#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_Mutation_Status	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_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
A2M	2	hgsc.bcm.edu	37	12	9246177	9246181	+	Splice_Site	DEL	TATGG	TATGG	-	rs1799759|rs3832852		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TATGG	TATGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:9246177_9246181delTATGG	ENST00000318602.7	-	18	2433		c.e18-2			NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin						blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	CATCTGACTCTATGGTGAGTGAGGA	0.42														734	0.146565	0.211	0.0965	5008	,	,		18777	0.0456		0.175	False		,,,				2504	0.1697				.		Pindel,Atlas-Indel	.											.	A2M	180	.	0			.	GRCh37	CD984159	A2M	D	rs3832852	PASS	.			640,3002		64,512,1245				http://www.ncbi.nlm.nih.gov/sites/varvu?gene		3.6	0.0		dbSNP_107	59	1227,6665		106,1015,2825	no	splice-3	A2M	NM_000014.4		170,1527,4070	A1A1,A1R,RR		15.5474,17.5728,16.1869				1867,9667				SO:0001630	splice_region_variant	2	.			.	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.2126-2CCATA>-	12.37:g.9246177_9246181delTATGG		Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	73	28	0.384	.	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Splice_Site	DEL	ENST00000318602.7	37	CCDS44827.1																																																																																			TATGG|0.860;-|0.140	0.140	strong		0.420	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	Intron
TPR	7175	hgsc.bcm.edu	37	1	186326758	186326758	+	Intron	DEL	A	A	-	rs3841803	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:186326758delA	ENST00000367478.4	-	14	1794				TPR_ENST00000474852.1_Intron	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein						carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		ACTCTAATCTAAAAACAAAGT	0.303			T	NTRK1	papillary thyroid								AAAAA|AAAAA|AAAA|deletion	693	0.138379	0.0182	0.0879	5008	,	,		17002	0.3929		0.0974	False		,,,				2504	0.1166				.		Pindel,Atlas-Indel	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.1498-2T>-						PASS	.			121,3363		3,115,1624	48.0	41.0	43.0			5.5	1.0	1	dbSNP_107	49	736,7060		41,654,3203	no	intron	TPR	NM_003292.2		44,769,4827	A1A1,A1R,RR		9.4407,3.473,7.5975			186326758	857,10423	1798	4062	5860	SO:0001627	intron_variant	7175	exon15			.	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.1498-3T>-	1.37:g.186326758delA		Somatic	56	.	.		WXS	Illumina HiSeq	Phase_I	90	35	0.389	NM_003292	Q15655|Q5SWY0|Q99968	Splice_Site	DEL	ENST00000367478.4	37	CCDS41446.1																																																																																			A|0.845;-|0.155	0.155	strong		0.303	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
OR2A14	135941	hgsc.bcm.edu	37	7	143826730	143826732	+	In_Frame_Del	DEL	CTT	CTT	-	rs66549240|rs34602346	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143826730_143826732delCTT	ENST00000408899.2	+	1	580_582	c.525_527delCTT	c.(523-528)cacttc>cac	p.F177del		NM_001001659.1	NP_001001659.1	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A, member 14	177				Missing (in Ref. 2; AAK95081). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(17)|skin(1)	22	Melanoma(164;0.0783)					AAATCAACCACTTCTTCTGTGAA	0.562														2897	0.578474	0.4652	0.7147	5008	,	,		20883	0.7371		0.4831	False		,,,				2504	0.5695				p.175_176del		Atlas-Indel	.											.	OR2A14	66	.	0			c.524_526del						PASS	.			1743,2055		447,849,603						4.2	1.0		dbSNP_130	199	4152,3826		1121,1910,958	no	coding	OR2A14	NM_001001659.1		1568,2759,1561	A1A1,A1R,RR		47.9569,45.8926,49.9406				5895,5881				SO:0001651	inframe_deletion	135941	exon1			.		CCDS43672.1	7q35	2013-09-20		2004-03-08	ENSG00000221938	ENSG00000221938		"""GPCR / Class A : Olfactory receptors"""	15084	protein-coding gene	gene with protein product				OR2A14P, OR2A6			Standard	NM_001001659		Approved	OST182	uc011kua.2	Q96R47	OTTHUMG00000158003	ENST00000408899.2:c.525_527delCTT	7.37:g.143826733_143826735delCTT	ENSP00000386137:p.Phe177del	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	241	86	0.356846	NM_001001659	Q6IF41|Q8NGT8	In_Frame_Del	DEL	ENST00000408899.2	37	CCDS43672.1																																																																																			CTT|0.441;-|0.559	0.559	strong		0.562	OR2A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349980.1		
OTOP1	133060	hgsc.bcm.edu	37	4	4198949	4198954	+	In_Frame_Del	DEL	CGTTGC	CGTTGC	-	rs200964011|rs374875261|rs547040796|rs141181262|rs200550998|rs112623841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CGTTGC	CGTTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:4198949_4198954delCGTTGC	ENST00000296358.4	-	5	1631_1636	c.1607_1612delGCAACG	c.(1606-1614)ggcaacgcc>gcc	p.GN536del		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	536					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TTTCTCTTGGCGTTGCCCTGTAAGAA	0.476														384	0.0766773	0.1074	0.1585	5008	,	,		20491	0.0		0.0457	False		,,,				2504	0.0879				p.536_538del		Pindel,Atlas-Indel	.											.	OTOP1	118	.	0			c.1608_1613del						PASS	.			431,3833		23,385,1724						0.8	0.0		dbSNP_132	60	431,7823		11,409,3707	no	coding	OTOP1	NM_177998.1		34,794,5431	A1A1,A1R,RR		5.2217,10.1079,6.8861				862,11656				SO:0001651	inframe_deletion	133060	exon5			.	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1607_1612delGCAACG	4.37:g.4198949_4198954delCGTTGC	ENSP00000296358:p.Gly536_Asn537del	Somatic	145	.	.		WXS	Illumina HiSeq	Phase_I	120	30	0.250	NM_177998	A1L476	In_Frame_Del	DEL	ENST00000296358.4	37	CCDS3372.1																																																																																			CGTTGC|0.943;-|0.057	0.057	strong		0.476	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
OR5M1	390168	hgsc.bcm.edu	37	11	56380547	56380550	+	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs71931749|rs72003051	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CAGA	CAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56380547_56380550delCAGA	ENST00000526538.1	-	1	428_431	c.429_432delTCTG	c.(427-432)tgtctgfs	p.CL143fs		NM_001004740.1	NP_001004740.1	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M, member 1	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|upper_aerodigestive_tract(1)	12						GGATAGTGACCAGACAGACACAGA	0.436														634	0.126597	0.031	0.098	5008	,	,		22572	0.1617		0.2008	False		,,,				2504	0.1636				p.144_145del		Pindel,Atlas-Indel	.											.	OR5M1	92	.	0			c.430_433del						PASS	.			236,3532		12,212,1660						3.7	0.0		dbSNP_130	118	1705,6265		205,1295,2485	no	frameshift	OR5M1	NM_001004740.1		217,1507,4145	A1A1,A1R,RR		21.3927,6.2633,16.536				1941,9797				SO:0001589	frameshift_variant	390168	exon1			.	AB065742	CCDS53631.1	11q11	2012-08-09				ENSG00000255012		"""GPCR / Class A : Olfactory receptors"""	8352	protein-coding gene	gene with protein product							Standard	NM_001004740		Approved	OST050	uc001nja.1	Q8NGP8		ENST00000526538.1:c.429_432delTCTG	11.37:g.56380551_56380554delCAGA	ENSP00000435416:p.Cys143fs	Somatic	235	.	.		WXS	Illumina HiSeq	Phase_I	278	88	0.317	NM_001004740	Q6IF60|Q96RB6	Frame_Shift_Del	DEL	ENST00000526538.1	37	CCDS53631.1																																																																																			CAGA|0.853;-|0.147	0.147	strong		0.436	OR5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391610.1	NM_001004740	
NCL	4691	hgsc.bcm.edu	37	2	232325382	232325384	+	In_Frame_Del	DEL	TCC	TCC	-	rs140018754		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:232325382_232325384delTCC	ENST00000322723.4	-	4	1047_1049	c.807_809delGGA	c.(805-810)gaggaa>gaa	p.269_270EE>E	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	269	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		TTAAGTACCTTCCTCCTCCTCTT	0.409																																					p.270_270del		Pindel,Atlas-Indel	.											.	NCL	80	.	0			c.808_810del						PASS	.			1,0,4265		0,0,1,0,0,2132						4.7	0.3			220	4,5,8245		0,0,4,0,5,4118	no	codingComplex	NCL	NM_005381.2		0,0,5,0,5,6250	A1A1,A1A2,A1R,A2A2,A2R,RR		0.109,0.0234,0.0799				5,5,12510				SO:0001651	inframe_deletion	4691	exon4			.		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.807_809delGGA	2.37:g.232325388_232325390delTCC	ENSP00000318195:p.Glu271del	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	153	50	0.327	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	In_Frame_Del	DEL	ENST00000322723.4	37	CCDS33397.1																																																																																			.	.	none		0.409	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10524657	10524659	+	In_Frame_Del	DEL	GAC	GAC	-	rs56252625|rs75627261|rs571414967|rs113642662	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GAC	GAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:10524657_10524659delGAC	ENST00000396560.2	+	3	407_409	c.180_182delGAC	c.(178-183)aggacg>agg	p.T62del	ATF7IP2_ENST00000324570.5_In_Frame_Del_p.T62del|ATF7IP2_ENST00000356427.2_In_Frame_Del_p.T62del|ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_In_Frame_Del_p.T62del	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	62					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						TCATAACTAGGACGACTGAAATA	0.374														3021	0.603235	0.5628	0.572	5008	,	,		18516	0.6994		0.5686	False		,,,				2504	0.6166				p.60_61del		Pindel,Atlas-Indel	.											.	ATF7IP2	40	.	0			c.179_181del						PASS	.			2445,1819		712,1021,399							0.1		dbSNP_131	58	4927,3327		1439,2049,639	no	coding	ATF7IP2	NM_024997.2		2151,3070,1038	A1A1,A1R,RR		40.3077,42.6595,41.1088				7372,5146				SO:0001651	inframe_deletion	80063	exon4			.	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.180_182delGAC	16.37:g.10524660_10524662delGAC	ENSP00000379808:p.Thr62del	Somatic	252	.	.		WXS	Illumina HiSeq	Phase_I	244	65	0.266	NM_001256160	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	In_Frame_Del	DEL	ENST00000396560.2	37	CCDS10540.1																																																																																			GAC|0.396;-|0.604	0.604	strong		0.374	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
EME1	146956	hgsc.bcm.edu	37	17	48452978	48452979	+	In_Frame_Ins	INS	-	-	AGC	rs76993288|rs36080231|rs67225428|rs558756129|rs3060668	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48452978_48452979insAGC	ENST00000338165.4	+	2	491_492	c.409_410insAGC	c.(409-411)aag>aAGCag	p.137_138insQ	MRPL27_ENST00000507088.1_5'Flank|EME1_ENST00000393271.2_In_Frame_Ins_p.137_138insQ|EME1_ENST00000511648.2_In_Frame_Ins_p.137_138insQ|MRPL27_ENST00000225969.4_5'Flank|MRPL27_ENST00000503633.1_5'Flank|MRPL27_ENST00000442592.3_5'Flank	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	137					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			TGACTGGAAAAAGCCCTTTCCA	0.47								Direct reversal of damage;Homologous recombination						2233	0.445887	0.7269	0.5836	5008	,	,		21332	0.1111		0.4473	False		,,,				2504	0.3119				p.K137delinsKQ		Pindel,Atlas-Indel	.											.	EME1	39	.	0			c.409_410insAGC						PASS	.		,	2895,1369		988,919,225					,	1.0	0.9		dbSNP_130	80	3907,4347		928,2051,1148	no	coding,coding	EME1	NM_152463.2,NM_001166131.1	,	1916,2970,1373	A1A1,A1R,RR		47.3346,32.106,45.6622	,	,		6802,5716				SO:0001652	inframe_insertion	146956	exon2			.	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"""SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"""	610885	"""essential meiotic endonuclease 1 homolog 1 (S. pombe)"""			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.410_412dupAGC	17.37:g.48452979_48452981dupAGC	ENSP00000339897:p.Lys137_Pro138insGln	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	172	49	0.285	NM_152463	Q96N62	In_Frame_Ins	INS	ENST00000338165.4	37	CCDS11565.1																																																																																			-|0.250;AGC|0.750	0.750	strong		0.470	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144915624	144915624	+	Frame_Shift_Del	DEL	G	G	-	rs66512216|rs1778112	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:144915624delG	ENST00000369354.3	-	14	1990	c.1801delC	c.(1801-1803)ctgfs	p.L602fs	PDE4DIP_ENST00000369351.3_Frame_Shift_Del_p.L602fs|PDE4DIP_ENST00000369349.3_Frame_Shift_Del_p.L602fs|PDE4DIP_ENST00000529945.1_Frame_Shift_Del_p.L765fs|PDE4DIP_ENST00000530740.1_Frame_Shift_Del_p.L739fs|PDE4DIP_ENST00000369356.4_Frame_Shift_Del_p.L602fs|PDE4DIP_ENST00000313382.9_Frame_Shift_Del_p.L668fs|PDE4DIP_ENST00000479408.2_Frame_Shift_Del_p.L389fs|PDE4DIP_ENST00000369359.4_Frame_Shift_Del_p.L739fs|PDE4DIP_ENST00000313431.9_Frame_Shift_Del_p.L765fs			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	602					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTGCAGAGCAGTGTTGCACTA	0.463			T	PDGFRB	MPD																																p.L764fs		Pindel,Atlas-Indel	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.2291delT						PASS	.		,,,,	205,4061		0,205,1928	117.0	102.0	107.0		,,,,	5.2	0.9	1	dbSNP_130	115	1400,6846		0,1400,2723	no	frameshift,frameshift,frameshift,frameshift,frameshift	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1,NM_001002812.1,NM_001002811.1	,,,,	0,1605,4651	A1A1,A1R,RR		16.9779,4.8054,12.8277	,,,,	,,,,	144915624	1605,10907	2203	4296	6499	SO:0001589	frameshift_variant	9659	exon10			.	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.1801delC	1.37:g.144915624delG	ENSP00000358360:p.Leu602fs	Somatic	123	.	.		WXS	Illumina HiSeq	Phase_I	196	30	0.153	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Frame_Shift_Del	DEL	ENST00000369354.3	37	CCDS30824.1																																																																																			G|0.808;-|0.192	0.192	strong		0.463	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
PCDH7	5099	hgsc.bcm.edu	37	4	30725858	30725859	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:30725858_30725859insA	ENST00000361762.2	+	1	3822_3823	c.2814_2815insA	c.(2815-2817)aaafs	p.K939fs	PCDH7_ENST00000543491.1_Frame_Shift_Ins_p.K939fs	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	939					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						AAAAGGACAAGAAAAACAAAAA	0.401																																					p.K938fs		Pindel,Atlas-Indel	.											.	PCDH7	215	.	0			c.2814_2815insA						PASS	.																																			SO:0001589	frameshift_variant	5099	exon1			.	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.2819dupA	4.37:g.30725863_30725863dupA	ENSP00000355243:p.Lys939fs	Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	91	38	0.418	NM_032457	O60246|O60247|Q4W5C4	Frame_Shift_Ins	INS	ENST00000361762.2	37	CCDS33971.1																																																																																			.	.	none		0.401	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589	
NEFH	4744	hgsc.bcm.edu	37	22	29885581	29885604	+	In_Frame_Del	DEL	AGGCCAAGTCCCCAGAGAAGGAAG	AGGCCAAGTCCCCAGAGAAGGAAG	-	rs267607534|rs373980795|rs267607533|rs149571560|rs79235463|rs200984527|rs370803228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGGCCAAGTCCCCAGAGAAGGAAG	AGGCCAAGTCCCCAGAGAAGGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29885581_29885604delAGGCCAAGTCCCCAGAGAAGGAAG	ENST00000310624.6	+	4	1985_2008	c.1952_1975delAGGCCAAGTCCCCAGAGAAGGAAG	c.(1951-1977)aaggccaagtccccagagaaggaagag>aag	p.AKSPEKEE652del		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	658	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						TCCCCTGAGAAGGCCAAGTCCCCAGAGAAGGAAGAGGCCAAGTC	0.562																																					p.651_658del		Atlas-Indel	.											.	NEFH	178	.	0			c.1951_1974del						PASS	.																																			SO:0001651	inframe_deletion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1952_1975delAGGCCAAGTCCCCAGAGAAGGAAG	22.37:g.29885581_29885604delAGGCCAAGTCCCCAGAGAAGGAAG	ENSP00000311997:p.Ala652_Glu659del	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Del	DEL	ENST00000310624.6	37	CCDS13858.1																																																																																			.	.	weak		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
RAI1	10743	hgsc.bcm.edu	37	17	17697102	17697102	+	Frame_Shift_Del	DEL	G	G	-	rs398124422|rs34083643|rs398124421|rs587780431		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17697102delG	ENST00000353383.1	+	3	1309	c.840delG	c.(838-840)cagfs	p.Q291fs	RAI1_ENST00000261641.6_Frame_Shift_Del_p.Q291fs	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	291	Gln-rich.|Poly-Gln.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)	p.Q280fs*84(1)		breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ACcagcagcagcagcagcagc	0.627																																					p.Q280fs		Atlas-Indel	.											RAI1,colon,carcinoma,-1,3	RAI1	121	3	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.839delA						PASS	.						20.0	25.0	23.0					17																	17697102		2038	4033	6071	SO:0001589	frameshift_variant	10743	exon3			.	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.840delG	17.37:g.17697102delG	ENSP00000323074:p.Gln291fs	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	89	25	0.280899	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Frame_Shift_Del	DEL	ENST00000353383.1	37	CCDS11188.1																																																																																			.	.	weak		0.627	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
TBP	6908	hgsc.bcm.edu	37	6	170871004	170871005	+	In_Frame_Ins	INS	-	-	CAA			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:170871004_170871005insCAA	ENST00000392092.2	+	3	459_460	c.180_181insCAA	c.(181-183)caa>CAAcaa	p.61_61Q>QQ	TBP_ENST00000540980.1_In_Frame_Ins_p.41_41Q>QQ|TBP_ENST00000230354.6_In_Frame_Ins_p.61_61Q>QQ	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	61	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaaca	0.54																																					p.Q60delinsQQ		Atlas-Indel	.											.	TBP	58	.	0			c.180_181insCAA						PASS	.																																			SO:0001652	inframe_insertion	6908	exon3			.	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.187_189dupCAA	6.37:g.170871011_170871013dupCAA	ENSP00000375942:p.Gln95dup	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	In_Frame_Ins	INS	ENST00000392092.2	37	CCDS5315.1																																																																																			.	.	none		0.540	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
ZNF271	10778	hgsc.bcm.edu	37	18	32888090	32888090	+	RNA	DEL	C	C	-	rs201643077|rs12965288	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:32888090delC	ENST00000399070.3	+	0	2484					NR_024565.1|NR_024566.1		Q14591	ZN271_HUMAN	zinc finger protein 271						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(9)	12						aaaaaaaaaaCCACCAATACC	0.393																																					.		Atlas-Indel	.											.	ZNF271	16	.	0			.						PASS	.																																					10778	.			.	X78930		18q12.2	2013-04-03			ENSG00000257267	ENSG00000257267		"""Zinc fingers, C2H2-type"""	13065	other	unknown		604754				7865130, 11777961	Standard	NR_024565		Approved	HZF7, ZNFEB	uc002kyp.4	Q14591	OTTHUMG00000132563		18.37:g.32888090delC		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	102	23	0.22549	.	B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	RNA	DEL	ENST00000399070.3	37																																																																																				C|0.747;-|0.253	0.253	strong		0.393	ZNF271-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255767.2	NR_024565	
ZNF560	147741	hgsc.bcm.edu	37	19	9578512	9578513	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9578512_9578513delTG	ENST00000301480.4	-	10	1323_1324	c.1110_1111delCA	c.(1108-1113)cacattfs	p.I371fs		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	371					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						TTTATCCCAATGTGGGTTTGCA	0.386																																					p.371_371del		Pindel,Atlas-Indel	.											.	ZNF560	162	.	0			c.1111_1112del						PASS	.																																			SO:0001589	frameshift_variant	147741	exon10			.	AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"""Zinc fingers, C2H2-type"", ""-"""	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.1110_1111delCA	19.37:g.9578514_9578515delTG	ENSP00000301480:p.Ile371fs	Somatic	233	.	.		WXS	Illumina HiSeq	Phase_I	238	62	0.261	NM_152476	Q495S9|Q495T1	Frame_Shift_Del	DEL	ENST00000301480.4	37	CCDS12214.1																																																																																			.	.	none		0.386	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476	
C10orf85	404216	hgsc.bcm.edu	37	10	122358877	122358878	+	3'UTR	DEL	GA	GA	-	rs71853551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122358877_122358878delGA	ENST00000369071.2	+	0	1157_1158									chromosome 10 open reading frame 85																		GCTCTGAGCTGAGAGAGAAGAA	0.545														1175	0.234625	0.1074	0.2406	5008	,	,		18302	0.2093		0.3101	False		,,,				2504	0.3507				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																			SO:0001624	3_prime_UTR_variant	100847064	.			.	AK094721		10q26.12	2013-09-20			ENSG00000177234	ENSG00000177234			31365	protein-coding gene	gene with protein product							Standard	NR_103717		Approved	FLJ37402, Em:AC023282.2		Q8N1V8	OTTHUMG00000019167	ENST00000369071.2:c.*669GA>-	10.37:g.122358883_122358884delGA		Somatic	91	.	.		WXS	Illumina HiSeq	Phase_I	101	28	0.277	.		RNA	DEL	ENST00000369071.2	37																																																																																				GA|0.769;-|0.231	0.231	strong		0.545	C10orf85-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050700.1		
TAF7L	54457	hgsc.bcm.edu	37	X	100531414	100531419	+	In_Frame_Del	DEL	TCATCC	TCATCC	-	rs377399072|rs199759165		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TCATCC	TCATCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:100531414_100531419delTCATCC	ENST00000372907.3	-	10	1058_1063	c.1047_1052delGGATGA	c.(1045-1053)gaggatgaa>gaa	p.349_351EDE>E	TAF7L_ENST00000324762.6_Intron|TAF7L_ENST00000356784.1_In_Frame_Del_p.263_265EDE>E|TAF7L_ENST00000372905.2_Intron	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	349	Glu-rich.		Missing. {ECO:0000269|PubMed:11279525, ECO:0000269|PubMed:16597641, ECO:0000269|PubMed:17714218}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						GTCTtcatcttcatcctcatcctcat	0.422														459	0.121589	0.084	0.0893	3775	,	,		14668	0.0317		0.1759	False		,,,				2504	0.0787				p.350_351del	Ovarian(104;431 1530 3210 15406 18594)	Pindel,Atlas-Indel	.											.	TAF7L	64	.	0			c.1048_1053del						PASS	.																																			SO:0001651	inframe_deletion	54457	exon10			.	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"""cancer/testis antigen 40"""	300314	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"""	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.1047_1052delGGATGA	X.37:g.100531420_100531425delTCATCC	ENSP00000361998:p.Glu353_Asp354del	Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	108	44	0.407	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	In_Frame_Del	DEL	ENST00000372907.3	37	CCDS35347.1																																																																																			TCATCC|0.871;-|0.129	0.129	strong		0.422	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2		
LARP7	51574	hgsc.bcm.edu	37	4	113569540	113569543	+	Intron	DEL	ACTT	ACTT	-	rs199971565	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	ACTT	ACTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:113569540_113569543delACTT	ENST00000344442.5	+	8	1420				MIR302A_ENST00000385192.1_RNA|MIR302B_ENST00000362188.1_RNA|MIR367_ENST00000362299.1_RNA|MIR302D_ENST00000362275.1_RNA|MIR302B_ENST00000509938.1_RNA|MIR302C_ENST00000362232.1_RNA|LARP7_ENST00000324052.6_Intron|MIR302B_ENST00000505215.1_RNA|MIR302B_ENST00000510655.1_RNA|LARP7_ENST00000509061.1_Intron	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7						RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		ACATGGAAGCACTTACTTTTGTTT	0.387														95	0.0189696	0.0038	0.0072	5008	,	,		17547	0.003		0.0239	False		,,,				2504	0.0593				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.		,	26,3950		3,20,1965					,	5.6	1.0			127	245,7237		11,223,3507	no	intron,intron	LARP7	NM_016648.2,NM_015454.1	,	14,243,5472	A1A1,A1R,RR		3.2745,0.6539,2.3652	,	,		271,11187				SO:0001627	intron_variant	442895	.			.	AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"""La ribonucleoprotein domain containing"", ""RNA binding motif (RRM) containing"""	24912	protein-coding gene	gene with protein product	"""P-TEFb-interaction protein for 7SK stability"""	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.1142+550ACTT>-	4.37:g.113569544_113569547delACTT		Somatic	129	.	.		WXS	Illumina HiSeq	Phase_I	158	59	0.373	.	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	RNA	DEL	ENST00000344442.5	37	CCDS3701.2																																																																																			ACTT|0.986;-|0.014	0.014	strong		0.387	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648	
SEC16A	9919	hgsc.bcm.edu	37	9	139370955	139370963	+	In_Frame_Del	DEL	AGCTCCTGA	AGCTCCTGA	-	rs545335424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGCTCCTGA	AGCTCCTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139370955_139370963delAGCTCCTGA	ENST00000371706.3	-	1	604_612	c.571_579delTCAGGAGCT	c.(571-579)tcaggagctdel	p.SGA191del	SEC16A_ENST00000431893.2_In_Frame_Del_p.SGA191del|SEC16A_ENST00000290037.6_In_Frame_Del_p.SGA191del|SEC16A_ENST00000313050.7_In_Frame_Del_p.SGA369del			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	191					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.S369_A371delSGA(1)		breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		ACATCGCCAGAGCTCCTGAAGCTCCTGAG	0.574														13	0.00259585	0.0008	0.0014	5008	,	,		18859	0.0		0.004	False		,,,				2504	0.0072				p.369_372del		Pindel,Atlas-Indel	.											.	SEC16A	249	.	1	Deletion - In frame(1)	breast(1)	c.1106_1114del						PASS	.			7,3561		0,7,1777						1.9	0.0			19	42,7812		1,40,3886	no	coding	SEC16A	NM_014866.1		1,47,5663	A1A1,A1R,RR		0.5348,0.1962,0.429				49,11373				SO:0001651	inframe_deletion	9919	exon3			.	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.571_579delTCAGGAGCT	9.37:g.139370964_139370972delAGCTCCTGA	ENSP00000360771:p.Ser191_Ala193del	Somatic	110	.	.		WXS	Illumina HiSeq	Phase_I	118	32	0.271	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	In_Frame_Del	DEL	ENST00000371706.3	37																																																																																				.	.	none		0.574	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
ABCF1	23	hgsc.bcm.edu	37	6	30558477	30558478	+	Stop_Codon_Ins	INS	-	-	A	rs76018112|rs548415581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30558477_30558478insA	ENST00000326195.8	+	0	2649_2650				ABCF1_ENST00000376545.3_Stop_Codon_Ins|ABCF1_ENST00000396515.4_Stop_Codon_Ins	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1						inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						CCCCGAGAGTGAGCTTTCCTTC	0.564													A|A|AA|insertion	3576	0.714058	0.73	0.5937	5008	,	,		19175	0.6736		0.6789	False		,,,				2504	0.8558				p.X846delinsX		Pindel,Atlas-Indel	.											.	ABCF1	61	.	0			c.2537_2538insA						PASS	.		,	2545,933		984,577,178					,	5.4	1.0		dbSNP_130	106	4558,2170		1686,1186,492	no	frameshift,frameshift	ABCF1	NM_001090.2,NM_001025091.1	,	2670,1763,670	A1A1,A1R,RR		32.2533,26.8258,30.4037	,	,		7103,3103				SO:0001567	stop_retained_variant	23	exon25			.	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"""ATP binding cassette transporters / subfamily F"""	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.2536dupA	6.37:g.30558478_30558478dupA		Somatic	192	.	.		WXS	Illumina HiSeq	Phase_I	224	58	0.259	NM_001025091	A2BF75|O14897|Q69YP6	Frame_Shift_Ins	INS	ENST00000326195.8	37	CCDS34380.1																																																																																			A|1.000;|0.000	1.000	strong		0.564	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3		
SPATA31A7	26165	hgsc.bcm.edu	37	9	65504156	65504156	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:65504156delG	ENST00000355045.2	-	4	3432	c.3404delC	c.(3403-3405)ccafs	p.P1135fs	SPATA31A7_ENST00000491812.2_5'Flank	NM_015667.2	NP_056482.2	Q8IWB4	S31A7_HUMAN	SPATA31 subfamily A, member 7	1135					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTTCCTGACTGGGGTAAGTTG	0.458																																					p.P1135fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.3405delA						PASS	.																																			SO:0001589	frameshift_variant	727905	exon4			.		CCDS75838.1	9q12	2014-04-11	2012-10-12	2012-10-12	ENSG00000234734	ENSG00000276040			32007	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A7"""	FAM75A7		20850414	Standard	NM_015667		Approved	OTTHUMG00000013196		Q8IWB4	OTTHUMG00000188536	ENST00000355045.2:c.3404delC	9.37:g.65504156delG	ENSP00000347153:p.Pro1135fs	Somatic	376	.	.		WXS	Illumina HiSeq	Phase_I	263	49	0.186	NM_001113541	Q5TZK4|Q9Y4Q5	Frame_Shift_Del	DEL	ENST00000355045.2	37	CCDS43825.1																																																																																			.	.	none		0.458	SPATA31A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036952.1	NM_015667	
TPSD1	23430	hgsc.bcm.edu	37	16	1306560	1306560	+	Frame_Shift_Del	DEL	G	G	-	rs3830782|rs397840555	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306560delG	ENST00000211076.3	+	2	274	c.126delG	c.(124-126)cagfs	p.Q42fs	TPSD1_ENST00000397534.2_Frame_Shift_Del_p.Q35fs|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	42	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TTGGGGGGCAGGAGGCCCCCA	0.697													|||unknown(ALL_OTHER_Ns)	1341	0.267772	0.4191	0.3401	5008	,	,		17418	0.1528		0.2217	False		,,,				2504	0.1779				p.Q42fs		Atlas-Indel	.											.	TPSD1	47	.	0			c.125delA						PASS	.			1594,2670		311,972,849	32.0	48.0	43.0			-2.8	0.0	16	dbSNP_114	55	1800,6452		185,1430,2511	no	frameshift	TPSD1	NM_012217.2		496,2402,3360	A1A1,A1R,RR		21.8129,37.3827,27.1173			1306560	3394,9122	2038	4218	6256	SO:0001589	frameshift_variant	23430	exon2			.	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.126delG	16.37:g.1306560delG	ENSP00000211076:p.Gln42fs	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	191	90	0.471204	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Frame_Shift_Del	DEL	ENST00000211076.3	37	CCDS10432.1																																																																																			G|0.731;-|0.269	0.269	strong		0.697	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
AFM	173	hgsc.bcm.edu	37	4	74347532	74347532	+	Frame_Shift_Del	DEL	T	T	-	rs145217978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:74347532delT	ENST00000226355.3	+	1	133	c.40delT	c.(40-42)tttfs	p.F15fs		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	15					vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTTTTCTTGTTTTTTTTGAC	0.313																																					p.L13fs		Atlas-Indel	.											.	AFM	101	.	0			c.39delG						PASS	.						41.0	44.0	43.0					4																	74347532		2193	4282	6475	SO:0001589	frameshift_variant	173	exon1			.	L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.40delT	4.37:g.74347532delT	ENSP00000226355:p.Phe15fs	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	181	12	0.0662983	NM_001133	A8K3E1|Q32MR3|Q4W5C5	Frame_Shift_Del	DEL	ENST00000226355.3	37	CCDS3557.1																																																																																			.	.	none		0.313	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2		
C21orf58	54058	hgsc.bcm.edu	37	21	47721985	47721986	+	In_Frame_Ins	INS	-	-	TGG	rs144178764|rs112899928|rs35902237|rs71318063	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47721985_47721986insTGG	ENST00000291691.7	-	8	2032_2033	c.896_897insCCA	c.(895-897)cat>caCCAt	p.299_299H>HH	C21orf58_ENST00000397683.1_In_Frame_Ins_p.193_193H>HH|C21orf58_ENST00000472607.1_5'UTR|C21orf58_ENST00000397680.1_In_Frame_Ins_p.193_193H>HH|C21orf58_ENST00000397679.1_In_Frame_Ins_p.193_193H>HH|C21orf58_ENST00000397682.3_In_Frame_Ins_p.193_193H>HH	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	299	Poly-His.							p.H299_A300insH(3)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		GCCACACAGCAtggtggtggtg	0.708														1382	0.275958	0.1384	0.4063	5008	,	,		16708	0.3046		0.3091	False		,,,				2504	0.3057				p.H299delinsHH		Pindel,Atlas-Indel	.											.	C21orf58	25	.	3	Insertion - In frame(3)	breast(2)|central_nervous_system(1)	c.897_898insCCA						PASS	.																																			SO:0001652	inframe_insertion	54058	exon8			.		CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.894_896dupCCA	21.37:g.47721992_47721994dupTGG	ENSP00000291691:p.His299dup	Somatic	56	.	.		WXS	Illumina HiSeq	Phase_I	50	13	0.260	NM_058180	B3KPI1	In_Frame_Ins	INS	ENST00000291691.7	37	CCDS13735.1																																																																																			-|0.500;TGG|0.500	0.500	strong		0.708	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180	
FOXD4L4	349334	hgsc.bcm.edu	37	9	70427650	70427652	+	Stop_Codon_Del	DEL	CAG	CAG	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:70427650_70427652delCAG	ENST00000377413.1	-	0	2079_2081					NM_199244.2	NP_954714.2	Q8WXT5	FX4L4_HUMAN	forkhead box D4-like 4						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C416delC(1)							GBM - Glioblastoma multiforme(29;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		CCTGATACCTCAGCAGCGCCGAC	0.65																																					p.417_417del		Atlas-Indel	.											.	FOXD4L2	4	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.1249_1251del						PASS	.																																			SO:0001567	stop_retained_variant	100036519	exon1			.		CCDS75845.1	9q13	2007-03-19			ENSG00000184659	ENSG00000184659			23762	protein-coding gene	gene with protein product		611085					Standard	NM_199244		Approved	bA460E7.2, OTTHUMG00000013337		Q8WXT5	OTTHUMG00000013337	Exception_encountered	9.37:g.70427653_70427655delCAG	Exception_encountered	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	158	11	0.0696203	NM_001099279	Q5RIB4	In_Frame_Del	DEL	ENST00000377413.1	37	CCDS6621.1																																																																																			.	.	none		0.650	FOXD4L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037143.2		
SPAG1	6674	hgsc.bcm.edu	37	8	101206459	101206460	+	In_Frame_Ins	INS	-	-	GAC	rs72062044|rs56246127	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:101206459_101206460insGAC	ENST00000388798.2	+	10	1250_1251	c.1059_1060insGAC	c.(1060-1062)agc>GACagc	p.353_354insD	SPAG1_ENST00000520508.1_In_Frame_Ins_p.353_354insD|SPAG1_ENST00000251809.3_In_Frame_Ins_p.353_354insD|SPAG1_ENST00000520643.1_In_Frame_Ins_p.353_354insD	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	353					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		AAGAAGGAAAAAGCGGAAGAAA	0.356														753	0.150359	0.0537	0.2392	5008	,	,		16467	0.0734		0.2117	False		,,,				2504	0.2342				p.K353delinsKD		Pindel,Atlas-Indel	.											.	SPAG1	80	.	0			c.1059_1060insGAC						PASS	.		,	320,3944		14,292,1826					,	0.9	0.0		dbSNP_130	64	1643,6611		162,1319,2646	no	coding,coding	SPAG1	NM_172218.2,NM_003114.4	,	176,1611,4472	A1A1,A1R,RR		19.9055,7.5047,15.6814	,	,		1963,10555				SO:0001652	inframe_insertion	6674	exon10			.	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"""Tetratricopeptide (TTC) repeat domain containing"""	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	Exception_encountered	8.37:g.101206459_101206460insGAC	ENSP00000373450:p.Lys353_Ser354insAsp	Somatic	308	.	.		WXS	Illumina HiSeq	Phase_I	247	64	0.259	NM_172218	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	In_Frame_Ins	INS	ENST00000388798.2	37	CCDS34930.1																																																																																			GAC|1.000;|0.000	1.000	weak		0.356	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218	
OR5M10	390167	hgsc.bcm.edu	37	11	56344844	56344851	+	Frame_Shift_Del	DEL	CATTGAAG	CATTGAAG	-	rs148438199	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CATTGAAG	CATTGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56344844_56344851delCATTGAAG	ENST00000526812.2	-	1	412_419	c.347_354delCTTCAATG	c.(346-354)gcttcaatgfs	p.ASM116fs		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						GATCCAATGCCATTGAAGCAAGGAAGTA	0.452														198	0.0395367	0.003	0.049	5008	,	,		24973	0.001		0.0974	False		,,,				2504	0.0624				p.116_119del		Pindel,Atlas-Indel	.											.	OR5M10	56	.	0			c.348_355del						PASS	.			44,3794		3,38,1878						3.1	0.9		dbSNP_134	159	644,7378		32,580,3399	no	frameshift	OR5M10	NM_001004741.1		35,618,5277	A1A1,A1R,RR		8.0279,1.1464,5.801				688,11172				SO:0001589	frameshift_variant	390167	exon1			.	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"""GPCR / Class A : Olfactory receptors"""	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.347_354delCTTCAATG	11.37:g.56344844_56344851delCATTGAAG	ENSP00000436004:p.Ala116fs	Somatic	203	.	.		WXS	Illumina HiSeq	Phase_I	207	60	0.290	NM_001004741	B9EIL9	Frame_Shift_Del	DEL	ENST00000526812.2	37	CCDS53630.1																																																																																			CATTGAAG|0.959;-|0.041	0.041	strong		0.452	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741	
MPHOSPH9	10198	hgsc.bcm.edu	37	12	123678972	123678974	+	In_Frame_Del	DEL	TTT	TTT	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:123678972_123678974delTTT	ENST00000606320.1	-	13	2406_2408	c.2200_2202delAAA	c.(2200-2202)aaadel	p.K734del	MPHOSPH9_ENST00000302349.5_In_Frame_Del_p.K582del|MPHOSPH9_ENST00000541076.2_In_Frame_Del_p.K704del|MPHOSPH9_ENST00000392425.3_In_Frame_Del_p.K582del			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	734						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		GTTGAGCTTCTTTATCATCTGAG	0.305																																					p.582_583del		Pindel,Atlas-Indel	.											.	MPHOSPH9	75	.	0			c.1745_1747del						PASS	.																																			SO:0001651	inframe_deletion	10198	exon9			.	X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.2200_2202delAAA	12.37:g.123678972_123678974delTTT	ENSP00000475489:p.Lys734del	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	162	50	0.309	NM_022782	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	In_Frame_Del	DEL	ENST00000606320.1	37																																																																																				.	.	none		0.305	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2		
TMSB4X	7114	hgsc.bcm.edu	37	X	12994443	12994444	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:12994443_12994444delAG	ENST00000380635.1	+	2	279_280	c.63_64delAG	c.(61-66)acagagfs	p.E22fs	TMSB4X_ENST00000380636.1_Frame_Shift_Del_p.E22fs|TMSB4X_ENST00000380633.1_Frame_Shift_Del_p.E22fs|TMSB4X_ENST00000451311.2_Frame_Shift_Del_p.E22fs			P62328	TYB4_HUMAN	thymosin beta 4, X-linked	22					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sequestering of actin monomers (GO:0042989)	cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	poly(A) RNA binding (GO:0044822)			upper_aerodigestive_tract(1)	1						TGAAGAAGACAGAGACGCAAGA	0.54																																					p.21_21del		Pindel,Atlas-Indel	.											.	TMSB4X	3	.	0			c.62_63del						PASS	.			0,3721		0,0,1592,537						4.7	1.0			58	1,6483		0,1,2356,1770	no	frameshift	TMSB4X	NM_021109.3		0,1,3948,2307	A1A1,A1R,RR,R		0.0154,0.0,0.0098				1,10204				SO:0001589	frameshift_variant	7114	exon2			.		CCDS35202.1	Xp22.2	2013-05-14	2008-02-25		ENSG00000205542	ENSG00000205542			11881	protein-coding gene	gene with protein product		300159	"""thymosin, beta 4, X chromosome"""	TMSB4		2677145, 9381176	Standard	NM_021109		Approved	TB4X	uc004cvf.3	P62328	OTTHUMG00000021144	ENST00000380635.1:c.63_64delAG	X.37:g.12994445_12994446delAG	ENSP00000370009:p.Glu22fs	Somatic	177	.	.		WXS	Illumina HiSeq	Phase_I	186	81	0.435	NM_021109	P01253|P01254|Q546P5|Q63576|Q9UE55	Frame_Shift_Del	DEL	ENST00000380635.1	37	CCDS35202.1																																																																																			.	.	none		0.540	TMSB4X-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000055779.1	NM_021109	
FOXD4L5	653427	hgsc.bcm.edu	37	9	70176734	70176736	+	Stop_Codon_Del	DEL	CAG	CAG	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:70176734_70176736delCAG	ENST00000377420.1	-	0	2079_2081					NM_001126334.1	NP_001119806.1	Q5VV16	FX4L5_HUMAN	forkhead box D4-like 5						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|lung(2)	7						CCTGATACCTCAGCAGCGCCGAC	0.65																																					p.417_417del		Atlas-Indel	.											.	FOXD4L5	27	.	0			c.1249_1251del						PASS	.																																			SO:0001567	stop_retained_variant	653427	exon1			.		CCDS47977.1	9q13	2008-07-21			ENSG00000204779	ENSG00000204779			18522	protein-coding gene	gene with protein product						12234674	Standard	NM_001126334		Approved	bA15J10.2, OTTHUMG00000013332	uc010moc.3	Q5VV16	OTTHUMG00000013332	Exception_encountered	9.37:g.70176737_70176739delCAG	Exception_encountered	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	176	28	0.159091	NM_001126334		In_Frame_Del	DEL	ENST00000377420.1	37	CCDS47977.1																																																																																			.	.	none		0.650	FOXD4L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037122.1	NM_001126334	
EMCN	51705	hgsc.bcm.edu	37	4	101401162	101401164	+	In_Frame_Del	DEL	AAC	AAC	-	rs199955415|rs367883693|rs80331904|rs201510590	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:101401162_101401164delAAC	ENST00000296420.4	-	2	275_277	c.97_99delGTT	c.(97-99)gttdel	p.V33del	EMCN_ENST00000502327.1_5'UTR|EMCN_ENST00000305864.3_In_Frame_Del_p.V33del|EMCN_ENST00000511970.1_In_Frame_Del_p.V33del	NM_001159694.1|NM_016242.3	NP_001153166.1|NP_057326.2	Q9ULC0	MUCEN_HUMAN	endomucin	33						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)		TTGTTGTAGTAACAACAAGTGAA	0.31														1741	0.347644	0.2458	0.4092	5008	,	,		16968	0.7202		0.0944	False		,,,				2504	0.318				p.33_34del		Pindel,Atlas-Indel	.											.	EMCN	37	.	0			c.98_100del						PASS	.		,	958,3302		118,722,1290					,	-3.3	0.0		dbSNP_54	133	803,7437		45,713,3362	no	coding,coding	EMCN	NM_016242.3,NM_001159694.1	,	163,1435,4652	A1A1,A1R,RR		9.7451,22.4883,14.088	,	,		1761,10739				SO:0001651	inframe_deletion	51705	exon2			.	AF205940	CCDS3655.1, CCDS54782.1	4q22.1	2008-02-05			ENSG00000164035	ENSG00000164035		"""Mucins"""	16041	protein-coding gene	gene with protein product		608350				11418125, 11594763	Standard	NM_016242		Approved	MUC14	uc003hvr.3	Q9ULC0	OTTHUMG00000131051	ENST00000296420.4:c.97_99delGTT	4.37:g.101401165_101401167delAAC	ENSP00000296420:p.Val33del	Somatic	195	.	.		WXS	Illumina HiSeq	Phase_I	220	57	0.259	NM_001159694	A8K716|B4E347|Q8NEY5|Q8WWE7|Q9NRM8	In_Frame_Del	DEL	ENST00000296420.4	37	CCDS3655.1																																																																																			AAC|0.680;-|0.320	0.320	strong		0.310	EMCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253699.2	NM_016242	
APLF	200558	hgsc.bcm.edu	37	2	68765135	68765137	+	In_Frame_Del	DEL	AAG	AAG	-	rs139666972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:68765135_68765137delAAG	ENST00000303795.4	+	7	1107_1109	c.936_938delAAG	c.(934-939)aaaaga>aaa	p.R313del	APLF_ENST00000471727.1_3'UTR	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	313				Missing (in Ref. 1; BAF83530). {ECO:0000305}.	cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						TTGCCACTAAAAGAACACCACAT	0.384														230	0.0459265	0.0045	0.0922	5008	,	,		18148	0.0119		0.0805	False		,,,				2504	0.0685				p.312_313del		Pindel,Atlas-Indel	.											.	APLF	69	.	0			c.935_937del						PASS	.			81,4185		7,67,2059						4.0	0.0		dbSNP_134	78	575,7679		21,533,3573	no	coding	APLF	NM_173545.2		28,600,5632	A1A1,A1R,RR		6.9663,1.8987,5.2396				656,11864				SO:0001651	inframe_deletion	200558	exon7			.	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.936_938delAAG	2.37:g.68765135_68765137delAAG	ENSP00000307004:p.Arg313del	Somatic	288	.	.		WXS	Illumina HiSeq	Phase_I	419	123	0.294	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	In_Frame_Del	DEL	ENST00000303795.4	37	CCDS1888.1																																																																																			AAG|0.949;-|0.051	0.051	strong		0.384	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
AHNAK	79026	hgsc.bcm.edu	37	11	62303555	62303556	+	In_Frame_Ins	INS	-	-	CTC	rs113658672|rs145590149|rs377504333	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62303555_62303556insCTC	ENST00000378024.4	-	3	289_290	c.15_16insGAG	c.(13-18)gagaca>gagGAGaca	p.5_6insE	RP11-864I4.3_ENST00000544108.1_RNA|AHNAK_ENST00000257247.7_In_Frame_Ins_p.5_6insE|AHNAK_ENST00000530124.1_In_Frame_Ins_p.5_6insE	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TCCCGGGTTGTCTCCTCCTTCT	0.614														430	0.0858626	0.2587	0.0375	5008	,	,		16210	0.0119		0.0258	False		,,,				2504	0.0245				p.T6delinsET		Pindel,Atlas-Indel	.											.	AHNAK	532	.	0			c.16_17insGAG						PASS	.		,	935,3329		99,737,1296					,	1.4	0.9		dbSNP_132	49	220,8034		4,212,3911	no	coding,coding	AHNAK	NM_024060.2,NM_001620.1	,	103,949,5207	A1A1,A1R,RR		2.6654,21.9278,9.2267	,	,		1155,11363				SO:0001652	inframe_insertion	79026	exon3			.	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.13_15dupGAG	11.37:g.62303559_62303561dupCTC	ENSP00000367263:p.Glu5_Glu5dup	Somatic	115	.	.		WXS	Illumina HiSeq	Phase_I	130	43	0.331	NM_001620	A1A586	In_Frame_Ins	INS	ENST00000378024.4	37	CCDS31584.1																																																																																			.	.	strong		0.614	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
PKD1	5310	hgsc.bcm.edu	37	16	2144160	2144161	+	In_Frame_Ins	INS	-	-	TGG			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2144160_2144161insTGG	ENST00000262304.4	-	35	10758_10759	c.10550_10551insCCA	c.(10549-10551)ggg>ggCCAg	p.3517_3518insQ	PKD1_ENST00000423118.1_In_Frame_Ins_p.3516_3517insQ|RP11-304L19.3_ENST00000565937.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3517					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GCCCCAGCTCCCCCAGCCTCTG	0.663																																					p.G3517delinsGQ		Pindel,Atlas-Indel	.											.	PKD1	184	.	0			c.10551_10552insCCA						PASS	.																																			SO:0001652	inframe_insertion	5310	exon35			.	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.10550_10551insCCA	16.37:g.2144160_2144161insTGG	ENSP00000262304:p.Gly3517_Glu3518insGln	Somatic	167	.	.		WXS	Illumina HiSeq	Phase_I	217	59	0.272	NM_001009944	Q15140|Q15141	In_Frame_Ins	INS	ENST00000262304.4	37	CCDS32369.1																																																																																			.	.	none		0.663	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
SPANXN4	441525	hgsc.bcm.edu	37	X	142121809	142121811	+	Splice_Site	DEL	AGA	AGA	-	rs368252596		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:142121809_142121811delAGA	ENST00000446864.1	+	2	175_176	c.78_79delAGA	c.(76-81)aaagaa>aaaa	p.E27del	SPANXN4_ENST00000370504.3_Intron	NM_001009613.2	NP_001009613.1	Q5MJ08	SPXN4_HUMAN	SPANX family, member N4	27										endometrium(2)|large_intestine(2)|lung(3)|ovary(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					TTTTTTTACCAGAAGAAGAAGAA	0.414																																					.		Pindel,Atlas-Indel	.											.	SPANXN4	10	.	0			.						PASS	.			28,3000		4,16,4,1234,516						0.8	0.0		dbSNP_131	21	265,5828		10,168,77,2059,1542	no	coding-near-splice	SPANXN4	NM_001009613.2		14,184,81,3293,2058	A1A1,A1R,A1,RR,R		4.3493,0.9247,3.2124				293,8828				SO:0001630	splice_region_variant	441525	.			.	DQ336126	CCDS48178.1	Xq27.3	2009-03-25			ENSG00000189326	ENSG00000189326			33177	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 9"""	300667				14973187, 17012309	Standard	NM_001009613		Approved	SPANX-N4, CT11.9	uc004fbv.4	Q5MJ08	OTTHUMG00000022575	ENST00000446864.1:c.79-1AGA>-	X.37:g.142121818_142121820delAGA		Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	229	39	0.170	.	Q0ZNK6|Q5W0S6	Splice_Site	DEL	ENST00000446864.1	37	CCDS48178.1																																																																																			.	.	none		0.414	SPANXN4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377539.1	NM_001009613	In_Frame_Del
FCRL5	83416	hgsc.bcm.edu	37	1	157488567	157488567	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:157488567delG	ENST00000361835.3	-	14	2823	c.2666delC	c.(2665-2667)cctfs	p.P889fs	FCRL5_ENST00000461387.1_5'UTR|FCRL5_ENST00000356953.4_Frame_Shift_Del_p.P889fs	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	889					negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				CGAGTCTGAAGGGCTCCTGTG	0.493																																					p.P889fs		Pindel,Atlas-Indel	.											FCRL5,NS,carcinoma,-1,1	FCRL5	177	1	0			c.2667delT						PASS	.						93.0	91.0	92.0					1																	157488567		2203	4300	6503	SO:0001589	frameshift_variant	83416	exon14			.	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.2666delC	1.37:g.157488567delG	ENSP00000354691:p.Pro889fs	Somatic	171	.	.		WXS	Illumina HiSeq	Phase_I	209	52	0.249	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Frame_Shift_Del	DEL	ENST00000361835.3	37	CCDS1165.1																																																																																			.	.	none		0.493	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
TOP3A	7156	hgsc.bcm.edu	37	17	18205751	18205760	+	Intron	DEL	GGAGAGTGAA	GGAGAGTGAA	-	rs398030477|rs56191269|rs376457096|rs66697088	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GGAGAGTGAA	GGAGAGTGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18205751_18205760delGGAGAGTGAA	ENST00000321105.5	-	7	858				TOP3A_ENST00000542570.1_Intron|TOP3A_ENST00000540524.1_5'Flank	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha						DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						GGCAGCTCCTGGAGAGTGAAGGAGAGTGAA	0.51														1135	0.226637	0.3275	0.268	5008	,	,		22295	0.0605		0.3082	False		,,,				2504	0.1483				.		Pindel,Atlas-Indel	.											.	TOP3A	85	.	0			.						PASS	.			1400,2860		219,962,949						6.1	1.0		dbSNP_126	37	2430,5820		352,1726,2047	no	intron	TOP3A	NM_004618.3		571,2688,2996	A1A1,A1R,RR		29.4545,32.8638,30.6155				3830,8680				SO:0001627	intron_variant	7156	.			.	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.644-3TTCACTCTCC>-	17.37:g.18205761_18205770delGGAGAGTGAA		Somatic	94	.	.		WXS	Illumina HiSeq	Phase_I	89	27	0.303	.	A8KA61|B4DK80|D3DXC7|Q13473	Splice_Site	DEL	ENST00000321105.5	37	CCDS11194.1																																																																																			GGAGAGTGAA|0.758;-|0.242	0.242	strong		0.510	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
PKD1L2	114780	hgsc.bcm.edu	37	16	81242149	81242150	+	RNA	DEL	TT	TT	-	rs55980345|rs75398810|rs532218091|rs548490632|rs386792900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81242149_81242150delTT	ENST00000525539.1	-	0	705_706				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.N236fs*26(6)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CGGACACAGGTTTCCAAAGTAG	0.554																																					p.236_236del		Atlas-Indel	.											.	PKD1L2	361	.	6	Deletion - Frameshift(6)	breast(4)|lung(2)	c.707_708del						PASS	.																																					114780	exon4			.	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242149_81242150delTT		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Frame_Shift_Del	DEL	ENST00000525539.1	37																																																																																				TT|0.500;-|0.500	0.500	strong		0.554	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
CLVS1	157807	hgsc.bcm.edu	37	8	62412051	62412053	+	In_Frame_Del	DEL	GAG	GAG	-	rs35623706	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:62412051_62412053delGAG	ENST00000519846.1	+	7	1487_1489	c.1015_1017delGAG	c.(1015-1017)gagdel	p.E340del	CLVS1_ENST00000518858.1_3'UTR|CLVS1_ENST00000518592.1_In_Frame_Del_p.E61del|CLVS1_ENST00000325897.4_In_Frame_Del_p.E340del			Q8IUQ0	CLVS1_HUMAN	clavesin 1	340					lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)			endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						CCTGAAACATGAGGAGAAGGGAG	0.498														8	0.00159744	0.0	0.0014	5008	,	,		18651	0.0		0.006	False		,,,				2504	0.001				p.338_339del		Pindel,Atlas-Indel	.											.	CLVS1	74	.	0			c.1014_1016del						PASS	.			6,4258		0,6,2126						2.0	1.0		dbSNP_126	118	75,8179		1,73,4053	no	coding	CLVS1	NM_173519.2		1,79,6179	A1A1,A1R,RR		0.9087,0.1407,0.6471				81,12437				SO:0001651	inframe_deletion	157807	exon6			.	AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"""retinaldehyde binding protein 1-like 1"""	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.1015_1017delGAG	8.37:g.62412054_62412056delGAG	ENSP00000428402:p.Glu340del	Somatic	129	.	.		WXS	Illumina HiSeq	Phase_I	136	50	0.368	NM_173519	B2R7M5|C8UZT3|Q8NB32	In_Frame_Del	DEL	ENST00000519846.1	37	CCDS6176.1																																																																																			GAG|0.500;-|0.500	0.500	weak		0.498	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519	
CWH43	80157	hgsc.bcm.edu	37	4	49034670	49034670	+	Frame_Shift_Del	DEL	A	A	-	rs147750792	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:49034670delA	ENST00000226432.4	+	12	1779	c.1596delA	c.(1594-1596)acafs	p.T532fs	CWH43_ENST00000513409.1_Frame_Shift_Del_p.T505fs	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	532					GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						CAGCCATCACATTGACCGTTA	0.473													A|A|-|deletion	67	0.0133786	0.0015	0.0173	5008	,	,		21594	0.0149		0.0288	False		,,,				2504	0.0092				p.T532fs		Pindel,Atlas-Indel	.											.	CWH43	101	.	0			c.1595delC						PASS	.			23,4243		0,23,2110	217.0	185.0	196.0			4.9	0.0	4	dbSNP_134	199	137,8117		1,135,3991	no	frameshift	CWH43	NM_025087.2		1,158,6101	A1A1,A1R,RR		1.6598,0.5391,1.278			49034670	160,12360	2203	4299	6502	SO:0001589	frameshift_variant	80157	exon12			.		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.1596delA	4.37:g.49034670delA	ENSP00000226432:p.Thr532fs	Somatic	231	.	.		WXS	Illumina HiSeq	Phase_I	240	65	0.271	NM_025087	B2RPD7	Frame_Shift_Del	DEL	ENST00000226432.4	37	CCDS3486.1																																																																																			A|0.980;-|0.020	0.020	strong		0.473	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087	
SPATA31A5	727905	hgsc.bcm.edu	37	9	41506129	41506129	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:41506129delC	ENST00000377621.1	+	4	3430	c.3401delC	c.(3400-3402)accfs	p.T1134fs	RP11-100J16.5_ENST00000429787.2_RNA	NM_001113541.1	NP_001107013.1	Q5VU36	S31A5_HUMAN	SPATA31 subfamily A, member 5	1134					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCTCAACTTACCCCAGTCAGG	0.463																																					p.T1134fs		Atlas-Indel	.											.	.	.	.	0			c.3400delA						PASS	.																																			SO:0001589	frameshift_variant	727905	exon4			.			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000233788				32005	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A5"""	FAM75A5		20850414	Standard	NM_001113541		Approved	OTTHUMG00000013204	uc004abu.4	Q5VU36	OTTHUMG00000013204	ENST00000377621.1:c.3401delC	9.37:g.41506129delC	ENSP00000366847:p.Thr1134fs	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	290	101	0.348276	NM_001113541		Frame_Shift_Del	DEL	ENST00000377621.1	37	CCDS47970.1																																																																																			.	.	none		0.463	SPATA31A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036962.1	NM_001113541	
IFNE	338376	hgsc.bcm.edu	37	9	21482239	21482241	+	5'UTR	DEL	AAT	AAT	-	rs3028326|rs397894161|rs34533918	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:21482239_21482241delAAT	ENST00000448696.3	-	0	71_73				MIR31HG_ENST00000304425.3_RNA	NM_176891.4	NP_795372.1	Q86WN2	IFNE_HUMAN	interferon, epsilon						adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(2)|lung(1)|skin(1)	4						TGCTTGAGCAAATAATTaatttt	0.261														783	0.15635	0.1604	0.0937	5008	,	,		15774	0.2083		0.0577	False		,,,				2504	0.2434				.		Pindel,Atlas-Indel	.											.	IFNE	16	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	338376	.			.	AY190045	CCDS34997.1	9p21.1	2008-12-12			ENSG00000184995	ENSG00000184995			18163	protein-coding gene	gene with protein product		615223				15546383, 17287131	Standard	NM_176891		Approved	IFNE1	uc003zpg.3	Q86WN2	OTTHUMG00000019672	ENST00000448696.3:c.-548ATT>-	9.37:g.21482242_21482244delAAT		Somatic	69	.	.		WXS	Illumina HiSeq	Phase_I	63	23	0.365	.		RNA	DEL	ENST00000448696.3	37	CCDS34997.1																																																																																			AAT|0.882;-|0.118	0.118	strong		0.261	IFNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051901.2	NM_176891	
CCDC66	285331	hgsc.bcm.edu	37	3	56650051	56650052	+	In_Frame_Ins	INS	-	-	CTT	rs67797937|rs77152637|rs74463118	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:56650051_56650052insCTT	ENST00000394672.3	+	13	1883_1884	c.1813_1814insCTT	c.(1813-1815)act>aCTTct	p.606_607insS	CCDC66_ENST00000436465.2_In_Frame_Ins_p.606_607insS|CCDC66_ENST00000326595.7_In_Frame_Ins_p.572_573insS	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	606					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		GAATTCTACGACTTCTAAGAAG	0.287																																					p.T605delinsTS		Pindel,Atlas-Indel	.											.	CCDC66	145	.	0			c.1813_1814insCTT						PASS	.		,	3586,680		1520,546,67					,	1.9	0.0		dbSNP_130	92	3788,4448		872,2044,1202	no	coding,coding	CCDC66	NM_001141947.1,NM_001012506.4	,	2392,2590,1269	A1A1,A1R,RR		45.9932,15.94,41.0174	,	,		7374,5128				SO:0001652	inframe_insertion	285331	exon13			.	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1814_1816dupCTT	3.37:g.56650052_56650054dupCTT	ENSP00000378167:p.Ser606_Ser606dup	Somatic	133	.	.		WXS	Illumina HiSeq	Phase_I	119	82	0.689	NM_001141947	B3KWL8|Q4VC34|Q8N949	In_Frame_Ins	INS	ENST00000394672.3	37	CCDS46852.1																																																																																			-|0.298;CTT|0.702	0.702	strong		0.287	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
ALPK2	115701	hgsc.bcm.edu	37	18	56204388	56204402	+	In_Frame_Del	DEL	CAGTTGATGTGTCCT	CAGTTGATGTGTCCT	-	rs199745034|rs201560823|rs386803723|rs149103820|rs60644017|rs67925233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CAGTTGATGTGTCCT	CAGTTGATGTGTCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56204388_56204402delCAGTTGATGTGTCCT	ENST00000361673.3	-	5	3230_3244	c.3017_3031delAGGACACATCAACTG	c.(3016-3033)gaggacacatcaactgtt>gtt	p.EDTST1006del	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1006						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GCAATGGTAACAGTTGATGTGTCCTCAGTCTCCCT	0.493														2013	0.401957	0.4274	0.4251	5008	,	,		24283	0.2371		0.5696	False		,,,				2504	0.3487				p.1006_1011del		Pindel,Atlas-Indel	.											.	ALPK2	487	.	0			c.3018_3032del						PASS	.																																			SO:0001651	inframe_deletion	115701	exon5			.	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.3017_3031delAGGACACATCAACTG	18.37:g.56204388_56204402delCAGTTGATGTGTCCT	ENSP00000354991:p.Glu1006_Thr1010del	Somatic	192	.	.		WXS	Illumina HiSeq	Phase_I	186	40	0.215	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	In_Frame_Del	DEL	ENST00000361673.3	37	CCDS11966.2																																																																																			.	.	strong		0.493	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
BTNL2	56244	hgsc.bcm.edu	37	6	32370970	32370970	+	Frame_Shift_Del	DEL	G	G	-	rs370253771|rs60740710	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32370970delG	ENST00000374993.1	-	3	450	c.451delC	c.(451-453)cacfs	p.H151fs	BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000454136.3_Frame_Shift_Del_p.H151fs|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000374995.3_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	151	Ig-like V-type 2.					integral component of membrane (GO:0016021)		p.H151fs*96(1)		central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CCCTCCATGTGGATGCTAGGG	0.602													GG|GG|G|deletion	672	0.134185	0.1369	0.1369	5008	,	,		18467	0.1984		0.0974	False		,,,				2504	0.1002				p.H151fs		Pindel,Atlas-Indel	.											.	BTNL2	50	.	1	Deletion - Frameshift(1)	kidney(1)	c.452delA						PASS	.			408,3086		47,314,1386	22.0	22.0	22.0			3.5	0.9	6	dbSNP_129	24	520,6118		63,394,2862	yes	frameshift	BTNL2	NM_019602.1		110,708,4248	A1A1,A1R,RR		7.8337,11.6772,9.1591			32370970	928,9204	1502	2696	4198	SO:0001589	frameshift_variant	56244	exon3			.	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.451delC	6.37:g.32370970delG	ENSP00000364132:p.His151fs	Somatic	53	.	.		WXS	Illumina HiSeq	Phase_I	68	17	0.250	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Frame_Shift_Del	DEL	ENST00000374993.1	37																																																																																				G|0.866;-|0.134	0.134	strong		0.602	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
SLC5A9	200010	hgsc.bcm.edu	37	1	48694606	48694609	+	Frame_Shift_Del	DEL	GTAG	GTAG	-	rs200805074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GTAG	GTAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:48694606_48694609delGTAG	ENST00000438567.2	+	3	371_374	c.319_322delGTAG	c.(319-324)gtaggtfs	p.VG107fs	RP5-1024N4.4_ENST00000606809.1_RNA|SLC5A9_ENST00000420136.2_Frame_Shift_Del_p.VG100fs|SLC5A9_ENST00000533824.1_Frame_Shift_Del_p.VG107fs|SLC5A9_ENST00000236495.5_Frame_Shift_Del_p.VG107fs	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	107					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						AGGCCTTGCCGTAGGTGGCTTCGA	0.569																																					p.106_107del		Pindel,Atlas-Indel	.											SLC5A9,rectum,carcinoma,0,1	SLC5A9	82	1	0			c.318_321del						PASS	.		,	0,4266		0,0,2133					,	0.2	1.0			80	1,8253		0,1,4126	no	frameshift,frameshift	SLC5A9	NM_001135181.1,NM_001011547.2	,	0,1,6259	A1A1,A1R,RR		0.0121,0.0,0.0080	,	,		1,12519				SO:0001589	frameshift_variant	200010	exon3			.	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.319_322delGTAG	1.37:g.48694606_48694609delGTAG	ENSP00000401730:p.Val107fs	Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	43	14	0.326	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Frame_Shift_Del	DEL	ENST00000438567.2	37	CCDS30709.2																																																																																			.	.	none		0.569	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
OR1B1	347169	hgsc.bcm.edu	37	9	125391770	125391771	+	Frame_Shift_Ins	INS	-	-	A	rs398102330|rs78126045|rs11421222	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:125391770_125391771insA	ENST00000304833.3	-	1	81_82	c.44_45insT	c.(43-45)ttgfs	p.L15fs	RP11-64P14.7_ENST00000431442.1_RNA|RP11-64P14.7_ENST00000419604.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	15						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						ACCCAAGGAGCAAAAAAACCGG	0.475													?|AAAAAAA|AAAAAAAA|unsure	2046	0.408546	0.3888	0.2954	5008	,	,		22113	0.3383		0.504	False		,,,				2504	0.4898				p.L15fs		Pindel,Atlas-Indel	.											.	OR1B1	48	.	0			c.45_46insT						PASS	.			1831,2421		393,1045,688						-0.3	0.5		dbSNP_134	87	4104,4128		1026,2052,1038	no	frameshift	OR1B1	NM_001004450.1		1419,3097,1726	A1A1,A1R,RR		49.8542,43.0621,47.5409				5935,6549				SO:0001589	frameshift_variant	347169	exon1			.	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"""GPCR / Class A : Olfactory receptors"""	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.45dupT	9.37:g.125391777_125391777dupA	ENSP00000303151:p.Leu15fs	Somatic	77	.	.		WXS	Illumina HiSeq	Phase_I	83	21	0.253	NM_001004450	Q6IFN3	Frame_Shift_Ins	INS	ENST00000304833.3	37	CCDS35126.1																																																																																			-|0.589;A|0.411	0.411	strong		0.475	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450	
KRT4	3851	hgsc.bcm.edu	37	12	53207602	53207603	+	Frame_Shift_Ins	INS	-	-	G	rs7135148|rs71092788		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53207602_53207603insG	ENST00000551956.1	-	1	732_733	c.240_241insC	c.(238-243)tttggcfs	p.G81fs	KRT4_ENST00000293774.4_Frame_Shift_Ins_p.G155fs|KRT4_ENST00000458244.2_Frame_Shift_Ins_p.G61fs			P19013	K2C4_HUMAN	keratin 4	81	Gly-rich.|Head.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CCACCAGTGCCAAAGCCTCCAG	0.599																																					p.G81fs	Pancreas(190;284 2995 41444 45903)	Atlas-Indel	.											.	KRT4	110	.	0			c.241_242insC						PASS	.																																			SO:0001589	frameshift_variant	3851	exon1			.		CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.240_241insC	12.37:g.53207602_53207603insG	ENSP00000448220:p.Gly81fs	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	101	40	0.39604	NM_002272	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Frame_Shift_Ins	INS	ENST00000551956.1	37	CCDS41787.2																																																																																			.	.	none		0.599	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
DNAH14	127602	hgsc.bcm.edu	37	1	225380562	225380565	+	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs191528375|rs144339803	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225380562_225380565delAAAG	ENST00000445597.2	+	25	4554_4557	c.4554_4557delAAAG	c.(4552-4557)acaaagfs	p.TK1518fs	DNAH14_ENST00000439375.2_Frame_Shift_Del_p.TK1923fs|DNAH14_ENST00000430092.1_Frame_Shift_Del_p.TK1923fs			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1518					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CAAAGAACACAAAGAAAGACATTG	0.289														98	0.0195687	0.0038	0.0231	5008	,	,		16043	0.0		0.0636	False		,,,				2504	0.0133				p.1923_1924del		Pindel,Atlas-Indel	.											.	DNAH14	300	.	0			c.5768_5771del						PASS	.			26,1986		3,20,983						3.0	0.0		dbSNP_134	171	216,3860		17,182,1839	no	frameshift	DNAH14	NM_001373.1		20,202,2822	A1A1,A1R,RR		5.2993,1.2922,3.975				242,5846				SO:0001589	frameshift_variant	127602	exon37			.	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.4554_4557delAAAG	1.37:g.225380566_225380569delAAAG	ENSP00000409472:p.Thr1518fs	Somatic	178	.	.		WXS	Illumina HiSeq	Phase_I	184	60	0.326	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Frame_Shift_Del	DEL	ENST00000445597.2	37																																																																																				AAAG|0.968;-|0.032	0.032	strong		0.289	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
MAN1A2	10905	hgsc.bcm.edu	37	1	117945057	117945067	+	Splice_Site	DEL	TAAAGAGGTAA	TAAAGAGGTAA	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TAAAGAGGTAA	TAAAGAGGTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:117945057_117945067delTAAAGAGGTAA	ENST00000356554.3	+	2	1287_1293	c.552_558delTAAAGAGGTAA	c.(550-558)attaaagag>at	p.IKE184fs	MAN1A2_ENST00000482811.1_Intron	NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	184					cellular protein metabolic process (GO:0044267)|lung alveolus development (GO:0048286)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	27	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		GGGAAAAAATTAAAGAGGTAATAAGCTGAGT	0.36																																					p.184_186del	Ovarian(33;199 881 8228 13687 31538)	Pindel,Atlas-Indel	.											.	MAN1A2	50	.	0			c.551_558del						PASS	.																																			SO:0001630	splice_region_variant	10905	exon2			.	AF027156	CCDS895.1	1p13	2008-02-05			ENSG00000198162	ENSG00000198162			6822	protein-coding gene	gene with protein product		604345				9592125	Standard	NM_006699		Approved	MAN1B	uc001ehd.1	O60476	OTTHUMG00000012149	ENST00000356554.3:c.558+1TAAAGAGGTAA>-	1.37:g.117945057_117945067delTAAAGAGGTAA		Somatic	114	.	.		WXS	Illumina HiSeq	Phase_I	95	30	0.316	NM_006699	Q9H510	Frame_Shift_Del	DEL	ENST00000356554.3	37	CCDS895.1																																																																																			.	.	none		0.360	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033593.1	NM_006699	Frame_Shift_Del
ACIN1	22985	hgsc.bcm.edu	37	14	23548787	23548788	+	In_Frame_Ins	INS	-	-	GTGAAT	rs55838227|rs34870944|rs61741619	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23548787_23548788insGTGAAT	ENST00000262710.1	-	6	2257_2258	c.1930_1931insATTCAC	c.(1930-1932)cgt>cATTCACgt	p.643_644insHS	ACIN1_ENST00000555053.1_In_Frame_Ins_p.643_644insHS|ACIN1_ENST00000457657.1_In_Frame_Ins_p.603_604insHS|ACIN1_ENST00000605057.1_In_Frame_Ins_p.585_586insHS|ACIN1_ENST00000555352.1_5'Flank	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	643	Ser-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S643_R644insHS(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		TGAACGAGAACGTGAACGTGAC	0.49																																					p.R644delinsHSR		Pindel,Atlas-Indel	.											.	ACIN1	147	.	1	Insertion - In frame(1)	upper_aerodigestive_tract(1)	c.1931_1932insATTCAC						PASS	.																																			SO:0001652	inframe_insertion	22985	exon6			.	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1930_1931insATTCAC	14.37:g.23548787_23548788insGTGAAT	ENSP00000262710:p.Ser643_Arg644insHisSer	Somatic	202	.	.		WXS	Illumina HiSeq	Phase_I	229	36	0.157	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	In_Frame_Ins	INS	ENST00000262710.1	37	CCDS9587.1																																																																																			-|0.604;GTGAAT|0.396	0.396	strong		0.490	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
BDNF	627	hgsc.bcm.edu	37	11	27681176	27681177	+	5'UTR	INS	-	-	TG	rs149254890|rs397725548|rs28722151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:27681176_27681177insTG	ENST00000525528.1	-	0	28_29				BDNF_ENST00000532997.1_Intron|BDNF_ENST00000533246.1_Intron|BDNF_ENST00000418212.1_Intron|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000395986.2_Intron|BDNF_ENST00000314915.6_Intron|BDNF-AS_ENST00000501176.2_RNA|BDNF_ENST00000395980.2_Intron|BDNF_ENST00000356660.4_Intron|BDNF_ENST00000439476.2_5'UTR|BDNF-AS_ENST00000499008.3_RNA|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000525950.1_Intron|BDNF_ENST00000395978.3_Intron|BDNF_ENST00000395981.3_Intron|BDNF_ENST00000584049.1_Intron|BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000420794.1_Intron|BDNF_ENST00000533131.1_Intron|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000438929.1_Intron|BDNF_ENST00000395983.3_Intron|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000530861.1_Intron|BDNF-AS_ENST00000532965.1_RNA	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor						axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						GATGTTCTCTCtgtgtgtgtgt	0.446																																					.		Atlas-Indel	.											.	BDNF	63	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	627	.			.	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"""Endogenous ligands"""	1033	protein-coding gene	gene with protein product	"""neurotrophin"""	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.-1066->CA	11.37:g.27681185_27681186dupTG		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	224	110	0.491071	.	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	RNA	INS	ENST00000525528.1	37	CCDS7866.1																																																																																			.	.	strong		0.446	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735	
PRDM2	7799	hgsc.bcm.edu	37	1	14106394	14106395	+	In_Frame_Ins	INS	-	-	CTC	rs2308040|rs148293494|rs59028030		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14106394_14106395insCTC	ENST00000235372.7	+	8	2960_2961	c.2104_2105insCTC	c.(2104-2106)act>aCTCct	p.703_704insP	PRDM2_ENST00000343137.4_In_Frame_Ins_p.502_503insP|PRDM2_ENST00000311066.5_In_Frame_Ins_p.703_704insP|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_In_Frame_Ins_p.502_503insP	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	703				P -> PP (in Ref. 1 and 7). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P703_A704insP(1)		endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		AGATAAACTAACTCCTGCAGGG	0.401																																					p.T702delinsTP		Pindel,Atlas-Indel	.											.	PRDM2	147	.	1	Insertion - In frame(1)	ovary(1)	c.2104_2105insCTC						PASS	.		,,,	2438,1826		699,1040,393					,,,	0.5	0.2		dbSNP_100	80	3443,4811		676,2091,1360	no	coding,coding,intron,coding	PRDM2	NM_015866.4,NM_012231.4,NM_001135610.1,NM_001007257.2	,,,	1375,3131,1753	A1A1,A1R,RR		41.7131,42.8236,46.9803	,,,	,,,		5881,6637				SO:0001652	inframe_insertion	7799	exon8			.	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.2105_2107dupCTC	1.37:g.14106395_14106397dupCTC	ENSP00000235372:p.Pro703_Pro703dup	Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	139	39	0.281	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	In_Frame_Ins	INS	ENST00000235372.7	37	CCDS150.1																																																																																			-|0.492;CTC|0.508	0.508	strong		0.401	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
DEFB126	81623	hgsc.bcm.edu	37	20	126311	126312	+	Frame_Shift_Del	DEL	CC	CC	-	rs376364807|rs11467417|rs386393058		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:126311_126312delCC	ENST00000382398.3	+	2	574_575	c.314_315delCC	c.(313-315)accfs	p.T105fs	DEFB126_ENST00000542572.1_3'UTR	NM_030931.3	NP_112193.1	Q9BYW3	DB126_HUMAN	defensin, beta 126	105					defense response to bacterium (GO:0042742)	cell surface (GO:0009986)|extracellular region (GO:0005576)|glycocalyx (GO:0030112)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			ATGGCTCCTACCCCCGTTTCTC	0.455																																					p.105_105del		Atlas-Indel	.											.	DEFB126	52	.	0			c.313_314del						PASS	.			2386,1878		678,1030,424						-4.7	0.0		dbSNP_120	113	4702,3552		1341,2020,766	no	frameshift	DEFB126	NM_030931.2		2019,3050,1190	A1A1,A1R,RR		43.0337,44.0432,43.3775				7088,5430				SO:0001589	frameshift_variant	81623	exon2			.		CCDS12990.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125788	ENSG00000125788		"""Defensins, beta"""	15900	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 8"""	C20orf8		11854508	Standard	NM_030931		Approved	bA530N10.1, DEFB-26	uc002wcx.3	Q9BYW3	OTTHUMG00000031616	ENST00000382398.3:c.314_315delCC	20.37:g.126313_126314delCC	ENSP00000371835:p.Thr105fs	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_030931	Q562G3|Q9H1M5	Frame_Shift_Del	DEL	ENST00000382398.3	37	CCDS12990.1																																																																																			CC|0.459;-|0.541	0.541	strong		0.455	DEFB126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077428.2	NM_030931	
KCNA7	3743	hgsc.bcm.edu	37	19	49573363	49573365	+	In_Frame_Del	DEL	GGA	GGA	-	rs10535426|rs12975537|rs375428032	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49573363_49573365delGGA	ENST00000221444.1	-	2	1681_1683	c.1326_1328delTCC	c.(1324-1329)cctcca>cca	p.442_443PP>P		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	442					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	TGCCCAGAGTGGAGGTGGTAGCT	0.631														725	0.144768	0.2988	0.1398	5008	,	,		15138	0.0486		0.0875	False		,,,				2504	0.0982				p.443_443del	Colon(74;686 1235 3793 23366 48562)	Pindel,Atlas-Indel	.											.	KCNA7	30	.	0			c.1327_1329del						PASS	.			1096,3166		123,850,1158						-0.9	0.9		dbSNP_107	73	770,7484		38,694,3395	no	coding	KCNA7	NM_031886.2		161,1544,4553	A1A1,A1R,RR		9.3288,25.7156,14.9089				1866,10650				SO:0001651	inframe_deletion	3743	exon2			.	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.1326_1328delTCC	19.37:g.49573363_49573365delGGA	ENSP00000221444:p.Pro443del	Somatic	58	.	.		WXS	Illumina HiSeq	Phase_I	82	51	0.622	NM_031886	A1KYX7|Q9BYS4	In_Frame_Del	DEL	ENST00000221444.1	37	CCDS12755.1																																																																																			GGA|0.851;-|0.149	0.149	strong		0.631	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886	
C2orf71	388939	hgsc.bcm.edu	37	2	29287926	29287927	+	In_Frame_Ins	INS	-	-	GCT	rs139768554|rs72122505|rs201781577|rs35753661	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29287926_29287927insGCT	ENST00000331664.5	-	2	3674_3675	c.3675_3676insAGC	c.(3673-3678)agcgag>agcAGCgag	p.1225_1226insS	C2orf71_ENST00000602958.1_5'Flank	NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1225			S -> SS. {ECO:0000269|PubMed:21412943}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)		p.S1225_E1226insS(2)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GGGCTCTCCTCGCTGCTGCTGC	0.624														1871	0.373602	0.5257	0.2637	5008	,	,		17644	0.4931		0.2545	False		,,,				2504	0.2454				p.E1226delinsSE		Pindel,Atlas-Indel	.											.	C2orf71	146	.	2	Insertion - In frame(2)	ovary(1)|breast(1)	c.3676_3677insAGC						PASS	.			1580,1994		462,656,669						5.2	1.0		dbSNP_130	16	1923,5511		406,1111,2200	no	coding	C2orf71	NM_001029883.1		868,1767,2869	A1A1,A1R,RR		25.8676,44.2082,31.8223				3503,7505				SO:0001652	inframe_insertion	388939	exon2			.		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3673_3675dupAGC	2.37:g.29287933_29287935dupGCT	ENSP00000332809:p.Ser1225_Ser1225dup	Somatic	43	.	.		WXS	Illumina HiSeq	Phase_I	61	18	0.295	NM_001029883		In_Frame_Ins	INS	ENST00000331664.5	37	CCDS42669.1																																																																																			.	.	strong		0.624	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
SSC5D	284297	hgsc.bcm.edu	37	19	56029616	56029617	+	In_Frame_Ins	INS	-	-	CCA	rs35104581|rs71181782|rs150781976	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56029616_56029617insCCA	ENST00000389623.6	+	14	3996_3997	c.3973_3974insCCA	c.(3973-3975)ccc>cCCAcc	p.1327_1328insT		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1327	Pro-rich.|Thr-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						gacccctcaccccACAACTCCT	0.599														1953	0.389976	0.4486	0.4193	5008	,	,		12005	0.5466		0.3012	False		,,,				2504	0.2198				p.P1325delinsPT		Atlas-Indel	.											.	SSC5D	65	.	0			c.3973_3974insCCA						PASS	.			1160,1648		342,476,586						2.2	0.0		dbSNP_126	332	1299,3745		266,767,1489	no	coding	SSC5D	NM_001144950.1		608,1243,2075	A1A1,A1R,RR		25.7534,41.3105,31.3169				2459,5393				SO:0001652	inframe_insertion	284297	exon14			.		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.3974_3976dupCCA	19.37:g.56029617_56029619dupCCA	ENSP00000374274:p.Thr1327_Thr1327dup	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	103	40	0.38835	NM_001144950	B5MDQ5|C7S7T9|C7S7U0|K7EP70	In_Frame_Ins	INS	ENST00000389623.6	37	CCDS46196.1																																																																																			.	.	strong		0.599	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
ZNF681	148213	hgsc.bcm.edu	37	19	23927742	23927743	+	Frame_Shift_Del	DEL	CA	CA	-	rs61397759	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:23927742_23927743delCA	ENST00000402377.3	-	4	750_751	c.609_610delTG	c.(607-612)tgtggafs	p.CG203fs	ZNF681_ENST00000395385.3_Frame_Shift_Del_p.CG134fs	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	203					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)	p.C134fs*5(1)|p.G135R(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				AAGGCTTTTCCACAGTCTTCAC	0.292														564	0.11262	0.0106	0.1441	5008	,	,		17190	0.0913		0.1998	False		,,,				2504	0.1605				p.204_204del		Pindel,Atlas-Indel	.											LOC148213,extremity,malignant_melanoma,-1,1	ZNF681	76	1	2	Substitution - Missense(1)|Deletion - Frameshift(1)	ovary(1)|skin(1)	c.610_611del						PASS	.			179,4075		8,163,1956						-2.8	0.0		dbSNP_129	28	1687,6547		180,1327,2610	yes	frameshift	ZNF681	NM_138286.2		188,1490,4566	A1A1,A1R,RR		20.4882,4.2078,14.9423				1866,10622				SO:0001589	frameshift_variant	148213	exon4			.	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"""Zinc fingers, C2H2-type"", ""-"""	26457	protein-coding gene	gene with protein product	"""hypothetical protein FLJ31526"""						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.609_610delTG	19.37:g.23927744_23927745delCA	ENSP00000384000:p.Cys203fs	Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	63	29	0.460	NM_138286	B3KVF7	Frame_Shift_Del	DEL	ENST00000402377.3	37	CCDS12414.2																																																																																			CA|0.870;-|0.130	0.130	strong		0.292	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	
GDPD4	220032	hgsc.bcm.edu	37	11	76954788	76954789	+	Frame_Shift_Ins	INS	-	-	A	rs34784710|rs76229203	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:76954788_76954789insA	ENST00000376217.2	-	12	1441_1442	c.1191_1192insT	c.(1189-1194)aatatcfs	p.I398fs	GDPD4_ENST00000315938.4_Frame_Shift_Ins_p.I398fs			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	398	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						ATTATACTGATATTGTTTTTAG	0.416													A|A|AA|insertion	1272	0.253994	0.0514	0.1916	5008	,	,		16545	0.256		0.3718	False		,,,				2504	0.4489				p.I398fs		Pindel,Atlas-Indel	.											.	GDPD4	49	.	0			c.1192_1193insT						PASS	.			442,3822		29,384,1719						1.2	0.7		dbSNP_126	119	2948,5306		503,1942,1682	no	frameshift	GDPD4	NM_182833.1		532,2326,3401	A1A1,A1R,RR		35.716,10.3659,27.081				3390,9128				SO:0001589	frameshift_variant	220032	exon12			.	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1192dupT	11.37:g.76954789_76954789dupA	ENSP00000365390:p.Ile398fs	Somatic	105	.	.		WXS	Illumina HiSeq	Phase_I	100	24	0.240	NM_182833	Q7Z5B0	Frame_Shift_Ins	INS	ENST00000376217.2	37																																																																																				-|0.773;A|0.227	0.227	strong		0.416	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
MED15	51586	hgsc.bcm.edu	37	22	20920813	20920814	+	In_Frame_Ins	INS	-	-	CAGCAGCAGCAG	rs67182670|rs361923|rs535773989|rs539945336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:20920813_20920814insCAGCAGCAGCAG	ENST00000263205.7	+	7	819_820	c.750_751insCAGCAGCAGCAG	c.(751-753)cag>CAGCAGCAGCAGcag	p.251_251Q>QQQQQ	MED15_ENST00000541476.1_In_Frame_Ins_p.225_225Q>QQQQQ|MED15_ENST00000425759.2_In_Frame_Ins_p.140_140Q>QQQQQ|MED15_ENST00000478831.1_3'UTR|MED15_ENST00000542773.1_In_Frame_Ins_p.56_56Q>QQQQQ|MED15_ENST00000292733.7_In_Frame_Ins_p.251_251Q>QQQQQ|MED15_ENST00000382974.2_In_Frame_Ins_p.180_180Q>QQQQQ|MED15_ENST00000406969.1_In_Frame_Ins_p.225_225Q>QQQQQ	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	251	Poly-Gln.			Missing (in Ref. 3; BAB85034). {ECO:0000305}.	gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.Q250_Q251insQ(4)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			aacaacagcaacagcagcagca	0.589																																					p.Q250delinsQQQQQ		Atlas-Indel	.											PCQAP,caecum,carcinoma,0,2	MED15	68	2	4	Insertion - In frame(4)	ovary(2)|large_intestine(2)	c.750_751insCAGCAGCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	51586	exon7			.	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.775_786dupCAGCAGCAGCAG	22.37:g.20920813_20920814insCAGCAGCAGCAG	ENSP00000263205:p.GlnGlnGlnGln259dup	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	13	0.185714	NM_015889	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	In_Frame_Ins	INS	ENST00000263205.7	37	CCDS33602.1																																																																																			.	.	alt		0.589	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889	
HTT	3064	hgsc.bcm.edu	37	4	3230411	3230413	+	In_Frame_Del	DEL	GAG	GAG	-	rs149109767|rs112304717	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:3230411_3230413delGAG	ENST00000355072.5	+	58	8063_8065	c.7918_7920delGAG	c.(7918-7920)gagdel	p.E2643del		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2643	Poly-Glu.				anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		ggacgaggaagaggaggaggagg	0.552														133	0.0265575	0.0045	0.0677	5008	,	,		18486	0.0		0.0606	False		,,,				2504	0.0194				p.2639_2640del		Pindel,Atlas-Indel	.											.	HTT	221	.	0			c.7917_7919del						PASS	.			80,3886		5,70,1908						-4.5	1.0		dbSNP_130	76	529,7479		20,489,3495	no	coding	HTT	NM_002111.6		25,559,5403	A1A1,A1R,RR		6.6059,2.0171,5.086				609,11365				SO:0001651	inframe_deletion	3064	exon58			.	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.7918_7920delGAG	4.37:g.3230420_3230422delGAG	ENSP00000347184:p.Glu2643del	Somatic	76	.	.		WXS	Illumina HiSeq	Phase_I	89	53	0.596	NM_002111	Q9UQB7	In_Frame_Del	DEL	ENST00000355072.5	37	CCDS43206.1																																																																																			GAG|0.965;-|0.035	0.035	strong		0.552	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
CEP162	22832	hgsc.bcm.edu	37	6	84896314	84896316	+	In_Frame_Del	DEL	TTC	TTC	-	rs199518175|rs202045843	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:84896314_84896316delTTC	ENST00000403245.3	-	12	1249_1251	c.1135_1137delGAA	c.(1135-1137)gaadel	p.E379del	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_In_Frame_Del_p.E303del	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		AAAATTCAGTTTCTTTTCTTTCG	0.345														208	0.0415335	0.0151	0.0937	5008	,	,		17340	0.0149		0.0398	False		,,,				2504	0.0695				p.379_380del		Pindel,Atlas-Indel	.											.	KIAA1009	119	.	0			c.1136_1138del						PASS	.			45,4215		1,43,2086						-1.2	0.9			74	359,7891		14,331,3780	no	coding	KIAA1009	NM_014895.2		15,374,5866	A1A1,A1R,RR		4.3515,1.0563,3.2294				404,12106				SO:0001651	inframe_deletion	22832	exon12			.																												ENST00000403245.3:c.1135_1137delGAA	6.37:g.84896314_84896316delTTC	ENSP00000385215:p.Glu379del	Somatic	55	.	.		WXS	Illumina HiSeq	Phase_I	81	27	0.333	NM_014895		In_Frame_Del	DEL	ENST00000403245.3	37	CCDS34494.2																																																																																			TTC|0.961;-|0.039	0.039	strong		0.345	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
DEFB126	81623	hgsc.bcm.edu	37	20	126156	126159	+	Frame_Shift_Del	DEL	CAAA	CAAA	-	rs200807952|rs397788846|rs11467497		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CAAA	CAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:126156_126159delCAAA	ENST00000382398.3	+	2	419_422	c.159_162delCAAA	c.(157-162)ggcaaafs	p.GK53fs	DEFB126_ENST00000542572.1_Intron	NM_030931.3	NP_112193.1	Q9BYW3	DB126_HUMAN	defensin, beta 126	53					defense response to bacterium (GO:0042742)	cell surface (GO:0009986)|extracellular region (GO:0005576)|glycocalyx (GO:0030112)		p.K54K(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			CAATGTGCGGCAAACAAAGGGACT	0.417																																					p.53_54del		Pindel,Atlas-Indel	.											.	DEFB126	52	.	1	Substitution - coding silent(1)	lung(1)	c.158_161del						PASS	.			1092,3172		148,796,1188						-7.1	0.0		dbSNP_120	185	1309,6945		109,1091,2927	yes	frameshift	DEFB126	NM_030931.2		257,1887,4115	A1A1,A1R,RR		15.859,25.6098,19.1804				2401,10117				SO:0001589	frameshift_variant	81623	exon2			.		CCDS12990.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125788	ENSG00000125788		"""Defensins, beta"""	15900	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 8"""	C20orf8		11854508	Standard	NM_030931		Approved	bA530N10.1, DEFB-26	uc002wcx.3	Q9BYW3	OTTHUMG00000031616	ENST00000382398.3:c.159_162delCAAA	20.37:g.126160_126163delCAAA	ENSP00000371835:p.Gly53fs	Somatic	143	.	.		WXS	Illumina HiSeq	Phase_I	165	52	0.315	NM_030931	Q562G3|Q9H1M5	Frame_Shift_Del	DEL	ENST00000382398.3	37	CCDS12990.1																																																																																			CAAA|0.834;-|0.166	0.166	strong		0.417	DEFB126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077428.2	NM_030931	
ALMS1	7840	hgsc.bcm.edu	37	2	73681184	73681184	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:73681184delA	ENST00000264448.6	+	8	7638	c.7527delA	c.(7525-7527)gtafs	p.V2509fs	ALMS1_ENST00000377715.1_Frame_Shift_Del_p.V2509fs|ALMS1_ENST00000409009.1_Frame_Shift_Del_p.V2467fs|ALMS1-IT1_ENST00000441587.2_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2509					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AAAGCCGGGTACGAGCACATG	0.368																																					p.V2509fs		Pindel,Atlas-Indel	.											ALMS1,NS,carcinoma,0,1	ALMS1	384	1	0			c.7526delT						PASS	.						34.0	32.0	33.0					2																	73681184		1889	4102	5991	SO:0001589	frameshift_variant	7840	exon8			.	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7527delA	2.37:g.73681184delA	ENSP00000264448:p.Val2509fs	Somatic	92	.	.		WXS	Illumina HiSeq	Phase_I	135	30	0.222	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Frame_Shift_Del	DEL	ENST00000264448.6	37	CCDS42697.1																																																																																			.	.	none		0.368	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
TNRC6A	27327	hgsc.bcm.edu	37	16	24788423	24788434	+	In_Frame_Del	DEL	GCAGCCACAGCC	GCAGCCACAGCC	-	rs10593507|rs60829899|rs71156436|rs11644562|rs71383714	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GCAGCCACAGCC	GCAGCCACAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:24788423_24788434delGCAGCCACAGCC	ENST00000395799.3	+	5	462_473	c.333_344delGCAGCCACAGCC	c.(331-345)cagcagccacagccg>cag	p.QPQP112del	TNRC6A_ENST00000315183.7_In_Frame_Del_p.QPQP112del	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	112	Gln-rich.|Interaction with argonaute family proteins.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		agccacagcagcagccacagccgcagccgcag	0.59														660	0.131789	0.0908	0.1455	5008	,	,		12550	0.126		0.162	False		,,,				2504	0.1524				p.111_115del		Atlas-Indel	.											.	TNRC6A	171	.	0			c.332_343del						PASS	.			502,3262		90,322,1470						1.3	0.2		dbSNP_130	23	1410,6010		189,1032,2489	no	coding	TNRC6A	NM_014494.2		279,1354,3959	A1A1,A1R,RR		19.0027,13.3369,17.0959				1912,9272				SO:0001651	inframe_deletion	27327	exon5			.	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.333_344delGCAGCCACAGCC	16.37:g.24788423_24788434delGCAGCCACAGCC	ENSP00000379144:p.Gln112_Pro115del	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	In_Frame_Del	DEL	ENST00000395799.3	37	CCDS10624.2																																																																																			GCAGCCACAGCC|0.906;-|0.094	0.094	strong		0.590	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
FRG2C	100288801	hgsc.bcm.edu	37	3	75713659	75713660	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:75713659_75713660delAG	ENST00000308062.3	+	1	179_180	c.129_130delAG	c.(127-132)aaaggcfs	p.G44fs	FRG2C_ENST00000464571.1_Frame_Shift_Del_p.G44fs	NM_001124759.1	NP_001118231.1	A6NGY1	FRG2C_HUMAN	FSHD region gene 2 family, member C	44						nucleus (GO:0005634)				breast(2)|ovary(1)	3						TCAAAGGAAAAGGCAAGACCGC	0.525																																					p.43_43del		Atlas-Indel	.											.	FRG2C	16	.	0			c.128_129del						PASS	.																																			SO:0001589	frameshift_variant	100288801	exon1			.		CCDS43108.1	3p12.3	2009-11-25			ENSG00000172969	ENSG00000172969			33626	protein-coding gene	gene with protein product							Standard	NM_001124759		Approved			A6NGY1	OTTHUMG00000158963	ENST00000308062.3:c.129_130delAG	3.37:g.75713659_75713660delAG	ENSP00000312299:p.Gly44fs	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	255	27	0.105882	NM_001124759		Frame_Shift_Del	DEL	ENST00000308062.3	37	CCDS43108.1																																																																																			.	.	none		0.525	FRG2C-001	KNOWN	NAGNAG_splice_site|not_best_in_genome_evidence|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352694.1	NM_001124759.1	
AKAP2	11217	hgsc.bcm.edu	37	9	112900341	112900342	+	In_Frame_Ins	INS	-	-	GAAGCT	rs373159646|rs34665027|rs150402481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:112900341_112900342insGAAGCT	ENST00000259318.7	+	2	2031_2032	c.1824_1825insGAAGCT	c.(1825-1827)gaa>GAAGCTgaa	p.609_609E>EAE	AKAP2_ENST00000434623.2_In_Frame_Ins_p.698_698E>EAE|AKAP2_ENST00000510514.5_In_Frame_Ins_p.840_840E>EAE|PALM2-AKAP2_ENST00000374530.3_In_Frame_Ins_p.840_840E>EAE|PALM2-AKAP2_ENST00000302798.7_In_Frame_Ins_p.840_840E>EAE|AKAP2_ENST00000555236.1_In_Frame_Ins_p.840_840E>EAE|AKAP2_ENST00000374525.1_In_Frame_Ins_p.698_698E>EAE	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	609								p.E839_E840insEA(1)|p.E697_E698insEA(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						CGACTGTAGAGGAAGCTGAAGC	0.505														656	0.13099	0.1309	0.0821	5008	,	,		20174	0.2133		0.1362	False		,,,				2504	0.0757				p.E839delinsEEA		Pindel,Atlas-Indel	.											.	PALM2-AKAP2	117	.	2	Insertion - In frame(2)	lung(2)	c.2517_2518insGAAGCT						PASS	.		,,,,	550,3714		39,472,1621					,,,,	2.7	0.9		dbSNP_134	39	1146,7108		82,982,3063	no	coding,coding,coding,coding,coding	AKAP2,PALM2-AKAP2	NM_147150.2,NM_007203.4,NM_001198656.1,NM_001136562.2,NM_001004065.4	,,,,	121,1454,4684	A1A1,A1R,RR		13.8842,12.8987,13.5485	,,,,	,,,,		1696,10822				SO:0001652	inframe_insertion	445815	exon8			.	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.1831_1836dupGAAGCT	9.37:g.112900342_112900347dupGAAGCT	Exception_encountered	Somatic	52	.	.		WXS	Illumina HiSeq	Phase_I	62	27	0.435	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	In_Frame_Ins	INS	ENST00000259318.7	37	CCDS48003.1																																																																																			.	.	strong		0.505	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065	
DYSF	8291	hgsc.bcm.edu	37	2	71871177	71871195	+	Splice_Site	DEL	ATTTTGACACCCTGAAGGT	ATTTTGACACCCTGAAGGT	-	rs7573406|rs199861501|rs200809348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	ATTTTGACACCCTGAAGGT	ATTTTGACACCCTGAAGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:71871177_71871195delATTTTGACACCCTGAAGGT	ENST00000258104.3	+	41	4770_4786	c.4493_4509delATTTTGACACCCTGAAGGT	c.(4492-4509)gattttgacaccctgaag>g	p.DFDTLK1498fs	DYSF_ENST00000409582.3_Splice_Site_p.DFDTLK1536fs|DYSF_ENST00000429174.2_Splice_Site_p.DFDTLK1519fs|DYSF_ENST00000409762.1_Splice_Site_p.DFDTLK1515fs|DYSF_ENST00000409366.1_Splice_Site_p.DFDTLK1520fs|DYSF_ENST00000409651.1_Splice_Site_p.DFDTLK1530fs|DYSF_ENST00000410020.3_Splice_Site_p.DFDTLK1537fs|DYSF_ENST00000410041.1_Splice_Site_p.DFDTLK1516fs|DYSF_ENST00000394120.2_Splice_Site_p.DFDTLK1499fs|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000413539.2_Splice_Site_p.DFDTLK1529fs|DYSF_ENST00000409744.1_Splice_Site_p.DFDTLK1506fs	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1498					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CTGGAGAAGGATTTTGACACCCTGAAGGTAAGGCCTCTC	0.493																																					p.1537_1542del		Pindel,Atlas-Indel	.											.	DYSF	536	.	0			c.4609_4626del	GRCh37	CD031501	DYSF	D		PASS	.																																			SO:0001630	splice_region_variant	8291	exon42			.	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4509+1ATTTTGACACCCTGAAGGT>-	2.37:g.71871177_71871195delATTTTGACACCCTGAAGGT		Somatic	180	.	.		WXS	Illumina HiSeq	Phase_I	211	57	0.270	NM_001130987	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	In_Frame_Del	DEL	ENST00000258104.3	37	CCDS1918.1																																																																																			.	.	none		0.493	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	Frame_Shift_Del
OR5B12	390191	hgsc.bcm.edu	37	11	58207036	58207036	+	Frame_Shift_Del	DEL	T	T	-	rs201567144|rs148519730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:58207036delT	ENST00000302572.2	-	1	610	c.589delA	c.(589-591)attfs	p.I197fs		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ACAAAAAAAATAACCATCTCA	0.393													T|T|-|deletion	23	0.00459265	0.0015	0.0058	5008	,	,		21092	0.0		0.0169	False		,,,				2504	0.0				p.I197fs		Pindel,Atlas-Indel	.											.	OR5B12	80	.	0			c.590delT						PASS	.			8,4256		0,8,2124	69.0	65.0	66.0			3.2	0.5	11		67	128,8126		0,128,3999	no	frameshift	OR5B12	NM_001004733.2		0,136,6123	A1A1,A1R,RR		1.5508,0.1876,1.0864			58207036	136,12382	2201	4295	6496	SO:0001589	frameshift_variant	390191	exon1			.	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"""GPCR / Class A : Olfactory receptors"""	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.589delA	11.37:g.58207036delT	ENSP00000306657:p.Ile197fs	Somatic	112	.	.		WXS	Illumina HiSeq	Phase_I	149	29	0.195	NM_001004733	B2RNL2|Q6IEV5	Frame_Shift_Del	DEL	ENST00000302572.2	37	CCDS31551.1																																																																																			T|0.994;-|0.006	0.006	strong		0.393	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733	
VSIG10	54621	hgsc.bcm.edu	37	12	118511660	118511677	+	In_Frame_Del	DEL	TGATCACCTCGGGCTGGG	TGATCACCTCGGGCTGGG	-	rs76814182|rs569997181|rs142627542|rs540996271	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TGATCACCTCGGGCTGGG	TGATCACCTCGGGCTGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:118511660_118511677delTGATCACCTCGGGCTGGG	ENST00000359236.5	-	5	1322_1339	c.1046_1063delCCCAGCCCGAGGTGATCA	c.(1045-1065)acccagcccgaggtgatcatc>atc	p.TQPEVI349del		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	349	Ig-like C2-type 4.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						CTAGGCTGGATGATCACCTCGGGCTGGGTAAGGTTCCT	0.583														26	0.00519169	0.0008	0.0072	5008	,	,		21969	0.0		0.0179	False		,,,				2504	0.002				p.349_355del		Pindel,Atlas-Indel	.											.	VSIG10	41	.	0			c.1047_1064del						PASS	.			16,3866		2,12,1927						4.4	0.9		dbSNP_134	58	206,7786		8,190,3798	no	coding	VSIG10	NM_019086.5		10,202,5725	A1A1,A1R,RR		2.5776,0.4122,1.8696				222,11652				SO:0001651	inframe_deletion	54621	exon5			.		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1046_1063delCCCAGCCCGAGGTGATCA	12.37:g.118511660_118511677delTGATCACCTCGGGCTGGG	ENSP00000352172:p.Thr349_Ile354del	Somatic	123	.	.		WXS	Illumina HiSeq	Phase_I	113	38	0.336	NM_019086	Q9NWQ7	In_Frame_Del	DEL	ENST00000359236.5	37	CCDS44992.1																																																																																			.	.	none		0.583	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
ZSCAN21	7589	hgsc.bcm.edu	37	7	99662512	99662515	+	3'UTR	DEL	TAGT	TAGT	-	rs56833874|rs71689664|rs202229615|rs200297846|rs200795752|rs398111646	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TAGT	TAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99662512_99662515delTAGT	ENST00000292450.4	+	0	1858_1861				ZSCAN21_ENST00000456748.2_3'UTR|ZSCAN21_ENST00000543588.1_3'UTR|ZNF3_ENST00000413658.2_Frame_Shift_Del_p.TT98fs	NM_145914.2	NP_666019.1	Q9Y5A6	ZSC21_HUMAN	zinc finger and SCAN domain containing 21						positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|skin(1)	21	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			ACCTTTTGCGTAGTTAAACAGACG	0.407														1393	0.278155	0.1573	0.232	5008	,	,		19468	0.4067		0.2763	False		,,,				2504	0.3436				p.98_99del		Pindel,Atlas-Indel	.											.	ZNF3	54	.	0			c.293_296del						PASS	.		,	697,3191		89,519,1336					,	-4.0	0.0		dbSNP_130	140	2233,5761		344,1545,2108	yes	utr-3,frameshift	ZNF3,ZSCAN21	NM_145914.2,NM_017715.2	,	433,2064,3444	A1A1,A1R,RR		27.9335,17.927,24.6591	,	,		2930,8952				SO:0001624	3_prime_UTR_variant	7551	exon6			.	AL136865	CCDS5681.1	7q11.1	2013-01-08	2006-10-06	2006-10-06	ENSG00000166529	ENSG00000166529		"""-"", ""Zinc fingers, C2H2-type"""	13104	protein-coding gene	gene with protein product		601261	"""zinc finger protein 38 (KOX 25)"", ""zinc finger protein 38"""	ZNF38		2288909, 2014798	Standard	NM_145914		Approved	DKFZp434L134, NY-REN-21, Zipro1	uc003uso.3	Q9Y5A6	OTTHUMG00000154583	ENST00000292450.4:c.*275TAGT>-	7.37:g.99662512_99662515delTAGT		Somatic	126	.	.		WXS	Illumina HiSeq	Phase_I	102	30	0.294	NM_017715	A4D2A6|D6W5T9|Q9H0B5	Frame_Shift_Del	DEL	ENST00000292450.4	37	CCDS5681.1																																																																																			TAGT|0.748;-|0.252	0.252	strong		0.407	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336166.1	NM_145914	
DNAJC28	54943	hgsc.bcm.edu	37	21	34860750	34860754	+	Frame_Shift_Del	DEL	AATTA	AATTA	-	rs139852262|rs3834674	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AATTA	AATTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:34860750_34860754delAATTA	ENST00000314399.3	-	2	1385_1389	c.947_951delTAATT	c.(946-951)ttaattfs	p.LI316fs	DNAJC28_ENST00000381947.3_Frame_Shift_Del_p.LI316fs|DNAJC28_ENST00000402202.1_Frame_Shift_Del_p.LI316fs	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	316				LIVPILTRQKVHFDAQKEIVRAQKIYETLIKTKEVTDRNPN NLDQGEGEKTPEIKKGFLNWMNLWKFIKIRSF -> CSHPD QAKSPF (in Ref. 2; BAA91185). {ECO:0000305}.				p.L316*(2)|p.L316fs*12(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						GGATGGGAACAATTAAATTAAAATC	0.341														760	0.151757	0.0151	0.2262	5008	,	,		20822	0.1667		0.2664	False		,,,				2504	0.1503				p.316_318del		Pindel,Atlas-Indel	.											.	DNAJC28	47	.	3	Substitution - Nonsense(2)|Deletion - Frameshift(1)	lung(3)	c.948_952del						PASS	.		,	229,4035		5,219,1908					,	5.1	1.0		dbSNP_130	84	1814,6438		207,1400,2519	no	frameshift,frameshift	DNAJC28	NM_017833.3,NM_001040192.1	,	212,1619,4427	A1A1,A1R,RR		21.9825,5.3705,16.3231	,	,		2043,10473				SO:0001589	frameshift_variant	54943	exon2			.	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"""Heat shock proteins / DNAJ (HSP40)"""	1297	protein-coding gene	gene with protein product	"""Orf28"""		"""chromosome 21 open reading frame 55"""	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.947_951delTAATT	21.37:g.34860755_34860759delAATTA	ENSP00000320303:p.Leu316fs	Somatic	176	.	.		WXS	Illumina HiSeq	Phase_I	189	65	0.344	NM_001040192	D3DSF2	Frame_Shift_Del	DEL	ENST00000314399.3	37	CCDS13626.1																																																																																			AATTA|0.826;-|0.174	0.174	strong		0.341	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3		
TRDN	10345	hgsc.bcm.edu	37	6	123594510	123594511	+	Splice_Site	INS	-	-	A	rs147062785|rs386359375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:123594510_123594511insA	ENST00000398178.3	-	28	1619		c.e28-2		TRDN_ENST00000334268.4_Splice_Site	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin						cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		CAGATATAGCTAAAATAAATAA	0.238													AAAAA|AAAA|AAAAA|deletion	1317	0.262979	0.0946	0.2104	5008	,	,		12974	0.5069		0.1859	False		,,,				2504	0.3558				.		Pindel,Atlas-Indel	.											.	TRDN	88	.	0			c.1598-2->T						PASS	.			198,1964		33,132,916						4.2	0.0		dbSNP_130	5	764,4058		183,398,1830	no	splice-3	TRDN	NM_006073.2		216,530,2746	A1A1,A1R,RR		15.844,9.1582,13.7743				962,6022				SO:0001630	splice_region_variant	10345	exon29			.	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1598-2->T	6.37:g.123594514_123594514dupA		Somatic	77	.	.		WXS	Illumina HiSeq	Phase_I	79	17	0.215	NM_006073	A5D6W5|F5H2W7|Q6NSB8	Splice_Site	INS	ENST00000398178.3	37	CCDS55053.1																																																																																			-|0.740;A|0.260	0.260	strong		0.238	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			Intron
ETFB	2109	hgsc.bcm.edu	37	19	51857874	51857875	+	Intron	INS	-	-	CCACAG	rs113835487|rs397825770|rs61361626	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51857874_51857875insCCACAG	ENST00000309244.4	-	2	149				ETFB_ENST00000354232.4_In_Frame_Ins_p.5_6insWL|CTD-2616J11.9_ENST00000600974.1_RNA|CTD-2616J11.11_ENST00000600067.1_Intron	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		TTTATGGTAACCCACAGTGAGA	0.381														409	0.0816693	0.2595	0.0375	5008	,	,		22079	0.001		0.005	False		,,,				2504	0.0348				p.V7delinsLWV		Pindel,Atlas-Indel	.											.	ETFB	46	.	0			c.19_20insCTGTGG						PASS	.		,	1043,3221		124,795,1213					,	-0.7	0.0		dbSNP_130	53	41,8213		0,41,4086	no	intron,coding	ETFB	NM_001985.2,NM_001014763.1	,	124,836,5299	A1A1,A1R,RR		0.4967,24.4606,8.6595	,	,		1084,11434				SO:0001627	intron_variant	2109	exon1			.	X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379			3482	protein-coding gene	gene with protein product		130410					Standard	NM_001014763		Approved		uc002pwg.3	P38117		ENST00000309244.4:c.58-312->CTGTGG	19.37:g.51857875_51857880dupCCACAG		Somatic	128	.	.		WXS	Illumina HiSeq	Phase_I	89	26	0.292	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	In_Frame_Ins	INS	ENST00000309244.4	37	CCDS12828.1																																																																																			-|0.937;CCACAG|0.063	0.063	strong		0.381	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
SPATA31A3	727830	hgsc.bcm.edu	37	9	40705744	40705744	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:40705744delC	ENST00000356699.5	+	4	3430	c.3401delC	c.(3400-3402)accfs	p.T1134fs	RP11-395E19.5_ENST00000432614.1_lincRNA	NM_001083124.1	NP_001076593.1	Q5VYP0	S31A3_HUMAN	SPATA31 subfamily A, member 3	1134					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCTCAACTTACCCCAGTCAGG	0.463																																					p.T1134fs		Atlas-Indel	.											.	.	.	.	0			c.3400delA						PASS	.						24.0	20.0	21.0					9																	40705744		919	2111	3030	SO:0001589	frameshift_variant	727830	exon4			.			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000147926				32003	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A3"""	FAM75A3		20850414	Standard	NM_001083124		Approved	OTTHUMG00000013164, DKFZp434B204	uc010mmj.3	Q5VYP0	OTTHUMG00000013164	ENST00000356699.5:c.3401delC	9.37:g.40705744delC	ENSP00000349132:p.Thr1134fs	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	504	37	0.0734127	NM_001083124		Frame_Shift_Del	DEL	ENST00000356699.5	37	CCDS47969.1																																																																																			.	.	none		0.463	SPATA31A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036919.1	NM_001083124	
DMKN	93099	hgsc.bcm.edu	37	19	36002410	36002412	+	In_Frame_Del	DEL	CTG	CTG	-	rs56743379|rs111543270|rs199498909		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:36002410_36002412delCTG	ENST00000339686.3	-	5	995_997	c.819_821delCAG	c.(817-822)agcagt>agt	p.273_274SS>S	DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000418261.1_In_Frame_Del_p.273_274SS>S|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_In_Frame_Del_p.273_274SS>S|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000424570.2_In_Frame_Del_p.273_274SS>S|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000447113.2_In_Frame_Del_p.273_274SS>S|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000440396.1_In_Frame_Del_p.273_274SS>S|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000436012.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	273	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			gctgctgccactgctgctgccac	0.655																																					p.274_274del		Atlas-Indel	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.820_822del						PASS	.																																			SO:0001651	inframe_deletion	93099	exon5			.	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.819_821delCAG	19.37:g.36002416_36002418delCTG	ENSP00000342012:p.Ser274del	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	67	21	0.313433	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	In_Frame_Del	DEL	ENST00000339686.3	37	CCDS12463.1																																																																																			CTG|0.500;-|0.500	0.500	weak		0.655	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
ZNF83	55769	hgsc.bcm.edu	37	19	53116646	53116648	+	In_Frame_Del	DEL	TGT	TGT	-	rs568637119|rs369554773	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53116646_53116648delTGT	ENST00000597597.1	-	2	3423_3425	c.1170_1172delACA	c.(1168-1173)caacat>cat	p.Q390del	ZNF83_ENST00000541777.2_In_Frame_Del_p.Q390del|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000545872.1_In_Frame_Del_p.Q390del|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000301096.3_In_Frame_Del_p.Q390del|ZNF83_ENST00000391789.4_In_Frame_Del_p.Q362del|ZNF83_ENST00000536937.1_In_Frame_Del_p.Q390del|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000544146.1_In_Frame_Del_p.Q390del			P51522	ZNF83_HUMAN	zinc finger protein 83	390					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		GATTCTGTGATGTTGTACAAGAT	0.365														67	0.0133786	0.0	0.0072	5008	,	,		24290	0.0		0.006	False		,,,				2504	0.0573				p.391_391del		Pindel,Atlas-Indel	.											.	ZNF83	73	.	0			c.1171_1173del						PASS	.		,,,,,,,,	116,4148		55,6,2071					,,,,,,,,	2.2	0.0			110	326,7928		107,112,3908	no	coding,coding,coding,coding,coding,coding,coding,coding,coding	ZNF83	NM_018300.3,NM_001242538.1,NM_001242531.1,NM_001105554.1,NM_001105553.1,NM_001105552.1,NM_001105551.1,NM_001105550.1,NM_001105549.1	,,,,,,,,	162,118,5979	A1A1,A1R,RR		3.9496,2.7205,3.5309	,,,,,,,,	,,,,,,,,		442,12076				SO:0001651	inframe_deletion	55769	exon5			.	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.1170_1172delACA	19.37:g.53116649_53116651delTGT	ENSP00000472619:p.Gln390del	Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	80	26	0.325	NM_001105551	A8MT75|Q3ZCX0|Q6PI08	In_Frame_Del	DEL	ENST00000597597.1	37	CCDS12854.1																																																																																			.	.	none		0.365	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
SCRN3	79634	hgsc.bcm.edu	37	2	175292581	175292593	+	Frame_Shift_Del	DEL	TCAAATTTATCAG	TCAAATTTATCAG	-	rs145699077|rs79038555	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TCAAATTTATCAG	TCAAATTTATCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:175292581_175292593delTCAAATTTATCAG	ENST00000272732.6	+	8	1315_1327	c.1233_1245delTCAAATTTATCAG	c.(1231-1245)attcaaatttatcagfs	p.IQIYQ411fs	SCRN3_ENST00000409673.3_Frame_Shift_Del_p.IQIYQ404fs|SCRN3_ENST00000548921.1_3'UTR	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	411							dipeptidase activity (GO:0016805)	p.I406V(1)|p.I413V(1)|p.N417fs*>4(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			AAGATGAAATTCAAATTTATCAGTCAAATTTAT	0.319														1062	0.212061	0.0832	0.1931	5008	,	,		19634	0.2113		0.3817	False		,,,				2504	0.226				p.411_415del		Pindel,Atlas-Indel	.											.	SCRN3	76	.	3	Substitution - Missense(2)|Deletion - Frameshift(1)	endometrium(2)|urinary_tract(1)	c.1232_1244del						PASS	.		,	515,3749		33,449,1650					,	5.6	1.0		dbSNP_134	72	2708,5524		474,1760,1882	no	frameshift,frameshift	SCRN3	NM_024583.4,NM_001193528.1	,	507,2209,3532	A1A1,A1R,RR		32.896,12.0779,25.7923	,	,		3223,9273				SO:0001589	frameshift_variant	79634	exon8			.	AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.1233_1245delTCAAATTTATCAG	2.37:g.175292581_175292593delTCAAATTTATCAG	ENSP00000272732:p.Ile411fs	Somatic	450	.	.		WXS	Illumina HiSeq	Phase_I	354	78	0.220	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Frame_Shift_Del	DEL	ENST00000272732.6	37	CCDS2258.1																																																																																			TCAAATTTATCAG|0.751;-|0.249	0.249	strong		0.319	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583	
KLF17	128209	hgsc.bcm.edu	37	1	44596380	44596382	+	In_Frame_Del	DEL	CAA	CAA	-	rs200059598|rs34057178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:44596380_44596382delCAA	ENST00000372299.3	+	3	1180_1182	c.1122_1124delCAA	c.(1120-1125)gccaac>gcc	p.N378del	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	378					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					ACCCACAGGCCAACAACAACAAT	0.493														1153	0.230232	0.0719	0.2723	5008	,	,		21631	0.2887		0.175	False		,,,				2504	0.411				p.374_375del		Pindel,Atlas-Indel	.											.	KLF17	92	.	0			c.1121_1123del						PASS	.			430,3836		27,376,1730						-0.7	0.0		dbSNP_126	87	1593,6661		149,1295,2683	no	coding	KLF17	NM_173484.3		176,1671,4413	A1A1,A1R,RR		19.2997,10.0797,16.1581				2023,10497				SO:0001651	inframe_deletion	128209	exon3			.	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.1122_1124delCAA	1.37:g.44596389_44596391delCAA	ENSP00000361373:p.Asn378del	Somatic	100	.	.		WXS	Illumina HiSeq	Phase_I	81	56	0.691	NM_173484	Q86VQ7|Q8N805	In_Frame_Del	DEL	ENST00000372299.3	37	CCDS508.1																																																																																			CAA|0.811;-|0.189	0.189	strong		0.493	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
OR8I2	120586	hgsc.bcm.edu	37	11	55861307	55861307	+	Frame_Shift_Del	DEL	A	A	-	rs201548817|rs112181516|rs144690814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55861307delA	ENST00000302124.2	+	1	555	c.524delA	c.(523-525)catfs	p.H175fs		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H175fs*10(1)|p.C178fs*2(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					AGCATCAATCATTTTTTTTGT	0.443													A|A|-|deletion	195	0.0389377	0.0121	0.0447	5008	,	,		21866	0.001		0.0944	False		,,,				2504	0.0532				p.H175fs		Atlas-Indel	.											.	OR8I2	119	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	ovary(1)|large_intestine(1)	c.523delC						PASS	.			95,4169		0,95,2037	153.0	141.0	145.0			4.3	1.0	11	dbSNP_134	151	669,7585		32,605,3490	no	frameshift	OR8I2	NM_001003750.1		32,700,5527	A1A1,A1R,RR		8.1052,2.228,6.1032			55861307	764,11754	2201	4296	6497	SO:0001589	frameshift_variant	120586	exon1			.	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.524delA	11.37:g.55861307delA	ENSP00000303864:p.His175fs	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	146	50	0.342466	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Frame_Shift_Del	DEL	ENST00000302124.2	37	CCDS31517.1																																																																																			.	.	strong		0.443	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
PRDM2	7799	hgsc.bcm.edu	37	1	14105121	14105122	+	In_Frame_Ins	INS	-	-	GAA	rs199679022|rs375577840		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14105121_14105122insGAA	ENST00000235372.7	+	8	1687_1688	c.831_832insGAA	c.(832-834)gaa>GAAgaa	p.278_278E>EE	PRDM2_ENST00000343137.4_In_Frame_Ins_p.77_77E>EE|PRDM2_ENST00000311066.5_In_Frame_Ins_p.278_278E>EE|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_In_Frame_Ins_p.77_77E>EE	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	278	Asp/Glu-rich (acidic).			EDEEEEEDDDDDELEDEG -> VGGGGGVVVVVSWKARGE (in Ref. 6; AAA87023). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		aggaggaggatgaagaagaaga	0.5																																					p.D277delinsDE		Pindel,Atlas-Indel	.											PRDM2,colon,carcinoma,0,1	PRDM2	147	1	0			c.831_832insGAA						PASS	.																																			SO:0001652	inframe_insertion	7799	exon8			.	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.844_846dupGAA	1.37:g.14105128_14105130dupGAA	ENSP00000235372:p.Glu282dup	Somatic	80	.	.		WXS	Illumina HiSeq	Phase_I	100	25	0.250	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	In_Frame_Ins	INS	ENST00000235372.7	37	CCDS150.1																																																																																			.	.	none		0.500	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
OR5B12	390191	hgsc.bcm.edu	37	11	58207035	58207036	+	Frame_Shift_Del	DEL	AT	AT	-	rs201567144|rs148519730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:58207035_58207036delAT	ENST00000302572.2	-	1	610_611	c.589_590delAT	c.(589-591)attfs	p.I197fs		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CACAAAAAAAATAACCATCTCA	0.391																																					p.197_197del		Atlas-Indel	.											.	OR5B12	80	.	0			c.590_591del						PASS	.																																			SO:0001589	frameshift_variant	390191	exon1			.	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"""GPCR / Class A : Olfactory receptors"""	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.589_590delAT	11.37:g.58207035_58207036delAT	ENSP00000306657:p.Ile197fs	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	146	14	0.0958904	NM_001004733	B2RNL2|Q6IEV5	Frame_Shift_Del	DEL	ENST00000302572.2	37	CCDS31551.1																																																																																			.	.	none		0.391	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733	
OR6C1	390321	hgsc.bcm.edu	37	12	55714406	55714407	+	Frame_Shift_Ins	INS	-	-	A	rs5798345|rs74350806|rs80197193	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:55714406_55714407insA	ENST00000379668.2	+	1	61_62	c.23_24insA	c.(22-27)acagagfs	p.E9fs		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						ACAGAAATAACAGAGTTTATTC	0.381													A|A|AA|insertion	1647	0.328874	0.1634	0.4496	5008	,	,		18561	0.3413		0.4264	False		,,,				2504	0.3538				p.T8fs		Pindel,Atlas-Indel	.											.	OR6C1	58	.	0			c.23_24insA						PASS	.			785,3479		74,637,1421						0.1	0.0		dbSNP_114	61	3536,4718		747,2042,1338	no	frameshift	OR6C1	NM_001005182.1		821,2679,2759	A1A1,A1R,RR		42.8398,18.4099,34.5183				4321,8197				SO:0001589	frameshift_variant	390321	exon1			.	AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"""GPCR / Class A : Olfactory receptors"""	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.24dupA	12.37:g.55714407_55714407dupA	ENSP00000368990:p.Glu9fs	Somatic	71	.	.		WXS	Illumina HiSeq	Phase_I	90	29	0.322	NM_001005182	B2RNM0	Frame_Shift_Ins	INS	ENST00000379668.2	37	CCDS31818.1																																																																																			-|0.656;A|0.344	0.344	strong		0.381	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182	
MAGI1	9223	hgsc.bcm.edu	37	3	65425560	65425561	+	In_Frame_Ins	INS	-	-	CTG	rs113903140|rs35698502|rs142043619|rs377562449	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:65425560_65425561insCTG	ENST00000497477.2	-	9	1262_1263	c.1263_1264insCAG	c.(1261-1266)cagaca>cagCAGaca	p.421_422insQ	MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000402939.2_In_Frame_Ins_p.421_422insQ|MAGI1_ENST00000330909.8_In_Frame_Ins_p.421_422insQ|MAGI1_ENST00000483466.1_In_Frame_Ins_p.421_422insQ			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	421	Poly-Gln.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		CAACCTTCTGTctgctgctgct	0.559											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T422delinsQT		Atlas-Indel	.											.	MAGI1	481	.	0			c.1264_1265insCAG						PASS	.																																			SO:0001652	inframe_insertion	9223	exon9			.	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.1261_1263dupCAG	3.37:g.65425567_65425569dupCTG	ENSP00000424369:p.Gln421_Gln421dup	Somatic	48	0	0	1084	WXS	Illumina HiSeq	Phase_I	61	21	0.344262	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	In_Frame_Ins	INS	ENST00000497477.2	37																																																																																				.	.	strong		0.559	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
AKAP9	10142	hgsc.bcm.edu	37	7	91652178	91652179	+	In_Frame_Ins	INS	-	-	AAC	rs111673064|rs10644111|rs397825978|rs34756483	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:91652178_91652179insAAC	ENST00000359028.2	+	15	4264_4265	c.4039_4040insAAC	c.(4039-4041)aaa>aAACaa	p.1347_1348insQ	AKAP9_ENST00000356239.3_In_Frame_Ins_p.1335_1336insQ|AKAP9_ENST00000358100.2_In_Frame_Ins_p.1347_1348insQ			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1347			K -> KQ. {ECO:0000269|PubMed:10202149}.		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.K1335_L1336insQ(1)|p.K1347_L1348insQ(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TGAAAAAACTAAACTTGAAGAA	0.312			T	BRAF	papillary thyroid									2127	0.42472	0.6657	0.3689	5008	,	,		15358	0.1825		0.3867	False		,,,				2504	0.4274				p.K1335delinsKQ		Pindel,Atlas-Indel	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	2	Insertion - In frame(2)	ovary(2)	c.4003_4004insAAC						PASS	.		,	2670,1594		824,1022,286					,	2.2	0.0		dbSNP_119	46	3327,4927		650,2027,1450	no	coding,coding	AKAP9	NM_147185.2,NM_005751.4	,	1474,3049,1736	A1A1,A1R,RR		40.3077,37.3827,47.907	,	,		5997,6521				SO:0001652	inframe_insertion	10142	exon14			.	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.4040_4042dupAAC	7.37:g.91652179_91652181dupAAC	ENSP00000351922:p.Lys1347_Leu1348insGln	Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	69	23	0.333	NM_147185	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	In_Frame_Ins	INS	ENST00000359028.2	37																																																																																				-|0.604;AAC|0.396	0.396	strong		0.312	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
FOXD4L2	100036519	hgsc.bcm.edu	37	9	42719309	42719311	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:42719309_42719311delGCT	ENST00000377590.1	+	1	2076_2078	c.1244_1246delGCT	c.(1243-1248)cgctgc>cgc	p.C416del		NM_001099279.1	NP_001092749.1	Q6VB85	FX4L2_HUMAN	forkhead box D4-like 2	416					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(1)	1				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		CCTCGTCGGCGCTGCTGAGGTAT	0.64																																					p.415_415del		Atlas-Indel	.											.	FOXD4L2	4	.	0			c.1243_1245del						PASS	.																																			SO:0001651	inframe_deletion	100036519	exon1			.			9p12	2008-07-21			ENSG00000204828				24813	protein-coding gene	gene with protein product						12421752	Standard			Approved	OTTHUMG00000066752	uc004acn.3	Q6VB85	OTTHUMG00000066752	ENST00000377590.1:c.1244_1246delGCT	9.37:g.42719312_42719314delGCT	ENSP00000366814:p.Cys416del	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	147	20	0.136054	NM_001099279		In_Frame_Del	DEL	ENST00000377590.1	37	CCDS43817.1																																																																																			.	.	none		0.640	FOXD4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143077.1	NM_001099279	
PTPRQ	374462	hgsc.bcm.edu	37	12	80943506	80943523	+	Splice_Site	DEL	TGAAACAGGTAACTAACG	TGAAACAGGTAACTAACG	-	rs141686707|rs190917077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TGAAACAGGTAACTAACG	TGAAACAGGTAACTAACG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:80943506_80943523delTGAAACAGGTAACTAACG	ENST00000266688.5	+	30	4266_4273	c.4266_4273delTGAAACAGGTAACTAACG	c.(4264-4275)cctgaaacaggt>ccgt	p.ETG1423del				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1469	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						GCACACTACCTGAAACAGGTAACTAACGTGAAACAGGT	0.381																																					p.1254_1257del		Pindel,Atlas-Indel	.											.	PTPRQ	119	.	0			c.3761_3769del						PASS	.			21,2253		2,17,1118						3.6	1.0		dbSNP_134	53	261,3959		31,199,1880	no	coding-near-splice	PTPRQ	NM_001145026.1		33,216,2998	A1A1,A1R,RR		6.1848,0.9235,4.3425				282,6212				SO:0001630	splice_region_variant	374462	exon22			.	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.4273+1TGAAACAGGTAACTAACG>-	12.37:g.80943506_80943523delTGAAACAGGTAACTAACG		Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	124	34	0.274	NM_001145026		In_Frame_Del	DEL	ENST00000266688.5	37																																																																																				.	.	strong		0.381	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	In_Frame_Del
OR52N5	390075	hgsc.bcm.edu	37	11	5799652	5799652	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5799652delA	ENST00000317093.2	-	1	245	c.213delT	c.(211-213)tttfs	p.F71fs	TRIM5_ENST00000380027.1_Intron	NM_001001922.2	NP_001001922.2	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N, member 5	71						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F71fs*59(1)		endometrium(2)|large_intestine(3)|liver(1)|lung(17)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		GAGCATGGCCAAAAAAAAAAT	0.428																																					p.G72fs		Pindel,Atlas-Indel	.											.	OR52N5	58	.	1	Deletion - Frameshift(1)	ovary(1)	c.214delG						PASS	.			21,37,4048		0,0,21,1,35,1996	123.0	117.0	119.0			2.7	0.6	11		123	37,129,7678		1,0,35,6,117,3763	no	codingComplex	OR52N5	NM_001001922.2		1,0,56,7,152,5759	A1A1,A1A2,A1R,A2A2,A2R,RR		2.1163,1.4126,1.8745			5799652	58,166,11726	2125	4088	6213	SO:0001589	frameshift_variant	390075	exon1			.	AB065535	CCDS31397.1	11p15.4	2012-08-09			ENSG00000181009	ENSG00000181009		"""GPCR / Class A : Olfactory receptors"""	15231	protein-coding gene	gene with protein product							Standard	NM_001001922		Approved	OR52N5Q	uc010qzn.2	Q8NH56	OTTHUMG00000168799	ENST00000317093.2:c.213delT	11.37:g.5799652delA	ENSP00000322866:p.Phe71fs	Somatic	0	.	.		WXS	Illumina HiSeq	Phase_I	100	18	0.180	NM_001001922	B9EH12|Q6IFG2	Frame_Shift_Del	DEL	ENST00000317093.2	37	CCDS31397.1																																																																																			.	.	none		0.428	OR52N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401141.1	NM_001001922	
CUL9	23113	hgsc.bcm.edu	37	6	43174057	43174065	+	Splice_Site	DEL	AGGAGGAAG	AGGAGGAAG	-	rs542758187	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGGAGGAAG	AGGAGGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:43174057_43174065delAGGAGGAAG	ENST00000252050.4	+	26	5106_5113	c.5022_5029delAGGAGGAAG	c.(5020-5031)gaaggaggaaga>gaga	p.GGR1675del	CUL9_ENST00000354495.3_Splice_Site_p.GGR1565del|CUL9_ENST00000372647.2_Splice_Site_p.GGR1675del	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1675	Glu-rich.				microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						TCTGTCCCTCAGGAGGAAGAGGAGGAAGA	0.517														9	0.00179712	0.0	0.0	5008	,	,		22978	0.0		0.004	False		,,,				2504	0.0051				p.1675_1676del		Pindel,Atlas-Indel	.											.	CUL9	248	.	0			c.5023_5028del						PASS	.			3,4261		0,3,2129						3.3	0.9			67	25,8229		0,25,4102	no	coding-near-splice	CUL9	NM_015089.2		0,28,6231	A1A1,A1R,RR		0.3029,0.0704,0.2237				28,12490				SO:0001630	splice_region_variant	23113	exon26			.	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.5023-1AGGAGGAAG>-	6.37:g.43174066_43174074delAGGAGGAAG		Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	50	20	0.400	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	In_Frame_Del	DEL	ENST00000252050.4	37	CCDS4890.1																																																																																			.	.	none		0.517	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	In_Frame_Del
NCOA3	8202	hgsc.bcm.edu	37	20	46279837	46279839	+	In_Frame_Del	DEL	CAG	CAG	-	rs147879509|rs2664555|rs397778717|rs3830809		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:46279837_46279839delCAG	ENST00000371998.3	+	20	3954_3956	c.3763_3765delCAG	c.(3763-3765)cagdel	p.Q1276del	NCOA3_ENST00000341724.6_In_Frame_Del_p.Q1202del|NCOA3_ENST00000372004.3_In_Frame_Del_p.Q1272del|NCOA3_ENST00000371997.3_In_Frame_Del_p.Q1267del			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1276	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q1255delQ(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						gcagcagcaacagcagcagcagc	0.552																																					p.1254_1255del		Atlas-Indel	.											NCOA3,NS,carcinoma,0,1	NCOA3	156	1	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.3762_3764del						PASS	.		,,,	586,1098,2378		46,154,340,141,662,688					,,,	0.5	0.0		dbSNP_107	50	208,3200,4626		14,44,136,605,1946,1272	no	codingComplex,codingComplex,codingComplex,codingComplex	NCOA3	NM_181659.2,NM_006534.3,NM_001174088.1,NM_001174087.1	,,,	60,198,476,746,2608,1960	A1A1,A1A2,A1R,A2A2,A2R,RR		42.4197,41.4574,42.0966	,,,	,,,		794,4298,7004				SO:0001651	inframe_deletion	8202	exon20			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3763_3765delCAG	20.37:g.46279846_46279848delCAG	ENSP00000361066:p.Gln1276del	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	115	37	0.321739	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	In_Frame_Del	DEL	ENST00000371998.3	37	CCDS13407.1																																																																																			CAG|0.669;-|0.331	0.331	strong		0.552	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
DNAJC9	23234	hgsc.bcm.edu	37	10	75005896	75005902	+	Frame_Shift_Del	DEL	GTATGTC	GTATGTC	-	rs36012375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GTATGTC	GTATGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:75005896_75005902delGTATGTC	ENST00000372950.4	-	3	2026_2032	c.354_360delGACATAC	c.(352-360)aagacatacfs	p.KTY118fs	DNAJC9_ENST00000453189.2_5'Flank|DNAJC9-AS1_ENST00000513954.1_RNA|DNAJC9-AS1_ENST00000440197.2_RNA|MRPS16_ENST00000479005.1_5'Flank	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	118					social behavior (GO:0035176)	nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					CCGAACCTTTGTATGTCTTTTCAAAAG	0.382																																					p.119_121del		Pindel,Atlas-Indel	.											.	DNAJC9	19	.	0			c.355_361del						PASS	.																																			SO:0001589	frameshift_variant	23234	exon3			.	AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"""Heat shock proteins / DNAJ (HSP40)"""	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.354_360delGACATAC	10.37:g.75005896_75005902delGTATGTC	ENSP00000362041:p.Lys118fs	Somatic	168	.	.		WXS	Illumina HiSeq	Phase_I	118	20	0.169	NM_015190	B2RMW6	Frame_Shift_Del	DEL	ENST00000372950.4	37	CCDS7322.1																																																																																			.	.	none		0.382	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190	
FAM74A7	100996582	hgsc.bcm.edu	37	9	40715923	40715924	+	lincRNA	DEL	AA	AA	-	rs374953827|rs62565543	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:40715923_40715924delAA	ENST00000432614.1	-	0	0				FAM74A3_ENST00000604146.1_lincRNA																							GAAGACGTGGAAAGAGCTCAGA	0.569																																					.		Atlas-Indel	.											.	FAM74A3	17	.	0			.						PASS	.																																					728495	.			.																													9.37:g.40715923_40715924delAA		Somatic	452	0	0		WXS	Illumina HiSeq	Phase_I	161	76	0.47205	.		RNA	DEL	ENST00000432614.1	37																																																																																				.	.	weak		0.569	RP11-395E19.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000143688.1		
PYGL	5836	hgsc.bcm.edu	37	14	51378591	51378591	+	Splice_Site	DEL	T	T	-	rs74464749|rs11356035|rs397852066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:51378591delT	ENST00000216392.7	-	16	2160		c.e16-2		RP11-218E20.5_ENST00000557343.1_RNA|PYGL_ENST00000532462.1_Splice_Site|PYGL_ENST00000544180.2_Splice_Site	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver						5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|necroptotic process (GO:0070266)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	AMP binding (GO:0016208)|ATP binding (GO:0005524)|bile acid binding (GO:0032052)|drug binding (GO:0008144)|glucose binding (GO:0005536)|glycogen phosphorylase activity (GO:0008184)|protein homodimerization activity (GO:0042803)|purine nucleobase binding (GO:0002060)|pyridoxal phosphate binding (GO:0030170)|vitamin binding (GO:0019842)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)	TGGGGCAGCCTTTGGGGAAGA	0.453													TT|TTT|TT|insertion	2764	0.551917	0.7133	0.5605	5008	,	,		22069	0.63		0.3519	False		,,,				2504	0.453				.		Pindel,Atlas-Indel	.											.	PYGL	77	.	0			c.1726-1A>-						PASS	.		,	2789,1475		899,991,242	49.0	78.0	68.0		,	5.6	1.0	14	dbSNP_120	120	2763,5491		460,1843,1824	no	splice-3,splice-3	PYGL	NM_002863.4,NM_001163940.1	,	1359,2834,2066	A1A1,A1R,RR		33.4747,34.5919,44.3521	,	,	51378591	5552,6966	2172	4288	6460	SO:0001630	splice_region_variant	5836	exon16			.		CCDS32080.1, CCDS53894.1	14q11.2-q24.3	2013-03-01	2008-07-31		ENSG00000100504	ENSG00000100504	2.4.1.1	"""Glycogen phosphorylases"""	9725	protein-coding gene	gene with protein product	"""Hers disease"", ""glycogen storage disease type VI"", ""glycogen phosphorylase, liver form"""	613741	"""phosphorylase, glycogen; liver"""			2877458	Standard	NM_002863		Approved		uc001wyu.3	P06737	OTTHUMG00000166596	ENST00000216392.7:c.1828-2A>-	14.37:g.51378591delT		Somatic	169	.	.		WXS	Illumina HiSeq	Phase_I	191	71	0.372	NM_001163940	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Splice_Site	DEL	ENST00000216392.7	37	CCDS32080.1																																																																																			T|0.468;-|0.532	0.532	strong		0.453	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863	Intron
HRCT1	646962	hgsc.bcm.edu	37	9	35906584	35906586	+	In_Frame_Del	DEL	CCA	CCA	-	rs143611048	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35906584_35906586delCCA	ENST00000354323.2	+	1	396_398	c.300_302delCCA	c.(298-303)ctccac>ctc	p.H105del	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	105	His-rich.					integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						ctcaccacctccaccaccaccac	0.66														929	0.185503	0.1619	0.1268	5008	,	,		6334	0.3085		0.1213	False		,,,				2504	0.1984				p.100_101del		Atlas-Indel	.											HRCT1,NS,malignant_melanoma,0,1	HRCT1	14	1	0			c.299_301del						PASS	.																																			SO:0001651	inframe_deletion	646962	exon1			.		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.300_302delCCA	9.37:g.35906593_35906595delCCA	ENSP00000346283:p.His105del	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	28	11	0.392857	NM_001039792	B7ZBJ1	In_Frame_Del	DEL	ENST00000354323.2	37	CCDS35012.1																																																																																			.	.	strong		0.660	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
LILRB4	11006	hgsc.bcm.edu	37	19	55179244	55179244	+	Splice_Site	DEL	G	G	-	rs571881532|rs386810941	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55179244delG	ENST00000391736.1	+	13	1515	c.1200delG	c.(1198-1200)gag>ga	p.E400fs	LILRB4_ENST00000430952.2_Splice_Site_p.E399fs|LILRB4_ENST00000391734.3_Intron|LILRB4_ENST00000391733.3_Splice_Site_p.E401fs|LILRB4_ENST00000270452.2_Splice_Site_p.E400fs	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	400					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		TGGACACTGAGGTGAGTCCTT	0.617													?|GG|G|unsure	97	0.019369	0.0461	0.0144	5008	,	,		16664	0.002		0.0169	False		,,,				2504	0.0072				p.E400fs		Atlas-Indel	.											.	LILRB4	86	.	0			c.1199delA						PASS	.		,	175,4085		12,151,1967	99.0	93.0	95.0		,	1.0	0.0	19		95	101,8151		5,91,4030	no	frameshift-near-splice,frameshift-near-splice	LILRB4	NM_006847.3,NM_001081438.1	,	17,242,5997	A1A1,A1R,RR		1.2239,4.108,2.2059	,	,	55179244	276,12236	2193	4296	6489	SO:0001630	splice_region_variant	11006	exon11			.	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1200+1G>-	19.37:g.55179244delG		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	218	32	0.146789	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Frame_Shift_Del	DEL	ENST00000391736.1	37	CCDS12902.1																																																																																			.	.	none		0.617	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		Frame_Shift_Del
ZNF772	400720	hgsc.bcm.edu	37	19	57988666	57988667	+	In_Frame_Ins	INS	-	-	GCC	rs77164240|rs528587884|rs34678661|rs193920834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57988666_57988667insGCC	ENST00000343280.4	-	1	271_272	c.11_12insGGC	c.(10-12)gct>gcGGCt	p.4_4A>AA	ZNF772_ENST00000425074.3_In_Frame_Ins_p.4_4A>AA|AC003005.2_ENST00000595422.1_lincRNA|AC004076.9_ENST00000596831.1_In_Frame_Ins_p.4_4A>AA|ZNF772_ENST00000601768.1_In_Frame_Ins_p.4_4A>AA|AC004076.9_ENST00000415705.3_5'UTR|ZNF772_ENST00000600175.1_In_Frame_Ins_p.4_4A>AA|ZNF772_ENST00000427512.2_5'UTR|ZNF772_ENST00000356584.3_In_Frame_Ins_p.4_4A>AA	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	4					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)	9		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		CCATCGGCTCAGCCGCCGCCAT	0.644											OREG0025695	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		2037	0.406749	0.3124	0.4481	5008	,	,		16965	0.5823		0.2753	False		,,,				2504	0.4591				p.A4delinsAA	Melanoma(5;289 436 14293 15924 30817)	Pindel,Atlas-Indel	.											ZNF772,colon,carcinoma,0,1	ZNF772	42	1	0			c.12_13insGGC						PASS	.		,	1273,2975		195,883,1046					,	-4.0	0.0		dbSNP_126	62	2294,5946		320,1654,2146	no	coding,coding	ZNF772	NM_001144068.1,NM_001024596.2	,	515,2537,3192	A1A1,A1R,RR		27.8398,29.967,28.5634	,	,		3567,8921				SO:0001652	inframe_insertion	400720	exon1			.	BX647068	CCDS33133.1, CCDS46210.1	19q13.43	2013-01-08				ENSG00000197128		"""Zinc fingers, C2H2-type"", ""-"""	33106	protein-coding gene	gene with protein product							Standard	NM_001024596		Approved	DKFZp686I1569	uc002qot.3	Q68DY9		ENST00000343280.4:c.9_11dupGGC	19.37:g.57988673_57988675dupGCC	ENSP00000341165:p.Ala4dup	Somatic	199	.	.	1027	WXS	Illumina HiSeq	Phase_I	214	59	0.276	NM_001024596	A6NJK9|B4DH56|B4DYS0	In_Frame_Ins	INS	ENST00000343280.4	37	CCDS33133.1																																																																																			GCC|1.000;|0.000	1.000	strong		0.644	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596	
OR8I2	120586	hgsc.bcm.edu	37	11	55861278	55861278	+	Frame_Shift_Del	DEL	T	T	-	rs145832034|rs138372442	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55861278delT	ENST00000302124.2	+	1	526	c.495delT	c.(493-495)agtfs	p.S165fs		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	165						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					TGATAAGCAGTTTGGCGTTCT	0.443													TTT|TTT|TT|deletion	195	0.0389377	0.0121	0.0447	5008	,	,		21572	0.001		0.0944	False		,,,				2504	0.0532				p.S165fs		Atlas-Indel	.											.	OR8I2	119	.	0			c.494delG						PASS	.			95,4169		0,95,2037	159.0	143.0	149.0			4.3	0.2	11	dbSNP_134	154	669,7585		32,605,3490	no	frameshift	OR8I2	NM_001003750.1		32,700,5527	A1A1,A1R,RR		8.1052,2.228,6.1032			55861278	764,11754	2201	4296	6497	SO:0001589	frameshift_variant	120586	exon1			.	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.495delT	11.37:g.55861278delT	ENSP00000303864:p.Ser165fs	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	124	45	0.362903	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Frame_Shift_Del	DEL	ENST00000302124.2	37	CCDS31517.1																																																																																			T|0.961;-|0.039	0.039	strong		0.443	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
IGSF3	3321	hgsc.bcm.edu	37	1	117122285	117122286	+	In_Frame_Ins	INS	-	-	TCC	rs576658823|rs367941869|rs151042895|rs114915440	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:117122285_117122286insTCC	ENST00000369486.3	-	10	3827_3828	c.3062_3063insGGA	c.(3061-3063)gac>gaGGAc	p.1020_1021insE	IGSF3_ENST00000369483.1_In_Frame_Ins_p.1040_1041insE|IGSF3_ENST00000318837.6_In_Frame_Ins_p.1040_1041insE	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1020	Ig-like C2-type 8.		D -> E (in dbSNP:rs647711). {ECO:0000269|PubMed:9790749}.		lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.D1041D(1)|p.D1021D(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		cgtcgtcgtcgtcgtcctcctc	0.634														1230	0.245607	0.1528	0.3069	5008	,	,		17681	0.1022		0.4284	False		,,,				2504	0.2873				p.D1041delinsED		Atlas-Indel	.											IGSF3_ENST00000369483,NS,carcinoma,0,4	IGSF3	294	4	2	Substitution - coding silent(2)	prostate(2)	c.3123_3124insGGA						PASS	.																																			SO:0001652	inframe_insertion	3321	exon11			.	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3062_3063insGGA	1.37:g.117122285_117122286insTCC	ENSP00000358498:p.Asp1020_Asp1021insGlu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	98	32	0.326531	NM_001542	A6NJZ6|A6NMC7	In_Frame_Ins	INS	ENST00000369486.3	37	CCDS30813.1																																																																																			.	.	none		0.634	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
CC2D2A	57545	hgsc.bcm.edu	37	4	15513005	15513007	+	In_Frame_Del	DEL	GAA	GAA	-	rs112367037|rs386833764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:15513005_15513007delGAA	ENST00000503292.1	+	9	856_858	c.676_678delGAA	c.(676-678)gaadel	p.E229del	CC2D2A_ENST00000389652.5_In_Frame_Del_p.E180del|CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000424120.1_In_Frame_Del_p.E229del|CC2D2A_ENST00000413206.1_In_Frame_Del_p.E229del	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	229	Poly-Glu.				cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						GGAGGAAGGGGAAGAAGAAGAAC	0.443														217	0.0433307	0.003	0.0778	5008	,	,		21113	0.0		0.0815	False		,,,				2504	0.0787				p.225_226del		Pindel,Atlas-Indel	.											.	CC2D2A	158	.	0			c.675_677del						PASS	.			59,3675		1,57,1809						-3.4	0.0		dbSNP_132	103	580,7314		24,532,3391	no	coding	CC2D2A	NM_001080522.2		25,589,5200	A1A1,A1R,RR		7.3474,1.5801,5.4954				639,10989				SO:0001651	inframe_deletion	57545	exon9			.	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"""Meckel syndrome, type 6"""	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.676_678delGAA	4.37:g.15513014_15513016delGAA	ENSP00000421809:p.Glu229del	Somatic	90	.	.		WXS	Illumina HiSeq	Phase_I	93	56	0.602	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	In_Frame_Del	DEL	ENST00000503292.1	37	CCDS47026.1																																																																																			GAA|0.958;-|0.042	0.042	strong		0.443	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522	
RAI1	10743	hgsc.bcm.edu	37	17	17697099	17697100	+	Frame_Shift_Del	DEL	GC	GC	-	rs35068024|rs587780431|rs587780429|rs398124422|rs11078398|rs144872134	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17697099_17697100delGC	ENST00000353383.1	+	3	1306_1307	c.837_838delGC	c.(835-840)cagcagfs	p.QQ279fs	RAI1_ENST00000261641.6_Frame_Shift_Del_p.QQ279fs	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	279	Gln-rich.|Poly-Gln.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ATGACcagcagcagcagcagca	0.634																																					p.279_279del		Atlas-Indel	.											.	RAI1	121	.	0			c.836_837del						PASS	.																																			SO:0001589	frameshift_variant	10743	exon3			.	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.837_838delGC	17.37:g.17697099_17697100delGC	ENSP00000323074:p.Gln279fs	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	89	25	0.280899	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Frame_Shift_Del	DEL	ENST00000353383.1	37	CCDS11188.1																																																																																			GC|0.875;-|0.125	0.125	strong		0.634	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
RIC8A	60626	hgsc.bcm.edu	37	11	209895	209897	+	In_Frame_Del	DEL	CCC	CCC	-	rs201633036|rs200641500|rs3832797|rs398102296|rs571957041	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:209895_209897delCCC	ENST00000526104.1	+	3	1965_1967	c.621_623delCCC	c.(619-624)aacccc>aac	p.P210del	BET1L_ENST00000382762.3_5'Flank|BET1L_ENST00000332865.6_5'Flank|BET1L_ENST00000410108.1_5'Flank|BET1L_ENST00000486280.1_5'Flank|BET1L_ENST00000529614.2_5'Flank|RIC8A_ENST00000325207.5_In_Frame_Del_p.P210del|RIC8A_ENST00000527696.1_In_Frame_Del_p.P204del|BET1L_ENST00000325147.9_5'Flank			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	210					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CTGAAGGGAACCCCCCACCCACG	0.601														2073	0.413938	0.2519	0.428	5008	,	,		21433	0.7629		0.327	False		,,,				2504	0.3528				p.207_208del		Pindel,Atlas-Indel	.											.	RIC8A	45	.	0			c.620_622del						PASS	.			1167,8,3089		173,0,821,4,0,1134						1.2	0.0		dbSNP_107	49	2820,12,5422		493,0,1834,6,0,1794	no	codingComplex	RIC8A	NM_021932.4		666,0,2655,10,0,2928	A1A1,A1A2,A1R,A2A2,A2R,RR		34.3106,27.5563,32.0099				3987,20,8511				SO:0001651	inframe_deletion	60626	exon3			.	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"""resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"""			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069	ENST00000526104.1:c.621_623delCCC	11.37:g.209898_209900delCCC	ENSP00000432008:p.Pro210del	Somatic	29	.	.		WXS	Illumina HiSeq	Phase_I	40	12	0.300	NM_021932	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	In_Frame_Del	DEL	ENST00000526104.1	37																																																																																				CCC|0.579;-|0.421	0.421	strong		0.601	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932	
FAM98B	283742	hgsc.bcm.edu	37	15	38776807	38776815	+	IGR	DEL	GGTGGTGGT	GGTGGTGGT	-	rs201831942|rs374461368		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GGTGGTGGT	GGTGGTGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:38776807_38776815delGGTGGTGGT	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_In_Frame_Del_p.GGG426del	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		ATATGGAGGAggtggtggtggtggtggtg	0.459																																					p.416_419del		Pindel,Atlas-Indel	.											.	FAM98B	53	.	0			c.1248_1256del						PASS	.																																			SO:0001628	intergenic_variant	283742	exon8			.		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		15.37:g.38776816_38776824delGGTGGTGGT		Somatic	56	.	.		WXS	Illumina HiSeq	Phase_I	73	14	0.192	NM_173611	A8MUW5|Q8N935	In_Frame_Del	DEL	ENST00000491535.1	37	CCDS42015.1																																																																																			GGTGGTGGT|0.896;-|0.104	0.104	strong		0.459	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611	
WDR81	124997	hgsc.bcm.edu	37	17	1631341	1631343	+	In_Frame_Del	DEL	GAG	GAG	-	rs577690948|rs200758098|rs35048651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1631341_1631343delGAG	ENST00000409644.1	+	1	3088_3090	c.3088_3090delGAG	c.(3088-3090)gagdel	p.E1033del	WDR81_ENST00000545662.1_5'Flank|WDR81_ENST00000419248.1_Intron|WDR81_ENST00000446363.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_5'UTR|WDR81_ENST00000437219.2_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1033				Missing (in Ref. 1; BAB84937). {ECO:0000305}.	negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGGGGCTGCTGAGGAGGAGGAGA	0.695														1061	0.211861	0.115	0.196	5008	,	,		16982	0.1835		0.1948	False		,,,				2504	0.4008				p.1029_1030del		Pindel,Atlas-Indel	.											.	WDR81	180	.	0			c.3087_3089del						PASS	.		,,,	549,3367		98,353,1507					,,,	-11.3	0.0		dbSNP_130	17	1642,6232		262,1118,2557	no	utr-5,intron,coding,intron	WDR81	NM_152348.3,NM_001163811.1,NM_001163809.1,NM_001163673.1	,,,	360,1471,4064	A1A1,A1R,RR		20.8534,14.0194,18.5835	,,,	,,,		2191,9599				SO:0001651	inframe_deletion	124997	exon1			.	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.3088_3090delGAG	17.37:g.1631350_1631352delGAG	ENSP00000386609:p.Glu1033del	Somatic	74	.	.		WXS	Illumina HiSeq	Phase_I	62	18	0.290	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	In_Frame_Del	DEL	ENST00000409644.1	37	CCDS54062.1																																																																																			-|0.172;GAG|0.828	0.172	strong		0.695	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
BAIAP2L2	80115	hgsc.bcm.edu	37	22	38483155	38483156	+	In_Frame_Ins	INS	-	-	TCATGGGTG	rs132924|rs142739979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38483155_38483156insTCATGGGTG	ENST00000381669.3	-	11	1378_1379	c.1234_1235insCACCCATGA	c.(1234-1236)aac>aCACCCATGAac	p.411_412insTPM	CTA-228A9.3_ENST00000609162.1_lincRNA	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	411				M -> MTPM (in Ref. 3; AAH15619). {ECO:0000305}.	filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					GTTCCCggggttcatgggtgtc	0.653														1505	0.300519	0.2814	0.3602	5008	,	,		13633	0.1796		0.3529	False		,,,				2504	0.3548				p.N412delinsTPMN		Pindel,Atlas-Indel	.											BAIAP2L2,NS,carcinoma,0,4	BAIAP2L2	39	4	0			c.1235_1236insCACCCATGA						PASS	.			1032,2628		159,714,957						-3.7	0.0		dbSNP_130	29	2800,5058		480,1840,1609	no	coding	BAIAP2L2	NM_025045.4		639,2554,2566	A1A1,A1R,RR		35.6325,28.1967,33.2697				3832,7686				SO:0001652	inframe_insertion	80115	exon11			.	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1226_1234dupCACCCATGA	22.37:g.38483156_38483164dupTCATGGGTG	ENSP00000371085:p.Thr409_Met411dup	Somatic	48	.	.		WXS	Illumina HiSeq	Phase_I	48	32	0.667	NM_025045	B0QYE2|Q96BG7	In_Frame_Ins	INS	ENST00000381669.3	37	CCDS43018.1																																																																																			.	.	strong		0.653	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045	
OR2T4	127074	hgsc.bcm.edu	37	1	248525328	248525329	+	Frame_Shift_Ins	INS	-	-	TA	rs370409078|rs61248663	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248525328_248525329insTA	ENST00000366475.1	+	1	446_447	c.446_447insTA	c.(445-450)accatgfs	p.M150fs		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M150fs*20(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTTCTAGCCACCATGGCCTATG	0.525														1358	0.271166	0.2284	0.2637	5008	,	,		20870	0.381		0.1779	False		,,,				2504	0.317				p.T149fs		Atlas-Indel	.											.	OR2T4	126	.	1	Insertion - Frameshift(1)	liver(1)	c.446_447insTA						PASS	.																																			SO:0001589	frameshift_variant	127074	exon1			.	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	Exception_encountered	1.37:g.248525328_248525329insTA	ENSP00000355431:p.Met150fs	Somatic	729	0	0		WXS	Illumina HiSeq	Phase_I	666	189	0.283784	NM_001004696	Q6IEZ8	Frame_Shift_Ins	INS	ENST00000366475.1	37	CCDS31113.1																																																																																			-|0.754;TA|0.246	0.246	strong		0.525	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
CNDP1	84735	hgsc.bcm.edu	37	18	72223591	72223592	+	In_Frame_Ins	INS	-	-	TGC	rs10663835|rs60017744|rs67791561	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:72223591_72223592insTGC	ENST00000358821.3	+	2	271_272	c.43_44insTGC	c.(43-45)gtg>gTGCtg	p.20_21insL	CNDP1_ENST00000585136.1_3'UTR|CNDP1_ENST00000582365.1_Intron	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	20			L -> LL. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16046297}.			extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.L20_E21insL(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		CCTGCTGGCTGTGCTGCTGCTG	0.559																																					p.V15delinsVL	Melanoma(32;1029 1042 25286 38395 44237)	Pindel,Atlas-Indel	.											.	CNDP1	98	.	1	Insertion - In frame(1)	kidney(1)	c.43_44insTGC						PASS	.																																			SO:0001652	inframe_insertion	84735	exon2			.		CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"""carnosinase 1"", ""glutamate carboxypeptidase-like protein 2"""	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.56_58dupTGC	18.37:g.72223598_72223600dupTGC	ENSP00000351682:p.Leu20_Leu20dup	Somatic	103	.	.		WXS	Illumina HiSeq	Phase_I	110	34	0.309	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	In_Frame_Ins	INS	ENST00000358821.3	37	CCDS12007.1																																																																																			-|0.500;TGC|0.500	0.500	strong		0.559	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
MAN2A1	4124	hgsc.bcm.edu	37	5	109190936	109190938	+	In_Frame_Del	DEL	CTC	CTC	-	rs200733039|rs3217225|rs200723635	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:109190936_109190938delCTC	ENST00000261483.4	+	20	4124_4126	c.3072_3074delCTC	c.(3070-3075)ttctcc>ttc	p.S1026del	MAN2A1_ENST00000505313.1_3'UTR	NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	1026				Missing (in Ref. 2; BAA10017). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		CAAATAAGTTCTCCTCACCTACC	0.404														1342	0.267971	0.0416	0.2507	5008	,	,		15500	0.6062		0.1521	False		,,,				2504	0.3569				p.1024_1025del		Pindel,Atlas-Indel	.											MAN2A1,NS,carcinoma,-1,2	MAN2A1	136	2	0			c.3071_3073del						PASS	.			490,3774		127,236,1769						-1.0	0.0		dbSNP_130	147	1753,6501		285,1183,2659	no	coding	MAN2A1	NM_002372.2		412,1419,4428	A1A1,A1R,RR		21.2382,11.4916,17.9182				2243,10275				SO:0001651	inframe_deletion	4124	exon20			.		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.3072_3074delCTC	5.37:g.109190939_109190941delCTC	ENSP00000261483:p.Ser1026del	Somatic	78	.	.		WXS	Illumina HiSeq	Phase_I	130	45	0.346	NM_002372	Q16767	In_Frame_Del	DEL	ENST00000261483.4	37	CCDS34209.1																																																																																			CTC|0.730;-|0.270	0.270	strong		0.404	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
AMOT	154796	hgsc.bcm.edu	37	X	112022297	112022298	+	In_Frame_Ins	INS	-	-	AGG	rs373265985|rs147791784		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:112022297_112022298insAGG	ENST00000524145.1	-	11	3158_3159	c.3084_3085insCCT	c.(3082-3087)cctgca>cctCCTgca	p.1028_1029insP	AMOT_ENST00000304758.1_In_Frame_Ins_p.619_620insP|AMOT_ENST00000371959.3_In_Frame_Ins_p.1028_1029insP|MIR4329_ENST00000582643.1_RNA|AMOT_ENST00000371962.1_In_Frame_Ins_p.796_797insP			Q4VCS5	AMOT_HUMAN	angiomotin	1028					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						GCTGGACTTGCAGGAACCTCAG	0.525														154	0.0407947	0.0242	0.0346	3775	,	,		13612	0.0		0.0706	False		,,,				2504	0.0276				p.A1029delinsPA		Pindel,Atlas-Indel	.											.	AMOT	204	.	0			c.3085_3086insCCT						PASS	.		,	118,3603		1,92,24,1499,513					,	3.4	1.0		dbSNP_134	104	510,5974		11,346,142,2000,1628	no	coding,coding	AMOT	NM_133265.2,NM_001113490.1	,	12,438,166,3499,2141	A1A1,A1R,A1,RR,R		7.8655,3.1712,6.1538	,	,		628,9577				SO:0001652	inframe_insertion	154796	exon10			.	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.3082_3084dupCCT	X.37:g.112022298_112022300dupAGG	ENSP00000429013:p.Pro1028_Pro1028dup	Somatic	104	.	.		WXS	Illumina HiSeq	Phase_I	153	78	0.510	NM_001113490	Q504X5|Q9HD27|Q9UPT1	In_Frame_Ins	INS	ENST00000524145.1	37	CCDS48154.1																																																																																			.	.	weak		0.525	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265	
IL32	9235	hgsc.bcm.edu	37	16	3119297	3119298	+	Frame_Shift_Ins	INS	-	-	G	rs71818662|rs531600758	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:3119297_3119298insG	ENST00000534507.1	+	6	857_858	c.646_647insG	c.(646-648)cggfs	p.R216fs	IL32_ENST00000382213.3_Frame_Shift_Ins_p.R161fs|IL32_ENST00000529550.1_Frame_Shift_Ins_p.R170fs|IL32_ENST00000548652.1_Frame_Shift_Ins_p.R161fs|IL32_ENST00000551513.1_Frame_Shift_Ins_p.R207fs|IL32_ENST00000530890.1_Frame_Shift_Ins_p.R150fs|IL32_ENST00000549213.1_Frame_Shift_Ins_p.R113fs|IL32_ENST00000444393.3_Frame_Shift_Ins_p.R170fs|IL32_ENST00000533097.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000530538.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000548476.1_Frame_Shift_Ins_p.R216fs|IL32_ENST00000552936.1_Frame_Shift_Ins_p.R194fs|IL32_ENST00000525643.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000396887.3_Frame_Shift_Ins_p.R113fs|IL32_ENST00000548246.1_Frame_Shift_Ins_p.R130fs|IL32_ENST00000396890.2_Frame_Shift_Ins_p.R216fs|IL32_ENST00000008180.9_Frame_Shift_Ins_p.R150fs|IL32_ENST00000552356.1_Frame_Shift_Ins_p.R150fs|IL32_ENST00000528163.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000325568.5_Frame_Shift_Ins_p.R170fs|IL32_ENST00000529699.1_Frame_Shift_Ins_p.R150fs|IL32_ENST00000552664.1_Frame_Shift_Ins_p.R170fs|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000551122.1_Frame_Shift_Ins_p.R113fs|IL32_ENST00000526464.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000440815.3_Frame_Shift_Ins_p.R170fs|IL32_ENST00000531965.1_Frame_Shift_Ins_p.R160fs			P24001	IL32_HUMAN	interleukin 32	216					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)		p.D172fs*12(3)		breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CGGAGCCCCACGGGGGGACAAG	0.579																																					p.R170fs		Pindel,Atlas-Indel	.											IL32,NS,carcinoma,0,1	IL32	32	1	3	Insertion - Frameshift(3)	urinary_tract(1)|breast(1)|pancreas(1)	c.508_509insG						PASS	.																																			SO:0001589	frameshift_variant	9235	exon7			.	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.652dupG	16.37:g.3119303_3119303dupG	ENSP00000431775:p.Arg216fs	Somatic	124	.	.		WXS	Illumina HiSeq	Phase_I	258	51	0.198	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Frame_Shift_Ins	INS	ENST00000534507.1	37																																																																																				.	.	strong		0.579	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
PDPK1	5170	hgsc.bcm.edu	37	16	2611896	2611899	+	Frame_Shift_Del	DEL	CGAC	CGAC	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CGAC	CGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2611896_2611899delCGAC	ENST00000342085.4	+	4	602_605	c.453_456delCGAC	c.(451-456)gacgacfs	p.DD151fs	PDPK1_ENST00000268673.7_Intron|PDPK1_ENST00000441549.3_Frame_Shift_Del_p.DD151fs|RP11-20I23.8_ENST00000569852.1_RNA|PDPK1_ENST00000389224.3_Frame_Shift_Del_p.DD124fs|PDPK1_ENST00000354836.5_Frame_Shift_Del_p.DD151fs	NM_002613.4	NP_002604.1	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase 1	151	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|focal adhesion assembly (GO:0048041)|hyperosmotic response (GO:0006972)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of endothelial cell migration (GO:0010594)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of mast cell degranulation (GO:0043304)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	3-phosphoinositide-dependent protein kinase activity (GO:0004676)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7		Ovarian(90;0.17)			Celecoxib(DB00482)	CATTTCAGGACGACGAGAAGCTGT	0.52																																					p.151_152del		Atlas-Indel	.											.	PDPK1	37	.	0			c.452_455del	GRCh37	CD072462	PDPK1	D		PASS	.																																			SO:0001589	frameshift_variant	5170	exon4			.	AF017995	CCDS10472.1, CCDS10473.1, CCDS58411.1	16p13.3	2014-03-20	2014-03-20		ENSG00000140992	ENSG00000140992			8816	protein-coding gene	gene with protein product	"""PkB kinase"""	605213				9094314, 9445477	Standard	NM_002613		Approved	PDK1	uc002cqs.4	O15530	OTTHUMG00000128874	ENST00000342085.4:c.453_456delCGAC	16.37:g.2611896_2611899delCGAC	ENSP00000344220:p.Asp151fs	Somatic	582	0	0		WXS	Illumina HiSeq	Phase_I	582	62	0.106529	NM_001261816	H0Y4Z0|Q59EH6|Q6FI20|Q8IV52|Q9BRD5	Frame_Shift_Del	DEL	ENST00000342085.4	37	CCDS10472.1																																																																																			.	.	none		0.520	PDPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250831.3		
ROBO3	64221	hgsc.bcm.edu	37	11	124750448	124750453	+	In_Frame_Del	DEL	CGGAGT	CGGAGT	-	rs55725290|rs56085444|rs71859853	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CGGAGT	CGGAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124750448_124750453delCGGAGT	ENST00000397801.1	+	27	4285_4290	c.4093_4098delCGGAGT	c.(4093-4098)cggagtdel	p.RS1367del	ROBO3_ENST00000525482.1_3'UTR|ROBO3_ENST00000543966.1_In_Frame_Del_p.RS130del|ROBO3_ENST00000538940.1_In_Frame_Del_p.RS1345del	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	1367					axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		TGgccggagccggagtcggagtcaga	0.66														2107	0.420727	0.6664	0.2392	5008	,	,		17575	0.378		0.2883	False		,,,				2504	0.3978				p.1364_1366del		Pindel,Atlas-Indel	.											.	ROBO3	199	.	0			c.4092_4097del						PASS	.			2069,1609		709,651,479						2.4	1.0		dbSNP_130	17	1833,5925		332,1169,2378	no	coding	ROBO3	NM_022370.3		1041,1820,2857	A1A1,A1R,RR		23.6272,43.7466,34.1203				3902,7534				SO:0001651	inframe_deletion	64221	exon27			.	AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13433	protein-coding gene	gene with protein product		608630	"""roundabout (axon guidance receptor, Drosophila) homolog 3"", ""horizontal gaze palsy with progressive scoliosis"""	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.4093_4098delCGGAGT	11.37:g.124750454_124750459delCGGAGT	ENSP00000380903:p.Arg1367_Ser1368del	Somatic	70	.	.		WXS	Illumina HiSeq	Phase_I	95	49	0.516	NM_022370		In_Frame_Del	DEL	ENST00000397801.1	37	CCDS44755.1																																																																																			CGGAGT|0.626;-|0.374	0.374	strong		0.660	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663	
TUT1	64852	hgsc.bcm.edu	37	11	62359061	62359061	+	5'UTR	DEL	G	G	-	rs577382133	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62359061delG	ENST00000476907.1	-	0	588				MIR3654_ENST00000496634.2_5'Flank|TUT1_ENST00000308436.7_Frame_Shift_Del_p.P4fs			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific						mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CGATCCGATAGGAAGTGACAT	0.572													GG|GG|G|deletion	4	0.000798722	0.0	0.0	5008	,	,		18693	0.0		0.003	False		,,,				2504	0.001				p.P4fs		Pindel,Atlas-Indel	.											.	TUT1	122	.	0			c.12delT						PASS	.			5,4215		0,5,2105	34.0	46.0	42.0			-4.7	0.0	11		42	32,8150		2,28,4061	no	frameshift	TUT1	NM_022830.2		2,33,6166	A1A1,A1R,RR		0.3911,0.1185,0.2983			62359061	37,12365	692	1591	2283	SO:0001623	5_prime_UTR_variant	64852	exon1			.	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"""RNA binding motif (RRM) containing"""	26184	protein-coding gene	gene with protein product	"""RNA uridylyltransferase"", ""U6 TUTase"", ""TUTase 6"""	610641	"""RNA binding motif protein 21"""	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.-104C>-	11.37:g.62359061delG		Somatic	46	.	.		WXS	Illumina HiSeq	Phase_I	50	12	0.240	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Frame_Shift_Del	DEL	ENST00000476907.1	37																																																																																				.	.	none		0.572	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830	
RP1L1	94137	hgsc.bcm.edu	37	8	10466004	10466024	+	In_Frame_Del	DEL	CTGGGCCTCCCCTTCAGCCTC	CTGGGCCTCCCCTTCAGCCTC	-	rs199577777|rs199959237|rs535482422|rs558932296|rs181718385|rs542254783	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CTGGGCCTCCCCTTCAGCCTC	CTGGGCCTCCCCTTCAGCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:10466004_10466024delCTGGGCCTCCCCTTCAGCCTC	ENST00000382483.3	-	4	5807_5827	c.5584_5604delGAGGCTGAAGGGGAGGCCCAG	c.(5584-5604)gaggctgaaggggaggcccagdel	p.EAEGEAQ1862del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1942					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.E1862E(1)|p.A1863D(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CTGACTCTGGCTGGGCCTCCCCTTCAGCCTCCTGGGCATCC	0.633																																					p.1862_1869del		Atlas-Indel	.											RP1L1,lower_third,carcinoma,+2,1	RP1L1	453	1	2	Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)	c.5585_5605del						PASS	.			85,3535		3,79,1728						0.5	0.0			170	854,7024		39,776,3124	no	coding	RP1L1	NM_178857.5		42,855,4852	A1A1,A1R,RR		10.8403,2.3481,8.1666				939,10559				SO:0001651	inframe_deletion	94137	exon4			.	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5584_5604delGAGGCTGAAGGGGAGGCCCAG	8.37:g.10466004_10466024delCTGGGCCTCCCCTTCAGCCTC	ENSP00000371923:p.Glu1862_Gln1868del	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	83	22	0.26506	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																			.	.	none		0.633	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
OR2W3	343171	hgsc.bcm.edu	37	1	248059779	248059780	+	Frame_Shift_Ins	INS	-	-	A	rs80255919|rs112696640	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248059779_248059780insA	ENST00000360358.3	+	1	891_892	c.891_892insA	c.(892-894)aagfs	p.K298fs	OR2W3_ENST00000537741.1_Frame_Shift_Ins_p.K298fs	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A300fs*>16(1)		breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			ACAGAGAGGTGAAGGGGGCACT	0.54													AA|AA|AAA|insertion	673	0.134385	0.1339	0.1931	5008	,	,		18884	0.0317		0.1312	False		,,,				2504	0.2025				p.V297fs		Pindel,Atlas-Indel	.											.	OR2W3	113	.	1	Insertion - Frameshift(1)	upper_aerodigestive_tract(1)	c.891_892insA						PASS	.			569,3697		41,487,1605						4.3	1.0		dbSNP_132	41	1288,6960		99,1090,2935	no	frameshift	OR2W3	NM_001001957.2		140,1577,4540	A1A1,A1R,RR		15.6159,13.338,14.8394				1857,10657				SO:0001589	frameshift_variant	343171	exon1			.	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.893dupA	1.37:g.248059781_248059781dupA	ENSP00000353516:p.Lys298fs	Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	140	44	0.314	NM_001001957	Q6IF06|Q8NG86	Frame_Shift_Ins	INS	ENST00000360358.3	37	CCDS31099.1																																																																																			-|0.876;A|0.124	0.124	strong		0.540	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957	
BAIAP2L2	80115	hgsc.bcm.edu	37	22	38482353	38482394	+	In_Frame_Del	DEL	TGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	TGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	-	rs371997714|rs66500630|rs113792005|rs376182024|rs541462698|rs369923129|rs553799224	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	TGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38482353_38482394delTGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	ENST00000381669.3	-	12	1466_1507	c.1322_1363delTAGCACCCTCGGAGTACTGGGATGGCCAGTCCCGCTCCCGCA	c.(1321-1365)atagcaccctcggagtactgggatggccagtcccgctcccgcacc>acc	p.IAPSEYWDGQSRSR441del	SLC16A8_ENST00000469516.1_5'Flank	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	441					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					CGGCTTGGGGTGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTATGGAGTTGCC	0.674														708	0.141374	0.0272	0.2291	5008	,	,		20774	0.0565		0.1918	False		,,,				2504	0.2689				p.441_455del		Pindel,Atlas-Indel	.											.	BAIAP2L2	39	.	0			c.1323_1364del						PASS	.			138,3818		23,92,1863						2.2	0.8		dbSNP_130	20	1131,6525		291,549,2988	no	coding	BAIAP2L2	NM_025045.4		314,641,4851	A1A1,A1R,RR		14.7727,3.4884,10.9283				1269,10343				SO:0001651	inframe_deletion	80115	exon12			.	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1322_1363delTAGCACCCTCGGAGTACTGGGATGGCCAGTCCCGCTCCCGCA	22.37:g.38482353_38482394delTGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	ENSP00000371085:p.Ile441_Arg454del	Somatic	129	.	.		WXS	Illumina HiSeq	Phase_I	32	22	0.688	NM_025045	B0QYE2|Q96BG7	In_Frame_Del	DEL	ENST00000381669.3	37	CCDS43018.1																																																																																			.	.	none		0.674	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045	
OR5K3	403277	hgsc.bcm.edu	37	3	98110406	98110407	+	Frame_Shift_Ins	INS	-	-	A	rs144759043|rs145803525|rs79045298	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:98110406_98110407insA	ENST00000383695.1	+	1	897_898	c.897_898insA	c.(898-900)aaafs	p.K300fs	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	300						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						TAAATATTATGAAAAAAATTAT	0.262													AAAAAAA|AAAAAAA|AAAAAAAA|insertion	1648	0.329073	0.208	0.3689	5008	,	,		12958	0.127		0.5964	False		,,,				2504	0.3978				p.M299fs		Pindel,Atlas-Indel	.											.	OR5K3	60	.	0			c.897_898insA						PASS	.																																			SO:0001589	frameshift_variant	403277	exon1			.		CCDS33803.1	3q11.2	2013-09-23			ENSG00000206536	ENSG00000206536		"""GPCR / Class A : Olfactory receptors"""	31290	protein-coding gene	gene with protein product							Standard	NM_001005516		Approved		uc011bgw.2	A6NET4	OTTHUMG00000160077	ENST00000383695.1:c.904dupA	3.37:g.98110413_98110413dupA	ENSP00000373194:p.Lys300fs	Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	36	28	0.778	NM_001005516		Frame_Shift_Ins	INS	ENST00000383695.1	37	CCDS33803.1																																																																																			-|0.649;A|0.351	0.351	strong		0.262	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359110.1		
MICA	100507436	hgsc.bcm.edu	37	6	31380161	31380162	+	Frame_Shift_Ins	INS	-	-	CT	rs41293539|rs547446871|rs138201170	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31380161_31380162insCT	ENST00000449934.2	+	5	1006_1007	c.952_953insCT	c.(952-954)ggcfs	p.G318fs	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				TGTTGCTGCTGGCTGCTGCTAT	0.45														1171	0.233826	0.2882	0.2579	5008	,	,		18959	0.127		0.2157	False		,,,				2504	0.272				p.G318fs		Pindel,Atlas-Indel	.											.	MICA	21	.	0			c.952_953insCT						PASS	.																																			SO:0001589	frameshift_variant	100507436	exon5			.	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	Exception_encountered	6.37:g.31380161_31380162insCT	ENSP00000413079:p.Gly318fs	Somatic	118	.	.		WXS	Illumina HiSeq	Phase_I	154	32	0.208	NM_001177519		Frame_Shift_Ins	INS	ENST00000449934.2	37	CCDS56412.1																																																																																			.	.	weak		0.450	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
OR5H6	79295	hgsc.bcm.edu	37	3	97983488	97983496	+	In_Frame_Del	DEL	TGTAACCAC	TGTAACCAC	-	rs145155372|rs149984587|rs369030566|rs398062605|rs74203917|rs372483864	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TGTAACCAC	TGTAACCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:97983488_97983496delTGTAACCAC	ENST00000383696.2	+	1	401_409	c.360_368delTGTAACCAC	c.(358-369)cttgtaaccact>ctt	p.VTT124del	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						TTTTTTCCCTTGTAACCACTGTAACCACA	0.383														1588	0.317093	0.2141	0.3372	5008	,	,		24385	0.1319		0.5616	False		,,,				2504	0.3814				p.120_123del		Pindel,Atlas-Indel	.											.	OR5H6	89	.	0			c.359_367del						PASS	.			1036,3228		131,774,1227						2.2	0.0		dbSNP_134	100	4355,3849		1213,1929,960	no	coding	OR5H6	NM_001005479.1		1344,2703,2187	A1A1,A1R,RR		46.9161,24.2964,43.2387				5391,7077				SO:0001651	inframe_deletion	79295	exon1			.	BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"""GPCR / Class A : Olfactory receptors"""	14767	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily H, member 6"""				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.360_368delTGTAACCAC	3.37:g.97983497_97983505delTGTAACCAC	ENSP00000373196:p.Val124_Thr126del	Somatic	248	.	.		WXS	Illumina HiSeq	Phase_I	230	59	0.257	NM_001005479	Q6IF88	In_Frame_Del	DEL	ENST00000383696.2	37	CCDS33800.1																																																																																			TGTAACCAC|0.673;-|0.327	0.327	strong		0.383	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2		
DDX20	11218	hgsc.bcm.edu	37	1	112305578	112305580	+	In_Frame_Del	DEL	ATG	ATG	-	rs538821511	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:112305578_112305580delATG	ENST00000369702.4	+	10	1881_1883	c.1261_1263delATG	c.(1261-1263)atgdel	p.M423del	DDX20_ENST00000475700.1_In_Frame_Del_p.M31del|DDX20_ENST00000536167.1_3'UTR	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	423	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGAAGAAAATATGATGATGAGAA	0.355														3	0.000599042	0.0	0.0	5008	,	,		21006	0.0		0.003	False		,,,				2504	0.0				p.420_421del		Pindel,Atlas-Indel	.											.	DDX20	50	.	0			c.1260_1262del						PASS	.			3,4263		0,3,2130						0.5	1.0			109	32,8220		0,32,4094	no	coding	DDX20	NM_007204.4		0,35,6224	A1A1,A1R,RR		0.3878,0.0703,0.2796				35,12483				SO:0001651	inframe_deletion	11218	exon10			.	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.1261_1263delATG	1.37:g.112305584_112305586delATG	ENSP00000358716:p.Met423del	Somatic	113	.	.		WXS	Illumina HiSeq	Phase_I	100	30	0.300	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	In_Frame_Del	DEL	ENST00000369702.4	37	CCDS842.1																																																																																			.	.	none		0.355	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
OR52A1	23538	hgsc.bcm.edu	37	11	5172795	5172796	+	Frame_Shift_Ins	INS	-	-	C	rs112098990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5172795_5172796insC	ENST00000380367.1	-	2	1221_1222	c.804_805insG	c.(802-807)gggtctfs	p.S269fs	OR52A1_ENST00000328942.1_Frame_Shift_Ins_p.S269fs			Q9UKL2	O52A1_HUMAN	olfactory receptor, family 52, subfamily A, member 1	269					sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	19		Medulloblastoma(188;0.00106)|Breast(177;0.0155)|all_neural(188;0.0189)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGATGTGAGACCCAAACCTAT	0.436													CCC|CCC|CCCC|insertion	980	0.195687	0.1399	0.2738	5008	,	,		18188	0.0278		0.2445	False		,,,				2504	0.3384				p.S269fs		Pindel,Atlas-Indel	.											OR52A1,NS,carcinoma,+1,1	OR52A1	58	1	0			c.805_806insG						PASS	.			597,3667		41,515,1576						-1.6	0.3		dbSNP_132	163	2117,6137		287,1543,2297	no	frameshift	OR52A1	NM_012375.2		328,2058,3873	A1A1,A1R,RR		25.6482,14.0009,21.6808				2714,9804				SO:0001589	frameshift_variant	23538	exon1			.	AF154673	CCDS31374.1	11p15.4	2012-08-09			ENSG00000182070	ENSG00000182070		"""GPCR / Class A : Olfactory receptors"""	8318	protein-coding gene	gene with protein product						10512676	Standard	NM_012375		Approved	HPFH1OR	uc010qyy.2	Q9UKL2	OTTHUMG00000066603	ENST00000380367.1:c.805dupG	11.37:g.5172798_5172798dupC	ENSP00000369725:p.Ser269fs	Somatic	116	.	.		WXS	Illumina HiSeq	Phase_I	108	36	0.333	NM_012375	Q6IF31	Frame_Shift_Ins	INS	ENST00000380367.1	37	CCDS31374.1																																																																																			-|0.838;C|0.162	0.162	strong		0.436	OR52A1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142810.2	NM_012375	
BBX	56987	hgsc.bcm.edu	37	3	107491759	107491761	+	In_Frame_Del	DEL	AGA	AGA	-	rs397757043|rs34531902	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:107491759_107491761delAGA	ENST00000325805.8	+	11	1478_1480	c.1191_1193delAGA	c.(1189-1194)ttagaa>tta	p.E399del	BBX_ENST00000402543.1_In_Frame_Del_p.E399del|BBX_ENST00000406780.1_In_Frame_Del_p.E399del|BBX_ENST00000415149.2_In_Frame_Del_p.E399del|BBX_ENST00000416476.2_Intron			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	399					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			AGGAAGAGTTAGAAGAAGATCAC	0.325														187	0.0373403	0.0076	0.0706	5008	,	,		18681	0.0		0.1074	False		,,,				2504	0.0204				p.397_398del		Pindel,Atlas-Indel	.											.	BBX	156	.	0			c.1190_1192del						PASS	.		,	130,4136		1,128,2004					,	2.6	1.0		dbSNP_126	71	978,7272		62,854,3209	no	coding,coding	BBX	NM_020235.5,NM_001142568.1	,	63,982,5213	A1A1,A1R,RR		11.8545,3.0474,8.8527	,	,		1108,11408				SO:0001651	inframe_deletion	56987	exon11			.	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"""x 001 protein"""					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1191_1193delAGA	3.37:g.107491765_107491767delAGA	ENSP00000319974:p.Glu399del	Somatic	152	.	.		WXS	Illumina HiSeq	Phase_I	173	57	0.329	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	In_Frame_Del	DEL	ENST00000325805.8	37	CCDS46881.1																																																																																			AGA|0.951;-|0.049	0.049	strong		0.325	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
UBAC1	10422	hgsc.bcm.edu	37	9	138836942	138836944	+	In_Frame_Del	DEL	CCT	CCT	-	rs66767056|rs140946801	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:138836942_138836944delCCT	ENST00000371756.3	-	7	1023_1025	c.806_808delAGG	c.(805-810)gaggcc>gcc	p.E269del	UBAC1_ENST00000465873.1_5'UTR	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	269				Missing (in Ref. 1; AAD51084). {ECO:0000305}.	protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.E269delE(1)|p.E269fs*6(1)		NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		TCATCTCTGGCCTCCTCATCGGT	0.621														851	0.169928	0.0197	0.2104	5008	,	,		17759	0.2183		0.2465	False		,,,				2504	0.2157				p.269_270del	NSCLC(78;973 1398 27381 29552 42415)	Pindel,Atlas-Indel	.											.	UBAC1	40	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	stomach(1)|kidney(1)	c.807_809del						PASS	.			274,3990		12,250,1870						0.6	0.8		dbSNP_130	124	2296,5958		312,1672,2143	no	coding	UBAC1	NM_016172.2		324,1922,4013	A1A1,A1R,RR		27.8168,6.4259,20.5304				2570,9948				SO:0001651	inframe_deletion	10422	exon7			.	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"""ubiquitin associated domain containing 1"""	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.806_808delAGG	9.37:g.138836945_138836947delCCT	ENSP00000360821:p.Glu269del	Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	106	39	0.368	NM_016172	O75500|Q9UMW7	In_Frame_Del	DEL	ENST00000371756.3	37	CCDS35177.1																																																																																			CCT|0.815;-|0.185	0.185	strong		0.621	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172	
OR2T12	127064	hgsc.bcm.edu	37	1	248458876	248458876	+	Frame_Shift_Del	DEL	T	T	-	rs11339452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248458876delT	ENST00000317996.1	-	1	4	c.5delA	c.(4-6)gagfs	p.E2fs		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	2						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E2fs*2(1)|p.E2G(1)		endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			ATTTCTCATCTCCATAATTTC	0.428													|||unknown(ALL_OTHER_Ns)	1075	0.214657	0.0159	0.245	5008	,	,		14731	0.3591		0.174	False		,,,				2504	0.3548				p.E2fs		Pindel,Atlas-Indel	.											OR2T12,NS,carcinoma,-1,1	OR2T12	113	1	2	Substitution - Missense(1)|Deletion - Frameshift(1)	lung(1)|pancreas(1)	c.6delG						PASS	.			202,4060		4,194,1933	66.0	61.0	62.0			-2.7	0.0	1	dbSNP_120	70	1430,6824		123,1184,2820	no	frameshift	OR2T12	NM_001004692.1		127,1378,4753	A1A1,A1R,RR		17.3249,4.7396,13.0393			248458876	1632,10884	2200	4211	6411	SO:0001589	frameshift_variant	127064	exon1			.	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.5delA	1.37:g.248458876delT	ENSP00000324583:p.Glu2fs	Somatic	293	.	.		WXS	Illumina HiSeq	Phase_I	302	56	0.185	NM_001004692		Frame_Shift_Del	DEL	ENST00000317996.1	37	CCDS31110.1																																																																																			T|0.803;-|0.197	0.197	strong		0.428	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
OR5K4	403278	hgsc.bcm.edu	37	3	98073592	98073592	+	Frame_Shift_Del	DEL	A	A	-	rs398102322|rs11288615	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:98073592delA	ENST00000354924.2	+	1	895	c.895delA	c.(895-897)aaafs	p.K300fs	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005517.1	NP_001005517.1	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K, member 4	300						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	21						AAATGTTCTTAAAAAAATTAT	0.254													AAAAAAA|AAAAAAA|AAAAAA|deletion	1683	0.336062	0.2352	0.3588	5008	,	,		16327	0.1319		0.5875	False		,,,				2504	0.408				p.L298fs		Pindel,Atlas-Indel	.											.	OR5K4	75	.	0			c.894delT						PASS	.						68.0	56.0	60.0					3																	98073592		2111	3952	6063	SO:0001589	frameshift_variant	403278	exon1			.		CCDS33802.1	3q11.2	2013-09-23			ENSG00000196098	ENSG00000196098		"""GPCR / Class A : Olfactory receptors"""	31291	protein-coding gene	gene with protein product							Standard	NM_001005517		Approved		uc011bgv.2	A6NMS3	OTTHUMG00000160081	ENST00000354924.2:c.895delA	3.37:g.98073592delA	ENSP00000347003:p.Lys300fs	Somatic	30	.	.		WXS	Illumina HiSeq	Phase_I	53	34	0.642	NM_001005517		Frame_Shift_Del	DEL	ENST00000354924.2	37	CCDS33802.1																																																																																			A|0.650;-|0.350	0.350	strong		0.254	OR5K4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359114.1		
CACNA1B	774	hgsc.bcm.edu	37	9	140918171	140918185	+	In_Frame_Del	DEL	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	-	rs145816559|rs11137342|rs370787788|rs551405755	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140918171_140918185delGGAGAAGGAGACCAC	ENST00000371372.1	+	19	3121_3135	c.2976_2990delGGAGAAGGAGACCAC	c.(2974-2991)gtggagaaggagaccacg>gtg	p.EKETT993del	CACNA1B_ENST00000277549.5_In_Frame_Del_p.EKETT185del|CACNA1B_ENST00000545473.1_5'Flank|CACNA1B_ENST00000371355.4_In_Frame_Del_p.EKETT994del|CACNA1B_ENST00000371363.1_In_Frame_Del_p.EKETT993del|CACNA1B_ENST00000277551.2_In_Frame_Del_p.EKETT993del|CACNA1B_ENST00000371357.1_In_Frame_Del_p.EKETT994del|CACNA1B_ENST00000371367.5_5'UTR	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	993					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.T996_E1000delTTEKE(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	ACGAGGCTGTGGAGAAGGAGACCACGGAGAAGGAG	0.735														1990	0.397364	0.6225	0.1282	5008	,	,		9031	0.6349		0.1521	False		,,,				2504	0.2914				p.992_997del		Pindel	.											.	CACNA1B	266	.	1	Deletion - In frame(1)	breast(1)	c.2975_2989del						PASS	.			1091,1197		364,363,417						-1.3	0.0		dbSNP_134	8	691,4399		126,439,1980	no	coding	CACNA1B	NM_000718.3		490,802,2397	A1A1,A1R,RR		13.5756,47.6836,24.1529				1782,5596				SO:0001651	inframe_deletion	774	exon19			.	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.2976_2990delGGAGAAGGAGACCAC	9.37:g.140918171_140918185delGGAGAAGGAGACCAC	ENSP00000360423:p.Glu993_Thr997del	Somatic	94	.	.		WXS	Illumina HiSeq	Phase_I	19	16	0.842	NM_001243812	B1AQK5	In_Frame_Del	DEL	ENST00000371372.1	37	CCDS59522.1																																																																																			GGAGAAGGAGACCAC|0.621;-|0.379	0.379	strong		0.735	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
IFIH1	64135	hgsc.bcm.edu	37	2	163128798	163128801	+	Frame_Shift_Del	DEL	TCTC	TCTC	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:163128798_163128801delTCTC	ENST00000263642.2	-	13	2946_2949	c.2551_2554delGAGA	c.(2551-2556)gagaagfs	p.EK851fs		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	851	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)	p.E851D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						TACATCATCTTCTCTCGGAAATCA	0.417																																					p.851_852del		Pindel	.											.	IFIH1	102	.	1	Substitution - Missense(1)	breast(1)	c.2552_2555del						PASS	.																																			SO:0001589	frameshift_variant	64135	exon13			.	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.2551_2554delGAGA	2.37:g.163128798_163128801delTCTC	ENSP00000263642:p.Glu851fs	Somatic	312	.	.		WXS	Illumina HiSeq	Phase_I	345	102	0.296	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Frame_Shift_Del	DEL	ENST00000263642.2	37	CCDS2217.1																																																																																			.	.	none		0.417	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168	
IQSEC1	9922	hgsc.bcm.edu	37	3	12942851	12942851	+	Intron	DEL	C	C	-	rs397988742|rs56387830		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:12942851delC	ENST00000273221.4	-	13	3064					NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1						actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GGGGGGGTGGCCAGGGCTGGG	0.697																																					p.P993fs		Pindel	.											.	IQSEC1	88	.	0			c.2977delC						PASS	.		,	1975,1		987,1,0	1.0	1.0	1.0		,	1.9	0.0	3	dbSNP_130	2	4412,6		2205,2,2	no	intron,frameshift	IQSEC1	NM_014869.4,NM_001134382.1	,	3192,3,2	A1A1,A1R,RR		0.1358,0.0506,0.1095	,	,	12942851	6387,7	180	413	593	SO:0001627	intron_variant	9922	exon15			.	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"""brefeldin A-resistant ARF-GEF2"""	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.2847+1421G>-	3.37:g.12942851delC		Somatic	17	.	.		WXS	Illumina HiSeq	Phase_I	16	12	0.750	NM_001134382	O94863|Q96D85	Frame_Shift_Del	DEL	ENST00000273221.4	37	CCDS33703.1																																																																																			C|0.010;-|0.990	0.990	strong		0.697	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242149	81242151	+	RNA	DEL	TTT	TTT	-	rs532218091|rs55980345|rs75398810|rs5818326|rs548490632|rs386792900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81242149_81242151delTTT	ENST00000525539.1	-	0	704_706				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.N236fs*26(6)|p.G235G(2)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CGGACACAGGTTTCCAAAGTAGG	0.557														146	0.0291534	0.0038	0.0101	5008	,	,		21632	0.0635		0.0119	False		,,,				2504	0.0593				p.236_236del		Pindel	.											.	PKD1L2	361	.	8	Deletion - Frameshift(6)|Substitution - coding silent(2)	lung(4)|breast(4)	c.706_708del						PASS	.		,	824,61,3211		115,28,566,0,33,1306					,	3.1	1.0		dbSNP_129	86	3173,330,4601		544,214,1871,1,114,1308	yes	codingComplex,codingComplex	PKD1L2	NM_052892.3,NM_001076780.1	,	659,242,2437,1,147,2614	A1A1,A1A2,A1R,A2A2,A2R,RR		43.2256,21.6064,35.9672	,	,		3997,391,7812						114780	exon4			.	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242149_81242151delTTT		Somatic	43	.	.		WXS	Illumina HiSeq	Phase_I	26	18	0.692	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	In_Frame_Del	DEL	ENST00000525539.1	37																																																																																				-|0.500;TT|0.500	0.500	alt		0.557	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
RHBG	57127	hgsc.bcm.edu	37	1	156354348	156354348	+	Frame_Shift_Del	DEL	C	C	-	rs11303415	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156354348delC	ENST00000368249.1	+	9	1303	c.1265delC	c.(1264-1266)tccfs	p.S422fs	RHBG_ENST00000255013.3_Frame_Shift_Del_p.S353fs|RHBG_ENST00000494874.1_Intron|RHBG_ENST00000400992.2_Frame_Shift_Del_p.S390fs|RHBG_ENST00000368246.2_Splice_Site	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	422	Interaction with ANK3.				ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)	p.R425fs*>17(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					TTTCTGGACTCCCCCCCCAGA	0.632											OREG0013871	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		2118	0.422923	0.6059	0.2925	5008	,	,		18146	0.5446		0.2396	False		,,,				2504	0.3313				p.S422fs		Pindel	.											.	RHBG	133	.	1	Deletion - Frameshift(1)	ovary(1)	c.1264delT						PASS	.						38.0	63.0	55.0					1																	156354348		1930	4140	6070	SO:0001589	frameshift_variant	57127	exon9			.	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.1265delC	1.37:g.156354348delC	ENSP00000357232:p.Ser422fs	Somatic	97	.	.	1777	WXS	Illumina HiSeq	Phase_I	114	66	0.579	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Frame_Shift_Del	DEL	ENST00000368249.1	37																																																																																				-|1.000;|0.000	1.000	strong		0.632	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
ACIN1	22985	hgsc.bcm.edu	37	14	23548783	23548784	+	In_Frame_Ins	INS	-	-	GAACGT	rs78164858|rs148403158|rs61741621|rs5807202|rs3077646	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23548783_23548784insGAACGT	ENST00000262710.1	-	6	2261_2262	c.1934_1935insACGTTC	c.(1933-1935)tct>tcACGTTCt	p.645_645S>SRS	ACIN1_ENST00000555053.1_In_Frame_Ins_p.645_645S>SRS|ACIN1_ENST00000457657.1_In_Frame_Ins_p.605_605S>SRS|ACIN1_ENST00000605057.1_In_Frame_Ins_p.587_587S>SRS|ACIN1_ENST00000555352.1_5'Flank	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	645	Ser-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		ATGCTGAACGAGAACGTGAACG	0.485														1942	0.38778	0.5318	0.2637	5008	,	,		21370	0.4226		0.2664	False		,,,				2504	0.3701				p.S645delinsSRS		Pindel	.											.	ACIN1	147	.	0			c.1935_1936insACGTTC						PASS	.		,,	2635,143,113,3,1370		775,98,106,3,878,1,1,0,42,0,0,6,0,0,222					,,	-4.2	0.3		dbSNP_126	219	3073,1,288,0,4892		417,1,253,0,1985,0,0,0,0,0,0,35,0,0,1436	no	codingComplex,codingComplex,codingComplex	ACIN1	NM_014977.3,NM_001164815.1,NM_001164814.1	,,	1192,99,359,3,2863,1,1,0,42,0,0,41,0,0,1658	A1A1,A1A2,A1A3,A1A4,A1R,A2A2,A2A3,A2A4,A2R,A3A3,A3A4,A3R,A4A4,A4R,RR		40.7318,38.2036,49.976	,,	,,		5708,144,401,3,6262				SO:0001652	inframe_insertion	22985	exon6			.	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1929_1934dupACGTTC	14.37:g.23548784_23548789dupGAACGT	ENSP00000262710:p.ArgSer647dup	Somatic	197	.	.		WXS	Illumina HiSeq	Phase_I	203	58	0.286	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	In_Frame_Ins	INS	ENST00000262710.1	37	CCDS9587.1																																																																																			.	.	strong		0.485	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
OR8I2	120586	hgsc.bcm.edu	37	11	55861280	55861307	+	Frame_Shift_Del	DEL	TGGCGTTCTGTGATTCCAGCATCAATCA	TGGCGTTCTGTGATTCCAGCATCAATCA	-	rs201548817|rs538399922|rs117967749|rs112181516|rs146622884|rs148972396|rs144690814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TGGCGTTCTGTGATTCCAGCATCAATCA	TGGCGTTCTGTGATTCCAGCATCAATCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55861280_55861307delTGGCGTTCTGTGATTCCAGCATCAATCA	ENST00000302124.2	+	1	528_555	c.497_524delTGGCGTTCTGTGATTCCAGCATCAATCA	c.(496-525)ttggcgttctgtgattccagcatcaatcatfs	p.LAFCDSSINH166fs		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H175fs*10(1)|p.C178fs*2(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					ATAAGCAGTTTGGCGTTCTGTGATTCCAGCATCAATCATTTTTTTTGT	0.443																																					p.166_175del		Pindel	.											.	OR8I2	119	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	ovary(1)|large_intestine(1)	c.496_523del						PASS	.																																			SO:0001589	frameshift_variant	120586	exon1			.	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.497_524delTGGCGTTCTGTGATTCCAGCATCAATCA	11.37:g.55861280_55861307delTGGCGTTCTGTGATTCCAGCATCAATCA	ENSP00000303864:p.Leu166fs	Somatic	134	.	.		WXS	Illumina HiSeq	Phase_I	137	23	0.168	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Frame_Shift_Del	DEL	ENST00000302124.2	37	CCDS31517.1																																																																																			.	.	none		0.443	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31106500	31106501	+	Frame_Shift_Ins	INS	-	-	C	rs138474986|rs9278990|rs373492377|rs375095896|rs386698869	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31106500_31106501insC	ENST00000259881.9	+	5	400_401	c.111_112insC	c.(112-114)cccfs	p.P38fs	PSORS1C1_ENST00000547221.1_5'UTR|PSORS1C2_ENST00000259845.4_Intron|PSORS1C1_ENST00000481450.2_Intron	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	38								p.H40fs*3(2)		kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGGAAACTCGTCCCCCCCACGT	0.564																																					p.R37fs		Pindel	.											.	PSORS1C1	11	.	2	Insertion - Frameshift(2)	ovary(1)|kidney(1)	c.111_112insC						PASS	.																																			SO:0001589	frameshift_variant	170679	exon5			.	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.118dupC	6.37:g.31106507_31106507dupC	ENSP00000259881:p.Pro38fs	Somatic	138	.	.		WXS	Illumina HiSeq	Phase_I	151	45	0.298	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Frame_Shift_Ins	INS	ENST00000259881.9	37	CCDS34390.1																																																																																			.	.	strong		0.564	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885568	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC	rs147489453|rs559153194|rs75808076|rs59279731		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29885567_29885568insAAGTCCCCTGAGAAGGCC	ENST00000310624.6	+	4	1971_1972	c.1938_1939insAAGTCCCCTGAGAAGGCC	c.(1939-1941)aag>AAGTCCCCTGAGAAGGCCaag	p.647_647K>KSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	653	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAGGAAGCAAAGTCCCCTGA	0.569																																					p.A646delinsAKSPEKA		Pindel	.											NEFH,rectum,carcinoma,0,1	NEFH	178	1	0			c.1938_1939insAAGTCCCCTGAGAAGGCC						PASS	.			2816,1448		937,942,253						-5.3	0.0		dbSNP_134	77	5046,3206		1537,1972,617	no	coding	NEFH	NM_021076.3		2474,2914,870	A1A1,A1R,RR		38.8512,33.9587,37.1844				7862,4654				SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1939_1956dupAAGTCCCCTGAGAAGGCC	22.37:g.29885567_29885568insAAGTCCCCTGAGAAGGCC	Exception_encountered	Somatic	47	.	.		WXS	Illumina HiSeq	Phase_I	44	16	0.364	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																			.	.	strong		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
CLEC17A	388512	hgsc.bcm.edu	37	19	14694175	14694176	+	In_Frame_Ins	INS	-	-	GGA	rs138602183|rs34295949|rs548360441	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14694175_14694176insGGA	ENST00000417570.1	+	2	88_89	c.50_51insGGA	c.(49-54)atggag>atGGAggag	p.22_23insE	CLEC17A_ENST00000397439.2_In_Frame_Ins_p.22_23insE|CLEC17A_ENST00000547437.1_In_Frame_Ins_p.22_23insE|RN7SL337P_ENST00000462468.2_RNA	NM_001204118.1	NP_001191047.1	Q6ZS10	CL17A_HUMAN	C-type lectin domain family 17, member A	22	Poly-Glu.					cell surface (GO:0009986)|integral component of membrane (GO:0016021)	fucose binding (GO:0042806)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)										GAAGGGACCATGGAGGAGGAGG	0.579														414	0.0826677	0.174	0.0346	5008	,	,		19484	0.004		0.0656	False		,,,				2504	0.092				p.M17delinsME		Pindel	.											.	CLEC17A	27	.	0			c.50_51insGGA						PASS	.																																			SO:0001652	inframe_insertion	388512	exon2			.	AK127809	CCDS46002.1, CCDS46002.2, CCDS56087.1	19p13.12	2009-06-26			ENSG00000187912	ENSG00000187912		"""C-type lectin domain containing"""	34520	protein-coding gene	gene with protein product	"""prolectin"""					19419970	Standard	NM_207390		Approved	FLJ45910	uc010dzn.2	Q6ZS10		ENST00000417570.1:c.66_68dupGGA	19.37:g.14694182_14694184dupGGA	ENSP00000393719:p.Glu22_Glu22dup	Somatic	238	.	.		WXS	Illumina HiSeq	Phase_I	243	48	0.198	NM_207390	A8MX68|B2RTX0|B7ZMM4	In_Frame_Ins	INS	ENST00000417570.1	37	CCDS56087.1																																																																																			-|0.500;GGA|0.500	0.500	weak		0.579	CLEC17A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403400.1	NM_207390	
RAI1	10743	hgsc.bcm.edu	37	17	17697094	17697096	+	In_Frame_Del	DEL	CAG	CAG	-	rs113303801|rs398124422|rs371983878|rs571229335|rs587780431	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17697094_17697096delCAG	ENST00000353383.1	+	3	1301_1303	c.832_834delCAG	c.(832-834)cagdel	p.Q291del	RAI1_ENST00000261641.6_In_Frame_Del_p.Q291del	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	291	Gln-rich.|Poly-Gln.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CAGCTATGACcagcagcagcagc	0.64																																					p.277_278del		Pindel	.											.	RAI1	121	.	0			c.831_833del						PASS	.																																			SO:0001651	inframe_deletion	10743	exon3			.	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.832_834delCAG	17.37:g.17697103_17697105delCAG	ENSP00000323074:p.Gln291del	Somatic	64	.	.		WXS	Illumina HiSeq	Phase_I	91	25	0.275	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	In_Frame_Del	DEL	ENST00000353383.1	37	CCDS11188.1																																																																																			.	.	weak		0.640	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
CEP162	22832	hgsc.bcm.edu	37	6	84884494	84884495	+	In_Frame_Ins	INS	-	-	TCCTGTTGTTTCTTTAGTTCTTCCAACTTATTTTCTAGTTCTTTC	rs539790644|rs143976780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:84884494_84884495insTCCTGTTGTTTCTTTAGTTCTTCCAACTTATTTTCTAGTTCTTTC	ENST00000403245.3	-	15	2090_2091	c.1976_1977insGAAAGAACTAGAAAATAAGTTGGAAGAACTAAAGAAACAACAGGA	c.(1975-1977)gaa>gaGAAAGAACTAGAAAATAAGTTGGAAGAACTAAAGAAACAACAGGAa	p.659_659E>EKELENKLEELKKQQE	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_In_Frame_Ins_p.583_583E>EKELENKLEELKKQQE	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		AGAGTTCTTTTTCCTGTTGTTT	0.302														208	0.0415335	0.0151	0.0937	5008	,	,		19552	0.0149		0.0417	False		,,,				2504	0.0675				p.E659delinsEKELENKLEELKKQQE		Pindel	.											.	KIAA1009	119	.	0			c.1977_1978insGAAAGAACTAGAAAATAAGTTGGAAGAACTAAAGAAACAACAGGA						PASS	.																																			SO:0001652	inframe_insertion	22832	exon15			.																												ENST00000403245.3:c.1932_1976dupGAAAGAACTAGAAAATAAGTTGGAAGAACTAAAGAAACAACAGGA	6.37:g.84884494_84884495insTCCTGTTGTTTCTTTAGTTCTTCCAACTTATTTTCTAGTTCTTTC	ENSP00000385215:p.LysGluLeuGluAsnLysLeuGluGluLeuLysLysGlnGlnGlu659dup	Somatic	156	.	.		WXS	Illumina HiSeq	Phase_I	185	35	0.189	NM_014895		In_Frame_Ins	INS	ENST00000403245.3	37	CCDS34494.2																																																																																			.	.	none		0.302	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
AK9	221264	hgsc.bcm.edu	37	6	109906330	109906332	+	In_Frame_Del	DEL	CTT	CTT	-	rs71770197|rs73519211|rs568921203|rs141134529	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:109906330_109906332delCTT	ENST00000424296.2	-	19	2184_2186	c.2108_2110delAAG	c.(2107-2112)gaagca>gca	p.E703del	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000368948.2_In_Frame_Del_p.E703del	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	703					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TTTTACCTTGCTTCTTCTTCTTC	0.227														1863	0.372005	0.2542	0.4092	5008	,	,		14640	0.377		0.4095	False		,,,				2504	0.4611				p.703_704del		Pindel	.											.	AKD1	223	.	0			c.2109_2111del						PASS	.			396,1116		113,170,473						-0.1	0.2		dbSNP_130	6	1116,1910		355,406,752	no	coding	AKD1	NM_001145128.2		468,576,1225	A1A1,A1R,RR		36.8804,26.1905,33.3186				1512,3026				SO:0001651	inframe_deletion	221264	exon19			.	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.2108_2110delAAG	6.37:g.109906339_109906341delCTT	ENSP00000410186:p.Glu703del	Somatic	61	.	.		WXS	Illumina HiSeq	Phase_I	51	15	0.294	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	In_Frame_Del	DEL	ENST00000424296.2	37	CCDS55048.1																																																																																			CTT|0.626;-|0.374	0.374	strong		0.227	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
ACTRT2	140625	hgsc.bcm.edu	37	1	2938408	2938410	+	In_Frame_Del	DEL	AGA	AGA	-	rs4013154|rs201580305	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:2938408_2938410delAGA	ENST00000378404.2	+	1	363_365	c.158_160delAGA	c.(157-162)cagaag>cag	p.K55del		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	55				Missing (in Ref. 5; AAH29499). {ECO:0000305}.		cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		GAGGCCAACCAGAAGAAGTACTT	0.611														563	0.11242	0.0106	0.2176	5008	,	,		17049	0.1925		0.1581	False		,,,				2504	0.046				p.53_53del		Pindel	.											ACTRT2,NS,carcinoma,-1,1	ACTRT2	69	1	0			c.157_159del						PASS	.			152,4114		9,134,1990						4.1	0.8		dbSNP_108	43	1412,6842		109,1194,2824	no	coding	ACTRT2	NM_080431.4		118,1328,4814	A1A1,A1R,RR		17.1069,3.5631,12.492				1564,10956				SO:0001651	inframe_deletion	140625	exon1			.	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.158_160delAGA	1.37:g.2938411_2938413delAGA	ENSP00000367658:p.Lys55del	Somatic	87	.	.		WXS	Illumina HiSeq	Phase_I	120	41	0.342	NM_080431	B1AN52|Q8NHS6|Q8TDG1	In_Frame_Del	DEL	ENST00000378404.2	37	CCDS45.1																																																																																			AGA|0.848;-|0.152	0.152	strong		0.611	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431	
DMKN	93099	hgsc.bcm.edu	37	19	36002362	36002412	+	In_Frame_Del	DEL	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	-	rs112672248|rs142519211|rs144877871|rs544198244|rs199498909|rs11667007|rs12981076|rs146822312|rs148799704|rs138902616|rs56743379|rs140071083|rs371511253|rs117522133|rs59309505|rs113540509|rs111543270|rs58579970|rs201369392	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:36002362_36002412delCTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	ENST00000339686.3	-	5	995_1045	c.819_869delCAGTGGCAGCAGCAGTGGCGGCAGCAGTGGCGGCAGCAGTGGTGGCAGCAG	c.(817-870)agcagtggcagcagcagtggcggcagcagtggcggcagcagtggtggcagcagt>agt	p.273_290SSGSSSGGSSGGSSGGSS>S	DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000418261.1_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000424570.2_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000447113.2_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000440396.1_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000436012.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	273	Gly-rich.		G -> S (in dbSNP:rs11667007). {ECO:0000269|PubMed:17380110}.	G -> GSSSG (in Ref. 4; AAQ88778). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			actgttgccactgctgccaccactgctgccgccactgctgccgccactgctgctgccactgctgctgccac	0.641																																					p.274_290del		Pindel	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.820_870del						PASS	.		,,,,,,	1051,3093		133,785,1154					,,,,,,	-3.2	0.0		dbSNP_130	28	1360,6640		184,992,2824	no	coding,coding,coding,intron,coding,coding,intron	DMKN	NM_033317.4,NM_001190349.1,NM_001190348.1,NM_001190347.1,NM_001126058.2,NM_001126057.2,NM_001126056.2	,,,,,,	317,1777,3978	A1A1,A1R,RR		17.0,25.362,19.8534	,,,,,,	,,,,,,		2411,9733				SO:0001651	inframe_deletion	93099	exon5			.	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.819_869delCAGTGGCAGCAGCAGTGGCGGCAGCAGTGGCGGCAGCAGTGGTGGCAGCAG	19.37:g.36002362_36002412delCTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	ENSP00000342012:p.Ser273_Ser289del	Somatic	49	.	.		WXS	Illumina HiSeq	Phase_I	65	25	0.385	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	In_Frame_Del	DEL	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	none		0.641	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
ZNF384	171017	hgsc.bcm.edu	37	12	6777070	6777072	+	In_Frame_Del	DEL	TGC	TGC	-	rs78573212|rs72393318|rs544124628|rs3835029	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TGC	TGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6777070_6777072delTGC	ENST00000396801.3	-	11	1749_1751	c.1542_1544delGCA	c.(1540-1545)cagcaa>caa	p.514_515QQ>Q	ZNF384_ENST00000396799.2_In_Frame_Del_p.453_454QQ>Q|RP4-761J14.8_ENST00000589924.1_RNA|ZNF384_ENST00000361959.3_In_Frame_Del_p.514_515QQ>Q|ZNF384_ENST00000319770.3_In_Frame_Del_p.437_438QQ>Q|ZNF384_ENST00000396795.1_In_Frame_Del_p.453_454QQ>Q|ZNF384_ENST00000355772.4_In_Frame_Del_p.398_399QQ>Q|RP4-761J14.8_ENST00000586338.1_RNA	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	514	Gln-rich.				nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.L139delL(6)|p.Q455delQ(3)|p.Q516delQ(3)	EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						TGGTGgctgttgctgctgctgct	0.665			T	"""EWSR1, TAF15 """	ALL									4006	0.79992	0.8253	0.8501	5008	,	,		14338	0.8125		0.7753	False		,,,				2504	0.7423				p.515_515del		Pindel	.		Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	ZNF384_ENST00000361959,caecum,carcinoma,0,4	ZNF384	102	4	12	Deletion - In frame(12)	breast(12)	c.1543_1545del						PASS	.																																			SO:0001651	inframe_deletion	171017	exon11			.	U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"""Zinc fingers, C2H2-type"""	11955	protein-coding gene	gene with protein product		609951	"""trinucleotide repeat containing 1"""	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.1542_1544delGCA	12.37:g.6777079_6777081delTGC	ENSP00000380019:p.Gln516del	Somatic	48	.	.		WXS	Illumina HiSeq	Phase_I	58	20	0.345	NM_001135734	O15407|Q7Z722|Q8N938	In_Frame_Del	DEL	ENST00000396801.3	37	CCDS44817.1																																																																																			.	.	strong		0.665	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400712.1		
OVGP1	5016	hgsc.bcm.edu	37	1	111957515	111957583	+	In_Frame_Del	DEL	ACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	ACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	-	rs61742558|rs568931117|rs12096782|rs112145355|rs113984808|rs201350653|rs375218077|rs79262073|rs201210901|rs75512011|rs1126656|rs368203827|rs150261549|rs3767609|rs3767608|rs201662631|rs376377993|rs145862799|rs45455292|rs74322126|rs374145757|rs140282461|rs549398942|rs369687480|rs386634633|rs144666939|rs551744565|rs139753199	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	ACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	ACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111957515_111957583delACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	ENST00000369732.3	-	11	1595_1663	c.1540_1608delTATCAGTCTGTGACCCCTGGGGAAAAGACCCTGACCCCTGTGGGTCATCAGTCTGTGACCCCTGTGAGT	c.(1540-1608)tatcagtctgtgacccctggggaaaagaccctgacccctgtgggtcatcagtctgtgacccctgtgagtdel	p.YQSVTPGEKTLTPVGHQSVTPVS514del		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	514			Y -> H (in dbSNP:rs1126656). {ECO:0000269|Ref.2}.		binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)	p.T597_V604delTPVSHQSV(2)|p.T533_V540delTPVSHQSV(2)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		CAGACTGATGACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATAACCCACAGAG	0.554																																					p.514_537del		Pindel	.											.	OVGP1	177	.	4	Deletion - In frame(4)	haematopoietic_and_lymphoid_tissue(2)|stomach(2)	c.1541_1609del						PASS	.																																			SO:0001651	inframe_deletion	5016	exon11			.	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1540_1608delTATCAGTCTGTGACCCCTGGGGAAAAGACCCTGACCCCTGTGGGTCATCAGTCTGTGACCCCTGTGAGT	1.37:g.111957515_111957583delACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	ENSP00000358747:p.Tyr514_Ser536del	Somatic	167	.	.		WXS	Illumina HiSeq	Phase_I	152	33	0.217	NM_002557	A0AV19|B9EGE1|Q15841	In_Frame_Del	DEL	ENST00000369732.3	37	CCDS834.1																																																																																			.	.	none		0.554	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
FAM74A7	100996582	hgsc.bcm.edu	37	9	40715911	40715944	+	lincRNA	DEL	GAGAAGACGTGGAAAGAGCTCAGAGGCTGTCCCA	GAGAAGACGTGGAAAGAGCTCAGAGGCTGTCCCA	-	rs199625563|rs370250075|rs62565542|rs62565543|rs535156143|rs374953827|rs112785686|rs557064091|rs62566171|rs62566172	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GAGAAGACGTGGAAAGAGCTCAGAGGCTGTCCCA	GAGAAGACGTGGAAAGAGCTCAGAGGCTGTCCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:40715911_40715944delGAGAAGACGTGGAAAGAGCTCAGAGGCTGTCCCA	ENST00000432614.1	-	0	0				FAM74A3_ENST00000604146.1_lincRNA																							GGCTGTCCCGGAGAAGACGTGGAAAGAGCTCAGAGGCTGTCCCAGAGAAGACGT	0.568																																					.		Pindel	.											FAM74A3,right_upper_lobe,carcinoma,-1,1	FAM74A3	17	1	0			.						PASS	.			490,3580		46,398,1591						-0.2	0.0			18	1765,6001		192,1381,2310	no	intergenic				238,1779,3901	A1A1,A1R,RR		22.7273,12.0393,19.052				2255,9581						728495	.			.																													9.37:g.40715911_40715944delGAGAAGACGTGGAAAGAGCTCAGAGGCTGTCCCA		Somatic	488	.	.		WXS	Illumina HiSeq	Phase_I	187	50	0.267	.		RNA	DEL	ENST00000432614.1	37																																																																																				.	.	none		0.568	RP11-395E19.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000143688.1		
PCDHA4	56144	hgsc.bcm.edu	37	5	140186979	140186990	+	In_Frame_Del	DEL	GGGCCGCGGAGG	GGGCCGCGGAGG	-	rs67934344|rs200172095|rs563991668|rs3822355|rs3822354|rs17844273|rs3822351|rs3822350|rs3822353|rs3822352|rs386692888|rs543774145|rs201303975|rs386692887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GGGCCGCGGAGG	GGGCCGCGGAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140186979_140186990delGGGCCGCGGAGG	ENST00000530339.1	+	1	207_218	c.207_218delGGGCCGCGGAGG	c.(205-219)aagggccgcggaggc>aac	p.69_73KGRGG>N	PCDHA4_ENST00000356878.4_In_Frame_Del_p.69_73KGRGG>N|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_In_Frame_Del_p.69_73KGRGG>N	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	69	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.G72R(2)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCGTCCAAGGGCCGCGGAGGCCTTCTGGAG	0.656																																					p.69_73del		Pindel	.											.	PCDHA4	419	.	2	Substitution - Missense(2)	lung(2)	c.206_217del						PASS	.																																			SO:0001651	inframe_deletion	56144	exon1			.	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.207_218delGGGCCGCGGAGG	5.37:g.140186979_140186990delGGGCCGCGGAGG	ENSP00000435300:p.Lys69_Gly73delinsAsn	Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	39	12	0.308	NM_031500	O75285|Q2M253	In_Frame_Del	DEL	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.656	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
FAM157B	100132403	hgsc.bcm.edu	37	9	141107537	141107548	+	lincRNA	DEL	GCAGCAGCAGCA	GCAGCAGCAGCA	-	rs199863448|rs370981092		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GCAGCAGCAGCA	GCAGCAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:141107537_141107548delGCAGCAGCAGCA	ENST00000446912.2	+	0	20_31							P0CG42	F157B_HUMAN	family with sequence similarity 157, member B																		Ggcagcggcggcagcagcagcagcagcagcag	0.547																																					p.73_77del		Pindel	.											.	.	.	.	0			c.218_229del						PASS	.			125,11,122,864		47,0,5,26,3,1,4,48,20,407							0.0			11	246,36,761,2189		64,0,32,86,6,3,21,223,280,901	no	codingComplex	FAM157B	NM_001145249.1		111,0,37,112,9,4,25,271,300,1308	A1A1,A1A2,A1A3,A1R,A2A2,A2A3,A2R,A3A3,A3R,RR		32.271,22.9947,29.8806				371,47,883,3053						100132403	exon2			.			9q34	2013-01-24			ENSG00000233013	ENSG00000233013			34080	other	unknown							Standard	NM_001145249		Approved		uc011mfe.1	P0CG42	OTTHUMG00000021000		9.37:g.141107537_141107548delGCAGCAGCAGCA		Somatic	565	.	.		WXS	Illumina HiSeq	Phase_I	220	40	0.182	NM_001145249		In_Frame_Del	DEL	ENST00000446912.2	37																																																																																				.	.	alt		0.547	FAM157B-001	KNOWN	mRNA_end_NF|basic	lincRNA	lincRNA	OTTHUMT00000055378.2	NM_001145249	
DCAF15	90379	hgsc.bcm.edu	37	19	14070706	14070707	+	Splice_Site	INS	-	-	GGTGGGCCCAGGGCGGGCAG	rs3217681|rs141180609|rs373011773	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14070706_14070707insGGTGGGCCCAGGGCGGGCAG	ENST00000254337.6	+	9	1460_1461	c.1439_1440insGGTGGGCCCAGGGCGGGCAG	c.(1438-1443)gaggtc>gaGGTGGGCCCAGGGCGGGCAGggtc	p.-481fs		NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15						protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						GTCATTCTGGAGGTGGGCCCAG	0.589											OREG0025301	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		1524	0.304313	0.2731	0.2277	5008	,	,		14914	0.3294		0.2843	False		,,,				2504	0.3957				p.E480fs		Pindel	.											.	DCAF15	30	.	0			c.1439_1440insGGTGGGCCCAGGGCGGGCAG						PASS	.																																			SO:0001630	splice_region_variant	90379	exon9			.	BC002926	CCDS32926.1	19p13.12	2009-07-17	2009-07-17	2009-07-17	ENSG00000132017	ENSG00000132017		"""DDB1 and CUL4 associated factors"""	25095	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 72"""	C19orf72			Standard	NM_138353		Approved	MGC99481	uc002mxt.3	Q66K64		ENST00000254337.6:c.1440+1->GGTGGGCCCAGGGCGGGCAG	19.37:g.14070706_14070707insGGTGGGCCCAGGGCGGGCAG		Somatic	145	.	.	692	WXS	Illumina HiSeq	Phase_I	95	17	0.179	NM_138353	B3KS86|Q96DW0|Q9BU31	Frame_Shift_Ins	INS	ENST00000254337.6	37	CCDS32926.1																																																																																			-|0.924;GGTGGGCCCAGGGCGGGCAG|0.076	0.076	strong		0.589	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353	Frame_Shift_Ins
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651614	1651643	+	In_Frame_Del	DEL	TACTGCTGCCAGTCCAGCTGCTGTAAGCCC	TACTGCTGCCAGTCCAGCTGCTGTAAGCCC	-	rs200756510|rs4752771|rs576867883|rs74396270|rs71025765|rs199686073|rs559627884|rs201911893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TACTGCTGCCAGTCCAGCTGCTGTAAGCCC	TACTGCTGCCAGTCCAGCTGCTGTAAGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1651614_1651643delTACTGCTGCCAGTCCAGCTGCTGTAAGCCC	ENST00000399676.2	+	1	582_611	c.544_573delTACTGCTGCCAGTCCAGCTGCTGTAAGCCC	c.(544-573)tactgctgccagtccagctgctgtaagcccdel	p.YCCQSSCCKP192del		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	192	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.Q185K(1)|p.Y182_P191delYCCQSSCCKP(1)|p.Y192_P201delYCCQSSCCKP(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CTGTAAGCCTTACTGCTGCCAGTCCAGCTGCTGTAAGCCCTACTGCTGCC	0.596																																					p.181_191del		Pindel	.											.	KRTAP5-5	86	.	3	Deletion - In frame(2)|Substitution - Missense(1)	urinary_tract(1)|ovary(1)|lung(1)	c.543_572del						PASS	.			1260,2356		122,1016,670						1.7	0.0		dbSNP_130	87	2762,4476		292,2178,1149	no	coding	KRTAP5-5	NM_001001480.2		414,3194,1819	A1A1,A1R,RR		38.1597,34.8451,37.0555				4022,6832				SO:0001651	inframe_deletion	439915	exon1			.	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.544_573delTACTGCTGCCAGTCCAGCTGCTGTAAGCCC	11.37:g.1651614_1651643delTACTGCTGCCAGTCCAGCTGCTGTAAGCCC	ENSP00000382584:p.Tyr192_Pro201del	Somatic	67	.	.		WXS	Illumina HiSeq	Phase_I	66	15	0.227	NM_001001480	A8MWN2	In_Frame_Del	DEL	ENST00000399676.2	37	CCDS41592.1																																																																																			.	.	none		0.596	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
MAB21L1	4081	hgsc.bcm.edu	37	13	36050434	36050451	+	5'UTR	DEL	CTGCTGCTGCTGCTGCTG	CTGCTGCTGCTGCTGCTG	-	rs146621732|rs376319884|rs372625772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CTGCTGCTGCTGCTGCTG	CTGCTGCTGCTGCTGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:36050434_36050451delCTGCTGCTGCTGCTGCTG	ENST00000379919.4	-	0	381_398				NBEA_ENST00000540320.1_Intron|NBEA_ENST00000537702.1_5'Flank|NBEA_ENST00000379939.2_Intron|NBEA_ENST00000310336.4_Intron|NBEA_ENST00000400445.3_Intron	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)						anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		GTTGGTTTCCctgctgctgctgctgctgctgctgctgc	0.56																																					.		Pindel	.											.	MAB21L1	52	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	4081	.			.	BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"""mab-21 (C. elegans)-like 1"""			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.-176CAGCAGCAGCAGCAGCAG>-	13.37:g.36050434_36050451delCTGCTGCTGCTGCTGCTG		Somatic	75	.	.		WXS	Illumina HiSeq	Phase_I	44	21	0.477	.	Q6I9T5	RNA	DEL	ENST00000379919.4	37	CCDS9353.1																																																																																			.	.	alt		0.560	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584	
PTPRQ	374462	hgsc.bcm.edu	37	12	81063246	81063246	+	Intron	DEL	A	A	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:81063246delA	ENST00000266688.5	+	46	6441							Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q						regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						TTGAAAGGGTAAAAAAAAAAG	0.328																																					.		Pindel	.											.	PTPRQ	119	.	0			c.5937+2A>-						PASS	.						60.0	54.0	56.0					12																	81063246		692	1591	2283	SO:0001627	intron_variant	374462	exon38			.	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.6441+3A>-	12.37:g.81063246delA		Somatic	37	.	.		WXS	Illumina HiSeq	Phase_I	42	11	0.262	NM_001145026		Splice_Site	DEL	ENST00000266688.5	37																																																																																				.	.	none		0.328	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
WNK1	65125	hgsc.bcm.edu	37	12	970297	970297	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:970297delA	ENST00000315939.6	+	7	2382	c.1739delA	c.(1738-1740)gaafs	p.E580fs	WNK1_ENST00000340908.4_Frame_Shift_Del_p.E173fs|WNK1_ENST00000535572.1_Frame_Shift_Del_p.E580fs|WNK1_ENST00000540360.1_3'UTR|WNK1_ENST00000537687.1_Frame_Shift_Del_p.E580fs|WNK1_ENST00000530271.2_Frame_Shift_Del_p.E580fs	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	580					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.?(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GAGGAGCAAGAAAAAAAAAAG	0.468																																					p.E580fs	Colon(19;451 567 6672 12618 28860)	Pindel	.											WNK1_ENST00000537687,rectum,carcinoma,-2,2	WNK1	403	2	1	Unknown(1)	skin(1)	c.1738delG						PASS	.						98.0	96.0	97.0					12																	970297		2203	4300	6503	SO:0001589	frameshift_variant	65125	exon7			.	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1739delA	12.37:g.970297delA	ENSP00000313059:p.Glu580fs	Somatic	50	.	.		WXS	Illumina HiSeq	Phase_I	72	13	0.181	NM_213655	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Frame_Shift_Del	DEL	ENST00000315939.6	37	CCDS8506.1																																																																																			.	.	none		0.468	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144923729	144923729	+	Frame_Shift_Del	DEL	T	T	-	rs3215779|rs369106087	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:144923729delT	ENST00000369354.3	-	6	918	c.729delA	c.(727-729)gaafs	p.E243fs	PDE4DIP_ENST00000369351.3_Frame_Shift_Del_p.E243fs|PDE4DIP_ENST00000369349.3_Frame_Shift_Del_p.E243fs|PDE4DIP_ENST00000529945.1_Frame_Shift_Del_p.E406fs|PDE4DIP_ENST00000530740.1_Frame_Shift_Del_p.E380fs|PDE4DIP_ENST00000369356.4_Frame_Shift_Del_p.E243fs|PDE4DIP_ENST00000313382.9_Frame_Shift_Del_p.E309fs|PDE4DIP_ENST00000479408.2_Frame_Shift_Del_p.E30fs|PDE4DIP_ENST00000369359.4_Frame_Shift_Del_p.E380fs|PDE4DIP_ENST00000313431.9_Frame_Shift_Del_p.E406fs			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	243					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTTCCTGGAGTTCTGCCAAGT	0.448			T	PDGFRB	MPD								TT|TT|T|deletion	928	0.185304	0.0113	0.2205	5008	,	,		39069	0.3988		0.1799	False		,,,				2504	0.181				p.L407fs		Pindel	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.1219delC						PASS	.						364.0	305.0	325.0					1																	144923729		2203	4300	6503	SO:0001589	frameshift_variant	9659	exon2			.	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.729delA	1.37:g.144923729delT	ENSP00000358360:p.Glu243fs	Somatic	400	.	.		WXS	Illumina HiSeq	Phase_I	431	74	0.172	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Frame_Shift_Del	DEL	ENST00000369354.3	37	CCDS30824.1																																																																																			.	.	weak		0.448	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1606121	1606150	+	In_Frame_Del	DEL	CCACAGCCACCCTTGGATCCCCCACAAGAG	CCACAGCCACCCTTGGATCCCCCACAAGAG	-	rs138363822|rs199501537|rs80025267|rs76191756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CCACAGCCACCCTTGGATCCCCCACAAGAG	CCACAGCCACCCTTGGATCCCCCACAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1606121_1606150delCCACAGCCACCCTTGGATCCCCCACAAGAG	ENST00000382171.2	-	1	363_392	c.330_359delCTCTTGTGGGGGATCCAAGGGTGGCTGTGG	c.(328-360)ggctcttgtgggggatccaagggtggctgtggt>ggt	p.110_120GSCGGSKGGCG>G	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	110	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACAGCCGGAACCACAGCCACCCTTGGATCCCCCACAAGAGCCACAGCCCC	0.661																																					p.111_120del		Pindel	.											.	KRTAP5-1	74	.	0			c.331_360del						PASS	.			2171,2035		609,953,541						-5.2	0.0			71	4129,4059		1127,1875,1092	no	coding	KRTAP5-1	NM_001005922.1		1736,2828,1633	A1A1,A1R,RR		49.5725,48.3833,49.169				6300,6094				SO:0001651	inframe_deletion	387264	exon1			.	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.330_359delCTCTTGTGGGGGATCCAAGGGTGGCTGTGG	11.37:g.1606121_1606150delCCACAGCCACCCTTGGATCCCCCACAAGAG	ENSP00000371606:p.Gly110_Cys119del	Somatic	162	.	.		WXS	Illumina HiSeq	Phase_I	74	15	0.203	NM_001005922		In_Frame_Del	DEL	ENST00000382171.2	37	CCDS31330.1																																																																																			.	.	none		0.661	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
CD33	945	hgsc.bcm.edu	37	19	51729104	51729107	+	Frame_Shift_Del	DEL	CCGG	CCGG	-	rs546468173|rs201074739|rs571957160|rs201342074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CCGG	CCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51729104_51729107delCCGG	ENST00000262262.4	+	3	485_488	c.464_467delCCGG	c.(463-468)cccggcfs	p.PG155fs	CD33_ENST00000391796.3_Frame_Shift_Del_p.PG155fs|CD33_ENST00000421133.2_Frame_Shift_Del_p.PG28fs|CD33_ENST00000436584.2_Frame_Shift_Del_p.PG28fs	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	155	Ig-like C2-type.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.G156C(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	ACTCTAGAACCCGGCCACTCCAAA	0.613														29	0.00579073	0.0015	0.0115	5008	,	,		18806	0.0		0.0189	False		,,,				2504	0.0				p.155_156del		Pindel	.											.	CD33	55	.	1	Substitution - Missense(1)	lung(1)	c.463_466del						PASS	.		,,	24,4240		1,22,2109					,,	-6.1	0.0		dbSNP_131	84	233,8017		5,223,3897	no	frameshift,frameshift,frameshift	CD33	NM_001772.3,NM_001177608.1,NM_001082618.1	,,	6,245,6006	A1A1,A1R,RR		2.8242,0.5629,2.0537	,,	,,		257,12257				SO:0001589	frameshift_variant	945	exon3			.	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.464_467delCCGG	19.37:g.51729104_51729107delCCGG	ENSP00000262262:p.Pro155fs	Somatic	72	.	.		WXS	Illumina HiSeq	Phase_I	88	28	0.318	NM_001177608	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Frame_Shift_Del	DEL	ENST00000262262.4	37	CCDS33084.1																																																																																			CCGG|0.992;-|0.008	0.008	strong		0.613	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
HEATR5A	25938	hgsc.bcm.edu	37	14	31856396	31856398	+	In_Frame_Del	DEL	AAG	AAG	-	rs142429257	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:31856396_31856398delAAG	ENST00000389961.3	-	7	1098_1100	c.1099_1101delCTT	c.(1099-1101)cttdel	p.L367del	HEATR5A_ENST00000543095.2_In_Frame_Del_p.L373del|HEATR5A_ENST00000404677.3_In_Frame_Del_p.L373del|HEATR5A_ENST00000439348.1_In_Frame_Del_p.L367del|HEATR5A_ENST00000439727.1_In_Frame_Del_p.L80del			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	367										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		CCTTTTCTCCAAGAAGACCACCT	0.453														34	0.00678914	0.0008	0.0058	5008	,	,		16529	0.0		0.0229	False		,,,				2504	0.0061				p.373_374del		Pindel	.											.	HEATR5A	181	.	0			c.1118_1120del						PASS	.			30,3614		5,20,1797						5.3	1.0		dbSNP_134	123	235,7667		12,211,3728	no	coding	HEATR5A	NM_015473.3		17,231,5525	A1A1,A1R,RR		2.9739,0.8233,2.2952				265,11281				SO:0001651	inframe_deletion	25938	exon8			.	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 125"""	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.1099_1101delCTT	14.37:g.31856399_31856401delAAG	ENSP00000374611:p.Leu367del	Somatic	184	.	.		WXS	Illumina HiSeq	Phase_I	216	65	0.301	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	In_Frame_Del	DEL	ENST00000389961.3	37																																																																																				AAG|0.989;-|0.011	0.011	strong		0.453	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461266	141461266	+	Silent	SNP	A	A	G	rs3735801	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:141461266A>G	ENST00000438773.2	-	2	340	c.207T>C	c.(205-207)ggT>ggC	p.G69G	TRAPPC9_ENST00000389328.4_Silent_p.G167G|TRAPPC9_ENST00000389327.3_Silent_p.G69G	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	69					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						TCTGGAAGTCACCCCACTCGT	0.577													a|||	2694	0.537939	0.5635	0.4121	5008	,	,		19938	0.5347		0.5586	False		,,,				2504	0.5746				p.G167G		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.T501C						PASS	.	G	,	2452,1954	619.0+/-393.3	674,1104,425	77.0	68.0	71.0		207,501	-3.1	1.0	8	dbSNP_107	71	4906,3694	620.6+/-397.1	1420,2066,814	yes	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	2094,3170,1239	GG,GA,AA		42.9535,44.3486,43.4261	,	69/1149,167/1247	141461266	7358,5648	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon2			GAAGTCACCCCAC	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.207T>C	8.37:g.141461266A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	73	0.948052	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1																																																																																			A|0.446;G|0.554	0.554	strong		0.577	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
BBS12	166379	hgsc.bcm.edu	37	4	123664446	123664446	+	Missense_Mutation	SNP	G	G	A	rs13135778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:123664446G>A	ENST00000314218.3	+	2	1592	c.1399G>A	c.(1399-1401)Gac>Aac	p.D467N	BBS12_ENST00000542236.1_Missense_Mutation_p.D467N	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	467			D -> N (in dbSNP:rs13135778). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TTGTGTGGGCGACGGGGTCTG	0.468									Bardet-Biedl syndrome				A|||	464	0.0926518	0.0514	0.1052	5008	,	,		19474	0.0		0.2127	False		,,,				2504	0.1115				p.D467N		Atlas-SNP	.											.	BBS12	63	.	0			c.G1399A						PASS	.	A	ASN/ASP,ASN/ASP	304,4102	798.2+/-415.5	15,274,1914	80.0	79.0	79.0		1399,1399	1.9	0.0	4	dbSNP_121	79	1941,6659	725.5+/-406.6	230,1481,2589	yes	missense,missense	BBS12	NM_001178007.1,NM_152618.2	23,23	245,1755,4503	AA,AG,GG		22.5698,6.8997,17.2613	benign,benign	467/711,467/711	123664446	2245,10761	2203	4300	6503	SO:0001583	missense	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GTGGGCGACGGGG	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1399G>A	4.37:g.123664446G>A	ENSP00000319062:p.Asp467Asn	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	161	69	0.428571	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	37	CCDS3728.1	238	0.10897435897435898	32	0.06504065040650407	42	0.11602209944751381	0	0.0	164	0.21635883905013192	A	0.015	-1.552873	0.00918	0.068997	0.225698	ENSG00000181004	ENST00000314218;ENST00000542236	T;T	0.78246	-1.16;-1.16	5.69	1.9	0.25705	.	1.320260	0.04713	N	0.418035	T	0.00039	0.0001	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05099	-1.0906	9	0.07813	T	0.8	-38.0042	9.6017	0.39607	0.7363:0.0:0.2637:0.0	rs13135778;rs17857450;rs13135778	467	Q6ZW61	BBS12_HUMAN	N	467	ENSP00000319062:D467N;ENSP00000438273:D467N	ENSP00000319062:D467N	D	+	1	0	BBS12	123883896	0.000000	0.05858	0.033000	0.17914	0.138000	0.21146	0.602000	0.24134	-0.117000	0.11872	-0.269000	0.10298	GAC	G|0.857;A|0.143	0.143	strong		0.468	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
MAP3K5	4217	hgsc.bcm.edu	37	6	137113248	137113248	+	Missense_Mutation	SNP	G	G	C	rs114489274	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:137113248G>C	ENST00000359015.4	-	1	408	c.48C>G	c.(46-48)ttC>ttG	p.F16L		NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	16					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		CCGAGGGGGCGAAGGGTGGCA	0.751													G|||	137	0.0273562	0.0545	0.0331	5008	,	,		10210	0.001		0.0368	False		,,,				2504	0.0041				p.F16L		Atlas-SNP	.											.	MAP3K5	136	.	0			c.C48G						PASS	.	G	LEU/PHE	125,3405		0,125,1640	5.0	5.0	5.0		48	-1.7	0.0	6	dbSNP_132	5	173,6697		1,171,3263	yes	missense	MAP3K5	NM_005923.3	22	1,296,4903	CC,CG,GG		2.5182,3.5411,2.8654	benign	16/1375	137113248	298,10102	1765	3435	5200	SO:0001583	missense	4217	exon1			GGGGGCGAAGGGT	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.48C>G	6.37:g.137113248G>C	ENSP00000351908:p.Phe16Leu	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Missense_Mutation	SNP	ENST00000359015.4	37	CCDS5179.1	71	0.03250915750915751	32	0.06504065040650407	12	0.03314917127071823	1	0.0017482517482517483	26	0.03430079155672823	G	0.004	-2.247563	0.00271	0.035411	0.025182	ENSG00000197442	ENST00000359015;ENST00000367768	T	0.67698	-0.28	3.56	-1.67	0.08238	.	0.551802	0.17811	N	0.161216	T	0.10766	0.0263	N	0.08118	0	0.18873	N	0.999987	B	0.02656	0.0	B	0.01281	0.0	T	0.21143	-1.0254	10	0.06236	T	0.91	.	0.5664	0.00687	0.2262:0.1463:0.3293:0.2982	.	16	Q99683	M3K5_HUMAN	L	16;96	ENSP00000351908:F16L	ENSP00000351908:F16L	F	-	3	2	MAP3K5	137154941	0.480000	0.25933	0.000000	0.03702	0.004000	0.04260	0.655000	0.24933	-0.505000	0.06568	-0.311000	0.09066	TTC	G|0.968;C|0.032	0.032	strong		0.751	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
INADL	10207	hgsc.bcm.edu	37	1	62261168	62261168	+	Missense_Mutation	SNP	A	A	G	rs7516332	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:62261168A>G	ENST00000371158.2	+	10	1312	c.1198A>G	c.(1198-1200)Ata>Gta	p.I400V	INADL_ENST00000316485.6_Missense_Mutation_p.I400V	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	400	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.		I -> V (in dbSNP:rs7516332).		cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.I400V(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TGTGAAAAGTATAATACCTGG	0.383													A|||	2178	0.434904	0.1808	0.5634	5008	,	,		17382	0.4514		0.493	False		,,,				2504	0.6104				p.I400V		Atlas-SNP	.											INADL,NS,carcinoma,0,1	INADL	179	1	1	Substitution - Missense(1)	prostate(1)	c.A1198G						PASS	.	A	VAL/ILE	1074,3332	387.2+/-326.4	136,802,1265	118.0	106.0	110.0		1198	-3.3	0.2	1	dbSNP_116	110	4169,4431	566.8+/-388.7	1023,2123,1154	yes	missense	INADL	NM_176877.2	29	1159,2925,2419	GG,GA,AA		48.4767,24.3759,40.3122	benign	400/1802	62261168	5243,7763	2203	4300	6503	SO:0001583	missense	10207	exon10			AAAAGTATAATAC	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.1198A>G	1.37:g.62261168A>G	ENSP00000360200:p.Ile400Val	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	164	161	0.981707	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	924	0.4230769230769231	122	0.24796747967479674	206	0.569060773480663	234	0.4090909090909091	362	0.47757255936675463	A	8.454	0.853778	0.17106	0.243759	0.484767	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.14266	2.52;2.52	5.29	-3.27	0.05048	PDZ/DHR/GLGF (4);	0.406531	0.24115	N	0.041412	T	0.00012	0.0000	N	0.13003	0.285	0.09310	P	0.9999999999995363	B;B;B	0.15473	0.013;0.008;0.008	B;B;B	0.21360	0.034;0.019;0.034	T	0.37619	-0.9698	9	0.21540	T	0.41	.	4.4158	0.11455	0.5466:0.0:0.2392:0.2142	rs7516332;rs52828363;rs56777942;rs7516332	400;400;400	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	V	400	ENSP00000360200:I400V;ENSP00000326199:I400V	ENSP00000255202:I400V	I	+	1	0	INADL	62033756	0.900000	0.30661	0.167000	0.22817	0.675000	0.39556	0.533000	0.23082	-0.790000	0.04492	-0.336000	0.08194	ATA	A|0.589;G|0.411	0.411	strong		0.383	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
RNF43	54894	hgsc.bcm.edu	37	17	56436109	56436109	+	Missense_Mutation	SNP	C	C	T	rs34523089	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:56436109C>T	ENST00000584437.1	-	8	2983	c.1028G>A	c.(1027-1029)cGc>cAc	p.R343H	RNF43_ENST00000577716.1_Missense_Mutation_p.R343H|RNF43_ENST00000500597.2_Missense_Mutation_p.R302H|RNF43_ENST00000407977.2_Missense_Mutation_p.R343H|RNF43_ENST00000581868.1_Missense_Mutation_p.R216H|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577625.1_Missense_Mutation_p.R216H|RNF43_ENST00000583753.1_Missense_Mutation_p.R302H			Q68DV7	RNF43_HUMAN	ring finger protein 43	343			R -> H (in dbSNP:rs34523089).		negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGGATGCTGGCGAATGAGGTG	0.597													C|||	327	0.0652955	0.0091	0.1167	5008	,	,		18742	0.001		0.163	False		,,,				2504	0.0706				p.R343H		Atlas-SNP	.											RNF43,NS,carcinoma,0,1	RNF43	157	1	0			c.G1028A						PASS	.	C	HIS/ARG	159,4239		3,153,2043	17.0	18.0	18.0		1028	2.7	1.0	17	dbSNP_126	18	1360,7218		135,1090,3064	yes	missense	RNF43	NM_017763.4	29	138,1243,5107	TT,TC,CC		15.8545,3.6153,11.7062	probably-damaging	343/784	56436109	1519,11457	2199	4289	6488	SO:0001583	missense	54894	exon9			TGCTGGCGAATGA		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.1028G>A	17.37:g.56436109C>T	ENSP00000463069:p.Arg343His	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	30	29	0.966667	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	166	0.076007326007326	3	0.006097560975609756	44	0.12154696132596685	1	0.0017482517482517483	118	0.15567282321899736	C	16.21	3.058842	0.55325	0.036153	0.158545	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.09350	3.14;2.99	3.66	2.69	0.31865	.	0.421385	0.24485	N	0.038106	T	0.00073	0.0002	L	0.27053	0.805	0.31011	P	0.71922	B;D;D	0.89917	0.007;1.0;0.999	B;D;D	0.79108	0.005;0.992;0.981	T	0.17258	-1.0375	9	0.45353	T	0.12	-21.2099	8.7609	0.34674	0.0:0.8913:0.0:0.1087	rs34523089	302;343;343	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	H	343;302	ENSP00000385328:R343H;ENSP00000441969:R302H	ENSP00000385328:R343H	R	-	2	0	RNF43	53791108	1.000000	0.71417	0.999000	0.59377	0.937000	0.57800	2.096000	0.41738	0.886000	0.36113	0.400000	0.26472	CGC	C|0.912;T|0.088	0.088	strong		0.597	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
PCDHA3	56145	hgsc.bcm.edu	37	5	140182101	140182101	+	Missense_Mutation	SNP	G	G	T	rs7701755	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140182101G>T	ENST00000522353.2	+	1	1319	c.1319G>T	c.(1318-1320)aGc>aTc	p.S440I	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.S440I|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	440	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> I (in dbSNP:rs7701755).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S440I(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCACGGCCAGCGTGTCCGTG	0.662													.|||	2962	0.591454	0.7194	0.6052	5008	,	,		19163	0.5327		0.5388	False		,,,				2504	0.5235				p.S440I		Atlas-SNP	.											PCDHA3_ENST00000522353,NS,carcinoma,0,2	PCDHA3	396	2	2	Substitution - Missense(2)	prostate(2)	c.G1319T						PASS	.	G	,,ILE/SER,,ILE/SER	3102,1304	695.1+/-405.9	1100,902,201	98.0	99.0	98.0		,,1319,,1319	3.9	1.0	5	dbSNP_116	98	4538,4060	592.0+/-392.9	1192,2154,953	no	intron,intron,missense,intron,missense	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,142,,142	2292,3056,1154	TT,TG,GG		47.2203,29.596,41.2488	,,,,	,,440/951,,440/825	140182101	7640,5364	2203	4299	6502	SO:0001583	missense	56145	exon1			CGGCCAGCGTGTC	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1319G>T	5.37:g.140182101G>T	ENSP00000429808:p.Ser440Ile	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	237	123	0.518987	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	1264	0.5787545787545788	345	0.7012195121951219	202	0.5580110497237569	311	0.5437062937062938	406	0.5356200527704486	g	12.25	1.880266	0.33162	0.70404	0.527797	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.52057	0.68;0.68	4.75	3.86	0.44501	Cadherin (5);Cadherin-like (1);	0.270257	0.25762	U	0.028479	T	0.00012	0.0000	N	0.20445	0.575	0.39934	P	0.025679000000000007	B;B	0.33212	0.189;0.402	B;B	0.43990	0.089;0.438	T	0.30238	-0.9985	9	0.45353	T	0.12	.	10.1855	0.42995	0.0:0.1486:0.6971:0.1542	rs7701755;rs17844260;rs56703455	440;440	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	I	440	ENSP00000429808:S440I;ENSP00000434086:S440I	ENSP00000429808:S440I	S	+	2	0	PCDHA3	140162285	0.000000	0.05858	1.000000	0.80357	0.938000	0.57974	-1.041000	0.03542	1.106000	0.41623	0.461000	0.40582	AGC	G|0.413;T|0.587	0.587	strong		0.662	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
TMEM247	388946	hgsc.bcm.edu	37	2	46707885	46707885	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:46707885A>G	ENST00000434431.1	+	2	459	c.459A>G	c.(457-459)caA>caG	p.Q153Q		NM_001145051.2	NP_001138523.1	A6NEH6	TM247_HUMAN	transmembrane protein 247	153						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											AGCTGCAGCAAGAGGCGGCGC	0.682																																					p.Q153Q		Atlas-SNP	.											ENSG00000187600_ENST00000434431,NS,carcinoma,+1,2	.	.	2	0			c.A459G						scavenged	.						16.0	21.0	19.0					2																	46707885		690	1589	2279	SO:0001819	synonymous_variant	388946	exon2			GCAGCAAGAGGCG		CCDS56117.1	2p21	2012-04-11			ENSG00000187600	ENSG00000187600			42967	protein-coding gene	gene with protein product							Standard	NM_001145051		Approved		uc010yod.3	A6NEH6	OTTHUMG00000153137	ENST00000434431.1:c.459A>G	2.37:g.46707885A>G		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	118	13	0.110169	NM_001145051		Silent	SNP	ENST00000434431.1	37	CCDS56117.1																																																																																			.	.	none		0.682	TMEM247-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329726.1	NM_001145051	
PDCD6IP	10015	hgsc.bcm.edu	37	3	33905566	33905566	+	Missense_Mutation	SNP	C	C	T	rs1127732	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33905566C>T	ENST00000307296.3	+	16	2566	c.2189C>T	c.(2188-2190)tCa>tTa	p.S730L	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.S735L			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	730	Interaction with EIAV p9.|Pro-rich.|Self-association.		S -> L (in dbSNP:rs1127732). {ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						TATCAGTCCTCACCAGCAGGA	0.433													C|||	1241	0.247804	0.1581	0.3112	5008	,	,		18749	0.3889		0.1332	False		,,,				2504	0.2965				p.S735L		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.C2204T						PASS	.	C	LEU/SER,LEU/SER	693,3713	291.8+/-281.7	58,577,1568	79.0	75.0	76.0		2204,2189	5.9	1.0	3	dbSNP_86	76	1313,7287	259.0+/-282.4	98,1117,3085	yes	missense,missense	PDCD6IP	NM_001162429.1,NM_013374.4	145,145	156,1694,4653	TT,TC,CC		15.2674,15.7286,15.4237	benign,benign	735/874,730/869	33905566	2006,11000	2203	4300	6503	SO:0001583	missense	10015	exon16			AGTCCTCACCAGC	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.2189C>T	3.37:g.33905566C>T	ENSP00000307387:p.Ser730Leu	Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	272	120	0.441176	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	504	0.23076923076923078	71	0.1443089430894309	109	0.3011049723756906	220	0.38461538461538464	104	0.13720316622691292	C	18.35	3.603869	0.66445	0.157286	0.152674	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.36157	1.27;1.27	5.94	5.94	0.96194	.	0.207357	0.40144	N	0.001180	T	0.00012	0.0000	L	0.47016	1.485	0.27577	P	0.9497123	P;B;P	0.36086	0.536;0.346;0.536	B;B;B	0.30943	0.115;0.122;0.115	T	0.48258	-0.9051	9	0.26408	T	0.33	-18.0067	16.5903	0.84763	0.0:0.8699:0.1301:0.0	rs1127732;rs52791786;rs61557319;rs1127732	511;735;730	B7Z5C1;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	L	730;735	ENSP00000307387:S730L;ENSP00000411825:S735L	ENSP00000307387:S730L	S	+	2	0	PDCD6IP	33880570	0.405000	0.25336	0.997000	0.53966	0.716000	0.41182	1.948000	0.40303	2.817000	0.96982	0.557000	0.71058	TCA	C|0.800;N|0.001	.	strong		0.433	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
MBL2	4153	hgsc.bcm.edu	37	10	54531235	54531235	+	Missense_Mutation	SNP	C	C	T	rs1800450	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:54531235C>T	ENST00000373968.3	-	1	225	c.161G>A	c.(160-162)gGc>gAc	p.G54D		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	54	Collagen-like.		G -> D (polymorphism associated with mannose-binding protein deficiency and recurrent infections; dbSNP:rs1800450). {ECO:0000269|PubMed:10447262, ECO:0000269|PubMed:12175909, ECO:0000269|PubMed:1303250, ECO:0000269|PubMed:1304173, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15994813, ECO:0000269|PubMed:1675710, ECO:0000269|PubMed:9743385}.		acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						TCCCTTGGTGCCATCACGCCC	0.542													C|||	611	0.122005	0.0136	0.219	5008	,	,		19637	0.1478		0.1412	False		,,,				2504	0.1534				p.G54D		Atlas-SNP	.											.	MBL2	55	.	0			c.G161A	GRCh37	CM920484	MBL2	M	rs1800450	PASS	.	C	ASP/GLY	127,4279	93.4+/-132.2	3,121,2079	137.0	123.0	128.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	161	4.0	1.0	10	dbSNP_89	128	1208,7392	244.0+/-273.4	83,1042,3175	yes	missense	MBL2	NM_000242.2	94	86,1163,5254	TT,TC,CC		14.0465,2.8824,10.2645	probably-damaging	54/249	54531235	1335,11671	2203	4300	6503	SO:0001583	missense	4153	exon1			TTGGTGCCATCAC	AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"""Collectins"""	6922	protein-coding gene	gene with protein product		154545	"""mannose-binding lectin (protein C) 2, soluble (opsonic defect)"""	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.161G>A	10.37:g.54531235C>T	ENSP00000363079:p.Gly54Asp	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	165	76	0.460606	NM_000242	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Missense_Mutation	SNP	ENST00000373968.3	37	CCDS7247.1	266	0.12179487179487179	14	0.028455284552845527	58	0.16022099447513813	97	0.16958041958041958	97	0.1279683377308707	C	20.6	4.011183	0.75046	0.028824	0.140465	ENSG00000165471	ENST00000373968	D	0.99353	-5.77	3.99	3.99	0.46301	.	0.117435	0.39341	N	0.001384	T	0.54255	0.1847	H	0.99249	4.485	0.20489	P	0.999895595	D	0.89917	1.0	D	0.91635	0.999	T	0.00007	-1.2495	9	0.87932	D	0	-18.6311	11.8851	0.52598	0.0:1.0:0.0:0.0	rs1800450;rs52803813;rs60780172;rs1800450	54	P11226	MBL2_HUMAN	D	54	ENSP00000363079:G54D	ENSP00000363079:G54D	G	-	2	0	MBL2	54201241	0.973000	0.33851	0.994000	0.49952	0.900000	0.52787	3.632000	0.54287	2.530000	0.85305	0.655000	0.94253	GGC	C|0.888;T|0.111	0.111	strong		0.542	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242	
PRKACA	5566	hgsc.bcm.edu	37	19	14200109	14200109	+	IGR	SNP	T	T	C	rs386807036|rs374448790|rs8062	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14200109T>C	ENST00000308677.4	-	0	2677				PRKACA_ENST00000350356.3_5'Flank|SAMD1_ENST00000533683.2_Silent_p.E234E|SAMD1_ENST00000541938.1_5'Flank	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha						activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						catcatcttcttcatcttcat	0.527													A|||	518	0.103435	0.0182	0.2608	5008	,	,		16803	0.0813		0.1163	False		,,,				2504	0.1166				p.E234E		Atlas-SNP	.											.	SAMD1	27	.	0			c.A702G						PASS	.						68.0	76.0	73.0					19																	14200109		2015	4073	6088	SO:0001628	intergenic_variant	90378	exon2			ATCTTCTTCATCT		CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	2.7.11.1		9380	protein-coding gene	gene with protein product		601639				8884279	Standard	NM_002730		Approved	PKACa	uc002myc.3	P17612			19.37:g.14200109T>C		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	232	131	0.564655	NM_138352	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Silent	SNP	ENST00000308677.4	37	CCDS12304.1																																																																																			T|0.928;C|0.002;A|0.070	0.002	strong		0.527	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730	
SUPT20H	55578	hgsc.bcm.edu	37	13	37583831	37583831	+	Missense_Mutation	SNP	G	G	A	rs9469	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:37583831G>A	ENST00000350612.6	-	26	2538	c.2318C>T	c.(2317-2319)aCg>aTg	p.T773M	SUPT20H_ENST00000464744.1_3'UTR|SUPT20H_ENST00000475892.1_3'UTR|SUPT20H_ENST00000360252.4_3'UTR|SUPT20H_ENST00000356185.3_3'UTR	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	773			T -> M (in dbSNP:rs9469). {ECO:0000269|PubMed:15498874}.		autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										AGTGGTTGGCGTGCCTCTCTT	0.398													G|||	2069	0.413139	0.0809	0.4222	5008	,	,		16399	0.7232		0.3787	False		,,,				2504	0.5716				p.T773M		Atlas-SNP	.											.	.	.	.	0			c.C2318T						PASS	.	G	MET/THR,	618,3788	266.8+/-267.5	45,528,1630	174.0	167.0	169.0		2318,	4.2	0.9	13	dbSNP_52	169	3425,5175	505.1+/-376.3	692,2041,1567	yes	missense,utr-3	FAM48A	NM_001014286.2,NM_017569.3	81,	737,2569,3197	AA,AG,GG		39.8256,14.0263,31.0857	probably-damaging,	773/780,	37583831	4043,8963	2203	4300	6503	SO:0001583	missense	55578	exon26			GTTGGCGTGCCTC	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"""p38 interacting protein"", ""transcription factor (p38 interacting protein)"""	613417	"""chromosome 13 open reading frame 19"", ""family with sequence similarity 48, member A"""	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.2318C>T	13.37:g.37583831G>A	ENSP00000218894:p.Thr773Met	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	134	124	0.925373	NM_001014286	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	37	CCDS31959.1	909|909	0.41620879120879123|0.41620879120879123	55|55	0.11178861788617886|0.11178861788617886	154|154	0.425414364640884|0.425414364640884	402|402	0.7027972027972028|0.7027972027972028	298|298	0.39313984168865435|0.39313984168865435	G|G	8.546|8.546	0.874397|0.874397	0.17395|0.17395	0.140263|0.140263	0.398256|0.398256	ENSG00000102710|ENSG00000102710	ENST00000469488|ENST00000350612	.|T	.|0.33654	.|1.4	5.92|5.92	4.18|4.18	0.49190|0.49190	.|.	.|0.112689	.|0.40064	.|N	.|0.001198	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.21448|0.21448	0.665|0.665	0.09310|0.09310	P|P	0.9999999999926429|0.9999999999926429	.|B	.|0.12630	.|0.006	.|B	.|0.09377	.|0.004	T|T	0.28776|0.28776	-1.0033|-1.0033	4|9	.|0.40728	.|T	.|0.16	.|.	10.3486|10.3486	0.43920|0.43920	0.1524:0.0:0.8476:0.0|0.1524:0.0:0.8476:0.0	rs9469;rs3168739;rs52812678;rs60675753;rs9469|rs9469;rs3168739;rs52812678;rs60675753;rs9469	.|773	.|Q8NEM7	.|FA48A_HUMAN	C|M	316|773	.|ENSP00000218894:T773M	.|ENSP00000218894:T773M	R|T	-|-	1|2	0|0	FAM48A|FAM48A	36481831|36481831	1.000000|1.000000	0.71417|0.71417	0.874000|0.874000	0.34290|0.34290	0.857000|0.857000	0.48899|0.48899	3.130000|3.130000	0.50508|0.50508	0.832000|0.832000	0.34804|0.34804	-0.373000|-0.373000	0.07131|0.07131	CGC|ACG	G|0.646;A|0.354	0.354	strong		0.398	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144906508	144906508	+	Missense_Mutation	SNP	C	C	T	rs34169189	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:144906508C>T	ENST00000369354.3	-	18	2538	c.2349G>A	c.(2347-2349)atG>atA	p.M783I	PDE4DIP_ENST00000369351.3_Missense_Mutation_p.M783I|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.M783I|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.M946I|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.M920I|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.M783I|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.M849I|PDE4DIP_ENST00000479408.2_Missense_Mutation_p.M570I|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.M920I|PDE4DIP_ENST00000524974.1_Intron|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.M946I			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	783				M -> I (in Ref. 4; CAD38529 and 6; AAI32718). {ECO:0000305}.	cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CCTGCACAGCCATCATGGACT	0.418			T	PDGFRB	MPD								C|||	467	0.0932508	0.0227	0.1974	5008	,	,		20695	0.0268		0.1342	False		,,,				2504	0.1411				p.M946I		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G2838A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	179,4227	111.2+/-149.4	6,167,2030	92.0	92.0	92.0		2349,2349,2547,2349,2838	2.0	1.0	1	dbSNP_126	92	1266,7320	243.8+/-273.2	80,1106,3107	yes	missense,missense,missense,missense,missense	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1,NM_001002812.1,NM_001002811.1	10,10,10,10,10	86,1273,5137	TT,TC,CC		14.7449,4.0626,11.1222	benign,benign,benign,benign,benign	783/2347,783/2363,849/2241,783/970,946/1133	144906508	1445,11547	2203	4293	6496	SO:0001583	missense	9659	exon14			CACAGCCATCATG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.2349G>A	1.37:g.144906508C>T	ENSP00000358360:p.Met783Ile	Somatic	355	0	0		WXS	Illumina HiSeq	Phase_I	401	208	0.518703	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	187	0.08562271062271062	10	0.02032520325203252	67	0.1850828729281768	13	0.022727272727272728	97	0.1279683377308707	C	10.64	1.407063	0.25378	0.040626	0.147449	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	T;T;T;T;T;T;T;T;T;T	0.10860	4.85;4.94;4.94;4.94;4.94;3.93;3.94;2.86;2.85;2.83	6.07	1.96	0.26148	.	.	.	.	.	T	0.01124	0.0037	N	0.12182	0.205	0.09310	P	0.9999999999993228	B;B;B;B;B	0.18461	0.0;0.0;0.0;0.028;0.0	B;B;B;B;B	0.13407	0.001;0.0;0.001;0.009;0.0	T	0.47018	-0.9149	8	0.06099	T	0.92	.	3.6148	0.08073	0.1196:0.5183:0.2102:0.1519	rs34169189	946;783;946;849;783	E9PL24;Q5VU43-7;Q5VU43-2;Q5VU43-3;Q5VU43	.;.;.;.;MYOME_HUMAN	I	849;783;783;946;920;920;783;783;946;946;570	ENSP00000327209:M849I;ENSP00000358360:M783I;ENSP00000358363:M783I;ENSP00000435654:M920I;ENSP00000358366:M920I;ENSP00000358357:M783I;ENSP00000358355:M783I;ENSP00000316434:M946I;ENSP00000433392:M946I;ENSP00000436791:M570I	ENSP00000327209:M849I	M	-	3	0	PDE4DIP	143617865	0.689000	0.27690	1.000000	0.80357	0.965000	0.64279	-0.084000	0.11268	0.929000	0.37192	0.638000	0.83543	ATG	C|0.898;T|0.102	0.102	strong		0.418	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
USP45	85015	hgsc.bcm.edu	37	6	99893938	99893938	+	Silent	SNP	T	T	C	rs4504482	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:99893938T>C	ENST00000327681.6	-	14	2242	c.1710A>G	c.(1708-1710)ggA>ggG	p.G570G	USP45_ENST00000369233.2_Silent_p.G522G|USP45_ENST00000539675.1_Intron|USP45_ENST00000392738.2_Silent_p.G250G|USP45_ENST00000500704.2_Silent_p.G570G	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	570	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		AATCTTGATCTCCAGTTACAG	0.388													T|||	1757	0.350839	0.2042	0.3689	5008	,	,		18479	0.4871		0.331	False		,,,				2504	0.4162				p.G570G		Atlas-SNP	.											.	USP45	56	.	0			c.A1710G						PASS	.	T		1015,3391	361.6+/-315.8	115,785,1303	57.0	60.0	59.0		1710	1.2	0.0	6	dbSNP_111	59	2538,6062	413.0+/-351.0	358,1822,2120	yes	coding-synonymous	USP45	NM_001080481.1		473,2607,3423	CC,CT,TT		29.5116,23.0368,27.3182		570/815	99893938	3553,9453	2203	4300	6503	SO:0001819	synonymous_variant	85015	exon14			TTGATCTCCAGTT	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"""Ubiquitin-specific peptidases"""	20080	protein-coding gene	gene with protein product			"""ubiquitin specific protease 45"""			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.1710A>G	6.37:g.99893938T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Silent	SNP	ENST00000327681.6	37	CCDS34501.1																																																																																			T|0.693;C|0.307	0.307	strong		0.388	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929	
SLAIN2	57606	hgsc.bcm.edu	37	4	48424058	48424058	+	Silent	SNP	C	C	T	rs17609614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:48424058C>T	ENST00000264313.6	+	8	2128	c.1710C>T	c.(1708-1710)agC>agT	p.S570S	SLAIN2_ENST00000512093.1_Silent_p.S403S	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	570					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						CCTATGGTAGCATGAAAGATG	0.373													C|||	151	0.0301518	0.0325	0.0591	5008	,	,		19100	0.0268		0.0229	False		,,,				2504	0.0174				p.S570S		Atlas-SNP	.											.	SLAIN2	31	.	0			c.C1710T						PASS	.	C		128,3588		2,124,1732	65.0	61.0	62.0		1710	3.7	1.0	4	dbSNP_123	62	231,7965		4,223,3871	no	coding-synonymous	SLAIN2	NM_020846.1		6,347,5603	TT,TC,CC		2.8184,3.4446,3.0138		570/582	48424058	359,11553	1858	4098	5956	SO:0001819	synonymous_variant	57606	exon8			TGGTAGCATGAAA	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"""KIAA1458"""	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.1710C>T	4.37:g.48424058C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_020846	A8K4P1|Q8N5R3	Silent	SNP	ENST00000264313.6	37	CCDS47051.1																																																																																			C|0.968;T|0.032	0.032	strong		0.373	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846	
ZNF645	158506	hgsc.bcm.edu	37	X	22291606	22291606	+	Missense_Mutation	SNP	C	C	A	rs5951426	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:22291606C>A	ENST00000323684.1	+	1	542	c.498C>A	c.(496-498)gaC>gaA	p.D166E		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	166			D -> E (in dbSNP:rs5951426). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20657603}.		protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						AAATCTCTGACATCCCTAAAA	0.463													A|||	1533	0.406093	0.5802	0.2954	3775	,	,		14986	0.3393		0.0845	False		,,,				2504	0.137				p.D166E		Atlas-SNP	.											.	ZNF645	67	.	0			c.C498A						PASS	.	A	GLU/ASP	2605,1230		768,679,390,185,181	93.0	90.0	91.0		498	0.8	0.0	X	dbSNP_114	91	752,5976		39,471,203,1918,1669	yes	missense	ZNF645	NM_152577.3	45	807,1150,593,2103,1850	AA,AC,A,CC,C		11.1772,32.073,31.7807	benign	166/426	22291606	3357,7206	2203	4300	6503	SO:0001583	missense	158506	exon1			CTCTGACATCCCT	AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.498C>A	X.37:g.22291606C>A	ENSP00000323348:p.Asp166Glu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	154	153	0.993506	NM_152577	A0AV29|A0AV31|E3SBK4|Q6DJY9	Missense_Mutation	SNP	ENST00000323684.1	37	CCDS14205.1	635	0.38276069921639544	201	0.6165644171779141	70	0.2229299363057325	125	0.2880184331797235	41	0.05742296918767507	A	3.325	-0.137835	0.06711	0.67927	0.111772	ENSG00000175809	ENST00000323684	T	0.32272	1.46	3.32	0.836	0.18891	.	0.285432	0.29253	N	0.012685	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40213	-0.9575	9	0.06365	T	0.9	.	0.5068	0.00588	0.3297:0.1861:0.1164:0.3678	rs5951426;rs6528101;rs60426202;rs5951426	166	Q8N7E2	ZN645_HUMAN	E	166	ENSP00000323348:D166E	ENSP00000323348:D166E	D	+	3	2	ZNF645	22201527	0.047000	0.20315	0.000000	0.03702	0.001000	0.01503	-0.180000	0.09754	-0.203000	0.10251	-1.309000	0.01313	GAC	C|0.602;0|0.023	.	strong		0.463	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577	
TRIM63	84676	hgsc.bcm.edu	37	1	26385003	26385003	+	Missense_Mutation	SNP	T	T	C	rs2275950	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26385003T>C	ENST00000374272.3	-	5	847	c.709A>G	c.(709-711)Aaa>Gaa	p.K237E	TRIM63_ENST00000483052.1_5'Flank	NM_032588.3	NP_115977.2	Q969Q1	TRI63_HUMAN	tripartite motif containing 63, E3 ubiquitin protein ligase	237			K -> E (in dbSNP:rs2275950). {ECO:0000269|PubMed:11243782, ECO:0000269|PubMed:15489334}.		cellular response to dexamethasone stimulus (GO:0071549)|muscle contraction (GO:0006936)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression (GO:0010468)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to interleukin-1 (GO:0070555)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|titin binding (GO:0031432)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K237E(1)		kidney(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;9.15e-26)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000767)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CTAAGCTTTTTCTCCTGCTCC	0.537													C|||	913	0.182308	0.267	0.1239	5008	,	,		20137	0.1706		0.2187	False		,,,				2504	0.0838				p.K237E		Atlas-SNP	.											TRIM63,NS,carcinoma,0,1	TRIM63	33	1	1	Substitution - Missense(1)	stomach(1)	c.A709G						PASS	.	C	GLU/LYS	1195,3211	710.2+/-407.8	175,845,1183	177.0	161.0	166.0		709	5.5	1.0	1	dbSNP_100	166	1862,6738	729.6+/-406.7	197,1468,2635	yes	missense	TRIM63	NM_032588.2	56	372,2313,3818	CC,CT,TT		21.6512,27.1221,23.5045	benign	237/354	26385003	3057,9949	2203	4300	6503	SO:0001583	missense	84676	exon5			GCTTTTTCTCCTG	AF353673	CCDS273.1	1p34-p33	2014-09-17	2012-02-23	2004-11-17	ENSG00000158022	ENSG00000158022		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	16007	protein-coding gene	gene with protein product	"""muscle-specific RING finger protein 1"", ""iris ring finger protein"", ""striated muscle RING zinc finger protein"""	606131	"""ring finger protein 28"", ""tripartite motif-containing 63"", ""tripartite motif containing 63"""	RNF28		11243782, 11283016	Standard	NM_032588		Approved	MURF-1, IRF, SMRZ	uc001bli.2	Q969Q1	OTTHUMG00000007510	ENST00000374272.3:c.709A>G	1.37:g.26385003T>C	ENSP00000363390:p.Lys237Glu	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	240	113	0.470833	NM_032588	B4DN95|Q5T2I1|Q96BD3|Q96KD9|Q9BYV4	Missense_Mutation	SNP	ENST00000374272.3	37	CCDS273.1	434	0.1987179487179487	127	0.258130081300813	43	0.11878453038674033	100	0.17482517482517482	164	0.21635883905013192	C	7.836	0.720876	0.15372	0.271221	0.216512	ENSG00000158022	ENST00000374272	T	0.40756	1.02	5.5	5.5	0.81552	.	0.198167	0.52532	N	0.000069	T	0.00012	0.0000	N	0.00043	-2.47	0.48830	P	2.889999999999837E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.33954	-0.9848	9	0.02654	T	1	.	14.2207	0.65826	0.0:0.9273:0.0:0.0727	rs2275950;rs52817885;rs60345068;rs2275950	237	Q969Q1	TRI63_HUMAN	E	237	ENSP00000363390:K237E	ENSP00000363390:K237E	K	-	1	0	TRIM63	26257590	0.957000	0.32711	1.000000	0.80357	0.788000	0.44548	2.222000	0.42926	1.336000	0.45506	-0.215000	0.12644	AAA	T|0.785;C|0.215	0.215	strong		0.537	TRIM63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019750.1	NM_032588	
TRIM58	25893	hgsc.bcm.edu	37	1	248039451	248039451	+	Missense_Mutation	SNP	C	C	T	rs3811444	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248039451C>T	ENST00000366481.3	+	6	1169	c.1121C>T	c.(1120-1122)aCg>aTg	p.T374M	OR2W3_ENST00000537741.1_Intron	NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	374	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		T -> M (in dbSNP:rs3811444). {ECO:0000269|Ref.1}.			intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.T374M(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GGGGAAACCACGCCATCTCCT	0.552													C|||	1139	0.227436	0.0401	0.2896	5008	,	,		18855	0.2292		0.3449	False		,,,				2504	0.3139				p.T374M		Atlas-SNP	.											TRIM58,colon,carcinoma,0,2	TRIM58	143	2	1	Substitution - Missense(1)	stomach(1)	c.C1121T						PASS	.	C	MET/THR	391,4015	195.0+/-219.7	20,351,1832	115.0	112.0	113.0		1121	2.2	0.0	1	dbSNP_107	113	2974,5626	460.6+/-365.2	507,1960,1833	yes	missense	TRIM58	NM_015431.3	81	527,2311,3665	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	34.5814,8.8743,25.8727	probably-damaging	374/487	248039451	3365,9641	2203	4300	6503	SO:0001583	missense	25893	exon6			AAACCACGCCATC	AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	24150	protein-coding gene	gene with protein product			"""tripartite motif-containing 58"""				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.1121C>T	1.37:g.248039451C>T	ENSP00000355437:p.Thr374Met	Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_015431	Q6B0H9	Missense_Mutation	SNP	ENST00000366481.3	37	CCDS1636.1	505	0.23122710622710624	23	0.046747967479674794	99	0.27348066298342544	132	0.23076923076923078	251	0.3311345646437995	C	5.325	0.245339	0.10077	0.088743	0.345814	ENSG00000162722	ENST00000366481	T	0.69435	-0.4	4.05	2.21	0.28008	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.334447	0.25964	N	0.027168	T	0.00012	0.0000	M	0.65320	2	0.50171	P	1.4099999999994672E-4	D	0.76494	0.999	D	0.69479	0.964	T	0.14643	-1.0465	9	0.34782	T	0.22	.	4.5153	0.11932	0.0:0.6178:0.1832:0.199	rs3811444;rs17672233;rs3811444	374	Q8NG06	TRI58_HUMAN	M	374	ENSP00000355437:T374M	ENSP00000355437:T374M	T	+	2	0	TRIM58	246106074	0.000000	0.05858	0.011000	0.14972	0.001000	0.01503	0.168000	0.16622	0.697000	0.31718	-0.133000	0.14855	ACG	C|0.752;N|0.000	.	strong		0.552	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431	
PJA1	64219	hgsc.bcm.edu	37	X	68381264	68381264	+	Missense_Mutation	SNP	C	C	A	rs11539157	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:68381264C>A	ENST00000361478.1	-	2	2195	c.1818G>T	c.(1816-1818)gaG>gaT	p.E606D	PJA1_ENST00000477231.1_5'Flank|PJA1_ENST00000374584.3_Missense_Mutation_p.E418D|PJA1_ENST00000374571.4_Missense_Mutation_p.E551D|PJA1_ENST00000374583.1_Missense_Mutation_p.E606D	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	606			E -> D (in dbSNP:rs11539157). {ECO:0000269|PubMed:15489334}.		protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						CAGTTGCCACCTCCCCCTTCA	0.577													C|||	271	0.0717881	0.0076	0.0865	3775	,	,		14297	0.0		0.1829	False		,,,				2504	0.0174				p.E606D		Atlas-SNP	.											.	PJA1	106	.	0			c.G1818T						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	148,3687		5,119,19,1508,552	92.0	67.0	75.0		1653,1254,1818	1.6	1.0	X	dbSNP_120	75	1594,5134		142,863,447,1423,1425	yes	missense,missense,missense	PJA1	NM_001032396.2,NM_022368.4,NM_145119.3	45,45,45	147,982,466,2931,1977	AA,AC,A,CC,C		23.692,3.8592,16.4915	possibly-damaging,possibly-damaging,possibly-damaging	551/589,418/456,606/644	68381264	1742,8821	2203	4300	6503	SO:0001583	missense	64219	exon2			TGCCACCTCCCCC	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"""RING-type (C3HC4) zinc fingers"""	16648	protein-coding gene	gene with protein product		300420	"""praja 1"", ""praja ring finger 1"""			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.1818G>T	X.37:g.68381264C>A	ENSP00000355014:p.Glu606Asp	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	89	78	0.876405	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Missense_Mutation	SNP	ENST00000361478.1	37	CCDS14393.1	185	0.11151295961422544	13	0.026422764227642278	21	0.06287425149700598	0	0.0	93	0.13963963963963963	C	2.066	-0.414175	0.04766	0.038592	0.23692	ENSG00000181191	ENST00000396010;ENST00000374584;ENST00000374583;ENST00000361478;ENST00000374571	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	3.53	1.65	0.23941	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.243443	0.26708	U	0.022906	T	0.00039	0.0001	N	0.11284	0.12	0.31236	P	0.6957530000000001	D;D	0.63046	0.992;0.975	D;D	0.77004	0.989;0.943	T	0.10314	-1.0635	9	0.13853	T	0.58	-11.7912	3.8141	0.08808	0.4375:0.439:0.0:0.1235	rs11539157;rs52823996;rs59105084;rs11539157	606;418	Q8NG27;Q8NG27-2	PJA1_HUMAN;.	D	521;418;606;606;551	ENSP00000363712:E418D;ENSP00000363711:E606D;ENSP00000355014:E606D;ENSP00000363699:E551D	ENSP00000355014:E606D	E	-	3	2	PJA1	68297989	1.000000	0.71417	0.990000	0.47175	0.003000	0.03518	1.134000	0.31442	0.306000	0.22856	-0.351000	0.07748	GAG	0|0.013;A|0.129	0.129	strong		0.577	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119	
TAP1	6890	hgsc.bcm.edu	37	6	32814942	32814942	+	Missense_Mutation	SNP	C	C	T	rs1057149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32814942C>T	ENST00000354258.4	-	10	2284	c.2123G>A	c.(2122-2124)cGa>cAa	p.R708Q	TAP1_ENST00000425148.2_Missense_Mutation_p.R447Q|PSMB9_ENST00000395330.1_Intron|PSMB8_ENST00000374881.2_5'Flank|TAPSAR1_ENST00000453426.1_lincRNA	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	708	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> Q (in allele TAP1*04:01; dbSNP:rs1057149). {ECO:0000269|PubMed:11250043, ECO:0000269|PubMed:12878362, ECO:0000269|PubMed:8168860, ECO:0000269|PubMed:8248212}.		antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	CACTGCCTGTCGCTGACCCCC	0.572													C|||	296	0.0591054	0.171	0.049	5008	,	,		19876	0.001		0.0338	False		,,,				2504	0.001				p.R708Q		Atlas-SNP	.											.	TAP1	39	.	0			c.G2123A						PASS	.	C	GLN/ARG	373,2649		21,331,1159	99.0	83.0	89.0		2123	4.6	1.0	6	dbSNP_86	89	158,5260		2,154,2553	yes	missense	TAP1	NM_000593.5	43	23,485,3712	TT,TC,CC		2.9162,12.3428,6.2915	probably-damaging	708/809	32814942	531,7909	1511	2709	4220	SO:0001583	missense	6890	exon10			GCCTGTCGCTGAC		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"""ATP binding cassette transporters / subfamily B"""	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.2123G>A	6.37:g.32814942C>T	ENSP00000346206:p.Arg708Gln	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_000593	Q16149|Q96CP4	Missense_Mutation	SNP	ENST00000354258.4	37	CCDS4758.1	132	0.06043956043956044	95	0.19308943089430894	16	0.04419889502762431	1	0.0017482517482517483	20	0.026385224274406333	C	26.8	4.772874	0.90108	0.123428	0.029162	ENSG00000168394	ENST00000354258;ENST00000425148	D;D	0.94138	-3.36;-3.36	5.43	4.56	0.56223	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.39146	N	0.001454	D	0.93465	0.7915	L	0.56124	1.755	0.29257	P	0.871604	D	0.89917	1.0	D	0.71870	0.975	D	0.93820	0.7118	9	0.72032	D	0.01	1.8168	8.8967	0.35470	0.0:0.8297:0.0:0.1703	rs1057149;rs17883085;rs45470196;rs52792188;rs59175449;rs1057149	708	Q03518	TAP1_HUMAN	Q	708;447	ENSP00000346206:R708Q;ENSP00000401919:R447Q	ENSP00000346206:R708Q	R	-	2	0	TAP1	32922920	0.979000	0.34478	1.000000	0.80357	0.997000	0.91878	1.782000	0.38654	2.552000	0.86080	0.643000	0.83706	CGA	.	.	weak		0.572	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593	
KRT40	125115	hgsc.bcm.edu	37	17	39140221	39140221	+	Missense_Mutation	SNP	C	C	T	rs1510068	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39140221C>T	ENST00000398486.2	-	3	465	c.305G>A	c.(304-306)aGc>aAc	p.S102N	KRT40_ENST00000377755.4_Missense_Mutation_p.S102N	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	102	Coil 1A.|Rod.		S -> N (in dbSNP:rs1510068).			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				CTCCAGATAGCTGGCGAGTCT	0.537													T|||	1808	0.361022	0.6861	0.2378	5008	,	,		20636	0.1716		0.2684	False		,,,				2504	0.2996				p.S102N		Atlas-SNP	.											.	KRT40	27	.	0			c.G305A						PASS	.	T	ASN/SER	2674,1732	486.9+/-360.8	825,1024,354	188.0	187.0	187.0		305	-5.8	0.8	17	dbSNP_88	187	2371,6217	685.4+/-404.0	316,1739,2239	yes	missense	KRT40	NM_182497.3	46	1141,2763,2593	TT,TC,CC		27.6083,39.31,38.8256	benign	102/432	39140221	5045,7949	2203	4294	6497	SO:0001583	missense	125115	exon3			AGATAGCTGGCGA	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.305G>A	17.37:g.39140221C>T	ENSP00000381500:p.Ser102Asn	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	198	104	0.525253	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	733	0.3356227106227106	338	0.6869918699186992	92	0.2541436464088398	96	0.16783216783216784	207	0.27308707124010556	T	3.418	-0.118818	0.06838	0.6069	0.276083	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.90788	-2.73;-2.73	5.06	-5.78	0.02362	Filament (1);	0.890113	0.09311	N	0.819550	T	0.00012	0.0000	N	0.11131	0.1	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.25641	-1.0126	9	0.21014	T	0.42	.	12.6385	0.56696	0.0:0.5662:0.2406:0.1932	rs1510068;rs52833989	102	Q6A162	K1C40_HUMAN	N	102	ENSP00000366984:S102N;ENSP00000381500:S102N	ENSP00000366984:S102N	S	-	2	0	KRT40	36393747	0.000000	0.05858	0.776000	0.31678	0.924000	0.55760	-1.867000	0.01646	-1.577000	0.01650	-1.120000	0.02017	AGC	C|0.662;T|0.338	0.338	strong		0.537	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
E4F1	1877	hgsc.bcm.edu	37	16	2285357	2285357	+	Silent	SNP	C	C	T	rs26840	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2285357C>T	ENST00000301727.4	+	14	2187	c.2139C>T	c.(2137-2139)atC>atT	p.I713I	RP11-304L19.12_ENST00000564055.1_lincRNA|DNASE1L2_ENST00000564065.1_5'Flank|E4F1_ENST00000564139.1_3'UTR|DNASE1L2_ENST00000382437.4_5'Flank|E4F1_ENST00000565090.1_Silent_p.I536I|DNASE1L2_ENST00000320700.5_5'Flank|DNASE1L2_ENST00000567494.1_5'Flank	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1	713					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						CCATCACCATCGCCACCCCCG	0.687													C|||	1554	0.310304	0.0726	0.3184	5008	,	,		15288	0.4018		0.4046	False		,,,				2504	0.4346				p.I713I		Atlas-SNP	.											.	E4F1	53	.	0			c.C2139T						PASS	.	C		482,3904		31,420,1742	31.0	36.0	34.0		2139	-1.6	1.0	16	dbSNP_76	34	3478,5096		725,2028,1534	no	coding-synonymous	E4F1	NM_004424.3		756,2448,3276	TT,TC,CC		40.5645,10.9895,30.5556		713/785	2285357	3960,9000	2193	4287	6480	SO:0001819	synonymous_variant	1877	exon14			CACCATCGCCACC	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.2139C>T	16.37:g.2285357C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_004424	A8K2R4|O00146	Silent	SNP	ENST00000301727.4	37	CCDS32370.1																																																																																			C|0.702;T|0.298	0.298	strong		0.687	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424	
GSG1L	146395	hgsc.bcm.edu	37	16	27974487	27974487	+	Silent	SNP	T	T	C	rs2051743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:27974487T>C	ENST00000447459.2	-	2	471	c.387A>G	c.(385-387)gcA>gcG	p.A129A	GSG1L_ENST00000380898.2_5'UTR|GSG1L_ENST00000395724.3_Silent_p.A129A	NM_001109763.1	NP_001103233.1	Q6UXU4	GSG1L_HUMAN	GSG1-like	129					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	asymmetric synapse (GO:0032279)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(4)	17						CTTTCTCCGATGCCGGGGCCA	0.542													C|||	2908	0.580671	0.4244	0.6787	5008	,	,		22024	0.754		0.5577	False		,,,				2504	0.5675				p.A129A		Atlas-SNP	.											.	GSG1L	82	.	0			c.A387G						PASS	.	C		1838,2154		432,974,590	73.0	79.0	77.0		387	-9.1	0.1	16	dbSNP_94	77	4833,3497		1441,1951,773	no	coding-synonymous	GSG1L	NM_001109763.1		1873,2925,1363	CC,CT,TT		41.9808,46.0421,45.8611		129/332	27974487	6671,5651	1996	4165	6161	SO:0001819	synonymous_variant	146395	exon2			CTCCGATGCCGGG	AK128775	CCDS10631.1, CCDS45450.1	16p11.2	2014-01-20			ENSG00000169181	ENSG00000169181			28283	protein-coding gene	gene with protein product						22813734	Standard	NM_001109763		Approved	MGC18079, PRO19651, KTSR5831	uc002doz.2	Q6UXU4	OTTHUMG00000131676	ENST00000447459.2:c.387A>G	16.37:g.27974487T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_001109763	Q7Z6F8|Q8TB81	Silent	SNP	ENST00000447459.2	37	CCDS45450.1																																																																																			T|0.424;C|0.576	0.576	strong		0.542	GSG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433832.2	NM_144675	
SLC9A9	285195	hgsc.bcm.edu	37	3	143371201	143371201	+	Splice_Site	SNP	C	C	T	rs1242069	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:143371201C>T	ENST00000316549.6	-	6	859	c.651G>A	c.(649-651)gtG>gtA	p.V217V		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	217					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)			breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						CCAGCACTGTCACTAGGAAGA	0.463													C|||	120	0.0239617	0.0038	0.0504	5008	,	,		20669	0.001		0.0497	False		,,,				2504	0.0297				p.V217V		Atlas-SNP	.											.	SLC9A9	117	.	0			c.G651A						PASS	.	C		51,4355	50.2+/-85.5	1,49,2153	114.0	88.0	97.0		651	5.5	1.0	3	dbSNP_87	97	388,8212	124.3+/-183.0	10,368,3922	yes	coding-synonymous-near-splice	SLC9A9	NM_173653.3		11,417,6075	TT,TC,CC		4.5116,1.1575,3.3754		217/646	143371201	439,12567	2203	4300	6503	SO:0001630	splice_region_variant	285195	exon6			CACTGTCACTAGG	AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"""Solute carriers"""	20653	protein-coding gene	gene with protein product		608396	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 9"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 9"""			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.650-1G>A	3.37:g.143371201C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	166	88	0.53012	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Silent	SNP	ENST00000316549.6	37	CCDS33872.1																																																																																			C|0.969;T|0.031	0.031	strong		0.463	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653	Silent
ACAT2	39	hgsc.bcm.edu	37	6	160198395	160198395	+	Silent	SNP	G	G	A	rs3465	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:160198395G>A	ENST00000367048.4	+	7	2579	c.819G>A	c.(817-819)ggG>ggA	p.G273G	ACAT2_ENST00000541436.1_Silent_p.G302G|SNORA20_ENST00000384662.1_RNA|ACAT2_ENST00000472052.1_3'UTR	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	273					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		ATAAACGTGGGCTTACACCTT	0.428													G|||	1178	0.235224	0.1362	0.3458	5008	,	,		20131	0.1042		0.3807	False		,,,				2504	0.2761				p.G273G		Atlas-SNP	.											.	ACAT2	32	.	0			c.G819A						PASS	.	G		735,3671	302.7+/-287.5	72,591,1540	154.0	142.0	146.0		819	-1.0	0.6	6	dbSNP_36	146	3421,5179	504.6+/-376.2	702,2017,1581	no	coding-synonymous	ACAT2	NM_005891.2		774,2608,3121	AA,AG,GG		39.7791,16.6818,31.9545		273/398	160198395	4156,8850	2203	4300	6503	SO:0001819	synonymous_variant	39	exon7			ACGTGGGCTTACA	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"""acetoacetyl Coenzyme A thiolase"""	100678	"""acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)"", ""acetyl-Coenzyme A acetyltransferase 2"""			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.819G>A	6.37:g.160198395G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	231	103	0.445887	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Silent	SNP	ENST00000367048.4	37	CCDS5268.1																																																																																			G|0.719;A|0.281	0.281	strong		0.428	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891	
FRMPD1	22844	hgsc.bcm.edu	37	9	37745413	37745413	+	Silent	SNP	G	G	A	rs3747541	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:37745413G>A	ENST00000539465.1	+	16	3977	c.3384G>A	c.(3382-3384)gaG>gaA	p.E1128E	FRMPD1_ENST00000377765.3_Silent_p.E1128E|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1128						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		TTCAGGAGGAGTCTAGGAAGG	0.428													A|||	1935	0.386382	0.5847	0.4193	5008	,	,		20725	0.2024		0.332	False		,,,				2504	0.3405				p.E1128E		Atlas-SNP	.											.	FRMPD1	237	.	0			c.G3384A						PASS	.	A		2298,2108	576.3+/-384.2	614,1070,519	69.0	72.0	71.0		3384	-1.8	0.0	9	dbSNP_107	71	3005,5595	664.5+/-402.2	526,1953,1821	no	coding-synonymous	FRMPD1	NM_014907.2		1140,3023,2340	AA,AG,GG		34.9419,47.8438,40.7735		1128/1579	37745413	5303,7703	2203	4300	6503	SO:0001819	synonymous_variant	22844	exon16			GGAGGAGTCTAGG	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.3384G>A	9.37:g.37745413G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	163	70	0.429448	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	37	CCDS6612.1																																																																																			G|0.618;A|0.382	0.382	strong		0.428	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
ZBTB46	140685	hgsc.bcm.edu	37	20	62378418	62378418	+	Silent	SNP	C	C	T	rs74552928	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62378418C>T	ENST00000245663.4	-	5	1785	c.1635G>A	c.(1633-1635)gcG>gcA	p.A545A	ZBTB46_ENST00000302995.2_Silent_p.A545A|RP4-583P15.10_ENST00000447343.2_RNA|RP4-583P15.10_ENST00000433905.2_RNA|ZBTB46_ENST00000395104.1_Silent_p.A545A	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	545					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					CCAGCTCCTCCGCCTCCCCTC	0.726													C|||	286	0.0571086	0.0038	0.0764	5008	,	,		9647	0.001		0.1044	False		,,,				2504	0.1247				p.A545A		Atlas-SNP	.											.	ZBTB46	72	.	0			c.G1635A						PASS	.	C		105,4299		0,105,2097	29.0	28.0	29.0		1635	0.3	1.0	20	dbSNP_131	29	930,7654		48,834,3410	no	coding-synonymous	ZBTB46	NM_025224.3		48,939,5507	TT,TC,CC		10.8341,2.3842,7.9689		545/590	62378418	1035,11953	2202	4292	6494	SO:0001819	synonymous_variant	140685	exon5			CTCCTCCGCCTCC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1635G>A	20.37:g.62378418C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	23	14	0.608696	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			C|0.926;T|0.074	0.074	strong		0.726	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
CAST	831	hgsc.bcm.edu	37	5	96076487	96076487	+	Splice_Site	SNP	G	G	A	rs7724759	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96076487G>A	ENST00000341926.3	+	11	831	c.669G>A	c.(667-669)tcG>tcA	p.S223S	CTC-506B8.1_ENST00000502568.1_RNA|CAST_ENST00000359176.4_Splice_Site_p.S287S|CAST_ENST00000395813.1_Splice_Site_p.S306S|CAST_ENST00000509903.1_Intron|CAST_ENST00000504465.1_Splice_Site_p.S151S|CAST_ENST00000325674.7_Intron|CAST_ENST00000511049.1_Splice_Site_p.S209S|CAST_ENST00000395812.2_Splice_Site_p.S265S|CAST_ENST00000348386.3_Intron|CAST_ENST00000510756.1_Splice_Site_p.S284S|CAST_ENST00000508830.1_Splice_Site_p.S306S|CAST_ENST00000338252.3_Intron|CAST_ENST00000508579.1_5'Flank|CAST_ENST00000508608.1_Splice_Site_p.S269S|CAST_ENST00000515663.1_5'Flank|CAST_ENST00000309190.5_Splice_Site_p.S201S|CAST_ENST00000511782.1_Splice_Site_p.S209S			P20810	ICAL_HUMAN	calpastatin	223					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		CAGACTCTTCGGTGAGTTTAC	0.353													G|||	876	0.17492	0.0688	0.2248	5008	,	,		18456	0.0942		0.338	False		,,,				2504	0.1984				p.S265S		Atlas-SNP	.											CAST,NS,carcinoma,+1,2	CAST	58	2	0			c.G795A						PASS	.	G	,,	518,3888	228.8+/-243.5	36,446,1721	75.0	81.0	79.0		795,,603	3.0	0.6	5	dbSNP_116	79	2695,5905	429.8+/-356.3	434,1827,2039	yes	coding-synonymous-near-splice,intron,coding-synonymous-near-splice	CAST	NM_001042440.2,NM_001190442.1,NM_173060.3	,,	470,2273,3760	AA,AG,GG		31.3372,11.7567,24.704	,,	265/751,,201/687	96076487	3213,9793	2203	4300	6503	SO:0001630	splice_region_variant	831	exon11			CTCTTCGGTGAGT	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.669+1G>A	5.37:g.96076487G>A		Somatic	366	1	0.00273224		WXS	Illumina HiSeq	Phase_I	367	172	0.468665	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Silent	SNP	ENST00000341926.3	37		440	0.20146520146520147	37	0.07520325203252033	88	0.2430939226519337	67	0.11713286713286714	248	0.32717678100263853	G	6.389	0.439934	0.12104	0.117567	0.313372	ENSG00000153113	ENST00000512620	.	.	.	4.86	2.98	0.34508	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999942473	.	.	.	.	.	.	T	0.29336	-1.0015	3	.	.	.	11.5549	9.9911	0.41872	0.0:0.0:0.6167:0.3833	rs7724759;rs17401060;rs7724759	.	.	.	Q	240	.	.	R	+	2	0	CAST	96102243	0.878000	0.30173	0.650000	0.29550	0.214000	0.24535	1.071000	0.30666	0.689000	0.31550	-0.188000	0.12872	CGA	G|0.780;A|0.220	0.220	strong		0.353	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062	Silent
TTF1	7270	hgsc.bcm.edu	37	9	135277130	135277130	+	Missense_Mutation	SNP	C	C	A	rs3739915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:135277130C>A	ENST00000334270.2	-	2	1118	c.1079G>T	c.(1078-1080)gGa>gTa	p.G360V		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	360			G -> V (in dbSNP:rs3739915).		chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		CACCTGTGATCCTTCAGGGTA	0.448													C|||	481	0.0960463	0.0408	0.0807	5008	,	,		20873	0.246		0.0527	False		,,,				2504	0.0716				p.G360V		Atlas-SNP	.											.	TTF1	82	.	0			c.G1079T						PASS	.	C	,VAL/GLY	215,4191	130.6+/-167.2	0,215,1988	155.0	140.0	145.0		,1079	1.1	0.0	9	dbSNP_107	145	404,8196	128.8+/-187.0	7,390,3903	yes	intron,missense	TTF1	NM_001205296.1,NM_007344.3	,109	7,605,5891	AA,AC,CC		4.6977,4.8797,4.7593	,probably-damaging	,360/906	135277130	619,12387	2203	4300	6503	SO:0001583	missense	7270	exon2			TGTGATCCTTCAG	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.1079G>T	9.37:g.135277130C>A	ENSP00000333920:p.Gly360Val	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	188	91	0.484043	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Missense_Mutation	SNP	ENST00000334270.2	37	CCDS6948.1	235	0.10760073260073261	21	0.042682926829268296	26	0.0718232044198895	148	0.25874125874125875	40	0.052770448548812667	C	14.18	2.459471	0.43736	0.048797	0.046977	ENSG00000125482	ENST00000334270;ENST00000245588	T	0.11063	2.81	5.09	1.12	0.20585	.	1.518420	0.03910	N	0.281816	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	P	0.50943	0.94	P	0.46144	0.505	T	0.35475	-0.9787	9	0.22706	T	0.39	.	4.2753	0.10806	0.0:0.5508:0.1695:0.2797	rs3739915;rs52828446;rs57984098;rs3739915	360	Q15361	TTF1_HUMAN	V	360	ENSP00000333920:G360V	ENSP00000245588:G360V	G	-	2	0	TTF1	134266951	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.088000	0.11198	0.255000	0.21593	-0.140000	0.14226	GGA	C|0.927;A|0.073	0.073	strong		0.448	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344	
CDC16	8881	hgsc.bcm.edu	37	13	115004935	115004935	+	Silent	SNP	T	T	C	rs2296970	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:115004935T>C	ENST00000356221.3	+	5	459	c.351T>C	c.(349-351)ccT>ccC	p.P117P	CDC16_ENST00000375310.1_Silent_p.P23P|CDC16_ENST00000375312.3_Silent_p.P23P|CDC16_ENST00000252458.6_Silent_p.P23P|CDC16_ENST00000252457.5_Silent_p.P116P|CDC16_ENST00000360383.3_Silent_p.P117P|CDC16_ENST00000375308.1_Silent_p.P23P			Q13042	CDC16_HUMAN	cell division cycle 16	117					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			TCAAAGATCCTTCCAGCGACT	0.453													C|||	2212	0.441693	0.8366	0.3516	5008	,	,		17862	0.2024		0.3191	False		,,,				2504	0.3446				p.P117P		Atlas-SNP	.											.	CDC16	50	.	0			c.T351C						PASS	.	C	,	3269,1137	400.4+/-331.6	1229,811,163	43.0	48.0	46.0		351,351	2.6	1.0	13	dbSNP_100	46	2445,6155	694.4+/-404.7	368,1709,2223	no	coding-synonymous,coding-synonymous	CDC16	NM_001078645.1,NM_003903.3	,	1597,2520,2386	CC,CT,TT		28.4302,25.8057,43.9336	,	117/621,117/621	115004935	5714,7292	2203	4300	6503	SO:0001819	synonymous_variant	8881	exon5			AGATCCTTCCAGC	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.351T>C	13.37:g.115004935T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																			T|0.563;C|0.437	0.437	strong		0.453	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240791	39240791	+	Silent	SNP	C	C	G	rs553572799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240791C>G	ENST00000391417.4	+	1	333	c.333C>G	c.(331-333)cgC>cgG	p.R111R		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	136	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						cctgctgccgccccagctgct	0.662																																					p.R111R		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,3	KRTAP4-7	49	3	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.C333G						scavenged	.																																			SO:0001819	synonymous_variant	100132476	exon1			CTGCCGCCCCAGC	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.333C>G	17.37:g.39240791C>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	32	5	0.15625	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	37	CCDS45673.1																																																																																			.	.	none		0.662	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
AKAP9	10142	hgsc.bcm.edu	37	7	91730338	91730338	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:91730338C>T	ENST00000359028.2	+	45	11302	c.11077C>T	c.(11077-11079)Ctg>Ttg	p.L3693L	AKAP9_ENST00000356239.3_Silent_p.L3689L|AKAP9_ENST00000358100.2_Silent_p.L3639L			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3693					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ACTTCAAACTCTGAGCCCTGA	0.393			T	BRAF	papillary thyroid																																p.L3689L		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C11065T						PASS	.						69.0	69.0	69.0					7																	91730338		2203	4300	6503	SO:0001819	synonymous_variant	10142	exon45			CAAACTCTGAGCC	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.11077C>T	7.37:g.91730338C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	98	4	0.0408163	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				.	.	none		0.393	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
PRRC2A	7916	hgsc.bcm.edu	37	6	31603045	31603045	+	Missense_Mutation	SNP	A	A	G	rs35201773	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31603045A>G	ENST00000376033.2	+	22	5531	c.5297A>G	c.(5296-5298)gAc>gGc	p.D1766G	PRRC2A_ENST00000376007.4_Missense_Mutation_p.D1766G	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1766	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GGCACTAGTGACAAGGTCTGT	0.562													A|||	50	0.00998403	0.0068	0.0389	5008	,	,		18924	0.0		0.0139	False		,,,				2504	0.0				p.D1766G		Atlas-SNP	.											.	PRRC2A	152	.	0			c.A5297G						PASS	.	A	GLY/ASP,GLY/ASP	27,4379	31.7+/-61.6	1,25,2177	86.0	77.0	80.0		5297,5297	5.5	1.0	6	dbSNP_126	80	162,8438	76.9+/-139.5	3,156,4141	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	94,94	4,181,6318	GG,GA,AA		1.8837,0.6128,1.4532	possibly-damaging,possibly-damaging	1766/2158,1766/2158	31603045	189,12817	2203	4300	6503	SO:0001583	missense	7916	exon22			CTAGTGACAAGGT	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5297A>G	6.37:g.31603045A>G	ENSP00000365201:p.Asp1766Gly	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	157	78	0.496815	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	30	0.013736263736263736	5	0.01016260162601626	15	0.04143646408839779	0	0.0	10	0.013192612137203167	A	10.30	1.312721	0.23908	0.006128	0.018837	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01685	4.69;4.69	5.51	5.51	0.81932	.	0.094899	0.46758	D	0.000270	T	0.01092	0.0036	L	0.36672	1.1	0.49051	D	0.999747	B	0.23377	0.084	B	0.25759	0.063	T	0.53542	-0.8424	10	0.87932	D	0	-11.5495	13.2493	0.60041	1.0:0.0:0.0:0.0	rs35201773	1766	P48634	PRC2A_HUMAN	G	1760;1749;1766;1766;991	ENSP00000365175:D1766G;ENSP00000365201:D1766G	ENSP00000365175:D1766G	D	+	2	0	PRRC2A	31711024	1.000000	0.71417	0.996000	0.52242	0.325000	0.28411	4.617000	0.61204	2.317000	0.78254	0.459000	0.35465	GAC	A|0.983;G|0.017;T|0.000	0.017	strong		0.562	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
CDR2L	30850	hgsc.bcm.edu	37	17	72999773	72999773	+	Silent	SNP	C	C	T	rs3744204	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72999773C>T	ENST00000337231.5	+	5	1414	c.1002C>T	c.(1000-1002)caC>caT	p.H334H		NM_014603.2	NP_055418.2	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like	334												all_lung(278;0.226)					CCAGCCGGCACGCGGGCAACC	0.672													C|||	1306	0.260783	0.0991	0.4438	5008	,	,		17180	0.1925		0.3598	False		,,,				2504	0.318				p.H334H		Atlas-SNP	.											.	.	.	.	0			c.C1002T						PASS	.	C		517,3707		37,443,1632	13.0	13.0	13.0		1002	2.1	1.0	17	dbSNP_107	13	2341,5835		333,1675,2080	no	coding-synonymous	CDR2L	NM_014603.2		370,2118,3712	TT,TC,CC		28.6326,12.2396,23.0484		334/466	72999773	2858,9542	2112	4088	6200	SO:0001819	synonymous_variant	30850	exon5			CCGGCACGCGGGC		CCDS11710.2	17q25.1	2006-03-28			ENSG00000109089	ENSG00000109089			29999	protein-coding gene	gene with protein product	"""paraneoplastic antigen"""						Standard	NM_014603		Approved	HUMPPA	uc002jml.4	Q86X02	OTTHUMG00000150435	ENST00000337231.5:c.1002C>T	17.37:g.72999773C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_014603	B4DFA7|Q15175	Silent	SNP	ENST00000337231.5	37	CCDS11710.2																																																																																			C|0.748;T|0.252	0.252	strong		0.672	CDR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318080.1	NM_014603	
ARSH	347527	hgsc.bcm.edu	37	X	2928170	2928170	+	Silent	SNP	C	C	T	rs77183343	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:2928170C>T	ENST00000381130.2	+	2	192	c.192C>T	c.(190-192)acC>acT	p.T64T		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	64					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CCTTCCTGACCGGCCGGTACC	0.493													C|||	252	0.066755	0.0726	0.0317	3775	,	,		13559	0.0079		0.0835	False		,,,				2504	0.0429				p.T64T		Atlas-SNP	.											.	ARSH	72	.	0			c.C192T						PASS	.	C		416,3419		16,311,73,1305,498	57.0	43.0	48.0		192	-7.2	0.0	X	dbSNP_131	48	758,5970		30,498,200,1900,1672	no	coding-synonymous	ARSH	NM_001011719.1		46,809,273,3205,2170	TT,TC,T,CC,C		11.2663,10.8475,11.1143		64/563	2928170	1174,9389	2203	4300	6503	SO:0001819	synonymous_variant	347527	exon2			CCTGACCGGCCGG	AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"""Arylsulfatase family"""	32488	protein-coding gene	gene with protein product		300586	"""arylsulfatase H"""			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.192C>T	X.37:g.2928170C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	93	0.911765	NM_001011719		Silent	SNP	ENST00000381130.2	37	CCDS35198.1																																																																																			C|0.899;T|0.101	0.101	strong		0.493	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
KIAA0753	9851	hgsc.bcm.edu	37	17	6511781	6511781	+	Silent	SNP	A	A	G	rs4796519	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:6511781A>G	ENST00000361413.3	-	10	2074	c.1716T>C	c.(1714-1716)gcT>gcC	p.A572A	KIAA0753_ENST00000575027.1_5'Flank|KIAA0753_ENST00000572370.1_Silent_p.A273A|KIAA0753_ENST00000542606.1_Silent_p.A273A|KIAA0753_ENST00000589033.1_Silent_p.A28A	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	572						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TTAGCCATGCAGCACTGAAAT	0.458													G|||	3322	0.663339	0.7307	0.6729	5008	,	,		16648	0.7103		0.5467	False		,,,				2504	0.637				p.A572A		Atlas-SNP	.											KIAA0753,colon,carcinoma,-1,1	KIAA0753	63	1	0			c.T1716C						PASS	.	G		2749,1123		976,797,163	205.0	198.0	200.0		1716	0.2	0.5	17	dbSNP_111	200	4751,3521		1370,2011,755	yes	coding-synonymous	KIAA0753	NM_014804.2		2346,2808,918	GG,GA,AA		42.5653,29.0031,38.2411		572/968	6511781	7500,4644	1936	4136	6072	SO:0001819	synonymous_variant	9851	exon10			CCATGCAGCACTG		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.1716T>C	17.37:g.6511781A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Silent	SNP	ENST00000361413.3	37	CCDS42247.1																																																																																			A|0.360;G|0.640	0.640	strong		0.458	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
PCDHA10	56139	hgsc.bcm.edu	37	5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	rs142356019	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140237158G>A	ENST00000307360.5	+	1	1525	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.V509M|PCDHA4_ENST00000512229.2_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	509	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTACGTGTCGGTGCACGCGGA	0.697													.|||	119	0.023762	0.0121	0.0346	5008	,	,		14546	0.0		0.0716	False		,,,				2504	0.0072				p.V509M		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1525A						PASS	.	G	,MET/VAL,,,,,,,,,,,MET/VAL,MET/VAL	120,4272		4,112,2080	66.0	73.0	71.0		,1525,,,,,,,,,,,1525,1525	3.6	1.0	5	dbSNP_134	71	477,8069		47,383,3843	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,21,,,,,,,,,,,21,21	51,495,5923	AA,AG,GG		5.5816,2.7322,4.6143	,,,,,,,,,,,,,	,509/949,,,,,,,,,,,509/845,509/686	140237158	597,12341	2196	4273	6469	SO:0001583	missense	56139	exon1			GTGTCGGTGCACG	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"""Cadherins / Protocadherins : Clustered"""	8664	other	complex locus constituent	"""KIAA0345-like 4"", ""ortholog to mouse CNR8"""	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1525G>A	5.37:g.140237158G>A	ENSP00000304234:p.Val509Met	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	87	0.03983516483516483	9	0.018292682926829267	19	0.052486187845303865	0	0.0	59	0.07783641160949868	G	14.28	2.487603	0.44249	0.027322	0.055816	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.67698	-0.28;-0.28	3.63	3.63	0.41609	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.17323	0.0416	M	0.64404	1.975	0.43489	P	0.004271000000000025	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.993	T	0.65446	-0.6166	8	0.59425	D	0.04	.	9.6727	0.40021	0.0974:0.0:0.9026:0.0	.	509;509;509	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	M	509	ENSP00000421030:V509M;ENSP00000304234:V509M	ENSP00000304234:V509M	V	+	1	0	PCDHA10	140217342	.	.	0.998000	0.56505	0.648000	0.38561	.	.	2.007000	0.58848	0.561000	0.74099	GTG	G|0.957;A|0.043	0.043	strong		0.697	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
HCFC1	3054	hgsc.bcm.edu	37	X	153215839	153215839	+	Silent	SNP	G	G	A	rs3027875		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153215839G>A	ENST00000310441.7	-	24	6825	c.5859C>T	c.(5857-5859)tgC>tgT	p.C1953C	HCFC1_ENST00000354233.3_Silent_p.C1884C|HCFC1_ENST00000369984.4_Silent_p.C1998C	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1953	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGCTGGGCCCGCAGTACACCC	0.652													G|||	722	0.191258	0.0197	0.1816	3775	,	,		11049	0.002		0.4821	False		,,,				2504	0.0849				p.C1953C		Atlas-SNP	.											.	HCFC1	284	.	0			c.C5859T						PASS	.	G		298,3211		22,216,38,1232,531	41.0	47.0	45.0		5859	-5.3	0.9	X	dbSNP_102	45	4106,2410		924,1122,1136,313,662	no	coding-synonymous	HCFC1	NM_005334.2		946,1338,1174,1545,1193	AA,AG,A,GG,G		36.9859,8.4924,43.9302		1953/2036	153215839	4404,5621	2039	4157	6196	SO:0001819	synonymous_variant	3054	exon24			GGGCCCGCAGTAC		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.5859C>T	X.37:g.153215839G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	119	69	0.579832	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1	475	0.2863170584689572	17	0.035269709543568464	46	0.15333333333333332	2	0.0034965034965034965	261	0.4943181818181818	G	10.91	1.485602	0.26686	0.084924	0.630141	ENSG00000172534	ENST00000444191	.	.	.	5.42	-5.26	0.02772	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11108	-1.0601	3	.	.	.	.	15.8112	0.78565	0.7732:0.0:0.2268:0.0	rs3027875	.	.	.	W	529	.	.	R	-	1	2	HCFC1	152869033	0.009000	0.17119	0.935000	0.37517	0.942000	0.58702	-0.600000	0.05693	-1.195000	0.02680	-0.411000	0.06167	CGG	G|0.712;A|0.288	0.288	strong		0.652	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334	
DCAF4L1	285429	hgsc.bcm.edu	37	4	41984118	41984118	+	Silent	SNP	C	C	T	rs2660320	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:41984118C>T	ENST00000333141.5	+	1	406	c.309C>T	c.(307-309)agC>agT	p.S103S		NM_001029955.3	NP_001025126.2	Q3SXM0	DC4L1_HUMAN	DDB1 and CUL4 associated factor 4-like 1	103										breast(1)|endometrium(5)|kidney(6)|large_intestine(11)|lung(12)|prostate(1)|skin(1)	37						GCATCATCAGCCTGCGAACTC	0.557													C|||	3300	0.658946	0.1452	0.7983	5008	,	,		22448	0.9593		0.7763	False		,,,				2504	0.8241				p.S103S		Atlas-SNP	.											.	DCAF4L1	70	.	0			c.C309T						PASS	.	C		1080,3326	391.0+/-327.9	130,820,1253	97.0	88.0	91.0		309	0.7	0.3	4	dbSNP_100	91	6679,1921	726.5+/-406.6	2580,1519,201	no	coding-synonymous	DCAF4L1	NM_001029955.3		2710,2339,1454	TT,TC,CC		22.3372,24.512,40.3429		103/397	41984118	7759,5247	2203	4300	6503	SO:0001819	synonymous_variant	285429	exon1			CATCAGCCTGCGA	BC035027	CCDS33978.1	4p13	2013-01-09	2009-07-17	2009-07-17		ENSG00000182308		"""WD repeat domain containing"""	27723	protein-coding gene	gene with protein product			"""WD repeat domain 21B"""	WDR21B			Standard	NM_001029955		Approved		uc003gwk.2	Q3SXM0		ENST00000333141.5:c.309C>T	4.37:g.41984118C>T		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	241	238	0.987552	NM_001029955	B3KVI3|Q3ZCW8|Q499Y5|Q9UFI0	Silent	SNP	ENST00000333141.5	37	CCDS33978.1																																																																																			C|0.375;T|0.625	0.625	strong		0.557	DCAF4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360958.1	NM_001029955	
ACTR5	79913	hgsc.bcm.edu	37	20	37383640	37383640	+	Silent	SNP	T	T	C	rs2748663	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:37383640T>C	ENST00000243903.4	+	4	853	c.816T>C	c.(814-816)aaT>aaC	p.N272N		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	272					DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|UV-damage excision repair (GO:0070914)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)				kidney(2)|large_intestine(2)|liver(1)|lung(5)|skin(2)	12		Myeloproliferative disorder(115;0.00878)				ATGAGAATAATGTCCACAAGA	0.428													T|||	1198	0.239217	0.205	0.2334	5008	,	,		18350	0.2669		0.2565	False		,,,				2504	0.2434				p.N272N		Atlas-SNP	.											.	ACTR5	44	.	0			c.T816C						PASS	.	T		946,3460	358.9+/-314.6	103,740,1360	73.0	77.0	76.0		816	-8.8	0.5	20	dbSNP_100	76	2263,6337	381.5+/-340.0	302,1659,2339	no	coding-synonymous	ACTR5	NM_024855.3		405,2399,3699	CC,CT,TT		26.314,21.4707,24.6732		272/608	37383640	3209,9797	2203	4300	6503	SO:0001819	synonymous_variant	79913	exon4			GAATAATGTCCAC	AK022847	CCDS13308.1	20q12	2011-07-06	2001-11-28		ENSG00000101442	ENSG00000101442		"""INO80 complex subunits"""	14671	protein-coding gene	gene with protein product	"""INO80 complex subunit M"""		"""ARP5 (actin-related protein 5, yeast) homolog"""			16230350	Standard	NM_024855		Approved	FLJ12785, Arp5, INO80M	uc002xjd.2	Q9H9F9	OTTHUMG00000032456	ENST00000243903.4:c.816T>C	20.37:g.37383640T>C		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	259	257	0.992278	NM_024855	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Silent	SNP	ENST00000243903.4	37	CCDS13308.1																																																																																			C|0.243;N|0.000	0.243	strong		0.428	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855	
IRS4	8471	hgsc.bcm.edu	37	X	107978342	107978342	+	Silent	SNP	T	T	A	rs375938401|rs80131334|rs1800993	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:107978342T>A	ENST00000372129.2	-	1	1309	c.1233A>T	c.(1231-1233)cgA>cgT	p.R411R	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	411					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GCAGTCTTCCTCGCCTGGAGT	0.642													T|||	171	0.045298	0.0401	0.0562	3775	,	,		13003	0.002		0.0398	False		,,,				2504	0.0378				p.R411R		Atlas-SNP	.											.	IRS4	253	.	0			c.A1233T						PASS	.	T		11,3824		0,0,11,1632,560	49.0	43.0	45.0		1233	0.9	0.1	X	dbSNP_131	45	29,6699		1,1,26,2426,1846	no	coding-synonymous	IRS4	NM_003604.2		1,1,37,4058,2406	AA,AT,A,TT,T		0.431,0.2868,0.3787		411/1258	107978342	40,10523	2203	4300	6503	SO:0001819	synonymous_variant	8471	exon1			TCTTCCTCGCCTG	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1233A>T	X.37:g.107978342T>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	84	81	0.964286	NM_003604		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																			T|0.950;A|0.050	0.050	strong		0.642	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
VRK1	7443	hgsc.bcm.edu	37	14	97299853	97299853	+	Silent	SNP	A	A	G	rs2145635	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:97299853A>G	ENST00000216639.3	+	2	194	c.45A>G	c.(43-45)gcA>gcG	p.A15A		NM_003384.2	NP_003375.1	Q99986	VRK1_HUMAN	vaccinia related kinase 1	15					Golgi disassembly (GO:0090166)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-T3 phosphorylation (GO:0072355)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi stack (GO:0005795)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H3-S10 specific) (GO:0035175)|histone kinase activity (H3-T3 specific) (GO:0072354)|nucleosomal histone binding (GO:0031493)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(1)|stomach(1)	12		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		AGAGCTCTGCAAAGAGACATC	0.388													A|||	1450	0.289537	0.211	0.3401	5008	,	,		19259	0.1161		0.3936	False		,,,				2504	0.4315				p.A15A		Atlas-SNP	.											.	VRK1	34	.	0			c.A45G						PASS	.	A		934,3472	356.9+/-313.7	102,730,1371	106.0	102.0	103.0		45	-4.5	0.5	14	dbSNP_96	103	3369,5229	500.5+/-375.2	669,2031,1599	no	coding-synonymous	VRK1	NM_003384.2		771,2761,2970	GG,GA,AA		39.1835,21.1984,33.0898		15/397	97299853	4303,8701	2203	4299	6502	SO:0001819	synonymous_variant	7443	exon2			CTCTGCAAAGAGA	AB000449	CCDS9947.1	14q32.2	2012-07-05			ENSG00000100749	ENSG00000100749			12718	protein-coding gene	gene with protein product		602168				9344656	Standard	XM_006720247		Approved		uc001yft.3	Q99986	OTTHUMG00000171459	ENST00000216639.3:c.45A>G	14.37:g.97299853A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	47	0.61039	NM_003384	Q3SYL2	Silent	SNP	ENST00000216639.3	37	CCDS9947.1																																																																																			A|0.687;G|0.313	0.313	strong		0.388	VRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413520.1	NM_003384	
FAM166B	730112	hgsc.bcm.edu	37	9	35562549	35562549	+	Silent	SNP	G	G	A	rs755774	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35562549G>A	ENST00000399742.2	-	5	637	c.567C>T	c.(565-567)tgC>tgT	p.C189C	FAM166B_ENST00000492890.1_Intron	NM_001099951.2|NM_001164310.1	NP_001093421.1|NP_001157782.1	A8MTA8	F166B_HUMAN	family with sequence similarity 166, member B	189										kidney(3)|large_intestine(1)|lung(4)|ovary(1)	9						GGAAGCGGGCGCAGGGCACAT	0.627													G|||	1671	0.333666	0.2148	0.5778	5008	,	,		16151	0.2817		0.4433	False		,,,				2504	0.2618				p.C189C		Atlas-SNP	.											.	FAM166B	19	.	0			c.C567T						PASS	.	G	,	1052,3294		153,746,1274	42.0	51.0	48.0		,567	-5.5	0.9	9	dbSNP_86	48	4007,4555		926,2155,1200	no	intron,coding-synonymous	FAM166B	NM_001099951.2,NM_001164310.1	,	1079,2901,2474	AA,AG,GG		46.7998,24.2062,39.1927	,	,189/276	35562549	5059,7849	2173	4281	6454	SO:0001819	synonymous_variant	730112	exon5			GCGGGCGCAGGGC	BC129999	CCDS47963.1, CCDS56572.1	9p13.3	2008-06-10			ENSG00000215187	ENSG00000215187			34242	protein-coding gene	gene with protein product							Standard	NM_001099951		Approved		uc010mkr.3	A8MTA8	OTTHUMG00000019858	ENST00000399742.2:c.567C>T	9.37:g.35562549G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_001164310	A1L3B2|B7ZBJ0	Silent	SNP	ENST00000399742.2	37	CCDS56572.1																																																																																			G|0.653;A|0.347	0.347	strong		0.627	FAM166B-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336563.1	NM_001099951	
BYSL	705	hgsc.bcm.edu	37	6	41889505	41889505	+	Missense_Mutation	SNP	C	C	T	rs144207756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41889505C>T	ENST00000230340.4	+	1	580	c.205C>T	c.(205-207)Ctc>Ttc	p.L69F	MED20_ENST00000409312.1_5'Flank|MED20_ENST00000467535.1_5'Flank|MED20_ENST00000265350.4_5'Flank|MED20_ENST00000409060.1_5'Flank	NM_004053.3	NP_004044.3	Q13895	BYST_HUMAN	bystin-like	69					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|female pregnancy (GO:0007565)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|trophectodermal cell differentiation (GO:0001829)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(5)|skin(1)	8	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			ACAGGAGGAACTCGAGGCCGA	0.677											OREG0017436	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0	0.0014	5008	,	,		12733	0.0		0.001	False		,,,				2504	0.0				p.L69F		Atlas-SNP	.											.	BYSL	17	.	0			c.C205T						PASS	.	C	PHE/LEU	4,4396		0,4,2196	16.0	20.0	19.0		205	5.1	1.0	6	dbSNP_134	19	24,8570		0,24,4273	yes	missense	BYSL	NM_004053.3	22	0,28,6469	TT,TC,CC		0.2793,0.0909,0.2155	probably-damaging	69/438	41889505	28,12966	2200	4297	6497	SO:0001583	missense	705	exon1			GAGGAACTCGAGG	L36720	CCDS34450.1	6p21.1	2008-08-29			ENSG00000112578	ENSG00000112578			1157	protein-coding gene	gene with protein product		603871				9925933, 17381424	Standard	NM_004053		Approved		uc003orl.3	Q13895	OTTHUMG00000014687	ENST00000230340.4:c.205C>T	6.37:g.41889505C>T	ENSP00000230340:p.Leu69Phe	Somatic	115	0	0	904	WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_004053	Q6P5W4|Q86W44|Q96IP8	Missense_Mutation	SNP	ENST00000230340.4	37	CCDS34450.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	29.3	4.996049	0.93167	9.09E-4	0.002793	ENSG00000112578	ENST00000230340	T	0.23950	1.88	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.44561	0.1299	M	0.82716	2.605	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.44682	-0.9312	10	0.59425	D	0.04	-26.2728	11.7533	0.51862	0.0:0.9191:0.0:0.0809	.	69	Q13895	BYST_HUMAN	F	69	ENSP00000230340:L69F	ENSP00000230340:L69F	L	+	1	0	BYSL	41997483	1.000000	0.71417	0.996000	0.52242	0.908000	0.53690	3.917000	0.56424	2.639000	0.89480	0.655000	0.94253	CTC	C|0.998;T|0.002	0.002	strong		0.677	BYSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040535.2		
MET	4233	hgsc.bcm.edu	37	7	116339672	116339672	+	Silent	SNP	C	C	T	rs35775721	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116339672C>T	ENST00000318493.6	+	2	721	c.534C>T	c.(532-534)agC>agT	p.S178S	MET_ENST00000436117.2_Silent_p.S178S|MET_ENST00000397752.3_Silent_p.S178S			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GTGTGGTGAGCGCCCTGGGAG	0.473			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				C|||	443	0.0884585	0.1664	0.0303	5008	,	,		20901	0.0526		0.0417	False		,,,				2504	0.1094				p.S178S		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	0			c.C534T						scavenged	.	C	,	514,3416		29,456,1480	104.0	105.0	105.0		534,534	-2.6	0.7	7	dbSNP_126	105	337,7949		10,317,3816	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	39,773,5296	TT,TC,CC		4.0671,13.0789,6.9663	,	178/1391,178/1409	116339672	851,11365	1965	4143	6108	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GGTGAGCGCCCTG	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.534C>T	7.37:g.116339672C>T		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	150	82	0.546667	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.935;T|0.065	0.065	strong		0.473	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
KDM4B	23030	hgsc.bcm.edu	37	19	5131955	5131955	+	Silent	SNP	C	C	T	rs45459493	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:5131955C>T	ENST00000159111.4	+	13	2061	c.1843C>T	c.(1843-1845)Ctg>Ttg	p.L615L	KDM4B_ENST00000536461.1_Silent_p.L649L	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	615					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						GCGCCATCCCCTGGGCCGGCC	0.637													C|||	53	0.0105831	0.0015	0.0187	5008	,	,		12016	0.0		0.0338	False		,,,				2504	0.0041				p.L615L		Atlas-SNP	.											.	KDM4B	120	.	0			c.C1843T						PASS	.	C		24,4372		0,24,2174	23.0	28.0	27.0		1843	2.0	1.0	19	dbSNP_127	27	237,8351		2,233,4059	no	coding-synonymous	KDM4B	NM_015015.2		2,257,6233	TT,TC,CC		2.7597,0.546,2.0102		615/1097	5131955	261,12723	2198	4294	6492	SO:0001819	synonymous_variant	23030	exon13			CATCCCCTGGGCC	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1843C>T	19.37:g.5131955C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	188	89	0.473404	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Silent	SNP	ENST00000159111.4	37	CCDS12138.1																																																																																			C|0.981;T|0.019	0.019	strong		0.637	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015	
FSHB	2488	hgsc.bcm.edu	37	11	30255185	30255185	+	Silent	SNP	C	C	T	rs6169	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:30255185C>T	ENST00000417547.1	+	3	267	c.228C>T	c.(226-228)taC>taT	p.Y76Y	FSHB_ENST00000254122.3_Silent_p.Y76Y|FSHB_ENST00000533718.1_Silent_p.Y76Y	NM_001018080.1	NP_001018090.1	P01225	FSHB_HUMAN	follicle stimulating hormone, beta polypeptide	76					cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|female pregnancy (GO:0007565)|follicle-stimulating hormone signaling pathway (GO:0042699)|peptide hormone processing (GO:0016486)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone biosynthetic process (GO:0006701)|regulation of osteoclast differentiation (GO:0045670)|Sertoli cell proliferation (GO:0060011)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	12						AACTGGTATACGAAACAGTGA	0.498													T|||	3079	0.614816	0.7572	0.5317	5008	,	,		18146	0.6696		0.4503	False		,,,				2504	0.5941				p.Y76Y		Atlas-SNP	.											.	FSHB	28	.	0			c.C228T						PASS	.	T	,	3124,1280	437.6+/-345.0	1100,924,178	107.0	94.0	99.0		228,228	-8.5	0.5	11	dbSNP_52	99	3747,4851	617.0+/-396.6	825,2097,1377	no	coding-synonymous,coding-synonymous	FSHB	NM_000510.2,NM_001018080.1	,	1925,3021,1555	TT,TC,CC		43.5799,29.0645,47.1543	,	76/130,76/130	30255185	6871,6131	2202	4299	6501	SO:0001819	synonymous_variant	2488	exon3			GGTATACGAAACA		CCDS7868.1	11p13	2013-02-26				ENSG00000131808		"""Endogenous ligands"""	3964	protein-coding gene	gene with protein product	"""follitropin, beta chain"", ""follicle-stimulating hormone beta subunit"""	136530				2885163, 3151250	Standard	NM_000510		Approved		uc001msm.3	P01225		ENST00000417547.1:c.228C>T	11.37:g.30255185C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_000510	A2TF08|A5JVV3|Q14D61	Silent	SNP	ENST00000417547.1	37	CCDS7868.1																																																																																			C|0.436;T|0.564	0.564	strong		0.498	FSHB-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389757.1	NM_000510	
NOP56	10528	hgsc.bcm.edu	37	20	2638579	2638579	+	Missense_Mutation	SNP	T	T	C	rs6753	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2638579T>C	ENST00000329276.5	+	12	1940	c.1424T>C	c.(1423-1425)aTg>aCg	p.M475T	SNORD57_ENST00000448188.1_RNA|SNORD56_ENST00000413522.1_RNA|IDH3B_ENST00000488299.1_5'Flank|SNORD86_ENST00000391196.1_RNA|SNORA51_ENST00000606420.1_RNA|NOP56_ENST00000492135.1_3'UTR	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	475	Lys-rich.		M -> T (in dbSNP:rs6753). {ECO:0000269|PubMed:9372940}.		cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						CTTTAGGAGATGAGTGAAAAA	0.458													C|||	1888	0.376997	0.6188	0.379	5008	,	,		17492	0.254		0.2654	False		,,,				2504	0.2904				p.M475T		Atlas-SNP	.											NOP56,caecum,carcinoma,-1,1	NOP56	73	1	0			c.T1424C						PASS	.	C	THR/MET	2294,2012		620,1054,479	139.0	155.0	150.0		1424	-3.1	0.0	20	dbSNP_52	150	2312,6232		339,1634,2299	no	missense	NOP56	NM_006392.3	81	959,2688,2778	CC,CT,TT		27.0599,46.7255,35.8444	benign	475/595	2638579	4606,8244	2153	4272	6425	SO:0001583	missense	10528	exon12			AGGAGATGAGTGA	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.1424T>C	20.37:g.2638579T>C	ENSP00000370589:p.Met475Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_006392	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	800	0.3663003663003663	330	0.6707317073170732	130	0.35911602209944754	136	0.23776223776223776	204	0.2691292875989446	C	0.012	-1.685592	0.00745	0.532745	0.270599	ENSG00000101361	ENST00000329276	T	0.39997	1.05	4.64	-3.07	0.05363	.	1.567430	0.03170	N	0.170662	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38929	-0.9638	9	0.11485	T	0.65	1.0538	11.6995	0.51562	0.0:0.3003:0.0:0.6997	rs6753;rs1071606;rs2273136;rs3177051;rs3182722;rs3182969;rs16907603;rs17419589;rs52816246;rs60600923;rs6753	475	O00567	NOP56_HUMAN	T	475	ENSP00000370589:M475T	ENSP00000370589:M475T	M	+	2	0	NOP56	2586579	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.138000	0.01303	-0.892000	0.03935	-0.748000	0.03510	ATG	T|0.637;C|0.363	0.363	strong		0.458	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
RAG1	5896	hgsc.bcm.edu	37	11	36595600	36595600	+	Missense_Mutation	SNP	A	A	G	rs3740955	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:36595600A>G	ENST00000299440.5	+	2	858	c.746A>G	c.(745-747)cAc>cGc	p.H249R		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	249	Interaction with importin alpha-1.		H -> R (in dbSNP:rs3740955). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2598259, ECO:0000269|PubMed:8844221}.		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				GCCCGTCAGCACAAGAGAAGA	0.498									Familial Hemophagocytic Lymphohistiocytosis				G|||	3072	0.613419	0.7708	0.6052	5008	,	,		24019	0.756		0.3648	False		,,,				2504	0.5153				p.H249R	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.A746G						PASS	.	G	ARG/HIS	3200,1204	420.4+/-339.0	1162,876,164	79.0	71.0	74.0		746	-2.0	0.0	11	dbSNP_107	74	2888,5708	672.0+/-402.9	470,1948,1880	yes	missense	RAG1	NM_000448.2	29	1632,2824,2044	GG,GA,AA		33.597,27.3388,46.8308	benign	249/1044	36595600	6088,6912	2202	4298	6500	SO:0001583	missense	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GTCAGCACAAGAG	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"""RING-type (C3HC4) zinc fingers"""	9831	protein-coding gene	gene with protein product	"""recombination activating protein 1"", ""RING finger protein 74"", ""V(D)J recombination-activating protein 1"""	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.746A>G	11.37:g.36595600A>G	ENSP00000299440:p.His249Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_000448	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	37	CCDS7902.1	1291	0.5911172161172161	364	0.7398373983739838	200	0.5524861878453039	448	0.7832167832167832	279	0.36807387862796836	G	0.188	-1.055818	0.01965	0.726612	0.33597	ENSG00000166349	ENST00000534663;ENST00000299440	T;T	0.36878	1.23;1.23	5.6	-1.98	0.07480	.	1.564430	0.03609	N	0.234553	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45920	-0.9228	9	0.51188	T	0.08	.	10.2304	0.43252	0.5804:0.1383:0.2812:0.0	rs3740955;rs12797306;rs17629075;rs17857143;rs56430511;rs58718336;rs3740955	249	P15918	RAG1_HUMAN	R	249	ENSP00000434610:H249R;ENSP00000299440:H249R	ENSP00000299440:H249R	H	+	2	0	RAG1	36552176	0.004000	0.15560	0.000000	0.03702	0.057000	0.15508	0.169000	0.16641	-0.541000	0.06257	-0.738000	0.03535	CAC	A|0.471;G|0.529	0.529	strong		0.498	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448	
DSC1	1823	hgsc.bcm.edu	37	18	28720147	28720147	+	Missense_Mutation	SNP	C	C	T	rs17800159	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:28720147C>T	ENST00000257198.5	-	10	1639	c.1378G>A	c.(1378-1380)Gtt>Att	p.V460I	RP11-408H20.2_ENST00000581836.1_RNA|DSC1_ENST00000257197.3_Missense_Mutation_p.V460I	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	460	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> I (in dbSNP:rs17800159).		homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V460I(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			ATAATTTTAACGGTGACAGTT	0.453													C|||	933	0.186302	0.0091	0.232	5008	,	,		14951	0.4792		0.1332	False		,,,				2504	0.1462				p.V460I		Atlas-SNP	.											DSC1_ENST00000257198,NS,carcinoma,0,2	DSC1	240	2	2	Substitution - Missense(2)	stomach(2)	c.G1378A						PASS	.	C	ILE/VAL,ILE/VAL	110,4296	86.3+/-125.0	2,106,2095	107.0	101.0	103.0		1378,1378	5.8	1.0	18	dbSNP_123	103	1108,7492	230.7+/-264.9	80,948,3272	yes	missense,missense	DSC1	NM_004948.3,NM_024421.2	29,29	82,1054,5367	TT,TC,CC		12.8837,2.4966,9.3649	possibly-damaging,possibly-damaging	460/841,460/895	28720147	1218,11788	2203	4300	6503	SO:0001583	missense	1823	exon10			TTTTAACGGTGAC	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1378G>A	18.37:g.28720147C>T	ENSP00000257198:p.Val460Ile	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	198	92	0.464646	NM_004948	Q9HB01	Missense_Mutation	SNP	ENST00000257198.5	37	CCDS11894.1	454	0.2078754578754579	11	0.022357723577235773	75	0.20718232044198895	279	0.48776223776223776	89	0.11741424802110818	C	14.76	2.631257	0.46944	0.024966	0.128837	ENSG00000134765	ENST00000257197;ENST00000257198	T;T	0.64260	-0.09;-0.09	5.83	5.83	0.93111	Cadherin (4);Cadherin-like (1);	0.000000	0.47852	D	0.000201	T	0.00012	0.0000	L	0.51914	1.62	0.24227	P	0.99541603	D;D	0.76494	0.999;0.997	D;P	0.81914	0.995;0.766	T	0.44682	-0.9312	9	0.14656	T	0.56	.	17.9032	0.88911	0.0:1.0:0.0:0.0	rs17800159;rs52809488;rs17800159	460;460	Q08554;Q9HB00	DSC1_HUMAN;.	I	460	ENSP00000257197:V460I;ENSP00000257198:V460I	ENSP00000257197:V460I	V	-	1	0	DSC1	26974145	1.000000	0.71417	0.996000	0.52242	0.261000	0.26267	3.858000	0.55979	2.761000	0.94854	0.650000	0.86243	GTT	C|0.860;T|0.140	0.140	strong		0.453	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
TBC1D19	55296	hgsc.bcm.edu	37	4	26719569	26719569	+	Silent	SNP	T	T	C	rs34600164	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:26719569T>C	ENST00000264866.4	+	14	1247	c.969T>C	c.(967-969)ttT>ttC	p.F323F	TBC1D19_ENST00000511789.1_Silent_p.F258F	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	323	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)	p.F323L(1)		breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				TACTTTGTTTTTCCCGGGATA	0.323													T|||	235	0.0469249	0.0038	0.0331	5008	,	,		18561	0.0149		0.0785	False		,,,				2504	0.1155				p.F323F		Atlas-SNP	.											TBC1D19,trunk,malignant_melanoma,0,1	TBC1D19	53	1	1	Substitution - Missense(1)	skin(1)	c.T969C						PASS	.	T		59,4347	56.2+/-92.4	1,57,2145	163.0	151.0	155.0		969	3.7	1.0	4	dbSNP_126	155	650,7950	165.5+/-217.6	31,588,3681	no	coding-synonymous	TBC1D19	NM_018317.2		32,645,5826	CC,CT,TT		7.5581,1.3391,5.4513		323/527	26719569	709,12297	2203	4300	6503	SO:0001819	synonymous_variant	55296	exon14			TTGTTTTTCCCGG	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.969T>C	4.37:g.26719569T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_018317	B9A6M0|Q9NUX1	Silent	SNP	ENST00000264866.4	37	CCDS3439.1																																																																																			T|0.953;C|0.047	0.047	strong		0.323	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317	
MYH6	4624	hgsc.bcm.edu	37	14	23874523	23874523	+	Silent	SNP	C	C	T	rs2277474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23874523C>T	ENST00000356287.3	-	4	440	c.411G>A	c.(409-411)gaG>gaA	p.E137E	MYH6_ENST00000405093.3_Silent_p.E137E			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	137	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CGGCCACCACCTCGGCATTGT	0.602													C|||	773	0.154353	0.1384	0.1513	5008	,	,		18207	0.0675		0.2485	False		,,,				2504	0.1708				p.E137E		Atlas-SNP	.											.	MYH6	274	.	0			c.G411A						PASS	.	C		728,3678		56,616,1531	92.0	96.0	95.0		411	1.5	1.0	14	dbSNP_100	95	2243,6357		300,1643,2357	no	coding-synonymous	MYH6	NM_002471.3		356,2259,3888	TT,TC,CC		26.0814,16.5229,22.8433		137/1940	23874523	2971,10035	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon5			CACCACCTCGGCA	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.411G>A	14.37:g.23874523C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			C|0.794;A|0.002	.	strong		0.602	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
FBXW10	10517	hgsc.bcm.edu	37	17	18682505	18682505	+	Missense_Mutation	SNP	T	T	C	rs1024657	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18682505T>C	ENST00000395665.4	+	14	3274	c.3053T>C	c.(3052-3054)gTc>gCc	p.V1018A	FBXW10_ENST00000308799.4_Missense_Mutation_p.V1027A|FBXW10_ENST00000301938.4_Missense_Mutation_p.V965A|TVP23B_ENST00000574226.1_5'Flank|TVP23B_ENST00000307767.8_5'Flank|FBXW10_ENST00000395667.1_Missense_Mutation_p.V1017A|TVP23B_ENST00000476139.1_5'Flank			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	1018								p.V1017A(1)		NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						CCAGGAAAAGTCAGCAAAGCT	0.488													N|||	744	0.148562	0.1846	0.2147	5008	,	,		13486	0.0903		0.2018	False		,,,				2504	0.0583				p.V1018A		Atlas-SNP	.											FBXW10,NS,carcinoma,0,2	FBXW10	82	2	1	Substitution - Missense(1)	prostate(1)	c.T3053C						scavenged	.						42.0	40.0	41.0					17																	18682505		1906	3581	5487	SO:0001583	missense	10517	exon14			GAAAAGTCAGCAA	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.3053T>C	17.37:g.18682505T>C	ENSP00000379025:p.Val1018Ala	Somatic	441	0	0		WXS	Illumina HiSeq	Phase_I	243	7	0.0288066	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	498	0.22802197802197802	92	0.18699186991869918	107	0.2955801104972376	65	0.11363636363636363	234	0.3087071240105541	C	0.015	-1.557317	0.00910	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84	3.38	2.36	0.29203	.	0.000000	0.31936	N	0.006834	T	0.00012	0.0000	N	0.00128	-2.045	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.24693	-1.0153	9	0.02654	T	1	.	4.0906	0.09968	0.4063:0.4743:0.0:0.1194	.	965;1027;1018;1017	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	A	1017;1027;965;1018	ENSP00000379026:V1017A;ENSP00000310382:V1027A;ENSP00000306937:V965A;ENSP00000379025:V1018A	ENSP00000306937:V965A	V	+	2	0	FBXW10	18623230	0.407000	0.25352	0.286000	0.24833	0.737000	0.42083	0.661000	0.25023	0.116000	0.18110	-0.473000	0.04963	GTC	T|0.778;C|0.222	0.222	strong		0.488	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
PRKG1	5592	hgsc.bcm.edu	37	10	53822301	53822301	+	Missense_Mutation	SNP	A	A	G	rs34997494	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:53822301A>G	ENST00000401604.2	+	7	994	c.800A>G	c.(799-801)aAt>aGt	p.N267S	PRKG1_ENST00000373985.1_Missense_Mutation_p.N255S|PRKG1_ENST00000373975.2_5'UTR|PRKG1_ENST00000373980.4_Missense_Mutation_p.N282S			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	267	cGMP-binding, low affinity.		N -> S (in dbSNP:rs34997494). {ECO:0000269|PubMed:17344846}.		actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTGCAGGTAAATGTCACTCGT	0.398													A|||	161	0.0321486	0.0076	0.0274	5008	,	,		16295	0.0516		0.0467	False		,,,				2504	0.0337				p.N282S		Atlas-SNP	.											PRKG1_ENST00000401604,NS,adenoma,0,3	PRKG1	167	3	0			c.A845G						PASS	.	A	SER/ASN,SER/ASN	75,4331	65.3+/-102.7	1,73,2129	65.0	63.0	64.0		800,845	5.8	1.0	10	dbSNP_126	64	413,8187	129.7+/-187.7	10,393,3897	yes	missense,missense	PRKG1	NM_001098512.2,NM_006258.3	46,46	11,466,6026	GG,GA,AA		4.8023,1.7022,3.7521	benign,benign	267/672,282/687	53822301	488,12518	2203	4300	6503	SO:0001583	missense	5592	exon7			AGGTAAATGTCAC		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.800A>G	10.37:g.53822301A>G	ENSP00000384200:p.Asn267Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	137	55	0.40146	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	69	0.03159340659340659	4	0.008130081300813009	10	0.027624309392265192	24	0.04195804195804196	31	0.040897097625329816	A	16.04	3.009579	0.54361	0.017022	0.048023	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	D;D;D;D	0.92397	-3.03;-3.03;-3.03;-3.03	5.76	5.76	0.90799	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.111572	0.64402	D	0.000014	T	0.45558	0.1348	N	0.02765	-0.5	0.52501	D	0.999954	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.67772	-0.5584	10	0.17369	T	0.5	-24.0012	14.0391	0.64663	1.0:0.0:0.0:0.0	rs34997494	282;267	Q13976-2;Q13976	.;KGP1_HUMAN	S	267;255;282;140	ENSP00000384200:N267S;ENSP00000363097:N255S;ENSP00000363092:N282S;ENSP00000363087:N140S	ENSP00000363087:N140S	N	+	2	0	PRKG1	53492307	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	6.824000	0.75288	2.202000	0.70862	0.533000	0.62120	AAT	A|0.962;G|0.038	0.038	strong		0.398	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PAK7	57144	hgsc.bcm.edu	37	20	9543622	9543622	+	Missense_Mutation	SNP	C	C	T	rs2297345	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:9543622C>T	ENST00000378429.3	-	7	2078	c.1532G>A	c.(1531-1533)aGc>aAc	p.S511N	PAK7_ENST00000378423.1_Missense_Mutation_p.S511N|PAK7_ENST00000353224.5_Missense_Mutation_p.S511N	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	511	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> N (in dbSNP:rs2297345). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			AAGGTAGCTGCTGTACATGTC	0.463													T|||	2577	0.514577	0.8782	0.3833	5008	,	,		19708	0.5427		0.3151	False		,,,				2504	0.2924				p.S511N		Atlas-SNP	.											.	PAK7	194	.	0			c.G1532A						PASS	.	T	ASN/SER,ASN/SER	3483,923	353.3+/-312.1	1393,697,113	191.0	170.0	177.0		1532,1532	5.9	1.0	20	dbSNP_100	177	2654,5946	686.2+/-404.1	409,1836,2055	yes	missense,missense	PAK7	NM_020341.3,NM_177990.2	46,46	1802,2533,2168	TT,TC,CC		30.8605,20.9487,47.1859	benign,benign	511/720,511/720	9543622	6137,6869	2203	4300	6503	SO:0001583	missense	57144	exon6			TAGCTGCTGTACA	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"""p21(CDKN1A)-activated kinase 7"""			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1532G>A	20.37:g.9543622C>T	ENSP00000367686:p.Ser511Asn	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	131	53	0.40458	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	1126	0.5155677655677655	429	0.8719512195121951	149	0.4116022099447514	312	0.5454545454545454	236	0.3113456464379947	T	9.638	1.138248	0.21123	0.790513	0.308605	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.13657	2.57;2.57;2.57	5.87	5.87	0.94306	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	L	0.33189	0.99	0.37336	P	0.08982500000000004	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.11966	-1.0566	8	.	.	.	.	12.3288	0.55026	0.0:0.0658:0.0:0.9342	rs2297345;rs61006606;rs2297345	511;511	B0AZM9;Q9P286	.;PAK7_HUMAN	N	511;511;511;459	ENSP00000367686:S511N;ENSP00000322957:S511N;ENSP00000367679:S511N	.	S	-	2	0	PAK7	9491622	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	6.239000	0.72356	1.158000	0.42547	-0.254000	0.11334	AGC	C|0.503;T|0.497	0.497	strong		0.463	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1		
SCN1A	6323	hgsc.bcm.edu	37	2	166930049	166930049	+	Missense_Mutation	SNP	C	C	T	rs398123601		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:166930049C>T	ENST00000303395.4	-	1	82	c.83G>A	c.(82-84)cGc>cAc	p.R28H	AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.R28H|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.R28H|SCN1A_ENST00000423058.2_Missense_Mutation_p.R28H			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	28					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTCTGCAATGCGTCTTTCAAT	0.448																																					p.R28H		Atlas-SNP	.											SCN1A_ENST00000303395,colon,carcinoma,-1,2	SCN1A	641	2	0			c.G83A						scavenged	.						219.0	208.0	212.0					2																	166930049		2203	4300	6503	SO:0001583	missense	6323	exon1			GCAATGCGTCTTT	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.83G>A	2.37:g.166930049C>T	ENSP00000303540:p.Arg28His	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	303	5	0.0165017	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.595805	0.86953	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97772	-4.53;-4.53;-4.51;-4.49	5.77	5.77	0.91146	.	0.000000	0.64402	D	0.000007	D	0.98861	0.9615	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	D	0.99585	1.0974	10	0.87932	D	0	.	19.3504	0.94381	0.0:1.0:0.0:0.0	.	28	P35498-2	.	H	28	ENSP00000407030:R28H;ENSP00000303540:R28H;ENSP00000364554:R28H;ENSP00000386312:R28H	ENSP00000303540:R28H	R	-	2	0	SCN1A	166638295	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.760000	0.85248	2.885000	0.99019	0.655000	0.94253	CGC	.	.	none		0.448	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
C19orf48	84798	hgsc.bcm.edu	37	19	51301456	51301456	+	Missense_Mutation	SNP	G	G	A	rs4802741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51301456G>A	ENST00000598463.1	-	5	1348	c.250C>T	c.(250-252)Cgc>Tgc	p.R84C	C19orf48_ENST00000595794.1_5'Flank|SNORD88A_ENST00000408314.1_RNA|C19orf48_ENST00000345523.4_Missense_Mutation_p.R84C|C19orf48_ENST00000596655.1_Missense_Mutation_p.R84C|C19orf48_ENST00000391812.1_Missense_Mutation_p.R84C|SNORD88B_ENST00000408454.1_RNA			Q6RUI8	CS048_HUMAN	chromosome 19 open reading frame 48	84			R -> C (in dbSNP:rs4802741).							endometrium(1)|kidney(1)|lung(1)|ovary(1)	4		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		TCACGGTGGCGTATGGACAGC	0.637													G|||	1652	0.329872	0.1309	0.2161	5008	,	,		19818	0.6538		0.3012	False		,,,				2504	0.3753				p.R84C		Atlas-SNP	.											.	C19orf48	11	.	0			c.C250T						PASS	.	G	CYS/ARG,CYS/ARG	682,3724		45,592,1566	110.0	100.0	103.0		250,250	0.9	0.0	19	dbSNP_111	103	2414,6186		350,1714,2236	yes	missense,missense	C19orf48	NM_199250.1,NM_199249.1	180,180	395,2306,3802	AA,AG,GG		28.0698,15.4789,23.8044	benign,benign	84/118,84/118	51301456	3096,9910	2203	4300	6503	SO:0001583	missense	84798	exon5			GGTGGCGTATGGA	BC037227	CCDS12803.1	19q13.33	2012-10-26			ENSG00000167747	ENSG00000167747			29667	protein-coding gene	gene with protein product	"""multidrug resistance-related protein"""					12452007	Standard	NM_001290154		Approved	MGC13170	uc002ptg.3	Q6RUI8		ENST00000598463.1:c.250C>T	19.37:g.51301456G>A	ENSP00000471463:p.Arg84Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	109	41	0.376147	NM_199249		Missense_Mutation	SNP	ENST00000598463.1	37	CCDS12803.1	769	0.35210622710622713	71	0.1443089430894309	80	0.22099447513812154	383	0.6695804195804196	235	0.3100263852242744	N	1.803	-0.476478	0.04414	0.154789	0.280698	ENSG00000167747	ENST00000391812;ENST00000345523	T;T	0.32023	1.47;1.47	1.92	0.845	0.18950	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.31779	-0.9931	8	0.44086	T	0.13	.	7.3421	0.26644	0.1625:0.0:0.8375:0.0	rs4802741;rs17657799;rs60128113;rs4802741	84	Q6RUI8	CS048_HUMAN	C	84	ENSP00000375688:R84C;ENSP00000301419:R84C	ENSP00000301419:R84C	R	-	1	0	C19orf48	55993268	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.160000	0.16462	-0.004000	0.14419	-1.786000	0.00637	CGC	G|0.713;A|0.287	0.287	strong		0.637	C19orf48-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464107.1	NM_032712	
ROBO4	54538	hgsc.bcm.edu	37	11	124756406	124756406	+	Silent	SNP	G	G	A	rs7104934	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124756406G>A	ENST00000306534.3	-	16	3233	c.2748C>T	c.(2746-2748)agC>agT	p.S916S	ROBO4_ENST00000533054.1_Silent_p.S771S|RP11-664I21.5_ENST00000524453.1_RNA	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	916					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		CGAAACCAAAGCTATCCACAG	0.582													G|||	1173	0.234225	0.4811	0.121	5008	,	,		17633	0.0883		0.163	False		,,,				2504	0.2045				p.S916S		Atlas-SNP	.											.	ROBO4	130	.	0			c.C2748T						PASS	.	G		1775,2627	507.9+/-366.8	350,1075,776	46.0	51.0	49.0		2748	3.8	1.0	11	dbSNP_116	49	1179,7419	230.4+/-264.8	78,1023,3198	no	coding-synonymous	ROBO4	NM_019055.5		428,2098,3974	AA,AG,GG		13.7125,40.3226,22.7231		916/1008	124756406	2954,10046	2201	4299	6500	SO:0001819	synonymous_variant	54538	exon16			ACCAAAGCTATCC	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.2748C>T	11.37:g.124756406G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	151	72	0.476821	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			G|0.783;A|0.217	0.217	strong		0.582	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
DOPEY2	9980	hgsc.bcm.edu	37	21	37617986	37617986	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:37617986C>T	ENST00000399151.3	+	19	3793	c.3708C>T	c.(3706-3708)gaC>gaT	p.D1236D		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1236					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						AGCCCTACGACTCTCGGCGGG	0.582																																					p.D1236D		Atlas-SNP	.											DOPEY2,NS,carcinoma,+2,1	DOPEY2	184	1	0			c.C3708T						scavenged	.						63.0	60.0	61.0					21																	37617986		2203	4300	6503	SO:0001819	synonymous_variant	9980	exon19			CTACGACTCTCGG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.3708C>T	21.37:g.37617986C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	106	2	0.0188679	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	37	CCDS13643.1																																																																																			.	.	none		0.582	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
CLDN14	23562	hgsc.bcm.edu	37	21	37833751	37833751	+	Silent	SNP	G	G	A	rs219779	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:37833751G>A	ENST00000399137.1	-	3	1109	c.243C>T	c.(241-243)cgC>cgT	p.R81R	CLDN14_ENST00000342108.2_Silent_p.R81R|AP000695.4_ENST00000454980.1_RNA|CLDN14_ENST00000399135.1_Silent_p.R81R|AP000695.4_ENST00000428667.1_RNA|CLDN14_ENST00000399136.1_Silent_p.R81R|CLDN14_ENST00000399139.1_Silent_p.R81R|AP000695.6_ENST00000429588.1_RNA	NM_144492.2	NP_652763.1	O95500	CLD14_HUMAN	claudin 14	81			R -> H (in DFNB29). {ECO:0000269|PubMed:22246673, ECO:0000269|PubMed:23235333}.		calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein complex assembly (GO:0006461)|tight junction assembly (GO:0070830)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|lung(5)|skin(1)	7						CCATGAGGGCGCGGGCAGCCT	0.652													A|||	952	0.190096	0.3086	0.2248	5008	,	,		19260	0.006		0.2485	False		,,,				2504	0.135				p.R81R		Atlas-SNP	.											.	CLDN14	25	.	0			c.C243T						PASS	.	A	,,,,	1380,3026	666.6+/-401.7	204,972,1027	51.0	41.0	45.0		243,243,243,243,243	-8.8	0.4	21	dbSNP_79	45	2213,6387	690.9+/-404.5	304,1605,2391	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLDN14	NM_001146077.1,NM_001146078.1,NM_001146079.1,NM_012130.2,NM_144492.2	,,,,	508,2577,3418	AA,AG,GG		25.7326,31.3209,27.6257	,,,,	81/240,81/240,81/240,81/240,81/240	37833751	3593,9413	2203	4300	6503	SO:0001819	synonymous_variant	23562	exon3			GAGGGCGCGGGCA	AJ132445	CCDS13645.1	21q22.3	2008-07-31			ENSG00000159261	ENSG00000159261		"""Claudins"""	2035	protein-coding gene	gene with protein product		605608		DFNB29		11163249	Standard	NM_144492		Approved		uc002yvk.2	O95500	OTTHUMG00000086638	ENST00000399137.1:c.243C>T	21.37:g.37833751G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_144492		Silent	SNP	ENST00000399137.1	37	CCDS13645.1																																																																																			G|0.759;A|0.241	0.241	strong		0.652	CLDN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194697.1	NM_144492	
NOTCH4	4855	hgsc.bcm.edu	37	6	32188642	32188642	+	Silent	SNP	T	T	C	rs520688|rs71556915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32188642T>C	ENST00000375023.3	-	5	951	c.813A>G	c.(811-813)ccA>ccG	p.P271P		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	271	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CCTCACAGTCTGGGCCTATGA	0.607													C|||	1403	0.280152	0.2095	0.2594	5008	,	,		18868	0.2421		0.3519	False		,,,				2504	0.3558				p.P271P		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A813G						PASS	.	C		939,3467	734.4+/-410.6	91,757,1355	94.0	85.0	88.0		813	-2.0	0.0	6	dbSNP_83	88	2747,5853	677.2+/-403.4	449,1849,2002	no	coding-synonymous	NOTCH4	NM_004557.3		540,2606,3357	CC,CT,TT		31.9419,21.3118,28.3408		271/2004	32188642	3686,9320	2203	4300	6503	SO:0001819	synonymous_variant	4855	exon5			ACAGTCTGGGCCT		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.813A>G	6.37:g.32188642T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			T|0.705;C|0.295	0.295	strong		0.607	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
EN1	2019	hgsc.bcm.edu	37	2	119604255	119604255	+	Silent	SNP	C	C	T	rs79126103	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:119604255C>T	ENST00000295206.6	-	1	999	c.489G>A	c.(487-489)gcG>gcA	p.A163A	EN1_ENST00000546667.1_5'Flank	NM_001426.3	NP_001417.3	Q05925	HME1_HUMAN	engrailed homeobox 1	163					anatomical structure morphogenesis (GO:0009653)|dorsal/ventral pattern formation (GO:0009953)|embryonic forelimb morphogenesis (GO:0035115)|hindbrain development (GO:0030902)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|multicellular organism growth (GO:0035264)|neuron development (GO:0048666)|pigmentation (GO:0043473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|response to cocaine (GO:0042220)|skeletal system development (GO:0001501)	membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	9						CAGCGCCTGGCGCCCGGGTGC	0.751													C|||	316	0.063099	0.028	0.183	5008	,	,		4825	0.0397		0.0497	False		,,,				2504	0.0634				p.A163A		Atlas-SNP	.											EN1,NS,carcinoma,0,1	EN1	33	1	0			c.G489A						PASS	.	C		98,4216		3,92,2062	10.0	13.0	12.0		489	-0.6	0.4	2	dbSNP_131	12	416,8046		6,404,3821	no	coding-synonymous	EN1	NM_001426.3		9,496,5883	TT,TC,CC		4.9161,2.2717,4.0232		163/393	119604255	514,12262	2157	4231	6388	SO:0001819	synonymous_variant	2019	exon1			GCCTGGCGCCCGG	L12699	CCDS2123.1	2q14.2	2011-06-20	2007-02-15		ENSG00000163064	ENSG00000163064		"""Homeoboxes / ANTP class : NKL subclass"""	3342	protein-coding gene	gene with protein product		131290				8094370	Standard	NM_001426		Approved		uc002tlm.3	Q05925	OTTHUMG00000131401	ENST00000295206.6:c.489G>A	2.37:g.119604255C>T		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001426	Q4ZG44	Silent	SNP	ENST00000295206.6	37	CCDS2123.1																																																																																			C|0.935;T|0.065	0.065	strong		0.751	EN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254191.3		
DNMBP	23268	hgsc.bcm.edu	37	10	101657880	101657880	+	Silent	SNP	G	G	A	rs7919323	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:101657880G>A	ENST00000324109.4	-	9	2974	c.2883C>T	c.(2881-2883)aaC>aaT	p.N961N	DNMBP_ENST00000540316.1_De_novo_Start_OutOfFrame|DNMBP_ENST00000342239.3_Silent_p.N961N|DNMBP_ENST00000543621.1_Silent_p.N207N	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	961	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TAATGTTAACGTTGATTTCCT	0.433													G|||	1375	0.274561	0.1589	0.3256	5008	,	,		17198	0.2183		0.3946	False		,,,				2504	0.3292				p.N961N		Atlas-SNP	.											.	DNMBP	173	.	0			c.C2883T						PASS	.			890,3516	345.4+/-308.5	84,722,1397	130.0	114.0	119.0		2883	-4.9	0.9	10	dbSNP_116	119	3322,5278	495.3+/-374.0	654,2014,1632	no	coding-synonymous	DNMBP	NM_015221.2		738,2736,3029	AA,AG,GG		38.6279,20.1997,32.3851		961/1578	101657880	4212,8794	2203	4300	6503	SO:0001819	synonymous_variant	23268	exon9			GTTAACGTTGATT	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.2883C>T	10.37:g.101657880G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	85	77	0.905882	NM_015221	Q8IVY3|Q9Y2L3	Silent	SNP	ENST00000324109.4	37	CCDS7485.1																																																																																			G|0.689;A|0.311	0.311	strong		0.433	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
RPUSD4	84881	hgsc.bcm.edu	37	11	126081403	126081403	+	Missense_Mutation	SNP	T	T	C	rs2282580	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:126081403T>C	ENST00000298317.4	-	1	184	c.131A>G	c.(130-132)cAg>cGg	p.Q44R	FAM118B_ENST00000360194.4_5'Flank|RNU4-86P_ENST00000410135.1_RNA|FAM118B_ENST00000529731.1_5'Flank|RPUSD4_ENST00000534393.1_5'Flank|RPUSD4_ENST00000533628.1_Missense_Mutation_p.Q44R|RP11-50B3.4_ENST00000532866.1_RNA|FAM118B_ENST00000533050.1_5'UTR	NM_032795.2	NP_116184.2	Q96CM3	RUSD4_HUMAN	RNA pseudouridylate synthase domain containing 4	44			Q -> R (in dbSNP:rs2282580). {ECO:0000269|PubMed:14702039}.		pseudouridine synthesis (GO:0001522)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0761)		CGCTAATCTCTGGGCATTTAT	0.582													T|||	2400	0.479233	0.2534	0.5576	5008	,	,		16167	0.8175		0.338	False		,,,				2504	0.5256				p.Q44R		Atlas-SNP	.											.	RPUSD4	36	.	0			c.A131G						PASS	.	T	ARG/GLN,ARG/GLN	1178,3224	413.0+/-336.3	162,854,1185	138.0	147.0	144.0		131,131	5.3	0.4	11	dbSNP_100	144	2674,5924	430.0+/-356.4	429,1816,2054	yes	missense,missense	RPUSD4	NM_001144827.1,NM_032795.2	43,43	591,2670,3239	CC,CT,TT		31.1003,26.7606,29.6308	probably-damaging,probably-damaging	44/347,44/378	126081403	3852,9148	2201	4299	6500	SO:0001583	missense	84881	exon1			AATCTCTGGGCAT	BC014131	CCDS8469.1, CCDS53721.1	11q24.2	2013-02-11			ENSG00000165526	ENSG00000165526		"""RNA pseudouridylate synthase domain containing"""	25898	protein-coding gene	gene with protein product							Standard	NM_032795		Approved	FLJ14494	uc001qde.3	Q96CM3	OTTHUMG00000165815	ENST00000298317.4:c.131A>G	11.37:g.126081403T>C	ENSP00000298317:p.Gln44Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_001144827	E9PML2|Q96K56	Missense_Mutation	SNP	ENST00000298317.4	37	CCDS8469.1	1044	0.47802197802197804	135	0.27439024390243905	184	0.5082872928176796	472	0.8251748251748252	253	0.3337730870712401	T	12.23	1.874132	0.33069	0.267606	0.311003	ENSG00000165526	ENST00000298317;ENST00000533628;ENST00000532674	T;T;T	0.41400	2.89;2.71;1.0	5.31	5.31	0.75309	.	0.524166	0.20250	N	0.096111	T	0.00012	0.0000	M	0.75447	2.3	0.09310	P	0.9999999999999989	P;P	0.45126	0.851;0.851	B;B	0.40165	0.321;0.253	T	0.27839	-1.0062	9	0.07325	T	0.83	-33.2137	11.581	0.50891	0.0:0.0:0.0:1.0	rs2282580;rs17803480;rs57431655;rs2282580	44;44	E9PML2;Q96CM3	.;RUSD4_HUMAN	R	44	ENSP00000298317:Q44R;ENSP00000433065:Q44R;ENSP00000433709:Q44R	ENSP00000298317:Q44R	Q	-	2	0	RPUSD4	125586613	0.992000	0.36948	0.370000	0.25965	0.024000	0.10985	2.462000	0.45049	2.224000	0.72417	0.528000	0.53228	CAG	T|0.608;C|0.392	0.392	strong		0.582	RPUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386336.1	NM_032795	
BTK	695	hgsc.bcm.edu	37	X	100612565	100612565	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:100612565A>G	ENST00000308731.7	-	13	1272	c.1109T>C	c.(1108-1110)aTa>aCa	p.I370T	BTK_ENST00000372880.1_Intron	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	370	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		I -> M (in XLA). {ECO:0000269|PubMed:7711734}.		adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)			breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						GAGCCTGGATATGAGTCCTGA	0.498									Agammaglobulinemia, X-linked																												p.I370T		Atlas-SNP	.											.	BTK	87	.	0			c.T1109C						PASS	.						304.0	239.0	261.0					X																	100612565		2203	4300	6503	SO:0001583	missense	695	exon13	Familial Cancer Database	Bruton Type Agammaglobulinemia	CTGGATATGAGTC	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.1109T>C	X.37:g.100612565A>G	ENSP00000308176:p.Ile370Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	150	140	0.933333	NM_000061	B2RAW1|Q32ML5	Missense_Mutation	SNP	ENST00000308731.7	37	CCDS14482.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.962940	0.53507	.	.	ENSG00000010671	ENST00000372855;ENST00000372859;ENST00000372860;ENST00000395179;ENST00000372869;ENST00000443591;ENST00000308731	D	0.92647	-3.08	5.76	5.76	0.90799	SH2 motif (2);	0.046830	0.85682	D	0.000000	D	0.88941	0.6574	L	0.42008	1.315	0.54753	D	0.999988	B;P;P	0.44734	0.227;0.645;0.842	B;B;B	0.39419	0.114;0.299;0.185	D	0.89837	0.4000	10	0.66056	D	0.02	.	14.7456	0.69488	1.0:0.0:0.0:0.0	.	41;370;370	Q3MS94;B2RAW1;Q06187	.;.;BTK_HUMAN	T	41;41;39;41;41;41;370	ENSP00000308176:I370T	ENSP00000308176:I370T	I	-	2	0	BTK	100499221	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.664000	0.83830	1.943000	0.56356	0.483000	0.47432	ATA	.	.	none		0.498	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061	
OBP2A	29991	hgsc.bcm.edu	37	9	138439806	138439806	+	Missense_Mutation	SNP	C	C	T	rs72766543	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:138439806C>T	ENST00000539850.1	+	4	393	c.367C>T	c.(367-369)Cgc>Tgc	p.R123C	OBP2A_ENST00000342114.4_Missense_Mutation_p.A78V|OBP2A_ENST00000371776.1_Missense_Mutation_p.R123C|OBP2A_ENST00000340780.3_Missense_Mutation_p.R123C			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	123					response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		TGGGGGCCTGCGCTACATGGG	0.617													.|||	734	0.146565	0.0303	0.1326	5008	,	,		16953	0.1567		0.2515	False		,,,				2504	0.1953				p.R123C		Atlas-SNP	.											OBP2A,NS,carcinoma,-1,1	OBP2A	21	1	0			c.C367T						PASS	.	C	CYS/ARG	288,4118	155.5+/-188.7	18,252,1933	43.0	39.0	40.0		367	-2.1	0.0	9	dbSNP_130	40	2254,6346	376.8+/-338.3	302,1650,2348	yes	missense	OBP2A	NM_014582.2	180	320,1902,4281	TT,TC,CC		26.2093,6.5365,19.5448	benign	123/171	138439806	2542,10464	2203	4300	6503	SO:0001583	missense	29991	exon4			GGCCTGCGCTACA	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.367C>T	9.37:g.138439806C>T	ENSP00000441028:p.Arg123Cys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	99	56	0.565657	NM_014582	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Missense_Mutation	SNP	ENST00000539850.1	37	CCDS6992.1	352|352	0.16117216117216118|0.16117216117216118	17|17	0.034552845528455285|0.034552845528455285	60|60	0.16574585635359115|0.16574585635359115	82|82	0.14335664335664336|0.14335664335664336	193|193	0.2546174142480211|0.2546174142480211	c|c	6.857|6.857	0.527344|0.527344	0.13066|0.13066	0.065365|0.065365	0.262093|0.262093	ENSG00000122136|ENSG00000122136	ENST00000342114|ENST00000340780;ENST00000371776;ENST00000539850	T|T;T;T	0.09073|0.11821	3.02|2.74;2.97;2.97	2.25|2.25	-2.08|-2.08	0.07254|0.07254	.|Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.|1.620130	.|0.03800	.|N	.|0.264331	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|P;P	0.02656|0.48911	0.0|0.832;0.917	B|B;B	0.01281|0.39738	0.0|0.308;0.109	T|T	0.21793|0.21793	-1.0235|-1.0235	8|9	0.45353|0.30854	T|T	0.12|0.27	-12.4885|-12.4885	2.1381|2.1381	0.03768|0.03768	0.2454:0.3235:0.0:0.4311|0.2454:0.3235:0.0:0.4311	.|.	78|123;123	Q5T8A4|Q5T8A5;Q9NY56	.|.;OBP2A_HUMAN	V|C	78|123	ENSP00000340950:A78V|ENSP00000342097:R123C;ENSP00000360841:R123C;ENSP00000441028:R123C	ENSP00000340950:A78V|ENSP00000342097:R123C	A|R	+|+	2|1	0|0	OBP2A|OBP2A	137579627|137579627	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-3.799000|-3.799000	0.00363|0.00363	-0.438000|-0.438000	0.07232|0.07232	-0.537000|-0.537000	0.04273|0.04273	GCG|CGC	C|0.813;T|0.187	0.187	strong		0.617	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582	
TTLL3	26140	hgsc.bcm.edu	37	3	9874914	9874914	+	Nonsense_Mutation	SNP	C	C	T	rs115917139	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9874914C>T	ENST00000547186.1	+	11	1897	c.1681C>T	c.(1681-1683)Cga>Tga	p.R561*	TTLL3_ENST00000430793.1_Nonsense_Mutation_p.R349*|ARPC4-TTLL3_ENST00000397256.1_Intron|TTLL3_ENST00000397241.1_Intron|TTLL3_ENST00000427853.3_Intron|TTLL3_ENST00000383827.1_Intron|TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000426895.4_Nonsense_Mutation_p.R704*	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	561					axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					GCTGACCCAGCGAGGCTCTGG	0.647													C|||	115	0.0229633	0.0	0.0231	5008	,	,		16546	0.001		0.0408	False		,,,				2504	0.0583				p.R704X		Atlas-SNP	.											.	TTLL3	51	.	0			c.C2110T						PASS	.	C	stop/ARG,	28,3784		0,28,1878	29.0	31.0	30.0		2110,	3.6	0.3	3	dbSNP_132	30	360,7860		10,340,3760	yes	stop-gained,intron	TTLL3,ARPC4-TTLL3	NM_001025930.3,NM_001198793.1	,	10,368,5638	TT,TC,CC		4.3796,0.7345,3.2247	,	704/916,	9874914	388,11644	1906	4110	6016	SO:0001587	stop_gained	26140	exon11			ACCCAGCGAGGCT		CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"""Tubulin tyrosine ligase-like family"""	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.1681C>T	3.37:g.9874914C>T	ENSP00000446659:p.Arg561*	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Nonsense_Mutation	SNP	ENST00000547186.1	37		43	0.019688644688644688	0	0.0	11	0.03038674033149171	0	0.0	32	0.04221635883905013	C	38	6.974468	0.97975	0.007345	0.043796	ENSG00000214021	ENST00000426895;ENST00000547186;ENST00000443148;ENST00000430793	.	.	.	5.39	3.58	0.41010	.	0.000000	0.27782	U	0.017874	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6056	0.33771	0.3092:0.5413:0.1495:0.0	rs3208837;rs17407417	.	.	.	X	704;561;499;349	.	ENSP00000392549:R704X	R	+	1	2	TTLL3	9849914	0.009000	0.17119	0.270000	0.24601	0.659000	0.38960	0.677000	0.25262	0.639000	0.30564	-0.152000	0.13540	CGA	C|0.975;T|0.025	0.025	strong		0.647	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2	
CSRNP3	80034	hgsc.bcm.edu	37	2	166535918	166535918	+	Silent	SNP	C	C	T	rs777346	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:166535918C>T	ENST00000342316.4	+	5	1685	c.1413C>T	c.(1411-1413)acC>acT	p.T471T	CSRNP3_ENST00000314499.7_Silent_p.T471T|CSRNP3_ENST00000409420.1_Silent_p.T503T	NM_024969.3	NP_079245.2	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	471					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						TGCCTTACACCATGACCCCGG	0.493													T|||	1849	0.369209	0.3434	0.3098	5008	,	,		17599	0.372		0.496	False		,,,				2504	0.3129				p.T471T		Atlas-SNP	.											.	CSRNP3	73	.	0			c.C1413T						PASS	.	T	,	1650,2756	658.7+/-400.4	295,1060,848	74.0	70.0	72.0		1413,1413	4.1	1.0	2	dbSNP_86	72	4191,4409	586.0+/-392.0	1025,2141,1134	no	coding-synonymous,coding-synonymous	CSRNP3	NM_001172173.1,NM_024969.3	,	1320,3201,1982	TT,TC,CC		48.7326,37.4489,44.91	,	471/586,471/586	166535918	5841,7165	2203	4300	6503	SO:0001819	synonymous_variant	80034	exon7			TTACACCATGACC	AB063300	CCDS2225.1	2q24.3	2012-04-17	2009-01-07	2009-01-07	ENSG00000178662	ENSG00000178662		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30729	protein-coding gene	gene with protein product	"""TGF beta induced apotosis protein 2"", ""protein phosphatase 1, regulatory subunit 73"""		"""family with sequence similarity 130, member A2"""	FAM130A2		17726538	Standard	NM_024969		Approved	FLJ32093, TAIP-2, PPP1R73	uc002udg.3	Q8WYN3	OTTHUMG00000132145	ENST00000342316.4:c.1413C>T	2.37:g.166535918C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_001172173	B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9	Silent	SNP	ENST00000342316.4	37	CCDS2225.1																																																																																			C|0.583;T|0.417	0.417	strong		0.493	CSRNP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255191.2	NM_024969	
ZNF28	7576	hgsc.bcm.edu	37	19	53304563	53304563	+	Missense_Mutation	SNP	T	T	C	rs13382164	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53304563T>C	ENST00000457749.2	-	4	654	c.535A>G	c.(535-537)Aga>Gga	p.R179G	ZNF28_ENST00000414252.2_Missense_Mutation_p.R126G|ZNF28_ENST00000360272.4_Missense_Mutation_p.R126G|ZNF28_ENST00000438150.2_Missense_Mutation_p.R126G	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	179			R -> G (in dbSNP:rs13382164).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		CAACAAATTCTTTGGGATGTT	0.378													-|||	1928	0.384984	0.2882	0.1873	5008	,	,		20926	0.7302		0.3082	False		,,,				2504	0.3793				p.R179G		Atlas-SNP	.											.	ZNF28	191	.	0			c.A535G						PASS	.	T	GLY/ARG	1192,3212		162,868,1172	119.0	131.0	127.0		535	1.8	0.0	19	dbSNP_121	127	2450,6134		352,1746,2194	no	missense	ZNF28	NM_006969.3	125	514,2614,3366	CC,CT,TT		28.5415,27.0663,28.0413	benign	179/719	53304563	3642,9346	2202	4292	6494	SO:0001583	missense	7576	exon4			AAATTCTTTGGGA	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"""Zinc fingers, C2H2-type"", ""-"""	13073	protein-coding gene	gene with protein product			"""zinc finger protein 28 (KOX 24)"""				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.535A>G	19.37:g.53304563T>C	ENSP00000397693:p.Arg179Gly	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	136	44	0.323529	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	37	CCDS33093.2	855	0.3914835164835165	144	0.2926829268292683	75	0.20718232044198895	398	0.6958041958041958	238	0.31398416886543534	-	12.51	1.959462	0.34565	0.270663	0.285415	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.09817	2.94;3.1;2.94;2.94;3.02	1.81	1.81	0.25067	.	.	.	.	.	T	0.00012	0.0000	M	0.81614	2.55	0.80722	P	0.0	P	0.38978	0.652	B	0.30855	0.121	T	0.18085	-1.0348	8	0.62326	D	0.03	.	7.2865	0.26342	0.0:0.0:0.0:1.0	rs13382164;rs60960175;rs13382164	179	P17035	ZNF28_HUMAN	G	126;179;126;126;126	ENSP00000412143:R126G;ENSP00000397693:R179G;ENSP00000353410:R126G;ENSP00000444965:R126G;ENSP00000375661:R126G	ENSP00000353410:R126G	R	-	1	2	ZNF28	57996375	0.000000	0.05858	0.003000	0.11579	0.016000	0.09150	-0.097000	0.11042	0.825000	0.34637	0.248000	0.18094	AGA	T|0.682;C|0.318	0.318	strong		0.378	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969	
TSC2	7249	hgsc.bcm.edu	37	16	2125834	2125834	+	Silent	SNP	T	T	C	rs13337626	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2125834T>C	ENST00000219476.3	+	23	3210	c.2580T>C	c.(2578-2580)ttT>ttC	p.F860F	TSC2_ENST00000401874.2_Silent_p.F860F|TSC2_ENST00000568454.1_Silent_p.F871F|TSC2_ENST00000353929.4_Silent_p.F860F|TSC2_ENST00000382538.6_Silent_p.F811F|TSC2_ENST00000439673.2_Silent_p.F823F|TSC2_ENST00000350773.4_Silent_p.F860F	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	860					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				ACAGGAACTTTGCCGCGGAGC	0.667			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				T|||	314	0.0626997	0.093	0.0418	5008	,	,		15856	0.002		0.0875	False		,,,				2504	0.0736				p.F860F		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	.	TSC2	364	.	0			c.T2580C						PASS	.	T	,,	381,4015	191.9+/-217.4	16,349,1833	82.0	62.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2580,2580,2580	-9.9	0.1	16	dbSNP_121	69	740,7860	176.9+/-226.6	26,688,3586	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	,,	42,1037,5419	CC,CT,TT		8.6047,8.667,8.6257	,,	860/1808,860/1741,860/1785	2125834	1121,11875	2198	4300	6498	SO:0001819	synonymous_variant	7249	exon23	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GAACTTTGCCGCG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.2580T>C	16.37:g.2125834T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	113	48	0.424779	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																			T|0.921;C|0.079	0.079	strong		0.667	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
PDE1C	5137	hgsc.bcm.edu	37	7	32209524	32209524	+	Missense_Mutation	SNP	G	G	C	rs377587504		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:32209524G>C	ENST00000396193.1	-	3	774	c.181C>G	c.(181-183)Ctc>Gtc	p.L61V		NM_001191058.1	NP_001177987.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	0					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	TTCCCTGTGAGCCCATCGATG	0.522																																					p.L61V		Atlas-SNP	.											.	PDE1C	465	.	0			c.C181G						PASS	.						263.0	223.0	235.0					7																	32209524		876	1991	2867	SO:0001583	missense	5137	exon3			CTGTGAGCCCATC	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396193.1:c.181C>G	7.37:g.32209524G>C	ENSP00000379496:p.Leu61Val	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	204	104	0.509804	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396193.1	37	CCDS55100.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.717510	0.68844	.	.	ENSG00000154678	ENST00000396193	T	0.77489	-1.1	5.75	4.88	0.63580	.	.	.	.	.	T	0.64294	0.2585	N	0.14661	0.345	0.80722	D	1	B	0.25667	0.131	B	0.21546	0.035	T	0.63945	-0.6522	9	0.72032	D	0.01	.	14.3935	0.66996	0.0714:0.0:0.9286:0.0	.	61	E9PE92	.	V	61	ENSP00000379496:L61V	ENSP00000379496:L61V	L	-	1	0	PDE1C	32176049	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	3.073000	0.50057	1.456000	0.47831	0.655000	0.94253	CTC	.	.	weak		0.522	PDE1C-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215075.1		
FBXW9	84261	hgsc.bcm.edu	37	19	12802009	12802009	+	Missense_Mutation	SNP	T	T	C	rs143596846	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12802009T>C	ENST00000380339.3	-	5	890	c.854A>G	c.(853-855)gAc>gGc	p.D285G	FBXW9_ENST00000587955.1_Missense_Mutation_p.D275G|FBXW9_ENST00000393261.3_Missense_Mutation_p.D285G|FBXW9_ENST00000544494.1_Missense_Mutation_p.D23G|CTD-2659N19.2_ENST00000585742.1_RNA			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	285					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CACCTTCTTGTCATAGGTGCC	0.607													T|||	2	0.000399361	0.0	0.0	5008	,	,		18570	0.0		0.002	False		,,,				2504	0.0				p.D285G		Atlas-SNP	.											.	FBXW9	30	.	0			c.A854G						PASS	.	T	GLY/ASP	1,4145		0,1,2072	127.0	128.0	127.0		854	4.7	1.0	19	dbSNP_134	127	16,8394		0,16,4189	yes	missense	FBXW9	NM_032301.2	94	0,17,6261	CC,CT,TT		0.1902,0.0241,0.1354	probably-damaging	285/459	12802009	17,12539	2073	4205	6278	SO:0001583	missense	84261	exon5			TTCTTGTCATAGG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.854A>G	19.37:g.12802009T>C	ENSP00000369696:p.Asp285Gly	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	19.32	3.804178	0.70682	2.41E-4	0.001902	ENSG00000132004	ENST00000544494;ENST00000393261;ENST00000380339	D;T;T	0.89270	-2.49;1.07;1.07	4.66	4.66	0.58398	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.90665	0.7072	L	0.32530	0.975	0.58432	D	0.999997	D;P;D	0.89917	1.0;0.872;0.999	D;P;D	0.81914	0.995;0.759;0.96	D	0.91740	0.5403	10	0.87932	D	0	-31.5318	13.2197	0.59881	0.0:0.0:0.0:1.0	.	275;285;285	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	G	23;285;285	ENSP00000442714:D23G;ENSP00000376945:D285G;ENSP00000369696:D285G	ENSP00000369696:D285G	D	-	2	0	FBXW9	12663009	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	6.197000	0.72100	1.957000	0.56846	0.379000	0.24179	GAC	T|0.999;C|0.001	0.001	strong		0.607	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
ZNF860	344787	hgsc.bcm.edu	37	3	32031615	32031615	+	Missense_Mutation	SNP	A	A	C	rs13064905	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:32031615A>C	ENST00000360311.4	+	2	1593	c.1044A>C	c.(1042-1044)gaA>gaC	p.E348D		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	348					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						AGGTTTGTGAAAAGGCTTTCA	0.393													C|||	2356	0.470447	0.7988	0.3602	5008	,	,		21648	0.4524		0.1968	False		,,,				2504	0.4049				p.E348D		Atlas-SNP	.											.	ZNF860	96	.	0			c.A1044C						PASS	.						45.0	47.0	46.0					3																	32031615		692	1591	2283	SO:0001583	missense	344787	exon2			TTGTGAAAAGGCT	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1044A>C	3.37:g.32031615A>C	ENSP00000373274:p.Glu348Asp	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	252	80	0.31746	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	911	0.41712454212454214	385	0.782520325203252	126	0.34806629834254144	248	0.43356643356643354	152	0.20052770448548812	C	3.265	-0.150374	0.06585	.	.	ENSG00000197385	ENST00000360311	T	0.01185	5.21	0.345	0.345	0.16011	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04148	-0.265	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02411	-1.1163	7	.	.	.	.	2.5267	0.04693	0.3212:0.3574:0.3213:0.0	rs13064905;rs61529855;rs13064905	348	A6NHJ4	ZN860_HUMAN	D	348	ENSP00000373274:E348D	.	E	+	3	2	ZNF860	32006619	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	-1.684000	0.01932	-0.518000	0.06452	-0.525000	0.04345	GAA	A|0.614;C|0.386	0.386	strong		0.393	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
IRF6	3664	hgsc.bcm.edu	37	1	209968684	209968684	+	Silent	SNP	C	C	A	rs2013162	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:209968684C>A	ENST00000367021.3	-	5	631	c.459G>T	c.(457-459)tcG>tcT	p.S153S	IRF6_ENST00000542854.1_Silent_p.S58S	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	153					cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		CATGGTGCTGCGACTGATCCA	0.502										HNSCC(57;0.16)			C|||	2022	0.403754	0.2428	0.4769	5008	,	,		23317	0.5843		0.3608	False		,,,				2504	0.4274				p.S153S		Atlas-SNP	.											.	IRF6	65	.	0			c.G459T						PASS	.	C	,	1284,3122	438.0+/-345.2	192,900,1111	341.0	247.0	279.0		174,459	-6.4	1.0	1	dbSNP_92	279	3169,5431	480.4+/-370.4	576,2017,1707	no	coding-synonymous,coding-synonymous	IRF6	NM_001206696.1,NM_006147.3	,	768,2917,2818	AA,AC,CC		36.8488,29.1421,34.238	,	58/373,153/468	209968684	4453,8553	2203	4300	6503	SO:0001819	synonymous_variant	3664	exon5			GTGCTGCGACTGA	AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595			6121	protein-coding gene	gene with protein product		607199	"""Van der Woude syndrome"""	VWS, LPS		12219090	Standard	NM_006147		Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.459G>T	1.37:g.209968684C>A		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_006147	B4DLE2|D3DT90|F5GWX8|G0ZTL0	Silent	SNP	ENST00000367021.3	37	CCDS1492.1																																																																																			C|0.631;A|0.369	0.369	strong		0.502	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088827.1	NM_006147	
REEP4	80346	hgsc.bcm.edu	37	8	21996453	21996453	+	Missense_Mutation	SNP	C	C	T	rs79793560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21996453C>T	ENST00000306306.3	-	6	1007	c.539G>A	c.(538-540)cGg>cAg	p.R180Q	REEP4_ENST00000334530.5_Intron|REEP4_ENST00000523293.1_Missense_Mutation_p.R180Q	NM_025232.2	NP_079508.2	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	180					mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|nuclear envelope organization (GO:0006998)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)	microtubule binding (GO:0008017)			kidney(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	7				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)		GGGTGGCCTCCGGTGGGACAC	0.652													C|||	46	0.0091853	0.0053	0.0187	5008	,	,		17285	0.002		0.0209	False		,,,				2504	0.0031				p.R180Q		Atlas-SNP	.											.	REEP4	13	.	0			c.G539A						PASS	.	C	GLN/ARG	24,4382		0,24,2179	25.0	26.0	26.0		539	1.9	0.1	8	dbSNP_131	26	158,8430		1,156,4137	yes	missense	REEP4	NM_025232.2	43	1,180,6316	TT,TC,CC		1.8398,0.5447,1.4006	benign	180/258	21996453	182,12812	2203	4294	6497	SO:0001583	missense	80346	exon6			GGCCTCCGGTGGG	BC013048	CCDS6024.1	8p21.3	2008-05-02	2006-02-07	2006-02-07	ENSG00000168476	ENSG00000168476		"""Receptor accessory proteins"""	26176	protein-coding gene	gene with protein product		609349	"""chromosome 8 open reading frame 20"""	C8orf20		16271481, 15550249	Standard	NM_025232		Approved	FLJ22246, FLJ22277, PP432	uc003xau.1	Q9H6H4	OTTHUMG00000131491	ENST00000306306.3:c.539G>A	8.37:g.21996453C>T	ENSP00000303482:p.Arg180Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	116	64	0.551724	NM_025232	D3DSQ9|Q86VL1|Q9H6I5|Q9HBP4	Missense_Mutation	SNP	ENST00000306306.3	37	CCDS6024.1	29	0.013278388278388278	5	0.01016260162601626	8	0.022099447513812154	2	0.0034965034965034965	14	0.018469656992084433	C	3.815	-0.038862	0.07497	0.005447	0.018398	ENSG00000168476	ENST00000306306;ENST00000523293;ENST00000518664	D;D;D	0.89617	-1.7;-2.39;-2.54	4.86	1.92	0.25849	.	0.768004	0.11073	N	0.602648	T	0.62405	0.2425	N	0.14661	0.345	0.29351	N	0.865351	B	0.10296	0.003	B	0.04013	0.001	T	0.57871	-0.7736	10	0.13853	T	0.58	-14.4627	6.2242	0.20698	0.0:0.6692:0.1536:0.1772	.	180	Q9H6H4	REEP4_HUMAN	Q	180	ENSP00000303482:R180Q;ENSP00000428709:R180Q;ENSP00000428160:R180Q	ENSP00000303482:R180Q	R	-	2	0	REEP4	22052398	0.000000	0.05858	0.147000	0.22382	0.291000	0.27294	-0.823000	0.04443	0.481000	0.27557	-0.749000	0.03505	CGG	C|0.985;T|0.015	0.015	strong		0.652	REEP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254337.2	NM_025232	
WDR17	116966	hgsc.bcm.edu	37	4	177082069	177082069	+	Missense_Mutation	SNP	G	G	C	rs7693453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:177082069G>C	ENST00000280190.4	+	21	2894	c.2738G>C	c.(2737-2739)tGt>tCt	p.C913S	WDR17_ENST00000393643.2_Missense_Mutation_p.C889S|WDR17_ENST00000507824.2_Missense_Mutation_p.C896S|WDR17_ENST00000508596.1_Missense_Mutation_p.C889S			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	913			C -> S (in dbSNP:rs7693453). {ECO:0000269|PubMed:15489334}.							breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		TAGGCTGCTTGTGAAGGAAAT	0.308													G|||	962	0.192093	0.1422	0.1354	5008	,	,		18427	0.1677		0.2545	False		,,,				2504	0.2607				p.C913S		Atlas-SNP	.											.	WDR17	198	.	0			c.G2738C						PASS	.	G	SER/CYS,SER/CYS	720,3686	297.0+/-284.5	64,592,1547	99.0	96.0	97.0		2738,2666	2.8	1.0	4	dbSNP_116	97	2236,6364	378.1+/-338.8	282,1672,2346	yes	missense,missense	WDR17	NM_170710.4,NM_181265.3	112,112	346,2264,3893	CC,CG,GG		26.0,16.3414,22.728	benign,benign	913/1323,889/1284	177082069	2956,10050	2203	4300	6503	SO:0001583	missense	116966	exon21			CTGCTTGTGAAGG	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"""WD repeat domain containing"""	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.2738G>C	4.37:g.177082069G>C	ENSP00000280190:p.Cys913Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	88	28	0.318182	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	395|395	0.18086080586080586|0.18086080586080586	57|57	0.11585365853658537|0.11585365853658537	59|59	0.16298342541436464|0.16298342541436464	86|86	0.15034965034965034|0.15034965034965034	193|193	0.2546174142480211|0.2546174142480211	G|G	6.694|6.694	0.496597|0.496597	0.12762|0.12762	0.163414|0.163414	0.26|0.26	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.56444|.	0.5;0.52;0.46|.	4.58|4.58	2.79|2.79	0.32731|0.32731	.|.	0.055200|.	0.64402|.	D|.	0.000001|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.59436|0.59436	1.845|1.845	0.09310|0.09310	P|P	0.99999694807|0.99999694807	B;P;P|.	0.40681|.	0.381;0.727;0.727|.	B;B;B|.	0.33521|.	0.064;0.165;0.165|.	T|T	0.03898|0.03898	-1.0994|-1.0994	9|4	0.15952|.	T|.	0.53|.	-10.3871|-10.3871	13.5714|13.5714	0.61849|0.61849	0.0:0.0:0.7169:0.2831|0.0:0.0:0.7169:0.2831	rs7693453;rs7693453|rs7693453;rs7693453	889;889;913|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	S|F	889;889;913;896|155	ENSP00000422763:C889S;ENSP00000377258:C889S;ENSP00000280190:C913S|.	ENSP00000280190:C913S|.	C|L	+|+	2|3	0|2	WDR17|WDR17	177319063|177319063	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.854000|0.854000	0.48673|0.48673	4.116000|4.116000	0.57871|0.57871	0.619000|0.619000	0.30197|0.30197	-0.188000|-0.188000	0.12872|0.12872	TGT|TTG	G|0.793;C|0.207	0.207	strong		0.308	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
HLA-C	3107	hgsc.bcm.edu	37	6	31239802	31239802	+	Missense_Mutation	SNP	C	C	G	rs1050451	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239802C>G	ENST00000376228.5	-	1	61	c.47G>C	c.(46-48)gGc>gCc	p.G16A	HLA-C_ENST00000383329.3_Missense_Mutation_p.G16A	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	16					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CAGGGCCAGGCCTCCCGAGAG	0.706													g|||	3897	0.778155	0.7867	0.8184	5008	,	,		12807	0.8135		0.7266	False		,,,				2504	0.7546				p.G16A		Atlas-SNP	.											.	HLA-C	92	.	0			c.G47C						PASS	.	G	ALA/GLY	2287,731		872,543,94	17.0	19.0	18.0		47	0.9	0.1	6	dbSNP_86	18	3715,1703		1284,1147,278	no	missense	HLA-C	NM_002117.5	60	2156,1690,372	GG,GC,CC		31.4323,24.2213,28.8525	benign	16/367	31239802	6002,2434	1509	2709	4218	SO:0001583	missense	3107	exon1			GCCAGGCCTCCCG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.47G>C	6.37:g.31239802C>G	ENSP00000365402:p.Gly16Ala	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1633|1633	0.7477106227106227|0.7477106227106227	376|376	0.7642276422764228|0.7642276422764228	280|280	0.7734806629834254|0.7734806629834254	454|454	0.7937062937062938|0.7937062937062938	523|523	0.6899736147757256|0.6899736147757256	-|-	5.303|5.303	0.241362|0.241362	0.10077|0.10077	0.757787|0.757787	0.685677|0.685677	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00666|.	5.91;5.91|.	2.71|2.71	0.875|0.875	0.19130|0.19130	.|.	0.899764|.	0.08995|.	N|.	0.863853|.	T|T	0.12646|0.12646	0.0307|0.0307	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.001;0.0;0.001|.	T|T	0.22977|0.22977	-1.0201|-1.0201	8|3	0.02654|.	T|.	1|.	.|.	3.0934|3.0934	0.06301|0.06301	0.2825:0.2324:0.4851:0.0|0.2825:0.2324:0.4851:0.0	rs2308529;rs3177899;rs11547342|rs2308529;rs3177899;rs11547342	16;16;16;16|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	A|S	16|15	ENSP00000365402:G16A;ENSP00000372819:G16A|.	ENSP00000365402:G16A|.	G|R	-|-	2|3	0|2	HLA-C|HLA-C	31347781|31347781	0.012000|0.012000	0.17670|0.17670	0.115000|0.115000	0.21578|0.21578	0.010000|0.010000	0.07245|0.07245	-0.014000|-0.014000	0.12656|0.12656	-0.050000|-0.050000	0.13356|0.13356	-0.676000|-0.676000	0.03789|0.03789	GGC|AGG	G|0.730;C|0.270	0.730	strong		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
TTC7A	57217	hgsc.bcm.edu	37	2	47301029	47301029	+	Silent	SNP	A	A	G	rs3739099	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:47301029A>G	ENST00000319190.5	+	20	2912	c.2544A>G	c.(2542-2544)gtA>gtG	p.V848V	C2orf61_ENST00000464527.2_Intron|TTC7A_ENST00000394850.2_Silent_p.V872V|RP11-761B3.1_ENST00000422269.1_Intron|TTC7A_ENST00000263737.6_Silent_p.V494V|TTC7A_ENST00000409245.1_Silent_p.V814V|AC073283.7_ENST00000421759.1_RNA	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	848					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GCAGCCCTGTACTGCCCTTCT	0.687													G|||	1665	0.332468	0.3064	0.2507	5008	,	,		17841	0.6577		0.0885	False		,,,				2504	0.3415				p.V848V		Atlas-SNP	.											TTC7A,NS,carcinoma,0,1	TTC7A	80	1	0			c.A2544G						PASS	.	G		1221,3183	692.2+/-405.5	177,867,1158	41.0	35.0	37.0		2544	1.0	1.0	2	dbSNP_107	37	641,7959	780.6+/-407.7	30,581,3689	no	coding-synonymous	TTC7A	NM_020458.2		207,1448,4847	GG,GA,AA		7.4535,27.7248,14.3187		848/859	47301029	1862,11142	2202	4300	6502	SO:0001819	synonymous_variant	57217	exon20			CCCTGTACTGCCC	AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"""Tetratricopeptide (TTC) repeat domain containing"""	19750	protein-coding gene	gene with protein product		609332	"""tetratricopeptide repeat domain 7"""	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.2544A>G	2.37:g.47301029A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	267	114	0.426966	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																			A|0.774;G|0.226	0.226	strong		0.687	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
CBR3	874	hgsc.bcm.edu	37	21	37518582	37518582	+	Silent	SNP	G	G	A	rs17849671	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:37518582G>A	ENST00000290354.5	+	3	887	c.606G>A	c.(604-606)acG>acA	p.T202T	CBR3-AS1_ENST00000608622.1_RNA|CBR3-AS1_ENST00000608632.1_RNA|CBR3-AS1_ENST00000608690.1_RNA|CBR3-AS1_ENST00000427491.1_RNA|CBR3-AS1_ENST00000608641.1_RNA|CBR3-AS1_ENST00000453159.1_RNA|CBR3-AS1_ENST00000413862.1_RNA	NM_001236.3	NP_001227.1	O75828	CBR3_HUMAN	carbonyl reductase 3	202					cognition (GO:0050890)|phylloquinone catabolic process (GO:0042376)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	3-keto sterol reductase activity (GO:0000253)|carbonyl reductase (NADPH) activity (GO:0004090)|NADPH binding (GO:0070402)			kidney(1)|large_intestine(1)|lung(1)	3					Doxorubicin(DB00997)	TGGGGGTCACGGTCTTATCGA	0.527													G|||	110	0.0219649	0.0	0.036	5008	,	,		18695	0.0		0.0606	False		,,,				2504	0.0245				p.T202T		Atlas-SNP	.											CBR3,NS,carcinoma,+1,1	CBR3	11	1	0			c.G606A						PASS	.	G		47,4359	48.9+/-83.8	0,47,2156	88.0	80.0	83.0		606	-9.6	0.4	21	dbSNP_123	83	478,8122	140.1+/-196.7	10,458,3832	no	coding-synonymous	CBR3	NM_001236.3		10,505,5988	AA,AG,GG		5.5581,1.0667,4.0366		202/278	37518582	525,12481	2203	4300	6503	SO:0001819	synonymous_variant	874	exon3			GGTCACGGTCTTA	AB004854	CCDS13642.1	21q22.2	2011-09-14			ENSG00000159231	ENSG00000159231	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	1549	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 21C, member 2"""	603608				9740676, 19027726	Standard	NM_001236		Approved	SDR21C2	uc002yve.3	O75828	OTTHUMG00000086617	ENST00000290354.5:c.606G>A	21.37:g.37518582G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_001236	Q6FHP2	Silent	SNP	ENST00000290354.5	37	CCDS13642.1																																																																																			G|0.964;A|0.036	0.036	strong		0.527	CBR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194632.1		
SPATA2	9825	hgsc.bcm.edu	37	20	48522585	48522585	+	Silent	SNP	G	G	A	rs492702	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:48522585G>A	ENST00000422556.1	-	3	1483	c.1134C>T	c.(1132-1134)tcC>tcT	p.S378S	SPATA2_ENST00000543716.1_Silent_p.S241S|SPATA2_ENST00000289431.5_Silent_p.S378S	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	378					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	20	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			TGGAGAGGGCGGACTCTTTGG	0.652													G|||	2447	0.488618	0.1225	0.585	5008	,	,		15619	0.7728		0.4503	False		,,,				2504	0.6616				p.S378S		Atlas-SNP	.											.	SPATA2	36	.	0			c.C1134T						PASS	.	G	,	800,3606	311.4+/-292.0	69,662,1472	47.0	44.0	45.0		1134,1134	-8.6	0.1	20	dbSNP_83	45	3988,4612	538.1+/-383.3	920,2148,1232	no	coding-synonymous,coding-synonymous	SPATA2	NM_001135773.1,NM_006038.3	,	989,2810,2704	AA,AG,GG		46.3721,18.1571,36.8138	,	378/521,378/521	48522585	4788,8218	2203	4300	6503	SO:0001819	synonymous_variant	9825	exon3			GAGGGCGGACTCT	AB018300	CCDS13422.1	20q13.13	2014-06-13			ENSG00000158480	ENSG00000158480			14681	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 145"""	607662					Standard	NM_001135773		Approved	KIAA0757, PD1, tamo, PPP1R145	uc002xuw.3	Q9UM82	OTTHUMG00000032704	ENST00000422556.1:c.1134C>T	20.37:g.48522585G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_006038	E1P626|O94857	Silent	SNP	ENST00000422556.1	37	CCDS13422.1																																																																																			G|0.593;A|0.407	0.407	strong		0.652	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038	
PCDH15	65217	hgsc.bcm.edu	37	10	55582905	55582905	+	Silent	SNP	G	G	T	rs10825114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:55582905G>T	ENST00000320301.6	-	33	4975	c.4581C>A	c.(4579-4581)ccC>ccA	p.P1527P	PCDH15_ENST00000437009.1_Silent_p.P1458P|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395430.1_Silent_p.P1524P|PCDH15_ENST00000395432.2_Silent_p.P1487P|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395433.1_Silent_p.P1504P|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000361849.3_Silent_p.P1529P	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1527					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CCTTATAAAGGGGATTATGGG	0.368										HNSCC(58;0.16)			G|||	1421	0.283746	0.1755	0.2277	5008	,	,		20280	0.7014		0.0447	False		,,,				2504	0.2853				p.P1534P		Atlas-SNP	.											PCDH15_ENST00000417177,NS,malignant_melanoma,-2,4	PCDH15	1715	4	0			c.C4602A						PASS	.	G	,,,,,,,,,,,	778,3628	311.4+/-292.0	73,632,1498	82.0	88.0	86.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4602,4587,4374,4572,4461,4521,,,,,4512,4581	-2.6	0.0	10	dbSNP_120	86	387,8211	122.4+/-181.4	10,367,3922	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,intron,intron,coding-synonymous,coding-synonymous	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	,,,,,,,,,,,	83,999,5420	TT,TG,GG		4.501,17.6577,8.9588	,,,,,,,,,,,	1534/1963,1529/1958,1458/1887,1524/1953,1487/1916,1507/1936,,,,,1504/1933,1527/1956	55582905	1165,11839	2203	4299	6502	SO:0001819	synonymous_variant	65217	exon35			ATAAAGGGGATTA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4581C>A	10.37:g.55582905G>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	134	59	0.440298	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			G|0.809;T|0.191	0.191	strong		0.368	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
PIR	8544	hgsc.bcm.edu	37	X	15415583	15415583	+	Silent	SNP	C	C	T	rs8094	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:15415583C>T	ENST00000380421.3	-	8	1141	c.681G>A	c.(679-681)caG>caA	p.Q227Q	PIR_ENST00000380420.5_Silent_p.Q227Q	NM_001018109.2|NM_003662.3	NP_001018119.1|NP_003653.1	O00625	PIR_HUMAN	pirin (iron-binding nuclear protein)	227					monocyte differentiation (GO:0030224)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|quercetin 2,3-dioxygenase activity (GO:0008127)|transcription cofactor activity (GO:0003712)	p.Q227Q(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9	Hepatocellular(33;0.183)					TGTTCTCCACCTGGACACTGT	0.378													C|||	1654	0.438146	0.2231	0.3689	3775	,	,		12947	0.3552		0.4344	False		,,,				2504	0.3149				p.Q227Q	Ovarian(180;1587 2015 10555 34192 51653)	Atlas-SNP	.											.	PIR	22	.	1	Substitution - coding silent(1)	stomach(1)	c.G681A						PASS	.	C	,	1271,2564		180,722,189,730,382	170.0	131.0	145.0		681,681	3.2	1.0	X	dbSNP_107	145	3912,2816		817,1184,1094,427,778	no	coding-synonymous,coding-synonymous	PIR	NM_001018109.2,NM_003662.3	,	997,1906,1283,1157,1160	TT,TC,T,CC,C		41.8549,33.1421,49.0675	,	227/291,227/291	15415583	5183,5380	2203	4300	6503	SO:0001819	synonymous_variant	8544	exon8			CTCCACCTGGACA	Y07868	CCDS14167.1	Xp22.31	2008-02-05			ENSG00000087842	ENSG00000087842			30048	protein-coding gene	gene with protein product		300931				9079676	Standard	NM_003662		Approved		uc004cwv.3	O00625	OTTHUMG00000021176	ENST00000380421.3:c.681G>A	X.37:g.15415583C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	197	196	0.994924	NM_001018109	Q5U0G0|Q6FHD2	Silent	SNP	ENST00000380421.3	37	CCDS14167.1																																																																																			0|0.003;T|0.470	0.470	strong		0.378	PIR-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055863.1	NM_003662	
FOCAD	54914	hgsc.bcm.edu	37	9	20764870	20764870	+	Missense_Mutation	SNP	T	T	C	rs10511687	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:20764870T>C	ENST00000380249.1	+	9	861	c.497T>C	c.(496-498)tTa>tCa	p.L166S	FOCAD_ENST00000338382.6_Missense_Mutation_p.L166S	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	166			L -> S (in dbSNP:rs10511687).			focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											TCTTATAGGTTAGAAGTTTCA	0.353													C|||	1407	0.28095	0.3094	0.2795	5008	,	,		24115	0.0437		0.3767	False		,,,				2504	0.3896				p.L166S		Atlas-SNP	.											.	.	.	.	0			c.T497C						PASS	.	C	SER/LEU	1420,2986	685.3+/-404.5	220,980,1003	123.0	116.0	118.0		497	6.0	1.0	9	dbSNP_119	118	3143,5457	656.3+/-401.3	579,1985,1736	yes	missense	KIAA1797	NM_017794.3	145	799,2965,2739	CC,CT,TT		36.5465,32.2288,35.0838	benign	166/1802	20764870	4563,8443	2203	4300	6503	SO:0001583	missense	54914	exon9			ATAGGTTAGAAGT	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.497T>C	9.37:g.20764870T>C	ENSP00000369599:p.Leu166Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	560	0.2564102564102564	145	0.29471544715447157	106	0.292817679558011	33	0.057692307692307696	276	0.3641160949868074	C	8.211	0.800362	0.16397	0.322288	0.365465	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.22945	1.93;1.93	5.98	5.98	0.97165	Domain of unknown function DUF3730 (1);	0.550410	0.19445	N	0.114095	T	0.00012	0.0000	N	0.01874	-0.695	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.38845	-0.9642	9	0.02654	T	1	-24.8529	8.723	0.34452	0.2532:0.6767:0.0:0.0701	rs10511687;rs52817455;rs58837776;rs10511687	166	Q5VW36	K1797_HUMAN	S	166	ENSP00000369599:L166S;ENSP00000344307:L166S	ENSP00000344307:L166S	L	+	2	0	KIAA1797	20754870	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	1.741000	0.38238	1.555000	0.49500	-0.186000	0.12905	TTA	T|0.745;C|0.255	0.255	strong		0.353	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
ITFG1	81533	hgsc.bcm.edu	37	16	47271876	47271876	+	Splice_Site	SNP	T	T	C	rs8044842	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:47271876T>C	ENST00000320640.6	-	13	1602	c.1374A>G	c.(1372-1374)acA>acG	p.T458T	ITFG1_ENST00000544001.2_Splice_Site_p.T345T|ITFG1_ENST00000568047.1_5'UTR	NM_030790.3	NP_110417.2	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	458						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	19		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				ATTTACTTACTGTTATCTTAC	0.254													T|||	355	0.0708866	0.1831	0.0447	5008	,	,		16229	0.0139		0.0388	False		,,,				2504	0.0297				p.T458T		Atlas-SNP	.											.	ITFG1	49	.	0			c.A1374G						PASS	.	T		727,3649		56,615,1517	21.0	21.0	21.0		1374	2.2	1.0	16	dbSNP_116	21	371,8139		11,349,3895	yes	coding-synonymous-near-splice	ITFG1	NM_030790.3		67,964,5412	CC,CT,TT		4.3596,16.6133,8.5209		458/613	47271876	1098,11788	2188	4255	6443	SO:0001630	splice_region_variant	81533	exon13			ACTTACTGTTATC	AF503339	CCDS10728.1	16q12.1	2008-02-05			ENSG00000129636	ENSG00000129636			30697	protein-coding gene	gene with protein product	"""T cell immunomodulatory protein"""	611803				12598909	Standard	NM_030790		Approved	CDA08, TIP	uc002eet.3	Q8TB96	OTTHUMG00000133103	ENST00000320640.6:c.1374+1A>G	16.37:g.47271876T>C		Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	244	126	0.516393	NM_030790	Q96SR4|Q9BRE2|Q9H2V9	Silent	SNP	ENST00000320640.6	37	CCDS10728.1																																																																																			T|0.925;C|0.075	0.075	strong		0.254	ITFG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256768.3	NM_030790	Silent
ZBTB38	253461	hgsc.bcm.edu	37	3	141163045	141163045	+	Silent	SNP	T	T	C	rs11714558	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:141163045T>C	ENST00000514251.1	+	4	2094	c.1815T>C	c.(1813-1815)gtT>gtC	p.V605V	ZBTB38_ENST00000441582.2_Silent_p.V605V|ZBTB38_ENST00000321464.5_Silent_p.V606V					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						CCTATGTTGTTCAGAATCCAC	0.433													T|||	50	0.00998403	0.0	0.0101	5008	,	,		20534	0.0		0.0318	False		,,,				2504	0.0112				p.V605V		Atlas-SNP	.											.	ZBTB38	92	.	0			c.T1815C						PASS	.	T		12,3922		0,12,1955	79.0	78.0	79.0		1815	0.3	0.6	3	dbSNP_120	79	206,8128		7,192,3968	no	coding-synonymous	ZBTB38	NM_001080412.2		7,204,5923	CC,CT,TT		2.4718,0.305,1.777		605/1196	141163045	218,12050	1967	4167	6134	SO:0001819	synonymous_variant	253461	exon8			TGTTGTTCAGAAT	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.1815T>C	3.37:g.141163045T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	164	84	0.512195	NM_001080412		Silent	SNP	ENST00000514251.1	37	CCDS43157.1																																																																																			T|0.985;C|0.015	0.015	strong		0.433	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505192	37505192	+	Missense_Mutation	SNP	C	C	T	rs1200875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:37505192C>T	ENST00000602533.1	+	32	2884	c.2785C>T	c.(2785-2787)Cgt>Tgt	p.R929C	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.R1048C|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.R929C			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	985					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CTGTGAACAACGTACAGGAAA	0.343													C|||	646	0.128994	0.0174	0.2666	5008	,	,		15629	0.0843		0.2644	False		,,,				2504	0.089				p.R929C		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.C2785T						PASS	.	C	CYS/ARG	168,3462		8,152,1655	75.0	71.0	72.0		2785	2.6	0.0	10	dbSNP_87	72	1889,6247		211,1467,2390	yes	missense	ANKRD30A	NM_052997.2	180	219,1619,4045	TT,TC,CC		23.2178,4.6281,17.4826	possibly-damaging	929/1342	37505192	2057,9709	1815	4068	5883	SO:0001583	missense	91074	exon32			GAACAACGTACAG	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.2785C>T	10.37:g.37505192C>T	ENSP00000473551:p.Arg929Cys	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	187	187	1	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		352	0.16117216117216118	9	0.018292682926829267	95	0.26243093922651933	52	0.09090909090909091	196	0.25857519788918204	c	3.321	-0.138837	0.06669	0.046281	0.232178	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.17213	2.29;2.29	2.63	2.63	0.31362	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.41784	0.762	B	0.16289	0.015	T	0.40813	-0.9543	8	0.72032	D	0.01	.	10.6339	0.45554	0.0:1.0:0.0:0.0	rs1200875;rs1782081;rs16937432;rs17591018;rs56561122;rs57985851;rs1200875	985	Q9BXX3	AN30A_HUMAN	C	929;1048	ENSP00000354432:R929C;ENSP00000363792:R1048C	ENSP00000354432:R929C	R	+	1	0	ANKRD30A	37545198	0.002000	0.14202	0.002000	0.10522	0.003000	0.03518	1.096000	0.30976	1.281000	0.44480	0.313000	0.20887	CGT	C|0.845;T|0.155	0.155	strong		0.343	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
ACTL8	81569	hgsc.bcm.edu	37	1	18149566	18149566	+	Silent	SNP	C	C	A	rs2296035	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18149566C>A	ENST00000375406.1	+	2	279	c.63C>A	c.(61-63)ggC>ggA	p.G21G		NM_030812.2	NP_110439.2	Q9H568	ACTL8_HUMAN	actin-like 8	21					epithelial cell differentiation (GO:0030855)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	28		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)		GCACGGCCGGCTGGAATGAGC	0.602													C|||	2418	0.482827	0.3215	0.5807	5008	,	,		18379	0.6865		0.4732	False		,,,				2504	0.4315				p.G21G		Atlas-SNP	.											.	ACTL8	58	.	0			c.C63A						PASS	.	C		1513,2893	483.2+/-359.6	276,961,966	75.0	63.0	67.0		63	-8.7	0.0	1	dbSNP_100	67	3975,4625	552.6+/-386.1	926,2123,1251	no	coding-synonymous	ACTL8	NM_030812.2		1202,3084,2217	AA,AC,CC		46.2209,34.3395,42.1959		21/367	18149566	5488,7518	2203	4300	6503	SO:0001819	synonymous_variant	81569	exon2			GGCCGGCTGGAAT	AK057339	CCDS183.1	1p36.2-p35	2009-03-25			ENSG00000117148	ENSG00000117148			24018	protein-coding gene	gene with protein product	"""cancer/testis antigen 57"""						Standard	NM_030812		Approved	CT57	uc001bat.3	Q9H568	OTTHUMG00000002512	ENST00000375406.1:c.63C>A	1.37:g.18149566C>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_030812	Q13104|Q96M75	Silent	SNP	ENST00000375406.1	37	CCDS183.1																																																																																			C|0.540;A|0.460	0.460	strong		0.602	ACTL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007143.1	NM_030812	
CR2	1380	hgsc.bcm.edu	37	1	207648173	207648173	+	Silent	SNP	T	T	C	rs61735651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207648173T>C	ENST00000367058.3	+	13	2340	c.2151T>C	c.(2149-2151)atT>atC	p.I717I	CR2_ENST00000367057.3_Silent_p.I776I|CR2_ENST00000367059.3_Silent_p.I717I|CR2_ENST00000458541.2_Silent_p.I690I	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	717	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CTGCAGTTATTCACTGTCACC	0.413													T|||	317	0.0632987	0.1203	0.0447	5008	,	,		19682	0.001		0.0865	False		,,,				2504	0.0399				p.I776I		Atlas-SNP	.											.	CR2	164	.	0			c.T2328C						PASS	.	T	,	429,3973		30,369,1802	76.0	84.0	81.0		2328,2151	2.3	0.4	1	dbSNP_129	81	899,7701		39,821,3440	no	coding-synonymous,coding-synonymous	CR2	NM_001006658.2,NM_001877.4	,	69,1190,5242	CC,CT,TT		10.4535,9.7456,10.2138	,	776/1093,717/1034	207648173	1328,11674	2201	4300	6501	SO:0001819	synonymous_variant	1380	exon14			AGTTATTCACTGT	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.2151T>C	1.37:g.207648173T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Silent	SNP	ENST00000367058.3	37	CCDS1478.1																																																																																			T|0.917;C|0.083	0.083	strong		0.413	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
TCOF1	6949	hgsc.bcm.edu	37	5	149755421	149755421	+	Silent	SNP	A	A	G	rs2071239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149755421A>G	ENST00000504761.2	+	12	1842	c.1842A>G	c.(1840-1842)tcA>tcG	p.S614S	TCOF1_ENST00000439160.2_Silent_p.S614S|TCOF1_ENST00000394269.3_Silent_p.S614S|TCOF1_ENST00000513346.1_Silent_p.S614S|TCOF1_ENST00000377797.3_Silent_p.S614S|TCOF1_ENST00000451292.1_Silent_p.S614S|TCOF1_ENST00000445265.2_Silent_p.S537S|TCOF1_ENST00000323668.7_Silent_p.S537S			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	614					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCGAGGAGTCATCGGACAGTG	0.632													G|||	814	0.16254	0.2511	0.0937	5008	,	,		17281	0.1448		0.1292	False		,,,				2504	0.1442				p.S614S		Atlas-SNP	.											.	TCOF1	154	.	0			c.A1842G						PASS	.	G	,,,,,	1116,3290	717.8+/-408.8	133,850,1220	62.0	62.0	62.0		1611,1842,1842,1842,1611,1842	-5.2	0.0	5	dbSNP_96	62	1365,7235	755.2+/-407.5	93,1179,3028	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	,,,,,	226,2029,4248	GG,GA,AA		15.8721,25.3291,19.0758	,,,,,	537/1412,614/959,614/1489,614/1452,537/1413,614/1451	149755421	2481,10525	2203	4300	6503	SO:0001819	synonymous_variant	6949	exon12			GGAGTCATCGGAC		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.1842A>G	5.37:g.149755421A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	203	91	0.448276	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Silent	SNP	ENST00000504761.2	37	CCDS54936.1																																																																																			A|0.832;G|0.168	0.168	strong		0.632	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
MUC16	94025	hgsc.bcm.edu	37	19	9047305	9047305	+	Silent	SNP	G	G	A	rs10415818	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9047305G>A	ENST00000397910.4	-	5	34529	c.34326C>T	c.(34324-34326)caC>caT	p.H11442H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11444	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGAACTTGTGTGTGTCTCAG	0.478													G|||	918	0.183307	0.177	0.1945	5008	,	,		23374	0.0258		0.2823	False		,,,				2504	0.2444				p.H11442H		Atlas-SNP	.											.	MUC16	4315	.	0			c.C34326T						PASS	.			696,3340		57,582,1379	187.0	188.0	187.0		34326	-6.2	0.0	19	dbSNP_119	187	2515,5805		401,1713,2046	no	coding-synonymous	MUC16	NM_024690.2		458,2295,3425	AA,AG,GG		30.2284,17.2448,25.9874		11442/14508	9047305	3211,9145	2018	4160	6178	SO:0001819	synonymous_variant	94025	exon5			ACTTGTGTGTGTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.34326C>T	19.37:g.9047305G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.797;A|0.203	0.203	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF860	344787	hgsc.bcm.edu	37	3	32031135	32031135	+	Silent	SNP	A	A	G	rs6419811	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:32031135A>G	ENST00000360311.4	+	2	1113	c.564A>G	c.(562-564)tcA>tcG	p.S188S		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	188					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						ATGCTTCCTCAGTTCTAACGT	0.358													G|||	2356	0.470447	0.7988	0.3602	5008	,	,		20726	0.4524		0.1968	False		,,,				2504	0.4049				p.S188S		Atlas-SNP	.											ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	0			c.A564G						PASS	.	G		938,446		325,288,79	58.0	44.0	48.0		564	0.3	0.0	3	dbSNP_116	48	608,2574		58,492,1041	no	coding-synonymous	ZNF860	NM_001137674.2		383,780,1120	GG,GA,AA		19.1075,32.2254,33.859		188/633	32031135	1546,3020	692	1591	2283	SO:0001819	synonymous_variant	344787	exon2			TTCCTCAGTTCTA	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.564A>G	3.37:g.32031135A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	151	62	0.410596	NM_001137674	B4DFA4	Silent	SNP	ENST00000360311.4	37	CCDS46784.1																																																																																			A|0.567;G|0.433	0.433	strong		0.358	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
FBXO47	494188	hgsc.bcm.edu	37	17	37093510	37093510	+	Missense_Mutation	SNP	T	T	C	rs113358400	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:37093510T>C	ENST00000378079.2	-	11	1476	c.1277A>G	c.(1276-1278)aAt>aGt	p.N426S		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	426										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						ATGGAACAAATTCAAAAAGCT	0.363													T|||	35	0.00698882	0.0008	0.0144	5008	,	,		15990	0.0		0.0239	False		,,,				2504	0.0				p.N426S		Atlas-SNP	.											.	FBXO47	34	.	0			c.A1277G						PASS	.	T	SER/ASN	36,4370	40.0+/-72.8	0,36,2167	127.0	111.0	116.0		1277	4.8	1.0	17	dbSNP_132	116	256,8344	99.9+/-161.4	3,250,4047	yes	missense	FBXO47	NM_001008777.2	46	3,286,6214	CC,CT,TT		2.9767,0.8171,2.2451	benign	426/453	37093510	292,12714	2203	4300	6503	SO:0001583	missense	494188	exon11			AACAAATTCAAAA		CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"""F-boxes /  ""other"""""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.1277A>G	17.37:g.37093510T>C	ENSP00000367319:p.Asn426Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	113	66	0.584071	NM_001008777	B2RTZ4	Missense_Mutation	SNP	ENST00000378079.2	37	CCDS32639.1	23	0.010531135531135532	0	0.0	7	0.019337016574585635	0	0.0	16	0.021108179419525065	T	14.00	2.405097	0.42613	0.008171	0.029767	ENSG00000204952	ENST00000378079	T	0.59502	0.26	5.88	4.81	0.61882	.	0.203730	0.50627	N	0.000112	T	0.19366	0.0465	L	0.29908	0.895	0.40423	D	0.979864	B	0.28350	0.208	B	0.20577	0.03	T	0.10965	-1.0607	10	0.33940	T	0.23	-5.6902	10.6903	0.45867	0.0:0.0748:0.0:0.9252	.	426	Q5MNV8	FBX47_HUMAN	S	426	ENSP00000367319:N426S	ENSP00000367319:N426S	N	-	2	0	FBXO47	34347036	1.000000	0.71417	0.984000	0.44739	0.974000	0.67602	3.816000	0.55658	1.066000	0.40716	0.528000	0.53228	AAT	T|0.981;C|0.019	0.019	strong		0.363	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777	
USP17L22	100287513	hgsc.bcm.edu	37	4	9270328	9270328	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:9270328G>A	ENST00000511280.1	+	1	984	c.984G>A	c.(982-984)tgG>tgA	p.W328*		NM_001256863.1	NP_001243792.1	D6RA61	U17LM_HUMAN	ubiquitin specific peptidase 17-like family member 22	328	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.W328*(1)									ACGCTGGGTGGAGTTGTCACA	0.498																																					p.W328X		Atlas-SNP	.											RP11-1286E23.17,NS,carcinoma,0,1	.	.	1	1	Substitution - Nonsense(1)	breast(1)	c.G984A						scavenged	.																																			SO:0001587	stop_gained	100287441	exon1			TGGGTGGAGTTGT		CCDS59463.1	4p16.1	2012-10-09			ENSG00000248933	ENSG00000248933			44450	protein-coding gene	gene with protein product							Standard	NM_001256863		Approved			D6RA61	OTTHUMG00000160159	ENST00000511280.1:c.984G>A	4.37:g.9270328G>A	ENSP00000423115:p.Trp328*	Somatic	217	5	0.0230415		WXS	Illumina HiSeq	Phase_I	321	15	0.046729	NM_001256861		Nonsense_Mutation	SNP	ENST00000511280.1	37	CCDS59463.1	.	.	.	.	.	.	.	.	.	.	.	12.24	1.878008	0.33162	.	.	ENSG00000248933	ENST00000511280	.	.	.	0.337	0.337	0.15966	.	1.191590	0.06372	N	0.713729	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	328	.	ENSP00000423115:W328X	W	+	3	0	RP11-1286E23.17	8965445	0.289000	0.24334	0.271000	0.24616	0.094000	0.18550	0.042000	0.13949	0.444000	0.26612	0.121000	0.15741	TGG	.	.	none		0.498	USP17L22-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359427.1	NM_001256863	
ADGB	79747	hgsc.bcm.edu	37	6	146993392	146993392	+	Silent	SNP	A	A	G	rs77104188	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:146993392A>G	ENST00000397944.3	+	8	952	c.876A>G	c.(874-876)aaA>aaG	p.K292K	ADGB_ENST00000367493.3_5'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	292	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						AGCTCCTGAAAGAAATATTGC	0.378													A|||	111	0.0221645	0.003	0.0274	5008	,	,		17411	0.0		0.0437	False		,,,				2504	0.045				p.K292K		Atlas-SNP	.											.	ADGB	93	.	0			c.A876G						PASS	.	A		13,1371		0,13,679	57.0	51.0	53.0		876	1.3	1.0	6	dbSNP_132	53	206,2976		9,188,1394	no	coding-synonymous	C6orf103	NM_024694.3		9,201,2073	GG,GA,AA		6.4739,0.9393,4.7963		292/1668	146993392	219,4347	692	1591	2283	SO:0001819	synonymous_variant	79747	exon8			CCTGAAAGAAATA	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.876A>G	6.37:g.146993392A>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	182	94	0.516484	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	37																																																																																				A|0.976;G|0.024	0.024	strong		0.378	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
LY75	4065	hgsc.bcm.edu	37	2	160673519	160673519	+	Missense_Mutation	SNP	G	G	A	rs35941588	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160673519G>A	ENST00000263636.4	-	30	4205	c.4178C>T	c.(4177-4179)aCt>aTt	p.T1393I	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.T1393I|LY75_ENST00000553424.1_Missense_Mutation_p.T1393I|LY75_ENST00000554112.1_Missense_Mutation_p.T1393I|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.T1393I	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1393			T -> I (in dbSNP:rs35941588).		endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		TGGCAGTGTAGTATTATATTC	0.289													G|||	176	0.0351438	0.003	0.0447	5008	,	,		18447	0.0248		0.0736	False		,,,				2504	0.0429				p.T1393I		Atlas-SNP	.											.	LY75	151	.	0			c.C4178T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR	54,4352	54.2+/-90.2	0,54,2149	85.0	83.0	84.0		4178,4178,4178	1.4	1.0	2	dbSNP_126	84	604,7996	157.3+/-211.0	18,568,3714	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	89,89,89	18,622,5863	AA,AG,GG		7.0233,1.2256,5.0592	benign,benign,benign	1393/1874,1393/1818,1393/1723	160673519	658,12348	2203	4300	6503	SO:0001583	missense	4065	exon30			AGTGTAGTATTAT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.4178C>T	2.37:g.160673519G>A	ENSP00000263636:p.Thr1393Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	94	55	0.585106	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	92	0.04212454212454213	2	0.0040650406504065045	15	0.04143646408839779	15	0.026223776223776224	60	0.079155672823219	G	11.44	1.640691	0.29157	0.012256	0.070233	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.17370	2.28;2.28;2.28;2.28;2.28	5.65	1.44	0.22558	.	1.477230	0.04826	N	0.437871	T	0.00845	0.0028	L	0.44542	1.39	0.20489	N	0.999892	B;B;B	0.34015	0.414;0.25;0.435	B;B;B	0.32677	0.15;0.052;0.117	T	0.30179	-0.9987	10	0.38643	T	0.18	-2.8581	10.4261	0.44378	0.0:0.3377:0.4523:0.21	rs35941588	1393;1393;1393	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	I	1393	ENSP00000451511:T1393I;ENSP00000451446:T1393I;ENSP00000263636:T1393I;ENSP00000423463:T1393I;ENSP00000421035:T1393I	ENSP00000423463:T1393I	T	-	2	0	LY75;LY75-CD302	160381765	0.975000	0.34042	0.995000	0.50966	0.968000	0.65278	1.327000	0.33746	0.789000	0.33779	0.650000	0.86243	ACT	G|0.954;A|0.046	0.046	strong		0.289	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
NFATC1	4772	hgsc.bcm.edu	37	18	77227476	77227476	+	Silent	SNP	A	A	G	rs25656	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:77227476A>G	ENST00000427363.2	+	8	1986	c.1986A>G	c.(1984-1986)ccA>ccG	p.P662P	NFATC1_ENST00000329101.4_Silent_p.P649P|NFATC1_ENST00000592223.1_Silent_p.P649P|NFATC1_ENST00000587635.1_Missense_Mutation_p.H634R|NFATC1_ENST00000591814.1_Silent_p.P662P|NFATC1_ENST00000545796.1_Silent_p.P190P|NFATC1_ENST00000586434.1_Silent_p.P649P|NFATC1_ENST00000397790.2_Silent_p.P190P|NFATC1_ENST00000318065.5_Silent_p.P649P|NFATC1_ENST00000542384.1_Silent_p.P662P|NFATC1_ENST00000253506.5_Silent_p.P662P			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	662					calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	AGATCCCGCCATTTCGGAATC	0.587													G|||	2028	0.404952	0.6717	0.379	5008	,	,		15486	0.374		0.2972	False		,,,				2504	0.2055				p.P662P	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.A1986G						PASS	.	G	,,,,	2671,1735	518.3+/-369.7	803,1065,335	99.0	76.0	84.0		1986,1947,570,1947,1986	-9.4	0.2	18	dbSNP_116	84	2780,5820	677.6+/-403.4	453,1874,1973	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	,,,,	1256,2939,2308	GG,GA,AA		32.3256,39.3781,41.9114	,,,,	662/826,649/931,190/354,649/813,662/717	77227476	5451,7555	2203	4300	6503	SO:0001819	synonymous_variant	4772	exon8			CCCGCCATTTCGG	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.1986A>G	18.37:g.77227476A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Silent	SNP	ENST00000427363.2	37																																																																																				A|0.576;G|0.424	0.424	strong		0.587	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
NOTCH4	4855	hgsc.bcm.edu	37	6	32188383	32188383	+	Missense_Mutation	SNP	T	T	C	rs422951	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32188383T>C	ENST00000375023.3	-	6	1096	c.958A>G	c.(958-960)Acc>Gcc	p.T320A		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	320	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		T -> A (in dbSNP:rs422951).		cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GGACCCTGGGTCTCACACTCA	0.637													T|||	1718	0.343051	0.2958	0.3112	5008	,	,		17396	0.2212		0.4553	False		,,,				2504	0.4397				p.T320A		Atlas-SNP	.											NOTCH4,NS,carcinoma,0,1	NOTCH4	201	1	0			c.A958G						PASS	.	T	ALA/THR	942,2080		144,654,713	49.0	50.0	50.0		958	-5.0	0.0	6	dbSNP_80	50	2436,2982		538,1360,811	yes	missense	NOTCH4	NM_004557.3	58	682,2014,1524	CC,CT,TT		44.9612,31.1714,40.0237	benign	320/2004	32188383	3378,5062	1511	2709	4220	SO:0001583	missense	4855	exon6			CCTGGGTCTCACA		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.958A>G	6.37:g.32188383T>C	ENSP00000364163:p.Thr320Ala	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	730	0.3342490842490842	138	0.2804878048780488	125	0.3453038674033149	127	0.22202797202797203	340	0.44854881266490765	T	1.333	-0.596204	0.03771	0.311714	0.449612	ENSG00000204301	ENST00000375023	D	0.92149	-2.98	4.6	-4.96	0.03038	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	1.178960	0.06410	N	0.720517	T	0.72867	0.3514	L	0.31752	0.955	0.09310	P	0.99999999997133	B;B	0.02656	0.0;0.0	B;B	0.13407	0.009;0.003	T	0.58736	-0.7584	9	0.37606	T	0.19	.	7.561	0.27851	0.1143:0.3195:0.0:0.5662	rs422951;rs2229976;rs17422277;rs17855878;rs58507746;rs422951	320;320	Q6P3V5;Q99466	.;NOTC4_HUMAN	A	320	ENSP00000364163:T320A	ENSP00000364163:T320A	T	-	1	0	NOTCH4	32296361	0.007000	0.16637	0.009000	0.14445	0.286000	0.27126	0.081000	0.14823	-1.001000	0.03434	-1.194000	0.01681	ACC	T|0.625;C|0.375	0.375	strong		0.637	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
MYO6	4646	hgsc.bcm.edu	37	6	76542585	76542585	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:76542585G>A	ENST00000369977.3	+	6	557	c.418G>A	c.(418-420)Gtg>Atg	p.V140M	MYO6_ENST00000369981.3_Missense_Mutation_p.V140M|MYO6_ENST00000369985.4_Missense_Mutation_p.V140M|MYO6_ENST00000369975.1_Missense_Mutation_p.V140M	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	140	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		AGACATGAAGGTGCTCAAGAT	0.333																																					p.V140M		Atlas-SNP	.											.	MYO6	124	.	0			c.G418A						PASS	.						85.0	90.0	88.0					6																	76542585		2203	4300	6503	SO:0001583	missense	4646	exon6			ATGAAGGTGCTCA	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"""Myosins / Myosin superfamily : Class VI"""	7605	protein-coding gene	gene with protein product		600970	"""deafness, autosomal recessive 37"""	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.418G>A	6.37:g.76542585G>A	ENSP00000358994:p.Val140Met	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914335	0.92178	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.91002	0.7170	L	0.55990	1.75	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.79784	0.957;0.993	D	0.89801	0.3975	10	0.46703	T	0.11	.	19.6547	0.95831	0.0:0.0:1.0:0.0	.	140;140	Q9UM54-2;Q9UM54-1	.;.	M	140	ENSP00000358998:V140M;ENSP00000359002:V140M;ENSP00000358994:V140M;ENSP00000358992:V140M	ENSP00000358992:V140M	V	+	1	0	MYO6	76599305	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.388000	0.97237	2.717000	0.92951	0.650000	0.86243	GTG	.	.	none		0.333	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999	
HMHA1	23526	hgsc.bcm.edu	37	19	1079959	1079959	+	Missense_Mutation	SNP	G	G	A	rs36084354	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1079959G>A	ENST00000313093.2	+	13	1776	c.1545G>A	c.(1543-1545)atG>atA	p.M515I	HMHA1_ENST00000539243.2_Missense_Mutation_p.M531I|HMHA1_ENST00000590214.1_Missense_Mutation_p.M542I|HMHA1_ENST00000543365.1_Missense_Mutation_p.M398I|HMHA1_ENST00000536472.1_Missense_Mutation_p.M355I|HMHA1_ENST00000590577.1_Missense_Mutation_p.M150I|HMHA1_ENST00000586866.1_Missense_Mutation_p.M519I	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	515			M -> I (in dbSNP:rs36084354).		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGATGCATATGCAGACGGCGC	0.682													G|||	146	0.0291534	0.0045	0.0548	5008	,	,		15433	0.0069		0.0855	False		,,,				2504	0.0092				p.M531I		Atlas-SNP	.											HMHA1,NS,carcinoma,0,2	HMHA1	78	2	0			c.G1593A						PASS	.	G	ILE/MET	82,4324	68.1+/-105.8	2,78,2123	74.0	83.0	80.0		1545	4.4	1.0	19	dbSNP_126	80	706,7894	170.9+/-221.9	37,632,3631	yes	missense	HMHA1	NM_012292.2	10	39,710,5754	AA,AG,GG		8.2093,1.8611,6.0587	benign	515/1137	1079959	788,12218	2203	4300	6503	SO:0001583	missense	23526	exon13			GCATATGCAGACG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.1545G>A	19.37:g.1079959G>A	ENSP00000316772:p.Met515Ile	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	37	CCDS32863.1	95	0.043498168498168496	7	0.014227642276422764	27	0.07458563535911603	4	0.006993006993006993	57	0.07519788918205805	G	17.24	3.339832	0.60963	0.018611	0.082093	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000544746;ENST00000536472;ENST00000412039;ENST00000543365	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	4.41	4.41	0.53225	.	0.044760	0.85682	U	0.000000	T	0.02688	0.0081	M	0.66939	2.045	0.54753	D	0.999981	P;B;B;B;B	0.38827	0.649;0.4;0.215;0.4;0.172	B;B;B;B;B	0.35770	0.21;0.173;0.062;0.077;0.035	T	0.01608	-1.1313	10	0.29301	T	0.29	-21.4743	14.4939	0.67670	0.0:0.0:1.0:0.0	rs36084354;rs62131203	355;531;150;398;515	F5H4A3;F6QP70;B3KVA9;F5H1R4;Q92619	.;.;.;.;HMHA1_HUMAN	I	531;515;515;355;509;398	ENSP00000439601:M531I;ENSP00000316772:M515I;ENSP00000445109:M355I;ENSP00000438979:M398I	ENSP00000316772:M515I	M	+	3	0	HMHA1	1030959	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.741000	0.47426	2.021000	0.59480	0.561000	0.74099	ATG	G|0.948;A|0.052	0.052	strong		0.682	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
OR56A4	120793	hgsc.bcm.edu	37	11	6023640	6023640	+	Missense_Mutation	SNP	T	T	C	rs11040249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6023640T>C	ENST00000330728.4	-	1	784	c.739A>G	c.(739-741)Atc>Gtc	p.I247V		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGAAAGTGATGTCATCACAA	0.423													.|||	824	0.164537	0.0582	0.1945	5008	,	,		24555	0.0794		0.2684	False		,,,				2504	0.2679				p.I247V		Atlas-SNP	.											.	OR56A4	66	.	0			c.A739G						PASS	.	T	VAL/ILE	477,3925	223.3+/-239.8	30,417,1754	50.0	50.0	50.0		739	3.7	0.0	11	dbSNP_120	50	2562,6030	417.3+/-352.4	397,1768,2131	yes	missense	OR56A4	NM_001005179.2	29	427,2185,3885	CC,CT,TT		29.8184,10.836,23.3877	benign	247/366	6023640	3039,9955	2201	4296	6497	SO:0001583	missense	120793	exon1			AAGTGATGTCATC	BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"""GPCR / Class A : Olfactory receptors"""	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.739A>G	11.37:g.6023640T>C	ENSP00000328215:p.Ile247Val	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	165	73	0.442424	NM_001005179	B9EH17	Missense_Mutation	SNP	ENST00000330728.4	37	CCDS31404.1	358	0.16391941391941392	36	0.07317073170731707	67	0.1850828729281768	46	0.08041958041958042	209	0.2757255936675462	T	8.238	0.806233	0.16467	0.10836	0.298184	ENSG00000183389	ENST00000330728	T	0.00107	8.72	3.72	3.72	0.42706	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36740	U	0.002434	T	0.00012	0.0000	L	0.51914	1.62	0.80722	P	0.0	B	0.06786	0.001	B	0.17722	0.019	T	0.21999	-1.0229	9	0.45353	T	0.12	.	11.6678	0.51383	0.0:0.0:0.0:1.0	rs11040249;rs59527403;rs11040249	195	Q8NGH8	O56A4_HUMAN	V	247	ENSP00000328215:I247V	ENSP00000328215:I247V	I	-	1	0	OR56A4	5980216	0.000000	0.05858	0.040000	0.18447	0.988000	0.76386	0.189000	0.17037	1.669000	0.50854	0.533000	0.62120	ATC	T|0.797;C|0.203	0.203	strong		0.423	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179	
C11orf16	56673	hgsc.bcm.edu	37	11	8942942	8942942	+	Missense_Mutation	SNP	C	C	T	rs2653601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:8942942C>T	ENST00000326053.5	-	6	1431	c.1325G>A	c.(1324-1326)cGg>cAg	p.R442Q	C11orf16_ENST00000525780.1_Intron	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	442				R -> Q (in Ref. 1; CAB92289). {ECO:0000305}.				p.R442Q(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	22				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		TGGCGGGGTCCGCGGTGGCTT	0.517													C|||	1347	0.26897	0.1059	0.2507	5008	,	,		18759	0.2232		0.3539	False		,,,				2504	0.4622				p.R442Q		Atlas-SNP	.											C11orf16,NS,carcinoma,0,1	C11orf16	43	1	1	Substitution - Missense(1)	stomach(1)	c.G1325A						scavenged	.	C	GLN/ARG	587,3815	259.8+/-263.3	42,503,1656	134.0	125.0	128.0		1325	-0.9	0.0	11	dbSNP_100	128	3049,5543	469.1+/-367.5	543,1963,1790	yes	missense	C11orf16	NM_020643.2	43	585,2466,3446	TT,TC,CC		35.4865,13.3348,27.9821	benign	442/468	8942942	3636,9358	2201	4296	6497	SO:0001583	missense	56673	exon6			GGGGTCCGCGGTG	AJ400877	CCDS7794.1	11p15.3	2008-06-25			ENSG00000176029	ENSG00000176029			1169	protein-coding gene	gene with protein product						11528127	Standard	NM_020643		Approved		uc001mhb.4	Q9NQ32	OTTHUMG00000165654	ENST00000326053.5:c.1325G>A	11.37:g.8942942C>T	ENSP00000318999:p.Arg442Gln	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	203	92	0.453202	NM_020643	Q53FB2|Q8N6Y9	Missense_Mutation	SNP	ENST00000326053.5	37	CCDS7794.1	551	0.2522893772893773	67	0.13617886178861788	113	0.31215469613259667	99	0.17307692307692307	272	0.35883905013192613	C	0.460	-0.889593	0.02511	0.133348	0.354865	ENSG00000176029	ENST00000326053	T	0.29655	1.56	4.09	-0.874	0.10631	.	0.767073	0.11168	N	0.592343	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41395	-0.9511	9	0.02654	T	1	-1.9265	4.093	0.09978	0.0:0.2956:0.1771:0.5273	rs2653601;rs3829274;rs52796858;rs60226138;rs2653601	442	Q9NQ32	CK016_HUMAN	Q	442	ENSP00000318999:R442Q	ENSP00000318999:R442Q	R	-	2	0	C11orf16	8899518	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.178000	0.09782	-0.182000	0.10602	-1.352000	0.01234	CGG	T|0.268;G|0.006	0.268	strong		0.517	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643	
PCM1	5108	hgsc.bcm.edu	37	8	17830005	17830005	+	Missense_Mutation	SNP	G	G	A	rs17514547	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:17830005G>A	ENST00000519253.1	+	23	4003	c.3752G>A	c.(3751-3753)cGc>cAc	p.R1251H	PCM1_ENST00000327578.8_5'Flank|PCM1_ENST00000524226.1_Missense_Mutation_p.R1252H|PCM1_ENST00000325083.8_Missense_Mutation_p.R1251H			Q15154	PCM1_HUMAN	pericentriolar material 1	1251			R -> H (in dbSNP:rs17514547).		centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		GGAAGAAGACGCCAGTTTGAT	0.378			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""								G|||	51	0.0101837	0.0008	0.0086	5008	,	,		17700	0.0		0.0268	False		,,,				2504	0.0174				p.R1251H		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	.	0			c.G3752A						PASS	.	G	HIS/ARG	17,3709		0,17,1846	102.0	96.0	98.0		3752	2.0	1.0	8	dbSNP_123	98	250,7948		5,240,3854	yes	missense	PCM1	NM_006197.3	29	5,257,5700	AA,AG,GG		3.0495,0.4563,2.2392	probably-damaging	1251/2025	17830005	267,11657	1863	4099	5962	SO:0001583	missense	5108	exon23			GAAGACGCCAGTT		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.3752G>A	8.37:g.17830005G>A	ENSP00000431099:p.Arg1251His	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	172	81	0.47093	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		27	0.012362637362637362	0	0.0	4	0.011049723756906077	0	0.0	23	0.030343007915567283	G	12.33	1.904852	0.33628	0.004563	0.030495	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.52983	0.64;0.64;0.64	4.81	2.01	0.26516	.	0.261491	0.45126	N	0.000386	T	0.25121	0.0610	N	0.25647	0.755	0.80722	D	1	B;D;B;D	0.89917	0.0;1.0;0.01;1.0	B;D;B;D	0.79784	0.001;0.993;0.007;0.993	T	0.13980	-1.0489	10	0.44086	T	0.13	-0.0745	7.4507	0.27237	0.3627:0.0:0.6373:0.0	rs17514547;rs52805963;rs56506649;rs17514547	113;1251;1252;1251	B4DJ00;E7ETA6;E7EV56;Q15154	.;.;.;PCM1_HUMAN	H	1251;1251;1252	ENSP00000327077:R1251H;ENSP00000431099:R1251H;ENSP00000430521:R1252H	ENSP00000327077:R1251H	R	+	2	0	PCM1	17874285	0.992000	0.36948	1.000000	0.80357	0.174000	0.22865	0.417000	0.21214	0.305000	0.22832	0.313000	0.20887	CGC	G|0.986;A|0.014	0.014	strong		0.378	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
MUC21	394263	hgsc.bcm.edu	37	6	30954939	30954939	+	Silent	SNP	A	A	T	rs140285853		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954939A>T	ENST00000376296.3	+	2	1228	c.987A>T	c.(985-987)acA>acT	p.T329T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	329	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GGGCCAGCACAGCCACCAACT	0.622																																					p.T329T		Atlas-SNP	.											.	MUC21	98	.	0			c.A987T						PASS	.						142.0	142.0	142.0					6																	30954939		2202	4297	6499	SO:0001819	synonymous_variant	394263	exon2			CAGCACAGCCACC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.987A>T	6.37:g.30954939A>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	128	26	0.203125	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			A|0.999;T|0.001	0.001	weak		0.622	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
PSG1	5669	hgsc.bcm.edu	37	19	43373078	43373078	+	Missense_Mutation	SNP	C	C	G	rs143301512	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:43373078C>G	ENST00000436291.2	-	4	934	c.818G>C	c.(817-819)tGg>tCg	p.W273S	PSG1_ENST00000244296.2_Missense_Mutation_p.W273S|PSG1_ENST00000403380.3_Missense_Mutation_p.W180S|PSG1_ENST00000595124.1_Missense_Mutation_p.W180S|PSG1_ENST00000595356.1_Missense_Mutation_p.W273S|PSG1_ENST00000312439.6_Missense_Mutation_p.W273S	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	273	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				ATTTAGCCACCAAATGTAGGT	0.473													.|||	158	0.0315495	0.0038	0.0576	5008	,	,		20871	0.0		0.0984	False		,,,				2504	0.0143				p.W273S		Atlas-SNP	.											.	PSG1	196	.	0			c.G818C						PASS	.	C	SER/TRP,SER/TRP,SER/TRP	57,2961		1,55,1453	67.0	75.0	72.0		818,818,818	1.5	0.0	19	dbSNP_134	72	503,4907		30,443,2232	no	missense,missense,missense	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	177,177,177	31,498,3685	GG,GC,CC		9.2976,1.8887,6.6445	,,	273/420,273/418,273/427	43373078	560,7868	1509	2705	4214	SO:0001583	missense	5669	exon4			AGCCACCAAATGT		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.818G>C	19.37:g.43373078C>G	ENSP00000413041:p.Trp273Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	CCDS54275.1	107	0.04899267399267399	1	0.0020325203252032522	26	0.0718232044198895	1	0.0017482517482517483	79	0.10422163588390501	N	8.612	0.889433	0.17540	0.018887	0.092976	ENSG00000231924	ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.62498	0.02;0.02;0.02;0.02	1.51	1.51	0.23008	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14700	0.0355	H	0.98426	4.23	0.80722	P	0.0	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;1.0;0.997;0.994	T	0.65557	-0.6139	8	0.51188	T	0.08	.	6.307	0.21145	0.0:1.0:0.0:0.0	.	273;180;273;180;273;145;273	P11464-4;G5E9F7;P11464;Q8NBY8;P11464-3;B4DTG5;P11464-2	.;.;PSG1_HUMAN;.;.;.;.	S	273;180;273;273	ENSP00000413041:W273S;ENSP00000385386:W180S;ENSP00000308970:W273S;ENSP00000244296:W273S	ENSP00000244296:W273S	W	-	2	0	PSG1	48064918	0.003000	0.15002	0.004000	0.12327	0.003000	0.03518	0.905000	0.28504	0.785000	0.33685	0.195000	0.17529	TGG	C|0.944;G|0.056	0.056	strong		0.473	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
SF3B1	23451	hgsc.bcm.edu	37	2	198266831	198266831	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:198266831C>T	ENST00000335508.6	-	15	2192	c.2101G>A	c.(2101-2103)Gtt>Att	p.V701I	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'UTR	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	701					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.V701F(2)|p.V701I(1)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ATGGTCCGAACTTTCTGCTGC	0.423			Mis		myelodysplastic syndrome																																p.V701I		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	SF3B1,NS,haematopoietic_neoplasm,0,4	SF3B1	1038	4	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(2)|NS(1)	c.G2101A						scavenged	.						79.0	77.0	78.0					2																	198266831		2203	4300	6503	SO:0001583	missense	23451	exon15			TCCGAACTTTCTG	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2101G>A	2.37:g.198266831C>T	ENSP00000335321:p.Val701Ile	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	180	3	0.0166667	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	35	5.564267	0.96527	.	.	ENSG00000115524	ENST00000335508	T	0.73363	-0.74	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.89619	0.6767	M	0.90814	3.15	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.90052	0.4150	10	0.62326	D	0.03	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	701	O75533	SF3B1_HUMAN	I	701	ENSP00000335321:V701I	ENSP00000335321:V701I	V	-	1	0	SF3B1	197975076	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.348000	0.79366	2.857000	0.98124	0.650000	0.86243	GTT	.	.	none		0.423	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
IGFBP5	3488	hgsc.bcm.edu	37	2	217543728	217543728	+	Missense_Mutation	SNP	G	G	A	rs11575194	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:217543728G>A	ENST00000233813.4	-	2	1161	c.412C>T	c.(412-414)Cgg>Tgg	p.R138W		NM_000599.3	NP_000590.1	P24593	IBP5_HUMAN	insulin-like growth factor binding protein 5	138			R -> W (in dbSNP:rs11575194). {ECO:0000269|Ref.6}.		cellular protein metabolic process (GO:0044267)|cellular response to cAMP (GO:0071320)|cellular response to organic cyclic compound (GO:0071407)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hair follicle morphogenesis (GO:0031069)|intracellular signal transduction (GO:0035556)|mammary gland involution (GO:0060056)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|striated muscle cell differentiation (GO:0051146)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|insulin-like growth factor binding protein complex (GO:0016942)	insulin-like growth factor I binding (GO:0031994)			endometrium(1)|large_intestine(3)|lung(1)	5		Renal(323;0.0822)		Epithelial(149;2.1e-06)|all cancers(144;0.000165)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGTTTGGGCCGGAAGATCTTG	0.602													G|||	58	0.0115815	0.0038	0.0288	5008	,	,		18505	0.0		0.0308	False		,,,				2504	0.002				p.R138W		Atlas-SNP	.											IGFBP5,NS,carcinoma,+2,1	IGFBP5	13	1	0			c.C412T	GRCh37	CM067683	IGFBP5	M	rs11575194	PASS	.	G	TRP/ARG	39,4367	43.1+/-76.7	0,39,2164	100.0	91.0	94.0		412	4.2	1.0	2	dbSNP_120	94	358,8242	119.9+/-179.2	10,338,3952	yes	missense	IGFBP5	NM_000599.3	101	10,377,6116	AA,AG,GG		4.1628,0.8852,3.0524	probably-damaging	138/273	217543728	397,12609	2203	4300	6503	SO:0001583	missense	3488	exon2			TGGGCCGGAAGAT		CCDS2405.1	2q35	2014-09-16			ENSG00000115461	ENSG00000115461			5474	protein-coding gene	gene with protein product		146734				7511611	Standard	NM_000599		Approved		uc002vgj.4	P24593	OTTHUMG00000133058	ENST00000233813.4:c.412C>T	2.37:g.217543728G>A	ENSP00000233813:p.Arg138Trp	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	183	93	0.508197	NM_000599	Q5U0A3	Missense_Mutation	SNP	ENST00000233813.4	37	CCDS2405.1	35	0.016025641025641024	3	0.006097560975609756	9	0.024861878453038673	0	0.0	23	0.030343007915567283	G	23.6	4.435229	0.83885	0.008852	0.041628	ENSG00000115461	ENST00000233813;ENST00000449583	T;T	0.42131	0.98;1.99	5.07	4.18	0.49190	.	0.358254	0.30118	N	0.010380	T	0.20210	0.0486	L	0.51422	1.61	0.52501	D	0.999958	D	0.76494	0.999	P	0.59171	0.853	T	0.12604	-1.0541	10	0.38643	T	0.18	-22.7157	12.4718	0.55792	0.0:0.0:0.8328:0.1672	rs11575194;rs52792956;rs11575194	138	P24593	IBP5_HUMAN	W	138;183	ENSP00000233813:R138W;ENSP00000413474:R183W	ENSP00000233813:R138W	R	-	1	2	IGFBP5	217251973	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.253000	0.51469	1.356000	0.45884	0.561000	0.74099	CGG	G|0.973;A|0.027	0.027	strong		0.602	IGFBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256674.2	NM_000599	
USP15	9958	hgsc.bcm.edu	37	12	62785663	62785663	+	Silent	SNP	T	T	C	rs11174457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:62785663T>C	ENST00000280377.5	+	17	2359	c.2301T>C	c.(2299-2301)gcT>gcC	p.A767A	USP15_ENST00000353364.3_Silent_p.A738A|USP15_ENST00000393654.3_Silent_p.A742A	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	767	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		AAAATGCTGCTGAGGTAAGTC	0.318													T|||	302	0.0603035	0.0635	0.0836	5008	,	,		15367	0.006		0.0875	False		,,,				2504	0.0675				p.A767A	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											USP15,NS,carcinoma,0,1	USP15	105	1	0			c.T2301C						PASS	.	T		249,4153	138.8+/-174.5	6,237,1958	65.0	63.0	63.0		2214	0.4	1.0	12	dbSNP_120	63	707,7877	169.3+/-220.7	33,641,3618	no	coding-synonymous	USP15	NM_006313.1		39,878,5576	CC,CT,TT		8.2363,5.6565,7.3618		738/953	62785663	956,12030	2201	4292	6493	SO:0001819	synonymous_variant	9958	exon17			TGCTGCTGAGGTA	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2301T>C	12.37:g.62785663T>C		Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	339	152	0.448378	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	37	CCDS58251.1																																																																																			T|0.933;C|0.067	0.067	strong		0.318	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
FRAS1	80144	hgsc.bcm.edu	37	4	79385719	79385719	+	Silent	SNP	G	G	A	rs6851427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:79385719G>A	ENST00000264895.6	+	49	7451	c.7011G>A	c.(7009-7011)gcG>gcA	p.A2337A		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2337					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AGCTTAAGGCGGTGGATGCTG	0.542													G|||	1490	0.297524	0.1422	0.4409	5008	,	,		20735	0.3194		0.3618	False		,,,				2504	0.317				p.A2337A		Atlas-SNP	.											.	FRAS1	779	.	0			c.G7011A						PASS	.	G		735,3483		64,607,1438	103.0	99.0	101.0		7011	-11.0	0.0	4	dbSNP_116	101	3199,5261		581,2037,1612	no	coding-synonymous	FRAS1	NM_025074.6		645,2644,3050	AA,AG,GG		37.8132,17.4253,31.0301		2337/4013	79385719	3934,8744	2109	4230	6339	SO:0001819	synonymous_variant	80144	exon49			TAAGGCGGTGGAT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.7011G>A	4.37:g.79385719G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	700	0.32051282051282054	85	0.17276422764227642	155	0.4281767955801105	180	0.3146853146853147	280	0.36939313984168864	G	0.089	-1.170149	0.01660	0.174253	0.378132	ENSG00000138759	ENST00000512123	.	.	.	5.49	-11.0	0.00169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999981	.	.	.	.	.	.	T	0.12477	-1.0546	3	.	.	.	.	5.2213	0.15370	0.5169:0.2383:0.0704:0.1744	rs6851427;rs6851427	.	.	.	S	566	.	.	G	+	1	0	FRAS1	79604743	0.000000	0.05858	0.029000	0.17559	0.016000	0.09150	-2.249000	0.01188	-3.583000	0.00137	-0.137000	0.14449	GGT	G|0.682;A|0.318	0.318	strong		0.542	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
DDR2	4921	hgsc.bcm.edu	37	1	162737116	162737116	+	Silent	SNP	C	C	G	rs2298258	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:162737116C>G	ENST00000367922.3	+	12	1698	c.1260C>G	c.(1258-1260)ctC>ctG	p.L420L	DDR2_ENST00000367921.3_Silent_p.L420L	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	420					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	TCATCATCCTCTGGAGGCAGT	0.473													C|||	1745	0.348442	0.5023	0.353	5008	,	,		20143	0.4077		0.1461	False		,,,				2504	0.2843				p.L420L	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											DDR2_ENST00000367922,NS,carcinoma,+2,1	DDR2	228	1	0			c.C1260G						PASS	.	C	,	2082,2324	572.6+/-383.4	502,1078,623	117.0	107.0	110.0		1260,1260	1.6	1.0	1	dbSNP_100	110	1264,7336	252.6+/-278.6	103,1058,3139	no	coding-synonymous,coding-synonymous	DDR2	NM_001014796.1,NM_006182.2	,	605,2136,3762	GG,GC,CC		14.6977,47.2537,25.7266	,	420/856,420/856	162737116	3346,9660	2203	4300	6503	SO:0001819	synonymous_variant	4921	exon12			CATCCTCTGGAGG	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"""discoidin domain receptor family, member 2"""	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.1260C>G	1.37:g.162737116C>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	234	123	0.525641	NM_001014796	Q7Z730	Silent	SNP	ENST00000367922.3	37	CCDS1241.1	705	0.3228021978021978	253	0.5142276422764228	113	0.31215469613259667	237	0.4143356643356643	102	0.1345646437994723	C	9.562	1.118647	0.20877	0.472537	0.146977	ENSG00000162733	ENST00000433757	T	0.74315	-0.83	5.79	1.65	0.23941	.	0.000000	0.85682	D	0.000000	T	0.67420	0.2891	.	.	.	0.31024	P	0.717955	.	.	.	.	.	.	T	0.68010	-0.5522	6	0.87932	D	0	.	9.3142	0.37924	0.0:0.5761:0.2821:0.1418	rs2298258;rs2298258	.	.	.	V	13	ENSP00000396864:L13V	ENSP00000396864:L13V	L	+	1	2	DDR2	161003740	0.991000	0.36638	0.998000	0.56505	0.995000	0.86356	0.218000	0.17622	0.034000	0.15491	0.655000	0.94253	CTG	C|0.718;G|0.282	0.282	strong		0.473	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182	
C22orf42	150297	hgsc.bcm.edu	37	22	32554985	32554985	+	Missense_Mutation	SNP	A	A	G	rs5998267	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:32554985A>G	ENST00000382097.3	-	1	290	c.218T>C	c.(217-219)cTg>cCg	p.L73P	RP1-90G24.8_ENST00000426354.1_lincRNA	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	73			L -> P (in dbSNP:rs5998267).							NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						GGACATCTTCAGCATCTTCGG	0.557													.|||	2917	0.582468	0.8495	0.4193	5008	,	,		17928	0.4167		0.4831	False		,,,				2504	0.6104				p.L73P		Atlas-SNP	.											.	C22orf42	37	.	0			c.T218C						PASS	.	G	PRO/LEU	3508,898	336.3+/-304.3	1393,722,88	159.0	158.0	158.0		218		0.0	22	dbSNP_114	158	3969,4631	583.1+/-391.5	947,2075,1278	yes	missense	C22orf42	NM_001010859.1	98	2340,2797,1366	GG,GA,AA		46.1512,20.3813,42.5111	benign	73/252	32554985	7477,5529	2203	4300	6503	SO:0001583	missense	150297	exon1			ATCTTCAGCATCT	BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.218T>C	22.37:g.32554985A>G	ENSP00000371529:p.Leu73Pro	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	297	144	0.484848	NM_001010859	A4QPH5	Missense_Mutation	SNP	ENST00000382097.3	37	CCDS33639.1	1168	0.5347985347985348	409	0.8313008130081301	157	0.43370165745856354	234	0.4090909090909091	368	0.48548812664907653	G	0.016	-1.533546	0.00951	0.796187	0.461512	ENSG00000205856	ENST00000382097	T	0.34472	1.36	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31052	-0.9957	6	0.41790	T	0.15	.	.	.	.	rs5998267;rs8141156;rs52829159;rs56619140;rs59525772;rs5998267	73	Q6IC83	CV042_HUMAN	P	73	ENSP00000371529:L73P	ENSP00000371529:L73P	L	-	2	0	C22orf42	30884985	0.003000	0.15002	0.021000	0.16686	0.021000	0.10359	-1.336000	0.02660	-2.036000	0.00922	-2.094000	0.00368	CTG	A|0.432;G|0.568	0.568	strong		0.557	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859	
UTP14A	10813	hgsc.bcm.edu	37	X	129054446	129054446	+	Missense_Mutation	SNP	G	G	A	rs35183830	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:129054446G>A	ENST00000394422.3	+	9	794	c.766G>A	c.(766-768)Gtg>Atg	p.V256M	RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000425117.2_Missense_Mutation_p.V204M|UTP14A_ENST00000371042.3_Missense_Mutation_p.V88M|UTP14A_ENST00000371051.5_Missense_Mutation_p.V202M	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	256					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(16)|ovary(3)|urinary_tract(1)	32						TCACAAAGTCGTGAAGAAAGG	0.468													G|||	27	0.00715232	0.0	0.0101	3775	,	,		15530	0.0		0.0199	False		,,,				2504	0.0				p.V256M		Atlas-SNP	.											.	UTP14A	74	.	0			c.G766A						PASS	.	G	MET/VAL,MET/VAL	21,3814		0,17,4,1615,567	119.0	117.0	117.0		610,766	0.3	0.0	X	dbSNP_126	117	213,6515		3,163,44,2262,1828	yes	missense,missense	UTP14A	NM_001166221.1,NM_006649.3	21,21	3,180,48,3877,2395	AA,AG,A,GG,G		3.1659,0.5476,2.2153	possibly-damaging,possibly-damaging	204/720,256/772	129054446	234,10329	2203	4300	6503	SO:0001583	missense	10813	exon9			AAAGTCGTGAAGA	AF039694	CCDS14615.1, CCDS55489.1	Xq26.1	2009-01-15	2004-06-01	2004-06-01	ENSG00000156697	ENSG00000156697			10665	protein-coding gene	gene with protein product		300508	"""serologically defined colon cancer antigen 16"""	SDCCAG16		9610721, 16354793	Standard	NM_006649		Approved	NY-CO-16	uc004euz.3	Q9BVJ6	OTTHUMG00000022378	ENST00000394422.3:c.766G>A	X.37:g.129054446G>A	ENSP00000377944:p.Val256Met	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	155	145	0.935484	NM_006649	A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Missense_Mutation	SNP	ENST00000394422.3	37	CCDS14615.1	18	0.0108499095840868	0	0.0	4	0.011049723756906077	0	0.0	12	0.015915119363395226	G	7.052	0.564612	0.13498	0.005476	0.031659	ENSG00000156697	ENST00000425117;ENST00000394422;ENST00000371051;ENST00000427972;ENST00000371042	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	6.17	0.291	0.15732	.	0.560306	0.20217	N	0.096775	T	0.03220	0.0094	L	0.36672	1.1	0.24976	N	0.991635	B;B;B	0.28470	0.178;0.06;0.213	B;B;B	0.24701	0.033;0.031;0.055	T	0.18777	-1.0326	10	0.45353	T	0.12	-0.769	4.3378	0.11095	0.273:0.4021:0.2538:0.0711	rs35183830;rs35183830	202;204;256	F8WD00;E9PEL7;Q9BVJ6	.;.;UT14A_HUMAN	M	204;256;202;88;88	ENSP00000388669:V204M;ENSP00000377944:V256M;ENSP00000360090:V202M;ENSP00000413187:V88M;ENSP00000360081:V88M	ENSP00000360081:V88M	V	+	1	0	UTP14A	128882127	0.999000	0.42202	0.011000	0.14972	0.010000	0.07245	2.143000	0.42187	-0.415000	0.07484	-0.849000	0.03036	GTG	G|0.984;A|0.016	0.016	strong		0.468	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058221.1	NM_006649	
FAT4	79633	hgsc.bcm.edu	37	4	126411594	126411594	+	Silent	SNP	G	G	A	rs62312781	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:126411594G>A	ENST00000394329.3	+	17	13630	c.13617G>A	c.(13615-13617)gaG>gaA	p.E4539E	FAT4_ENST00000335110.5_Silent_p.E2780E	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4539					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						ATCCCAAAGAGGAGAAGAAAC	0.522													G|||	786	0.156949	0.236	0.2349	5008	,	,		19314	0.0		0.1819	False		,,,				2504	0.1309				p.E4539E		Atlas-SNP	.											.	FAT4	1752	.	0			c.G13617A						PASS	.	G		916,3490	348.2+/-309.8	108,700,1395	69.0	72.0	71.0		13617	1.8	0.9	4	dbSNP_129	71	1587,7013	293.9+/-301.6	145,1297,2858	no	coding-synonymous	FAT4	NM_024582.4		253,1997,4253	AA,AG,GG		18.4535,20.7898,19.245		4539/4982	126411594	2503,10503	2203	4300	6503	SO:0001819	synonymous_variant	79633	exon17			CAAAGAGGAGAAG	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.13617G>A	4.37:g.126411594G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			G|0.825;A|0.175	0.175	strong		0.522	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
HSPD1	3329	hgsc.bcm.edu	37	2	198363534	198363534	+	Silent	SNP	C	C	T	rs565153254		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:198363534C>T	ENST00000388968.3	-	2	306	c.39G>A	c.(37-39)ccG>ccA	p.P13P	HSPD1_ENST00000544407.1_Silent_p.P13P|HSPE1_ENST00000409729.1_5'Flank|HSPE1_ENST00000409468.1_5'Flank|HSPE1_ENST00000233893.5_5'Flank|HSPD1_ENST00000345042.2_Silent_p.P13P|HSPE1-MOB4_ENST00000604458.1_5'Flank	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	13					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)	p.P13P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			CCCTGGACACCGGTCTCATCT	0.502																																					p.P13P		Atlas-SNP	.											HSPD1_ENST00000426480,NS,haematopoietic_neoplasm,0,3	HSPD1	68	3	1	Substitution - coding silent(1)	breast(1)	c.G39A						scavenged	.						52.0	49.0	50.0					2																	198363534		2203	4300	6503	SO:0001819	synonymous_variant	3329	exon2			GGACACCGGTCTC	M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"""Heat Shock Proteins / Chaperonins"""	5261	protein-coding gene	gene with protein product		118190	"""heat shock 60kD protein 1 (chaperonin)"", ""spastic paraplegia 13 (autosomal dominant)"""	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.39G>A	2.37:g.198363534C>T		Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	279	4	0.0143369	NM_002156	B2R5M6|B7Z712|Q38L19|Q9UCR6	Silent	SNP	ENST00000388968.3	37	CCDS33357.1																																																																																			.	.	none		0.502	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156	
SHQ1	55164	hgsc.bcm.edu	37	3	72799703	72799703	+	Missense_Mutation	SNP	C	C	T	rs35178407	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:72799703C>T	ENST00000325599.8	-	11	1605	c.1466G>A	c.(1465-1467)aGt>aAt	p.S489N	SHQ1_ENST00000468371.1_5'UTR|SHQ1_ENST00000463369.1_Missense_Mutation_p.S461N	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	489	Ser-rich.		S -> N (in dbSNP:rs35178407). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		TTGCAAAGAACTGACTGTCTC	0.473													c|||	1462	0.291933	0.6936	0.2003	5008	,	,		21525	0.0367		0.2406	False		,,,				2504	0.1299				p.S489N		Atlas-SNP	.											SHQ1,NS,carcinoma,+1,1	SHQ1	60	1	0			c.G1466A						PASS	.	C	ASN/SER	2724,1682	656.5+/-400.1	852,1020,331	124.0	120.0	122.0		1466	-11.0	0.0	3	dbSNP_126	122	2148,6452	369.7+/-335.6	267,1614,2419	yes	missense	SHQ1	NM_018130.2	46	1119,2634,2750	TT,TC,CC		24.9767,38.1752,37.4596	benign	489/578	72799703	4872,8134	2203	4300	6503	SO:0001583	missense	55164	exon11			AAAGAACTGACTG	BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"""SHQ1 homolog (S. cerevisiae)"""			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.1466G>A	3.37:g.72799703C>T	ENSP00000315182:p.Ser489Asn	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	226	100	0.442478	NM_018130	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Missense_Mutation	SNP	ENST00000325599.8	37	CCDS33788.1	604	0.2765567765567766	328	0.6666666666666666	66	0.18232044198895028	18	0.03146853146853147	192	0.2532981530343008	c	4.444	0.082137	0.08533	0.618248	0.249767	ENSG00000144736	ENST00000325599;ENST00000463369	T;T	0.30182	1.56;1.54	5.52	-11.0	0.00169	.	2.458750	0.01385	N	0.013072	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24799	-1.0150	9	0.02654	T	1	5.7921	5.1688	0.15099	0.0852:0.378:0.3244:0.2124	rs35178407	489	Q6PI26	SHQ1_HUMAN	N	489;461	ENSP00000315182:S489N;ENSP00000417452:S461N	ENSP00000315182:S489N	S	-	2	0	SHQ1	72882393	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.307000	0.08167	-4.380000	0.00053	-1.925000	0.00514	AGT	C|0.666;T|0.334	0.334	strong		0.473	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130	
GATAD2A	54815	hgsc.bcm.edu	37	19	19606634	19606634	+	Silent	SNP	G	G	A	rs1047361	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19606634G>A	ENST00000360315.3	+	6	1008	c.696G>A	c.(694-696)tcG>tcA	p.S232S	GATAD2A_ENST00000358713.3_Silent_p.S232S|GATAD2A_ENST00000429563.2_Silent_p.S59S|GATAD2A_ENST00000252577.5_Silent_p.S232S|GATAD2A_ENST00000404158.1_Silent_p.S232S|GATAD2A_ENST00000537887.1_Intron	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	232					anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						AGGCGTCCTCGAAGCTGGGGC	0.652													G|||	2375	0.474241	0.6566	0.4798	5008	,	,		13831	0.3194		0.325	False		,,,				2504	0.5368				p.S232S		Atlas-SNP	.											.	GATAD2A	81	.	0			c.G696A						PASS	.	G		2733,1673	653.2+/-399.5	833,1067,303	51.0	46.0	48.0		696	-9.9	0.0	19	dbSNP_86	48	3031,5569	465.6+/-366.6	535,1961,1804	no	coding-synonymous	GATAD2A	NM_017660.3		1368,3028,2107	AA,AG,GG		35.2442,37.9709,44.318		232/634	19606634	5764,7242	2203	4300	6503	SO:0001819	synonymous_variant	54815	exon6			GTCCTCGAAGCTG	AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"""GATA zinc finger domain containing"""	29989	protein-coding gene	gene with protein product	"""p66 alpha"""	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.696G>A	19.37:g.19606634G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Silent	SNP	ENST00000360315.3	37	CCDS12402.2																																																																																			A|0.431;G|0.569;T|0.000	0.431	strong		0.652	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660	
STK17B	9262	hgsc.bcm.edu	37	2	197021276	197021276	+	Silent	SNP	T	T	C	rs10931726	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:197021276T>C	ENST00000263955.4	-	3	508	c.222A>G	c.(220-222)cgA>cgG	p.R74R	RP11-347P5.1_ENST00000606818.1_RNA|STK17B_ENST00000409228.1_Silent_p.R74R	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	74	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(10)	15			OV - Ovarian serous cystadenocarcinoma(117;0.141)			AAATTTCTGCTCGACAATCCT	0.358													T|||	2355	0.470248	0.1006	0.5893	5008	,	,		16480	0.5536		0.6103	False		,,,				2504	0.6554				p.R74R		Atlas-SNP	.											STK17B,NS,carcinoma,-1,1	STK17B	28	1	0			c.A222G						PASS	.	T		817,3589	325.9+/-299.3	84,649,1470	97.0	91.0	93.0		222	1.4	1.0	2	dbSNP_120	93	5060,3540	630.1+/-398.3	1482,2096,722	no	coding-synonymous	STK17B	NM_004226.3		1566,2745,2192	CC,CT,TT		41.1628,18.5429,45.1868		74/373	197021276	5877,7129	2203	4300	6503	SO:0001819	synonymous_variant	9262	exon3			TTCTGCTCGACAA	AB011421	CCDS2315.1	2q33.1	2008-02-05	2007-02-12		ENSG00000081320	ENSG00000081320			11396	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 2"""	604727	"""serine/threonine kinase 17b (apoptosis-inducing)"""			9786912	Standard	NM_004226		Approved	DRAK2	uc002utk.3	O94768	OTTHUMG00000132735	ENST00000263955.4:c.222A>G	2.37:g.197021276T>C		Somatic	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	244	95	0.389344	NM_004226		Silent	SNP	ENST00000263955.4	37	CCDS2315.1																																																																																			T|0.540;C|0.460	0.460	strong		0.358	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2		
KRTAP10-5	386680	hgsc.bcm.edu	37	21	45999716	45999716	+	Missense_Mutation	SNP	T	T	C	rs7509970	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:45999716T>C	ENST00000400372.1	-	1	765	c.740A>G	c.(739-741)tAc>tGc	p.Y247C	TSPEAR_ENST00000323084.4_Intron	NM_198694.2	NP_941967.2	P60370	KR105_HUMAN	keratin associated protein 10-5	247	22 X 5 AA repeats of C-C-X(3).		Y -> C (in dbSNP:rs7509970).			keratin filament (GO:0045095)				endometrium(2)|kidney(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	14						GCTGGCCTGGTAGGAGGAGGC	0.721													.|||	681	0.135982	0.2133	0.0706	5008	,	,		18145	0.1756		0.0537	False		,,,				2504	0.1217				p.Y247C		Atlas-SNP	.											.	KRTAP10-5	43	.	0			c.A740G						PASS	.	C	,CYS/TYR	732,3670		73,586,1542	32.0	43.0	40.0		,740	3.4	0.2	21	dbSNP_116	40	349,8239		10,329,3955	no	intron,missense	TSPEAR,KRTAP10-5	NM_144991.2,NM_198694.2	,194	83,915,5497	CC,CT,TT		4.0638,16.6288,8.3218	,benign	,247/272	45999716	1081,11909	2201	4294	6495	SO:0001583	missense	386680	exon1			GCCTGGTAGGAGG	AJ566384	CCDS42958.1	21q22.3	2007-10-05			ENSG00000241123	ENSG00000241123		"""Keratin associated proteins"""	22969	protein-coding gene	gene with protein product				KRTAP18-5			Standard	NM_198694		Approved	KAP10.5, KAP18.5	uc002zfl.1	P60370	OTTHUMG00000057638	ENST00000400372.1:c.740A>G	21.37:g.45999716T>C	ENSP00000383223:p.Tyr247Cys	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_198694	Q0VAR7|Q0VAR8|Q70LJ3	Missense_Mutation	SNP	ENST00000400372.1	37	CCDS42958.1	269	0.12316849816849818	104	0.21138211382113822	27	0.07458563535911603	107	0.18706293706293706	31	0.040897097625329816	c	0	-2.696963	0.00098	0.166288	0.040638	ENSG00000241123	ENST00000400372	T	0.00651	5.97	3.43	3.43	0.39272	.	.	.	.	.	T	0.00012	0.0000	N	0.00012	-2.955	0.80722	P	0.0	B	0.12013	0.005	B	0.01281	0.0	T	0.29119	-1.0022	8	0.02654	T	1	.	5.1866	0.15187	0.0:0.6694:0.2103:0.1203	rs7509970	247	P60370	KR105_HUMAN	C	247	ENSP00000383223:Y247C	ENSP00000383223:Y247C	Y	-	2	0	KRTAP10-5	44824144	1.000000	0.71417	0.234000	0.24042	0.007000	0.05969	1.325000	0.33724	0.785000	0.33685	-0.374000	0.07098	TAC	T|0.893;C|0.107	0.107	strong		0.721	KRTAP10-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128042.1		
TSC22D2	9819	hgsc.bcm.edu	37	3	150128154	150128154	+	Silent	SNP	T	T	C	rs61734437	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:150128154T>C	ENST00000361875.3	+	1	2033	c.1017T>C	c.(1015-1017)ccT>ccC	p.P339P	TSC22D2_ENST00000361136.2_Silent_p.P339P	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	339					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TGTCCCTGCCTCCGCAGCCGG	0.731													T|||	425	0.0848642	0.0408	0.0879	5008	,	,		12811	0.0317		0.174	False		,,,				2504	0.1053				p.P339P		Atlas-SNP	.											TSC22D2,colon,carcinoma,0,1	TSC22D2	42	1	0			c.T1017C						scavenged	.	T		203,3721		5,193,1764	6.0	7.0	7.0		1017	-6.9	0.0	3	dbSNP_129	7	1191,6657		98,995,2831	no	coding-synonymous	TSC22D2	NM_014779.2		103,1188,4595	CC,CT,TT		15.1758,5.1733,11.8417		339/781	150128154	1394,10378	1962	3924	5886	SO:0001819	synonymous_variant	9819	exon1			CCTGCCTCCGCAG	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.1017T>C	3.37:g.150128154T>C		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	3	3	1	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Silent	SNP	ENST00000361875.3	37	CCDS3149.1																																																																																			T|0.904;C|0.096	0.096	strong		0.731	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779	
FRMPD1	22844	hgsc.bcm.edu	37	9	37735680	37735680	+	Silent	SNP	G	G	A	rs61740795	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:37735680G>A	ENST00000539465.1	+	13	1943	c.1350G>A	c.(1348-1350)acG>acA	p.T450T	FRMPD1_ENST00000536622.1_Silent_p.T272T|FRMPD1_ENST00000377765.3_Silent_p.T450T|FRMPD1_ENST00000541302.1_Silent_p.T319T|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	450	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		TAGAGCTAACGGAAGAGTCTG	0.458													G|||	284	0.0567093	0.0091	0.1066	5008	,	,		15661	0.0		0.1849	False		,,,				2504	0.0123				p.T450T		Atlas-SNP	.											FRMPD1,NS,carcinoma,0,1	FRMPD1	237	1	0			c.G1350A						PASS	.	G		169,4237	112.1+/-150.2	2,165,2036	117.0	114.0	115.0		1350	-11.2	0.0	9	dbSNP_129	115	1549,7051	292.1+/-300.7	122,1305,2873	no	coding-synonymous	FRMPD1	NM_014907.2		124,1470,4909	AA,AG,GG		18.0116,3.8357,13.2093		450/1579	37735680	1718,11288	2203	4300	6503	SO:0001819	synonymous_variant	22844	exon13			GCTAACGGAAGAG	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1350G>A	9.37:g.37735680G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	37	CCDS6612.1																																																																																			G|0.877;A|0.123	0.123	strong		0.458	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
KIF27	55582	hgsc.bcm.edu	37	9	86474115	86474115	+	Missense_Mutation	SNP	T	T	C	rs55654273	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:86474115T>C	ENST00000297814.2	-	14	3249	c.3106A>G	c.(3106-3108)Aat>Gat	p.N1036D	RP11-575L7.4_ENST00000590417.1_RNA|RP11-575L7.4_ENST00000586206.1_RNA|RP11-575L7.4_ENST00000591217.1_RNA|RP11-575L7.4_ENST00000608866.1_RNA|RP11-575L7.4_ENST00000586211.1_RNA|KIF27_ENST00000334204.2_Missense_Mutation_p.N939D|RP11-575L7.4_ENST00000589817.1_RNA|RP11-575L7.4_ENST00000590368.1_RNA|RP11-575L7.4_ENST00000590813.1_RNA|RP11-575L7.4_ENST00000589233.1_RNA|RP11-575L7.4_ENST00000421734.3_RNA|RP11-575L7.4_ENST00000592283.1_RNA|KIF27_ENST00000413982.1_Missense_Mutation_p.N970D	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	1036			N -> D (in dbSNP:rs55654273). {ECO:0000269|PubMed:17974005}.		ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						TCATCCACATTGTGTCTGCGT	0.413													T|||	605	0.120807	0.146	0.0937	5008	,	,		18178	0.1071		0.1312	False		,,,				2504	0.1094				p.N1036D		Atlas-SNP	.											.	KIF27	103	.	0			c.A3106G						PASS	.	T	ASP/ASN	642,3762	275.7+/-272.7	51,540,1611	225.0	194.0	205.0		3106	4.5	1.0	9	dbSNP_129	205	1182,7418	240.8+/-271.4	83,1016,3201	yes	missense	KIF27	NM_017576.1	23	134,1556,4812	CC,CT,TT		13.7442,14.5777,14.0265	benign	1036/1402	86474115	1824,11180	2202	4300	6502	SO:0001583	missense	55582	exon14			CCACATTGTGTCT	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.3106A>G	9.37:g.86474115T>C	ENSP00000297814:p.Asn1036Asp	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	302	123	0.407285	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	251	0.11492673992673992	70	0.14227642276422764	33	0.09116022099447514	47	0.08216783216783216	101	0.13324538258575197	T	8.103	0.777160	0.16120	0.145777	0.137442	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.69040	-0.37;-0.37;-0.24	4.5	4.5	0.54988	.	0.000000	0.64402	D	0.000004	T	0.00210	0.0006	N	0.02539	-0.55	0.58432	P	5.000000000032756E-6	B;B;B	0.17038	0.0;0.003;0.02	B;B;B	0.11329	0.0;0.006;0.004	T	0.04991	-1.0913	9	0.18276	T	0.48	.	8.6475	0.34013	0.0:0.0858:0.0:0.9142	rs55654273	939;970;1036	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	D	1036;970;939	ENSP00000297814:N1036D;ENSP00000401688:N970D;ENSP00000333928:N939D	ENSP00000297814:N1036D	N	-	1	0	KIF27	85663935	0.992000	0.36948	0.989000	0.46669	0.023000	0.10783	2.997000	0.49457	1.883000	0.54544	0.402000	0.26972	AAT	T|0.869;C|0.131	0.131	strong		0.413	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
SERPINB6	5269	hgsc.bcm.edu	37	6	2959513	2959513	+	Silent	SNP	C	C	T	rs2236277	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:2959513C>T	ENST00000380520.1	-	1	2048	c.54G>A	c.(52-54)acG>acA	p.T18T	SERPINB6_ENST00000380524.1_Silent_p.T18T|SERPINB6_ENST00000380539.1_Silent_p.T18T|SERPINB6_ENST00000380546.3_Silent_p.T18T|SERPINB6_ENST00000380529.1_Silent_p.T18T|SERPINB6_ENST00000335686.5_Silent_p.T18T			P35237	SPB6_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 6	18					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T18T(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|stomach(1)|upper_aerodigestive_tract(2)	17	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	CTTTACCCAGCGTTTTCAAAA	0.468													C|||	1709	0.341254	0.1513	0.4539	5008	,	,		21942	0.4841		0.338	False		,,,				2504	0.3742				p.T37T		Atlas-SNP	.											SERPINB6,NS,carcinoma,0,1	SERPINB6	31	1	1	Substitution - coding silent(1)	stomach(1)	c.G111A						PASS	.	C	,	805,3601	323.7+/-298.2	76,653,1474	148.0	134.0	139.0		54,54	-1.1	0.3	6	dbSNP_98	139	2761,5839	439.8+/-359.3	427,1907,1966	no	coding-synonymous,coding-synonymous	SERPINB6	NM_001195291.1,NM_004568.5	,	503,2560,3440	TT,TC,CC		32.1047,18.2705,27.4181	,	18/377,18/377	2959513	3566,9440	2203	4300	6503	SO:0001819	synonymous_variant	5269	exon2			ACCCAGCGTTTTC	Z22658	CCDS4479.1, CCDS75386.1, CCDS75387.1	6p25.2	2014-02-18	2005-08-18		ENSG00000124570	ENSG00000124570		"""Serine (or cysteine) peptidase inhibitors"""	8950	protein-coding gene	gene with protein product	"""cytoplasmic antiproteinase"""	173321	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6"", ""deafness, autosomal recessive 91"""	PI6, DFNB91		8415716, 9858835, 20451170, 24172014	Standard	NM_004568		Approved	PTI, CAP	uc031smo.1	P35237	OTTHUMG00000016170	ENST00000380520.1:c.54G>A	6.37:g.2959513C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	168	167	0.994048	NM_001271823	B2RBA8|Q59F97|Q5TD06|Q7Z2Y7|Q96J44|Q9UDI7	Silent	SNP	ENST00000380520.1	37	CCDS4479.1	735	0.33653846153846156	61	0.12398373983739837	162	0.44751381215469616	274	0.479020979020979	238	0.31398416886543534	C	7.310	0.614766	0.14129	0.182705	0.321047	ENSG00000124570	ENST00000380500	.	.	.	5.11	-1.14	0.09741	.	.	.	.	.	T	0.11879	0.0289	.	.	.	0.46185	P	0.0010879999999999779	.	.	.	.	.	.	T	0.24835	-1.0149	3	.	.	.	.	4.0275	0.09693	0.4755:0.2285:0.0:0.296	rs2236277;rs59298149;rs2236277	.	.	.	H	7	.	.	R	-	2	0	SERPINB6	2904512	0.000000	0.05858	0.317000	0.25265	0.860000	0.49131	-0.626000	0.05527	-0.034000	0.13713	0.591000	0.81541	CGC	C|0.691;A|0.002	.	strong		0.468	SERPINB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043422.1		
FOXD4	2298	hgsc.bcm.edu	37	9	116800	116800	+	Nonstop_Mutation	SNP	C	C	G	rs79220013	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:116800C>G	ENST00000382500.2	-	1	1617	c.1320G>C	c.(1318-1320)taG>taC	p.*440Y		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	0					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.*440Y(1)		endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		CCACCTGGCTCTAGGAGGGCC	0.642																																					p.X440Y		Atlas-SNP	.											FOXD4_ENST00000382500,NS,carcinoma,0,1	FOXD4	75	1	1	Nonstop extension(1)	large_intestine(1)	c.G1320C						PASS	.	C	TYR/stop	490,3462		34,422,1520	16.0	20.0	19.0		1320	1.5	0.7	9	dbSNP_131	19	1918,5986		195,1528,2229	no	stop-lost	FOXD4	NM_207305.3		229,1950,3749	GG,GC,CC		24.2662,12.3988,20.3104		440/440	116800	2408,9448	1976	3952	5928	SO:0001578	stop_lost	2298	exon1			CTGGCTCTAGGAG	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.1320G>C	9.37:g.116800C>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	242	77	0.318182	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	502	0.22985347985347984	49	0.09959349593495935	69	0.19060773480662985	166	0.2902097902097902	218	0.287598944591029	.	4.305	0.055848	0.08291	0.123988	0.242662	ENSG00000170122	ENST00000382500	.	.	.	2.41	1.47	0.22746	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7839	0.23662	0.0:0.8374:0.0:0.1626	.	.	.	.	Y	440	.	.	X	-	3	2	FOXD4	106800	0.004000	0.15560	0.657000	0.29651	0.049000	0.14656	1.312000	0.33574	1.347000	0.45714	0.473000	0.43528	TAG	C|0.766;G|0.234	0.234	strong		0.642	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
SNX16	64089	hgsc.bcm.edu	37	8	82727569	82727569	+	Silent	SNP	T	T	C	rs16909651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:82727569T>C	ENST00000345957.4	-	5	950	c.672A>G	c.(670-672)gaA>gaG	p.E224E	SNX16_ENST00000396330.2_Silent_p.E224E|SNX16_ENST00000353788.4_Silent_p.E195E|RP13-923O23.6_ENST00000524337.1_RNA	NM_152836.2	NP_690049.1	P57768	SNX16_HUMAN	sorting nexin 16	224					early endosome to late endosome transport (GO:0045022)|endosome to lysosome transport (GO:0008333)|protein targeting to lysosome (GO:0006622)	early endosome (GO:0005769)|extrinsic component of endosome membrane (GO:0031313)|late endosome (GO:0005770)|lysosome (GO:0005764)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			large_intestine(1)|ovary(1)|pancreas(1)|skin(2)	5						CCCTGCTTTCTTCTAGGCTAT	0.353													T|||	786	0.156949	0.0144	0.147	5008	,	,		16427	0.1974		0.1978	False		,,,				2504	0.273				p.E224E		Atlas-SNP	.											SNX16,caecum,carcinoma,0,1	SNX16	21	1	0			c.A672G						PASS	.	T	,,	192,4214	121.3+/-158.8	4,184,2015	101.0	90.0	94.0		672,672,585	4.6	1.0	8	dbSNP_123	94	1600,7000	297.7+/-303.5	165,1270,2865	no	coding-synonymous,coding-synonymous,coding-synonymous	SNX16	NM_022133.3,NM_152836.2,NM_152837.2	,,	169,1454,4880	CC,CT,TT		18.6047,4.3577,13.7783	,,	224/345,224/345,195/316	82727569	1792,11214	2203	4300	6503	SO:0001819	synonymous_variant	64089	exon5			GCTTTCTTCTAGG	AF305779	CCDS6234.1, CCDS6235.1	8q21.13	2011-05-03			ENSG00000104497	ENSG00000104497		"""Sorting nexins"""	14980	protein-coding gene	gene with protein product		614903				12461558, 12813048	Standard	NM_152837		Approved		uc003ycn.3	P57768	OTTHUMG00000164727	ENST00000345957.4:c.672A>G	8.37:g.82727569T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	136	54	0.397059	NM_152836	A8K4D8|Q658L0|Q8N4U3	Silent	SNP	ENST00000345957.4	37	CCDS6234.1																																																																																			T|0.855;C|0.145	0.145	strong		0.353	SNX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379929.1	NM_022133	
FMN1	342184	hgsc.bcm.edu	37	15	33359574	33359574	+	Intron	SNP	C	C	A	rs11858145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:33359574C>A	ENST00000559047.1	-	3	2043				FMN1_ENST00000559150.1_Intron|FMN1_ENST00000558197.1_Missense_Mutation_p.G171V|FMN1_ENST00000334528.9_Missense_Mutation_p.G171V|FMN1_ENST00000561249.1_Intron			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		AGATAAAACACCACTAGGGGA	0.532													A|||	3622	0.723243	0.587	0.7795	5008	,	,		19433	0.8284		0.6481	False		,,,				2504	0.8364				p.G171V		Atlas-SNP	.											.	FMN1	174	.	0			c.G512T						PASS	.	A	VAL/GLY	2309,1539		695,919,310	59.0	59.0	59.0		512	1.0	0.0	15	dbSNP_120	59	5361,2913		1753,1855,529	yes	missense	FMN1	NM_001103184.2	109	2448,2774,839	AA,AC,CC		35.2067,39.9948,36.7266	benign	171/1197	33359574	7670,4452	1924	4137	6061	SO:0001627	intron_variant	342184	exon1			AAAACACCACTAG	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-2299G>T	15.37:g.33359574C>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		1553	0.7110805860805861	295	0.5995934959349594	281	0.7762430939226519	489	0.8548951048951049	488	0.6437994722955145	A	0.037	-1.303150	0.01353	0.600052	0.647933	ENSG00000248905	ENST00000334528	T	0.35421	1.31	4.84	1.03	0.20045	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38950	-0.9637	7	0.02654	T	1	.	5.7546	0.18166	0.2735:0.5962:0.1303:0.0	rs11858145;rs52816131;rs56844861;rs11858145	171;171	Q68DA7-3;Q68DA7-5	.;.	V	171	ENSP00000333950:G171V	ENSP00000333950:G171V	G	-	2	0	FMN1	31146866	0.000000	0.05858	0.000000	0.03702	0.200000	0.23975	-0.756000	0.04777	0.018000	0.15052	-0.362000	0.07510	GGT	C|0.298;A|0.702	0.702	strong		0.532	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
ZNF571	51276	hgsc.bcm.edu	37	19	38056763	38056763	+	Missense_Mutation	SNP	C	C	G	rs8111790	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:38056763C>G	ENST00000328550.2	-	4	666	c.567G>C	c.(565-567)caG>caC	p.Q189H	ZNF571-AS1_ENST00000587121.1_RNA|ZNF571-AS1_ENST00000592392.1_RNA|ZNF571-AS1_ENST00000590838.1_RNA|ZNF571_ENST00000590751.1_Intron|ZNF571_ENST00000358744.3_Missense_Mutation_p.Q189H|ZNF571-AS1_ENST00000591430.1_RNA|ZNF571-AS1_ENST00000589802.1_RNA|ZNF540_ENST00000592533.1_Intron|ZNF571-AS1_ENST00000586139.1_RNA|ZNF571-AS1_ENST00000585578.1_RNA|ZNF571_ENST00000593133.1_Missense_Mutation_p.Q189H|ZNF571-AS1_ENST00000586013.1_RNA|ZNF571_ENST00000451802.2_Missense_Mutation_p.Q189H|ZNF571-AS1_ENST00000589750.1_RNA			Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	189			Q -> H (in dbSNP:rs8111790). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	25			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCTCACCAGTCTGAATTCTCT	0.343													C|||	901	0.179912	0.0885	0.2651	5008	,	,		21454	0.0288		0.3618	False		,,,				2504	0.2117				p.Q189H		Atlas-SNP	.											ZNF571,colon,carcinoma,0,1	ZNF571	54	1	0			c.G567C						PASS	.	C	HIS/GLN	587,3819	258.6+/-262.5	37,513,1653	93.0	93.0	93.0		567	-7.0	0.0	19	dbSNP_116	93	3138,5462	476.9+/-369.5	580,1978,1742	yes	missense	ZNF571	NM_016536.3	24	617,2491,3395	GG,GC,CC		36.4884,13.3227,28.6406	benign	189/610	38056763	3725,9281	2203	4300	6503	SO:0001583	missense	51276	exon4			ACCAGTCTGAATT	AF161544	CCDS12505.1	19q13.12	2013-09-20			ENSG00000180479	ENSG00000180479		"""Zinc fingers, C2H2-type"", ""-"""	25000	protein-coding gene	gene with protein product						11042152	Standard	XM_005258977		Approved	HSPC059	uc002ogt.3	Q7Z3V5	OTTHUMG00000182016	ENST00000328550.2:c.567G>C	19.37:g.38056763C>G	ENSP00000333660:p.Gln189His	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_016536	Q2HIY0|Q3ZCU3|Q9NZX7	Missense_Mutation	SNP	ENST00000328550.2	37	CCDS12505.1	437	0.2000915750915751	42	0.08536585365853659	95	0.26243093922651933	21	0.03671328671328671	279	0.36807387862796836	C	0.983	-0.696452	0.03279	0.133227	0.364884	ENSG00000180479	ENST00000328550;ENST00000451802;ENST00000358744	T;T;T	0.01584	4.75;4.75;4.75	3.49	-6.98	0.01611	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00022	-2.725	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.44651	-0.9314	8	0.02654	T	1	.	3.9809	0.09495	0.5001:0.1224:0.2896:0.0879	rs8111790;rs52805879;rs8111790	189	Q7Z3V5	ZN571_HUMAN	H	189	ENSP00000333660:Q189H;ENSP00000392638:Q189H;ENSP00000351594:Q189H	ENSP00000333660:Q189H	Q	-	3	2	ZNF571	42748603	0.000000	0.05858	0.000000	0.03702	0.706000	0.40770	-2.048000	0.01406	-1.791000	0.01261	0.313000	0.20887	CAG	C|0.737;G|0.263	0.263	strong		0.343	ZNF571-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458669.1	NM_016536	
PDGFRA	5156	hgsc.bcm.edu	37	4	55152040	55152040	+	Silent	SNP	C	C	T	rs2228230	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55152040C>T	ENST00000257290.5	+	18	2803	c.2472C>T	c.(2470-2472)gtC>gtT	p.V824V	FIP1L1_ENST00000507166.1_Silent_p.V584V	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	824	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.V824V(15)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	CTCGCAACGTCCTCCTGGCAC	0.498			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)			C|||	1204	0.240415	0.3449	0.2767	5008	,	,		22168	0.1726		0.1451	False		,,,				2504	0.2413				p.V824V	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	PDGFRA,NS,carcinoma,0,17	PDGFRA	1583	17	15	Substitution - coding silent(15)	soft_tissue(11)|central_nervous_system(3)|endometrium(1)	c.C2472T						PASS	.	C		1381,3025	455.5+/-351.0	211,959,1033	186.0	168.0	174.0		2472	2.4	1.0	4	dbSNP_98	174	1198,7402	241.0+/-271.5	95,1008,3197	no	coding-synonymous	PDGFRA	NM_006206.4		306,1967,4230	TT,TC,CC		13.9302,31.3436,19.8293		824/1090	55152040	2579,10427	2203	4300	6503	SO:0001819	synonymous_variant	5156	exon18	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	CAACGTCCTCCTG	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.2472C>T	4.37:g.55152040C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	64	24	0.375	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																			C|0.801;T|0.199	0.199	strong		0.498	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
TNS1	7145	hgsc.bcm.edu	37	2	218758200	218758200	+	Missense_Mutation	SNP	T	T	G	rs61745748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:218758200T>G	ENST00000171887.4	-	8	756	c.304A>C	c.(304-306)Aat>Cat	p.N102H	TNS1_ENST00000430930.1_Missense_Mutation_p.N102H|TNS1_ENST00000419504.1_Missense_Mutation_p.N102H|TNS1_ENST00000310858.6_Missense_Mutation_p.N133H	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	102	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GGGTCTGCATTGAGCCATGTG	0.562													T|||	63	0.0125799	0.0023	0.0086	5008	,	,		19412	0.0		0.0199	False		,,,				2504	0.0348				p.N102H		Atlas-SNP	.											.	TNS1	251	.	0			c.A304C						PASS	.	T	HIS/ASN	19,4387	26.2+/-53.5	0,19,2184	144.0	113.0	123.0		304	5.1	1.0	2	dbSNP_129	123	190,8410	85.0+/-147.5	0,190,4110	yes	missense	TNS1	NM_022648.4	68	0,209,6294	GG,GT,TT		2.2093,0.4312,1.607	possibly-damaging	102/1736	218758200	209,12797	2203	4300	6503	SO:0001583	missense	7145	exon8			CTGCATTGAGCCA	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.304A>C	2.37:g.218758200T>G	ENSP00000171887:p.Asn102His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	152	77	0.506579	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	26	0.011904761904761904	3	0.006097560975609756	4	0.011049723756906077	0	0.0	19	0.025065963060686015	T	18.57	3.652558	0.67472	0.004312	0.022093	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554;ENST00000310858;ENST00000413280	D;D;D;D;D;D;D	0.98617	-5.03;-5.03;-5.03;-5.03;-5.03;-5.03;-5.03	5.09	5.09	0.68999	Phosphatase tensin type (1);	0.098933	0.64402	D	0.000002	D	0.96361	0.8813	L	0.49350	1.555	0.54753	D	0.99998	D;B;D;D;D;D	0.89917	0.988;0.086;1.0;0.976;0.963;0.963	P;B;D;P;P;P	0.91635	0.819;0.112;0.999;0.867;0.498;0.498	D	0.92353	0.5891	10	0.72032	D	0.01	.	14.6945	0.69110	0.0:0.0:0.0:1.0	.	102;156;133;102;102;102	B2RU35;A1L0S7;Q6IPI5;Q9HBL0;E9PGF5;E9PF55	.;.;.;TENS1_HUMAN;.;.	H	102;102;102;227;170;133;102	ENSP00000171887:N102H;ENSP00000408724:N102H;ENSP00000406016:N102H;ENSP00000405460:N227H;ENSP00000400383:N170H;ENSP00000308321:N133H;ENSP00000395615:N102H	ENSP00000171887:N102H	N	-	1	0	TNS1	218466445	1.000000	0.71417	0.961000	0.40146	0.927000	0.56198	6.097000	0.71452	2.142000	0.66516	0.460000	0.39030	AAT	T|0.986;G|0.014	0.014	strong		0.562	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
EDDM3A	10876	hgsc.bcm.edu	37	14	21215997	21215997	+	Silent	SNP	C	C	T	rs11847654	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21215997C>T	ENST00000326842.2	+	2	385	c.258C>T	c.(256-258)agC>agT	p.S86S		NM_006683.4	NP_006674.2	Q14507	EP3A_HUMAN	epididymal protein 3A	86					sperm displacement (GO:0007321)	extracellular space (GO:0005615)				breast(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						AGAAGGGGAGCGACCGATATA	0.448													C|||	1416	0.282748	0.1135	0.3228	5008	,	,		20153	0.4573		0.2316	False		,,,				2504	0.3558				p.S86S		Atlas-SNP	.											.	EDDM3A	15	.	0			c.C258T						PASS	.	C		587,3819	259.2+/-262.9	38,511,1654	98.0	93.0	95.0		258	-3.4	0.0	14	dbSNP_120	95	2012,6588	352.6+/-328.8	228,1556,2516	no	coding-synonymous	EDDM3A	NM_006683.4		266,2067,4170	TT,TC,CC		23.3953,13.3227,19.9831		86/148	21215997	2599,10407	2203	4300	6503	SO:0001819	synonymous_variant	10876	exon2			GGGGAGCGACCGA	X76383	CCDS9556.1	14q11.1	2010-03-19	2010-01-27	2010-01-27	ENSG00000181562	ENSG00000181562			16978	protein-coding gene	gene with protein product		611580	"""family with sequence similarity 12, member A"""	FAM12A		7514008	Standard	NM_006683		Approved	HE3-ALPHA	uc001vyc.3	Q14507	OTTHUMG00000029581	ENST00000326842.2:c.258C>T	14.37:g.21215997C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	144	68	0.472222	NM_006683	Q4KN33	Silent	SNP	ENST00000326842.2	37	CCDS9556.1																																																																																			C|0.754;T|0.246	0.246	strong		0.448	EDDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073742.3		
VWF	7450	hgsc.bcm.edu	37	12	6128170	6128170	+	Missense_Mutation	SNP	C	C	G	rs1800383	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6128170C>G	ENST00000261405.5	-	28	4668	c.4414G>C	c.(4414-4416)Gac>Cac	p.D1472H		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1472			D -> H (in dbSNP:rs1800383). {ECO:0000269|PubMed:1988024, ECO:0000269|PubMed:2584182, ECO:0000269|PubMed:3489923}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	TGTGCCATGTCGGGGGGCAGA	0.617													G|||	1168	0.233227	0.5507	0.1153	5008	,	,		18385	0.1081		0.1004	False		,,,				2504	0.1534				p.D1472H		Atlas-SNP	.											.	VWF	338	.	0			c.G4414C	GRCh37	CI034194|HM070121	VWF	I|M	rs1800383	PASS	.	G	HIS/ASP	1717,2649		417,883,883	24.0	35.0	31.0		4414	0.8	0.0	12	dbSNP_89	31	565,8029		27,511,3759	no	missense	VWF	NM_000552.3	81	444,1394,4642	GG,GC,CC		6.5744,39.3266,17.608	benign	1472/2814	6128170	2282,10678	2183	4297	6480	SO:0001583	missense	7450	exon28			CCATGTCGGGGGG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.4414G>C	12.37:g.6128170C>G	ENSP00000261405:p.Asp1472His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	327	0.14972527472527472	188	0.3821138211382114	40	0.11049723756906077	51	0.08916083916083917	48	0.0633245382585752	.	0.040	-1.288300	0.01387	0.393266	0.065744	ENSG00000110799	ENST00000261405	T	0.77620	-1.11	4.88	0.812	0.18744	.	1.932190	0.02536	N	0.094083	T	0.00012	0.0000	N	0.00972	-1.085	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.16364	-1.0405	9	0.41790	T	0.15	.	10.0439	0.42175	0.0:0.2371:0.3857:0.3772	rs1800383;rs7303267	1472	P04275	VWF_HUMAN	H	1472	ENSP00000261405:D1472H	ENSP00000261405:D1472H	D	-	1	0	VWF	5998431	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.229000	0.09098	-0.533000	0.06323	-5.080000	0.00001	GAC	.	.	weak		0.617	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
KIAA1551	55196	hgsc.bcm.edu	37	12	32135186	32135186	+	Missense_Mutation	SNP	T	T	A	rs3759302	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:32135186T>A	ENST00000312561.4	+	4	1711	c.1297T>A	c.(1297-1299)Tct>Act	p.S433T	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	433			S -> T (in dbSNP:rs3759302).														GACTAATACTTCTTATAGTGA	0.343													T|||	733	0.146366	0.0756	0.1254	5008	,	,		19387	0.121		0.1869	False		,,,				2504	0.2413				p.S433T		Atlas-SNP	.											.	.	.	.	0			c.T1297A						PASS	.	T	THR/SER	387,4019	180.5+/-208.7	15,357,1831	69.0	82.0	78.0		1297	-1.1	0.0	12	dbSNP_107	78	1720,6880	298.2+/-303.8	168,1384,2748	yes	missense	C12orf35	NM_018169.3	58	183,1741,4579	AA,AT,TT		20.0,8.7835,16.2002	possibly-damaging	433/1748	32135186	2107,10899	2203	4300	6503	SO:0001583	missense	55196	exon4			AATACTTCTTATA	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.1297T>A	12.37:g.32135186T>A	ENSP00000310338:p.Ser433Thr	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	313	0.1433150183150183	43	0.08739837398373984	47	0.1298342541436464	85	0.1486013986013986	138	0.1820580474934037	T	9.919	1.211573	0.22289	0.087835	0.2	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.08807	3.7;3.05	5.72	-1.13	0.09775	.	0.495198	0.19035	N	0.124441	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D	0.76494	0.999	D	0.65443	0.935	T	0.33599	-0.9862	8	.	.	.	.	5.5119	0.16886	0.0:0.2805:0.2503:0.4692	rs3759302;rs3759302	433	Q9HCM1	CL035_HUMAN	T	433	ENSP00000310338:S433T;ENSP00000370442:S433T	.	S	+	1	0	C12orf35	32026453	0.000000	0.05858	0.001000	0.08648	0.111000	0.19643	-0.055000	0.11807	-0.438000	0.07232	0.533000	0.62120	TCT	T|0.847;A|0.153	0.153	strong		0.343	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
CHRNA9	55584	hgsc.bcm.edu	37	4	40356041	40356041	+	Missense_Mutation	SNP	C	C	T	rs55633891	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:40356041C>T	ENST00000310169.2	+	5	1083	c.944C>T	c.(943-945)gCg>gTg	p.A315V		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	315			A -> V (in dbSNP:rs55633891).		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|inner ear morphogenesis (GO:0042472)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine-activated cation-selective channel activity (GO:0004889)|calcium channel activity (GO:0005262)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(4)|stomach(1)	33					Galantamine(DB00674)|Nicotine(DB00184)	GCCTCCACTGCGTTGACCATC	0.502													C|||	710	0.141773	0.1241	0.1124	5008	,	,		21268	0.1468		0.164	False		,,,				2504	0.1585				p.A315V	Esophageal Squamous(115;1297 1602 22235 25158 43327)	Atlas-SNP	.											.	CHRNA9	53	.	0			c.C944T						PASS	.	C	VAL/ALA	630,3776	271.3+/-270.1	48,534,1621	129.0	132.0	131.0		944	4.9	1.0	4	dbSNP_129	131	1127,7473	233.6+/-266.8	77,973,3250	yes	missense	CHRNA9	NM_017581.2	64	125,1507,4871	TT,TC,CC		13.1047,14.2987,13.5091	benign	315/480	40356041	1757,11249	2203	4300	6503	SO:0001583	missense	55584	exon5			CCACTGCGTTGAC	AF227732	CCDS3459.1	4p14	2012-02-11	2012-02-07		ENSG00000174343	ENSG00000174343		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	14079	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 9 (neuronal)"""	605116	"""cholinergic receptor, nicotinic, alpha polypeptide 9"""				Standard	NM_017581		Approved	NACHRA9	uc003gva.2	Q9UGM1	OTTHUMG00000099375	ENST00000310169.2:c.944C>T	4.37:g.40356041C>T	ENSP00000312663:p.Ala315Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	77	30	0.38961	NM_017581	Q14CY7|Q4W5A2|Q9NYV2	Missense_Mutation	SNP	ENST00000310169.2	37	CCDS3459.1	314	0.14377289377289376	63	0.12804878048780488	33	0.09116022099447514	94	0.16433566433566432	124	0.16358839050131926	C	11.56	1.674234	0.29693	0.142987	0.131047	ENSG00000174343	ENST00000310169	D	0.83673	-1.75	5.72	4.87	0.63330	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.155728	0.64402	D	0.000019	T	0.00496	0.0016	N	0.05031	-0.125	0.09310	P	0.999999809154	P	0.44659	0.84	P	0.45343	0.477	T	0.48547	-0.9026	9	0.02654	T	1	.	14.1356	0.65287	0.0:0.9283:0.0:0.0717	rs55633891	315	Q9UGM1	ACHA9_HUMAN	V	315	ENSP00000312663:A315V	ENSP00000312663:A315V	A	+	2	0	CHRNA9	40050798	1.000000	0.71417	0.999000	0.59377	0.870000	0.49936	5.772000	0.68889	2.709000	0.92574	0.561000	0.74099	GCG	C|0.863;T|0.137	0.137	strong		0.502	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1		
GPR111	222611	hgsc.bcm.edu	37	6	47649222	47649222	+	Silent	SNP	T	T	G	rs8180544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:47649222T>G	ENST00000296862.1	+	6	927	c.927T>G	c.(925-927)tcT>tcG	p.S309S	GPR111_ENST00000507065.1_Silent_p.S241S|GPR111_ENST00000398742.2_Silent_p.S241S			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	309					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						TCACTTTTTCTATGAGAATTA	0.393																																					p.S241S		Atlas-SNP	.											GPR111_ENST00000296862,upper_leg,malignant_melanoma,+1,2	GPR111	123	2	0			c.T723G						PASS	.	G		1788,1962		422,944,509	126.0	119.0	121.0		723	-10.4	0.4	6	dbSNP_117	121	5323,2901		1732,1859,521	no	coding-synonymous	GPR111	NM_153839.6		2154,2803,1030	GG,GT,TT		35.2748,47.68,40.613		241/643	47649222	7111,4863	1875	4112	5987	SO:0001819	synonymous_variant	222611	exon7			TTTTTCTATGAGA	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.927T>G	6.37:g.47649222T>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	164	89	0.542683	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Silent	SNP	ENST00000296862.1	37																																																																																				T|0.468;G|0.532	0.532	strong		0.393	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
CNTNAP4	85445	hgsc.bcm.edu	37	16	76587331	76587331	+	Silent	SNP	T	T	C	rs7184958	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:76587331T>C	ENST00000563764.1	+	1	18	c.18T>C	c.(16-18)acT>acC	p.T6T	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000307431.8_Silent_p.T1197T|CNTNAP4_ENST00000478060.1_Silent_p.T1125T|CNTNAP4_ENST00000476707.1_Silent_p.T1201T|CNTNAP4_ENST00000377504.4_Silent_p.T1149T																							GACACGTGACTGAGTCCAGCT	0.582													C|||	1506	0.300719	0.3449	0.1945	5008	,	,		17303	0.2867		0.2773	False		,,,				2504	0.3548				p.T1125T		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.T3375C						PASS	.	C	,	1424,2818		233,958,930	47.0	51.0	49.0		3593,3375	-8.7	0.2	16	dbSNP_116	49	2380,6088		331,1718,2185	yes	coding-synonymous,coding-synonymous	CNTNAP4	NM_033401.3,NM_138994.3	,	564,2676,3115	CC,CT,TT		28.1058,33.5691,29.9292	,	1198/1309,1125/1236	76587331	3804,8906	2121	4234	6355	SO:0001819	synonymous_variant	85445	exon21			CGTGACTGAGTCC																												ENST00000563764.1:c.18T>C	16.37:g.76587331T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	178	95	0.533708	NM_138994		Silent	SNP	ENST00000563764.1	37																																																																																				T|0.714;C|0.286	0.286	strong		0.582	RP11-58C22.1-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000421971.1		
SP2	6668	hgsc.bcm.edu	37	17	46000406	46000406	+	Missense_Mutation	SNP	T	T	C	rs62067380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:46000406T>C	ENST00000376741.4	+	4	1275	c.1138T>C	c.(1138-1140)Tct>Cct	p.S380P	AC003665.1_ENST00000411573.2_RNA|AC003665.1_ENST00000451140.2_RNA|AC003665.1_ENST00000433001.1_RNA|AC003665.1_ENST00000585280.1_RNA	NM_003110.5	NP_003101.3	Q02086	SP2_HUMAN	Sp2 transcription factor	380					cardiovascular system development (GO:0072358)|embryonic organ development (GO:0048568)|fibroblast proliferation (GO:0048144)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	13						TGCAGCCACCTCTAACACCAC	0.597													T|||	478	0.0954473	0.0204	0.1398	5008	,	,		18745	0.0605		0.1511	False		,,,				2504	0.1442				p.S380P		Atlas-SNP	.											.	SP2	38	.	0			c.T1138C						PASS	.	T	PRO/SER	180,4226	115.0+/-153.0	4,172,2027	82.0	78.0	79.0		1138	3.8	1.0	17	dbSNP_129	79	1212,7388	243.3+/-273.0	83,1046,3171	yes	missense	SP2	NM_003110.5	74	87,1218,5198	CC,CT,TT		14.093,4.0853,10.7028	benign	380/614	46000406	1392,11614	2203	4300	6503	SO:0001583	missense	6668	exon4			GCCACCTCTAACA		CCDS11521.2	17q21.3-q22	2013-01-08			ENSG00000167182	ENSG00000167182		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11207	protein-coding gene	gene with protein product		601801				1341900, 9730617	Standard	NM_003110		Approved	KIAA0048	uc002imk.3	Q02086	OTTHUMG00000150196	ENST00000376741.4:c.1138T>C	17.37:g.46000406T>C	ENSP00000365931:p.Ser380Pro	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_003110	A6NK74	Missense_Mutation	SNP	ENST00000376741.4	37	CCDS11521.2	214	0.09798534798534798	12	0.024390243902439025	54	0.14917127071823205	30	0.05244755244755245	118	0.15567282321899736	T	15.74	2.922421	0.52653	0.040853	0.14093	ENSG00000167182	ENST00000376741	T	0.10382	2.88	6.17	3.84	0.44239	.	0.294876	0.32802	N	0.005632	T	0.00039	0.0001	L	0.36672	1.1	0.25600	P	0.9866029	B	0.06786	0.001	B	0.06405	0.002	T	0.34453	-0.9828	9	0.25751	T	0.34	.	3.6607	0.08237	0.1331:0.0707:0.1394:0.6568	rs62067380	380	Q02086	SP2_HUMAN	P	380	ENSP00000365931:S380P	ENSP00000365931:S380P	S	+	1	0	SP2	43355405	0.844000	0.29557	0.985000	0.45067	0.987000	0.75469	1.773000	0.38563	1.116000	0.41820	0.533000	0.62120	TCT	T|0.895;C|0.105	0.105	strong		0.597	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110	
ATP2A1	487	hgsc.bcm.edu	37	16	28898793	28898793	+	Silent	SNP	T	T	C	rs6565259	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28898793T>C	ENST00000357084.3	+	8	945	c.678T>C	c.(676-678)acT>acC	p.T226T	ATP2A1_ENST00000395503.4_Silent_p.T226T|ATP2A1_ENST00000536376.1_Silent_p.T101T	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	226					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						TGGCCACCACTGGTGTGGGCA	0.602													t|||	1697	0.338858	0.5189	0.4942	5008	,	,		18719	0.1617		0.3131	False		,,,				2504	0.1943				p.T226T		Atlas-SNP	.											.	ATP2A1	116	.	0			c.T678C						PASS	.	C	,	2225,2169	590.6+/-387.4	538,1149,510	97.0	93.0	94.0		678,678	-11.0	0.0	16	dbSNP_116	94	3020,5580	464.7+/-366.3	540,1940,1820	no	coding-synonymous,coding-synonymous	ATP2A1	NM_004320.4,NM_173201.3	,	1078,3089,2330	CC,CT,TT		35.1163,49.3628,40.3648	,	226/995,226/1002	28898793	5245,7749	2197	4300	6497	SO:0001819	synonymous_variant	487	exon8			CACCACTGGTGTG		CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.678T>C	16.37:g.28898793T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	83	49	0.590361	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																			T|0.631;C|0.369	0.369	strong		0.602	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183541	11183541	+	Missense_Mutation	SNP	T	T	C	rs78152338	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11183541T>C	ENST00000390675.2	-	1	465	c.394A>G	c.(394-396)Atg>Gtg	p.M132V	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	132					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						CCCAACAGCATCACCAGAATG	0.363																																					p.M132V		Atlas-SNP	.											.	TAS2R31	24	.	0			c.A394G						PASS	.						90.0	100.0	97.0					12																	11183541		2040	4253	6293	SO:0001583	missense	259290	exon1			ACAGCATCACCAG	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.394A>G	12.37:g.11183541T>C	ENSP00000375093:p.Met132Val	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	184	33	0.179348	NM_176885	P59547|Q17R84|Q645X5	Missense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	.	.	.	.	.	.	.	.	.	.	.	3.560	-0.089826	0.07053	.	.	ENSG00000256436	ENST00000390675	T	0.00737	5.76	2.45	-0.352	0.12598	.	.	.	.	.	T	0.00815	0.0027	L	0.49699	1.58	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.46803	-0.9165	9	0.35671	T	0.21	.	1.9424	0.03349	0.2663:0.1698:0.0:0.5639	.	132	P59538	T2R31_HUMAN	V	132	ENSP00000375093:M132V	ENSP00000375093:M132V	M	-	1	0	TAS2R31	11074808	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-1.005000	0.03674	-0.194000	0.10399	0.163000	0.16589	ATG	T|0.750;C|0.250	0.250	strong		0.363	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
KAT6B	23522	hgsc.bcm.edu	37	10	76789416	76789416	+	Missense_Mutation	SNP	C	C	T	rs140992439	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:76789416C>T	ENST00000287239.4	+	18	5323	c.4834C>T	c.(4834-4836)Cgt>Tgt	p.R1612C	KAT6B_ENST00000372711.1_Missense_Mutation_p.R1429C|KAT6B_ENST00000372714.1_Missense_Mutation_p.R1320C|KAT6B_ENST00000372725.1_Missense_Mutation_p.R1320C|KAT6B_ENST00000372724.1_Missense_Mutation_p.R1320C	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1612	Interaction with RUNX1 and RUNX2.|Ser-rich.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CCAGTCCGTACGTTCTGTCAA	0.547													C|||	2	0.000399361	0.0	0.0	5008	,	,		21694	0.002		0.0	False		,,,				2504	0.0				p.R1612C		Atlas-SNP	.											MYST4,colon,carcinoma,-1,1	.	.	1	0			c.C4834T						scavenged	.	C	CYS/ARG	0,4406		0,0,2203	164.0	139.0	148.0		4834	4.8	1.0	10	dbSNP_134	148	1,8599	1.2+/-3.3	0,1,4299	no	missense	KAT6B	NM_012330.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1612/2074	76789416	1,13005	2203	4300	6503	SO:0001583	missense	23522	exon18			TCCGTACGTTCTG	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	17582	protein-coding gene	gene with protein product	"""MOZ-related factor"""	605880	"""MYST histone acetyltransferase (monocytic leukemia) 4"""	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.4834C>T	10.37:g.76789416C>T	ENSP00000287239:p.Arg1612Cys	Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	113	3	0.0265487	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	13.44	2.236414	0.39498	0.0	1.16E-4	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	D;D;D;D;D	0.85702	-1.96;-1.96;-2.02;-1.96;-1.97	4.77	4.77	0.60923	.	0.000000	0.51477	D	0.000100	D	0.87704	0.6244	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.99	P;D;P	0.85130	0.862;0.997;0.726	D	0.88877	0.3337	10	0.87932	D	0	-7.0229	12.8499	0.57852	0.1632:0.8368:0.0:0.0	.	1429;1320;1612	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	C	1320;1320;1612;1320;1429	ENSP00000361810:R1320C;ENSP00000361809:R1320C;ENSP00000287239:R1612C;ENSP00000361799:R1320C;ENSP00000361796:R1429C	ENSP00000287239:R1612C	R	+	1	0	KAT6B	76459422	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.385000	0.59613	2.191000	0.70037	0.563000	0.77884	CGT	C|1.000;T|0.000	0.000	strong		0.547	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
ABCA7	10347	hgsc.bcm.edu	37	19	1054583	1054583	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1054583C>T	ENST00000263094.6	+	28	3972	c.3741C>T	c.(3739-3741)gcC>gcT	p.A1247A	ABCA7_ENST00000433129.1_Silent_p.A1247A|ABCA7_ENST00000435683.2_Silent_p.A1109A	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1247					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCTGCCTGCCCTCTTTGTGG	0.632																																					p.A1247A		Atlas-SNP	.											.	ABCA7	174	.	0			c.C3741T						PASS	.						93.0	70.0	78.0					19																	1054583		2203	4300	6503	SO:0001819	synonymous_variant	10347	exon28			GCCTGCCCTCTTT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.3741C>T	19.37:g.1054583C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	80	31	0.3875	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			.	.	none		0.632	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
CTCFL	140690	hgsc.bcm.edu	37	20	56090807	56090807	+	Silent	SNP	A	A	G	rs6025601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:56090807A>G	ENST00000608263.1	-	5	1804	c.1143T>C	c.(1141-1143)gaT>gaC	p.D381D	CTCFL_ENST00000243914.3_Silent_p.D381D|CTCFL_ENST00000423479.3_Silent_p.D381D|CTCFL_ENST00000608903.1_Silent_p.D119D|CTCFL_ENST00000539382.1_Silent_p.D176D|CTCFL_ENST00000502686.2_Silent_p.D119D|CTCFL_ENST00000609232.1_Silent_p.D381D|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000422869.2_Silent_p.D381D|CTCFL_ENST00000371196.2_Silent_p.D381D|CTCFL_ENST00000608440.1_Silent_p.D381D|CTCFL_ENST00000429804.3_Silent_p.D381D|CTCFL_ENST00000433949.3_Silent_p.D176D|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000608425.1_Silent_p.D381D	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	381					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GCTTGTAGGTATCTCTGCTGG	0.473													G|||	1645	0.328474	0.4092	0.33	5008	,	,		18536	0.369		0.2097	False		,,,				2504	0.2986				p.D381D		Atlas-SNP	.											CTCFL,bladder,carcinoma,-2,2	CTCFL	97	2	0			c.T1143C						PASS	.	G		1579,2827	666.5+/-401.7	259,1061,883	176.0	166.0	170.0		1143	2.9	1.0	20	dbSNP_114	170	1675,6925	739.7+/-407.1	172,1331,2797	no	coding-synonymous	CTCFL	NM_080618.2		431,2392,3680	GG,GA,AA		19.4767,35.8375,25.0192		381/664	56090807	3254,9752	2203	4300	6503	SO:0001819	synonymous_variant	140690	exon5			GTAGGTATCTCTG		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1143T>C	20.37:g.56090807A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	94	52	0.553191	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Silent	SNP	ENST00000608263.1	37	CCDS13459.1																																																																																			A|0.717;G|0.283	0.283	strong		0.473	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
FADD	8772	hgsc.bcm.edu	37	11	70049752	70049752	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:70049752C>T	ENST00000301838.4	+	1	484	c.187C>T	c.(187-189)Ctg>Ttg	p.L63L	RP11-805J14.5_ENST00000527232.1_RNA|RP11-805J14.5_ENST00000526174.1_RNA	NM_003824.3	NP_003815.1	Q13158	FADD_HUMAN	Fas (TNFRSF6)-associated via death domain	63	DED. {ECO:0000255|PROSITE- ProRule:PRU00065}.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|motor neuron apoptotic process (GO:0097049)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of activation-induced cell death of T cells (GO:0070236)|negative regulation of necroptotic process (GO:0060546)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000454)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of proteolysis (GO:0045862)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|protein heterooligomerization (GO:0051291)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|ripoptosome (GO:0097342)	death effector domain binding (GO:0035877)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|tumor necrosis factor receptor superfamily binding (GO:0032813)			endometrium(1)|lung(4)|ovary(1)|pancreas(1)|urinary_tract(2)	9	Esophageal squamous(2;1.19e-45)		LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			CACCGAGCTCCTGCGCGAGCT	0.736																																					p.L63L		Atlas-SNP	.											.	FADD	14	.	0			c.C187T						PASS	.						18.0	23.0	21.0					11																	70049752		2140	4217	6357	SO:0001819	synonymous_variant	8772	exon1			GAGCTCCTGCGCG	U24231	CCDS8196.1	11q13.3	2014-09-17			ENSG00000168040	ENSG00000168040			3573	protein-coding gene	gene with protein product	"""Fas-associating protein with death domain"", ""Fas-associating death domain-containing protein"", ""mediator of receptor-induced toxicity"", ""growth-inhibiting gene 3 protein"""	602457				7536190, 7538907	Standard	NM_003824		Approved	MORT1, GIG3	uc001opm.2	Q13158	OTTHUMG00000167264	ENST00000301838.4:c.187C>T	11.37:g.70049752C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_003824	Q14866|Q6IBR4	Silent	SNP	ENST00000301838.4	37	CCDS8196.1																																																																																			.	.	none		0.736	FADD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393902.1	NM_003824	
PIEZO1	9780	hgsc.bcm.edu	37	16	88791458	88791458	+	Missense_Mutation	SNP	G	G	A	rs11645197	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:88791458G>A	ENST00000301015.9	-	30	4439	c.4193C>T	c.(4192-4194)cCa>cTa	p.P1398L		NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1398					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						CTGCCTCCGTGGCGGGGAGGA	0.701													G|||	878	0.175319	0.0121	0.1643	5008	,	,		17170	0.0873		0.3171	False		,,,				2504	0.3487				p.P1398L		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C4193T						PASS	.						5.0	11.0	9.0					16																	88791458		644	1514	2158	SO:0001583	missense	9780	exon30			CTCCGTGGCGGGG	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.4193C>T	16.37:g.88791458G>A	ENSP00000301015:p.Pro1398Leu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	103	57	0.553398	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	356	0.163003663003663	12	0.024390243902439025	72	0.19889502762430938	46	0.08041958041958042	226	0.29815303430079154	G	13.18	2.159529	0.38119	.	.	ENSG00000103335	ENST00000301015	T	0.71934	-0.61	4.33	4.33	0.51752	.	0.581104	0.16407	N	0.215765	T	0.00012	0.0000	L	0.54323	1.7	0.53688	P	2.4000000000024002E-5	B	0.29716	0.255	B	0.26614	0.071	T	0.06391	-1.0829	9	0.36615	T	0.2	-9.1253	11.3569	0.49621	0.0:0.0:0.8181:0.1819	rs11645197;rs11645197	1398	Q92508	PIEZ1_HUMAN	L	1398	ENSP00000301015:P1398L	ENSP00000301015:P1398L	P	-	2	0	FAM38A	87318959	.	.	0.902000	0.35471	0.960000	0.62799	.	.	2.406000	0.81754	0.462000	0.41574	CCA	G|0.827;A|0.173	0.173	strong		0.701	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
NOTCH4	4855	hgsc.bcm.edu	37	6	32163274	32163274	+	Silent	SNP	G	G	A	rs8192583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32163274G>A	ENST00000375023.3	-	30	6090	c.5952C>T	c.(5950-5952)gaC>gaT	p.D1984D	GPSM3_ENST00000375040.3_5'Flank|GPSM3_ENST00000375043.3_5'UTR|GPSM3_ENST00000487761.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1984					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GGGGACCACAGTCAAGTTGAG	0.537													G|||	261	0.0521166	0.0598	0.0274	5008	,	,		18364	0.0099		0.0557	False		,,,				2504	0.0992				p.D1984D		Atlas-SNP	.											.	NOTCH4	201	.	0			c.C5952T						PASS	.	G	,	167,2851		4,159,1346	95.0	114.0	107.0		5952,	-4.2	0.0	6	dbSNP_117	107	270,5146		9,252,2447	no	coding-synonymous,utr-5	NOTCH4,GPSM3	NM_004557.3,NM_022107.1	,	13,411,3793	AA,AG,GG		4.9852,5.5335,5.1814	,	1984/2004,	32163274	437,7997	1509	2708	4217	SO:0001819	synonymous_variant	4855	exon30			ACCACAGTCAAGT		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.5952C>T	6.37:g.32163274G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			G|0.952;A|0.048	0.048	strong		0.537	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
KLHL24	54800	hgsc.bcm.edu	37	3	183368891	183368891	+	Silent	SNP	C	C	T	rs2293031	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:183368891C>T	ENST00000454652.2	+	4	1133	c.747C>T	c.(745-747)caC>caT	p.H249H	KLHL24_ENST00000242810.6_Silent_p.H249H|KLHL24_ENST00000476808.1_Silent_p.H249H	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24	249	BACK.					cell projection (GO:0042995)|cytoplasm (GO:0005737)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			CACTGTTACACGAGCTCCTGA	0.443													T|||	1769	0.353235	0.5151	0.2867	5008	,	,		20428	0.4355		0.2714	False		,,,				2504	0.181				p.H249H		Atlas-SNP	.											.	KLHL24	56	.	0			c.C747T						PASS	.	T		2139,2267	597.0+/-388.8	533,1073,597	132.0	122.0	125.0		747	-3.9	0.6	3	dbSNP_100	125	2403,6197	699.6+/-405.1	348,1707,2245	no	coding-synonymous	KLHL24	NM_017644.3		881,2780,2842	TT,TC,CC		27.9419,48.5474,34.9223		249/601	183368891	4542,8464	2203	4300	6503	SO:0001819	synonymous_variant	54800	exon3			GTTACACGAGCTC		CCDS3246.1	3q27.1	2013-02-22	2013-02-22		ENSG00000114796	ENSG00000114796		"""Kelch-like"", ""BTB/POZ domain containing"""	25947	protein-coding gene	gene with protein product		611295	"""kelch-like 24 (Drosophila)"""				Standard	XM_005247552		Approved	DRE1, FLJ20059	uc003flv.3	Q6TFL4	OTTHUMG00000156911	ENST00000454652.2:c.747C>T	3.37:g.183368891C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	186	100	0.537634	NM_017644	A5PLN8|Q9H620|Q9NXT9	Silent	SNP	ENST00000454652.2	37	CCDS3246.1																																																																																			C|0.626;T|0.374	0.374	strong		0.443	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	NM_017644	
FAM217A	222826	hgsc.bcm.edu	37	6	4069133	4069133	+	Missense_Mutation	SNP	T	T	C	rs10485172	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:4069133T>C	ENST00000274673.3	-	7	1727	c.1324A>G	c.(1324-1326)Atg>Gtg	p.M442V	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	442			M -> V (in dbSNP:rs10485172).														GAAACTGGCATTGGAGACCTC	0.413													T|||	402	0.0802716	0.1377	0.0937	5008	,	,		18737	0.006		0.1243	False		,,,				2504	0.0245				p.M442V		Atlas-SNP	.											.	.	.	.	0			c.A1324G						PASS	.	T	VAL/MET	662,3744	281.1+/-275.7	54,554,1595	100.0	97.0	98.0		1324	1.0	0.2	6	dbSNP_119	98	971,7629	211.8+/-252.3	54,863,3383	yes	missense	C6orf146	NM_173563.2	21	108,1417,4978	CC,CT,TT		11.2907,15.025,12.5557	benign	442/509	4069133	1633,11373	2203	4300	6503	SO:0001583	missense	222826	exon7			CTGGCATTGGAGA	BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 146"""	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.1324A>G	6.37:g.4069133T>C	ENSP00000274673:p.Met442Val	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	174	85	0.488506	NM_173563	Q5JYK1	Missense_Mutation	SNP	ENST00000274673.3	37	CCDS4489.1	213	0.09752747252747253	71	0.1443089430894309	35	0.09668508287292818	5	0.008741258741258742	102	0.1345646437994723	T	0.925	-0.714704	0.03206	0.15025	0.112907	ENSG00000145975	ENST00000274673;ENST00000538080;ENST00000470599	T	0.14022	2.54	4.94	1.03	0.20045	.	0.772232	0.12048	N	0.504377	T	0.03434	0.0099	L	0.46157	1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37686	-0.9695	9	0.30854	T	0.27	-0.9412	4.0433	0.09761	0.0:0.1922:0.1795:0.6283	rs10485172;rs17734154;rs60013304;rs10485172	442	Q8IXS0	CF146_HUMAN	V	442;289;570	ENSP00000274673:M442V	ENSP00000274673:M442V	M	-	1	0	C6orf146	4014132	0.001000	0.12720	0.190000	0.23270	0.195000	0.23768	-0.040000	0.12104	0.384000	0.24942	-0.361000	0.07541	ATG	T|0.913;C|0.086;A|0.000	0.086	strong		0.413	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563	
ZXDC	79364	hgsc.bcm.edu	37	3	126194076	126194076	+	Silent	SNP	T	T	C	rs812367	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:126194076T>C	ENST00000389709.3	-	1	686	c.633A>G	c.(631-633)ccA>ccG	p.P211P	ZXDC_ENST00000336332.5_Silent_p.P211P	NM_025112.4	NP_079388.3	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C	211					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|LRR domain binding (GO:0030275)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(1)	17				GBM - Glioblastoma multiforme(114;0.155)		AGCCCTCCAGTGGGCACTTGA	0.682													C|||	2741	0.547324	0.2753	0.5749	5008	,	,		11019	0.5724		0.673	False		,,,				2504	0.7403				p.P211P		Atlas-SNP	.											.	ZXDC	87	.	0			c.A633G						PASS	.	C	,	1522,2592		316,890,851	11.0	13.0	13.0		633,633	-2.2	1.0	3	dbSNP_86	13	5693,2645		2000,1693,476	no	coding-synonymous,coding-synonymous	ZXDC	NM_001040653.2,NM_025112.4	,	2316,2583,1327	CC,CT,TT		31.7222,36.9956,42.0575	,	211/711,211/859	126194076	7215,5237	2057	4169	6226	SO:0001819	synonymous_variant	79364	exon1			CTCCAGTGGGCAC	AK023923	CCDS43145.1, CCDS43146.1	3q21.3	2014-02-12			ENSG00000070476	ENSG00000070476		"""Zinc fingers, C2H2-type"""	28160	protein-coding gene	gene with protein product		615746				8619474, 9110174	Standard	XM_005247757		Approved	MGC11349, FLJ13861	uc003eiv.3	Q2QGD7	OTTHUMG00000162754	ENST00000389709.3:c.633A>G	3.37:g.126194076T>C		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	249	248	0.995984	NM_025112	C5J0H9|Q6DKI8|Q7L3L1|Q8NAU2	Silent	SNP	ENST00000389709.3	37	CCDS43145.1																																																																																			T|0.442;C|0.558	0.558	strong		0.682	ZXDC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370327.2	NM_025112	
ALPK2	115701	hgsc.bcm.edu	37	18	56205262	56205262	+	Missense_Mutation	SNP	A	A	C	rs12103986	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56205262A>C	ENST00000361673.3	-	5	2370	c.2157T>G	c.(2155-2157)caT>caG	p.H719Q	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	719			H -> Q (in dbSNP:rs12103986). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GTTTTTCTTCATGCTGTGGAC	0.448													C|||	2025	0.404353	0.4312	0.4294	5008	,	,		23677	0.2361		0.5736	False		,,,				2504	0.3497				p.H719Q		Atlas-SNP	.											.	ALPK2	487	.	0			c.T2157G						PASS	.	C	GLN/HIS	1987,2419	616.7+/-392.8	446,1095,662	169.0	145.0	153.0		2157	-5.1	0.0	18	dbSNP_120	153	4593,4007	555.2+/-386.6	1237,2119,944	yes	missense	ALPK2	NM_052947.3	24	1683,3214,1606	CC,CA,AA		46.593,45.0976,49.408	benign	719/2171	56205262	6580,6426	2203	4300	6503	SO:0001583	missense	115701	exon5			TTCTTCATGCTGT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2157T>G	18.37:g.56205262A>C	ENSP00000354991:p.His719Gln	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	385	193	0.501299	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	955	0.43727106227106227	189	0.38414634146341464	184	0.5082872928176796	137	0.2395104895104895	445	0.5870712401055409	C	0.376	-0.931153	0.02359	0.450976	0.53407	ENSG00000198796	ENST00000361673	T	0.39592	1.07	5.64	-5.12	0.02893	.	0.972088	0.08477	N	0.940021	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39800	-0.9596	9	0.02654	T	1	0.6961	10.1225	0.42630	0.3517:0.2202:0.4281:0.0	rs12103986;rs52837847;rs58231351;rs12103986	719;719	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	Q	719	ENSP00000354991:H719Q	ENSP00000354991:H719Q	H	-	3	2	ALPK2	54356242	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.093000	0.03362	-1.351000	0.02197	-2.084000	0.00378	CAT	A|0.529;C|0.471	0.471	strong		0.448	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
CA3	761	hgsc.bcm.edu	37	8	86351997	86351997	+	Missense_Mutation	SNP	G	G	A	rs20571	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:86351997G>A	ENST00000285381.2	+	2	174	c.91G>A	c.(91-93)Gtt>Att	p.V31I	RP11-317J10.2_ENST00000521761.1_RNA|RP11-317J10.2_ENST00000517697.1_RNA	NM_005181.3	NP_005172.1	P07451	CAH3_HUMAN	carbonic anhydrase III, muscle specific	31			V -> I (in dbSNP:rs20571). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|response to ethanol (GO:0045471)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	carbonate dehydratase activity (GO:0004089)|nickel cation binding (GO:0016151)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23					Acetazolamide(DB00819)|Zonisamide(DB00909)	CCAGTCGCCCGTTGAGCTGCA	0.483													G|||	2201	0.439497	0.2837	0.5159	5008	,	,		18877	0.4474		0.6282	False		,,,				2504	0.3937				p.V31I		Atlas-SNP	.											.	CA3	47	.	0			c.G91A						PASS	.	G	ILE/VAL	1464,2942	471.1+/-356.0	239,986,978	85.0	73.0	77.0		91	4.7	1.0	8	dbSNP_67	77	5224,3376	641.6+/-399.7	1598,2028,674	yes	missense	CA3	NM_005181.3	29	1837,3014,1652	AA,AG,GG		39.2558,33.2274,48.5776	benign	31/261	86351997	6688,6318	2203	4300	6503	SO:0001583	missense	761	exon2			TCGCCCGTTGAGC	AJ006473	CCDS6238.1	8q21.2	2012-10-02					4.2.1.1	"""Carbonic anhydrases"""	1374	protein-coding gene	gene with protein product		114750				6221502	Standard	NM_005181		Approved	Car3, CAIII	uc003ydj.3	P07451		ENST00000285381.2:c.91G>A	8.37:g.86351997G>A	ENSP00000285381:p.Val31Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_005181	B2R867|B3KUC8|O60842	Missense_Mutation	SNP	ENST00000285381.2	37	CCDS6238.1	1067	0.48855311355311354	141	0.2865853658536585	185	0.511049723756906	268	0.46853146853146854	473	0.6240105540897097	G	5.881	0.346611	0.11126	0.332274	0.607442	ENSG00000164879	ENST00000285381	T	0.21361	2.01	5.81	4.66	0.58398	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.044063	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00408	-1.53	0.40549	P	0.01889099999999999	B	0.02656	0.0	B	0.01281	0.0	T	0.43196	-0.9406	9	0.02654	T	1	-13.3439	11.0395	0.47823	0.9276:0.0:0.0724:0.0	rs20571;rs17849877;rs59654767;rs20571	31	P07451	CAH3_HUMAN	I	31	ENSP00000285381:V31I	ENSP00000285381:V31I	V	+	1	0	CA3	86539249	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	4.497000	0.60367	1.032000	0.39892	-0.247000	0.11927	GTT	G|0.511;A|0.489	0.489	strong		0.483	CA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381090.1	NM_005181	
PCDHGB1	56104	hgsc.bcm.edu	37	5	140730384	140730384	+	Missense_Mutation	SNP	G	G	T	rs62378414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140730384G>T	ENST00000523390.1	+	1	557	c.557G>T	c.(556-558)aGt>aTt	p.S186I	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	186	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGATGGAAGTAAATATCCG	0.468													.|||	118	0.0235623	0.0356	0.0288	5008	,	,		20557	0.001		0.0298	False		,,,				2504	0.0204				p.S186I		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.G557T						PASS	.	G	,,,ILE/SER,ILE/SER	118,3644		2,114,1765	151.0	148.0	149.0		,,,557,557	1.3	1.0	5	dbSNP_129	149	241,7983		3,235,3874	yes	intron,intron,intron,missense,missense	PCDHGB1,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018922.2,NM_032095.1	,,,142,142	5,349,5639	TT,TG,GG		2.9304,3.1366,2.9952	,,,,	,,,186/928,186/811	140730384	359,11627	1881	4112	5993	SO:0001583	missense	56104	exon1			ATGGAAGTAAATA	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.557G>T	5.37:g.140730384G>T	ENSP00000429273:p.Ser186Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	134	47	0.350746	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	37	CCDS54923.1	53	0.024267399267399268	16	0.032520325203252036	16	0.04419889502762431	0	0.0	21	0.027704485488126648	.	12.14	1.849715	0.32699	0.031366	0.029304	ENSG00000254221	ENST00000523390	T	0.22336	1.96	5.36	1.34	0.21922	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.04452	0.0122	M	0.62088	1.915	0.09310	N	1	B;B	0.32467	0.125;0.372	B;B	0.35727	0.094;0.209	T	0.24764	-1.0151	9	0.40728	T	0.16	.	1.2756	0.02030	0.2205:0.1214:0.4089:0.2492	rs62378414	186;186	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	I	186	ENSP00000429273:S186I	ENSP00000429273:S186I	S	+	2	0	PCDHGB1	140710568	0.000000	0.05858	0.998000	0.56505	0.897000	0.52465	-0.393000	0.07305	0.019000	0.15079	-0.253000	0.11424	AGT	G|0.975;T|0.025	0.025	strong		0.468	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
CNDP1	84735	hgsc.bcm.edu	37	18	72228136	72228136	+	Missense_Mutation	SNP	G	G	A	rs150779486	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:72228136G>A	ENST00000358821.3	+	4	577	c.349G>A	c.(349-351)Gaa>Aaa	p.E117K	CNDP1_ENST00000585136.1_Intron|CNDP1_ENST00000582365.1_Missense_Mutation_p.E74K|RP11-231E4.3_ENST00000583702.1_RNA	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	117						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		CATCCTGGCCGAACTGGGGAG	0.552													G|||	12	0.00239617	0.0091	0.0	5008	,	,		16481	0.0		0.0	False		,,,				2504	0.0				p.E117K	Melanoma(32;1029 1042 25286 38395 44237)	Atlas-SNP	.											.	CNDP1	98	.	0			c.G349A						PASS	.	G	LYS/GLU	47,4359	48.9+/-83.8	0,47,2156	135.0	136.0	136.0		349	4.2	0.1	18	dbSNP_134	136	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CNDP1	NM_032649.5	56	0,49,6454	AA,AG,GG		0.0233,1.0667,0.3767	possibly-damaging	117/508	72228136	49,12957	2203	4300	6503	SO:0001583	missense	84735	exon4			CTGGCCGAACTGG		CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"""carnosinase 1"", ""glutamate carboxypeptidase-like protein 2"""	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.349G>A	18.37:g.72228136G>A	ENSP00000351682:p.Glu117Lys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Missense_Mutation	SNP	ENST00000358821.3	37	CCDS12007.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	5.843	0.339732	0.11069	0.010667	2.33E-4	ENSG00000150656	ENST00000358821	T	0.08896	3.04	5.11	4.22	0.49857	.	0.189436	0.45606	D	0.000347	T	0.03564	0.0102	L	0.45228	1.405	0.19300	N	0.99998	P	0.36633	0.562	B	0.14578	0.011	T	0.37641	-0.9697	10	0.13853	T	0.58	-25.2873	9.5834	0.39501	0.0785:0.1446:0.7769:0.0	.	117	Q96KN2	CNDP1_HUMAN	K	117	ENSP00000351682:E117K	ENSP00000351682:E117K	E	+	1	0	CNDP1	70379116	0.997000	0.39634	0.058000	0.19502	0.362000	0.29581	3.719000	0.54926	1.116000	0.41820	0.655000	0.94253	GAA	G|0.996;A|0.004	0.004	strong		0.552	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
GPRC6A	222545	hgsc.bcm.edu	37	6	117130544	117130544	+	Missense_Mutation	SNP	A	A	C	rs28360548	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:117130544A>C	ENST00000310357.3	-	2	452	c.431T>G	c.(430-432)aTa>aGa	p.I144R	GPRC6A_ENST00000530250.1_Missense_Mutation_p.I144R|GPRC6A_ENST00000368549.3_Missense_Mutation_p.I144R	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	144			I -> R (in dbSNP:rs28360548).		calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		CCCAGAACCTATGACAGCCTT	0.433													A|||	939	0.1875	0.1657	0.17	5008	,	,		19939	0.0218		0.33	False		,,,				2504	0.2536				p.I144R		Atlas-SNP	.											.	GPRC6A	152	.	0			c.T431G						PASS	.	A	ARG/ILE	822,3584	325.9+/-299.3	86,650,1467	93.0	89.0	90.0		431	4.9	1.0	6	dbSNP_125	90	2897,5703	454.1+/-363.4	486,1925,1889	yes	missense	GPRC6A	NM_148963.2	97	572,2575,3356	CC,CA,AA		33.686,18.6564,28.5945	probably-damaging	144/927	117130544	3719,9287	2203	4300	6503	SO:0001583	missense	222545	exon2			GAACCTATGACAG	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.431T>G	6.37:g.117130544A>C	ENSP00000309493:p.Ile144Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	140	65	0.464286	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	CCDS5112.1	402	0.18406593406593408	78	0.15853658536585366	66	0.18232044198895028	13	0.022727272727272728	245	0.3232189973614776	A	18.19	3.568339	0.65651	0.186564	0.33686	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.87179	-2.22;-2.22;-2.22	4.86	4.86	0.63082	Extracellular ligand-binding receptor (1);	0.063736	0.56097	D	0.000023	D	0.91828	0.7414	M	0.88775	2.98	0.27601	P	0.9489647999999999	D;D;D	0.69078	0.997;0.996;0.996	D;D;D	0.69479	0.949;0.931;0.964	D	0.93396	0.6756	9	0.87932	D	0	.	9.4609	0.38785	0.9097:0.0:0.0903:0.0	rs28360548	144;144;144	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	R	144	ENSP00000309493:I144R;ENSP00000357537:I144R;ENSP00000433465:I144R	ENSP00000309493:I144R	I	-	2	0	GPRC6A	117237237	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.904000	0.56325	2.047000	0.60756	0.477000	0.44152	ATA	A|0.747;C|0.253	0.253	strong		0.433	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
FRAS1	80144	hgsc.bcm.edu	37	4	79300993	79300993	+	Missense_Mutation	SNP	G	G	A	rs12512164	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:79300993G>A	ENST00000325942.6	+	27	3846	c.3406G>A	c.(3406-3408)Gaa>Aaa	p.E1136K	FRAS1_ENST00000264895.6_Missense_Mutation_p.E1136K	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1136			E -> K (in dbSNP:rs12512164).		cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.E1136K(4)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GGGTAGGGTCGAAGATCTCCT	0.483													G|||	1068	0.213259	0.1195	0.3487	5008	,	,		19674	0.2173		0.2704	False		,,,				2504	0.181				p.E1136K		Atlas-SNP	.											FRAS1_ENST00000325942,NS,carcinoma,0,3	FRAS1	779	3	4	Substitution - Missense(4)	prostate(4)	c.G3406A						scavenged	.	G	LYS/GLU,LYS/GLU	560,3214		46,468,1373	84.0	81.0	82.0		3406,3406	3.5	0.8	4	dbSNP_120	82	2256,5954		308,1640,2157	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	56,56	354,2108,3530	AA,AG,GG		27.4787,14.8384,23.498	benign,benign	1136/1977,1136/4013	79300993	2816,9168	1887	4105	5992	SO:0001583	missense	80144	exon27			AGGGTCGAAGATC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.3406G>A	4.37:g.79300993G>A	ENSP00000326330:p.Glu1136Lys	Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	164	76	0.463415	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	510	0.23351648351648352	63	0.12804878048780488	115	0.31767955801104975	125	0.21853146853146854	207	0.27308707124010556	G	3.779	-0.046038	0.07452	0.148384	0.274787	ENSG00000138759	ENST00000325942;ENST00000264895	T;T	0.76186	-1.0;-1.0	5.63	3.55	0.40652	.	0.341617	0.29348	N	0.012411	T	0.00012	0.0000	L	0.44542	1.39	0.58432	P	1.0000000000287557E-6	P;P	0.45986	0.867;0.87	B;B	0.30716	0.085;0.119	T	0.21042	-1.0257	9	0.23302	T	0.38	.	7.925	0.29870	0.1533:0.1598:0.6869:0.0	rs12512164;rs17460067;rs52813123;rs60971831;rs12512164	1136;1136	E9PHH6;A2RRR8	.;.	K	1136	ENSP00000326330:E1136K;ENSP00000264895:E1136K	ENSP00000264895:E1136K	E	+	1	0	FRAS1	79520017	1.000000	0.71417	0.837000	0.33122	0.031000	0.12232	3.882000	0.56160	1.351000	0.45789	0.591000	0.81541	GAA	G|0.776;A|0.224	0.224	strong		0.483	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
MST1L	11223	hgsc.bcm.edu	37	1	17083778	17083778	+	RNA	SNP	C	C	T	rs28455793	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17083778C>T	ENST00000455405.2	-	0	810							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										CAGAGACACGCGTGAAGACGG	0.542																																					p.T673T		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	0			c.G2019A						scavenged	.																																					11223	exon15			GACACGCGTGAAG	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17083778C>T		Somatic	245	18	0.0734694		WXS	Illumina HiSeq	Phase_I	168	83	0.494048	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				C|0.312;T|0.688	0.688	strong		0.542	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
MRAP2	112609	hgsc.bcm.edu	37	6	84799059	84799059	+	Silent	SNP	C	C	T	rs9449776	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:84799059C>T	ENST00000257776.4	+	4	612	c.477C>T	c.(475-477)aaC>aaT	p.N159N		NM_138409.2	NP_612418.2	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	159					energy homeostasis (GO:0097009)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|positive regulation of cAMP biosynthetic process (GO:0030819)|protein localization to cell surface (GO:0034394)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	corticotropin hormone receptor binding (GO:0031780)|identical protein binding (GO:0042802)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)|type 5 melanocortin receptor binding (GO:0031783)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(4)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	19						AGGAGCTGAACAGGCTCATGA	0.502													C|||	1039	0.207468	0.5802	0.1455	5008	,	,		18995	0.0099		0.0726	False		,,,				2504	0.09				p.N159N		Atlas-SNP	.											.	MRAP2	40	.	0			c.C477T						PASS	.	C		2295,2111	602.0+/-389.8	603,1089,511	123.0	120.0	121.0		477	2.4	1.0	6	dbSNP_119	121	638,7962	165.2+/-217.4	35,568,3697	no	coding-synonymous	MRAP2	NM_138409.2		638,1657,4208	TT,TC,CC		7.4186,47.9119,22.5511		159/206	84799059	2933,10073	2203	4300	6503	SO:0001819	synonymous_variant	112609	exon4			GCTGAACAGGCTC	AK090775	CCDS5001.1	6q14.3	2009-10-06	2008-07-16	2008-07-16	ENSG00000135324	ENSG00000135324			21232	protein-coding gene	gene with protein product		615410	"""chromosome 6 open reading frame 117"""	C6orf117			Standard	NM_138409		Approved	bA51G5.2	uc003pkg.4	Q96G30	OTTHUMG00000015121	ENST00000257776.4:c.477C>T	6.37:g.84799059C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	157	73	0.464968	NM_138409	A8K9M1|Q8IXM9|Q8N2D1	Silent	SNP	ENST00000257776.4	37	CCDS5001.1																																																																																			C|0.783;T|0.217	0.217	strong		0.502	MRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041367.1	NM_138409	
IFNGR1	3459	hgsc.bcm.edu	37	6	137519588	137519588	+	Silent	SNP	A	A	C	rs11914	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:137519588A>C	ENST00000367739.4	-	7	1171	c.1050T>G	c.(1048-1050)tcT>tcG	p.S350S	IFNGR1_ENST00000543628.1_Silent_p.S322S	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	350					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)			central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	CTGTTATACTAGAAAGTTCTT	0.453													A|||	471	0.0940495	0.0492	0.111	5008	,	,		17682	0.1062		0.1471	False		,,,				2504	0.0757				p.S350S		Atlas-SNP	.											.	IFNGR1	46	.	0			c.T1050G						PASS	.	A		267,4139	152.9+/-186.6	9,249,1945	120.0	118.0	119.0		1050	-11.4	0.0	6	dbSNP_52	119	1406,7194	273.1+/-290.5	109,1188,3003	no	coding-synonymous	IFNGR1	NM_000416.2		118,1437,4948	CC,CA,AA		16.3488,6.0599,12.8633		350/490	137519588	1673,11333	2203	4300	6503	SO:0001819	synonymous_variant	3459	exon7			TATACTAGAAAGT		CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"""Interferons"", ""CD molecules"""	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.1050T>G	6.37:g.137519588A>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_000416	B4DFT7|E1P587|Q53Y96	Silent	SNP	ENST00000367739.4	37	CCDS5185.1																																																																																			A|0.874;C|0.126	0.126	strong		0.453	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1		
TLR8	51311	hgsc.bcm.edu	37	X	12939412	12939412	+	Silent	SNP	C	C	A	rs3747414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:12939412C>A	ENST00000218032.6	+	2	2340	c.2253C>A	c.(2251-2253)atC>atA	p.I751I	TLR8_ENST00000311912.5_Silent_p.I769I	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	751					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.I769I(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TAAAAACAATCAACAAATCCG	0.423													C|||	2048	0.542517	0.289	0.4712	3775	,	,		15702	0.6131		0.2416	False		,,,				2504	0.4888				p.I751I		Atlas-SNP	.											.	TLR8	134	.	1	Substitution - coding silent(1)	stomach(1)	c.C2253A						PASS	.	C		1450,2385		241,759,209,632,362	102.0	93.0	96.0		2253	4.0	0.1	X	dbSNP_107	96	2320,4408		289,1095,647,1044,1225	no	coding-synonymous	TLR8	NM_138636.4		530,1854,856,1676,1587	AA,AC,A,CC,C		34.4828,37.8096,35.6906		751/1042	12939412	3770,6793	2203	4300	6503	SO:0001819	synonymous_variant	51311	exon2			AACAATCAACAAA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2253C>A	X.37:g.12939412C>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	104	98	0.942308	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	37	CCDS14152.1																																																																																			0|0.006;A|0.430	0.430	strong		0.423	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
MCM5	4174	hgsc.bcm.edu	37	22	35802661	35802661	+	Missense_Mutation	SNP	C	C	G	rs2307340	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:35802661C>G	ENST00000216122.4	+	5	693	c.539C>G	c.(538-540)aCc>aGc	p.T180S	MCM5_ENST00000382011.5_Missense_Mutation_p.T137S	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	180			T -> S (in dbSNP:rs2307340). {ECO:0000269|Ref.5}.		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						AACACCCTCACCAACATTGCC	0.637													C|||	208	0.0415335	0.0234	0.0288	5008	,	,		21179	0.006		0.0855	False		,,,				2504	0.0665				p.T180S		Atlas-SNP	.											.	MCM5	54	.	0			c.C539G						PASS	.	C	SER/THR	121,4285	91.1+/-129.8	3,115,2085	75.0	55.0	61.0		539	0.2	1.0	22	dbSNP_100	61	735,7865	177.3+/-227.0	27,681,3592	yes	missense	MCM5	NM_006739.3	58	30,796,5677	GG,GC,CC		8.5465,2.7463,6.5816	benign	180/735	35802661	856,12150	2203	4300	6503	SO:0001583	missense	4174	exon5			CCCTCACCAACAT		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"""minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)"", ""MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"""	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.539C>G	22.37:g.35802661C>G	ENSP00000216122:p.Thr180Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	NM_006739	O60785|Q14578|Q9BTJ4|Q9BWL8	Missense_Mutation	SNP	ENST00000216122.4	37	CCDS13915.1	90	0.04120879120879121	14	0.028455284552845527	9	0.024861878453038673	3	0.005244755244755245	64	0.08443271767810026	C	5.317	0.243830	0.10077	0.027463	0.085465	ENSG00000100297	ENST00000216122;ENST00000382011;ENST00000444582;ENST00000416905;ENST00000444778	T;T;T;T	0.04654	3.58;3.58;3.58;3.58	3.94	0.199	0.15175	Nucleic acid-binding, OB-fold-like (1);	0.558871	0.18678	N	0.134238	T	0.00109	0.0003	N	0.11255	0.115	0.24550	N	0.994025	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.49163	-0.8968	10	0.10636	T	0.68	-30.8481	8.3315	0.32189	0.302:0.3613:0.3367:0.0	rs2307340;rs17720368;rs52837575;rs2307340	137;180	B1AHB1;P33992	.;MCM5_HUMAN	S	180;137;89;212;37	ENSP00000216122:T180S;ENSP00000371441:T137S;ENSP00000393977:T212S;ENSP00000408705:T37S	ENSP00000216122:T180S	T	+	2	0	MCM5	34132661	0.701000	0.27806	1.000000	0.80357	0.998000	0.95712	-0.180000	0.09754	0.397000	0.25310	0.561000	0.74099	ACC	C|0.945;G|0.055	0.055	strong		0.637	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3		
ZNF207	7756	hgsc.bcm.edu	37	17	30677325	30677325	+	Silent	SNP	G	G	A	rs140451700	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:30677325G>A	ENST00000321233.6	+	1	175	c.21G>A	c.(19-21)aaG>aaA	p.K7K	ZNF207_ENST00000577908.1_Silent_p.K7K|RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000394673.2_Silent_p.K7K|ZNF207_ENST00000341711.6_Silent_p.K7K|ZNF207_ENST00000394670.4_Silent_p.K7K|ZNF207_ENST00000342555.6_5'UTR|MIR632_ENST00000385193.1_RNA	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	7	Microtubule-binding region.				attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			AGAAGAAGAAGCAGCTGAAGC	0.537													G|||	4	0.000798722	0.0	0.0043	5008	,	,		19354	0.0		0.001	False		,,,				2504	0.0				p.K7K		Atlas-SNP	.											.	ZNF207	32	.	0			c.G21A						PASS	.	G	,,	4,4402	8.1+/-20.4	0,4,2199	209.0	197.0	201.0		21,21,21	3.5	1.0	17	dbSNP_134	201	65,8535	39.3+/-95.6	0,65,4235	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF207	NM_001032293.2,NM_001098507.1,NM_003457.3	,,	0,69,6434	AA,AG,GG		0.7558,0.0908,0.5305	,,	7/464,7/495,7/479	30677325	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	7756	exon1			GAAGAAGCAGCTG	AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"""Zinc fingers, C2H2-type"""	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.21G>A	17.37:g.30677325G>A		Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	322	172	0.534162	NM_003457	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Silent	SNP	ENST00000321233.6	37	CCDS11271.1																																																																																			G|0.996;A|0.004	0.004	strong		0.537	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2		
OR51G1	79324	hgsc.bcm.edu	37	11	4945233	4945233	+	Missense_Mutation	SNP	C	C	T	rs35264256	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:4945233C>T	ENST00000321961.2	-	1	404	c.337G>A	c.(337-339)Gag>Aag	p.E113K	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACTGATGACTCCATTGAAGAC	0.502													C|||	385	0.076877	0.062	0.1527	5008	,	,		22495	0.0079		0.1083	False		,,,				2504	0.0818				p.E113K		Atlas-SNP	.											.	OR51G1	74	.	0			c.G337A						PASS	.	C	LYS/GLU	277,4125	154.8+/-188.1	3,271,1927	101.0	94.0	97.0		337	4.2	0.5	11	dbSNP_126	97	930,7666	206.2+/-248.4	61,808,3429	no	missense	OR51G1	NM_001005237.1	56	64,1079,5356	TT,TC,CC		10.819,6.2926,9.286	probably-damaging	113/322	4945233	1207,11791	2201	4298	6499	SO:0001583	missense	79324	exon1			ATGACTCCATTGA	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.337G>A	11.37:g.4945233C>T	ENSP00000322546:p.Glu113Lys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	171	0.0782967032967033	34	0.06910569105691057	30	0.08287292817679558	5	0.008741258741258742	102	0.1345646437994723	C	12.66	2.005934	0.35415	0.062926	0.10819	ENSG00000176879	ENST00000321961	T	0.40225	1.04	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39475	U	0.001355	T	0.02119	0.0066	H	0.95504	3.68	0.36263	P	0.145324	D	0.89917	1.0	D	0.91635	0.999	T	0.58092	-0.7697	9	0.87932	D	0	.	15.2651	0.73654	0.0:1.0:0.0:0.0	rs35264256;rs61737945	113	Q8NGK1	O51G1_HUMAN	K	113	ENSP00000322546:E113K	ENSP00000322546:E113K	E	-	1	0	OR51G1	4901809	0.634000	0.27190	0.508000	0.27688	0.043000	0.13939	1.261000	0.32980	2.169000	0.68431	0.557000	0.71058	GAG	C|0.912;T|0.088	0.088	strong		0.502	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
ZNF286B	729288	hgsc.bcm.edu	37	17	18584123	18584123	+	Silent	SNP	A	A	G	rs200143783	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18584123A>G	ENST00000545289.1	-	3	307	c.57T>C	c.(55-57)tcT>tcC	p.S19S	ZNF286B_ENST00000285274.5_Silent_p.S19S	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	19					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)			endometrium(1)|lung(1)	2						GGAAATGGGGAGAATCCTGGG	0.463																																					p.S19S		Atlas-SNP	.											.	ZNF286B	75	.	0			c.T57C						PASS	.						92.0	99.0	97.0					17																	18584123		692	1591	2283	SO:0001819	synonymous_variant	729288	exon3			ATGGGGAGAATCC		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.57T>C	17.37:g.18584123A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	135	38	0.281481	NM_001145045		Silent	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			A|0.962;G|0.038	0.038	strong		0.463	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
TBL3	10607	hgsc.bcm.edu	37	16	2028402	2028402	+	Silent	SNP	A	A	C	rs8460	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2028402A>C	ENST00000568546.1	+	21	2351	c.2223A>C	c.(2221-2223)cgA>cgC	p.R741R		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	741					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						TCTTGAGGCGAGAGGCCCCCG	0.677													N|||	2142	0.427716	0.6725	0.3732	5008	,	,		15492	0.3413		0.3062	False		,,,				2504	0.3497				p.R741R	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											TBL3,NS,carcinoma,0,1	TBL3	54	1	0			c.A2223C						PASS	.	G		2661,1735		815,1031,352	45.0	50.0	48.0		2223	-10.3	0.0	16	dbSNP_52	48	2595,6001		389,1817,2092	no	coding-synonymous	TBL3	NM_006453.2		1204,2848,2444	CC,CA,AA		30.1885,39.4677,40.4557		741/809	2028402	5256,7736	2198	4298	6496	SO:0001819	synonymous_variant	10607	exon21			GAGGCGAGAGGCC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.2223A>C	16.37:g.2028402A>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			A|0.592;C|0.408	0.408	strong		0.677	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
KRI1	65095	hgsc.bcm.edu	37	19	10668673	10668673	+	Missense_Mutation	SNP	A	A	G	rs1982074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10668673A>G	ENST00000312962.6	-	14	1371	c.1352T>C	c.(1351-1353)cTg>cCg	p.L451P	KRI1_ENST00000361821.5_Missense_Mutation_p.L447P	NM_023008.3	NP_075384.3	Q8N9T8	KRI1_HUMAN	KRI1 homolog (S. cerevisiae)	445						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			CTCACAGTGCAGCTCCTGCTG	0.647													A|||	886	0.176917	0.0378	0.33	5008	,	,		15709	0.2192		0.163	False		,,,				2504	0.227				p.L451P		Atlas-SNP	.											.	KRI1	65	.	0			c.T1352C						PASS	.	A	PRO/LEU	268,4138	151.0+/-185.0	17,234,1952	61.0	57.0	58.0		1352	-5.3	0.1	19	dbSNP_92	58	1668,6932	306.8+/-308.1	158,1352,2790	yes	missense	KRI1	NM_023008.3	98	175,1586,4742	GG,GA,AA		19.3953,6.0826,14.8854	benign	451/710	10668673	1936,11070	2203	4300	6503	SO:0001583	missense	65095	exon14			CAGTGCAGCTCCT		CCDS12242.1	19p13.2	2008-02-05			ENSG00000129347	ENSG00000129347			25769	protein-coding gene	gene with protein product						12878157	Standard	NM_023008		Approved	FLJ12949	uc002moy.1	Q8N9T8	OTTHUMG00000150343	ENST00000312962.6:c.1352T>C	19.37:g.10668673A>G	ENSP00000320917:p.Leu451Pro	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	103	43	0.417476	NM_023008	Q2M1R5|Q2M1R7|Q7L5J7|Q96G92|Q9BU50|Q9H6I1|Q9H978	Missense_Mutation	SNP	ENST00000312962.6	37	CCDS12242.1	352	0.16117216117216118	16	0.032520325203252036	96	0.26519337016574585	124	0.21678321678321677	116	0.15303430079155672	A	8.178	0.793193	0.16327	0.060826	0.193953	ENSG00000129347	ENST00000312962;ENST00000361821;ENST00000541101	T;T	0.07444	3.35;3.19	5.35	-5.26	0.02772	.	0.498159	0.23183	N	0.050983	T	0.00012	0.0000	N	0.05050	-0.12	0.26942	P	0.9662262	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.48043	-0.9069	9	0.27785	T	0.31	-1.4891	12.8203	0.57690	0.2679:0.0:0.7321:0.0	rs1982074;rs3745254;rs52816528;rs57112278;rs1982074	451;447	Q8N9T8;D3YTE0	KRI1_HUMAN;.	P	451;447;451	ENSP00000320917:L451P;ENSP00000355366:L447P	ENSP00000320917:L451P	L	-	2	0	KRI1	10529673	0.095000	0.21747	0.063000	0.19743	0.485000	0.33311	0.533000	0.23082	-0.810000	0.04375	-0.385000	0.06624	CTG	A|0.850;G|0.150	0.150	strong		0.647	KRI1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317705.1	NM_023008	
C4BPA	722	hgsc.bcm.edu	37	1	207287446	207287446	+	Splice_Site	SNP	C	C	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207287446C>G	ENST00000367070.3	+	3	338	c.144C>G	c.(142-144)ggC>ggG	p.G48G		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	48					complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						GGTGTCCAGGCAATTGTGGTC	0.443																																					p.G48G		Atlas-SNP	.											.	C4BPA	70	.	0			c.C144G						PASS	.						182.0	169.0	174.0					1																	207287446		2203	4300	6503	SO:0001630	splice_region_variant	722	exon3			TCCAGGCAATTGT	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"""complement component 4-binding protein, alpha"""	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.143-1C>G	1.37:g.207287446C>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	144	69	0.479167	NM_000715	Q5VVQ8	Silent	SNP	ENST00000367070.3	37	CCDS1477.1																																																																																			.	.	none		0.443	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		Silent
PHKB	5257	hgsc.bcm.edu	37	16	47697618	47697618	+	Missense_Mutation	SNP	A	A	G	rs16945474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:47697618A>G	ENST00000323584.5	+	24	2333	c.2309A>G	c.(2308-2310)tAt>tGt	p.Y770C	PHKB_ENST00000566044.1_Missense_Mutation_p.Y763C|PHKB_ENST00000299167.8_Missense_Mutation_p.Y770C|PHKB_ENST00000455779.1_Missense_Mutation_p.Y763C	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	770	Calmodulin-binding. {ECO:0000255}.		Y -> C (in dbSNP:rs16945474). {ECO:0000269|PubMed:12825073, ECO:0000269|PubMed:9326319}.		carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				GAGAGAGTCTATAGAAGAGCT	0.333													A|||	324	0.0646965	0.1649	0.0375	5008	,	,		18074	0.0149		0.0368	False		,,,				2504	0.0286				p.Y770C		Atlas-SNP	.											PHKB_ENST00000323584,NS,carcinoma,0,3	PHKB	298	3	0			c.A2309G	GRCh37	CM031328	PHKB	M	rs16945474	scavenged	.	A	CYS/TYR,CYS/TYR	671,3731	285.2+/-278.0	50,571,1580	227.0	204.0	212.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2309,2288	5.7	1.0	16	dbSNP_123	212	375,8225	123.1+/-182.0	9,357,3934	yes	missense,missense	PHKB	NM_000293.2,NM_001031835.2	194,194	59,928,5514	GG,GA,AA		4.3605,15.2431,8.0449	possibly-damaging,possibly-damaging	770/1094,763/1087	47697618	1046,11956	2201	4300	6501	SO:0001583	missense	5257	exon24			GAGTCTATAGAAG		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.2309A>G	16.37:g.47697618A>G	ENSP00000313504:p.Tyr770Cys	Somatic	272	2	0.00735294		WXS	Illumina HiSeq	Phase_I	270	155	0.574074	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	37	CCDS10729.1	129	0.059065934065934064	80	0.16260162601626016	18	0.049723756906077346	4	0.006993006993006993	27	0.03562005277044855	A	20.4	3.992193	0.74703	0.152431	0.043605	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.91407	-2.84;-2.84	5.73	5.73	0.89815	Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	T	0.04497	0.0123	M	0.78223	2.4	0.09310	P	0.99999999996013	B;P	0.48350	0.413;0.909	P;B	0.46479	0.518;0.425	T	0.40478	-0.9561	9	0.54805	T	0.06	-23.0012	16.0152	0.80434	1.0:0.0:0.0:0.0	rs16945474;rs52820357;rs16945474	770;763	Q93100;Q93100-4	KPBB_HUMAN;.	C	763;763;770	ENSP00000414345:Y763C;ENSP00000313504:Y770C	ENSP00000299167:Y763C	Y	+	2	0	PHKB	46255119	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.569000	0.90744	2.180000	0.69256	0.533000	0.62120	TAT	A|0.929;G|0.071	0.071	strong		0.333	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1		
TBC1D32	221322	hgsc.bcm.edu	37	6	121642790	121642790	+	Silent	SNP	T	T	C	rs10499110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:121642790T>C	ENST00000398212.2	-	2	355	c.306A>G	c.(304-306)caA>caG	p.Q102Q	TBC1D32_ENST00000275159.6_Silent_p.Q102Q	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	102					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										CTTTAGATTCTTGAGTTCTTT	0.393													C|||	368	0.0734824	0.1021	0.1268	5008	,	,		18526	0.124		0.0109	False		,,,				2504	0.0092				p.Q102Q		Atlas-SNP	.											.	C6orf170	146	.	0			c.A306G						PASS	.	C		308,3492		13,282,1605	248.0	230.0	236.0		306	2.4	1.0	6	dbSNP_119	236	102,8136		0,102,4017	no	coding-synonymous	C6orf170	NM_152730.4		13,384,5622	CC,CT,TT		1.2382,8.1053,3.4059		102/1258	121642790	410,11628	1900	4119	6019	SO:0001819	synonymous_variant	221322	exon2			AGATTCTTGAGTT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.306A>G	6.37:g.121642790T>C		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	294	139	0.472789	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																			T|0.924;C|0.076	0.076	strong		0.393	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
MADCAM1	8174	hgsc.bcm.edu	37	19	501701	501701	+	Missense_Mutation	SNP	G	G	A	rs71171990|rs72970252	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:501701G>A	ENST00000215637.3	+	4	746	c.700G>A	c.(700-702)Gac>Aac	p.D234N	MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.D15N	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	234	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAGCCTCCCGACACCACCTC	0.652																																					p.D234N		Atlas-SNP	.											MADCAM1,NS,lymphoid_neoplasm,0,2	MADCAM1	29	2	0			c.G700A						PASS	.						31.0	45.0	40.0					19																	501701		2203	4299	6502	SO:0001583	missense	8174	exon4			CCTCCCGACACCA	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.700G>A	19.37:g.501701G>A	ENSP00000215637:p.Asp234Asn	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	308	0.14102564102564102	38	0.07723577235772358	55	0.15193370165745856	90	0.15734265734265734	125	0.16490765171503957	g	8.795	0.931415	0.18131	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.10382	2.88	4.28	-4.55	0.03441	.	3.221950	0.01471	N	0.016293	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.37641	-0.9697	9	0.13853	T	0.58	.	12.1068	0.53818	0.7972:0.0:0.2028:0.0	.	234	Q13477	MADCA_HUMAN	N	258;250;242;234	ENSP00000215637:D234N	ENSP00000215637:D234N	D	+	1	0	MADCAM1	452701	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.470000	0.06639	-0.806000	0.04398	-0.199000	0.12753	GAC	G|0.865;A|0.135	0.135	strong		0.652	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
OR5D13	390142	hgsc.bcm.edu	37	11	55541620	55541620	+	Missense_Mutation	SNP	G	G	T	rs7124871	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55541620G>T	ENST00000361760.1	+	1	707	c.707G>T	c.(706-708)cGc>cTc	p.R236L		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	236			R -> L (in dbSNP:rs7124871).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R236H(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				GCAAGTGGGCGCCAGAAAACT	0.408													G|||	123	0.0245607	0.003	0.0259	5008	,	,		20084	0.001		0.0616	False		,,,				2504	0.0389				p.R236L		Atlas-SNP	.											OR5D13,bladder,carcinoma,+1,4	OR5D13	96	4	1	Substitution - Missense(1)	pancreas(1)	c.G707T						PASS	.	G	LEU/ARG	42,4358	44.6+/-78.6	0,42,2158	131.0	116.0	121.0		707	2.8	0.0	11	dbSNP_116	121	534,8058	147.6+/-202.9	24,486,3786	yes	missense	OR5D13	NM_001001967.1	102	24,528,5944	TT,TG,GG		6.2151,0.9545,4.4335	benign	236/315	55541620	576,12416	2200	4296	6496	SO:0001583	missense	390142	exon1			GTGGGCGCCAGAA	BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"""GPCR / Class A : Olfactory receptors"""	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.707G>T	11.37:g.55541620G>T	ENSP00000354800:p.Arg236Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	164	79	0.481707	NM_001001967	Q6IF68|Q6IFC9	Missense_Mutation	SNP	ENST00000361760.1	37	CCDS31507.1	50	0.022893772893772892	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	43	0.05672823218997362	G	10.55	1.382164	0.24944	0.009545	0.062151	ENSG00000198877	ENST00000361760	T	0.00330	8.08	3.82	2.85	0.33270	GPCR, rhodopsin-like superfamily (1);	0.690085	0.10966	U	0.614455	T	0.00039	0.0001	M	0.73372	2.23	0.09310	N	1	B	0.14438	0.01	B	0.17098	0.017	T	0.45086	-0.9285	10	0.62326	D	0.03	-0.5898	6.2567	0.20877	0.1054:0.0:0.7013:0.1933	rs7124871;rs17592523;rs58941873;rs7124871	236	Q8NGL4	OR5DD_HUMAN	L	236	ENSP00000354800:R236L	ENSP00000354800:R236L	R	+	2	0	OR5D13	55298196	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.634000	0.05477	0.679000	0.31345	0.486000	0.48141	CGC	A|0.001;G|0.964;T|0.036	0.036	strong		0.408	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967	
CAPSL	133690	hgsc.bcm.edu	37	5	35910529	35910529	+	Missense_Mutation	SNP	C	C	T	rs1445898	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:35910529C>T	ENST00000397367.2	-	3	380	c.254G>A	c.(253-255)cGg>cAg	p.R85Q	CAPSL_ENST00000397366.1_Missense_Mutation_p.R85Q|CAPSL_ENST00000514524.1_Missense_Mutation_p.R85Q	NM_144647.3	NP_653248.3	Q8WWF8	CAPSL_HUMAN	calcyphosine-like	85	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		R -> Q (in dbSNP:rs1445898).			cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(10)|skin(1)|urinary_tract(1)	19	all_lung(31;0.000268)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.167)|Colorectal(62;0.202)			ATCAAACCTCCGGAAAAGTTC	0.358													c|||	2631	0.525359	0.2277	0.5937	5008	,	,		18925	0.7609		0.4523	False		,,,				2504	0.7117				p.R85Q		Atlas-SNP	.											.	CAPSL	68	.	0			c.G254A						PASS	.	T	GLN/ARG,GLN/ARG	1220,3186	423.8+/-340.2	172,876,1155	117.0	115.0	115.0	http://www.ncbi.nlm.nih.gov/pubmed?term	254,254	0.5	1.0	5	dbSNP_88	115	3821,4779	538.4+/-383.4	854,2113,1333	yes	missense,missense	CAPSL	NM_001042625.1,NM_144647.3	43,43	1026,2989,2488	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	44.4302,27.6895,38.759	benign,benign	85/209,85/209	35910529	5041,7965	2203	4300	6503	SO:0001583	missense	133690	exon3			AACCTCCGGAAAA	BC017586	CCDS3912.2	5p13.2	2013-01-10			ENSG00000152611	ENSG00000152611		"""EF-hand domain containing"""	28375	protein-coding gene	gene with protein product						12477932	Standard	NM_001042625		Approved	MGC26610	uc003jju.1	Q8WWF8	OTTHUMG00000131109	ENST00000397367.2:c.254G>A	5.37:g.35910529C>T	ENSP00000380524:p.Arg85Gln	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	208	94	0.451923	NM_144647		Missense_Mutation	SNP	ENST00000397367.2	37	CCDS3912.2	1124	0.5146520146520146	124	0.25203252032520324	202	0.5580110497237569	455	0.7954545454545454	343	0.4525065963060686	c	2.980	-0.210599	0.06140	0.276895	0.444302	ENSG00000152611	ENST00000397367;ENST00000397366;ENST00000513623;ENST00000514524	T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67	5.38	0.531	0.17108	EF-hand-like domain (1);	0.583831	0.19450	N	0.113949	T	0.00012	0.0000	L	0.33137	0.985	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.35895	-0.9770	9	0.22109	T	0.4	-2.3175	6.8704	0.24117	0.0:0.4281:0.117:0.4549	rs1445898;rs17643269;rs52822159;rs58733553;rs1445898	85	Q8WWF8	CAPSL_HUMAN	Q	85	ENSP00000380524:R85Q;ENSP00000380523:R85Q;ENSP00000424806:R85Q;ENSP00000421018:R85Q	ENSP00000380523:R85Q	R	-	2	0	CAPSL	35946286	0.000000	0.05858	0.995000	0.50966	0.133000	0.20885	-1.012000	0.03649	0.016000	0.14998	-1.212000	0.01626	CGG	C|0.556;T|0.444	0.444	strong		0.358	CAPSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253772.2	NM_144647	
ALPK2	115701	hgsc.bcm.edu	37	18	56203120	56203120	+	Silent	SNP	C	C	T	rs3809981	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56203120C>T	ENST00000361673.3	-	5	4512	c.4299G>A	c.(4297-4299)ggG>ggA	p.G1433G	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1433						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TTGATTGACCCCCTTCTCTGG	0.502													C|||	1652	0.329872	0.2103	0.3847	5008	,	,		18692	0.2391		0.5308	False		,,,				2504	0.3395				p.G1433G		Atlas-SNP	.											ALPK2_ENST00000361673,NS,carcinoma,-1,4	ALPK2	487	4	0			c.G4299A						scavenged	.	C		1144,3262	397.0+/-330.2	141,862,1200	55.0	55.0	55.0		4299	1.0	0.0	18	dbSNP_107	55	4171,4429	542.7+/-384.2	1015,2141,1144	no	coding-synonymous	ALPK2	NM_052947.3		1156,3003,2344	TT,TC,CC		48.5,25.9646,40.8658		1433/2171	56203120	5315,7691	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			TTGACCCCCTTCT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4299G>A	18.37:g.56203120C>T		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	170	91	0.535294	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			C|0.606;T|0.394	0.394	strong		0.502	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
MORC1	27136	hgsc.bcm.edu	37	3	108754214	108754214	+	Missense_Mutation	SNP	T	T	C	rs3762697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:108754214T>C	ENST00000483760.1	-	15	1475	c.1432A>G	c.(1432-1434)Atg>Gtg	p.M478V	MORC1_ENST00000232603.5_Missense_Mutation_p.M478V					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						GGGATACCCATGGCTTGTCTT	0.318													T|||	741	0.147963	0.2262	0.0922	5008	,	,		17273	0.0823		0.163	False		,,,				2504	0.1339				p.M478V		Atlas-SNP	.											.	MORC1	211	.	0			c.A1432G						PASS	.	T	VAL/MET	983,3423	366.4+/-317.8	109,765,1329	112.0	105.0	107.0		1432	3.6	1.0	3	dbSNP_107	107	1212,7388	245.6+/-274.3	76,1060,3164	yes	missense	MORC1	NM_014429.3	21	185,1825,4493	CC,CT,TT		14.093,22.3105,16.8768	benign	478/985	108754214	2195,10811	2203	4300	6503	SO:0001583	missense	27136	exon15			TACCCATGGCTTG	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.1432A>G	3.37:g.108754214T>C	ENSP00000417282:p.Met478Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	135	55	0.407407	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	37		313	0.1433150183150183	119	0.241869918699187	42	0.11602209944751381	28	0.04895104895104895	124	0.16358839050131926	T	9.688	1.151217	0.21371	0.223105	0.14093	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.05925	3.37;3.39	4.76	3.58	0.41010	Zinc finger, CW-type (1);	0.103731	0.43747	D	0.000528	T	0.00012	0.0000	M	0.66939	2.045	0.33868	P	0.365425	B;B	0.20887	0.013;0.049	B;B	0.25987	0.006;0.065	T	0.36480	-0.9746	9	0.30078	T	0.28	-14.86	8.6446	0.33998	0.0:0.0:0.1935:0.8065	rs3762697;rs52811107;rs3762697	478;478	E7ERX1;Q86VD1	.;MORC1_HUMAN	V	478	ENSP00000232603:M478V;ENSP00000417282:M478V	ENSP00000232603:M478V	M	-	1	0	MORC1	110236904	0.984000	0.35163	1.000000	0.80357	0.814000	0.46013	-0.070000	0.11523	0.930000	0.37217	0.402000	0.26972	ATG	T|0.839;C|0.161	0.161	strong		0.318	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
IRS4	8471	hgsc.bcm.edu	37	X	107976940	107976940	+	Missense_Mutation	SNP	G	G	C	rs1801164	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:107976940G>C	ENST00000372129.2	-	1	2711	c.2635C>G	c.(2635-2637)Cat>Gat	p.H879D	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	879			H -> D (in dbSNP:rs1801164).		positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GGGGGCTCATGATCTGAAGGC	0.443													C|||	2023	0.535894	0.5197	0.4236	3775	,	,		13623	0.5268		0.173	False		,,,				2504	0.3446				p.H879D		Atlas-SNP	.											.	IRS4	253	.	0			c.C2635G						PASS	.	C	ASP/HIS	2353,1482		614,771,354,247,217	173.0	180.0	178.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2635	4.2	0.0	X	dbSNP_89	178	1412,5316		109,803,391,1516,1481	yes	missense	IRS4	NM_003604.2	81	723,1574,745,1763,1698	CC,CG,C,GG,G		20.9869,38.6441,35.6433	benign	879/1258	107976940	3765,6798	2203	4300	6503	SO:0001583	missense	8471	exon1			GCTCATGATCTGA	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.2635C>G	X.37:g.107976940G>C	ENSP00000361202:p.His879Asp	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	103	0.895652	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	807	0.4864376130198915	168	0.48	94	0.3643410852713178	193	0.5216216216216216	85	0.12648809523809523	C	0	-2.692727	0.00098	0.613559	0.209869	ENSG00000133124	ENST00000372129	T	0.30981	1.51	5.05	4.16	0.48862	.	0.577573	0.18090	N	0.152035	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46735	-0.9170	9	0.05351	T	0.99	-1.8372	9.2295	0.37428	0.0:0.775:0.1408:0.0842	rs1801164;rs17847226;rs59727900	879	O14654	IRS4_HUMAN	D	879	ENSP00000361202:H879D	ENSP00000361202:H879D	H	-	1	0	IRS4	107863596	0.365000	0.25006	0.005000	0.12908	0.008000	0.06430	1.017000	0.29989	0.480000	0.27534	-0.273000	0.10243	CAT	G|0.583;C|0.417	0.417	strong		0.443	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
NPHP3	27031	hgsc.bcm.edu	37	3	132401603	132401603	+	Missense_Mutation	SNP	G	G	C	rs143451766	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:132401603G>C	ENST00000337331.5	-	26	3842	c.3756C>G	c.(3754-3756)agC>agG	p.S1252R	NPHP3_ENST00000326682.8_3'UTR	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	1252			S -> R (in NPHP3; dbSNP:rs143451766). {ECO:0000269|PubMed:12872122}.		atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TCCGACCCAGGCTATCTTCAT	0.348													G|||	2	0.000399361	0.0	0.0	5008	,	,		18145	0.0		0.002	False		,,,				2504	0.0				p.S1252R		Atlas-SNP	.											.	NPHP3	110	.	0			c.C3756G	GRCh37	CM032020	NPHP3	M	rs143451766	PASS	.	G	ARG/SER	3,4403	6.2+/-15.9	0,3,2200	109.0	115.0	113.0		3756	4.4	1.0	3	dbSNP_134	113	8,8592	6.4+/-24.3	0,8,4292	yes	missense	NPHP3	NM_153240.4	110	0,11,6492	CC,CG,GG		0.093,0.0681,0.0846	probably-damaging	1252/1331	132401603	11,12995	2203	4300	6503	SO:0001583	missense	27031	exon26			ACCCAGGCTATCT	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"""Tetratricopeptide (TTC) repeat domain containing"""	7907	protein-coding gene	gene with protein product	"""nephrocystin-3"", ""Meckel syndrome, type 7"", ""cilia and flagella associated protein 31"""	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.3756C>G	3.37:g.132401603G>C	ENSP00000338766:p.Ser1252Arg	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	177	70	0.39548	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	37	CCDS3078.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.67	3.188670	0.57909	6.81E-4	9.3E-4	ENSG00000113971	ENST00000393144;ENST00000393156;ENST00000337331	T	0.76839	-1.05	6.16	4.38	0.52667	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.77267	0.4105	N	0.20881	0.62	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.966	T	0.72057	-0.4405	10	0.21014	T	0.42	-24.6133	9.7792	0.40639	0.2093:0.0:0.7907:0.0	.	1252;134	Q7Z494;Q7Z491	NPHP3_HUMAN;.	R	532;314;1252	ENSP00000338766:S1252R	ENSP00000338766:S1252R	S	-	3	2	NPHP3	133884293	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	2.446000	0.44908	0.937000	0.37394	0.650000	0.86243	AGC	G|0.999;C|0.001	0.001	strong		0.348	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240	
COL27A1	85301	hgsc.bcm.edu	37	9	116931666	116931666	+	Missense_Mutation	SNP	A	A	T	rs2567705	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:116931666A>T	ENST00000356083.3	+	3	2222	c.1831A>T	c.(1831-1833)Atc>Ttc	p.I611F		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	611	Pro-rich.		I -> F (in dbSNP:rs2567705). {ECO:0000269|PubMed:15489334}.		extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TGGCTATTCGATCTTCCACCT	0.647													T|||	1457	0.290935	0.3654	0.2795	5008	,	,		16947	0.1151		0.4215	False		,,,				2504	0.2454				p.I611F		Atlas-SNP	.											.	COL27A1	200	.	0			c.A1831T						PASS	.	T	PHE/ILE	1664,2742	652.9+/-399.5	313,1038,852	59.0	66.0	64.0		1831	4.7	0.7	9	dbSNP_100	64	3368,5232	639.6+/-399.5	666,2036,1598	yes	missense	COL27A1	NM_032888.2	21	979,3074,2450	TT,TA,AA		39.1628,37.7667,38.6898	benign	611/1861	116931666	5032,7974	2203	4300	6503	SO:0001583	missense	85301	exon3			TATTCGATCTTCC	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.1831A>T	9.37:g.116931666A>T	ENSP00000348385:p.Ile611Phe	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	657	0.3008241758241758	180	0.36585365853658536	114	0.3149171270718232	58	0.10139860139860139	305	0.4023746701846966	T	11.39	1.623941	0.28889	0.377667	0.391628	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	D;D	0.96136	-3.92;-2.73	4.66	4.66	0.58398	.	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.48087	P	4.1400000000002546E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27262	-1.0079	8	0.02654	T	1	.	7.5893	0.28012	0.1893:0.0:0.0:0.8107	rs2567705;rs17801180;rs59019220;rs2567705	611;558	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	F	611;611;558;558	ENSP00000348385:I611F;ENSP00000391328:I558F	ENSP00000348385:I611F	I	+	1	0	COL27A1	115971487	0.777000	0.28628	0.708000	0.30435	0.682000	0.39822	0.927000	0.28818	0.823000	0.34589	-0.364000	0.07487	ATC	A|0.648;T|0.352	0.352	strong		0.647	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
ACP5	54	hgsc.bcm.edu	37	19	11687195	11687195	+	Missense_Mutation	SNP	C	C	T	rs2229531	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11687195C>T	ENST00000592828.1	-	6	1000	c.598G>A	c.(598-600)Gtg>Atg	p.V200M	ACP5_ENST00000433365.2_Missense_Mutation_p.V200M|ACP5_ENST00000590420.1_Intron|ACP5_ENST00000412435.2_Missense_Mutation_p.V200M|ACP5_ENST00000218758.5_Missense_Mutation_p.V200M	NM_001111034.1	NP_001104504.1	P13686	PPA5_HUMAN	acid phosphatase 5, tartrate resistant	200			V -> M (in dbSNP:rs2229531). {ECO:0000269|Ref.3}.		bone morphogenesis (GO:0060349)|bone resorption (GO:0045453)|defense response to Gram-positive bacterium (GO:0050830)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of superoxide anion generation (GO:0032929)|negative regulation of tumor necrosis factor production (GO:0032720)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	acid phosphatase activity (GO:0003993)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	9						GCCACCAGCACGTAGTCCTCC	0.662													C|||	357	0.0712859	0.0083	0.0677	5008	,	,		16995	0.1012		0.1153	False		,,,				2504	0.0828				p.V200M		Atlas-SNP	.											.	ACP5	30	.	0			c.G598A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL	126,4278	84.8+/-123.5	1,124,2077	30.0	30.0	30.0		598,598,598,598	1.7	0.9	19	dbSNP_98	30	942,7656	195.4+/-240.6	55,832,3412	yes	missense,missense,missense,missense	ACP5	NM_001111034.1,NM_001111035.1,NM_001111036.1,NM_001611.3	21,21,21,21	56,956,5489	TT,TC,CC		10.956,2.861,8.2141	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	200/326,200/326,200/326,200/326	11687195	1068,11934	2202	4299	6501	SO:0001583	missense	54	exon5			CCAGCACGTAGTC	X14618	CCDS12265.1	19p13.2	2012-10-02			ENSG00000102575	ENSG00000102575	3.1.3.2		124	protein-coding gene	gene with protein product	"""tartrate-resistant acid phosphatase"""	171640				8449511, 2338077	Standard	NM_001611		Approved	TRAP	uc002msj.4	P13686	OTTHUMG00000182036	ENST00000592828.1:c.598G>A	19.37:g.11687195C>T	ENSP00000468767:p.Val200Met	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	71	26	0.366197	NM_001111034	A8K3V2|Q2TAB1|Q6IAS6|Q9UCJ5|Q9UCJ6|Q9UCJ7	Missense_Mutation	SNP	ENST00000592828.1	37	CCDS12265.1	171	0.0782967032967033	5	0.01016260162601626	30	0.08287292817679558	48	0.08391608391608392	88	0.11609498680738786	c	13.33	2.204010	0.38905	0.02861	0.10956	ENSG00000102575	ENST00000218758;ENST00000412435;ENST00000433365	D;D;D	0.86230	-2.09;-2.09;-2.09	5.32	1.74	0.24563	Metallophosphoesterase domain (1);	0.130324	0.52532	D	0.000075	T	0.13114	0.0318	M	0.79926	2.475	0.09310	P	0.9999999999976482	D	0.57899	0.981	P	0.53649	0.731	T	0.64437	-0.6408	9	0.49607	T	0.09	-20.4341	8.7675	0.34711	0.2331:0.3011:0.4658:0.0	rs2229531;rs59380162;rs2229531	200	P13686	PPA5_HUMAN	M	200	ENSP00000218758:V200M;ENSP00000392374:V200M;ENSP00000413456:V200M	ENSP00000218758:V200M	V	-	1	0	ACP5	11548195	0.964000	0.33143	0.899000	0.35326	0.000000	0.00434	0.812000	0.27211	0.595000	0.29777	-0.176000	0.13171	GTG	C|0.925;T|0.075	0.075	strong		0.662	ACP5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458881.1		
IL32	9235	hgsc.bcm.edu	37	16	3119167	3119167	+	Silent	SNP	T	T	C	rs34184287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:3119167T>C	ENST00000534507.1	+	6	727	c.516T>C	c.(514-516)gtT>gtC	p.V172V	IL32_ENST00000382213.3_Silent_p.V117V|IL32_ENST00000529550.1_Silent_p.V126V|IL32_ENST00000548652.1_Silent_p.V117V|IL32_ENST00000551513.1_Silent_p.V163V|IL32_ENST00000530890.1_Silent_p.V106V|IL32_ENST00000549213.1_Intron|IL32_ENST00000444393.3_Silent_p.V126V|IL32_ENST00000533097.2_Silent_p.V126V|IL32_ENST00000530538.2_Silent_p.V126V|IL32_ENST00000548476.1_Silent_p.V172V|IL32_ENST00000552936.1_Silent_p.V150V|IL32_ENST00000525643.2_Silent_p.V126V|IL32_ENST00000396887.3_Intron|IL32_ENST00000548246.1_Silent_p.V86V|IL32_ENST00000396890.2_Silent_p.V172V|IL32_ENST00000008180.9_Silent_p.V106V|IL32_ENST00000552356.1_Silent_p.V106V|IL32_ENST00000528163.2_Silent_p.V126V|IL32_ENST00000325568.5_Silent_p.V126V|IL32_ENST00000529699.1_Silent_p.V106V|IL32_ENST00000552664.1_Silent_p.V126V|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000551122.1_Intron|IL32_ENST00000526464.2_Silent_p.V126V|IL32_ENST00000440815.3_Silent_p.V126V|IL32_ENST00000531965.1_Silent_p.V116V			P24001	IL32_HUMAN	interleukin 32	172					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						GGCACGGGGTTCTGGCCTGGG	0.597													T|||	1775	0.354433	0.2307	0.366	5008	,	,		18195	0.3839		0.4046	False		,,,				2504	0.4315				p.V126V		Atlas-SNP	.											.	IL32	32	.	0			c.T378C						PASS	.						21.0	25.0	24.0					16																	3119167		2192	4276	6468	SO:0001819	synonymous_variant	9235	exon7			CGGGGTTCTGGCC	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.516T>C	16.37:g.3119167T>C		Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	410	200	0.487805	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Silent	SNP	ENST00000534507.1	37																																																																																				T|0.235;C|0.765	0.765	strong		0.597	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
IFNA17	3451	hgsc.bcm.edu	37	9	21227821	21227821	+	Missense_Mutation	SNP	T	T	C	rs141849715	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:21227821T>C	ENST00000413767.2	-	1	400	c.352A>G	c.(352-354)Aac>Gac	p.N118D		NM_021268.2	NP_067091.1	P01571	IFN17_HUMAN	interferon, alpha 17	118					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(2)|lung(4)|ovary(1)|skin(1)	9				Lung(24;2.13e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		GCTTCCAGGTTATTCAGTTGC	0.473																																					p.N118D		Atlas-SNP	.											.	IFNA17	17	.	0			c.A352G						PASS	.	T	ASP/ASN	4,4402	4.2+/-10.8	0,4,2199	149.0	155.0	153.0		352	-0.6	0.0	9	dbSNP_134	153	34,8566	17.9+/-57.8	1,32,4267	no	missense	IFNA17	NM_021268.2	23	1,36,6466	CC,CT,TT		0.3953,0.0908,0.2922	benign	118/190	21227821	38,12968	2203	4300	6503	SO:0001583	missense	3451	exon1			CCAGGTTATTCAG		CCDS6500.1	9p22	2010-12-10			ENSG00000234829	ENSG00000234829		"""Interferons"""	5422	protein-coding gene	gene with protein product		147583				1385305	Standard	NM_021268		Approved	LEIF2C1, IFN-alphaI	uc003zos.1	P01571	OTTHUMG00000019667	ENST00000413767.2:c.352A>G	9.37:g.21227821T>C	ENSP00000411940:p.Asn118Asp	Somatic	454	0	0		WXS	Illumina HiSeq	Phase_I	365	127	0.347945	NM_021268	Q14639|Q4KMT4|Q5VZ53|Q7M4Q4	Missense_Mutation	SNP	ENST00000413767.2	37	CCDS6500.1	7	0.003205128205128205	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	t	0.009	-1.820432	0.00595	9.08E-4	0.003953	ENSG00000234829	ENST00000413767	T	0.02890	4.12	2.87	-0.61	0.11604	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.099480	0.06778	N	0.784835	T	0.00356	0.0011	N	0.00014	-2.915	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.50013	-0.8877	10	0.02654	T	1	.	3.954	0.09382	0.0:0.356:0.3901:0.2539	.	118	P01571	IFN17_HUMAN	D	118	ENSP00000411940:N118D	ENSP00000411940:N118D	N	-	1	0	IFNA17	21217821	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-0.698000	0.05092	0.082000	0.17018	-0.702000	0.03669	AAC	T|0.997;C|0.003	0.003	strong		0.473	IFNA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051896.1	NM_021268	
ZNF845	91664	hgsc.bcm.edu	37	19	53848779	53848779	+	Silent	SNP	T	T	C	rs75887836	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53848779T>C	ENST00000595091.1	+	4	255	c.36T>C	c.(34-36)gaT>gaC	p.D12D	ZNF845_ENST00000458035.1_Silent_p.D12D			Q96IR2	ZN845_HUMAN	zinc finger protein 845	12	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						CATTCAGGGATGTGGCCATAG	0.443													.|||	673	0.134385	0.1536	0.0893	5008	,	,		18186	0.1617		0.1083	False		,,,				2504	0.1391				p.D12D		Atlas-SNP	.											.	ZNF845	101	.	0			c.T36C						PASS	.	C		194,1190		11,172,509	87.0	83.0	84.0		36	-0.7	0.8	19	dbSNP_131	84	316,2866		22,272,1297	no	coding-synonymous	ZNF845	NM_138374.1		33,444,1806	CC,CT,TT		9.9309,14.0173,11.1695		12/971	53848779	510,4056	692	1591	2283	SO:0001819	synonymous_variant	91664	exon3			CAGGGATGTGGCC	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.36T>C	19.37:g.53848779T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	48	30	0.625	NM_138374		Silent	SNP	ENST00000595091.1	37	CCDS46170.1																																																																																			T|0.880;C|0.120	0.120	strong		0.443	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
GCC2	9648	hgsc.bcm.edu	37	2	109087167	109087167	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:109087167G>T	ENST00000309863.6	+	6	2096	c.1382G>T	c.(1381-1383)gGt>gTt	p.G461V		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	461					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						GAAATACAGGGTCTTAAGGAA	0.294																																					p.G461V		Atlas-SNP	.											GCC2,NS,carcinoma,-1,1	GCC2	129	1	0			c.G1382T						PASS	.						35.0	37.0	37.0					2																	109087167		2203	4289	6492	SO:0001583	missense	9648	exon6			TACAGGGTCTTAA	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.1382G>T	2.37:g.109087167G>T	ENSP00000307939:p.Gly461Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	153	58	0.379085	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	37	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	G	9.716	1.158335	0.21454	.	.	ENSG00000135968	ENST00000309863;ENST00000409896;ENST00000393318	T	0.31247	1.5	5.41	4.51	0.55191	.	0.374008	0.26163	N	0.025964	T	0.25344	0.0616	L	0.57536	1.79	0.44330	D	0.99721	B	0.30763	0.294	B	0.30251	0.113	T	0.07770	-1.0755	10	0.30078	T	0.28	.	5.137	0.14939	0.1494:0.0:0.6492:0.2014	.	461	Q8IWJ2	GCC2_HUMAN	V	461;424;206	ENSP00000307939:G461V	ENSP00000307939:G461V	G	+	2	0	GCC2	108453599	1.000000	0.71417	1.000000	0.80357	0.601000	0.36947	2.328000	0.43867	2.688000	0.91661	0.655000	0.94253	GGT	.	.	none		0.294	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635	
FTCD	10841	hgsc.bcm.edu	37	21	47558552	47558552	+	Missense_Mutation	SNP	G	G	A	rs61735841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47558552G>A	ENST00000291670.5	-	12	1356	c.1313C>T	c.(1312-1314)gCg>gTg	p.A438V	FTCD_ENST00000397748.1_Missense_Mutation_p.A438V|FTCD_ENST00000397743.1_Silent_p.G423G|FTCD_ENST00000397746.3_Missense_Mutation_p.A438V|FTCD_ENST00000359679.2_Missense_Mutation_p.A438V|FTCD_ENST00000498355.2_5'UTR|FTCD_ENST00000355384.2_Silent_p.G423G	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	438	Cyclodeaminase/cyclohydrolase. {ECO:0000250}.		A -> E. {ECO:0000269|PubMed:12815595}.		cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	CTGTAGGGCCGCCGTGCGCCT	0.682													G|||	145	0.0289537	0.0068	0.0331	5008	,	,		15702	0.0069		0.0954	False		,,,				2504	0.0102				p.A438V		Atlas-SNP	.											FTCD,caecum,carcinoma,-1,1	FTCD	59	1	0			c.C1313T						PASS	.	G	VAL/ALA,VAL/ALA	94,4234		1,92,2071	9.0	11.0	10.0		1313,1313	3.5	0.0	21	dbSNP_129	10	863,7621		42,779,3421	yes	missense,missense	FTCD	NM_006657.2,NM_206965.1	64,64	43,871,5492	AA,AG,GG		10.1721,2.1719,7.4696	benign,benign	438/542,438/542	47558552	957,11855	2164	4242	6406	SO:0001583	missense	10841	exon12			AGGGCCGCCGTGC	U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"""formiminotransferase cyclodeaminase"""			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.1313C>T	21.37:g.47558552G>A	ENSP00000291670:p.Ala438Val	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	23	11	0.478261	NM_206965	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Missense_Mutation	SNP	ENST00000291670.5	37	CCDS13731.1	95	0.043498168498168496	5	0.01016260162601626	16	0.04419889502762431	5	0.008741258741258742	69	0.09102902374670185	G	12.64	1.998345	0.35226	0.021719	0.101721	ENSG00000160282	ENST00000291670;ENST00000397748;ENST00000359679;ENST00000397746	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	4.39	3.47	0.39725	Cyclodeaminase/cyclohydrolase (2);	0.364773	0.26700	N	0.022944	T	0.01189	0.0039	L	0.55481	1.735	0.80722	D	1	B;B	0.30482	0.281;0.058	B;B	0.26202	0.027;0.067	T	0.00899	-1.1522	10	0.39692	T	0.17	0.9566	9.6865	0.40103	0.0819:0.1469:0.7713:0.0	.	438;438	O95954-2;O95954	.;FTCD_HUMAN	V	438	ENSP00000291670:A438V;ENSP00000380856:A438V;ENSP00000352707:A438V;ENSP00000380854:A438V	ENSP00000291670:A438V	A	-	2	0	FTCD	46382980	0.546000	0.26457	0.002000	0.10522	0.014000	0.08584	1.492000	0.35594	0.913000	0.36797	0.557000	0.71058	GCG	G|0.952;A|0.048	0.048	strong		0.682	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657	
ATP9A	10079	hgsc.bcm.edu	37	20	50287736	50287736	+	Silent	SNP	C	C	T	rs2255341	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:50287736C>T	ENST00000338821.5	-	12	1362	c.1098G>A	c.(1096-1098)tcG>tcA	p.S366S	ATP9A_ENST00000311637.5_Silent_p.S230S|ATP9A_ENST00000402822.1_Silent_p.S245S	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	366					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CGGGGATTTTCGAGTCCCTTC	0.532													C|||	2669	0.532947	0.292	0.5173	5008	,	,		19347	0.7937		0.5318	False		,,,				2504	0.6022				p.S366S		Atlas-SNP	.											.	ATP9A	135	.	0			c.G1098A						PASS	.	C		1552,2854	488.8+/-361.3	257,1038,908	96.0	81.0	86.0		1098	-10.7	0.0	20	dbSNP_100	86	4503,4097	592.7+/-393.0	1177,2149,974	no	coding-synonymous	ATP9A	NM_006045.1		1434,3187,1882	TT,TC,CC		47.6395,35.2247,46.5554		366/1048	50287736	6055,6951	2203	4300	6503	SO:0001819	synonymous_variant	10079	exon12			GATTTTCGAGTCC	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1098G>A	20.37:g.50287736C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	37	CCDS33489.1																																																																																			C|0.500;T|0.500	0.500	strong		0.532	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
KMT2D	8085	hgsc.bcm.edu	37	12	49427652	49427652	+	Silent	SNP	C	C	T	rs3782357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:49427652C>T	ENST00000301067.7	-	39	10835	c.10836G>A	c.(10834-10836)caG>caA	p.Q3612Q	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3612	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CAGCTGAGtgctgttgctgtt	0.587													T|||	2221	0.44349	0.5726	0.2911	5008	,	,		20317	0.4444		0.3489	False		,,,				2504	0.4734				p.Q3612Q		Atlas-SNP	.											MLL2_ENST00000301067,NS,carcinoma,0,2	MLL2	1173	2	0			c.G10836A						PASS	.	T		2316,2066		635,1046,510	10.0	10.0	10.0		10836	0.3	1.0	12	dbSNP_107	10	3142,5418		634,1874,1772	no	coding-synonymous	MLL2	NM_003482.3		1269,2920,2282	TT,TC,CC		36.7056,47.1474,42.1728		3612/5538	49427652	5458,7484	2191	4280	6471	SO:0001819	synonymous_variant	8085	exon39			TGAGTGCTGTTGC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.10836G>A	12.37:g.49427652C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			C|0.590;T|0.410	0.410	strong		0.587	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
SCYL1	57410	hgsc.bcm.edu	37	11	65293819	65293819	+	Silent	SNP	G	G	A	rs75169347	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65293819G>A	ENST00000270176.5	+	4	677	c.600G>A	c.(598-600)aaG>aaA	p.K200K	SCYL1_ENST00000525364.1_Silent_p.K200K|SCYL1_ENST00000420247.2_Silent_p.K200K|SCYL1_ENST00000279270.6_Silent_p.K200K|SCYL1_ENST00000524944.1_Silent_p.K200K|SCYL1_ENST00000533862.1_Silent_p.K200K|SCYL1_ENST00000527009.1_Silent_p.K57K	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	200	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						TCAGAGAGAAGTGGTGGGTGA	0.657													G|||	91	0.0181709	0.0015	0.0303	5008	,	,		16563	0.0		0.0616	False		,,,				2504	0.0061				p.K200K		Atlas-SNP	.											.	SCYL1	76	.	0			c.G600A						PASS	.	G	,	34,4166		0,34,2066	16.0	19.0	18.0		600,600	-1.8	0.8	11	dbSNP_131	18	504,7942		14,476,3733	no	coding-synonymous,coding-synonymous	SCYL1	NM_001048218.1,NM_020680.3	,	14,510,5799	AA,AG,GG		5.9673,0.8095,4.2543	,	200/792,200/809	65293819	538,12108	2100	4223	6323	SO:0001819	synonymous_variant	57410	exon4			AGAGAAGTGGTGG	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"""teratoma-associated tyrosine kinase"", ""telomerase transcriptional elements-interacting factor"", ""telomerase regulation-associated protein"""	607982	"""N-terminal kinase-like"""	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.600G>A	11.37:g.65293819G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Silent	SNP	ENST00000270176.5	37	CCDS41672.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680	
GART	2618	hgsc.bcm.edu	37	21	34883618	34883618	+	Missense_Mutation	SNP	T	T	C	rs8971	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:34883618T>C	ENST00000381831.3	-	17	2518	c.2255A>G	c.(2254-2256)gAt>gGt	p.D752G	GART_ENST00000381815.4_Missense_Mutation_p.D752G|GART_ENST00000381839.3_Missense_Mutation_p.D752G|GART_ENST00000543717.1_Missense_Mutation_p.D304G	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	752	AIRS.		D -> G (in dbSNP:rs8971).		'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	CTGCTGGATATCCCTCAGAAT	0.473													T|||	762	0.152157	0.0166	0.2262	5008	,	,		18600	0.1647		0.2694	False		,,,				2504	0.1493				p.D752G		Atlas-SNP	.											.	GART	81	.	0			c.A2255G						PASS	.	T	GLY/ASP,GLY/ASP,GLY/ASP	265,4141	150.7+/-184.7	6,253,1944	223.0	209.0	214.0		2255,2255,2255	4.4	0.0	21	dbSNP_52	214	1993,6607	349.2+/-327.3	225,1543,2532	yes	missense,missense,missense	GART	NM_000819.4,NM_001136005.1,NM_001136006.1	94,94,94	231,1796,4476	CC,CT,TT		23.1744,6.0145,17.3612	benign,benign,benign	752/1011,752/1011,752/1011	34883618	2258,10748	2203	4300	6503	SO:0001583	missense	2618	exon17			TGGATATCCCTCA	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2255A>G	21.37:g.34883618T>C	ENSP00000371253:p.Asp752Gly	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	179	84	0.469274	NM_001136005	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	37	CCDS13627.1	381	0.17445054945054944	12	0.024390243902439025	91	0.2513812154696133	87	0.1520979020979021	191	0.2519788918205805	T	13.62	2.290807	0.40494	0.060145	0.231744	ENSG00000159131	ENST00000414353;ENST00000381815;ENST00000381831;ENST00000381839;ENST00000543717	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	5.6	4.42	0.53409	AIR synthase-related protein, C-terminal (2);	0.253151	0.40728	N	0.001031	T	0.00012	0.0000	L	0.52126	1.63	0.20638	P	0.999876375	B	0.19935	0.04	B	0.29440	0.102	T	0.36672	-0.9738	9	0.23891	T	0.37	-9.7444	12.6803	0.56918	0.0:0.0:0.1379:0.8621	rs8971;rs1050984;rs3171429;rs17353783;rs17382501;rs52807185;rs58505477;rs8971	752	P22102	PUR2_HUMAN	G	16;752;752;752;304	ENSP00000371236:D752G;ENSP00000371253:D752G;ENSP00000371261:D752G;ENSP00000443579:D304G	ENSP00000371236:D752G	D	-	2	0	GART	33805488	1.000000	0.71417	0.033000	0.17914	0.963000	0.63663	5.737000	0.68606	0.929000	0.37192	0.533000	0.62120	GAT	T|0.835;C|0.165	0.165	strong		0.473	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819	
HLA-C	3107	hgsc.bcm.edu	37	6	31239057	31239057	+	Missense_Mutation	SNP	C	C	T	rs2308575	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239057C>T	ENST00000376228.5	-	3	426	c.412G>A	c.(412-414)Gac>Aac	p.D138N	HLA-C_ENST00000383329.3_Missense_Mutation_p.D138N	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	138	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GCGGACTGGTCATACCCGCGG	0.701													c|||	1286	0.256789	0.357	0.3401	5008	,	,		13284	0.1627		0.2495	False		,,,				2504	0.1667				p.D138N		Atlas-SNP	.											.	HLA-C	92	.	0			c.G412A						PASS	.	C	ASN/ASP	1500,2858		126,1248,805	33.0	25.0	28.0		412	-5.6	0.0	6	dbSNP_124	28	2101,6393		152,1797,2298	no	missense	HLA-C	NM_002117.5	23	278,3045,3103	TT,TC,CC		24.7351,34.4195,28.019	benign	138/367	31239057	3601,9251	2179	4247	6426	SO:0001583	missense	3107	exon3			ACTGGTCATACCC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.412G>A	6.37:g.31239057C>T	ENSP00000365402:p.Asp138Asn	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	177	104	0.587571	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	724	0.3315018315018315	205	0.4166666666666667	137	0.3784530386740331	151	0.263986013986014	231	0.30474934036939316	.	0.004	-2.366963	0.00212	0.344195	0.247351	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00010	9.45;9.45	2.81	-5.62	0.02481	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	15.640400	0.00481	N	0.000122	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.09377	0.004;0.002;0.002;0.001	T	0.60767	-0.7198	8	0.22706	T	0.39	.	2.0724	0.03616	0.2359:0.1761:0.389:0.199	rs2308575;rs9264659;rs17839984	138;138;138;138	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	N	138;138;138;175	ENSP00000365402:D138N;ENSP00000372819:D138N	ENSP00000365402:D138N	D	-	1	0	HLA-C	31347036	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-20.000000	0.00000	-8.536000	0.00000	-3.984000	0.00014	GAC	T|0.306;C|0.694	0.306	strong		0.701	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
SLC7A13	157724	hgsc.bcm.edu	37	8	87229948	87229948	+	Silent	SNP	T	T	A	rs4621787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:87229948T>A	ENST00000297524.3	-	3	1033	c.930A>T	c.(928-930)tcA>tcT	p.S310S	SLC7A13_ENST00000419776.2_Silent_p.S301S|SLC7A13_ENST00000520624.1_5'UTR	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	310						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						TTGGTCTCGATGATTTAAATA	0.388													T|||	843	0.168331	0.1921	0.2363	5008	,	,		15021	0.1419		0.0845	False		,,,				2504	0.2014				p.S310S		Atlas-SNP	.											.	SLC7A13	97	.	0			c.A930T						PASS	.	T		797,3609	283.1+/-276.9	114,569,1520	82.0	95.0	91.0		930	-1.8	0.0	8	dbSNP_111	91	774,7818	179.5+/-228.6	31,712,3553	no	coding-synonymous	SLC7A13	NM_138817.2		145,1281,5073	AA,AT,TT		9.0084,18.089,12.0865		310/471	87229948	1571,11427	2203	4296	6499	SO:0001819	synonymous_variant	157724	exon3			TCTCGATGATTTA	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.930A>T	8.37:g.87229948T>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_138817	Q05C37|Q08AH9|Q96N84	Silent	SNP	ENST00000297524.3	37	CCDS34917.1																																																																																			A|0.126;G|0.000;T|0.873	0.126	strong		0.388	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
MUC4	4585	hgsc.bcm.edu	37	3	195517909	195517909	+	Missense_Mutation	SNP	G	G	T	rs729593	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:195517909G>T	ENST00000463781.3	-	2	1001	c.542C>A	c.(541-543)aCa>aAa	p.T181K	MUC4_ENST00000475231.1_Missense_Mutation_p.T181K|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	186					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCAGGAAGTTGTTCGTGATTG	0.502													g|||	464	0.0926518	0.0045	0.2709	5008	,	,		21900	0.002		0.0924	False		,,,				2504	0.1789				p.T181K		Atlas-SNP	.											MUC4_ENST00000463781,lymph_node,lymphoid_neoplasm,0,2	MUC4	1505	2	0			c.C542A						PASS	.		LYS/THR,,	90,4026		3,84,1971	229.0	210.0	216.0		542,,	-1.1	0.0	3	dbSNP_86	216	870,7552		60,750,3401	no	missense,intron,intron	MUC4	NM_018406.6,NM_004532.5,NM_138297.4	78,,	63,834,5372	TT,TG,GG		10.3301,2.1866,7.6567	possibly-damaging,,	181/5413,,	195517909	960,11578	2058	4211	6269	SO:0001583	missense	4585	exon2			GAAGTTGTTCGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.542C>A	3.37:g.195517909G>T	ENSP00000417498:p.Thr181Lys	Somatic	311	1	0.00321543		WXS	Illumina HiSeq	Phase_I	369	169	0.457995	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	176	0.08058608058608059	2	0.0040650406504065045	97	0.26795580110497236	1	0.0017482517482517483	76	0.10026385224274406	-	6.375	0.437311	0.12104	0.021866	0.103301	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.36157	1.27;1.27	3.56	-1.11	0.09840	.	1.063610	0.07524	U	0.911007	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P;P	0.41041	0.736;0.652	B;B	0.34093	0.175;0.084	T	0.24333	-1.0163	9	0.35671	T	0.21	.	3.7402	0.08527	0.3096:0.4039:0.2865:0.0	rs729593;rs17455416;rs729593	181;186	E7ESK3;Q99102	.;MUC4_HUMAN	K	181;181;155	ENSP00000417498:T181K;ENSP00000420243:T181K	ENSP00000376209:T155K	T	-	2	0	MUC4	197002304	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.160000	0.10041	-0.181000	0.10619	-0.358000	0.07595	ACA	T|0.073;G|0.923;A|0.004	0.073	strong		0.502	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
C9orf24	84688	hgsc.bcm.edu	37	9	34385757	34385757	+	Missense_Mutation	SNP	C	C	T	rs112332239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:34385757C>T	ENST00000297623.2	-	2	356	c.158G>A	c.(157-159)cGa>cAa	p.R53Q		NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	53					cell differentiation (GO:0030154)|cellular protein complex assembly (GO:0043623)|spermatogenesis (GO:0007283)	manchette (GO:0002177)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)		ATCCACATGTCGCTCCATGGT	0.567													C|||	29	0.00579073	0.0008	0.0101	5008	,	,		16546	0.0		0.0199	False		,,,				2504	0.001				p.R53Q		Atlas-SNP	.											.	C9orf24	15	.	0			c.G158A						PASS	.	C	GLN/ARG	15,4391	22.3+/-47.3	0,15,2188	102.0	98.0	100.0		158	0.2	0.0	9	dbSNP_132	100	141,8459	70.7+/-133.2	3,135,4162	yes	missense	C9orf24	NM_032596.3	43	3,150,6350	TT,TC,CC		1.6395,0.3404,1.1994	possibly-damaging	53/263	34385757	156,12850	2203	4300	6503	SO:0001583	missense	84688	exon2			ACATGTCGCTCCA	BC029484	CCDS6553.1, CCDS6554.1, CCDS6555.1, CCDS59121.1	9p11.2	2013-01-11			ENSG00000164972	ENSG00000164972			19919	protein-coding gene	gene with protein product	"""ciliated bronchial epithelium 1"", ""spermatid-specific manchette-related protein 1"""					12029067	Standard	NM_147168		Approved	bA573M23.4, NYD-SP22, MGC32921, MGC33614, CBE1, SMRP1	uc003zuh.1	Q8NCR6	OTTHUMG00000000437	ENST00000297623.2:c.158G>A	9.37:g.34385757C>T	ENSP00000297623:p.Arg53Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_032596	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Missense_Mutation	SNP	ENST00000297623.2	37	CCDS6554.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	C	10.89	1.479396	0.26511	0.003404	0.016395	ENSG00000164972	ENST00000297623	T	0.49720	0.77	5.89	0.165	0.14995	.	0.947922	0.08816	N	0.889535	T	0.14527	0.0351	N	0.19112	0.55	0.09310	N	1	B	0.24675	0.109	B	0.15870	0.014	T	0.13683	-1.0500	10	0.25751	T	0.34	-8.2018	5.5465	0.17067	0.0:0.4781:0.1404:0.3815	.	53	Q8NCR6	CI024_HUMAN	Q	53	ENSP00000297623:R53Q	ENSP00000297623:R53Q	R	-	2	0	C9orf24	34375757	0.003000	0.15002	0.001000	0.08648	0.048000	0.14542	0.273000	0.18662	-0.081000	0.12662	-0.797000	0.03246	CGA	C|0.989;T|0.011	0.011	strong		0.567	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169	
NFASC	23114	hgsc.bcm.edu	37	1	204948659	204948659	+	Silent	SNP	A	A	G	rs6667532	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:204948659A>G	ENST00000401399.1	+	18	2347	c.2148A>G	c.(2146-2148)ccA>ccG	p.P716P	NFASC_ENST00000338586.6_Silent_p.P716P|NFASC_ENST00000539706.1_Silent_p.P712P|NFASC_ENST00000367169.4_Silent_p.P716P|NFASC_ENST00000367170.4_Silent_p.P716P|NFASC_ENST00000404076.1_Silent_p.P695P|NFASC_ENST00000513543.1_Silent_p.P712P|NFASC_ENST00000367171.4_Silent_p.P701P|NFASC_ENST00000367172.4_Silent_p.P716P|NFASC_ENST00000360049.4_Silent_p.P712P|NFASC_ENST00000404907.1_Silent_p.P712P|NFASC_ENST00000338515.6_Silent_p.P716P|NFASC_ENST00000339876.6_Silent_p.P716P			O94856	NFASC_HUMAN	neurofascin	716	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CCAGCCTCCCATCCGAGCGCT	0.617													G|||	486	0.0970447	0.205	0.0692	5008	,	,		17159	0.0139		0.0775	False		,,,				2504	0.0767				p.P727P		Atlas-SNP	.											.	NFASC	396	.	0			c.A2181G						PASS	.	G	,,,	951,3453	726.1+/-409.7	106,739,1357	92.0	96.0	95.0		2148,2181,2136,2136	-10.5	0.0	1	dbSNP_116	95	995,7605	760.3+/-407.6	65,865,3370	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFASC	NM_001005388.2,NM_001160331.1,NM_001160332.1,NM_015090.3	,,,	171,1604,4727	GG,GA,AA		11.5698,21.594,14.9646	,,,	716/1241,727/1190,712/1175,712/1170	204948659	1946,11058	2202	4300	6502	SO:0001819	synonymous_variant	23114	exon17			CCTCCCATCCGAG	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.2148A>G	1.37:g.204948659A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	162	83	0.512346	NM_001160331	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	210	0.09615384615384616	116	0.23577235772357724	26	0.0718232044198895	9	0.015734265734265736	59	0.07783641160949868	G	8.629	0.893166	0.17613	0.21594	0.115698	ENSG00000163531	ENST00000367173	.	.	.	5.24	-10.5	0.00291	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999775	.	.	.	.	.	.	T	0.39702	-0.9601	3	.	.	.	.	11.333	0.49487	0.4535:0.4306:0.0637:0.0522	rs6667532;rs6667532	.	.	.	R	686	.	.	H	+	2	0	NFASC	203215282	0.000000	0.05858	0.002000	0.10522	0.885000	0.51271	-2.604000	0.00890	-5.484000	0.00014	-1.664000	0.00749	CAT	A|0.875;G|0.125	0.125	strong		0.617	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
ATRNL1	26033	hgsc.bcm.edu	37	10	117228794	117228794	+	Silent	SNP	A	A	G	rs10885721	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:117228794A>G	ENST00000355044.3	+	24	3735	c.3609A>G	c.(3607-3609)acA>acG	p.T1203T	ATRNL1_ENST00000423111.2_Silent_p.T254T|ATRNL1_ENST00000303745.7_Intron	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1203					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CTAACATTACATTCTATGTGT	0.303													A|||	1725	0.344449	0.2935	0.4654	5008	,	,		13018	0.1677		0.4911	False		,,,				2504	0.3589				p.T1203T		Atlas-SNP	.											.	ATRNL1	219	.	0			c.A3609G						PASS	.	A		1525,2869	443.9+/-347.2	262,1001,934	56.0	61.0	59.0		3609	0.7	1.0	10	dbSNP_120	59	4374,4182	568.5+/-389.0	1115,2144,1019	no	coding-synonymous	ATRNL1	NM_207303.2		1377,3145,1953	GG,GA,AA		48.878,34.7064,45.5521		1203/1380	117228794	5899,7051	2197	4278	6475	SO:0001819	synonymous_variant	26033	exon24			CATTACATTCTAT	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3609A>G	10.37:g.117228794A>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	169	168	0.994083	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1																																																																																			A|0.586;G|0.414	0.414	strong		0.303	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	
WNK1	65125	hgsc.bcm.edu	37	12	968489	968489	+	Silent	SNP	T	T	C	rs2286006	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:968489T>C	ENST00000315939.6	+	6	2122	c.1479T>C	c.(1477-1479)gaT>gaC	p.D493D	WNK1_ENST00000340908.4_Silent_p.D86D|WNK1_ENST00000535572.1_Silent_p.D493D|WNK1_ENST00000540360.1_3'UTR|WNK1_ENST00000537687.1_Silent_p.D493D|WNK1_ENST00000530271.2_Silent_p.D493D	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	493					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CAGAAGAAGATGATGGAGAAA	0.338													C|||	468	0.0934505	0.0378	0.0692	5008	,	,		16590	0.0675		0.171	False		,,,				2504	0.1329				p.D493D	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.T1479C						PASS	.	C	,,,	209,4197	797.7+/-415.4	6,197,2000	77.0	82.0	80.0		1479,1479,1479,1479	0.2	1.0	12	dbSNP_100	80	1292,7306	756.3+/-407.5	104,1084,3111	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WNK1	NM_001184985.1,NM_014823.2,NM_018979.3,NM_213655.4	,,,	110,1281,5111	CC,CT,TT		15.0268,4.7435,11.5426	,,,	493/2643,493/2135,493/2383,493/2635	968489	1501,11503	2203	4299	6502	SO:0001819	synonymous_variant	65125	exon6			AGAAGATGATGGA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1479T>C	12.37:g.968489T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																			T|0.899;C|0.101	0.101	strong		0.338	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
FAM153B	202134	hgsc.bcm.edu	37	5	175528584	175528584	+	Splice_Site	SNP	C	C	T	rs200684937		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:175528584C>T	ENST00000253490.4	+	12	721	c.664C>T	c.(664-666)Ctt>Ttt	p.L222F	FAM153B_ENST00000512862.1_Intron|FAM153B_ENST00000510151.1_Splice_Site_p.L145F|FAM153B_ENST00000515817.1_Splice_Site_p.L145F			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	222								p.L222F(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	16	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		ACTGGCCGAACGTACGTATTC	0.463																																					p.L145F		Atlas-SNP	.											FAM153B,NS,carcinoma,0,1	FAM153B	28	1	1	Substitution - Missense(1)	prostate(1)	c.C433T						scavenged	.																																			SO:0001630	splice_region_variant	202134	exon11			GCCGAACGTACGT	AK055006	CCDS43401.1, CCDS43401.2	5q35.2	2010-05-12			ENSG00000182230	ENSG00000182230			27323	protein-coding gene	gene with protein product							Standard	NM_001265615		Approved		uc031smb.1	P0C7A2	OTTHUMG00000163181	ENST00000253490.4:c.664+1C>T	5.37:g.175528584C>T		Somatic	551	0	0		WXS	Illumina HiSeq	Phase_I	464	10	0.0215517	NM_001265615	A8MTI1	Missense_Mutation	SNP	ENST00000253490.4	37		.	.	.	.	.	.	.	.	.	.	C	6.188	0.402789	0.11696	.	.	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	0.752	-0.292	0.12839	.	.	.	.	.	T	0.10423	0.0255	N	0.08118	0	0.09310	N	1	D	0.60575	0.988	B	0.40982	0.345	T	0.17410	-1.0370	8	0.38643	T	0.18	.	4.5589	0.12151	0.0:0.421:0.579:0.0	.	222	P0C7A2	F153B_HUMAN	F	145;222	.	ENSP00000253490:L222F	L	+	1	0	FAM153B	175461190	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	-4.439000	0.00234	-0.089000	0.12484	-1.402000	0.01139	CTT	C|0.500;T|0.500	0.500	strong		0.463	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001079529	Missense_Mutation
SH2D7	646892	hgsc.bcm.edu	37	15	78390414	78390414	+	Missense_Mutation	SNP	T	T	C	rs2289524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:78390414T>C	ENST00000328828.5	+	3	410	c.410T>C	c.(409-411)aTg>aCg	p.M137T	SH2D7_ENST00000409568.2_Start_Codon_SNP_p.M1T	NM_001101404.1	NP_001094874.1	A6NKC9	SH2D7_HUMAN	SH2 domain containing 7	137	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		M -> T (in dbSNP:rs2289524).							endometrium(2)|kidney(2)|lung(3)	7						TTCAAAGAGATGCTGACTGCT	0.617													c|||	2092	0.417732	0.5287	0.3415	5008	,	,		18189	0.252		0.4493	False		,,,				2504	0.4601				p.M137T		Atlas-SNP	.											.	SH2D7	26	.	0			c.T410C						PASS	.		THR/MET	2159,2021		581,997,512	31.0	34.0	33.0		410	1.3	1.0	15	dbSNP_100	33	3563,4831		757,2049,1391	yes	missense	SH2D7	NM_001101404.1	81	1338,3046,1903	CC,CT,TT		42.447,48.3493,45.5066	benign	137/452	78390414	5722,6852	2090	4197	6287	SO:0001583	missense	646892	exon3			AAGAGATGCTGAC		CCDS45315.1	15q25.1	2013-02-14			ENSG00000183476	ENSG00000183476		"""SH2 domain containing"""	34549	protein-coding gene	gene with protein product							Standard	NM_001101404		Approved	LOC646892	uc010blb.1	A6NKC9	OTTHUMG00000154271	ENST00000328828.5:c.410T>C	15.37:g.78390414T>C	ENSP00000327846:p.Met137Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_001101404		Missense_Mutation	SNP	ENST00000328828.5	37	CCDS45315.1	910	0.4166666666666667	260	0.5284552845528455	149	0.4116022099447514	159	0.27797202797202797	342	0.45118733509234826	c	4.851	0.158248	0.09236	0.516507	0.42447	ENSG00000183476	ENST00000409568;ENST00000328828	T;T	0.39592	1.49;1.07	4.73	1.28	0.21552	SH2 motif (2);	.	.	.	.	T	0.00012	0.0000	N	0.02865	-0.47	0.54753	P	1.3000000000040757E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.46978	-0.9152	8	0.05351	T	0.99	.	4.7848	0.13220	0.2197:0.5727:0.12:0.0876	rs2289524;rs17399674;rs59279842;rs2289524	137	A6NKC9	SH2D7_HUMAN	T	1;137	ENSP00000386676:M1T;ENSP00000327846:M137T	ENSP00000327846:M137T	M	+	2	0	SH2D7	76177469	0.104000	0.21937	0.971000	0.41717	0.037000	0.13140	0.337000	0.19841	0.420000	0.25954	-1.338000	0.01255	ATG	T|0.570;C|0.430	0.430	strong		0.617	SH2D7-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000334660.2	NM_001101404	
ANKRD44	91526	hgsc.bcm.edu	37	2	198001319	198001319	+	Silent	SNP	A	A	G	rs3731569	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:198001319A>G	ENST00000328737.2	-	4	259	c.183T>C	c.(181-183)agT>agC	p.S61S	ANKRD44_ENST00000337207.5_Silent_p.S61S|ANKRD44_ENST00000539527.1_Silent_p.S14S|ANKRD44_ENST00000450567.1_Silent_p.S61S|ANKRD44_ENST00000409153.1_Silent_p.S86S|ANKRD44_ENST00000282272.8_Silent_p.S78S|ANKRD44_ENST00000409919.1_Silent_p.S86S			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	86								p.S61S(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CACTCACTTCACTTCTGGAAG	0.428													a|||	1633	0.326078	0.5862	0.2997	5008	,	,		19780	0.2153		0.2247	False		,,,				2504	0.2117				p.S86S		Atlas-SNP	.											ANKRD44,NS,carcinoma,0,1	ANKRD44	281	1	1	Substitution - coding silent(1)	stomach(1)	c.T258C						PASS	.	G	,	2245,2161	593.1+/-387.9	584,1077,542	83.0	84.0	83.0		258,258	0.2	1.0	2	dbSNP_107	83	2018,6582	353.0+/-328.9	227,1564,2509	no	coding-synonymous,coding-synonymous	ANKRD44	NM_001195144.1,NM_153697.2	,	811,2641,3051	GG,GA,AA		23.4651,49.0468,32.7772	,	86/994,86/368	198001319	4263,8743	2203	4300	6503	SO:0001819	synonymous_variant	91526	exon4			CACTTCACTTCTG	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.183T>C	2.37:g.198001319A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_153697	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	37																																																																																				A|0.672;G|0.328	0.328	strong		0.428	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	
SLC37A2	219855	hgsc.bcm.edu	37	11	124949044	124949044	+	Silent	SNP	C	C	T	rs33932952|rs373958961	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124949044C>T	ENST00000403796.2	+	5	652	c.351C>T	c.(349-351)taC>taT	p.Y117Y	SLC37A2_ENST00000407458.1_Silent_p.Y117Y|SLC37A2_ENST00000298280.5_Silent_p.Y117Y|SLC37A2_ENST00000308074.4_Silent_p.Y117Y	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	117					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.Y117Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		TCCGTTACTACCTCTCAGCTG	0.542													C|||	664	0.132588	0.18	0.1023	5008	,	,		20435	0.0605		0.1918	False		,,,				2504	0.1033				p.Y117Y	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											SLC37A2,NS,carcinoma,0,1	SLC37A2	105	1	1	Substitution - coding silent(1)	stomach(1)	c.C351T						PASS	.	C	,	887,3515	344.1+/-307.9	92,703,1406	153.0	147.0	149.0		351,351	4.6	1.0	11	dbSNP_126	149	1719,6879	314.6+/-311.9	172,1375,2752	no	coding-synonymous,coding-synonymous	SLC37A2	NM_001145290.1,NM_198277.2	,	264,2078,4158	TT,TC,CC		19.993,20.1499,20.0462	,	117/502,117/506	124949044	2606,10394	2201	4299	6500	SO:0001819	synonymous_variant	219855	exon5			TTACTACCTCTCA	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.351C>T	11.37:g.124949044C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	208	106	0.509615	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Silent	SNP	ENST00000403796.2	37	CCDS44757.1																																																																																			C|0.814;T|0.186	0.186	strong		0.542	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
ZNF407	55628	hgsc.bcm.edu	37	18	72344509	72344509	+	Missense_Mutation	SNP	G	G	A	rs7227263	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:72344509G>A	ENST00000299687.5	+	1	1534	c.1534G>A	c.(1534-1536)Ggg>Agg	p.G512R	ZNF407_ENST00000582337.1_Missense_Mutation_p.G512R|ZNF407_ENST00000577538.1_Missense_Mutation_p.G512R|ZNF407_ENST00000309902.6_Missense_Mutation_p.G512R	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	512			G -> R (in dbSNP:rs7227263).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TCCGGACTCCGGGCTGCATTC	0.562													G|||	339	0.0676917	0.112	0.0663	5008	,	,		18648	0.001		0.1064	False		,,,				2504	0.0378				p.G512R		Atlas-SNP	.											.	ZNF407	231	.	0			c.G1534A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY	404,3640		17,370,1635	85.0	93.0	90.0		1534,1534,1534	-9.6	0.0	18	dbSNP_116	90	1156,7212		87,982,3115	yes	missense,missense,missense	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	125,125,125	104,1352,4750	AA,AG,GG		13.8145,9.9901,12.5685	benign,benign,benign	512/1816,512/1661,512/2249	72344509	1560,10852	2022	4184	6206	SO:0001583	missense	55628	exon1			GACTCCGGGCTGC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1534G>A	18.37:g.72344509G>A	ENSP00000299687:p.Gly512Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	173	0.07921245421245421	59	0.11991869918699187	26	0.0718232044198895	0	0.0	88	0.11609498680738786	G	8.956	0.969380	0.18659	0.099901	0.138145	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.08984	3.03;3.44	5.78	-9.59	0.00556	.	0.000000	0.18108	U	0.151444	T	0.00039	0.0001	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.01281	0.0;0.0;0.0	T	0.40059	-0.9583	9	0.27785	T	0.31	.	5.3187	0.15870	0.1757:0.2898:0.4351:0.0994	rs7227263;rs57563446;rs7227263	512;512;512	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	R	512	ENSP00000299687:G512R;ENSP00000310359:G512R	ENSP00000299687:G512R	G	+	1	0	ZNF407	70473497	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.751000	0.04803	-0.515000	0.06479	-0.806000	0.03193	GGG	G|0.910;A|0.090	0.090	strong		0.562	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
TLN2	83660	hgsc.bcm.edu	37	15	63111739	63111739	+	Missense_Mutation	SNP	T	T	C	rs3816988	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:63111739T>C	ENST00000561311.1	+	52	7026	c.6796T>C	c.(6796-6798)Ttc>Ctc	p.F2266L	TLN2_ENST00000306829.6_Missense_Mutation_p.F2266L			Q9Y4G6	TLN2_HUMAN	talin 2	2266			F -> L (in dbSNP:rs3816988).		cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						AACCCCAGAATTCAAGCAGCA	0.547													C|||	811	0.161941	0.2216	0.1441	5008	,	,		19114	0.0615		0.166	False		,,,				2504	0.1933				p.F2266L		Atlas-SNP	.											.	TLN2	253	.	0			c.T6796C						PASS	.	C	LEU/PHE	851,3555	745.3+/-411.6	87,677,1439	85.0	87.0	87.0		6796	4.6	1.0	15	dbSNP_107	87	1472,7128	749.3+/-407.4	125,1222,2953	yes	missense	TLN2	NM_015059.2	22	212,1899,4392	CC,CT,TT		17.1163,19.3146,17.861	benign	2266/2543	63111739	2323,10683	2203	4300	6503	SO:0001583	missense	83660	exon50			CCAGAATTCAAGC	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.6796T>C	15.37:g.63111739T>C	ENSP00000453508:p.Phe2266Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	31	0.3875	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	335	0.1533882783882784	113	0.22967479674796748	49	0.13535911602209943	44	0.07692307692307693	129	0.17018469656992086	C	13.73	2.323027	0.41096	0.193146	0.171163	ENSG00000171914	ENST00000306829	T	0.64618	-0.11	5.51	4.59	0.56863	.	0.187066	0.48286	N	0.000199	T	0.00012	0.0000	N	0.01003	-1.06	0.58432	P	9.99999999995449E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.08066	-1.0740	9	0.22706	T	0.39	-6.6987	7.4237	0.27085	0.1332:0.7271:0.0:0.1397	rs3816988;rs52797772;rs56500415;rs61482176;rs3816988	2266	Q9Y4G6	TLN2_HUMAN	L	2266	ENSP00000303476:F2266L	ENSP00000303476:F2266L	F	+	1	0	TLN2	60898792	0.965000	0.33210	1.000000	0.80357	0.983000	0.72400	1.848000	0.39309	1.348000	0.45733	-0.119000	0.15052	TTC	T|0.827;C|0.173	0.173	strong		0.547	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
METAP2	10988	hgsc.bcm.edu	37	12	95879734	95879734	+	Silent	SNP	C	C	T	rs2305293	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:95879734C>T	ENST00000323666.5	+	4	634	c.405C>T	c.(403-405)tgC>tgT	p.C135C	METAP2_ENST00000546753.1_Silent_p.C112C|METAP2_ENST00000551840.1_Silent_p.C134C|METAP2_ENST00000550777.1_Silent_p.C99C|METAP2_ENST00000261220.9_Silent_p.C112C	NM_006838.3	NP_006829.1			methionyl aminopeptidase 2											endometrium(3)|large_intestine(2)|lung(7)|prostate(1)	13						GACAAGAATGCGAATACCCAC	0.388													C|||	184	0.0367412	0.0038	0.0317	5008	,	,		17962	0.0238		0.0716	False		,,,				2504	0.0624				p.C135C		Atlas-SNP	.											.	METAP2	28	.	0			c.C405T						PASS	.	C		66,4340	61.1+/-98.1	0,66,2137	165.0	153.0	157.0		405	1.8	1.0	12	dbSNP_100	157	584,8016	155.8+/-209.8	13,558,3729	no	coding-synonymous	METAP2	NM_006838.3		13,624,5866	TT,TC,CC		6.7907,1.498,4.9977		135/479	95879734	650,12356	2203	4300	6503	SO:0001819	synonymous_variant	10988	exon4			AGAATGCGAATAC	U13261	CCDS9052.1	12q22	2014-09-04			ENSG00000111142		3.4.11.18		16672	protein-coding gene	gene with protein product	"""Peptidase M"""	601870				7644482, 8858118	Standard	NM_006838		Approved	MNPEP, p67, MAP2	uc001tec.3	P50579	OTTHUMG00000170280	ENST00000323666.5:c.405C>T	12.37:g.95879734C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_006838		Silent	SNP	ENST00000323666.5	37	CCDS9052.1																																																																																			C|0.954;T|0.046	0.046	strong		0.388	METAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408296.1	NM_006838	
DNAH3	55567	hgsc.bcm.edu	37	16	20966362	20966362	+	Missense_Mutation	SNP	T	T	C	rs34051490	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20966362T>C	ENST00000261383.3	-	55	10843	c.10844A>G	c.(10843-10845)tAt>tGt	p.Y3615C	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3615	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.Y3615F(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CTCTGATGGATAGCTGGTTAG	0.438													T|||	440	0.0878594	0.0204	0.0706	5008	,	,		16990	0.1716		0.0746	False		,,,				2504	0.1186				p.Y3615C		Atlas-SNP	.											.	DNAH3	1142	.	2	Substitution - Missense(2)	kidney(2)	c.A10844G						PASS	.	T	CYS/TYR	122,4280	90.2+/-128.9	3,116,2082	96.0	93.0	94.0		10844	5.4	1.0	16	dbSNP_126	94	715,7885	175.9+/-225.9	28,659,3613	yes	missense	DNAH3	NM_017539.1	194	31,775,5695	CC,CT,TT		8.314,2.7715,6.4375	probably-damaging	3615/4117	20966362	837,12165	2201	4300	6501	SO:0001583	missense	55567	exon55			GATGGATAGCTGG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.10844A>G	16.37:g.20966362T>C	ENSP00000261383:p.Tyr3615Cys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	120	118	0.983333	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	183	0.08379120879120878	16	0.032520325203252036	19	0.052486187845303865	83	0.1451048951048951	65	0.08575197889182058	T	17.67	3.447041	0.63178	0.027715	0.08314	ENSG00000158486	ENST00000261383	T	0.08807	3.05	5.43	5.43	0.79202	Dynein heavy chain (1);	0.151822	0.44688	D	0.000424	T	0.00210	0.0006	M	0.90814	3.15	0.09310	P	0.9999999999999944	D	0.89917	1.0	D	0.77557	0.99	T	0.04495	-1.0947	9	0.54805	T	0.06	.	11.4825	0.50333	0.0:0.0:0.1501:0.8499	rs34051490;rs58030299	3615	Q8TD57	DYH3_HUMAN	C	3615	ENSP00000261383:Y3615C	ENSP00000261383:Y3615C	Y	-	2	0	DNAH3	20873863	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.910000	0.69931	2.058000	0.61347	0.533000	0.62120	TAT	T|0.927;C|0.073	0.073	strong		0.438	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
GIMAP8	155038	hgsc.bcm.edu	37	7	150163837	150163837	+	Silent	SNP	A	A	G	rs2140595	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:150163837A>G	ENST00000307271.3	+	2	625	c.51A>G	c.(49-51)ggA>ggG	p.G17G		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	17	AIG1-type G 1.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		TCCTCCTGGGAAAATGCCGCT	0.512													G|||	1613	0.322085	0.3086	0.2334	5008	,	,		19150	0.4177		0.3708	False		,,,				2504	0.2546				p.G17G		Atlas-SNP	.											GIMAP8,trunk,malignant_melanoma,+1,1	GIMAP8	136	1	0			c.A51G						PASS	.	G		1393,3013		226,941,1036	58.0	60.0	59.0		51	-1.1	0.4	7	dbSNP_96	59	2989,5611		551,1887,1862	no	coding-synonymous	GIMAP8	NM_175571.2		777,2828,2898	GG,GA,AA		34.7558,31.616,33.6921		17/666	150163837	4382,8624	2203	4300	6503	SO:0001819	synonymous_variant	155038	exon2			CCTGGGAAAATGC	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.51A>G	7.37:g.150163837A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_175571		Silent	SNP	ENST00000307271.3	37	CCDS34777.1																																																																																			A|0.649;G|0.351	0.351	strong		0.512	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
DCST1	149095	hgsc.bcm.edu	37	1	155019710	155019710	+	Missense_Mutation	SNP	A	A	C	rs11264300	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:155019710A>C	ENST00000295542.1	+	14	1630	c.1534A>C	c.(1534-1536)Atg>Ctg	p.M512L	RP11-307C12.11_ENST00000452962.1_RNA|DCST1_ENST00000368419.2_Missense_Mutation_p.M512L|DCST1_ENST00000423025.2_Missense_Mutation_p.M487L|DCST1_ENST00000392480.1_Missense_Mutation_p.M512L	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	512			M -> L (in dbSNP:rs11264300). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			GGGAGACTCCATGCTAGCCCG	0.532													A|||	2777	0.554513	0.3858	0.5865	5008	,	,		18637	0.8849		0.3569	False		,,,				2504	0.6227				p.M512L		Atlas-SNP	.											DCST1,rectum,carcinoma,0,1	DCST1	69	1	0			c.A1534C						PASS	.	A	LEU/MET,LEU/MET	1798,2608	527.6+/-372.2	350,1098,755	88.0	86.0	87.0		1459,1534	3.7	1.0	1	dbSNP_120	87	2984,5616	462.0+/-365.6	524,1936,1840	yes	missense,missense	DCST1	NM_001143687.2,NM_152494.3	15,15	874,3034,2595	CC,CA,AA		34.6977,40.808,36.7676	benign,benign	487/682,512/707	155019710	4782,8224	2203	4300	6503	SO:0001583	missense	149095	exon14			GACTCCATGCTAG	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.1534A>C	1.37:g.155019710A>C	ENSP00000295542:p.Met512Leu	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	201	72	0.358209	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	37	CCDS1083.1	1163	0.5325091575091575	179	0.3638211382113821	193	0.5331491712707183	517	0.9038461538461539	274	0.36147757255936674	A	11.83	1.756878	0.31137	0.40808	0.346977	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	4.88	3.73	0.42828	Dendritic cell-specific transmembrane protein-like (1);	0.190127	0.51477	N	0.000086	T	0.06416	0.0165	L	0.31420	0.93	0.36215	P	0.148416	B;B	0.16166	0.016;0.016	B;B	0.18561	0.022;0.022	T	0.24048	-1.0171	9	0.06494	T	0.89	-31.4022	8.753	0.34629	0.8085:0.1915:0.0:0.0	rs11264300;rs52800761;rs60521342;rs11264300	487;512	E9PHV3;Q5T197	.;DCST1_HUMAN	L	512;512;487;512	ENSP00000295542:M512L;ENSP00000376271:M512L;ENSP00000387369:M487L;ENSP00000357404:M512L	ENSP00000295542:M512L	M	+	1	0	DCST1	153286334	1.000000	0.71417	1.000000	0.80357	0.492000	0.33523	3.293000	0.51779	0.960000	0.38005	0.533000	0.62120	ATG	A|0.559;C|0.441	0.441	strong		0.532	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416994	105416994	+	Silent	SNP	A	A	G	rs191772734	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105416994A>G	ENST00000333244.5	-	7	4913	c.4794T>C	c.(4792-4794)gtT>gtC	p.V1598V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1598						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGGGGCCCTTAACATCTATCT	0.602													.|||	51	0.0101837	0.0015	0.013	5008	,	,		15713	0.0		0.0268	False		,,,				2504	0.0133				p.V1598V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T4794C						PASS	.	G		12,3588		0,12,1788	105.0	116.0	113.0		4794	-3.1	0.0	14		113	131,7909		8,115,3897	no	coding-synonymous	AHNAK2	NM_138420.2		8,127,5685	GG,GA,AA		1.6294,0.3333,1.2285		1598/5796	105416994	143,11497	1800	4020	5820	SO:0001819	synonymous_variant	113146	exon7			GCCCTTAACATCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4794T>C	14.37:g.105416994A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	165	81	0.490909	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.991;G|0.009	0.009	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TTN	7273	hgsc.bcm.edu	37	2	179464527	179464527	+	Missense_Mutation	SNP	T	T	C	rs1001238	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179464527T>C	ENST00000591111.1	-	239	51402	c.51178A>G	c.(51178-51180)Aat>Gat	p.N17060D	TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.N9636D|TTN_ENST00000342992.6_Missense_Mutation_p.N16133D|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.N18701D|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.N9761D|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.N9828D|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17060	Ig-like 102.		N -> D. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGTTAACATTGGTTCCTTCT	0.383													C|||	2568	0.51278	0.5688	0.4078	5008	,	,		19770	0.7252		0.2535	False		,,,				2504	0.5593				p.N18701D		Atlas-SNP	.											.	TTN	18412	.	0			c.A56101G						PASS	.	C	ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN	1980,1734		541,898,418	95.0	87.0	90.0		29482,29281,48397,28906	5.6	1.0	2	dbSNP_86	90	1846,6320		195,1456,2432	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	23,23,23,23	736,2354,2850	CC,CT,TT		22.6059,46.6882,32.2054	benign,benign,benign,benign	9828/27119,9761/27052,16133/33424,9636/26927	179464527	3826,8054	1857	4083	5940	SO:0001583	missense	7273	exon289			TAACATTGGTTCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.51178A>G	2.37:g.179464527T>C	ENSP00000465570:p.Asn17060Asp	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		998	0.45695970695970695	285	0.5792682926829268	131	0.36187845303867405	395	0.6905594405594405	187	0.24670184696569922	C	15.22	2.767580	0.49574	0.533118	0.226059	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.6	5.6	0.85130	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.02751	-0.505	0.38372	P	0.05510300000000001	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.34030	-0.9845	8	0.87932	D	0	.	14.7926	0.69854	0.0:0.9306:0.0:0.0694	rs1001238;rs52825036;rs60652051;rs1001238	9636;9761;9828;17060	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	16133;9636;9828;9761;9634	ENSP00000343764:N16133D;ENSP00000434586:N9636D;ENSP00000340554:N9828D;ENSP00000352154:N9761D	ENSP00000340554:N9828D	N	-	1	0	TTN	179172772	1.000000	0.71417	0.998000	0.56505	0.770000	0.43624	6.042000	0.70996	1.386000	0.46466	-0.226000	0.12346	AAT	T|0.561;C|0.439	0.439	strong		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
OR8J1	219477	hgsc.bcm.edu	37	11	56128081	56128081	+	Missense_Mutation	SNP	A	A	G	rs10896290	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56128081A>G	ENST00000303039.3	+	1	391	c.359A>G	c.(358-360)tAt>tGt	p.Y120C		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	120			Y -> C (in dbSNP:rs10896290). {ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:14983052, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					TTGATGGCCTATGACCGCTAT	0.488													A|||	1103	0.220248	0.2542	0.1873	5008	,	,		18213	0.1369		0.328	False		,,,				2504	0.1728				p.Y120C		Atlas-SNP	.											OR8J1,head_neck,carcinoma,0,1	OR8J1	87	1	0			c.A359G						scavenged	.	A	CYS/TYR	1238,3164	425.5+/-340.8	183,872,1146	149.0	137.0	141.0		359	4.8	1.0	11	dbSNP_120	141	2939,5653	458.5+/-364.6	521,1897,1878	yes	missense	OR8J1	NM_001005205.2	194	704,2769,3024	GG,GA,AA		34.2062,28.1236,32.1456	benign	120/317	56128081	4177,8817	2201	4296	6497	SO:0001583	missense	219477	exon1			TGGCCTATGACCG	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.359A>G	11.37:g.56128081A>G	ENSP00000304060:p.Tyr120Cys	Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	257	115	0.447471	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	37	CCDS31529.1	524	0.23992673992673993	112	0.22764227642276422	68	0.1878453038674033	88	0.15384615384615385	256	0.33773087071240104	A	12.19	1.863321	0.32884	0.281236	0.342062	ENSG00000172487	ENST00000303039	T	0.00490	7.03	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000031	T	0.00012	0.0000	M	0.91196	3.185	0.33499	P	0.41034099999999996	B	0.24651	0.108	B	0.29942	0.109	T	0.39014	-0.9634	9	0.72032	D	0.01	.	13.3744	0.60730	1.0:0.0:0.0:0.0	rs10896290;rs52824219;rs59409905;rs10896290	120	Q8NGP2	OR8J1_HUMAN	C	120	ENSP00000304060:Y120C	ENSP00000304060:Y120C	Y	+	2	0	OR8J1	55884657	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	3.624000	0.54231	1.910000	0.55303	0.523000	0.50628	TAT	A|0.712;G|0.288	0.288	strong		0.488	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
ZP1	22917	hgsc.bcm.edu	37	11	60638461	60638461	+	Silent	SNP	C	C	T	rs10897122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:60638461C>T	ENST00000278853.5	+	5	858	c.858C>T	c.(856-858)ttC>ttT	p.F286F		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	286	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						ATGGCTACTTCGTCCTCGTAG	0.577													C|||	1551	0.309704	0.034	0.3098	5008	,	,		20608	0.626		0.2207	False		,,,				2504	0.4479				p.F286F		Atlas-SNP	.											.	ZP1	69	.	0			c.C858T						PASS	.	C		298,4108	162.5+/-194.5	11,276,1916	249.0	216.0	227.0		858	-1.5	0.0	11	dbSNP_120	227	1961,6637	345.4+/-325.7	228,1505,2566	no	coding-synonymous	ZP1	NM_207341.2		239,1781,4482	TT,TC,CC		22.8076,6.7635,17.3716		286/639	60638461	2259,10745	2203	4299	6502	SO:0001819	synonymous_variant	22917	exon5			CTACTTCGTCCTC	BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"""Zona pellucida glycoproteins"""	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.858C>T	11.37:g.60638461C>T		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_207341		Silent	SNP	ENST00000278853.5	37	CCDS31572.1																																																																																			C|0.776;N|0.000	.	strong		0.577	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341	
FAM131B	9715	hgsc.bcm.edu	37	7	143053723	143053723	+	Missense_Mutation	SNP	C	C	T	rs17854363	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143053723C>T	ENST00000409408.1	-	6	2627	c.919G>A	c.(919-921)Gct>Act	p.A307T	FAM131B_ENST00000443739.2_Missense_Mutation_p.A335T|FAM131B_ENST00000409222.3_Missense_Mutation_p.A307T|FAM131B_ENST00000409578.1_Missense_Mutation_p.A323T|FAM131B_ENST00000409346.1_Missense_Mutation_p.A307T			Q86XD5	F131B_HUMAN	family with sequence similarity 131, member B	307			A -> T (in dbSNP:rs17854363). {ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24	Melanoma(164;0.205)					CGGCTGAGAGCGGTAGACATC	0.582													C|||	941	0.187899	0.112	0.2406	5008	,	,		19428	0.2679		0.2087	False		,,,				2504	0.1493				p.A335T		Atlas-SNP	.											.	FAM131B	104	.	0			c.G1003A						PASS	.	C	THR/ALA,THR/ALA	546,3860	244.0+/-253.5	36,474,1693	180.0	162.0	168.0		919,1003	5.8	1.0	7	dbSNP_123	168	1662,6938	308.1+/-308.7	168,1326,2806	yes	missense,missense	FAM131B	NM_014690.4,NM_001031690.2	58,58	204,1800,4499	TT,TC,CC		19.3256,12.3922,16.9768	benign,benign	307/333,335/361	143053723	2208,10798	2203	4300	6503	SO:0001583	missense	9715	exon7			TGAGAGCGGTAGA	BC045611	CCDS5882.1, CCDS47734.1	7q34	2007-03-20			ENSG00000159784	ENSG00000159784			22202	protein-coding gene	gene with protein product							Standard	NM_014690		Approved	KIAA0773	uc010lpa.3	Q86XD5	OTTHUMG00000152697	ENST00000409408.1:c.919G>A	7.37:g.143053723C>T	ENSP00000387017:p.Ala307Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	160	74	0.4625	NM_001031690	A4D2H6|A6NDW3|A8K605|B8ZZN2|D3DXE3|J3KQX2|Q7L0D6|Q86T97	Missense_Mutation	SNP	ENST00000409408.1	37	CCDS5882.1	487	0.222985347985348	63	0.12804878048780488	86	0.23756906077348067	165	0.28846153846153844	173	0.22823218997361477	C	15.60	2.881674	0.51908	0.123922	0.193256	ENSG00000159784	ENST00000443739;ENST00000409578;ENST00000409346;ENST00000452076;ENST00000409408;ENST00000409222	T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88	5.81	5.81	0.92471	.	0.539404	0.18955	N	0.126564	T	0.00012	0.0000	L	0.40543	1.245	0.26047	P	0.9815394	B;P	0.38642	0.198;0.641	B;B	0.28305	0.088;0.08	T	0.48843	-0.8999	9	0.17832	T	0.49	-6.3713	15.5509	0.76152	0.0:0.8627:0.1373:0.0	rs17854363	323;307	Q86XD5-2;Q86XD5	.;F131B_HUMAN	T	335;323;307;311;307;307	ENSP00000410603:A335T;ENSP00000386568:A323T;ENSP00000386984:A307T;ENSP00000387017:A307T;ENSP00000387147:A307T	ENSP00000387147:A307T	A	-	1	0	FAM131B	142763845	0.962000	0.33011	0.959000	0.39883	0.790000	0.44656	3.776000	0.55356	2.746000	0.94184	0.655000	0.94253	GCT	C|0.809;T|0.191	0.191	strong		0.582	FAM131B-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328057.1	NM_014690	
PLEKHH3	79990	hgsc.bcm.edu	37	17	40824339	40824339	+	Missense_Mutation	SNP	G	G	A	rs200210041	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:40824339G>A	ENST00000591022.1	-	7	1228	c.841C>T	c.(841-843)Cgg>Tgg	p.R281W	PLEKHH3_ENST00000293349.6_Missense_Mutation_p.R281W|PLEKHH3_ENST00000412503.1_Missense_Mutation_p.R281W|PLEKHH3_ENST00000456950.2_Intron	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	281	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		ccggggcgccgcgcccccTCC	0.716													G|||	11	0.00219649	0.0	0.0014	5008	,	,		11523	0.0		0.008	False		,,,				2504	0.002				p.R281W		Atlas-SNP	.											.	PLEKHH3	49	.	0			c.C841T						PASS	.	G	TRP/ARG	10,3544		0,10,1767	7.0	7.0	7.0		841	4.4	1.0	17		7	83,6727		1,81,3323	no	missense	PLEKHH3	NM_024927.4	101	1,91,5090	AA,AG,GG		1.2188,0.2814,0.8973	probably-damaging	281/794	40824339	93,10271	1777	3405	5182	SO:0001583	missense	79990	exon7			GGCGCCGCGCCCC	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.841C>T	17.37:g.40824339G>A	ENSP00000468678:p.Arg281Trp	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	15	12	0.8	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Missense_Mutation	SNP	ENST00000591022.1	37	CCDS11434.1	9	0.004120879120879121	3	0.006097560975609756	0	0.0	0	0.0	6	0.0079155672823219	G	33	5.272087	0.95429	0.002814	0.012188	ENSG00000068137	ENST00000293349;ENST00000412503	D;D	0.88354	-2.06;-2.37	5.41	4.43	0.53597	MyTH4 domain (1);	0.000000	0.45361	D	0.000363	D	0.88862	0.6552	L	0.36672	1.1	0.50467	D	0.999874	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.90716	0.4631	10	0.66056	D	0.02	-15.0434	15.2543	0.73573	0.0:0.0:0.8583:0.1417	.	281;281	Q7Z736-2;Q7Z736	.;PKHH3_HUMAN	W	281	ENSP00000293349:R281W;ENSP00000411885:R281W	ENSP00000293349:R281W	R	-	1	2	PLEKHH3	38077865	0.977000	0.34250	1.000000	0.80357	0.995000	0.86356	2.205000	0.42770	1.486000	0.48398	0.655000	0.94253	CGG	G|0.996;A|0.004	0.004	strong		0.716	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	
SPG11	80208	hgsc.bcm.edu	37	15	44943757	44943757	+	Missense_Mutation	SNP	A	A	G	rs3759871	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:44943757A>G	ENST00000261866.7	-	6	1404	c.1388T>C	c.(1387-1389)tTt>tCt	p.F463S	SPG11_ENST00000535302.2_Missense_Mutation_p.F463S|SPG11_ENST00000559193.1_Missense_Mutation_p.F463S|SPG11_ENST00000558319.1_Missense_Mutation_p.F463S|SPG11_ENST00000427534.2_Missense_Mutation_p.F463S	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	463			F -> S (in dbSNP:rs3759871). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:15489334}.		cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.F463S(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		GCCAAGGGAAAAACACTGCAT	0.463													A|||	2378	0.47484	0.5234	0.5893	5008	,	,		20546	0.4653		0.4513	False		,,,				2504	0.362				p.F463S		Atlas-SNP	.											SPG11,NS,carcinoma,0,1	SPG11	207	1	1	Substitution - Missense(1)	stomach(1)	c.T1388C						PASS	.	A	SER/PHE,SER/PHE	2310,2086	603.0+/-390.0	609,1092,497	118.0	110.0	113.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1388,1388	4.9	0.9	15	dbSNP_107	113	3917,4679	547.6+/-385.2	924,2069,1305	yes	missense,missense	SPG11	NM_001160227.1,NM_025137.3	155,155	1533,3161,1802	GG,GA,AA		45.5677,47.4522,47.9295	benign,benign	463/2331,463/2444	44943757	6227,6765	2198	4298	6496	SO:0001583	missense	80208	exon6			AGGGAAAAACACT		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"""spatacsin"""	610844	"""KIAA1840"""	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.1388T>C	15.37:g.44943757A>G	ENSP00000261866:p.Phe463Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	72	65	0.902778	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	1075	0.49221611721611724	254	0.516260162601626	206	0.569060773480663	283	0.49475524475524474	332	0.43799472295514513	A	10.01	1.234381	0.22626	0.525478	0.455677	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.76060	-0.99;-0.73;-0.73	6.06	4.93	0.64822	.	0.209291	0.42053	D	0.000773	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B;B;B;B	0.22211	0.021;0.066;0.053;0.021	B;B;B;B	0.18561	0.009;0.02;0.022;0.008	T	0.48514	-0.9029	9	0.26408	T	0.33	.	3.1014	0.06327	0.6352:0.1486:0.0744:0.1418	rs3759871;rs52807288;rs59538210;rs3759871	463;463;463;463	C4B7M2;F5H3N6;B9EK60;Q96JI7	.;.;.;SPTCS_HUMAN	S	463	ENSP00000261866:F463S;ENSP00000445278:F463S;ENSP00000396110:F463S	ENSP00000261866:F463S	F	-	2	0	SPG11	42731049	0.042000	0.20092	0.856000	0.33681	0.991000	0.79684	1.226000	0.32563	1.092000	0.41356	0.533000	0.62120	TTT	A|0.523;G|0.477	0.477	strong		0.463	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1		
DMXL1	1657	hgsc.bcm.edu	37	5	118480316	118480316	+	Missense_Mutation	SNP	G	G	A	rs4895362	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:118480316G>A	ENST00000311085.8	+	15	2632	c.2552G>A	c.(2551-2553)aGc>aAc	p.S851N	DMXL1_ENST00000539542.1_Missense_Mutation_p.S851N	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	851			S -> N (in dbSNP:rs4895362).							breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GGCAAAGACAGCATTTTATCT	0.313													G|||	108	0.0215655	0.003	0.0288	5008	,	,		16639	0.0		0.0497	False		,,,				2504	0.0348				p.S851N		Atlas-SNP	.											.	DMXL1	268	.	0			c.G2552A						PASS	.	G	ASN/SER	55,4349	53.6+/-89.4	0,55,2147	93.0	102.0	99.0		2552	-2.8	0.0	5	dbSNP_111	99	580,8008	154.6+/-208.8	23,534,3737	yes	missense	DMXL1	NM_005509.4	46	23,589,5884	AA,AG,GG		6.7536,1.2489,4.8876	benign	851/3028	118480316	635,12357	2202	4294	6496	SO:0001583	missense	1657	exon15			AAGACAGCATTTT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.2552G>A	5.37:g.118480316G>A	ENSP00000309690:p.Ser851Asn	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	272	125	0.459559	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	53	0.024267399267399268	3	0.006097560975609756	14	0.03867403314917127	0	0.0	36	0.047493403693931395	G	0.012	-1.691464	0.00731	0.012489	0.067536	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.30448	1.53;1.53	5.24	-2.79	0.05841	.	1.281360	0.04515	N	0.383583	T	0.01592	0.0051	L	0.29908	0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.20075	-1.0286	10	0.22109	T	0.4	1.8738	10.3433	0.43891	0.5093:0.0873:0.4034:0.0	rs4895362;rs52827504;rs4895362	851;851	F5H269;Q9Y485	.;DMXL1_HUMAN	N	851	ENSP00000309690:S851N;ENSP00000439479:S851N	ENSP00000309690:S851N	S	+	2	0	DMXL1	118508215	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.559000	0.05971	-1.556000	0.01695	-1.786000	0.00637	AGC	G|0.959;A|0.041	0.041	strong		0.313	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
ISM2	145501	hgsc.bcm.edu	37	14	77944624	77944624	+	Missense_Mutation	SNP	T	T	C	rs149849326	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77944624T>C	ENST00000342219.4	-	6	1215	c.1159A>G	c.(1159-1161)Aag>Gag	p.K387E	ISM2_ENST00000393684.3_Missense_Mutation_p.K299E|ISM2_ENST00000412904.1_Missense_Mutation_p.K306E|ISM2_ENST00000493585.1_Silent_p.G271G|ISM2_ENST00000429906.1_Missense_Mutation_p.K306E	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	387						extracellular region (GO:0005576)				endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						GCCAGGAGCTTCCACTCCTCA	0.637													T|||	41	0.0081869	0.003	0.0086	5008	,	,		19142	0.0		0.0159	False		,,,				2504	0.0153				p.K387E		Atlas-SNP	.											.	ISM2	68	.	0			c.A1159G						PASS	.	T	,GLU/LYS	12,4394	17.9+/-39.9	0,12,2191	160.0	139.0	146.0		813,1159	4.0	0.1	14	dbSNP_134	146	179,8421	81.8+/-144.4	4,171,4125	yes	coding-synonymous,missense	ISM2	NM_182509.3,NM_199296.2	,56	4,183,6316	CC,CT,TT		2.0814,0.2724,1.4686	,benign	271/293,387/572	77944624	191,12815	2203	4300	6503	SO:0001583	missense	145501	exon6			GGAGCTTCCACTC	AK056709	CCDS9864.1, CCDS45143.1	14q24.3	2013-05-15	2013-05-15	2008-12-23	ENSG00000100593	ENSG00000100593			23176	protein-coding gene	gene with protein product	"""thrombospondin and AMOP containing isthmin-like 1"""	612684	"""thrombospondin, type I domain-containing 3"", ""thrombospondin, type I, domain containing 3"", ""isthmin 2 homolog (zebrafish)"""	THSD3		15194193	Standard	NM_199296		Approved	FLJ32147, TAIL1	uc001xtz.3	Q6H9L7	OTTHUMG00000158563	ENST00000342219.4:c.1159A>G	14.37:g.77944624T>C	ENSP00000341490:p.Lys387Glu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_199296	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Missense_Mutation	SNP	ENST00000342219.4	37	CCDS9864.1	16	0.007326007326007326	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	10	0.013192612137203167	T	0.025	-1.384359	0.01194	0.002724	0.020814	ENSG00000100593	ENST00000342219;ENST00000412904;ENST00000429906;ENST00000393684	T;T;T;T	0.21734	1.99;2.0;2.0;2.31	4.91	4.02	0.46733	.	0.727256	0.11876	N	0.520968	T	0.07188	0.0182	.	.	.	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.11329	0.006;0.003	T	0.24119	-1.0169	9	0.23302	T	0.38	-16.3633	10.822	0.46610	0.0:0.0:0.8104:0.1896	.	306;387	Q6H9L7-5;Q6H9L7	.;ISM2_HUMAN	E	387;306;306;299	ENSP00000341490:K387E;ENSP00000416773:K306E;ENSP00000395387:K306E;ENSP00000377289:K299E	ENSP00000341490:K387E	K	-	1	0	ISM2	77014377	0.530000	0.26330	0.071000	0.20095	0.024000	0.10985	1.079000	0.30766	1.071000	0.40834	-0.384000	0.06662	AAG	T|0.987;C|0.013	0.013	strong		0.637	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509	
BAAT	570	hgsc.bcm.edu	37	9	104130469	104130469	+	Missense_Mutation	SNP	C	C	G	rs41281027	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:104130469C>G	ENST00000395051.3	-	2	672	c.602G>C	c.(601-603)cGc>cCc	p.R201P	BAAT_ENST00000259407.2_Missense_Mutation_p.R201P			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	201					acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	TTCTGGTTTGCGGGGCAGGTC	0.498													G|||	777	0.155152	0.236	0.1383	5008	,	,		12055	0.0456		0.1571	False		,,,				2504	0.1687				p.R201P		Atlas-SNP	.											BAAT,bladder,carcinoma,-1,1	BAAT	52	1	0			c.G602C						scavenged	.	G	PRO/ARG,PRO/ARG	957,3449	730.6+/-410.2	104,749,1350	74.0	80.0	78.0		602,602	-3.1	0.0	9	dbSNP_127	78	1250,7350	760.2+/-407.6	90,1070,3140	yes	missense,missense	BAAT	NM_001127610.1,NM_001701.3	103,103	194,1819,4490	GG,GC,CC		14.5349,21.7204,16.9691	benign,benign	201/419,201/419	104130469	2207,10799	2203	4300	6503	SO:0001583	missense	570	exon3			GGTTTGCGGGGCA	L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	2.3.1.65		932	protein-coding gene	gene with protein product	"""glycine N-choloyltransferase"""	602938	"""bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase)"", ""bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)"""				Standard	NM_001701		Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.602G>C	9.37:g.104130469C>G	ENSP00000378491:p.Arg201Pro	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	131	52	0.396947	NM_001127610	Q3B7W9|Q96L31	Missense_Mutation	SNP	ENST00000395051.3	37	CCDS6752.1	314	0.14377289377289376	118	0.23983739837398374	53	0.1464088397790055	27	0.0472027972027972	116	0.15303430079155672	G	5.108	0.205558	0.09704	0.217204	0.145349	ENSG00000136881	ENST00000259407;ENST00000395051	T;T	0.45276	0.9;0.9	4.47	-3.11	0.05299	.	3.070920	0.00995	N	0.003597	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16158	-1.0412	9	0.42905	T	0.14	7.5868	0.7619	0.01008	0.2513:0.3284:0.1798:0.2405	rs41281027;rs61755097	201	Q14032	BAAT_HUMAN	P	201	ENSP00000259407:R201P;ENSP00000378491:R201P	ENSP00000259407:R201P	R	-	2	0	BAAT	103170290	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.429000	0.02437	-0.719000	0.04942	-0.216000	0.12614	CGC	C|0.839;G|0.161	0.161	strong		0.498	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1		
DACT1	51339	hgsc.bcm.edu	37	14	59112732	59112732	+	Missense_Mutation	SNP	C	C	T	rs17832998	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:59112732C>T	ENST00000335867.4	+	4	1415	c.1391C>T	c.(1390-1392)gCt>gTt	p.A464V	DACT1_ENST00000556859.1_Missense_Mutation_p.A183V|DACT1_ENST00000395153.3_Missense_Mutation_p.A427V|DACT1_ENST00000541264.2_Missense_Mutation_p.A183V			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	464			A -> V (in dbSNP:rs17832998). {ECO:0000269|Ref.3}.		dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						CAAGAACATGCTCGGTGTTCC	0.637													C|||	1350	0.269569	0.2443	0.1902	5008	,	,		16542	0.2738		0.3161	False		,,,				2504	0.3078				p.A464V		Atlas-SNP	.											.	DACT1	119	.	0			c.C1391T						PASS	.	C	VAL/ALA,VAL/ALA	1148,3256	381.4+/-324.0	158,832,1212	47.0	55.0	52.0		1280,1391	2.4	0.0	14	dbSNP_123	52	2747,5853	407.0+/-349.0	435,1877,1988	yes	missense,missense	DACT1	NM_001079520.1,NM_016651.5	64,64	593,2709,3200	TT,TC,CC		31.9419,26.0672,29.9523	benign,benign	427/800,464/837	59112732	3895,9109	2202	4300	6502	SO:0001583	missense	51339	exon4			AACATGCTCGGTG	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.1391C>T	14.37:g.59112732C>T	ENSP00000337439:p.Ala464Val	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_016651	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	37	CCDS9736.1	590	0.27014652014652013	141	0.2865853658536585	79	0.21823204419889503	137	0.2395104895104895	233	0.3073878627968338	C	7.265	0.606015	0.14002	0.260672	0.319419	ENSG00000165617	ENST00000556859;ENST00000395151;ENST00000395153;ENST00000335867;ENST00000541264	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	5.35	2.42	0.29668	.	0.626485	0.16134	N	0.228059	T	0.00012	0.0000	N	0.25144	0.715	0.80722	P	0.0	B;B	0.19073	0.007;0.033	B;B	0.17979	0.006;0.02	T	0.37753	-0.9692	9	0.27785	T	0.31	-0.8406	8.5845	0.33649	0.0:0.6186:0.2537:0.1277	rs17832998;rs52807238;rs57262719;rs17832998	427;464	A8MYJ2;Q9NYF0	.;DACT1_HUMAN	V	183;183;427;464;183	ENSP00000451598:A183V;ENSP00000378581:A183V;ENSP00000378582:A427V;ENSP00000337439:A464V;ENSP00000442850:A183V	ENSP00000337439:A464V	A	+	2	0	DACT1	58182485	0.000000	0.05858	0.000000	0.03702	0.418000	0.31294	0.062000	0.14389	0.206000	0.20587	0.563000	0.77884	GCT	C|0.713;T|0.287	0.287	strong		0.637	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
OR2J3	442186	hgsc.bcm.edu	37	6	29080344	29080344	+	Missense_Mutation	SNP	G	G	A	rs3749977	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29080344G>A	ENST00000377169.1	+	1	677	c.677G>A	c.(676-678)cGa>cAa	p.R226Q		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	226			R -> Q (in allele 6M1-3*02; decreased response to C3HEX; dbSNP:rs3749977). {ECO:0000269|PubMed:22714804, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						GCCATCGTCCGAGCTATACTG	0.458													G|||	1861	0.371605	0.6021	0.2752	5008	,	,		22524	0.252		0.2286	False		,,,				2504	0.3988				p.R226Q		Atlas-SNP	.											.	OR2J3	53	.	0			c.G677A						PASS	.	G	GLN/ARG	1332,1250		337,658,296	110.0	118.0	116.0		677	-4.1	0.0	6	dbSNP_107	116	1194,3948		151,892,1528	yes	missense	OR2J3	NM_001005216.2	43	488,1550,1824	AA,AG,GG		23.2205,48.4121,32.7033	benign	226/312	29080344	2526,5198	1291	2571	3862	SO:0001583	missense	442186	exon1			TCGTCCGAGCTAT		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.677G>A	6.37:g.29080344G>A	ENSP00000366374:p.Arg226Gln	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	370	169	0.456757	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	704	0.32234432234432236	305	0.6199186991869918	95	0.26243093922651933	133	0.23251748251748253	171	0.22559366754617413	G	0.012	-1.666039	0.00765	0.515879	0.232205	ENSG00000204701	ENST00000377169	T	0.39406	1.08	2.78	-4.13	0.03904	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.08403	0.0209	L	0.31294	0.92	0.80722	P	0.0	B	0.12630	0.006	B	0.15870	0.014	T	0.32981	-0.9886	8	0.12766	T	0.61	.	8.1363	0.31056	0.1874:0.1869:0.6257:0.0	rs3749977;rs6923417;rs3749977	226	O76001	OR2J3_HUMAN	Q	226	ENSP00000366374:R226Q	ENSP00000366374:R226Q	R	+	2	0	OR2J3	29188323	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-3.580000	0.00424	-1.536000	0.01738	-0.602000	0.04101	CGA	G|0.651;A|0.349	0.349	strong		0.458	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
WDR25	79446	hgsc.bcm.edu	37	14	100996312	100996312	+	Silent	SNP	T	T	C	rs13065	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100996312T>C	ENST00000335290.6	+	7	1795	c.1569T>C	c.(1567-1569)taT>taC	p.Y523Y	WDR25_ENST00000402312.3_Silent_p.Y523Y|WDR25_ENST00000542471.2_Silent_p.Y266Y|WDR25_ENST00000554998.1_Silent_p.Y523Y|WDR25_ENST00000557502.1_3'UTR	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	523										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				GCACCACCTATCACCCCGTGC	0.642													C|||	3212	0.641374	0.9705	0.611	5008	,	,		19149	0.6974		0.4155	False		,,,				2504	0.3926				p.Y523Y		Atlas-SNP	.											WDR25,NS,carcinoma,0,1	WDR25	37	1	0			c.T1569C						PASS	.	C	,	3873,533	242.1+/-252.3	1710,453,40	82.0	75.0	77.0		1569,1569	0.8	1.0	14	dbSNP_52	77	3368,5232	640.7+/-399.6	670,2028,1602	no	coding-synonymous,coding-synonymous	WDR25	NM_001161476.1,NM_024515.4	,	2380,2481,1642	CC,CT,TT		39.1628,12.0971,44.3257	,	523/545,523/545	100996312	7241,5765	2203	4300	6503	SO:0001819	synonymous_variant	79446	exon7			CACCTATCACCCC	BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"""WD repeat domain containing"""	21064	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 67"""	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.1569T>C	14.37:g.100996312T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	151	74	0.490066	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Silent	SNP	ENST00000335290.6	37	CCDS32157.1																																																																																			T|0.409;C|0.591	0.591	strong		0.642	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515	
EPHX2	2053	hgsc.bcm.edu	37	8	27394366	27394366	+	Silent	SNP	C	C	T	rs13439459	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27394366C>T	ENST00000521400.1	+	13	1666	c.1236C>T	c.(1234-1236)agC>agT	p.S412S	EPHX2_ENST00000518379.1_Silent_p.S380S|EPHX2_ENST00000380476.3_Silent_p.S359S|EPHX2_ENST00000521780.1_Silent_p.S346S|EPHX2_ENST00000517536.1_Silent_p.S229S	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	412	Epoxide hydrolase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		TCAGAGCAAGCGATGAGGTGA	0.527													C|||	314	0.0626997	0.084	0.0807	5008	,	,		15715	0.001		0.0845	False		,,,				2504	0.0624				p.S412S		Atlas-SNP	.											.	EPHX2	57	.	0			c.C1236T						PASS	.	C		359,4047	184.7+/-212.0	17,325,1861	63.0	65.0	64.0		1236	0.1	0.0	8	dbSNP_121	64	874,7726	197.8+/-242.3	44,786,3470	no	coding-synonymous	EPHX2	NM_001979.4		61,1111,5331	TT,TC,CC		10.1628,8.148,9.4802		412/556	27394366	1233,11773	2203	4300	6503	SO:0001819	synonymous_variant	2053	exon13			AGCAAGCGATGAG	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.1236C>T	8.37:g.27394366C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Silent	SNP	ENST00000521400.1	37	CCDS6060.1																																																																																			C|0.918;T|0.082	0.082	strong		0.527	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		
HLA-C	3107	hgsc.bcm.edu	37	6	31237124	31237124	+	Missense_Mutation	SNP	T	T	C	rs1130838	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31237124T>C	ENST00000376228.5	-	7	1101	c.1087A>G	c.(1087-1089)Act>Gct	p.T363A	HLA-C_ENST00000383329.3_Missense_Mutation_p.T369A	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	369					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CCTTTACAAGTGATGAGAGAC	0.532													C|||	3933	0.785343	0.8139	0.8184	5008	,	,		17056	0.8135		0.7266	False		,,,				2504	0.7546				p.T363A		Atlas-SNP	.											.	HLA-C	92	.	0			c.A1087G						PASS	.	C	ALA/THR	2396,624		955,486,69	39.0	46.0	44.0		1087	0.5	0.0	6	dbSNP_86	44	3724,1694		1281,1162,266	yes	missense	HLA-C	NM_002117.5	58	2236,1648,335	CC,CT,TT		31.2661,20.6623,27.471	benign	363/367	31237124	6120,2318	1510	2709	4219	SO:0001583	missense	3107	exon7			TACAAGTGATGAG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.1087A>G	6.37:g.31237124T>C	ENSP00000365402:p.Thr363Ala	Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	137	134	0.978102	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1702	0.7793040293040293	401	0.8150406504065041	291	0.8038674033149171	461	0.8059440559440559	549	0.7242744063324539	.	1.561	-0.536687	0.04082	0.793377	0.687339	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000539307	T;T	0.01043	5.41;5.41	2.34	0.456	0.16655	MHC class I, alpha chain, C-terminal (1);	.	.	.	.	T	0.00144	0.0004	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.32268	-0.9913	7	0.02654	T	1	.	2.992	0.05986	0.0:0.4647:0.2366:0.2987	rs1130838;rs2308656;rs3177816;rs3190167;rs3998382;rs17413262;rs45552931	369;363	A2AEA2;P10321	.;1C07_HUMAN	A	363;369;400	ENSP00000365402:T363A;ENSP00000372819:T369A	ENSP00000365402:T363A	T	-	1	0	HLA-C	31345103	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.365000	0.01079	-0.161000	0.10983	-0.711000	0.03637	ACT	T|0.266;C|0.734	0.734	strong		0.532	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
IQCC	55721	hgsc.bcm.edu	37	1	32672908	32672908	+	Missense_Mutation	SNP	T	T	G	rs3903683	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32672908T>G	ENST00000291358.6	+	5	647	c.626T>G	c.(625-627)tTc>tGc	p.F209C	RP4-622L5.7_ENST00000373604.4_RNA|RP4-622L5.7_ENST00000421616.1_RNA|DCDC2B_ENST00000409358.1_5'Flank|IQCC_ENST00000537469.1_Missense_Mutation_p.F289C	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	209			F -> C (in dbSNP:rs3903683). {ECO:0000269|Ref.2}.							endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CCCCGCGTGTTCCTAGAACAT	0.547													G|||	1139	0.227436	0.3056	0.2378	5008	,	,		17838	0.2302		0.0567	False		,,,				2504	0.2873				p.F289C		Atlas-SNP	.											.	IQCC	46	.	0			c.T866G						PASS	.	G	CYS/PHE,CYS/PHE	1285,3121	699.3+/-406.5	211,863,1129	69.0	69.0	69.0		626,866	2.3	0.0	1	dbSNP_108	69	560,8040	794.2+/-407.5	19,522,3759	yes	missense,missense	IQCC	NM_018134.2,NM_001160042.1	205,205	230,1385,4888	GG,GT,TT		6.5116,29.1648,14.1858	benign,benign	209/467,289/547	32672908	1845,11161	2203	4300	6503	SO:0001583	missense	55721	exon5			GCGTGTTCCTAGA	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.626T>G	1.37:g.32672908T>G	ENSP00000291358:p.Phe209Cys	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	173	97	0.560694	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Missense_Mutation	SNP	ENST00000291358.6	37	CCDS355.1	379	0.17353479853479853	152	0.3089430894308943	55	0.15193370165745856	127	0.22202797202797203	45	0.059366754617414245	G	0.013	-1.607113	0.00842	0.291648	0.065116	ENSG00000160051	ENST00000537469;ENST00000291358	T;T	0.08282	3.11;3.11	3.46	2.32	0.28847	.	0.368381	0.20522	N	0.090682	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44982	-0.9292	9	0.02654	T	1	-0.5815	2.9321	0.05803	0.187:0.0:0.5649:0.2481	rs3903683;rs61163302;rs3903683	289;209	F5H7T8;Q4KMZ1	.;IQCC_HUMAN	C	289;209	ENSP00000442291:F289C;ENSP00000291358:F209C	ENSP00000291358:F209C	F	+	2	0	IQCC	32445495	0.023000	0.18921	0.001000	0.08648	0.011000	0.07611	1.192000	0.32150	0.305000	0.22832	-0.217000	0.12591	TTC	T|0.842;G|0.158	0.158	strong		0.547	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134	
AMZ1	155185	hgsc.bcm.edu	37	7	2748803	2748803	+	Silent	SNP	C	C	T	rs58726146	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:2748803C>T	ENST00000312371.4	+	5	1064	c.696C>T	c.(694-696)gaC>gaT	p.D232D	AMZ1_ENST00000407112.1_Intron|AMZ1_ENST00000489665.1_Intron	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	232							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		CAGCAGCAGACGGCCCCGAGG	0.687													C|||	1451	0.289736	0.3011	0.1297	5008	,	,		14749	0.5714		0.1252	False		,,,				2504	0.2669				p.D232D		Atlas-SNP	.											AMZ1,NS,carcinoma,0,1	AMZ1	41	1	0			c.C696T						PASS	.	C		1183,3211		177,829,1191	14.0	18.0	16.0		696	-8.6	0.0	7	dbSNP_129	16	1168,7426		83,1002,3212	no	coding-synonymous	AMZ1	NM_133463.1		260,1831,4403	TT,TC,CC		13.5909,26.9231,18.1013		232/499	2748803	2351,10637	2197	4297	6494	SO:0001819	synonymous_variant	155185	exon5			AGCAGACGGCCCC	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.696C>T	7.37:g.2748803C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	37	CCDS34589.1																																																																																			C|0.791;T|0.209	0.209	strong		0.687	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735857	55735857	+	Missense_Mutation	SNP	A	A	G	rs76700680	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55735857A>G	ENST00000312345.2	-	1	133	c.83T>C	c.(82-84)aTg>aCg	p.M28T		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					CATCAGGATCATCAAATACAT	0.333													G|||	191	0.038139	0.0129	0.0389	5008	,	,		16224	0.001		0.0934	False		,,,				2504	0.0532				p.M28T		Atlas-SNP	.											.	OR10AG1	100	.	0			c.T83C						PASS	.	G	THR/MET	106,4286		3,100,2093	41.0	47.0	45.0		83	-1.9	0.0	11	dbSNP_131	45	677,7909		31,615,3647	yes	missense	OR10AG1	NM_001005491.1	81	34,715,5740	GG,GA,AA		7.8849,2.4135,6.0333	benign	28/302	55735857	783,12195	2196	4293	6489	SO:0001583	missense	282770	exon1			AGGATCATCAAAT	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.83T>C	11.37:g.55735857A>G	ENSP00000311477:p.Met28Thr	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	149	46	0.308725	NM_001005491	B2RNH4|Q6IEU3	Missense_Mutation	SNP	ENST00000312345.2	37	CCDS31514.1	82	0.037545787545787544	4	0.008130081300813009	10	0.027624309392265192	0	0.0	68	0.08970976253298153	G	1.859	-0.462999	0.04476	0.024135	0.078849	ENSG00000174970	ENST00000312345	T	0.00424	7.45	5.27	-1.85	0.07784	.	0.642260	0.13667	N	0.371153	T	0.00012	0.0000	N	0.02412	-0.56	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.10965	-1.0607	10	0.28530	T	0.3	.	6.955	0.24565	0.5575:0.2587:0.1837:0.0	.	28	Q8NH19	O10AG_HUMAN	T	28	ENSP00000311477:M28T	ENSP00000311477:M28T	M	-	2	0	OR10AG1	55492433	0.000000	0.05858	0.000000	0.03702	0.303000	0.27691	0.401000	0.20948	-0.367000	0.08052	-1.753000	0.00675	ATG	A|0.951;G|0.049	0.049	strong		0.333	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
MARCH10	162333	hgsc.bcm.edu	37	17	60814473	60814473	+	Silent	SNP	C	C	T	rs567796772		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:60814473C>T	ENST00000311269.5	-	6	1030	c.756G>A	c.(754-756)tcG>tcA	p.S252S	RP11-156L14.1_ENST00000582564.1_RNA|MARCH10_ENST00000456609.2_Silent_p.S252S|RP11-156L14.1_ENST00000579201.1_RNA|RP11-156L14.1_ENST00000577270.1_RNA|RP11-156L14.1_ENST00000584597.1_RNA|MARCH10_ENST00000583600.1_Silent_p.S290S|MARCH10_ENST00000544856.2_Silent_p.S251S	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	252					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						GTGGTGGCCCCGAGAACTCAC	0.493																																					p.S252S		Atlas-SNP	.											MARCH10,colon,carcinoma,-1,1	MARCH10	102	1	0			c.G756A						scavenged	.						110.0	111.0	110.0					17																	60814473		2203	4300	6503	SO:0001819	synonymous_variant	162333	exon6			TGGCCCCGAGAAC	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	26655	protein-coding gene	gene with protein product		613337	"""ring finger protein 190"", ""membrane-associated ring finger (C3HC4) 10"""	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.756G>A	17.37:g.60814473C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	200	2	0.01	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Silent	SNP	ENST00000311269.5	37	CCDS11635.1																																																																																			.	.	none		0.493	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598	
OR4D6	219983	hgsc.bcm.edu	37	11	59224885	59224885	+	Missense_Mutation	SNP	G	G	C	rs1453542	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:59224885G>C	ENST00000300127.2	+	1	475	c.452G>C	c.(451-453)aGt>aCt	p.S151T		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	151			S -> T (in dbSNP:rs1453542).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						TCTTGGGTGAGTGGTGGTTTG	0.517													G|||	888	0.177316	0.0477	0.2305	5008	,	,		19531	0.1746		0.2793	False		,,,				2504	0.2127				p.S151T		Atlas-SNP	.											.	OR4D6	65	.	0			c.G452C						PASS	.	G	THR/SER	329,4073	176.2+/-205.4	11,307,1883	283.0	250.0	261.0		452	5.0	1.0	11	dbSNP_88	261	2540,6050	415.1+/-351.7	365,1810,2120	yes	missense	OR4D6	NM_001004708.1	58	376,2117,4003	CC,CG,GG		29.5693,7.4739,22.0828	benign	151/315	59224885	2869,10123	2201	4295	6496	SO:0001583	missense	219983	exon1			GGGTGAGTGGTGG	AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"""GPCR / Class A : Olfactory receptors"""	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.452G>C	11.37:g.59224885G>C	ENSP00000300127:p.Ser151Thr	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	181	91	0.502762	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	460	0.21062271062271062	28	0.056910569105691054	95	0.26243093922651933	114	0.1993006993006993	223	0.2941952506596306	G	12.41	1.928327	0.34002	0.074739	0.295693	ENSG00000166884	ENST00000300127	T	0.36699	1.24	6.0	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.374604	0.22876	N	0.054573	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.17465	0.022	B	0.28305	0.088	T	0.27400	-1.0075	9	0.87932	D	0	-5.4983	15.5056	0.75739	0.0:0.1386:0.8614:0.0	rs1453542;rs17500408;rs1453542	151	Q8NGJ1	OR4D6_HUMAN	T	151	ENSP00000300127:S151T	ENSP00000300127:S151T	S	+	2	0	OR4D6	58981461	0.000000	0.05858	0.956000	0.39512	0.935000	0.57460	-0.059000	0.11731	2.846000	0.97976	0.650000	0.86243	AGT	G|0.782;C|0.218	0.218	strong		0.517	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708	
IRG1	730249	hgsc.bcm.edu	37	13	77531361	77531361	+	Silent	SNP	C	C	T	rs41287034	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:77531361C>T	ENST00000377462.1	+	5	749	c.687C>T	c.(685-687)ctC>ctT	p.L229L	IRG1_ENST00000449753.1_Silent_p.L229L	NM_001258406.1	NP_001245335.1	A6NK06	IRG1_HUMAN	immunoresponsive 1 homolog (mouse)	229					cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to progesterone stimulus (GO:0071393)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of type I interferon production (GO:0032480)|positive regulation of antimicrobial humoral response (GO:0002760)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|propionate catabolic process (GO:0019543)|tolerance induction to lipopolysaccharide (GO:0072573)	mitochondrion (GO:0005739)	2-methylcitrate dehydratase activity (GO:0047547)|aconitate decarboxylase activity (GO:0047613)										TGTTGGGTCTCCAAGGAAACA	0.527													C|||	112	0.0223642	0.0015	0.0605	5008	,	,		22273	0.0		0.0557	False		,,,				2504	0.0123				p.L225L		Atlas-SNP	.											.	IRG1	1	.	0			c.C675T						PASS	.																																			SO:0001819	synonymous_variant	730249	exon4			GGGTCTCCAAGGA		CCDS58299.1	13q22.3	2013-04-29			ENSG00000102794	ENSG00000102794			33904	protein-coding gene	gene with protein product		615275				23610393	Standard	NM_001258406		Approved		uc031qmi.1	A6NK06	OTTHUMG00000017098	ENST00000377462.1:c.687C>T	13.37:g.77531361C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	161	85	0.52795	NM_001258406		Silent	SNP	ENST00000377462.1	37	CCDS58299.1																																																																																			C|0.960;T|0.040	0.040	strong		0.527	IRG1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045311.1	XM_001133269	
PDCD6IP	10015	hgsc.bcm.edu	37	3	33907945	33907945	+	Silent	SNP	A	A	G	rs3183987	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33907945A>G	ENST00000307296.3	+	18	2912	c.2535A>G	c.(2533-2535)ccA>ccG	p.P845P	PDCD6IP_ENST00000457054.2_Silent_p.P850P			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	845	Interaction with EIAV p9.|Pro-rich.|Self-association.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						GACAGGCTCCATACCCGGGAC	0.522													A|||	1655	0.330471	0.2943	0.4035	5008	,	,		15976	0.4117		0.2326	False		,,,				2504	0.3446				p.P850P		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.A2550G						PASS	.	A	,	1318,3088	444.3+/-347.3	179,960,1064	88.0	87.0	87.0		2550,2535	-11.6	0.7	3	dbSNP_105	87	2277,6323	383.6+/-340.8	281,1715,2304	no	coding-synonymous,coding-synonymous	PDCD6IP	NM_001162429.1,NM_013374.4	,	460,2675,3368	GG,GA,AA		26.4767,29.9138,27.6411	,	850/874,845/869	33907945	3595,9411	2203	4300	6503	SO:0001819	synonymous_variant	10015	exon18			GGCTCCATACCCG	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.2535A>G	3.37:g.33907945A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	177	89	0.502825	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Silent	SNP	ENST00000307296.3	37	CCDS2660.1																																																																																			A|0.707;G|0.293	0.293	strong		0.522	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
HOPX	84525	hgsc.bcm.edu	37	4	57522134	57522134	+	Silent	SNP	C	C	T	rs11555052	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:57522134C>T	ENST00000337881.7	-	2	689	c.33G>A	c.(31-33)gaG>gaA	p.E11E	HOPX_ENST00000554144.1_Silent_p.E29E|HOPX_ENST00000555760.2_Silent_p.E11E|HOPX_ENST00000317745.7_Silent_p.E11E|HOPX_ENST00000553379.2_Silent_p.E11E|HOPX_ENST00000508121.1_Silent_p.E29E|HOPX_ENST00000381260.3_Silent_p.E11E|HOPX_ENST00000556614.2_Silent_p.E11E|HOPX_ENST00000556376.2_Silent_p.E11E|HOPX_ENST00000420433.1_Silent_p.E29E|HOPX_ENST00000503639.3_Silent_p.E11E|HOPX_ENST00000381255.3_Silent_p.E11E	NM_139212.3	NP_631958.1	Q9BPY8	HOP_HUMAN	HOP homeobox	11					heart development (GO:0007507)|histone deacetylation (GO:0016575)|lung alveolus development (GO:0048286)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of heart contraction (GO:0008016)|regulation of protein binding (GO:0043393)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(2)|lung(5)|skin(1)	8	Glioma(25;0.08)|all_neural(26;0.101)					CCACCTGGTCCTCTGTGGGGC	0.687													C|||	223	0.0445288	0.0159	0.0288	5008	,	,		11377	0.0575		0.0099	False		,,,				2504	0.1166				p.E29E		Atlas-SNP	.											HOPX_ENST00000554144,NS,carcinoma,-1,2	HOPX	28	2	0			c.G87A						PASS	.	C	,,,,	69,4335	58.7+/-95.3	0,69,2133	73.0	64.0	67.0		33,87,87,33,33	3.8	1.0	4	dbSNP_120	67	119,8481	59.5+/-121.1	0,119,4181	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HOPX	NM_001145459.1,NM_001145460.1,NM_032495.5,NM_139211.4,NM_139212.3	,,,,	0,188,6314	TT,TC,CC		1.3837,1.5668,1.4457	,,,,	11/74,29/113,29/92,11/74,11/74	57522134	188,12816	2202	4300	6502	SO:0001819	synonymous_variant	84525	exon3			CTGGTCCTCTGTG		CCDS3507.1, CCDS47062.1, CCDS54767.1	4q12	2011-06-20			ENSG00000171476	ENSG00000171476		"""Homeoboxes / PRD class"""	24961	protein-coding gene	gene with protein product	"""homeobox only domain"""	607275				12297045	Standard	NM_032495		Approved	LAGY, HOP, OB1, NECC1, SMAP31	uc003hbz.2	Q9BPY8	OTTHUMG00000128768	ENST00000337881.7:c.33G>A	4.37:g.57522134C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_032495	A8K0Z2|E9PB55|G3V294|Q8N0V6|Q96CI1	Silent	SNP	ENST00000337881.7	37	CCDS3507.1																																																																																			C|0.981;T|0.019	0.019	strong		0.687	HOPX-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250689.4		
CCSER2	54462	hgsc.bcm.edu	37	10	86131059	86131059	+	Missense_Mutation	SNP	A	A	G	rs3814205	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:86131059A>G	ENST00000224756.8	+	2	436	c.251A>G	c.(250-252)aAt>aGt	p.N84S	CCSER2_ENST00000372088.2_Missense_Mutation_p.N84S|CCSER2_ENST00000359979.4_Missense_Mutation_p.N84S	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	84			N -> S (in dbSNP:rs3814205).		microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)											GAGCCTAACAATACTCAAAAT	0.333													.|||	1068	0.213259	0.1392	0.3617	5008	,	,		19838	0.2312		0.1958	False		,,,				2504	0.2076				p.N84S		Atlas-SNP	.											FAM190B,NS,carcinoma,+1,1	CCSER2	7	1	0			c.A251G						PASS	.	A	SER/ASN	688,3718	282.8+/-276.7	62,564,1577	50.0	50.0	50.0		251	-11.6	0.0	10	dbSNP_107	50	1723,6873	310.9+/-310.1	174,1375,2749	yes	missense	FAM190B	NM_018999.2	46	236,1939,4326	GG,GA,AA		20.0442,15.6151,18.5433	benign	84/835	86131059	2411,10591	2203	4298	6501	SO:0001583	missense	54462	exon2			CTAACAATACTCA		CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771			29197	protein-coding gene	gene with protein product			"""KIAA1128"", ""family with sequence similarity 190, member B"""	KIAA1128, FAM190B		10574461	Standard	XM_005269905		Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.251A>G	10.37:g.86131059A>G	ENSP00000224756:p.Asn84Ser	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	111	11	0.0990991	NM_018999	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Missense_Mutation	SNP	ENST00000224756.8	37	CCDS31235.1	502	0.22985347985347984	79	0.16056910569105692	119	0.3287292817679558	145	0.2534965034965035	159	0.20976253298153033	A	0.035	-1.314141	0.01331	0.156151	0.200442	ENSG00000107771	ENST00000359979;ENST00000224756;ENST00000372088	T;T;T	0.44482	0.92;2.26;2.27	5.82	-11.6	0.00059	.	1.497990	0.03607	N	0.234277	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.09377	0.004;0.002;0.002	T	0.24404	-1.0161	9	0.07175	T	0.84	-0.0082	14.4781	0.67562	0.316:0.1002:0.5839:0.0	rs3814205;rs11565098;rs52798571;rs59323515;rs3814205	84;84;84	Q9H7U1-3;Q9H7U1;Q9H7U1-2	.;F190B_HUMAN;.	S	84	ENSP00000353068:N84S;ENSP00000224756:N84S;ENSP00000361160:N84S	ENSP00000224756:N84S	N	+	2	0	FAM190B	86121039	0.000000	0.05858	0.000000	0.03702	0.413000	0.31143	-0.193000	0.09573	-2.350000	0.00617	-0.290000	0.09829	AAT	A|0.798;G|0.202	0.202	strong		0.333	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999	
HECTD4	283450	hgsc.bcm.edu	37	12	112638486	112638486	+	Silent	SNP	G	G	T	rs61739678	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:112638486G>T	ENST00000430131.2	-	54	8402	c.7257C>A	c.(7255-7257)acC>acA	p.T2419T	HECTD4_ENST00000550722.1_Silent_p.T2695T|HECTD4_ENST00000377560.5_Silent_p.T2669T			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2419					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CCAGCCCATTGGTGGCAGTCC	0.512													G|||	39	0.00778754	0.0015	0.0173	5008	,	,		16462	0.0		0.0229	False		,,,				2504	0.002				p.T2707T		Atlas-SNP	.											.	.	.	.	0			c.C8121A						PASS	.	G		6,4010		0,6,2002	131.0	128.0	129.0		8007	1.8	1.0	12	dbSNP_129	129	130,8226		0,130,4048	no	coding-synonymous	C12orf51	NM_001109662.2		0,136,6050	TT,TG,GG		1.5558,0.1494,1.0993		2669/4247	112638486	136,12236	2008	4178	6186	SO:0001819	synonymous_variant	283450	exon55			CCCATTGGTGGCA	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.7257C>A	12.37:g.112638486G>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	265	120	0.45283	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																				G|0.989;T|0.011	0.011	strong		0.512	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
ERRFI1	54206	hgsc.bcm.edu	37	1	8074334	8074334	+	Missense_Mutation	SNP	C	C	T	rs34781518	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:8074334C>T	ENST00000377482.5	-	4	548	c.325G>A	c.(325-327)Gat>Aat	p.D109N	ERRFI1_ENST00000467067.1_3'UTR|ERRFI1_ENST00000469499.1_3'UTR|ERRFI1_ENST00000474874.1_Intron	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	109			D -> N (in dbSNP:rs34781518).		lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		ACAACTTGATCCTCTTCATGT	0.473													C|||	28	0.00559105	0.0023	0.0072	5008	,	,		19585	0.0		0.0129	False		,,,				2504	0.0072				p.D109N		Atlas-SNP	.											.	ERRFI1	42	.	0			c.G325A						PASS	.	C	ASN/ASP	9,4397	14.3+/-33.2	0,9,2194	133.0	135.0	134.0		325	3.6	0.1	1	dbSNP_126	134	125,8475	63.5+/-125.6	2,121,4177	yes	missense	ERRFI1	NM_018948.3	23	2,130,6371	TT,TC,CC		1.4535,0.2043,1.0303	benign	109/463	8074334	134,12872	2203	4300	6503	SO:0001583	missense	54206	exon4			CTTGATCCTCTTC	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.325G>A	1.37:g.8074334C>T	ENSP00000366702:p.Asp109Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_018948	B2RDX9|Q9NTG9|Q9UD05	Missense_Mutation	SNP	ENST00000377482.5	37	CCDS94.1	16	0.007326007326007326	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	11	0.014511873350923483	C	14.65	2.599372	0.46318	0.002043	0.014535	ENSG00000116285	ENST00000377482	T	0.73469	-0.75	5.46	3.6	0.41247	.	0.166510	0.49916	D	0.000130	T	0.64349	0.2590	M	0.72894	2.215	0.80722	D	1	B	0.14012	0.009	B	0.14023	0.01	T	0.64449	-0.6405	10	0.46703	T	0.11	0.9342	10.6084	0.45408	0.0:0.8467:0.0:0.1533	rs34781518	109	Q9UJM3	ERRFI_HUMAN	N	109	ENSP00000366702:D109N	ENSP00000366702:D109N	D	-	1	0	ERRFI1	7996921	1.000000	0.71417	0.096000	0.21009	0.300000	0.27592	4.293000	0.59037	0.671000	0.31185	0.655000	0.94253	GAT	C|0.989;T|0.011	0.011	strong		0.473	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948	
WDFY4	57705	hgsc.bcm.edu	37	10	50022040	50022040	+	Silent	SNP	G	G	A	rs41283275	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50022040G>A	ENST00000325239.5	+	30	5280	c.5253G>A	c.(5251-5253)agG>agA	p.R1751R	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1751						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						TCCTGCAGAGGCACCACCAGG	0.582													G|||	749	0.149561	0.2322	0.1484	5008	,	,		19475	0.1022		0.1213	False		,,,				2504	0.1166				p.R1751R		Atlas-SNP	.											.	WDFY4	205	.	0			c.G5253A						PASS	.	G		318,1066		31,256,405	36.0	40.0	39.0		5253	-4.1	0.0	10	dbSNP_127	39	342,2840		19,304,1268	no	coding-synonymous	WDFY4	NM_020945.1		50,560,1673	AA,AG,GG		10.748,22.9769,14.4547		1751/3185	50022040	660,3906	692	1591	2283	SO:0001819	synonymous_variant	57705	exon31			GCAGAGGCACCAC	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.5253G>A	10.37:g.50022040G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	23	11	0.478261	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	313	0.1433150183150183	105	0.21341463414634146	48	0.13259668508287292	68	0.11888111888111888	92	0.12137203166226913	G	5.144	0.212184	0.09757	0.229769	0.10748	ENSG00000128815	ENST00000312002;ENST00000374161	.	.	.	5.83	-4.12	0.03916	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.30698	P	0.750638	.	.	.	.	.	.	T	0.34104	-0.9842	3	.	.	.	.	2.7652	0.05318	0.5275:0.1495:0.21:0.1131	rs41283275;rs61838867	.	.	.	T	842;298	.	.	A	+	1	0	WDFY4	49692046	0.590000	0.26815	0.009000	0.14445	0.628000	0.37860	-0.339000	0.07832	-0.628000	0.05582	-0.964000	0.02622	GCA	G|0.855;A|0.145	0.145	strong		0.582	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
SPTA1	6708	hgsc.bcm.edu	37	1	158631171	158631171	+	Silent	SNP	A	A	C	rs2518493	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:158631171A>C	ENST00000368147.4	-	18	2673	c.2493T>G	c.(2491-2493)ctT>ctG	p.L831L		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	831					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					GCCTATTCAGAAGCTTTTTGG	0.418													A|||	1220	0.24361	0.1407	0.3026	5008	,	,		17801	0.4087		0.2525	False		,,,				2504	0.1616				p.L831L		Atlas-SNP	.											.	SPTA1	720	.	0			c.T2493G						PASS	.	A		691,3077		57,577,1250	160.0	151.0	153.0		2493	1.2	1.0	1	dbSNP_100	153	2016,6228		274,1468,2380	no	coding-synonymous	SPTA1	NM_003126.2		331,2045,3630	CC,CA,AA		24.4541,18.3386,22.5358		831/2420	158631171	2707,9305	1884	4122	6006	SO:0001819	synonymous_variant	6708	exon18			ATTCAGAAGCTTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2493T>G	1.37:g.158631171A>C		Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	269	129	0.479554	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			A|0.736;C|0.264	0.264	strong		0.418	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
OR2T27	403239	hgsc.bcm.edu	37	1	248813821	248813821	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248813821C>T	ENST00000344889.3	-	1	364	c.365G>A	c.(364-366)cGc>cAc	p.R122H		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGCTACGTAGCGATCATAGGA	0.542																																					p.R122H		Atlas-SNP	.											OR2T27,NS,carcinoma,-1,1	OR2T27	52	1	0			c.G365A						scavenged	.						102.0	44.0	63.0					1																	248813821		2201	4269	6470	SO:0001583	missense	403239	exon1			ACGTAGCGATCAT		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.365G>A	1.37:g.248813821C>T	ENSP00000342008:p.Arg122His	Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	217	4	0.0184332	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	37	CCDS31124.1	.	.	.	.	.	.	.	.	.	.	.	8.762	0.923941	0.18056	.	.	ENSG00000187701	ENST00000344889	T	0.77489	-1.1	3.3	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40385	N	0.001119	T	0.75532	0.3862	M	0.87381	2.88	0.24518	N	0.994177	B	0.32382	0.368	B	0.27608	0.081	T	0.68712	-0.5336	10	0.62326	D	0.03	.	8.2532	0.31739	0.0:0.7898:0.0:0.2101	.	122	Q8NH04	O2T27_HUMAN	H	122	ENSP00000342008:R122H	ENSP00000342008:R122H	R	-	2	0	OR2T27	246880444	0.982000	0.34865	0.207000	0.23584	0.151000	0.21798	3.869000	0.56062	0.236000	0.21180	0.194000	0.17425	CGC	.	.	none		0.542	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
SLC16A13	201232	hgsc.bcm.edu	37	17	6942108	6942108	+	Silent	SNP	C	C	T	rs11078663	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:6942108C>T	ENST00000308027.6	+	3	1289	c.981C>T	c.(979-981)tcC>tcT	p.S327S		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	327						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						TGGCCTTCTCCGTGCTGCCTG	0.607													C|||	1763	0.352037	0.0469	0.4035	5008	,	,		18080	0.5149		0.6044	False		,,,				2504	0.3006				p.S327S		Atlas-SNP	.											.	SLC16A13	28	.	0			c.C981T						PASS	.	C		571,3835	247.5+/-255.7	51,469,1683	72.0	79.0	76.0		981	-0.4	1.0	17	dbSNP_120	76	5171,3429	621.5+/-397.2	1612,1947,741	no	coding-synonymous	SLC16A13	NM_201566.2		1663,2416,2424	TT,TC,CC		39.8721,12.9596,44.1489		327/427	6942108	5742,7264	2203	4300	6503	SO:0001819	synonymous_variant	201232	exon3			CTTCTCCGTGCTG	BN000145	CCDS11085.1	17p13.1	2013-07-18	2013-07-18		ENSG00000174327	ENSG00000174327		"""Solute carriers"""	31037	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 13"""		"""solute carrier family 16 (monocarboxylic acid transporters), member 13"""				Standard	NM_201566		Approved	MCT13	uc002geh.3	Q7RTY0	OTTHUMG00000102089	ENST00000308027.6:c.981C>T	17.37:g.6942108C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_201566	A3KMG3|A5PKU5|Q2VP92	Silent	SNP	ENST00000308027.6	37	CCDS11085.1																																																																																			C|0.571;T|0.429	0.429	strong		0.607	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2		
OR2T4	127074	hgsc.bcm.edu	37	1	248525657	248525657	+	Missense_Mutation	SNP	G	G	A	rs28718027	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248525657G>A	ENST00000366475.1	+	1	775	c.775G>A	c.(775-777)Ggg>Agg	p.G259R		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACCATCCACGGGATGAACTC	0.507													a|||	1476	0.294728	0.2405	0.2709	5008	,	,		21255	0.4296		0.1799	False		,,,				2504	0.364				p.G259R		Atlas-SNP	.											OR2T4,right_upper_lobe,carcinoma,-1,1	OR2T4	126	1	0			c.G775A						scavenged	.	A	ARG/GLY	1056,3350	722.6+/-409.3	140,776,1287	128.0	126.0	127.0		775	0.2	0.8	1	dbSNP_125	127	1386,7214	752.1+/-407.4	111,1164,3025	no	missense	OR2T4	NM_001004696.1	125	251,1940,4312	AA,AG,GG		16.1163,23.9673,18.7759	benign	259/349	248525657	2442,10564	2203	4300	6503	SO:0001583	missense	127074	exon1			ATCCACGGGATGA	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.775G>A	1.37:g.248525657G>A	ENSP00000355431:p.Gly259Arg	Somatic	660	8	0.0121212		WXS	Illumina HiSeq	Phase_I	703	330	0.469417	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	539	0.2467948717948718	113	0.22967479674796748	73	0.20165745856353592	221	0.38636363636363635	132	0.1741424802110818	A	0.003	-2.467723	0.00169	0.239673	0.161163	ENSG00000196944	ENST00000366475	T	0.00019	9.06	3.09	0.223	0.15292	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	N	0.000181	T	0.00012	0.0000	N	0.00101	-2.135	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38436	-0.9661	9	0.02654	T	1	.	5.6019	0.17359	0.5788:0.3259:0.0954:0.0	rs28718027	259	Q8NH00	OR2T4_HUMAN	R	259	ENSP00000355431:G259R	ENSP00000355431:G259R	G	+	1	0	OR2T4	246592280	0.000000	0.05858	0.777000	0.31699	0.114000	0.19823	0.443000	0.21644	-0.098000	0.12285	-0.340000	0.08031	GGG	G|0.795;A|0.205	0.205	strong		0.507	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10575824	10575824	+	Silent	SNP	C	C	A	rs1970817	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:10575824C>A	ENST00000396560.2	+	12	1994	c.1767C>A	c.(1765-1767)ccC>ccA	p.P589P	ATF7IP2_ENST00000324570.5_3'UTR|ATF7IP2_ENST00000356427.2_Silent_p.P589P|ATF7IP2_ENST00000543967.1_Silent_p.P133P|ATF7IP2_ENST00000396559.1_3'UTR	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	589	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						TTTTCAGACCCAATGGCATTG	0.463													C|||	2334	0.466054	0.2958	0.5173	5008	,	,		17249	0.5704		0.5179	False		,,,				2504	0.499				p.P589P		Atlas-SNP	.											ATF7IP2_ENST00000396560,NS,adenoma,0,1	ATF7IP2	40	1	0			c.C1767A						PASS	.	C		1458,2936	470.2+/-355.7	247,964,986	106.0	104.0	104.0		1767	2.7	0.5	16	dbSNP_92	104	4484,4116	590.1+/-392.6	1132,2220,948	no	coding-synonymous	ATF7IP2	NM_024997.2		1379,3184,1934	AA,AC,CC		47.8605,33.1816,45.7288		589/683	10575824	5942,7052	2197	4300	6497	SO:0001819	synonymous_variant	80063	exon12			CAGACCCAATGGC	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.1767C>A	16.37:g.10575824C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Silent	SNP	ENST00000396560.2	37	CCDS10540.1																																																																																			C|0.529;A|0.471	0.471	strong		0.463	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
SPATA31A6	389730	hgsc.bcm.edu	37	9	43626820	43626820	+	Missense_Mutation	SNP	G	G	C	rs138779714	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:43626820G>C	ENST00000332857.6	-	4	1895	c.1867C>G	c.(1867-1869)Cgg>Ggg	p.R623G	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	623					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GATTCGTCCCGAAGCTGCATC	0.542													G|||	1620	0.323482	0.0764	0.5303	5008	,	,		10590	0.2411		0.4334	False		,,,				2504	0.4826				p.R623G		Atlas-SNP	.											FAM75A6,NS,carcinoma,0,2	.	.	2	0			c.C1867G						scavenged	.						2.0	2.0	2.0					9																	43626820		38	330	368	SO:0001583	missense	389730	exon4			CGTCCCGAAGCTG		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A6"""	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.1867C>G	9.37:g.43626820G>C	ENSP00000329825:p.Arg623Gly	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_001145196		Missense_Mutation	SNP	ENST00000332857.6	37	CCDS47973.1	524	0.23992673992673993	19	0.03861788617886179	149	0.4116022099447514	95	0.1660839160839161	261	0.34432717678100266	G	6.183	0.401995	0.11696	.	.	ENSG00000185775	ENST00000332857	T	0.06687	3.27	2.97	2.06	0.26882	.	0.721119	0.12036	N	0.505462	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.45629	-0.9248	9	0.52906	T	0.07	-2.4748	6.1646	0.20384	0.1491:0.0:0.8509:0.0	.	623	Q5VVP1	F75A6_HUMAN	G	623	ENSP00000329825:R623G	ENSP00000329825:R623G	R	-	1	2	FAM75A6	43566816	0.028000	0.19301	0.001000	0.08648	0.001000	0.01503	0.853000	0.27777	0.610000	0.30035	-0.559000	0.04183	CGG	G|0.760;C|0.240	0.240	strong		0.542	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196	
CAMLG	819	hgsc.bcm.edu	37	5	134076812	134076812	+	Missense_Mutation	SNP	G	G	A	rs12657663	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:134076812G>A	ENST00000297156.2	+	2	352	c.232G>A	c.(232-234)Gtt>Att	p.V78I	CAMLG_ENST00000514518.1_Intron	NM_001745.3	NP_001736.1	P49069	CAMLG_HUMAN	calcium modulating ligand	78			V -> I (in dbSNP:rs12657663).		defense response (GO:0006952)|epidermal growth factor receptor signaling pathway (GO:0007173)|receptor recycling (GO:0001881)|signal transduction (GO:0007165)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|cervix(1)|kidney(3)|lung(3)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Cyclosporine(DB00091)	CTCCCTCAGCGTTCCTTCCGT	0.453													G|||	734	0.146565	0.0136	0.1787	5008	,	,		19311	0.2808		0.1332	False		,,,				2504	0.1789				p.V78I		Atlas-SNP	.											.	CAMLG	27	.	0			c.G232A						PASS	.	G	ILE/VAL	112,4294	86.3+/-125.0	2,108,2093	86.0	84.0	85.0		232	-11.7	0.0	5	dbSNP_120	85	885,7715	200.4+/-244.2	47,791,3462	yes	missense	CAMLG	NM_001745.3	29	49,899,5555	AA,AG,GG		10.2907,2.542,7.6657	benign	78/297	134076812	997,12009	2203	4300	6503	SO:0001583	missense	819	exon2			CTCAGCGTTCCTT	AF068179.1	CCDS4178.1	5q23	2008-07-18			ENSG00000164615	ENSG00000164615			1471	protein-coding gene	gene with protein product	"""calcium-modulating cyclophilin ligand"", ""calcium-signal modulating cyclophilin ligand"", ""cyclophilin B-binding protein"""	601118				8824814	Standard	NM_001745		Approved	CAML	uc003kzt.3	P49069	OTTHUMG00000129116	ENST00000297156.2:c.232G>A	5.37:g.134076812G>A	ENSP00000297156:p.Val78Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	113	71	0.628319	NM_001745	A1L3Y3	Missense_Mutation	SNP	ENST00000297156.2	37	CCDS4178.1	330	0.1510989010989011	11	0.022357723577235773	50	0.13812154696132597	168	0.2937062937062937	101	0.13324538258575197	G	5.074	0.199353	0.09652	0.02542	0.102907	ENSG00000164615	ENST00000297156	T	0.30981	1.51	5.86	-11.7	0.00046	.	1.190980	0.05515	N	0.561025	T	0.00012	0.0000	N	0.12182	0.205	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.09662	-1.0664	9	0.05620	T	0.96	-1.7125	3.5917	0.07991	0.5114:0.2134:0.1321:0.1431	rs12657663;rs52822059;rs12657663	78	P49069	CAMLG_HUMAN	I	78	ENSP00000297156:V78I	ENSP00000297156:V78I	V	+	1	0	CAMLG	134104711	0.000000	0.05858	0.000000	0.03702	0.958000	0.62258	-1.489000	0.02306	-3.248000	0.00205	-0.812000	0.03155	GTT	G|0.890;A|0.110	0.110	strong		0.453	CAMLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251161.1	NM_001745	
TMEM131	23505	hgsc.bcm.edu	37	2	98409046	98409046	+	Missense_Mutation	SNP	G	G	A	rs12995673	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:98409046G>A	ENST00000186436.5	-	31	4175	c.3947C>T	c.(3946-3948)cCg>cTg	p.P1316L		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1316	Pro-rich.					integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						TTCAGGCTGCGGCTCCTGGGG	0.682													G|||	737	0.147165	0.0522	0.2046	5008	,	,		15915	0.0119		0.3917	False		,,,				2504	0.1227				p.P1316L		Atlas-SNP	.											.	TMEM131	258	.	0			c.C3947T						PASS	.	G	LEU/PRO	409,3805		21,367,1719	20.0	24.0	23.0		3947	3.9	0.9	2	dbSNP_121	23	3100,5366		567,1966,1700	yes	missense	TMEM131	NM_015348.1	98	588,2333,3419	AA,AG,GG		36.6171,9.7057,27.6735	benign	1316/1884	98409046	3509,9171	2107	4233	6340	SO:0001583	missense	23505	exon31			GGCTGCGGCTCCT	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.3947C>T	2.37:g.98409046G>A	ENSP00000186436:p.Pro1316Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	139	78	0.561151	NM_015348		Missense_Mutation	SNP	ENST00000186436.5	37	CCDS46368.1	416	0.19047619047619047	24	0.04878048780487805	75	0.20718232044198895	6	0.01048951048951049	311	0.4102902374670185	G	11.78	1.741897	0.30865	0.097057	0.366171	ENSG00000075568	ENST00000186436	T	0.19105	2.17	5.91	3.94	0.45596	.	0.779755	0.12489	N	0.464371	T	0.00012	0.0000	N	0.22421	0.69	0.31392	P	0.677675	B	0.11235	0.004	B	0.04013	0.001	T	0.45877	-0.9231	9	0.30078	T	0.28	-4.2451	8.8937	0.35451	0.0823:0.0:0.6775:0.2402	rs12995673	1316	Q92545	TM131_HUMAN	L	1316	ENSP00000186436:P1316L	ENSP00000186436:P1316L	P	-	2	0	TMEM131	97775478	0.977000	0.34250	0.930000	0.37139	0.781000	0.44180	1.805000	0.38883	1.505000	0.48720	0.655000	0.94253	CCG	G|0.781;A|0.219	0.219	strong		0.682	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542	
EMP2	2013	hgsc.bcm.edu	37	16	10631912	10631912	+	Silent	SNP	C	C	T	rs2279868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:10631912C>T	ENST00000359543.3	-	4	398	c.189G>A	c.(187-189)gcG>gcA	p.A63A	EMP2_ENST00000536829.1_Silent_p.A63A	NM_001424.4	NP_001415.1	P54851	EMP2_HUMAN	epithelial membrane protein 2	63					cell proliferation (GO:0008283)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|regulation of glomerular filtration (GO:0003093)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	integrin binding (GO:0005178)			NS(1)|endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6						TGGCCTGGACCGCCTGCAGCG	0.627													c|||	1363	0.272165	0.3555	0.2219	5008	,	,		17949	0.1984		0.165	False		,,,				2504	0.3814				p.A63A	GBM(158;2021 2691 14714 39478)	Atlas-SNP	.											.	EMP2	21	.	0			c.G189A						PASS	.	T		1315,3079	695.2+/-405.9	185,945,1067	144.0	132.0	136.0		189	-7.2	0.4	16	dbSNP_100	136	1639,6961	741.6+/-407.2	170,1299,2831	no	coding-synonymous	EMP2	NM_001424.4		355,2244,3898	TT,TC,CC		19.0581,29.9272,22.7336		63/168	10631912	2954,10040	2197	4300	6497	SO:0001819	synonymous_variant	2013	exon4			CTGGACCGCCTGC	U52100	CCDS10541.1	16p13.2	2008-08-01			ENSG00000213853	ENSG00000213853			3334	protein-coding gene	gene with protein product		602334				8996089, 10331954, 16216233	Standard	NM_001424		Approved	XMP	uc002czx.3	P54851	OTTHUMG00000129752	ENST00000359543.3:c.189G>A	16.37:g.10631912C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_001424	B2R7V6|D3DUF8	Silent	SNP	ENST00000359543.3	37	CCDS10541.1																																																																																			C|0.762;T|0.238	0.238	strong		0.627	EMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251965.1	NM_001424	
TMEM116	89894	hgsc.bcm.edu	37	12	112375990	112375990	+	Missense_Mutation	SNP	A	A	C	rs3752630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:112375990A>C	ENST00000550831.3	-	5	432	c.64T>G	c.(64-66)Tgt>Ggt	p.C22G	TMEM116_ENST00000355445.3_Missense_Mutation_p.C79G|TMEM116_ENST00000552374.2_Missense_Mutation_p.C114G|TMEM116_ENST00000549537.2_5'UTR|TMEM116_ENST00000354825.3_Missense_Mutation_p.C22G|TMEM116_ENST00000437003.2_Missense_Mutation_p.C22G	NM_138341.2	NP_612350.1	Q8NCL8	TM116_HUMAN	transmembrane protein 116	22			C -> G (in dbSNP:rs3752630).			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)	8						GCCATTTGACAAACTCGACAA	0.328													C|||	1126	0.22484	0.3116	0.1383	5008	,	,		17904	0.2728		0.165	False		,,,				2504	0.181				p.C114G		Atlas-SNP	.											.	TMEM116	17	.	0			c.T340G						PASS	.	C	GLY/CYS,GLY/CYS,GLY/CYS	1224,3182		160,904,1139	74.0	77.0	76.0		235,340,64	3.8	0.8	12	dbSNP_107	76	1419,7181		124,1171,3005	yes	missense,missense,missense	TMEM116	NM_001193453.1,NM_001193531.1,NM_138341.2	159,159,159	284,2075,4144	CC,CA,AA		16.5,27.7803,20.3214	benign,benign,benign	79/303,114/338,22/246	112375990	2643,10363	2203	4300	6503	SO:0001583	missense	89894	exon6			TTTGACAAACTCG	AK074648	CCDS9157.1, CCDS55886.1, CCDS55887.1	12q24.13	2012-03-02			ENSG00000198270	ENSG00000198270			25084	protein-coding gene	gene with protein product						12477932	Standard	NM_001193453		Approved	FLJ90167	uc001ttd.2	Q8NCL8	OTTHUMG00000169606	ENST00000550831.3:c.64T>G	12.37:g.112375990A>C	ENSP00000450377:p.Cys22Gly	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	209	97	0.464115	NM_001193531	G3V1W7|G5E985|Q6NSH5|Q8IZ66	Missense_Mutation	SNP	ENST00000550831.3	37	CCDS9157.1	490	0.22435897435897437	155	0.3150406504065041	57	0.1574585635359116	157	0.2744755244755245	121	0.15963060686015831	N	9.079	0.998886	0.19121	0.277803	0.165	ENSG00000198270	ENST00000355445;ENST00000354825;ENST00000550831;ENST00000437003;ENST00000552374;ENST00000550037	T;T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13;1.13	5.65	3.84	0.44239	.	0.212377	0.39985	N	0.001208	T	0.00012	0.0000	N	0.00268	-1.735	0.58432	P	1.999999999946489E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.39800	-0.9596	9	0.02654	T	1	-1.49	5.6836	0.17790	0.1556:0.6817:0.0:0.1627	rs3752630;rs57885084;rs3752630	114;79;114;22	F8VNZ8;G5E985;G3V1W7;Q8NCL8	.;.;.;TM116_HUMAN	G	79;22;22;22;114;114	ENSP00000347620:C79G;ENSP00000346883:C22G;ENSP00000450377:C22G;ENSP00000395861:C22G;ENSP00000447731:C114G;ENSP00000446516:C114G	ENSP00000346883:C22G	C	-	1	0	TMEM116	110860373	0.997000	0.39634	0.823000	0.32752	0.743000	0.42351	0.422000	0.21296	0.363000	0.24346	-1.207000	0.01640	TGT	A|0.783;C|0.217	0.217	strong		0.328	TMEM116-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405026.3	NM_138341	
ZNF577	84765	hgsc.bcm.edu	37	19	52376507	52376507	+	Missense_Mutation	SNP	T	T	C	rs2288868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52376507T>C	ENST00000301399.5	-	7	1101	c.736A>G	c.(736-738)Aaa>Gaa	p.K246E	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.K187E|ZNF577_ENST00000451628.2_Missense_Mutation_p.K187E|ZNF577_ENST00000412216.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	246			K -> E (in dbSNP:rs2288868). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TTTCCGCATTTGCTGCATCTG	0.498													C|||	2537	0.506589	0.6808	0.4553	5008	,	,		20982	0.3026		0.3897	False		,,,				2504	0.638				p.K246E		Atlas-SNP	.											.	ZNF577	63	.	0			c.A736G						PASS	.	C	GLU/LYS,GLU/LYS	2801,1605		911,979,313	71.0	66.0	68.0		559,736	0.9	0.0	19	dbSNP_100	68	3326,5274		637,2052,1611	yes	missense,missense	ZNF577	NM_001135590.1,NM_032679.2	56,56	1548,3031,1924	CC,CT,TT		38.6744,36.4276,47.109	benign,benign	187/427,246/486	52376507	6127,6879	2203	4300	6503	SO:0001583	missense	84765	exon7			CGCATTTGCTGCA	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.736A>G	19.37:g.52376507T>C	ENSP00000301399:p.Lys246Glu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	37	CCDS12842.2	989	0.45283882783882784	335	0.6808943089430894	175	0.48342541436464087	177	0.3094405594405594	302	0.39841688654353563	.	0.004	-2.338582	0.00224	0.635724	0.386744	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.07444	3.19;3.19;3.19;3.19	3.1	0.885	0.19188	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00991	-1.07	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33445	-0.9868	8	0.02654	T	1	.	7.5218	0.27633	0.0:0.6874:0.0:0.3126	rs2288868;rs17856122;rs52818789;rs60409315;rs2288868	246;187	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	E	246;187;187;246	ENSP00000301399:K246E;ENSP00000413476:K187E;ENSP00000389652:K187E;ENSP00000404509:K246E	ENSP00000301399:K246E	K	-	1	0	ZNF577	57068319	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	-0.289000	0.08365	-0.108000	0.12066	-0.119000	0.15052	AAA	T|0.520;C|0.480	0.480	strong		0.498	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
CR2	1380	hgsc.bcm.edu	37	1	207648456	207648456	+	Missense_Mutation	SNP	G	G	T	rs144572703	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207648456G>T	ENST00000367058.3	+	13	2623	c.2434G>T	c.(2434-2436)Gtg>Ttg	p.V812L	CR2_ENST00000367057.3_Missense_Mutation_p.V871L|CR2_ENST00000367059.3_Missense_Mutation_p.V812L|CR2_ENST00000458541.2_Missense_Mutation_p.V785L	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	812	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CAATGACATAGTGTATGTTGA	0.448													G|||	10	0.00199681	0.0008	0.0014	5008	,	,		23285	0.0		0.002	False		,,,				2504	0.0061				p.V871L		Atlas-SNP	.											.	CR2	164	.	0			c.G2611T						PASS	.	G	LEU/VAL,LEU/VAL	18,4388	26.2+/-53.5	0,18,2185	177.0	156.0	163.0		2611,2434	0.4	0.0	1	dbSNP_134	163	49,8551	32.3+/-84.9	0,49,4251	yes	missense,missense	CR2	NM_001006658.2,NM_001877.4	32,32	0,67,6436	TT,TG,GG		0.5698,0.4085,0.5151	benign,benign	871/1093,812/1034	207648456	67,12939	2203	4300	6503	SO:0001583	missense	1380	exon14			GACATAGTGTATG	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.2434G>T	1.37:g.207648456G>T	ENSP00000356025:p.Val812Leu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	173	83	0.479769	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	4	0.0018315018315018315	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	5.431	0.264713	0.10294	0.004085	0.005698	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	4.7	0.427	0.16489	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.49287	0.1548	L	0.60845	1.875	0.09310	N	1	B;B;B	0.21520	0.039;0.012;0.057	B;B;B	0.27796	0.083;0.027;0.05	T	0.52215	-0.8605	9	0.56958	D	0.05	.	2.2553	0.04053	0.1786:0.1505:0.516:0.1549	.	812;812;871	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	L	812;871;812;785	ENSP00000356025:V812L;ENSP00000356024:V871L;ENSP00000356026:V812L;ENSP00000404222:V785L	ENSP00000356024:V871L	V	+	1	0	CR2	205715079	0.006000	0.16342	0.000000	0.03702	0.195000	0.23768	0.157000	0.16402	-0.007000	0.14345	0.655000	0.94253	GTG	G|0.996;T|0.004	0.004	strong		0.448	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
PLG	5340	hgsc.bcm.edu	37	6	161152240	161152240	+	Missense_Mutation	SNP	G	G	A	rs4252125	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:161152240G>A	ENST00000308192.9	+	11	1477	c.1414G>A	c.(1414-1416)Gat>Aat	p.D472N		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	472			D -> N (in dbSNP:rs4252125). {ECO:0000269|PubMed:2318848, ECO:0000269|Ref.4, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CCTGCTTCCAGATGTAGAGAC	0.502													A|||	700	0.139776	0.152	0.1787	5008	,	,		19629	0.0		0.2962	False		,,,				2504	0.0787				p.D472N		Atlas-SNP	.											.	PLG	150	.	0			c.G1414A	GRCh37	CM043559	PLG	M	rs4252125	PASS	.	A	ASN/ASP	804,3602	749.7+/-412.0	66,672,1465	95.0	87.0	90.0		1414	2.1	0.0	6	dbSNP_111	90	2604,5996	688.3+/-404.3	368,1868,2064	yes	missense	PLG	NM_000301.3	23	434,2540,3529	AA,AG,GG		30.2791,18.2478,26.2033	benign	472/811	161152240	3408,9598	2203	4300	6503	SO:0001583	missense	5340	exon11			CTTCCAGATGTAG	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1414G>A	6.37:g.161152240G>A	ENSP00000308938:p.Asp472Asn	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	NM_000301	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	ENST00000308192.9	37	CCDS5279.1	354	0.1620879120879121	69	0.1402439024390244	73	0.20165745856353592	0	0.0	212	0.2796833773087071	A	4.858	0.159413	0.09236	0.182478	0.302791	ENSG00000122194	ENST00000308192	T	0.62105	0.05	4.5	2.08	0.27032	.	0.677337	0.12596	N	0.455126	T	0.18593	0.0446	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.03993	-1.0986	9	0.34782	T	0.22	.	8.3175	0.32108	0.7311:0.0:0.2689:0.0	rs4252125;rs17639358;rs52806400;rs60784473;rs4252125	472	P00747	PLMN_HUMAN	N	472	ENSP00000308938:D472N	ENSP00000308938:D472N	D	+	1	0	PLG	161072230	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.058000	0.14301	-0.295000	0.08960	-2.697000	0.00138	GAT	G|0.784;A|0.216	0.216	strong		0.502	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
ASB15	142685	hgsc.bcm.edu	37	7	123264804	123264804	+	Silent	SNP	C	C	T	rs11769381	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:123264804C>T	ENST00000451558.1	+	10	1154	c.633C>T	c.(631-633)gtC>gtT	p.V211V	ASB15_ENST00000451215.1_Silent_p.V211V|RP11-390E23.3_ENST00000418409.1_RNA|ASB15_ENST00000434204.1_Silent_p.V211V|ASB15_ENST00000540573.1_Silent_p.V211V|RP11-390E23.3_ENST00000422401.1_RNA|ASB15_ENST00000275699.3_Silent_p.V211V|RP11-390E23.3_ENST00000440504.1_RNA|RP11-390E23.3_ENST00000451016.1_RNA|RP11-390E23.3_ENST00000429396.1_RNA			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	211					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						GATTTGGAGTCACACCACTAG	0.483											OREG0018282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2352	0.469649	0.3033	0.4193	5008	,	,		21132	0.5446		0.4324	False		,,,				2504	0.6912				p.V211V		Atlas-SNP	.											.	ASB15	94	.	0			c.C633T						PASS	.	C		1431,2975	466.6+/-354.6	237,957,1009	165.0	120.0	135.0		633	2.5	1.0	7	dbSNP_120	135	3901,4699	546.0+/-384.9	878,2145,1277	no	coding-synonymous	ASB15	NM_080928.3		1115,3102,2286	TT,TC,CC		45.3605,32.4784,40.9965		211/589	123264804	5332,7674	2203	4300	6503	SO:0001819	synonymous_variant	142685	exon6			TGGAGTCACACCA	AF403033	CCDS34742.1	7q31.31	2013-01-10	2011-01-25		ENSG00000146809	ENSG00000146809		"""Ankyrin repeat domain containing"""	19767	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 15"""			12076535	Standard	XM_005250149		Approved	FLJ43370	uc003vkw.1	Q8WXK1	OTTHUMG00000157114	ENST00000451558.1:c.633C>T	7.37:g.123264804C>T		Somatic	213	0	0	1525	WXS	Illumina HiSeq	Phase_I	210	209	0.995238	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Silent	SNP	ENST00000451558.1	37	CCDS34742.1																																																																																			C|0.569;N|0.000	.	strong		0.483	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1		
SPAG16	79582	hgsc.bcm.edu	37	2	214727221	214727221	+	Missense_Mutation	SNP	A	A	C	rs2042791	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:214727221A>C	ENST00000331683.5	+	11	1178	c.1083A>C	c.(1081-1083)caA>caC	p.Q361H	SPAG16_ENST00000374309.3_Missense_Mutation_p.Q267H	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	361			Q -> H (in dbSNP:rs2042791). {ECO:0000269|PubMed:11867345}.		cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.Q361H(1)		endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		TCTCCATGCAACCCCACAAAG	0.463													C|||	1924	0.384185	0.205	0.4006	5008	,	,		21486	0.501		0.3688	False		,,,				2504	0.5102				p.Q361H		Atlas-SNP	.											SPAG16,NS,carcinoma,0,1	SPAG16	134	1	1	Substitution - Missense(1)	stomach(1)	c.A1083C						PASS	.	C	HIS/GLN	1008,3398	729.1+/-410.0	117,774,1312	125.0	112.0	116.0		1083	-1.4	0.9	2	dbSNP_94	116	3250,5350	648.1+/-400.5	623,2004,1673	yes	missense	SPAG16	NM_024532.3	24	740,2778,2985	CC,CA,AA		37.7907,22.8779,32.7387	benign	361/632	214727221	4258,8748	2203	4300	6503	SO:0001583	missense	79582	exon11			CATGCAACCCCAC	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.1083A>C	2.37:g.214727221A>C	ENSP00000332592:p.Gln361His	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	824	0.3772893772893773	109	0.22154471544715448	133	0.3674033149171271	294	0.513986013986014	288	0.37994722955145116	C	0.007	-1.962849	0.00461	0.228779	0.377907	ENSG00000144451	ENST00000331683;ENST00000374309;ENST00000451561	T;T;T	0.57907	0.37;0.37;0.37	5.74	-1.4	0.08968	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.227351	0.31233	N	0.008011	T	0.00012	0.0000	N	0.00170	-1.935	0.58432	P	2.9999999999752447E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.47995	-0.9073	9	0.23302	T	0.38	.	7.967	0.30104	0.1068:0.3532:0.0:0.5401	rs2042791;rs52830989;rs60027582;rs2042791	267;212;361	B4DYB5;Q8N0X2-2;Q8N0X2	.;.;SPG16_HUMAN	H	361;267;47	ENSP00000332592:Q361H;ENSP00000363428:Q267H;ENSP00000416600:Q47H	ENSP00000332592:Q361H	Q	+	3	2	SPAG16	214435466	0.352000	0.24895	0.906000	0.35671	0.004000	0.04260	-0.692000	0.05127	-0.330000	0.08514	-0.756000	0.03474	CAA	A|0.653;C|0.347	0.347	strong		0.463	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
TNIK	23043	hgsc.bcm.edu	37	3	170802910	170802910	+	Missense_Mutation	SNP	C	C	T	rs17857452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:170802910C>T	ENST00000436636.2	-	25	3339	c.2995G>A	c.(2995-2997)Gca>Aca	p.A999T	TNIK_ENST00000341852.6_Missense_Mutation_p.A915T|TNIK_ENST00000488470.1_Missense_Mutation_p.A944T|TNIK_ENST00000369326.5_Missense_Mutation_p.A977T|TNIK_ENST00000475336.1_Missense_Mutation_p.A907T|TNIK_ENST00000284483.8_Missense_Mutation_p.A991T|TNIK_ENST00000470834.1_Missense_Mutation_p.A962T|TNIK_ENST00000357327.5_Missense_Mutation_p.A970T|TNIK_ENST00000538048.1_Missense_Mutation_p.A951T|TNIK_ENST00000460047.1_Missense_Mutation_p.A936T	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	999	Mediates interaction with NEDD4.		A -> T (in dbSNP:rs17857452). {ECO:0000269|PubMed:17344846}.		actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			TGCTTACCTGCGGCTGATGAT	0.483													c|||	202	0.0403355	0.0045	0.0634	5008	,	,		17196	0.0		0.0934	False		,,,				2504	0.0593				p.A999T		Atlas-SNP	.											.	TNIK	313	.	0			c.G2995A						PASS	.	T	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	53,3761		0,53,1854	58.0	59.0	59.0		2971,2908,2884,2830,2806,2743,2719,2995	0.1	0.0	3	dbSNP_123	59	721,7523		28,665,3429	yes	missense,missense,missense,missense,missense,missense,missense,missense	TNIK	NM_001161560.1,NM_001161561.1,NM_001161562.1,NM_001161563.1,NM_001161564.1,NM_001161565.1,NM_001161566.1,NM_015028.2	58,58,58,58,58,58,58,58	28,718,5283	TT,TC,CC		8.7458,1.3896,6.419	benign,benign,benign,benign,benign,benign,benign,benign	991/1353,970/1332,962/1324,944/1306,936/1298,915/1277,907/1269,999/1361	170802910	774,11284	1907	4122	6029	SO:0001583	missense	23043	exon25			TACCTGCGGCTGA	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.2995G>A	3.37:g.170802910C>T	ENSP00000399511:p.Ala999Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	97	0.044413919413919416	4	0.008130081300813009	24	0.06629834254143646	0	0.0	69	0.09102902374670185	c	0.015	-1.562875	0.00903	0.013896	0.087458	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	T;T;T;T;T;T;T;T;T;T	0.72394	-0.64;-0.63;-0.63;-0.64;-0.64;-0.64;-0.65;-0.64;-0.64;-0.65	5.37	0.144	0.14824	.	0.582061	0.19613	N	0.110097	T	0.03053	0.0090	L	0.35723	1.085	0.53688	P	2.8000000000028002E-5	B;B;B;B;B;B;B;B	0.24651	0.001;0.006;0.0;0.001;0.108;0.013;0.0;0.066	B;B;B;B;B;B;B;B	0.22753	0.001;0.01;0.001;0.001;0.041;0.005;0.001;0.018	T	0.19386	-1.0307	9	0.07482	T	0.82	.	8.3344	0.32206	0.0:0.3338:0.0:0.6662	rs17857452;rs17857452	907;962;936;915;991;970;944;999	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	T	999;977;951;915;991;907;970;936;944;962	ENSP00000399511:A999T;ENSP00000358332:A977T;ENSP00000443278:A951T;ENSP00000345352:A915T;ENSP00000284483:A991T;ENSP00000418156:A907T;ENSP00000349880:A970T;ENSP00000418916:A936T;ENSP00000418378:A944T;ENSP00000419990:A962T	ENSP00000284483:A991T	A	-	1	0	TNIK	172285604	0.048000	0.20356	0.047000	0.18901	0.005000	0.04900	0.181000	0.16880	0.104000	0.17725	-0.970000	0.02610	GCA	C|0.934;G|0.013;T|0.052	0.052	strong		0.483	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
IGFN1	91156	hgsc.bcm.edu	37	1	201183402	201183402	+	Silent	SNP	T	T	C	rs1568810	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:201183402T>C	ENST00000335211.4	+	13	8956	c.8826T>C	c.(8824-8826)ccT>ccC	p.P2942P	IGFN1_ENST00000295591.8_Silent_p.P102P|IGFN1_ENST00000451870.2_Silent_p.P485P	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	485						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACCTGGGACCTGGCACCTGGT	0.617													C|||	1581	0.315695	0.1891	0.3256	5008	,	,		16461	0.3403		0.3509	False		,,,				2504	0.4182				p.P2942P		Atlas-SNP	.											.	IGFN1	220	.	0			c.T8826C						PASS	.	C		966,3440	727.6+/-409.9	100,766,1337	69.0	54.0	59.0		8826	-4.1	0.2	1	dbSNP_88	59	2869,5731	666.2+/-402.3	494,1881,1925	no	coding-synonymous	IGFN1	NM_001164586.1		594,2647,3262	CC,CT,TT		33.3605,21.9246,29.4864		2942/3709	201183402	3835,9171	2203	4300	6503	SO:0001819	synonymous_variant	91156	exon13			GGGACCTGGCACC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.8826T>C	1.37:g.201183402T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	710	0.3250915750915751	114	0.23170731707317074	115	0.31767955801104975	214	0.3741258741258741	267	0.35224274406332456	C	12.92	2.083537	0.36758	0.219246	0.333605	ENSG00000163395	ENST00000412892	.	.	.	3.39	-4.06	0.03986	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999858896	.	.	.	.	.	.	T	0.20273	-1.0280	3	.	.	.	.	11.6598	0.51339	0.0:0.1592:0.0:0.8408	rs1568810;rs17424132;rs58560287;rs1568810	.	.	.	R	360	.	.	W	+	1	0	IGFN1	199450025	0.001000	0.12720	0.205000	0.23548	0.697000	0.40408	-0.981000	0.03766	-1.670000	0.01468	-0.642000	0.03964	TGG	T|0.698;C|0.302	0.302	strong		0.617	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
CWH43	80157	hgsc.bcm.edu	37	4	49063872	49063872	+	Missense_Mutation	SNP	C	C	A	rs1051447	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:49063872C>A	ENST00000226432.4	+	16	2248	c.2065C>A	c.(2065-2067)Cat>Aat	p.H689N	CWH43_ENST00000513409.1_Missense_Mutation_p.H662N	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	689			H -> N (in dbSNP:rs1051447). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						AAACAACCATCATTTTCATAT	0.254													.|||	2387	0.476637	0.1967	0.7536	5008	,	,		15036	0.3681		0.7475	False		,,,				2504	0.4918				p.H689N		Atlas-SNP	.											.	CWH43	101	.	0			c.C2065A						PASS	.	C	ASN/HIS	1204,3162		177,850,1156	28.0	27.0	27.0		2065	4.6	1.0	4	dbSNP_86	27	6045,2429		2185,1675,377	yes	missense	CWH43	NM_025087.2	68	2362,2525,1533	AA,AC,CC		28.6641,27.5767,43.5436	probably-damaging	689/700	49063872	7249,5591	2183	4237	6420	SO:0001583	missense	80157	exon16			AACCATCATTTTC		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.2065C>A	4.37:g.49063872C>A	ENSP00000226432:p.His689Asn	Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	218	101	0.463303	NM_025087	B2RPD7	Missense_Mutation	SNP	ENST00000226432.4	37	CCDS3486.1	1195	0.5471611721611722	109	0.22154471544715448	284	0.7845303867403315	227	0.3968531468531469	575	0.758575197889182	C	14.38	2.518520	0.44763	0.275767	0.713359	ENSG00000109182	ENST00000226432;ENST00000513409	T;T	0.42513	1.55;0.97	4.59	4.59	0.56863	.	0.209202	0.34025	N	0.004323	T	0.00012	0.0000	M	0.66939	2.045	0.28466	P	0.9156359000000001	D	0.53619	0.961	P	0.52159	0.691	T	0.29671	-1.0004	8	.	.	.	.	13.2029	0.59778	0.0:1.0:0.0:0.0	rs1051447;rs2768949;rs3087790;rs52789586;rs58129284;rs1051447	689	Q9H720	PG2IP_HUMAN	N	689;662	ENSP00000226432:H689N;ENSP00000422802:H662N	.	H	+	1	0	CWH43	48758629	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.679000	0.54634	2.838000	0.97847	0.561000	0.74099	CAT	C|0.458;A|0.542	0.542	strong		0.254	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319488	21319488	+	Silent	SNP	C	C	T	rs77176173	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:21319488C>T	ENST00000583088.1	+	3	1729	c.834C>T	c.(832-834)agC>agT	p.S278S	KCNJ12_ENST00000331718.5_Silent_p.S278S	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	278					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.S278S(1)		NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	ACGAGGCCAGCCCGCTCTTCG	0.607										Prostate(3;0.18)																											p.S278S		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	lung(1)	c.C834T						scavenged	.						104.0	85.0	91.0					17																	21319488		2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			GGCCAGCCCGCTC	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.834C>T	17.37:g.21319488C>T		Somatic	174	25	0.143678		WXS	Illumina HiSeq	Phase_I	217	37	0.170507	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			C|0.625;T|0.375	0.375	strong		0.607	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
C15orf39	56905	hgsc.bcm.edu	37	15	75499995	75499995	+	Missense_Mutation	SNP	T	T	G	rs28509789	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75499995T>G	ENST00000360639.2	+	2	1926	c.1606T>G	c.(1606-1608)Tca>Gca	p.S536A	C15orf39_ENST00000567617.1_Missense_Mutation_p.S536A|C15orf39_ENST00000394987.4_Missense_Mutation_p.S536A			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	536			S -> A (in dbSNP:rs28509789). {ECO:0000269|PubMed:15498874}.			cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						TGAGCCTGACTCAGCCCCAGC	0.617													T|||	1965	0.392372	0.4697	0.4078	5008	,	,		18530	0.3264		0.2773	False		,,,				2504	0.4632				p.S536A		Atlas-SNP	.											C15orf39,bladder,carcinoma,-1,1	C15orf39	64	1	0			c.T1606G						PASS	.	T	ALA/SER	1955,2437		448,1059,689	25.0	26.0	26.0		1606	-3.5	0.0	15	dbSNP_125	26	2337,6247		327,1683,2282	yes	missense	C15orf39	NM_015492.4	99	775,2742,2971	GG,GT,TT		27.2251,44.5128,33.0764	benign	536/1048	75499995	4292,8684	2196	4292	6488	SO:0001583	missense	56905	exon2			CCTGACTCAGCCC	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 38~Name Same As HGNC:28782"""				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.1606T>G	15.37:g.75499995T>G	ENSP00000353854:p.Ser536Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	37	CCDS10276.1	749	0.34294871794871795	224	0.45528455284552843	141	0.38950276243093923	189	0.3304195804195804	195	0.25725593667546176	T	3.832	-0.035507	0.07497	0.445128	0.272251	ENSG00000167173	ENST00000360639;ENST00000394987	T;T	0.80393	-1.37;-1.37	4.84	-3.54	0.04653	.	1.653880	0.03470	N	0.213444	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.31888	-0.9927	9	0.08381	T	0.77	.	0.2702	0.00230	0.2813:0.1842:0.2851:0.2495	rs28509789	536	Q6ZRI6	CO039_HUMAN	A	536	ENSP00000353854:S536A;ENSP00000378438:S536A	ENSP00000353854:S536A	S	+	1	0	C15orf39	73287048	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.873000	0.04214	-0.640000	0.05495	0.460000	0.39030	TCA	T|0.662;G|0.338	0.338	strong		0.617	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492	
HAP1	9001	hgsc.bcm.edu	37	17	39884065	39884065	+	Missense_Mutation	SNP	C	C	A	rs35612698	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39884065C>A	ENST00000310778.5	-	8	1233	c.1224G>T	c.(1222-1224)ttG>ttT	p.L408F	RN7SL399P_ENST00000471648.2_RNA|HAP1_ENST00000341193.5_Intron|HAP1_ENST00000393939.2_Intron|JUP_ENST00000540235.1_Intron|HAP1_ENST00000347901.4_Missense_Mutation_p.L408F			P54257	HAP1_HUMAN	huntingtin-associated protein 1	408	Glu-rich.|HAP1 N-terminal.		L -> F (in dbSNP:rs35612698).		anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			GCTGCTTCTGCAACTTTTCAG	0.602													C|||	1184	0.236422	0.1793	0.2493	5008	,	,		20399	0.1935		0.4016	False		,,,				2504	0.1789				p.L408F		Atlas-SNP	.											.	HAP1	48	.	0			c.G1224T						PASS	.	C	,,PHE/LEU	939,3467	354.6+/-312.7	107,725,1371	48.0	42.0	44.0		,,1224	1.3	0.9	17	dbSNP_126	44	3381,5219	496.5+/-374.3	634,2113,1553	yes	intron,intron,missense	HAP1	NM_001079870.1,NM_001079871.1,NM_177977.2	,,22	741,2838,2924	AA,AC,CC		39.314,21.3118,33.2154	,,probably-damaging	,,408/620	39884065	4320,8686	2203	4300	6503	SO:0001583	missense	9001	exon8			CTTCTGCAACTTT	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"""neuroan 1"""	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.1224G>T	17.37:g.39884065C>A	ENSP00000309392:p.Leu408Phe	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_177977	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	37		570	0.260989010989011	85	0.17276422764227642	105	0.2900552486187845	84	0.14685314685314685	296	0.39050131926121373	C	14.34	2.505980	0.44558	0.213118	0.39314	ENSG00000173805	ENST00000310778;ENST00000347901	T;T	0.35605	1.3;1.3	3.45	1.28	0.21552	.	.	.	.	.	T	0.00012	0.0000	M	0.79475	2.455	0.31296	P	0.68889	D;D	0.61697	0.99;0.986	P;P	0.62382	0.901;0.894	T	0.36237	-0.9756	8	0.72032	D	0.01	-4.5459	3.4576	0.07521	0.2534:0.6089:0.0:0.1377	rs35612698;rs62065872	408;408	P54257-2;P54257	.;HAP1_HUMAN	F	408	ENSP00000309392:L408F;ENSP00000334002:L408F	ENSP00000309392:L408F	L	-	3	2	HAP1	37137591	0.980000	0.34600	0.928000	0.36995	0.592000	0.36648	0.135000	0.15952	1.809000	0.52856	0.549000	0.68633	TTG	C|0.692;A|0.308	0.308	strong		0.602	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949	
MUC21	394263	hgsc.bcm.edu	37	6	30954434	30954434	+	Missense_Mutation	SNP	A	A	G	rs9262337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954434A>G	ENST00000376296.3	+	2	723	c.482A>G	c.(481-483)gAg>gGg	p.E161G	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	161	28 X 15 AA approximate tandem repeats.|Ser-rich.		E -> G (in dbSNP:rs9262337). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404}.		cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E161G(1)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACCTCCAGTGAGGCCAGCACA	0.617													G|||	458	0.0914537	0.093	0.1383	5008	,	,		25853	0.0685		0.0845	False		,,,				2504	0.0869				p.E161G		Atlas-SNP	.											MUC21,NS,carcinoma,0,3	MUC21	98	3	1	Substitution - Missense(1)	prostate(1)	c.A482G						scavenged	.						144.0	135.0	138.0					6																	30954434		2202	4300	6502	SO:0001583	missense	394263	exon2			CCAGTGAGGCCAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.482A>G	6.37:g.30954434A>G	ENSP00000365473:p.Glu161Gly	Somatic	63	6	0.0952381		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	2.769	-0.256080	0.05829	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.01178	5.22	3.76	-7.51	0.01346	.	.	.	.	.	T	0.00178	0.0005	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43015	-0.9417	8	.	.	.	3.8375	8.9823	0.35972	0.4863:0.3865:0.1271:0.0	rs9262337	161	Q5SSG8	MUC21_HUMAN	G	161	ENSP00000365473:E161G	.	E	+	2	0	MUC21	31062413	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-3.965000	0.00324	-2.460000	0.00537	-0.330000	0.08379	GAG	A|0.875;G|0.125	0.125	strong		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
TSPYL1	7259	hgsc.bcm.edu	37	6	116600774	116600774	+	Missense_Mutation	SNP	C	C	G	rs3749895	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:116600774C>G	ENST00000368608.3	-	1	292	c.220G>C	c.(220-222)Gcc>Ccc	p.A74P	DSE_ENST00000540275.1_Intron|DSE_ENST00000452085.3_5'Flank|RP1-93H18.1_ENST00000449314.1_lincRNA	NM_003309.3	NP_003300.1	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	74			A -> P (in dbSNP:rs3749895). {ECO:0000269|PubMed:11230166}.		nucleosome assembly (GO:0006334)	nucleus (GO:0005634)	enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(3)|urinary_tract(1)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)		CGGCCCGCGGCATCCTGGGGT	0.711													G|||	2325	0.464257	0.348	0.3847	5008	,	,		14160	0.6448		0.3082	False		,,,				2504	0.6524				p.A74P		Atlas-SNP	.											TSPYL1,NS,carcinoma,0,1	TSPYL1	28	1	0			c.G220C						PASS	.	G	PRO/ALA	1399,2907		244,911,998	25.0	29.0	27.0		220	1.4	0.0	6	dbSNP_107	27	2333,6069		345,1643,2213	no	missense	TSPYL1	NM_003309.3	27	589,2554,3211	GG,GC,CC		27.7672,32.4895,29.3673	benign	74/438	116600774	3732,8976	2153	4201	6354	SO:0001583	missense	7259	exon1			CCGCGGCATCCTG	AF042181	CCDS34518.1	6q22.1	2014-09-17	2004-04-05	2004-04-07	ENSG00000189241	ENSG00000189241			12382	protein-coding gene	gene with protein product		604714	"""TSPY-like"""	TSPYL		9730615	Standard	NM_003309		Approved		uc003pwp.4	Q9H0U9	OTTHUMG00000015427	ENST00000368608.3:c.220G>C	6.37:g.116600774C>G	ENSP00000357597:p.Ala74Pro	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	27	10	0.37037	NM_003309	O75885|Q5TFE6	Missense_Mutation	SNP	ENST00000368608.3	37	CCDS34518.1	887	0.40613553113553114	157	0.31910569105691056	131	0.36187845303867405	370	0.6468531468531469	229	0.3021108179419525	G	2.250	-0.371714	0.05034	0.324895	0.277672	ENSG00000189241	ENST00000368608;ENST00000545830	T	0.20738	2.05	4.22	1.42	0.22433	.	.	.	.	.	T	0.00998	0.0033	N	0.00554	-1.385	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46952	-0.9154	8	0.02654	T	1	-0.2268	4.9149	0.13840	0.1909:0.3357:0.4734:0.0	rs3749895;rs56769178;rs3749895	74	Q9H0U9	TSYL1_HUMAN	P	74	ENSP00000357597:A74P	ENSP00000357597:A74P	A	-	1	0	TSPYL1	116707467	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.032000	0.13732	0.050000	0.15949	-0.120000	0.15030	GCC	C|0.657;G|0.343	0.343	strong		0.711	TSPYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041929.1		
EHBP1L1	254102	hgsc.bcm.edu	37	11	65349063	65349063	+	Missense_Mutation	SNP	G	G	A	rs3741380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65349063G>A	ENST00000309295.4	+	9	1185	c.920G>A	c.(919-921)cGg>cAg	p.R307Q		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	307			R -> Q (in dbSNP:rs3741380). {ECO:0000269|PubMed:14702039}.			membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CCTCGGCTCCGGAAAGGCTCT	0.677													g|||	2303	0.459864	0.4501	0.3876	5008	,	,		13992	0.4504		0.4881	False		,,,				2504	0.5051				p.R307Q		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G920A						PASS	.	A	GLN/ARG	1663,2001		405,853,574	7.0	9.0	8.0		920	-3.8	0.8	11	dbSNP_107	8	3726,4332		931,1864,1234	yes	missense	EHBP1L1	NM_001099409.1	43	1336,2717,1808	AA,AG,GG		46.2398,45.3876,45.9734	possibly-damaging	307/1524	65349063	5389,6333	1832	4029	5861	SO:0001583	missense	254102	exon9			GGCTCCGGAAAGG	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.920G>A	11.37:g.65349063G>A	ENSP00000312671:p.Arg307Gln	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	177	87	0.491525	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	37	CCDS44649.1	996	0.45604395604395603	229	0.4654471544715447	141	0.38950276243093923	259	0.4527972027972028	367	0.4841688654353562	g	11.09	1.537701	0.27475	0.453876	0.462398	ENSG00000173442	ENST00000309295;ENST00000533237	T;T	0.81415	-0.15;-1.49	4.66	-3.82	0.04281	.	1.262800	0.05598	N	0.575772	T	0.00012	0.0000	N	0.24115	0.695	0.31386	P	0.678381	B	0.24533	0.105	B	0.12156	0.007	T	0.23084	-1.0198	9	0.51188	T	0.08	.	5.5934	0.17313	0.5222:0.0:0.3399:0.1378	rs3741380;rs61037855	307	Q8N3D4	EH1L1_HUMAN	Q	307	ENSP00000312671:R307Q;ENSP00000431996:R307Q	ENSP00000312671:R307Q	R	+	2	0	EHBP1L1	65105639	0.961000	0.32948	0.783000	0.31826	0.039000	0.13416	0.141000	0.16076	-0.401000	0.07644	-2.163000	0.00326	CGG	G|0.543;A|0.457	0.457	strong		0.677	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
UMODL1	89766	hgsc.bcm.edu	37	21	43557559	43557559	+	Silent	SNP	T	T	A	rs3819141	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:43557559T>A	ENST00000408910.2	+	22	3786	c.3786T>A	c.(3784-3786)ccT>ccA	p.P1262P	UMODL1_ENST00000408989.2_Silent_p.P1390P|UMODL1_ENST00000400424.2_Silent_p.P1190P|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400427.1_Silent_p.P1318P	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1262					adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						GTGAGCCTCCTCATGCAGAAG	0.612													A|||	1680	0.335463	0.1785	0.3703	5008	,	,		16653	0.4097		0.3718	False		,,,				2504	0.409				p.P1390P	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.T4170A						PASS	.	A	,,,	875,3285		99,677,1304	145.0	155.0	152.0		3786,3954,3570,4170	-4.8	0.0	21	dbSNP_107	152	3189,5253		592,2005,1624	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	691,2682,2928	AA,AT,TT		37.7754,21.0337,32.2488	,,,	1262/1319,1318/1375,1190/1247,1390/1447	43557559	4064,8538	2080	4221	6301	SO:0001819	synonymous_variant	89766	exon21			GCCTCCTCATGCA		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.3786T>A	21.37:g.43557559T>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	168	87	0.517857	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			T|0.652;A|0.348	0.348	strong		0.612	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
CAPN14	440854	hgsc.bcm.edu	37	2	31411184	31411184	+	Splice_Site	SNP	C	C	A	rs1465972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:31411184C>A	ENST00000403897.3	-	14	1671	c.1530G>T	c.(1528-1530)aaG>aaT	p.K510N	CAPN14_ENST00000444918.2_Splice_Site_p.K510N	NM_001145122.1	NP_001138594.1	A8MX76	CAN14_HUMAN	calpain 14	510	Linker.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)	p.K510N(1)		NS(1)|endometrium(2)|prostate(1)|skin(1)|stomach(2)	7						GACTACTCACCTTTGAGAAGA	0.463													C|||	1654	0.330272	0.5908	0.389	5008	,	,		21271	0.1558		0.1899	False		,,,				2504	0.2607				p.K510N		Atlas-SNP	.											CAPN14,NS,carcinoma,0,1	CAPN14	36	1	1	Substitution - Missense(1)	stomach(1)	c.G1530T						PASS	.	C	ASN/LYS	716,668		183,350,159	88.0	97.0	95.0		1530	3.3	0.2	2	dbSNP_88	95	530,2652		50,430,1111	yes	missense-near-splice	CAPN14	NM_001145122.1	94	233,780,1270	AA,AC,CC		16.6562,48.2659,27.2887	possibly-damaging	510/685	31411184	1246,3320	692	1591	2283	SO:0001630	splice_region_variant	440854	exon14			ACTCACCTTTGAG	AC015980	CCDS46254.1	2p23.1-p21	2013-01-10			ENSG00000214711	ENSG00000214711		"""EF-hand domain containing"""	16664	protein-coding gene	gene with protein product		610229				11675017	Standard	NM_001145122		Approved		uc010yms.2	A8MX76	OTTHUMG00000152039	ENST00000403897.3:c.1530+1G>T	2.37:g.31411184C>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_001145122	B3KRU9	Missense_Mutation	SNP	ENST00000403897.3	37	CCDS46254.1	648	0.2967032967032967	273	0.5548780487804879	131	0.36187845303867405	94	0.16433566433566432	150	0.19788918205804748	C	10.43	1.349387	0.24426	0.517341	0.166562	ENSG00000214711	ENST00000444918;ENST00000403897	D;D	0.87334	-2.24;-2.24	4.16	3.26	0.37387	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.37244	P	0.09373900000000002	B;P	0.44429	0.18;0.835	B;B	0.42798	0.112;0.398	T	0.44190	-0.9344	7	.	.	.	.	11.0223	0.47726	0.0:0.8103:0.1897:0.0	rs1465972;rs52798796;rs57316229;rs1465972	510;334	A8MX76;A8MX76-2	CAN14_HUMAN;.	N	510	ENSP00000398670:K510N;ENSP00000385247:K510N	.	K	-	3	2	CAPN14	31264688	1.000000	0.71417	0.214000	0.23707	0.017000	0.09413	3.590000	0.53979	0.702000	0.31825	0.655000	0.94253	AAG	C|0.704;A|0.296	0.296	strong		0.463	CAPN14-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325010.1	NM_001145122	Missense_Mutation
TSKS	60385	hgsc.bcm.edu	37	19	50249950	50249950	+	Missense_Mutation	SNP	C	C	T	rs76911687|rs550916960|rs59626794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50249950C>T	ENST00000246801.3	-	6	851	c.769G>A	c.(769-771)Gag>Aag	p.E257K	TSKS_ENST00000358830.3_Missense_Mutation_p.E57K	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	257					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		tcctccggctcctgcttctcc	0.721																																					p.E257K		Atlas-SNP	.											TSKS,NS,carcinoma,0,1	TSKS	97	1	0			c.G769A						scavenged	.						13.0	13.0	13.0					19																	50249950		2192	4287	6479	SO:0001583	missense	60385	exon6			CCGGCTCCTGCTT	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 161"""	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.769G>A	19.37:g.50249950C>T	ENSP00000246801:p.Glu257Lys	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	31	3	0.0967742	NM_021733	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	.	.	.	.	.	.	.	.	.	.	C	10.29	1.310367	0.23821	.	.	ENSG00000126467	ENST00000246801;ENST00000358830	T;T	0.44482	1.53;0.92	.	.	.	.	0.000000	0.47852	D	0.000216	T	0.14570	0.0352	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.23297	-1.0192	9	0.06494	T	0.89	-7.4983	3.9611	0.09410	0.0:0.4649:0.5351:0.0	.	257	Q9UJT2	TSKS_HUMAN	K	257;57	ENSP00000246801:E257K;ENSP00000351691:E57K	ENSP00000246801:E257K	E	-	1	0	TSKS	54941762	0.937000	0.31787	0.589000	0.28718	0.411000	0.31082	0.639000	0.24690	-0.000000	0.14550	0.000000	0.15137	GAG	.	.	weak		0.721	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	
TTLL12	23170	hgsc.bcm.edu	37	22	43568512	43568512	+	Missense_Mutation	SNP	C	C	T	rs34074034	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:43568512C>T	ENST00000216129.6	-	10	1453	c.1390G>A	c.(1390-1392)Gtg>Atg	p.V464M	TTLL12_ENST00000484118.1_5'Flank|TTLL12_ENST00000494035.1_5'Flank	NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	464	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.		V -> M (in dbSNP:rs34074034).		cellular protein modification process (GO:0006464)					central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				ACCTTTCCCACGTCTTCTCGA	0.572													C|||	1014	0.202476	0.0598	0.1643	5008	,	,		16640	0.2351		0.2465	False		,,,				2504	0.3436				p.V464M		Atlas-SNP	.											.	TTLL12	50	.	0			c.G1390A						PASS	.	C	MET/VAL	385,4021	193.6+/-218.7	16,353,1834	209.0	150.0	170.0		1390	5.3	1.0	22	dbSNP_126	170	2043,6557	356.5+/-330.3	249,1545,2506	yes	missense	TTLL12	NM_015140.3	21	265,1898,4340	TT,TC,CC		23.7558,8.7381,18.6683	probably-damaging	464/645	43568512	2428,10578	2203	4300	6503	SO:0001583	missense	23170	exon10			TTCCCACGTCTTC	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"""Tubulin tyrosine ligase-like family"""	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.1390G>A	22.37:g.43568512C>T	ENSP00000216129:p.Val464Met	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	227	89	0.39207	NM_015140	Q20WK5|Q9UGU3	Missense_Mutation	SNP	ENST00000216129.6	37	CCDS14047.1	436	0.19963369963369965	39	0.07926829268292683	67	0.1850828729281768	132	0.23076923076923078	198	0.2612137203166227	C	22.3	4.264974	0.80358	0.087381	0.237558	ENSG00000100304	ENST00000216129;ENST00000423379	T	0.08193	3.12	5.31	5.31	0.75309	.	0.059184	0.64402	D	0.000002	T	0.00012	0.0000	M	0.82323	2.585	0.09310	P	0.9999999844361	D;D	0.76494	0.999;0.999	D;D	0.75484	0.971;0.986	T	0.00883	-1.1528	9	0.87932	D	0	-21.7077	18.9677	0.92702	0.0:1.0:0.0:0.0	rs34074034;rs60598679	464;464	B1AH89;Q14166	.;TTL12_HUMAN	M	464	ENSP00000216129:V464M	ENSP00000216129:V464M	V	-	1	0	TTLL12	41898456	1.000000	0.71417	0.985000	0.45067	0.367000	0.29736	5.546000	0.67243	2.466000	0.83321	0.561000	0.74099	GTG	C|0.803;G|0.000;T|0.197	0.197	strong		0.572	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
PLEC	5339	hgsc.bcm.edu	37	8	144996408	144996408	+	Silent	SNP	T	T	G	rs11778026	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144996408T>G	ENST00000322810.4	-	32	8161	c.7992A>C	c.(7990-7992)gcA>gcC	p.A2664A	PLEC_ENST00000398774.2_Silent_p.A2495A|PLEC_ENST00000345136.3_Silent_p.A2527A|PLEC_ENST00000354589.3_Silent_p.A2527A|PLEC_ENST00000354958.2_Silent_p.A2505A|PLEC_ENST00000436759.2_Silent_p.A2554A|PLEC_ENST00000527096.1_Silent_p.A2550A|PLEC_ENST00000356346.3_Silent_p.A2513A|PLEC_ENST00000357649.2_Silent_p.A2531A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2664	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCAGCTGCTGTGCCTTGGCCA	0.657													T|||	1157	0.23103	0.028	0.2968	5008	,	,		16590	0.1429		0.4284	False		,,,				2504	0.3466				p.A2664A		Atlas-SNP	.											.	PLEC	1144	.	0			c.A7992C						PASS	.	T	,,,,,,,	382,4000		24,334,1833	12.0	13.0	13.0		7662,7539,7515,7992,7485,7581,7593,7581	-5.4	0.9	8	dbSNP_120	13	3440,5132		731,1978,1577	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	755,2312,3410	GG,GT,TT		40.1307,8.7175,29.5044	,,,,,,,	2554/4575,2513/4534,2505/4526,2664/4685,2495/4516,2527/4548,2531/4552,2527/4548	144996408	3822,9132	2191	4286	6477	SO:0001819	synonymous_variant	5339	exon32			CTGCTGTGCCTTG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.7992A>C	8.37:g.144996408T>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1	538	0.24633699633699635	15	0.03048780487804878	108	0.2983425414364641	94	0.16433566433566432	321	0.4234828496042216	t	9.155	1.017286	0.19355	0.087175	0.401307	ENSG00000178209	ENST00000527303	.	.	.	4.38	-5.41	0.02648	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999983	.	.	.	.	.	.	T	0.47509	-0.9112	3	.	.	.	.	1.205	0.01893	0.195:0.1813:0.155:0.4687	rs11778026	.	.	.	P	97	.	.	H	-	2	0	PLEC	145068396	0.000000	0.05858	0.870000	0.34147	0.990000	0.78478	-2.721000	0.00811	-0.830000	0.04262	0.364000	0.22116	CAC	A|0.000;G|0.248;T|0.752	0.248	strong		0.657	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
DEFB118	117285	hgsc.bcm.edu	37	20	29956480	29956480	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:29956480T>C	ENST00000253381.2	+	1	60	c.27T>C	c.(25-27)ccT>ccC	p.P9P		NM_054112.2	NP_473453.1	Q96PH6	DB118_HUMAN	defensin, beta 118	9					cell-matrix adhesion (GO:0007160)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(1)|lung(7)|ovary(3)|pancreas(1)|prostate(1)	14	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			TGGCTCTTCCTATGCTTGTGC	0.473																																					p.P9P		Atlas-SNP	.											DEFB118,NS,malignant_melanoma,+2,1	DEFB118	30	1	0			c.T27C						scavenged	.						144.0	117.0	126.0					20																	29956480		2203	4300	6503	SO:0001819	synonymous_variant	117285	exon1			TCTTCCTATGCTT	AF347073	CCDS13177.1	20q11.21	2008-02-01	2002-05-09	2002-05-10	ENSG00000131068	ENSG00000131068		"""Defensins, beta"""	16196	protein-coding gene	gene with protein product		607650	"""chromosome 20 open reading frame 63"""	C20orf63		11564719, 15033915	Standard	NM_054112		Approved	dJ1018D12.3, DEFB-18, ESC42	uc002wvr.3	Q96PH6	OTTHUMG00000032161	ENST00000253381.2:c.27T>C	20.37:g.29956480T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	137	3	0.0218978	NM_054112	Q17RC4|Q8N691|Q9NUH0	Silent	SNP	ENST00000253381.2	37	CCDS13177.1																																																																																			.	.	none		0.473	DEFB118-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078501.2	NM_054112	
APOBR	55911	hgsc.bcm.edu	37	16	28508048	28508048	+	Silent	SNP	A	A	G	rs180744	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28508048A>G	ENST00000431282.1	+	3	1669	c.1659A>G	c.(1657-1659)caA>caG	p.Q553Q	CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000328423.5_Silent_p.Q553Q|APOBR_ENST00000564831.1_Silent_p.Q562Q|CLN3_ENST00000569430.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	553	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						CCAAAGGCCAAGGACCTGAGC	0.637													G|||	1581	0.315695	0.4599	0.4352	5008	,	,		18185	0.1042		0.3489	False		,,,				2504	0.2198				p.Q562Q		Atlas-SNP	.											.	APOBR	89	.	0			c.A1686G						PASS	.	G		1784,2268		427,930,669	10.0	11.0	11.0		1659	0.1	0.0	16	dbSNP_79	11	3212,5150		670,1872,1639	no	coding-synonymous	APOBR	NM_018690.3		1097,2802,2308	GG,GA,AA		38.4119,44.0276,40.2449		553/1089	28508048	4996,7418	2026	4181	6207	SO:0001819	synonymous_variant	55911	exon2			AGGCCAAGGACCT	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1659A>G	16.37:g.28508048A>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	155	65	0.419355	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	37																																																																																				A|0.690;G|0.310	0.310	strong		0.637	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
ABCC12	94160	hgsc.bcm.edu	37	16	48164777	48164777	+	Silent	SNP	T	T	C	rs12149826	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:48164777T>C	ENST00000311303.3	-	8	1503	c.1158A>G	c.(1156-1158)gtA>gtG	p.V386V	ABCC12_ENST00000448542.1_Silent_p.V386V|ABCC12_ENST00000416054.1_Silent_p.V386V	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	386	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				AAAACTTCATTACATTAAACA	0.408													T|||	605	0.120807	0.0091	0.1931	5008	,	,		23511	0.0		0.2714	False		,,,				2504	0.1902				p.V386V		Atlas-SNP	.											.	ABCC12	190	.	0			c.A1158G						PASS	.	T		270,4132	150.3+/-184.3	10,250,1941	84.0	75.0	78.0		1158	-1.4	1.0	16	dbSNP_120	78	2634,5966	425.1+/-354.9	409,1816,2075	no	coding-synonymous	ABCC12	NM_033226.2		419,2066,4016	CC,CT,TT		30.6279,6.1336,22.335		386/1360	48164777	2904,10098	2201	4300	6501	SO:0001819	synonymous_variant	94160	exon8			CTTCATTACATTA	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.1158A>G	16.37:g.48164777T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	37	CCDS10730.1																																																																																			T|0.827;C|0.173	0.173	strong		0.408	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
TLE1	7088	hgsc.bcm.edu	37	9	84302311	84302311	+	Silent	SNP	A	A	G	rs147523347	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:84302311A>G	ENST00000376499.3	-	2	1127	c.63T>C	c.(61-63)acT>acC	p.T21T	RP11-154D17.1_ENST00000437181.1_lincRNA|TLE1_ENST00000376472.1_5'UTR|TLE1_ENST00000376463.1_5'Flank	NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	21	Gln-rich.				multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						ACTCCGGGATAGTGAACTTGA	0.642											OREG0019267	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	30	0.00599042	0.0	0.0029	5008	,	,		13712	0.0		0.007	False		,,,				2504	0.0215				p.T21T	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	Atlas-SNP	.											TLE1,NS,haematopoietic_neoplasm,0,1	TLE1	81	1	0			c.T63C						scavenged	.	A		6,4396	9.9+/-24.2	0,6,2195	25.0	26.0	25.0		63	-3.5	1.0	9	dbSNP_134	25	55,8545	30.1+/-81.4	2,51,4247	no	coding-synonymous	TLE1	NM_005077.3		2,57,6442	GG,GA,AA		0.6395,0.1363,0.4692		21/771	84302311	61,12941	2201	4300	6501	SO:0001819	synonymous_variant	7088	exon2			CGGGATAGTGAAC		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"""WD repeat domain containing"""	11837	protein-coding gene	gene with protein product	"""enhancer of split groucho 1"""	600189	"""transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"""			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.63T>C	9.37:g.84302311A>G		Somatic	97	1	0.0103093	1228	WXS	Illumina HiSeq	Phase_I	132	61	0.462121	NM_005077	A8K495|Q5T3G4|Q969V9	Silent	SNP	ENST00000376499.3	37	CCDS6661.1																																																																																			A|0.995;G|0.005	0.005	strong		0.642	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077	
LRRC3B	116135	hgsc.bcm.edu	37	3	26751493	26751493	+	Silent	SNP	A	A	T	rs35497952	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:26751493A>T	ENST00000396641.2	+	2	922	c.330A>T	c.(328-330)ggA>ggT	p.G110G	AC114877.3_ENST00000446601.1_lincRNA|LRRC3B_ENST00000417744.1_Silent_p.G110G|LRRC3B_ENST00000456208.2_Silent_p.G110G	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	110						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						CCTTCAAAGGAGTAGCTGAAA	0.438													A|||	739	0.147564	0.1036	0.1556	5008	,	,		21624	0.2421		0.0805	False		,,,				2504	0.1728				p.G110G		Atlas-SNP	.											.	LRRC3B	51	.	0			c.A330T						PASS	.	A		439,3967	212.5+/-232.4	20,399,1784	65.0	62.0	63.0		330	-4.1	0.9	3	dbSNP_126	63	764,7836	181.8+/-230.4	43,678,3579	no	coding-synonymous	LRRC3B	NM_052953.2		63,1077,5363	TT,TA,AA		8.8837,9.9637,9.2496		110/260	26751493	1203,11803	2203	4300	6503	SO:0001819	synonymous_variant	116135	exon2			CAAAGGAGTAGCT	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.330A>T	3.37:g.26751493A>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	153	78	0.509804	NM_052953	Q5M8T0	Silent	SNP	ENST00000396641.2	37	CCDS2644.1																																																																																			A|0.898;T|0.102	0.102	strong		0.438	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953	
POLQ	10721	hgsc.bcm.edu	37	3	121151812	121151812	+	Missense_Mutation	SNP	G	G	C	rs3218634	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121151812G>C	ENST00000264233.5	-	29	7740	c.7612C>G	c.(7612-7614)Ctc>Gtc	p.L2538V		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2538					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TCATCATGGAGTTGAAGGATG	0.413								DNA polymerases (catalytic subunits)					G|||	423	0.0844649	0.2209	0.0576	5008	,	,		20550	0.0		0.0845	False		,,,				2504	0.0061				p.L2538V	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C7612G						PASS	.	G	VAL/LEU	878,3528	340.7+/-306.4	86,706,1411	133.0	126.0	129.0		7612	5.0	1.0	3	dbSNP_106	129	547,8053	150.9+/-205.7	15,517,3768	yes	missense	POLQ	NM_199420.3	32	101,1223,5179	CC,CG,GG		6.3605,19.9274,10.9565	possibly-damaging	2538/2591	121151812	1425,11581	2203	4300	6503	SO:0001583	missense	10721	exon29			CATGGAGTTGAAG	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.7612C>G	3.37:g.121151812G>C	ENSP00000264233:p.Leu2538Val	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	146	68	0.465753	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	205	0.09386446886446886	122	0.24796747967479674	20	0.055248618784530384	0	0.0	63	0.08311345646437995	G	21.9	4.219102	0.79464	0.199274	0.063605	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	D	0.93604	-3.25	6.07	5.03	0.67393	DNA-directed DNA polymerase, family A, palm domain (2);	0.000000	0.85682	D	0.000000	T	0.00178	0.0005	N	0.04148	-0.265	0.32829	P	0.49616099999999996	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.99	T	0.32025	-0.9922	9	0.45353	T	0.12	.	15.195	0.73081	0.0802:0.0:0.9198:0.0	rs3218634;rs52830932;rs3218634	2538;1710	O75417;O75417-2	DPOLQ_HUMAN;.	V	2161;2538;2674	ENSP00000264233:L2538V	ENSP00000264233:L2538V	L	-	1	0	POLQ	122634502	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	6.731000	0.74785	2.885000	0.99019	0.655000	0.94253	CTC	A|0.000;C|0.102;G|0.898	0.102	strong		0.413	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
SCN7A	6332	hgsc.bcm.edu	37	2	167269629	167269629	+	Silent	SNP	T	T	G	rs33922582	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:167269629T>G	ENST00000409855.1	-	21	3543	c.3417A>C	c.(3415-3417)gcA>gcC	p.A1139A		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1139					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	CATTAAATGTTGCCTGTAAAA	0.294													T|||	303	0.0605032	0.059	0.0288	5008	,	,		17441	0.0129		0.0775	False		,,,				2504	0.1166				p.A1139A		Atlas-SNP	.											.	SCN7A	410	.	0			c.A3417C						PASS	.	T		183,3423		3,177,1623	39.0	36.0	36.0		3417	1.5	1.0	2	dbSNP_126	36	743,7377		30,683,3347	no	coding-synonymous	SCN7A	NM_002976.3		33,860,4970	GG,GT,TT		9.1502,5.0749,7.897		1139/1683	167269629	926,10800	1803	4060	5863	SO:0001819	synonymous_variant	6332	exon21			AAATGTTGCCTGT	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.3417A>C	2.37:g.167269629T>G		Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	424	192	0.45283	NM_002976		Silent	SNP	ENST00000409855.1	37	CCDS46442.1																																																																																			T|0.945;G|0.055	0.055	strong		0.294	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
GAL3ST2	64090	hgsc.bcm.edu	37	2	242742875	242742875	+	Missense_Mutation	SNP	C	C	T	rs62620233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242742875C>T	ENST00000192314.6	+	4	622	c.491C>T	c.(490-492)gCc>gTc	p.A164V	AC114730.5_ENST00000437438.1_RNA	NM_022134.2	NP_071417.2	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2	164					biosynthetic process (GO:0009058)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|skin(1)	14		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TTCCGGGGCGCCCCGAGCCTG	0.607													C|||	790	0.157748	0.1581	0.2032	5008	,	,		14441	0.1964		0.1044	False		,,,				2504	0.1401				p.A164V		Atlas-SNP	.											GAL3ST2,colon,carcinoma,+1,1	GAL3ST2	34	1	0			c.C491T						PASS	.	C	VAL/ALA	700,3702	252.4+/-258.8	62,576,1563	31.0	32.0	31.0		491	-1.0	0.0	2	dbSNP_129	31	827,7769	176.5+/-226.3	40,747,3511	yes	missense	GAL3ST2	NM_022134.2	64	102,1323,5074	TT,TC,CC		9.6208,15.9019,11.748	benign	164/399	242742875	1527,11471	2201	4298	6499	SO:0001583	missense	64090	exon4			GGGGCGCCCCGAG	AB040610	CCDS33427.1	2q37.2	2014-05-19			ENSG00000154252	ENSG00000154252		"""Sulfotransferases, membrane-bound"""	24869	protein-coding gene	gene with protein product		608237				11029462	Standard	NM_022134		Approved	GP3ST	uc002wcj.1	Q9H3Q3	OTTHUMG00000151473	ENST00000192314.6:c.491C>T	2.37:g.242742875C>T	ENSP00000192314:p.Ala164Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	66	0.528	NM_022134	Q17RK0|Q57Z52	Missense_Mutation	SNP	ENST00000192314.6	37	CCDS33427.1	307	0.14056776556776557	74	0.15040650406504066	59	0.16298342541436464	103	0.18006993006993008	71	0.09366754617414248	C	11.77	1.737866	0.30774	0.159019	0.096208	ENSG00000154252	ENST00000192314	T	0.12147	2.71	4.39	-0.998	0.10212	.	1.225170	0.05750	N	0.602914	T	0.00012	0.0000	N	0.11870	0.19	0.80722	P	0.0	B	0.14805	0.011	B	0.16289	0.015	T	0.45205	-0.9277	9	0.23891	T	0.37	-7.5969	8.759	0.34663	0.0:0.5757:0.0:0.4243	rs62620233	164	Q9H3Q3	G3ST2_HUMAN	V	164	ENSP00000192314:A164V	ENSP00000192314:A164V	A	+	2	0	GAL3ST2	242391548	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.125000	0.10579	-0.193000	0.10415	-0.391000	0.06502	GCC	C|0.884;T|0.116	0.116	strong		0.607	GAL3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322792.1	NM_022134	
MAP9	79884	hgsc.bcm.edu	37	4	156276289	156276289	+	Silent	SNP	C	C	T	rs2341894	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:156276289C>T	ENST00000311277.4	-	10	1577	c.1314G>A	c.(1312-1314)gtG>gtA	p.V438V	AC097467.2_ENST00000596165.1_RNA|MAP9_ENST00000515654.1_Silent_p.V414V|AC097467.2_ENST00000609486.1_RNA|AC097467.2_ENST00000600928.1_RNA|AC097467.2_ENST00000608463.1_RNA|AC097467.2_ENST00000594666.1_RNA|AC097467.2_ENST00000610249.1_RNA|AC097467.2_ENST00000609254.1_RNA|AC097467.2_ENST00000598252.1_RNA|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000594492.1_RNA|AC097467.2_ENST00000598890.1_RNA|AC097467.2_ENST00000608092.1_RNA|AC097467.2_ENST00000596754.1_RNA|AC097467.2_ENST00000597831.1_RNA|AC097467.2_ENST00000601977.1_RNA|AC097467.2_ENST00000417474.1_RNA|AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000597939.1_RNA|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000593387.2_RNA|AC097467.2_ENST00000608544.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	438					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		CATGTAAATACACATTTTTCT	0.244													T|||	3705	0.739816	0.9546	0.5533	5008	,	,		13242	0.9266		0.5616	False		,,,				2504	0.5726				p.V438V		Atlas-SNP	.											.	MAP9	79	.	0			c.G1314A						PASS	.	T		3899,469		1752,395,37	56.0	60.0	59.0		1314	-10.3	0.1	4	dbSNP_100	59	4588,3938		1248,2092,923	no	coding-synonymous	MAP9	NM_001039580.1		3000,2487,960	TT,TC,CC		46.1881,10.7372,34.1787		438/648	156276289	8487,4407	2184	4263	6447	SO:0001819	synonymous_variant	79884	exon10			TAAATACACATTT	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"""aster-associated protein"""	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.1314G>A	4.37:g.156276289C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	200	89	0.445	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Silent	SNP	ENST00000311277.4	37	CCDS35493.1																																																																																			C|0.324;T|0.676	0.676	strong		0.244	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	
ALPK2	115701	hgsc.bcm.edu	37	18	56202768	56202768	+	Missense_Mutation	SNP	C	C	A	rs3809983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56202768C>A	ENST00000361673.3	-	5	4864	c.4651G>T	c.(4651-4653)Gct>Tct	p.A1551S	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1551			A -> S (in dbSNP:rs3809983). {ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCAAGAGAAGCGTGAGTCATT	0.468													C|||	1660	0.33147	0.2118	0.3862	5008	,	,		20824	0.2381		0.5348	False		,,,				2504	0.3415				p.A1551S		Atlas-SNP	.											.	ALPK2	487	.	0			c.G4651T						PASS	.	C	SER/ALA	1145,3261	406.6+/-333.9	140,865,1198	114.0	109.0	110.0		4651	-0.1	0.0	18	dbSNP_107	110	4191,4409	568.8+/-389.1	1025,2141,1134	yes	missense	ALPK2	NM_052947.3	99	1165,3006,2332	AA,AC,CC		48.7326,25.9873,41.0272	benign	1551/2171	56202768	5336,7670	2203	4300	6503	SO:0001583	missense	115701	exon5			GAGAAGCGTGAGT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4651G>T	18.37:g.56202768C>A	ENSP00000354991:p.Ala1551Ser	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	212	108	0.509434	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	834	0.38186813186813184	113	0.22967479674796748	165	0.4558011049723757	139	0.243006993006993	417	0.5501319261213721	C	13.02	2.113587	0.37339	0.259873	0.487326	ENSG00000198796	ENST00000361673	T	0.46819	0.86	5.71	-0.0922	0.13658	.	2.375810	0.01312	N	0.010641	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	P;B	0.37955	0.612;0.145	B;B	0.30401	0.115;0.055	T	0.46176	-0.9210	9	0.15952	T	0.53	-3.1963	0.4633	0.00520	0.1895:0.3075:0.1652:0.3378	rs3809983;rs17728545;rs52816616;rs60880749;rs3809983	1546;1551	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	S	1551	ENSP00000354991:A1551S	ENSP00000354991:A1551S	A	-	1	0	ALPK2	54353748	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.557000	0.05985	0.043000	0.15746	-0.137000	0.14449	GCT	C|0.609;N|0.000	.	strong		0.468	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
AIM1L	55057	hgsc.bcm.edu	37	1	26673108	26673108	+	5'Flank	SNP	C	C	T	rs11247925	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26673108C>T	ENST00000308182.5	-	0	0				AIM1L_ENST00000527815.1_5'Flank|RN7SL490P_ENST00000579210.1_RNA			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like								carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		ACTTACCACTCGGGCCTTGGC	0.637													C|||	898	0.179313	0.1505	0.1931	5008	,	,		16282	0.1438		0.1918	False		,,,				2504	0.2321				p.R14Q		Atlas-SNP	.											.	AIM1L	98	.	0			c.G41A						PASS	.	C	GLN/ARG	533,3273		35,463,1405	9.0	10.0	10.0		41	2.4	1.0	1	dbSNP_120	10	1557,6629		156,1245,2692	yes	missense	AIM1L	NM_001039775.3	43	191,1708,4097	TT,TC,CC		19.0203,14.0042,17.4283	benign	14/1662	26673108	2090,9902	1903	4093	5996	SO:0001631	upstream_gene_variant	55057	exon2			ACCACTCGGGCCT			1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490		1.37:g.26673108C>T	Exception_encountered	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_001039775	B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	37		375	0.1717032967032967	71	0.1443089430894309	73	0.20165745856353592	99	0.17307692307692307	132	0.1741424802110818	C	13.55	2.270057	0.40194	0.140042	0.190203	ENSG00000176092	ENST00000538018;ENST00000449629;ENST00000475866	T	0.18657	2.2	5.29	2.41	0.29592	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.46028	P	0.0011759999999999549	P	0.40230	0.708	B	0.28232	0.087	T	0.25572	-1.0128	8	0.02654	T	1	.	5.4485	0.16550	0.0:0.6438:0.1767:0.1795	rs11247925;rs61517510;rs11247925	14	E7ET48	.	Q	14	ENSP00000428746:R14Q	ENSP00000363323:R14Q	R	-	2	0	AIM1L	26545695	0.405000	0.25336	0.996000	0.52242	0.572000	0.35998	0.092000	0.15066	0.242000	0.21303	0.655000	0.94253	CGA	C|0.834;T|0.166	0.166	strong		0.637	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2	
POLD1	5424	hgsc.bcm.edu	37	19	50905074	50905074	+	Missense_Mutation	SNP	G	G	A	rs1726801	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50905074G>A	ENST00000440232.2	+	4	409	c.356G>A	c.(355-357)cGc>cAc	p.R119H	POLD1_ENST00000595904.1_Missense_Mutation_p.R119H|POLD1_ENST00000599857.1_Missense_Mutation_p.R119H	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	119			R -> H (in dbSNP:rs1726801). {ECO:0000269|PubMed:1542570, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CCACCATCCCGCGGCTCCGTG	0.677								DNA polymerases (catalytic subunits)					G|||	943	0.188299	0.3222	0.1023	5008	,	,		12711	0.1607		0.0706	False		,,,				2504	0.2178				p.R119H		Atlas-SNP	.											.	POLD1	174	.	0			c.G356A						PASS	.	G	HIS/ARG	1305,3099	415.7+/-337.3	206,893,1103	36.0	40.0	39.0		356	-8.1	0.0	19	dbSNP_89	39	619,7977	153.7+/-208.1	22,575,3701	yes	missense	POLD1	NM_002691.2	29	228,1468,4804	AA,AG,GG		7.201,29.6322,14.8	benign	119/1108	50905074	1924,11076	2202	4298	6500	SO:0001583	missense	5424	exon4			CATCCCGCGGCTC		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.356G>A	19.37:g.50905074G>A	ENSP00000406046:p.Arg119His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	37	CCDS12795.1	354	0.1620879120879121	149	0.30284552845528456	40	0.11049723756906077	110	0.19230769230769232	55	0.07255936675461741	G	9.914	1.210250	0.22289	0.296322	0.07201	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.22743	1.94	4.04	-8.08	0.01094	Ribonuclease H-like (1);	1.185790	0.05994	N	0.646591	T	0.00012	0.0000	L	0.39898	1.24	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.41233	-0.9520	9	0.13108	T	0.6	-1.863	6.6121	0.22757	0.4495:0.3218:0.2288:0.0	rs1726801;rs2230241;rs17850396;rs58282823;rs1726801	119;119	E7EVW0;P28340	.;DPOD1_HUMAN	H	119;120	ENSP00000406046:R119H	ENSP00000366129:R120H	R	+	2	0	POLD1	55596886	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.860000	0.04272	-1.701000	0.01413	-1.576000	0.00868	CGC	G|0.838;A|0.162	0.162	strong		0.677	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
TECTA	7007	hgsc.bcm.edu	37	11	121038810	121038810	+	Silent	SNP	C	C	T	rs2155369	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:121038810C>T	ENST00000392793.1	+	19	5905	c.5634C>T	c.(5632-5634)agC>agT	p.S1878S	TECTA_ENST00000264037.2_Silent_p.S1878S			O75443	TECTA_HUMAN	tectorin alpha	1878	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		S -> R (in dbSNP:rs2155369).		cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GGATCGAAAGCGCCAACAACA	0.453													C|||	928	0.185304	0.0136	0.1571	5008	,	,		22018	0.3105		0.1402	False		,,,				2504	0.3548				p.S1878S		Atlas-SNP	.											TECTA,colon,carcinoma,+2,1	TECTA	329	1	0			c.C5634T						PASS	.	C		144,4262	100.7+/-139.4	7,130,2066	233.0	199.0	211.0		5634	-0.1	1.0	11	dbSNP_96	211	1141,7457	235.0+/-267.7	84,973,3242	no	coding-synonymous	TECTA	NM_005422.2		91,1103,5308	TT,TC,CC		13.2705,3.2683,9.8816		1878/2156	121038810	1285,11719	2203	4299	6502	SO:0001819	synonymous_variant	7007	exon18			CGAAAGCGCCAAC	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.5634C>T	11.37:g.121038810C>T		Somatic	273	1	0.003663		WXS	Illumina HiSeq	Phase_I	301	127	0.421927	NM_005422		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																			T|0.129;G|0.000;C|0.871	0.129	strong		0.453	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
PXMP2	5827	hgsc.bcm.edu	37	12	133272590	133272590	+	Silent	SNP	G	G	T	rs145883118	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133272590G>T	ENST00000317479.3	+	3	422	c.357G>T	c.(355-357)ccG>ccT	p.P119P	RP13-672B3.2_ENST00000537262.1_Intron|PXMP2_ENST00000428960.2_Silent_p.P26P|PXMP2_ENST00000545677.1_Intron|PXMP2_ENST00000543589.1_Intron|PXMP2_ENST00000539093.1_Intron	NM_018663.1	NP_061133.1	Q9NR77	PXMP2_HUMAN	peroxisomal membrane protein 2, 22kDa	119						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|protein complex (GO:0043234)				large_intestine(1)|liver(2)|lung(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.86e-08)|Epithelial(86;2.47e-07)|all cancers(50;6.85e-06)		TCTTTGCACCGGCCTTCCTCA	0.537													G|||	3	0.000599042	0.0	0.0	5008	,	,		16181	0.0		0.002	False		,,,				2504	0.001				p.P119P		Atlas-SNP	.											.	PXMP2	15	.	0			c.G357T						PASS	.						89.0	85.0	87.0					12																	133272590		2203	4300	6503	SO:0001819	synonymous_variant	5827	exon3			TGCACCGGCCTTC		CCDS9279.1	12q24	2010-08-18	2002-08-29		ENSG00000176894	ENSG00000176894			9716	protein-coding gene	gene with protein product			"""peroxisomal membrane protein 2 (22kD)"""			11590176	Standard	NM_018663		Approved	PMP22	uc001ukt.3	Q9NR77	OTTHUMG00000168019	ENST00000317479.3:c.357G>T	12.37:g.133272590G>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_018663		Silent	SNP	ENST00000317479.3	37	CCDS9279.1																																																																																			G|0.999;T|0.001	0.001	strong		0.537	PXMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397553.1	NM_018663	
EXOC3L4	91828	hgsc.bcm.edu	37	14	103576444	103576444	+	Missense_Mutation	SNP	C	C	G	rs744153|rs34558946	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:103576444C>G	ENST00000380069.3	+	11	2129	c.2053C>G	c.(2053-2055)Caa>Gaa	p.Q685E		NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	685			Q -> E (in dbSNP:rs744153). {ECO:0000269|PubMed:15489334}.		exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						GCAGCACACTCAAGACCTGCT	0.682													C|||	2824	0.563898	0.9198	0.5447	5008	,	,		13814	0.631		0.2435	False		,,,				2504	0.3569				p.Q685E		Atlas-SNP	.											.	EXOC3L4	35	.	0			c.C2053G						PASS	.	C	GLU/GLN	328,4040		30,268,1886	9.0	10.0	10.0		2053	3.2	0.0	14	dbSNP_86	10	87,8461		3,81,4190	no	missense	EXOC3L4	NM_001077594.1	29	33,349,6076	GG,GC,CC		1.0178,7.5092,3.2131	benign	685/723	103576444	415,12501	2184	4274	6458	SO:0001583	missense	91828	exon11			CACACTCAAGACC	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 73"""	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.2053C>G	14.37:g.103576444C>G	ENSP00000369409:p.Gln685Glu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	NM_001077594	Q14CR2	Missense_Mutation	SNP	ENST00000380069.3	37	CCDS32163.1	1136	0.5201465201465202	435	0.8841463414634146	190	0.5248618784530387	343	0.5996503496503497	168	0.22163588390501318	C	6.740	0.505332	0.12822	0.075092	0.010178	ENSG00000205436	ENST00000380069	T	0.05649	3.41	4.05	3.15	0.36227	.	0.607756	0.15328	N	0.268190	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B	0.30179	0.271	B	0.35655	0.207	T	0.04840	-1.0923	9	0.28530	T	0.3	-11.326	9.8244	0.40903	0.0:0.7902:0.2098:0.0	rs744153;rs4362322;rs57475976;rs4362322	685	Q17RC7	EX3L4_HUMAN	E	685	ENSP00000369409:Q685E	ENSP00000369409:Q685E	Q	+	1	0	EXOC3L4	102646197	0.003000	0.15002	0.002000	0.10522	0.016000	0.09150	1.275000	0.33144	1.053000	0.40415	-0.518000	0.04402	CAA	C|0.580;G|0.420	0.420	strong		0.682	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093	
MICAL2	9645	hgsc.bcm.edu	37	11	12183846	12183846	+	Silent	SNP	C	C	T	rs28625145|rs111445151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:12183846C>T	ENST00000256194.4	+	3	432	c.144C>T	c.(142-144)aaC>aaT	p.N48N	MICAL2_ENST00000527546.1_Silent_p.N48N|MICAL2_ENST00000342902.5_Silent_p.N48N|MICAL2_ENST00000537344.1_Silent_p.N48N|MICAL2_ENST00000379612.3_Silent_p.N48N	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	48	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		ACCACAGAAACTTTTATTCCA	0.493													C|||	885	0.176717	0.1702	0.2118	5008	,	,		19646	0.1528		0.2107	False		,,,				2504	0.1503				p.N48N		Atlas-SNP	.											.	MICAL2	114	.	0			c.C144T						PASS	.	C		756,3646	307.7+/-290.2	71,614,1516	66.0	65.0	66.0		144	2.7	1.0	11	dbSNP_125	66	1693,6895	311.4+/-310.3	160,1373,2761	no	coding-synonymous	MICAL2	NM_014632.2		231,1987,4277	TT,TC,CC		19.7136,17.174,18.853		48/1125	12183846	2449,10541	2201	4294	6495	SO:0001819	synonymous_variant	9645	exon3			CAGAAACTTTTAT	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.144C>T	11.37:g.12183846C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																			C|0.813;T|0.187	0.187	strong		0.493	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
RADIL	55698	hgsc.bcm.edu	37	7	4876057	4876057	+	Missense_Mutation	SNP	C	C	T	rs3763384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:4876057C>T	ENST00000399583.3	-	3	902	c.715G>A	c.(715-717)Gac>Aac	p.D239N	RADIL_ENST00000536091.1_Missense_Mutation_p.D239N|RADIL_ENST00000538469.1_5'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	239			D -> N (in dbSNP:rs3763384). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:19690332}.		multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CGCATGGCGTCGGGGCCGGGC	0.706													C|||	1257	0.250998	0.0401	0.2853	5008	,	,		13192	0.3264		0.2873	False		,,,				2504	0.3967				p.D239N		Atlas-SNP	.											.	RADIL	110	.	0			c.G715A						PASS	.	C	ASN/ASP	305,3815		19,267,1774	13.0	20.0	18.0		715	4.8	0.1	7	dbSNP_107	18	2586,5772		412,1762,2005	yes	missense	RADIL	NM_018059.4	23	431,2029,3779	TT,TC,CC		30.9404,7.4029,23.1688	benign	239/1076	4876057	2891,9587	2060	4179	6239	SO:0001583	missense	55698	exon3			TGGCGTCGGGGCC	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.715G>A	7.37:g.4876057C>T	ENSP00000382492:p.Asp239Asn	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	50	31	0.62	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	524	0.23992673992673993	22	0.044715447154471545	94	0.2596685082872928	195	0.3409090909090909	213	0.28100263852242746	C	10.16	1.274597	0.23307	0.074029	0.309404	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000536091	T;T	0.24538	3.27;1.85	4.85	4.85	0.62838	.	0.607882	0.16897	N	0.195056	T	0.00012	0.0000	L	0.35414	1.06	0.80722	P	0.0	P	0.39782	0.688	B	0.25291	0.059	T	0.45411	-0.9263	9	0.14252	T	0.57	-25.6462	10.7848	0.46398	0.0:0.9079:0.0:0.0921	rs3763384;rs58768759;rs3763384	239	Q96JH8	RADIL_HUMAN	N	239;213;239	ENSP00000382492:D239N;ENSP00000442533:D239N	ENSP00000320946:D213N	D	-	1	0	RADIL	4842583	0.018000	0.18449	0.055000	0.19348	0.004000	0.04260	0.996000	0.29719	2.243000	0.73865	0.462000	0.41574	GAC	C|0.745;T|0.255	0.255	strong		0.706	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
MYOM1	8736	hgsc.bcm.edu	37	18	3129297	3129297	+	Silent	SNP	C	C	T	rs72860212	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:3129297C>T	ENST00000356443.4	-	18	3060	c.2727G>A	c.(2725-2727)ccG>ccA	p.P909P	MYOM1_ENST00000400569.3_Silent_p.P909P|MYOM1_ENST00000582016.1_5'UTR|MYOM1_ENST00000261606.7_Intron	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	909					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TCTGTGGTGGCGGGGTAAGCT	0.493											OREG0024838	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3	0.000599042	0.0	0.0014	5008	,	,		19213	0.0		0.002	False		,,,				2504	0.0				p.P909P		Atlas-SNP	.											MYOM1,bladder,carcinoma,-1,1	MYOM1	192	1	0			c.G2727A						PASS	.	C	,	0,3830		0,0,1915	112.0	118.0	116.0		2727,	-5.7	0.0	18	dbSNP_130	116	28,8192		0,28,4082	no	coding-synonymous,intron	MYOM1	NM_003803.3,NM_019856.1	,	0,28,5997	TT,TC,CC		0.3406,0.0,0.2324	,	909/1686,	3129297	28,12022	1915	4110	6025	SO:0001819	synonymous_variant	8736	exon18			TGGTGGCGGGGTA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2727G>A	18.37:g.3129297C>T		Somatic	253	0	0	608	WXS	Illumina HiSeq	Phase_I	231	121	0.52381	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			C|0.998;T|0.002	0.002	strong		0.493	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291597	1291597	+	Missense_Mutation	SNP	C	C	G	rs144979264	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1291597C>G	ENST00000338844.3	+	4	429	c.396C>G	c.(394-396)aaC>aaG	p.N132K	TPSAB1_ENST00000461509.2_Missense_Mutation_p.N139K	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	132	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		N -> K (in dbSNP:rs1800991). {ECO:0000269|PubMed:10898108, ECO:0000269|PubMed:15489334}.		defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				AGCCGGTGAACGTCTCCAGCC	0.662													C|||	2475	0.494209	0.4092	0.3991	5008	,	,		15322	0.754		0.4563	False		,,,				2504	0.4479				p.N132K		Atlas-SNP	.											.	TPSAB1	24	.	0			c.C396G						PASS	.	C	LYS/ASN	1538,2778		228,1082,848	17.0	13.0	14.0		396	-0.1	0.0	16	dbSNP_134	14	3309,5111		655,1999,1556	no	missense	TPSAB1	NM_003294.3	94	883,3081,2404	GG,GC,CC		39.2993,35.6348,38.0575	benign	132/276	1291597	4847,7889	2158	4210	6368	SO:0001583	missense	7177	exon4			GGTGAACGTCTCC	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.396C>G	16.37:g.1291597C>G	ENSP00000343577:p.Asn132Lys	Somatic	481	0	0		WXS	Illumina HiSeq	Phase_I	575	204	0.354783	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	37	CCDS10431.1	976	0.4468864468864469	144	0.2926829268292683	123	0.3397790055248619	410	0.7167832167832168	299	0.3944591029023747	C	0.004	-2.348130	0.00219	0.356348	0.392993	ENSG00000172236	ENST00000338844;ENST00000461509	D;D	0.87966	-2.32;-2.32	3.51	-0.139	0.13460	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.707462	0.12783	N	0.439558	T	0.00012	0.0000	N	0.01649	-0.78	0.80722	P	0.0	B;B	0.20780	0.017;0.048	B;B	0.25506	0.024;0.061	T	0.42732	-0.9434	9	0.17832	T	0.49	.	1.0697	0.01619	0.177:0.4138:0.1741:0.235	.	123;132	Q15661-2;Q15661	.;TRYB1_HUMAN	K	132;139	ENSP00000343577:N132K;ENSP00000418247:N139K	ENSP00000343577:N132K	N	+	3	2	TPSAB1	1231598	0.000000	0.05858	0.010000	0.14722	0.028000	0.11728	-2.880000	0.00715	0.121000	0.18284	-0.492000	0.04666	AAC	C|0.500;G|0.500	0.500	strong		0.662	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
ZSWIM6	57688	hgsc.bcm.edu	37	5	60628414	60628414	+	Silent	SNP	G	G	T	rs111274143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:60628414G>T	ENST00000252744.5	+	1	315	c.315G>T	c.(313-315)gtG>gtT	p.V105V		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	105	Gly-rich.				neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						CGGAGCCGGTGCAGCGCCGCA	0.711													G|||	509	0.101637	0.0794	0.1037	5008	,	,		2581	0.0724		0.1431	False		,,,				2504	0.1176				p.V105V		Atlas-SNP	.											.	ZSWIM6	51	.	0			c.G315T						PASS	.						6.0	11.0	9.0					5																	60628414		679	1570	2249	SO:0001819	synonymous_variant	57688	exon1			GCCGGTGCAGCGC	BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449		"""Zinc fingers, SWIM-type"""	29316	protein-coding gene	gene with protein product		615951				10997877, 16427614	Standard	NM_020928		Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.315G>T	5.37:g.60628414G>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	134	133	0.992537	NM_020928		Silent	SNP	ENST00000252744.5	37	CCDS47215.1																																																																																			G|0.894;T|0.106	0.106	strong		0.711	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368710.1	NM_020928	
TNC	3371	hgsc.bcm.edu	37	9	117804544	117804544	+	Silent	SNP	T	T	C	rs1061495	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:117804544T>C	ENST00000350763.4	-	18	5613	c.5202A>G	c.(5200-5202)acA>acG	p.T1734T	TNC_ENST00000537320.1_Silent_p.T1097T|TNC_ENST00000340094.3_Silent_p.T1370T|TNC_ENST00000535648.1_Silent_p.T1279T|TNC_ENST00000341037.4_Silent_p.T1552T|TNC_ENST00000345230.3_Silent_p.T1097T|TNC_ENST00000346706.3_Silent_p.T1188T|TNC_ENST00000423613.2_Silent_p.T1461T|TNC_ENST00000542877.1_Silent_p.T1371T	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1734	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CCACTTGGGCTGTGGGTGCCC	0.517													t|||	1417	0.282947	0.528	0.2795	5008	,	,		17872	0.1478		0.2575	False		,,,				2504	0.1196				p.T1734T		Atlas-SNP	.											.	TNC	282	.	0			c.A5202G						PASS	.	T		2170,2236	585.4+/-386.2	545,1080,578	102.0	98.0	100.0		5202	-7.2	0.6	9	dbSNP_86	100	2197,6403	374.9+/-337.6	295,1607,2398	no	coding-synonymous	TNC	NM_002160.3		840,2687,2976	CC,CT,TT		25.5465,49.251,33.5768		1734/2202	117804544	4367,8639	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon18			TTGGGCTGTGGGT		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5202A>G	9.37:g.117804544T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1	623	0.28525641025641024	262	0.532520325203252	95	0.26243093922651933	68	0.11888111888111888	198	0.2612137203166227	t	0.947	-0.707721	0.03230	0.49251	0.255465	ENSG00000041982	ENST00000544972	.	.	.	6.08	-7.17	0.01511	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.46289	-0.9202	3	.	.	.	.	2.9726	0.05927	0.1397:0.4085:0.1194:0.3325	rs1061495;rs3202589;rs17435046;rs1061495	.	.	.	G	297	.	.	S	-	1	0	TNC	116844365	0.056000	0.20664	0.591000	0.28745	0.159000	0.22180	0.132000	0.15891	-1.139000	0.02881	-2.708000	0.00134	AGC	T|0.688;C|0.312	0.312	strong		0.517	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
MED27	9442	hgsc.bcm.edu	37	9	134735980	134735980	+	Missense_Mutation	SNP	G	G	A	rs557626461	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:134735980G>A	ENST00000292035.5	-	8	944	c.881C>T	c.(880-882)cCg>cTg	p.P294L	MED27_ENST00000357028.2_Missense_Mutation_p.P258L	NM_004269.3	NP_004260.2	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	294					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.P294L(4)|p.P294fs*>18(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	18		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		CCTCCATGTCGGGGGAAGGCC	0.597													G|||	40	0.00798722	0.003	0.0072	5008	,	,		18345	0.0		0.0169	False		,,,				2504	0.0143				p.P294L	Colon(41;784 923 6932 42329 52483)	Atlas-SNP	.											MED27,NS,carcinoma,0,4	MED27	37	4	5	Substitution - Missense(4)|Deletion - Frameshift(1)	endometrium(2)|kidney(2)|large_intestine(1)	c.C881T						scavenged	.						30.0	29.0	29.0					9																	134735980		2203	4300	6503	SO:0001583	missense	9442	exon8			CATGTCGGGGGAA	AF104252	CCDS6945.1, CCDS59153.1, CCDS69689.1	9q34.13	2008-02-05	2007-07-30	2007-07-30	ENSG00000160563	ENSG00000160563			2377	protein-coding gene	gene with protein product		605044	"""cofactor required for Sp1 transcriptional activation, subunit 8, 34kDa"""	CRSP8		9989412	Standard	NM_004269		Approved	TRAP37, CRSP34	uc004cbe.2	Q6P2C8	OTTHUMG00000020833	ENST00000292035.5:c.881C>T	9.37:g.134735980G>A	ENSP00000292035:p.Pro294Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	131	5	0.0381679	NM_004269	O95401|Q4F964|Q5VTA4|Q5VTA5|Q9BU57|Q9NYR4|V9GYV9	Missense_Mutation	SNP	ENST00000292035.5	37	CCDS6945.1	.	.	.	.	.	.	.	.	.	.	G	31	5.095595	0.94197	.	.	ENSG00000160563	ENST00000292035;ENST00000357028;ENST00000372184	.	.	.	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.84014	0.5379	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	D	0.86894	0.2050	9	0.87932	D	0	-0.1478	16.105	0.81213	0.0:0.0:1.0:0.0	.	258;294	Q6P2C8-2;Q6P2C8	.;MED27_HUMAN	L	294;220;258	.	ENSP00000292035:P294L	P	-	2	0	MED27	133725801	1.000000	0.71417	0.949000	0.38748	0.987000	0.75469	7.762000	0.85270	2.472000	0.83506	0.655000	0.94253	CCG	.	.	none		0.597	MED27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054770.2	NM_004269	
NOL10	79954	hgsc.bcm.edu	37	2	10740989	10740989	+	Missense_Mutation	SNP	T	T	C	rs115424813	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:10740989T>C	ENST00000381685.5	-	17	1517	c.1412A>G	c.(1411-1413)aAg>aGg	p.K471R	NOL10_ENST00000538384.1_Missense_Mutation_p.K445R|NOL10_ENST00000542668.1_Missense_Mutation_p.K421R|AC092687.5_ENST00000414538.1_RNA|NOL10_ENST00000345985.3_Missense_Mutation_p.K421R	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	471						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		CTTAACTTTCTTTTTCCATGT	0.303													T|||	5	0.000998403	0.0008	0.0	5008	,	,		14204	0.0		0.004	False		,,,				2504	0.0				p.K471R		Atlas-SNP	.											.	NOL10	22	.	0			c.A1412G						PASS	.	T	ARG/LYS	1,4363		0,1,2181	147.0	126.0	133.0		1412	5.4	1.0	2	dbSNP_133	133	34,8502		0,34,4234	yes	missense	NOL10	NM_024894.2	26	0,35,6415	CC,CT,TT		0.3983,0.0229,0.2713	benign	471/689	10740989	35,12865	2182	4268	6450	SO:0001583	missense	79954	exon17			ACTTTCTTTTTCC	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1412A>G	2.37:g.10740989T>C	ENSP00000371101:p.Lys471Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Missense_Mutation	SNP	ENST00000381685.5	37	CCDS1673.2	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	12.48	1.950627	0.34377	2.29E-4	0.003983	ENSG00000115761	ENST00000345985;ENST00000381685;ENST00000542668;ENST00000538384	T;T;T;T	0.48522	0.81;2.21;1.42;2.21	5.39	5.39	0.77823	.	0.041560	0.85682	D	0.000000	T	0.35248	0.0925	L	0.41573	1.285	0.53688	D	0.999975	B;B;B	0.12630	0.001;0.003;0.006	B;B;B	0.15052	0.007;0.012;0.005	T	0.15492	-1.0435	10	0.11182	T	0.66	-7.9689	10.455	0.44546	0.0:0.0825:0.0:0.9174	.	445;471;421	B4DLV0;Q9BSC4;Q9BSC4-2	.;NOL10_HUMAN;.	R	421;471;421;445	ENSP00000263837:K421R;ENSP00000371101:K471R;ENSP00000437625:K421R;ENSP00000439663:K445R	ENSP00000263837:K421R	K	-	2	0	NOL10	10658440	1.000000	0.71417	1.000000	0.80357	0.404000	0.30871	4.072000	0.57563	2.170000	0.68504	0.460000	0.39030	AAG	T|0.998;C|0.002	0.002	strong		0.303	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
LY75	4065	hgsc.bcm.edu	37	2	160710922	160710922	+	Silent	SNP	T	T	C	rs2729705	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160710922T>C	ENST00000263636.4	-	18	2571	c.2544A>G	c.(2542-2544)gcA>gcG	p.A848A	LY75-CD302_ENST00000505052.1_Silent_p.A848A|LY75_ENST00000553424.1_Silent_p.A848A|LY75_ENST00000554112.1_Silent_p.A848A|LY75-CD302_ENST00000504764.1_Silent_p.A848A	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	848	C-type lectin 5. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		ATGTTATAGTTGCAAGAAAGC	0.299													C|||	2616	0.522364	0.7413	0.438	5008	,	,		15220	0.4583		0.5736	False		,,,				2504	0.2996				p.A848A		Atlas-SNP	.											.	LY75	151	.	0			c.A2544G						PASS	.	C	,,	3148,1258	428.5+/-341.9	1113,922,168	82.0	80.0	81.0		2544,2544,2544	-0.9	0.8	2	dbSNP_100	81	4858,3742	532.9+/-382.3	1360,2138,802	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	2473,3060,970	CC,CT,TT		43.5116,28.552,38.4438	,,	848/1874,848/1818,848/1723	160710922	8006,5000	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon18			TATAGTTGCAAGA	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.2544A>G	2.37:g.160710922T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			T|0.417;C|0.583	0.583	strong		0.299	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
EID2B	126272	hgsc.bcm.edu	37	19	40023308	40023308	+	Silent	SNP	A	A	G	rs1123301	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40023308A>G	ENST00000326282.4	-	1	186	c.135T>C	c.(133-135)gcT>gcC	p.A45A	CTB-60E11.9_ENST00000594676.1_RNA|EID2B_ENST00000601837.1_Intron	NM_152361.1	NP_689574.1			EP300 interacting inhibitor of differentiation 2B											endometrium(1)|lung(1)|urinary_tract(1)	3	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;8.61e-26)|all cancers(26;2.76e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GGCCTTCCCGAGCCTCCTGCA	0.751													.|||	4013	0.801318	0.8646	0.6484	5008	,	,		13555	0.8442		0.7425	False		,,,				2504	0.8405				p.A45A		Atlas-SNP	.											EID2B,NS,carcinoma,0,1	EID2B	9	1	0			c.T135C						scavenged	.	G		3691,533		1630,431,51	7.0	9.0	8.0		135	0.0	0.0	19	dbSNP_86	8	6168,2264		2313,1542,361	no	coding-synonymous	EID2B	NM_152361.1		3943,1973,412	GG,GA,AA		26.8501,12.6184,22.1002		45/162	40023308	9859,2797	2112	4216	6328	SO:0001819	synonymous_variant	126272	exon1			TTCCCGAGCCTCC	AK096263	CCDS12539.1	19q13.2	2008-02-05				ENSG00000176401			26796	protein-coding gene	gene with protein product						15970276	Standard	NM_152361		Approved	EID-3, FLJ38944	uc002olz.1	Q96D98		ENST00000326282.4:c.135T>C	19.37:g.40023308A>G		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_152361		Silent	SNP	ENST00000326282.4	37	CCDS12539.1																																																																																			A|0.234;G|0.766	0.766	strong		0.751	EID2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464961.1	NM_152361	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499228	59499228	+	Missense_Mutation	SNP	C	C	T	rs3809529	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:59499228C>T	ENST00000307144.4	+	1	187	c.89C>T	c.(88-90)cCg>cTg	p.P30L	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	30			P -> L (in dbSNP:rs3809529). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						GCCCTGTGTCCGCGTCAAGCA	0.597													C|||	2460	0.491214	0.4735	0.4409	5008	,	,		20601	0.6131		0.34	False		,,,				2504	0.5808				p.P30L		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.C89T						PASS	.	C	,LEU/PRO	1879,2503	542.2+/-376.0	414,1051,726	61.0	55.0	57.0		,89	1.5	0.0	15	dbSNP_107	57	2756,5824	439.8+/-359.3	438,1880,1972	yes	intron,missense	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,98	852,2931,2698	TT,TC,CC		32.1212,42.88,35.7584	,benign	,30/382	59499228	4635,8327	2191	4290	6481	SO:0001583	missense	92483	exon1			TGTGTCCGCGTCA	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.89C>T	15.37:g.59499228C>T	ENSP00000302393:p.Pro30Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	131	67	0.51145	NM_033195	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	37	CCDS10171.1	984	0.45054945054945056	217	0.4410569105691057	146	0.40331491712707185	363	0.6346153846153846	258	0.3403693931398417	C	7.523	0.657174	0.14580	0.4288	0.321212	ENSG00000171989	ENST00000307144	T	0.68765	-0.35	1.49	1.49	0.22878	.	0.733878	0.10584	U	0.657625	T	0.00012	0.0000	L	0.29908	0.895	0.45946	P	0.0012299999999999534	B	0.15719	0.014	B	0.06405	0.002	T	0.47005	-0.9150	9	0.30854	T	0.27	.	6.8004	0.23748	0.0:1.0:0.0:0.0	rs3809529;rs17856654;rs52793037;rs57306412;rs3809529	30	Q9BYZ2	LDH6B_HUMAN	L	30	ENSP00000302393:P30L	ENSP00000302393:P30L	P	+	2	0	LDHAL6B	57286520	0.011000	0.17503	0.018000	0.16275	0.036000	0.12997	1.945000	0.40273	0.710000	0.31997	0.305000	0.20034	CCG	C|0.613;T|0.387	0.387	strong		0.597	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
KLK14	43847	hgsc.bcm.edu	37	19	51584916	51584916	+	Missense_Mutation	SNP	G	G	A	rs2569491	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51584916G>A	ENST00000156499.2	-	4	351	c.133C>T	c.(133-135)Cat>Tat	p.H45Y	KLK14_ENST00000391802.1_Missense_Mutation_p.H45Y			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	45	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		H -> Y (in dbSNP:rs2569491). {ECO:0000269|PubMed:15489334}.		epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		GTGCACGTATGGCCACCAATT	0.617													N|||	2032	0.405751	0.7436	0.2637	5008	,	,		16271	0.0952		0.3201	False		,,,				2504	0.4581				p.H45Y	GBM(117;2161 2172 2448 22911)	Atlas-SNP	.											.	KLK14	49	.	0			c.C133T						PASS	.		TYR/HIS	2483,1457		821,841,308	36.0	36.0	36.0		133	2.9	0.2	19	dbSNP_100	36	2584,5656		468,1648,2004	yes	missense	KLK14	NM_022046.4	83	1289,2489,2312	AA,AG,GG		31.3592,36.9797,41.601	benign	45/268	51584916	5067,7113	1970	4120	6090	SO:0001583	missense	43847	exon4			ACGTATGGCCACC	AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"""Kallikreins"""	6362	protein-coding gene	gene with protein product		606135	"""kallikrein 14"""			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.133C>T	19.37:g.51584916G>A	ENSP00000156499:p.His45Tyr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_022046	A7UNK5|Q1RMZ2|Q6B089	Missense_Mutation	SNP	ENST00000156499.2	37	CCDS12823.2	714	0.3269230769230769	341	0.693089430894309	102	0.281767955801105	43	0.07517482517482517	228	0.3007915567282322	.	0.011	-1.694889	0.00731	0.630203	0.313592	ENSG00000129437	ENST00000156499;ENST00000391802	D;D	0.88818	-2.43;-2.43	5.04	2.91	0.33838	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	N	0.11698	0.16	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43475	-0.9389	8	0.02654	T	1	.	4.6001	0.12348	0.5856:0.1572:0.2572:0.0	rs2569491;rs56473998;rs59256883;rs2569491	45	Q9P0G3	KLK14_HUMAN	Y	45	ENSP00000156499:H45Y;ENSP00000375678:H45Y	ENSP00000156499:H45Y	H	-	1	0	KLK14	56276728	0.992000	0.36948	0.154000	0.22540	0.287000	0.27160	2.724000	0.47285	0.411000	0.25702	-0.355000	0.07637	CAT	G|0.632;A|0.368	0.368	strong		0.617	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046	
REPS1	85021	hgsc.bcm.edu	37	6	139229872	139229872	+	Missense_Mutation	SNP	C	C	T	rs1044418	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:139229872C>T	ENST00000450536.2	-	18	2723	c.2149G>A	c.(2149-2151)Gtt>Att	p.V717I	REPS1_ENST00000415951.2_Missense_Mutation_p.V658I|REPS1_ENST00000367663.4_Missense_Mutation_p.V690I|REPS1_ENST00000258062.5_Missense_Mutation_p.V716I|REPS1_ENST00000409812.2_Missense_Mutation_p.V626I			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	717	Interaction with RALBP1. {ECO:0000250}.			V -> I (in Ref. 6; CAD38569). {ECO:0000305}.	receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		TGTTCATCAACTTCTGGCCTT	0.393													C|||	513	0.102436	0.1672	0.0937	5008	,	,		19494	0.0347		0.1382	False		,,,				2504	0.0542				p.V716I		Atlas-SNP	.											.	REPS1	58	.	0			c.G2146A						PASS	.	C	ILE/VAL,ILE/VAL	777,3629	315.8+/-294.3	73,631,1499	194.0	175.0	182.0		2068,2146	5.3	0.9	6	dbSNP_86	182	1395,7205	271.1+/-289.3	115,1165,3020	yes	missense,missense	REPS1	NM_001128617.1,NM_031922.3	29,29	188,1796,4519	TT,TC,CC		16.2209,17.635,16.7	benign,benign	690/770,716/796	139229872	2172,10834	2203	4300	6503	SO:0001583	missense	85021	exon18			CATCAACTTCTGG		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"""EF-hand domain containing"""	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.2149G>A	6.37:g.139229872C>T	ENSP00000392065:p.Val717Ile	Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	290	147	0.506897	NM_031922	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	ENST00000450536.2	37		217	0.09935897435897435	60	0.12195121951219512	36	0.09944751381215469	14	0.024475524475524476	107	0.14116094986807387	C	21.1	4.099557	0.76983	0.17635	0.162209	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668	T;T;T;T;T;T	0.32023	1.52;1.5;1.5;1.49;1.52;1.47	5.35	5.35	0.76521	.	0.320820	0.32503	N	0.006003	T	0.24661	0.0598	N	0.22421	0.69	0.24898	P	0.99212115	B;B;P;B;B	0.52692	0.0;0.0;0.955;0.0;0.084	B;B;P;B;B	0.53401	0.002;0.001;0.725;0.001;0.024	T	0.01074	-1.1460	9	0.32370	T	0.25	-1.7825	19.2467	0.93905	0.0:1.0:0.0:0.0	rs1044418;rs3184165;rs57483293;rs1044418	716;665;626;717;658	Q96D71-3;B2R7D3;Q96D71-2;Q96D71;E9PMG1	.;.;.;REPS1_HUMAN;.	I	717;690;675;626;716;658;665	ENSP00000392065:V717I;ENSP00000356635:V690I;ENSP00000434251:V675I;ENSP00000386699:V626I;ENSP00000258062:V716I;ENSP00000397941:V658I	ENSP00000258062:V716I	V	-	1	0	REPS1	139271565	0.998000	0.40836	0.862000	0.33874	0.941000	0.58515	4.270000	0.58896	2.784000	0.95788	0.585000	0.79938	GTT	C|0.886;T|0.114	0.114	strong		0.393	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3		
CEMIP	57214	hgsc.bcm.edu	37	15	81230195	81230195	+	Silent	SNP	G	G	A	rs376777316		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:81230195G>A	ENST00000394685.3	+	25	3701	c.3282G>A	c.(3280-3282)tcG>tcA	p.S1094S	RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Silent_p.S1094S|KIAA1199_ENST00000356249.5_Silent_p.S1094S			Q8WUJ3	CEMIP_HUMAN		1094					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CCATCCTCTCGGATGTTCACA	0.577																																					p.S1094S		Atlas-SNP	.											KIAA1199,NS,carcinoma,+1,1	KIAA1199	118	1	0			c.G3282A						scavenged	.						76.0	72.0	73.0					15																	81230195		2203	4300	6503	SO:0001819	synonymous_variant	57214	exon24			CCTCTCGGATGTT																												ENST00000394685.3:c.3282G>A	15.37:g.81230195G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	154	2	0.012987	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																			.	.	weak		0.577	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
VWA3B	200403	hgsc.bcm.edu	37	2	98709684	98709684	+	Silent	SNP	T	T	C	rs298917	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:98709684T>C	ENST00000477737.1	+	2	333	c.129T>C	c.(127-129)caT>caC	p.H43H	VWA3B_ENST00000451075.2_5'UTR|VWA3B_ENST00000435344.1_Silent_p.H43H	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	43										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TTCAACTGCATGGGCTTAAGA	0.458													T|||	535	0.106829	0.0877	0.1427	5008	,	,		17580	0.0407		0.1938	False		,,,				2504	0.0859				p.H43H		Atlas-SNP	.											.	VWA3B	138	.	0			c.T129C						PASS	.	T		380,3546		24,332,1607	126.0	117.0	120.0		129	-1.3	0.9	2	dbSNP_79	120	1680,6646		174,1332,2657	no	coding-synonymous	VWA3B	NM_144992.4		198,1664,4264	CC,CT,TT		20.1778,9.6791,16.8136		43/1295	98709684	2060,10192	1963	4163	6126	SO:0001819	synonymous_variant	200403	exon2			ACTGCATGGGCTT	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.129T>C	2.37:g.98709684T>C		Somatic	265	1	0.00377358		WXS	Illumina HiSeq	Phase_I	274	116	0.423358	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Silent	SNP	ENST00000477737.1	37	CCDS42718.1																																																																																			T|0.871;C|0.129	0.129	strong		0.458	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
EPHA10	284656	hgsc.bcm.edu	37	1	38187447	38187447	+	Silent	SNP	A	A	G	rs579908	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:38187447A>G	ENST00000373048.4	-	11	2030	c.2031T>C	c.(2029-2031)caT>caC	p.H677H	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000330210.7_Silent_p.H172H|EPHA10_ENST00000427468.2_Silent_p.H677H|EPHA10_ENST00000540011.1_3'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	677	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCCTCAGCATATGCACGGCTA	0.657													G|||	945	0.188698	0.3048	0.1556	5008	,	,		17306	0.0288		0.2634	False		,,,				2504	0.1431				p.H677H		Atlas-SNP	.											.	EPHA10	120	.	0			c.T2031C						PASS	.	G		1205,2893		188,829,1032	17.0	22.0	20.0		2031	1.4	0.9	1	dbSNP_83	20	2191,6177		279,1633,2272	no	coding-synonymous	EPHA10	NM_001099439.1		467,2462,3304	GG,GA,AA		26.1831,29.4046,27.2421		677/1009	38187447	3396,9070	2049	4184	6233	SO:0001819	synonymous_variant	284656	exon11			CAGCATATGCACG	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2031T>C	1.37:g.38187447A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	236	124	0.525424	NM_001099439	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	37	CCDS41305.1																																																																																			A|0.805;G|0.195	0.195	strong		0.657	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
FERMT1	55612	hgsc.bcm.edu	37	20	6093177	6093177	+	Missense_Mutation	SNP	A	A	G	rs16991866	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:6093177A>G	ENST00000217289.4	-	4	1267	c.479T>C	c.(478-480)aTa>aCa	p.I160T	FERMT1_ENST00000536936.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	160	FERM.		I -> T (in dbSNP:rs16991866).		cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						ATCTTCAATTATGGGTTCCTT	0.343													A|||	416	0.0830671	0.1172	0.0519	5008	,	,		15189	0.0794		0.0905	False		,,,				2504	0.0552				p.I160T		Atlas-SNP	.											.	FERMT1	106	.	0			c.T479C						PASS	.	A	THR/ILE	546,3860	245.6+/-254.5	41,464,1698	132.0	134.0	133.0		479	5.8	0.0	20	dbSNP_123	133	807,7793	189.0+/-235.8	33,741,3526	yes	missense	FERMT1	NM_017671.4	89	74,1205,5224	GG,GA,AA		9.3837,12.3922,10.4029	benign	160/678	6093177	1353,11653	2203	4300	6503	SO:0001583	missense	55612	exon4			TCAATTATGGGTT	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.479T>C	20.37:g.6093177A>G	ENSP00000217289:p.Ile160Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Missense_Mutation	SNP	ENST00000217289.4	37	CCDS13098.1	193	0.08836996336996338	68	0.13821138211382114	16	0.04419889502762431	45	0.07867132867132867	64	0.08443271767810026	A	9.186	1.024830	0.19433	0.123922	0.093837	ENSG00000101311	ENST00000217289;ENST00000339538	T	0.41758	0.99	5.77	5.77	0.91146	FERM, N-terminal (1);Band 4.1 domain (1);	0.968169	0.08542	N	0.930408	T	0.00210	0.0006	N	0.08118	0	0.28873	P	0.894859	B;B	0.18968	0.007;0.032	B;B	0.20955	0.026;0.032	T	0.09509	-1.0671	9	0.13108	T	0.6	-13.0329	12.212	0.54386	0.9318:0.0:0.0682:0.0	rs16991866;rs52791370;rs16991866	160;160	Q9BQL6-4;Q9BQL6	.;FERM1_HUMAN	T	160	ENSP00000217289:I160T	ENSP00000217289:I160T	I	-	2	0	FERMT1	6041177	0.093000	0.21703	0.013000	0.15412	0.754000	0.42855	3.679000	0.54634	2.326000	0.78906	0.533000	0.62120	ATA	A|0.898;G|0.102	0.102	strong		0.343	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
TSPYL1	7259	hgsc.bcm.edu	37	6	116600810	116600810	+	Missense_Mutation	SNP	G	G	A	rs3828743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:116600810G>A	ENST00000368608.3	-	1	256	c.184C>T	c.(184-186)Cca>Tca	p.P62S	DSE_ENST00000540275.1_Intron|DSE_ENST00000452085.3_5'Flank|RP1-93H18.1_ENST00000449314.1_lincRNA	NM_003309.3	NP_003300.1	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	62			P -> S (in dbSNP:rs3828743). {ECO:0000269|PubMed:11230166}.		nucleosome assembly (GO:0006334)	nucleus (GO:0005634)	enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(3)|urinary_tract(1)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)		GAAGGCGGTGGAGGCGGGAGC	0.692													G|||	1752	0.34984	0.0643	0.3458	5008	,	,		14958	0.6319		0.2614	False		,,,				2504	0.5389				p.P62S		Atlas-SNP	.											.	TSPYL1	28	.	0			c.C184T						PASS	.	G	SER/PRO	333,3909		25,283,1813	31.0	33.0	32.0		184	-1.1	0.0	6	dbSNP_107	32	2067,6317		241,1585,2366	no	missense	TSPYL1	NM_003309.3	74	266,1868,4179	AA,AG,GG		24.6541,7.8501,19.0084	possibly-damaging	62/438	116600810	2400,10226	2121	4192	6313	SO:0001583	missense	7259	exon1			GCGGTGGAGGCGG	AF042181	CCDS34518.1	6q22.1	2014-09-17	2004-04-05	2004-04-07	ENSG00000189241	ENSG00000189241			12382	protein-coding gene	gene with protein product		604714	"""TSPY-like"""	TSPYL		9730615	Standard	NM_003309		Approved		uc003pwp.4	Q9H0U9	OTTHUMG00000015427	ENST00000368608.3:c.184C>T	6.37:g.116600810G>A	ENSP00000357597:p.Pro62Ser	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_003309	O75885|Q5TFE6	Missense_Mutation	SNP	ENST00000368608.3	37	CCDS34518.1	715	0.3273809523809524	44	0.08943089430894309	116	0.32044198895027626	358	0.6258741258741258	197	0.2598944591029024	G	12.61	1.988214	0.35036	0.078501	0.246541	ENSG00000189241	ENST00000368608;ENST00000545830	T	0.30981	1.51	3.94	-1.11	0.09840	.	.	.	.	.	T	0.07863	0.0197	L	0.47190	1.495	0.80722	P	0.0	B	0.17038	0.02	B	0.09377	0.004	T	0.30504	-0.9976	8	0.27082	T	0.32	-0.2852	4.2248	0.10575	0.2952:0.3263:0.3785:0.0	rs3828743;rs61228315;rs3828743	62	Q9H0U9	TSYL1_HUMAN	S	62	ENSP00000357597:P62S	ENSP00000357597:P62S	P	-	1	0	TSPYL1	116707503	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.197000	0.09518	-0.249000	0.09569	0.655000	0.94253	CCA	G|0.757;A|0.243	0.243	strong		0.692	TSPYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041929.1		
ZNF821	55565	hgsc.bcm.edu	37	16	71893981	71893981	+	Silent	SNP	C	C	T	rs17850869	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:71893981C>T	ENST00000565601.1	-	7	1586	c.1179G>A	c.(1177-1179)ttG>ttA	p.L393L	ZNF821_ENST00000564134.1_3'UTR|ZNF821_ENST00000425432.1_Silent_p.L393L|ATXN1L_ENST00000569119.1_Intron|ZNF821_ENST00000446827.2_Silent_p.L351L|ZNF821_ENST00000313565.6_Silent_p.L351L	NM_001201553.1	NP_001188482.1	O75541	ZN821_HUMAN	zinc finger protein 821	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(2)	13						GCTGGCTGTCCAACTCCACCC	0.562													C|||	34	0.00678914	0.0038	0.0072	5008	,	,		17374	0.0		0.0209	False		,,,				2504	0.0031				p.L393L		Atlas-SNP	.											.	ZNF821	25	.	0			c.G1179A						PASS	.	C	,,,,	14,4382	22.3+/-47.3	0,14,2184	71.0	56.0	61.0		1179,1179,1053,,1053	4.2	1.0	16	dbSNP_123	61	154,8446	73.5+/-136.2	2,150,4148	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous	ZNF821	NM_001201552.1,NM_001201553.1,NM_001201554.1,NM_001201556.1,NM_017530.2	,,,,	2,164,6332	TT,TC,CC		1.7907,0.3185,1.2927	,,,,	393/413,393/413,351/371,,351/371	71893981	168,12828	2198	4300	6498	SO:0001819	synonymous_variant	55565	exon7			GCTGTCCAACTCC	AF070588	CCDS32481.1, CCDS56006.1, CCDS73911.1	16q22.3	2008-05-02				ENSG00000102984		"""Zinc fingers, C2H2-type"""	28043	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_017530		Approved		uc021tlb.1	O75541		ENST00000565601.1:c.1179G>A	16.37:g.71893981C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	54	0.675	NM_001201553	A6NK48|B4DKK4|D3DWS3	Silent	SNP	ENST00000565601.1	37	CCDS56006.1																																																																																			C|0.988;T|0.012	0.012	strong		0.562	ZNF821-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434180.1	NM_017530	
TSEN2	80746	hgsc.bcm.edu	37	3	12544829	12544829	+	Missense_Mutation	SNP	G	G	A	rs33955793	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:12544829G>A	ENST00000284995.6	+	5	764	c.377G>A	c.(376-378)cGc>cAc	p.R126H	TSEN2_ENST00000415684.1_Missense_Mutation_p.R126H|TSEN2_ENST00000402228.3_Missense_Mutation_p.R126H|TSEN2_ENST00000314571.7_Missense_Mutation_p.R126H|TSEN2_ENST00000454502.2_Missense_Mutation_p.R126H|RNU6-404P_ENST00000515968.1_RNA|TSEN2_ENST00000444864.1_Missense_Mutation_p.R126H|TSEN2_ENST00000383797.5_Missense_Mutation_p.R126H	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	126			R -> H (in dbSNP:rs33955793).		mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						AGTACAGTGCGCAGAATCCTC	0.483													G|||	294	0.0587061	0.0469	0.1816	5008	,	,		19207	0.0188		0.0577	False		,,,				2504	0.0297				p.R126H		Atlas-SNP	.											.	TSEN2	46	.	0			c.G377A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	268,4138	151.8+/-185.6	9,250,1944	117.0	106.0	110.0		377,377,377,377,377	-9.2	0.0	3	dbSNP_126	110	569,8031	153.0+/-207.5	18,533,3749	yes	missense,missense,missense,missense,missense	TSEN2	NM_001145392.1,NM_001145393.1,NM_001145394.1,NM_001145395.1,NM_025265.3	29,29,29,29,29	27,783,5693	AA,AG,GG		6.6163,6.0826,6.4355	benign,benign,benign,benign,benign	126/466,126/440,126/407,126/403,126/466	12544829	837,12169	2203	4300	6503	SO:0001583	missense	80746	exon5			CAGTGCGCAGAAT	BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"""tRNA splicing endonuclease subunits"""	28422	protein-coding gene	gene with protein product		608753	"""tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)"", ""tRNA splicing endonuclease 2 homolog (S. cerevisiae)"""			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.377G>A	3.37:g.12544829G>A	ENSP00000284995:p.Arg126His	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	160	70	0.4375	NM_001145394	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Missense_Mutation	SNP	ENST00000284995.6	37	CCDS2611.1	147	0.0673076923076923	31	0.06300813008130081	67	0.1850828729281768	6	0.01048951048951049	43	0.05672823218997362	G	9.134	1.012176	0.19277	0.060826	0.066163	ENSG00000154743	ENST00000446004;ENST00000314571;ENST00000454502;ENST00000383797;ENST00000402228;ENST00000284995;ENST00000444864;ENST00000537959;ENST00000415684	T;T;T;T;T;T;T;T	0.55930	0.51;0.52;0.49;0.52;0.5;0.5;0.52;0.52	4.92	-9.22	0.00675	.	1.471840	0.03899	N	0.280054	T	0.00073	0.0002	N	0.16307	0.4	0.09310	N	1	B;B;B;B	0.12013	0.005;0.001;0.001;0.0	B;B;B;B	0.11329	0.006;0.001;0.002;0.0	T	0.05599	-1.0875	10	0.39692	T	0.17	-0.0042	16.8759	0.86051	0.3149:0.0:0.6851:0.0	rs33955793	126;126;126;126	G5E9Q3;Q8NCE0;Q8NCE0-3;C9IZI7	.;SEN2_HUMAN;.;.	H	126;126;126;126;126;126;126;99;126	ENSP00000406238:R126H;ENSP00000323188:R126H;ENSP00000392029:R126H;ENSP00000373307:R126H;ENSP00000385976:R126H;ENSP00000284995:R126H;ENSP00000407974:R126H;ENSP00000416510:R126H	ENSP00000284995:R126H	R	+	2	0	TSEN2	12519829	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.393000	0.07305	-1.893000	0.01106	-1.133000	0.01973	CGC	G|0.936;A|0.064	0.064	strong		0.483	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1	NM_025265	
FAT4	79633	hgsc.bcm.edu	37	4	126412106	126412106	+	Missense_Mutation	SNP	C	C	G	rs147662558	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:126412106C>G	ENST00000394329.3	+	17	14142	c.14129C>G	c.(14128-14130)tCt>tGt	p.S4710C	FAT4_ENST00000335110.5_Missense_Mutation_p.S2951C	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4710	Necessary and sufficient for interaction with MPDZ. {ECO:0000250}.				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						TCCAAATCTTCTACGTTCTAT	0.483													C|||	30	0.00599042	0.0008	0.0058	5008	,	,		20671	0.0		0.0179	False		,,,				2504	0.0072				p.S4710C		Atlas-SNP	.											.	FAT4	1752	.	0			c.C14129G						PASS	.	C	CYS/SER	22,4384	30.8+/-60.4	0,22,2181	103.0	109.0	107.0		14129	4.9	0.3	4	dbSNP_134	107	177,8423	80.6+/-143.3	1,175,4124	yes	missense	FAT4	NM_024582.4	112	1,197,6305	GG,GC,CC		2.0581,0.4993,1.5301	probably-damaging	4710/4982	126412106	199,12807	2203	4300	6503	SO:0001583	missense	79633	exon17			AATCTTCTACGTT	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.14129C>G	4.37:g.126412106C>G	ENSP00000377862:p.Ser4710Cys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	20	0.009157509157509158	0	0.0	5	0.013812154696132596	0	0.0	15	0.01978891820580475	C	15.14	2.744809	0.49151	0.004993	0.020581	ENSG00000196159	ENST00000394329;ENST00000335110	T;D	0.82081	-1.36;-1.57	4.93	4.93	0.64822	.	0.000000	0.33732	U	0.004612	T	0.73760	0.3628	L	0.36672	1.1	0.41081	D	0.985527	D;D;D	0.61697	0.982;0.983;0.99	P;P;P	0.53313	0.639;0.533;0.723	T	0.82729	-0.0313	10	0.72032	D	0.01	.	17.1555	0.86791	0.0:1.0:0.0:0.0	.	2951;4710;4709	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	C	4710;2951	ENSP00000377862:S4710C;ENSP00000335169:S2951C	ENSP00000335169:S2951C	S	+	2	0	FAT4	126631556	0.998000	0.40836	0.267000	0.24556	0.798000	0.45092	5.643000	0.67895	2.283000	0.76528	0.561000	0.74099	TCT	C|0.986;G|0.014	0.014	strong		0.483	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
DPY19L3	147991	hgsc.bcm.edu	37	19	32973077	32973077	+	Silent	SNP	C	C	T	rs7253039	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:32973077C>T	ENST00000342179.5	+	19	2297	c.2082C>T	c.(2080-2082)taC>taT	p.Y694Y	DPY19L3_ENST00000392250.2_Silent_p.Y694Y|DPY19L3_ENST00000586987.1_3'UTR	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	694						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					TGCCTCCCTACGTGGCCTACT	0.468													C|||	897	0.179113	0.2474	0.1916	5008	,	,		18018	0.119		0.161	False		,,,				2504	0.1585				p.Y694Y		Atlas-SNP	.											.	DPY19L3	70	.	0			c.C2082T						PASS	.	C	,	1056,3350	386.8+/-326.2	127,802,1274	169.0	169.0	169.0		2082,2082	2.5	0.2	19	dbSNP_116	169	1415,7185	272.0+/-289.9	108,1199,2993	no	coding-synonymous,coding-synonymous	DPY19L3	NM_001172774.1,NM_207325.2	,	235,2001,4267	TT,TC,CC		16.4535,23.9673,18.9989	,	694/717,694/717	32973077	2471,10535	2203	4300	6503	SO:0001819	synonymous_variant	147991	exon19			TCCCTACGTGGCC		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.2082C>T	19.37:g.32973077C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Silent	SNP	ENST00000342179.5	37	CCDS12422.1																																																																																			C|0.821;T|0.179	0.179	strong		0.468	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325	
THAP8	199745	hgsc.bcm.edu	37	19	36530343	36530343	+	Missense_Mutation	SNP	C	C	T	rs10421966	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:36530343C>T	ENST00000292894.1	-	3	1098	c.554G>A	c.(553-555)cGg>cAg	p.R185Q	AC002116.7_ENST00000586962.1_RNA|THAP8_ENST00000538849.1_Missense_Mutation_p.R40Q|THAP8_ENST00000524106.1_5'Flank	NM_152658.2	NP_689871.1	Q8NA92	THAP8_HUMAN	THAP domain containing 8	185			R -> Q (in dbSNP:rs10421966). {ECO:0000269|PubMed:14702039}.				DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TTGCAGCCTCCGCACCCGGCG	0.711													c|||	1294	0.258387	0.2239	0.2233	5008	,	,		15755	0.3274		0.33	False		,,,				2504	0.1851				p.R185Q		Atlas-SNP	.											.	THAP8	11	.	0			c.G554A						PASS	.	C	GLN/ARG	927,3425		105,717,1354	8.0	7.0	7.0		554	-5.1	0.0	19	dbSNP_119	7	2538,5980		398,1742,2119	no	missense	THAP8	NM_152658.2	43	503,2459,3473	TT,TC,CC		29.7957,21.3006,26.9231	benign	185/275	36530343	3465,9405	2176	4259	6435	SO:0001583	missense	199745	exon3			AGCCTCCGCACCC	AK057453	CCDS33000.1	19q13.13	2013-01-25			ENSG00000161277	ENSG00000161277		"""THAP (C2CH-type zinc finger) domain containing"""	23191	protein-coding gene	gene with protein product		612536				12575992	Standard	NM_152658		Approved	FLJ32891	uc002oda.1	Q8NA92	OTTHUMG00000048138	ENST00000292894.1:c.554G>A	19.37:g.36530343C>T	ENSP00000292894:p.Arg185Gln	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	26	20	0.769231	NM_152658	Q0P5Z7|Q96M21	Missense_Mutation	SNP	ENST00000292894.1	37	CCDS33000.1	666	0.30494505494505497	125	0.2540650406504065	90	0.24861878453038674	196	0.34265734265734266	255	0.33641160949868076	c	10.87	1.471684	0.26423	0.213006	0.297957	ENSG00000161277	ENST00000292894;ENST00000392182;ENST00000538849	D;T	0.88354	-2.37;1.87	4.54	-5.09	0.02920	.	0.939552	0.08854	N	0.883987	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02464	-1.1155	9	0.17832	T	0.49	-19.0278	12.6285	0.56644	0.0:0.4052:0.0:0.5948	rs10421966;rs10421966	185	Q8NA92	THAP8_HUMAN	Q	185;185;40	ENSP00000292894:R185Q;ENSP00000445493:R40Q	ENSP00000292894:R185Q	R	-	2	0	THAP8	41222183	0.492000	0.26027	0.006000	0.13384	0.039000	0.13416	-0.273000	0.08548	-1.335000	0.02241	-1.316000	0.01300	CGG	C|0.695;T|0.305	0.305	strong		0.711	THAP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379036.1	NM_152658	
PCDHGB3	56102	hgsc.bcm.edu	37	5	140751696	140751696	+	Missense_Mutation	SNP	C	C	A	rs62620756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140751696C>A	ENST00000576222.1	+	1	1866	c.1735C>A	c.(1735-1737)Ccg>Acg	p.P579T	PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	579	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGATATGGTGCCGCGCTCTGC	0.642													.|||	141	0.028155	0.0386	0.0346	5008	,	,		18070	0.001		0.0348	False		,,,				2504	0.0307				p.P579T		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.C1735A						PASS	.	C	,,,,,,,THR/PRO,THR/PRO	159,4247		3,153,2047	52.0	62.0	59.0		,,,,,,,1735,1735	5.3	0.8	5	dbSNP_129	59	320,8280		5,310,3985	yes	intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032097.1	,,,,,,,38,38	8,463,6032	AA,AC,CC		3.7209,3.6087,3.6829	,,,,,,,,	,,,,,,,579/930,579/815	140751696	479,12527	2203	4300	6503	SO:0001583	missense	56102	exon1			ATGGTGCCGCGCT	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1735C>A	5.37:g.140751696C>A	ENSP00000461862:p.Pro579Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	163	97	0.595092	NM_018924	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			C|0.968;A|0.032	0.032	strong		0.642	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
LPCAT3	10162	hgsc.bcm.edu	37	12	7125672	7125672	+	Silent	SNP	C	C	G	rs61733160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7125672C>G	ENST00000261407.4	-	1	142	c.57G>C	c.(55-57)ctG>ctC	p.L19L	C1S_ENST00000406697.1_Intron	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	19					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						AACCCGACTGCAGAACCCCCG	0.667													C|||	254	0.0507188	0.1142	0.0216	5008	,	,		-128	0.0188		0.0258	False		,,,				2504	0.044				p.L19L		Atlas-SNP	.											.	LPCAT3	33	.	0			c.G57C						PASS	.	C		419,3987	176.2+/-205.4	18,383,1802	43.0	43.0	43.0		57	3.2	0.0	12	dbSNP_129	43	161,8439	66.7+/-129.0	0,161,4139	no	coding-synonymous	LPCAT3	NM_005768.5		18,544,5941	GG,GC,CC		1.8721,9.5098,4.4595		19/488	7125672	580,12426	2203	4300	6503	SO:0001819	synonymous_variant	10162	exon1			CGACTGCAGAACC	U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"""O-acyltransferase (membrane bound) domain containing 5"", ""membrane bound O-acyltransferase domain containing 5"""	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970	ENST00000261407.4:c.57G>C	12.37:g.7125672C>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	108	43	0.398148	NM_005768	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Silent	SNP	ENST00000261407.4	37	CCDS8572.1																																																																																			C|0.950;G|0.050	0.050	strong		0.667	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768	
RPUSD2	27079	hgsc.bcm.edu	37	15	40862064	40862064	+	Silent	SNP	C	C	T	rs1058734	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:40862064C>T	ENST00000315616.7	+	1	566	c.528C>T	c.(526-528)gcC>gcT	p.A176A	RPUSD2_ENST00000559271.1_Intron	NM_152260.1	NP_689473.1	Q8IZ73	RUSD2_HUMAN	RNA pseudouridylate synthase domain containing 2	176					pseudouridine synthesis (GO:0001522)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			kidney(4)|lung(4)|skin(3)	11		all_cancers(109;2.74e-14)|all_epithelial(112;1.64e-11)|Lung NSC(122;6.69e-09)|all_lung(180;1.22e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;3.1e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0786)		AGCCCCTGGCCTACTATGAGG	0.627													C|||	1323	0.264177	0.2247	0.2939	5008	,	,		13198	0.0942		0.4712	False		,,,				2504	0.2587				p.A176A		Atlas-SNP	.											.	RPUSD2	28	.	0			c.C528T						PASS	.	C		1165,3241		168,829,1206	16.0	15.0	15.0		528	-1.0	1.0	15	dbSNP_86	15	3813,4787		847,2119,1334	no	coding-synonymous	RPUSD2	NM_152260.1		1015,2948,2540	TT,TC,CC		44.3372,26.4412,38.2746		176/546	40862064	4978,8028	2203	4300	6503	SO:0001819	synonymous_variant	27079	exon1			CCTGGCCTACTAT	AK055971	CCDS10061.1, CCDS66737.1	15q13.3	2013-02-11	2005-01-31	2005-02-07	ENSG00000166133	ENSG00000166133		"""RNA pseudouridylate synthase domain containing"""	24180	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 19"""	C15orf19		12477932	Standard	NM_001286407		Approved	C18B11, FLJ31409	uc001zmd.1	Q8IZ73	OTTHUMG00000130031	ENST00000315616.7:c.528C>T	15.37:g.40862064C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	29	27	0.931035	NM_152260	B4DDD1|Q7L989|Q92939|Q96IA7|Q96N50	Silent	SNP	ENST00000315616.7	37	CCDS10061.1																																																																																			C|0.669;T|0.331	0.331	strong		0.627	RPUSD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252308.2	NM_152260	
YME1L1	10730	hgsc.bcm.edu	37	10	27437964	27437964	+	Silent	SNP	T	T	C	rs11538750	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:27437964T>C	ENST00000326799.3	-	2	187	c.39A>G	c.(37-39)acA>acG	p.T13T	YME1L1_ENST00000477432.1_Silent_p.T13T|YME1L1_ENST00000375972.3_Silent_p.T13T|YME1L1_ENST00000376016.3_Silent_p.T13T	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	13					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						TCAGAGGAACTGTAACCTAGA	0.333													T|||	651	0.129992	0.0106	0.1167	5008	,	,		17774	0.2798		0.1093	False		,,,				2504	0.1677				p.T13T		Atlas-SNP	.											.	YME1L1	71	.	0			c.A39G						PASS	.	T	,	129,4277	94.4+/-133.1	3,123,2077	161.0	167.0	165.0		39,39	1.4	1.0	10	dbSNP_121	165	711,7889	174.6+/-224.8	28,655,3617	no	coding-synonymous,coding-synonymous	YME1L1	NM_014263.2,NM_139312.1	,	31,778,5694	CC,CT,TT		8.2674,2.9278,6.4586	,	13/717,13/774	27437964	840,12166	2203	4300	6503	SO:0001819	synonymous_variant	10730	exon2			AGGAACTGTAACC	AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"""ATPases / AAA-type"""	12843	protein-coding gene	gene with protein product		607472	"""YME1 (S.cerevisiae)-like 1"", ""YME1-like 1 (S. cerevisiae)"""			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.39A>G	10.37:g.27437964T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_139312	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Silent	SNP	ENST00000326799.3	37	CCDS7152.1																																																																																			T|0.905;C|0.095	0.095	strong		0.333	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312	
TARBP1	6894	hgsc.bcm.edu	37	1	234584231	234584231	+	Silent	SNP	C	C	T	rs2102596	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:234584231C>T	ENST00000040877.1	-	11	1955	c.1956G>A	c.(1954-1956)caG>caA	p.Q652Q		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	652					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			ATTACCTATACTGAGTCTTCA	0.358													T|||	1438	0.287141	0.2564	0.3732	5008	,	,		17667	0.3036		0.2893	False		,,,				2504	0.2485				p.Q652Q		Atlas-SNP	.											.	TARBP1	111	.	0			c.G1956A						PASS	.	T		1255,3151	703.5+/-407.0	181,893,1129	89.0	87.0	88.0		1956	-10.6	0.0	1	dbSNP_96	88	2315,6285	705.4+/-405.5	302,1711,2287	no	coding-synonymous	TARBP1	NM_005646.3		483,2604,3416	TT,TC,CC		26.9186,28.4839,27.4489		652/1622	234584231	3570,9436	2203	4300	6503	SO:0001819	synonymous_variant	6894	exon11			CCTATACTGAGTC		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"""tRNA methyltransferase 3 homolog (S. cerevisiae)"""	605052	"""Tar (HIV-1) RNA binding protein 1"""			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.1956G>A	1.37:g.234584231C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			C|0.714;T|0.286	0.286	strong		0.358	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
FAM90A1	55138	hgsc.bcm.edu	37	12	8375112	8375112	+	Missense_Mutation	SNP	G	G	T	rs9668582	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:8375112G>T	ENST00000538603.1	-	7	1259	c.701C>A	c.(700-702)gCg>gAg	p.A234E	FAM90A1_ENST00000307435.6_Missense_Mutation_p.A234E	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	234			A -> E (in dbSNP:rs9668582). {ECO:0000269|PubMed:15489334}.				nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		ACAGCCACCCGCAGGGCTGCT	0.657																																					p.A234E		Atlas-SNP	.											.	FAM90A1	68	.	0			c.C701A						PASS	.						39.0	63.0	55.0					12																	8375112		2070	4218	6288	SO:0001583	missense	55138	exon7			CCACCCGCAGGGC	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.701C>A	12.37:g.8375112G>T	ENSP00000445418:p.Ala234Glu	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	48	46	0.958333	NM_018088	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	454	0.2078754578754579	85	0.17276422764227642	67	0.1850828729281768	197	0.34440559440559443	105	0.13852242744063326	.	0.004	-2.244152	0.00271	.	.	ENSG00000171847	ENST00000307435;ENST00000538603	T;T	0.06608	3.28;3.28	0.713	-1.43	0.08884	.	.	.	.	.	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34204	-0.9838	7	0.02654	T	1	7.4118	.	.	.	rs9668582;rs17857268	234	Q86YD7	F90A1_HUMAN	E	234	ENSP00000307798:A234E;ENSP00000445418:A234E	ENSP00000307798:A234E	A	-	2	0	FAM90A1	8266379	0.005000	0.15991	0.000000	0.03702	0.014000	0.08584	-0.767000	0.04720	-1.652000	0.01502	-1.448000	0.01049	GCG	G|0.793;T|0.207	0.207	strong		0.657	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
PITRM1	10531	hgsc.bcm.edu	37	10	3180288	3180288	+	Missense_Mutation	SNP	C	C	T	rs35779348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:3180288C>T	ENST00000224949.4	-	27	3083	c.3049G>A	c.(3049-3051)Ggc>Agc	p.G1017S	PITRM1_ENST00000464395.1_5'UTR|PITRM1_ENST00000380994.1_Missense_Mutation_p.G575S|PITRM1_ENST00000451104.2_Missense_Mutation_p.G919S|PITRM1_ENST00000380989.2_Missense_Mutation_p.G1018S			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	1017					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						ATGGCCAGGCCGTGTGTGCTC	0.612													C|||	45	0.00898562	0.0008	0.0231	5008	,	,		17586	0.0		0.0268	False		,,,				2504	0.001				p.G1018S		Atlas-SNP	.											.	PITRM1	109	.	0			c.G3052A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	26,4230		1,24,2103	48.0	53.0	52.0		3052,2755,3049	3.0	0.0	10	dbSNP_126	52	266,8210		6,254,3978	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	56,56,56	7,278,6081	TT,TC,CC		3.1383,0.6109,2.2934	possibly-damaging,possibly-damaging,possibly-damaging	1018/1039,919/940,1017/1038	3180288	292,12440	2128	4238	6366	SO:0001583	missense	10531	exon27			CCAGGCCGTGTGT	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.3049G>A	10.37:g.3180288C>T	ENSP00000224949:p.Gly1017Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	29	0.013278388278388278	0	0.0	8	0.022099447513812154	0	0.0	21	0.027704485488126648	c	15.07	2.724507	0.48728	0.006109	0.031383	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	5.83	3.02	0.34903	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.146245	0.64402	N	0.000007	T	0.29223	0.0727	M	0.61703	1.905	0.49798	D	0.99982	P;D;P	0.62365	0.898;0.991;0.87	B;P;B	0.50049	0.312;0.629;0.355	T	0.25187	-1.0139	10	0.23891	T	0.37	-27.4489	9.9005	0.41344	0.0:0.7891:0.0:0.2109	rs35779348	919;1017;952	E7ES23;Q5JRX3;E9PDX7	.;PREP_HUMAN;.	S	1017;1010;1018;575;919	ENSP00000224949:G1017S;ENSP00000370377:G1018S;ENSP00000370382:G575S;ENSP00000401201:G919S	ENSP00000224949:G1017S	G	-	1	0	PITRM1	3170288	0.938000	0.31826	0.006000	0.13384	0.000000	0.00434	3.590000	0.53979	0.394000	0.25230	-1.075000	0.02238	GGC	T|0.016;G|0.000;C|0.984	0.016	strong		0.612	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
ATRN	8455	hgsc.bcm.edu	37	20	3515951	3515951	+	Silent	SNP	C	C	T	rs151519	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3515951C>T	ENST00000262919.5	+	2	530	c.462C>T	c.(460-462)taC>taT	p.Y154Y	ATRN_ENST00000446916.2_Silent_p.Y154Y	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	154	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						ATTATAAATACAAAACGAAGT	0.338													T|||	962	0.192093	0.3306	0.1945	5008	,	,		10237	0.0169		0.2893	False		,,,				2504	0.0838				p.Y154Y		Atlas-SNP	.											.	ATRN	118	.	0			c.C462T						PASS	.	T	,,	1424,2982	675.4+/-403.1	221,982,1000	70.0	74.0	72.0		114,462,462	3.1	1.0	20	dbSNP_79	72	2367,6233	698.7+/-405.0	321,1725,2254	no	coding-synonymous,coding-synonymous,coding-synonymous	ATRN	NM_001207047.1,NM_139321.2,NM_139322.2	,,	542,2707,3254	TT,TC,CC		27.5233,32.3196,29.1481	,,	38/1157,154/1430,154/1273	3515951	3791,9215	2203	4300	6503	SO:0001819	synonymous_variant	8455	exon2			TAAATACAAAACG	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"""mahogany protein"""	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.462C>T	20.37:g.3515951C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	152	59	0.388158	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Silent	SNP	ENST00000262919.5	37	CCDS13053.1																																																																																			C|0.751;T|0.249	0.249	strong		0.338	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321	
OR12D2	26529	hgsc.bcm.edu	37	6	29364615	29364615	+	Missense_Mutation	SNP	G	G	T	rs9257834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29364615G>T	ENST00000383555.2	+	1	200	c.139G>T	c.(139-141)Gtc>Ttc	p.V47F	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	47			V -> F (in dbSNP:rs9257834).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						TCTGATGATTGTCATCTCCGA	0.463													G|||	1597	0.31889	0.1921	0.3458	5008	,	,		20479	0.3641		0.4523	False		,,,				2504	0.2873				p.V47F		Atlas-SNP	.											.	OR12D2	42	.	0			c.G139T						PASS	.	G	PHE/VAL	668,2352		75,518,917	127.0	133.0	131.0		139	3.2	0.0	6	dbSNP_118	131	2411,3007		536,1339,834	yes	missense	OR12D2	NM_013936.3	50	611,1857,1751	TT,TG,GG		44.4998,22.1192,36.4897	probably-damaging	47/308	29364615	3079,5359	1510	2709	4219	SO:0001583	missense	26529	exon1			ATGATTGTCATCT		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.139G>T	6.37:g.29364615G>T	ENSP00000373047:p.Val47Phe	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	231	110	0.47619	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	788	0.3608058608058608	102	0.2073170731707317	123	0.3397790055248619	208	0.36363636363636365	355	0.4683377308707124	G	10.62	1.402237	0.25291	0.221192	0.444998	ENSG00000168787	ENST00000383555	T	0.03496	3.91	4.07	3.19	0.36642	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000073	T	0.07503	0.0189	M	0.87456	2.885	0.80722	P	0.0	D	0.62365	0.991	P	0.60345	0.873	T	0.02698	-1.1122	9	0.72032	D	0.01	.	5.9657	0.19325	0.0988:0.0:0.7097:0.1915	rs9257834;rs59373671;rs9257834	47	P58182	O12D2_HUMAN	F	47	ENSP00000373047:V47F	ENSP00000373047:V47F	V	+	1	0	OR12D2	29472594	0.000000	0.05858	0.005000	0.12908	0.002000	0.02628	-0.520000	0.06252	0.897000	0.36392	0.411000	0.27672	GTC	G|0.636;T|0.364	0.364	strong		0.463	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
GGT7	2686	hgsc.bcm.edu	37	20	33451148	33451148	+	Silent	SNP	G	G	A	rs11546155	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:33451148G>A	ENST00000336431.5	-	2	417	c.373C>T	c.(373-375)Ctg>Ttg	p.L125L		NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	125					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						TGCATGACCAGCGCCACGGTG	0.647													g|||	693	0.138379	0.1362	0.0533	5008	,	,		13649	0.1071		0.1074	False		,,,				2504	0.2658				p.L125L		Atlas-SNP	.											GGT7,NS,carcinoma,0,2	GGT7	41	2	0			c.C373T						scavenged	.			635,3771	263.8+/-265.7	43,549,1611	35.0	32.0	33.0		373	5.3	0.8	20	dbSNP_120	33	1202,7398	236.0+/-268.3	90,1022,3188	no	coding-synonymous	GGT7	NM_178026.2		133,1571,4799	AA,AG,GG		13.9767,14.4122,14.1243		125/663	33451148	1837,11169	2203	4300	6503	SO:0001819	synonymous_variant	2686	exon2			TGACCAGCGCCAC	AL049709	CCDS13242.2	20q11.22	2008-11-24	2008-03-10	2008-03-10	ENSG00000131067	ENSG00000131067		"""Gamma-glutamyltransferases"""	4259	protein-coding gene	gene with protein product		612342	"""gamma-glutamyltransferase-like 3"""	GGTL5, GGTL3		8104871, 18357469	Standard	NM_178026		Approved	D20S101, dJ18C9.2	uc002xay.3	Q9UJ14	OTTHUMG00000032314	ENST00000336431.5:c.373C>T	20.37:g.33451148G>A		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	217	109	0.502304	NM_178026	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Silent	SNP	ENST00000336431.5	37	CCDS13242.2																																																																																			G|0.875;A|0.125	0.125	strong		0.647	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2	NM_178026	
OR8B2	26595	hgsc.bcm.edu	37	11	124253147	124253147	+	Silent	SNP	A	A	G	rs530704	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124253147A>G	ENST00000375013.2	-	1	111	c.93T>C	c.(91-93)ttT>ttC	p.F31F		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		AGATCACTAGAAACAGGAAAA	0.418																																					p.F31F		Atlas-SNP	.											.	OR8B2	42	.	0			c.T93C						PASS	.						210.0	177.0	188.0					11																	124253147		2201	4299	6500	SO:0001819	synonymous_variant	26595	exon1			CACTAGAAACAGG	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"""GPCR / Class A : Olfactory receptors"""	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.93T>C	11.37:g.124253147A>G		Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	326	76	0.233129	NM_001005468	Q8NGH2	Silent	SNP	ENST00000375013.2	37	CCDS31708.1																																																																																			A|0.680;G|0.320	0.320	strong		0.418	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468	
ZNF57	126295	hgsc.bcm.edu	37	19	2917287	2917287	+	Missense_Mutation	SNP	C	C	A	rs2288958	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:2917287C>A	ENST00000306908.5	+	4	816	c.668C>A	c.(667-669)aCc>aAc	p.T223N	AC006277.2_ENST00000520090.2_RNA|ZNF57_ENST00000523428.1_Missense_Mutation_p.T191N	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	223			T -> N (in dbSNP:rs2288958).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAGAGAAAACCTACAAATGC	0.468													C|||	2345	0.468251	0.2398	0.5447	5008	,	,		22421	0.631		0.4642	False		,,,				2504	0.5593				p.T223N	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.C668A						PASS	.	C	ASN/THR	1204,3202	419.6+/-338.7	167,870,1166	104.0	89.0	94.0		668	-4.0	0.0	19	dbSNP_100	94	3845,4755	540.9+/-383.9	841,2163,1296	yes	missense	ZNF57	NM_173480.2	65	1008,3033,2462	AA,AC,CC		44.7093,27.3264,38.8205	benign	223/556	2917287	5049,7957	2203	4300	6503	SO:0001583	missense	126295	exon4			AGAAAACCTACAA	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.668C>A	19.37:g.2917287C>A	ENSP00000303696:p.Thr223Asn	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	40	0.645161	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	1026	0.4697802197802198	114	0.23170731707317074	187	0.5165745856353591	371	0.6486013986013986	354	0.46701846965699206	C	13.02	2.111658	0.37242	0.273264	0.447093	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.15372	2.43;2.43	2.02	-4.04	0.04010	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.25890	0.77	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.39272	-0.9622	8	0.66056	D	0.02	.	4.7224	0.12924	0.5138:0.3621:0.0:0.1241	rs2288958;rs61415421;rs2288958	223	Q68EA5	ZNF57_HUMAN	N	223;225;191	ENSP00000303696:T223N;ENSP00000430223:T191N	ENSP00000303696:T223N	T	+	2	0	ZNF57	2868287	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-2.633000	0.00869	-1.718000	0.01383	-0.535000	0.04281	ACC	C|0.581;A|0.419	0.419	strong		0.468	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
UCP3	7352	hgsc.bcm.edu	37	11	73717254	73717254	+	Silent	SNP	A	A	G	rs1800006	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:73717254A>G	ENST00000314032.4	-	3	849	c.297T>C	c.(295-297)taT>taC	p.Y99Y	UCP3_ENST00000348534.4_Silent_p.Y99Y|UCP3_ENST00000426995.2_Silent_p.Y99Y	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	99					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to hormone stimulus (GO:0032870)|fatty acid metabolic process (GO:0006631)|lipid metabolic process (GO:0006629)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to activity (GO:0014823)|response to cold (GO:0009409)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					TGACGGAGTCATAGAGGCCGA	0.622													G|||	1719	0.343251	0.6445	0.1556	5008	,	,		18847	0.2808		0.2416	False		,,,				2504	0.2382				p.Y99Y		Atlas-SNP	.											.	UCP3	31	.	0			c.T297C						PASS	.	G	,	2599,1801	528.9+/-372.5	772,1055,373	44.0	44.0	44.0		297,297	-7.6	0.3	11	dbSNP_89	44	2091,6495	715.0+/-406.0	256,1579,2458	no	coding-synonymous,coding-synonymous	UCP3	NM_003356.3,NM_022803.2	,	1028,2634,2831	GG,GA,AA		24.3536,40.9318,36.1158	,	99/313,99/276	73717254	4690,8296	2200	4293	6493	SO:0001819	synonymous_variant	7352	exon3			GGAGTCATAGAGG	AF001787	CCDS8229.1, CCDS44677.1	11q13.4	2013-05-22				ENSG00000175564		"""Solute carriers"""	12519	protein-coding gene	gene with protein product		602044				9480760, 9196039	Standard	NM_003356		Approved	SLC25A9	uc001our.3	P55916		ENST00000314032.4:c.297T>C	11.37:g.73717254A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_003356	O60475|Q96HL3	Silent	SNP	ENST00000314032.4	37	CCDS8229.1																																																																																			A|0.651;G|0.349	0.349	strong		0.622	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356	
SVOPL	136306	hgsc.bcm.edu	37	7	138363746	138363746	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:138363746C>T	ENST00000419765.3	-	1	78	c.45G>A	c.(43-45)cgG>cgA	p.R15R	SVOPL_ENST00000421622.1_Silent_p.R15R	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	15						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						GGCTCAATTTCCGAAGGCTGA	0.493																																					p.R15R		Atlas-SNP	.											SVOPL_ENST00000419765,colon,carcinoma,-1,2	SVOPL	111	2	0			c.G45A						scavenged	.						99.0	96.0	97.0					7																	138363746		692	1591	2283	SO:0001819	synonymous_variant	136306	exon1			CAATTTCCGAAGG	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"""SV2 related protein homolog (rat)-like"""				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.45G>A	7.37:g.138363746C>T		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	203	6	0.0295567	NM_001139456		Silent	SNP	ENST00000419765.3	37	CCDS47721.1																																																																																			.	.	none		0.493	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959	
KCNMA1	3778	hgsc.bcm.edu	37	10	78944590	78944590	+	Silent	SNP	G	G	A	rs1131824	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:78944590G>A	ENST00000286628.8	-	4	686	c.687C>T	c.(685-687)ttC>ttT	p.F229F	KCNMA1_ENST00000404857.1_Silent_p.F229F|KCNMA1_ENST00000404771.3_Silent_p.F229F|KCNMA1_ENST00000372440.1_Silent_p.F229F|KCNMA1_ENST00000406533.3_Silent_p.F229F|KCNMA1_ENST00000286627.5_Silent_p.F229F|KCNMA1_ENST00000354353.5_Silent_p.F229F|KCNMA1_ENST00000372443.1_Silent_p.F229F	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	229					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	CCCGCAAGCCGAAGTAGAGAA	0.468													A|||	2033	0.40595	0.705	0.2695	5008	,	,		18937	0.249		0.335	False		,,,				2504	0.3333				p.F229F		Atlas-SNP	.											.	KCNMA1	370	.	0			c.C687T						PASS	.	A	,,,	2735,1671	508.4+/-367.0	857,1021,325	155.0	140.0	145.0		687,687,687,687	5.3	1.0	10	dbSNP_86	145	3109,5491	658.9+/-401.6	549,2011,1740	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNMA1	NM_001014797.2,NM_001161352.1,NM_001161353.1,NM_002247.3	,,,	1406,3032,2065	AA,AG,GG		36.1512,37.9256,44.9331	,,,	229/1183,229/1237,229/1220,229/1179	78944590	5844,7162	2203	4300	6503	SO:0001819	synonymous_variant	3778	exon4			CAAGCCGAAGTAG	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6284	protein-coding gene	gene with protein product	"""BK channel alpha subunit"""	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.687C>T	10.37:g.78944590G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001161352	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Silent	SNP	ENST00000286628.8	37		835|835	0.3823260073260073|0.3823260073260073	335|335	0.6808943089430894|0.6808943089430894	108|108	0.2983425414364641|0.2983425414364641	138|138	0.24125874125874125|0.24125874125874125	254|254	0.33509234828496043|0.33509234828496043	A|A	6.974|6.974	0.549742|0.549742	0.13374|0.13374	0.620744|0.620744	0.361512|0.361512	ENSG00000156113|ENSG00000156113	ENST00000372421|ENST00000372403	.|.	.|.	.|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.45366|0.45366	-0.9266|-0.9266	3|3	.|.	.|.	.|.	-11.1608|-11.1608	10.553|10.553	0.45101|0.45101	0.8628:0.0:0.1372:0.0|0.8628:0.0:0.1372:0.0	rs1131824;rs2227912;rs2296678;rs3192016;rs7098260;rs17414082;rs17482985;rs41318619;rs57078861;rs1131824|rs1131824;rs2227912;rs2296678;rs3192016;rs7098260;rs17414082;rs17482985;rs41318619;rs57078861;rs1131824	.|.	.|.	.|.	W|L	218|180	.|.	.|.	R|S	-|-	1|2	2|0	KCNMA1|KCNMA1	78614596|78614596	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.952000|0.952000	0.60782|0.60782	1.408000|1.408000	0.34668|0.34668	1.101000|1.101000	0.41535|0.41535	-0.254000|-0.254000	0.11334|0.11334	CGG|TCG	G|0.579;A|0.421	0.421	strong		0.468	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247	
GRIN2D	2906	hgsc.bcm.edu	37	19	48908597	48908597	+	Missense_Mutation	SNP	G	G	A	rs372406980		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48908597G>A	ENST00000263269.3	+	3	1160	c.1072G>A	c.(1072-1074)Gag>Aag	p.E358K		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	358					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCACCGCGGCGAGAGTCTGCA	0.622																																					p.E358K		Atlas-SNP	.											.	GRIN2D	76	.	0			c.G1072A						PASS	.						14.0	15.0	15.0					19																	48908597		2201	4295	6496	SO:0001583	missense	2906	exon3			CGCGGCGAGAGTC	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.1072G>A	19.37:g.48908597G>A	ENSP00000263269:p.Glu358Lys	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	40	25	0.625	NM_000836		Missense_Mutation	SNP	ENST00000263269.3	37	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.833830	0.50951	.	.	ENSG00000105464	ENST00000263269	T	0.05319	3.46	4.32	4.32	0.51571	.	0.845492	0.10398	N	0.679577	T	0.06280	0.0162	L	0.31926	0.97	0.42288	D	0.992125	P	0.48230	0.907	B	0.33620	0.167	T	0.50285	-0.8846	10	0.54805	T	0.06	.	15.9622	0.79939	0.0:0.0:1.0:0.0	.	358	O15399	NMDE4_HUMAN	K	358	ENSP00000263269:E358K	ENSP00000263269:E358K	E	+	1	0	GRIN2D	53600409	0.989000	0.36119	0.999000	0.59377	0.911000	0.54048	3.506000	0.53364	2.116000	0.64780	0.561000	0.74099	GAG	.	.	alt		0.622	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
ABHD12B	145447	hgsc.bcm.edu	37	14	51368610	51368610	+	Missense_Mutation	SNP	A	A	G	rs28564871|rs386777431	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:51368610A>G	ENST00000337334.2	+	10	859	c.844A>G	c.(844-846)Atc>Gtc	p.I282V	ABHD12B_ENST00000353130.1_Missense_Mutation_p.I205V|ABHD12B_ENST00000395752.1_Missense_Mutation_p.I175V|PYGL_ENST00000532462.1_Intron	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	282			I -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.				hydrolase activity (GO:0016787)	p.I205V(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					AGACAAAATAATCTTTCCTAA	0.313													G|||	1421	0.283746	0.1649	0.3876	5008	,	,		18507	0.4573		0.2028	False		,,,				2504	0.2751				p.I282V		Atlas-SNP	.											ABHD12B_ENST00000337334,colon,carcinoma,-1,5	ABHD12B	53	5	1	Substitution - Missense(1)	breast(1)	c.A844G						PASS	.	G	VAL/ILE,VAL/ILE	673,3733	760.5+/-413.0	54,565,1584	75.0	72.0	73.0		844,613	3.3	1.0	14	dbSNP_125	73	1637,6955	738.4+/-407.1	151,1335,2810	yes	missense,missense	ABHD12B	NM_001206673.1,NM_181814.1	29,29	205,1900,4394	GG,GA,AA		19.0526,15.2746,17.772	benign,benign	282/363,205/286	51368610	2310,10688	2203	4296	6499	SO:0001583	missense	145447	exon10			AAAATAATCTTTC	BG698443	CCDS9702.1, CCDS55916.1	14q21.3	2009-10-09	2007-04-03	2007-04-03	ENSG00000131969	ENSG00000131969		"""Abhydrolase domain containing"""	19837	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 29"""	C14orf29			Standard	NM_181814		Approved	BEM46L3	uc001wys.3	Q7Z5M8	OTTHUMG00000140286	ENST00000337334.2:c.844A>G	14.37:g.51368610A>G	ENSP00000336693:p.Ile282Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	118	47	0.398305	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Missense_Mutation	SNP	ENST00000337334.2	37	CCDS55916.1	657	0.3008241758241758	90	0.18292682926829268	139	0.3839779005524862	268	0.46853146853146854	160	0.21108179419525067	G	6.676	0.493340	0.12702	0.152746	0.190526	ENSG00000131969	ENST00000353130;ENST00000337334;ENST00000395752	T;T;T	0.41065	2.23;1.01;2.27	5.24	3.35	0.38373	.	0.502898	0.21095	N	0.080253	T	0.00012	0.0000	N	0.11789	0.175	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.47611	-0.9104	9	0.09843	T	0.71	-9.4496	5.205	0.15285	0.175:0.0:0.6608:0.1641	rs28564871;rs28564871	282;205	Q7Z5M8;Q7Z5M8-2	AB12B_HUMAN;.	V	205;282;175	ENSP00000343951:I205V;ENSP00000336693:I282V;ENSP00000379101:I175V	ENSP00000336693:I282V	I	+	1	0	ABHD12B	50438360	0.799000	0.28903	0.998000	0.56505	0.960000	0.62799	0.331000	0.19733	0.401000	0.25424	-0.119000	0.15052	ATC	A|0.765;G|0.235	0.235	strong		0.313	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1		
MYBPH	4608	hgsc.bcm.edu	37	1	203140671	203140671	+	Silent	SNP	G	G	A	rs3737875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:203140671G>A	ENST00000255416.4	-	5	690	c.633C>T	c.(631-633)aaC>aaT	p.N211N		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H	211	Ig-like C2-type 1.				cell adhesion (GO:0007155)|regulation of striated muscle contraction (GO:0006942)	myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			endometrium(5)|large_intestine(6)|lung(7)|skin(1)|urinary_tract(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.153)	Colorectal(1306;0.0306)		GGGCATGGCCGTTGTGGGTCC	0.662													G|||	848	0.169329	0.1021	0.1153	5008	,	,		19650	0.3968		0.0944	False		,,,				2504	0.1411				p.N211N	NSCLC(32;174 1025 14462 23899 42933)	Atlas-SNP	.											.	MYBPH	41	.	0			c.C633T						PASS	.	G		421,3985	206.2+/-227.9	18,385,1800	43.0	46.0	45.0		633	-4.7	0.3	1	dbSNP_107	45	811,7789	187.3+/-234.6	41,729,3530	yes	coding-synonymous	MYBPH	NM_004997.2		59,1114,5330	AA,AG,GG		9.4302,9.5552,9.4726		211/478	203140671	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	4608	exon5			ATGGCCGTTGTGG	BC044226	CCDS30975.1	1q32.1	2013-02-11	2001-11-28		ENSG00000133055	ENSG00000133055		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7552	protein-coding gene	gene with protein product		160795	"""myosin-binding protein H"""			8486381	Standard	NM_004997		Approved		uc001gzh.1	Q13203	OTTHUMG00000042121	ENST00000255416.4:c.633C>T	1.37:g.203140671G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_004997	Q16886|Q86YC5	Silent	SNP	ENST00000255416.4	37	CCDS30975.1																																																																																			G|0.870;A|0.130	0.130	strong		0.662	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	NM_004997	
GRIN2A	2903	hgsc.bcm.edu	37	16	9862741	9862741	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:9862741G>A	ENST00000396573.2	-	13	2871	c.2562C>T	c.(2560-2562)tcC>tcT	p.S854S	GRIN2A_ENST00000535259.1_Silent_p.S697S|GRIN2A_ENST00000330684.3_Silent_p.S854S|GRIN2A_ENST00000562109.1_Silent_p.S854S|GRIN2A_ENST00000396575.2_Silent_p.S854S|GRIN2A_ENST00000404927.2_Silent_p.S854S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	854					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CAGGCCGGTCGGAGCACACGC	0.562																																					p.S854S		Atlas-SNP	.											.	GRIN2A	366	.	0			c.C2562T						PASS	.						89.0	91.0	91.0					16																	9862741		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon13			CCGGTCGGAGCAC		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.2562C>T	16.37:g.9862741G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																			.	.	none		0.562	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
USPL1	10208	hgsc.bcm.edu	37	13	31231806	31231806	+	Missense_Mutation	SNP	T	T	C	rs7984952	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:31231806T>C	ENST00000255304.4	+	9	1934	c.1592T>C	c.(1591-1593)tTa>tCa	p.L531S		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	531			L -> S (in dbSNP:rs7984952). {ECO:0000269|PubMed:15489334}.		Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		CCAGTATCTTTAACATCGTGT	0.433													C|||	2397	0.478634	0.823	0.389	5008	,	,		20093	0.1796		0.4016	False		,,,				2504	0.4642				p.L531S	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.T1592C						PASS	.	C	SER/LEU	3409,997	371.7+/-320.1	1322,765,116	128.0	123.0	125.0		1592	3.5	0.0	13	dbSNP_116	125	3537,5063	631.3+/-398.5	724,2089,1487	yes	missense	USPL1	NM_005800.4	145	2046,2854,1603	CC,CT,TT		41.1279,22.6282,46.5939	benign	531/1093	31231806	6946,6060	2203	4300	6503	SO:0001583	missense	10208	exon9			TATCTTTAACATC	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 22"""	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.1592T>C	13.37:g.31231806T>C	ENSP00000255304:p.Leu531Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	85	81	0.952941	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	956	0.43772893772893773	408	0.8292682926829268	154	0.425414364640884	100	0.17482517482517482	294	0.38786279683377306	C	10.88	1.475572	0.26511	0.773718	0.411279	ENSG00000132952	ENST00000255304	T	0.07908	3.15	5.54	3.46	0.39613	.	1.048920	0.07340	N	0.880541	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15235	-1.0444	9	0.10636	T	0.68	-0.3858	8.089	0.30790	0.1311:0.7144:0.0:0.1545	rs7984952;rs17609480;rs17857154;rs61445569;rs7984952	531	Q5W0Q7	USPL1_HUMAN	S	531	ENSP00000255304:L531S	ENSP00000255304:L531S	L	+	2	0	USPL1	30129806	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.369000	0.20416	0.715000	0.32103	-0.119000	0.15052	TTA	T|0.507;C|0.493	0.493	strong		0.433	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800	
SEMA3E	9723	hgsc.bcm.edu	37	7	83037751	83037751	+	Silent	SNP	C	C	A	rs2722985	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:83037751C>A	ENST00000307792.3	-	6	1070	c.603G>T	c.(601-603)gcG>gcT	p.A201A	SEMA3E_ENST00000427262.1_Silent_p.A141A	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	201	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TGCGGAAGATCGCAGCGTCTC	0.463													C|||	2786	0.55631	0.1339	0.6801	5008	,	,		15839	0.8413		0.5984	False		,,,				2504	0.7025				p.A201A		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G603T						PASS	.	C	,	950,3456	361.6+/-315.8	104,742,1357	62.0	57.0	59.0		423,603	-11.8	0.0	7	dbSNP_100	59	5054,3546	629.2+/-398.2	1501,2052,747	no	coding-synonymous,coding-synonymous	SEMA3E	NM_001178129.1,NM_012431.2	,	1605,2794,2104	AA,AC,CC		41.2326,21.5615,46.1633	,	141/716,201/776	83037751	6004,7002	2203	4300	6503	SO:0001819	synonymous_variant	9723	exon6			GAAGATCGCAGCG	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.603G>T	7.37:g.83037751C>A		Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	198	196	0.989899	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	37	CCDS34674.1																																																																																			C|0.504;A|0.496	0.496	strong		0.463	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
BPIFB3	359710	hgsc.bcm.edu	37	20	31656632	31656632	+	Missense_Mutation	SNP	C	C	G	rs6057717	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:31656632C>G	ENST00000375494.3	+	10	1002	c.1002C>G	c.(1000-1002)caC>caG	p.H334Q		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	334			H -> Q (in dbSNP:rs6057717).		innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TGCCCCTGCACCAGCAACTCC	0.562													C|||	2414	0.482029	0.3086	0.4741	5008	,	,		17133	0.7698		0.3837	False		,,,				2504	0.5266				p.H334Q		Atlas-SNP	.											C20orf185,NS,carcinoma,0,1	.	.	1	0			c.C1002G						PASS	.	C	GLN/HIS	1307,3099	442.3+/-346.6	202,903,1098	89.0	66.0	74.0		1002	2.3	0.6	20	dbSNP_114	74	3124,5476	475.9+/-369.2	578,1968,1754	yes	missense	BPIFB3	NM_182658.1	24	780,2871,2852	GG,GC,CC		36.3256,29.6641,34.0689	benign	334/477	31656632	4431,8575	2203	4300	6503	SO:0001583	missense	359710	exon10			CCTGCACCAGCAA	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1002C>G	20.37:g.31656632C>G	ENSP00000364643:p.His334Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	37	CCDS13212.1	1051	0.48122710622710624	163	0.3313008130081301	160	0.4419889502762431	438	0.7657342657342657	290	0.38258575197889183	C	2.285	-0.363791	0.05103	0.296641	0.363256	ENSG00000186190	ENST00000375494	T	0.08193	3.12	4.25	2.26	0.28386	.	2.005100	0.02461	N	0.086613	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	9.99999999995449E-6	B	0.26635	0.155	B	0.29785	0.107	T	0.28332	-1.0047	9	0.13853	T	0.58	0.2314	6.1232	0.20164	0.0:0.7579:0.0:0.2421	rs6057717;rs6057717	334	P59826	BPIB3_HUMAN	Q	334	ENSP00000364643:H334Q	ENSP00000364643:H334Q	H	+	3	2	BPIFB3	31120293	0.019000	0.18553	0.644000	0.29465	0.068000	0.16541	0.094000	0.15107	0.519000	0.28406	0.591000	0.81541	CAC	C|0.625;G|0.375	0.375	strong		0.562	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
TINAGL1	64129	hgsc.bcm.edu	37	1	32050533	32050533	+	Silent	SNP	G	G	A	rs372554073		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32050533G>A	ENST00000271064.7	+	7	829	c.753G>A	c.(751-753)acG>acA	p.T251T	TINAGL1_ENST00000457433.2_Silent_p.T220T|TINAGL1_ENST00000537531.1_3'UTR|TINAGL1_ENST00000481165.1_3'UTR	NM_001204415.1|NM_022164.2	NP_001191344.1|NP_071447.1	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1	251					endosomal transport (GO:0016197)|immune response (GO:0006955)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type peptidase activity (GO:0008234)|extracellular matrix structural constituent (GO:0005201)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			breast(2)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(4)|prostate(1)|skin(3)|urinary_tract(1)	18		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		GACACATGACGCCTGTCCTGT	0.637																																					p.T251T		Atlas-SNP	.											TINAGL1,colon,carcinoma,+1,1	TINAGL1	35	1	0			c.G753A						scavenged	.	G	,,	8,4398		0,8,2195	79.0	73.0	75.0		660,438,753	-7.1	0.4	1		75	2,8598		0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	TINAGL1	NM_001204414.1,NM_001204415.1,NM_022164.2	,,	0,10,6493	AA,AG,GG		0.0233,0.1816,0.0769	,,	220/437,146/363,251/468	32050533	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	64129	exon7			CATGACGCCTGTC	AB050716	CCDS343.1, CCDS55586.1, CCDS72745.1	1p34.3	2014-04-22	2005-08-18	2005-08-18	ENSG00000142910	ENSG00000142910			19168	protein-coding gene	gene with protein product			"""lipocalin 7"", ""TINAG-like 1"""	LCN7		11170462	Standard	NM_022164		Approved	P3ECSL, LIECG3, ARG1, TINAGRP	uc001bta.3	Q9GZM7	OTTHUMG00000003884	ENST00000271064.7:c.753G>A	1.37:g.32050533G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	202	3	0.0148515	NM_022164	A8K9Q5|B4DPK6|D3DPN8|Q8TEJ9|Q8WZ23|Q96GZ4|Q96JW3	Silent	SNP	ENST00000271064.7	37	CCDS343.1																																																																																			.	.	none		0.637	TINAGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011072.1	NM_022164	
ERAP2	64167	hgsc.bcm.edu	37	5	96249115	96249115	+	Silent	SNP	C	C	T	rs2255546	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96249115C>T	ENST00000437043.3	+	17	3322	c.2611C>T	c.(2611-2613)Cta>Tta	p.L871L	CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000379904.4_Silent_p.L826L	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	871					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		GGGGCAGCAACTAGCATGGGA	0.423													T|||	2768	0.552716	0.6021	0.5807	5008	,	,		17104	0.5258		0.5199	False		,,,				2504	0.5276				p.L871L		Atlas-SNP	.											.	ERAP2	77	.	0			c.C2611T						PASS	.	T	,	2556,1850	537.9+/-374.9	724,1108,371	69.0	65.0	66.0		2611,2611	-3.7	0.0	5	dbSNP_100	66	4488,4112	563.5+/-388.1	1154,2180,966	no	coding-synonymous,coding-synonymous	ERAP2	NM_001130140.1,NM_022350.3	,	1878,3288,1337	TT,TC,CC		47.814,41.9882,45.8404	,	871/961,871/961	96249115	7044,5962	2203	4300	6503	SO:0001819	synonymous_variant	64167	exon17			CAGCAACTAGCAT	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.2611C>T	5.37:g.96249115C>T		Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	277	134	0.483755	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Silent	SNP	ENST00000437043.3	37	CCDS4086.1	1210	0.5540293040293041	272	0.5528455284552846	213	0.5883977900552486	329	0.5751748251748252	396	0.5224274406332454	T	0.052	-1.247794	0.01469	0.580118	0.52186	ENSG00000164308	ENST00000512869	.	.	.	4.78	-3.71	0.04424	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53005	P	3.6000000000036E-5	.	.	.	.	.	.	T	0.36986	-0.9725	3	.	.	.	.	8.9931	0.36037	0.0:0.4507:0.1107:0.4387	rs2255546;rs3959887;rs17408795;rs58750029;rs2255546	.	.	.	I	25	.	.	T	+	2	0	ERAP2	96274871	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-0.599000	0.05700	-1.522000	0.01769	-2.697000	0.00138	ACT	C|0.452;T|0.548	0.548	strong		0.423	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242102	81242102	+	RNA	SNP	G	G	A	rs6420424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81242102G>A	ENST00000525539.1	-	0	753				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TCACCTTCCCGGCACTGGTAC	0.552													G|||	2832	0.565495	0.4629	0.5086	5008	,	,		21299	0.881		0.4632	False		,,,				2504	0.5245				p.R252W		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C754T						PASS	.	G	TRP/ARG,TRP/ARG	1858,2332		449,960,686	80.0	77.0	78.0	http://omim.org/entry/115300	754,754	2.0	0.6	16	dbSNP_116	78	3958,4490		918,2122,1184	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	101,101	1367,3082,1870	AA,AG,GG		46.8513,44.3437,46.0199	benign,benign	252/992,252/2460	81242102	5816,6822	2095	4224	6319			114780	exon4			CTTCCCGGCACTG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242102G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1278	0.5851648351648352	235	0.47764227642276424	180	0.4972375690607735	493	0.8618881118881119	370	0.48812664907651715	G	2.983	-0.209849	0.06140	0.443437	0.468513	ENSG00000166473	ENST00000337114	T	0.01397	4.94	4.11	2.0	0.26442	D-galactoside/L-rhamnose binding SUEL lectin domain (1);	2.014490	0.02501	N	0.090491	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.15930	0.015;0.013	B;B	0.08055	0.003;0.002	T	0.26916	-1.0089	8	0.48119	T	0.1	-0.1764	2.9711	0.05923	0.1018:0.1597:0.4865:0.252	rs6420424;rs61420732;rs6420424	252;252	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	W	252	ENSP00000337397:R252W	ENSP00000337397:R252W	R	-	1	2	PKD1L2	79799603	0.965000	0.33210	0.580000	0.28601	0.086000	0.17979	1.700000	0.37815	0.223000	0.20920	-1.598000	0.00824	CGG	G|0.437;A|0.563	0.563	strong		0.552	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
ROR2	4920	hgsc.bcm.edu	37	9	94538040	94538040	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:94538040G>A	ENST00000375708.3	-	2	356	c.158C>T	c.(157-159)cCg>cTg	p.P53L	ROR2_ENST00000375715.1_5'UTR|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	53					cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						AGTTGGAATCGGGCCGTCCTG	0.522											OREG0019308	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P53L		Atlas-SNP	.											ROR2,NS,carcinoma,0,1	ROR2	167	1	0			c.C158T						scavenged	.						84.0	70.0	75.0					9																	94538040		2203	4300	6503	SO:0001583	missense	4920	exon2			GGAATCGGGCCGT	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.158C>T	9.37:g.94538040G>A	ENSP00000364860:p.Pro53Leu	Somatic	79	1	0.0126582	1306	WXS	Illumina HiSeq	Phase_I	106	3	0.0283019	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	G	0.824	-0.747690	0.03065	.	.	ENSG00000169071	ENST00000375708	T	0.77229	-1.08	4.37	4.37	0.52481	.	0.000000	0.41938	D	0.000793	T	0.61073	0.2318	N	0.14661	0.345	0.51012	D	0.999906	B;B	0.06786	0.001;0.0	B;B	0.04013	0.0;0.001	T	0.56335	-0.7996	10	0.30078	T	0.28	.	12.705	0.57056	0.0:0.0:1.0:0.0	.	53;53	A1L4F5;Q01974	.;ROR2_HUMAN	L	53	ENSP00000364860:P53L	ENSP00000364860:P53L	P	-	2	0	ROR2	93577861	0.976000	0.34144	0.782000	0.31804	0.155000	0.21991	2.457000	0.45005	2.720000	0.93068	0.561000	0.74099	CCG	.	.	none		0.522	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
PSMC5	5705	hgsc.bcm.edu	37	17	61903445	61903445	+	5'Flank	SNP	G	G	C	rs2584625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:61903445G>C	ENST00000310144.6	+	0	0				PSMC5_ENST00000580864.1_5'Flank|PSMC5_ENST00000375812.4_5'Flank|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000581882.1_5'Flank|FTSJ3_ENST00000427159.2_Missense_Mutation_p.Q91E	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						GTGATGTCCTGCTGGAGAGTC	0.478													C|||	3670	0.732827	0.9796	0.6816	5008	,	,		20984	0.5556		0.5984	False		,,,				2504	0.7566				p.Q91E		Atlas-SNP	.											.	FTSJ3	63	.	0			c.C271G						PASS	.	C	GLU/GLN	4014,392	196.0+/-220.5	1829,356,18	143.0	145.0	145.0		271	4.7	1.0	17	dbSNP_100	145	5216,3384	501.5+/-375.5	1599,2018,683	yes	missense	FTSJ3	NM_017647.3	29	3428,2374,701	CC,CG,GG		39.3488,8.897,29.0328	benign	91/848	61903445	9230,3776	2203	4300	6503	SO:0001631	upstream_gene_variant	117246	exon5			TGTCCTGCTGGAG	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195			17.37:g.61903445G>C	Exception_encountered	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	131	71	0.541985	NM_017647	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	37	CCDS11645.1	1496	0.684981684981685	477	0.9695121951219512	230	0.6353591160220995	333	0.5821678321678322	456	0.6015831134564644	C	15.39	2.818139	0.50633	0.91103	0.606512	ENSG00000108592	ENST00000427159	T	0.28454	1.61	4.74	4.74	0.60224	Ribosomal RNA methyltransferase RrmJ/FtsJ (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00246	-1.78	0.49389	P	2.1099999999996122E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.40720	-0.9548	9	0.02654	T	1	-24.6385	13.1779	0.59637	0.0:0.8383:0.1617:0.0	rs2584625;rs3760246;rs17552334;rs52828289;rs57321735;rs2584625	91	Q8IY81	RRMJ3_HUMAN	E	91	ENSP00000396673:Q91E	ENSP00000396673:Q91E	Q	-	1	0	FTSJ3	59257177	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.111000	0.64628	1.367000	0.46095	-0.216000	0.12614	CAG	G|0.317;C|0.682	0.682	strong		0.478	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72503344	72503344	+	Silent	SNP	G	G	A	rs10999502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:72503344G>A	ENST00000373207.1	+	13	1965	c.1965G>A	c.(1963-1965)acG>acA	p.T655T	ADAMTS14_ENST00000373208.1_Silent_p.T658T	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	655	Cys-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CGGCGGACACGGGGGACGTGG	0.622													G|||	1560	0.311502	0.1641	0.2089	5008	,	,		19688	0.5387		0.2167	False		,,,				2504	0.4468				p.T658T		Atlas-SNP	.											ADAMTS14,NS,adenoma,0,1	ADAMTS14	148	1	0			c.G1974A						PASS	.	G	,	760,3646	308.0+/-290.3	51,658,1494	95.0	76.0	82.0		1965,1974	-10.0	0.4	10	dbSNP_120	82	1824,6776	328.1+/-318.2	192,1440,2668	no	coding-synonymous,coding-synonymous	ADAMTS14	NM_080722.3,NM_139155.2	,	243,2098,4162	AA,AG,GG		21.2093,17.2492,19.8678	,	655/1224,658/1227	72503344	2584,10422	2203	4300	6503	SO:0001819	synonymous_variant	140766	exon13			GGACACGGGGGAC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1965G>A	10.37:g.72503344G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	189	92	0.486772	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			G|0.768;A|0.232	0.232	strong		0.622	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
CCDC159	126075	hgsc.bcm.edu	37	19	11465316	11465316	+	Missense_Mutation	SNP	G	G	C	rs6887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11465316G>C	ENST00000588790.1	+	12	1280	c.833G>C	c.(832-834)tGt>tCt	p.C278S	DKFZP761J1410_ENST00000251473.5_5'Flank|DKFZP761J1410_ENST00000591608.1_5'Flank|CCDC159_ENST00000458408.1_Missense_Mutation_p.C278S			P0C7I6	CC159_HUMAN	coiled-coil domain containing 159	393										endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	5						GACTCCGACTGTGACCAGGAC	0.642													C|||	1886	0.376597	0.4486	0.3718	5008	,	,		15852	0.2788		0.4533	False		,,,				2504	0.3047				p.C278S		Atlas-SNP	.											.	CCDC159	35	.	0			c.G833C						PASS	.	C	SER/CYS	1954,2438		433,1088,675	32.0	39.0	36.0		833	0.3	0.0	19	dbSNP_52	36	3992,4592		955,2082,1255	yes	missense	CCDC159	NM_001080503.2	112	1388,3170,1930	CC,CG,GG		46.5051,44.49,45.8231	benign	278/298	11465316	5946,7030	2196	4292	6488	SO:0001583	missense	126075	exon10			CCGACTGTGACCA	BC038439	CCDS45976.1	19p13.2	2010-02-17			ENSG00000183401	ENSG00000183401			26996	protein-coding gene	gene with protein product							Standard	NM_001080503		Approved		uc010xlt.2	P0C7I6		ENST00000588790.1:c.833G>C	19.37:g.11465316G>C	ENSP00000468232:p.Cys278Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	102	60	0.588235	NM_001080503	B4DEG3|B4DWR8|B4E133|B7ZAM4	Missense_Mutation	SNP	ENST00000588790.1	37	CCDS45976.1	849	0.38873626373626374	219	0.4451219512195122	143	0.39502762430939226	143	0.25	344	0.45382585751978893	C	0.343	-0.949288	0.02304	0.4449	0.465051	ENSG00000183401	ENST00000458408;ENST00000427879	T	0.39406	1.08	4.13	0.299	0.15771	.	.	.	.	.	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47156	-0.9139	8	0.08381	T	0.77	4.0E-4	8.6764	0.34181	0.1452:0.2636:0.5912:0.0	rs6887;rs3167723;rs17702516;rs59712669;rs6887	393;278	P0C7I6;P0C7I6-2	CC159_HUMAN;.	S	278;393	ENSP00000402239:C278S	ENSP00000390400:C393S	C	+	2	0	CCDC159	11326316	0.001000	0.12720	0.000000	0.03702	0.069000	0.16628	-0.055000	0.11807	0.121000	0.18284	-0.322000	0.08575	TGT	G|0.619;C|0.381	0.381	strong		0.642	CCDC159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458761.1	NM_001080503	
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97922875	97922875	+	Silent	SNP	G	G	A	rs13008	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:97922875G>A	ENST00000005260.8	-	14	1709	c.1494C>T	c.(1492-1494)cgC>cgT	p.R498R		NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	498	Binds F-actin.				filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			TCACAGTCGGGCGGAGTTTCA	0.537													G|||	739	0.147564	0.0144	0.2637	5008	,	,		16327	0.001		0.4284	False		,,,				2504	0.1074				p.R498R		Atlas-SNP	.											.	BAIAP2L1	61	.	0			c.C1494T						PASS	.	G		433,3973	208.5+/-229.5	21,391,1791	129.0	127.0	128.0		1494	-4.7	0.0	7	dbSNP_52	128	4026,4574	556.9+/-386.9	945,2136,1219	no	coding-synonymous	BAIAP2L1	NM_018842.4		966,2527,3010	AA,AG,GG		46.814,9.8275,34.2842		498/512	97922875	4459,8547	2203	4300	6503	SO:0001819	synonymous_variant	55971	exon14			AGTCGGGCGGAGT	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.1494C>T	7.37:g.97922875G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	120	41	0.341667	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	37	CCDS34687.1																																																																																			G|0.717;A|0.283	0.283	strong		0.537	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842	
PITRM1	10531	hgsc.bcm.edu	37	10	3207632	3207632	+	Missense_Mutation	SNP	A	A	G	rs3814596	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:3207632A>G	ENST00000224949.4	-	5	540	c.506T>C	c.(505-507)tTc>tCc	p.F169S	PITRM1_ENST00000451104.2_Missense_Mutation_p.F137S|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.F169S			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	169			F -> S (in dbSNP:rs3814596). {ECO:0000269|PubMed:10360838}.		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TAAACATGGGAAAAAGGTGGC	0.383													A|||	667	0.133187	0.1407	0.1066	5008	,	,		18416	0.0526		0.1869	False		,,,				2504	0.1697				p.F169S		Atlas-SNP	.											PITRM1,colon,carcinoma,0,1	PITRM1	109	1	0			c.T506C						scavenged	.	A	SER/PHE,SER/PHE,SER/PHE	523,3215		49,425,1395	98.0	99.0	99.0		506,410,506	5.4	0.8	10	dbSNP_107	99	1599,6625		159,1281,2672	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	155,155,155	208,1706,4067	GG,GA,AA		19.4431,13.9914,17.7395	possibly-damaging,possibly-damaging,possibly-damaging	169/1039,137/940,169/1038	3207632	2122,9840	1869	4112	5981	SO:0001583	missense	10531	exon5			CATGGGAAAAAGG	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.506T>C	10.37:g.3207632A>G	ENSP00000224949:p.Phe169Ser	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	219	112	0.511416	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	274	0.12545787545787546	60	0.12195121951219512	42	0.11602209944751381	29	0.050699300699300696	143	0.18865435356200527	a	17.90	3.501492	0.64298	0.139914	0.194431	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.27104	1.69;1.69;1.69	5.37	5.37	0.77165	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	M	0.79693	2.465	0.09310	P	0.99999623526	B;B;P;P;P	0.41498	0.377;0.11;0.708;0.752;0.752	B;B;P;P;P	0.53760	0.146;0.215;0.615;0.734;0.734	T	0.01105	-1.1450	9	0.33141	T	0.24	.	15.4166	0.74974	1.0:0.0:0.0:0.0	rs3814596;rs52789691;rs57308152;rs3814596	162;137;169;169;169	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3	.;.;.;.;PREP_HUMAN	S	169;162;169;137	ENSP00000224949:F169S;ENSP00000370377:F169S;ENSP00000401201:F137S	ENSP00000224949:F169S	F	-	2	0	PITRM1	3197632	1.000000	0.71417	0.829000	0.32907	0.889000	0.51656	8.663000	0.91134	2.037000	0.60232	0.477000	0.44152	TTC	A|0.857;G|0.143	0.143	strong		0.383	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
RYR2	6262	hgsc.bcm.edu	37	1	237841390	237841390	+	Missense_Mutation	SNP	A	A	G	rs34967813	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:237841390A>G	ENST00000366574.2	+	61	9190	c.8873A>G	c.(8872-8874)cAa>cGa	p.Q2958R	RYR2_ENST00000609119.1_Intron|RYR2_ENST00000542537.1_Missense_Mutation_p.Q2942R|RYR2_ENST00000360064.6_Missense_Mutation_p.Q2956R	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2958			Q -> R (in dbSNP:rs34967813). {ECO:0000269|PubMed:11157710}.		BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CCTTATGAACAAGAAATCAAG	0.358													A|||	497	0.0992412	0.0113	0.1988	5008	,	,		19250	0.0		0.2942	False		,,,				2504	0.0491				p.Q2958R		Atlas-SNP	.											.	RYR2	1273	.	0			c.A8873G						PASS	.	A	ARG/GLN	199,3583		7,185,1699	109.0	106.0	107.0		8873	5.7	1.0	1	dbSNP_126	107	2499,5717		379,1741,1988	yes	missense	RYR2	NM_001035.2	43	386,1926,3687	GG,GA,AA		30.4163,5.2618,22.4871	possibly-damaging	2958/4968	237841390	2698,9300	1891	4108	5999	SO:0001583	missense	6262	exon61			ATGAACAAGAAAT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.8873A>G	1.37:g.237841390A>G	ENSP00000355533:p.Gln2958Arg	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	151	66	0.437086	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	313	0.1433150183150183	10	0.02032520325203252	77	0.212707182320442	0	0.0	226	0.29815303430079154	A	17.35	3.367905	0.61513	0.052618	0.304163	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;D;D	0.96745	-0.29;-4.08;-4.11	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000013	T	0.00039	0.0001	L	0.38649	1.16	0.09310	P	1.0	B	0.30605	0.287	B	0.20955	0.032	T	0.04708	-1.0932	9	0.21014	T	0.42	.	10.2872	0.43575	0.9266:0.0:0.0734:0.0	rs34967813	2958	Q92736	RYR2_HUMAN	R	2958;2956;2942	ENSP00000355533:Q2958R;ENSP00000353174:Q2956R;ENSP00000443798:Q2942R	ENSP00000353174:Q2956R	Q	+	2	0	RYR2	235908013	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.168000	0.77570	2.164000	0.68074	0.482000	0.46254	CAA	A|0.827;G|0.173	0.173	strong		0.358	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
ZC3H7A	29066	hgsc.bcm.edu	37	16	11852354	11852354	+	Silent	SNP	A	A	C	rs8743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:11852354A>C	ENST00000396516.2	-	19	2558	c.2361T>G	c.(2359-2361)gtT>gtG	p.V787V	ZC3H7A_ENST00000575984.1_5'UTR|ZC3H7A_ENST00000355758.4_Silent_p.V787V			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	787						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						AACAGTTTCCAACATATTGAC	0.363													A|||	2670	0.533147	0.6407	0.5504	5008	,	,		19419	0.5863		0.4085	False		,,,				2504	0.4489				p.V787V		Atlas-SNP	.											.	ZC3H7A	72	.	0			c.T2361G						PASS	.	A		2580,1814	637.4+/-396.7	741,1098,358	110.0	102.0	105.0		2361	5.7	1.0	16	dbSNP_52	105	3652,4948	522.7+/-380.2	784,2084,1432	no	coding-synonymous	ZC3H7A	NM_014153.3		1525,3182,1790	CC,CA,AA		42.4651,41.2836,47.9606		787/972	11852354	6232,6762	2197	4300	6497	SO:0001819	synonymous_variant	29066	exon20			GTTTCCAACATAT	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"""Zinc fingers, CCCH-type domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30959	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 7"", ""zinc finger CCCH-type containing 7"""	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.2361T>G	16.37:g.11852354A>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	NM_014153	D3DUG5|Q9NPE9	Silent	SNP	ENST00000396516.2	37	CCDS10550.1																																																																																			A|0.507;C|0.493	0.493	strong		0.363	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153	
COG6	57511	hgsc.bcm.edu	37	13	40229891	40229891	+	Missense_Mutation	SNP	G	G	A	rs3812882	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:40229891G>A	ENST00000455146.3	+	1	78	c.28G>A	c.(28-30)Gca>Aca	p.A10T	COG6_ENST00000416691.1_Missense_Mutation_p.A10T	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	10			A -> T (in dbSNP:rs3812882). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.6}.		glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		GGAAGTGGTCGCAGTGTCTGC	0.687													G|||	2426	0.484425	0.5008	0.5879	5008	,	,		13338	0.4573		0.3777	False		,,,				2504	0.5266				p.A10T		Atlas-SNP	.											.	COG6	49	.	0			c.G28A						PASS	.	G	THR/ALA,THR/ALA	2156,2206		575,1006,600	13.0	14.0	14.0		28,28	2.7	0.0	13	dbSNP_107	14	3484,5028		840,1804,1612	yes	missense,missense	COG6	NM_001145079.1,NM_020751.2	58,58	1415,2810,2212	AA,AG,GG		40.9305,49.4269,43.8092	possibly-damaging,possibly-damaging	10/616,10/658	40229891	5640,7234	2181	4256	6437	SO:0001583	missense	57511	exon1			GTGGTCGCAGTGT	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"""Components of oligomeric golgi complex"""	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.28G>A	13.37:g.40229891G>A	ENSP00000397441:p.Ala10Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	36	34	0.944444	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	37	CCDS9370.1	1021	0.4674908424908425	253	0.5142276422764228	211	0.5828729281767956	262	0.458041958041958	295	0.3891820580474934	G	27.1	4.802264	0.90538	0.494269	0.409305	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000422759;ENST00000455146	T;T;T	0.38077	1.16;1.17;1.18	5.52	2.68	0.31781	.	0.801127	0.11428	N	0.565084	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B;B	0.10296	0.003;0.003	B;B	0.04013	0.001;0.001	T	0.43686	-0.9376	9	0.23891	T	0.37	-20.1481	4.4269	0.11507	0.0858:0.1523:0.6047:0.1571	rs3812882;rs58038583;rs3812882	31;10	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	T	10;41;10;10	ENSP00000403733:A10T;ENSP00000412877:A10T;ENSP00000397441:A10T	ENSP00000255468:A41T	A	+	1	0	COG6	39127891	0.000000	0.05858	0.003000	0.11579	0.521000	0.34408	-0.010000	0.12743	0.621000	0.30232	0.561000	0.74099	GCA	G|0.525;A|0.475	0.475	strong		0.687	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3		
PRRT3	285368	hgsc.bcm.edu	37	3	9991101	9991101	+	Missense_Mutation	SNP	C	C	G	rs55847233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9991101C>G	ENST00000412055.1	-	2	828	c.699G>C	c.(697-699)ttG>ttC	p.L233F	PRRT3_ENST00000411976.2_Missense_Mutation_p.L233F|PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	233			L -> F (in dbSNP:rs55847233). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						CTGCCTCCTGCAAGTGTTCCT	0.602													G|||	1915	0.382388	0.8154	0.3271	5008	,	,		19213	0.1558		0.2147	False		,,,				2504	0.2423				p.L233F		Atlas-SNP	.											.	PRRT3	35	.	0			c.G699C						PASS	.	G	PHE/LEU	2991,1367		1061,869,249	47.0	57.0	54.0		699	1.9	0.8	3	dbSNP_129	54	2095,6471		271,1553,2459	yes	missense	PRRT3	NM_207351.3	22	1332,2422,2708	GG,GC,CC		24.4572,31.3676,39.3531	benign	233/982	9991101	5086,7838	2179	4283	6462	SO:0001583	missense	285368	exon2			CTCCTGCAAGTGT	AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"""Proline-rich transmembrane proteins"""	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.699G>C	3.37:g.9991101C>G	ENSP00000392511:p.Leu233Phe	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	69	27	0.391304	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Missense_Mutation	SNP	ENST00000412055.1	37	CCDS43049.1	806	0.36904761904761907	398	0.8089430894308943	124	0.3425414364640884	118	0.2062937062937063	166	0.21899736147757257	G	0.003	-2.526495	0.00147	0.686324	0.244572	ENSG00000163704	ENST00000412055;ENST00000411976	T;T	0.17691	2.56;2.26	3.73	1.9	0.25705	.	0.446559	0.19299	N	0.117687	T	0.00012	0.0000	N	0.03050	-0.425	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.10823	-1.0613	8	.	.	.	-4.8059	6.9449	0.24512	0.0:0.366:0.4455:0.1885	rs55847233;rs61441802;rs62245483	233;233	Q5FWE3-3;Q5FWE3	.;PRRT3_HUMAN	F	233	ENSP00000392511:L233F;ENSP00000404512:L233F	.	L	-	3	2	PRRT3	9966101	0.897000	0.30589	0.796000	0.32109	0.027000	0.11550	0.979000	0.29500	0.191000	0.20236	-0.127000	0.14921	TTG	C|0.673;G|0.327	0.327	strong		0.602	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351	
CABP5	56344	hgsc.bcm.edu	37	19	48537585	48537585	+	Missense_Mutation	SNP	A	A	G	rs3745746	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48537585A>G	ENST00000293255.2	-	5	513	c.383T>C	c.(382-384)gTg>gCg	p.V128A		NM_019855.4	NP_062829.1	Q9NP86	CABP5_HUMAN	calcium binding protein 5	128	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.		V -> A (in dbSNP:rs3745746).		signal transduction (GO:0007165)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	11		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)		CTGTAGCTCCACCAGGGTGAT	0.522													g|||	1113	0.222244	0.1399	0.281	5008	,	,		16208	0.0645		0.3569	False		,,,				2504	0.316				p.V128A		Atlas-SNP	.											.	CABP5	28	.	0			c.T383C						PASS	.	G	ALA/VAL	756,3650	754.6+/-412.5	68,620,1515	59.0	56.0	57.0		383	-5.2	0.3	19	dbSNP_107	57	3333,5267	644.2+/-400.0	647,2039,1614	yes	missense	CABP5	NM_019855.4	64	715,2659,3129	GG,GA,AA		38.7558,17.1584,31.4393	benign	128/174	48537585	4089,8917	2203	4300	6503	SO:0001583	missense	56344	exon5			AGCTCCACCAGGG	AF169159	CCDS12709.1	19q13.33	2014-08-12			ENSG00000105507	ENSG00000105507		"""EF-hand domain containing"""	13714	protein-coding gene	gene with protein product		607315	"""calcium binding protein 3"""	CABP3		10625670	Standard	NM_019855		Approved	CaBP3	uc002phu.2	Q9NP86	OTTHUMG00000183139	ENST00000293255.2:c.383T>C	19.37:g.48537585A>G	ENSP00000293255:p.Val128Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	97	36	0.371134	NM_019855	A0AUY4	Missense_Mutation	SNP	ENST00000293255.2	37	CCDS12709.1	508	0.2326007326007326	70	0.14227642276422764	120	0.3314917127071823	52	0.09090909090909091	266	0.35092348284960423	G	0.023	-1.402989	0.01165	0.171584	0.387558	ENSG00000105507	ENST00000293255	T	0.68765	-0.35	5.01	-5.16	0.02857	EF-hand-like domain (1);	0.442432	0.23732	N	0.045101	T	0.00012	0.0000	N	0.00300	-1.685	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.17258	-1.0375	9	0.02654	T	1	-9.6053	8.8389	0.35129	0.3967:0.2939:0.3094:0.0	rs3745746;rs17663756;rs52805288;rs60664550;rs3745746	128	Q9NP86	CABP5_HUMAN	A	128	ENSP00000293255:V128A	ENSP00000293255:V128A	V	-	2	0	CABP5	53229397	0.000000	0.05858	0.314000	0.25224	0.351000	0.29236	-2.822000	0.00748	-0.593000	0.05844	-0.930000	0.02707	GTG	G|0.275;N|0.000	0.275	strong		0.522	CABP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465212.1	NM_019855	
TEAD2	8463	hgsc.bcm.edu	37	19	49862722	49862722	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49862722C>T	ENST00000311227.2	-	3	357	c.267G>A	c.(265-267)ctG>ctA	p.L89L	TEAD2_ENST00000598397.1_5'Flank|AC010524.4_ENST00000596488.1_RNA|TEAD2_ENST00000377214.4_Silent_p.L89L|DKKL1_ENST00000594268.1_5'Flank|TEAD2_ENST00000598810.1_Silent_p.L89L|TEAD2_ENST00000601519.1_Silent_p.L89L|TEAD2_ENST00000593945.1_Silent_p.L89L|TEAD2_ENST00000539846.1_5'UTR	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	89					gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		TCCCCGTTCTCAGCTTGATGT	0.522																																					p.L89L		Atlas-SNP	.											.	TEAD2	70	.	0			c.G267A						PASS	.						254.0	214.0	228.0					19																	49862722		2203	4300	6503	SO:0001819	synonymous_variant	8463	exon3			CGTTCTCAGCTTG	X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.267G>A	19.37:g.49862722C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	197	86	0.436548	NM_001256658	B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Silent	SNP	ENST00000311227.2	37	CCDS12761.1																																																																																			.	.	none		0.522	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465465.1	NM_003598	
CCDC60	160777	hgsc.bcm.edu	37	12	119916900	119916900	+	Splice_Site	SNP	A	A	G	rs2519540	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:119916900A>G	ENST00000327554.2	+	4	808	c.343A>G	c.(343-345)Aca>Gca	p.T115A	RP11-768F21.1_ENST00000509470.2_lincRNA|CCDC60_ENST00000546345.1_3'UTR	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	115			T -> A (in dbSNP:rs2519540).							endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		GTCCTTCAGCACATATGATGA	0.488													A|||	269	0.0537141	0.0159	0.0965	5008	,	,		20974	0.0		0.164	False		,,,				2504	0.0164				p.T115A		Atlas-SNP	.											.	CCDC60	84	.	0			c.A343G						PASS	.	A	ALA/THR	134,4272	97.1+/-135.8	2,130,2071	167.0	129.0	142.0		343	-1.0	0.0	12	dbSNP_100	142	1377,7223	267.1+/-287.1	126,1125,3049	yes	missense-near-splice	CCDC60	NM_178499.3	58	128,1255,5120	GG,GA,AA		16.0116,3.0413,11.6177	probably-damaging	115/551	119916900	1511,11495	2203	4300	6503	SO:0001630	splice_region_variant	160777	exon4			TTCAGCACATATG	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.342-1A>G	12.37:g.119916900A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	39	13	0.333333	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	183	0.08379120879120878	15	0.03048780487804878	38	0.10497237569060773	0	0.0	130	0.17150395778364116	A	9.951	1.220027	0.22373	0.030413	0.160116	ENSG00000183273	ENST00000327554	T	0.22945	1.93	4.44	-0.979	0.10276	.	0.373833	0.22507	N	0.059159	T	0.00073	0.0002	M	0.72118	2.19	0.80722	P	0.0	B	0.14438	0.01	B	0.13407	0.009	T	0.10245	-1.0638	8	.	.	.	-8.2784	3.9529	0.09377	0.5034:0.1866:0.3099:0.0	rs2519540;rs17482695;rs52797827;rs57050119;rs2519540	115	Q8IWA6	CCD60_HUMAN	A	115	ENSP00000333374:T115A	.	T	+	1	0	CCDC60	118401283	0.000000	0.05858	0.012000	0.15200	0.135000	0.20990	-0.272000	0.08560	0.024000	0.15214	0.528000	0.53228	ACA	A|0.905;G|0.095	0.095	strong		0.488	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	Missense_Mutation
FAM160B2	64760	hgsc.bcm.edu	37	8	21954017	21954017	+	Silent	SNP	C	C	T	rs117838157|rs577506980	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21954017C>T	ENST00000289921.7	+	3	340	c.294C>T	c.(292-294)gcC>gcT	p.A98A		NM_022749.5	NP_073586.5	Q86V87	F16B2_HUMAN	family with sequence similarity 160, member B2	98										endometrium(2)|kidney(1)|lung(2)|prostate(3)|urinary_tract(1)	9						TGGGCAAGGCCGAGGTGGGAG	0.716													c|||	50	0.00998403	0.0219	0.0072	5008	,	,		14888	0.0		0.0139	False		,,,				2504	0.002				p.A98A		Atlas-SNP	.											.	FAM160B2	35	.	0			c.C294T						PASS	.	T		95,3757		2,91,1833	13.0	16.0	15.0		294	-10.0	0.0	8	dbSNP_132	15	87,7943		1,85,3929	no	coding-synonymous	FAM160B2	NM_022749.5		3,176,5762	TT,TC,CC		1.0834,2.4663,1.5317		98/744	21954017	182,11700	1926	4015	5941	SO:0001819	synonymous_variant	64760	exon3			CAAGGCCGAGGTG	AK025454	CCDS6021.2	8p21.3	2012-11-30	2008-06-05	2008-06-05	ENSG00000158863	ENSG00000158863			16492	protein-coding gene	gene with protein product			"""retinoic acid induced 16"""	RAI16		22971576, 15626329	Standard	XR_247128		Approved	FLJ21801	uc011kyx.2	Q86V87	OTTHUMG00000097088	ENST00000289921.7:c.294C>T	8.37:g.21954017C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	48	0.648649	NM_022749	B2RDQ5|B3KNX1|Q2M211|Q71JB5|Q7L3J6|Q969T0|Q9H6W4	Silent	SNP	ENST00000289921.7	37	CCDS6021.2																																																																																			C|0.990;T|0.010	0.010	strong		0.716	FAM160B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375334.2		
PGM3	5238	hgsc.bcm.edu	37	6	83881740	83881740	+	Silent	SNP	T	T	C	rs542948	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:83881740T>C	ENST00000283977.4	-	10	1164	c.1038A>G	c.(1036-1038)gaA>gaG	p.E346E	PGM3_ENST00000513973.1_Silent_p.E427E|PGM3_ENST00000512866.1_Silent_p.E427E|PGM3_ENST00000506587.1_Silent_p.E455E					phosphoglucomutase 3											NS(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	18		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)		CCAAGATTGCTTCAATCACCA	0.423													C|||	1795	0.358427	0.5976	0.2795	5008	,	,		19708	0.2897		0.2962	False		,,,				2504	0.226				p.E455E		Atlas-SNP	.											.	PGM3	39	.	0			c.A1365G						PASS	.	C	,,,	2445,1961	553.2+/-378.7	666,1113,424	131.0	115.0	120.0		1365,1038,1281,1281	1.7	1.0	6	dbSNP_83	120	2181,6419	712.2+/-405.9	288,1605,2407	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PGM3	NM_001199917.1,NM_001199918.1,NM_001199919.1,NM_015599.2	,,,	954,2718,2831	CC,CT,TT		25.3605,44.5075,35.5682	,,,	455/571,346/442,427/567,427/543	83881740	4626,8380	2203	4300	6503	SO:0001819	synonymous_variant	5238	exon12			GATTGCTTCAATC	BC001258	CCDS4997.1, CCDS56435.1, CCDS56436.1, CCDS75487.1	6q14.1-q15	2012-10-02			ENSG00000013375	ENSG00000013375	5.4.2.3		8907	protein-coding gene	gene with protein product	"""acetylglucosamine phosphomutase"""	172100				12174217, 10721701	Standard	NM_001199917		Approved	AGM1, DKFZP434B187, PAGM	uc011dyz.2	O95394	OTTHUMG00000015110	ENST00000283977.4:c.1038A>G	6.37:g.83881740T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_001199917		Silent	SNP	ENST00000283977.4	37																																																																																				T|0.636;G|0.002	.	strong		0.423	PGM3-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000366385.2	NM_015599	
C5orf60	285679	hgsc.bcm.edu	37	5	179071947	179071947	+	Silent	SNP	A	A	G	rs4645306	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:179071947A>G	ENST00000448248.2	-	1	100	c.75T>C	c.(73-75)atT>atC	p.I25I	C5orf60_ENST00000506142.1_5'UTR	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	25						integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						GCTCTGTACCAATAACACTGT	0.517																																					p.I25I		Atlas-SNP	.											.	C5orf60	24	.	0			c.T75C						PASS	.						72.0	71.0	71.0					5																	179071947		692	1591	2283	SO:0001819	synonymous_variant	285679	exon1			TGTACCAATAACA	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.75T>C	5.37:g.179071947A>G		Somatic	271	1	0.00369004		WXS	Illumina HiSeq	Phase_I	357	169	0.473389	NM_001142306	A1L488|B7ZM52|B7ZM53	Silent	SNP	ENST00000448248.2	37	CCDS47353.1																																																																																			A|0.743;G|0.257	0.257	strong		0.517	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
RPP40	10799	hgsc.bcm.edu	37	6	4998963	4998963	+	Silent	SNP	A	A	G	rs1749144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:4998963A>G	ENST00000380051.2	-	5	590	c.546T>C	c.(544-546)gcT>gcC	p.A182A	RPP40_ENST00000319533.5_Silent_p.A159A|RPP40_ENST00000464646.1_Silent_p.A122A	NM_006638.2	NP_006629.2	O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	182					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			NS(1)|breast(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	14	Ovarian(93;0.11)	all_hematologic(90;0.0895)				TTTTATGCCAAGCCAAAAGAA	0.294													A|||	1714	0.342252	0.5242	0.3156	5008	,	,		15043	0.1677		0.2773	False		,,,				2504	0.362				p.A182A		Atlas-SNP	.											.	RPP40	36	.	0			c.T546C						PASS	.	A		2085,2287		535,1015,636	39.0	41.0	41.0		546	0.4	1.0	6	dbSNP_89	41	2264,6292		313,1638,2327	no	coding-synonymous	RPP40	NM_006638.2		848,2653,2963	GG,GA,AA		26.461,47.6898,33.6402		182/364	4998963	4349,8579	2186	4278	6464	SO:0001819	synonymous_variant	10799	exon5			ATGCCAAGCCAAA	U94317	CCDS34333.1, CCDS69040.1, CCDS75391.1	6p25.1	2012-05-21	2007-06-26	2004-03-19	ENSG00000124787	ENSG00000124787			20992	protein-coding gene	gene with protein product		606117	"""ribonuclease P1"", ""ribonuclease P 40kDa subunit"""	RNASEP1		9630247	Standard	NM_006638		Approved	bA428J1.3	uc003mwl.3	O75818	OTTHUMG00000014168	ENST00000380051.2:c.546T>C	6.37:g.4998963A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	159	81	0.509434	NM_006638	Q5VX97|Q8WVK8	Silent	SNP	ENST00000380051.2	37	CCDS34333.1																																																																																			A|0.671;G|0.329	0.329	strong		0.294	RPP40-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039733.2	NM_006638	
OR51Q1	390061	hgsc.bcm.edu	37	11	5444061	5444061	+	Missense_Mutation	SNP	G	G	A	rs2736586	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5444061G>A	ENST00000300778.4	+	1	721	c.631G>A	c.(631-633)Gtg>Atg	p.V211M	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	211			V -> M (in dbSNP:rs2736586).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATTATTATCGTGGATCCTCT	0.498													A|||	2272	0.453674	0.2799	0.3991	5008	,	,		22644	0.7024		0.3986	False		,,,				2504	0.5276				p.V211M		Atlas-SNP	.											.	OR51Q1	79	.	0			c.G631A						PASS	.	A	MET/VAL	1332,3070	694.1+/-405.8	203,926,1072	176.0	150.0	159.0		631	-6.4	0.0	11	dbSNP_100	159	3373,5221	641.9+/-399.7	676,2021,1600	yes	missense	OR51Q1	NM_001004757.2	21	879,2947,2672	AA,AG,GG		39.2483,30.259,36.2034	benign	211/318	5444061	4705,8291	2201	4297	6498	SO:0001583	missense	390061	exon1			ATTATCGTGGATC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.631G>A	11.37:g.5444061G>A	ENSP00000300778:p.Val211Met	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	304	152	0.5	NM_001004757	B2RNN1	Missense_Mutation	SNP	ENST00000300778.4	37	CCDS31381.1	966	0.4423076923076923	139	0.28252032520325204	148	0.4088397790055249	395	0.6905594405594405	284	0.37467018469656993	A	1.024	-0.684014	0.03353	0.30259	0.392483	ENSG00000167360	ENST00000300778	T	0.40225	1.04	5.0	-6.36	0.01969	GPCR, rhodopsin-like superfamily (1);	0.797893	0.10688	N	0.645565	T	0.00012	0.0000	N	0.16066	0.365	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.41893	-0.9483	9	0.34782	T	0.22	.	2.3076	0.04178	0.162:0.4157:0.2302:0.1921	rs2736586;rs17359689;rs56459839;rs60685018;rs2736586	211	Q8NH59	O51Q1_HUMAN	M	211	ENSP00000300778:V211M	ENSP00000300778:V211M	V	+	1	0	OR51Q1	5400637	0.000000	0.05858	0.034000	0.17996	0.033000	0.12548	-3.921000	0.00334	-1.154000	0.02825	-1.540000	0.00911	GTG	G|0.599;A|0.401	0.401	strong		0.498	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
CATSPER1	117144	hgsc.bcm.edu	37	11	65787666	65787666	+	Silent	SNP	G	G	A	rs34769321|rs3829937	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65787666G>A	ENST00000312106.5	-	9	2207	c.2070C>T	c.(2068-2070)gcC>gcT	p.A690A		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	690					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						GGATCCGGGCGGCCCTCTGGG	0.662													G|||	814	0.16254	0.2065	0.1254	5008	,	,		15119	0.1181		0.16	False		,,,				2504	0.1779				p.A690A		Atlas-SNP	.											.	CATSPER1	101	.	0			c.C2070T						PASS	.	G		904,3498	344.9+/-308.3	95,714,1392	43.0	45.0	44.0		2070	-9.2	0.0	11	dbSNP_107	44	1331,7261	257.5+/-281.5	102,1127,3067	no	coding-synonymous	CATSPER1	NM_053054.3		197,1841,4459	AA,AG,GG		15.4912,20.5361,17.2002		690/781	65787666	2235,10759	2201	4296	6497	SO:0001819	synonymous_variant	117144	exon9			CCGGGCGGCCCTC	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.2070C>T	11.37:g.65787666G>A		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	135	134	0.992593	NM_053054	Q96P76	Silent	SNP	ENST00000312106.5	37	CCDS8127.1																																																																																			G|0.834;A|0.166	0.166	strong		0.662	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
GUCY2D	3000	hgsc.bcm.edu	37	17	7915920	7915920	+	Silent	SNP	G	G	A	rs56130505	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7915920G>A	ENST00000254854.4	+	10	2259	c.2109G>A	c.(2107-2109)gcG>gcA	p.A703A		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	703	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				CTCCCAGAGCGGAGGGTAAGA	0.592													G|||	404	0.0806709	0.1914	0.0519	5008	,	,		15383	0.002		0.0815	False		,,,				2504	0.0317				p.A703A		Atlas-SNP	.											.	GUCY2D	82	.	0			c.G2109A						PASS	.	G		829,3577	324.0+/-298.4	85,659,1459	53.0	53.0	53.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2109	-10.7	0.0	17	dbSNP_129	53	839,7761	191.3+/-237.5	43,753,3504	no	coding-synonymous	GUCY2D	NM_000180.3		128,1412,4963	AA,AG,GG		9.7558,18.8153,12.8249		703/1104	7915920	1668,11338	2203	4300	6503	SO:0001819	synonymous_variant	3000	exon10			CAGAGCGGAGGGT	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"""cone rod dystrophy 6"""	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.2109G>A	17.37:g.7915920G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_000180	Q6LEA7	Silent	SNP	ENST00000254854.4	37	CCDS11127.1																																																																																			G|0.888;A|0.112	0.112	strong		0.592	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
ALPP	250	hgsc.bcm.edu	37	2	233244930	233244930	+	Missense_Mutation	SNP	G	G	C	rs1048988	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233244930G>C	ENST00000392027.2	+	6	961	c.692G>C	c.(691-693)cGc>cCc	p.R231P	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	231			R -> P (in dbSNP:rs1048988). {ECO:0000269|PubMed:3512548}.		dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		TACATGTTTCGCATGGGAACC	0.617													C|||	704	0.140575	0.0393	0.183	5008	,	,		17811	0.0327		0.2952	False		,,,				2504	0.1994				p.R231P		Atlas-SNP	.											.	ALPP	53	.	0			c.G692C						PASS	.	G	PRO/ARG	288,4118		13,262,1928	120.0	101.0	107.0		692	0.3	0.2	2	dbSNP_86	107	2180,6414		313,1554,2430	no	missense	ALPP	NM_001632.3	103	326,1816,4358	CC,CG,GG		25.3665,6.5365,18.9846	benign	231/536	233244930	2468,10532	2203	4297	6500	SO:0001583	missense	250	exon6			TGTTTCGCATGGG	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.692G>C	2.37:g.233244930G>C	ENSP00000375881:p.Arg231Pro	Somatic	437	0	0		WXS	Illumina HiSeq	Phase_I	451	21	0.0465632	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	315	0.14423076923076922	37	0.07520325203252033	71	0.19613259668508287	31	0.05419580419580419	176	0.23218997361477572	.	0.004	-2.332974	0.00227	0.065365	0.253665	ENSG00000163283	ENST00000392027	D	0.94723	-3.5	2.31	0.318	0.15867	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.107337	0.64402	N	0.000004	T	0.00039	0.0001	N	0.00001	-3.68	0.38425	P	0.05372900000000003	B	0.02656	0.0	B	0.01281	0.0	T	0.58165	-0.7684	9	0.02654	T	1	.	12.9635	0.58472	0.0:0.8242:0.1758:0.0	rs1048988;rs2678510;rs3189061;rs17412784;rs1048988	231	P05187	PPB1_HUMAN	P	231	ENSP00000375881:R231P	ENSP00000375881:R231P	R	+	2	0	ALPP	232953174	0.991000	0.36638	0.168000	0.22838	0.172000	0.22775	3.488000	0.53229	-0.072000	0.12864	-0.735000	0.03563	CGC	G|0.823;C|0.177	0.177	strong		0.617	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
SPARCL1	8404	hgsc.bcm.edu	37	4	88415636	88415636	+	Missense_Mutation	SNP	G	G	C	rs1049544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:88415636G>C	ENST00000282470.6	-	4	786	c.316C>G	c.(316-318)Cac>Gac	p.H106D	SPARCL1_ENST00000503414.1_5'UTR|SPARCL1_ENST00000418378.1_Missense_Mutation_p.H106D	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	106			H -> D (in dbSNP:rs1049544). {ECO:0000269|PubMed:7600298}.		signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.H106D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		ACACTTAAGTGACCATCACTG	0.428													C|||	2883	0.575679	0.8828	0.5043	5008	,	,		19259	0.4375		0.3787	False		,,,				2504	0.5562				p.H106D		Atlas-SNP	.											SPARCL1,NS,carcinoma,0,1	SPARCL1	59	1	1	Substitution - Missense(1)	stomach(1)	c.C316G						PASS	.	C	ASP/HIS,ASP/HIS	3557,849	333.3+/-302.9	1435,687,81	146.0	137.0	140.0		316,316	4.2	0.0	4	dbSNP_86	140	3197,5403	652.8+/-401.0	601,1995,1704	yes	missense,missense	SPARCL1	NM_001128310.1,NM_004684.4	81,81	2036,2682,1785	CC,CG,GG		37.1744,19.2692,48.0701	benign,benign	106/665,106/665	88415636	6754,6252	2203	4300	6503	SO:0001583	missense	8404	exon4			TTAAGTGACCATC	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.316C>G	4.37:g.88415636G>C	ENSP00000282470:p.His106Asp	Somatic	327	1	0.0030581		WXS	Illumina HiSeq	Phase_I	282	130	0.460993	NM_004684	B4E2Z0|E7ESU2|Q14800	Missense_Mutation	SNP	ENST00000282470.6	37	CCDS3622.1	1128	0.5164835164835165	433	0.8800813008130082	189	0.5220994475138122	231	0.40384615384615385	275	0.3627968337730871	C	0.004	-2.345033	0.00222	0.807308	0.371744	ENSG00000152583	ENST00000282470;ENST00000418378;ENST00000509407;ENST00000434434;ENST00000535835;ENST00000512317	T;T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05;1.05	5.1	4.25	0.50352	.	0.302477	0.31760	N	0.007107	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39333	-0.9619	9	0.02654	T	1	-9.5256	7.9807	0.30181	0.0:0.7512:0.1608:0.088	rs1049544;rs3189722;rs3763393;rs17846057;rs17859050;rs52829980;rs59760974;rs1049544	106	Q14515	SPRL1_HUMAN	D	106	ENSP00000282470:H106D;ENSP00000414856:H106D;ENSP00000423483:H106D;ENSP00000416971:H106D;ENSP00000438188:H106D;ENSP00000423448:H106D	ENSP00000282470:H106D	H	-	1	0	SPARCL1	88634660	0.001000	0.12720	0.015000	0.15790	0.002000	0.02628	0.940000	0.28992	0.820000	0.34516	-0.120000	0.15030	CAC	G|0.488;C|0.512	0.512	strong		0.428	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		
LMLN	89782	hgsc.bcm.edu	37	3	197712759	197712759	+	Silent	SNP	T	T	C	rs7373242	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:197712759T>C	ENST00000330198.4	+	8	949	c.927T>C	c.(925-927)taT>taC	p.Y309Y	LMLN_ENST00000420910.2_Silent_p.Y309Y|LMLN_ENST00000482695.1_Silent_p.Y257Y|LMLN_ENST00000332636.5_Silent_p.Y257Y	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	309					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		CTTTTAATTATAGGTATTTTT	0.378													T|||	1052	0.210064	0.5204	0.1023	5008	,	,		17831	0.0109		0.1173	False		,,,				2504	0.1677				p.Y309Y		Atlas-SNP	.											.	LMLN	53	.	0			c.T927C						PASS	.	T	,	1994,2412	558.9+/-380.1	448,1098,657	75.0	73.0	73.0		927,927	-1.2	1.0	3	dbSNP_116	73	947,7653	207.3+/-249.1	38,871,3391	no	coding-synonymous,coding-synonymous	LMLN	NM_001136049.2,NM_033029.3	,	486,1969,4048	CC,CT,TT		11.0116,45.2565,22.6126	,	309/693,309/656	197712759	2941,10065	2203	4300	6503	SO:0001819	synonymous_variant	89782	exon8			TAATTATAGGTAT	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.927T>C	3.37:g.197712759T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_001136049	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Silent	SNP	ENST00000330198.4	37	CCDS3332.1																																																																																			T|0.785;C|0.215	0.215	strong		0.378	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029	
GAB1	2549	hgsc.bcm.edu	37	4	144359490	144359490	+	Missense_Mutation	SNP	C	C	T	rs28925904	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:144359490C>T	ENST00000262994.4	+	4	1234	c.932C>T	c.(931-933)cCa>cTa	p.P311L	GAB1_ENST00000505913.1_Missense_Mutation_p.P208L|GAB1_ENST00000262995.4_Missense_Mutation_p.P311L	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	311			P -> L (in dbSNP:rs28925904). {ECO:0000269|Ref.2}.		activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					GACATTCCTCCAACACCTGGT	0.423													C|||	39	0.00778754	0.0	0.0173	5008	,	,		15521	0.0		0.0249	False		,,,				2504	0.002				p.P311L		Atlas-SNP	.											.	GAB1	80	.	0			c.C932T						PASS	.	C	LEU/PRO,LEU/PRO	20,4386	28.1+/-56.4	0,20,2183	96.0	87.0	90.0		932,932	5.8	1.0	4	dbSNP_125	90	175,8425	80.4+/-143.0	0,175,4125	yes	missense,missense	GAB1	NM_002039.3,NM_207123.2	98,98	0,195,6308	TT,TC,CC		2.0349,0.4539,1.4993	probably-damaging,probably-damaging	311/695,311/725	144359490	195,12811	2203	4300	6503	SO:0001583	missense	2549	exon4			TTCCTCCAACACC	U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"""Pleckstrin homology (PH) domain containing"""	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.932C>T	4.37:g.144359490C>T	ENSP00000262994:p.Pro311Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_207123	A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	ENST00000262994.4	37	CCDS3759.1	23	0.010531135531135532	0	0.0	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	33	5.225676	0.95173	0.004539	0.020349	ENSG00000109458	ENST00000262995;ENST00000262994;ENST00000505913	T;T;T	0.42131	0.98;0.98;0.98	5.8	5.8	0.92144	.	0.048415	0.85682	D	0.000000	T	0.35653	0.0939	M	0.65975	2.015	0.80722	D	1	P;P	0.52577	0.954;0.947	B;P	0.46320	0.439;0.512	T	0.48570	-0.9024	10	0.59425	D	0.04	1.2408	20.063	0.97692	0.0:1.0:0.0:0.0	rs28925904;rs28925904	311;311	Q13480;Q13480-2	GAB1_HUMAN;.	L	311;311;208	ENSP00000262995:P311L;ENSP00000262994:P311L;ENSP00000424554:P208L	ENSP00000262994:P311L	P	+	2	0	GAB1	144578940	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.564000	0.67359	2.735000	0.93741	0.655000	0.94253	CCA	C|0.986;T|0.014	0.014	strong		0.423	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039	
DOPEY1	23033	hgsc.bcm.edu	37	6	83838673	83838673	+	Missense_Mutation	SNP	G	G	A	rs4706980	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:83838673G>A	ENST00000349129.2	+	16	2047	c.1787G>A	c.(1786-1788)cGa>cAa	p.R596Q	DOPEY1_ENST00000237163.5_Missense_Mutation_p.R577Q|DOPEY1_ENST00000369739.3_Missense_Mutation_p.R587Q	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	596			R -> Q (in dbSNP:rs4706980).		protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CCAAGTAGTCGATCATCAGAG	0.413													G|||	436	0.0870607	0.003	0.0893	5008	,	,		20778	0.1468		0.1431	False		,,,				2504	0.0798				p.R596Q		Atlas-SNP	.											.	DOPEY1	190	.	0			c.G1787A						PASS	.	G	GLN/ARG,GLN/ARG	105,4301	81.4+/-119.9	2,101,2100	90.0	92.0	91.0		1760,1787	3.8	1.0	6	dbSNP_111	91	1059,7541	224.3+/-260.7	76,907,3317	yes	missense,missense	DOPEY1	NM_001199942.1,NM_015018.3	43,43	78,1008,5417	AA,AG,GG		12.314,2.3831,8.9497	probably-damaging,probably-damaging	587/2477,596/2466	83838673	1164,11842	2203	4300	6503	SO:0001583	missense	23033	exon16			GTAGTCGATCATC	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.1787G>A	6.37:g.83838673G>A	ENSP00000195654:p.Arg596Gln	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	235	0.10760073260073261	3	0.006097560975609756	30	0.08287292817679558	88	0.15384615384615385	114	0.1503957783641161	G	16.09	3.025541	0.54683	0.023831	0.12314	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.25250	1.85;1.81	5.66	3.76	0.43208	.	0.686210	0.12799	N	0.438200	T	0.24314	0.0589	L	0.59436	1.845	0.09310	P	1.0	B;D;D	0.71674	0.024;0.998;0.998	B;P;P	0.55965	0.005;0.709;0.788	T	0.03706	-1.1011	9	0.36615	T	0.2	.	11.1733	0.48584	0.1584:0.0:0.8416:0.0	rs4706980;rs52817056;rs60343229;rs4706980	487;587;596	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	Q	596;577;577	ENSP00000195654:R596Q;ENSP00000237163:R577Q	ENSP00000237163:R577Q	R	+	2	0	DOPEY1	83895392	1.000000	0.71417	0.982000	0.44146	0.991000	0.79684	4.374000	0.59543	0.641000	0.30601	0.655000	0.94253	CGA	G|0.899;A|0.101	0.101	strong		0.413	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
DDX41	51428	hgsc.bcm.edu	37	5	176940384	176940384	+	Silent	SNP	G	G	A	rs335438	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:176940384G>A	ENST00000507955.1	-	11	1723	c.1200C>T	c.(1198-1200)cgC>cgT	p.R400R	DDX41_ENST00000506965.1_5'Flank|DOK3_ENST00000312943.6_5'Flank	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	400					apoptotic process (GO:0006915)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)|RNA processing (GO:0006396)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)					all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			CAGCCCCAGCGCGCCCCACAT	0.592													G|||	1935	0.386382	0.4539	0.3199	5008	,	,		17281	0.2063		0.4712	False		,,,				2504	0.4407				p.R400R		Atlas-SNP	.											.	DDX41	49	.	0			c.C1200T						PASS	.	G		2005,2401	557.6+/-379.8	456,1093,654	86.0	93.0	91.0		1200	-10.5	0.0	5	dbSNP_79	91	3989,4611	548.4+/-385.4	923,2143,1234	no	coding-synonymous	DDX41	NM_016222.2		1379,3236,1888	AA,AG,GG		46.3837,45.5061,46.0864		400/623	176940384	5994,7012	2203	4300	6503	SO:0001819	synonymous_variant	51428	exon11			CCCAGCGCGCCCC	AF195417	CCDS4427.1	5q35.3	2008-02-05			ENSG00000183258	ENSG00000183258		"""DEAD-boxes"""	18674	protein-coding gene	gene with protein product		608170				10607561	Standard	NM_016222		Approved	ABS, MGC8828	uc003mho.3	Q9UJV9	OTTHUMG00000130858	ENST00000507955.1:c.1200C>T	5.37:g.176940384G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	154	67	0.435065	NM_016222	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Silent	SNP	ENST00000507955.1	37	CCDS4427.1																																																																																			G|0.576;A|0.424	0.424	strong		0.592	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222	
DCSTAMP	81501	hgsc.bcm.edu	37	8	105368408	105368408	+	Silent	SNP	A	A	G	rs4734780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:105368408A>G	ENST00000297581.2	+	4	1444	c.1395A>G	c.(1393-1395)gcA>gcG	p.A465A	DCSTAMP_ENST00000520080.1_3'UTR|DCSTAMP_ENST00000517991.1_3'UTR|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	465					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											TGGACATGGCAAGTGCAGACA	0.458													A|||	397	0.0792732	0.1331	0.0317	5008	,	,		20678	0.0744		0.0467	False		,,,				2504	0.0787				p.A465A		Atlas-SNP	.											.	.	.	.	0			c.A1395G						PASS	.	A		492,3914	228.8+/-243.5	27,438,1738	100.0	95.0	97.0		1395	-4.5	0.0	8	dbSNP_111	97	413,8187	129.5+/-187.6	13,387,3900	no	coding-synonymous	TM7SF4	NM_030788.2		40,825,5638	GG,GA,AA		4.8023,11.1666,6.9583		465/471	105368408	905,12101	2203	4300	6503	SO:0001819	synonymous_variant	81501	exon4			CATGGCAAGTGCA	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"""Dendritic cells (DC)-specific transmembrane protein"", ""IL-Four INDuced"""	605933	"""transmembrane 7 superfamily member 4"""	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.1395A>G	8.37:g.105368408A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_030788	B7ZVW2|E7ESG0|Q2M2D5	Silent	SNP	ENST00000297581.2	37	CCDS6301.1																																																																																			A|0.929;G|0.071	0.071	strong		0.458	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788	
POLD1	5424	hgsc.bcm.edu	37	19	50905042	50905042	+	Silent	SNP	G	G	A	rs20582	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50905042G>A	ENST00000440232.2	+	4	377	c.324G>A	c.(322-324)gcG>gcA	p.A108A	POLD1_ENST00000595904.1_Silent_p.A108A|POLD1_ENST00000599857.1_Silent_p.A108A	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	108					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CAGGCCCAGCGCAGCCTGTGC	0.672								DNA polymerases (catalytic subunits)					G|||	946	0.188898	0.3245	0.1023	5008	,	,		11288	0.1607		0.0706	False		,,,				2504	0.2178				p.A108A		Atlas-SNP	.											.	POLD1	174	.	0			c.G324A						PASS	.	G		1266,3124		224,818,1153	27.0	34.0	31.0		324	-7.7	0.0	19	dbSNP_67	31	602,7940		24,554,3693	no	coding-synonymous	POLD1	NM_002691.2		248,1372,4846	AA,AG,GG		7.0475,28.8383,14.4448		108/1108	50905042	1868,11064	2195	4271	6466	SO:0001819	synonymous_variant	5424	exon4			CCCAGCGCAGCCT		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.324G>A	19.37:g.50905042G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	64	43	0.671875	NM_002691	Q8NER3|Q96H98	Silent	SNP	ENST00000440232.2	37	CCDS12795.1																																																																																			A|0.170;G|0.829;T|0.000	0.170	strong		0.672	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
LVRN	206338	hgsc.bcm.edu	37	5	115351066	115351066	+	Silent	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:115351066T>A	ENST00000357872.4	+	17	2692	c.2568T>A	c.(2566-2568)atT>atA	p.I856I	AQPEP_ENST00000515454.1_3'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		856						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AAGAAAAGATTCAACTTGCTT	0.343																																					p.I856I		Atlas-SNP	.											FLJ90650,caecum,carcinoma,0,1	.	.	1	0			c.T2568A						scavenged	.						91.0	87.0	88.0					5																	115351066		2202	4300	6502	SO:0001819	synonymous_variant	0	exon17			AAAGATTCAACTT																												ENST00000357872.4:c.2568T>A	5.37:g.115351066T>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	54	2	0.037037	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			.	.	none		0.343	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
PLIN4	729359	hgsc.bcm.edu	37	19	4511908	4511908	+	Silent	SNP	C	C	T	rs10423606	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:4511908C>T	ENST00000301286.3	-	3	2021	c.2022G>A	c.(2020-2022)acG>acA	p.T674T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	674	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)		p.T602T(1)|p.T674T(1)		NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CGGTCTTGGCCGTGTCTACAC	0.577																																					p.T674T		Atlas-SNP	.											.	PLIN4	191	.	2	Substitution - coding silent(2)	lung(2)	c.G2022A						PASS	.						149.0	159.0	156.0					19																	4511908		2123	4223	6346	SO:0001819	synonymous_variant	729359	exon3			CTTGGCCGTGTCT	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2022G>A	19.37:g.4511908C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	289	97	0.33564	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			C|0.500;T|0.500	0.500	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
KIAA1211	57482	hgsc.bcm.edu	37	4	57180473	57180473	+	Missense_Mutation	SNP	C	C	A	rs6823339	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:57180473C>A	ENST00000504228.1	+	6	910	c.805C>A	c.(805-807)Ctc>Atc	p.L269I	KIAA1211_ENST00000541073.1_Missense_Mutation_p.L262I|KIAA1211_ENST00000264229.6_Missense_Mutation_p.L269I			Q6ZU35	K1211_HUMAN	KIAA1211	269	Glu-rich.		L -> I (in dbSNP:rs6823339).							endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					AAGGCAGGAGCTCTTGGAGGA	0.657													C|||	1472	0.29393	0.3616	0.2839	5008	,	,		13368	0.0675		0.4095	False		,,,				2504	0.3241				p.L269I		Atlas-SNP	.											.	KIAA1211	178	.	0			c.C805A						PASS	.	C	ILE/LEU	1223,2587		219,785,901	12.0	15.0	14.0		805	3.0	1.0	4	dbSNP_116	14	3113,4891		682,1749,1571	yes	missense	KIAA1211	NM_020722.1	5	901,2534,2472	AA,AC,CC		38.8931,32.0997,36.7022	possibly-damaging	269/1234	57180473	4336,7478	1905	4002	5907	SO:0001583	missense	57482	exon8			CAGGAGCTCTTGG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.805C>A	4.37:g.57180473C>A	ENSP00000423366:p.Leu269Ile	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	644	0.2948717948717949	180	0.36585365853658536	114	0.3149171270718232	33	0.057692307692307696	317	0.4182058047493404	C	12.18	1.859468	0.32884	0.320997	0.388931	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.12672	2.67;2.67;2.66	4.77	3.02	0.34903	.	.	.	.	.	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	P;P;P	0.51537	0.946;0.86;0.86	B;B;B	0.43052	0.406;0.328;0.328	T	0.41592	-0.9500	8	0.16420	T	0.52	-7.7337	2.6747	0.05078	0.1513:0.5402:0.1465:0.162	rs6823339	262;262;269	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	I	269;269;262;179	ENSP00000264229:L269I;ENSP00000423366:L269I;ENSP00000444006:L262I	ENSP00000264229:L269I	L	+	1	0	KIAA1211	56875230	0.004000	0.15560	0.975000	0.42487	0.959000	0.62525	0.877000	0.28106	0.428000	0.26173	0.462000	0.41574	CTC	C|0.703;A|0.297	0.297	strong		0.657	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
CTAGE1	64693	hgsc.bcm.edu	37	18	19996805	19996805	+	5'Flank	SNP	T	T	C	rs12961009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:19996805T>C	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Missense_Mutation_p.I324V			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					AGATTTTTAATATGCTCTGTA	0.313													T|||	78	0.0155751	0.0015	0.0245	5008	,	,		18989	0.001		0.0497	False		,,,				2504	0.0082				p.I324V		Atlas-SNP	.											.	CTAGE1	146	.	0			c.A970G						PASS	.	T	VAL/ILE	43,4211		0,43,2084	34.0	38.0	37.0		970	0.7	0.0	18	dbSNP_121	37	371,8155		6,359,3898	no	missense	CTAGE1	NM_172241.2	29	6,402,5982	CC,CT,TT		4.3514,1.0108,3.2394	benign	324/746	19996805	414,12366	2127	4263	6390	SO:0001631	upstream_gene_variant	64693	exon1			TTTTAATATGCTC	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 1"", ""cutaneous T-cell lymphoma-associated antigen 2"", ""cancer/testis antigen family 21, member 1"", ""cancer/testis antigen family 21, member 2"""	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			18.37:g.19996805T>C	Exception_encountered	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	NM_172241	B0YIZ3	Missense_Mutation	SNP	ENST00000525417.1	37		45	0.020604395604395604	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	34	0.044854881266490766	T	6.941	0.543343	0.13250	0.010108	0.043514	ENSG00000212710	ENST00000391403	T	0.37584	1.19	0.741	0.741	0.18336	.	.	.	.	.	T	0.10252	0.0251	M	0.77486	2.375	0.09310	N	1	B	0.33940	0.433	B	0.35470	0.203	T	0.15838	-1.0423	8	.	.	.	.	3.7843	0.08694	0.0:0.0:0.0:1.0	rs12961009	324	Q96RT6	CTGE2_HUMAN	V	324	ENSP00000375220:I324V	.	I	-	1	0	CTAGE1	18250803	1.000000	0.71417	0.034000	0.17996	0.294000	0.27393	2.665000	0.46791	0.560000	0.29169	0.369000	0.22263	ATT	T|0.976;C|0.024	0.024	strong		0.313	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241	
RNASE3	6037	hgsc.bcm.edu	37	14	21360157	21360157	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21360157G>A	ENST00000304639.3	+	2	370	c.312G>A	c.(310-312)cgG>cgA	p.R104R		NM_002935.2	NP_002926.2	P12724	ECP_HUMAN	ribonuclease, RNase A family, 3	104					antibacterial humoral response (GO:0019731)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)	9	all_cancers(95;0.00453)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)	Pranlukast(DB01411)	GTAGATTCCGGGTGCCTTTAC	0.423																																					p.R104R		Atlas-SNP	.											RNASE3,NS,carcinoma,+2,2	RNASE3	24	2	0			c.G312A						scavenged	.						100.0	103.0	102.0					14																	21360157		2191	4300	6491	SO:0001819	synonymous_variant	6037	exon2			ATTCCGGGTGCCT	X55990	CCDS9560.1	14q11.2	2014-03-13	2010-05-07		ENSG00000169397	ENSG00000169397	3.1.27.-	"""Ribonucleases, RNase A"""	10046	protein-coding gene	gene with protein product	"""eosinophil cationic protein"""	131398		RNS3		1577491	Standard	NM_002935		Approved	ECP	uc001vyj.3	P12724	OTTHUMG00000029604	ENST00000304639.3:c.312G>A	14.37:g.21360157G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	185	4	0.0216216	NM_002935	Q4VBC1|Q8WTP7|Q8WZ62|Q9GZN9	Silent	SNP	ENST00000304639.3	37	CCDS9560.1																																																																																			.	.	none		0.423	RNASE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073795.2	NM_002935	
ZC3H7A	29066	hgsc.bcm.edu	37	16	11873158	11873158	+	Missense_Mutation	SNP	T	T	C	rs16958654	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:11873158T>C	ENST00000396516.2	-	3	367	c.170A>G	c.(169-171)cAt>cGt	p.H57R	ZC3H7A_ENST00000575170.1_5'UTR|ZC3H7A_ENST00000355758.4_Missense_Mutation_p.H57R			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	57			H -> R (in dbSNP:rs16958654).			nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						GTTCCAATCATGTTCCCGATA	0.333													C|||	289	0.0577077	0.0946	0.0634	5008	,	,		15894	0.0		0.0835	False		,,,				2504	0.0368				p.H57R		Atlas-SNP	.											.	ZC3H7A	72	.	0			c.A170G						PASS	.	C	ARG/HIS	455,3937	782.1+/-414.5	31,393,1772	134.0	140.0	138.0		170	1.5	0.5	16	dbSNP_123	138	579,8021	792.7+/-407.5	15,549,3736	yes	missense	ZC3H7A	NM_014153.3	29	46,942,5508	CC,CT,TT		6.7326,10.3597,7.9587	benign	57/972	11873158	1034,11958	2196	4300	6496	SO:0001583	missense	29066	exon4			CAATCATGTTCCC	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"""Zinc fingers, CCCH-type domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30959	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 7"", ""zinc finger CCCH-type containing 7"""	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.170A>G	16.37:g.11873158T>C	ENSP00000379773:p.His57Arg	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	167	75	0.449102	NM_014153	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	37	CCDS10550.1	126	0.057692307692307696	41	0.08333333333333333	24	0.06629834254143646	0	0.0	61	0.08047493403693931	C	11.44	1.639891	0.29157	0.103597	0.067326	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.73152	-0.72;-0.72	5.7	1.53	0.23141	Tetratricopeptide-like helical (1);	0.413589	0.31566	N	0.007424	T	0.01156	0.0038	N	0.02345	-0.59	0.09310	P	0.9999999750082	B	0.02656	0.0	B	0.01281	0.0	T	0.05162	-1.0902	9	0.15066	T	0.55	.	8.9212	0.35612	0.0:0.5485:0.0:0.4515	rs16958654;rs52808221;rs61248391;rs16958654	57	Q8IWR0	Z3H7A_HUMAN	R	57	ENSP00000347999:H57R;ENSP00000379773:H57R	ENSP00000347999:H57R	H	-	2	0	ZC3H7A	11780659	0.001000	0.12720	0.453000	0.27007	0.919000	0.55068	0.446000	0.21694	-0.130000	0.11599	-0.349000	0.07799	CAT	T|0.928;C|0.072	0.072	strong		0.333	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153	
PITRM1	10531	hgsc.bcm.edu	37	10	3191823	3191823	+	Missense_Mutation	SNP	C	C	T	rs2388556	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:3191823C>T	ENST00000224949.4	-	16	1895	c.1861G>A	c.(1861-1863)Gtc>Atc	p.V621I	PITRM1_ENST00000464395.1_5'Flank|PITRM1_ENST00000380994.1_Missense_Mutation_p.V179I|PITRM1_ENST00000451104.2_Missense_Mutation_p.V589I|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.V621I			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	621			V -> I (in dbSNP:rs2388556). {ECO:0000269|PubMed:10360838}.		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TTGGTGAGGACGCTGCAGAAG	0.517													C|||	579	0.115615	0.1346	0.0893	5008	,	,		15779	0.0536		0.1571	False		,,,				2504	0.1299				p.V621I		Atlas-SNP	.											.	PITRM1	109	.	0			c.G1861A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	532,3574		45,442,1566	185.0	189.0	188.0		1861,1765,1861	4.5	1.0	10	dbSNP_100	188	1444,6974		128,1188,2893	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	29,29,29	173,1630,4459	TT,TC,CC		17.1537,12.9566,15.7777	possibly-damaging,possibly-damaging,possibly-damaging	621/1039,589/940,621/1038	3191823	1976,10548	2053	4209	6262	SO:0001583	missense	10531	exon16			TGAGGACGCTGCA	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1861G>A	10.37:g.3191823C>T	ENSP00000224949:p.Val621Ile	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	245	0.11217948717948718	58	0.11788617886178862	38	0.10497237569060773	30	0.05244755244755245	119	0.15699208443271767	c	23.1	4.376667	0.82682	0.129566	0.171537	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104	T;T;T;T	0.22336	1.96;1.96;1.96;2.17	5.41	4.51	0.55191	Peptidase M16C associated (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.057779	0.64402	D	0.000001	T	0.00109	0.0003	M	0.71036	2.16	0.09310	P	0.9999943181	P;P;D;D	0.56287	0.792;0.9;0.975;0.975	B;P;P;P	0.55222	0.177;0.459;0.771;0.771	T	0.04115	-1.0976	9	0.33940	T	0.23	.	13.8585	0.63545	0.0:0.9265:0.0:0.0735	rs2388556;rs59691732;rs2388556	614;589;621;621	E9PDX6;E7ES23;C9JSL2;Q5JRX3	.;.;.;PREP_HUMAN	I	621;614;621;179;589	ENSP00000224949:V621I;ENSP00000370377:V621I;ENSP00000370382:V179I;ENSP00000401201:V589I	ENSP00000224949:V621I	V	-	1	0	PITRM1	3181823	1.000000	0.71417	0.982000	0.44146	0.973000	0.67179	5.780000	0.68956	1.294000	0.44707	0.555000	0.69702	GTC	C|0.892;T|0.108	0.108	strong		0.517	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
BCAM	4059	hgsc.bcm.edu	37	19	45316804	45316804	+	Silent	SNP	C	C	T	rs3810141	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:45316804C>T	ENST00000270233.6	+	6	733	c.711C>T	c.(709-711)tgC>tgT	p.C237C	BCAM_ENST00000589651.1_Silent_p.C237C	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	237	Ig-like V-type 2.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GCTTCCACTGCGCCGCCCACT	0.692													C|||	501	0.10004	0.087	0.0893	5008	,	,		14090	0.0466		0.0815	False		,,,				2504	0.1994				p.C237C		Atlas-SNP	.											.	BCAM	53	.	0			c.C711T	GRCh37	CM973376	BCAM	M	rs3810141	PASS	.	C	,	401,4001		20,361,1820	39.0	45.0	43.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	711,711	-3.5	0.1	19	dbSNP_107	43	526,8060		18,490,3785	no	coding-synonymous,coding-synonymous	BCAM	NM_001013257.1,NM_005581.3	,	38,851,5605	TT,TC,CC		6.1263,9.1095,7.1374	,	237/589,237/629	45316804	927,12061	2201	4293	6494	SO:0001819	synonymous_variant	4059	exon6			CCACTGCGCCGCC	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6722	protein-coding gene	gene with protein product		612773	"""Lutheran blood group (Auberger b antigen included)"", ""basal cell adhesion molecule (Lu and Au blood groups)"""	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.711C>T	19.37:g.45316804C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	55	0.56701	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Silent	SNP	ENST00000270233.6	37	CCDS12644.1																																																																																			T|0.064;C|0.936	0.064	strong		0.692	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	
BTNL2	56244	hgsc.bcm.edu	37	6	32370975	32370975	+	Missense_Mutation	SNP	C	C	T	rs60263670	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32370975C>T	ENST00000374993.1	-	3	445	c.446G>A	c.(445-447)aGc>aAc	p.S149N	BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000454136.3_Missense_Mutation_p.S149N|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000374995.3_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	149	Ig-like V-type 2.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CATGTGGATGCTAGGGGCAGA	0.607													T|||	699	0.139577	0.1543	0.1427	5008	,	,		18117	0.1984		0.0974	False		,,,				2504	0.1002				p.S149N		Atlas-SNP	.											.	BTNL2	50	.	0			c.G446A						PASS	.	T	ASN/SER	390,2626		23,344,1141	22.0	22.0	22.0		446	3.4	0.0	6	dbSNP_129	22	417,4999		15,387,2306	yes	missense	BTNL2	NM_019602.1	46	38,731,3447	TT,TC,CC		7.6994,12.931,9.5707	benign	149/456	32370975	807,7625	1508	2708	4216	SO:0001583	missense	56244	exon3			TGGATGCTAGGGG	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.446G>A	6.37:g.32370975C>T	ENSP00000364132:p.Ser149Asn	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		302	0.1382783882783883	66	0.13414634146341464	53	0.1464088397790055	106	0.1853146853146853	77	0.10158311345646438	T	6.111	0.388689	0.11581	0.12931	0.076994	ENSG00000204290	ENST00000468270;ENST00000374993	T	0.15487	2.42	4.6	3.39	0.38822	Immunoglobulin-like fold (1);	2.076250	0.02101	N	0.053915	T	0.01905	0.0060	N	0.01751	-0.74	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37291	-0.9712	9	0.20519	T	0.43	.	6.822	0.23862	0.0:0.1909:0.0:0.8091	rs60263670;rs61743082	149	Q9UIR0	BTNL2_HUMAN	N	149	ENSP00000364132:S149N	ENSP00000364132:S149N	S	-	2	0	BTNL2	32478953	0.000000	0.05858	0.000000	0.03702	0.243000	0.25628	-0.190000	0.09615	0.340000	0.23745	-0.377000	0.06932	AGC	C|0.893;T|0.107	0.107	strong		0.607	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
TRIM3	10612	hgsc.bcm.edu	37	11	6486914	6486914	+	Silent	SNP	C	C	T	rs144521953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6486914C>T	ENST00000525074.1	-	2	406	c.12G>A	c.(10-12)agG>agA	p.R4R	TRIM3_ENST00000536344.1_Intron|TRIM3_ENST00000345851.3_Silent_p.R4R|TRIM3_ENST00000537602.1_Silent_p.R4R|TRIM3_ENST00000359518.3_Silent_p.R4R	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	4					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCTGTCCTCCCTCTTTGCCA	0.602																																					p.R4R	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.G12A						PASS	.	C	,	1,4401	2.1+/-5.4	0,1,2200	148.0	113.0	125.0		12,12	3.3	1.0	11	dbSNP_134	125	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous,coding-synonymous	TRIM3	NM_006458.2,NM_033278.2	,	0,6,6491	TT,TC,CC		0.0582,0.0227,0.0462	,	4/745,4/745	6486914	6,12988	2201	4296	6497	SO:0001819	synonymous_variant	10612	exon2			GTCCTCCCTCTTT	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.12G>A	11.37:g.6486914C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																			C|0.999;T|0.001	0.001	strong		0.602	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
PCCA	5095	hgsc.bcm.edu	37	13	100888122	100888122	+	Silent	SNP	A	A	G	rs538229	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:100888122A>G	ENST00000376285.1	+	8	665	c.627A>G	c.(625-627)gcA>gcG	p.A209A	PCCA_ENST00000376279.3_Silent_p.A209A|PCCA_ENST00000376286.4_Silent_p.A183A	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	209	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	TCAGAATTGCAAGGGAAATTG	0.388													A|||	516	0.103035	0.0885	0.1455	5008	,	,		19089	0.0159		0.174	False		,,,				2504	0.1094				p.A209A		Atlas-SNP	.											PCCA,colon,carcinoma,+2,1	PCCA	59	1	0			c.A627G						PASS	.	A	,,	493,3913	231.4+/-245.2	26,441,1736	158.0	135.0	143.0		627,549,627	4.3	1.0	13	dbSNP_83	143	1478,7122	281.0+/-294.8	133,1212,2955	no	coding-synonymous,coding-synonymous,coding-synonymous	PCCA	NM_000282.3,NM_001127692.2,NM_001178004.1	,,	159,1653,4691	GG,GA,AA		17.186,11.1893,15.1545	,,	209/729,183/703,209/682	100888122	1971,11035	2203	4300	6503	SO:0001819	synonymous_variant	5095	exon8			AATTGCAAGGGAA	X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"""propionyl Coenzyme A carboxylase, alpha polypeptide"""			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.627A>G	13.37:g.100888122A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	168	74	0.440476	NM_001178004	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Silent	SNP	ENST00000376285.1	37	CCDS9496.2																																																																																			A|0.862;G|0.138	0.138	strong		0.388	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2		
ABCC1	4363	hgsc.bcm.edu	37	16	16162039	16162039	+	Silent	SNP	C	C	T	rs8187858	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:16162039C>T	ENST00000399410.3	+	13	1879	c.1704C>T	c.(1702-1704)taC>taT	p.Y568Y	ABCC1_ENST00000349029.5_Silent_p.Y568Y|ABCC1_ENST00000346370.5_Silent_p.Y568Y|ABCC1_ENST00000351154.5_Silent_p.Y568Y|ABCC1_ENST00000399408.2_Silent_p.Y568Y|ABCC1_ENST00000345148.5_Silent_p.Y568Y	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	568	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	TTGCCGTCTACGTGACCATTG	0.562													C|||	179	0.0357428	0.0053	0.0504	5008	,	,		19559	0.001		0.0984	False		,,,				2504	0.0378				p.Y568Y		Atlas-SNP	.											.	ABCC1	156	.	0			c.C1704T						PASS	.	C	,,,,	66,4202		0,66,2068	182.0	177.0	179.0		1704,1704,1704,1704,1704	0.1	1.0	16	dbSNP_123	179	791,7693		41,709,3492	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	41,775,5560	TT,TC,CC		9.3234,1.5464,6.7205	,,,,	568/1532,568/1473,568/1476,568/1417,568/1467	16162039	857,11895	2134	4242	6376	SO:0001819	synonymous_variant	4363	exon13			CGTCTACGTGACC	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.1704C>T	16.37:g.16162039C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	154	79	0.512987	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			C|0.953;T|0.047	0.047	strong		0.562	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
PIWIL4	143689	hgsc.bcm.edu	37	11	94320237	94320237	+	Silent	SNP	T	T	C	rs7110167	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:94320237T>C	ENST00000299001.6	+	7	949	c.738T>C	c.(736-738)ttT>ttC	p.F246F	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	246					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GGCCTGGGTTTGCCATTTCTG	0.358													T|||	2772	0.553514	0.8124	0.4524	5008	,	,		19065	0.5		0.4016	False		,,,				2504	0.4867				p.F246F		Atlas-SNP	.											PIWIL4,NS,carcinoma,+2,1	PIWIL4	70	1	0			c.T738C						PASS	.	T		3284,1118	717.2+/-408.7	1239,806,156	144.0	153.0	150.0		738	-0.4	0.2	11	dbSNP_116	150	3427,5169	504.7+/-376.2	705,2017,1576	no	coding-synonymous	PIWIL4	NM_152431.2		1944,2823,1732	CC,CT,TT		39.8674,25.3975,48.369		246/853	94320237	6711,6287	2201	4298	6499	SO:0001819	synonymous_variant	143689	exon7			TGGGTTTGCCATT	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.738T>C	11.37:g.94320237T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			T|0.476;C|0.524	0.524	strong		0.358	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
DVL2	1856	hgsc.bcm.edu	37	17	7129840	7129840	+	Silent	SNP	T	T	C	rs35594616	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7129840T>C	ENST00000005340.5	-	14	1944	c.1662A>G	c.(1660-1662)caA>caG	p.Q554Q	DVL2_ENST00000575458.1_Silent_p.Q548Q|DVL2_ENST00000574642.1_5'Flank	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	554					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						GGGCAGGGTATTGGTAGGAGA	0.617													T|||	2602	0.519569	0.416	0.4957	5008	,	,		15735	0.4732		0.6233	False		,,,				2504	0.6176				p.Q554Q		Atlas-SNP	.											.	DVL2	49	.	0			c.A1662G						PASS	.	T		1944,2462	545.8+/-376.9	413,1118,672	51.0	55.0	54.0		1662	-2.7	0.9	17	dbSNP_126	54	5380,3220	646.5+/-400.3	1695,1990,615	no	coding-synonymous	DVL2	NM_004422.2		2108,3108,1287	CC,CT,TT		37.4419,44.1217,43.6875		554/737	7129840	7324,5682	2203	4300	6503	SO:0001819	synonymous_variant	1856	exon14			AGGGTATTGGTAG	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.1662A>G	17.37:g.7129840T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_004422	D3DTN3|Q53XM0	Silent	SNP	ENST00000005340.5	37	CCDS11091.1																																																																																			T|0.449;C|0.551	0.551	strong		0.617	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
GLI1	2735	hgsc.bcm.edu	37	12	57865821	57865821	+	Missense_Mutation	SNP	G	G	C	rs2228226	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57865821G>C	ENST00000228682.2	+	12	3389	c.3298G>C	c.(3298-3300)Gaa>Caa	p.E1100Q	GLI1_ENST00000546141.1_Missense_Mutation_p.E1059Q|GLI1_ENST00000543426.1_Missense_Mutation_p.E972Q	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	1100			E -> Q (in dbSNP:rs2228226). {ECO:0000269|PubMed:10951255, ECO:0000269|Ref.2}.		cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			TGGGGAAACAGAATTCCTCAA	0.527													C|||	2936	0.586262	0.7882	0.4755	5008	,	,		19363	0.3958		0.674	False		,,,				2504	0.498				p.E1100Q	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.G3298C						PASS	.	C	GLN/GLU,GLN/GLU,GLN/GLU	3394,1012	375.9+/-321.8	1314,766,123	56.0	57.0	56.0		2914,3175,3298	4.7	1.0	12	dbSNP_98	56	5864,2736	432.3+/-357.1	2008,1848,444	yes	missense,missense,missense	GLI1	NM_001160045.1,NM_001167609.1,NM_005269.2	29,29,29	3322,2614,567	CC,CG,GG		31.814,22.9687,28.8175	benign,benign,benign	972/979,1059/1066,1100/1107	57865821	9258,3748	2203	4300	6503	SO:0001583	missense	2735	exon12			GAAACAGAATTCC		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.3298G>C	12.37:g.57865821G>C	ENSP00000228682:p.Glu1100Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	37	CCDS8940.1	1303	0.5966117216117216	397	0.806910569105691	186	0.5138121546961326	215	0.3758741258741259	505	0.6662269129287599	C	1.093	-0.663397	0.03428	0.770313	0.68186	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	T;T;T;T	0.10573	2.99;2.86;2.93;2.93	4.69	4.69	0.59074	.	0.000000	0.43747	N	0.000525	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.13150	-1.0520	9	0.22109	T	0.4	.	10.0074	0.41965	0.1557:0.6938:0.1504:0.0	rs2228226;rs3182229;rs17548454;rs58463097;rs2228226	1100	P08151	GLI1_HUMAN	Q	972;1100;1059;1059;568	ENSP00000437607:E972Q;ENSP00000228682:E1100Q;ENSP00000441006:E1059Q;ENSP00000434408:E1059Q	ENSP00000228682:E1100Q	E	+	1	0	GLI1	56152088	1.000000	0.71417	0.999000	0.59377	0.948000	0.59901	2.147000	0.42226	1.603000	0.50134	-0.120000	0.15030	GAA	G|0.340;C|0.660	0.660	strong		0.527	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
HTT	3064	hgsc.bcm.edu	37	4	3240312	3240312	+	Silent	SNP	G	G	A	rs141927489	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:3240312G>A	ENST00000355072.5	+	65	9175	c.9030G>A	c.(9028-9030)caG>caA	p.Q3010Q		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	3010					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CATACCCCCAGTTCATGGCCA	0.557													G|||	9	0.00179712	0.0	0.0058	5008	,	,		14198	0.0		0.004	False		,,,				2504	0.001				p.Q3010Q		Atlas-SNP	.											.	HTT	221	.	0			c.G9030A						PASS	.	G		6,4064		0,6,2029	75.0	82.0	79.0		9030	4.1	1.0	4	dbSNP_134	79	35,8345		0,35,4155	no	coding-synonymous	HTT	NM_002111.6		0,41,6184	AA,AG,GG		0.4177,0.1474,0.3293		3010/3143	3240312	41,12409	2035	4190	6225	SO:0001819	synonymous_variant	3064	exon65			CCCCCAGTTCATG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.9030G>A	4.37:g.3240312G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			G|0.998;A|0.002	0.002	strong		0.557	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
MUC21	394263	hgsc.bcm.edu	37	6	30954977	30954977	+	Missense_Mutation	SNP	C	C	T	rs55638653		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954977C>T	ENST00000376296.3	+	2	1266	c.1025C>T	c.(1024-1026)gCc>gTc	p.A342V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	342	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGTGGGGCCAGCACAGCC	0.637																																					p.A342V		Atlas-SNP	.											MUC21,NS,carcinoma,0,1	MUC21	98	1	0			c.C1025T						PASS	.						134.0	134.0	134.0					6																	30954977		2203	4298	6501	SO:0001583	missense	394263	exon2			GTGGGGCCAGCAC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1025C>T	6.37:g.30954977C>T	ENSP00000365473:p.Ala342Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	132	24	0.181818	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	c	5.899	0.350041	0.11182	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02737	4.18	4.68	0.808	0.18719	.	.	.	.	.	T	0.00468	0.0015	N	0.04508	-0.205	0.09310	N	0.999998	B	0.12013	0.005	B	0.09377	0.004	T	0.44143	-0.9347	9	0.33940	T	0.23	1.1431	5.6626	0.17676	0.0:0.6071:0.1425:0.2504	rs55638653	342	Q5SSG8	MUC21_HUMAN	V	192;342	ENSP00000365473:A342V	ENSP00000365473:A342V	A	+	2	0	MUC21	31062956	0.000000	0.05858	0.014000	0.15608	0.396000	0.30629	-0.234000	0.09028	0.023000	0.15187	-0.942000	0.02676	GCC	C|0.999;T|0.001	0.001	weak		0.637	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
ELAVL3	1995	hgsc.bcm.edu	37	19	11569397	11569397	+	Silent	SNP	G	G	A	rs61744781	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11569397G>A	ENST00000359227.3	-	4	787	c.363C>T	c.(361-363)tcC>tcT	p.S121S	ELAVL3_ENST00000438662.2_Silent_p.S121S	NM_001420.3|NM_032281.2	NP_001411.2|NP_115657.2	Q14576	ELAV3_HUMAN	ELAV like neuron-specific RNA binding protein 3	121					cell differentiation (GO:0030154)|nervous system development (GO:0007399)		AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15						CATCCCGGATGGATGCTGAAC	0.587													G|||	438	0.0874601	0.1029	0.1412	5008	,	,		21068	0.0337		0.0825	False		,,,				2504	0.089				p.S121S		Atlas-SNP	.											ELAVL3,NS,carcinoma,-2,1	ELAVL3	58	1	0			c.C363T						scavenged	.	G	,	424,3982	208.5+/-229.5	22,380,1801	110.0	101.0	104.0		363,363	-1.0	0.7	19	dbSNP_129	104	524,8076	147.3+/-202.7	16,492,3792	no	coding-synonymous,coding-synonymous	ELAVL3	NM_001420.3,NM_032281.2	,	38,872,5593	AA,AG,GG		6.093,9.6232,7.2889	,	121/368,121/361	11569397	948,12058	2203	4300	6503	SO:0001819	synonymous_variant	1995	exon4			CCGGATGGATGCT		CCDS32912.1, CCDS45978.1	19p13.2	2013-10-03	2013-10-03			ENSG00000196361		"""RNA binding motif (RRM) containing"""	3314	protein-coding gene	gene with protein product	"""Hu antigen C"", ""paraneoplastic limbic encephalitis antigen 21"", ""paraneoplastic cerebellar degeneration-associated antigen"", ""ELAV-like protein 3"""	603458	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)"""			9799595	Standard	NM_001420		Approved	HUC, PLE21, DKFZp547J036, HUCL, MGC20653	uc002mry.1	Q14576		ENST00000359227.3:c.363C>T	19.37:g.11569397G>A		Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_032281	Q16135|Q96CL8|Q96QS9	Silent	SNP	ENST00000359227.3	37	CCDS32912.1																																																																																			G|0.922;A|0.078	0.078	strong		0.587	ELAVL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458827.2	NM_001420	
MTUS1	57509	hgsc.bcm.edu	37	8	17611924	17611924	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:17611924G>A	ENST00000262102.6	-	2	1617	c.1393C>T	c.(1393-1395)Cca>Tca	p.P465S	MTUS1_ENST00000519263.1_Missense_Mutation_p.P465S|MTUS1_ENST00000381862.3_Missense_Mutation_p.P465S|MTUS1_ENST00000381869.3_Missense_Mutation_p.P465S	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	465					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TTCGAGTCTGGTATGTTTTTA	0.418																																					p.P465S		Atlas-SNP	.											.	MTUS1	144	.	0			c.C1393T						PASS	.						155.0	147.0	149.0					8																	17611924		1868	4121	5989	SO:0001583	missense	57509	exon2			AGTCTGGTATGTT	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.1393C>T	8.37:g.17611924G>A	ENSP00000262102:p.Pro465Ser	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	244	48	0.196721	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	G	6.988	0.552322	0.13374	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.18960	3.16;3.17;3.16;2.18	5.0	-1.15	0.09709	.	0.579128	0.16128	N	0.228351	T	0.09598	0.0236	N	0.16656	0.425	0.09310	N	1	B;B;B	0.23377	0.084;0.041;0.041	B;B;B	0.21917	0.037;0.011;0.011	T	0.18745	-1.0327	10	0.52906	T	0.07	-0.6007	2.2436	0.04025	0.3516:0.1319:0.4048:0.1117	.	465;465;465	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	S	465	ENSP00000371293:P465S;ENSP00000262102:P465S;ENSP00000430167:P465S;ENSP00000371286:P465S	ENSP00000262102:P465S	P	-	1	0	MTUS1	17656204	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.204000	0.17335	-0.351000	0.08249	-1.623000	0.00790	CCA	.	.	none		0.418	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
MDH2	4191	hgsc.bcm.edu	37	7	75677504	75677504	+	Missense_Mutation	SNP	C	C	T	rs6720	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:75677504C>T	ENST00000315758.5	+	1	120	c.26C>T	c.(25-27)gCc>gTc	p.A9V	STYXL1_ENST00000248600.1_5'Flank|STYXL1_ENST00000431581.1_5'Flank|STYXL1_ENST00000451157.1_5'Flank|MDH2_ENST00000432020.2_Missense_Mutation_p.A9V|MDH2_ENST00000443006.1_5'UTR|STYXL1_ENST00000460184.2_5'Flank|STYXL1_ENST00000360591.3_5'Flank|STYXL1_ENST00000359697.3_5'Flank|STYXL1_ENST00000340062.5_5'Flank|MDH2_ENST00000490105.1_3'UTR|MDH2_ENST00000461263.2_Missense_Mutation_p.A9V	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	9			A -> V (in dbSNP:rs17849553). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|internal protein amino acid acetylation (GO:0006475)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	L-malate dehydrogenase activity (GO:0030060)|malate dehydrogenase (NADP+) activity (GO:0046554)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(2)	14						GCCCGGCCTGCCAGCGCTGCT	0.741													c|||	2615	0.522165	0.7073	0.4164	5008	,	,		14327	0.6071		0.327	False		,,,				2504	0.4601				p.A9V		Atlas-SNP	.											MDH2,NS,carcinoma,0,1	MDH2	35	1	0			c.C26T						PASS	.	C	VAL/ALA	2410,1644		759,892,376	9.0	7.0	8.0		26	0.6	0.0	7	dbSNP_123	8	2255,5607		413,1429,2089	no	missense	MDH2	NM_005918.2	64	1172,2321,2465	TT,TC,CC		28.6823,40.5525,39.149	benign	9/339	75677504	4665,7251	2027	3931	5958	SO:0001583	missense	4191	exon1			GGCCTGCCAGCGC		CCDS5581.1, CCDS64691.1, CCDS75622.1	7q11.23	2013-09-20			ENSG00000146701	ENSG00000146701	1.1.1.37		6971	protein-coding gene	gene with protein product		154100					Standard	NM_005918		Approved		uc003ueo.3	P40926	OTTHUMG00000023827	ENST00000315758.5:c.26C>T	7.37:g.75677504C>T	ENSP00000327070:p.Ala9Val	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Missense_Mutation	SNP	ENST00000315758.5	37	CCDS5581.1	1104	0.5054945054945055	353	0.717479674796748	147	0.40607734806629836	356	0.6223776223776224	248	0.32717678100263853	C	15.67	2.903178	0.52333	0.594475	0.286823	ENSG00000146701	ENST00000315758;ENST00000432020	T;T	0.41758	0.99;0.99	5.57	0.558	0.17266	.	0.307415	0.35262	N	0.003322	T	0.00012	0.0000	L	0.33624	1.015	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34054	-0.9844	9	0.25751	T	0.34	-8.1463	9.0275	0.36239	0.0:0.6206:0.0:0.3794	rs6720	9;9	E9PDB2;P40926	.;MDHM_HUMAN	V	9	ENSP00000327070:A9V;ENSP00000408649:A9V	ENSP00000327070:A9V	A	+	2	0	MDH2	75515440	0.001000	0.12720	0.004000	0.12327	0.754000	0.42855	0.356000	0.20181	0.047000	0.15862	0.650000	0.86243	GCC	C|0.494;T|0.506	0.506	strong		0.741	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1		
ACTL7B	10880	hgsc.bcm.edu	37	9	111617341	111617341	+	Silent	SNP	A	A	G	rs3750467	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:111617341A>G	ENST00000374667.3	-	1	1898	c.870T>C	c.(868-870)acT>acC	p.T290T		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	290						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						CCTGGCCAATAGTGATGAGTT	0.667													G|||	642	0.128195	0.0469	0.1009	5008	,	,		18533	0.1379		0.1451	False		,,,				2504	0.2301				p.T290T		Atlas-SNP	.											.	ACTL7B	57	.	0			c.T870C						PASS	.	G		257,4141		12,233,1954	47.0	54.0	52.0		870	3.1	1.0	9	dbSNP_107	52	1127,7457		70,987,3235	no	coding-synonymous	ACTL7B	NM_006686.3		82,1220,5189	GG,GA,AA		13.1291,5.8436,10.6609		290/416	111617341	1384,11598	2199	4292	6491	SO:0001819	synonymous_variant	10880	exon1			GCCAATAGTGATG	BC033789	CCDS6771.1	9q31	2009-05-15			ENSG00000148156	ENSG00000148156			162	protein-coding gene	gene with protein product		604304				10373328, 12907721	Standard	NM_006686		Approved	Tact1	uc004bdi.3	Q9Y614	OTTHUMG00000020462	ENST00000374667.3:c.870T>C	9.37:g.111617341A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_006686	B2R9Q2|Q5JSV1	Silent	SNP	ENST00000374667.3	37	CCDS6771.1																																																																																			A|0.890;G|0.110	0.110	strong		0.667	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686	
RB1CC1	9821	hgsc.bcm.edu	37	8	53569680	53569680	+	Silent	SNP	C	C	T	rs62499947	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:53569680C>T	ENST00000025008.5	-	15	3232	c.2709G>A	c.(2707-2709)gaG>gaA	p.E903E	RB1CC1_ENST00000435644.2_Silent_p.E903E|RB1CC1_ENST00000539297.1_Silent_p.E903E|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	903					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				GTAAAACCTCCTCAAGGCATA	0.308													C|||	74	0.0147764	0.0008	0.0259	5008	,	,		17739	0.0		0.0497	False		,,,				2504	0.0051				p.E903E	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.G2709A						PASS	.	C	,	48,4352		0,48,2152	64.0	70.0	68.0		2709,2709	-0.2	1.0	8	dbSNP_129	68	396,8188		10,376,3906	no	coding-synonymous,coding-synonymous	RB1CC1	NM_001083617.1,NM_014781.4	,	10,424,6058	TT,TC,CC		4.6132,1.0909,3.4196	,	903/1592,903/1595	53569680	444,12540	2200	4292	6492	SO:0001819	synonymous_variant	9821	exon15			AACCTCCTCAAGG	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.2709G>A	8.37:g.53569680C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	127	68	0.535433	NM_001083617	Q86YR4|Q8WVU9|Q92601	Silent	SNP	ENST00000025008.5	37	CCDS34892.1																																																																																			C|0.970;T|0.030	0.030	strong		0.308	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	
SERPINF2	5345	hgsc.bcm.edu	37	17	1648502	1648502	+	Missense_Mutation	SNP	C	C	T	rs2070863	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1648502C>T	ENST00000324015.3	+	3	174	c.97C>T	c.(97-99)Cgg>Tgg	p.R33W	SERPINF2_ENST00000382061.4_Missense_Mutation_p.R33W|SERPINF2_ENST00000450523.2_Missense_Mutation_p.R33W	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	33			R -> W (in dbSNP:rs2070863). {ECO:0000269|PubMed:10583218}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of proteolysis (GO:0030162)|response to organic substance (GO:0010033)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Ocriplasmin(DB08888)	GCCCTTGGGCCGGCAGGTACT	0.672													C|||	1197	0.239018	0.2201	0.2089	5008	,	,		9905	0.1855		0.1988	False		,,,				2504	0.3824				p.R33W		Atlas-SNP	.											.	SERPINF2	33	.	0			c.C97T	GRCh37	CM073337	SERPINF2	M	rs2070863	PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	894,3468		90,714,1377	23.0	18.0	20.0		97,97,97	3.0	0.0	17	dbSNP_96	20	1705,6805		177,1351,2727	yes	missense,missense,missense	SERPINF2	NM_000934.3,NM_001165920.1,NM_001165921.1	101,101,101	267,2065,4104	TT,TC,CC		20.0353,20.4952,20.1911	probably-damaging,probably-damaging,probably-damaging	33/492,33/492,33/428	1648502	2599,10273	2181	4255	6436	SO:0001583	missense	5345	exon3			TTGGGCCGGCAGG	D00174	CCDS11011.1, CCDS54064.1	17p13.3	2014-02-18	2005-08-18		ENSG00000167711	ENSG00000167711		"""Serine (or cysteine) peptidase inhibitors"""	9075	protein-coding gene	gene with protein product	"""alpha-2-plasmin inhibitor"", ""alpha-2-antiplasmin"""	613168	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2"""	PLI		3416655, 24172014	Standard	NM_000934		Approved	API, ALPHA-2-PI, A2AP, AAP	uc002ftk.1	P08697	OTTHUMG00000090552	ENST00000324015.3:c.97C>T	17.37:g.1648502C>T	ENSP00000321853:p.Arg33Trp	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_000934	B4E1B7|Q8N5U7|Q9UCG2|Q9UCG3	Missense_Mutation	SNP	ENST00000324015.3	37	CCDS11011.1	419	0.19184981684981686	99	0.20121951219512196	71	0.19613259668508287	103	0.18006993006993008	146	0.19261213720316622	C	11.31	1.601548	0.28534	0.204952	0.200353	ENSG00000167711	ENST00000453066;ENST00000324015;ENST00000450523;ENST00000423861;ENST00000453723;ENST00000382061	D;D;D;D;D	0.87809	-2.3;-1.97;-2.03;-1.72;-1.97	4.98	2.96	0.34315	.	1.515610	0.03304	N	0.189536	T	0.00356	0.0011	L	0.29908	0.895	0.80722	P	0.0	D;P	0.55172	0.97;0.946	B;B	0.42087	0.375;0.12	T	0.32295	-0.9912	9	0.52906	T	0.07	.	10.6516	0.45651	0.0:0.8237:0.0:0.1763	rs2070863;rs2234833;rs61057008;rs2070863	33;33	B4E1B7;P08697	.;A2AP_HUMAN	W	33	ENSP00000402286:R33W;ENSP00000321853:R33W;ENSP00000403877:R33W;ENSP00000402056:R33W;ENSP00000371493:R33W	ENSP00000321853:R33W	R	+	1	2	SERPINF2	1595252	0.001000	0.12720	0.003000	0.11579	0.006000	0.05464	0.793000	0.26944	0.235000	0.21160	-1.626000	0.00786	CGG	C|0.794;T|0.206	0.206	strong		0.672	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207078.3	NM_000934	
MT-ND5	4540	hgsc.bcm.edu	37	M	13135	13135	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:13135G>A	ENST00000361567.2	+	1	799	c.799G>A	c.(799-801)Gca>Aca	p.A267T	MT-TE_ENST00000387459.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	267					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TCCACCCCCTAGCAGAAAATA	0.498																																					p.A267T		Atlas-SNP	.											.	.	.	.	0			c.G799A						PASS	.																																			SO:0001583	missense	0	exon1			CCCCTAGCAGAAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.799G>A	M.37:g.13135G>A	ENSP00000354813:p.Ala267Thr	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.498	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
KIAA1614	57710	hgsc.bcm.edu	37	1	180897634	180897634	+	Missense_Mutation	SNP	G	G	A	rs140222211	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:180897634G>A	ENST00000367588.4	+	4	1185	c.1130G>A	c.(1129-1131)cGt>cAt	p.R377H	KIAA1614_ENST00000367587.1_5'UTR	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	377										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CTGCTGCAGCGTGCCCGCATG	0.687													G|||	14	0.00279553	0.0	0.0029	5008	,	,		14999	0.001		0.005	False		,,,				2504	0.0061				p.R377H		Atlas-SNP	.											.	KIAA1614	75	.	0			c.G1130A						PASS	.	G	HIS/ARG	5,4137		0,5,2066	49.0	56.0	54.0		1130	1.1	1.0	1	dbSNP_134	54	54,8378		1,52,4163	yes	missense	KIAA1614	NM_020950.1	29	1,57,6229	AA,AG,GG		0.6404,0.1207,0.4692	probably-damaging	377/1191	180897634	59,12515	2071	4216	6287	SO:0001583	missense	57710	exon4			TGCAGCGTGCCCG	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.1130G>A	1.37:g.180897634G>A	ENSP00000356560:p.Arg377His	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	202	95	0.470297	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	37	CCDS41442.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	14.72	2.618956	0.46736	0.001207	0.006404	ENSG00000135835	ENST00000367588	T	0.22336	1.96	5.56	1.09	0.20402	.	0.498887	0.17274	N	0.180243	T	0.14874	0.0359	L	0.58101	1.795	0.37966	D	0.933112	B	0.13145	0.007	B	0.10450	0.005	T	0.13872	-1.0493	9	0.72032	D	0.01	-0.6487	9.816	0.40853	0.2886:0.0:0.7114:0.0	.	377	Q5VZ46	K1614_HUMAN	H	377	ENSP00000356560:R377H	ENSP00000356560:R377H	R	+	2	0	KIAA1614	179164257	0.993000	0.37304	0.971000	0.41717	0.997000	0.91878	2.386000	0.44380	0.254000	0.21573	0.650000	0.86243	CGT	G|0.997;A|0.003	0.003	strong		0.687	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
PTPRH	5794	hgsc.bcm.edu	37	19	55698955	55698955	+	Missense_Mutation	SNP	C	C	T	rs36092369	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55698955C>T	ENST00000376350.3	-	14	2514	c.2492G>A	c.(2491-2493)gGc>gAc	p.G831D	PTPRH_ENST00000263434.5_Missense_Mutation_p.G653D	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	831	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		G -> D (in dbSNP:rs36092369).		apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CTGGCTGTGGCCCACCAGGGA	0.582													C|||	35	0.00698882	0.0008	0.0115	5008	,	,		13434	0.0		0.0258	False		,,,				2504	0.0				p.G831D		Atlas-SNP	.											.	PTPRH	139	.	0			c.G2492A						PASS	.	C	ASP/GLY,ASP/GLY	26,4380	30.8+/-60.4	0,26,2177	86.0	71.0	76.0		1958,2492	0.4	0.0	19	dbSNP_126	76	184,8416	82.0+/-144.6	0,184,4116	yes	missense,missense	PTPRH	NM_001161440.1,NM_002842.3	94,94	0,210,6293	TT,TC,CC		2.1395,0.5901,1.6146	benign,benign	653/938,831/1116	55698955	210,12796	2203	4300	6503	SO:0001583	missense	5794	exon14			CTGTGGCCCACCA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.2492G>A	19.37:g.55698955C>T	ENSP00000365528:p.Gly831Asp	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	98	53	0.540816	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	20	0.009157509157509158	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	16	0.021108179419525065	C	10.21	1.286919	0.23478	0.005901	0.021395	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.11277	2.79;2.79	5.11	0.41	0.16387	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.972561	0.08370	N	0.956268	T	0.03915	0.0110	L	0.31752	0.955	0.46061	D	0.998842	B;B	0.20887	0.049;0.022	B;B	0.19666	0.026;0.018	T	0.13818	-1.0495	10	0.49607	T	0.09	.	7.556	0.27824	0.0:0.6382:0.1229:0.2389	rs36092369;rs61746916	653;831	C9JCH2;Q9HD43	.;PTPRH_HUMAN	D	831;653	ENSP00000365528:G831D;ENSP00000263434:G653D	ENSP00000263434:G653D	G	-	2	0	PTPRH	60390767	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.443000	0.21644	-0.238000	0.09724	-0.797000	0.03246	GGC	C|0.985;T|0.015	0.015	strong		0.582	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
PARP12	64761	hgsc.bcm.edu	37	7	139724555	139724555	+	Silent	SNP	C	C	G	rs3735352	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:139724555C>G	ENST00000263549.3	-	12	2784	c.1911G>C	c.(1909-1911)ccG>ccC	p.P637P		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	637	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					CCTTGGCCGGCGGACGGACAA	0.592													G|||	368	0.0734824	0.205	0.0389	5008	,	,		19852	0.0		0.0408	False		,,,				2504	0.0297				p.P637P		Atlas-SNP	.											.	PARP12	59	.	0			c.G1911C						PASS	.						111.0	93.0	99.0					7																	139724555		2203	4300	6503	SO:0001819	synonymous_variant	64761	exon12			GGCCGGCGGACGG	AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	21919	protein-coding gene	gene with protein product		612481	"""zinc finger CCCH-type domain containing 1"""	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1911G>C	7.37:g.139724555C>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	148	76	0.513514	NM_022750	Q9H610|Q9NP36|Q9NTI3	Silent	SNP	ENST00000263549.3	37	CCDS5857.1																																																																																			T|0.364;G|0.008;C|0.628	0.008	strong		0.592	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750	
TPCN2	219931	hgsc.bcm.edu	37	11	68846399	68846399	+	Missense_Mutation	SNP	A	A	T	rs35264875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:68846399A>T	ENST00000294309.3	+	16	1551	c.1450A>T	c.(1450-1452)Atg>Ttg	p.M484L	TPCN2_ENST00000442692.2_3'UTR|TPCN2_ENST00000542467.1_Missense_Mutation_p.M484L	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	484			M -> L (associated with SHEP10; dbSNP:rs35264875). {ECO:0000269|PubMed:18488028}.		calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CCTGTTGGAGATGCTGCTCAA	0.587													A|||	499	0.0996406	0.0212	0.085	5008	,	,		19355	0.0109		0.1988	False		,,,				2504	0.2055				p.M484L		Atlas-SNP	.											.	TPCN2	63	.	0			c.A1450T	GRCh37	CM083199	TPCN2	M	rs35264875	PASS	.	A	LEU/MET	154,4246	106.9+/-145.3	1,152,2047	134.0	116.0	122.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1450	-3.9	1.0	11	dbSNP_126	122	1516,7072	288.6+/-298.9	129,1258,2907	yes	missense	TPCN2	NM_139075.3	15	130,1410,4954	TT,TA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	17.6525,3.5,12.858	benign	484/753	68846399	1670,11318	2200	4294	6494	SO:0001583	missense	219931	exon16			TTGGAGATGCTGC	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1450A>T	11.37:g.68846399A>T	ENSP00000294309:p.Met484Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	143	74	0.517483	NM_139075	Q9NT82	Missense_Mutation	SNP	ENST00000294309.3	37	CCDS8189.1	221|221	0.10119047619047619|0.10119047619047619	20|20	0.04065040650406504|0.04065040650406504	37|37	0.10220994475138122|0.10220994475138122	1|1	0.0017482517482517483|0.0017482517482517483	163|163	0.21503957783641162|0.21503957783641162	A|A	1.170|1.170	-0.641124|-0.641124	0.03557|0.03557	0.035|0.035	0.176525|0.176525	ENSG00000162341|ENSG00000162341	ENST00000294309;ENST00000535009;ENST00000542467|ENST00000356782	D;D|.	0.97352|.	-4.35;-4.35|.	4.35|4.35	-3.89|-3.89	0.04193|0.04193	Ion transport (1);|.	0.610626|.	0.16272|.	N|.	0.221759|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.45228|0.45228	1.405|1.405	0.32294|0.32294	P|P	0.56594|0.56594	B;B;B|.	0.13145|.	0.007;0.004;0.005|.	B;B;B|.	0.12156|.	0.007;0.005;0.004|.	T|T	0.30851|0.30851	-0.9964|-0.9964	9|5	0.07325|0.51188	T|T	0.83|0.08	-9.7887|-9.7887	10.1342|10.1342	0.42697|0.42697	0.32:0.5707:0.0:0.1092|0.32:0.5707:0.0:0.1092	rs35264875|rs35264875	484;484;399|.	E7ETX0;Q8NHX9;F5H1G5|.	.;TPC2_HUMAN;.|.	L|S	484;399;484|357	ENSP00000294309:M484L;ENSP00000445551:M484L|.	ENSP00000294309:M484L|ENSP00000349231:R357S	M|R	+|+	1|3	0|2	TPCN2|TPCN2	68602975|68602975	0.977000|0.977000	0.34250|0.34250	0.985000|0.985000	0.45067|0.45067	0.406000|0.406000	0.30931|0.30931	0.673000|0.673000	0.25203|0.25203	-0.538000|-0.538000	0.06281|0.06281	-0.689000|-0.689000	0.03729|0.03729	ATG|AGA	A|0.879;T|0.121	0.121	strong		0.587	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
WDR81	124997	hgsc.bcm.edu	37	17	1636934	1636934	+	Missense_Mutation	SNP	A	A	G	rs587780503|rs3809870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1636934A>G	ENST00000409644.1	+	7	4603	c.4603A>G	c.(4603-4605)Atg>Gtg	p.M1535V	WDR81_ENST00000545662.1_Missense_Mutation_p.M166V|WDR81_ENST00000419248.1_Missense_Mutation_p.M308V|WDR81_ENST00000446363.1_Missense_Mutation_p.M174V|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Missense_Mutation_p.M484V|WDR81_ENST00000437219.2_Missense_Mutation_p.M332V	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1535			M -> V (in dbSNP:rs3809870). {ECO:0000269|PubMed:14702039}.		negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GGAGCCCACCATGCCCGGCAC	0.672													G|||	1397	0.278954	0.177	0.2219	5008	,	,		15718	0.4861		0.2744	False		,,,				2504	0.2485				p.M1535V		Atlas-SNP	.											.	WDR81	180	.	0			c.A4603G						PASS	.	G	VAL/MET,VAL/MET,VAL/MET,VAL/MET	804,3596		59,686,1455	31.0	37.0	35.0		1450,922,4603,994	-1.0	0.0	17	dbSNP_107	35	2261,6319		300,1661,2329	yes	missense,missense,missense,missense	WDR81	NM_152348.3,NM_001163811.1,NM_001163809.1,NM_001163673.1	21,21,21,21	359,2347,3784	GG,GA,AA		26.352,18.2727,23.6133	benign,benign,benign,benign	484/891,308/715,1535/1942,332/739	1636934	3065,9915	2200	4290	6490	SO:0001583	missense	124997	exon7			CCCACCATGCCCG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.4603A>G	17.37:g.1636934A>G	ENSP00000386609:p.Met1535Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	67	25	0.373134	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	662	0.3031135531135531	87	0.17682926829268292	86	0.23756906077348067	283	0.49475524475524474	206	0.2717678100263852	G	0.001	-3.187157	0.00026	0.182727	0.26352	ENSG00000167716	ENST00000437219;ENST00000309182;ENST00000446363;ENST00000419248;ENST00000418841;ENST00000409644;ENST00000354680;ENST00000545662	T;T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	4.26	-1.04	0.10068	.	1.449160	0.03756	N	0.257327	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.22452	-1.0216	9	0.13108	T	0.6	.	9.6648	0.39977	0.5735:0.0:0.4265:0.0	rs3809870;rs61272730	166;332;662;484	B7Z6V3;B7Z579;Q8TEL1;Q562E7	.;.;.;WDR81_HUMAN	V	332;484;174;308;120;1535;286;166	ENSP00000391074:M332V;ENSP00000312074:M484V;ENSP00000401560:M174V;ENSP00000407845:M308V;ENSP00000395198:M120V;ENSP00000386609:M1535V;ENSP00000442726:M166V	ENSP00000312074:M484V	M	+	1	0	WDR81	1583684	0.000000	0.05858	0.001000	0.08648	0.035000	0.12851	-0.684000	0.05173	-0.539000	0.06273	-0.971000	0.02607	ATG	A|0.743;G|0.257	0.257	strong		0.672	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
AKAP13	11214	hgsc.bcm.edu	37	15	86124419	86124419	+	Silent	SNP	C	C	T	rs4843073	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86124419C>T	ENST00000394518.2	+	7	3215	c.3120C>T	c.(3118-3120)tcC>tcT	p.S1040S	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Silent_p.S1040S	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1040					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						ACAACAGCTCCGCTCTGTTGC	0.572													C|||	2912	0.58147	0.5461	0.6153	5008	,	,		21032	0.5784		0.6153	False		,,,				2504	0.5736				p.S1040S	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C3120T						PASS	.	C	,	2605,1799	638.8+/-397.0	778,1049,375	65.0	60.0	62.0		3120,3120	-9.9	0.0	15	dbSNP_111	62	5538,3060	658.2+/-401.5	1797,1944,558	no	coding-synonymous,coding-synonymous	AKAP13	NM_006738.4,NM_007200.3	,	2575,2993,933	TT,TC,CC		35.5897,40.8492,37.3712	,	1040/2818,1040/2814	86124419	8143,4859	2202	4299	6501	SO:0001819	synonymous_variant	11214	exon7			CAGCTCCGCTCTG	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.3120C>T	15.37:g.86124419C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	37	CCDS32319.1																																																																																			C|0.387;T|0.613	0.613	strong		0.572	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
MUC21	394263	hgsc.bcm.edu	37	6	30955019	30955019	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30955019G>A	ENST00000376296.3	+	2	1308	c.1067G>A	c.(1066-1068)gGg>gAg	p.G356E	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	356	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACCTCCAGTGGGGCCAGCACA	0.637																																					p.G356E		Atlas-SNP	.											MUC21,NS,carcinoma,0,3	MUC21	98	3	0			c.G1067A						scavenged	.						136.0	135.0	136.0					6																	30955019		2203	4300	6503	SO:0001583	missense	394263	exon2			CCAGTGGGGCCAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1067G>A	6.37:g.30955019G>A	ENSP00000365473:p.Gly356Glu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	107	6	0.0560748	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	g	7.208	0.594777	0.13875	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.03035	4.07	3.8	-1.27	0.09347	.	.	.	.	.	T	0.00724	0.0024	L	0.29908	0.895	0.09310	N	1	P	0.41393	0.748	B	0.36959	0.237	T	0.44159	-0.9346	9	0.15952	T	0.53	0.3604	4.2322	0.10608	0.4907:0.0:0.345:0.1644	.	356	Q5SSG8	MUC21_HUMAN	E	206;356	ENSP00000365473:G356E	ENSP00000365473:G356E	G	+	2	0	MUC21	31062998	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	-0.756000	0.04777	-0.290000	0.09025	0.586000	0.80456	GGG	.	.	none		0.637	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
TTBK1	84630	hgsc.bcm.edu	37	6	43231048	43231048	+	Missense_Mutation	SNP	C	C	G	rs35175743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:43231048C>G	ENST00000259750.4	+	13	2029	c.1946C>G	c.(1945-1947)cCt>cGt	p.P649R	TTBK1_ENST00000304139.5_Missense_Mutation_p.P598R	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	649			P -> R (in dbSNP:rs35175743). {ECO:0000269|PubMed:17344846}.		substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			GGACCCCGCCCTCGACGGAGA	0.677													C|||	46	0.0091853	0.003	0.0086	5008	,	,		16590	0.0		0.0328	False		,,,				2504	0.0031				p.P649R		Atlas-SNP	.											.	TTBK1	124	.	0			c.C1946G						PASS	.	C	ARG/PRO	19,4261		0,19,2121	10.0	12.0	11.0		1946	5.0	1.0	6	dbSNP_126	11	196,8196		2,192,4002	yes	missense	TTBK1	NM_032538.1	103	2,211,6123	GG,GC,CC		2.3356,0.4439,1.6967	probably-damaging	649/1322	43231048	215,12457	2140	4196	6336	SO:0001583	missense	84630	exon13			CCCGCCCTCGACG	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.1946C>G	6.37:g.43231048C>G	ENSP00000259750:p.Pro649Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	34	0.015567765567765568	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	29	0.03825857519788918	C	18.88	3.718137	0.68844	0.004439	0.023356	ENSG00000146216	ENST00000259750	T	0.24538	1.85	5.03	5.03	0.67393	.	0.083494	0.47455	D	0.000230	T	0.15305	0.0369	L	0.46157	1.445	0.80722	D	1	B;P	0.46912	0.386;0.886	B;B	0.42771	0.167;0.397	T	0.02115	-1.1211	10	0.72032	D	0.01	.	11.044	0.47849	0.1856:0.8144:0.0:0.0	rs35175743;rs61729327	172;649	Q9H6N8;Q5TCY1	.;TTBK1_HUMAN	R	649	ENSP00000259750:P649R	ENSP00000259750:P649R	P	+	2	0	TTBK1	43339026	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.189000	0.65098	2.329000	0.79093	0.563000	0.77884	CCT	C|0.984;G|0.016	0.016	strong		0.677	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
RARS2	57038	hgsc.bcm.edu	37	6	88231226	88231226	+	Missense_Mutation	SNP	T	T	C	rs3757370	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:88231226T>C	ENST00000369536.5	-	12	1036	c.991A>G	c.(991-993)Ata>Gta	p.I331V	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	331			I -> V (in dbSNP:rs3757370). {ECO:0000269|PubMed:14702039}.		arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		ATTCGATCTATAGCAGCTGCA	0.338													T|||	234	0.0467252	0.0023	0.0144	5008	,	,		14966	0.13		0.0308	False		,,,				2504	0.0603				p.I331V		Atlas-SNP	.											.	RARS2	61	.	0			c.A991G						PASS	.	T	VAL/ILE	25,4381	31.7+/-61.6	0,25,2178	87.0	87.0	87.0		991	5.8	1.0	6	dbSNP_107	87	196,8404	85.6+/-148.0	5,186,4109	yes	missense	RARS2	NM_020320.3	29	5,211,6287	CC,CT,TT		2.2791,0.5674,1.6992	benign	331/579	88231226	221,12785	2203	4300	6503	SO:0001583	missense	57038	exon12			GATCTATAGCAGC	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	21406	protein-coding gene	gene with protein product	"""arginine tRNA ligase 2, mitochondrial (putative)"""	611524	"""arginyl-tRNA synthetase-like"""	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.991A>G	6.37:g.88231226T>C	ENSP00000358549:p.Ile331Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	127	70	0.551181	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	93	0.042582417582417584	1	0.0020325203252032522	3	0.008287292817679558	67	0.11713286713286714	22	0.029023746701846966	T	13.68	2.308999	0.40895	0.005674	0.022791	ENSG00000146282	ENST00000369536	T	0.62788	-0.0	5.83	5.83	0.93111	Arginyl-tRNA synthetase, class Ia, core (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.099876	0.64402	D	0.000002	T	0.39145	0.1067	N	0.26130	0.795	0.46356	D	0.999	B	0.28713	0.22	B	0.39119	0.291	T	0.38950	-0.9637	10	0.22706	T	0.39	.	12.1103	0.53836	0.0:0.0:0.1431:0.8569	rs3757370;rs52804813;rs3757370	331	Q5T160	SYRM_HUMAN	V	331	ENSP00000358549:I331V	ENSP00000358549:I331V	I	-	1	0	RARS2	88287945	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.440000	0.44855	2.236000	0.73375	0.533000	0.62120	ATA	T|0.970;C|0.030	0.030	strong		0.338	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
SEC14L3	266629	hgsc.bcm.edu	37	22	30860830	30860830	+	Missense_Mutation	SNP	C	C	T	rs2269961	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:30860830C>T	ENST00000215812.4	-	8	731	c.641G>A	c.(640-642)cGc>cAc	p.R214H	SEC14L3_ENST00000402286.1_Missense_Mutation_p.R137H|SEC14L3_ENST00000540910.1_Missense_Mutation_p.R137H|SEC14L3_ENST00000401751.1_Missense_Mutation_p.R155H|SEC14L3_ENST00000539629.1_Missense_Mutation_p.R155H|SEC14L3_ENST00000403066.1_Missense_Mutation_p.R155H|SEC14L3_ENST00000415957.2_Missense_Mutation_p.R155H	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	214	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		R -> H (in dbSNP:rs2269961).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	AATTTTCCTGCGAGTGTCCTC	0.443													C|||	1102	0.220048	0.2209	0.1427	5008	,	,		23188	0.3194		0.2167	False		,,,				2504	0.1748				p.R214H	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.G641A						PASS	.	C	HIS/ARG	1012,3394	374.9+/-321.4	117,778,1308	176.0	151.0	160.0		641	4.5	1.0	22	dbSNP_100	160	1833,6767	328.2+/-318.2	187,1459,2654	yes	missense	SEC14L3	NM_174975.4	29	304,2237,3962	TT,TC,CC		21.314,22.9687,21.8745	probably-damaging	214/401	30860830	2845,10161	2203	4300	6503	SO:0001583	missense	266629	exon8			TTCCTGCGAGTGT	AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.641G>A	22.37:g.30860830C>T	ENSP00000215812:p.Arg214His	Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	127	123	0.968504	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	502|502	0.22985347985347984|0.22985347985347984	94|94	0.1910569105691057|0.1910569105691057	60|60	0.16574585635359115|0.16574585635359115	182|182	0.3181818181818182|0.3181818181818182	166|166	0.21899736147757257|0.21899736147757257	C|C	24.0|24.0	4.480823|4.480823	0.84747|0.84747	0.229687|0.229687	0.21314|0.21314	ENSG00000100012|ENSG00000100012	ENST00000435069|ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	.|T;T;T;T;T;T;T	.|0.79352	.|-1.26;-1.26;-1.26;-1.26;-1.26;-1.26;-1.26	5.5|5.5	4.49|4.49	0.54785|0.54785	.|Cellular retinaldehyde-binding/triple function, C-terminal (5);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.80982|0.80982	2.52|2.52	0.09310|0.09310	P|P	1.0|1.0	.|D;D	.|0.76494	.|0.974;0.999	.|B;D	.|0.63597	.|0.419;0.916	T|T	0.00001|0.00001	-1.2690|-1.2690	4|9	.|0.72032	.|D	.|0.01	-11.635|-11.635	14.2373|14.2373	0.65934|0.65934	0.0:0.9272:0.0:0.0728|0.0:0.9272:0.0:0.0728	rs2269961;rs17659246;rs52827962;rs61243443;rs2269961|rs2269961;rs17659246;rs52827962;rs61243443;rs2269961	.|137;214	.|E9PE57;Q9UDX4	.|.;S14L3_HUMAN	T|H	180|155;155;214;137;155;155;137	.|ENSP00000385941:R155H;ENSP00000401864:R155H;ENSP00000215812:R214H;ENSP00000385004:R137H;ENSP00000383896:R155H;ENSP00000444691:R155H;ENSP00000439752:R137H	.|ENSP00000215812:R214H	A|R	-|-	1|2	0|0	SEC14L3|SEC14L3	29190830|29190830	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.701000|0.701000	0.40568|0.40568	4.589000|4.589000	0.61006|0.61006	1.334000|1.334000	0.45468|0.45468	0.655000|0.655000	0.94253|0.94253	GCA|CGC	C|0.774;N|0.001	.	strong		0.443	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
HIGD1B	51751	hgsc.bcm.edu	37	17	42927721	42927721	+	Missense_Mutation	SNP	G	G	A	rs1071682	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:42927721G>A	ENST00000253410.2	+	3	508	c.257G>A	c.(256-258)aGc>aAc	p.S86N	HIGD1B_ENST00000587021.1_Missense_Mutation_p.S41N|HIGD1B_ENST00000591513.1_Missense_Mutation_p.S86N|EFTUD2_ENST00000426333.2_3'UTR	NM_016438.2	NP_057522.1	Q9P298	HIG1B_HUMAN	HIG1 hypoxia inducible domain family, member 1B	86	HIG1. {ECO:0000255|PROSITE- ProRule:PRU00836}.		S -> N (in dbSNP:rs1071682). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)	5		Prostate(33;0.109)				ACAATGTACAGCGATTACGTC	0.527													G|||	1128	0.22524	0.1959	0.2334	5008	,	,		19254	0.0843		0.3439	False		,,,				2504	0.2822				p.S86N		Atlas-SNP	.											.	HIGD1B	8	.	0			c.G257A						PASS	.	G	,,ASN/SER	971,3435	364.6+/-317.1	112,747,1344	107.0	99.0	102.0		,,257	4.2	1.0	17	dbSNP_86	102	3111,5489	470.9+/-367.9	578,1955,1767	yes	utr-3,utr-3,missense	EFTUD2,HIGD1B	NM_001142605.1,NM_004247.3,NM_016438.2	,,46	690,2702,3111	AA,AG,GG		36.1744,22.0381,31.3855	,,benign	,,86/100	42927721	4082,8924	2203	4300	6503	SO:0001583	missense	51751	exon4			TGTACAGCGATTA	AB038021	CCDS11488.1	17q21.31	2009-03-17	2009-03-17			ENSG00000131097			24318	protein-coding gene	gene with protein product			"""HIG1 domain family, member 1B"""			12477932	Standard	NM_016438		Approved	CLST11240, CLST11240-15	uc031rau.1	Q9P298		ENST00000253410.2:c.257G>A	17.37:g.42927721G>A	ENSP00000253410:p.Ser86Asn	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_001271880	D3DX57|Q9P297	Missense_Mutation	SNP	ENST00000253410.2	37	CCDS11488.1	510	0.23351648351648352	104	0.21138211382113822	108	0.2983425414364641	46	0.08041958041958042	252	0.3324538258575198	G	8.023	0.760046	0.15846	0.220381	0.361744	ENSG00000131097	ENST00000253410	T	0.29917	1.55	5.24	4.23	0.50019	Hypoxia induced protein, domain (1);	0.358919	0.30201	N	0.010170	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999955091	B	0.02656	0.0	B	0.01281	0.0	T	0.42464	-0.9450	8	0.35671	T	0.21	-5.9784	7.5238	0.27643	0.2083:0.0:0.7917:0.0	rs1071682;rs2231649;rs3197382;rs3206868;rs11556249;rs17627800;rs52796922;rs61288939;rs1071682	86	Q9P298	HIG1B_HUMAN	N	86	ENSP00000253410:S86N	ENSP00000253410:S86N	S	+	2	0	HIGD1B	40283247	1.000000	0.71417	1.000000	0.80357	0.158000	0.22134	1.774000	0.38573	1.112000	0.41740	-0.466000	0.05196	AGC	G|0.720;A|0.280	0.280	strong		0.527	HIGD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448669.1	NM_016438	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036971	33036971	+	Silent	SNP	C	C	T	rs2308928	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33036971C>T	ENST00000419277.1	-	4	582	c.453G>A	c.(451-453)acG>acA	p.T151T	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Silent_p.T151T	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	151	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						TGCACAGCCACGTGACGTTGA	0.567													.|||	2198	0.438898	0.5802	0.2839	5008	,	,		19188	0.6796		0.1889	False		,,,				2504	0.3671				p.T151T		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G453A						PASS	.	C	,,	1423,1595		327,769,413	144.0	168.0	160.0		453,453,453	-2.0	0.9	6	dbSNP_126	160	960,4456		72,816,1820	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	399,1585,2233	TT,TC,CC		17.7253,47.1504,28.2547	,,	151/261,151/261,151/261	33036971	2383,6051	1509	2708	4217	SO:0001819	synonymous_variant	3113	exon3			CAGCCACGTGACG	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.453G>A	6.37:g.33036971C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	121	51	0.421488	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1	864	0.3956043956043956	274	0.556910569105691	89	0.24585635359116023	371	0.6486013986013986	130	0.17150395778364116	C	9.336	1.061867	0.19987	0.471504	0.177253	ENSG00000231389	ENST00000437811	.	.	.	3.4	-1.99	0.07457	.	.	.	.	.	T	0.06096	0.0158	.	.	.	0.09310	P	0.9999999999999838	.	.	.	.	.	.	T	0.35649	-0.9780	3	.	.	.	.	0.2576	0.00214	0.3011:0.282:0.1489:0.2681	rs2308928;rs17850579	.	.	.	M	19	.	.	V	-	1	0	HLA-DPA1	33144949	0.000000	0.05858	0.911000	0.35937	0.725000	0.41563	-5.615000	0.00109	-0.669000	0.05289	-0.165000	0.13383	GTG	C|0.695;T|0.305	0.305	strong		0.567	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
PTCHD2	57540	hgsc.bcm.edu	37	1	11561593	11561593	+	Missense_Mutation	SNP	G	G	A	rs2817580	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:11561593G>A	ENST00000294484.6	+	2	682	c.544G>A	c.(544-546)Ggc>Agc	p.G182S	PTCHD2_ENST00000389575.3_Missense_Mutation_p.G182S	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	182			G -> S (in dbSNP:rs2817580). {ECO:0000269|PubMed:10718198}.		cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CTCACTCGGTGGCCCAGGCCC	0.692													G|||	1862	0.371805	0.143	0.6311	5008	,	,		13855	0.2718		0.659	False		,,,				2504	0.3047				p.G182S		Atlas-SNP	.											.	PTCHD2	193	.	0			c.G544A						PASS	.	G	SER/GLY	960,2852		150,660,1096	12.0	15.0	14.0		544	0.8	0.0	1	dbSNP_100	14	5214,3008		1659,1896,556	yes	missense	PTCHD2	NM_020780.1	56	1809,2556,1652	AA,AG,GG		36.5848,25.1836,48.6954	benign	182/1393	11561593	6174,5860	1906	4111	6017	SO:0001583	missense	57540	exon2			CTCGGTGGCCCAG	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.544G>A	1.37:g.11561593G>A	ENSP00000294484:p.Gly182Ser	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	949	0.43452380952380953	71	0.1443089430894309	219	0.6049723756906077	157	0.2744755244755245	502	0.662269129287599	G	3.922	-0.017933	0.07681	0.251836	0.634152	ENSG00000204624	ENST00000294484;ENST00000389575	T;T	0.21734	1.99;1.99	2.78	0.794	0.18638	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.13594	0.008	B	0.14578	0.011	T	0.33420	-0.9869	8	0.12430	T	0.62	.	6.4306	0.21794	0.2544:0.0:0.7456:0.0	rs2817580;rs3738160;rs2817580	182	Q9P2K9	PTHD2_HUMAN	S	182	ENSP00000294484:G182S;ENSP00000374226:G182S	ENSP00000294484:G182S	G	+	1	0	PTCHD2	11484180	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	0.106000	0.15354	0.058000	0.16222	0.561000	0.74099	GGC	G|0.586;A|0.414	0.414	strong		0.692	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
JMJD4	65094	hgsc.bcm.edu	37	1	227920186	227920186	+	Silent	SNP	G	G	A	rs35575794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:227920186G>A	ENST00000366758.3	-	6	1298	c.1299C>T	c.(1297-1299)gaC>gaT	p.D433D	SNAP47_ENST00000480897.1_3'UTR|SNAP47_ENST00000366760.1_Intron|JMJD4_ENST00000485807.1_5'UTR|SNAP47_ENST00000315781.5_5'Flank|SNAP47_ENST00000366759.4_5'Flank|JMJD4_ENST00000438896.2_Silent_p.D417D	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	433										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				CTCTCTGGAAGTCGGGGTGCG	0.617													G|||	98	0.0195687	0.0023	0.0202	5008	,	,		19261	0.0		0.0656	False		,,,				2504	0.0153				p.D433D		Atlas-SNP	.											.	JMJD4	28	.	0			c.C1299T						PASS	.	G	,	64,4342	59.9+/-96.7	1,62,2140	77.0	67.0	70.0		1251,1299	3.9	1.0	1	dbSNP_126	70	571,8029	152.8+/-207.3	21,529,3750	no	coding-synonymous,coding-synonymous	JMJD4	NM_001161465.1,NM_023007.2	,	22,591,5890	AA,AG,GG		6.6395,1.4526,4.8824	,	417/448,433/464	227920186	635,12371	2203	4300	6503	SO:0001819	synonymous_variant	65094	exon6			CTGGAAGTCGGGG	AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692			25724	protein-coding gene	gene with protein product						12477932	Standard	NM_023007		Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.1299C>T	1.37:g.227920186G>A		Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	271	145	0.535055	NM_023007	Q5TBZ1|Q5TBZ6|Q9H970	Silent	SNP	ENST00000366758.3	37	CCDS1561.1	57	0.0260989010989011	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	47	0.06200527704485488	G	1.043	-0.678172	0.03378	0.014526	0.066395	ENSG00000081692	ENST00000438896	.	.	.	4.9	3.91	0.45181	.	.	.	.	.	T	0.10551	0.0258	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.08743	-1.0707	4	.	.	.	-40.3933	10.0022	0.41935	0.107:0.0:0.893:0.0	rs35575794;rs61750987	.	.	.	I	410	.	.	T	-	2	0	JMJD4	225986809	1.000000	0.71417	0.996000	0.52242	0.091000	0.18340	2.793000	0.47845	2.544000	0.85801	0.462000	0.41574	ACT	G|0.956;A|0.044	0.044	strong		0.617	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007	
SLIT2	9353	hgsc.bcm.edu	37	4	20490493	20490493	+	Silent	SNP	C	C	T	rs117793863	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:20490493C>T	ENST00000504154.1	+	8	915	c.663C>T	c.(661-663)tcC>tcT	p.S221S	SLIT2_ENST00000503837.1_Silent_p.S221S|SLIT2_ENST00000503823.1_Silent_p.S221S|SLIT2_ENST00000273739.5_Silent_p.S221S	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	221	LRRCT 1.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						CCTGGCTCTCCGACTGGCTTC	0.483													C|||	155	0.0309505	0.0	0.0	5008	,	,		16187	0.0446		0.0099	False		,,,				2504	0.1022				p.S221S		Atlas-SNP	.											.	SLIT2	290	.	0			c.C663T						PASS	.	C		18,4388	24.3+/-50.5	0,18,2185	152.0	163.0	160.0		663	-10.9	0.0	4	dbSNP_132	160	118,8482	62.4+/-124.4	0,118,4182	no	coding-synonymous	SLIT2	NM_004787.1		0,136,6367	TT,TC,CC		1.3721,0.4085,1.0457		221/1530	20490493	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	9353	exon8			GCTCTCCGACTGG	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.663C>T	4.37:g.20490493C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	165	80	0.484848	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																			C|0.989;T|0.011	0.011	strong		0.483	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
NOL10	79954	hgsc.bcm.edu	37	2	10784491	10784491	+	Silent	SNP	A	A	G	rs3732111	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:10784491A>G	ENST00000381685.5	-	13	1086	c.981T>C	c.(979-981)ctT>ctC	p.L327L	NOL10_ENST00000538384.1_Silent_p.L301L|NOL10_ENST00000542668.1_Silent_p.L277L|NOL10_ENST00000345985.3_Silent_p.L277L	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	327						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		TGGCCGTCAGAAGCATGCCTA	0.358													A|||	1245	0.248602	0.3011	0.3012	5008	,	,		16564	0.4157		0.1193	False		,,,				2504	0.1012				p.L327L		Atlas-SNP	.											.	NOL10	22	.	0			c.T981C						PASS	.	A		1222,3098		178,866,1116	42.0	41.0	41.0		981	-1.8	0.4	2	dbSNP_107	41	843,7517		47,749,3384	no	coding-synonymous	NOL10	NM_024894.2		225,1615,4500	GG,GA,AA		10.0837,28.287,16.2855		327/689	10784491	2065,10615	2160	4180	6340	SO:0001819	synonymous_variant	79954	exon13			CGTCAGAAGCATG	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.981T>C	2.37:g.10784491A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	161	65	0.403727	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Silent	SNP	ENST00000381685.5	37	CCDS1673.2																																																																																			A|0.770;G|0.230	0.230	strong		0.358	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
MUC21	394263	hgsc.bcm.edu	37	6	30955043	30955043	+	Missense_Mutation	SNP	G	G	A	rs9262385	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30955043G>A	ENST00000376296.3	+	2	1332	c.1091G>A	c.(1090-1092)gGg>gAg	p.G364E	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	364	28 X 15 AA approximate tandem repeats.|Ser-rich.			G -> E (in Ref. 3; AAQ88781 and 4; CAQ08321). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACCAACTCTGGGTCCAGCACG	0.632													a|||	106	0.0211661	0.0197	0.0576	5008	,	,		18768	0.0079		0.0179	False		,,,				2504	0.0143				p.G364E		Atlas-SNP	.											MUC21,NS,neuroblastoma,0,1	MUC21	98	1	0			c.G1091A						scavenged	.	A	GLU/GLY	25,4361		2,21,2170	143.0	141.0	141.0		1091	-6.6	0.0	6	dbSNP_118	141	46,8528		4,38,4245	no	missense	MUC21	NM_001010909.2	98	6,59,6415	AA,AG,GG		0.5365,0.57,0.5478	benign	364/567	30955043	71,12889	2193	4287	6480	SO:0001583	missense	394263	exon2			ACTCTGGGTCCAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1091G>A	6.37:g.30955043G>A	ENSP00000365473:p.Gly364Glu	Somatic	90	2	0.0222222		WXS	Illumina HiSeq	Phase_I	75	17	0.226667	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	a	0.072	-1.201075	0.01581	0.0057	0.005365	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02323	4.34	4.44	-6.61	0.01818	.	.	.	.	.	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.46830	-0.9163	9	0.02654	T	1	0.4928	3.9243	0.09257	0.1415:0.3445:0.3555:0.1585	rs9262385	364	Q5SSG8	MUC21_HUMAN	E	214;364	ENSP00000365473:G364E	ENSP00000365473:G364E	G	+	2	0	MUC21	31063022	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.474000	0.02337	-1.580000	0.01644	-2.305000	0.00258	GGG	G|0.992;A|0.008	0.008	strong		0.632	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735808	55735808	+	Silent	SNP	G	G	A	rs78226543	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55735808G>A	ENST00000312345.2	-	1	182	c.132C>T	c.(130-132)ccC>ccT	p.P44P		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					TCTGGAGAGCGGGGTGAATTT	0.343													G|||	192	0.0383387	0.0129	0.0389	5008	,	,		16381	0.002		0.0934	False		,,,				2504	0.0532				p.P44P		Atlas-SNP	.											.	OR10AG1	100	.	0			c.C132T						PASS	.	G		104,4292	70.3+/-108.2	3,98,2097	49.0	56.0	54.0		132	-2.7	0.0	11	dbSNP_132	54	670,7916	154.6+/-208.8	32,606,3655	no	coding-synonymous	OR10AG1	NM_001005491.1		35,704,5752	AA,AG,GG		7.8034,2.3658,5.9621		44/302	55735808	774,12208	2198	4293	6491	SO:0001819	synonymous_variant	282770	exon1			GAGAGCGGGGTGA	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.132C>T	11.37:g.55735808G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	161	50	0.310559	NM_001005491	B2RNH4|Q6IEU3	Silent	SNP	ENST00000312345.2	37	CCDS31514.1																																																																																			G|0.951;A|0.049	0.049	strong		0.343	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4455266	4455266	+	Missense_Mutation	SNP	G	G	T	rs117615621	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4455266G>T	ENST00000254718.4	-	8	1238	c.932C>A	c.(931-933)gCg>gAg	p.A311E	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.A311E			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	311	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						GGGCAGGGCCGCGCCCAGCAG	0.627													g|||	34	0.00678914	0.0	0.0043	5008	,	,		17646	0.0		0.0159	False		,,,				2504	0.0153				p.A311E		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C932A						PASS	.		GLU/ALA,GLU/ALA	21,4385	28.1+/-56.4	0,21,2182	77.0	77.0	77.0		932,932	4.1	0.0	17	dbSNP_132	77	183,8417	83.1+/-145.7	1,181,4118	yes	missense,missense	MYBBP1A	NM_001105538.1,NM_014520.3	107,107	1,202,6300	TT,TG,GG		2.1279,0.4766,1.5685	possibly-damaging,possibly-damaging	311/1333,311/1329	4455266	204,12802	2203	4300	6503	SO:0001583	missense	10514	exon8			AGGGCCGCGCCCA	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.932C>A	17.37:g.4455266G>T	ENSP00000254718:p.Ala311Glu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	0	0.0	13	0.017150395778364115	g	11.41	1.630660	0.28978	0.004766	0.021279	ENSG00000132382	ENST00000381556;ENST00000254718;ENST00000426435	T;T	0.46819	0.86;0.86	5.12	4.11	0.48088	Armadillo-type fold (1);	0.772320	0.12521	N	0.461686	T	0.31606	0.0802	L	0.43152	1.355	0.09310	N	1	P;P	0.49862	0.929;0.913	P;P	0.54431	0.752;0.637	T	0.25847	-1.0120	10	0.02654	T	1	-3.0486	12.5437	0.56186	0.0:0.2572:0.7428:0.0	.	311;311	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	E	311	ENSP00000370968:A311E;ENSP00000254718:A311E	ENSP00000254718:A311E	A	-	2	0	MYBBP1A	4402015	0.048000	0.20356	0.008000	0.14137	0.298000	0.27526	1.234000	0.32660	2.677000	0.91161	0.457000	0.33378	GCG	G|0.987;T|0.013	0.013	strong		0.627	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
PDLIM2	64236	hgsc.bcm.edu	37	8	22449181	22449181	+	Splice_Site	SNP	C	C	T	rs73229817	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22449181C>T	ENST00000397760.4	+	9	1281	c.881C>T	c.(880-882)gCg>gTg	p.A294V	PDLIM2_ENST00000339162.7_Intron|PDLIM2_ENST00000265810.4_Splice_Site_p.A294V|PDLIM2_ENST00000308354.7_Splice_Site_p.A544V|PDLIM2_ENST00000409141.1_Intron|AC037459.4_ENST00000430850.2_Splice_Site_p.A88V|PDLIM2_ENST00000448520.1_3'UTR|PDLIM2_ENST00000409417.1_Splice_Site_p.A294V|PDLIM2_ENST00000397761.2_Splice_Site_p.A294V			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)	294	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		ACCAGCATCGCGTGAGTGTGG	0.677													C|||	75	0.014976	0.0008	0.0259	5008	,	,		13301	0.0		0.0507	False		,,,				2504	0.0051				p.A544V		Atlas-SNP	.											.	PDLIM2	42	.	0			c.C1631T						PASS	.	C	VAL/ALA,VAL/ALA,	59,4335		0,59,2138	15.0	16.0	15.0		1631,881,	4.0	1.0	8	dbSNP_130	15	484,8090		15,454,3818	yes	missense-near-splice,missense-near-splice,intron	PDLIM2	NM_021630.5,NM_176871.3,NM_198042.3	64,64,	15,513,5956	TT,TC,CC		5.645,1.3427,4.1872	benign,benign,	544/603,294/367,	22449181	543,12425	2197	4287	6484	SO:0001630	splice_region_variant	64236	exon9			GCATCGCGTGAGT	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270	ENST00000397760.4:c.881+1C>T	8.37:g.22449181C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	96	42	0.4375	NM_021630	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	37		45	0.020604395604395604	0	0.0	8	0.022099447513812154	0	0.0	37	0.048812664907651716	C	5.401	0.259185	0.10239	0.013427	0.05645	ENSG00000120913;ENSG00000120913;ENSG00000120913;ENSG00000120913;ENSG00000120913;ENSG00000248235	ENST00000308354;ENST00000397760;ENST00000397761;ENST00000265810;ENST00000409417;ENST00000430850	D;D;D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27;-2.27;-2.27	4.89	3.98	0.46160	Zinc finger, LIM-type (5);	0.806538	0.11006	N	0.610011	T	0.18923	0.0454	N	0.02539	-0.55	0.80722	D	1	B;B	0.17667	0.023;0.002	B;B	0.12156	0.007;0.002	T	0.48570	-0.9024	10	0.02654	T	1	-4.4182	7.3807	0.26854	0.0:0.7362:0.1669:0.097	.	294;294	Q96JY6-3;Q96JY6	.;PDLI2_HUMAN	V	544;294;294;294;294;88	ENSP00000312634:A544V;ENSP00000380867:A294V;ENSP00000380868:A294V;ENSP00000265810:A294V;ENSP00000387084:A294V;ENSP00000428700:A88V	ENSP00000428700:A88V	A	+	2	0	AC037459.4;PDLIM2	22505126	0.679000	0.27596	0.980000	0.43619	0.979000	0.70002	0.646000	0.24797	0.988000	0.38734	0.491000	0.48974	GCG	C|0.969;T|0.031	0.031	strong		0.677	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1		Missense_Mutation
LIPC	3990	hgsc.bcm.edu	37	15	58838010	58838010	+	Missense_Mutation	SNP	A	A	G	rs6083	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:58838010A>G	ENST00000356113.6	+	7	1259	c.644A>G	c.(643-645)aAt>aGt	p.N215S	LIPC_ENST00000299022.5_Missense_Mutation_p.N215S|LIPC_ENST00000433326.2_Missense_Mutation_p.N154S|LIPC_ENST00000414170.3_Missense_Mutation_p.N215S			P11150	LIPC_HUMAN	lipase, hepatic	215			N -> S (in dbSNP:rs6083). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:12966036, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2324091, ECO:0000269|PubMed:2447084, ECO:0000269|PubMed:2828141}.		cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		GATGATGCCAATTTTGTGGAT	0.547													A|||	3048	0.608626	0.7141	0.4928	5008	,	,		17425	0.7917		0.3847	False		,,,				2504	0.59				p.N215S		Atlas-SNP	.											.	LIPC	56	.	0			c.A644G	GRCh37	CM910256	LIPC	M	rs6083	PASS	.	A	SER/ASN	2974,1410	683.7+/-404.3	1008,958,226	102.0	97.0	99.0		644	-0.1	0.2	15	dbSNP_52	99	3117,5467	477.4+/-369.6	585,1947,1760	yes	missense	LIPC	NM_000236.2	46	1593,2905,1986	GG,GA,AA		36.3117,32.1624,46.9695	benign	215/500	58838010	6091,6877	2192	4292	6484	SO:0001583	missense	3990	exon5			ATGCCAATTTTGT		CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.644A>G	15.37:g.58838010A>G	ENSP00000348425:p.Asn215Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	48	0.55814	NM_000236	A2RUB4|A8K9B6|O43571|P78529|Q99465	Missense_Mutation	SNP	ENST00000356113.6	37	CCDS10166.1	1284	0.5879120879120879	340	0.6910569105691057	173	0.47790055248618785	484	0.8461538461538461	287	0.3786279683377309	A	10.60	1.396310	0.25205	0.678376	0.363117	ENSG00000166035	ENST00000356113;ENST00000414170;ENST00000299022;ENST00000433326	D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61	5.44	-0.0709	0.13745	Lipase, N-terminal (1);	0.579236	0.19650	N	0.109222	T	0.00012	0.0000	L	0.47190	1.495	0.80722	P	0.0	B;B	0.18461	0.028;0.003	B;B	0.15870	0.014;0.011	T	0.31420	-0.9944	9	0.59425	D	0.04	.	2.8406	0.05528	0.5107:0.2771:0.0788:0.1334	rs6083;rs3184021;rs17269369;rs58086367;rs6083	154;215	E7EUK6;P11150	.;LIPC_HUMAN	S	215;215;215;154	ENSP00000348425:N215S;ENSP00000395569:N215S;ENSP00000299022:N215S;ENSP00000395002:N154S	ENSP00000299022:N215S	N	+	2	0	LIPC	56625302	0.005000	0.15991	0.226000	0.23910	0.397000	0.30659	2.059000	0.41384	0.025000	0.15241	-0.490000	0.04691	AAT	A|0.457;G|0.543	0.543	strong		0.547	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1		
PRDM2	7799	hgsc.bcm.edu	37	1	14105049	14105049	+	Missense_Mutation	SNP	C	C	A	rs61747667	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14105049C>A	ENST00000235372.7	+	8	1615	c.759C>A	c.(757-759)gaC>gaA	p.D253E	PRDM2_ENST00000343137.4_Missense_Mutation_p.D52E|PRDM2_ENST00000311066.5_Missense_Mutation_p.D253E|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.D52E	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		CAGAACCAGACGAGCGATTAG	0.577													C|||	160	0.0319489	0.0015	0.0	5008	,	,		18148	0.0218		0.0169	False		,,,				2504	0.1217				p.D253E		Atlas-SNP	.											.	PRDM2	147	.	0			c.C759A						PASS	.	C	GLU/ASP,,GLU/ASP,GLU/ASP	12,4394	17.9+/-39.9	0,12,2191	51.0	55.0	54.0		156,,759,759	-11.3	0.0	1	dbSNP_129	54	173,8427	73.2+/-135.9	2,169,4129	yes	missense,intron,missense,missense	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	45,,45,45	2,181,6320	AA,AC,CC		2.0116,0.2724,1.4224	benign,,benign,benign	52/1482,,253/1719,253/1683	14105049	185,12821	2203	4300	6503	SO:0001583	missense	7799	exon8			ACCAGACGAGCGA	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.759C>A	1.37:g.14105049C>A	ENSP00000235372:p.Asp253Glu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	121	62	0.512397	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	23	0.010531135531135532	1	0.0020325203252032522	1	0.0027624309392265192	9	0.015734265734265736	12	0.0158311345646438	C	1.830	-0.470076	0.04445	0.002724	0.020116	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137;ENST00000407521	T;T;T;T	0.01430	5.02;4.92;4.9;4.9	5.66	-11.3	0.00108	.	0.717944	0.14194	N	0.335143	T	0.00356	0.0011	L	0.35414	1.06	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.52624	-0.8551	10	0.02654	T	1	.	1.8264	0.03122	0.2114:0.1:0.3026:0.3861	rs61747667	111;253;253	Q5THJ0;Q13029;Q13029-2	.;PRDM2_HUMAN;.	E	253;253;253;52;52;52	ENSP00000235372:D253E;ENSP00000312352:D253E;ENSP00000411103:D52E;ENSP00000341621:D52E	ENSP00000235372:D253E	D	+	3	2	PRDM2	13977636	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-1.461000	0.02366	-2.802000	0.00351	-0.263000	0.10527	GAC	A|0.016;C|0.984;T|0.000	0.016	strong		0.577	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
NEB	4703	hgsc.bcm.edu	37	2	152500449	152500449	+	Missense_Mutation	SNP	C	C	G	rs13013209	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:152500449C>G	ENST00000172853.10	-	57	7986	c.7839G>C	c.(7837-7839)aaG>aaC	p.K2613N	NEB_ENST00000603639.1_Missense_Mutation_p.K2613N|NEB_ENST00000397345.3_Missense_Mutation_p.K2613N|NEB_ENST00000409198.1_Missense_Mutation_p.K2613N|NEB_ENST00000604864.1_Missense_Mutation_p.K2613N|NEB_ENST00000427231.2_Missense_Mutation_p.K2613N			P20929	NEBU_HUMAN	nebulin	2613			K -> N (in dbSNP:rs13013209).	K -> Y (in Ref. 1; CAA58788). {ECO:0000305}.	muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCTGGCACTTCTTGGCCAACA	0.562													C|||	1469	0.293331	0.031	0.4438	5008	,	,		19755	0.2609		0.4662	False		,,,				2504	0.3967				p.K2613N		Atlas-SNP	.											.	NEB	1697	.	0			c.G7839C						PASS	.	C	ASN/LYS,ASN/LYS,ASN/LYS	407,3733		27,353,1690	360.0	346.0	351.0		7839,7839,7839	5.8	1.0	2	dbSNP_121	351	3979,4421		941,2097,1162	no	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	94,94,94	968,2450,2852	GG,GC,CC		47.369,9.8309,34.9761	probably-damaging,probably-damaging,probably-damaging	2613/8526,2613/8526,2613/6670	152500449	4386,8154	2070	4200	6270	SO:0001583	missense	4703	exon57			GCACTTCTTGGCC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.7839G>C	2.37:g.152500449C>G	ENSP00000172853:p.Lys2613Asn	Somatic	297	1	0.003367		WXS	Illumina HiSeq	Phase_I	356	354	0.994382	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		656	0.30036630036630035	16	0.032520325203252036	140	0.3867403314917127	154	0.2692307692307692	346	0.45646437994722955	C	22.7	4.323892	0.81580	0.098309	0.47369	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.38560	1.13;1.13;1.13;1.13	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.88775	2.98	0.09310	P	1.0	D	0.76494	0.999	D	0.87578	0.998	T	0.35847	-0.9772	9	0.66056	D	0.02	.	19.9941	0.97377	0.0:1.0:0.0:0.0	rs13013209;rs52797571	2613	P20929	NEBU_HUMAN	N	2613	ENSP00000386259:K2613N;ENSP00000380505:K2613N;ENSP00000416578:K2613N;ENSP00000172853:K2613N	ENSP00000172853:K2613N	K	-	3	2	NEB	152208695	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.897000	0.63231	2.729000	0.93468	0.557000	0.71058	AAG	C|0.678;G|0.322	0.322	strong		0.562	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
FAM86A	196483	hgsc.bcm.edu	37	16	5140561	5140561	+	Silent	SNP	C	C	T	rs9673770	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:5140561C>T	ENST00000427587.4	-	5	416	c.348G>A	c.(346-348)tcG>tcA	p.S116S	FAM86A_ENST00000587133.1_Silent_p.S55S|FAM86A_ENST00000458008.4_Silent_p.S82S	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	116						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						CCGAGCCTCCCGAGGGCTGCA	0.582													c|||	459	0.0916534	0.0242	0.17	5008	,	,		20650	0.128		0.1402	False		,,,				2504	0.0399				p.S116S		Atlas-SNP	.											FAM86A,NS,carcinoma,0,1	FAM86A	32	1	0			c.G348A						PASS	.	C	,	138,4256	98.5+/-137.1	3,132,2062	62.0	63.0	63.0		348,246	-10.0	0.0	16	dbSNP_119	63	1084,7516	225.2+/-261.4	74,936,3290	no	coding-synonymous,coding-synonymous	FAM86A	NM_201400.2,NM_201598.2	,	77,1068,5352	TT,TC,CC		12.6047,3.1406,9.4043	,	116/331,82/297	5140561	1222,11772	2197	4300	6497	SO:0001819	synonymous_variant	196483	exon5			GCCTCCCGAGGGC	BC010084	CCDS10529.1, CCDS10530.1, CCDS73823.1	16p13.3	2012-11-07			ENSG00000118894	ENSG00000118894			32221	protein-coding gene	gene with protein product		615263					Standard	NM_201400		Approved	SB153, MGC19636	uc002cyo.2	Q96G04	OTTHUMG00000129527	ENST00000427587.4:c.348G>A	16.37:g.5140561C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	137	74	0.540146	NM_201400	D3DUF0|Q96S85	Silent	SNP	ENST00000427587.4	37	CCDS10529.1																																																																																			C|0.896;T|0.104	0.104	strong		0.582	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400	
C7orf72	100130988	hgsc.bcm.edu	37	7	50143938	50143938	+	Silent	SNP	C	C	T	rs17133685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:50143938C>T	ENST00000297001.6	+	2	632	c.582C>T	c.(580-582)ccC>ccT	p.P194P		NM_001161834.2	NP_001155306	A4D263	CG072_HUMAN	chromosome 7 open reading frame 72	194										NS(1)|breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|prostate(2)	9						AAGTTACTCCCTTACAACCTC	0.348													T|||	380	0.0758786	0.1263	0.0274	5008	,	,		12752	0.0476		0.0547	False		,,,				2504	0.093				p.P194P		Atlas-SNP	.											.	C7orf72	26	.	0			c.C582T						PASS	.						175.0	138.0	149.0					7																	50143938		692	1591	2283	SO:0001819	synonymous_variant	100130988	exon2			TACTCCCTTACAA		CCDS47585.1	7p12.2	2009-10-15			ENSG00000164500	ENSG00000164500			22564	protein-coding gene	gene with protein product							Standard	NM_001161834		Approved		uc011kcj.2	A4D263	OTTHUMG00000155883	ENST00000297001.6:c.582C>T	7.37:g.50143938C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	185	92	0.497297	NM_001161834	A6NDX9	Silent	SNP	ENST00000297001.6	37	CCDS47585.1																																																																																			C|0.927;T|0.073	0.073	strong		0.348	C7orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342124.1	NM_001161834	
APIP	51074	hgsc.bcm.edu	37	11	34910397	34910397	+	Missense_Mutation	SNP	C	C	T	rs1977420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:34910397C>T	ENST00000395787.3	-	4	441	c.227G>A	c.(226-228)tGt>tAt	p.C76Y	APIP_ENST00000278359.5_Missense_Mutation_p.C93Y|APIP_ENST00000527830.1_5'UTR	NM_015957.2	NP_057041.2			APAF1 interacting protein											kidney(2)|lung(1)|skin(1)	4	all_epithelial(35;0.161)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.000425)			ATTTATATCACAAACAAACAT	0.333													C|||	2291	0.457468	0.3056	0.4035	5008	,	,		14661	0.7371		0.3559	False		,,,				2504	0.5174				p.C76Y		Atlas-SNP	.											.	APIP	21	.	0			c.G227A						PASS	.	C	TYR/CYS	1360,3042	448.7+/-348.8	223,914,1064	86.0	80.0	82.0		227	5.8	1.0	11	dbSNP_92	82	3072,5524	467.2+/-367.0	556,1960,1782	yes	missense	APIP	NM_015957.2	194	779,2874,2846	TT,TC,CC		35.7376,30.895,34.0976	benign	76/243	34910397	4432,8566	2201	4298	6499	SO:0001583	missense	51074	exon4			ATATCACAAACAA	AF132963	CCDS7895.1	11p13	2014-05-12				ENSG00000149089	4.2.1.109		17581	protein-coding gene	gene with protein product	"""methylthioribulose-1-phosphate dehydratase"""	612491				10810093, 15262985, 24367089	Standard	NM_015957		Approved	CGI-29, Mmrp19, APIP2	uc001mvs.2	Q96GX9		ENST00000395787.3:c.227G>A	11.37:g.34910397C>T	ENSP00000379133:p.Cys76Tyr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_015957		Missense_Mutation	SNP	ENST00000395787.3	37	CCDS7895.1	998	0.45695970695970695	176	0.35772357723577236	145	0.4005524861878453	406	0.7097902097902098	271	0.3575197889182058	C	15.65	2.895387	0.52121	0.30895	0.357376	ENSG00000149089	ENST00000278359;ENST00000395787	T;T	0.21031	2.03;2.03	5.85	5.85	0.93711	Class II aldolase/adducin, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.35723	1.085	0.09310	P	0.999999999737726	B;B	0.15141	0.012;0.01	B;B	0.21708	0.036;0.021	T	0.38585	-0.9654	9	0.27785	T	0.31	-14.1985	20.1775	0.98187	0.0:1.0:0.0:0.0	rs1977420;rs17845553;rs17858450;rs61147536;rs1977420	93;76	B4DY17;Q96GX9	.;MTNB_HUMAN	Y	93;76	ENSP00000278359:C93Y;ENSP00000379133:C76Y	ENSP00000278359:C93Y	C	-	2	0	APIP	34866973	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.655000	0.61476	2.771000	0.95319	0.561000	0.74099	TGT	C|0.611;T|0.389	0.389	strong		0.333	APIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389864.1	NM_015957	
BMP2	650	hgsc.bcm.edu	37	20	6759115	6759115	+	Missense_Mutation	SNP	A	A	T	rs235768	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:6759115A>T	ENST00000378827.4	+	3	1789	c.570A>T	c.(568-570)agA>agT	p.R190S		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	190			R -> S (in dbSNP:rs235768).		activation of MAPK activity (GO:0000187)|atrioventricular valve morphogenesis (GO:0003181)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|bone mineralization (GO:0030282)|bone mineralization involved in bone maturation (GO:0035630)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiocyte differentiation (GO:0035051)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation (GO:0002062)|corticotropin hormone secreting cell differentiation (GO:0060128)|embryo development (GO:0009790)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchyme development (GO:0060485)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of calcium-independent cell-cell adhesion (GO:0051042)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|pericardium development (GO:0060039)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of odontogenesis (GO:0042482)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of Wnt signaling pathway by BMP signaling pathway (GO:0060804)|protein destabilization (GO:0031648)|protein phosphorylation (GO:0006468)|proteoglycan metabolic process (GO:0006029)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP receptor binding (GO:0070700)|phosphatase activator activity (GO:0019211)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)|retinol dehydrogenase activity (GO:0004745)|SMAD binding (GO:0046332)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	13						CCGTGACCAGACTTTTGGACA	0.468													A|||	3840	0.766773	0.9803	0.7291	5008	,	,		19497	0.8284		0.6223	False		,,,				2504	0.59				p.R190S		Atlas-SNP	.											.	BMP2	45	.	0			c.A570T						PASS	.	A	SER/ARG	4086,318	760.0+/-412.9	1900,286,16	58.0	63.0	61.0		570	5.7	1.0	20	dbSNP_79	61	5398,3202	643.9+/-400.0	1665,2068,567	yes	missense	BMP2	NM_001200.2	110	3565,2354,583	TT,TA,AA		37.2326,7.2207,27.0686	possibly-damaging	190/397	6759115	9484,3520	2202	4300	6502	SO:0001583	missense	650	exon3			GACCAGACTTTTG		CCDS13099.1	20p12	2014-01-30			ENSG00000125845	ENSG00000125845		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1069	protein-coding gene	gene with protein product		112261		BMP2A		2376592	Standard	NM_001200		Approved		uc002wmu.1	P12643	OTTHUMG00000031833	ENST00000378827.4:c.570A>T	20.37:g.6759115A>T	ENSP00000368104:p.Arg190Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	149	62	0.416107	NM_001200		Missense_Mutation	SNP	ENST00000378827.4	37	CCDS13099.1	1666	0.7628205128205128	480	0.975609756097561	251	0.6933701657458563	459	0.8024475524475524	476	0.6279683377308707	A	15.85	2.955336	0.53293	0.927793	0.627674	ENSG00000125845	ENST00000378827	T	0.70045	-0.45	5.72	5.72	0.89469	Transforming growth factor-beta, N-terminal (1);	0.083194	0.85682	D	0.000000	T	0.00012	0.0000	M	0.87038	2.855	0.09310	P	0.999999362888	D	0.56968	0.978	P	0.60236	0.871	T	0.15292	-1.0442	9	0.72032	D	0.01	.	16.3625	0.83273	1.0:0.0:0.0:0.0	rs235768;rs52826407;rs235768	190	P12643	BMP2_HUMAN	S	190	ENSP00000368104:R190S	ENSP00000368104:R190S	R	+	3	2	BMP2	6707115	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.861000	0.62969	2.319000	0.78375	0.524000	0.50904	AGA	A|0.265;T|0.735	0.735	strong		0.468	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3		
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18777422	18777422	+	Silent	SNP	G	G	A	rs45579937	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:18777422G>A	ENST00000380548.4	+	19	3534	c.3195G>A	c.(3193-3195)ctG>ctA	p.L1065L		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1065						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		AAGTGCTCCTGCACCTGCCCT	0.682													G|||	501	0.10004	0.0136	0.0807	5008	,	,		16632	0.123		0.171	False		,,,				2504	0.1339				p.L1065L		Atlas-SNP	.											ADAMTSL1_ENST00000380548,NS,carcinoma,0,1	ADAMTSL1	306	1	0			c.G3195A						scavenged	.	G		186,3920		4,178,1871	12.0	16.0	14.0		3195	2.8	0.7	9	dbSNP_127	14	1652,6722		169,1314,2704	no	coding-synonymous	ADAMTSL1	NM_001040272.5		173,1492,4575	AA,AG,GG		19.7277,4.53,14.7276		1065/1763	18777422	1838,10642	2053	4187	6240	SO:0001819	synonymous_variant	92949	exon19			GCTCCTGCACCTG	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.3195G>A	9.37:g.18777422G>A		Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	CCDS47954.1																																																																																			G|0.884;A|0.116	0.116	strong		0.682	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
DNAH3	55567	hgsc.bcm.edu	37	16	20981162	20981162	+	Missense_Mutation	SNP	T	T	C	rs12929546	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20981162T>C	ENST00000261383.3	-	52	8409	c.8410A>G	c.(8410-8412)Atc>Gtc	p.I2804V	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2804	Stalk. {ECO:0000250}.		I -> V (in dbSNP:rs12929546).		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CCTTTCATGATGCAGATGCTC	0.592													C|||	861	0.171925	0.2383	0.1052	5008	,	,		20774	0.1895		0.1054	False		,,,				2504	0.18				p.I2804V		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A8410G						PASS	.	C	VAL/ILE	908,3494	739.9+/-411.1	92,724,1385	142.0	127.0	132.0		8410	4.8	1.0	16	dbSNP_121	132	897,7703	778.0+/-407.7	44,809,3447	yes	missense	DNAH3	NM_017539.1	29	136,1533,4832	CC,CT,TT		10.4302,20.627,13.8825	benign	2804/4117	20981162	1805,11197	2201	4300	6501	SO:0001583	missense	55567	exon52			TCATGATGCAGAT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.8410A>G	16.37:g.20981162T>C	ENSP00000261383:p.Ile2804Val	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	322	0.14743589743589744	112	0.22764227642276422	32	0.08839779005524862	90	0.15734265734265734	88	0.11609498680738786	C	0.030	-1.339308	0.01287	0.20627	0.104302	ENSG00000158486	ENST00000261383	T	0.72615	-0.67	5.79	4.85	0.62838	Dynein heavy chain, coiled coil stalk (1);	0.153629	0.43579	N	0.000552	T	0.00039	0.0001	N	0.05177	-0.1	0.09310	P	1.0	B	0.02656	0.0	B	0.06405	0.002	T	0.03259	-1.1055	9	0.10377	T	0.69	.	11.8457	0.52383	0.0:0.8061:0.0:0.1939	rs12929546;rs52792526;rs56469197;rs12929546	2804	Q8TD57	DYH3_HUMAN	V	2804	ENSP00000261383:I2804V	ENSP00000261383:I2804V	I	-	1	0	DNAH3	20888663	0.998000	0.40836	0.997000	0.53966	0.039000	0.13416	2.152000	0.42272	0.829000	0.34733	-0.772000	0.03388	ATC	T|0.856;C|0.144	0.144	strong		0.592	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
NXPE4	54827	hgsc.bcm.edu	37	11	114453549	114453549	+	Silent	SNP	G	G	A	rs371147789		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:114453549G>A	ENST00000375478.3	-	3	471	c.291C>T	c.(289-291)gcC>gcT	p.A97A	NXPE4_ENST00000424261.2_5'UTR	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	97						extracellular vesicular exosome (GO:0070062)											TGCTATGTGTGGCGCTGGTGG	0.537																																					p.A97A		Atlas-SNP	.											FAM55D,NS,carcinoma,-2,1	.	.	1	0			c.C291T						PASS	.	G	,	1,4331		0,1,2165	251.0	250.0	250.0		291,	-1.0	0.0	11		250	2,8546		0,2,4272	no	coding-synonymous,utr-5	FAM55D	NM_001077639.1,NM_017678.2	,	0,3,6437	AA,AG,GG		0.0234,0.0231,0.0233	,	97/545,	114453549	3,12877	2166	4274	6440	SO:0001819	synonymous_variant	54827	exon3			ATGTGTGGCGCTG	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.291C>T	11.37:g.114453549G>A		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	325	142	0.436923	NM_001077639	Q6QDB4|Q9NXP5	Silent	SNP	ENST00000375478.3	37	CCDS41718.1																																																																																			.	.	weak		0.537	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
CFH	3075	hgsc.bcm.edu	37	1	196682947	196682947	+	Silent	SNP	G	G	A	rs2274700	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:196682947G>A	ENST00000367429.4	+	10	1659	c.1419G>A	c.(1417-1419)gcG>gcA	p.A473A		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	473	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						AAGAAAAAGCGAAATATCAAT	0.353													A|||	2399	0.479034	0.4735	0.5389	5008	,	,		16109	0.4246		0.4235	False		,,,				2504	0.5573				p.A473A		Atlas-SNP	.											.	CFH	251	.	0			c.G1419A	GRCh37	CM062504	CFH	M	rs2274700	PASS	.	A		2066,2340	606.9+/-390.8	497,1072,634	86.0	82.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1419	0.1	0.0	1	dbSNP_100	83	3477,5123	632.1+/-398.6	698,2081,1521	no	coding-synonymous	CFH	NM_000186.3		1195,3153,2155	AA,AG,GG		40.4302,46.8906,42.6188		473/1232	196682947	5543,7463	2203	4300	6503	SO:0001819	synonymous_variant	3075	exon10			AAAAGCGAAATAT	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.1419G>A	1.37:g.196682947G>A		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	321	129	0.401869	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000367429.4	37	CCDS1385.1																																																																																			G|0.570;A|0.430	0.430	strong		0.353	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
IDUA	3425	hgsc.bcm.edu	37	4	994452	994452	+	Silent	SNP	C	C	T	rs3755954	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:994452C>T	ENST00000247933.4	+	3	440	c.352C>T	c.(352-354)Ctg>Ttg	p.L118L	IDUA_ENST00000514224.1_5'UTR|IDUA_ENST00000453894.1_Silent_p.L71L	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	118					carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGACGGGTACCTGGACCTTCT	0.672													C|||	812	0.162141	0.1626	0.2046	5008	,	,		16145	0.1478		0.2505	False		,,,				2504	0.0552				p.L118L		Atlas-SNP	.											.	IDUA	33	.	0			c.C352T						PASS	.	C		859,3543	333.3+/-302.9	105,649,1447	71.0	63.0	66.0		352	-0.7	0.6	4	dbSNP_107	66	2075,6525	358.1+/-331.0	250,1575,2475	yes	coding-synonymous	IDUA	NM_000203.3		355,2224,3922	TT,TC,CC		24.1279,19.5139,22.5658		118/654	994452	2934,10068	2201	4300	6501	SO:0001819	synonymous_variant	3425	exon3			GGGTACCTGGACC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.352C>T	4.37:g.994452C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	240	124	0.516667	NM_000203	B3KWK6	Silent	SNP	ENST00000247933.4	37	CCDS3343.1																																																																																			C|0.784;T|0.216	0.216	strong		0.672	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
CNTN4	152330	hgsc.bcm.edu	37	3	3081750	3081750	+	Silent	SNP	A	A	T	rs6802588	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:3081750A>T	ENST00000397461.1	+	19	2577	c.2193A>T	c.(2191-2193)cgA>cgT	p.R731R	CNTN4_ENST00000358480.3_Silent_p.R512R|CNTN4_ENST00000448906.2_Silent_p.R403R|CNTN4_ENST00000418658.1_Silent_p.R731R|CNTN4_ENST00000397459.2_Silent_p.R403R|CNTN4_ENST00000427331.1_Silent_p.R731R|CNTN4-AS1_ENST00000442749.2_RNA	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	731	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		AGAATGGTCGAGGCTTTGGTT	0.473													A|||	1827	0.364816	0.09	0.4107	5008	,	,		20561	0.5873		0.3668	False		,,,				2504	0.4724				p.R731R		Atlas-SNP	.											CNTN4_ENST00000418658,caecum,carcinoma,+1,6	CNTN4	335	6	0			c.A2193T						PASS	.	A	,,,	593,3813	259.5+/-263.1	35,523,1645	119.0	105.0	110.0		2193,1206,2193,1209	-1.8	0.2	3	dbSNP_116	110	3419,5181	505.2+/-376.3	698,2023,1579	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CNTN4	NM_001206955.1,NM_001206956.1,NM_175607.2,NM_175613.2	,,,	733,2546,3224	TT,TA,AA		39.7558,13.4589,30.8473	,,,	731/1027,402/698,731/1027,403/699	3081750	4012,8994	2203	4300	6503	SO:0001819	synonymous_variant	152330	exon20			TGGTCGAGGCTTT	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.2193A>T	3.37:g.3081750A>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	223	99	0.443946	NM_175607	B2RAX3|Q8IX14|Q8TC35	Silent	SNP	ENST00000397461.1	37	CCDS43041.1																																																																																			A|0.660;T|0.340	0.340	strong		0.473	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
HTATIP2	10553	hgsc.bcm.edu	37	11	20403763	20403763	+	Missense_Mutation	SNP	C	C	T	rs376468659		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:20403763C>T	ENST00000451739.2	+	4	922	c.481C>T	c.(481-483)Cgt>Tgt	p.R161C	HTATIP2_ENST00000421577.2_Missense_Mutation_p.R161C|HTATIP2_ENST00000531058.1_Missense_Mutation_p.R115C|HTATIP2_ENST00000443524.2_Missense_Mutation_p.R161C|HTATIP2_ENST00000419348.2_Missense_Mutation_p.R195C	NM_001098522.1	NP_001091992.1			HIV-1 Tat interactive protein 2, 30kDa											large_intestine(2)|lung(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	8						AAAATTTGATCGTTACTCTGT	0.343																																					p.R195C		Atlas-SNP	.											.	HTATIP2	30	.	0			c.C583T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4404		0,0,2202	125.0	141.0	136.0		583,481,481,481	5.6	1.0	11		136	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	HTATIP2	NM_001098520.1,NM_001098521.1,NM_001098522.1,NM_006410.4	180,180,180,180	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	195/277,161/243,161/243,161/243	20403763	1,13003	2202	4300	6502	SO:0001583	missense	10553	exon5			TTTGATCGTTACT	AF039103	CCDS7852.1, CCDS44553.1, CCDS53613.1	11p15.1	2011-09-14	2002-08-29		ENSG00000109854	ENSG00000109854	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	16637	protein-coding gene	gene with protein product	"""Tat-interacting protein (30kD)"", ""short chain dehydrogenase/reductase family 44U, member 1"""	605628	"""HIV-1 Tat interactive protein 2, 30 kDa"""			9482853, 9174052, 19027726	Standard	NM_006410		Approved	TIP30, CC3, FLJ26963, SDR44U1	uc001mpx.2	Q9BUP3	OTTHUMG00000166015	ENST00000451739.2:c.481C>T	11.37:g.20403763C>T	ENSP00000394259:p.Arg161Cys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	4	0.0487805	NM_001098520		Missense_Mutation	SNP	ENST00000451739.2	37	CCDS7852.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.666405	0.88251	0.0	1.16E-4	ENSG00000109854	ENST00000421577;ENST00000443524;ENST00000419348;ENST00000451739;ENST00000531058	T;T;T;T;T	0.32753	1.5;1.5;1.5;1.5;1.44	5.62	5.62	0.85841	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.57007	0.2024	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.69654	0.939;0.965	T	0.55438	-0.8141	10	0.46703	T	0.11	-19.1679	17.5131	0.87765	0.0:1.0:0.0:0.0	.	161;195	Q9BUP3;Q9BUP3-3	HTAI2_HUMAN;.	C	161;161;195;161;115	ENSP00000397752:R161C;ENSP00000387876:R161C;ENSP00000392985:R195C;ENSP00000394259:R161C;ENSP00000436729:R115C	ENSP00000392985:R195C	R	+	1	0	HTATIP2	20360339	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.464000	0.53057	2.809000	0.96659	0.655000	0.94253	CGT	.	.	weak		0.343	HTATIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387445.2	NM_001098521	
OR1S2	219958	hgsc.bcm.edu	37	11	57970967	57970967	+	Silent	SNP	G	G	A	rs138762515		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57970967G>A	ENST00000302592.6	-	1	686	c.687C>T	c.(685-687)ttC>ttT	p.F229F		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	229						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F229F(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				AGACATAGGAGAAGAAGATGA	0.438																																					p.F229F		Atlas-SNP	.											OR1S2,NS,carcinoma,0,2	OR1S2	119	2	1	Substitution - coding silent(1)	kidney(1)	c.C687T						scavenged	.						154.0	129.0	138.0					11																	57970967		2201	4296	6497	SO:0001819	synonymous_variant	219958	exon1			ATAGGAGAAGAAG	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.687C>T	11.37:g.57970967G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	136	7	0.0514706	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	37	CCDS31545.1																																																																																			G|0.999;A|0.001	0.001	weak		0.438	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
TRIM9	114088	hgsc.bcm.edu	37	14	51446216	51446216	+	Missense_Mutation	SNP	T	T	G	rs2275462	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:51446216T>G	ENST00000298355.3	-	9	3080	c.1959A>C	c.(1957-1959)ttA>ttC	p.L653F	TRIM9_ENST00000338969.5_Missense_Mutation_p.L734F	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	653	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		L -> F (in dbSNP:rs2275462). {ECO:0000269|PubMed:11331580, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9179496}.		negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					TTTTTCTATTTAAGTCGAGGA	0.448													T|||	2954	0.589856	0.4372	0.7262	5008	,	,		19323	0.6925		0.5537	False		,,,				2504	0.6309				p.L653F		Atlas-SNP	.											TRIM9_ENST00000338969,NS,carcinoma,-2,2	TRIM9	188	2	0			c.A1959C						scavenged	.	T	PHE/LEU	1944,2462	551.4+/-378.3	432,1080,691	198.0	218.0	211.0		1959	3.5	1.0	14	dbSNP_100	211	4883,3717	618.6+/-396.8	1386,2111,803	yes	missense	TRIM9	NM_015163.5	22	1818,3191,1494	GG,GT,TT		43.2209,44.1217,47.5088	benign	653/711	51446216	6827,6179	2203	4300	6503	SO:0001583	missense	114088	exon9			TCTATTTAAGTCG	AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16288	protein-coding gene	gene with protein product		606555	"""tripartite motif-containing 9"""			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.1959A>C	14.37:g.51446216T>G	ENSP00000298355:p.Leu653Phe	Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_015163	D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Missense_Mutation	SNP	ENST00000298355.3	37	CCDS9703.1	1278	0.5851648351648352	207	0.42073170731707316	241	0.6657458563535912	408	0.7132867132867133	422	0.5567282321899736	T	15.58	2.876985	0.51801	0.441217	0.567791	ENSG00000100505	ENST00000298355;ENST00000338969	T;T	0.73363	-0.44;-0.74	5.89	3.54	0.40534	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.122414	0.56097	N	0.000032	T	0.00012	0.0000	L	0.41236	1.265	0.09310	P	1.0	B;B	0.21606	0.058;0.012	B;B	0.29663	0.105;0.077	T	0.48387	-0.9040	9	0.11182	T	0.66	.	1.0846	0.01650	0.1734:0.1282:0.1816:0.5167	rs2275462;rs17795996;rs17855888;rs60258718;rs2275462	734;653	Q9C026-4;Q9C026	.;TRIM9_HUMAN	F	653;734	ENSP00000298355:L653F;ENSP00000342970:L734F	ENSP00000298355:L653F	L	-	3	2	TRIM9	50515966	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	0.502000	0.22594	1.035000	0.39972	0.455000	0.32223	TTA	T|0.451;G|0.549	0.549	strong		0.448	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163	
CCDC83	220047	hgsc.bcm.edu	37	11	85627108	85627108	+	Silent	SNP	T	T	C	rs7927222	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:85627108T>C	ENST00000342404.3	+	10	1128	c.912T>C	c.(910-912)agT>agC	p.S304S	CCDC83_ENST00000376067.1_Silent_p.S204S|CCDC83_ENST00000280245.4_Silent_p.S335S|RP11-90K17.2_ENST00000531414.1_RNA			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	304										breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				AAGTAGAAAGTAGAGACTTGA	0.323													T|||	631	0.125998	0.1399	0.1585	5008	,	,		19840	0.0		0.2604	False		,,,				2504	0.0757				p.S335S		Atlas-SNP	.											.	CCDC83	48	.	0			c.T1005C						PASS	.	T		662,3744	280.8+/-275.6	57,548,1598	113.0	114.0	114.0		1005	-10.3	0.0	11	dbSNP_116	114	2106,6492	363.6+/-333.2	275,1556,2468	no	coding-synonymous	CCDC83	NM_173556.3		332,2104,4066	CC,CT,TT		24.4941,15.025,21.2858		335/445	85627108	2768,10236	2203	4299	6502	SO:0001819	synonymous_variant	220047	exon11			AGAAAGTAGAGAC	AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.912T>C	11.37:g.85627108T>C		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	179	82	0.458101	NM_173556	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Silent	SNP	ENST00000342404.3	37		320	0.14652014652014653	61	0.12398373983739837	64	0.17679558011049723	0	0.0	195	0.25725593667546176	T	4.888	0.165049	0.09339	0.15025	0.244941	ENSG00000150676	ENST00000526729	.	.	.	5.17	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.15867	-1.0422	3	.	.	.	0.2638	4.5566	0.12140	0.2081:0.4914:0.1158:0.1848	rs7927222;rs17744860;rs57862723;rs7927222	.	.	.	A	209	.	.	V	+	2	0	CCDC83	85304756	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.837000	0.01689	-1.808000	0.01234	-0.468000	0.05107	GTA	T|0.812;C|0.188	0.188	strong		0.323	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037419	33037419	+	Splice_Site	SNP	G	G	A	rs17850584|rs1126543	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33037419G>A	ENST00000419277.1	-	3	474	c.345C>T	c.(343-345)aaC>aaT	p.N115N	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Splice_Site_p.N115N	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	115	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						AGGGCGTACCGTTGGTGGCCT	0.542													.|||	2200	0.439297	0.5809	0.2853	5008	,	,		19932	0.6796		0.1889	False		,,,				2504	0.3671				p.N115N		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C345T						PASS	.	A	,,	1387,1633		327,733,450	137.0	126.0	130.0		345,345,345	-3.5	0.0	6	dbSNP_86	130	942,4476		70,802,1837	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	397,1535,2287	AA,AG,GG		17.3865,45.9272,27.6013	,,	115/261,115/261,115/261	33037419	2329,6109	1510	2709	4219	SO:0001630	splice_region_variant	3113	exon2			CGTACCGTTGGTG	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.346+1C>T	6.37:g.33037419G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	154	45	0.292208	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1																																																																																			G|0.700;A|0.300	0.300	strong		0.542	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	Silent
SLC4A7	9497	hgsc.bcm.edu	37	3	27490194	27490194	+	Silent	SNP	T	T	C	rs13096477	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:27490194T>C	ENST00000295736.5	-	3	280	c.210A>G	c.(208-210)agA>agG	p.R70R	SLC4A7_ENST00000440156.1_Silent_p.R79R|SLC4A7_ENST00000428386.1_Silent_p.R70R|SLC4A7_ENST00000445684.1_Silent_p.R79R|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000454389.1_Silent_p.R79R|SLC4A7_ENST00000425128.2_Silent_p.R75R|SLC4A7_ENST00000446700.1_Silent_p.R75R|SLC4A7_ENST00000435667.2_Silent_p.R79R|SLC4A7_ENST00000455077.1_Silent_p.R75R|SLC4A7_ENST00000437179.1_Silent_p.R75R	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	70					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	TATCTTTTCTTCTCCGGTGGT	0.403													T|||	605	0.120807	0.034	0.1527	5008	,	,		14346	0.0565		0.2107	False		,,,				2504	0.1892				p.R75R		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A225G						PASS	.	T		300,4106	162.9+/-194.8	7,286,1910	238.0	214.0	222.0		210	0.6	1.0	3	dbSNP_121	222	1989,6611	347.9+/-326.8	221,1547,2532	no	coding-synonymous	SLC4A7	NM_003615.3		228,1833,4442	CC,CT,TT		23.1279,6.8089,17.5996		70/1215	27490194	2289,10717	2203	4300	6503	SO:0001819	synonymous_variant	9497	exon3			TTTTCTTCTCCGG	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.210A>G	3.37:g.27490194T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	225	94	0.417778	NM_001258379	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			T|0.851;C|0.149	0.149	strong		0.403	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
ADRA1D	146	hgsc.bcm.edu	37	20	4228735	4228735	+	Silent	SNP	C	C	T	rs35105284	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:4228735C>T	ENST00000379453.4	-	1	986	c.870G>A	c.(868-870)gcG>gcA	p.A290A		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	290					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			endometrium(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	14					Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	GCTTGACGCCCGCCTCGAGGC	0.716													c|||	1026	0.204872	0.1679	0.317	5008	,	,		12525	0.0546		0.2753	False		,,,				2504	0.2577				p.A290A		Atlas-SNP	.											.	ADRA1D	36	.	0			c.G870A						PASS	.			748,3524		84,580,1472	13.0	11.0	12.0		870	-2.3	1.0	20	dbSNP_126	12	2056,6376		285,1486,2445	no	coding-synonymous	ADRA1D	NM_000678.3		369,2066,3917	TT,TC,CC		24.3833,17.5094,22.0718		290/573	4228735	2804,9900	2136	4216	6352	SO:0001819	synonymous_variant	146	exon1			GACGCCCGCCTCG	U03864	CCDS13079.1	20p13	2012-08-08	2012-05-09		ENSG00000171873	ENSG00000171873		"""GPCR / Class A : Adrenoceptors : alpha"""	280	protein-coding gene	gene with protein product		104219	"""adrenergic, alpha-1D-, receptor"""			8039425	Standard	NM_000678		Approved	ADRA1R, ADRA1A, ADRA1	uc002wkr.2	P25100	OTTHUMG00000031779	ENST00000379453.4:c.870G>A	20.37:g.4228735C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_000678	Q9NPY0	Silent	SNP	ENST00000379453.4	37	CCDS13079.1																																																																																			C|0.787;T|0.213	0.213	strong		0.716	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678	
UBR5	51366	hgsc.bcm.edu	37	8	103276753	103276753	+	Silent	SNP	T	T	G	rs12707772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:103276753T>G	ENST00000520539.1	-	54	8241	c.7635A>C	c.(7633-7635)ctA>ctC	p.L2545L	UBR5_ENST00000518205.1_Silent_p.L273L|UBR5_ENST00000521922.1_Silent_p.L2538L|UBR5_ENST00000220959.4_Silent_p.L2544L	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2545	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TGATAGGACATAGTTCATTCT	0.289													T|||	340	0.0678914	0.0605	0.062	5008	,	,		15307	0.0139		0.171	False		,,,				2504	0.0317				p.L2545L	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.A7635C						PASS	.	T		344,4048	172.3+/-202.3	8,328,1860	49.0	49.0	49.0		7635	-8.1	0.9	8	dbSNP_121	49	1476,7066	270.1+/-288.8	133,1210,2928	no	coding-synonymous	UBR5	NM_015902.5		141,1538,4788	GG,GT,TT		17.2793,7.8324,14.0714		2545/2800	103276753	1820,11114	2196	4271	6467	SO:0001819	synonymous_variant	51366	exon54			AGGACATAGTTCA	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.7635A>C	8.37:g.103276753T>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	185	185	1	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	37	CCDS34933.1																																																																																			T|0.889;G|0.111	0.111	strong		0.289	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	
GPR50	9248	hgsc.bcm.edu	37	X	150349871	150349871	+	Missense_Mutation	SNP	A	A	G	rs13440581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:150349871A>G	ENST00000218316.3	+	2	1885	c.1816A>G	c.(1816-1818)Att>Gtt	p.I606V	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	606	Pro-rich.		I -> V (higher fasting circulating triglyceride levels; dbSNP:rs13440581). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8647286}.		cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					TGTCGTGGTTATTGATGTTGA	0.478													A|||	1032	0.273377	0.18	0.196	3775	,	,		17863	0.0129		0.4443	False		,,,				2504	0.2025				p.I606V		Atlas-SNP	.											.	GPR50	195	.	0			c.A1816G						PASS	.	A	VAL/ILE	996,2675		130,591,145,829,426	123.0	122.0	122.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1816	2.1	0.0	X	dbSNP_121	122	3870,2763		797,1197,1079,408,750	yes	missense	GPR50	NM_004224.3	29	927,1788,1224,1237,1176	GG,GA,G,AA,A		41.6554,27.1316,47.2244	benign	606/618	150349871	4866,5438	2121	4231	6352	SO:0001583	missense	9248	exon2			GTGGTTATTGATG	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.1816A>G	X.37:g.150349871A>G	ENSP00000218316:p.Ile606Val	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	45	27	0.6	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	516	0.31103074141048825	75	0.16968325791855204	53	0.17434210526315788	4	0.007017543859649123	225	0.41058394160583944	A	6.036	0.375080	0.11409	0.271316	0.583446	ENSG00000102195	ENST00000218316	T	0.70282	-0.47	3.33	2.13	0.27403	.	0.209202	0.24136	N	0.041201	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.14438	0.01	B	0.06405	0.002	T	0.43081	-0.9413	9	0.51188	T	0.08	-4.0928	4.235	0.10621	0.8259:0.0:0.1741:0.0	rs13440581	606	Q13585	MTR1L_HUMAN	V	606	ENSP00000218316:I606V	ENSP00000218316:I606V	I	+	1	0	GPR50	150100529	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-1.224000	0.02959	0.493000	0.27837	0.430000	0.28490	ATT	A|0.687;G|0.313	0.313	strong		0.478	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
WDR90	197335	hgsc.bcm.edu	37	16	711712	711712	+	Silent	SNP	C	C	T	rs3177415	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:711712C>T	ENST00000293879.4	+	31	3789	c.3789C>T	c.(3787-3789)ggC>ggT	p.G1263G	WDR90_ENST00000549091.1_Silent_p.G1263G			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1263										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GGGACGCCGGCGAGCTCACCT	0.682													C|||	3497	0.698283	0.8865	0.5951	5008	,	,		16897	0.9841		0.3708	False		,,,				2504	0.5593				p.G1263G		Atlas-SNP	.											.	WDR90	107	.	0			c.C3789T						PASS	.	C		3230,1016		1248,734,141	36.0	43.0	41.0		3789	-5.2	0.0	16	dbSNP_105	41	2960,5490		548,1864,1813	no	coding-synonymous	WDR90	NM_145294.4		1796,2598,1954	TT,TC,CC		35.0296,23.9284,48.7555		1263/1749	711712	6190,6506	2123	4225	6348	SO:0001819	synonymous_variant	197335	exon31			CGCCGGCGAGCTC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.3789C>T	16.37:g.711712C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	141	134	0.950355	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			C|0.451;T|0.549	0.549	strong		0.682	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
MIIP	60672	hgsc.bcm.edu	37	1	12082334	12082334	+	Missense_Mutation	SNP	A	A	T	rs11553925	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:12082334A>T	ENST00000235332.4	+	3	466	c.297A>T	c.(295-297)aaA>aaT	p.K99N	MIIP_ENST00000436478.2_Missense_Mutation_p.K99N|MIIP_ENST00000466860.1_3'UTR|Y_RNA_ENST00000365591.1_RNA	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein	99			K -> N (in dbSNP:rs11553925). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15867349}.							autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						CACCTGCCAAATGCCAGCACC	0.701													A|||	812	0.162141	0.1762	0.1398	5008	,	,		18127	0.0685		0.2515	False		,,,				2504	0.1636				p.K99N		Atlas-SNP	.											MIIP,brain,glioma,0,1	MIIP	34	1	0			c.A297T						PASS	.	A	ASN/LYS	744,3662	280.2+/-275.2	61,622,1520	45.0	49.0	48.0		297	-1.2	0.0	1	dbSNP_120	48	2149,6443	336.4+/-321.9	276,1597,2423	yes	missense	MIIP	NM_021933.3	94	337,2219,3943	TT,TA,AA		25.0116,16.8861,22.2573	possibly-damaging	99/389	12082334	2893,10105	2203	4296	6499	SO:0001583	missense	60672	exon3			TGCCAAATGCCAG	AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"""invasion inhibitory protein 45"""	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.297A>T	1.37:g.12082334A>T	ENSP00000235332:p.Lys99Asn	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_021933	C0KL22|Q96HU6|Q9H839|Q9HA00	Missense_Mutation	SNP	ENST00000235332.4	37	CCDS143.1	346	0.15842490842490842	81	0.16463414634146342	51	0.1408839779005525	21	0.03671328671328671	193	0.2546174142480211	A	20.4	3.982609	0.74474	0.168861	0.250116	ENSG00000116691	ENST00000235332;ENST00000436478	T;T	0.21543	2.0;2.0	4.49	-1.21	0.09524	.	1.829550	0.02773	N	0.119944	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	P	0.52316	0.952	P	0.51701	0.677	T	0.13469	-1.0508	9	0.41790	T	0.15	-0.001	8.0747	0.30710	0.4922:0.0:0.5077:0.0	rs11553925;rs17856239;rs61368770	99	Q5JXC2	MIIP_HUMAN	N	99	ENSP00000235332:K99N;ENSP00000392417:K99N	ENSP00000235332:K99N	K	+	3	2	MIIP	12004921	0.000000	0.05858	0.000000	0.03702	0.740000	0.42216	-0.465000	0.06680	-0.287000	0.09064	-0.285000	0.09966	AAA	A|0.799;T|0.201	0.201	strong		0.701	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933	
IL17RE	132014	hgsc.bcm.edu	37	3	9952706	9952706	+	Silent	SNP	A	A	G	rs279572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9952706A>G	ENST00000383814.3	+	9	1065	c.960A>G	c.(958-960)acA>acG	p.T320T	IL17RE_ENST00000295980.3_Silent_p.T320T|IL17RE_ENST00000454190.2_Silent_p.T320T|IL17RE_ENST00000421412.1_Silent_p.T353T	NM_153480.1	NP_705613.1	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E	320					inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(11)|skin(1)	21				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		CGAATGCCACAGCTCGAGAGT	0.617													G|||	2138	0.426917	0.6384	0.4683	5008	,	,		17881	0.0942		0.5527	False		,,,				2504	0.3252				p.T360T		Atlas-SNP	.											.	IL17RE	62	.	0			c.A1080G						PASS	.	G	,,	2733,1673	509.6+/-367.3	863,1007,333	59.0	60.0	59.0		960,960,1080	-6.6	0.3	3	dbSNP_79	59	4624,3976	552.1+/-386.1	1229,2166,905	no	coding-synonymous,coding-synonymous,coding-synonymous	IL17RE	NM_001193380.1,NM_153480.1,NM_153483.2	,,	2092,3173,1238	GG,GA,AA		46.2326,37.9709,43.4338	,,	320/534,320/668,360/708	9952706	7357,5649	2203	4300	6503	SO:0001819	synonymous_variant	132014	exon10			TGCCACAGCTCGA	AF458069	CCDS2589.1, CCDS54552.1	3p25.3	2008-02-05			ENSG00000163701	ENSG00000163701		"""Interleukins and interleukin receptors"""	18439	protein-coding gene	gene with protein product		614995					Standard	NM_153480		Approved	FLJ23658	uc003btu.3	Q8NFR9	OTTHUMG00000128649	ENST00000383814.3:c.960A>G	3.37:g.9952706A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_153483	B2RB34|B2RNR1|B9EH65|Q6P532|Q8N8H7|Q8N8H8|Q8TEC2	Silent	SNP	ENST00000383814.3	37	CCDS2589.1																																																																																			A|0.492;G|0.508	0.508	strong		0.617	IL17RE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250529.1	NM_153480	
FAT3	120114	hgsc.bcm.edu	37	11	92623877	92623877	+	Silent	SNP	G	G	A	rs12277422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:92623877G>A	ENST00000298047.6	+	27	13385	c.13368G>A	c.(13366-13368)ccG>ccA	p.P4456P	FAT3_ENST00000409404.2_Silent_p.P4424P|FAT3_ENST00000489716.1_3'UTR|FAT3_ENST00000533797.1_Silent_p.P759P|FAT3_ENST00000525166.1_Silent_p.P4306P			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4456	Pro-rich.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CTCCTCTCCCGGAGGACTTCC	0.577										TCGA Ovarian(4;0.039)			G|||	1133	0.226238	0.2148	0.2954	5008	,	,		17038	0.2381		0.2455	False		,,,				2504	0.1605				p.P4424P		Atlas-SNP	.											.	FAT3	1822	.	0			c.G13272A						PASS	.	G		884,3136		90,704,1216	30.0	34.0	33.0		13272	-11.3	0.0	11	dbSNP_120	33	2081,6257		268,1545,2356	yes	coding-synonymous	FAT3	NM_001008781.2		358,2249,3572	AA,AG,GG		24.958,21.99,23.9926		4424/4558	92623877	2965,9393	2010	4169	6179	SO:0001819	synonymous_variant	120114	exon25			TCTCCCGGAGGAC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.13368G>A	11.37:g.92623877G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				A|0.259;G|0.741	0.259	strong		0.577	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
VARS2	57176	hgsc.bcm.edu	37	6	30882689	30882689	+	Missense_Mutation	SNP	C	C	T	rs6926224	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30882689C>T	ENST00000321897.5	+	1	708	c.76C>T	c.(76-78)Cac>Tac	p.H26Y	VARS2_ENST00000416670.2_Missense_Mutation_p.H26Y|VARS2_ENST00000542001.1_Intron|VARS2_ENST00000541562.1_Missense_Mutation_p.H56Y			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	26			H -> Y (in dbSNP:rs6926224).		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						CCCCAGGTTTCACTCCGTTTC	0.592													C|||	325	0.0648962	0.121	0.0706	5008	,	,		18573	0.0476		0.0358	False		,,,				2504	0.0327				p.H56Y		Atlas-SNP	.											.	VARS2	60	.	0			c.C166T						PASS	.	C	,TYR/HIS,TYR/HIS	365,2655		27,311,1172	60.0	67.0	64.0		,166,76	2.2	0.0	6	dbSNP_116	64	195,5223		8,179,2522	yes	intron,missense,missense	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,83,83	35,490,3694	TT,TC,CC		3.5991,12.0861,6.6366	,benign,benign	,56/1094,26/1064	30882689	560,7878	1510	2709	4219	SO:0001583	missense	57176	exon2			AGGTTTCACTCCG	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.76C>T	6.37:g.30882689C>T	ENSP00000316092:p.His26Tyr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	168	0.07692307692307693	74	0.15040650406504066	35	0.09668508287292818	33	0.057692307692307696	26	0.03430079155672823	C	11.77	1.738479	0.30774	0.120861	0.035991	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000428017;ENST00000413959;ENST00000541562;ENST00000421263	T;T;T;T;T	0.32023	3.54;3.54;1.53;3.53;1.47	4.95	2.22	0.28083	.	1.675560	0.03247	N	0.181311	T	0.12433	0.0302	L	0.44542	1.39	0.54753	P	1.3000000000040757E-5	B;B;B	0.29716	0.0;0.255;0.022	B;B;B	0.28784	0.0;0.094;0.026	T	0.24764	-1.0151	9	0.72032	D	0.01	1.0156	7.1536	0.25624	0.0:0.7217:0.0:0.2783	rs6926224;rs6926224	26;56;26	B7ZL25;F5GXJ0;Q5ST30	.;.;SYVM_HUMAN	Y	26;26;26;26;56;26	ENSP00000316092:H26Y;ENSP00000394802:H26Y;ENSP00000403749:H26Y;ENSP00000441000:H56Y;ENSP00000416390:H26Y	ENSP00000316092:H26Y	H	+	1	0	VARS2	30990668	0.000000	0.05858	0.001000	0.08648	0.660000	0.38997	0.072000	0.14617	0.375000	0.24679	0.650000	0.86243	CAC	C|0.929;T|0.071	0.071	strong		0.592	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
TAB1	10454	hgsc.bcm.edu	37	22	39813801	39813801	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:39813801C>A	ENST00000216160.6	+	5	559	c.497C>A	c.(496-498)gCc>gAc	p.A166D	TAB1_ENST00000331454.3_Missense_Mutation_p.A166D	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	166	PP2C-like.				activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						TCGGGAGGGGCCATGGCCGTT	0.577																																					p.A166D		Atlas-SNP	.											.	TAB1	36	.	0			c.C497A						PASS	.						86.0	73.0	77.0					22																	39813801		2203	4300	6503	SO:0001583	missense	10454	exon5			GAGGGGCCATGGC	U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"""TAK1-binding protein 1"", ""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	602615	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.497C>A	22.37:g.39813801C>A	ENSP00000216160:p.Ala166Asp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_153497	Q2PP09|Q8IZW2	Missense_Mutation	SNP	ENST00000216160.6	37	CCDS13993.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.967710	0.92855	.	.	ENSG00000100324	ENST00000216160;ENST00000331454	T;T	0.10960	2.82;2.82	5.34	5.34	0.76211	Protein phosphatase 2C-like (4);	0.225313	0.44097	D	0.000492	T	0.36248	0.0960	M	0.76170	2.325	0.80722	D	1	P;P;D	0.89917	0.944;0.814;1.0	P;B;D	0.87578	0.531;0.393;0.998	T	0.10109	-1.0644	10	0.72032	D	0.01	.	19.0356	0.92976	0.0:1.0:0.0:0.0	.	166;166;310	Q15750-2;Q15750;Q59FT7	.;TAB1_HUMAN;.	D	166	ENSP00000216160:A166D;ENSP00000333049:A166D	ENSP00000216160:A166D	A	+	2	0	TAB1	38143747	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.726000	0.74758	2.496000	0.84212	0.655000	0.94253	GCC	.	.	none		0.577	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497	
ZNF287	57336	hgsc.bcm.edu	37	17	16455760	16455760	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:16455760A>G	ENST00000395824.1	-	6	2313	c.1696T>C	c.(1696-1698)Tgt>Cgt	p.C566R	ZNF287_ENST00000395825.3_Missense_Mutation_p.C566R			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	559					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		CATTCATTACATTTATAACAC	0.348																																					p.C566R		Atlas-SNP	.											.	ZNF287	60	.	0			c.T1696C						PASS	.						89.0	92.0	91.0					17																	16455760		2203	4300	6503	SO:0001583	missense	57336	exon6			CATTACATTTATA	AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.1696T>C	17.37:g.16455760A>G	ENSP00000379168:p.Cys566Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	96	4	0.0416667	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	37	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	A	17.56	3.420080	0.62622	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	D;D	0.99974	-10.2;-10.2	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000025	D	0.99984	0.9995	H	0.99225	4.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99087	1.0839	10	0.87932	D	0	.	13.3294	0.60477	1.0:0.0:0.0:0.0	.	559	Q9HBT7	ZN287_HUMAN	R	566	ENSP00000379169:C566R;ENSP00000379168:C566R	ENSP00000379168:C566R	C	-	1	0	ZNF287	16396485	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.014000	0.93635	2.317000	0.78254	0.459000	0.35465	TGT	.	.	none		0.348	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1		
VCAN	1462	hgsc.bcm.edu	37	5	82789647	82789647	+	Silent	SNP	A	A	G	rs4470745	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:82789647A>G	ENST00000265077.3	+	5	1210	c.645A>G	c.(643-645)gtA>gtG	p.V215V	VCAN_ENST00000342785.4_Silent_p.V215V|VCAN_ENST00000513984.1_Silent_p.V215V|VCAN_ENST00000512590.2_Silent_p.V167V|VCAN_ENST00000343200.5_Silent_p.V215V|VCAN_ENST00000502527.2_Silent_p.V215V	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	215	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CTCCCAGAGTAGGCTGTTATG	0.473													A|||	1194	0.238419	0.2292	0.281	5008	,	,		19615	0.0893		0.4135	False		,,,				2504	0.1943				p.V215V		Atlas-SNP	.											.	VCAN	498	.	0			c.A645G						PASS	.	A	,,,	1066,3340	387.5+/-326.5	120,826,1257	138.0	132.0	134.0		645,645,645,645	3.4	1.0	5	dbSNP_111	134	3493,5107	511.9+/-377.8	697,2099,1504	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	817,2925,2761	GG,GA,AA		40.6163,24.1943,35.0531	,,,	215/656,215/2410,215/1643,215/3397	82789647	4559,8447	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon5			CAGAGTAGGCTGT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.645A>G	5.37:g.82789647A>G		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	287	283	0.986063	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			A|0.691;G|0.309	0.309	strong		0.473	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
LRP1B	53353	hgsc.bcm.edu	37	2	141260668	141260668	+	Silent	SNP	A	A	G	rs4444457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:141260668A>G	ENST00000389484.3	-	54	9497	c.8526T>C	c.(8524-8526)taT>taC	p.Y2842Y		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2842					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CACACTGTCGATATCCTAGAG	0.398										TSP Lung(27;0.18)			G|||	2720	0.543131	0.466	0.451	5008	,	,		17484	0.7222		0.5388	False		,,,				2504	0.5327				p.Y2842Y	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T8526C						PASS	.	G		2201,2205	587.3+/-386.7	557,1087,559	118.0	110.0	113.0		8526	1.6	1.0	2	dbSNP_111	113	4728,3872	543.0+/-384.3	1306,2116,878	no	coding-synonymous	LRP1B	NM_018557.2		1863,3203,1437	GG,GA,AA		45.0233,49.9546,46.7246		2842/4600	141260668	6929,6077	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon54			CTGTCGATATCCT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8526T>C	2.37:g.141260668A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	192	95	0.494792	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			A|0.460;G|0.540	0.540	strong		0.398	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
OR1S2	219958	hgsc.bcm.edu	37	11	57971195	57971195	+	Silent	SNP	G	G	A	rs11229279	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57971195G>A	ENST00000302592.6	-	1	458	c.459C>T	c.(457-459)ttC>ttT	p.F153F		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F153F(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				GCAAAGTGCCGAACCTGGCCC	0.483													G|||	2137	0.426717	0.2239	0.3876	5008	,	,		21853	0.752		0.3161	False		,,,				2504	0.5072				p.F153F		Atlas-SNP	.											OR1S2,caecum,carcinoma,-2,2	OR1S2	119	2	1	Substitution - coding silent(1)	stomach(1)	c.C459T						PASS	.	G		1096,3306	396.5+/-330.1	131,834,1236	175.0	164.0	168.0		459	1.5	0.0	11	dbSNP_120	168	2804,5788	443.7+/-360.5	477,1850,1969	no	coding-synonymous	OR1S2	NM_001004459.1		608,2684,3205	AA,AG,GG		32.635,24.8978,30.0139		153/326	57971195	3900,9094	2201	4296	6497	SO:0001819	synonymous_variant	219958	exon1			AGTGCCGAACCTG	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.459C>T	11.37:g.57971195G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	261	100	0.383142	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	37	CCDS31545.1																																																																																			G|0.677;A|0.323	0.323	strong		0.483	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
CATSPER4	378807	hgsc.bcm.edu	37	1	26517891	26517891	+	Silent	SNP	C	C	T	rs11247867	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26517891C>T	ENST00000456354.2	+	2	394	c.327C>T	c.(325-327)atC>atT	p.I109I		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	109					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		CCATCACCATCGCTCTCCGTA	0.592													C|||	586	0.117013	0.2042	0.0893	5008	,	,		19617	0.0089		0.1879	False		,,,				2504	0.0573				p.I109I		Atlas-SNP	.											CATSPER4,caecum,carcinoma,0,1	CATSPER4	59	1	0			c.C327T						scavenged	.	C		921,3485	354.6+/-312.7	111,699,1393	92.0	75.0	80.0		327	-0.8	1.0	1	dbSNP_120	80	1628,6972	301.0+/-305.2	152,1324,2824	no	coding-synonymous	CATSPER4	NM_198137.1		263,2023,4217	TT,TC,CC		18.9302,20.9033,19.5986		109/473	26517891	2549,10457	2203	4300	6503	SO:0001819	synonymous_variant	378807	exon2			CACCATCGCTCTC	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.327C>T	1.37:g.26517891C>T		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	180	69	0.383333	NM_198137	A1A4W6|Q5VY71	Silent	SNP	ENST00000456354.2	37	CCDS30645.1																																																																																			C|0.822;T|0.178	0.178	strong		0.592	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
CACNA1D	776	hgsc.bcm.edu	37	3	53769479	53769479	+	Silent	SNP	C	C	T	rs1045958	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:53769479C>T	ENST00000350061.5	+	20	3211	c.2700C>T	c.(2698-2700)agC>agT	p.S900S	CACNA1D_ENST00000288139.4_Silent_p.S920S|CACNA1D_ENST00000422281.2_Silent_p.S900S	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	900					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGCTGAGCAGCGCTGCCCTGG	0.617													C|||	963	0.192292	0.0159	0.3112	5008	,	,		19700	0.2153		0.3191	False		,,,				2504	0.1922				p.S920S		Atlas-SNP	.											.	CACNA1D	324	.	0			c.C2760T						PASS	.	C	,,	307,4099	165.1+/-196.6	18,271,1914	112.0	93.0	100.0		2760,2700,2700	-6.5	0.2	3	dbSNP_86	100	3003,5597	464.9+/-366.4	529,1945,1826	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA1D	NM_000720.2,NM_001128839.1,NM_001128840.1	,,	547,2216,3740	TT,TC,CC		34.9186,6.9678,25.4498	,,	920/2182,900/2138,900/2162	53769479	3310,9696	2203	4300	6503	SO:0001819	synonymous_variant	776	exon21			GAGCAGCGCTGCC	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.2700C>T	3.37:g.53769479C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	164	161	0.981707	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Silent	SNP	ENST00000350061.5	37	CCDS46848.1																																																																																			C|0.761;T|0.239	0.239	strong		0.617	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720	
NASP	4678	hgsc.bcm.edu	37	1	46073489	46073489	+	Silent	SNP	G	G	A	rs2230657	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:46073489G>A	ENST00000350030.3	+	6	993	c.906G>A	c.(904-906)ccG>ccA	p.P302P	NASP_ENST00000537798.1_Silent_p.P238P|NASP_ENST00000402363.3_Silent_p.P304P|NASP_ENST00000351223.3_Intron|NASP_ENST00000372052.4_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	302	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					CTTTAGACCCGACAGTCAAGC	0.522													G|||	2872	0.573482	0.6831	0.5346	5008	,	,		17281	0.6329		0.4861	False		,,,				2504	0.4816				p.P302P		Atlas-SNP	.											NASP,colon,carcinoma,0,1	NASP	77	1	0			c.G906A						scavenged	.	G	,,	2933,1473	672.8+/-402.7	988,957,258	46.0	47.0	47.0		714,906,	-8.8	0.0	1	dbSNP_98	47	4098,4502	556.7+/-386.9	986,2126,1188	no	coding-synonymous,coding-synonymous,intron	NASP	NM_001195193.1,NM_002482.3,NM_152298.3	,,	1974,3083,1446	AA,AG,GG		47.6512,33.4317,45.9403	,,	238/725,302/789,	46073489	7031,5975	2203	4300	6503	SO:0001819	synonymous_variant	4678	exon6			AGACCCGACAGTC	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"""Tetratricopeptide (TTC) repeat domain containing"""	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.906G>A	1.37:g.46073489G>A		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	130	74	0.569231	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Silent	SNP	ENST00000350030.3	37	CCDS524.1																																																																																			G|0.444;A|0.556	0.556	strong		0.522	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482	
TLN2	83660	hgsc.bcm.edu	37	15	63127983	63127983	+	Silent	SNP	G	G	A	rs8038919	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:63127983G>A	ENST00000561311.1	+	55	7406	c.7176G>A	c.(7174-7176)caG>caA	p.Q2392Q	RP11-1069G10.1_ENST00000558404.1_RNA|TLN2_ENST00000306829.6_Silent_p.Q2392Q|RP11-1069G10.1_ENST00000558888.1_RNA			Q9Y4G6	TLN2_HUMAN	talin 2	2392	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						AGTGGTCACAGGGGCTGATTT	0.582													G|||	487	0.0972444	0.062	0.0951	5008	,	,		20090	0.0873		0.1163	False		,,,				2504	0.137				p.Q2392Q		Atlas-SNP	.											.	TLN2	253	.	0			c.G7176A						PASS	.	G		219,4187	132.9+/-169.3	10,199,1994	211.0	215.0	214.0		7176	2.9	1.0	15	dbSNP_116	214	953,7647	210.3+/-251.2	47,859,3394	no	coding-synonymous	TLN2	NM_015059.2		57,1058,5388	AA,AG,GG		11.0814,4.9705,9.0112		2392/2543	63127983	1172,11834	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon53			GTCACAGGGGCTG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.7176G>A	15.37:g.63127983G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	224	115	0.513393	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			G|0.912;A|0.088	0.088	strong		0.582	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
SPPL2C	162540	hgsc.bcm.edu	37	17	43923703	43923703	+	Silent	SNP	C	C	T	rs12185235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43923703C>T	ENST00000329196.5	+	1	1448	c.1431C>T	c.(1429-1431)acC>acT	p.T477T	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	477						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										TGGCCTGCACCGTGGCCTATG	0.577													C|||	430	0.0858626	0.0151	0.1571	5008	,	,		22489	0.001		0.2396	False		,,,				2504	0.0603				p.T477T		Atlas-SNP	.											.	.	.	.	0			c.C1431T						PASS	.	C		203,4203	127.0+/-164.0	6,191,2006	120.0	92.0	102.0		1431	-9.2	0.0	17	dbSNP_120	102	1927,6673	340.7+/-323.7	221,1485,2594	no	coding-synonymous	IMP5	NM_175882.2		227,1676,4600	TT,TC,CC		22.407,4.6074,16.3771		477/685	43923703	2130,10876	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			CTGCACCGTGGCC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1431C>T	17.37:g.43923703C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	110	47	0.427273	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			C|0.853;T|0.147	0.147	strong		0.577	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
SLC12A2	6558	hgsc.bcm.edu	37	5	127488456	127488456	+	Silent	SNP	A	A	C	rs115357531	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:127488456A>C	ENST00000262461.2	+	15	2511	c.2322A>C	c.(2320-2322)tcA>tcC	p.S774S	SLC12A2_ENST00000343225.4_Silent_p.S774S	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	774					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	TGCAGCATTCAATTCGTCTTT	0.413													A|||	2	0.000399361	0.0	0.0	5008	,	,		18737	0.0		0.002	False		,,,				2504	0.0				p.S774S		Atlas-SNP	.											.	SLC12A2	119	.	0			c.A2322C						PASS	.	A		0,4406		0,0,2203	127.0	119.0	122.0		2322	-10.5	0.2	5	dbSNP_132	122	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous	SLC12A2	NM_001046.2		0,21,6482	CC,CA,AA		0.2442,0.0,0.1615		774/1213	127488456	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	6558	exon15			GCATTCAATTCGT		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"""Solute carriers"""	10911	protein-coding gene	gene with protein product	"""bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1"", ""basolateral Na-K-Cl symporter"", ""protein phosphatase 1, regulatory subunit 141"""	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.2322A>C	5.37:g.127488456A>C		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	339	165	0.486726	NM_001046	Q8N713|Q8WWH7	Silent	SNP	ENST00000262461.2	37	CCDS4144.1																																																																																			A|0.999;C|0.001	0.001	strong		0.413	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046	
METTL11B	149281	hgsc.bcm.edu	37	1	170135828	170135828	+	Silent	SNP	C	C	T	rs41272487	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:170135828C>T	ENST00000439373.2	+	3	623	c.516C>T	c.(514-516)taC>taT	p.Y172Y	METTL11B_ENST00000367764.3_3'UTR	NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	172						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						ACCACTGCTACAGCCTGCAGG	0.493													C|||	293	0.0585064	0.1067	0.0562	5008	,	,		17807	0.004		0.0915	False		,,,				2504	0.0174				p.Y172Y		Atlas-SNP	.											.	METTL11B	18	.	0			c.C516T						PASS	.	C		157,1227		14,129,549	101.0	87.0	91.0		516	2.4	1.0	1	dbSNP_127	91	212,2970		6,200,1385	no	coding-synonymous	METTL11B	NM_001136107.1		20,329,1934	TT,TC,CC		6.6625,11.3439,8.0815		172/284	170135828	369,4197	692	1591	2283	SO:0001819	synonymous_variant	149281	exon3			CTGCTACAGCCTG	AL445203, CAH72139	CCDS44275.1	1q24.2	2012-11-05	2008-06-11	2008-06-11	ENSG00000203740	ENSG00000203740			31932	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 184"""	C1orf184			Standard	NM_001136107		Approved	HOMT1B	uc009wvv.1	Q5VVY1	OTTHUMG00000035959	ENST00000439373.2:c.516C>T	1.37:g.170135828C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	231	231	1	NM_001136107	B2RXI0	Silent	SNP	ENST00000439373.2	37	CCDS44275.1																																																																																			C|0.929;T|0.071	0.071	strong		0.493	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
OR2G2	81470	hgsc.bcm.edu	37	1	247752109	247752109	+	Missense_Mutation	SNP	A	A	G	rs61732336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:247752109A>G	ENST00000320065.1	+	1	448	c.448A>G	c.(448-450)Atg>Gtg	p.M150V	RP11-978I15.10_ENST00000435333.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			CTTGGCATCTATGGCATGGCT	0.557													G|||	337	0.0672923	0.0938	0.1095	5008	,	,		21707	0.0		0.1034	False		,,,				2504	0.0337				p.M150V		Atlas-SNP	.											.	OR2G2	88	.	0			c.A448G						PASS	.	G	VAL/MET	393,4013	790.2+/-415.0	16,361,1826	237.0	205.0	215.0		448	-5.3	0.0	1	dbSNP_129	215	848,7752	780.9+/-407.6	46,756,3498	yes	missense	OR2G2	NM_001001915.1	21	62,1117,5324	GG,GA,AA		9.8605,8.9197,9.5417	benign	150/318	247752109	1241,11765	2203	4300	6503	SO:0001583	missense	81470	exon1			GCATCTATGGCAT	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.448A>G	1.37:g.247752109A>G	ENSP00000326349:p.Met150Val	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	312	162	0.519231	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	160	0.07326007326007326	51	0.10365853658536585	33	0.09116022099447514	0	0.0	76	0.10026385224274406	G	0	-2.729325	0.00091	0.089197	0.098605	ENSG00000177489	ENST00000320065	T	0.33865	1.39	4.29	-5.33	0.02713	GPCR, rhodopsin-like superfamily (1);	1.021920	0.07888	N	0.970689	T	0.00210	0.0006	N	0.00514	-1.41	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.08743	-1.0707	9	0.02654	T	1	.	3.6913	0.08347	0.3747:0.1023:0.4062:0.1167	rs61732336	150	Q8NGZ5	OR2G2_HUMAN	V	150	ENSP00000326349:M150V	ENSP00000326349:M150V	M	+	1	0	OR2G2	245818732	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-3.255000	0.00538	-1.465000	0.01899	-1.221000	0.01599	ATG	A|0.915;G|0.085	0.085	strong		0.557	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
SLC11A1	6556	hgsc.bcm.edu	37	2	219249013	219249013	+	Silent	SNP	C	C	T	rs2276631	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:219249013C>T	ENST00000233202.6	+	3	538	c.198C>T	c.(196-198)ttC>ttT	p.F66F	SLC11A1_ENST00000539932.1_5'UTR|SLC11A1_ENST00000473367.1_Intron	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	66	Pro/Ser-rich.				activation of protein kinase activity (GO:0032147)|antigen processing and presentation of peptide antigen (GO:0048002)|cadmium ion transmembrane transport (GO:0070574)|cellular cadmium ion homeostasis (GO:0006876)|cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|divalent metal ion export (GO:0070839)|inflammatory response (GO:0006954)|interaction with host (GO:0051701)|interleukin-2 production (GO:0032623)|interleukin-3 production (GO:0032632)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|L-arginine import (GO:0043091)|macrophage activation (GO:0042116)|manganese ion transport (GO:0006828)|MHC class II biosynthetic process (GO:0045342)|mRNA stabilization (GO:0048255)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cytokine production (GO:0001818)|nitrite transport (GO:0015707)|phagocytosis (GO:0006909)|phagosome maturation (GO:0090382)|positive regulation of cytokine production (GO:0001819)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of gene expression (GO:0010628)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus, translocation (GO:0000060)|respiratory burst (GO:0045730)|response to bacterium (GO:0009617)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|T cell cytokine production (GO:0002369)|T cell proliferation involved in immune response (GO:0002309)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|wound healing (GO:0042060)	cell outer membrane (GO:0009279)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|tertiary granule membrane (GO:0070821)	manganese ion transmembrane transporter activity (GO:0005384)|metal ion:proton antiporter activity (GO:0051139)|protein homodimerization activity (GO:0042803)|transition metal ion transmembrane transporter activity (GO:0046915)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGCCTGGCTTCCTCATGAGCA	0.597													C|||	841	0.167931	0.1452	0.2695	5008	,	,		14695	0.0982		0.2505	False		,,,				2504	0.1135				p.F66F		Atlas-SNP	.											.	SLC11A1	41	.	0			c.C198T	GRCh37	CM057841	SLC11A1	M	rs2276631	PASS	.	C		758,3648	311.1+/-291.9	69,620,1514	110.0	105.0	107.0		198	2.0	1.0	2	dbSNP_100	107	2313,6287	389.5+/-342.9	323,1667,2310	no	coding-synonymous	SLC11A1	NM_000578.3		392,2287,3824	TT,TC,CC		26.8953,17.2038,23.6122		66/551	219249013	3071,9935	2203	4300	6503	SO:0001819	synonymous_variant	6556	exon3			TGGCTTCCTCATG	D38171	CCDS2415.1	2q35	2013-07-18	2013-07-18		ENSG00000018280	ENSG00000018280		"""Solute carriers"""	10907	protein-coding gene	gene with protein product	"""natural resistance-associated macrophage protein 1"""	600266		LSH, NRAMP, NRAMP1		7964458, 7980580	Standard	NM_000578		Approved		uc002vhv.3	P49279	OTTHUMG00000086747	ENST00000233202.6:c.198C>T	2.37:g.219249013C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_000578	C0H5Y3	Silent	SNP	ENST00000233202.6	37	CCDS2415.1																																																																																			C|0.789;T|0.211	0.211	strong		0.597	SLC11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195076.2	NM_000578	
HLA-B	3106	hgsc.bcm.edu	37	6	31323134	31323134	+	Silent	SNP	T	T	C	rs1050240		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323134T>C	ENST00000412585.2	-	4	883	c.855A>G	c.(853-855)gtA>gtG	p.V285V		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	285	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CCTCATGCTGTACATGGCATG	0.572									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.V285V		Atlas-SNP	.											.	HLA-B	54	.	0			c.A855G						PASS	.						73.0	65.0	68.0					6																	31323134		2203	4300	6503	SO:0001819	synonymous_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	ATGCTGTACATGG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.855A>G	6.37:g.31323134T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	177	46	0.259887	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	weak		0.572	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
DNASE1L3	1776	hgsc.bcm.edu	37	3	58183636	58183636	+	Missense_Mutation	SNP	G	G	A	rs35677470	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:58183636G>A	ENST00000394549.2	-	6	932	c.616C>T	c.(616-618)Cgc>Tgc	p.R206C	DNASE1L3_ENST00000486455.1_Missense_Mutation_p.R176C|DNASE1L3_ENST00000318316.3_Missense_Mutation_p.R206C|DNASE1L3_ENST00000483681.1_Missense_Mutation_p.R206C	NM_004944.3	NP_004935.1	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3	206			R -> C (in dbSNP:rs35677470). {ECO:0000269|PubMed:22019780}.		apoptotic DNA fragmentation (GO:0006309)|developmental programmed cell death (GO:0010623)|DNA metabolic process (GO:0006259)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			breast(2)|large_intestine(4)|lung(6)	12				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)		GTCCTCAAGCGGATGTTCTTC	0.517													G|||	100	0.0199681	0.003	0.0317	5008	,	,		20492	0.0		0.0527	False		,,,				2504	0.0215				p.R206C	Esophageal Squamous(96;1069 1424 4841 43466 52325)	Atlas-SNP	.											DNASE1L3,colon,carcinoma,+1,1	DNASE1L3	36	1	0			c.C616T						PASS	.	G	CYS/ARG	57,4349	55.5+/-91.7	1,55,2147	113.0	105.0	108.0		616	5.2	1.0	3	dbSNP_126	108	646,7954	166.2+/-218.2	26,594,3680	yes	missense	DNASE1L3	NM_004944.2	180	27,649,5827	AA,AG,GG		7.5116,1.2937,5.4052	probably-damaging	206/306	58183636	703,12303	2203	4300	6503	SO:0001583	missense	1776	exon6			TCAAGCGGATGTT	AF047354	CCDS2886.1, CCDS58836.1	3p14.3	2008-05-15			ENSG00000163687	ENSG00000163687			2959	protein-coding gene	gene with protein product	"""DNase gamma"""	602244				9205125, 9714828, 14646506	Standard	NM_004944		Approved	DNAS1L3, LSD	uc003djo.2	Q13609	OTTHUMG00000159153	ENST00000394549.2:c.616C>T	3.37:g.58183636G>A	ENSP00000378053:p.Arg206Cys	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	238	133	0.558824	NM_004944	B2R8B1|B7Z707|O75803	Missense_Mutation	SNP	ENST00000394549.2	37	CCDS2886.1	58	0.026556776556776556	3	0.006097560975609756	12	0.03314917127071823	0	0.0	43	0.05672823218997362	G	23.6	4.431643	0.83776	0.012937	0.075116	ENSG00000163687	ENST00000486455;ENST00000450710;ENST00000318316;ENST00000483681;ENST00000477209;ENST00000394549	D;D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56;-1.56	5.25	5.25	0.73442	Endonuclease/exonuclease/phosphatase (2);	0.000000	0.85682	D	0.000000	T	0.54240	0.1846	M	0.93808	3.46	0.09310	P	0.99999999771482	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.79266	-0.1874	9	0.87932	D	0	.	14.7337	0.69402	0.0:0.0:0.8549:0.1451	rs35677470	176;206;206	B7Z707;E9PES0;Q13609	.;.;DNSL3_HUMAN	C	176;206;206;206;80;206	ENSP00000419052:R176C;ENSP00000316193:R206C;ENSP00000417047:R206C;ENSP00000417976:R80C;ENSP00000378053:R206C	ENSP00000316193:R206C	R	-	1	0	DNASE1L3	58158676	1.000000	0.71417	0.999000	0.59377	0.751000	0.42716	5.173000	0.65010	2.738000	0.93877	0.591000	0.81541	CGC	G|0.954;A|0.046	0.046	strong		0.517	DNASE1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353533.1	NM_004944	
UBE3C	9690	hgsc.bcm.edu	37	7	157000176	157000176	+	Silent	SNP	T	T	C	rs2301914	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:157000176T>C	ENST00000348165.5	+	12	1863	c.1503T>C	c.(1501-1503)taT>taC	p.Y501Y		NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	501					protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		CACTCTTTTATCTTTTTAGCT	0.373													C|||	2552	0.509585	0.8253	0.3934	5008	,	,		18213	0.4534		0.3648	False		,,,				2504	0.3722				p.Y501Y		Atlas-SNP	.											.	UBE3C	124	.	0			c.T1503C						PASS	.	C		3334,1072	391.9+/-328.3	1256,822,125	151.0	147.0	148.0		1503	3.4	1.0	7	dbSNP_100	148	3034,5566	663.7+/-402.1	530,1974,1796	no	coding-synonymous	UBE3C	NM_014671.2		1786,2796,1921	CC,CT,TT		35.2791,24.3305,48.962		501/1084	157000176	6368,6638	2203	4300	6503	SO:0001819	synonymous_variant	9690	exon12			CTTTTATCTTTTT	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.1503T>C	7.37:g.157000176T>C		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	226	120	0.530973	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Silent	SNP	ENST00000348165.5	37	CCDS34789.1																																																																																			T|0.498;C|0.502	0.502	strong		0.373	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671	
FRAS1	80144	hgsc.bcm.edu	37	4	79240063	79240063	+	Missense_Mutation	SNP	A	A	G	rs345513	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:79240063A>G	ENST00000325942.6	+	18	2500	c.2060A>G	c.(2059-2061)gAc>gGc	p.D687G	FRAS1_ENST00000264895.6_Missense_Mutation_p.D687G|FRAS1_ENST00000264899.6_Missense_Mutation_p.D687G	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	687			D -> G (in dbSNP:rs345513).		cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CAGCTGTCTGACGTGGGCATC	0.542													G|||	2175	0.434305	0.5091	0.4539	5008	,	,		17068	0.4038		0.3946	False		,,,				2504	0.3916				p.D687G		Atlas-SNP	.											.	FRAS1	779	.	0			c.A2060G						PASS	.	G	GLY/ASP,GLY/ASP	1864,2090		450,964,563	136.0	136.0	136.0		2060,2060	4.0	0.0	4	dbSNP_79	136	3188,5138		595,1998,1570	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	94,94	1045,2962,2133	GG,GA,AA		38.2897,47.1421,41.1401	benign,benign	687/1977,687/4013	79240063	5052,7228	1977	4163	6140	SO:0001583	missense	80144	exon18			TGTCTGACGTGGG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.2060A>G	4.37:g.79240063A>G	ENSP00000326330:p.Asp687Gly	Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	943|943|943	0.4317765567765568|0.4317765567765568|0.4317765567765568	254|254|254	0.516260162601626|0.516260162601626|0.516260162601626	159|159|159	0.43922651933701656|0.43922651933701656|0.43922651933701656	230|230|230	0.4020979020979021|0.4020979020979021|0.4020979020979021	300|300|300	0.39577836411609496|0.39577836411609496|0.39577836411609496	G|G|G	0.003|0.003|0.003	-2.396851|-2.396851|-2.396851	0.00198|0.00198|0.00198	0.471421|0.471421|0.471421	0.382897|0.382897|0.382897	ENSG00000138759|ENSG00000138759|ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000264899|ENST00000502446|ENST00000508900	T;T;T|.|.	0.18960|.|.	2.18;2.58;2.33|.|.	5.71|5.71|5.71	3.96|3.96|3.96	0.45880|0.45880|0.45880	.|.|.	0.462954|.|.	0.22144|.|.	N|.|.	0.064015|.|.	T|T|.	0.00012|0.00012|.	0.0000|0.0000|.	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	P|P|P	0.0|0.0|0.0	B;B;B|.|.	0.02656|.|.	0.0;0.0;0.0|.|.	B;B;B|.|.	0.01281|.|.	0.0;0.0;0.0|.|.	T|T|.	0.48990|0.48990|.	-0.8985|-0.8985|.	8|3|.	0.02654|.|.	T|.|.	1|.|.	.|.|.	5.4424|5.4424|5.4424	0.16517|0.16517|0.16517	0.2232:0.272:0.5048:0.0|0.2232:0.272:0.5048:0.0|0.2232:0.272:0.5048:0.0	rs345513;rs61476559;rs345513|rs345513;rs61476559;rs345513|rs345513;rs61476559;rs345513	687;687;687|.|.	E9PHH6;E7EWM9;A2RRR8|.|.	.;.;.|.|.	G|A|W	687|616|529	ENSP00000326330:D687G;ENSP00000264895:D687G;ENSP00000264899:D687G|.|.	ENSP00000264895:D687G|.|.	D|T|X	+|+|+	2|1|3	0|0|0	FRAS1|FRAS1|FRAS1	79459087|79459087|79459087	0.016000|0.016000|0.016000	0.18221|0.18221|0.18221	0.003000|0.003000|0.003000	0.11579|0.11579|0.11579	0.000000|0.000000|0.000000	0.00434|0.00434|0.00434	0.432000|0.432000|0.432000	0.21461|0.21461|0.21461	0.343000|0.343000|0.343000	0.23821|0.23821|0.23821	-0.735000|-0.735000|-0.735000	0.03563|0.03563|0.03563	GAC|ACG|TGA	A|0.566;G|0.434	0.434	strong		0.542	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
ITGB4	3691	hgsc.bcm.edu	37	17	73725481	73725481	+	Silent	SNP	C	C	T	rs61751843	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73725481C>T	ENST00000200181.3	+	7	889	c.702C>T	c.(700-702)ggC>ggT	p.G234G	ITGB4_ENST00000339591.3_Silent_p.G234G|ITGB4_ENST00000449880.2_Silent_p.G234G|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000450894.3_Silent_p.G234G|ITGB4_ENST00000579662.1_Silent_p.G234G	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	234	VWFA.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTCCTGAGGGCGGCTTCGATG	0.592													C|||	81	0.0161741	0.0038	0.0274	5008	,	,		20621	0.0		0.0497	False		,,,				2504	0.0072				p.G234G		Atlas-SNP	.											.	ITGB4	165	.	0			c.C702T						PASS	.	C	,,	35,4371	39.2+/-71.8	1,33,2169	76.0	69.0	71.0		702,702,702	-11.3	0.1	17	dbSNP_129	71	366,8234	121.7+/-180.7	8,350,3942	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	,,	9,383,6111	TT,TC,CC		4.2558,0.7944,3.0832	,,	234/1823,234/1806,234/1753	73725481	401,12605	2203	4300	6503	SO:0001819	synonymous_variant	3691	exon7			TGAGGGCGGCTTC		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.702C>T	17.37:g.73725481C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	37	CCDS11727.1																																																																																			C|0.972;T|0.028	0.028	strong		0.592	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
OR8H2	390151	hgsc.bcm.edu	37	11	55873293	55873293	+	Missense_Mutation	SNP	T	T	C	rs61731255	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55873293T>C	ENST00000313503.1	+	1	775	c.775T>C	c.(775-777)Tat>Cat	p.Y259H		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					GATTTTTACTTATTTAAAACC	0.368										HNSCC(53;0.14)			t|||	195	0.0389377	0.0121	0.0447	5008	,	,		18285	0.001		0.0944	False		,,,				2504	0.0532				p.Y259H		Atlas-SNP	.											.	OR8H2	117	.	0			c.T775C						PASS	.	T	HIS/TYR	97,4305	75.7+/-113.9	0,97,2104	79.0	82.0	81.0		775	3.6	0.9	11	dbSNP_129	81	694,7898	170.3+/-221.5	35,624,3637	yes	missense	OR8H2	NM_001005200.1	83	35,721,5741	CC,CT,TT		8.0773,2.2035,6.0874	benign	259/313	55873293	791,12203	2201	4296	6497	SO:0001583	missense	390151	exon1			TTTACTTATTTAA	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.775T>C	11.37:g.55873293T>C	ENSP00000323982:p.Tyr259His	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	214	118	0.551402	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	86	0.039377289377289376	4	0.008130081300813009	14	0.03867403314917127	0	0.0	68	0.08970976253298153	t	10.79	1.450190	0.26074	0.022035	0.080773	ENSG00000181767	ENST00000313503	T	0.00291	8.27	3.58	3.58	0.41010	GPCR, rhodopsin-like superfamily (1);	0.143357	0.32918	N	0.005489	T	0.00012	0.0000	M	0.75777	2.31	0.22001	N	0.999428	B	0.31581	0.329	B	0.40375	0.327	T	0.27191	-1.0081	10	0.72032	D	0.01	.	8.5487	0.33438	0.1725:0.0:0.0:0.8275	rs61731255	259	Q8N162	OR8H2_HUMAN	H	259	ENSP00000323982:Y259H	ENSP00000323982:Y259H	Y	+	1	0	OR8H2	55629869	0.634000	0.27190	0.867000	0.34043	0.288000	0.27193	2.179000	0.42528	1.590000	0.49995	0.362000	0.22060	TAT	T|0.947;C|0.053	0.053	strong		0.368	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
DEPDC5	9681	hgsc.bcm.edu	37	22	32211412	32211412	+	Silent	SNP	A	A	C	rs5749334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:32211412A>C	ENST00000400242.3	+	22	1833	c.1677A>C	c.(1675-1677)ggA>ggC	p.G559G	DEPDC5_ENST00000382105.2_Intron|DEPDC5_ENST00000400249.2_Intron|DEPDC5_ENST00000536766.1_Intron|DEPDC5_ENST00000382112.3_Intron|DEPDC5_ENST00000535622.1_Intron|DEPDC5_ENST00000400246.1_Intron|DEPDC5_ENST00000400248.2_Intron|DEPDC5_ENST00000382111.2_Intron|DEPDC5_ENST00000266091.3_Intron	NM_001007188.2	NP_001007189.1	O75140	DEPD5_HUMAN	DEP domain containing 5	0					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						agcacctaggataaagtgcag	0.418													C|||	3335	0.665935	0.826	0.7147	5008	,	,		12523	0.6726		0.5139	False		,,,				2504	0.5644				p.G559G		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A1677C						PASS	.	C	,,,,	1588,446		616,356,45	43.0	43.0	43.0		1677,,,,	-0.4	0.0	22	dbSNP_114	43	2275,1945		618,1039,453	no	coding-synonymous,intron,intron,intron,intron	DEPDC5	NM_001007188.2,NM_001136029.2,NM_001242896.1,NM_001242897.1,NM_014662.3	,,,,	1234,1395,498	CC,CA,AA		46.09,21.9272,38.2315	,,,,	559/560,,,,	32211412	3863,2391	1017	2110	3127	SO:0001819	synonymous_variant	9681	exon22			CCTAGGATAAAGT	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000400242.3:c.1677A>C	22.37:g.32211412A>C		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_001007188	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Silent	SNP	ENST00000400242.3	37	CCDS43007.1																																																																																			A|0.346;C|0.654	0.654	strong		0.418	DEPDC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000129083.2	NM_014662	
CCT4	10575	hgsc.bcm.edu	37	2	62103327	62103327	+	Silent	SNP	G	G	T	rs115496486	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:62103327G>T	ENST00000394440.3	-	8	1116	c.820C>A	c.(820-822)Cga>Aga	p.R274R	CCT4_ENST00000544185.1_Silent_p.R124R|AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000538252.1_Silent_p.R218R|CCT4_ENST00000461540.2_5'UTR|CCT4_ENST00000544079.1_Silent_p.R244R	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	274					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			CGCAGCACTCGGTCCATCTGG	0.328													G|||	14	0.00279553	0.0	0.0058	5008	,	,		16234	0.0		0.0099	False		,,,				2504	0.0				p.R274R		Atlas-SNP	.											.	CCT4	38	.	0			c.C820A						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	103.0	107.0	106.0		820	2.1	1.0	2	dbSNP_132	106	44,8556	29.0+/-79.6	0,44,4256	no	coding-synonymous	CCT4	NM_006430.2		0,50,6453	TT,TG,GG		0.5116,0.1362,0.3844		274/540	62103327	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	10575	exon8			GCACTCGGTCCAT		CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"""Heat Shock Proteins / Chaperonins"""	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.820C>A	2.37:g.62103327G>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	231	87	0.376623	NM_006430	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Silent	SNP	ENST00000394440.3	37	CCDS33206.1																																																																																			G|0.996;T|0.004	0.004	strong		0.328	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2		
ADAR	103	hgsc.bcm.edu	37	1	154561925	154561925	+	Silent	SNP	C	C	T	rs1127309	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:154561925C>T	ENST00000368474.4	-	9	2881	c.2682G>A	c.(2680-2682)gtG>gtA	p.V894V	ADAR_ENST00000368471.3_Silent_p.V599V|ADAR_ENST00000292205.5_Silent_p.V937V	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	894	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		AATCTCCTTTCACACAGCGAT	0.438													C|||	1407	0.28095	0.2927	0.2133	5008	,	,		21281	0.3244		0.3221	False		,,,				2504	0.226				p.V894V		Atlas-SNP	.											.	ADAR	113	.	0			c.G2682A						PASS	.	C	,,,,	1357,3049	451.0+/-349.5	205,947,1051	90.0	81.0	84.0		1797,2682,1797,2604,2547	3.4	1.0	1	dbSNP_86	84	2519,6081	413.4+/-351.1	391,1737,2172	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADAR	NM_001025107.2,NM_001111.4,NM_001193495.1,NM_015840.3,NM_015841.3	,,,,	596,2684,3223	TT,TC,CC		29.2907,30.7989,29.8016	,,,,	599/932,894/1227,599/932,868/1201,849/1182	154561925	3876,9130	2203	4300	6503	SO:0001819	synonymous_variant	103	exon9			TCCTTTCACACAG	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.2682G>A	1.37:g.154561925C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_001111	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Silent	SNP	ENST00000368474.4	37	CCDS1071.1																																																																																			T|0.294;G|0.003;C|0.701;A|0.002	0.294	strong		0.438	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
HDAC4	9759	hgsc.bcm.edu	37	2	240078400	240078400	+	Silent	SNP	G	G	A	rs148880349	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:240078400G>A	ENST00000345617.3	-	7	1472	c.681C>T	c.(679-681)caC>caT	p.H227H	HDAC4_ENST00000541256.1_Silent_p.H196H|HDAC4_ENST00000543185.1_5'Flank|HDAC4_ENST00000553145.1_5'Flank	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	227	Interaction with MEF2A.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CCAGGACCGGGTGGTTATAGG	0.567																																					p.H227H		Atlas-SNP	.											.	HDAC4	127	.	0			c.C681T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	126.0	120.0	122.0		681	3.5	1.0	2	dbSNP_134	122	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	HDAC4	NM_006037.3		0,12,6491	AA,AG,GG		0.1047,0.0681,0.0923		227/1085	240078400	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon7			GACCGGGTGGTTA	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.681C>T	2.37:g.240078400G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.999;A|0.001	0.001	strong		0.567	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
KRTAP10-5	386680	hgsc.bcm.edu	37	21	46000398	46000398	+	Missense_Mutation	SNP	C	C	T	rs2020221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:46000398C>T	ENST00000400372.1	-	1	83	c.58G>A	c.(58-60)Gac>Aac	p.D20N	TSPEAR_ENST00000323084.4_Intron	NM_198694.2	NP_941967.2	P60370	KR105_HUMAN	keratin associated protein 10-5	20			D -> N (in dbSNP:rs2020221). {ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				endometrium(2)|kidney(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	14						GGGCAGTCGTCCACTCGCCAG	0.687													.|||	1848	0.36901	0.4054	0.4553	5008	,	,		18004	0.4425		0.2505	False		,,,				2504	0.3047				p.D20N		Atlas-SNP	.											.	KRTAP10-5	43	.	0			c.G58A						PASS	.	C	ASN/ASP,	1761,2643	496.0+/-363.4	360,1041,801	73.0	77.0	76.0		58,	2.5	1.0	21	dbSNP_92	76	2116,6482	356.0+/-330.1	258,1600,2441	no	missense,intron	TSPEAR,KRTAP10-5	NM_198694.2,NM_144991.2	23,	618,2641,3242	TT,TC,CC		24.6104,39.9864,29.8185	possibly-damaging,	20/272,	46000398	3877,9125	2202	4299	6501	SO:0001583	missense	386680	exon1			AGTCGTCCACTCG	AJ566384	CCDS42958.1	21q22.3	2007-10-05			ENSG00000241123	ENSG00000241123		"""Keratin associated proteins"""	22969	protein-coding gene	gene with protein product				KRTAP18-5			Standard	NM_198694		Approved	KAP10.5, KAP18.5	uc002zfl.1	P60370	OTTHUMG00000057638	ENST00000400372.1:c.58G>A	21.37:g.46000398C>T	ENSP00000383223:p.Asp20Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_198694	Q0VAR7|Q0VAR8|Q70LJ3	Missense_Mutation	SNP	ENST00000400372.1	37	CCDS42958.1	766	0.3507326007326007	183	0.3719512195121951	141	0.38950276243093923	251	0.4388111888111888	191	0.2519788918205805	c	10.66	1.413075	0.25465	0.399864	0.246104	ENSG00000241123	ENST00000400372	T	0.14893	2.47	3.39	2.47	0.30058	.	.	.	.	.	T	0.00012	0.0000	M	0.90198	3.095	0.39600	P	0.03029000000000004	P	0.34522	0.455	B	0.34301	0.179	T	0.33111	-0.9881	8	0.52906	T	0.07	.	8.749	0.34605	0.0:0.7672:0.2328:0.0	rs2020221;rs17004669;rs52824986;rs2020221	20	P60370	KR105_HUMAN	N	20	ENSP00000383223:D20N	ENSP00000383223:D20N	D	-	1	0	KRTAP10-5	44824826	0.023000	0.18921	0.997000	0.53966	0.107000	0.19398	0.648000	0.24828	0.739000	0.32628	0.298000	0.19748	GAC	C|0.669;T|0.331	0.331	strong		0.687	KRTAP10-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128042.1		
CLIP1	6249	hgsc.bcm.edu	37	12	122817580	122817580	+	Missense_Mutation	SNP	A	A	G	rs17883517	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:122817580A>G	ENST00000540338.1	-	14	2862	c.2821T>C	c.(2821-2823)Tct>Cct	p.S941P	CLIP1_ENST00000361654.4_Missense_Mutation_p.S819P|CLIP1_ENST00000537178.1_Missense_Mutation_p.S895P|CLIP1_ENST00000302528.7_Missense_Mutation_p.S930P|CLIP1_ENST00000358808.2_Missense_Mutation_p.S930P|CLIP1_ENST00000545889.1_Missense_Mutation_p.S516P			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	941			S -> P (in dbSNP:rs17883517). {ECO:0000269|PubMed:15489334}.		microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		AGCTGAGAAGAGTTATCTCCT	0.388													A|||	157	0.0313498	0.003	0.0591	5008	,	,		18646	0.001		0.1034	False		,,,				2504	0.0072				p.S941P		Atlas-SNP	.											.	CLIP1	126	.	0			c.T2821C						PASS	.	A	PRO/SER,PRO/SER	75,4331	67.0+/-104.6	1,73,2129	191.0	164.0	173.0		2788,2683	5.6	1.0	12	dbSNP_124	173	848,7748	193.0+/-238.8	37,774,3487	yes	missense,missense	CLIP1	NM_002956.2,NM_198240.1	74,74	38,847,5616	GG,GA,AA		9.8651,1.7022,7.0989	probably-damaging,probably-damaging	930/1428,895/1393	122817580	923,12079	2203	4298	6501	SO:0001583	missense	6249	exon15			GAGAAGAGTTATC		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.2821T>C	12.37:g.122817580A>G	ENSP00000439093:p.Ser941Pro	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	288	163	0.565972	NM_001247997	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	90	0.04120879120879121	1	0.0020325203252032522	20	0.055248618784530384	1	0.0017482517482517483	68	0.08970976253298153	A	27.9	4.876504	0.91664	0.017022	0.098651	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304	T;T;T;T;T;T	0.78126	2.31;-1.15;-1.15;0.29;0.29;-1.0	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.19765	0.0475	M	0.72894	2.215	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.74348	0.983;0.97;0.961	T	0.63269	-0.6675	10	0.56958	D	0.05	-9.4204	15.837	0.78805	1.0:0.0:0.0:0.0	rs17883517;rs17883517	895;930;941	P30622-2;P30622-1;P30622	.;.;CLIP1_HUMAN	P	516;930;930;660;895;941;788	ENSP00000438743:S516P;ENSP00000303585:S930P;ENSP00000351665:S930P;ENSP00000445531:S895P;ENSP00000439093:S941P;ENSP00000437786:S788P	ENSP00000303585:S930P	S	-	1	0	CLIP1	121383533	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.663000	0.91134	2.140000	0.66376	0.460000	0.39030	TCT	A|0.939;G|0.061	0.061	strong		0.388	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956	
KRT32	3882	hgsc.bcm.edu	37	17	39623431	39623431	+	Silent	SNP	C	C	T	rs117028403	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39623431C>T	ENST00000225899.3	-	1	250	c.147G>A	c.(145-147)tcG>tcA	p.S49S	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	49	Head.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				GCAGGCAGACCGAAGGCAGGC	0.662													C|||	75	0.014976	0.0008	0.0086	5008	,	,		17040	0.0		0.0318	False		,,,				2504	0.0368				p.S49S		Atlas-SNP	.											.	KRT32	57	.	0			c.G147A						PASS	.	C		28,4378	32.6+/-62.9	1,26,2176	36.0	39.0	38.0		147	-8.6	0.0	17	dbSNP_132	38	266,8334	98.8+/-160.4	6,254,4040	no	coding-synonymous	KRT32	NM_002278.3		7,280,6216	TT,TC,CC		3.093,0.6355,2.2605		49/449	39623431	294,12712	2203	4300	6503	SO:0001819	synonymous_variant	3882	exon1			GCAGACCGAAGGC	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.147G>A	17.37:g.39623431C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_002278		Silent	SNP	ENST00000225899.3	37	CCDS11393.1																																																																																			C|0.981;T|0.019	0.019	strong		0.662	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
ACP2	53	hgsc.bcm.edu	37	11	47261762	47261762	+	Missense_Mutation	SNP	A	A	G	rs145420520	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:47261762A>G	ENST00000256997.3	-	11	1293	c.1177T>C	c.(1177-1179)Ttc>Ctc	p.F393L	ACP2_ENST00000527256.1_Missense_Mutation_p.F361L|ACP2_ENST00000533929.1_Missense_Mutation_p.F365L|ACP2_ENST00000525230.1_5'UTR|ACP2_ENST00000529444.1_Missense_Mutation_p.F330L|ACP2_ENST00000537863.1_Missense_Mutation_p.F206L	NM_001610.2	NP_001601.1	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal	393					dephosphorylation (GO:0016311)|lysosome organization (GO:0007040)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)	acid phosphatase activity (GO:0003993)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)	10						ATGAGGAGGAAGAGGATGGAG	0.592													A|||	28	0.00559105	0.0015	0.0086	5008	,	,		22440	0.0		0.0149	False		,,,				2504	0.0051				p.F393L	Melanoma(90;262 1440 11488 44828 48531)	Atlas-SNP	.											.	ACP2	36	.	0			c.T1177C						PASS	.	A	LEU/PHE	9,4393	14.3+/-33.2	0,9,2192	121.0	83.0	96.0		1177	5.7	1.0	11	dbSNP_134	96	85,8511	49.8+/-109.6	1,83,4214	yes	missense	ACP2	NM_001610.2	22	1,92,6406	GG,GA,AA		0.9888,0.2045,0.7232	benign	393/424	47261762	94,12904	2201	4298	6499	SO:0001583	missense	53	exon11			GGAGGAAGAGGAT	X15525	CCDS7928.1, CCDS44583.1	11p11.2	2008-02-05			ENSG00000134575	ENSG00000134575	3.1.3.2		123	protein-coding gene	gene with protein product		171650				975882	Standard	NM_001610		Approved		uc001nei.3	P11117	OTTHUMG00000166949	ENST00000256997.3:c.1177T>C	11.37:g.47261762A>G	ENSP00000256997:p.Phe393Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_001610	E9PCI1|Q561W5|Q9BTU7	Missense_Mutation	SNP	ENST00000256997.3	37	CCDS7928.1	19	0.0086996336996337	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	13	0.017150395778364115	A	11.49	1.654886	0.29425	0.002045	0.009888	ENSG00000134575	ENST00000256997;ENST00000529444;ENST00000527256;ENST00000537863;ENST00000540414;ENST00000533929	T;T;T;T;T	0.10288	3.17;3.08;3.2;2.89;3.05	5.66	5.66	0.87406	.	0.156460	0.64402	D	0.000019	T	0.02418	0.0074	N	0.08118	0	0.34188	D	0.67174	B;B;B;B	0.12013	0.001;0.005;0.001;0.005	B;B;B;B	0.08055	0.001;0.003;0.001;0.003	T	0.32188	-0.9916	10	0.25106	T	0.35	.	9.2012	0.37260	0.9119:0.0:0.0881:0.0	.	330;361;365;393	E9PHY0;B7Z7D2;E9PQY3;P11117	.;.;.;PPAL_HUMAN	L	393;330;361;206;383;365	ENSP00000256997:F393L;ENSP00000436658:F330L;ENSP00000432205:F361L;ENSP00000441933:F206L;ENSP00000432439:F365L	ENSP00000256997:F393L	F	-	1	0	ACP2	47218338	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.024000	0.57218	2.158000	0.67659	0.482000	0.46254	TTC	A|0.991;G|0.009	0.009	strong		0.592	ACP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392022.2	NM_001610	
DMTN	2039	hgsc.bcm.edu	37	8	21924633	21924633	+	Missense_Mutation	SNP	G	G	A	rs113145439	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21924633G>A	ENST00000523266.1	+	3	518	c.56G>A	c.(55-57)cGa>cAa	p.R19Q	DMTN_ENST00000519907.1_Missense_Mutation_p.R19Q|DMTN_ENST00000265800.5_Missense_Mutation_p.R19Q|DMTN_ENST00000517600.1_Intron|DMTN_ENST00000443491.2_Intron|DMTN_ENST00000432128.1_Missense_Mutation_p.R19Q|DMTN_ENST00000415253.1_Missense_Mutation_p.R19Q|DMTN_ENST00000523782.2_Intron|DMTN_ENST00000358242.3_Missense_Mutation_p.R19Q|DMTN_ENST00000381470.3_Missense_Mutation_p.R19Q	NM_001978.2	NP_001969.2	Q08495	DEMA_HUMAN	dematin actin binding protein	19					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|actin filament capping (GO:0051693)|actin filament reorganization (GO:0090527)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cellular response to calcium ion (GO:0071277)|cellular response to cAMP (GO:0071320)|cytoskeleton organization (GO:0007010)|erythrocyte development (GO:0048821)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of platelet aggregation (GO:1901731)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of wound healing (GO:0090303)|protein complex assembly (GO:0006461)|protein secretion by platelet (GO:0070560)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)|regulation of lamellipodium assembly (GO:0010591)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection membrane (GO:0031253)|cortical cytoskeleton (GO:0030863)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|protein self-association (GO:0043621)|receptor binding (GO:0005102)|spectrin binding (GO:0030507)										AGCCCCTCCCGAGATTCCAGT	0.721													G|||	35	0.00698882	0.0053	0.0058	5008	,	,		10465	0.003		0.0149	False		,,,				2504	0.0061				p.R19Q		Atlas-SNP	.											.	EPB49	35	.	0			c.G56A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG	26,4372	33.5+/-64.1	0,26,2173	30.0	31.0	31.0		56,56,56,56,,56	4.9	1.0	8	dbSNP_132	31	111,8487	56.8+/-118.0	0,111,4188	yes	missense,missense,missense,missense,intron,missense	EPB49	NM_001114135.2,NM_001114136.1,NM_001114137.1,NM_001114138.1,NM_001114139.1,NM_001978.2	43,43,43,43,,43	0,137,6361	AA,AG,GG		1.291,0.5912,1.0542	probably-damaging,probably-damaging,probably-damaging,probably-damaging,,probably-damaging	19/406,19/406,19/384,19/384,,19/406	21924633	137,12859	2199	4299	6498	SO:0001583	missense	2039	exon3			CCTCCCGAGATTC	U28389	CCDS6020.1, CCDS47820.1, CCDS47821.1	8p21.1	2013-05-03	2013-05-03	2013-05-03	ENSG00000158856	ENSG00000158856			3382	protein-coding gene	gene with protein product		125305	"""erythrocyte membrane protein band 4.9 (dematin)"""	EPB49		8341682, 12011427	Standard	NM_001978		Approved	DMT		Q08495	OTTHUMG00000097087	ENST00000523266.1:c.56G>A	8.37:g.21924633G>A	ENSP00000427866:p.Arg19Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	127	65	0.511811	NM_001978	A8K0T5|B3KP70|B3KRH3|E9PEJ0|Q13215|Q9BRE3	Missense_Mutation	SNP	ENST00000523266.1	37	CCDS6020.1	16	0.007326007326007326	4	0.008130081300813009	1	0.0027624309392265192	3	0.005244755244755245	8	0.010554089709762533	G	23.7	4.448739	0.84101	0.005912	0.01291	ENSG00000158856	ENST00000519850;ENST00000381470;ENST00000432128;ENST00000517804;ENST00000265800;ENST00000517418;ENST00000358242;ENST00000415253;ENST00000523266;ENST00000519907	T;T;T;T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97	4.86	4.86	0.63082	.	.	.	.	.	T	0.48502	0.1503	L	0.46157	1.445	0.44652	D	0.997638	D;D	0.69078	0.997;0.997	D;D	0.67725	0.953;0.947	T	0.57027	-0.7881	9	0.72032	D	0.01	.	15.4743	0.75465	0.0:0.0:1.0:0.0	.	19;19	Q08495;Q08495-2	DEMA_HUMAN;.	Q	19	ENSP00000430600:R19Q;ENSP00000370879:R19Q;ENSP00000416111:R19Q;ENSP00000428415:R19Q;ENSP00000265800:R19Q;ENSP00000429948:R19Q;ENSP00000350977:R19Q;ENSP00000401291:R19Q;ENSP00000427866:R19Q;ENSP00000429377:R19Q	ENSP00000265800:R19Q	R	+	2	0	EPB49	21980579	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	5.310000	0.65780	2.249000	0.74217	0.462000	0.41574	CGA	G|0.989;A|0.011	0.011	strong		0.721	DMTN-009	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375178.1	NM_001978	
NEDD9	4739	hgsc.bcm.edu	37	6	11185533	11185533	+	Silent	SNP	G	G	A	rs1050775	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:11185533G>A	ENST00000379446.5	-	7	2533	c.2367C>T	c.(2365-2367)acC>acT	p.T789T	NEDD9_ENST00000504387.1_Silent_p.T789T|RP3-510L9.1_ENST00000500636.2_RNA	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	789					actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.T789T(1)		endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			CCATGACTATGGTCTTGAGCT	0.557													A|||	2464	0.492013	0.6452	0.4236	5008	,	,		17248	0.3492		0.5477	False		,,,				2504	0.4233				p.T789T		Atlas-SNP	.											NEDD9_ENST00000379446,NS,carcinoma,0,1	NEDD9	191	1	1	Substitution - coding silent(1)	stomach(1)	c.C2367T						PASS	.	A	,	2778,1628	500.5+/-364.7	870,1038,295	193.0	170.0	178.0		2367,2367	-11.6	0.0	6	dbSNP_86	178	4595,4005	554.3+/-386.5	1241,2113,946	no	coding-synonymous,coding-synonymous	NEDD9	NM_001142393.1,NM_006403.3	,	2111,3151,1241	AA,AG,GG		46.5698,36.9496,43.3108	,	789/835,789/835	11185533	7373,5633	2203	4300	6503	SO:0001819	synonymous_variant	4739	exon8			GACTATGGTCTTG	L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"""Cas scaffolding proteins"""	7733	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 2"", ""Cas-like"""	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.2367C>T	6.37:g.11185533G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	226	224	0.99115	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Silent	SNP	ENST00000379446.5	37	CCDS4520.1																																																																																			G|0.457;A|0.543	0.543	strong		0.557	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403	
MUC16	94025	hgsc.bcm.edu	37	19	9060125	9060125	+	Silent	SNP	G	G	A	rs12972088	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9060125G>A	ENST00000397910.4	-	3	27524	c.27321C>T	c.(27319-27321)caC>caT	p.H9107H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9109	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATGCAGTTGAGTGGGTCCCTG	0.483													G|||	1053	0.210264	0.2595	0.2118	5008	,	,		23165	0.0099		0.3121	False		,,,				2504	0.2444				p.H9107H		Atlas-SNP	.											.	MUC16	4315	.	0			c.C27321T						PASS	.	G		945,2921		98,749,1086	126.0	116.0	119.0		27321	-3.1	0.0	19	dbSNP_121	119	2804,5482		499,1806,1838	no	coding-synonymous	MUC16	NM_024690.2		597,2555,2924	AA,AG,GG		33.8402,24.4439,30.8509		9107/14508	9060125	3749,8403	1933	4143	6076	SO:0001819	synonymous_variant	94025	exon3			AGTTGAGTGGGTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27321C>T	19.37:g.9060125G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	171	171	1	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.760;A|0.240	0.240	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SCN9A	6335	hgsc.bcm.edu	37	2	167144974	167144974	+	Silent	SNP	A	A	T	rs6747673	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:167144974A>T	ENST00000409435.1	-	9	1286	c.1287T>A	c.(1285-1287)cgT>cgA	p.R429R	SCN9A_ENST00000303354.6_Silent_p.R430R|SCN9A_ENST00000375387.4_Silent_p.R430R|SCN9A_ENST00000409672.1_Silent_p.R429R|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	429					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTTTTTTAAGACGGTCTAACA	0.388													T|||	2738	0.546725	0.8041	0.5432	5008	,	,		14394	0.3839		0.4871	False		,,,				2504	0.4305				p.R429R		Atlas-SNP	.											.	SCN9A	296	.	0			c.T1287A						PASS	.	T		2765,915		1042,681,117	138.0	147.0	145.0		1287	-7.4	0.0	2	dbSNP_116	145	3907,4277		907,2093,1092	no	coding-synonymous	SCN9A	NM_002977.3		1949,2774,1209	TT,TA,AA		47.7395,24.8641,43.7626		429/1978	167144974	6672,5192	1840	4092	5932	SO:0001819	synonymous_variant	6335	exon10			TTTAAGACGGTCT	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1287T>A	2.37:g.167144974A>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			A|0.462;T|0.538	0.538	strong		0.388	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
IL23R	149233	hgsc.bcm.edu	37	1	67633812	67633812	+	Missense_Mutation	SNP	G	G	T	rs1884444	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:67633812G>T	ENST00000347310.5	+	2	180	c.9G>T	c.(7-9)caG>caT	p.Q3H	IL23R_ENST00000371002.1_Missense_Mutation_p.Q3H|C1orf141_ENST00000371007.2_Intron	NM_144701.2	NP_653302.2	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor	3			Q -> H (in dbSNP:rs1884444). {ECO:0000269|PubMed:17068223}.		defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|interleukin-23-mediated signaling pathway (GO:0038155)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)	interleukin-23 receptor complex (GO:0072536)|receptor complex (GO:0043235)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	21						ACATGAATCAGGTCACTATTC	0.323													G|||	2655	0.530152	0.4713	0.3689	5008	,	,		17689	0.6369		0.5239	False		,,,				2504	0.6207				p.Q3H		Atlas-SNP	.											.	IL23R	52	.	0			c.G9T						PASS	.	G	HIS/GLN	2203,2203	589.1+/-387.1	549,1105,549	216.0	182.0	193.0		9	2.0	0.9	1	dbSNP_92	193	4540,4060	595.0+/-393.4	1203,2134,963	yes	missense	IL23R	NM_144701.2	24	1752,3239,1512	TT,TG,GG		47.2093,50.0,48.1547	benign	3/630	67633812	6743,6263	2203	4300	6503	SO:0001583	missense	149233	exon2			GAATCAGGTCACT	AF461422	CCDS637.1	1p31.2	2008-02-05			ENSG00000162594	ENSG00000162594			19100	protein-coding gene	gene with protein product		607562				12023369	Standard	NM_144701		Approved	IL-23R	uc001ddo.3	Q5VWK5	OTTHUMG00000009092	ENST00000347310.5:c.9G>T	1.37:g.67633812G>T	ENSP00000321345:p.Gln3His	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_144701	C9JGX4|Q4VGP1|Q4VGP2|Q4VGP3|Q4VGP4|Q4VGP5|Q4VGP6|Q5VWK7|Q8IW84|Q8NFQ9|Q96AS1	Missense_Mutation	SNP	ENST00000347310.5	37	CCDS637.1	1129	0.516941391941392	226	0.45934959349593496	142	0.39226519337016574	360	0.6293706293706294	401	0.5290237467018469	G	4.001	-0.002532	0.07819	0.5	0.527907	ENSG00000162594	ENST00000347310;ENST00000371002	D;D	0.85339	-1.97;-1.97	5.41	2.03	0.26663	.	0.684055	0.14296	N	0.328617	T	0.53738	0.1815	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.19844	-1.0293	9	0.18276	T	0.48	-8.8637	5.912	0.19033	0.1103:0.4066:0.4832:0.0	rs1884444;rs41538148;rs52798390;rs57078543;rs1884444	3	Q5VWK5	IL23R_HUMAN	H	3	ENSP00000321345:Q3H;ENSP00000360041:Q3H	ENSP00000321345:Q3H	Q	+	3	2	IL23R	67406400	0.352000	0.24895	0.917000	0.36280	0.002000	0.02628	0.723000	0.25939	1.232000	0.43678	0.591000	0.81541	CAG	G|0.477;T|0.523	0.523	strong		0.323	IL23R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025199.2	NM_144701	
TSPAN18	90139	hgsc.bcm.edu	37	11	44940828	44940828	+	Missense_Mutation	SNP	G	G	A	rs2291334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:44940828G>A	ENST00000520358.2	+	7	812	c.397G>A	c.(397-399)Gtc>Atc	p.V133I	TSPAN18_ENST00000340160.3_Missense_Mutation_p.V133I			Q96SJ8	TSN18_HUMAN	tetraspanin 18	133			V -> I (in dbSNP:rs2291334). {ECO:0000269|PubMed:12975309}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						CGACACAGACGTCTTCTCTGC	0.557													G|||	1738	0.347045	0.034	0.415	5008	,	,		21259	0.5575		0.329	False		,,,				2504	0.5235				p.V133I		Atlas-SNP	.											TSPAN18,colon,carcinoma,-2,1	TSPAN18	38	1	0			c.G397A						PASS	.	G	ILE/VAL	440,3966	212.5+/-232.4	25,390,1788	199.0	154.0	170.0		397	2.4	0.5	11	dbSNP_100	170	2937,5661	458.0+/-364.5	502,1933,1864	yes	missense	TSPAN18	NM_130783.4	29	527,2323,3652	AA,AG,GG		34.1591,9.9864,25.9689	benign	133/249	44940828	3377,9627	2203	4299	6502	SO:0001583	missense	90139	exon6			ACAGACGTCTTCT	AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"""Tetraspanins"""	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.397G>A	11.37:g.44940828G>A	ENSP00000429993:p.Val133Ile	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	127	47	0.370079	NM_130783	Q6UY44|Q8NBI9	Missense_Mutation	SNP	ENST00000520358.2	37	CCDS7910.1	743|743	0.3402014652014652|0.3402014652014652	20|20	0.04065040650406504|0.04065040650406504	154|154	0.425414364640884|0.425414364640884	316|316	0.5524475524475524|0.5524475524475524	253|253	0.3337730870712401|0.3337730870712401	G|G	11.55|11.55	1.671289|1.671289	0.29693|0.29693	0.099864|0.099864	0.341591|0.341591	ENSG00000157570|ENSG00000157570	ENST00000518429|ENST00000533786;ENST00000533080;ENST00000520358;ENST00000520999;ENST00000340160	.|T;D;D;T;D	.|0.86956	.|-1.27;-2.19;-2.19;-1.27;-2.19	5.29|5.29	2.4|2.4	0.29515|0.29515	.|Tetraspanin, EC2 domain (1);	.|0.405863	.|0.28989	.|N	.|0.013489	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38838|0.38838	1.175|1.175	0.09310|0.09310	P|P	0.9999999999999999|0.9999999999999999	.|B;B	.|0.32302	.|0.205;0.363	.|B;B	.|0.34385	.|0.04;0.181	T|T	0.44651|0.44651	-0.9314|-0.9314	4|9	.|0.36615	.|T	.|0.2	.|.	9.2617|9.2617	0.37616|0.37616	0.2416:0.0:0.7584:0.0|0.2416:0.0:0.7584:0.0	rs2291334;rs17787220;rs58600094;rs2291334|rs2291334;rs17787220;rs58600094;rs2291334	.|133;133	.|Q8WUV1;Q96SJ8	.|.;TSN18_HUMAN	H|I	136|133;68;133;143;133	.|ENSP00000433592:V133I;ENSP00000433362:V68I;ENSP00000429993:V133I;ENSP00000427942:V143I;ENSP00000339820:V133I	.|ENSP00000339820:V133I	R|V	+|+	2|1	0|0	TSPAN18|TSPAN18	44897404|44897404	1.000000|1.000000	0.71417|0.71417	0.546000|0.546000	0.28166|0.28166	0.227000|0.227000	0.25037|0.25037	5.142000|5.142000	0.64820|0.64820	0.622000|0.622000	0.30249|0.30249	0.462000|0.462000	0.41574|0.41574	CGT|GTC	G|0.711;A|0.289	0.289	strong		0.557	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783	
RNF213	57674	hgsc.bcm.edu	37	17	78261805	78261805	+	Silent	SNP	A	A	G	rs7215243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78261805A>G	ENST00000582970.1	+	4	596	c.453A>G	c.(451-453)ccA>ccG	p.P151P	RNF213_ENST00000508628.2_Silent_p.P200P|RNF213_ENST00000456466.1_Silent_p.P151P|RNF213_ENST00000319921.4_Silent_p.P151P	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	151					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCCAGCCCCCAGGCACAGCCA	0.692													G|||	1481	0.295727	0.5885	0.1873	5008	,	,		12591	0.131		0.1988	False		,,,				2504	0.2464				p.P151P		Atlas-SNP	.											RNF213_ENST00000456466,NS,carcinoma,0,3	RNF213	766	3	0			c.A453G						PASS	.	G	,	2141,2209		550,1041,584	11.0	13.0	12.0		600,453	-4.2	0.0	17	dbSNP_116	12	1773,6779		200,1373,2703	no	coding-synonymous,coding-synonymous	RNF213	NM_020914.4,NM_020954.2	,	750,2414,3287	GG,GA,AA		20.732,49.2184,30.3364	,	200/5257,151/1064	78261805	3914,8988	2175	4276	6451	SO:0001819	synonymous_variant	57674	exon4			GCCCCCAGGCACA	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.453A>G	17.37:g.78261805A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			A|0.731;G|0.269	0.269	strong		0.692	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
HSPG2	3339	hgsc.bcm.edu	37	1	22200473	22200473	+	Missense_Mutation	SNP	C	C	T	rs28546127	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22200473C>T	ENST00000374695.3	-	29	3767	c.3688G>A	c.(3688-3690)Ggc>Agc	p.G1230S		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1230	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GTGGGGTGGCCGTCTGTGTCC	0.642													C|||	311	0.0621006	0.1921	0.0403	5008	,	,		17490	0.0		0.0219	False		,,,				2504	0.0072				p.G1230S		Atlas-SNP	.											.	HSPG2	311	.	0			c.G3688A						PASS	.	C	SER/GLY	756,3650	289.5+/-280.5	55,646,1502	63.0	54.0	57.0		3688	3.6	1.0	1	dbSNP_125	57	257,8339	92.8+/-154.8	4,249,4045	yes	missense	HSPG2	NM_005529.5	56	59,895,5547	TT,TC,CC		2.9898,17.1584,7.7911	probably-damaging	1230/4392	22200473	1013,11989	2203	4298	6501	SO:0001583	missense	3339	exon29			GGTGGCCGTCTGT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.3688G>A	1.37:g.22200473C>T	ENSP00000363827:p.Gly1230Ser	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	207	98	0.47343	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	124|124	0.056776556776556776|0.056776556776556776	91|91	0.18495934959349594|0.18495934959349594	15|15	0.04143646408839779|0.04143646408839779	0|0	0.0|0.0	18|18	0.023746701846965697|0.023746701846965697	C|C	18.88|18.88	3.717149|3.717149	0.68844|0.68844	0.171584|0.171584	0.029898|0.029898	ENSG00000142798|ENSG00000142798	ENST00000374695|ENST00000427897	T|.	0.62232|.	0.04|.	5.49|5.49	3.62|3.62	0.41486|0.41486	EGF-like, laminin (3);|.	0.000000|.	0.40728|.	N|.	0.001040|.	T|T	0.00178|0.00178	0.0005|0.0005	L|L	0.57536|0.57536	1.79|1.79	0.23616|0.23616	P|P	0.99728566|0.99728566	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.05869|0.05869	-1.0859|-1.0859	9|4	0.49607|.	T|.	0.09|.	.|.	9.8758|9.8758	0.41202|0.41202	0.0:0.832:0.0:0.168|0.0:0.832:0.0:0.168	rs28546127|rs28546127	1230|.	P98160|.	PGBM_HUMAN|.	S|Q	1230|84	ENSP00000363827:G1230S|.	ENSP00000363827:G1230S|.	G|R	-|-	1|2	0|0	HSPG2|HSPG2	22073060|22073060	0.382000|0.382000	0.25148|0.25148	0.992000|0.992000	0.48379|0.48379	0.989000|0.989000	0.77384|0.77384	1.738000|1.738000	0.38207|0.38207	0.683000|0.683000	0.31428|0.31428	0.407000|0.407000	0.27541|0.27541	GGC|CGG	C|0.928;G|0.000;T|0.071	0.071	strong		0.642	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
SPPL2C	162540	hgsc.bcm.edu	37	17	43924200	43924200	+	Missense_Mutation	SNP	C	C	G	rs12373142	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43924200C>G	ENST00000329196.5	+	1	1945	c.1928C>G	c.(1927-1929)cCg>cGg	p.P643R	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	643			P -> R (in dbSNP:rs12373142).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										CTGATGCCCCCGCCCTCAGAG	0.627													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		18729	0.001		0.2396	False		,,,				2504	0.0613				p.P643R		Atlas-SNP	.											.	.	.	.	0			c.C1928G						PASS	.	C	ARG/PRO	200,4206	121.3+/-158.8	5,190,2008	43.0	41.0	42.0		1928	-0.3	0.0	17	dbSNP_120	42	1916,6684	328.1+/-318.2	221,1474,2605	yes	missense	IMP5	NM_175882.2	103	226,1664,4613	GG,GC,CC		22.2791,4.5393,16.2694	possibly-damaging	643/685	43924200	2116,10890	2203	4300	6503	SO:0001583	missense	162540	exon1			TGCCCCCGCCCTC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1928C>G	17.37:g.43924200C>G	ENSP00000332488:p.Pro643Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	253	0.11584249084249085	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	174	0.22955145118733508	C	0.238	-1.015902	0.02078	0.045393	0.222791	ENSG00000185294	ENST00000329196	T	0.04406	3.63	4.23	-0.281	0.12882	.	0.237510	0.22293	N	0.061965	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.21309	0.054	B	0.14023	0.01	T	0.48490	-0.9031	9	0.48119	T	0.1	-18.8908	2.3936	0.04384	0.382:0.3664:0.1536:0.098	rs12373142;rs12373142	643	Q8IUH8	IMP5_HUMAN	R	643	ENSP00000332488:P643R	ENSP00000332488:P643R	P	+	2	0	AC217771.1	41279980	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.094000	0.11094	-0.001000	0.14495	-1.047000	0.02352	CCG	C|0.473;G|0.527	0.527	strong		0.627	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
ITGA7	3679	hgsc.bcm.edu	37	12	56082025	56082025	+	Silent	SNP	G	G	C	rs17117883	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56082025G>C	ENST00000555728.1	-	24	3178	c.3150C>G	c.(3148-3150)tcC>tcG	p.S1050S	ITGA7_ENST00000553804.1_Silent_p.S1010S|ITGA7_ENST00000347027.6_Silent_p.S1000S|ITGA7_ENST00000257880.7_Silent_p.S1050S|ITGA7_ENST00000394230.2_Silent_p.S1010S|ITGA7_ENST00000394229.2_Silent_p.S1006S|ITGA7_ENST00000257879.6_Silent_p.S1006S|ITGA7_ENST00000452168.2_Silent_p.S913S			Q13683	ITA7_HUMAN	integrin, alpha 7	1050					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)	p.S1006S(2)|p.S1010S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						TCTTTATGGAGGACTTCACTG	0.542													G|||	222	0.0443291	0.0651	0.0375	5008	,	,		20542	0.001		0.0666	False		,,,				2504	0.0429				p.S1010S		Atlas-SNP	.											ITGA7_ENST00000553804,NS,carcinoma,0,2	ITGA7	194	2	3	Substitution - coding silent(3)	prostate(3)	c.C3030G						PASS	.	G	,,	283,4123	158.9+/-191.5	8,267,1928	156.0	138.0	144.0		3030,2739,3018	-5.6	0.9	12	dbSNP_123	144	399,8201	126.8+/-185.2	8,383,3909	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGA7	NM_001144996.1,NM_001144997.1,NM_002206.2	,,	16,650,5837	CC,CG,GG		4.6395,6.4231,5.2437	,,	1010/1142,913/1045,1006/1138	56082025	682,12324	2203	4300	6503	SO:0001819	synonymous_variant	3679	exon23			TATGGAGGACTTC		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"""Integrins"""	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.3150C>G	12.37:g.56082025G>C		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	227	88	0.387665	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Silent	SNP	ENST00000555728.1	37																																																																																				G|0.944;C|0.056	0.056	strong		0.542	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	
GLDC	2731	hgsc.bcm.edu	37	9	6645251	6645251	+	Silent	SNP	C	C	T	rs12341698	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:6645251C>T	ENST00000321612.6	-	1	399	c.249G>A	c.(247-249)ggG>ggA	p.G83G	RP11-390F4.6_ENST00000413145.1_lincRNA	NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	83					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	TTACCGCCAGCCCCAAGGTCT	0.711													C|||	1248	0.249201	0.2269	0.2464	5008	,	,		11058	0.2083		0.2266	False		,,,				2504	0.3466				p.G83G		Atlas-SNP	.											.	GLDC	118	.	0			c.G249A						PASS	.	C		912,3494		99,714,1390	24.0	20.0	22.0		249	4.0	1.0	9	dbSNP_120	22	1800,6800		181,1438,2681	no	coding-synonymous	GLDC	NM_000170.2		280,2152,4071	TT,TC,CC		20.9302,20.699,20.8519		83/1021	6645251	2712,10294	2203	4300	6503	SO:0001819	synonymous_variant	2731	exon1			CGCCAGCCCCAAG	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"""glycine cleavage system protein P"", ""glycine decarboxylase"""	238300	"""glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"""			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.249G>A	9.37:g.6645251C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			C|0.786;T|0.214	0.214	strong		0.711	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
NAT16	375607	hgsc.bcm.edu	37	7	100817901	100817901	+	Missense_Mutation	SNP	A	A	G	rs34985488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100817901A>G	ENST00000300303.2	-	2	426	c.188T>C	c.(187-189)tTt>tCt	p.F63S	NAT16_ENST00000443096.1_Missense_Mutation_p.F63S|NAT16_ENST00000455377.1_Missense_Mutation_p.F63S	NM_198571.2	NP_940973.2	Q8N8M0	NAT16_HUMAN	N-acetyltransferase 16 (GCN5-related, putative)	63	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.		F -> S (in dbSNP:rs34985488). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.				N-acetyltransferase activity (GO:0008080)										CACTTCCTCAAACTCCCGTTC	0.682													A|||	952	0.190096	0.2814	0.098	5008	,	,		13601	0.2302		0.0934	False		,,,				2504	0.1902				p.F63S		Atlas-SNP	.											.	.	.	.	0			c.T188C						PASS	.	A	SER/PHE	1061,3345	385.1+/-325.6	120,821,1262	71.0	64.0	66.0		188	2.5	1.0	7	dbSNP_126	66	682,7918	170.4+/-221.6	29,624,3647	yes	missense	C7orf52	NM_198571.2	155	149,1445,4909	GG,GA,AA		7.9302,24.0808,13.4015	probably-damaging	63/370	100817901	1743,11263	2203	4300	6503	SO:0001583	missense	375607	exon2			TCCTCAAACTCCC	AK096556	CCDS5713.1	7q22.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000167011	ENSG00000167011			22030	protein-coding gene	gene with protein product		615783	"""chromosome 7 open reading frame 52"""	C7orf52			Standard	NM_198571		Approved	FLJ39237	uc003uxy.2	Q8N8M0	OTTHUMG00000157110	ENST00000300303.2:c.188T>C	7.37:g.100817901A>G	ENSP00000300303:p.Phe63Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_198571	B3KRS2|Q8NDR1	Missense_Mutation	SNP	ENST00000300303.2	37	CCDS5713.1	364	0.16666666666666666	145	0.29471544715447157	38	0.10497237569060773	115	0.20104895104895104	66	0.0870712401055409	A	20.3	3.964128	0.74131	0.240808	0.079302	ENSG00000167011	ENST00000300303;ENST00000455377;ENST00000444446;ENST00000443096	T;T;T;T	0.58060	0.95;0.95;0.95;0.36	3.72	2.5	0.30297	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (1);	0.172675	0.36703	U	0.002455	T	0.00012	0.0000	L	0.44542	1.39	0.26939	P	0.966288	D;P	0.54964	0.969;0.94	P;P	0.53313	0.723;0.723	T	0.09862	-1.0655	9	0.87932	D	0	.	7.3923	0.26917	0.8851:0.0:0.1149:0.0	rs34985488;rs60060124	63;63	B3KRS2;Q8N8M0	.;CG052_HUMAN	S	63	ENSP00000300303:F63S;ENSP00000395125:F63S;ENSP00000391769:F63S;ENSP00000394435:F63S	ENSP00000300303:F63S	F	-	2	0	C7orf52	100604621	1.000000	0.71417	0.955000	0.39395	0.937000	0.57800	4.055000	0.57441	1.558000	0.49541	0.334000	0.21626	TTT	A|0.859;G|0.141	0.141	strong		0.682	NAT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347465.1	NM_198571	
AKAP13	11214	hgsc.bcm.edu	37	15	86124555	86124555	+	Missense_Mutation	SNP	G	G	A	rs4843075	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86124555G>A	ENST00000394518.2	+	7	3351	c.3256G>A	c.(3256-3258)Gat>Aat	p.D1086N	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.D1086N	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1086			D -> N (in dbSNP:rs4843075). {ECO:0000269|Ref.3}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						GGTGAGTGGAGATGTGACGGT	0.483													A|||	2911	0.58127	0.5469	0.6182	5008	,	,		24126	0.5784		0.6153	False		,,,				2504	0.5695				p.D1086N	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G3256A						PASS	.	A	ASN/ASP,ASN/ASP	2606,1798	528.7+/-372.5	778,1050,374	86.0	86.0	86.0		3256,3256	-0.3	0.0	15	dbSNP_111	86	5538,3060	468.4+/-367.3	1797,1944,558	yes	missense,missense	AKAP13	NM_006738.4,NM_007200.3	23,23	2575,2994,932	AA,AG,GG		35.5897,40.8265,37.3635	benign,benign	1086/2818,1086/2814	86124555	8144,4858	2202	4299	6501	SO:0001583	missense	11214	exon7			AGTGGAGATGTGA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.3256G>A	15.37:g.86124555G>A	ENSP00000378026:p.Asp1086Asn	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	156	153	0.980769	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	1277	0.5847069597069597	261	0.5304878048780488	221	0.6104972375690608	334	0.583916083916084	461	0.6081794195250659	A	1.068	-0.670763	0.03403	0.591735	0.644103	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.07800	3.16;3.16	4.94	-0.344	0.12628	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36237	-0.9756	8	0.02654	T	1	.	4.2114	0.10514	0.4523:0.0:0.3833:0.1644	rs4843075;rs58229576;rs4843075	1086;1086	Q12802;Q12802-2	AKP13_HUMAN;.	N	1086;1086;1085;1085	ENSP00000354718:D1086N;ENSP00000378026:D1086N	ENSP00000354718:D1086N	D	+	1	0	AKAP13	83925559	0.000000	0.05858	0.002000	0.10522	0.040000	0.13550	0.180000	0.16860	-0.293000	0.08986	-0.254000	0.11334	GAT	G|0.387;A|0.613	0.613	strong		0.483	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
IBSP	3381	hgsc.bcm.edu	37	4	88732911	88732911	+	Missense_Mutation	SNP	C	C	T	rs1054628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:88732911C>T	ENST00000226284.5	+	7	870	c.803C>T	c.(802-804)gCc>gTc	p.A268V		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	268			A -> V (in dbSNP:rs1054628). {ECO:0000269|PubMed:2404984}.		biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		TACACGGGCGCCAATGAATAC	0.463													C|||	1060	0.211661	0.2685	0.2493	5008	,	,		19940	0.2927		0.1272	False		,,,				2504	0.1115				p.A268V		Atlas-SNP	.											IBSP,colon,carcinoma,+1,1	IBSP	53	1	0			c.C803T						PASS	.	C	VAL/ALA	1147,3259	407.1+/-334.1	146,855,1202	66.0	62.0	63.0		803	3.5	1.0	4	dbSNP_86	63	1326,7274	262.0+/-284.2	92,1142,3066	yes	missense	IBSP	NM_004967.3	64	238,1997,4268	TT,TC,CC		15.4186,26.0327,19.0143	benign	268/318	88732911	2473,10533	2203	4300	6503	SO:0001583	missense	3381	exon7			CGGGCGCCAATGA		CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"""bone sialoprotein"", ""bone sialoprotein II"""	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.803C>T	4.37:g.88732911C>T	ENSP00000226284:p.Ala268Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_004967		Missense_Mutation	SNP	ENST00000226284.5	37	CCDS3624.1	478	0.21886446886446886	122	0.24796747967479674	95	0.26243093922651933	167	0.291958041958042	94	0.12401055408970976	C	13.96	2.391875	0.42410	0.260327	0.154186	ENSG00000029559	ENST00000226284	T	0.13901	2.55	5.36	3.47	0.39725	.	0.644144	0.15037	N	0.284091	T	0.00012	0.0000	N	0.22421	0.69	0.48135	P	4.030000000000422E-4	B	0.16396	0.017	B	0.22880	0.042	T	0.44483	-0.9325	9	0.35671	T	0.21	.	13.2444	0.60016	0.222:0.778:0.0:0.0	rs1054628;rs59614959;rs1054628	268	P21815	SIAL_HUMAN	V	268	ENSP00000226284:A268V	ENSP00000226284:A268V	A	+	2	0	IBSP	88951935	0.004000	0.15560	0.951000	0.38953	0.638000	0.38207	0.359000	0.20233	0.487000	0.27698	0.591000	0.81541	GCC	C|0.800;T|0.200	0.200	strong		0.463	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2		
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885567	+	Silent	SNP	A	A	C	rs147489453|rs75808076|rs59279731		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29885567A>C	ENST00000310624.6	+	4	1971	c.1938A>C	c.(1936-1938)gcA>gcC	p.A646A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	652	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAGGAAGCAAAGTCCCCTG	0.567																																					p.A646A		Atlas-SNP	.											NEFH,rectum,carcinoma,0,1	NEFH	178	1	0			c.A1938C						PASS	.						78.0	77.0	77.0					22																	29885567		2133	4127	6260	SO:0001819	synonymous_variant	4744	exon4			GGAAGCAAAGTCC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1938A>C	22.37:g.29885567A>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			.	.	weak		0.567	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
ABCA8	10351	hgsc.bcm.edu	37	17	66878099	66878099	+	Missense_Mutation	SNP	C	C	T	rs34987539	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:66878099C>T	ENST00000269080.2	-	29	3868	c.3731G>A	c.(3730-3732)tGt>tAt	p.C1244Y	ABCA8_ENST00000430352.2_Missense_Mutation_p.C1284Y|ABCA8_ENST00000586539.1_Missense_Mutation_p.C1284Y	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1244					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					CTTGCGTAGACAGCTGGCAAT	0.408													C|||	26	0.00519169	0.0008	0.0029	5008	,	,		23456	0.001		0.0169	False		,,,				2504	0.0051				p.C1244Y		Atlas-SNP	.											.	ABCA8	213	.	0			c.G3731A						PASS	.	C	TYR/CYS	13,4393	19.1+/-41.9	0,13,2190	135.0	126.0	129.0		3731	4.8	1.0	17	dbSNP_126	129	101,8499	56.0+/-117.1	1,99,4200	yes	missense	ABCA8	NM_007168.2	194	1,112,6390	TT,TC,CC		1.1744,0.2951,0.8765	probably-damaging	1244/1582	66878099	114,12892	2203	4300	6503	SO:0001583	missense	10351	exon29			CGTAGACAGCTGG	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3731G>A	17.37:g.66878099C>T	ENSP00000269080:p.Cys1244Tyr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	15	0.006868131868131868	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	13	0.017150395778364115	C	16.93	3.258878	0.59321	0.002951	0.011744	ENSG00000141338	ENST00000269080;ENST00000430352	D;D	0.85629	-2.01;-2.01	4.75	4.75	0.60458	.	0.000000	0.64402	D	0.000018	D	0.88081	0.6341	M	0.89840	3.065	0.39548	D	0.968927	D;D;D	0.89917	1.0;0.993;1.0	D;D;D	0.79784	0.993;0.964;0.984	D	0.90611	0.4552	10	0.62326	D	0.03	.	12.7575	0.57343	0.0:0.9174:0.0:0.0826	rs34987539	1284;1284;1244	A1L3U3;C9JQE6;O94911	.;.;ABCA8_HUMAN	Y	1244;1284	ENSP00000269080:C1244Y;ENSP00000402814:C1284Y	ENSP00000269080:C1244Y	C	-	2	0	ABCA8	64389694	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	0.751000	0.26348	2.623000	0.88846	0.563000	0.77884	TGT	C|0.992;T|0.008	0.008	strong		0.408	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
EXO1	9156	hgsc.bcm.edu	37	1	242048674	242048674	+	Missense_Mutation	SNP	C	C	T	rs9350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:242048674C>T	ENST00000366548.3	+	15	2863	c.2270C>T	c.(2269-2271)cCt>cTt	p.P757L	EXO1_ENST00000348581.5_Missense_Mutation_p.P757L|EXO1_ENST00000518483.1_Missense_Mutation_p.P757L	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	757	Interaction with MSH2.		P -> L (may be associated with a reduced risk of colorectal cancer; dbSNP:rs9350). {ECO:0000269|PubMed:14756672, ECO:0000269|PubMed:15550454, ECO:0000269|PubMed:9788596, ECO:0000269|Ref.5}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			AAGATCAAACCTCTAGGACCT	0.463								Editing and processing nucleases					C|||	1260	0.251597	0.1808	0.3199	5008	,	,		11488	0.4683		0.1521	False		,,,				2504	0.1779				p.P757L		Atlas-SNP	.											.	EXO1	103	.	0			c.C2270T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	810,3596	321.5+/-297.2	82,646,1475	55.0	59.0	58.0		2270,2270,2270	6.0	0.0	1	dbSNP_52	58	1367,7233	265.6+/-286.2	110,1147,3043	yes	missense,missense,missense	EXO1	NM_003686.4,NM_006027.4,NM_130398.3	98,98,98	192,1793,4518	TT,TC,CC		15.8953,18.384,16.7384	probably-damaging,probably-damaging,probably-damaging	757/804,757/847,757/847	242048674	2177,10829	2203	4300	6503	SO:0001583	missense	9156	exon13			TCAAACCTCTAGG	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"""rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"""	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.2270C>T	1.37:g.242048674C>T	ENSP00000355506:p.Pro757Leu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_006027	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	37	CCDS1620.1	566	0.2591575091575092	99	0.20121951219512196	100	0.27624309392265195	249	0.4353146853146853	118	0.15567282321899736	C	18.42	3.620253	0.66787	0.18384	0.158953	ENSG00000174371	ENST00000366548;ENST00000348581;ENST00000518483	T;T;T	0.64803	-0.12;-0.12;-0.12	6.0	6.0	0.97389	.	0.230334	0.45361	D	0.000364	T	0.00012	0.0000	M	0.69823	2.125	0.39013	P	0.04041899999999998	P;P;P	0.44139	0.827;0.702;0.577	B;B;B	0.42495	0.344;0.389;0.202	T	0.31392	-0.9945	9	0.62326	D	0.03	-8.0137	19.2545	0.93940	0.0:1.0:0.0:0.0	rs9350;rs1047846;rs3171065;rs16842285;rs52791110;rs57175702;rs9350	756;757;757	A8K5H6;Q9UQ84-4;Q9UQ84	.;.;EXO1_HUMAN	L	757	ENSP00000355506:P757L;ENSP00000311873:P757L;ENSP00000430251:P757L	ENSP00000311873:P757L	P	+	2	0	EXO1	240115297	0.490000	0.26012	0.044000	0.18714	0.917000	0.54804	6.128000	0.71650	2.836000	0.97738	0.655000	0.94253	CCT	C|0.786;T|0.214	0.214	strong		0.463	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027	
SPATA9	83890	hgsc.bcm.edu	37	5	94994467	94994467	+	Missense_Mutation	SNP	T	T	C	rs34297786	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:94994467T>C	ENST00000274432.8	-	5	766	c.625A>G	c.(625-627)Aaa>Gaa	p.K209E	SPATA9_ENST00000477047.2_Intron|RFESD_ENST00000508206.1_Intron	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	209			K -> E (in dbSNP:rs34297786). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)	7		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)		GGTTTTGCTTTGATTTCACCT	0.403													T|||	175	0.0349441	0.0877	0.0303	5008	,	,		6749	0.0		0.0258	False		,,,				2504	0.0123				p.K209E		Atlas-SNP	.											.	SPATA9	17	.	0			c.A625G						PASS	.	T	GLU/LYS	336,4070	175.5+/-204.9	21,294,1888	105.0	100.0	102.0		625	0.5	1.0	5	dbSNP_126	102	289,8309	106.6+/-167.4	4,281,4014	yes	missense	SPATA9	NM_031952.3	56	25,575,5902	CC,CT,TT		3.3612,7.626,4.8062	benign	209/255	94994467	625,12379	2203	4299	6502	SO:0001583	missense	83890	exon5			TTGCTTTGATTTC	AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.625A>G	5.37:g.94994467T>C	ENSP00000274432:p.Lys209Glu	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Missense_Mutation	SNP	ENST00000274432.8	37	CCDS4076.1	69	0.03159340659340659	34	0.06910569105691057	12	0.03314917127071823	0	0.0	23	0.030343007915567283	T	11.21	1.570681	0.28003	0.07626	0.033612	ENSG00000145757	ENST00000274432	T	0.30981	1.51	5.37	0.482	0.16815	.	0.776698	0.12019	N	0.507118	T	0.00906	0.0030	N	0.24115	0.695	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.10382	-1.0632	10	0.51188	T	0.08	-5.3492	6.9651	0.24619	0.0:0.418:0.0:0.582	rs34297786	209	Q9BWV2	SPAT9_HUMAN	E	209	ENSP00000274432:K209E	ENSP00000274432:K209E	K	-	1	0	SPATA9	95020223	0.921000	0.31238	0.997000	0.53966	0.255000	0.26057	0.013000	0.13310	0.174000	0.19809	0.528000	0.53228	AAA	T|0.957;C|0.043	0.043	strong		0.403	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952	
SLC7A13	157724	hgsc.bcm.edu	37	8	87226700	87226700	+	Missense_Mutation	SNP	A	A	G	rs9656982	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:87226700A>G	ENST00000297524.3	-	4	1458	c.1355T>C	c.(1354-1356)aTg>aCg	p.M452T	CTD-3118D11.3_ENST00000523112.1_RNA|SLC7A13_ENST00000419776.2_3'UTR	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	452			M -> T (in dbSNP:rs9656982).			integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						ATAGCAAGTCATCTTCTCAAA	0.328													A|||	848	0.169329	0.1967	0.2363	5008	,	,		17057	0.1419		0.0835	False		,,,				2504	0.2014				p.M452T		Atlas-SNP	.											.	SLC7A13	97	.	0			c.T1355C						PASS	.	A	THR/MET	768,3638	301.0+/-286.6	66,636,1501	63.0	69.0	67.0		1355	4.2	0.4	8	dbSNP_119	67	779,7821	183.9+/-232.0	31,717,3552	yes	missense	SLC7A13	NM_138817.2	81	97,1353,5053	GG,GA,AA		9.0581,17.4308,11.8945	benign	452/471	87226700	1547,11459	2203	4300	6503	SO:0001583	missense	157724	exon4			CAAGTCATCTTCT	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.1355T>C	8.37:g.87226700A>G	ENSP00000297524:p.Met452Thr	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_138817	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	302	0.1382783882783883	81	0.16463414634146342	80	0.22099447513812154	67	0.11713286713286714	74	0.09762532981530343	A	12.56	1.973178	0.34848	0.174308	0.090581	ENSG00000164893	ENST00000297524	D	0.87966	-2.32	4.15	4.15	0.48705	.	0.647706	0.14488	N	0.316524	T	0.00109	0.0003	N	0.08118	0	0.09310	P	1.0	B	0.19817	0.039	B	0.18263	0.021	T	0.08066	-1.0740	9	0.27785	T	0.31	.	11.775	0.51981	1.0:0.0:0.0:0.0	rs9656982;rs52795070;rs61261684;rs9656982	452	Q8TCU3	S7A13_HUMAN	T	452	ENSP00000297524:M452T	ENSP00000297524:M452T	M	-	2	0	SLC7A13	87295816	0.152000	0.22762	0.373000	0.26003	0.957000	0.61999	3.243000	0.51392	1.808000	0.52836	0.533000	0.62120	ATG	A|0.866;G|0.134	0.134	strong		0.328	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
SMARCAL1	50485	hgsc.bcm.edu	37	2	217315787	217315787	+	Splice_Site	SNP	T	T	C	rs2066527	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:217315787T>C	ENST00000357276.4	+	12	2400	c.2070T>C	c.(2068-2070)acT>acC	p.T690T	SMARCAL1_ENST00000358207.5_Splice_Site_p.T690T	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	690					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		AGGACAAAACTGTGAGTCCAG	0.527									Schimke Immuno-Osseous Dysplasia				T|||	423	0.0844649	0.0431	0.0476	5008	,	,		20873	0.0079		0.1044	False		,,,				2504	0.2249				p.T690T		Atlas-SNP	.											SMARCAL1,NS,carcinoma,0,1	SMARCAL1	93	1	0			c.T2070C						PASS	.	T	,	214,4192	123.7+/-161.0	10,194,1999	34.0	36.0	35.0		2070,2070	-3.5	0.9	2	dbSNP_98	35	1086,7514	222.0+/-259.2	63,960,3277	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	SMARCAL1	NM_001127207.1,NM_014140.3	,	73,1154,5276	CC,CT,TT		12.6279,4.857,9.9954	,	690/955,690/955	217315787	1300,11706	2203	4300	6503	SO:0001630	splice_region_variant	50485	exon12	Familial Cancer Database	SIOD	CAAAACTGTGAGT	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"""HepA-related protein"", ""ATP-driven annealing helicase"""	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.2070+1T>C	2.37:g.217315787T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Silent	SNP	ENST00000357276.4	37	CCDS2403.1																																																																																			T|0.912;C|0.088	0.088	strong		0.527	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2		Silent
C21orf58	54058	hgsc.bcm.edu	37	21	47734659	47734659	+	Missense_Mutation	SNP	G	G	A	rs13047478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47734659G>A	ENST00000291691.7	-	5	1716	c.580C>T	c.(580-582)Cca>Tca	p.P194S	C21orf58_ENST00000397683.1_Missense_Mutation_p.P88S|C21orf58_ENST00000397680.1_Missense_Mutation_p.P88S|C21orf58_ENST00000397679.1_Missense_Mutation_p.P88S|C21orf58_ENST00000397682.3_Missense_Mutation_p.P88S	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	194										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		GGCGGGTCTGGGGCCAGCGGG	0.657													G|||	1442	0.287939	0.1263	0.4409	5008	,	,		14807	0.3115		0.33	False		,,,				2504	0.3303				p.P194S		Atlas-SNP	.											.	C21orf58	25	.	0			c.C580T						PASS	.	G	SER/PRO	649,3555		54,541,1507	16.0	15.0	15.0		580	4.7	0.1	21	dbSNP_121	15	2687,5655		448,1791,1932	yes	missense	C21orf58	NM_058180.3	74	502,2332,3439	AA,AG,GG		32.2105,15.4377,26.5901	benign	194/323	47734659	3336,9210	2102	4171	6273	SO:0001583	missense	54058	exon5			GGTCTGGGGCCAG		CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.580C>T	21.37:g.47734659G>A	ENSP00000291691:p.Pro194Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_058180	B3KPI1	Missense_Mutation	SNP	ENST00000291691.7	37	CCDS13735.1	625	0.28617216117216115	67	0.13617886178861788	154	0.425414364640884	160	0.27972027972027974	244	0.32189973614775724	G	16.55	3.155161	0.57259	0.154377	0.322105	ENSG00000160298	ENST00000397683;ENST00000417060;ENST00000397682;ENST00000291691;ENST00000397679;ENST00000397680	T;T;T;T;T;T	0.60171	0.65;0.21;0.65;0.21;0.65;0.65	4.68	4.68	0.58851	.	0.162937	0.39475	N	0.001354	T	0.00012	0.0000	L	0.38175	1.15	0.09310	P	0.9999999999999938	D;D;D	0.67145	0.996;0.996;0.989	P;P;P	0.62813	0.848;0.907;0.848	T	0.42068	-0.9473	9	0.66056	D	0.02	-5.0994	13.4601	0.61223	0.0:0.0:1.0:0.0	rs13047478	194;88;194	P58505;Q8N7N9;P58505-2	CU058_HUMAN;.;.	S	88;156;88;194;88;88	ENSP00000380799:P88S;ENSP00000402356:P156S;ENSP00000380798:P88S;ENSP00000291691:P194S;ENSP00000380796:P88S;ENSP00000380797:P88S	ENSP00000291691:P194S	P	-	1	0	C21orf58	46559087	0.118000	0.22208	0.141000	0.22245	0.007000	0.05969	0.807000	0.27140	2.317000	0.78254	0.563000	0.77884	CCA	G|0.726;A|0.274	0.274	strong		0.657	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180	
TBC1D28	254272	hgsc.bcm.edu	37	17	18542519	18542519	+	Missense_Mutation	SNP	T	T	G	rs74452761		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18542519T>G	ENST00000345096.4	-	5	866	c.167A>C	c.(166-168)gAg>gCg	p.E56A	TBC1D28_ENST00000405044.1_Missense_Mutation_p.E56A|TBC1D28_ENST00000575570.1_5'Flank			Q2M2D7	TBC28_HUMAN	TBC1 domain family, member 28	56				E -> A (in Ref. 1; AAI12013). {ECO:0000305}.			Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(5)|lung(2)|ovary(1)	9						GCGGGGCAGCTCCATCTCACT	0.647																																					p.E56A		Atlas-SNP	.											.	TBC1D28	14	.	0			c.A167C						PASS	.						92.0	101.0	98.0					17																	18542519		2192	4297	6489	SO:0001583	missense	254272	exon6			GGCAGCTCCATCT		CCDS42273.1	17p11.2	2008-10-27			ENSG00000189375	ENSG00000189375			26858	protein-coding gene	gene with protein product							Standard	NM_001039397		Approved	FLJ40244	uc002gud.2	Q2M2D7	OTTHUMG00000059054	ENST00000345096.4:c.167A>C	17.37:g.18542519T>G	ENSP00000339973:p.Glu56Ala	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	209	94	0.449761	NM_001039397	Q2M2E1	Missense_Mutation	SNP	ENST00000345096.4	37	CCDS42273.1	1125	0.5151098901098901	248	0.5040650406504065	183	0.505524861878453	377	0.6590909090909091	317	0.4182058047493404	N	7.143	0.582264	0.13749	.	.	ENSG00000189375	ENST00000345096;ENST00000405044	T;T	0.44881	0.91;0.91	0.418	0.418	0.16429	.	0.321547	0.28187	U	0.016280	T	0.00012	0.0000	M	0.78916	2.43	0.80722	P	0.0	B	0.19331	0.035	B	0.08055	0.003	T	0.36578	-0.9742	8	0.59425	D	0.04	.	.	.	.	.	56	Q2M2D7	TBC28_HUMAN	A	56	ENSP00000339973:E56A;ENSP00000385821:E56A	ENSP00000339973:E56A	E	-	2	0	TBC1D28	18483244	0.334000	0.24739	0.001000	0.08648	0.001000	0.01503	0.493000	0.22451	0.402000	0.25451	0.392000	0.25879	GAG	T|0.485;G|0.515	0.515	strong		0.647	TBC1D28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130672.2	NM_001039397	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798823	55798823	+	Missense_Mutation	SNP	A	A	G	rs17600939	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55798823A>G	ENST00000313555.1	+	1	929	c.929A>G	c.(928-930)tAt>tGt	p.Y310C		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	310			Y -> C (in dbSNP:rs17600939).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					AGAATTGGATATTCAAATGAA	0.279													A|||	192	0.0383387	0.0129	0.0403	5008	,	,		19098	0.001		0.0934	False		,,,				2504	0.0532				p.Y310C		Atlas-SNP	.											OR5AS1,NS,carcinoma,0,1	OR5AS1	121	1	0			c.A929G						PASS	.	A	CYS/TYR	110,4284	78.8+/-117.2	3,104,2090	45.0	53.0	50.0		929	-6.7	0.0	11	dbSNP_123	50	690,7894	166.8+/-218.7	34,622,3636	yes	missense	OR5AS1	NM_001001921.1	194	37,726,5726	GG,GA,AA		8.0382,2.5034,6.1643	benign	310/325	55798823	800,12178	2197	4292	6489	SO:0001583	missense	219447	exon1			TTGGATATTCAAA	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.929A>G	11.37:g.55798823A>G	ENSP00000324111:p.Tyr310Cys	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_001001921	Q6IFB8	Missense_Mutation	SNP	ENST00000313555.1	37	CCDS31516.1	83	0.038003663003663	4	0.008130081300813009	11	0.03038674033149171	0	0.0	68	0.08970976253298153	A	7.586	0.669661	0.14776	0.025034	0.080382	ENSG00000181785	ENST00000313555	T	0.00359	7.87	4.55	-6.67	0.01783	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	N	1	B	0.21688	0.059	B	0.24394	0.053	T	0.16276	-1.0408	9	0.40728	T	0.16	.	1.5267	0.02526	0.3768:0.3258:0.1268:0.1706	rs17600939;rs52804281;rs17600939	310	Q8N127	O5AS1_HUMAN	C	310	ENSP00000324111:Y310C	ENSP00000324111:Y310C	Y	+	2	0	OR5AS1	55555399	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.358000	0.07641	-0.785000	0.04522	-1.296000	0.01341	TAT	A|0.948;G|0.052	0.052	strong		0.279	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
BTBD11	121551	hgsc.bcm.edu	37	12	108051406	108051406	+	Missense_Mutation	SNP	G	G	A	rs12303478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:108051406G>A	ENST00000280758.5	+	17	3754	c.3226G>A	c.(3226-3228)Ggc>Agc	p.G1076S	BTBD11_ENST00000494235.2_Missense_Mutation_p.G155S|BTBD11_ENST00000357167.4_Missense_Mutation_p.G613S|BTBD11_ENST00000420571.2_Missense_Mutation_p.G957S	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	1076			G -> S (in dbSNP:rs12303478).			integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TGAAGGGACCGGCCAGGATGT	0.478													G|||	525	0.104832	0.1989	0.0692	5008	,	,		20662	0.001		0.0964	False		,,,				2504	0.1186				p.G1076S		Atlas-SNP	.											.	BTBD11	122	.	0			c.G3226A						PASS	.	G	SER/GLY,SER/GLY	721,3685	299.0+/-285.6	45,631,1527	123.0	112.0	116.0		1837,3226	5.6	1.0	12	dbSNP_120	116	808,7792	189.3+/-236.1	37,734,3529	yes	missense,missense	BTBD11	NM_001017523.1,NM_001018072.1	56,56	82,1365,5056	AA,AG,GG		9.3953,16.364,11.7561	benign,benign	613/642,1076/1105	108051406	1529,11477	2203	4300	6503	SO:0001583	missense	121551	exon17			GGGACCGGCCAGG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.3226G>A	12.37:g.108051406G>A	ENSP00000280758:p.Gly1076Ser	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	245	143	0.583673	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	181	0.08287545787545787	80	0.16260162601626016	33	0.09116022099447514	1	0.0017482517482517483	67	0.08839050131926121	G	16.12	3.031635	0.54790	0.16364	0.093953	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000357167;ENST00000494235	T;T;T;T	0.39056	1.28;1.46;1.1;1.26	5.6	5.6	0.85130	.	0.095314	0.64402	D	0.000001	T	0.00178	0.0005	L	0.46157	1.445	0.20307	P	0.9999127565	B;B	0.25312	0.123;0.123	B;B	0.12837	0.008;0.008	T	0.02668	-1.1126	9	0.26408	T	0.33	.	19.6296	0.95694	0.0:0.0:1.0:0.0	rs12303478;rs52798261;rs57558542;rs12303478	613;1076	E9PHS4;A6QL63	.;BTBDB_HUMAN	S	1076;957;613;155	ENSP00000280758:G1076S;ENSP00000413889:G957S;ENSP00000349690:G613S;ENSP00000448322:G155S	ENSP00000280758:G1076S	G	+	1	0	BTBD11	106575536	1.000000	0.71417	0.971000	0.41717	0.758000	0.43043	3.360000	0.52299	2.644000	0.89710	0.655000	0.94253	GGC	G|0.891;A|0.109	0.109	strong		0.478	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
NHSL1	57224	hgsc.bcm.edu	37	6	138745896	138745896	+	Silent	SNP	A	A	G	rs117203533	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:138745896A>G	ENST00000427025.2	-	7	4783	c.4155T>C	c.(4153-4155)caT>caC	p.H1385H	NHSL1_ENST00000343505.5_Silent_p.H1381H	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	1385										breast(2)|endometrium(4)|kidney(1)	7						GGGAGGGAGAATGGTTTCGGG	0.527													A|||	57	0.0113818	0.0015	0.0504	5008	,	,		15079	0.0		0.0179	False		,,,				2504	0.002				p.H1385H		Atlas-SNP	.											.	NHSL1	99	.	0			c.T4155C						PASS	.	A	,	5,1379		0,5,687	42.0	43.0	43.0		4143,4155	-2.2	1.0	6	dbSNP_132	43	35,3147		2,31,1558	no	coding-synonymous,coding-synonymous	NHSL1	NM_001144060.1,NM_020464.1	,	2,36,2245	GG,GA,AA		1.0999,0.3613,0.876	,	1381/1607,1385/1611	138745896	40,4526	692	1591	2283	SO:0001819	synonymous_variant	57224	exon7			GGGAGAATGGTTT	AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.4155T>C	6.37:g.138745896A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	117	55	0.470085	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Silent	SNP	ENST00000427025.2	37	CCDS55063.1																																																																																			A|0.989;G|0.011	0.011	strong		0.527	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	
MAP2K7	5609	hgsc.bcm.edu	37	19	7975183	7975183	+	Silent	SNP	C	C	T	rs34562033	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7975183C>T	ENST00000397979.3	+	4	426	c.372C>T	c.(370-372)ggC>ggT	p.G124G	MAP2K7_ENST00000545011.1_Silent_p.G166G|CTD-3193O13.13_ENST00000595655.1_RNA|MAP2K7_ENST00000397983.3_Silent_p.G140G|MAP2K7_ENST00000397981.3_Silent_p.G124G	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	124	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						AGAACTTGGGCGAGATGGGCA	0.672													C|||	47	0.00938498	0.0008	0.0216	5008	,	,		17296	0.001		0.0179	False		,,,				2504	0.0123				p.G124G		Atlas-SNP	.											.	MAP2K7	66	.	0			c.C372T						PASS	.	C		10,4052		0,10,2021	32.0	38.0	36.0		372	-10.2	0.4	19	dbSNP_126	36	151,8205		0,151,4027	no	coding-synonymous	MAP2K7	NM_145185.2		0,161,6048	TT,TC,CC		1.8071,0.2462,1.2965		124/420	7975183	161,12257	2031	4178	6209	SO:0001819	synonymous_variant	5609	exon4			CTTGGGCGAGATG	AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.372C>T	19.37:g.7975183C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_145185	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Silent	SNP	ENST00000397979.3	37	CCDS42491.1																																																																																			C|0.990;T|0.010	0.010	strong		0.672	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1		
ABCG8	64241	hgsc.bcm.edu	37	2	44102491	44102491	+	Silent	SNP	C	C	T	rs4148221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:44102491C>T	ENST00000272286.2	+	11	1785	c.1695C>T	c.(1693-1695)gcC>gcT	p.A565A		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	565	ABC transmembrane type-2.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	TCAGCAATGCCCTCTACAACT	0.617													C|||	639	0.127596	0.1694	0.1556	5008	,	,		18103	0.0188		0.1759	False		,,,				2504	0.1135				p.A565A		Atlas-SNP	.											.	ABCG8	98	.	0			c.C1695T						PASS	.	C		727,3679	299.8+/-286.0	60,607,1536	56.0	58.0	57.0		1695	-3.5	0.1	2	dbSNP_110	57	1524,7076	287.1+/-298.1	128,1268,2904	no	coding-synonymous	ABCG8	NM_022437.2		188,1875,4440	TT,TC,CC		17.7209,16.5002,17.3074		565/674	44102491	2251,10755	2203	4300	6503	SO:0001819	synonymous_variant	64241	exon11			CAATGCCCTCTAC	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"""ATP binding cassette transporters / subfamily G"""	13887	protein-coding gene	gene with protein product	"""gallbladder disease 4"", ""sterolin 2"""	605460	"""ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"""			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.1695C>T	2.37:g.44102491C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_022437	Q53QN8	Silent	SNP	ENST00000272286.2	37	CCDS1815.1																																																																																			C|0.850;T|0.150	0.150	strong		0.617	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
EDNRA	1909	hgsc.bcm.edu	37	4	148461073	148461073	+	Silent	SNP	G	G	A	rs5334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:148461073G>A	ENST00000324300.5	+	6	1520	c.1005G>A	c.(1003-1005)gaG>gaA	p.E335E	EDNRA_ENST00000503721.1_3'UTR|EDNRA_ENST00000511804.1_Silent_p.E110E|EDNRA_ENST00000339690.5_3'UTR|EDNRA_ENST00000506066.1_Silent_p.E226E|EDNRA_ENST00000358556.4_Silent_p.E226E	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	335					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|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 ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TGTATAACGAGATGGACAAGA	0.348													G|||	1924	0.384185	0.6498	0.3372	5008	,	,		18834	0.2381		0.2237	False		,,,				2504	0.3742				p.E335E		Atlas-SNP	.											EDNRA,NS,carcinoma,+1,2	EDNRA	48	2	0			c.G1005A						scavenged	.	G	,	2444,1962	621.4+/-393.7	684,1076,443	182.0	182.0	182.0		678,1005	3.6	1.0	4	dbSNP_52	182	2140,6460	367.3+/-334.7	275,1590,2435	no	coding-synonymous,coding-synonymous	EDNRA	NM_001166055.1,NM_001957.3	,	959,2666,2878	AA,AG,GG		24.8837,44.5302,35.2453	,	226/319,335/428	148461073	4584,8422	2203	4300	6503	SO:0001819	synonymous_variant	1909	exon6			TAACGAGATGGAC	D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"""GPCR / Class A : Endothelin receptors"""	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.1005G>A	4.37:g.148461073G>A		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	192	89	0.463542	NM_001957	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Silent	SNP	ENST00000324300.5	37	CCDS3769.1																																																																																			G|0.644;A|0.356	0.356	strong		0.348	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1		
IRAK2	3656	hgsc.bcm.edu	37	3	10251340	10251340	+	Silent	SNP	C	C	G	rs464286	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:10251340C>G	ENST00000256458.4	+	4	582	c.492C>G	c.(490-492)tcC>tcG	p.S164S		NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	164					activation of MAPK activity (GO:0000187)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						CCCCTCATTCCTTGAGAAGCG	0.582													C|||	485	0.096845	0.0068	0.0519	5008	,	,		16367	0.2123		0.0895	False		,,,				2504	0.1391				p.S164S		Atlas-SNP	.											.	IRAK2	113	.	0			c.C492G						PASS	.	C		78,4328	68.1+/-105.8	0,78,2125	150.0	154.0	153.0		492	1.2	0.0	3	dbSNP_80	153	603,7997	158.3+/-211.8	21,561,3718	no	coding-synonymous	IRAK2	NM_001570.3		21,639,5843	GG,GC,CC		7.0116,1.7703,5.236		164/626	10251340	681,12325	2203	4300	6503	SO:0001819	synonymous_variant	3656	exon4			TCATTCCTTGAGA	AF026273	CCDS33697.1	3p25.2	2008-08-18			ENSG00000134070	ENSG00000134070			6113	protein-coding gene	gene with protein product		603304				9374458	Standard	XR_245126		Approved		uc003bve.1	O43187	OTTHUMG00000155358	ENST00000256458.4:c.492C>G	3.37:g.10251340C>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_001570	B4DQZ6|Q08AG6|Q5K546	Silent	SNP	ENST00000256458.4	37	CCDS33697.1																																																																																			C|0.933;G|0.067	0.067	strong		0.582	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339623.1		
CACNA1H	8912	hgsc.bcm.edu	37	16	1268494	1268494	+	Silent	SNP	C	C	T	rs2745136	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1268494C>T	ENST00000348261.5	+	33	5978	c.5730C>T	c.(5728-5730)gaC>gaT	p.D1910D	CACNA1H_ENST00000358590.4_Silent_p.D1904D|CACNA1H_ENST00000565831.1_Silent_p.D1904D	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1910					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GCGCCAGGGACGCCCCAAACC	0.701													C|||	3501	0.699081	0.7156	0.7075	5008	,	,		14381	0.8661		0.6441	False		,,,				2504	0.5552				p.D1910D		Atlas-SNP	.											CACNA1H_ENST00000358590,NS,carcinoma,0,2	CACNA1H	317	2	0			c.C5730T						scavenged	.	C	,	2908,1158		1072,764,197	23.0	30.0	28.0		5712,5730	-5.8	0.0	16	dbSNP_100	28	5076,3122		1657,1762,680	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	2729,2526,877	TT,TC,CC		38.0825,28.4801,34.8989	,	1904/2348,1910/2354	1268494	7984,4280	2033	4099	6132	SO:0001819	synonymous_variant	8912	exon33			CAGGGACGCCCCA	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.5730C>T	16.37:g.1268494C>T		Somatic	42	1	0.0238095		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.275;G|0.000;T|0.724	0.724	strong		0.701	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
TIMELESS	8914	hgsc.bcm.edu	37	12	56825311	56825311	+	Silent	SNP	C	C	T	rs774033	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56825311C>T	ENST00000553532.1	-	8	915	c.765G>A	c.(763-765)gtG>gtA	p.V255V	TIMELESS_ENST00000229201.4_Silent_p.V254V|TIMELESS_ENST00000554616.1_Silent_p.V255V					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						GCTGGCGCAACACCTCCAGTT	0.552													C|||	2525	0.504193	0.2526	0.6816	5008	,	,		14831	0.7371		0.4503	False		,,,				2504	0.5337				p.V255V		Atlas-SNP	.											.	TIMELESS	107	.	0			c.G765A						PASS	.	C		1189,3217	413.9+/-336.6	150,889,1164	123.0	104.0	111.0		765	2.4	0.9	12	dbSNP_86	111	3907,4693	547.2+/-385.1	873,2161,1266	no	coding-synonymous	TIMELESS	NM_003920.3		1023,3050,2430	TT,TC,CC		45.4302,26.9859,39.1819		255/1209	56825311	5096,7910	2203	4300	6503	SO:0001819	synonymous_variant	8914	exon8			GCGCAACACCTCC	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.765G>A	12.37:g.56825311C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_003920		Silent	SNP	ENST00000553532.1	37	CCDS8918.1																																																																																			C|0.565;T|0.435	0.435	strong		0.552	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
NID2	22795	hgsc.bcm.edu	37	14	52520368	52520368	+	Missense_Mutation	SNP	C	C	T	rs2101919	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:52520368C>T	ENST00000216286.5	-	5	1357	c.1358G>A	c.(1357-1359)gGt>gAt	p.G453D	NID2_ENST00000541773.1_Missense_Mutation_p.G400D	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	453			G -> D (in dbSNP:rs2101919). {ECO:0000269|PubMed:9733643}.		basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					TGTAGTGTGACCTGAAGCAGG	0.512													C|||	2860	0.571086	0.447	0.5648	5008	,	,		20220	0.4425		0.7525	False		,,,				2504	0.6892				p.G453D		Atlas-SNP	.											.	NID2	201	.	0			c.G1358A						PASS	.	C	ASP/GLY	2206,2200	588.8+/-387.0	565,1076,562	132.0	132.0	132.0		1358	-5.0	0.0	14	dbSNP_96	132	6463,2137	715.2+/-406.0	2416,1631,253	yes	missense	NID2	NM_007361.3	94	2981,2707,815	TT,TC,CC		24.8488,49.9319,33.3461	benign	453/1376	52520368	8669,4337	2203	4300	6503	SO:0001583	missense	22795	exon5			GTGTGACCTGAAG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1358G>A	14.37:g.52520368C>T	ENSP00000216286:p.Gly453Asp	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	196	104	0.530612	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	1267	0.5801282051282052	223	0.4532520325203252	205	0.5662983425414365	263	0.4597902097902098	576	0.7598944591029023	C	6.095	0.385827	0.11524	0.500681	0.751512	ENSG00000087303	ENST00000216286;ENST00000541773;ENST00000395707	D;D	0.83335	-1.71;-1.6	5.61	-5.03	0.02973	.	1.291090	0.05087	N	0.484656	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.12630	0.006;0.001	B;B	0.13407	0.009;0.002	T	0.25916	-1.0118	9	0.14252	T	0.57	.	10.746	0.46181	0.0:0.4433:0.4289:0.1277	rs2101919;rs52833324;rs56866817;rs2101919	400;453	Q14112-2;Q14112	.;NID2_HUMAN	D	453;400;455	ENSP00000216286:G453D;ENSP00000443730:G400D	ENSP00000216286:G453D	G	-	2	0	NID2	51590118	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.119000	0.10676	-0.995000	0.03459	-0.165000	0.13383	GGT	T|0.617;G|0.003	0.617	strong		0.512	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
MTMR2	8898	hgsc.bcm.edu	37	11	95578270	95578270	+	Silent	SNP	C	C	T	rs113897932	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:95578270C>T	ENST00000346299.5	-	11	1573	c.1233G>A	c.(1231-1233)acG>acA	p.T411T	MTMR2_ENST00000393223.3_Silent_p.T339T|MTMR2_ENST00000409459.1_Silent_p.T339T|MTMR2_ENST00000352297.7_Silent_p.T339T	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	411	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTACCACAGACGTCTTCCCTG	0.443													C|||	31	0.0061901	0.0023	0.0058	5008	,	,		18111	0.0		0.0239	False		,,,				2504	0.0				p.T411T		Atlas-SNP	.											MTMR2_ENST00000346299,NS,carcinoma,-1,2	MTMR2	79	2	0			c.G1233A						PASS	.	C	,,	19,4383	26.2+/-53.5	0,19,2182	140.0	123.0	128.0		1233,1017,1017	-8.2	0.2	11	dbSNP_132	128	239,8357	96.3+/-158.1	5,229,4064	no	coding-synonymous,coding-synonymous,coding-synonymous	MTMR2	NM_016156.5,NM_201278.2,NM_201281.2	,,	5,248,6246	TT,TC,CC		2.7804,0.4316,1.9849	,,	411/644,339/572,339/572	95578270	258,12740	2201	4298	6499	SO:0001819	synonymous_variant	8898	exon11			CACAGACGTCTTC	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.1233G>A	11.37:g.95578270C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_016156	A6NN98|Q9UPS9	Silent	SNP	ENST00000346299.5	37	CCDS8305.1																																																																																			C|0.983;G|0.000;T|0.017	0.017	strong		0.443	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156	
AASDHPPT	60496	hgsc.bcm.edu	37	11	105950335	105950335	+	Missense_Mutation	SNP	A	A	G	rs528924003		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:105950335A>G	ENST00000278618.4	+	2	547	c.325A>G	c.(325-327)Atc>Gtc	p.I109V	KBTBD3_ENST00000526793.1_5'Flank|KBTBD3_ENST00000531837.1_5'Flank|KBTBD3_ENST00000534815.1_5'Flank	NM_015423.2	NP_056238.2	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	109	Coenzyme A binding.				macromolecule biosynthetic process (GO:0009059)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	holo-[acyl-carrier-protein] synthase activity (GO:0008897)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)	17		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		CAACTTTAACATCTCTCATCA	0.393																																					p.I109V		Atlas-SNP	.											.	AASDHPPT	40	.	0			c.A325G						PASS	.						116.0	115.0	115.0					11																	105950335		2201	4299	6500	SO:0001583	missense	60496	exon2			TTTAACATCTCTC	AF302110	CCDS31664.1	11q22	2010-12-09			ENSG00000149313	ENSG00000149313	1.2.1.31		14235	protein-coding gene	gene with protein product		607756				12815048, 11286508	Standard	NM_015423		Approved	LYS5, CGI-80, AASD-PPT	uc001pjc.1	Q9NRN7	OTTHUMG00000166253	ENST00000278618.4:c.325A>G	11.37:g.105950335A>G	ENSP00000278618:p.Ile109Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	138	72	0.521739	NM_015423	B2R6D1|B4DDW7|Q9C068|Q9P0Q3|Q9UG80|Q9Y389	Missense_Mutation	SNP	ENST00000278618.4	37	CCDS31664.1	.	.	.	.	.	.	.	.	.	.	A	2.118	-0.402119	0.04865	.	.	ENSG00000149313	ENST00000533423;ENST00000524411;ENST00000278618	.	.	.	5.91	3.59	0.41128	4&apos (1);-phosphopantetheinyl transferase (1);	0.472007	0.24312	N	0.039629	T	0.16428	0.0395	N	0.01817	-0.705	0.36736	D	0.881978	B	0.02656	0.0	B	0.01281	0.0	T	0.20472	-1.0274	9	0.05620	T	0.96	.	7.3013	0.26422	0.6388:0.0:0.3612:0.0	.	109	Q9NRN7	ADPPT_HUMAN	V	44;44;109	.	ENSP00000278618:I109V	I	+	1	0	AASDHPPT	105455545	0.998000	0.40836	1.000000	0.80357	0.985000	0.73830	1.307000	0.33516	0.485000	0.27652	0.533000	0.62120	ATC	.	.	none		0.393	AASDHPPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388734.1	NM_015423	
MTMR11	10903	hgsc.bcm.edu	37	1	149906413	149906413	+	Missense_Mutation	SNP	T	T	C	rs11205303	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:149906413T>C	ENST00000439741.2	-	6	725	c.475A>G	c.(475-477)Atg>Gtg	p.M159V	MTMR11_ENST00000361405.6_Missense_Mutation_p.M159V|MTMR11_ENST00000406732.3_Missense_Mutation_p.M131V|MTMR11_ENST00000492824.1_5'UTR|MTMR11_ENST00000369140.3_Missense_Mutation_p.M87V	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	159			M -> V (in dbSNP:rs11205303). {ECO:0000269|PubMed:15489334}.				phosphatase activity (GO:0016791)	p.M87V(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			ACAATGGCCATGGTCACCTGC	0.498													T|||	1145	0.228634	0.0151	0.2637	5008	,	,		21469	0.2837		0.3688	False		,,,				2504	0.2914				p.M159V		Atlas-SNP	.											MTMR11,NS,carcinoma,0,1	MTMR11	136	1	1	Substitution - Missense(1)	stomach(1)	c.A475G						PASS	.	T	VAL/MET,VAL/MET	383,4023	194.3+/-219.2	20,343,1840	118.0	94.0	102.0		475,259	2.7	1.0	1	dbSNP_120	102	3473,5127	509.2+/-377.2	717,2039,1544	yes	missense,missense	MTMR11	NM_001145862.1,NM_181873.3	21,21	737,2382,3384	CC,CT,TT		40.3837,8.6927,29.6479	benign,benign	159/710,87/641	149906413	3856,9150	2203	4300	6503	SO:0001583	missense	10903	exon6			TGGCCATGGTCAC	AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	24307	protein-coding gene	gene with protein product	"""cisplatin resistance associated"""					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.475A>G	1.37:g.149906413T>C	ENSP00000391668:p.Met159Val	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	278	273	0.982014	NM_001145862	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Missense_Mutation	SNP	ENST00000439741.2	37	CCDS53360.1	576	0.26373626373626374	8	0.016260162601626018	98	0.27071823204419887	179	0.3129370629370629	291	0.3839050131926121	T	10.96	1.498377	0.26861	0.086927	0.403837	ENSG00000014914	ENST00000369140;ENST00000439741;ENST00000361405;ENST00000406732;ENST00000405710	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	6.17	2.65	0.31530	.	0.439521	0.27429	N	0.019403	T	0.60444	0.2269	L	0.57536	1.79	0.37780	P	0.073017	B;B;B;B	0.25850	0.0;0.038;0.136;0.084	B;B;B;B	0.26864	0.001;0.023;0.074;0.034	T	0.41378	-0.9512	9	0.16420	T	0.52	.	7.499	0.27507	0.0:0.241:0.0:0.759	rs11205303;rs17582922;rs52819798;rs11205303	1;131;87;159	F8W8W0;A4FU01-6;A4FU01-4;A4FU01	.;.;.;MTMRB_HUMAN	V	87;159;159;131;1	ENSP00000358136:M87V;ENSP00000391668:M159V;ENSP00000354941:M159V;ENSP00000383948:M131V	ENSP00000354941:M159V	M	-	1	0	MTMR11	148173037	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.553000	0.23391	0.214000	0.20742	-0.256000	0.11100	ATG	T|0.730;C|0.270	0.270	strong		0.498	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873	
RNF135	84282	hgsc.bcm.edu	37	17	29326155	29326155	+	Missense_Mutation	SNP	G	G	T	rs61749868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:29326155G>T	ENST00000328381.5	+	5	2118	c.1245G>T	c.(1243-1245)tgG>tgT	p.W415C	RNF135_ENST00000443677.2_3'UTR|RNF135_ENST00000535306.2_3'UTR|RNF135_ENST00000324689.4_3'UTR	NM_032322.3	NP_115698.3	Q8IUD6	RN135_HUMAN	ring finger protein 135	415	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		W -> C (in dbSNP:rs61749868). {ECO:0000269|PubMed:19291764}.		innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-beta production (GO:0032728)|protein ubiquitination (GO:0016567)|regulation of innate immune response (GO:0045088)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|ribonucleoprotein complex binding (GO:0043021)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|skin(2)|urinary_tract(1)	10		all_cancers(10;8.65e-08)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Myeloproliferative disorder(56;0.0255)				CTGCCTTCTGGCTGTATGGCT	0.458													G|||	12	0.00239617	0.0015	0.0	5008	,	,		21128	0.0		0.0099	False		,,,				2504	0.0				p.W415C		Atlas-SNP	.											.	RNF135	19	.	1	Unknown(1)	central_nervous_system(1)	c.G1245T						PASS	.	G	,CYS/TRP,	10,4396	16.8+/-37.8	0,10,2193	104.0	106.0	105.0		,1245,	5.2	1.0	17	dbSNP_129	105	86,8514	49.4+/-109.1	0,86,4214	yes	utr-3,missense,utr-3	RNF135	NM_001184992.1,NM_032322.3,NM_197939.1	,215,	0,96,6407	TT,TG,GG		1.0,0.227,0.7381	,probably-damaging,	,415/433,	29326155	96,12910	2203	4300	6503	SO:0001583	missense	84282	exon5			CTTCTGGCTGTAT	AJ496729	CCDS11262.1, CCDS11263.1, CCDS54104.1	17q11.2	2013-01-09			ENSG00000181481	ENSG00000181481		"""RING-type (C3HC4) zinc fingers"""	21158	protein-coding gene	gene with protein product	"""riplet"""	611358				11468690, 19017631	Standard	NM_001184992		Approved	MGC13061	uc002hfz.3	Q8IUD6	OTTHUMG00000132867	ENST00000328381.5:c.1245G>T	17.37:g.29326155G>T	ENSP00000328340:p.Trp415Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	102	40	0.392157	NM_032322	A0AVM5|B2R7G9|B6ZLM5|F5GX60|Q9BSE9	Missense_Mutation	SNP	ENST00000328381.5	37	CCDS11262.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	G	15.55	2.867158	0.51588	0.00227	0.01	ENSG00000181481	ENST00000328381;ENST00000535605	T	0.69926	-0.44	5.21	5.21	0.72293	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.176168	0.28072	N	0.016704	T	0.72244	0.3436	L	0.56280	1.765	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73852	-0.3852	10	0.38643	T	0.18	-10.0145	16.6225	0.84934	0.0:0.0:1.0:0.0	rs61749868	415	Q8IUD6	RN135_HUMAN	C	415;234	ENSP00000328340:W415C	ENSP00000328340:W415C	W	+	3	0	RNF135	26350281	1.000000	0.71417	0.995000	0.50966	0.297000	0.27493	6.437000	0.73421	2.613000	0.88420	0.655000	0.94253	TGG	G|0.995;T|0.005	0.005	strong		0.458	RNF135-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256342.3	NM_032322	
TRPV4	59341	hgsc.bcm.edu	37	12	110226379	110226379	+	Silent	SNP	G	G	A	rs3742037	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:110226379G>A	ENST00000418703.2	-	12	2128	c.2034C>T	c.(2032-2034)atC>atT	p.I678I	TRPV4_ENST00000392719.2_Silent_p.I631I|TRPV4_ENST00000537083.1_Silent_p.I618I|TRPV4_ENST00000346520.2_Silent_p.I618I|TRPV4_ENST00000536838.1_Silent_p.I644I|TRPV4_ENST00000541794.1_Silent_p.I631I|TRPV4_ENST00000544971.1_Silent_p.I571I|TRPV4_ENST00000261740.2_Silent_p.I678I	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	678					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						CGCCCATGCCGATGGTCAGCT	0.572													G|||	903	0.180312	0.1059	0.2738	5008	,	,		23121	0.1905		0.1352	False		,,,				2504	0.2505				p.I678I		Atlas-SNP	.											.	TRPV4	88	.	0			c.C2034T						PASS	.	G	,,,,	494,3912	232.6+/-246.1	32,430,1741	240.0	175.0	197.0		1893,1932,1713,2034,1854	1.3	1.0	12	dbSNP_107	197	1200,7400	243.6+/-273.1	95,1010,3195	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV4	NM_001177428.1,NM_001177431.1,NM_001177433.1,NM_021625.4,NM_147204.2	,,,,	127,1440,4936	AA,AG,GG		13.9535,11.212,13.0248	,,,,	631/825,644/838,571/765,678/872,618/812	110226379	1694,11312	2203	4300	6503	SO:0001819	synonymous_variant	59341	exon13			CATGCCGATGGTC	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18083	protein-coding gene	gene with protein product	"""osmosensitive transient receptor potential channel 4"""	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.2034C>T	12.37:g.110226379G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	118	49	0.415254	NM_021625	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Silent	SNP	ENST00000418703.2	37	CCDS9134.1																																																																																			G|0.862;A|0.138	0.138	strong		0.572	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625	
TRPV2	51393	hgsc.bcm.edu	37	17	16326005	16326005	+	Silent	SNP	A	A	C	rs1129235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:16326005A>C	ENST00000338560.7	+	4	826	c.427A>C	c.(427-429)Agg>Cgg	p.R143R	TRPV2_ENST00000577397.1_5'UTR	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	143	Required for interaction with SLC50A1. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		GCAGATCGACAGGGACTCTGG	0.557													C|||	1861	0.371605	0.5938	0.366	5008	,	,		20463	0.2302		0.3867	False		,,,				2504	0.2055				p.R143R		Atlas-SNP	.											.	TRPV2	74	.	0			c.A427C						PASS	.	C		2362,2044	561.1+/-380.6	643,1076,484	73.0	60.0	64.0		427	-2.9	0.0	17	dbSNP_86	64	3361,5239	636.2+/-399.1	648,2065,1587	no	coding-synonymous	TRPV2	NM_016113.4		1291,3141,2071	CC,CA,AA		39.0814,46.3913,44.0028		143/765	16326005	5723,7283	2203	4300	6503	SO:0001819	synonymous_variant	51393	exon4			ATCGACAGGGACT	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.427A>C	17.37:g.16326005A>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	127	68	0.535433	NM_016113	A6NML2|A8K0Z0|Q9Y670	Silent	SNP	ENST00000338560.7	37	CCDS32576.1	867	0.39697802197802196	285	0.5792682926829268	148	0.4088397790055249	147	0.256993006993007	287	0.3786279683377309	C	8.991	0.977622	0.18812	0.536087	0.390814	ENSG00000187688	ENST00000455666	.	.	.	5.24	-2.87	0.05700	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.40404	P	0.020321000000000033	.	.	.	.	.	.	T	0.37056	-0.9722	3	.	.	.	-11.1604	14.0002	0.64429	0.6578:0.2566:0.0856:0.0	rs1129235;rs3186911;rs16959673;rs58276834;rs1129235	.	.	.	P	100	.	.	Q	+	2	0	TRPV2	16266730	0.001000	0.12720	0.005000	0.12908	0.899000	0.52679	-0.477000	0.06583	-0.859000	0.04105	-0.121000	0.15023	CAG	A|0.578;C|0.422	0.422	strong		0.557	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
MPDZ	8777	hgsc.bcm.edu	37	9	13150531	13150531	+	Silent	SNP	T	T	C	rs10756457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:13150531T>C	ENST00000319217.7	-	25	3856	c.3609A>G	c.(3607-3609)aaA>aaG	p.K1203K	MPDZ_ENST00000447879.1_Silent_p.K1203K|MPDZ_ENST00000381022.2_Silent_p.K1203K|MPDZ_ENST00000546205.1_Silent_p.K1217K|MPDZ_ENST00000541718.1_Silent_p.K1203K|MPDZ_ENST00000381015.4_Silent_p.K1203K|MPDZ_ENST00000536827.1_Silent_p.K1203K|MPDZ_ENST00000538841.1_Silent_p.K95K	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1203	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TATCTCCAGGTTTCAAGGTTC	0.368													T|||	2392	0.477636	0.6982	0.3473	5008	,	,		13929	0.496		0.33	False		,,,				2504	0.4049				p.K1203K		Atlas-SNP	.											.	MPDZ	324	.	0			c.A3609G						PASS	.	T		2224,1466		675,874,296	164.0	162.0	163.0		3609	0.9	1.0	9	dbSNP_120	163	2645,5529		442,1761,1884	no	coding-synonymous	MPDZ	NM_003829.3		1117,2635,2180	CC,CT,TT		32.3587,39.729,41.0401		1203/2042	13150531	4869,6995	1845	4087	5932	SO:0001819	synonymous_variant	8777	exon25			TCCAGGTTTCAAG	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.3609A>G	9.37:g.13150531T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																				T|0.540;C|0.460	0.460	strong		0.368	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111611076	111611076	+	Silent	SNP	A	A	G	rs12521830	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:111611076A>G	ENST00000261486.5	-	4	558	c.282T>C	c.(280-282)ttT>ttC	p.F94F		NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	94	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		ATTTAATACCAAAATACAAAG	0.264													A|||	1616	0.322684	0.4077	0.3545	5008	,	,		17567	0.3413		0.337	False		,,,				2504	0.1513				p.F94F		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.T282C						PASS	.	A		1431,2089		312,807,641	48.0	54.0	52.0		282	4.4	1.0	5	dbSNP_120	52	2837,5193		528,1781,1706	no	coding-synonymous	EPB41L4A	NM_022140.3		840,2588,2347	GG,GA,AA		35.33,40.6534,36.9524		94/687	111611076	4268,7282	1760	4015	5775	SO:0001819	synonymous_variant	64097	exon4			AATACCAAAATAC	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.282T>C	5.37:g.111611076A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	160	157	0.98125	NM_022140	A4FUI6	Silent	SNP	ENST00000261486.5	37	CCDS43350.1																																																																																			A|0.639;G|0.361	0.361	strong		0.264	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		
ZFHX4	79776	hgsc.bcm.edu	37	8	77763355	77763355	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:77763355A>C	ENST00000521891.2	+	10	4646	c.4198A>C	c.(4198-4200)Aac>Cac	p.N1400H	ZFHX4_ENST00000455469.2_Missense_Mutation_p.N1355H|ZFHX4_ENST00000518282.1_Missense_Mutation_p.N1374H|ZFHX4_ENST00000050961.6_Missense_Mutation_p.N1355H	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1355					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.N1400D(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GTATCGCTGTAACCATTGTAG	0.453										HNSCC(33;0.089)																											p.N1400H		Atlas-SNP	.											ZFHX4,NS,carcinoma,0,1	ZFHX4	878	1	1	Substitution - Missense(1)	lung(1)	c.A4198C						PASS	.						87.0	82.0	83.0					8																	77763355		1894	4118	6012	SO:0001583	missense	79776	exon10			CGCTGTAACCATT		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.4198A>C	8.37:g.77763355A>C	ENSP00000430497:p.Asn1400His	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	238	108	0.453782	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	13.28	2.190004	0.38707	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.65	4.65	0.58169	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.48286	U	0.000184	T	0.48077	0.1480	M	0.73962	2.25	0.40800	D	0.98333	P;P;P	0.50528	0.894;0.936;0.936	P;P;P	0.53809	0.548;0.735;0.735	T	0.56414	-0.7983	10	0.72032	D	0.01	.	14.5713	0.68213	1.0:0.0:0.0:0.0	.	1355;1355;1400	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	H	1400;1400;1355;1355;1374	ENSP00000430497:N1400H;ENSP00000399605:N1355H;ENSP00000050961:N1355H;ENSP00000430848:N1374H	ENSP00000050961:N1355H	N	+	1	0	ZFHX4	77925910	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.066000	0.76734	2.096000	0.63516	0.454000	0.30748	AAC	.	.	none		0.453	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
ATP2A3	489	hgsc.bcm.edu	37	17	3828702	3828702	+	Silent	SNP	T	T	C	rs887387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:3828702T>C	ENST00000352011.3	-	22	3156	c.3102A>G	c.(3100-3102)agA>agG	p.R1034R	ATP2A3_ENST00000397039.1_Silent_p.R208R|ATP2A3_ENST00000397041.3_3'UTR|ATP2A3_ENST00000309890.7_3'UTR|ATP2A3_ENST00000359983.3_3'UTR|ATP2A3_ENST00000397043.3_3'UTR|ATP2A3_ENST00000397035.3_3'UTR			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	1034					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		GAGACTCCACTCTGTTCCCAG	0.577													T|||	1434	0.286342	0.1823	0.4424	5008	,	,		15994	0.2857		0.335	False		,,,				2504	0.2669				p.R1034R	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.A3102G						PASS	.	T	,,,,,,	978,3428	366.1+/-317.7	111,756,1336	131.0	122.0	125.0		,,,3102,,,	3.4	0.7	17	dbSNP_86	125	3267,5333	487.8+/-372.2	601,2065,1634	no	utr-3,utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	712,2821,2970	CC,CT,TT		37.9884,22.197,32.6388	,,,,,,	,,,1034/1044,,,	3828702	4245,8761	2203	4300	6503	SO:0001819	synonymous_variant	489	exon22			CTCCACTCTGTTC		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.3102A>G	17.37:g.3828702T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_174955	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			T|0.680;C|0.320	0.320	strong		0.577	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48598785	48598785	+	Missense_Mutation	SNP	G	G	A	rs1380657	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48598785G>A	ENST00000323776.5	+	9	1432	c.1270G>A	c.(1270-1272)Gca>Aca	p.A424T	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.A387T	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			TGAAGACACAGCATACTTGTG	0.547													A|||	4060	0.810703	0.913	0.6988	5008	,	,		20382	0.8879		0.7336	False		,,,				2504	0.7515				p.A424T		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.G1270A						PASS	.	A	THR/ALA	3921,485		1750,421,32	64.0	65.0	65.0		1270	-4.3	0.0	17	dbSNP_88	65	6246,2354		2285,1676,339	yes	missense	MYCBPAP	NM_032133.4	58	4035,2097,371	AA,AG,GG		27.3721,11.0077,21.8284	benign	424/985	48598785	10167,2839	2203	4300	6503	SO:0001583	missense	84073	exon9			GACACAGCATACT	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.1270G>A	17.37:g.48598785G>A	ENSP00000323184:p.Ala424Thr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	171	83	0.48538	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	1777	0.8136446886446886	453	0.9207317073170732	258	0.712707182320442	510	0.8916083916083916	556	0.7335092348284961	A	5.695	0.312728	0.10789	0.889923	0.726279	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.45276	0.9;0.9	4.68	-4.29	0.03721	.	2.770710	0.01165	N	0.006722	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28808	-1.0032	9	0.11182	T	0.66	1.3766	8.3331	0.32197	0.5198:0.0:0.3793:0.1009	rs1380657;rs17856808;rs58822805;rs1380657	387	Q8TBZ2	MYBPP_HUMAN	T	424;387	ENSP00000323184:A424T;ENSP00000397209:A387T	ENSP00000323184:A424T	A	+	1	0	MYCBPAP	45953784	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.797000	0.04570	-1.013000	0.03383	-1.007000	0.02485	GCA	G|0.199;A|0.801	0.801	strong		0.547	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
LONRF2	164832	hgsc.bcm.edu	37	2	100917109	100917109	+	Silent	SNP	C	C	T	rs13006224	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:100917109C>T	ENST00000393437.3	-	4	1701	c.1062G>A	c.(1060-1062)tcG>tcA	p.S354S	LONRF2_ENST00000409647.1_Silent_p.S111S	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	354							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						GTCATACCTCCGAGCTCCCTG	0.413													C|||	1896	0.378594	0.0325	0.4467	5008	,	,		16541	0.7252		0.498	False		,,,				2504	0.318				p.S354S		Atlas-SNP	.											.	LONRF2	62	.	0			c.G1062A						PASS	.	C		499,3907	231.4+/-245.2	27,445,1731	134.0	118.0	124.0		1062	1.9	0.0	2	dbSNP_121	124	4167,4433	568.9+/-389.1	1031,2105,1164	no	coding-synonymous	LONRF2	NM_198461.3		1058,2550,2895	TT,TC,CC		48.4535,11.3255,35.8757		354/755	100917109	4666,8340	2203	4300	6503	SO:0001819	synonymous_variant	164832	exon4			TACCTCCGAGCTC	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"""RING-type (C3HC4) zinc fingers"""	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1062G>A	2.37:g.100917109C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	31	0.378049	NM_198461	B9A006|Q6ZSR4	Silent	SNP	ENST00000393437.3	37	CCDS2046.2																																																																																			C|0.610;T|0.390	0.390	strong		0.413	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461	
STEAP1B	256227	hgsc.bcm.edu	37	7	22533033	22533033	+	Missense_Mutation	SNP	C	C	G	rs148687847	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:22533033C>G	ENST00000406890.2	-	3	544	c.450G>C	c.(448-450)ttG>ttC	p.L150F	STEAP1B_ENST00000404369.4_Missense_Mutation_p.L169F	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	150						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						CAGCAAAAAACAAACTGAGAA	0.398													g|||	302	0.0603035	0.1309	0.0519	5008	,	,		19399	0.0		0.0666	False		,,,				2504	0.0266				p.L169F		Atlas-SNP	.											.	STEAP1B	22	.	0			c.G507C						PASS	.						207.0	168.0	180.0					7																	22533033		692	1591	2283	SO:0001583	missense	256227	exon3			AAAAAACAAACTG		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.450G>C	7.37:g.22533033C>G	ENSP00000385239:p.Leu150Phe	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	269	96	0.356877	NM_001164460	B5MCI2	Missense_Mutation	SNP	ENST00000406890.2	37	CCDS55094.1	112	0.05128205128205128	50	0.1016260162601626	17	0.04696132596685083	1	0.0017482517482517483	44	0.05804749340369393	N	0.001	-2.895021	0.00059	.	.	ENSG00000105889	ENST00000406890;ENST00000404369;ENST00000424363;ENST00000439708	D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83	1.23	1.23	0.21249	Flavoprotein transmembrane component (1);	0.000000	0.45361	N	0.000376	T	0.04092	0.0114	N	0.01417	-0.88	0.47819	P	4.7200000000002795E-4	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.45440	-0.9261	9	0.05620	T	0.96	-8.6244	2.7391	0.05248	0.2042:0.3141:0.4817:0.0	.	169;150	B5MCI2;Q6NZ63	.;STEAL_HUMAN	F	150;169;169;169	ENSP00000385239:L150F;ENSP00000384370:L169F;ENSP00000416608:L169F;ENSP00000408954:L169F	ENSP00000384370:L169F	L	-	3	2	STEAP1B	22499558	1.000000	0.71417	0.999000	0.59377	0.143000	0.21401	1.116000	0.31221	0.125000	0.18397	-1.976000	0.00459	TTG	C|0.942;G|0.058	0.058	strong		0.398	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		
CATSPER3	347732	hgsc.bcm.edu	37	5	134343799	134343799	+	Silent	SNP	A	A	G	rs177252	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:134343799A>G	ENST00000282611.6	+	4	731	c.645A>G	c.(643-645)gcA>gcG	p.A215A		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	215					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACCTGGCTGCAGCTTTTTTCA	0.542													G|||	2549	0.508986	0.6415	0.4078	5008	,	,		15572	0.5615		0.3191	False		,,,				2504	0.5429				p.A215A		Atlas-SNP	.											.	CATSPER3	38	.	0			c.A645G						PASS	.	G		2542,1864	536.5+/-374.5	734,1074,395	117.0	105.0	109.0		645	-0.7	0.0	5	dbSNP_79	109	2576,6024	689.8+/-404.4	382,1812,2106	no	coding-synonymous	CATSPER3	NM_178019.2		1116,2886,2501	GG,GA,AA		29.9535,42.3059,39.3511		215/399	134343799	5118,7888	2203	4300	6503	SO:0001819	synonymous_variant	347732	exon4			GGCTGCAGCTTTT	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.645A>G	5.37:g.134343799A>G		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	237	105	0.443038	NM_178019	Q86XS6	Silent	SNP	ENST00000282611.6	37	CCDS4181.1																																																																																			A|0.562;G|0.438	0.438	strong		0.542	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
CDH19	28513	hgsc.bcm.edu	37	18	64176386	64176386	+	Silent	SNP	C	C	T	rs150353589	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:64176386C>T	ENST00000262150.2	-	11	1966	c.1674G>A	c.(1672-1674)ccG>ccA	p.P558P	CDH19_ENST00000540086.1_Intron	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	1833	Cadherin 5. {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)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				TTGTAAGTGACGGGATTCCAT	0.448													c|||	21	0.00419329	0.0008	0.0086	5008	,	,		16460	0.0		0.0139	False		,,,				2504	0.0				p.P558P		Atlas-SNP	.											CDH19,mucosal,malignant_melanoma,-2,2	CDH19	141	2	0			c.G1674A						PASS	.	T		6,4400	11.4+/-27.6	0,6,2197	199.0	172.0	181.0		1674	1.3	0.1	18	dbSNP_134	181	58,8542	36.4+/-91.3	0,58,4242	no	coding-synonymous	CDH19	NM_021153.2		0,64,6439	TT,TC,CC		0.6744,0.1362,0.4921		558/773	64176386	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	28513	exon11			AAGTGACGGGATT	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"""Cadherins / Major cadherins"""	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000262150.2:c.1674G>A	18.37:g.64176386C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	221	125	0.565611	NM_021153	O15098	Silent	SNP	ENST00000262150.2	37	CCDS11994.1																																																																																			A|0.000;C|0.996;T|0.004	0.004	strong		0.448	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693104	187693104	+	Silent	SNP	C	C	T	rs10172225	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:187693104C>T	ENST00000295131.2	-	9	1548	c.1509G>A	c.(1507-1509)gtG>gtA	p.V503V		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	503					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			TCCCAAATGACACAGTGGGTA	0.333													T|||	872	0.174121	0.4213	0.1066	5008	,	,		18832	0.0208		0.1103	False		,,,				2504	0.1115				p.V503V		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.G1509A						PASS	.	T		1766,2640	643.0+/-397.8	353,1060,790	64.0	64.0	64.0		1509	1.2	0.0	2	dbSNP_119	64	979,7621	773.0+/-407.7	44,891,3365	no	coding-synonymous	ZSWIM2	NM_182521.2		397,1951,4155	TT,TC,CC		11.3837,40.0817,21.1056		503/634	187693104	2745,10261	2203	4300	6503	SO:0001819	synonymous_variant	151112	exon9			AAATGACACAGTG	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1509G>A	2.37:g.187693104C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Silent	SNP	ENST00000295131.2	37	CCDS33348.1																																																																																			C|0.805;T|0.195	0.195	strong		0.333	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
PJA1	64219	hgsc.bcm.edu	37	X	68381787	68381787	+	Missense_Mutation	SNP	C	C	T	rs5937160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:68381787C>T	ENST00000361478.1	-	2	1672	c.1295G>A	c.(1294-1296)aGt>aAt	p.S432N	PJA1_ENST00000477231.1_5'Flank|PJA1_ENST00000374584.3_Missense_Mutation_p.S244N|PJA1_ENST00000374571.4_Missense_Mutation_p.S377N|PJA1_ENST00000374583.1_Missense_Mutation_p.S432N	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	432			S -> N (in dbSNP:rs5937160). {ECO:0000269|PubMed:15489334}.		protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						GCTGCCAGCACTGGCCCCGGC	0.597													c|||	331	0.0876821	0.0507	0.0879	3775	,	,		12070	0.0		0.1829	False		,,,				2504	0.0194				p.S432N		Atlas-SNP	.											.	PJA1	106	.	0			c.G1295A						PASS	.		ASN/SER,ASN/SER,ASN/SER	327,3502		15,255,42,1361,525	40.0	45.0	43.0		1130,731,1295	1.5	0.0	X	dbSNP_114	43	1589,5129		142,859,446,1426,1418	yes	missense,missense,missense	PJA1	NM_001032396.2,NM_022368.4,NM_145119.3	46,46,46	157,1114,488,2787,1943	TT,TC,T,CC,C		23.6529,8.5401,18.1663	benign,benign,benign	377/589,244/456,432/644	68381787	1916,8631	2198	4291	6489	SO:0001583	missense	64219	exon2			CCAGCACTGGCCC	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"""RING-type (C3HC4) zinc fingers"""	16648	protein-coding gene	gene with protein product		300420	"""praja 1"", ""praja ring finger 1"""			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.1295G>A	X.37:g.68381787C>T	ENSP00000355014:p.Ser432Asn	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	73	70	0.958904	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Missense_Mutation	SNP	ENST00000361478.1	37	CCDS14393.1	212	0.12778782399035563	30	0.06329113924050633	21	0.06287425149700598	0	0.0	92	0.13813813813813813	c	6.439	0.449078	0.12223	0.085401	0.236529	ENSG00000181191	ENST00000396010;ENST00000374584;ENST00000374583;ENST00000361478;ENST00000374571	T;T;T;T	0.06449	3.3;3.3;3.3;3.3	1.51	1.51	0.23008	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.27700	0.18;0.186	B;B	0.22152	0.038;0.011	T	0.45542	-0.9254	8	0.14656	T	0.56	.	5.8838	0.18870	0.0:1.0:0.0:0.0	rs5937160;rs17846437;rs17859486;rs5937160	432;244	Q8NG27;Q8NG27-2	PJA1_HUMAN;.	N	347;244;432;432;377	ENSP00000363712:S244N;ENSP00000363711:S432N;ENSP00000355014:S432N;ENSP00000363699:S377N	ENSP00000355014:S432N	S	-	2	0	PJA1	68298512	0.000000	0.05858	0.004000	0.12327	0.081000	0.17604	0.031000	0.13710	1.029000	0.39812	0.417000	0.27973	AGT	C|0.855;T|0.145	0.145	strong		0.597	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119	
CSPG4	1464	hgsc.bcm.edu	37	15	75982239	75982239	+	Silent	SNP	G	G	A	rs148229217	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75982239G>A	ENST00000308508.5	-	3	1259	c.1167C>T	c.(1165-1167)gaC>gaT	p.D389D		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	389	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CATAGGCATCGTCCTCATACT	0.627													G|||	467	0.0932508	0.0688	0.0908	5008	,	,		21001	0.001		0.1342	False		,,,				2504	0.181				p.D389D		Atlas-SNP	.											CSPG4,NS,carcinoma,0,2	CSPG4	175	2	0			c.C1167T						PASS	.	G		270,4096		6,258,1919	16.0	18.0	17.0		1167	-8.7	0.3	15	dbSNP_134	17	1141,7421		60,1021,3200	no	coding-synonymous	CSPG4	NM_001897.4		66,1279,5119	AA,AG,GG		13.3263,6.1842,10.9143		389/2323	75982239	1411,11517	2183	4281	6464	SO:0001819	synonymous_variant	1464	exon3			GGCATCGTCCTCA	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1167C>T	15.37:g.75982239G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	116	42	0.362069	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			G|0.899;A|0.101	0.101	strong		0.627	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
HIVEP1	3096	hgsc.bcm.edu	37	6	12120588	12120588	+	Missense_Mutation	SNP	C	C	T	rs2228209	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:12120588C>T	ENST00000379388.2	+	4	892	c.560C>T	c.(559-561)aCg>aTg	p.T187M		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	187			T -> M (in dbSNP:rs2228209).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TGTGGCACTACGTCCCCCTCC	0.453													C|||	1039	0.207468	0.0204	0.245	5008	,	,		21426	0.2232		0.339	False		,,,				2504	0.2822				p.T187M		Atlas-SNP	.											.	HIVEP1	242	.	0			c.C560T						PASS	.	C	MET/THR	273,3831		9,255,1788	115.0	107.0	110.0		560	3.7	0.0	6	dbSNP_98	110	2934,5488		512,1910,1789	yes	missense	HIVEP1	NM_002114.2	81	521,2165,3577	TT,TC,CC		34.8373,6.652,25.6027	probably-damaging	187/2719	12120588	3207,9319	2052	4211	6263	SO:0001583	missense	3096	exon4			GCACTACGTCCCC	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.560C>T	6.37:g.12120588C>T	ENSP00000368698:p.Thr187Met	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	134	133	0.992537	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	489	0.2239010989010989	15	0.03048780487804878	88	0.2430939226519337	134	0.23426573426573427	252	0.3324538258575198	C	13.07	2.128471	0.37533	0.06652	0.348373	ENSG00000095951	ENST00000379388	T	0.10382	2.88	5.5	3.68	0.42216	.	0.678176	0.12199	N	0.490468	T	0.06188	0.0160	L	0.56769	1.78	0.80722	P	0.0	D	0.58268	0.982	P	0.47528	0.549	T	0.30504	-0.9976	8	.	.	.	-1.54	4.9232	0.13880	0.263:0.5365:0.1291:0.0714	rs2228209;rs3800500;rs17609127;rs52832234;rs60943307;rs2228209	187	P15822	ZEP1_HUMAN	M	187	ENSP00000368698:T187M	.	T	+	2	0	HIVEP1	12228574	0.000000	0.05858	0.000000	0.03702	0.656000	0.38851	0.644000	0.24766	0.651000	0.30788	0.591000	0.81541	ACG	C|0.744;N|0.001	.	strong		0.453	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
NXPE1	120400	hgsc.bcm.edu	37	11	114398591	114398591	+	Missense_Mutation	SNP	C	C	T	rs143110380		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:114398591C>T	ENST00000424269.1	-	3	865	c.866G>A	c.(865-867)cGt>cAt	p.R289H	NXPE1_ENST00000536312.1_3'UTR|snoU13_ENST00000459372.1_RNA|NXPE1_ENST00000251921.2_Missense_Mutation_p.R147H|NXPE1_ENST00000536271.1_Missense_Mutation_p.R5H			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	289						extracellular region (GO:0005576)		p.R147H(1)									AATGTGTTTACGATCCTTCAT	0.373																																					p.R147H		Atlas-SNP	.											FAM55A,NS,carcinoma,0,1	NXPE1	8	1	1	Substitution - Missense(1)	endometrium(1)	c.G440A						scavenged	.	C	HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	163.0	129.0	141.0		440	-2.2	0.0	11	dbSNP_134	141	0,8592		0,0,4296	no	missense	FAM55A	NM_152315.2	29	0,1,6496	TT,TC,CC		0.0,0.0227,0.0077	benign	147/406	114398591	1,12993	2201	4296	6497	SO:0001583	missense	120400	exon4			TGTTTACGATCCT	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member A"""	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.866G>A	11.37:g.114398591C>T	ENSP00000411690:p.Arg289His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	116	4	0.0344828	NM_152315	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	37		.	.	.	.	.	.	.	.	.	.	C	6.501	0.460553	0.12342	2.27E-4	0.0	ENSG00000095110	ENST00000536271;ENST00000251921;ENST00000424269	T;T;T	0.14266	2.55;2.52;2.74	3.16	-2.19	0.07015	.	2.260390	0.02681	N	0.109654	T	0.05502	0.0145	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.20974	-1.0259	8	0.13108	T	0.6	.	0.9383	0.01350	0.3542:0.2954:0.2062:0.1443	.	.	.	.	H	5;147;289	ENSP00000445200:R5H;ENSP00000251921:R147H;ENSP00000411690:R289H	ENSP00000251921:R147H	R	-	2	0	FAM55A	113903801	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.253000	0.08794	-0.840000	0.04206	-2.337000	0.00247	CGT	C|1.000;T|0.000	0.000	weak		0.373	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315	
PBRM1	55193	hgsc.bcm.edu	37	3	52676038	52676038	+	Missense_Mutation	SNP	C	C	G	rs200106731		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52676038C>G	ENST00000296302.7	-	10	1020	c.1019G>C	c.(1018-1020)gGt>gCt	p.G340A	PBRM1_ENST00000356770.4_Missense_Mutation_p.G308A|PBRM1_ENST00000337303.4_Missense_Mutation_p.G340A|PBRM1_ENST00000409767.1_Missense_Mutation_p.G340A|PBRM1_ENST00000409114.3_Missense_Mutation_p.G340A|PBRM1_ENST00000410007.1_Missense_Mutation_p.G340A|PBRM1_ENST00000394830.3_Missense_Mutation_p.G340A|PBRM1_ENST00000409057.1_Missense_Mutation_p.G340A			Q86U86	PB1_HUMAN	polybromo 1	340			G -> A (found in a malignant melanoma cell line). {ECO:0000269|PubMed:21248752}.		chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TGATAAACGACCTCCTTGTAC	0.363			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																p.G340A		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.G1019C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY	0,4406		0,0,2203	260.0	245.0	250.0		923,1019,1019	4.8	1.0	3		250	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	60,60,60	0,3,6500	GG,GC,CC		0.0349,0.0,0.0231	benign,benign,benign	308/1603,340/1583,340/1583	52676038	3,13003	2203	4300	6503	SO:0001583	missense	55193	exon11			AAACGACCTCCTT	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1019G>C	3.37:g.52676038C>G	ENSP00000296302:p.Gly340Ala	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	54	0.529412	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	C	15.82	2.945034	0.53079	0.0	3.49E-4	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	T;T;T;T;T;T;T;T;T;T	0.33216	1.45;1.43;1.46;1.42;1.43;1.42;1.89;1.42;1.43;1.44	5.71	4.83	0.62350	Bromodomain (1);	0.049850	0.85682	D	0.000000	T	0.13543	0.0328	N	0.08118	0	0.46113	D	0.998875	B;B;B;B;B;B;B;B;B	0.23377	0.03;0.03;0.058;0.066;0.017;0.082;0.084;0.066;0.066	B;B;B;B;B;B;B;B;B	0.29267	0.019;0.02;0.031;0.046;0.024;0.1;0.034;0.046;0.046	T	0.20806	-1.0264	10	0.11794	T	0.64	-18.8331	5.4588	0.16606	0.0:0.7329:0.0:0.2671	.	340;340;340;340;340;340;340;308;340	Q86U86-9;Q86U86-6;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;.;PB1_HUMAN;.;.	A	308;340;340;340;340;340;340;340;340;284	ENSP00000349213:G308A;ENSP00000378307:G340A;ENSP00000296302:G340A;ENSP00000338302:G340A;ENSP00000386593:G340A;ENSP00000386529:G340A;ENSP00000386643:G340A;ENSP00000386601:G340A;ENSP00000387775:G340A;ENSP00000397662:G284A	ENSP00000296302:G340A	G	-	2	0	PBRM1	52651078	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.354000	0.66040	2.700000	0.92200	0.650000	0.86243	GGT	C|0.999;G|0.001	0.001	weak		0.363	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
COL6A1	1291	hgsc.bcm.edu	37	21	47423389	47423389	+	Missense_Mutation	SNP	G	G	A	rs1053312	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47423389G>A	ENST00000361866.3	+	35	2663	c.2549G>A	c.(2548-2550)cGc>cAc	p.R850H	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	850	C-terminal globular domain.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.		R -> H (in dbSNP:rs1053312). {ECO:0000269|PubMed:15689448}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		ACCACCAAGCGCTTCGCCAAG	0.706													G|||	1353	0.270168	0.4198	0.281	5008	,	,		14974	0.1339		0.2724	False		,,,				2504	0.1984				p.R850H		Atlas-SNP	.											.	COL6A1	101	.	0			c.G2549A						PASS	.	G	HIS/ARG	1739,2625		376,987,819	16.0	19.0	18.0		2549	0.7	1.0	21	dbSNP_86	18	2627,5865		454,1719,2073	yes	missense	COL6A1	NM_001848.2	29	830,2706,2892	AA,AG,GG		30.935,39.8488,33.9608	probably-damaging	850/1029	47423389	4366,8490	2182	4246	6428	SO:0001583	missense	1291	exon35			CCAAGCGCTTCGC	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2549G>A	21.37:g.47423389G>A	ENSP00000355180:p.Arg850His	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	16	8	0.5	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	37	CCDS13727.1	607	0.27793040293040294	208	0.42276422764227645	107	0.2955801104972376	87	0.1520979020979021	205	0.2704485488126649	G	19.07	3.755932	0.69648	0.398488	0.30935	ENSG00000142156	ENST00000361866	D	0.83673	-1.75	4.84	0.709	0.18150	von Willebrand factor, type A (3);	0.771200	0.12213	N	0.489117	T	0.00012	0.0000	N	0.14661	0.345	0.43868	P	0.003523000000000054	B	0.09022	0.002	B	0.06405	0.002	T	0.21415	-1.0246	9	0.41790	T	0.15	-7.3617	3.4558	0.07515	0.2694:0.0:0.4037:0.3269	rs1053312;rs3193825;rs17845675;rs17858614;rs59583777;rs1053312	850	P12109	CO6A1_HUMAN	H	850	ENSP00000355180:R850H	ENSP00000355180:R850H	R	+	2	0	COL6A1	46247817	0.006000	0.16342	0.992000	0.48379	0.989000	0.77384	-0.001000	0.12947	0.063000	0.16370	0.530000	0.56133	CGC	G|0.703;A|0.297	0.297	strong		0.706	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
DRC7	84229	hgsc.bcm.edu	37	16	57735900	57735900	+	Missense_Mutation	SNP	G	G	C	rs7196016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:57735900G>C	ENST00000360716.3	+	6	778	c.557G>C	c.(556-558)tGc>tCc	p.C186S	CCDC135_ENST00000394337.4_Missense_Mutation_p.C186S|CCDC135_ENST00000336825.8_Intron|RP11-405F3.4_ENST00000563062.1_RNA			Q8IY82	CC135_HUMAN		186			C -> S (in dbSNP:rs7196016). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						AAGGGGAACTGCTTTGACTTC	0.607													g|||	1425	0.284545	0.2368	0.2824	5008	,	,		23547	0.376		0.2604	False		,,,				2504	0.2812				p.C186S		Atlas-SNP	.											.	CCDC135	97	.	0			c.G557C						PASS	.	G	SER/CYS	1160,3236	409.5+/-335.0	163,834,1201	173.0	129.0	144.0		557	4.1	1.0	16	dbSNP_116	144	2178,6422	373.0+/-336.8	264,1650,2386	yes	missense	CCDC135	NM_032269.5	112	427,2484,3587	CC,CG,GG		25.3256,26.3876,25.6848	benign	186/875	57735900	3338,9658	2198	4300	6498	SO:0001583	missense	84229	exon5			GGAACTGCTTTGA																												ENST00000360716.3:c.557G>C	16.37:g.57735900G>C	ENSP00000353942:p.Cys186Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	616	0.28205128205128205	95	0.19308943089430894	99	0.27348066298342544	217	0.3793706293706294	205	0.2704485488126649	G	13.22	2.171631	0.38315	0.263876	0.253256	ENSG00000159625	ENST00000394337;ENST00000360716	T;T	0.57273	0.41;0.41	5.09	4.11	0.48088	.	0.102047	0.64402	D	0.000002	T	0.00012	0.0000	N	0.25332	0.735	0.09310	P	1.0	P	0.37158	0.585	B	0.30782	0.12	T	0.41360	-0.9513	9	0.30078	T	0.28	-26.8835	14.4722	0.67523	0.0:0.148:0.852:0.0	rs7196016;rs17853688;rs52823892;rs61693255;rs7196016	186	Q8IY82	CC135_HUMAN	S	186	ENSP00000377869:C186S;ENSP00000353942:C186S	ENSP00000353942:C186S	C	+	2	0	CCDC135	56293401	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	9.207000	0.95064	1.095000	0.41419	0.446000	0.29264	TGC	G|0.731;C|0.269	0.269	strong		0.607	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
LSG1	55341	hgsc.bcm.edu	37	3	194387186	194387186	+	Silent	SNP	C	C	T	rs35670721	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:194387186C>T	ENST00000265245.5	-	3	656	c.342G>A	c.(340-342)ccG>ccA	p.P114P	AC046143.1_ENST00000408791.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	114					GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		CTCACCTCCTCGGTATACACA	0.413													C|||	487	0.0972444	0.1384	0.1037	5008	,	,		17505	0.0744		0.0616	False		,,,				2504	0.0971				p.P114P		Atlas-SNP	.											.	LSG1	38	.	0			c.G342A						PASS	.	C		540,3866	245.3+/-254.3	37,466,1700	109.0	106.0	107.0		342	-4.7	1.0	3	dbSNP_126	107	530,8070	147.9+/-203.2	14,502,3784	no	coding-synonymous	LSG1	NM_018385.2		51,968,5484	TT,TC,CC		6.1628,12.256,8.227		114/659	194387186	1070,11936	2203	4300	6503	SO:0001819	synonymous_variant	55341	exon3			CCTCCTCGGTATA		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"""large subunit GTPase 1 homolog (S. cerevisiae)"""			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.342G>A	3.37:g.194387186C>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	189	83	0.439153	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Silent	SNP	ENST00000265245.5	37	CCDS33922.1																																																																																			C|0.920;T|0.080	0.080	strong		0.413	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	
IQGAP3	128239	hgsc.bcm.edu	37	1	156499969	156499969	+	Silent	SNP	T	T	C	rs386635735|rs1171566	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156499969T>C	ENST00000361170.2	-	34	4342	c.4332A>G	c.(4330-4332)ctA>ctG	p.L1444L	snoU13_ENST00000458777.1_RNA	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1444					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAAGTCGGCGTAGGTTCCGCA	0.647													C|||	3033	0.605631	0.8449	0.4424	5008	,	,		406	0.6022		0.33	False		,,,				2504	0.6851				p.L1444L		Atlas-SNP	.											IQGAP3,NS,carcinoma,0,1	IQGAP3	146	1	0			c.A4332G						scavenged	.	C		3226,1180	404.0+/-332.9	1179,868,156	52.0	46.0	48.0		4332	4.5	1.0	1	dbSNP_87	48	2795,5805	665.5+/-402.3	475,1845,1980	no	coding-synonymous	IQGAP3	NM_178229.4		1654,2713,2136	CC,CT,TT		32.5,26.7817,46.294		1444/1632	156499969	6021,6985	2203	4300	6503	SO:0001819	synonymous_variant	128239	exon34			TCGGCGTAGGTTC	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.4332A>G	1.37:g.156499969T>C		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	135	58	0.42963	NM_178229	Q5T3H8	Silent	SNP	ENST00000361170.2	37	CCDS1144.1																																																																																			T|0.489;C|0.511	0.511	strong		0.647	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
ECH1	1891	hgsc.bcm.edu	37	19	39307103	39307103	+	Missense_Mutation	SNP	C	C	T	rs2229259	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:39307103C>T	ENST00000221418.4	-	7	881	c.649G>A	c.(649-651)Ggg>Agg	p.G217R		NM_001398.2	NP_001389.2	Q13011	ECH1_HUMAN	enoyl CoA hydratase 1, peroxisomal	217			G -> R (in dbSNP:rs2229259).		fatty acid beta-oxidation (GO:0006635)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	isomerase activity (GO:0016853)|receptor binding (GO:0005102)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	6	all_cancers(60;9.36e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			CTCTGGTTCCCGATGACCTTG	0.652													t|||	380	0.0758786	0.0121	0.1571	5008	,	,		13675	0.0823		0.0795	False		,,,				2504	0.0941				p.G217R		Atlas-SNP	.											.	ECH1	14	.	0			c.G649A						PASS	.	C	ARG/GLY	114,4292	815.0+/-416.2	1,112,2090	65.0	60.0	62.0		649	4.9	1.0	19	dbSNP_98	62	955,7645	774.6+/-407.7	65,825,3410	yes	missense	ECH1	NM_001398.2	125	66,937,5500	TT,TC,CC		11.1047,2.5874,8.2193		217/329	39307103	1069,11937	2203	4300	6503	SO:0001583	missense	1891	exon7			GGTTCCCGATGAC	U16660	CCDS33014.1	19q13.1	2010-04-30	2010-04-30			ENSG00000104823			3149	protein-coding gene	gene with protein product		600696	"""enoyl Coenzyme A hydratase 1, peroxisomal"""			7558027	Standard	XM_005258610		Approved	HPXEL		Q13011		ENST00000221418.4:c.649G>A	19.37:g.39307103C>T	ENSP00000221418:p.Gly217Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_001398	A8K745|Q8WVX0|Q96EZ9	Missense_Mutation	SNP	ENST00000221418.4	37	CCDS33014.1	158	0.07234432234432235	12	0.024390243902439025	56	0.15469613259668508	37	0.06468531468531469	53	0.06992084432717678	t	33	5.204563	0.95033	0.025874	0.111047	ENSG00000104823	ENST00000221418	D	0.86627	-2.15	4.92	4.92	0.64577	Crotonase, core (1);	0.000000	0.85682	D	0.000000	T	0.11367	0.0277	M	0.91140	3.18	0.09310	P	0.99999999817355	D	0.89917	1.0	D	0.76575	0.988	T	0.54403	-0.8299	9	0.87932	D	0	.	17.0279	0.86453	0.0:1.0:0.0:0.0	rs2229259;rs2303173;rs11549274;rs2229259	217	Q13011	ECH1_HUMAN	R	217	ENSP00000221418:G217R	ENSP00000221418:G217R	G	-	1	0	ECH1	43998943	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.830000	0.75319	2.539000	0.85634	0.561000	0.74099	GGG	C|0.921;T|0.079	0.079	strong		0.652	ECH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462650.1		
PDF	64146	hgsc.bcm.edu	37	16	69364030	69364030	+	Silent	SNP	G	G	A	rs3852691	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:69364030G>A	ENST00000288022.1	-	1	468	c.444C>T	c.(442-444)ttC>ttT	p.F148F	RP11-343C2.12_ENST00000562949.1_Intron|COG8_ENST00000306875.4_Intron|COG8_ENST00000564419.1_5'Flank	NM_022341.1	NP_071736.1	Q9HBH1	DEFM_HUMAN	peptide deformylase (mitochondrial)	148					N-terminal protein amino acid modification (GO:0031365)|peptidyl-methionine modification (GO:0018206)|positive regulation of cell proliferation (GO:0008284)|translation (GO:0006412)	mitochondrion (GO:0005739)	iron ion binding (GO:0005506)|peptide deformylase activity (GO:0042586)	p.F148F(1)		NS(1)|prostate(1)	2						CGCGCAGGGGGAAGGGCTCCA	0.731													-|||	383	0.0764776	0.1331	0.0692	5008	,	,		11967	0.0258		0.0547	False		,,,				2504	0.0798				p.F148F		Atlas-SNP	.											PDF,NS,carcinoma,0,1	PDF	4	1	1	Substitution - coding silent(1)	prostate(1)	c.C444T						PASS	.		,	488,3644		35,418,1613	10.0	10.0	10.0		444,	-0.1	1.0	16	dbSNP_108	10	439,7599		14,411,3594	no	coding-synonymous,intron	PDF,COG8	NM_022341.1,NM_032382.4	,	49,829,5207	AA,AG,GG		5.4616,11.8103,7.6171	,	148/244,	69364030	927,11243	2066	4019	6085	SO:0001819	synonymous_variant	64146	exon1			CAGGGGGAAGGGC	AF239156	CCDS10875.1	16q22.1	2008-02-05				ENSG00000258429	3.5.1.88		30012	protein-coding gene	gene with protein product						11060042, 15489958	Standard	NM_022341		Approved		uc002ewx.1	Q9HBH1		ENST00000288022.1:c.444C>T	16.37:g.69364030G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	33	22	0.666667	NM_022341	Q8WUN6	Silent	SNP	ENST00000288022.1	37	CCDS10875.1																																																																																			G|0.930;A|0.070	0.070	strong		0.731	PDF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413022.1	NM_022341	
SLC13A2	9058	hgsc.bcm.edu	37	17	26824156	26824156	+	Missense_Mutation	SNP	A	A	G	rs11567842	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:26824156A>G	ENST00000314669.5	+	12	2068	c.1648A>G	c.(1648-1650)Atc>Gtc	p.I550V	SLC13A2_ENST00000444914.3_Missense_Mutation_p.I599V|SLC13A2_ENST00000545060.1_Missense_Mutation_p.I507V|SLC13A2_ENST00000537681.1_Missense_Mutation_p.I479V	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	550			I -> V (in dbSNP:rs11567842). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17470169}.		dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)	p.I550V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	TGGAGTCCTGATCATCGCACT	0.612													G|||	2371	0.473442	0.6415	0.5346	5008	,	,		19203	0.3452		0.3698	False		,,,				2504	0.4417				p.I599V		Atlas-SNP	.											SLC13A2,NS,carcinoma,0,1	SLC13A2	125	1	1	Substitution - Missense(1)	stomach(1)	c.A1795G						PASS	.	G	VAL/ILE,VAL/ILE,VAL/ILE	2552,1854	538.7+/-375.1	761,1030,412	153.0	125.0	135.0		1648,1519,1795	3.2	1.0	17	dbSNP_120	135	2975,5625	667.1+/-402.4	526,1923,1851	yes	missense,missense,missense	SLC13A2	NM_003984.3,NM_001145976.1,NM_001145975.1	29,29,29	1287,2953,2263	GG,GA,AA		34.593,42.079,42.4958	benign,benign,benign	550/593,507/550,599/642	26824156	5527,7479	2203	4300	6503	SO:0001583	missense	9058	exon12			GTCCTGATCATCG	U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"""Solute carriers"""	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.1648A>G	17.37:g.26824156A>G	ENSP00000316202:p.Ile550Val	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	309	138	0.446602	NM_001145975	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	37	CCDS11231.1	1012	0.4633699633699634	330	0.6707317073170732	193	0.5331491712707183	223	0.38986013986013984	266	0.35092348284960423	G	0.131	-1.113770	0.01799	0.57921	0.34593	ENSG00000007216	ENST00000314669;ENST00000444914;ENST00000545060;ENST00000537681	T;T;T;T	0.03272	3.99;3.99;3.99;3.99	5.27	3.21	0.36854	.	0.772693	0.12195	N	0.490860	T	0.00012	0.0000	N	0.00504	-1.425	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.27054	-1.0085	9	0.02654	T	1	-21.18	8.1201	0.30965	0.4377:0.0:0.5623:0.0	rs11567842;rs11568454;rs52804705;rs56617498;rs57825258;rs11567842	507;599;479;550	F5GWV6;E7ETH5;G3V1L2;Q13183	.;.;.;S13A2_HUMAN	V	550;599;507;479	ENSP00000316202:I550V;ENSP00000392411:I599V;ENSP00000441935:I507V;ENSP00000440802:I479V	ENSP00000316202:I550V	I	+	1	0	SLC13A2	23848283	0.529000	0.26322	1.000000	0.80357	0.420000	0.31355	0.555000	0.23422	0.590000	0.29694	-0.215000	0.12644	ATC	A|0.560;G|0.440	0.440	strong		0.612	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984	
CASS4	57091	hgsc.bcm.edu	37	20	55033647	55033647	+	Silent	SNP	T	T	C	rs3746625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:55033647T>C	ENST00000360314.3	+	7	2430	c.2205T>C	c.(2203-2205)cgT>cgC	p.R735R	CASS4_ENST00000371336.3_Silent_p.R735R|AL121914.1_ENST00000390795.2_RNA|CASS4_ENST00000434344.1_Silent_p.R298R	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	735					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						AGATCCTCCGTGGCAGCAGTC	0.627													C|||	2633	0.525759	0.4138	0.5245	5008	,	,		19307	0.9196		0.339	False		,,,				2504	0.4642				p.R735R		Atlas-SNP	.											.	CASS4	121	.	0			c.T2205C						PASS	.	C	,,,	1774,2632	643.3+/-397.8	369,1036,798	66.0	53.0	57.0		2043,894,2205,2205	-3.2	0.0	20	dbSNP_107	57	2929,5671	669.0+/-402.6	470,1989,1841	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	,,,	839,3025,2639	CC,CT,TT		34.0581,40.2633,36.1602	,,,	681/733,298/350,735/787,735/787	55033647	4703,8303	2203	4300	6503	SO:0001819	synonymous_variant	57091	exon6			CCTCCGTGGCAGC	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.2205T>C	20.37:g.55033647T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Silent	SNP	ENST00000360314.3	37	CCDS33492.1																																																																																			T|0.588;C|0.412	0.412	strong		0.627	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
TTN	7273	hgsc.bcm.edu	37	2	179427536	179427536	+	Missense_Mutation	SNP	T	T	C	rs3829746	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179427536T>C	ENST00000591111.1	-	276	78624	c.78400A>G	c.(78400-78402)Ata>Gta	p.I26134V	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I18710V|TTN_ENST00000342992.6_Missense_Mutation_p.I25207V|TTN_ENST00000589042.1_Missense_Mutation_p.I27775V|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I18835V|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I18902V|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26134	Fibronectin type-III 90. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> V. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTTCTCTTATGGTCAAATTC	0.408													C|||	2546	0.508387	0.5658	0.4078	5008	,	,		21726	0.7153		0.2535	False		,,,				2504	0.5511				p.I27775V		Atlas-SNP	.											.	TTN	18412	.	0			c.A83323G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	2013,1773		546,921,426	64.0	58.0	60.0		56704,56503,75619,56128	5.2	1.0	2	dbSNP_107	60	1841,6417		193,1455,2481	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	739,2376,2907	CC,CT,TT		22.2935,46.8304,31.9993	benign,benign,benign,benign	18902/27119,18835/27052,25207/33424,18710/26927	179427536	3854,8190	1893	4129	6022	SO:0001583	missense	7273	exon326			CTCTTATGGTCAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.78400A>G	2.37:g.179427536T>C	ENSP00000465570:p.Ile26134Val	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	160	80	0.5	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		980	0.44871794871794873	281	0.5711382113821138	129	0.356353591160221	385	0.6730769230769231	185	0.24406332453825857	C	9.433	1.086053	0.20390	0.531696	0.222935	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	6.04	5.15	0.70609	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.02275	-0.615	0.39703	P	0.028781999999999974	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.37314	-0.9711	8	0.87932	D	0	.	9.6301	0.39774	0.0:0.6833:0.0:0.3167	rs3829746;rs11565883;rs56750589;rs3829746	18710;18835;18902;26134	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	25207;18710;18902;18835;18708	ENSP00000343764:I25207V;ENSP00000434586:I18710V;ENSP00000340554:I18902V;ENSP00000352154:I18835V	ENSP00000340554:I18902V	I	-	1	0	TTN	179135782	0.155000	0.22806	0.994000	0.49952	0.900000	0.52787	0.683000	0.25349	0.883000	0.36040	-0.215000	0.12644	ATA	T|0.555;C|0.445	0.445	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KIF2B	84643	hgsc.bcm.edu	37	17	51900729	51900729	+	Missense_Mutation	SNP	C	C	T	rs3803824	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:51900729C>T	ENST00000268919.4	+	1	491	c.335C>T	c.(334-336)gCc>gTc	p.A112V		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	112			A -> V (in dbSNP:rs3803824). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CAGCGTACCGCCACGAAATGG	0.597													C|||	1053	0.210264	0.025	0.268	5008	,	,		15495	0.2034		0.3847	False		,,,				2504	0.2474				p.A112V		Atlas-SNP	.											KIF2B,NS,carcinoma,+1,3	KIF2B	254	3	0			c.C335T						PASS	.	C	VAL/ALA	377,4029	190.5+/-216.4	18,341,1844	77.0	83.0	81.0		335	4.0	0.0	17	dbSNP_107	81	3525,5075	513.5+/-378.2	730,2065,1505	yes	missense	KIF2B	NM_032559.4	64	748,2406,3349	TT,TC,CC		40.9884,8.5565,30.0015	benign	112/674	51900729	3902,9104	2203	4300	6503	SO:0001583	missense	84643	exon1			GTACCGCCACGAA	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.335C>T	17.37:g.51900729C>T	ENSP00000268919:p.Ala112Val	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	72	29	0.402778	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	520	0.23809523809523808	16	0.032520325203252036	104	0.287292817679558	96	0.16783216783216784	304	0.40105540897097625	C	1.990	-0.432000	0.04669	0.085565	0.409884	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.75154	-0.91	4.99	4.02	0.46733	.	0.344162	0.20835	N	0.084805	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.12630	0.006	B	0.14023	0.01	T	0.30851	-0.9964	9	0.18276	T	0.48	.	7.5842	0.27982	0.0:0.811:0.0:0.189	rs3803824;rs17654285;rs52812737;rs61204455;rs3803824	112	Q8N4N8	KIF2B_HUMAN	V	112;35	ENSP00000268919:A112V	ENSP00000268919:A112V	A	+	2	0	KIF2B	49255728	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.532000	0.23067	1.446000	0.47643	0.655000	0.94253	GCC	C|0.741;T|0.259	0.259	strong		0.597	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
BDP1	55814	hgsc.bcm.edu	37	5	70840233	70840233	+	Silent	SNP	C	C	T	rs182190	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:70840233C>T	ENST00000358731.4	+	31	6725	c.6462C>T	c.(6460-6462)ctC>ctT	p.L2154L	BDP1_ENST00000380675.2_Silent_p.L290L	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2154					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		ATAAAAACCTCGGACCAGTTA	0.348													C|||	1998	0.398962	0.3797	0.3055	5008	,	,		17770	0.3591		0.4583	False		,,,				2504	0.4714				p.L2154L		Atlas-SNP	.											.	BDP1	204	.	0			c.C6462T						PASS	.	C		1334,2334		248,838,748	102.0	95.0	97.0		6462	-1.6	0.0	5	dbSNP_79	97	3740,4442		880,1980,1231	no	coding-synonymous	BDP1	NM_018429.2		1128,2818,1979	TT,TC,CC		45.7101,36.3686,42.8186		2154/2625	70840233	5074,6776	1834	4091	5925	SO:0001819	synonymous_variant	55814	exon31			AAACCTCGGACCA	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.6462C>T	5.37:g.70840233C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	222	104	0.468468	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Silent	SNP	ENST00000358731.4	37	CCDS43328.1																																																																																			C|0.591;T|0.408	0.408	strong		0.348	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
EGF	1950	hgsc.bcm.edu	37	4	110901198	110901198	+	Missense_Mutation	SNP	G	G	A	rs2237051	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:110901198G>A	ENST00000265171.5	+	14	2569	c.2124G>A	c.(2122-2124)atG>atA	p.M708I	EGF_ENST00000509793.1_Missense_Mutation_p.M666I|EGF_ENST00000503392.1_Missense_Mutation_p.M708I	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	708			M -> I (in dbSNP:rs2237051). {ECO:0000269|Ref.2}.		activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	CATCAGTAATGAGAGTAAACA	0.443													A|||	3094	0.617812	0.8759	0.5764	5008	,	,		21586	0.6726		0.3628	False		,,,				2504	0.5041				p.M708I		Atlas-SNP	.											.	EGF	113	.	0			c.G2124A						PASS	.	A	ILE/MET,ILE/MET,ILE/MET	3553,853	335.5+/-303.9	1444,665,94	207.0	203.0	204.0		2124,1998,2124	1.5	0.9	4	dbSNP_98	204	3277,5323	647.3+/-400.4	639,1999,1662	yes	missense,missense,missense	EGF	NM_001178130.1,NM_001178131.1,NM_001963.4	10,10,10	2083,2664,1756	AA,AG,GG		38.1047,19.36,47.4858	benign,benign,benign	708/1167,666/1166,708/1208	110901198	6830,6176	2203	4300	6503	SO:0001583	missense	1950	exon14			AGTAATGAGAGTA	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"""epidermal growth factor (beta-urogastrone)"""				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.2124G>A	4.37:g.110901198G>A	ENSP00000265171:p.Met708Ile	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	224	106	0.473214	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	37	CCDS3689.1	1297	0.5938644688644689	416	0.8455284552845529	201	0.5552486187845304	394	0.6888111888111889	286	0.37730870712401055	A	0.766	-0.767643	0.02974	0.8064	0.381047	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.90676	-2.71;-2.71;-2.71	5.56	1.54	0.23209	Six-bladed beta-propeller, TolB-like (1);	0.333541	0.38897	N	0.001539	T	0.00012	0.0000	N	0.00504	-1.425	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42616	-0.9441	9	0.19147	T	0.46	.	1.6533	0.02776	0.4909:0.1309:0.2513:0.1269	rs2237051;rs17319162;rs52789322;rs58647950;rs2237051	708;666;708	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	I	666;708;708	ENSP00000424316:M666I;ENSP00000265171:M708I;ENSP00000421384:M708I	ENSP00000265171:M708I	M	+	3	0	EGF	111120647	0.008000	0.16893	0.927000	0.36925	0.771000	0.43674	-0.107000	0.10873	-0.200000	0.10300	-1.061000	0.02294	ATG	G|0.425;A|0.575	0.575	strong		0.443	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1		
HS6ST1	9394	hgsc.bcm.edu	37	2	129075939	129075939	+	Nonsense_Mutation	SNP	T	T	A	rs202247387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:129075939T>A	ENST00000259241.6	-	1	212	c.199A>T	c.(199-201)Aag>Tag	p.K67*	HS6ST1_ENST00000494089.1_5'UTR	NM_004807.2	NP_004798.3	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	67					angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|labyrinthine layer blood vessel development (GO:0060716)|lung alveolus development (GO:0048286)|neuron development (GO:0048666)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)|sulfotransferase activity (GO:0008146)	p.K67*(1)		endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		AAGTAGTACTTCTTCTCGTAG	0.692																																					p.K67X		Atlas-SNP	.											HS6ST1,NS,carcinoma,0,1	HS6ST1	31	1	1	Substitution - Nonsense(1)	prostate(1)	c.A199T						scavenged	.						19.0	29.0	26.0					2																	129075939		1938	4149	6087	SO:0001587	stop_gained	9394	exon1			AGTACTTCTTCTC	AB006179	CCDS42748.1	2q21	2010-03-19		2002-08-23	ENSG00000136720	ENSG00000136720		"""Sulfotransferases, membrane-bound"""	5201	protein-coding gene	gene with protein product		604846		HS6ST		9535912	Standard	NM_004807		Approved		uc002tpt.4	O60243	OTTHUMG00000153542	ENST00000259241.6:c.199A>T	2.37:g.129075939T>A	ENSP00000259241:p.Lys67*	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	101	11	0.108911	NM_004807	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	Nonsense_Mutation	SNP	ENST00000259241.6	37	CCDS42748.1	.	.	.	.	.	.	.	.	.	.	t	37	6.448341	0.97577	.	.	ENSG00000136720	ENST00000259241	.	.	.	3.16	3.16	0.36331	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3631	0.38208	0.0:0.0:0.0:1.0	.	.	.	.	X	67	.	.	K	-	1	0	HS6ST1	128792409	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	2.437000	0.44828	1.308000	0.44962	0.260000	0.18958	AAG	T|0.992;A|0.008	0.008	strong		0.692	HS6ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331572.1	NM_004807	
OR52E4	390081	hgsc.bcm.edu	37	11	5906203	5906203	+	Missense_Mutation	SNP	T	T	G	rs11823828	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5906203T>G	ENST00000316987.2	+	1	703	c.681T>G	c.(679-681)ttT>ttG	p.F227L		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	227			F -> L (in dbSNP:rs11823828).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGCTGTTTTTCGCCTTCCCT	0.383													T|||	1792	0.357827	0.3207	0.402	5008	,	,		21849	0.3641		0.4085	False		,,,				2504	0.318				p.F227L		Atlas-SNP	.											.	OR52E4	65	.	0			c.T681G						PASS	.	T	LEU/PHE	1495,2907	476.3+/-357.6	259,977,965	302.0	259.0	273.0		681	0.4	0.2	11	dbSNP_120	273	3625,4967	522.6+/-380.1	780,2065,1451	yes	missense	OR52E4	NM_001005165.1	22	1039,3042,2416	GG,GT,TT		42.1904,33.9618,39.4028	benign	227/313	5906203	5120,7874	2201	4296	6497	SO:0001583	missense	390081	exon1			TGTTTTTCGCCTT	AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"""GPCR / Class A : Olfactory receptors"""	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.681T>G	11.37:g.5906203T>G	ENSP00000321426:p.Phe227Leu	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	348	168	0.482759	NM_001005165	Q6IFG0	Missense_Mutation	SNP	ENST00000316987.2	37	CCDS31401.1	828	0.3791208791208791	154	0.3130081300813008	153	0.42265193370165743	204	0.35664335664335667	317	0.4182058047493404	T	11.25	1.582573	0.28180	0.339618	0.421904	ENSG00000180974	ENST00000316987	T	0.00013	9.26	5.15	0.395	0.16304	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000087	T	0.00012	0.0000	L	0.28054	0.825	0.80722	P	0.0	B	0.19331	0.035	B	0.29785	0.107	T	0.13710	-1.0499	9	0.38643	T	0.18	.	5.2374	0.15454	0.0:0.2102:0.4221:0.3677	rs11823828;rs59269559	227	Q8NGH9	O52E4_HUMAN	L	227	ENSP00000321426:F227L	ENSP00000321426:F227L	F	+	3	2	OR52E4	5862779	0.000000	0.05858	0.241000	0.24154	0.768000	0.43524	-0.301000	0.08232	0.202000	0.20498	0.523000	0.50628	TTT	T|0.612;G|0.388	0.388	strong		0.383	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165	
CFAP46	54777	hgsc.bcm.edu	37	10	134698678	134698678	+	Missense_Mutation	SNP	G	G	A	rs185087227		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:134698678G>A	ENST00000368586.5	-	27	3656	c.3556C>T	c.(3556-3558)Cgc>Tgc	p.R1186C	TTC40_ENST00000368582.2_Missense_Mutation_p.R1186C	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						AGGGCCAGGCGGTGCCACATG	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		15096	0.0		0.001	False		,,,				2504	0.0				p.R1186C		Atlas-SNP	.											.	TTC40	100	.	0			c.C3556T						PASS	.																																			SO:0001583	missense	54777	exon27			CCAGGCGGTGCCA																												ENST00000368586.5:c.3556C>T	10.37:g.134698678G>A	ENSP00000357575:p.Arg1186Cys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	15.93	2.977814	0.53720	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.50001	2.74;0.76	4.16	3.2	0.36748	.	.	.	.	.	T	0.55481	0.1923	.	.	.	0.32430	N	0.548168	.	.	.	.	.	.	T	0.67313	-0.5702	6	0.87932	D	0	.	12.0765	0.53647	0.0:0.0:0.8275:0.1725	.	.	.	.	C	1186	ENSP00000357575:R1186C;ENSP00000357571:R1186C	ENSP00000357571:R1186C	R	-	1	0	C10orf93	134548668	1.000000	0.71417	0.998000	0.56505	0.460000	0.32559	4.225000	0.58600	1.843000	0.53566	0.460000	0.39030	CGC	G|1.000;A|0.000	0.000	strong		0.582	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
NOXRED1	122945	hgsc.bcm.edu	37	14	77880305	77880305	+	Silent	SNP	C	C	T	rs10130481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77880305C>T	ENST00000380835.2	-	2	487	c.321G>A	c.(319-321)cgG>cgA	p.R107R	FKSG61_ENST00000595520.1_5'Flank|NOXRED1_ENST00000298358.3_Silent_p.R107R	NM_001113475.2	NP_001106946.1	Q6NXP6	NXRD1_HUMAN	NADP-dependent oxidoreductase domain containing 1	107					proline biosynthetic process (GO:0006561)		pyrroline-5-carboxylate reductase activity (GO:0004735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9						GAGTGGAGATCCGCAGGCTTT	0.567													C|||	755	0.150759	0.1029	0.2651	5008	,	,		16107	0.0159		0.1928	False		,,,				2504	0.2301				p.R107R		Atlas-SNP	.											NOXRED1,NS,carcinoma,-1,2	NOXRED1	23	2	0			c.G321A						PASS	.	C		578,3828	254.3+/-259.9	40,498,1665	41.0	39.0	39.0		321	0.6	1.0	14	dbSNP_119	39	1574,7026	289.8+/-299.5	155,1264,2881	no	coding-synonymous	NOXRED1	NM_001113475.2		195,1762,4546	TT,TC,CC		18.3023,13.1185,16.5462		107/360	77880305	2152,10854	2203	4300	6503	SO:0001819	synonymous_variant	122945	exon2			GGAGATCCGCAGG	AK057371	CCDS45142.1	14q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000165555	ENSG00000165555			20487	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 148"""	C14orf148			Standard	NM_001113475		Approved	FLJ32809	uc001xtr.3	Q6NXP6	OTTHUMG00000171554	ENST00000380835.2:c.321G>A	14.37:g.77880305C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_001113475	B3KQ47|O95435	Silent	SNP	ENST00000380835.2	37	CCDS45142.1																																																																																			C|0.851;T|0.149	0.149	strong		0.567	NOXRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414103.1	NM_138791	
AHNAK	79026	hgsc.bcm.edu	37	11	62285665	62285665	+	Silent	SNP	C	C	T	rs61625484	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62285665C>T	ENST00000378024.4	-	5	16498	c.16224G>A	c.(16222-16224)ctG>ctA	p.L5408L	AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5408					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CAAATTGGGGCAGCTTCATTT	0.532													C|||	220	0.0439297	0.1036	0.0303	5008	,	,		19832	0.0119		0.0258	False		,,,				2504	0.0245				p.L5408L		Atlas-SNP	.											.	AHNAK	532	.	0			c.G16224A						PASS	.	C	,	420,3984	206.5+/-228.1	18,384,1800	66.0	68.0	67.0		16224,	-0.9	1.0	11	dbSNP_129	67	221,8377	92.6+/-154.6	4,213,4082	yes	coding-synonymous,intron	AHNAK	NM_001620.1,NM_024060.2	,	22,597,5882	TT,TC,CC		2.5704,9.5368,4.93	,	5408/5891,	62285665	641,12361	2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			TTGGGGCAGCTTC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.16224G>A	11.37:g.62285665C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	141	63	0.446809	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																			A|0.000;C|0.950;G|0.000;T|0.050	0.050	strong		0.532	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
FBN3	84467	hgsc.bcm.edu	37	19	8176009	8176009	+	Silent	SNP	C	C	T	rs17160196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8176009C>T	ENST00000600128.1	-	33	4557	c.4143G>A	c.(4141-4143)gcG>gcA	p.A1381A	FBN3_ENST00000270509.2_Silent_p.A1381A|FBN3_ENST00000601739.1_Silent_p.A1381A			Q75N90	FBN3_HUMAN	fibrillin 3	1381	EGF-like 21; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						ACCCGCCGGGCGCATTGAGGC	0.657													C|||	497	0.0992412	0.0658	0.1182	5008	,	,		18434	0.128		0.1213	False		,,,				2504	0.0787				p.A1381A		Atlas-SNP	.											.	FBN3	300	.	0			c.G4143A						PASS	.	C		355,4051	181.2+/-209.3	15,325,1863	76.0	69.0	72.0		4143	-2.2	0.7	19	dbSNP_123	72	978,7622	212.1+/-252.5	47,884,3369	no	coding-synonymous	FBN3	NM_032447.3		62,1209,5232	TT,TC,CC		11.3721,8.0572,10.2491		1381/2810	8176009	1333,11673	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon32			GCCGGGCGCATTG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.4143G>A	19.37:g.8176009C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			C|0.891;T|0.109	0.109	strong		0.657	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
ANKRD53	79998	hgsc.bcm.edu	37	2	71212405	71212405	+	Missense_Mutation	SNP	T	T	C	rs61732279	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:71212405T>C	ENST00000360589.3	+	6	1602	c.1568T>C	c.(1567-1569)cTg>cCg	p.L523P	AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000441349.1_3'UTR|ANKRD53_ENST00000272421.6_3'UTR|ANKRD53_ENST00000457410.1_Missense_Mutation_p.L489P	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	523				L -> P (in Ref. 1; BAC04181). {ECO:0000305}.				p.L523P(1)		endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						CTCCCCACCCTGCCCTCCCCA	0.562											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	742	0.148163	0.1316	0.1282	5008	,	,		13076	0.1617		0.2276	False		,,,				2504	0.089				p.L523P		Atlas-SNP	.											ANKRD53_ENST00000360589,NS,carcinoma,0,2	ANKRD53	55	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T1568C						scavenged	.	T	PRO/LEU,	187,1197		12,163,517	15.0	15.0	15.0		1568,	0.8	0.0	2	dbSNP_129	15	637,2545		75,487,1029	yes	missense,utr-3	ANKRD53	NM_001115116.1,NM_024933.3	98,	87,650,1546	CC,CT,TT		20.0189,13.5116,18.0464	benign,	523/531,	71212405	824,3742	692	1591	2283	SO:0001583	missense	79998	exon6			CCACCCTGCCCTC	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"""Ankyrin repeat domain containing"""	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.1568T>C	2.37:g.71212405T>C	ENSP00000353796:p.Leu523Pro	Somatic	141	2	0.0141844	1128	WXS	Illumina HiSeq	Phase_I	219	87	0.39726	NM_001115116	Q8IYP8	Missense_Mutation	SNP	ENST00000360589.3	37	CCDS46321.1	375	0.1717032967032967	55	0.11178861788617886	49	0.13535911602209943	101	0.17657342657342656	170	0.22427440633245382	T	13.31	2.199486	0.38806	0.135116	0.200189	ENSG00000144031	ENST00000457410;ENST00000360589	T;T	0.75704	-0.83;-0.96	4.63	0.842	0.18927	.	0.443867	0.16837	N	0.197499	T	0.00039	0.0001	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	B	0.25007	0.116	B	0.23852	0.049	T	0.04216	-1.0968	9	0.46703	T	0.11	-8.7589	1.2754	0.02030	0.1821:0.102:0.1894:0.5266	rs61732279	523	Q8N9V6	ANR53_HUMAN	P	489;523	ENSP00000407004:L489P;ENSP00000353796:L523P	ENSP00000353796:L523P	L	+	2	0	ANKRD53	71065913	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.054000	0.11826	0.139000	0.18822	0.533000	0.62120	CTG	T|0.841;C|0.159	0.159	strong		0.562	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933	
KLHDC8A	55220	hgsc.bcm.edu	37	1	205308347	205308347	+	Silent	SNP	C	C	A	rs1105386	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:205308347C>A	ENST00000367156.3	-	7	1548	c.732G>T	c.(730-732)acG>acT	p.T244T	KLHDC8A_ENST00000539253.1_Silent_p.T244T|KLHDC8A_ENST00000367155.3_Silent_p.T244T|KLHDC8A_ENST00000537168.1_Silent_p.T131T|KLHDC8A_ENST00000460687.1_Silent_p.T110T	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	244										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			ACACGTCCATCGTCCGCAGGA	0.622													C|||	137	0.0273562	0.0219	0.0259	5008	,	,		18386	0.005		0.0199	False		,,,				2504	0.0665				p.T244T		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.G732T						PASS	.	C		81,4325	70.9+/-108.8	0,81,2122	51.0	44.0	46.0		732	-10.9	0.6	1	dbSNP_86	46	148,8452	72.6+/-135.2	2,144,4154	no	coding-synonymous	KLHDC8A	NM_018203.1		2,225,6276	AA,AC,CC		1.7209,1.8384,1.7607		244/351	205308347	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	55220	exon4			GTCCATCGTCCGC		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.732G>T	1.37:g.205308347C>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_018203	B3KU70|Q9NVG5	Silent	SNP	ENST00000367156.3	37	CCDS30985.1																																																																																			C|0.980;A|0.020	0.020	strong		0.622	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203	
ITPKB	3707	hgsc.bcm.edu	37	1	226923264	226923264	+	Silent	SNP	G	G	A	rs708775	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:226923264G>A	ENST00000272117.3	-	1	1895	c.1896C>T	c.(1894-1896)gcC>gcT	p.A632A	ITPKB_ENST00000429204.1_Silent_p.A632A|ITPKB_ENST00000366784.1_Silent_p.A632A			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	632					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)	p.A632A(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				TATGCAGGAAGGCTGAGTTGG	0.547													G|||	1410	0.28155	0.2428	0.317	5008	,	,		20089	0.2639		0.3141	False		,,,				2504	0.2935				p.A632A	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	1	Substitution - coding silent(1)	stomach(1)	c.C1896T						PASS	.	G		1123,3283	401.5+/-332.0	133,857,1213	130.0	123.0	125.0		1896	2.8	1.0	1	dbSNP_86	125	2530,6070	413.4+/-351.1	390,1750,2160	yes	coding-synonymous	ITPKB	NM_002221.3		523,2607,3373	AA,AG,GG		29.4186,25.488,28.087		632/947	226923264	3653,9353	2203	4300	6503	SO:0001819	synonymous_variant	3707	exon2			CAGGAAGGCTGAG	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1896C>T	1.37:g.226923264G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	201	95	0.472637	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	37	CCDS1555.1																																																																																			G|0.716;A|0.284	0.284	strong		0.547	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
CCPG1	9236	hgsc.bcm.edu	37	15	55652969	55652969	+	Missense_Mutation	SNP	C	C	G	rs200417770		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55652969C>G	ENST00000310958.6	-	8	1300	c.1002G>C	c.(1000-1002)caG>caC	p.Q334H	CCPG1_ENST00000442196.3_Missense_Mutation_p.Q334H|CCPG1_ENST00000569205.1_Missense_Mutation_p.Q334H|CCPG1_ENST00000425574.3_Intron|DYX1C1-CCPG1_ENST00000565113.1_RNA	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	334					cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		ATATTCTAATCTGTTCTCTTA	0.343																																					p.Q334H		Atlas-SNP	.											CCPG1,NS,carcinoma,0,1	CCPG1	74	1	0			c.G1002C						scavenged	.						124.0	115.0	118.0					15																	55652969		1815	4071	5886	SO:0001583	missense	9236	exon8			TCTAATCTGTTCT	AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.1002G>C	15.37:g.55652969C>G	ENSP00000311656:p.Gln334His	Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	161	57	0.354037	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Missense_Mutation	SNP	ENST00000310958.6	37	CCDS42039.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.799689	0.50208	.	.	ENSG00000256061	ENST00000310958;ENST00000442196	T;T	0.36157	1.27;1.27	5.72	2.86	0.33363	.	0.153716	0.64402	D	0.000014	T	0.53546	0.1803	M	0.66939	2.045	0.47214	D	0.999356	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.75484	0.986;0.976;0.986;0.979	T	0.52109	-0.8619	10	0.72032	D	0.01	.	9.2561	0.37584	0.0:0.6926:0.0:0.3074	.	334;334;334;190	A8K9T0;Q9ULG6-4;Q9ULG6;Q9ULG6-2	.;.;CCPG1_HUMAN;.	H	334	ENSP00000311656:Q334H;ENSP00000403400:Q334H	ENSP00000311656:Q334H	Q	-	3	2	DYX1C1	53440261	1.000000	0.71417	0.997000	0.53966	0.943000	0.58893	0.759000	0.26461	0.450000	0.26774	-0.145000	0.13849	CAG	C|0.999;G|0.001	0.001	weak		0.343	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748	
MADD	8567	hgsc.bcm.edu	37	11	47303275	47303275	+	Silent	SNP	T	T	C	rs326217	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:47303275T>C	ENST00000311027.5	+	8	1605	c.1440T>C	c.(1438-1440)aaT>aaC	p.N480N	MADD_ENST00000395336.3_Silent_p.N480N|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000395344.3_Silent_p.N480N|MADD_ENST00000342922.4_Silent_p.N480N|MADD_ENST00000406482.1_Silent_p.N480N|MADD_ENST00000402192.2_Silent_p.N480N|MADD_ENST00000402799.1_Silent_p.N480N|MADD_ENST00000349238.3_Silent_p.N480N|MADD_ENST00000407859.3_Silent_p.N480N	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		TCTATGGCAATGATGTGGATT	0.468													T|||	1483	0.296126	0.2481	0.4352	5008	,	,		18300	0.252		0.3042	False		,,,				2504	0.2996				p.N480N		Atlas-SNP	.											.	MADD	172	.	0			c.T1440C						PASS	.	T	,,,,,,,,,	1066,3336	389.1+/-327.2	115,836,1250	80.0	75.0	77.0		1440,1440,1440,1440,1440,1440,1440,1440,1440,1440	-4.1	0.7	11	dbSNP_79	77	2635,5961	426.0+/-355.2	391,1853,2054	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MADD	NM_001135943.1,NM_001135944.1,NM_003682.3,NM_130470.2,NM_130471.2,NM_130472.2,NM_130473.2,NM_130474.2,NM_130475.2,NM_130476.2	,,,,,,,,,	506,2689,3304	CC,CT,TT		30.6538,24.2163,28.4736	,,,,,,,,,	480/1545,480/1542,480/1648,480/1589,480/1566,480/1546,480/1609,480/1480,480/1582,480/1588	47303275	3701,9297	2201	4298	6499	SO:0001819	synonymous_variant	8567	exon8			TGGCAATGATGTG	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1440T>C	11.37:g.47303275T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	NM_130474		Silent	SNP	ENST00000311027.5	37	CCDS7930.1																																																																																			T|0.698;C|0.302	0.302	strong		0.468	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
LLGL2	3993	hgsc.bcm.edu	37	17	73565171	73565171	+	Missense_Mutation	SNP	T	T	C	rs1671021	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73565171T>C	ENST00000392550.3	+	13	1552	c.1435T>C	c.(1435-1437)Ttc>Ctc	p.F479L	LLGL2_ENST00000167462.5_Missense_Mutation_p.F479L|LLGL2_ENST00000577200.1_Missense_Mutation_p.F479L	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	479			F -> L (in dbSNP:rs1671021). {ECO:0000269|PubMed:15489334}.		cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CAACGAGAACTTCAGTGCCCA	0.667													C|||	2328	0.464856	0.907	0.3372	5008	,	,		17795	0.2639		0.3738	False		,,,				2504	0.2587				p.F479L		Atlas-SNP	.											.	LLGL2	155	.	0			c.T1435C						PASS	.	C	LEU/PHE,LEU/PHE	3630,776	303.5+/-288.0	1501,628,74	45.0	44.0	45.0		1435,1435	4.3	0.9	17	dbSNP_89	45	3320,5280	632.4+/-398.6	673,1974,1653	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	22,22	2174,2602,1727	CC,CT,TT		38.6047,17.6123,46.5631	benign,benign	479/1021,479/1016	73565171	6950,6056	2203	4300	6503	SO:0001583	missense	3993	exon13			GAGAACTTCAGTG	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1435T>C	17.37:g.73565171T>C	ENSP00000376333:p.Phe479Leu	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	142	65	0.457746	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	982	0.44963369963369965	442	0.8983739837398373	128	0.35359116022099446	125	0.21853146853146854	287	0.3786279683377309	C	10.65	1.409361	0.25378	0.823877	0.386047	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.09538	2.97;2.97	5.29	4.33	0.51752	WD40 repeat-like-containing domain (1);	0.192645	0.49916	N	0.000140	T	0.00012	0.0000	N	0.01267	-0.92	0.46542	P	9.050000000000447E-4	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.23476	-1.0187	9	0.18710	T	0.47	-3.4459	2.7305	0.05226	0.1772:0.5462:0.1184:0.1582	rs1671021;rs17492156;rs17855940;rs61228063;rs1671021	468;468;479;479	B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;L2GL2_HUMAN	L	479;479;468	ENSP00000167462:F479L;ENSP00000376333:F479L	ENSP00000167462:F479L	F	+	1	0	LLGL2	71076766	1.000000	0.71417	0.896000	0.35187	0.404000	0.30871	2.038000	0.41184	0.637000	0.30526	-0.222000	0.12452	TTC	T|0.486;C|0.514	0.514	strong		0.667	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
MFSD6	54842	hgsc.bcm.edu	37	2	191302144	191302144	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:191302144C>T	ENST00000392328.1	+	3	1713	c.1389C>T	c.(1387-1389)ttC>ttT	p.F463F	MFSD6_ENST00000281416.7_Silent_p.F463F	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	463					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						GATATGGCTTCGTGTTCACCT	0.493																																					p.F463F		Atlas-SNP	.											MFSD6,rectum,carcinoma,0,1	MFSD6	58	1	0			c.C1389T						scavenged	.						310.0	251.0	271.0					2																	191302144		2203	4300	6503	SO:0001819	synonymous_variant	54842	exon3			TGGCTTCGTGTTC		CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.1389C>T	2.37:g.191302144C>T		Somatic	372	13	0.0349462		WXS	Illumina HiSeq	Phase_I	408	38	0.0931373	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Silent	SNP	ENST00000392328.1	37	CCDS2306.1																																																																																			.	.	none		0.493	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1		
IFIT1B	439996	hgsc.bcm.edu	37	10	91143529	91143529	+	Silent	SNP	T	T	A	rs304494	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:91143529T>A	ENST00000371809.3	+	2	539	c.459T>A	c.(457-459)ggT>ggA	p.G153G	LIPA_ENST00000371837.1_Intron	NM_001010987.2	NP_001010987.1	Q5T764	IFT1B_HUMAN	interferon-induced protein with tetratricopeptide repeats 1B	153										endometrium(2)|large_intestine(3)|lung(8)	13						CGAAGTGTGGTGGAAAGAATT	0.493													A|||	3564	0.711661	0.9493	0.5144	5008	,	,		20237	0.873		0.5258	False		,,,				2504	0.5552				p.G153G		Atlas-SNP	.											IFIT1B,right_upper_lobe,carcinoma,+2,1	IFIT1B	39	1	0			c.T459A						PASS	.	A		3846,560	251.8+/-258.4	1680,486,37	85.0	85.0	85.0		459	1.9	0.4	10	dbSNP_79	85	4210,4390	584.5+/-391.7	1031,2148,1121	no	coding-synonymous	IFIT1B	NM_001010987.2		2711,2634,1158	AA,AT,TT		48.9535,12.7099,38.0594		153/475	91143529	8056,4950	2203	4300	6503	SO:0001819	synonymous_variant	439996	exon2			GTGTGGTGGAAAG		CCDS31242.1	10q23.31	2014-05-22	2010-03-22	2010-03-22	ENSG00000204010	ENSG00000204010		"""Tetratricopeptide (TTC) repeat domain containing"""	23442	protein-coding gene	gene with protein product			"""interferon-induced protein with tetratricopeptide repeats 1-like"""	IFIT1L			Standard	NM_001010987		Approved	bA149I23.6	uc001kgh.3	Q5T764	OTTHUMG00000018709	ENST00000371809.3:c.459T>A	10.37:g.91143529T>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	61	55	0.901639	NM_001010987	A7E245	Silent	SNP	ENST00000371809.3	37	CCDS31242.1																																																																																			.	.	weak		0.493	IFIT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049296.3	NM_001010987	
SYK	6850	hgsc.bcm.edu	37	9	93637015	93637015	+	Silent	SNP	C	C	T	rs2290890	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:93637015C>T	ENST00000375754.4	+	9	1213	c.1065C>T	c.(1063-1065)ccC>ccT	p.P355P	SYK_ENST00000375747.1_Silent_p.P332P|SYK_ENST00000375751.4_Silent_p.P332P|SYK_ENST00000375746.1_Silent_p.P355P	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	355	Interdomain B.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						ACGCGGACCCCGAGGAGATCA	0.562			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								C|||	981	0.195887	0.2088	0.366	5008	,	,		17794	0.2321		0.1362	False		,,,				2504	0.0818				p.P355P		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.C1065T						PASS	.	C	,,,	918,3488	352.6+/-311.8	90,738,1375	145.0	159.0	154.0		996,1065,996,1065	-8.3	0.4	9	dbSNP_100	154	1216,7384	245.4+/-274.3	88,1040,3172	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	178,1778,4547	TT,TC,CC		14.1395,20.8352,16.4078	,,,	332/613,355/636,332/613,355/636	93637015	2134,10872	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon9			GGACCCCGAGGAG	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1065C>T	9.37:g.93637015C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	94	53	0.56383	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			C|0.825;T|0.175	0.175	strong		0.562	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
SH2D4B	387694	hgsc.bcm.edu	37	10	82348395	82348395	+	Missense_Mutation	SNP	G	G	A	rs140909202		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:82348395G>A	ENST00000470604.2	+	4	502	c.502G>A	c.(502-504)Gaa>Aaa	p.E168K	SH2D4B_ENST00000339284.2_Missense_Mutation_p.E169K|SH2D4B_ENST00000313455.4_Missense_Mutation_p.E120K			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	168	Glu-rich.									endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			GAGGAAAGAGGAAGAGGAGAG	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		20999	0.0		0.001	False		,,,				2504	0.0				p.E169K		Atlas-SNP	.											.	SH2D4B	44	.	0			c.G505A						PASS	.	G	LYS/GLU,LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	78.0	73.0	75.0		358,505	4.2	1.0	10	dbSNP_134	75	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	SH2D4B	NM_001145719.1,NM_207372.2	56,56	0,7,6496	AA,AG,GG		0.0465,0.0681,0.0538	probably-damaging,probably-damaging	120/310,169/358	82348395	7,12999	2203	4300	6503	SO:0001583	missense	387694	exon4			AAAGAGGAAGAGG		CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"""SH2 domain containing"""	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.502G>A	10.37:g.82348395G>A	ENSP00000417953:p.Glu168Lys	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	32	12	0.375	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Missense_Mutation	SNP	ENST00000470604.2	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.52	3.409626	0.62399	6.81E-4	4.65E-4	ENSG00000178217	ENST00000339284;ENST00000372147;ENST00000470604;ENST00000313455	T;T;T	0.13657	2.57;2.57;2.57	5.16	4.24	0.50183	.	0.062098	0.64402	D	0.000007	T	0.32194	0.0821	L	0.58669	1.825	0.45930	D	0.998765	D;D	0.89917	0.998;1.0	D;D	0.85130	0.919;0.997	T	0.01829	-1.1265	10	0.45353	T	0.12	-11.6747	13.3192	0.60424	0.0:0.1602:0.8398:0.0	.	120;169	Q5SQS7-3;Q5SQS7-2	.;.	K	169;168;168;120	ENSP00000345295:E169K;ENSP00000417953:E168K;ENSP00000314242:E120K	ENSP00000314242:E120K	E	+	1	0	SH2D4B	82338375	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	4.750000	0.62162	1.143000	0.42306	0.655000	0.94253	GAA	G|0.999;A|0.001	0.001	strong		0.507	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984	
OR2AK2	391191	hgsc.bcm.edu	37	1	248128929	248128929	+	Missense_Mutation	SNP	G	G	A	rs6664332	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248128929G>A	ENST00000366480.3	+	1	395	c.296G>A	c.(295-297)aGc>aAc	p.S99N	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, member 2	99			S -> N (in dbSNP:rs6664332).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			ATGGCAGTCAGCTTCCTCTCA	0.483													.|||	1861	0.371605	0.2882	0.3646	5008	,	,		20363	0.4633		0.328	False		,,,				2504	0.4397				p.S99N	Melanoma(45;390 1181 23848 28461 41504)	Atlas-SNP	.											.	OR2AK2	90	.	0			c.G296A						PASS	.	A	ASN/SER,	1281,3125		189,903,1111	232.0	204.0	214.0		296,	1.9	0.0	1	dbSNP_116	214	2872,5728		471,1930,1899	yes	missense,intron	OR2L13,OR2AK2	NM_001004491.1,NM_175911.2	46,	660,2833,3010	AA,AG,GG		33.3953,29.074,31.9314	benign,	99/336,	248128929	4153,8853	2203	4300	6503	SO:0001583	missense	391191	exon1			CAGTCAGCTTCCT	BK004457	CCDS31102.1	1q44	2012-08-09			ENSG00000187080	ENSG00000187080		"""GPCR / Class A : Olfactory receptors"""	19569	protein-coding gene	gene with protein product				OR2AK1P			Standard	NM_001004491		Approved		uc010pzd.2	Q8NG84	OTTHUMG00000040201	ENST00000366480.3:c.296G>A	1.37:g.248128929G>A	ENSP00000355436:p.Ser99Asn	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	182	99	0.543956	NM_001004491	B2RND1|Q6IF05	Missense_Mutation	SNP	ENST00000366480.3	37	CCDS31102.1	776	0.3553113553113553	131	0.266260162601626	140	0.3867403314917127	252	0.4405594405594406	253	0.3337730870712401	.	0.010	-1.794300	0.00617	0.29074	0.333953	ENSG00000187080	ENST00000366480	T	0.01126	5.3	3.15	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00337	-1.62	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17349	-1.0372	8	0.07813	T	0.8	.	2.7483	0.05273	0.4798:0.0:0.1224:0.3979	rs6664332;rs58317680;rs6664332	99	Q8NG84	O2AK2_HUMAN	N	99	ENSP00000355436:S99N	ENSP00000355436:S99N	S	+	2	0	OR2AK2	246195552	0.000000	0.05858	0.002000	0.10522	0.030000	0.12068	0.001000	0.13038	-0.026000	0.13895	-0.556000	0.04195	AGC	G|0.663;A|0.337	0.337	strong		0.483	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	NM_001004491	
FCN2	2220	hgsc.bcm.edu	37	9	137775155	137775155	+	Silent	SNP	T	T	C	rs4520243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:137775155T>C	ENST00000291744.6	+	3	232	c.222T>C	c.(220-222)cgT>cgC	p.R74R	FCN2_ENST00000350339.2_Silent_p.R36R	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	74	Collagen-like.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		CAGGAGAACGTGGCCCCCCTG	0.597													C|||	1880	0.375399	0.3222	0.2997	5008	,	,		16091	0.4097		0.3718	False		,,,				2504	0.4693				p.R74R		Atlas-SNP	.											.	FCN2	55	.	0			c.T222C						PASS	.	C	,	1509,2897	675.0+/-403.0	253,1003,947	85.0	82.0	83.0		222,108	-3.0	0.0	9	dbSNP_111	83	2986,5614	665.3+/-402.3	547,1892,1861	no	coding-synonymous,coding-synonymous	FCN2	NM_004108.2,NM_015837.2	,	800,2895,2808	CC,CT,TT		34.7209,34.2488,34.561	,	74/314,36/276	137775155	4495,8511	2203	4300	6503	SO:0001819	synonymous_variant	2220	exon3			AGAACGTGGCCCC	D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"""Fibrinogen C domain containing"""	3624	protein-coding gene	gene with protein product	"""hucolin"", ""collagen/fibrinogen domain-containing protein 2"", ""ficolin B"", ""serum lectin p35"", ""L-ficolin"""	601624	"""ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"""			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.222T>C	9.37:g.137775155T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Silent	SNP	ENST00000291744.6	37	CCDS6983.1																																																																																			T|0.642;C|0.358	0.358	strong		0.597	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	
AMY2B	280	hgsc.bcm.edu	37	1	104117892	104117892	+	Missense_Mutation	SNP	T	T	C	rs140209167	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:104117892T>C	ENST00000361355.4	+	8	1542	c.926T>C	c.(925-927)gTc>gCc	p.V309A	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	309					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|kidney(4)|large_intestine(1)|lung(30)|prostate(1)|skin(1)|urinary_tract(1)	46		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		AGAGCACTTGTCTTTGTGGAT	0.408													.|||	6	0.00119808	0.0	0.0014	5008	,	,		14681	0.0		0.005	False		,,,				2504	0.0				p.V309A		Atlas-SNP	.											.	AMY2B	80	.	0			c.T926C						PASS	.	T	ALA/VAL	2,4404	4.2+/-10.8	0,2,2201	275.0	274.0	275.0		926	4.1	1.0	1	dbSNP_134	275	30,8566	21.0+/-64.5	0,30,4268	no	missense	AMY2B	NM_020978.3	64	0,32,6469	CC,CT,TT		0.349,0.0454,0.2461	probably-damaging	309/512	104117892	32,12970	2203	4298	6501	SO:0001583	missense	280	exon8			CACTTGTCTTTGT	M24895	CCDS782.1	1p21	2010-08-02	2006-04-27		ENSG00000240038	ENSG00000240038	3.2.1.1		478	protein-coding gene	gene with protein product		104660	"""amylase, alpha 2B; pancreatic"""	AMY2		8268204	Standard	NM_020978		Approved		uc001duq.3	P19961	OTTHUMG00000011024	ENST00000361355.4:c.926T>C	1.37:g.104117892T>C	ENSP00000354610:p.Val309Ala	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	261	137	0.524904	NM_020978	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	37	CCDS782.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	T	22.1	4.248687	0.80024	4.54E-4	0.00349	ENSG00000240038	ENST00000361355	D	0.98400	-4.91	5.26	4.12	0.48240	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98372	0.9459	M	0.82323	2.585	0.80722	D	1	P	0.40681	0.727	P	0.57204	0.815	D	0.99818	1.1045	10	0.66056	D	0.02	.	11.3322	0.49484	0.0:0.0734:0.0:0.9266	.	309	P19961	AMY2B_HUMAN	A	309	ENSP00000354610:V309A	ENSP00000354610:V309A	V	+	2	0	AMY2B	103919415	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.096000	0.64535	1.992000	0.58205	0.456000	0.33151	GTC	T|0.998;C|0.002	0.002	strong		0.408	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1	NM_020978	
MAPT	4137	hgsc.bcm.edu	37	17	44061036	44061036	+	Missense_Mutation	SNP	T	T	C	rs62063787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44061036T>C	ENST00000571987.1	+	5	866	c.866T>C	c.(865-867)gTa>gCa	p.V289A	MAPT_ENST00000576518.1_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.V289A|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.V289A|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.V289A|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	289			V -> A (risk factor for PSNP1; dbSNP:rs62063787). {ECO:0000269|PubMed:10534245, ECO:0000269|PubMed:9629852}.		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GGGCCCAGTGTAGGGCGGGCC	0.617													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		16077	0.001		0.2406	False		,,,				2504	0.0613				p.V289A		Atlas-SNP	.											.	MAPT	135	.	0			c.T866C						PASS	.	C	ALA/VAL,,,,,,ALA/VAL,	227,4179	791.3+/-415.1	7,213,1983	41.0	46.0	44.0		866,,,,,,866,	-1.4	0.0	17	dbSNP_129	44	1928,6672	716.3+/-406.1	221,1486,2593	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	64,,,,,,64,	228,1699,4576	CC,CT,TT		22.4186,5.1521,16.5693	benign,,,,,,benign,	289/777,,,,,,289/759,	44061036	2155,10851	2203	4300	6503	SO:0001583	missense	4137	exon6			CCAGTGTAGGGCG	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.866T>C	17.37:g.44061036T>C	ENSP00000458742:p.Val289Ala	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	0.533	-0.857132	0.02630	0.051521	0.224186	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.09723	2.95;2.95;2.95	4.68	-1.36	0.09085	.	1.284980	0.05582	N	0.573067	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43589	-0.9382	9	0.05620	T	0.96	1.7099	0.2163	0.00162	0.3062:0.2538:0.1395:0.3005	rs62063787	289;289	P10636-9;P10636	.;TAU_HUMAN	A	289	ENSP00000340820:V289A;ENSP00000262410:V289A;ENSP00000410838:V289A	ENSP00000262410:V289A	V	+	2	0	MAPT	41416873	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.211000	0.17474	-0.068000	0.12953	-1.163000	0.01768	GTA	T|0.849;C|0.151	0.151	strong		0.617	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
OR1S1	219959	hgsc.bcm.edu	37	11	57982726	57982726	+	Silent	SNP	G	G	T	rs1993089	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57982726G>T	ENST00000309433.6	+	1	510	c.510G>T	c.(508-510)ctG>ctT	p.L170L		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	170						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L170L(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTATTGCTCTGACACACACCC	0.478													G|||	2620	0.523163	0.2844	0.5418	5008	,	,		18215	0.8036		0.4225	False		,,,				2504	0.6472				p.L170L		Atlas-SNP	.											OR1S1,NS,carcinoma,0,1	OR1S1	139	1	1	Substitution - coding silent(1)	stomach(1)	c.G510T						PASS	.	G		1158,3244		197,764,1240	214.0	189.0	197.0		510	1.2	1.0	11	dbSNP_92	197	3386,5206		781,1824,1691	no	coding-synonymous	OR1S1	NM_001004458.1		978,2588,2931	TT,TG,GG		39.4088,26.3062,34.97		170/326	57982726	4544,8450	2201	4296	6497	SO:0001819	synonymous_variant	219959	exon1			TGCTCTGACACAC	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.510G>T	11.37:g.57982726G>T		Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	260	82	0.315385	NM_001004458	Q6IFG3	Silent	SNP	ENST00000309433.6	37	CCDS31546.1																																																																																			G|0.609;T|0.391	0.391	strong		0.478	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
ZSWIM6	57688	hgsc.bcm.edu	37	5	60628411	60628411	+	Silent	SNP	G	G	T	rs75429795	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:60628411G>T	ENST00000252744.5	+	1	312	c.312G>T	c.(310-312)ccG>ccT	p.P104P		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	104	Gly-rich.				neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						TCCCGGAGCCGGTGCAGCGCC	0.711													G|||	510	0.101837	0.0802	0.1037	5008	,	,		2584	0.0724		0.1431	False		,,,				2504	0.1176				p.P104P		Atlas-SNP	.											.	ZSWIM6	51	.	0			c.G312T						PASS	.						6.0	11.0	9.0					5																	60628411		679	1570	2249	SO:0001819	synonymous_variant	57688	exon1			GGAGCCGGTGCAG	BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449		"""Zinc fingers, SWIM-type"""	29316	protein-coding gene	gene with protein product		615951				10997877, 16427614	Standard	NM_020928		Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.312G>T	5.37:g.60628411G>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_020928		Silent	SNP	ENST00000252744.5	37	CCDS47215.1																																																																																			G|0.881;T|0.119	0.119	strong		0.711	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368710.1	NM_020928	
DNAH3	55567	hgsc.bcm.edu	37	16	20976360	20976360	+	Missense_Mutation	SNP	T	T	G	rs33928718	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20976360T>G	ENST00000261383.3	-	53	8845	c.8846A>C	c.(8845-8847)aAg>aCg	p.K2949T	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2949	Stalk. {ECO:0000250}.		K -> T (in dbSNP:rs33928718).		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GTCCTTTTTCTTGGTGTTCAT	0.502													T|||	426	0.0850639	0.0204	0.0663	5008	,	,		20691	0.1716		0.0726	False		,,,				2504	0.1094				p.K2949T		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A8846C						PASS	.	T	THR/LYS	113,4289	86.3+/-125.0	3,107,2091	177.0	170.0	172.0		8846	3.7	0.8	16	dbSNP_126	172	669,7931	169.4+/-220.8	23,623,3654	yes	missense	DNAH3	NM_017539.1	78	26,730,5745	GG,GT,TT		7.7791,2.567,6.0145	probably-damaging	2949/4117	20976360	782,12220	2201	4300	6501	SO:0001583	missense	55567	exon53			TTTTTCTTGGTGT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.8846A>C	16.37:g.20976360T>G	ENSP00000261383:p.Lys2949Thr	Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	184	184	1	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	179	0.08195970695970696	16	0.032520325203252036	17	0.04696132596685083	83	0.1451048951048951	63	0.08311345646437995	T	10.18	1.280449	0.23392	0.02567	0.077791	ENSG00000158486	ENST00000261383	T	0.74421	-0.84	5.93	3.71	0.42584	Dynein heavy chain, coiled coil stalk (1);	0.190997	0.43919	D	0.000509	T	0.02230	0.0069	M	0.84156	2.68	0.09310	P	0.9999999999995628	D	0.71674	0.998	D	0.72982	0.979	T	0.54275	-0.8318	9	0.52906	T	0.07	.	9.0659	0.36462	0.0:0.2405:0.0:0.7595	rs33928718	2949	Q8TD57	DYH3_HUMAN	T	2949	ENSP00000261383:K2949T	ENSP00000261383:K2949T	K	-	2	0	DNAH3	20883861	1.000000	0.71417	0.804000	0.32291	0.006000	0.05464	3.268000	0.51585	1.077000	0.40990	0.533000	0.62120	AAG	T|0.933;G|0.067	0.067	strong		0.502	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
BPIFB4	149954	hgsc.bcm.edu	37	20	31673846	31673846	+	Missense_Mutation	SNP	A	A	G	rs2070325	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:31673846A>G	ENST00000375483.3	+	5	802	c.802A>G	c.(802-804)Atc>Gtc	p.I268V		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	268			I -> V (in dbSNP:rs2070325).			cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										CTTCCTGGACATCGCAGTAGA	0.612													A|||	2331	0.465455	0.2693	0.4611	5008	,	,		20190	0.7569		0.3797	False		,,,				2504	0.5215				p.I268V		Atlas-SNP	.											.	.	.	.	0			c.A802G						PASS	.	A	VAL/ILE	1173,3233	414.1+/-336.7	172,829,1202	138.0	121.0	127.0		802	3.9	1.0	20	dbSNP_96	127	3112,5488	475.3+/-369.1	575,1962,1763	yes	missense	BPIFB4	NM_182519.2	29	747,2791,2965	GG,GA,AA		36.186,26.6228,32.9463	possibly-damaging	268/615	31673846	4285,8721	2203	4300	6503	SO:0001583	missense	149954	exon5			CTGGACATCGCAG	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.802A>G	20.37:g.31673846A>G	ENSP00000364632:p.Ile268Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	1025	0.4693223443223443	141	0.2865853658536585	155	0.4281767955801105	435	0.7604895104895105	294	0.38786279683377306	A	15.21	2.766176	0.49574	0.266228	0.36186	ENSG00000186191	ENST00000375483	T	0.06528	3.29	3.94	3.94	0.45596	.	0.165701	0.40818	N	0.001009	T	0.00012	0.0000	L	0.46157	1.445	0.32473	P	0.542564	P	0.39535	0.677	B	0.43445	0.42	T	0.00414	-1.1754	9	0.41790	T	0.15	-16.0856	9.1151	0.36753	1.0:0.0:0.0:0.0	rs2070325;rs61233760;rs2070325	268	P59827	BPIB4_HUMAN	V	268	ENSP00000364632:I268V	ENSP00000364632:I268V	I	+	1	0	BPIFB4	31137507	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.418000	0.52721	1.649000	0.50652	0.402000	0.26972	ATC	A|0.615;G|0.385	0.385	strong		0.612	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
SH2B1	25970	hgsc.bcm.edu	37	16	28883241	28883241	+	Missense_Mutation	SNP	A	A	G	rs7498665	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28883241A>G	ENST00000322610.8	+	8	1889	c.1450A>G	c.(1450-1452)Aca>Gca	p.T484A	SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000545570.1_Missense_Mutation_p.T174A|SH2B1_ENST00000337120.5_Missense_Mutation_p.T484A|SH2B1_ENST00000359285.5_Missense_Mutation_p.T484A|SH2B1_ENST00000395532.4_Missense_Mutation_p.T484A|SH2B1_ENST00000538342.1_Missense_Mutation_p.T148A			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	484	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation). {ECO:0000250}.		T -> A (in dbSNP:rs7498665). {ECO:0000269|PubMed:15767667, ECO:0000269|PubMed:17974005}.		blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.T484A(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						GGGACCCCCAACAGGGACAGT	0.622													G|||	1309	0.261382	0.2277	0.4856	5008	,	,		14129	0.126		0.329	False		,,,				2504	0.2178				p.T484A		Atlas-SNP	.											SH2B1,NS,carcinoma,0,1	SH2B1	160	1	1	Substitution - Missense(1)	stomach(1)	c.A1450G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	1188,3206	708.1+/-407.6	147,894,1156	54.0	54.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1450,1450,1450,1450,1450	3.1	1.0	16	dbSNP_116	54	3280,5320	644.9+/-400.1	645,1990,1665	yes	missense,missense,missense,missense,missense	SH2B1	NM_001145795.1,NM_001145796.1,NM_001145797.1,NM_001145812.1,NM_015503.2	58,58,58,58,58	792,2884,2821	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	38.1395,27.0369,34.3851	benign,benign,benign,benign,benign	484/757,484/672,484/684,484/672,484/672	28883241	4468,8526	2197	4300	6497	SO:0001583	missense	25970	exon6			CCCCCAACAGGGA	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	30417	protein-coding gene	gene with protein product	"""SH2-B homolog"""	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.1450A>G	16.37:g.28883241A>G	ENSP00000321221:p.Thr484Ala	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	196	95	0.484694	NM_001145796	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	ENST00000322610.8	37	CCDS53996.1	582	0.2664835164835165	101	0.20528455284552846	146	0.40331491712707185	77	0.1346153846153846	258	0.3403693931398417	G	4.100	0.016531	0.07959	0.270369	0.381395	ENSG00000178188	ENST00000322610;ENST00000545570;ENST00000359285;ENST00000538342;ENST00000395532;ENST00000337120	T;T;T;T;T;T	0.42513	0.98;1.66;0.97;1.56;0.98;0.98	5.14	3.08	0.35506	.	0.786081	0.11222	N	0.586567	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.44682	-0.9312	9	0.06494	T	0.89	-34.7926	4.2204	0.10554	0.0868:0.3268:0.4473:0.1391	rs7498665;rs17856339;rs60209196;rs7498665	148;174;484;484;484	B4DLN5;F5GXU7;Q9NRF2-2;Q9NRF2-3;Q9NRF2	.;.;.;.;SH2B1_HUMAN	A	484;174;484;148;484;484	ENSP00000321221:T484A;ENSP00000440354:T174A;ENSP00000352232:T484A;ENSP00000438784:T148A;ENSP00000378903:T484A;ENSP00000337163:T484A	ENSP00000321221:T484A	T	+	1	0	SH2B1	28790742	0.001000	0.12720	0.999000	0.59377	0.987000	0.75469	0.782000	0.26788	0.567000	0.29293	-0.186000	0.12905	ACA	A|0.711;G|0.289	0.289	strong		0.622	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503	
KLC2	64837	hgsc.bcm.edu	37	11	66033430	66033430	+	Missense_Mutation	SNP	C	C	T	rs2276036	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:66033430C>T	ENST00000417856.1	+	13	1792	c.1549C>T	c.(1549-1551)Cct>Tct	p.P517S	KLC2_ENST00000316924.5_Missense_Mutation_p.P517S|RP11-867G23.1_ENST00000530805.1_RNA|KLC2_ENST00000394067.2_Missense_Mutation_p.P517S|KLC2_ENST00000421552.1_Missense_Mutation_p.P440S|KLC2_ENST00000394066.2_Missense_Mutation_p.P440S|RP11-867G23.2_ENST00000533287.1_RNA|KLC2_ENST00000394078.1_Intron|RAB1B_ENST00000527397.1_5'Flank|RAB1B_ENST00000311481.6_5'Flank|KLC2_ENST00000394065.2_Missense_Mutation_p.P378S	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2	517			P -> S (in dbSNP:rs2276036).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon cargo transport (GO:0008088)|blood coagulation (GO:0007596)|microtubule-based movement (GO:0007018)	ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinesin I complex (GO:0016938)|membrane (GO:0016020)|microtubule (GO:0005874)|neuron projection (GO:0043005)|protein complex (GO:0043234)	kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						GGGTGCCGGGCCTCGGTCTGA	0.682													C|||	970	0.19369	0.1823	0.1268	5008	,	,		13064	0.2887		0.173	False		,,,				2504	0.18				p.P517S		Atlas-SNP	.											.	KLC2	50	.	0			c.C1549T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	762,3634	295.0+/-283.4	70,622,1506	36.0	43.0	41.0		1318,1549,1549,1549	0.4	1.0	11	dbSNP_100	41	1488,7096	269.1+/-288.2	137,1214,2941	yes	missense,missense,missense,missense	KLC2	NM_001134774.1,NM_001134775.1,NM_001134776.1,NM_022822.2	74,74,74,74	207,1836,4447	TT,TC,CC		17.3346,17.3339,17.3344	benign,benign,benign,benign	440/546,517/623,517/623,517/623	66033430	2250,10730	2198	4292	6490	SO:0001583	missense	64837	exon13			GCCGGGCCTCGGT	AK022449	CCDS8130.1, CCDS44653.1	11q13.1	2013-01-10			ENSG00000174996	ENSG00000174996		"""Tetratricopeptide (TTC) repeat domain containing"""	20716	protein-coding gene	gene with protein product		611729				9624122	Standard	NM_022822		Approved	FLJ12387	uc001ohb.2	Q9H0B6	OTTHUMG00000133757	ENST00000417856.1:c.1549C>T	11.37:g.66033430C>T	ENSP00000399403:p.Pro517Ser	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	219	205	0.936073	NM_022822	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Missense_Mutation	SNP	ENST00000417856.1	37	CCDS8130.1	422	0.19322344322344323	77	0.1565040650406504	49	0.13535911602209943	160	0.27972027972027974	136	0.17941952506596306	C	4.543	0.100733	0.08731	0.173339	0.173346	ENSG00000174996	ENST00000417856;ENST00000394067;ENST00000316924;ENST00000421552;ENST00000394066;ENST00000394065	T;T;T;T;T;D	0.82081	-0.94;-0.94;-0.94;-0.95;-0.95;-1.57	3.71	0.365	0.16131	.	0.603350	0.14605	N	0.309400	T	0.00012	0.0000	L	0.29908	0.895	0.34550	P	0.288802	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.03453	-1.1035	9	0.18276	T	0.48	-0.0827	7.7791	0.29054	0.0:0.6758:0.1993:0.1249	rs2276036;rs59407109;rs2276036	378;440;517	A8MZ87;A8MXL7;Q9H0B6	.;.;KLC2_HUMAN	S	517;517;517;440;440;378	ENSP00000399403:P517S;ENSP00000377631:P517S;ENSP00000314837:P517S;ENSP00000408484:P440S;ENSP00000377630:P440S;ENSP00000377629:P378S	ENSP00000314837:P517S	P	+	1	0	KLC2	65790006	0.000000	0.05858	0.986000	0.45419	0.343000	0.28985	-0.074000	0.11450	0.241000	0.21283	0.491000	0.48974	CCT	C|0.818;T|0.182	0.182	strong		0.682	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822	
PDE2A	5138	hgsc.bcm.edu	37	11	72289291	72289291	+	Silent	SNP	T	T	C	rs1135029	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:72289291T>C	ENST00000334456.5	-	30	2846	c.2601A>G	c.(2599-2601)gcA>gcG	p.A867A	PDE2A_ENST00000444035.2_Silent_p.A858A|PDE2A_ENST00000418754.2_Silent_p.A752A|PDE2A_ENST00000376450.3_Silent_p.A611A|PDE2A_ENST00000540345.1_Silent_p.A858A|PDE2A_ENST00000544570.1_Silent_p.A860A	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated	867	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	AGATGGGCATTGCAATGTGCT	0.562													T|||	1494	0.298323	0.0885	0.3213	5008	,	,		22174	0.245		0.5298	False		,,,				2504	0.3824				p.A867A		Atlas-SNP	.											PDE2A,caecum,carcinoma,-1,2	PDE2A	156	2	0			c.A2601G						PASS	.	T	,,	773,3627	312.5+/-292.6	70,633,1497	196.0	160.0	172.0		2580,2574,2601	-11.2	0.4	11	dbSNP_86	172	4604,3982	601.4+/-394.4	1236,2132,925	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE2A	NM_001143839.3,NM_001146209.2,NM_002599.4	,,	1306,2765,2422	CC,CT,TT		46.3778,17.5682,41.4061	,,	860/935,858/933,867/942	72289291	5377,7609	2200	4293	6493	SO:0001819	synonymous_variant	5138	exon30			GGGCATTGCAATG	U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"""Phosphodiesterases"""	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.2601A>G	11.37:g.72289291T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_002599	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Silent	SNP	ENST00000334456.5	37	CCDS8216.1																																																																																			T|0.638;C|0.362	0.362	strong		0.562	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599	
STEAP1B	256227	hgsc.bcm.edu	37	7	22533350	22533350	+	Missense_Mutation	SNP	C	C	T	rs146447808	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:22533350C>T	ENST00000406890.2	-	3	227	c.133G>A	c.(133-135)Gca>Aca	p.A45T	STEAP1B_ENST00000404369.4_Missense_Mutation_p.A64T	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	45						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						AGTTCCTGTGCGTGCTGAAGT	0.463													t|||	256	0.0511182	0.0968	0.0504	5008	,	,		19661	0.0		0.0666	False		,,,				2504	0.0266				p.A64T		Atlas-SNP	.											.	STEAP1B	22	.	0			c.G190A						PASS	.						98.0	77.0	83.0					7																	22533350		692	1591	2283	SO:0001583	missense	256227	exon3			CCTGTGCGTGCTG		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.133G>A	7.37:g.22533350C>T	ENSP00000385239:p.Ala45Thr	Somatic	377	0	0		WXS	Illumina HiSeq	Phase_I	367	142	0.386921	NM_001164460	B5MCI2	Missense_Mutation	SNP	ENST00000406890.2	37	CCDS55094.1	112	0.05128205128205128	35	0.07113821138211382	19	0.052486187845303865	1	0.0017482517482517483	57	0.07519788918205805	t	1.177	-0.639187	0.03557	.	.	ENSG00000105889	ENST00000406890;ENST00000404369;ENST00000424363;ENST00000439708	T;T;T;T	0.11385	2.78;2.94;2.99;2.81	1.06	-0.194	0.13240	.	0.644709	0.10852	N	0.627012	T	0.00144	0.0004	N	0.00347	-1.61	0.80722	P	0.0	B;B	0.12630	0.006;0.0	B;B	0.04013	0.001;0.0	T	0.42155	-0.9468	9	0.29301	T	0.29	-0.0084	2.3091	0.04182	0.2555:0.3907:0.0:0.3538	.	64;45	B5MCI2;Q6NZ63	.;STEAL_HUMAN	T	45;64;64;64	ENSP00000385239:A45T;ENSP00000384370:A64T;ENSP00000416608:A64T;ENSP00000408954:A64T	ENSP00000384370:A64T	A	-	1	0	STEAP1B	22499875	0.984000	0.35163	0.003000	0.11579	0.015000	0.08874	0.064000	0.14437	-0.581000	0.05937	-1.950000	0.00486	GCA	.	.	weak		0.463	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		
NAT1	9	hgsc.bcm.edu	37	8	18080128	18080128	+	Missense_Mutation	SNP	C	C	T	rs141552883		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:18080128C>T	ENST00000517492.1	+	3	1210	c.572C>T	c.(571-573)tCc>tTc	p.S191F	NAT1_ENST00000539092.1_Missense_Mutation_p.S191F|NAT1_ENST00000517441.1_3'UTR|NAT1_ENST00000541942.1_Missense_Mutation_p.S191F|NAT1_ENST00000520546.1_Missense_Mutation_p.S191F|NAT1_ENST00000545197.1_Missense_Mutation_p.S253F|NAT1_ENST00000535084.1_Missense_Mutation_p.S191F|NAT1_ENST00000518029.1_Missense_Mutation_p.S191F|NAT1_ENST00000307719.4_Missense_Mutation_p.S191F			Q8IZM9	S38A6_HUMAN	N-acetyltransferase 1 (arylamine N-acetyltransferase)	0					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(2)|urinary_tract(1)	9				Colorectal(111;0.0519)|COAD - Colon adenocarcinoma(73;0.208)		AAAATCTACTCCTTTACTCTT	0.358													C|||	1	0.000199681	0.0	0.0	5008	,	,		19441	0.0		0.001	False		,,,				2504	0.0				p.S253F		Atlas-SNP	.											.	NAT1	38	.	0			c.C758T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER	0,4406		0,0,2203	112.0	115.0	114.0		572,572,572,572,572,572,758,758,572	3.1	0.5	8	dbSNP_134	114	1,8599		0,1,4299	no	missense,missense,missense,missense,missense,missense,missense,missense,missense	NAT1	NM_000662.5,NM_001160170.1,NM_001160171.1,NM_001160172.1,NM_001160173.1,NM_001160174.1,NM_001160175.1,NM_001160176.1,NM_001160179.1	155,155,155,155,155,155,155,155,155	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	191/291,191/291,191/291,191/291,191/291,191/291,253/353,253/353,191/291	18080128	1,13005	2203	4300	6503	SO:0001583	missense	9	exon4			TCTACTCCTTTAC	BC047666	CCDS6007.1, CCDS55205.1	8p22	2012-01-18			ENSG00000171428	ENSG00000171428	2.3.1.5		7645	protein-coding gene	gene with protein product		108345		AAC1		7773298	Standard	NM_001160174		Approved		uc003wyt.3	P18440	OTTHUMG00000097001	ENST00000517492.1:c.572C>T	8.37:g.18080128C>T	ENSP00000429407:p.Ser191Phe	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	138	62	0.449275	NM_001160176	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000517492.1	37	CCDS6007.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	7.210	0.595309	0.13875	0.0	1.16E-4	ENSG00000171428	ENST00000535084;ENST00000307719;ENST00000545197;ENST00000539092;ENST00000541942;ENST00000518029;ENST00000517492;ENST00000520546	T;T;T;T;T;T;T;T	0.02177	4.41;4.41;4.41;4.41;4.41;4.41;4.41;4.41	4.05	3.13	0.36017	.	0.492839	0.21479	N	0.073870	T	0.07279	0.0184	M	0.90252	3.1	0.32873	D	0.50949	P;P	0.47409	0.895;0.851	P;P	0.52909	0.713;0.658	T	0.12811	-1.0533	10	0.10111	T	0.7	.	5.0238	0.14374	0.2107:0.6782:0.0:0.1111	.	253;191	F5H5R8;P18440	.;ARY1_HUMAN	F	191;191;253;191;191;191;191;191	ENSP00000444609:S191F;ENSP00000307218:S191F;ENSP00000443194:S253F;ENSP00000440434:S191F;ENSP00000440900:S191F;ENSP00000428270:S191F;ENSP00000429407:S191F;ENSP00000429341:S191F	ENSP00000307218:S191F	S	+	2	0	NAT1	18124408	0.952000	0.32445	0.453000	0.27007	0.784000	0.44337	0.616000	0.24344	0.767000	0.33267	0.460000	0.39030	TCC	C|1.000;T|0.000	0.000	strong		0.358	NAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374828.1	NM_000662	
TSPAN11	441631	hgsc.bcm.edu	37	12	31135579	31135579	+	Missense_Mutation	SNP	T	T	C	rs2075333	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:31135579T>C	ENST00000261177.9	+	6	628	c.569T>C	c.(568-570)gTg>gCg	p.V190A	TSPAN11_ENST00000535215.1_Missense_Mutation_p.V119A|TSPAN11_ENST00000546076.1_Missense_Mutation_p.V190A|TSPAN11_ENST00000544427.1_Missense_Mutation_p.V180A	NM_001080509.2	NP_001073978.1	A1L157	TSN11_HUMAN	tetraspanin 11	190			V -> A (in dbSNP:rs2075333). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)	11	all_lung(12;3.11e-10)|Lung NSC(12;5.24e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					ACAGTGGTGGTGCGCTGCGGC	0.662													C|||	3544	0.707668	0.6415	0.7478	5008	,	,		15450	0.7242		0.6998	False		,,,				2504	0.7597				p.V190A		Atlas-SNP	.											TSPAN11,NS,carcinoma,0,1	TSPAN11	30	1	0			c.T569C						PASS	.	C	ALA/VAL	2782,1614		890,1002,306	17.0	18.0	18.0		569	-1.8	0.0	12	dbSNP_96	18	5848,2738		2022,1804,467	yes	missense	TSPAN11	NM_001080509.2	64	2912,2806,773	CC,CT,TT		31.8891,36.7152,33.5233	benign	190/254	31135579	8630,4352	2198	4293	6491	SO:0001583	missense	441631	exon6			TGGTGGTGCGCTG		CCDS31765.1	12p11.21	2013-02-14				ENSG00000110900		"""Tetraspanins"""	30795	protein-coding gene	gene with protein product							Standard	NM_001080509		Approved		uc001rjp.3	A1L157		ENST00000261177.9:c.569T>C	12.37:g.31135579T>C	ENSP00000261177:p.Val190Ala	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	117	37	0.316239	NM_001080509	A1L158|B2RUX6	Missense_Mutation	SNP	ENST00000261177.9	37	CCDS31765.1	1525	0.6982600732600732	297	0.6036585365853658	265	0.7320441988950276	423	0.7395104895104895	540	0.712401055408971	C	0.003	-2.517694	0.00151	0.632848	0.681109	ENSG00000110900	ENST00000546076;ENST00000535215;ENST00000544427;ENST00000261177	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	4.01	-1.76	0.08006	Tetraspanin, EC2 domain (1);	0.775582	0.11273	N	0.581263	T	0.00012	0.0000	N	0.04355	-0.22	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.38585	-0.9654	9	0.06494	T	0.89	.	3.9487	0.09360	0.2594:0.2386:0.0:0.5019	rs2075333;rs3892968;rs17749073;rs59578843	180;190	F5H0F0;A1L157	.;TSN11_HUMAN	A	190;119;180;190	ENSP00000437403:V190A;ENSP00000445503:V119A;ENSP00000439895:V180A;ENSP00000261177:V190A	ENSP00000261177:V190A	V	+	2	0	TSPAN11	31026846	0.000000	0.05858	0.008000	0.14137	0.033000	0.12548	-0.471000	0.06631	-0.273000	0.09246	-1.741000	0.00685	GTG	T|0.327;C|0.673	0.673	strong		0.662	TSPAN11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399888.1	XM_497334	
PLEKHH2	130271	hgsc.bcm.edu	37	2	43989525	43989525	+	Missense_Mutation	SNP	C	C	G	rs76859622	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:43989525C>G	ENST00000282406.4	+	28	4264	c.4154C>G	c.(4153-4155)tCc>tGc	p.S1385C		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	1385	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GAATACAACTCCATGGTAAGT	0.373													C|||	73	0.0145767	0.0053	0.0259	5008	,	,		17853	0.0		0.0467	False		,,,				2504	0.001				p.S1385C		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.C4154G						PASS	.	C	CYS/SER	27,4379	32.6+/-62.9	0,27,2176	139.0	124.0	129.0		4154	5.2	1.0	2	dbSNP_131	129	294,8306	107.8+/-168.5	9,276,4015	yes	missense	PLEKHH2	NM_172069.3	112	9,303,6191	GG,GC,CC		3.4186,0.6128,2.4681	possibly-damaging	1385/1494	43989525	321,12685	2203	4300	6503	SO:0001583	missense	130271	exon28			ACAACTCCATGGT	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"""Pleckstrin homology (PH) domain containing"""	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.4154C>G	2.37:g.43989525C>G	ENSP00000282406:p.Ser1385Cys	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	184	69	0.375	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	53	0.024267399267399268	3	0.006097560975609756	14	0.03867403314917127	0	0.0	36	0.047493403693931395	C	21.4	4.147837	0.78001	0.006128	0.034186	ENSG00000152527	ENST00000282406	T	0.74632	-0.86	5.19	5.19	0.71726	FERM domain (1);	0.171104	0.52532	D	0.000063	T	0.30070	0.0753	L	0.44542	1.39	0.51767	D	0.99993	B	0.29571	0.249	B	0.25884	0.064	T	0.60332	-0.7284	10	0.87932	D	0	-10.2459	18.7342	0.91748	0.0:1.0:0.0:0.0	.	1385	Q8IVE3	PKHH2_HUMAN	C	1385	ENSP00000282406:S1385C	ENSP00000282406:S1385C	S	+	2	0	PLEKHH2	43843029	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.399000	0.66314	2.398000	0.81561	0.655000	0.94253	TCC	C|0.975;G|0.025	0.025	strong		0.373	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069	
EGR2	1959	hgsc.bcm.edu	37	10	64575663	64575663	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:64575663C>T	ENST00000242480.3	-	1	452	c.127G>A	c.(127-129)Gaa>Aaa	p.E43K	EGR2_ENST00000411732.1_5'UTR|EGR2_ENST00000493899.2_5'UTR|EGR2_ENST00000439032.1_Missense_Mutation_p.E43K	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	43					brain development (GO:0007420)|brain segmentation (GO:0035284)|cell death (GO:0008219)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|facial nerve structural organization (GO:0021612)|fat cell differentiation (GO:0045444)|learning or memory (GO:0007611)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein sumoylation (GO:0016925)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ossification (GO:0030278)|response to insulin (GO:0032868)|rhombomere 3 formation (GO:0021660)|rhombomere 5 formation (GO:0021666)|rhythmic behavior (GO:0007622)|Schwann cell differentiation (GO:0014037)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	36	Prostate(12;0.0297)|all_hematologic(501;0.228)					CCTCCCAGTTCGGCATTGGGA	0.622																																					p.E43K		Atlas-SNP	.											EGR2,bladder,carcinoma,0,1	EGR2	77	1	0			c.G127A						scavenged	.						109.0	103.0	105.0					10																	64575663		2203	4300	6503	SO:0001583	missense	1959	exon1			CCAGTTCGGCATT	BC035625	CCDS7267.1, CCDS44409.1	10q21.1	2014-09-17	2009-04-23		ENSG00000122877	ENSG00000122877		"""Zinc fingers, C2H2-type"""	3239	protein-coding gene	gene with protein product	"""Krox-20 homolog, Drosophila"""	129010	"""early growth response 2 (Krox-20 homolog, Drosophila)"""	KROX20			Standard	NM_000399		Approved		uc001jmi.3	P11161	OTTHUMG00000018308	ENST00000242480.3:c.127G>A	10.37:g.64575663C>T	ENSP00000242480:p.Glu43Lys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	191	3	0.0157068	NM_000399	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Missense_Mutation	SNP	ENST00000242480.3	37	CCDS7267.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.146518	0.77888	.	.	ENSG00000122877	ENST00000242480;ENST00000439032;ENST00000432380	T;T	0.14266	2.52;2.52	5.1	5.1	0.69264	.	0.054626	0.64402	D	0.000001	T	0.07863	0.0197	N	0.14661	0.345	0.80722	D	1	P	0.44006	0.824	B	0.27608	0.081	T	0.21415	-1.0246	10	0.62326	D	0.03	-12.6597	17.7043	0.88304	0.0:1.0:0.0:0.0	.	43	P11161	EGR2_HUMAN	K	43;43;56	ENSP00000242480:E43K;ENSP00000402040:E43K	ENSP00000242480:E43K	E	-	1	0	EGR2	64245669	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	5.190000	0.65104	2.548000	0.85928	0.556000	0.70494	GAA	.	.	none		0.622	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399	
DKKL1	27120	hgsc.bcm.edu	37	19	49878115	49878115	+	Missense_Mutation	SNP	G	G	A	rs1054770	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49878115G>A	ENST00000221498.2	+	5	964	c.559G>A	c.(559-561)Ggc>Agc	p.G187S	AC010524.2_ENST00000599433.1_RNA|DKKL1_ENST00000594268.1_Missense_Mutation_p.G45S	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	187			G -> S (in dbSNP:rs1054770).		anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		CCTGGAGGGCGGCCACTGGCT	0.652													G|||	1583	0.316094	0.2844	0.2464	5008	,	,		15776	0.3373		0.2406	False		,,,				2504	0.4642				p.G187S		Atlas-SNP	.											.	DKKL1	23	.	0			c.G559A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	1216,3190		169,878,1156	26.0	28.0	28.0		466,334,559	-3.2	0.0	19	dbSNP_86	28	2242,6356		296,1650,2353	yes	missense,missense,missense	DKKL1	NM_001197301.1,NM_001197302.1,NM_014419.3	56,56,56	465,2528,3509	AA,AG,GG		26.0758,27.5987,26.5918	benign,benign,benign	156/212,112/168,187/243	49878115	3458,9546	2203	4299	6502	SO:0001583	missense	27120	exon5			GAGGGCGGCCACT	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"""cancer/testis antigen 34"", ""soggy"""	605418	"""dickkopf-like 1 (soggy)"""			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.559G>A	19.37:g.49878115G>A	ENSP00000221498:p.Gly187Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	37	CCDS12762.1	586	0.2683150183150183	130	0.26422764227642276	90	0.24861878453038674	186	0.32517482517482516	180	0.23746701846965698	G	9.816	1.184396	0.21870	0.275987	0.260758	ENSG00000104901	ENST00000221498	T	0.11385	2.78	4.15	-3.2	0.05156	.	0.951199	0.08710	N	0.905096	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B	0.27117	0.168	B	0.17979	0.02	T	0.43228	-0.9404	9	0.41790	T	0.15	-4.4785	8.8013	0.34909	0.5829:0.0:0.4171:0.0	rs1054770;rs3195287;rs1054770	187	Q9UK85	DKKL1_HUMAN	S	187	ENSP00000221498:G187S	ENSP00000221498:G187S	G	+	1	0	DKKL1	54569927	0.000000	0.05858	0.000000	0.03702	0.529000	0.34654	-1.471000	0.02344	-0.443000	0.07180	-0.302000	0.09304	GGC	G|0.733;A|0.267	0.267	strong		0.652	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419	
SPZ1	84654	hgsc.bcm.edu	37	5	79616936	79616936	+	Missense_Mutation	SNP	A	A	C	rs35337118	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:79616936A>C	ENST00000296739.4	+	1	1147	c.902A>C	c.(901-903)cAt>cCt	p.H301P		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	301				H -> P (in Ref. 1; AAK17995). {ECO:0000305}.	transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		TCGGCTAAGCATGAGCTGGAG	0.413													A|||	475	0.0948482	0.0749	0.1138	5008	,	,		19598	0.0		0.162	False		,,,				2504	0.137				p.H301P		Atlas-SNP	.											.	SPZ1	60	.	0			c.A902C						PASS	.	A	PRO/HIS	302,3508		11,280,1614	116.0	112.0	113.0		902	-3.4	0.0	5	dbSNP_126	113	1422,6828		122,1178,2825	yes	missense	SPZ1	NM_032567.3	77	133,1458,4439	CC,CA,AA		17.2364,7.9265,14.2952	probably-damaging	301/431	79616936	1724,10336	1905	4125	6030	SO:0001583	missense	84654	exon1			CTAAGCATGAGCT		CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 148"""					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.902A>C	5.37:g.79616936A>C	ENSP00000369611:p.His301Pro	Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	179	93	0.519553	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	208	0.09523809523809523	31	0.06300813008130081	52	0.143646408839779	0	0.0	125	0.16490765171503957	A	13.73	2.323161	0.41096	0.079265	0.172364	ENSG00000164299	ENST00000296739	T	0.32753	1.44	4.4	-3.41	0.04839	.	1.849150	0.02670	N	0.108464	T	0.00073	0.0002	L	0.47190	1.495	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.16660	-1.0395	9	0.32370	T	0.25	-12.8598	0.6407	0.00810	0.2254:0.1397:0.2897:0.3452	rs35337118;rs62364057	301	Q9BXG8	SPZ1_HUMAN	P	301	ENSP00000369611:H301P	ENSP00000369611:H301P	H	+	2	0	SPZ1	79652692	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.033000	0.13754	-0.560000	0.06102	-0.503000	0.04515	CAT	A|0.872;C|0.128	0.128	strong		0.413	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567	
USP32	84669	hgsc.bcm.edu	37	17	58285542	58285542	+	Missense_Mutation	SNP	G	G	A	rs147413172	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:58285542G>A	ENST00000300896.4	-	24	2997	c.2803C>T	c.(2803-2805)Cgg>Tgg	p.R935W	USP32_ENST00000592339.1_Missense_Mutation_p.R605W	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	935	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R935W(2)		NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			AGTCCATACCGTACAGGGGTA	0.353																																					p.R935W		Atlas-SNP	.											USP32,NS,malignant_melanoma,0,2	USP32	128	2	2	Substitution - Missense(2)	NS(1)|pancreas(1)	c.C2803T						scavenged	.						37.0	43.0	41.0					17																	58285542		2202	4289	6491	SO:0001583	missense	84669	exon24			CATACCGTACAGG	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"""Ubiquitin-specific peptidases"", ""EF-hand domain containing"""	19143	protein-coding gene	gene with protein product		607740	"""ubiquitin specific protease 32"""			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.2803C>T	17.37:g.58285542G>A	ENSP00000300896:p.Arg935Trp	Somatic	461	3	0.00650759		WXS	Illumina HiSeq	Phase_I	563	138	0.245115	NM_032582	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.294566	0.81025	.	.	ENSG00000170832	ENST00000300896	T	0.53206	0.63	5.22	5.22	0.72569	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.72550	0.3474	M	0.82433	2.59	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.77376	-0.2611	10	0.87932	D	0	.	18.7745	0.91904	0.0:0.0:1.0:0.0	.	935	Q8NFA0	UBP32_HUMAN	W	935	ENSP00000300896:R935W	ENSP00000300896:R935W	R	-	1	2	USP32	55640324	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	5.540000	0.67205	2.436000	0.82500	0.563000	0.77884	CGG	.	.	weak		0.353	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582	
PLCG2	5336	hgsc.bcm.edu	37	16	81990441	81990441	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81990441A>T	ENST00000359376.3	+	32	3926	c.3712A>T	c.(3712-3714)Aat>Tat	p.N1238Y		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1238					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						GTTCAGTGTTAATGAGAACCA	0.512																																					p.N1238Y		Atlas-SNP	.											.	PLCG2	276	.	0			c.A3712T						PASS	.						99.0	100.0	100.0					16																	81990441		1953	4145	6098	SO:0001583	missense	5336	exon32			AGTGTTAATGAGA		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.3712A>T	16.37:g.81990441A>T	ENSP00000352336:p.Asn1238Tyr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	A	18.00	3.525302	0.64747	.	.	ENSG00000197943	ENST00000359376	T	0.67171	-0.25	5.49	5.49	0.81192	.	0.250471	0.46758	D	0.000266	T	0.71082	0.3298	L	0.36672	1.1	0.52099	D	0.999942	D	0.67145	0.996	P	0.59703	0.862	T	0.74414	-0.3673	10	0.72032	D	0.01	.	13.83	0.63375	1.0:0.0:0.0:0.0	.	1238	P16885	PLCG2_HUMAN	Y	1238	ENSP00000352336:N1238Y	ENSP00000352336:N1238Y	N	+	1	0	PLCG2	80547942	1.000000	0.71417	0.990000	0.47175	0.448000	0.32197	6.593000	0.74100	2.078000	0.62432	0.413000	0.27773	AAT	.	.	none		0.512	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
WNT8B	7479	hgsc.bcm.edu	37	10	102241724	102241724	+	Silent	SNP	G	G	A	rs76078607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:102241724G>A	ENST00000343737.5	+	5	551	c.423G>A	c.(421-423)gcG>gcA	p.A141A		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	141					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|negative regulation of gene expression (GO:0010629)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of gene expression (GO:0010628)|response to estradiol (GO:0032355)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)		TCGGAGAGGCGATTTCCAAGC	0.607											OREG0020440	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	9	0.00179712	0.0	0.0	5008	,	,		17905	0.0		0.008	False		,,,				2504	0.001				p.A141A		Atlas-SNP	.											.	WNT8B	31	.	0			c.G423A						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	122.0	105.0	111.0		423	-10.4	0.9	10	dbSNP_132	111	32,8568	22.2+/-67.0	0,32,4268	no	coding-synonymous	WNT8B	NM_003393.3		0,37,6466	AA,AG,GG		0.3721,0.1135,0.2845		141/352	102241724	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	7479	exon5			AGAGGCGATTTCC	X91940	CCDS7494.1	10q24	2003-11-12			ENSG00000075290	ENSG00000075290		"""Wingless-type MMTV integration sites"""	12789	protein-coding gene	gene with protein product		601396				8661156	Standard	NM_003393		Approved		uc001krb.3	Q93098	OTTHUMG00000018912	ENST00000343737.5:c.423G>A	10.37:g.102241724G>A		Somatic	92	0	0	1365	WXS	Illumina HiSeq	Phase_I	68	7	0.102941	NM_003393	O00771|Q5VX55|Q8WYK9	Silent	SNP	ENST00000343737.5	37	CCDS7494.1																																																																																			G|0.998;A|0.002	0.002	strong		0.607	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393	
PAPL	390928	hgsc.bcm.edu	37	19	39592138	39592138	+	Silent	SNP	C	C	T	rs1313617	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:39592138C>T	ENST00000331256.5	+	11	1348	c.1074C>T	c.(1072-1074)acC>acT	p.T358T	PAPL_ENST00000594229.1_Missense_Mutation_p.P317L	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		358						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										TGCCCTACACCAACCCGCGAG	0.582													C|||	1136	0.226837	0.3359	0.1671	5008	,	,		16890	0.1488		0.2018	False		,,,				2504	0.228				p.T358T		Atlas-SNP	.											.	.	.	.	0			c.C1074T						PASS	.	C		1424,2982	462.3+/-353.2	231,962,1010	60.0	52.0	55.0		1074	4.2	1.0	19	dbSNP_87	55	1798,6802	319.9+/-314.4	180,1438,2682	no	coding-synonymous	PAPL	NM_001004318.2		411,2400,3692	TT,TC,CC		20.907,32.3196,24.7732		358/439	39592138	3222,9784	2203	4300	6503	SO:0001819	synonymous_variant	0	exon11			CTACACCAACCCG																												ENST00000331256.5:c.1074C>T	19.37:g.39592138C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_001004318	B2RN68	Silent	SNP	ENST00000331256.5	37	CCDS33018.1																																																																																			C|0.765;T|0.235	0.235	strong		0.582	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		
GIMAP8	155038	hgsc.bcm.edu	37	7	150171710	150171710	+	Silent	SNP	T	T	C	rs60114833	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:150171710T>C	ENST00000307271.3	+	4	1867	c.1293T>C	c.(1291-1293)tgT>tgC	p.C431C		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	431	AIG1-type G 2.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		ACAAGCATTGTGTTTTCAGAG	0.343													T|||	1301	0.259784	0.1097	0.2233	5008	,	,		15551	0.4187		0.3698	False		,,,				2504	0.2117				p.C431C		Atlas-SNP	.											.	GIMAP8	136	.	0			c.T1293C						PASS	.	T		697,3709	291.3+/-281.4	59,579,1565	67.0	71.0	70.0		1293	-3.3	0.0	7	dbSNP_129	70	3020,5580	463.4+/-366.0	550,1920,1830	no	coding-synonymous	GIMAP8	NM_175571.2		609,2499,3395	CC,CT,TT		35.1163,15.8193,28.5791		431/666	150171710	3717,9289	2203	4300	6503	SO:0001819	synonymous_variant	155038	exon4			GCATTGTGTTTTC	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.1293T>C	7.37:g.150171710T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_175571		Silent	SNP	ENST00000307271.3	37	CCDS34777.1																																																																																			T|0.704;C|0.296	0.296	strong		0.343	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
RBMXL3	139804	hgsc.bcm.edu	37	X	114424505	114424505	+	Silent	SNP	G	G	A	rs62601528		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:114424505G>A	ENST00000424776.3	+	1	543	c.501G>A	c.(499-501)ccG>ccA	p.P167P	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	167							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						GGGCCACGCCGTCGAGCCTGG	0.706													g||||g|||	221|221	0.058543|0.058543	0.0038|0.0038	0.0548|0.0548	3775|3775	,|,	,|,		12084|12084	0.002|0.002		0.1123|0.1123	False|False		,,,|,,,				2504|2504	0.0644|0.0644				p.P167P		Atlas-SNP	.											.	RBMXL3	83	.	0			c.G501A						PASS	.						5.0	8.0	8.0					X																	114424505		648	1508	2156	SO:0001819	synonymous_variant	139804	exon1			CACGCCGTCGAGC	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.501G>A	X.37:g.114424505G>A		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	17	14	0.823529	NM_001145346	B4DXC0	Silent	SNP	ENST00000424776.3	37	CCDS55478.1																																																																																			G|0.928;A|0.072	0.072	strong		0.706	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
FLNB	2317	hgsc.bcm.edu	37	3	58154327	58154327	+	Silent	SNP	C	C	T	rs8640	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:58154327C>T	ENST00000295956.4	+	44	7524	c.7359C>T	c.(7357-7359)agC>agT	p.S2453S	FLNB_ENST00000484981.1_3'UTR|FLNB_ENST00000490882.1_Silent_p.S2484S|FLNB_ENST00000358537.3_Silent_p.S2429S|FLNB-AS1_ENST00000488720.1_RNA|FLNB_ENST00000493452.1_Silent_p.S2260S|FLNB_ENST00000348383.5_Silent_p.S2412S|FLNB_ENST00000419752.2_Silent_p.S2273S|FLNB_ENST00000429972.2_Silent_p.S2442S|FLNB_ENST00000357272.4_3'UTR	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	2453	Interaction with INPPL1.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		ACCTGATCAGCGTCAAATACG	0.537													C|||	2861	0.571286	0.5719	0.4597	5008	,	,		20342	0.9216		0.2664	False		,,,				2504	0.6022				p.S2484S		Atlas-SNP	.											.	FLNB	430	.	0			c.C7452T						PASS	.	C	,,,	2213,2193	592.1+/-387.7	532,1149,522	113.0	95.0	101.0		7452,7326,7287,7359	-4.1	0.2	3	dbSNP_52	101	2167,6433	371.5+/-336.3	275,1617,2408	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	807,2766,2930	TT,TC,CC		25.1977,49.773,33.6768	,,,	2484/2634,2442/2592,2429/2579,2453/2603	58154327	4380,8626	2203	4300	6503	SO:0001819	synonymous_variant	2317	exon45			GATCAGCGTCAAA	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.7359C>T	3.37:g.58154327C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																			C|0.573;T|0.427	0.427	strong		0.537	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
CASC5	57082	hgsc.bcm.edu	37	15	40915190	40915190	+	Missense_Mutation	SNP	A	A	G	rs8040502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:40915190A>G	ENST00000346991.5	+	11	3196	c.2806A>G	c.(2806-2808)Agg>Ggg	p.R936G	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Missense_Mutation_p.R910G			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	936	2 X 104 AA approximate repeats.		R -> G (in dbSNP:rs8040502). {ECO:0000269|PubMed:10980622, ECO:0000269|PubMed:12087463, ECO:0000269|PubMed:12618768}.		acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.R936G(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		ATATACATGTAGGCAGGATGA	0.368													G|||	3534	0.705671	0.9228	0.6225	5008	,	,		19341	0.3532		0.8559	False		,,,				2504	0.68				p.R936G		Atlas-SNP	.											CASC5,NS,carcinoma,0,1	CASC5	269	1	1	Substitution - Missense(1)	stomach(1)	c.A2806G						PASS	.	G	GLY/ARG,GLY/ARG	3490,286		1615,260,13	82.0	82.0	82.0		2728,2806	3.0	0.7	15	dbSNP_116	82	6921,1277		2926,1069,104	yes	missense,missense	CASC5	NM_144508.3,NM_170589.3	125,125	4541,1329,117	GG,GA,AA		15.577,7.5742,13.0533	benign,benign	910/2317,936/2343	40915190	10411,1563	1888	4099	5987	SO:0001583	missense	57082	exon11			ACATGTAGGCAGG	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.2806A>G	15.37:g.40915190A>G	ENSP00000335463:p.Arg936Gly	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	1531	0.701007326007326	451	0.9166666666666666	243	0.6712707182320442	183	0.31993006993006995	654	0.862796833773087	G	4.825	0.153406	0.09185	0.924258	0.84423	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.13657	2.57;2.57	5.09	3.03	0.35002	.	0.549745	0.17569	N	0.169531	T	0.00012	0.0000	N	0.00114	-2.085	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.24941	-1.0146	9	0.02654	T	1	.	7.4849	0.27427	0.0764:0.0:0.5097:0.4139	rs8040502;rs52826293;rs8040502	910;936;910	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	G	936;910;910	ENSP00000335463:R936G;ENSP00000382576:R910G	ENSP00000260369:R910G	R	+	1	2	CASC5	38702482	0.041000	0.20044	0.735000	0.30896	0.422000	0.31414	0.612000	0.24283	0.529000	0.28599	-0.226000	0.12346	AGG	A|0.259;G|0.741	0.741	strong		0.368	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53639448	53639448	+	Silent	SNP	G	G	A	rs144924117		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:53639448G>A	ENST00000379925.3	-	26	3830	c.3780C>T	c.(3778-3780)gtC>gtT	p.V1260V	RPGRIP1L_ENST00000564374.1_Silent_p.V1214V|RPGRIP1L_ENST00000563746.1_Silent_p.V1226V|RPGRIP1L_ENST00000262135.4_Silent_p.V1180V	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1260					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)			endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CGGCAAGGTCGACGTGAGCCA	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		18112	0.0		0.001	False		,,,				2504	0.0				p.V1260V		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.C3780T						PASS	.	G	,	2,4394	4.2+/-10.8	0,2,2196	181.0	134.0	150.0		3540,3780	-7.5	0.0	16	dbSNP_134	150	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	RPGRIP1L	NM_001127897.1,NM_015272.2	,	0,9,6489	AA,AG,GG		0.0814,0.0455,0.0693	,	1180/1236,1260/1316	53639448	9,12987	2198	4300	6498	SO:0001819	synonymous_variant	23322	exon26			AAGGTCGACGTGA		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"""fantom homolog"", ""Meckel syndrome, type 5"", ""protein phosphatase 1, regulatory subunit 134"""	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.3780C>T	16.37:g.53639448G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	105	65	0.619048	NM_015272	A0PJ88|Q9Y2K8	Silent	SNP	ENST00000379925.3	37	CCDS32447.1																																																																																			G|1.000;A|0.000	0.000	strong		0.532	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
MUC21	394263	hgsc.bcm.edu	37	6	30954356	30954356	+	Missense_Mutation	SNP	C	C	T	rs138756149		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954356C>T	ENST00000376296.3	+	2	645	c.404C>T	c.(403-405)gCc>gTc	p.A135V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	135	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GCCAGCACAGCCACCAACTCT	0.602																																					p.A135V		Atlas-SNP	.											MUC21,NS,carcinoma,0,3	MUC21	98	3	0			c.C404T						PASS	.						167.0	155.0	159.0					6																	30954356		2203	4300	6503	SO:0001583	missense	394263	exon2			GCACAGCCACCAA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.404C>T	6.37:g.30954356C>T	ENSP00000365473:p.Ala135Val	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	142	20	0.140845	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	C	2.845	-0.239645	0.05944	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02787	4.16	3.56	1.69	0.24217	.	.	.	.	.	T	0.01189	0.0039	N	0.24115	0.695	0.09310	N	1	P	0.50156	0.932	P	0.53146	0.719	T	0.46091	-0.9216	8	.	.	.	0.0524	2.4129	0.04429	0.1933:0.5064:0.1886:0.1118	.	135	Q5SSG8	MUC21_HUMAN	V	135	ENSP00000365473:A135V	.	A	+	2	0	MUC21	31062335	0.000000	0.05858	0.005000	0.12908	0.208000	0.24298	-0.443000	0.06862	0.285000	0.22329	0.485000	0.47835	GCC	.	.	weak		0.602	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
FAM179A	165186	hgsc.bcm.edu	37	2	29246044	29246044	+	Missense_Mutation	SNP	T	T	C	rs6721861	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29246044T>C	ENST00000379558.4	+	12	1955	c.1604T>C	c.(1603-1605)gTg>gCg	p.V535A	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Missense_Mutation_p.V480A	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	535			V -> A (in dbSNP:rs6721861).							breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GTGTGCTTGGTGGTGACTGGG	0.632													C|||	2376	0.474441	0.6218	0.3991	5008	,	,		18661	0.7044		0.3191	False		,,,				2504	0.2515				p.V535A		Atlas-SNP	.											FAM179A,NS,carcinoma,0,1	FAM179A	106	1	0			c.T1604C						PASS	.	C	ALA/VAL	2279,1877		635,1009,434	26.0	32.0	30.0		1604	4.6	0.6	2	dbSNP_116	30	2777,5625		504,1769,1928	yes	missense	FAM179A	NM_199280.2	64	1139,2778,2362	CC,CT,TT		33.0517,45.1636,40.2612	benign	535/1020	29246044	5056,7502	2078	4201	6279	SO:0001583	missense	165186	exon12			GCTTGGTGGTGAC	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.1604T>C	2.37:g.29246044T>C	ENSP00000368876:p.Val535Ala	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	182	68	0.373626	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	1135	0.5196886446886447	336	0.6829268292682927	153	0.42265193370165743	413	0.722027972027972	233	0.3073878627968338	C	4.363	0.066975	0.08388	0.548364	0.330517	ENSG00000189350	ENST00000379558;ENST00000403861;ENST00000440012	T;T;T	0.14022	2.54;2.54;2.54	5.5	4.61	0.57282	Armadillo-like helical (1);Armadillo-type fold (1);CLASP N-terminal domain (1);	0.095117	0.45867	N	0.000327	T	0.00012	0.0000	N	0.00325	-1.645	0.53688	P	2.199999999996649E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38802	-0.9644	9	0.02654	T	1	.	10.4738	0.44652	0.1336:0.7963:0.0:0.07	rs6721861;rs6721861	480;535	F8W8E4;Q6ZUX3	.;F179A_HUMAN	A	535;480;30	ENSP00000368876:V535A;ENSP00000384699:V480A;ENSP00000396739:V30A	ENSP00000368876:V535A	V	+	2	0	FAM179A	29099548	0.997000	0.39634	0.553000	0.28255	0.740000	0.42216	3.939000	0.56591	0.680000	0.31366	-0.128000	0.14901	GTG	T|0.456;C|0.544	0.544	strong		0.632	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
TMEM88B	643965	hgsc.bcm.edu	37	1	1361633	1361633	+	Silent	SNP	G	G	A	rs12022947	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:1361633G>A	ENST00000378821.3	+	1	126	c.126G>A	c.(124-126)tcG>tcA	p.S42S		NM_001146685.1	NP_001140157.1	A6NKF7	TM88B_HUMAN	transmembrane protein 88B	42						integral component of membrane (GO:0016021)											CAGGGTGGTCGGGGCCCCCGC	0.766													G|||	2003	0.39996	0.1989	0.3631	5008	,	,		12109	0.875		0.1193	False		,,,				2504	0.4969				p.S42S		Atlas-SNP	.											.	.	.	.	0			c.G126A						PASS	.						5.0	8.0	7.0					1																	1361633		648	1523	2171	SO:0001819	synonymous_variant	643965	exon1			GTGGTCGGGGCCC		CCDS57964.1	1p36.33	2013-01-16			ENSG00000205116	ENSG00000205116			37099	protein-coding gene	gene with protein product							Standard	NM_001146685		Approved		uc010nyp.2	A6NKF7	OTTHUMG00000153395	ENST00000378821.3:c.126G>A	1.37:g.1361633G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	11	8	0.727273	NM_001146685		Silent	SNP	ENST00000378821.3	37	CCDS57964.1																																																																																			G|0.633;A|0.367	0.367	strong		0.766	TMEM88B-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331012.2	NM_001146685	
EYS	346007	hgsc.bcm.edu	37	6	66005857	66005857	+	Missense_Mutation	SNP	T	T	A	rs17411795	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:66005857T>A	ENST00000370621.3	-	12	2448	c.1922A>T	c.(1921-1923)gAg>gTg	p.E641V	EYS_ENST00000503581.1_Missense_Mutation_p.E641V|EYS_ENST00000370616.2_Missense_Mutation_p.E641V			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	641			E -> V (in dbSNP:rs17411795). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.E641V(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AGTATCTATCTCACAGATGTT	0.438													T|||	522	0.104233	0.0582	0.1585	5008	,	,		13592	0.0655		0.2018	False		,,,				2504	0.0675				p.E641V		Atlas-SNP	.											EYS_ENST00000370621,NS,carcinoma,0,1	EYS	527	1	1	Substitution - Missense(1)	kidney(1)	c.A1922T						PASS	.	T	VAL/GLU	114,1270		6,102,584	157.0	124.0	134.0		1922	0.4	0.4	6	dbSNP_123	134	666,2516		60,546,985	yes	missense	EYS	NM_001142800.1	121	66,648,1569	AA,AT,TT		20.9302,8.237,17.0828	probably-damaging	641/3145	66005857	780,3786	692	1591	2283	SO:0001583	missense	346007	exon12			TCTATCTCACAGA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1922A>T	6.37:g.66005857T>A	ENSP00000359655:p.Glu641Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	162	72	0.444444	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		293	0.13415750915750915	34	0.06910569105691057	63	0.17403314917127072	38	0.06643356643356643	158	0.20844327176781002	.	12.97	2.098574	0.37048	0.08237	0.209302	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.80480	-1.38;-1.38;-1.38	5.48	0.452	0.16634	.	.	.	.	.	T	0.75213	0.3819	L	0.55481	1.735	0.09310	P	0.99999830371	D	0.55385	0.971	P	0.58454	0.839	T	0.70605	-0.4826	8	0.66056	D	0.02	.	7.9912	0.30242	0.0:0.3484:0.0:0.6516	rs17411795;rs17411795	641	Q5T1H1-1	.	V	641	ENSP00000424243:E641V;ENSP00000359655:E641V;ENSP00000359650:E641V	ENSP00000359650:E641V	E	-	2	0	EYS	66062578	0.526000	0.26298	0.371000	0.25978	0.109000	0.19521	0.278000	0.18753	0.091000	0.17302	0.482000	0.46254	GAG	A|0.141;N|0.000	0.141	strong		0.438	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
ZNF667	63934	hgsc.bcm.edu	37	19	56952615	56952615	+	Silent	SNP	A	A	G	rs61740673	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56952615A>G	ENST00000504904.3	-	7	2468	c.1749T>C	c.(1747-1749)taT>taC	p.Y583Y	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Silent_p.Y711Y|ZNF667_ENST00000292069.6_Silent_p.Y583Y			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	583					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		TACTACATTCATAGGGTTTCT	0.398													A|||	158	0.0315495	0.0961	0.0159	5008	,	,		20645	0.0		0.0159	False		,,,				2504	0.0041				p.Y583Y		Atlas-SNP	.											ZNF667,NS,NS,-2,1	ZNF667	95	1	0			c.T1749C						PASS	.	A		393,4013	197.7+/-221.8	16,361,1826	120.0	115.0	117.0		1749	-0.7	0.4	19	dbSNP_129	117	96,8504	53.1+/-113.8	0,96,4204	no	coding-synonymous	ZNF667	NM_022103.3		16,457,6030	GG,GA,AA		1.1163,8.9197,3.7598		583/611	56952615	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	63934	exon5			ACATTCATAGGGT		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1749T>C	19.37:g.56952615A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Silent	SNP	ENST00000504904.3	37	CCDS12944.1																																																																																			A|0.965;G|0.035	0.035	strong		0.398	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
INHA	3623	hgsc.bcm.edu	37	2	220439678	220439678	+	Silent	SNP	C	C	T	rs12720063	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:220439678C>T	ENST00000243786.2	+	2	711	c.531C>T	c.(529-531)gcC>gcT	p.A177A	INHA_ENST00000489456.1_3'UTR	NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	177					cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|erythrocyte differentiation (GO:0030218)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|ovarian follicle development (GO:0001541)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|regulation of cell cycle (GO:0051726)|regulation of cell proliferation (GO:0042127)|response to external stimulus (GO:0009605)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|inhibin A complex (GO:0043512)|inhibin-betaglycan-ActRII complex (GO:0034673)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|receptor binding (GO:0005102)			large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10		Renal(207;0.0183)		Epithelial(149;4.58e-07)|all cancers(144;4.31e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CTCACTGGGCCGTGCTGCACC	0.672													C|||	768	0.153355	0.0809	0.2464	5008	,	,		19024	0.2103		0.1968	False		,,,				2504	0.0818				p.A177A		Atlas-SNP	.											.	INHA	30	.	0			c.C531T						PASS	.	C		504,3902	232.6+/-246.1	35,434,1734	84.0	78.0	80.0		531	-11.0	0.5	2	dbSNP_121	80	1757,6843	317.9+/-313.4	179,1399,2722	no	coding-synonymous	INHA	NM_002191.3		214,1833,4456	TT,TC,CC		20.4302,11.4389,17.3843		177/367	220439678	2261,10745	2203	4300	6503	SO:0001819	synonymous_variant	3623	exon2			CTGGGCCGTGCTG		CCDS2444.1	2q35	2013-09-19			ENSG00000123999	ENSG00000123999			6065	protein-coding gene	gene with protein product		147380				3345731	Standard	NM_002191		Approved		uc002vmk.2	P05111	OTTHUMG00000059237	ENST00000243786.2:c.531C>T	2.37:g.220439678C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	119	65	0.546219	NM_002191	A8K8H5	Silent	SNP	ENST00000243786.2	37	CCDS2444.1																																																																																			C|0.826;T|0.174	0.174	strong		0.672	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1		
BRPF3	27154	hgsc.bcm.edu	37	6	36185759	36185759	+	Missense_Mutation	SNP	A	A	G	rs145016452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:36185759A>G	ENST00000357641.6	+	9	3308	c.3055A>G	c.(3055-3057)Agt>Ggt	p.S1019G	BRPF3_ENST00000339717.7_Missense_Mutation_p.S749G|BRPF3_ENST00000543502.1_Missense_Mutation_p.S749G|BRPF3_ENST00000534400.1_Missense_Mutation_p.S1019G|BRPF3_ENST00000443324.2_Intron|BRPF3_ENST00000534694.1_Intron	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	1019					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						TTTGGGTCTCAGTGGTGGACT	0.498													A|||	4	0.000798722	0.0008	0.0029	5008	,	,		21651	0.0		0.001	False		,,,				2504	0.0				p.S1019G		Atlas-SNP	.											.	BRPF3	93	.	0			c.A3055G						PASS	.	A	GLY/SER	3,4403	6.2+/-15.9	0,3,2200	183.0	146.0	159.0		3055	3.4	1.0	6	dbSNP_134	159	27,8573	19.2+/-60.6	0,27,4273	yes	missense	BRPF3	NM_015695.2	56	0,30,6473	GG,GA,AA		0.314,0.0681,0.2307	benign	1019/1206	36185759	30,12976	2203	4300	6503	SO:0001583	missense	27154	exon9			GGTCTCAGTGGTG	AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.3055A>G	6.37:g.36185759A>G	ENSP00000350267:p.Ser1019Gly	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	243	99	0.407407	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Missense_Mutation	SNP	ENST00000357641.6	37	CCDS34437.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	14.27	2.484908	0.44147	6.81E-4	0.00314	ENSG00000096070	ENST00000357641;ENST00000339717;ENST00000543502;ENST00000534400	T;T;T;T	0.19394	2.27;2.28;2.28;2.15	6.05	3.37	0.38596	.	0.607803	0.19087	N	0.123094	T	0.05135	0.0137	N	0.24115	0.695	0.80722	D	1	B;B	0.17465	0.022;0.0	B;B	0.18263	0.021;0.0	T	0.17501	-1.0367	10	0.25751	T	0.34	.	8.2232	0.31554	0.7652:0.0:0.2348:0.0	.	749;1019	Q17RB6;Q9ULD4	.;BRPF3_HUMAN	G	1019;749;749;1019	ENSP00000350267:S1019G;ENSP00000345419:S749G;ENSP00000445352:S749G;ENSP00000436504:S1019G	ENSP00000345419:S749G	S	+	1	0	BRPF3	36293737	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.870000	0.39529	1.116000	0.41820	0.528000	0.53228	AGT	A|0.997;G|0.003	0.003	strong		0.498	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695	
GDPD4	220032	hgsc.bcm.edu	37	11	76954833	76954833	+	Missense_Mutation	SNP	G	G	A	rs11237146	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:76954833G>A	ENST00000376217.2	-	12	1397	c.1147C>T	c.(1147-1149)Cat>Tat	p.H383Y	GDPD4_ENST00000315938.4_Missense_Mutation_p.H383Y			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	383	GP-PDE.		H -> Y (in dbSNP:rs11237146).		glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						CGGCCCACATGCTGAAAACCA	0.408													G|||	1213	0.242212	0.0257	0.1873	5008	,	,		15839	0.256		0.3608	False		,,,				2504	0.4376				p.H383Y		Atlas-SNP	.											.	GDPD4	49	.	0			c.C1147T						PASS	.	G	TYR/HIS	361,4039	183.3+/-210.9	23,315,1862	97.0	92.0	93.0		1147	3.3	0.9	11	dbSNP_120	93	2937,5647	459.0+/-364.8	484,1969,1839	yes	missense	GDPD4	NM_182833.1	83	507,2284,3701	AA,AG,GG		34.2148,8.2045,25.4005	possibly-damaging	383/521	76954833	3298,9686	2200	4292	6492	SO:0001583	missense	220032	exon12			CCACATGCTGAAA	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1147C>T	11.37:g.76954833G>A	ENSP00000365390:p.His383Tyr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	77	27	0.350649	NM_182833	Q7Z5B0	Missense_Mutation	SNP	ENST00000376217.2	37		475	0.2174908424908425	13	0.026422764227642278	74	0.20441988950276244	130	0.22727272727272727	258	0.3403693931398417	G	14.59	2.581875	0.46006	0.082045	0.342148	ENSG00000178795	ENST00000376217;ENST00000315938	T;T	0.10960	2.82;2.82	4.27	3.34	0.38264	.	0.431410	0.27433	N	0.019382	T	0.00012	0.0000	M	0.62723	1.935	0.36466	P	0.13304899999999997	P	0.52316	0.952	P	0.47075	0.536	T	0.51196	-0.8736	9	0.36615	T	0.2	-1.6698	10.9709	0.47438	0.0:0.0:0.8135:0.1865	rs11237146;rs17824232;rs58856218;rs11237146	383	Q6W3E5-2	.	Y	383	ENSP00000365390:H383Y;ENSP00000320815:H383Y	ENSP00000320815:H383Y	H	-	1	0	GDPD4	76632481	1.000000	0.71417	0.883000	0.34634	0.439000	0.31926	3.107000	0.50329	1.112000	0.41740	0.655000	0.94253	CAT	G|0.770;A|0.229	0.229	strong		0.408	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
TTN	7273	hgsc.bcm.edu	37	2	179587130	179587130	+	Missense_Mutation	SNP	C	C	G	rs12693166	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179587130C>G	ENST00000591111.1	-	75	21657	c.21433G>C	c.(21433-21435)Gat>Cat	p.D7145H	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.D6218H|TTN_ENST00000589042.1_Missense_Mutation_p.D7462H|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.1_ENST00000590024.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12720	Ig-like 53.			D -> H (in Ref. 1; CAA62189). {ECO:0000305}.	adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGATTTTCATCGTCTCTTAAA	0.408													C|||	1237	0.247005	0.202	0.1844	5008	,	,		19242	0.4375		0.1581	False		,,,				2504	0.2474				p.D7462H		Atlas-SNP	.											.	TTN	18412	.	0			c.G22384C						PASS	.	C	HIS/ASP,,,	623,3087		52,519,1284	61.0	59.0	60.0		18652,,,	6.2	1.0	2	dbSNP_121	60	1252,6966		97,1058,2954	yes	missense,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	81,,,	149,1577,4238	GG,GC,CC		15.2349,16.7925,15.7193	probably-damaging,,,	6218/33424,,,	179587130	1875,10053	1855	4109	5964	SO:0001583	missense	7273	exon77			TTTCATCGTCTCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.21433G>C	2.37:g.179587130C>G	ENSP00000465570:p.Asp7145His	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		513	0.2348901098901099	98	0.1991869918699187	55	0.15193370165745856	244	0.42657342657342656	116	0.15303430079155672	C	13.78	2.338338	0.41398	0.167925	0.152349	ENSG00000155657	ENST00000342992	T	0.73897	-0.79	6.16	6.16	0.99307	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.76328	2.33	0.09310	P	1.0	D	0.89917	1.0	D	0.81914	0.995	T	0.06698	-1.0812	8	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	rs12693166;rs56624981;rs12693166	7145	Q8WZ42	TITIN_HUMAN	H	6218	ENSP00000343764:D6218H	ENSP00000343764:D6218H	D	-	1	0	TTN	179295375	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.786000	0.85741	2.937000	0.99478	0.650000	0.86243	GAT	C|0.765;G|0.235	0.235	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KIAA0586	9786	hgsc.bcm.edu	37	14	58943847	58943847	+	Silent	SNP	G	G	A	rs373201020		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:58943847G>A	ENST00000556134.1	+	21	3061	c.2787G>A	c.(2785-2787)gaG>gaA	p.E929E	KIAA0586_ENST00000354386.6_Silent_p.E997E|KIAA0586_ENST00000423743.3_Silent_p.E900E|KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000261244.5_Silent_p.E868E	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	929					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCAGGGTAGAGCAAGAAATAA	0.388																																					p.E997E		Atlas-SNP	.											.	KIAA0586	180	.	0			c.G2991A						PASS	.	G		0,3666		0,0,1833	84.0	73.0	76.0		2604	-0.5	1.0	14		76	1,8181		0,1,4090	no	coding-synonymous	KIAA0586	NM_014749.3		0,1,5923	AA,AG,GG		0.0122,0.0,0.0084		868/1473	58943847	1,11847	1833	4091	5924	SO:0001819	synonymous_variant	9786	exon22			GGTAGAGCAAGAA	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.2787G>A	14.37:g.58943847G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Silent	SNP	ENST00000556134.1	37	CCDS58321.1																																																																																			.	.	weak		0.388	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749	
IQCF6	440956	hgsc.bcm.edu	37	3	51812952	51812952	+	Missense_Mutation	SNP	C	C	T	rs11130296|rs35586812	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:51812952C>T	ENST00000398780.3	-	1	57	c.11G>A	c.(10-12)cGg>cAg	p.R4Q		NM_001143833.3	NP_001137305.2	A8MYZ5	IQCF6_HUMAN	IQ motif containing F6	4										breast(1)	1						CAGTAACGTCCGGCGCACCAT	0.547													C|||	663	0.132388	0.0098	0.1787	5008	,	,		20767	0.0764		0.2873	False		,,,				2504	0.1636				p.R4Q		Atlas-SNP	.											.	IQCF6	2	.	0			c.G11A						PASS	.	C	GLN/ARG	64,1320		0,64,628	19.0	17.0	18.0		11	1.8	0.8	3	dbSNP_120	18	853,2329		111,631,849	yes	missense	IQCF6	NM_001143833.3	43	111,695,1477	TT,TC,CC		26.807,4.6243,20.0832	probably-damaging	4/108	51812952	917,3649	692	1591	2283	SO:0001583	missense	440956	exon2			AACGTCCGGCGCA		CCDS54590.1	3p21.1	2008-10-16			ENSG00000214686	ENSG00000214686			35158	protein-coding gene	gene with protein product							Standard	NM_001143833		Approved		uc021wyv.1	A8MYZ5		ENST00000398780.3:c.11G>A	3.37:g.51812952C>T	ENSP00000381760:p.Arg4Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_001143833		Missense_Mutation	SNP	ENST00000398780.3	37	CCDS54590.1	355	0.16254578754578755	5	0.01016260162601626	70	0.19337016574585636	53	0.09265734265734266	227	0.2994722955145119	C	15.40	2.822346	0.50739	0.046243	0.26807	ENSG00000214686	ENST00000398780	T	0.57595	0.39	4.9	1.79	0.24919	.	.	.	.	.	T	0.00012	0.0000	M	0.66939	2.045	0.43267	P	0.004781999999999953	B	0.02656	0.0	B	0.06405	0.002	T	0.09596	-1.0667	8	0.66056	D	0.02	-28.0976	6.1264	0.20182	0.0:0.6293:0.0:0.3707	rs11130296;rs60424990;rs11130296	27	A8MYZ5	IQCF6_HUMAN	Q	4	ENSP00000381760:R4Q	ENSP00000381760:R4Q	R	-	2	0	IQCF6	51787992	0.081000	0.21417	0.777000	0.31699	0.943000	0.58893	0.131000	0.15870	0.156000	0.19299	0.655000	0.94253	CGG	C|0.837;T|0.163	0.163	strong		0.547	IQCF6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496643	
LYPD3	27076	hgsc.bcm.edu	37	19	43965594	43965594	+	Missense_Mutation	SNP	C	C	T	rs149095976	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:43965594C>T	ENST00000244333.3	-	5	1038	c.950G>A	c.(949-951)gGg>gAg	p.G317E		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	317					cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				CTGCTGGGGCCCCCCTTTTGC	0.622													C|||	4	0.000798722	0.0	0.0014	5008	,	,		16242	0.0		0.003	False		,,,				2504	0.0				p.G317E		Atlas-SNP	.											.	LYPD3	24	.	0			c.G950A						PASS	.	C	GLU/GLY	2,4404	4.2+/-10.8	0,2,2201	43.0	46.0	45.0		950	0.4	0.0	19	dbSNP_134	45	11,8589	8.4+/-32.0	0,11,4289	yes	missense	LYPD3	NM_014400.2	98	0,13,6490	TT,TC,CC		0.1279,0.0454,0.1	benign	317/347	43965594	13,12993	2203	4300	6503	SO:0001583	missense	27076	exon5			TGGGGCCCCCCTT	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.950G>A	19.37:g.43965594C>T	ENSP00000244333:p.Gly317Glu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	48	0.466019	NM_014400	Q9UJ74	Missense_Mutation	SNP	ENST00000244333.3	37	CCDS12620.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.42	1.345506	0.24426	4.54E-4	0.001279	ENSG00000124466	ENST00000244333;ENST00000377995	T	0.12879	2.64	5.13	0.434	0.16539	.	0.666605	0.13500	N	0.383293	T	0.07098	0.0180	N	0.14661	0.345	0.09310	N	1	B	0.20368	0.044	B	0.18263	0.021	T	0.31336	-0.9947	10	0.72032	D	0.01	.	4.5533	0.12124	0.3053:0.5268:0.0:0.1679	.	317	O95274	LYPD3_HUMAN	E	317;265	ENSP00000244333:G317E	ENSP00000244333:G317E	G	-	2	0	LYPD3	48657434	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.324000	0.07986	0.018000	0.15052	-0.143000	0.13931	GGG	C|0.999;T|0.001	0.001	strong		0.622	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400	
DSC3	1825	hgsc.bcm.edu	37	18	28586964	28586964	+	Silent	SNP	A	A	G	rs1313586	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:28586964A>G	ENST00000360428.4	-	12	1877	c.1797T>C	c.(1795-1797)ccT>ccC	p.P599P	DSC3_ENST00000434452.1_Silent_p.P599P	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	599	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.P599P(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			CAGGTTCATCAGGATCAACAG	0.368													G|||	2976	0.594249	0.8268	0.3833	5008	,	,		14919	0.7917		0.3121	False		,,,				2504	0.5164				p.P599P		Atlas-SNP	.											DSC3,NS,carcinoma,0,1	DSC3	225	1	1	Substitution - coding silent(1)	stomach(1)	c.T1797C						PASS	.	G	,	3339,1067	388.6+/-327.0	1275,789,139	118.0	113.0	115.0		1797,1797	-10.2	0.0	18	dbSNP_87	115	2767,5833	679.2+/-403.5	434,1899,1967	no	coding-synonymous,coding-synonymous	DSC3	NM_001941.3,NM_024423.2	,	1709,2688,2106	GG,GA,AA		32.1744,24.217,46.9476	,	599/897,599/840	28586964	6106,6900	2203	4300	6503	SO:0001819	synonymous_variant	1825	exon12			TTCATCAGGATCA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.1797T>C	18.37:g.28586964A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_024423	A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	37	CCDS32810.1																																																																																			A|0.478;G|0.521	0.521	strong		0.368	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
ART3	419	hgsc.bcm.edu	37	4	77033590	77033590	+	Missense_Mutation	SNP	C	C	T	rs1128864	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:77033590C>T	ENST00000355810.4	+	12	1207	c.1088C>T	c.(1087-1089)tCg>tTg	p.S363L	ART3_ENST00000341029.5_Missense_Mutation_p.S341L|ART3_ENST00000349321.3_Missense_Mutation_p.S352L	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	363			S -> L (in dbSNP:rs1128864). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|stomach(1)	16			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TCTGCATCCTCGGGCAAACTG	0.418													C|||	2423	0.483826	0.7035	0.4035	5008	,	,		18814	0.5982		0.2346	False		,,,				2504	0.3824				p.S363L		Atlas-SNP	.											.	ART3	34	.	0			c.C1088T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER	2772,1634	661.0+/-400.8	881,1010,312	224.0	200.0	208.0		1088,1022,1055	2.5	0.8	4	dbSNP_86	208	2074,6526	359.3+/-331.5	247,1580,2473	yes	missense,missense,missense	ART3	NM_001130016.1,NM_001130017.1,NM_001179.4	145,145,145	1128,2590,2785	TT,TC,CC		24.1163,37.0858,37.2597	benign,benign,benign	363/390,341/368,352/379	77033590	4846,8160	2203	4300	6503	SO:0001583	missense	419	exon12			CATCCTCGGGCAA	X95827	CCDS3575.1, CCDS47079.1, CCDS47080.1	4q21.1	2008-05-15			ENSG00000156219	ENSG00000156219			725	protein-coding gene	gene with protein product		603086				9119374	Standard	NM_001130017		Approved		uc003hjo.3	Q13508	OTTHUMG00000130110	ENST00000355810.4:c.1088C>T	4.37:g.77033590C>T	ENSP00000348064:p.Ser363Leu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	46	0.422018	NM_001130016	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Missense_Mutation	SNP	ENST00000355810.4	37	CCDS47079.1	1031	0.47206959706959706	360	0.7317073170731707	139	0.3839779005524862	347	0.6066433566433567	185	0.24406332453825857	C	6.004	0.369077	0.11352	0.629142	0.241163	ENSG00000156219	ENST00000341029;ENST00000355810;ENST00000349321	T;T;T	0.11604	2.98;2.8;2.76	5.6	2.52	0.30459	.	1.300790	0.05293	N	0.521410	T	0.00012	0.0000	N	0.15975	0.35	0.58432	P	4.000000000004E-6	B;B;B;B	0.18013	0.015;0.004;0.007;0.025	B;B;B;B	0.11329	0.003;0.003;0.006;0.006	T	0.38672	-0.9650	9	0.37606	T	0.19	-13.2551	11.0566	0.47922	0.0:0.8105:0.0:0.1895	rs1128864;rs3186179;rs17001419;rs17845165;rs17857971;rs52804370;rs60186754;rs1128864	312;363;352;341	D6RBN3;Q13508;Q13508-3;Q13508-2	.;NAR3_HUMAN;.;.	L	341;363;352	ENSP00000343843:S341L;ENSP00000348064:S363L;ENSP00000304313:S352L	ENSP00000343843:S341L	S	+	2	0	ART3	77252614	0.275000	0.24201	0.818000	0.32626	0.003000	0.03518	0.816000	0.27267	0.741000	0.32674	-1.175000	0.01729	TCG	C|0.574;T|0.426	0.426	strong		0.418	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179	
ACTB	60	hgsc.bcm.edu	37	7	5567677	5567677	+	Silent	SNP	C	C	T	rs11546939	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:5567677C>T	ENST00000331789.5	-	5	1133	c.942G>A	c.(940-942)caG>caA	p.Q314Q	AC006483.1_ENST00000579427.1_RNA|ACTB_ENST00000464611.1_5'UTR	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	314					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		TGATCTCCTTCTGCATCCTGT	0.587													C|||	136	0.0271565	0.0386	0.0303	5008	,	,		24087	0.0149		0.0278	False		,,,				2504	0.0215				p.Q314Q		Atlas-SNP	.											.	ACTB	45	.	0			c.G942A						PASS	.	C		175,4231	112.5+/-150.6	2,171,2030	139.0	133.0	135.0		942	5.6	1.0	7	dbSNP_120	135	281,8319	105.4+/-166.3	3,275,4022	no	coding-synonymous	ACTB	NM_001101.3		5,446,6052	TT,TC,CC		3.2674,3.9719,3.5061		314/376	5567677	456,12550	2203	4300	6503	SO:0001819	synonymous_variant	60	exon5			CTCCTTCTGCATC	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.942G>A	7.37:g.5567677C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	126	50	0.396825	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Silent	SNP	ENST00000331789.5	37	CCDS5341.1																																																																																			C|0.965;T|0.035	0.035	strong		0.587	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101	
MUC17	140453	hgsc.bcm.edu	37	7	100684149	100684149	+	Missense_Mutation	SNP	G	G	A	rs201455288	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100684149G>A	ENST00000306151.4	+	3	9516	c.9452G>A	c.(9451-9453)gGt>gAt	p.G3151D		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3151	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					ACTTCTGAAGGTACCAGCATG	0.478													G|||	22	0.00439297	0.0	0.0216	5008	,	,		26584	0.0		0.006	False		,,,				2504	0.001				p.G3151D		Atlas-SNP	.											MUC17,colon,carcinoma,+1,1	MUC17	804	1	0			c.G9452A						PASS	.						297.0	303.0	301.0					7																	100684149		2203	4300	6503	SO:0001583	missense	140453	exon3			CTGAAGGTACCAG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.9452G>A	7.37:g.100684149G>A	ENSP00000302716:p.Gly3151Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	55	13	0.236364	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	5.194	0.221285	0.09863	.	.	ENSG00000169876	ENST00000306151	T	0.02085	4.46	0.905	-0.156	0.13391	.	.	.	.	.	T	0.02267	0.0070	N	0.14661	0.345	0.09310	N	1	D	0.55385	0.971	P	0.54629	0.757	T	0.46512	-0.9186	9	0.22706	T	0.39	.	2.5626	0.04775	0.2435:0.3118:0.4446:0.0	.	3151	Q685J3	MUC17_HUMAN	D	3151	ENSP00000302716:G3151D	ENSP00000302716:G3151D	G	+	2	0	MUC17	100470869	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-3.513000	0.00446	-0.037000	0.13646	0.121000	0.15741	GGT	G|0.997;A|0.003	0.003	strong		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
C6orf195	154386	hgsc.bcm.edu	37	6	2623930	2623930	+	Missense_Mutation	SNP	G	G	A	rs9503233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:2623930G>A	ENST00000296847.3	-	3	650	c.127C>T	c.(127-129)Ccc>Tcc	p.P43S		NM_152554.2	NP_689767.2	Q96MT4	CF195_HUMAN	chromosome 6 open reading frame 195	43			P -> S (in dbSNP:rs9503233). {ECO:0000269|PubMed:15489334}.							cervix(1)|endometrium(1)|lung(2)|skin(1)	5	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				CTTAGAGCGGGCCTGGCTCCT	0.622													G|||	542	0.108227	0.0832	0.1009	5008	,	,		18472	0.0337		0.2107	False		,,,				2504	0.1186				p.P43S		Atlas-SNP	.											.	C6orf195	10	.	0			c.C127T						PASS	.	G	SER/PRO	406,3626		22,362,1632	45.0	53.0	50.0		127	-2.5	0.0	6	dbSNP_119	50	1691,6643		167,1357,2643	yes	missense	C6orf195	NM_152554.2	74	189,1719,4275	AA,AG,GG		20.2904,10.0694,16.9578	benign	43/128	2623930	2097,10269	2016	4167	6183	SO:0001583	missense	154386	exon3			GAGCGGGCCTGGC	AK056496	CCDS43416.1	6p25.2	2008-10-21			ENSG00000164385	ENSG00000164385			21600	protein-coding gene	gene with protein product							Standard	NM_152554		Approved	FLJ31934, bA145H9.2	uc003mtw.2	Q96MT4	OTTHUMG00000014122	ENST00000296847.3:c.127C>T	6.37:g.2623930G>A	ENSP00000296847:p.Pro43Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_152554	Q3SY08|Q3SY09|Q3SY10|Q5TAW4	Missense_Mutation	SNP	ENST00000296847.3	37	CCDS43416.1	255	0.11675824175824176	46	0.09349593495934959	34	0.09392265193370165	19	0.033216783216783216	156	0.20580474934036938	G	5.756	0.323829	0.10900	0.100694	0.202904	ENSG00000164385	ENST00000296847	T	0.39787	1.06	3.16	-2.52	0.06346	.	.	.	.	.	T	0.07279	0.0184	N	0.08118	0	0.80722	P	0.0	B	0.24823	0.112	B	0.17979	0.02	T	0.24512	-1.0158	8	0.87932	D	0	.	6.064	0.19854	0.1051:0.0:0.2675:0.6274	rs9503233;rs52796843;rs60879034;rs9503233	43	Q96MT4	CF195_HUMAN	S	43	ENSP00000296847:P43S	ENSP00000296847:P43S	P	-	1	0	C6orf195	2568929	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.080000	0.11339	-0.617000	0.05664	-0.229000	0.12294	CCC	G|0.875;A|0.125	0.125	strong		0.622	C6orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039633.1	NM_152554	
ASB5	140458	hgsc.bcm.edu	37	4	177142611	177142611	+	Silent	SNP	G	G	A	rs35698542	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:177142611G>A	ENST00000296525.3	-	4	638	c.525C>T	c.(523-525)gcC>gcT	p.A175A	ASB5_ENST00000512254.1_Silent_p.A122A|ASB5_ENST00000511879.1_5'Flank	NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	175					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.A175A(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		CTTTACTGGCGGCCTCATGCG	0.498													G|||	65	0.0129792	0.0008	0.0288	5008	,	,		20188	0.0		0.0388	False		,,,				2504	0.0051				p.A175A		Atlas-SNP	.											ASB5,NS,carcinoma,0,1	ASB5	88	1	1	Substitution - coding silent(1)	prostate(1)	c.C525T						PASS	.	G		24,4382	30.8+/-60.4	0,24,2179	117.0	118.0	118.0		525	-6.8	1.0	4	dbSNP_126	118	266,8334	102.9+/-164.1	4,258,4038	no	coding-synonymous	ASB5	NM_080874.3		4,282,6217	AA,AG,GG		3.093,0.5447,2.2297		175/330	177142611	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	140458	exon4			ACTGGCGGCCTCA	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"""Ankyrin repeat domain containing"""	17180	protein-coding gene	gene with protein product		615050	"""ankyrin repeat and SOCS box-containing 5"""				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.525C>T	4.37:g.177142611G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	145	79	0.544828	NM_080874	Q8N7B5	Silent	SNP	ENST00000296525.3	37	CCDS3827.1																																																																																			G|0.978;A|0.022	0.022	strong		0.498	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1		
DFNB31	25861	hgsc.bcm.edu	37	9	117166246	117166246	+	Missense_Mutation	SNP	A	A	G	rs2274159	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:117166246A>G	ENST00000362057.3	-	10	2516	c.2348T>C	c.(2347-2349)gTg>gCg	p.V783A	DFNB31_ENST00000374059.3_Missense_Mutation_p.V432A|DFNB31_ENST00000265134.6_Missense_Mutation_p.V400A	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	783			V -> A (in dbSNP:rs2274159). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTTGGTGGACACCGACTGCCT	0.652													G|||	2035	0.40635	0.1906	0.4914	5008	,	,		17404	0.4742		0.4732	False		,,,				2504	0.499				p.V783A		Atlas-SNP	.											.	DFNB31	100	.	0			c.T2348C						PASS	.	G	ALA/VAL,ALA/VAL,ALA/VAL	1043,3363	725.1+/-409.6	140,763,1300	106.0	89.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1199,2345,2348	1.1	0.0	9	dbSNP_100	95	4299,4301	577.4+/-390.6	1060,2179,1061	yes	missense,missense,missense	DFNB31	NM_001083885.2,NM_001173425.1,NM_015404.3	64,64,64	1200,2942,2361	GG,GA,AA		49.9884,23.6723,41.0734	benign,benign,benign	400/525,782/907,783/908	117166246	5342,7664	2203	4300	6503	SO:0001583	missense	25861	exon10			GTGGACACCGACT	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"""whirlin"""	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.2348T>C	9.37:g.117166246A>G	ENSP00000354623:p.Val783Ala	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_015404	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Missense_Mutation	SNP	ENST00000362057.3	37	CCDS6806.1	919	0.4207875457875458	96	0.1951219512195122	184	0.5082872928176796	283	0.49475524475524474	356	0.46965699208443273	G	0.104	-1.148602	0.01714	0.236723	0.499884	ENSG00000095397	ENST00000265134;ENST00000374059;ENST00000362057	T;T;T	0.07216	4.13;4.11;3.21	5.03	1.09	0.20402	.	0.302854	0.27518	N	0.019005	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.42327	-0.9458	9	0.02654	T	1	-0.8461	6.5105	0.22218	0.4212:0.1714:0.4074:0.0	rs2274159;rs58704054;rs2274159	782;783;432	B9EGE6;Q9P202;Q9P202-4	.;WHRN_HUMAN;.	A	400;432;783	ENSP00000265134:V400A;ENSP00000363172:V432A;ENSP00000354623:V783A	ENSP00000265134:V400A	V	-	2	0	DFNB31	116206067	0.000000	0.05858	0.000000	0.03702	0.624000	0.37722	0.845000	0.27668	-0.048000	0.13401	-0.355000	0.07637	GTG	A|0.575;G|0.425	0.425	strong		0.652	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798764	55798764	+	Silent	SNP	T	T	C	rs61889975	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55798764T>C	ENST00000313555.1	+	1	870	c.870T>C	c.(868-870)taT>taC	p.Y290Y		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					CAATAATTTATAGTTTCAGAA	0.318													T|||	192	0.0383387	0.0129	0.0403	5008	,	,		18974	0.001		0.0934	False		,,,				2504	0.0532				p.Y290Y		Atlas-SNP	.											.	OR5AS1	121	.	0			c.T870C						PASS	.	T		110,4292	84.4+/-122.9	3,104,2094	48.0	50.0	49.0		870	-3.2	0.1	11	dbSNP_129	49	690,7900	169.6+/-220.9	34,622,3639	no	coding-synonymous	OR5AS1	NM_001001921.1		37,726,5733	CC,CT,TT		8.0326,2.4989,6.1576		290/325	55798764	800,12192	2201	4295	6496	SO:0001819	synonymous_variant	219447	exon1			AATTTATAGTTTC	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.870T>C	11.37:g.55798764T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_001001921	Q6IFB8	Silent	SNP	ENST00000313555.1	37	CCDS31516.1																																																																																			T|0.948;C|0.052	0.052	strong		0.318	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
GLTSCR1	29998	hgsc.bcm.edu	37	19	48183771	48183771	+	Silent	SNP	C	C	T	rs1035938	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48183771C>T	ENST00000396720.3	+	6	1538	c.1344C>T	c.(1342-1344)agC>agT	p.S448S	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	448										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		AACCCATGAGCGTCCACCTCC	0.711													C|||	1734	0.346246	0.4781	0.317	5008	,	,		12067	0.3214		0.2545	False		,,,				2504	0.3088				p.S448S		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.C1344T	GRCh37	CM052883	GLTSCR1	M	rs1035938	PASS	.	C		1510,2392		286,938,727	19.0	24.0	22.0		1344	-2.1	1.0	19	dbSNP_86	22	1980,6080		270,1440,2320	yes	coding-synonymous	GLTSCR1	NM_015711.3		556,2378,3047	TT,TC,CC		24.5658,38.6981,29.1757		448/1561	48183771	3490,8472	1951	4030	5981	SO:0001819	synonymous_variant	29998	exon6			CATGAGCGTCCAC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.1344C>T	19.37:g.48183771C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	37	CCDS46134.1																																																																																			C|0.666;T|0.334	0.334	strong		0.711	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711	
LPO	4025	hgsc.bcm.edu	37	17	56326521	56326521	+	Silent	SNP	G	G	C	rs8178329	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:56326521G>C	ENST00000262290.4	+	5	742	c.426G>C	c.(424-426)acG>acC	p.T142T	LPO_ENST00000543544.1_Silent_p.T83T|LPO_ENST00000582328.1_Silent_p.T59T|LPO_ENST00000421678.2_Silent_p.T59T	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	142					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						GCACCATTACGGGAGACTGCA	0.637													G|||	223	0.0445288	0.0492	0.0476	5008	,	,		15543	0.0		0.0795	False		,,,				2504	0.046				p.T142T		Atlas-SNP	.											.	LPO	73	.	0			c.G426C						PASS	.	G	,	264,4142	149.2+/-183.4	13,238,1952	73.0	63.0	66.0		177,426	-10.7	0.0	17	dbSNP_117	66	741,7859	178.5+/-227.8	29,683,3588	no	coding-synonymous,coding-synonymous	LPO	NM_001160102.1,NM_006151.2	,	42,921,5540	CC,CG,GG		8.6163,5.9918,7.7272	,	59/630,142/713	56326521	1005,12001	2203	4300	6503	SO:0001819	synonymous_variant	4025	exon5			CATTACGGGAGAC	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.426G>C	17.37:g.56326521G>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Silent	SNP	ENST00000262290.4	37	CCDS32689.1																																																																																			G|0.937;C|0.063	0.063	strong		0.637	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1		
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807897	18807897	+	Missense_Mutation	SNP	C	C	G	rs2992755	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18807897C>G	ENST00000400664.1	+	1	474	c.422C>G	c.(421-423)cCc>cGc	p.P141R		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	141			P -> R (in dbSNP:rs2992755).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CCTTGCTGCCCCAGCCAGGAA	0.637													G|||	3240	0.646965	0.5688	0.7147	5008	,	,		17597	0.8958		0.6113	False		,,,				2504	0.4847				p.P141R		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C422G						PASS	.	G	ARG/PRO	2422,1644		728,966,339	29.0	35.0	33.0		422	1.2	0.0	1	dbSNP_101	33	5311,3069		1682,1947,561	yes	missense	KLHDC7A	NM_152375.2	103	2410,2913,900	GG,GC,CC		36.6229,40.4329,37.8676	benign	141/778	18807897	7733,4713	2033	4190	6223	SO:0001583	missense	127707	exon1			GCTGCCCCAGCCA	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.422C>G	1.37:g.18807897C>G	ENSP00000383505:p.Pro141Arg	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	1523	0.6973443223443223	286	0.5813008130081301	247	0.6823204419889503	523	0.9143356643356644	467	0.6160949868073878	G	10.17	1.275745	0.23307	0.595671	0.633771	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.72725	-0.68	5.16	1.18	0.20946	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24799	-1.0150	8	0.22706	T	0.39	.	5.2538	0.15537	0.3998:0.1386:0.4616:0.0	rs2992755	141	Q5VTJ3	KLD7A_HUMAN	R	141;78	ENSP00000383505:P141R	ENSP00000383505:P141R	P	+	2	0	KLHDC7A	18680484	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.040000	0.12104	-0.168000	0.10853	-0.946000	0.02672	CCC	C|0.324;G|0.676	0.676	strong		0.637	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
TMC2	117532	hgsc.bcm.edu	37	20	2552884	2552884	+	Missense_Mutation	SNP	A	A	G	rs11908093	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2552884A>G	ENST00000358864.1	+	5	629	c.614A>G	c.(613-615)cAa>cGa	p.Q205R		NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	205	Arg/Asp/Glu/Lys-rich (highly charged).		Q -> R (in dbSNP:rs11908093).		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						AAAGGCAAGCAACTATATGCC	0.493													G|||	508	0.101438	0.2277	0.0418	5008	,	,		17373	0.0288		0.1024	False		,,,				2504	0.047				p.Q205R		Atlas-SNP	.											.	TMC2	121	.	0			c.A614G						PASS	.	G	ARG/GLN	919,3487	738.3+/-411.0	94,731,1378	118.0	111.0	113.0		614	0.1	0.0	20	dbSNP_120	113	896,7704	778.3+/-407.7	46,804,3450	yes	missense	TMC2	NM_080751.2	43	140,1535,4828	GG,GA,AA		10.4186,20.8579,13.9551	benign	205/907	2552884	1815,11191	2203	4300	6503	SO:0001583	missense	117532	exon5			GCAAGCAACTATA	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"""transmembrane, cochlear expressed, 2"""	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.614A>G	20.37:g.2552884A>G	ENSP00000351732:p.Gln205Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	92	31	0.336957	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	37	CCDS13029.2	200	0.09157509157509157	96	0.1951219512195122	16	0.04419889502762431	8	0.013986013986013986	80	0.10554089709762533	G	0.025	-1.379991	0.01204	0.208579	0.104186	ENSG00000149488	ENST00000358864	T	0.52983	0.64	5.16	0.0895	0.14460	.	0.309974	0.33691	N	0.004644	T	0.00012	0.0000	N	0.00972	-1.085	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.0	T	0.25779	-1.0122	9	0.10111	T	0.7	-0.6606	4.9191	0.13860	0.5438:0.1682:0.288:0.0	rs11908093;rs52819631;rs56539404;rs59606490;rs11908093	36;37;205;205	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	R	205	ENSP00000351732:Q205R	ENSP00000351732:Q205R	Q	+	2	0	TMC2	2500884	1.000000	0.71417	0.013000	0.15412	0.314000	0.28054	2.903000	0.48711	-0.010000	0.14271	-1.082000	0.02213	CAA	A|0.878;G|0.122	0.122	strong		0.493	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
SMG6	23293	hgsc.bcm.edu	37	17	2203025	2203025	+	Missense_Mutation	SNP	T	T	G	rs1885987	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:2203025T>G	ENST00000263073.6	-	2	1072	c.1022A>C	c.(1021-1023)aAc>aCc	p.N341T	SMG6_ENST00000544865.1_Missense_Mutation_p.N310T	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	341	Interaction with telomeric DNA.		N -> T (in dbSNP:rs1885987). {ECO:0000269|PubMed:12676087, ECO:0000269|PubMed:9872452}.		gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TTTAGCACTGTTTTTCTGCTC	0.473													T|||	1149	0.229433	0.0469	0.438	5008	,	,		19830	0.1716		0.3827	False		,,,				2504	0.2301				p.N341T	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											SMG6,NS,carcinoma,+1,1	SMG6	97	1	0			c.A1022C						PASS	.	T	THR/ASN,THR/ASN	414,3992	201.5+/-224.5	24,366,1813	132.0	115.0	121.0		929,1022	2.3	1.0	17	dbSNP_92	121	3325,5275	492.6+/-373.4	640,2045,1615	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	65,65	664,2411,3428	GG,GT,TT		38.6628,9.3963,28.7483	benign,benign	310/1389,341/1420	2203025	3739,9267	2203	4300	6503	SO:0001583	missense	23293	exon2			GCACTGTTTTTCT	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.1022A>C	17.37:g.2203025T>G	ENSP00000263073:p.Asn341Thr	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	278	132	0.47482	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	569	0.26053113553113555	30	0.06097560975609756	162	0.44751381215469616	99	0.17307692307692307	278	0.36675461741424803	T	8.744	0.919722	0.17982	0.093963	0.386628	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.07908	3.15;3.15	5.35	2.3	0.28687	.	0.902977	0.09887	N	0.742929	T	0.00012	0.0000	N	0.08118	0	0.46279	P	0.0010320000000000329	B	0.06786	0.001	B	0.09377	0.004	T	0.43426	-0.9392	9	0.21540	T	0.41	-2.6793	10.1357	0.42706	0.0:0.7847:0.0:0.2153	rs1885987;rs56772408;rs1885987	341	Q86US8	EST1A_HUMAN	T	341;310	ENSP00000263073:N341T;ENSP00000443920:N310T	ENSP00000263073:N341T	N	-	2	0	SMG6	2149775	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	3.302000	0.51849	0.252000	0.21531	-0.146000	0.13790	AAC	T|0.736;G|0.264	0.264	strong		0.473	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
FXR2	9513	hgsc.bcm.edu	37	17	7497292	7497292	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7497292G>A	ENST00000250113.7	-	11	1385	c.1051C>T	c.(1051-1053)Cga>Tga	p.R351*	FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	351						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		ATGTTCTCTCGGGTGCCAACA	0.502																																					p.R351X		Atlas-SNP	.											FXR2,NS,carcinoma,+2,1	FXR2	44	1	0			c.C1051T						scavenged	.						68.0	67.0	67.0					17																	7497292		1905	4118	6023	SO:0001587	stop_gained	9513	exon11			TCTCTCGGGTGCC	U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.1051C>T	17.37:g.7497292G>A	ENSP00000250113:p.Arg351*	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	73	3	0.0410959	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Nonsense_Mutation	SNP	ENST00000250113.7	37	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	G	39	7.571676	0.98365	.	.	ENSG00000129245	ENST00000250113	.	.	.	5.52	4.54	0.55810	.	0.209774	0.41605	D	0.000848	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-0.0119	11.2846	0.49214	0.0:0.0:0.6676:0.3324	.	.	.	.	X	351	.	ENSP00000250113:R351X	R	-	1	2	FXR2	7438017	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	3.669000	0.54561	1.555000	0.49500	0.563000	0.77884	CGA	.	.	none		0.502	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1		
VRK2	7444	hgsc.bcm.edu	37	2	58316814	58316814	+	Missense_Mutation	SNP	A	A	G	rs1051061	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:58316814A>G	ENST00000435505.2	+	10	1244	c.499A>G	c.(499-501)Ata>Gta	p.I167V	VRK2_ENST00000417641.2_Missense_Mutation_p.I167V|VRK2_ENST00000340157.4_Missense_Mutation_p.I167V|VRK2_ENST00000440705.2_Missense_Mutation_p.I144V|VRK2_ENST00000412104.2_Missense_Mutation_p.I167V			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	167	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		I -> V (in dbSNP:rs1051061). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16704422, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9344656}.		cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						TCATGGTGATATAAAAGCAGC	0.279													A|||	1512	0.301917	0.0651	0.3703	5008	,	,		18572	0.4117		0.3966	False		,,,				2504	0.363				p.I167V		Atlas-SNP	.											.	VRK2	46	.	0			c.A499G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	469,3937	220.7+/-238.1	42,385,1776	77.0	83.0	81.0		499,499,430,499,499	5.7	1.0	2	dbSNP_86	81	3473,5113	505.6+/-376.4	708,2057,1528	yes	missense,missense,missense,missense,missense	VRK2	NM_001130480.2,NM_001130481.2,NM_001130482.2,NM_001130483.2,NM_006296.5	29,29,29,29,29	750,2442,3304	GG,GA,AA		40.4496,10.6446,30.3417	benign,benign,benign,benign,benign	167/509,167/509,144/486,167/397,167/509	58316814	3942,9050	2203	4293	6496	SO:0001583	missense	7444	exon7			GGTGATATAAAAG	AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.499A>G	2.37:g.58316814A>G	ENSP00000408002:p.Ile167Val	Somatic	293	1	0.00341297		WXS	Illumina HiSeq	Phase_I	429	202	0.470862	NM_001130480	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Missense_Mutation	SNP	ENST00000435505.2	37	CCDS1859.1	742	0.33974358974358976	45	0.09146341463414634	146	0.40331491712707185	247	0.4318181818181818	304	0.40105540897097625	A	20.6	4.021668	0.75275	0.106446	0.404496	ENSG00000028116	ENST00000435505;ENST00000417641;ENST00000423109;ENST00000412104;ENST00000340157;ENST00000394539;ENST00000440705	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65	5.67	5.67	0.87782	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.75615	2.305	0.24250	P	0.99532689	D;D;P;P	0.69078	0.988;0.997;0.927;0.544	D;D;P;P	0.80764	0.994;0.99;0.727;0.569	T	0.43956	-0.9359	9	0.49607	T	0.09	-24.1341	14.8794	0.70519	1.0:0.0:0.0:0.0	rs1051061;rs17845825;rs17858793;rs52838242;rs1051061	171;167;167;167	B7Z2X1;Q86Y07-2;Q86Y07-5;Q86Y07	.;.;.;VRK2_HUMAN	V	167;167;171;167;167;167;144	ENSP00000408002:I167V;ENSP00000402375:I167V;ENSP00000404156:I167V;ENSP00000342381:I167V;ENSP00000398323:I144V	ENSP00000342381:I167V	I	+	1	0	VRK2	58170318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.798000	0.55522	2.150000	0.67090	0.477000	0.44152	ATA	A|0.683;G|0.317	0.317	strong		0.279	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296	
GRIN2B	2904	hgsc.bcm.edu	37	12	14019128	14019128	+	Silent	SNP	C	C	T	rs34315573	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:14019128C>T	ENST00000609686.1	-	2	224	c.15G>A	c.(13-15)gcG>gcA	p.A5A		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	5					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AACAGCACTCCGCTCTGGGCT	0.522													C|||	292	0.0583067	0.0023	0.0202	5008	,	,		19998	0.1399		0.0368	False		,,,				2504	0.0992				p.A5A		Atlas-SNP	.											GRIN2B,NS,carcinoma,-1,1	GRIN2B	303	1	0			c.G15A						PASS	.	C		40,4366	40.8+/-73.8	0,40,2163	38.0	42.0	41.0		15	-5.8	0.9	12	dbSNP_126	41	278,8320	104.4+/-165.4	2,274,4023	no	coding-synonymous	GRIN2B	NM_000834.3		2,314,6186	TT,TC,CC		3.2333,0.9079,2.4454		5/1485	14019128	318,12686	2203	4299	6502	SO:0001819	synonymous_variant	2904	exon2			GCACTCCGCTCTG		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.15G>A	12.37:g.14019128C>T		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			C|0.972;T|0.028	0.028	strong		0.522	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
ERICH3	127254	hgsc.bcm.edu	37	1	75078423	75078423	+	Missense_Mutation	SNP	C	C	T	rs150709786	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:75078423C>T	ENST00000326665.5	-	9	1289	c.1071G>A	c.(1069-1071)atG>atA	p.M357I	RP4-612J11.1_ENST00000416017.1_RNA|C1orf173_ENST00000420661.2_Missense_Mutation_p.M160I	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		357										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TGTTCACCTGCATCCCATTCA	0.423													C|||	7	0.00139776	0.0	0.0014	5008	,	,		18608	0.0		0.001	False		,,,				2504	0.0051				p.M357I		Atlas-SNP	.											C1orf173,NS,lymphoid_neoplasm,-2,1	C1orf173	380	1	0			c.G1071A						PASS	.	C	ILE/MET	2,4404	4.2+/-10.8	0,2,2201	99.0	95.0	97.0		1071	-6.5	0.9	1	dbSNP_134	97	14,8586	9.8+/-36.6	0,14,4286	yes	missense	C1orf173	NM_001002912.4	10	0,16,6487	TT,TC,CC		0.1628,0.0454,0.123	benign	357/1531	75078423	16,12990	2203	4300	6503	SO:0001583	missense	127254	exon9			CACCTGCATCCCA																												ENST00000326665.5:c.1071G>A	1.37:g.75078423C>T	ENSP00000322609:p.Met357Ile	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	11.61	1.691085	0.30052	4.54E-4	0.001628	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.16073	2.87;2.37	5.63	-6.51	0.01878	.	.	.	.	.	T	0.01287	0.0042	N	0.17474	0.49	0.30304	N	0.789207	B;B	0.16396	0.001;0.017	B;B	0.12837	0.003;0.008	T	0.33854	-0.9852	9	0.02654	T	1	-0.6393	1.2823	0.02043	0.2419:0.2826:0.0937:0.3818	.	160;357	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	I	357;160	ENSP00000322609:M357I;ENSP00000398581:M160I	ENSP00000322609:M357I	M	-	3	0	C1orf173	74851011	0.009000	0.17119	0.871000	0.34182	0.994000	0.84299	-0.981000	0.03766	-1.229000	0.02564	-0.140000	0.14226	ATG	C|0.999;T|0.001	0.001	strong		0.423	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
UBR5	51366	hgsc.bcm.edu	37	8	103307533	103307533	+	Silent	SNP	T	T	C	rs9650002	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:103307533T>C	ENST00000520539.1	-	31	4563	c.3957A>G	c.(3955-3957)ttA>ttG	p.L1319L	UBR5_ENST00000521922.1_Silent_p.L1313L|UBR5_ENST00000220959.4_Silent_p.L1319L|UBR5_ENST00000519528.1_5'Flank	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	1319					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TTGGAGGCTCTAAATCATGAT	0.373													T|||	263	0.052516	0.0416	0.0548	5008	,	,		20572	0.005		0.1481	False		,,,				2504	0.0164				p.L1319L	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.A3957G						PASS	.	T		275,4131	152.5+/-186.2	7,261,1935	59.0	55.0	56.0		3957	5.7	1.0	8	dbSNP_119	56	1298,7302	252.6+/-278.6	103,1092,3105	no	coding-synonymous	UBR5	NM_015902.5		110,1353,5040	CC,CT,TT		15.093,6.2415,12.0944		1319/2800	103307533	1573,11433	2203	4300	6503	SO:0001819	synonymous_variant	51366	exon31			AGGCTCTAAATCA	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.3957A>G	8.37:g.103307533T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	37	CCDS34933.1																																																																																			T|0.905;C|0.095	0.095	strong		0.373	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	
FEZ2	9637	hgsc.bcm.edu	37	2	36782886	36782886	+	Missense_Mutation	SNP	G	G	A	rs848642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:36782886G>A	ENST00000405912.3	-	7	984	c.985C>T	c.(985-987)Cgt>Tgt	p.R329C	FEZ2_ENST00000487919.1_5'UTR|FEZ2_ENST00000379245.4_Missense_Mutation_p.R356C|FEZ2_ENST00000305852.7_Missense_Mutation_p.R158C	NM_005102.2	NP_005093.2	Q9UHY8	FEZ2_HUMAN	fasciculation and elongation protein zeta 2 (zygin II)	329			R -> C (in dbSNP:rs848642).		axon guidance (GO:0007411)|nervous system development (GO:0007399)|signal transduction (GO:0007165)					breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	7		all_hematologic(82;0.21)				TTCATGGCACGAAGAACTGCA	0.338													G|||	2721	0.543331	0.5938	0.5159	5008	,	,		16726	0.7768		0.2893	False		,,,				2504	0.5153				p.R356C		Atlas-SNP	.											.	FEZ2	13	.	0			c.C1066T						PASS	.	G	CYS/ARG,CYS/ARG	2058,1562		593,872,345	57.0	54.0	55.0		985,1066	2.9	0.8	2	dbSNP_86	55	2544,5588		425,1694,1947	yes	missense,missense	FEZ2	NM_005102.2,NM_001042548.1	180,180	1018,2566,2292	AA,AG,GG		31.2838,43.1492,39.1593	benign,benign	329/354,356/381	36782886	4602,7150	1810	4066	5876	SO:0001583	missense	9637	exon8			TGGCACGAAGAAC	U60061	CCDS46257.1, CCDS46258.1	2p21	2008-05-15			ENSG00000171055	ENSG00000171055			3660	protein-coding gene	gene with protein product		604826				9096408	Standard	NM_005102		Approved		uc002rpg.2	Q9UHY8	OTTHUMG00000152148	ENST00000405912.3:c.985C>T	2.37:g.36782886G>A	ENSP00000385112:p.Arg329Cys	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	163	88	0.539877	NM_001042548	Q5EBN3|Q76LN0|Q99690	Missense_Mutation	SNP	ENST00000405912.3	37	CCDS46257.1	1145|1145	0.5242673992673993|0.5242673992673993	293|293	0.5955284552845529|0.5955284552845529	177|177	0.4889502762430939|0.4889502762430939	457|457	0.798951048951049|0.798951048951049	218|218	0.287598944591029|0.287598944591029	G|G	12.93|12.93	2.086010|2.086010	0.36855|0.36855	0.568508|0.568508	0.312838|0.312838	ENSG00000171055|ENSG00000171055	ENST00000379245;ENST00000305852;ENST00000405912;ENST00000357996|ENST00000441005	T;T;T;T|.	0.46451|.	4.13;0.9;1.87;0.87|.	5.59|5.59	2.87|2.87	0.33458|0.33458	.|.	0.293474|.	0.42682|.	N|.	0.000676|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38175|0.38175	1.15|1.15	0.26331|0.26331	P|P	0.9775287|0.9775287	P;B;B|.	0.48503|.	0.911;0.019;0.001|.	P;B;B|.	0.44860|.	0.462;0.004;0.001|.	T|T	0.20505|0.20505	-1.0273|-1.0273	9|4	0.38643|.	T|.	0.18|.	-25.4913|-25.4913	10.2732|10.2732	0.43495|0.43495	0.2133:0.0:0.7867:0.0|0.2133:0.0:0.7867:0.0	rs848642;rs1132438;rs3178168;rs3193188;rs3770804;rs11545206;rs17417887;rs52807216;rs58380546;rs848642|rs848642;rs1132438;rs3178168;rs3193188;rs3770804;rs11545206;rs17417887;rs52807216;rs58380546;rs848642	329;356;158|.	Q9UHY8;Q9UHY8-2;Q7Z674|.	FEZ2_HUMAN;.;.|.	C|L	356;158;329;228|158	ENSP00000368547:R356C;ENSP00000305843:R158C;ENSP00000385112:R329C;ENSP00000350685:R228C|.	ENSP00000305843:R158C|.	R|S	-|-	1|2	0|0	FEZ2|FEZ2	36636390|36636390	0.999000|0.999000	0.42202|0.42202	0.820000|0.820000	0.32676|0.32676	0.852000|0.852000	0.48524|0.48524	1.855000|1.855000	0.39378|0.39378	0.334000|0.334000	0.23590|0.23590	-0.759000|-0.759000	0.03464|0.03464	CGT|TCG	G|0.476;T|0.006	.	strong		0.338	FEZ2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325432.1		
KCNA6	3742	hgsc.bcm.edu	37	12	4920767	4920767	+	Silent	SNP	T	T	C	rs34642709	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:4920767T>C	ENST00000280684.3	+	1	2426	c.1560T>C	c.(1558-1560)taT>taC	p.Y520Y	RP11-234B24.4_ENST00000542988.1_lincRNA|KCNA6_ENST00000433855.1_Silent_p.Y520Y			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	520					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	ATCGGGCCTATGCAGAGAAAA	0.577										HNSCC(72;0.22)			T|||	67	0.0133786	0.0015	0.0043	5008	,	,		20418	0.0		0.0189	False		,,,				2504	0.044				p.Y520Y		Atlas-SNP	.											.	KCNA6	122	.	0			c.T1560C						PASS	.	T		7,4399	12.9+/-30.5	0,7,2196	55.0	59.0	58.0		1560	1.4	0.1	12	dbSNP_126	58	154,8446	72.6+/-135.2	2,150,4148	no	coding-synonymous	KCNA6	NM_002235.3		2,157,6344	CC,CT,TT		1.7907,0.1589,1.2379		520/530	4920767	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	3742	exon1			GGCCTATGCAGAG	X17622	CCDS8534.1	12p13	2014-06-12						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6225	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 96"""	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.1560T>C	12.37:g.4920767T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_002235		Silent	SNP	ENST00000280684.3	37	CCDS8534.1																																																																																			T|0.987;C|0.013	0.013	strong		0.577	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235	
JAG1	182	hgsc.bcm.edu	37	20	10625624	10625624	+	Missense_Mutation	SNP	C	C	T	rs147809756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:10625624C>T	ENST00000254958.5	-	18	2746	c.2231G>A	c.(2230-2232)cGa>cAa	p.R744Q	JAG1_ENST00000423891.2_Missense_Mutation_p.R585Q|JAG1_ENST00000488480.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	744	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						GCTACTGTTTCGGGCTATAAA	0.567									Alagille Syndrome				C|||	5	0.000998403	0.0	0.0029	5008	,	,		16903	0.0		0.002	False		,,,				2504	0.001				p.R744Q		Atlas-SNP	.											JAG1_ENST00000254958,NS,malignant_melanoma,-1,6	JAG1	213	6	0			c.G2231A						scavenged	.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	149.0	156.0	154.0		2231	6.1	1.0	20	dbSNP_134	154	9,8591	7.1+/-27.0	0,9,4291	yes	missense	JAG1	NM_000214.2	43	0,10,6493	TT,TC,CC		0.1047,0.0227,0.0769	possibly-damaging	744/1219	10625624	10,12996	2203	4300	6503	SO:0001583	missense	182	exon18	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CTGTTTCGGGCTA	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2231G>A	20.37:g.10625624C>T	ENSP00000254958:p.Arg744Gln	Somatic	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	116	63	0.543103	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	37	CCDS13112.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	18.43	3.623272	0.66901	2.27E-4	0.001047	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.87256	-2.23;-2.23	6.07	6.07	0.98685	Epidermal growth factor-like, type 3 (1);	0.047287	0.85682	D	0.000000	D	0.83294	0.5223	L	0.49778	1.585	0.58432	D	0.999995	P	0.36768	0.569	B	0.26614	0.071	T	0.80915	-0.1169	10	0.29301	T	0.29	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	744	P78504	JAG1_HUMAN	Q	744;585	ENSP00000254958:R744Q;ENSP00000389519:R585Q	ENSP00000254958:R744Q	R	-	2	0	JAG1	10573624	0.994000	0.37717	0.999000	0.59377	0.872000	0.50106	4.742000	0.62103	2.884000	0.98904	0.655000	0.94253	CGA	C|0.999;T|0.001	0.001	strong		0.567	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
ZNF705A	440077	hgsc.bcm.edu	37	12	8329676	8329676	+	Missense_Mutation	SNP	C	C	T	rs10743252	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:8329676C>T	ENST00000359286.4	+	5	489	c.400C>T	c.(400-402)Cgt>Tgt	p.R134C		NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	134			R -> C (in dbSNP:rs10743252).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R134C(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		AATAACTCAGCGTTTGTTAAC	0.388													t|||	2511	0.501398	0.4992	0.4914	5008	,	,		-128	0.5288		0.5845	False		,,,				2504	0.3978				p.R134C		Atlas-SNP	.											ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	1	Substitution - Missense(1)	stomach(1)	c.C400T						PASS	.	T	CYS/ARG	1857,2549		567,723,913	112.0	110.0	111.0		400	-2.7	0.0	12	dbSNP_120	111	4182,4414		1355,1472,1471	no	missense	ZNF705A	NM_001004328.2	180	1922,2195,2384	TT,TC,CC		48.6505,42.1471,46.4467	benign	134/301	8329676	6039,6963	2203	4298	6501	SO:0001583	missense	440077	exon5			ACTCAGCGTTTGT	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"""Zinc fingers, C2H2-type"", ""-"""	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.400C>T	12.37:g.8329676C>T	ENSP00000352233:p.Arg134Cys	Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	258	114	0.44186	NM_001004328		Missense_Mutation	SNP	ENST00000359286.4	37	CCDS31737.1	996	0.45604395604395603	179	0.3638211382113821	164	0.4530386740331492	274	0.479020979020979	379	0.5	.	1.048	-0.676742	0.03378	0.421471	0.486505	ENSG00000196946	ENST00000396570;ENST00000359286	T;T	0.08634	3.07;3.07	1.35	-2.7	0.06004	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45220	-0.9276	8	0.56958	D	0.05	.	3.8537	0.08967	0.4174:0.3552:0.0:0.2273	rs10743252;rs61402447	134	Q6ZN79	Z705A_HUMAN	C	134	ENSP00000379816:R134C;ENSP00000352233:R134C	ENSP00000352233:R134C	R	+	1	0	ZNF705A	8220943	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.071000	0.03437	-2.873000	0.00322	-1.619000	0.00793	CGT	C|0.481;T|0.519	0.519	strong		0.388	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328	
TTC27	55622	hgsc.bcm.edu	37	2	32961858	32961858	+	Missense_Mutation	SNP	A	A	G	rs2273660	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:32961858A>G	ENST00000317907.4	+	12	1658	c.1427A>G	c.(1426-1428)tAt>tGt	p.Y476C		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	476			Y -> C (in dbSNP:rs2273660).							breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						GTCATTTGTTATGAAAGAGCC	0.433													A|||	643	0.128395	0.1997	0.111	5008	,	,		15672	0.0923		0.1133	False		,,,				2504	0.0971				p.Y476C		Atlas-SNP	.											.	TTC27	71	.	0			c.A1427G						PASS	.	A	CYS/TYR,CYS/TYR	760,3646	311.6+/-292.2	62,636,1505	105.0	102.0	103.0		1277,1427	5.7	1.0	2	dbSNP_100	103	975,7625	211.5+/-252.1	60,855,3385	yes	missense,missense	TTC27	NM_001193509.1,NM_017735.4	194,194	122,1491,4890	GG,GA,AA		11.3372,17.2492,13.34	probably-damaging,probably-damaging	426/794,476/844	32961858	1735,11271	2203	4300	6503	SO:0001583	missense	55622	exon12			TTTGTTATGAAAG	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"""Tetratricopeptide (TTC) repeat domain containing"""	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1427A>G	2.37:g.32961858A>G	ENSP00000313953:p.Tyr476Cys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	134	70	0.522388	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	276	0.12637362637362637	88	0.17886178861788618	40	0.11049723756906077	68	0.11888111888111888	80	0.10554089709762533	A	21.2	4.106295	0.77096	0.172492	0.113372	ENSG00000018699	ENST00000317907	T	0.28895	1.59	5.7	5.7	0.88788	Tetratricopeptide-like helical (1);	0.266971	0.38164	N	0.001786	T	0.00109	0.0003	L	0.51422	1.61	0.18873	P	0.9999863401	D	0.71674	0.998	P	0.57371	0.819	T	0.01024	-1.1477	9	0.52906	T	0.07	-5.3293	14.9571	0.71124	1.0:0.0:0.0:0.0	rs2273660;rs58045822;rs2273660	476	Q6P3X3	TTC27_HUMAN	C	476	ENSP00000313953:Y476C	ENSP00000313953:Y476C	Y	+	2	0	TTC27	32815362	1.000000	0.71417	0.986000	0.45419	0.960000	0.62799	3.107000	0.50329	2.168000	0.68352	0.533000	0.62120	TAT	A|0.866;G|0.134	0.134	strong		0.433	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735	
ZNF468	90333	hgsc.bcm.edu	37	19	53345321	53345321	+	Silent	SNP	T	T	G	rs8100893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53345321T>G	ENST00000595646.1	-	4	346	c.226A>C	c.(226-228)Aga>Cga	p.R76R	ZNF468_ENST00000243639.4_Missense_Mutation_p.Q115P|ZNF468_ENST00000390651.4_Silent_p.R23R|ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000396409.4_Silent_p.R23R			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	76	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R76R(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		CTTGCTTGTCTGTGCAATGTC	0.398													-|||	888	0.177316	0.0847	0.3401	5008	,	,		21070	0.2153		0.1461	False		,,,				2504	0.18				p.R76R		Atlas-SNP	.											ZNF468,NS,carcinoma,0,1	ZNF468	46	1	1	Substitution - coding silent(1)	stomach(1)	c.A226C						PASS	.	T	,	454,3952		25,404,1774	155.0	146.0	149.0		226,67	1.2	0.0	19	dbSNP_116	149	1275,7325		104,1067,3129	yes	coding-synonymous,coding-synonymous	ZNF468	NM_001008801.1,NM_199132.1	,	129,1471,4903	GG,GT,TT		14.8256,10.3041,13.2939	,	76/523,23/470	53345321	1729,11277	2203	4300	6503	SO:0001819	synonymous_variant	90333	exon4			CTTGTCTGTGCAA	AK023558	CCDS33094.1, CCDS62781.1	19q13.41	2013-01-08				ENSG00000204604		"""Zinc fingers, C2H2-type"", ""-"""	33105	protein-coding gene	gene with protein product						16144304	Standard	NM_001277120		Approved		uc002qaf.3	Q5VIY5		ENST00000595646.1:c.226A>C	19.37:g.53345321T>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	104	60	0.576923	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Silent	SNP	ENST00000595646.1	37	CCDS33094.1																																																																																			T|0.847;G|0.153	0.153	strong		0.398	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801	
PANK1	53354	hgsc.bcm.edu	37	10	91344169	91344169	+	Silent	SNP	G	G	A	rs1063943	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:91344169G>A	ENST00000307534.4	-	7	1946	c.1791C>T	c.(1789-1791)gaC>gaT	p.D597D	PANK1_ENST00000371774.2_Silent_p.D399D|PANK1_ENST00000322191.6_Silent_p.D313D|PANK1_ENST00000342512.3_Silent_p.D372D	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	597					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell periphery (GO:0071944)|clathrin coat (GO:0030118)|cytosol (GO:0005829)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			cervix(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	11						GTCTCTACTTGTCATCAGTCA	0.448													G|||	366	0.0730831	0.1067	0.1023	5008	,	,		16245	0.0198		0.0696	False		,,,				2504	0.0654				p.D597D		Atlas-SNP	.											.	PANK1	35	.	0			c.C1791T						PASS	.	G	,,	467,3939	221.3+/-238.5	33,401,1769	174.0	168.0	170.0		939,1791,1116	-2.5	0.9	10	dbSNP_86	170	922,7678	205.1+/-247.6	39,844,3417	no	coding-synonymous,coding-synonymous,coding-synonymous	PANK1	NM_138316.3,NM_148977.2,NM_148978.2	,,	72,1245,5186	AA,AG,GG		10.7209,10.5992,10.6797	,,	313/315,597/599,372/374	91344169	1389,11617	2203	4300	6503	SO:0001819	synonymous_variant	53354	exon7			CTACTTGTCATCA	AF355198	CCDS7405.1, CCDS7406.1, CCDS31244.1	10q23.31	2008-05-14	2002-11-13	2002-11-15	ENSG00000152782	ENSG00000152782			8598	protein-coding gene	gene with protein product		606160	"""pantothenate kinase"""	PANK		11809413	Standard	NM_148977		Approved	MGC24596, PANK1a, PANK1b	uc001kgp.2	Q8TE04	OTTHUMG00000018718	ENST00000307534.4:c.1791C>T	10.37:g.91344169G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	65	5	0.0769231	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Silent	SNP	ENST00000307534.4	37	CCDS31244.1																																																																																			G|0.912;A|0.088	0.088	strong		0.448	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
MUC2	4583	hgsc.bcm.edu	37	11	1103873	1103873	+	Silent	SNP	C	C	T	rs11245957	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1103873C>T	ENST00000441003.2	+	48	8199	c.8172C>T	c.(8170-8172)taC>taT	p.Y2724Y		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5086					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	AGGTTTCGTACGCCGGCTGCA	0.657													c|||	753	0.150359	0.385	0.072	5008	,	,		14924	0.0357		0.0934	False		,,,				2504	0.0654				p.Y2720Y		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	0			c.C8160T						scavenged	.	T		1236,2906		166,904,1001	26.0	30.0	28.0		8157	-7.6	0.0	11	dbSNP_120	28	693,7677		30,633,3522	no	coding-synonymous	MUC2	NM_002457.2		196,1537,4523	TT,TC,CC		8.2796,29.8407,15.4172		2719/2813	1103873	1929,10583	2071	4185	6256	SO:0001819	synonymous_variant	4583	exon49			TTCGTACGCCGGC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.8172C>T	11.37:g.1103873C>T		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	107	46	0.429907	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.867;T|0.133	0.133	strong		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
PARP15	165631	hgsc.bcm.edu	37	3	122296647	122296647	+	Missense_Mutation	SNP	G	G	A	rs7632426	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:122296647G>A	ENST00000464300.2	+	1	199	c.133G>A	c.(133-135)Gcc>Acc	p.A45T	PARP15_ENST00000483793.1_Missense_Mutation_p.A45T	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	45					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		CGTGCTGCCGGCCGGGAACCG	0.692													G|||	847	0.169129	0.1528	0.0908	5008	,	,		14070	0.2331		0.1193	False		,,,				2504	0.2321				p.A45T		Atlas-SNP	.											.	PARP15	115	.	0			c.G133A						PASS	.						24.0	27.0	26.0					3																	122296647		692	1591	2283	SO:0001583	missense	165631	exon1			CTGCCGGCCGGGA	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.133G>A	3.37:g.122296647G>A	ENSP00000417214:p.Ala45Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	99	61	0.616162	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	325	0.1488095238095238	74	0.15040650406504066	25	0.06906077348066299	125	0.21853146853146854	101	0.13324538258575197	G	9.266	1.044407	0.19748	.	.	ENSG00000173200	ENST00000464300;ENST00000483793	T;T	0.18016	2.63;2.24	2.55	-2.4	0.06583	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	4.000000000004E-6	B;B	0.11235	0.004;0.004	B;B	0.08055	0.003;0.003	T	0.45145	-0.9281	8	0.11182	T	0.66	.	3.3144	0.07027	0.3969:0.0:0.4141:0.189	rs7632426;rs7632426	45;23	C9J7L3;Q460N3	.;PAR15_HUMAN	T	45	ENSP00000417214:A45T;ENSP00000417785:A45T	ENSP00000417214:A45T	A	+	1	0	PARP15	123779337	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.172000	0.09868	-0.618000	0.05656	-0.367000	0.07326	GCC	G|0.835;A|0.165	0.165	strong		0.692	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
LPP	4026	hgsc.bcm.edu	37	3	188327461	188327461	+	Silent	SNP	C	C	T	rs1059380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:188327461C>T	ENST00000312675.4	+	6	1188	c.942C>T	c.(940-942)gaC>gaT	p.D314D	LPP_ENST00000448637.1_Silent_p.D314D|LPP_ENST00000543006.1_Silent_p.D314D|LPP_ENST00000471917.1_3'UTR	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	314	Pro-rich.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		ATGACTCTGACCCTACCTATG	0.562			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								T|||	2937	0.586462	0.7322	0.5591	5008	,	,		18456	0.4355		0.5726	False		,,,				2504	0.5787				p.D314D		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	LPP	72	.	0			c.C942T						PASS	.	T	,,	3082,1324	443.9+/-347.2	1084,914,205	64.0	59.0	61.0		942,,942	-1.5	0.8	3	dbSNP_86	61	5048,3552	516.5+/-378.8	1489,2070,741	no	coding-synonymous,intron,coding-synonymous	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	,,	2573,2984,946	TT,TC,CC		41.3023,30.0499,37.4904	,,	314/613,,314/613	188327461	8130,4876	2203	4300	6503	SO:0001819	synonymous_variant	4026	exon6			CTCTGACCCTACC	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.942C>T	3.37:g.188327461C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	37	CCDS3291.1																																																																																			C|0.403;T|0.597	0.597	strong		0.562	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
PATZ1	23598	hgsc.bcm.edu	37	22	31741067	31741067	+	Silent	SNP	G	G	A	rs714909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:31741067G>A	ENST00000266269.5	-	1	1151	c.522C>T	c.(520-522)ctC>ctT	p.L174L	PATZ1_ENST00000215919.3_Silent_p.L174L|PATZ1_ENST00000405309.3_Silent_p.L174L|PATZ1_ENST00000351933.4_Silent_p.L174L|AC005003.1_ENST00000504184.2_5'Flank	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	174					male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)		EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						GGGGGCGAAAGAGCATTATAT	0.587													G|||	777	0.155152	0.0144	0.2536	5008	,	,		17894	0.121		0.2763	False		,,,				2504	0.1861				p.L174L		Atlas-SNP	.											.	PATZ1	24	.	0			c.C522T						PASS	.	G	,,,	241,4165	136.9+/-172.8	8,225,1970	84.0	92.0	89.0		522,522,522,522	-2.0	1.0	22	dbSNP_86	89	2371,6229	388.6+/-342.6	320,1731,2249	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PATZ1	NM_014323.2,NM_032050.1,NM_032051.1,NM_032052.1	,,,	328,1956,4219	AA,AG,GG		27.5698,5.4698,20.083	,,,	174/688,174/642,174/538,174/538	31741067	2612,10394	2203	4300	6503	SO:0001819	synonymous_variant	23598	exon1			GCGAAAGAGCATT	AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13071	protein-coding gene	gene with protein product		605165	"""zinc finger protein 278"""	ZNF278		10591208, 18241078, 18401526	Standard	NM_014323		Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.522C>T	22.37:g.31741067G>A		Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_032050	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Silent	SNP	ENST00000266269.5	37	CCDS13894.1																																																																																			G|0.818;A|0.182	0.182	strong		0.587	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052	
TBC1D31	93594	hgsc.bcm.edu	37	8	124121798	124121798	+	Silent	SNP	A	A	G	rs16897969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:124121798A>G	ENST00000287380.1	+	10	1464	c.1374A>G	c.(1372-1374)gcA>gcG	p.A458A	TBC1D31_ENST00000521676.1_Silent_p.A335A|TBC1D31_ENST00000378080.2_Silent_p.A353A|TBC1D31_ENST00000309336.3_Silent_p.A458A|TBC1D31_ENST00000327098.5_Silent_p.A458A|TBC1D31_ENST00000522420.1_Silent_p.A353A|TBC1D31_ENST00000518805.1_Silent_p.A91A	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	458	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										CTCATGTGGCATTTCTCAACC	0.388													a|||	1459	0.291334	0.3865	0.3588	5008	,	,		15919	0.1538		0.2903	False		,,,				2504	0.2577				p.A458A		Atlas-SNP	.											.	WDR67	97	.	0			c.A1374G						PASS	.	G	,	1633,2773	500.7+/-364.8	324,985,894	130.0	134.0	132.0		1374,1374	-10.0	0.6	8	dbSNP_123	132	2570,6030	417.1+/-352.3	363,1844,2093	no	coding-synonymous,coding-synonymous	WDR67	NM_001145088.1,NM_145647.3	,	687,2829,2987	GG,GA,AA		29.8837,37.0631,32.3159	,	458/971,458/1067	124121798	4203,8803	2203	4300	6503	SO:0001819	synonymous_variant	93594	exon10			TGTGGCATTTCTC	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.1374A>G	8.37:g.124121798A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	103	38	0.368932	NM_001145088	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Silent	SNP	ENST00000287380.1	37	CCDS6338.1																																																																																			A|0.694;G|0.306	0.306	strong		0.388	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	
PSEN2	5664	hgsc.bcm.edu	37	1	227071525	227071525	+	Silent	SNP	C	C	T	rs1046240	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:227071525C>T	ENST00000366783.3	+	5	697	c.261C>T	c.(259-261)caC>caT	p.H87H	PSEN2_ENST00000366782.1_Silent_p.H120H|PSEN2_ENST00000391872.2_Silent_p.H120H|PSEN2_ENST00000340188.4_Silent_p.H87H|PSEN2_ENST00000422240.2_Silent_p.H87H|PSEN2_ENST00000472139.2_5'Flank	NM_000447.2|NM_012486.2	NP_000438.2|NP_036618.2	P49810	PSN2_HUMAN	presenilin 2	87					amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|brain morphogenesis (GO:0048854)|calcium ion transport (GO:0006816)|cardiac muscle contraction (GO:0060048)|cell fate specification (GO:0001708)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|forebrain development (GO:0030900)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|locomotion (GO:0040011)|lung alveolus development (GO:0048286)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|memory (GO:0007613)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of protein phosphorylation (GO:0001933)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of synaptic plasticity (GO:0048167)|response to hypoxia (GO:0001666)|somitogenesis (GO:0001756)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear inner membrane (GO:0005637)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|urinary_tract(1)	20		Prostate(94;0.0771)				GAGCGAAGCACGTGATCATGC	0.577													C|||	2220	0.443291	0.3646	0.4827	5008	,	,		14633	0.3859		0.5934	False		,,,				2504	0.4264				p.H87H		Atlas-SNP	.											.	PSEN2	55	.	0			c.C261T						PASS	.	C	,	1735,2671	519.3+/-369.9	342,1051,810	132.0	115.0	121.0		261,261	1.5	1.0	1	dbSNP_86	121	4640,3960	602.1+/-394.5	1273,2094,933	no	coding-synonymous,coding-synonymous	PSEN2	NM_000447.2,NM_012486.2	,	1615,3145,1743	TT,TC,CC		46.0465,39.3781,49.0158	,	87/449,87/448	227071525	6375,6631	2203	4300	6503	SO:0001819	synonymous_variant	5664	exon5			GAAGCACGTGATC	BC006365	CCDS1556.1, CCDS44324.1	1q42.13	2014-09-17	2014-02-24		ENSG00000143801	ENSG00000143801			9509	protein-coding gene	gene with protein product		600759	"""Alzheimer disease 4"""	AD4		7638621	Standard	NM_000447		Approved	AD3L, STM2, PS2	uc009xeo.1	P49810	OTTHUMG00000037563	ENST00000366783.3:c.261C>T	1.37:g.227071525C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_012486	A8K8D4|B1AP21|Q96P32	Silent	SNP	ENST00000366783.3	37	CCDS1556.1																																																																																			C|0.514;T|0.486	0.486	strong		0.577	PSEN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091539.1	NM_000447	
CEP55	55165	hgsc.bcm.edu	37	10	95259979	95259979	+	Missense_Mutation	SNP	C	C	G	rs3740370	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:95259979C>G	ENST00000371485.3	+	2	475	c.171C>G	c.(169-171)caC>caG	p.H57Q		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	57			H -> Q (in dbSNP:rs3740370). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16406728}.		establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)				kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				AAGAGAGACACAGACTTTTGG	0.383													C|||	1345	0.26857	0.3238	0.1715	5008	,	,		18932	0.2887		0.2207	False		,,,				2504	0.2914				p.H57Q		Atlas-SNP	.											.	CEP55	35	.	0			c.C171G						PASS	.	C	GLN/HIS,GLN/HIS	1263,3143	430.1+/-342.5	192,879,1132	117.0	128.0	124.0		171,171	-1.1	0.9	10	dbSNP_107	124	1955,6645	345.8+/-325.9	210,1535,2555	yes	missense,missense	CEP55	NM_001127182.1,NM_018131.4	24,24	402,2414,3687	GG,GC,CC		22.7326,28.6655,24.7424	benign,benign	57/465,57/465	95259979	3218,9788	2203	4300	6503	SO:0001583	missense	55165	exon2			GAGACACAGACTT	AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"""cancer/testis antigen 111"""	610000	"""chromosome 10 open reading frame 3"""	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.171C>G	10.37:g.95259979C>G	ENSP00000360540:p.His57Gln	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	26	25	0.961538	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Missense_Mutation	SNP	ENST00000371485.3	37	CCDS7428.1	540	0.24725274725274726	160	0.3252032520325203	64	0.17679558011049723	161	0.28146853146853146	155	0.20448548812664907	C	4.002	-0.002321	0.07819	0.286655	0.227326	ENSG00000138180	ENST00000371485;ENST00000358339	T	0.15952	2.38	5.39	-1.15	0.09709	.	0.772035	0.12648	N	0.450712	T	0.00012	0.0000	L	0.47716	1.5	0.50632	P	1.1099999999997223E-4	B	0.06786	0.001	B	0.04013	0.001	T	0.46386	-0.9195	9	0.10377	T	0.69	-0.1339	2.9794	0.05948	0.2209:0.3378:0.3252:0.1162	rs3740370;rs11546296;rs52801109;rs3740370	57	Q53EZ4	CEP55_HUMAN	Q	57	ENSP00000360540:H57Q	ENSP00000351102:H57Q	H	+	3	2	CEP55	95249969	0.799000	0.28903	0.864000	0.33941	0.730000	0.41778	-0.508000	0.06344	-0.016000	0.14127	-1.121000	0.02013	CAC	C|0.756;G|0.244	0.244	strong		0.383	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131	
SCGB1D2	10647	hgsc.bcm.edu	37	11	62010863	62010863	+	Missense_Mutation	SNP	C	C	T	rs2232950	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62010863C>T	ENST00000244926.3	+	2	256	c.158C>T	c.(157-159)cCg>cTg	p.P53L	RP11-703H8.9_ENST00000529875.1_RNA	NM_006551.3	NP_006542.1	O95969	SG1D2_HUMAN	secretoglobin, family 1D, member 2	53			P -> L (in dbSNP:rs2232950).			extracellular space (GO:0005615)				breast(1)|endometrium(1)|lung(1)	3						GATGCCCCTCCGGAAGCTGTT	0.473													C|||	2359	0.471046	0.2322	0.4251	5008	,	,		20799	0.7927		0.337	False		,,,				2504	0.6329				p.P53L		Atlas-SNP	.											.	SCGB1D2	11	.	0			c.C158T						PASS	.	C	LEU/PRO	1039,3365	382.1+/-324.3	123,793,1286	136.0	126.0	130.0		158	-4.9	0.0	11	dbSNP_98	130	2813,5785	445.9+/-361.1	449,1915,1935	yes	missense	SCGB1D2	NM_006551.3	98	572,2708,3221	TT,TC,CC		32.7169,23.5922,29.6262	possibly-damaging	53/91	62010863	3852,9150	2202	4299	6501	SO:0001583	missense	10647	exon2			CCCCTCCGGAAGC	AJ224172	CCDS8017.1	11q13	2011-12-14			ENSG00000124935	ENSG00000124935		"""Secretoglobins"""	18396	protein-coding gene	gene with protein product	"""prostatein-like lipophilin B"", ""lipophilin B (uteroglobin family member), prostatein-like"""	615061				10066439, 9720917, 22155607	Standard	XM_006718422		Approved	LPHB, LIPB	uc001ntb.3	O95969	OTTHUMG00000167508	ENST00000244926.3:c.158C>T	11.37:g.62010863C>T	ENSP00000244926:p.Pro53Leu	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	244	243	0.995902	NM_006551	Q2M3N9	Missense_Mutation	SNP	ENST00000244926.3	37	CCDS8017.1	1008	0.46153846153846156	129	0.2621951219512195	161	0.4447513812154696	458	0.8006993006993007	260	0.34300791556728233	C	7.537	0.659889	0.14645	0.235922	0.327169	ENSG00000124935	ENST00000244926	T	0.16073	2.37	2.44	-4.87	0.03123	.	3.173700	0.01291	N	0.010028	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.47545	0.897	B	0.39465	0.3	T	0.42599	-0.9442	8	0.27785	T	0.31	.	5.5062	0.16856	0.66:0.2146:0.0:0.1254	rs2232950;rs3855295;rs17542874;rs58183460;rs2232950	53	O95969	SG1D2_HUMAN	L	53	ENSP00000244926:P53L	ENSP00000244926:P53L	P	+	2	0	SCGB1D2	61767439	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-6.574000	0.00061	-1.209000	0.02631	0.313000	0.20887	CCG	C|0.614;N|0.000	.	strong		0.473	SCGB1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394859.1	NM_006551	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048457	33048457	+	Missense_Mutation	SNP	C	C	G	rs1126504|rs386699868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33048457C>G	ENST00000418931.2	+	2	225	c.109C>G	c.(109-111)Ctt>Gtt	p.L37V	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPA1_ENST00000419277.1_5'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.L37V	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	37	Beta-1.		L -> V (in allele DPB1*01:01, allele DPB1*03:01, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*09:01, allele DPB1*09:02, allele DPB1*10:01, allele DPB1*11:01, allele DPB1*11:02, allele DPB1*13:01, allele DPB1*13:02, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*15:01, allele DPB1*16:02, allele DPB1*17:01, allele DPB1*17:02, allele DPB1*18:01, allele DPB1*20:02, allele DPB1*21:01, allele DPB1*21:02, allele DPB1*20:01, allele DPB1*22:02, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*27:01, allele DPB1*29:01, allele DPB1*30:01, allele DPB1*35:01, allele DPB1*36:01, allele DPB1*37:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*50:01, allele DPB1*52:01, allele DPB1*54:01, allele DPB1*55:01, allele DPB1*56:01, allele DPB1*58:01, allele DPB1*66:01, allele DPB1*67:01, allele DPB1*69:01, allele DPB1*70:01, allele DPB1*74:01, allele DPB1*76:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*85:01, allele DPB1*86:01, allele DPB1*87:01, allele DPB1*88:01, allele DPB1*89:01, allele DPB1*90:01, allele DPB1*91:01, allele DPB1*92:01, allele DPB1*93:01 and allele DPB1*98:01; dbSNP:rs1126504).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						AGAGAATTACCTTTTCCAGGG	0.537													.|||	1999	0.399161	0.6641	0.3357	5008	,	,		14928	0.2351		0.2992	False		,,,				2504	0.3579				p.L37V		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.C109G						PASS	.	G	,,VAL/LEU	1586,1434		521,544,445	45.0	51.0	49.0		,,109	-6.8	0.0	6	dbSNP_86	49	968,4440		180,608,1916	yes	utr-5,utr-5,missense	HLA-DPA1,HLA-DPB1	NM_001242524.1,NM_001242525.1,NM_002121.5	,,32	701,1152,2361	GG,GC,CC		17.8994,47.4834,30.3037	,,benign	,,37/259	33048457	2554,5874	1510	2704	4214	SO:0001583	missense	3115	exon2			AATTACCTTTTCC		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.109C>G	6.37:g.33048457C>G	ENSP00000408146:p.Leu37Val	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	59	21	0.355932	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	734	0.3360805860805861	308	0.6260162601626016	103	0.2845303867403315	121	0.21153846153846154	202	0.26649076517150394	c	2.784	-0.252744	0.05829	0.525166	0.178994	ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942	T;T	0.03831	3.79;4.79	3.4	-6.79	0.01715	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);	0.852977	0.09420	N	0.804589	T	0.00666	0.0022	N	0.04655	-0.195	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.48019	-0.9071	9	0.29301	T	0.29	.	14.1409	0.65320	0.0:0.5892:0.2384:0.1724	rs1126504;rs3176933;rs3181572;rs9277343;rs17221087;rs17421612	47;37	Q59GY1;P04440	.;DPB1_HUMAN	V	37	ENSP00000408146:L37V;ENSP00000439674:L37V	ENSP00000389210:L37V	L	+	1	0	HLA-DPB1	33156435	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.681000	0.00105	-3.728000	0.00114	-2.784000	0.00117	CTT	C|0.687;G|0.313	0.313	strong		0.537	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
KLHDC8A	55220	hgsc.bcm.edu	37	1	205308368	205308368	+	Silent	SNP	C	C	T	rs1105387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:205308368C>T	ENST00000367156.3	-	7	1527	c.711G>A	c.(709-711)cgG>cgA	p.R237R	KLHDC8A_ENST00000539253.1_Silent_p.R237R|KLHDC8A_ENST00000367155.3_Silent_p.R237R|KLHDC8A_ENST00000537168.1_Silent_p.R124R|KLHDC8A_ENST00000460687.1_Silent_p.R103R	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	237										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			ACTTGGGCTGCCGGTAGAGGC	0.597													C|||	902	0.180112	0.2247	0.134	5008	,	,		19267	0.0308		0.2813	False		,,,				2504	0.2025				p.R237R		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.G711A						PASS	.	C		984,3422	370.3+/-319.5	108,768,1327	54.0	47.0	49.0		711	3.2	1.0	1	dbSNP_86	49	2558,6042	416.8+/-352.2	346,1866,2088	no	coding-synonymous	KLHDC8A	NM_018203.1		454,2634,3415	TT,TC,CC		29.7442,22.3332,27.2336		237/351	205308368	3542,9464	2203	4300	6503	SO:0001819	synonymous_variant	55220	exon4			GGGCTGCCGGTAG		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.711G>A	1.37:g.205308368C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_018203	B3KU70|Q9NVG5	Silent	SNP	ENST00000367156.3	37	CCDS30985.1																																																																																			C|0.754;T|0.246	0.246	strong		0.597	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203	
RGL3	57139	hgsc.bcm.edu	37	19	11508177	11508177	+	Missense_Mutation	SNP	G	G	A	rs2291516	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11508177G>A	ENST00000380456.3	-	17	1906	c.1843C>T	c.(1843-1845)Cgt>Tgt	p.R615C	RGL3_ENST00000393423.3_Missense_Mutation_p.R621C|RGL3_ENST00000568628.1_5'UTR	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	615	Interaction with HRAS, MRAS and RIT1. {ECO:0000250}.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.		R -> C (in dbSNP:rs2291516).		small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						CGGATGACACGGGCCTCCGAG	0.682													G|||	1054	0.210463	0.0998	0.2983	5008	,	,		14214	0.3482		0.0915	False		,,,				2504	0.2781				p.R621C	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.C1861T						PASS	.	G	CYS/ARG,CYS/ARG	479,3925		29,421,1752	24.0	26.0	26.0		1861,1843	2.3	0.7	19	dbSNP_100	26	869,7721		39,791,3465	yes	missense,missense	RGL3	NM_001161616.1,NM_001035223.2	180,180	68,1212,5217	AA,AG,GG		10.1164,10.8765,10.374	benign,benign	621/717,615/711	11508177	1348,11646	2202	4295	6497	SO:0001583	missense	57139	exon17			TGACACGGGCCTC	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.1843C>T	19.37:g.11508177G>A	ENSP00000369823:p.Arg615Cys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	68	0.586207	NM_001161616	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	37	CCDS32910.1	414	0.18956043956043955	61	0.12398373983739837	91	0.2513812154696133	190	0.3321678321678322	72	0.09498680738786279	G	0.058	-1.230692	0.01518	0.108765	0.101164	ENSG00000205517	ENST00000342684;ENST00000393423;ENST00000380456	T;T	0.17213	2.29;2.29	4.48	2.32	0.28847	Ras-association (3);	0.051745	0.85682	D	0.000000	T	0.00012	0.0000	N	0.03084	-0.415	0.20638	P	0.999877051	B;B;B	0.14805	0.011;0.005;0.004	B;B;B	0.08055	0.003;0.001;0.002	T	0.49031	-0.8981	9	0.17369	T	0.5	.	5.9146	0.19048	0.3018:0.0:0.6982:0.0	rs2291516;rs61295577;rs2291516	615;621;621	Q3MIN7;B5ME84;B7ZL22	RGL3_HUMAN;.;.	C	412;621;615	ENSP00000377075:R621C;ENSP00000369823:R615C	ENSP00000344665:R412C	R	-	1	0	RGL3	11369177	1.000000	0.71417	0.674000	0.29902	0.017000	0.09413	2.240000	0.43088	1.224000	0.43551	0.555000	0.69702	CGT	G|0.856;A|0.144	0.144	strong		0.682	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	
AHNAK	79026	hgsc.bcm.edu	37	11	62299517	62299517	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62299517T>C	ENST00000378024.4	-	5	2646	c.2372A>G	c.(2371-2373)gAt>gGt	p.D791G	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	791					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				AATGCTCACATCAGGAGCAGT	0.507																																					p.D791G		Atlas-SNP	.											AHNAK,caecum,carcinoma,0,1	AHNAK	532	1	0			c.A2372G						scavenged	.						144.0	148.0	147.0					11																	62299517		2202	4299	6501	SO:0001583	missense	79026	exon5			CTCACATCAGGAG	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.2372A>G	11.37:g.62299517T>C	ENSP00000367263:p.Asp791Gly	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	174	2	0.0114943	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	12.73	2.026983	0.35797	.	.	ENSG00000124942	ENST00000378024	T	0.01838	4.61	5.46	5.46	0.80206	.	0.322433	0.21766	N	0.069426	T	0.12347	0.0300	M	0.91818	3.245	0.28945	N	0.890733	P	0.35894	0.526	P	0.51701	0.677	T	0.01401	-1.1364	10	0.32370	T	0.25	-7.6525	10.6905	0.45869	0.0:0.0767:0.0:0.9233	.	791	Q09666	AHNK_HUMAN	G	791	ENSP00000367263:D791G	ENSP00000367263:D791G	D	-	2	0	AHNAK	62056093	0.371000	0.25056	0.743000	0.31040	0.086000	0.17979	2.611000	0.46334	2.085000	0.62840	0.374000	0.22700	GAT	.	.	none		0.507	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
NCKAP5	344148	hgsc.bcm.edu	37	2	133541107	133541107	+	Missense_Mutation	SNP	T	T	A	rs16841277	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:133541107T>A	ENST00000409261.1	-	14	3650	c.3277A>T	c.(3277-3279)Aat>Tat	p.N1093Y	NCKAP5_ENST00000317721.6_Missense_Mutation_p.N1093Y|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1093	Ser-rich.		N -> Y (in dbSNP:rs16841277).							NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						GCGCTATCATTCAATTGTCCT	0.502													T|||	894	0.178514	0.0446	0.1888	5008	,	,		17828	0.251		0.2256	False		,,,				2504	0.229				p.N1093Y		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A3277T						PASS	.	T	TYR/ASN,	280,3714		13,254,1730	256.0	267.0	263.0		3277,	3.0	0.0	2	dbSNP_123	263	1972,6352		218,1536,2408	yes	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	143,	231,1790,4138	AA,AT,TT		23.6905,7.0105,18.2822	benign,	1093/1910,	133541107	2252,10066	1997	4162	6159	SO:0001583	missense	344148	exon14			TATCATTCAATTG	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.3277A>T	2.37:g.133541107T>A	ENSP00000387128:p.Asn1093Tyr	Somatic	278	1	0.00359712		WXS	Illumina HiSeq	Phase_I	277	130	0.469314	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	421	0.19276556776556777	29	0.05894308943089431	60	0.16574585635359115	152	0.26573426573426573	180	0.23746701846965698	T	11.70	1.718039	0.30503	0.070105	0.236905	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.11821	2.74;2.74	5.41	3.01	0.34805	.	0.789167	0.10545	U	0.662156	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	4.000000000004E-6	D	0.54964	0.969	P	0.47827	0.558	T	0.47394	-0.9121	9	0.66056	D	0.02	.	8.714	0.34401	0.0:0.1506:0.0:0.8494	rs16841277;rs16841277	1093	O14513	NCKP5_HUMAN	Y	1093	ENSP00000387128:N1093Y;ENSP00000380603:N1093Y	ENSP00000380603:N1093Y	N	-	1	0	NCKAP5	133257577	0.000000	0.05858	0.007000	0.13788	0.127000	0.20565	0.514000	0.22786	1.086000	0.41228	0.533000	0.62120	AAT	T|0.780;A|0.220	0.220	strong		0.502	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
NAV1	89796	hgsc.bcm.edu	37	1	201777250	201777250	+	Missense_Mutation	SNP	C	C	T	rs2820289	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:201777250C>T	ENST00000367296.4	+	18	4238	c.3818C>T	c.(3817-3819)tCg>tTg	p.S1273L	NAV1_ENST00000367297.4_Missense_Mutation_p.S1265L|NAV1_ENST00000367302.1_Missense_Mutation_p.S1226L|NAV1_ENST00000367295.1_Missense_Mutation_p.S879L|NAV1_ENST00000367300.3_Missense_Mutation_p.S1213L|NAV1_ENST00000295624.6_Missense_Mutation_p.S1270L|IPO9-AS1_ENST00000413035.1_RNA|MIR1231_ENST00000408101.1_RNA	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1273			S -> L (in dbSNP:rs2820289). {ECO:0000269|PubMed:12079279}.		microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						TCCTCCACCTCGTCCTCCGTG	0.562													c|||	429	0.0856629	0.0023	0.1398	5008	,	,		19061	0.1756		0.0636	False		,,,				2504	0.09				p.S1273L		Atlas-SNP	.											NAV1,NS,carcinoma,-1,1	NAV1	143	1	0			c.C3818T						PASS	.		LEU/SER,LEU/SER	79,4327	70.3+/-108.2	1,77,2125	122.0	114.0	117.0		2636,3818	4.4	0.5	1	dbSNP_100	117	632,7968	163.9+/-216.4	23,586,3691	yes	missense,missense	NAV1	NM_001167738.1,NM_020443.4	145,145	24,663,5816	TT,TC,CC		7.3488,1.793,5.4667	probably-damaging,probably-damaging	879/1484,1273/1878	201777250	711,12295	2203	4300	6503	SO:0001583	missense	89796	exon18			CCACCTCGTCCTC	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"""neuron navigator-1"", ""pore membrane and/or filament interacting like protein 3"""	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.3818C>T	1.37:g.201777250C>T	ENSP00000356265:p.Ser1273Leu	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	184	90	0.48913	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	37	CCDS1414.2	205	0.09386446886446886	3	0.006097560975609756	26	0.0718232044198895	118	0.2062937062937063	58	0.07651715039577836	c	24.6	4.545266	0.86022	0.01793	0.073488	ENSG00000134369	ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000367295	D;D;D;D;D;D	0.95821	-3.82;-3.82;-3.82;-3.82;-3.82;-3.82	5.33	4.42	0.53409	.	0.143822	0.47093	D	0.000248	T	0.01489	0.0048	L	0.60455	1.87	0.21553	P	0.999645964	D;P	0.67145	0.996;0.939	P;B	0.56127	0.792;0.406	T	0.00000	-1.2953	9	0.87932	D	0	-5.7771	13.6033	0.62033	0.0:0.9243:0.0:0.0757	rs2820289;rs52802753;rs57412406;rs2820289	879;1270	Q8NEY1-5;Q8NEY1-3	.;.	L	1226;1273;1270;1265;1213;879	ENSP00000356271:S1226L;ENSP00000356265:S1273L;ENSP00000295624:S1270L;ENSP00000356266:S1265L;ENSP00000356269:S1213L;ENSP00000356264:S879L	ENSP00000295624:S1270L	S	+	2	0	NAV1	200043873	1.000000	0.71417	0.489000	0.27452	0.642000	0.38348	4.617000	0.61204	1.257000	0.44085	0.552000	0.68991	TCG	C|0.922;T|0.078	0.078	strong		0.562	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28338423	28338423	+	Silent	SNP	C	C	G	rs55933916	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:28338423C>G	ENST00000284987.5	-	1	409	c.288G>C	c.(286-288)cgG>cgC	p.R96R		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	96					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						AGAGGAACCTCCGGCCGCCCG	0.697													C|||	497	0.0992412	0.1036	0.0951	5008	,	,		14001	0.0069		0.2048	False		,,,				2504	0.0828				p.R96R	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											ADAMTS5,NS,carcinoma,0,1	ADAMTS5	184	1	0			c.G288C						PASS	.	C		490,3904		24,442,1731	55.0	52.0	53.0		288	0.3	1.0	21	dbSNP_129	53	1678,6908		166,1346,2781	no	coding-synonymous	ADAMTS5	NM_007038.3		190,1788,4512	GG,GC,CC		19.5434,11.1516,16.7026		96/931	28338423	2168,10812	2197	4293	6490	SO:0001819	synonymous_variant	11096	exon1			GAACCTCCGGCCG	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.288G>C	21.37:g.28338423C>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	151	82	0.543046	NM_007038	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	37	CCDS13579.1																																																																																			C|0.849;G|0.151	0.151	strong		0.697	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
OR8B2	26595	hgsc.bcm.edu	37	11	124253170	124253170	+	Missense_Mutation	SNP	G	G	A	rs530765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124253170G>A	ENST00000375013.2	-	1	88	c.70C>T	c.(70-72)Cgg>Tgg	p.R24W		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		AGGGGTTGCCGGAACTCTGGA	0.413																																					p.R24W		Atlas-SNP	.											.	OR8B2	42	.	0			c.C70T						PASS	.						191.0	167.0	175.0					11																	124253170		2201	4299	6500	SO:0001583	missense	26595	exon1			GTTGCCGGAACTC	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"""GPCR / Class A : Olfactory receptors"""	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.70C>T	11.37:g.124253170G>A	ENSP00000364152:p.Arg24Trp	Somatic	423	0	0		WXS	Illumina HiSeq	Phase_I	340	73	0.214706	NM_001005468	Q8NGH2	Missense_Mutation	SNP	ENST00000375013.2	37	CCDS31708.1	.	.	.	.	.	.	.	.	.	.	g	10.77	1.443125	0.25987	.	.	ENSG00000204293	ENST00000375013	T	0.02812	4.15	4.2	3.29	0.37713	.	0.233085	0.30686	N	0.009087	T	0.02571	0.0078	L	0.37800	1.135	0.09310	N	1	P	0.34934	0.476	B	0.15870	0.014	T	0.42548	-0.9445	10	0.87932	D	0	.	12.0923	0.53733	0.0858:0.0:0.9142:0.0	rs530765	24	Q96RD0	OR8B2_HUMAN	W	24	ENSP00000364152:R24W	ENSP00000364152:R24W	R	-	1	2	OR8B2	123758380	0.904000	0.30761	0.005000	0.12908	0.017000	0.09413	2.272000	0.43373	1.142000	0.42291	0.400000	0.26472	CGG	G|0.878;A|0.122	0.122	strong		0.413	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468	
SASH1	23328	hgsc.bcm.edu	37	6	148865257	148865257	+	Missense_Mutation	SNP	A	A	G	rs208696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:148865257A>G	ENST00000367467.3	+	18	3126	c.2651A>G	c.(2650-2652)cAa>cGa	p.Q884R		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	884			Q -> R (in dbSNP:rs208696). {ECO:0000269|PubMed:12771949, ECO:0000269|PubMed:9872452, ECO:0000269|Ref.2}.		positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		CCCCTGGAGCAAGACTCTGCT	0.537													G|||	2930	0.585064	0.7035	0.6196	5008	,	,		18519	0.3631		0.5716	False		,,,				2504	0.6431				p.Q884R		Atlas-SNP	.											.	SASH1	123	.	0			c.A2651G						PASS	.	G	ARG/GLN	3011,1395	458.8+/-352.1	1045,921,237	127.0	141.0	136.0		2651	-1.6	0.0	6	dbSNP_79	136	5127,3473	510.5+/-377.5	1532,2063,705	yes	missense	SASH1	NM_015278.3	43	2577,2984,942	GG,GA,AA		40.3837,31.6614,37.4289	benign	884/1248	148865257	8138,4868	2203	4300	6503	SO:0001583	missense	23328	exon18			TGGAGCAAGACTC	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.2651A>G	6.37:g.148865257A>G	ENSP00000356437:p.Gln884Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	93	38	0.408602	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	37	CCDS5212.1	1222	0.5595238095238095	361	0.733739837398374	228	0.6298342541436464	203	0.3548951048951049	430	0.5672823218997362	G	0.007	-1.981279	0.00448	0.683386	0.596163	ENSG00000111961	ENST00000367467;ENST00000535767;ENST00000537769	T	0.34859	1.34	5.21	-1.65	0.08291	.	1.079950	0.07233	N	0.862863	T	0.02267	0.0070	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36261	-0.9755	9	0.02654	T	1	-0.004	6.5061	0.22196	0.4592:0.0:0.4235:0.1173	rs208696;rs209314;rs3734178;rs17715966;rs17846622;rs17859712;rs52829168;rs56933894;rs208696	884	O94885	SASH1_HUMAN	R	884;645;294	ENSP00000356437:Q884R	ENSP00000356437:Q884R	Q	+	2	0	SASH1	148906950	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.382000	0.07408	-0.570000	0.06022	-0.128000	0.14901	CAA	A|0.398;G|0.602	0.602	strong		0.537	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278	
EPX	8288	hgsc.bcm.edu	37	17	56272390	56272390	+	Silent	SNP	A	A	G	rs2240815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:56272390A>G	ENST00000225371.5	+	6	770	c.660A>G	c.(658-660)cgA>cgG	p.R220R		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	220					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	ACCGTGGCCGAGCCCTCATGT	0.607													G|||	2511	0.501398	0.8495	0.2968	5008	,	,		18384	0.244		0.4354	False		,,,				2504	0.5092				p.R220R		Atlas-SNP	.											.	EPX	95	.	0			c.A660G						PASS	.	G		3430,976	365.6+/-317.5	1339,752,112	63.0	59.0	60.0		660	2.2	0.0	17	dbSNP_98	60	3795,4805	613.5+/-396.1	842,2111,1347	no	coding-synonymous	EPX	NM_000502.4		2181,2863,1459	GG,GA,AA		44.1279,22.1516,44.4487		220/716	56272390	7225,5781	2203	4300	6503	SO:0001819	synonymous_variant	8288	exon6			TGGCCGAGCCCTC	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.660A>G	17.37:g.56272390A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	96	55	0.572917	NM_000502	Q4TVP3	Silent	SNP	ENST00000225371.5	37	CCDS11602.1																																																																																			A|0.474;G|0.526	0.526	strong		0.607	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502	
TRIM67	440730	hgsc.bcm.edu	37	1	231339713	231339713	+	Silent	SNP	C	C	T	rs11806609	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:231339713C>T	ENST00000366653.5	+	6	1635	c.1635C>T	c.(1633-1635)gaC>gaT	p.D545D	TRIM67_ENST00000444294.3_Silent_p.D543D|TRIM67_ENST00000449018.3_Silent_p.D483D|TRIM67_ENST00000366652.2_Silent_p.D545D			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	545	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				GCCCCGTGGACGGCTACATCC	0.632													C|||	650	0.129792	0.1536	0.0389	5008	,	,		17177	0.2272		0.0358	False		,,,				2504	0.1585				p.D545D		Atlas-SNP	.											.	TRIM67	160	.	0			c.C1635T						PASS	.	C		560,3596		31,498,1549	49.0	63.0	58.0		1635	-7.7	0.6	1	dbSNP_120	58	302,8092		3,296,3898	no	coding-synonymous	TRIM67	NM_001004342.3		34,794,5447	TT,TC,CC		3.5978,13.4745,6.8685		545/784	231339713	862,11688	2078	4197	6275	SO:0001819	synonymous_variant	440730	exon6			CGTGGACGGCTAC	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"""Tripartite motif containing / Tripartite motif containing"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	31859	protein-coding gene	gene with protein product		610584	"""tripartite motif-containing 67"""				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.1635C>T	1.37:g.231339713C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	55	19	0.345455	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	37	CCDS44333.1																																																																																			C|0.892;T|0.108	0.108	strong		0.632	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342	
GALNT10	55568	hgsc.bcm.edu	37	5	153783753	153783753	+	Silent	SNP	C	C	T	rs6580076	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:153783753C>T	ENST00000297107.6	+	8	1283	c.1146C>T	c.(1144-1146)gcC>gcT	p.A382A	GALNT10_ENST00000377661.2_Silent_p.A320A|GALNT10_ENST00000519544.1_3'UTR|SAP30L-AS1_ENST00000524264.1_RNA|SAP30L-AS1_ENST00000519727.1_RNA|GALNT10_ENST00000377657.3_Silent_p.A53A	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	382	Flexible loop.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.A382A(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			AGGTCCCGGCCGGAGTCAGCC	0.632													C|||	1429	0.285343	0.5083	0.1585	5008	,	,		19763	0.1637		0.1571	False		,,,				2504	0.3313				p.A382A		Atlas-SNP	.											GALNT10,NS,carcinoma,0,1	GALNT10	70	1	1	Substitution - coding silent(1)	stomach(1)	c.C1146T						PASS	.	C		1935,2471	545.4+/-376.8	432,1071,700	63.0	56.0	59.0		1146	-10.8	0.7	5	dbSNP_116	59	1471,7129	279.3+/-293.9	110,1251,2939	no	coding-synonymous	GALNT10	NM_198321.3		542,2322,3639	TT,TC,CC		17.1047,43.9174,26.1879		382/604	153783753	3406,9600	2203	4300	6503	SO:0001819	synonymous_variant	55568	exon8			CCCGGCCGGAGTC	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19873	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 10"""	608043	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"""			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.1146C>T	5.37:g.153783753C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	141	64	0.453901	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Silent	SNP	ENST00000297107.6	37	CCDS4325.1																																																																																			C|0.733;T|0.267	0.267	strong		0.632	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321	
TMEM156	80008	hgsc.bcm.edu	37	4	39000305	39000305	+	Missense_Mutation	SNP	A	A	G	rs11542133	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:39000305A>G	ENST00000381938.3	-	2	420	c.313T>C	c.(313-315)Tct>Cct	p.S105P	TMEM156_ENST00000372489.2_5'UTR	NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156	105			S -> P (in dbSNP:rs11542133). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						TTTCCTTTAGACTCACAAACC	0.343													A|||	1384	0.276358	0.1127	0.2536	5008	,	,		15695	0.4196		0.2843	False		,,,				2504	0.3579				p.S105P		Atlas-SNP	.											.	TMEM156	31	.	0			c.T313C						PASS	.	A	PRO/SER	616,3790	266.2+/-267.1	50,516,1637	69.0	64.0	65.0		313	3.5	1.0	4	dbSNP_120	65	2371,6229	390.9+/-343.5	335,1701,2264	yes	missense	TMEM156	NM_024943.1	74	385,2217,3901	GG,GA,AA		27.5698,13.9809,22.9663	benign	105/297	39000305	2987,10019	2203	4300	6503	SO:0001583	missense	80008	exon2			CTTTAGACTCACA	AK026888	CCDS3448.1	4p14	2008-02-05			ENSG00000121895	ENSG00000121895			26260	protein-coding gene	gene with protein product						12477932	Standard	NM_024943		Approved	FLJ23235	uc003gto.3	Q8N614	OTTHUMG00000128582	ENST00000381938.3:c.313T>C	4.37:g.39000305A>G	ENSP00000371364:p.Ser105Pro	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_024943	Q9H5N9	Missense_Mutation	SNP	ENST00000381938.3	37	CCDS3448.1	616	0.28205128205128205	66	0.13414634146341464	89	0.24585635359116023	246	0.43006993006993005	215	0.2836411609498681	A	11.93	1.785547	0.31593	0.139809	0.275698	ENSG00000121895	ENST00000381938	T	0.37752	1.18	4.73	3.54	0.40534	.	0.090855	0.49305	N	0.000159	T	0.00012	0.0000	L	0.61218	1.895	0.29643	P	0.8445860000000001	B	0.19935	0.04	B	0.23018	0.043	T	0.38929	-0.9638	9	0.52906	T	0.07	-4.5098	6.1953	0.20546	0.8757:0.0:0.1243:0.0	rs11542133;rs17852834;rs52808222;rs58873184;rs11542133	105	Q8N614	TM156_HUMAN	P	105	ENSP00000371364:S105P	ENSP00000371364:S105P	S	-	1	0	TMEM156	38676700	0.989000	0.36119	0.995000	0.50966	0.574000	0.36063	2.110000	0.41873	0.927000	0.37143	0.496000	0.49642	TCT	A|0.747;G|0.253	0.253	strong		0.343	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943	
MOGS	7841	hgsc.bcm.edu	37	2	74690378	74690378	+	Missense_Mutation	SNP	C	C	T	rs1063588	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:74690378C>T	ENST00000233616.4	-	3	877	c.715G>A	c.(715-717)Gac>Aac	p.D239N	MOGS_ENST00000535045.1_3'UTR|MOGS_ENST00000452063.2_Missense_Mutation_p.D133N|MOGS_ENST00000462443.1_5'UTR|MOGS_ENST00000409065.1_Intron	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	239			D -> N (in dbSNP:rs1063588). {ECO:0000269|PubMed:7635146}.		cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						AAGCGGAAGTCACCAAGTTCA	0.527													C|||	2598	0.51877	0.8086	0.3127	5008	,	,		20904	0.8214		0.1581	False		,,,				2504	0.3323				p.D239N		Atlas-SNP	.											.	MOGS	58	.	0			c.G715A						PASS	.	C	ASN/ASP,ASN/ASP	2661,1287		899,863,212	116.0	119.0	118.0		397,715	4.8	1.0	2	dbSNP_86	118	1138,7210		82,974,3118	yes	missense,missense	MOGS	NM_001146158.1,NM_006302.2	23,23	981,1837,3330	TT,TC,CC		13.632,32.5988,30.8962	benign,benign	133/732,239/838	74690378	3799,8497	1974	4174	6148	SO:0001583	missense	7841	exon3			GGAAGTCACCAAG	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"""glucosidase I"", ""processing A-glucosidase I"""	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.715G>A	2.37:g.74690378C>T	ENSP00000233616:p.Asp239Asn	Somatic	292	1	0.00342466		WXS	Illumina HiSeq	Phase_I	433	280	0.646651	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	37	CCDS42700.1	1064	0.48717948717948717	387	0.7865853658536586	94	0.2596685082872928	469	0.8199300699300699	114	0.1503957783641161	C	12.59	1.983034	0.34942	0.674012	0.13632	ENSG00000115275	ENST00000233616;ENST00000452063;ENST00000448666;ENST00000414701	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	4.85	4.85	0.62838	.	0.243944	0.41194	D	0.000925	T	0.00012	0.0000	N	0.17800	0.525	0.09310	P	1.0	P	0.36616	0.561	B	0.36666	0.23	T	0.07558	-1.0766	9	0.21014	T	0.42	-20.9003	13.3472	0.60580	0.0:1.0:0.0:0.0	rs1063588;rs3204621;rs58978224;rs1063588	239	Q13724	MOGS_HUMAN	N	239;133;133;120	ENSP00000233616:D239N;ENSP00000388201:D133N;ENSP00000410992:D133N;ENSP00000396298:D120N	ENSP00000233616:D239N	D	-	1	0	MOGS	74543886	0.998000	0.40836	1.000000	0.80357	0.950000	0.60333	0.994000	0.29693	2.504000	0.84457	0.655000	0.94253	GAC	C|0.531;T|0.469	0.469	strong		0.527	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302	
FREM1	158326	hgsc.bcm.edu	37	9	14775859	14775859	+	Silent	SNP	G	G	A	rs10733289	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:14775859G>A	ENST00000380880.3	-	25	5568	c.4785C>T	c.(4783-4785)gcC>gcT	p.A1595A	FREM1_ENST00000422223.2_Silent_p.A1595A|FREM1_ENST00000380881.4_Silent_p.A1596A|FREM1_ENST00000486223.1_5'UTR|FREM1_ENST00000380894.1_Silent_p.A131A			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1595					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TCCCATCTGTGGCCATGAAAG	0.463													G|||	2087	0.416733	0.2905	0.4366	5008	,	,		19227	0.3294		0.5845	False		,,,				2504	0.4908				p.A1595A		Atlas-SNP	.											.	FREM1	261	.	0			c.C4785T						PASS	.	G	,	1401,2495		259,883,806	109.0	102.0	104.0		393,4785	4.9	1.0	9	dbSNP_120	104	4939,3377		1465,2009,684	no	coding-synonymous,coding-synonymous	FREM1	NM_001177704.1,NM_144966.5	,	1724,2892,1490	AA,AG,GG		40.6085,35.96,48.0839	,	131/716,1595/2180	14775859	6340,5872	1948	4158	6106	SO:0001819	synonymous_variant	158326	exon26			ATCTGTGGCCATG	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.4785C>T	9.37:g.14775859G>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	234	122	0.521368	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			G|0.593;A|0.407	0.407	strong		0.463	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
SLC26A8	116369	hgsc.bcm.edu	37	6	35967772	35967772	+	Missense_Mutation	SNP	T	T	C	rs17713154	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:35967772T>C	ENST00000490799.1	-	4	795	c.442A>G	c.(442-444)Att>Gtt	p.I148V	SLC26A8_ENST00000355574.2_Missense_Mutation_p.I148V|SLC26A8_ENST00000394602.2_Missense_Mutation_p.I148V	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						AACTCACCAATGGACATTTGA	0.393													T|||	525	0.104832	0.0885	0.1427	5008	,	,		18752	0.0506		0.1402	False		,,,				2504	0.1196				p.I148V		Atlas-SNP	.											SLC26A8,colon,carcinoma,+2,1	SLC26A8	95	1	0			c.A442G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	396,4010	196.4+/-220.7	15,366,1822	164.0	167.0	166.0		442,442,442	1.7	1.0	6	dbSNP_123	166	1145,7455	234.6+/-267.5	90,965,3245	yes	missense,missense,missense	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	29,29,29	105,1331,5067	CC,CT,TT		13.314,8.9877,11.8484	benign,benign,benign	148/971,148/971,148/866	35967772	1541,11465	2203	4300	6503	SO:0001583	missense	116369	exon4			CACCAATGGACAT	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"""Solute carriers"""	14468	protein-coding gene	gene with protein product		608480	"""solute carrier family 26, member 8"""			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.442A>G	6.37:g.35967772T>C	ENSP00000417638:p.Ile148Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_052961		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	236	0.10805860805860806	36	0.07317073170731707	62	0.1712707182320442	33	0.057692307692307696	105	0.13852242744063326	T	7.036	0.561555	0.13498	0.089877	0.13314	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574	D;D;D	0.90444	-2.67;-2.67;-2.67	5.4	1.73	0.24493	.	0.168304	0.42420	N	0.000709	T	0.56411	0.1983	N	0.12853	0.265	0.31338	P	0.6840010000000001	P;B	0.38129	0.619;0.336	B;B	0.33890	0.172;0.075	T	0.59413	-0.7459	9	0.06365	T	0.9	.	6.6044	0.22718	0.0:0.2787:0.0:0.7213	rs17713154;rs52813917;rs17713154	148;148	Q96RN1;Q96RN1-2	S26A8_HUMAN;.	V	148	ENSP00000417638:I148V;ENSP00000378100:I148V;ENSP00000347778:I148V	ENSP00000347778:I148V	I	-	1	0	SLC26A8	36075750	0.990000	0.36364	1.000000	0.80357	0.996000	0.88848	0.851000	0.27751	0.443000	0.26582	0.533000	0.62120	ATT	T|0.887;C|0.113	0.113	strong		0.393	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
FAM187A	100528020	hgsc.bcm.edu	37	17	42979026	42979026	+	Intron	SNP	T	T	C	rs74349463	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:42979026T>C	ENST00000331733.4	+	3	371				CCDC103_ENST00000417826.2_Intron|CCDC103_ENST00000410027.1_Intron|AC015936.3_ENST00000441312.1_RNA|EFTUD2_ENST00000591382.1_5'Flank|FAM187A_ENST00000412523.2_Intron|EFTUD2_ENST00000592576.1_5'Flank|EFTUD2_ENST00000402521.3_5'Flank|CCDC103_ENST00000410006.2_Intron|EFTUD2_ENST00000426333.2_5'Flank	NM_001258399.1|NM_213607.2	NP_001245328.1|NP_998772.1	A6NFU0	F187A_HUMAN	family with sequence similarity 187, member A							integral component of membrane (GO:0016021)											CCCCGGTAGGTGAGGCCCTGC	0.458													T|||	474	0.0946486	0.0635	0.1037	5008	,	,		21708	0.005		0.166	False		,,,				2504	0.1493				.		Atlas-SNP	.											.	CCDC103	15	.	0			c.280+2T>C						PASS	.	T		309,4097	167.3+/-198.3	7,295,1901	88.0	76.0	80.0			-0.4	0.2	17	dbSNP_132	80	1457,7143	278.4+/-293.4	112,1233,2955	no	intron	CCDC103	NM_213607.1		119,1528,4856	CC,CT,TT		16.9419,7.0132,13.5783			42979026	1766,11240	2203	4300	6503	SO:0001627	intron_variant	388389	exon3			GGTAGGTGAGGCC			17q21.31	2013-01-11			ENSG00000214447	ENSG00000214447		"""Immunoglobulin superfamily / V-set domain containing"""	35153	protein-coding gene	gene with protein product							Standard			Approved		uc002ihp.1	A6NFU0	OTTHUMG00000154266	ENST00000331733.4:c.-1466+6T>C	17.37:g.42979026T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_001258399		Splice_Site	SNP	ENST00000331733.4	37																																																																																				T|0.873;C|0.127	0.127	strong		0.458	FAM187A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334584.1		
OR5T2	219464	hgsc.bcm.edu	37	11	56000288	56000288	+	Missense_Mutation	SNP	G	G	A	rs7122514	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56000288G>A	ENST00000313264.4	-	1	449	c.374C>T	c.(373-375)aCg>aTg	p.T125M		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	125			T -> M (in dbSNP:rs7122514).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					ATTCTTTGTCGTAAAATCTAC	0.403													g|||	185	0.0369409	0.003	0.0432	5008	,	,		22881	0.001		0.0944	False		,,,				2504	0.0562				p.T125M		Atlas-SNP	.											.	OR5T2	107	.	0			c.C374T						PASS	.	G	MET/THR	58,4344	55.5+/-91.7	0,58,2143	106.0	100.0	102.0		374	3.7	0.0	11	dbSNP_116	102	692,7900	171.0+/-222.0	34,624,3638	yes	missense	OR5T2	NM_001004746.1	81	34,682,5781	AA,AG,GG		8.054,1.3176,5.7719	benign	125/360	56000288	750,12244	2201	4296	6497	SO:0001583	missense	219464	exon1			TTTGTCGTAAAAT	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.374C>T	11.37:g.56000288G>A	ENSP00000323688:p.Thr125Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	83	0.038003663003663	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	69	0.09102902374670185	G	6.334	0.429739	0.11987	0.013176	0.08054	ENSG00000181718	ENST00000313264	T	0.01335	5.0	4.87	3.74	0.42951	GPCR, rhodopsin-like superfamily (1);	1.123250	0.06941	N	0.812812	T	0.00039	0.0001	N	0.02357	-0.585	0.09310	N	1	B	0.14805	0.011	B	0.08055	0.003	T	0.48559	-0.9025	10	0.49607	T	0.09	.	5.3798	0.16186	0.7601:0.0:0.0856:0.1543	rs7122514;rs52804091;rs61219207;rs7122514	125	Q8NGG2	OR5T2_HUMAN	M	125	ENSP00000323688:T125M	ENSP00000323688:T125M	T	-	2	0	OR5T2	55756864	0.280000	0.24249	0.001000	0.08648	0.000000	0.00434	4.695000	0.61767	0.818000	0.34468	-0.511000	0.04467	ACG	G|0.953;A|0.047	0.047	strong		0.403	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
SLC9C2	284525	hgsc.bcm.edu	37	1	173516871	173516871	+	Missense_Mutation	SNP	G	G	C	rs16846206	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:173516871G>C	ENST00000367714.3	-	13	1936	c.1514C>G	c.(1513-1515)gCt>gGt	p.A505G	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Missense_Mutation_p.A403G	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	505			A -> G (in dbSNP:rs16846206).		sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										CTCCATTAAAGCTTCATCTGT	0.348													G|||	1676	0.334665	0.1293	0.3256	5008	,	,		18034	0.6448		0.2107	False		,,,				2504	0.4264				p.A505G		Atlas-SNP	.											.	.	.	.	0			c.C1514G						PASS	.	G	GLY/ALA	584,3822	256.7+/-261.4	38,508,1657	158.0	142.0	147.0		1514	-0.2	1.0	1	dbSNP_123	147	1771,6829	319.3+/-314.1	183,1405,2712	yes	missense	SLC9A11	NM_178527.3	60	221,1913,4369	CC,CG,GG		20.593,13.2547,18.107	benign	505/1125	173516871	2355,10651	2203	4300	6503	SO:0001583	missense	284525	exon13			ATTAAAGCTTCAT	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1514C>G	1.37:g.173516871G>C	ENSP00000356687:p.Ala505Gly	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	149	66	0.442953	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	700	0.32051282051282054	69	0.1402439024390244	112	0.30939226519337015	355	0.6206293706293706	164	0.21635883905013192	G	10.10	1.258637	0.23051	0.132547	0.20593	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.25414	1.8;1.8	5.5	-0.206	0.13193	.	0.673556	0.13000	N	0.421735	T	0.03053	0.0090	N	0.08118	0	0.46241	P	0.0010580000000000034	B	0.27068	0.167	B	0.21360	0.034	T	0.42068	-0.9473	9	0.30854	T	0.27	-6.9082	4.5975	0.12336	0.3998:0.0:0.0905:0.5097	rs16846206;rs52835556;rs61192359;rs16846206	505	Q5TAH2	S9A11_HUMAN	G	505;403	ENSP00000356687:A505G;ENSP00000445437:A403G	ENSP00000356687:A505G	A	-	2	0	SLC9A11	171783494	0.999000	0.42202	0.997000	0.53966	0.401000	0.30781	0.324000	0.19610	0.035000	0.15519	-0.440000	0.05779	GCT	G|0.763;C|0.237	0.237	strong		0.348	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
MUC2	4583	hgsc.bcm.edu	37	11	1090343	1090343	+	Silent	SNP	T	T	C	rs12221966	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1090343T>C	ENST00000441003.2	+	27	3666	c.3639T>C	c.(3637-3639)tgT>tgC	p.C1213C	MUC2_ENST00000361558.6_5'Flank|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1213					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCAGCGTGTGTACCAACTCCT	0.647													C|||	422	0.0842652	0.0537	0.0893	5008	,	,		17608	0.0685		0.1163	False		,,,				2504	0.1053				p.C1213C		Atlas-SNP	.											.	MUC2	614	.	0			c.T3639C						PASS	.			298,4082		12,274,1904	64.0	73.0	70.0		3639	0.3	0.0	11	dbSNP_120	70	945,7609		47,851,3379	no	coding-synonymous	MUC2	NM_002457.2		59,1125,5283	CC,CT,TT		11.0475,6.8037,9.6103		1213/2813	1090343	1243,11691	2190	4277	6467	SO:0001819	synonymous_variant	4583	exon27			CGTGTGTACCAAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3639T>C	11.37:g.1090343T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	189	106	0.560847	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.916;C|0.084	0.084	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
HLA-DMA	3108	hgsc.bcm.edu	37	6	32917544	32917544	+	Missense_Mutation	SNP	C	C	T	rs1063478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32917544C>T	ENST00000374843.4	-	3	581	c.496G>A	c.(496-498)Gtc>Atc	p.V166I	XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000464392.1_5'UTR|HLA-DMA_ENST00000395305.3_Missense_Mutation_p.V71I|HLA-DMA_ENST00000395303.3_Missense_Mutation_p.V132I	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	166	Alpha-2.|Ig-like C1-type.		V -> I (in allele DMA*01:02 and allele DMA*01:04; dbSNP:rs1063478).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						TCCACAGGGACGGAATGATGC	0.498													c|||	870	0.173722	0.0915	0.1974	5008	,	,		20678	0.2391		0.1292	False		,,,				2504	0.2464				p.V166I		Atlas-SNP	.											.	HLA-DMA	20	.	0			c.G496A						PASS	.	T	ILE/VAL	283,2739		13,257,1241	78.0	71.0	73.0		496	1.5	0.0	6	dbSNP_86	73	696,4722		34,628,2047	yes	missense	HLA-DMA	NM_006120.3	29	47,885,3288	TT,TC,CC		12.8461,9.3647,11.5995	benign	166/262	32917544	979,7461	1511	2709	4220	SO:0001583	missense	3108	exon3			CAGGGACGGAATG		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.496G>A	6.37:g.32917544C>T	ENSP00000363976:p.Val166Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_006120	Q29639|Q29640	Missense_Mutation	SNP	ENST00000374843.4	37	CCDS4761.1	328	0.15018315018315018	50	0.1016260162601626	55	0.15193370165745856	129	0.22552447552447552	94	0.12401055408970976	c	2.325	-0.354828	0.05138	0.093647	0.128461	ENSG00000204257	ENST00000395305;ENST00000395303;ENST00000374843;ENST00000456800;ENST00000422832	T;T;T;T;T	0.03004	4.08;4.08;4.08;4.08;4.08	5.28	1.54	0.23209	.	1.512590	0.03389	N	0.201603	T	0.00784	0.0026	N	0.16130	0.375	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46830	-0.9163	9	0.33141	T	0.24	.	4.0461	0.09773	0.1635:0.5772:0.0:0.2594	rs1063478;rs13209997;rs17214050;rs17617501;rs17882348;rs45482294;rs52831176;rs1063478	166	Q31604	.	I	71;132;166;196;133	ENSP00000378716:V71I;ENSP00000378714:V132I;ENSP00000363976:V166I;ENSP00000409668:V196I;ENSP00000403122:V133I	ENSP00000363976:V166I	V	-	1	0	HLA-DMA	33025522	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.119000	0.10676	0.095000	0.17434	-0.131000	0.14894	GTC	.	.	weak		0.498	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	NM_006120	
OR2T3	343173	hgsc.bcm.edu	37	1	248637065	248637065	+	Silent	SNP	A	A	G	rs139758663	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248637065A>G	ENST00000359594.2	+	1	439	c.414A>G	c.(412-414)ccA>ccG	p.P138P		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCATTACCCACTGCTGATGA	0.542																																					p.P138P		Atlas-SNP	.											.	OR2T3	79	.	0			c.A414G						PASS	.						33.0	31.0	31.0					1																	248637065		2194	4274	6468	SO:0001819	synonymous_variant	343173	exon1			TTACCCACTGCTG		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.414A>G	1.37:g.248637065A>G		Somatic	454	0	0		WXS	Illumina HiSeq	Phase_I	655	169	0.258015	NM_001005495	B2RNJ1	Silent	SNP	ENST00000359594.2	37	CCDS31117.1																																																																																			A|0.884;G|0.116	0.116	strong		0.542	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
CCDC129	223075	hgsc.bcm.edu	37	7	31682853	31682853	+	Silent	SNP	T	T	C	rs38397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:31682853T>C	ENST00000407970.3	+	11	1907	c.1869T>C	c.(1867-1869)agT>agC	p.S623S	CCDC129_ENST00000409210.1_Silent_p.S531S|CCDC129_ENST00000451887.2_Silent_p.S649S|CCDC129_ENST00000319386.3_Silent_p.S475S	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	623										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AGGAAAGCAGTGGATTCTGTC	0.473													T|||	680	0.135783	0.0182	0.1556	5008	,	,		23363	0.1786		0.2177	False		,,,				2504	0.1524				p.S649S		Atlas-SNP	.											LOC223075,caecum,carcinoma,+1,2	CCDC129	127	2	0			c.T1947C						PASS	.	T		222,4184	132.9+/-169.3	9,204,1990	128.0	115.0	120.0		1869	-4.1	0.0	7	dbSNP_76	120	1729,6871	315.0+/-312.1	183,1363,2754	no	coding-synonymous	CCDC129	NM_194300.2		192,1567,4744	CC,CT,TT		20.1047,5.0386,15.0008		623/1045	31682853	1951,11055	2203	4300	6503	SO:0001819	synonymous_variant	223075	exon11			AAGCAGTGGATTC	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.1869T>C	7.37:g.31682853T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Silent	SNP	ENST00000407970.3	37	CCDS5435.2																																																																																			T|0.862;C|0.138	0.138	strong		0.473	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10524957	10524957	+	Silent	SNP	G	G	T	rs34430103	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:10524957G>T	ENST00000396560.2	+	3	707	c.480G>T	c.(478-480)ggG>ggT	p.G160G	ATF7IP2_ENST00000324570.5_Silent_p.G160G|ATF7IP2_ENST00000356427.2_Silent_p.G160G|ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Silent_p.G160G	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	160					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AGCATGAGGGGGCTTGTAGTC	0.448													G|||	899	0.179513	0.2436	0.2061	5008	,	,		20164	0.1577		0.1004	False		,,,				2504	0.1779				p.G160G		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.G480T						PASS	.	G		948,3446	360.6+/-315.3	98,752,1347	106.0	96.0	99.0		480	-1.1	0.0	16	dbSNP_126	99	1002,7598	216.3+/-255.4	56,890,3354	no	coding-synonymous	ATF7IP2	NM_024997.2		154,1642,4701	TT,TG,GG		11.6512,21.5749,15.0069		160/683	10524957	1950,11044	2197	4300	6497	SO:0001819	synonymous_variant	80063	exon3			TGAGGGGGCTTGT	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.480G>T	16.37:g.10524957G>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	228	95	0.416667	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Silent	SNP	ENST00000396560.2	37	CCDS10540.1																																																																																			G|0.848;T|0.152	0.152	strong		0.448	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
OR8H3	390152	hgsc.bcm.edu	37	11	55890355	55890355	+	Silent	SNP	T	T	C	rs78856925	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55890355T>C	ENST00000313472.3	+	1	507	c.507T>C	c.(505-507)tgT>tgC	p.C169C		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	169						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TGCATTTCTGTGACTCAAACA	0.433													T|||	182	0.0363419	0.003	0.0432	5008	,	,		22119	0.001		0.0944	False		,,,				2504	0.0532				p.C169C		Atlas-SNP	.											.	OR8H3	92	.	0			c.T507C						PASS	.						251.0	222.0	232.0					11																	55890355		2201	4296	6497	SO:0001819	synonymous_variant	390152	exon1			TTTCTGTGACTCA	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.507T>C	11.37:g.55890355T>C		Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	282	114	0.404255	NM_001005201	Q6IFB7	Silent	SNP	ENST00000313472.3	37	CCDS31519.1																																																																																			T|0.952;C|0.048	0.048	strong		0.433	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
COL18A1	80781	hgsc.bcm.edu	37	21	46898243	46898243	+	Silent	SNP	C	C	G	rs13046486	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:46898243C>G	ENST00000359759.4	+	8	2490	c.2469C>G	c.(2467-2469)ggC>ggG	p.G823G	COL18A1_ENST00000355480.5_Silent_p.G588G|COL18A1_ENST00000400337.2_Silent_p.G408G			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	823	Triple-helical region 2 (COL2).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		ACACCCAGGGCGACCCCGGTG	0.552											OREG0026262	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	370	0.0738818	0.0779	0.0749	5008	,	,		14896	0.0565		0.1034	False		,,,				2504	0.0552				p.G588G		Atlas-SNP	.											.	COL18A1	129	.	0			c.C1764G						PASS	.	T	,	311,3585		13,285,1650	128.0	139.0	135.0		1764,1224	-6.8	0.2	21	dbSNP_121	135	827,7443		44,739,3352	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	57,1024,5002	GG,GC,CC		10.0,7.9825,9.3539	,	588/1520,408/1340	46898243	1138,11028	1948	4135	6083	SO:0001819	synonymous_variant	80781	exon8			CCAGGGCGACCCC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2469C>G	21.37:g.46898243C>G		Somatic	275	1	0.00363636	942	WXS	Illumina HiSeq	Phase_I	330	166	0.50303	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.921;G|0.079	0.079	strong		0.552	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
SLC16A12	387700	hgsc.bcm.edu	37	10	91222287	91222287	+	5'UTR	SNP	A	A	C	rs3740030	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:91222287A>C	ENST00000341233.4	-	0	349				RP11-168O10.6_ENST00000423474.1_RNA|RP11-168O10.6_ENST00000454270.1_RNA|SLC16A12_ENST00000371790.4_Missense_Mutation_p.W17G	NM_213606.3	NP_998771.3	Q6ZSM3	MOT12_HUMAN	solute carrier family 16, member 12							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|skin(1)|stomach(1)	14						TCCAACAGCCAAGTTATGATC	0.478													A|||	345	0.0688898	0.0045	0.0375	5008	,	,		19194	0.2242		0.0736	False		,,,				2504	0.0133				p.W17G		Atlas-SNP	.											.	SLC16A12	40	.	0			c.T49G						PASS	.	A	GLY/TRP	97,4309	61.1+/-98.1	2,93,2108	39.0	37.0	38.0		49	0.6	0.5	10	dbSNP_107	38	731,7869	140.3+/-196.8	37,657,3606	yes	missense	SLC16A12	NM_213606.3	184	39,750,5714	CC,CA,AA		8.5,2.2015,6.3663		17/517	91222287	828,12178	2203	4300	6503	SO:0001623	5_prime_UTR_variant	387700	exon3			ACAGCCAAGTTAT		CCDS7404.1, CCDS7404.2	10q23.32	2013-07-18	2013-07-18		ENSG00000152779	ENSG00000152779		"""Solute carriers"""	23094	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 12"""	611910	"""solute carrier family 16 (monocarboxylic acid transporters), member 12"", ""solute carrier family 16, member 12 (monocarboxylic acid transporter 12)"""				Standard	NM_213606		Approved	MCT12	uc001kgm.3	Q6ZSM3	OTTHUMG00000018714	ENST00000341233.4:c.-42T>G	10.37:g.91222287A>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	28	24	0.857143	NM_213606	Q5M9M9|Q5T7J2|Q6ZV76	Missense_Mutation	SNP	ENST00000341233.4	37		196	0.08974358974358974	1	0.0020325203252032522	18	0.049723756906077346	121	0.21153846153846154	56	0.07387862796833773	A	7.041	0.562625	0.13498	0.022015	0.085	ENSG00000152779	ENST00000371790;ENST00000475682	T	0.18657	2.2	5.66	0.616	0.17613	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.51233	P	8.20000000000265E-5	.	.	.	.	.	.	T	0.45396	-0.9264	6	0.26408	T	0.33	.	9.0335	0.36273	0.2463:0.6418:0.0:0.1119	rs3740030;rs17122031;rs56505202;rs59939587;rs3740030	.	.	.	G	17	ENSP00000360855:W17G	ENSP00000360855:W17G	W	-	1	0	SLC16A12	91212267	0.766000	0.28496	0.496000	0.27539	0.171000	0.22731	0.772000	0.26647	0.530000	0.28619	-0.265000	0.10407	TGG	A|0.895;C|0.105	0.105	strong		0.478	SLC16A12-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_213606	
SMCR8	140775	hgsc.bcm.edu	37	17	18221134	18221134	+	Silent	SNP	C	C	T	rs1563631	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18221134C>T	ENST00000406438.3	+	1	2511	c.2031C>T	c.(2029-2031)taC>taT	p.Y677Y	TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank|TOP3A_ENST00000582230.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	677						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						CCACCAGCTACGTGAGCAGTG	0.577													C|||	895	0.178714	0.1611	0.2421	5008	,	,		20625	0.0605		0.3062	False		,,,				2504	0.1483				p.Y677Y		Atlas-SNP	.											SMCR8,colon,carcinoma,0,1	SMCR8	62	1	0			c.C2031T						scavenged	.	C		922,3484	355.1+/-312.9	87,748,1368	77.0	75.0	76.0		2031	-9.4	0.0	17	dbSNP_88	76	2597,6003	423.1+/-354.3	382,1833,2085	yes	coding-synonymous	SMCR8	NM_144775.2		469,2581,3453	TT,TC,CC		30.1977,20.926,27.0567		677/938	18221134	3519,9487	2203	4300	6503	SO:0001819	synonymous_variant	140775	exon1			CAGCTACGTGAGC	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.2031C>T	17.37:g.18221134C>T		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Silent	SNP	ENST00000406438.3	37	CCDS11195.2																																																																																			C|0.770;T|0.230	0.230	strong		0.577	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
SLC1A4	6509	hgsc.bcm.edu	37	2	65248271	65248271	+	Silent	SNP	G	G	A	rs7563131	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:65248271G>A	ENST00000234256.3	+	8	1833	c.1590G>A	c.(1588-1590)tcG>tcA	p.S530S	SLC1A4_ENST00000531327.1_Silent_p.S232S	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	530					amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	CCAAGGAGTCGGTTCTGTGAT	0.632													G|||	645	0.128794	0.2663	0.1009	5008	,	,		18789	0.0109		0.1193	False		,,,				2504	0.0941				p.S530S		Atlas-SNP	.											.	SLC1A4	33	.	0			c.G1590A						PASS	.	G	,	1282,3124	429.3+/-342.2	187,908,1108	36.0	39.0	38.0		696,1590	-6.6	0.8	2	dbSNP_116	38	1072,7528	224.3+/-260.7	67,938,3295	no	coding-synonymous,coding-synonymous	SLC1A4	NM_001193493.1,NM_003038.4	,	254,1846,4403	AA,AG,GG		12.4651,29.0967,18.0993	,	232/235,530/533	65248271	2354,10652	2203	4300	6503	SO:0001819	synonymous_variant	6509	exon8			GGAGTCGGTTCTG		CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"""Solute carriers"""	10942	protein-coding gene	gene with protein product	"""alanine/serine/cysteine/threonine transporter"""	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.1590G>A	2.37:g.65248271G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	110	40	0.363636	NM_003038	B7Z3C0|D6W5F0	Silent	SNP	ENST00000234256.3	37	CCDS1879.1																																																																																			G|0.846;A|0.154	0.154	strong		0.632	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038	
DNAH5	1767	hgsc.bcm.edu	37	5	13701536	13701536	+	Missense_Mutation	SNP	T	T	C	rs3734110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13701536T>C	ENST00000265104.4	-	77	13452	c.13348A>G	c.(13348-13350)Att>Gtt	p.I4450V		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4450			I -> V (in dbSNP:rs3734110). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039}.		cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GTACTAGAAATCCAAGAAGCC	0.363									Kartagener syndrome				C|||	2522	0.503594	0.5295	0.5187	5008	,	,		16237	0.4474		0.5457	False		,,,				2504	0.4724				p.I4450V		Atlas-SNP	.											DNAH5,NS,carcinoma,+2,1	DNAH5	868	1	0			c.A13348G						PASS	.	C	VAL/ILE	2223,2183	555.7+/-379.3	587,1049,567	63.0	70.0	68.0		13348	4.9	1.0	5	dbSNP_107	68	4726,3874	530.4+/-381.8	1275,2176,849	yes	missense	DNAH5	NM_001369.2	29	1862,3225,1416	CC,CT,TT		45.0465,49.5461,46.5708	benign	4450/4625	13701536	6949,6057	2203	4300	6503	SO:0001583	missense	1767	exon77	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TAGAAATCCAAGA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.13348A>G	5.37:g.13701536T>C	ENSP00000265104:p.Ile4450Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	1113	0.5096153846153846	267	0.5426829268292683	195	0.5386740331491713	234	0.4090909090909091	417	0.5501319261213721	C	9.791	1.178017	0.21787	0.504539	0.549535	ENSG00000039139	ENST00000265104	T	0.08282	3.11	5.78	4.91	0.64330	Dynein heavy chain (1);	0.377697	0.27478	N	0.019187	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.100000000000325E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.34650	-0.9820	9	0.28530	T	0.3	.	7.6741	0.28476	0.0:0.6802:0.1197:0.2002	rs3734110;rs13162128;rs61544221;rs3734110	4450	Q8TE73	DYH5_HUMAN	V	4450	ENSP00000265104:I4450V	ENSP00000265104:I4450V	I	-	1	0	DNAH5	13754536	0.999000	0.42202	1.000000	0.80357	0.812000	0.45895	1.084000	0.30828	0.804000	0.34136	-0.186000	0.12905	ATT	T|0.482;C|0.518	0.518	strong		0.363	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
UTP18	51096	hgsc.bcm.edu	37	17	49350802	49350802	+	Silent	SNP	A	A	C	rs2318789	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:49350802A>C	ENST00000225298.7	+	5	759	c.702A>C	c.(700-702)ggA>ggC	p.G234G		NM_016001.2	NP_057085.2	Q9Y5J1	UTP18_HUMAN	UTP18 small subunit (SSU) processome component homolog (yeast)	234					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			TTCCAAGAGGAATCTTGAAGG	0.398													A|||	2134	0.426118	0.1248	0.4424	5008	,	,		13944	0.6071		0.4791	False		,,,				2504	0.5808				p.G234G		Atlas-SNP	.											.	UTP18	28	.	0			c.A702C						PASS	.	A		655,3107		56,543,1282	131.0	123.0	125.0		702	0.6	1.0	17	dbSNP_100	125	3821,4393		903,2015,1189	no	coding-synonymous	UTP18	NM_016001.2		959,2558,2471	CC,CA,AA		46.5181,17.411,37.3747		234/557	49350802	4476,7500	1881	4107	5988	SO:0001819	synonymous_variant	51096	exon5			AAGAGGAATCTTG	AF151806	CCDS42362.1	17q21.33	2013-05-21	2011-12-09	2006-05-16	ENSG00000011260	ENSG00000011260		"""WD repeat domain containing"""	24274	protein-coding gene	gene with protein product		612816	"""WD repeat domain 50"""	WDR50		10810093, 8619474, 15590835	Standard	NM_016001		Approved	CGI-48	uc002its.3	Q9Y5J1	OTTHUMG00000162370	ENST00000225298.7:c.702A>C	17.37:g.49350802A>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_016001	Q9H4N6	Silent	SNP	ENST00000225298.7	37	CCDS42362.1																																																																																			A|0.569;C|0.431	0.431	strong		0.398	UTP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368654.1	NM_016001	
CACNA1A	773	hgsc.bcm.edu	37	19	13414594	13414594	+	Silent	SNP	C	C	T	rs16016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:13414594C>T	ENST00000360228.5	-	16	2090	c.2091G>A	c.(2089-2091)acG>acA	p.T697T	CACNA1A_ENST00000573710.2_Silent_p.T698T	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	698					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TCCCAAAGAGCGTCAGTACAA	0.567													c|||	927	0.185104	0.0673	0.2205	5008	,	,		13056	0.2887		0.1203	False		,,,				2504	0.2791				p.T698T		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G2094A						PASS	.	T	,,,,	328,3650		13,302,1674	149.0	151.0	150.0		2094,2094,2091,2094,2094	-9.2	0.1	19	dbSNP_54	150	1076,7250		71,934,3158	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	84,1236,4832	TT,TC,CC		12.9234,8.2453,11.4109	,,,,	698/2267,698/2262,697/2507,698/2264,698/2513	13414594	1404,10900	1989	4163	6152	SO:0001819	synonymous_variant	773	exon16			AAAGAGCGTCAGT	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.2091G>A	19.37:g.13414594C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			C|0.834;T|0.166	0.166	strong		0.567	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
IL4R	3566	hgsc.bcm.edu	37	16	27373972	27373972	+	Silent	SNP	T	T	C	rs2234900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:27373972T>C	ENST00000395762.2	+	11	1558	c.1299T>C	c.(1297-1299)ctT>ctC	p.L433L	IL4R_ENST00000380922.3_Silent_p.L418L|IL4R_ENST00000543915.2_Silent_p.L433L|IL4R_ENST00000170630.2_Silent_p.L433L	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	433					defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						CATGCCTTCTTCCACCTTCGG	0.617													t|||	1319	0.263379	0.6876	0.1758	5008	,	,		19679	0.0992		0.1262	False		,,,				2504	0.0624				p.L433L		Atlas-SNP	.											.	IL4R	70	.	0			c.T1299C						PASS	.	C		2502,1892	625.5+/-394.5	714,1074,409	73.0	73.0	73.0		1299	-10.2	0.0	16	dbSNP_98	73	1024,7576	215.7+/-255.0	67,890,3343	no	coding-synonymous	IL4R	NM_000418.2		781,1964,3752	CC,CT,TT		11.907,43.0587,27.1356		433/826	27373972	3526,9468	2197	4300	6497	SO:0001819	synonymous_variant	3566	exon11			CCTTCTTCCACCT	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1299T>C	16.37:g.27373972T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Silent	SNP	ENST00000395762.2	37	CCDS10629.1																																																																																			T|0.727;C|0.273	0.273	strong		0.617	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
CASP10	843	hgsc.bcm.edu	37	2	202082459	202082459	+	Intron	SNP	T	T	A	rs13006529	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:202082459T>A	ENST00000272879.5	+	9	1599				CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000492363.1_3'UTR|CASP10_ENST00000313728.7_Missense_Mutation_p.L455I|CASP10_ENST00000346817.5_Missense_Mutation_p.L479I|CASP10_ENST00000286186.6_Missense_Mutation_p.L522I|CASP10_ENST00000448480.1_Intron	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						TGCACTTTCATTATAGCAGAG	0.478													T|||	1648	0.329073	0.3328	0.3876	5008	,	,		17669	0.2073		0.4742	False		,,,				2504	0.2587				p.L522I		Atlas-SNP	.											.	CASP10	95	.	0			c.T1564A						PASS	.	T	ILE/LEU,,ILE/LEU,,,ILE/LEU	1547,2859	486.5+/-360.6	259,1029,915	152.0	143.0	146.0		1363,,1435,,,1564	-1.4	0.0	2	dbSNP_121	146	4211,4389	570.8+/-389.4	1042,2127,1131	yes	missense,intron,missense,intron,utr-3,missense	CASP10	NM_001206524.1,NM_001206542.1,NM_001230.4,NM_032974.4,NM_032976.3,NM_032977.3	5,,5,,,5	1301,3156,2046	AA,AT,TT		48.9651,35.1112,44.2719	probably-damaging,,probably-damaging,,,probably-damaging	455/456,,479/480,,,522/523	202082459	5758,7248	2203	4300	6503	SO:0001627	intron_variant	843	exon10			CTTTCATTATAGC	U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	3.4.22.63	"""Caspases"""	1500	protein-coding gene	gene with protein product		601762	"""caspase 10, apoptosis-related cysteine protease"""			8755496	Standard	NM_032974		Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000272879.5:c.1415+8174T>A	2.37:g.202082459T>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_032977	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Missense_Mutation	SNP	ENST00000272879.5	37	CCDS2338.1	768	0.3516483516483517	164	0.3333333333333333	144	0.39779005524861877	105	0.18356643356643357	355	0.4683377308707124	T	12.36	1.914818	0.33815	0.351112	0.489651	ENSG00000003400	ENST00000286186;ENST00000346817;ENST00000313728	T;T;T	0.03004	4.43;4.38;4.08	4.54	-1.39	0.08997	.	2.876120	0.01827	N	0.034467	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.32160	0.358;0.358;0.358	B;B;B	0.28139	0.086;0.086;0.086	T	0.41627	-0.9498	8	0.29301	T	0.29	.	1.0832	0.01647	0.1337:0.2388:0.273:0.3546	rs13006529;rs17616734;rs17860406;rs52811683;rs13006529	455;479;522	Q92851-6;Q92851-2;Q92851-4	.;.;.	I	522;479;455	ENSP00000286186:L522I;ENSP00000237865:L479I;ENSP00000314599:L455I	ENSP00000286186:L522I	L	+	1	2	CASP10	201790704	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.247000	0.18179	-0.138000	0.11434	-0.316000	0.08728	TTA	A|0.399;N|0.000	0.399	strong		0.478	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977	
PTPN3	5774	hgsc.bcm.edu	37	9	112219474	112219474	+	Missense_Mutation	SNP	C	C	G	rs3793524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:112219474C>G	ENST00000374541.2	-	4	372	c.268G>C	c.(268-270)Gcc>Ccc	p.A90P	PTPN3_ENST00000262539.3_Missense_Mutation_p.S7T	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	90	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		A -> P (in dbSNP:rs3793524). {ECO:0000269|PubMed:1648725}.		negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						TTCCTGATGGCTTTGCTTGCT	0.408													G|||	2045	0.408347	0.5318	0.2939	5008	,	,		23696	0.3442		0.3439	False		,,,				2504	0.455				p.A90P		Atlas-SNP	.											.	PTPN3	106	.	0			c.G268C						PASS	.	G	PRO/ALA,PRO/ALA	2124,2282	598.3+/-389.1	495,1134,574	185.0	160.0	169.0		268,268	5.6	1.0	9	dbSNP_107	169	2915,5685	670.0+/-402.7	485,1945,1870	yes	missense,missense	PTPN3	NM_001145368.1,NM_002829.3	27,27	980,3079,2444	GG,GC,CC		33.8953,48.207,38.7437	benign,benign	90/869,90/914	112219474	5039,7967	2203	4300	6503	SO:0001583	missense	5774	exon4			TGATGGCTTTGCT		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.268G>C	9.37:g.112219474C>G	ENSP00000363667:p.Ala90Pro	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_001145368	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	37	CCDS6776.1	829|829	0.37957875457875456|0.37957875457875456	244|244	0.4959349593495935|0.4959349593495935	118|118	0.3259668508287293|0.3259668508287293	202|202	0.3531468531468531|0.3531468531468531	265|265	0.3496042216358839|0.3496042216358839	G|G	24.4|24.4	4.525557|4.525557	0.85600|0.85600	0.48207|0.48207	0.338953|0.338953	ENSG00000070159|ENSG00000070159	ENST00000394831;ENST00000374541|ENST00000262539	T|T	0.76709|0.67865	-1.04|-0.29	5.56|5.56	5.56|5.56	0.83823|0.83823	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);FERM conserved site (1);|.	0.052669|.	0.85682|.	N|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00073|0.00073	-2.26|-2.26	0.09310|0.09310	P|P	1.0|1.0	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|T	0.33189|0.33189	-0.9878|-0.9878	9|6	0.02654|0.16896	T|T	1|0.51	.|.	16.3119|16.3119	0.82874|0.82874	0.0:0.1326:0.8674:0.0|0.0:0.1326:0.8674:0.0	rs3793524;rs52793477;rs59962731;rs3793524|rs3793524;rs52793477;rs59962731;rs3793524	90;90;90|.	B7Z9V1;Q45VJ3;P26045|.	.;.;PTN3_HUMAN|.	P|T	90|7	ENSP00000363667:A90P|ENSP00000262539:S7T	ENSP00000363667:A90P|ENSP00000262539:S7T	A|S	-|-	1|2	0|0	PTPN3|PTPN3	111259295|111259295	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.957000|0.957000	0.61999|0.61999	6.534000|6.534000	0.73833|0.73833	1.370000|1.370000	0.46153|0.46153	-0.371000|-0.371000	0.07208|0.07208	GCC|AGC	C|0.619;G|0.380	0.380	strong		0.408	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
EPHA8	2046	hgsc.bcm.edu	37	1	22903102	22903102	+	Silent	SNP	C	C	T	rs55844027	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22903102C>T	ENST00000166244.3	+	3	624	c.552C>T	c.(550-552)gcC>gcT	p.A184A	EPHA8_ENST00000374644.4_Silent_p.A184A|EPHA8_ENST00000538803.1_Silent_p.A184A	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	184	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TCTACCTGGCCTTCCAGGACA	0.612													C|||	278	0.0555112	0.0144	0.0764	5008	,	,		16921	0.1012		0.0368	False		,,,				2504	0.0685				p.A184A		Atlas-SNP	.											.	EPHA8	221	.	0			c.C552T						PASS	.	C	,	76,4330	67.6+/-105.2	0,76,2127	73.0	66.0	68.0		552,552	3.0	1.0	1	dbSNP_129	68	345,8255	117.9+/-177.5	6,333,3961	no	coding-synonymous,coding-synonymous	EPHA8	NM_001006943.1,NM_020526.3	,	6,409,6088	TT,TC,CC		4.0116,1.7249,3.237	,	184/496,184/1006	22903102	421,12585	2203	4300	6503	SO:0001819	synonymous_variant	2046	exon3			CCTGGCCTTCCAG	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.552C>T	1.37:g.22903102C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	155	74	0.477419	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	37	CCDS225.1																																																																																			C|0.960;T|0.040	0.040	strong		0.612	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
SERPINF2	5345	hgsc.bcm.edu	37	17	1657653	1657653	+	Missense_Mutation	SNP	G	G	A	rs1057335	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1657653G>A	ENST00000324015.3	+	10	1378	c.1301G>A	c.(1300-1302)aGg>aAg	p.R434K	SERPINF2_ENST00000382061.4_Missense_Mutation_p.R434K|SERPINF2_ENST00000450523.2_Missense_Mutation_p.R370K	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	434			R -> K (in dbSNP:rs1057335). {ECO:0000269|PubMed:10583218}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of proteolysis (GO:0030162)|response to organic substance (GO:0010033)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Ocriplasmin(DB08888)	GGCAGCGTGAGGAACCCCAAC	0.622													G|||	1110	0.221645	0.2057	0.2003	5008	,	,		14969	0.1567		0.173	False		,,,				2504	0.3753				p.R434K		Atlas-SNP	.											.	SERPINF2	33	.	0			c.G1301A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	932,3474	355.9+/-313.2	90,752,1361	129.0	114.0	119.0		1301,1301,1109	0.7	1.0	17	dbSNP_86	119	1547,7053	290.5+/-299.9	129,1289,2882	yes	missense,missense,missense	SERPINF2	NM_000934.3,NM_001165920.1,NM_001165921.1	26,26,26	219,2041,4243	AA,AG,GG		17.9884,21.153,19.0604	benign,benign,benign	434/492,434/492,370/428	1657653	2479,10527	2203	4300	6503	SO:0001583	missense	5345	exon10			GCGTGAGGAACCC	D00174	CCDS11011.1, CCDS54064.1	17p13.3	2014-02-18	2005-08-18		ENSG00000167711	ENSG00000167711		"""Serine (or cysteine) peptidase inhibitors"""	9075	protein-coding gene	gene with protein product	"""alpha-2-plasmin inhibitor"", ""alpha-2-antiplasmin"""	613168	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2"""	PLI		3416655, 24172014	Standard	NM_000934		Approved	API, ALPHA-2-PI, A2AP, AAP	uc002ftk.1	P08697	OTTHUMG00000090552	ENST00000324015.3:c.1301G>A	17.37:g.1657653G>A	ENSP00000321853:p.Arg434Lys	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	163	97	0.595092	NM_000934	B4E1B7|Q8N5U7|Q9UCG2|Q9UCG3	Missense_Mutation	SNP	ENST00000324015.3	37	CCDS11011.1	356	0.163003663003663	78	0.15853658536585366	67	0.1850828729281768	82	0.14335664335664336	129	0.17018469656992086	G	7.810	0.715570	0.15306	0.21153	0.179884	ENSG00000167711	ENST00000324015;ENST00000450523;ENST00000382061	D;D;D	0.84298	-1.83;-1.83;-1.83	5.4	0.742	0.18341	Serpin domain (3);	0.502118	0.23367	N	0.048942	T	0.00144	0.0004	N	0.25789	0.76	0.40390	P	0.02046800000000004	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.03221	-1.1059	8	.	.	.	.	7.7076	0.28659	0.4774:0.0:0.5226:0.0	rs1057335;rs3174717;rs3744770;rs57227120;rs1057335	370;434	B4E1B7;P08697	.;A2AP_HUMAN	K	434;370;434	ENSP00000321853:R434K;ENSP00000403877:R370K;ENSP00000371493:R434K	.	R	+	2	0	SERPINF2	1604403	0.874000	0.30092	0.999000	0.59377	0.787000	0.44495	-0.017000	0.12590	0.281000	0.22233	-1.036000	0.02392	AGG	G|0.814;A|0.186	0.186	strong		0.622	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207078.3	NM_000934	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435443	7435443	+	Silent	SNP	G	G	A	rs6843370	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:7435443G>A	ENST00000319098.4	-	1	1257	c.1164C>T	c.(1162-1164)gaC>gaT	p.D388D	SORCS2_ENST00000507866.2_Intron|SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000511199.1_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	388					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						GGTTCTCCGCGTCCCACTCTG	0.622													G|||	512	0.102236	0.1203	0.1052	5008	,	,		19768	0.0317		0.1362	False		,,,				2504	0.1135				p.D388D		Atlas-SNP	.											.	PSAPL1	51	.	0			c.C1164T						PASS	.	G	,	404,3794		21,362,1716	47.0	51.0	50.0		1164,	-7.1	0.0	4	dbSNP_116	50	1343,7079		115,1113,2983	no	coding-synonymous,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	,	136,1475,4699	AA,AG,GG		15.9463,9.6236,13.8431	,	388/522,	7435443	1747,10873	2099	4211	6310	SO:0001819	synonymous_variant	768239	exon1			CTCCGCGTCCCAC	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.1164C>T	4.37:g.7435443G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_001085382	A0A184|Q8N7T4	Silent	SNP	ENST00000319098.4	37	CCDS47009.1																																																																																			G|0.886;A|0.114	0.114	strong		0.622	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
OVGP1	5016	hgsc.bcm.edu	37	1	111966291	111966291	+	Silent	SNP	C	C	T	rs954739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111966291C>T	ENST00000369732.3	-	5	412	c.357G>A	c.(355-357)aaG>aaA	p.K119K	OVGP1_ENST00000481495.1_5'Flank|OVGP1_ENST00000540696.1_Silent_p.K59K	NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	119					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		AAGCAATAAACTTTTCACGGT	0.448													C|||	752	0.15016	0.0598	0.1282	5008	,	,		20675	0.1389		0.2366	False		,,,				2504	0.2106				p.K119K		Atlas-SNP	.											.	OVGP1	177	.	0			c.G357A						PASS	.	C		390,4016	196.4+/-220.7	13,364,1826	128.0	111.0	117.0		357	1.3	0.0	1	dbSNP_86	117	2274,6326	384.6+/-341.2	280,1714,2306	no	coding-synonymous	OVGP1	NM_002557.3		293,2078,4132	TT,TC,CC		26.4419,8.8516,20.4829		119/679	111966291	2664,10342	2203	4300	6503	SO:0001819	synonymous_variant	5016	exon5			AATAAACTTTTCA	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.357G>A	1.37:g.111966291C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	188	79	0.420213	NM_002557	A0AV19|B9EGE1|Q15841	Silent	SNP	ENST00000369732.3	37	CCDS834.1																																																																																			C|0.825;T|0.175	0.175	strong		0.448	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
PREX2	80243	hgsc.bcm.edu	37	8	68968171	68968171	+	Silent	SNP	G	G	A	rs1434775	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:68968171G>A	ENST00000288368.4	+	10	1477	c.1200G>A	c.(1198-1200)aaG>aaA	p.K400K	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	400	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AAGACCGAAAGAGAAAACTGA	0.403													A|||	2813	0.561701	0.8865	0.4755	5008	,	,		18889	0.2688		0.5239	False		,,,				2504	0.5245				p.K400K		Atlas-SNP	.											.	PREX2	614	.	0			c.G1200A						PASS	.	A	,	3619,787	315.8+/-294.3	1498,623,82	119.0	130.0	126.0		1200,1200	3.0	1.0	8	dbSNP_88	126	4215,4385	583.0+/-391.5	1038,2139,1123	no	coding-synonymous,coding-synonymous	PREX2	NM_024870.2,NM_025170.4	,	2536,2762,1205	AA,AG,GG		49.0116,17.862,39.7663	,	400/1607,400/980	68968171	7834,5172	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon10			CCGAAAGAGAAAA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1200G>A	8.37:g.68968171G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			G|0.421;A|0.579	0.579	strong		0.403	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
ALPK2	115701	hgsc.bcm.edu	37	18	56204945	56204945	+	Missense_Mutation	SNP	C	C	G	rs3809972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56204945C>G	ENST00000361673.3	-	5	2687	c.2474G>C	c.(2473-2475)aGa>aCa	p.R825T	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	825			R -> T (in dbSNP:rs3809972). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						ATCAACTGGTCTCCCAACAAG	0.418													G|||	2024	0.404153	0.4312	0.4294	5008	,	,		22836	0.2361		0.5726	False		,,,				2504	0.3497				p.R825T		Atlas-SNP	.											.	ALPK2	487	.	0			c.G2474C						PASS	.	G	THR/ARG	1984,2422	618.1+/-393.1	446,1092,665	97.0	93.0	94.0		2474	1.3	0.0	18	dbSNP_107	94	4589,4011	555.2+/-386.6	1237,2115,948	yes	missense	ALPK2	NM_052947.3	71	1683,3207,1613	GG,GC,CC		46.6395,45.0295,49.4618	benign	825/2171	56204945	6573,6433	2203	4300	6503	SO:0001583	missense	115701	exon5			ACTGGTCTCCCAA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2474G>C	18.37:g.56204945C>G	ENSP00000354991:p.Arg825Thr	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	243	120	0.493827	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	955	0.43727106227106227	189	0.38414634146341464	184	0.5082872928176796	137	0.2395104895104895	445	0.5870712401055409	G	0.989	-0.694484	0.03303	0.450295	0.533605	ENSG00000198796	ENST00000361673	T	0.38887	1.11	5.57	1.3	0.21679	.	1.325910	0.04699	N	0.415427	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45264	-0.9273	9	0.22109	T	0.4	-0.0267	5.5085	0.16868	0.3499:0.1423:0.5078:0.0	rs3809972;rs17309802;rs52836407;rs3809972	825;825	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	T	825	ENSP00000354991:R825T	ENSP00000354991:R825T	R	-	2	0	ALPK2	54355925	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.435000	0.06931	0.072000	0.16694	-0.901000	0.02856	AGA	C|0.531;G|0.469	0.469	strong		0.418	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
EPHA10	284656	hgsc.bcm.edu	37	1	38184470	38184470	+	Silent	SNP	C	C	G	rs610213	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:38184470C>G	ENST00000373048.4	-	16	2774	c.2775G>C	c.(2773-2775)gcG>gcC	p.A925A	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000330210.7_Silent_p.A420A|EPHA10_ENST00000427468.2_Silent_p.A925A|EPHA10_ENST00000540011.1_3'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	925					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGGCACGGTCCGCTAGTGGGG	0.677													C|||	561	0.112021	0.1793	0.0865	5008	,	,		17325	0.001		0.1551	False		,,,				2504	0.1094				p.A925A		Atlas-SNP	.											.	EPHA10	120	.	0			c.G2775C						PASS	.	C		702,3364		57,588,1388	19.0	24.0	22.0		2775	-3.1	1.0	1	dbSNP_83	22	1373,6981		115,1143,2919	no	coding-synonymous	EPHA10	NM_001099439.1		172,1731,4307	GG,GC,CC		16.4352,17.2651,16.7069		925/1009	38184470	2075,10345	2033	4177	6210	SO:0001819	synonymous_variant	284656	exon16			ACGGTCCGCTAGT	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2775G>C	1.37:g.38184470C>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	169	88	0.52071	NM_001099439	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	37	CCDS41305.1																																																																																			C|0.889;G|0.111	0.111	strong		0.677	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
SLC35G5	83650	hgsc.bcm.edu	37	8	11188703	11188703	+	Missense_Mutation	SNP	C	C	T	rs4841520	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11188703C>T	ENST00000382435.4	+	1	307	c.88C>T	c.(88-90)Cgc>Tgc	p.R30C		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	30						integral component of membrane (GO:0016021)											CTGGCACCAGCGCTGCCAGCC	0.662													C|||	557	0.111222	0.0877	0.232	5008	,	,		16315	0.1647		0.0527	False		,,,				2504	0.0624				p.R30C		Atlas-SNP	.											.	.	.	.	0			c.C88T						PASS	.	C	CYS/ARG	249,4157	129.8+/-166.5	7,235,1961	56.0	60.0	59.0		88	0.3	0.1	8	dbSNP_111	59	262,8334	89.4+/-151.6	3,256,4039	no	missense	SLC35G5	NM_054028.1	180	10,491,6000	TT,TC,CC		3.0479,5.6514,3.9302	benign	30/339	11188703	511,12491	2203	4298	6501	SO:0001583	missense	83650	exon1			CACCAGCGCTGCC	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.88C>T	8.37:g.11188703C>T	ENSP00000371872:p.Arg30Cys	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	95	57	0.6	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	243	0.11126373626373626	47	0.09552845528455285	63	0.17403314917127072	91	0.1590909090909091	42	0.055408970976253295	C	5.869	0.344573	0.11126	0.056514	0.030479	ENSG00000177710	ENST00000382435	T	0.30981	1.51	0.34	0.34	0.15985	.	0.206174	0.24657	N	0.036675	T	0.00039	0.0001	L	0.27053	0.805	0.38416	P	0.053956000000000004	B	0.09022	0.002	B	0.06405	0.002	T	0.13926	-1.0491	8	0.56958	D	0.05	-3.2098	.	.	.	rs4841520	30	Q96KT7	S35G5_HUMAN	C	30	ENSP00000371872:R30C	ENSP00000371872:R30C	R	+	1	0	SLC35G5	11226113	0.610000	0.26983	0.085000	0.20634	0.037000	0.13140	0.593000	0.23999	0.426000	0.26116	0.089000	0.15464	CGC	C|0.939;T|0.061	0.061	strong		0.662	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
FAM71B	153745	hgsc.bcm.edu	37	5	156590355	156590355	+	Silent	SNP	A	A	G	rs31220	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:156590355A>G	ENST00000302938.4	-	2	1016	c.921T>C	c.(919-921)ggT>ggC	p.G307G		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	307	Ala-rich.					nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGGTCACTTGACCTGGGCCTG	0.522													G|||	763	0.152356	0.3631	0.1138	5008	,	,		21181	0.0139		0.1372	False		,,,				2504	0.0532				p.G307G		Atlas-SNP	.											.	FAM71B	145	.	0			c.T921C						PASS	.	G		1483,2923	676.6+/-403.3	246,991,966	118.0	113.0	115.0		921	0.8	0.0	5	dbSNP_76	115	1271,7329	760.1+/-407.6	89,1093,3118	no	coding-synonymous	FAM71B	NM_130899.2		335,2084,4084	GG,GA,AA		14.7791,33.6586,21.1748		307/606	156590355	2754,10252	2203	4300	6503	SO:0001819	synonymous_variant	153745	exon2			CACTTGACCTGGG		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.921T>C	5.37:g.156590355A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Silent	SNP	ENST00000302938.4	37	CCDS4335.1																																																																																			A|0.813;G|0.187	0.187	strong		0.522	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899	
RUFY4	285180	hgsc.bcm.edu	37	2	218940418	218940418	+	Silent	SNP	C	C	T	rs4674246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:218940418C>T	ENST00000344321.7	+	9	1721	c.1203C>T	c.(1201-1203)gcC>gcT	p.A401A	RUFY4_ENST00000441828.2_3'UTR|RUFY4_ENST00000463872.1_3'UTR|RUFY4_ENST00000374155.3_Silent_p.A421A	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	401							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CCCTTGTGGCCAGAAGGGAGG	0.567													C|||	847	0.169129	0.152	0.111	5008	,	,		18551	0.1508		0.1372	False		,,,				2504	0.2853				p.A401A		Atlas-SNP	.											.	RUFY4	59	.	0			c.C1203T						PASS	.	C		507,3501		26,455,1523	86.0	82.0	83.0		1203	0.9	0.0	2	dbSNP_111	83	1020,7316		67,886,3215	no	coding-synonymous	RUFY4	NM_198483.3		93,1341,4738	TT,TC,CC		12.2361,12.6497,12.3704		401/572	218940418	1527,10817	2004	4168	6172	SO:0001819	synonymous_variant	285180	exon9			TGTGGCCAGAAGG	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"""Zinc fingers, FYVE domain containing"""	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.1203C>T	2.37:g.218940418C>T		Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	289	147	0.508651	NM_198483	Q6ZR96	Silent	SNP	ENST00000344321.7	37																																																																																				C|0.836;T|0.164	0.164	strong		0.567	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483	
FEM1C	56929	hgsc.bcm.edu	37	5	114860161	114860161	+	Silent	SNP	G	G	A	rs73253005	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:114860161G>A	ENST00000274457.3	-	3	2259	c.1698C>T	c.(1696-1698)gaC>gaT	p.D566D		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	566					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		CATCCAGCAAGTCACTAGCAG	0.378													G|||	457	0.091254	0.1263	0.049	5008	,	,		19914	0.0962		0.0746	False		,,,				2504	0.0859				p.D566D		Atlas-SNP	.											.	FEM1C	50	.	0			c.C1698T						PASS	.	G		536,3868	242.1+/-252.3	38,460,1704	148.0	143.0	145.0		1698	4.1	1.0	5	dbSNP_130	145	757,7843	181.0+/-229.8	37,683,3580	no	coding-synonymous	FEM1C	NM_020177.2		75,1143,5284	AA,AG,GG		8.8023,12.1708,9.9431		566/618	114860161	1293,11711	2202	4300	6502	SO:0001819	synonymous_variant	56929	exon3			CAGCAAGTCACTA		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"""Ankyrin repeat domain containing"""	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1698C>T	5.37:g.114860161G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	202	110	0.544554	NM_020177	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Silent	SNP	ENST00000274457.3	37	CCDS4118.1																																																																																			G|0.899;A|0.101	0.101	strong		0.378	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177	
PFKP	5214	hgsc.bcm.edu	37	10	3172145	3172145	+	Silent	SNP	C	C	T	rs1052337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:3172145C>T	ENST00000381125.4	+	17	1894	c.1818C>T	c.(1816-1818)ttC>ttT	p.F606F	PFKP_ENST00000381072.1_Silent_p.F24F|PFKP_ENST00000381075.2_Silent_p.F598F	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	606	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		CATACATTTTCGAAGAGCCCT	0.627													C|||	625	0.1248	0.1967	0.0821	5008	,	,		16234	0.0526		0.1292	False		,,,				2504	0.1278				p.F606F		Atlas-SNP	.											PFKP_ENST00000381075,colon,carcinoma,0,2	PFKP	182	2	0			c.C1818T						scavenged	.	C	,	828,3578	313.6+/-293.2	76,676,1451	45.0	42.0	43.0		1794,1818	-5.4	0.2	10	dbSNP_86	43	1252,7348	243.5+/-273.1	99,1054,3147	no	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	175,1730,4598	TT,TC,CC		14.5581,18.7926,15.9926	,	598/777,606/785	3172145	2080,10926	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon17			CATTTTCGAAGAG	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1818C>T	10.37:g.3172145C>T		Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1																																																																																			C|0.856;G|0.000;T|0.144	0.144	strong		0.627	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
C1orf74	148304	hgsc.bcm.edu	37	1	209956542	209956542	+	Missense_Mutation	SNP	C	C	A	rs7550857	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:209956542C>A	ENST00000294811.1	-	2	694	c.438G>T	c.(436-438)ttG>ttT	p.L146F		NM_152485.2	NP_689698.1	Q96LT6	CA074_HUMAN	chromosome 1 open reading frame 74	146			L -> F (in dbSNP:rs7550857).							endometrium(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	15				OV - Ovarian serous cystadenocarcinoma(81;0.0328)		GCAGCCCCTGCAAATGTGTGA	0.542													C|||	777	0.155152	0.2231	0.1009	5008	,	,		19943	0.0744		0.1412	False		,,,				2504	0.1994				p.L146F		Atlas-SNP	.											.	C1orf74	30	.	0			c.G438T						PASS	.	C	PHE/LEU	1019,3387	379.0+/-323.1	120,779,1304	63.0	62.0	62.0		438	0.9	0.7	1	dbSNP_116	62	1380,7220	267.9+/-287.5	129,1122,3049	yes	missense	C1orf74	NM_152485.2	22	249,1901,4353	AA,AC,CC		16.0465,23.1276,18.4453	benign	146/270	209956542	2399,10607	2203	4300	6503	SO:0001583	missense	148304	exon2			CCCCTGCAAATGT	AK057807	CCDS1491.1	1q32.2	2008-02-05			ENSG00000162757	ENSG00000162757			26319	protein-coding gene	gene with protein product						12477932	Standard	NM_152485		Approved	FLJ25078	uc001hhp.1	Q96LT6	OTTHUMG00000036483	ENST00000294811.1:c.438G>T	1.37:g.209956542C>A	ENSP00000294811:p.Leu146Phe	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_152485		Missense_Mutation	SNP	ENST00000294811.1	37	CCDS1491.1	293	0.13415750915750915	101	0.20528455284552846	42	0.11602209944751381	41	0.07167832167832168	109	0.1437994722955145	C	8.471	0.857540	0.17106	0.231276	0.160465	ENSG00000162757	ENST00000294811	T	0.47177	0.85	5.51	0.855	0.19013	.	0.159946	0.39210	N	0.001423	T	0.00012	0.0000	N	0.17872	0.535	0.53688	P	2.199999999996649E-5	B	0.32203	0.36	B	0.29176	0.099	T	0.16424	-1.0403	9	0.33940	T	0.23	-1.7483	0.8982	0.01268	0.246:0.3399:0.1149:0.2993	rs7550857;rs56864706;rs7550857	146	Q96LT6	CA074_HUMAN	F	146	ENSP00000294811:L146F	ENSP00000294811:L146F	L	-	3	2	C1orf74	208023165	0.002000	0.14202	0.669000	0.29828	0.692000	0.40212	-0.169000	0.09911	0.270000	0.21984	0.655000	0.94253	TTG	C|0.831;A|0.169	0.169	strong		0.542	C1orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088745.1	NM_152485	
UNC13B	10497	hgsc.bcm.edu	37	9	35398605	35398605	+	Missense_Mutation	SNP	G	G	A	rs41315995	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35398605G>A	ENST00000378495.3	+	31	3862	c.3640G>A	c.(3640-3642)Gtt>Att	p.V1214I	UNC13B_ENST00000378496.4_Missense_Mutation_p.V1214I|UNC13B_ENST00000481299.1_3'UTR|UNC13B_ENST00000396787.1_Missense_Mutation_p.V1226I	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1214					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			ACTGAATACGGTTCTGGATGA	0.527													G|||	40	0.00798722	0.0015	0.0101	5008	,	,		21287	0.0		0.0239	False		,,,				2504	0.0072				p.V1214I		Atlas-SNP	.											.	UNC13B	153	.	0			c.G3640A						PASS	.	G	ILE/VAL	19,4387	26.2+/-53.5	0,19,2184	142.0	135.0	138.0		3640	5.7	1.0	9	dbSNP_127	138	151,8449	72.9+/-135.5	2,147,4151	yes	missense	UNC13B	NM_006377.3	29	2,166,6335	AA,AG,GG		1.7558,0.4312,1.3071	possibly-damaging	1214/1592	35398605	170,12836	2203	4300	6503	SO:0001583	missense	10497	exon31			AATACGGTTCTGG	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.3640G>A	9.37:g.35398605G>A	ENSP00000367756:p.Val1214Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	19	0.0086996336996337	0	0.0	5	0.013812154696132596	0	0.0	14	0.018469656992084433	G	31	5.075214	0.94000	0.004312	0.017558	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.34472	1.36;1.36;1.36	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.45377	0.1339	M	0.86573	2.825	0.80722	D	1	B;D	0.58268	0.314;0.982	B;P	0.54924	0.068;0.764	T	0.61997	-0.6947	10	0.56958	D	0.05	-16.6564	19.8236	0.96607	0.0:0.0:1.0:0.0	rs41315995	1214;1214	F8W8M9;O14795	.;UN13B_HUMAN	I	1226;1214;1214;801	ENSP00000380006:V1226I;ENSP00000367756:V1214I;ENSP00000367757:V1214I	ENSP00000367756:V1214I	V	+	1	0	UNC13B	35388605	1.000000	0.71417	0.996000	0.52242	0.914000	0.54420	6.586000	0.74067	2.695000	0.91970	0.455000	0.32223	GTT	G|0.987;A|0.013	0.013	strong		0.527	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	
DNAH17	8632	hgsc.bcm.edu	37	17	76503585	76503585	+	Silent	SNP	G	G	C	rs12943086	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:76503585G>C	ENST00000585328.1	-	28	4654	c.4530C>G	c.(4528-4530)ctC>ctG	p.L1510L	DNAH17_ENST00000389840.5_Silent_p.L1509L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1509	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			AGTCCCCCGGGAGCTGGGTGC	0.597													G|||	60	0.0119808	0.0015	0.0317	5008	,	,		19330	0.0		0.0338	False		,,,				2504	0.002				p.L1513L		Atlas-SNP	.											.	DNAH17	347	.	0			c.C4539G						PASS	.	G		19,4133		0,19,2057	45.0	50.0	48.0		4539	-1.1	0.9	17	dbSNP_121	48	286,8196		6,274,3961	no	coding-synonymous	DNAH17	NM_173628.3		6,293,6018	CC,CG,GG		3.3718,0.4576,2.4141		1513/4463	76503585	305,12329	2076	4241	6317	SO:0001819	synonymous_variant	8632	exon28			CCCCGGGAGCTGG	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.4530C>G	17.37:g.76503585G>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.977;C|0.023	0.023	strong		0.597	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
MDM2	4193	hgsc.bcm.edu	37	12	69233215	69233215	+	Silent	SNP	A	A	G	rs769412	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:69233215A>G	ENST00000350057.5	+	9	987	c.987A>G	c.(985-987)gaA>gaG	p.E329E	RP11-611O2.5_ENST00000553141.1_RNA|MDM2_ENST00000540827.1_Silent_p.E159E|MDM2_ENST00000478070.1_3'UTR|MDM2_ENST00000348801.2_Silent_p.E128E|MDM2_ENST00000517852.1_Intron|MDM2_ENST00000428863.2_Silent_p.E133E|MDM2_ENST00000356290.4_Silent_p.E184E|MDM2_ENST00000393410.1_Silent_p.E106E|MDM2_ENST00000360430.2_Silent_p.E159E|MDM2_ENST00000545204.1_Intron|MDM2_ENST00000258149.5_Silent_p.E299E|MDM2_ENST00000393413.3_Silent_p.E81E|MDM2_ENST00000299252.4_Silent_p.E184E|MDM2_ENST00000393412.3_Silent_p.E81E|MDM2_ENST00000462284.1_Silent_p.E360E|MDM2_ENST00000258148.7_Silent_p.E305E|MDM2_ENST00000544561.1_Intron			Q00987	MDM2_HUMAN	MDM2 proto-oncogene, E3 ubiquitin protein ligase	354	Necessary for interaction with USP2.|Region II.				cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1)	19	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			CACAAGCTGAAGAGGGCTTTG	0.388			A		"""sarcoma, glioma, colorectal, other"""								A|||	391	0.0780751	0.1505	0.072	5008	,	,		20089	0.0179		0.0676	False		,,,				2504	0.0573				p.E360E		Atlas-SNP	.		Dom	yes		12	12q15	4193	Mdm2 p53 binding protein homolog		"""M, O, E, L"""	.	MDM2	92	.	0			c.A1080G						PASS	.	A		453,3245		29,395,1425	102.0	96.0	98.0		1080	1.7	0.7	12	dbSNP_86	98	485,7673		16,453,3610	no	coding-synonymous	MDM2	NM_002392.3		45,848,5035	GG,GA,AA		5.9451,12.2499,7.9116		360/498	69233215	938,10918	1849	4079	5928	SO:0001819	synonymous_variant	4193	exon11			AGCTGAAGAGGGC		CCDS8986.2, CCDS61189.1	12q13-q14	2014-06-26	2014-06-26		ENSG00000135679	ENSG00000135679			6973	protein-coding gene	gene with protein product		164785	"""mouse double minute 2, human homolog of; p53-binding protein"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)"", ""Mdm2 p53 binding protein homolog (mouse)"""			1614537, 16905769	Standard	NM_002392		Approved	HDM2, MGC5370	uc001sui.4	Q00987	OTTHUMG00000142827	ENST00000350057.5:c.987A>G	12.37:g.69233215A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	123	53	0.430894	NM_002392	A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8	Silent	SNP	ENST00000350057.5	37																																																																																				A|0.927;G|0.073	0.073	strong		0.388	MDM2-033	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000402665.1	NM_006880	
ELL2	22936	hgsc.bcm.edu	37	5	95234392	95234392	+	Silent	SNP	A	A	C	rs3777202	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:95234392A>C	ENST00000237853.4	-	8	1426	c.1077T>G	c.(1075-1077)tcT>tcG	p.S359S	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	359					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		GGCCTGCAGCAGATTTTTCAC	0.498													A|||	1930	0.385383	0.5318	0.2464	5008	,	,		15337	0.4325		0.2803	False		,,,				2504	0.3456				p.S359S		Atlas-SNP	.											ELL2,NS,carcinoma,-1,1	ELL2	63	1	0			c.T1077G						PASS	.	A		2118,2282		532,1054,614	85.0	105.0	99.0		1077	-6.7	0.0	5	dbSNP_107	99	2233,6363		292,1649,2357	no	coding-synonymous	ELL2	NM_012081.5		824,2703,2971	CC,CA,AA		25.9772,48.1364,33.4795		359/641	95234392	4351,8645	2200	4298	6498	SO:0001819	synonymous_variant	22936	exon8			TGCAGCAGATTTT	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1077T>G	5.37:g.95234392A>C		Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	316	150	0.474684	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	37	CCDS4080.1																																																																																			A|0.674;C|0.326	0.326	strong		0.498	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
ZNF780B	163131	hgsc.bcm.edu	37	19	40541845	40541845	+	Silent	SNP	A	A	G	rs371876870		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40541845A>G	ENST00000434248.1	-	5	986	c.921T>C	c.(919-921)tgT>tgC	p.C307C	ZNF780B_ENST00000221355.6_Silent_p.C159C	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	307					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)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CACATTCCCTACATACAAAGG	0.373																																					p.C307C		Atlas-SNP	.											.	ZNF780B	143	.	0			c.T921C						PASS	.	A		0,4406		0,0,2203	116.0	118.0	117.0		921	1.1	0.5	19		117	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF780B	NM_001005851.2		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		307/834	40541845	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	163131	exon5			TTCCCTACATACA	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"""Zinc fingers, C2H2-type"", ""-"""	33109	protein-coding gene	gene with protein product			"""zinc finger protein 779"""	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.921T>C	19.37:g.40541845A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	99	38	0.383838	NM_001005851	B9EH00	Silent	SNP	ENST00000434248.1	37	CCDS46077.1																																																																																			.	.	weak		0.373	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851	
ADCY10	55811	hgsc.bcm.edu	37	1	167825485	167825485	+	Missense_Mutation	SNP	T	T	C	rs2071921	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:167825485T>C	ENST00000367851.4	-	17	2273	c.2089A>G	c.(2089-2091)Att>Gtt	p.I697V	ADCY10_ENST00000367848.1_Missense_Mutation_p.I605V|ADCY10_ENST00000545172.1_Missense_Mutation_p.I544V	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	697			I -> V (in dbSNP:rs2071921). {ECO:0000269|PubMed:11423534, ECO:0000269|PubMed:11932268, ECO:0000269|PubMed:12609998}.		cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						ACTGCACCAATGACAATGTAG	0.458													t|||	2527	0.504593	0.4599	0.5749	5008	,	,		19993	0.7113		0.4105	False		,,,				2504	0.3988				p.I697V		Atlas-SNP	.											.	ADCY10	175	.	0			c.A2089G						PASS	.	T	VAL/ILE,VAL/ILE	2032,2374	563.4+/-381.2	471,1090,642	303.0	255.0	271.0		1630,2089	-2.4	0.0	1	dbSNP_96	271	3436,5164	506.2+/-376.5	692,2052,1556	yes	missense,missense	ADCY10	NM_001167749.1,NM_018417.4	29,29	1163,3142,2198	CC,CT,TT		39.9535,46.1189,42.0421	benign,benign	544/1458,697/1611	167825485	5468,7538	2203	4300	6503	SO:0001583	missense	55811	exon17			CACCAATGACAAT	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"""Adenylate cyclases"""	21285	protein-coding gene	gene with protein product	"""soluble adenylyl cyclase"", ""Hypercalciuria, absorptive, 2"""	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.2089A>G	1.37:g.167825485T>C	ENSP00000356825:p.Ile697Val	Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	290	286	0.986207	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	37	CCDS1265.1	1129	0.516941391941392	220	0.44715447154471544	188	0.5193370165745856	408	0.7132867132867133	313	0.4129287598944591	t	0.819	-0.749259	0.03065	0.461189	0.399535	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	T;T;T	0.33438	1.41;1.41;1.41	5.16	-2.43	0.06522	.	0.557476	0.16133	N	0.228103	T	0.09555	0.0235	L	0.46157	1.445	0.09310	P	0.999995	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.24870	-1.0148	9	0.38643	T	0.18	-4.5789	8.8481	0.35184	0.0:0.2154:0.3222:0.4624	rs2071921;rs52793140;rs60587593;rs2071921	544;605;697	F5GWS5;Q96PN6-2;Q96PN6	.;.;ADCYA_HUMAN	V	544;697;605	ENSP00000441992:I544V;ENSP00000356825:I697V;ENSP00000356822:I605V	ENSP00000356822:I605V	I	-	1	0	ADCY10	166092109	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	0.086000	0.14935	-0.260000	0.09418	-2.765000	0.00121	ATT	C|0.470;N|0.000	0.470	strong		0.458	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417	
MAMLD1	10046	hgsc.bcm.edu	37	X	149639035	149639035	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:149639035C>A	ENST00000370401.2	+	4	1500	c.1190C>A	c.(1189-1191)gCt>gAt	p.A397D	MAMLD1_ENST00000426613.2_Missense_Mutation_p.A372D|MAMLD1_ENST00000455522.2_5'Flank|MAMLD1_ENST00000262858.5_Missense_Mutation_p.A397D|MAMLD1_ENST00000432680.2_Missense_Mutation_p.A372D			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	397					male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					AGCAGCAATGCTGCCCTGGGG	0.597																																					p.A397D		Atlas-SNP	.											.	MAMLD1	263	.	0			c.C1190A						PASS	.						107.0	102.0	104.0					X																	149639035		2203	4300	6503	SO:0001583	missense	10046	exon3			GCAATGCTGCCCT	U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"""chromosome X open reading frame 6"""	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.1190C>A	X.37:g.149639035C>A	ENSP00000359428:p.Ala397Asp	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	124	20	0.16129	NM_005491	B2RCQ4|B4DG93|B9EGA5	Missense_Mutation	SNP	ENST00000370401.2	37	CCDS14693.2	.	.	.	.	.	.	.	.	.	.	C	7.869	0.727815	0.15507	.	.	ENSG00000013619	ENST00000445612;ENST00000370401;ENST00000432680;ENST00000262858;ENST00000426613	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.03	3.2	0.36748	.	0.474459	0.21020	N	0.081532	T	0.76054	0.3934	L	0.47716	1.5	0.21290	N	0.999735	D;D;D;D	0.71674	0.996;0.96;0.998;0.96	P;B;D;P	0.66351	0.899;0.408;0.943;0.59	T	0.66228	-0.5976	9	.	.	.	-2.4414	11.1467	0.48434	0.1443:0.7201:0.1356:0.0	.	359;372;372;397	F6WVG1;Q13495-4;Q13495-3;Q13495	.;.;.;MAMD1_HUMAN	D	359;397;372;397;372	ENSP00000359428:A397D;ENSP00000414517:A372D;ENSP00000262858:A397D;ENSP00000397438:A372D	.	A	+	2	0	MAMLD1	149389693	0.101000	0.21875	0.000000	0.03702	0.046000	0.14306	4.214000	0.58527	0.358000	0.24211	0.529000	0.55759	GCT	.	.	none		0.597	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491	
MOGS	7841	hgsc.bcm.edu	37	2	74690039	74690039	+	Missense_Mutation	SNP	G	G	A	rs2268416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:74690039G>A	ENST00000233616.4	-	4	1039	c.877C>T	c.(877-879)Ccc>Tcc	p.P293S	MOGS_ENST00000535045.1_3'UTR|MOGS_ENST00000452063.2_Missense_Mutation_p.P187S|MOGS_ENST00000462443.1_5'UTR|MOGS_ENST00000409065.1_3'UTR	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	293			P -> S (in dbSNP:rs2268416). {ECO:0000269|PubMed:7635146}.		cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						CGTTCAGGGGGGGCCCCTGGG	0.592													A|||	2698	0.538738	0.8714	0.3242	5008	,	,		18027	0.8214		0.159	False		,,,				2504	0.3405				p.P293S		Atlas-SNP	.											.	MOGS	58	.	0			c.C877T						PASS	.	A	SER/PRO,SER/PRO	2873,1041		1062,749,146	112.0	120.0	118.0		559,877	0.9	0.1	2	dbSNP_100	118	1202,7096		95,1012,3042	yes	missense,missense	MOGS	NM_001146158.1,NM_006302.2	74,74	1157,1761,3188	AA,AG,GG		14.4854,26.5968,33.3688	benign,benign	187/732,293/838	74690039	4075,8137	1957	4149	6106	SO:0001583	missense	7841	exon4			CAGGGGGGGCCCC	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"""glucosidase I"", ""processing A-glucosidase I"""	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.877C>T	2.37:g.74690039G>A	ENSP00000233616:p.Pro293Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	61	40	0.655738	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	37	CCDS42700.1	1100	0.5036630036630036	419	0.8516260162601627	97	0.26795580110497236	469	0.8199300699300699	115	0.1517150395778364	A	0.007	-1.939376	0.00484	0.734032	0.144854	ENSG00000115275	ENST00000233616;ENST00000452063;ENST00000448666	T;T;T	0.35973	1.28;1.28;1.28	4.85	0.945	0.19543	.	0.491884	0.22259	N	0.062440	T	0.00012	0.0000	N	0.01168	-0.975	0.09310	P	0.99999454037	B	0.02656	0.0	B	0.01281	0.0	T	0.33954	-0.9848	9	0.05721	T	0.95	-3.9946	1.0778	0.01636	0.5087:0.1551:0.1865:0.1497	rs2268416;rs58722329	293	Q13724	MOGS_HUMAN	S	293;187;187	ENSP00000233616:P293S;ENSP00000388201:P187S;ENSP00000410992:P187S	ENSP00000233616:P293S	P	-	1	0	MOGS	74543547	0.263000	0.24083	0.094000	0.20943	0.518000	0.34316	0.754000	0.26390	-0.235000	0.09767	-0.254000	0.11334	CCC	G|0.582;A|0.418	0.418	strong		0.592	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302	
KIAA1462	57608	hgsc.bcm.edu	37	10	30317826	30317826	+	Silent	SNP	A	A	G	rs7920682	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:30317826A>G	ENST00000375377.1	-	3	1352	c.1251T>C	c.(1249-1251)taT>taC	p.Y417Y		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	417					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						CGAAGCCGTCATAGGCAGTGA	0.547													G|||	2671	0.533347	0.9138	0.3847	5008	,	,		19040	0.3413		0.4841	False		,,,				2504	0.3732				p.Y417Y		Atlas-SNP	.											.	KIAA1462	162	.	0			c.T1251C						PASS	.	G		3295,605		1396,503,51	71.0	77.0	75.0		1251	-5.2	0.0	10	dbSNP_116	75	3945,4335		928,2089,1123	no	coding-synonymous	KIAA1462	NM_020848.2		2324,2592,1174	GG,GA,AA		47.6449,15.5128,40.5583		417/1360	30317826	7240,4940	1950	4140	6090	SO:0001819	synonymous_variant	57608	exon3			GCCGTCATAGGCA	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.1251T>C	10.37:g.30317826A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																			A|0.463;G|0.537	0.537	strong		0.547	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
ALX4	60529	hgsc.bcm.edu	37	11	44331509	44331509	+	Missense_Mutation	SNP	C	C	G	rs3824915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:44331509C>G	ENST00000329255.3	-	1	207	c.104G>C	c.(103-105)aGg>aCg	p.R35T		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	35			R -> T (in dbSNP:rs3824915). {ECO:0000269|PubMed:11106354, ECO:0000269|PubMed:11137991}.		anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						GGGAAATGCCCTAAAAGGCGA	0.642													C|||	2367	0.472644	0.2443	0.3833	5008	,	,		12277	0.5079		0.4682	False		,,,				2504	0.8129				p.R35T		Atlas-SNP	.											.	ALX4	58	.	0			c.G104C						PASS	.		THR/ARG	1324,3076		198,928,1074	16.0	19.0	18.0		104	4.6	1.0	11	dbSNP_107	18	4189,4407		1013,2163,1122	yes	missense	ALX4	NM_021926.3	71	1211,3091,2196	GG,GC,CC		48.732,30.0909,42.4207	probably-damaging	35/412	44331509	5513,7483	2200	4298	6498	SO:0001583	missense	60529	exon1			AATGCCCTAAAAG	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"""Homeoboxes / PRD class"""	450	protein-coding gene	gene with protein product		605420	"""parietal foramina 2"", ""aristaless-like homeobox 4"""	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.104G>C	11.37:g.44331509C>G	ENSP00000332744:p.Arg35Thr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	160	79	0.49375	NM_021926	Q96JN7|Q9H198|Q9HAY9	Missense_Mutation	SNP	ENST00000329255.3	37	CCDS31468.1	913	0.41804029304029305	126	0.25609756097560976	136	0.3756906077348066	280	0.48951048951048953	371	0.4894459102902375	c	28.2	4.901377	0.92035	0.300909	0.48732	ENSG00000052850	ENST00000329255	D	0.96427	-4.01	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	0.99999604534	B	0.34103	0.437	B	0.30401	0.115	T	0.00995	-1.1487	9	0.72032	D	0.01	.	17.4764	0.87660	0.0:1.0:0.0:0.0	rs3824915;rs3824915	35	Q9H161	ALX4_HUMAN	T	35	ENSP00000332744:R35T	ENSP00000332744:R35T	R	-	2	0	ALX4	44288085	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.269000	0.65542	2.108000	0.64289	0.457000	0.33378	AGG	C|0.594;G|0.406	0.406	strong		0.642	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1		
SLC2A14	144195	hgsc.bcm.edu	37	12	7967076	7967076	+	Silent	SNP	A	A	G	rs10845983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7967076A>G	ENST00000543909.1	-	16	2158	c.1399T>C	c.(1399-1401)Ttg>Ctg	p.L467L	SLC2A14_ENST00000431042.2_Silent_p.L444L|SLC2A14_ENST00000542505.1_Silent_p.L108L|SLC2A14_ENST00000396589.2_Silent_p.L467L|SLC2A14_ENST00000542546.1_Silent_p.L358L|SLC2A14_ENST00000539924.1_Silent_p.L482L|SLC2A14_ENST00000535295.1_Silent_p.L358L|SLC2A14_ENST00000340749.5_Silent_p.L444L			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	467					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		GTAAAGGCCAAGAAGGTAATG	0.453													A|||	1049	0.209465	0.0204	0.3674	5008	,	,		-128	0.1181		0.338	False		,,,				2504	0.3149				p.L467L		Atlas-SNP	.											SLC2A14,NS,carcinoma,+2,1	SLC2A14	78	1	0			c.T1399C						PASS	.	A		333,4073	173.0+/-202.9	18,297,1888	66.0	66.0	66.0		1399	2.4	0.2	12	dbSNP_120	66	2898,5702	449.7+/-362.2	459,1980,1861	no	coding-synonymous	SLC2A14	NM_153449.2		477,2277,3749	GG,GA,AA		33.6977,7.5579,24.8424		467/521	7967076	3231,9775	2203	4300	6503	SO:0001819	synonymous_variant	144195	exon12			AGGCCAAGAAGGT	AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"""Solute carriers"""	18301	protein-coding gene	gene with protein product		611039	"""solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"""	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.1399T>C	12.37:g.7967076A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	127	54	0.425197	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Silent	SNP	ENST00000543909.1	37	CCDS8585.1																																																																																			A|0.760;G|0.240	0.240	strong		0.453	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449	
PLEC	5339	hgsc.bcm.edu	37	8	144996029	144996029	+	Missense_Mutation	SNP	A	A	G	rs7833924	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144996029A>G	ENST00000322810.4	-	32	8540	c.8371T>C	c.(8371-8373)Tca>Cca	p.S2791P	PLEC_ENST00000398774.2_Missense_Mutation_p.S2622P|PLEC_ENST00000345136.3_Missense_Mutation_p.S2654P|PLEC_ENST00000354589.3_Missense_Mutation_p.S2654P|PLEC_ENST00000354958.2_Missense_Mutation_p.S2632P|PLEC_ENST00000436759.2_Missense_Mutation_p.S2681P|PLEC_ENST00000527096.1_Missense_Mutation_p.S2677P|PLEC_ENST00000356346.3_Missense_Mutation_p.S2640P|PLEC_ENST00000357649.2_Missense_Mutation_p.S2658P	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2791	Globular 2.		S -> P (in dbSNP:rs7833924).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CTCTGAGCTGACACCTTCCGC	0.687													G|||	2337	0.466653	0.8775	0.3674	5008	,	,		16760	0.1429		0.4354	False		,,,				2504	0.3476				p.S2791P		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,9	PLEC	1144	9	0			c.T8371C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER	3507,739		1479,549,95	13.0	16.0	15.0		8041,7918,7894,8371,7864,7960,7972,7960	1.3	0.6	8	dbSNP_116	15	3635,4801		854,1927,1437	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	74,74,74,74,74,74,74,74	2333,2476,1532	GG,GA,AA		43.0891,17.4046,43.684	benign,benign,benign,benign,benign,benign,benign,benign	2681/4575,2640/4534,2632/4526,2791/4685,2622/4516,2654/4548,2658/4552,2654/4548	144996029	7142,5540	2123	4218	6341	SO:0001583	missense	5339	exon32			GAGCTGACACCTT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8371T>C	8.37:g.144996029A>G	ENSP00000323856:p.Ser2791Pro	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	26	7	0.269231	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	978	0.4478021978021978	423	0.8597560975609756	137	0.3784530386740331	94	0.16433566433566432	324	0.42744063324538256	G	9.708	1.156295	0.21454	0.825954	0.430891	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43	4.16	1.26	0.21427	.	0.000000	0.64402	N	0.000006	T	0.00012	0.0000	N	0.05441	-0.05	0.46678	P	8.430000000000382E-4	B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.42766	-0.9432	9	0.02654	T	1	.	3.6953	0.08361	0.4852:0.1979:0.317:0.0	rs7833924	2681;2640;2632;2791;2622;2654;2658;2654	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	P	2654;2658;2654;2622;2791;2632;2640;2681;2677	ENSP00000344848:S2654P;ENSP00000350277:S2658P;ENSP00000346602:S2654P;ENSP00000381756:S2622P;ENSP00000323856:S2791P;ENSP00000347044:S2632P;ENSP00000348702:S2640P;ENSP00000388180:S2681P;ENSP00000434583:S2677P	ENSP00000323856:S2791P	S	-	1	0	PLEC	145068017	0.803000	0.28956	0.551000	0.28230	0.791000	0.44710	0.441000	0.21611	0.147000	0.19030	-0.380000	0.06706	TCA	A|0.560;G|0.440	0.440	strong		0.687	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
METTL7B	196410	hgsc.bcm.edu	37	12	56077599	56077599	+	Silent	SNP	A	A	T	rs73117273	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56077599A>T	ENST00000394252.3	+	2	710	c.501A>T	c.(499-501)ggA>ggT	p.G167G		NM_152637.2	NP_689850.2	Q6UX53	MET7B_HUMAN	methyltransferase like 7B	167							methyltransferase activity (GO:0008168)			kidney(1)|large_intestine(1)|lung(4)	6						CCTCCCAGGGAGGTGTGCTCT	0.527													A|||	25	0.00499201	0.0008	0.0043	5008	,	,		18463	0.0		0.0179	False		,,,				2504	0.0031				p.G167G		Atlas-SNP	.											.	METTL7B	35	.	0			c.A501T						PASS	.	A		12,4394	20.2+/-43.8	0,12,2191	129.0	127.0	128.0		501	2.8	1.0	12	dbSNP_130	128	67,8533	41.7+/-99.0	1,65,4234	no	coding-synonymous	METTL7B	NM_152637.2		1,77,6425	TT,TA,AA		0.7791,0.2724,0.6074		167/245	56077599	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	196410	exon2			CCAGGGAGGTGTG		CCDS8887.2	12q13.2	2012-06-12			ENSG00000170439	ENSG00000170439			28276	protein-coding gene	gene with protein product	"""associated with lipid droplets 1"""					17004324	Standard	NM_152637		Approved	MGC17301, ALDI	uc010spr.2	Q6UX53	OTTHUMG00000152665	ENST00000394252.3:c.501A>T	12.37:g.56077599A>T		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	250	126	0.504	NM_152637	A8K247|Q8WUI1	Silent	SNP	ENST00000394252.3	37	CCDS8887.2																																																																																			A|0.993;T|0.007	0.007	strong		0.527	METTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327271.1	NM_152637	
GPER1	2852	hgsc.bcm.edu	37	7	1131411	1131411	+	Missense_Mutation	SNP	C	C	T	rs11544331	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1131411C>T	ENST00000297469.3	+	2	738	c.47C>T	c.(46-48)cCa>cTa	p.P16L	C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|GPER1_ENST00000397088.3_Missense_Mutation_p.P16L|C7orf50_ENST00000357429.6_Intron|GPER1_ENST00000397092.1_Missense_Mutation_p.P16L|GPER1_ENST00000401670.1_Missense_Mutation_p.P16L	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	16			P -> L (in dbSNP:rs11544331). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19054851}.		apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										GAGATGTACCCAGGCACCGCG	0.652													C|||	696	0.138978	0.1021	0.2104	5008	,	,		16292	0.0248		0.2048	False		,,,				2504	0.1881				p.P16L		Atlas-SNP	.											.	GPER	25	.	0			c.C47T						PASS	.		LEU/PRO,LEU/PRO,,,LEU/PRO,	507,3897	232.0+/-245.7	34,439,1729	53.0	57.0	55.0		47,47,,,47,	-0.1	0.0	7	dbSNP_120	55	2106,6494	358.5+/-331.2	276,1554,2470	yes	missense,missense,intron,intron,missense,intron	GPER,C7orf50	NM_001039966.1,NM_001098201.1,NM_001134395.1,NM_001134396.1,NM_001505.2,NM_032350.5	98,98,,,98,	310,1993,4199	TT,TC,CC		24.4884,11.5123,20.0938	benign,benign,,,benign,	16/376,16/376,,,16/376,	1131411	2613,10391	2202	4300	6502	SO:0001583	missense	2852	exon2			TGTACCCAGGCAC	U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"""G protein-coupled receptor 30"""	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.47C>T	7.37:g.1131411C>T	ENSP00000297469:p.Pro16Leu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	153	80	0.522876	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Missense_Mutation	SNP	ENST00000297469.3	37	CCDS5322.1	319	0.14606227106227107	70	0.14227642276422764	66	0.18232044198895028	19	0.033216783216783216	164	0.21635883905013192	C	10.93	1.490502	0.26686	0.115123	0.244884	ENSG00000164850	ENST00000401670;ENST00000413368;ENST00000397092;ENST00000297469;ENST00000397088;ENST00000508834	T;T;T;T;T	0.67171	-0.25;1.03;-0.25;-0.25;-0.25	5.02	-0.101	0.13618	.	0.664049	0.13173	N	0.408117	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.09640	-1.0665	9	0.31617	T	0.26	.	8.8766	0.35350	0.0:0.5996:0.0:0.4004	rs11544331;rs17850769	16	Q99527	GPER_HUMAN	L	16	ENSP00000385151:P16L;ENSP00000410487:P16L;ENSP00000380281:P16L;ENSP00000297469:P16L;ENSP00000380277:P16L	ENSP00000297469:P16L	P	+	2	0	GPER	1097937	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.053000	0.14184	-0.347000	0.08299	0.655000	0.94253	CCA	C|0.808;T|0.192	0.192	strong		0.652	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966	
AMPD3	272	hgsc.bcm.edu	37	11	10503756	10503756	+	Silent	SNP	G	G	A	rs16907852	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:10503756G>A	ENST00000396554.3	+	4	941	c.600G>A	c.(598-600)ccG>ccA	p.P200P	AMPD3_ENST00000444303.2_Silent_p.P32P	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	191					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		CTGCACCTCCGGAAGAGGGCC	0.607													G|||	657	0.13119	0.3253	0.0879	5008	,	,		17518	0.003		0.0994	False		,,,				2504	0.0644				p.P200P		Atlas-SNP	.											.	AMPD3	68	.	0			c.G600A						PASS	.	G	,,,,	1210,3188		160,890,1149	37.0	42.0	40.0		600,573,594,573,96	-4.3	0.0	11	dbSNP_123	40	796,7790		30,736,3527	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMPD3	NM_000480.2,NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1	,,,,	190,1626,4676	AA,AG,GG		9.2709,27.5125,15.4498	,,,,	200/777,191/768,198/775,191/768,32/609	10503756	2006,10978	2199	4293	6492	SO:0001819	synonymous_variant	272	exon4			ACCTCCGGAAGAG	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.600G>A	11.37:g.10503756G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	37	CCDS7802.1																																																																																			G|0.846;A|0.154	0.154	strong		0.607	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
UCP3	7352	hgsc.bcm.edu	37	11	73715542	73715542	+	Silent	SNP	G	G	A	rs2075577	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:73715542G>A	ENST00000314032.4	-	5	1182	c.630C>T	c.(628-630)taC>taT	p.Y210Y	UCP3_ENST00000545271.1_5'Flank|UCP3_ENST00000348534.4_Intron|UCP3_ENST00000426995.2_Silent_p.Y210Y	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	210					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to hormone stimulus (GO:0032870)|fatty acid metabolic process (GO:0006631)|lipid metabolic process (GO:0006629)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to activity (GO:0014823)|response to cold (GO:0009409)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					TGAGCAGGTGGTAGTCCAGCA	0.587													A|||	2958	0.590655	0.8555	0.5418	5008	,	,		20118	0.4246		0.5378	False		,,,				2504	0.4928				p.Y210Y		Atlas-SNP	.											.	UCP3	31	.	0			c.C630T						PASS	.	A	,	3531,869	340.5+/-306.2	1424,683,93	138.0	104.0	116.0		630,630	-4.0	0.0	11	dbSNP_96	116	4706,3880	544.7+/-384.6	1294,2118,881	no	coding-synonymous,coding-synonymous	UCP3	NM_003356.3,NM_022803.2	,	2718,2801,974	AA,AG,GG		45.1898,19.75,36.5702	,	210/313,210/276	73715542	8237,4749	2200	4293	6493	SO:0001819	synonymous_variant	7352	exon5			CAGGTGGTAGTCC	AF001787	CCDS8229.1, CCDS44677.1	11q13.4	2013-05-22				ENSG00000175564		"""Solute carriers"""	12519	protein-coding gene	gene with protein product		602044				9480760, 9196039	Standard	NM_003356		Approved	SLC25A9	uc001our.3	P55916		ENST00000314032.4:c.630C>T	11.37:g.73715542G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	153	150	0.980392	NM_003356	O60475|Q96HL3	Silent	SNP	ENST00000314032.4	37	CCDS8229.1																																																																																			G|0.383;A|0.617	0.617	strong		0.587	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356	
SMIM8	57150	hgsc.bcm.edu	37	6	88046800	88046800	+	Silent	SNP	G	G	A	rs1048893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:88046800G>A	ENST00000392863.1	+	3	140	c.51G>A	c.(49-51)gaG>gaA	p.E17E	SMIM8_ENST00000229570.5_Silent_p.E17E|SMIM8_ENST00000608868.1_Silent_p.E17E|SMIM8_ENST00000608525.1_Silent_p.E17E|RP1-102H19.8_ENST00000448282.2_Silent_p.E17E|SMIM8_ENST00000608353.1_Silent_p.E17E	NM_001042493.1	NP_001035958.1	Q96KF7	SMIM8_HUMAN	small integral membrane protein 8	17						integral component of membrane (GO:0016021)											CACCCAAAGAGAAAGAGTTTC	0.388													G|||	559	0.111621	0.0976	0.0706	5008	,	,		15362	0.1349		0.1153	False		,,,				2504	0.1319				p.E17E		Atlas-SNP	.											.	.	.	.	0			c.G51A						PASS	.	G	,	427,3979	208.2+/-229.3	19,389,1795	85.0	87.0	86.0		51,51	0.8	1.0	6	dbSNP_86	86	957,7643	209.8+/-250.9	51,855,3394	no	coding-synonymous,coding-synonymous	C6orf162	NM_001042493.1,NM_020425.4	,	70,1244,5189	AA,AG,GG		11.1279,9.6913,10.6412	,	17/98,17/98	88046800	1384,11622	2203	4300	6503	SO:0001819	synonymous_variant	57150	exon3			CAAAGAGAAAGAG	AL050201	CCDS34496.1, CCDS75493.1	6q15	2013-06-21	2012-11-20	2012-11-20	ENSG00000111850	ENSG00000111850			21401	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 162"""	C6orf162			Standard	NM_001287445		Approved	DKFZP586E1923, dJ102H19.2	uc003plq.1	Q96KF7	OTTHUMG00000015168	ENST00000392863.1:c.51G>A	6.37:g.88046800G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_001042493	B2R4V6|E1P505|Q5TEZ3|Q6NSD2|Q8IZ10	Silent	SNP	ENST00000392863.1	37	CCDS34496.1																																																																																			G|0.896;A|0.104	0.104	strong		0.388	SMIM8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472479.2	NM_020425	
ZNF577	84765	hgsc.bcm.edu	37	19	52376952	52376952	+	Silent	SNP	T	T	A	rs8107969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52376952T>A	ENST00000301399.5	-	7	656	c.291A>T	c.(289-291)gtA>gtT	p.V97V	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Intron|ZNF577_ENST00000451628.2_Intron|ZNF577_ENST00000412216.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	97					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TACTCTGGATTACAAAACCTA	0.353													A|||	2536	0.50639	0.68	0.4553	5008	,	,		20806	0.3026		0.3897	False		,,,				2504	0.638				p.V97V		Atlas-SNP	.											.	ZNF577	63	.	0			c.A291T						PASS	.	A	,	2797,1609		908,981,314	39.0	36.0	37.0		,291	0.5	0.0	19	dbSNP_116	37	3324,5274		639,2046,1614	no	intron,coding-synonymous	ZNF577	NM_001135590.1,NM_032679.2	,	1547,3027,1928	AA,AT,TT		38.6602,36.5184,47.0701	,	,97/486	52376952	6121,6883	2203	4299	6502	SO:0001819	synonymous_variant	84765	exon7			CTGGATTACAAAA	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.291A>T	19.37:g.52376952T>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			T|0.527;A|0.473	0.473	strong		0.353	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
SPTBN1	6711	hgsc.bcm.edu	37	2	54886347	54886347	+	Silent	SNP	G	G	A	rs1052820	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:54886347G>A	ENST00000356805.4	+	31	6581	c.6300G>A	c.(6298-6300)ccG>ccA	p.P2100P	AC093110.3_ENST00000456363.1_RNA|SPTBN1_ENST00000333896.5_Silent_p.P2087P	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	2100					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)	p.P2100P(1)		NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			AGAGGCGGCCGCCTTCTCCCG	0.572													G|||	1393	0.278155	0.1498	0.3617	5008	,	,		15704	0.2877		0.3469	False		,,,				2504	0.3119				p.P2100P		Atlas-SNP	.											SPTBN1,NS,carcinoma,0,1	SPTBN1	378	1	1	Substitution - coding silent(1)	stomach(1)	c.G6300A						PASS	.	G	,	818,3588	324.5+/-298.6	80,658,1465	115.0	139.0	131.0		6300,6261	-2.9	1.0	2	dbSNP_86	131	2771,5829	440.9+/-359.6	415,1941,1944	no	coding-synonymous,coding-synonymous	SPTBN1	NM_003128.2,NM_178313.2	,	495,2599,3409	AA,AG,GG		32.2209,18.5656,27.595	,	2100/2365,2087/2156	54886347	3589,9417	2203	4300	6503	SO:0001819	synonymous_variant	6711	exon31			GCGGCCGCCTTCT		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.6300G>A	2.37:g.54886347G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	142	82	0.577465	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			G|0.724;A|0.276	0.276	strong		0.572	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
HPS5	11234	hgsc.bcm.edu	37	11	18319180	18319180	+	Missense_Mutation	SNP	G	G	T	rs7128017	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18319180G>T	ENST00000349215.3	-	11	1526	c.1249C>A	c.(1249-1251)Ctg>Atg	p.L417M	HPS5_ENST00000352460.3_5'Flank|HPS5_ENST00000531848.1_Missense_Mutation_p.L303M|HPS5_ENST00000438420.2_Missense_Mutation_p.L303M|HPS5_ENST00000396253.3_Missense_Mutation_p.L303M	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	417			L -> M (in dbSNP:rs7128017). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:12548288}.		blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.L417M(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						AATTCTTCCAGTTGAGAAATT	0.358									Hermansky-Pudlak syndrome				G|||	765	0.152756	0.1936	0.1657	5008	,	,		18531	0.124		0.1262	False		,,,				2504	0.1452				p.L417M		Atlas-SNP	.											HPS5,NS,carcinoma,0,1	HPS5	70	1	1	Substitution - Missense(1)	stomach(1)	c.C1249A						PASS	.	G	MET/LEU,MET/LEU,MET/LEU	833,3565	327.7+/-300.2	70,693,1436	98.0	97.0	97.0		907,1249,907	2.3	1.0	11	dbSNP_116	97	848,7738	193.4+/-239.1	44,760,3489	yes	missense,missense,missense	HPS5	NM_007216.3,NM_181507.1,NM_181508.1	15,15,15	114,1453,4925	TT,TG,GG		9.8765,18.9404,12.9467	probably-damaging,probably-damaging,probably-damaging	303/1016,417/1130,303/1016	18319180	1681,11303	2199	4293	6492	SO:0001583	missense	11234	exon11	Familial Cancer Database	HPS, HPS1-8	CTTCCAGTTGAGA	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.1249C>A	11.37:g.18319180G>T	ENSP00000265967:p.Leu417Met	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	37	CCDS7836.1	311	0.1423992673992674	96	0.1951219512195122	51	0.1408839779005525	73	0.12762237762237763	91	0.12005277044854881	G	13.44	2.239111	0.39598	0.189404	0.098765	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000531848	T;T;T;T	0.69175	-0.38;-0.38;-0.35;0.82	5.23	2.32	0.28847	.	0.000000	0.85682	D	0.000000	T	0.00271	0.0008	M	0.71581	2.175	0.18873	P	0.9999899422	D	0.89917	1.0	D	0.91635	0.999	T	0.22695	-1.0209	9	0.72032	D	0.01	.	10.7986	0.46474	0.1974:0.0:0.8026:0.0	rs7128017;rs52795518;rs59220261;rs7128017	417	Q9UPZ3	HPS5_HUMAN	M	303;303;417;303	ENSP00000379552:L303M;ENSP00000399590:L303M;ENSP00000265967:L417M;ENSP00000431758:L303M	ENSP00000265967:L417M	L	-	1	2	HPS5	18275756	1.000000	0.71417	0.988000	0.46212	0.121000	0.20230	3.161000	0.50747	0.218000	0.20820	0.462000	0.41574	CTG	G|0.868;T|0.132	0.132	strong		0.358	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
MET	4233	hgsc.bcm.edu	37	7	116436097	116436097	+	Silent	SNP	G	G	A	rs41737	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116436097G>A	ENST00000318493.6	+	21	4333	c.4146G>A	c.(4144-4146)ccG>ccA	p.P1382P	MET_ENST00000397752.3_Silent_p.P1364P|MET_ENST00000539704.1_Silent_p.P234P			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P1382P(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GTGTCGCTCCGTATCCTTCTC	0.468			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	1776	0.354633	0.0356	0.4726	5008	,	,		19834	0.4673		0.4433	False		,,,				2504	0.4949				p.P1382P		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.G4146A						PASS	.	A	,	418,3602		15,388,1607	193.0	176.0	181.0		4092,4146	-3.1	1.0	7	dbSNP_76	181	3563,4817		777,2009,1404	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	792,2397,3011	AA,AG,GG		42.5179,10.398,32.1048	,	1364/1391,1382/1409	116436097	3981,8419	2010	4190	6200	SO:0001819	synonymous_variant	4233	exon21	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CGCTCCGTATCCT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.4146G>A	7.37:g.116436097G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	192	88	0.458333	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.615;A|0.385	0.385	strong		0.468	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
DHRS3	9249	hgsc.bcm.edu	37	1	12640650	12640650	+	Silent	SNP	C	C	T	rs11540058	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:12640650C>T	ENST00000376223.2	-	2	623	c.240G>A	c.(238-240)acG>acA	p.T80T	DHRS3_ENST00000482265.1_5'UTR	NM_004753.4	NP_004744.2	O75911	DHRS3_HUMAN	dehydrogenase/reductase (SDR family) member 3	80					bone morphogenesis (GO:0060349)|cardiac septum morphogenesis (GO:0060411)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|phototransduction, visible light (GO:0007603)|regulation of ossification (GO:0030278)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|photoreceptor outer segment membrane (GO:0042622)	electron carrier activity (GO:0009055)|NADP-retinol dehydrogenase activity (GO:0052650)|nucleotide binding (GO:0000166)|retinol dehydrogenase activity (GO:0004745)			cervix(1)|large_intestine(4)|lung(2)|prostate(1)|skin(1)	9	Ovarian(185;0.249)	Lung NSC(185;4.11e-05)|all_lung(284;4.58e-05)|Renal(390;0.000147)|Colorectal(325;0.000585)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;9.25e-07)|COAD - Colon adenocarcinoma(227;0.000326)|BRCA - Breast invasive adenocarcinoma(304;0.000344)|Kidney(185;0.00235)|KIRC - Kidney renal clear cell carcinoma(229;0.00656)|STAD - Stomach adenocarcinoma(313;0.00798)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	GGATCTCCTCCGTCGTCTCCT	0.537													C|||	399	0.0796725	0.0446	0.0764	5008	,	,		17584	0.002		0.1918	False		,,,				2504	0.0941				p.T80T		Atlas-SNP	.											.	DHRS3	18	.	0			c.G240A						PASS	.	C		294,4112	161.1+/-193.3	10,274,1919	74.0	71.0	72.0		240	-4.2	0.4	1	dbSNP_120	72	1781,6819	321.8+/-315.3	194,1393,2713	no	coding-synonymous	DHRS3	NM_004753.4		204,1667,4632	TT,TC,CC		20.7093,6.6727,15.9542		80/303	12640650	2075,10931	2203	4300	6503	SO:0001819	synonymous_variant	9249	exon2			CTCCTCCGTCGTC	AF061741	CCDS146.1	1p36.1	2011-09-20			ENSG00000162496	ENSG00000162496	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	17693	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 16C, member 1"""	612830				9705317, 12226107, 19027726	Standard	XM_005263533		Approved	retSDR1, Rsdr1, SDR1, RDH17, SDR16C1	uc001auc.3	O75911	OTTHUMG00000001885	ENST00000376223.2:c.240G>A	1.37:g.12640650C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	191	88	0.460733	NM_004753	B2R7F3|Q5VUY3|Q6UY38|Q9BUC8	Silent	SNP	ENST00000376223.2	37	CCDS146.1																																																																																			C|0.868;T|0.132	0.132	strong		0.537	DHRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005318.1	NM_004753	
PNPT1	87178	hgsc.bcm.edu	37	2	55883317	55883317	+	Silent	SNP	G	G	T	rs2627765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:55883317G>T	ENST00000447944.2	-	17	1476	c.1390C>A	c.(1390-1392)Cga>Aga	p.R464R		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	464					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GGAAAATCTCGGGGAATAACA	0.328													T|||	1786	0.356629	0.3185	0.4899	5008	,	,		17660	0.1429		0.5785	False		,,,				2504	0.3057				p.R464R		Atlas-SNP	.											.	PNPT1	68	.	0			c.C1390A						PASS	.	T		1541,2865	660.1+/-400.7	280,981,942	86.0	83.0	84.0		1390	4.8	1.0	2	dbSNP_100	84	4787,3807	533.0+/-382.3	1337,2113,847	no	coding-synonymous	PNPT1	NM_033109.3		1617,3094,1789	TT,TG,GG		44.2983,34.975,48.6769		464/784	55883317	6328,6672	2203	4297	6500	SO:0001819	synonymous_variant	87178	exon17			AATCTCGGGGAAT	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"""polynucleotide phosphorylase"", ""3'-5' RNA exonuclease"""	610316	"""deafness, autosomal recessive 70"""	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.1390C>A	2.37:g.55883317G>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	229	227	0.991266	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Silent	SNP	ENST00000447944.2	37	CCDS1856.1																																																																																			G|0.559;T|0.441	0.441	strong		0.328	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109	
GBP4	115361	hgsc.bcm.edu	37	1	89652097	89652097	+	Missense_Mutation	SNP	C	C	T	rs1142886	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89652097C>T	ENST00000355754.6	-	10	1723	c.1626G>A	c.(1624-1626)atG>atA	p.M542I	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	542			M -> I (in dbSNP:rs1142886).	YM -> NI (in Ref. 1; AAL02054 and 3; BAC85144). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		CCATTTGGGCCATGTATTCCT	0.473													C|||	1801	0.359625	0.1445	0.3141	5008	,	,		18628	0.3998		0.4891	False		,,,				2504	0.5082				p.M542I		Atlas-SNP	.											.	GBP4	89	.	0			c.G1626A						PASS	.	C	ILE/MET	446,3960		119,208,1876	168.0	105.0	126.0		1626	-7.4	0.0	1	dbSNP_86	126	2956,5644		1064,828,2408	no	missense	GBP4	NM_052941.4	10	1183,1036,4284	TT,TC,CC		34.3721,10.1226,26.1572	benign	542/641	89652097	3402,9604	2203	4300	6503	SO:0001583	missense	115361	exon10			TTGGGCCATGTAT	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1626G>A	1.37:g.89652097C>T	ENSP00000359490:p.Met542Ile	Somatic	357	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	617	0.2825091575091575	38	0.07723577235772358	113	0.31215469613259667	182	0.3181818181818182	284	0.37467018469656993	C	0.034	-1.318603	0.01320	0.101226	0.343721	ENSG00000162654	ENST00000355754	T	0.49432	0.78	4.29	-7.4	0.01397	Guanylate-binding protein, C-terminal (3);	1.121610	0.06584	N	0.750755	T	0.02083	0.0065	N	0.00256	-1.76	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.21518	-1.0243	9	0.02654	T	1	.	5.4902	0.16771	0.2068:0.3872:0.0:0.4059	rs1142886;rs3180072;rs3206368;rs34488490	542	Q96PP9	GBP4_HUMAN	I	542	ENSP00000359490:M542I	ENSP00000359490:M542I	M	-	3	0	GBP4	89424685	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-4.744000	0.00191	-1.145000	0.02858	-1.326000	0.01283	ATG	C|0.619;T|0.381	0.381	strong		0.473	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
DNAH14	127602	hgsc.bcm.edu	37	1	225452983	225452983	+	Missense_Mutation	SNP	A	A	G	rs76767146	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225452983A>G	ENST00000445597.2	+	32	5684	c.5684A>G	c.(5683-5685)aAt>aGt	p.N1895S	DNAH14_ENST00000439375.2_Missense_Mutation_p.N2435S|DNAH14_ENST00000430092.1_Missense_Mutation_p.N2435S			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1895					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TTTAGCACCAATGTAACAGCT	0.328													A|||	163	0.0325479	0.0038	0.0375	5008	,	,		15142	0.0129		0.0686	False		,,,				2504	0.0511				p.N2435S		Atlas-SNP	.											.	DNAH14	300	.	0			c.A7304G						PASS	.	A	SER/ASN	18,1366		0,18,674	96.0	80.0	85.0		7304	-4.4	0.0	1	dbSNP_131	85	199,2981		4,191,1395	yes	missense	DNAH14	NM_001373.1	46	4,209,2069	GG,GA,AA		6.2579,1.3006,4.7546	benign	2435/4516	225452983	217,4347	692	1590	2282	SO:0001583	missense	127602	exon48			GCACCAATGTAAC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.5684A>G	1.37:g.225452983A>G	ENSP00000409472:p.Asn1895Ser	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	175	94	0.537143	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		84|84	0.038461538461538464|0.038461538461538464	3|3	0.006097560975609756|0.006097560975609756	16|16	0.04419889502762431|0.04419889502762431	9|9	0.015734265734265736|0.015734265734265736	56|56	0.07387862796833773|0.07387862796833773	A|A	8.743|8.743	0.919471|0.919471	0.17982|0.17982	0.013006|0.013006	0.062579|0.062579	ENSG00000185842|ENSG00000185842	ENST00000450490|ENST00000445597;ENST00000430092;ENST00000439375	.|T;T;T	.|0.34859	.|2.57;1.34;1.34	5.42|5.42	-4.42|-4.42	0.03579|0.03579	.|.	.|.	.|.	.|.	.|.	T|T	0.01189|0.01189	0.0039|0.0039	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.13145	.|0.007	.|B	.|0.08055	.|0.003	T|T	0.27502|0.27502	-1.0072|-1.0072	5|9	.|0.07990	.|T	.|0.79	.|.	7.3639|7.3639	0.26762|0.26762	0.4497:0.1284:0.4218:0.0|0.4497:0.1284:0.4218:0.0	.|.	.|2435	.|Q0VDD8-4	.|.	V|S	207|1895;2435;2435	.|ENSP00000409472:N1895S;ENSP00000414402:N2435S;ENSP00000392061:N2435S	.|ENSP00000414402:N2435S	M|N	+|+	1|2	0|0	DNAH14|DNAH14	223519606|223519606	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.773000|0.773000	0.43773|0.43773	-0.001000|-0.001000	0.12947|0.12947	-1.190000|-1.190000	0.02698|0.02698	-0.419000|-0.419000	0.06015|0.06015	ATG|AAT	A|0.953;G|0.047	0.047	strong		0.328	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
ALAD	210	hgsc.bcm.edu	37	9	116153900	116153900	+	Silent	SNP	A	A	G	rs1139488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:116153900A>G	ENST00000409155.3	-	4	364	c.168T>C	c.(166-168)taT>taC	p.Y56Y	ALAD_ENST00000482001.1_5'UTR|ALAD_ENST00000277315.5_Silent_p.Y39Y	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	56					cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270)	p.Y85Y(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1)	9					Aminolevulinic acid(DB00855)	GCTTCACACCATACCTGTGTG	0.582													A|||	1764	0.352236	0.3011	0.3674	5008	,	,		19245	0.497		0.3757	False		,,,				2504	0.2372				p.Y56Y		Atlas-SNP	.											ALAD,NS,carcinoma,0,1	ALAD	36	1	1	Substitution - coding silent(1)	stomach(1)	c.T168C						PASS	.	A		1431,2975	465.3+/-354.1	228,975,1000	67.0	62.0	64.0		168	2.0	1.0	9	dbSNP_86	64	3176,5424	479.9+/-370.2	603,1970,1727	no	coding-synonymous	ALAD	NM_000031.5		831,2945,2727	GG,GA,AA		36.9302,32.4784,35.4221		56/331	116153900	4607,8399	2203	4300	6503	SO:0001819	synonymous_variant	210	exon4			CACACCATACCTG	M13928	CCDS6794.2	9q32	2010-04-29	2010-04-29		ENSG00000148218	ENSG00000148218	4.2.1.24		395	protein-coding gene	gene with protein product	"""porphobilinogen synthase"""	125270	"""aminolevulinate, delta-, dehydratase"""			6839527, 6378062	Standard	NM_000031		Approved	ALADH, PBGS	uc011lxf.2	P13716	OTTHUMG00000020522	ENST00000409155.3:c.168T>C	9.37:g.116153900A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_000031	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Silent	SNP	ENST00000409155.3	37	CCDS6794.2																																																																																			G|0.353;N|0.001	0.353	strong		0.582	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945	
MET	4233	hgsc.bcm.edu	37	7	116340262	116340262	+	Missense_Mutation	SNP	A	A	G	rs33917957	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116340262A>G	ENST00000318493.6	+	2	1311	c.1124A>G	c.(1123-1125)aAc>aGc	p.N375S	MET_ENST00000436117.2_Missense_Mutation_p.N375S|MET_ENST00000397752.3_Missense_Mutation_p.N375S			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.N375S(2)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GACTTCTTCAACAAGATCGTC	0.443			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	165	0.0329473	0.0053	0.0101	5008	,	,		19354	0.0526		0.0209	False		,,,				2504	0.0787				p.N375S		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,3	MET	412	3	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|kidney(1)	c.A1124G						PASS	.	A	SER/ASN,SER/ASN	26,3828		0,26,1901	101.0	93.0	96.0		1124,1124	4.9	1.0	7	dbSNP_126	96	151,8127		0,151,3988	yes	missense,missense	MET	NM_000245.2,NM_001127500.1	46,46	0,177,5889	GG,GA,AA		1.8241,0.6746,1.459	benign,benign	375/1391,375/1409	116340262	177,11955	1927	4139	6066	SO:0001583	missense	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TCTTCAACAAGAT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1124A>G	7.37:g.116340262A>G	ENSP00000317272:p.Asn375Ser	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	46	0.021062271062271064	0	0.0	3	0.008287292817679558	27	0.0472027972027972	16	0.021108179419525065	A	10.97	1.502020	0.26949	0.006746	0.018241	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.04551	3.6;3.6;3.6	6.04	4.91	0.64330	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.135646	0.64402	D	0.000003	T	0.00906	0.0030	L	0.52364	1.645	0.80722	D	1	B;B;B;B;B;B;B;B;B;B;B;B;B	0.21071	0.051;0.044;0.008;0.011;0.024;0.024;0.044;0.044;0.005;0.02;0.025;0.043;0.043	B;B;B;B;B;B;B;B;B;B;B;B;B	0.26310	0.018;0.026;0.047;0.034;0.047;0.026;0.068;0.038;0.007;0.015;0.026;0.026;0.026	T	0.36601	-0.9741	10	0.40728	T	0.16	.	9.6723	0.40019	0.869:0.0:0.131:0.0	rs33917957	375;375;375;375;375;375;375;375;375;375;375;375;375	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;B5A939;B5A941;B5A940;P08581-2;B5A942;P08581;A1L467	.;.;.;.;.;.;.;.;.;.;.;MET_HUMAN;.	S	375	ENSP00000380860:N375S;ENSP00000317272:N375S;ENSP00000410980:N375S	ENSP00000317272:N375S	N	+	2	0	MET	116127498	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	2.866000	0.48420	2.317000	0.78254	0.460000	0.39030	AAC	A|0.977;G|0.023	0.023	strong		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383027	39383027	+	Missense_Mutation	SNP	G	G	T	rs71371478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39383027G>T	ENST00000377721.3	+	1	128	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.A41S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	41	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)		p.A41S(1)		large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CTGCCAGCCCGCCTGCTGTGT	0.637																																					p.A41S		Atlas-SNP	.											KRTAP9-2,extremity,malignant_melanoma,0,1	KRTAP9-2	24	1	1	Substitution - Missense(1)	skin(1)	c.G121T						scavenged	.						59.0	53.0	55.0					17																	39383027		2203	4300	6503	SO:0001583	missense	83899	exon1			CAGCCCGCCTGCT	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.121G>T	17.37:g.39383027G>T	ENSP00000366950:p.Ala41Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	66	12	0.181818	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.020245	0.00418	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01192	5.2;5.4	2.86	-2.81	0.05805	.	.	.	.	.	T	0.00328	0.0010	N	0.00368	-1.59	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.39742	-0.9599	9	0.02654	T	1	.	5.0512	0.14508	0.3642:0.0:0.0934:0.5425	.	41	Q9BYQ4	KRA92_HUMAN	S	41	ENSP00000366950:A41S;ENSP00000398325:A41S	ENSP00000366950:A41S	A	+	1	0	KRTAP9-2	36636553	0.000000	0.05858	0.088000	0.20740	0.203000	0.24098	-1.973000	0.01500	-1.243000	0.02519	-4.519000	0.00005	GCC	G|0.997;T|0.003	0.003	strong		0.637	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
GTF2IRD2	84163	hgsc.bcm.edu	37	7	74212048	74212048	+	Silent	SNP	C	C	T	rs707395	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:74212048C>T	ENST00000405086.2	-	16	1992	c.1803G>A	c.(1801-1803)aaG>aaA	p.K601K	GTF2IRD2_ENST00000451013.2_Silent_p.K148K	NM_173537.2	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2	601					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	11						ttttcaggctcttctcaacac	0.502													C|||	580	0.115815	0.0915	0.1124	5008	,	,		20612	0.0397		0.1849	False		,,,				2504	0.1585				p.K601K	NSCLC(40;560 1096 7501 40315 49546)	Atlas-SNP	.											.	GTF2IRD2	38	.	0			c.G1803A						PASS	.	C		495,3911	224.9+/-240.9	21,453,1729	52.0	50.0	51.0		1803	-0.6	0.9	7	dbSNP_86	51	1675,6921	304.9+/-307.2	166,1343,2789	no	coding-synonymous	GTF2IRD2	NM_173537.2		187,1796,4518	TT,TC,CC		19.4858,11.2347,16.6897		601/950	74212048	2170,10832	2203	4298	6501	SO:0001819	synonymous_variant	84163	exon16			CAGGCTCTTCTCA	BC047706	CCDS5576.1, CCDS64682.1	7q11.23	2014-05-06			ENSG00000196275	ENSG00000196275			30775	protein-coding gene	gene with protein product	"""transcription factor GTF2IRD2"""	608899				15243160	Standard	NM_173537		Approved	FLJ37938, GTF2IRD2A	uc003ubd.1	Q86UP8	OTTHUMG00000181527	ENST00000405086.2:c.1803G>A	7.37:g.74212048C>T		Somatic	688	2	0.00290698		WXS	Illumina HiSeq	Phase_I	770	351	0.455844	NM_173537	A8K5W6|B3KUZ2|Q69G40|Q6EKI8|Q6EKI9|Q6NVW2|Q6P7N8|Q86WX4|Q8ND85|Q8NDE5	Silent	SNP	ENST00000405086.2	37	CCDS5576.1																																																																																			C|0.860;T|0.140	0.140	strong		0.502	GTF2IRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252712.3	NM_173537	
ZNF462	58499	hgsc.bcm.edu	37	9	109685748	109685748	+	Silent	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:109685748G>T	ENST00000277225.5	+	2	373	c.84G>T	c.(82-84)acG>acT	p.T28T	ZNF462_ENST00000457913.1_Silent_p.T28T|RP11-508N12.4_ENST00000451160.2_Silent_p.T28T			Q96JM2	ZN462_HUMAN	zinc finger protein 462	28					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						ATGTCCACACGGCATTTCTGC	0.498																																					p.T28T		Atlas-SNP	.											.	ZNF462	322	.	0			c.G84T						PASS	.						241.0	216.0	224.0					9																	109685748		2203	4300	6503	SO:0001819	synonymous_variant	58499	exon2			CCACACGGCATTT	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.84G>T	9.37:g.109685748G>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	231	81	0.350649	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			.	.	none		0.498	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
ITGA2	3673	hgsc.bcm.edu	37	5	52351413	52351413	+	Silent	SNP	G	G	A	rs1062535	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:52351413G>A	ENST00000296585.5	+	8	968	c.825G>A	c.(823-825)acG>acA	p.T275T		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	275	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				GAAGTGCTACGAAAGTAATGG	0.368																																					p.T275T		Atlas-SNP	.											.	ITGA2	211	.	0			c.G825A	GRCh37	CM993454	ITGA2	M	rs1062535	PASS	.	A		1442,2964	467.6+/-354.9	240,962,1001	165.0	157.0	160.0		825	0.4	0.9	5	dbSNP_86	160	3426,5174	504.5+/-376.2	655,2116,1529	no	coding-synonymous	ITGA2	NM_002203.3		895,3078,2530	AA,AG,GG		39.8372,32.7281,37.4289		275/1182	52351413	4868,8138	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon8			TGCTACGAAAGTA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.825G>A	5.37:g.52351413G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	118	47	0.398305	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			G|0.627;A|0.373	0.373	strong		0.368	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
OR2Z1	284383	hgsc.bcm.edu	37	19	8841558	8841558	+	Silent	SNP	T	T	C	rs28324	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8841558T>C	ENST00000324060.2	+	1	243	c.168T>C	c.(166-168)caT>caC	p.H56H		NM_001004699.1	NP_001004699.1	Q8NG97	OR2Z1_HUMAN	olfactory receptor, family 2, subfamily Z, member 1	56						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCCGGCTCCATACACCCATGT	0.557													C|||	3202	0.639377	0.9652	0.6182	5008	,	,		20064	0.4563		0.6133	False		,,,				2504	0.4294				p.H56H		Atlas-SNP	.											.	OR2Z1	53	.	0			c.T168C						PASS	.	C		4031,375	191.2+/-216.9	1844,343,16	159.0	141.0	147.0		168	1.6	1.0	19	dbSNP_76	147	5401,3199	484.1+/-371.3	1710,1981,609	no	coding-synonymous	OR2Z1	NM_001004699.1		3554,2324,625	CC,CT,TT		37.1977,8.5111,27.4796		56/315	8841558	9432,3574	2203	4300	6503	SO:0001819	synonymous_variant	284383	exon1			GCTCCATACACCC	AC008753	CCDS32895.1	19p13.2	2013-09-20	2002-11-13		ENSG00000181733	ENSG00000181733		"""GPCR / Class A : Olfactory receptors"""	15391	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily Z, member 2"""	OR2Z2			Standard	NM_001004699		Approved		uc010xkg.2	Q8NG97	OTTHUMG00000182195	ENST00000324060.2:c.168T>C	19.37:g.8841558T>C		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	191	190	0.994764	NM_001004699	B9EH50|Q6IFK0|Q96R25	Silent	SNP	ENST00000324060.2	37	CCDS32895.1																																																																																			T|0.299;C|0.701	0.701	strong		0.557	OR2Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459954.1		
CILP2	148113	hgsc.bcm.edu	37	19	19655670	19655670	+	Silent	SNP	C	C	T	rs11669558	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19655670C>T	ENST00000291495.5	+	8	2401	c.2316C>T	c.(2314-2316)tcC>tcT	p.S772S	CILP2_ENST00000586018.1_Silent_p.S778S	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	772						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCGGCTTCTCCGCCAACCCCC	0.701													c|||	586	0.117013	0.177	0.1167	5008	,	,		12706	0.0		0.166	False		,,,				2504	0.1063				p.S772S		Atlas-SNP	.											.	CILP2	84	.	0			c.C2316T						PASS	.	T		623,3431		40,543,1444	9.0	11.0	10.0		2316	-9.3	0.7	19	dbSNP_120	10	1261,7031		94,1073,2979	no	coding-synonymous	CILP2	NM_153221.2		134,1616,4423	TT,TC,CC		15.2074,15.3675,15.26		772/1157	19655670	1884,10462	2027	4146	6173	SO:0001819	synonymous_variant	148113	exon8			CTTCTCCGCCAAC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.2316C>T	19.37:g.19655670C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	19	11	0.578947	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			C|0.874;T|0.126	0.126	strong		0.701	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
CR2	1380	hgsc.bcm.edu	37	1	207646322	207646322	+	Silent	SNP	G	G	A	rs1048971	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207646322G>A	ENST00000367058.3	+	10	1965	c.1776G>A	c.(1774-1776)ctG>ctA	p.L592L	CR2_ENST00000367057.3_Silent_p.L592L|CR2_ENST00000367059.3_Silent_p.L592L|CR2_ENST00000458541.2_Silent_p.L565L	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	592	Sushi 9. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CTGCTCCCCTGTGTAAACTTT	0.488													A|||	2005	0.400359	0.7595	0.2666	5008	,	,		19953	0.2024		0.3499	False		,,,				2504	0.2658				p.L592L		Atlas-SNP	.											.	CR2	164	.	0			c.G1776A						PASS	.	A	,	3036,1370	454.7+/-350.8	1052,932,219	79.0	76.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1776,1776	1.5	0.0	1	dbSNP_86	77	3056,5544	661.7+/-401.9	544,1968,1788	no	coding-synonymous,coding-synonymous	CR2	NM_001006658.2,NM_001877.4	,	1596,2900,2007	AA,AG,GG		35.5349,31.094,46.8399	,	592/1093,592/1034	207646322	6092,6914	2203	4300	6503	SO:0001819	synonymous_variant	1380	exon10			TCCCCTGTGTAAA	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1776G>A	1.37:g.207646322G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Silent	SNP	ENST00000367058.3	37	CCDS1478.1																																																																																			G|0.556;A|0.444	0.444	strong		0.488	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
CABS1	85438	hgsc.bcm.edu	37	4	71201943	71201943	+	Silent	SNP	A	A	G	rs13039	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:71201943A>G	ENST00000273936.5	+	1	1261	c.1187A>G	c.(1186-1188)tAa>tGa	p.*396*		NM_033122.3	NP_149113.3	Q96KC9	CABS1_HUMAN	calcium-binding protein, spermatid-specific 1	0					spermatogenesis (GO:0007283)	mitochondrial inner membrane (GO:0005743)|motile cilium (GO:0031514)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(4)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TTCATGATTTAAAAGCAACAA	0.373													G|||	991	0.197883	0.2247	0.1902	5008	,	,		20279	0.1726		0.1948	False		,,,				2504	0.1963				p.X396X		Atlas-SNP	.											.	CABS1	75	.	0			c.A1187G						PASS	.	G		851,3551		74,703,1424	37.0	38.0	38.0		1187	1.9	1.0	4	dbSNP_52	38	1350,7246		99,1152,3047	no	coding-synonymous	CABS1	NM_033122.3		173,1855,4471	GG,GA,AA		15.705,19.3321,16.9334		396/396	71201943	2201,10797	2201	4298	6499	SO:0001819	synonymous_variant	85438	exon1			TGATTTAAAAGCA	AF380838	CCDS3539.1	4q13.3	2013-10-11	2011-01-25	2011-01-25	ENSG00000145309	ENSG00000145309			30710	protein-coding gene	gene with protein product	"""casein-like phosphoprotein"""		"""chromosome 4 open reading frame 35"""	C4orf35		19208547, 19271754	Standard	NM_033122		Approved	NYD-SP26, FLJ32897, CLPH	uc003hff.3	Q96KC9	OTTHUMG00000129405	ENST00000273936.5:c.1187A>G	4.37:g.71201943A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_033122	B2RCB5|Q86UE0|Q96M17	Silent	SNP	ENST00000273936.5	37	CCDS3539.1																																																																																			A|0.812;G|0.188	0.188	strong		0.373	CABS1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251561.3	NM_033122	
CPVL	54504	hgsc.bcm.edu	37	7	29070209	29070209	+	Missense_Mutation	SNP	G	G	A	rs7313	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:29070209G>A	ENST00000409850.1	-	16	1950	c.1304C>T	c.(1303-1305)gCg>gTg	p.A435V	CPVL_ENST00000396276.3_Missense_Mutation_p.A435V|CPVL_ENST00000265394.5_Missense_Mutation_p.A435V			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	435			A -> V (in dbSNP:rs7313). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743}.			extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						GAAGTCACCCGCTTGCCGGAT	0.478													A|||	1478	0.295128	0.23	0.3559	5008	,	,		19512	0.1508		0.4622	False		,,,				2504	0.317				p.A435V		Atlas-SNP	.											CPVL,bladder,carcinoma,-1,2	CPVL	60	2	0			c.C1304T						PASS	.	A	VAL/ALA,VAL/ALA	1240,3166	705.1+/-407.2	154,932,1117	144.0	141.0	142.0		1304,1304	3.2	0.9	7	dbSNP_52	142	3994,4606	599.8+/-394.1	911,2172,1217	yes	missense,missense	CPVL	NM_019029.2,NM_031311.3	64,64	1065,3104,2334	AA,AG,GG		46.4419,28.1434,40.243	benign,benign	435/477,435/477	29070209	5234,7772	2203	4300	6503	SO:0001583	missense	54504	exon12			TCACCCGCTTGCC	AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"""carboxypeptidase WUG"", ""vitellogenic carboxypeptidase-like protein"", ""CP-Mac carboxypeptidase"""	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.1304C>T	7.37:g.29070209G>A	ENSP00000387164:p.Ala435Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	186	181	0.973118	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Missense_Mutation	SNP	ENST00000409850.1	37	CCDS5419.1	691	0.3163919413919414	118	0.23983739837398374	142	0.39226519337016574	83	0.1451048951048951	348	0.45910290237467016	A	1.332	-0.596422	0.03771	0.281434	0.464419	ENSG00000106066	ENST00000265394;ENST00000396276;ENST00000455893;ENST00000409850	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	5.5	3.15	0.36227	.	0.118062	0.56097	N	0.000025	T	0.00012	0.0000	N	0.01122	-1.005	0.51767	P	6.700000000003925E-5	B	0.11235	0.004	B	0.06405	0.002	T	0.47661	-0.9100	9	0.19590	T	0.45	-15.4544	8.4307	0.32755	0.6001:0.0:0.3999:0.0	rs7313;rs1008522;rs1132141;rs1637477;rs10360496;rs17675032;rs17856516;rs52799931;rs59772656;rs7313	435	Q9H3G5	CPVL_HUMAN	V	435;435;100;435	ENSP00000265394:A435V;ENSP00000379572:A435V;ENSP00000403580:A100V;ENSP00000387164:A435V	ENSP00000265394:A435V	A	-	2	0	CPVL	29036734	0.996000	0.38824	0.872000	0.34217	0.809000	0.45718	2.155000	0.42301	0.081000	0.16988	-0.352000	0.07741	GCG	G|0.638;T|0.004	.	strong		0.478	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
NDC80	10403	hgsc.bcm.edu	37	18	2616457	2616457	+	Missense_Mutation	SNP	G	G	C	rs9051	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:2616457G>C	ENST00000261597.4	+	17	1995	c.1813G>C	c.(1813-1815)Gct>Cct	p.A605P		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	605	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.		A -> P (in dbSNP:rs1983346).		attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GGAGCAGATTGCTAAAGTTGA	0.259													G|||	919	0.183506	0.1241	0.1354	5008	,	,		16739	0.125		0.2286	False		,,,				2504	0.3119				p.A605P		Atlas-SNP	.											.	NDC80	62	.	0			c.G1813C						PASS	.	G	PRO/ALA	664,3738	254.6+/-260.1	53,558,1590	44.0	47.0	46.0		1813	1.3	1.0	18	dbSNP_92	46	2000,6572	333.7+/-320.7	235,1530,2521	yes	missense	NDC80	NM_006101.2	27	288,2088,4111	CC,CG,GG		23.3318,15.0841,20.5334	benign	605/643	2616457	2664,10310	2201	4286	6487	SO:0001583	missense	10403	exon17			CAGATTGCTAAAG	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"""highly expressed in cancer, rich in leucine heptad repeats (yeast)"", ""kinetochore associated 2"", ""NDC80 kinetochore complex component homolog (S. cerevisiae)"""	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1813G>C	18.37:g.2616457G>C	ENSP00000261597:p.Ala605Pro	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	218	109	0.5	NM_006101	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	37	CCDS11827.1	383	0.17536630036630035	66	0.13414634146341464	61	0.1685082872928177	70	0.12237762237762238	186	0.24538258575197888	G	9.867	1.197860	0.22037	0.150841	0.233318	ENSG00000080986	ENST00000261597	T	0.48522	0.81	5.32	1.29	0.21616	.	1.211720	0.05314	N	0.525294	T	0.00012	0.0000	N	0.08118	0	0.49051	P	2.550000000000052E-4	B	0.26876	0.162	B	0.25614	0.062	T	0.20472	-1.0274	9	0.31617	T	0.26	-0.0998	5.5394	0.17030	0.24:0.247:0.513:0.0	rs9051	605	O14777	NDC80_HUMAN	P	605	ENSP00000261597:A605P	ENSP00000261597:A605P	A	+	1	0	NDC80	2606457	0.018000	0.18449	0.985000	0.45067	0.503000	0.33858	-0.152000	0.10159	0.332000	0.23536	0.555000	0.69702	GCT	G|0.806;C|0.194	0.194	strong		0.259	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	
NXPE4	54827	hgsc.bcm.edu	37	11	114441936	114441936	+	Silent	SNP	A	A	G	rs12421748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:114441936A>G	ENST00000375478.3	-	6	1539	c.1359T>C	c.(1357-1359)aaT>aaC	p.N453N	NXPE4_ENST00000424261.2_Silent_p.N169N	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	453						extracellular vesicular exosome (GO:0070062)											CTTTGTGGACATTGAGGGCCC	0.418													A|||	516	0.103035	0.0091	0.2017	5008	,	,		17881	0.0		0.1292	False		,,,				2504	0.2393				p.N453N		Atlas-SNP	.											.	.	.	.	0			c.T1359C						PASS	.	A	,	114,3654		4,106,1774	136.0	124.0	128.0		1359,507	-3.8	0.0	11	dbSNP_120	128	1110,7108		86,938,3085	no	coding-synonymous,coding-synonymous	FAM55D	NM_001077639.1,NM_017678.2	,	90,1044,4859	GG,GA,AA		13.5069,3.0255,10.2119	,	453/545,169/261	114441936	1224,10762	1884	4109	5993	SO:0001819	synonymous_variant	54827	exon6			GTGGACATTGAGG	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1359T>C	11.37:g.114441936A>G		Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	271	133	0.490775	NM_001077639	Q6QDB4|Q9NXP5	Silent	SNP	ENST00000375478.3	37	CCDS41718.1																																																																																			A|0.894;G|0.106	0.106	strong		0.418	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
DEGS1	8560	hgsc.bcm.edu	37	1	224377383	224377383	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:224377383G>A	ENST00000323699.4	+	2	353	c.187G>A	c.(187-189)Gac>Aac	p.D63N	DEGS1_ENST00000391877.3_Missense_Mutation_p.D63N|DEGS1_ENST00000465848.1_3'UTR	NM_003676.3	NP_003667.1	O15121	DEGS1_HUMAN	delta(4)-desaturase, sphingolipid 1	63					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|unsaturated fatty acid biosynthetic process (GO:0006636)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|kidney(3)|large_intestine(2)|lung(4)	10	Breast(184;0.193)			GBM - Glioblastoma multiforme(131;0.00643)		CATAGTAAAAGACTTGGACTG	0.413																																					p.D63N		Atlas-SNP	.											DEGS1,NS,carcinoma,0,1	DEGS1	24	1	0			c.G187A						scavenged	.						119.0	123.0	121.0					1																	224377383		2203	4300	6503	SO:0001583	missense	8560	exon2			GTAAAAGACTTGG	AF002668	CCDS1540.1	1q42.11	2013-09-02	2011-12-09	2004-12-14	ENSG00000143753	ENSG00000143753		"""Fatty acid desaturases"""	13709	protein-coding gene	gene with protein product	"""sphingolipid delta(4)-desaturase 1"", ""dihydroceramide desaturase 1"""	615843	"""degenerative spermatocyte homolog 1, lipid desaturase (Drosophila)"""			9188692, 20105137	Standard	NM_003676		Approved	MLD, Des-1, DES1, FADS7, DEGS-1	uc001hoj.3	O15121	OTTHUMG00000037496	ENST00000323699.4:c.187G>A	1.37:g.224377383G>A	ENSP00000316476:p.Asp63Asn	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	166	3	0.0180723	NM_003676		Missense_Mutation	SNP	ENST00000323699.4	37	CCDS1540.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.413285	0.62511	.	.	ENSG00000143753	ENST00000415210;ENST00000323699;ENST00000391877	T;T;T	0.44083	0.93;1.49;1.49	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.58935	0.2157	L	0.46614	1.455	0.80722	D	1	B;D	0.89917	0.004;1.0	B;D	0.83275	0.008;0.996	T	0.43686	-0.9376	10	0.20046	T	0.44	.	20.2418	0.98377	0.0:0.0:1.0:0.0	.	63;42	O15121;E7EMA0	DEGS1_HUMAN;.	N	42;63;63	ENSP00000400545:D42N;ENSP00000316476:D63N;ENSP00000375749:D63N	ENSP00000316476:D63N	D	+	1	0	DEGS1	222444006	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.001000	0.88508	2.863000	0.98299	0.549000	0.68633	GAC	.	.	none		0.413	DEGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091285.2		
KRT40	125115	hgsc.bcm.edu	37	17	39135214	39135214	+	Silent	SNP	T	T	C	rs8068970	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39135214T>C	ENST00000398486.2	-	8	1198	c.1038A>G	c.(1036-1038)caA>caG	p.Q346Q	KRT40_ENST00000377755.4_Silent_p.Q346Q	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	346	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				GACACTGAATTTGGGCCAGCT	0.572													C|||	1841	0.367612	0.7231	0.2435	5008	,	,		16216	0.1736		0.2704	False		,,,				2504	0.2751				p.Q346Q		Atlas-SNP	.											.	KRT40	27	.	0			c.A1038G						PASS	.	C		2819,1575	463.4+/-353.5	915,989,293	89.0	98.0	95.0		1038	3.5	1.0	17	dbSNP_116	95	2378,6204	683.1+/-403.9	322,1734,2235	no	coding-synonymous	KRT40	NM_182497.3		1237,2723,2528	CC,CT,TT		27.7092,35.8443,40.0509		346/432	39135214	5197,7779	2197	4291	6488	SO:0001819	synonymous_variant	125115	exon8			CTGAATTTGGGCC	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.1038A>G	17.37:g.39135214T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_182497	Q6IFU5	Silent	SNP	ENST00000398486.2	37	CCDS42320.1																																																																																			T|0.653;C|0.347	0.347	strong		0.572	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
CEACAM18	729767	hgsc.bcm.edu	37	19	51981946	51981946	+	Missense_Mutation	SNP	T	T	C	rs75588884	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51981946T>C	ENST00000396477.4	+	1	71	c.50T>C	c.(49-51)aTg>aCg	p.M17T	CEACAM18_ENST00000451626.1_Missense_Mutation_p.M78T	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	17										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GTCTTCCTCATGGGTAAGAGA	0.632													t|||	84	0.0167732	0.0091	0.0202	5008	,	,		14636	0.0089		0.0209	False		,,,				2504	0.0286				p.M78T		Atlas-SNP	.											CEACAM18_ENST00000451626,NS,chondrosarcoma,-1,1	CEACAM18	96	1	0			c.T233C						PASS	.	T	THR/MET	31,3875		0,31,1922	25.0	28.0	27.0		233	1.8	0.3	19	dbSNP_132	27	231,8097		3,225,3936	yes	missense	CEACAM18	NM_001080405.1	81	3,256,5858	CC,CT,TT		2.7738,0.7937,2.1416	benign	78/399	51981946	262,11972	1953	4164	6117	SO:0001583	missense	729767	exon2			TCCTCATGGGTAA			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.50T>C	19.37:g.51981946T>C	ENSP00000379738:p.Met17Thr	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		33	0.01510989010989011	7	0.014227642276422764	6	0.016574585635359115	5	0.008741258741258742	15	0.01978891820580475	.	0.006	-2.073812	0.00379	0.007937	0.027738	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.03689	3.84	2.8	1.76	0.24704	.	.	.	.	.	T	0.00580	0.0019	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.47328	-0.9126	9	0.02654	T	1	.	4.8465	0.13516	0.0:0.1495:0.0:0.8505	.	78	A8MTB9	CEA18_HUMAN	T	78;17;17	ENSP00000402203:M78T	ENSP00000379738:M17T	M	+	2	0	CEACAM18	56673758	0.270000	0.24152	0.270000	0.24601	0.080000	0.17528	1.352000	0.34033	0.480000	0.27534	0.533000	0.62120	ATG	T|0.977;C|0.023	0.023	strong		0.632	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
TMEM132D	121256	hgsc.bcm.edu	37	12	130184612	130184612	+	Silent	SNP	C	C	T	rs140064887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:130184612C>T	ENST00000422113.2	-	2	1037	c.711G>A	c.(709-711)ggG>ggA	p.G237G	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	237					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGACGCAGTCCCCTCTCTCAC	0.667													C|||	15	0.00299521	0.0015	0.0029	5008	,	,		15848	0.0		0.0099	False		,,,				2504	0.001				p.G237G		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G711A						PASS	.	C		8,4398	12.9+/-30.5	0,8,2195	81.0	74.0	76.0		711	-7.6	0.0	12	dbSNP_134	76	66,8534	39.8+/-96.3	0,66,4234	no	coding-synonymous	TMEM132D	NM_133448.2		0,74,6429	TT,TC,CC		0.7674,0.1816,0.569		237/1100	130184612	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	121256	exon2			GCAGTCCCCTCTC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.711G>A	12.37:g.130184612C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																			C|0.995;T|0.005	0.005	strong		0.667	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
CACNA1E	777	hgsc.bcm.edu	37	1	181725110	181725110	+	Silent	SNP	T	T	C	rs4652678	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:181725110T>C	ENST00000367573.2	+	29	4008	c.4008T>C	c.(4006-4008)caT>caC	p.H1336H	CACNA1E_ENST00000358338.5_Silent_p.H1268H|CACNA1E_ENST00000357570.5_Silent_p.H1287H|CACNA1E_ENST00000367567.4_Silent_p.H943H|CACNA1E_ENST00000360108.3_Silent_p.H1317H|CACNA1E_ENST00000367570.1_Silent_p.H1336H|CACNA1E_ENST00000526775.1_Silent_p.H1317H	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1336					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						ATGTAGATCATGAGAAAAACA	0.483													T|||	1594	0.318291	0.4856	0.3256	5008	,	,		18946	0.0754		0.2863	False		,,,				2504	0.3701				p.H1336H		Atlas-SNP	.											.	CACNA1E	778	.	0			c.T4008C						PASS	.	T	,,	1605,2223		339,927,648	79.0	80.0	80.0		4008,4008,3951	0.3	1.0	1	dbSNP_111	80	2240,6028		299,1642,2193	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	,,	638,2569,2841	CC,CT,TT		27.0924,41.9279,31.7874	,,	1336/2271,1336/2314,1317/2252	181725110	3845,8251	1914	4134	6048	SO:0001819	synonymous_variant	777	exon29			AGATCATGAGAAA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.4008T>C	1.37:g.181725110T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																			T|0.710;C|0.290	0.290	strong		0.483	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
GLTSCR1	29998	hgsc.bcm.edu	37	19	48182946	48182946	+	Silent	SNP	T	T	C	rs2911006	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48182946T>C	ENST00000396720.3	+	6	713	c.519T>C	c.(517-519)ccT>ccC	p.P173P	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	173										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		AGGGCCCGCCTACCGTGCTGA	0.731													C|||	4087	0.816094	0.7973	0.7954	5008	,	,		11247	0.9593		0.7227	False		,,,				2504	0.8047				p.P173P		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.T519C						PASS	.						6.0	8.0	7.0					19																	48182946		672	1552	2224	SO:0001819	synonymous_variant	29998	exon6			CCCGCCTACCGTG	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.519T>C	19.37:g.48182946T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	37	CCDS46134.1																																																																																			T|0.191;C|0.809	0.809	strong		0.731	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33576602	33576602	+	Missense_Mutation	SNP	A	A	G	rs3813474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:33576602A>G	ENST00000504830.1	-	19	3864	c.3529T>C	c.(3529-3531)Tgg>Cgg	p.W1177R	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.W1092R|ADAMTS12_ENST00000504582.1_5'Flank	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1177	Spacer 2.		W -> R (in dbSNP:rs3813474).		cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						ATCTTGGTCCATATTACAGGA	0.473										HNSCC(64;0.19)			A|||	257	0.0513179	0.003	0.0706	5008	,	,		22201	0.0446		0.1282	False		,,,				2504	0.0307				p.W1177R		Atlas-SNP	.											ADAMTS12,NS,carcinoma,+1,1	ADAMTS12	464	1	0			c.T3529C						PASS	.	A	ARG/TRP	117,4289	87.8+/-126.4	2,113,2088	198.0	179.0	185.0		3529	2.8	0.2	5	dbSNP_107	185	887,7713	199.7+/-243.7	43,801,3456	yes	missense	ADAMTS12	NM_030955.2	101	45,914,5544	GG,GA,AA		10.314,2.6555,7.7195	benign	1177/1595	33576602	1004,12002	2203	4300	6503	SO:0001583	missense	81792	exon19			TGGTCCATATTAC	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.3529T>C	5.37:g.33576602A>G	ENSP00000422554:p.Trp1177Arg	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	227	98	0.431718	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	169	0.07738095238095238	3	0.006097560975609756	32	0.08839779005524862	31	0.05419580419580419	103	0.1358839050131926	A	0.013	-1.623965	0.00820	0.026555	0.10314	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.58506	0.33;0.33	5.28	2.83	0.33086	.	0.596637	0.18452	N	0.140782	T	0.00328	0.0010	L	0.36672	1.1	0.29060	P	0.8839589999999999	B;B	0.12013	0.005;0.002	B;B	0.11329	0.006;0.003	T	0.06110	-1.0845	9	0.22706	T	0.39	.	3.9121	0.09207	0.6663:0.0:0.1695:0.1643	rs3813474;rs17567595;rs52822063;rs59098925;rs3813474	1092;1177	P58397-3;P58397	.;ATS12_HUMAN	R	1177;1092	ENSP00000422554:W1177R;ENSP00000344847:W1092R	ENSP00000344847:W1092R	W	-	1	0	ADAMTS12	33612359	0.962000	0.33011	0.200000	0.23457	0.053000	0.15095	2.322000	0.43814	0.428000	0.26173	0.533000	0.62120	TGG	A|0.925;G|0.075	0.075	strong		0.473	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
HLA-B	3106	hgsc.bcm.edu	37	6	31324151	31324151	+	Missense_Mutation	SNP	C	C	G	rs709055	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324151C>G	ENST00000412585.2	-	3	440	c.412G>C	c.(412-414)Gac>Cac	p.D138H		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	138	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GCGTACTGGTCATGCCCGCGG	0.706									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				C|||	132	0.0263578	0.0166	0.0245	5008	,	,		8671	0.0149		0.0547	False		,,,				2504	0.0235				p.D138H		Atlas-SNP	.											.	HLA-B	54	.	0			c.G412C						PASS	.						24.0	20.0	21.0					6																	31324151		2077	4174	6251	SO:0001583	missense	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	ACTGGTCATGCCC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.412G>C	6.37:g.31324151C>G	ENSP00000399168:p.Asp138His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	1.155	-0.645580	0.03531	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.00009	9.46;9.46	3.18	-6.36	0.01969	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	11.996900	0.00839	U	0.001730	T	0.00012	0.0000	N	0.03016	-0.435	0.09310	N	1	B	0.10296	0.003	B	0.20955	0.032	T	0.34775	-0.9815	10	0.21540	T	0.41	.	1.9609	0.03386	0.1105:0.2127:0.2728:0.4041	rs709055;rs1050378;rs3173354;rs3175252;rs4997053;rs9266151;rs16896610;rs28695853	138	P01889	1B07_HUMAN	H	138;17;17;149	ENSP00000399168:D138H;ENSP00000405931:D149H	ENSP00000399168:D138H	D	-	1	0	HLA-B	31432130	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-20.000000	0.00000	-4.183000	0.00067	-0.712000	0.03635	GAC	T|0.462;G|0.008;C|0.530	0.008	strong		0.706	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ALOX15B	247	hgsc.bcm.edu	37	17	7951819	7951819	+	Missense_Mutation	SNP	A	A	G	rs4792147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7951819A>G	ENST00000380183.4	+	14	2106	c.1967A>G	c.(1966-1968)cAg>cGg	p.Q656R	ALOX15B_ENST00000380173.2_Missense_Mutation_p.Q627R|ALOX15B_ENST00000572022.1_Missense_Mutation_p.Q644R|ALOX15B_ENST00000573359.1_Missense_Mutation_p.Q582R	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	656	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		Q -> R (in dbSNP:rs4792147). {ECO:0000269|PubMed:11350124, ECO:0000269|PubMed:11839751, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9177185}.		apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						GAGCGGAACCAGGGCCTGGTG	0.617													G|||	3257	0.650359	0.8775	0.5778	5008	,	,		16415	0.5506		0.5119	False		,,,				2504	0.6401				p.Q656R		Atlas-SNP	.											.	ALOX15B	66	.	0			c.A1967G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN	3558,848	334.1+/-303.3	1444,670,89	87.0	90.0	89.0		1880,1745,1967	-1.7	0.0	17	dbSNP_111	89	4308,4292	577.2+/-390.5	1079,2150,1071	yes	missense,missense,missense	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	43,43,43	2523,2820,1160	GG,GA,AA		49.907,19.2465,39.5202	benign,benign,benign	627/648,582/603,656/677	7951819	7866,5140	2203	4300	6503	SO:0001583	missense	247	exon14			GGAACCAGGGCCT	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1967A>G	17.37:g.7951819A>G	ENSP00000369530:p.Gln656Arg	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	1303	0.5966117216117216	413	0.8394308943089431	195	0.5386740331491713	321	0.5611888111888111	374	0.49340369393139843	G	7.178	0.589071	0.13812	0.807535	0.50093	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	T;T	0.76316	-1.01;-1.01	3.74	-1.69	0.08186	Lipoxygenase, C-terminal (3);	1.304660	0.04587	N	0.396096	T	0.00012	0.0000	N	0.12961	0.28	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.10450	0.005;0.001;0.001	T	0.40961	-0.9535	9	0.25751	T	0.34	-5.7717	10.5555	0.45114	0.7064:0.0:0.2936:0.0	rs4792147;rs17855861;rs17857053;rs52802887;rs60011980;rs4792147	582;627;656	O15296-2;O15296-4;O15296	.;.;LX15B_HUMAN	R	627;582;656	ENSP00000369520:Q627R;ENSP00000369530:Q656R	ENSP00000344337:Q582R	Q	+	2	0	ALOX15B	7892544	0.000000	0.05858	0.017000	0.16124	0.445000	0.32107	0.081000	0.14823	-0.947000	0.03673	-0.974000	0.02594	CAG	A|0.391;C|0.000;G|0.609	0.609	strong		0.617	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
ALDH1A3	220	hgsc.bcm.edu	37	15	101440917	101440917	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:101440917C>T	ENST00000329841.5	+	9	1553	c.1021C>T	c.(1021-1023)Cgg>Tgg	p.R341W	ALDH1A3_ENST00000346623.6_Missense_Mutation_p.R234W|RP11-66B24.4_ENST00000560351.1_RNA	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3	341					embryonic eye morphogenesis (GO:0048048)|face development (GO:0060324)|inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|nucleus accumbens development (GO:0021768)|olfactory pit development (GO:0060166)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|positive regulation of apoptotic process (GO:0043065)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoic acid metabolic process (GO:0042573)|retinol metabolic process (GO:0042572)|righting reflex (GO:0060013)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|thyroid hormone binding (GO:0070324)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(7)|lung(9)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	27	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		Vitamin A(DB00162)	TGCCAAGAAACGGCCCGTGGG	0.577																																					p.R341W		Atlas-SNP	.											ALDH1A3,NS,carcinoma,-1,1	ALDH1A3	61	1	0			c.C1021T						scavenged	.						65.0	62.0	63.0					15																	101440917		2203	4300	6503	SO:0001583	missense	220	exon9			AAGAAACGGCCCG	U07919	CCDS10389.1	15q26	2010-05-07			ENSG00000184254	ENSG00000184254	1.2.1.5	"""Aldehyde dehydrogenases"""	409	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 3"""	600463		ALDH6		7698756	Standard	XR_111558		Approved	RALDH3	uc002bwn.4	P47895	OTTHUMG00000149870	ENST00000329841.5:c.1021C>T	15.37:g.101440917C>T	ENSP00000332256:p.Arg341Trp	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	135	3	0.0222222	NM_000693	Q6NT64	Missense_Mutation	SNP	ENST00000329841.5	37	CCDS10389.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.116961	0.37339	.	.	ENSG00000184254	ENST00000329841;ENST00000346623	T	0.75821	-0.97	5.7	-1.37	0.09056	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.214262	0.42682	D	0.000671	T	0.68723	0.3032	N	0.02736	-0.51	0.21822	N	0.999522	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.988	T	0.72033	-0.4412	10	0.66056	D	0.02	.	17.8998	0.88900	0.6403:0.3597:0.0:0.0	.	245;341	Q7Z3A2;P47895	.;AL1A3_HUMAN	W	341;245	ENSP00000332256:R341W	ENSP00000332256:R341W	R	+	1	2	ALDH1A3	99258440	0.004000	0.15560	0.018000	0.16275	0.097000	0.18754	0.095000	0.15127	-0.100000	0.12241	-0.274000	0.10170	CGG	.	.	none		0.577	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313620.2		
PHC1	1911	hgsc.bcm.edu	37	12	9086553	9086553	+	Silent	SNP	G	G	A	rs1805773	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:9086553G>A	ENST00000543824.1	+	10	2318	c.1986G>A	c.(1984-1986)aaG>aaA	p.K662K	PHC1_ENST00000433847.2_3'UTR|PHC1_ENST00000536844.1_Silent_p.K268K|PHC1_ENST00000433083.2_Silent_p.K617K|PHC1_ENST00000544916.1_Silent_p.K662K			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	662					cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						TTCCTGCCAAGGCATCTCCAG	0.498													G|||	706	0.140974	0.2216	0.1311	5008	,	,		-128	0.0129		0.167	False		,,,				2504	0.1442				p.K662K		Atlas-SNP	.											.	PHC1	67	.	0			c.G1986A						PASS	.	G		937,3469	356.4+/-313.5	93,751,1359	90.0	82.0	85.0		1986	5.7	1.0	12	dbSNP_92	85	1426,7168	273.8+/-290.9	102,1222,2973	no	coding-synonymous	PHC1	NM_004426.2		195,1973,4332	AA,AG,GG		16.593,21.2665,18.1769		662/1005	9086553	2363,10637	2203	4297	6500	SO:0001819	synonymous_variant	1911	exon9			TGCCAAGGCATCT	U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"""Sterile alpha motif (SAM) domain containing"""	3182	protein-coding gene	gene with protein product		602978	"""early development regulator 1 (homolog of polyhomeotic 1)"", ""polyhomeotic-like 1 (Drosophila)"""	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.1986G>A	12.37:g.9086553G>A		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	227	124	0.546256	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Silent	SNP	ENST00000543824.1	37	CCDS8597.1	283	0.1295787545787546	112	0.22764227642276422	51	0.1408839779005525	3	0.005244755244755245	117	0.15435356200527706	G	7.561	0.664728	0.14710	0.212665	0.16593	ENSG00000111752	ENST00000537610	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.05194	-1.0900	3	.	.	.	-17.4092	12.0036	0.53246	0.0801:0.0:0.9199:0.0	rs1805773	.	.	.	K	173	.	.	R	+	2	0	PHC1	8977820	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.402000	0.59722	2.703000	0.92315	0.655000	0.94253	AGG	G|0.834;A|0.166	0.166	strong		0.498	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	
PTPRQ	374462	hgsc.bcm.edu	37	12	80935345	80935345	+	Missense_Mutation	SNP	T	T	C	rs6539524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:80935345T>C	ENST00000266688.5	+	26	3154	c.3154T>C	c.(3154-3156)Ttt>Ctt	p.F1052L				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1098	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						ACCTGAAGGGTTTGTTGGAAA	0.388													C|||	1993	0.397963	0.7988	0.3069	5008	,	,		15600	0.2192		0.2783	False		,,,				2504	0.228				p.F884L		Atlas-SNP	.											.	PTPRQ	119	.	0			c.T2650C						PASS	.	C	LEU/PHE	982,402		347,288,57	102.0	85.0	90.0		2712	-5.1	0.0	12	dbSNP_116	90	891,2291		140,611,840	yes	missense	PTPRQ	NM_001145026.1	22	487,899,897	CC,CT,TT		28.0013,29.0462,41.0206	benign	1056/2300	80935345	1873,2693	692	1591	2283	SO:0001583	missense	374462	exon18			GAAGGGTTTGTTG	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.3154T>C	12.37:g.80935345T>C	ENSP00000266688:p.Phe1052Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	37		841	0.3850732600732601	375	0.7621951219512195	132	0.36464088397790057	135	0.23601398601398602	199	0.262532981530343	C	5.204	0.223162	0.09863	0.709538	0.280013	ENSG00000139304	ENST00000266688	T	0.34667	1.35	5.89	-5.06	0.02946	Fibronectin, type III (3);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36187	-0.9758	7	0.13108	T	0.6	.	3.4758	0.07583	0.0926:0.2491:0.1919:0.4664	rs6539524;rs17713148;rs6539524	1098	Q9UMZ3	PTPRQ_HUMAN	L	1052	ENSP00000266688:F1052L	ENSP00000266688:F1052L	F	+	1	0	PTPRQ	79459476	0.028000	0.19301	0.042000	0.18584	0.996000	0.88848	-0.877000	0.04197	-1.392000	0.02082	-0.119000	0.15052	TTT	T|0.587;C|0.413	0.413	strong		0.388	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
OR5A2	219981	hgsc.bcm.edu	37	11	59189912	59189912	+	Missense_Mutation	SNP	G	G	A	rs1453547	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:59189912G>A	ENST00000302040.4	-	1	537	c.515C>T	c.(514-516)cCc>cTc	p.P172L		NM_001001954.1	NP_001001954.1	Q8NGI9	OR5A2_HUMAN	olfactory receptor, family 5, subfamily A, member 2	172			P -> L (in dbSNP:rs1453547).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	21						GATCATATAGGGCCCACAGAA	0.463													G|||	631	0.125998	0.0242	0.1311	5008	,	,		22596	0.1121		0.2515	False		,,,				2504	0.1452				p.P172L		Atlas-SNP	.											.	OR5A2	35	.	0			c.C515T						PASS	.	G	LEU/PRO	256,4146	148.8+/-183.1	10,236,1955	95.0	88.0	91.0		515	4.6	0.3	11	dbSNP_88	91	2258,6332	382.8+/-340.5	282,1694,2319	yes	missense	OR5A2	NM_001001954.1	98	292,1930,4274	AA,AG,GG		26.2864,5.8155,19.3504	probably-damaging	172/325	59189912	2514,10478	2201	4295	6496	SO:0001583	missense	219981	exon1			ATATAGGGCCCAC	AB065805	CCDS31560.1	11q12.1	2012-08-09			ENSG00000172324	ENSG00000172324		"""GPCR / Class A : Olfactory receptors"""	15249	protein-coding gene	gene with protein product							Standard	NM_001001954		Approved		uc010rkt.2	Q8NGI9	OTTHUMG00000167419	ENST00000302040.4:c.515C>T	11.37:g.59189912G>A	ENSP00000303834:p.Pro172Leu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_001001954	B9EH21|Q6IFF4|Q96RB0	Missense_Mutation	SNP	ENST00000302040.4	37	CCDS31560.1	349	0.15979853479853479	19	0.03861788617886179	59	0.16298342541436464	71	0.12412587412587413	200	0.2638522427440633	G	19.64	3.865680	0.71949	0.058155	0.262864	ENSG00000172324	ENST00000302040	T	0.00076	8.76	5.47	4.55	0.56014	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34932	U	0.003564	T	0.00012	0.0000	M	0.79343	2.45	0.30789	P	0.741141	D	0.69078	0.997	D	0.79784	0.993	T	0.68070	-0.5506	9	0.72032	D	0.01	.	13.8893	0.63729	0.0:0.0:0.8469:0.1531	rs1453547;rs17499129;rs57323320;rs1453547	172	Q8NGI9	OR5A2_HUMAN	L	172	ENSP00000303834:P172L	ENSP00000303834:P172L	P	-	2	0	OR5A2	58946488	0.328000	0.24687	0.276000	0.24689	0.826000	0.46750	3.157000	0.50716	1.428000	0.47296	0.585000	0.79938	CCC	G|0.820;A|0.180	0.180	strong		0.463	OR5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394552.1	NM_001001954	
MYOM1	8736	hgsc.bcm.edu	37	18	3215158	3215158	+	Missense_Mutation	SNP	C	C	G	rs386800438|rs1791085	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:3215158C>G	ENST00000356443.4	-	2	397	c.64G>C	c.(64-66)Gtg>Ctg	p.V22L	MYOM1_ENST00000400569.3_Missense_Mutation_p.V22L|MYOM1_ENST00000261606.7_Missense_Mutation_p.V22L|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	22			V -> L (in dbSNP:rs1791085).		muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GTGCTGCGCACGTCCTTGTTG	0.612													G|||	641	0.127995	0.1339	0.0879	5008	,	,		16535	0.1845		0.0915	False		,,,				2504	0.1278				p.V22L		Atlas-SNP	.											.	MYOM1	192	.	0			c.G64C						PASS	.	G	LEU/VAL,LEU/VAL	501,3711		30,441,1635	56.0	60.0	59.0		64,64	5.7	1.0	18	dbSNP_89	59	729,7753		30,669,3542	yes	missense,missense	MYOM1	NM_003803.3,NM_019856.1	32,32	60,1110,5177	GG,GC,CC		8.5947,11.8946,9.6896	benign,benign	22/1686,22/1590	3215158	1230,11464	2106	4241	6347	SO:0001583	missense	8736	exon2			TGCGCACGTCCTT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.64G>C	18.37:g.3215158C>G	ENSP00000348821:p.Val22Leu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	253	0.11584249084249085	65	0.13211382113821138	29	0.08011049723756906	91	0.1590909090909091	68	0.08970976253298153	G	2.140	-0.397132	0.04899	0.118946	0.085947	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.37235	1.33;1.33;1.21	5.67	5.67	0.87782	.	0.312462	0.30959	N	0.008527	T	0.00039	0.0001	N	0.01874	-0.695	0.58432	P	6.999999999979245E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.14896	-1.0456	9	0.02654	T	1	.	9.338	0.38062	0.0761:0.1468:0.7771:0.0	rs1791085;rs1791085	22;22	P52179-2;P52179	.;MYOM1_HUMAN	L	22	ENSP00000348821:V22L;ENSP00000383413:V22L;ENSP00000261606:V22L	ENSP00000261606:V22L	V	-	1	0	MYOM1	3205158	1.000000	0.71417	0.984000	0.44739	0.481000	0.33189	2.152000	0.42272	1.414000	0.47017	-0.120000	0.15030	GTG	C|0.887;G|0.113	0.113	strong		0.612	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
ATP13A2	23400	hgsc.bcm.edu	37	1	17313654	17313654	+	Silent	SNP	C	C	T	rs761421	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17313654C>T	ENST00000326735.8	-	26	3003	c.2970G>A	c.(2968-2970)gtG>gtA	p.V990V	ATP13A2_ENST00000452699.1_Silent_p.V985V|ATP13A2_ENST00000341676.5_Silent_p.V946V|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2	990					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CCGGTGGCCGCACCCGTCCCA	0.687													C|||	1734	0.346246	0.171	0.4582	5008	,	,		13199	0.252		0.508	False		,,,				2504	0.4346				p.V990V		Atlas-SNP	.											.	ATP13A2	85	.	0			c.G2970A						PASS	.	C	,,	1046,3360	380.6+/-323.8	133,780,1290	46.0	43.0	44.0		2955,2838,2970	-5.5	0.9	1	dbSNP_86	44	4488,4110	583.2+/-391.5	1155,2178,966	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	1288,2958,2256	TT,TC,CC		47.8018,23.7404,42.5561	,,	985/1176,946/1159,990/1181	17313654	5534,7470	2203	4299	6502	SO:0001819	synonymous_variant	23400	exon26			TGGCCGCACCCGT	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2970G>A	1.37:g.17313654C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			C|0.600;T|0.400	0.400	strong		0.687	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
SLC10A6	345274	hgsc.bcm.edu	37	4	87769929	87769929	+	Missense_Mutation	SNP	T	T	C	rs13106574	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:87769929T>C	ENST00000273905.6	-	1	487	c.340A>G	c.(340-342)Att>Gtt	p.I114V	SLC10A6_ENST00000505535.1_5'UTR	NM_197965.2	NP_932069.1	Q3KNW5	SOAT_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 6	114			I -> V (in dbSNP:rs13106574). {ECO:0000269|PubMed:15489334}.		sodium-dependent organic anion transport (GO:0043251)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)|sodium-dependent organic anion transmembrane transporter activity (GO:0043250)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	9		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.00099)		AAGGTGAAAATGTTAGAGATG	0.488													T|||	495	0.0988419	0.118	0.1268	5008	,	,		17437	0.001		0.1769	False		,,,				2504	0.0736				p.I114V		Atlas-SNP	.											.	SLC10A6	40	.	0			c.A340G						PASS	.	T	VAL/ILE	518,3888	237.4+/-249.2	30,458,1715	78.0	84.0	82.0		340	2.6	1.0	4	dbSNP_121	82	1726,6874	315.7+/-312.4	178,1370,2752	yes	missense	SLC10A6	NM_197965.2	29	208,1828,4467	CC,CT,TT		20.0698,11.7567,17.2536	benign	114/378	87769929	2244,10762	2203	4300	6503	SO:0001583	missense	345274	exon1			TGAAAATGTTAGA	AJ583502	CCDS3614.1	4q22.1	2013-07-18	2013-07-18		ENSG00000145283	ENSG00000145283		"""Solute carriers"""	30603	protein-coding gene	gene with protein product		613366				15020217, 17491011	Standard	NM_197965		Approved	SOAT	uc003hqd.2	Q3KNW5	OTTHUMG00000130596	ENST00000273905.6:c.340A>G	4.37:g.87769929T>C	ENSP00000273905:p.Ile114Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_197965	Q70EX7	Missense_Mutation	SNP	ENST00000273905.6	37	CCDS3614.1	224	0.10256410256410256	54	0.10975609756097561	46	0.1270718232044199	0	0.0	124	0.16358839050131926	T	10.69	1.422271	0.25639	0.117567	0.200698	ENSG00000145283	ENST00000273905	T	0.08984	3.03	5.59	2.64	0.31445	.	0.077016	0.52532	N	0.000071	T	0.00012	0.0000	N	0.13272	0.32	0.41065	P	0.014599000000000029	B	0.25169	0.119	B	0.31812	0.136	T	0.47394	-0.9121	9	0.15066	T	0.55	-17.4279	5.4631	0.16627	0.0:0.1238:0.1603:0.7158	rs13106574;rs52789983;rs59733764;rs13106574	114	Q3KNW5	SOAT_HUMAN	V	114	ENSP00000273905:I114V	ENSP00000273905:I114V	I	-	1	0	SLC10A6	87988953	1.000000	0.71417	0.956000	0.39512	0.893000	0.52053	1.263000	0.33004	0.751000	0.32900	0.533000	0.62120	ATT	T|0.854;C|0.146	0.146	strong		0.488	SLC10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253043.2	NM_197965	
PAX5	5079	hgsc.bcm.edu	37	9	37020669	37020669	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:37020669C>T	ENST00000358127.4	-	2	250	c.176G>A	c.(175-177)cGg>cAg	p.R59Q	PAX5_ENST00000523145.1_Intron|PAX5_ENST00000522003.1_Intron|PAX5_ENST00000523241.1_Missense_Mutation_p.R59Q|PAX5_ENST00000520154.1_Missense_Mutation_p.R59Q|PAX5_ENST00000414447.1_Missense_Mutation_p.R59Q|PAX5_ENST00000377847.2_Missense_Mutation_p.R59Q|PAX5_ENST00000377852.2_Missense_Mutation_p.R59Q|PAX5_ENST00000446742.1_Missense_Mutation_p.R59Q|PAX5_ENST00000520281.1_Missense_Mutation_p.R59Q|PAX5_ENST00000377853.2_Missense_Mutation_p.R59Q	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	59	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.		R -> G. {ECO:0000269|PubMed:24013638}.		humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.?(41)	PAX5/JAK2(18)	NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(151)|kidney(1)|lung(10)|prostate(1)|skin(1)	171		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		ATGGCTGACCCGAAGCTGCCT	0.512			"""T, Mis, D, F, S"""	"""IGH@, ETV6, PML, FOXP1, ZNF521, ELN"""	"""NHL, ALL, B-ALL"""																																p.R59Q		Atlas-SNP	.		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	PAX5,lymph_node,lymphoid_neoplasm,-1,1	PAX5	250	1	41	Unknown(41)	haematopoietic_and_lymphoid_tissue(41)	c.G176A						scavenged	.						119.0	117.0	118.0					9																	37020669		2203	4300	6503	SO:0001583	missense	5079	exon2			CTGACCCGAAGCT		CCDS6607.1, CCDS65039.1, CCDS65040.1, CCDS65041.1, CCDS65042.1, CCDS65043.1, CCDS65044.1, CCDS65045.1, CCDS65046.1, CCDS65047.1, CCDS65048.1	9p13.2	2011-06-20	2007-07-12		ENSG00000196092	ENSG00000196092		"""Paired boxes"", ""Homeoboxes / PRD class"""	8619	protein-coding gene	gene with protein product	"""B-cell lineage specific activator"""	167414	"""paired box gene 5 (B-cell lineage specific activator protein)"", ""paired box gene 5 (B-cell lineage specific activator)"""			1516825, 8431641	Standard	NM_016734		Approved	BSAP	uc003zzo.1	Q02548	OTTHUMG00000019907	ENST00000358127.4:c.176G>A	9.37:g.37020669C>T	ENSP00000350844:p.Arg59Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	105	2	0.0190476	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	37	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.773505	0.90108	.	.	ENSG00000196092	ENST00000358127;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000520281;ENST00000446742;ENST00000414447;ENST00000377847	D;D;D;D;D;D;D;D;D	0.99479	-5.81;-5.81;-5.81;-5.81;-5.81;-5.81;-5.98;-5.81;-5.81	5.59	5.59	0.84812	Paired box protein, N-terminal (5);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99387	0.9784	M	0.67625	2.065	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.996;1.0;1.0;0.996;1.0;1.0;0.998;0.996;0.996	D;P;D;D;P;D;D;P;P;P	0.87578	0.992;0.893;0.992;0.998;0.893;0.993;0.988;0.801;0.893;0.893	D	0.99937	1.1367	10	0.23302	T	0.38	.	19.5898	0.95506	0.0:1.0:0.0:0.0	.	58;59;59;59;59;59;59;59;59;59	C0KTF2;C0KTF8;C0KTF7;C0KTF9;C0KTF6;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.;.;.;.;.;.;.;.;.;PAX5_HUMAN	Q	59	ENSP00000350844:R59Q;ENSP00000367084:R59Q;ENSP00000367083:R59Q;ENSP00000429637:R59Q;ENSP00000429291:R59Q;ENSP00000430773:R59Q;ENSP00000404687:R59Q;ENSP00000412188:R59Q;ENSP00000367078:R59Q	ENSP00000350844:R59Q	R	-	2	0	PAX5	37010669	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.775000	0.85489	2.624000	0.88883	0.655000	0.94253	CGG	.	.	none		0.512	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1		
C19orf44	84167	hgsc.bcm.edu	37	19	16611978	16611978	+	Silent	SNP	T	T	C	rs728116	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:16611978T>C	ENST00000221671.3	+	2	531	c.375T>C	c.(373-375)gcT>gcC	p.A125A	CTD-3222D19.2_ENST00000409035.1_Intron|C19orf44_ENST00000594035.1_Silent_p.A125A	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	125										endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						CCGCCGATGCTGGTCTTCCAA	0.537													C|||	1830	0.365415	0.6407	0.3386	5008	,	,		17193	0.1736		0.3221	False		,,,				2504	0.2546				p.A125A		Atlas-SNP	.											.	C19orf44	47	.	0			c.T375C						PASS	.	C		2687,1719	510.1+/-367.4	836,1015,352	54.0	62.0	59.0		375	-1.2	0.0	19	dbSNP_86	59	2639,5961	683.9+/-403.9	411,1817,2072	no	coding-synonymous	C19orf44	NM_032207.2		1247,2832,2424	CC,CT,TT		30.686,39.015,40.9503		125/658	16611978	5326,7680	2203	4300	6503	SO:0001819	synonymous_variant	84167	exon2			CGATGCTGGTCTT	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.375T>C	19.37:g.16611978T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_032207	Q8N6Y7	Silent	SNP	ENST00000221671.3	37	CCDS12345.1																																																																																			T|0.621;C|0.379	0.379	strong		0.537	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207	
SUMF1	285362	hgsc.bcm.edu	37	3	4508802	4508802	+	Missense_Mutation	SNP	G	G	A	rs200789939	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:4508802G>A	ENST00000272902.5	-	1	163	c.128C>T	c.(127-129)gCg>gTg	p.A43V	SUMF1_ENST00000405420.2_Missense_Mutation_p.A43V|SUMF1_ENST00000534863.1_Missense_Mutation_p.A43V|SUMF1_ENST00000383843.5_Missense_Mutation_p.A43V|SUMF1_ENST00000458465.2_Missense_Mutation_p.A43V	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	43					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(3)	13		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		AAGGGACCCCGCGCCCGCACC	0.711													G|||	2	0.000399361	0.0	0.0	5008	,	,		13188	0.0		0.002	False		,,,				2504	0.0				p.A43V		Atlas-SNP	.											.	SUMF1	23	.	0			c.C128T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	0,4178		0,0,2089	5.0	7.0	6.0		128,128,128	2.7	0.0	3		6	3,8223		0,3,4110	no	missense,missense,missense	SUMF1	NM_001164674.1,NM_001164675.1,NM_182760.3	64,64,64	0,3,6199	AA,AG,GG		0.0365,0.0,0.0242	benign,benign,benign	43/350,43/355,43/375	4508802	3,12401	2089	4113	6202	SO:0001583	missense	285362	exon1			GACCCCGCGCCCG	BC017005	CCDS2564.1, CCDS54548.1, CCDS54549.1	3p26.1	2009-07-23			ENSG00000144455	ENSG00000144455			20376	protein-coding gene	gene with protein product		607939				12757705, 12757706	Standard	NM_182760		Approved	FGE, UNQ3037	uc003bpz.2	Q8NBK3	OTTHUMG00000090269	ENST00000272902.5:c.128C>T	3.37:g.4508802G>A	ENSP00000272902:p.Ala43Val	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	19	12	0.631579	NM_001164675	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Missense_Mutation	SNP	ENST00000272902.5	37	CCDS2564.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	11.94	1.790063	0.31685	0.0	3.65E-4	ENSG00000144455	ENST00000534982;ENST00000534863;ENST00000272902;ENST00000383843;ENST00000458465;ENST00000405420	D;D;D;D;D	0.92805	-2.68;-3.11;-3.09;-2.33;-3.11	4.54	2.71	0.32032	.	0.485588	0.20903	N	0.083614	D	0.87418	0.6172	L	0.59436	1.845	0.09310	N	1	B;B;B;B	0.19200	0.034;0.023;0.014;0.014	B;B;B;B	0.12156	0.003;0.007;0.005;0.005	T	0.75808	-0.3187	10	0.34782	T	0.22	-14.8698	5.3757	0.16164	0.1034:0.0:0.6962:0.2003	.	43;43;43;43	E9PF05;G5E9B0;E9PGL0;Q8NBK3	.;.;.;SUMF1_HUMAN	V	43	ENSP00000440421:A43V;ENSP00000272902:A43V;ENSP00000373355:A43V;ENSP00000410060:A43V;ENSP00000384977:A43V	ENSP00000272902:A43V	A	-	2	0	SUMF1	4483802	0.027000	0.19231	0.013000	0.15412	0.135000	0.20990	1.099000	0.31013	0.615000	0.30124	0.591000	0.81541	GCG	G|0.999;A|0.001	0.001	strong		0.711	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760	
RDH8	50700	hgsc.bcm.edu	37	19	10129552	10129552	+	Missense_Mutation	SNP	C	C	G	rs1122206	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10129552C>G	ENST00000171214.1	+	3	657	c.408C>G	c.(406-408)caC>caG	p.H136Q	RDH8_ENST00000591589.1_Missense_Mutation_p.H156Q	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	136			H -> Q (in dbSNP:rs1122206).		estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)	p.H136Q(1)		endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	GGCAGGGCCACATCGTGGTGA	0.582													C|||	973	0.194289	0.3381	0.1513	5008	,	,		19017	0.0853		0.1541	False		,,,				2504	0.184				p.H156Q		Atlas-SNP	.											RDH8,NS,carcinoma,0,1	RDH8	51	1	1	Substitution - Missense(1)	prostate(1)	c.C468G						PASS	.	C	GLN/HIS	1338,3068	447.7+/-348.4	215,908,1080	80.0	77.0	78.0		408	0.9	1.0	19	dbSNP_86	78	1153,7447	236.8+/-268.9	82,989,3229	yes	missense	RDH8	NM_015725.2	24	297,1897,4309	GG,GC,CC		13.407,30.3677,19.1527	probably-damaging	136/312	10129552	2491,10515	2203	4300	6503	SO:0001583	missense	50700	exon3			GGGCCACATCGTG	AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	14423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 28C, member 2"""	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.408C>G	19.37:g.10129552C>G	ENSP00000171214:p.His136Gln	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_015725	Q9H838	Missense_Mutation	SNP	ENST00000171214.1	37		382	0.1749084249084249	165	0.3353658536585366	51	0.1408839779005525	54	0.0944055944055944	112	0.14775725593667546	C	17.96	3.517049	0.64634	0.303677	0.13407	ENSG00000080511	ENST00000171214	D	0.93189	-3.18	5.34	0.86	0.19042	NAD(P)-binding domain (1);	0.099894	0.64402	D	0.000002	T	0.00012	0.0000	N	0.16233	0.39	0.22866	P	0.9986305	D	0.76494	0.999	D	0.81914	0.995	T	0.01472	-1.1346	9	0.49607	T	0.09	.	7.313	0.26485	0.0:0.5793:0.0:0.4207	rs1122206;rs2233794;rs57809919;rs1122206	136	Q9NYR8	RDH8_HUMAN	Q	136	ENSP00000171214:H136Q	ENSP00000171214:H136Q	H	+	3	2	RDH8	9990552	0.998000	0.40836	1.000000	0.80357	0.918000	0.54935	0.608000	0.24223	0.635000	0.30488	0.491000	0.48974	CAC	C|0.810;G|0.190	0.190	strong		0.582	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
CES5A	221223	hgsc.bcm.edu	37	16	55880534	55880534	+	Silent	SNP	G	G	C	rs11860488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:55880534G>C	ENST00000290567.9	-	13	1678	c.1557C>G	c.(1555-1557)ctC>ctG	p.L519L	CES5A_ENST00000520435.1_Silent_p.L489L|CES5A_ENST00000518005.1_Silent_p.L413L|CES5A_ENST00000319165.9_Silent_p.L469L|CES5A_ENST00000521992.1_Silent_p.L548L|CES5A_ENST00000541580.1_5'UTR	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	519						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						AGTCCAGCTGGAGGTACTGCT	0.532													C|||	1533	0.30611	0.4327	0.1873	5008	,	,		16694	0.2817		0.2783	False		,,,				2504	0.273				p.L548L		Atlas-SNP	.											.	CES5A	206	.	0			c.C1644G						PASS	.	C	,,	1885,2511		397,1091,710	205.0	202.0	203.0		1557,1644,1407	3.5	0.8	16	dbSNP_120	203	2083,6517		262,1559,2479	yes	coding-synonymous,coding-synonymous,coding-synonymous	CES5A	NM_001143685.1,NM_001190158.1,NM_145024.2	,,	659,2650,3189	CC,CG,GG		24.2209,42.8799,30.5325	,,	519/576,548/605,469/526	55880534	3968,9028	2198	4300	6498	SO:0001819	synonymous_variant	221223	exon14			CAGCTGGAGGTAC	AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"""Carboxylesterases"""	26459	protein-coding gene	gene with protein product			"""carboxylesterase 7"""	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1557C>G	16.37:g.55880534G>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	156	82	0.525641	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Silent	SNP	ENST00000290567.9	37	CCDS45490.1																																																																																			G|0.695;C|0.305	0.305	strong		0.532	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	
AP1G2	8906	hgsc.bcm.edu	37	14	24033027	24033027	+	Missense_Mutation	SNP	G	G	A	rs12897422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24033027G>A	ENST00000308724.5	-	11	1885	c.1130C>T	c.(1129-1131)tCc>tTc	p.S377F	AP1G2_ENST00000397120.3_Missense_Mutation_p.S377F|RP11-66N24.3_ENST00000555968.1_RNA|AP1G2_ENST00000556277.1_5'Flank	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	377	Essential for ubiquitin-binding.		S -> F (in dbSNP:rs12897422).		intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		TCGCACATTGGAGCTATTTAC	0.592													G|||	218	0.0435304	0.0061	0.0778	5008	,	,		19276	0.001		0.1372	False		,,,				2504	0.0174				p.S377F		Atlas-SNP	.											.	AP1G2	75	.	0			c.C1130T						PASS	.	G	PHE/SER	131,4275	93.4+/-132.2	4,123,2076	65.0	60.0	62.0		1130	4.7	1.0	14	dbSNP_121	62	1185,7415	238.3+/-269.8	89,1007,3204	yes	missense	AP1G2	NM_003917.2	155	93,1130,5280	AA,AG,GG		13.7791,2.9732,10.1184	possibly-damaging	377/786	24033027	1316,11690	2203	4300	6503	SO:0001583	missense	8906	exon12			ACATTGGAGCTAT	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1130C>T	14.37:g.24033027G>A	ENSP00000312442:p.Ser377Phe	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	119	68	0.571429	NM_003917	D3DS51|O75504	Missense_Mutation	SNP	ENST00000308724.5	37	CCDS9602.1	132	0.06043956043956044	5	0.01016260162601626	32	0.08839779005524862	1	0.0017482517482517483	94	0.12401055408970976	G	18.60	3.659856	0.67586	0.029732	0.137791	ENSG00000213983	ENST00000308724;ENST00000397120;ENST00000545295;ENST00000535852	T;T	0.15017	2.46;2.46	4.71	4.71	0.59529	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.208622	0.42548	D	0.000700	T	0.00356	0.0011	M	0.85630	2.765	0.25795	P	0.9845778	D;D	0.63046	0.992;0.992	D;D	0.70487	0.944;0.969	T	0.08452	-1.0721	9	0.87932	D	0	-9.9215	10.2873	0.43575	0.0:0.0:0.8032:0.1968	rs12897422;rs17794465;rs57359597;rs12897422	377;232	O75843;Q86V28	AP1G2_HUMAN;.	F	377;377;146;232	ENSP00000312442:S377F;ENSP00000380309:S377F	ENSP00000312442:S377F	S	-	2	0	AP1G2	23102867	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.364000	0.52328	2.425000	0.82216	0.557000	0.71058	TCC	G|0.919;A|0.081	0.081	strong		0.592	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917	
PRKD3	23683	hgsc.bcm.edu	37	2	37518045	37518045	+	Silent	SNP	G	G	C	rs10177176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:37518045G>C	ENST00000379066.1	-	4	1287	c.525C>G	c.(523-525)ctC>ctG	p.L175L	PRKD3_ENST00000234179.2_Silent_p.L175L			O94806	KPCD3_HUMAN	protein kinase D3	175					intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				CCAATCCCCAGAGCATCTCAC	0.378													G|||	1535	0.30651	0.171	0.3343	5008	,	,		18877	0.4097		0.4274	False		,,,				2504	0.2393				p.L175L	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.C525G						PASS	.	G		834,3572	330.2+/-301.4	76,682,1445	159.0	153.0	155.0		525	0.1	1.0	2	dbSNP_119	155	3472,5128	509.6+/-377.3	719,2034,1547	no	coding-synonymous	PRKD3	NM_005813.3		795,2716,2992	CC,CG,GG		40.3721,18.9287,33.1078		175/891	37518045	4306,8700	2203	4300	6503	SO:0001819	synonymous_variant	23683	exon3			TCCCCAGAGCATC	AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"""Pleckstrin homology (PH) domain containing"""	9408	protein-coding gene	gene with protein product		607077	"""protein kinase C, nu"""	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.525C>G	2.37:g.37518045G>C		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1																																																																																			G|0.650;C|0.350	0.350	strong		0.378	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	
PIK3CG	5294	hgsc.bcm.edu	37	7	106522592	106522592	+	Missense_Mutation	SNP	A	A	G	rs28763991	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:106522592A>G	ENST00000359195.3	+	7	2879	c.2569A>G	c.(2569-2571)Act>Gct	p.T857A	PIK3CG_ENST00000440650.2_Missense_Mutation_p.T857A|PIK3CG_ENST00000496166.1_Missense_Mutation_p.T857A	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	857	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						TATTTGGGAGACTGAATCTTT	0.358													A|||	316	0.063099	0.0772	0.0836	5008	,	,		12998	0.0317		0.0378	False		,,,				2504	0.0879				p.T857A		Atlas-SNP	.											.	PIK3CG	279	.	0			c.A2569G						PASS	.	A	ALA/THR	309,4097	161.1+/-193.3	12,285,1906	128.0	114.0	119.0		2569	3.2	1.0	7	dbSNP_125	119	386,8214	122.5+/-181.5	19,348,3933	yes	missense	PIK3CG	NM_002649.2	58	31,633,5839	GG,GA,AA		4.4884,7.0132,5.3437	benign	857/1103	106522592	695,12311	2203	4300	6503	SO:0001583	missense	5294	exon7			TGGGAGACTGAAT		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2569A>G	7.37:g.106522592A>G	ENSP00000352121:p.Thr857Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	121	0.0554029304029304	37	0.07520325203252033	28	0.07734806629834254	24	0.04195804195804196	32	0.04221635883905013	A	7.177	0.588795	0.13812	0.070132	0.044884	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000473541;ENST00000359195	T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41	5.92	3.17	0.36434	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.362286	0.35525	N	0.003155	T	0.06600	0.0169	N	0.13235	0.315	0.34510	D	0.706987	B	0.02656	0.0	B	0.06405	0.002	T	0.25676	-1.0125	10	0.08179	T	0.78	-9.1635	6.297	0.21091	0.6604:0.0:0.3396:0.0	rs28763991	857	P48736	PK3CG_HUMAN	A	857;857;130;857	ENSP00000392258:T857A;ENSP00000419260:T857A;ENSP00000417623:T130A;ENSP00000352121:T857A	ENSP00000352121:T857A	T	+	1	0	PIK3CG	106309828	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	3.432000	0.52824	1.015000	0.39444	0.533000	0.62120	ACT	A|0.942;G|0.058	0.058	strong		0.358	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1		
UBXN6	80700	hgsc.bcm.edu	37	19	4454000	4454000	+	Silent	SNP	G	G	A	rs11909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:4454000G>A	ENST00000301281.6	-	2	298	c.174C>T	c.(172-174)gcC>gcT	p.A58A	UBXN6_ENST00000394765.3_Silent_p.A5A|CTB-50L17.9_ENST00000592034.1_RNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	58						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						GGGCTAGGGCGGCAGCGGCTG	0.682													G|||	1563	0.312101	0.2595	0.2205	5008	,	,		14553	0.2867		0.4115	False		,,,				2504	0.3722				p.A58A		Atlas-SNP	.											.	UBXN6	27	.	0			c.C174T						PASS	.	G	,	1279,3127	422.5+/-339.8	196,887,1120	67.0	83.0	78.0		15,174	-8.5	0.2	19	dbSNP_52	78	3475,5123	493.1+/-373.5	709,2057,1533	no	coding-synonymous,coding-synonymous	UBXN6	NM_001171091.1,NM_025241.2	,	905,2944,2653	AA,AG,GG		40.4164,29.0286,36.558	,	5/389,58/442	4454000	4754,8250	2203	4299	6502	SO:0001819	synonymous_variant	80700	exon2			TAGGGCGGCAGCG	AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"""UBX domain containing"""	14928	protein-coding gene	gene with protein product		611946	"""UBX domain-containing 1"", ""UBX domain containing 1"""	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.174C>T	19.37:g.4454000G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Silent	SNP	ENST00000301281.6	37	CCDS12129.1																																																																																			G|0.653;A|0.347	0.347	strong		0.682	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
PCNT	5116	hgsc.bcm.edu	37	21	47841933	47841933	+	Silent	SNP	T	T	C	rs61735815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47841933T>C	ENST00000359568.5	+	32	7181	c.7074T>C	c.(7072-7074)ccT>ccC	p.P2358P	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2358					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CAGGAGGCCCTGAGGCTCAAA	0.612													T|||	115	0.0229633	0.0151	0.0303	5008	,	,		15470	0.001		0.0686	False		,,,				2504	0.0041				p.P2358P		Atlas-SNP	.											.	PCNT	283	.	0			c.T7074C						PASS	.	T		137,4269	96.2+/-134.9	3,131,2069	74.0	79.0	77.0		7074	-8.4	0.0	21	dbSNP_129	77	532,8068	148.5+/-203.7	11,510,3779	no	coding-synonymous	PCNT	NM_006031.5		14,641,5848	CC,CT,TT		6.186,3.1094,5.1438		2358/3337	47841933	669,12337	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon32			AGGCCCTGAGGCT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7074T>C	21.37:g.47841933T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	88	34	0.386364	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			T|0.952;C|0.048	0.048	strong		0.612	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
WDR11	55717	hgsc.bcm.edu	37	10	122665489	122665489	+	Silent	SNP	C	C	T	rs12268298	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122665489C>T	ENST00000263461.6	+	27	3639	c.3393C>T	c.(3391-3393)ctC>ctT	p.L1131L	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					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						TCCTGGTTCTCCTCTCTCTGG	0.522													C|||	335	0.066893	0.2231	0.0187	5008	,	,		15929	0.0268		0.0	False		,,,				2504	0.0				p.L1131L		Atlas-SNP	.											.	WDR11	95	.	0			c.C3393T						PASS	.	C		866,3540	338.4+/-305.3	95,676,1432	119.0	107.0	111.0		3393	-3.8	0.9	10	dbSNP_120	111	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	WDR11	NM_018117.11		95,679,5729	TT,TC,CC		0.0349,19.655,6.6815		1131/1225	122665489	869,12137	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon27			GGTTCTCCTCTCT	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.3393C>T	10.37:g.122665489C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	107	64	0.598131	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			C|0.933;T|0.067	0.067	strong		0.522	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
DSG4	147409	hgsc.bcm.edu	37	18	28968426	28968426	+	Missense_Mutation	SNP	C	C	T	rs374554073		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:28968426C>T	ENST00000308128.4	+	4	448	c.313C>T	c.(313-315)Cgc>Tgc	p.R105C	DSG4_ENST00000359747.4_Missense_Mutation_p.R105C|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	105	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CATTAATCCTCGCACTGGGGA	0.393																																					p.R105C		Atlas-SNP	.											DSG4_ENST00000359747,NS,carcinoma,-1,2	DSG4	343	2	0			c.C313T						scavenged	.	C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	116.0	108.0	111.0		313,313	4.9	1.0	18		111	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	DSG4	NM_001134453.1,NM_177986.3	180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	105/1060,105/1041	28968426	1,13005	2203	4300	6503	SO:0001583	missense	147409	exon4			AATCCTCGCACTG	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.313C>T	18.37:g.28968426C>T	ENSP00000311859:p.Arg105Cys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	87	3	0.0344828	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.393045	0.83011	0.0	1.16E-4	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.53206	0.63;0.63	5.88	4.94	0.65067	Cadherin (5);Cadherin-like (1);	0.000000	0.32473	N	0.006056	T	0.59142	0.2172	L	0.55990	1.75	0.44937	D	0.997958	D;D	0.76494	0.999;0.995	D;P	0.64321	0.924;0.849	T	0.59177	-0.7503	10	0.59425	D	0.04	.	11.1538	0.48476	0.3051:0.6949:0.0:0.0	.	105;105	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	C	105	ENSP00000311859:R105C;ENSP00000352785:R105C	ENSP00000311859:R105C	R	+	1	0	DSG4	27222424	0.057000	0.20700	1.000000	0.80357	0.988000	0.76386	2.078000	0.41567	2.785000	0.95823	0.650000	0.86243	CGC	.	.	weak		0.393	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
RHOT2	89941	hgsc.bcm.edu	37	16	719592	719592	+	Missense_Mutation	SNP	G	G	A	rs11557858	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:719592G>A	ENST00000315082.4	+	5	376	c.262G>A	c.(262-264)Gcc>Acc	p.A88T	RHOT2_ENST00000569943.2_Intron	NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	88	Miro 1.				cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				CTCTGAGGAGGCCACCATTGA	0.622													G|||	1387	0.276957	0.5348	0.1801	5008	,	,		18724	0.2946		0.1153	False		,,,				2504	0.1452				p.A88T		Atlas-SNP	.											.	RHOT2	35	.	0			c.G262A						PASS	.	G	THR/ALA	2063,2333	566.1+/-381.8	477,1109,612	156.0	102.0	121.0		262	-1.1	0.8	16	dbSNP_120	121	1092,7502	227.2+/-262.7	63,966,3268	yes	missense	RHOT2	NM_138769.1	58	540,2075,3880	AA,AG,GG		12.7065,46.929,24.2879	benign	88/619	719592	3155,9835	2198	4297	6495	SO:0001583	missense	89941	exon5			GAGGAGGCCACCA	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"""EF-hand domain containing"""	21169	protein-coding gene	gene with protein product	"""mitochondrial Rho (MIRO) GTPase 2"""	613889	"""chromosome 16 open reading frame 39"", ""ras homolog gene family, member T2"""	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.262G>A	16.37:g.719592G>A	ENSP00000321971:p.Ala88Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Missense_Mutation	SNP	ENST00000315082.4	37	CCDS10417.1	552	0.25274725274725274	259	0.5264227642276422	48	0.13259668508287292	169	0.29545454545454547	76	0.10026385224274406	G	8.543	0.873637	0.17322	0.46929	0.127065	ENSG00000140983	ENST00000315082	T	0.76968	-1.06	5.07	-1.08	0.09936	MIRO (1);	0.589164	0.18158	N	0.149874	T	0.00012	0.0000	N	0.05608	-0.01	0.51233	P	8.399999999997299E-5	B	0.06786	0.001	B	0.12837	0.008	T	0.43507	-0.9387	9	0.13853	T	0.58	-5.7558	6.5124	0.22228	0.3047:0.0:0.5681:0.1272	rs11557858;rs28637938	88	Q8IXI1	MIRO2_HUMAN	T	88	ENSP00000321971:A88T	ENSP00000321971:A88T	A	+	1	0	RHOT2	659593	0.026000	0.19158	0.822000	0.32727	0.564000	0.35744	0.433000	0.21477	0.169000	0.19679	0.555000	0.69702	GCC	G|0.760;A|0.240	0.240	strong		0.622	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769	
ZNF658	26149	hgsc.bcm.edu	37	9	40772563	40772563	+	Silent	SNP	G	G	A	rs62561229	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:40772563G>A	ENST00000602553.1	-	5	3006	c.2712C>T	c.(2710-2712)cgC>cgT	p.R904R	ZNF658_ENST00000441795.1_Intron|ZNF658_ENST00000377626.3_Silent_p.R904R			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	904					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TCTCCCCTGAGCGAGTTCTAA	0.453													G|||	913	0.182308	0.2776	0.1167	5008	,	,		18539	0.1964		0.1789	False		,,,				2504	0.089				p.R904R		Atlas-SNP	.											ZNF658,NS,carcinoma,-1,1	ZNF658	100	1	0			c.C2712T						scavenged	.	G		1147,3255	406.0+/-333.7	121,905,1175	78.0	77.0	78.0		2712	-1.4	0.0	9	dbSNP_131	78	1305,7257	258.4+/-282.1	94,1117,3070	no	coding-synonymous	ZNF658	NM_033160.5		215,2022,4245	AA,AG,GG		15.2418,26.0563,18.9139		904/1060	40772563	2452,10512	2201	4281	6482	SO:0001819	synonymous_variant	26149	exon5			CCCTGAGCGAGTT	AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"""Zinc fingers, C2H2-type"", ""-"""	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.2712C>T	9.37:g.40772563G>A		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	206	98	0.475728	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Silent	SNP	ENST00000602553.1	37	CCDS35023.1																																																																																			G|0.814;A|0.186	0.186	strong		0.453	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160	
GRIN2A	2903	hgsc.bcm.edu	37	16	9916204	9916204	+	Silent	SNP	C	C	G	rs9806806	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:9916204C>G	ENST00000396573.2	-	11	2394	c.2085G>C	c.(2083-2085)cgG>cgC	p.R695R	GRIN2A_ENST00000535259.1_Silent_p.R538R|GRIN2A_ENST00000330684.3_Silent_p.R695R|GRIN2A_ENST00000562109.1_Silent_p.R695R|GRIN2A_ENST00000396575.2_Silent_p.R695R|GRIN2A_ENST00000404927.2_Silent_p.R695R	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	695					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GATAGTTATTCCGAATGTTTC	0.458													C|||	1408	0.28115	0.5272	0.2176	5008	,	,		20970	0.0794		0.2873	False		,,,				2504	0.1953				p.R695R		Atlas-SNP	.											.	GRIN2A	366	.	0			c.G2085C						PASS	.	C	,,	2155,2239	583.6+/-385.9	532,1091,574	168.0	143.0	152.0		2085,2085,2085	2.5	1.0	16	dbSNP_119	152	2407,6193	399.1+/-346.3	315,1777,2208	no	coding-synonymous,coding-synonymous,coding-synonymous	GRIN2A	NM_000833.3,NM_001134407.1,NM_001134408.1	,,	847,2868,2782	GG,GC,CC		27.9884,49.0442,35.1085	,,	695/1465,695/1465,695/1282	9916204	4562,8432	2197	4300	6497	SO:0001819	synonymous_variant	2903	exon11			GTTATTCCGAATG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.2085G>C	16.37:g.9916204C>G		Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	359	161	0.448468	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																			C|0.671;G|0.329	0.329	strong		0.458	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
CAMK2B	816	hgsc.bcm.edu	37	7	44259871	44259871	+	Silent	SNP	C	C	T	rs1127065	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:44259871C>T	ENST00000395749.2	-	23	1867	c.1791G>A	c.(1789-1791)ccG>ccA	p.P597P	CAMK2B_ENST00000258682.6_Silent_p.P448P|CAMK2B_ENST00000395747.2_Silent_p.P449P|CAMK2B_ENST00000440254.2_Silent_p.P473P|CAMK2B_ENST00000457475.1_Silent_p.P449P|CAMK2B_ENST00000358707.3_Silent_p.P434P|CAMK2B_ENST00000346990.4_Silent_p.P380P|CAMK2B_ENST00000347193.4_Silent_p.P423P|CAMK2B_ENST00000353625.4_Silent_p.P410P|CAMK2B_ENST00000502837.2_3'UTR|CAMK2B_ENST00000489429.1_5'UTR|CAMK2B_ENST00000350811.3_Silent_p.P473P	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	597					activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						TCGTGTGGATCGGCTTGCTGT	0.627													C|||	1711	0.341653	0.1694	0.3213	5008	,	,		16956	0.3998		0.4076	False		,,,				2504	0.4611				p.P597P		Atlas-SNP	.											CAMK2B,NS,carcinoma,0,1	CAMK2B	56	1	0			c.G1791A						PASS	.	C	,,,,,,,	1004,3402	352.8+/-311.9	125,754,1324	107.0	59.0	75.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1791,1419,1347,1344,1302,1269,1230,1140	-8.5	0.9	7	dbSNP_86	75	3673,4927	498.7+/-374.8	817,2039,1444	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2B	NM_001220.4,NM_172078.2,NM_172079.2,NM_172080.2,NM_172081.2,NM_172082.2,NM_172083.2,NM_172084.2	,,,,,,,	942,2793,2768	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	42.7093,22.7871,35.9603	,,,,,,,	597/667,473/543,449/519,448/518,434/504,423/493,410/480,380/450	44259871	4677,8329	2203	4300	6503	SO:0001819	synonymous_variant	816	exon23			GTGGATCGGCTTG	U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"""CaM-kinase II beta chain"", ""calcium/calmodulin-dependent protein kinase type II beta chain"", ""CaM kinase II beta subunit"", ""proline rich calmodulin-dependent protein kinase"""	607707	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"""	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.1791G>A	7.37:g.44259871C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	216	100	0.462963	NM_001220	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Silent	SNP	ENST00000395749.2	37	CCDS5483.1																																																																																			T|0.361;G|0.004;C|0.635	0.361	strong		0.627	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084	
TRERF1	55809	hgsc.bcm.edu	37	6	42233518	42233518	+	Silent	SNP	C	C	T	rs17704222	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:42233518C>T	ENST00000372922.4	-	6	2017	c.1455G>A	c.(1453-1455)ggG>ggA	p.G485G	TRERF1_ENST00000354325.2_Silent_p.G485G|TRERF1_ENST00000340840.2_Silent_p.G485G|TRERF1_ENST00000372917.4_Silent_p.G485G|TRERF1_ENST00000541110.1_Silent_p.G485G	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	485	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GCTGGGCTCTCCCATCAGGTA	0.493													C|||	178	0.0355431	0.0045	0.0375	5008	,	,		19050	0.004		0.0726	False		,,,				2504	0.0706				p.G485G		Atlas-SNP	.											.	TRERF1	124	.	0			c.G1455A						PASS	.	C		79,4327	67.6+/-105.2	1,77,2125	57.0	55.0	56.0		1455	3.8	1.0	6	dbSNP_123	56	764,7836	180.8+/-229.6	32,700,3568	no	coding-synonymous	TRERF1	NM_033502.2		33,777,5693	TT,TC,CC		8.8837,1.793,6.4816		485/1201	42233518	843,12163	2203	4300	6503	SO:0001819	synonymous_variant	55809	exon6			GGCTCTCCCATCA	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1455G>A	6.37:g.42233518C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	37	CCDS4867.1																																																																																			C|0.950;T|0.050	0.050	strong		0.493	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
SLC41A1	254428	hgsc.bcm.edu	37	1	205779231	205779231	+	Silent	SNP	G	G	A	rs11240569	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:205779231G>A	ENST00000367137.3	-	2	1353	c.339C>T	c.(337-339)acC>acT	p.T113T		NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	113					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)	p.T113T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	17	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			CAGCAGCCACGGTCCCAAAGC	0.607													G|||	1385	0.276558	0.0174	0.1873	5008	,	,		20273	0.5198		0.2883	False		,,,				2504	0.4274				p.T113T		Atlas-SNP	.											SLC41A1,NS,carcinoma,0,1	SLC41A1	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C339T						PASS	.	G		280,4126	156.3+/-189.4	12,256,1935	102.0	95.0	98.0		339	-11.2	0.4	1	dbSNP_120	98	2466,6134	406.9+/-349.0	350,1766,2184	no	coding-synonymous	SLC41A1	NM_173854.4		362,2022,4119	AA,AG,GG		28.6744,6.355,21.1133		113/514	205779231	2746,10260	2203	4300	6503	SO:0001819	synonymous_variant	254428	exon2			AGCCACGGTCCCA	AJ514402	CCDS30988.1	1q32.1	2013-07-17	2013-07-17		ENSG00000133065	ENSG00000133065		"""Solute carriers"""	19429	protein-coding gene	gene with protein product		610801				12810078, 18367447	Standard	NM_173854		Approved	MgtE	uc001hdh.1	Q8IVJ1	OTTHUMG00000036000	ENST00000367137.3:c.339C>T	1.37:g.205779231G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_173854	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Silent	SNP	ENST00000367137.3	37	CCDS30988.1																																																																																			G|0.761;A|0.239	0.239	strong		0.607	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1		
DST	667	hgsc.bcm.edu	37	6	56484758	56484758	+	Silent	SNP	C	C	T	rs2230862	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:56484758C>T	ENST00000370765.6	-	23	4181	c.4074G>A	c.(4072-4074)aaG>aaA	p.K1358K	DST_ENST00000370769.4_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000370754.5_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	0					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CTGCTTTCTGCTTGTCATGTT	0.443													T|||	1685	0.336462	0.4523	0.3746	5008	,	,		19178	0.2034		0.3946	False		,,,				2504	0.2301				p.K1358K		Atlas-SNP	.											.	DST	1427	.	0			c.G4074A						PASS	.	T	,	1918,2488	626.8+/-394.8	399,1120,684	194.0	180.0	185.0		4074,	-2.8	0.0	6	dbSNP_98	185	3584,5016	627.4+/-398.0	762,2060,1478	no	coding-synonymous,intron	DST	NM_001723.5,NM_015548.4	,	1161,3180,2162	TT,TC,CC		41.6744,43.5315,42.3036	,	1358/2650,	56484758	5502,7504	2203	4300	6503	SO:0001819	synonymous_variant	667	exon23			TTTCTGCTTGTCA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.4074G>A	6.37:g.56484758C>T		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	267	123	0.460674	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000370765.6	37	CCDS4959.1																																																																																			C|0.609;T|0.391	0.391	strong		0.443	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723	
FBN3	84467	hgsc.bcm.edu	37	19	8159339	8159339	+	Missense_Mutation	SNP	G	G	C	rs34167077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8159339G>C	ENST00000600128.1	-	47	6310	c.5896C>G	c.(5896-5898)Cac>Gac	p.H1966D	FBN3_ENST00000270509.2_Missense_Mutation_p.H1966D|FBN3_ENST00000601739.1_Missense_Mutation_p.H1966D			Q75N90	FBN3_HUMAN	fibrillin 3	1966	EGF-like 31; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		H -> D (in dbSNP:rs34167077).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CCAATGCAGTGGTCACTCTGC	0.592													G|||	271	0.0541134	0.0068	0.0663	5008	,	,		19075	0.0		0.1163	False		,,,				2504	0.1012				p.H1966D		Atlas-SNP	.											.	FBN3	300	.	0			c.C5896G						PASS	.	G	ASP/HIS	84,4322	73.1+/-111.1	0,84,2119	69.0	53.0	58.0		5896	2.4	0.1	19	dbSNP_126	58	923,7677	203.1+/-246.2	59,805,3436	yes	missense	FBN3	NM_032447.3	81	59,889,5555	CC,CG,GG		10.7326,1.9065,7.7426	benign	1966/2810	8159339	1007,11999	2203	4300	6503	SO:0001583	missense	84467	exon46			TGCAGTGGTCACT		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5896C>G	19.37:g.8159339G>C	ENSP00000470498:p.His1966Asp	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	73	26	0.356164	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	113	0.051739926739926737	2	0.0040650406504065045	26	0.0718232044198895	0	0.0	85	0.11213720316622691	G	9.353	1.066075	0.20067	0.019065	0.107326	ENSG00000142449	ENST00000270509	D	0.87256	-2.23	4.69	2.4	0.29515	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.613082	0.15924	U	0.237993	T	0.04861	0.0131	N	0.13003	0.285	0.47037	P	7.009999999999517E-4	B	0.31193	0.312	B	0.30251	0.113	T	0.49133	-0.8971	9	0.20046	T	0.44	.	10.7785	0.46363	0.0:0.0:0.3634:0.6366	rs34167077	1966	Q75N90	FBN3_HUMAN	D	1966	ENSP00000270509:H1966D	ENSP00000270509:H1966D	H	-	1	0	FBN3	8065339	1.000000	0.71417	0.139000	0.22197	0.818000	0.46254	2.275000	0.43399	0.921000	0.36994	0.462000	0.41574	CAC	G|0.937;C|0.063	0.063	strong		0.592	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
KANSL1	284058	hgsc.bcm.edu	37	17	44248814	44248814	+	Silent	SNP	G	G	A	rs535019273	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44248814G>A	ENST00000262419.6	-	2	1166	c.696C>T	c.(694-696)tcC>tcT	p.S232S	KANSL1_ENST00000574590.1_Silent_p.S232S|KANSL1_ENST00000575318.1_Silent_p.S232S|KANSL1_ENST00000572904.1_Silent_p.S232S|KANSL1_ENST00000432791.1_Silent_p.S232S|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000393476.3_5'UTR	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	232					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											AATTGACAGAGGATTTGTTTG	0.458													A|||	433	0.0864617	0.0151	0.1571	5008	,	,		24585	0.001		0.2406	False		,,,				2504	0.0624				p.S232S		Atlas-SNP	.											.	.	.	.	0			c.C696T						PASS	.	A	,,	203,4203	807.8+/-415.9	5,193,2005	118.0	146.0	136.0		696,696,696	5.0	1.0	17	dbSNP_92	136	1935,6665	725.7+/-406.6	220,1495,2585	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	225,1688,4590	AA,AG,GG		22.5,4.6074,16.4386	,,	232/1105,232/1106,232/1106	44248814	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon2			GACAGAGGATTTG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.696C>T	17.37:g.44248814G>A		Somatic	426	0	0		WXS	Illumina HiSeq	Phase_I	514	216	0.420233	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			G|0.848;A|0.152	0.152	strong		0.458	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
FLNA	2316	hgsc.bcm.edu	37	X	153594932	153594932	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153594932T>G	ENST00000369850.3	-	7	1299	c.1063A>C	c.(1063-1065)Aag>Cag	p.K355Q	FLNA_ENST00000344736.4_Missense_Mutation_p.K355Q|FLNA_ENST00000422373.1_Missense_Mutation_p.K355Q|FLNA_ENST00000360319.4_Missense_Mutation_p.K355Q	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	355					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGGCTCACCTTATGAGTCCCC	0.632																																					p.K355Q		Atlas-SNP	.											.	FLNA	373	.	0			c.A1063C						PASS	.						89.0	91.0	91.0					X																	153594932		2009	4148	6157	SO:0001583	missense	2316	exon7			TCACCTTATGAGT	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.1063A>C	X.37:g.153594932T>G	ENSP00000358866:p.Lys355Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	231	126	0.545455	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.346167	0.41599	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95	4.87	4.87	0.63330	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.85605	0.5735	L	0.50993	1.605	0.80722	D	1	B;B	0.29612	0.251;0.18	B;B	0.42163	0.23;0.378	D	0.84661	0.0706	10	0.51188	T	0.08	.	13.3412	0.60545	0.0:0.0:0.0:1.0	.	355;355	P21333-2;P21333	.;FLNA_HUMAN	Q	355;328;355;355;355	ENSP00000353467:K355Q;ENSP00000416926:K355Q;ENSP00000358866:K355Q;ENSP00000358863:K355Q	ENSP00000358863:K355Q	K	-	1	0	FLNA	153248126	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.134000	0.71689	1.607000	0.50170	0.427000	0.28365	AAG	.	.	none		0.632	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
DPP6	1804	hgsc.bcm.edu	37	7	154684153	154684153	+	Missense_Mutation	SNP	T	T	C	rs3734960	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:154684153T>C	ENST00000377770.3	+	26	2702	c.2561T>C	c.(2560-2562)cTg>cCg	p.L854P	DPP6_ENST00000427557.1_Missense_Mutation_p.L747P|DPP6_ENST00000332007.3_Missense_Mutation_p.L792P|DPP6_ENST00000404039.1_Missense_Mutation_p.L790P			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	854			L -> P (in dbSNP:rs3734960). {ECO:0000269|PubMed:8103397}.		cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GACAAACTGCTGACAGTCACA	0.507													C|||	1783	0.35603	0.5234	0.4611	5008	,	,		17698	0.2738		0.2644	False		,,,				2504	0.2342				p.L854P	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.T2561C						PASS	.	C	PRO/LEU,PRO/LEU,PRO/LEU	2119,2151		542,1035,558	134.0	145.0	142.0		2015,1934,1934	2.9	0.0	7	dbSNP_107	142	2325,6155		357,1611,2272	yes	missense,missense,missense	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	98,98,98	899,2646,2830	CC,CT,TT		27.4175,49.6253,34.8549	benign,benign,benign	672/684,645/657,645/657	154684153	4444,8306	2135	4240	6375	SO:0001583	missense	1804	exon26			AACTGCTGACAGT	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"""dipeptidylpeptidase VI"", ""dipeptidylpeptidase 6"""			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.2561T>C	7.37:g.154684153T>C	ENSP00000367001:p.Leu854Pro	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	142	83	0.584507	NM_130797		Missense_Mutation	SNP	ENST00000377770.3	37		729	0.33379120879120877	241	0.4898373983739837	149	0.4116022099447514	147	0.256993006993007	192	0.2532981530343008	C	3.365	-0.129586	0.06753	0.496253	0.274175	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.15487	2.44;2.42;2.46;2.45	4.66	2.86	0.33363	.	0.518379	0.21248	N	0.077690	T	0.00012	0.0000	N	0.00823	-1.155	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.41034	-0.9531	9	0.52906	T	0.07	-8.5465	9.9808	0.41813	0.0:0.7772:0.0:0.2228	rs3734960;rs10386252;rs52799412;rs58782221;rs3734960	747;792;854;790	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	P	790;854;792;747	ENSP00000385578:L790P;ENSP00000367001:L854P;ENSP00000328226:L792P;ENSP00000397303:L747P	ENSP00000328226:L792P	L	+	2	0	DPP6	154315086	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.182000	0.16900	0.095000	0.17434	-0.735000	0.03563	CTG	T|0.670;C|0.330	0.330	strong		0.507	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189601	11189601	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11189601G>T	ENST00000382435.4	+	1	1205	c.986G>T	c.(985-987)aGc>aTc	p.S329I		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	329						integral component of membrane (GO:0016021)											CGGAACCTCAGCTGTGAGAGG	0.517																																					p.S329I		Atlas-SNP	.											AMAC1L2,NS,carcinoma,-1,1	.	.	1	0			c.G986T						scavenged	.						67.0	68.0	68.0					8																	11189601		2203	4300	6503	SO:0001583	missense	83650	exon1			ACCTCAGCTGTGA	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.986G>T	8.37:g.11189601G>T	ENSP00000371872:p.Ser329Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	113	10	0.0884956	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	g	0.299	-0.974907	0.02215	.	.	ENSG00000177710	ENST00000382435	T	0.28666	1.6	.	.	.	.	0.000000	0.52532	D	0.000061	T	0.22244	0.0536	L	0.54323	1.7	0.26188	N	0.979621	B	0.02656	0.0	B	0.06405	0.002	T	0.18241	-1.0343	8	0.22706	T	0.39	-1.3917	.	.	.	.	329	Q96KT7	S35G5_HUMAN	I	329	ENSP00000371872:S329I	ENSP00000371872:S329I	S	+	2	0	SLC35G5	11227011	0.173000	0.23056	0.298000	0.25002	0.299000	0.27559	0.335000	0.19806	0.064000	0.16427	0.064000	0.15345	AGC	.	.	none		0.517	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
TTN	7273	hgsc.bcm.edu	37	2	179543217	179543217	+	Silent	SNP	C	C	T	rs35112591	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179543217C>T	ENST00000591111.1	-	142	33107	c.32883G>A	c.(32881-32883)gaG>gaA	p.E10961E	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.E10034E|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Silent_p.E11278E|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33597	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E10034E(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTGGGTACCTCTGGCACTT	0.373													C|||	1194	0.238419	0.1362	0.183	5008	,	,		13346	0.4454		0.1581	False		,,,				2504	0.2853				p.E11278E		Atlas-SNP	.											TTN_ENST00000356127,NS,carcinoma,0,1	TTN	18412	1	1	Substitution - coding silent(1)	prostate(1)	c.G33834A						scavenged	.	C	,,,	498,3178		42,414,1382	36.0	33.0	34.0		,30102,,	1.4	1.0	2	dbSNP_126	34	1313,6871		103,1107,2882	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	145,1521,4264	TT,TC,CC		16.0435,13.5473,15.2698	,,,	,10034/33424,,	179543217	1811,10049	1838	4092	5930	SO:0001819	synonymous_variant	7273	exon144			GGGTACCTCTGGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.32883G>A	2.37:g.179543217C>T		Somatic	164	3	0.0182927		WXS	Illumina HiSeq	Phase_I	142	57	0.401408	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				C|0.788;T|0.212	0.212	strong		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MAGEB2	4113	hgsc.bcm.edu	37	X	30236913	30236913	+	Silent	SNP	G	G	A	rs5973792	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:30236913G>A	ENST00000378988.4	+	2	317	c.216G>A	c.(214-216)gcG>gcA	p.A72A		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	72										breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						CCGCTGCTGCGGCTGCGGGTG	0.557													G|||	646	0.171126	0.1679	0.1499	3775	,	,		12005	0.0218		0.2087	False		,,,				2504	0.09				p.A72A		Atlas-SNP	.											.	MAGEB2	133	.	0			c.G216A						PASS	.	G		874,2947		88,563,135,980,424	12.0	11.0	12.0		216	-1.7	0.0	X	dbSNP_114	12	1906,4790		189,1006,522,1230,1324	no	coding-synonymous	MAGEB2	NM_002364.4		277,1569,657,2210,1748	AA,AG,A,GG,G		28.4648,22.8736,26.4334		72/320	30236913	2780,7737	2190	4271	6461	SO:0001819	synonymous_variant	4113	exon2			TGCTGCGGCTGCG	AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"""DSS/AHC critical interval MAGE superfamily 6"", ""melanoma-associated antigen B2"", ""cancer/testis antigen family 3, member 2"""	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.216G>A	X.37:g.30236913G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	68	64	0.941176	NM_002364	O75860	Silent	SNP	ENST00000378988.4	37	CCDS14219.1																																																																																			G|0.782;A|0.218	0.218	strong		0.557	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102514227	102514227	+	Silent	SNP	T	T	C	rs13749	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102514227T>C	ENST00000360184.4	+	73	13244	c.13080T>C	c.(13078-13080)acT>acC	p.T4360T	RP11-1017G21.4_ENST00000557242.1_RNA|RP11-1017G21.4_ENST00000553701.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4360					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.T4360T(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ACGCAGAGACTGAGAAGAAGA	0.597													C|||	1739	0.347244	0.6505	0.2392	5008	,	,		15280	0.2897		0.1421	False		,,,				2504	0.2843				p.T4360T		Atlas-SNP	.											DYNC1H1,NS,carcinoma,0,1	DYNC1H1	395	1	1	Substitution - coding silent(1)	stomach(1)	c.T13080C						PASS	.	C		2522,1884	542.8+/-376.1	727,1068,408	160.0	107.0	125.0		13080	-8.9	0.5	14	dbSNP_52	125	1427,7173	752.5+/-407.4	137,1153,3010	no	coding-synonymous	DYNC1H1	NM_001376.4		864,2221,3418	CC,CT,TT		16.593,42.7599,30.3629		4360/4647	102514227	3949,9057	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon73			AGAGACTGAGAAG	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.13080T>C	14.37:g.102514227T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			T|0.681;C|0.319	0.319	strong		0.597	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
CAPN9	10753	hgsc.bcm.edu	37	1	230914729	230914729	+	Missense_Mutation	SNP	A	A	C	rs1933631	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:230914729A>C	ENST00000271971.2	+	9	1077	c.964A>C	c.(964-966)Aag>Cag	p.K322Q	RP11-99J16__A.2_ENST00000412344.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000452640.1_RNA|CAPN9_ENST00000354537.1_Missense_Mutation_p.K296Q|CAPN9_ENST00000366666.2_Missense_Mutation_p.K259Q	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	322	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		K -> Q (in dbSNP:rs1933631). {ECO:0000269|Ref.3}.		digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				GATGGCATTTAAGGACTTCAA	0.493													A|||	1659	0.33127	0.3888	0.2075	5008	,	,		17427	0.1875		0.3201	False		,,,				2504	0.501				p.K322Q		Atlas-SNP	.											.	CAPN9	116	.	0			c.A964C						PASS	.	A	GLN/LYS,GLN/LYS	1669,2737	506.6+/-366.4	316,1037,850	65.0	54.0	58.0		964,886	-3.5	0.0	1	dbSNP_92	58	2765,5835	437.6+/-358.7	422,1921,1957	yes	missense,missense	CAPN9	NM_006615.2,NM_016452.1	53,53	738,2958,2807	CC,CA,AA		32.1512,37.8802,34.092	benign,benign	322/691,296/665	230914729	4434,8572	2203	4300	6503	SO:0001583	missense	10753	exon9			GCATTTAAGGACT	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.964A>C	1.37:g.230914729A>C	ENSP00000271971:p.Lys322Gln	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	37	CCDS1586.1	631	0.2889194139194139	196	0.3983739837398374	76	0.20994475138121546	103	0.18006993006993008	256	0.33773087071240104	A	4.329	0.060364	0.08339	0.378802	0.321512	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	T;T;T	0.15603	2.41;2.41;2.41	5.24	-3.49	0.04724	Peptidase C2, calpain, catalytic domain (3);	0.854162	0.10872	N	0.624846	T	0.00012	0.0000	N	0.01686	-0.76	0.80722	P	0.0	B;B;B	0.25105	0.017;0.118;0.017	B;B;B	0.20384	0.005;0.029;0.005	T	0.37267	-0.9713	9	0.02654	T	1	.	2.0781	0.03628	0.2162:0.282:0.3632:0.1385	rs1933631;rs17788932;rs52813786;rs60788299;rs1933631	259;296;322	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	Q	322;296;259	ENSP00000271971:K322Q;ENSP00000346538:K296Q;ENSP00000355626:K259Q	ENSP00000271971:K322Q	K	+	1	0	CAPN9	228981352	0.990000	0.36364	0.001000	0.08648	0.294000	0.27393	1.483000	0.35497	-0.677000	0.05231	-0.490000	0.04691	AAG	A|0.692;C|0.308	0.308	strong		0.493	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
ABCC2	1244	hgsc.bcm.edu	37	10	101563815	101563815	+	Missense_Mutation	SNP	G	G	A	rs2273697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:101563815G>A	ENST00000370449.4	+	10	1362	c.1249G>A	c.(1249-1251)Gtt>Att	p.V417I		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	417	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.		V -> I (in dbSNP:rs2273697). {ECO:0000269|PubMed:11266082, ECO:0000269|PubMed:11477083}.		cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	GGAGTACACCGTTGGAGAAAC	0.463													G|||	934	0.186502	0.1891	0.1585	5008	,	,		23541	0.0962		0.2038	False		,,,				2504	0.2781				p.V417I		Atlas-SNP	.											ABCC2,NS,adenoma,0,1	ABCC2	160	1	0			c.G1249A	GRCh37	CM067967	ABCC2	M	rs2273697	PASS	.		ILE/VAL	824,3582	325.9+/-299.3	81,662,1460	184.0	151.0	162.0		1249	-10.3	0.1	10	dbSNP_100	162	1675,6925	307.6+/-308.5	174,1327,2799	yes	missense	ABCC2	NM_000392.3	29	255,1989,4259	AA,AG,GG		19.4767,18.7018,19.2142	benign	417/1546	101563815	2499,10507	2203	4300	6503	SO:0001583	missense	1244	exon10			TACACCGTTGGAG	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.1249G>A	10.37:g.101563815G>A	ENSP00000359478:p.Val417Ile	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	137	7	0.0510949	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	379	0.17353479853479853	98	0.1991869918699187	57	0.1574585635359116	73	0.12762237762237763	151	0.19920844327176782	G	12.32	1.903578	0.33628	0.187018	0.194767	ENSG00000023839	ENST00000370449	D	0.90955	-2.76	5.48	-10.3	0.00346	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.601291	0.17938	N	0.156921	T	0.00300	0.0009	N	0.17474	0.49	0.25643	P	0.9861835	B	0.13594	0.008	B	0.20955	0.032	T	0.04153	-1.0973	9	0.41790	T	0.15	-1.4461	20.1781	0.98191	0.3045:0.0:0.6955:0.0	rs2273697;rs17216184;rs60620335;rs2273697	417	Q92887	MRP2_HUMAN	I	417	ENSP00000359478:V417I	ENSP00000359478:V417I	V	+	1	0	ABCC2	101553805	0.000000	0.05858	0.132000	0.22025	0.617000	0.37484	-0.363000	0.07593	-1.996000	0.00970	-1.022000	0.02435	GTT	A|0.183;C|0.005	0.183	strong		0.463	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
OR1B1	347169	hgsc.bcm.edu	37	9	125391409	125391409	+	Silent	SNP	A	A	G	rs1536928	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:125391409A>G	ENST00000304833.3	-	1	443	c.406T>C	c.(406-408)Ttg>Ctg	p.L136L	RP11-64P14.7_ENST00000431442.1_RNA|RP11-64P14.7_ENST00000419604.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						TTCATTACCAAAGCATAGTGC	0.502													A|||	2054	0.410144	0.3896	0.2954	5008	,	,		21672	0.3403		0.504	False		,,,				2504	0.4949				p.L136L		Atlas-SNP	.											.	OR1B1	48	.	0			c.T406C						PASS	.	A		1912,2494	546.6+/-377.1	405,1102,696	101.0	81.0	88.0		406	-0.0	0.6	9	dbSNP_88	88	4275,4325	574.8+/-390.1	1042,2191,1067	yes	coding-synonymous	OR1B1	NM_001004450.1		1447,3293,1763	GG,GA,AA		49.7093,43.3954,47.5704		136/319	125391409	6187,6819	2203	4300	6503	SO:0001819	synonymous_variant	347169	exon1			TTACCAAAGCATA	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"""GPCR / Class A : Olfactory receptors"""	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.406T>C	9.37:g.125391409A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_001004450	Q6IFN3	Silent	SNP	ENST00000304833.3	37	CCDS35126.1																																																																																			A|0.554;G|0.446	0.446	strong		0.502	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450	
FERMT3	83706	hgsc.bcm.edu	37	11	63974995	63974995	+	Splice_Site	SNP	C	C	G	rs142815441	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:63974995C>G	ENST00000279227.5	+	2	254	c.159C>G	c.(157-159)atC>atG	p.I53M	FERMT3_ENST00000345728.5_Splice_Site_p.I53M	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	53					integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						TGGAGCAGATCAGTGAGTGTC	0.657													C|||	7	0.00139776	0.0	0.0029	5008	,	,		12110	0.0		0.005	False		,,,				2504	0.0				p.I53M		Atlas-SNP	.											.	FERMT3	51	.	0			c.C159G						PASS	.	C	MET/ILE,MET/ILE	4,4398	8.1+/-20.4	0,4,2197	36.0	40.0	39.0		159,159	4.5	1.0	11	dbSNP_134	39	46,8548	29.6+/-80.5	0,46,4251	yes	missense-near-splice,missense-near-splice	FERMT3	NM_031471.5,NM_178443.2	10,10	0,50,6448	GG,GC,CC		0.5353,0.0909,0.3847	benign,benign	53/664,53/668	63974995	50,12946	2201	4297	6498	SO:0001630	splice_region_variant	83706	exon2			GCAGATCAGTGAG	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	23151	protein-coding gene	gene with protein product	"""kindlin-3"""	607901	"""fermitin family homolog 3 (Drosophila)"""				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.160+1C>G	11.37:g.63974995C>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_031471	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	37	CCDS8060.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	12.17	1.857249	0.32791	9.09E-4	0.005353	ENSG00000149781	ENST00000544997;ENST00000345728;ENST00000279227	T;T;T	0.59083	1.55;0.29;0.29	4.48	4.48	0.54585	.	0.210781	0.37715	N	0.001977	T	0.39627	0.1085	L	0.54323	1.7	0.37691	D	0.923865	P;B	0.45011	0.848;0.031	B;B	0.36885	0.235;0.024	T	0.56183	-0.8021	10	0.49607	T	0.09	-30.3298	10.1956	0.43051	0.3098:0.6902:0.0:0.0	.	53;53	Q86UX7-2;Q86UX7	.;URP2_HUMAN	M	53	ENSP00000445778:I53M;ENSP00000339950:I53M;ENSP00000279227:I53M	ENSP00000279227:I53M	I	+	3	3	FERMT3	63731571	0.223000	0.23663	1.000000	0.80357	0.325000	0.28411	0.067000	0.14510	2.502000	0.84385	0.561000	0.74099	ATC	C|0.997;G|0.003	0.003	strong		0.657	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471	Missense_Mutation
PPARG	5468	hgsc.bcm.edu	37	3	12475557	12475557	+	Silent	SNP	C	C	T	rs3856806	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:12475557C>T	ENST00000287820.6	+	7	1552	c.1431C>T	c.(1429-1431)caC>caT	p.H477H	PPARG_ENST00000397026.2_Silent_p.H455H|PPARG_ENST00000397000.1_3'UTR|PPARG_ENST00000397015.2_Silent_p.H449H|PPARG_ENST00000539812.1_3'UTR|PPARG_ENST00000309576.6_Silent_p.H449H|PPARG_ENST00000397010.2_Silent_p.H449H|PPARG_ENST00000397012.2_Silent_p.H449H	NM_015869.4	NP_056953.2	P37231	PPARG_HUMAN	peroxisome proliferator-activated receptor gamma	477	Ligand-binding.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|brown fat cell differentiation (GO:0050873)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|cellular response to lithium ion (GO:0071285)|epithelial cell differentiation (GO:0030855)|fatty acid oxidation (GO:0019395)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|innate immune response (GO:0045087)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|lipoprotein transport (GO:0042953)|long-chain fatty acid transport (GO:0015909)|low-density lipoprotein particle receptor biosynthetic process (GO:0045713)|monocyte differentiation (GO:0030224)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of cell growth (GO:0030308)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ regeneration (GO:0031100)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|placenta development (GO:0001890)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fatty acid oxidation (GO:0046321)|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)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood pressure (GO:0008217)|regulation of cholesterol transporter activity (GO:0060694)|regulation of transcription involved in cell fate commitment (GO:0060850)|response to caffeine (GO:0031000)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to lipid (GO:0033993)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|arachidonic acid binding (GO:0050544)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|prostaglandin receptor activity (GO:0004955)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)		PAX8/PPARG(117)	breast(2)|endometrium(4)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20					Balsalazide(DB01014)|Bezafibrate(DB01393)|Glipizide(DB01067)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Mesalazine(DB00244)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Pioglitazone(DB01132)|Repaglinide(DB00912)|Rosiglitazone(DB00412)|Sulfasalazine(DB00795)|Telmisartan(DB00966)	TCACGGAACACGTGCAGCTAC	0.532			T	PAX8	follicular thyroid		"""Insulin resistance ; lipodystrophy, familial partial L;diabetes mellitus, insulin-resistantI, with acanthosis nigricans and hypertension"""						C|||	634	0.126597	0.0484	0.1138	5008	,	,		15722	0.2113		0.1213	False		,,,				2504	0.1595				p.H477H		Atlas-SNP	.		Dom	yes		3	3p25	5468	"""peroxisome proliferative activated receptor, gamma"""	yes	E	.	PPARG	49	.	0			c.C1431T	GRCh37	CM994587	PPARG	M	rs3856806	PASS	.	C	,,,	282,4124	158.5+/-191.2	13,256,1934	81.0	71.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1347,1431,1347,1347	-1.0	1.0	3	dbSNP_108	74	1105,7495	230.4+/-264.8	76,953,3271	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPARG	NM_005037.5,NM_015869.4,NM_138711.3,NM_138712.3	,,,	89,1209,5205	TT,TC,CC		12.8488,6.4004,10.6643	,,,	449/478,477/506,449/478,449/478	12475557	1387,11619	2203	4300	6503	SO:0001819	synonymous_variant	5468	exon7			GGAACACGTGCAG	X90563	CCDS2609.1, CCDS2610.2	3p25	2013-01-16	2006-10-17		ENSG00000132170	ENSG00000132170		"""Nuclear hormone receptors"""	9236	protein-coding gene	gene with protein product		601487	"""peroxisome proliferative activated receptor, gamma"""			7862171, 9750197	Standard	NM_005037		Approved	PPARG1, PPARG2, NR1C3, PPARgamma	uc003bwx.3	P37231	OTTHUMG00000129764	ENST00000287820.6:c.1431C>T	3.37:g.12475557C>T		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	211	206	0.976303	NM_015869	A8K3G6|B5BUA1|O00684|O00710|O14515|Q0QJH8|Q15178|Q15179|Q15180|Q15832|Q86U60|Q96J12	Silent	SNP	ENST00000287820.6	37	CCDS2609.1																																																																																			C|0.887;T|0.113	0.113	strong		0.532	PPARG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251979.2	NM_005037	
CCDC174	51244	hgsc.bcm.edu	37	3	14712473	14712473	+	Silent	SNP	G	G	A	rs1901	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:14712473G>A	ENST00000383794.3	+	11	1249	c.1176G>A	c.(1174-1176)ccG>ccA	p.P392P	CCDC174_ENST00000303688.7_Silent_p.P316P|CCDC174_ENST00000476763.1_3'UTR	NM_016474.4	NP_057558.3	Q6PII3	CC174_HUMAN	coiled-coil domain containing 174	392						cytoplasm (GO:0005737)|nucleus (GO:0005634)											AGTTTGCCCCGCCGTCAGATT	0.507													A|||	1730	0.345447	0.4614	0.4568	5008	,	,		16410	0.2262		0.3499	False		,,,				2504	0.228				p.P392P		Atlas-SNP	.											.	.	.	.	0			c.G1176A						PASS	.	A		2007,2399	614.5+/-392.4	465,1077,661	50.0	47.0	48.0		1176	1.4	1.0	3	dbSNP_36	48	2909,5691	670.3+/-402.7	460,1989,1851	no	coding-synonymous	C3orf19	NM_016474.4		925,3066,2512	AA,AG,GG		33.8256,45.5515,37.7979		392/468	14712473	4916,8090	2203	4300	6503	SO:0001819	synonymous_variant	51244	exon11			TGCCCCGCCGTCA	AF151046	CCDS2620.2	3p25.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000154781	ENSG00000154781			28033	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 19"""	C3orf19		11042152	Standard	NM_016474		Approved	FLJ33839	uc003byw.3	Q6PII3	OTTHUMG00000129837	ENST00000383794.3:c.1176G>A	3.37:g.14712473G>A		Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	188	187	0.994681	NM_016474	Q96CS5	Silent	SNP	ENST00000383794.3	37	CCDS2620.2																																																																																			G|0.630;A|0.370	0.370	strong		0.507	CCDC174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252077.2	NM_016474	
LDHA	3939	hgsc.bcm.edu	37	11	18422487	18422487	+	Silent	SNP	C	C	A	rs61736803	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18422487C>A	ENST00000422447.3	+	4	621	c.348C>A	c.(346-348)atC>atA	p.I116I	LDHA_ENST00000227157.4_Silent_p.I116I|LDHA_ENST00000379412.5_Silent_p.I116I|LDHA_ENST00000396222.2_Silent_p.I116I|LDHA_ENST00000540430.1_Silent_p.I145I|LDHA_ENST00000430553.2_Intron|LDHA_ENST00000542179.1_Silent_p.I116I	NM_001135239.1|NM_005566.3	NP_001128711.1|NP_005557.1	P00338	LDHA_HUMAN	lactate dehydrogenase A	116					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|cellular response to extracellular stimulus (GO:0031668)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	L-lactate dehydrogenase activity (GO:0004459)			central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(4)	12						ACGTGAACATCTTTAAATTCA	0.413													C|||	488	0.0974441	0.0469	0.1527	5008	,	,		11417	0.0645		0.1521	False		,,,				2504	0.1043				p.I145I		Atlas-SNP	.											.	LDHA	118	.	0			c.C435A						PASS	.	C	,,,,	333,4065	174.8+/-204.3	17,299,1883	94.0	78.0	84.0		,435,348,348,348	5.0	1.0	11	dbSNP_129	84	1464,7122	279.1+/-293.8	109,1246,2938	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LDHA	NM_001135239.1,NM_001165414.1,NM_001165415.1,NM_001165416.1,NM_005566.3	,,,,	126,1545,4821	AA,AC,CC		17.051,7.5716,13.8401	,,,,	,145/362,116/275,116/242,116/333	18422487	1797,11187	2199	4293	6492	SO:0001819	synonymous_variant	3939	exon4			GAACATCTTTAAA	X02152	CCDS7839.1, CCDS44549.1, CCDS53609.1, CCDS53610.1, CCDS53611.1	11p15.1	2012-10-02			ENSG00000134333	ENSG00000134333	1.1.1.27		6535	protein-coding gene	gene with protein product		150000				3000353	Standard	NM_005566		Approved		uc010rdd.2	P00338	OTTHUMG00000167721	ENST00000422447.3:c.348C>A	11.37:g.18422487C>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_001165414	B4DKQ2|B7Z5E3|D3DQY3|F8W819|Q53G53|Q6IBM7|Q6ZNV1|Q9UDE8|Q9UDE9	Silent	SNP	ENST00000422447.3	37	CCDS7839.1																																																																																			C|0.911;A|0.089	0.089	strong		0.413	LDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258172.2	NM_005566	
STEAP1B	256227	hgsc.bcm.edu	37	7	22533182	22533182	+	Missense_Mutation	SNP	T	T	C	rs62619777	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:22533182T>C	ENST00000406890.2	-	3	395	c.301A>G	c.(301-303)Atg>Gtg	p.M101V	STEAP1B_ENST00000404369.4_Missense_Mutation_p.M120V	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	101						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						ATGGAAACCATTGGCAAGACT	0.383													t|||	302	0.0603035	0.1309	0.0519	5008	,	,		19722	0.0		0.0666	False		,,,				2504	0.0266				p.M120V		Atlas-SNP	.											.	STEAP1B	22	.	0			c.A358G						PASS	.						103.0	89.0	93.0					7																	22533182		692	1591	2283	SO:0001583	missense	256227	exon3			AAACCATTGGCAA		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.301A>G	7.37:g.22533182T>C	ENSP00000385239:p.Met101Val	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	337	119	0.353116	NM_001164460	B5MCI2	Missense_Mutation	SNP	ENST00000406890.2	37	CCDS55094.1	126	0.057692307692307696	58	0.11788617886178862	17	0.04696132596685083	0	0.0	51	0.06728232189973615	t	0.009	-1.842652	0.00573	.	.	ENSG00000105889	ENST00000406890;ENST00000404369;ENST00000424363;ENST00000439708	D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.64	1.06	-1.75	0.08031	Flavoprotein transmembrane component (1);	0.166886	0.26662	U	0.023149	T	0.03348	0.0097	N	0.12182	0.205	0.52501	P	4.300000000001525E-5	B;B	0.06786	0.001;0.0	B;B	0.12837	0.008;0.002	T	0.35525	-0.9785	9	0.11485	T	0.65	-11.9862	6.1797	0.20463	0.0:0.6349:0.0:0.3651	rs62619777	120;101	B5MCI2;Q6NZ63	.;STEAL_HUMAN	V	101;120;120;120	ENSP00000385239:M101V;ENSP00000384370:M120V;ENSP00000416608:M120V;ENSP00000408954:M120V	ENSP00000384370:M120V	M	-	1	0	STEAP1B	22499707	0.982000	0.34865	0.802000	0.32245	0.529000	0.34654	0.180000	0.16860	-0.574000	0.05990	0.102000	0.15555	ATG	T|0.936;C|0.064	0.064	strong		0.383	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		
TM4SF4	7104	hgsc.bcm.edu	37	3	149192676	149192676	+	Silent	SNP	G	G	A	rs12488126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:149192676G>A	ENST00000305354.4	+	1	916	c.12G>A	c.(10-12)ggG>ggA	p.G4G		NM_004617.3	NP_004608.1	P48230	T4S4_HUMAN	transmembrane 4 L six family member 4	4					tissue regeneration (GO:0042246)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)|ovary(1)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TGTGCACTGGGGGCTGTGCCA	0.532													G|||	945	0.188698	0.0514	0.3602	5008	,	,		18015	0.0208		0.4066	False		,,,				2504	0.2014				p.G4G		Atlas-SNP	.											.	TM4SF4	27	.	0			c.G12A						PASS	.	G		382,3480		24,334,1573	59.0	62.0	61.0		12	-0.5	0.0	3	dbSNP_120	61	3223,5043		631,1961,1541	no	coding-synonymous	TM4SF4	NM_004617.3		655,2295,3114	AA,AG,GG		38.991,9.8912,29.7246		4/203	149192676	3605,8523	1931	4133	6064	SO:0001819	synonymous_variant	7104	exon1			CACTGGGGGCTGT		CCDS46932.1	3q25	2005-03-21	2005-03-21		ENSG00000169903	ENSG00000169903			11856	protein-coding gene	gene with protein product		606567	"""transmembrane 4 superfamily member 4"""			7665614	Standard	NM_004617		Approved	il-TMP	uc003exd.2	P48230	OTTHUMG00000159619	ENST00000305354.4:c.12G>A	3.37:g.149192676G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	136	72	0.529412	NM_004617	B2RDA4	Silent	SNP	ENST00000305354.4	37	CCDS46932.1																																																																																			G|0.791;A|0.209	0.209	strong		0.532	TM4SF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356528.1		
ADCY8	114	hgsc.bcm.edu	37	8	131921956	131921956	+	Silent	SNP	A	A	G	rs12547243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:131921956A>G	ENST00000286355.5	-	6	3730	c.1638T>C	c.(1636-1638)ccT>ccC	p.P546P	ADCY8_ENST00000377928.3_Silent_p.P546P	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	546					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)			TATCTTACCCAGGGATTCCTC	0.453										HNSCC(32;0.087)			G|||	2728	0.544728	0.3343	0.6297	5008	,	,		20272	0.6815		0.6958	False		,,,				2504	0.4724				p.P546P		Atlas-SNP	.											.	ADCY8	291	.	0			c.T1638C						PASS	.	G		1581,2825	666.9+/-401.8	286,1009,908	224.0	203.0	210.0		1638	-9.6	0.5	8	dbSNP_120	210	5879,2721	435.9+/-358.1	2034,1811,455	no	coding-synonymous	ADCY8	NM_001115.2		2320,2820,1363	GG,GA,AA		31.6395,35.8829,42.6419		546/1252	131921956	7460,5546	2203	4300	6503	SO:0001819	synonymous_variant	114	exon6			TTACCCAGGGATT	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.1638T>C	8.37:g.131921956A>G		Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	247	245	0.991903	NM_001115		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																			A|0.424;G|0.576	0.576	strong		0.453	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
TUBD1	51174	hgsc.bcm.edu	37	17	57963537	57963537	+	Missense_Mutation	SNP	A	A	G	rs1292053	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:57963537A>G	ENST00000592426.1	-	2	227	c.227T>C	c.(226-228)aTg>aCg	p.M76T	TUBD1_ENST00000376094.4_Missense_Mutation_p.M76T|TUBD1_ENST00000539018.1_Intron|TUBD1_ENST00000394239.3_Missense_Mutation_p.M76T|TUBD1_ENST00000346141.6_Intron|TUBD1_ENST00000591611.1_5'UTR|TUBD1_ENST00000325752.3_Missense_Mutation_p.M76T|TUBD1_ENST00000340993.6_Missense_Mutation_p.M76T			Q9UJT1	TBD_HUMAN	tubulin, delta 1	76			M -> T (in dbSNP:rs1292053). {ECO:0000269|PubMed:10620804, ECO:0000269|PubMed:15081367}.		cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|protein polymerization (GO:0051258)|spermatogenesis (GO:0007283)	centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.M76T(1)		NS(2)|breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(2)	21	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)		Vinblastine(DB00570)	CTTTGACAGCATTTGATTGAT	0.418													G|||	2410	0.48123	0.5204	0.4597	5008	,	,		17567	0.5754		0.4175	False		,,,				2504	0.4121				p.M76T		Atlas-SNP	.											TUBD1,NS,carcinoma,0,1	TUBD1	38	1	1	Substitution - Missense(1)	stomach(1)	c.T227C						PASS	.	G	THR/MET,THR/MET,THR/MET,,,THR/MET	2123,2283	599.7+/-389.3	520,1083,600	99.0	96.0	97.0		227,227,227,,,227	4.1	0.7	17	dbSNP_87	97	3751,4849	617.5+/-396.7	846,2059,1395	yes	missense,missense,missense,utr-5,intron,missense	TUBD1	NM_001193609.1,NM_001193610.1,NM_001193611.1,NM_001193612.1,NM_001193613.1,NM_016261.3	81,81,81,,,81	1366,3142,1995	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	43.6163,48.1843,45.1638	benign,benign,benign,,,benign	76/399,76/397,76/352,,,76/454	57963537	5874,7132	2203	4300	6503	SO:0001583	missense	51174	exon3			GACAGCATTTGAT	AF201333	CCDS11620.1, CCDS54151.1, CCDS54152.1, CCDS54153.1, CCDS54154.1	17q23.1	2007-03-16						"""Tubulins"""	16811	protein-coding gene	gene with protein product		607344				10620804	Standard	NM_016261		Approved	FLJ12709, TUBD	uc002ixw.2	Q9UJT1		ENST00000592426.1:c.227T>C	17.37:g.57963537A>G	ENSP00000468518:p.Met76Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	151	62	0.410596	NM_016261	B4DPT8|B4DW01|D3DU02|E9PCA7|E9PCQ8|Q5KU36|Q9BWG9|Q9H7Z8	Missense_Mutation	SNP	ENST00000592426.1	37	CCDS11620.1	1077	0.49313186813186816	261	0.5304878048780488	159	0.43922651933701656	342	0.5979020979020979	315	0.4155672823218997	G	2.326	-0.354555	0.05138	0.481843	0.436163	ENSG00000108423	ENST00000325752;ENST00000340993;ENST00000394239;ENST00000376094	T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47	6.08	4.1	0.47936	Tubulin/FtsZ, GTPase domain (4);	0.183702	0.64402	N	0.000019	T	0.00012	0.0000	N	0.00960	-1.095	0.52099	P	5.299999999996974E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.45425	-0.9262	9	0.11485	T	0.65	-1.7956	11.3011	0.49306	0.1943:0.0:0.8057:0.0	rs1292053;rs59005131;rs1292053	76;76;76;76	E9PCA7;E9PCQ8;Q9UJT1-2;Q9UJT1	.;.;.;TBD_HUMAN	T	76	ENSP00000320797:M76T;ENSP00000342399:M76T;ENSP00000377785:M76T;ENSP00000365262:M76T	ENSP00000320797:M76T	M	-	2	0	TUBD1	55318319	1.000000	0.71417	0.705000	0.30386	0.931000	0.56810	4.164000	0.58190	0.476000	0.27440	-0.119000	0.15052	ATG	A|0.522;G|0.478	0.478	strong		0.418	TUBD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448815.1	NM_016261	
IRS2	8660	hgsc.bcm.edu	37	13	110435953	110435953	+	Silent	SNP	A	A	G	rs4773092	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:110435953A>G	ENST00000375856.3	-	1	2962	c.2448T>C	c.(2446-2448)tgT>tgC	p.C816C		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	816					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			TGTCCCCGCCACAGGTGTAGG	0.711													.|||	2824	0.563898	0.59	0.7089	5008	,	,		9606	0.4514		0.5905	False		,,,				2504	0.5143				p.C816C	Melanoma(100;613 2409 40847)	Atlas-SNP	.											IRS2,NS,carcinoma,0,1	IRS2	44	1	0			c.T2448C						PASS	.	G		2520,1602		831,858,372	5.0	7.0	6.0		2448	-1.1	0.0	13	dbSNP_111	6	4936,3332		1596,1744,794	no	coding-synonymous	IRS2	NM_003749.2		2427,2602,1166	GG,GA,AA		40.3,38.8646,39.8224		816/1339	110435953	7456,4934	2061	4134	6195	SO:0001819	synonymous_variant	8660	exon1			CCCGCCACAGGTG	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"""Pleckstrin homology (PH) domain containing"""	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.2448T>C	13.37:g.110435953A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	50	16	0.32	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Silent	SNP	ENST00000375856.3	37	CCDS9510.1																																																																																			A|0.452;G|0.548	0.548	strong		0.711	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749	
TTC39A	22996	hgsc.bcm.edu	37	1	51767352	51767352	+	Silent	SNP	G	G	A	rs41287290	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:51767352G>A	ENST00000447632.2	-	12	1101	c.1053C>T	c.(1051-1053)ttC>ttT	p.F351F	TTC39A_ENST00000371747.3_Silent_p.F350F|TTC39A_ENST00000262676.5_3'UTR|TTC39A_ENST00000451380.1_Silent_p.F315F|TTC39A_ENST00000413473.2_Silent_p.F319F|TTC39A_ENST00000371750.5_Silent_p.F316F|TTC39A_ENST00000262675.7_Silent_p.F288F			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	351								p.0?(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(2)|prostate(2)|skin(3)|urinary_tract(1)	17						ACATGTGGTGGAACTGCTTCC	0.602													G|||	267	0.0533147	0.0106	0.0836	5008	,	,		20364	0.0		0.1441	False		,,,				2504	0.0511				p.F319F		Atlas-SNP	.											TTC39A,colon,carcinoma,0,2	TTC39A	40	2	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.C957T						PASS	.	G	,	99,4159		1,97,2031	67.0	70.0	69.0		948,957	0.7	1.0	1	dbSNP_127	69	1047,7399		70,907,3246	no	coding-synonymous,coding-synonymous	TTC39A	NM_001080494.2,NM_001144832.1	,	71,1004,5277	AA,AG,GG		12.3964,2.325,9.0208	,	316/579,319/582	51767352	1146,11558	2129	4223	6352	SO:0001819	synonymous_variant	22996	exon12			GTGGTGGAACTGC	AB007921	CCDS44143.1, CCDS44144.1, CCDS72789.1, CCDS72790.1	1p32.3	2013-01-11	2008-06-23	2008-06-23	ENSG00000085831	ENSG00000085831		"""Tetratricopeptide (TTC) repeat domain containing"""	18657	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 34"""	C1orf34		9455484, 9461476	Standard	XM_005270643		Approved	KIAA0452, DEME-6	uc010onf.2	Q5SRH9	OTTHUMG00000008193	ENST00000447632.2:c.1053C>T	1.37:g.51767352G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Silent	SNP	ENST00000447632.2	37																																																																																				A|0.083;C|0.000;G|0.917	0.083	strong		0.602	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2		
PHF20L1	51105	hgsc.bcm.edu	37	8	133851776	133851776	+	Missense_Mutation	SNP	A	A	G	rs184173196		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:133851776A>G	ENST00000395386.2	+	18	2635	c.2336A>G	c.(2335-2337)tAt>tGt	p.Y779C	PHF20L1_ENST00000220847.7_Missense_Mutation_p.Y166C|AF230666.2_ENST00000429151.1_RNA|PHF20L1_ENST00000395390.2_Missense_Mutation_p.Y754C|AF230666.2_ENST00000608375.1_RNA	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	779							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			GCTGATGTCTATGGTGTTACA	0.403													A|||	1	0.000199681	0.0008	0.0	5008	,	,		21222	0.0		0.0	False		,,,				2504	0.0				p.Y779C		Atlas-SNP	.											.	PHF20L1	129	.	0			c.A2336G						PASS	.	A	CYS/TYR	1,3787		0,1,1893	123.0	112.0	115.0		2336	0.3	1.0	8		115	1,8241		0,1,4120	no	missense	PHF20L1	NM_016018.4	194	0,2,6013	GG,GA,AA		0.0121,0.0264,0.0166	benign	779/1018	133851776	2,12028	1894	4121	6015	SO:0001583	missense	51105	exon18			ATGTCTATGGTGT	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24280	protein-coding gene	gene with protein product	"""tudor domain containing 20B"""					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2336A>G	8.37:g.133851776A>G	ENSP00000378784:p.Tyr779Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	37	CCDS6367.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	12.42	1.932270	0.34096	2.64E-4	1.21E-4	ENSG00000129292	ENST00000395386;ENST00000220847;ENST00000395390	T;T	0.31247	1.5;1.5	5.41	0.304	0.15796	.	0.868678	0.10032	U	0.724554	T	0.24431	0.0592	L	0.51422	1.61	0.35848	D	0.826539	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.13926	-1.0491	10	0.40728	T	0.16	-14.4995	4.697	0.12809	0.5762:0.0:0.2929:0.1309	.	754;779	F8W9L8;A8MW92	.;P20L1_HUMAN	C	779;166;754	ENSP00000378784:Y779C;ENSP00000378788:Y754C	ENSP00000220847:Y166C	Y	+	2	0	PHF20L1	133920958	0.994000	0.37717	0.990000	0.47175	0.999000	0.98932	1.529000	0.35996	-0.163000	0.10946	0.533000	0.62120	TAT	A|1.000;G|0.000	0.000	strong		0.403	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
S100A5	6276	hgsc.bcm.edu	37	1	153509890	153509890	+	Missense_Mutation	SNP	T	T	C	rs3795393	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:153509890T>C	ENST00000368718.1	-	4	442	c.161A>G	c.(160-162)gAc>gGc	p.D54G	BX470102.3_ENST00000420695.1_RNA|S100A6_ENST00000368719.4_5'Flank|S100A6_ENST00000368720.2_5'Flank|S100A6_ENST00000496817.1_5'Flank|S100A5_ENST00000359215.1_Missense_Mutation_p.D72G|S100A5_ENST00000368717.2_Missense_Mutation_p.D54G	NM_002962.1	NP_002953.2	P33763	S10A5_HUMAN	S100 calcium binding protein A5	54	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		D -> G.			neuronal cell body (GO:0043025)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)	p.D72G(1)		endometrium(1)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	4	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTTCATCAAGTCATCGATGCT	0.557													T|||	536	0.107029	0.0045	0.1254	5008	,	,		20624	0.244		0.0805	False		,,,				2504	0.1186				p.D54G		Atlas-SNP	.											S100A5,NS,carcinoma,-1,2	S100A5	10	2	1	Substitution - Missense(1)	stomach(1)	c.A161G						scavenged	.	T	GLY/ASP	72,4334	66.4+/-103.9	1,70,2132	248.0	205.0	220.0		161	3.3	0.2	1	dbSNP_107	220	660,7940	168.0+/-219.6	27,606,3667	yes	missense	S100A5	NM_002962.1	94	28,676,5799	CC,CT,TT		7.6744,1.6341,5.6282	benign	54/93	153509890	732,12274	2203	4300	6503	SO:0001583	missense	6276	exon4			ATCAAGTCATCGA	Z18954	CCDS1041.1, CCDS1041.2	1q21	2013-01-10	2001-11-28		ENSG00000196420	ENSG00000196420		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	10495	protein-coding gene	gene with protein product		176991	"""S100 calcium-binding protein A5"""	S100D		8341667	Standard	NM_002962		Approved		uc001fbx.3	P33763	OTTHUMG00000013547	ENST00000368718.1:c.161A>G	1.37:g.153509890T>C	ENSP00000357707:p.Asp54Gly	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	156	66	0.423077	NM_002962	Q52LE7|Q5RHS3	Missense_Mutation	SNP	ENST00000368718.1	37	CCDS1041.2	253	0.11584249084249085	3	0.006097560975609756	48	0.13259668508287292	144	0.2517482517482518	58	0.07651715039577836	T	11.21	1.571260	0.28003	0.016341	0.076744	ENSG00000196420	ENST00000368718;ENST00000359215;ENST00000368717	T;T;T	0.06933	3.24;3.24;3.24	4.41	3.27	0.37495	.	0.844215	0.10933	N	0.618156	T	0.02455	0.0075	.	.	.	0.80722	P	0.0	B	0.20261	0.043	B	0.19946	0.027	T	0.37079	-0.9721	8	0.56958	D	0.05	.	6.6544	0.22979	0.0:0.1089:0.0:0.8911	rs3795393;rs60039031;rs3795393	72	Q52LE7	.	G	54;72;54	ENSP00000357707:D54G;ENSP00000352148:D72G;ENSP00000357706:D54G	ENSP00000352148:D72G	D	-	2	0	S100A5	151776514	0.053000	0.20554	0.164000	0.22755	0.796000	0.44982	2.454000	0.44979	0.826000	0.34661	0.533000	0.62120	GAC	T|0.916;C|0.084	0.084	strong		0.557	S100A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037719.1	NM_002962	
KDR	3791	hgsc.bcm.edu	37	4	55946171	55946171	+	Silent	SNP	G	G	A	rs35961234	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55946171G>A	ENST00000263923.4	-	30	4303	c.4008C>T	c.(4006-4008)acC>acT	p.T1336T	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	1336					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.T1336T(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGTGCTACCGGTTTGCACTC	0.532			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			G|||	48	0.00958466	0.0008	0.013	5008	,	,		17550	0.0		0.0348	False		,,,				2504	0.0031				p.T1336T		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,colon,carcinoma,0,5	KDR	307	5	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C4008T						PASS	.	G		26,4380	33.5+/-64.1	0,26,2177	220.0	204.0	209.0		4008	-5.9	0.0	4	dbSNP_126	209	228,8372	94.5+/-156.4	3,222,4075	no	coding-synonymous	KDR	NM_002253.2		3,248,6252	AA,AG,GG		2.6512,0.5901,1.9529		1336/1357	55946171	254,12752	2203	4300	6503	SO:0001819	synonymous_variant	3791	exon30			GCTACCGGTTTGC	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.4008C>T	4.37:g.55946171G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	211	109	0.516588	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	37	CCDS3497.1																																																																																			G|0.983;A|0.017	0.017	strong		0.532	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
OCSTAMP	128506	hgsc.bcm.edu	37	20	45174632	45174632	+	Silent	SNP	A	A	G	rs184507425	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:45174632A>G	ENST00000279028.2	-	2	394	c.381T>C	c.(379-381)acT>acC	p.T127T		NM_080721.1	NP_542452.1	Q9BR26	OCSTP_HUMAN	osteoclast stimulatory transmembrane protein	127					cellular response to estrogen stimulus (GO:0071391)|cellular response to tumor necrosis factor (GO:0071356)|multinuclear osteoclast differentiation (GO:0072674)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of osteoclast proliferation (GO:0090290)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)	2						CCAGGGTGGCAGTGCTGTAGG	0.682													A|||	14	0.00279553	0.0	0.0058	5008	,	,		18377	0.0		0.0099	False		,,,				2504	0.0				p.T127T		Atlas-SNP	.											.	OCSTAMP	34	.	0			c.T381C						PASS	.	A		4,1380		0,4,688	31.0	36.0	35.0		381	-4.0	0.2	20		35	45,3137		1,43,1547	yes	coding-synonymous	C20orf123	NM_080721.1		1,47,2235	GG,GA,AA		1.4142,0.289,1.0731		127/567	45174632	49,4517	692	1591	2283	SO:0001819	synonymous_variant	128506	exon2			GGTGGCAGTGCTG	AL034424	CCDS54468.1	20q13.12	2012-03-27	2012-03-27	2012-03-27	ENSG00000149635	ENSG00000149635			16116	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 123"""	C20orf123		18064667	Standard	NM_080721		Approved	dJ257E24.3	uc010zxu.2	Q9BR26	OTTHUMG00000032652	ENST00000279028.2:c.381T>C	20.37:g.45174632A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_080721		Silent	SNP	ENST00000279028.2	37	CCDS54468.1																																																																																			A|0.994;G|0.006	0.006	strong		0.682	OCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079573.2	XM_496476	
GABRR1	2569	hgsc.bcm.edu	37	6	89926966	89926966	+	Missense_Mutation	SNP	T	T	C	rs12200969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:89926966T>C	ENST00000454853.2	-	1	186	c.76A>G	c.(76-78)Atg>Gtg	p.M26V	GABRR1_ENST00000481493.1_5'UTR|GABRR1_ENST00000369451.3_Intron|GABRR1_ENST00000435811.1_Missense_Mutation_p.M26V	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	26			M -> V (in dbSNP:rs12200969). {ECO:0000269|PubMed:14702039}.		gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	GGCCAGTGCATTCTGCTTTCA	0.463													C|||	1533	0.30611	0.5272	0.2118	5008	,	,		18075	0.0942		0.3529	False		,,,				2504	0.2444				p.M26V		Atlas-SNP	.											.	GABRR1	63	.	0			c.A76G						PASS	.	C	VAL/MET	2072,2334	606.9+/-390.8	483,1106,614	95.0	80.0	85.0		76	2.9	1.0	6	dbSNP_120	85	3000,5600	665.5+/-402.3	550,1900,1850	yes	missense	GABRR1	NM_002042.3	21	1033,3006,2464	CC,CT,TT		34.8837,47.0268,38.9974	benign	26/480	89926966	5072,7934	2203	4300	6503	SO:0001583	missense	2569	exon1			AGTGCATTCTGCT		CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4090	protein-coding gene	gene with protein product	"""GABA(A) receptor, rho 1"""	137161	"""gamma-aminobutyric acid (GABA) receptor, rho 1"""			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.76A>G	6.37:g.89926966T>C	ENSP00000412673:p.Met26Val	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	227	117	0.515419	NM_001256703	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Missense_Mutation	SNP	ENST00000454853.2	37	CCDS5019.2	641	0.2934981684981685	243	0.49390243902439024	76	0.20994475138121546	56	0.0979020979020979	266	0.35092348284960423	C	9.759	1.169648	0.21621	0.470268	0.348837	ENSG00000146276	ENST00000454853;ENST00000435811	T;T	0.23754	1.89;1.89	5.75	2.91	0.33838	.	0.428050	0.21492	N	0.073662	T	0.02571	0.0078	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46442	-0.9191	8	.	.	.	-4.2998	5.3971	0.16275	0.0:0.4594:0.246:0.2946	rs12200969;rs61289123;rs12200969	26;26	P24046-2;P24046	.;GBRR1_HUMAN	V	26	ENSP00000412673:M26V;ENSP00000394687:M26V	.	M	-	1	0	GABRR1	89983685	0.989000	0.36119	0.992000	0.48379	0.995000	0.86356	0.261000	0.18442	0.051000	0.15978	-0.128000	0.14901	ATG	T|0.651;C|0.349	0.349	strong		0.463	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2		
ACP1	52	hgsc.bcm.edu	37	2	272203	272203	+	Intron	SNP	C	C	T	rs11553746	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:272203C>T	ENST00000272065.5	+	3	324				ACP1_ENST00000484464.1_Intron|ACP1_ENST00000405233.1_Missense_Mutation_p.T53I|ACP1_ENST00000439645.2_Silent_p.D43D|ACP1_ENST00000407983.3_Missense_Mutation_p.T95I|ACP1_ENST00000272067.6_Silent_p.D43D	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble							cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	GGGTCATTGACAGCGGTGCTG	0.542													C|||	1219	0.243411	0.1286	0.232	5008	,	,		16562	0.249		0.334	False		,,,				2504	0.3078				p.T95I		Atlas-SNP	.											ACP1_ENST00000272067,NS,carcinoma,+1,1	ACP1	42	1	0			c.C284T						scavenged	.	C	ILE/THR,,	749,3657	306.3+/-289.4	63,623,1517	185.0	149.0	161.0		284,,129	5.9	1.0	2	dbSNP_120	161	2963,5637	459.5+/-364.9	486,1991,1823	yes	missense,intron,coding-synonymous	ACP1	NM_001040649.2,NM_004300.3,NM_007099.3	89,,	549,2614,3340	TT,TC,CC		34.4535,16.9995,28.5407	,,	95/113,,43/159	272203	3712,9294	2203	4300	6503	SO:0001627	intron_variant	52	exon3			CATTGACAGCGGT	M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"""Protein tyrosine phosphatases / Class II Cys-based PTPs"""	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.231+53C>T	2.37:g.272203C>T		Somatic	198	2	0.010101		WXS	Illumina HiSeq	Phase_I	229	126	0.550218	NM_001040649	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Missense_Mutation	SNP	ENST00000272065.5	37	CCDS1639.1	520	0.23809523809523808	56	0.11382113821138211	86	0.23756906077348067	126	0.2202797202797203	252	0.3324538258575198	C	17.56	3.419926	0.62622	0.169995	0.344535	ENSG00000143727	ENST00000407983;ENST00000405233;ENST00000449425	T;T	0.47528	0.91;0.84	5.87	5.87	0.94306	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.28039	P	0.9338388	D	0.76494	0.999	D	0.83275	0.996	T	0.01697	-1.1293	7	0.44086	T	0.13	-21.5954	17.6971	0.88285	0.0:1.0:0.0:0.0	rs11553746	95	B5MCC7	.	I	95;53;53	ENSP00000385404:T95I;ENSP00000384307:T53I	ENSP00000384307:T53I	T	+	2	0	ACP1	262203	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.667000	0.68067	2.779000	0.95612	0.655000	0.94253	ACA	C|0.738;T|0.262	0.262	strong		0.542	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3		
SSC5D	284297	hgsc.bcm.edu	37	19	56011915	56011915	+	Silent	SNP	G	G	A	rs61107130	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56011915G>A	ENST00000389623.6	+	11	2384	c.2361G>A	c.(2359-2361)gtG>gtA	p.V787V	SSC5D_ENST00000587166.1_Silent_p.V787V	NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	787	SRCR 5. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						GGCTGGAAGTGTGGCATGCCG	0.662													G|||	922	0.184105	0.0726	0.1873	5008	,	,		16639	0.3859		0.1511	False		,,,				2504	0.1585				p.V787V		Atlas-SNP	.											.	SSC5D	65	.	0			c.G2361A						PASS	.	G	,	87,1297		1,85,606	46.0	47.0	47.0		2361,2361	2.5	1.0	19	dbSNP_129	47	436,2746		27,382,1182	no	coding-synonymous,coding-synonymous	SSC5D	NM_001144950.1,NM_001195267.1	,	28,467,1788	AA,AG,GG		13.7021,6.2861,11.4542	,	787/1574,787/952	56011915	523,4043	692	1591	2283	SO:0001819	synonymous_variant	284297	exon11			GGAAGTGTGGCAT		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.2361G>A	19.37:g.56011915G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	161	84	0.521739	NM_001195267	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Silent	SNP	ENST00000389623.6	37	CCDS46196.1																																																																																			G|0.790;A|0.210	0.210	strong		0.662	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
COL3A1	1281	hgsc.bcm.edu	37	2	189864080	189864080	+	Missense_Mutation	SNP	G	G	A	rs1800255	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:189864080G>A	ENST00000304636.3	+	30	2262	c.2092G>A	c.(2092-2094)Gct>Act	p.A698T	COL3A1_ENST00000317840.5_Missense_Mutation_p.A698T	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	698	Triple-helical region.		A -> T (in dbSNP:rs1800255). {ECO:0000269|PubMed:18272325, ECO:0000269|PubMed:2235526}.		aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TAGAGGTGGAGCTGGTCCCCC	0.463													G|||	1094	0.21845	0.1051	0.2522	5008	,	,		15459	0.2331		0.2624	False		,,,				2504	0.2873				p.A698T		Atlas-SNP	.											.	COL3A1	292	.	0			c.G2092A	GRCh37	CM086593	COL3A1	M	rs1800255	PASS	.	G	THR/ALA	592,3814		40,512,1651	36.0	38.0	37.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2092	0.9	1.0	2	dbSNP_89	37	2190,6410		297,1596,2407	yes	missense	COL3A1	NM_000090.3	58	337,2108,4058	AA,AG,GG		25.4651,13.4362,21.3901	benign	698/1467	189864080	2782,10224	2203	4300	6503	SO:0001583	missense	1281	exon30			GGTGGAGCTGGTC	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.2092G>A	2.37:g.189864080G>A	ENSP00000304408:p.Ala698Thr	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	456	0.2087912087912088	39	0.07926829268292683	85	0.23480662983425415	139	0.243006993006993	193	0.2546174142480211	G	14.88	2.666284	0.47677	0.134362	0.254651	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.93488	-3.23;-3.22	4.96	0.873	0.19118	.	0.169588	0.27912	N	0.017354	T	0.00073	0.0002	N	0.16266	0.395	0.34524	P	0.291559	B	0.02656	0.0	B	0.01281	0.0	T	0.11767	-1.0574	9	0.28530	T	0.3	.	1.7367	0.02943	0.2601:0.2137:0.4107:0.1155	rs1800255;rs3817316;rs17831227;rs52832986;rs1800255	698	P02461	CO3A1_HUMAN	T	698	ENSP00000304408:A698T;ENSP00000315243:A698T	ENSP00000304408:A698T	A	+	1	0	COL3A1	189572325	0.046000	0.20272	0.979000	0.43373	0.998000	0.95712	0.487000	0.22356	0.246000	0.21394	0.650000	0.86243	GCT	G|0.808;A|0.192	0.192	strong		0.463	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
CSPG4	1464	hgsc.bcm.edu	37	15	75982428	75982428	+	Silent	SNP	C	C	T	rs7182906	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75982428C>T	ENST00000308508.5	-	3	1070	c.978G>A	c.(976-978)ggG>ggA	p.G326G		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	326	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTGCATCCAGCCCCCCGAGAA	0.632													C|||	1423	0.284145	0.2277	0.4006	5008	,	,		20377	0.1865		0.3817	False		,,,				2504	0.2781				p.G326G		Atlas-SNP	.											CSPG4,NS,carcinoma,0,1	CSPG4	175	1	0			c.G978A						PASS	.						20.0	18.0	18.0					15																	75982428		2192	4291	6483	SO:0001819	synonymous_variant	1464	exon3			ATCCAGCCCCCCG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.978G>A	15.37:g.75982428C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	148	81	0.547297	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			C|0.702;T|0.298	0.298	strong		0.632	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
STARD13	90627	hgsc.bcm.edu	37	13	33703666	33703666	+	Missense_Mutation	SNP	C	C	G	rs34425674	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:33703666C>G	ENST00000336934.5	-	5	1264	c.1148G>C	c.(1147-1149)cGt>cCt	p.R383P	STARD13_ENST00000399365.3_Missense_Mutation_p.R265P|STARD13_ENST00000255486.4_Missense_Mutation_p.R375P	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	383			R -> P (in dbSNP:rs34425674).		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		TTCATGCATACGGCTTTGGTC	0.537													C|||	51	0.0101837	0.0	0.0072	5008	,	,		18202	0.0		0.0268	False		,,,				2504	0.0194				p.R383P		Atlas-SNP	.											STARD13,NS,carcinoma,0,1	STARD13	100	1	0			c.G1148C						PASS	.	C	PRO/ARG,PRO/ARG,PRO/ARG	28,4378	31.7+/-61.6	0,28,2175	74.0	74.0	74.0		794,1148,1124	2.0	0.4	13	dbSNP_126	74	250,8350	97.2+/-158.9	1,248,4051	yes	missense,missense,missense	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	103,103,103	1,276,6226	GG,GC,CC		2.907,0.6355,2.1375	benign,benign,benign	265/996,383/1114,375/1106	33703666	278,12728	2203	4300	6503	SO:0001583	missense	90627	exon5			TGCATACGGCTTT	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.1148G>C	13.37:g.33703666C>G	ENSP00000338785:p.Arg383Pro	Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	77	75	0.974026	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	23	0.010531135531135532	0	0.0	4	0.011049723756906077	0	0.0	19	0.025065963060686015	C	11.55	1.671535	0.29693	0.006355	0.02907	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934;ENST00000399364	T;T;T	0.06528	3.3;3.29;3.3	5.82	2.03	0.26663	.	0.215824	0.46442	D	0.000297	T	0.02610	0.0079	L	0.48642	1.525	0.80722	D	1	P;B;B;B	0.45594	0.862;0.451;0.116;0.451	P;B;B;B	0.47941	0.562;0.411;0.154;0.411	T	0.32955	-0.9887	10	0.35671	T	0.21	.	8.9615	0.35849	0.0:0.2181:0.0:0.7819	rs34425674	375;348;383;375	Q9Y3M8-5;Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;.;STA13_HUMAN;.	P	265;375;383;375	ENSP00000382300:R265P;ENSP00000255486:R375P;ENSP00000338785:R383P	ENSP00000255486:R375P	R	-	2	0	STARD13	32601666	0.222000	0.23652	0.427000	0.26684	0.190000	0.23558	0.474000	0.22148	0.963000	0.38082	-0.436000	0.05848	CGT	C|0.981;G|0.019	0.019	strong		0.537	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
TTC23L	153657	hgsc.bcm.edu	37	5	34863034	34863034	+	Silent	SNP	A	A	T	rs3906383	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:34863034A>T	ENST00000505624.1	+	5	514	c.411A>T	c.(409-411)acA>acT	p.T137T	TTC23L_ENST00000514080.1_3'UTR	NM_144725.3	NP_653326.3	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like	137										breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(9)|prostate(2)|stomach(1)|urinary_tract(1)	22						AACATGCTACATCAGCCAAGA	0.468													a|||	196	0.0391374	0.0023	0.0317	5008	,	,		21723	0.0367		0.0447	False		,,,				2504	0.091				p.T137T		Atlas-SNP	.											.	TTC23L	47	.	0			c.A411T						PASS	.	G		45,3837		1,43,1897	95.0	91.0	92.0		411	-4.5	0.0	5	dbSNP_108	92	513,7777		18,477,3650	no	coding-synonymous	TTC23L	NM_144725.3		19,520,5547	TT,TA,AA		6.1882,1.1592,4.5843		137/362	34863034	558,11614	1941	4145	6086	SO:0001819	synonymous_variant	153657	exon5			TGCTACATCAGCC		CCDS54840.1	5p13.2	2008-07-14			ENSG00000205838	ENSG00000205838			26355	protein-coding gene	gene with protein product						12477932	Standard	NM_144725		Approved	FLJ25439	uc003jiu.3	Q6PF05	OTTHUMG00000162020	ENST00000505624.1:c.411A>T	5.37:g.34863034A>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_144725	Q6RGS4|Q8N7R3|Q96LJ2	Silent	SNP	ENST00000505624.1	37	CCDS54840.1																																																																																			A|0.947;T|0.053	0.053	strong		0.468	TTC23L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366819.1	NM_144725	
H2BFM	286436	hgsc.bcm.edu	37	X	103294760	103294760	+	Nonsense_Mutation	SNP	C	C	T	rs2301384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:103294760C>T	ENST00000355016.3	+	1	245	c.217C>T	c.(217-219)Cag>Tag	p.Q73*	H2BFM_ENST00000243297.5_Nonsense_Mutation_p.Q176*	NM_001164416.1	NP_001157888.1	P0C1H6	H2BFM_HUMAN	H2B histone family, member M	73						nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(1)|ovary(1)	3						GCAGGTTCACCAGGGCCTCAG	0.632													.|||	1157	0.30649	0.0272	0.1902	3775	,	,		13564	0.2986		0.3211	False		,,,				2504	0.3732				p.Q73X		Atlas-SNP	.											.	H2BFM	25	.	0			c.C217T						PASS	.	C	stop/GLN	78,1131		4,56,14,457,161	33.0	36.0	35.0		217	-5.1	0.0	X	dbSNP_100	35	1054,1337		163,388,340,249,451	yes	stop-gained	H2BFM	NM_001164416.1		167,444,354,706,612	TT,TC,T,CC,C		44.082,6.4516,31.4444		73/155	103294760	1132,2468	692	1591	2283	SO:0001587	stop_gained	286436	exon1			GTTCACCAGGGCC	AK093522	CCDS55468.1	Xq22.2	2011-01-27			ENSG00000101812	ENSG00000101812		"""Histones / Replication-independent"""	27867	protein-coding gene	gene with protein product							Standard	NM_001164416		Approved		uc004els.2	P0C1H6	OTTHUMG00000022122	ENST00000355016.3:c.217C>T	X.37:g.103294760C>T	ENSP00000347119:p.Gln73*	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	145	137	0.944828	NM_001164416	A6NP82	Nonsense_Mutation	SNP	ENST00000355016.3	37	CCDS55468.1	542	0.32670283303194697	13	0.026970954356846474	56	0.1891891891891892	122	0.26991150442477874	179	0.2934426229508197	.	14.19	2.462579	0.43736	0.064516	0.44082	ENSG00000101812	ENST00000243297;ENST00000355016	.	.	.	2.54	-5.08	0.02929	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999982547	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	2.3382	0.04252	0.135:0.2701:0.3961:0.1989	rs2301384	.	.	.	X	176;73	.	ENSP00000243297:Q176X	Q	+	1	0	H2BFM	103181416	0.834000	0.29399	0.000000	0.03702	0.002000	0.02628	0.930000	0.28858	-2.587000	0.00458	-0.389000	0.06534	CAG	C|0.676;T|0.324	0.324	strong		0.632	H2BFM-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057758.2	XM_210048	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74196686	74196686	+	Silent	SNP	T	T	C	rs2075025	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:74196686T>C	ENST00000286523.5	-	4	2534	c.1752A>G	c.(1750-1752)gcA>gcG	p.A584A	ELMSAN1_ENST00000394071.2_Silent_p.A584A	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	584					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										TCATGTCCTCTGCCTGGAGAA	0.567													t|||	3025	0.604034	0.649	0.4524	5008	,	,		16050	0.8323		0.3887	False		,,,				2504	0.637				p.A584A		Atlas-SNP	.											.	.	.	.	0			c.A1752G						PASS	.	C	,	2618,1786		784,1050,368	31.0	30.0	30.0		1752,1752	-7.0	0.6	14	dbSNP_96	30	3179,5419		605,1969,1725	no	coding-synonymous,coding-synonymous	C14orf43	NM_001043318.1,NM_194278.3	,	1389,3019,2093	CC,CT,TT		36.9737,40.554,44.5854	,	584/1046,584/1046	74196686	5797,7205	2202	4299	6501	SO:0001819	synonymous_variant	91748	exon4			GTCCTCTGCCTGG	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.1752A>G	14.37:g.74196686T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Silent	SNP	ENST00000286523.5	37	CCDS9819.1																																																																																			T|0.490;C|0.510	0.510	strong		0.567	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278	
DDN	23109	hgsc.bcm.edu	37	12	49390677	49390677	+	Missense_Mutation	SNP	T	T	C	rs10783299	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:49390677T>C	ENST00000421952.2	-	2	2003	c.1982A>G	c.(1981-1983)gAg>gGg	p.E661G	RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	661	Interaction with CD2AP and NPHS1. {ECO:0000250}.		E -> G (in dbSNP:rs10783299).			cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E607G(1)		NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						GTTTCCAACCTCGGGCAGGGT	0.602											OREG0021778	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2197	0.438698	0.553	0.2939	5008	,	,		15899	0.4425		0.3539	False		,,,				2504	0.4703				p.E661G		Atlas-SNP	.											DDN_ENST00000421952,NS,carcinoma,0,3	DDN	54	3	1	Substitution - Missense(1)	stomach(1)	c.A1982G						scavenged	.	C	GLY/GLU	2254,2152	563.1+/-381.1	580,1094,529	39.0	35.0	36.0		1982	-5.8	0.0	12	dbSNP_120	36	3211,5389	638.0+/-399.3	621,1969,1710	yes	missense	DDN	NM_015086.1	98	1201,3063,2239	CC,CT,TT		37.3372,48.8425,42.0191	benign	661/712	49390677	5465,7541	2203	4300	6503	SO:0001583	missense	23109	exon2			CCAACCTCGGGCA	AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.1982A>G	12.37:g.49390677T>C	ENSP00000390590:p.Glu661Gly	Somatic	117	1	0.00854701	961	WXS	Illumina HiSeq	Phase_I	127	48	0.377953	NM_015086		Missense_Mutation	SNP	ENST00000421952.2	37	CCDS31791.2	879	0.4024725274725275	269	0.5467479674796748	108	0.2983425414364641	232	0.40559440559440557	270	0.3562005277044855	C	3.227	-0.158200	0.06544	0.511575	0.373372	ENSG00000181418	ENST00000421952	T	0.43688	0.94	4.55	-5.81	0.02340	.	1.555000	0.03978	N	0.292861	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33650	-0.9860	9	0.08179	T	0.78	-28.7637	2.4931	0.04615	0.124:0.1427:0.291:0.4424	rs10783299;rs59932751;rs10783299	661	O94850	DEND_HUMAN	G	661	ENSP00000390590:E661G	ENSP00000390590:E661G	E	-	2	0	DDN	47676944	0.000000	0.05858	0.000000	0.03702	0.228000	0.25075	-1.178000	0.03093	-2.010000	0.00953	-0.355000	0.07637	GAG	T|0.588;C|0.412	0.412	strong		0.602	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1		
PLXNB3	5365	hgsc.bcm.edu	37	X	153041868	153041868	+	Missense_Mutation	SNP	T	T	A	rs146832392	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153041868T>A	ENST00000361971.5	+	28	4901	c.4787T>A	c.(4786-4788)gTg>gAg	p.V1596E	PLXNB3_ENST00000538966.1_Missense_Mutation_p.V1619E|PLXNB3_ENST00000538776.1_Missense_Mutation_p.V1249E|SRPK3_ENST00000489426.1_5'UTR	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1596					axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					TTGACCTCCGTGACCCAAAAC	0.632													T|||	70	0.018543	0.0015	0.0144	3775	,	,		5576	0.0		0.0577	False		,,,				2504	0.0				p.V1619E		Atlas-SNP	.											.	PLXNB3	208	.	0			c.T4856A						PASS	.		GLU/VAL,GLU/VAL	30,3803		0,27,3,1605,566	73.0	58.0	63.0		4856,4787	4.8	1.0	X	dbSNP_134	63	421,6303		8,296,109,2124,1759	yes	missense,missense	PLXNB3	NM_001163257.1,NM_005393.2	121,121	8,323,112,3729,2325	AA,AT,A,TT,T		6.2612,0.7827,4.272	possibly-damaging,possibly-damaging	1619/1933,1596/1910	153041868	451,10106	2201	4296	6497	SO:0001583	missense	5365	exon29			CCTCCGTGACCCA	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.4787T>A	X.37:g.153041868T>A	ENSP00000355378:p.Val1596Glu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	230	131	0.569565	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	48|48	0.028933092224231464|0.028933092224231464	2|2	0.0040650406504065045|0.0040650406504065045	4|4	0.011111111111111112|0.011111111111111112	0|0	0.0|0.0	33|33	0.04483695652173913|0.04483695652173913	t|t	9.741|9.741	1.164866|1.164866	0.21538|0.21538	0.007827|0.007827	0.062612|0.062612	ENSG00000198753|ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776|ENST00000411613	T;T;T|.	0.11277|.	2.79;2.79;2.79|.	4.82|4.82	4.82|4.82	0.62117|0.62117	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);|.	0.221383|.	0.38111|.	N|.	0.001803|.	T|.	0.09992|.	0.0245|.	L|L	0.38692|0.38692	1.165|1.165	0.09310|0.09310	P|P	1.0|1.0	D;B;P|.	0.55800|.	0.973;0.155;0.934|.	P;B;P|.	0.62491|.	0.903;0.187;0.903|.	T|.	0.46414|.	-0.9193|.	9|.	0.05833|.	T|.	0.94|.	.|.	12.712|12.712	0.57094|0.57094	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1249;1619;1596|.	B7Z3H9;F5H773;Q9ULL4|.	.;.;PLXB3_HUMAN|.	E|R	1619;1596;1249|220	ENSP00000442736:V1619E;ENSP00000355378:V1596E;ENSP00000445569:V1249E|.	ENSP00000355378:V1596E|.	V|X	+|+	2|1	0|0	PLXNB3|PLXNB3	152695062|152695062	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.065000|0.065000	0.16274|0.16274	5.057000|5.057000	0.64294|0.64294	1.709000|1.709000	0.51313|0.51313	0.378000|0.378000	0.23410|0.23410	GTG|TGA	T|0.965;A|0.035	0.035	strong		0.632	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
PIGN	23556	hgsc.bcm.edu	37	18	59774037	59774037	+	Silent	SNP	C	C	T	rs9319997	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:59774037C>T	ENST00000357637.5	-	19	2167	c.1752G>A	c.(1750-1752)ctG>ctA	p.L584L	PIGN_ENST00000400334.3_Silent_p.L584L	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	584					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				CTCGAGTCCACAGCCGAGTGA	0.403													C|||	468	0.0934505	0.0061	0.1239	5008	,	,		19226	0.0069		0.2694	False		,,,				2504	0.0982				p.L584L		Atlas-SNP	.											.	PIGN	62	.	0			c.G1752A						PASS	.	C	,	191,3641		5,181,1730	52.0	50.0	51.0		1752,1752	2.2	1.0	18	dbSNP_119	51	2034,6216		242,1550,2333	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	247,1731,4063	TT,TC,CC		24.6545,4.9843,18.4158	,	584/932,584/932	59774037	2225,9857	1916	4125	6041	SO:0001819	synonymous_variant	23556	exon19			AGTCCACAGCCGA	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.1752G>A	18.37:g.59774037C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	159	50	0.314465	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			C|0.912;T|0.088	0.088	strong		0.403	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
GALP	85569	hgsc.bcm.edu	37	19	56694505	56694505	+	Splice_Site	SNP	C	C	T	rs575756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56694505C>T	ENST00000357330.2	+	5	301	c.219C>T	c.(217-219)gaC>gaT	p.D73D	GALP_ENST00000440823.1_3'UTR	NM_033106.3	NP_149097.1	Q9UBC7	GALP_HUMAN	galanin-like peptide	73					behavioral response to starvation (GO:0042595)|defense response to bacterium (GO:0042742)|neuropeptide signaling pathway (GO:0007218)|regulation of appetite (GO:0032098)|response to insulin (GO:0032868)	extracellular region (GO:0005576)				lung(4)	4		Colorectal(82;0.000147)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0507)		tgtttctAGACGGGCTCCCCT	0.488													C|||	1575	0.314497	0.1369	0.3617	5008	,	,		18590	0.3383		0.3529	False		,,,				2504	0.4571				p.D73D		Atlas-SNP	.											.	GALP	13	.	0			c.C219T						PASS	.	C	,	811,3595	324.8+/-298.8	96,619,1488	118.0	104.0	109.0		,219	-1.4	0.1	19	dbSNP_83	109	3287,5313	491.7+/-373.1	642,2003,1655	yes	utr-3,coding-synonymous-near-splice	GALP	NM_001145546.1,NM_033106.3	,	738,2622,3143	TT,TC,CC		38.2209,18.4067,31.5085	,	,73/117	56694505	4098,8908	2203	4300	6503	SO:0001630	splice_region_variant	85569	exon5			TCTAGACGGGCTC	AF188493	CCDS12940.1, CCDS46202.1	19q13.42	2013-02-26	2007-08-24			ENSG00000197487		"""Endogenous ligands"""	24840	protein-coding gene	gene with protein product		611178				10601261	Standard	NM_033106		Approved		uc002qmo.1	Q9UBC7		ENST00000357330.2:c.218-1C>T	19.37:g.56694505C>T		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	222	222	1	NM_033106	A1KXL3	Silent	SNP	ENST00000357330.2	37	CCDS12940.1																																																																																			C|0.685;N|0.001	.	strong		0.488	GALP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457832.1	NM_033106	Silent
EPG5	57724	hgsc.bcm.edu	37	18	43534824	43534824	+	Missense_Mutation	SNP	T	T	C	rs59422275	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:43534824T>C	ENST00000282041.5	-	2	578	c.544A>G	c.(544-546)Aaa>Gaa	p.K182E		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	182			K -> E (in dbSNP:rs59422275). {ECO:0000269|PubMed:10997877}.		autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						AGGCCTTGTTTGTCTTCTTTA	0.418													T|||	564	0.11262	0.2466	0.0692	5008	,	,		20092	0.0268		0.0815	False		,,,				2504	0.0828				p.K182E		Atlas-SNP	.											.	EPG5	199	.	0			c.A544G						PASS	.	T	GLU/LYS	784,3070		76,632,1219	51.0	51.0	51.0		544	2.7	0.1	18	dbSNP_129	51	687,7567		23,641,3463	yes	missense	EPG5	NM_020964.2	56	99,1273,4682	CC,CT,TT		8.3232,20.3425,12.149	benign	182/2580	43534824	1471,10637	1927	4127	6054	SO:0001583	missense	57724	exon2			CTTGTTTGTCTTC	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.544A>G	18.37:g.43534824T>C	ENSP00000282041:p.Lys182Glu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	154	88	0.571429	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	215	0.09844322344322344	119	0.241869918699187	22	0.06077348066298342	12	0.02097902097902098	62	0.08179419525065963	T	5.546	0.285680	0.10513	0.203425	0.083232	ENSG00000152223	ENST00000282041	T	0.10763	2.84	5.16	2.73	0.32206	.	1.752500	0.02376	N	0.078330	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.002	T	0.38286	-0.9668	9	0.02654	T	1	0.0102	6.3859	0.21559	0.0:0.0826:0.1584:0.759	rs59422275;rs61751868	182;182	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	E	182	ENSP00000282041:K182E	ENSP00000282041:K182E	K	-	1	0	EPG5	41788822	0.002000	0.14202	0.058000	0.19502	0.041000	0.13682	1.089000	0.30890	0.280000	0.22209	0.460000	0.39030	AAA	T|0.904;C|0.096	0.096	strong		0.418	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390086	208390086	+	Silent	SNP	G	G	C	rs1664227	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:208390086G>C	ENST00000367033.3	-	2	1939	c.1182C>G	c.(1180-1182)acC>acG	p.T394T		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	394	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TTACCGCCTTGGTGCACTGGA	0.622													G|||	1839	0.367212	0.3623	0.3343	5008	,	,		20651	0.4048		0.3042	False		,,,				2504	0.4233				p.T394T		Atlas-SNP	.											.	PLXNA2	178	.	0			c.C1182G						PASS	.	G		1551,2855	488.5+/-361.2	287,977,939	80.0	74.0	76.0		1182	4.9	1.0	1	dbSNP_89	76	2810,5790	443.7+/-360.5	479,1852,1969	no	coding-synonymous	PLXNA2	NM_025179.3		766,2829,2908	CC,CG,GG		32.6744,35.202,33.5307		394/1895	208390086	4361,8645	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon2			CGCCTTGGTGCAC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.1182C>G	1.37:g.208390086G>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			G|0.664;C|0.336	0.336	strong		0.622	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
HMHA1	23526	hgsc.bcm.edu	37	19	1085966	1085966	+	Silent	SNP	A	A	G	rs3761028	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1085966A>G	ENST00000313093.2	+	23	3603	c.3372A>G	c.(3370-3372)acA>acG	p.T1124T	HMHA1_ENST00000539243.2_Silent_p.T1140T|HMHA1_ENST00000590214.1_Silent_p.T1151T|HMHA1_ENST00000591169.1_3'UTR|HMHA1_ENST00000543365.1_Silent_p.T1007T|HMHA1_ENST00000536472.1_Silent_p.T992T|POLR2E_ENST00000585838.1_5'Flank|HMHA1_ENST00000590577.1_Silent_p.T759T|HMHA1_ENST00000586866.1_Silent_p.T1128T	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	1124					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCGGATGACACTGGGCTCCT	0.657													g|||	2659	0.53095	0.5764	0.6744	5008	,	,		11914	0.3294		0.6352	False		,,,				2504	0.4683				p.T1140T		Atlas-SNP	.											HMHA1,NS,carcinoma,0,1	HMHA1	78	1	0			c.A3420G						PASS	.	G		2495,1865		724,1047,409	45.0	49.0	48.0		3372	-8.4	0.0	19	dbSNP_107	48	5321,3223		1722,1877,673	no	coding-synonymous	HMHA1	NM_012292.2		2446,2924,1082	GG,GA,AA		37.7224,42.7752,39.4296		1124/1137	1085966	7816,5088	2180	4272	6452	SO:0001819	synonymous_variant	23526	exon23			GATGACACTGGGC	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.3372A>G	19.37:g.1085966A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	115	46	0.4	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			T|0.000;G|0.587;C|0.000;A|0.413	0.587	strong		0.657	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
MKI67	4288	hgsc.bcm.edu	37	10	129899543	129899543	+	Silent	SNP	C	C	T	rs10082504	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:129899543C>T	ENST00000368654.3	-	14	10059	c.9684G>A	c.(9682-9684)agG>agA	p.R3228R	MKI67_ENST00000368653.3_Silent_p.R2868R	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3228					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.R3228R(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTTCTGCACACCTCTTGACAC	0.433													C|||	519	0.103634	0.0666	0.1556	5008	,	,		21188	0.1389		0.0785	False		,,,				2504	0.1063				p.R3228R		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - coding silent(1)	stomach(1)	c.G9684A						scavenged	.	C	,	301,4105	164.4+/-196.0	13,275,1915	130.0	121.0	124.0		8604,9684	-0.4	0.0	10	dbSNP_119	124	803,7797	188.0+/-235.1	40,723,3537	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	53,998,5452	TT,TC,CC		9.3372,6.8316,8.4884	,	2868/2897,3228/3257	129899543	1104,11902	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon14			TGCACACCTCTTG	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.9684G>A	10.37:g.129899543C>T		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	136	59	0.433824	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			C|0.913;T|0.087	0.087	strong		0.433	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209190070	209190070	+	Silent	SNP	T	T	C	rs138885638	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:209190070T>C	ENST00000264380.4	+	20	2693	c.2535T>C	c.(2533-2535)tcT>tcC	p.S845S		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	845					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						GAGGAGGCTCTGATTATGAGC	0.378													T|||	3	0.000599042	0.0015	0.0	5008	,	,		20316	0.0		0.001	False		,,,				2504	0.0				p.S845S		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.T2535C						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	97.0	91.0	93.0		2535	1.9	1.0	2	dbSNP_134	93	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	PIKFYVE	NM_015040.3		0,15,6488	CC,CT,TT		0.1512,0.0454,0.1153		845/2099	209190070	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	200576	exon20			AGGCTCTGATTAT	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.2535T>C	2.37:g.209190070T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	37	CCDS2382.1																																																																																			T|0.999;C|0.001	0.001	strong		0.378	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
ABCA13	154664	hgsc.bcm.edu	37	7	48563913	48563913	+	Silent	SNP	A	A	G	rs61705907	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:48563913A>G	ENST00000435803.1	+	54	14145	c.14121A>G	c.(14119-14121)agA>agG	p.R4707R	ABCA13_ENST00000544596.1_Silent_p.R437R	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4707					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AGGAAAAGAGAGTGTTTGAAG	0.378													G|||	427	0.0852636	0.2171	0.0389	5008	,	,		18917	0.003		0.0308	False		,,,				2504	0.0808				p.R4707R		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A14121G						PASS	.	G		710,3024		65,580,1222	115.0	115.0	115.0		14121	-2.2	0.3	7	dbSNP_129	115	322,7874		6,310,3782	no	coding-synonymous	ABCA13	NM_152701.3		71,890,5004	GG,GA,AA		3.9287,19.0145,8.6505		4707/5059	48563913	1032,10898	1867	4098	5965	SO:0001819	synonymous_variant	154664	exon54			AAAGAGAGTGTTT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.14121A>G	7.37:g.48563913A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	227	113	0.497797	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			A|0.939;G|0.061	0.061	strong		0.378	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
DMKN	93099	hgsc.bcm.edu	37	19	36002404	36002404	+	Missense_Mutation	SNP	C	C	T	rs56743379|rs138902616		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:36002404C>T	ENST00000339686.3	-	5	1003	c.827G>A	c.(826-828)aGc>aAc	p.S276N	DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000418261.1_Missense_Mutation_p.S276N|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.S276N|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.S276N|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.S276N|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.S276N|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000436012.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	276	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			gccactgctgctgccactgct	0.647																																					p.S276N		Atlas-SNP	.											DMKN,NS,carcinoma,0,2	DMKN	116	2	1	Deletion - In frame(1)	ovary(1)	c.G827A						PASS	.						28.0	21.0	23.0					19																	36002404		2176	4255	6431	SO:0001583	missense	93099	exon5			CTGCTGCTGCCAC	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.827G>A	19.37:g.36002404C>T	ENSP00000342012:p.Ser276Asn	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	55	11	0.2	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	C	7.414	0.635437	0.14322	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1	3.2	-1.74	0.08056	.	0.904855	0.09337	N	0.815985	T	0.30696	0.0773	L	0.48642	1.525	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.08055	0.001;0.001;0.001;0.001;0.003	T	0.32241	-0.9914	10	0.16896	T	0.51	5.0393	8.4003	0.32581	0.0:0.7659:0.0:0.2341	.	276;276;276;276;276	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	N	276	ENSP00000342012:S276N;ENSP00000394908:S276N;ENSP00000415277:S276N;ENSP00000414743:S276N;ENSP00000388404:S276N;ENSP00000409513:S276N	ENSP00000342012:S276N	S	-	2	0	DMKN	40694244	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.213000	0.09305	-0.013000	0.14199	-1.984000	0.00453	AGC	.	.	weak		0.647	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
C20orf141	128653	hgsc.bcm.edu	37	20	2796007	2796007	+	Silent	SNP	G	G	A	rs12625619	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2796007G>A	ENST00000380589.4	+	1	351	c.177G>A	c.(175-177)ctG>ctA	p.L59L	TMEM239_ENST00000554164.1_Silent_p.L59L|TMEM239_ENST00000380585.1_5'Flank|TMEM239_ENST00000361033.1_5'Flank|C20orf141_ENST00000603872.1_Silent_p.L59L|TMEM239_ENST00000380593.4_Silent_p.L59L	NM_080739.2	NP_542777.1	Q9NUB4	CT141_HUMAN	chromosome 20 open reading frame 141	59	Leu-rich.					integral component of membrane (GO:0016021)				endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	10						CACTAGGACTGACAATCCAGG	0.617													G|||	732	0.146166	0.2549	0.1225	5008	,	,		16000	0.1319		0.0726	False		,,,				2504	0.1063				p.L59L		Atlas-SNP	.											.	C20orf141	21	.	0			c.G177A						PASS	.	G		965,3441	361.9+/-315.9	100,765,1338	109.0	106.0	107.0		177	2.9	0.7	20	dbSNP_120	107	859,7741	194.9+/-240.2	38,783,3479	no	coding-synonymous	C20orf141	NM_080739.2		138,1548,4817	AA,AG,GG		9.9884,21.902,14.0243		59/166	2796007	1824,11182	2203	4300	6503	SO:0001819	synonymous_variant	128653	exon1			AGGACTGACAATC		CCDS13034.1	20p13	2012-10-30			ENSG00000258713	ENSG00000258713			16134	protein-coding gene	gene with protein product							Standard	NM_001256538		Approved	dJ860F19.4	uc002wgw.3	Q9NUB4	OTTHUMG00000031707	ENST00000380589.4:c.177G>A	20.37:g.2796007G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_080739		Silent	SNP	ENST00000380589.4	37	CCDS13034.1																																																																																			G|0.860;A|0.140	0.140	strong		0.617	C20orf141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077644.2	NM_080739	
SALL1	6299	hgsc.bcm.edu	37	16	51172677	51172677	+	Silent	SNP	G	G	A	rs11645288	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:51172677G>A	ENST00000251020.4	-	2	3489	c.3456C>T	c.(3454-3456)caC>caT	p.H1152H	SALL1_ENST00000440970.1_Silent_p.H1055H|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1152					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GAGTTCTCTCGTGAATCTGCA	0.512													G|||	707	0.141174	0.1868	0.147	5008	,	,		24279	0.0248		0.2247	False		,,,				2504	0.1094				p.H1152H	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C3456T						PASS	.	G	,	722,3674	300.7+/-286.5	66,590,1542	100.0	90.0	94.0		3165,3456	1.8	1.0	16	dbSNP_120	94	1862,6738	333.3+/-320.5	189,1484,2627	no	coding-synonymous,coding-synonymous	SALL1	NM_001127892.1,NM_002968.2	,	255,2074,4169	AA,AG,GG		21.6512,16.424,19.883	,	1055/1228,1152/1325	51172677	2584,10412	2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			TCTCTCGTGAATC	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3456C>T	16.37:g.51172677G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	194	89	0.458763	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																			G|0.822;A|0.178	0.178	strong		0.512	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
DDX20	11218	hgsc.bcm.edu	37	1	112298582	112298582	+	Silent	SNP	A	A	G	rs197392	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:112298582A>G	ENST00000369702.4	+	1	656	c.36A>G	c.(34-36)gcA>gcG	p.A12A	FAM212B_ENST00000412270.1_5'Flank|DDX20_ENST00000536167.1_Silent_p.A12A|FAM212B_ENST00000444059.2_5'Flank	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	12					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAGCCTTAGCAGCAGTGGCGA	0.662													g|||	1214	0.242412	0.5666	0.147	5008	,	,		11743	0.0367		0.1978	False		,,,				2504	0.1299				p.A12A		Atlas-SNP	.											DDX20,NS,carcinoma,0,1	DDX20	50	1	0			c.A36G						scavenged	.			1915,2403		428,1059,672	12.0	13.0	13.0		36	-5.7	0.0	1	dbSNP_79	13	1610,6958		184,1242,2858	no	coding-synonymous	DDX20	NM_007204.4		612,2301,3530	GG,GA,AA		18.7908,44.3492,27.3553		12/825	112298582	3525,9361	2159	4284	6443	SO:0001819	synonymous_variant	11218	exon1			CTTAGCAGCAGTG	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.36A>G	1.37:g.112298582A>G		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	239	109	0.456067	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Silent	SNP	ENST00000369702.4	37	CCDS842.1																																																																																			A|0.755;G|0.245	0.245	strong		0.662	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
PLXNA2	5362	hgsc.bcm.edu	37	1	208391085	208391085	+	Silent	SNP	G	G	A	rs12120681	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:208391085G>A	ENST00000367033.3	-	2	940	c.183C>T	c.(181-183)gcC>gcT	p.A61A		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	61	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CCACATAGACGGCCCCCGTCC	0.582													G|||	413	0.0824681	0.0129	0.1412	5008	,	,		18311	0.0159		0.159	False		,,,				2504	0.1247				p.A61A		Atlas-SNP	.											PLXNA2,colon,carcinoma,-1,1	PLXNA2	178	1	0			c.C183T						PASS	.	G		197,4209	122.9+/-160.3	6,185,2012	105.0	101.0	102.0		183	-11.7	0.1	1	dbSNP_120	102	1434,7166	275.4+/-291.8	120,1194,2986	no	coding-synonymous	PLXNA2	NM_025179.3		126,1379,4998	AA,AG,GG		16.6744,4.4712,12.5404		61/1895	208391085	1631,11375	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon2			ATAGACGGCCCCC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.183C>T	1.37:g.208391085G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	263	138	0.524715	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			G|0.894;A|0.106	0.106	strong		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
OR2D3	120775	hgsc.bcm.edu	37	11	6942695	6942695	+	Missense_Mutation	SNP	C	C	T	rs12806437	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6942695C>T	ENST00000317834.3	+	1	491	c.463C>T	c.(463-465)Cgg>Tgg	p.R155W		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	155			R -> W (in dbSNP:rs12806437). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R155W(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATGACACAACGGGTGTGTCT	0.532													C|||	856	0.170927	0.0408	0.17	5008	,	,		19587	0.2143		0.1581	False		,,,				2504	0.316				p.R155W		Atlas-SNP	.											OR2D3,NS,carcinoma,0,1	OR2D3	51	1	1	Substitution - Missense(1)	stomach(1)	c.C463T						PASS	.	C	TRP/ARG	306,4096	165.8+/-197.2	5,296,1900	141.0	122.0	129.0		463	-3.0	0.0	11	dbSNP_121	129	1532,7060	290.5+/-299.9	130,1272,2894	yes	missense	OR2D3	NM_001004684.1	101	135,1568,4794	TT,TC,CC		17.8305,6.9514,14.145	benign	155/331	6942695	1838,11156	2201	4296	6497	SO:0001583	missense	120775	exon1			ACACAACGGGTGT	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"""GPCR / Class A : Olfactory receptors"""	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.463C>T	11.37:g.6942695C>T	ENSP00000320560:p.Arg155Trp	Somatic	283	1	0.00353357		WXS	Illumina HiSeq	Phase_I	328	170	0.518293	NM_001004684	B2RP06|Q6IFG8|Q96R51	Missense_Mutation	SNP	ENST00000317834.3	37	CCDS31417.1	321	0.14697802197802198	22	0.044715447154471545	59	0.16298342541436464	115	0.20104895104895104	125	0.16490765171503957	C	3.804	-0.041195	0.07452	0.069514	0.178305	ENSG00000178358	ENST00000317834	T	0.00949	5.51	5.17	-2.95	0.05564	GPCR, rhodopsin-like superfamily (1);	2.457810	0.02011	N	0.047015	T	0.00012	0.0000	L	0.56280	1.765	0.80722	P	0.0	B	0.26845	0.161	B	0.24269	0.052	T	0.44590	-0.9318	9	0.36615	T	0.2	-0.698	4.0012	0.09580	0.3231:0.2905:0.0:0.3864	rs12806437;rs52811082;rs59333628;rs12806437	155	Q8NGH3	OR2D3_HUMAN	W	155	ENSP00000320560:R155W	ENSP00000320560:R155W	R	+	1	2	OR2D3	6899271	0.000000	0.05858	0.000000	0.03702	0.061000	0.15899	-0.952000	0.03881	-0.292000	0.08999	0.655000	0.94253	CGG	C|0.859;T|0.141	0.141	strong		0.532	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
BEST1	7439	hgsc.bcm.edu	37	11	61722645	61722645	+	Silent	SNP	C	C	A	rs1109748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61722645C>A	ENST00000378043.4	+	3	862	c.219C>A	c.(217-219)atC>atA	p.I73I	BEST1_ENST00000526988.1_5'UTR|BEST1_ENST00000449131.2_Silent_p.I13I|BEST1_ENST00000534553.1_5'UTR|BEST1_ENST00000301774.9_5'UTR|BEST1_ENST00000378042.3_Silent_p.I13I|BEST1_ENST00000435278.2_Silent_p.I73I	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	73			I -> N (in VMD2). {ECO:0000269|PubMed:11241846}.		chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						ACAGCTACATCCAGCTCATCC	0.602													C|||	1590	0.317492	0.0825	0.2839	5008	,	,		13980	0.6498		0.0726	False		,,,				2504	0.5685				p.I73I		Atlas-SNP	.											.	BEST1	85	.	0			c.C219A						PASS	.	C	,	366,4038	187.1+/-213.8	19,328,1855	187.0	155.0	166.0	http://www.ncbi.nlm.nih.gov/pubmed?term	39,219	3.9	1.0	11	dbSNP_86	166	629,7969	162.0+/-214.8	30,569,3700	no	coding-synonymous,coding-synonymous	BEST1	NM_001139443.1,NM_004183.3	,	49,897,5555	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	7.3157,8.3106,7.6527	,	13/605,73/586	61722645	995,12007	2202	4299	6501	SO:0001819	synonymous_variant	7439	exon3			CTACATCCAGCTC	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.219C>A	11.37:g.61722645C>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	153	69	0.45098	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			C|0.838;A|0.162	0.162	strong		0.602	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
MUC20	200958	hgsc.bcm.edu	37	3	195453406	195453406	+	Silent	SNP	G	G	C	rs3210209	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:195453406G>C	ENST00000447234.2	+	2	2058	c.1932G>C	c.(1930-1932)acG>acC	p.T644T	MUC20_ENST00000445522.2_Silent_p.T609T|MUC20_ENST00000436408.1_Silent_p.T644T|MUC20_ENST00000320736.6_Silent_p.T473T	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	644	Involved in oligomerization.|Thr-rich.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CCACGCCCACGACTGCCCGGA	0.607																																					p.T473T		Atlas-SNP	.											MUC20_ENST00000381954,NS,carcinoma,0,2	MUC20	84	2	0			c.G1419C						PASS	.						95.0	104.0	101.0					3																	195453406		2094	4219	6313	SO:0001819	synonymous_variant	200958	exon3			GCCCACGACTGCC	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1932G>C	3.37:g.195453406G>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	28	0.321839	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Silent	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	C	3.515	-0.099070	0.07010	.	.	ENSG00000176945	ENST00000423938	.	.	.	4.94	0.0954	0.14485	.	.	.	.	.	T	0.20210	0.0486	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.22208	-1.0223	4	.	.	.	-0.7226	1.1024	0.01687	0.1592:0.4292:0.1556:0.2559	rs3210209;rs3828404;rs9871135;rs17414553	.	.	.	H	56	.	.	D	+	1	0	MUC20	196939077	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.296000	0.08287	0.094000	0.17404	-0.123000	0.14984	GAC	G|0.915;C|0.085	0.085	strong		0.607	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
FAM118A	55007	hgsc.bcm.edu	37	22	45723842	45723842	+	Silent	SNP	G	G	A	rs17851057	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:45723842G>A	ENST00000216214.3	+	5	1254	c.420G>A	c.(418-420)agG>agA	p.R140R	FAM118A_ENST00000441876.2_Silent_p.R140R|FAM118A_ENST00000405673.1_Silent_p.R140R|FAM118A_ENST00000405548.3_5'Flank	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	140						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TGATGGACAGGGGCGCCATGG	0.597													G|||	2686	0.536342	0.851	0.4006	5008	,	,		18320	0.5268		0.2932	False		,,,				2504	0.4673				p.R140R		Atlas-SNP	.											.	FAM118A	32	.	0			c.G420A						PASS	.	G	,	3316,1090	717.8+/-408.8	1258,800,145	58.0	48.0	52.0		420,420	-0.2	0.9	22	dbSNP_123	52	2444,6156	402.6+/-347.5	354,1736,2210	no	coding-synonymous,coding-synonymous	FAM118A	NM_001104595.1,NM_017911.2	,	1612,2536,2355	AA,AG,GG		28.4186,24.739,44.2873	,	140/358,140/358	45723842	5760,7246	2203	4300	6503	SO:0001819	synonymous_variant	55007	exon4			GGACAGGGGCGCC	BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 8"""	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.420G>A	22.37:g.45723842G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	168	98	0.583333	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Silent	SNP	ENST00000216214.3	37	CCDS14065.1																																																																																			G|0.539;A|0.461	0.461	strong		0.597	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
RNF175	285533	hgsc.bcm.edu	37	4	154644537	154644537	+	Missense_Mutation	SNP	T	T	C	rs10517577	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:154644537T>C	ENST00000347063.4	-	5	847	c.475A>G	c.(475-477)Atg>Gtg	p.M159V	RP11-153M7.5_ENST00000505051.1_RNA|RNF175_ENST00000506505.1_5'UTR|RNF175_ENST00000274068.4_Missense_Mutation_p.M31V	NM_173662.2	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	159			M -> V (in dbSNP:rs10517577).			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	13	all_hematologic(180;0.093)	Renal(120;0.118)				ATTGTAAACATGATCGCCAAG	0.388													T|||	467	0.0932508	0.0053	0.1628	5008	,	,		16695	0.004		0.2247	False		,,,				2504	0.1196				p.M159V		Atlas-SNP	.											.	RNF175	40	.	0			c.A475G						PASS	.	T	VAL/MET	160,3704		4,152,1776	100.0	86.0	90.0		475	0.7	1.0	4	dbSNP_119	90	1923,6345		194,1535,2405	yes	missense	RNF175	NM_173662.2	21	198,1687,4181	CC,CT,TT		23.2583,4.1408,17.1695	benign	159/329	154644537	2083,10049	1932	4134	6066	SO:0001583	missense	285533	exon5			TAAACATGATCGC	BC034385	CCDS47149.1	4q31.3	2008-02-05			ENSG00000145428	ENSG00000145428		"""RING-type (C3HC4) zinc fingers"""	27735	protein-coding gene	gene with protein product							Standard	NM_173662		Approved	FLJ34190	uc003int.3	Q8N4F7	OTTHUMG00000161557	ENST00000347063.4:c.475A>G	4.37:g.154644537T>C	ENSP00000340979:p.Met159Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	147	75	0.510204	NM_173662	C9JL66|Q8NB61	Missense_Mutation	SNP	ENST00000347063.4	37	CCDS47149.1	245	0.11217948717948718	2	0.0040650406504065045	61	0.1685082872928177	1	0.0017482517482517483	181	0.23878627968337732	T	13.82	2.350213	0.41599	0.041408	0.232583	ENSG00000145428	ENST00000347063;ENST00000274068;ENST00000508248	T;T;T	0.77229	-1.08;-1.08;-1.08	4.34	0.707	0.18139	.	0.198777	0.49916	N	0.000139	T	0.00039	0.0001	L	0.55481	1.735	0.25431	P	0.9881882	P;B	0.36683	0.565;0.002	B;B	0.36335	0.222;0.008	T	0.01894	-1.1252	9	0.30854	T	0.27	-5.8208	7.4098	0.27011	0.0:0.2644:0.0:0.7356	rs10517577;rs17370896;rs52808550;rs57008646;rs10517577	31;159	Q8NB61;Q8N4F7	.;RN175_HUMAN	V	159;31;99	ENSP00000340979:M159V;ENSP00000274068:M31V;ENSP00000427472:M99V	ENSP00000274068:M31V	M	-	1	0	RNF175	154863987	1.000000	0.71417	0.996000	0.52242	0.935000	0.57460	3.291000	0.51764	0.136000	0.18733	0.455000	0.32223	ATG	T|0.917;C|0.083	0.083	strong		0.388	RNF175-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365286.1	NM_173662	
CASQ2	845	hgsc.bcm.edu	37	1	116243877	116243877	+	Silent	SNP	G	G	A	rs7413162|rs397516641	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:116243877G>A	ENST00000261448.5	-	11	1424	c.1185C>T	c.(1183-1185)gaC>gaT	p.D395D	CASQ2_ENST00000456138.2_Silent_p.D324D	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	395	Asp/Glu-rich (acidic).				cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		catcatcatcgtcatcactgt	0.398													A|||	2132	0.425719	0.4599	0.464	5008	,	,		23773	0.3224		0.4135	False		,,,				2504	0.4714				p.D395D		Atlas-SNP	.											.	CASQ2	54	.	0			c.C1185T						PASS	.	A		1973,2433	619.6+/-393.4	458,1057,688	231.0	197.0	208.0		1185	-9.6	0.5	1	dbSNP_116	208	3073,5527	660.2+/-401.7	565,1943,1792	no	coding-synonymous	CASQ2	NM_001232.3		1023,3000,2480	AA,AG,GG		35.7326,44.7798,38.7975		395/400	116243877	5046,7960	2203	4300	6503	SO:0001819	synonymous_variant	845	exon11			ATCATCGTCATCA	BC022288	CCDS884.1	1p13.1	2014-09-17			ENSG00000118729	ENSG00000118729		"""Protein disulfide isomerases"""	1513	protein-coding gene	gene with protein product		114251				8406504	Standard	NM_001232		Approved	PDIB2	uc001efx.4	O14958	OTTHUMG00000011970	ENST00000261448.5:c.1185C>T	1.37:g.116243877G>A		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	342	342	1	NM_001232	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Silent	SNP	ENST00000261448.5	37	CCDS884.1																																																																																			G|0.586;A|0.414	0.414	strong		0.398	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232	
OR2T6	254879	hgsc.bcm.edu	37	1	248550970	248550970	+	Missense_Mutation	SNP	A	A	G	rs7417616	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248550970A>G	ENST00000355728.2	+	1	61	c.61A>G	c.(61-63)Aat>Gat	p.N21D		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	21			N -> D (in dbSNP:rs7417616).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTTCACTCACAATAAATGCTC	0.433													g|||	1890	0.377396	0.5234	0.3156	5008	,	,		15093	0.4375		0.1769	False		,,,				2504	0.3681				p.N21D		Atlas-SNP	.											.	OR2T6	101	.	0			c.A61G						PASS	.	G	ASP/ASN	2003,2403	615.1+/-392.5	466,1071,666	148.0	142.0	144.0		61	-6.2	0.0	1	dbSNP_116	144	1299,7301	758.8+/-407.5	92,1115,3093	yes	missense	OR2T6	NM_001005471.1	23	558,2186,3759	GG,GA,AA		15.1047,45.4607,25.3883	benign	21/309	248550970	3302,9704	2203	4300	6503	SO:0001583	missense	254879	exon1			ACTCACAATAAAT	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"""GPCR / Class A : Olfactory receptors"""	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.61A>G	1.37:g.248550970A>G	ENSP00000347965:p.Asn21Asp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_001005471	A6NE36	Missense_Mutation	SNP	ENST00000355728.2	37	CCDS31114.1	744	0.34065934065934067	262	0.532520325203252	96	0.26519337016574585	243	0.42482517482517484	143	0.18865435356200527	G	11.81	1.749870	0.30955	0.454607	0.151047	ENSG00000198104	ENST00000355728	T	0.02974	4.09	4.48	-6.15	0.02105	.	1.525930	0.03801	N	0.264518	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41070	-0.9529	9	0.62326	D	0.03	.	4.0254	0.09685	0.4105:0.1039:0.3836:0.102	rs7417616;rs60973717;rs7417616	21	Q8NHC8	OR2T6_HUMAN	D	21	ENSP00000347965:N21D	ENSP00000347965:N21D	N	+	1	0	OR2T6	246617593	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-3.757000	0.00374	-1.171000	0.02765	-1.555000	0.00892	AAT	A|0.702;G|0.298	0.298	strong		0.433	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471	
CELF4	56853	hgsc.bcm.edu	37	18	34850846	34850846	+	Silent	SNP	G	G	A	rs1443638	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:34850846G>A	ENST00000591282.1	-	8	983	c.984C>T	c.(982-984)gcC>gcT	p.A328A	CELF4_ENST00000361795.5_Silent_p.A326A|CELF4_ENST00000601019.1_Silent_p.A326A|CELF4_ENST00000412753.1_Silent_p.A327A|CELF4_ENST00000420428.2_Silent_p.A328A|CELF4_ENST00000591287.1_Silent_p.A327A|CELF4_ENST00000588597.1_Silent_p.A317A|CELF4_ENST00000603232.1_Silent_p.A327A|CELF4_ENST00000334919.5_Silent_p.A318A|RP11-797E24.3_ENST00000588766.1_RNA			Q9BZC1	CELF4_HUMAN	CUGBP, Elav-like family member 4	328					alternative mRNA splicing, via spliceosome (GO:0000380)|embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA splice site selection (GO:0006376)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of translation (GO:0017148)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	44						TGCTAGGCACGGCTGGTGCAG	0.632													G|||	1079	0.215455	0.1324	0.17	5008	,	,		18519	0.2272		0.3529	False		,,,				2504	0.2065				p.A328A		Atlas-SNP	.											.	CELF4	90	.	0			c.C984T						PASS	.	G	,,,	818,3588	320.2+/-296.5	79,660,1464	39.0	34.0	36.0		981,978,954,984	-4.0	1.0	18	dbSNP_88	36	3152,5448	474.8+/-368.9	589,1974,1737	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CELF4	NM_001025087.1,NM_001025088.1,NM_001025089.1,NM_020180.3	,,,	668,2634,3201	AA,AG,GG		36.6512,18.5656,30.5244	,,,	327/486,326/485,318/449,328/487	34850846	3970,9036	2203	4300	6503	SO:0001819	synonymous_variant	56853	exon8			AGGCACGGCTGGT	AF248651	CCDS32818.1, CCDS45857.1, CCDS45858.1	18q12	2013-02-12	2010-02-19	2010-02-19				"""RNA binding motif (RRM) containing"""	14015	protein-coding gene	gene with protein product		612679	"""Bruno (Drosophila) -like 4, RNA binding protein"", ""bruno-like 4, RNA binding protein (Drosophila)"""	BRUNOL4		10893231	Standard	NM_020180		Approved		uc002lae.2	Q9BZC1		ENST00000591282.1:c.984C>T	18.37:g.34850846G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_020180	Q59EN7|Q86XB9|Q8N2M6|Q9BQ96|Q9NR84|Q9NR85	Silent	SNP	ENST00000591282.1	37	CCDS32818.1	535	0.24496336996336995	61	0.12398373983739837	71	0.19613259668508287	130	0.22727272727272727	273	0.36015831134564646	G	9.731	1.162181	0.21538	0.185656	0.366512	ENSG00000101489	ENST00000361683	.	.	.	4.66	-3.97	0.04094	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999956	.	.	.	.	.	.	T	0.39761	-0.9598	4	0.62326	D	0.03	-9.1122	13.6895	0.62537	0.7368:0.0:0.2632:0.0	rs1443638;rs52790871;rs59351053;rs1443638	.	.	.	C	211	.	ENSP00000355189:R211C	R	-	1	0	CELF4	33104844	0.169000	0.23002	0.977000	0.42913	0.946000	0.59487	-0.355000	0.07671	-0.730000	0.04869	-1.031000	0.02408	CGT	G|0.726;A|0.274	0.274	strong		0.632	CELF4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440892.1	NM_020180	
ZNF229	7772	hgsc.bcm.edu	37	19	44934653	44934653	+	Silent	SNP	T	T	C	rs8113370	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:44934653T>C	ENST00000588931.1	-	6	736	c.303A>G	c.(301-303)aaA>aaG	p.K101K	ZNF229_ENST00000291187.4_Silent_p.K95K|CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	101	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				AGGAGAGCTCTTTGTGTGAAA	0.413													T|||	817	0.163139	0.1906	0.3228	5008	,	,		20023	0.1558		0.1074	False		,,,				2504	0.0777				p.K101K		Atlas-SNP	.											.	ZNF229	123	.	0			c.A303G						PASS	.	T		625,3057		51,523,1267	61.0	58.0	59.0		303	0.9	0.0	19	dbSNP_116	59	905,7281		54,797,3242	no	coding-synonymous	ZNF229	NM_014518.2		105,1320,4509	CC,CT,TT		11.0555,16.9745,12.8918		101/826	44934653	1530,10338	1841	4093	5934	SO:0001819	synonymous_variant	7772	exon6			GAGCTCTTTGTGT	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.303A>G	19.37:g.44934653T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	114	61	0.535088	NM_014518	B2RWN3|Q59FV2|Q86WL9	Silent	SNP	ENST00000588931.1	37	CCDS42574.1																																																																																			T|0.846;C|0.154	0.154	strong		0.413	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
RBM19	9904	hgsc.bcm.edu	37	12	114386639	114386639	+	Splice_Site	SNP	A	A	G	rs7966348|rs17849837	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:114386639A>G	ENST00000545145.2	-	10	1353	c.1275T>C	c.(1273-1275)taT>taC	p.Y425Y	RBM19_ENST00000261741.5_Splice_Site_p.Y425Y|RBM19_ENST00000392561.3_Splice_Site_p.Y425Y	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	425	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Y425Y(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					CACCCCTACCATATTTGGAGA	0.607													G|||	992	0.198083	0.3457	0.0764	5008	,	,		18272	0.1885		0.1133	False		,,,				2504	0.182				p.Y425Y		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - coding silent(1)	stomach(1)	c.T1275C						PASS	.	G	,,	1441,2965	683.3+/-404.2	253,935,1015	76.0	66.0	69.0		1275,1275,1275	0.8	0.8	12	dbSNP_116	69	887,7713	778.8+/-407.7	38,811,3451	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	291,1746,4466	GG,GA,AA		10.314,32.7054,17.8994	,,	425/961,425/961,425/961	114386639	2328,10678	2203	4300	6503	SO:0001630	splice_region_variant	9904	exon10			CCTACCATATTTG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1276+1T>C	12.37:g.114386639A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			A|0.823;G|0.177	0.177	strong		0.607	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	Silent
HKR1	284459	hgsc.bcm.edu	37	19	37854235	37854235	+	Missense_Mutation	SNP	G	G	T	rs3745765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:37854235G>T	ENST00000324411.4	+	6	1807	c.1538G>T	c.(1537-1539)aGc>aTc	p.S513I	HKR1_ENST00000591471.1_Missense_Mutation_p.S240I|HKR1_ENST00000392153.3_Missense_Mutation_p.S494I|HKR1_ENST00000544914.1_Missense_Mutation_p.S240I|HKR1_ENST00000589392.1_Missense_Mutation_p.S495I|HKR1_ENST00000591134.1_Intron|HKR1_ENST00000541583.2_Missense_Mutation_p.S452I	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	513			S -> I (in dbSNP:rs3745765). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9813242}.		multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCAACCCTGAGCACGCACCAG	0.512													T|||	1739	0.347244	0.534	0.2695	5008	,	,		21012	0.2986		0.159	False		,,,				2504	0.3937				p.S513I		Atlas-SNP	.											.	HKR1	74	.	0			c.G1538T						PASS	.	T	ILE/SER	2120,2286	600.6+/-389.5	515,1090,598	77.0	73.0	74.0		1538	1.5	0.6	19	dbSNP_107	74	1466,7134	750.0+/-407.4	139,1188,2973	yes	missense	HKR1	NM_181786.2	142	654,2278,3571	TT,TG,GG		17.0465,48.1162,27.5719	benign	513/660	37854235	3586,9420	2203	4300	6503	SO:0001583	missense	284459	exon6			CCCTGAGCACGCA	M20675	CCDS12502.1	19q13.13	2013-01-08	2010-05-04			ENSG00000181666		"""Zinc fingers, C2H2-type"", ""-"""	4928	protein-coding gene	gene with protein product	"""oncogene HKR1"""	165250	"""GLI-Kruppel family member HKR1"""			2850480, 9813242	Standard	NM_181786		Approved	ZNF875	uc002ogb.3	P10072		ENST00000324411.4:c.1538G>T	19.37:g.37854235G>T	ENSP00000315505:p.Ser513Ile	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_181786	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Missense_Mutation	SNP	ENST00000324411.4	37	CCDS12502.1	677	0.309981684981685	260	0.5284552845528455	109	0.3011049723756906	189	0.3304195804195804	119	0.15699208443271767	T	0.006	-2.050625	0.00394	0.481162	0.170465	ENSG00000181666	ENST00000544914;ENST00000414402;ENST00000392153;ENST00000542144;ENST00000324411;ENST00000541583	T;T;T;T	0.20069	2.38;2.1;2.1;2.1	2.58	1.52	0.23074	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.02985	-0.445	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.09377	0.002;0.002;0.004;0.0	T	0.46275	-0.9203	8	0.02654	T	1	.	4.178	0.10362	0.351:0.0:0.1804:0.4686	rs3745765;rs52831370;rs57747062;rs3745765	452;494;513;495	Q7Z6E1;P10072-2;P10072;B4DSY3	.;.;HKR1_HUMAN;.	I	240;292;494;549;513;452	ENSP00000437774:S240I;ENSP00000375994:S494I;ENSP00000315505:S513I;ENSP00000438261:S452I	ENSP00000315505:S513I	S	+	2	0	HKR1	42546075	0.000000	0.05858	0.625000	0.29200	0.782000	0.44232	-1.475000	0.02335	0.004000	0.14682	-1.198000	0.01671	AGC	G|0.704;T|0.296	0.296	strong		0.512	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786	
CACNA1G	8913	hgsc.bcm.edu	37	17	48703986	48703986	+	Silent	SNP	G	G	A	rs9893223	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48703986G>A	ENST00000359106.5	+	38	7008	c.7008G>A	c.(7006-7008)ccG>ccA	p.P2336P	CACNA1G_ENST00000354983.4_Silent_p.P2302P|CACNA1G_ENST00000515411.1_Silent_p.P2273P|CACNA1G_ENST00000514717.1_Silent_p.P2186P|CACNA1G_ENST00000507336.1_Silent_p.P2325P|CACNA1G_ENST00000515765.1_Silent_p.P2280P|CACNA1G_ENST00000515165.1_Silent_p.P2243P|CACNA1G_ENST00000514079.1_Silent_p.P2250P|CACNA1G_ENST00000513689.2_Silent_p.P2246P|CACNA1G_ENST00000507609.1_Silent_p.P2236P|CACNA1G_ENST00000502264.1_Silent_p.P2265P|CACNA1G_ENST00000505165.1_Silent_p.P2164P|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000360761.4_Silent_p.P2220P|CACNA1G_ENST00000514181.1_Silent_p.P2218P|CACNA1G_ENST00000510366.1_Silent_p.P2191P|CACNA1G_ENST00000513964.1_Silent_p.P2198P|CACNA1G_ENST00000352832.5_Silent_p.P2209P|CACNA1G_ENST00000512389.1_Silent_p.P2232P|CACNA1G_ENST00000503485.1_Silent_p.P2209P|CACNA1G_ENST00000358244.5_Silent_p.P2130P|CACNA1G_ENST00000442258.2_Silent_p.P2202P|CACNA1G_ENST00000507896.1_Silent_p.P2153P|CACNA1G_ENST00000510115.1_Silent_p.P2257P|CACNA1G_ENST00000429973.2_Silent_p.P2225P|CACNA1G_ENST00000507510.2_Silent_p.P2291P	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2336					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GGAGGGCTCCGTCCAGCGACT	0.622											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	965	0.192692	0.3858	0.1369	5008	,	,		14554	0.0813		0.0557	False		,,,				2504	0.227				p.P2336P		Atlas-SNP	.											CACNA1G_ENST00000359106,NS,carcinoma,0,6	CACNA1G	659	6	0			c.G7008A						PASS	.	G	,,,,,,,,,,,,,	1251,2609		202,847,881	27.0	32.0	30.0		7008,6390,6939,6696,6771,6840,6660,6795,6729,6873,6675,6627,6606,6906	-8.3	0.2	17	dbSNP_119	30	423,7815		13,397,3709	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1G	NM_018896.3,NM_198376.1,NM_198377.1,NM_198378.1,NM_198379.1,NM_198380.1,NM_198382.1,NM_198383.1,NM_198384.1,NM_198385.1,NM_198386.1,NM_198387.1,NM_198388.1,NM_198396.1	,,,,,,,,,,,,,	215,1244,4590	AA,AG,GG		5.1347,32.4093,13.837	,,,,,,,,,,,,,	2336/2378,2130/2172,2313/2355,2232/2274,2257/2299,2280/2322,2220/2262,2265/2307,2243/2285,2291/2333,2225/2267,2209/2251,2202/2244,2302/2344	48703986	1674,10424	1930	4119	6049	SO:0001819	synonymous_variant	8913	exon38			GGCTCCGTCCAGC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.7008G>A	17.37:g.48703986G>A		Somatic	87	0	0	956	WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	CCDS45730.1																																																																																			G|0.876;A|0.124	0.124	strong		0.622	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194827	18194827	+	Missense_Mutation	SNP	C	C	G	rs2468774	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18194827C>G	ENST00000314254.3	+	1	444	c.24C>G	c.(22-24)ttC>ttG	p.F8L	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	8			F -> L (in dbSNP:rs2468774). {ECO:0000269|PubMed:11850634}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						TCCCAGTCTTCGGTACAAAAC	0.522													G|||	1654	0.330272	0.2549	0.3415	5008	,	,		19349	0.4395		0.3062	False		,,,				2504	0.3364				p.F8L		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.C24G						PASS	.	G	LEU/PHE	1080,3318	721.3+/-409.2	130,820,1249	164.0	155.0	158.0		24	1.5	0.0	11	dbSNP_100	158	2449,6137	695.9+/-404.8	338,1773,2182	no	missense	MRGPRX4	NM_054032.3	22	468,2593,3431	GG,GC,CC		28.5232,24.5566,27.1796	benign	8/323	18194827	3529,9455	2199	4293	6492	SO:0001583	missense	117196	exon1			AGTCTTCGGTACA	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.24C>G	11.37:g.18194827C>G	ENSP00000314042:p.Phe8Leu	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	37	CCDS7831.1	750	0.3434065934065934	114	0.23170731707317074	120	0.3314917127071823	275	0.4807692307692308	241	0.3179419525065963	G	1.256	-0.617153	0.03663	0.245566	0.285232	ENSG00000179817	ENST00000314254	T	0.16324	2.35	2.42	1.49	0.22878	.	1.996180	0.02024	N	0.048015	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45190	-0.9278	9	0.09590	T	0.72	.	3.8504	0.08953	0.152:0.2516:0.5964:0.0	rs2468774;rs16934999;rs52794849;rs2468774	8	Q96LA9	MRGX4_HUMAN	L	8	ENSP00000314042:F8L	ENSP00000314042:F8L	F	+	3	2	MRGPRX4	18151403	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.053000	0.14184	0.135000	0.18707	-1.305000	0.01319	TTC	C|0.699;G|0.301	0.301	strong		0.522	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39190954	39190954	+	Silent	SNP	G	G	A	rs71300033|rs75033421		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39190954G>A	ENST00000344363.5	-	1	153	c.120C>T	c.(118-120)tgC>tgT	p.C40C		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	40						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCTGGTCTGGCAGCAGCTTG	0.607																																					p.C40C		Atlas-SNP	.											.	KRTAP1-3	18	.	0			c.C120T						PASS	.						44.0	52.0	49.0					17																	39190954		1969	4174	6143	SO:0001819	synonymous_variant	81850	exon1			GGTCTGGCAGCAG	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"""Keratin associated proteins"""	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.120C>T	17.37:g.39190954G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	179	31	0.173184	NM_030966	Q07628|Q8IUG0|Q9BYS2	Silent	SNP	ENST00000344363.5	37	CCDS42323.1																																																																																			A|1.000;|0.000	1.000	weak		0.607	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1		
PARP1	142	hgsc.bcm.edu	37	1	226589958	226589958	+	Silent	SNP	G	G	A	rs1805404	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:226589958G>A	ENST00000366794.5	-	2	386	c.243C>T	c.(241-243)gaC>gaT	p.D81D	PARP1_ENST00000366792.1_Silent_p.D81D|PARP1_ENST00000366791.5_Silent_p.D81D|PARP1_ENST00000366790.3_Silent_p.D81D	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	81					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CTTTCTGCTGGTCATCCCACC	0.587								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					G|||	1093	0.218251	0.115	0.3573	5008	,	,		18540	0.4365		0.1541	False		,,,				2504	0.1002				p.D81D		Atlas-SNP	.											PARP1,colon,carcinoma,-1,1	PARP1	100	1	0			c.C243T						PASS	.	G		553,3853	250.3+/-257.4	37,479,1687	102.0	88.0	93.0		243	3.3	1.0	1	dbSNP_92	93	1368,7232	267.2+/-287.2	124,1120,3056	no	coding-synonymous	PARP1	NM_001618.3		161,1599,4743	AA,AG,GG		15.907,12.5511,14.7701		81/1015	226589958	1921,11085	2203	4300	6503	SO:0001819	synonymous_variant	142	exon2			CTGCTGGTCATCC	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.243C>T	1.37:g.226589958G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_001618	B1ANJ4|Q8IUZ9	Silent	SNP	ENST00000366794.5	37	CCDS1554.1																																																																																			G|0.811;A|0.189	0.189	strong		0.587	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
PKD1	5310	hgsc.bcm.edu	37	16	2164294	2164294	+	Silent	SNP	G	G	A	rs35965348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2164294G>A	ENST00000262304.4	-	11	2938	c.2730C>T	c.(2728-2730)gaC>gaT	p.D910D	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Silent_p.D910D	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	910	PKD 3. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CCACCACCACGTCCACCACGT	0.697													g|||	145	0.0289537	0.0015	0.036	5008	,	,		15926	0.0		0.0716	False		,,,				2504	0.047				p.D910D		Atlas-SNP	.											.	PKD1	184	.	0			c.C2730T						PASS	.	G	,	61,4321	56.2+/-92.4	0,61,2130	34.0	28.0	30.0		2730,2730	0.2	0.6	16	dbSNP_126	30	630,7958	156.7+/-210.5	25,580,3689	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	25,641,5819	AA,AG,GG		7.3358,1.3921,5.3277	,	910/4303,910/4304	2164294	691,12279	2191	4294	6485	SO:0001819	synonymous_variant	5310	exon11			CACCACGTCCACC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.2730C>T	16.37:g.2164294G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			G|0.950;A|0.050	0.050	strong		0.697	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
MPHOSPH9	10198	hgsc.bcm.edu	37	12	123664514	123664514	+	Silent	SNP	G	G	A	rs1727301	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:123664514G>A	ENST00000606320.1	-	15	2519	c.2313C>T	c.(2311-2313)aaC>aaT	p.N771N	MPHOSPH9_ENST00000302349.5_Silent_p.N619N|MPHOSPH9_ENST00000541076.2_Silent_p.N741N|MPHOSPH9_ENST00000392425.3_Silent_p.N619N			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	771						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		CAAGCAATTTGTTCTCAGTTG	0.269													G|||	1970	0.393371	0.0234	0.4179	5008	,	,		19244	0.6855		0.3956	False		,,,				2504	0.5726				p.N619N		Atlas-SNP	.											.	MPHOSPH9	75	.	0			c.C1857T						PASS	.	G		353,4041	177.6+/-206.5	17,319,1861	72.0	66.0	68.0		1857	2.7	1.0	12	dbSNP_89	68	3226,5366	474.7+/-368.9	587,2052,1657	no	coding-synonymous	MPHOSPH9	NM_022782.2		604,2371,3518	AA,AG,GG		37.5466,8.0337,27.5604		619/1032	123664514	3579,9407	2197	4296	6493	SO:0001819	synonymous_variant	10198	exon11			CAATTTGTTCTCA	X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.2313C>T	12.37:g.123664514G>A		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	224	109	0.486607	NM_022782	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	Silent	SNP	ENST00000606320.1	37																																																																																				G|0.666;A|0.334	0.334	strong		0.269	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2		
TULP4	56995	hgsc.bcm.edu	37	6	158924595	158924595	+	Silent	SNP	A	A	G	rs3749853	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:158924595A>G	ENST00000367097.3	+	13	5257	c.3900A>G	c.(3898-3900)caA>caG	p.Q1300Q	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	1300					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CCGACCTCCAAAGCCACTTGG	0.612													A|||	726	0.144968	0.1672	0.1037	5008	,	,		16677	0.1389		0.1889	False		,,,				2504	0.1053				p.Q1300Q		Atlas-SNP	.											.	TULP4	137	.	0			c.A3900G						PASS	.	A	,	705,3701	286.9+/-279.0	60,585,1558	55.0	59.0	58.0		,3900	-3.0	1.0	6	dbSNP_107	58	1684,6916	298.2+/-303.8	162,1360,2778	no	intron,coding-synonymous	TULP4	NM_001007466.1,NM_020245.3	,	222,1945,4336	GG,GA,AA		19.5814,16.0009,18.3684	,	,1300/1544	158924595	2389,10617	2203	4300	6503	SO:0001819	synonymous_variant	56995	exon13			CCTCCAAAGCCAC		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.3900A>G	6.37:g.158924595A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	127	54	0.425197	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Silent	SNP	ENST00000367097.3	37	CCDS34561.1																																																																																			A|0.827;G|0.173	0.173	strong		0.612	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
TTC32	130502	hgsc.bcm.edu	37	2	20101487	20101487	+	Silent	SNP	G	G	A	rs2304589	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:20101487G>A	ENST00000333610.3	-	1	260	c.129C>T	c.(127-129)tcC>tcT	p.S43S	TTC32_ENST00000402414.1_Silent_p.S43S|RP11-79O8.1_ENST00000607190.1_lincRNA	NM_001008237.1	NP_001008238.1	Q5I0X7	TTC32_HUMAN	tetratricopeptide repeat domain 32	43										kidney(2)|large_intestine(1)|lung(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTCGTCGCTGGAGGCCGCGC	0.637													g|||	1411	0.281749	0.208	0.2305	5008	,	,		16050	0.4028		0.175	False		,,,				2504	0.4029				p.S43S		Atlas-SNP	.											.	TTC32	13	.	0			c.C129T						PASS	.	A		904,3502	349.8+/-310.5	102,700,1401	57.0	58.0	58.0		129	-8.4	0.0	2	dbSNP_100	58	1392,7208	269.4+/-288.4	127,1138,3035	no	coding-synonymous	TTC32	NM_001008237.1		229,1838,4436	AA,AG,GG		16.186,20.5175,17.6534		43/152	20101487	2296,10710	2203	4300	6503	SO:0001819	synonymous_variant	130502	exon1			GTCGCTGGAGGCC	BC057850	CCDS33151.1	2p24.1	2013-01-10			ENSG00000183891	ENSG00000183891		"""Tetratricopeptide (TTC) repeat domain containing"""	32954	protein-coding gene	gene with protein product							Standard	NM_001008237		Approved		uc002rdg.3	Q5I0X7	OTTHUMG00000151776	ENST00000333610.3:c.129C>T	2.37:g.20101487G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001008237		Silent	SNP	ENST00000333610.3	37	CCDS33151.1																																																																																			G|0.740;A|0.260	0.260	strong		0.637	TTC32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323868.1	NM_001008237	
MAST3	23031	hgsc.bcm.edu	37	19	18234441	18234441	+	Silent	SNP	C	C	T	rs740691	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18234441C>T	ENST00000262811.6	+	7	522	c.522C>T	c.(520-522)caC>caT	p.H174H	MAST3_ENST00000608648.1_3'UTR	NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	174							ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						TGATGAATCACGTGTACCGGG	0.582													T|||	2827	0.564497	0.4425	0.5331	5008	,	,		15958	0.6706		0.504	False		,,,				2504	0.7045				p.H174H		Atlas-SNP	.											.	MAST3	83	.	0			c.C522T						PASS	.	T		1885,2029		469,947,541	42.0	43.0	43.0		522	-9.4	0.0	19	dbSNP_86	43	4406,3866		1208,1990,938	no	coding-synonymous	MAST3	NM_015016.1		1677,2937,1479	TT,TC,CC		46.736,48.1604,48.3752		174/1310	18234441	6291,5895	1957	4136	6093	SO:0001819	synonymous_variant	23031	exon7			GAATCACGTGTAC	AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.522C>T	19.37:g.18234441C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_015016	Q7LDZ8|Q9UPI0	Silent	SNP	ENST00000262811.6	37	CCDS46014.1																																																																																			C|0.468;N|0.000	.	strong		0.582	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150	
PEPD	5184	hgsc.bcm.edu	37	19	33882222	33882222	+	Silent	SNP	G	G	A	rs17569	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:33882222G>A	ENST00000244137.7	-	13	1164	c.1131C>T	c.(1129-1131)caC>caT	p.H377H	PEPD_ENST00000397032.4_Silent_p.H336H|PEPD_ENST00000436370.3_Silent_p.H313H|PEPD_ENST00000591968.1_5'UTR	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	377					cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					CTCCCACGTCGTGCACGTCAA	0.667													G|||	493	0.0984425	0.0068	0.0562	5008	,	,		17793	0.2192		0.1392	False		,,,				2504	0.0859				p.H377H		Atlas-SNP	.											.	PEPD	48	.	0			c.C1131T						PASS	.	G	,,	96,4118		1,94,2012	26.0	31.0	29.0		1131,1008,939	-1.8	1.0	19	dbSNP_63	29	1242,7202		88,1066,3068	no	coding-synonymous,coding-synonymous,coding-synonymous	PEPD	NM_000285.3,NM_001166056.1,NM_001166057.1	,,	89,1160,5080	AA,AG,GG		14.7087,2.2781,10.5704	,,	377/494,336/453,313/430	33882222	1338,11320	2107	4222	6329	SO:0001819	synonymous_variant	5184	exon13			CACGTCGTGCACG	BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"""prolidase"""	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.1131C>T	19.37:g.33882222G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	151	79	0.523179	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Silent	SNP	ENST00000244137.7	37	CCDS42544.1																																																																																			T|0.045;G|0.545;C|0.327;A|0.083	0.083	strong		0.667	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285	
SERHL2	253190	hgsc.bcm.edu	37	22	42970032	42970032	+	Missense_Mutation	SNP	T	T	C	rs137055	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:42970032T>C	ENST00000327678.5	+	12	1018	c.916T>C	c.(916-918)Tgc>Cgc	p.C306R	SERHL2_ENST00000340239.4_3'UTR|RRP7B_ENST00000357802.2_RNA|SERHL2_ENST00000407614.4_Missense_Mutation_p.C126R|SERHL2_ENST00000335879.5_Missense_Mutation_p.C242R	NM_014509.3	NP_055324.2	Q9NQF3	SERHL_HUMAN	serine hydrolase-like 2	0							hydrolase activity (GO:0016787)	p.C306R(1)		breast(1)|endometrium(2)|lung(3)|skin(1)|stomach(1)	8						CTTCTTACAGTGCACACACAT	0.562													.|||	1865	0.372404	0.5265	0.1801	5008	,	,		21842	0.7093		0.1004	False		,,,				2504	0.2331				p.C306R		Atlas-SNP	.											SERHL2,NS,carcinoma,0,1	SERHL2	23	1	1	Substitution - Missense(1)	stomach(1)	c.T916C						PASS	.	T	ARG/CYS	2011,2395	612.7+/-392.0	424,1163,616	139.0	119.0	126.0		916	-0.9	0.0	22	dbSNP_78	126	816,7782	781.9+/-407.6	45,726,3528	no	missense	SERHL2	NM_014509.3	180	469,1889,4144	CC,CT,TT		9.4906,45.6423,21.7395	benign	306/315	42970032	2827,10177	2203	4299	6502	SO:0001583	missense	253190	exon12			TTACAGTGCACAC		CCDS14037.1, CCDS63498.1	22q13	2005-08-09			ENSG00000183569	ENSG00000183569			29446	protein-coding gene	gene with protein product							Standard	NM_014509		Approved		uc003bcr.3	Q9H4I8	OTTHUMG00000150892	ENST00000327678.5:c.916T>C	22.37:g.42970032T>C	ENSP00000331376:p.Cys306Arg	Somatic	485	0	0		WXS	Illumina HiSeq	Phase_I	470	218	0.46383	NM_014509	Q5JZ95|Q9UH21	Missense_Mutation	SNP	ENST00000327678.5	37	CCDS14037.1	795	0.364010989010989	270	0.5487804878048781	66	0.18232044198895028	384	0.6713286713286714	75	0.09894459102902374	C	5.546	0.285594	0.10513	0.456423	0.094906	ENSG00000183569	ENST00000327678;ENST00000356720;ENST00000407614;ENST00000335879	T;T;T	0.41400	2.86;1.0;1.04	4.05	-0.864	0.10666	.	1.070450	0.07397	N	0.890154	T	0.00012	0.0000	N	0.00661	-1.28	0.52099	P	5.999999999994898E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41928	-0.9481	9	0.17369	T	0.5	.	1.1602	0.01804	0.3199:0.3417:0.1963:0.1421	rs137055;rs3201029;rs3747190;rs60116198;rs137055	242;306	Q9H4I8-2;Q9H4I8	.;SEHL2_HUMAN	R	306;126;126;242	ENSP00000331376:C306R;ENSP00000385691:C126R;ENSP00000336578:C242R	ENSP00000331376:C306R	C	+	1	0	SERHL2	41299976	0.000000	0.05858	0.006000	0.13384	0.009000	0.06853	-1.099000	0.03343	-0.094000	0.12374	-2.546000	0.00178	TGC	.	.	weak		0.562	SERHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320454.1	NM_014509	
RRM2B	50484	hgsc.bcm.edu	37	8	103250991	103250991	+	Intron	SNP	C	C	T	rs28999669	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:103250991C>T	ENST00000251810.3	-	1	292				KB-431C1.4_ENST00000520820.1_RNA|RRM2B_ENST00000519962.1_Intron|RRM2B_ENST00000519317.1_Intron|RRM2B_ENST00000395912.2_Intron	NM_001172478.1|NM_015713.4	NP_001165949.1|NP_056528.2	Q7LG56	RIR2B_HUMAN	ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process (GO:0009186)|deoxyribonucleoside triphosphate metabolic process (GO:0009200)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA repair (GO:0006281)|kidney development (GO:0001822)|mitochondrial DNA replication (GO:0006264)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|renal system process (GO:0003014)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	9	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000728)		Cladribine(DB00242)	AGCGGTCCTGCAACTTGCAAT	0.647								Modulation of nucleotide pools					C|||	254	0.0507188	0.0325	0.0519	5008	,	,		13859	0.005		0.1521	False		,,,				2504	0.0174				p.L20L		Atlas-SNP	.											.	RRM2B	31	.	0			c.G60A						PASS	.	C	,,	56,1328		0,56,636	38.0	47.0	44.0		60,,	1.3	0.0	8	dbSNP_125	44	493,2689		35,423,1133	no	coding-synonymous,intron,intron	RRM2B	NM_001172477.1,NM_001172478.1,NM_015713.4	,,	35,479,1769	TT,TC,CC		15.4934,4.0462,12.0237	,,	20/424,,	103250991	549,4017	692	1591	2283	SO:0001627	intron_variant	50484	exon1			GTCCTGCAACTTG	AB036532	CCDS34932.1, CCDS55267.1	8q23.1	2014-09-17			ENSG00000048392	ENSG00000048392			17296	protein-coding gene	gene with protein product		604712				10716435, 10980602, 17486094	Standard	NM_015713		Approved	p53R2	uc022azl.1	Q7LG56	OTTHUMG00000164776	ENST00000251810.3:c.48+63G>A	8.37:g.103250991C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_001172477	B4E2N4|Q17R22|Q75PQ6|Q75PQ7|Q75PY8|Q75PY9|Q86YE3|Q9NPD6|Q9NTD8|Q9NUW3	Silent	SNP	ENST00000251810.3	37	CCDS34932.1	169	0.07738095238095238	16	0.032520325203252036	25	0.06906077348066299	7	0.012237762237762238	121	0.15963060686015831	C	5.858	0.342551	0.11069	0.040462	0.154934	ENSG00000048392	ENST00000522368	.	.	.	3.1	1.27	0.21489	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.58432	P	5.999999999950489E-6	.	.	.	.	.	.	T	0.10590	-1.0623	3	.	.	.	.	5.244	0.15487	0.0:0.726:0.0:0.274	rs28999669	.	.	.	T	5	.	.	A	-	1	0	RRM2B	103320167	0.004000	0.15560	0.000000	0.03702	0.116000	0.19942	0.643000	0.24750	0.332000	0.23536	-0.350000	0.07774	GCA	C|0.922;T|0.078	0.078	strong		0.647	RRM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380191.3		
BAIAP2	10458	hgsc.bcm.edu	37	17	79089590	79089590	+	Missense_Mutation	SNP	A	A	G	rs4969391	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79089590A>G	ENST00000321300.6	+	14	1649	c.1556A>G	c.(1555-1557)cAg>cGg	p.Q519R	BAIAP2_ENST00000435091.3_3'UTR|BAIAP2_ENST00000575245.1_3'UTR|BAIAP2_ENST00000428708.2_Missense_Mutation_p.Q519R|BAIAP2_ENST00000392411.3_Missense_Mutation_p.Q441R	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	519			Q -> R (in dbSNP:rs4969391).		actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GCCCACGTCCAGCTGAAGCCG	0.582													A|||	863	0.172324	0.1059	0.3631	5008	,	,		17328	0.1478		0.1561	False		,,,				2504	0.1687				p.Q519R		Atlas-SNP	.											BAIAP2_ENST00000321300,colon,carcinoma,0,1	BAIAP2	74	1	0			c.A1556G						scavenged	.	A	ARG/GLN,,ARG/GLN	516,3890	234.6+/-247.4	35,446,1722	90.0	91.0	91.0		1556,,1556	5.0	1.0	17	dbSNP_111	91	1330,7270	259.8+/-282.9	98,1134,3068	yes	missense,utr-3,missense	BAIAP2	NM_001144888.1,NM_006340.2,NM_017451.2	43,,43	133,1580,4790	GG,GA,AA		15.4651,11.7113,14.1934	benign,,benign	519/535,,519/553	79089590	1846,11160	2203	4300	6503	SO:0001583	missense	10458	exon14			ACGTCCAGCTGAA	AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.1556A>G	17.37:g.79089590A>G	ENSP00000316338:p.Gln519Arg	Somatic	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Missense_Mutation	SNP	ENST00000321300.6	37	CCDS11775.1	410	0.18772893772893773	84	0.17073170731707318	112	0.30939226519337015	92	0.16083916083916083	122	0.16094986807387862	A	13.79	2.343165	0.41498	0.117113	0.154651	ENSG00000175866	ENST00000321300;ENST00000428708;ENST00000392411	T;T;T	0.38560	1.13;1.13;1.13	4.96	4.96	0.65561	.	1.320840	0.04637	N	0.404645	T	0.00012	0.0000	N	0.04508	-0.205	0.43761	P	0.0037289999999999823	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.18935	-1.0321	9	0.30854	T	0.27	-1.4439	8.529	0.33321	0.9135:0.0:0.0865:0.0	rs4969391;rs52805958;rs56955834;rs4969391	441;519;519	F8W878;Q9UQB8;Q9UQB8-2	.;BAIP2_HUMAN;.	R	519;519;441	ENSP00000316338:Q519R;ENSP00000401022:Q519R;ENSP00000376211:Q441R	ENSP00000316338:Q519R	Q	+	2	0	BAIAP2	76704185	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	4.516000	0.60496	1.862000	0.54008	0.379000	0.24179	CAG	A|0.843;G|0.157	0.157	strong		0.582	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		
OR5F1	338674	hgsc.bcm.edu	37	11	55761256	55761256	+	Silent	SNP	A	A	G	rs77110658	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55761256A>G	ENST00000278409.1	-	1	845	c.846T>C	c.(844-846)atT>atC	p.I282I		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	282					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					TCAACATGGGAATCACCACTG	0.443													G|||	191	0.038139	0.0129	0.0389	5008	,	,		17735	0.001		0.0934	False		,,,				2504	0.0532				p.I282I		Atlas-SNP	.											.	OR5F1	116	.	0			c.T846C						PASS	.	G		103,4299	814.0+/-416.2	3,97,2101	78.0	78.0	78.0		846	-0.4	0.8	11	dbSNP_131	78	669,7923	785.0+/-407.6	34,601,3661	no	coding-synonymous	OR5F1	NM_003697.1		37,698,5762	GG,GA,AA		7.7863,2.3398,5.9412		282/315	55761256	772,12222	2201	4296	6497	SO:0001819	synonymous_variant	338674	exon1			CATGGGAATCACC	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"""GPCR / Class A : Olfactory receptors"""	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.846T>C	11.37:g.55761256A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_003697	Q495D1|Q6IFB9	Silent	SNP	ENST00000278409.1	37	CCDS31515.1																																																																																			A|0.952;G|0.048	0.048	strong		0.443	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697	
DGKE	8526	hgsc.bcm.edu	37	17	54912339	54912339	+	Silent	SNP	G	G	A	rs1048159	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:54912339G>A	ENST00000284061.3	+	2	363	c.183G>A	c.(181-183)ggG>ggA	p.G61G	C17orf67_ENST00000575658.1_5'Flank|DGKE_ENST00000576869.1_3'UTR|C17orf67_ENST00000397861.2_5'Flank|DGKE_ENST00000572810.1_Silent_p.G61G|C17orf67_ENST00000487705.1_Intron	NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	61					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					GCAAGCACGGGTGGCGCGACA	0.677													G|||	511	0.102037	0.0666	0.1066	5008	,	,		16751	0.0179		0.1799	False		,,,				2504	0.1534				p.G61G		Atlas-SNP	.											DGKE,NS,carcinoma,+2,1	DGKE	47	1	0			c.G183A						PASS	.	G		395,4011	192.3+/-217.7	18,359,1826	52.0	60.0	57.0		183	-4.0	1.0	17	dbSNP_86	57	1264,7334	249.4+/-276.7	92,1080,3127	no	coding-synonymous	DGKE	NM_003647.2		110,1439,4953	AA,AG,GG		14.7011,8.965,12.7576		61/568	54912339	1659,11345	2203	4299	6502	SO:0001819	synonymous_variant	8526	exon2			GCACGGGTGGCGC	U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"""diacylglycerol kinase, epsilon (64kD)"""			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.183G>A	17.37:g.54912339G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	48	0.631579	NM_003647	Q8TBM4|Q9UKQ3	Silent	SNP	ENST00000284061.3	37	CCDS11590.1																																																																																			G|0.882;A|0.118	0.118	strong		0.677	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647	
ERAP2	64167	hgsc.bcm.edu	37	5	96215680	96215680	+	Silent	SNP	C	C	T	rs41506651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96215680C>T	ENST00000437043.3	+	2	1002	c.291C>T	c.(289-291)atC>atT	p.I97I	CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000510309.1_Silent_p.I97I|ERAP2_ENST00000379904.4_Silent_p.I97I	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	97					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		CTGAGAAGATCGAAGTCTTGG	0.473													C|||	244	0.048722	0.0061	0.0663	5008	,	,		22981	0.003		0.1004	False		,,,				2504	0.0879				p.I97I		Atlas-SNP	.											.	ERAP2	77	.	0			c.C291T						PASS	.	C	,	112,4294	87.3+/-125.9	1,110,2092	82.0	71.0	75.0		291,291	-4.0	0.5	5	dbSNP_127	75	924,7676	205.4+/-247.8	45,834,3421	no	coding-synonymous,coding-synonymous	ERAP2	NM_001130140.1,NM_022350.3	,	46,944,5513	TT,TC,CC		10.7442,2.542,7.9656	,	97/961,97/961	96215680	1036,11970	2203	4300	6503	SO:0001819	synonymous_variant	64167	exon2			GAAGATCGAAGTC	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.291C>T	5.37:g.96215680C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	165	86	0.521212	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Silent	SNP	ENST00000437043.3	37	CCDS4086.1																																																																																			C|0.928;T|0.072	0.072	strong		0.473	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
GALNT2	2590	hgsc.bcm.edu	37	1	230386238	230386238	+	Missense_Mutation	SNP	A	A	C	rs78164071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:230386238A>C	ENST00000366672.4	+	10	1013	c.941A>C	c.(940-942)gAt>gCt	p.D314A	GALNT2_ENST00000541865.1_Intron|GALNT2_ENST00000543760.1_Missense_Mutation_p.D276A	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	314	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				TTTGTGATGGATAAGTTCTAT	0.488													A|||	6	0.00119808	0.0	0.0014	5008	,	,		19543	0.0		0.005	False		,,,				2504	0.0				p.D314A		Atlas-SNP	.											.	GALNT2	83	.	0			c.A941C						PASS	.	A	ALA/ASP	4,4402	9.9+/-24.2	0,4,2199	176.0	157.0	164.0		941	4.4	1.0	1	dbSNP_133	164	30,8570	22.2+/-67.0	0,30,4270	yes	missense	GALNT2	NM_004481.3	126	0,34,6469	CC,CA,AA		0.3488,0.0908,0.2614	benign	314/572	230386238	34,12972	2203	4300	6503	SO:0001583	missense	2590	exon10			TGATGGATAAGTT	BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4124	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 2"""	602274	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"""			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.941A>C	1.37:g.230386238A>C	ENSP00000355632:p.Asp314Ala	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_004481	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	16.68	3.189190	0.57909	9.08E-4	0.003488	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291	T;T	0.59772	0.24;0.24	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.50514	0.1620	M	0.80746	2.51	0.80722	D	1	B;B	0.32573	0.376;0.213	B;B	0.28305	0.088;0.018	T	0.63479	-0.6628	10	0.66056	D	0.02	.	13.6391	0.62239	1.0:0.0:0.0:0.0	.	314;276	Q10471;G3V1S6	GALT2_HUMAN;.	A	276;314;195	ENSP00000445017:D276A;ENSP00000355632:D314A	ENSP00000355632:D314A	D	+	2	0	GALNT2	228452861	1.000000	0.71417	0.986000	0.45419	0.977000	0.68977	8.799000	0.91895	1.761000	0.52028	0.379000	0.24179	GAT	A|0.997;C|0.003	0.003	strong		0.488	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	
PCNT	5116	hgsc.bcm.edu	37	21	47766113	47766113	+	Missense_Mutation	SNP	T	T	G	rs34500739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47766113T>G	ENST00000359568.5	+	4	818	c.711T>G	c.(709-711)caT>caG	p.H237Q	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	237	Glu-rich.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CTGGCCTGCATCAGAGTCAGG	0.602													G|||	128	0.0255591	0.028	0.0303	5008	,	,		16755	0.001		0.0646	False		,,,				2504	0.0041				p.H237Q		Atlas-SNP	.											.	PCNT	283	.	0			c.T711G						PASS	.	G	GLN/HIS	192,4214	807.9+/-415.9	5,182,2016	83.0	74.0	77.0		711	3.3	1.0	21	dbSNP_126	77	528,8072	795.4+/-407.5	11,506,3783	yes	missense	PCNT	NM_006031.5	24	16,688,5799	GG,GT,TT		6.1395,4.3577,5.5359	benign	237/3337	47766113	720,12286	2203	4300	6503	SO:0001583	missense	5116	exon4			CCTGCATCAGAGT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.711T>G	21.37:g.47766113T>G	ENSP00000352572:p.His237Gln	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	150	80	0.533333	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	92	0.04212454212454213	21	0.042682926829268296	16	0.04419889502762431	1	0.0017482517482517483	54	0.0712401055408971	G	2.436	-0.329782	0.05314	0.043577	0.061395	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01279	5.06	3.27	3.27	0.37495	.	.	.	.	.	T	0.00073	0.0002	N	0.00926	-1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45145	-0.9281	9	0.09084	T	0.74	.	8.0049	0.30319	0.0:0.0:0.7564:0.2436	rs34500739	119;237	O95613-2;O95613	.;PCNT_HUMAN	Q	237;224	ENSP00000352572:H237Q	ENSP00000338675:H224Q	H	+	3	2	PCNT	46590541	0.057000	0.20700	0.965000	0.40720	0.171000	0.22731	0.660000	0.25009	0.988000	0.38734	-0.648000	0.03929	CAT	T|0.949;G|0.051	0.051	strong		0.602	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
MT-ND4	4538	hgsc.bcm.edu	37	M	11299	11299	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:11299T>C	ENST00000361381.2	+	1	540	c.540T>C	c.(538-540)acT>acC	p.T180T	MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	180					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						CTACTACTCACTCTCACTGCC	0.418																																					p.T180T		Atlas-SNP	.											.	.	.	.	0			c.T540C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ACTCACTCTCACT			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.540T>C	M.37:g.11299T>C		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.418	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
PSMA7	5688	hgsc.bcm.edu	37	20	60713311	60713311	+	Silent	SNP	G	G	A	rs7076	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60713311G>A	ENST00000370873.4	-	5	633	c.507C>T	c.(505-507)cgC>cgT	p.R169R	PSMA7_ENST00000484488.1_5'UTR|PSMA7_ENST00000370861.1_Silent_p.R99R	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 7	169					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	identical protein binding (GO:0042802)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|lung(2)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			CCAGGAACTCGCGCACTGACT	0.507													G|||	2996	0.598243	0.143	0.7392	5008	,	,		23907	0.7738		0.8032	False		,,,				2504	0.7219				p.R169R		Atlas-SNP	.											.	PSMA7	13	.	0			c.C507T						PASS	.	G		1121,3285		162,797,1244	178.0	123.0	142.0		507	-1.7	0.9	20	dbSNP_52	142	6854,1746		2747,1360,193	no	coding-synonymous	PSMA7	NM_002792.2		2909,2157,1437	AA,AG,GG		20.3023,25.4426,38.6821		169/249	60713311	7975,5031	2203	4300	6503	SO:0001819	synonymous_variant	5688	exon5			GAACTCGCGCACT	AF022815	CCDS13489.1	20q13.33	2008-07-02			ENSG00000101182	ENSG00000101182		"""Proteasome (prosome, macropain) subunits"""	9536	protein-coding gene	gene with protein product	"""proteasome subunit XAPC7"", ""proteasome subunit RC6-1"""	606607				8764072	Standard	NM_002792		Approved	XAPC7, C6, HSPC, RC6-1	uc002ybx.2	O14818	OTTHUMG00000032895	ENST00000370873.4:c.507C>T	20.37:g.60713311G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	156	153	0.980769	NM_002792	B2R515|Q5JXJ2|Q9BR53|Q9H4K5|Q9UEU8	Silent	SNP	ENST00000370873.4	37	CCDS13489.1	1429	0.6543040293040293	81	0.16463414634146342	276	0.7624309392265194	455	0.7954545454545454	617	0.8139841688654353	.	1.999	-0.429897	0.04701	0.254426	0.796977	ENSG00000101182	ENST00000442551	.	.	.	5.12	-1.69	0.08186	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.25502	-1.0130	3	.	.	.	.	6.494	0.22132	0.5381:0.1241:0.3378:0.0	rs7076;rs1058341;rs3171398;rs6089329;rs17849854	.	.	.	V	95	.	.	A	-	2	0	PSMA7	60146706	0.112000	0.22096	0.946000	0.38457	0.151000	0.21798	-0.355000	0.07671	-0.567000	0.06046	-1.008000	0.02478	GCG	G|0.369;A|0.631	0.631	strong		0.507	PSMA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079975.1	NM_002792	
ARL17B	100506084	hgsc.bcm.edu	37	17	44430254	44430254	+	Missense_Mutation	SNP	G	G	C	rs35595570	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44430254G>C	ENST00000450673.3	-	3	296	c.191C>G	c.(190-192)gCt>gGt	p.A64G	ARL17B_ENST00000575698.1_Missense_Mutation_p.A64G|ARL17B_ENST00000434041.2_Missense_Mutation_p.A64G|ARL17B_ENST00000570618.1_Missense_Mutation_p.A64G|ARL17B_ENST00000575960.1_Missense_Mutation_p.A64G|ARL17B_ENST00000571246.1_Missense_Mutation_p.A64G	NM_001039083.3	NP_001034172.3	Q8IVW1	ARL17_HUMAN	ADP-ribosylation factor-like 17B	64					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)	GTP binding (GO:0005525)	p.A64G(1)		pancreas(1)	1						ATCCCAGACAGCGAAGGTGTT	0.378																																					p.A64G		Atlas-SNP	.											ARL17B,NS,other,0,1	ARL17B	3	1	1	Substitution - Missense(1)	pancreas(1)	c.C191G						scavenged	.						3.0	3.0	3.0					17																	44430254		1275	3002	4277	SO:0001583	missense	100506084	exon3			CAGACAGCGAAGG	AF493886	CCDS54137.1, CCDS58557.1	17q21.31	2014-05-09	2009-11-17	2009-11-17	ENSG00000228696	ENSG00000228696		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	32387	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 17"""	ARL17			Standard	NM_001039083		Approved			Q8IVW1	OTTHUMG00000178031	ENST00000450673.3:c.191C>G	17.37:g.44430254G>C	ENSP00000404247:p.Ala64Gly	Somatic	739	2	0.00270636		WXS	Illumina HiSeq	Phase_I	967	179	0.185109	NM_001039083	B0AZR6|Q59FW5|Q8N6E2|Q8TD73|Q8WW54|Q9NZD5|Q9P158	Missense_Mutation	SNP	ENST00000450673.3	37	CCDS58557.1	.	.	.	.	.	.	.	.	.	.	g	4.858	0.159467	0.09236	.	.	ENSG00000228696	ENST00000434041;ENST00000450673	T;T	0.63744	-0.06;-0.06	2.89	2.89	0.33648	.	.	.	.	.	T	0.51736	0.1692	.	.	.	0.29739	N	0.837233	B;B;B	0.31817	0.164;0.054;0.341	B;B;B	0.31686	0.134;0.038;0.08	T	0.55768	-0.8089	8	0.52906	T	0.07	.	11.9465	0.52930	0.0:0.0:1.0:0.0	.	64;64;64	Q8IVW1;Q8IVW1-2;F8VZA5	ARL17_HUMAN;.;.	G	64	ENSP00000391751:A64G;ENSP00000404247:A64G	ENSP00000391751:A64G	A	-	2	0	ARL17B	41786010	1.000000	0.71417	0.999000	0.59377	0.006000	0.05464	8.736000	0.91554	1.898000	0.54952	0.393000	0.25936	GCT	G|0.905;C|0.095	0.095	strong		0.378	ARL17B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440297.1	NM_001039083	
NDNF	79625	hgsc.bcm.edu	37	4	121958697	121958697	+	Silent	SNP	G	G	A	rs3733560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:121958697G>A	ENST00000379692.4	-	4	955	c.429C>T	c.(427-429)tcC>tcT	p.S143S	NDNF_ENST00000506900.1_5'UTR	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	143	Poly-Ser.				cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						GATATAAACCGGATGGGGAAC	0.408													G|||	1999	0.399161	0.0756	0.4438	5008	,	,		18898	0.5962		0.5656	False		,,,				2504	0.4305				p.S143S		Atlas-SNP	.											.	NDNF	72	.	0			c.C429T						PASS	.	G		605,3271		43,519,1376	130.0	126.0	127.0		429	-7.6	0.4	4	dbSNP_107	127	4868,3450		1442,1984,733	no	coding-synonymous	NDNF	NM_024574.3		1485,2503,2109	AA,AG,GG		41.4763,15.6089,44.8827		143/569	121958697	5473,6721	1938	4159	6097	SO:0001819	synonymous_variant	79625	exon4			TAAACCGGATGGG	BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 31"""	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.429C>T	4.37:g.121958697G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	NM_024574	A8K0Q0|Q6UWE5|Q9H5P7	Silent	SNP	ENST00000379692.4	37	CCDS3717.2																																																																																			G|0.554;A|0.446	0.446	strong		0.408	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574	
SEMA3G	56920	hgsc.bcm.edu	37	3	52476246	52476246	+	Silent	SNP	G	G	A	rs34900551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52476246G>A	ENST00000231721.2	-	4	413	c.414C>T	c.(412-414)gcC>gcT	p.A138A		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	138	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		TGGGCTGGAAGGCCCCAGTGC	0.657													G|||	49	0.00978435	0.0008	0.0101	5008	,	,		16416	0.0		0.0358	False		,,,				2504	0.0051				p.A138A		Atlas-SNP	.											.	SEMA3G	58	.	0			c.C414T						PASS	.	G		35,4371	40.0+/-72.8	0,35,2168	47.0	45.0	45.0		414	4.7	1.0	3	dbSNP_126	45	325,8275	112.0+/-172.2	3,319,3978	no	coding-synonymous	SEMA3G	NM_020163.1		3,354,6146	AA,AG,GG		3.7791,0.7944,2.768		138/783	52476246	360,12646	2203	4300	6503	SO:0001819	synonymous_variant	56920	exon4			CTGGAAGGCCCCA		CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.414C>T	3.37:g.52476246G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	211	109	0.516588	NM_020163	Q7L9D9|Q9H7Q3	Silent	SNP	ENST00000231721.2	37	CCDS2856.1																																																																																			G|0.978;A|0.022	0.022	strong		0.657	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163	
MUC16	94025	hgsc.bcm.edu	37	19	9057704	9057704	+	Silent	SNP	G	G	T	rs12984130	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9057704G>T	ENST00000397910.4	-	3	29945	c.29742C>A	c.(29740-29742)atC>atA	p.I9914I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9916	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TAGAGGACATGATTTCTGTCA	0.463													G|||	1046	0.208866	0.2352	0.219	5008	,	,		21195	0.0258		0.3121	False		,,,				2504	0.2485				p.I9914I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C29742A						PASS	.	G		912,3046		97,718,1164	186.0	176.0	179.0		29742	1.4	0.0	19	dbSNP_121	179	2817,5499		498,1821,1839	no	coding-synonymous	MUC16	NM_024690.2		595,2539,3003	TT,TG,GG		33.8745,23.0419,30.3813		9914/14508	9057704	3729,8545	1979	4158	6137	SO:0001819	synonymous_variant	94025	exon3			GGACATGATTTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29742C>A	19.37:g.9057704G>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	269	268	0.996283	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.768;T|0.232	0.232	strong		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DUS2	54920	hgsc.bcm.edu	37	16	68087517	68087517	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:68087517C>T	ENST00000565263.1	+	5	717	c.223C>T	c.(223-225)Cgc>Tgc	p.R75C	AC130462.1_ENST00000408862.1_RNA|DUS2_ENST00000358896.6_Missense_Mutation_p.R75C|DUS2_ENST00000432752.1_Missense_Mutation_p.R75C	NM_017803.3	NP_060273.1	Q9NX74	DUS2L_HUMAN	dihydrouridine synthase 2	75					negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	double-stranded RNA binding (GO:0003725)|flavin adenine dinucleotide binding (GO:0050660)|protein kinase inhibitor activity (GO:0004860)|tRNA dihydrouridine synthase activity (GO:0017150)										AGTTGTCTTCCGCACCTGTGA	0.522																																					p.R75C		Atlas-SNP	.											DUS2L,NS,carcinoma,-1,2	DUS2L	39	2	0			c.C223T						scavenged	.						188.0	145.0	160.0					16																	68087517		2198	4300	6498	SO:0001583	missense	54920	exon4			GTCTTCCGCACCT		CCDS10859.1, CCDS61970.1	16q22.1	2013-07-23	2013-07-23	2013-07-23	ENSG00000167264	ENSG00000167264			26014	protein-coding gene	gene with protein product	"""SMM1 homolog (S. cerevisiae)"""	609707	"""dihydrouridine synthase 2-like (SMM1, S. cerevisiae)"", ""dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)"", ""dihydrouridine synthase 2-like"""	DUS2L		15994936, 22741570	Standard	NM_017803		Approved	FLJ20399, SMM1	uc002evj.4	Q9NX74	OTTHUMG00000137538	ENST00000565263.1:c.223C>T	16.37:g.68087517C>T	ENSP00000455229:p.Arg75Cys	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	127	3	0.023622	NM_001271762	A8K3G3|Q4H4D9	Missense_Mutation	SNP	ENST00000565263.1	37	CCDS10859.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.777629	0.31502	.	.	ENSG00000167264	ENST00000358896;ENST00000432752	T;T	0.33438	1.41;1.91	5.97	5.97	0.96955	Aldolase-type TIM barrel (1);	0.062771	0.64402	D	0.000011	T	0.65790	0.2725	H	0.94771	3.58	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.993	T	0.74216	-0.3737	10	0.87932	D	0	-34.6484	12.8506	0.57855	0.1627:0.8373:0.0:0.0	.	75;75	E7EUN9;Q9NX74	.;DUS2L_HUMAN	C	75	ENSP00000351769:R75C;ENSP00000409498:R75C	ENSP00000351769:R75C	R	+	1	0	DUS2L	66645018	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	1.931000	0.40134	2.834000	0.97654	0.557000	0.71058	CGC	.	.	none		0.522	DUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268869.2	NM_017803	
CDH17	1015	hgsc.bcm.edu	37	8	95161102	95161102	+	Splice_Site	SNP	G	G	A	rs35792427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:95161102G>A	ENST00000027335.3	-	14	1921	c.1797C>T	c.(1795-1797)agC>agT	p.S599S	CDH17_ENST00000450165.2_Splice_Site_p.S599S|CDH17_ENST00000441892.2_Splice_Site_p.S385S	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	599	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			TCAGTGAATAGCTTCATCAAA	0.418													G|||	635	0.126797	0.0106	0.2305	5008	,	,		15416	0.1587		0.1143	False		,,,				2504	0.1902				p.S599S		Atlas-SNP	.											.	CDH17	119	.	0			c.C1797T						PASS	.	G	,	134,4272	95.3+/-134.0	3,128,2072	99.0	84.0	89.0		1797,1797	-6.6	0.9	8	dbSNP_126	89	1166,7434	237.8+/-269.5	82,1002,3216	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	CDH17	NM_001144663.1,NM_004063.3	,	85,1130,5288	AA,AG,GG		13.5581,3.0413,9.9954	,	599/833,599/833	95161102	1300,11706	2203	4300	6503	SO:0001630	splice_region_variant	1015	exon14			TGAATAGCTTCAT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1797-1C>T	8.37:g.95161102G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	108	59	0.546296	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			G|0.892;A|0.108	0.108	strong		0.418	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	Silent
C2orf54	79919	hgsc.bcm.edu	37	2	241828012	241828012	+	Silent	SNP	T	T	C	rs6708304	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241828012T>C	ENST00000388934.4	-	4	1106	c.948A>G	c.(946-948)gaA>gaG	p.E316E	C2orf54_ENST00000307486.8_Silent_p.E167E|C2orf54_ENST00000402775.2_Silent_p.E148E	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	316										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		CGCCCTGCAGTTCTGCCCAGT	0.697													C|||	2843	0.567692	0.8192	0.366	5008	,	,		9793	0.5278		0.5219	False		,,,				2504	0.4591				p.E316E		Atlas-SNP	.											C2orf54,colon,carcinoma,0,1	C2orf54	14	1	0			c.A948G						PASS	.	C	,	3233,979		1276,681,149	10.0	14.0	13.0		948,444	1.1	0.9	2	dbSNP_116	13	4211,4237		1104,2003,1117	no	coding-synonymous,coding-synonymous	C2orf54	NM_001085437.1,NM_024861.2	,	2380,2684,1266	CC,CT,TT		49.8461,23.2431,41.2006	,	316/448,148/280	241828012	7444,5216	2106	4224	6330	SO:0001819	synonymous_variant	79919	exon4			CTGCAGTTCTGCC	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.948A>G	2.37:g.241828012T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	65	63	0.969231	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	37	CCDS42839.1																																																																																			T|0.464;C|0.536	0.536	strong		0.697	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
ACSM1	116285	hgsc.bcm.edu	37	16	20648702	20648702	+	Silent	SNP	G	G	A	rs151328	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20648702G>A	ENST00000307493.4	-	8	1255	c.1188C>T	c.(1186-1188)taC>taT	p.Y396Y	ACSM1_ENST00000219151.4_Silent_p.Y15Y|ACSM1_ENST00000520010.1_Silent_p.Y396Y	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	396					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						CCTGGACGTCGTAGGGTGGAG	0.542													G|||	1737	0.346845	0.5416	0.1916	5008	,	,		20252	0.3512		0.1799	False		,,,				2504	0.3609				p.Y396Y		Atlas-SNP	.											.	ACSM1	118	.	0			c.C1188T						PASS	.	G		2177,2225	586.1+/-386.4	540,1097,564	126.0	117.0	120.0		1188	-9.1	0.0	16	dbSNP_79	120	1726,6874	315.1+/-312.1	176,1374,2750	no	coding-synonymous	ACSM1	NM_052956.2		716,2471,3314	AA,AG,GG		20.0698,49.4548,30.0185		396/578	20648702	3903,9099	2201	4300	6501	SO:0001819	synonymous_variant	116285	exon8			GACGTCGTAGGGT	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"""Acyl-CoA synthetase family"""	18049	protein-coding gene	gene with protein product		614357	"""butyryl Coenzyme A synthetase 1"""	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.1188C>T	16.37:g.20648702G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_052956	Q08AH2|Q96A20	Silent	SNP	ENST00000307493.4	37	CCDS10587.1	674	0.3086080586080586	255	0.5182926829268293	73	0.20165745856353592	196	0.34265734265734266	150	0.19788918205804748	G	0.019	-1.451414	0.01080	0.494548	0.200698	ENSG00000166743	ENST00000524149	.	.	.	5.07	-9.12	0.00707	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.01920	-1.1247	3	.	.	.	.	17.3287	0.87257	0.8454:0.0:0.1546:0.0	rs151328;rs1262366;rs16970472;rs61455665;rs151328	.	.	.	M	102	.	.	T	-	2	0	ACSM1	20556203	0.000000	0.05858	0.015000	0.15790	0.014000	0.08584	-2.456000	0.01002	-1.806000	0.01237	-0.192000	0.12808	ACG	G|0.685;A|0.315	0.315	strong		0.542	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956	
SYNRG	11276	hgsc.bcm.edu	37	17	35896123	35896123	+	Silent	SNP	T	T	C	rs1045000	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:35896123T>C	ENST00000339208.6	-	19	3764	c.3624A>G	c.(3622-3624)gtA>gtG	p.V1208V	SYNRG_ENST00000346661.4_Silent_p.V1208V|SYNRG_ENST00000345615.4_Silent_p.V1130V|SYNRG_ENST00000591288.1_Silent_p.V1002V|SYNRG_ENST00000585472.1_Silent_p.V1129V|SYNRG_ENST00000502449.2_Silent_p.V1085V|SYNRG_ENST00000394378.2_Silent_p.V1130V	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	1208					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GGTTATTCCATACTTTATCGA	0.468													T|||	1174	0.234425	0.1793	0.366	5008	,	,		22803	0.255		0.2197	False		,,,				2504	0.2096				p.V1208V		Atlas-SNP	.											.	SYNRG	101	.	0			c.A3624G						PASS	.	T	,,,,,,	870,3536	340.2+/-306.1	99,672,1432	196.0	163.0	174.0		3390,3387,3255,3006,3624,3390,3390	-11.3	0.2	17	dbSNP_86	174	1928,6672	341.2+/-323.9	215,1498,2587	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYNRG	NM_001163544.1,NM_001163545.1,NM_001163546.1,NM_001163547.1,NM_007247.4,NM_080550.3,NM_198882.1	,,,,,,	314,2170,4019	CC,CT,TT		22.4186,19.7458,21.5131	,,,,,,	1130/1237,1129/1236,1085/1180,1002/1109,1208/1315,1130/1225,1130/1260	35896123	2798,10208	2203	4300	6503	SO:0001819	synonymous_variant	11276	exon19			ATTCCATACTTTA	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"""gamma-synergin"", ""adaptor-related protein complex 1 gamma subunit-binding protein 1"""	607291	"""AP1 gamma subunit binding protein 1"""	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.3624A>G	17.37:g.35896123T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	119	117	0.983193	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Silent	SNP	ENST00000339208.6	37	CCDS11321.1																																																																																			T|0.778;C|0.222	0.222	strong		0.468	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	
CCDC170	80129	hgsc.bcm.edu	37	6	151894505	151894505	+	Missense_Mutation	SNP	T	T	C	rs953767	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:151894505T>C	ENST00000239374.7	+	6	1070	c.971T>C	c.(970-972)tTc>tCc	p.F324S	CCDC170_ENST00000367290.5_Missense_Mutation_p.F324S	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	324			F -> S (in dbSNP:rs953767). {ECO:0000269|PubMed:14702039}.														AGCCAGTACTTCTCATTTAGG	0.488													C|||	4716	0.941693	0.9932	0.9352	5008	,	,		19378	0.996		0.8757	False		,,,				2504	0.8885				p.F324S		Atlas-SNP	.											.	.	.	.	0			c.T971C						PASS	.	C	SER/PHE	3893,85		1904,85,0	83.0	89.0	87.0		971	2.5	0.0	6	dbSNP_86	87	7325,975		3224,877,49	yes	missense	C6orf97	NM_025059.3	155	5128,962,49	CC,CT,TT		11.747,2.1368,8.6333	benign	324/716	151894505	11218,1060	1989	4150	6139	SO:0001583	missense	80129	exon6			AGTACTTCTCATT	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.971T>C	6.37:g.151894505T>C	ENSP00000239374:p.Phe324Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	170	170	1	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	2051	0.9391025641025641	486	0.9878048780487805	332	0.9171270718232044	571	0.9982517482517482	662	0.8733509234828496	C	0.229	-1.022154	0.02061	0.978632	0.88253	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.06849	3.25;3.25	5.36	2.45	0.29901	.	1.188190	0.05678	N	0.589912	T	0.00608	0.0020	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45454	-0.9260	9	0.10111	T	0.7	-0.1204	1.6293	0.02729	0.2503:0.4547:0.1206:0.1744	rs953767;rs52813389;rs57743841;rs953767	324	Q8IYT3	CF097_HUMAN	S	324	ENSP00000239374:F324S;ENSP00000356259:F324S	ENSP00000239374:F324S	F	+	2	0	C6orf97	151936198	0.000000	0.05858	0.012000	0.15200	0.759000	0.43091	-0.169000	0.09911	0.769000	0.33313	-0.131000	0.14894	TTC	T|0.077;G|0.001	.	strong		0.488	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
LRCH4	4034	hgsc.bcm.edu	37	7	100172858	100172858	+	Missense_Mutation	SNP	C	C	T	rs3197597	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100172858C>T	ENST00000310300.6	-	18	1976	c.1924G>A	c.(1924-1926)Gtg>Atg	p.V642M	SAP25_ENST00000538735.1_5'Flank|LRCH4_ENST00000497245.1_Missense_Mutation_p.V190M	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	642	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.		V -> M (in dbSNP:rs3197597). {ECO:0000269|PubMed:15489334}.		nervous system development (GO:0007399)	PML body (GO:0016605)				NS(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	23	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACCCGCTTCACGGCCTCCAGC	0.692													C|||	312	0.0623003	0.0053	0.1167	5008	,	,		13947	0.001		0.1282	False		,,,				2504	0.0961				p.V642M		Atlas-SNP	.											.	LRCH4	53	.	0			c.G1924A						PASS	.	C	MET/VAL	129,4257		1,127,2065	25.0	22.0	23.0		1924	3.5	0.9	7	dbSNP_105	23	1235,7339		88,1059,3140	no	missense	LRCH4	NM_002319.3	21	89,1186,5205	TT,TC,CC		14.404,2.9412,10.5247	probably-damaging	642/684	100172858	1364,11596	2193	4287	6480	SO:0001583	missense	4034	exon18			GCTTCACGGCCTC	AF053356	CCDS34706.1	7q22	2008-05-20	2004-05-27	2004-05-28	ENSG00000077454	ENSG00000077454			6691	protein-coding gene	gene with protein product				LRN, LRRN1		9799793	Standard	XM_005250346		Approved		uc003uvj.3	O75427	OTTHUMG00000159544	ENST00000310300.6:c.1924G>A	7.37:g.100172858C>T	ENSP00000309689:p.Val642Met	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	38	29	0.763158	NM_002319	A4D2D5|Q8WV85|Q96ID0	Missense_Mutation	SNP	ENST00000310300.6	37	CCDS34706.1	153	0.07005494505494506	3	0.006097560975609756	52	0.143646408839779	0	0.0	98	0.12928759894459102	C	16.00	2.998121	0.54147	0.029412	0.14404	ENSG00000077454	ENST00000310300;ENST00000422462;ENST00000497245	T;T	0.52526	1.23;0.66	4.43	3.54	0.40534	Calponin homology domain (1);	0.470515	0.20703	N	0.087237	T	0.00384	0.0012	M	0.67397	2.05	0.32707	P	0.512149	B	0.18968	0.032	B	0.19391	0.025	T	0.12993	-1.0526	9	0.87932	D	0	-3.4562	8.223	0.31552	0.0:0.8915:0.0:0.1085	rs3197597;rs17162358	642	O75427	LRCH4_HUMAN	M	642;101;190	ENSP00000309689:V642M;ENSP00000419870:V190M	ENSP00000309689:V642M	V	-	1	0	LRCH4	100010794	0.996000	0.38824	0.926000	0.36857	0.352000	0.29268	2.559000	0.45888	1.104000	0.41587	0.555000	0.69702	GTG	C|0.922;T|0.078	0.078	strong		0.692	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319	
TPCN2	219931	hgsc.bcm.edu	37	11	68854012	68854012	+	Silent	SNP	A	A	G	rs35337391	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:68854012A>G	ENST00000294309.3	+	23	2126	c.2025A>G	c.(2023-2025)gtA>gtG	p.V675V	TPCN2_ENST00000442692.2_3'UTR|TPCN2_ENST00000542467.1_Intron	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	675					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TCTATTTTGTATTGTGGTGGC	0.537													A|||	517	0.103235	0.0401	0.085	5008	,	,		16938	0.0109		0.2038	False		,,,				2504	0.1933				p.V675V		Atlas-SNP	.											.	TPCN2	63	.	0			c.A2025G						PASS	.	A		219,4181	134.1+/-170.4	3,213,1984	281.0	208.0	233.0		2025	-0.6	0.1	11	dbSNP_126	233	1533,7055	290.9+/-300.1	133,1267,2894	no	coding-synonymous	TPCN2	NM_139075.3		136,1480,4878	GG,GA,AA		17.8505,4.9773,13.4894		675/753	68854012	1752,11236	2200	4294	6494	SO:0001819	synonymous_variant	219931	exon23			TTTTGTATTGTGG	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.2025A>G	11.37:g.68854012A>G		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	293	143	0.488055	NM_139075	Q9NT82	Silent	SNP	ENST00000294309.3	37	CCDS8189.1																																																																																			A|0.871;G|0.129	0.129	strong		0.537	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
NRAP	4892	hgsc.bcm.edu	37	10	115374670	115374670	+	Silent	SNP	A	A	G	rs3121453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:115374670A>G	ENST00000359988.3	-	28	3358	c.3114T>C	c.(3112-3114)gaT>gaC	p.D1038D	NRAP_ENST00000369360.3_Silent_p.D1011D|NRAP_ENST00000369358.4_Silent_p.D1046D|NRAP_ENST00000360478.3_Silent_p.D1003D	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TATAGCCACCATCTCGAAGTT	0.468													G|||	625	0.1248	0.1293	0.1614	5008	,	,		20413	0.0218		0.2058	False		,,,				2504	0.1155				p.D1038D		Atlas-SNP	.											.	NRAP	208	.	0			c.T3114C						PASS	.	G	,	709,3697	760.0+/-412.9	54,601,1548	184.0	164.0	171.0		3009,3114	-3.0	0.4	10	dbSNP_103	171	1935,6665	725.8+/-406.6	227,1481,2592	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	281,2082,4140	GG,GA,AA		22.5,16.0917,20.3291	,	1003/1696,1038/1731	115374670	2644,10362	2203	4300	6503	SO:0001819	synonymous_variant	4892	exon28			GCCACCATCTCGA		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3114T>C	10.37:g.115374670A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	146	67	0.458904	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			A|0.825;G|0.175	0.175	strong		0.468	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
RBMXL1	494115	hgsc.bcm.edu	37	1	89448812	89448812	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89448812T>G	ENST00000321792.5	-	2	1125	c.698A>C	c.(697-699)gAt>gCt	p.D233A	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.D233A|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000413769.1_5'Flank|CCBL2_ENST00000370491.3_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	233					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.D233A(3)									TGGTGCATAATCTCTTGTATC	0.423																																					p.D233A		Atlas-SNP	.											CCBL2,NS,carcinoma,0,3	.	.	3	3	Substitution - Missense(3)	kidney(3)	c.A698C						scavenged	.						205.0	178.0	187.0					1																	89448812		2203	4300	6503	SO:0001583	missense	494115	exon3			GCATAATCTCTTG	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.698A>C	1.37:g.89448812T>G	ENSP00000318415:p.Asp233Ala	Somatic	260	3	0.0115385		WXS	Illumina HiSeq	Phase_I	346	7	0.0202312	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.084835	0.76642	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	D;D	0.83163	-1.69;-1.69	1.53	1.53	0.23141	.	0.000000	0.85682	D	0.000000	T	0.79100	0.4389	M	0.71036	2.16	0.46499	D	0.999078	D	0.59357	0.985	P	0.53102	0.718	T	0.78889	-0.2026	10	0.66056	D	0.02	.	6.8078	0.23786	0.0:0.0:0.0:1.0	.	233	Q96E39	RBMXL_HUMAN	A	233	ENSP00000318415:D233A;ENSP00000446099:D233A	ENSP00000318415:D233A	D	-	2	0	RBMXL1	89221400	1.000000	0.71417	0.996000	0.52242	0.787000	0.44495	5.062000	0.64326	0.706000	0.31912	0.254000	0.18369	GAT	.	.	none		0.423	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33408542	33408542	+	Silent	SNP	G	G	A	rs587780472|rs411136	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33408542G>A	ENST00000418600.2	+	11	1814	c.1713G>A	c.(1711-1713)tcG>tcA	p.S571S	SYNGAP1_ENST00000293748.5_Silent_p.S571S|MIR5004_ENST00000579078.1_RNA|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Silent_p.S512S	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	571	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)	p.S556S(1)|p.S571S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						TGTTTGCTTCGTGGCGGCTGC	0.632													G|||	2192	0.4377	0.2716	0.4035	5008	,	,		17633	0.6319		0.3837	False		,,,				2504	0.5419				p.S571S		Atlas-SNP	.											SYNGAP1_ENST00000293748,NS,carcinoma,0,2	SYNGAP1	202	2	2	Substitution - coding silent(2)	stomach(2)	c.G1713A						PASS	.	G		1228,3176		187,854,1161	23.0	23.0	23.0		1713	-10.5	0.2	6	dbSNP_80	23	3424,5172		694,2036,1568	no	coding-synonymous	SYNGAP1	NM_006772.2		881,2890,2729	AA,AG,GG		39.8325,27.8837,35.7846		571/1344	33408542	4652,8348	2202	4298	6500	SO:0001819	synonymous_variant	8831	exon11			TGCTTCGTGGCGG	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.1713G>A	6.37:g.33408542G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			G|0.608;A|0.392	0.392	strong		0.632	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
ZNF705A	440077	hgsc.bcm.edu	37	12	8329700	8329700	+	Missense_Mutation	SNP	A	A	C	rs10743253	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:8329700A>C	ENST00000359286.4	+	5	513	c.424A>C	c.(424-426)Aaa>Caa	p.K142Q		NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	142			K -> Q (in dbSNP:rs10743253).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K142Q(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		CAGTGGAAAGAAACCCTATGT	0.373													a|||	2152	0.429712	0.2882	0.4683	5008	,	,		-128	0.5198		0.5616	False		,,,				2504	0.365				p.K142Q		Atlas-SNP	.											ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	1	Substitution - Missense(1)	stomach(1)	c.A424C						PASS	.	A	GLN/LYS	1390,3016		224,942,1037	125.0	128.0	127.0		424	1.4	0.1	12	dbSNP_120	127	4659,3941		1319,2021,960	no	missense	ZNF705A	NM_001004328.2	53	1543,2963,1997	CC,CA,AA		45.8256,31.5479,46.5093	probably-damaging	142/301	8329700	6049,6957	2203	4300	6503	SO:0001583	missense	440077	exon5			GGAAAGAAACCCT	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"""Zinc fingers, C2H2-type"", ""-"""	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.424A>C	12.37:g.8329700A>C	ENSP00000352233:p.Lys142Gln	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	309	146	0.472492	NM_001004328		Missense_Mutation	SNP	ENST00000359286.4	37	CCDS31737.1	1021	0.4674908424908425	136	0.2764227642276423	170	0.4696132596685083	300	0.5244755244755245	415	0.5474934036939314	.	16.40	3.111296	0.56398	0.315479	0.541744	ENSG00000196946	ENST00000396570;ENST00000359286	T;T	0.02280	4.36;4.36	1.35	1.35	0.21983	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.88450	2.955	0.44309	P	0.0028200000000000447	D	0.57899	0.981	P	0.59221	0.854	T	0.39860	-0.9593	8	0.87932	D	0	.	6.8118	0.23809	1.0:0.0:0.0:0.0	rs10743253;rs17801815	142	Q6ZN79	Z705A_HUMAN	Q	142	ENSP00000379816:K142Q;ENSP00000352233:K142Q	ENSP00000352233:K142Q	K	+	1	0	ZNF705A	8220967	0.311000	0.24536	0.078000	0.20375	0.253000	0.25986	3.275000	0.51639	0.891000	0.36235	0.329000	0.21502	AAA	A|0.528;C|0.471	0.471	strong		0.373	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328	
OR7A17	26333	hgsc.bcm.edu	37	19	14992042	14992042	+	Silent	SNP	A	A	G	rs10405136	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14992042A>G	ENST00000327462.2	-	1	222	c.126T>C	c.(124-126)aaT>aaC	p.N42N		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	42						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					TGATGAGCAGATTCCCGAGCA	0.498													.|||	2815	0.562101	0.3737	0.5591	5008	,	,		14102	0.6984		0.5149	False		,,,				2504	0.727				p.N42N		Atlas-SNP	.											.	OR7A17	37	.	0			c.T126C						PASS	.	A		1800,2606	632.7+/-395.9	367,1066,770	60.0	51.0	54.0		126	0.5	0.9	19	dbSNP_119	54	4390,4208	553.8+/-386.4	1163,2064,1072	no	coding-synonymous	OR7A17	NM_030901.1		1530,3130,1842	GG,GA,AA		48.9416,40.8534,47.6007		42/310	14992042	6190,6814	2203	4299	6502	SO:0001819	synonymous_variant	26333	exon1			GAGCAGATTCCCG	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"""GPCR / Class A : Olfactory receptors"""	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.126T>C	19.37:g.14992042A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_030901	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	37	CCDS12319.1																																																																																			.	.	weak		0.498	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
ARHGAP44	9912	hgsc.bcm.edu	37	17	12852459	12852459	+	Silent	SNP	A	A	G	rs2072254	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:12852459A>G	ENST00000379672.5	+	11	1164	c.864A>G	c.(862-864)ggA>ggG	p.G288G	ARHGAP44_ENST00000262444.9_Silent_p.G288G|ARHGAP44_ENST00000340825.3_Silent_p.G288G	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	288	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						GTTGGTAGGGACTCTTCCGAG	0.577													A|||	527	0.105232	0.0325	0.1138	5008	,	,		18166	0.1845		0.0765	False		,,,				2504	0.1452				p.G288G		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.A864G						PASS	.	A		192,4000		5,182,1909	29.0	31.0	30.0		864	-1.0	1.0	17	dbSNP_96	30	686,7716		23,640,3538	no	coding-synonymous	ARHGAP44	NM_014859.4		28,822,5447	GG,GA,AA		8.1647,4.5802,6.9716		288/819	12852459	878,11716	2096	4201	6297	SO:0001819	synonymous_variant	9912	exon11			GTAGGGACTCTTC		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"""Rho GTPase activating proteins"""	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.864A>G	17.37:g.12852459A>G		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Silent	SNP	ENST00000379672.5	37	CCDS45616.1																																																																																			A|0.902;G|0.098	0.098	strong		0.577	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859	
EFS	10278	hgsc.bcm.edu	37	14	23826822	23826822	+	Silent	SNP	C	C	T	rs2231809	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23826822C>T	ENST00000216733.3	-	6	1906	c.1299G>A	c.(1297-1299)ctG>ctA	p.L433L	EFS_ENST00000429593.2_Silent_p.L264L|EFS_ENST00000351354.3_Silent_p.L340L|RP11-124D2.3_ENST00000554010.1_RNA	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	433					cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		ACAGGAGCTGCAGATCTCCGG	0.592													T|||	2280	0.455272	0.8767	0.2493	5008	,	,		17090	0.3036		0.2734	False		,,,				2504	0.3753				p.L433L		Atlas-SNP	.											.	EFS	37	.	0			c.G1299A						PASS	.	T	,	3442,964	347.5+/-309.5	1350,742,111	34.0	38.0	37.0		1299,1020	-9.4	0.0	14	dbSNP_98	37	2599,5999	662.1+/-401.9	394,1811,2094	no	coding-synonymous,coding-synonymous	EFS	NM_005864.2,NM_032459.1	,	1744,2553,2205	TT,TC,CC		30.228,21.8793,46.4549	,	433/562,340/469	23826822	6041,6963	2203	4299	6502	SO:0001819	synonymous_variant	10278	exon6			GAGCTGCAGATCT	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"""Cas scaffolding proteins"""	16898	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 3"""	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.1299G>A	14.37:g.23826822C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	128	54	0.421875	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Silent	SNP	ENST00000216733.3	37	CCDS9595.1																																																																																			C|0.549;T|0.451	0.451	strong		0.592	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2		
CIDEC	63924	hgsc.bcm.edu	37	3	9918861	9918861	+	Silent	SNP	C	C	A	rs456168	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9918861C>A	ENST00000336832.2	-	3	235	c.96G>T	c.(94-96)ctG>ctT	p.L32L	CIDEC_ENST00000383817.1_Silent_p.L32L|CIDEC_ENST00000455015.1_Intron|CIDEC_ENST00000430427.1_Silent_p.L32L|CIDEC_ENST00000443115.1_Silent_p.L32L|CIDEC_ENST00000423850.1_Intron	NM_001199552.1|NM_001199623.1|NM_022094.3	NP_001186481.1|NP_001186552.1|NP_071377.2	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	32					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|lipid particle organization (GO:0034389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	8	Medulloblastoma(99;0.227)					TGGGCTCCGACAGCAGCTGCT	0.647													C|||	1569	0.313299	0.4962	0.3458	5008	,	,		18973	0.248		0.1998	False		,,,				2504	0.227				p.L45L		Atlas-SNP	.											CIDEC,NS,carcinoma,0,1	CIDEC	22	1	0			c.G135T						PASS	.	C	,,,	1785,2463		385,1015,724	27.0	27.0	27.0		96,96,135,96	4.2	0.0	3	dbSNP_80	27	1568,6736		155,1258,2739	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIDEC	NM_001199551.1,NM_001199552.1,NM_001199623.1,NM_022094.3	,,,	540,2273,3463	AA,AC,CC		18.8825,42.0198,26.7129	,,,	32/249,32/239,45/252,32/239	9918861	3353,9199	2124	4152	6276	SO:0001819	synonymous_variant	63924	exon3			CTCCGACAGCAGC		CCDS2587.1, CCDS56239.1, CCDS74897.1	3p25	2004-07-26			ENSG00000187288	ENSG00000187288			24229	protein-coding gene	gene with protein product		612120				12429024	Standard	NM_001199623		Approved	CIDE-3, FLJ20871, Fsp27	uc021wsw.1	Q96AQ7	OTTHUMG00000128522	ENST00000336832.2:c.96G>T	3.37:g.9918861C>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	72	46	0.638889	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Silent	SNP	ENST00000336832.2	37	CCDS2587.1																																																																																			C|0.678;A|0.322	0.322	strong		0.647	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094	
CYB5A	1528	hgsc.bcm.edu	37	18	71959075	71959075	+	Silent	SNP	G	G	A	rs76198400	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:71959075G>A	ENST00000340533.4	-	1	176	c.36C>T	c.(34-36)taC>taT	p.Y12Y	CYB5A_ENST00000494131.2_Silent_p.Y12Y|CYB5A_ENST00000299438.9_5'Flank|CYB5A_ENST00000397914.4_Silent_p.Y12Y	NM_148923.3	NP_683725.1	P00167	CYB5_HUMAN	cytochrome b5 type A (microsomal)	12	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				hydrogen ion transmembrane transport (GO:1902600)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	aldo-keto reductase (NADP) activity (GO:0004033)|cytochrome-c oxidase activity (GO:0004129)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(1)|lung(1)|skin(1)	4		Esophageal squamous(42;0.0749)|Prostate(75;0.157)|Melanoma(33;0.211)				CCTCTAGGGTGTAGTACTTCA	0.587											OREG0025052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	477	0.0952476	0.0068	0.2046	5008	,	,		13141	0.0704		0.1322	False		,,,				2504	0.1247				p.Y12Y	NSCLC(176;1530 2076 2606 27426 50572)|Ovarian(151;328 1870 2837 37860 52175)	Atlas-SNP	.											.	CYB5A	9	.	0			c.C36T						PASS	.	G	,,	149,4257	103.0+/-141.5	2,145,2056	237.0	199.0	212.0		36,36,36	2.6	1.0	18	dbSNP_131	212	1294,7306	256.5+/-280.9	93,1108,3099	no	coding-synonymous,coding-synonymous,coding-synonymous	CYB5A	NM_001190807.2,NM_001914.3,NM_148923.3	,,	95,1253,5155	AA,AG,GG		15.0465,3.3818,11.0949	,,	12/125,12/99,12/135	71959075	1443,11563	2203	4300	6503	SO:0001819	synonymous_variant	1528	exon1			TAGGGTGTAGTAC	M22865	CCDS12004.1, CCDS12005.1, CCDS54188.1	18q23	2006-01-30	2006-01-30	2006-01-30	ENSG00000166347	ENSG00000166347		"""Cytochrome b genes"""	2570	protein-coding gene	gene with protein product		613218	"""cytochrome b-5"", ""cytochrome b5 (microsomal)"""	CYB5		1840560	Standard	NM_148923		Approved		uc002lli.3	P00167	OTTHUMG00000132843	ENST00000340533.4:c.36C>T	18.37:g.71959075G>A		Somatic	107	0	0	1134	WXS	Illumina HiSeq	Phase_I	179	90	0.502793	NM_148923	A8MV91|F8WEU4|Q6IB14	Silent	SNP	ENST00000340533.4	37	CCDS12004.1																																																																																			A|0.107;C|0.000;G|0.893	0.107	strong		0.587	CYB5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256316.1	NM_001914, NM_148923	
CILP2	148113	hgsc.bcm.edu	37	19	19654189	19654189	+	Silent	SNP	G	G	A	rs45556231	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19654189G>A	ENST00000291495.5	+	7	1195	c.1110G>A	c.(1108-1110)tcG>tcA	p.S370S	CILP2_ENST00000586018.1_Silent_p.S376S	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	370	Ig-like C2-type.					extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.S370S(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCGTGCGCTCGGGCACTGCCC	0.647													G|||	593	0.118411	0.1634	0.1167	5008	,	,		14555	0.0		0.166	False		,,,				2504	0.1319				p.S370S		Atlas-SNP	.											CILP2,NS,carcinoma,0,1	CILP2	84	1	1	Substitution - coding silent(1)	prostate(1)	c.G1110A						PASS	.	G		716,3690		51,614,1538	43.0	43.0	43.0		1110	-8.9	0.0	19	dbSNP_127	43	1420,7178		113,1194,2992	no	coding-synonymous	CILP2	NM_153221.2		164,1808,4530	AA,AG,GG		16.5155,16.2506,16.4257		370/1157	19654189	2136,10868	2203	4299	6502	SO:0001819	synonymous_variant	148113	exon7			GCGCTCGGGCACT	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1110G>A	19.37:g.19654189G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	219	100	0.456621	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			G|0.842;A|0.158	0.158	strong		0.647	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
LAMA1	284217	hgsc.bcm.edu	37	18	6977844	6977844	+	Missense_Mutation	SNP	A	A	G	rs671871	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:6977844A>G	ENST00000389658.3	-	44	6320	c.6227T>C	c.(6226-6228)aTt>aCt	p.I2076T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2076	Domain II and I.		I -> T (in dbSNP:rs671871).		axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GTTGGCTTGAATTTCCACGTC	0.418													G|||	1372	0.273962	0.6309	0.2089	5008	,	,		20170	0.0893		0.172	False		,,,				2504	0.1329				p.I2076T		Atlas-SNP	.											.	LAMA1	458	.	0			c.T6227C						PASS	.	G	THR/ILE	2401,2005	560.5+/-380.5	669,1063,471	60.0	58.0	58.0		6227	2.2	0.9	18	dbSNP_83	58	1522,7078	746.3+/-407.3	130,1262,2908	yes	missense	LAMA1	NM_005559.3	89	799,2325,3379	GG,GA,AA		17.6977,45.5061,30.163	benign	2076/3076	6977844	3923,9083	2203	4300	6503	SO:0001583	missense	284217	exon44			GCTTGAATTTCCA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6227T>C	18.37:g.6977844A>G	ENSP00000374309:p.Ile2076Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	553	0.2532051282051282	294	0.5975609756097561	71	0.19613259668508287	59	0.10314685314685315	129	0.17018469656992086	G	5.574	0.290674	0.10567	0.544939	0.176977	ENSG00000101680	ENST00000389658	T	0.41400	1.0	5.1	2.15	0.27550	Laminin II (1);	0.565454	0.17247	N	0.181313	T	0.00012	0.0000	N	0.00926	-1.1	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.42849	-0.9427	9	0.15952	T	0.53	.	5.0817	0.14661	0.3013:0.0:0.5527:0.1461	rs671871;rs56554268;rs58305327;rs671871	2076	P25391	LAMA1_HUMAN	T	2076	ENSP00000374309:I2076T	ENSP00000374309:I2076T	I	-	2	0	LAMA1	6967844	0.989000	0.36119	0.949000	0.38748	0.939000	0.58152	1.200000	0.32247	0.209000	0.20645	-0.119000	0.15052	ATT	A|0.717;G|0.283	0.283	strong		0.418	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
ACP5	54	hgsc.bcm.edu	37	19	11687908	11687908	+	Silent	SNP	G	G	A	rs62638747	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11687908G>A	ENST00000592828.1	-	4	627	c.225C>T	c.(223-225)ttC>ttT	p.F75F	ACP5_ENST00000433365.2_Silent_p.F75F|ACP5_ENST00000590420.1_Intron|ACP5_ENST00000412435.2_Silent_p.F75F|ACP5_ENST00000218758.5_Silent_p.F75F	NM_001111034.1	NP_001104504.1	P13686	PPA5_HUMAN	acid phosphatase 5, tartrate resistant	75					bone morphogenesis (GO:0060349)|bone resorption (GO:0045453)|defense response to Gram-positive bacterium (GO:0050830)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of superoxide anion generation (GO:0032929)|negative regulation of tumor necrosis factor production (GO:0032720)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	acid phosphatase activity (GO:0003993)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)	p.F75F(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	9						GCACACCAGTGAAGTAAAAAT	0.572													G|||	324	0.0646965	0.031	0.0749	5008	,	,		17330	0.0238		0.1292	False		,,,				2504	0.0787				p.F75F		Atlas-SNP	.											ACP5,NS,carcinoma,0,1	ACP5	30	1	1	Substitution - coding silent(1)	pancreas(1)	c.C225T						PASS	.	G	,,,	171,4235	111.2+/-149.4	2,167,2034	77.0	75.0	76.0		225,225,225,225	3.7	0.8	19	dbSNP_129	76	1020,7580	218.5+/-256.9	65,890,3345	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACP5	NM_001111034.1,NM_001111035.1,NM_001111036.1,NM_001611.3	,,,	67,1057,5379	AA,AG,GG		11.8605,3.8811,9.1573	,,,	75/326,75/326,75/326,75/326	11687908	1191,11815	2203	4300	6503	SO:0001819	synonymous_variant	54	exon3			ACCAGTGAAGTAA	X14618	CCDS12265.1	19p13.2	2012-10-02			ENSG00000102575	ENSG00000102575	3.1.3.2		124	protein-coding gene	gene with protein product	"""tartrate-resistant acid phosphatase"""	171640				8449511, 2338077	Standard	NM_001611		Approved	TRAP	uc002msj.4	P13686	OTTHUMG00000182036	ENST00000592828.1:c.225C>T	19.37:g.11687908G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	170	88	0.517647	NM_001111034	A8K3V2|Q2TAB1|Q6IAS6|Q9UCJ5|Q9UCJ6|Q9UCJ7	Silent	SNP	ENST00000592828.1	37	CCDS12265.1																																																																																			G|0.911;A|0.089	0.089	strong		0.572	ACP5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458881.1		
TPSD1	23430	hgsc.bcm.edu	37	16	1306927	1306927	+	Silent	SNP	C	C	T	rs79472859		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306927C>T	ENST00000211076.3	+	3	532	c.384C>T	c.(382-384)gaC>gaT	p.D128D	TPSD1_ENST00000397534.2_Silent_p.D121D|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	128	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.D128D(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CCGGGGCGGACATCGCCCTGC	0.647																																					p.D128D		Atlas-SNP	.											TPSD1,NS,carcinoma,0,1	TPSD1	47	1	1	Substitution - coding silent(1)	stomach(1)	c.C384T						PASS	.						75.0	72.0	73.0					16																	1306927		2199	4300	6499	SO:0001819	synonymous_variant	23430	exon3			GGCGGACATCGCC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.384C>T	16.37:g.1306927C>T		Somatic	407	0	0		WXS	Illumina HiSeq	Phase_I	596	113	0.189597	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			C|0.643;T|0.357	0.357	strong		0.647	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
IPO4	79711	hgsc.bcm.edu	37	14	24649669	24649669	+	Silent	SNP	C	C	T	rs2273912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24649669C>T	ENST00000354464.6	-	30	3401	c.3225G>A	c.(3223-3225)caG>caA	p.Q1075Q	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	1075					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)		p.Q1075Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CCAGTACAGCCTGGAGCTCCT	0.592													C|||	667	0.133187	0.1104	0.2983	5008	,	,		19218	0.1022		0.0865	False		,,,				2504	0.1268				p.Q1075Q		Atlas-SNP	.											IPO4,NS,carcinoma,0,1	IPO4	74	1	1	Substitution - coding silent(1)	stomach(1)	c.G3225A						PASS	.	C		384,3634		17,350,1642	37.0	40.0	39.0		3225	3.1	1.0	14	dbSNP_100	39	776,7568		29,718,3425	no	coding-synonymous	IPO4	NM_024658.3		46,1068,5067	TT,TC,CC		9.3001,9.557,9.3836		1075/1082	24649669	1160,11202	2009	4172	6181	SO:0001819	synonymous_variant	79711	exon30			TACAGCCTGGAGC	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.3225G>A	14.37:g.24649669C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	37	CCDS9616.1																																																																																			C|0.876;T|0.124	0.124	strong		0.592	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
EXD3	54932	hgsc.bcm.edu	37	9	140243968	140243968	+	Missense_Mutation	SNP	C	C	T	rs79140116	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140243968C>T	ENST00000340951.4	-	15	1705	c.1510G>A	c.(1510-1512)Gtg>Atg	p.V504M	EXD3_ENST00000342129.4_Missense_Mutation_p.V184M	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						GGGGCTGGCACGCTCGCCACC	0.697													c|||	524	0.104633	0.0507	0.2695	5008	,	,		14938	0.0427		0.1541	False		,,,				2504	0.0736				p.V504M		Atlas-SNP	.											.	EXD3	86	.	0			c.G1510A						PASS	.		MET/VAL	254,3978		10,234,1872	16.0	19.0	18.0		1510	-5.4	0.0	9	dbSNP_131	18	1194,7212		98,998,3107	no	missense	EXD3	NM_017820.3	21	108,1232,4979	TT,TC,CC		14.2041,6.0019,11.4575	benign	504/877	140243968	1448,11190	2116	4203	6319	SO:0001583	missense	54932	exon15			CTGGCACGCTCGC		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.1510G>A	9.37:g.140243968C>T	ENSP00000340474:p.Val504Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	284	0.13003663003663005	25	0.0508130081300813	105	0.2900552486187845	30	0.05244755244755245	124	0.16358839050131926	t	3.449	-0.112483	0.06881	0.060019	0.142041	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.68025	-0.3;-0.3	2.72	-5.44	0.02624	-5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2);	2.595330	0.01201	N	0.007563	T	0.00012	0.0000	N	0.03253	-0.375	0.80722	P	0.0	B;B	0.15930	0.001;0.015	B;B	0.01281	0.0;0.0	T	0.03060	-1.1077	9	0.46703	T	0.11	.	1.1609	0.01805	0.2635:0.3154:0.2657:0.1554	.	184;504	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	M	184;504	ENSP00000343705:V184M;ENSP00000340474:V504M	ENSP00000340474:V504M	V	-	1	0	EXD3	139363789	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.924000	0.01565	-1.820000	0.01215	-1.902000	0.00527	GTG	C|0.870;T|0.130	0.130	strong		0.697	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
N4BP2L2	10443	hgsc.bcm.edu	37	13	33017043	33017043	+	Missense_Mutation	SNP	T	T	C	rs3742318	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:33017043T>C	ENST00000504114.1	-	6	1677	c.1586A>G	c.(1585-1587)aAt>aGt	p.N529S	N4BP2L2_ENST00000446957.2_Intron|N4BP2L2_ENST00000380121.3_5'UTR|N4BP2L2_ENST00000399396.3_Missense_Mutation_p.N544S|N4BP2L2_ENST00000357505.6_Missense_Mutation_p.N529S			Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	0					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TTTTTGTTTATTCTCCTCTTC	0.333													T|||	1321	0.263778	0.1876	0.3732	5008	,	,		17811	0.2292		0.2038	False		,,,				2504	0.3865				p.N544S		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.A1631G						PASS	.	T	SER/ASN	791,2883		92,607,1138	77.0	68.0	70.0		1631	-0.3	0.0	13	dbSNP_107	70	1650,6540		161,1328,2606	yes	missense	N4BP2L2	NM_033111.3	46	253,1935,3744	CC,CT,TT		20.1465,21.5297,20.5748	benign	544/753	33017043	2441,9423	1837	4095	5932	SO:0001583	missense	10443	exon7			TGTTTATTCTCCT	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"""phosphonoformate immuno-associated protein 5"""	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000504114.1:c.1586A>G	13.37:g.33017043T>C	ENSP00000427477:p.Asn529Ser	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	120	6	0.05	NM_033111	A3KME8	Missense_Mutation	SNP	ENST00000504114.1	37		485	0.22206959706959706	86	0.17479674796747968	127	0.35082872928176795	122	0.21328671328671328	150	0.19788918205804748	T	9.575	1.122085	0.20877	0.215297	0.201465	ENSG00000139617;ENSG00000139617;ENSG00000244754;ENSG00000244754;ENSG00000244754	ENST00000380121;ENST00000503296;ENST00000504114;ENST00000357505;ENST00000399396	.	.	.	5.12	-0.351	0.12602	.	0.768603	0.11295	N	0.578799	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B;B;B	0.24368	0.021;0.021;0.102;0.102	B;B;B;B	0.21917	0.025;0.025;0.037;0.037	T	0.38243	-0.9670	8	0.31617	T	0.26	0.8588	1.2916	0.02061	0.1368:0.1577:0.2838:0.4217	rs3742318;rs52817721;rs60092837;rs3742318	529;544;427;427	B4DPY1;Q92802-3;Q96KV2;Q9Y3H6	.;.;.;.	S	427;456;529;529;544	.	ENSP00000350104:N529S	N	-	2	0	N4BP2L2;RP11-298P3.4	31915043	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.958000	0.03857	-0.278000	0.09180	-0.321000	0.08615	AAT	T|0.777;C|0.223	0.223	strong		0.333	N4BP2L2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000361380.1	NM_014887	
P2RY2	5029	hgsc.bcm.edu	37	11	72946140	72946140	+	Missense_Mutation	SNP	G	G	C	rs3741156	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:72946140G>C	ENST00000311131.2	+	3	1403	c.936G>C	c.(934-936)agG>agC	p.R312S	P2RY2_ENST00000393597.2_Missense_Mutation_p.R312S|P2RY2_ENST00000393596.2_Missense_Mutation_p.R312S	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	312			R -> S (in dbSNP:rs3741156). {ECO:0000269|PubMed:15489334}.		cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	CTGGGCAGAGGCTCGTACGCT	0.647													G|||	1364	0.272364	0.0121	0.4107	5008	,	,		17319	0.5397		0.2266	False		,,,				2504	0.2975				p.R312S		Atlas-SNP	.											.	P2RY2	54	.	0			c.G936C						PASS	.	G	SER/ARG,SER/ARG,SER/ARG	261,4139	143.5+/-178.5	3,255,1942	64.0	54.0	57.0		936,936,936	2.2	1.0	11	dbSNP_107	57	2036,6550	346.9+/-326.4	248,1540,2505	yes	missense,missense,missense	P2RY2	NM_002564.2,NM_176071.1,NM_176072.1	110,110,110	251,1795,4447	CC,CG,GG		23.713,5.9318,17.6883	benign,benign,benign	312/378,312/378,312/378	72946140	2297,10689	2200	4293	6493	SO:0001583	missense	5029	exon3			GCAGAGGCTCGTA	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.936G>C	11.37:g.72946140G>C	ENSP00000310305:p.Arg312Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	37	CCDS8219.1	625	0.28617216117216115	6	0.012195121951219513	132	0.36464088397790057	312	0.5454545454545454	175	0.23087071240105542	G	5.105	0.205055	0.09704	0.059318	0.23713	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.27720	1.65;1.65;1.65	4.09	2.16	0.27623	.	0.464574	0.23797	N	0.044477	T	0.00012	0.0000	N	0.21448	0.665	0.34061	P	0.34272100000000005	B	0.15930	0.015	B	0.12837	0.008	T	0.46289	-0.9202	9	0.15066	T	0.55	.	6.0799	0.19935	0.3699:0.0:0.6301:0.0	rs3741156;rs17850859	312	P41231	P2RY2_HUMAN	S	312	ENSP00000377222:R312S;ENSP00000310305:R312S;ENSP00000377221:R312S	ENSP00000310305:R312S	R	+	3	2	P2RY2	72623788	1.000000	0.71417	0.983000	0.44433	0.022000	0.10575	1.609000	0.36858	0.305000	0.22832	-0.254000	0.11334	AGG	C|0.211;G|0.789	0.211	strong		0.647	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072	
DOCK6	57572	hgsc.bcm.edu	37	19	11326119	11326119	+	Silent	SNP	A	A	G	rs2304155	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11326119A>G	ENST00000294618.7	-	32	4061	c.4050T>C	c.(4048-4050)aaT>aaC	p.N1350N	DOCK6_ENST00000319867.7_Silent_p.N689N|CTC-510F12.2_ENST00000588634.1_RNA	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1350					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GCCAGCGCACATTCTCCGGAT	0.557													G|||	2508	0.500799	0.41	0.5101	5008	,	,		18057	0.5119		0.6292	False		,,,				2504	0.4734				p.N1350N		Atlas-SNP	.											.	DOCK6	104	.	0			c.T4050C						PASS	.	G		1911,2141		456,999,571	53.0	52.0	53.0		4050	-7.4	0.2	19	dbSNP_100	53	5217,3123		1623,1971,576	no	coding-synonymous	DOCK6	NM_020812.2		2079,2970,1147	GG,GA,AA		37.446,47.1619,42.479		1350/2048	11326119	7128,5264	2026	4170	6196	SO:0001819	synonymous_variant	57572	exon32			GCGCACATTCTCC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.4050T>C	19.37:g.11326119A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			G|0.539;N|0.001	0.539	strong		0.557	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
WDR90	197335	hgsc.bcm.edu	37	16	708275	708275	+	Missense_Mutation	SNP	C	C	A	rs45613635	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:708275C>A	ENST00000293879.4	+	22	2697	c.2697C>A	c.(2695-2697)caC>caA	p.H899Q	LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Missense_Mutation_p.H899Q			Q96KV7	WDR90_HUMAN	WD repeat domain 90	899				H -> Q (in Ref. 1; BAD18654). {ECO:0000305}.						endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CTCTGGGCCACCTGCTGGTGT	0.667													C|||	1707	0.340855	0.0968	0.3804	5008	,	,		18278	0.6766		0.2565	False		,,,				2504	0.3834				p.H899Q		Atlas-SNP	.											.	WDR90	107	.	0			c.C2697A						PASS	.	C	GLN/HIS	490,3792		27,436,1678	57.0	63.0	61.0		2697	3.1	1.0	16	dbSNP_127	61	1923,6587		206,1511,2538	yes	missense	WDR90	NM_145294.4	24	233,1947,4216	AA,AC,CC		22.5969,11.4433,18.8634	possibly-damaging	899/1749	708275	2413,10379	2141	4255	6396	SO:0001583	missense	197335	exon22			GGGCCACCTGCTG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.2697C>A	16.37:g.708275C>A	ENSP00000293879:p.His899Gln	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	775	0.35485347985347987	47	0.09552845528455285	135	0.3729281767955801	385	0.6730769230769231	208	0.27440633245382584	C	15.64	2.893432	0.52121	0.114433	0.225969	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.49720	0.77;3.6	5.28	3.07	0.35406	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.126543	0.51477	U	0.000100	T	0.00012	0.0000	L	0.52759	1.655	0.09310	P	0.9999999999999999	D;P	0.67145	0.996;0.852	P;B	0.62089	0.898;0.314	T	0.43212	-0.9405	9	0.13108	T	0.6	.	5.1499	0.15004	0.0:0.5613:0.1906:0.2481	rs45613635;rs62032462	899;899	F8VUX9;Q96KV7	.;WDR90_HUMAN	Q	899	ENSP00000448122:H899Q;ENSP00000293879:H899Q	ENSP00000293879:H899Q	H	+	3	2	WDR90	648276	0.999000	0.42202	0.998000	0.56505	0.836000	0.47400	0.623000	0.24447	1.194000	0.43101	0.555000	0.69702	CAC	C|0.694;A|0.306	0.306	strong		0.667	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377918	49377918	+	Missense_Mutation	SNP	G	G	T	rs35087747	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49377918G>T	ENST00000200453.5	+	2	1697	c.1428G>T	c.(1426-1428)agG>agT	p.R476S		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	476	4 X 34 AA approximate repeats.|Glu-rich.|Interaction with SMAD7.		R -> S (in dbSNP:rs35087747). {ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CGGACCAGAGGGCCCACTTCA	0.572													T|||	421	0.0840655	0.087	0.0793	5008	,	,		17447	0.003		0.164	False		,,,				2504	0.0849				p.R476S		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G1428T						PASS	.	T	SER/ARG	578,3828	771.4+/-413.8	35,508,1660	71.0	70.0	70.0		1428	-5.6	0.0	19	dbSNP_126	70	1549,7051	745.0+/-407.3	129,1291,2880	yes	missense	PPP1R15A	NM_014330.3	110	164,1799,4540	TT,TG,GG		18.0116,13.1185,16.354	benign	476/675	49377918	2127,10879	2203	4300	6503	SO:0001583	missense	23645	exon2			CCAGAGGGCCCAC	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1428G>T	19.37:g.49377918G>T	ENSP00000200453:p.Arg476Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	84	36	0.428571	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	198	0.09065934065934066	45	0.09146341463414634	30	0.08287292817679558	1	0.0017482517482517483	122	0.16094986807387862	T	0.463	-0.888184	0.02511	0.131185	0.180116	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05139	3.49	4.19	-5.56	0.02529	.	0.890365	0.09631	N	0.776241	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34925	-0.9809	9	0.02654	T	1	2.4026	3.0039	0.06023	0.2444:0.4426:0.1244:0.1886	rs35087747	476	O75807	PR15A_HUMAN	S	476;316;434	ENSP00000200453:R476S	ENSP00000200453:R476S	R	+	3	2	PPP1R15A	54069730	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.597000	0.00894	-1.820000	0.01215	-1.089000	0.02181	AGG	A|0.000;C|0.000;G|0.864;T|0.136	0.136	strong		0.572	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
COL6A3	1293	hgsc.bcm.edu	37	2	238253149	238253149	+	Silent	SNP	G	G	A	rs2646258	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:238253149G>A	ENST00000295550.4	-	36	7964	c.7512C>T	c.(7510-7512)aaC>aaT	p.N2504N	COL6A3_ENST00000409809.1_Silent_p.N2298N|COL6A3_ENST00000472056.1_Silent_p.N1897N|COL6A3_ENST00000353578.4_Silent_p.N2298N|COL6A3_ENST00000346358.4_Silent_p.N2304N|COL6A3_ENST00000347401.3_Silent_p.N2303N	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2504	Nonhelical region.|VWFA 11. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTAGGAATCCGTTCCTCACAC	0.507													G|||	543	0.108427	0.09	0.1729	5008	,	,		21892	0.0536		0.1282	False		,,,				2504	0.1237				p.N2504N		Atlas-SNP	.											.	COL6A3	608	.	0			c.C7512T						PASS	.	G	,,	404,4002	199.4+/-223.0	17,370,1816	136.0	129.0	131.0		7512,5691,6894	-6.7	0.0	2	dbSNP_100	131	902,7698	201.6+/-245.0	53,796,3451	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	70,1166,5267	AA,AG,GG		10.4884,9.1693,10.0415	,,	2504/3178,1897/2571,2298/2972	238253149	1306,11700	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon36			GAATCCGTTCCTC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7512C>T	2.37:g.238253149G>A		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	348	163	0.468391	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.896;A|0.104	0.104	strong		0.507	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
FAM153B	202134	hgsc.bcm.edu	37	5	175528119	175528119	+	Splice_Site	SNP	T	T	C	rs199710353		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:175528119T>C	ENST00000253490.4	+	11	689	c.632T>C	c.(631-633)aTg>aCg	p.M211T	FAM153B_ENST00000512862.1_Intron|FAM153B_ENST00000510151.1_Splice_Site_p.M134T|FAM153B_ENST00000515817.1_Splice_Site_p.M134T			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	211								p.M211T(4)		endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	16	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		GAAGTTCACATGGTAAAGTCG	0.433													N|||	1	0.000199681	0.0	0.0014	5008	,	,		30376	0.0		0.0	False		,,,				2504	0.0				p.M134T		Atlas-SNP	.											FAM153B,NS,carcinoma,0,4	FAM153B	28	4	4	Substitution - Missense(4)	endometrium(3)|kidney(1)	c.T401C						scavenged	.						258.0	307.0	289.0					5																	175528119		1510	2708	4218	SO:0001630	splice_region_variant	202134	exon10			TTCACATGGTAAA	AK055006	CCDS43401.1, CCDS43401.2	5q35.2	2010-05-12			ENSG00000182230	ENSG00000182230			27323	protein-coding gene	gene with protein product							Standard	NM_001265615		Approved		uc031smb.1	P0C7A2	OTTHUMG00000163181	ENST00000253490.4:c.633+1T>C	5.37:g.175528119T>C		Somatic	732	0	0		WXS	Illumina HiSeq	Phase_I	598	6	0.0100334	NM_001265615	A8MTI1	Missense_Mutation	SNP	ENST00000253490.4	37		.	.	.	.	.	.	.	.	.	.	T	0.008	-1.861446	0.00552	.	.	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	0.917	-0.575	0.11734	.	.	.	.	.	T	0.20292	0.0488	N	0.24115	0.695	0.09310	N	1	B	0.33528	0.416	B	0.35470	0.203	T	0.18618	-1.0331	8	0.35671	T	0.21	.	2.9058	0.05720	0.5811:0.0:0.0:0.4189	.	211	P0C7A2	F153B_HUMAN	T	134;211	.	ENSP00000253490:M211T	M	+	2	0	FAM153B	175460725	0.015000	0.18098	0.001000	0.08648	0.003000	0.03518	-0.418000	0.07080	-0.147000	0.11254	-0.935000	0.02700	ATG	T|0.500;C|0.500	0.500	weak		0.433	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001079529	Missense_Mutation
SIGLEC8	27181	hgsc.bcm.edu	37	19	51957556	51957556	+	Missense_Mutation	SNP	T	T	C	rs3829659	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51957556T>C	ENST00000321424.3	-	6	1228	c.1162A>G	c.(1162-1164)Agg>Ggg	p.R388G	SIGLEC8_ENST00000597352.1_5'Flank|SIGLEC8_ENST00000340550.5_Missense_Mutation_p.R295G|SIGLEC8_ENST00000430817.1_Missense_Mutation_p.R279G	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	388			R -> G (in dbSNP:rs3829659).		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.R388G(1)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GATTTCTTCCTGCAGGACCTC	0.592													t|||	1637	0.326877	0.5461	0.255	5008	,	,		17901	0.2321		0.2714	False		,,,				2504	0.2362				p.R388G		Atlas-SNP	.											SIGLEC8,NS,carcinoma,0,1	SIGLEC8	130	1	1	Substitution - Missense(1)	stomach(1)	c.A1162G						PASS	.	C	GLY/ARG	2365,2041		638,1089,476	96.0	90.0	92.0		1162	-0.1	0.0	19	dbSNP_107	92	2089,6511		251,1587,2462	no	missense	SIGLEC8	NM_014442.2	125	889,2676,2938	CC,CT,TT		24.2907,46.3232,34.2457	probably-damaging	388/500	51957556	4454,8552	2203	4300	6503	SO:0001583	missense	27181	exon6			TCTTCCTGCAGGA	AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.1162A>G	19.37:g.51957556T>C	ENSP00000321077:p.Arg388Gly	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_014442	Q7Z728	Missense_Mutation	SNP	ENST00000321424.3	37	CCDS33086.1	725	0.33195970695970695	262	0.532520325203252	107	0.2955801104972376	135	0.23601398601398602	221	0.29155672823219	.	11.33	1.607566	0.28623	0.536768	0.242907	ENSG00000105366	ENST00000430817;ENST00000321424;ENST00000340550	T;T;T	0.73681	0.62;-0.77;0.19	2.09	-0.0729	0.13737	.	.	.	.	.	T	0.00012	0.0000	M	0.86502	2.82	0.80722	P	0.0	D;P;P	0.89917	1.0;0.909;0.915	D;B;B	0.69142	0.962;0.382;0.236	T	0.38067	-0.9678	8	0.62326	D	0.03	.	4.3104	0.10967	0.0:0.361:0.0:0.639	rs3829659;rs3829659	279;295;388	C9JT30;Q9NYZ4-2;Q9NYZ4	.;.;SIGL8_HUMAN	G	279;388;295	ENSP00000389142:R279G;ENSP00000321077:R388G;ENSP00000339448:R295G	ENSP00000321077:R388G	R	-	1	2	SIGLEC8	56649368	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.711000	0.05019	-0.079000	0.12707	-0.475000	0.04921	AGG	T|0.647;C|0.353	0.353	strong		0.592	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442	
CTSF	8722	hgsc.bcm.edu	37	11	66331458	66331458	+	Silent	SNP	A	A	G	rs572846	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:66331458A>G	ENST00000310325.5	-	13	1510	c.1401T>C	c.(1399-1401)cgT>cgC	p.R467R	CTSF_ENST00000533168.1_5'Flank|ACTN3_ENST00000513398.1_RNA|ACTN3_ENST00000502692.1_RNA	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F	467				SDVPFWAIKNSWGTDWGEKGYYYLHRGSGACGVNTMASSAV VD -> EFRCLSCIQPGHRQGWDHSISGPLEGK (in Ref. 9). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)			endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						CCCCGGACCCACGATGCAAGT	0.667													G|||	2950	0.589058	0.879	0.4207	5008	,	,		17133	0.5536		0.5497	False		,,,				2504	0.3937				p.R467R		Atlas-SNP	.											.	CTSF	42	.	0			c.T1401C						PASS	.	G		3575,825	322.3+/-297.6	1467,641,92	34.0	38.0	37.0		1401	-6.4	0.7	11	dbSNP_83	37	4564,4026	552.7+/-386.2	1199,2166,930	no	coding-synonymous	CTSF	NM_003793.3		2666,2807,1022	GG,GA,AA		46.8685,18.75,37.3441		467/485	66331458	8139,4851	2200	4295	6495	SO:0001819	synonymous_variant	8722	exon13			GGACCCACGATGC	AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"""Cathepsins"""	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090	ENST00000310325.5:c.1401T>C	11.37:g.66331458A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_003793	B2R964|O95240|Q9NSU4|Q9UKQ5	Silent	SNP	ENST00000310325.5	37	CCDS8144.1																																																																																			A|0.380;G|0.620	0.620	strong		0.667	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793	
PSMG2	56984	hgsc.bcm.edu	37	18	12718593	12718593	+	Silent	SNP	A	A	G	rs2302768	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:12718593A>G	ENST00000317615.6	+	4	1048	c.366A>G	c.(364-366)tcA>tcG	p.S122S	PSMG2_ENST00000590217.1_Silent_p.S122S|PSMG2_ENST00000585331.2_Silent_p.S91S	NM_020232.4	NP_064617.2			proteasome (prosome, macropain) assembly chaperone 2											lung(1)|prostate(2)|skin(1)	4						TTGTTCTTTCAAGCAGTCATT	0.383													G|||	1469	0.293331	0.2466	0.281	5008	,	,		16839	0.3046		0.4324	False		,,,				2504	0.2106				p.S122S		Atlas-SNP	.											.	PSMG2	17	.	0			c.A366G						PASS	.	G	,	1337,3069	693.3+/-405.7	193,951,1059	146.0	135.0	139.0		366,273	-10.9	0.0	18	dbSNP_100	139	3853,4747	609.1+/-395.5	874,2105,1321	yes	coding-synonymous,coding-synonymous	PSMG2	NM_020232.4,NM_147163.1	,	1067,3056,2380	GG,GA,AA		44.8023,30.345,39.9047	,	122/265,91/234	12718593	5190,7816	2203	4300	6503	SO:0001819	synonymous_variant	56984	exon4			TCTTTCAAGCAGT	AF276707	CCDS11862.1, CCDS67440.1	18p11.21	2012-01-25	2007-10-23	2007-10-23	ENSG00000128789	ENSG00000128789			24929	protein-coding gene	gene with protein product	"""hepatocellular carcinoma susceptibility protein"", ""CD40 ligand-activated specific transcript 3"""	609702	"""tumor necrosis factor superfamily, member 5-induced protein 1"""	TNFSF5IP1		11854909, 12147697, 17189198	Standard	NM_147163		Approved	HCCA3, MDS003, MGC15092, CLAST3, HsT1707, PAC2	uc002krk.3	Q969U7	OTTHUMG00000131703	ENST00000317615.6:c.366A>G	18.37:g.12718593A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	113	111	0.982301	NM_020232		Silent	SNP	ENST00000317615.6	37	CCDS11862.1																																																																																			A|0.636;G|0.364	0.364	strong		0.383	PSMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254615.1	NM_020232	
CACNA1E	777	hgsc.bcm.edu	37	1	181701799	181701799	+	Missense_Mutation	SNP	T	T	A	rs35737760	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:181701799T>A	ENST00000367573.2	+	20	2577	c.2577T>A	c.(2575-2577)gaT>gaA	p.D859E	CACNA1E_ENST00000358338.5_Missense_Mutation_p.D791E|CACNA1E_ENST00000357570.5_Missense_Mutation_p.D810E|CACNA1E_ENST00000367567.4_Missense_Mutation_p.D466E|CACNA1E_ENST00000360108.3_Missense_Mutation_p.D840E|CACNA1E_ENST00000367570.1_Missense_Mutation_p.D859E|CACNA1E_ENST00000526775.1_Missense_Mutation_p.D840E	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	859			D -> E (in dbSNP:rs35737760).		calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TCAAGGGGGATGGAGGGGACC	0.667													T|||	751	0.14996	0.1664	0.1311	5008	,	,		16409	0.0506		0.1382	False		,,,				2504	0.2556				p.D859E		Atlas-SNP	.											CACNA1E,trunk,malignant_melanoma,+2,1	CACNA1E	778	1	0			c.T2577A						PASS	.	T	GLU/ASP,GLU/ASP,GLU/ASP	505,3345		37,431,1457	12.0	16.0	15.0		2577,2577,2520	-6.0	0.0	1	dbSNP_126	15	1038,7180		63,912,3134	yes	missense,missense,missense	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	45,45,45	100,1343,4591	AA,AT,TT		12.6308,13.1169,12.7859	benign,benign,benign	859/2271,859/2314,840/2252	181701799	1543,10525	1925	4109	6034	SO:0001583	missense	777	exon20			GGGGGATGGAGGG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2577T>A	1.37:g.181701799T>A	ENSP00000356545:p.Asp859Glu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	177	95	0.536723	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	261	0.11950549450549451	77	0.1565040650406504	52	0.143646408839779	23	0.04020979020979021	109	0.1437994722955145	T	0.132	-1.111794	0.01813	0.131169	0.126308	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.95788	-3.76;-3.76;-3.76;-3.76;-3.81;-3.75;-3.76	3.73	-5.99	0.02213	.	4.946150	0.00550	N	0.000244	T	0.01523	0.0049	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.73075	-0.4097	9	0.02654	T	1	.	3.2695	0.06876	0.098:0.2208:0.1936:0.4876	rs35737760	840;859;859	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	E	859;840;810;791;466;840;859	ENSP00000356542:D859E;ENSP00000434814:D840E;ENSP00000350183:D810E;ENSP00000351101:D791E;ENSP00000356539:D466E;ENSP00000353222:D840E;ENSP00000356545:D859E	ENSP00000350183:D810E	D	+	3	2	CACNA1E	179968422	0.000000	0.05858	0.006000	0.13384	0.622000	0.37654	-1.730000	0.01855	-1.491000	0.01840	-1.386000	0.01163	GAT	T|0.879;A|0.121	0.121	strong		0.667	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
ERI1	90459	hgsc.bcm.edu	37	8	8869199	8869199	+	Silent	SNP	T	T	G	rs9650616	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:8869199T>G	ENST00000523898.1	+	4	1114	c.435T>G	c.(433-435)ccT>ccG	p.P145P	ERI1_ENST00000250263.7_Silent_p.P145P|ERI1_ENST00000519292.1_Silent_p.P145P|ERI1_ENST00000520332.1_3'UTR			Q8IV48	ERI1_HUMAN	exoribonuclease 1	145	Exonuclease.				gene silencing by RNA (GO:0031047)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|rRNA 3'-end processing (GO:0031125)	cytoplasm (GO:0005737)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|histone pre-mRNA stem-loop binding (GO:0071207)|metal ion binding (GO:0046872)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11						GAAACCCACCTGAGTTTGTAC	0.323													T|||	1507	0.300919	0.4448	0.2767	5008	,	,		18799	0.003		0.4662	False		,,,				2504	0.2607				p.P145P		Atlas-SNP	.											.	ERI1	20	.	0			c.T435G						PASS	.	T		1917,2489	539.9+/-375.4	421,1075,707	70.0	72.0	72.0		435	-1.5	1.0	8	dbSNP_119	72	3879,4721	539.4+/-383.6	853,2173,1274	no	coding-synonymous	ERI1	NM_153332.3		1274,3248,1981	GG,GT,TT		45.1047,43.5089,44.564		145/350	8869199	5796,7210	2203	4300	6503	SO:0001819	synonymous_variant	90459	exon3			CCCACCTGAGTTT	BC035279	CCDS5972.1	8p23.1	2008-12-16	2008-12-16	2008-12-16	ENSG00000104626	ENSG00000104626		"""Enhanced RNAi three prime mRNA exonucleases"""	23994	protein-coding gene	gene with protein product	"""exoribonuclease 1"", ""enhanced RNAi three prime mRNA exonuclease homolog 1 (C.elegans)"""	608739	"""three prime histone mRNA exonuclease 1"""	THEX1		14536070	Standard	NM_153332		Approved	3'HEXO	uc003wsk.2	Q8IV48	OTTHUMG00000129328	ENST00000523898.1:c.435T>G	8.37:g.8869199T>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_153332	A8K4U7|Q9NSX3	Silent	SNP	ENST00000523898.1	37	CCDS5972.1																																																																																			T|0.605;G|0.395	0.395	strong		0.323	ERI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251471.2	NM_153332	
HLA-C	3107	hgsc.bcm.edu	37	6	31239518	31239518	+	Silent	SNP	C	C	T	rs1050420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239518C>T	ENST00000376228.5	-	2	215	c.201G>A	c.(199-201)ccG>ccA	p.P67P	HLA-C_ENST00000383329.3_Silent_p.P67P	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	67	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GCTCCCCTCTCGGACTCGCGG	0.701													t|||	2230	0.445288	0.5363	0.513	5008	,	,		12078	0.2808		0.4314	False		,,,				2504	0.4581				p.P67P		Atlas-SNP	.											.	HLA-C	92	.	0			c.G201A						PASS	.	T		1449,1571		354,741,415	38.0	40.0	39.0		201	-0.2	0.0	6	dbSNP_86	39	2233,3179		465,1303,938	no	coding-synonymous	HLA-C	NM_002117.5		819,2044,1353	TT,TC,CC		41.2602,47.9801,43.667		67/367	31239518	3682,4750	1510	2706	4216	SO:0001819	synonymous_variant	3107	exon2			CCCTCTCGGACTC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.201G>A	6.37:g.31239518C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	151	148	0.980132	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	910	0.4166666666666667	245	0.49796747967479676	195	0.5386740331491713	155	0.270979020979021	315	0.4155672823218997	-	6.921	0.539543	0.13250	0.479801	0.412602	ENSG00000204525	ENST00000415537	.	.	.	2.81	-0.177	0.13307	.	.	.	.	.	T	0.11793	0.0287	.	.	.	0.51233	P	8.699999999994823E-5	.	.	.	.	.	.	T	0.24476	-1.0159	3	.	.	.	.	3.289	0.06942	0.0:0.5067:0.2214:0.2719	rs1050420;rs2308551;rs3173347;rs16868214;rs17849592	.	.	.	K	67	.	.	E	-	1	0	HLA-C	31347497	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-0.011000	0.12721	-0.051000	0.13334	-0.679000	0.03777	GAG	C|0.581;T|0.419	0.419	strong		0.701	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
ZNF471	57573	hgsc.bcm.edu	37	19	57036653	57036653	+	Missense_Mutation	SNP	G	G	A	rs3752176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57036653G>A	ENST00000308031.5	+	5	1350	c.1217G>A	c.(1216-1218)gGt>gAt	p.G406D	ZNF471_ENST00000591537.1_3'UTR|ZNF471_ENST00000593197.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	406			G -> D (in dbSNP:rs3752176). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		TACAAATGTGGTGTGTGTGGA	0.398													A|||	1910	0.38139	0.4289	0.3213	5008	,	,		21368	0.2292		0.4891	False		,,,				2504	0.4059				p.G406D	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.G1217A						PASS	.	A	ASP/GLY	2022,2384	611.9+/-391.9	481,1060,662	85.0	85.0	85.0		1217	3.3	0.7	19	dbSNP_107	85	4055,4545	595.8+/-393.5	979,2097,1224	yes	missense	ZNF471	NM_020813.2	94	1460,3157,1886	AA,AG,GG		47.1512,45.892,46.7246	benign	406/627	57036653	6077,6929	2203	4300	6503	SO:0001583	missense	57573	exon5			AATGTGGTGTGTG	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"""Zinc fingers, C2H2-type"", ""-"""	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1217G>A	19.37:g.57036653G>A	ENSP00000309161:p.Gly406Asp	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	868	0.3974358974358974	224	0.45528455284552843	142	0.39226519337016574	138	0.24125874125874125	364	0.48021108179419525	A	6.025	0.372926	0.11409	0.45892	0.471512	ENSG00000196263	ENST00000308031	T	0.07216	3.21	3.35	3.35	0.38373	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.02865	-0.47	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.42068	-0.9473	8	0.38643	T	0.18	.	3.2288	0.06741	0.5506:0.2145:0.2349:0.0	rs3752176;rs58477375;rs3752176	406	Q9BX82	ZN471_HUMAN	D	406	ENSP00000309161:G406D	ENSP00000309161:G406D	G	+	2	0	ZNF471	61728465	0.000000	0.05858	0.706000	0.30403	0.790000	0.44656	-1.550000	0.02180	0.388000	0.25054	-0.521000	0.04368	GGT	G|0.559;A|0.441	0.441	strong		0.398	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813	
SPARCL1	8404	hgsc.bcm.edu	37	4	88412806	88412806	+	Missense_Mutation	SNP	T	T	C	rs1130643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:88412806T>C	ENST00000282470.6	-	5	1725	c.1255A>G	c.(1255-1257)Acg>Gcg	p.T419A	SPARCL1_ENST00000503414.1_Missense_Mutation_p.T294A|SPARCL1_ENST00000418378.1_Missense_Mutation_p.T419A	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	419			T -> A (in dbSNP:rs1130643).		signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		TCACTTGACGTTTCCTCCTCA	0.393													T|||	1101	0.219848	0.5061	0.1311	5008	,	,		19417	0.1538		0.1243	False		,,,				2504	0.0624				p.T419A		Atlas-SNP	.											.	SPARCL1	59	.	0			c.A1255G						PASS	.	T	ALA/THR,ALA/THR	1998,2408	558.6+/-380.0	441,1116,646	298.0	237.0	258.0		1255,1255	-4.3	0.0	4	dbSNP_86	258	1118,7482	231.4+/-265.4	67,984,3249	yes	missense,missense	SPARCL1	NM_001128310.1,NM_004684.4	58,58	508,2100,3895	CC,CT,TT		13.0,45.3473,23.9582	benign,benign	419/665,419/665	88412806	3116,9890	2203	4300	6503	SO:0001583	missense	8404	exon5			TTGACGTTTCCTC	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.1255A>G	4.37:g.88412806T>C	ENSP00000282470:p.Thr419Ala	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	161	64	0.397516	NM_004684	B4E2Z0|E7ESU2|Q14800	Missense_Mutation	SNP	ENST00000282470.6	37	CCDS3622.1	429	0.19642857142857142	211	0.42886178861788615	52	0.143646408839779	66	0.11538461538461539	100	0.13192612137203166	T	4.774	0.143962	0.09134	0.453473	0.13	ENSG00000152583	ENST00000282470;ENST00000418378;ENST00000438050;ENST00000503414	D;D;D	0.89343	-2.5;-2.5;-2.5	5.18	-4.28	0.03732	.	1.245570	0.04943	N	0.459008	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.19257	-1.0311	9	0.07644	T	0.81	3.0442	1.8177	0.03104	0.1153:0.2416:0.3399:0.3033	rs1130643;rs2219682;rs3189727;rs52819302;rs60236995;rs1130643	419	Q14515	SPRL1_HUMAN	A	419;419;294;294	ENSP00000282470:T419A;ENSP00000414856:T419A;ENSP00000422903:T294A	ENSP00000282470:T419A	T	-	1	0	SPARCL1	88631830	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.309000	0.08145	-0.779000	0.04560	-0.327000	0.08410	ACG	T|0.777;C|0.223	0.223	strong		0.393	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		
CEP162	22832	hgsc.bcm.edu	37	6	84884544	84884544	+	Missense_Mutation	SNP	T	T	G	rs149892489		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:84884544T>G	ENST00000403245.3	-	15	2041	c.1927A>C	c.(1927-1929)Aag>Cag	p.K643Q	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_Missense_Mutation_p.K567Q	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TCTTTCTCCTTTTCTGAGAAT	0.348																																					p.K643Q		Atlas-SNP	.											.	KIAA1009	119	.	0			c.A1927C						PASS	.						78.0	70.0	72.0					6																	84884544		2203	4297	6500	SO:0001583	missense	22832	exon15			TCTCCTTTTCTGA																												ENST00000403245.3:c.1927A>C	6.37:g.84884544T>G	ENSP00000385215:p.Lys643Gln	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	205	17	0.0829268	NM_014895		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	T	21.8	4.205158	0.79127	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.24723	1.84;1.85	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.44540	0.1298	M	0.77616	2.38	0.38548	D	0.949389	D	0.89917	1.0	D	0.85130	0.997	T	0.48222	-0.9054	10	0.52906	T	0.07	-30.2168	15.7393	0.77876	0.0:0.0:0.0:1.0	.	643	Q5TB80	QN1_HUMAN	Q	567;643	ENSP00000257766:K567Q;ENSP00000385215:K643Q	ENSP00000257766:K567Q	K	-	1	0	KIAA1009	84941263	1.000000	0.71417	0.993000	0.49108	0.784000	0.44337	5.561000	0.67339	2.184000	0.69523	0.460000	0.39030	AAG	.	.	weak		0.348	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
SMPD4	55627	hgsc.bcm.edu	37	2	130912789	130912789	+	Missense_Mutation	SNP	A	A	C	rs148027738		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:130912789A>C	ENST00000409031.1	-	15	2598	c.1450T>G	c.(1450-1452)Ttt>Gtt	p.F484V	SMPD4_ENST00000426662.2_Missense_Mutation_p.F120V|SMPD4_ENST00000453750.1_Missense_Mutation_p.F233V|SMPD4_ENST00000431183.2_Missense_Mutation_p.F382V|SMPD4_ENST00000351288.6_Missense_Mutation_p.F455V|SMPD4_ENST00000443958.2_Missense_Mutation_p.F148V|SMPD4_ENST00000473720.1_5'Flank|SMPD4_ENST00000452225.2_Missense_Mutation_p.F225V|SMPD4_ENST00000339679.7_Missense_Mutation_p.F342V	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	445					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	AAGCCCACAAACAACTTGGTG	0.602																																					p.F484V		Atlas-SNP	.											SMPD4,NS,adenoma,0,1	SMPD4	67	1	0			c.T1450G						PASS	.						97.0	88.0	91.0					2																	130912789		2203	4300	6503	SO:0001583	missense	55627	exon15			CCACAAACAACTT	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.1450T>G	2.37:g.130912789A>C	ENSP00000386531:p.Phe484Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	150	11	0.0733333	NM_017951	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Missense_Mutation	SNP	ENST00000409031.1	37	CCDS42751.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	15.92|15.92|15.92	2.974600|2.974600|2.974600	0.53720|0.53720|0.53720	.|.|.	.|.|.	ENSG00000136699|ENSG00000136699|ENSG00000136699	ENST00000439886|ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750;ENST00000443958;ENST00000339679;ENST00000452225;ENST00000426662;ENST00000457039;ENST00000449159;ENST00000451542|ENST00000430682	.|.|.	.|.|.	.|.|.	4.24|4.24|4.24	4.24|4.24|4.24	0.50183|0.50183|0.50183	.|.|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|T	0.73636|0.73636|0.73636	0.3612|0.3612|0.3612	M|M|M	0.81497|0.81497|0.81497	2.545|2.545|2.545	0.58432|0.58432|0.58432	D|D|D	0.999999|0.999999|0.999999	.|D;D;P;P;D;P;D;D;D|.	.|0.76494|.	.|0.982;0.982;0.907;0.896;0.999;0.885;0.991;0.998;0.992|.	.|P;P;P;P;D;P;D;D;D|.	.|0.78314|.	.|0.849;0.888;0.751;0.818;0.991;0.492;0.94;0.981;0.974|.	T|T|T	0.75340|0.75340|0.75340	-0.3352|-0.3352|-0.3352	5|9|5	.|0.37606|.	.|T|.	.|0.19|.	.|.|.	11.314|11.314|11.314	0.49381|0.49381|0.49381	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|120;225;382;342;233;416;445;484;491|.	.|B4E0L6;B4DQ31;E7ESA2;B4E0T5;B4DM23;Q9NXE4-2;Q9NXE4;B1PBA3;Q9NXE4-4|.	.|.;.;.;.;.;.;NSMA3_HUMAN;.;.|.	W|V|G	358|455;484;382;233;148;342;225;120;81;20;226|165	.|.|.	.|ENSP00000339721:F342V|.	C|F|V	-|-|-	3|1|2	2|0|0	SMPD4|SMPD4|SMPD4	130629259|130629259|130629259	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.969000|0.969000|0.969000	0.41365|0.41365|0.41365	0.096000|0.096000|0.096000	0.18686|0.18686|0.18686	6.723000|6.723000|6.723000	0.74742|0.74742|0.74742	1.538000|1.538000|1.538000	0.49270|0.49270|0.49270	0.254000|0.254000|0.254000	0.18369|0.18369|0.18369	TGT|TTT|GTT	A|0.999;C|0.001	0.001	weak		0.602	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751	
RHNO1	83695	hgsc.bcm.edu	37	12	2997397	2997397	+	Silent	SNP	G	G	A	rs2907608	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:2997397G>A	ENST00000489288.2	+	3	641	c.489G>A	c.(487-489)tcG>tcA	p.S163S	RHNO1_ENST00000461997.2_Silent_p.S149S|RHNO1_ENST00000464682.2_3'UTR|TULP3_ENST00000448120.2_5'Flank|TULP3_ENST00000397132.2_5'Flank	NM_001252499.2|NM_001257097.1|NM_001257098.1	NP_001239428.1|NP_001244026.1|NP_001244027.1	Q9BSD3	RHNO1_HUMAN	RAD9-HUS1-RAD1 interacting nuclear orphan 1	163					cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|positive regulation of G0 to G1 transition (GO:0070318)|recombinational repair (GO:0000725)	chromosome (GO:0005694)|nucleus (GO:0005634)											CAGAGTCATCGTCTGTGAAGG	0.507													G|||	2634	0.525958	0.5976	0.5706	5008	,	,		19325	0.6458		0.3489	False		,,,				2504	0.456				p.S163S		Atlas-SNP	.											.	.	.	.	0			c.G489A						PASS	.	G		2426,1980	618.6+/-393.2	660,1106,437	128.0	125.0	126.0			-9.9	0.0	12	dbSNP_101	126	2965,5635	461.8+/-365.5	516,1933,1851	no	intergenic				1176,3039,2288	AA,AG,GG		34.4767,44.9387,41.4501			2997397	5391,7615	2203	4300	6503	SO:0001819	synonymous_variant	83695	exon3			GTCATCGTCTGTG	AK021945	CCDS8518.1, CCDS58199.1	12p13.33	2012-08-23	2012-08-23	2012-08-23	ENSG00000171792	ENSG00000171792			28206	protein-coding gene	gene with protein product	"""Rad9, Rad1, Hus1 interacting nuclear orphan"""	614085	"""chromosome 12 open reading frame 32"""	C12orf32		20811708, 21659603	Standard	NM_001252499		Approved	HKMT1188, MGC13204, RHINO	uc031qfq.1	Q9BSD3	OTTHUMG00000158557	ENST00000489288.2:c.489G>A	12.37:g.2997397G>A		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	154	153	0.993506	NM_001257098	B7Z989	Silent	SNP	ENST00000489288.2	37	CCDS8518.1																																																																																			G|0.532;A|0.468	0.468	strong		0.507	RHNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351286.2	NM_031465	
DTHD1	401124	hgsc.bcm.edu	37	4	36345377	36345377	+	Silent	SNP	G	G	A	rs2270880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:36345377G>A	ENST00000456874.2	+	9	2335	c.2277G>A	c.(2275-2277)gaG>gaA	p.E759E	DTHD1_ENST00000357504.3_Silent_p.E594E|RP11-431M7.2_ENST00000504344.1_RNA|DTHD1_ENST00000503528.1_3'UTR|DTHD1_ENST00000507598.1_Silent_p.E799E	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	759	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						TTGCAGAAGAGCTCAAATTCA	0.458													G|||	541	0.108027	0.0106	0.062	5008	,	,		19226	0.121		0.165	False		,,,				2504	0.2004				p.E759E		Atlas-SNP	.											.	DTHD1	63	.	0			c.G2277A						PASS	.	G	,	62,1322		3,56,633	19.0	17.0	18.0		1782,2277	4.3	1.0	4	dbSNP_100	18	526,2656		43,440,1108	no	coding-synonymous,coding-synonymous	DTHD1	NM_001136536.3,NM_001170700.1	,	46,496,1741	AA,AG,GG		16.5305,4.4798,12.8778	,	594/617,759/782	36345377	588,3978	692	1591	2283	SO:0001819	synonymous_variant	401124	exon9			AGAAGAGCTCAAA	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.2277G>A	4.37:g.36345377G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_001170700	B2RXK4|B4E2N7	Silent	SNP	ENST00000456874.2	37	CCDS54754.1																																																																																			G|0.895;A|0.105	0.105	strong		0.458	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
MARCH7	64844	hgsc.bcm.edu	37	2	160604452	160604452	+	Silent	SNP	C	C	T	rs11555185	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160604452C>T	ENST00000259050.4	+	5	773	c.651C>T	c.(649-651)gaC>gaT	p.D217D	MARCH7_ENST00000539065.1_Silent_p.D161D|MARCH7_ENST00000473749.1_3'UTR|MARCH7_ENST00000409175.1_Silent_p.D217D|MARCH7_ENST00000409591.1_Silent_p.D179D	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	217	Ser-rich.				protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D217D(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						GTTCTAGGGACTCCAGAAATT	0.378													C|||	1104	0.220447	0.0287	0.4928	5008	,	,		17238	0.2698		0.33	False		,,,				2504	0.1227				p.D217D		Atlas-SNP	.											MARCH7,colon,carcinoma,0,2	MARCH7	48	2	1	Substitution - coding silent(1)	stomach(1)	c.C651T						PASS	.	C		305,4101	165.1+/-196.6	10,285,1908	84.0	85.0	85.0		651	2.8	0.9	2	dbSNP_120	85	2715,5885	431.8+/-356.9	425,1865,2010	no	coding-synonymous	MARCH7	NM_022826.2		435,2150,3918	TT,TC,CC		31.5698,6.9224,23.2201		217/705	160604452	3020,9986	2203	4300	6503	SO:0001819	synonymous_variant	64844	exon5			TAGGGACTCCAGA	AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	17393	protein-coding gene	gene with protein product		613334	"""axotrophin"", ""membrane-associated ring finger (C3HC4) 7"""	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.651C>T	2.37:g.160604452C>T		Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	348	166	0.477012	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Silent	SNP	ENST00000259050.4	37	CCDS2210.1																																																																																			C|0.761;T|0.239	0.239	strong		0.378	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
FZD10	11211	hgsc.bcm.edu	37	12	130648246	130648246	+	Silent	SNP	G	G	C	rs80190592	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:130648246G>C	ENST00000229030.4	+	1	1243	c.759G>C	c.(757-759)ccG>ccC	p.P253P	FZD10-AS1_ENST00000505807.2_RNA|FZD10_ENST00000539839.1_Missense_Mutation_p.G221R			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	253					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		TCATCGACCCGGCCCGCTTCC	0.657													G|||	49	0.00978435	0.0015	0.0216	5008	,	,		15646	0.0		0.0298	False		,,,				2504	0.002				p.P253P		Atlas-SNP	.											.	FZD10	95	.	0			c.G759C						PASS	.	G		16,4390	23.3+/-48.9	0,16,2187	111.0	100.0	103.0		759	-9.9	0.0	12	dbSNP_131	103	208,8392	89.4+/-151.6	5,198,4097	no	coding-synonymous	FZD10	NM_007197.3		5,214,6284	CC,CG,GG		2.4186,0.3631,1.7223		253/582	130648246	224,12782	2203	4300	6503	SO:0001819	synonymous_variant	11211	exon1			CGACCCGGCCCGC	AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"""GPCR / Class F : Frizzled receptors"", ""CD molecules"""	4039	protein-coding gene	gene with protein product		606147	"""frizzled (Drosophila) homolog 10"", ""frizzled homolog 10 (Drosophila)"", ""frizzled 10, seven transmembrane spanning receptor"", ""frizzled family receptor 10"""			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.759G>C	12.37:g.130648246G>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_007197		Silent	SNP	ENST00000229030.4	37	CCDS9267.1	31	0.014194139194139194	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	19	0.025065963060686015	G	5.513	0.279581	0.10458	0.003631	0.024186	ENSG00000111432	ENST00000539839	.	.	.	4.96	-9.93	0.00452	.	.	.	.	.	T	0.23806	0.0576	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60265	-0.7297	5	0.87932	D	0	.	1.7667	0.03003	0.1909:0.337:0.2398:0.2323	.	.	.	.	R	221	.	ENSP00000438460:G221R	G	+	1	0	FZD10	129214199	0.000000	0.05858	0.000000	0.03702	0.995000	0.86356	-5.094000	0.00152	-2.807000	0.00349	0.561000	0.74099	GGC	G|0.981;C|0.019	0.019	strong		0.657	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ZNF304	57343	hgsc.bcm.edu	37	19	57868879	57868879	+	Silent	SNP	T	T	C	rs34411126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57868879T>C	ENST00000282286.5	+	3	1815	c.1642T>C	c.(1642-1644)Ttg>Ctg	p.L548L	ZNF304_ENST00000391705.3_Silent_p.L548L|ZNF304_ENST00000443917.2_Silent_p.L595L|ZNF304_ENST00000598744.1_Silent_p.L506L			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	548					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		CAGCCTCATTTTGCACCAGAG	0.453													C|||	702	0.140176	0.1997	0.0735	5008	,	,		21030	0.0784		0.1362	False		,,,				2504	0.1748				p.L548L		Atlas-SNP	.											.	ZNF304	74	.	0			c.T1642C						PASS	.	C		851,3555	746.2+/-411.7	74,703,1426	63.0	60.0	61.0		1642	3.4	1.0	19	dbSNP_126	61	1192,7408	763.4+/-407.6	92,1008,3200	no	coding-synonymous	ZNF304	NM_020657.2		166,1711,4626	CC,CT,TT		13.8605,19.3146,15.7081		548/660	57868879	2043,10963	2203	4300	6503	SO:0001819	synonymous_variant	57343	exon3			CTCATTTTGCACC	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"""Zinc fingers, C2H2-type"", ""-"""	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.1642T>C	19.37:g.57868879T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	33	14	0.424242	NM_020657		Silent	SNP	ENST00000282286.5	37	CCDS12950.1																																																																																			T|0.850;C|0.150	0.150	strong		0.453	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1		
CCDC88B	283234	hgsc.bcm.edu	37	11	64124515	64124515	+	Silent	SNP	T	T	C	rs612448	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64124515T>C	ENST00000356786.5	+	27	4424	c.4380T>C	c.(4378-4380)ccT>ccC	p.P1460P	CCDC88B_ENST00000359902.2_Missense_Mutation_p.L565P|RPS6KA4_ENST00000334205.4_5'Flank|RPS6KA4_ENST00000528057.1_5'Flank|RPS6KA4_ENST00000294261.4_5'Flank|CCDC88B_ENST00000301897.4_Silent_p.P123P|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	1460						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTCTAGGCCCTGAGGTACAGG	0.632													C|||	1303	0.260184	0.0303	0.4107	5008	,	,		17803	0.1845		0.4334	False		,,,				2504	0.364				p.P1460P		Atlas-SNP	.											CCDC88B_ENST00000359902,NS,carcinoma,-1,1	CCDC88B	89	1	0			c.T4380C						PASS	.	C		426,3976		23,380,1798	133.0	102.0	112.0		4380	0.6	0.0	11	dbSNP_83	112	3738,4856		794,2150,1353	no	coding-synonymous	CCDC88B	NM_032251.5		817,2530,3151	CC,CT,TT		43.4955,9.6774,32.0406		1460/1477	64124515	4164,8832	2201	4297	6498	SO:0001819	synonymous_variant	283234	exon27			AGGCCCTGAGGTA	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.4380T>C	11.37:g.64124515T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2	605	0.27701465201465203	21	0.042682926829268296	141	0.38950276243093923	104	0.18181818181818182	339	0.4472295514511873	N	11.12	1.545644	0.27652	0.096774	0.434955	ENSG00000168071	ENST00000359902	T	0.57907	0.37	3.89	0.573	0.17363	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46652	-0.9176	6	.	.	.	.	3.3622	0.07190	0.0:0.4118:0.2053:0.3829	rs612448;rs58613170;rs612448	549	A6NC98-5	.	P	565	ENSP00000352974:L565P	.	L	+	2	0	CCDC88B	63881091	0.000000	0.05858	0.010000	0.14722	0.161000	0.22273	-0.393000	0.07305	0.007000	0.14760	-0.511000	0.04467	CTG	T|0.706;C|0.294	0.294	strong		0.632	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
ICE2	79664	hgsc.bcm.edu	37	15	60745788	60745788	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:60745788A>G	ENST00000561114.1	-	9	1301	c.1139T>C	c.(1138-1140)tTt>tCt	p.F380S	NARG2_ENST00000261520.4_Intron|NARG2_ENST00000439632.1_Intron	NM_001276385.1	NP_001263314.1														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						GGGGAAAAAAAAAGCATTACA	0.328																																					p.F380S		Atlas-SNP	.											.	NARG2	82	.	0			c.T1139C						PASS	.						54.0	55.0	55.0					15																	60745788		2203	4297	6500	SO:0001583	missense	79664	exon9			AAAAAAAAAGCAT																												ENST00000561114.1:c.1139T>C	15.37:g.60745788A>G	ENSP00000454162:p.Phe380Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	163	74	0.453988	NM_001276385		Missense_Mutation	SNP	ENST00000561114.1	37																																																																																				.	.	none		0.328	NARG2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000416605.1		
PARP10	84875	hgsc.bcm.edu	37	8	145060112	145060112	+	Silent	SNP	G	G	A	rs11136345	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:145060112G>A	ENST00000313028.7	-	3	307	c.213C>T	c.(211-213)caC>caT	p.H71H	PARP10_ENST00000525773.1_Silent_p.H83H|PARP10_ENST00000533665.1_5'UTR|PARP10_ENST00000524918.1_Silent_p.H71H	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	71					negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CATGTAGTTCGTGATCTGCCT	0.667													G|||	1959	0.391174	0.6165	0.2795	5008	,	,		15706	0.1458		0.4314	False		,,,				2504	0.3773				p.H71H		Atlas-SNP	.											.	PARP10	57	.	0			c.C213T						PASS	.			2616,1788		782,1052,368	18.0	20.0	19.0		213	-2.5	0.0	8	dbSNP_120	19	3620,4976		794,2032,1472	no	coding-synonymous	PARP10	NM_032789.3		1576,3084,1840	AA,AG,GG		42.1126,40.5995,47.9692		71/1026	145060112	6236,6764	2202	4298	6500	SO:0001819	synonymous_variant	84875	exon3			TAGTTCGTGATCT	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"""Poly (ADP-ribose) polymerases"""	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.213C>T	8.37:g.145060112G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Silent	SNP	ENST00000313028.7	37	CCDS34960.1																																																																																			G|0.551;A|0.449	0.449	strong		0.667	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789	
CYB5RL	606495	hgsc.bcm.edu	37	1	54661150	54661150	+	Missense_Mutation	SNP	C	C	T	rs946448	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:54661150C>T	ENST00000534324.1	-	1	139	c.140G>A	c.(139-141)aGg>aAg	p.R47K	CYB5RL_ENST00000537208.1_Missense_Mutation_p.R47K|CYB5RL_ENST00000287899.8_Missense_Mutation_p.R47K|CYB5RL_ENST00000497820.1_Missense_Mutation_p.R47K|CYB5RL_ENST00000419823.2_Missense_Mutation_p.R47K|MRPL37_ENST00000487096.1_Intron|CYB5RL_ENST00000401046.3_5'UTR|CYB5RL_ENST00000542737.1_Missense_Mutation_p.R47K|RP11-446E24.4_ENST00000311841.7_Missense_Mutation_p.R47K			Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like	47	Oxidoreductase-like.		R -> K (in dbSNP:rs946448). {ECO:0000269|PubMed:15489334}.				cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|urinary_tract(1)	8						TGCCTCCCACCTTGCCAGATC	0.607													C|||	1584	0.316294	0.2118	0.3213	5008	,	,		14903	0.255		0.3519	False		,,,				2504	0.4806				p.R47K		Atlas-SNP	.											.	CYB5RL	17	.	0			c.G140A						PASS	.	C	LYS/ARG	875,3219		95,685,1267	46.0	48.0	47.0		140	4.2	1.0	1	dbSNP_86	47	2866,5494		514,1838,1828	yes	missense	CYB5RL	NM_001031672.2	26	609,2523,3095	TT,TC,CC		34.2823,21.3727,30.0385	benign	47/316	54661150	3741,8713	2047	4180	6227	SO:0001583	missense	606495	exon3			TCCCACCTTGCCA		CCDS44151.1	1p32.3	2011-04-08			ENSG00000215883	ENSG00000215883			32220	protein-coding gene	gene with protein product						12477932	Standard	NM_001031672		Approved	LOC606495	uc009vzo.3	Q6IPT4	OTTHUMG00000008082	ENST00000534324.1:c.140G>A	1.37:g.54661150C>T	ENSP00000434343:p.Arg47Lys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_001031672	B7ZBS4|Q8NF25	Missense_Mutation	SNP	ENST00000534324.1	37	CCDS44151.1	669	0.30631868131868134	110	0.22357723577235772	144	0.39779005524861877	143	0.25	272	0.35883905013192613	C	20.2	3.956210	0.73902	0.213727	0.342823	ENSG00000215883	ENST00000419823;ENST00000534324;ENST00000287899;ENST00000542737;ENST00000537208;ENST00000497820	T;T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03;1.03	5.17	4.24	0.50183	Oxidoreductase-like, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.26092	0.79	0.42558	P	0.006867999999999985	B	0.26775	0.159	B	0.24848	0.056	T	0.41088	-0.9528	8	0.29301	T	0.29	.	8.214	0.31501	0.0:0.8334:0.0:0.1666	rs946448;rs3737834;rs17390104;rs60484336;rs946448	47	Q6IPT4	NB5R5_HUMAN	K	47	ENSP00000409075:R47K;ENSP00000434343:R47K;ENSP00000287899:R47K;ENSP00000438151:R47K;ENSP00000443797:R47K;ENSP00000431157:R47K	ENSP00000287899:R47K	R	-	2	0	CYB5RL	54433738	0.172000	0.23043	1.000000	0.80357	0.997000	0.91878	0.880000	0.28159	2.689000	0.91719	0.561000	0.74099	AGG	C|0.708;T|0.292	0.292	strong		0.607	CYB5RL-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388318.1	NM_001031672	
WDR35	57539	hgsc.bcm.edu	37	2	20189015	20189015	+	Missense_Mutation	SNP	T	T	C	rs1060742	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:20189015T>C	ENST00000345530.3	-	2	168	c.53A>G	c.(52-54)cAg>cGg	p.Q18R	WDR35_ENST00000281405.4_Missense_Mutation_p.Q18R|AC079145.4_ENST00000416575.1_RNA	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	18			Q -> R (in dbSNP:rs1060742).		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)		p.Q18R(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGATACACACTGCAGCTTCAC	0.443													T|||	594	0.11861	0.0038	0.1196	5008	,	,		18787	0.1736		0.1123	False		,,,				2504	0.2229				p.Q18R		Atlas-SNP	.											WDR35,NS,carcinoma,0,1	WDR35	92	1	1	Substitution - Missense(1)	stomach(1)	c.A53G						PASS	.	T	ARG/GLN,ARG/GLN	93,4313	76.8+/-115.0	1,91,2111	173.0	156.0	161.0		53,53	5.3	0.9	2	dbSNP_86	161	758,7842	181.5+/-230.2	37,684,3579	yes	missense,missense	WDR35	NM_001006657.1,NM_020779.3	43,43	38,775,5690	CC,CT,TT		8.814,2.1108,6.5431	benign,benign	18/1182,18/1171	20189015	851,12155	2203	4300	6503	SO:0001583	missense	57539	exon2			ACACACTGCAGCT	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.53A>G	2.37:g.20189015T>C	ENSP00000314444:p.Gln18Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	154	72	0.467532	NM_020779	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	37	CCDS33152.1	228	0.1043956043956044	4	0.008130081300813009	45	0.12430939226519337	97	0.16958041958041958	82	0.10817941952506596	T	11.66	1.704882	0.30232	0.021108	0.08814	ENSG00000118965	ENST00000345530;ENST00000281405	T;T	0.28454	1.61;1.61	5.31	5.31	0.75309	WD40/YVTN repeat-like-containing domain (1);	0.137051	0.64402	N	0.000004	T	0.00039	0.0001	N	0.00210	-1.845	0.09310	P	0.9999999999999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19549	-1.0302	9	0.14252	T	0.57	-11.4416	9.392	0.38378	0.0:0.0828:0.0:0.9172	rs1060742;rs3172016;rs3731662;rs52824687;rs1060742	18;18	Q9P2L0-2;Q9P2L0	.;WDR35_HUMAN	R	18	ENSP00000314444:Q18R;ENSP00000281405:Q18R	ENSP00000281405:Q18R	Q	-	2	0	WDR35	20052496	1.000000	0.71417	0.918000	0.36340	0.962000	0.63368	2.239000	0.43079	2.232000	0.73038	0.533000	0.62120	CAG	T|0.913;C|0.087	0.087	strong		0.443	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	
FAM103A1	83640	hgsc.bcm.edu	37	15	83657894	83657894	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:83657894G>A	ENST00000304191.3	+	3	345	c.124G>A	c.(124-126)Gaa>Aaa	p.E42K	RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000538348.2_Missense_Mutation_p.P128S	NM_031452.3	NP_113640.1	Q9BTL3	RAM_HUMAN	family with sequence similarity 103, member A1	42	Interaction with RNMT.				7-methylguanosine mRNA capping (GO:0006370)|methylation (GO:0032259)|recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex (GO:0036031)	mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			prostate(1)	1						AATTGTTGAGGAATGGAATAG	0.418																																					p.P128S		Atlas-SNP	.											.	C15orf40	18	.	0			c.C382T						PASS	.																																			SO:0001583	missense	123207	exon4			GTTGAGGAATGGA	CR597724	CCDS10321.1	15q25.2	2012-06-13			ENSG00000169612	ENSG00000169612			31022	protein-coding gene	gene with protein product	"""RNMT-activating mini protein"""	614547				22099306	Standard	NM_031452		Approved	HsT19360, C15orf18, MGC2560, RAM	uc002bjl.2	Q9BTL3	OTTHUMG00000147357	ENST00000304191.3:c.124G>A	15.37:g.83657894G>A	ENSP00000307181:p.Glu42Lys	Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	352	151	0.428977	NM_001160116	Q2M1J8	Missense_Mutation	SNP	ENST00000304191.3	37	CCDS10321.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.4|25.4	4.630726|4.630726	0.87660|0.87660	.|.	.|.	ENSG00000169612|ENSG00000169609	ENST00000304191|ENST00000538348	.|.	.|.	.|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.167238|.	0.51477|.	D|.	0.000085|.	T|T	0.76659|0.76659	0.4018|0.4018	M|M	0.70595|0.70595	2.14|2.14	0.80722|0.80722	D|D	1|1	P|D	0.42692|0.67145	0.787|0.996	B|P	0.37601|0.61658	0.254|0.892	T|T	0.72350|0.72350	-0.4320|-0.4320	9|8	0.66056|0.29301	D|T	0.02|0.29	-9.1412|-9.1412	19.6657|19.6657	0.95891|0.95891	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	42|128	Q9BTL3|F5GX92	F103A_HUMAN|.	K|S	42|128	.|.	ENSP00000307181:E42K|ENSP00000441077:P128S	E|P	+|-	1|1	0|0	FAM103A1|C15orf40	81448898|81448898	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	7.848000|7.848000	0.86902|0.86902	2.744000|2.744000	0.94065|0.94065	0.655000|0.655000	0.94253|0.94253	GAA|CCT	.	.	none		0.418	FAM103A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304001.1	NM_031452	
PGR	5241	hgsc.bcm.edu	37	11	100998771	100998771	+	Missense_Mutation	SNP	C	C	G	rs3740753	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:100998771C>G	ENST00000325455.5	-	1	2484	c.1031G>C	c.(1030-1032)aGt>aCt	p.S344T	PGR_ENST00000263463.5_Missense_Mutation_p.S344T|PGR_ENST00000534013.1_Intron	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	344	Modulating, Pro-Rich.		S -> T (in dbSNP:rs3740753). {ECO:0000269|PubMed:2328727, ECO:0000269|Ref.8}.		cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	ACAGGGTGAACTCCGCGGCGG	0.682													C|||	361	0.0720847	0.0061	0.1398	5008	,	,		11093	0.0099		0.1769	False		,,,				2504	0.0695				p.S344T	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.G1031C						PASS	.	C	THR/SER,THR/SER	106,4056		1,104,1976	14.0	19.0	18.0		1031,539	1.8	1.0	11	dbSNP_107	18	1244,7046		88,1068,2989	yes	missense,missense	PGR	NM_000926.4,NM_001202474.1	58,58	89,1172,4965	GG,GC,CC		15.006,2.5469,10.8416	benign,benign	344/934,180/770	100998771	1350,11102	2081	4145	6226	SO:0001583	missense	5241	exon1			GGTGAACTCCGCG	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.1031G>C	11.37:g.100998771C>G	ENSP00000325120:p.Ser344Thr	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	208	0.09523809523809523	6	0.012195121951219513	55	0.15193370165745856	4	0.006993006993006993	143	0.18865435356200527	C	7.606	0.673794	0.14841	0.025469	0.15006	ENSG00000082175	ENST00000325455;ENST00000263463;ENST00000537623	T;T	0.10288	2.89;2.89	3.84	1.76	0.24704	.	1.096570	0.07012	N	0.825310	T	0.00012	0.0000	L	0.27053	0.805	0.53688	P	2.1000000000048757E-5	B;B	0.26483	0.094;0.15	B;B	0.24394	0.034;0.053	T	0.43766	-0.9371	9	0.34782	T	0.22	.	5.4483	0.16548	0.0:0.5358:0.2446:0.2196	rs3740753	344;344	Q8TDS3;P06401	.;PRGR_HUMAN	T	344	ENSP00000325120:S344T;ENSP00000263463:S344T	ENSP00000263463:S344T	S	-	2	0	PGR	100503981	0.000000	0.05858	0.978000	0.43139	0.038000	0.13279	-0.179000	0.09768	0.816000	0.34421	0.561000	0.74099	AGT	C|0.884;G|0.116	0.116	strong		0.682	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
TMC2	117532	hgsc.bcm.edu	37	20	2593863	2593863	+	Silent	SNP	T	T	C	rs6515646	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2593863T>C	ENST00000358864.1	+	14	1782	c.1767T>C	c.(1765-1767)tcT>tcC	p.S589S	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	589			S -> C (in dbSNP:rs16987592).		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TGACGGTGTCTGACATGCTGG	0.552													C|||	1331	0.265775	0.208	0.2767	5008	,	,		17643	0.2937		0.2416	False		,,,				2504	0.3323				p.S589S		Atlas-SNP	.											.	TMC2	121	.	0			c.T1767C						PASS	.	C		963,3443	734.0+/-410.5	111,741,1351	182.0	138.0	153.0		1767	-9.9	0.3	20	dbSNP_116	153	2080,6520	717.8+/-406.2	256,1568,2476	yes	coding-synonymous	TMC2	NM_080751.2		367,2309,3827	CC,CT,TT		24.186,21.8566,23.3969		589/907	2593863	3043,9963	2203	4300	6503	SO:0001819	synonymous_variant	117532	exon14			GGTGTCTGACATG	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"""transmembrane, cochlear expressed, 2"""	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1767T>C	20.37:g.2593863T>C		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	269	131	0.486989	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Silent	SNP	ENST00000358864.1	37	CCDS13029.2																																																																																			T|0.752;C|0.248	0.248	strong		0.552	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
OR12D3	81797	hgsc.bcm.edu	37	6	29342630	29342630	+	Silent	SNP	C	C	T	rs34525583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29342630C>T	ENST00000396806.3	-	1	438	c.435G>A	c.(433-435)gcG>gcA	p.A145A	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						TGAGCCAGGCCGCAGCTGCCA	0.483													C|||	363	0.072484	0.0257	0.0461	5008	,	,		19687	0.1052		0.0487	False		,,,				2504	0.1452				p.A145A		Atlas-SNP	.											OR12D3,NS,carcinoma,-1,1	OR12D3	55	1	0			c.G435A						PASS	.	C		88,2932		2,84,1424	55.0	56.0	56.0		435	-1.3	0.0	6	dbSNP_126	56	327,5091		12,303,2394	no	coding-synonymous	OR12D3	NM_030959.2		14,387,3818	TT,TC,CC		6.0354,2.9139,4.9182		145/317	29342630	415,8023	1510	2709	4219	SO:0001819	synonymous_variant	81797	exon1			CCAGGCCGCAGCT		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"""GPCR / Class A : Olfactory receptors"""	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.435G>A	6.37:g.29342630C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Silent	SNP	ENST00000396806.3	37	CCDS4658.1																																																																																			C|0.949;T|0.051	0.051	strong		0.483	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3		
TUBA1B	10376	hgsc.bcm.edu	37	12	49522605	49522605	+	Silent	SNP	C	C	T	rs1057548	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:49522605C>T	ENST00000336023.5	-	4	586	c.492G>A	c.(490-492)aaG>aaA	p.K164K	RP11-386G11.10_ENST00000547712.1_RNA|RP11-386G11.10_ENST00000548149.1_RNA|RP11-386G11.10_ENST00000547387.1_RNA|RP11-386G11.10_ENST00000551496.1_RNA|RP11-386G11.10_ENST00000552893.1_RNA	NM_006082.2	NP_006073.2	P68363	TBA1B_HUMAN	tubulin, alpha 1b	164					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(4)	12						CCAGCTTGGACTTCTTGCCAT	0.537													C|||	2270	0.453275	0.3427	0.3415	5008	,	,		17051	0.6806		0.327	False		,,,				2504	0.5777				p.K164K		Atlas-SNP	.											.	TUBA1B	24	.	0			c.G492A						PASS	.						53.0	63.0	59.0					12																	49522605		2203	4300	6503	SO:0001819	synonymous_variant	10376	exon4			CTTGGACTTCTTG	AF081484	CCDS31792.1	12q13.12	2007-02-12				ENSG00000123416		"""Tubulins"""	18809	protein-coding gene	gene with protein product	"""tubulin, alpha, ubiquitous"""	602530				12054644, 6646120	Standard	NM_006082		Approved	K-ALPHA-1	uc001rtm.3	P68363	OTTHUMG00000170410	ENST00000336023.5:c.492G>A	12.37:g.49522605C>T		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	219	90	0.410959	NM_006082	P04687|P05209|Q27I68|Q8WU19	Silent	SNP	ENST00000336023.5	37	CCDS31792.1																																																																																			C|0.576;T|0.424	0.424	strong		0.537	TUBA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409005.1	NM_006082	
GPR55	9290	hgsc.bcm.edu	37	2	231774844	231774844	+	Silent	SNP	G	G	A	rs2396777	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:231774844G>A	ENST00000392040.1	-	2	1026	c.834C>T	c.(832-834)aaC>aaT	p.N278N	AC012507.4_ENST00000454890.1_RNA|GPR55_ENST00000392039.2_Silent_p.N278N	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	278					activation of phospholipase C activity (GO:0007202)|bone resorption (GO:0045453)|cannabinoid signaling pathway (GO:0038171)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho protein signal transduction (GO:0035025)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|G-protein coupled receptor activity (GO:0004930)	p.N278N(1)		endometrium(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)		AGCAGTTGACGTTGGAGAAAC	0.507													G|||	1731	0.345647	0.6815	0.1686	5008	,	,		23399	0.2331		0.1471	False		,,,				2504	0.3374				p.N278N		Atlas-SNP	.											GPR55,NS,carcinoma,0,1	GPR55	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C834T						PASS	.	G		2555,1851	633.8+/-396.1	754,1047,402	107.0	105.0	106.0		834	0.4	0.4	2	dbSNP_100	106	1442,7158	275.3+/-291.7	135,1172,2993	no	coding-synonymous	GPR55	NM_005683.3		889,2219,3395	AA,AG,GG		16.7674,42.0109,30.732		278/320	231774844	3997,9009	2203	4300	6503	SO:0001819	synonymous_variant	9290	exon2			GTTGACGTTGGAG	AF096786	CCDS2480.1	2q37	2012-08-21			ENSG00000135898	ENSG00000135898		"""GPCR / Class A : Orphans"""	4511	protein-coding gene	gene with protein product		604107				9931487	Standard	NM_005683		Approved		uc002vrg.3	Q9Y2T6	OTTHUMG00000133224	ENST00000392040.1:c.834C>T	2.37:g.231774844G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	147	71	0.482993	NM_005683	Q8N580	Silent	SNP	ENST00000392040.1	37	CCDS2480.1																																																																																			G|0.690;N|0.000	.	strong		0.507	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683	
MAPK13	5603	hgsc.bcm.edu	37	6	36098410	36098410	+	Silent	SNP	A	A	C	rs1059227	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:36098410A>C	ENST00000211287.4	+	1	313	c.51A>C	c.(49-51)acA>acC	p.T17T	MAPK13_ENST00000373766.5_Silent_p.T17T|MAPK13_ENST00000373759.1_5'Flank|MAPK13_ENST00000373761.6_Silent_p.T17T	NM_002754.4	NP_002745.1	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	17					cell cycle (GO:0007049)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 production (GO:0032755)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|prostate(2)|skin(1)	12						TCAACAAGACAGCCTGGGAGC	0.701													C|||	3749	0.748602	0.8064	0.7176	5008	,	,		6731	0.9454		0.6441	False		,,,				2504	0.5971				p.T17T		Atlas-SNP	.											MAPK13_ENST00000211287,NS,carcinoma,0,4	MAPK13	65	4	0			c.A51C						PASS	.	C		3351,1051		1279,793,129	29.0	28.0	28.0		51	-3.5	1.0	6	dbSNP_86	28	5675,2921		1897,1881,520	no	coding-synonymous	MAPK13	NM_002754.3		3176,2674,649	CC,CA,AA		33.9809,23.8755,30.5585		17/366	36098410	9026,3972	2201	4298	6499	SO:0001819	synonymous_variant	5603	exon1			CAAGACAGCCTGG	Y10488	CCDS4818.1	6p21	2011-06-09			ENSG00000156711	ENSG00000156711	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6875	protein-coding gene	gene with protein product		602899		PRKM13		9295308, 9218798	Standard	NM_002754		Approved	SAPK4, p38delta	uc003ols.4	O15264	OTTHUMG00000014587	ENST00000211287.4:c.51A>C	6.37:g.36098410A>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_002754	O14739|O15124|Q5U4A5|Q6FI46|Q9UNU0	Silent	SNP	ENST00000211287.4	37	CCDS4818.1																																																																																			A|0.271;C|0.729	0.729	strong		0.701	MAPK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040328.1		
SPTBN5	51332	hgsc.bcm.edu	37	15	42154738	42154738	+	Splice_Site	SNP	G	G	A	rs16972193	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:42154738G>A	ENST00000320955.6	-	43	7611	c.7384C>T	c.(7384-7386)Cgg>Tgg	p.R2462W		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2462					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GGTTCATACCGCTTCTGGGCC	0.667													G|||	807	0.161142	0.0091	0.1239	5008	,	,		16546	0.4603		0.1143	False		,,,				2504	0.1329				p.R2427W		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C7279T						PASS	.	G	TRP/ARG	134,3994		3,128,1933	10.0	14.0	13.0		7279	-5.0	0.8	15	dbSNP_123	13	1015,7375		59,897,3239	yes	missense-near-splice	SPTBN5	NM_016642.2	101	62,1025,5172	AA,AG,GG		12.0977,3.2461,9.1788	benign	2427/3640	42154738	1149,11369	2064	4195	6259	SO:0001630	splice_region_variant	51332	exon43			CATACCGCTTCTG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.7385+1C>T	15.37:g.42154738G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	85	75	0.882353	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		413	0.1891025641025641	6	0.012195121951219513	49	0.13535911602209943	269	0.47027972027972026	89	0.11741424802110818	.	13.00	2.105295	0.37145	0.032461	0.120977	ENSG00000137877	ENST00000320955	T	0.61510	0.1	4.93	-4.96	0.03038	.	0.308670	0.24012	N	0.042364	T	0.00012	0.0000	L	0.47716	1.5	0.34186	P	0.328453	B	0.28470	0.213	B	0.26517	0.07	T	0.38023	-0.9680	9	0.49607	T	0.09	.	2.189	0.03894	0.4277:0.1027:0.3245:0.1451	rs16972193;rs16972193	2462	Q9NRC6	SPTN5_HUMAN	W	2462	ENSP00000317790:R2462W	ENSP00000317790:R2462W	R	-	1	2	SPTBN5	39942030	0.326000	0.24669	0.837000	0.33122	0.659000	0.38960	-1.520000	0.02241	-0.730000	0.04869	0.467000	0.42956	CGG	G|0.799;A|0.201	0.201	strong		0.667	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	Missense_Mutation
C3orf20	84077	hgsc.bcm.edu	37	3	14724345	14724345	+	Missense_Mutation	SNP	G	G	A	rs17040154	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:14724345G>A	ENST00000253697.3	+	3	577	c.125G>A	c.(124-126)gGc>gAc	p.G42D	C3orf20_ENST00000412910.1_Intron|C3orf20_ENST00000435614.1_Intron	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	42			G -> D (in dbSNP:rs17040154).			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						GTACCAAAAGGCATCAGAAAC	0.517													G|||	299	0.0597045	0.0008	0.098	5008	,	,		21526	0.0823		0.0676	False		,,,				2504	0.0808				p.G42D		Atlas-SNP	.											.	C3orf20	109	.	0			c.G125A						PASS	.	G	,,ASP/GLY	65,4341	60.5+/-97.4	0,65,2138	132.0	135.0	134.0		,,125	5.3	1.0	3	dbSNP_123	134	504,8096	145.1+/-200.9	18,468,3814	yes	intron,intron,missense	C3orf20	NM_001184957.1,NM_001184958.1,NM_032137.4	,,94	18,533,5952	AA,AG,GG		5.8605,1.4753,4.3749	,,probably-damaging	,,42/905	14724345	569,12437	2203	4300	6503	SO:0001583	missense	84077	exon3			CAAAAGGCATCAG	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.125G>A	3.37:g.14724345G>A	ENSP00000253697:p.Gly42Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	126	0.057692307692307696	0	0.0	32	0.08839779005524862	45	0.07867132867132867	49	0.06464379947229551	G	21.2	4.116651	0.77323	0.014753	0.058605	ENSG00000131379	ENST00000253697	T	0.25250	1.81	5.28	5.28	0.74379	.	0.000000	0.48767	D	0.000170	T	0.01976	0.0062	L	0.36672	1.1	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.02610	-1.1134	9	0.87932	D	0	-26.0886	15.8379	0.78814	0.0:0.0:1.0:0.0	rs17040154;rs52822220;rs56495265;rs17040154	42	Q8ND61	CC020_HUMAN	D	42	ENSP00000253697:G42D	ENSP00000253697:G42D	G	+	2	0	C3orf20	14699349	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	5.001000	0.63946	2.465000	0.83290	0.591000	0.81541	GGC	G|0.950;A|0.050	0.050	strong		0.517	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	
VANGL2	57216	hgsc.bcm.edu	37	1	160395003	160395003	+	Silent	SNP	G	G	A	rs17380141	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:160395003G>A	ENST00000368061.2	+	8	1875	c.1401G>A	c.(1399-1401)ccG>ccA	p.P467P		NM_020335.2	NP_065068.1	Q9ULK5	VANG2_HUMAN	VANGL planar cell polarity protein 2	467					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|cell migration involved in kidney development (GO:0035787)|cochlea morphogenesis (GO:0090103)|convergent extension involved in axis elongation (GO:0060028)|convergent extension involved in neural plate elongation (GO:0022007)|digestive tract morphogenesis (GO:0048546)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity involved in neural tube closure (GO:0090177)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|glomerulus development (GO:0032835)|hair follicle development (GO:0001942)|heart looping (GO:0001947)|inner ear receptor stereocilium organization (GO:0060122)|kidney morphogenesis (GO:0060993)|lateral sprouting involved in lung morphogenesis (GO:0060490)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in axis elongation (GO:0003402)|planar cell polarity pathway involved in heart morphogenesis (GO:0061346)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|positive regulation of JUN kinase activity (GO:0043507)|post-anal tail morphogenesis (GO:0036342)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Wnt signaling pathway (GO:0030111)|Rho protein signal transduction (GO:0007266)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell pole (GO:0060187)|cell-cell junction (GO:0005911)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)		p.P467P(1)		biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	37	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCGAGGAGCCGGTGACCAACG	0.557													G|||	1137	0.227037	0.2375	0.219	5008	,	,		14885	0.0843		0.2793	False		,,,				2504	0.3119				p.P467P		Atlas-SNP	.											VANGL2,NS,carcinoma,0,1	VANGL2	83	1	1	Substitution - coding silent(1)	stomach(1)	c.G1401A						scavenged	.	G		1046,3360	384.0+/-325.1	127,792,1284	88.0	77.0	81.0		1401	-7.8	0.9	1	dbSNP_123	81	2515,6085	412.4+/-350.8	386,1743,2171	no	coding-synonymous	VANGL2	NM_020335.2		513,2535,3455	AA,AG,GG		29.2442,23.7404,27.3797		467/522	160395003	3561,9445	2203	4300	6503	SO:0001819	synonymous_variant	57216	exon8			GGAGCCGGTGACC	AB033041	CCDS30915.1	1q22-q23	2013-03-05	2013-03-05		ENSG00000162738	ENSG00000162738			15511	protein-coding gene	gene with protein product	"""vang, van gogh-like 2"", ""loop-tail-associated protein"", ""strabismus"""	600533	"""vang (van gogh, Drosophila)-like 2, vang, van gogh-like 2 (Drosophila)"", ""vang-like 2 (van gogh, Drosophila)"""			11431695	Standard	NM_020335		Approved	KIAA1215, LTAP, LPP1, STBM, STB1, STBM1, MGC119403, MGC119404	uc001fwc.2	Q9ULK5	OTTHUMG00000033122	ENST00000368061.2:c.1401G>A	1.37:g.160395003G>A		Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_020335	D3DVE9|Q5T212	Silent	SNP	ENST00000368061.2	37	CCDS30915.1																																																																																			G|0.745;A|0.255	0.255	strong		0.557	VANGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080677.1	NM_020335	
PLCH1	23007	hgsc.bcm.edu	37	3	155203301	155203301	+	Missense_Mutation	SNP	C	C	T	rs143905522	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:155203301C>T	ENST00000340059.7	-	22	2841	c.2842G>A	c.(2842-2844)Gag>Aag	p.E948K	PLCH1_ENST00000414191.1_Missense_Mutation_p.E910K|PLCH1_ENST00000447496.2_Missense_Mutation_p.E948K|PLCH1_ENST00000334686.6_Missense_Mutation_p.E910K|PLCH1_ENST00000460012.1_Missense_Mutation_p.E910K|PLCH1-AS2_ENST00000472913.1_RNA|PLCH1_ENST00000494598.1_Missense_Mutation_p.E928K	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	948					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CTTGTGGCCTCGGACACAGAA	0.517																																					p.E948K		Atlas-SNP	.											PLCH1_ENST00000340059,bladder,carcinoma,+1,2	PLCH1	406	2	0			c.G2842A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	154.0	144.0	147.0		2842,2842,2728	5.9	1.0	3	dbSNP_134	147	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense	PLCH1	NM_001130960.1,NM_001130961.1,NM_014996.2	56,56,56	0,7,6496	TT,TC,CC		0.0581,0.0454,0.0538	benign,benign,benign	948/1694,948/1003,910/1656	155203301	7,12999	2203	4300	6503	SO:0001583	missense	23007	exon22			TGGCCTCGGACAC	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.2842G>A	3.37:g.155203301C>T	ENSP00000345988:p.Glu948Lys	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	200	100	0.5	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.382670	0.61845	4.54E-4	5.81E-4	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.34275	1.8;1.65;1.37;1.68;1.65;1.65	5.88	5.88	0.94601	.	0.244558	0.40385	N	0.001102	T	0.35941	0.0949	L	0.54323	1.7	0.80722	D	1	B;P;B	0.52061	0.222;0.95;0.039	B;B;B	0.37601	0.099;0.254;0.031	T	0.19679	-1.0298	10	0.39692	T	0.17	.	20.2228	0.98330	0.0:1.0:0.0:0.0	.	910;948;948	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	K	928;910;948;948;910;910	ENSP00000419100:E928K;ENSP00000417502:E910K;ENSP00000402759:E948K;ENSP00000345988:E948K;ENSP00000335469:E910K;ENSP00000412977:E910K	ENSP00000335469:E910K	E	-	1	0	PLCH1	156685995	0.993000	0.37304	0.975000	0.42487	0.446000	0.32137	3.168000	0.50801	2.789000	0.95967	0.655000	0.94253	GAG	C|1.000;T|0.000	0.000	strong		0.517	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49376582	49376582	+	Missense_Mutation	SNP	G	G	A	rs564196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49376582G>A	ENST00000200453.5	+	2	361	c.92G>A	c.(91-93)cGc>cAc	p.R31H		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	31	Required for localization in the endoplasmic reticulum.		R -> H (in dbSNP:rs564196).		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CTCCTCAGCCGCGCCTGGAGC	0.652													G|||	1372	0.273962	0.5325	0.2262	5008	,	,		16179	0.0873		0.1501	False		,,,				2504	0.2781				p.R31H		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G92A						PASS	.	G	HIS/ARG	2111,2289		524,1063,613	25.0	28.0	27.0		92	2.2	0.9	19	dbSNP_83	27	1232,7358		75,1082,3138	yes	missense	PPP1R15A	NM_014330.3	29	599,2145,3751	AA,AG,GG		14.3423,47.9773,25.7352	probably-damaging	31/675	49376582	3343,9647	2200	4295	6495	SO:0001583	missense	23645	exon2			TCAGCCGCGCCTG	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.92G>A	19.37:g.49376582G>A	ENSP00000200453:p.Arg31His	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	499	0.22847985347985347	249	0.5060975609756098	82	0.2265193370165746	54	0.0944055944055944	114	0.1503957783641161	G	17.76	3.468799	0.63625	0.479773	0.143423	ENSG00000087074	ENST00000200453	T	0.05996	3.36	4.28	2.16	0.27623	.	0.226254	0.28606	N	0.014748	T	0.00012	0.0000	L	0.43923	1.385	0.33266	P	0.43964800000000004	D	0.76494	0.999	P	0.57846	0.828	T	0.45264	-0.9273	9	0.72032	D	0.01	-4.0888	6.5741	0.22555	0.2149:0.0:0.7851:0.0	rs564196;rs564196	31	O75807	PR15A_HUMAN	H	31	ENSP00000200453:R31H	ENSP00000200453:R31H	R	+	2	0	PPP1R15A	54068394	0.865000	0.29922	0.897000	0.35233	0.378000	0.30076	1.188000	0.32102	0.758000	0.33059	0.561000	0.74099	CGC	G|0.729;A|0.271	0.271	strong		0.652	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
DACT2	168002	hgsc.bcm.edu	37	6	168708816	168708816	+	Missense_Mutation	SNP	T	T	G	rs10945501	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168708816T>G	ENST00000366795.3	-	4	1709	c.1621A>C	c.(1621-1623)Aca>Cca	p.T541P	DACT2_ENST00000610183.1_Missense_Mutation_p.T371P|DACT2_ENST00000607983.1_Missense_Mutation_p.T133P|DACT2_ENST00000366796.3_Intron	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	541			T -> P (in dbSNP:rs10945501).		epithelial cell morphogenesis (GO:0003382)|hematopoietic progenitor cell differentiation (GO:0002244)|inner medullary collecting duct development (GO:0072061)|negative regulation of cell adhesion (GO:0007162)|negative regulation of nodal signaling pathway (GO:1900108)|skin development (GO:0043588)	mitochondrion (GO:0005739)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)|transcription factor binding (GO:0008134)			endometrium(1)	1		Breast(66;1.46e-05)|Ovarian(120;0.0728)		OV - Ovarian serous cystadenocarcinoma(33;5.33e-21)|BRCA - Breast invasive adenocarcinoma(81;1.18e-06)|GBM - Glioblastoma multiforme(31;0.000957)		CCCCTCCCTGTGGGCCAGTGG	0.701													G|||	2526	0.504393	0.7905	0.4107	5008	,	,		11834	0.3234		0.3688	False		,,,				2504	0.5102				p.T541P		Atlas-SNP	.											DACT2_ENST00000366795,rectum,carcinoma,0,2	DACT2	46	2	0			c.A1621C						PASS	.						8.0	12.0	11.0					6																	168708816		690	1585	2275	SO:0001583	missense	168002	exon4			TCCCTGTGGGCCA	AF318336	CCDS47519.1, CCDS69241.1, CCDS75554.1	6q27	2013-05-15	2013-05-15	2003-09-17	ENSG00000164488	ENSG00000164488			21231	protein-coding gene	gene with protein product		608966	"""chromosome 6 open reading frame 116"", ""dapper homolog 2, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 2 (Xenopus laevis)"""	C6orf116			Standard	NM_001286351		Approved	bA503C24.7, DAPPER2	uc003qwq.3	Q5SW24	OTTHUMG00000016046	ENST00000366795.3:c.1621A>C	6.37:g.168708816T>G	ENSP00000355760:p.Thr541Pro	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	30	10	0.333333	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Missense_Mutation	SNP	ENST00000366795.3	37	CCDS47519.1	1004	0.4597069597069597	386	0.7845528455284553	152	0.4198895027624309	197	0.34440559440559443	269	0.3548812664907652	G	4.150	0.026308	0.08054	.	.	ENSG00000164488	ENST00000366795	T	0.41758	0.99	3.05	2.17	0.27698	.	1.930070	0.03734	N	0.253953	T	0.03871	0.0109	N	0.00729	-1.24	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.19160	-1.0314	9	0.18276	T	0.48	.	4.6907	0.12780	0.1176:0.0:0.6679:0.2145	rs10945501	541	Q5SW24	DACT2_HUMAN	P	541	ENSP00000355760:T541P	ENSP00000355760:T541P	T	-	1	0	DACT2	168451665	0.016000	0.18221	0.003000	0.11579	0.001000	0.01503	1.035000	0.30216	0.060000	0.16281	-0.225000	0.12378	ACA	T|0.545;G|0.455	0.455	strong		0.701	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
OR8B3	390271	hgsc.bcm.edu	37	11	124266906	124266906	+	Missense_Mutation	SNP	C	C	T	rs530992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124266906C>T	ENST00000354597.3	-	1	358	c.342G>A	c.(340-342)atG>atA	p.M114I		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	114			M -> I (in dbSNP:rs530992). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TTGAGGTCAACATGTAACATT	0.388																																					p.M114I		Atlas-SNP	.											.	OR8B3	36	.	0			c.G342A						PASS	.	C	ILE/MET	1554,2848		145,1264,792	87.0	77.0	81.0		342	1.5	0.9	11	dbSNP_83	81	2312,6286		180,1952,2167	no	missense	OR8B3	NM_001005467.1	10	325,3216,2959	TT,TC,CC		26.89,35.3021,29.7385	benign	114/314	124266906	3866,9134	2201	4299	6500	SO:0001583	missense	390271	exon1			GGTCAACATGTAA	AB065827	CCDS31709.1	11q24.1	2012-08-09			ENSG00000196661	ENSG00000196661		"""GPCR / Class A : Olfactory receptors"""	8472	protein-coding gene	gene with protein product							Standard	NM_001005467		Approved		uc010saj.2	Q8NGG8	OTTHUMG00000165983	ENST00000354597.3:c.342G>A	11.37:g.124266906C>T	ENSP00000346611:p.Met114Ile	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	439	191	0.43508	NM_001005467	Q6IFQ8|Q8NGH1	Missense_Mutation	SNP	ENST00000354597.3	37	CCDS31709.1	708	0.3241758241758242	223	0.4532520325203252	112	0.30939226519337015	141	0.2465034965034965	232	0.30606860158311344	N	0.008	-1.927147	0.00493	0.353021	0.2689	ENSG00000196661	ENST00000354597	T	0.00382	7.61	3.49	1.5	0.22942	GPCR, rhodopsin-like superfamily (1);	0.076028	0.56097	D	0.000028	T	0.00012	0.0000	N	0.05230	-0.09	0.36345	P	0.14026300000000003	B	0.19706	0.038	B	0.23275	0.045	T	0.00601	-1.1650	9	0.23891	T	0.37	.	6.5217	0.22279	0.3904:0.3203:0.2893:0.0	rs530992	114	Q8NGG8	OR8B3_HUMAN	I	114	ENSP00000346611:M114I	ENSP00000346611:M114I	M	-	3	0	OR8B3	123772116	0.000000	0.05858	0.931000	0.37212	0.006000	0.05464	-2.276000	0.01161	0.416000	0.25844	-0.196000	0.12772	ATG	C|0.689;T|0.311	0.311	strong		0.388	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467	
UROC1	131669	hgsc.bcm.edu	37	3	126202257	126202257	+	Silent	SNP	G	G	A	rs1687477	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:126202257G>A	ENST00000290868.2	-	19	1898	c.1845C>T	c.(1843-1845)gcC>gcT	p.A615A	UROC1_ENST00000383579.3_Silent_p.A675A	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	615					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		CTCTCCCCTCGGCCTCCGGGG	0.622													g|||	2049	0.409145	0.1853	0.4697	5008	,	,		20269	0.4901		0.5239	False		,,,				2504	0.4673				p.A675A		Atlas-SNP	.											UROC1_ENST00000383579,NS,carcinoma,0,4	UROC1	150	4	0			c.C2025T						PASS	.		,	1025,3381	375.1+/-321.5	124,777,1302	67.0	61.0	63.0		2025,1845	-10.3	0.5	3	dbSNP_89	63	4524,4076	592.7+/-393.0	1177,2170,953	no	coding-synonymous,coding-synonymous	UROC1	NM_001165974.1,NM_144639.2	,	1301,2947,2255	AA,AG,GG		47.3953,23.2637,42.6649	,	675/737,615/677	126202257	5549,7457	2203	4300	6503	SO:0001819	synonymous_variant	131669	exon20			CCCCTCGGCCTCC	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"""urocanase 1"""	613012	"""urocanase domain containing 1"""			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.1845C>T	3.37:g.126202257G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001165974	E9PE13|Q14C64|Q68CJ7	Silent	SNP	ENST00000290868.2	37	CCDS3038.1																																																																																			G|0.576;A|0.424	0.424	strong		0.622	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639	
TMEM259	91304	hgsc.bcm.edu	37	19	1010406	1010406	+	Silent	SNP	G	G	A	rs62131162	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1010406G>A	ENST00000356663.3	-	11	1927	c.1806C>T	c.(1804-1806)ggC>ggT	p.G602G	TMEM259_ENST00000333175.5_3'UTR	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	602						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GGCTAGGCCCGCCTACCGCAG	0.741													N|||	505	0.100839	0.1278	0.098	5008	,	,		11980	0.001		0.1322	False		,,,				2504	0.137				p.G602G		Atlas-SNP	.											.	.	.	.	0			c.C1806T						PASS	.		,	328,3510		20,288,1611	3.0	4.0	4.0		1806,	-2.6	0.0	19	dbSNP_129	4	874,6922		40,794,3064	no	coding-synonymous,utr-3	C19orf6	NM_001033026.1,NM_033420.3	,	60,1082,4675	AA,AG,GG		11.2109,8.5461,10.3318	,	602/621,	1010406	1202,10432	1919	3898	5817	SO:0001819	synonymous_variant	91304	exon11			AGGCCCGCCTACC	BC008957	CCDS12052.1, CCDS32862.1	19p13.3	2013-02-06	2013-02-06	2013-02-06	ENSG00000182087	ENSG00000182087			17039	protein-coding gene	gene with protein product	"""membralin"", ""aspecific BCL2 ARE-binding protein 1"""	611011	"""chromosome 19 open reading frame 6"""	C19orf6		12638133, 16084606	Standard	XM_005259675		Approved	MGC4022, ASBABP1, MBRL	uc002lqr.1	Q4ZIN3		ENST00000356663.3:c.1806C>T	19.37:g.1010406G>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_001033026	O60392|Q8NF79|Q96H30	Silent	SNP	ENST00000356663.3	37	CCDS32862.1																																																																																			G|0.903;A|0.097	0.097	strong		0.741	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420	
EFCAB12	90288	hgsc.bcm.edu	37	3	129134242	129134242	+	Silent	SNP	G	G	A	rs16859327	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129134242G>A	ENST00000505956.1	-	4	846	c.684C>T	c.(682-684)gtC>gtT	p.V228V	EFCAB12_ENST00000326085.3_Silent_p.V228V	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	228	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)										GAGGGACTCCGACCTGAGGAG	0.537													G|||	758	0.151358	0.1309	0.1239	5008	,	,		21003	0.4603		0.002	False		,,,				2504	0.0337				p.V228V		Atlas-SNP	.											.	.	.	.	0			c.C684T						PASS	.	G		402,3570		22,358,1606	102.0	98.0	99.0		684	-9.7	0.0	3	dbSNP_123	99	35,8287		1,33,4127	no	coding-synonymous	C3orf25	NM_207307.1		23,391,5733	AA,AG,GG		0.4206,10.1208,3.5546		228/573	129134242	437,11857	1986	4161	6147	SO:0001819	synonymous_variant	90288	exon4			GACTCCGACCTGA	AK096099	CCDS54638.1	3q21.3	2013-01-10	2012-07-20	2012-07-20	ENSG00000172771	ENSG00000172771		"""EF-hand domain containing"""	28061	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 25"""	C3orf25			Standard	NM_207307		Approved		uc003emg.3	Q6NXP0	OTTHUMG00000159464	ENST00000505956.1:c.684C>T	3.37:g.129134242G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	211	96	0.454976	NM_207307	Q69YX4	Silent	SNP	ENST00000505956.1	37	CCDS54638.1																																																																																			G|0.849;A|0.151	0.151	strong		0.537	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	
EPB41L2	2037	hgsc.bcm.edu	37	6	131190838	131190838	+	Silent	SNP	G	G	A	rs17059736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:131190838G>A	ENST00000337057.3	-	15	2653	c.2472C>T	c.(2470-2472)ccC>ccT	p.P824P	EPB41L2_ENST00000527659.1_Intron|EPB41L2_ENST00000530481.1_Intron|EPB41L2_ENST00000525193.1_Intron|EPB41L2_ENST00000524581.1_Silent_p.P202P|EPB41L2_ENST00000530757.1_Intron|EPB41L2_ENST00000529208.1_Silent_p.P754P|EPB41L2_ENST00000531410.1_Intron|EPB41L2_ENST00000528282.1_Intron|EPB41L2_ENST00000525271.1_Intron|EPB41L2_ENST00000392427.3_Intron|EPB41L2_ENST00000445890.2_Intron|EPB41L2_ENST00000368128.2_Silent_p.P824P|EPB41L2_ENST00000527411.1_Silent_p.P754P	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	824					cortical actin cytoskeleton organization (GO:0030866)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|spectrin (GO:0008091)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2)	44	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		TCTTCTCTCCGGGTATCTTTT	0.507													G|||	799	0.159545	0.2489	0.2104	5008	,	,		19065	0.0873		0.1262	False		,,,				2504	0.1115				p.P824P		Atlas-SNP	.											.	EPB41L2	96	.	0			c.C2472T						PASS	.	G	,,,,	1149,3257	408.4+/-334.6	155,839,1209	266.0	248.0	254.0		,,,,2472	-0.6	0.6	6	dbSNP_123	254	988,7612	212.5+/-252.8	51,886,3363	no	intron,intron,intron,intron,coding-synonymous	EPB41L2	NM_001135554.1,NM_001135555.2,NM_001199388.1,NM_001199389.1,NM_001431.3	,,,,	206,1725,4572	AA,AG,GG		11.4884,26.0781,16.4309	,,,,	,,,,824/1006	131190838	2137,10869	2203	4300	6503	SO:0001819	synonymous_variant	2037	exon15			CTCTCCGGGTATC	AF027299	CCDS5141.1, CCDS47474.1, CCDS56450.1, CCDS59037.1	6q23	2008-08-29			ENSG00000079819	ENSG00000079819			3379	protein-coding gene	gene with protein product		603237				9598318, 9828140	Standard	NM_001431		Approved	4.1-G	uc003qch.2	O43491	OTTHUMG00000015560	ENST00000337057.3:c.2472C>T	6.37:g.131190838G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	222	116	0.522523	NM_001431	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Silent	SNP	ENST00000337057.3	37	CCDS5141.1	336	0.15384615384615385	110	0.22357723577235772	71	0.19613259668508287	61	0.10664335664335664	94	0.12401055408970976	G	0.169	-1.073530	0.01918	0.260781	0.114884	ENSG00000079819	ENST00000456097	.	.	.	5.71	-0.641	0.11490	.	.	.	.	.	T	0.31389	0.0795	.	.	.	0.09310	P	0.9999999765644	.	.	.	.	.	.	T	0.18053	-1.0349	3	.	.	.	.	10.824	0.46620	0.5978:0.0:0.4022:0.0	rs17059736;rs17059736	.	.	.	W	367	.	.	R	-	1	2	EPB41L2	131232531	0.003000	0.15002	0.625000	0.29200	0.157000	0.22087	-0.125000	0.10579	-0.095000	0.12351	-1.587000	0.00848	CGG	G|0.841;A|0.159	0.159	strong		0.507	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3		
SPHKAP	80309	hgsc.bcm.edu	37	2	228855993	228855993	+	Missense_Mutation	SNP	C	C	T	rs61752221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:228855993C>T	ENST00000392056.3	-	10	4817	c.4771G>A	c.(4771-4773)Gag>Aag	p.E1591K	SPHKAP_ENST00000344657.5_Missense_Mutation_p.E1562K	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1591						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GGCTTACCCTCTGTGCTTTCT	0.418													C|||	24	0.00479233	0.0015	0.0086	5008	,	,		19744	0.0		0.0159	False		,,,				2504	0.0				p.E1591K		Atlas-SNP	.											.	SPHKAP	750	.	0			c.G4771A						PASS	.	C	LYS/GLU,LYS/GLU	8,4398	14.3+/-33.2	0,8,2195	184.0	175.0	178.0		4771,4684	4.2	0.9	2	dbSNP_129	178	121,8479	63.5+/-125.6	0,121,4179	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	56,56	0,129,6374	TT,TC,CC		1.407,0.1816,0.9918	benign,benign	1591/1701,1562/1672	228855993	129,12877	2203	4300	6503	SO:0001583	missense	80309	exon10			TACCCTCTGTGCT		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4771G>A	2.37:g.228855993C>T	ENSP00000375909:p.Glu1591Lys	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	237	102	0.43038	NM_001142644	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	16	0.007326007326007326	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	11	0.014511873350923483	C	12.78	2.039722	0.35989	0.001816	0.01407	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.12147	2.73;2.71	6.17	4.25	0.50352	.	0.480270	0.24755	N	0.035878	T	0.05547	0.0146	N	0.22421	0.69	0.33424	D	0.580224	B;B	0.15473	0.011;0.013	B;B	0.18561	0.022;0.013	T	0.23940	-1.0174	10	0.19590	T	0.45	.	6.1421	0.20265	0.0:0.7401:0.0:0.2599	rs61752221	1591;1562	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	K	1591;1562	ENSP00000375909:E1591K;ENSP00000339886:E1562K	ENSP00000339886:E1562K	E	-	1	0	SPHKAP	228564237	0.988000	0.35896	0.850000	0.33497	0.996000	0.88848	2.406000	0.44557	0.778000	0.33520	0.655000	0.94253	GAG	C|0.991;T|0.009	0.009	strong		0.418	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
CDH12	1010	hgsc.bcm.edu	37	5	21752056	21752056	+	Silent	SNP	A	A	G	rs6451993	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:21752056A>G	ENST00000382254.1	-	15	3261	c.2175T>C	c.(2173-2175)gaT>gaC	p.D725D	RP11-804N13.1_ENST00000522350.1_RNA|CDH12_ENST00000522262.1_Silent_p.D685D|CDH12_ENST00000504376.2_Silent_p.D725D|CDH12_ENST00000521384.1_5'UTR	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	725					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D725D(1)		NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TTGGATCCACATCATTTTCCT	0.478										HNSCC(59;0.17)			A|||	2750	0.549121	0.3775	0.6282	5008	,	,		16061	0.4365		0.7485	False		,,,				2504	0.636				p.D725D		Atlas-SNP	.											CDH12,NS,carcinoma,0,1	CDH12	238	1	1	Substitution - coding silent(1)	stomach(1)	c.T2175C						PASS	.	A		2000,2406	560.5+/-380.5	451,1098,654	257.0	218.0	231.0		2175	-7.7	0.0	5	dbSNP_116	231	6333,2267	708.1+/-405.6	2338,1657,305	no	coding-synonymous	CDH12	NM_004061.3		2789,2755,959	GG,GA,AA		26.3605,45.3926,35.9296		725/795	21752056	8333,4673	2203	4300	6503	SO:0001819	synonymous_variant	1010	exon15			ATCCACATCATTT	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"""Cadherins / Major cadherins"""	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.2175T>C	5.37:g.21752056A>G		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	232	114	0.491379	NM_004061	B2RBT1|B7Z2U6|Q86UD2	Silent	SNP	ENST00000382254.1	37	CCDS3890.1																																																																																			A|0.402;G|0.598	0.598	strong		0.478	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061	
WDR18	57418	hgsc.bcm.edu	37	19	984533	984533	+	Silent	SNP	T	T	C	rs2301810	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:984533T>C	ENST00000251289.5	+	1	203	c.180T>C	c.(178-180)aaT>aaC	p.N60N	WDR18_ENST00000587001.2_Silent_p.N60N|WDR18_ENST00000591997.1_Intron	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	60					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGCAAGAATTACATCAGCG	0.711													.|||	2246	0.448482	0.4667	0.438	5008	,	,		11366	0.3899		0.5577	False		,,,				2504	0.3793				p.N60N		Atlas-SNP	.											.	WDR18	20	.	0			c.T180C						PASS	.	C		1857,2351		456,945,703	7.0	9.0	9.0		180	3.3	1.0	19	dbSNP_100	9	4066,4176		1101,1864,1156	no	coding-synonymous	WDR18	NM_024100.3		1557,2809,1859	CC,CT,TT		49.3327,44.1302,47.5743		60/433	984533	5923,6527	2104	4121	6225	SO:0001819	synonymous_variant	57418	exon1			CAAGAATTACATC		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.180T>C	19.37:g.984533T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	22	8	0.363636	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	37	CCDS12051.1																																																																																			T|0.552;C|0.448	0.448	strong		0.711	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
TACC2	10579	hgsc.bcm.edu	37	10	123996970	123996970	+	Missense_Mutation	SNP	G	G	A	rs61753077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:123996970G>A	ENST00000369005.1	+	17	8528	c.8188G>A	c.(8188-8190)Ggg>Agg	p.G2730R	TACC2_ENST00000368999.1_Missense_Mutation_p.G820R|TACC2_ENST00000358010.1_Missense_Mutation_p.G876R|TACC2_ENST00000453444.2_Missense_Mutation_p.G2657R|TACC2_ENST00000369004.3_Missense_Mutation_p.G790R|TACC2_ENST00000515603.1_Missense_Mutation_p.G2608R|TACC2_ENST00000515273.1_Missense_Mutation_p.G2657R|TACC2_ENST00000369001.1_Missense_Mutation_p.G357R|TACC2_ENST00000334433.3_Missense_Mutation_p.G2730R|TACC2_ENST00000260733.3_Missense_Mutation_p.G808R|TACC2_ENST00000360561.3_Missense_Mutation_p.G778R|TACC2_ENST00000369000.1_Missense_Mutation_p.G353R|TACC2_ENST00000513429.1_Missense_Mutation_p.G876R	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2730					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CTCCCGCATCGGGACCGCTGA	0.527													G|||	66	0.0131789	0.003	0.0216	5008	,	,		17550	0.0		0.0467	False		,,,				2504	0.0				p.G2730R		Atlas-SNP	.											.	TACC2	271	.	0			c.G8188A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	40,4366	46.0+/-80.4	0,40,2163	57.0	55.0	56.0		2422,2332,2626,8188	4.1	1.0	10	dbSNP_129	56	313,8287	111.6+/-171.8	2,309,3989	yes	missense,missense,missense,missense	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	125,125,125,125	2,349,6152	AA,AG,GG		3.6395,0.9079,2.7141	probably-damaging,probably-damaging,probably-damaging,probably-damaging	808/1027,778/997,876/1095,2730/2949	123996970	353,12653	2203	4300	6503	SO:0001583	missense	10579	exon17			CGCATCGGGACCG	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.8188G>A	10.37:g.123996970G>A	ENSP00000358001:p.Gly2730Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	46	0.021062271062271064	3	0.006097560975609756	9	0.024861878453038673	0	0.0	34	0.044854881266490766	G	12.82	2.052838	0.36181	0.009079	0.036395	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000369001;ENST00000369000;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000496913	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.20200	3.68;3.39;4.13;4.14;3.68;3.39;4.13;2.27;2.31;3.52;3.29;3.52;3.27;2.09	5.04	4.14	0.48551	.	0.000000	0.34245	N	0.004131	T	0.06872	0.0175	L	0.27053	0.805	0.26040	N	0.981621	D;D;D;D;D;D;D;D;D	0.89917	0.999;0.998;0.999;1.0;0.982;0.982;0.998;0.997;1.0	D;D;D;D;P;P;P;P;D	0.73380	0.924;0.925;0.949;0.98;0.525;0.739;0.906;0.832;0.975	T	0.04115	-1.0976	10	0.16896	T	0.51	-20.0163	9.4031	0.38444	0.1642:0.0:0.8358:0.0	rs61753077	2657;790;2608;2657;778;808;353;876;2730	E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-2;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	R	2730;876;2657;2608;2730;876;2657;2643;357;353;778;820;790;808;388	ENSP00000358001:G2730R;ENSP00000425062:G876R;ENSP00000424467:G2657R;ENSP00000427618:G2608R;ENSP00000334280:G2730R;ENSP00000350701:G876R;ENSP00000395048:G2657R;ENSP00000357997:G357R;ENSP00000357996:G353R;ENSP00000353763:G778R;ENSP00000357995:G820R;ENSP00000422815:G790R;ENSP00000260733:G808R;ENSP00000422725:G388R	ENSP00000260733:G808R	G	+	1	0	TACC2	123986960	1.000000	0.71417	0.963000	0.40424	0.109000	0.19521	3.162000	0.50755	1.253000	0.44018	-0.136000	0.14681	GGG	G|0.976;A|0.024	0.024	strong		0.527	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
FCRLA	84824	hgsc.bcm.edu	37	1	161682975	161682975	+	Silent	SNP	G	G	T	rs6688140	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:161682975G>T	ENST00000236938.6	+	5	1178	c.936G>T	c.(934-936)ccG>ccT	p.P312P	FCRLA_ENST00000546024.1_Silent_p.P223P|FCRLA_ENST00000540521.1_Silent_p.P178P|FCRLA_ENST00000294796.4_Silent_p.P161P|FCRLA_ENST00000349527.4_Silent_p.P200P|FCRLA_ENST00000350710.3_Silent_p.P77P|FCRLA_ENST00000367959.2_Silent_p.P318P|FCRLA_ENST00000367950.1_Silent_p.P88P|FCRLA_ENST00000309691.6_Silent_p.P206P|FCRLA_ENST00000367957.2_Silent_p.P172P|FCRLA_ENST00000367949.2_Silent_p.P128P|FCRLA_ENST00000540926.1_Silent_p.P301P|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000367953.3_Silent_p.P301P	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	295	Pro-rich.				cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			CTCTGCCTCCGCCGCCAACCC	0.572													G|||	63	0.0125799	0.0008	0.0346	5008	,	,		17957	0.0		0.0338	False		,,,				2504	0.0041				p.P318P		Atlas-SNP	.											.	FCRLA	101	.	0			c.G954T						PASS	.	G	,,,,,,	21,4385	28.1+/-56.4	0,21,2182	60.0	65.0	63.0		954,669,534,231,516,384,936	-6.3	0.0	1	dbSNP_116	63	281,8319	106.0+/-166.9	7,267,4026	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCRLA	NM_001184866.1,NM_001184867.1,NM_001184870.1,NM_001184871.1,NM_001184872.1,NM_001184873.1,NM_032738.3	,,,,,,	7,288,6208	TT,TG,GG		3.2674,0.4766,2.322	,,,,,,	318/383,223/288,178/243,77/142,172/237,128/193,312/377	161682975	302,12704	2203	4300	6503	SO:0001819	synonymous_variant	84824	exon6			GCCTCCGCCGCCA	AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18504	protein-coding gene	gene with protein product		606891	"""Fc receptor-like and mucin-like 1"""	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.936G>T	1.37:g.161682975G>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	167	83	0.497006	NM_001184866	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Silent	SNP	ENST00000236938.6	37	CCDS30926.1																																																																																			A|0.000;G|0.978;T|0.022	0.022	strong		0.572	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738	
SHKBP1	92799	hgsc.bcm.edu	37	19	41082868	41082868	+	Silent	SNP	T	T	C	rs16974365	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:41082868T>C	ENST00000291842.5	+	1	112	c.63T>C	c.(61-63)atT>atC	p.I21I	SHKBP1_ENST00000600733.1_Silent_p.I21I	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	21	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein homooligomerization (GO:0051260)					breast(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(3)|urinary_tract(1)	29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGGAAGTCATTCATCTGAATG	0.697													T|||	743	0.148363	0.0053	0.121	5008	,	,		10244	0.251		0.2107	False		,,,				2504	0.1912				p.I21I		Atlas-SNP	.											SHKBP1,NS,carcinoma,0,1	SHKBP1	68	1	0			c.T63C						PASS	.	T		161,4215		3,155,2030	8.0	10.0	10.0		63	3.5	1.0	19	dbSNP_123	10	1571,6963		137,1297,2833	no	coding-synonymous	SHKBP1	NM_138392.3		140,1452,4863	CC,CT,TT		18.4087,3.6792,13.416		21/708	41082868	1732,11178	2188	4267	6455	SO:0001819	synonymous_variant	92799	exon1			AGTCATTCATCTG	AF258553	CCDS12560.1	19q13.2	2013-01-10				ENSG00000160410		"""WD repeat domain containing"""	19214	protein-coding gene	gene with protein product						11152963	Standard	NM_138392		Approved	PP203, Sb1	uc002oob.3	Q8TBC3		ENST00000291842.5:c.63T>C	19.37:g.41082868T>C		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	19	7	0.368421	NM_138392	Q8N2I6|Q8WY93|Q96IB8	Silent	SNP	ENST00000291842.5	37	CCDS12560.1																																																																																			T|0.842;C|0.158	0.158	strong		0.697	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462613.2	NM_138392	
EPHX2	2053	hgsc.bcm.edu	37	8	27358505	27358505	+	Missense_Mutation	SNP	A	A	G	rs41507953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27358505A>G	ENST00000521400.1	+	2	594	c.164A>G	c.(163-165)aAa>aGa	p.K55R	EPHX2_ENST00000518379.1_Missense_Mutation_p.K55R|EPHX2_ENST00000520666.1_3'UTR|EPHX2_ENST00000380476.3_Missense_Mutation_p.K2R|EPHX2_ENST00000521780.1_Intron|EPHX2_ENST00000517536.1_Missense_Mutation_p.K55R	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	55	Phosphatase.		K -> R (decreased phosphatase activity; no effect on epoxyde hydrolase activity; dbSNP:rs41507953). {ECO:0000269|Ref.6}.		arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		CGGCTTATGAAAGGAGAGATC	0.527													G|||	504	0.100639	0.2201	0.0836	5008	,	,		18406	0.001		0.0865	False		,,,				2504	0.0685				p.K55R		Atlas-SNP	.											.	EPHX2	57	.	0			c.A164G	GRCh37	CM033767	EPHX2	M	rs41507953	PASS	.	G	ARG/LYS	959,3447	734.1+/-410.5	114,731,1358	103.0	97.0	99.0		164	-5.8	0.0	8	dbSNP_127	99	895,7705	778.4+/-407.7	47,801,3452	yes	missense	EPHX2	NM_001979.4	26	161,1532,4810	GG,GA,AA		10.407,21.7658,14.255	benign	55/556	27358505	1854,11152	2203	4300	6503	SO:0001583	missense	2053	exon2			TTATGAAAGGAGA	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.164A>G	8.37:g.27358505A>G	ENSP00000430269:p.Lys55Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Missense_Mutation	SNP	ENST00000521400.1	37	CCDS6060.1	220|220	0.10073260073260074|0.10073260073260074	121|121	0.2459349593495935|0.2459349593495935	30|30	0.08287292817679558|0.08287292817679558	1|1	0.0017482517482517483|0.0017482517482517483	68|68	0.08970976253298153|0.08970976253298153	G|G	0.069|0.069	-1.206660|-1.206660	0.01568|0.01568	0.217658|0.217658	0.10407|0.10407	ENSG00000120915|ENSG00000120915	ENST00000521684|ENST00000521400;ENST00000518328;ENST00000517536;ENST00000380476;ENST00000415449;ENST00000518379	T|T;T;T;T;T	0.09538|0.09073	2.97|3.02;3.02;3.02;3.02;3.02	4.33|4.33	-5.81|-5.81	0.02340|0.02340	.|Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);	0.650048|0.650048	0.15154|0.15154	N|N	0.277528|0.277528	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01729|0.01729	-0.75|-0.75	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.10450	.|0.002;0.005;0.001	T|T	0.18304|0.18304	-1.0341|-1.0341	7|9	0.59425|0.02654	D|T	0.04|1	-3.2011|-3.2011	7.5338|7.5338	0.27697|0.27697	0.6253:0.2288:0.146:0.0|0.6253:0.2288:0.146:0.0	rs41507953;rs56620636;rs57378862;rs62504273;rs41507953|rs41507953;rs56620636;rs57378862;rs62504273;rs41507953	.|55;55;55	.|E5RFU2;E7ETW9;P34913	.|.;.;HYES_HUMAN	E|R	55|55;55;55;2;55;55	ENSP00000428191:K55E|ENSP00000430269:K55R;ENSP00000430779:K55R;ENSP00000428875:K55R;ENSP00000369843:K2R;ENSP00000427956:K55R	ENSP00000428191:K55E|ENSP00000369843:K2R	K|K	+|+	1|2	0|0	EPHX2|EPHX2	27414422|27414422	0.085000|0.085000	0.21516|0.21516	0.023000|0.023000	0.16930|0.16930	0.464000|0.464000	0.32679|0.32679	-1.570000|-1.570000	0.02140|0.02140	-1.722000|-1.722000	0.01377|0.01377	-0.349000|-0.349000	0.07799|0.07799	AAG|AAA	A|0.878;G|0.122	0.122	strong		0.527	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		
MYRIP	25924	hgsc.bcm.edu	37	3	40251392	40251392	+	Silent	SNP	T	T	C	rs1799418	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:40251392T>C	ENST00000302541.6	+	11	2055	c.1713T>C	c.(1711-1713)gaT>gaC	p.D571D	MYRIP_ENST00000444716.1_Silent_p.D571D|MYRIP_ENST00000425621.1_Silent_p.D571D|MYRIP_ENST00000396217.3_Silent_p.D482D|MYRIP_ENST00000539167.1_Silent_p.D384D|RN7SL411P_ENST00000585204.1_RNA|MYRIP_ENST00000459828.1_3'UTR	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	571	Actin-binding.			D -> E (in Ref. 1; AAM43954). {ECO:0000305}.	intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		AGGCTCGGGATCCCCAGACTC	0.483													C|||	1843	0.368011	0.2791	0.5216	5008	,	,		19456	0.2589		0.5517	False		,,,				2504	0.3027				p.D571D		Atlas-SNP	.											.	MYRIP	98	.	0			c.T1713C						PASS	.	C		1331,3075	695.1+/-405.9	198,935,1070	108.0	103.0	105.0		1713	1.0	0.0	3	dbSNP_89	105	4601,3999	554.4+/-386.5	1261,2079,960	no	coding-synonymous	MYRIP	NM_015460.2		1459,3014,2030	CC,CT,TT		46.5,30.2088,45.6097		571/860	40251392	5932,7074	2203	4300	6503	SO:0001819	synonymous_variant	25924	exon11			TCGGGATCCCCAG	AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"""A-kinase anchor proteins"""	19156	protein-coding gene	gene with protein product	"""synaptotagmin-like protein homologue lacking C2 domains-c"", ""rab effector MYRIP"", ""Slp homologue lacking C2 domains"""	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.1713T>C	3.37:g.40251392T>C		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	212	104	0.490566	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Silent	SNP	ENST00000302541.6	37	CCDS2689.1																																																																																			C|0.439;N|0.001	0.439	strong		0.483	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
UBA1	7317	hgsc.bcm.edu	37	X	47062534	47062534	+	Splice_Site	SNP	G	G	A	rs2070169	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:47062534G>A	ENST00000335972.6	+	13	1523	c.1340G>A	c.(1339-1341)cGc>cAc	p.R447H	INE1_ENST00000456273.1_RNA|UBA1_ENST00000377351.4_Splice_Site_p.R447H|UBA1_ENST00000490869.1_3'UTR	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	447	2 approximate repeats.		R -> H (in dbSNP:rs2070169).		cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATTCCTTAGCGCCAGAACCGT	0.557													G|||	877	0.232318	0.0832	0.2507	3775	,	,		13568	0.127		0.0885	False		,,,				2504	0.3845				p.R447H		Atlas-SNP	.											.	UBA1	89	.	0			c.G1340A						PASS	.	G	HIS/ARG,HIS/ARG	496,3339		31,371,63,1230,508	127.0	102.0	110.0		1340,1340	3.7	0.8	X	dbSNP_96	110	778,5950		41,493,203,1894,1669	yes	missense-near-splice,missense-near-splice	UBA1	NM_003334.3,NM_153280.2	29,29	72,864,266,3124,2177	AA,AG,A,GG,G		11.5636,12.9335,12.061	benign,benign	447/1059,447/1059	47062534	1274,9289	2203	4300	6503	SO:0001630	splice_region_variant	7317	exon13			CTTAGCGCCAGAA	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"""Ubiquitin-like modifier activating enzymes"""	12469	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog (yeast)"", ""POC20 centriolar protein homolog (Chlamydomonas)"""	314370	"""ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)"", ""ubiquitin-activating enzyme E1"""	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.1339-1G>A	X.37:g.47062534G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	168	16	0.0952381	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	37	CCDS14275.1	246	0.14828209764918626	26	0.05603448275862069	61	0.20333333333333334	37	0.06954887218045112	38	0.05277777777777778	G	6.438	0.448939	0.12223	0.129335	0.115636	ENSG00000130985	ENST00000377351;ENST00000335972	T;T	0.18338	2.22;2.22	5.42	3.66	0.41972	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.098654	0.64402	D	0.000005	T	0.00012	0.0000	L	0.51914	1.62	0.09310	P	0.9999999999959204	B	0.06786	0.001	B	0.06405	0.002	T	0.18085	-1.0348	9	0.45353	T	0.12	-3.192	7.3242	0.26545	0.28:0.0:0.72:0.0	rs2070169;rs2230146;rs11558783;rs17336348;rs2070169	447	P22314	UBA1_HUMAN	H	447	ENSP00000366568:R447H;ENSP00000338413:R447H	ENSP00000338413:R447H	R	+	2	0	UBA1	46947478	0.996000	0.38824	0.750000	0.31169	0.028000	0.11728	2.767000	0.47637	0.582000	0.29556	-0.195000	0.12781	CGC	0|0.003;A|0.142	0.142	strong		0.557	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	Missense_Mutation
STRN3	29966	hgsc.bcm.edu	37	14	31381351	31381351	+	Missense_Mutation	SNP	T	T	C	rs2273171	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:31381351T>C	ENST00000357479.5	-	11	1608	c.1412A>G	c.(1411-1413)aAt>aGt	p.N471S	STRN3_ENST00000355683.5_Missense_Mutation_p.N387S|STRN3_ENST00000366206.2_5'UTR	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	471			N -> S (in dbSNP:rs2273171). {ECO:0000269|PubMed:10748158, ECO:0000269|PubMed:7864889}.		negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N387S(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		ATACTTGGGATTCCATGTCTT	0.423													T|||	1948	0.388978	0.3139	0.4553	5008	,	,		17850	0.4692		0.4632	False		,,,				2504	0.2843				p.N471S		Atlas-SNP	.											STRN3,NS,carcinoma,0,1	STRN3	117	1	1	Substitution - Missense(1)	stomach(1)	c.A1412G						PASS	.	T	SER/ASN,SER/ASN	1515,2891	481.2+/-359.0	271,973,959	130.0	124.0	126.0		1412,1160	5.6	1.0	14	dbSNP_100	126	3983,4617	552.8+/-386.2	904,2175,1221	yes	missense,missense	STRN3	NM_001083893.1,NM_014574.3	46,46	1175,3148,2180	CC,CT,TT		46.314,34.3849,42.2728	possibly-damaging,possibly-damaging	471/798,387/714	31381351	5498,7508	2203	4300	6503	SO:0001583	missense	29966	exon11			TTGGGATTCCATG		CCDS9641.1, CCDS41938.1	14q13-q21	2013-01-10			ENSG00000196792	ENSG00000196792		"""WD repeat domain containing"""	15720	protein-coding gene	gene with protein product	"""cell cycle S/G2 nuclear autoantigen"""	614766				7864889, 10681496	Standard	NM_014574		Approved	SG2NA	uc001wqu.2	Q13033	OTTHUMG00000140201	ENST00000357479.5:c.1412A>G	14.37:g.31381351T>C	ENSP00000350071:p.Asn471Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Missense_Mutation	SNP	ENST00000357479.5	37	CCDS41938.1	941	0.4308608058608059	165	0.3353658536585366	166	0.4585635359116022	250	0.4370629370629371	360	0.47493403693931396	T	24.6	4.544097	0.86022	0.343849	0.46314	ENSG00000196792	ENST00000355683;ENST00000357479	T;T	0.59772	0.24;0.24	5.63	5.63	0.86233	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.083501	0.85682	D	0.000000	T	0.00012	0.0000	L	0.28400	0.85	0.09310	P	0.99999999782838	B;B	0.33135	0.029;0.399	B;B	0.31946	0.037;0.138	T	0.44922	-0.9296	9	0.72032	D	0.01	-10.5307	15.7875	0.78319	0.0:0.0:0.0:1.0	rs2273171;rs57146647;rs2273171	387;471	Q13033-2;Q13033	.;STRN3_HUMAN	S	387;471	ENSP00000347909:N387S;ENSP00000350071:N471S	ENSP00000347909:N387S	N	-	2	0	STRN3	30451102	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.153000	0.71819	2.257000	0.74773	0.533000	0.62120	AAT	C|0.414;N|0.000	0.414	strong		0.423	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
PCMTD1	115294	hgsc.bcm.edu	37	8	52733050	52733050	+	Missense_Mutation	SNP	T	T	A	rs12335014	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:52733050T>A	ENST00000360540.5	-	7	1341	c.935A>T	c.(934-936)aAc>aTc	p.N312I	PCMTD1_ENST00000544451.1_Missense_Mutation_p.N236I|PCMTD1_ENST00000522514.1_Missense_Mutation_p.N312I|PCMTD1_ENST00000519559.1_5'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	312			N -> I (in dbSNP:rs12335014). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				ctcttctttgttatcctcttc	0.398													T|||	2231	0.445487	0.0514	0.6254	5008	,	,		15882	0.4792		0.6292	False		,,,				2504	0.6268				p.N312I		Atlas-SNP	.											.	PCMTD1	73	.	0			c.A935T						PASS	.	T	ILE/ASN	717,3689	293.8+/-282.8	72,573,1558	101.0	84.0	90.0		935	0.4	0.9	8	dbSNP_120	90	5648,2952	633.8+/-398.8	1797,2054,449	no	missense	PCMTD1	NM_052937.2	149	1869,2627,2007	AA,AT,TT		34.3256,16.2733,48.939	benign	312/358	52733050	6365,6641	2203	4300	6503	SO:0001583	missense	115294	exon6			TCTTTGTTATCCT		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.935A>T	8.37:g.52733050T>A	ENSP00000353739:p.Asn312Ile	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	194	94	0.484536	NM_052937	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	954	0.4368131868131868	29	0.05894308943089431	216	0.5966850828729282	253	0.4423076923076923	456	0.6015831134564644	T	13.01	2.110648	0.37242	0.162733	0.656744	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.49139	0.79;0.79;0.79	5.97	0.36	0.16097	.	0.799495	0.12261	N	0.484695	T	0.00012	0.0000	N	0.22421	0.69	0.27279	P	0.9581572	P;B	0.34757	0.467;0.004	B;B	0.31614	0.133;0.008	T	0.39522	-0.9610	9	0.44086	T	0.13	-11.6135	5.5868	0.17279	0.0:0.3404:0.1421:0.5175	rs12335014;rs17853079;rs52825998;rs12335014	236;312	F5H1M8;Q96MG8	.;PCMD1_HUMAN	I	312;236;312	ENSP00000353739:N312I;ENSP00000444026:N236I;ENSP00000428099:N312I	ENSP00000353739:N312I	N	-	2	0	PCMTD1	52895603	0.969000	0.33509	0.925000	0.36789	0.993000	0.82548	0.918000	0.28678	0.044000	0.15775	0.533000	0.62120	AAC	T|0.570;A|0.430	0.430	strong		0.398	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
EPPK1	83481	hgsc.bcm.edu	37	8	144941181	144941181	+	Missense_Mutation	SNP	G	G	C	rs7839934	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144941181G>C	ENST00000525985.1	-	2	6312	c.6241C>G	c.(6241-6243)Ctg>Gtg	p.L2081V				P58107	EPIPL_HUMAN	epiplakin 1	2081						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGGAACAGCAGCCAGCCCGTG	0.592													g|||	1432	0.285942	0.2254	0.2997	5008	,	,		20148	0.2669		0.2575	False		,,,				2504	0.407				p.L2081V		Atlas-SNP	.											.	EPPK1	199	.	0			c.C6241G						PASS	.	C	VAL/LEU	960,3348		104,752,1298	66.0	73.0	71.0		6241	-1.8	0.0	8	dbSNP_116	71	2179,6351		285,1609,2371	yes	missense	EPPK1	NM_031308.1	32	389,2361,3669	CC,CG,GG		25.5451,22.2841,24.4508	benign	2081/2420	144941181	3139,9699	2154	4265	6419	SO:0001583	missense	83481	exon1			ACAGCAGCCAGCC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6241C>G	8.37:g.144941181G>C	ENSP00000436337:p.Leu2081Val	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		567	0.25961538461538464	116	0.23577235772357724	104	0.287292817679558	148	0.25874125874125875	199	0.262532981530343	g	3.474	-0.107219	0.06924	0.222841	0.255451	ENSG00000227184	ENST00000525985	T	0.69040	-0.37	4.41	-1.77	0.07982	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17440	-1.0369	7	0.15952	T	0.53	.	5.5162	0.16908	0.0:0.3982:0.2789:0.3229	rs7839934;rs7839934	2081	E9PPU0	.	V	2081	ENSP00000436337:L2081V	ENSP00000436337:L2081V	L	-	1	2	EPPK1	145013169	0.000000	0.05858	0.005000	0.12908	0.000000	0.00434	-2.297000	0.01141	-0.861000	0.04094	-3.661000	0.00025	CTG	G|0.737;C|0.263	0.263	strong		0.592	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
TRMT61B	55006	hgsc.bcm.edu	37	2	29092850	29092850	+	Silent	SNP	G	G	T	rs4666122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29092850G>T	ENST00000306108.5	-	1	317	c.294C>A	c.(292-294)tcC>tcA	p.S98S		NM_017910.3	NP_060380.3	Q9BVS5	TR61B_HUMAN	tRNA methyltransferase 61 homolog B (S. cerevisiae)	98					mitochondrial tRNA methylation (GO:0070901)|protein homooligomerization (GO:0051260)	mitochondrion (GO:0005739)|tRNA (m1A) methyltransferase complex (GO:0031515)	tRNA (adenine-N1-)-methyltransferase activity (GO:0016429)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	13						GCTCTCGAGGGGATGACTCTT	0.612													G|||	2530	0.505192	0.3933	0.5735	5008	,	,		18327	0.7817		0.4115	False		,,,				2504	0.4192				p.S98S		Atlas-SNP	.											.	TRMT61B	28	.	0			c.C294A						PASS	.	G		1694,2712	509.4+/-367.2	329,1036,838	59.0	61.0	60.0		294	0.2	0.0	2	dbSNP_111	60	3649,4951	522.9+/-380.2	765,2119,1416	no	coding-synonymous	TRMT61B	NM_017910.3		1094,3155,2254	TT,TG,GG		42.4302,38.4476,41.081		98/478	29092850	5343,7663	2203	4300	6503	SO:0001819	synonymous_variant	55006	exon1			TCGAGGGGATGAC	BC010365	CCDS1768.1	2p23.2	2009-01-09			ENSG00000171103	ENSG00000171103			26070	protein-coding gene	gene with protein product						11230166	Standard	NM_017910		Approved	FLJ20628	uc002rmm.3	Q9BVS5	OTTHUMG00000128433	ENST00000306108.5:c.294C>A	2.37:g.29092850G>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_017910	Q9H0Q9|Q9NWS7	Silent	SNP	ENST00000306108.5	37	CCDS1768.1																																																																																			G|0.539;N|0.000	.	strong		0.612	TRMT61B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250224.1	NM_017910	
RERE	473	hgsc.bcm.edu	37	1	8421186	8421186	+	Missense_Mutation	SNP	G	G	A	rs201922249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:8421186G>A	ENST00000337907.3	-	19	3015	c.2381C>T	c.(2380-2382)cCt>cTt	p.P794L	RERE_ENST00000476556.1_Missense_Mutation_p.P240L|RERE_ENST00000400907.2_Intron|RERE_ENST00000400908.2_Missense_Mutation_p.P794L|RERE_ENST00000377464.1_Missense_Mutation_p.P526L	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	794	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GTGGGGAACAGGCGCTGTGGG	0.731													G|||	25	0.00499201	0.0	0.0101	5008	,	,		12737	0.0		0.0159	False		,,,				2504	0.002				p.P794L		Atlas-SNP	.											.	RERE	129	.	0			c.C2381T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	16,4116		0,16,2050	8.0	9.0	9.0		2381,719,2381	4.2	0.0	1		9	135,8059		1,133,3963	yes	missense,missense,missense	RERE	NM_012102.3,NM_001042682.1,NM_001042681.1	98,98,98	1,149,6013	AA,AG,GG		1.6475,0.3872,1.2251	benign,benign,benign	794/1567,240/1013,794/1567	8421186	151,12175	2066	4097	6163	SO:0001583	missense	473	exon19			GGAACAGGCGCTG	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2381C>T	1.37:g.8421186G>A	ENSP00000338629:p.Pro794Leu	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	19	13	0.684211	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	14	0.00641025641025641	0	0.0	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	20.8	4.057756	0.76074	0.003872	0.016475	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908	T;T;T	0.46063	0.88;0.89;0.88	5.15	4.24	0.50183	.	.	.	.	.	T	0.22513	0.0543	L	0.44542	1.39	0.37189	D	0.903842	B;B	0.27910	0.193;0.005	B;B	0.31390	0.129;0.038	T	0.35599	-0.9782	9	0.54805	T	0.06	-2.2502	12.4483	0.55664	0.0824:0.0:0.9176:0.0	.	526;794	B1AKN3;Q9P2R6	.;RERE_HUMAN	L	794;526;240;794	ENSP00000338629:P794L;ENSP00000366684:P526L;ENSP00000383700:P794L	ENSP00000338629:P794L	P	-	2	0	RERE	8343773	0.692000	0.27719	0.002000	0.10522	0.010000	0.07245	4.289000	0.59013	1.299000	0.44798	0.561000	0.74099	CCT	G|0.994;A|0.006	0.006	strong		0.731	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
SLC25A52	147407	hgsc.bcm.edu	37	18	29340051	29340051	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:29340051C>T	ENST00000579441.2	-	1	573	c.574G>A	c.(574-576)Ggc>Agc	p.G192S	SLC25A52_ENST00000269205.5_Missense_Mutation_p.G202S			Q3SY17	S2552_HUMAN	solute carrier family 25, member 52	192					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											CCTCGAAGGCCGAAAAACAAG	0.473																																					p.G202S		Atlas-SNP	.											MCART2_ENST00000269205,NS,carcinoma,+1,2	.	.	2	0			c.G604A						scavenged	.						71.0	70.0	70.0					18																	29340051		2203	4297	6500	SO:0001583	missense	147407	exon1			GAAGGCCGAAAAA		CCDS32812.1, CCDS32812.2	18q12.1	2013-07-15	2012-03-29	2012-03-29	ENSG00000141437	ENSG00000141437		"""Solute carriers"""	23324	protein-coding gene	gene with protein product			"""mitochondrial carrier triple repeat 2"""	MCART2			Standard	NM_001034172		Approved		uc002kxa.3	Q3SY17	OTTHUMG00000179617	ENST00000579441.2:c.574G>A	18.37:g.29340051C>T	ENSP00000462754:p.Gly192Ser	Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	292	19	0.0650685	NM_001034172		Missense_Mutation	SNP	ENST00000579441.2	37		.	.	.	.	.	.	.	.	.	.	C	13.46	2.243739	0.39697	.	.	ENSG00000141437	ENST00000269205;ENST00000535708	T	0.79141	-1.24	1.22	0.273	0.15650	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.65544	0.2701	L	0.54323	1.7	0.48511	D	0.999667	B	0.24483	0.104	B	0.19391	0.025	T	0.51052	-0.8754	10	0.26408	T	0.33	.	5.5522	0.17097	0.0:0.7844:0.0:0.2156	.	192	Q3SY17	MCAR2_HUMAN	S	202;192	ENSP00000372612:G202S	ENSP00000372612:G202S	G	-	1	0	MCART2	27594049	1.000000	0.71417	0.108000	0.21378	0.927000	0.56198	4.925000	0.63425	0.084000	0.17077	0.505000	0.49811	GGC	.	.	none		0.473	SLC25A52-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_084000	
CCHCR1	54535	hgsc.bcm.edu	37	6	31124849	31124849	+	5'UTR	SNP	C	C	T	rs3130453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31124849C>T	ENST00000376266.5	-	0	89				CCHCR1_ENST00000396263.2_5'UTR|TCF19_ENST00000376255.4_5'Flank|TCF19_ENST00000376257.3_5'Flank|CCHCR1_ENST00000396268.3_Nonsense_Mutation_p.W78*|CCHCR1_ENST00000480060.1_5'UTR|CCHCR1_ENST00000451521.2_Nonsense_Mutation_p.W78*	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						GATTCTGTCTCCAGCCATCTA	0.473													C|||	2350	0.469249	0.4977	0.5202	5008	,	,		18983	0.3968		0.4612	False		,,,				2504	0.4775				p.W78X		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G234A						PASS	.	C	stop/TRP,stop/TRP,	1483,1537		355,773,382	51.0	38.0	43.0		234,234,	3.7	1.0	6	dbSNP_103	43	2610,2808		642,1326,741	yes	stop-gained,stop-gained,utr-5	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	997,2099,1123	TT,TC,CC		48.1728,49.106,48.5068	,,	78/836,78/872,	31124849	4093,4345	1510	2709	4219	SO:0001623	5_prime_UTR_variant	54535	exon2			CTGTCTCCAGCCA	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.-34G>A	6.37:g.31124849C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001105563	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Nonsense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	996	0.45604395604395603	247	0.5020325203252033	188	0.5193370165745856	203	0.3548951048951049	358	0.47229551451187335	C	37	6.045963	0.97231	0.49106	0.481728	ENSG00000204536	ENST00000396268;ENST00000451521;ENST00000426967	.	.	.	5.51	3.71	0.42584	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	6.2217	0.20685	0.1856:0.7216:0.0:0.0928	rs3130453;rs3180339;rs6910883;rs17516449;rs59308567;rs3130453	.	.	.	X	78;78;87	.	ENSP00000379566:W78X	W	-	3	0	CCHCR1	31232828	0.752000	0.28338	1.000000	0.80357	0.995000	0.86356	0.244000	0.18124	1.298000	0.44778	0.549000	0.68633	TGG	C|0.528;T|0.472	0.472	strong		0.473	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
FANCA	2175	hgsc.bcm.edu	37	16	89815152	89815152	+	Missense_Mutation	SNP	G	G	A	rs17233497	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89815152G>A	ENST00000389301.3	-	33	3293	c.3263C>T	c.(3262-3264)tCt>tTt	p.S1088F	FANCA_ENST00000568369.1_Missense_Mutation_p.S1088F	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1088			S -> F (in FA; dbSNP:rs17233497). {ECO:0000269|PubMed:10094191, ECO:0000269|PubMed:18987736}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GCAGAGGACAGACGAAGGCAG	0.587			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	117	0.0233626	0.0038	0.0187	5008	,	,		21735	0.0218		0.0646	False		,,,				2504	0.0123				p.S1088F		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,lymph_node,lymphoid_neoplasm,0,1	FANCA	99	1	0			c.C3263T	GRCh37	CM992318	FANCA	M	rs17233497	PASS	.	G	PHE/SER	73,4323	62.9+/-100.1	0,73,2125	80.0	59.0	66.0		3263	3.7	0.0	16	dbSNP_123	66	697,7903	172.7+/-223.4	27,643,3630	yes	missense	FANCA	NM_000135.2	155	27,716,5755	AA,AG,GG		8.1047,1.6606,5.9249	possibly-damaging	1088/1456	89815152	770,12226	2198	4300	6498	SO:0001583	missense	2175	exon33	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGGACAGACGAAG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3263C>T	16.37:g.89815152G>A	ENSP00000373952:p.Ser1088Phe	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	59	19	0.322034	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	73	0.033424908424908424	3	0.006097560975609756	9	0.024861878453038673	11	0.019230769230769232	50	0.06596306068601583	G	14.27	2.484066	0.44147	0.016606	0.081047	ENSG00000187741	ENST00000389301;ENST00000305699	D	0.85955	-2.05	4.63	3.68	0.42216	.	0.363675	0.24115	N	0.041417	T	0.32556	0.0833	M	0.72118	2.19	0.21020	N	0.999803	P;P;P	0.50272	0.906;0.933;0.933	P;B;B	0.49665	0.618;0.401;0.401	T	0.58589	-0.7610	10	0.66056	D	0.02	-6.0479	8.8363	0.35115	0.1022:0.0:0.8978:0.0	rs17233497;rs17233497	65;1088;1088	B7Z6Y4;B4DRI7;O15360	.;.;FANCA_HUMAN	F	1088;65	ENSP00000373952:S1088F	ENSP00000306281:S65F	S	-	2	0	FANCA	88342653	0.024000	0.19004	0.003000	0.11579	0.202000	0.24057	2.054000	0.41335	1.329000	0.45376	0.462000	0.41574	TCT	G|0.954;A|0.046	0.046	strong		0.587	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
ITIH4	3700	hgsc.bcm.edu	37	3	52861211	52861211	+	Missense_Mutation	SNP	A	A	T	rs13072536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52861211A>T	ENST00000266041.4	-	3	350	c.254T>A	c.(253-255)aTc>aAc	p.I85N	ITIH4-AS1_ENST00000478366.1_RNA|RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000485816.1_Missense_Mutation_p.I85N|RP5-966M1.6_ENST00000513520.1_5'Flank|ITIH4_ENST00000406595.1_Missense_Mutation_p.I85N|ITIH4_ENST00000434759.3_5'UTR|ITIH4_ENST00000346281.5_Missense_Mutation_p.I85N	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	85	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.		I -> N (in dbSNP:rs13072536). {ECO:0000269|PubMed:7775381}.	I -> K (in Ref. 3; AAD05198). {ECO:0000305}.	acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GCCATCGATGATCCTGGGGGC	0.612													A|||	1228	0.245208	0.1997	0.379	5008	,	,		20759	0.3175		0.2584	False		,,,				2504	0.1237				p.I85N		Atlas-SNP	.											.	ITIH4	74	.	0			c.T254A						PASS	.	A	ASN/ILE,ASN/ILE	949,3457	362.6+/-316.2	89,771,1343	108.0	102.0	104.0		254,254	3.0	1.0	3	dbSNP_121	104	2005,6595	350.3+/-327.8	265,1475,2560	yes	missense,missense	ITIH4	NM_001166449.1,NM_002218.4	149,149	354,2246,3903	TT,TA,AA		23.314,21.5388,22.7126	benign,benign	85/901,85/931	52861211	2954,10052	2203	4300	6503	SO:0001583	missense	3700	exon3			TCGATGATCCTGG	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"""plasma Kallikrein-sensitive glycoprotein"""	600564	"""inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"""	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.254T>A	3.37:g.52861211A>T	ENSP00000266041:p.Ile85Asn	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	130	64	0.492308	NM_001166449	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Missense_Mutation	SNP	ENST00000266041.4	37	CCDS2865.1	627	0.28708791208791207	83	0.16869918699186992	134	0.3701657458563536	214	0.3741258741258741	196	0.25857519788918204	A	15.32	2.798959	0.50208	0.215388	0.23314	ENSG00000055955	ENST00000266041;ENST00000346281;ENST00000485816;ENST00000406595;ENST00000538421	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	5.44	3.03	0.35002	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.497556	0.19130	N	0.121954	T	0.00012	0.0000	L	0.39245	1.2	0.09310	P	0.9999999510011	D;D;D	0.57257	0.957;0.979;0.979	P;D;D	0.63703	0.776;0.917;0.917	T	0.43212	-0.9405	9	0.37606	T	0.19	-17.459	6.9091	0.24325	0.6491:0.0:0.3509:0.0	rs13072536;rs52823976;rs13072536	85;85;85	E9PGN5;B7ZKJ8;Q14624	.;.;ITIH4_HUMAN	N	85	ENSP00000266041:I85N;ENSP00000340520:I85N;ENSP00000417824:I85N;ENSP00000384425:I85N	ENSP00000266041:I85N	I	-	2	0	ITIH4	52836251	0.983000	0.35010	0.996000	0.52242	0.387000	0.30353	2.393000	0.44442	0.363000	0.24346	-0.451000	0.05528	ATC	A|0.744;T|0.256	0.256	strong		0.612	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
ADAM7	8756	hgsc.bcm.edu	37	8	24339679	24339679	+	Missense_Mutation	SNP	G	G	A	rs13255694	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:24339679G>A	ENST00000175238.6	+	9	813	c.730G>A	c.(730-732)Gtg>Atg	p.V244M	RP11-624C23.1_ENST00000523578.1_RNA|ADAM7_ENST00000520720.1_Missense_Mutation_p.V16M|ADAM7_ENST00000380789.1_Missense_Mutation_p.V244M|RP11-624C23.1_ENST00000519689.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	244	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.		V -> M (in dbSNP:rs13255694).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		AAACATCCATGTGACGTTGGT	0.294													G|||	1309	0.261382	0.1006	0.428	5008	,	,		18287	0.1875		0.3032	False		,,,				2504	0.3937				p.V244M		Atlas-SNP	.											.	ADAM7	165	.	0			c.G730A						PASS	.	G	MET/VAL	560,3846	247.5+/-255.7	38,484,1681	86.0	84.0	85.0		730	5.6	1.0	8	dbSNP_121	85	2833,5763	443.1+/-360.3	474,1885,1939	yes	missense	ADAM7	NM_003817.2	21	512,2369,3620	AA,AG,GG		32.9572,12.7099,26.096	probably-damaging	244/755	24339679	3393,9609	2203	4298	6501	SO:0001583	missense	8756	exon9			ATCCATGTGACGT	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.730G>A	8.37:g.24339679G>A	ENSP00000175238:p.Val244Met	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	539	0.2467948717948718	47	0.09552845528455285	149	0.4116022099447514	109	0.19055944055944055	234	0.3087071240105541	G	17.31	3.357026	0.61293	0.127099	0.329572	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.72942	-0.7;-0.7;-0.7	5.63	5.63	0.86233	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.49305	D	0.000147	T	0.00012	0.0000	H	0.94886	3.595	0.19945	P	0.9999442786	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.01630	-1.1308	9	0.87932	D	0	.	15.176	0.72913	0.0:0.0:1.0:0.0	rs13255694;rs17811530;rs52806960;rs61591583;rs13255694	16;244	E5RK87;Q9H2U9	.;ADAM7_HUMAN	M	244;244;16;59	ENSP00000175238:V244M;ENSP00000370166:V244M;ENSP00000430400:V16M	ENSP00000175238:V244M	V	+	1	0	ADAM7	24395569	1.000000	0.71417	0.990000	0.47175	0.429000	0.31625	4.064000	0.57506	2.652000	0.90054	0.655000	0.94253	GTG	G|0.755;A|0.245	0.245	strong		0.294	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
MYNN	55892	hgsc.bcm.edu	37	3	169492101	169492101	+	Silent	SNP	C	C	T	rs10936599	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:169492101C>T	ENST00000349841.5	+	2	681	c.18C>T	c.(16-18)caC>caT	p.H6H	MYNN_ENST00000356716.4_Silent_p.H6H|MYNN_ENST00000544106.1_Silent_p.H6H|RP11-816J6.3_ENST00000602879.1_RNA|MYNN_ENST00000392733.1_Silent_p.H6H|RP11-362K14.5_ENST00000602342.1_RNA	NM_018657.4	NP_061127.1	Q9NPC7	MYNN_HUMAN	myoneurin	6					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			ATTCGCACCACTGTGAGCACC	0.393													C|||	1355	0.270567	0.0371	0.3545	5008	,	,		21836	0.5784		0.2425	False		,,,				2504	0.2382				p.H6H		Atlas-SNP	.											.	MYNN	36	.	0			c.C18T						PASS	.	C	,,	305,4101	164.0+/-195.7	5,295,1903	172.0	165.0	168.0	http://www.ncbi.nlm.nih.gov/pubmed?term	18,18,18	3.9	1.0	3	dbSNP_120	168	2128,6472	366.6+/-334.4	279,1570,2451	yes	coding-synonymous,coding-synonymous,coding-synonymous	MYNN	NM_001185118.1,NM_001185119.1,NM_018657.4	,,	284,1865,4354	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	24.7442,6.9224,18.7068	,,	6/611,6/582,6/611	169492101	2433,10573	2203	4300	6503	SO:0001819	synonymous_variant	55892	exon3			GCACCACTGTGAG	AF148848	CCDS3207.1, CCDS54671.1	3q26.31	2013-01-09			ENSG00000085274	ENSG00000085274		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	14955	protein-coding gene	gene with protein product		606042				10873615	Standard	NM_001185118		Approved	SBBIZ1, ZBTB31, ZNF902	uc010hwo.3	Q9NPC7		ENST00000349841.5:c.18C>T	3.37:g.169492101C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	152	77	0.506579	NM_001185118	B2R6C9|Q6QHA6|Q6QHA7|Q6R3G1|Q6R3G2|Q6R4A0|Q7Z716|Q7Z717|Q86Z11|Q86Z12|Q9NS01|Q9UIW8	Silent	SNP	ENST00000349841.5	37	CCDS3207.1																																																																																			C|0.763;T|0.237	0.237	strong		0.393	MYNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467801.1	NM_018657	
CXCR1	3577	hgsc.bcm.edu	37	2	219029932	219029932	+	Start_Codon_SNP	SNP	C	C	T	rs55808468	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:219029932C>T	ENST00000295683.2	-	2	123	c.3G>A	c.(1-3)atG>atA	p.M1I		NM_000634.2	NP_000625.1	P25024	CXCR1_HUMAN	chemokine (C-X-C motif) receptor 1	1					cell surface receptor signaling pathway (GO:0007166)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|receptor internalization (GO:0031623)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)			endometrium(1)|large_intestine(2)|lung(7)|prostate(3)	13					Ketoprofen(DB01009)	TAATATTTGACATGTCCTCTT	0.403													C|||	6	0.00119808	0.0008	0.0014	5008	,	,		25559	0.0		0.004	False		,,,				2504	0.0				p.M1I		Atlas-SNP	.											.	CXCR1	42	.	0			c.G3A						PASS	.	C	ILE/MET	9,4397	15.5+/-35.6	0,9,2194	107.0	104.0	105.0		3	-7.0	0.0	2	dbSNP_129	105	69,8531	42.2+/-99.7	2,65,4233	yes	missense	CXCR1	NM_000634.2	10	2,74,6427	TT,TC,CC		0.8023,0.2043,0.5997	benign	1/351	219029932	78,12928	2203	4300	6503	SO:0001582	initiator_codon_variant	3577	exon2			ATTTGACATGTCC	U11870	CCDS2409.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000163464	ENSG00000163464		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"", ""Interleukins and interleukin receptors"""	6026	protein-coding gene	gene with protein product		146929	"""interleukin 8 receptor, alpha"""	CMKAR1, IL8RA		1303245, 1427896	Standard	NM_000634		Approved	CKR-1, CDw128a, CD181	uc002vhc.3	P25024	OTTHUMG00000133108	ENST00000295683.2:c.3G>A	2.37:g.219029932C>T	ENSP00000295683:p.Met1Ile	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_000634	B2R6Q3|Q2YEF8|Q2YEG4|Q2YEG5|Q2YEG7|Q2YEG8|Q53R18|Q6IN95|Q8N6T6|Q9P2T8|Q9P2T9|Q9P2U0|Q9P2U1|Q9P2U2	Missense_Mutation	SNP	ENST00000295683.2	37	CCDS2409.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	C	10.73	1.433980	0.25813	0.002043	0.008023	ENSG00000163464	ENST00000295683;ENST00000421691	T	0.64085	-0.08	4.29	-7.02	0.01589	.	2.764150	0.01362	N	0.012266	T	0.31136	0.0787	.	.	.	0.21802	N	0.999532	B	0.19706	0.038	B	0.16722	0.016	T	0.10359	-1.0633	9	0.33141	T	0.24	.	2.2979	0.04154	0.1065:0.3398:0.1472:0.4066	rs55808468;rs61752207	1	P25024	CXCR1_HUMAN	I	1	ENSP00000295683:M1I	ENSP00000295683:M1I	M	-	3	0	CXCR1	218738177	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.941000	0.00329	-0.947000	0.03673	0.313000	0.20887	ATG	C|0.996;T|0.004	0.004	strong		0.403	CXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256773.2	NM_000634	Missense_Mutation
OR5I1	10798	hgsc.bcm.edu	37	11	55703861	55703861	+	Missense_Mutation	SNP	T	T	C	rs17597625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55703861T>C	ENST00000301532.3	-	1	15	c.16A>G	c.(16-18)Aga>Gga	p.R6G		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	6			R -> G (in dbSNP:rs17597625).		signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R6R(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GTGTAGTTTCTATCTGTAAAT	0.328													C|||	178	0.0355431	0.0136	0.0346	5008	,	,		15490	0.001		0.0905	False		,,,				2504	0.045				p.R6G		Atlas-SNP	.											OR5I1,caecum,carcinoma,0,1	OR5I1	110	1	1	Substitution - coding silent(1)	large_intestine(1)	c.A16G						PASS	.	C	GLY/ARG	105,4295	798.8+/-415.5	2,101,2097	37.0	36.0	36.0		16	4.1	0.2	11	dbSNP_123	36	682,7900	778.3+/-407.7	34,614,3643	yes	missense	OR5I1	NM_006637.1	125	36,715,5740	CC,CT,TT		7.9469,2.3864,6.0622	benign	6/315	55703861	787,12195	2200	4291	6491	SO:0001583	missense	10798	exon1			AGTTTCTATCTGT	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.16A>G	11.37:g.55703861T>C	ENSP00000301532:p.Arg6Gly	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	37	CCDS7949.1	81	0.03708791208791209	4	0.008130081300813009	10	0.027624309392265192	0	0.0	67	0.08839050131926121	C	0.703	-0.790212	0.02884	0.023864	0.079469	ENSG00000167825	ENST00000301532	T	0.02158	4.42	4.97	4.06	0.47325	.	0.153192	0.30446	N	0.009603	T	0.00073	0.0002	N	0.02391	-0.57	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.50866	-0.8777	10	0.17369	T	0.5	.	10.0478	0.42197	0.0:0.8312:0.0:0.1688	rs17597625;rs52838199;rs58739552;rs17597625	6	Q13606	OR5I1_HUMAN	G	6	ENSP00000301532:R6G	ENSP00000301532:R6G	R	-	1	2	OR5I1	55460437	0.000000	0.05858	0.238000	0.24106	0.113000	0.19764	0.224000	0.17738	0.610000	0.30035	-0.154000	0.13518	AGA	T|0.952;C|0.048	0.048	strong		0.328	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
MAML1	9794	hgsc.bcm.edu	37	5	179201847	179201847	+	Missense_Mutation	SNP	G	G	A	rs6895902	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:179201847G>A	ENST00000292599.3	+	5	3283	c.3020G>A	c.(3019-3021)aGt>aAt	p.S1007N	MAML1_ENST00000503050.1_Intron	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGTGGATGAGTGATTTGGAC	0.463													A|||	1146	0.228834	0.1967	0.2594	5008	,	,		19614	0.1518		0.3579	False		,,,				2504	0.1973				p.S1007N		Atlas-SNP	.											MAML1,brain,glioma,0,1	MAML1	118	1	0			c.G3020A						PASS	.	A	ASN/SER	977,3427	707.4+/-407.5	109,759,1334	123.0	114.0	117.0		3020	1.6	0.6	5	dbSNP_116	117	2925,5675	643.1+/-399.9	503,1919,1878	yes	missense	MAML1	NM_014757.4	46	612,2678,3212	AA,AG,GG		34.0116,22.1844,30.0062	benign	1007/1017	179201847	3902,9102	2202	4300	6502	SO:0001583	missense	9794	exon5			GGATGAGTGATTT	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.3020G>A	5.37:g.179201847G>A	ENSP00000292599:p.Ser1007Asn	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_014757		Missense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	551	0.2522893772893773	96	0.1951219512195122	97	0.26795580110497236	77	0.1346153846153846	281	0.370712401055409	A	0.840	-0.742301	0.03088	0.221844	0.340116	ENSG00000161021	ENST00000292599	T	0.21734	1.99	5.28	1.61	0.23674	.	0.198509	0.44285	N	0.000479	T	0.00012	0.0000	N	0.00392	-1.555	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48091	-0.9065	9	0.02654	T	1	-2.2874	9.1608	0.37021	0.7206:0.0:0.2794:0.0	rs6895902;rs57675371;rs6895902	1007	Q92585	MAML1_HUMAN	N	1007	ENSP00000292599:S1007N	ENSP00000292599:S1007N	S	+	2	0	MAML1	179134453	0.882000	0.30256	0.579000	0.28588	0.991000	0.79684	1.053000	0.30442	-0.182000	0.10602	-0.361000	0.07541	AGT	G|0.733;A|0.267	0.267	strong		0.463	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
POU5F1	5460	hgsc.bcm.edu	37	6	31138107	31138107	+	Silent	SNP	G	G	A	rs1062630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31138107G>A	ENST00000259915.8	-	1	363	c.291C>T	c.(289-291)ggC>ggT	p.G97G	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	97					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)		EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	CTCCTGCTTCGCCCTCAGGCT	0.672			T	EWSR1	sarcoma								G|||	847	0.169129	0.2678	0.1412	5008	,	,		15076	0.0377		0.2008	False		,,,				2504	0.1585				p.G97G		Atlas-SNP	.		Dom	yes		6	6p21.31	5460	"""POU domain, class 5, transcription factor 1"""		M	POU5F1,colon,carcinoma,0,2	POU5F1	25	2	0			c.C291T						PASS	.	G		809,2213		106,597,808	33.0	34.0	33.0		291	0.1	0.4	6	dbSNP_86	33	1252,4160		159,934,1613	no	coding-synonymous	POU5F1	NM_002701.4		265,1531,2421	AA,AG,GG		23.1338,26.7704,24.4368		97/361	31138107	2061,6373	1511	2706	4217	SO:0001819	synonymous_variant	5460	exon1			TGCTTCGCCCTCA	Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"""Homeoboxes / POU class"""	9221	protein-coding gene	gene with protein product		164177	"""POU domain class 5, transcription factor 1"""	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.291C>T	6.37:g.31138107G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	86	52	0.604651	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Silent	SNP	ENST00000259915.8	37	CCDS34391.1																																																																																			G|0.784;A|0.216	0.216	strong		0.672	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701	
TSHZ2	128553	hgsc.bcm.edu	37	20	51871489	51871489	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:51871489T>C	ENST00000371497.5	+	2	2379	c.1492T>C	c.(1492-1494)Tat>Cat	p.Y498H	TSHZ2_ENST00000603338.2_Missense_Mutation_p.Y495H|TSHZ2_ENST00000329613.6_Missense_Mutation_p.Y495H|RP4-678D15.1_ENST00000606932.1_RNA	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	498					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			TACAATCAAATATCAATACCT	0.418																																					p.Y498H		Atlas-SNP	.											TSHZ2,colon,carcinoma,-1,1	TSHZ2	209	1	0			c.T1492C						scavenged	.						68.0	73.0	71.0					20																	51871489		2203	4300	6503	SO:0001583	missense	128553	exon2			ATCAAATATCAAT	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.1492T>C	20.37:g.51871489T>C	ENSP00000360552:p.Tyr498His	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	151	2	0.013245	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.885352	0.51908	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.52295	0.67;0.67	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.70544	0.3236	M	0.78456	2.415	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.74426	-0.3669	10	0.87932	D	0	-3.8498	16.3964	0.83607	0.0:0.0:0.0:1.0	.	498	Q9NRE2	TSH2_HUMAN	H	498;495;24	ENSP00000360552:Y498H;ENSP00000333114:Y495H	ENSP00000333114:Y495H	Y	+	1	0	TSHZ2	51304896	1.000000	0.71417	0.971000	0.41717	0.392000	0.30506	7.693000	0.84214	2.275000	0.75901	0.523000	0.50628	TAT	.	.	none		0.418	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
ECSIT	51295	hgsc.bcm.edu	37	19	11618630	11618630	+	Missense_Mutation	SNP	G	G	A	rs34803265	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11618630G>A	ENST00000270517.7	-	6	967	c.832C>T	c.(832-834)Cgc>Tgc	p.R278C	ZNF653_ENST00000293771.5_5'Flank|ECSIT_ENST00000252440.7_Intron|CTC-398G3.6_ENST00000585656.1_5'Flank|ECSIT_ENST00000417981.2_Missense_Mutation_p.R64C|ECSIT_ENST00000591352.1_5'UTR|ECSIT_ENST00000592312.1_Silent_p.P208P|ECSIT_ENST00000591104.1_Intron|ZNF653_ENST00000593191.1_5'Flank|ECSIT_ENST00000588998.1_Intron	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	278			R -> C (in dbSNP:rs34803265). {ECO:0000269|Ref.1}.		BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						GGATTGTGGCGGGCCAGGGCG	0.627													G|||	119	0.023762	0.0023	0.036	5008	,	,		15521	0.0		0.0835	False		,,,				2504	0.0072				p.R278C		Atlas-SNP	.											.	ECSIT	32	.	0			c.C832T						PASS	.						31.0	35.0	34.0					19																	11618630		2203	4300	6503	SO:0001583	missense	51295	exon6			TGTGGCGGGCCAG	BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"""Mitochondrial respiratory chain complex assembly factors"""	29548	protein-coding gene	gene with protein product	"""signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"""	608388	"""ECSIT homolog (Drosophila)"""			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.832C>T	19.37:g.11618630G>A	ENSP00000270517:p.Arg278Cys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_016581	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	37	CCDS12262.1	82	0.037545787545787544	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	69	0.09102902374670185	G	14.20	2.463549	0.43736	.	.	ENSG00000130159	ENST00000270517;ENST00000417981	T;T	0.45668	0.89;0.89	4.83	4.83	0.62350	.	0.366146	0.28659	N	0.014573	T	0.02119	0.0066	L	0.31926	0.97	0.09310	P	0.9999999999998158	D;B	0.76494	0.999;0.041	P;B	0.53861	0.736;0.007	T	0.18335	-1.0340	9	0.51188	T	0.08	-10.7648	12.602	0.56503	0.0:0.1675:0.8325:0.0	rs34803265;rs34803265	64;278	E9PAN9;Q9BQ95	.;ECSIT_HUMAN	C	278;64	ENSP00000270517:R278C;ENSP00000412712:R64C	ENSP00000270517:R278C	R	-	1	0	ECSIT	11479630	0.529000	0.26322	1.000000	0.80357	0.819000	0.46315	0.913000	0.28611	2.216000	0.71823	0.491000	0.48974	CGC	G|0.959;A|0.041	0.041	strong		0.627	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581	
GPBP1	65056	hgsc.bcm.edu	37	5	56526783	56526783	+	Silent	SNP	G	G	A	rs1130203	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:56526783G>A	ENST00000506184.2	+	4	1279	c.174G>A	c.(172-174)ggG>ggA	p.G58G	GPBP1_ENST00000514387.2_5'UTR|GPBP1_ENST00000454432.2_Silent_p.G58G|GPBP1_ENST00000538707.1_Silent_p.G65G|GPBP1_ENST00000511209.1_Silent_p.G65G|GPBP1_ENST00000424459.3_Silent_p.G58G|GPBP1_ENST00000264779.6_Silent_p.G65G			Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1	58					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	19		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		CTGCTATTGGGCGTCCTAATG	0.353													A|||	4276	0.853834	0.9713	0.8314	5008	,	,		16812	0.998		0.6541	False		,,,				2504	0.7679				p.G65G		Atlas-SNP	.											.	GPBP1	51	.	0			c.G195A						PASS	.	A	,,,	4078,328	168.7+/-199.5	1891,296,16	149.0	158.0	155.0		195,195,,174	4.5	1.0	5	dbSNP_86	155	5847,2753	435.7+/-358.1	1991,1865,444	no	coding-synonymous,coding-synonymous,utr-5,coding-synonymous	GPBP1	NM_001127235.2,NM_001127236.2,NM_001203246.1,NM_022913.3	,,,	3882,2161,460	AA,AG,GG		32.0116,7.4444,23.6891	,,,	65/466,65/481,,58/474	56526783	9925,3081	2203	4300	6503	SO:0001819	synonymous_variant	65056	exon3			TATTGGGCGTCCT		CCDS34162.1, CCDS47211.1, CCDS47212.1, CCDS47212.2, CCDS56368.1	5q11.2	2008-02-05				ENSG00000062194			29520	protein-coding gene	gene with protein product		608412				12842993	Standard	NM_022913		Approved	DKFZp761C169, vasculin	uc003jrk.4	Q86WP2		ENST00000506184.2:c.174G>A	5.37:g.56526783G>A		Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	260	114	0.438462	NM_001127236	A6NKW3|Q6NSH6|Q9H0D4|Q9H785|Q9NSN4	Silent	SNP	ENST00000506184.2	37	CCDS34162.1																																																																																			G|0.224;A|0.776	0.776	strong		0.353	GPBP1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374496.1	NM_022913	
TIAM2	26230	hgsc.bcm.edu	37	6	155569168	155569168	+	Silent	SNP	C	C	T	rs41284218	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:155569168C>T	ENST00000461783.3	+	22	4960	c.3687C>T	c.(3685-3687)gaC>gaT	p.D1229D	TIAM2_ENST00000456144.1_Silent_p.D1229D|TIAM2_ENST00000529824.2_Silent_p.D1229D|TIAM2_ENST00000456877.2_Silent_p.D541D|TIAM2_ENST00000275246.7_Silent_p.D154D|TIAM2_ENST00000367174.2_Silent_p.D605D|TIAM2_ENST00000360366.4_Silent_p.D1253D|TIAM2_ENST00000528391.2_Silent_p.D565D|TIAM2_ENST00000318981.5_Silent_p.D1229D			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1229	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		CTTTTCTGGACGCCCGGAACC	0.507											OREG0017745	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	388	0.077476	0.1657	0.0562	5008	,	,		16514	0.0		0.0855	False		,,,				2504	0.045				p.D1229D		Atlas-SNP	.											.	TIAM2	161	.	0			c.C3687T						PASS	.	C	,	625,3781	271.9+/-270.5	42,541,1620	78.0	80.0	79.0		462,3687	-8.8	0.7	6	dbSNP_127	79	649,7951	164.8+/-217.1	25,599,3676	no	coding-synonymous,coding-synonymous	TIAM2	NM_001010927.2,NM_012454.3	,	67,1140,5296	TT,TC,CC		7.5465,14.1852,9.7955	,	154/627,1229/1702	155569168	1274,11732	2203	4300	6503	SO:0001819	synonymous_variant	26230	exon19			TCTGGACGCCCGG		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.3687C>T	6.37:g.155569168C>T		Somatic	117	0	0	1771	WXS	Illumina HiSeq	Phase_I	128	52	0.40625	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	CCDS34558.1																																																																																			C|0.903;T|0.097	0.097	strong		0.507	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
PARP4	143	hgsc.bcm.edu	37	13	25052261	25052261	+	Silent	SNP	C	C	T	rs4770696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25052261C>T	ENST00000381989.3	-	13	1707	c.1602G>A	c.(1600-1602)tcG>tcA	p.S534S		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	534	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		AGGCTGTTTGCGAAACTCCAT	0.443													.|||	2727	0.544529	0.4289	0.5677	5008	,	,		16176	0.5992		0.5	False		,,,				2504	0.6738				p.S534S		Atlas-SNP	.											PARP4,mouth,carcinoma,-1,1	PARP4	142	1	0			c.G1602A						scavenged	.	T		1900,2506	626.8+/-394.8	410,1080,713	74.0	65.0	68.0		1602	-0.2	0.0	13	dbSNP_111	68	4549,4051	557.5+/-387.1	1197,2155,948	no	coding-synonymous	PARP4	NM_006437.3		1607,3235,1661	TT,TC,CC		47.1047,43.123,49.5848		534/1725	25052261	6449,6557	2203	4300	6503	SO:0001819	synonymous_variant	143	exon13			TGTTTGCGAAACT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1602G>A	13.37:g.25052261C>T		Somatic	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			C|0.494;T|0.506	0.506	strong		0.443	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
SLC6A18	348932	hgsc.bcm.edu	37	5	1240757	1240757	+	Nonsense_Mutation	SNP	C	C	G	rs7447815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1240757C>G	ENST00000324642.3	+	7	1080	c.957C>G	c.(955-957)taC>taG	p.Y319*	SLC6A18_ENST00000296821.4_Intron	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	319					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CTAATGACTACGAGCACTGCC	0.612													C|||	1746	0.348642	0.3638	0.3775	5008	,	,		19420	0.2351		0.3688	False		,,,				2504	0.4039				p.Y319X		Atlas-SNP	.											.	SLC6A18	84	.	0			c.C957G	GRCh37	CM086962	SLC6A18	M	rs7447815	PASS	.	C	stop/TYR	1534,2872	484.6+/-360.1	249,1036,918	142.0	107.0	119.0		957	-3.1	0.0	5	dbSNP_116	119	3206,5394	484.0+/-371.3	622,1962,1716	yes	stop-gained	SLC6A18	NM_182632.2		871,2998,2634	GG,GC,CC		37.2791,34.8162,36.4447		319/629	1240757	4740,8266	2203	4300	6503	SO:0001587	stop_gained	348932	exon7			TGACTACGAGCAC	AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"""Solute carriers"""	26441	protein-coding gene	gene with protein product		610300	"""solute carrier family 6 (neurotransmitter transporter), member 18"", ""solute carrier family 6, member 18"""			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.957C>G	5.37:g.1240757C>G	ENSP00000323549:p.Tyr319*	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	NM_182632		Nonsense_Mutation	SNP	ENST00000324642.3	37	CCDS3860.1	743	0.3402014652014652	188	0.3821138211382114	135	0.3729281767955801	140	0.24475524475524477	280	0.36939313984168864	C	13.94	2.386926	0.42308	0.348162	0.372791	ENSG00000164363	ENST00000324642	.	.	.	4.51	-3.14	0.05250	.	0.627859	0.15102	N	0.280472	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.214	0.59844	0.0:0.2103:0.0:0.7897	rs7447815;rs7447815	.	.	.	X	319	.	ENSP00000323549:Y319X	Y	+	3	2	SLC6A18	1293757	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.005000	0.00650	-0.907000	0.03862	-1.743000	0.00684	TAC	C|0.649;G|0.351	0.351	strong		0.612	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632	
ZNF789	285989	hgsc.bcm.edu	37	7	99081730	99081730	+	Missense_Mutation	SNP	A	A	G	rs6962772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99081730A>G	ENST00000331410.5	+	4	499	c.229A>G	c.(229-231)Act>Gct	p.T77A	ZNF789_ENST00000494186.1_3'UTR|ZNF789_ENST00000448667.1_Missense_Mutation_p.T70A|ZNF789_ENST00000493485.1_Intron	NM_213603.2	NP_998768.2	Q5FWF6	ZN789_HUMAN	zinc finger protein 789	77	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		T -> A (in dbSNP:rs6962772). {ECO:0000269|PubMed:15489334}.		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)			endometrium(2)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)	11	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					TCTACCGAGAACTGGGAATAG	0.527													G|||	2321	0.463458	0.9372	0.2839	5008	,	,		19277	0.3393		0.165	False		,,,				2504	0.3855				p.T77A		Atlas-SNP	.											.	ZNF789	33	.	0			c.A229G						PASS	.	G	ALA/THR	3483,923	354.6+/-312.7	1372,739,92	127.0	125.0	126.0		229	-2.8	0.0	7	dbSNP_116	126	1238,7362	762.4+/-407.6	102,1034,3164	yes	missense	ZNF789	NM_213603.2	58	1474,1773,3256	GG,GA,AA		14.3953,20.9487,36.2986	benign	77/426	99081730	4721,8285	2203	4300	6503	SO:0001583	missense	285989	exon4			CCGAGAACTGGGA	AK093141	CCDS34693.1, CCDS34694.1	7q22.1	2013-01-08			ENSG00000198556	ENSG00000198556		"""Zinc fingers, C2H2-type"", ""-"""	27801	protein-coding gene	gene with protein product						12477932	Standard	XM_005250281		Approved		uc003uqq.1	Q5FWF6	OTTHUMG00000154601	ENST00000331410.5:c.229A>G	7.37:g.99081730A>G	ENSP00000331927:p.Thr77Ala	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_213603	A4D282|A6NH61|Q6ZMZ9	Missense_Mutation	SNP	ENST00000331410.5	37	CCDS34693.1	876	0.4010989010989011	447	0.9085365853658537	112	0.30939226519337015	191	0.3339160839160839	126	0.1662269129287599	G	0.984	-0.696284	0.03279	0.790513	0.143953	ENSG00000198556	ENST00000331410;ENST00000448667	T;T	0.04917	3.53;5.48	4.15	-2.85	0.05734	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	N	0.11201	0.11	0.30939	P	0.7259880000000001	B	0.02656	0.0	B	0.01281	0.0	T	0.30297	-0.9983	8	0.07644	T	0.81	.	0.9601	0.01393	0.4435:0.1255:0.1777:0.2534	rs6962772;rs10358546;rs56621679;rs60618959;rs6962772	77	Q5FWF6	ZN789_HUMAN	A	77;70	ENSP00000331927:T77A;ENSP00000405206:T70A	ENSP00000331927:T77A	T	+	1	0	ZNF789	98919666	0.000000	0.05858	0.007000	0.13788	0.922000	0.55478	-0.578000	0.05841	-0.645000	0.05458	-0.119000	0.15052	ACT	A|0.607;G|0.393	0.393	strong		0.527	ZNF789-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336266.1	NM_213603	
MUC17	140453	hgsc.bcm.edu	37	7	100679720	100679720	+	Missense_Mutation	SNP	G	G	A	rs140695064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100679720G>A	ENST00000306151.4	+	3	5087	c.5023G>A	c.(5023-5025)Gct>Act	p.A1675T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1675	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCCTACACCTGCTGAAGGTAC	0.493													G|||	4	0.000798722	0.0008	0.0	5008	,	,		26161	0.0		0.003	False		,,,				2504	0.0				p.A1675T		Atlas-SNP	.											.	MUC17	804	.	0			c.G5023A						PASS	.						208.0	220.0	216.0					7																	100679720		2203	4300	6503	SO:0001583	missense	140453	exon3			ACACCTGCTGAAG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5023G>A	7.37:g.100679720G>A	ENSP00000302716:p.Ala1675Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	52	32	0.615385	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	2.769	-0.256106	0.05829	.	.	ENSG00000169876	ENST00000306151	T	0.02085	4.46	0.932	-0.0747	0.13730	.	.	.	.	.	T	0.00998	0.0033	N	0.08118	0	0.09310	N	1	B	0.27286	0.174	B	0.16722	0.016	T	0.47114	-0.9142	9	0.08179	T	0.78	.	3.5105	0.07706	0.297:0.0:0.703:0.0	.	1675	Q685J3	MUC17_HUMAN	T	1675	ENSP00000302716:A1675T	ENSP00000302716:A1675T	A	+	1	0	MUC17	100466440	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-3.486000	0.00455	-0.003000	0.14444	0.134000	0.15878	GCT	.	.	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SSTR3	6753	hgsc.bcm.edu	37	22	37603051	37603051	+	Silent	SNP	C	C	T	rs229569	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:37603051C>T	ENST00000328544.3	-	2	1325	c.792G>A	c.(790-792)gcG>gcA	p.A264A	SSTR3_ENST00000402501.1_Silent_p.A264A	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	264					cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	GCACGAAGAGCGCCACCACGG	0.672													C|||	1957	0.390775	0.4811	0.3343	5008	,	,		14335	0.5863		0.2227	False		,,,				2504	0.2802				p.A264A		Atlas-SNP	.											.	SSTR3	42	.	0			c.G792A						PASS	.	C		1905,2501	528.6+/-372.4	400,1105,698	83.0	64.0	70.0		792	-10.2	0.8	22	dbSNP_79	70	1744,6856	306.4+/-307.9	178,1388,2734	no	coding-synonymous	SSTR3	NM_001051.2		578,2493,3432	TT,TC,CC		20.2791,43.2365,28.0563		264/419	37603051	3649,9357	2203	4300	6503	SO:0001819	synonymous_variant	6753	exon2			GAAGAGCGCCACC		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"""GPCR / Class A : Somatostatin receptors"""	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.792G>A	22.37:g.37603051C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	54	34	0.62963	NM_001051	A8K550|Q53ZR7	Silent	SNP	ENST00000328544.3	37	CCDS13944.1																																																																																			C|0.666;T|0.334	0.334	strong		0.672	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1		
PLG	5340	hgsc.bcm.edu	37	6	161139857	161139857	+	Silent	SNP	A	A	G	rs13231	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:161139857A>G	ENST00000308192.9	+	9	1146	c.1083A>G	c.(1081-1083)caA>caG	p.Q361Q		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	361				Q -> E (in Ref. 7; AA sequence and 9; AA sequence). {ECO:0000305}.	blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CCACGGAACAATTGGCTCCCA	0.498													G|||	683	0.136382	0.1452	0.1744	5008	,	,		17688	0.0		0.2922	False		,,,				2504	0.0777				p.Q361Q		Atlas-SNP	.											.	PLG	150	.	0			c.A1083G						PASS	.	G		777,3629	752.2+/-412.3	59,659,1485	76.0	72.0	73.0		1083	-8.7	0.0	6	dbSNP_52	73	2587,6013	689.3+/-404.3	365,1857,2078	no	coding-synonymous	PLG	NM_000301.3		424,2516,3563	GG,GA,AA		30.0814,17.635,25.865		361/811	161139857	3364,9642	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon9			GGAACAATTGGCT	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1083A>G	6.37:g.161139857A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			A|0.787;G|0.213	0.213	strong		0.498	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
LAMA1	284217	hgsc.bcm.edu	37	18	6985631	6985631	+	Silent	SNP	C	C	T	rs617206	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:6985631C>T	ENST00000389658.3	-	38	5484	c.5391G>A	c.(5389-5391)ctG>ctA	p.L1797L		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1797	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CTTGAACATGCAGCTTTTTAT	0.448													C|||	2765	0.552117	0.5174	0.5908	5008	,	,		17146	0.6687		0.4374	False		,,,				2504	0.5695				p.L1797L		Atlas-SNP	.											.	LAMA1	458	.	0			c.G5391A						PASS	.	C		2195,2211	588.3+/-386.9	551,1093,559	110.0	96.0	101.0		5391	0.4	0.3	18	dbSNP_83	101	3672,4928	526.2+/-380.9	761,2150,1389	no	coding-synonymous	LAMA1	NM_005559.3		1312,3243,1948	TT,TC,CC		42.6977,49.8184,45.1099		1797/3076	6985631	5867,7139	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon38			AACATGCAGCTTT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5391G>A	18.37:g.6985631C>T		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	240	116	0.483333	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			C|0.506;T|0.494	0.494	strong		0.448	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
HTR3C	170572	hgsc.bcm.edu	37	3	183774762	183774762	+	Missense_Mutation	SNP	C	C	A	rs6766410	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:183774762C>A	ENST00000318351.1	+	5	523	c.489C>A	c.(487-489)aaC>aaA	p.N163K		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	163			N -> K (in dbSNP:rs6766410). {ECO:0000269|PubMed:12801637}.		ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.N163K(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	GCATCTGTAACCTGGACATCT	0.453													C|||	2327	0.464657	0.3933	0.5274	5008	,	,		20078	0.6508		0.4632	False		,,,				2504	0.3262				p.N163K		Atlas-SNP	.											HTR3C,NS,carcinoma,0,1	HTR3C	65	1	1	Substitution - Missense(1)	stomach(1)	c.C489A						PASS	.	T	LYS/ASN	1833,2573		380,1073,750	264.0	233.0	244.0		489	1.0	1.0	3	dbSNP_116	244	3661,4939		806,2049,1445	yes	missense	HTR3C	NM_130770.2	94	1186,3122,2195	AA,AC,CC		42.5698,41.6024,42.242	benign	163/448	183774762	5494,7512	2203	4300	6503	SO:0001583	missense	170572	exon5			CTGTAACCTGGAC	AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24003	protein-coding gene	gene with protein product		610121	"""5-hydroxytryptamine (serotonin) receptor 3, family member C"""			12801637, 15157181	Standard	NM_130770		Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	ENST00000318351.1:c.489C>A	3.37:g.183774762C>A	ENSP00000322617:p.Asn163Lys	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	182	90	0.494505	NM_130770	A2RRR5	Missense_Mutation	SNP	ENST00000318351.1	37	CCDS3250.1	1081	0.49496336996337	190	0.3861788617886179	176	0.4861878453038674	358	0.6258741258741258	357	0.470976253298153	.	12.56	1.974677	0.34848	0.416024	0.425698	ENSG00000178084	ENST00000318351	T	0.78246	-1.16	4.92	0.975	0.19721	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.452396	0.24975	N	0.034101	T	0.00012	0.0000	N	0.17723	0.515	0.46701	P	8.350000000000302E-4	B	0.20368	0.044	B	0.19666	0.026	T	0.45571	-0.9252	9	0.12103	T	0.63	-22.9762	4.0035	0.09590	0.1547:0.5056:0.0:0.3397	rs6766410;rs52821884;rs57343081;rs6766410	163	Q8WXA8	5HT3C_HUMAN	K	163	ENSP00000322617:N163K	ENSP00000322617:N163K	N	+	3	2	HTR3C	185257456	0.013000	0.17824	0.997000	0.53966	0.991000	0.79684	-0.501000	0.06398	0.296000	0.22592	-0.119000	0.15052	AAC	C|0.546;A|0.454	0.454	strong		0.453	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770	
CTRC	11330	hgsc.bcm.edu	37	1	15767036	15767036	+	Silent	SNP	C	C	T	rs497078	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:15767036C>T	ENST00000375949.4	+	3	206	c.180C>T	c.(178-180)ggC>ggT	p.G60G	CTRC_ENST00000483406.1_3'UTR|CTRC_ENST00000375943.2_Intron	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	60	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATACGTGTGGCGGGACTTTGA	0.627													C|||	415	0.0828674	0.1498	0.0778	5008	,	,		14713	0.003		0.0865	False		,,,				2504	0.0746				p.G60G		Atlas-SNP	.											.	CTRC	28	.	0			c.C180T						PASS	.	C		635,3771		55,525,1623	144.0	95.0	111.0		180	-10.1	0.0	1	dbSNP_83	111	926,7674		36,854,3410	no	coding-synonymous	CTRC	NM_007272.2		91,1379,5033	TT,TC,CC		10.7674,14.4122,12.0022		60/269	15767036	1561,11445	2203	4300	6503	SO:0001819	synonymous_variant	11330	exon3			GTGTGGCGGGACT	BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"""elastase 4"""	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.180C>T	1.37:g.15767036C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_007272	A8K082|O00765|Q9NUH5	Silent	SNP	ENST00000375949.4	37	CCDS156.1																																																																																			A|0.000;C|0.887;T|0.113	0.113	strong		0.627	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272	
NUDT18	79873	hgsc.bcm.edu	37	8	21965801	21965801	+	Silent	SNP	C	C	A	rs184414226	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21965801C>A	ENST00000309188.6	-	4	337	c.219G>T	c.(217-219)ctG>ctT	p.L73L	NUDT18_ENST00000522405.1_5'UTR|NUDT18_ENST00000521807.2_3'UTR	NM_024815.3	NP_079091.3	Q6ZVK8	NUD18_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 18	73	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				dADP catabolic process (GO:0046057)|dGDP catabolic process (GO:0046067)|GDP catabolic process (GO:0046712)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	8-hydroxy-dADP phosphatase activity (GO:0044717)|8-oxo-dGDP phosphatase activity (GO:0044715)|8-oxo-GDP phosphatase activity (GO:0044716)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|lung(2)	4				Colorectal(74;0.00185)|COAD - Colon adenocarcinoma(73;0.0608)|READ - Rectum adenocarcinoma(5;0.0986)		TCCCCGCAGGCAGGTACCACG	0.647													C|||	20	0.00399361	0.0015	0.0159	5008	,	,		17574	0.0		0.005	False		,,,				2504	0.002				p.L73L		Atlas-SNP	.											.	NUDT18	13	.	0			c.G219T						PASS	.	C		3,4253		0,3,2125	29.0	35.0	33.0		221	-6.9	0.4	8		33	74,8356		1,72,4142	yes	coding-synonymous	NUDT18	NM_024815.3		1,75,6267	AA,AC,CC		0.8778,0.0705,0.607		73/324	21965801	77,12609	2128	4215	6343	SO:0001819	synonymous_variant	79873	exon4			CGCAGGCAGGTAC		CCDS75706.1	8p21.3	2012-07-31				ENSG00000275074		"""Nudix motif containing"""	26194	protein-coding gene	gene with protein product	"""mutT human homolog 3"""	615791				22556419	Standard	NM_024815		Approved	FLJ22494, MTH3	uc003xaq.1	Q6ZVK8		ENST00000309188.6:c.219G>T	8.37:g.21965801C>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	81	48	0.592593	NM_024815	Q8IZ75|Q9H687	Silent	SNP	ENST00000309188.6	37		8	0.003663003663003663	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	0	0.0	C	9.689	1.151432	0.21371	7.05E-4	0.008778	ENSG00000173566	ENST00000522379	.	.	.	5.1	-6.89	0.01660	.	.	.	.	.	T	0.20981	0.0505	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36016	-0.9765	4	.	.	.	.	2.7266	0.05215	0.1919:0.4767:0.2185:0.113	.	.	.	.	S	109	.	.	A	-	1	0	NUDT18	22021746	0.082000	0.21442	0.361000	0.25849	0.984000	0.73092	-0.870000	0.04228	-1.380000	0.02115	0.561000	0.74099	GCC	C|0.996;A|0.004	0.004	strong		0.647	NUDT18-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_024815	
BLM	641	hgsc.bcm.edu	37	15	91337479	91337479	+	Silent	SNP	G	G	A	rs2227933	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91337479G>A	ENST00000355112.3	+	16	3220	c.3102G>A	c.(3100-3102)acG>acA	p.T1034T	BLM_ENST00000560509.1_Silent_p.T1034T|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1034					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			AAAATATAACGGAATGCAGGA	0.338			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome				G|||	757	0.151158	0.1974	0.1124	5008	,	,		13066	0.1855		0.165	False		,,,				2504	0.0665				p.T1034T		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.G3102A						PASS	.	G		833,3563	328.8+/-300.7	79,675,1444	104.0	106.0	106.0		3102	-8.5	0.9	15	dbSNP_98	106	1564,7028	292.0+/-300.6	141,1282,2873	no	coding-synonymous	BLM	NM_000057.2		220,1957,4317	AA,AG,GG		18.203,18.949,18.4555		1034/1418	91337479	2397,10591	2198	4296	6494	SO:0001819	synonymous_variant	641	exon16	Familial Cancer Database		TATAACGGAATGC	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3102G>A	15.37:g.91337479G>A		Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	235	113	0.480851	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	37	CCDS10363.1																																																																																			A|0.170;G|0.830	0.170	strong		0.338	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
SBNO2	22904	hgsc.bcm.edu	37	19	1122147	1122147	+	Silent	SNP	G	G	A	rs2072280	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1122147G>A	ENST00000361757.3	-	11	1377	c.1140C>T	c.(1138-1140)ttC>ttT	p.F380F	SBNO2_ENST00000587024.1_Silent_p.F380F|SBNO2_ENST00000438103.2_Silent_p.F323F	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	380					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGACGCCCTCGAAGGCCTCCC	0.677													g|||	2204	0.440096	0.5	0.6066	5008	,	,		15083	0.2371		0.4642	False		,,,				2504	0.4254				p.F380F		Atlas-SNP	.											.	SBNO2	112	.	0			c.C1140T						PASS	.	A	,	1946,2156		517,912,622	18.0	21.0	20.0		969,1140	-4.3	0.9	19	dbSNP_96	20	3583,4681		844,1895,1393	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	1361,2807,2015	AA,AG,GG		43.3567,47.4403,44.7113	,	323/1310,380/1367	1122147	5529,6837	2051	4132	6183	SO:0001819	synonymous_variant	22904	exon11			GCCCTCGAAGGCC	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.1140C>T	19.37:g.1122147G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			G|0.572;A|0.428	0.428	strong		0.677	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
SLC7A3	84889	hgsc.bcm.edu	37	X	70146398	70146398	+	Silent	SNP	A	A	G	rs4360450	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:70146398A>G	ENST00000374299.3	-	10	1743	c.1599T>C	c.(1597-1599)agT>agC	p.S533S	SLC7A3_ENST00000298085.4_Silent_p.S533S			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	533					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GGGGAGTGGAACTCTGTGGCT	0.468													G|||	3066	0.812185	0.5658	0.6081	3775	,	,		14725	0.754		0.4791	False		,,,				2504	0.6687				p.S533S		Atlas-SNP	.											.	SLC7A3	76	.	0			c.T1599C						PASS	.	G	,	2907,924		934,598,441,99,128	47.0	39.0	42.0		1599,1599	1.1	0.1	X	dbSNP_111	42	4337,2385		992,1138,1215,297,653	no	coding-synonymous,coding-synonymous	SLC7A3	NM_001048164.2,NM_032803.5	,	1926,1736,1656,396,781	GG,GA,G,AA,A		35.4805,24.119,31.356	,	533/620,533/620	70146398	7244,3309	2200	4295	6495	SO:0001819	synonymous_variant	84889	exon10			AGTGGAACTCTGT	AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"""Solute carriers"""	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.1599T>C	X.37:g.70146398A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	119	9	0.0756303	NM_032803	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Silent	SNP	ENST00000374299.3	37	CCDS14404.1																																																																																			A|0.284;G|0.716	0.716	strong		0.468	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803	
MAN2A2	4122	hgsc.bcm.edu	37	15	91455455	91455455	+	Silent	SNP	C	C	T	rs140404658	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91455455C>T	ENST00000559717.1	+	15	2751	c.2292C>T	c.(2290-2292)gcC>gcT	p.A764A	MAN2A2_ENST00000360468.3_Silent_p.A764A|MAN2A2_ENST00000431652.2_Silent_p.A272A|MAN2A2_ENST00000430376.2_5'UTR			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	764					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GCGACTTCGCCCTCAGCAACC	0.627													C|||	29	0.00579073	0.0	0.013	5008	,	,		22039	0.0		0.0189	False		,,,				2504	0.001				p.A764A		Atlas-SNP	.											MAN2A2,NS,carcinoma,+2,2	MAN2A2	99	2	0			c.C2292T						PASS	.	C		8,4388	14.3+/-33.2	0,8,2190	95.0	93.0	94.0		2292	2.4	1.0	15	dbSNP_134	94	100,8496	54.4+/-115.2	0,100,4198	no	coding-synonymous	MAN2A2	NM_006122.2		0,108,6388	TT,TC,CC		1.1633,0.182,0.8313		764/1151	91455455	108,12884	2198	4298	6496	SO:0001819	synonymous_variant	4122	exon14			CTTCGCCCTCAGC	L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.2292C>T	15.37:g.91455455C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	174	169	0.971264	NM_006122	A6NH12|A8K1E8|Q13754	Silent	SNP	ENST00000559717.1	37	CCDS32332.1																																																																																			C|0.991;T|0.009	0.009	strong		0.627	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122	
PRDM7	11105	hgsc.bcm.edu	37	16	90130136	90130136	+	Missense_Mutation	SNP	C	C	T	rs2078478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90130136C>T	ENST00000449207.2	-	5	411	c.392G>A	c.(391-393)aGa>aAa	p.R131K	PRDM7_ENST00000407825.1_5'UTR|PRDM7_ENST00000325921.6_5'Flank	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	131			R -> K (in dbSNP:rs2078478).		regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)			lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		TGACAATTCTCTCAAACTAGA	0.418													.|||	1440	0.28754	0.1195	0.2781	5008	,	,		20389	0.7798		0.1571	False		,,,				2504	0.1483				p.R131K		Atlas-SNP	.											.	PRDM7	53	.	0			c.G392A						PASS	.	T	LYS/ARG	460,3272		27,406,1433	93.0	87.0	89.0		392	1.6	0.1	16	dbSNP_96	89	1186,7026		80,1026,3000	yes	missense	PRDM7	NM_001098173.1	26	107,1432,4433	TT,TC,CC		14.4423,12.3258,13.781	benign	131/493	90130136	1646,10298	1866	4106	5972	SO:0001583	missense	11105	exon5			AATTCTCTCAAAC	AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"""Zinc fingers, C2H2-type"", ""-"""	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.392G>A	16.37:g.90130136C>T	ENSP00000396732:p.Arg131Lys	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	280	118	0.421429	NM_001098173	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	37	CCDS45557.1	731	0.3347069597069597	76	0.15447154471544716	78	0.2154696132596685	445	0.777972027972028	132	0.1741424802110818	.	0.016	-1.514500	0.00975	0.123258	0.144423	ENSG00000126856	ENST00000449207	T	0.09350	2.99	1.6	1.6	0.23607	.	.	.	.	.	T	0.00012	0.0000	N	0.00186	-1.895	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.13072	-1.0523	7	.	.	.	-7.7225	3.5217	0.07744	0.0:0.2185:0.0:0.7815	rs2078478;rs17784778;rs58861284;rs2078478	131	Q9NQW5	PRDM7_HUMAN	K	131	ENSP00000396732:R131K	.	R	-	2	0	PRDM7	88657637	0.021000	0.18746	0.057000	0.19452	0.003000	0.03518	0.341000	0.19909	0.113000	0.18004	-0.490000	0.04691	AGA	C|0.693;T|0.307	0.307	strong		0.418	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1		
OR2T3	343173	hgsc.bcm.edu	37	1	248637480	248637480	+	Missense_Mutation	SNP	A	A	G	rs74498773	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248637480A>G	ENST00000359594.2	+	1	854	c.829A>G	c.(829-831)Atg>Gtg	p.M277V		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGAGCAGGACATGATGGTGTC	0.532																																					p.M277V		Atlas-SNP	.											.	OR2T3	79	.	0			c.A829G						PASS	.	A	VAL/MET	584,3822		1,582,1620	283.0	269.0	273.0		829	2.4	0.1	1	dbSNP_131	273	589,8009		1,587,3711	no	missense	OR2T3	NM_001005495.1	21	2,1169,5331	GG,GA,AA		6.8504,13.2547,9.0203	benign	277/319	248637480	1173,11831	2203	4299	6502	SO:0001583	missense	343173	exon1			CAGGACATGATGG		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.829A>G	1.37:g.248637480A>G	ENSP00000352604:p.Met277Val	Somatic	965	1	0.00103627		WXS	Illumina HiSeq	Phase_I	1053	266	0.252612	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	a	7.636	0.679773	0.14907	0.132547	0.068504	ENSG00000196539	ENST00000359594	T	0.00054	8.8	2.37	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	L	0.42008	1.315	0.09310	N	1	B	0.23128	0.08	B	0.24006	0.05	T	0.34675	-0.9819	9	0.87932	D	0	.	8.2762	0.31874	1.0:0.0:0.0:0.0	.	277	Q8NH03	OR2T3_HUMAN	V	277	ENSP00000352604:M277V	ENSP00000352604:M277V	M	+	1	0	OR2T3	246704103	0.000000	0.05858	0.081000	0.20488	0.192000	0.23643	0.197000	0.17197	0.841000	0.35020	0.156000	0.16432	ATG	A|0.974;G|0.026	0.026	strong		0.532	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
CFAP46	54777	hgsc.bcm.edu	37	10	134748331	134748331	+	Missense_Mutation	SNP	C	C	T	rs12781609	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:134748331C>T	ENST00000368586.5	-	8	891	c.791G>A	c.(790-792)aGt>aAt	p.S264N	TTC40_ENST00000368582.2_Missense_Mutation_p.S264N|TTC40_ENST00000368585.3_Missense_Mutation_p.S264N	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CAGAATGACACTGATGTCACC	0.373													C|||	1870	0.373403	0.323	0.5014	5008	,	,		19190	0.3413		0.3459	False		,,,				2504	0.4121				p.S264N		Atlas-SNP	.											.	TTC40	100	.	0			c.G791A						PASS	.	C	ASN/SER	1569,2837	488.3+/-361.2	288,993,922	107.0	105.0	106.0		791	-5.5	0.0	10	dbSNP_121	106	3258,5342	488.5+/-372.4	619,2020,1661	yes	missense	C10orf93	NM_173572.3	46	907,3013,2583	TT,TC,CC		37.8837,35.6105,37.1136	benign	264/406	134748331	4827,8179	2203	4300	6503	SO:0001583	missense	54777	exon8			ATGACACTGATGT																												ENST00000368586.5:c.791G>A	10.37:g.134748331C>T	ENSP00000357575:p.Ser264Asn	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	93	91	0.978495	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	809	0.37042124542124544	174	0.35365853658536583	165	0.4558011049723757	205	0.3583916083916084	265	0.3496042216358839	C	4.040	0.004943	0.07866	0.356105	0.378837	ENSG00000171811	ENST00000368586;ENST00000368582;ENST00000368585	T;T;T	0.53857	0.6;0.6;0.6	4.08	-5.5	0.02576	.	2.977290	0.01403	N	0.013680	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.26467	-1.0102	9	0.18276	T	0.48	.	2.0833	0.03640	0.1451:0.3896:0.1483:0.3171	rs12781609;rs52809580;rs58199946;rs12781609	264	Q5SR76-1	.	N	264	ENSP00000357575:S264N;ENSP00000357571:S264N;ENSP00000357574:S264N	ENSP00000357571:S264N	S	-	2	0	C10orf93	134598321	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.323000	0.01117	-1.228000	0.02568	-0.320000	0.08662	AGT	C|0.636;T|0.364	0.364	strong		0.373	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
CATSPER4	378807	hgsc.bcm.edu	37	1	26520292	26520292	+	Missense_Mutation	SNP	G	G	T	rs12138368	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26520292G>T	ENST00000456354.2	+	3	439	c.372G>T	c.(370-372)ttG>ttT	p.L124F		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	124			L -> F (in dbSNP:rs12138368).		calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		ACTATGAGTTGTTCTCTACCA	0.507													G|||	117	0.0233626	0.0023	0.036	5008	,	,		21477	0.0		0.0835	False		,,,				2504	0.0051				p.L124F		Atlas-SNP	.											CATSPER4,NS,carcinoma,0,1	CATSPER4	59	1	0			c.G372T						scavenged	.	G	PHE/LEU	64,4342	60.5+/-97.4	0,64,2139	190.0	162.0	171.0		372	-1.4	1.0	1	dbSNP_120	171	763,7837	181.2+/-229.9	27,709,3564	yes	missense	CATSPER4	NM_198137.1	22	27,773,5703	TT,TG,GG		8.8721,1.4526,6.3586	benign	124/473	26520292	827,12179	2203	4300	6503	SO:0001583	missense	378807	exon3			TGAGTTGTTCTCT	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.372G>T	1.37:g.26520292G>T	ENSP00000390423:p.Leu124Phe	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	124	56	0.451613	NM_198137	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	74	0.03388278388278388	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	55	0.07255936675461741	G	10.80	1.452939	0.26161	0.014526	0.088721	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.97598	-4.45;-4.45	5.05	-1.38	0.09027	.	0.178796	0.26677	N	0.023065	T	0.38295	0.1035	N	0.25485	0.75	0.24893	N	0.992154	B	0.12013	0.005	B	0.12156	0.007	T	0.71244	-0.4650	10	0.48119	T	0.1	-10.6819	4.6883	0.12769	0.3142:0.2831:0.4027:0.0	rs12138368;rs52809738;rs59959266;rs12138368	124	Q7RTX7	CTSR4_HUMAN	F	124	ENSP00000341006:L124F;ENSP00000390423:L124F	ENSP00000341006:L124F	L	+	3	2	CATSPER4	26392879	0.991000	0.36638	0.993000	0.49108	0.850000	0.48378	-0.030000	0.12308	-0.205000	0.10219	-1.410000	0.01125	TTG	G|0.946;T|0.054	0.054	strong		0.507	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
EHBP1	23301	hgsc.bcm.edu	37	2	63176139	63176139	+	Missense_Mutation	SNP	A	A	C	rs17432615	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:63176139A>C	ENST00000263991.5	+	14	2745	c.2263A>C	c.(2263-2265)Aaa>Caa	p.K755Q	EHBP1_ENST00000405289.1_Missense_Mutation_p.K720Q|EHBP1_ENST00000354487.3_Missense_Mutation_p.K720Q|EHBP1_ENST00000431489.1_Missense_Mutation_p.K720Q|EHBP1_ENST00000405015.3_Missense_Mutation_p.K720Q	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	755			K -> Q (in dbSNP:rs17432615).			cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TCCTATCAAAAAAACAAGTTT	0.373													A|||	307	0.0613019	0.0219	0.0764	5008	,	,		18003	0.0347		0.1083	False		,,,				2504	0.0828				p.K755Q		Atlas-SNP	.											.	EHBP1	127	.	0			c.A2263C						PASS	.	A	GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS	174,4230	108.2+/-146.6	6,162,2034	41.0	45.0	44.0		2158,2158,2158,2263	6.0	1.0	2	dbSNP_123	44	1145,7453	225.7+/-261.6	79,987,3233	yes	missense,missense,missense,missense	EHBP1	NM_001142614.1,NM_001142615.2,NM_001142616.1,NM_015252.3	53,53,53,53	85,1149,5267	CC,CA,AA		13.3171,3.951,10.1446	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	720/1197,720/1161,720/1161,755/1232	63176139	1319,11683	2202	4299	6501	SO:0001583	missense	23301	exon14			ATCAAAAAAACAA	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.2263A>C	2.37:g.63176139A>C	ENSP00000263991:p.Lys755Gln	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	341	226	0.662757	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	37	CCDS1872.1	144|144	0.06593406593406594|0.06593406593406594	10|10	0.02032520325203252|0.02032520325203252	25|25	0.06906077348066299|0.06906077348066299	20|20	0.03496503496503497|0.03496503496503497	89|89	0.11741424802110818|0.11741424802110818	A|A	17.80|17.80	3.478474|3.478474	0.63849|0.63849	0.03951|0.03951	0.133171|0.133171	ENSG00000115504|ENSG00000115504	ENST00000454124|ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T|T;T;T;T;T	0.46451|0.75050	0.87|-0.9;-0.9;-0.88;-0.88;-0.88	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.172511|0.172511	0.50627|0.50627	D|D	0.000112|0.000112	T|T	0.03651|0.03651	0.0104|0.0104	L|L	0.59436|0.59436	1.845|1.845	0.31326|0.31326	P|P	0.685439|0.685439	.|D;P;D	.|0.56746	.|0.977;0.763;0.977	.|P;B;P	.|0.59221	.|0.854;0.372;0.827	T|T	0.33497|0.33497	-0.9866|-0.9866	7|9	0.62326|0.22706	D|T	0.03|0.39	.|.	16.5582|16.5582	0.84512|0.84512	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs17432615;rs52811992;rs17432615|rs17432615;rs52811992;rs17432615	.|720;720;755	.|Q8NDI1-2;Q8NDI1-3;Q8NDI1	.|.;.;EHBP1_HUMAN	N|Q	24|720;720;755;720;720	ENSP00000396186:K24N|ENSP00000384143:K720Q;ENSP00000403783:K720Q;ENSP00000263991:K755Q;ENSP00000346482:K720Q;ENSP00000385524:K720Q	ENSP00000396186:K24N|ENSP00000263991:K755Q	K|K	+|+	3|1	2|0	EHBP1|EHBP1	63029643|63029643	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.397000|0.397000	0.30659|0.30659	6.179000|6.179000	0.71974|0.71974	2.308000|2.308000	0.77769|0.77769	0.533000|0.533000	0.62120|0.62120	AAA|AAA	A|0.917;C|0.083	0.083	strong		0.373	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
GPER1	2852	hgsc.bcm.edu	37	7	1132456	1132456	+	Silent	SNP	C	C	T	rs10246354	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1132456C>T	ENST00000297469.3	+	2	1783	c.1092C>T	c.(1090-1092)acC>acT	p.T364T	C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|GPER1_ENST00000397088.3_Silent_p.T364T|C7orf50_ENST00000357429.6_Intron|GPER1_ENST00000397092.1_Silent_p.T364T|GPER1_ENST00000401670.1_Silent_p.T364T	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	364					apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										CAGACAGCACCGAGCAGTCGG	0.592													c|||	647	0.129193	0.0764	0.2032	5008	,	,		18945	0.0278		0.1968	False		,,,				2504	0.183				p.T364T		Atlas-SNP	.											.	GPER	25	.	0			c.C1092T						PASS	.		,,,,,	434,3972	210.2+/-230.7	23,388,1792	55.0	45.0	48.0		1092,1092,,,1092,	-11.3	0.0	7	dbSNP_119	48	2028,6570	350.8+/-328.0	257,1514,2528	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron	GPER,C7orf50	NM_001039966.1,NM_001098201.1,NM_001134395.1,NM_001134396.1,NM_001505.2,NM_032350.5	,,,,,	280,1902,4320	TT,TC,CC		23.5869,9.8502,18.9326	,,,,,	364/376,364/376,,,364/376,	1132456	2462,10542	2203	4299	6502	SO:0001819	synonymous_variant	2852	exon2			CAGCACCGAGCAG	U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"""G protein-coupled receptor 30"""	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.1092C>T	7.37:g.1132456C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	179	97	0.541899	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Silent	SNP	ENST00000297469.3	37	CCDS5322.1																																																																																			C|0.820;T|0.180	0.180	strong		0.592	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966	
CRISP3	10321	hgsc.bcm.edu	37	6	49696473	49696473	+	Silent	SNP	G	G	T	rs488132	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:49696473G>T	ENST00000393666.1	-	7	714	c.708C>A	c.(706-708)gcC>gcA	p.A236A	CRISP3_ENST00000263045.4_Silent_p.A249A|CRISP3_ENST00000371159.4_Silent_p.A267A|CRISP3_ENST00000423399.2_Silent_p.A146A|CRISP3_ENST00000433368.2_Silent_p.A259A			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	236	ShKT. {ECO:0000255|PROSITE- ProRule:PRU01005}.				defense response (GO:0006952)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|specific granule (GO:0042581)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|skin(6)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			AATTGCAGGAGGCCTTGCAAC	0.403													G|||	778	0.155351	0.2413	0.0634	5008	,	,		17608	0.1875		0.1103	False		,,,				2504	0.1176				p.A259A		Atlas-SNP	.											.	CRISP3	67	.	0			c.C777A						PASS	.	G	,	853,3553	334.9+/-303.7	68,717,1418	186.0	167.0	174.0		777,747	-2.8	0.0	6	dbSNP_83	174	961,7639	209.4+/-250.6	61,839,3400	no	coding-synonymous,coding-synonymous	CRISP3	NM_001190986.1,NM_006061.2	,	129,1556,4818	TT,TG,GG		11.1744,19.36,13.9474	,	259/269,249/259	49696473	1814,11192	2203	4300	6503	SO:0001819	synonymous_variant	10321	exon8			GCAGGAGGCCTTG	X94323	CCDS4929.1, CCDS4929.2, CCDS55019.1	6p12.3	2008-02-05			ENSG00000096006	ENSG00000096006			16904	protein-coding gene	gene with protein product						8665901, 12223513	Standard	NM_006061		Approved	SGP28, CRISP-3, CRS3, dJ442L6.3, Aeg2	uc003ozs.3	P54108	OTTHUMG00000014823	ENST00000393666.1:c.708C>A	6.37:g.49696473G>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	NM_001190986	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Silent	SNP	ENST00000393666.1	37																																																																																				G|0.848;T|0.152	0.152	strong		0.403	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061	
C17orf64	124773	hgsc.bcm.edu	37	17	58508618	58508618	+	Silent	SNP	T	T	C	rs3760332	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:58508618T>C	ENST00000269127.4	+	6	786	c.702T>C	c.(700-702)acT>acC	p.T234T	RPL12P38_ENST00000588627.1_RNA	NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	234										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			CTCCAGAGACTGAACCGTAAG	0.458													C|||	1541	0.307708	0.8608	0.1023	5008	,	,		17422	0.1716		0.0765	False		,,,				2504	0.0838				p.T234T		Atlas-SNP	.											.	C17orf64	19	.	0			c.T702C						PASS	.	C		3104,1302		1120,864,219	43.0	55.0	51.0		702	-1.2	0.0	17	dbSNP_107	51	774,7826		30,714,3556	no	coding-synonymous	C17orf64	NM_181707.2		1150,1578,3775	CC,CT,TT		9.0,29.5506,29.817		234/237	58508618	3878,9128	2203	4300	6503	SO:0001819	synonymous_variant	124773	exon6			AGAGACTGAACCG	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.702T>C	17.37:g.58508618T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_181707	Q8IY87	Silent	SNP	ENST00000269127.4	37	CCDS32698.2																																																																																			T|0.702;C|0.298	0.298	strong		0.458	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707	
XDH	7498	hgsc.bcm.edu	37	2	31593265	31593265	+	Missense_Mutation	SNP	T	T	C	rs17323225	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:31593265T>C	ENST00000379416.3	-	18	1984	c.1936A>G	c.(1936-1938)Ata>Gta	p.I646V		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	646			I -> V (in dbSNP:rs17323225). {ECO:0000269|Ref.6}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	ATTCCAGTTATGTTACTCCCA	0.353													T|||	97	0.019369	0.0053	0.0159	5008	,	,		20409	0.004		0.0467	False		,,,				2504	0.0286				p.I646V	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.A1936G						PASS	.	T	VAL/ILE	30,4376	36.8+/-68.6	0,30,2173	105.0	99.0	101.0		1936	-9.7	0.0	2	dbSNP_123	101	292,8308	107.0+/-167.8	4,284,4012	yes	missense	XDH	NM_000379.3	29	4,314,6185	CC,CT,TT		3.3953,0.6809,2.4758	benign	646/1334	31593265	322,12684	2203	4300	6503	SO:0001583	missense	7498	exon18			CAGTTATGTTACT	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.1936A>G	2.37:g.31593265T>C	ENSP00000368727:p.Ile646Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	37	CCDS1775.1	38	0.0173992673992674	6	0.012195121951219513	6	0.016574585635359115	0	0.0	26	0.03430079155672823	T	2.440	-0.328875	0.05314	0.006809	0.033953	ENSG00000158125	ENST00000379416	T	0.16457	2.34	6.17	-9.66	0.00534	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead (3);	1.433710	0.03555	N	0.226175	T	0.02688	0.0081	N	0.20401	0.57	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.16041	-1.0416	10	0.15066	T	0.55	.	10.4692	0.44626	0.0:0.4161:0.1475:0.4365	rs17323225;rs52823262;rs60097147;rs17323225	646	P47989	XDH_HUMAN	V	646	ENSP00000368727:I646V	ENSP00000368727:I646V	I	-	1	0	XDH	31446769	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-2.756000	0.00789	-2.073000	0.00878	-1.231000	0.01572	ATA	T|0.978;C|0.022	0.022	strong		0.353	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
CYB5D1	124637	hgsc.bcm.edu	37	17	7761926	7761926	+	Silent	SNP	C	C	T	rs3744252	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7761926C>T	ENST00000332439.4	+	3	392	c.240C>T	c.(238-240)atC>atT	p.I80I	LSMD1_ENST00000575208.1_5'Flank|CYB5D1_ENST00000571846.1_Silent_p.I80I|LSMD1_ENST00000576861.1_Intron|LSMD1_ENST00000570555.1_Intron|LSMD1_ENST00000576384.1_5'Flank|LSMD1_ENST00000575771.1_5'Flank|LSMD1_ENST00000333775.5_5'Flank|CYB5D1_ENST00000570446.1_Intron|LSMD1_ENST00000575071.1_5'Flank|LSMD1_ENST00000335155.5_5'Flank	NM_144607.4	NP_653208.2	Q6P9G0	CB5D1_HUMAN	cytochrome b5 domain containing 1	80	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.						heme binding (GO:0020037)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(2)|skin(2)	6		all_cancers(10;0.11)|Prostate(122;0.219)				CTTTAAAGATCCGCAAGCACA	0.622											OREG0024147	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	477	0.0952476	0.0083	0.1383	5008	,	,		17067	0.1429		0.1004	False		,,,				2504	0.1278				p.I80I		Atlas-SNP	.											CYB5D1,NS,carcinoma,0,1	CYB5D1	16	1	0			c.C240T						PASS	.	C		82,4324	69.8+/-107.6	0,82,2121	55.0	55.0	55.0		240	1.0	1.0	17	dbSNP_107	55	838,7762	188.6+/-235.5	48,742,3510	no	coding-synonymous	CYB5D1	NM_144607.4		48,824,5631	TT,TC,CC		9.7442,1.8611,7.0737		80/229	7761926	920,12086	2203	4300	6503	SO:0001819	synonymous_variant	124637	exon3			AAAGATCCGCAAG	AK057061	CCDS11123.1	17p13.1	2006-01-12	2006-01-12						26516	protein-coding gene	gene with protein product						12477932	Standard	NM_144607		Approved	FLJ32499	uc002gjb.4	Q6P9G0		ENST00000332439.4:c.240C>T	17.37:g.7761926C>T		Somatic	120	0	0	644	WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_144607	D3DTQ8|Q96DM7	Silent	SNP	ENST00000332439.4	37	CCDS11123.1																																																																																			C|0.920;T|0.080	0.080	strong		0.622	CYB5D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440841.1	NM_144607	
CYB5RL	606495	hgsc.bcm.edu	37	1	54644859	54644859	+	Missense_Mutation	SNP	C	C	T	rs61738851	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:54644859C>T	ENST00000534324.1	-	5	706	c.707G>A	c.(706-708)cGt>cAt	p.R236H	CYB5RL_ENST00000537208.1_Intron|CYB5RL_ENST00000287899.8_Intron|CYB5RL_ENST00000419823.2_Missense_Mutation_p.R236H|CYB5RL_ENST00000401046.3_Missense_Mutation_p.R88H|CYB5RL_ENST00000542737.1_Missense_Mutation_p.R236H|RP11-446E24.4_ENST00000311841.7_Intron			Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like	236							cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|urinary_tract(1)	8						ATTCCAGAAACGGGCCTGCTC	0.488													C|||	258	0.0515176	0.003	0.0648	5008	,	,		23044	0.001		0.1004	False		,,,				2504	0.1094				p.R236H		Atlas-SNP	.											.	CYB5RL	17	.	0			c.G707A						PASS	.	C	HIS/ARG	61,3935		2,57,1939	66.0	70.0	69.0		707	3.3	0.5	1	dbSNP_129	69	880,7476		49,782,3347	yes	missense	CYB5RL	NM_001031672.2	29	51,839,5286	TT,TC,CC		10.5314,1.5265,7.6182	probably-damaging	236/316	54644859	941,11411	1998	4178	6176	SO:0001583	missense	606495	exon7			CAGAAACGGGCCT		CCDS44151.1	1p32.3	2011-04-08			ENSG00000215883	ENSG00000215883			32220	protein-coding gene	gene with protein product						12477932	Standard	NM_001031672		Approved	LOC606495	uc009vzo.3	Q6IPT4	OTTHUMG00000008082	ENST00000534324.1:c.707G>A	1.37:g.54644859C>T	ENSP00000434343:p.Arg236His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_001031672	B7ZBS4|Q8NF25	Missense_Mutation	SNP	ENST00000534324.1	37	CCDS44151.1	118	0.05402930402930403	3	0.006097560975609756	31	0.0856353591160221	0	0.0	84	0.11081794195250659	C	11.78	1.741169	0.30865	0.015265	0.105314	ENSG00000215883	ENST00000419823;ENST00000401046;ENST00000534324;ENST00000542737;ENST00000493530	D;D;D;D;D	0.95656	-2.17;-2.17;-2.17;-2.17;-3.77	5.19	3.33	0.38152	Oxidoreductase FAD/NAD(P)-binding (1);	0.225621	0.18555	U	0.137795	T	0.25005	0.0607	L	0.58101	1.795	0.19945	N	0.999947	P;P	0.37423	0.529;0.594	B;B	0.29785	0.107;0.031	T	0.58487	-0.7628	10	0.46703	T	0.11	-10.291	8.5464	0.33424	0.0:0.7619:0.0:0.2381	.	236;88	Q6IPT4;Q6IPT4-3	NB5R5_HUMAN;.	H	236;88;236;236;150	ENSP00000409075:R236H;ENSP00000383825:R88H;ENSP00000434343:R236H;ENSP00000438151:R236H;ENSP00000434606:R150H	ENSP00000383825:R88H	R	-	2	0	CYB5RL	54417447	0.735000	0.28153	0.467000	0.27180	0.732000	0.41865	1.081000	0.30791	0.700000	0.31782	0.655000	0.94253	CGT	C|0.933;T|0.067	0.067	strong		0.488	CYB5RL-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388318.1	NM_001031672	
ZSCAN12	9753	hgsc.bcm.edu	37	6	28358335	28358335	+	Intron	SNP	G	G	C	rs1416918	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28358335G>C	ENST00000361028.1	-	4	1840				ZSCAN12_ENST00000396827.3_Intron			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|urinary_tract(1)	6						TAGGTACCACGTCTATTATGG	0.428													C|||	1935	0.386382	0.5582	0.3271	5008	,	,		21477	0.2996		0.2893	False		,,,				2504	0.3855				p.R578G		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.C1732G						PASS	.	C	GLY/ARG	644,740		147,350,195	291.0	256.0	267.0		1732	-0.5	0.1	6	dbSNP_88	267	1003,2179		161,681,749	yes	missense	ZSCAN12	NM_001163391.1	125	308,1031,944	CC,CG,GG		31.5211,46.5318,36.071		578/612	28358335	1647,2919	692	1591	2283	SO:0001627	intron_variant	9753	exon4			TACCACGTCTATT	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"""-"", ""Zinc fingers, C2H2-type"""	13172	protein-coding gene	gene with protein product		603978	"""zinc finger protein 305"", ""zinc finger protein 96"""	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.1694+37C>G	6.37:g.28358335G>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	185	95	0.513514	NM_001163391	O43724	Missense_Mutation	SNP	ENST00000361028.1	37																																																																																				G|0.614;C|0.386	0.386	strong		0.428	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724	
CYP4A22	284541	hgsc.bcm.edu	37	1	47609489	47609489	+	Missense_Mutation	SNP	T	T	C	rs10789501	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:47609489T>C	ENST00000371891.3	+	6	722	c.691T>C	c.(691-693)Tgt>Cgt	p.C231R	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000294337.3_Missense_Mutation_p.C231R|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000371890.3_Intron	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	231			C -> R (allele CYP4A22*2, allele CYP4A22*3, allele CYP4A22*4, allele CYP4A22*5, allele CYP4A22*6, allele CYP4A22*7, allele CYP4A22*8, allele CYP4A22*9, allele CYP4A22*10, allele CYP4A22*11, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs10789501). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGTTTTTTGCTGTATGAGGAA	0.552													C|||	2908	0.580671	0.5015	0.464	5008	,	,		20346	0.9335		0.3489	False		,,,				2504	0.6452				p.C231R	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.T691C						PASS	.	C	ARG/CYS	2187,2219		554,1079,570	137.0	125.0	129.0		691	1.9	0.0	1	dbSNP_120	129	2907,5693		483,1941,1876	yes	missense	CYP4A22	NM_001010969.2	180	1037,3020,2446	CC,CT,TT		33.8023,49.6369,39.1665	benign	231/520	47609489	5094,7912	2203	4300	6503	SO:0001583	missense	284541	exon6			TTTTGCTGTATGA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.691T>C	1.37:g.47609489T>C	ENSP00000360958:p.Cys231Arg	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	262	137	0.522901	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	1188	0.5439560439560439	243	0.49390243902439024	151	0.4171270718232044	539	0.9423076923076923	255	0.33641160949868076	N	0.003	-2.442517	0.00180	0.496369	0.338023	ENSG00000162365	ENST00000371891;ENST00000294337	T;T	0.65732	-0.17;-0.17	1.94	1.94	0.25998	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00000	-3.89	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44922	-0.9296	9	0.02654	T	1	.	3.8065	0.08779	0.4389:0.412:0.0:0.1491	rs10789501;rs56846047;rs10789501	231	Q5TCH4	CP4AM_HUMAN	R	231	ENSP00000360958:C231R;ENSP00000294337:C231R	ENSP00000294337:C231R	C	+	1	0	CYP4A22	47382076	0.014000	0.17966	0.002000	0.10522	0.001000	0.01503	0.053000	0.14184	0.188000	0.20168	-1.033000	0.02402	TGT	T|0.527;C|0.473	0.473	strong		0.552	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
DACT2	168002	hgsc.bcm.edu	37	6	168708751	168708751	+	Silent	SNP	A	A	G	rs10945499	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168708751A>G	ENST00000366795.3	-	4	1774	c.1686T>C	c.(1684-1686)tcT>tcC	p.S562S	DACT2_ENST00000610183.1_Silent_p.S392S|DACT2_ENST00000607983.1_Silent_p.S154S|DACT2_ENST00000366796.3_Intron	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	562					epithelial cell morphogenesis (GO:0003382)|hematopoietic progenitor cell differentiation (GO:0002244)|inner medullary collecting duct development (GO:0072061)|negative regulation of cell adhesion (GO:0007162)|negative regulation of nodal signaling pathway (GO:1900108)|skin development (GO:0043588)	mitochondrion (GO:0005739)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)|transcription factor binding (GO:0008134)			endometrium(1)	1		Breast(66;1.46e-05)|Ovarian(120;0.0728)		OV - Ovarian serous cystadenocarcinoma(33;5.33e-21)|BRCA - Breast invasive adenocarcinoma(81;1.18e-06)|GBM - Glioblastoma multiforme(31;0.000957)		GGGTGGACTCAGAACAGGAGC	0.706													G|||	2547	0.508586	0.8056	0.4107	5008	,	,		11419	0.3244		0.3688	False		,,,				2504	0.5102				p.S562S		Atlas-SNP	.											DACT2_ENST00000366795,NS,carcinoma,0,2	DACT2	46	2	0			c.T1686C						scavenged	.	G		1006,378		366,274,52	29.0	39.0	36.0		1686	-8.6	0.7	6	dbSNP_120	36	1150,2032		213,724,654	no	coding-synonymous	DACT2	NM_214462.3		579,998,706	GG,GA,AA		36.1408,27.3121,47.2186		562/775	168708751	2156,2410	692	1591	2283	SO:0001819	synonymous_variant	168002	exon4			GGACTCAGAACAG	AF318336	CCDS47519.1, CCDS69241.1, CCDS75554.1	6q27	2013-05-15	2013-05-15	2003-09-17	ENSG00000164488	ENSG00000164488			21231	protein-coding gene	gene with protein product		608966	"""chromosome 6 open reading frame 116"", ""dapper homolog 2, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 2 (Xenopus laevis)"""	C6orf116			Standard	NM_001286351		Approved	bA503C24.7, DAPPER2	uc003qwq.3	Q5SW24	OTTHUMG00000016046	ENST00000366795.3:c.1686T>C	6.37:g.168708751A>G		Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Silent	SNP	ENST00000366795.3	37	CCDS47519.1																																																																																			A|0.525;G|0.475	0.475	strong		0.706	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
SPATA31D1	389763	hgsc.bcm.edu	37	9	84609057	84609057	+	Silent	SNP	C	C	T	rs12340419	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:84609057C>T	ENST00000344803.2	+	4	3719	c.3672C>T	c.(3670-3672)gaC>gaT	p.D1224D		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1224					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											ATTTCACTGACATGTCTTTTG	0.453													C|||	291	0.058107	0.1089	0.0504	5008	,	,		21941	0.0119		0.0875	False		,,,				2504	0.0123				p.D1224D		Atlas-SNP	.											.	.	.	.	0			c.C3672T						PASS	.	C		321,3591		8,305,1643	159.0	154.0	155.0		3672	1.8	0.0	9	dbSNP_120	155	613,7669		24,565,3552	no	coding-synonymous	FAM75D1	NM_001001670.2		32,870,5195	TT,TC,CC		7.4016,8.2055,7.6595		1224/1577	84609057	934,11260	1956	4141	6097	SO:0001819	synonymous_variant	389763	exon4			CACTGACATGTCT		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.3672C>T	9.37:g.84609057C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	147	90	0.612245	NM_001001670		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																			C|0.944;T|0.056	0.056	strong		0.453	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
TRIM69	140691	hgsc.bcm.edu	37	15	45047402	45047402	+	Missense_Mutation	SNP	A	A	G	rs17588988	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:45047402A>G	ENST00000559390.1	+	3	1239	c.311A>G	c.(310-312)aAg>aGg	p.K104R	TRIM69_ENST00000561043.1_Intron|TRIM69_ENST00000338264.4_Intron|TRIM69_ENST00000558173.1_5'UTR|TRIM69_ENST00000560442.1_Intron|TRIM69_ENST00000558329.1_Intron|TRIM69_ENST00000329464.4_Missense_Mutation_p.K104R			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	104	Necessary for nuclear localization. {ECO:0000250}.		K -> R (in dbSNP:rs17588988).		apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		GAGAAGATTAAGAAGTTACCC	0.438													A|||	255	0.0509185	0.0968	0.0432	5008	,	,		22016	0.006		0.0567	False		,,,				2504	0.0348				p.K104R	Pancreas(84;519 1450 1802 20427 34706)	Atlas-SNP	.											.	TRIM69	47	.	0			c.A311G						PASS	.	A	,ARG/LYS	366,4030	187.1+/-213.8	23,320,1855	115.0	102.0	106.0		,311	4.0	1.0	15	dbSNP_123	106	508,8088	142.5+/-198.7	16,476,3806	yes	intron,missense	TRIM69	NM_080745.3,NM_182985.3	,26	39,796,5661	GG,GA,AA		5.9097,8.3258,6.7272	,benign	,104/501	45047402	874,12118	2198	4298	6496	SO:0001583	missense	140691	exon2			AGATTAAGAAGTT	AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	17857	protein-coding gene	gene with protein product			"""ring finger protein 36"", ""tripartite motif-containing 69"""	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.311A>G	15.37:g.45047402A>G	ENSP00000453177:p.Lys104Arg	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	213	97	0.455399	NM_182985	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Missense_Mutation	SNP	ENST00000559390.1	37	CCDS32220.1	115	0.052655677655677656	46	0.09349593495934959	20	0.055248618784530384	1	0.0017482517482517483	48	0.0633245382585752	A	12.00	1.806778	0.31961	0.083258	0.059097	ENSG00000185880	ENST00000329464	T	0.16897	2.31	5.17	4.04	0.47022	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.53938	D	0.000059	T	0.00300	0.0009	N	0.24115	0.695	0.24382	N	0.994781	P	0.36438	0.553	B	0.32149	0.141	T	0.27971	-1.0058	10	0.07644	T	0.81	.	7.0985	0.25323	0.9002:0.0:0.0998:0.0	rs17588988;rs58042584;rs17588988	104	Q86WT6	TRI69_HUMAN	R	104	ENSP00000332284:K104R	ENSP00000332284:K104R	K	+	2	0	TRIM69	42834694	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	2.265000	0.43311	2.089000	0.63090	0.455000	0.32223	AAG	A|0.936;G|0.064	0.064	strong		0.438	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1		
RNF126	55658	hgsc.bcm.edu	37	19	651852	651852	+	Missense_Mutation	SNP	C	C	T	rs2285751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:651852C>T	ENST00000292363.5	-	4	357	c.202G>A	c.(202-204)Gtg>Atg	p.V68M		NM_194460.2	NP_919442.1			ring finger protein 126											lung(1)	1		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCTGGTCCACGTGCTGGGGA	0.647													C|||	302	0.0603035	0.0446	0.0317	5008	,	,		12078	0.1448		0.0437	False		,,,				2504	0.0317				p.V68M		Atlas-SNP	.											.	RNF126	15	.	0			c.G202A						PASS	.	C	MET/VAL	199,4207	114.6+/-152.6	1,197,2005	37.0	36.0	37.0		202	3.3	1.0	19	dbSNP_100	37	454,8146	128.8+/-187.0	19,416,3865	no	missense	RNF126	NM_194460.2	21	20,613,5870	TT,TC,CC		5.2791,4.5166,5.0208	benign	68/312	651852	653,12353	2203	4300	6503	SO:0001583	missense	55658	exon4			GGTCCACGTGCTG	BC025374	CCDS12039.1	19p13.3	2013-01-09				ENSG00000070423		"""RING-type (C3HC4) zinc fingers"""	21151	protein-coding gene	gene with protein product		615177					Standard	NM_194460		Approved	FLJ20552	uc010drs.3	Q9BV68		ENST00000292363.5:c.202G>A	19.37:g.651852C>T	ENSP00000292363:p.Val68Met	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_194460		Missense_Mutation	SNP	ENST00000292363.5	37	CCDS12039.1	151	0.06913919413919414	24	0.04878048780487805	11	0.03038674033149171	78	0.13636363636363635	38	0.05013192612137203	c	11.70	1.716178	0.30413	0.045166	0.052791	ENSG00000070423	ENST00000292363;ENST00000340092	T	0.14766	2.48	4.39	3.34	0.38264	.	0.596976	0.15720	N	0.247950	T	0.00073	0.0002	L	0.38175	1.15	0.31485	P	0.66673	B	0.33694	0.421	B	0.21360	0.034	T	0.20042	-1.0287	9	0.39692	T	0.17	.	9.4092	0.38480	0.0:0.8993:0.0:0.1007	rs2285751;rs11554786;rs52824573;rs57007366;rs2285751	68	Q9BV68-2	.	M	68	ENSP00000292363:V68M	ENSP00000292363:V68M	V	-	1	0	RNF126	602852	0.801000	0.28930	0.996000	0.52242	0.420000	0.31355	0.840000	0.27600	2.150000	0.67090	0.561000	0.74099	GTG	C|0.942;T|0.058	0.058	strong		0.647	RNF126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452104.2	NM_017876	
PCDH19	57526	hgsc.bcm.edu	37	X	99663194	99663194	+	Silent	SNP	G	G	T	rs41300169	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:99663194G>T	ENST00000373034.4	-	1	2077	c.402C>A	c.(400-402)atC>atA	p.I134I	PCDH19_ENST00000420881.2_Silent_p.I134I|PCDH19_ENST00000255531.7_Silent_p.I134I	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	134	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						TCTCCAGCTCGATCTGTGCTG	0.582													G|||	606	0.16053	0.0272	0.1844	3775	,	,		13549	0.2044		0.0368	False		,,,				2504	0.2035				p.I134I		Atlas-SNP	.											.	PCDH19	269	.	0			c.C402A						PASS	.	G	,,	126,3562		2,104,18,1453,552	112.0	107.0	109.0		402,402,402	-11.4	0.0	X	dbSNP_127	109	360,6268		4,235,117,2160,1713	no	coding-synonymous,coding-synonymous,coding-synonymous	PCDH19	NM_001105243.1,NM_001184880.1,NM_020766.2	,,	6,339,135,3613,2265	TT,TG,T,GG,G		5.4315,3.4165,4.7111	,,	134/1102,134/1149,134/1101	99663194	486,9830	2129	4229	6358	SO:0001819	synonymous_variant	57526	exon1			CAGCTCGATCTGT	AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"""Cadherins / Protocadherins : Non-clustered"""	14270	protein-coding gene	gene with protein product		300460	"""epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"""	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.402C>A	X.37:g.99663194G>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	131	7	0.0534351	NM_001184880	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Silent	SNP	ENST00000373034.4	37	CCDS55462.1																																																																																			G|0.871;T|0.129	0.129	strong		0.582	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766	
CDRT15	146822	hgsc.bcm.edu	37	17	14139702	14139702	+	Missense_Mutation	SNP	G	G	A	rs138924466	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:14139702G>A	ENST00000420162.2	-	2	323	c.308C>T	c.(307-309)gCg>gTg	p.A103V	CDRT15_ENST00000431716.2_Missense_Mutation_p.A37V	NM_001007530.1	NP_001007531.1	Q96T59	CDRTF_HUMAN	CMT1A duplicated region transcript 15	103										endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		CTCTGGCTCCGCCGCTGGTGC	0.582																																					p.A103V		Atlas-SNP	.											CDRT15,NS,carcinoma,0,1	CDRT15	20	1	0			c.C308T						scavenged	.						28.0	28.0	28.0					17																	14139702		2202	4277	6479	SO:0001583	missense	146822	exon2			GGCTCCGCCGCTG	AF355097	CCDS32569.1	17p12	2012-11-19			ENSG00000223510	ENSG00000223510			14395	protein-coding gene	gene with protein product						11381029	Standard	NM_001007530		Approved		uc010vvu.2	Q96T59	OTTHUMG00000179686	ENST00000420162.2:c.308C>T	17.37:g.14139702G>A	ENSP00000402355:p.Ala103Val	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	136	27	0.198529	NM_001007530	B2RUU5	Missense_Mutation	SNP	ENST00000420162.2	37	CCDS32569.1	59	0.027014652014652016	15	0.03048780487804878	13	0.03591160220994475	0	0.0	31	0.040897097625329816	g	0.003	-2.463165	0.00171	.	.	ENSG00000223510	ENST00000431716;ENST00000420162	T	0.43294	0.95	.	.	.	.	.	.	.	.	T	0.01976	0.0062	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09509	-1.0671	7	0.02654	T	1	.	.	.	.	.	103	Q96T59	CDRTF_HUMAN	V	37;103	ENSP00000402355:A103V	ENSP00000402355:A103V	A	-	2	0	CDRT15	14080427	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-3.002000	0.00652	-1.914000	0.01078	-1.958000	0.00481	GCG	G|0.979;A|0.021	0.021	strong		0.582	CDRT15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252853.1	NM_001007530	
MUC20	200958	hgsc.bcm.edu	37	3	195453412	195453412	+	Silent	SNP	C	C	T	rs1063306	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:195453412C>T	ENST00000447234.2	+	2	2064	c.1938C>T	c.(1936-1938)gcC>gcT	p.A646A	MUC20_ENST00000445522.2_Silent_p.A611A|MUC20_ENST00000436408.1_Silent_p.A646A|MUC20_ENST00000320736.6_Silent_p.A475A	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	646	Involved in oligomerization.|Thr-rich.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)		p.A646A(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CCACGACTGCCCGGACGAGGC	0.597																																					p.A475A		Atlas-SNP	.											MUC20,NS,carcinoma,0,1	MUC20	84	1	1	Substitution - coding silent(1)	stomach(1)	c.C1425T						PASS	.						95.0	104.0	101.0					3																	195453412		2091	4211	6302	SO:0001819	synonymous_variant	200958	exon3			GACTGCCCGGACG	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1938C>T	3.37:g.195453412C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	79	26	0.329114	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Silent	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	c	5.109	0.205776	0.09704	.	.	ENSG00000176945	ENST00000423938	.	.	.	4.94	-2.01	0.07410	.	.	.	.	.	T	0.23094	0.0558	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.29397	-1.0013	4	.	.	.	0.1557	5.102	0.14764	0.0:0.352:0.1579:0.4901	rs1063306;rs3204354;rs3828403;rs9837249;rs17404447	.	.	.	S	58	.	.	P	+	1	0	MUC20	196939083	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.403000	0.07214	-0.402000	0.07633	-1.140000	0.01884	CCG	C|0.928;T|0.072	0.072	strong		0.597	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
OR10AD1	121275	hgsc.bcm.edu	37	12	48597053	48597053	+	Missense_Mutation	SNP	A	A	G	rs17122812	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48597053A>G	ENST00000310248.2	-	1	117	c.23T>C	c.(22-24)gTg>gCg	p.V8A		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	8			V -> A (in dbSNP:rs17122812).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						AAATTCCGTCACTATGCTGCC	0.517													A|||	705	0.140775	0.0628	0.1643	5008	,	,		22063	0.1935		0.2107	False		,,,				2504	0.1033				p.V8A		Atlas-SNP	.											OR10AD1,NS,carcinoma,0,1	OR10AD1	24	1	0			c.T23C						PASS	.	A	ALA/VAL	348,4058	176.9+/-206.0	10,328,1865	50.0	47.0	48.0		23	3.9	0.3	12	dbSNP_123	48	1853,6747	323.2+/-315.9	196,1461,2643	yes	missense	OR10AD1	NM_001004134.1	64	206,1789,4508	GG,GA,AA		21.5465,7.8983,16.923	benign	8/318	48597053	2201,10805	2203	4300	6503	SO:0001583	missense	121275	exon1			TCCGTCACTATGC		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.23T>C	12.37:g.48597053A>G	ENSP00000308689:p.Val8Ala	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	372	0.17032967032967034	34	0.06910569105691057	66	0.18232044198895028	121	0.21153846153846154	151	0.19920844327176782	A	7.785	0.710317	0.15239	0.078983	0.215465	ENSG00000172640	ENST00000310248	T	0.00892	5.57	5.07	3.93	0.45458	.	0.599767	0.12846	N	0.434418	T	0.00012	0.0000	M	0.68317	2.08	0.43381	P	0.0045199999999999685	B	0.31077	0.307	B	0.31946	0.138	T	0.40478	-0.9561	9	0.56958	D	0.05	-15.4666	7.5959	0.28048	0.9023:0.0:0.0977:0.0	rs17122812;rs17122812	8	Q8NGE0	O10AD_HUMAN	A	8	ENSP00000308689:V8A	ENSP00000308689:V8A	V	-	2	0	OR10AD1	46883320	0.038000	0.19896	0.286000	0.24833	0.014000	0.08584	3.127000	0.50484	0.894000	0.36317	0.460000	0.39030	GTG	A|0.830;G|0.170	0.170	strong		0.517	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
FXYD3	5349	hgsc.bcm.edu	37	19	35612168	35612168	+	Intron	SNP	T	T	A	rs1688016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:35612168T>A	ENST00000344013.6	+	5	293				FXYD3_ENST00000454903.2_Missense_Mutation_p.L39H|FXYD3_ENST00000346446.5_Intron|FXYD3_ENST00000535103.1_Intron|FXYD3_ENST00000603449.1_Missense_Mutation_p.L39H|FXYD3_ENST00000604804.1_Intron|FXYD3_ENST00000406988.1_Intron|FXYD3_ENST00000604621.1_Intron|FXYD3_ENST00000603524.1_Intron|FXYD3_ENST00000406242.3_Intron|FXYD3_ENST00000605550.1_Intron|FXYD3_ENST00000605552.1_Missense_Mutation_p.L39H|FXYD3_ENST00000604404.1_Intron|FXYD3_ENST00000603181.1_Intron|FXYD3_ENST00000605677.1_Intron|FXYD3_ENST00000435734.2_Intron|FXYD3_ENST00000604255.1_Intron			Q14802	FXYD3_HUMAN	FXYD domain containing ion transport regulator 3						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of catalytic activity (GO:0050790)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.L39H(1)		endometrium(1)|lung(2)|prostate(1)	4	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CCGTGCCCCCTTTCCCCTCCC	0.517													A|||	1783	0.35603	0.2958	0.2493	5008	,	,		16537	0.2679		0.3698	False		,,,				2504	0.59				p.L39H		Atlas-SNP	.											.	FXYD3	15	.	1	Substitution - Missense(1)	kidney(1)	c.T116A						PASS	.	A	,,HIS/LEU,HIS/LEU,,,,	1396,3010	687.1+/-404.8	215,966,1022	69.0	73.0	71.0		,,116,116,,,,	0.7	0.0	19	dbSNP_89	71	3066,5534	658.0+/-401.5	527,2012,1761	yes	intron,intron,missense,missense,intron,intron,intron,intron	FXYD3	NM_001136007.1,NM_001136008.1,NM_001136009.1,NM_001136010.1,NM_001136011.1,NM_001136012.1,NM_005971.3,NM_021910.2	,,99,99,,,,	742,2978,2783	AA,AT,TT		35.6512,31.6841,34.3072	,,,,,,,	,,39/62,39/62,,,,	35612168	4462,8544	2203	4300	6503	SO:0001627	intron_variant	5349	exon5			GCCCCCTTTCCCC	X93036	CCDS12442.1, CCDS12443.1, CCDS46048.1, CCDS46049.1, CCDS46050.1	19q13.11-q13.12	2008-05-14	2002-01-14			ENSG00000089356			4027	protein-coding gene	gene with protein product		604996	"""FXYD domain-containing ion transport regulator 3"""	PLML		7836447, 10950925	Standard	NM_005971		Approved	MAT-8	uc010xsm.2	Q14802		ENST00000344013.6:c.97+19T>A	19.37:g.35612168T>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	230	139	0.604348	NM_001136010	A6NDE0|C9JDU2|F5H174|F8WB34|Q13211|Q6IB59	Missense_Mutation	SNP	ENST00000344013.6	37	CCDS12442.1	668	0.3058608058608059	157	0.31910569105691056	85	0.23480662983425415	137	0.2395104895104895	289	0.3812664907651715	A	2.768	-0.256355	0.05829	0.316841	0.356512	ENSG00000089356	ENST00000454903	.	.	.	2.85	0.693	0.18056	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45745	-0.9240	5	.	.	.	.	2.5324	0.04706	0.2797:0.4271:0.0:0.2932	rs1688016	39	C9JDU2	.	H	39	.	.	L	+	2	0	FXYD3	40304008	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.057000	0.11768	-0.034000	0.13713	-0.336000	0.08194	CTT	T|0.672;A|0.328	0.328	strong		0.517	FXYD3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000468985.1	NM_021910	
ARHGAP9	64333	hgsc.bcm.edu	37	12	57869681	57869681	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57869681G>A	ENST00000356411.2	-	10	1384	c.1246C>T	c.(1246-1248)Cag>Tag	p.Q416*	ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000424809.2_Nonsense_Mutation_p.Q416*|ARHGAP9_ENST00000430041.2_Nonsense_Mutation_p.Q232*|ARHGAP9_ENST00000550288.1_Nonsense_Mutation_p.Q495*|ARHGAP9_ENST00000393791.3_Nonsense_Mutation_p.Q416*|ARHGAP9_ENST00000393797.2_Nonsense_Mutation_p.Q487*			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	416	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			TGGTCCGACTGCAGCAGGAAC	0.647																																					p.Q416X		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.C1246T						PASS	.						27.0	30.0	29.0					12																	57869681		2201	4296	6497	SO:0001587	stop_gained	64333	exon9			CCGACTGCAGCAG	AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.1246C>T	12.37:g.57869681G>A	ENSP00000348782:p.Gln416*	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	117	47	0.401709	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Nonsense_Mutation	SNP	ENST00000356411.2	37		.	.	.	.	.	.	.	.	.	.	G	40	7.946108	0.98574	.	.	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000423291;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000430041;ENST00000548139	.	.	.	3.97	3.97	0.46021	.	0.139059	0.48767	D	0.000170	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.468	0.61266	0.0:0.0:1.0:0.0	.	.	.	.	X	416;416;86;416;487;465;232;232	.	ENSP00000344852:Q465X	Q	-	1	0	ARHGAP9	56155948	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.206000	0.65192	2.235000	0.73313	0.561000	0.74099	CAG	.	.	none		0.647	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496	
HLA-C	3107	hgsc.bcm.edu	37	6	31238179	31238179	+	Missense_Mutation	SNP	C	C	T	rs41562012	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238179C>T	ENST00000376228.5	-	4	717	c.703G>A	c.(703-705)Gcg>Acg	p.A235T	HLA-C_ENST00000383329.3_Missense_Mutation_p.A235T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	235	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GTGATCTCCGCAGGGTAGAAG	0.627													c|||	83	0.0165735	0.0136	0.0202	5008	,	,		16224	0.001		0.0437	False		,,,				2504	0.0061				p.A235T		Atlas-SNP	.											.	HLA-C	92	.	0			c.G703A						PASS	.	C	THR/ALA	53,4353		0,53,2150	41.0	42.0	42.0		703	1.8	0.3	6	dbSNP_127	42	340,8250		5,330,3960	no	missense	HLA-C	NM_002117.5	58	5,383,6110	TT,TC,CC		3.9581,1.2029,3.024	possibly-damaging	235/367	31238179	393,12603	2203	4295	6498	SO:0001583	missense	3107	exon4			TCTCCGCAGGGTA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.703G>A	6.37:g.31238179C>T	ENSP00000365402:p.Ala235Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	95	62	0.652632	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	41	0.018772893772893772	7	0.014227642276422764	5	0.013812154696132596	1	0.0017482517482517483	28	0.036939313984168866	.	4.284	0.051806	0.08291	0.012029	0.039581	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.14766	2.48;2.48	2.67	1.79	0.24919	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.402896	0.17690	U	0.165292	T	0.14830	0.0358	H	0.97758	4.07	0.09310	N	1	B;B;B;B	0.19200	0.034;0.001;0.004;0.009	B;B;B;B	0.28232	0.087;0.013;0.022;0.017	T	0.23726	-1.0180	10	0.87932	D	0	.	5.5522	0.17097	0.0:0.84:0.0:0.16	rs41562012	235;235;235;235	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	T	235;235;235;272	ENSP00000365402:A235T;ENSP00000372819:A235T	ENSP00000365402:A235T	A	-	1	0	HLA-C	31346158	0.000000	0.05858	0.342000	0.25602	0.447000	0.32167	-1.515000	0.02252	0.702000	0.31825	0.298000	0.19748	GCG	C|0.973;T|0.027	0.027	strong		0.627	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
TSC22D2	9819	hgsc.bcm.edu	37	3	150128994	150128994	+	Silent	SNP	T	T	G	rs34647320	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:150128994T>G	ENST00000361875.3	+	1	2873	c.1857T>G	c.(1855-1857)ccT>ccG	p.P619P	TSC22D2_ENST00000361136.2_Silent_p.P619P	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	619					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TGAAGCCGCCTGTTGCAGATT	0.468													T|||	413	0.0824681	0.0386	0.0879	5008	,	,		18932	0.0317		0.172	False		,,,				2504	0.0982				p.P619P		Atlas-SNP	.											.	TSC22D2	42	.	0			c.T1857G						PASS	.	T		314,4092	166.9+/-198.0	10,294,1899	85.0	94.0	91.0		1857	1.2	1.0	3	dbSNP_126	91	1717,6883	311.8+/-310.5	165,1387,2748	no	coding-synonymous	TSC22D2	NM_014779.2		175,1681,4647	GG,GT,TT		19.9651,7.1266,15.6159		619/781	150128994	2031,10975	2203	4300	6503	SO:0001819	synonymous_variant	9819	exon1			GCCGCCTGTTGCA	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.1857T>G	3.37:g.150128994T>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Silent	SNP	ENST00000361875.3	37	CCDS3149.1	203|203	0.09294871794871795|0.09294871794871795	15|15	0.03048780487804878|0.03048780487804878	33|33	0.09116022099447514|0.09116022099447514	29|29	0.050699300699300696|0.050699300699300696	126|126	0.1662269129287599|0.1662269129287599	T|T	8.025|8.025	0.760446|0.760446	0.15914|0.15914	0.071266|0.071266	0.199651|0.199651	ENSG00000196428|ENSG00000196428	ENST00000466814|ENST00000480589	.|.	.|.	.|.	5.05|5.05	1.23|1.23	0.21249|0.21249	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999991805|0.9999999999991805	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.18967|0.18967	-1.0320|-1.0320	3|3	.|.	.|.	.|.	.|.	3.3184|3.3184	0.07041|0.07041	0.1903:0.3818:0.0:0.4278|0.1903:0.3818:0.0:0.4278	rs34647320|rs34647320	.|.	.|.	.|.	G|R	67|80	.|.	.|.	C|L	+|+	1|2	0|0	TSC22D2|TSC22D2	151611684|151611684	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	0.378000|0.378000	0.20569|0.20569	0.244000|0.244000	0.21351|0.21351	0.374000|0.374000	0.22700|0.22700	TGT|CTG	T|0.866;G|0.134;A|0.000	0.134	strong		0.468	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779	
MICA	100507436	hgsc.bcm.edu	37	6	31382911	31382911	+	3'UTR	SNP	A	A	G	rs1882	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31382911A>G	ENST00000449934.2	+	0	1205				HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CACtgagggcacctagactct	0.552													g|||	3622	0.723243	0.6982	0.8112	5008	,	,		14191	0.7778		0.5805	False		,,,				2504	0.7853				p.T383A		Atlas-SNP	.											.	MICA	21	.	0			c.A1147G						PASS	.	A		895,489		295,305,92	107.0	103.0	104.0			-0.9	0.0	6	dbSNP_36	104	1634,1548		435,764,392	yes	utr-3	MICA	NM_001177519.1		730,1069,484	GG,GA,AA		48.6486,35.3324,44.6124			31382911	2529,2037	692	1591	2283	SO:0001624	3_prime_UTR_variant	100507436	exon7			GAGGGCACCTAGA	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.*152A>G	6.37:g.31382911A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_000247		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			A|0.320;G|0.680	0.680	strong		0.552	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
FRG2B	441581	hgsc.bcm.edu	37	10	135438967	135438967	+	Missense_Mutation	SNP	C	C	T	rs145018822		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135438967C>T	ENST00000425520.1	-	4	525	c.473G>A	c.(472-474)cGg>cAg	p.R158Q	FRG2B_ENST00000443774.1_Missense_Mutation_p.R159Q	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	158						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		AGACCTATGCCGCTTGCTGCG	0.542																																					p.R158Q		Atlas-SNP	.											FRG2B,NS,carcinoma,+1,1	FRG2B	47	1	0			c.G473A						scavenged	.						120.0	141.0	134.0					10																	135438967		2197	4298	6495	SO:0001583	missense	441581	exon4			CTATGCCGCTTGC	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.473G>A	10.37:g.135438967C>T	ENSP00000401310:p.Arg158Gln	Somatic	367	4	0.0108992		WXS	Illumina HiSeq	Phase_I	352	124	0.352273	NM_001080998	Q5VSQ1	Missense_Mutation	SNP	ENST00000425520.1	37	CCDS44502.1	.	.	.	.	.	.	.	.	.	.	.	5.581	0.292050	0.10567	.	.	ENSG00000225899	ENST00000443774;ENST00000425520	T;T	0.55588	0.51;0.51	.	.	.	.	1.696950	0.04119	N	0.316034	T	0.33990	0.0882	N	0.14661	0.345	0.09310	N	1	B	0.19935	0.04	B	0.08055	0.003	T	0.27938	-1.0059	8	0.52906	T	0.07	-2.5282	.	.	.	.	158	Q96QU4	FRG2B_HUMAN	Q	159;158	ENSP00000408343:R159Q;ENSP00000401310:R158Q	ENSP00000401310:R158Q	R	-	2	0	FRG2B	135288957	0.001000	0.12720	0.088000	0.20740	0.089000	0.18198	-2.060000	0.01392	0.119000	0.18210	0.121000	0.15741	CGG	.	.	weak		0.542	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
ALPP	250	hgsc.bcm.edu	37	2	233243796	233243796	+	Splice_Site	SNP	T	T	C	rs200958062|rs1130338	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233243796T>C	ENST00000392027.2	+	2	461	c.192T>C	c.(190-192)gaT>gaC	p.D64D	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	64					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		TCCTGGGCGATGGTGAGTGAG	0.667													t|||	60	0.0119808	0.0008	0.0101	5008	,	,		17060	0.0		0.0258	False		,,,				2504	0.0266				p.D64D		Atlas-SNP	.											.	ALPP	53	.	0			c.T192C						PASS	.	C		9,4397		0,9,2194	72.0	79.0	77.0		192	-5.0	0.0	2		77	144,8456		4,136,4160	no	coding-synonymous-near-splice	ALPP	NM_001632.3		4,145,6354	CC,CT,TT		1.6744,0.2043,1.1764		64/536	233243796	153,12853	2203	4300	6503	SO:0001630	splice_region_variant	250	exon2			GGGCGATGGTGAG	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.193+1T>C	2.37:g.233243796T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_001632	P05188|P06861|Q53S78|Q96DB7	Silent	SNP	ENST00000392027.2	37	CCDS2490.1																																																																																			T|0.989;C|0.011	0.011	strong		0.667	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	Silent
CRACR2A	84766	hgsc.bcm.edu	37	12	3782701	3782701	+	Silent	SNP	C	C	T	rs17697920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:3782701C>T	ENST00000252322.1	-	7	1050	c.582G>A	c.(580-582)ctG>ctA	p.L194L	EFCAB4B_ENST00000440314.2_Silent_p.L194L|EFCAB4B_ENST00000444507.1_Silent_p.L194L	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		194					activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			CAAAGTTGGACAGTAAATGAG	0.502													T|||	858	0.171326	0.1172	0.2363	5008	,	,		20281	0.127		0.1471	False		,,,				2504	0.2689				p.L194L		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.G582A						PASS	.	T	,	554,3852	775.2+/-414.1	37,480,1686	156.0	141.0	146.0		582,582	1.9	0.9	12	dbSNP_123	146	1228,7372	762.3+/-407.6	91,1046,3163	no	coding-synonymous,coding-synonymous	EFCAB4B	NM_001144958.1,NM_032680.3	,	128,1526,4849	TT,TC,CC		14.2791,12.5738,13.7014	,	194/732,194/396	3782701	1782,11224	2203	4300	6503	SO:0001819	synonymous_variant	84766	exon7			GTTGGACAGTAAA																												ENST00000252322.1:c.582G>A	12.37:g.3782701C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	150	66	0.44	NM_001144958	B4E1X0|B9EK63	Silent	SNP	ENST00000252322.1	37	CCDS8522.1																																																																																			C|0.860;N|0.000	.	strong		0.502	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
WDR90	197335	hgsc.bcm.edu	37	16	716494	716494	+	Missense_Mutation	SNP	G	G	A	rs373898012		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:716494G>A	ENST00000293879.4	+	38	4780	c.4780G>A	c.(4780-4782)Gct>Act	p.A1594T	RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000547944.1_Missense_Mutation_p.A193T|WDR90_ENST00000549091.1_Missense_Mutation_p.A1596T|WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000315764.4_Intron			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1594										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCTATGGCTGGCTGCCAGTGG	0.632																																					p.A1594T		Atlas-SNP	.											.	WDR90	107	.	0			c.G4780A						PASS	.	G	THR/ALA	0,4066		0,0,2033	30.0	40.0	37.0		4780	4.5	1.0	16		37	2,8340		0,2,4169	no	missense	WDR90	NM_145294.4	58	0,2,6202	AA,AG,GG		0.024,0.0,0.0161	probably-damaging	1594/1749	716494	2,12406	2033	4171	6204	SO:0001583	missense	197335	exon38			TGGCTGGCTGCCA	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.4780G>A	16.37:g.716494G>A	ENSP00000293879:p.Ala1594Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.919032	0.92249	0.0	2.4E-4	ENSG00000161996	ENST00000549091;ENST00000293879;ENST00000547944	T;T;T	0.62788	1.43;1.4;-0.0	4.49	4.49	0.54785	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.235790	0.42420	D	0.000715	T	0.78534	0.4298	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.981	T	0.78352	-0.2237	10	0.33141	T	0.24	.	16.1987	0.82053	0.0:0.0:1.0:0.0	.	193;1594	G3V201;Q96KV7	.;WDR90_HUMAN	T	1596;1594;193	ENSP00000448122:A1596T;ENSP00000293879:A1594T;ENSP00000449576:A193T	ENSP00000293879:A1594T	A	+	1	0	WDR90	656495	1.000000	0.71417	0.981000	0.43875	0.970000	0.65996	6.432000	0.73400	2.045000	0.60652	0.561000	0.74099	GCT	.	.	weak		0.632	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
CYP2W1	54905	hgsc.bcm.edu	37	7	1023013	1023013	+	Silent	SNP	C	C	T	rs2272375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1023013C>T	ENST00000308919.7	+	1	179	c.166C>T	c.(166-168)Ctg>Ttg	p.L56L	CYP2W1_ENST00000340150.6_5'UTR	NM_017781.2	NP_060251.2	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W, polypeptide 1	56					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		GGACCGGTCCCTGATGGAGGT	0.711													C|||	1804	0.360224	0.5098	0.3343	5008	,	,		12799	0.3115		0.2744	False		,,,				2504	0.3149				p.L56L		Atlas-SNP	.											.	CYP2W1	28	.	0			c.C166T						PASS	.	C		1532,2094		347,838,628	11.0	10.0	10.0		166	4.5	0.8	7	dbSNP_100	10	1881,5021		306,1269,1876	no	coding-synonymous	CYP2W1	NM_017781.2		653,2107,2504	TT,TC,CC		27.253,42.2504,32.4183		56/491	1023013	3413,7115	1813	3451	5264	SO:0001819	synonymous_variant	54905	exon1			CGGTCCCTGATGG	AK000366	CCDS5319.2	7p22.3	2004-07-05			ENSG00000073067	ENSG00000073067		"""Cytochrome P450s"""	20243	protein-coding gene	gene with protein product		615967					Standard	XM_005249792		Approved	FLJ20359, MGC34287	uc003sjq.1	Q8TAV3	OTTHUMG00000074071	ENST00000308919.7:c.166C>T	7.37:g.1023013C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	15	4	0.266667	NM_017781		Silent	SNP	ENST00000308919.7	37	CCDS5319.2																																																																																			C|0.645;T|0.355	0.355	strong		0.711	CYP2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157249.1	NM_017781	
UNC119	9094	hgsc.bcm.edu	37	17	26874803	26874803	+	Missense_Mutation	SNP	G	G	A	rs146916036	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:26874803G>A	ENST00000335765.4	-	4	612	c.502C>T	c.(502-504)Cgc>Tgc	p.R168C	UNC119_ENST00000484980.1_Missense_Mutation_p.R73C|UNC119_ENST00000301032.4_Missense_Mutation_p.R168C|UNC119_ENST00000470125.1_Missense_Mutation_p.R73C	NM_005148.3	NP_005139.1	Q13432	U119A_HUMAN	unc-119 homolog (C. elegans)	168	Required for centrosome localization.				cytokinesis, completion of separation (GO:0007109)|endocytosis (GO:0006897)|lipoprotein transport (GO:0042953)|negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of clathrin-mediated endocytosis (GO:1900186)|phototransduction (GO:0007602)|positive regulation of protein tyrosine kinase activity (GO:0061098)|synaptic transmission (GO:0007268)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	lipid binding (GO:0008289)			breast(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	7	Lung NSC(42;0.00431)					AGCTGGTTGCGGAAGTAGTGC	0.537											OREG0024277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R168C		Atlas-SNP	.											.	UNC119	27	.	0			c.C502T						PASS	.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	173.0	156.0	162.0		502,502	4.8	1.0	17	dbSNP_134	162	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	UNC119	NM_005148.3,NM_054035.2	180,180	0,11,6492	AA,AG,GG		0.1279,0.0,0.0846	probably-damaging,probably-damaging	168/241,168/221	26874803	11,12995	2203	4300	6503	SO:0001583	missense	9094	exon4			GGTTGCGGAAGTA	U40998	CCDS11233.1, CCDS11234.1	17q11.2	2014-09-17	2001-11-28		ENSG00000109103	ENSG00000109103			12565	protein-coding gene	gene with protein product	"""POC7 centriolar protein homolog A (Chlamydomonas)"""	604011	"""unc119 (C.elegans) homolog"""			8576185, 9538874	Standard	NM_005148		Approved	HRG4, POC7, POC7A	uc002hbk.2	Q13432	OTTHUMG00000132606	ENST00000335765.4:c.502C>T	17.37:g.26874803G>A	ENSP00000337040:p.Arg168Cys	Somatic	216	0	0	790	WXS	Illumina HiSeq	Phase_I	259	122	0.471042	NM_005148	A8K8G4|F1T095|O95126	Missense_Mutation	SNP	ENST00000335765.4	37	CCDS11233.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221194	0.79464	0.0	0.001279	ENSG00000109103	ENST00000335765;ENST00000301032;ENST00000444148	D;D;D	0.82344	-1.51;-1.59;-1.6	5.81	4.83	0.62350	Immunoglobulin E-set (1);	0.000000	0.85682	D	0.000000	D	0.93259	0.7852	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	D	0.95030	0.8168	10	0.87932	D	0	-19.9144	16.2568	0.82522	0.0:0.0:0.8662:0.1338	.	168;168	F1T095;Q13432	.;U119A_HUMAN	C	168;168;161	ENSP00000337040:R168C;ENSP00000301032:R168C;ENSP00000414639:R161C	ENSP00000301032:R168C	R	-	1	0	UNC119	23898930	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.862000	0.56009	1.437000	0.47472	0.462000	0.41574	CGC	G|0.999;A|0.001	0.001	strong		0.537	UNC119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255842.2		
CTIF	9811	hgsc.bcm.edu	37	18	46163049	46163049	+	Missense_Mutation	SNP	C	C	T	rs2277712	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:46163049C>T	ENST00000256413.3	+	3	540	c.245C>T	c.(244-246)cCa>cTa	p.P82L	CTIF_ENST00000382998.4_Missense_Mutation_p.P82L	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	82	Interaction with NCBP1/CBP80.		P -> L (in dbSNP:rs2277712).		nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						CGAGCCCCCCCACAGCAGGTA	0.637													C|||	303	0.0605032	0.0182	0.0403	5008	,	,		18667	0.1052		0.0288	False		,,,				2504	0.1186				p.P82L		Atlas-SNP	.											.	CTIF	102	.	0			c.C245T						PASS	.	C	LEU/PRO,LEU/PRO	92,4314	72.0+/-110.0	1,90,2112	30.0	30.0	30.0		245,245	3.3	0.1	18	dbSNP_100	30	340,8260	107.8+/-168.5	9,322,3969	yes	missense,missense	CTIF	NM_001142397.1,NM_014772.2	98,98	10,412,6081	TT,TC,CC		3.9535,2.0881,3.3215	benign,benign	82/601,82/599	46163049	432,12574	2203	4300	6503	SO:0001583	missense	9811	exon3			CCCCCCCACAGCA	AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"""KIAA0427"""	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.245C>T	18.37:g.46163049C>T	ENSP00000256413:p.Pro82Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_014772	B3KTR8|Q8IVD5	Missense_Mutation	SNP	ENST00000256413.3	37	CCDS11935.1	113	0.051739926739926737	12	0.024390243902439025	16	0.04419889502762431	61	0.10664335664335664	24	0.0316622691292876	C	12.70	2.017640	0.35606	0.020881	0.039535	ENSG00000134030	ENST00000256413;ENST00000382998;ENST00000420275	T;T	0.43294	0.95;0.96	5.23	3.34	0.38264	.	0.830161	0.10581	N	0.657940	T	0.00496	0.0016	N	0.14661	0.345	0.22424	N	0.999117	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.06954	-1.0798	10	0.51188	T	0.08	-26.7866	7.8083	0.29215	0.0:0.7976:0.0:0.2024	rs2277712;rs2277712	82;82	O43310-2;O43310	.;CTIF_HUMAN	L	82;82;34	ENSP00000256413:P82L;ENSP00000372459:P82L	ENSP00000256413:P82L	P	+	2	0	CTIF	44417047	0.001000	0.12720	0.099000	0.21106	0.966000	0.64601	0.595000	0.24029	0.627000	0.30340	0.561000	0.74099	CCA	A|0.000;C|0.956;T|0.044	0.044	strong		0.637	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772	
PLEC	5339	hgsc.bcm.edu	37	8	145011204	145011204	+	Silent	SNP	A	A	G	rs6993938	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:145011204A>G	ENST00000322810.4	-	5	958	c.789T>C	c.(787-789)gcT>gcC	p.A263A	PLEC_ENST00000398774.2_Silent_p.A94A|PLEC_ENST00000345136.3_Silent_p.A126A|PLEC_ENST00000354589.3_Silent_p.A126A|PLEC_ENST00000354958.2_Silent_p.A104A|PLEC_ENST00000436759.2_Silent_p.A153A|PLEC_ENST00000527096.1_Silent_p.A153A|PLEC_ENST00000356346.3_Silent_p.A112A|PLEC_ENST00000357649.2_Silent_p.A130A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	263	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.|Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.A153A(1)|p.A263A(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GGTTGCCGTCAGCGATGTCAT	0.622													G|||	1164	0.232428	0.0613	0.2882	5008	,	,		17817	0.1458		0.4066	False		,,,				2504	0.3344				p.A263A		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,-2,8	PLEC	1144	8	2	Substitution - coding silent(2)	stomach(2)	c.T789C						scavenged	.	G	,,,,,,,	453,3867		28,397,1735	96.0	103.0	101.0		459,336,312,789,282,378,390,378	-11.4	0.0	8	dbSNP_116	101	3317,5259		646,2025,1617	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	674,2422,3352	GG,GA,AA		38.6777,10.4861,29.2339	,,,,,,,	153/4575,112/4534,104/4526,263/4685,94/4516,126/4548,130/4552,126/4548	145011204	3770,9126	2160	4288	6448	SO:0001819	synonymous_variant	5339	exon5			GCCGTCAGCGATG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.789T>C	8.37:g.145011204A>G		Somatic	167	1	0.00598802		WXS	Illumina HiSeq	Phase_I	159	73	0.459119	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			A|0.729;C|0.001;G|0.270	0.270	strong		0.622	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
FAM120AOS	158293	hgsc.bcm.edu	37	9	96209943	96209943	+	Missense_Mutation	SNP	T	T	C	rs10821128	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:96209943T>C	ENST00000375412.5	-	3	1603	c.721A>G	c.(721-723)Aag>Gag	p.K241E	FAM120AOS_ENST00000423591.1_Missense_Mutation_p.K59E|FAM120AOS_ENST00000479094.1_5'UTR	NM_198841.2	NP_942138.2	Q5T036	F120S_HUMAN	family with sequence similarity 120A opposite strand	241			K -> E (in dbSNP:rs10821128). {ECO:0000269|PubMed:14702039}.							kidney(1)|large_intestine(1)|lung(3)|skin(1)	6						GTGGTTTTCTTTGAGACTTTG	0.338													T|||	1138	0.227236	0.0363	0.3069	5008	,	,		20145	0.4117		0.3479	False		,,,				2504	0.1145				p.K241E		Atlas-SNP	.											.	FAM120AOS	13	.	0			c.A721G						PASS	.	-	GLU/LYS	403,4003	197.1+/-221.3	22,359,1822	224.0	207.0	213.0		721	-1.4	0.0	9	dbSNP_120	213	2898,5702	453.0+/-363.1	507,1884,1909	yes	missense	FAM120AOS	NM_198841.2	56	529,2243,3731	CC,CT,TT		33.6977,9.1466,25.3806	benign	241/257	96209943	3301,9705	2203	4300	6503	SO:0001583	missense	158293	exon3			TTTTCTTTGAGAC	AK056096	CCDS6705.1	9q22.32	2008-02-05	2006-07-04	2006-07-04	ENSG00000188938	ENSG00000188938			23389	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 10 opposite strand"""	C9orf10OS		14585507	Standard	NM_198841		Approved		uc004atu.4	Q5T036	OTTHUMG00000020251	ENST00000375412.5:c.721A>G	9.37:g.96209943T>C	ENSP00000364561:p.Lys241Glu	Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	197	106	0.538071	NM_198841	A6NN20	Missense_Mutation	SNP	ENST00000375412.5	37	CCDS6705.1	686	0.3141025641025641	26	0.052845528455284556	132	0.36464088397790057	257	0.4493006993006993	271	0.3575197889182058	T	2.509	-0.313505	0.05422	0.091466	0.336977	ENSG00000188938	ENST00000423591;ENST00000375412;ENST00000375409;ENST00000428378	T;T;T	0.57595	0.44;0.63;0.39	1.77	-1.41	0.08941	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43458	-0.9390	8	0.87932	D	0	.	5.3583	0.16073	0.0:0.5975:0.0:0.4025	rs10821128;rs10821128	241	Q5T036	F120S_HUMAN	E	59;241;58;58	ENSP00000414298:K59E;ENSP00000364561:K241E;ENSP00000416978:K58E	ENSP00000364558:K58E	K	-	1	0	FAM120AOS	95249764	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.584000	0.02114	-0.371000	0.08004	-0.280000	0.10049	AAG	T|0.734;C|0.266	0.266	strong		0.338	FAM120AOS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053154.1		
PREX2	80243	hgsc.bcm.edu	37	8	69143589	69143589	+	Silent	SNP	A	A	G	rs2280637	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:69143589A>G	ENST00000288368.4	+	40	5074	c.4797A>G	c.(4795-4797)ccA>ccG	p.P1599P		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1599					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TGTGCGAGCCACCTCCCCCAG	0.443													G|||	1666	0.332668	0.1861	0.3761	5008	,	,		15846	0.3879		0.2992	False		,,,				2504	0.4775				p.P1599P		Atlas-SNP	.											.	PREX2	614	.	0			c.A4797G						PASS	.	G		765,3641	749.6+/-412.0	69,627,1507	64.0	57.0	59.0		4797	-8.5	0.5	8	dbSNP_100	59	2409,6191	693.2+/-404.6	335,1739,2226	no	coding-synonymous	PREX2	NM_024870.2		404,2366,3733	GG,GA,AA		28.0116,17.3627,24.4041		1599/1607	69143589	3174,9832	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon40			CGAGCCACCTCCC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4797A>G	8.37:g.69143589A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			A|0.724;G|0.276	0.276	strong		0.443	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
PRSS16	10279	hgsc.bcm.edu	37	6	27216699	27216699	+	Missense_Mutation	SNP	G	G	T	rs5030965	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:27216699G>T	ENST00000230582.3	+	3	326	c.311G>T	c.(310-312)aGc>aTc	p.S104I	PRSS16_ENST00000421826.2_Intron	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	104			S -> I (in dbSNP:rs5030965).		protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						GGTGAGGGCAGCCTTGGGCCT	0.557													G|||	330	0.0658946	0.1241	0.0562	5008	,	,		18857	0.0129		0.0308	False		,,,				2504	0.0849				p.S104I	NSCLC(178;1118 2105 17078 23587 44429)	Atlas-SNP	.											.	PRSS16	66	.	0			c.G311T						PASS	.	G	ILE/SER	464,3942	221.0+/-238.3	20,424,1759	92.0	78.0	82.0		311	3.2	1.0	6	dbSNP_113	82	454,8146	136.4+/-193.5	9,436,3855	yes	missense	PRSS16	NM_005865.3	142	29,860,5614	TT,TG,GG		5.2791,10.5311,7.0583	possibly-damaging	104/515	27216699	918,12088	2203	4300	6503	SO:0001583	missense	10279	exon3			AGGGCAGCCTTGG	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"""Serine peptidases / Serine peptidases"""	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.311G>T	6.37:g.27216699G>T	ENSP00000230582:p.Ser104Ile	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_005865	O75416	Missense_Mutation	SNP	ENST00000230582.3	37	CCDS4623.1	88	0.040293040293040296	46	0.09349593495934959	19	0.052486187845303865	5	0.008741258741258742	18	0.023746701846965697	g	15.62	2.887304	0.52014	0.105311	0.052791	ENSG00000112812	ENST00000230582;ENST00000343467;ENST00000348953	T	0.26373	1.74	4.14	3.24	0.37175	.	0.303446	0.36409	N	0.002611	T	0.27765	0.0683	M	0.67625	2.065	0.32813	D	0.501663	D	0.57899	0.981	P	0.59221	0.854	T	0.09335	-1.0679	10	0.52906	T	0.07	-6.5812	9.8532	0.41070	0.0:0.2089:0.7911:0.0	rs5030965	104	Q9NQE7	TSSP_HUMAN	I	104	ENSP00000230582:S104I	ENSP00000230582:S104I	S	+	2	0	PRSS16	27324678	1.000000	0.71417	0.983000	0.44433	0.718000	0.41266	3.424000	0.52764	1.051000	0.40369	0.557000	0.71058	AGC	G|0.940;T|0.060	0.060	strong		0.557	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2		
NBEAL2	23218	hgsc.bcm.edu	37	3	47033970	47033970	+	Silent	SNP	C	C	T	rs201015016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:47033970C>T	ENST00000450053.3	+	10	1217	c.1038C>T	c.(1036-1038)taC>taT	p.Y346Y	NBEAL2_ENST00000292309.5_Silent_p.Y346Y|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	346					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CACAGCTGTACCTGCAGTCCC	0.642													C|||	2	0.000399361	0.0	0.0014	5008	,	,		17796	0.0		0.001	False		,,,				2504	0.0				p.Y346Y		Atlas-SNP	.											.	NBEAL2	267	.	0			c.C1038T						PASS	.	C		3,3859		0,3,1928	26.0	28.0	27.0		1038	3.4	1.0	3		27	23,8219		0,23,4098	no	coding-synonymous	NBEAL2	NM_015175.1		0,26,6026	TT,TC,CC		0.2791,0.0777,0.2148		346/2755	47033970	26,12078	1931	4121	6052	SO:0001819	synonymous_variant	23218	exon10			GCTGTACCTGCAG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.1038C>T	3.37:g.47033970C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1																																																																																			C|0.998;T|0.002	0.002	weak		0.642	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
RFX5	5993	hgsc.bcm.edu	37	1	151315287	151315287	+	Missense_Mutation	SNP	G	G	C	rs2233854	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:151315287G>C	ENST00000290524.4	-	11	1404	c.1226C>G	c.(1225-1227)cCc>cGc	p.P409R	RFX5_ENST00000368870.2_Missense_Mutation_p.P409R|RFX5_ENST00000452513.2_Missense_Mutation_p.P369R|RFX5_ENST00000452671.2_Missense_Mutation_p.P409R|RFX5_ENST00000478564.1_5'Flank|RP11-126K1.8_ENST00000422153.1_RNA	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	409			P -> R (in dbSNP:rs2233854).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TGTGCCCCGGGGCTGAGTGAG	0.577													G|||	318	0.0634984	0.003	0.0994	5008	,	,		17803	0.0		0.171	False		,,,				2504	0.0746				p.P409R		Atlas-SNP	.											.	RFX5	69	.	0			c.C1226G						PASS	.	G	ARG/PRO,ARG/PRO	154,4252	106.0+/-144.5	0,154,2049	145.0	153.0	150.0		1226,1226	3.3	0.3	1	dbSNP_98	150	1392,7208	268.7+/-288.0	111,1170,3019	yes	missense,missense	RFX5	NM_000449.3,NM_001025603.1	103,103	111,1324,5068	CC,CG,GG		16.186,3.4952,11.8868	benign,benign	409/617,409/617	151315287	1546,11460	2203	4300	6503	SO:0001583	missense	5993	exon11			CCCCGGGGCTGAG		CCDS994.1	1q21	2014-09-17			ENSG00000143390	ENSG00000143390			9986	protein-coding gene	gene with protein product		601863				9401005	Standard	XM_005245405		Approved		uc001exw.1	P48382	OTTHUMG00000012495	ENST00000290524.4:c.1226C>G	1.37:g.151315287G>C	ENSP00000290524:p.Pro409Arg	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	NM_000449	B7Z848|D3DV19|E9PFU4|Q5VWC3	Missense_Mutation	SNP	ENST00000290524.4	37	CCDS994.1	173	0.07921245421245421	1	0.0020325203252032522	37	0.10220994475138122	0	0.0	135	0.17810026385224276	G	10.08	1.252305	0.22880	0.034952	0.16186	ENSG00000143390	ENST00000290524;ENST00000368870;ENST00000452671;ENST00000452513;ENST00000392746	T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32	5.11	3.26	0.37387	.	0.513188	0.18988	N	0.125669	T	0.13798	0.0334	L	0.50333	1.59	0.40855	P	0.016218999999999983	B;P	0.39216	0.435;0.664	B;B	0.30782	0.12;0.109	T	0.04767	-1.0928	9	0.87932	D	0	-2.0525	8.7495	0.34607	0.175:0.0:0.825:0.0	rs2233854;rs52795020;rs2233854	369;409	B7Z848;P48382	.;RFX5_HUMAN	R	409;409;409;369;409	ENSP00000290524:P409R;ENSP00000357864:P409R;ENSP00000389130:P409R;ENSP00000398388:P369R;ENSP00000376502:P409R	ENSP00000290524:P409R	P	-	2	0	RFX5	149581911	0.809000	0.29036	0.256000	0.24389	0.663000	0.39108	1.746000	0.38288	0.749000	0.32854	0.491000	0.48974	CCC	G|0.896;C|0.104	0.104	strong		0.577	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449	
HIVEP1	3096	hgsc.bcm.edu	37	6	12120445	12120445	+	Silent	SNP	A	A	G	rs2228215	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:12120445A>G	ENST00000379388.2	+	4	749	c.417A>G	c.(415-417)caA>caG	p.Q139Q		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	139					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TTCTGCAGCAACCATCTGAAC	0.443													T|||	1101	0.219848	0.0628	0.2478	5008	,	,		19938	0.2242		0.34	False		,,,				2504	0.2843				p.Q139Q		Atlas-SNP	.											.	HIVEP1	242	.	0			c.A417G						PASS	.	T		369,3537		21,327,1605	95.0	90.0	92.0		417	-7.9	0.0	6	dbSNP_98	92	2909,5385		510,1889,1748	no	coding-synonymous	HIVEP1	NM_002114.2		531,2216,3353	GG,GA,AA		35.0735,9.447,26.8689		139/2719	12120445	3278,8922	1953	4147	6100	SO:0001819	synonymous_variant	3096	exon4			GCAGCAACCATCT	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.417A>G	6.37:g.12120445A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Silent	SNP	ENST00000379388.2	37	CCDS43426.1																																																																																			A|0.745;C|0.002	.	strong		0.443	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
CCDC114	93233	hgsc.bcm.edu	37	19	48806094	48806094	+	Missense_Mutation	SNP	C	C	T	rs35361179	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48806094C>T	ENST00000315396.7	-	10	1668	c.986G>A	c.(985-987)cGt>cAt	p.R329H		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	329			R -> H (in dbSNP:rs35361179).		outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		CTTGCTGGCACGTGCGCTCAC	0.622													C|||	74	0.0147764	0.0015	0.0447	5008	,	,		19284	0.001		0.0288	False		,,,				2504	0.0112				p.R329H		Atlas-SNP	.											CCDC114,caecum,carcinoma,-1,1	CCDC114	100	1	0			c.G986A						PASS	.	C	HIS/ARG	31,4375	37.6+/-69.7	0,31,2172	87.0	81.0	83.0		986	-1.1	0.0	19	dbSNP_126	83	324,8276	112.9+/-173.0	11,302,3987	yes	missense	CCDC114	NM_144577.3	29	11,333,6159	TT,TC,CC		3.7674,0.7036,2.7295	benign	329/671	48806094	355,12651	2203	4300	6503	SO:0001583	missense	93233	exon10			CTGGCACGTGCGC	BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.986G>A	19.37:g.48806094C>T	ENSP00000318429:p.Arg329His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Missense_Mutation	SNP	ENST00000315396.7	37	CCDS12714.2	31	0.014194139194139194	1	0.0020325203252032522	13	0.03591160220994475	1	0.0017482517482517483	16	0.021108179419525065	C	8.260	0.811019	0.16537	0.007036	0.037674	ENSG00000105479	ENST00000315396	T	0.29397	1.57	3.6	-1.15	0.09709	.	.	.	.	.	T	0.03136	0.0092	N	0.14661	0.345	0.09310	N	1	B;B;B	0.18166	0.009;0.026;0.012	B;B;B	0.12837	0.003;0.008;0.002	T	0.25433	-1.0132	9	0.24483	T	0.36	-7.3408	6.2299	0.20728	0.0:0.4832:0.0:0.5168	rs35361179	122;329;329	Q96M63-4;Q96M63;Q96M63-5	.;CC114_HUMAN;.	H	329	ENSP00000318429:R329H	ENSP00000318429:R329H	R	-	2	0	CCDC114	53497906	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	-0.128000	0.10531	-0.211000	0.10124	-0.320000	0.08662	CGT	C|0.977;T|0.023	0.023	strong		0.622	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
P2RY2	5029	hgsc.bcm.edu	37	11	72946279	72946279	+	Missense_Mutation	SNP	T	T	C	rs74472890	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:72946279T>C	ENST00000311131.2	+	3	1542	c.1075T>C	c.(1075-1077)Tct>Cct	p.S359P	P2RY2_ENST00000393597.2_Missense_Mutation_p.S359P|P2RY2_ENST00000393596.2_Missense_Mutation_p.S359P	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	359				S -> F (in Ref. 1; AAC04923). {ECO:0000305}.	cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	CAGTGAGGACTCTAGGCGGAC	0.597													T|||	107	0.0213658	0.0023	0.0231	5008	,	,		19669	0.002		0.0467	False		,,,				2504	0.0399				p.S359P		Atlas-SNP	.											.	P2RY2	54	.	0			c.T1075C						PASS	.	T	PRO/SER,PRO/SER,PRO/SER	50,4304		0,50,2127	89.0	93.0	92.0		1075,1075,1075	-0.2	0.2	11	dbSNP_131	92	376,8144		8,360,3892	yes	missense,missense,missense	P2RY2	NM_002564.2,NM_176071.1,NM_176072.1	74,74,74	8,410,6019	CC,CT,TT		4.4131,1.1484,3.309	benign,benign,benign	359/378,359/378,359/378	72946279	426,12448	2177	4260	6437	SO:0001583	missense	5029	exon3			GAGGACTCTAGGC	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.1075T>C	11.37:g.72946279T>C	ENSP00000310305:p.Ser359Pro	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	37	CCDS8219.1	40	0.018315018315018316	1	0.0020325203252032522	7	0.019337016574585635	1	0.0017482517482517483	31	0.040897097625329816	T	12.54	1.967865	0.34754	0.011484	0.044131	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.73789	-0.78;-0.78;-0.78	3.87	-0.188	0.13264	.	1.570370	0.04200	N	0.329931	T	0.21962	0.0529	N	0.08118	0	0.20975	N	0.999818	P	0.36733	0.567	B	0.33568	0.166	T	0.37056	-0.9722	10	0.45353	T	0.12	.	7.1556	0.25635	0.5501:0.0:0.0:0.4499	.	359	P41231	P2RY2_HUMAN	P	359	ENSP00000377222:S359P;ENSP00000310305:S359P;ENSP00000377221:S359P	ENSP00000310305:S359P	S	+	1	0	P2RY2	72623927	0.008000	0.16893	0.241000	0.24154	0.534000	0.34807	0.514000	0.22786	-0.040000	0.13580	0.459000	0.35465	TCT	T|0.971;C|0.029	0.029	strong		0.597	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072	
EZH2	2146	hgsc.bcm.edu	37	7	148508727	148508727	+	Missense_Mutation	SNP	T	T	G	rs267601394		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:148508727T>G	ENST00000460911.1	-	16	2010	c.1922A>C	c.(1921-1923)tAc>tCc	p.Y641S	EZH2_ENST00000541220.1_Missense_Mutation_p.Y590S|EZH2_ENST00000478654.1_Missense_Mutation_p.Y590S|EZH2_ENST00000483967.1_Missense_Mutation_p.Y632S|EZH2_ENST00000320356.2_Missense_Mutation_p.Y646S|EZH2_ENST00000350995.2_Missense_Mutation_p.Y602S|EZH2_ENST00000476773.1_Missense_Mutation_p.Y590S			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	641	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		Y -> C (in a patient with diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> F (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> H (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> N (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> S (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.		cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)	p.Y646F(59)|p.Y646S(22)|p.Y602F(8)|p.Y646C(6)|p.Y602S(4)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			CTCTCCACAGTATTCTGAGAT	0.378			Mis		DLBCL																																p.Y646S		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,face,carcinoma,-1,214	EZH2	823	214	99	Substitution - Missense(99)	haematopoietic_and_lymphoid_tissue(99)	c.A1937C						PASS	.						96.0	89.0	91.0					7																	148508727		2203	4300	6503	SO:0001583	missense	2146	exon16			CCACAGTATTCTG		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.1922A>C	7.37:g.148508727T>G	ENSP00000419711:p.Tyr641Ser	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	t	25.3	4.619614	0.87460	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967	D;D;D;D;D;D;D	0.93307	-3.2;-1.94;-1.94;-1.94;-3.2;-3.2;-1.94	5.63	5.63	0.86233	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.97654	0.9231	H	0.99516	4.605	0.80722	D	1	D;P;P;D;P	0.63880	0.986;0.918;0.543;0.993;0.688	P;P;B;P;B	0.52481	0.7;0.577;0.395;0.7;0.318	D	0.99066	1.0832	10	0.87932	D	0	.	15.87	0.79108	0.0:0.0:0.0:1.0	.	632;590;641;602;646	Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;EZH2_HUMAN;.;.	S	590;646;641;602;590;590;632	ENSP00000417062:Y590S;ENSP00000320147:Y646S;ENSP00000419711:Y641S;ENSP00000223193:Y602S;ENSP00000443219:Y590S;ENSP00000419050:Y590S;ENSP00000419856:Y632S	ENSP00000320147:Y646S	Y	-	2	0	EZH2	148139660	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.789000	0.85783	2.145000	0.66743	0.533000	0.62120	TAC	.	.	none		0.378	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
TUBD1	51174	hgsc.bcm.edu	37	17	57951973	57951973	+	Silent	SNP	G	G	A	rs2250526	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:57951973G>A	ENST00000592426.1	-	5	861	c.861C>T	c.(859-861)taC>taT	p.Y287Y	TUBD1_ENST00000376094.4_Intron|TUBD1_ENST00000539018.1_Silent_p.Y71Y|TUBD1_ENST00000394239.3_Silent_p.Y287Y|TUBD1_ENST00000346141.6_Intron|TUBD1_ENST00000325752.3_Silent_p.Y287Y|TUBD1_ENST00000340993.6_Intron			Q9UJT1	TBD_HUMAN	tubulin, delta 1	287					cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|protein polymerization (GO:0051258)|spermatogenesis (GO:0007283)	centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.Y287Y(1)		NS(2)|breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(2)	21	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)		Vinblastine(DB00570)	TAAATGTGGTGTATGCCAATG	0.413													G|||	1163	0.232228	0.2005	0.1441	5008	,	,		17170	0.4107		0.1551	False		,,,				2504	0.2331				p.Y287Y		Atlas-SNP	.											TUBD1,NS,carcinoma,0,1	TUBD1	38	1	1	Substitution - coding silent(1)	stomach(1)	c.C861T						PASS	.	G	,,,,,	795,3611	320.7+/-296.8	84,627,1492	204.0	191.0	195.0		,861,,,213,861	1.1	1.0	17	dbSNP_100	195	1594,7006	296.3+/-302.9	151,1292,2857	no	intron,coding-synonymous,intron,intron,coding-synonymous,coding-synonymous	TUBD1	NM_001193609.1,NM_001193610.1,NM_001193611.1,NM_001193612.1,NM_001193613.1,NM_016261.3	,,,,,	235,1919,4349	AA,AG,GG		18.5349,18.0436,18.3684	,,,,,	,287/397,,,71/238,287/454	57951973	2389,10617	2203	4300	6503	SO:0001819	synonymous_variant	51174	exon6			TGTGGTGTATGCC	AF201333	CCDS11620.1, CCDS54151.1, CCDS54152.1, CCDS54153.1, CCDS54154.1	17q23.1	2007-03-16						"""Tubulins"""	16811	protein-coding gene	gene with protein product		607344				10620804	Standard	NM_016261		Approved	FLJ12709, TUBD	uc002ixw.2	Q9UJT1		ENST00000592426.1:c.861C>T	17.37:g.57951973G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	163	66	0.404908	NM_016261	B4DPT8|B4DW01|D3DU02|E9PCA7|E9PCQ8|Q5KU36|Q9BWG9|Q9H7Z8	Silent	SNP	ENST00000592426.1	37	CCDS11620.1																																																																																			G|0.781;A|0.219	0.219	strong		0.413	TUBD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448815.1	NM_016261	
SACS	26278	hgsc.bcm.edu	37	13	23929842	23929842	+	Silent	SNP	T	T	C	rs41315020	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:23929842T>C	ENST00000382292.3	-	7	1182	c.909A>G	c.(907-909)gcA>gcG	p.A303A	SACS_ENST00000476776.1_5'Flank|SACS_ENST00000402364.1_5'UTR|SACS_ENST00000382298.3_Silent_p.A303A			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	303					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.A156A(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GCACTGTGTCTGCATCTGCCC	0.443													T|||	255	0.0509185	0.0113	0.0288	5008	,	,		20441	0.1627		0.0378	False		,,,				2504	0.0184				p.A303A		Atlas-SNP	.											SACS,NS,carcinoma,0,1	SACS	871	1	1	Substitution - coding silent(1)	stomach(1)	c.A909G						PASS	.	T		104,4302	81.9+/-120.4	0,104,2099	97.0	96.0	96.0		909	-7.7	0.8	13	dbSNP_127	96	364,8236	121.3+/-180.4	3,358,3939	no	coding-synonymous	SACS	NM_014363.4		3,462,6038	CC,CT,TT		4.2326,2.3604,3.5983		303/4580	23929842	468,12538	2203	4300	6503	SO:0001819	synonymous_variant	26278	exon8			TGTGTCTGCATCT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.909A>G	13.37:g.23929842T>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	258	125	0.484496	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2	129	0.059065934065934064	11	0.022357723577235773	12	0.03314917127071823	77	0.1346153846153846	29	0.03825857519788918	T	10.28	1.306139	0.23736	0.023604	0.042326	ENSG00000151835	ENST00000455470	.	.	.	5.86	-7.73	0.01245	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.25745	-1.0123	3	.	.	.	.	0.0814	0.00032	0.2669:0.2137:0.1838:0.3356	rs41315020;rs57420292;rs61736775	.	.	.	G	203	.	.	R	-	1	2	SACS	22827842	0.023000	0.18921	0.775000	0.31657	0.974000	0.67602	-0.897000	0.04110	-1.501000	0.01817	-0.309000	0.09137	AGA	T|0.956;C|0.044	0.044	strong		0.443	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
MUC2	4583	hgsc.bcm.edu	37	11	1103855	1103855	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1103855C>T	ENST00000441003.2	+	48	8181	c.8154C>T	c.(8152-8154)gtC>gtT	p.V2718V		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5080					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCGTCCCCGTCACCACGGAGG	0.642																																					p.V2714V		Atlas-SNP	.											.	MUC2	614	.	0			c.C8142T						PASS	.						22.0	25.0	24.0					11																	1103855		2048	4156	6204	SO:0001819	synonymous_variant	4583	exon49			CCCCGTCACCACG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.8154C>T	11.37:g.1103855C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	106	62	0.584906	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
LAMC1	3915	hgsc.bcm.edu	37	1	182993025	182993025	+	Silent	SNP	C	C	T	rs10911194	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:182993025C>T	ENST00000258341.4	+	1	431	c.174C>T	c.(172-174)gcC>gcT	p.A58A		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	58	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TCAACGCCGCCTTCAACGTGA	0.697													C|||	2602	0.519569	0.3192	0.611	5008	,	,		11827	0.628		0.5338	False		,,,				2504	0.5992				p.A58A		Atlas-SNP	.											.	LAMC1	176	.	0			c.C174T						PASS	.	C		1571,2835	469.6+/-355.5	304,963,936	32.0	34.0	33.0		174	4.2	1.0	1	dbSNP_120	33	4679,3921	588.7+/-392.4	1223,2233,844	no	coding-synonymous	LAMC1	NM_002293.3		1527,3196,1780	TT,TC,CC		45.593,35.6559,48.0547		58/1610	182993025	6250,6756	2203	4300	6503	SO:0001819	synonymous_variant	3915	exon1			CGCCGCCTTCAAC	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.174C>T	1.37:g.182993025C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	169	75	0.443787	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																			C|0.512;T|0.488	0.488	strong		0.697	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
TRUB1	142940	hgsc.bcm.edu	37	10	116719543	116719543	+	Missense_Mutation	SNP	G	G	A	rs7099565	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:116719543G>A	ENST00000298746.3	+	4	561	c.500G>A	c.(499-501)aGg>aAg	p.R167K	TRUB1_ENST00000485065.1_3'UTR	NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase family member 1	167			R -> K (in dbSNP:rs7099565). {ECO:0000269|PubMed:14702039}.		pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		TCTACGGGGAGGGTAACAGAA	0.413													A|||	2117	0.422724	0.7844	0.2968	5008	,	,		18735	0.0367		0.4503	False		,,,				2504	0.3926				p.R167K		Atlas-SNP	.											.	TRUB1	30	.	0			c.G500A						PASS	.	A	LYS/ARG	3254,1152	407.1+/-334.1	1216,822,165	87.0	85.0	86.0		500	4.6	1.0	10	dbSNP_116	86	3964,4636	601.9+/-394.4	902,2160,1238	yes	missense	TRUB1	NM_139169.4	26	2118,2982,1403	AA,AG,GG		46.093,26.1462,44.5025	benign	167/350	116719543	7218,5788	2203	4300	6503	SO:0001583	missense	142940	exon4			CGGGGAGGGTAAC	AF448144	CCDS7591.1	10q25.3	2013-09-02	2013-09-02		ENSG00000165832	ENSG00000165832			16060	protein-coding gene	gene with protein product		610726	"""TruB pseudouridine (psi) synthase homolog 1 (E. coli)"""			12736709	Standard	NM_139169		Approved	PUS4	uc001lcd.3	Q8WWH5	OTTHUMG00000019094	ENST00000298746.3:c.500G>A	10.37:g.116719543G>A	ENSP00000298746:p.Arg167Lys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_139169	B2R716|Q53ES2	Missense_Mutation	SNP	ENST00000298746.3	37	CCDS7591.1	846	0.3873626373626374	365	0.741869918699187	114	0.3149171270718232	22	0.038461538461538464	345	0.4551451187335092	A	5.009	0.187410	0.09547	0.738538	0.46093	ENSG00000165832	ENST00000298746	T	0.48522	0.81	5.69	4.56	0.56223	Pseudouridine synthase, catalytic domain (1);	0.240920	0.47455	N	0.000229	T	0.00012	0.0000	N	0.01761	-0.735	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.45205	-0.9277	9	0.02654	T	1	-6.3728	8.283	0.31910	0.842:0.0:0.158:0.0	rs7099565;rs11543158;rs17325262;rs59183827;rs7099565	167	Q8WWH5	TRUB1_HUMAN	K	167	ENSP00000298746:R167K	ENSP00000298746:R167K	R	+	2	0	TRUB1	116709533	1.000000	0.71417	0.993000	0.49108	0.666000	0.39218	1.997000	0.40786	0.440000	0.26502	-0.254000	0.11334	AGG	G|0.500;A|0.500	0.500	strong		0.413	TRUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050504.1	NM_139169	
FAM189B	10712	hgsc.bcm.edu	37	1	155217614	155217614	+	Missense_Mutation	SNP	T	T	C	rs553505679		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:155217614T>C	ENST00000361361.2	-	12	2475	c.1966A>G	c.(1966-1968)Agc>Ggc	p.S656G	FAM189B_ENST00000368368.3_Missense_Mutation_p.S638G|FAM189B_ENST00000472550.1_5'Flank|FAM189B_ENST00000350210.2_Missense_Mutation_p.S560G	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	656						integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						AGGCTGAGGCTGTGGGGGCGG	0.647													T|||	1	0.000199681	0.0008	0.0	5008	,	,		14418	0.0		0.0	False		,,,				2504	0.0				p.S656G		Atlas-SNP	.											.	FAM189B	51	.	0			c.A1966G						PASS	.						11.0	11.0	11.0					1																	155217614		2144	4211	6355	SO:0001583	missense	10712	exon12			TGAGGCTGTGGGG	AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 2"""	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.1966A>G	1.37:g.155217614T>C	ENSP00000354958:p.Ser656Gly	Somatic	373	0	0		WXS	Illumina HiSeq	Phase_I	400	205	0.5125	NM_006589	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	37	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.066640	0.76301	.	.	ENSG00000160767	ENST00000350210;ENST00000368368;ENST00000361361	T;T;T	0.03272	3.99;3.99;3.99	4.51	4.51	0.55191	.	0.000000	0.64402	D	0.000008	T	0.03959	0.0111	N	0.19112	0.55	0.31239	N	0.695389	D;P;P;P	0.59767	0.986;0.924;0.954;0.924	D;P;D;P	0.70935	0.971;0.878;0.916;0.827	T	0.21348	-1.0248	10	0.87932	D	0	.	12.1475	0.54031	0.0:0.0:0.0:1.0	.	421;638;560;656	B1AVS2;B1AVS5;P81408-2;P81408	.;.;.;F189B_HUMAN	G	560;638;656	ENSP00000307128:S560G;ENSP00000357352:S638G;ENSP00000354958:S656G	ENSP00000307128:S560G	S	-	1	0	FAM189B	153484238	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.099000	0.64554	2.037000	0.60232	0.529000	0.55759	AGC	.	.	none		0.647	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589	
OR6Y1	391112	hgsc.bcm.edu	37	1	158517353	158517353	+	Silent	SNP	G	G	A	rs16840314	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:158517353G>A	ENST00000302617.3	-	1	542	c.543C>T	c.(541-543)caC>caT	p.H181H		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					CACAAAAGTAGTGATTGATCT	0.473													G|||	974	0.194489	0.028	0.219	5008	,	,		24176	0.376		0.2416	False		,,,				2504	0.1667				p.H181H		Atlas-SNP	.											.	OR6Y1	73	.	0			c.C543T						PASS	.	G		308,4098	165.8+/-197.2	16,276,1911	65.0	55.0	59.0		543	4.4	1.0	1	dbSNP_123	59	1984,6616	345.4+/-325.7	251,1482,2567	no	coding-synonymous	OR6Y1	NM_001005189.1		267,1758,4478	AA,AG,GG		23.0698,6.9905,17.6226		181/326	158517353	2292,10714	2203	4300	6503	SO:0001819	synonymous_variant	391112	exon1			AAAGTAGTGATTG	BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"""GPCR / Class A : Olfactory receptors"""	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.543C>T	1.37:g.158517353G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_001005189	Q6IFS0	Silent	SNP	ENST00000302617.3	37	CCDS30899.1																																																																																			G|0.800;A|0.200	0.200	strong		0.473	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189	
HLA-B	3106	hgsc.bcm.edu	37	6	31323116	31323116	+	Silent	SNP	C	C	T	rs1131446	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323116C>T	ENST00000412585.2	-	4	901	c.873G>A	c.(871-873)ccG>ccA	p.P291P		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	291	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TGAGGGGCTTCGGCAGCCCCT	0.577									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				C|||	485	0.096845	0.0749	0.0922	5008	,	,		21693	0.0754		0.1074	False		,,,				2504	0.1411				p.P291P		Atlas-SNP	.											HLA-B,rectum,carcinoma,0,1	HLA-B	54	1	0			c.G873A						PASS	.						60.0	57.0	58.0					6																	31323116		2203	4300	6503	SO:0001819	synonymous_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	GGGCTTCGGCAGC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.873G>A	6.37:g.31323116C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	173	15	0.0867052	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			C|0.943;T|0.057	0.057	strong		0.577	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
FRG2B	441581	hgsc.bcm.edu	37	10	135438753	135438753	+	Silent	SNP	G	G	A	rs375000694		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135438753G>A	ENST00000425520.1	-	4	739	c.687C>T	c.(685-687)acC>acT	p.T229T	FRG2B_ENST00000443774.1_Silent_p.T230T	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	229						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		AAGCTGCCTGGGTGGCCATGG	0.597																																					p.T229T		Atlas-SNP	.											FRG2B,NS,carcinoma,0,3	FRG2B	47	3	0			c.C687T						scavenged	.						3.0	4.0	4.0					10																	135438753		1467	3364	4831	SO:0001819	synonymous_variant	441581	exon4			TGCCTGGGTGGCC	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.687C>T	10.37:g.135438753G>A		Somatic	271	28	0.103321		WXS	Illumina HiSeq	Phase_I	258	57	0.22093	NM_001080998	Q5VSQ1	Silent	SNP	ENST00000425520.1	37	CCDS44502.1																																																																																			.	.	none		0.597	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
NKAIN2	154215	hgsc.bcm.edu	37	6	124604203	124604203	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:124604203C>T	ENST00000368417.1	+	2	167	c.107C>T	c.(106-108)cCt>cTt	p.P36L	NKAIN2_ENST00000368416.1_Missense_Mutation_p.P36L|NKAIN2_ENST00000476571.1_3'UTR|NKAIN2_ENST00000545433.1_Missense_Mutation_p.P21L|NKAIN2_ENST00000546092.1_Missense_Mutation_p.P36L	NM_001040214.1	NP_001035304.1	Q5VXU1	NKAI2_HUMAN	Na+/K+ transporting ATPase interacting 2	36						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|large_intestine(3)|lung(12)|skin(2)	19				GBM - Glioblastoma multiforme(226;0.104)		CAGTGGGCACCTATCCTGGCA	0.383																																					p.P36L		Atlas-SNP	.											NKAIN2,NS,carcinoma,-1,1	NKAIN2	34	1	0			c.C107T						scavenged	.						227.0	212.0	217.0					6																	124604203		2203	4300	6503	SO:0001583	missense	154215	exon2			GGGCACCTATCCT	AB070452	CCDS34526.1	6q21	2008-02-05	2007-10-04	2007-10-04	ENSG00000188580	ENSG00000188580		"""Na+/K+ transporting ATPase interacting"""	16443	protein-coding gene	gene with protein product		609758	"""T-cell lymphoma breakpoint associated target 1"""	TCBA1		17606467	Standard	XM_005266833		Approved	FAM77B	uc003pzo.3	Q5VXU1	OTTHUMG00000015500	ENST00000368417.1:c.107C>T	6.37:g.124604203C>T	ENSP00000357402:p.Pro36Leu	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	190	2	0.0105263	NM_153355	Q8IYR4|Q8TF67	Missense_Mutation	SNP	ENST00000368417.1	37	CCDS34526.1	.	.	.	.	.	.	.	.	.	.	C	32	5.115603	0.94339	.	.	ENSG00000188580	ENST00000368416;ENST00000368417;ENST00000546092;ENST00000539866;ENST00000545433	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.41096	0.1144	M	0.83774	2.66	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.91635	0.991;0.994;0.995;0.999	T	0.25257	-1.0137	10	0.48119	T	0.1	-8.5993	19.8344	0.96650	0.0:1.0:0.0:0.0	.	36;35;36;36	F5GY48;Q5VXU1-3;Q5VXU1;Q5VXU1-2	.;.;NKAI2_HUMAN;.	L	36;36;36;35;21	ENSP00000357401:P36L;ENSP00000357402:P36L;ENSP00000440287:P36L;ENSP00000437798:P21L	ENSP00000357401:P36L	P	+	2	0	NKAIN2	124645902	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.717000	0.84732	2.692000	0.91855	0.655000	0.94253	CCT	.	.	none		0.383	NKAIN2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042057.1	NM_001040214	
OR4N2	390429	hgsc.bcm.edu	37	14	20295834	20295834	+	Missense_Mutation	SNP	T	T	C	rs2801164	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20295834T>C	ENST00000315947.1	+	1	227	c.227T>C	c.(226-228)aTt>aCt	p.I76T	OR4N2_ENST00000568211.1_Missense_Mutation_p.I76T	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	76			I -> T (in dbSNP:rs2801164).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TACTCCTTCATTGTGGCTCCC	0.493																																					p.I76T		Atlas-SNP	.											.	OR4N2	125	.	0			c.T227C						PASS	.	T	THR/ILE	2451,1955		531,1389,283	151.0	177.0	168.0		227	4.3	1.0	14	dbSNP_100	168	3783,4813		526,2731,1041	no	missense	OR4N2	NM_001004723.1	89	1057,4120,1324	CC,CT,TT		44.0088,44.3713,47.9465	benign	76/308	20295834	6234,6768	2203	4298	6501	SO:0001583	missense	390429	exon1			CCTTCATTGTGGC		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.227T>C	14.37:g.20295834T>C	ENSP00000319601:p.Ile76Thr	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	184	180	0.978261	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	1034	0.4734432234432234	294	0.5975609756097561	158	0.43646408839779005	242	0.4230769230769231	340	0.44854881266490765	.	10.30	1.311947	0.23821	0.556287	0.440088	ENSG00000176294	ENST00000557677;ENST00000315947	T;T	0.00512	6.89;6.89	4.3	4.3	0.51218	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000151	T	0.00012	0.0000	N	0.00985	-1.075	0.42474	P	0.007167999999999952	B	0.12630	0.006	B	0.17433	0.018	T	0.00099	-1.2068	9	0.16420	T	0.52	-16.0998	11.7038	0.51585	0.0:0.0:0.0:1.0	rs2801164	76	Q8NGD1	OR4N2_HUMAN	T	76	ENSP00000452022:I76T;ENSP00000319601:I76T	ENSP00000319601:I76T	I	+	2	0	OR4N2	19365674	0.000000	0.05858	1.000000	0.80357	0.971000	0.66376	0.524000	0.22940	1.922000	0.55676	0.482000	0.46254	ATT	.	.	weak		0.493	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
AHNAK	79026	hgsc.bcm.edu	37	11	62290719	62290719	+	Missense_Mutation	SNP	A	A	G	rs11231128	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62290719A>G	ENST00000378024.4	-	5	11444	c.11170T>C	c.(11170-11172)Tca>Cca	p.S3724P	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3724			S -> P (in dbSNP:rs11231128).		protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TTACCCTCTGAGCCTTCGATG	0.473													N|||	224	0.0447284	0.1067	0.0303	5008	,	,		20040	0.0119		0.0258	False		,,,				2504	0.0245				p.S3724P		Atlas-SNP	.											.	AHNAK	532	.	0			c.T11170C						PASS	.	G	PRO/SER,	428,3976		18,392,1792	130.0	137.0	135.0		11170,	4.4	0.9	11	dbSNP_120	135	222,8376		4,214,4081	yes	missense,intron	AHNAK	NM_001620.1,NM_024060.2	74,	22,606,5873	GG,GA,AA		2.582,9.7184,4.9992	benign,	3724/5891,	62290719	650,12352	2202	4299	6501	SO:0001583	missense	79026	exon5			CCTCTGAGCCTTC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11170T>C	11.37:g.62290719A>G	ENSP00000367263:p.Ser3724Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	99	0.04532967032967033	60	0.12195121951219512	15	0.04143646408839779	7	0.012237762237762238	17	0.022427440633245383	-	0.603	-0.828266	0.02734	0.097184	0.02582	ENSG00000124942	ENST00000378024	T	0.00476	7.15	5.32	4.4	0.53042	.	0.000000	0.37577	N	0.002037	T	0.00012	0.0000	N	0.00005	-3.27	0.21762	N	0.99955	B	0.02656	0.0	B	0.01281	0.0	T	0.42137	-0.9469	10	0.02654	T	1	.	12.0519	0.53511	0.1443:0.0:0.8557:0.0	rs11231128;rs57558876;rs11231128	3724	Q09666	AHNK_HUMAN	P	3724	ENSP00000367263:S3724P	ENSP00000367263:S3724P	S	-	1	0	AHNAK	62047295	0.942000	0.31987	0.946000	0.38457	0.042000	0.13812	0.401000	0.20948	1.262000	0.44165	-0.200000	0.12747	TCA	A|0.947;G|0.053	0.053	strong		0.473	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
PDE9A	5152	hgsc.bcm.edu	37	21	44189166	44189166	+	Silent	SNP	T	T	C	rs1045382	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:44189166T>C	ENST00000291539.6	+	17	1551	c.1491T>C	c.(1489-1491)ccT>ccC	p.P497P	PDE9A_ENST00000380328.2_Silent_p.P444P|PDE9A_ENST00000335512.4_Silent_p.P437P|PDE9A_ENST00000335440.6_Silent_p.P395P|PDE9A_ENST00000398232.3_Silent_p.P430P|PDE9A_ENST00000398229.3_Silent_p.P363P|PDE9A_ENST00000349112.3_Silent_p.P369P|PDE9A_ENST00000539837.1_Silent_p.P369P|PDE9A_ENST00000398224.3_Silent_p.P370P|PDE9A_ENST00000398227.3_Silent_p.P337P|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000328862.6_Silent_p.P471P|PDE9A_ENST00000398234.3_Silent_p.P396P|PDE9A_ENST00000398236.3_Silent_p.P411P|PDE9A_ENST00000398225.3_Silent_p.P456P	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	497	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	AAGGCCTTCCTGTGGCACCGT	0.512													C|||	2569	0.512979	0.6853	0.4352	5008	,	,		24371	0.4236		0.3718	False		,,,				2504	0.5726				p.P497P		Atlas-SNP	.											.	PDE9A	69	.	0			c.T1491C						PASS	.	C	,,,,,,,,,,,,,,,,,,,	2761,1645	502.9+/-365.4	856,1049,298	171.0	147.0	155.0		1311,1110,1107,1332,1188,870,870,1233,1011,840,1089,1185,870,840,1290,1368,1413,870,870,1491	-9.5	0.1	21	dbSNP_86	155	3112,5488	658.8+/-401.6	587,1938,1775	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	,,,,,,,,,,,,,,,,,,,	1443,2987,2073	CC,CT,TT		36.186,37.3355,45.1561	,,,,,,,,,,,,,,,,,,,	437/534,370/467,369/466,444/541,396/493,290/387,290/387,411/508,337/434,280/377,363/460,395/492,290/387,280/377,430/527,456/553,471/568,290/387,290/387,497/594	44189166	5873,7133	2203	4300	6503	SO:0001819	synonymous_variant	5152	exon17			CCTTCCTGTGGCA	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.1491T>C	21.37:g.44189166T>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	189	80	0.42328	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Silent	SNP	ENST00000291539.6	37	CCDS13690.1																																																																																			T|0.555;C|0.445	0.445	strong		0.512	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
ZNF688	146542	hgsc.bcm.edu	37	16	30582855	30582855	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30582855G>A	ENST00000223459.6	-	1	1200	c.96C>T	c.(94-96)gcC>gcT	p.A32A	ZNF688_ENST00000395219.1_Intron|AC002310.7_ENST00000486926.1_RNA|ZNF688_ENST00000567855.1_Silent_p.A32A|AC002310.7_ENST00000492040.1_RNA|ZNF688_ENST00000563707.1_Silent_p.A32A	NM_145271.3	NP_660314.1	P0C7X2	ZN688_HUMAN	zinc finger protein 688	32	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						AGAAGTACACGGCCACGTCCG	0.741																																					p.A32A		Atlas-SNP	.											.	ZNF688	37	.	0			c.C96T						PASS	.						12.0	14.0	13.0					16																	30582855		2187	4293	6480	SO:0001819	synonymous_variant	146542	exon1			GTACACGGCCACG	AK122680	CCDS10684.1	16p11.2	2013-01-08			ENSG00000229809	ENSG00000229809		"""Zinc fingers, C2H2-type"", ""-"""	30489	protein-coding gene	gene with protein product						10493829	Standard	XM_005255139		Approved		uc002dys.2	P0C7X2	OTTHUMG00000132408	ENST00000223459.6:c.96C>T	16.37:g.30582855G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	103	41	0.398058	NM_145271	A8MV39|B3KV51|O75701|Q8IW91|Q8WV14|Q96MN0	Silent	SNP	ENST00000223459.6	37	CCDS10684.1																																																																																			.	.	none		0.741	ZNF688-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255544.2	NM_145271	
SLC11A2	4891	hgsc.bcm.edu	37	12	51386017	51386017	+	Missense_Mutation	SNP	G	G	T	rs144863268	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:51386017G>T	ENST00000262051.7	-	13	1390	c.1303C>A	c.(1303-1305)Cta>Ata	p.L435I	SLC11A2_ENST00000262052.5_Missense_Mutation_p.L435I|SLC11A2_ENST00000547688.1_Missense_Mutation_p.L464I|SLC11A2_ENST00000394904.3_Missense_Mutation_p.L464I|SLC11A2_ENST00000547198.1_Missense_Mutation_p.L435I|SLC11A2_ENST00000541174.2_Missense_Mutation_p.L435I|SLC11A2_ENST00000545993.2_Missense_Mutation_p.L431I|SLC11A2_ENST00000546743.1_Missense_Mutation_p.L356I	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	435			L -> I (in dbSNP:rs144863268). {ECO:0000269|PubMed:9642100}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						ATCCCTGTTAGATGCTCTACA	0.468													G|||	3	0.000599042	0.0015	0.0	5008	,	,		21375	0.0		0.001	False		,,,				2504	0.0				p.L464I		Atlas-SNP	.											.	SLC11A2	51	.	0			c.C1390A						PASS	.	G	ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU	1,4405	2.1+/-5.4	0,1,2202	152.0	126.0	135.0		1303,1390,1303,1303,1303,1303,1291	4.7	0.9	12	dbSNP_134	135	25,8575	17.3+/-56.4	0,25,4275	yes	missense,missense,missense,missense,missense,missense,missense	SLC11A2	NM_000617.2,NM_001174125.1,NM_001174126.1,NM_001174127.1,NM_001174128.1,NM_001174129.1,NM_001174130.1	5,5,5,5,5,5,5	0,26,6477	TT,TG,GG		0.2907,0.0227,0.1999	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	435/562,464/591,435/569,435/569,435/562,435/562,431/558	51386017	26,12980	2203	4300	6503	SO:0001583	missense	4891	exon13			CTGTTAGATGCTC	AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"""Solute carriers"""	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.1303C>A	12.37:g.51386017G>T	ENSP00000262051:p.Leu435Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Missense_Mutation	SNP	ENST00000262051.7	37	CCDS53792.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	19.37	3.814690	0.70912	2.27E-4	0.002907	ENSG00000110911	ENST00000262051;ENST00000547198;ENST00000262052;ENST00000394904;ENST00000547688;ENST00000541174;ENST00000545993;ENST00000546743	T;T;T;T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41	5.59	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.73361	0.3577	L	0.49256	1.55	0.58432	D	0.999993	D;D;D;D;D;P	0.64830	0.985;0.981;0.994;0.994;0.985;0.883	D;D;D;D;D;P	0.67382	0.951;0.919;0.919;0.919;0.951;0.665	T	0.72191	-0.4365	9	.	.	.	-6.39	9.6058	0.39632	0.1786:0.0:0.8214:0.0	.	398;431;464;435;284;435	B7Z9M2;F5H741;P49281-3;P49281-2;B3KY44;P49281	.;.;.;.;.;NRAM2_HUMAN	I	435;435;435;464;464;435;431;356	ENSP00000262051:L435I;ENSP00000446769:L435I;ENSP00000262052:L435I;ENSP00000378364:L464I;ENSP00000449200:L464I;ENSP00000444542:L435I;ENSP00000442810:L431I;ENSP00000446914:L356I	.	L	-	1	2	SLC11A2	49672284	1.000000	0.71417	0.949000	0.38748	0.975000	0.68041	2.010000	0.40913	1.408000	0.46895	0.655000	0.94253	CTA	G|0.998;T|0.002	0.002	strong		0.468	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1		
ADCY2	108	hgsc.bcm.edu	37	5	7802363	7802363	+	Silent	SNP	C	C	T	rs2290910	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7802363C>T	ENST00000338316.4	+	21	2750	c.2661C>T	c.(2659-2661)tgC>tgT	p.C887C	ADCY2_ENST00000537121.1_Silent_p.C707C	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	887					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)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|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)|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)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						ACTGCGTCTGCGTCATGTTTG	0.483													C|||	1169	0.233427	0.1203	0.4164	5008	,	,		20942	0.2768		0.2644	False		,,,				2504	0.18				p.C887C		Atlas-SNP	.											ADCY2,rectum,carcinoma,0,1	ADCY2	337	1	0			c.C2661T						PASS	.	C		684,3722	288.4+/-279.8	53,578,1572	82.0	77.0	79.0		2661	-2.6	1.0	5	dbSNP_100	79	2285,6315	385.4+/-341.5	289,1707,2304	no	coding-synonymous	ADCY2	NM_020546.2		342,2285,3876	TT,TC,CC		26.5698,15.5243,22.8279		887/1092	7802363	2969,10037	2203	4300	6503	SO:0001819	synonymous_variant	108	exon21			CGTCTGCGTCATG	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"""Adenylate cyclases"""	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2661C>T	5.37:g.7802363C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																			C|0.772;T|0.228	0.228	strong		0.483	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
PRUNE2	158471	hgsc.bcm.edu	37	9	79322711	79322711	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:79322711G>A	ENST00000376718.3	-	8	4602	c.4479C>T	c.(4477-4479)gaC>gaT	p.D1493D	PRUNE2_ENST00000428286.1_Silent_p.D1134D	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1493					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CTATAGGGACGTCCCCAAAAT	0.468																																					p.D1493D		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C4479T						PASS	.						43.0	42.0	43.0					9																	79322711		1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			AGGGACGTCCCCA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.4479C>T	9.37:g.79322711G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	G	3.028	-0.200220	0.06219	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.49	-1.57	0.08506	.	.	.	.	.	T	0.20129	0.0484	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.24404	-1.0161	4	.	.	.	-1.5436	2.2159	0.03959	0.4355:0.2533:0.0685:0.2427	.	.	.	.	C	815	.	.	R	-	1	0	PRUNE2	78512531	0.011000	0.17503	0.001000	0.08648	0.002000	0.02628	0.261000	0.18442	-0.420000	0.07427	-0.238000	0.12139	CGT	.	.	none		0.468	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
PPL	5493	hgsc.bcm.edu	37	16	4935146	4935146	+	Silent	SNP	C	C	T	rs1049206	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:4935146C>T	ENST00000345988.2	-	22	3599	c.3510G>A	c.(3508-3510)gtG>gtA	p.V1170V	PPL_ENST00000590782.2_Silent_p.V1168V	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1170					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.V1170V(1)		breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CCTTCTCCTGCACCACCACTT	0.622													C|||	1841	0.367612	0.3359	0.4135	5008	,	,		18711	0.2907		0.3241	False		,,,				2504	0.502				p.V1170V		Atlas-SNP	.											PPL,NS,carcinoma,0,1	PPL	168	1	1	Substitution - coding silent(1)	stomach(1)	c.G3510A						PASS	.	C		1539,2855	487.3+/-360.9	274,991,932	120.0	110.0	113.0		3510	2.1	1.0	16	dbSNP_86	113	2550,6050	414.9+/-351.6	376,1798,2126	no	coding-synonymous	PPL	NM_002705.4		650,2789,3058	TT,TC,CC		29.6512,35.025,31.4684		1170/1757	4935146	4089,8905	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			CTCCTGCACCACC	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3510G>A	16.37:g.4935146C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	135	76	0.562963	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			C|0.673;T|0.327	0.327	strong		0.622	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
ZNF768	79724	hgsc.bcm.edu	37	16	30536672	30536672	+	Silent	SNP	A	A	G	rs3751847	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30536672A>G	ENST00000380412.5	-	2	964	c.789T>C	c.(787-789)tgT>tgC	p.C263C	ZNF768_ENST00000562803.1_Silent_p.C232C	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	263					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	DNA-directed RNA polymerase II, core complex (GO:0005665)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						CGCAGATGCCACAGATGTTAG	0.652													G|||	3163	0.631589	0.9644	0.4424	5008	,	,		15017	0.1468		0.5924	False		,,,				2504	0.8558				p.C263C		Atlas-SNP	.											.	ZNF768	28	.	0			c.T789C						PASS	.	G		3900,494	225.6+/-241.4	1736,428,33	41.0	43.0	43.0		789	-9.0	0.1	16	dbSNP_107	43	5168,3432	494.0+/-373.7	1556,2056,688	no	coding-synonymous	ZNF768	NM_024671.3		3292,2484,721	GG,GA,AA		39.907,11.2426,30.2139		263/541	30536672	9068,3926	2197	4300	6497	SO:0001819	synonymous_variant	79724	exon2			GATGCCACAGATG	BC013760	CCDS10681.2	16p11.2	2013-01-08			ENSG00000169957	ENSG00000169957		"""Zinc fingers, C2H2-type"""	26273	protein-coding gene	gene with protein product						12477932	Standard	NM_024671		Approved	FLJ23436	uc002dyk.4	Q9H5H4	OTTHUMG00000132392	ENST00000380412.5:c.789T>C	16.37:g.30536672A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_024671	Q569L7|Q96CX4	Silent	SNP	ENST00000380412.5	37	CCDS10681.2																																																																																			A|0.389;G|0.611	0.611	strong		0.652	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671	
UAP1L1	91373	hgsc.bcm.edu	37	9	139973820	139973820	+	Missense_Mutation	SNP	C	C	T	rs7037849	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139973820C>T	ENST00000409858.3	+	5	988	c.956C>T	c.(955-957)gCc>gTc	p.A319V	UAP1L1_ENST00000360271.3_Missense_Mutation_p.A196V	NM_207309.2	NP_997192.2	Q3KQV9	UAP1L_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1 like 1	319			A -> V (in dbSNP:rs7037849). {ECO:0000269|PubMed:14702039}.				uridylyltransferase activity (GO:0070569)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		CAGCTACGTGCCTCCGACGGG	0.637													C|||	2450	0.489217	0.4834	0.4452	5008	,	,		14974	0.6528		0.3996	False		,,,				2504	0.4519				p.A319V		Atlas-SNP	.											.	UAP1L1	46	.	0			c.C956T						PASS	.	C	VAL/ALA	2072,2334	570.2+/-382.8	489,1094,620	134.0	115.0	122.0		956	0.1	0.0	9	dbSNP_116	122	3320,5280	494.2+/-373.8	648,2024,1628	yes	missense	UAP1L1	NM_207309.2	64	1137,3118,2248	TT,TC,CC		38.6047,47.0268,41.4578	benign	319/508	139973820	5392,7614	2203	4300	6503	SO:0001583	missense	91373	exon5			TACGTGCCTCCGA	AK022632	CCDS7028.2	9q34.3	2014-07-31	2014-07-31		ENSG00000197355	ENSG00000197355			28082	protein-coding gene	gene with protein product							Standard	NM_207309		Approved		uc010ncb.3	Q3KQV9	OTTHUMG00000020962	ENST00000409858.3:c.956C>T	9.37:g.139973820C>T	ENSP00000386935:p.Ala319Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	131	70	0.534351	NM_207309	A2AMJ8|Q5SPZ2|Q69YQ3|Q6ZR38	Missense_Mutation	SNP	ENST00000409858.3	37	CCDS7028.2	1056	0.4835164835164835	216	0.43902439024390244	165	0.4558011049723757	377	0.6590909090909091	298	0.39313984168865435	C	10.17	1.276808	0.23307	0.470268	0.386047	ENSG00000197355	ENST00000409858;ENST00000360271	T;T	0.17691	2.26;2.26	4.91	0.0909	0.14465	.	0.722083	0.13651	N	0.372274	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B;P	0.42692	0.173;0.787	B;B	0.40782	0.158;0.34	T	0.28522	-1.0041	9	0.59425	D	0.04	.	11.7893	0.52059	0.1378:0.1826:0.6796:0.0	rs7037849;rs60377984;rs7037849	319;196	Q3KQV9;Q3KQV9-2	UAP1L_HUMAN;.	V	319;196	ENSP00000386935:A319V;ENSP00000353409:A196V	ENSP00000353409:A196V	A	+	2	0	UAP1L1	139093641	0.000000	0.05858	0.000000	0.03702	0.136000	0.21042	1.006000	0.29847	0.092000	0.17331	0.491000	0.48974	GCC	C|0.558;T|0.442	0.442	strong		0.637	UAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055216.2	XM_038063	
SMIM8	57150	hgsc.bcm.edu	37	6	88046818	88046818	+	Silent	SNP	A	A	G	rs138902411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:88046818A>G	ENST00000392863.1	+	3	158	c.69A>G	c.(67-69)ccA>ccG	p.P23P	SMIM8_ENST00000229570.5_Silent_p.P23P|SMIM8_ENST00000608868.1_Silent_p.P23P|SMIM8_ENST00000608525.1_Silent_p.P23P|RP1-102H19.8_ENST00000448282.2_Silent_p.P23P|SMIM8_ENST00000608353.1_Silent_p.P23P	NM_001042493.1	NP_001035958.1	Q96KF7	SMIM8_HUMAN	small integral membrane protein 8	23						integral component of membrane (GO:0016021)											TTCAAAGCCCAGGGCTCAGAG	0.408													A|||	2	0.000399361	0.0	0.0	5008	,	,		14790	0.0		0.002	False		,,,				2504	0.0				p.P23P		Atlas-SNP	.											.	.	.	.	0			c.A69G						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	94.0	96.0	95.0		69,69	2.1	1.0	6	dbSNP_134	95	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous,coding-synonymous	C6orf162	NM_001042493.1,NM_020425.4	,	0,23,6480	GG,GA,AA		0.2093,0.1135,0.1768	,	23/98,23/98	88046818	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	57150	exon3			AAGCCCAGGGCTC	AL050201	CCDS34496.1, CCDS75493.1	6q15	2013-06-21	2012-11-20	2012-11-20	ENSG00000111850	ENSG00000111850			21401	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 162"""	C6orf162			Standard	NM_001287445		Approved	DKFZP586E1923, dJ102H19.2	uc003plq.1	Q96KF7	OTTHUMG00000015168	ENST00000392863.1:c.69A>G	6.37:g.88046818A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_001042493	B2R4V6|E1P505|Q5TEZ3|Q6NSD2|Q8IZ10	Silent	SNP	ENST00000392863.1	37	CCDS34496.1																																																																																			A|0.998;G|0.002	0.002	strong		0.408	SMIM8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472479.2	NM_020425	
RADIL	55698	hgsc.bcm.edu	37	7	4874250	4874250	+	Silent	SNP	G	G	A	rs76862906	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:4874250G>A	ENST00000399583.3	-	4	1591	c.1404C>T	c.(1402-1404)cgC>cgT	p.R468R	RADIL_ENST00000536091.1_Silent_p.R468R|RADIL_ENST00000538469.1_Silent_p.R228R	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	468					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		AGACAGTCTCGCGGATCAGCC	0.701													G|||	414	0.0826677	0.0938	0.0389	5008	,	,		10722	0.1508		0.0586	False		,,,				2504	0.0532				p.R468R		Atlas-SNP	.											.	RADIL	110	.	0			c.C1404T						PASS	.						15.0	20.0	18.0					7																	4874250		2045	4178	6223	SO:0001819	synonymous_variant	55698	exon4			AGTCTCGCGGATC	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.1404C>T	7.37:g.4874250G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			G|0.921;A|0.079	0.079	strong		0.701	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
TULP2	7288	hgsc.bcm.edu	37	19	49391404	49391404	+	Missense_Mutation	SNP	C	C	T	rs8112811	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49391404C>T	ENST00000221399.3	-	8	895	c.751G>A	c.(751-753)Gac>Aac	p.D251N		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	251			D -> N (in dbSNP:rs8112811).		visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		CTCATATGGTCGCTGTCCGTG	0.622													C|||	1076	0.214856	0.41	0.2017	5008	,	,		19229	0.0665		0.1262	False		,,,				2504	0.2045				p.D251N		Atlas-SNP	.											.	TULP2	60	.	0			c.G751A						PASS	.	C	ASN/ASP	1491,2915	474.6+/-357.0	251,989,963	94.0	63.0	73.0		751	-7.8	0.0	19	dbSNP_116	73	1028,7572	219.0+/-257.2	61,906,3333	yes	missense	TULP2	NM_003323.2	23	312,1895,4296	TT,TC,CC		11.9535,33.8402,19.368	benign	251/521	49391404	2519,10487	2203	4300	6503	SO:0001583	missense	7288	exon8			TATGGTCGCTGTC	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"""cancer/testis antigen 65"""	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.751G>A	19.37:g.49391404C>T	ENSP00000221399:p.Asp251Asn	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	153	81	0.529412	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	37	CCDS12739.1	423	0.1936813186813187	203	0.41260162601626016	74	0.20441988950276244	42	0.07342657342657342	104	0.13720316622691292	C	0.828	-0.746256	0.03065	0.338402	0.119535	ENSG00000104804	ENST00000221399;ENST00000518572	D;T	0.82433	-1.61;2.26	3.9	-7.8	0.01214	.	21.342800	0.00166	N	0.000000	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	P	0.34615	0.459	B	0.18871	0.023	T	0.08764	-1.0706	9	0.14656	T	0.56	5.8448	4.3174	0.11000	0.1014:0.4134:0.3042:0.181	rs8112811;rs17847565;rs52800287;rs59119925;rs8112811	251	O00295	TULP2_HUMAN	N	251;205	ENSP00000221399:D251N;ENSP00000428420:D205N	ENSP00000221399:D251N	D	-	1	0	TULP2	54083216	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.866000	0.01647	-2.765000	0.00368	-1.113000	0.02065	GAC	C|0.790;T|0.210	0.210	strong		0.622	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	
CEMP1	752014	hgsc.bcm.edu	37	16	2580755	2580755	+	Missense_Mutation	SNP	G	G	C	rs76722821	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2580755G>C	ENST00000567119.1	-	1	654	c.320C>G	c.(319-321)gCg>gGg	p.A107G	AMDHD2_ENST00000413459.3_Missense_Mutation_p.A594P|AMDHD2_ENST00000302956.4_3'UTR|CEMP1_ENST00000565480.1_Intron|MIR3178_ENST00000581887.1_RNA|AMDHD2_ENST00000565570.1_3'UTR|CEMP1_ENST00000382350.1_Missense_Mutation_p.A107G	NM_001048212.3	NP_001041677.1	Q6PRD7	CEMP1_HUMAN	cementum protein 1	107						cytoplasm (GO:0005737)				lung(1)|skin(1)	2						GCAGGGCCTCGCCTGAGGGAG	0.627													G|||	40	0.00798722	0.0	0.0173	5008	,	,		18584	0.0		0.0258	False		,,,				2504	0.002				p.A594P		Atlas-SNP	.											.	AMDHD2	33	.	0			c.G1780C						PASS	.	G	PRO/ALA,GLY/ALA	12,3928		0,12,1958	31.0	36.0	35.0		1780,320	0.6	0.0	16	dbSNP_131	35	141,8143		5,131,4006	yes	missense,missense	AMDHD2,CEMP1	NM_001145815.1,NM_001048212.3	27,60	5,143,5964	CC,CG,GG		1.7021,0.3046,1.2516	probably-damaging,probably-damaging	594/595,107/248	2580755	153,12071	1970	4142	6112	SO:0001583	missense	51005	exon11			GGCCTCGCCTGAG	AY584596	CCDS42108.1	16p13.3	2006-09-22							32553	protein-coding gene	gene with protein product	"""cementum protein-23"""	611113				16263347	Standard	NM_001048212		Approved	CP-23	uc002cqr.3	Q6PRD7		ENST00000567119.1:c.320C>G	16.37:g.2580755G>C	ENSP00000457380:p.Ala107Gly	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_001145815	B2RUY1	Missense_Mutation	SNP	ENST00000567119.1	37	CCDS42108.1	20|20	0.009157509157509158|0.009157509157509158	0|0	0.0|0.0	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	14|14	0.018469656992084433|0.018469656992084433	G|G	3.474|3.474	-0.107349|-0.107349	0.06924|0.06924	0.003046|0.003046	0.017021|0.017021	ENSG00000205923|ENSG00000162066	ENST00000382350|ENST00000413459	T|.	0.55234|.	0.53|.	0.559|0.559	0.559|0.559	0.17272|0.17272	.|.	.|.	.|.	.|.	.|.	T|T	0.38241|0.38241	0.1033|0.1033	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	D|D	0.65815|0.56968	0.995|0.978	D|P	0.69142|0.61800	0.962|0.894	T|T	0.28618|0.28618	-1.0038|-1.0038	7|6	0.87932|0.87932	D|D	0|0	.|.	.|.	.|.	.|.	.|.	107|594	Q6PRD7|Q9Y303-3	CEMP1_HUMAN|.	G|P	107|594	ENSP00000371787:A107G|.	ENSP00000371787:A107G|ENSP00000391596:A594P	A|A	-|+	2|1	0|0	CEMP1|AMDHD2	2520756|2520756	0.005000|0.005000	0.15991|0.15991	0.001000|0.001000	0.08648|0.08648	0.002000|0.002000	0.02628|0.02628	-0.342000|-0.342000	0.07801|0.07801	0.556000|0.556000	0.29098|0.29098	0.561000|0.561000	0.74099|0.74099	GCG|GCC	G|0.990;C|0.010	0.010	strong		0.627	CEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435686.1	NM_001048212	
SPATA20	64847	hgsc.bcm.edu	37	17	48625928	48625928	+	Missense_Mutation	SNP	C	C	G	rs8076632	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48625928C>G	ENST00000356488.4	+	3	345	c.262C>G	c.(262-264)Cag>Gag	p.Q88E	SPATA20_ENST00000006658.6_Missense_Mutation_p.Q104E|SPATA20_ENST00000393244.3_Missense_Mutation_p.Q44E|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	88			Q -> E (in dbSNP:rs8076632). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CCCCTGGGGACAGGAAGCCTT	0.637													C|||	1690	0.33746	0.6831	0.2767	5008	,	,		18074	0.0625		0.3499	False		,,,				2504	0.184				p.Q104E		Atlas-SNP	.											SPATA20,NS,carcinoma,0,1	SPATA20	59	1	0			c.C310G						PASS	.	C	GLU/GLN	2797,1607	646.3+/-398.3	904,989,309	72.0	81.0	78.0		310	4.6	1.0	17	dbSNP_116	78	3108,5492	464.2+/-366.2	561,1986,1753	yes	missense	SPATA20	NM_022827.2	29	1465,2975,2062	GG,GC,CC		36.1395,36.4896,45.4091	benign	104/803	48625928	5905,7099	2202	4300	6502	SO:0001583	missense	64847	exon4			TGGGGACAGGAAG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.262C>G	17.37:g.48625928C>G	ENSP00000348878:p.Gln88Glu	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	746	0.3415750915750916	324	0.6585365853658537	113	0.31215469613259667	48	0.08391608391608392	261	0.34432717678100266	C	10.44	1.351888	0.24512	0.635104	0.361395	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.35973	1.28;1.28;1.28	4.59	4.59	0.56863	Thioredoxin-like fold (2);Domain of unknown function DUF255 (1);	0.057503	0.64402	D	0.000001	T	0.00012	0.0000	N	0.00507	-1.42	0.20403	P	0.9999042779	B;B;B	0.14012	0.009;0.009;0.003	B;B;B	0.12156	0.007;0.007;0.007	T	0.39375	-0.9617	9	0.02654	T	1	-19.6545	15.7482	0.77962	0.0:1.0:0.0:0.0	rs8076632;rs11559097;rs17855972;rs57357545;rs8076632	88;88;104	B4DZC5;Q8TB22;Q8TB22-2	.;SPT20_HUMAN;.	E	104;88;44	ENSP00000006658:Q104E;ENSP00000348878:Q88E;ENSP00000376935:Q44E	ENSP00000006658:Q104E	Q	+	1	0	SPATA20	45980927	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.181000	0.65054	2.368000	0.80403	0.561000	0.74099	CAG	C|0.583;G|0.417	0.417	strong		0.637	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
VIPR1	7433	hgsc.bcm.edu	37	3	42568929	42568929	+	Silent	SNP	T	T	C	rs2229722	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:42568929T>C	ENST00000325123.4	+	5	557	c.444T>C	c.(442-444)atT>atC	p.I148I	VIPR1_ENST00000543411.1_Silent_p.I100I|VIPR1-AS1_ENST00000593611.1_RNA|VIPR1_ENST00000473575.1_3'UTR|VIPR1_ENST00000438259.2_Intron|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1-AS1_ENST00000602176.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|VIPR1_ENST00000433647.1_Silent_p.I107I|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000593621.1_RNA|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000601312.1_RNA	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	148					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		GCTACACCATTGGCTACGGCC	0.607													C|||	1859	0.371206	0.4667	0.2839	5008	,	,		16535	0.5784		0.1511	False		,,,				2504	0.317				p.I148I		Atlas-SNP	.											.	VIPR1	45	.	0			c.T444C						PASS	.	C		1915,2491	627.0+/-394.8	389,1137,677	122.0	108.0	113.0		444	0.6	0.8	3	dbSNP_98	113	1389,7211	754.1+/-407.5	107,1175,3018	no	coding-synonymous	VIPR1	NM_004624.3		496,2312,3695	CC,CT,TT		16.1512,43.4635,25.4037		148/458	42568929	3304,9702	2203	4300	6503	SO:0001819	synonymous_variant	7433	exon5			CACCATTGGCTAC	AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12694	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 1"""	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.444T>C	3.37:g.42568929T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	49	0.576471	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Silent	SNP	ENST00000325123.4	37	CCDS2698.1																																																																																			T|0.722;C|0.278	0.278	strong		0.607	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624	
FRG1	2483	hgsc.bcm.edu	37	4	190878589	190878589	+	Missense_Mutation	SNP	A	A	G	rs561930100	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:190878589A>G	ENST00000226798.4	+	6	691	c.469A>G	c.(469-471)Att>Gtt	p.I157V	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	157					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TAGCTGCTTTATTAGATGCAA	0.363													.|||	11	0.00219649	0.0015	0.0058	5008	,	,		28209	0.001		0.004	False		,,,				2504	0.0				p.I157V		Atlas-SNP	.											FRG1,NS,carcinoma,0,1	FRG1	76	1	0			c.A469G						scavenged	.						15.0	18.0	17.0					4																	190878589		2157	4266	6423	SO:0001583	missense	2483	exon6			TGCTTTATTAGAT	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.469A>G	4.37:g.190878589A>G	ENSP00000226798:p.Ile157Val	Somatic	172	3	0.0174419		WXS	Illumina HiSeq	Phase_I	191	6	0.0314136	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	10.14	1.269261	0.23221	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.42900	2.02;0.96	4.19	4.19	0.49359	Actin cross-linking (1);	0.049103	0.85682	D	0.000000	T	0.25938	0.0632	L	0.28014	0.82	0.48696	D	0.999699	B	0.09022	0.002	B	0.18871	0.023	T	0.08086	-1.0739	10	0.20519	T	0.43	-23.3336	6.6273	0.22837	0.8897:0.0:0.1103:0.0	.	157	Q14331	FRG1_HUMAN	V	157;29;94	ENSP00000226798:I157V;ENSP00000435943:I94V	ENSP00000226798:I157V	I	+	1	0	FRG1	191115583	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	5.196000	0.65136	1.677000	0.50941	0.373000	0.22412	ATT	.	.	none		0.363	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036951	33036951	+	Missense_Mutation	SNP	A	A	G	rs386699855|rs2308930	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33036951A>G	ENST00000419277.1	-	4	602	c.473T>C	c.(472-474)cTg>cCg	p.L158P	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.L158P	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	158	Alpha-2.|Ig-like C1-type.		L -> P (in allele DPA1*02:01, allele DPA1*02:02 and allele DPA1*04:01; dbSNP:rs2308930).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CTCAGTGACCAGCTCCCCGTT	0.567													G|||	2199	0.439097	0.5802	0.2839	5008	,	,		19044	0.6796		0.1899	False		,,,				2504	0.3671				p.L158P		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.T473C						PASS	.	G	PRO/LEU,PRO/LEU,PRO/LEU	1408,1610		327,754,428	163.0	188.0	179.0		473,473,473	1.5	0.0	6	dbSNP_126	179	937,4479		72,793,1843	no	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	98,98,98	399,1547,2271	GG,GA,AA		17.3006,46.6534,27.8041	benign,benign,benign	158/261,158/261,158/261	33036951	2345,6089	1509	2708	4217	SO:0001583	missense	3113	exon3			GTGACCAGCTCCC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.473T>C	6.37:g.33036951A>G	ENSP00000393566:p.Leu158Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	112	45	0.401786	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	830	0.38003663003663	264	0.5365853658536586	80	0.22099447513812154	364	0.6363636363636364	122	0.16094986807387862	G	0.004	-2.279822	0.00254	0.466534	0.173006	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.02656	4.21;4.21;4.21	3.4	1.52	0.23074	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.841204	0.10189	N	0.704860	T	0.00144	0.0004	N	0.00066	-2.3	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38757	-0.9646	9	0.02654	T	1	.	3.676	0.08292	0.3205:0.0:0.5087:0.1708	rs2308930	158	P20036	DPA1_HUMAN	P	158;158;125;158	ENSP00000393566:L158P;ENSP00000402872:L158P;ENSP00000390929:L158P	ENSP00000393566:L158P	L	-	2	0	HLA-DPA1	33144929	0.000000	0.05858	0.007000	0.13788	0.408000	0.30992	-1.645000	0.02000	-0.065000	0.13021	-0.131000	0.14894	CTG	A|0.698;G|0.302	0.302	strong		0.567	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
NRCAM	4897	hgsc.bcm.edu	37	7	107800936	107800936	+	Splice_Site	SNP	C	C	T	rs17155094	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:107800936C>T	ENST00000425651.2	-	28	3467	c.3468G>A	c.(3466-3468)gcG>gcA	p.A1156A	NRCAM_ENST00000379022.4_Splice_Site_p.A1156A|NRCAM_ENST00000351718.4_Splice_Site_p.A1035A|NRCAM_ENST00000413765.2_Splice_Site_p.A1032A|NRCAM_ENST00000379028.3_Splice_Site_p.A1156A|NRCAM_ENST00000379024.4_Splice_Site_p.A1044A	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1156	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GGCTTGCCATCGCTGGAAAAC	0.453													C|||	113	0.0225639	0.0038	0.0144	5008	,	,		16131	0.0129		0.0378	False		,,,				2504	0.0481				p.A1156A		Atlas-SNP	.											.	NRCAM	267	.	0			c.G3468A						PASS	.	C	,,,,	29,4377	35.2+/-66.4	0,29,2174	81.0	71.0	74.0		3468,3189,3132,3096,3105	-10.9	0.2	7	dbSNP_123	74	303,8297	110.4+/-170.8	5,293,4002	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	,,,,	5,322,6176	TT,TC,CC		3.5233,0.6582,2.5527	,,,,	1156/1305,1063/1212,1044/1193,1032/1181,1035/1184	107800936	332,12674	2203	4300	6503	SO:0001630	splice_region_variant	4897	exon28			TGCCATCGCTGGA		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3467-1G>A	7.37:g.107800936C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	37	CCDS47686.1	43	0.019688644688644688	3	0.006097560975609756	7	0.019337016574585635	6	0.01048951048951049	27	0.03562005277044855	C	1.690	-0.504279	0.04261	0.006582	0.035233	ENSG00000091129	ENST00000445634	.	.	.	5.45	-10.9	0.00192	.	.	.	.	.	T	0.17704	0.0425	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63056	-0.6722	4	.	.	.	.	10.2814	0.43541	0.0:0.3164:0.3742:0.3094	rs17155094;rs17155094	.	.	.	Q	55	.	.	R	-	2	0	NRCAM	107588172	0.072000	0.21174	0.240000	0.24138	0.871000	0.50021	-0.651000	0.05372	-3.512000	0.00149	-0.980000	0.02579	CGA	C|0.975;T|0.025	0.025	strong		0.453	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	Silent
ZFPM2	23414	hgsc.bcm.edu	37	8	106814029	106814029	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:106814029C>A	ENST00000407775.2	+	8	1969	c.1719C>A	c.(1717-1719)agC>agA	p.S573R	RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|ZFPM2_ENST00000517361.1_Missense_Mutation_p.S441R|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000524045.2_RNA|ZFPM2_ENST00000378472.4_Missense_Mutation_p.S304R|ZFPM2_ENST00000522296.1_3'UTR|ZFPM2_ENST00000520492.1_Missense_Mutation_p.S441R|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000521622.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	573					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			ATTGCAGCAGCCGATGGCAGC	0.448																																					p.S573R		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C1719A						PASS	.						128.0	131.0	130.0					8																	106814029		1929	4136	6065	SO:0001583	missense	23414	exon8			CAGCAGCCGATGG	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.1719C>A	8.37:g.106814029C>A	ENSP00000384179:p.Ser573Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	185	93	0.502703	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.842831	0.51057	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.25579	1.79;2.28;2.28;3.53	5.86	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.48059	0.1479	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44711	-0.9310	10	0.44086	T	0.13	.	11.619	0.51106	0.0:0.8135:0.0:0.1865	.	573	Q8WW38	FOG2_HUMAN	R	573;441;441;304	ENSP00000384179:S573R;ENSP00000430757:S441R;ENSP00000428720:S441R;ENSP00000367733:S304R	ENSP00000367733:S304R	S	+	3	2	ZFPM2	106883205	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.698000	0.37794	1.485000	0.48380	0.655000	0.94253	AGC	.	.	none		0.448	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
CARS2	79587	hgsc.bcm.edu	37	13	111293915	111293915	+	Missense_Mutation	SNP	T	T	G	rs1043886	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:111293915T>G	ENST00000257347.4	-	15	1727	c.1664A>C	c.(1663-1665)cAa>cCa	p.Q555P	CARS2_ENST00000535398.1_5'Flank	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	555			Q -> P (in dbSNP:rs1043886). {ECO:0000269|PubMed:15489334}.		cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	TTTTGTCCTTTGATCCAGCAG	0.537													T|||	410	0.081869	0.0477	0.0778	5008	,	,		20456	0.0903		0.159	False		,,,				2504	0.0429				p.Q555P		Atlas-SNP	.											.	CARS2	37	.	0			c.A1664C						PASS	.	T	PRO/GLN	256,4150	146.1+/-180.8	6,244,1953	369.0	292.0	318.0		1664	-0.9	0.0	13	dbSNP_86	318	1102,7498	228.9+/-263.8	67,968,3265	yes	missense	CARS2	NM_024537.2	76	73,1212,5218	GG,GT,TT		12.814,5.8103,10.4413	benign	555/565	111293915	1358,11648	2203	4300	6503	SO:0001583	missense	79587	exon15			GTCCTTTGATCCA	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.1664A>C	13.37:g.111293915T>G	ENSP00000257347:p.Gln555Pro	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	197	89	0.451777	NM_024537	Q8NI84|Q96IV4	Missense_Mutation	SNP	ENST00000257347.4	37	CCDS9514.1	223	0.1021062271062271	28	0.056910569105691054	27	0.07458563535911603	48	0.08391608391608392	120	0.158311345646438	T	11.37	1.619830	0.28801	0.058103	0.12814	ENSG00000134905	ENST00000257347	T	0.30714	1.52	4.51	-0.906	0.10524	.	0.609617	0.15893	N	0.239458	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27502	-1.0072	9	0.33141	T	0.24	-28.0496	7.7764	0.29039	0.1167:0.0:0.5896:0.2937	rs1043886;rs3183552;rs17845109;rs17857900;rs60947481;rs1043886	555	Q9HA77	SYCM_HUMAN	P	555	ENSP00000257347:Q555P	ENSP00000257347:Q555P	Q	-	2	0	CARS2	110091916	0.085000	0.21516	0.002000	0.10522	0.652000	0.38707	0.017000	0.13399	-0.031000	0.13781	0.379000	0.24179	CAA	T|0.901;G|0.099	0.099	strong		0.537	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537	
MUC17	140453	hgsc.bcm.edu	37	7	100682571	100682571	+	Missense_Mutation	SNP	T	T	C	rs142739196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100682571T>C	ENST00000306151.4	+	3	7938	c.7874T>C	c.(7873-7875)aTc>aCc	p.I2625T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2625	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AGCATGCCAATCTCAACTCCT	0.448																																					p.I2625T		Atlas-SNP	.											.	MUC17	804	.	0			c.T7874C						PASS	.	C	THR/ILE	14,4392	823.9+/-416.5	0,14,2189	240.0	244.0	243.0		7874	-1.4	0.0	7	dbSNP_134	243	53,8547	815.6+/-407.0	0,53,4247	yes	missense	MUC17	NM_001040105.1	89	0,67,6436	CC,CT,TT		0.6163,0.3177,0.5151	benign	2625/4494	100682571	67,12939	2203	4300	6503	SO:0001583	missense	140453	exon3			TGCCAATCTCAAC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.7874T>C	7.37:g.100682571T>C	ENSP00000302716:p.Ile2625Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	54	13	0.240741	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	14	0.00641025641025641	0	0.0	8	0.022099447513812154	0	0.0	6	0.0079155672823219	C	0.004	-2.245422	0.00271	0.003177	0.006163	ENSG00000169876	ENST00000306151	T	0.02421	4.3	0.673	-1.35	0.09114	.	.	.	.	.	T	0.00524	0.0017	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.43507	-0.9387	9	0.02654	T	1	.	1.0372	0.01551	0.1756:0.3823:0.1583:0.2838	.	2625	Q685J3	MUC17_HUMAN	T	2625	ENSP00000302716:I2625T	ENSP00000302716:I2625T	I	+	2	0	MUC17	100469291	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-7.796000	0.00029	-3.904000	0.00093	-3.178000	0.00056	ATC	T|0.993;C|0.007	0.007	strong		0.448	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
H6PD	9563	hgsc.bcm.edu	37	1	9307033	9307033	+	Silent	SNP	G	G	A	rs7524046	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:9307033G>A	ENST00000377403.2	+	3	938	c.636G>A	c.(634-636)gcG>gcA	p.A212A	H6PD_ENST00000602477.1_Silent_p.A223A	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	212	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		AGGCTGTGGCGCAGATCCTGC	0.602													g|||	1115	0.222644	0.1074	0.2622	5008	,	,		15526	0.4038		0.2445	False		,,,				2504	0.1411				p.A212A		Atlas-SNP	.											.	H6PD	71	.	0			c.G636A						PASS	.	A		698,3708	294.4+/-283.1	51,596,1556	94.0	91.0	92.0		636	-10.1	0.6	1	dbSNP_116	92	2054,6546	357.1+/-330.6	238,1578,2484	no	coding-synonymous	H6PD	NM_004285.3		289,2174,4040	AA,AG,GG		23.8837,15.842,21.1595		212/792	9307033	2752,10254	2203	4300	6503	SO:0001819	synonymous_variant	9563	exon3			TGTGGCGCAGATC	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"""glucose dehyrogenase"""	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.636G>A	1.37:g.9307033G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	109	54	0.495413	NM_004285	Q4TT33|Q66I35|Q68DT3	Silent	SNP	ENST00000377403.2	37	CCDS101.1																																																																																			G|0.772;A|0.228	0.228	strong		0.602	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
IGSF9B	22997	hgsc.bcm.edu	37	11	133815981	133815981	+	Silent	SNP	C	C	G	rs10894768	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:133815981C>G	ENST00000321016.8	-	2	467	c.237G>C	c.(235-237)ccG>ccC	p.P79P	IGSF9B_ENST00000533871.2_Silent_p.P79P			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	79	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CCACGTGCGGCGGGTAGTAGC	0.617													G|||	1776	0.354633	0.3011	0.438	5008	,	,		16482	0.5208		0.2992	False		,,,				2504	0.2536				p.P79P		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G237C						PASS	.	G		1154,3082		154,846,1118	48.0	59.0	55.0		237	-11.4	0.0	11	dbSNP_120	55	2510,5934		370,1770,2082	no	coding-synonymous	IGSF9B	NM_014987.1		524,2616,3200	GG,GC,CC		29.7252,27.2427,28.8959		79/1350	133815981	3664,9016	2118	4222	6340	SO:0001819	synonymous_variant	22997	exon2			GTGCGGCGGGTAG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.237G>C	11.37:g.133815981C>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	130	36	0.276923	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				C|0.633;G|0.367	0.367	strong		0.617	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189215	11189215	+	Silent	SNP	C	C	A	rs151245433	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11189215C>A	ENST00000382435.4	+	1	819	c.600C>A	c.(598-600)ggC>ggA	p.G200G		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	200						integral component of membrane (GO:0016021)		p.G200G(1)									TCCTGGGAGGCCTGGCGCTGT	0.592																																					p.G200G		Atlas-SNP	.											AMAC1L2,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C600A						PASS	.						106.0	112.0	110.0					8																	11189215		2203	4300	6503	SO:0001819	synonymous_variant	83650	exon1			GGGAGGCCTGGCG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.600C>A	8.37:g.11189215C>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	173	25	0.144509	NM_054028	A2RRL6	Silent	SNP	ENST00000382435.4	37	CCDS5980.1																																																																																			C|0.988;A|0.011	0.011	strong		0.592	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
KCNJ9	3765	hgsc.bcm.edu	37	1	160057522	160057522	+	Missense_Mutation	SNP	C	C	T	rs3001040	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:160057522C>T	ENST00000368088.3	+	3	1339	c.1097C>T	c.(1096-1098)gCg>gTg	p.A366V		NM_004983.2	NP_004974.2	Q92806	KCNJ9_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 9	366			A -> V (in dbSNP:rs3001040). {ECO:0000269|PubMed:10659995, ECO:0000269|PubMed:10913335}.		synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein activated inward rectifier potassium channel activity (GO:0015467)			biliary_tract(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|skin(2)	16	all_cancers(52;5.86e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			gaggagggggcgggggagggg	0.662													c|||	1243	0.248203	0.1475	0.2824	5008	,	,		3073	0.2718		0.3688	False		,,,				2504	0.2117				p.A366V		Atlas-SNP	.											.	KCNJ9	35	.	0			c.C1097T	GRCh37	CM012776	KCNJ9	M	rs3001040	PASS	.		VAL/ALA	421,3293		34,353,1470	5.0	5.0	5.0		1097	3.5	0.0	1	dbSNP_101	5	1609,5435		218,1173,2131	yes	missense	KCNJ9	NM_004983.2	64	252,1526,3601	TT,TC,CC		22.8421,11.3355,18.8697	benign	366/394	160057522	2030,8728	1857	3522	5379	SO:0001583	missense	3765	exon3			AGGGGGCGGGGGA	U52152	CCDS1194.1	1q23.2	2011-07-05			ENSG00000162728	ENSG00000162728		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6270	protein-coding gene	gene with protein product		600932				8575783, 16382105	Standard	NM_004983		Approved	Kir3.3, GIRK3	uc001fuy.1	Q92806	OTTHUMG00000024072	ENST00000368088.3:c.1097C>T	1.37:g.160057522C>T	ENSP00000357067:p.Ala366Val	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	34	9	0.264706	NM_004983	Q5JW75	Missense_Mutation	SNP	ENST00000368088.3	37	CCDS1194.1	635	0.2907509157509158	83	0.16869918699186992	108	0.2983425414364641	160	0.27972027972027974	284	0.37467018469656993	c	11.19	1.564343	0.27915	0.113355	0.228421	ENSG00000162728	ENST00000368088	D	0.88431	-2.38	4.42	3.51	0.40186	.	0.659602	0.12116	U	0.498063	T	0.61961	0.2389	N	0.08118	0	0.80722	P	0.0	B	0.24132	0.098	B	0.12837	0.008	T	0.42137	-0.9469	9	0.33141	T	0.24	.	9.8547	0.41079	0.0:0.901:0.0:0.099	rs3001040;rs3795338	366	Q92806	IRK9_HUMAN	V	366	ENSP00000357067:A366V	ENSP00000357067:A366V	A	+	2	0	KCNJ9	158324146	0.286000	0.24305	0.007000	0.13788	0.815000	0.46073	1.910000	0.39927	0.865000	0.35603	0.550000	0.68814	GCG	C|0.709;T|0.291	0.291	strong		0.662	KCNJ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060628.1	NM_004983	
ZNF516	9658	hgsc.bcm.edu	37	18	74091541	74091541	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:74091541C>T	ENST00000443185.2	-	4	2846	c.2529G>A	c.(2527-2529)ggG>ggA	p.G843G	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	843					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		ACCCCGGCATCCCCCCTGGCA	0.637																																					p.G843G		Atlas-SNP	.											ZNF516,NS,carcinoma,-1,2	ZNF516	102	2	0			c.G2529A						scavenged	.						59.0	71.0	67.0					18																	74091541		1927	4118	6045	SO:0001819	synonymous_variant	9658	exon4			CGGCATCCCCCCT	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.2529G>A	18.37:g.74091541C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	174	2	0.0114943	NM_014643		Silent	SNP	ENST00000443185.2	37																																																																																				.	.	none		0.637	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
MICAL2	9645	hgsc.bcm.edu	37	11	12225946	12225946	+	Silent	SNP	T	T	G	rs3763823	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:12225946T>G	ENST00000256194.4	+	4	702	c.414T>G	c.(412-414)cgT>cgG	p.R138R	MICAL2_ENST00000527546.1_Silent_p.R138R|MICAL2_ENST00000342902.5_Silent_p.R138R|MICAL2_ENST00000537344.1_Silent_p.R138R|MICAL2_ENST00000379612.3_Silent_p.R138R|MICAL2_ENST00000527195.1_3'UTR	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	138	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		ATGACCTTCGTGGCCTGGGAG	0.547													G|||	3511	0.701078	0.8911	0.7089	5008	,	,		20509	0.6508		0.5905	False		,,,				2504	0.6043				p.R138R		Atlas-SNP	.											MICAL2,colon,carcinoma,0,2	MICAL2	114	2	0			c.T414G						PASS	.	G		3683,719	295.9+/-283.9	1531,621,49	114.0	101.0	105.0		414	0.2	1.0	11	dbSNP_107	105	4804,3784	535.8+/-382.9	1333,2138,823	no	coding-synonymous	MICAL2	NM_014632.2		2864,2759,872	GG,GT,TT		44.0615,16.3335,34.6651		138/1125	12225946	8487,4503	2201	4294	6495	SO:0001819	synonymous_variant	9645	exon4			CCTTCGTGGCCTG	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.414T>G	11.37:g.12225946T>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																			T|0.332;G|0.668	0.668	strong		0.547	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
PICALM	8301	hgsc.bcm.edu	37	11	85692181	85692181	+	Silent	SNP	A	A	C	rs76719109	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:85692181A>C	ENST00000393346.3	-	17	1918	c.1770T>G	c.(1768-1770)gcT>gcG	p.A590A	PICALM_ENST00000528398.1_Silent_p.A489A|PICALM_ENST00000356360.5_Silent_p.A590A|PICALM_ENST00000532317.1_Silent_p.A540A|PICALM_ENST00000526033.1_Silent_p.A583A			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	590					axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)	p.A590A(1)		endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				CCATTGTTGCAGCATTCCAAG	0.343			T	"""MLLT10, MLL"""	"""TALL, AML, """								A|||	3119	0.622804	0.6097	0.585	5008	,	,		17069	0.6577		0.5875	False		,,,				2504	0.6677				p.A590A		Atlas-SNP	.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	PICALM,colon,carcinoma,0,4	PICALM	82	4	1	Substitution - coding silent(1)	urinary_tract(1)	c.T1770G						PASS	.	A	,,,	2726,1680	655.1+/-399.9	837,1052,314	137.0	131.0	133.0		1620,1749,1467,1770	3.2	1.0	11	dbSNP_130	133	5119,3479	635.7+/-399.0	1546,2027,726	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PICALM	NM_001008660.2,NM_001206946.1,NM_001206947.1,NM_007166.3	,,,	2383,3079,1040	CC,CA,AA		40.4629,38.1298,39.6724	,,,	540/611,583/646,489/552,590/653	85692181	7845,5159	2203	4299	6502	SO:0001819	synonymous_variant	8301	exon17			TGTTGCAGCATTC	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.1770T>G	11.37:g.85692181A>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_007166	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Silent	SNP	ENST00000393346.3	37	CCDS8272.1	1306|1306	0.597985347985348|0.597985347985348	296|296	0.6016260162601627|0.6016260162601627	205|205	0.5662983425414365|0.5662983425414365	363|363	0.6346153846153846|0.6346153846153846	442|442	0.58311345646438|0.58311345646438	A|A	10.76|10.76	1.440820|1.440820	0.25900|0.25900	0.618702|0.618702	0.595371|0.595371	ENSG00000073921|ENSG00000073921	ENST00000529760;ENST00000532603;ENST00000526961;ENST00000530542|ENST00000530692;ENST00000529016	.|.	.|.	.|.	5.51|5.51	3.17|3.17	0.36434|0.36434	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.44236|0.44236	-0.9341|-0.9341	3|3	.|.	.|.	.|.	-4.4033|-4.4033	5.7025|5.7025	0.17891|0.17891	0.7376:0.0:0.1307:0.1317|0.7376:0.0:0.1307:0.1317	rs694353;rs1127490;rs1804605;rs2508687;rs3183524;rs11553488;rs17434978;rs17817702;rs56960791;rs694353|rs694353;rs1127490;rs1804605;rs2508687;rs3183524;rs11553488;rs17434978;rs17817702;rs56960791;rs694353	.|.	.|.	.|.	G|R	238;92;194;288|119;237	.|.	.|.	C|L	-|-	1|2	0|0	PICALM|PICALM	85369829|85369829	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.399000|2.399000	0.44495|0.44495	1.010000|1.010000	0.39314|0.39314	0.477000|0.477000	0.44152|0.44152	TGC|CTG	A|0.399;C|0.601	0.601	strong		0.343	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166	
BLM	641	hgsc.bcm.edu	37	15	91354505	91354505	+	Silent	SNP	C	C	T	rs1063147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91354505C>T	ENST00000355112.3	+	21	4063	c.3945C>T	c.(3943-3945)ctC>ctT	p.L1315L	BLM_ENST00000560509.1_Silent_p.L1184L|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1315					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			CTGAGGAGCTCGACGAGGAAA	0.493			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome				C|||	665	0.132788	0.1278	0.1037	5008	,	,		17547	0.1875		0.167	False		,,,				2504	0.0685				p.L1315L		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.C3945T						PASS	.	C		559,3837	251.2+/-258.0	33,493,1672	78.0	79.0	79.0		3945	-6.6	0.0	15	dbSNP_86	79	1579,7017	295.4+/-302.4	142,1295,2861	no	coding-synonymous	BLM	NM_000057.2		175,1788,4533	TT,TC,CC		18.369,12.7161,16.4563		1315/1418	91354505	2138,10854	2198	4298	6496	SO:0001819	synonymous_variant	641	exon21	Familial Cancer Database		GGAGCTCGACGAG	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3945C>T	15.37:g.91354505C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	127	69	0.543307	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	37	CCDS10363.1																																																																																			C|0.847;T|0.153	0.153	strong		0.493	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
HSPG2	3339	hgsc.bcm.edu	37	1	22214127	22214127	+	Silent	SNP	A	A	G	rs2229478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22214127A>G	ENST00000374695.3	-	8	823	c.744T>C	c.(742-744)ctT>ctC	p.L248L		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	248					angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TCGTCTCCACAAGGAGAGAGA	0.592													G|||	2686	0.536342	0.7065	0.5793	5008	,	,		17253	0.6498		0.3191	False		,,,				2504	0.3824				p.L248L		Atlas-SNP	.											.	HSPG2	311	.	0			c.T744C						PASS	.	G		2774,1632	500.3+/-364.7	854,1066,283	103.0	115.0	110.0		744	0.1	0.0	1	dbSNP_98	110	2784,5816	678.5+/-403.5	446,1892,1962	no	coding-synonymous	HSPG2	NM_005529.5		1300,2958,2245	GG,GA,AA		32.3721,37.0404,42.7341		248/4392	22214127	5558,7448	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon8			CTCCACAAGGAGA	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.744T>C	1.37:g.22214127A>G		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	221	114	0.515837	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1	1139	0.5215201465201466	315	0.6402439024390244	198	0.5469613259668509	372	0.6503496503496503	254	0.33509234828496043	G	10.30	1.311032	0.23821	0.629596	0.323721	ENSG00000142798	ENST00000412328;ENST00000374673	T;D	0.91945	0.45;-2.94	4.36	0.117	0.14652	.	0.787170	0.10376	N	0.682166	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.42344	-0.9457	8	0.15499	T	0.54	.	0.6232	0.00782	0.277:0.3437:0.1377:0.2416	rs2229478;rs2254495;rs57283009	171	Q5SZI5	.	S	171;75	ENSP00000405412:L171S;ENSP00000363805:L75S	ENSP00000363805:L75S	L	-	2	0	HSPG2	22086714	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.260000	0.08708	-0.307000	0.08804	-1.325000	0.01285	TTG	A|0.549;G|0.451	0.451	strong		0.592	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
DNAH14	127602	hgsc.bcm.edu	37	1	225211422	225211422	+	Missense_Mutation	SNP	T	T	C	rs75568712	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225211422T>C	ENST00000445597.2	+	9	1270	c.1270T>C	c.(1270-1272)Ttc>Ctc	p.F424L	DNAH14_ENST00000439375.2_Missense_Mutation_p.F405L|DNAH14_ENST00000366849.1_Missense_Mutation_p.F382L|DNAH14_ENST00000430092.1_Missense_Mutation_p.F405L|DNAH14_ENST00000400952.3_Missense_Mutation_p.F405L			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	424				F -> L (in Ref. 3; AAI19718). {ECO:0000305}.	microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AGAAACATTTTTCAAGTTTGT	0.328													T|||	169	0.033746	0.0045	0.036	5008	,	,		16444	0.0129		0.0736	False		,,,				2504	0.0521				p.F405L		Atlas-SNP	.											.	DNAH14	300	.	0			c.T1213C						PASS	.						158.0	138.0	144.0					1																	225211422		692	1589	2281	SO:0001583	missense	127602	exon11			ACATTTTTCAAGT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.1270T>C	1.37:g.225211422T>C	ENSP00000409472:p.Phe424Leu	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	280	133	0.475	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		85	0.03891941391941392	4	0.008130081300813009	15	0.04143646408839779	9	0.015734265734265736	57	0.07519788918205805	T	0.742	-0.776128	0.02951	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000400952;ENST00000366849;ENST00000439375	T;T;T;T;T	0.28895	2.65;1.65;1.6;1.59;1.65	5.37	-0.367	0.12541	.	0.811230	0.10693	N	0.644943	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.26677	-1.0096	10	0.08837	T	0.75	.	1.0652	0.01609	0.1512:0.1812:0.1566:0.511	.	405;405;424	Q0VDD8-4;Q0VDD8-2;Q0VDD8	.;.;DYH14_HUMAN	L	424;405;405;382;405	ENSP00000409472:F424L;ENSP00000414402:F405L;ENSP00000383737:F405L;ENSP00000355814:F382L;ENSP00000392061:F405L	ENSP00000355814:F382L	F	+	1	0	DNAH14	223278045	0.000000	0.05858	0.000000	0.03702	0.592000	0.36648	-0.636000	0.05465	-0.234000	0.09782	0.421000	0.28195	TTC	T|0.955;C|0.045	0.045	strong		0.328	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744127	31744127	+	Nonsense_Mutation	SNP	A	A	T	rs877346	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:31744127A>T	ENST00000399889.2	-	1	430	c.405T>A	c.(403-405)tgT>tgA	p.C135*		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	135						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						AAGGGAAGCCACAGCTTCCAT	0.572													A|||	1593	0.318091	0.1679	0.3473	5008	,	,		17991	0.2688		0.4483	False		,,,				2504	0.4172				p.C135X		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.T405A						PASS	.	A	stop/CYS	948,3458	360.4+/-315.2	101,746,1356	67.0	63.0	64.0		405	2.3	0.1	21	dbSNP_86	64	4176,4424	568.4+/-389.0	1014,2148,1138	yes	stop-gained	KRTAP13-2	NM_181621.3		1115,2894,2494	TT,TA,AA		48.5581,21.5161,39.3972		135/176	31744127	5124,7882	2203	4300	6503	SO:0001587	stop_gained	337959	exon1			GAAGCCACAGCTT	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"""Keratin associated proteins"""	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.405T>A	21.37:g.31744127A>T	ENSP00000382777:p.Cys135*	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_181621		Nonsense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	676	0.30952380952380953	79	0.16056910569105692	127	0.35082872928176795	131	0.229020979020979	339	0.4472295514511873	A	10.96	1.499213	0.26861	0.215161	0.485581	ENSG00000182816	ENST00000399889	.	.	.	4.63	2.31	0.28768	.	1.593970	0.04788	U	0.431189	.	.	.	.	.	.	0.41237	P	0.013387999999999955	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	5.6289	0.17499	0.7863:0.0:0.2137:0.0	rs877346;rs3804009;rs52833590;rs877346	.	.	.	X	135	.	ENSP00000382777:C135X	C	-	3	2	KRTAP13-2	30665998	0.001000	0.12720	0.081000	0.20488	0.063000	0.16089	0.246000	0.18160	0.865000	0.35603	-0.274000	0.10170	TGT	A|0.636;T|0.364	0.364	strong		0.572	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1		
PTGFR	5737	hgsc.bcm.edu	37	1	78958491	78958491	+	Silent	SNP	C	C	T	rs35227129	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:78958491C>T	ENST00000370757.3	+	2	300	c.63C>T	c.(61-63)acC>acT	p.T21T	PTGFR_ENST00000370756.3_Silent_p.T21T|PTGFR_ENST00000370758.1_Silent_p.T21T	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	21					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)			breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	CAAACACAACCTGCCAGACGG	0.453													C|||	157	0.0313498	0.0076	0.0476	5008	,	,		20761	0.001		0.0944	False		,,,				2504	0.0184				p.T21T		Atlas-SNP	.											.	PTGFR	121	.	0			c.C63T						PASS	.	C	,	73,4333	66.4+/-103.9	0,73,2130	75.0	79.0	78.0		63,63	2.4	1.0	1	dbSNP_126	78	831,7769	191.5+/-237.7	32,767,3501	no	coding-synonymous,coding-synonymous	PTGFR	NM_000959.3,NM_001039585.1	,	32,840,5631	TT,TC,CC		9.6628,1.6568,6.9506	,	21/360,21/298	78958491	904,12102	2203	4300	6503	SO:0001819	synonymous_variant	5737	exon2			CACAACCTGCCAG	AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"""GPCR / Class A : Prostanoid receptors"""	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.63C>T	1.37:g.78958491C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	NM_000959	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Silent	SNP	ENST00000370757.3	37	CCDS686.1																																																																																			C|0.937;T|0.063	0.063	strong		0.453	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959	
UBXN2B	137886	hgsc.bcm.edu	37	8	59329438	59329438	+	Silent	SNP	A	A	G	rs13277646	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:59329438A>G	ENST00000399598.2	+	2	236	c.114A>G	c.(112-114)gaA>gaG	p.E38E	UBXN2B_ENST00000522978.1_3'UTR	NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	38						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						ATGAAGATGAAGTGAAGTGCA	0.378													A|||	1292	0.257987	0.1369	0.513	5008	,	,		15223	0.2411		0.2853	False		,,,				2504	0.2301				p.E38E		Atlas-SNP	.											.	UBXN2B	36	.	0			c.A114G						PASS	.	A		695,3061		64,567,1247	97.0	88.0	91.0		114	5.6	1.0	8	dbSNP_121	91	2352,5842		344,1664,2089	no	coding-synonymous	UBXN2B	NM_001077619.1		408,2231,3336	GG,GA,AA		28.7039,18.5037,25.4979		38/332	59329438	3047,8903	1878	4097	5975	SO:0001819	synonymous_variant	137886	exon2			AGATGAAGTGAAG	AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"""UBX domain containing"""	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.114A>G	8.37:g.59329438A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	67	21	0.313433	NM_001077619	B3KWZ3	Silent	SNP	ENST00000399598.2	37	CCDS43741.1																																																																																			A|0.746;G|0.254	0.254	strong		0.378	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619	
DCLRE1C	64421	hgsc.bcm.edu	37	10	14976727	14976727	+	Missense_Mutation	SNP	G	G	C	rs35441642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:14976727G>C	ENST00000378278.2	-	7	549	c.512C>G	c.(511-513)cCa>cGa	p.P171R	DCLRE1C_ENST00000396817.2_Missense_Mutation_p.P51R|DCLRE1C_ENST00000357717.2_Missense_Mutation_p.P56R|DCLRE1C_ENST00000378254.1_Missense_Mutation_p.P51R|DCLRE1C_ENST00000453695.2_Missense_Mutation_p.P51R|DCLRE1C_ENST00000378258.1_Missense_Mutation_p.P51R|DCLRE1C_ENST00000378249.1_Missense_Mutation_p.P56R|DCLRE1C_ENST00000378289.4_Missense_Mutation_p.P171R|DCLRE1C_ENST00000378246.2_Missense_Mutation_p.P56R|DCLRE1C_ENST00000378255.1_Missense_Mutation_p.P51R			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	171			P -> R (in dbSNP:rs35441642). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.P171R(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						GTAAAATCTTGGATCACAGAA	0.388								Non-homologous end-joining					G|||	585	0.116813	0.1362	0.1455	5008	,	,		20942	0.1815		0.0646	False		,,,				2504	0.0573				p.P171R		Atlas-SNP	.											DCLRE1C_ENST00000378278,NS,carcinoma,0,1	DCLRE1C	136	1	1	Substitution - Missense(1)	stomach(1)	c.C512G						PASS	.	G	ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO	564,3842	252.4+/-258.8	38,488,1677	142.0	137.0	139.0		512,152,152,167	4.7	0.5	10	dbSNP_126	139	622,7978	162.0+/-214.8	24,574,3702	yes	missense,missense,missense,missense	DCLRE1C	NM_001033855.1,NM_001033857.1,NM_001033858.1,NM_022487.2	103,103,103,103	62,1062,5379	CC,CG,GG		7.2326,12.8007,9.1189	benign,benign,benign,benign	171/693,51/573,51/573,56/578	14976727	1186,11820	2203	4300	6503	SO:0001583	missense	64421	exon7			AATCTTGGATCAC	BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"""PSO2 homolog (S. cerevisiae)"""	605988	"""severe combined immunodeficiency, type a (Athabascan)"", ""DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"""	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.512C>G	10.37:g.14976727G>C	ENSP00000367527:p.Pro171Arg	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	148	61	0.412162	NM_001033855	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Missense_Mutation	SNP	ENST00000378278.2	37	CCDS31149.1	274	0.12545787545787546	62	0.12601626016260162	46	0.1270718232044199	112	0.1958041958041958	54	0.0712401055408971	G	15.65	2.896364	0.52121	0.128007	0.072326	ENSG00000152457	ENST00000378289;ENST00000453695;ENST00000378246;ENST00000357717;ENST00000378249;ENST00000396817;ENST00000378255;ENST00000378254;ENST00000378278;ENST00000378258;ENST00000418843;ENST00000378241;ENST00000456122	T;T;T;T;T;T;T;T;T;T;T;T;D	0.95238	-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-1.38;-0.81;-3.65	4.73	4.73	0.59995	Beta-lactamase-like (1);	0.102510	0.64402	D	0.000001	T	0.03827	0.0108	M	0.83603	2.65	0.09310	P	0.9999999727978	P;D;B	0.89917	0.589;1.0;0.014	B;D;B	0.97110	0.413;1.0;0.098	T	0.00000	-1.2801	9	0.54805	T	0.06	.	18.0404	0.89317	0.0:0.0:1.0:0.0	rs35441642;rs61749164	171;56;171	Q96SD1-4;Q96SD1-3;Q96SD1	.;.;DCR1C_HUMAN	R	171;51;56;56;56;51;51;51;171;51;25;51;56	ENSP00000367538:P171R;ENSP00000400529:P51R;ENSP00000367492:P56R;ENSP00000350349:P56R;ENSP00000367496:P56R;ENSP00000380030:P51R;ENSP00000367503:P51R;ENSP00000367502:P51R;ENSP00000367527:P171R;ENSP00000367506:P51R;ENSP00000391428:P25R;ENSP00000367487:P51R;ENSP00000413180:P56R	ENSP00000350349:P56R	P	-	2	0	DCLRE1C	15016733	1.000000	0.71417	0.522000	0.27862	0.643000	0.38383	9.556000	0.98127	2.323000	0.78572	0.557000	0.71058	CCA	G|0.900;C|0.100	0.100	strong		0.388	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487	
CLDN14	23562	hgsc.bcm.edu	37	21	37833307	37833307	+	Silent	SNP	C	C	T	rs219780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:37833307C>T	ENST00000399137.1	-	3	1553	c.687G>A	c.(685-687)acG>acA	p.T229T	CLDN14_ENST00000342108.2_Silent_p.T229T|AP000695.4_ENST00000454980.1_RNA|CLDN14_ENST00000399135.1_Silent_p.T229T|AP000695.4_ENST00000428667.1_RNA|CLDN14_ENST00000399136.1_Silent_p.T229T|CLDN14_ENST00000399139.1_Silent_p.T229T|AP000695.6_ENST00000429588.1_RNA	NM_144492.2	NP_652763.1	O95500	CLD14_HUMAN	claudin 14	229					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein complex assembly (GO:0006461)|tight junction assembly (GO:0070830)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|lung(5)|skin(1)	7						ACCCGCTGTGCGTGGCCGAGG	0.667													C|||	678	0.135383	0.2269	0.1138	5008	,	,		16019	0.002		0.2048	False		,,,				2504	0.093				p.T229T		Atlas-SNP	.											.	CLDN14	25	.	0			c.G687A						PASS	.	C	,,,,	1095,3311	393.5+/-328.9	129,837,1237	77.0	65.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	687,687,687,687,687	-11.0	0.0	21	dbSNP_79	69	1807,6793	323.0+/-315.8	193,1421,2686	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLDN14	NM_001146077.1,NM_001146078.1,NM_001146079.1,NM_012130.2,NM_144492.2	,,,,	322,2258,3923	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	21.0116,24.8525,22.3128	,,,,	229/240,229/240,229/240,229/240,229/240	37833307	2902,10104	2203	4300	6503	SO:0001819	synonymous_variant	23562	exon3			GCTGTGCGTGGCC	AJ132445	CCDS13645.1	21q22.3	2008-07-31			ENSG00000159261	ENSG00000159261		"""Claudins"""	2035	protein-coding gene	gene with protein product		605608		DFNB29		11163249	Standard	NM_144492		Approved		uc002yvk.2	O95500	OTTHUMG00000086638	ENST00000399137.1:c.687G>A	21.37:g.37833307C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	215	88	0.409302	NM_144492		Silent	SNP	ENST00000399137.1	37	CCDS13645.1																																																																																			C|0.804;T|0.196	0.196	strong		0.667	CLDN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194697.1	NM_144492	
PACSIN2	11252	hgsc.bcm.edu	37	22	43278220	43278220	+	Silent	SNP	C	C	T	rs2899365	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:43278220C>T	ENST00000263246.3	-	7	1077	c.876G>A	c.(874-876)ccG>ccA	p.P292P	PACSIN2_ENST00000337959.4_Silent_p.P292P|PACSIN2_ENST00000402229.1_Silent_p.P292P|PACSIN2_ENST00000407585.1_Silent_p.P292P|PACSIN2_ENST00000403744.3_Silent_p.P292P	NM_001184970.1	NP_001171899.1	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in neurons 2	292	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cell projection morphogenesis (GO:0048858)|membrane tubulation (GO:0097320)|negative regulation of endocytosis (GO:0045806)|protein localization to endosome (GO:0036010)	caveola (GO:0005901)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	19		Glioma(61;0.222)				TGGCCATGCCCGGCCCGTGAT	0.562													C|||	1707	0.340855	0.3631	0.3761	5008	,	,		20424	0.0933		0.4622	False		,,,				2504	0.4162				p.P292P		Atlas-SNP	.											.	PACSIN2	48	.	0			c.G876A						PASS	.	C	,,	1711,2415		376,959,728	66.0	71.0	69.0		876,876,876	-10.8	0.0	22	dbSNP_101	69	4023,4431		994,2035,1198	no	coding-synonymous,coding-synonymous,coding-synonymous	PACSIN2	NM_001184970.1,NM_001184971.1,NM_007229.3	,,	1370,2994,1926	TT,TC,CC		47.5869,41.4687,45.5803	,,	292/487,292/446,292/487	43278220	5734,6846	2063	4227	6290	SO:0001819	synonymous_variant	11252	exon7			CATGCCCGGCCCG	AF128536	CCDS43023.1, CCDS54536.1	22q13.2-q13.33	2009-05-08			ENSG00000100266	ENSG00000100266			8571	protein-coding gene	gene with protein product	"""syndapin II"""	604960				10431838, 11082044	Standard	NM_007229		Approved	SDPII	uc003bdg.4	Q9UNF0	OTTHUMG00000150701	ENST00000263246.3:c.876G>A	22.37:g.43278220C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_007229	O95921|Q96HV9|Q9H0D3|Q9NPN1|Q9Y4V2	Silent	SNP	ENST00000263246.3	37	CCDS43023.1																																																																																			C|0.642;T|0.358	0.358	strong		0.562	PACSIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319665.1	NM_007229	
OR14I1	401994	hgsc.bcm.edu	37	1	248844959	248844959	+	Missense_Mutation	SNP	T	T	C	rs55871516	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248844959T>C	ENST00000342623.3	-	1	670	c.647A>G	c.(646-648)tAt>tGt	p.Y216C		NM_001004734.1	NP_001004734.1	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I, member 1	216			Y -> C (in dbSNP:rs55871516).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y216C(1)		NS(1)|breast(4)|large_intestine(2)|lung(24)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	35						GATTTGGAAATAGGAGATCAT	0.483													T|||	665	0.132788	0.1649	0.0865	5008	,	,		20268	0.128		0.1173	False		,,,				2504	0.1431				p.Y216C		Atlas-SNP	.											OR14I1,right_lower_lobe,carcinoma,-1,2	OR14I1	64	2	1	Substitution - Missense(1)	stomach(1)	c.A647G						PASS	.	T	CYS/TYR	674,3732		47,580,1576	78.0	83.0	82.0		647	3.5	0.0	1	dbSNP_129	82	992,7608		58,876,3366	yes	missense	OR14I1	NM_001004734.1	194	105,1456,4942	CC,CT,TT		11.5349,15.2973,12.8095	probably-damaging	216/312	248844959	1666,11340	2203	4300	6503	SO:0001583	missense	401994	exon1			TGGAAATAGGAGA		CCDS31125.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000189181	ENSG00000189181		"""GPCR / Class A : Olfactory receptors"""	19575	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BU, member 1"""	OR5BU1P, OR5BU1			Standard	NM_001004734		Approved		uc001ieu.1	A6ND48	OTTHUMG00000040378	ENST00000342623.3:c.647A>G	1.37:g.248844959T>C	ENSP00000339726:p.Tyr216Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_001004734		Missense_Mutation	SNP	ENST00000342623.3	37	CCDS31125.1	291	0.13324175824175824	89	0.18089430894308944	37	0.10220994475138122	73	0.12762237762237763	92	0.12137203166226913	.	20.4	3.983867	0.74474	0.152973	0.115349	ENSG00000189181	ENST00000342623	T	0.00520	6.85	3.49	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41938	D	0.000794	T	0.00012	0.0000	H	0.99104	4.43	0.31092	P	0.710709	D	0.89917	1.0	D	0.97110	1.0	T	0.01966	-1.1238	9	0.87932	D	0	.	9.9498	0.41631	0.0:0.0:0.0:1.0	rs55871516	216	A6ND48	O14I1_HUMAN	C	216	ENSP00000339726:Y216C	ENSP00000339726:Y216C	Y	-	2	0	OR14I1	246911582	0.989000	0.36119	0.016000	0.15963	0.659000	0.38960	2.521000	0.45563	1.422000	0.47177	0.443000	0.29094	TAT	T|0.871;C|0.129	0.129	strong		0.483	OR14I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097128.1	NM_001004734	
MYLK4	340156	hgsc.bcm.edu	37	6	2749381	2749381	+	Missense_Mutation	SNP	C	C	T	rs2296356	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:2749381C>T	ENST00000274643.7	-	2	490	c.148G>A	c.(148-150)Gga>Aga	p.G50R	MYLK4_ENST00000268446.5_Missense_Mutation_p.G50R	NM_001012418.3	NP_001012418.2	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4	50			G -> R (in dbSNP:rs2296356). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.			extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23	Ovarian(93;0.0412)	all_hematologic(90;0.0897)				TCATTATGTCCAGATCTTGAA	0.383													C|||	786	0.156949	0.0325	0.2651	5008	,	,		19893	0.3194		0.1153	False		,,,				2504	0.1237				p.G50R		Atlas-SNP	.											.	MYLK4	74	.	0			c.G148A						PASS	.	C	ARG/GLY	270,4136	153.3+/-186.9	9,252,1942	129.0	134.0	132.0		148	4.8	0.2	6	dbSNP_100	132	1176,7424	239.7+/-270.7	78,1020,3202	yes	missense	MYLK4	NM_001012418.3	125	87,1272,5144	TT,TC,CC		13.6744,6.128,11.1179	possibly-damaging	50/389	2749381	1446,11560	2203	4300	6503	SO:0001583	missense	340156	exon2			TATGTCCAGATCT		CCDS34330.1	6p25.2	2008-01-23			ENSG00000145949	ENSG00000145949			27972	protein-coding gene	gene with protein product	"""caMLCK like"""						Standard	NM_001012418		Approved	SgK085	uc003mty.4	Q86YV6	OTTHUMG00000014121	ENST00000274643.7:c.148G>A	6.37:g.2749381C>T	ENSP00000274643:p.Gly50Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	136	60	0.441176	NM_001012418	A2RUC0|Q5TAW2	Missense_Mutation	SNP	ENST00000274643.7	37	CCDS34330.1	371	0.16987179487179488	20	0.04065040650406504	79	0.21823204419889503	184	0.32167832167832167	88	0.11609498680738786	C	10.14	1.269128	0.23221	0.06128	0.136744	ENSG00000145949	ENST00000268446;ENST00000274643	T;T	0.66638	0.11;-0.22	5.65	4.79	0.61399	.	.	.	.	.	T	0.29882	0.0747	N	0.08118	0	0.38215	P	0.05940500000000004	B	0.16396	0.017	B	0.12837	0.008	T	0.09122	-1.0689	8	0.38643	T	0.18	.	13.8942	0.63761	0.0:0.8476:0.1524:0.0	rs2296356;rs52819487;rs2296356	50	Q86YV6	MYLK4_HUMAN	R	50	ENSP00000268446:G50R;ENSP00000274643:G50R	ENSP00000268446:G50R	G	-	1	0	MYLK4	2694380	0.094000	0.21725	0.169000	0.22859	0.186000	0.23388	2.859000	0.48364	1.398000	0.46701	-0.127000	0.14921	GGA	C|0.865;T|0.135	0.135	strong		0.383	MYLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039632.2	NM_001012418	
COL10A1	1300	hgsc.bcm.edu	37	6	116441470	116441470	+	Silent	SNP	C	C	G	rs2228548	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:116441470C>G	ENST00000327673.4	-	2	2216	c.1809G>C	c.(1807-1809)gtG>gtC	p.V603V	NT5DC1_ENST00000319550.4_Intron|COL10A1_ENST00000243222.4_Silent_p.V603V|AL121963.1_ENST00000430695.1_5'Flank			Q03692	COAA1_HUMAN	collagen, type X, alpha 1	603	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Nonhelical region (NC1).		V -> M. {ECO:0000269|PubMed:15880705}.		cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	cell cortex (GO:0005938)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	13		all_cancers(87;0.0176)|all_epithelial(87;0.0263)|Colorectal(196;0.234)		all cancers(137;0.0157)|OV - Ovarian serous cystadenocarcinoma(136;0.0325)|GBM - Glioblastoma multiforme(226;0.0446)|Epithelial(106;0.0711)		CTTTCACATGCACGTGGTATG	0.403													C|||	137	0.0273562	0.0303	0.0173	5008	,	,		21345	0.0		0.0487	False		,,,				2504	0.0368				p.V603V		Atlas-SNP	.											.	COL10A1	51	.	0			c.G1809C						PASS	.	C	,	160,4246	109.1+/-147.4	4,152,2047	130.0	119.0	123.0		1809,	1.9	0.8	6	dbSNP_98	123	508,8092	145.3+/-201.0	20,468,3812	no	coding-synonymous,intron	COL10A1,NT5DC1	NM_000493.3,NM_152729.2	,	24,620,5859	GG,GC,CC		5.907,3.6314,5.1361	,	603/681,	116441470	668,12338	2203	4300	6503	SO:0001819	synonymous_variant	1300	exon3			CACATGCACGTGG		CCDS5105.1	6q21-q22	2013-01-16	2008-07-29		ENSG00000123500	ENSG00000123500		"""Collagens"""	2185	protein-coding gene	gene with protein product	"""Schmid metaphyseal chondrodysplasia"""	120110				2037056	Standard	XM_006715332		Approved		uc003pwm.3	Q03692	OTTHUMG00000015426	ENST00000327673.4:c.1809G>C	6.37:g.116441470C>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	192	75	0.390625	NM_000493	A1L4P2	Silent	SNP	ENST00000327673.4	37	CCDS5105.1																																																																																			C|0.955;G|0.045	0.045	strong		0.403	COL10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041926.1		
SLFNL1	200172	hgsc.bcm.edu	37	1	41485902	41485902	+	Missense_Mutation	SNP	C	C	G	rs3738368	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:41485902C>G	ENST00000359345.1	-	1	3007	c.431G>C	c.(430-432)aGa>aCa	p.R144T	SLFNL1_ENST00000439569.2_Missense_Mutation_p.R144T|SLFNL1_ENST00000302946.8_Missense_Mutation_p.R144T|SLFNL1_ENST00000372613.2_Missense_Mutation_p.R144T|SLFNL1_ENST00000397197.2_Missense_Mutation_p.R144T|SLFNL1_ENST00000372611.1_Missense_Mutation_p.R144T	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	144			R -> T (in dbSNP:rs3738368).				ATP binding (GO:0005524)			endometrium(3)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				ACTTACCTCTCTGTGGCTGAA	0.617													C|||	912	0.182109	0.0166	0.2896	5008	,	,		16809	0.1687		0.3042	False		,,,				2504	0.2178				p.R144T		Atlas-SNP	.											.	SLFNL1	37	.	0			c.G431C						PASS	.	C	THR/ARG,THR/ARG	329,4077	171.2+/-201.5	12,305,1886	62.0	64.0	63.0		431,431	3.8	0.2	1	dbSNP_107	63	2645,5955	425.6+/-355.0	428,1789,2083	yes	missense,missense	SLFNL1	NM_001168247.1,NM_144990.3	71,71	440,2094,3969	GG,GC,CC		30.7558,7.4671,22.8664	probably-damaging,probably-damaging	144/408,144/408	41485902	2974,10032	2203	4300	6503	SO:0001583	missense	200172	exon3			ACCTCTCTGTGGC	BC022037	CCDS460.1, CCDS72766.1	1p34.2	2008-02-05			ENSG00000171790	ENSG00000171790			26313	protein-coding gene	gene with protein product							Standard	NM_144990		Approved	FLJ23878	uc001cgm.2	Q499Z3	OTTHUMG00000005719	ENST00000359345.1:c.431G>C	1.37:g.41485902C>G	ENSP00000352299:p.Arg144Thr	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_001168247	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	37	CCDS460.1	442	0.20238095238095238	12	0.024390243902439025	108	0.2983425414364641	101	0.17657342657342656	221	0.29155672823219	C	9.864	1.197201	0.22037	0.074671	0.307558	ENSG00000171790	ENST00000302946;ENST00000372613;ENST00000372611;ENST00000359345;ENST00000439569;ENST00000397197	T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24	5.63	3.77	0.43336	.	0.397216	0.23740	N	0.045022	T	0.00012	0.0000	L	0.59436	1.845	0.37239	P	0.09398899999999999	P;P;D	0.55605	0.946;0.86;0.972	P;P;B	0.48840	0.592;0.453;0.335	T	0.10683	-1.0619	9	0.72032	D	0.01	-0.14	8.5891	0.33677	0.0:0.8238:0.0:0.1762	rs3738368;rs17357926;rs58566626;rs3738368	144;144;144	Q499Z3-3;Q499Z3-2;Q499Z3	.;.;SLNL1_HUMAN	T	144	ENSP00000304401:R144T;ENSP00000361696:R144T;ENSP00000361694:R144T;ENSP00000352299:R144T;ENSP00000398938:R144T;ENSP00000380381:R144T	ENSP00000304401:R144T	R	-	2	0	SLFNL1	41258489	0.301000	0.24444	0.233000	0.24025	0.015000	0.08874	0.322000	0.19576	0.746000	0.32786	-0.291000	0.09656	AGA	C|0.777;G|0.222	0.222	strong		0.617	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990	
FAM171A2	284069	hgsc.bcm.edu	37	17	42437000	42437000	+	Missense_Mutation	SNP	G	G	A	rs71371993	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:42437000G>A	ENST00000293443.7	-	3	546	c.386C>T	c.(385-387)cCg>cTg	p.P129L		NM_198475.2	NP_940877.2	A8MVW0	F1712_HUMAN	family with sequence similarity 171, member A2	129						integral component of membrane (GO:0016021)											GAGCGTGGCCGGCCGCTCAGG	0.642													G|||	217	0.0433307	0.0068	0.0591	5008	,	,		12413	0.0288		0.0815	False		,,,				2504	0.0573				p.P129L		Atlas-SNP	.											.	FAM171A2	13	.	0			c.C386T						PASS	.	G	LEU/PRO	23,1361		0,23,669	47.0	57.0	54.0		386	3.7	1.0	17	dbSNP_130	54	223,2959		10,203,1378	yes	missense	FAM171A2	NM_198475.2	98	10,226,2047	AA,AG,GG		7.0082,1.6618,5.3876	probably-damaging	129/827	42437000	246,4320	692	1591	2283	SO:0001583	missense	284069	exon3			GTGGCCGGCCGCT		CCDS45701.1	17q21.31	2008-06-16			ENSG00000161682	ENSG00000161682			30480	protein-coding gene	gene with protein product						12477932	Standard	NM_198475		Approved	MGC34829	uc002igs.2	A8MVW0	OTTHUMG00000132421	ENST00000293443.7:c.386C>T	17.37:g.42437000G>A	ENSP00000293443:p.Pro129Leu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_198475	A8MQB4	Missense_Mutation	SNP	ENST00000293443.7	37	CCDS45701.1	185	0.08470695970695971	26	0.052845528455284556	32	0.08839779005524862	34	0.05944055944055944	93	0.12269129287598944	G	26.8	4.769736	0.90020	0.016618	0.070082	ENSG00000161682	ENST00000293443	T	0.31769	1.48	3.73	3.73	0.42828	.	0.000000	0.64402	U	0.000005	T	0.00845	0.0028	L	0.48642	1.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00456	-1.1728	10	0.72032	D	0.01	-20.1101	14.5063	0.67755	0.0:0.0:1.0:0.0	.	129	A8MVW0	F1712_HUMAN	L	129	ENSP00000293443:P129L	ENSP00000293443:P129L	P	-	2	0	FAM171A2	39792526	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.062000	0.76706	1.911000	0.55334	0.456000	0.33151	CCG	G|0.915;A|0.085	0.085	strong		0.642	FAM171A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255559.2	NM_198475	
TCOF1	6949	hgsc.bcm.edu	37	5	149763305	149763305	+	Intron	SNP	A	A	G	rs7715100	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149763305A>G	ENST00000504761.2	+	17	2859				TCOF1_ENST00000439160.2_Intron|TCOF1_ENST00000394269.3_Missense_Mutation_p.Q955R|TCOF1_ENST00000513346.1_Intron|TCOF1_ENST00000377797.3_Intron|TCOF1_ENST00000451292.1_Intron|TCOF1_ENST00000445265.2_Intron|TCOF1_ENST00000323668.7_Intron			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1						skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTTTAGGACCAGGAGTCTTCT	0.512													a|||	790	0.157748	0.2383	0.0908	5008	,	,		21551	0.1438		0.1292	False		,,,				2504	0.1401				p.Q955R		Atlas-SNP	.											.	TCOF1	154	.	0			c.A2864G						PASS	.	A	,ARG/GLN,,,,	764,2936		71,622,1157	85.0	92.0	89.0		,2864,,,,	-4.3	0.0	5	dbSNP_116	89	1077,6761		66,945,2908	yes	intron,missense,intron,intron,intron,intron	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	,43,,,,	137,1567,4065	GG,GA,AA		13.7408,20.6486,15.956	,,,,,	,955/959,,,,	149763305	1841,9697	1850	3919	5769	SO:0001627	intron_variant	6949	exon18			AGGACCAGGAGTC		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.2859+4010A>G	5.37:g.149763305A>G		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	237	113	0.476793	NM_001008657	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	308|308	0.14102564102564102|0.14102564102564102	120|120	0.24390243902439024|0.24390243902439024	38|38	0.10497237569060773|0.10497237569060773	57|57	0.09965034965034965|0.09965034965034965	93|93	0.12269129287598944|0.12269129287598944	a|a	4.342|4.342	0.062949|0.062949	0.08388|0.08388	0.206486|0.206486	0.137408|0.137408	ENSG00000070814|ENSG00000070814	ENST00000394269|ENST00000513538	D|.	0.82526|.	-1.62|.	2.69|2.69	-4.27|-4.27	0.03744|0.03744	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.32824|0.32824	-0.9892|-0.9892	7|3	0.37606|.	T|.	0.19|.	.|.	1.2733|1.2733	0.02025|0.02025	0.464:0.1563:0.2213:0.1584|0.464:0.1563:0.2213:0.1584	rs7715100;rs17656788;rs7715100|rs7715100;rs17656788;rs7715100	955|.	Q13428-5|.	.|.	R|G	955|64	ENSP00000377811:Q955R|.	ENSP00000377811:Q955R|.	Q|R	+|+	2|1	0|2	TCOF1|TCOF1	149743498|149743498	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-0.942000|-0.942000	0.03921|0.03921	-1.314000|-1.314000	0.02300|0.02300	-1.049000|-1.049000	0.02347|0.02347	CAG|AGG	A|0.847;G|0.153	0.153	strong		0.512	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
SERPING1	710	hgsc.bcm.edu	37	11	57381989	57381989	+	Missense_Mutation	SNP	G	G	A	rs4926	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57381989G>A	ENST00000278407.4	+	8	1665	c.1438G>A	c.(1438-1440)Gtg>Atg	p.V480M	SERPING1_ENST00000403558.1_Missense_Mutation_p.V523M|SERPING1_ENST00000340687.6_Missense_Mutation_p.V443M|SERPING1_ENST00000378323.4_Missense_Mutation_p.V485M|SERPING1_ENST00000378324.2_Missense_Mutation_p.V428M	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	480			V -> M (in dbSNP:rs4926). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16409206, ECO:0000269|PubMed:22994404, ECO:0000269|Ref.7, ECO:0000269|Ref.8, ECO:0000269|Ref.9}.		blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						CTTCCTCTTCGTGCTCTGGGA	0.622													G|||	749	0.149561	0.0855	0.1657	5008	,	,		18565	0.0942		0.2664	False		,,,				2504	0.1616				p.V480M		Atlas-SNP	.											.	SERPING1	57	.	0			c.G1438A						PASS	.	G	MET/VAL,MET/VAL	468,3934	220.4+/-237.8	25,418,1758	40.0	40.0	40.0		1438,1438	-0.9	1.0	11	dbSNP_52	40	2413,6179	398.7+/-346.2	364,1685,2247	yes	missense,missense	SERPING1	NM_000062.2,NM_001032295.1	21,21	389,2103,4005	AA,AG,GG		28.0843,10.6315,22.1718	benign,benign	480/501,480/501	57381989	2881,10113	2201	4296	6497	SO:0001583	missense	710	exon7			CTCTTCGTGCTCT	X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"""Serine (or cysteine) peptidase inhibitors"""	1228	protein-coding gene	gene with protein product	"""plasma protease C1 inhibitor"", ""angioedema, hereditary"""	606860	"""serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"""	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.1438G>A	11.37:g.57381989G>A	ENSP00000278407:p.Val480Met	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	156	80	0.512821	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	37	CCDS7962.1	371	0.16987179487179488	45	0.09146341463414634	67	0.1850828729281768	63	0.11013986013986014	196	0.25857519788918204	G	11.21	1.570632	0.28003	0.106315	0.280843	ENSG00000149131	ENST00000278407;ENST00000340687;ENST00000378323;ENST00000378324;ENST00000403558	D;D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94;-1.94	4.68	-0.867	0.10655	Serpin domain (3);Protease inhibitor I4, serpin, conserved site (1);	0.321108	0.26116	N	0.026252	T	0.00039	0.0001	L	0.45470	1.425	0.58432	P	2.9999999999752447E-6	B;B;B	0.20780	0.048;0.014;0.014	B;B;B	0.21360	0.034;0.034;0.034	T	0.37619	-0.9698	9	0.52906	T	0.07	.	20.9307	0.99941	0.0:0.2407:0.7593:0.0	rs4926;rs17745;rs3198011;rs17611360;rs17850724;rs52802567;rs4926	485;480;480	B4E1F0;E9KL26;P05155	.;.;IC1_HUMAN	M	480;443;485;428;523	ENSP00000278407:V480M;ENSP00000341861:V443M;ENSP00000367574:V485M;ENSP00000367575:V428M;ENSP00000384420:V523M	ENSP00000278407:V480M	V	+	1	0	SERPING1	57138565	0.003000	0.15002	0.964000	0.40570	0.328000	0.28507	-1.524000	0.02233	-0.365000	0.08076	-1.104000	0.02111	GTG	G|0.799;A|0.200	0.200	strong		0.622	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062	
RASGRF1	5923	hgsc.bcm.edu	37	15	79277511	79277511	+	Silent	SNP	A	A	G	rs2230518	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:79277511A>G	ENST00000419573.3	-	24	3574	c.3300T>C	c.(3298-3300)aaT>aaC	p.N1100N	RP11-16K12.1_ENST00000316148.4_RNA|RASGRF1_ENST00000394745.3_Silent_p.N316N|RASGRF1_ENST00000558480.2_Silent_p.N1084N|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1100	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TGATGTCCTCATTGCGGATGA	0.473													G|||	1411	0.281749	0.4697	0.1945	5008	,	,		20696	0.1865		0.2644	False		,,,				2504	0.2055				p.N1100N		Atlas-SNP	.											.	RASGRF1	168	.	0			c.T3300C						PASS	.	G	,,	1782,2610	640.9+/-397.4	346,1090,760	138.0	118.0	125.0		3252,3300,948	-7.9	0.5	15	dbSNP_98	125	2295,6291	704.9+/-405.4	301,1693,2299	no	coding-synonymous,coding-synonymous,coding-synonymous	RASGRF1	NM_001145648.1,NM_002891.4,NM_153815.2	,,	647,2783,3059	GG,GA,AA		26.7296,40.5738,31.4147	,,	1084/1258,1100/1274,316/490	79277511	4077,8901	2196	4293	6489	SO:0001819	synonymous_variant	5923	exon24			GTCCTCATTGCGG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3300T>C	15.37:g.79277511A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	145	144	0.993103	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	37	CCDS10309.1																																																																																			T|0.132;G|0.239;C|0.053;N|0.000;A|0.576	0.239	strong		0.473	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
WDFY4	57705	hgsc.bcm.edu	37	10	50013402	50013402	+	Missense_Mutation	SNP	T	T	C	rs2170132	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50013402T>C	ENST00000325239.5	+	25	4609	c.4582T>C	c.(4582-4584)Tcc>Ccc	p.S1528P	WDFY4_ENST00000413659.2_Intron	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1528						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CTCCAAGATCTCCACCATCAT	0.587													C|||	2889	0.576877	0.7905	0.3977	5008	,	,		17153	0.8304		0.2962	False		,,,				2504	0.4427				p.S1528P		Atlas-SNP	.											.	WDFY4	205	.	0			c.T4582C						PASS	.	C	PRO/SER	1011,373		373,265,54	92.0	82.0	85.0		4582	1.5	1.0	10	dbSNP_96	85	996,2186		136,724,731	yes	missense	WDFY4	NM_020945.1	74	509,989,785	CC,CT,TT		31.3011,26.9509,43.9553	benign	1528/3185	50013402	2007,2559	692	1591	2283	SO:0001583	missense	57705	exon26			AAGATCTCCACCA	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.4582T>C	10.37:g.50013402T>C	ENSP00000320563:p.Ser1528Pro	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	1202|1202	0.5503663003663004|0.5503663003663004	377|377	0.766260162601626|0.766260162601626	139|139	0.3839779005524862|0.3839779005524862	465|465	0.8129370629370629|0.8129370629370629	221|221	0.29155672823219|0.29155672823219	C|C	7.506|7.506	0.653714|0.653714	0.14580|0.14580	0.730491|0.730491	0.313011|0.313011	ENSG00000128815|ENSG00000128815	ENST00000312002;ENST00000374161|ENST00000426033;ENST00000325239	.|T	.|0.55234	.|0.53	5.01|5.01	1.47|1.47	0.22746|0.22746	.|.	.|0.231982	.|0.36101	.|N	.|0.002791	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	P|P	0.99999999718745|0.99999999718745	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	T|T	0.28038|0.28038	-1.0056|-1.0056	4|8	.|.	.|.	.|.	.|.	4.1496|4.1496	0.10232|0.10232	0.4526:0.3487:0.0:0.1987|0.4526:0.3487:0.0:0.1987	rs2170132;rs17772022;rs52834656;rs2170132|rs2170132;rs17772022;rs52834656;rs2170132	.|56;1528	.|F2Z372;Q6ZS81	.|.;WDFY4_HUMAN	P|P	618;74|1528	.|ENSP00000320563:S1528P	.|.	L|S	+|+	2|1	0|0	WDFY4|WDFY4	49683408|49683408	0.490000|0.490000	0.26012|0.26012	0.989000|0.989000	0.46669|0.46669	0.577000|0.577000	0.36160|0.36160	-0.165000|-0.165000	0.09968|0.09968	0.219000|0.219000	0.20840|0.20840	-0.821000|-0.821000	0.03111|0.03111	CTC|TCC	T|0.443;C|0.557	0.557	strong		0.587	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
CRLF1	9244	hgsc.bcm.edu	37	19	18710535	18710535	+	Silent	SNP	G	G	A	rs2238647	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18710535G>A	ENST00000392386.3	-	2	430	c.237C>T	c.(235-237)aaC>aaT	p.N79N		NM_004750.4	NP_004741.1	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1	79	Ig-like C2-type.				negative regulation of motor neuron apoptotic process (GO:2000672)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|ureteric bud development (GO:0001657)	CRLF-CLCF1 complex (GO:0097058)|extracellular space (GO:0005615)	cytokine binding (GO:0019955)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	9						GGCGGCGCCCGTTGAGGGTCC	0.682													G|||	1341	0.267772	0.0779	0.3458	5008	,	,		2009	0.5258		0.2266	False		,,,				2504	0.2454				p.N79N		Atlas-SNP	.											.	CRLF1	32	.	0			c.C237T						PASS	.	G		458,3934		30,398,1768	19.0	19.0	19.0		237	-6.0	0.8	19	dbSNP_98	19	1632,6956		154,1324,2816	no	coding-synonymous	CRLF1	NM_004750.4		184,1722,4584	AA,AG,GG		19.0033,10.4281,16.1017		79/423	18710535	2090,10890	2196	4294	6490	SO:0001819	synonymous_variant	9244	exon2			GCGCCCGTTGAGG	AF059293	CCDS32962.1	19p12	2013-02-11				ENSG00000006016		"""Fibronectin type III domain containing"""	2364	protein-coding gene	gene with protein product	"""cold-induced sweating syndrome"""	604237				9686600	Standard	NM_004750		Approved	CLF-1, CLF, CISS, CISS1	uc010ebt.2	O75462		ENST00000392386.3:c.237C>T	19.37:g.18710535G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	196	93	0.47449	NM_004750	Q9UHH5	Silent	SNP	ENST00000392386.3	37	CCDS32962.1																																																																																			G|0.781;A|0.219	0.219	strong		0.682	CRLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465129.1		
ZNF772	400720	hgsc.bcm.edu	37	19	57984918	57984918	+	Silent	SNP	A	A	G	rs2074058	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57984918A>G	ENST00000343280.4	-	5	1454	c.1194T>C	c.(1192-1194)agT>agC	p.S398S	ZNF772_ENST00000425074.3_3'UTR|AC004076.9_ENST00000596831.1_Intron|ZNF772_ENST00000601768.1_Intron|AC004076.9_ENST00000415705.3_Intron|ZNF772_ENST00000600175.1_Intron|ZNF772_ENST00000427512.2_Silent_p.S286S|ZNF772_ENST00000356584.3_Silent_p.S357S	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	398					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)	9		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		CAGTATGAACACTCCAATGTT	0.413													A|||	2073	0.413938	0.3154	0.4524	5008	,	,		22319	0.5893		0.2783	False		,,,				2504	0.4785				p.S398S	Melanoma(5;289 436 14293 15924 30817)	Atlas-SNP	.											.	ZNF772	42	.	0			c.T1194C						PASS	.	A	,	1364,3042	454.2+/-350.6	198,968,1037	132.0	121.0	125.0		1194,1071	-1.1	1.0	19	dbSNP_96	125	2446,6154	402.6+/-347.5	329,1788,2183	no	coding-synonymous,coding-synonymous	ZNF772	NM_001024596.2,NM_001144068.1	,	527,2756,3220	GG,GA,AA		28.4419,30.9578,29.2942	,	398/490,357/449	57984918	3810,9196	2203	4300	6503	SO:0001819	synonymous_variant	400720	exon5			ATGAACACTCCAA	BX647068	CCDS33133.1, CCDS46210.1	19q13.43	2013-01-08				ENSG00000197128		"""Zinc fingers, C2H2-type"", ""-"""	33106	protein-coding gene	gene with protein product							Standard	NM_001024596		Approved	DKFZp686I1569	uc002qot.3	Q68DY9		ENST00000343280.4:c.1194T>C	19.37:g.57984918A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_001024596	A6NJK9|B4DH56|B4DYS0	Silent	SNP	ENST00000343280.4	37	CCDS33133.1																																																																																			A|0.659;G|0.341	0.341	strong		0.413	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596	
PLXNB3	5365	hgsc.bcm.edu	37	X	153041544	153041544	+	Missense_Mutation	SNP	T	T	C	rs5987155	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153041544T>C	ENST00000361971.5	+	27	4718	c.4604T>C	c.(4603-4605)aTg>aCg	p.M1535T	PLXNB3_ENST00000538966.1_Missense_Mutation_p.M1558T|PLXNB3_ENST00000538776.1_Missense_Mutation_p.M1188T|SRPK3_ENST00000489426.1_5'Flank	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1535			M -> T (in dbSNP:rs5987155). {ECO:0000269|PubMed:14702039}.		axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					AGCAGCGAGATGCAGCGCGTG	0.667													t|||	3139	0.831523	0.6694	0.6354	3775	,	,		8235	0.5863		0.6103	False		,,,				2504	0.6217				p.M1558T		Atlas-SNP	.											.	PLXNB3	208	.	0			c.T4673C						PASS	.		THR/MET,THR/MET	3331,467		1246,358,481,17,75	37.0	28.0	31.0		4673,4604	-5.5	0.0	X	dbSNP_114	31	5256,1456		1501,802,1452,123,408	yes	missense,missense	PLXNB3	NM_001163257.1,NM_005393.2	81,81	2747,1160,1933,140,483	CC,CT,C,TT,T		21.6925,12.2959,18.2969	possibly-damaging,possibly-damaging	1558/1933,1535/1910	153041544	8587,1923	2177	4286	6463	SO:0001583	missense	5365	exon28			GCGAGATGCAGCG	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.4604T>C	X.37:g.153041544T>C	ENSP00000355378:p.Met1535Thr	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	1353	0.8155515370705244	229	0.8178571428571428	151	0.7122641509433962	224	0.6086956521739131	323	0.684322033898305	t	0.009	-1.836143	0.00579	0.877041	0.783075	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776	T;T;T	0.01527	5.41;5.38;4.8	4.93	-5.5	0.02576	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	276.708000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.01081	-1.03	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.24440	-1.0160	9	0.15499	T	0.54	.	9.4446	0.38690	0.0:0.5607:0.1071:0.3322	rs5987155;rs5987155	1188;1558;1535	B7Z3H9;F5H773;Q9ULL4	.;.;PLXB3_HUMAN	T	1558;1535;1188	ENSP00000442736:M1558T;ENSP00000355378:M1535T;ENSP00000445569:M1188T	ENSP00000355378:M1535T	M	+	2	0	PLXNB3	152694738	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.560000	0.00921	-1.237000	0.02539	-1.471000	0.01009	ATG	T|0.184;C|0.816	0.816	strong		0.667	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
RHPN2	85415	hgsc.bcm.edu	37	19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:33517507C>T	ENST00000254260.3	-	3	252	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	RHPN2_ENST00000400226.4_De_novo_Start_OutOfFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	73					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.V73M(2)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TCCAGCCGCACTTGCTCCCGC	0.552																																					p.V73M		Atlas-SNP	.											RHPN2,face,carcinoma,0,2	RHPN2	107	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G217A						scavenged	.						84.0	83.0	83.0					19																	33517507		2203	4300	6503	SO:0001583	missense	85415	exon3			GCCGCACTTGCTC	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.217G>A	19.37:g.33517507C>T	ENSP00000254260:p.Val73Met	Somatic	15	1	0.0666667		WXS	Illumina HiSeq	Phase_I	39	5	0.128205	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542997	0.65198	.	.	ENSG00000131941	ENST00000254260	T	0.39787	1.06	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71984	-0.4427	10	0.87932	D	0	11.9954	16.025	0.80536	0.0:1.0:0.0:0.0	.	73	Q8IUC4	RHPN2_HUMAN	M	73	ENSP00000254260:V73M	ENSP00000254260:V73M	V	-	1	0	RHPN2	38209347	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.267000	0.78462	2.167000	0.68274	0.557000	0.71058	GTG	.	.	none		0.552	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
TRIM4	89122	hgsc.bcm.edu	37	7	99500899	99500899	+	Silent	SNP	T	T	C	rs2247762	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99500899T>C	ENST00000355947.2	-	6	990	c.861A>G	c.(859-861)gtA>gtG	p.V287V	TRIM4_ENST00000354241.5_Silent_p.V261V|TRIM4_ENST00000349062.2_Silent_p.V261V	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	287					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				TCTTCACCTTTACAGCTTCAA	0.458													T|||	1612	0.321885	0.1498	0.3357	5008	,	,		21228	0.2937		0.4235	False		,,,				2504	0.4693				p.V287V		Atlas-SNP	.											.	TRIM4	33	.	0			c.A861G						PASS	.	T	,	934,3472	359.4+/-314.8	101,732,1370	135.0	127.0	130.0		861,783	-0.2	0.0	7	dbSNP_100	130	3964,4636	552.3+/-386.1	897,2170,1233	no	coding-synonymous,coding-synonymous	TRIM4	NM_033017.3,NM_033091.2	,	998,2902,2603	CC,CT,TT		46.093,21.1984,37.6595	,	287/501,261/475	99500899	4898,8108	2203	4300	6503	SO:0001819	synonymous_variant	89122	exon6			CACCTTTACAGCT	AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16275	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM4"", ""tripartite motif protein 4"""		"""tripartite motif-containing 4"""			11331580	Standard	NM_033017		Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.861A>G	7.37:g.99500899T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Silent	SNP	ENST00000355947.2	37	CCDS5679.1	687	0.31456043956043955	68	0.13821138211382114	133	0.3674033149171271	155	0.270979020979021	331	0.4366754617414248	T	0.026	-1.374714	0.01214	0.211984	0.46093	ENSG00000146833	ENST00000447480	.	.	.	2.16	-0.222	0.13122	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47711	-0.9096	3	.	.	.	.	4.2291	0.10594	0.0:0.3632:0.0:0.6368	rs2247762;rs10373684;rs17277887;rs2247762	.	.	.	E	163	.	.	K	-	1	0	TRIM4	99338835	0.000000	0.05858	0.023000	0.16930	0.054000	0.15201	-2.459000	0.01000	-0.051000	0.13334	0.528000	0.53228	AAA	T|0.658;C|0.342	0.342	strong		0.458	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017	
KCNG4	93107	hgsc.bcm.edu	37	16	84256103	84256103	+	Missense_Mutation	SNP	C	C	T	rs35649980	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84256103C>T	ENST00000308251.4	-	3	1348	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H		NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	427			R -> H (in dbSNP:rs35649980).		protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						TGGCACACTGCGGGGCACCAT	0.632													C|||	321	0.0640974	0.0159	0.0375	5008	,	,		19028	0.1002		0.0855	False		,,,				2504	0.089				p.R427H		Atlas-SNP	.											.	KCNG4	71	.	0			c.G1280A						PASS	.	C	HIS/ARG	104,4296	81.4+/-119.9	1,102,2097	53.0	50.0	51.0		1280	5.6	1.0	16	dbSNP_126	51	649,7951	163.5+/-216.0	19,611,3670	yes	missense	KCNG4	NM_172347.2	29	20,713,5767	TT,TC,CC		7.5465,2.3636,5.7923	benign	427/520	84256103	753,12247	2200	4300	6500	SO:0001583	missense	93107	exon3			ACACTGCGGGGCA	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.1280G>A	16.37:g.84256103C>T	ENSP00000312129:p.Arg427His	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	138	65	0.471014	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	149	0.06822344322344322	11	0.022357723577235773	20	0.055248618784530384	55	0.09615384615384616	63	0.08311345646437995	C	26.8	4.771200	0.90108	0.023636	0.075465	ENSG00000168418	ENST00000308251	T	0.44881	0.91	5.61	5.61	0.85477	Ion transport (1);	0.165528	0.48286	D	0.000200	T	0.01092	0.0036	L	0.31207	0.915	0.80722	D	1	P	0.47191	0.891	B	0.42282	0.382	T	0.00374	-1.1780	10	0.56958	D	0.05	.	18.6265	0.91342	0.0:1.0:0.0:0.0	rs35649980	427	Q8TDN1	KCNG4_HUMAN	H	427	ENSP00000312129:R427H	ENSP00000312129:R427H	R	-	2	0	KCNG4	82813604	0.899000	0.30636	0.999000	0.59377	0.974000	0.67602	4.934000	0.63491	2.631000	0.89168	0.655000	0.94253	CGC	C|0.935;T|0.065	0.065	strong		0.632	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
LAMA2	3908	hgsc.bcm.edu	37	6	129371106	129371106	+	Silent	SNP	C	C	T	rs1140366	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:129371106C>T	ENST00000421865.2	+	2	205	c.156C>T	c.(154-156)atC>atT	p.I52I		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	52	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ATGCTCTTATCACGACCAATG	0.433													C|||	354	0.0706869	0.0015	0.0749	5008	,	,		17055	0.125		0.1282	False		,,,				2504	0.046				p.I52I		Atlas-SNP	.											.	LAMA2	481	.	0			c.C156T						PASS	.	C	,	104,4302	80.4+/-118.8	1,102,2100	196.0	176.0	183.0		156,156	4.6	1.0	6	dbSNP_86	183	1001,7599	216.4+/-255.5	62,877,3361	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	63,979,5461	TT,TC,CC		11.6395,2.3604,8.4961	,	52/3123,52/3119	129371106	1105,11901	2203	4300	6503	SO:0001819	synonymous_variant	3908	exon2			TCTTATCACGACC	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.156C>T	6.37:g.129371106C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	259	130	0.50193	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			C|0.907;T|0.093	0.093	strong		0.433	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
DTX2	113878	hgsc.bcm.edu	37	7	76131650	76131650	+	Silent	SNP	G	G	A	rs6958774	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:76131650G>A	ENST00000324432.5	+	9	1776	c.1266G>A	c.(1264-1266)gcG>gcA	p.A422A	DTX2_ENST00000446820.2_Silent_p.A375A|DTX2_ENST00000307569.8_Silent_p.A375A|DTX2_ENST00000446600.1_Silent_p.A331A|DTX2_ENST00000430490.2_Silent_p.A422A|DTX2_ENST00000413936.2_Silent_p.A422A	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	422					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						TGTCCACAGCGTCTGGATACA	0.597																																					p.A422A		Atlas-SNP	.											.	DTX2	64	.	0			c.G1266A						PASS	.						81.0	62.0	68.0					7																	76131650		2201	4296	6497	SO:0001819	synonymous_variant	113878	exon8			CACAGCGTCTGGA		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.1266G>A	7.37:g.76131650G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	157	53	0.33758	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			G|0.701;A|0.299	0.299	strong		0.597	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
TMEM232	642987	hgsc.bcm.edu	37	5	109960989	109960989	+	Silent	SNP	A	A	G	rs61730920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:109960989A>G	ENST00000455884.2	-	7	797	c.747T>C	c.(745-747)taT>taC	p.Y249Y	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Silent_p.Y249Y			C9JQI7	TM232_HUMAN	transmembrane protein 232	249						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						CTGTGTTCTCATATCTTTTCT	0.363													A|||	798	0.159345	0.3457	0.1354	5008	,	,		17424	0.0833		0.0905	False		,,,				2504	0.0736				p.Y249Y		Atlas-SNP	.											.	TMEM232	57	.	0			c.T747C						PASS	.	A		427,957		71,285,336	262.0	227.0	238.0		747	3.3	0.0	5	dbSNP_129	238	293,2889		14,265,1312	no	coding-synonymous	TMEM232	NM_001039763.3		85,550,1648	GG,GA,AA		9.208,30.8526,15.7687		249/658	109960989	720,3846	692	1591	2283	SO:0001819	synonymous_variant	642987	exon7			GTTCTCATATCTT	AK125070	CCDS47253.1, CCDS47253.2	5q22.1	2014-02-12	2009-10-02		ENSG00000186952	ENSG00000186952			37270	protein-coding gene	gene with protein product							Standard	NM_001039763		Approved	FLJ43080	uc011cvh.2	C9JQI7	OTTHUMG00000163297	ENST00000455884.2:c.747T>C	5.37:g.109960989A>G		Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	292	126	0.431507	NM_001039763	B4DKF4	Silent	SNP	ENST00000455884.2	37	CCDS47253.2																																																																																			A|0.859;G|0.141	0.141	strong		0.363	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
NFAT5	10725	hgsc.bcm.edu	37	16	69727273	69727273	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:69727273C>T	ENST00000354436.2	+	12	3809	c.3491C>T	c.(3490-3492)cCg>cTg	p.P1164L	NFAT5_ENST00000566899.1_Missense_Mutation_p.P1088L|NFAT5_ENST00000349945.1_Missense_Mutation_p.P1088L|NFAT5_ENST00000567239.1_Missense_Mutation_p.P1181L|NFAT5_ENST00000432919.1_Missense_Mutation_p.P1182L|NFAT5_ENST00000393742.2_Missense_Mutation_p.P1088L	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	1164					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TTTGCAGCACCGAACTCAATT	0.433																																					p.P1182L		Atlas-SNP	.											NFAT5_ENST00000432919,NS,carcinoma,-1,2	NFAT5	184	2	0			c.C3545T						scavenged	.						135.0	126.0	129.0					16																	69727273		2198	4300	6498	SO:0001583	missense	10725	exon13			CAGCACCGAACTC	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"""Nuclear factor of activated T-cells"""	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.3491C>T	16.37:g.69727273C>T	ENSP00000346420:p.Pro1164Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	164	3	0.0182927	NM_138713	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Missense_Mutation	SNP	ENST00000354436.2	37	CCDS10881.1	.	.	.	.	.	.	.	.	.	.	C	8.752	0.921504	0.17982	.	.	ENSG00000102908	ENST00000432919;ENST00000426654;ENST00000349945;ENST00000354436;ENST00000393742	T;T;T;T	0.46451	0.94;0.87;0.87;0.87	5.82	4.73	0.59995	.	0.291843	0.34386	N	0.004007	T	0.30510	0.0767	N	0.22421	0.69	0.41933	D	0.990576	B;B;B	0.21688	0.059;0.024;0.024	B;B;B	0.14023	0.008;0.01;0.005	T	0.07635	-1.0762	10	0.66056	D	0.02	0.4953	12.7519	0.57314	0.7127:0.2873:0.0:0.0	.	1181;1164;1182	A2RRB4;O94916;E9PHR7	.;NFAT5_HUMAN;.	L	1182;1181;1088;1164;1088	ENSP00000396538:P1182L;ENSP00000338806:P1088L;ENSP00000346420:P1164L;ENSP00000377343:P1088L	ENSP00000338806:P1088L	P	+	2	0	NFAT5	68284774	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.946000	0.49050	1.038000	0.40049	-0.271000	0.10264	CCG	.	.	none		0.433	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714	
CSPG4	1464	hgsc.bcm.edu	37	15	75970070	75970070	+	Missense_Mutation	SNP	C	C	T	rs8023621	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75970070C>T	ENST00000308508.5	-	9	5200	c.5108G>A	c.(5107-5109)cGc>cAc	p.R1703H	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1703	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.		R -> H (in dbSNP:rs8023621).		activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GTGGCTGGGGCGCTGGGGACA	0.632													C|||	1317	0.262979	0.1634	0.3919	5008	,	,		18353	0.1885		0.3787	False		,,,				2504	0.2638				p.R1703H		Atlas-SNP	.											.	CSPG4	175	.	0			c.G5108A						PASS	.	C	HIS/ARG	887,3507	328.5+/-300.6	90,707,1400	82.0	84.0	83.0		5108	3.1	1.0	15	dbSNP_116	83	3435,5153	481.0+/-370.5	696,2043,1555	yes	missense	CSPG4	NM_001897.4	29	786,2750,2955	TT,TC,CC		39.9977,20.1866,33.2923	benign	1703/2323	75970070	4322,8660	2197	4294	6491	SO:0001583	missense	1464	exon9			CTGGGGCGCTGGG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.5108G>A	15.37:g.75970070C>T	ENSP00000312506:p.Arg1703His	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	131	80	0.610687	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	573	0.2623626373626374	73	0.1483739837398374	129	0.356353591160221	80	0.13986013986013987	291	0.3839050131926121	C	15.05	2.717852	0.48622	0.201866	0.399977	ENSG00000173546	ENST00000308508	T	0.20200	2.09	4.96	3.09	0.35607	.	0.176621	0.40302	N	0.001133	T	0.00012	0.0000	L	0.38531	1.155	0.25196	P	0.99009862	B	0.09022	0.002	B	0.04013	0.001	T	0.45877	-0.9231	9	0.41790	T	0.15	.	5.5851	0.17269	0.1563:0.6778:0.0:0.1659	rs8023621;rs8023621	1703	Q6UVK1	CSPG4_HUMAN	H	1703	ENSP00000312506:R1703H	ENSP00000312506:R1703H	R	-	2	0	CSPG4	73757125	0.994000	0.37717	0.998000	0.56505	0.997000	0.91878	1.492000	0.35594	0.521000	0.28445	0.555000	0.69702	CGC	C|0.707;T|0.293	0.293	strong		0.632	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
TPRN	286262	hgsc.bcm.edu	37	9	140094306	140094306	+	Silent	SNP	G	G	A	rs375619082	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140094306G>A	ENST00000409012.4	-	1	944	c.858C>T	c.(856-858)tgC>tgT	p.C286C	TPRN_ENST00000541945.1_Intron|TPRN_ENST00000321773.2_Silent_p.C225C	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	286					sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						CTGCGGAGACGCACTGGCGCT	0.711													G|||	15	0.00299521	0.0	0.0043	5008	,	,		9338	0.0		0.0109	False		,,,				2504	0.001				p.C286C		Atlas-SNP	.											.	TPRN	28	.	0			c.C858T						PASS	.	-		5,1333		0,5,664	4.0	6.0	5.0		858	1.2	1.0	9		5	51,3043		0,51,1496	no	coding-synonymous	TPRN	NM_001128228.2		0,56,2160	AA,AG,GG		1.6484,0.3737,1.2635		286/712	140094306	56,4376	669	1547	2216	SO:0001819	synonymous_variant	286262	exon1			GGAGACGCACTGG	AK074735	CCDS56594.1	9q34.3	2011-01-06	2010-03-24	2010-03-24	ENSG00000176058	ENSG00000176058			26894	protein-coding gene	gene with protein product		613354	"""chromosome 9 open reading frame 75"", ""deafness, autosomal recessive 79"""	C9orf75, DFNB79		20170898, 20170899	Standard	NM_001128228		Approved	FLJ90254	uc004clu.3	Q4KMQ1	OTTHUMG00000020984	ENST00000409012.4:c.858C>T	9.37:g.140094306G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_001128228	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Silent	SNP	ENST00000409012.4	37	CCDS56594.1																																																																																			.	.	weak		0.711	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691	
OR51S1	119692	hgsc.bcm.edu	37	11	4869649	4869649	+	Missense_Mutation	SNP	G	G	A	rs12361955	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:4869649G>A	ENST00000322101.2	-	1	865	c.790C>T	c.(790-792)Ctc>Ttc	p.L264F	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	264			L -> F (in dbSNP:rs12361955).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGTGCCAGGAGGATCATAGGG	0.498													G|||	1499	0.299321	0.3411	0.2608	5008	,	,		19746	0.0675		0.4046	False		,,,				2504	0.4008				p.L264F		Atlas-SNP	.											OR51S1,NS,carcinoma,+2,1	OR51S1	83	1	0			c.C790T						scavenged	.	G	PHE/LEU	1535,2867	485.3+/-360.3	273,989,939	112.0	96.0	102.0		790	3.3	1.0	11	dbSNP_120	102	3700,4896	528.7+/-381.4	805,2090,1403	yes	missense	OR51S1	NM_001004758.1	22	1078,3079,2342	AA,AG,GG		43.0433,34.8705,40.2754	benign	264/324	4869649	5235,7763	2201	4298	6499	SO:0001583	missense	119692	exon1			CCAGGAGGATCAT	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"""GPCR / Class A : Olfactory receptors"""	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.790C>T	11.37:g.4869649G>A	ENSP00000322754:p.Leu264Phe	Somatic	127	2	0.015748		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	621	0.28434065934065933	168	0.34146341463414637	120	0.3314917127071823	32	0.055944055944055944	301	0.3970976253298153	G	8.217	0.801715	0.16397	0.348705	0.430433	ENSG00000176922	ENST00000322101	T	0.73363	-0.74	5.25	3.29	0.37713	GPCR, rhodopsin-like superfamily (1);	0.176237	0.27469	N	0.019222	T	0.00012	0.0000	N	0.04746	-0.17	0.58432	P	1.0000000000287557E-6	B	0.10296	0.003	B	0.12156	0.007	T	0.31668	-0.9935	9	0.87932	D	0	-11.6636	8.9594	0.35838	0.0843:0.295:0.6207:0.0	rs12361955;rs58301091;rs12361955	264	Q8NGJ8	O51S1_HUMAN	F	264	ENSP00000322754:L264F	ENSP00000322754:L264F	L	-	1	0	OR51S1	4826225	0.000000	0.05858	1.000000	0.80357	0.400000	0.30750	0.704000	0.25661	1.445000	0.47624	0.655000	0.94253	CTC	G|0.658;A|0.342	0.342	strong		0.498	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
TAPBPL	55080	hgsc.bcm.edu	37	12	6562293	6562293	+	Missense_Mutation	SNP	C	C	T	rs2041385	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6562293C>T	ENST00000266556.7	+	2	290	c.125C>T	c.(124-126)gCg>gTg	p.A42V	CD27-AS1_ENST00000545339.1_RNA|TAPBPL_ENST00000544021.1_Intron|CD27-AS1_ENST00000399492.2_RNA|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	42			A -> V (in dbSNP:rs2041385). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						TGCTTCCTGGCGAAGGACGGT	0.662													C|||	1140	0.227636	0.1074	0.1628	5008	,	,		17324	0.3204		0.2932	False		,,,				2504	0.273				p.A42V		Atlas-SNP	.											.	TAPBPL	21	.	0			c.C125T						PASS	.	C	VAL/ALA	535,3869		38,459,1705	43.0	37.0	39.0		125	-5.2	0.0	12	dbSNP_94	39	2476,6124		356,1764,2180	yes	missense	TAPBPL	NM_018009.4	64	394,2223,3885	TT,TC,CC		28.7907,12.148,23.1544	benign	42/469	6562293	3011,9993	2202	4300	6502	SO:0001583	missense	55080	exon2			TCCTGGCGAAGGA	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.125C>T	12.37:g.6562293C>T	ENSP00000266556:p.Ala42Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_018009	Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	37	CCDS8546.1	513	0.2348901098901099	48	0.0975609756097561	60	0.16574585635359115	187	0.3269230769230769	218	0.287598944591029	C	1.218	-0.627843	0.03610	0.12148	0.287907	ENSG00000139192	ENST00000266556	T	0.05580	3.42	4.05	-5.24	0.02789	.	0.507396	0.21121	N	0.079815	T	0.00012	0.0000	N	0.00823	-1.155	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.21381	-1.0247	9	0.02654	T	1	-2.2272	7.3675	0.26781	0.0:0.5521:0.1639:0.284	rs2041385;rs17725581;rs17845450;rs17858323;rs57312329;rs2041385	42	Q9BX59	TPSNR_HUMAN	V	42	ENSP00000266556:A42V	ENSP00000266556:A42V	A	+	2	0	TAPBPL	6432554	0.717000	0.27966	0.004000	0.12327	0.001000	0.01503	0.287000	0.18920	-0.736000	0.04831	-1.830000	0.00593	GCG	C|0.784;T|0.216	0.216	strong		0.662	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178634547	178634547	+	Silent	SNP	G	G	A	rs66565583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:178634547G>A	ENST00000251582.7	-	4	959	c.858C>T	c.(856-858)caC>caT	p.H286H	ADAMTS2_ENST00000274609.5_Silent_p.H286H	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	286	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		ACTTCTGTACGTGCTCCTTCC	0.637													A|||	680	0.135783	0.1309	0.1369	5008	,	,		14807	0.0089		0.2078	False		,,,				2504	0.1984				p.H286H		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C858T						PASS	.	A	,	567,3839	773.4+/-414.0	44,479,1680	153.0	125.0	135.0		858,858	1.1	1.0	5	dbSNP_130	135	1691,6909	738.3+/-407.0	174,1343,2783	no	coding-synonymous,coding-synonymous	ADAMTS2	NM_014244.4,NM_021599.2	,	218,1822,4463	AA,AG,GG		19.6628,12.8688,17.3612	,	286/1212,286/567	178634547	2258,10748	2203	4300	6503	SO:0001819	synonymous_variant	9509	exon4			CTGTACGTGCTCC	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.858C>T	5.37:g.178634547G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	193	95	0.492228	NM_021599		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			G|0.834;A|0.166	0.166	strong		0.637	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
TTN	7273	hgsc.bcm.edu	37	2	179421694	179421694	+	Missense_Mutation	SNP	A	A	G	rs9808377	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179421694A>G	ENST00000591111.1	-	280	83488	c.83264T>C	c.(83263-83265)aTc>aCc	p.I27755T	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I20331T|TTN_ENST00000342992.6_Missense_Mutation_p.I26828T|TTN_ENST00000589042.1_Missense_Mutation_p.I29396T|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I20456T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I20523T|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27755	Fibronectin type-III 102. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> T. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCAGAGATGATGAATTGAGT	0.463													G|||	2540	0.507188	0.5666	0.4049	5008	,	,		20211	0.7153		0.2495	False		,,,				2504	0.5501				p.I29396T		Atlas-SNP	.											.	TTN	18412	.	0			c.T88187C						PASS	.	G	THR/ILE,THR/ILE,THR/ILE,THR/ILE	2066,1878		556,954,462	92.0	95.0	94.0		61568,61367,80483,60992	-2.9	0.1	2	dbSNP_119	94	1831,6469		187,1457,2506	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	743,2411,2968	GG,GA,AA		22.0602,47.6166,31.8278	benign,benign,benign,benign	20523/27119,20456/27052,26828/33424,20331/26927	179421694	3897,8347	1972	4150	6122	SO:0001583	missense	7273	exon330			GAGATGATGAATT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.83264T>C	2.37:g.179421694A>G	ENSP00000465570:p.Ile27755Thr	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	203	109	0.536946	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		979	0.4482600732600733	282	0.573170731707317	129	0.356353591160221	385	0.6730769230769231	183	0.24142480211081793	G	3.223	-0.159019	0.06544	0.523834	0.220602	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	5.87	-2.9	0.05648	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00044	-2.455	0.51482	P	7.299999999998974E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.50617	-0.8807	8	0.87932	D	0	.	12.5594	0.56273	0.6079:0.0:0.3921:0.0	rs9808377;rs56743405;rs9808377	20331;20456;20523;27755	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	26828;20331;20523;20456;20328	ENSP00000343764:I26828T;ENSP00000434586:I20331T;ENSP00000340554:I20523T;ENSP00000352154:I20456T	ENSP00000340554:I20523T	I	-	2	0	TTN	179129940	0.202000	0.23423	0.094000	0.20943	0.170000	0.22686	0.686000	0.25392	-1.202000	0.02655	-0.726000	0.03593	ATC	A|0.549;G|0.451	0.451	strong		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SRPK1	6732	hgsc.bcm.edu	37	6	35803192	35803192	+	Silent	SNP	C	C	A	rs1049649	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:35803192C>A	ENST00000373825.2	-	16	2142	c.1857G>T	c.(1855-1857)tcG>tcT	p.S619S	SRPK1_ENST00000423325.2_Silent_p.S603S|SRPK1_ENST00000373822.1_Silent_p.S511S					SRSF protein kinase 1											endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						CCTCTTCCTGCGACCACTCAT	0.527													A|||	1473	0.294129	0.3071	0.2781	5008	,	,		18125	0.1607		0.3231	False		,,,				2504	0.3957				p.S619S	NSCLC(31;67 978 16289 24856 26454)	Atlas-SNP	.											.	SRPK1	61	.	0			c.G1857T						PASS	.	A		1161,2725		173,815,955	53.0	57.0	56.0		1857	4.3	1.0	6	dbSNP_86	56	2575,5715		422,1731,1992	no	coding-synonymous	SRPK1	NM_003137.4		595,2546,2947	AA,AC,CC		31.0615,29.8765,30.6833		619/656	35803192	3736,8440	1943	4145	6088	SO:0001819	synonymous_variant	6732	exon16			TTCCTGCGACCAC	U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063			11305	protein-coding gene	gene with protein product	"""SR protein kinase 1"", ""serine/arginine-rich splicing factor kinase 1"""	601939	"""SFRS protein kinase 1"""			8208298, 10198174	Standard	NM_003137		Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.1857G>T	6.37:g.35803192C>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_003137		Silent	SNP	ENST00000373825.2	37	CCDS47415.1																																																																																			C|0.707;A|0.293	0.293	strong		0.527	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040319.3	NM_003137	
BEST1	7439	hgsc.bcm.edu	37	11	61730553	61730553	+	Intron	SNP	T	T	C	rs17185413	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61730553T>C	ENST00000378043.4	+	10	2382				FTH1_ENST00000529631.1_Intron|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000449131.2_Missense_Mutation_p.S583P|BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000301774.9_Missense_Mutation_p.S271P|BEST1_ENST00000378042.3_Intron	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						AGGGAAGTGTTCGGGACCTTT	0.537													T|||	523	0.104433	0.0151	0.1268	5008	,	,		21309	0.002		0.2247	False		,,,				2504	0.1912				p.S583P		Atlas-SNP	.											BEST1_ENST00000449131,colon,carcinoma,-1,2	BEST1	85	2	0			c.T1747C						PASS	.	T	PRO/SER,	73,1311		1,71,620	52.0	45.0	47.0		1747,	-2.9	0.0	11	dbSNP_123	47	798,2384		102,594,895	yes	missense,intron	BEST1	NM_001139443.1,NM_004183.3	74,	103,665,1515	CC,CT,TT		25.0786,5.2746,19.0758	,	583/605,	61730553	871,3695	692	1591	2283	SO:0001627	intron_variant	7439	exon9			AAGTGTTCGGGAC	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1739+188T>C	11.37:g.61730553T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_001139443	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Missense_Mutation	SNP	ENST00000378043.4	37	CCDS31580.1	230	0.10531135531135531	9	0.018292682926829267	60	0.16574585635359115	0	0.0	161	0.21240105540897097	T	17.59	3.427298	0.62733	0.052746	0.250786	ENSG00000167995	ENST00000301774;ENST00000449131	T;D	0.97209	-0.36;-4.29	4.35	-2.91	0.05631	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.50448	-0.8827	7	.	.	.	.	2.0384	0.03545	0.1365:0.3758:0.2746:0.2131	rs17185413	583	O76090-3	.	P	271;583	ENSP00000301774:S271P;ENSP00000399709:S583P	.	S	+	1	0	BEST1	61487129	0.000000	0.05858	0.000000	0.03702	0.259000	0.26198	-0.347000	0.07750	-0.344000	0.08338	0.459000	0.35465	TCG	T|0.906;C|0.094	0.094	strong		0.537	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
WNK2	65268	hgsc.bcm.edu	37	9	96055063	96055063	+	Silent	SNP	C	C	T	rs41278286	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:96055063C>T	ENST00000297954.4	+	23	5427	c.5427C>T	c.(5425-5427)gaC>gaT	p.D1809D	WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000427277.2_Silent_p.D1384D|WNK2_ENST00000356055.3_Silent_p.D136D|WNK2_ENST00000349097.3_Silent_p.D1421D|WNK2_ENST00000395477.2_Silent_p.D1772D	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1809					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CCCCACCCGACGTCTACCTGG	0.692													C|||	1965	0.392372	0.3487	0.2954	5008	,	,		13856	0.4206		0.3131	False		,,,				2504	0.5726				p.D1772D		Atlas-SNP	.											WNK2_ENST00000297954,colon,carcinoma,+2,4	WNK2	277	4	0			c.C5316T						PASS	.	C		1467,2891		252,963,964	15.0	15.0	15.0		5316	-1.8	0.9	9	dbSNP_127	15	2457,6027		393,1671,2178	no	coding-synonymous	WNK2	NM_006648.3		645,2634,3142	TT,TC,CC		28.9604,33.6622,30.556		1772/2218	96055063	3924,8918	2179	4242	6421	SO:0001819	synonymous_variant	65268	exon22			ACCCGACGTCTAC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.5427C>T	9.37:g.96055063C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	192	98	0.510417	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		777|777	0.3557692307692308|0.3557692307692308	176|176	0.35772357723577236|0.35772357723577236	105|105	0.2900552486187845|0.2900552486187845	256|256	0.44755244755244755|0.44755244755244755	240|240	0.316622691292876|0.316622691292876	C|C	0.625|0.625	-0.819743|-0.819743	0.02776|0.02776	0.336622|0.336622	0.289604|0.289604	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730;ENST00000448251;ENST00000453718	.|.	.|.	.|.	5.39|5.39	-1.75|-1.75	0.08031|0.08031	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999996005|0.9999999999996005	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.46005|0.46005	-0.9222|-0.9222	3|3	.|.	.|.	.|.	.|.	11.3977|11.3977	0.49851|0.49851	0.0:0.3577:0.0:0.6423|0.0:0.3577:0.0:0.6423	rs41278286;rs57682323;rs61738874|rs41278286;rs57682323;rs61738874	.|.	.|.	.|.	C|M	1376|1768;569;294	.|.	.|.	R|T	+|+	1|2	0|0	WNK2|WNK2	95094884|95094884	0.000000|0.000000	0.05858|0.05858	0.908000|0.908000	0.35775|0.35775	0.064000|0.064000	0.16182|0.16182	-2.297000|-2.297000	0.01141|0.01141	-0.195000|-0.195000	0.10382|0.10382	-1.010000|-1.010000	0.02471|0.02471	CGT|ACG	C|0.672;T|0.328	0.328	strong		0.692	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
CNGA2	1260	hgsc.bcm.edu	37	X	150909307	150909307	+	Missense_Mutation	SNP	G	G	T	rs35350051	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:150909307G>T	ENST00000329903.4	+	4	449	c.416G>T	c.(415-417)tGg>tTg	p.W139L		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	139			W -> L (in dbSNP:rs35350051).		phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					GCTGGGGATTGGTACTACTGC	0.552													G|||	457	0.12106	0.0068	0.1081	3775	,	,		13777	0.1974		0.0954	False		,,,				2504	0.0798				p.W139L		Atlas-SNP	.											.	CNGA2	136	.	0			c.G416T						PASS	.	G	LEU/TRP	108,3727		1,91,15,1540,556	212.0	183.0	193.0		416	5.4	1.0	X	dbSNP_126	193	986,5742		59,595,273,1774,1599	yes	missense	CNGA2	NM_005140.1	61	60,686,288,3314,2155	TT,TG,T,GG,G		14.6552,2.8162,10.3569	benign	139/665	150909307	1094,9469	2203	4300	6503	SO:0001583	missense	1260	exon5			GGGATTGGTACTA	S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.416G>T	X.37:g.150909307G>T	ENSP00000328478:p.Trp139Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	176	173	0.982955	NM_005140	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	196	0.11814345991561181	5	0.01020408163265306	25	0.07352941176470588	58	0.11372549019607843	50	0.06868131868131869	G	1.518	-0.547556	0.04024	0.028162	0.146552	ENSG00000183862	ENST00000329903	D	0.97161	-4.27	5.44	5.44	0.79542	.	0.329033	0.34133	N	0.004228	T	0.05273	0.0140	N	0.04724	-0.175	0.32707	P	0.512141	B	0.06786	0.001	B	0.06405	0.002	T	0.68678	-0.5345	9	0.09843	T	0.71	.	15.5522	0.76161	0.0:0.0:1.0:0.0	rs35350051	139	Q16280	CNGA2_HUMAN	L	139	ENSP00000328478:W139L	ENSP00000328478:W139L	W	+	2	0	CNGA2	150659963	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	2.216000	0.42871	2.267000	0.75376	0.544000	0.68410	TGG	G|0.898;T|0.102	0.102	strong		0.552	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140	
NOP9	161424	hgsc.bcm.edu	37	14	24773387	24773387	+	Silent	SNP	T	T	C	rs2144494	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24773387T>C	ENST00000267425.3	+	8	1644	c.1551T>C	c.(1549-1551)ctT>ctC	p.L517L	NOP9_ENST00000396802.3_Silent_p.L517L	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	517							poly(A) RNA binding (GO:0044822)										TTCTGTCCCTTGCCCAAAGTC	0.587													G|||	720	0.14377	0.1346	0.3444	5008	,	,		19048	0.004		0.1849	False		,,,				2504	0.1155				p.L517L		Atlas-SNP	.											.	.	.	.	0			c.T1551C						PASS	.	G		650,3756		54,542,1607	64.0	55.0	58.0		1551	1.5	1.0	14	dbSNP_96	58	1782,6818		188,1406,2706	no	coding-synonymous	C14orf21	NM_174913.1		242,1948,4313	CC,CT,TT		20.7209,14.7526,18.6991		517/637	24773387	2432,10574	2203	4300	6503	SO:0001819	synonymous_variant	161424	exon8			GTCCCTTGCCCAA		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.1551T>C	14.37:g.24773387T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	CCDS9624.1																																																																																			T|0.835;C|0.165	0.165	strong		0.587	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
VCAN	1462	hgsc.bcm.edu	37	5	82834299	82834299	+	Missense_Mutation	SNP	G	G	A	rs188703	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:82834299G>A	ENST00000265077.3	+	8	6042	c.5477G>A	c.(5476-5478)cGt>cAt	p.R1826H	VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.R839H|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1826	GAG-beta.		R -> H (in dbSNP:rs188703).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	ACTCTCCCACGTAGTCCTGCC	0.483													G|||	1795	0.358427	0.3449	0.4611	5008	,	,		16825	0.3234		0.4254	False		,,,				2504	0.271				p.R1826H		Atlas-SNP	.											VCAN,NS,carcinoma,-1,1	VCAN	498	1	0			c.G5477A						PASS	.	G	,HIS/ARG,,HIS/ARG	1549,2857	445.5+/-347.7	261,1027,915	69.0	77.0	74.0		,2516,,5477	0.2	0.0	5	dbSNP_79	74	3441,5159	478.3+/-369.9	704,2033,1563	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,29,,29	965,3060,2478	AA,AG,GG		40.0116,35.1566,38.3669	,benign,,benign	,839/2410,,1826/3397	82834299	4990,8016	2203	4300	6503	SO:0001583	missense	1462	exon8			TCCCACGTAGTCC	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.5477G>A	5.37:g.82834299G>A	ENSP00000265077:p.Arg1826His	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	832	0.38095238095238093	139	0.28252032520325204	169	0.46685082872928174	203	0.3548951048951049	321	0.4234828496042216	G	12.50	1.956712	0.34565	0.351566	0.400116	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.84660	-1.85;-1.88;3.27	5.82	0.253	0.15551	.	0.983187	0.08317	N	0.964443	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.31931	0.347;0.235	B;B	0.27170	0.077;0.035	T	0.21415	-1.0246	9	0.49607	T	0.09	.	2.0501	0.03569	0.1803:0.1061:0.4634:0.2501	rs188703;rs309558;rs479344;rs52807291;rs60541692;rs188703	839;1826	P13611-2;P13611	.;CSPG2_HUMAN	H	1826;839;839	ENSP00000265077:R1826H;ENSP00000340062:R839H;ENSP00000426251:R839H	ENSP00000265077:R1826H	R	+	2	0	VCAN	82870055	0.003000	0.15002	0.001000	0.08648	0.027000	0.11550	0.786000	0.26844	0.328000	0.23435	0.655000	0.94253	CGT	G|0.623;A|0.377	0.377	strong		0.483	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
ZPBP	11055	hgsc.bcm.edu	37	7	50097697	50097697	+	Silent	SNP	A	A	G	rs76027725	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:50097697A>G	ENST00000046087.2	-	4	444	c.375T>C	c.(373-375)ctT>ctC	p.L125L	ZPBP_ENST00000491129.1_5'Flank|ZPBP_ENST00000419417.1_Silent_p.L124L	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	125					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					TTTGGAATACAAGGCTTCCTG	0.338													A|||	87	0.0173722	0.0083	0.0187	5008	,	,		19651	0.0		0.0547	False		,,,				2504	0.0082				p.L125L		Atlas-SNP	.											.	ZPBP	65	.	0			c.T375C						PASS	.	A	,	60,4346	58.1+/-94.6	1,58,2144	112.0	113.0	112.0		372,375	3.3	0.9	7	dbSNP_131	112	389,8211	125.6+/-184.2	9,371,3920	yes	coding-synonymous,coding-synonymous	ZPBP	NM_001159878.1,NM_007009.2	,	10,429,6064	GG,GA,AA		4.5233,1.3618,3.4523	,	124/351,125/352	50097697	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	11055	exon4			GAATACAAGGCTT	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.375T>C	7.37:g.50097697A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	170	98	0.576471	NM_007009	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Silent	SNP	ENST00000046087.2	37	CCDS5509.1																																																																																			A|0.965;G|0.035	0.035	strong		0.338	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009	
TP53BP2	7159	hgsc.bcm.edu	37	1	223989966	223989966	+	Silent	SNP	C	C	T	rs1153933	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:223989966C>T	ENST00000343537.7	-	9	1368	c.1077G>A	c.(1075-1077)tcG>tcA	p.S359S	TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391879.2_5'Flank|TP53BP2_ENST00000391878.2_Silent_p.S230S	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	353					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		GCATAGTAGACGACTGGATAT	0.552													C|||	1066	0.212859	0.416	0.2147	5008	,	,		15374	0.1935		0.0934	False		,,,				2504	0.0798				p.S359S		Atlas-SNP	.											.	TP53BP2	144	.	0			c.G1077A						PASS	.	C	,	1527,2879	483.2+/-359.6	249,1029,925	69.0	70.0	70.0		1077,690	-11.4	0.0	1	dbSNP_87	70	586,8014	156.3+/-210.2	26,534,3740	no	coding-synonymous,coding-synonymous	TP53BP2	NM_001031685.2,NM_005426.2	,	275,1563,4665	TT,TC,CC		6.814,34.6573,16.2463	,	359/1135,230/1006	223989966	2113,10893	2203	4300	6503	SO:0001819	synonymous_variant	7159	exon9			AGTAGACGACTGG	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	12000	protein-coding gene	gene with protein product		602143	"""tumor protein p53-binding protein, 2"""			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.1077G>A	1.37:g.223989966C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Silent	SNP	ENST00000343537.7	37	CCDS44319.1																																																																																			C|0.815;N|0.000	.	strong		0.552	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426	
RFXANK	8625	hgsc.bcm.edu	37	19	19304899	19304899	+	Missense_Mutation	SNP	G	G	C	rs34282046	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19304899G>C	ENST00000303088.4	+	3	618	c.144G>C	c.(142-144)gaG>gaC	p.E48D	RFXANK_ENST00000353145.1_Missense_Mutation_p.E48D|RFXANK_ENST00000456252.3_Missense_Mutation_p.E48D|MEF2BNB-MEF2B_ENST00000514819.3_5'Flank|MEF2BNB-MEF2B_ENST00000444486.3_5'Flank|MEF2B_ENST00000162023.5_5'Flank|MEF2BNB_ENST00000585679.1_5'Flank|MEF2B_ENST00000602424.2_5'Flank|MEF2BNB_ENST00000462790.3_5'Flank|MEF2BNB_ENST00000477565.3_5'Flank|MEF2BNB_ENST00000494489.2_5'Flank|RFXANK_ENST00000407360.3_Missense_Mutation_p.E48D|RFXANK_ENST00000392324.4_Missense_Mutation_p.E48D	NM_003721.2	NP_003712.1	O14593	RFXK_HUMAN	regulatory factor X-associated ankyrin-containing protein	48			E -> D (in dbSNP:rs34282046).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			NS(1)|breast(1)|endometrium(1)|lung(8)|ovary(2)|prostate(1)	14			Epithelial(12;0.00228)			GCACCCCTGAGCCTGTGAATC	0.572													G|||	220	0.0439297	0.0053	0.111	5008	,	,		17509	0.0139		0.0467	False		,,,				2504	0.0767				p.E48D		Atlas-SNP	.											.	RFXANK	31	.	0			c.G144C						PASS	.	G	ASP/GLU,ASP/GLU	42,4364	46.7+/-81.2	1,40,2162	142.0	113.0	123.0		144,144	0.4	0.9	19	dbSNP_126	123	482,8118	141.4+/-197.7	14,454,3832	yes	missense,missense	RFXANK	NM_003721.2,NM_134440.1	45,45	15,494,5994	CC,CG,GG		5.6047,0.9532,4.0289	benign,benign	48/261,48/238	19304899	524,12482	2203	4300	6503	SO:0001583	missense	8625	exon3			CCCTGAGCCTGTG	AF094760	CCDS12395.1, CCDS12396.1, CCDS62611.1	19p12	2014-09-17			ENSG00000064490	ENSG00000064490		"""Ankyrin repeat domain containing"""	9987	protein-coding gene	gene with protein product	"""ankyrin repeat-containing regulatory factor X-associated protein"", ""regulatory factor X subunit B"", ""RFX-Bdelta4"", ""DNA-binding protein RFXANK"""	603200				9806546, 10072068	Standard	NM_003721		Approved	BLS, RFX-B, ANKRA1, F14150_1, MGC138628	uc002nls.3	O14593	OTTHUMG00000169224	ENST00000303088.4:c.144G>C	19.37:g.19304899G>C	ENSP00000305071:p.Glu48Asp	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	140	69	0.492857	NM_003721	O95839|Q24JQ1|Q6FGA8	Missense_Mutation	SNP	ENST00000303088.4	37	CCDS12395.1	77	0.035256410256410256	5	0.01016260162601626	36	0.09944751381215469	8	0.013986013986013986	28	0.036939313984168866	G	0.254	-1.004566	0.02112	0.009532	0.056047	ENSG00000064490	ENST00000353145;ENST00000421262;ENST00000456252;ENST00000303088;ENST00000407360;ENST00000543652;ENST00000540981;ENST00000541873;ENST00000392324;ENST00000535017	T;T;T;T;T;T;T;T;T	0.47177	1.19;0.85;1.16;1.2;1.13;1.81;1.68;1.19;1.42	4.22	0.432	0.16529	.	0.379447	0.25951	N	0.027255	T	0.00496	0.0016	N	0.02916	-0.46	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.001	T	0.10776	-1.0615	10	0.52906	T	0.07	-16.4163	6.1793	0.20461	0.1271:0.5086:0.3643:0.0	rs34282046	48;48;48;48	Q6IB23;Q24JQ1;O14593-2;O14593	.;.;.;RFXK_HUMAN	D	48;48;48;48;48;48;48;48;48;13	ENSP00000262804:E48D;ENSP00000393159:E48D;ENSP00000409138:E48D;ENSP00000305071:E48D;ENSP00000384572:E48D;ENSP00000439581:E48D;ENSP00000440325:E48D;ENSP00000376138:E48D;ENSP00000444280:E13D	ENSP00000305071:E48D	E	+	3	2	RFXANK	19165899	0.030000	0.19436	0.914000	0.36105	0.118000	0.20060	-0.136000	0.10405	0.234000	0.21139	0.462000	0.41574	GAG	G|0.957;C|0.043	0.043	strong		0.572	RFXANK-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402923.2	NM_003721	
ANAPC1	64682	hgsc.bcm.edu	37	2	112551673	112551673	+	Silent	SNP	G	G	A	rs200630962		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:112551673G>A	ENST00000341068.3	-	37	5272	c.4500C>T	c.(4498-4500)tcC>tcT	p.S1500S		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	1500					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.S1500S(4)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						CATTAGGTGCGGACAAATAAG	0.279																																					p.S1500S		Atlas-SNP	.											ANAPC1,NS,carcinoma,0,2	ANAPC1	116	2	4	Substitution - coding silent(4)	prostate(4)	c.C4500T						scavenged	.						11.0	13.0	13.0					2																	112551673		1952	4023	5975	SO:0001819	synonymous_variant	64682	exon37			AGGTGCGGACAAA	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"""Anaphase promoting complex subunits"""	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.4500C>T	2.37:g.112551673G>A		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Silent	SNP	ENST00000341068.3	37	CCDS2093.1	.	.	.	.	.	.	.	.	.	.	A	7.932	0.740923	0.15642	.	.	ENSG00000153107	ENST00000427997	.	.	.	4.54	1.89	0.25635	.	.	.	.	.	T	0.27063	0.0663	.	.	.	0.09310	P	0.999999999999997	.	.	.	.	.	.	T	0.26395	-1.0104	3	.	.	.	-16.0881	1.4848	0.02444	0.5341:0.1136:0.1479:0.2044	.	.	.	.	C	1035	.	.	R	-	1	0	ANAPC1	112268144	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	0.500000	0.22562	0.212000	0.20703	-0.352000	0.07741	CGC	G|0.500;A|0.500	0.500	strong		0.279	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	
MEP1A	4224	hgsc.bcm.edu	37	6	46806809	46806809	+	Missense_Mutation	SNP	C	C	T	rs1804211	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46806809C>T	ENST00000230588.4	+	14	2186	c.2177C>T	c.(2176-2178)aCg>aTg	p.T726M		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	726			T -> M (in dbSNP:rs1804211). {ECO:0000269|PubMed:14702039}.		digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			ATCGGAGGCACGGCTGGCGTG	0.602													C|||	1272	0.253994	0.09	0.3646	5008	,	,		18798	0.1944		0.3469	False		,,,				2504	0.363				p.T726M		Atlas-SNP	.											.	MEP1A	93	.	0			c.C2177T						PASS	.	C	MET/THR	547,3859	246.5+/-255.1	36,475,1692	124.0	104.0	111.0		2177	-1.3	0.0	6	dbSNP_89	111	3046,5554	470.1+/-367.7	541,1964,1795	no	missense	MEP1A	NM_005588.2	81	577,2439,3487	TT,TC,CC		35.4186,12.4149,27.6257	possibly-damaging	726/747	46806809	3593,9413	2203	4300	6503	SO:0001583	missense	4224	exon14			GAGGCACGGCTGG		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.2177C>T	6.37:g.46806809C>T	ENSP00000230588:p.Thr726Met	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	205	110	0.536585	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	37	CCDS4918.1	524	0.23992673992673993	40	0.08130081300813008	128	0.35359116022099446	83	0.1451048951048951	273	0.36015831134564646	C	14.06	2.423088	0.43020	0.124149	0.354186	ENSG00000112818	ENST00000230588	T	0.26373	1.74	5.8	-1.33	0.09172	.	0.909437	0.09810	N	0.752909	T	0.07007	0.0178	L	0.29908	0.895	0.80722	P	0.0	P;P	0.48998	0.918;0.918	B;B	0.39738	0.308;0.289	T	0.20907	-1.0261	9	0.66056	D	0.02	0.1704	8.2215	0.31543	0.0:0.3658:0.1088:0.5254	rs1804211;rs16875099;rs52810040	754;726	B7ZL91;Q16819	.;MEP1A_HUMAN	M	726	ENSP00000230588:T726M	ENSP00000230588:T726M	T	+	2	0	MEP1A	46914768	0.000000	0.05858	0.027000	0.17364	0.128000	0.20619	-0.788000	0.04614	-0.097000	0.12307	0.650000	0.86243	ACG	C|0.738;T|0.262	0.262	strong		0.602	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588	
OTOF	9381	hgsc.bcm.edu	37	2	26700700	26700700	+	Intron	SNP	G	G	A	rs4665855	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:26700700G>A	ENST00000272371.2	-	19	2341				OTOF_ENST00000403946.3_Intron|OTOF_ENST00000339598.3_Intron|OTOF_ENST00000402415.3_Missense_Mutation_p.P21L|OTOF_ENST00000338581.6_Intron	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin						membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTTGATCAGGGGAGTGAGGGA	0.572													G|||	3018	0.602636	0.4561	0.5994	5008	,	,		18953	0.9841		0.4414	False		,,,				2504	0.5757				p.P21L	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											OTOF_ENST00000402415,NS,carcinoma,0,2	OTOF	524	2	0			c.C62T						scavenged	.	G	,,LEU/PRO,	1167,1487		265,637,425	46.0	53.0	50.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,62,	-0.6	0.0	2	dbSNP_111	50	1821,2795		348,1125,835	yes	intron,intron,missense,intron	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,98,	613,1762,1260	AA,AG,GG		39.4497,43.9714,41.1004	,,,	,,21/1308,	26700700	2988,4282	1327	2308	3635	SO:0001627	intron_variant	9381	exon1			ATCAGGGGAGTGA	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2215-83C>T	2.37:g.26700700G>A		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	266	124	0.466165	NM_194322	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	1357	0.6213369963369964	231	0.4695121951219512	211	0.5828729281767956	561	0.9807692307692307	354	0.46701846965699206	G	2.955	-0.215799	0.06101	0.439714	0.394497	ENSG00000115155	ENST00000402415	T	0.76839	-1.05	3.62	-0.572	0.11745	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.29971	-0.9994	6	.	.	.	.	0.7994	0.01072	0.2277:0.1857:0.3963:0.1903	rs4665855;rs58375897;rs4665855	21	Q9HC10-3	.	L	21	ENSP00000383906:P21L	.	P	-	2	0	OTOF	26554204	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.242000	0.18087	-0.112000	0.11979	-1.581000	0.00855	CCC	G|0.410;A|0.590	0.590	strong		0.572	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
NWD1	284434	hgsc.bcm.edu	37	19	16872794	16872794	+	Silent	SNP	C	C	T	rs61995711	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:16872794C>T	ENST00000552788.1	+	6	1978	c.1978C>T	c.(1978-1980)Ctg>Ttg	p.L660L	NWD1_ENST00000523826.1_Silent_p.L454L|NWD1_ENST00000339803.6_Silent_p.L525L|NWD1_ENST00000379808.3_Silent_p.L660L|NWD1_ENST00000524140.2_Silent_p.L660L|NWD1_ENST00000549814.1_Silent_p.L660L			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	660	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CTGTAGACAGCTGGTCGAGGT	0.582													C|||	33	0.00658946	0.0008	0.0086	5008	,	,		16843	0.0		0.0229	False		,,,				2504	0.0031				p.L660L		Atlas-SNP	.											.	NWD1	303	.	0			c.C1978T						PASS	.	C		17,4389	24.3+/-50.5	0,17,2186	89.0	70.0	76.0		1978	3.3	1.0	19	dbSNP_129	76	198,8402	86.6+/-149.0	2,194,4104	no	coding-synonymous	NWD1	NM_001007525.3		2,211,6290	TT,TC,CC		2.3023,0.3858,1.6531		660/1433	16872794	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	284434	exon8			AGACAGCTGGTCG	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1978C>T	19.37:g.16872794C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_001007525	C9J021|Q68CT3	Silent	SNP	ENST00000552788.1	37																																																																																				C|0.986;T|0.014	0.014	strong		0.582	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
HTN3	3347	hgsc.bcm.edu	37	4	70898907	70898907	+	Silent	SNP	C	C	T	rs1849937	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:70898907C>T	ENST00000530128.1	+	5	201	c.126C>T	c.(124-126)ggC>ggT	p.G42G	HTN3_ENST00000381057.3_Silent_p.G32G|HTN3_ENST00000526767.1_Silent_p.G42G			P15516	HIS3_HUMAN	histatin 3	42					biomineral tissue development (GO:0031214)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)	p.G42G(1)		breast(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	8						CACATCGAGGCTATAGATCAA	0.368													C|||	563	0.11242	0.0151	0.1614	5008	,	,		19306	0.2024		0.1143	False		,,,				2504	0.1145				p.G42G		Atlas-SNP	.											HTN3,NS,carcinoma,0,1	HTN3	16	1	1	Substitution - coding silent(1)	prostate(1)	c.C126T						PASS	.	C		151,4255	103.8+/-142.4	5,141,2057	140.0	125.0	130.0		126	-2.2	0.0	4	dbSNP_92	130	831,7769	191.0+/-237.3	44,743,3513	no	coding-synonymous	HTN3	NM_000200.2		49,884,5570	TT,TC,CC		9.6628,3.4271,7.5504		42/52	70898907	982,12024	2203	4300	6503	SO:0001819	synonymous_variant	3347	exon5			TCGAGGCTATAGA		CCDS33999.1	4q13	2008-08-29							5284	protein-coding gene	gene with protein product		142702					Standard	NM_000200		Approved	HIS2	uc003hew.2	P15516		ENST00000530128.1:c.126C>T	4.37:g.70898907C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	161	62	0.385093	NM_000200	Q16243|Q502Z1	Silent	SNP	ENST00000530128.1	37	CCDS33999.1																																																																																			C|0.911;T|0.089	0.089	strong		0.368	HTN3-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387375.1	NM_000200	
CFAP44	55779	hgsc.bcm.edu	37	3	113128051	113128051	+	Silent	SNP	G	G	T	rs13059888	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:113128051G>T	ENST00000295868.2	-	7	954	c.792C>A	c.(790-792)ccC>ccA	p.P264P	WDR52-AS1_ENST00000498480.1_RNA|WDR52-AS1_ENST00000473329.1_RNA|WDR52_ENST00000393845.2_Silent_p.P264P	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						TCCTTAGTATGGGTTGTTCTT	0.423													G|||	248	0.0495208	0.0136	0.0807	5008	,	,		16702	0.001		0.1412	False		,,,				2504	0.0317				p.P264P		Atlas-SNP	.											.	WDR52	151	.	0			c.C792A						PASS	.	G	,	98,4308	79.3+/-117.8	1,96,2106	144.0	139.0	141.0		792,792	2.0	1.0	3	dbSNP_121	141	1129,7471	232.8+/-266.3	80,969,3251	no	coding-synonymous,coding-synonymous	WDR52	NM_001164496.1,NM_018338.3	,	81,1065,5357	TT,TG,GG		13.1279,2.2242,9.4341	,	264/1855,264/983	113128051	1227,11779	2203	4300	6503	SO:0001819	synonymous_variant	55779	exon7			TAGTATGGGTTGT																												ENST00000295868.2:c.792C>A	3.37:g.113128051G>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_001164496		Silent	SNP	ENST00000295868.2	37	CCDS2972.1																																																																																			G|0.919;T|0.081	0.081	strong		0.423	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
FTSJ3	117246	hgsc.bcm.edu	37	17	61901197	61901197	+	Missense_Mutation	SNP	T	T	A	rs2727288	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:61901197T>A	ENST00000427159.2	-	13	1915	c.1270A>T	c.(1270-1272)Agc>Tgc	p.S424C		NM_017647.3	NP_060117.3			FtsJ homolog 3 (E. coli)											breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CGGATGGTGCTCAAGGAGAAC	0.577													G|||	3638	0.726438	0.9569	0.6787	5008	,	,		16633	0.5556		0.5984	False		,,,				2504	0.7566				p.S424C		Atlas-SNP	.											.	FTSJ3	63	.	0			c.A1270T						PASS	.	G	CYS/SER	3940,466		1759,422,22	131.0	126.0	127.0		1270	4.7	0.9	17	dbSNP_100	127	5216,3384		1599,2018,683	yes	missense	FTSJ3	NM_017647.3	112	3358,2440,705	AA,AT,TT		39.3488,10.5765,29.6017	benign	424/848	61901197	9156,3850	2203	4300	6503	SO:0001583	missense	117246	exon13			TGGTGCTCAAGGA	AF327355	CCDS11644.1	17q23.3	2014-09-11			ENSG00000108592	ENSG00000108592			17136	protein-coding gene	gene with protein product	"""SPB1 RNA methyltransferase homolog (S. cerevisiae)"""						Standard	NM_017647		Approved	SPB1	uc002jca.3	Q8IY81	OTTHUMG00000179012	ENST00000427159.2:c.1270A>T	17.37:g.61901197T>A	ENSP00000396673:p.Ser424Cys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	191	84	0.439791	NM_017647		Missense_Mutation	SNP	ENST00000427159.2	37	CCDS11644.1	1488	0.6813186813186813	470	0.9552845528455285	229	0.6325966850828729	333	0.5821678321678322	456	0.6015831134564644	G	6.589	0.477083	0.12521	0.894235	0.606512	ENSG00000108592	ENST00000427159	T	0.33216	1.42	5.65	4.68	0.58851	.	0.266108	0.37857	N	0.001907	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.39624	0.681	B	0.35971	0.215	T	0.18999	-1.0319	9	0.72032	D	0.01	-3.2134	8.945	0.35753	0.0769:0.0:0.7739:0.1492	rs2727288;rs3744292;rs11549663;rs17639101;rs17844828;rs17857126;rs17857539;rs52805130;rs56861461;rs2727288	424	Q8IY81	RRMJ3_HUMAN	C	424	ENSP00000396673:S424C	ENSP00000396673:S424C	S	-	1	0	FTSJ3	59254929	0.000000	0.05858	0.934000	0.37439	0.950000	0.60333	0.028000	0.13644	0.948000	0.37687	-0.121000	0.15023	AGC	T|0.319;A|0.681	0.681	strong		0.577	FTSJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444386.1		
OR1S1	219959	hgsc.bcm.edu	37	11	57982763	57982763	+	Missense_Mutation	SNP	A	A	G	rs1993088	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57982763A>G	ENST00000309433.6	+	1	547	c.547A>G	c.(547-549)Aac>Gac	p.N183D		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	183			N -> D (in dbSNP:rs1993088).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N183D(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				GCTCTTCTGTAACCACAACAC	0.463																																					p.N183D		Atlas-SNP	.											OR1S1,NS,carcinoma,0,2	OR1S1	139	2	1	Substitution - Missense(1)	stomach(1)	c.A547G						scavenged	.	A	ASP/ASN	839,3563		197,445,1559	211.0	172.0	185.0		547	-1.1	0.0	11	dbSNP_92	185	2540,6040		772,996,2522	no	missense	OR1S1	NM_001004458.1	23	969,1441,4081	GG,GA,AA		29.6037,19.0595,26.0283	benign	183/326	57982763	3379,9603	2201	4290	6491	SO:0001583	missense	219959	exon1			TTCTGTAACCACA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.547A>G	11.37:g.57982763A>G	ENSP00000311688:p.Asn183Asp	Somatic	271	1	0.00369004		WXS	Illumina HiSeq	Phase_I	209	44	0.210526	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	962	0.44047619047619047	111	0.22560975609756098	174	0.48066298342541436	408	0.7132867132867133	269	0.3548812664907652	A	0.009	-1.849961	0.00563	0.190595	0.296037	ENSG00000172774	ENST00000309433	T	0.00241	8.46	3.45	-1.1	0.09872	GPCR, rhodopsin-like superfamily (1);	0.551977	0.16162	N	0.226699	T	0.00012	0.0000	N	0.02802	-0.49	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38286	-0.9668	9	0.37606	T	0.19	.	5.0446	0.14477	0.2795:0.278:0.4425:0.0	rs1993088	183	Q8NH92	OR1S1_HUMAN	D	183	ENSP00000311688:N183D	ENSP00000311688:N183D	N	+	1	0	OR1S1	57739339	0.000000	0.05858	0.017000	0.16124	0.033000	0.12548	0.105000	0.15333	-0.506000	0.06558	-1.305000	0.01319	AAC	A|0.671;G|0.329	0.329	strong		0.463	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
LZTS3	9762	hgsc.bcm.edu	37	20	3147744	3147744	+	Silent	SNP	G	G	A	rs151258888	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3147744G>A	ENST00000329152.3	-	1	1463	c.66C>T	c.(64-66)gcC>gcT	p.A22A	LZTS3_ENST00000360342.3_Silent_p.A22A|LZTS3_ENST00000337576.5_Silent_p.A22A			O60299	LZTS3_HUMAN		22						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)											AGGGCCGTGGGGCAAAGGCCA	0.701													g|||	29	0.00579073	0.0	0.0086	5008	,	,		14211	0.001		0.0219	False		,,,				2504	0.0				p.A22A		Atlas-SNP	.											ProSAPiP1,NS,carcinoma,0,2	.	.	2	0			c.C66T						PASS	.	A		16,4328		1,14,2157	7.0	9.0	9.0		66	3.2	0.9	20	dbSNP_134	9	164,8370		3,158,4106	no	coding-synonymous	ProSAPiP1	NM_014731.2		4,172,6263	AA,AG,GG		1.9217,0.3683,1.3977		22/674	3147744	180,12698	2172	4267	6439	SO:0001819	synonymous_variant	0	exon1			CCGTGGGGCAAAG																												ENST00000329152.3:c.66C>T	20.37:g.3147744G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	27	17	0.62963	NM_014731	A2A2Q7|D3DVX6|Q8IXX8	Silent	SNP	ENST00000329152.3	37	CCDS13049.1																																																																																			G|0.988;A|0.012	0.012	strong		0.701	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2		
RABGGTA	5875	hgsc.bcm.edu	37	14	24736027	24736027	+	Silent	SNP	G	G	A	rs14193	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24736027G>A	ENST00000399409.3	-	14	1905	c.1422C>T	c.(1420-1422)cgC>cgT	p.R474R	RABGGTA_ENST00000559586.1_5'Flank|RABGGTA_ENST00000216840.6_Silent_p.R474R|RABGGTA_ENST00000560777.1_Silent_p.R83R	NM_004581.5	NP_004572.3	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase, alpha subunit	474					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)	12				GBM - Glioblastoma multiforme(265;0.0184)		GGGTTCGGAGGCGATTGTGTG	0.582													A|||	2934	0.585863	0.7254	0.5461	5008	,	,		21076	0.6151		0.3628	False		,,,				2504	0.6247				p.R474R		Atlas-SNP	.											.	RABGGTA	43	.	0			c.C1422T						PASS	.	A	,	2847,1481		957,933,274	91.0	110.0	104.0		1422,1422	-1.6	1.0	14	dbSNP_52	104	3068,5482		551,1966,1758	no	coding-synonymous,coding-synonymous	RABGGTA	NM_004581.3,NM_182836.1	,	1508,2899,2032	AA,AG,GG		35.883,34.219,45.931	,	474/568,474/568	24736027	5915,6963	2164	4275	6439	SO:0001819	synonymous_variant	5875	exon14			TCGGAGGCGATTG		CCDS45088.1	14q11.2	2011-06-27				ENSG00000100949		"""Prenyltransferase alpha subunit repeat containing"""	9795	protein-coding gene	gene with protein product	"""protein prenyltransferase alpha subunit repeat containing 3"""	601905				8954794	Standard	NM_182836		Approved	PTAR3	uc001wog.4	Q92696		ENST00000399409.3:c.1422C>T	14.37:g.24736027G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	194	85	0.438144	NM_004581	A8K5N2|D3DS69	Silent	SNP	ENST00000399409.3	37	CCDS45088.1																																																																																			T|0.000;G|0.465;A|0.534	0.534	strong		0.582	RABGGTA-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415308.5	NM_182836	
KIF13A	63971	hgsc.bcm.edu	37	6	17781450	17781450	+	Silent	SNP	G	G	A	rs942376	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:17781450G>A	ENST00000259711.6	-	30	3732	c.3627C>T	c.(3625-3627)agC>agT	p.S1209S	KIF13A_ENST00000378843.2_Silent_p.S1196S|KIF13A_ENST00000378816.5_Silent_p.S1209S|KIF13A_ENST00000378814.5_Silent_p.S1196S|KIF13A_ENST00000378826.2_Silent_p.S1209S	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1209					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			AGAAAAACTGGCTGCCATGCT	0.512													G|||	822	0.164137	0.0598	0.2997	5008	,	,		15964	0.2014		0.2097	False		,,,				2504	0.1237				p.S1209S		Atlas-SNP	.											.	KIF13A	276	.	0			c.C3627T						PASS	.	G	,,,	349,3525		18,313,1606	93.0	93.0	93.0		3627,3588,3588,3627	3.1	1.0	6	dbSNP_86	93	1579,6727		160,1259,2734	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	178,1572,4340	AA,AG,GG		19.0104,9.0088,15.8292	,,,	1209/1771,1196/1758,1196/1750,1209/1806	17781450	1928,10252	1937	4153	6090	SO:0001819	synonymous_variant	63971	exon30			AAACTGGCTGCCA	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.3627C>T	6.37:g.17781450G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_001105566	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1	419	0.19184981684981686	37	0.07520325203252033	94	0.2596685082872928	137	0.2395104895104895	151	0.19920844327176782	G	10.33	1.320761	0.23994	0.090088	0.190104	ENSG00000137177	ENST00000358380	.	.	.	5.29	3.07	0.35406	.	.	.	.	.	T	0.26702	0.0653	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09662	-1.0664	3	.	.	.	.	7.1879	0.25809	0.3069:0.0:0.6931:0.0	rs942376;rs3734233;rs58734397;rs942376	.	.	.	V	603	.	.	A	-	2	0	KIF13A	17889429	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.524000	0.35942	1.333000	0.45449	0.561000	0.74099	GCC	G|0.825;A|0.175	0.175	strong		0.512	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
BTNL2	56244	hgsc.bcm.edu	37	6	32370908	32370908	+	Silent	SNP	T	T	A	rs59129682	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32370908T>A	ENST00000374993.1	-	3	512	c.513A>T	c.(511-513)ccA>ccT	p.P171P	BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000454136.3_Silent_p.P171P|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000374995.3_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	171	Ig-like V-type 2.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CCTGGGGCTCTGGGAACCAGC	0.597													T|||	672	0.134185	0.1369	0.1369	5008	,	,		19203	0.1984		0.0974	False		,,,				2504	0.1002				p.P171P		Atlas-SNP	.											BTNL2,NS,adenoma,0,1	BTNL2	50	1	0			c.A513T						PASS	.	T		339,2677		12,315,1181	48.0	48.0	48.0		513	0.4	1.0	6	dbSNP_129	48	428,4990		15,398,2296	no	coding-synonymous	BTNL2	NM_019602.1		27,713,3477	AA,AT,TT		7.8996,11.2401,9.0941		171/456	32370908	767,7667	1508	2709	4217	SO:0001819	synonymous_variant	56244	exon3			GGGCTCTGGGAAC	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.513A>T	6.37:g.32370908T>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Silent	SNP	ENST00000374993.1	37																																																																																				T|0.894;A|0.106	0.106	strong		0.597	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
HOMER3	9454	hgsc.bcm.edu	37	19	19049198	19049198	+	Silent	SNP	G	G	A	rs1064351	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19049198G>A	ENST00000539827.1	-	3	919	c.267C>T	c.(265-267)taC>taT	p.Y89Y	HOMER3_ENST00000542541.2_Silent_p.Y89Y|HOMER3_ENST00000594794.1_Intron|HOMER3_ENST00000594439.1_Silent_p.Y89Y|HOMER3_ENST00000221222.11_Silent_p.Y89Y|HOMER3_ENST00000355887.6_Silent_p.Y89Y|AC005932.1_ENST00000601106.1_RNA|HOMER3_ENST00000392351.3_Silent_p.Y89Y|HOMER3_ENST00000433218.2_Silent_p.Y89Y			Q9NSC5	HOME3_HUMAN	homer homolog 3 (Drosophila)	89	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				G-protein coupled glutamate receptor signaling pathway (GO:0007216)|protein targeting (GO:0006605)	basal part of cell (GO:0045178)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				endometrium(3)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	10			Epithelial(12;0.0107)			AGCCCAGGCCGTAGACTGTGT	0.597													G|||	1405	0.280551	0.1051	0.5231	5008	,	,		15444	0.1736		0.4423	False		,,,				2504	0.2894				p.Y89Y		Atlas-SNP	.											.	HOMER3	19	.	0			c.C267T						PASS	.	G	,,,	657,3749	278.7+/-274.4	47,563,1593	110.0	103.0	106.0		267,267,267,267	-4.1	0.7	19	dbSNP_86	106	3755,4845	533.5+/-382.4	810,2135,1355	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HOMER3	NM_001145721.1,NM_001145722.1,NM_001145724.1,NM_004838.3	,,,	857,2698,2948	AA,AG,GG		43.6628,14.9115,33.9228	,,,	89/359,89/362,89/326,89/362	19049198	4412,8594	2203	4300	6503	SO:0001819	synonymous_variant	9454	exon4			CAGGCCGTAGACT	Y18894	CCDS12391.1, CCDS46022.1, CCDS46023.1	19p13.1	2008-02-05				ENSG00000051128			17514	protein-coding gene	gene with protein product		604800				10653696, 9808459	Standard	NM_004838		Approved	HOMER-3	uc002nkv.2	Q9NSC5		ENST00000539827.1:c.267C>T	19.37:g.19049198G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	177	174	0.983051	NM_001145722	E9PCW9|O14580|O95350|Q9NSB9|Q9NSC0|Q9NSC1	Silent	SNP	ENST00000539827.1	37	CCDS12391.1																																																																																			G|0.682;A|0.318	0.318	strong		0.597	HOMER3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464607.1		
TRPV2	51393	hgsc.bcm.edu	37	17	16325968	16325968	+	Silent	SNP	A	A	G	rs8121	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:16325968A>G	ENST00000338560.7	+	4	789	c.390A>G	c.(388-390)ggA>ggG	p.G130G	TRPV2_ENST00000577397.1_5'UTR	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	130	Required for interaction with SLC50A1. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.G130G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TTAAGGACGGAGTCAATGCCT	0.572													G|||	1960	0.391374	0.6475	0.3818	5008	,	,		18556	0.2321		0.3877	False		,,,				2504	0.2198				p.G130G		Atlas-SNP	.											TRPV2,right_upper_lobe,carcinoma,+1,2	TRPV2	74	2	1	Substitution - coding silent(1)	stomach(1)	c.A390G						scavenged	.	G		2586,1820	532.3+/-373.4	765,1056,382	82.0	67.0	72.0		390	-5.9	0.0	17	dbSNP_52	72	3364,5236	641.2+/-399.7	648,2068,1584	no	coding-synonymous	TRPV2	NM_016113.4		1413,3124,1966	GG,GA,AA		39.1163,41.3073,45.7481		130/765	16325968	5950,7056	2203	4300	6503	SO:0001819	synonymous_variant	51393	exon4			GGACGGAGTCAAT	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.390A>G	17.37:g.16325968A>G		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	121	66	0.545455	NM_016113	A6NML2|A8K0Z0|Q9Y670	Silent	SNP	ENST00000338560.7	37	CCDS32576.1	889	0.40705128205128205	301	0.6117886178861789	153	0.42265193370165743	148	0.25874125874125875	287	0.3786279683377309	G	0.717	-0.784796	0.02907	0.586927	0.391163	ENSG00000187688	ENST00000455666	.	.	.	5.24	-5.94	0.02247	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999865	.	.	.	.	.	.	T	0.46569	-0.9182	3	.	.	.	-7.0661	0.4381	0.00482	0.2267:0.1978:0.2647:0.3108	rs8121;rs1129232;rs3186904;rs60740001;rs8121	.	.	.	G	88	.	.	S	+	1	0	TRPV2	16266693	0.000000	0.05858	0.029000	0.17559	0.089000	0.18198	-1.548000	0.02184	-1.326000	0.02266	-0.812000	0.03155	AGT	A|0.561;G|0.439	0.439	strong		0.572	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
ADTRP	84830	hgsc.bcm.edu	37	6	11714728	11714728	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:11714728G>A	ENST00000414691.3	-	6	1086	c.676C>T	c.(676-678)Cgg>Tgg	p.R226W	ADTRP_ENST00000514824.1_5'UTR|ADTRP_ENST00000229583.5_Missense_Mutation_p.R244W	NM_032744.3	NP_116133.1	Q96IZ2	ADTRP_HUMAN	androgen-dependent TFPI-regulating protein	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CTCTTCTTCCGTGGCTGCCTC	0.413																																					p.R244W		Atlas-SNP	.											C6orf105,bladder,carcinoma,+1,1	ADTRP	3	1	0			c.C730T						scavenged	.						144.0	138.0	140.0					6																	11714728		2203	4300	6503	SO:0001583	missense	84830	exon7			TCTTCCGTGGCTG	AJ420520	CCDS4521.1, CCDS47374.1	6p24.1	2012-01-30	2012-01-27	2012-01-27	ENSG00000111863	ENSG00000111863			21214	protein-coding gene	gene with protein product	"""androgen-induced 1-like"""	614348	"""chromosome 6 open reading frame 105"""	C6orf105		21868574	Standard	NM_032744		Approved	dJ413H6.1, AIG1L	uc011dip.2	Q96IZ2	OTTHUMG00000014260	ENST00000414691.3:c.676C>T	6.37:g.11714728G>A	ENSP00000404416:p.Arg226Trp	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	306	3	0.00980392	NM_001143948	B2R7T9|B4DV39|Q5THW1	Missense_Mutation	SNP	ENST00000414691.3	37	CCDS4521.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835963	0.71373	.	.	ENSG00000111863	ENST00000414691;ENST00000229583	T;T	0.33216	1.43;1.42	6.15	-2.23	0.06930	.	.	.	.	.	T	0.12347	0.0300	L	0.53249	1.67	0.18873	N	0.999987	D;B	0.60160	0.987;0.005	P;B	0.46825	0.528;0.001	T	0.07385	-1.0775	9	0.66056	D	0.02	.	1.3421	0.02156	0.2376:0.0981:0.2128:0.4515	.	244;226	Q96IZ2-2;Q96IZ2	.;ADTRP_HUMAN	W	226;244	ENSP00000404416:R226W;ENSP00000229583:R244W	ENSP00000229583:R244W	R	-	1	2	C6orf105	11822714	0.000000	0.05858	0.000000	0.03702	0.624000	0.37722	-0.905000	0.04075	-0.388000	0.07797	-0.148000	0.13756	CGG	.	.	none		0.413	ADTRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039864.3	NM_032744	
PLEC	5339	hgsc.bcm.edu	37	8	144992552	144992552	+	Missense_Mutation	SNP	G	G	A	rs201666443		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144992552G>A	ENST00000322810.4	-	32	12017	c.11848C>T	c.(11848-11850)Cgc>Tgc	p.R3950C	PLEC_ENST00000398774.2_Missense_Mutation_p.R3781C|PLEC_ENST00000345136.3_Missense_Mutation_p.R3813C|PLEC_ENST00000354589.3_Missense_Mutation_p.R3813C|PLEC_ENST00000354958.2_Missense_Mutation_p.R3791C|PLEC_ENST00000436759.2_Missense_Mutation_p.R3840C|PLEC_ENST00000527096.1_Missense_Mutation_p.R3836C|PLEC_ENST00000356346.3_Missense_Mutation_p.R3799C|PLEC_ENST00000357649.2_Missense_Mutation_p.R3817C	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3950	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						AAGCCCAGGCGGGGGTCCACG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15094	0.0		0.0	False		,,,				2504	0.001				p.R3950C		Atlas-SNP	.											.	PLEC	1144	.	0			c.C11848T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4044		0,0,2022	12.0	17.0	16.0		11518,11395,11371,11848,11341,11437,11449,11437	3.8	0.6	8		16	2,8328		0,2,4163	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	180,180,180,180,180,180,180,180	0,2,6185	AA,AG,GG		0.024,0.0,0.0162	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	3840/4575,3799/4534,3791/4526,3950/4685,3781/4516,3813/4548,3817/4552,3813/4548	144992552	2,12372	2022	4165	6187	SO:0001583	missense	5339	exon32			CCAGGCGGGGGTC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.11848C>T	8.37:g.144992552G>A	ENSP00000323856:p.Arg3950Cys	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	28	11	0.392857	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	G	8.746	0.920155	0.17982	0.0	2.4E-4	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78;-0.78;-0.78;-0.78;-0.78;-0.78	3.78	3.78	0.43462	.	0.335440	0.24089	U	0.041652	T	0.67135	0.2861	L	0.46157	1.445	0.35517	D	0.801081	P;D;P;P;P;P;P;P	0.54772	0.894;0.968;0.894;0.913;0.894;0.894;0.894;0.894	B;B;B;B;B;B;B;B	0.43990	0.311;0.311;0.311;0.438;0.311;0.311;0.311;0.311	T	0.74300	-0.3710	10	0.38643	T	0.18	.	10.3245	0.43785	0.0:0.0:0.8027:0.1973	.	3840;3799;3791;3950;3781;3813;3817;3813	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	C	3813;3817;3813;3781;3950;3791;3799;3840;3836	ENSP00000344848:R3813C;ENSP00000350277:R3817C;ENSP00000346602:R3813C;ENSP00000381756:R3781C;ENSP00000323856:R3950C;ENSP00000347044:R3791C;ENSP00000348702:R3799C;ENSP00000388180:R3840C;ENSP00000434583:R3836C	ENSP00000323856:R3950C	R	-	1	0	PLEC	145064540	0.957000	0.32711	0.639000	0.29394	0.951000	0.60555	2.993000	0.49425	2.103000	0.63969	0.297000	0.19635	CGC	.	.	weak		0.652	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
OR2A25	392138	hgsc.bcm.edu	37	7	143771536	143771536	+	Missense_Mutation	SNP	G	G	A	rs6951485	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143771536G>A	ENST00000408898.2	+	1	262	c.224G>A	c.(223-225)aGc>aAc	p.S75N		NM_001004488.1	NP_001004488.1	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A, member 25	75			S -> N (in dbSNP:rs6951485). {ECO:0000269|PubMed:12690205}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(16)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	24	Melanoma(164;0.0783)					TGTGCTTGCAGCACGGTGCCC	0.562													.|||	3192	0.63738	0.7769	0.7147	5008	,	,		20464	0.6379		0.496	False		,,,				2504	0.5389				p.S75N		Atlas-SNP	.											.	OR2A25	66	.	0			c.G224A						PASS	.	A	ASN/SER	3220,1186	414.8+/-337.0	1183,854,166	80.0	82.0	81.0		224	2.5	1.0	7	dbSNP_116	81	4541,4059	556.5+/-386.9	1205,2131,964	yes	missense	OR2A25	NM_001004488.1	46	2388,2985,1130	AA,AG,GG		47.1977,26.9178,40.3275	benign	75/311	143771536	7761,5245	2203	4300	6503	SO:0001583	missense	392138	exon1			CTTGCAGCACGGT		CCDS43669.1	7q35	2012-08-09		2004-03-10	ENSG00000221933	ENSG00000221933		"""GPCR / Class A : Olfactory receptors"""	19562	protein-coding gene	gene with protein product				OR2A25P, OR2A27			Standard	NM_001004488		Approved		uc011ktx.2	A4D2G3	OTTHUMG00000158013	ENST00000408898.2:c.224G>A	7.37:g.143771536G>A	ENSP00000386167:p.Ser75Asn	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	153	65	0.424837	NM_001004488	B2RNC9	Missense_Mutation	SNP	ENST00000408898.2	37	CCDS43669.1	1367	0.6259157509157509	384	0.7804878048780488	250	0.6906077348066298	371	0.6486013986013986	362	0.47757255936675463	A	0.006	-2.020272	0.00418	0.730822	0.528023	ENSG00000221933	ENST00000408898	T	0.00433	7.43	4.88	2.52	0.30459	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	L	0.28556	0.865	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24119	-1.0169	8	0.10902	T	0.67	-3.3808	4.2596	0.10735	0.565:0.1674:0.2676:0.0	rs6951485;rs6951485	75	A4D2G3	O2A25_HUMAN	N	75	ENSP00000386167:S75N	ENSP00000386167:S75N	S	+	2	0	OR2A25	143402469	0.000000	0.05858	0.997000	0.53966	0.172000	0.22775	-0.086000	0.11233	0.059000	0.16252	-1.204000	0.01649	AGC	G|0.399;A|0.601	0.601	strong		0.562	OR2A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350000.1		
EMR1	2015	hgsc.bcm.edu	37	19	6921868	6921868	+	Missense_Mutation	SNP	G	G	A	rs7256147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:6921868G>A	ENST00000312053.4	+	14	1802	c.1765G>A	c.(1765-1767)Gtt>Att	p.V589I	EMR1_ENST00000381404.4_Missense_Mutation_p.V537I|EMR1_ENST00000381407.5_Missense_Mutation_p.V448I|EMR1_ENST00000450315.3_Missense_Mutation_p.V412I|EMR1_ENST00000250572.8_Missense_Mutation_p.V589I	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	589	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.|Ser/Thr-rich.		V -> I (in dbSNP:rs7256147). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					AAATCTTGCCGTTATCATGGC	0.458													G|||	1132	0.226038	0.2534	0.1758	5008	,	,		20422	0.2024		0.2177	False		,,,				2504	0.2577				p.V589I		Atlas-SNP	.											.	EMR1	153	.	0			c.G1765A						PASS	.	G	ILE/VAL	1017,3389	378.3+/-322.8	119,779,1305	168.0	142.0	151.0		1765	-2.5	0.2	19	dbSNP_116	151	1720,6880	313.7+/-311.4	152,1416,2732	yes	missense	EMR1	NM_001974.3	29	271,2195,4037	AA,AG,GG		20.0,23.0822,21.0441	benign	589/887	6921868	2737,10269	2203	4300	6503	SO:0001583	missense	2015	exon14			CTTGCCGTTATCA	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"""-"", ""GPCR / Class B : Orphans"""	3336	protein-coding gene	gene with protein product		600493	"""egf-like module containing, mucin-like, hormone receptor-like sequence 1"""	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.1765G>A	19.37:g.6921868G>A	ENSP00000311545:p.Val589Ile	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	150	63	0.42	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	440	0.20146520146520147	144	0.2926829268292683	51	0.1408839779005525	92	0.16083916083916083	153	0.20184696569920843	G	0.088	-1.171130	0.01660	0.230822	0.2	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4;-0.4	4.43	-2.52	0.06346	GPS domain (3);	.	.	.	.	T	0.00012	0.0000	N	0.04387	-0.21	0.58432	P	6.999999999979245E-6	B;B;B;B	0.22604	0.012;0.017;0.072;0.021	B;B;B;B	0.17722	0.006;0.011;0.019;0.011	T	0.10567	-1.0624	8	0.02654	T	1	.	11.3457	0.49559	0.4153:0.0:0.5847:0.0	rs7256147;rs17855005;rs52793961;rs60313628;rs7256147	412;589;537;589	E7EPX9;Q14246-2;E9PD45;Q14246	.;.;.;EMR1_HUMAN	I	589;589;537;589;448;412	ENSP00000311545:V589I;ENSP00000370811:V537I;ENSP00000250572:V589I;ENSP00000370814:V448I;ENSP00000405974:V412I	ENSP00000250572:V589I	V	+	1	0	EMR1	6872868	0.001000	0.12720	0.158000	0.22627	0.004000	0.04260	-0.809000	0.04510	-0.787000	0.04510	-0.811000	0.03165	GTT	G|0.783;A|0.217	0.217	strong		0.458	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
PRDM2	7799	hgsc.bcm.edu	37	1	14105946	14105946	+	Silent	SNP	T	T	C	rs61747661	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14105946T>C	ENST00000235372.7	+	8	2512	c.1656T>C	c.(1654-1656)gaT>gaC	p.D552D	PRDM2_ENST00000343137.4_Silent_p.D351D|PRDM2_ENST00000311066.5_Silent_p.D552D|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Silent_p.D351D	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	552					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		AAGCAGATGATGTGTACATCA	0.448													C|||	189	0.0377396	0.0015	0.0	5008	,	,		20098	0.0218		0.0169	False		,,,				2504	0.1513				p.D552D		Atlas-SNP	.											PRDM2,NS,carcinoma,+1,1	PRDM2	147	1	0			c.T1656C						PASS	.	C	,,,	12,4394	823.7+/-416.5	0,12,2191	82.0	87.0	85.0		1053,,1656,1656	-0.6	1.0	1	dbSNP_129	85	175,8425	810.3+/-407.1	2,171,4127	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	,,,	2,183,6318	CC,CT,TT		2.0349,0.2724,1.4378	,,,	351/1482,,552/1719,552/1683	14105946	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	7799	exon8			AGATGATGTGTAC	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.1656T>C	1.37:g.14105946T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Silent	SNP	ENST00000235372.7	37	CCDS150.1																																																																																			T|0.983;C|0.017	0.017	strong		0.448	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
HINT3	135114	hgsc.bcm.edu	37	6	126278230	126278230	+	Missense_Mutation	SNP	G	G	C	rs2295005	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:126278230G>C	ENST00000229633.5	+	1	304	c.107G>C	c.(106-108)gGc>gCc	p.G36A		NM_138571.4	NP_612638.3	Q9NQE9	HINT3_HUMAN	histidine triad nucleotide binding protein 3	36			G -> A (2.5-fold increase in affinity for indolepropinoic acyl-adenylate and cytosine; 2-fold decrease in hypoxanthine affinity; nearly no change in affinity for adenine, guanine and uracil; dbSNP:rs2295005). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17870088, ECO:0000269|Ref.1}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)			endometrium(1)|large_intestine(1)|lung(1)|stomach(1)	4				UCEC - Uterine corpus endometrioid carcinoma (4;0.153)|GBM - Glioblastoma multiforme(226;0.0321)		GAAGCCGCTGGCAAGTCACCA	0.672											OREG0017649	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3479	0.694688	0.6944	0.6844	5008	,	,		14861	0.9534		0.495	False		,,,				2504	0.6411				p.G36A		Atlas-SNP	.											HINT3,NS,carcinoma,0,1	HINT3	14	1	0			c.G107C						PASS	.	C	ALA/GLY	2578,1154		926,726,214	26.0	20.0	22.0		107	4.5	0.0	6	dbSNP_100	22	3795,3485		1052,1691,897	yes	missense	HINT3	NM_138571.4	60	1978,2417,1111	CC,CG,GG		47.8709,30.9218,42.1268	benign	36/183	126278230	6373,4639	1866	3640	5506	SO:0001583	missense	135114	exon1			CCGCTGGCAAGTC	AK057688	CCDS5133.1	6q22.33	2007-12-04			ENSG00000111911	ENSG00000111911			18468	protein-coding gene	gene with protein product		609998				11805111	Standard	NM_138571		Approved	FLJ33126	uc003qal.4	Q9NQE9	OTTHUMG00000015514	ENST00000229633.5:c.107G>C	6.37:g.126278230G>C	ENSP00000229633:p.Gly36Ala	Somatic	83	0	0	1548	WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_138571	B3KQ91|Q8N0Y9	Missense_Mutation	SNP	ENST00000229633.5	37	CCDS5133.1	1538	0.7042124542124543	372	0.7560975609756098	243	0.6712707182320442	545	0.9527972027972028	378	0.49868073878627966	C	3.977	-0.007271	0.07773	0.690782	0.521291	ENSG00000111911	ENST00000229633	D	0.90844	-2.74	4.51	4.51	0.55191	Histidine triad-like motif (1);	1.657570	0.03007	N	0.148899	T	0.55893	0.1949	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48714	-0.9011	9	0.02654	T	1	-18.9857	11.9951	0.53196	0.0:0.8247:0.1753:0.0	rs2295005;rs17292865;rs52818664;rs2295005	36	Q9NQE9	HINT3_HUMAN	A	36	ENSP00000229633:G36A	ENSP00000229633:G36A	G	+	2	0	HINT3	126319923	0.001000	0.12720	0.016000	0.15963	0.016000	0.09150	0.449000	0.21744	1.129000	0.42072	-0.371000	0.07208	GGC	G|0.358;C|0.642	0.642	strong		0.672	HINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042090.1	NM_138571	
PGAP1	80055	hgsc.bcm.edu	37	2	197781288	197781288	+	Missense_Mutation	SNP	T	T	C	rs142320636	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:197781288T>C	ENST00000354764.4	-	3	445	c.331A>G	c.(331-333)Aaa>Gaa	p.K111E	PGAP1_ENST00000485830.1_5'UTR|PGAP1_ENST00000409188.1_Missense_Mutation_p.K69E|PGAP1_ENST00000409475.1_Missense_Mutation_p.K111E	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	111					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TCCTCTGCTTTTCTAAGTGCA	0.388													T|||	4	0.000798722	0.0	0.0014	5008	,	,		18296	0.0		0.003	False		,,,				2504	0.0				p.K111E		Atlas-SNP	.											.	PGAP1	84	.	0			c.A331G						PASS	.	T	GLU/LYS	2,4404	4.2+/-10.8	0,2,2201	77.0	71.0	73.0		331	5.6	1.0	2	dbSNP_134	73	13,8587	9.8+/-36.6	0,13,4287	yes	missense	PGAP1	NM_024989.3	56	0,15,6488	CC,CT,TT		0.1512,0.0454,0.1153	possibly-damaging	111/923	197781288	15,12991	2203	4300	6503	SO:0001583	missense	80055	exon3			CTGCTTTTCTAAG		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.331A>G	2.37:g.197781288T>C	ENSP00000346809:p.Lys111Glu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	24.3	4.516548	0.85495	4.54E-4	0.001512	ENSG00000197121	ENST00000354764;ENST00000409475;ENST00000409188	D;D;D	0.85955	-2.05;-2.05;-2.05	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.91503	0.7317	M	0.79123	2.44	0.80722	D	1	P;D	0.76494	0.873;0.999	B;D	0.83275	0.403;0.996	D	0.89403	0.3697	10	0.18276	T	0.48	-17.7348	16.0983	0.81144	0.0:0.0:0.0:1.0	.	111;111	Q75T13-3;Q75T13	.;PGAP1_HUMAN	E	111;111;69	ENSP00000346809:K111E;ENSP00000387028:K111E;ENSP00000386802:K69E	ENSP00000346809:K111E	K	-	1	0	PGAP1	197489533	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.643000	0.83403	2.256000	0.74724	0.524000	0.50904	AAA	T|0.999;C|0.001	0.001	strong		0.388	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
PCDHGA1	56114	hgsc.bcm.edu	37	5	140712299	140712299	+	Missense_Mutation	SNP	A	A	T	rs62378404	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140712299A>T	ENST00000517417.1	+	1	2048	c.2048A>T	c.(2047-2049)aAa>aTa	p.K683I	PCDHGA1_ENST00000378105.3_Missense_Mutation_p.K683I	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	683					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCTCCGCCAAACCCAACGAT	0.692																																					p.K683I		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.A2048T						PASS	.						67.0	80.0	76.0					5																	140712299		2203	4296	6499	SO:0001583	missense	56114	exon1			CCGCCAAACCCAA	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.2048A>T	5.37:g.140712299A>T	ENSP00000431083:p.Lys683Ile	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	173	81	0.468208	NM_018912	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	113	0.051739926739926737	45	0.09146341463414634	18	0.049723756906077346	14	0.024475524475524476	36	0.047493403693931395	A	13.01	2.110756	0.37242	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.51817	0.73;0.69	3.87	-0.312	0.12758	.	3.140790	0.01069	N	0.004795	T	0.01661	0.0053	L	0.38175	1.15	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.15870	0.014;0.002	T	0.15723	-1.0427	10	0.59425	D	0.04	.	4.888	0.13713	0.6559:0.1574:0.1867:0.0	rs62378404	683;683	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	I	683	ENSP00000431083:K683I;ENSP00000367345:K683I	ENSP00000367345:K683I	K	+	2	0	PCDHGA1	140692483	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	1.355000	0.34068	0.173000	0.19788	0.477000	0.44152	AAA	A|0.958;T|0.042	0.042	strong		0.692	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912	
ROBO4	54538	hgsc.bcm.edu	37	11	124767125	124767125	+	Silent	SNP	G	G	A	rs73016370	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124767125G>A	ENST00000306534.3	-	2	588	c.103C>T	c.(103-105)Cta>Tta	p.L35L	ROBO4_ENST00000533054.1_Intron|ROBO4_ENST00000526899.1_5'UTR	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	35	Ig-like C2-type 1.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GGGTGGACTAGGATCTGGGGC	0.652													G|||	498	0.0994409	0.003	0.0735	5008	,	,		15800	0.2054		0.0974	False		,,,				2504	0.1411				p.L35L		Atlas-SNP	.											.	ROBO4	130	.	0			c.C103T						PASS	.	G		91,4271		1,89,2091	11.0	10.0	11.0		103	2.6	0.6	11	dbSNP_130	11	797,7743		47,703,3520	no	coding-synonymous	ROBO4	NM_019055.5		48,792,5611	AA,AG,GG		9.3326,2.0862,6.8827		35/1008	124767125	888,12014	2181	4270	6451	SO:0001819	synonymous_variant	54538	exon2			GGACTAGGATCTG	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.103C>T	11.37:g.124767125G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			G|0.919;A|0.081	0.081	strong		0.652	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
FAM208A	23272	hgsc.bcm.edu	37	3	56667682	56667682	+	Missense_Mutation	SNP	G	G	C	rs9835332	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:56667682G>C	ENST00000493960.2	-	18	3147	c.3137C>G	c.(3136-3138)aCa>aGa	p.T1046R	FAM208A_ENST00000355628.5_Missense_Mutation_p.T985R|FAM208A_ENST00000431842.2_Missense_Mutation_p.T609R	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1046			T -> R (in dbSNP:rs9835332). {ECO:0000269|PubMed:10470851, ECO:0000269|PubMed:11149944, ECO:0000269|PubMed:18726359}.				poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						TGTGGAAACTGTACTGACATA	0.393													C|||	3928	0.784345	0.9259	0.7147	5008	,	,		21224	0.9514		0.4592	False		,,,				2504	0.8047				p.T1046R		Atlas-SNP	.											.	FAM208A	113	.	0			c.C3137G						PASS	.	C	ARG/THR,ARG/THR	3727,679	287.5+/-279.3	1590,547,66	119.0	128.0	125.0	http://www.ncbi.nlm.nih.gov/pubmed?term	3137,1826	0.8	0.1	3	dbSNP_119	125	3967,4633	601.5+/-394.4	912,2143,1245	yes	missense,missense	FAM208A	NM_001112736.1,NM_015224.3	71,71	2502,2690,1311	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	46.1279,15.4108,40.8427	benign,benign	1046/1513,609/1234	56667682	7694,5312	2203	4300	6503	SO:0001583	missense	23272	exon18			GAAACTGTACTGA	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.3137C>G	3.37:g.56667682G>C	ENSP00000417509:p.Thr1046Arg	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	1566	0.717032967032967	450	0.9146341463414634	243	0.6712707182320442	538	0.9405594405594405	335	0.4419525065963061	C	0.007	-2.008918	0.00426	0.845892	0.461279	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.10960	2.82;3.02;3.03	5.76	0.788	0.18601	.	0.648587	0.16563	N	0.208976	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.18524	-1.0334	9	0.07325	T	0.83	4.0E-4	7.7966	0.29150	0.0:0.3353:0.4221:0.2426	rs9835332;rs52798848;rs57620855;rs9835332	1046;985;609;1046	Q9UK61-3;Q9UK61-4;Q9UK61-2;Q9UK61	.;.;.;F208A_HUMAN	R	609;1046;985	ENSP00000399410:T609R;ENSP00000417509:T1046R;ENSP00000347845:T985R	ENSP00000347845:T985R	T	-	2	0	C3orf63	56642722	0.113000	0.22115	0.089000	0.20774	0.774000	0.43823	-0.360000	0.07622	-0.279000	0.09167	-0.829000	0.03081	ACA	G|0.365;C|0.635	0.635	strong		0.393	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110447512	110447512	+	Missense_Mutation	SNP	G	G	C	rs142972518	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110447512G>C	ENST00000378402.5	+	29	3538	c.3434G>C	c.(3433-3435)gGg>gCg	p.G1145A		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1145	IPT/TIG 4.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CAGAATGTAGGGGGTGAAGAG	0.443										HNSCC(38;0.096)			G|||	58	0.0115815	0.0015	0.0101	5008	,	,		18338	0.0		0.0268	False		,,,				2504	0.0225				p.G1145A		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G3434C						PASS	.	G	ALA/GLY	15,3743		0,15,1864	197.0	197.0	197.0		3434	-2.3	0.0	8	dbSNP_134	197	167,8083		3,161,3961	yes	missense	PKHD1L1	NM_177531.4	60	3,176,5825	CC,CG,GG		2.0242,0.3991,1.5157	benign	1145/4244	110447512	182,11826	1879	4125	6004	SO:0001583	missense	93035	exon29			ATGTAGGGGGTGA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.3434G>C	8.37:g.110447512G>C	ENSP00000367655:p.Gly1145Ala	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	222	102	0.459459	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	27	0.012362637362637362	0	0.0	5	0.013812154696132596	0	0.0	22	0.029023746701846966	G	2.585	-0.296544	0.05532	0.003991	0.020242	ENSG00000205038	ENST00000378402	D	0.85702	-2.02	6.07	-2.3	0.06785	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.912531	0.09435	N	0.802529	T	0.53142	0.1778	L	0.34521	1.04	0.09310	N	1	B	0.16396	0.017	B	0.21360	0.034	T	0.50074	-0.8870	10	0.12103	T	0.63	.	12.0147	0.53307	0.3405:0.0:0.6595:0.0	.	1145	Q86WI1	PKHL1_HUMAN	A	1145	ENSP00000367655:G1145A	ENSP00000367655:G1145A	G	+	2	0	PKHD1L1	110516688	0.005000	0.15991	0.000000	0.03702	0.004000	0.04260	0.643000	0.24750	-0.303000	0.08856	-0.768000	0.03414	GGG	G|0.986;C|0.014	0.014	strong		0.443	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
CASP7	840	hgsc.bcm.edu	37	10	115489152	115489152	+	Missense_Mutation	SNP	C	C	G	rs2227310	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:115489152C>G	ENST00000345633.4	+	8	1149	c.765C>G	c.(763-765)gaC>gaG	p.D255E	CASP7_ENST00000452490.2_Missense_Mutation_p.D230E|CASP7_ENST00000369318.3_Missense_Mutation_p.D255E|CASP7_ENST00000369321.2_Missense_Mutation_p.D288E|CASP7_ENST00000369315.1_Missense_Mutation_p.D255E|CASP7_ENST00000369331.4_Missense_Mutation_p.T244S	NM_033339.4	NP_203125.1	P55210	CASP7_HUMAN	caspase 7, apoptosis-related cysteine peptidase	255			D -> E (in dbSNP:rs2227310).		activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway (GO:0097193)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)	8		Colorectal(252;0.0946)|Breast(234;0.188)		Epithelial(162;0.012)|all cancers(201;0.014)		ACGGAAAAGACCTGGAAATCA	0.522													C|||	1251	0.2498	0.1278	0.2579	5008	,	,		18522	0.4157		0.2535	False		,,,				2504	0.2342				p.D340E		Atlas-SNP	.											.	CASP7	21	.	0			c.C1020G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP,SER/THR	638,3768	276.0+/-272.9	60,518,1625	139.0	131.0	133.0		765,864,765,731	1.7	0.5	10	dbSNP_98	133	2172,6428	371.4+/-336.2	274,1624,2402	yes	missense,missense,missense,missense	CASP7	NM_001227.3,NM_033338.4,NM_033339.3,NM_033340.2	45,45,45,58	334,2142,4027	GG,GC,CC		25.2558,14.4803,21.6054	benign,benign,benign,benign	255/304,288/337,255/304,244/254	115489152	2810,10196	2203	4300	6503	SO:0001583	missense	840	exon7			AAAAGACCTGGAA	U37448	CCDS7580.1, CCDS7581.1, CCDS7582.1, CCDS58096.1, CCDS73200.1	10q25	2006-02-17	2005-08-17		ENSG00000165806	ENSG00000165806		"""Caspases"""	1508	protein-coding gene	gene with protein product		601761	"""caspase 7, apoptosis-related cysteine protease"""			8521391, 8576161	Standard	NM_033338		Approved	MCH3, CMH-1, ICE-LAP3	uc010qsa.3	P55210	OTTHUMG00000019076	ENST00000345633.4:c.765C>G	10.37:g.115489152C>G	ENSP00000298701:p.Asp255Glu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_001267057	B4DQU7|B5BU45|D3DRB8|Q13364|Q53YD5|Q5SVL0|Q5SVL3|Q96BA0	Missense_Mutation	SNP	ENST00000345633.4	37	CCDS7581.1	591|591	0.2706043956043956|0.2706043956043956	65|65	0.13211382113821138|0.13211382113821138	100|100	0.27624309392265195|0.27624309392265195	245|245	0.42832167832167833|0.42832167832167833	181|181	0.23878627968337732|0.23878627968337732	C|C	3.097|3.097	-0.185662|-0.185662	0.06340|0.06340	0.144803|0.144803	0.252558|0.252558	ENSG00000165806|ENSG00000165806	ENST00000369321;ENST00000345633;ENST00000369318;ENST00000442393;ENST00000369315;ENST00000452490|ENST00000369331	T;T;T;T;T|T	0.23552|0.08193	1.9;1.9;1.9;1.9;1.9|3.12	5.85|5.85	1.66|1.66	0.24008|0.24008	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);|.	0.816620|.	0.11948|.	N|.	0.513957|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.53688|0.53688	P|P	2.5000000000052758E-5|2.5000000000052758E-5	B;B;B;B|B	0.02656|0.10296	0.0;0.0;0.0;0.0|0.003	B;B;B;B|B	0.04013|0.08055	0.0;0.001;0.0;0.0|0.003	T|T	0.46679|0.46679	-0.9174|-0.9174	8|7	0.02654|0.02654	T|T	1|1	.|.	6.1143|6.1143	0.20117|0.20117	0.1949:0.2422:0.4924:0.0705|0.1949:0.2422:0.4924:0.0705	rs2227310;rs56575824;rs58910029;rs2227310|rs2227310;rs56575824;rs58910029;rs2227310	230;263;288;255|244	B4DQU7;B4DWA2;P55210-3;P55210|P55210-2	.;.;.;CASP7_HUMAN|.	E|S	288;255;255;216;255;230|244	ENSP00000358327:D288E;ENSP00000298701:D255E;ENSP00000358324:D255E;ENSP00000358321:D255E;ENSP00000398107:D230E|ENSP00000358337:T244S	ENSP00000298701:D255E|ENSP00000358337:T244S	D|T	+|+	3|2	2|0	CASP7|CASP7	115479142|115479142	0.004000|0.004000	0.15560|0.15560	0.493000|0.493000	0.27502|0.27502	0.997000|0.997000	0.91878|0.91878	-0.776000|-0.776000	0.04674|0.04674	0.362000|0.362000	0.24319|0.24319	0.655000|0.655000	0.94253|0.94253	GAC|ACC	C|0.761;G|0.239	0.239	strong		0.522	CASP7-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050439.1	NM_033338	
KIAA1683	80726	hgsc.bcm.edu	37	19	18368810	18368810	+	Missense_Mutation	SNP	G	G	T	rs999813	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18368810G>T	ENST00000600328.3	-	4	2916	c.2723C>A	c.(2722-2724)cCt>cAt	p.P908H	PDE4C_ENST00000596647.1_5'Flank|PDE4C_ENST00000355502.3_5'Flank|KIAA1683_ENST00000392413.4_Missense_Mutation_p.P1095H|KIAA1683_ENST00000600359.3_Missense_Mutation_p.P862H			Q9H0B3	K1683_HUMAN	KIAA1683	908			P -> H (in dbSNP:rs999813). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						CCGCCTGGGAGGCACCACCGC	0.672													g|||	2760	0.551118	0.6876	0.6037	5008	,	,		15679	0.5536		0.4662	False		,,,				2504	0.4141				p.P1095H		Atlas-SNP	.											KIAA1683_ENST00000392413,NS,carcinoma,0,2	KIAA1683	190	2	0			c.C3284A						scavenged	.	G	HIS/PRO,HIS/PRO,HIS/PRO	2962,1438		1011,940,249	61.0	58.0	59.0		3284,2585,2723	-1.6	0.0	19	dbSNP_86	59	3903,4679		920,2063,1308	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	77,77,77	1931,3003,1557	TT,TG,GG		45.4789,32.6818,47.1191	benign,benign,benign	1095/1368,862/1135,908/1181	18368810	6865,6117	2200	4291	6491	SO:0001583	missense	80726	exon4			CTGGGAGGCACCA	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2723C>A	19.37:g.18368810G>T	ENSP00000470780:p.Pro908His	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	1174	0.5375457875457875	326	0.6626016260162602	196	0.5414364640883977	298	0.5209790209790209	354	0.46701846965699206	g	6.262	0.416402	0.11870	0.673182	0.454789	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000392412;ENST00000411671	T;T;T	0.03441	4.03;4.01;3.93	3.59	-1.61	0.08399	.	1.073180	0.07438	N	0.896811	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.12553	-1.0543	9	0.39692	T	0.17	-0.7752	1.3507	0.02172	0.1782:0.1122:0.3686:0.3411	rs999813;rs17654930;rs52810202;rs59590619;rs999813	1095;908	E9PDE0;Q9H0B3	.;K1683_HUMAN	H	1095;908;862;172;522	ENSP00000376213:P1095H;ENSP00000352774:P908H;ENSP00000404501:P862H	ENSP00000352774:P908H	P	-	2	0	KIAA1683	18229810	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.447000	0.06828	-0.155000	0.11098	-0.546000	0.04227	CCT	G|0.473;T|0.527	0.527	strong		0.672	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
TRIM67	440730	hgsc.bcm.edu	37	1	231344908	231344908	+	Missense_Mutation	SNP	A	A	G	rs114415891	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:231344908A>G	ENST00000366653.5	+	8	2035	c.2035A>G	c.(2035-2037)Atg>Gtg	p.M679V	TRIM67_ENST00000444294.3_Missense_Mutation_p.M677V|TRIM67_ENST00000449018.3_Missense_Mutation_p.M617V|TRIM67_ENST00000366652.2_Missense_Mutation_p.M679V			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	679	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.			M -> V (in Ref. 3; BAC86689). {ECO:0000305}.	negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)	p.M679V(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				GGTCAAGGACATGATGCTGGG	0.617													A|||	30	0.00599042	0.0	0.0072	5008	,	,		20231	0.0		0.0229	False		,,,				2504	0.002				p.M679V		Atlas-SNP	.											TRIM67_ENST00000366653,colon,carcinoma,-1,7	TRIM67	160	7	1	Substitution - Missense(1)	breast(1)	c.A2035G						PASS	.	A	VAL/MET	20,4368	26.2+/-53.5	0,20,2174	91.0	99.0	96.0		2035	5.7	1.0	1	dbSNP_132	96	142,8458	68.7+/-131.2	1,140,4159	yes	missense	TRIM67	NM_001004342.3	21	1,160,6333	GG,GA,AA		1.6512,0.4558,1.2473	benign	679/784	231344908	162,12826	2194	4300	6494	SO:0001583	missense	440730	exon8			AAGGACATGATGC	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"""Tripartite motif containing / Tripartite motif containing"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	31859	protein-coding gene	gene with protein product		610584	"""tripartite motif-containing 67"""				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.2035A>G	1.37:g.231344908A>G	ENSP00000355613:p.Met679Val	Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	263	127	0.48289	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	37	CCDS44333.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	A	4.607	0.112797	0.08831	0.004558	0.016512	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000449018;ENST00000366653	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.73	5.73	0.89815	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.28400	0.0702	N	0.02721	-0.515	0.46981	D	0.999274	B	0.14012	0.009	B	0.17098	0.017	T	0.27739	-1.0065	10	0.28530	T	0.3	.	16.3197	0.82945	1.0:0.0:0.0:0.0	.	679	Q6ZTA4	TRI67_HUMAN	V	677;679;617;679	ENSP00000412124:M677V;ENSP00000355612:M679V;ENSP00000400163:M617V;ENSP00000355613:M679V	ENSP00000355612:M679V	M	+	1	0	TRIM67	229411531	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.313000	0.65798	2.302000	0.77476	0.533000	0.62120	ATG	A|0.990;G|0.010	0.010	strong		0.617	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342	
ATP8B3	148229	hgsc.bcm.edu	37	19	1783185	1783185	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1783185G>A	ENST00000310127.6	-	29	3983	c.3745C>T	c.(3745-3747)Cgt>Tgt	p.R1249C	ATP8B3_ENST00000539485.1_Missense_Mutation_p.R1259C|ATP8B3_ENST00000525591.1_Missense_Mutation_p.R1212C	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1249					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R1259C(1)		central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TAGCTGGAACGGCGGGCACGA	0.587																																					p.R1249C		Atlas-SNP	.											ATP8B3,caecum,carcinoma,0,1	ATP8B3	108	1	1	Substitution - Missense(1)	large_intestine(1)	c.C3745T						PASS	.						48.0	49.0	49.0					19																	1783185		1993	4151	6144	SO:0001583	missense	148229	exon29			TGGAACGGCGGGC	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.3745C>T	19.37:g.1783185G>A	ENSP00000311336:p.Arg1249Cys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	145	67	0.462069	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611889	0.66558	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.65732	-0.17;-0.05;-0.07	4.57	4.57	0.56435	.	0.144065	0.47852	D	0.000201	T	0.78710	0.4326	M	0.76727	2.345	0.54753	D	0.999983	D;D	0.89917	1.0;1.0	D;D	0.79108	0.988;0.992	T	0.82323	-0.0514	10	0.87932	D	0	.	16.3466	0.83134	0.0:0.0:1.0:0.0	.	1249;1212	O60423;Q7Z485	AT8B3_HUMAN;.	C	1249;1259;1212	ENSP00000311336:R1249C;ENSP00000443574:R1259C;ENSP00000437115:R1212C	ENSP00000311336:R1249C	R	-	1	0	ATP8B3	1734185	1.000000	0.71417	0.937000	0.37676	0.253000	0.25986	7.161000	0.77505	2.088000	0.63022	0.549000	0.68633	CGT	.	.	none		0.587	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
C19orf44	84167	hgsc.bcm.edu	37	19	16612011	16612011	+	Silent	SNP	T	T	C	rs728117	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:16612011T>C	ENST00000221671.3	+	2	564	c.408T>C	c.(406-408)tcT>tcC	p.S136S	CTD-3222D19.2_ENST00000409035.1_Intron|C19orf44_ENST00000594035.1_Silent_p.S136S	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	136										endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						GAATCCTCTCTGGGGGTGCAC	0.512													C|||	1835	0.366414	0.643	0.3415	5008	,	,		17337	0.1736		0.3221	False		,,,				2504	0.2546				p.S136S		Atlas-SNP	.											.	C19orf44	47	.	0			c.T408C						PASS	.	C		2698,1708	509.6+/-367.3	843,1012,348	55.0	61.0	59.0		408	-2.9	0.0	19	dbSNP_86	59	2642,5958	684.2+/-403.9	411,1820,2069	no	coding-synonymous	C19orf44	NM_032207.2		1254,2832,2417	CC,CT,TT		30.7209,38.7653,41.058		136/658	16612011	5340,7666	2203	4300	6503	SO:0001819	synonymous_variant	84167	exon2			CCTCTCTGGGGGT	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.408T>C	19.37:g.16612011T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_032207	Q8N6Y7	Silent	SNP	ENST00000221671.3	37	CCDS12345.1																																																																																			T|0.663;C|0.337	0.337	strong		0.512	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207	
UBASH3B	84959	hgsc.bcm.edu	37	11	122659918	122659918	+	Silent	SNP	T	T	G	rs955051	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:122659918T>G	ENST00000284273.5	+	6	1257	c.882T>G	c.(880-882)ggT>ggG	p.G294G		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	294	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.G294G(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		CCAGCGAGGGTTGGATCTATG	0.527													T|||	469	0.0936502	0.0295	0.0778	5008	,	,		20220	0.0387		0.1511	False		,,,				2504	0.1892				p.G294G		Atlas-SNP	.											UBASH3B,NS,carcinoma,0,1	UBASH3B	73	1	1	Substitution - coding silent(1)	stomach(1)	c.T882G						scavenged	.	T		221,4183	132.9+/-169.3	4,213,1985	179.0	172.0	174.0		882	4.0	1.0	11	dbSNP_86	174	1529,7069	287.5+/-298.3	143,1243,2913	no	coding-synonymous	UBASH3B	NM_032873.4		147,1456,4898	GG,GT,TT		17.7832,5.0182,13.4595		294/650	122659918	1750,11252	2202	4299	6501	SO:0001819	synonymous_variant	84959	exon6			CGAGGGTTGGATC	AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"""SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"""	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.882T>G	11.37:g.122659918T>G		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	138	55	0.398551	NM_032873	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Silent	SNP	ENST00000284273.5	37	CCDS31694.1																																																																																			A|0.005;C|0.000	.	strong		0.527	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873	
EML5	161436	hgsc.bcm.edu	37	14	89206861	89206861	+	Missense_Mutation	SNP	G	G	A	rs139652502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:89206861G>A	ENST00000380664.5	-	5	580	c.581C>T	c.(580-582)aCg>aTg	p.T194M	EML5_ENST00000554922.1_Missense_Mutation_p.T194M|EML5_ENST00000352093.5_Missense_Mutation_p.T194M			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	194						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AAGGTCACCCGTCTTACCAAA	0.378													G|||	17	0.00339457	0.0015	0.0014	5008	,	,		16789	0.0		0.0119	False		,,,				2504	0.002				p.T194M		Atlas-SNP	.											EML5,colon,NS,+1,1	EML5	141	1	0			c.C581T						PASS	.	G	MET/THR	11,3737		0,11,1863	154.0	145.0	148.0		581	5.2	1.0	14	dbSNP_134	148	112,8122		0,112,4005	yes	missense	EML5	NM_183387.2	81	0,123,5868	AA,AG,GG		1.3602,0.2935,1.0265	benign	194/1978	89206861	123,11859	1874	4117	5991	SO:0001583	missense	161436	exon5			TCACCCGTCTTAC	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.581C>T	14.37:g.89206861G>A	ENSP00000370039:p.Thr194Met	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	234	114	0.487179	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	8	0.003663003663003663	1	0.0020325203252032522	0	0.0	0	0.0	7	0.009234828496042216	G	15.13	2.742905	0.49151	0.002935	0.013602	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.22134	1.97;1.97;1.97	5.21	5.21	0.72293	WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.195228	0.43919	D	0.000501	T	0.18173	0.0436	L	0.49640	1.575	0.54753	D	0.999982	B	0.24368	0.102	B	0.24394	0.053	T	0.02208	-1.1195	10	0.46703	T	0.11	-17.6021	18.7549	0.91828	0.0:0.0:1.0:0.0	.	194	Q05BV3	EMAL5_HUMAN	M	194	ENSP00000451998:T194M;ENSP00000298315:T194M;ENSP00000370039:T194M	ENSP00000298315:T194M	T	-	2	0	EML5	88276614	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.542000	0.82095	2.417000	0.82017	0.591000	0.81541	ACG	G|0.994;A|0.006	0.006	strong		0.378	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
ITGA2	3673	hgsc.bcm.edu	37	5	52379277	52379277	+	Silent	SNP	C	C	T	rs2303122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:52379277C>T	ENST00000296585.5	+	27	3395	c.3252C>T	c.(3250-3252)ttC>ttT	p.F1084F		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	1084					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)	p.F1084L(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				ACGGGACTTTCGCATCAGTAA	0.368													C|||	1662	0.331869	0.2806	0.4323	5008	,	,		19643	0.2946		0.3708	False		,,,				2504	0.3282				p.F1084F		Atlas-SNP	.											ITGA2,colon,carcinoma,0,1	ITGA2	211	1	1	Substitution - Missense(1)	large_intestine(1)	c.C3252T						scavenged	.	C		1316,3090	442.9+/-346.8	197,922,1084	103.0	96.0	98.0		3252	-2.5	1.0	5	dbSNP_100	98	3138,5462	477.9+/-369.8	554,2030,1716	no	coding-synonymous	ITGA2	NM_002203.3		751,2952,2800	TT,TC,CC		36.4884,29.8684,34.2457		1084/1182	52379277	4454,8552	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon27			GACTTTCGCATCA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.3252C>T	5.37:g.52379277C>T		Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			T|0.351;G|0.004	0.351	strong		0.368	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
FARP2	9855	hgsc.bcm.edu	37	2	242371101	242371101	+	Missense_Mutation	SNP	C	C	T	rs757978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242371101C>T	ENST00000264042.3	+	9	949	c.779C>T	c.(778-780)aCc>aTc	p.T260I	FARP2_ENST00000373287.4_Missense_Mutation_p.T260I|FARP2_ENST00000545004.1_Missense_Mutation_p.T260I	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	260	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		T -> I (in dbSNP:rs757978).		actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		CAGGGCACCACCAAAATCAAC	0.383													C|||	403	0.0804712	0.1082	0.0807	5008	,	,		11204	0.0238		0.0974	False		,,,				2504	0.0838				p.T260I		Atlas-SNP	.											.	FARP2	92	.	0			c.C779T						PASS	.	C	ILE/THR	426,3980	206.2+/-227.9	22,382,1799	118.0	106.0	110.0	http://www.ncbi.nlm.nih.gov/pubmed?term	779	4.8	1.0	2	dbSNP_86	110	961,7639	210.5+/-251.4	47,867,3386	yes	missense	FARP2	NM_014808.2	89	69,1249,5185	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	11.1744,9.6686,10.6643	probably-damaging	260/1055	242371101	1387,11619	2203	4300	6503	SO:0001583	missense	9855	exon9			GCACCACCAAAAT	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.779C>T	2.37:g.242371101C>T	ENSP00000264042:p.Thr260Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	171	0.0782967032967033	51	0.10365853658536585	22	0.06077348066298342	19	0.033216783216783216	79	0.10422163588390501	c	21.0	4.075661	0.76415	0.096686	0.111744	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287	D;D;D	0.87179	-2.22;-2.22;-2.22	4.79	4.79	0.61399	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.126402	0.53938	D	0.000056	T	0.23688	0.0573	L	0.49640	1.575	0.09310	P	0.999999999237139	D;D;D	0.89917	1.0;0.988;1.0	D;D;D	0.97110	0.999;0.944;1.0	T	0.65092	-0.6252	9	0.30078	T	0.28	.	18.2564	0.90021	0.0:1.0:0.0:0.0	rs757978;rs17452163;rs59395776;rs757978	260;260;260	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	I	260	ENSP00000264042:T260I;ENSP00000443876:T260I;ENSP00000362384:T260I	ENSP00000264042:T260I	T	+	2	0	FARP2	242019774	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.828000	0.69307	2.382000	0.81193	0.539000	0.68188	ACC	C|0.901;T|0.099	0.099	strong		0.383	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31239827	31239827	+	Missense_Mutation	SNP	C	C	T	rs2308525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239827C>T	ENST00000376228.5	-	1	36	c.22G>A	c.(22-24)Gcc>Acc	p.A8T	HLA-C_ENST00000383329.3_Missense_Mutation_p.A8T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	8			QA -> RT (in allele Cw*17:02).		antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						AGGAGGAGGGCTCGGGGCGCC	0.682													t|||	3772	0.753195	0.7095	0.8026	5008	,	,		13502	0.8135		0.7157	False		,,,				2504	0.7536				p.A8T		Atlas-SNP	.											.	HLA-C	92	.	0			c.G22A						PASS	.	T	THR/ALA	2088,932		716,656,138	18.0	19.0	19.0		22	-3.2	0.0	6	dbSNP_119	19	3676,1742		1255,1166,288	no	missense	HLA-C	NM_002117.5	58	1971,1822,426	TT,TC,CC		32.1521,30.8609,31.69	benign	8/367	31239827	5764,2674	1510	2709	4219	SO:0001583	missense	3107	exon1			GGAGGGCTCGGGG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.22G>A	6.37:g.31239827C>T	ENSP00000365402:p.Ala8Thr	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	81	78	0.962963	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1605|1605	0.7348901098901099|0.7348901098901099	333|333	0.676829268292683|0.676829268292683	285|285	0.787292817679558|0.787292817679558	455|455	0.7954545454545454|0.7954545454545454	532|532	0.7018469656992085|0.7018469656992085	-|-	7.571|7.571	0.666781|0.666781	0.14710|0.14710	0.691391|0.691391	0.678479|0.678479	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00760|.	5.73;5.73|.	2.71|2.71	-3.23|-3.23	0.05109|0.05109	.|.	5.988920|.	0.01249|.	N|.	0.008827|.	T|T	0.11793|0.11793	0.0287|0.0287	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.001;0.0;0.001|.	T|T	0.23226|0.23226	-1.0194|-1.0194	8|3	0.02654|.	T|.	1|.	.|.	5.6062|5.6062	0.17381|0.17381	0.0:0.5036:0.1875:0.3089|0.0:0.5036:0.1875:0.3089	rs2308525;rs9264673|rs2308525;rs9264673	8;8;8;8|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	T|N	8|7	ENSP00000365402:A8T;ENSP00000372819:A8T|.	ENSP00000365402:A8T|.	A|S	-|-	1|2	0|0	HLA-C|HLA-C	31347806|31347806	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.008000|0.008000	0.06430|0.06430	-0.588000|-0.588000	0.05774|0.05774	-1.188000|-1.188000	0.02705|0.02705	-0.893000|-0.893000	0.02921|0.02921	GCC|AGC	C|0.297;T|0.703	0.703	strong		0.682	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
HOXA7	3204	hgsc.bcm.edu	37	7	27196113	27196113	+	Missense_Mutation	SNP	C	C	T	rs2301721	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:27196113C>T	ENST00000242159.3	-	1	185	c.52G>A	c.(52-54)Gct>Act	p.A18T	HOXA-AS3_ENST00000518947.2_RNA|RP1-170O19.21_ENST00000602610.1_lincRNA|HOXA7_ENST00000523796.2_5'Flank	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	18			A -> T (in dbSNP:rs2301721). {ECO:0000269|PubMed:10911612, ECO:0000269|PubMed:11435435, ECO:0000269|PubMed:9804983, ECO:0000269|Ref.4, ECO:0000269|Ref.8}.		angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						AACAGAGAAGCCCCCGCCGTA	0.532													C|||	3097	0.618411	0.1014	0.6499	5008	,	,		11557	0.8581		0.83	False		,,,				2504	0.8303				p.A18T		Atlas-SNP	.											.	HOXA7	34	.	0			c.G52A						PASS	.	C	THR/ALA	924,3476		117,690,1393	62.0	77.0	72.0		52	4.3	1.0	7	dbSNP_100	72	7180,1414		3008,1164,125	yes	missense	HOXA7	NM_006896.3	58	3125,1854,1518	TT,TC,CC		16.4533,21.0,37.6328	benign	18/231	27196113	8104,4890	2200	4297	6497	SO:0001583	missense	3204	exon1			GAGAAGCCCCCGC		CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"""Homeoboxes / ANTP class : HOXL subclass"""	5108	protein-coding gene	gene with protein product		142950	"""homeo box A7"""	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.52G>A	7.37:g.27196113C>T	ENSP00000242159:p.Ala18Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	124	110	0.887097	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	37	CCDS5408.1	1439	0.6588827838827839	81	0.16463414634146342	243	0.6712707182320442	483	0.8444055944055944	632	0.8337730870712401	C	13.23	2.173748	0.38413	0.21	0.835467	ENSG00000122592	ENST00000242159;ENST00000519842	T;T	0.63096	1.58;-0.02	5.21	4.34	0.51931	.	0.190595	0.43919	N	0.000503	T	0.00012	0.0000	N	0.19112	0.55	0.25878	P	0.9836271	B	0.23128	0.08	B	0.16289	0.015	T	0.25433	-1.0132	9	0.21540	T	0.41	.	13.6625	0.62376	0.0:0.9241:0.0:0.0759	rs2301721;rs58981696;rs2301721	18	P31268	HXA7_HUMAN	T	18	ENSP00000242159:A18T;ENSP00000428563:A18T	ENSP00000242159:A18T	A	-	1	0	HOXA7	27162638	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.781000	0.47750	1.341000	0.45600	0.561000	0.74099	GCT	C|0.328;T|0.672	0.672	strong		0.532	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1		
CFH	3075	hgsc.bcm.edu	37	1	196659237	196659237	+	Missense_Mutation	SNP	C	C	T	rs1061170	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:196659237C>T	ENST00000359637.2	+	8	1074	c.1012C>T	c.(1012-1014)Cat>Tat	p.H338Y	CFH_ENST00000367429.4_Missense_Mutation_p.H402Y|CFH_ENST00000439155.2_Missense_Mutation_p.H402Y			P08603	CFAH_HUMAN	complement factor H	402	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						TAATCAAAATCATGGAAGAAA	0.348													T|||	3673	0.733427	0.6377	0.7666	5008	,	,		16067	0.9514		0.6382	False		,,,				2504	0.7127				p.H402Y		Atlas-SNP	.											CFH,NS,carcinoma,0,1	CFH	251	1	0			c.C1204T	GRCh37	CM051020	CFH	M	rs1061170	PASS	.	T	TYR/HIS,TYR/HIS	2808,1598	496.0+/-363.4	889,1030,284	51.0	52.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1204,1204	-9.1	0.0	1	dbSNP_86	51	5312,3288	490.0+/-372.7	1649,2014,637	yes	missense,missense	CFH	NM_000186.3,NM_001014975.2	83,83	2538,3044,921	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	38.2326,36.2687,37.5673	benign,benign	402/1232,402/450	196659237	8120,4886	2203	4300	6503	SO:0001583	missense	3075	exon9			CAAAATCATGGAA	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000359637.2:c.1012C>T	1.37:g.196659237C>T	ENSP00000352658:p.His338Tyr	Somatic	390	1	0.0025641		WXS	Illumina HiSeq	Phase_I	394	203	0.515228	NM_001014975	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000359637.2	37		1576	0.7216117216117216	303	0.6158536585365854	265	0.7320441988950276	533	0.9318181818181818	475	0.6266490765171504	T	0.004	-2.252215	0.00268	0.637313	0.617674	ENSG00000000971	ENST00000367429;ENST00000439155;ENST00000391986;ENST00000359637	T;T;T	0.63255	-0.03;-0.03;-0.03	4.54	-9.09	0.00717	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.27606	-1.0069	7	0.02654	T	1	.	2.0714	0.03614	0.4236:0.2638:0.0834:0.2293	rs1061170;rs60173482;rs1061170	338;402	Q5TFM2;F8WDX4	.;.	Y	402;402;402;338	ENSP00000356399:H402Y;ENSP00000402656:H402Y;ENSP00000352658:H338Y	ENSP00000352658:H338Y	H	+	1	0	CFH	194925860	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.715000	0.00056	-4.010000	0.00082	-4.388000	0.00006	CAT	C|0.341;T|0.659	0.659	strong		0.348	CFH-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000087502.1	NM_000186	
KIAA1804	84451	hgsc.bcm.edu	37	1	233489617	233489617	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:233489617G>A	ENST00000366624.3	+	3	1312	c.1051G>A	c.(1051-1053)Gcc>Acc	p.A351T	MLK4_ENST00000366623.3_Missense_Mutation_p.A351T	NM_032435.2	NP_115811.2																					TGATGGCCTCGCCGTGGCTTA	0.517																																					p.A351T		Atlas-SNP	.											KIAA1804,NS,carcinoma,-1,1	KIAA1804	129	1	0			c.G1051A						scavenged	.						120.0	108.0	112.0					1																	233489617		2203	4300	6503	SO:0001583	missense	0	exon3			GGCCTCGCCGTGG																												ENST00000366624.3:c.1051G>A	1.37:g.233489617G>A	ENSP00000355583:p.Ala351Thr	Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	218	3	0.0137615	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.187846	0.78789	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	D;D	0.82526	-1.62;-1.62	4.91	4.91	0.64330	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85725	0.5763	N	0.21194	0.64	0.80722	D	1	D;D	0.71674	0.998;0.984	D;P	0.72338	0.977;0.843	D	0.87906	0.2694	10	0.72032	D	0.01	.	18.301	0.90163	0.0:0.0:1.0:0.0	.	351;351	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	T	351	ENSP00000355582:A351T;ENSP00000355583:A351T	ENSP00000355582:A351T	A	+	1	0	RP5-862P8.2	231556240	1.000000	0.71417	0.258000	0.24420	0.403000	0.30841	9.648000	0.98483	2.538000	0.85594	0.563000	0.77884	GCC	.	.	none		0.517	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
DAAM1	23002	hgsc.bcm.edu	37	14	59789892	59789892	+	Silent	SNP	G	G	T	rs17096074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:59789892G>T	ENST00000395125.1	+	5	746	c.723G>T	c.(721-723)ctG>ctT	p.L241L	DAAM1_ENST00000360909.3_Silent_p.L241L|DAAM1_ENST00000351081.1_Silent_p.L241L	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	241	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AGAAGGTTCTGCAGGCCATGC	0.552													G|||	147	0.029353	0.0053	0.0375	5008	,	,		18273	0.0109		0.0865	False		,,,				2504	0.0164				p.L241L		Atlas-SNP	.											DAAM1,NS,carcinoma,+2,1	DAAM1	95	1	0			c.G723T						PASS	.	G		67,4339	64.1+/-101.4	0,67,2136	26.0	26.0	26.0		723	5.1	1.0	14	dbSNP_123	26	784,7816	180.3+/-229.3	32,720,3548	no	coding-synonymous	DAAM1	NM_014992.1		32,787,5684	TT,TG,GG		9.1163,1.5207,6.5431		241/1079	59789892	851,12155	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon6			GGTTCTGCAGGCC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.723G>T	14.37:g.59789892G>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.945;T|0.055	0.055	strong		0.552	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
CRHR1	1394	hgsc.bcm.edu	37	17	43907896	43907896	+	Silent	SNP	T	T	C	rs16940665	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43907896T>C	ENST00000398285.3	+	8	756	c.756T>C	c.(754-756)acT>acC	p.T252T	CRHR1_ENST00000339069.5_Silent_p.T122T|CRHR1_ENST00000293493.7_Silent_p.T48T|CRHR1_ENST00000314537.5_Silent_p.T223T|CRHR1_ENST00000352855.5_Silent_p.T183T|CRHR1_ENST00000577353.1_Silent_p.T223T	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	252					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CCTACTCCACTGACCGGCTGC	0.622													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		20880	0.001		0.2396	False		,,,				2504	0.0613				p.T252T	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.T756C						PASS	.	C	,,,	200,4202	777.7+/-414.2	5,190,2006	91.0	94.0	93.0		756,549,669,669	-4.0	0.9	17	dbSNP_123	93	1925,6675	717.6+/-406.2	221,1483,2596	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CRHR1	NM_001145146.1,NM_001145147.1,NM_001145148.1,NM_004382.4	,,,	226,1673,4602	CC,CT,TT		22.3837,4.5434,16.3436	,,,	252/445,183/376,223/402,223/416	43907896	2125,10877	2201	4300	6501	SO:0001819	synonymous_variant	1394	exon8			CTCCACTGACCGG	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2357	protein-coding gene	gene with protein product	"""corticotropin-releasing factor receptor"""	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.756T>C	17.37:g.43907896T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	99	37	0.373737	NM_001145146	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Silent	SNP	ENST00000398285.3	37	CCDS45712.1																																																																																			T|0.862;C|0.138	0.138	strong		0.622	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3		
ZNF438	220929	hgsc.bcm.edu	37	10	31134214	31134214	+	Silent	SNP	A	A	G	rs3740236	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:31134214A>G	ENST00000361310.3	-	7	2492	c.2163T>C	c.(2161-2163)caT>caC	p.H721H	ZNF438_ENST00000436087.2_Silent_p.H721H|ZNF438_ENST00000331737.6_Silent_p.H711H|ZNF438_ENST00000442986.1_Silent_p.H721H|ZNF438_ENST00000375311.1_Silent_p.H285H|ZNF438_ENST00000413025.1_Silent_p.H721H|ZNF438_ENST00000538351.2_Silent_p.H672H|ZNF438_ENST00000444692.2_Silent_p.H711H|ZNF438_ENST00000452305.1_Silent_p.H711H			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	721					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(15)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(175;0.0587)				TTGGACATGCATGTGATTCCT	0.537													G|||	737	0.147165	0.0227	0.2954	5008	,	,		20833	0.3274		0.0954	False		,,,				2504	0.0777				p.H721H		Atlas-SNP	.											.	ZNF438	90	.	0			c.T2163C						PASS	.	G	,,,,,,	186,4220	809.7+/-416.0	4,178,2021	93.0	89.0	90.0		2163,2163,2163,2016,2133,2133,2163	-10.2	0.0	10	dbSNP_107	90	896,7704	778.3+/-407.7	31,834,3435	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF438	NM_001143766.1,NM_001143767.1,NM_001143768.1,NM_001143769.1,NM_001143770.1,NM_001143771.1,NM_182755.2	,,,,,,	35,1012,5456	GG,GA,AA		10.4186,4.2215,8.3192	,,,,,,	721/829,721/829,721/829,672/780,711/819,711/819,721/829	31134214	1082,11924	2203	4300	6503	SO:0001819	synonymous_variant	220929	exon8			ACATGCATGTGAT	AK057323	CCDS7168.1, CCDS44369.1, CCDS53504.1	10p11.23	2006-02-15			ENSG00000183621	ENSG00000183621		"""Zinc fingers, C2H2-type"""	21029	protein-coding gene	gene with protein product							Standard	NM_182755		Approved	bA330O11.1	uc010qeb.2	Q7Z4V0	OTTHUMG00000017904	ENST00000361310.3:c.2163T>C	10.37:g.31134214A>G		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	206	101	0.490291	NM_182755	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Silent	SNP	ENST00000361310.3	37	CCDS7168.1																																																																																			A|0.883;G|0.117	0.117	strong		0.537	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755	
GPATCH2	55105	hgsc.bcm.edu	37	1	217604654	217604654	+	Missense_Mutation	SNP	T	T	C	rs35737297	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:217604654T>C	ENST00000366935.3	-	10	1530	c.1420A>G	c.(1420-1422)Atg>Gtg	p.M474V		NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	474	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)	p.M474V(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		TTCTGAAGCATTCGGTTTCCA	0.458													T|||	146	0.0291534	0.0008	0.0159	5008	,	,		18380	0.0417		0.0417	False		,,,				2504	0.0511				p.M474V		Atlas-SNP	.											GPATCH2,NS,carcinoma,0,1	GPATCH2	53	1	1	Substitution - Missense(1)	stomach(1)	c.A1420G						PASS	.	T	VAL/MET	40,4366	43.8+/-77.6	0,40,2163	99.0	101.0	100.0		1420	4.7	1.0	1	dbSNP_126	100	338,8262	116.6+/-176.3	6,326,3968	yes	missense	GPATCH2	NM_018040.2	21	6,366,6131	CC,CT,TT		3.9302,0.9079,2.9064	possibly-damaging	474/529	217604654	378,12628	2203	4300	6503	SO:0001583	missense	55105	exon10			GAAGCATTCGGTT	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.1420A>G	1.37:g.217604654T>C	ENSP00000355902:p.Met474Val	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	173	82	0.473988	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Missense_Mutation	SNP	ENST00000366935.3	37	CCDS1518.1	67	0.030677655677655676	1	0.0020325203252032522	10	0.027624309392265192	31	0.05419580419580419	25	0.032981530343007916	T	21.1	4.094621	0.76870	0.009079	0.039302	ENSG00000092978	ENST00000366935	T	0.38077	1.16	5.83	4.68	0.58851	D111/G-patch (3);	0.040812	0.85682	D	0.000000	T	0.23094	0.0558	M	0.87971	2.92	0.80722	D	1	D	0.60160	0.987	D	0.67382	0.951	T	0.55749	-0.8092	10	0.87932	D	0	.	13.121	0.59327	0.0:0.0:0.1338:0.8662	rs35737297	474	Q9NW75	GPTC2_HUMAN	V	474	ENSP00000355902:M474V	ENSP00000355902:M474V	M	-	1	0	GPATCH2	215671277	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.156000	0.77453	1.002000	0.39104	0.528000	0.53228	ATG	T|0.969;C|0.031	0.031	strong		0.458	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040	
B3GALT5	10317	hgsc.bcm.edu	37	21	41033062	41033062	+	Silent	SNP	G	G	A	rs734412	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:41033062G>A	ENST00000380620.4	+	5	1168	c.576G>A	c.(574-576)agG>agA	p.R192R	B3GALT5_ENST00000380618.1_Silent_p.R192R|B3GALT5_ENST00000398714.2_Silent_p.R192R|AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000343118.4_Silent_p.R192R			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	192					protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				TTCCCATCAGGCAGCCATTCA	0.468													G|||	106	0.0211661	0.0038	0.036	5008	,	,		16476	0.0		0.0656	False		,,,				2504	0.0102				p.R192R		Atlas-SNP	.											.	B3GALT5	40	.	0			c.G576A						PASS	.	G	,,,,	79,4327	70.3+/-108.2	3,73,2127	67.0	67.0	67.0		576,576,576,576,576	2.7	0.1	21	dbSNP_86	67	723,7877	175.9+/-225.9	36,651,3613	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	B3GALT5	NM_006057.1,NM_033170.1,NM_033171.1,NM_033172.1,NM_033173.1	,,,,	39,724,5740	AA,AG,GG		8.407,1.793,6.1664	,,,,	192/311,192/311,192/311,192/311,192/311	41033062	802,12204	2203	4300	6503	SO:0001819	synonymous_variant	10317	exon3			CATCAGGCAGCCA	AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"""Beta 3-glycosyltransferases"""	920	protein-coding gene	gene with protein product	"""homolog of C. elegans Bt toxin resistance gene bre-5"", ""GlcNAc-beta-1,3-galactosyltransferase 5"""	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.576G>A	21.37:g.41033062G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_033170	A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Silent	SNP	ENST00000380620.4	37	CCDS13667.1																																																																																			G|0.950;A|0.050	0.050	strong		0.468	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	NM_033170	
SLC4A11	83959	hgsc.bcm.edu	37	20	3214581	3214581	+	Silent	SNP	C	C	T	rs3803956	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3214581C>T	ENST00000380056.3	-	5	686	c.639G>A	c.(637-639)tcG>tcA	p.S213S	SLC4A11_ENST00000539553.2_Silent_p.S197S|SLC4A11_ENST00000380059.3_Silent_p.S240S	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	213			S -> L (in CHED2). {ECO:0000269|PubMed:17679935}.|S -> P (in CDPD). {ECO:0000269|PubMed:17220209}.		bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						TGCAGAGCCACGACTGCTGGT	0.627													C|||	833	0.166334	0.2186	0.1254	5008	,	,		17524	0.128		0.1779	False		,,,				2504	0.1524				p.S240S	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.G720A						PASS	.	C	,,	933,3473	355.6+/-313.1	107,719,1377	123.0	114.0	117.0		591,720,639	-10.4	0.0	20	dbSNP_107	117	1489,7111	283.3+/-296.1	121,1247,2932	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	,,	228,1966,4309	TT,TC,CC		17.314,21.1757,18.6222	,,	197/876,240/919,213/892	3214581	2422,10584	2203	4300	6503	SO:0001819	synonymous_variant	83959	exon6			GAGCCACGACTGC	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.639G>A	20.37:g.3214581C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Silent	SNP	ENST00000380056.3	37	CCDS13052.1																																																																																			C|0.820;T|0.180	0.180	strong		0.627	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
PAXIP1	22976	hgsc.bcm.edu	37	7	154738409	154738409	+	Missense_Mutation	SNP	T	T	C	rs3501	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:154738409T>C	ENST00000404141.1	-	18	3191	c.3037A>G	c.(3037-3039)Atg>Gtg	p.M1013V	PAXIP1_ENST00000397192.1_Missense_Mutation_p.M1013V|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	1013	BRCT 6. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with TP53BP1.		M -> V (in dbSNP:rs3501). {ECO:0000269|PubMed:17974005}.		adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)		p.M979V(1)		NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		TTGTGCTCCATGAGCTTCCGG	0.512													T|||	1179	0.235423	0.0726	0.3818	5008	,	,		15607	0.2083		0.3012	False		,,,				2504	0.3119				p.M1013V		Atlas-SNP	.											PAXIP1_ENST00000397192,caecum,carcinoma,0,3	PAXIP1	150	3	1	Substitution - Missense(1)	stomach(1)	c.A3037G						PASS	.	T	VAL/MET	391,3623		19,353,1635	76.0	74.0	75.0		3037	0.2	1.0	7	dbSNP_36	75	2251,6097		310,1631,2233	yes	missense	PAXIP1	NM_007349.3	21	329,1984,3868	CC,CT,TT		26.9645,9.7409,21.3719	benign	1013/1070	154738409	2642,9720	2007	4174	6181	SO:0001583	missense	22976	exon18			GCTCCATGAGCTT	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.3037A>G	7.37:g.154738409T>C	ENSP00000384048:p.Met1013Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	505	0.23122710622710624	40	0.08130081300813008	130	0.35911602209944754	118	0.2062937062937063	217	0.2862796833773087	T	12.30	1.897499	0.33535	0.097409	0.269645	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.41758	0.99;0.99	5.34	0.184	0.15086	BRCT (1);	0.162750	0.40640	N	0.001047	T	0.00012	0.0000	L	0.36672	1.1	0.26425	P	0.9760338	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45011	-0.9290	9	0.13853	T	0.58	-19.4618	5.5358	0.17011	0.0:0.2232:0.1342:0.6426	rs3501;rs52823645;rs3501	979;1013	Q6ZW49-1;Q6ZW49	.;PAXI1_HUMAN	V	1013;1013;837;966	ENSP00000384048:M1013V;ENSP00000380376:M1013V	ENSP00000319149:M966V	M	-	1	0	PAXIP1	154369342	1.000000	0.71417	0.964000	0.40570	0.940000	0.58332	1.156000	0.31712	-0.203000	0.10251	0.454000	0.30748	ATG	T|0.770;C|0.230	0.230	strong		0.512	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037424	33037424	+	Missense_Mutation	SNP	T	T	C	rs1126542	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33037424T>C	ENST00000419277.1	-	3	469	c.340A>G	c.(340-342)Acc>Gcc	p.T114A	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.T114A	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	114	Alpha-1.		T -> A (in allele DPA1*01:05, allele DPA1*02:01, allele DPA1*02:02, allele DPA1*02:03, allele DPA1*02:04 and allele DPA1*04:01; dbSNP:rs1126542).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						GTACCGTTGGTGGCCTGAGTG	0.542													.|||	2199	0.439097	0.5802	0.2853	5008	,	,		19850	0.6796		0.1889	False		,,,				2504	0.3671				p.T114A		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.A340G						PASS	.						140.0	128.0	132.0					6																	33037424		1510	2709	4219	SO:0001583	missense	3113	exon2			CGTTGGTGGCCTG	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.340A>G	6.37:g.33037424T>C	ENSP00000393566:p.Thr114Ala	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	159	47	0.295597	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	858	0.39285714285714285	270	0.5487804878048781	88	0.2430939226519337	370	0.6468531468531469	130	0.17150395778364116	C	0.073	-1.198952	0.01581	.	.	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000453337	T;T;T	0.00816	5.66;5.66;5.66	3.11	-6.22	0.02058	MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);Immunoglobulin-like fold (1);	1.036210	0.07665	N	0.934335	T	0.00328	0.0010	M	0.69523	2.12	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43861	-0.9365	9	0.34782	T	0.22	.	0.6691	0.00856	0.1954:0.1808:0.2729:0.351	rs1126542;rs2308922;rs3181639;rs12722008;rs17424589	114	P20036	DPA1_HUMAN	A	114	ENSP00000393566:T114A;ENSP00000402872:T114A;ENSP00000390929:T114A	ENSP00000393566:T114A	T	-	1	0	HLA-DPA1	33145402	0.000000	0.05858	0.063000	0.19743	0.003000	0.03518	-1.634000	0.02020	-3.515000	0.00149	-1.145000	0.01858	ACC	T|0.680;G|0.000;C|0.319;A|0.000	0.319	strong		0.542	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
OTOGL	283310	hgsc.bcm.edu	37	12	80761411	80761411	+	Missense_Mutation	SNP	G	G	T	rs11114416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:80761411G>T	ENST00000547103.1	+	53	6345	c.6339G>T	c.(6337-6339)ttG>ttT	p.L2113F	OTOGL_ENST00000546620.1_Missense_Mutation_p.L144F|OTOGL_ENST00000458043.2_Missense_Mutation_p.L2125F			Q3ZCN5	OTOGL_HUMAN	otogelin-like	2113					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TAAAGTATTTGGAAGAAGACT	0.323													G|||	851	0.169928	0.1846	0.2075	5008	,	,		14825	0.0417		0.1819	False		,,,				2504	0.2434				p.L2125F		Atlas-SNP	.											C12orf64,NS,carcinoma,-1,1	OTOGL	235	1	0			c.G6375T						PASS	.	G	PHE/LEU	807,3593		72,663,1465	68.0	65.0	66.0		6375	2.7	1.0	12	dbSNP_120	66	1648,6936		165,1318,2809	yes	missense	OTOGL	NM_173591.3	22	237,1981,4274	TT,TG,GG		19.1985,18.3409,18.9079	benign	2125/2345	80761411	2455,10529	2200	4292	6492	SO:0001583	missense	283310	exon53			GTATTTGGAAGAA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.6339G>T	12.37:g.80761411G>T	ENSP00000447211:p.Leu2113Phe	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		323|323	0.1478937728937729|0.1478937728937729	86|86	0.17479674796747968|0.17479674796747968	75|75	0.20718232044198895|0.20718232044198895	26|26	0.045454545454545456|0.045454545454545456	136|136	0.17941952506596306|0.17941952506596306	G|G	7.587|7.587	0.670053|0.670053	0.14776|0.14776	0.183409|0.183409	0.191985|0.191985	ENSG00000165899|ENSG00000165899	ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182|ENST00000298820	T;T;T;T|.	0.45276|.	2.32;2.32;2.23;0.9|.	5.53|5.53	2.66|2.66	0.31614|0.31614	.|.	0.498844|.	0.17868|.	N|.	0.159272|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.41027|0.41027	1.25|1.25	0.38267|0.38267	P|P	0.057950999999999975|0.057950999999999975	B|.	0.13594|.	0.008|.	B|.	0.16722|.	0.016|.	T|T	0.08889|0.08889	-1.0700|-1.0700	9|4	0.10636|.	T|.	0.68|.	.|.	9.0285|9.0285	0.36245|0.36245	0.1297:0.0:0.7494:0.1209|0.1297:0.0:0.7494:0.1209	rs11114416;rs52818722;rs11114416|rs11114416;rs52818722;rs11114416	490|.	Q3ZCN5|.	OTOGL_HUMAN|.	F|L	2113;2125;144;142|533	ENSP00000447211:L2113F;ENSP00000400895:L2125F;ENSP00000449094:L144F;ENSP00000449641:L142F|.	ENSP00000400895:L2125F|.	L|W	+|+	3|2	2|0	OTOGL|OTOGL	79285542|79285542	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.341000|0.341000	0.28922|0.28922	1.200000|1.200000	0.32247|0.32247	0.354000|0.354000	0.24105|0.24105	-0.198000|-0.198000	0.12761|0.12761	TTG|TGG	G|0.827;T|0.173	0.173	strong		0.323	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
FAAH2	158584	hgsc.bcm.edu	37	X	57475132	57475132	+	Silent	SNP	T	T	C	rs1367830	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:57475132T>C	ENST00000374900.4	+	10	1524	c.1404T>C	c.(1402-1404)ccT>ccC	p.P468P	FAAH2_ENST00000491179.1_3'UTR	NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	468						integral component of membrane (GO:0016021)	carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3)	22						TAACACGGCCTTTCAACTTTG	0.398										HNSCC(52;0.14)			T|||	1777	0.470728	0.0295	0.402	3775	,	,		9355	0.4663		0.5457	False		,,,				2504	0.4499				p.P468P		Atlas-SNP	.											.	FAAH2	66	.	0			c.T1404C						PASS	.	T		451,3384		30,328,63,1274,508	202.0	146.0	165.0		1404	1.3	1.0	X	dbSNP_88	165	4917,1811		1311,944,1351,173,521	no	coding-synonymous	FAAH2	NM_174912.3		1341,1272,1414,1447,1029	CC,CT,C,TT,T		26.9174,11.7601,49.1811		468/533	57475132	5368,5195	2203	4300	6503	SO:0001819	synonymous_variant	158584	exon10			ACGGCCTTTCAAC	AK055766	CCDS14375.1	Xp11.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000165591	ENSG00000165591			26440	protein-coding gene	gene with protein product		300654	"""amidase domain containing"""	AMDD		17015445	Standard	NM_174912		Approved	RP11-479E16.1, FLJ31204, FAAH-2	uc004dvc.3	Q6GMR7	OTTHUMG00000021684	ENST00000374900.4:c.1404T>C	X.37:g.57475132T>C		Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	120	115	0.958333	NM_174912	Q86VT2|Q96N98	Silent	SNP	ENST00000374900.4	37	CCDS14375.1																																																																																			T|0.496;0|0.015	.	strong		0.398	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912	
IRF2	3660	hgsc.bcm.edu	37	4	185310218	185310218	+	Silent	SNP	C	C	T	rs1131553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:185310218C>T	ENST00000393593.3	-	9	951	c.744G>A	c.(742-744)ggG>ggA	p.G248G		NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	248					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G248G(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		AGTGTGGCCGCCCCTTTCAAG	0.498													C|||	2119	0.423123	0.3548	0.5245	5008	,	,		20139	0.4216		0.3598	False		,,,				2504	0.5102				p.G248G		Atlas-SNP	.											IRF2,NS,carcinoma,0,1	IRF2	53	1	1	Substitution - coding silent(1)	stomach(1)	c.G744A						PASS	.	C		1525,2881	483.3+/-359.7	262,1001,940	129.0	111.0	117.0		744	-4.0	0.9	4	dbSNP_107	117	3376,5224	500.1+/-375.1	677,2022,1601	no	coding-synonymous	IRF2	NM_002199.3		939,3023,2541	TT,TC,CC		39.2558,34.6119,37.6826		248/350	185310218	4901,8105	2203	4300	6503	SO:0001819	synonymous_variant	3660	exon9			TGGCCGCCCCTTT		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.744G>A	4.37:g.185310218C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Silent	SNP	ENST00000393593.3	37	CCDS3835.1	869	0.39789377289377287	184	0.37398373983739835	192	0.5303867403314917	211	0.3688811188811189	282	0.3720316622691293	C	4.681	0.126624	0.08931	0.346119	0.392558	ENSG00000168310	ENST00000505067	.	.	.	5.31	-4.03	0.04021	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999610463	.	.	.	.	.	.	T	0.48151	-0.9060	3	.	.	.	.	1.1333	0.01749	0.3733:0.1003:0.2741:0.2523	rs3775543;rs17417214;rs3775543	.	.	.	T	182	.	.	A	-	1	0	IRF2	185547212	0.073000	0.21202	0.901000	0.35422	0.846000	0.48090	-1.266000	0.02842	-0.699000	0.05077	-0.324000	0.08512	GCG	C|0.617;T|0.383	0.383	strong		0.498	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1		
RB1	5925	hgsc.bcm.edu	37	13	48947553	48947553	+	Silent	SNP	C	C	T	rs117865557		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:48947553C>T	ENST00000267163.4	+	12	1278	c.1140C>T	c.(1138-1140)aaC>aaT	p.N380N		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	380	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	CTGTTATGAACACTATCCAAC	0.294		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			C|||	1	0.000199681	0.0	0.0	5008	,	,		14986	0.001		0.0	False		,,,				2504	0.0				p.N380N		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	.	RB1	1068	.	23	Whole gene deletion(15)|Unknown(8)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.C1140T						PASS	.	C		0,4406		0,0,2203	103.0	110.0	107.0		1140	4.3	1.0	13	dbSNP_132	107	3,8577	3.0+/-9.4	0,3,4287	no	coding-synonymous	RB1	NM_000321.2		0,3,6490	TT,TC,CC		0.035,0.0,0.0231		380/929	48947553	3,12983	2203	4290	6493	SO:0001819	synonymous_variant	5925	exon12	Familial Cancer Database		TATGAACACTATC	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1140C>T	13.37:g.48947553C>T		Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	135	118	0.874074	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																			C|1.000;T|0.000	0.000	strong		0.294	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
HDAC4	9759	hgsc.bcm.edu	37	2	240003813	240003813	+	Silent	SNP	G	G	A	rs61754649	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:240003813G>A	ENST00000345617.3	-	21	3413	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	HDAC4_ENST00000543185.1_Silent_p.S458S	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	874	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CAGGAGCCCCGCTGCCTGGGA	0.642													G|||	44	0.00878594	0.0015	0.0144	5008	,	,		13690	0.0		0.0298	False		,,,				2504	0.002				p.S874S		Atlas-SNP	.											.	HDAC4	127	.	0			c.C2622T						PASS	.	G		25,4381	31.7+/-61.6	0,25,2178	99.0	95.0	97.0		2622	1.0	1.0	2	dbSNP_129	97	218,8382	92.6+/-154.6	1,216,4083	no	coding-synonymous	HDAC4	NM_006037.3		1,241,6261	AA,AG,GG		2.5349,0.5674,1.8684		874/1085	240003813	243,12763	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon21			AGCCCCGCTGCCT	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.2622C>T	2.37:g.240003813G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	178	87	0.488764	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.982;A|0.018	0.018	strong		0.642	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
KMT2C	58508	hgsc.bcm.edu	37	7	151970797	151970797	+	Silent	SNP	A	A	T	rs141993954	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:151970797A>T	ENST00000262189.6	-	7	1223	c.1005T>A	c.(1003-1005)ccT>ccA	p.P335P	KMT2C_ENST00000355193.2_Silent_p.P335P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	335					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TACATCTTTCAGGAGCTTGGT	0.388																																					p.P335P		Atlas-SNP	.											MLL3_ENST00000355193,NS,adenoma,0,4	MLL3	1564	4	0			c.T1005A						PASS	.	A		49,4357	29.0+/-57.7	0,49,2154	236.0	218.0	224.0		1005	2.3	1.0	7	dbSNP_134	224	176,8424	61.0+/-122.8	0,176,4124	no	coding-synonymous	MLL3	NM_170606.2		0,225,6278	TT,TA,AA		2.0465,1.1121,1.73		335/4912	151970797	225,12781	2203	4300	6503	SO:0001819	synonymous_variant	58508	exon7			TCTTTCAGGAGCT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1005T>A	7.37:g.151970797A>T		Somatic	381	0	0		WXS	Illumina HiSeq	Phase_I	332	23	0.0692771	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																			A|0.985;T|0.015	0.015	strong		0.388	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
LGALS14	56891	hgsc.bcm.edu	37	19	40196611	40196611	+	Intron	SNP	C	C	T	rs35541195	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40196611C>T	ENST00000392052.3	+	2	238				LGALS14_ENST00000360675.3_Missense_Mutation_p.R22C	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14						apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			TAATGTGTGCCGCTTCTGGGA	0.493													C|||	252	0.0503195	0.0356	0.0648	5008	,	,		19968	0.0		0.1451	False		,,,				2504	0.0143				p.R22C		Atlas-SNP	.											.	LGALS14	38	.	0			c.C64T						PASS	.	C	,CYS/ARG	239,4167		9,221,1973	202.0	150.0	168.0		,64	-0.5	0.0	19	dbSNP_126	168	1098,7502		66,966,3268	yes	intron,missense	LGALS14	NM_020129.2,NM_203471.1	,180	75,1187,5241	TT,TC,CC		12.7674,5.4244,10.2799	,	,22/169	40196611	1337,11669	2203	4300	6503	SO:0001627	intron_variant	56891	exon2			GTGTGCCGCTTCT	AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"""Lectins, galactoside-binding"""	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.16-626C>T	19.37:g.40196611C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	208	110	0.528846	NM_203471	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Missense_Mutation	SNP	ENST00000392052.3	37	CCDS46073.1	159	0.07280219780219781	26	0.052845528455284556	31	0.0856353591160221	0	0.0	102	0.1345646437994723	.	5.101	0.204247	0.09704	0.054244	0.127674	ENSG00000006659	ENST00000360675	T	0.09163	3.01	0.906	-0.462	0.12168	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.30937	0.301	B	0.04013	0.001	T	0.41910	-0.9482	8	0.56958	D	0.05	.	3.7318	0.08496	0.5522:0.4478:0.0:0.0	rs35541195;rs60146906	22	A8MPV8	.	C	22	ENSP00000353893:R22C	ENSP00000353893:R22C	R	+	1	0	LGALS14	44888451	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.305000	0.08188	-0.197000	0.10350	0.313000	0.20887	CGC	C|0.907;T|0.093	0.093	strong		0.493	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129	
PBRM1	55193	hgsc.bcm.edu	37	3	52668776	52668776	+	Silent	SNP	A	A	G	rs34173244	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52668776A>G	ENST00000296302.7	-	11	1144	c.1143T>C	c.(1141-1143)gaT>gaC	p.D381D	PBRM1_ENST00000356770.4_Silent_p.D349D|PBRM1_ENST00000337303.4_Silent_p.D381D|PBRM1_ENST00000409767.1_Silent_p.D381D|PBRM1_ENST00000409114.3_Silent_p.D381D|PBRM1_ENST00000410007.1_Silent_p.D381D|PBRM1_ENST00000394830.3_Silent_p.D381D|PBRM1_ENST00000409057.1_Silent_p.D381D			Q86U86	PB1_HUMAN	polybromo 1	381					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GATTTGAAACATCCATAAAGG	0.388			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								A|||	368	0.0734824	0.2201	0.0403	5008	,	,		17023	0.0		0.0089	False		,,,				2504	0.0409				p.D381D		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.T1143C						PASS	.	A	,,	949,3457	360.6+/-315.3	103,743,1357	103.0	102.0	103.0		1047,1143,1143	4.5	1.0	3	dbSNP_126	103	184,8416	82.6+/-145.2	1,182,4117	no	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	104,925,5474	GG,GA,AA		2.1395,21.5388,8.7114	,,	349/1603,381/1583,381/1583	52668776	1133,11873	2203	4300	6503	SO:0001819	synonymous_variant	55193	exon12			TGAAACATCCATA	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1143T>C	3.37:g.52668776A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	130	55	0.423077	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				A|0.925;G|0.075	0.075	strong		0.388	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
MMP2	4313	hgsc.bcm.edu	37	16	55536763	55536763	+	Silent	SNP	C	C	G	rs11541998	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:55536763C>G	ENST00000219070.4	+	12	2351	c.1842C>G	c.(1840-1842)ccC>ccG	p.P614P	MMP2_ENST00000543485.1_Silent_p.P538P|MMP2_ENST00000570308.1_Silent_p.P538P|MMP2_ENST00000437642.2_Silent_p.P564P	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	614	Required for inhibitor TIMP2 binding.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	ATGCCATCCCCGATAACCTGG	0.582													C|||	186	0.0371406	0.0053	0.0605	5008	,	,		19457	0.001		0.1103	False		,,,				2504	0.0256				p.P614P		Atlas-SNP	.											.	MMP2	119	.	0			c.C1842G						PASS	.	C	,	108,4288	81.4+/-119.9	3,102,2093	76.0	63.0	67.0		1692,1842	-11.3	0.0	16	dbSNP_120	67	945,7655	202.8+/-246.0	53,839,3408	no	coding-synonymous,coding-synonymous	MMP2	NM_001127891.1,NM_004530.4	,	56,941,5501	GG,GC,CC		10.9884,2.4568,8.1025	,	564/611,614/661	55536763	1053,11943	2198	4300	6498	SO:0001819	synonymous_variant	4313	exon12			CATCCCCGATAAC		CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"""matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)"", ""matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"""	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.1842C>G	16.37:g.55536763C>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_004530	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Silent	SNP	ENST00000219070.4	37	CCDS10752.1																																																																																			C|0.933;G|0.067	0.067	strong		0.582	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3		
TPO	7173	hgsc.bcm.edu	37	2	1418192	1418192	+	Silent	SNP	C	C	G	rs9678281	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:1418192C>G	ENST00000345913.4	+	2	103	c.12C>G	c.(10-12)ctC>ctG	p.L4L	TPO_ENST00000329066.4_Silent_p.L4L|TPO_ENST00000382201.3_Silent_p.L4L|TPO_ENST00000382198.1_Silent_p.L4L|TPO_ENST00000539820.1_Silent_p.L4L|TPO_ENST00000346956.3_Silent_p.L4L|TPO_ENST00000382269.3_Silent_p.L4L|TPO_ENST00000497517.2_Intron|TPO_ENST00000349624.3_Silent_p.L4L|TPO_ENST00000337415.3_Silent_p.L4L	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	4					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TGAGAGCGCTCGCTGTGCTGT	0.512													C|||	1561	0.311701	0.2769	0.3703	5008	,	,		16931	0.2361		0.3887	False		,,,				2504	0.316				p.L4L		Atlas-SNP	.											TPO,colon,carcinoma,0,1	TPO	224	1	0			c.C12G						scavenged	.	C	,,,,,	1280,3126	431.4+/-342.9	186,908,1109	76.0	73.0	74.0		12,12,12,12,12,12	-10.3	0.0	2	dbSNP_119	74	3341,5259	494.8+/-373.9	662,2017,1621	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	,,,,,	848,2925,2730	GG,GC,CC		38.8488,29.0513,35.5298	,,,,,	4/934,4/934,4/877,4/877,4/890,4/761	1418192	4621,8385	2203	4300	6503	SO:0001819	synonymous_variant	7173	exon2			AGCGCTCGCTGTG		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.12C>G	2.37:g.1418192C>G		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	166	69	0.415663	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1																																																																																			C|0.654;G|0.346;T|0.000	0.346	strong		0.512	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
DNAH6	1768	hgsc.bcm.edu	37	2	84945469	84945469	+	Silent	SNP	G	G	A	rs1192344	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:84945469G>A	ENST00000237449.6	+	58	9761	c.9753G>A	c.(9751-9753)ctG>ctA	p.L3251L	DNAH6_ENST00000389394.3_Silent_p.L3251L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3251	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GAAATATTCTGGACAATGAAG	0.338													G|||	345	0.0688898	0.1505	0.0331	5008	,	,		19884	0.002		0.0636	False		,,,				2504	0.0583				p.L3251L		Atlas-SNP	.											.	DNAH6	194	.	0			c.G9753A						PASS	.	G		153,1231		12,129,551	107.0	96.0	99.0		9753	-0.2	1.0	2	dbSNP_87	99	171,3011		4,163,1424	no	coding-synonymous	DNAH6	NM_001370.1		16,292,1975	AA,AG,GG		5.374,11.0549,7.0959		3251/4159	84945469	324,4242	692	1591	2283	SO:0001819	synonymous_variant	1768	exon59			TATTCTGGACAAT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.9753G>A	2.37:g.84945469G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	174	87	0.5	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			G|0.933;A|0.067	0.067	strong		0.338	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
PAIP2	51247	hgsc.bcm.edu	37	5	138700404	138700404	+	Missense_Mutation	SNP	G	G	A	rs151194423	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:138700404G>A	ENST00000394795.2	+	3	1281	c.290G>A	c.(289-291)aGt>aAt	p.S97N	PAIP2_ENST00000510080.1_Missense_Mutation_p.S97N|PAIP2_ENST00000265192.4_Missense_Mutation_p.S97N|CTB-43P18.1_ENST00000503553.3_RNA|PAIP2_ENST00000511381.1_3'UTR|PAIP2_ENST00000511706.1_Intron			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	97					memory (GO:0007613)|negative regulation of translational initiation (GO:0045947)|regulation of long-term synaptic potentiation (GO:1900271)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mRNA binding (GO:0003729)|translation repressor activity (GO:0030371)			kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTTGTTATCAGTGATGGCTCT	0.398													G|||	2	0.000399361	0.0	0.0029	5008	,	,		20179	0.0		0.0	False		,,,				2504	0.0				p.S97N		Atlas-SNP	.											.	PAIP2	10	.	0			c.G290A						PASS	.						108.0	94.0	99.0					5																	138700404		2203	4300	6503	SO:0001583	missense	51247	exon3			TTATCAGTGATGG	AF151052	CCDS4211.1	5q32	2008-02-05			ENSG00000120727	ENSG00000120727			17970	protein-coding gene	gene with protein product		605604				11172725, 16804161	Standard	NM_016480		Approved	PAIP2A	uc003led.3	Q9BPZ3	OTTHUMG00000129227	ENST00000394795.2:c.290G>A	5.37:g.138700404G>A	ENSP00000378275:p.Ser97Asn	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	143	66	0.461538	NM_001033112	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	Missense_Mutation	SNP	ENST00000394795.2	37	CCDS4211.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	13.16	2.153214	0.38021	.	.	ENSG00000120727	ENST00000265192;ENST00000394795;ENST00000510080	.	.	.	5.93	3.13	0.36017	.	0.483405	0.25916	N	0.027466	T	0.27629	0.0679	L	0.34521	1.04	0.35331	D	0.785643	B	0.02656	0.0	B	0.01281	0.0	T	0.22034	-1.0228	8	.	.	.	-10.2094	6.1013	0.20049	0.2021:0.2583:0.5396:0.0	.	97	Q9BPZ3	PAIP2_HUMAN	N	97	.	.	S	+	2	0	PAIP2	138728303	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.347000	0.44036	0.381000	0.24851	-0.165000	0.13383	AGT	G|0.999;A|0.001	0.001	strong		0.398	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373002.1	NM_016480	
TELO2	9894	hgsc.bcm.edu	37	16	1544301	1544301	+	Missense_Mutation	SNP	G	G	C	rs35400877|rs2667660	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1544301G>C	ENST00000262319.6	+	2	298	c.19G>C	c.(19-21)Gag>Cag	p.E7Q		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	7			E -> G (in dbSNP:rs2667661).|E -> Q (in dbSNP:rs2667660).	E -> R (in Ref. 1; BAA31658). {ECO:0000305}.	regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				AGCACCCTCAGAGGTTCGACT	0.607											OREG0023547	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1442	0.287939	0.2352	0.196	5008	,	,		16375	0.5119		0.2416	False		,,,				2504	0.2413				p.E7Q		Atlas-SNP	.											TELO2,NS,carcinoma,-2,1	TELO2	44	1	0			c.G19C						PASS	.	G	GLN/GLU	78,4320		29,20,2150	58.0	56.0	56.0		19	0.1	0.0	16	dbSNP_100	56	134,8466		42,50,4208	yes	missense	TELO2	NM_016111.3	29	71,70,6358	CC,CG,GG		1.5581,1.7735,1.631	benign	7/838	1544301	212,12786	2199	4300	6499	SO:0001583	missense	9894	exon2			CCCTCAGAGGTTC	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"""TEL2, telomere maintenance 2, homolog (S. cerevisiae)"""			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.19G>C	16.37:g.1544301G>C	ENSP00000262319:p.Glu7Gln	Somatic	48	0	0	596	WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	575	0.2632783882783883	83	0.16869918699186992	61	0.1685082872928177	272	0.4755244755244755	159	0.20976253298153033	G	6.874	0.530569	0.13127	0.017735	0.015581	ENSG00000100726	ENST00000262319	T	0.14893	2.47	4.69	0.132	0.14762	.	1.140400	0.06530	N	0.741364	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.47886	-0.9082	9	0.15499	T	0.54	-0.28	1.8711	0.03208	0.1855:0.1566:0.4967:0.1611	rs2667660;rs3752928;rs8048710;rs28482852	7	Q9Y4R8	TELO2_HUMAN	Q	7	ENSP00000262319:E7Q	ENSP00000262319:E7Q	E	+	1	0	TELO2	1484302	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	1.489000	0.35562	0.066000	0.16515	-0.254000	0.11334	GAG	CG|0.500;GA|0.500	.	alt		0.607	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
EIF5B	9669	hgsc.bcm.edu	37	2	99978048	99978048	+	Silent	SNP	G	G	A	rs12233086	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:99978048G>A	ENST00000289371.6	+	4	886	c.684G>A	c.(682-684)gtG>gtA	p.V228V		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	228					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TTAAGACAGTGGCCCAAAAGA	0.398													G|||	848	0.169329	0.1051	0.2839	5008	,	,		17320	0.25		0.1481	False		,,,				2504	0.1135				p.V228V	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											.	EIF5B	95	.	0			c.G684A						PASS	.	G		460,3224		38,384,1420	53.0	53.0	53.0		684	4.0	1.0	2	dbSNP_120	53	1104,7056		81,942,3057	no	coding-synonymous	EIF5B	NM_015904.3		119,1326,4477	AA,AG,GG		13.5294,12.4864,13.205		228/1221	99978048	1564,10280	1842	4080	5922	SO:0001819	synonymous_variant	9669	exon4			GACAGTGGCCCAA	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"""translation initiation factor IF2"""	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.684G>A	2.37:g.99978048G>A		Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	233	116	0.497854	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	37	CCDS42721.1																																																																																			G|0.842;A|0.158	0.158	strong		0.398	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904	
EP400	57634	hgsc.bcm.edu	37	12	132445675	132445675	+	Missense_Mutation	SNP	G	G	A	rs61745448	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:132445675G>A	ENST00000333577.4	+	2	620	c.511G>A	c.(511-513)Gtg>Atg	p.V171M	EP400_ENST00000332482.4_Missense_Mutation_p.V171M|EP400_ENST00000389561.2_Missense_Mutation_p.V171M|EP400_ENST00000389562.2_Missense_Mutation_p.V171M|EP400_ENST00000330386.6_Missense_Mutation_p.V171M			Q96L91	EP400_HUMAN	E1A binding protein p400	171					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		AGGGGGCTTCGTGGATGCCAG	0.672													G|||	61	0.0121805	0.0008	0.0231	5008	,	,		15923	0.0		0.0408	False		,,,				2504	0.0031				p.V171M		Atlas-SNP	.											.	EP400	370	.	0			c.G511A						PASS	.	G	MET/VAL	44,4360	43.8+/-77.6	0,44,2158	55.0	42.0	46.0		511	4.9	1.0	12	dbSNP_129	46	411,8187	121.7+/-180.7	15,381,3903	no	missense	EP400	NM_015409.4	21	15,425,6061	AA,AG,GG		4.7802,0.9991,3.4995	probably-damaging	171/3124	132445675	455,12547	2202	4299	6501	SO:0001583	missense	57634	exon2			GGCTTCGTGGATG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.511G>A	12.37:g.132445675G>A	ENSP00000333602:p.Val171Met	Somatic	426	0	0		WXS	Illumina HiSeq	Phase_I	478	237	0.495816	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		42	0.019230769230769232	0	0.0	10	0.027624309392265192	0	0.0	32	0.04221635883905013	G	6.433	0.448071	0.12223	0.009991	0.047802	ENSG00000183495	ENST00000537902;ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000423130;ENST00000541296;ENST00000542457	D;D;D;D;D	0.94232	-3.23;-3.38;-3.38;-3.38;-3.38	5.79	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.83312	0.5227	M	0.75447	2.3	0.37260	D	0.906958	D;D;D;D;D	0.67145	0.996;0.996;0.996;0.995;0.996	P;P;P;P;P	0.59487	0.753;0.753;0.753;0.858;0.753	D	0.87512	0.2440	10	0.87932	D	0	.	15.0397	0.71781	0.0684:0.0:0.9316:0.0	rs61745448	171;171;171;171;171	Q96L91-2;Q96L91-4;Q96L91-5;F8WCN8;Q96L91-3	.;.;.;.;.	M	171	ENSP00000333602:V171M;ENSP00000374212:V171M;ENSP00000374213:V171M;ENSP00000331737:V171M;ENSP00000330620:V171M	ENSP00000330620:V171M	V	+	1	0	EP400	131011628	1.000000	0.71417	0.961000	0.40146	0.048000	0.14542	9.461000	0.97646	1.453000	0.47775	0.563000	0.77884	GTG	G|0.976;A|0.024	0.024	strong		0.672	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
POU5F1	5460	hgsc.bcm.edu	37	6	31138377	31138377	+	Silent	SNP	C	C	T	rs2077010	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31138377C>T	ENST00000259915.8	-	1	93	c.21G>A	c.(19-21)tcG>tcA	p.S7S	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	7					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)		EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	AGGCGAAATCCGAAGCCAGGT	0.672			T	EWSR1	sarcoma								C|||	2113	0.421925	0.4478	0.4726	5008	,	,		12960	0.3859		0.4105	False		,,,				2504	0.3998				p.S7S		Atlas-SNP	.		Dom	yes		6	6p21.31	5460	"""POU domain, class 5, transcription factor 1"""		M	.	POU5F1	25	.	0			c.G21A						PASS	.	C		1050,1698		242,566,566	4.0	4.0	4.0		21	-7.4	0.8	6	dbSNP_96	4	1810,3054		399,1012,1021	no	coding-synonymous	POU5F1	NM_002701.4		641,1578,1587	TT,TC,CC		37.2122,38.2096,37.5723		7/361	31138377	2860,4752	1374	2432	3806	SO:0001819	synonymous_variant	5460	exon1			GAAATCCGAAGCC	Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"""Homeoboxes / POU class"""	9221	protein-coding gene	gene with protein product		164177	"""POU domain class 5, transcription factor 1"""	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.21G>A	6.37:g.31138377C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	48	29	0.604167	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Silent	SNP	ENST00000259915.8	37	CCDS34391.1																																																																																			C|0.592;T|0.408	0.408	strong		0.672	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701	
DNAJC6	9829	hgsc.bcm.edu	37	1	65858145	65858145	+	Silent	SNP	G	G	A	rs4325172	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:65858145G>A	ENST00000395325.3	+	12	1486	c.1329G>A	c.(1327-1329)gaG>gaA	p.E443E	DNAJC6_ENST00000371069.4_Silent_p.E500E|DNAJC6_ENST00000263441.7_Silent_p.E430E	NM_014787.3	NP_055602.1	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	443					cell death (GO:0008219)|clathrin coat disassembly (GO:0072318)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytosol (GO:0005829)|synapse (GO:0045202)	protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(22)|ovary(1)|prostate(2)|skin(1)	39						TCTGTGAGGAGGACCACGCTG	0.448													G|||	1773	0.354034	0.2784	0.4323	5008	,	,		21332	0.1885		0.5338	False		,,,				2504	0.3865				p.E500E		Atlas-SNP	.											.	DNAJC6	104	.	0			c.G1500A						PASS	.	G		1412,2994	462.4+/-353.2	217,978,1008	57.0	53.0	55.0		1329	2.5	1.0	1	dbSNP_111	55	4592,4008	596.6+/-393.6	1213,2166,921	no	coding-synonymous	DNAJC6	NM_014787.2		1430,3144,1929	AA,AG,GG		46.6047,32.0472,46.1633		443/914	65858145	6004,7002	2203	4300	6503	SO:0001819	synonymous_variant	9829	exon12			TGAGGAGGACCAC	AB007942	CCDS30739.1, CCDS58004.1, CCDS58005.1	1p31.3	2011-09-02			ENSG00000116675	ENSG00000116675		"""Heat shock proteins / DNAJ (HSP40)"""	15469	protein-coding gene	gene with protein product	"""auxilin"""	608375				9455484, 11147971	Standard	NM_001256864		Approved	KIAA0473	uc001dce.2	O75061	OTTHUMG00000009066	ENST00000395325.3:c.1329G>A	1.37:g.65858145G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	194	193	0.994845	NM_001256864	B7Z3V8|D3DQ65|D3DQ66|Q32M66|Q4G0K1|Q5T614|Q5T615	Silent	SNP	ENST00000395325.3	37	CCDS30739.1																																																																																			G|0.575;A|0.425	0.425	strong		0.448	DNAJC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025134.1		
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048459	33048459	+	Silent	SNP	T	T	G	rs1126506|rs386699868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33048459T>G	ENST00000418931.2	+	2	227	c.111T>G	c.(109-111)ctT>ctG	p.L37L	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPA1_ENST00000419277.1_5'UTR|HLA-DPB1_ENST00000535465.1_Silent_p.L37L	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	37	Beta-1.		L -> V (in allele DPB1*01:01, allele DPB1*03:01, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*09:01, allele DPB1*09:02, allele DPB1*10:01, allele DPB1*11:01, allele DPB1*11:02, allele DPB1*13:01, allele DPB1*13:02, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*15:01, allele DPB1*16:02, allele DPB1*17:01, allele DPB1*17:02, allele DPB1*18:01, allele DPB1*20:02, allele DPB1*21:01, allele DPB1*21:02, allele DPB1*20:01, allele DPB1*22:02, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*27:01, allele DPB1*29:01, allele DPB1*30:01, allele DPB1*35:01, allele DPB1*36:01, allele DPB1*37:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*50:01, allele DPB1*52:01, allele DPB1*54:01, allele DPB1*55:01, allele DPB1*56:01, allele DPB1*58:01, allele DPB1*66:01, allele DPB1*67:01, allele DPB1*69:01, allele DPB1*70:01, allele DPB1*74:01, allele DPB1*76:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*85:01, allele DPB1*86:01, allele DPB1*87:01, allele DPB1*88:01, allele DPB1*89:01, allele DPB1*90:01, allele DPB1*91:01, allele DPB1*92:01, allele DPB1*93:01 and allele DPB1*98:01; dbSNP:rs1126504).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						AGAATTACCTTTTCCAGGGAC	0.547													.|||	1999	0.399161	0.6641	0.3357	5008	,	,		14846	0.2351		0.2992	False		,,,				2504	0.3579				p.L37L		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.T111G						PASS	.	G	,,	1550,1470		518,514,478	46.0	51.0	49.0		,,111	1.6	0.0	6	dbSNP_86	49	855,4553		171,513,2020	no	utr-5,utr-5,coding-synonymous	HLA-DPA1,HLA-DPB1	NM_001242524.1,NM_001242525.1,NM_002121.5	,,	689,1027,2498	GG,GT,TT		15.8099,48.6755,28.5358	,,	,,37/259	33048459	2405,6023	1510	2704	4214	SO:0001819	synonymous_variant	3115	exon2			TTACCTTTTCCAG		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.111T>G	6.37:g.33048459T>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	59	20	0.338983	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Silent	SNP	ENST00000418931.2	37	CCDS4765.1	711	0.32554945054945056	301	0.6117886178861789	99	0.27348066298342544	114	0.1993006993006993	197	0.2598944591029024	t	9.495	1.101747	0.20632	0.513245	0.158099	ENSG00000223865	ENST00000416804	.	.	.	3.4	1.56	0.23342	.	.	.	.	.	T	0.33059	0.0850	.	.	.	0.45777	P	0.0013339999999999463	.	.	.	.	.	.	T	0.10823	-1.0613	3	.	.	.	.	9.7986	0.40751	0.0:0.1471:0.695:0.1579	rs1126506;rs3176934;rs3181576;rs9277344;rs17214692;rs17418629;rs17851008	.	.	.	C	4	.	.	F	+	2	0	HLA-DPB1	33156437	0.004000	0.15560	0.001000	0.08648	0.000000	0.00434	0.061000	0.14366	0.097000	0.17492	-0.948000	0.02665	TTT	T|0.677;G|0.323	0.323	strong		0.547	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
ZC3H7A	29066	hgsc.bcm.edu	37	16	11876203	11876203	+	Missense_Mutation	SNP	T	T	C	rs1429077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:11876203T>C	ENST00000396516.2	-	1	205	c.8A>G	c.(7-9)aAt>aGt	p.N3S	ZC3H7A_ENST00000575170.1_5'UTR|ZC3H7A_ENST00000355758.4_Missense_Mutation_p.N3S			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	3			N -> S (in dbSNP:rs1429077).			nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						CTCGGACACATTGGACATGTT	0.438													C|||	291	0.058107	0.0953	0.0634	5008	,	,		19921	0.0		0.0845	False		,,,				2504	0.0368				p.N3S		Atlas-SNP	.											.	ZC3H7A	72	.	0			c.A8G						PASS	.	C	SER/ASN	459,3935	782.2+/-414.5	32,395,1770	228.0	196.0	207.0		8	4.3	1.0	16	dbSNP_88	207	579,8021	792.8+/-407.5	15,549,3736	yes	missense	ZC3H7A	NM_014153.3	46	47,944,5506	CC,CT,TT		6.7326,10.4461,7.9883	benign	3/972	11876203	1038,11956	2197	4300	6497	SO:0001583	missense	29066	exon2			GACACATTGGACA	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"""Zinc fingers, CCCH-type domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30959	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 7"", ""zinc finger CCCH-type containing 7"""	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.8A>G	16.37:g.11876203T>C	ENSP00000379773:p.Asn3Ser	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_014153	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	37	CCDS10550.1	127	0.05815018315018315	41	0.08333333333333333	24	0.06629834254143646	0	0.0	62	0.08179419525065963	C	2.940	-0.219000	0.06101	0.104461	0.067326	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.09538	2.97;2.97	5.28	4.31	0.51392	.	0.322769	0.42294	N	0.000728	T	0.00109	0.0003	N	0.03115	-0.41	0.09310	P	0.999999999800655	B	0.02656	0.0	B	0.01281	0.0	T	0.33854	-0.9852	9	0.02654	T	1	.	7.1432	0.25568	0.0:0.6799:0.0:0.3201	rs1429077;rs52833537;rs1429077	3	Q8IWR0	Z3H7A_HUMAN	S	3	ENSP00000347999:N3S;ENSP00000379773:N3S	ENSP00000347999:N3S	N	-	2	0	ZC3H7A	11783704	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	0.430000	0.21428	1.377000	0.46286	-0.320000	0.08662	AAT	T|0.926;C|0.074	0.074	strong		0.438	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153	
MMP2	4313	hgsc.bcm.edu	37	16	55536727	55536727	+	Silent	SNP	C	C	T	rs14070	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:55536727C>T	ENST00000219070.4	+	12	2315	c.1806C>T	c.(1804-1806)ttC>ttT	p.F602F	MMP2_ENST00000543485.1_Silent_p.F526F|MMP2_ENST00000570308.1_Silent_p.F526F|MMP2_ENST00000437642.2_Silent_p.F552F	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	602	Required for inhibitor TIMP2 binding.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	ATCCTGGCTTCCCCAAGCTCA	0.567													C|||	1522	0.303914	0.1505	0.4769	5008	,	,		19770	0.246		0.4533	False		,,,				2504	0.2945				p.F602F		Atlas-SNP	.											.	MMP2	119	.	0			c.C1806T						PASS	.	C	,	909,3487	351.1+/-311.1	84,741,1373	87.0	74.0	78.0		1656,1806	0.4	1.0	16	dbSNP_52	78	3853,4747	540.8+/-383.9	836,2181,1283	no	coding-synonymous,coding-synonymous	MMP2	NM_001127891.1,NM_004530.4	,	920,2922,2656	TT,TC,CC		44.8023,20.6779,36.642	,	552/611,602/661	55536727	4762,8234	2198	4300	6498	SO:0001819	synonymous_variant	4313	exon12			TGGCTTCCCCAAG		CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"""matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)"", ""matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"""	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.1806C>T	16.37:g.55536727C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_004530	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Silent	SNP	ENST00000219070.4	37	CCDS10752.1																																																																																			C|0.641;T|0.359	0.359	strong		0.567	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3		
MUSK	4593	hgsc.bcm.edu	37	9	113457726	113457726	+	Silent	SNP	G	G	A	rs10980531	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:113457726G>A	ENST00000374448.4	+	4	536	c.402G>A	c.(400-402)gaG>gaA	p.E134E	MUSK_ENST00000416899.2_Silent_p.E134E|MUSK_ENST00000374439.1_Silent_p.E16E|MUSK_ENST00000374440.3_Silent_p.E16E|MUSK_ENST00000189978.5_Silent_p.E134E	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	134	Ig-like 2.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						AAATAATAGAGGGATTAAAAG	0.358													G|||	852	0.170128	0.1452	0.1167	5008	,	,		16625	0.2192		0.1899	False		,,,				2504	0.1708				p.E134E		Atlas-SNP	.											.	MUSK	112	.	0			c.G402A						PASS	.	G	,,	438,3196		27,384,1406	47.0	43.0	45.0		402,402,402	-1.2	1.0	9	dbSNP_120	45	1379,6749		120,1139,2805	no	coding-synonymous,coding-synonymous,coding-synonymous	MUSK	NM_001166280.1,NM_001166281.1,NM_005592.3	,,	147,1523,4211	AA,AG,GG		16.966,12.0528,15.4481	,,	134/784,134/774,134/870	113457726	1817,9945	1817	4064	5881	SO:0001819	synonymous_variant	4593	exon4			AATAGAGGGATTA	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.402G>A	9.37:g.113457726G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	NM_001166281	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Silent	SNP	ENST00000374448.4	37	CCDS48005.1																																																																																			G|0.813;A|0.187	0.187	strong		0.358	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
ZFHX3	463	hgsc.bcm.edu	37	16	72993706	72993706	+	Silent	SNP	G	G	A	rs62053191	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72993706G>A	ENST00000268489.5	-	2	1011	c.339C>T	c.(337-339)gcC>gcT	p.A113A	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	113					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CGGTGTCGCTGGCGCTCTCCT	0.672													G|||	137	0.0273562	0.0061	0.0303	5008	,	,		12816	0.002		0.0596	False		,,,				2504	0.047				p.A113A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C339T						PASS	.	G	,	72,4324		1,70,2127	22.0	23.0	23.0		,339	-0.8	1.0	16	dbSNP_129	23	584,8000		21,542,3729	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	22,612,5856	AA,AG,GG		6.8034,1.6379,5.0539	,	,113/3704	72993706	656,12324	2198	4292	6490	SO:0001819	synonymous_variant	463	exon2			GTCGCTGGCGCTC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.339C>T	16.37:g.72993706G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			G|0.958;A|0.042	0.042	strong		0.672	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
NMS	129521	hgsc.bcm.edu	37	2	101086966	101086966	+	Missense_Mutation	SNP	C	C	T	rs13411940	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:101086966C>T	ENST00000376865.1	+	1	23	c.16C>T	c.(16-18)Ccc>Tcc	p.P6S		NM_001011717.1	NP_001011717.1	Q5H8A3	NMS_HUMAN	neuromedin S	6			P -> S (in dbSNP:rs13411940).		neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)		p.P6S(1)		breast(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)	14						ACATCTTCGTCCCCAGTTCCC	0.542													C|||	1356	0.270767	0.2776	0.1931	5008	,	,		18141	0.3502		0.2048	False		,,,				2504	0.3027				p.P6S		Atlas-SNP	.											NMS,NS,carcinoma,0,1	NMS	26	1	1	Substitution - Missense(1)	stomach(1)	c.C16T						PASS	.	C	SER/PRO	1196,3210	417.6+/-338.0	164,868,1171	394.0	340.0	358.0		16	2.5	0.0	2	dbSNP_121	358	1896,6704	336.8+/-322.0	217,1462,2621	yes	missense	NMS	NM_001011717.1	74	381,2330,3792	TT,TC,CC		22.0465,27.1448,23.7736	benign	6/154	101086966	3092,9914	2203	4300	6503	SO:0001583	missense	129521	exon1			CTTCGTCCCCAGT	AB164464	CCDS33259.1	2q11.2	2013-02-26			ENSG00000204640	ENSG00000204640		"""Endogenous ligands"""	32203	protein-coding gene	gene with protein product	"""prepro-NMS"""					15635449	Standard	NM_001011717		Approved		uc002tan.1	Q5H8A3	OTTHUMG00000153142	ENST00000376865.1:c.16C>T	2.37:g.101086966C>T	ENSP00000366061:p.Pro6Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_001011717		Missense_Mutation	SNP	ENST00000376865.1	37	CCDS33259.1	578	0.26465201465201466	138	0.2804878048780488	79	0.21823204419889503	193	0.3374125874125874	168	0.22163588390501318	C	11.18	1.563248	0.27915	0.271448	0.220465	ENSG00000204640	ENST00000376865	T	0.50813	0.73	4.33	2.53	0.30540	.	0.194078	0.32287	N	0.006318	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	B	0.32302	0.363	B	0.28916	0.096	T	0.28459	-1.0043	9	0.54805	T	0.06	-6.7097	5.9059	0.19001	0.0:0.6767:0.2141:0.1092	rs13411940;rs56567182;rs58703521;rs13411940	6	Q5H8A3	NMS_HUMAN	S	6	ENSP00000366061:P6S	ENSP00000366061:P6S	P	+	1	0	NMS	100453398	0.001000	0.12720	0.003000	0.11579	0.004000	0.04260	0.009000	0.13219	0.579000	0.29504	0.655000	0.94253	CCC	C|0.746;T|0.254	0.254	strong		0.542	NMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329737.1	NM_001011717	
AQP12B	653437	hgsc.bcm.edu	37	2	241621866	241621866	+	Missense_Mutation	SNP	C	C	T	rs62187796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241621866C>T	ENST00000407834.3	-	1	451	c.389G>A	c.(388-390)cGc>cAc	p.R130H		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	118						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		CCAGCAGAGGCGCGTCAGGGT	0.701													N|||	467	0.0932508	0.0265	0.0994	5008	,	,		16334	0.003		0.2296	False		,,,				2504	0.1319				p.R130H		Atlas-SNP	.											.	AQP12B	33	.	0			c.G389A						PASS	.		HIS/ARG	317,4067		21,275,1896	22.0	22.0	22.0		389	-2.1	0.0	2	dbSNP_129	22	1975,6579		290,1395,2592	no	missense	AQP12B	NM_001102467.1	29	311,1670,4488	TT,TC,CC		23.0886,7.2308,17.7153	probably-damaging	130/308	241621866	2292,10646	2192	4277	6469	SO:0001583	missense	653437	exon1			CAGAGGCGCGTCA	BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"""Ion channels / Aquaporins"""	6096	protein-coding gene	gene with protein product			"""insulin synthesis associated 3"""	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263	ENST00000407834.3:c.389G>A	2.37:g.241621866C>T	ENSP00000384894:p.Arg130His	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	38	25	0.657895	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	37	CCDS46560.1	247	0.1130952380952381	25	0.0508130081300813	41	0.1132596685082873	5	0.008741258741258742	176	0.23218997361477572	.	2.205	-0.382095	0.04966	0.072308	0.230886	ENSG00000185176	ENST00000407834	T	0.15718	2.4	2.84	-2.13	0.07144	.	0.821421	0.11042	N	0.605947	T	0.00012	0.0000	L	0.35723	1.085	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.37314	-0.9711	9	0.44086	T	0.13	0.9342	8.3463	0.32275	0.0:0.4802:0.0:0.5198	rs62187796	130	A6NM10-2	.	H	130	ENSP00000384894:R130H	ENSP00000384894:R130H	R	-	2	0	AQP12B	241270539	0.000000	0.05858	0.001000	0.08648	0.109000	0.19521	-1.901000	0.01597	-0.508000	0.06540	-1.338000	0.01255	CGC	C|0.877;T|0.123	0.123	strong		0.701	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
ADIPOR2	79602	hgsc.bcm.edu	37	12	1893170	1893170	+	Silent	SNP	C	C	T	rs9805042	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:1893170C>T	ENST00000357103.4	+	7	1214	c.963C>T	c.(961-963)taC>taT	p.Y321Y		NM_024551.2	NP_078827.2	Q86V24	ADR2_HUMAN	adiponectin receptor 2	321					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|female pregnancy (GO:0007565)|heart development (GO:0007507)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of cell growth (GO:0030308)|positive regulation of glucose import (GO:0046326)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|receptor activity (GO:0004872)	p.Y321Y(1)		endometrium(1)|large_intestine(3)|lung(7)|stomach(1)	12	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			CCAGCCTCTACATCACAGGAG	0.547													C|||	1189	0.23742	0.5416	0.111	5008	,	,		18023	0.1111		0.1302	False		,,,				2504	0.1564				p.Y321Y		Atlas-SNP	.											ADIPOR2,NS,carcinoma,0,1	ADIPOR2	30	1	1	Substitution - coding silent(1)	stomach(1)	c.C963T						PASS	.	C		2031,2375	565.5+/-381.7	484,1063,656	90.0	84.0	86.0		963	-5.4	0.2	12	dbSNP_119	86	1097,7503	228.6+/-263.6	61,975,3264	no	coding-synonymous	ADIPOR2	NM_024551.2		545,2038,3920	TT,TC,CC		12.7558,46.0962,24.0504		321/387	1893170	3128,9878	2203	4300	6503	SO:0001819	synonymous_variant	79602	exon7			CCTCTACATCACA	AY424280	CCDS8511.1	12p13	2012-08-22			ENSG00000006831	ENSG00000006831		"""GPCR / Unclassified : Adiponectin receptors"""	24041	protein-coding gene	gene with protein product		607946				12802337	Standard	NM_024551		Approved	PAQR2, ACDCR2	uc001qjm.3	Q86V24	OTTHUMG00000130139	ENST00000357103.4:c.963C>T	12.37:g.1893170C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	175	79	0.451429	NM_024551	Q53YY5|Q9H737	Silent	SNP	ENST00000357103.4	37	CCDS8511.1																																																																																			C|0.770;T|0.230	0.230	strong		0.547	ADIPOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252447.2	NM_024551	
TMEM39A	55254	hgsc.bcm.edu	37	3	119150836	119150836	+	Missense_Mutation	SNP	C	C	T	rs1132200	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:119150836C>T	ENST00000319172.5	-	9	1879	c.1459G>A	c.(1459-1461)Gca>Aca	p.A487T		NM_018266.1	NP_060736.1	Q9NV64	TM39A_HUMAN	transmembrane protein 39A	487			A -> T (in dbSNP:rs1132200). {ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	13				GBM - Glioblastoma multiforme(114;0.244)		GCTTAGTTTGCCTTGAGTTCA	0.338													C|||	444	0.0886581	0.0083	0.0663	5008	,	,		16204	0.0724		0.1441	False		,,,				2504	0.1728				p.A487T		Atlas-SNP	.											.	TMEM39A	36	.	0			c.G1459A						PASS	.	C	THR/ALA	157,4249	104.3+/-142.8	2,153,2048	58.0	55.0	56.0		1459	5.7	1.0	3	dbSNP_86	56	1372,7226	265.3+/-286.1	116,1140,3043	yes	missense	TMEM39A	NM_018266.1	58	118,1293,5091	TT,TC,CC		15.9572,3.5633,11.7579	possibly-damaging	487/489	119150836	1529,11475	2203	4299	6502	SO:0001583	missense	55254	exon9			AGTTTGCCTTGAG	BC021277	CCDS2987.1	3q13.33	2005-01-10			ENSG00000176142	ENSG00000176142			25600	protein-coding gene	gene with protein product						12477932	Standard	NM_018266		Approved	FLJ10902	uc003eck.2	Q9NV64	OTTHUMG00000159361	ENST00000319172.5:c.1459G>A	3.37:g.119150836C>T	ENSP00000326063:p.Ala487Thr	Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	128	126	0.984375	NM_018266	D3DN80|Q53FN4|Q53GI1|Q6PKB5	Missense_Mutation	SNP	ENST00000319172.5	37	CCDS2987.1	189	0.08653846153846154	7	0.014227642276422764	31	0.0856353591160221	43	0.07517482517482517	108	0.1424802110817942	C	16.08	3.021427	0.54576	0.035633	0.159572	ENSG00000176142	ENST00000319172	T	0.48201	0.82	5.65	5.65	0.86999	.	0.410299	0.27202	N	0.020441	T	0.00109	0.0003	N	0.08118	0	0.26539	P	0.9741145	B	0.20261	0.043	B	0.19946	0.027	T	0.03587	-1.1022	9	0.34782	T	0.22	3.3393	14.4815	0.67587	0.0:0.8536:0.1464:0.0	rs1132200;rs3087626;rs3192765;rs17203111;rs56414853;rs57535001;rs1132200	487	Q9NV64	TM39A_HUMAN	T	487	ENSP00000326063:A487T	ENSP00000326063:A487T	A	-	1	0	TMEM39A	120633526	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.236000	0.43052	2.941000	0.99782	0.655000	0.94253	GCA	C|0.901;T|0.099	0.099	strong		0.338	TMEM39A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354941.3	NM_018266	
WDR18	57418	hgsc.bcm.edu	37	19	984554	984554	+	Silent	SNP	C	C	G	rs4806884	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:984554C>G	ENST00000251289.5	+	1	224	c.201C>G	c.(199-201)ctC>ctG	p.L67L	WDR18_ENST00000587001.2_Silent_p.L67L|WDR18_ENST00000591997.1_Intron	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	67					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGGGAGCTCCAGCGGAAGG	0.711													.|||	1837	0.366813	0.3283	0.4092	5008	,	,		11315	0.2768		0.5567	False		,,,				2504	0.2863				p.L67L		Atlas-SNP	.											.	WDR18	20	.	0			c.C201G						PASS	.	G		1233,2751		232,769,991	5.0	7.0	7.0		201	-1.1	1.0	19	dbSNP_111	7	3627,4195		956,1715,1240	no	coding-synonymous	WDR18	NM_024100.3		1188,2484,2231	GG,GC,CC		46.3692,30.9488,41.1655		67/433	984554	4860,6946	1992	3911	5903	SO:0001819	synonymous_variant	57418	exon1			GGAGCTCCAGCGG		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.201C>G	19.37:g.984554C>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	22	6	0.272727	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	37	CCDS12051.1																																																																																			C|0.614;G|0.386	0.386	strong		0.711	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
AFMID	125061	hgsc.bcm.edu	37	17	76198587	76198587	+	Silent	SNP	A	A	G	rs72897838	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:76198587A>G	ENST00000327898.5	+	3	171	c.162A>G	c.(160-162)acA>acG	p.T54T	AFMID_ENST00000591952.1_Intron|AFMID_ENST00000409257.5_Silent_p.T54T|AFMID_ENST00000588800.1_Intron					arylformamidase											autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|skin(1)	19			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.134)			CAGCCACCACAAGGGCCCGGG	0.517													G|||	300	0.0599042	0.0802	0.062	5008	,	,		9299	0.001		0.0845	False		,,,				2504	0.0665				p.T54T		Atlas-SNP	.											.	AFMID	38	.	0			c.A162G						PASS	.	G	,	381,4025	788.8+/-414.9	23,335,1845	57.0	60.0	59.0		162,162	2.2	0.0	17	dbSNP_130	59	855,7745	778.4+/-407.7	50,755,3495	no	coding-synonymous,coding-synonymous	AFMID	NM_001010982.4,NM_001145526.2	,	73,1090,5340	GG,GA,AA		9.9419,8.6473,9.5033	,	54/304,54/309	76198587	1236,11770	2203	4300	6503	SO:0001819	synonymous_variant	125061	exon3			CACCACAAGGGCC	BX648442	CCDS32750.2, CCDS45801.1	17q25.3	2005-11-09			ENSG00000183077	ENSG00000183077	3.5.1.9		20910	protein-coding gene	gene with protein product							Standard	NR_027083		Approved	DKFZp686F03259, KF	uc002juz.3	Q63HM1	OTTHUMG00000153957	ENST00000327898.5:c.162A>G	17.37:g.76198587A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	28	0.595745	NM_001145526		Silent	SNP	ENST00000327898.5	37	CCDS45801.1																																																																																			A|0.911;G|0.089	0.089	strong		0.517	AFMID-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333203.1	XM_058889	
PDCD6IP	10015	hgsc.bcm.edu	37	3	33895391	33895391	+	Silent	SNP	A	A	G	rs3183982	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33895391A>G	ENST00000307296.3	+	14	2288	c.1911A>G	c.(1909-1911)tcA>tcG	p.S637S	PDCD6IP_ENST00000457054.2_Silent_p.S642S			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	637	Interaction with EIAV p9.|Self-association.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						AGGAATTTTCAAAAATGAAAC	0.249													G|||	1654	0.330272	0.2943	0.4035	5008	,	,		16027	0.4107		0.2326	False		,,,				2504	0.3446				p.S642S		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.A1926G						PASS	.	G	,	1184,3206		162,860,1173	17.0	17.0	17.0		1926,1911	-9.9	0.8	3	dbSNP_105	17	2114,6460		272,1570,2445	no	coding-synonymous,coding-synonymous	PDCD6IP	NM_001162429.1,NM_013374.4	,	434,2430,3618	GG,GA,AA		24.6559,26.9704,25.4397	,	642/874,637/869	33895391	3298,9666	2195	4287	6482	SO:0001819	synonymous_variant	10015	exon14			ATTTTCAAAAATG	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.1911A>G	3.37:g.33895391A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Silent	SNP	ENST00000307296.3	37	CCDS2660.1																																																																																			A|0.616;G|0.384	0.384	strong		0.249	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
UTP14C	9724	hgsc.bcm.edu	37	13	52603896	52603896	+	Missense_Mutation	SNP	G	G	A	rs17402034	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:52603896G>A	ENST00000521776.2	+	2	1689	c.956G>A	c.(955-957)cGc>cAc	p.R319H		NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	319			R -> H (in dbSNP:rs17402034).		cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)				breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		CTGGAGGCTCGCCAAGCTATG	0.483													G|||	153	0.0305511	0.0038	0.0346	5008	,	,		19323	0.0		0.0994	False		,,,				2504	0.0245				p.R319H		Atlas-SNP	.											.	UTP14C	67	.	0			c.G956A						PASS	.	G	HIS/ARG	98,4308	78.8+/-117.2	1,96,2106	120.0	123.0	122.0		956	0.7	0.0	13	dbSNP_123	122	914,7686	203.0+/-246.1	50,814,3436	yes	missense	UTP14C	NM_021645.5	29	51,910,5542	AA,AG,GG		10.6279,2.2242,7.781	probably-damaging	319/767	52603896	1012,11994	2203	4300	6503	SO:0001583	missense	9724	exon2			AGGCTCGCCAAGC	D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"""KIAA0266"""	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.956G>A	13.37:g.52603896G>A	ENSP00000428619:p.Arg319His	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	148	9	0.0608108	NM_021645	Q5FWG3|Q92555	Missense_Mutation	SNP	ENST00000521776.2	37	CCDS31978.1	98	0.04487179487179487	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	79	0.10422163588390501	G	13.30	2.197270	0.38806	0.022242	0.106279	ENSG00000253797	ENST00000521776	T	0.38401	1.14	2.58	0.736	0.18307	.	0.103239	0.64402	N	0.000002	T	0.02267	0.0070	M	0.92268	3.29	0.48830	D	0.999717	D	0.89917	1.0	D	0.97110	1.0	T	0.03344	-1.1046	9	.	.	.	-9.4065	6.3491	0.21365	0.2764:0.0:0.7236:0.0	rs17402034;rs52791623;rs17402034	319	Q5TAP6	UT14C_HUMAN	H	319	ENSP00000428619:R319H	.	R	+	2	0	UTP14C	51501897	1.000000	0.71417	0.028000	0.17463	0.912000	0.54170	5.938000	0.70170	0.021000	0.15133	0.448000	0.29417	CGC	G|0.934;A|0.066	0.066	strong		0.483	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645	
ARHGAP21	57584	hgsc.bcm.edu	37	10	24908686	24908686	+	Missense_Mutation	SNP	T	T	C	rs3748222	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:24908686T>C	ENST00000396432.2	-	9	2624	c.2138A>G	c.(2137-2139)aAt>aGt	p.N713S	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.N500S	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	712					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)	p.N712S(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						TAAATCTTGATTCCTTTGACT	0.448													T|||	2195	0.438299	0.4395	0.4669	5008	,	,		19155	0.369		0.5129	False		,,,				2504	0.411				p.N713S		Atlas-SNP	.											ARHGAP21,NS,carcinoma,0,1	ARHGAP21	185	1	1	Substitution - Missense(1)	stomach(1)	c.A2138G						scavenged	.	T	SER/ASN	2018,2388	561.4+/-380.7	470,1078,655	50.0	49.0	49.0		2138	1.2	0.0	10	dbSNP_107	49	4609,3991	597.8+/-393.8	1248,2113,939	no	missense	ARHGAP21	NM_020824.3	46	1718,3191,1594	CC,CT,TT		46.407,45.8012,49.0466	benign	713/1959	24908686	6627,6379	2203	4300	6503	SO:0001583	missense	57584	exon9			TCTTGATTCCTTT	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.2138A>G	10.37:g.24908686T>C	ENSP00000379709:p.Asn713Ser	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	141	78	0.553191	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	961	0.440018315018315	217	0.4410569105691057	167	0.4613259668508287	192	0.3356643356643357	385	0.5079155672823219	T	0.138	-1.105936	0.01828	0.458012	0.53593	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	4.68	1.19	0.21007	.	0.538244	0.20359	N	0.093890	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B;B	0.17667	0.023;0.013	B;B	0.19148	0.024;0.011	T	0.46275	-0.9203	9	0.08599	T	0.76	.	1.0351	0.01547	0.2179:0.3383:0.1391:0.3047	rs3748222;rs3748222	703;712	F8W9U9;Q5T5U3	.;RHG21_HUMAN	S	713;500;703;713;548	ENSP00000379709:N713S;ENSP00000365604:N500S;ENSP00000365592:N703S;ENSP00000405018:N713S	ENSP00000365604:N500S	N	-	2	0	ARHGAP21	24948692	0.000000	0.05858	0.001000	0.08648	0.652000	0.38707	-0.783000	0.04638	0.367000	0.24454	0.533000	0.62120	AAT	T|0.510;C|0.490	0.490	strong		0.448	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133955427	133955427	+	Missense_Mutation	SNP	A	A	G	rs11592585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:133955427A>G	ENST00000298622.4	+	10	1615	c.1477A>G	c.(1477-1479)Atg>Gtg	p.M493V		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	493			M -> V (in dbSNP:rs11592585).			Golgi apparatus (GO:0005794)		p.M493V(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TCTCCAGGGCATGGCCAAGGA	0.642													A|||	935	0.186701	0.0408	0.232	5008	,	,		16582	0.2371		0.3419	False		,,,				2504	0.1401				p.M493V		Atlas-SNP	.											JAKMIP3,NS,carcinoma,0,1	JAKMIP3	69	1	1	Substitution - Missense(1)	prostate(1)	c.A1477G						PASS	.	A	VAL/MET	417,3981		20,377,1802	75.0	54.0	61.0		1477	-1.7	1.0	10	dbSNP_120	61	3041,5545		522,1997,1774	yes	missense	JAKMIP3	NM_001105521.2	21	542,2374,3576	GG,GA,AA		35.4181,9.4816,26.6328	benign	493/845	133955427	3458,9526	2199	4293	6492	SO:0001583	missense	282973	exon10			CAGGGCATGGCCA	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.1477A>G	10.37:g.133955427A>G	ENSP00000298622:p.Met493Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	500	0.22893772893772893	18	0.036585365853658534	91	0.2513812154696133	131	0.229020979020979	260	0.34300791556728233	A	10.98	1.503688	0.26949	0.094816	0.354181	ENSG00000188385	ENST00000298622	T	0.20598	2.06	3.87	-1.72	0.08107	.	0.570968	0.17020	N	0.190165	T	0.00012	0.0000	L	0.47716	1.5	0.20074	P	0.999933551	B	0.02656	0.0	B	0.01281	0.0	T	0.45205	-0.9277	9	0.27785	T	0.31	-14.708	4.6571	0.12622	0.4005:0.3058:0.2937:0.0	rs11592585;rs57375718;rs11592585	493	Q5VZ66	JKIP3_HUMAN	V	493	ENSP00000298622:M493V	ENSP00000298622:M493V	M	+	1	0	JAKMIP3	133805417	0.001000	0.12720	0.986000	0.45419	0.976000	0.68499	-0.349000	0.07731	-0.382000	0.07870	0.459000	0.35465	ATG	A|0.782;G|0.218	0.218	strong		0.642	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
FYCO1	79443	hgsc.bcm.edu	37	3	46009491	46009491	+	Silent	SNP	C	C	T	rs3796376	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:46009491C>T	ENST00000296137.2	-	8	1540	c.1335G>A	c.(1333-1335)ctG>ctA	p.L445L	FYCO1_ENST00000535325.1_Silent_p.L445L	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	445					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CCAGGCGCTCCAGGCTGGCCC	0.627													C|||	808	0.161342	0.0333	0.1542	5008	,	,		17595	0.2927		0.2078	False		,,,				2504	0.1564				p.L445L		Atlas-SNP	.											.	FYCO1	115	.	0			c.G1335A						PASS	.	C		293,4113	161.1+/-193.3	6,281,1916	138.0	151.0	147.0		1335	2.3	0.9	3	dbSNP_107	147	1686,6914	309.2+/-309.3	161,1364,2775	no	coding-synonymous	FYCO1	NM_024513.2		167,1645,4691	TT,TC,CC		19.6047,6.65,15.2161		445/1479	46009491	1979,11027	2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			GCGCTCCAGGCTG	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.1335G>A	3.37:g.46009491C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	154	154	1	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																			C|0.825;T|0.175	0.175	strong		0.627	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
GRM6	2916	hgsc.bcm.edu	37	5	178417654	178417654	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:178417654C>T	ENST00000517717.1	-	5	989	c.951G>A	c.(949-951)ttG>ttA	p.L317L	GRM6_ENST00000231188.5_Silent_p.L317L|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	317					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		CCTCCAGGCTCAAGATGGGTG	0.662																																					p.L317L		Atlas-SNP	.											GRM6,NS,lymphoid_neoplasm,-2,1	GRM6	149	1	0			c.G951A						scavenged	.						38.0	32.0	34.0					5																	178417654		2203	4300	6503	SO:0001819	synonymous_variant	2916	exon4			CAGGCTCAAGATG	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.951G>A	5.37:g.178417654C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	201	4	0.0199005	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																			.	.	none		0.662	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
HNRNPH2	3188	hgsc.bcm.edu	37	X	100668296	100668296	+	Silent	SNP	C	C	T	rs3027574	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:100668296C>T	ENST00000316594.5	+	2	1398	c.1320C>T	c.(1318-1320)aaC>aaT	p.N440N		NM_001032393.2|NM_001199973.1|NM_001199974.1|NM_019597.4	NP_001027565.1|NP_001186902.1|NP_001186903.1|NP_062543.1	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2 (H')	440					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|large_intestine(2)|lung(6)|skin(1)	12						TGCAGGAAAACTCCAGTGACT	0.453													C|||	84	0.0222517	0.028	0.0101	3775	,	,		14616	0.0		0.0288	False		,,,				2504	0.0112				p.N440N		Atlas-SNP	.											.	HNRNPH2	50	.	0			c.C1320T						PASS	.	C	,,,	111,3710		3,90,15,1532,556	173.0	165.0	168.0		1320,,,1320	3.5	1.0	X	dbSNP_102	168	324,6400		6,218,94,2203,1776	no	coding-synonymous,utr-3,utr-3,coding-synonymous	HNRNPH2,RPL36A-HNRNPH2	NM_001032393.2,NM_001199973.1,NM_001199974.1,NM_019597.4	,,,	9,308,109,3735,2332	TT,TC,T,CC,C		4.8186,2.905,4.1252	,,,	440/450,,,440/450	100668296	435,10110	2196	4297	6493	SO:0001819	synonymous_variant	3188	exon2			GGAAAACTCCAGT	U01923	CCDS14485.1	Xq22	2013-02-12		2008-04-18	ENSG00000126945	ENSG00000126945		"""RNA binding motif (RRM) containing"""	5042	protein-coding gene	gene with protein product		300610		HNRPH2		7499401	Standard	NM_019597		Approved	hnRNPH', FTP3, HNRPH'	uc004ehn.3	P55795	OTTHUMG00000022029	ENST00000316594.5:c.1320C>T	X.37:g.100668296C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	165	154	0.933333	NM_001032393	A1L400|Q9HHA7	Silent	SNP	ENST00000316594.5	37	CCDS14485.1																																																																																			C|0.964;T|0.036	0.036	strong		0.453	HNRNPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057556.1	NM_019597	
TOX4	9878	hgsc.bcm.edu	37	14	21960969	21960969	+	Silent	SNP	G	G	A	rs7617	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21960969G>A	ENST00000405508.1	+	8	1470	c.1194G>A	c.(1192-1194)cgG>cgA	p.R398R	TOX4_ENST00000262709.3_Silent_p.R398R|TOX4_ENST00000448790.2_Silent_p.R375R			O94842	TOX4_HUMAN	TOX high mobility group box family member 4	398						chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)			large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		TGACCTCCCGGGGGCTCCAAC	0.512													G|||	2480	0.495208	0.4274	0.3746	5008	,	,		18365	0.6488		0.502	False		,,,				2504	0.5072				p.R398R		Atlas-SNP	.											.	TOX4	50	.	0			c.G1194A						PASS	.	G		2060,2346	569.2+/-382.6	473,1114,616	92.0	100.0	98.0		1194	1.9	1.0	14	dbSNP_52	98	4322,4278	579.2+/-390.9	1127,2068,1105	no	coding-synonymous	TOX4	NM_014828.2		1600,3182,1721	AA,AG,GG		49.7442,46.7544,49.0697		398/622	21960969	6382,6624	2203	4300	6503	SO:0001819	synonymous_variant	9878	exon7			CTCCCGGGGGCTC	AB018280	CCDS32043.1	14q11.2	2007-03-20	2007-03-20	2007-03-20	ENSG00000092203	ENSG00000092203			20161	protein-coding gene	gene with protein product		614032	"""chromosome 14 open reading frame 92"", ""KIAA0737"""	C14orf92, KIAA0737			Standard	NM_014828		Approved	LCP1	uc001waz.3	O94842	OTTHUMG00000150278	ENST00000405508.1:c.1194G>A	14.37:g.21960969G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	168	79	0.470238	NM_014828	B4DPY8|B4DSM0|E7EV69	Silent	SNP	ENST00000405508.1	37	CCDS32043.1																																																																																			G|0.511;A|0.489	0.489	strong		0.512	TOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317287.2	NM_014828	
NUP155	9631	hgsc.bcm.edu	37	5	37333727	37333727	+	Silent	SNP	A	A	G	rs150594	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:37333727A>G	ENST00000231498.3	-	13	1559	c.1356T>C	c.(1354-1356)gcT>gcC	p.A452A	NUP155_ENST00000381843.2_Silent_p.A393A|NUP155_ENST00000513532.1_Silent_p.A452A	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	452					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CATCAACACCAGCTGTCATCT	0.279													G|||	1778	0.355032	0.854	0.2219	5008	,	,		16393	0.123		0.1531	False		,,,				2504	0.2219				p.A452A		Atlas-SNP	.											NUP155,NS,carcinoma,-1,1	NUP155	116	1	0			c.T1356C						PASS	.	G	,	3224,1182	411.9+/-335.9	1178,868,157	53.0	54.0	54.0		1179,1356	-1.2	1.0	5	dbSNP_79	54	1375,7225	754.1+/-407.5	102,1171,3027	no	coding-synonymous,coding-synonymous	NUP155	NM_004298.2,NM_153485.1	,	1280,2039,3184	GG,GA,AA		15.9884,26.8271,35.3606	,	393/1333,452/1392	37333727	4599,8407	2203	4300	6503	SO:0001819	synonymous_variant	9631	exon13			AACACCAGCTGTC	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"""nucleoporin 155kD"""			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.1356T>C	5.37:g.37333727A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_153485	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	37	CCDS3921.1																																																																																			A|0.658;G|0.342	0.342	strong		0.279	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298	
PCOLCE2	26577	hgsc.bcm.edu	37	3	142542449	142542449	+	Missense_Mutation	SNP	G	G	T	rs17554211	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:142542449G>T	ENST00000295992.3	-	7	1180	c.874C>A	c.(874-876)Ccc>Acc	p.P292T	PCOLCE2_ENST00000485766.1_Intron	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	292			P -> T (in dbSNP:rs17554211).		positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						GCCACGGTGGGTTTTAAACCT	0.353													G|||	210	0.0419329	0.0091	0.0908	5008	,	,		17279	0.001		0.1252	False		,,,				2504	0.0082				p.P292T		Atlas-SNP	.											.	PCOLCE2	63	.	0			c.C874A						PASS	.	G	THR/PRO	95,4311	70.9+/-108.8	3,89,2111	65.0	70.0	68.0		874	5.4	1.0	3	dbSNP_123	68	961,7639	199.4+/-243.5	57,847,3396	yes	missense	PCOLCE2	NM_013363.3	38	60,936,5507	TT,TG,GG		11.1744,2.1562,8.1193	benign	292/416	142542449	1056,11950	2203	4300	6503	SO:0001583	missense	26577	exon7			CGGTGGGTTTTAA	AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.874C>A	3.37:g.142542449G>T	ENSP00000295992:p.Pro292Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	161	82	0.509317	NM_013363	B2RCH9|D3DNG4|Q9BRH3	Missense_Mutation	SNP	ENST00000295992.3	37	CCDS3127.1	139	0.06364468864468864	6	0.012195121951219513	37	0.10220994475138122	0	0.0	96	0.1266490765171504	G	11.63	1.695488	0.30052	0.021562	0.111744	ENSG00000163710	ENST00000295992	T	0.20069	2.1	5.41	5.41	0.78517	Tissue inhibitor of metalloproteinases-like, OB-fold (1);	0.000000	0.85682	D	0.000000	T	0.00328	0.0010	M	0.78637	2.42	0.09310	P	1.0	B	0.13145	0.007	B	0.12156	0.007	T	0.02269	-1.1185	9	0.54805	T	0.06	-19.3292	18.3636	0.90383	0.0:0.0:1.0:0.0	rs17554211;rs52837289;rs17554211	292	Q9UKZ9	PCOC2_HUMAN	T	292	ENSP00000295992:P292T	ENSP00000295992:P292T	P	-	1	0	PCOLCE2	144025139	1.000000	0.71417	0.958000	0.39756	0.239000	0.25481	6.431000	0.73395	2.803000	0.96430	0.655000	0.94253	CCC	G|0.926;T|0.074	0.074	strong		0.353	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354509.1	NM_013363	
KPNA2	3838	hgsc.bcm.edu	37	17	66039350	66039350	+	Silent	SNP	A	A	G	rs4638	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:66039350A>G	ENST00000537025.2	+	7	1421	c.801A>G	c.(799-801)gtA>gtG	p.V267V	KPNA2_ENST00000330459.3_Silent_p.V267V			P52292	IMA1_HUMAN	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	267					cytokine-mediated signaling pathway (GO:0019221)|DNA metabolic process (GO:0006259)|NLS-bearing protein import into nucleus (GO:0006607)|regulation of DNA recombination (GO:0000018)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|kidney(2)|lung(9)|prostate(1)|urinary_tract(2)	22	all_cancers(12;1.18e-09)		BRCA - Breast invasive adenocarcinoma(8;1.03e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			ATCCAGAAGTATTAGCAGATA	0.473													a|||	2597	0.51857	0.4024	0.6585	5008	,	,		19618	0.2847		0.7276	False		,,,				2504	0.6022				p.V267V		Atlas-SNP	.											.	KPNA2	55	.	0			c.A801G						PASS	.	A		1967,2439	555.1+/-379.2	455,1057,691	167.0	174.0	172.0		801	-6.0	1.0	17	dbSNP_52	172	6375,2225	709.1+/-405.7	2367,1641,292	no	coding-synonymous	KPNA2	NM_002266.2		2822,2698,983	GG,GA,AA		25.8721,44.6437,35.8604		267/530	66039350	8342,4664	2203	4300	6503	SO:0001819	synonymous_variant	3838	exon7			AGAAGTATTAGCA	U09559	CCDS32713.1	17q24.2	2013-02-14						"""Importins"", ""Armadillo repeat containing"""	6395	protein-coding gene	gene with protein product		600685		RCH1		8016130, 7754385	Standard	NM_002266		Approved	SRP1alpha, IPOA1, QIP2	uc002jgk.3	P52292		ENST00000537025.2:c.801A>G	17.37:g.66039350A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	122	73	0.598361	NM_002266	B9EJD6|Q53YE3|Q9BRU5	Silent	SNP	ENST00000537025.2	37	CCDS32713.1																																																																																			A|0.406;G|0.594	0.594	strong		0.473	KPNA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448111.1	NM_002266	
ITGAX	3687	hgsc.bcm.edu	37	16	31371674	31371674	+	Missense_Mutation	SNP	G	G	A	rs2230428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31371674G>A	ENST00000268296.4	+	8	872	c.751G>A	c.(751-753)Gcc>Acc	p.A251T	ITGAX_ENST00000562522.1_Missense_Mutation_p.A251T	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	251	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		A -> T (in dbSNP:rs2230428). {ECO:0000269|PubMed:2303426, ECO:0000269|PubMed:3327687}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						TAGGGATGCCGCCAAAATTCT	0.522													G|||	413	0.0824681	0.1067	0.0605	5008	,	,		18946	0.006		0.164	False		,,,				2504	0.0603				p.A251T		Atlas-SNP	.											ITGAX,colon,carcinoma,0,1	ITGAX	198	1	0			c.G751A						PASS	.	G	THR/ALA	476,3918	224.6+/-240.7	21,434,1742	103.0	107.0	105.0		751	1.1	1.0	16	dbSNP_98	105	1618,6982	301.0+/-305.2	158,1302,2840	yes	missense	ITGAX	NM_000887.3	58	179,1736,4582	AA,AG,GG		18.814,10.833,16.1151	benign	251/1164	31371674	2094,10900	2197	4300	6497	SO:0001583	missense	3687	exon8			GATGCCGCCAAAA	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.751G>A	16.37:g.31371674G>A	ENSP00000268296:p.Ala251Thr	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	242	126	0.520661	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	222	0.10164835164835165	61	0.12398373983739837	25	0.06906077348066299	2	0.0034965034965034965	134	0.17678100263852242	G	3.517	-0.098475	0.07010	0.10833	0.18814	ENSG00000140678	ENST00000268296	D	0.82984	-1.67	4.73	1.14	0.20703	von Willebrand factor, type A (3);	.	.	.	.	T	0.00109	0.0003	N	0.01761	-0.735	0.43226	P	0.004882999999999971	B	0.06786	0.001	B	0.01281	0.0	T	0.05733	-1.0867	8	0.02654	T	1	.	5.7375	0.18075	0.7138:0.0:0.0978:0.1884	rs2230428;rs3087446;rs12928508;rs56605064;rs2230428	251	P20702	ITAX_HUMAN	T	251	ENSP00000268296:A251T	ENSP00000268296:A251T	A	+	1	0	ITGAX	31279175	1.000000	0.71417	0.999000	0.59377	0.217000	0.24651	2.344000	0.44010	0.063000	0.16370	-0.312000	0.09012	GCC	G|0.860;A|0.140	0.140	strong		0.522	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
CASR	846	hgsc.bcm.edu	37	3	122003757	122003757	+	Missense_Mutation	SNP	G	G	T	rs1801725	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:122003757G>T	ENST00000490131.1	+	7	3328	c.2956G>T	c.(2956-2958)Gcc>Tcc	p.A986S	CASR_ENST00000296154.5_Missense_Mutation_p.A986S|CASR_ENST00000498619.1_Missense_Mutation_p.A996S|AC068754.1_ENST00000408547.1_RNA	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	986			A -> S (associated with high serum level of calcium; is also a potential predisposing factor in disorders of bone and mineral metabolism; dbSNP:rs1801725). {ECO:0000269|PubMed:10023897, ECO:0000269|PubMed:11161843, ECO:0000269|PubMed:14985373, ECO:0000269|PubMed:15531522, ECO:0000269|PubMed:16598859, ECO:0000269|PubMed:17698911, ECO:0000269|PubMed:18756473, ECO:0000269|Ref.5}.		anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	TCAGAAGAACGCCATGGCCCA	0.582													G|||	472	0.0942492	0.0098	0.1066	5008	,	,		20250	0.0367		0.1451	False		,,,				2504	0.2065				p.A996S		Atlas-SNP	.											.	CASR	190	.	0			c.G2986T	GRCh37	CM012741	CASR	M	rs1801725	PASS	.	G	SER/ALA,SER/ALA	179,4227	115.0+/-153.0	1,177,2025	69.0	65.0	67.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2956,2986	4.9	0.6	3	dbSNP_89	67	1272,7328	254.3+/-279.6	109,1054,3137	yes	missense,missense	CASR	NM_000388.3,NM_001178065.1	99,99	110,1231,5162	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.7907,4.0626,11.1564	benign,benign	986/1079,996/1089	122003757	1451,11555	2203	4300	6503	SO:0001583	missense	846	exon7			AAGAACGCCATGG	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"""GPCR / Class C : Calcium-sensing receptors"""	1514	protein-coding gene	gene with protein product	"""severe neonatal hyperparathyroidism"""	601199	"""hypocalciuric hypercalcemia 1"""	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.2956G>T	3.37:g.122003757G>T	ENSP00000418685:p.Ala986Ser	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	330	155	0.469697	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	37	CCDS3010.1	166	0.076007326007326	2	0.0040650406504065045	49	0.13535911602209943	10	0.017482517482517484	105	0.13852242744063326	G	10.51	1.370984	0.24771	0.040626	0.147907	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.91237	-2.81;-2.8;-2.81	5.79	4.92	0.64577	.	0.112422	0.64402	D	0.000010	T	0.01627	0.0052	N	0.11201	0.11	0.22989	P	0.99846151	B;B	0.27951	0.195;0.195	B;B	0.22753	0.041;0.041	T	0.52388	-0.8582	9	0.39692	T	0.17	.	13.8067	0.63236	0.0731:0.0:0.9269:0.0	rs1801725;rs17251741;rs17838787;rs60137063;rs1801725	996;986	E7ENE0;P41180	.;CASR_HUMAN	S	986;996;986	ENSP00000418685:A986S;ENSP00000420194:A996S;ENSP00000296154:A986S	ENSP00000296154:A986S	A	+	1	0	CASR	123486447	0.999000	0.42202	0.567000	0.28434	0.776000	0.43924	3.138000	0.50570	1.465000	0.48006	0.561000	0.74099	GCC	G|0.904;T|0.096	0.096	strong		0.582	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388	
VANGL2	57216	hgsc.bcm.edu	37	1	160393905	160393905	+	Silent	SNP	A	A	G	rs12086448	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:160393905A>G	ENST00000368061.2	+	7	1611	c.1137A>G	c.(1135-1137)aaA>aaG	p.K379K	VANGL2_ENST00000483408.1_3'UTR	NM_020335.2	NP_065068.1	Q9ULK5	VANG2_HUMAN	VANGL planar cell polarity protein 2	379					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|cell migration involved in kidney development (GO:0035787)|cochlea morphogenesis (GO:0090103)|convergent extension involved in axis elongation (GO:0060028)|convergent extension involved in neural plate elongation (GO:0022007)|digestive tract morphogenesis (GO:0048546)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity involved in neural tube closure (GO:0090177)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|glomerulus development (GO:0032835)|hair follicle development (GO:0001942)|heart looping (GO:0001947)|inner ear receptor stereocilium organization (GO:0060122)|kidney morphogenesis (GO:0060993)|lateral sprouting involved in lung morphogenesis (GO:0060490)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in axis elongation (GO:0003402)|planar cell polarity pathway involved in heart morphogenesis (GO:0061346)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|positive regulation of JUN kinase activity (GO:0043507)|post-anal tail morphogenesis (GO:0036342)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Wnt signaling pathway (GO:0030111)|Rho protein signal transduction (GO:0007266)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell pole (GO:0060187)|cell-cell junction (GO:0005911)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)		p.K379K(1)		biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	37	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGGAGCAGAAAAACCCCAGGG	0.617													G|||	2888	0.576677	0.8003	0.4524	5008	,	,		15789	0.371		0.497	False		,,,				2504	0.6564				p.K379K		Atlas-SNP	.											VANGL2,NS,carcinoma,0,1	VANGL2	83	1	1	Substitution - coding silent(1)	stomach(1)	c.A1137G						PASS	.	G		3395,1011	376.8+/-322.2	1323,749,131	85.0	90.0	88.0		1137	2.7	1.0	1	dbSNP_120	88	4522,4078	560.2+/-387.5	1201,2120,979	no	coding-synonymous	VANGL2	NM_020335.2		2524,2869,1110	GG,GA,AA		47.4186,22.946,39.1281		379/522	160393905	7917,5089	2203	4300	6503	SO:0001819	synonymous_variant	57216	exon7			GCAGAAAAACCCC	AB033041	CCDS30915.1	1q22-q23	2013-03-05	2013-03-05		ENSG00000162738	ENSG00000162738			15511	protein-coding gene	gene with protein product	"""vang, van gogh-like 2"", ""loop-tail-associated protein"", ""strabismus"""	600533	"""vang (van gogh, Drosophila)-like 2, vang, van gogh-like 2 (Drosophila)"", ""vang-like 2 (van gogh, Drosophila)"""			11431695	Standard	NM_020335		Approved	KIAA1215, LTAP, LPP1, STBM, STB1, STBM1, MGC119403, MGC119404	uc001fwc.2	Q9ULK5	OTTHUMG00000033122	ENST00000368061.2:c.1137A>G	1.37:g.160393905A>G		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	306	148	0.48366	NM_020335	D3DVE9|Q5T212	Silent	SNP	ENST00000368061.2	37	CCDS30915.1																																																																																			A|0.412;G|0.588	0.588	strong		0.617	VANGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080677.1	NM_020335	
GAL3ST1	9514	hgsc.bcm.edu	37	22	30953295	30953295	+	Missense_Mutation	SNP	C	C	T	rs2267161	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:30953295C>T	ENST00000402321.1	-	2	402	c.85G>A	c.(85-87)Gtg>Atg	p.V29M	GAL3ST1_ENST00000443111.2_Missense_Mutation_p.V29M|GAL3ST1_ENST00000401975.1_Missense_Mutation_p.V29M|GAL3ST1_ENST00000406361.1_Missense_Mutation_p.V29M|GAL3ST1_ENST00000406955.1_Missense_Mutation_p.V29M|GAL3ST1_ENST00000338911.5_Missense_Mutation_p.V29M|GAL3ST1_ENST00000402369.1_Missense_Mutation_p.V29M			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	29			V -> M (in dbSNP:rs2267161). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.		galactosylceramide biosynthetic process (GO:0006682)|glycosphingolipid metabolic process (GO:0006687)|myelination (GO:0042552)|protein N-linked glycosylation (GO:0006487)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21						TAGGAGTACACCAGCAGCAGG	0.652													C|||	1552	0.309904	0.3646	0.2536	5008	,	,		17788	0.3502		0.326	False		,,,				2504	0.2178				p.V29M		Atlas-SNP	.											.	GAL3ST1	44	.	0			c.G85A						PASS	.	C	MET/VAL	1647,2759	502.0+/-365.1	326,995,882	89.0	91.0	91.0		85	1.1	0.9	22	dbSNP_100	91	2732,5868	436.8+/-358.4	420,1892,1988	yes	missense	GAL3ST1	NM_004861.1	21	746,2887,2870	TT,TC,CC		31.7674,37.3808,33.6691	benign	29/424	30953295	4379,8627	2203	4300	6503	SO:0001583	missense	9514	exon3			AGTACACCAGCAG	D88667	CCDS13879.1	22q12.2	2007-04-02			ENSG00000128242	ENSG00000128242		"""Sulfotransferases, membrane-bound"""	24240	protein-coding gene	gene with protein product	"""cerebroside (3' phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase"""	602300				9847074, 9030544	Standard	NM_004861		Approved	CST	uc003aii.1	Q99999	OTTHUMG00000151200	ENST00000402321.1:c.85G>A	22.37:g.30953295C>T	ENSP00000385735:p.Val29Met	Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	347	159	0.458213	NM_004861	Q96C63	Missense_Mutation	SNP	ENST00000402321.1	37	CCDS13879.1	691	0.3163919413919414	167	0.3394308943089431	90	0.24861878453038674	197	0.34440559440559443	237	0.31266490765171506	C	13.74	2.327313	0.41197	0.373808	0.317674	ENSG00000128242	ENST00000406955;ENST00000402321;ENST00000402369;ENST00000401975;ENST00000338911;ENST00000406361;ENST00000443111;ENST00000441967;ENST00000431313;ENST00000452827;ENST00000437282;ENST00000416358;ENST00000427899;ENST00000423299;ENST00000443136;ENST00000423371;ENST00000428682;ENST00000453479;ENST00000426220;ENST00000447224;ENST00000411821;ENST00000445645;ENST00000448604	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.18960	2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18	5.58	1.09	0.20402	.	0.269973	0.36268	N	0.002686	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.9999999999999958	B	0.25904	0.137	B	0.29716	0.106	T	0.49495	-0.8934	9	0.33141	T	0.24	-10.4855	7.6791	0.28502	0.2039:0.1191:0.677:0.0	rs2267161;rs17845430;rs17856591;rs17858302;rs61593263;rs2267161	29	Q99999	G3ST1_HUMAN	M	29	ENSP00000385825:V29M;ENSP00000385735:V29M;ENSP00000384122:V29M;ENSP00000384388:V29M;ENSP00000343234:V29M;ENSP00000385207:V29M;ENSP00000402587:V29M;ENSP00000390545:V29M;ENSP00000395080:V29M;ENSP00000405017:V29M;ENSP00000401426:V29M;ENSP00000391485:V29M;ENSP00000397092:V29M;ENSP00000391996:V29M;ENSP00000405381:V29M;ENSP00000401074:V29M;ENSP00000389876:V29M;ENSP00000398380:V29M;ENSP00000414542:V29M;ENSP00000412995:V29M;ENSP00000394912:V29M;ENSP00000399649:V29M;ENSP00000390068:V29M	ENSP00000343234:V29M	V	-	1	0	GAL3ST1	29283295	1.000000	0.71417	0.931000	0.37212	0.726000	0.41606	1.007000	0.29860	0.316000	0.23135	-0.147000	0.13772	GTG	C|0.671;T|0.329	0.329	strong		0.652	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321745.1	NM_004861	
SLC17A2	10246	hgsc.bcm.edu	37	6	25916979	25916979	+	Silent	SNP	C	C	T	rs1865760	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:25916979C>T	ENST00000265425.3	-	7	884	c.864G>A	c.(862-864)ttG>ttA	p.L288L	SLC17A2_ENST00000360488.3_Silent_p.L288L|SLC17A2_ENST00000377850.3_Silent_p.L288L			O00624	NPT3_HUMAN	solute carrier family 17, member 2	288					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	31						TGATGGTGCACAACCAGAAAT	0.448													C|||	2004	0.40016	0.143	0.4568	5008	,	,		22991	0.6964		0.4026	False		,,,				2504	0.3998				p.L288L		Atlas-SNP	.											.	SLC17A2	70	.	0			c.G864A						PASS	.	C		817,3589	325.6+/-299.2	73,671,1459	129.0	114.0	119.0		864	-5.0	0.9	6	dbSNP_96	119	3350,5250	498.8+/-374.8	670,2010,1620	no	coding-synonymous	SLC17A2	NM_005835.2		743,2681,3079	TT,TC,CC		38.9535,18.5429,32.0391		288/437	25916979	4167,8839	2203	4300	6503	SO:0001819	synonymous_variant	10246	exon8			GGTGCACAACCAG	U90544	CCDS4567.1, CCDS69060.1	6p22.2	2013-07-18	2013-07-18		ENSG00000112337	ENSG00000112337		"""Solute carriers"""	10930	protein-coding gene	gene with protein product		611049	"""solute carrier family 17 (sodium phosphate), member 2"""			9149941	Standard	NM_001286123		Approved	NPT3	uc003nfl.3	O00624	OTTHUMG00000014413	ENST00000265425.3:c.864G>A	6.37:g.25916979C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	99	55	0.555556	NM_005835	A6NK81|A6NLD6|Q5TB84|Q76P85	Silent	SNP	ENST00000265425.3	37																																																																																				C|0.634;T|0.366	0.366	strong		0.448	SLC17A2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040075.1		
SRRM4	84530	hgsc.bcm.edu	37	12	119540062	119540062	+	Silent	SNP	C	C	T	rs73213729	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:119540062C>T	ENST00000267260.4	+	2	541	c.153C>T	c.(151-153)ccC>ccT	p.P51P	RP11-364C11.2_ENST00000537730.1_RNA	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	51					cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						AGAATAACCCCGTTGTCCCAG	0.468													C|||	146	0.0291534	0.056	0.0231	5008	,	,		19674	0.004		0.0219	False		,,,				2504	0.0307				p.P51P		Atlas-SNP	.											.	SRRM4	131	.	0			c.C153T						PASS	.	C		196,3542		9,178,1682	54.0	53.0	53.0		153	0.6	0.3	12	dbSNP_130	53	349,7869		8,333,3768	no	coding-synonymous	SRRM4	NM_194286.3		17,511,5450	TT,TC,CC		4.2468,5.2434,4.5584		51/612	119540062	545,11411	1869	4109	5978	SO:0001819	synonymous_variant	84530	exon2			TAACCCCGTTGTC	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.153C>T	12.37:g.119540062C>T		Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	167	80	0.479042	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Silent	SNP	ENST00000267260.4	37	CCDS44994.1																																																																																			C|0.973;T|0.027	0.027	strong		0.468	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
AKAP9	10142	hgsc.bcm.edu	37	7	91641928	91641928	+	Silent	SNP	A	A	G	rs13245393	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:91641928A>G	ENST00000359028.2	+	10	3765	c.3540A>G	c.(3538-3540)gaA>gaG	p.E1180E	AKAP9_ENST00000356239.3_Silent_p.E1168E|AKAP9_ENST00000358100.2_Silent_p.E1180E			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1180					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ACCAGTTAGAACTACAGACTA	0.328			T	BRAF	papillary thyroid								G|||	1872	0.373802	0.5076	0.3573	5008	,	,		18366	0.1617		0.3867	False		,,,				2504	0.41				p.E1168E		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.A3504G						PASS	.	G	,	2279,2127	576.6+/-384.3	583,1113,507	75.0	77.0	76.0		3504,3504	-0.3	1.0	7	dbSNP_121	76	3467,5133	632.0+/-398.6	678,2111,1511	no	coding-synonymous,coding-synonymous	AKAP9	NM_005751.4,NM_147185.2	,	1261,3224,2018	GG,GA,AA		40.314,48.2751,44.1796	,	1168/3908,1168/3900	91641928	5746,7260	2203	4300	6503	SO:0001819	synonymous_variant	10142	exon9			GTTAGAACTACAG	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.3540A>G	7.37:g.91641928A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				A|0.589;G|0.411	0.411	strong		0.328	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735518	55735518	+	Missense_Mutation	SNP	G	G	A	rs61896165	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55735518G>A	ENST00000312345.2	-	1	472	c.422C>T	c.(421-423)aCc>aTc	p.T141I		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	141						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					AATTGTGATGGTCCAGGAAGC	0.428													A|||	191	0.038139	0.0129	0.0389	5008	,	,		19255	0.001		0.0934	False		,,,				2504	0.0532				p.T141I		Atlas-SNP	.											.	OR10AG1	100	.	0			c.C422T						PASS	.	A	ILE/THR	108,4294	814.6+/-416.2	3,102,2096	79.0	76.0	77.0		422	5.5	0.1	11	dbSNP_129	77	693,7899	786.9+/-407.6	34,625,3637	yes	missense	OR10AG1	NM_001005491.1	89	37,727,5733	AA,AG,GG		8.0656,2.4534,6.1644	benign	141/302	55735518	801,12193	2201	4296	6497	SO:0001583	missense	282770	exon1			GTGATGGTCCAGG	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.422C>T	11.37:g.55735518G>A	ENSP00000311477:p.Thr141Ile	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_001005491	B2RNH4|Q6IEU3	Missense_Mutation	SNP	ENST00000312345.2	37	CCDS31514.1	82	0.037545787545787544	4	0.008130081300813009	10	0.027624309392265192	0	0.0	68	0.08970976253298153	A	0.012	-1.653074	0.00785	0.024534	0.080656	ENSG00000174970	ENST00000312345	T	0.33865	1.39	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.889433	0.09682	N	0.769573	T	0.00608	0.0020	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.14811	-1.0459	10	0.02654	T	1	.	10.1447	0.42755	0.9194:0.0:0.0806:0.0	rs61896165	141	Q8NH19	O10AG_HUMAN	I	141	ENSP00000311477:T141I	ENSP00000311477:T141I	T	-	2	0	OR10AG1	55492094	0.000000	0.05858	0.070000	0.20053	0.035000	0.12851	-0.042000	0.12063	0.904000	0.36572	-1.264000	0.01445	ACC	G|0.948;A|0.052	0.052	strong		0.428	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
GRIA4	2893	hgsc.bcm.edu	37	11	105842740	105842740	+	Silent	SNP	G	G	A	rs61736488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:105842740G>A	ENST00000530497.1	+	14	2394	c.2394G>A	c.(2392-2394)aaG>aaA	p.K798K	RNU6-277P_ENST00000516272.1_RNA|GRIA4_ENST00000533094.1_Intron|GRIA4_ENST00000393127.2_Intron|GRIA4_ENST00000525187.1_Intron|GRIA4_ENST00000282499.5_Silent_p.K798K			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	798					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		GTGGACCCAAGGACTCTGGAA	0.463													G|||	355	0.0708866	0.1263	0.0418	5008	,	,		14620	0.0248		0.0865	False		,,,				2504	0.0481				p.K798K		Atlas-SNP	.											.	GRIA4	380	.	0			c.G2394A						PASS	.	G	,	543,3859	245.0+/-254.1	42,459,1700	106.0	106.0	106.0		2394,	5.6	1.0	11	dbSNP_129	106	646,7952	165.1+/-217.3	25,596,3678	no	coding-synonymous,intron	GRIA4	NM_000829.3,NM_001077243.2	,	67,1055,5378	AA,AG,GG		7.5134,12.3353,9.1462	,	798/903,	105842740	1189,11811	2201	4299	6500	SO:0001819	synonymous_variant	2893	exon15			ACCCAAGGACTCT	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4574	protein-coding gene	gene with protein product		138246	"""glutamate receptor, ionotrophic, AMPA 4"""	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.2394G>A	11.37:g.105842740G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_000829	Q86XE8	Silent	SNP	ENST00000530497.1	37	CCDS8333.1																																																																																			G|0.919;A|0.081	0.081	strong		0.463	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1		
GCDH	2639	hgsc.bcm.edu	37	19	13010520	13010520	+	3'UTR	SNP	A	A	G	rs8012	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:13010520A>G	ENST00000222214.5	+	0	1693				GCDH_ENST00000422947.2_3'UTR|GCDH_ENST00000588242.2_3'UTR|GCDH_ENST00000457854.1_Missense_Mutation_p.Q417R|SYCE2_ENST00000293695.7_Intron|GCDH_ENST00000591470.1_3'UTR			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase						cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	GAAGTCGTTCAGATGTGTTCC	0.438													G|||	3608	0.720447	0.8563	0.6988	5008	,	,		16551	0.7768		0.5219	False		,,,				2504	0.6984				p.L417R	GBM(123;875 1636 7726 16444 26754)	Atlas-SNP	.											GCDH_ENST00000457854,NS,carcinoma,+1,1	GCDH	76	1	0			c.T1250G						scavenged	.	G	,,ARG/GLN	3530,752		1455,620,66	73.0	87.0	83.0		,,1250	-1.4	0.0	19	dbSNP_52	83	4635,3863		1306,2023,920	yes	utr-3,intron,missense	GCDH,SYCE2	NM_000159.2,NM_001105578.1,NM_013976.2	,,43	2761,2643,986	GG,GA,AA		45.4578,17.5619,36.1111	,,	,,417/429	13010520	8165,4615	2141	4249	6390	SO:0001624	3_prime_UTR_variant	2639	exon12			TCGTTCAGATGTG	AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"""glutaryl-Coenzyme A dehydrogenase"""			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.*165A>G	19.37:g.13010520A>G		Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	167	75	0.449102	NM_013976	A8K2Z2|O14719	Missense_Mutation	SNP	ENST00000222214.5	37	CCDS12286.1	1499	0.6863553113553114	416	0.8455284552845529	242	0.6685082872928176	461	0.8059440559440559	380	0.5013192612137203	G	0.525	-0.860606	0.02610	0.824381	0.545422	ENSG00000105607	ENST00000457854	D	0.97455	-4.39	4.81	-1.41	0.08941	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42882	-0.9425	7	0.62326	D	0.03	.	6.9724	0.24656	0.5991:0.2464:0.1545:0.0	rs8012;rs3170319;rs17639268;rs60041561;rs8012	417	Q92947-2	.	R	417	ENSP00000394872:Q417R	ENSP00000394872:Q417R	Q	+	2	0	GCDH	12871520	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.326000	0.19646	-0.796000	0.04456	-4.229000	0.00009	CAG	A|0.293;G|0.706	0.706	strong		0.438	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1		
PCDHA3	56145	hgsc.bcm.edu	37	5	140181648	140181648	+	Missense_Mutation	SNP	T	T	C	rs3733709	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140181648T>C	ENST00000522353.2	+	1	866	c.866T>C	c.(865-867)aTt>aCt	p.I289T	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.I289T|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	289	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> T (in dbSNP:rs3733709).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.I289T(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAGCAGATATTCTGTCAAAA	0.403													.|||	423	0.0844649	0.0681	0.0706	5008	,	,		23696	0.0714		0.1213	False		,,,				2504	0.092				p.I289T		Atlas-SNP	.											PCDHA3_ENST00000522353,NS,carcinoma,0,2	PCDHA3	396	2	2	Substitution - Missense(2)	stomach(2)	c.T866C						PASS	.	T	,,THR/ILE,,THR/ILE	317,4089	167.6+/-198.6	13,291,1899	106.0	106.0	106.0		,,866,,866	2.5	0.3	5	dbSNP_107	106	1039,7561	222.0+/-259.2	58,923,3319	yes	intron,intron,missense,intron,missense	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,89,,89	71,1214,5218	CC,CT,TT		12.0814,7.1947,10.426	,,,,	,,289/951,,289/825	140181648	1356,11650	2203	4300	6503	SO:0001583	missense	56145	exon1			CAGATATTCTGTC	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.866T>C	5.37:g.140181648T>C	ENSP00000429808:p.Ile289Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	194	0.08882783882783883	33	0.06707317073170732	32	0.08839779005524862	40	0.06993006993006994	89	0.11741424802110818	t	3.551	-0.091651	0.07053	0.071947	0.120814	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.52754	0.72;0.65	4.79	2.45	0.29901	Cadherin (4);Cadherin-like (1);	1.221100	0.06378	N	0.714716	T	0.00496	0.0016	N	0.17838	0.53	0.80722	P	0.0	B;B	0.13145	0.006;0.007	B;B	0.22152	0.026;0.038	T	0.13818	-1.0495	9	0.33141	T	0.24	.	7.7169	0.28710	0.0:0.2189:0.0:0.7811	rs3733709;rs17286766;rs17844254;rs52815327;rs56754038;rs3733709	289;289	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	T	289	ENSP00000429808:I289T;ENSP00000434086:I289T	ENSP00000429808:I289T	I	+	2	0	PCDHA3	140161832	0.001000	0.12720	0.315000	0.25238	0.541000	0.35023	0.535000	0.23114	0.313000	0.23062	0.383000	0.25322	ATT	T|0.906;C|0.094	0.094	strong		0.403	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
CHD1L	9557	hgsc.bcm.edu	37	1	146740502	146740502	+	Missense_Mutation	SNP	C	C	G	rs17356233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:146740502C>G	ENST00000369258.4	+	10	1070	c.1050C>G	c.(1048-1050)caC>caG	p.H350Q	CHD1L_ENST00000369259.3_Missense_Mutation_p.H146Q|CHD1L_ENST00000431239.1_Intron|CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000361293.5_Missense_Mutation_p.H69Q	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	350			H -> Q (in dbSNP:rs17356233). {ECO:0000269|PubMed:17974005}.		ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					GGAAGCTTCACCTGCTGGATA	0.488													C|||	737	0.147165	0.0076	0.1931	5008	,	,		19944	0.1111		0.2306	False		,,,				2504	0.2546				p.H350Q		Atlas-SNP	.											.	CHD1L	72	.	0			c.C1050G	GRCh37	CM067658	CHD1L	M	rs17356233	PASS	.	C	GLN/HIS	208,4198	130.2+/-166.9	5,198,2000	160.0	138.0	145.0		1050	-0.8	1.0	1	dbSNP_123	145	2010,6590	351.2+/-328.2	226,1558,2516	yes	missense	CHD1L	NM_004284.3	24	231,1756,4516	GG,GC,CC		23.3721,4.7208,17.0537	benign	350/898	146740502	2218,10788	2203	4300	6503	SO:0001583	missense	9557	exon10			GCTTCACCTGCTG	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.1050C>G	1.37:g.146740502C>G	ENSP00000358262:p.His350Gln	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	249	117	0.46988	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	37	CCDS927.1	302	0.1382783882783883	4	0.008130081300813009	69	0.19060773480662985	59	0.10314685314685315	170	0.22427440633245382	C	11.03	1.518680	0.27211	0.047208	0.233721	ENSG00000131778	ENST00000369259;ENST00000369258;ENST00000436230;ENST00000361293	T;T;T	0.65178	-0.14;-0.14;-0.14	5.54	-0.764	0.11027	.	0.458298	0.27437	N	0.019376	T	0.13114	0.0318	N	0.01128	-1	0.44807	P	0.0021889999999999965	B;B	0.33073	0.396;0.246	B;B	0.37422	0.249;0.082	T	0.17501	-1.0367	9	0.29301	T	0.29	.	8.959	0.35836	0.0:0.5036:0.0:0.4964	rs17356233;rs52837843;rs17356233	146;350	Q86WJ1-3;Q86WJ1	.;CHD1L_HUMAN	Q	146;350;250;69	ENSP00000358263:H146Q;ENSP00000358262:H350Q;ENSP00000355100:H69Q	ENSP00000355100:H69Q	H	+	3	2	CHD1L	145207126	0.252000	0.23972	0.967000	0.41034	0.521000	0.34408	0.211000	0.17474	-0.148000	0.11234	0.650000	0.86243	CAC	C|0.849;G|0.151	0.151	strong		0.488	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284	
IFT122	55764	hgsc.bcm.edu	37	3	129214358	129214358	+	Missense_Mutation	SNP	T	T	C	rs73204230		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129214358T>C	ENST00000348417.2	+	18	2193	c.2116T>C	c.(2116-2118)Ttc>Ctc	p.F706L	IFT122_ENST00000440957.2_Missense_Mutation_p.F497L|IFT122_ENST00000504021.1_Missense_Mutation_p.F582L|IFT122_ENST00000431818.2_Missense_Mutation_p.F556L|IFT122_ENST00000513932.1_3'UTR|IFT122_ENST00000349441.2_Missense_Mutation_p.F595L|IFT122_ENST00000296266.3_Missense_Mutation_p.F757L|IFT122_ENST00000347300.2_Missense_Mutation_p.F647L|IFT122_ENST00000507564.1_Missense_Mutation_p.F698L	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	706					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						CCAGGGGAAGTTCCATGAGGC	0.498																																					p.F757L		Atlas-SNP	.											IFT122,colon,carcinoma,0,2	IFT122	117	2	0			c.T2269C						scavenged	.						108.0	92.0	98.0					3																	129214358		2203	4300	6503	SO:0001583	missense	55764	exon19			GGGAAGTTCCATG	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.2116T>C	3.37:g.129214358T>C	ENSP00000324005:p.Phe706Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	4	0.0298507	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	37	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	T	18.27	3.586407	0.66105	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000454840;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957;ENST00000509522;ENST00000507221	D;D;D;D;T;D;D;D;T	0.87412	-2.25;-2.25;-2.25;-2.25;0.39;-2.25;-2.25;-2.25;0.51	5.29	5.29	0.74685	.	0.047626	0.85682	D	0.000000	D	0.92143	0.7509	M	0.83118	2.625	0.58432	D	0.999999	B;B;D;B;B;B;B;B;B	0.61697	0.001;0.103;0.99;0.024;0.26;0.136;0.041;0.001;0.002	B;B;P;B;B;B;B;B;B	0.60541	0.004;0.03;0.876;0.057;0.117;0.191;0.17;0.002;0.004	D	0.92052	0.5649	10	0.44086	T	0.13	-26.7424	12.0946	0.53747	0.0:0.0:0.1434:0.8566	.	497;698;93;582;546;595;647;706;757	E9PDG2;E7EQF4;B3KT43;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;.;IF122_HUMAN;.	L	647;757;698;647;556;582;595;706;546;497;203;68	ENSP00000323973:F647L;ENSP00000296266:F757L;ENSP00000425536:F698L;ENSP00000410946:F556L;ENSP00000422179:F582L;ENSP00000324165:F595L;ENSP00000324005:F706L;ENSP00000401569:F497L;ENSP00000424727:F203L	ENSP00000296266:F757L	F	+	1	0	IFT122	130697048	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.917000	0.69989	2.107000	0.64212	0.533000	0.62120	TTC	T|0.500;C|0.500	0.500	strong		0.498	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
COL4A1	1282	hgsc.bcm.edu	37	13	110818598	110818598	+	Missense_Mutation	SNP	T	T	G	rs3742207	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:110818598T>G	ENST00000375820.4	-	45	4123	c.4002A>C	c.(4000-4002)caA>caC	p.Q1334H	COL4A1_ENST00000467182.1_5'Flank	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1334	Triple-helical region.		Q -> H (in dbSNP:rs3742207). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21527998}.		axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CCGGGACGCCTTGATCGCCTT	0.473													T|||	1444	0.288339	0.2882	0.2334	5008	,	,		18983	0.2629		0.325	False		,,,				2504	0.316				p.Q1334H		Atlas-SNP	.											.	COL4A1	372	.	0			c.A4002C	GRCh37	CM083606	COL4A1	M	rs3742207	PASS	.	T	HIS/GLN	1243,3163	428.5+/-341.9	179,885,1139	183.0	167.0	173.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4002	-1.2	0.9	13	dbSNP_107	173	2935,5665	457.2+/-364.3	501,1933,1866	yes	missense	COL4A1	NM_001845.4	24	680,2818,3005	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	34.1279,28.2115,32.1236	benign	1334/1670	110818598	4178,8828	2203	4300	6503	SO:0001583	missense	1282	exon45			GACGCCTTGATCG	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.4002A>C	13.37:g.110818598T>G	ENSP00000364979:p.Gln1334His	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	198	198	1	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	37	CCDS9511.1	639	0.2925824175824176	142	0.2886178861788618	89	0.24585635359116023	142	0.24825174825174826	266	0.35092348284960423	T	6.850	0.526111	0.13066	0.282115	0.341279	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198	D	0.93307	-3.2	4.68	-1.19	0.09585	.	0.072729	0.56097	D	0.000024	T	0.00012	0.0000	L	0.33093	0.98	0.09310	P	0.9999999999992717	B	0.29988	0.264	B	0.37550	0.253	T	0.04065	-1.0980	9	0.39692	T	0.17	.	10.2129	0.43152	0.0:0.3302:0.0:0.6698	rs3742207;rs17517176;rs61457243;rs3742207	1334	P02462	CO4A1_HUMAN	H	977;1334;983	ENSP00000364979:Q1334H	ENSP00000364973:Q977H	Q	-	3	2	COL4A1	109616599	1.000000	0.71417	0.874000	0.34290	0.050000	0.14768	0.460000	0.21924	-0.086000	0.12550	-1.070000	0.02257	CAA	T|0.688;G|0.312	0.312	strong		0.473	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
NPLOC4	55666	hgsc.bcm.edu	37	17	79589242	79589242	+	Silent	SNP	G	G	A	rs6565604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79589242G>A	ENST00000331134.6	-	3	374	c.159C>T	c.(157-159)acC>acT	p.T53T	NPLOC4_ENST00000539314.1_5'UTR|NPLOC4_ENST00000374747.5_Silent_p.T53T	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	53					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			TTATCTCTCCGGTCTTGTTTC	0.433													G|||	3219	0.642772	0.7065	0.6628	5008	,	,		17313	0.7768		0.4076	False		,,,				2504	0.6462				p.T53T		Atlas-SNP	.											.	NPLOC4	27	.	0			c.C159T						PASS	.	G		2526,1202		854,818,192	113.0	108.0	110.0		159	-7.4	1.0	17	dbSNP_116	110	3762,4440		868,2026,1207	no	coding-synonymous	NPLOC4	NM_017921.2		1722,2844,1399	AA,AG,GG		45.8669,32.2425,47.2925		53/609	79589242	6288,5642	1864	4101	5965	SO:0001819	synonymous_variant	55666	exon3			CTCTCCGGTCTTG	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.159C>T	17.37:g.79589242G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	85	50	0.588235	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Silent	SNP	ENST00000331134.6	37	CCDS45812.1																																																																																			G|0.403;A|0.597	0.597	strong		0.433	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1		
PGBD1	84547	hgsc.bcm.edu	37	6	28269663	28269663	+	Missense_Mutation	SNP	A	A	G	rs1997660	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28269663A>G	ENST00000405948.2	+	7	2452	c.2032A>G	c.(2032-2034)Ata>Gta	p.I678V	PGBD1_ENST00000259883.3_Missense_Mutation_p.I678V	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	678			I -> V (in dbSNP:rs1997660).			membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						TGATTTCCGAATAGAAGAAAA	0.403													G|||	2963	0.591653	0.9501	0.4597	5008	,	,		21228	0.6012		0.3091	False		,,,				2504	0.4816				p.I678V		Atlas-SNP	.											.	PGBD1	106	.	0			c.A2032G						PASS	.	G	VAL/ILE,VAL/ILE	3672,734	301.8+/-287.1	1540,592,71	127.0	130.0	129.0		2032,2032	3.6	0.7	6	dbSNP_92	129	2750,5850	680.9+/-403.7	452,1846,2002	yes	missense,missense	PGBD1	NM_001184743.1,NM_032507.3	29,29	1992,2438,2073	GG,GA,AA		31.9767,16.6591,49.3772	benign,benign	678/810,678/810	28269663	6422,6584	2203	4300	6503	SO:0001583	missense	84547	exon7			TTCCGAATAGAAG	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.2032A>G	6.37:g.28269663A>G	ENSP00000385213:p.Ile678Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	188	99	0.526596	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	1199	0.548992673992674	461	0.9369918699186992	169	0.46685082872928174	346	0.6048951048951049	223	0.2941952506596306	G	0.005	-2.168088	0.00315	0.833409	0.319767	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.16743	2.32;2.32	4.48	3.61	0.41365	.	0.600559	0.12776	N	0.440090	T	0.01124	0.0037	N	0.01109	-1.01	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48502	-0.9030	9	0.02654	T	1	-9.75	7.387	0.26888	0.1999:0.0:0.8001:0.0	rs1997660;rs41538181;rs52791434;rs60280230;rs1997660	678	Q96JS3	PGBD1_HUMAN	V	678	ENSP00000385213:I678V;ENSP00000259883:I678V	ENSP00000259883:I678V	I	+	1	0	PGBD1	28377642	0.082000	0.21442	0.675000	0.29917	0.339000	0.28857	1.091000	0.30915	0.640000	0.30582	-0.186000	0.12905	ATA	A|0.464;G|0.536	0.536	strong		0.403	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
CEP135	9662	hgsc.bcm.edu	37	4	56874517	56874517	+	Missense_Mutation	SNP	A	A	C	rs3214045	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:56874517A>C	ENST00000257287.4	+	18	2429	c.2305A>C	c.(2305-2307)Ata>Cta	p.I769L		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	769			I -> L (in dbSNP:rs3214045).		centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					TCAAATGAAGATAATGATCTC	0.289													a|||	697	0.139177	0.087	0.1182	5008	,	,		18162	0.0913		0.2714	False		,,,				2504	0.138				p.I769L		Atlas-SNP	.											.	CEP135	115	.	0			c.A2305C						PASS	.	C	LEU/ILE	529,3877	237.1+/-249.0	28,473,1702	77.0	80.0	79.0		2305	-6.1	0.0	4	dbSNP_106	79	2212,6386	373.7+/-337.1	267,1678,2354	yes	missense	CEP135	NM_025009.3	5	295,2151,4056	CC,CA,AA		25.7269,12.0064,21.0781	benign	769/1141	56874517	2741,10263	2203	4299	6502	SO:0001583	missense	9662	exon18			ATGAAGATAATGA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"""KIAA0635"", ""centrosomal protein 4"""	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.2305A>C	4.37:g.56874517A>C	ENSP00000257287:p.Ile769Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	360	0.16483516483516483	40	0.08130081300813008	45	0.12430939226519337	63	0.11013986013986014	212	0.2796833773087071	a	0.064	-1.216297	0.01542	0.120064	0.257269	ENSG00000174799	ENST00000257287	T	0.16597	2.33	5.62	-6.14	0.02111	.	0.837336	0.11284	N	0.580002	T	0.00012	0.0000	N	0.00879	-1.12	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48525	-0.9028	9	0.27082	T	0.32	.	7.6315	0.28243	0.3133:0.323:0.3638:0.0	rs3214045;rs52815254;rs61495232;rs3214045	769	Q66GS9	CP135_HUMAN	L	769	ENSP00000257287:I769L	ENSP00000257287:I769L	I	+	1	0	CEP135	56569274	0.062000	0.20869	0.003000	0.11579	0.010000	0.07245	-1.014000	0.03641	-0.994000	0.03463	-3.568000	0.00029	ATA	A|0.815;C|0.185;G|0.000	0.185	strong		0.289	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009	
GRPR	2925	hgsc.bcm.edu	37	X	16168467	16168467	+	Silent	SNP	T	T	C	rs4986945	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:16168467T>C	ENST00000380289.2	+	2	851	c.453T>C	c.(451-453)tcT>tcC	p.S151S	RP11-431J24.2_ENST00000422438.1_RNA|RP11-431J24.2_ENST00000454712.2_RNA|RP11-431J24.2_ENST00000435789.1_RNA	NM_005314.2	NP_005305.1	P30550	GRPR_HUMAN	gastrin-releasing peptide receptor	151					cell proliferation (GO:0008283)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cell proliferation (GO:0042127)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)|G-protein coupled peptide receptor activity (GO:0008528)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(3)|stomach(1)|upper_aerodigestive_tract(3)	25	Hepatocellular(33;0.183)					TCCAGGCCTCTCATGCCCTGA	0.507													T|||	1038	0.274967	0.2307	0.2089	3775	,	,		13968	0.122		0.2545	False		,,,				2504	0.2137				p.S151S		Atlas-SNP	.											.	GRPR	51	.	0			c.T453C						PASS	.	T		1282,2553		182,710,208,740,363	92.0	90.0	91.0		453	0.9	1.0	X	dbSNP_111	91	2321,4407		299,1083,640,1046,1232	no	coding-synonymous	GRPR	NM_005314.2		481,1793,848,1786,1595	CC,CT,C,TT,T		34.4976,33.4289,34.1096		151/385	16168467	3603,6960	2203	4300	6503	SO:0001819	synonymous_variant	2925	exon2			GGCCTCTCATGCC		CCDS14174.1	Xp22.2	2014-02-21			ENSG00000126010	ENSG00000126010		"""GPCR / Class A : Bombesin receptors"""	4609	protein-coding gene	gene with protein product	"""bombesin receptor 2"""	305670					Standard	NM_005314		Approved	BB2	uc004cxj.3	P30550	OTTHUMG00000021189	ENST00000380289.2:c.453T>C	X.37:g.16168467T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	137	128	0.934307	NM_005314	B2R910	Silent	SNP	ENST00000380289.2	37	CCDS14174.1																																																																																			T|0.694;C|0.306	0.306	strong		0.507	GRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055901.1	NM_005314	
PGBD1	84547	hgsc.bcm.edu	37	6	28264692	28264692	+	Missense_Mutation	SNP	C	C	G	rs3800325	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28264692C>G	ENST00000405948.2	+	5	1162	c.742C>G	c.(742-744)Cag>Gag	p.Q248E	PGBD1_ENST00000259883.3_Missense_Mutation_p.Q248E	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	248			Q -> E (in dbSNP:rs3800325).			membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						GAACTCAGCTCAGGAGACAGT	0.562													C|||	1321	0.263778	0.4743	0.1787	5008	,	,		18210	0.1448		0.1372	False		,,,				2504	0.2924				p.Q248E		Atlas-SNP	.											.	PGBD1	106	.	0			c.C742G						PASS	.	C	GLU/GLN,GLU/GLN	1677,2729	510.6+/-367.6	333,1011,859	109.0	101.0	104.0		742,742	2.0	0.0	6	dbSNP_107	104	1097,7503	228.4+/-263.5	60,977,3263	yes	missense,missense	PGBD1	NM_001184743.1,NM_032507.3	29,29	393,1988,4122	GG,GC,CC		12.7558,38.0617,21.3286	benign,benign	248/810,248/810	28264692	2774,10232	2203	4300	6503	SO:0001583	missense	84547	exon5			TCAGCTCAGGAGA	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.742C>G	6.37:g.28264692C>G	ENSP00000385213:p.Gln248Glu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	458	0.2097069597069597	227	0.4613821138211382	67	0.1850828729281768	73	0.12762237762237763	91	0.12005277044854881	C	7.843	0.722359	0.15439	0.380617	0.127558	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.01505	4.82;4.82	3.81	2.03	0.26663	.	0.573096	0.13206	N	0.405600	T	0.00468	0.0015	N	0.24115	0.695	0.80722	P	0.0	B	0.29037	0.231	B	0.19666	0.026	T	0.48364	-0.9042	9	0.34782	T	0.22	-6.1494	5.9479	0.19229	0.0:0.7644:0.0:0.2356	rs3800325;rs57265126;rs3800325	248	Q96JS3	PGBD1_HUMAN	E	248	ENSP00000385213:Q248E;ENSP00000259883:Q248E	ENSP00000259883:Q248E	Q	+	1	0	PGBD1	28372671	0.000000	0.05858	0.003000	0.11579	0.477000	0.33069	0.589000	0.23939	0.579000	0.29504	0.655000	0.94253	CAG	C|0.785;G|0.215	0.215	strong		0.562	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
MAP3K1	4214	hgsc.bcm.edu	37	5	56177843	56177843	+	Missense_Mutation	SNP	C	C	G	rs45556841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:56177843C>G	ENST00000399503.3	+	14	2816	c.2816C>G	c.(2815-2817)tCt>tGt	p.S939C		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	939					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GTAGGACCTTCTAGTTcaaca	0.423													C|||	37	0.00738818	0.0015	0.0259	5008	,	,		20934	0.0		0.0139	False		,,,				2504	0.0031				p.S939C		Atlas-SNP	.											.	MAP3K1	355	.	0			c.C2816G						PASS	.	C	CYS/SER	20,3788		0,20,1884	73.0	70.0	71.0		2816	3.9	1.0	5	dbSNP_127	71	191,8093		5,181,3956	yes	missense	MAP3K1	NM_005921.1	112	5,201,5840	GG,GC,CC		2.3056,0.5252,1.745	benign	939/1513	56177843	211,11881	1904	4142	6046	SO:0001583	missense	4214	exon14			GACCTTCTAGTTC	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.2816C>G	5.37:g.56177843C>G	ENSP00000382423:p.Ser939Cys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	139	75	0.539568	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	23	0.010531135531135532	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	9	0.011873350923482849	C	11.21	1.571845	0.28003	0.005252	0.023056	ENSG00000095015	ENST00000399503	T	0.32272	1.46	5.71	3.87	0.44632	.	0.150855	0.47093	D	0.000259	T	0.04182	0.0116	N	0.08118	0	0.26331	N	0.977519	B	0.24368	0.102	B	0.27262	0.078	T	0.15578	-1.0432	10	0.87932	D	0	.	13.0984	0.59206	0.1278:0.7495:0.1227:0.0	rs45556841	939	Q13233	M3K1_HUMAN	C	939	ENSP00000382423:S939C	ENSP00000382423:S939C	S	+	2	0	MAP3K1	56213600	0.989000	0.36119	0.986000	0.45419	0.965000	0.64279	2.061000	0.41403	1.414000	0.47017	0.655000	0.94253	TCT	C|0.985;G|0.015	0.015	strong		0.423	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
THAP10	56906	hgsc.bcm.edu	37	15	71184278	71184278	+	Silent	SNP	G	G	T	rs2959174	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:71184278G>T	ENST00000249861.4	-	1	846	c.334C>A	c.(334-336)Cga>Aga	p.R112R	LRRC49_ENST00000544974.2_Intron|LRRC49_ENST00000560369.1_5'Flank|LRRC49_ENST00000260382.5_5'Flank|LRRC49_ENST00000443425.2_5'Flank	NM_020147.3	NP_064532.1	Q9P2Z0	THA10_HUMAN	THAP domain containing 10	112							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						AGCTCTCCTCGCGTGTCCAGG	0.687													T|||	2750	0.549121	0.7731	0.2954	5008	,	,		14020	0.5823		0.4066	False		,,,				2504	0.5389				p.R112R		Atlas-SNP	.											.	THAP10	19	.	0			c.C334A						PASS	.	T		3117,1281	427.2+/-341.4	1113,891,195	33.0	34.0	34.0		334	-1.1	0.0	15	dbSNP_101	34	3501,5093	620.8+/-397.1	700,2101,1496	no	coding-synonymous	THAP10	NM_020147.3		1813,2992,1691	TT,TG,GG		40.7377,29.1269,49.061		112/258	71184278	6618,6374	2199	4297	6496	SO:0001819	synonymous_variant	56906	exon1			CTCCTCGCGTGTC	AL360202	CCDS10237.1	15q22.32	2013-01-25			ENSG00000129028	ENSG00000129028		"""THAP (C2CH-type zinc finger) domain containing"""	23193	protein-coding gene	gene with protein product		612538				12575992	Standard	NM_020147		Approved		uc002asv.3	Q9P2Z0	OTTHUMG00000133388	ENST00000249861.4:c.334C>A	15.37:g.71184278G>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_020147	B2R8R0	Silent	SNP	ENST00000249861.4	37	CCDS10237.1																																																																																			G|0.471;T|0.529	0.529	strong		0.687	THAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257242.2	NM_020147	
IRX4	50805	hgsc.bcm.edu	37	5	1878440	1878440	+	Silent	SNP	C	C	T	rs1689717	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1878440C>T	ENST00000505790.1	-	6	1659	c.1203G>A	c.(1201-1203)gcG>gcA	p.A401A	IRX4_ENST00000505938.1_5'Flank|IRX4_ENST00000231357.2_Silent_p.A401A|IRX4_ENST00000513692.1_Silent_p.A401A	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	401					establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		CCGCAGGGGCCGCGGGACCTT	0.721													c|||	552	0.110224	0.2451	0.0749	5008	,	,		12499	0.006		0.1014	False		,,,				2504	0.0695				p.A401A		Atlas-SNP	.											.	IRX4	45	.	0			c.G1203A						PASS	.			879,3265		87,705,1280	5.0	8.0	7.0		1203	-7.3	0.0	5	dbSNP_89	7	654,7600		25,604,3498	no	coding-synonymous	IRX4	NM_016358.2		112,1309,4778	TT,TC,CC		7.9234,21.2114,12.3649		401/520	1878440	1533,10865	2072	4127	6199	SO:0001819	synonymous_variant	50805	exon5			AGGGGCCGCGGGA	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"""Homeoboxes / TALE class"""	6129	protein-coding gene	gene with protein product		606199	"""iroquois homeobox protein 4"""			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.1203G>A	5.37:g.1878440C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	24	18	0.75	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Silent	SNP	ENST00000505790.1	37	CCDS3867.1																																																																																			C|0.900;T|0.100	0.100	strong		0.721	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358	
CCDC149	91050	hgsc.bcm.edu	37	4	24836619	24836619	+	Silent	SNP	C	C	T	rs16876194	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:24836619C>T	ENST00000389609.4	-	9	914	c.771G>A	c.(769-771)caG>caA	p.Q257Q	CCDC149_ENST00000428116.2_Intron|CCDC149_ENST00000502801.1_Intron|CCDC149_ENST00000504487.1_Silent_p.Q257Q	NM_173463.4	NP_775734.2	Q6ZUS6	CC149_HUMAN	coiled-coil domain containing 149	202										cervix(1)|endometrium(1)|large_intestine(2)|lung(3)	7		Breast(46;0.173)				TGGATTTACCCTGGCCCTTCG	0.473													C|||	403	0.0804712	0.1611	0.0576	5008	,	,		18114	0.002		0.0835	False		,,,				2504	0.0654				p.Q257Q		Atlas-SNP	.											.	CCDC149	41	.	0			c.G771A						PASS	.	C	,	679,3727	286.3+/-278.7	51,577,1575	130.0	123.0	125.0		771,771	3.6	0.9	4	dbSNP_123	125	698,7902	173.2+/-223.7	20,658,3622	no	coding-synonymous,coding-synonymous	CCDC149	NM_001130726.2,NM_173463.4	,	71,1235,5197	TT,TC,CC		8.1163,15.4108,10.5874	,	257/530,257/530	24836619	1377,11629	2203	4300	6503	SO:0001819	synonymous_variant	91050	exon9			TTTACCCTGGCCC		CCDS33967.1, CCDS47036.1, CCDS33967.2	4p15.2	2008-03-03				ENSG00000181982			25405	protein-coding gene	gene with protein product						17457313	Standard	NM_173463		Approved	DKFZp761B107	uc003grc.3	Q6ZUS6		ENST00000389609.4:c.771G>A	4.37:g.24836619C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	121	56	0.46281	NM_173463	A6NJE7|B4DK90|B4DZG3|G5EA04|Q6NW41|Q8N3K8	Silent	SNP	ENST00000389609.4	37	CCDS33967.2																																																																																			C|0.904;T|0.096	0.096	strong		0.473	CCDC149-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360157.1	NM_173463	
ASXL2	55252	hgsc.bcm.edu	37	2	25972936	25972936	+	Missense_Mutation	SNP	C	C	T	rs192716734	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:25972936C>T	ENST00000435504.4	-	12	1782	c.1489G>A	c.(1489-1491)Gct>Act	p.A497T	ASXL2_ENST00000272341.4_Missense_Mutation_p.A237T|ASXL2_ENST00000336112.4_Missense_Mutation_p.A469T|ASXL2_ENST00000404843.1_Missense_Mutation_p.A237T			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	497					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCTGTTCAGCAGAGGTGACT	0.453													C|||	7	0.00139776	0.0	0.0058	5008	,	,		20730	0.0		0.003	False		,,,				2504	0.0				p.A497T		Atlas-SNP	.											.	ASXL2	217	.	0			c.G1489A						PASS	.	C	THR/ALA	2,3826		0,2,1912	173.0	158.0	163.0		1489	4.2	1.0	2		163	44,8222		1,42,4090	yes	missense	ASXL2	NM_018263.4	58	1,44,6002	TT,TC,CC		0.5323,0.0522,0.3804	benign	497/1436	25972936	46,12048	1914	4133	6047	SO:0001583	missense	55252	exon11			GTTCAGCAGAGGT			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"""additional sex combs like 2 (Drosophila)"""			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.1489G>A	2.37:g.25972936C>T	ENSP00000391447:p.Ala497Thr	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	C	11.46	1.644550	0.29246	5.22E-4	0.005323	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	T;T;T;T	0.18338	2.24;2.24;2.22;2.22	6.01	4.22	0.49857	.	0.445872	0.26951	N	0.021661	T	0.10208	0.0250	L	0.48362	1.52	0.26143	N	0.980241	B;B	0.17852	0.006;0.024	B;B	0.13407	0.005;0.009	T	0.19811	-1.0294	10	0.14252	T	0.57	-2.402	11.1814	0.48631	0.0:0.8518:0.0:0.1482	.	237;497	Q76L83-2;Q76L83	.;ASXL2_HUMAN	T	497;469;237;237	ENSP00000391447:A497T;ENSP00000337250:A469T;ENSP00000383920:A237T;ENSP00000272341:A237T	ENSP00000272341:A237T	A	-	1	0	ASXL2	25826440	0.000000	0.05858	1.000000	0.80357	0.627000	0.37826	0.440000	0.21592	1.566000	0.49654	-0.142000	0.14014	GCT	C|0.997;T|0.003	0.003	strong		0.453	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263	
HSPG2	3339	hgsc.bcm.edu	37	1	22160043	22160043	+	Missense_Mutation	SNP	C	C	T	rs2229493	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22160043C>T	ENST00000374695.3	-	79	10974	c.10895G>A	c.(10894-10896)cGa>cAa	p.R3632Q	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3632	Ig-like C2-type 22.		R -> Q (in dbSNP:rs2229493). {ECO:0000269|PubMed:1730768}.		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GTCCTGGGGTCGGACTGAGGG	0.622													c|||	430	0.0858626	0.1672	0.0504	5008	,	,		19458	0.0		0.0676	False		,,,				2504	0.1084				p.R3632Q		Atlas-SNP	.											.	HSPG2	311	.	0			c.G10895A						PASS	.	T	GLN/ARG	763,3643	310.8+/-291.8	66,631,1506	62.0	49.0	54.0		10895	-1.1	0.1	1	dbSNP_98	54	661,7939	166.7+/-218.6	26,609,3665	yes	missense	HSPG2	NM_005529.5	43	92,1240,5171	TT,TC,CC		7.686,17.3173,10.9488	benign	3632/4392	22160043	1424,11582	2203	4300	6503	SO:0001583	missense	3339	exon79			TGGGGTCGGACTG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.10895G>A	1.37:g.22160043C>T	ENSP00000363827:p.Arg3632Gln	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	194	90	0.463918	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	165	0.07554945054945054	93	0.18902439024390244	23	0.06353591160220995	0	0.0	49	0.06464379947229551	c	3.442	-0.113760	0.06881	0.173173	0.07686	ENSG00000142798	ENST00000374695;ENST00000426143	T;T	0.65364	-0.15;2.78	4.19	-1.15	0.09709	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.976806	0.08314	N	0.964930	T	0.00073	0.0002	N	0.11673	0.155	0.80722	P	0.0	B;B	0.23806	0.003;0.091	B;B	0.19666	0.015;0.026	T	0.09640	-1.0665	9	0.14252	T	0.57	.	8.8503	0.35194	0.0:0.4632:0.0:0.5368	rs2229493;rs11552566;rs52806904;rs2229493	1572;3632	Q59EG0;P98160	.;PGBM_HUMAN	Q	3632;184	ENSP00000363827:R3632Q;ENSP00000392022:R184Q	ENSP00000363827:R3632Q	R	-	2	0	HSPG2	22032630	0.001000	0.12720	0.061000	0.19648	0.123000	0.20343	-0.065000	0.11617	-0.314000	0.08716	-1.984000	0.00453	CGA	T|0.098;G|0.000;C|0.902;A|0.000	0.098	strong		0.622	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
SIRPB1	10326	hgsc.bcm.edu	37	20	1600524	1600524	+	Missense_Mutation	SNP	T	T	C	rs1535882	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:1600524T>C	ENST00000381605.4	-	1	131	c.67A>G	c.(67-69)Aga>Gga	p.R23G	SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000381603.3_Missense_Mutation_p.R23G|RP4-576H24.4_ENST00000564763.1_Missense_Mutation_p.R23G|SIRPB1_ENST00000279477.7_Missense_Mutation_p.R23G|SIRPB1_ENST00000568365.1_Missense_Mutation_p.R23G	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	23			R -> G (in dbSNP:rs1535882).		cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CCTGTGAGTCTCCCCAGCAGT	0.562													-|||	1217	0.243011	0.1263	0.4164	5008	,	,		19223	0.2212		0.3499	False		,,,				2504	0.1902				p.R23G		Atlas-SNP	.											SIRPB1_ENST00000279477,NS,adenoma,0,2	SIRPB1	83	2	0			c.A67G						PASS	.	-	GLY/ARG,GLY/ARG,GLY/ARG	714,3692		67,580,1556	97.0	87.0	90.0		67,67,67	0.2	0.0	20	dbSNP_88	90	2946,5654		513,1920,1867	yes	missense,missense,missense	SIRPB1	NM_001083910.2,NM_001135844.2,NM_006065.3	125,125,125	580,2500,3423	CC,CT,TT		34.2558,16.2052,28.1409	benign,benign,benign	23/182,23/399,23/399	1600524	3660,9346	2203	4300	6503	SO:0001583	missense	10326	exon1			TGAGTCTCCCCAG	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.67A>G	20.37:g.1600524T>C	ENSP00000371018:p.Arg23Gly	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_001083910	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	606	0.2774725274725275	71	0.1443089430894309	134	0.3701657458563536	131	0.229020979020979	270	0.3562005277044855	.	0.502	-0.870473	0.02570	0.162052	0.342558	ENSG00000101307	ENST00000381605;ENST00000381603;ENST00000279477;ENST00000381596	T;T;T	0.09630	4.47;4.83;2.96	0.15	0.15	0.14883	Immunoglobulin-like (2);	3.043770	0.01395	N	0.013381	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.48917	-0.8992	8	0.25106	T	0.35	.	.	.	.	rs1535882;rs52800175;rs60047757;rs1535882	23;23;23	O00241;Q5TFQ8;O00241-2	SIRB1_HUMAN;SIRBL_HUMAN;.	G	23	ENSP00000371018:R23G;ENSP00000371016:R23G;ENSP00000279477:R23G	ENSP00000279477:R23G	R	-	1	2	SIRPB1	1548524	0.145000	0.22656	0.006000	0.13384	0.002000	0.02628	-0.970000	0.03810	-1.047000	0.03242	-1.042000	0.02369	AGA	T|0.729;C|0.271	0.271	strong		0.562	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
CLUH	23277	hgsc.bcm.edu	37	17	2595964	2595964	+	Silent	SNP	G	G	A	rs2302199	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:2595964G>A	ENST00000570628.2	-	21	3327	c.3222C>T	c.(3220-3222)gcC>gcT	p.A1074A	CLUH_ENST00000538975.1_Silent_p.A1074A|CLUH_ENST00000435359.1_Silent_p.A1074A			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	1074					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											GCTGGCTGCTGGCGAAGCAGT	0.721													G|||	2291	0.457468	0.5219	0.3689	5008	,	,		14392	0.501		0.4235	False		,,,				2504	0.4233				p.A1074A		Atlas-SNP	.											KIAA0664_ENST00000322335,NS,carcinoma,0,2	.	.	2	0			c.C3222T						PASS	.	G		2207,2129		583,1041,544	21.0	28.0	26.0		3222	3.2	1.0	17	dbSNP_100	26	3114,5350		599,1916,1717	no	coding-synonymous	KIAA0664	NM_015229.3		1182,2957,2261	AA,AG,GG		36.7911,49.1006,41.5703		1074/1310	2595964	5321,7479	2168	4232	6400	SO:0001819	synonymous_variant	23277	exon21			GCTGCTGGCGAAG	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"""KIAA0664"""	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.3222C>T	17.37:g.2595964G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	46	28	0.608696	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	37	CCDS45572.1																																																																																			G|0.545;A|0.455	0.455	strong		0.721	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
GGT1	2678	hgsc.bcm.edu	37	22	25016442	25016442	+	Missense_Mutation	SNP	C	C	T	rs3895576		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25016442C>T	ENST00000400382.1	+	8	1285	c.530C>T	c.(529-531)gCc>gTc	p.A177V	GGT1_ENST00000406383.2_Missense_Mutation_p.A177V|GGT1_ENST00000400380.1_Missense_Mutation_p.A177V|GGT1_ENST00000248923.4_Missense_Mutation_p.A177V|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400383.1_Missense_Mutation_p.A177V			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	177			A -> V (in dbSNP:rs3895576).		arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.A177V(1)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	TTGGCGGCAGCCCTGGAAAAC	0.687																																					p.A177V		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	prostate(1)	c.C530T						scavenged	.						25.0	28.0	27.0					22																	25016442		1906	4095	6001	SO:0001583	missense	2678	exon8			CGGCAGCCCTGGA	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.530C>T	22.37:g.25016442C>T	ENSP00000383232:p.Ala177Val	Somatic	380	7	0.0184211		WXS	Illumina HiSeq	Phase_I	396	16	0.040404	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	14.08	2.430183	0.43122	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383	T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23	3.35	3.35	0.38373	.	0.067565	0.64402	U	0.000018	T	0.09730	0.0239	L	0.56340	1.77	0.09310	N	1	B	0.12013	0.005	B	0.20577	0.03	T	0.15065	-1.0450	10	0.46703	T	0.11	-6.9103	10.3241	0.43783	0.0:0.7987:0.2013:0.0	rs3895576;rs4049845	177	P19440	GGT1_HUMAN	V	177	ENSP00000248923:A177V;ENSP00000393537:A177V;ENSP00000383232:A177V;ENSP00000383233:A177V;ENSP00000383231:A177V;ENSP00000385975:A177V	ENSP00000248923:A177V	A	+	2	0	GGT1	23346442	0.997000	0.39634	0.256000	0.24389	0.047000	0.14425	3.457000	0.53007	1.588000	0.49971	0.455000	0.32223	GCC	.	.	weak		0.687	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
C5orf60	285679	hgsc.bcm.edu	37	5	179069468	179069468	+	Missense_Mutation	SNP	A	A	G	rs62405726	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:179069468A>G	ENST00000448248.2	-	5	731	c.706T>C	c.(706-708)Tgg>Cgg	p.W236R	C5orf60_ENST00000506142.1_5'Flank	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	0	Ser-rich.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						CCCTGCCTCCACCTGCCTGCA	0.572													a|||	2302	0.459665	0.2935	0.5548	5008	,	,		17330	0.6806		0.2753	False		,,,				2504	0.5787				p.W236R		Atlas-SNP	.											C5orf60,caecum,carcinoma,+1,1	C5orf60	24	1	0			c.T706C						PASS	.						60.0	54.0	56.0					5																	179069468		692	1589	2281	SO:0001583	missense	285679	exon5			GCCTCCACCTGCC	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.706T>C	5.37:g.179069468A>G	ENSP00000404583:p.Trp236Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	37	CCDS47353.1	.	.	.	.	.	.	.	.	.	.	a	0.017	-1.489861	0.01018	.	.	ENSG00000204661	ENST00000448248	T	0.19938	2.11	0.517	-1.03	0.10102	.	.	.	.	.	T	0.21347	0.0514	.	.	.	0.80722	P	0.0	D;D	0.58268	0.982;0.982	P;P	0.61592	0.891;0.891	T	0.25745	-1.0123	6	0.07175	T	0.84	.	.	.	.	rs62405726	240;236	A6NFR6-2;A6NFR6-4	.;.	R	236	ENSP00000404583:W236R	ENSP00000404583:W236R	W	-	1	0	C5orf60	179002074	0.006000	0.16342	0.002000	0.10522	0.006000	0.05464	0.475000	0.22164	-0.672000	0.05266	-0.967000	0.02615	TGG	A|0.713;G|0.287	0.287	strong		0.572	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
DNAH3	55567	hgsc.bcm.edu	37	16	20948142	20948142	+	Silent	SNP	A	A	G	rs140126023	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20948142A>G	ENST00000261383.3	-	60	11687	c.11688T>C	c.(11686-11688)aaT>aaC	p.N3896N	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3896					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CTCGGCCAAGATTGATGAGGC	0.562													A|||	2	0.000399361	0.0	0.0	5008	,	,		17157	0.0		0.001	False		,,,				2504	0.001				p.N3896N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T11688C						PASS	.	A		6,4396	11.4+/-27.6	0,6,2195	59.0	52.0	54.0		11688	2.0	0.6	16	dbSNP_134	54	29,8571	21.0+/-64.5	0,29,4271	no	coding-synonymous	DNAH3	NM_017539.1		0,35,6466	GG,GA,AA		0.3372,0.1363,0.2692		3896/4117	20948142	35,12967	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon60			GCCAAGATTGATG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.11688T>C	16.37:g.20948142A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	47	15	0.319149	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			A|0.998;G|0.002	0.002	strong		0.562	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
CEP89	84902	hgsc.bcm.edu	37	19	33370070	33370070	+	Nonstop_Mutation	SNP	A	A	G	rs745961	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:33370070A>G	ENST00000305768.5	-	19	2438	c.2350T>C	c.(2350-2352)Tag>Cag	p.*784Q	CTD-2085J24.4_ENST00000586628.2_lincRNA	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	0					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CGCAGATTCTAGCAGGTGGGG	0.637													G|||	823	0.164337	0.0703	0.1527	5008	,	,		13364	0.1071		0.334	False		,,,				2504	0.184				p.X784Q		Atlas-SNP	.											.	CEP89	82	.	0			c.T2350C						PASS	.	G	GLN/stop	480,3926	781.4+/-414.5	25,430,1748	56.0	54.0	55.0		2350	1.1	0.0	19	dbSNP_86	55	3049,5551	659.9+/-401.7	565,1919,1816	yes	stop-lost	CEP89	NM_032816.3		590,2349,3564	GG,GA,AA		35.4535,10.8942,27.1336		784/784	33370070	3529,9477	2203	4300	6503	SO:0001578	stop_lost	84902	exon19			GATTCTAGCAGGT	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.2350T>C	19.37:g.33370070A>G	ENSP00000306105:p.*784Gluext*8	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	401	0.18360805860805862	31	0.06300813008130081	66	0.18232044198895028	53	0.09265734265734266	251	0.3311345646437995	G	7.755	0.704137	0.15172	0.108942	0.354535	ENSG00000121289	ENST00000305768	.	.	.	4.59	1.07	0.20283	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.4374	0.21831	0.1629:0.2782:0.5589:0.0	rs745961;rs17272253;rs58732563;rs745961	.	.	.	Q	784	.	.	X	-	1	0	CEP89	38061910	0.003000	0.15002	0.001000	0.08648	0.001000	0.01503	0.663000	0.25053	-0.012000	0.14223	-2.506000	0.00189	TAG	A|0.778;G|0.222	0.222	strong		0.637	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
DHX57	90957	hgsc.bcm.edu	37	2	39082344	39082344	+	Missense_Mutation	SNP	T	T	C	rs7598922	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:39082344T>C	ENST00000295373.6	-	8	1886	c.1760A>G	c.(1759-1761)aAt>aGt	p.N587S	DHX57_ENST00000479345.2_5'Flank	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	587	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		N -> S (in dbSNP:rs7598922). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.				ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				AGGTGGTCCATTCAGAGAATC	0.428													T|||	2950	0.589058	0.3018	0.572	5008	,	,		15761	0.8026		0.6342	False		,,,				2504	0.7229				p.N587S	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.A1760G						PASS	.	T	SER/ASN	1533,2873	483.9+/-359.9	279,975,949	146.0	139.0	141.0		1760	1.6	0.9	2	dbSNP_116	141	5437,3163	655.2+/-401.2	1722,1993,585	yes	missense	DHX57	NM_198963.1	46	2001,2968,1534	CC,CT,TT		36.7791,34.7935,46.4093	benign	587/1387	39082344	6970,6036	2203	4300	6503	SO:0001583	missense	90957	exon8			GGTCCATTCAGAG	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.1760A>G	2.37:g.39082344T>C	ENSP00000295373:p.Asn587Ser	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	189	187	0.989418	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	1312	0.6007326007326007	152	0.3089430894308943	209	0.5773480662983426	461	0.8059440559440559	490	0.6464379947229552	T	7.504	0.653311	0.14580	0.347935	0.632209	ENSG00000163214	ENST00000295373	T	0.02395	4.31	5.26	1.59	0.23543	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.594351	0.15931	N	0.237700	T	0.00012	0.0000	N	0.05230	-0.09	0.44927	P	0.0020540000000000003	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.11329	0.004;0.004;0.006	T	0.04153	-1.0973	9	0.10636	T	0.68	.	9.1946	0.37220	0.0:0.2:0.0:0.8	rs7598922;rs17422506;rs52811978;rs57694271;rs7598922	587;587;587	Q6P158-2;Q6P158;B4DKW2	.;DHX57_HUMAN;.	S	587	ENSP00000295373:N587S	ENSP00000295373:N587S	N	-	2	0	DHX57	38935848	0.135000	0.22499	0.887000	0.34795	0.973000	0.67179	0.621000	0.24418	0.097000	0.17492	0.528000	0.53228	AAT	T|0.439;C|0.561	0.561	strong		0.428	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
C2orf73	129852	hgsc.bcm.edu	37	2	54562012	54562012	+	Missense_Mutation	SNP	C	C	A	rs55714450	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:54562012C>A	ENST00000398634.2	+	2	127	c.85C>A	c.(85-87)Cac>Aac	p.H29N	C2orf73_ENST00000405749.1_Intron|C2orf73_ENST00000491538.1_Intron	NM_001100396.1	NP_001093866.1	Q8N5S3	CB073_HUMAN	chromosome 2 open reading frame 73	29			H -> N (in dbSNP:rs55714450).							breast(2)	2						AGAAATTAAACACGAAGAAAA	0.303													C|||	1021	0.203874	0.1619	0.2954	5008	,	,		18549	0.0456		0.3419	False		,,,				2504	0.2168				p.H29N		Atlas-SNP	.											.	C2orf73	17	.	0			c.C85A						PASS	.	C	ASN/HIS	671,2967		80,511,1228	62.0	52.0	55.0		85	0.3	1.0	2	dbSNP_129	55	2761,5371		485,1791,1790	yes	missense	C2orf73	NM_001100396.1	68	565,2302,3018	AA,AC,CC		33.9523,18.4442,29.1589	benign	29/288	54562012	3432,8338	1819	4066	5885	SO:0001583	missense	129852	exon2			ATTAAACACGAAG	BC031669, AK097617	CCDS46285.1	2p16.2	2008-07-07			ENSG00000177994	ENSG00000177994			26861	protein-coding gene	gene with protein product						14702039	Standard	NM_001100396		Approved	FLJ40298	uc002rxt.1	Q8N5S3	OTTHUMG00000151826	ENST00000398634.2:c.85C>A	2.37:g.54562012C>A	ENSP00000381631:p.His29Asn	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	265	123	0.464151	NM_001100396	A0AV79|A0AV81|Q8N7V4	Missense_Mutation	SNP	ENST00000398634.2	37	CCDS46285.1	481	0.22023809523809523	78	0.15853658536585366	107	0.2955801104972376	22	0.038461538461538464	274	0.36147757255936674	C	1.011	-0.687753	0.03328	0.184442	0.339523	ENSG00000177994	ENST00000486488;ENST00000398634	T;T	0.31247	1.5;1.5	4.5	0.334	0.15948	.	0.885835	0.09662	N	0.772356	T	0.00012	0.0000	N	0.08118	0	0.52099	P	5.299999999996974E-5	B	0.09022	0.002	B	0.10450	0.005	T	0.46400	-0.9194	9	0.35671	T	0.21	-24.6075	1.7904	0.03050	0.1957:0.3112:0.3535:0.1395	rs55714450;rs62141760	29	Q8N5S3	CB073_HUMAN	N	35;29	ENSP00000417971:H35N;ENSP00000381631:H29N	ENSP00000381631:H29N	H	+	1	0	C2orf73	54415516	0.249000	0.23941	0.972000	0.41901	0.150000	0.21749	-0.629000	0.05508	0.169000	0.19679	-0.300000	0.09419	CAC	C|0.747;A|0.253	0.253	strong		0.303	C2orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324075.2	NM_001100396	
ASB2	51676	hgsc.bcm.edu	37	14	94417531	94417531	+	Missense_Mutation	SNP	T	T	C	rs11555542	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:94417531T>C	ENST00000315988.4	-	4	1038	c.550A>G	c.(550-552)Aac>Gac	p.N184D	MIR4506_ENST00000584693.1_RNA|ASB2_ENST00000555019.1_Missense_Mutation_p.N232D|ASB2_ENST00000556337.1_Intron	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	184					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		CAGCGGTGGTTGGTGTCTGCA	0.632													T|||	104	0.0207668	0.0023	0.0605	5008	,	,		19972	0.001		0.0567	False		,,,				2504	0.001				p.N232D		Atlas-SNP	.											.	ASB2	71	.	0			c.A694G						PASS	.	T	ASP/ASN,ASP/ASN	50,4356	50.9+/-86.3	0,50,2153	76.0	63.0	67.0		694,550	5.6	1.0	14	dbSNP_120	67	469,8131	139.0+/-195.8	10,449,3841	yes	missense,missense	ASB2	NM_001202429.1,NM_016150.4	23,23	10,499,5994	CC,CT,TT		5.4535,1.1348,3.9905	possibly-damaging,possibly-damaging	232/636,184/588	94417531	519,12487	2203	4300	6503	SO:0001583	missense	51676	exon6			GGTGGTTGGTGTC	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.550A>G	14.37:g.94417531T>C	ENSP00000320675:p.Asn184Asp	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	71	42	0.591549	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	37	CCDS9915.1	67	0.030677655677655676	2	0.0040650406504065045	25	0.06906077348066299	1	0.0017482517482517483	39	0.051451187335092345	T	27.5	4.840814	0.91197	0.011348	0.054535	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988;ENST00000543546;ENST00000555507;ENST00000556062	T;T;T;T	0.73789	-0.5;-0.5;-0.5;-0.78	5.62	5.62	0.85841	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	N	0.25201	0.72	0.54753	D	0.999986	P;D;P	0.76494	0.922;0.999;0.922	P;D;P	0.83275	0.841;0.996;0.677	T	0.60742	-0.7203	10	0.30078	T	0.28	-2.7607	15.8384	0.78818	0.0:0.0:0.0:1.0	rs11555542;rs11555542	200;232;184	B3KPZ6;B4E166;Q96Q27	.;.;ASB2_HUMAN	D	232;200;184;130;130;78	ENSP00000451575:N232D;ENSP00000320675:N184D;ENSP00000450940:N130D;ENSP00000451694:N78D	ENSP00000320675:N184D	N	-	1	0	ASB2	93487284	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.258000	0.72487	2.137000	0.66172	0.459000	0.35465	AAC	T|0.964;C|0.036	0.036	strong		0.632	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
PLEC	5339	hgsc.bcm.edu	37	8	145007187	145007187	+	Missense_Mutation	SNP	G	G	A	rs11136336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:145007187G>A	ENST00000322810.4	-	14	2091	c.1922C>T	c.(1921-1923)gCc>gTc	p.A641V	PLEC_ENST00000398774.2_Missense_Mutation_p.A472V|PLEC_ENST00000345136.3_Missense_Mutation_p.A504V|PLEC_ENST00000354589.3_Missense_Mutation_p.A504V|PLEC_ENST00000354958.2_Missense_Mutation_p.A482V|PLEC_ENST00000436759.2_Missense_Mutation_p.A531V|PLEC_ENST00000527096.1_Missense_Mutation_p.A527V|PLEC_ENST00000356346.3_Missense_Mutation_p.A490V|PLEC_ENST00000357649.2_Missense_Mutation_p.A508V	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	641	Globular 1.		A -> V (in dbSNP:rs11136336).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						AGTCACCTGGGCCACCTGGGT	0.672													G|||	1159	0.23143	0.0605	0.2867	5008	,	,		15300	0.1399		0.4066	False		,,,				2504	0.3374				p.A641V		Atlas-SNP	.											.	PLEC	1144	.	0			c.C1922T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	410,3576		24,362,1607	13.0	18.0	16.0		1511,1523,1511,1415,1922,1445,1469,1592	3.9	0.7	8	dbSNP_120	16	3151,5161		610,1931,1615	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_201384.1,NM_201383.1,NM_201382.2,NM_201381.1,NM_201380.2,NM_201379.1,NM_201378.2,NM_000445.3	64,64,64,64,64,64,64,64	634,2293,3222	AA,AG,GG		37.909,10.286,28.9559	benign,benign,benign,benign,benign,benign,benign,benign	504/4548,508/4552,504/4548,472/4516,641/4685,482/4526,490/4534,531/4575	145007187	3561,8737	1993	4156	6149	SO:0001583	missense	5339	exon14			ACCTGGGCCACCT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.1922C>T	8.37:g.145007187G>A	ENSP00000323856:p.Ala641Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	524	0.23992673992673993	28	0.056910569105691054	104	0.287292817679558	89	0.1555944055944056	303	0.3997361477572559	G	9.379	1.072611	0.20147	0.10286	0.37909	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096;ENST00000528025	T;T;T;T;T;T;T;T;T;D	0.90069	-1.03;-1.04;-1.06;-1.06;-1.05;-1.03;-1.03;-1.03;-1.03;-2.61	4.87	3.92	0.45320	.	0.283995	0.25801	U	0.028215	T	0.00012	0.0000	N	0.02539	-0.55	0.48571	P	3.2200000000004447E-4	B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.08289	-1.0729	9	0.45353	T	0.12	.	7.8835	0.29635	0.0914:0.1662:0.7424:0.0	rs11136336;rs11136336	531;490;482;641;472;504;508;504	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	V	504;508;504;472;641;482;490;531;527;548	ENSP00000344848:A504V;ENSP00000350277:A508V;ENSP00000346602:A504V;ENSP00000381756:A472V;ENSP00000323856:A641V;ENSP00000347044:A482V;ENSP00000348702:A490V;ENSP00000388180:A531V;ENSP00000434583:A527V;ENSP00000437303:A548V	ENSP00000323856:A641V	A	-	2	0	PLEC	145079175	1.000000	0.71417	0.707000	0.30419	0.197000	0.23852	1.952000	0.40343	2.261000	0.74972	0.643000	0.83706	GCC	G|0.772;A|0.228	0.228	strong		0.672	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150526270	150526270	+	Missense_Mutation	SNP	C	C	T	rs41317517	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:150526270C>T	ENST00000369038.2	+	4	1004	c.803C>T	c.(802-804)tCc>tTc	p.S268F	ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.S268F|MIR4257_ENST00000581735.1_RNA|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.S268F|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.S268F|RP11-54A4.2_ENST00000442435.2_RNA			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	268					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CCCACGCACTCCTTAGGAGAA	0.657													C|||	17	0.00339457	0.0015	0.0072	5008	,	,		15387	0.001		0.008	False		,,,				2504	0.001				p.S268F		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.C803T						PASS	.	C	PHE/SER,PHE/SER	16,4390	23.3+/-48.9	0,16,2187	50.0	49.0	49.0		803,803	0.4	0.0	1	dbSNP_127	49	100,8500	55.2+/-116.2	1,98,4201	yes	missense,missense	ADAMTSL4	NM_019032.4,NM_025008.3	155,155	1,114,6388	TT,TC,CC		1.1628,0.3631,0.8919	possibly-damaging,possibly-damaging	268/1075,268/878	150526270	116,12890	2203	4300	6503	SO:0001583	missense	54507	exon6			CGCACTCCTTAGG	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.803C>T	1.37:g.150526270C>T	ENSP00000358034:p.Ser268Phe	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	143	73	0.51049	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	37	CCDS955.1	13	0.005952380952380952	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	6	0.0079155672823219	C	8.618	0.890660	0.17613	0.003631	0.011628	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000369039;ENST00000369038	T;T;T;T	0.64085	0.02;-0.08;0.2;-0.08	4.73	0.378	0.16204	.	.	.	.	.	T	0.26304	0.0642	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.12013	0.001;0.005;0.002;0.005	B;B;B;B	0.09377	0.002;0.004;0.002;0.004	T	0.32851	-0.9891	9	0.72032	D	0.01	.	7.3289	0.26571	0.0:0.5416:0.0:0.4584	rs41317517	268;268;268;268	B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2	.;.;ATL4_HUMAN;.	F	268	ENSP00000358037:S268F;ENSP00000271643:S268F;ENSP00000358035:S268F;ENSP00000358034:S268F	ENSP00000271643:S268F	S	+	2	0	ADAMTSL4	148792894	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.115000	0.10741	0.034000	0.15491	0.484000	0.47621	TCC	C|0.991;T|0.009	0.009	strong		0.657	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
OR2T6	254879	hgsc.bcm.edu	37	1	248551560	248551560	+	Silent	SNP	C	C	T	rs954474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248551560C>T	ENST00000355728.2	+	1	651	c.651C>T	c.(649-651)tcC>tcT	p.S217S		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGACTGCATCCTACACCAGGA	0.522													c|||	1471	0.29373	0.2247	0.2867	5008	,	,		22601	0.4365		0.175	False		,,,				2504	0.3671				p.S217S		Atlas-SNP	.											OR2T6,rectum,carcinoma,+1,2	OR2T6	101	2	0			c.C651T						PASS	.	C		988,3418	369.1+/-318.9	120,748,1335	295.0	225.0	249.0		651	3.2	0.7	1	dbSNP_86	249	1286,7314	255.4+/-280.3	90,1106,3104	no	coding-synonymous	OR2T6	NM_001005471.1		210,1854,4439	TT,TC,CC		14.9535,22.424,17.4842		217/309	248551560	2274,10732	2203	4300	6503	SO:0001819	synonymous_variant	254879	exon1			TGCATCCTACACC	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"""GPCR / Class A : Olfactory receptors"""	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.651C>T	1.37:g.248551560C>T		Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	315	158	0.501587	NM_001005471	A6NE36	Silent	SNP	ENST00000355728.2	37	CCDS31114.1																																																																																			C|0.780;T|0.220	0.220	strong		0.522	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471	
TTN	7273	hgsc.bcm.edu	37	2	179598228	179598228	+	Silent	SNP	A	A	G	rs12993099	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179598228A>G	ENST00000591111.1	-	52	15065	c.14841T>C	c.(14839-14841)atT>atC	p.I4947I	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.I4020I|TTN_ENST00000589042.1_Silent_p.I5264I|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12327	Ig-like 30.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGCTCGCTCAATGATTTTGG	0.438													A|||	148	0.0295527	0.0023	0.062	5008	,	,		17704	0.0		0.0895	False		,,,				2504	0.0123				p.I5264I		Atlas-SNP	.											.	TTN	18412	.	0			c.T15792C						PASS	.	A	,,,	59,3795		1,57,1869	215.0	217.0	216.0		,12060,,	3.5	1.0	2	dbSNP_121	216	656,7622		18,620,3501	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	19,677,5370	GG,GA,AA		7.9246,1.5309,5.8935	,,,	,4020/33424,,	179598228	715,11417	1927	4139	6066	SO:0001819	synonymous_variant	7273	exon54			TCGCTCAATGATT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.14841T>C	2.37:g.179598228A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.957;G|0.043	0.043	strong		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SLCO1B7	338821	hgsc.bcm.edu	37	12	21196424	21196424	+	Missense_Mutation	SNP	T	T	A	rs11045676	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:21196424T>A	ENST00000421593.2	+	6	743	c.743T>A	c.(742-744)tTt>tAt	p.F248Y	LST3_ENST00000540229.1_Intron|SLCO1B3_ENST00000553473.1_Intron|LST3_ENST00000381541.3_Missense_Mutation_p.F295Y|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.F295Y	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						GTTTCACTATTTTTGCATGTG	0.299													T|||	359	0.0716853	0.0083	0.1354	5008	,	,		17505	0.003		0.1879	False		,,,				2504	0.0634				p.F248Y		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.T743A						PASS	.	T	TYR/PHE	178,4216		8,162,2027	71.0	72.0	72.0		743	-0.2	0.0	12	dbSNP_120	72	1709,6885		173,1363,2761	yes	missense	SLCO1B7	NM_001009562.4	22	181,1525,4788	AA,AT,TT		19.886,4.051,14.5288		248/641	21196424	1887,11101	2197	4297	6494	SO:0001583	missense	338821	exon6			CACTATTTTTGCA	AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.743T>A	12.37:g.21196424T>A	ENSP00000394168:p.Phe248Tyr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	89	34	0.382022	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	197	0.0902014652014652	6	0.012195121951219513	48	0.13259668508287292	1	0.0017482517482517483	142	0.18733509234828497	.	6.090	0.384882	0.11524	0.04051	0.19886	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.38401	1.14;1.14;1.14	3.17	-0.223	0.13118	.	3.846580	0.00397	N	0.000059	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.30709	0.291;0.078	B;B	0.25884	0.064;0.025	T	0.16988	-1.0384	9	0.62326	D	0.03	.	2.4823	0.04590	0.2331:0.4843:0.0:0.2825	rs11045676;rs52823168	248;295	G3V0H7;F5H094	.;.	Y	295;295;248	ENSP00000370952:F295Y;ENSP00000452013:F295Y;ENSP00000394168:F248Y	ENSP00000370952:F295Y	F	+	2	0	SLCO1B7;RP11-545J16.1	21087691	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	0.207000	0.17395	0.144000	0.18951	-0.756000	0.03474	TTT	T|0.895;A|0.105	0.105	strong		0.299	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
PADI1	29943	hgsc.bcm.edu	37	1	17531763	17531763	+	Silent	SNP	C	C	T	rs2293911	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17531763C>T	ENST00000375471.4	+	1	143	c.51C>T	c.(49-51)gcC>gcT	p.A17A		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	17					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	CTACCCATGCCGTGTGTGTGG	0.592													C|||	220	0.0439297	0.0061	0.0317	5008	,	,		18559	0.0228		0.0944	False		,,,				2504	0.0736				p.A17A	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.C51T						PASS	.	C		78,4328	68.7+/-106.4	1,76,2126	167.0	125.0	139.0		51	-7.3	0.0	1	dbSNP_100	139	718,7882	174.6+/-224.8	22,674,3604	no	coding-synonymous	PADI1	NM_013358.2		23,750,5730	TT,TC,CC		8.3488,1.7703,6.1203		17/664	17531763	796,12210	2203	4300	6503	SO:0001819	synonymous_variant	29943	exon1			CCATGCCGTGTGT	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"""Peptidyl arginine deiminases"""	18367	protein-coding gene	gene with protein product	"""peptidylarginine deiminase type I"", ""protein-arginine deiminase type-1"", ""hPAD-colony 10"""	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.51C>T	1.37:g.17531763C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	184	94	0.51087	NM_013358	A1L4K6|Q70SX6	Silent	SNP	ENST00000375471.4	37	CCDS178.1																																																																																			C|0.944;T|0.056	0.056	strong		0.592	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358	
CLSTN2	64084	hgsc.bcm.edu	37	3	140178381	140178381	+	Missense_Mutation	SNP	T	T	C	rs17348572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:140178381T>C	ENST00000458420.3	+	7	1182	c.992T>C	c.(991-993)aTt>aCt	p.I331T	RP11-68L1.2_ENST00000503357.1_RNA|RP11-68L1.1_ENST00000483759.2_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	331			I -> T (in dbSNP:rs17348572).		homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.I331T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						TCTGGCATCATTGACCTCTTG	0.552										HNSCC(16;0.037)			T|||	151	0.0301518	0.0204	0.0144	5008	,	,		19373	0.0268		0.0477	False		,,,				2504	0.0399				p.I331T	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											CLSTN2,NS,carcinoma,0,1	CLSTN2	190	1	1	Substitution - Missense(1)	stomach(1)	c.T992C						PASS	.	T	THR/ILE	90,4316	75.2+/-113.4	0,90,2113	90.0	85.0	87.0		992	5.4	1.0	3	dbSNP_123	87	451,8149	135.7+/-192.9	16,419,3865	yes	missense	CLSTN2	NM_022131.2	89	16,509,5978	CC,CT,TT		5.2442,2.0427,4.1596	benign	331/956	140178381	541,12465	2203	4300	6503	SO:0001583	missense	64084	exon7			GCATCATTGACCT	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.992T>C	3.37:g.140178381T>C	ENSP00000402460:p.Ile331Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	66	0.03021978021978022	6	0.012195121951219513	9	0.024861878453038673	12	0.02097902097902098	39	0.051451187335092345	T	10.57	1.385910	0.25031	0.020427	0.052442	ENSG00000158258	ENST00000458420	T	0.22945	1.93	5.41	5.41	0.78517	Concanavalin A-like lectin/glucanase (1);	0.055407	0.64402	D	0.000001	T	0.02610	0.0079	N	0.20685	0.6	0.37350	D	0.910753	B	0.14438	0.01	B	0.11329	0.006	T	0.10109	-1.0644	10	0.27785	T	0.31	-20.372	13.4033	0.60896	0.0:0.0:0.0:1.0	rs17348572;rs52815627;rs61656456;rs17348572	331	Q9H4D0	CSTN2_HUMAN	T	331	ENSP00000402460:I331T	ENSP00000402460:I331T	I	+	2	0	CLSTN2	141661071	0.996000	0.38824	0.974000	0.42286	0.994000	0.84299	2.713000	0.47194	2.064000	0.61679	0.533000	0.62120	ATT	T|0.968;C|0.032	0.032	strong		0.552	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
BOD1L1	259282	hgsc.bcm.edu	37	4	13615174	13615174	+	Missense_Mutation	SNP	G	G	A	rs2035820	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:13615174G>A	ENST00000040738.5	-	5	1421	c.1286C>T	c.(1285-1287)aCg>aTg	p.T429M		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	429	Lys-rich.		T -> M (in dbSNP:rs2035820).			nucleus (GO:0005634)	DNA binding (GO:0003677)										GCTATCAGACGTTACAACTTC	0.383													A|||	688	0.13738	0.1558	0.2147	5008	,	,		11755	0.003		0.1501	False		,,,				2504	0.183				p.T429M		Atlas-SNP	.											BOD1L,NS,carcinoma,+1,1	.	.	1	0			c.C1286T						PASS	.	A	MET/THR	691,3715	761.7+/-413.1	44,603,1556	168.0	158.0	161.0		1286	4.0	0.7	4	dbSNP_94	161	1295,7305	758.9+/-407.5	86,1123,3091	yes	missense	BOD1L	NM_148894.2	81	130,1726,4647	AA,AG,GG		15.0581,15.6832,15.2699	benign	429/3052	13615174	1986,11020	2203	4300	6503	SO:0001583	missense	259282	exon5			TCAGACGTTACAA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.1286C>T	4.37:g.13615174G>A	ENSP00000040738:p.Thr429Met	Somatic	390	0	0		WXS	Illumina HiSeq	Phase_I	362	138	0.381215	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	269	0.12316849816849818	85	0.17276422764227642	73	0.20165745856353592	0	0.0	111	0.14643799472295516	A	0.018	-1.474986	0.01035	0.156832	0.150581	ENSG00000038219	ENST00000040738	T	0.06371	3.31	5.18	3.99	0.46301	.	0.580206	0.15617	N	0.253098	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45116	-0.9283	9	0.27082	T	0.32	-3.2621	9.6555	0.39923	0.8567:0.0:0.1433:0.0	rs2035820;rs17807749;rs58395303;rs2035820	429	Q8NFC6	BOD1L_HUMAN	M	429	ENSP00000040738:T429M	ENSP00000040738:T429M	T	-	2	0	BOD1L	13224272	0.969000	0.33509	0.676000	0.29932	0.496000	0.33645	2.391000	0.44424	0.387000	0.25024	-1.120000	0.02017	ACG	G|0.852;A|0.148	0.148	strong		0.383	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
ZNF268	10795	hgsc.bcm.edu	37	12	133780587	133780587	+	Missense_Mutation	SNP	G	G	A	rs373286359		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133780587G>A	ENST00000536435.2	+	6	2645	c.2315G>A	c.(2314-2316)cGa>cAa	p.R772Q	ZNF268_ENST00000228289.5_Missense_Mutation_p.R772Q|ZNF268_ENST00000537565.1_Missense_Mutation_p.R611Q|ZNF268_ENST00000542986.2_3'UTR|ZNF268_ENST00000541009.2_3'UTR|ZNF268_ENST00000536899.2_3'UTR	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	772					cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TCACATCAGCGAACTCATGCA	0.423																																					p.R772Q		Atlas-SNP	.											ZNF268,NS,carcinoma,0,1	ZNF268	71	1	0			c.G2315A						PASS	.						31.0	31.0	31.0					12																	133780587		692	1590	2282	SO:0001583	missense	10795	exon6			ATCAGCGAACTCA	X78926	CCDS45012.1, CCDS53851.1, CCDS53852.1, CCDS53853.1, CCDS53854.1, CCDS59239.1, CCDS59240.1	12q24.33	2013-01-08				ENSG00000090612		"""Zinc fingers, C2H2-type"", ""-"""	13061	protein-coding gene	gene with protein product		604753				7865130	Standard	NM_003415		Approved	HZF3	uc010tcf.2	Q14587	OTTHUMG00000167946	ENST00000536435.2:c.2315G>A	12.37:g.133780587G>A	ENSP00000444412:p.Arg772Gln	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_001165881	Q8TDG8|Q96RH4|Q9BZJ9	Missense_Mutation	SNP	ENST00000536435.2	37	CCDS45012.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.191297	0.58017	.	.	ENSG00000090612	ENST00000541009;ENST00000228289;ENST00000537565;ENST00000541019	T;T	0.24723	1.84;1.84	3.98	0.988	0.19796	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18130	0.0435	L	0.60957	1.885	0.21416	N	0.999694	B;P	0.36495	0.42;0.556	B;B	0.15484	0.01;0.013	T	0.10382	-1.0632	8	.	.	.	.	7.3383	0.26623	0.3109:0.0:0.6891:0.0	.	772;611	Q14587;Q14587-2	ZN268_HUMAN;.	Q	772;772;611;611	ENSP00000228289:R772Q;ENSP00000445713:R611Q	.	R	+	2	0	ZNF268	.	0.000000	0.05858	0.096000	0.21009	0.817000	0.46193	-0.126000	0.10563	0.332000	0.23536	0.650000	0.86243	CGA	.	.	alt		0.423	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943	
HELZ2	85441	hgsc.bcm.edu	37	20	62196033	62196033	+	Missense_Mutation	SNP	C	C	T	rs3810487	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62196033C>T	ENST00000467148.1	-	8	4211	c.4142G>A	c.(4141-4143)aGg>aAg	p.R1381K	HELZ2_ENST00000427522.2_Missense_Mutation_p.R812K	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1381			R -> K (in dbSNP:rs3810487).		cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CACCCCGTCCCTGGGCACGAA	0.687													C|||	1099	0.219449	0.0076	0.0994	5008	,	,		16931	0.5317		0.1958	False		,,,				2504	0.2935				p.R1381K		Atlas-SNP	.											.	.	.	.	0			c.G4142A						PASS	.	C	LYS/ARG,LYS/ARG	191,4159		5,181,1989	13.0	11.0	12.0		4142,2435	-0.3	0.1	20	dbSNP_107	12	1595,6957		167,1261,2848	yes	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	26,26	172,1442,4837	TT,TC,CC		18.6506,4.3908,13.8428	benign,benign	1381/2650,812/2081	62196033	1786,11116	2175	4276	6451	SO:0001583	missense	85441	exon9			CCGTCCCTGGGCA	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.4142G>A	20.37:g.62196033C>T	ENSP00000417401:p.Arg1381Lys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	523	0.23946886446886448	6	0.012195121951219513	44	0.12154696132596685	317	0.5541958041958042	156	0.20580474934036938	C	0.010	-1.760787	0.00657	0.043908	0.186506	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.33654	1.4;1.4	4.66	-0.274	0.12910	Ribonuclease II/R (2);	0.704916	0.14555	N	0.312409	T	0.00012	0.0000	N	0.02379	-0.575	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.09377	0.004;0.004	T	0.44574	-0.9319	9	0.02654	T	1	-26.0318	4.9363	0.13943	0.0:0.212:0.1822:0.6059	rs3810487;rs3810487	1381;812	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	K	812;1381	ENSP00000393257:R812K;ENSP00000417401:R1381K	ENSP00000393257:R812K	R	-	2	0	RP4-697K14.7	61666477	0.573000	0.26676	0.059000	0.19551	0.015000	0.08874	0.738000	0.26158	0.069000	0.16605	0.491000	0.48974	AGG	C|0.809;T|0.191	0.191	strong		0.687	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
CCDC33	80125	hgsc.bcm.edu	37	15	74622678	74622678	+	Missense_Mutation	SNP	G	G	A	rs1564782	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:74622678G>A	ENST00000398814.3	+	12	1870	c.1439G>A	c.(1438-1440)aGt>aAt	p.S480N	CCDC33_ENST00000558821.1_Missense_Mutation_p.S73N|CCDC33_ENST00000321288.5_Missense_Mutation_p.S683N|CCDC33_ENST00000268082.4_Missense_Mutation_p.S73N	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	683										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GGCAAAGCCAGTGAGGCCCAG	0.652													G|||	2144	0.428115	0.2716	0.3919	5008	,	,		18331	0.3611		0.665	False		,,,				2504	0.4908				p.S480N		Atlas-SNP	.											CCDC33_ENST00000321288,NS,carcinoma,0,3	CCDC33	160	3	0			c.G1439A						PASS	.	G	ASN/SER,ASN/SER	1337,2755		237,863,946	34.0	45.0	41.0		1439,218	1.5	0.0	15	dbSNP_88	41	5799,2571		2023,1753,409	yes	missense,missense	CCDC33	NM_025055.3,NM_182791.2	46,46	2260,2616,1355	AA,AG,GG		30.7168,32.6735,42.7379	benign,benign	480/756,73/368	74622678	7136,5326	2046	4185	6231	SO:0001583	missense	80125	exon12			AAGCCAGTGAGGC	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.1439G>A	15.37:g.74622678G>A	ENSP00000381795:p.Ser480Asn	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	CCDS42058.1	1007	0.4610805860805861	142	0.2886178861788618	165	0.4558011049723757	192	0.3356643356643357	508	0.6701846965699209	G	4.262	0.047652	0.08243	0.326735	0.692832	ENSG00000140481	ENST00000321288;ENST00000398814;ENST00000321374;ENST00000268082	T;T;T;T	0.35973	1.28;2.31;1.97;1.97	4.62	1.52	0.23074	.	2.105930	0.01933	N	0.041358	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B;B;B;B	0.09022	0.001;0.001;0.001;0.002	B;B;B;B	0.06405	0.001;0.002;0.0;0.001	T	0.44967	-0.9293	9	0.27082	T	0.32	.	4.3065	0.10949	0.5366:0.3273:0.1361:0.0	rs1564782;rs16968185;rs60264189;rs1564782	73;73;683;480	Q8N5R6-4;Q8N5R6-5;C9JFX2;Q8N5R6-6	.;.;.;.	N	683;480;73;73	ENSP00000325012:S683N;ENSP00000381795:S480N;ENSP00000325661:S73N;ENSP00000268082:S73N	ENSP00000268082:S73N	S	+	2	0	CCDC33	72409731	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.430000	0.21428	0.030000	0.15379	-0.366000	0.07423	AGT	G|0.560;A|0.440	0.440	strong		0.652	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
ZNF41	7592	hgsc.bcm.edu	37	X	47308795	47308795	+	Missense_Mutation	SNP	A	A	C	rs17147624	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:47308795A>C	ENST00000377065.4	-	5	1013	c.374T>G	c.(373-375)aTa>aGa	p.I125R	ZNF41_ENST00000313116.7_Missense_Mutation_p.I125R|ZNF41_ENST00000465311.1_5'UTR|ZNF41_ENST00000397050.2_Missense_Mutation_p.I135R	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	167	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				ATCTTCTCCTATGGGTTGATC	0.378													A|||	127	0.0336424	0.0552	0.013	3775	,	,		14063	0.005		0.0219	False		,,,				2504	0.0184				p.I125R		Atlas-SNP	.											.	ZNF41	71	.	0			c.T374G						PASS	.	A	ARG/ILE,ARG/ILE	265,3570		6,213,40,1413,531	56.0	48.0	51.0		374,374	-1.3	0.0	X	dbSNP_123	51	196,6532		2,139,53,2287,1819	yes	missense,missense	ZNF41	NM_007130.2,NM_153380.2	97,97	8,352,93,3700,2350	CC,CA,C,AA,A		2.9132,6.91,4.3643	benign,benign	125/780,125/780	47308795	461,10102	2203	4300	6503	SO:0001583	missense	7592	exon5			TCTCCTATGGGTT	X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"""Zinc fingers, C2H2-type"", ""-"""	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.374T>G	X.37:g.47308795A>C	ENSP00000366265:p.Ile125Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	164	7	0.0426829	NM_007130	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	37	CCDS14279.1	50	0.030138637733574444	18	0.0379746835443038	3	0.008379888268156424	2	0.0035211267605633804	8	0.010723860589812333	A	0.029	-1.345848	0.01266	0.0691	0.029132	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050;ENST00000432977	T;T;T;T	0.07444	3.19;3.19;3.19;5.87	3.1	-1.26	0.09376	.	0.188581	0.26048	N	0.026660	T	0.00328	0.0010	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B;B	0.17268	0.021;0.021;0.001;0.021;0.012	B;B;B;B;B	0.13407	0.009;0.009;0.003;0.009;0.004	T	0.35001	-0.9806	9	0.33141	T	0.24	.	6.4767	0.22039	0.4505:0.0:0.5495:0.0	rs17147624;rs52810092;rs17147624	125;127;135;159;167	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	R	125;125;135;135	ENSP00000315173:I125R;ENSP00000366265:I125R;ENSP00000380243:I135R;ENSP00000390385:I135R	ENSP00000315173:I125R	I	-	2	0	ZNF41	47193739	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-0.692000	0.05127	-0.351000	0.08249	-0.321000	0.08615	ATA	A|0.944;0|0.015	.	strong		0.378	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380	
CPM	1368	hgsc.bcm.edu	37	12	69260779	69260779	+	Silent	SNP	C	C	T	rs33925480	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:69260779C>T	ENST00000551568.1	-	7	897	c.837G>A	c.(835-837)acG>acA	p.T279T	CPM_ENST00000338356.3_Silent_p.T279T|CPM_ENST00000546373.1_Silent_p.T279T	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	279					anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			ACAGCTCCAACGTAATTTCAA	0.383													C|||	334	0.0666933	0.0129	0.0807	5008	,	,		19671	0.0159		0.1342	False		,,,				2504	0.1125				p.T279T		Atlas-SNP	.											.	CPM	30	.	0			c.G837A						PASS	.	C	,,	145,4261	100.7+/-139.4	2,141,2060	105.0	101.0	102.0		837,837,837	-11.1	0.0	12	dbSNP_126	102	1174,7426	240.1+/-271.0	81,1012,3207	no	coding-synonymous,coding-synonymous,coding-synonymous	CPM	NM_001005502.2,NM_001874.4,NM_198320.3	,,	83,1153,5267	TT,TC,CC		13.6512,3.291,10.1415	,,	279/444,279/444,279/444	69260779	1319,11687	2203	4300	6503	SO:0001819	synonymous_variant	1368	exon7			CTCCAACGTAATT	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"""renal carboxypeptidase"", ""urinary carboxypeptidase B"""	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.837G>A	12.37:g.69260779C>T		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	257	134	0.521401	NM_001005502	B2R800|Q9H2K9	Silent	SNP	ENST00000551568.1	37	CCDS8987.1	142	0.06501831501831502	4	0.008130081300813009	37	0.10220994475138122	6	0.01048951048951049	95	0.12532981530343007	C	6.995	0.553768	0.13374	0.03291	0.136512	ENSG00000135678	ENST00000551897	.	.	.	5.54	-11.1	0.00147	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.9999999999999961	.	.	.	.	.	.	T	0.05869	-1.0859	3	.	.	.	-16.4712	9.2735	0.37686	0.1531:0.0757:0.0795:0.6918	rs33925480	.	.	.	H	82	.	.	R	-	2	0	CPM	67547046	0.000000	0.05858	0.019000	0.16419	0.860000	0.49131	-3.148000	0.00583	-2.582000	0.00461	-0.890000	0.02929	CGT	C|0.903;T|0.097	0.097	strong		0.383	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320	
RAD1	5810	hgsc.bcm.edu	37	5	34908877	34908877	+	Missense_Mutation	SNP	T	T	C	rs1805327	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:34908877T>C	ENST00000382038.2	-	6	2261	c.842A>G	c.(841-843)gAg>gGg	p.E281G	RAD1_ENST00000341754.4_Missense_Mutation_p.E281G	NM_002853.3	NP_002844.1	O60671	RAD1_HUMAN	RAD1 checkpoint DNA exonuclease	281			E -> G (in dbSNP:rs1805327). {ECO:0000269|Ref.11}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|meiotic recombination checkpoint (GO:0051598)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|substantia nigra development (GO:0021762)	chromosome (GO:0005694)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|damaged DNA binding (GO:0003684)|exodeoxyribonuclease III activity (GO:0008853)			endometrium(3)|large_intestine(1)|lung(5)|urinary_tract(1)	10	all_lung(31;0.000107)	Lung NSC(810;5.19e-05)|Ovarian(839;0.0448)|Breast(839;0.198)	COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			TACTCAAGACTCAGATTCAGG	0.323								Other conserved DNA damage response genes					T|||	227	0.0453275	0.0023	0.0375	5008	,	,		19465	0.0347		0.0557	False		,,,				2504	0.1094				p.E281G		Atlas-SNP	.											.	RAD1	17	.	0			c.A842G						PASS	.	T	GLY/GLU	60,4346	57.4+/-93.9	2,56,2145	79.0	76.0	77.0		842	5.7	1.0	5	dbSNP_96	77	673,7923	168.1+/-219.7	29,615,3654	no	missense	RAD1	NM_002853.3	98	31,671,5799	CC,CT,TT		7.8292,1.3618,5.6376	benign	281/283	34908877	733,12269	2203	4298	6501	SO:0001583	missense	5810	exon6			CAAGACTCAGATT	AF074717	CCDS3905.1	5p13	2014-08-08	2014-08-08		ENSG00000113456	ENSG00000113456	3.1.11.2		9806	protein-coding gene	gene with protein product	"""exonuclease homolog RAD1"", ""checkpoint control protein HRAD1"", ""cell cycle checkpoint protein Hrad1"", ""Rad1-like DNA damage checkpoint"", ""DNA repair exonuclease REC1"""	603153	"""RAD1 (S. pombe) homolog"", ""RAD1 homolog (S. pombe)"""			9716408, 9828137	Standard	NR_026591		Approved	HRAD1, REC1	uc003jix.3	O60671	OTTHUMG00000090783	ENST00000382038.2:c.842A>G	5.37:g.34908877T>C	ENSP00000371469:p.Glu281Gly	Somatic	501	0	0		WXS	Illumina HiSeq	Phase_I	591	309	0.522843	NM_002853	O75572|O95304|Q1W161|Q5KSM0|Q5KSM1|Q9UEP1	Missense_Mutation	SNP	ENST00000382038.2	37	CCDS3905.1	76	0.0347985347985348	3	0.006097560975609756	13	0.03591160220994475	20	0.03496503496503497	40	0.052770448548812667	T	17.22	3.334864	0.60853	0.013618	0.078292	ENSG00000113456	ENST00000382038;ENST00000341754;ENST00000542494	T;T	0.15718	2.4;2.4	5.73	5.73	0.89815	.	0.185949	0.34725	N	0.003734	T	0.00967	0.0032	L	0.50333	1.59	0.28288	N	0.923675	B	0.24186	0.099	B	0.19946	0.027	T	0.01312	-1.1388	10	0.59425	D	0.04	.	16.0048	0.80354	0.0:0.0:0.0:1.0	rs1805327;rs52830916;rs56497649;rs1805327	281	O60671	RAD1_HUMAN	G	281;281;245	ENSP00000371469:E281G;ENSP00000340879:E281G	ENSP00000340879:E281G	E	-	2	0	RAD1	34944634	0.980000	0.34600	0.996000	0.52242	0.753000	0.42808	2.691000	0.47010	2.190000	0.69967	0.533000	0.62120	GAG	T|0.946;G|0.000	.	strong		0.323	RAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207567.1	NM_002853	
PCDHB12	56124	hgsc.bcm.edu	37	5	140589738	140589738	+	Missense_Mutation	SNP	C	C	T	rs2910327	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140589738C>T	ENST00000239450.2	+	1	1448	c.1259C>T	c.(1258-1260)aCc>aTc	p.T420I	PCDHB12_ENST00000541609.1_Missense_Mutation_p.T83I	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	420	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		T -> I (in dbSNP:rs2910327).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TACAACATCACCATCACCGTC	0.522													C|||	601	0.120008	0.1036	0.0937	5008	,	,		18305	0.0933		0.1412	False		,,,				2504	0.1667				p.T420I		Atlas-SNP	.											.	PCDHB12	179	.	0			c.C1259T						PASS	.	C	ILE/THR	523,3883	239.6+/-250.7	33,457,1713	98.0	95.0	96.0		1259	3.0	1.0	5	dbSNP_101	96	1412,7188	273.4+/-290.6	134,1144,3022	yes	missense	PCDHB12	NM_018932.3	89	167,1601,4735	TT,TC,CC		16.4186,11.8702,14.8777	probably-damaging	420/796	140589738	1935,11071	2203	4300	6503	SO:0001583	missense	56124	exon1			ACATCACCATCAC	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1259C>T	5.37:g.140589738C>T	ENSP00000239450:p.Thr420Ile	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	261	0.11950549450549451	50	0.1016260162601626	43	0.11878453038674033	53	0.09265734265734266	115	0.1517150395778364	C	14.49	2.550541	0.45383	0.118702	0.164186	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.03358	3.96;3.96	3.83	2.96	0.34315	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00039	0.0001	M	0.87381	2.88	0.28256	P	0.9250636	B	0.25105	0.118	B	0.37346	0.247	T	0.01993	-1.1233	8	0.87932	D	0	.	10.8885	0.46981	0.0:0.9041:0.0:0.0959	rs2910327;rs17844600;rs52810894;rs57414218;rs2910327	420	Q9Y5F1	PCDBC_HUMAN	I	83;420;40	ENSP00000440199:T83I;ENSP00000239450:T420I	ENSP00000239450:T420I	T	+	2	0	PCDHB12	140569922	0.829000	0.29322	0.986000	0.45419	0.299000	0.27559	2.700000	0.47085	0.730000	0.32425	0.485000	0.47835	ACC	C|0.860;T|0.140	0.140	strong		0.522	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
MT-ND6	4541	hgsc.bcm.edu	37	M	14167	14167	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:14167C>T	ENST00000361681.2	-	1	506	c.507G>A	c.(505-507)gaG>gaA	p.E169E	MT-TE_ENST00000387459.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	169					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						CCCCGAGCAATCTCAATTACA	0.413																																					p.E169E		Atlas-SNP	.											.	.	.	.	0			c.G507A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			AGCAATCTCAATT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7462	protein-coding gene	gene with protein product	"""complex I ND6 subunit"", ""NADH-ubiquinone oxidoreductase chain 6"""	516006	"""NADH dehydrogenase 6"""	MTND6			Standard			Approved	NAD6, ND6		P03923		ENST00000361681.2:c.507G>A	M.37:g.14167C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	ENST00000361681	Q34774|Q8HG30	Silent	SNP	ENST00000361681.2	37																																																																																				.	.	none		0.413	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
SLC22A1	6580	hgsc.bcm.edu	37	6	160543148	160543148	+	Missense_Mutation	SNP	C	C	T	rs12208357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:160543148C>T	ENST00000366963.4	+	1	328	c.181C>T	c.(181-183)Cgc>Tgc	p.R61C	SLC22A1_ENST00000324965.4_Missense_Mutation_p.R61C|SLC22A1_ENST00000457470.2_Missense_Mutation_p.R61C	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	61			R -> C (reduction of the MPP uptake. Reduction of the MPP uptake; when associated with V-408; dbSNP:rs12208357). {ECO:0000269|PubMed:12439218, ECO:0000269|PubMed:12719534}.		dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|epinephrine transport (GO:0048241)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|norepinephrine transport (GO:0015874)|organic cation transport (GO:0015695)|protein homooligomerization (GO:0051260)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)|dopamine transmembrane transporter activity (GO:0005329)|norepinephrine transmembrane transporter activity (GO:0005333)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)		SLC22A1/CUTA(2)	breast(1)|endometrium(3)|large_intestine(3)|lung(13)|upper_aerodigestive_tract(1)	21		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)	Acebutolol(DB01193)|Acepromazine(DB01614)|Aciclovir(DB00787)|Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Caspofungin(DB00520)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Choline(DB00122)|Cimetidine(DB00501)|Cladribine(DB00242)|Clonidine(DB00575)|Codeine(DB00318)|Cytarabine(DB00987)|Desipramine(DB01151)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Estropipate(DB04574)|Ganciclovir(DB01004)|Gentian Violet(DB00406)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Lamivudine(DB00709)|Latanoprost(DB00654)|Metformin(DB00331)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rocuronium(DB00728)|Saquinavir(DB01232)|Spermine(DB00127)|Testosterone(DB00624)|Thiamine(DB00152)|Thioproperazine(DB01622)|Thiothixene(DB01623)|Tubocurarine(DB01199)|Vecuronium(DB01339)|Verapamil(DB00661)	GCTGAGCCAGCGCTGTGGCTG	0.652													C|||	102	0.0203674	0.0038	0.0202	5008	,	,		18506	0.0		0.0626	False		,,,				2504	0.0204				p.R61C		Atlas-SNP	.											.	SLC22A1	69	.	0			c.C181T	GRCh37	CM072040	SLC22A1	M	rs12208357	PASS	.	C	CYS/ARG,CYS/ARG	62,4344	58.7+/-95.3	1,60,2142	63.0	71.0	68.0		181,181	2.7	0.2	6	dbSNP_120	68	695,7905	170.6+/-221.7	28,639,3633	yes	missense,missense	SLC22A1	NM_003057.2,NM_153187.1	180,180	29,699,5775	TT,TC,CC		8.0814,1.4072,5.8204	probably-damaging,probably-damaging	61/555,61/507	160543148	757,12249	2203	4300	6503	SO:0001583	missense	6580	exon1			AGCCAGCGCTGTG	U77086	CCDS5274.1, CCDS5275.1	6q25.3	2013-05-22			ENSG00000175003	ENSG00000175003		"""Solute carriers"""	10963	protein-coding gene	gene with protein product		602607				9605850	Standard	NM_003057		Approved	OCT1	uc003qtc.3	O15245	OTTHUMG00000015947	ENST00000366963.4:c.181C>T	6.37:g.160543148C>T	ENSP00000355930:p.Arg61Cys	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	Missense_Mutation	SNP	ENST00000366963.4	37	CCDS5274.1	59	0.027014652014652016	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	46	0.06068601583113457	C	16.11	3.029636	0.54790	0.014072	0.080814	ENSG00000175003	ENST00000366963;ENST00000324965;ENST00000457470	T;T;T	0.75050	-0.74;-0.9;-0.89	5.5	2.69	0.31865	.	0.239275	0.35067	N	0.003473	T	0.75882	0.3910	M	0.82630	2.6	0.20926	N	0.999822	D;D	0.89917	1.0;1.0	D;D	0.75020	0.975;0.985	T	0.68561	-0.5376	10	0.72032	D	0.01	.	4.8751	0.13653	0.3844:0.4224:0.1244:0.0688	rs12208357;rs56982873	61;61	O15245-2;O15245	.;S22A1_HUMAN	C	61	ENSP00000355930:R61C;ENSP00000318103:R61C;ENSP00000409557:R61C	ENSP00000318103:R61C	R	+	1	0	SLC22A1	160463138	0.070000	0.21116	0.228000	0.23943	0.895000	0.52256	0.292000	0.19011	0.260000	0.21731	0.561000	0.74099	CGC	C|0.961;T|0.039	0.039	strong		0.652	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		
ISL2	64843	hgsc.bcm.edu	37	15	76630717	76630717	+	Silent	SNP	C	C	T	rs62028361	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:76630717C>T	ENST00000290759.4	+	3	533	c.373C>T	c.(373-375)Ctg>Ttg	p.L125L	RP11-685G9.2_ENST00000559539.1_RNA	NM_145805.1	NP_665804.1	Q96A47	ISL2_HUMAN	ISL LIM homeobox 2	125	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|peripheral nervous system neuron development (GO:0048935)|regulation of transcription, DNA-templated (GO:0006355)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord motor neuron cell fate specification (GO:0021520)|visceral motor neuron differentiation (GO:0021524)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6						CCGCCAGCTGCTGCCTGGGGA	0.726													C|||	265	0.0529153	0.0484	0.0418	5008	,	,		9628	0.0367		0.0954	False		,,,				2504	0.0399				p.L125L	GBM(97;953 1391 16164 31496 36951)	Atlas-SNP	.											.	ISL2	20	.	0			c.C373T						PASS	.	C		262,4084		11,240,1922	13.0	12.0	13.0		373	3.5	1.0	15	dbSNP_129	13	752,7766		42,668,3549	no	coding-synonymous	ISL2	NM_145805.1		53,908,5471	TT,TC,CC		8.8284,6.0285,7.8825		125/360	76630717	1014,11850	2173	4259	6432	SO:0001819	synonymous_variant	64843	exon3			CAGCTGCTGCCTG	AK001022	CCDS10290.1	15q24.3	2012-03-09	2007-07-13		ENSG00000159556	ENSG00000159556		"""Homeoboxes / LIM class"""	18524	protein-coding gene	gene with protein product		609481	"""ISL2 transcription factor, LIM/homeodomain, (islet-2)"""				Standard	NM_145805		Approved	FLJ10160	uc002bbw.1	Q96A47	OTTHUMG00000143723	ENST00000290759.4:c.373C>T	15.37:g.76630717C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	18	10	0.555556	NM_145805	B3KM37	Silent	SNP	ENST00000290759.4	37	CCDS10290.1																																																																																			C|0.925;T|0.075	0.075	strong		0.726	ISL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289779.1		
FAT2	2196	hgsc.bcm.edu	37	5	150945931	150945931	+	Silent	SNP	C	C	T	rs3734058	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150945931C>T	ENST00000261800.5	-	1	2574	c.2562G>A	c.(2560-2562)agG>agA	p.R854R		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	854	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTAGCGAACCCTGCCATTGT	0.547													C|||	2101	0.419529	0.441	0.4539	5008	,	,		21887	0.3562		0.4901	False		,,,				2504	0.3589				p.R854R		Atlas-SNP	.											.	FAT2	465	.	0			c.G2562A						PASS	.	C		1958,2448	554.6+/-379.1	422,1114,667	104.0	99.0	101.0		2562	1.4	1.0	5	dbSNP_107	101	4498,4102	592.5+/-393.0	1183,2132,985	no	coding-synonymous	FAT2	NM_001447.2		1605,3246,1652	TT,TC,CC		47.6977,44.4394,49.6386		854/4350	150945931	6456,6550	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			GCGAACCCTGCCA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2562G>A	5.37:g.150945931C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			C|0.525;T|0.475	0.475	strong		0.547	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
CSF2RB	1439	hgsc.bcm.edu	37	22	37333804	37333804	+	Missense_Mutation	SNP	G	G	A	rs1801114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:37333804G>A	ENST00000403662.3	+	14	2176	c.1954G>A	c.(1954-1956)Gtg>Atg	p.V652M	CSF2RB_ENST00000262825.5_Missense_Mutation_p.V658M|CSF2RB_ENST00000406230.1_Missense_Mutation_p.V658M|CSF2RB_ENST00000536485.1_Missense_Mutation_p.V599M			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	652			V -> M (in dbSNP:rs1801114).		cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	AGGACAGGCCGTGGAAGTGGA	0.697													G|||	304	0.0607029	0.1558	0.0331	5008	,	,		13581	0.0		0.0229	False		,,,				2504	0.0532				p.V652M		Atlas-SNP	.											.	CSF2RB	104	.	0			c.G1954A						PASS	.	G	MET/VAL	588,3790		36,516,1637	11.0	13.0	12.0		1954	-7.8	0.0	22	dbSNP_89	12	168,8364		3,162,4101	yes	missense	CSF2RB	NM_000395.2	21	39,678,5738	AA,AG,GG		1.9691,13.4308,5.8559	benign	652/898	37333804	756,12154	2189	4266	6455	SO:0001583	missense	1439	exon14			CAGGCCGTGGAAG	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.1954G>A	22.37:g.37333804G>A	ENSP00000384053:p.Val652Met	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	37	CCDS13936.1	114	0.0521978021978022	88	0.17886178861788618	12	0.03314917127071823	0	0.0	14	0.018469656992084433	G	8.665	0.901468	0.17760	0.134308	0.019691	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.91792	-2.4;-2.91;-2.91;-2.91	4.99	-7.79	0.01218	.	6.560840	0.00166	N	0.000015	T	0.00695	0.0023	N	0.22421	0.69	0.80722	P	0.0	B;B	0.18968	0.032;0.019	B;B	0.09377	0.004;0.002	T	0.56384	-0.7988	9	0.27082	T	0.32	0.4157	8.8555	0.35225	0.2452:0.2362:0.5186:0.0	rs1801114;rs1801114	658;652	P32927-2;P32927	.;IL3RB_HUMAN	M	652;652;658;658;599	ENSP00000384053:V652M;ENSP00000262825:V658M;ENSP00000385271:V658M;ENSP00000440003:V599M	ENSP00000262825:V658M	V	+	1	0	CSF2RB	35663750	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.431000	0.06965	-1.885000	0.01118	-1.628000	0.00784	GTG	G|0.949;A|0.051	0.051	strong		0.697	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
PRDM5	11107	hgsc.bcm.edu	37	4	121706201	121706201	+	Silent	SNP	A	A	G	rs12499000	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:121706201A>G	ENST00000264808.3	-	11	1474	c.1234T>C	c.(1234-1236)Ttg>Ctg	p.L412L	PRDM5_ENST00000428209.2_Silent_p.L381L|PRDM5_ENST00000515109.1_Silent_p.L381L	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	412					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.L412L(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GTCCGGAACAAAGCTTTACAT	0.408													A|||	688	0.13738	0.0113	0.1931	5008	,	,		15439	0.1895		0.2674	False		,,,				2504	0.0808				p.L412L		Atlas-SNP	.											PRDM5,NS,carcinoma,0,1	PRDM5	76	1	1	Substitution - coding silent(1)	stomach(1)	c.T1234C						PASS	.	A		255,4151	146.9+/-181.5	11,233,1959	108.0	97.0	101.0		1234	-1.3	0.8	4	dbSNP_120	101	2344,6256	392.4+/-344.0	329,1686,2285	no	coding-synonymous	PRDM5	NM_018699.2		340,1919,4244	GG,GA,AA		27.2558,5.7876,19.9831		412/631	121706201	2599,10407	2203	4300	6503	SO:0001819	synonymous_variant	11107	exon11			GGAACAAAGCTTT	AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"""Zinc fingers, C2H2-type"""	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.1234T>C	4.37:g.121706201A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Silent	SNP	ENST00000264808.3	37	CCDS3716.1																																																																																			A|0.807;G|0.193	0.193	strong		0.408	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2		
HECTD3	79654	hgsc.bcm.edu	37	1	45475881	45475881	+	Silent	SNP	T	T	C	rs146960255	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:45475881T>C	ENST00000372172.4	-	3	686	c.615A>G	c.(613-615)caA>caG	p.Q205Q	UROD_ENST00000246337.4_5'Flank|HECTD3_ENST00000372168.3_5'Flank	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	205					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					ACAGTAGCCTTTGTACAGCTT	0.582													T|||	17	0.00339457	0.0	0.0072	5008	,	,		18680	0.0		0.0119	False		,,,				2504	0.0				p.Q205Q		Atlas-SNP	.											.	HECTD3	158	.	0			c.A615G						PASS	.	T		5,4165		0,5,2080	132.0	135.0	134.0		615	-2.2	1.0	1	dbSNP_134	134	80,8368		0,80,4144	no	coding-synonymous	HECTD3	NM_024602.5		0,85,6224	CC,CT,TT		0.947,0.1199,0.6736		205/862	45475881	85,12533	2085	4224	6309	SO:0001819	synonymous_variant	79654	exon3			TAGCCTTTGTACA	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"""HECT domain containing 3"""			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.615A>G	1.37:g.45475881T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Silent	SNP	ENST00000372172.4	37	CCDS41318.1																																																																																			T|0.994;C|0.006	0.006	strong		0.582	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602	
POMGNT1	55624	hgsc.bcm.edu	37	1	46655645	46655645	+	Missense_Mutation	SNP	C	C	T	rs74374973	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:46655645C>T	ENST00000371984.3	-	20	1823	c.1666G>A	c.(1666-1668)Gac>Aac	p.D556N	POMGNT1_ENST00000371992.1_Missense_Mutation_p.D556N|POMGNT1_ENST00000371986.3_Missense_Mutation_p.D556N|POMGNT1_ENST00000535522.1_Missense_Mutation_p.D534N|POMGNT1_ENST00000485714.1_5'Flank|POMGNT1_ENST00000396420.3_3'UTR	NM_017739.3	NP_060209	Q8WZA1	PMGT1_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)	556			D -> N (in MDDGC3; normal enzyme activity but altered kinetic properties; dbSNP:rs74374973). {ECO:0000269|PubMed:18195152}.		protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)			breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(166;0.155)					TTGCTGTGGTCCAGAACCTCA	0.527													C|||	26	0.00519169	0.0008	0.0101	5008	,	,		15236	0.0		0.0179	False		,,,				2504	0.0				p.D556N		Atlas-SNP	.											.	POMGNT1	96	.	0			c.G1666A	GRCh37	CM074441	POMGNT1	M	rs74374973	PASS	.	C	ASN/ASP	10,4396	16.8+/-37.8	0,10,2193	62.0	57.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1666	6.1	1.0	1	dbSNP_131	59	102,8498	56.0+/-117.1	2,98,4200	yes	missense	POMGNT1	NM_017739.3	23	2,108,6393	TT,TC,CC		1.186,0.227,0.8611	probably-damaging	556/661	46655645	112,12894	2203	4300	6503	SO:0001583	missense	55624	exon20			TGTGGTCCAGAAC		CCDS531.1, CCDS57995.1	1p34.1	2014-09-17	2013-07-31		ENSG00000085998	ENSG00000085998	2.4.1.-	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	19139	protein-coding gene	gene with protein product	"""protein O-mannose beta-1,2-N-acetylglucosaminyltransferase"""	606822	"""muscle-eye-brain disease"", ""protein O-linked mannose beta1,2-N-acetylglucosaminyltransferase"""	MEB		11742540, 12788071	Standard	NM_017739		Approved	FLJ20277, MGAT1.2, LGMD2O	uc001cpg.3	Q8WZA1	OTTHUMG00000007604	ENST00000371984.3:c.1666G>A	1.37:g.46655645C>T	ENSP00000361052:p.Asp556Asn	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	45	0.584416	NM_017739	D3DQ16|Q5VST2|Q5VST3|Q9BV55|Q9H9L8|Q9NXF9|Q9NYF7	Missense_Mutation	SNP	ENST00000371984.3	37	CCDS531.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	C	36	5.604935	0.96626	0.00227	0.01186	ENSG00000085998	ENST00000371984;ENST00000371992;ENST00000535522;ENST00000371986	D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59	6.06	6.06	0.98353	.	0.089068	0.85682	D	0.000000	T	0.81494	0.4834	L	0.52126	1.63	0.80722	A	1	D;D;D;D	0.71674	0.998;0.993;0.98;0.997	P;P;P;D	0.63283	0.895;0.896;0.824;0.913	D	0.83528	0.0089	9	0.45353	T	0.12	-32.5843	20.6208	0.99490	0.0:1.0:0.0:0.0	.	534;556;413;556	F5H827;Q5VST3;B7Z7F2;Q8WZA1	.;.;.;PMGT1_HUMAN	N	556;556;534;556	ENSP00000361052:D556N;ENSP00000361060:D556N;ENSP00000443767:D534N;ENSP00000361054:D556N	ENSP00000361052:D556N	D	-	1	0	POMGNT1	46428232	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.757000	0.68766	2.882000	0.98803	0.655000	0.94253	GAC	C|0.992;T|0.008	0.008	strong		0.527	POMGNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020146.1	NM_017739	
TTC31	64427	hgsc.bcm.edu	37	2	74710491	74710491	+	Missense_Mutation	SNP	C	C	T	rs6707475	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:74710491C>T	ENST00000233623.5	+	2	90	c.83C>T	c.(82-84)gCa>gTa	p.A28V	TTC31_ENST00000442235.2_5'UTR|TTC31_ENST00000463189.1_3'UTR|CCDC142_ENST00000290418.4_5'Flank|CCDC142_ENST00000393965.3_5'Flank|CCDC142_ENST00000471713.1_5'Flank|TTC31_ENST00000410003.1_Missense_Mutation_p.A28V	NM_022492.4	NP_071937.4	Q49AM3	TTC31_HUMAN	tetratricopeptide repeat domain 31	28			A -> V (in dbSNP:rs6707475). {ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						GTCGCTGCTGCACCCAAACTT	0.582											OREG0014719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2741	0.547324	0.907	0.3256	5008	,	,		17254	0.8224		0.159	False		,,,				2504	0.3344				p.A28V		Atlas-SNP	.											.	TTC31	23	.	0			c.C83T						PASS	.	T	VAL/ALA	2987,943		1146,695,124	63.0	71.0	68.0		83	0.3	0.8	2	dbSNP_116	68	1204,7124		95,1014,3055	yes	missense	TTC31	NM_022492.4	64	1241,1709,3179	TT,TC,CC		14.4573,23.9949,34.1899	benign	28/520	74710491	4191,8067	1965	4164	6129	SO:0001583	missense	64427	exon2			CTGCTGCACCCAA	AK026819	CCDS42701.1	2p13.1	2013-01-11			ENSG00000115282	ENSG00000115282		"""Tetratricopeptide (TTC) repeat domain containing"""	25759	protein-coding gene	gene with protein product						12477932	Standard	NM_022492		Approved	FLJ12788	uc002slt.2	Q49AM3	OTTHUMG00000152887	ENST00000233623.5:c.83C>T	2.37:g.74710491C>T	ENSP00000233623:p.Ala28Val	Somatic	83	0	0	1154	WXS	Illumina HiSeq	Phase_I	139	101	0.726619	NM_022492	Q4KN40|Q53FD4|Q9H9F7	Missense_Mutation	SNP	ENST00000233623.5	37	CCDS42701.1	1119	0.5123626373626373	436	0.8861788617886179	98	0.27071823204419887	470	0.8216783216783217	115	0.1517150395778364	T	14.44	2.534928	0.45073	0.760051	0.144573	ENSG00000115282	ENST00000410003;ENST00000435361;ENST00000441635;ENST00000233623	T;T	0.38077	1.16;1.16	4.27	0.28	0.15682	.	0.280031	0.23373	N	0.048891	T	0.00012	0.0000	N	0.00347	-1.61	0.09310	P	0.9999999999531156	B	0.02656	0.0	B	0.01281	0.0	T	0.29579	-1.0007	9	0.02654	T	1	-1.4487	3.1691	0.06546	0.1962:0.3671:0.0:0.4367	rs6707475;rs52813769;rs59381657;rs6707475	28	Q49AM3	TTC31_HUMAN	V	28	ENSP00000387213:A28V;ENSP00000233623:A28V	ENSP00000233623:A28V	A	+	2	0	TTC31	74563999	0.061000	0.20836	0.771000	0.31576	0.900000	0.52787	-0.054000	0.11826	-0.006000	0.14370	-0.254000	0.11334	GCA	C|0.514;T|0.486	0.486	strong		0.582	TTC31-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328422.1	NM_022492	
DNMBP	23268	hgsc.bcm.edu	37	10	101639877	101639877	+	Missense_Mutation	SNP	A	A	C	rs11190305	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:101639877A>C	ENST00000324109.4	-	16	4330	c.4239T>G	c.(4237-4239)tgT>tgG	p.C1413W	DNMBP_ENST00000540316.1_Missense_Mutation_p.C349W|DNMBP_ENST00000342239.3_Missense_Mutation_p.C1437W|DNMBP_ENST00000543621.1_Missense_Mutation_p.C659W	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1413	Ser-rich.		C -> W (in dbSNP:rs11190305). {ECO:0000269|PubMed:15489334}.		intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TTCCTTGGTCACATTCTTTTG	0.542													A|||	1388	0.277157	0.1437	0.3329	5008	,	,		19778	0.244		0.3917	False		,,,				2504	0.3344				p.C1413W		Atlas-SNP	.											.	DNMBP	173	.	0			c.T4239G						PASS	.		TRP/CYS	827,3579	328.5+/-300.6	82,663,1458	194.0	191.0	192.0		4239	0.6	0.0	10	dbSNP_120	192	3271,5329	490.7+/-372.9	638,1995,1667	yes	missense	DNMBP	NM_015221.2	215	720,2658,3125	CC,CA,AA		38.0349,18.7699,31.5085	benign	1413/1578	101639877	4098,8908	2203	4300	6503	SO:0001583	missense	23268	exon16			TTGGTCACATTCT	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.4239T>G	10.37:g.101639877A>C	ENSP00000315659:p.Cys1413Trp	Somatic	273	2	0.00732601		WXS	Illumina HiSeq	Phase_I	177	162	0.915254	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	630	0.28846153846153844	55	0.11178861788617886	133	0.3674033149171271	150	0.26223776223776224	292	0.38522427440633245	A	9.817	1.184720	0.21870	0.187699	0.380349	ENSG00000107554	ENST00000342239;ENST00000324109;ENST00000393570;ENST00000543621;ENST00000540316	T;T;T;T	0.34275	2.81;2.76;2.42;1.37	5.77	0.604	0.17547	.	2.318410	0.01492	N	0.017126	T	0.00012	0.0000	N	0.14661	0.345	0.44104	P	0.003125999999999962	B;P;B	0.37573	0.328;0.6;0.102	B;B;B	0.41202	0.094;0.35;0.078	T	0.28618	-1.0038	9	0.37606	T	0.19	11.0357	1.0338	0.01543	0.3826:0.2917:0.1845:0.1411	rs11190305;rs17495998;rs17846312;rs17859342;rs52793133;rs56919867;rs11190305	1413;659;1437	Q6XZF7;Q6XZF7-2;Q5SVK8	DNMBP_HUMAN;.;.	W	1437;1413;659;659;349	ENSP00000344914:C1437W;ENSP00000315659:C1413W;ENSP00000443657:C659W;ENSP00000443573:C349W	ENSP00000315659:C1413W	C	-	3	2	DNMBP	101629867	0.000000	0.05858	0.006000	0.13384	0.005000	0.04900	-0.874000	0.04210	-0.132000	0.11557	-0.366000	0.07423	TGT	A|0.708;C|0.292	0.292	strong		0.542	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
PCDHA8	56140	hgsc.bcm.edu	37	5	140221139	140221139	+	Missense_Mutation	SNP	G	G	A	rs3756331	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140221139G>A	ENST00000531613.1	+	1	233	c.233G>A	c.(232-234)aGt>aAt	p.S78N	PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.S78N|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	78	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> N (in dbSNP:rs3756331).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S78N(2)		NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGAGGTAAGTCTGCAGAAT	0.642													.|||	2981	0.595248	0.7383	0.6009	5008	,	,		18152	0.5337		0.5338	False		,,,				2504	0.5245				p.S78N		Atlas-SNP	.											PCDHA8_ENST00000531613,NS,carcinoma,0,2	PCDHA8	366	2	2	Substitution - Missense(2)	stomach(2)	c.G233A						PASS	.	A	,,,,,,,ASN/SER,,,ASN/SER	2941,1439		1111,719,360	56.0	82.0	73.0		,,,,,,,233,,,233	2.7	1.0	5	dbSNP_107	73	4120,4444		1149,1822,1311	no	intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,missense	PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031856.1	,,,,,,,46,,,46	2260,2541,1671	AA,AG,GG		48.1084,32.8539,45.4496	,,,,,,,,,,	,,,,,,,78/951,,,78/815	140221139	7061,5883	2190	4282	6472	SO:0001583	missense	56140	exon1			AGGTAAGTCTGCA	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.233G>A	5.37:g.140221139G>A	ENSP00000434655:p.Ser78Asn	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	69	40	0.57971	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	1164	0.532967032967033	319	0.6483739837398373	187	0.5165745856353591	290	0.506993006993007	368	0.48548812664907653	A	0.403	-0.917356	0.02396	0.671461	0.481084	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.34859	1.34;1.34	3.91	2.73	0.32206	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	0.000000	0.39083	N	0.001480	T	0.00012	0.0000	N	0.00125	-2.05	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42882	-0.9425	9	0.02654	T	1	.	4.5167	0.11939	0.6189:0.0:0.2461:0.1351	rs3756331;rs6881677;rs17844315;rs59428168	78;78	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	N	78	ENSP00000434655:S78N;ENSP00000367363:S78N	ENSP00000367363:S78N	S	+	2	0	PCDHA8	140201323	0.478000	0.25917	0.985000	0.45067	0.851000	0.48451	3.070000	0.50033	0.083000	0.17047	-0.389000	0.06534	AGT	G|0.466;A|0.534	0.534	strong		0.642	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
PCDHB16	57717	hgsc.bcm.edu	37	5	140563574	140563574	+	Silent	SNP	A	A	G	rs2697534	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140563574A>G	ENST00000361016.2	+	1	2595	c.1440A>G	c.(1438-1440)tcA>tcG	p.S480S		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	480	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACAGAGACTCAGGCACCAACG	0.657																																					p.S480S		Atlas-SNP	.											PCDHB16,NS,carcinoma,+2,1	PCDHB16	159	1	0			c.A1440G						scavenged	.						59.0	55.0	56.0					5																	140563574		2203	4278	6481	SO:0001819	synonymous_variant	57717	exon1			AGACTCAGGCACC	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1440A>G	5.37:g.140563574A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	93	12	0.129032	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Silent	SNP	ENST00000361016.2	37	CCDS4251.1																																																																																			A|0.320;G|0.680	0.680	strong		0.657	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
ITIH4	3700	hgsc.bcm.edu	37	3	52852538	52852538	+	Missense_Mutation	SNP	G	G	T	rs4687657	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52852538G>T	ENST00000266041.4	-	18	2188	c.2092C>A	c.(2092-2094)Cca>Aca	p.P698T	RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000467462.1_5'Flank|ITIH4_ENST00000485816.1_Missense_Mutation_p.P703T|ITIH4_ENST00000406595.1_Missense_Mutation_p.P668T|ITIH4_ENST00000346281.5_Missense_Mutation_p.P668T	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	698			P -> T (in dbSNP:rs4687657).		acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GTGGCTGGTGGTGCTGAAGCA	0.587													G|||	1291	0.257788	0.1997	0.3919	5008	,	,		18673	0.3155		0.3022	False		,,,				2504	0.136				p.P698T		Atlas-SNP	.											.	ITIH4	74	.	0			c.C2092A						PASS	.	G	THR/PRO,THR/PRO	965,3437		97,771,1333	59.0	55.0	56.0		2002,2092	1.6	0.0	3	dbSNP_111	56	2288,6306		327,1634,2336	yes	missense,missense	ITIH4	NM_001166449.1,NM_002218.4	38,38	424,2405,3669	TT,TG,GG		26.6232,21.9219,25.0308	benign,benign	668/901,698/931	52852538	3253,9743	2201	4297	6498	SO:0001583	missense	3700	exon18			CTGGTGGTGCTGA	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"""plasma Kallikrein-sensitive glycoprotein"""	600564	"""inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"""	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.2092C>A	3.37:g.52852538G>T	ENSP00000266041:p.Pro698Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	174	75	0.431034	NM_002218	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Missense_Mutation	SNP	ENST00000266041.4	37	CCDS2865.1	672|672	0.3076923076923077|0.3076923076923077	86|86	0.17479674796747968|0.17479674796747968	143|143	0.39502762430939226|0.39502762430939226	213|213	0.3723776223776224|0.3723776223776224	230|230	0.3034300791556728|0.3034300791556728	G|G	7.544|7.544	0.661216|0.661216	0.14645|0.14645	0.219219|0.219219	0.266232|0.266232	ENSG00000055955|ENSG00000055955	ENST00000266041;ENST00000346281;ENST00000485816;ENST00000406595;ENST00000538421|ENST00000441637	T;T;T;T|.	0.01474|.	4.91;4.89;4.91;4.85|.	3.44|3.44	1.62|1.62	0.23740|0.23740	.|.	15.761600|.	0.00166|.	N|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.55481|0.55481	1.735|1.735	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.15719|.	0.011;0.014;0.011;0.005|.	B;B;B;B|.	0.13407|.	0.009;0.008;0.009;0.004|.	T|T	0.40794|0.40794	-0.9544|-0.9544	9|4	0.19590|.	T|.	0.45|.	2.2572|2.2572	4.1556|4.1556	0.10260|0.10260	0.1216:0.0:0.6499:0.2285|0.1216:0.0:0.6499:0.2285	rs4687657;rs60446728;rs4687657|rs4687657;rs60446728;rs4687657	668;703;698;668|.	E9PGN5;B7ZKJ8;Q14624;Q14624-2|.	.;.;ITIH4_HUMAN;.|.	T|N	698;668;703;668;656|525	ENSP00000266041:P698T;ENSP00000340520:P668T;ENSP00000417824:P703T;ENSP00000384425:P668T|.	ENSP00000266041:P698T|.	P|T	-|-	1|2	0|0	ITIH4|ITIH4	52827578|52827578	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	-0.314000|-0.314000	0.08092|0.08092	0.447000|0.447000	0.26695|0.26695	-0.890000|-0.890000	0.02929|0.02929	CCA|ACC	G|0.736;N|0.000	.	strong		0.587	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
TFRC	7037	hgsc.bcm.edu	37	3	195778972	195778972	+	Silent	SNP	C	C	T	rs1805051	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:195778972C>T	ENST00000360110.4	-	19	2293	c.2124G>A	c.(2122-2124)acG>acA	p.T708T	TFRC_ENST00000420415.1_Silent_p.T627T|TFRC_ENST00000535031.1_Silent_p.T426T|TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000392396.3_Silent_p.T708T	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	708	Ligand-binding.				cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|osteoclast differentiation (GO:0030316)|positive regulation of bone resorption (GO:0045780)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transferrin receptor activity (GO:0004998)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)	Gallium nitrate(DB05260)	AAGCTGGCAGCGTGTGAGAGC	0.468			T	BCL6	NHL								C|||	242	0.0483227	0.003	0.0706	5008	,	,		18754	0.002		0.0875	False		,,,				2504	0.1012				p.T708T		Atlas-SNP	.		Dom	yes		3	3q29	7037	"""transferrin receptor (p90, CD71)"""		L	.	TFRC	54	.	0			c.G2124A						PASS	.	C	,	86,4320	72.5+/-110.5	1,84,2118	67.0	68.0	68.0		2124,2124	-3.1	0.4	3	dbSNP_89	68	928,7672	205.2+/-247.7	52,824,3424	no	coding-synonymous,coding-synonymous	TFRC	NM_001128148.1,NM_003234.2	,	53,908,5542	TT,TC,CC		10.7907,1.9519,7.7964	,	708/761,708/761	195778972	1014,11992	2203	4300	6503	SO:0001819	synonymous_variant	7037	exon19			TGGCAGCGTGTGA	X01060	CCDS3312.1	3q29	2013-09-19	2013-09-19		ENSG00000072274	ENSG00000072274		"""CD molecules"""	11763	protein-coding gene	gene with protein product		190010	"""transferrin receptor (p90, CD71)"""				Standard	NM_003234		Approved	CD71, TFR1, p90	uc003fwa.4	P02786	OTTHUMG00000155714	ENST00000360110.4:c.2124G>A	3.37:g.195778972C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	216	103	0.476852	NM_001128148	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Silent	SNP	ENST00000360110.4	37	CCDS3312.1																																																																																			C|0.929;T|0.071	0.071	strong		0.468	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1		
KAT6A	7994	hgsc.bcm.edu	37	8	41794934	41794934	+	Silent	SNP	C	C	T	rs13748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:41794934C>T	ENST00000396930.3	-	17	3735	c.3192G>A	c.(3190-3192)acG>acA	p.T1064T	KAT6A_ENST00000406337.1_Silent_p.T1064T|KAT6A_ENST00000265713.2_Silent_p.T1064T	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1064					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CGATCTCAAACGTGGGTTCTA	0.438													C|||	1049	0.209465	0.4849	0.1484	5008	,	,		18800	0.004		0.2704	False		,,,				2504	0.0297				p.T1064T		Atlas-SNP	.											.	.	.	.	0			c.G3192A						PASS	.	C	,,	1890,2516	543.4+/-376.3	417,1056,730	122.0	117.0	119.0		3192,3192,3192	-11.3	0.2	8	dbSNP_52	119	2019,6581	353.5+/-329.1	243,1533,2524	no	coding-synonymous,coding-synonymous,coding-synonymous	KAT6A	NM_001099412.1,NM_001099413.1,NM_006766.3	,,	660,2589,3254	TT,TC,CC		23.4767,42.8961,30.0554	,,	1064/2005,1064/2005,1064/2005	41794934	3909,9097	2203	4300	6503	SO:0001819	synonymous_variant	7994	exon17			CTCAAACGTGGGT	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.3192G>A	8.37:g.41794934C>T		Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	351	177	0.504274	NM_001099412	Q76L81	Silent	SNP	ENST00000396930.3	37	CCDS6124.1																																																																																			C|0.720;T|0.280	0.280	strong		0.438	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
MURC	347273	hgsc.bcm.edu	37	9	103348208	103348208	+	Silent	SNP	A	A	T	rs28623148	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:103348208A>T	ENST00000307584.5	+	2	635	c.570A>T	c.(568-570)tcA>tcT	p.S190S		NM_001018116.1	NP_001018126.1	Q5BKX8	MURC_HUMAN	muscle-related coiled-coil protein	190					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Z disc (GO:0030018)				endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)	16		Acute lymphoblastic leukemia(62;0.0461)				TTAGGAAGTCAGGCAAGGAGC	0.393													A|||	590	0.117812	0.0514	0.0418	5008	,	,		21179	0.2232		0.0258	False		,,,				2504	0.2474				p.S190S		Atlas-SNP	.											.	MURC	43	.	0			c.A570T						PASS	.	A		235,4171	138.4+/-174.2	6,223,1974	79.0	80.0	79.0		570	1.4	1.0	9	dbSNP_125	79	203,8397	87.4+/-149.7	1,201,4098	no	coding-synonymous	MURC	NM_001018116.1		7,424,6072	TT,TA,AA		2.3605,5.3336,3.3677		190/365	103348208	438,12568	2203	4300	6503	SO:0001819	synonymous_variant	347273	exon2			GAAGTCAGGCAAG	BC090888	CCDS35083.1	9q31.1	2014-09-17			ENSG00000170681	ENSG00000170681			33742	protein-coding gene	gene with protein product	"""muscle-restricted coiled-coil protein"""					18508909, 18332105	Standard	NM_001018116		Approved	cavin-4, CAVIN4	uc004bba.3	Q5BKX8	OTTHUMG00000020368	ENST00000307584.5:c.570A>T	9.37:g.103348208A>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_001018116	B1PRL3|B4DT88	Silent	SNP	ENST00000307584.5	37	CCDS35083.1																																																																																			A|0.955;T|0.045	0.045	strong		0.393	MURC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053419.2	NM_001018116	
SETD4	54093	hgsc.bcm.edu	37	21	37410477	37410477	+	Missense_Mutation	SNP	T	T	C	rs2835239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:37410477T>C	ENST00000399215.1	-	9	2531	c.1159A>G	c.(1159-1161)Ata>Gta	p.I387V	SETD4_ENST00000481477.1_5'UTR|SETD4_ENST00000399212.1_Missense_Mutation_p.I363V|SETD4_ENST00000332131.4_Missense_Mutation_p.I387V|AP000688.1_ENST00000600312.1_Intron			Q9NVD3	SETD4_HUMAN	SET domain containing 4	387			I -> V (in dbSNP:rs2835239).	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						GTCTCTTCTATGAAATAATAG	0.348													T|||	128	0.0255591	0.0	0.036	5008	,	,		19033	0.002		0.0636	False		,,,				2504	0.0378				p.I387V		Atlas-SNP	.											.	SETD4	37	.	0			c.A1159G						PASS	.	T	VAL/ILE	56,4348	54.9+/-90.9	2,52,2148	164.0	159.0	161.0		1159	3.2	0.2	21	dbSNP_100	161	498,8102	144.3+/-200.2	8,482,3810	yes	missense	SETD4	NM_017438.3	29	10,534,5958	CC,CT,TT		5.7907,1.2716,4.2602	possibly-damaging	387/441	37410477	554,12450	2202	4300	6502	SO:0001583	missense	54093	exon10			CTTCTATGAAATA	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.1159A>G	21.37:g.37410477T>C	ENSP00000382163:p.Ile387Val	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	245	126	0.514286	NM_017438	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Missense_Mutation	SNP	ENST00000399215.1	37	CCDS13640.1	62	0.028388278388278388	0	0.0	13	0.03591160220994475	0	0.0	49	0.06464379947229551	T	14.91	2.676807	0.47886	0.012716	0.057907	ENSG00000185917	ENST00000399215;ENST00000399212;ENST00000332131	T;T;T	0.18016	2.24;2.24;2.24	5.79	3.22	0.36961	Rubisco LS methyltransferase, substrate-binding domain (1);	0.377760	0.30762	N	0.008935	T	0.02083	0.0065	M	0.70595	2.14	0.38358	D	0.94451	B;P	0.36789	0.27;0.57	B;B	0.41202	0.151;0.35	T	0.04294	-1.0962	10	0.24483	T	0.36	-25.5361	7.6719	0.28463	0.1314:0.0:0.2735:0.5951	rs2835239;rs17228507;rs52822224;rs59296148;rs2835239	363;387	Q9NVD3-3;Q9NVD3	.;SETD4_HUMAN	V	387;363;387	ENSP00000382163:I387V;ENSP00000382161:I363V;ENSP00000329189:I387V	ENSP00000329189:I387V	I	-	1	0	SETD4	36332347	0.986000	0.35501	0.209000	0.23619	0.729000	0.41735	0.337000	0.19841	0.970000	0.38263	0.459000	0.35465	ATA	T|0.963;C|0.037	0.037	strong		0.348	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438	
R3HCC1	203069	hgsc.bcm.edu	37	8	23148930	23148930	+	Silent	SNP	A	A	G	rs200790441|rs2272762	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:23148930A>G	ENST00000411463.1	+	6	1029	c.1029A>G	c.(1027-1029)acA>acG	p.T343T	R3HCC1_ENST00000265806.6_Silent_p.T116T|R3HCC1_ENST00000518454.1_Silent_p.T116T|R3HCC1_ENST00000522012.1_3'UTR			Q9Y3T6	R3HC1_HUMAN	R3H domain and coiled-coil containing 1	343							nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)			central_nervous_system(1)|skin(2)	3						ATTTGGACACATCCTCCTTCG	0.532													G|||	2791	0.557308	0.4312	0.4597	5008	,	,		21514	0.7996		0.5427	False		,,,				2504	0.5624				p.T116T		Atlas-SNP	.											R3HCC1,colon,carcinoma,0,1	R3HCC1	11	1	0			c.A348G						PASS	.	G		630,754		147,336,209	131.0	119.0	123.0		348	-7.5	0.3	8	dbSNP_100	123	1849,1333		528,793,270	no	coding-synonymous	R3HCC1	NM_001136108.1		675,1129,479	GG,GA,AA		41.8919,45.5202,45.7074		116/254	23148930	2479,2087	692	1591	2283	SO:0001819	synonymous_variant	203069	exon5			GGACACATCCTCC		CCDS47826.1	8p21.3	2012-05-23		2005-11-20	ENSG00000104679	ENSG00000104679			27329	protein-coding gene	gene with protein product						12477932	Standard	XM_005273427		Approved	DKFZp564N123	uc003xdf.3	Q9Y3T6	OTTHUMG00000163786	ENST00000411463.1:c.1029A>G	8.37:g.23148930A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	111	45	0.405405	NM_001136108	B7ZLI1	Silent	SNP	ENST00000411463.1	37																																																																																				A|0.395;G|0.605	0.605	strong		0.532	R3HCC1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001136108	
GNPAT	8443	hgsc.bcm.edu	37	1	231401902	231401902	+	Silent	SNP	G	G	A	rs574553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:231401902G>A	ENST00000366647.4	+	7	1084	c.915G>A	c.(913-915)gaG>gaA	p.E305E	GNPAT_ENST00000366646.3_Silent_p.E244E	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	305					cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				AACCAAAAGAGTCTACAACTG	0.358													A|||	3148	0.628594	0.7012	0.6254	5008	,	,		19809	0.6339		0.5318	False		,,,				2504	0.6268				p.E305E		Atlas-SNP	.											.	GNPAT	73	.	0			c.G915A						PASS	.	A		3020,1386	455.9+/-351.1	1038,944,221	107.0	110.0	109.0		915	3.2	1.0	1	dbSNP_83	109	4716,3884	544.7+/-384.6	1291,2134,875	no	coding-synonymous	GNPAT	NM_014236.3		2329,3078,1096	AA,AG,GG		45.1628,31.4571,40.5198		305/681	231401902	7736,5270	2203	4300	6503	SO:0001819	synonymous_variant	8443	exon7			AAAAGAGTCTACA	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.915G>A	1.37:g.231401902G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_014236	B4DNM9|Q5TBH7|Q9BWC2	Silent	SNP	ENST00000366647.4	37	CCDS1592.1																																																																																			G|0.396;A|0.604	0.604	strong		0.358	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1		
LINS	55180	hgsc.bcm.edu	37	15	101110265	101110265	+	Silent	SNP	T	T	A	rs2411836	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:101110265T>A	ENST00000314742.8	-	7	1674	c.1452A>T	c.(1450-1452)acA>acT	p.T484T	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	484								p.T484T(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						CATTTTCATGTGTGTGATGGT	0.353													T|||	1560	0.311502	0.2375	0.2493	5008	,	,		17495	0.246		0.4513	False		,,,				2504	0.3793				p.T484T		Atlas-SNP	.											LINS,NS,carcinoma,0,1	LINS	62	1	1	Substitution - coding silent(1)	stomach(1)	c.A1452T						scavenged	.	T		1242,3164	413.7+/-336.6	157,928,1118	56.0	55.0	55.0		1452	-0.9	0.8	15	dbSNP_100	55	4032,4566	526.5+/-381.0	961,2110,1228	no	coding-synonymous	LINS	NM_001040616.2		1118,3038,2346	AA,AT,TT		46.8946,28.1888,40.5568		484/758	101110265	5274,7730	2203	4299	6502	SO:0001819	synonymous_variant	55180	exon7			TTCATGTGTGTGA	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"""lines homolog 1 (Drosophila)"""	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1452A>T	15.37:g.101110265T>A		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	11	7	0.636364	NM_001040616	Q96FW2|Q9NVQ3	Silent	SNP	ENST00000314742.8	37	CCDS10385.1																																																																																			T|0.624;A|0.376	0.376	strong		0.353	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148	
HECTD4	283450	hgsc.bcm.edu	37	12	112601517	112601517	+	Silent	SNP	C	C	T	rs61748839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:112601517C>T	ENST00000430131.2	-	73	12605	c.11460G>A	c.(11458-11460)gcG>gcA	p.A3820A	HECTD4_ENST00000549141.1_5'Flank|HECTD4_ENST00000550722.1_Silent_p.A4096A|HECTD4_ENST00000377560.5_Silent_p.A4070A			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3820	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GGATGGCTGCCGCGTAGATGT	0.682													c|||	9	0.00179712	0.0023	0.0029	5008	,	,		16972	0.0		0.004	False		,,,				2504	0.0				p.A4108A		Atlas-SNP	.											.	.	.	.	0			c.G12324A						PASS	.	T		1,2955		0,1,1477	5.0	9.0	7.0		12210	-11.5	0.0	12	dbSNP_129	7	22,5824		0,22,2901	no	coding-synonymous	C12orf51	NM_001109662.2		0,23,4378	TT,TC,CC		0.3763,0.0338,0.2613		4070/4247	112601517	23,8779	1478	2923	4401	SO:0001819	synonymous_variant	283450	exon74			GGCTGCCGCGTAG	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.11460G>A	12.37:g.112601517C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																				C|0.996;T|0.004	0.004	strong		0.682	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
FOXN1	8456	hgsc.bcm.edu	37	17	26864302	26864302	+	Missense_Mutation	SNP	G	G	C	rs532648	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:26864302G>C	ENST00000226247.2	+	8	1824	c.1795G>C	c.(1795-1797)Gcc>Ccc	p.A599P	FOXN1_ENST00000579795.1_Missense_Mutation_p.A599P	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	599			A -> P (in dbSNP:rs532648).		defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					TGACTTGGCAGCCCCGGGCAG	0.677													C|||	1967	0.392772	0.6309	0.3862	5008	,	,		16861	0.2212		0.334	False		,,,				2504	0.3129				p.A599P		Atlas-SNP	.											.	FOXN1	51	.	0			c.G1795C						PASS	.	C	PRO/ALA	2506,1900	539.4+/-375.3	695,1116,392	39.0	40.0	39.0		1795	2.2	0.9	17	dbSNP_83	39	2419,6181	693.8+/-404.7	333,1753,2214	yes	missense	FOXN1	NM_003593.2	27	1028,2869,2606	CC,CG,GG		28.1279,43.123,37.8671	benign	599/649	26864302	4925,8081	2203	4300	6503	SO:0001583	missense	8456	exon8			TTGGCAGCCCCGG	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"""Forkhead boxes"""	12765	protein-coding gene	gene with protein product		600838	"""winged-helix nude"", ""Rowett nude"""	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.1795G>C	17.37:g.26864302G>C	ENSP00000226247:p.Ala599Pro	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	200	106	0.53	NM_003593	B2R9Q7|O15352	Missense_Mutation	SNP	ENST00000226247.2	37	CCDS11232.1	829	0.37957875457875456	313	0.6361788617886179	137	0.3784530386740331	144	0.2517482517482518	235	0.3100263852242744	C	0.003	-2.391997	0.00200	0.56877	0.281279	ENSG00000109101	ENST00000226247	D	0.92348	-3.02	4.2	2.18	0.27775	.	0.393102	0.22159	N	0.063817	T	0.00012	0.0000	N	0.00335	-1.625	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41822	-0.9487	9	0.02654	T	1	.	5.1473	0.14991	0.1624:0.5975:0.0991:0.141	rs532648;rs3744636	599	O15353	FOXN1_HUMAN	P	599	ENSP00000226247:A599P	ENSP00000226247:A599P	A	+	1	0	FOXN1	23888429	0.000000	0.05858	0.918000	0.36340	0.306000	0.27790	0.598000	0.24074	-0.141000	0.11374	-2.896000	0.00094	GCC	G|0.618;C|0.382	0.382	strong		0.677	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1		
MYPN	84665	hgsc.bcm.edu	37	10	69933969	69933969	+	Missense_Mutation	SNP	G	G	A	rs7916821	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:69933969G>A	ENST00000358913.5	+	11	2608	c.2120G>A	c.(2119-2121)aGt>aAt	p.S707N	MYPN_ENST00000540630.1_Missense_Mutation_p.S707N|MYPN_ENST00000354393.2_Missense_Mutation_p.S432N	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	707			S -> N (in dbSNP:rs7916821). {ECO:0000269|PubMed:11309420, ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						ACAACATCCAGTAAGCAGGTG	0.532													G|||	1628	0.32508	0.1762	0.4035	5008	,	,		18267	0.2163		0.4851	False		,,,				2504	0.4182				p.S707N		Atlas-SNP	.											.	MYPN	189	.	0			c.G2120A						PASS	.	G	ASN/SER	977,3429	367.3+/-318.2	109,759,1335	126.0	122.0	123.0		2120	4.7	1.0	10	dbSNP_116	123	4126,4474	564.6+/-388.3	1042,2042,1216	yes	missense	MYPN	NM_032578.2	46	1151,2801,2551	AA,AG,GG		47.9767,22.1743,39.2357	benign	707/1321	69933969	5103,7903	2203	4300	6503	SO:0001583	missense	84665	exon11			CATCCAGTAAGCA	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2120G>A	10.37:g.69933969G>A	ENSP00000351790:p.Ser707Asn	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	242	118	0.487603	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	752	0.3443223443223443	103	0.20934959349593496	152	0.4198895027624309	129	0.22552447552447552	368	0.48548812664907653	G	11.58	1.680407	0.29872	0.221743	0.479767	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.58210	0.35;0.44;0.42	5.64	4.68	0.58851	.	0.566496	0.20639	N	0.088436	T	0.00012	0.0000	L	0.36672	1.1	0.40218	P	0.022298999999999958	B;B;B	0.23806	0.045;0.091;0.026	B;B;B	0.26310	0.068;0.032;0.031	T	0.44360	-0.9333	8	.	.	.	.	8.7519	0.34620	0.1116:0.0:0.7493:0.1391	rs7916821;rs17536754;rs52812363;rs56567864;rs57392128;rs7916821	707;432;707	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	N	432;432;707;707	ENSP00000346369:S432N;ENSP00000351790:S707N;ENSP00000441668:S707N	.	S	+	2	0	MYPN	69603975	0.513000	0.26194	1.000000	0.80357	0.719000	0.41307	0.501000	0.22578	2.832000	0.97577	0.655000	0.94253	AGT	G|0.638;A|0.362	0.362	strong		0.532	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
FRMD1	79981	hgsc.bcm.edu	37	6	168457966	168457966	+	Silent	SNP	G	G	A	rs3734899	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168457966G>A	ENST00000283309.6	-	11	1525	c.1461C>T	c.(1459-1461)gaC>gaT	p.D487D	FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000537786.1_Silent_p.D258D|FRMD1_ENST00000440994.2_Silent_p.D419D	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	487						cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		GCTGCATGTCGTCCAGGCCAT	0.672													G|||	1981	0.395567	0.1074	0.353	5008	,	,		17417	0.4871		0.493	False		,,,				2504	0.6207				p.D487D	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.C1461T						PASS	.	G	,	746,3660	296.1+/-284.1	69,608,1526	37.0	34.0	35.0		1257,1461	-5.5	0.0	6	dbSNP_107	35	3924,4676	536.6+/-383.0	877,2170,1253	no	coding-synonymous,coding-synonymous	FRMD1	NM_001122841.1,NM_024919.3	,	946,2778,2779	AA,AG,GG		45.6279,16.9315,35.9065	,	419/482,487/550	168457966	4670,8336	2203	4300	6503	SO:0001819	synonymous_variant	79981	exon11			CATGTCGTCCAGG		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.1461C>T	6.37:g.168457966G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Silent	SNP	ENST00000283309.6	37	CCDS5306.1																																																																																			G|0.633;A|0.367	0.367	strong		0.672	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919	
AKAP13	11214	hgsc.bcm.edu	37	15	86124483	86124483	+	Missense_Mutation	SNP	C	C	G	rs4843074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86124483C>G	ENST00000394518.2	+	7	3279	c.3184C>G	c.(3184-3186)Cct>Gct	p.P1062A	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.P1062A	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1062			P -> A (in dbSNP:rs4843074). {ECO:0000269|Ref.3}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CTGCAGTCAGCCTTCTCCTCT	0.532													C|||	2914	0.581869	0.5469	0.6182	5008	,	,		22712	0.5784		0.6153	False		,,,				2504	0.5726				p.P1062A	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C3184G						PASS	.	C	ALA/PRO,ALA/PRO	2605,1799	638.8+/-397.0	778,1049,375	77.0	74.0	75.0		3184,3184	-0.9	0.0	15	dbSNP_111	75	5533,3065	656.1+/-401.3	1797,1939,563	yes	missense,missense	AKAP13	NM_006738.4,NM_007200.3	27,27	2575,2988,938	GG,GC,CC		35.6478,40.8492,37.4096	benign,benign	1062/2818,1062/2814	86124483	8138,4864	2202	4299	6501	SO:0001583	missense	11214	exon7			AGTCAGCCTTCTC	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.3184C>G	15.37:g.86124483C>G	ENSP00000378026:p.Pro1062Ala	Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	217	216	0.995392	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	1277	0.5847069597069597	261	0.5304878048780488	221	0.6104972375690608	334	0.583916083916084	461	0.6081794195250659	C	11.12	1.546134	0.27652	0.591508	0.643522	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.15718	2.4;2.4	4.55	-0.872	0.10638	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.42050	P	0.008888000000000007	B;B	0.32101	0.243;0.356	B;B	0.33454	0.079;0.164	T	0.31392	-0.9945	8	0.31617	T	0.26	.	0.5594	0.00676	0.1915:0.3321:0.1914:0.285	rs4843074;rs52828149;rs4843074	1062;1062	Q12802;Q12802-2	AKP13_HUMAN;.	A	1062;1062;1061;1061	ENSP00000354718:P1062A;ENSP00000378026:P1062A	ENSP00000354718:P1062A	P	+	1	0	AKAP13	83925487	0.000000	0.05858	0.028000	0.17463	0.038000	0.13279	-0.511000	0.06321	-0.005000	0.14395	0.655000	0.94253	CCT	C|0.377;G|0.623	0.623	strong		0.532	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
FAM179A	165186	hgsc.bcm.edu	37	2	29221040	29221040	+	Silent	SNP	C	C	T	rs72786173	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29221040C>T	ENST00000379558.4	+	3	411	c.60C>T	c.(58-60)tgC>tgT	p.C20C	FAM179A_ENST00000403861.2_Silent_p.C20C	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	20										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCGTGTACTGCGGGAGCATCC	0.622													C|||	62	0.0123802	0.0015	0.0231	5008	,	,		15479	0.0		0.0408	False		,,,				2504	0.0031				p.C20C		Atlas-SNP	.											.	FAM179A	106	.	0			c.C60T						PASS	.	C		27,3951		0,27,1962	19.0	21.0	20.0		60	1.1	0.1	2	dbSNP_130	20	275,8023		2,271,3876	no	coding-synonymous	FAM179A	NM_199280.2		2,298,5838	TT,TC,CC		3.3141,0.6787,2.4601		20/1020	29221040	302,11974	1989	4149	6138	SO:0001819	synonymous_variant	165186	exon3			GTACTGCGGGAGC	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.60C>T	2.37:g.29221040C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	261	130	0.498084	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			C|0.978;T|0.022	0.022	strong		0.622	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
LRIT3	345193	hgsc.bcm.edu	37	4	110791543	110791543	+	Silent	SNP	C	C	T	rs2347133	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:110791543C>T	ENST00000594814.1	+	4	1638	c.1638C>T	c.(1636-1638)ccC>ccT	p.P546P	LRIT3_ENST00000409621.2_Silent_p.P363P|LRIT3_ENST00000327908.3_Silent_p.P363P|LRIT3_ENST00000379920.3_Silent_p.P501P	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	546	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		GCTTGGAACCCGGTGGGCAAT	0.488													C|||	1246	0.248802	0.27	0.3804	5008	,	,		20723	0.2728		0.1481	False		,,,				2504	0.2055				p.P546P		Atlas-SNP	.											.	LRIT3	107	.	0			c.C1638T						PASS	.	C		1072,3334	389.3+/-327.3	133,806,1264	101.0	96.0	98.0		1503	-10.3	0.0	4	dbSNP_100	98	1186,7414	241.4+/-271.8	100,986,3214	no	coding-synonymous	LRIT3	NM_198506.2		233,1792,4478	TT,TC,CC		13.7907,24.3305,17.3612		501/635	110791543	2258,10748	2203	4300	6503	SO:0001819	synonymous_variant	345193	exon4			GGAACCCGGTGGG	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1638C>T	4.37:g.110791543C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	166	78	0.46988	NM_198506	C9J1C2|Q6ZTG1	Silent	SNP	ENST00000594814.1	37	CCDS3688.3																																																																																			C|0.804;T|0.196	0.196	strong		0.488	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
TBX18	9096	hgsc.bcm.edu	37	6	85473758	85473758	+	Missense_Mutation	SNP	C	C	T	rs172562	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:85473758C>T	ENST00000369663.5	-	1	479	c.142G>A	c.(142-144)Ggg>Agg	p.G48R	TBX18_ENST00000606521.1_5'Flank|TBX18_ENST00000606784.1_5'Flank	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	48			G -> R (in dbSNP:rs172562). {ECO:0000269|PubMed:15489334}.		anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.G48R(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		tccacggcccccgccgccTCT	0.711													C|||	2052	0.409744	0.0862	0.3847	5008	,	,		9197	0.4683		0.501	False		,,,				2504	0.7106				p.G48R		Atlas-SNP	.											TBX18,NS,carcinoma,0,1	TBX18	131	1	1	Substitution - Missense(1)	prostate(1)	c.G142A						scavenged	.	C	ARG/GLY	558,3286		91,376,1455	3.0	4.0	4.0		142	4.4	0.1	6	dbSNP_79	4	3522,4434		896,1730,1352	yes	missense	TBX18	NM_001080508.1	125	987,2106,2807	TT,TC,CC		44.2685,14.5161,34.5763	benign	48/608	85473758	4080,7720	1922	3978	5900	SO:0001583	missense	9096	exon1			CGGCCCCCGCCGC	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"""T-boxes"""	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.142G>A	6.37:g.85473758C>T	ENSP00000358677:p.Gly48Arg	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	14	6	0.428571	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Missense_Mutation	SNP	ENST00000369663.5	37	CCDS34495.1	861	0.3942307692307692	51	0.10365853658536585	152	0.4198895027624309	273	0.4772727272727273	385	0.5079155672823219	C	14.67	2.603923	0.46423	0.145161	0.442685	ENSG00000112837	ENST00000369663	D	0.86366	-2.11	5.33	4.45	0.53987	.	0.989186	0.08254	N	0.974149	T	0.62600	0.2441	N	0.08118	0	0.80722	P	0.0	B	0.14438	0.01	B	0.12156	0.007	T	0.16988	-1.0384	9	0.17369	T	0.5	.	14.0585	0.64786	0.0:0.9244:0.0:0.0756	rs172562	48	O95935	TBX18_HUMAN	R	48	ENSP00000358677:G48R	ENSP00000358677:G48R	G	-	1	0	TBX18	85530477	0.007000	0.16637	0.127000	0.21898	0.591000	0.36615	2.304000	0.43655	2.495000	0.84180	0.305000	0.20034	GGG	C|0.605;T|0.395	0.395	strong		0.711	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508	
LRRN2	10446	hgsc.bcm.edu	37	1	204587047	204587047	+	Missense_Mutation	SNP	G	G	A	rs11588857	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:204587047G>A	ENST00000367175.1	-	1	4286	c.2074C>T	c.(2074-2076)Cca>Tca	p.P692S	LRRN2_ENST00000367176.3_Missense_Mutation_p.P692S|RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367177.3_Missense_Mutation_p.P692S			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	692			P -> S (in dbSNP:rs11588857).		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			TTCCTCCCTGGATTCCAGGGC	0.587													G|||	923	0.184305	0.0575	0.0922	5008	,	,		8413	0.3075		0.2237	False		,,,				2504	0.2536				p.P692S		Atlas-SNP	.											.	LRRN2	81	.	0			c.C2074T						PASS	.	G	SER/PRO,SER/PRO	357,4049	183.6+/-211.2	16,325,1862	92.0	98.0	96.0		2074,2074	5.2	1.0	1	dbSNP_120	96	1832,6768	326.2+/-317.3	182,1468,2650	yes	missense,missense	LRRN2	NM_006338.2,NM_201630.1	74,74	198,1793,4512	AA,AG,GG		21.3023,8.1026,16.8307	possibly-damaging,possibly-damaging	692/714,692/714	204587047	2189,10817	2203	4300	6503	SO:0001583	missense	10446	exon3			TCCCTGGATTCCA	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.2074C>T	1.37:g.204587047G>A	ENSP00000356143:p.Pro692Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	132	61	0.462121	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	418	0.19139194139194138	38	0.07723577235772358	39	0.10773480662983426	172	0.3006993006993007	169	0.22295514511873352	G	16.07	3.018815	0.54576	0.081026	0.213023	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.58358	0.34;0.34;0.34	5.16	5.16	0.70880	.	0.206931	0.24115	N	0.041409	T	0.00012	0.0000	N	0.08118	0	0.30449	P	0.775467	B	0.20671	0.047	B	0.19391	0.025	T	0.15549	-1.0433	9	0.10636	T	0.68	.	11.3325	0.49484	0.0854:0.0:0.9146:0.0	rs11588857;rs57344872;rs11588857	692	O75325	LRRN2_HUMAN	S	692	ENSP00000356144:P692S;ENSP00000356145:P692S;ENSP00000356143:P692S	ENSP00000356143:P692S	P	-	1	0	LRRN2	202853670	0.999000	0.42202	0.996000	0.52242	0.824000	0.46624	3.223000	0.51231	2.688000	0.91661	0.561000	0.74099	CCA	G|0.827;A|0.173	0.173	strong		0.587	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
MUC21	394263	hgsc.bcm.edu	37	6	30954485	30954485	+	Missense_Mutation	SNP	G	G	A	rs140951082	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954485G>A	ENST00000376296.3	+	2	774	c.533G>A	c.(532-534)aGc>aAc	p.S178N	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	178	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S178N(1)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AGTGGGGCCAGCACAGCCACC	0.617													G|||	8	0.00159744	0.0008	0.0014	5008	,	,		28215	0.0		0.005	False		,,,				2504	0.001				p.S178N		Atlas-SNP	.											MUC21,NS,malignant_melanoma,0,1	MUC21	98	1	1	Substitution - Missense(1)	NS(1)	c.G533A						scavenged	.						150.0	143.0	145.0					6																	30954485		2202	4299	6501	SO:0001583	missense	394263	exon2			GGGCCAGCACAGC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.533G>A	6.37:g.30954485G>A	ENSP00000365473:p.Ser178Asn	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	136	7	0.0514706	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	10.17	1.277242	0.23307	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02863	4.13	3.72	-3.6	0.04570	.	.	.	.	.	T	0.00608	0.0020	L	0.34521	1.04	0.09310	N	1	B	0.16802	0.019	B	0.19946	0.027	T	0.48198	-0.9056	8	.	.	.	-1.0525	1.0899	0.01661	0.3623:0.2667:0.2352:0.1358	.	178	Q5SSG8	MUC21_HUMAN	N	178	ENSP00000365473:S178N	.	S	+	2	0	MUC21	31062464	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-2.096000	0.01349	-0.539000	0.06273	-0.330000	0.08379	AGC	.	.	weak		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
AATK	9625	hgsc.bcm.edu	37	17	79095629	79095629	+	Missense_Mutation	SNP	C	C	A	rs7503604|rs386799844	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79095629C>A	ENST00000326724.4	-	11	2131	c.2107G>T	c.(2107-2109)Ggc>Tgc	p.G703C	AATK_ENST00000417379.1_Missense_Mutation_p.G600C	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	703			G -> C (in dbSNP:rs7503604). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9734811}.		brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			TCAGCGTGGCCGCCCGCAGAG	0.721													A|||	2787	0.55651	0.4463	0.6772	5008	,	,		12566	0.6419		0.4911	False		,,,				2504	0.5992				p.G703C		Atlas-SNP	.											AATK_ENST00000326724,NS,carcinoma,0,2	AATK	102	2	0			c.G2107T						PASS	.	A	CYS/GLY,CYS/GLY	1514,2030		367,780,625	5.0	7.0	6.0		2107,1798	-7.1	0.0	17	dbSNP_116	6	3740,4026		1007,1726,1150	yes	missense,missense	AATK	NM_001080395.2,NM_004920.2	159,159	1374,2506,1775	AA,AC,CC		48.1586,42.7201,46.4545	benign,benign	703/1375,600/1272	79095629	5254,6056	1772	3883	5655	SO:0001583	missense	9625	exon11			CGTGGCCGCCCGC	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.2107G>T	17.37:g.79095629C>A	ENSP00000324196:p.Gly703Cys	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	15	14	0.933333	NM_001080395	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	37	CCDS45807.1	1170	0.5357142857142857	212	0.43089430894308944	229	0.6325966850828729	346	0.6048951048951049	383	0.5052770448548812	A	9.655	1.142554	0.21205	0.427201	0.481586	ENSG00000181409	ENST00000326724;ENST00000374792	T;T	0.79247	-1.11;-1.25	3.91	-7.07	0.01563	.	1.777830	0.03483	N	0.215355	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.29882	-0.9997	9	0.38643	T	0.18	.	1.6467	0.02763	0.278:0.4625:0.1:0.1595	rs7503604;rs59349021	703	Q6ZMQ8	LMTK1_HUMAN	C	703;667	ENSP00000324196:G703C;ENSP00000363924:G667C	ENSP00000324196:G703C	G	-	1	0	AATK	76710224	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.384000	0.01063	-1.190000	0.02698	-1.672000	0.00744	GGC	C|0.463;A|0.537	0.537	strong		0.721	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
MORC1	27136	hgsc.bcm.edu	37	3	108677910	108677910	+	Missense_Mutation	SNP	C	C	T	rs78212601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:108677910C>T	ENST00000483760.1	-	27	2837	c.2794G>A	c.(2794-2796)Gaa>Aaa	p.E932K	MORC1_ENST00000232603.5_Missense_Mutation_p.E953K					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						AGATTATCTTCTTTAAGCAAA	0.378													C|||	40	0.00798722	0.0	0.0101	5008	,	,		15018	0.001		0.0288	False		,,,				2504	0.0031				p.E953K		Atlas-SNP	.											.	MORC1	211	.	0			c.G2857A						PASS	.	C	LYS/GLU	18,4388	20.2+/-43.8	0,18,2185	46.0	48.0	47.0		2857	5.2	1.0	3	dbSNP_131	47	191,8407	78.4+/-141.0	2,187,4110	yes	missense	MORC1	NM_014429.3	56	2,205,6295	TT,TC,CC		2.2214,0.4085,1.6072	probably-damaging	953/985	108677910	209,12795	2203	4299	6502	SO:0001583	missense	27136	exon28			TATCTTCTTTAAG	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2794G>A	3.37:g.108677910C>T	ENSP00000417282:p.Glu932Lys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	105	44	0.419048	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	37		31	0.014194139194139194	0	0.0	8	0.022099447513812154	0	0.0	23	0.030343007915567283	C	22.9	4.346692	0.82022	0.004085	0.022214	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.10005	2.92;2.92	5.2	5.2	0.72013	.	0.143592	0.32640	N	0.005834	T	0.04092	0.0114	L	0.32530	0.975	0.29995	N	0.816578	P;P	0.46784	0.884;0.884	P;P	0.46419	0.516;0.516	T	0.01048	-1.1469	10	0.44086	T	0.13	-17.6497	14.1073	0.65099	0.0:1.0:0.0:0.0	.	932;953	E7ERX1;Q86VD1	.;MORC1_HUMAN	K	953;932	ENSP00000232603:E953K;ENSP00000417282:E932K	ENSP00000232603:E953K	E	-	1	0	MORC1	110160600	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.944000	0.40263	2.716000	0.92895	0.650000	0.86243	GAA	C|0.984;T|0.016	0.016	strong		0.378	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
HR	55806	hgsc.bcm.edu	37	8	21978578	21978578	+	Splice_Site	SNP	A	A	G	rs58080661	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21978578A>G	ENST00000381418.4	-	10	3847	c.2367T>C	c.(2365-2367)agT>agC	p.S789S	HR_ENST00000312841.8_Splice_Site_p.S789S	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	789					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CCTCACTCACACTGGGCAGGG	0.662													A|||	566	0.113019	0.3525	0.0562	5008	,	,		16124	0.0149		0.0209	False		,,,				2504	0.0256				p.S789S		Atlas-SNP	.											.	HR	71	.	0			c.T2367C						PASS	.	A	,	1464,2940	441.0+/-346.2	245,974,983	35.0	39.0	38.0		2367,2367	-4.1	1.0	8	dbSNP_129	38	167,8431	74.2+/-136.8	1,165,4133	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	HR	NM_005144.4,NM_018411.4	,	246,1139,5116	GG,GA,AA		1.9423,33.2425,12.5442	,	789/1190,789/1135	21978578	1631,11371	2202	4299	6501	SO:0001630	splice_region_variant	55806	exon10			ACTCACACTGGGC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.2367+1T>C	8.37:g.21978578A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	145	61	0.42069	NM_018411	Q6GS30|Q96H33|Q9NPE1	Silent	SNP	ENST00000381418.4	37	CCDS6022.1																																																																																			A|0.881;G|0.119	0.119	strong		0.662	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		Silent
CD226	10666	hgsc.bcm.edu	37	18	67534632	67534632	+	Silent	SNP	C	C	T	rs72481819	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:67534632C>T	ENST00000280200.4	-	6	1114	c.846G>A	c.(844-846)gaG>gaA	p.E282E	CD226_ENST00000577287.1_Silent_p.E127E|CD226_ENST00000581982.1_Silent_p.E127E|CD226_ENST00000582621.1_Silent_p.E282E	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	282	Poly-Arg.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)|cytokine production (GO:0001816)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	24		Esophageal squamous(42;0.129)				GATCTCTTCTCTCTCTCCTTC	0.348													C|||	110	0.0219649	0.0045	0.036	5008	,	,		16692	0.0		0.0755	False		,,,				2504	0.0031				p.E282E	NSCLC(184;838 2130 8673 21498 50749)	Atlas-SNP	.											.	CD226	51	.	0			c.G846A						PASS	.	C		68,4338	61.7+/-98.7	0,68,2135	243.0	239.0	241.0		846	-0.6	0.0	18	dbSNP_130	241	570,8030	153.6+/-207.9	27,516,3757	no	coding-synonymous	CD226	NM_006566.2		27,584,5892	TT,TC,CC		6.6279,1.5433,4.9054		282/337	67534632	638,12368	2203	4300	6503	SO:0001819	synonymous_variant	10666	exon6			TCTTCTCTCTCTC	U56102	CCDS11997.1	18q22.3	2013-01-11	2006-03-28		ENSG00000150637	ENSG00000150637		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	16961	protein-coding gene	gene with protein product		605397	"""CD226 antigen"""			8673704	Standard	NM_006566		Approved	DNAM-1, DNAM1, PTA1, TLiSA1	uc002lkm.4	Q15762	OTTHUMG00000132809	ENST00000280200.4:c.846G>A	18.37:g.67534632C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_006566	B2R818	Silent	SNP	ENST00000280200.4	37	CCDS11997.1																																																																																			C|0.957;T|0.043	0.043	strong		0.348	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566	
MCPH1	79648	hgsc.bcm.edu	37	8	6302106	6302106	+	Missense_Mutation	SNP	C	C	A	rs35590577	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:6302106C>A	ENST00000344683.5	+	8	939	c.863C>A	c.(862-864)cCt>cAt	p.P288H	MCPH1_ENST00000522905.1_Missense_Mutation_p.P240H|MCPH1_ENST00000519480.1_Missense_Mutation_p.P288H	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	288			P -> H (in dbSNP:rs35590577).		cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		AAATCAAGTCCTCAGAAATTT	0.343													C|||	347	0.0692891	0.2254	0.0288	5008	,	,		19953	0.0		0.0239	False		,,,				2504	0.0051				p.P288H	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.C863A						PASS	.	C	HIS/PRO,HIS/PRO,HIS/PRO	680,2980		67,546,1217	56.0	52.0	53.0		863,719,863	4.4	0.0	8	dbSNP_126	53	89,8071		0,89,3991	yes	missense,missense,missense	MCPH1	NM_001172574.1,NM_001172575.1,NM_024596.3	77,77,77	67,635,5208	AA,AC,CC		1.0907,18.5792,6.5059	probably-damaging,probably-damaging,probably-damaging	288/611,240/563,288/836	6302106	769,11051	1830	4080	5910	SO:0001583	missense	79648	exon8			CAAGTCCTCAGAA	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.863C>A	8.37:g.6302106C>A	ENSP00000342924:p.Pro288His	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	168	83	0.494048	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	130	0.05952380952380952	104	0.21138211382113822	8	0.022099447513812154	0	0.0	18	0.023746701846965697	C	18.11	3.550319	0.65311	0.185792	0.010907	ENSG00000147316	ENST00000344683;ENST00000519480;ENST00000522905	T;T;T	0.34472	1.36;1.36;1.36	5.26	4.38	0.52667	.	0.265904	0.36778	N	0.002415	T	0.00073	0.0002	M	0.67397	2.05	0.80722	P	0.0	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.04153	-1.0973	9	0.44086	T	0.13	-14.7477	10.5155	0.44887	0.0:0.9093:0.0:0.0907	rs35590577	240;288;288	E9PH63;Q8NEM0;E9PGU5	.;MCPH1_HUMAN;.	H	288;288;240	ENSP00000342924:P288H;ENSP00000430962:P288H;ENSP00000430768:P240H	ENSP00000342924:P288H	P	+	2	0	MCPH1	6289514	0.224000	0.23674	0.049000	0.19019	0.549000	0.35272	2.195000	0.42677	1.344000	0.45657	0.655000	0.94253	CCT	C|0.953;A|0.047	0.047	strong		0.343	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
FLG	2312	hgsc.bcm.edu	37	1	152283605	152283605	+	Nonsense_Mutation	SNP	C	C	A	rs199895224		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152283605C>A	ENST00000368799.1	-	3	3792	c.3757G>T	c.(3757-3759)Gga>Tga	p.G1253*	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1253	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTTCCTGTCCCACCTGTGAG	0.557									Ichthyosis																												p.G1253X		Atlas-SNP	.											.	FLG	900	.	0			c.G3757T						PASS	.						276.0	263.0	267.0					1																	152283605		2203	4300	6503	SO:0001587	stop_gained	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCTGTCCCACCTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.3757G>T	1.37:g.152283605C>A	ENSP00000357789:p.Gly1253*	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	223	101	0.452915	NM_002016	Q01720|Q5T583|Q9UC71	Nonsense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	38	6.749215	0.97809	.	.	ENSG00000143631	ENST00000368799	.	.	.	2.72	0.669	0.17918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	.	5.0097	0.14306	0.0:0.6754:0.0:0.3246	.	.	.	.	X	1253	.	ENSP00000357789:G1253X	G	-	1	0	FLG	150550229	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.711000	0.05019	0.347000	0.23924	0.186000	0.17326	GGA	.	.	weak		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CLEC4M	10332	hgsc.bcm.edu	37	19	7831628	7831628	+	Missense_Mutation	SNP	G	G	A	rs2277998	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7831628G>A	ENST00000327325.5	+	5	989	c.871G>A	c.(871-873)Gac>Aac	p.D291N	CLEC4M_ENST00000394122.2_Missense_Mutation_p.D279N|CLEC4M_ENST00000595496.1_Missense_Mutation_p.D155N|CLEC4M_ENST00000596363.1_Missense_Mutation_p.D263N|CLEC4M_ENST00000596707.1_Missense_Mutation_p.D224N|CLEC4M_ENST00000597522.1_Missense_Mutation_p.D199N|CLEC4M_ENST00000334806.5_Missense_Mutation_p.D240N|CLEC4M_ENST00000248228.4_Missense_Mutation_p.D269N|CLEC4M_ENST00000357361.2_Missense_Mutation_p.D291N|CLEC4M_ENST00000359059.5_Missense_Mutation_p.D224N	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	291	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		D -> N (in dbSNP:rs2277998). {ECO:0000269|Ref.5}.		antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						GAACTGGCACGACTCCGTCAC	0.602													g|||	887	0.177117	0.0113	0.3573	5008	,	,		15081	0.1389		0.2962	False		,,,				2504	0.1902				p.D291N		Atlas-SNP	.											CLEC4M,right_lower_lobe,carcinoma,-2,2	CLEC4M	58	2	0			c.G871A						scavenged	.	A	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	302,4104	162.9+/-194.8	11,280,1912	99.0	90.0	93.0		718,799,463,670,595,733,802,787,871	-5.1	0.0	19	dbSNP_100	93	2704,5896	433.6+/-357.5	430,1844,2026	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense	CLEC4M	NM_001144904.1,NM_001144905.1,NM_001144906.1,NM_001144907.1,NM_001144908.1,NM_001144909.1,NM_001144910.1,NM_001144911.1,NM_014257.4	23,23,23,23,23,23,23,23,23	441,2124,3938	AA,AG,GG		31.4419,6.8543,23.1124	benign,benign,benign,benign,benign,benign,benign,benign,benign	240/349,267/376,155/264,224/333,199/233,245/354,268/377,263/297,291/400	7831628	3006,10000	2203	4300	6503	SO:0001583	missense	10332	exon5			TGGCACGACTCCG	AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"""C-type lectin domain containing"", ""CD molecules"""	13523	protein-coding gene	gene with protein product		605872	"""CD299 antigen"""	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.871G>A	19.37:g.7831628G>A	ENSP00000316228:p.Asp291Asn	Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	157	73	0.464968	NM_014257	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Missense_Mutation	SNP	ENST00000327325.5	37	CCDS12187.1	438	0.20054945054945056	10	0.02032520325203252	110	0.30386740331491713	88	0.15384615384615385	230	0.3034300791556728	g	3.314	-0.140125	0.06669	0.068543	0.314419	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000248228;ENST00000334806;ENST00000359059;ENST00000357361;ENST00000358690	T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1	2.57	-5.14	0.02875	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.00012	0.0000	M	0.67700	2.07	0.80722	P	0.0	B;B;B;B;B;B;B;B	0.24258	0.056;0.029;0.1;0.009;0.003;0.006;0.075;0.01	B;B;B;B;B;B;B;B	0.19946	0.014;0.004;0.012;0.027;0.002;0.008;0.017;0.013	T	0.25433	-1.0132	8	0.40728	T	0.16	.	1.8763	0.03219	0.2781:0.1053:0.4222:0.1944	rs2277998;rs17303108;rs52822524;rs2277998	240;224;291;279;268;263;155;199	B4E2Z5;Q9H2X3-5;Q9H2X3;E7ENS9;Q9H2X3-8;Q9H2X3-9;Q9H2X3-7;Q9H2X3-4	.;.;CLC4M_HUMAN;.;.;.;.;.	N	291;279;269;240;224;291;235	ENSP00000316228:D291N;ENSP00000377680:D279N;ENSP00000248228:D269N;ENSP00000335228:D240N;ENSP00000351954:D224N;ENSP00000349924:D291N	ENSP00000248228:D269N	D	+	1	0	CLEC4M	7737628	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.143000	0.01297	-3.295000	0.00194	-3.689000	0.00024	GAC	G|0.787;A|0.213	0.213	strong		0.602	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257	
CUBN	8029	hgsc.bcm.edu	37	10	17152994	17152994	+	Silent	SNP	G	G	A	rs1801223	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:17152994G>A	ENST00000377833.4	-	9	1004	c.939C>T	c.(937-939)aaC>aaT	p.N313N		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	313	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)	AACAGCCGCCGTTATTTATCT	0.473													G|||	1076	0.214856	0.1944	0.2262	5008	,	,		16541	0.25		0.2584	False		,,,				2504	0.1534				p.N313N		Atlas-SNP	.											.	CUBN	515	.	0			c.C939T						PASS	.	G		956,3450	361.4+/-315.7	109,738,1356	95.0	92.0	93.0		939	-0.5	0.9	10	dbSNP_89	93	1607,6993	299.3+/-304.4	157,1293,2850	no	coding-synonymous	CUBN	NM_001081.3		266,2031,4206	AA,AG,GG		18.686,21.6977,19.7063		313/3624	17152994	2563,10443	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon9			GCCGCCGTTATTT	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.939C>T	10.37:g.17152994G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			G|0.680;T|0.036	.	strong		0.473	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
PCDHA6	56142	hgsc.bcm.edu	37	5	140209467	140209467	+	Silent	SNP	T	T	G	rs7710794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140209467T>G	ENST00000529310.1	+	1	1905	c.1791T>G	c.(1789-1791)gtT>gtG	p.V597V	PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	597	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCGCGCAGTTGACGCCGACT	0.677													.|||	3006	0.60024	0.7534	0.6052	5008	,	,		16573	0.5327		0.5378	False		,,,				2504	0.5235				p.V597V		Atlas-SNP	.											.	PCDHA6	442	.	0			c.T1791G						PASS	.	G	,,,,,,,,	3192,1214	421.3+/-339.3	1167,858,178	88.0	88.0	88.0		,,,,,1791,,1791,	1.5	0.9	5	dbSNP_116	88	4543,4057	559.0+/-387.3	1194,2155,951	no	intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous,intron	PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_031411.1,NM_031848.1,NM_031849.1	,,,,,,,,	2361,3013,1129	GG,GT,TT		47.1744,27.5533,40.5274	,,,,,,,,	,,,,,597/951,,597/804,	140209467	7735,5271	2203	4300	6503	SO:0001819	synonymous_variant	56142	exon1			CGCAGTTGACGCC	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"""Cadherins / Protocadherins : Clustered"""	8672	other	complex locus constituent	"""KIAA0345-like 8"""	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1791T>G	5.37:g.140209467T>G		Somatic	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	181	99	0.546961	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	CCDS47281.1																																																																																			T|0.407;G|0.593	0.593	strong		0.677	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
WRN	7486	hgsc.bcm.edu	37	8	30999075	30999075	+	Missense_Mutation	SNP	C	C	T	rs143954702		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:30999075C>T	ENST00000298139.5	+	25	3346	c.3097C>T	c.(3097-3099)Cgg>Tgg	p.R1033W		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	1033					aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		AGAAGTTTCTCGGTATAACAA	0.423			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.R1033W	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.C3097T						PASS	.	C	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	106.0	104.0	105.0		3097	3.2	0.1	8	dbSNP_134	105	2,8598	2.2+/-6.3	0,2,4298	yes	missense	WRN	NM_000553.4	101	0,5,6498	TT,TC,CC		0.0233,0.0681,0.0384	benign	1033/1433	30999075	5,13001	2203	4300	6503	SO:0001583	missense	7486	exon25	Familial Cancer Database	WS, Adult Progeria	GTTTCTCGGTATA		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.3097C>T	8.37:g.30999075C>T	ENSP00000298139:p.Arg1033Trp	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	145	77	0.531034	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	C	13.66	2.304314	0.40795	6.81E-4	2.33E-4	ENSG00000165392	ENST00000298139	T	0.30448	1.53	5.9	3.15	0.36227	RQC domain (2);	0.406919	0.26176	N	0.025894	T	0.18841	0.0452	L	0.36672	1.1	0.21950	N	0.999455	B;P	0.38565	0.098;0.637	B;B	0.26614	0.044;0.071	T	0.11494	-1.0585	10	0.72032	D	0.01	-1.5776	8.5727	0.33578	0.1396:0.1272:0.7332:0.0	.	443;1033	Q59F09;Q14191	.;WRN_HUMAN	W	1033	ENSP00000298139:R1033W	ENSP00000298139:R1033W	R	+	1	2	WRN	31118617	0.089000	0.21612	0.091000	0.20842	0.002000	0.02628	0.474000	0.22148	0.400000	0.25396	-0.134000	0.14843	CGG	C|1.000;T|0.000	0.000	weak		0.423	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
SLC4A11	83959	hgsc.bcm.edu	37	20	3218634	3218634	+	5'Flank	SNP	G	G	C	rs3810562	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3218634G>C	ENST00000380056.3	-	0	0				SLC4A11_ENST00000539553.2_Intron|SLC4A11_ENST00000380059.3_Missense_Mutation_p.P26R	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11						bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)	p.P26R(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						CTCTCTCCTCGGATGCCAAGG	0.637													C|||	3213	0.641573	0.8215	0.5807	5008	,	,		15857	0.6766		0.5795	False		,,,				2504	0.4693				p.P26R	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											SLC4A11_ENST00000380059,NS,lymphoid_neoplasm,0,1	SLC4A11	188	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C77G						PASS	.																																			SO:0001631	upstream_gene_variant	83959	exon1			CTCCTCGGATGCC	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740		20.37:g.3218634G>C	Exception_encountered	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	37	CCDS13052.1	1403	0.6423992673992674	385	0.782520325203252	209	0.5773480662983426	382	0.6678321678321678	427	0.5633245382585752	C	3.200	-0.163983	0.06502	.	.	ENSG00000088836	ENST00000380059	T	0.80909	-1.43	3.5	-1.98	0.07480	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.38001	-0.9681	8	0.11182	T	0.66	.	4.6723	0.12694	0.1395:0.2058:0.5427:0.112	rs3810562	26	B4DKC8	.	R	26	ENSP00000369399:P26R	ENSP00000369399:P26R	P	-	2	0	SLC4A11	3166634	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.858000	0.04281	-0.398000	0.07679	-1.307000	0.01316	CCG	G|0.367;C|0.633	0.633	strong		0.637	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
KRT83	3889	hgsc.bcm.edu	37	12	52711747	52711747	+	Nonsense_Mutation	SNP	C	C	A	rs146753414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:52711747C>A	ENST00000293670.3	-	3	663	c.601G>T	c.(601-603)Gaa>Taa	p.E201*		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	201	Coil 1B.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GCTACTTCTTCTTCATACCTG	0.542													c|||	37	0.00738818	0.0008	0.0072	5008	,	,		18864	0.0		0.0308	False		,,,				2504	0.0				p.E201X	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											.	KRT83	64	.	0			c.G601T						PASS	.	C	stop/GLU	8,4398	14.3+/-33.2	0,8,2195	154.0	157.0	156.0		601	5.2	1.0	12	dbSNP_134	156	169,8431	80.1+/-142.7	3,163,4134	yes	stop-gained	KRT83	NM_002282.3		3,171,6329	AA,AC,CC		1.9651,0.1816,1.3609		201/494	52711747	177,12829	2203	4300	6503	SO:0001587	stop_gained	3889	exon3			CTTCTTCTTCATA	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.601G>T	12.37:g.52711747C>A	ENSP00000293670:p.Glu201*	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	35	0.364583	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Nonsense_Mutation	SNP	ENST00000293670.3	37	CCDS8823.1	28	0.01282051282051282	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	24	0.0316622691292876	C	36	5.618880	0.96649	0.001816	0.019651	ENSG00000170523	ENST00000293670	.	.	.	5.15	5.15	0.70609	.	0.000000	0.42548	U	0.000691	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.6426	0.91400	0.0:1.0:0.0:0.0	.	.	.	.	X	201	.	ENSP00000293670:E201X	E	-	1	0	KRT83	50998014	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	4.682000	0.61671	2.411000	0.81874	0.655000	0.94253	GAA	C|0.984;A|0.016	0.016	strong		0.542	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
PARP10	84875	hgsc.bcm.edu	37	8	145058986	145058986	+	Missense_Mutation	SNP	A	A	G	rs11136343	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:145058986A>G	ENST00000313028.7	-	5	1278	c.1184T>C	c.(1183-1185)cTg>cCg	p.L395P	PARP10_ENST00000525773.1_Missense_Mutation_p.L407P|PARP10_ENST00000533665.1_5'Flank|PARP10_ENST00000524918.1_Missense_Mutation_p.L395P	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	395			L -> P (in dbSNP:rs11136343).		negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTCCTGCCCCAGCAACCCCTT	0.642													a|||	1825	0.364417	0.5915	0.255	5008	,	,		17752	0.124		0.3926	False		,,,				2504	0.3538				p.L395P		Atlas-SNP	.											.	PARP10	57	.	0			c.T1184C						PASS	.		PRO/LEU	2513,1893	608.3+/-391.1	717,1079,407	60.0	70.0	67.0		1184	-6.0	0.0	8	dbSNP_120	67	3271,5329	476.9+/-369.5	645,1981,1674	yes	missense	PARP10	NM_032789.3	98	1362,3060,2081	GG,GA,AA		38.0349,42.9641,44.4718	possibly-damaging	395/1026	145058986	5784,7222	2203	4300	6503	SO:0001583	missense	84875	exon5			TGCCCCAGCAACC	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"""Poly (ADP-ribose) polymerases"""	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.1184T>C	8.37:g.145058986A>G	ENSP00000325618:p.Leu395Pro	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	103	58	0.563107	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Missense_Mutation	SNP	ENST00000313028.7	37	CCDS34960.1	758	0.34706959706959706	293	0.5955284552845529	102	0.281767955801105	73	0.12762237762237763	290	0.38258575197889183	a	6.469	0.454757	0.12283	0.570359	0.380349	ENSG00000178685	ENST00000524918;ENST00000534861;ENST00000313028;ENST00000525773;ENST00000313059	T;T;T;T	0.37058	2.87;2.86;2.86;1.22	3.0	-5.99	0.02213	.	0.984329	0.08211	N	0.980735	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43572	-0.9383	9	0.24483	T	0.36	.	6.835	0.23931	0.2596:0.0:0.5805:0.16	rs11136343;rs52810958;rs11136343	407;395;395	E9PNI7;E9PK67;Q53GL7	.;.;PAR10_HUMAN	P	395;101;395;407;310	ENSP00000431620:L395P;ENSP00000325618:L395P;ENSP00000434776:L407P;ENSP00000314320:L310P	ENSP00000325618:L395P	L	-	2	0	PARP10	145130974	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.851000	0.00732	-1.692000	0.01428	-1.612000	0.00800	CTG	A|0.597;G|0.403	0.403	strong		0.642	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789	
NANS	54187	hgsc.bcm.edu	37	9	100823135	100823135	+	Missense_Mutation	SNP	G	G	C	rs1058446	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:100823135G>C	ENST00000210444.5	+	2	274	c.204G>C	c.(202-204)gaG>gaC	p.E68D		NM_018946.3	NP_061819.2	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid synthase	68			E -> D (in dbSNP:rs1058446). {ECO:0000269|PubMed:15489334}.		lipopolysaccharide biosynthetic process (GO:0009103)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	N-acetylneuraminate synthase activity (GO:0050462)|N-acylneuraminate cytidylyltransferase activity (GO:0008781)|N-acylneuraminate-9-phosphate synthase activity (GO:0047444)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	11		Acute lymphoblastic leukemia(62;0.0559)				AAGCCTTGGAGAGGCCATACA	0.502													G|||	963	0.192292	0.2224	0.2622	5008	,	,		18731	0.2004		0.2207	False		,,,				2504	0.0644				p.E68D		Atlas-SNP	.											.	NANS	24	.	0			c.G204C						PASS	.	G	ASP/GLU	937,3469	357.4+/-313.9	105,727,1371	182.0	180.0	181.0		204	3.0	1.0	9	dbSNP_86	181	2075,6525	359.9+/-331.7	269,1537,2494	yes	missense	NANS	NM_018946.3	45	374,2264,3865	CC,CG,GG		24.1279,21.2665,23.1585	benign	68/360	100823135	3012,9994	2203	4300	6503	SO:0001583	missense	54187	exon2			CTTGGAGAGGCCA	AF161387	CCDS6733.1	9p24.1-p23	2008-07-31	2008-07-31		ENSG00000095380	ENSG00000095380			19237	protein-coding gene	gene with protein product	"""sialic acid synthase"""	605202				10749855	Standard	NM_018946		Approved	SAS	uc004ayc.3	Q9NR45	OTTHUMG00000020341	ENST00000210444.5:c.204G>C	9.37:g.100823135G>C	ENSP00000210444:p.Glu68Asp	Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	151	149	0.986755	NM_018946	B2RE98|Q8WUV9|Q9BWS6|Q9NVD4	Missense_Mutation	SNP	ENST00000210444.5	37	CCDS6733.1	498	0.22802197802197802	120	0.24390243902439024	88	0.2430939226519337	125	0.21853146853146854	165	0.21767810026385223	G	12.90	2.077207	0.36662	0.212665	0.241279	ENSG00000095380	ENST00000210444	T	0.43294	0.95	5.73	2.95	0.34219	Aldolase-type TIM barrel (1);N-acetylneuraminic acid synthase, N-terminal (1);	0.043833	0.85682	D	0.000000	T	0.00012	0.0000	N	0.02751	-0.505	0.22754	P	0.99877242	B	0.02656	0.0	B	0.11329	0.006	T	0.29150	-1.0021	9	0.27082	T	0.32	-17.3272	9.6941	0.40147	0.2239:0.0:0.7761:0.0	rs1058446;rs3199071;rs17858509;rs52795099;rs1058446	68	Q9NR45	SIAS_HUMAN	D	68	ENSP00000210444:E68D	ENSP00000210444:E68D	E	+	3	2	NANS	99862956	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	2.315000	0.43752	0.470000	0.27294	0.655000	0.94253	GAG	G|0.775;C|0.225	0.225	strong		0.502	NANS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053359.1	NM_018946	
IGF1R	3480	hgsc.bcm.edu	37	15	99491842	99491842	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:99491842C>T	ENST00000268035.6	+	20	4238	c.3627C>T	c.(3625-3627)gcC>gcT	p.A1209A	IGF1R_ENST00000558762.1_Silent_p.A1208A	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1209	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	CCACACTGGCCGAGCAGCCCT	0.582																																					p.A1209A		Atlas-SNP	.											IGF1R,NS,carcinoma,+2,1	IGF1R	147	1	0			c.C3627T						scavenged	.						105.0	102.0	103.0					15																	99491842		2197	4297	6494	SO:0001819	synonymous_variant	3480	exon20			ACTGGCCGAGCAG	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.3627C>T	15.37:g.99491842C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	77	2	0.025974	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	37	CCDS10378.1																																																																																			.	.	none		0.582	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
HLA-C	3107	hgsc.bcm.edu	37	6	31237862	31237862	+	Splice_Site	SNP	T	T	C	rs9264621|rs281860578	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31237862T>C	ENST00000376228.5	-	5	910	c.896A>G	c.(895-897)gAg>gGg	p.E299G	HLA-C_ENST00000383329.3_Splice_Site_p.E299G	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	299	Connecting peptide.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GGAAGATGGCTCTGGGAAAGG	0.592													t|||	452	0.0902556	0.0628	0.1441	5008	,	,		15914	0.1022		0.1133	False		,,,				2504	0.0532				p.E299G		Atlas-SNP	.											HLA-C_ENST00000383329,caecum,carcinoma,0,4	HLA-C	92	4	0			c.A896G						PASS	.	C	GLY/GLU	324,4076		19,286,1895	40.0	42.0	41.0		896	1.5	0.1	6	dbSNP_118	41	1002,7594		85,832,3381	no	missense-near-splice	HLA-C	NM_002117.5	98	104,1118,5276	CC,CT,TT		11.6566,7.3636,10.2031	benign	299/367	31237862	1326,11670	2200	4298	6498	SO:0001630	splice_region_variant	3107	exon5			GATGGCTCTGGGA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.896-1A>G	6.37:g.31237862T>C		Somatic	293	1	0.00341297		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	246	0.11263736263736264	38	0.07723577235772358	64	0.17679558011049723	56	0.0979020979020979	88	0.11609498680738786	.	3.388	-0.124932	0.06795	0.073636	0.116566	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.15718	2.4;2.4	2.67	1.47	0.22746	Immunoglobulin-like fold (1);	0.450646	0.15943	N	0.237111	T	0.03915	0.0110	.	.	.	0.09310	P	1.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.29579	-1.0007	8	0.51188	T	0.08	.	4.7418	0.13015	0.0:0.1536:0.0:0.8464	rs9264621	299;299;299;299	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	G	299;299;299;336	ENSP00000365402:E299G;ENSP00000372819:E299G	ENSP00000365402:E299G	E	-	2	0	HLA-C	31345841	0.850000	0.29656	0.069000	0.20011	0.066000	0.16364	1.082000	0.30803	0.446000	0.26666	-0.925000	0.02716	GAG	T|0.893;C|0.107	0.107	strong		0.592	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	Missense_Mutation
SAA1	6288	hgsc.bcm.edu	37	11	18290866	18290866	+	Silent	SNP	T	T	C	rs1136745	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18290866T>C	ENST00000405158.2	+	3	400	c.216T>C	c.(214-216)gcT>gcC	p.A72A	SAA1_ENST00000532858.1_Silent_p.A72A|SAA1_ENST00000356524.4_Silent_p.A72A|RNA5SP334_ENST00000364825.1_RNA	NM_000331.4	NP_000322	P0DJI8	SAA1_HUMAN	serum amyloid A1	72					acute-phase response (GO:0006953)|innate immune response (GO:0045087)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of inflammatory response (GO:0050728)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of interleukin-1 secretion (GO:0050716)|regulation of protein secretion (GO:0050708)	endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	G-protein coupled receptor binding (GO:0001664)|heparin binding (GO:0008201)	p.A72A(1)		endometrium(1)|large_intestine(3)|lung(2)|stomach(3)	9					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	GTGCCTGGGCTGCAGAAGTGA	0.562																																					p.A72A		Atlas-SNP	.											SAA1,NS,carcinoma,0,1	SAA1	14	1	1	Substitution - coding silent(1)	stomach(1)	c.T216C						scavenged	.						20.0	21.0	20.0					11																	18290866		2190	4260	6450	SO:0001819	synonymous_variant	6288	exon3			CTGGGCTGCAGAA	M10906	CCDS7835.1	11p15.1	2014-01-30			ENSG00000173432	ENSG00000173432		"""Endogenous ligands"""	10513	protein-coding gene	gene with protein product		104750		SAA		2595451, 9305847	Standard	NM_199161		Approved	PIG4, TP53I4	uc021qeo.1	P0DJI8	OTTHUMG00000166147	ENST00000405158.2:c.216T>C	11.37:g.18290866T>C		Somatic	96	7	0.0729167		WXS	Illumina HiSeq	Phase_I	140	33	0.235714	NM_199161	P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Silent	SNP	ENST00000405158.2	37	CCDS7835.1																																																																																			C|1.000;|0.000	1.000	weak		0.562	SAA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395864.1	NM_199161	
MS4A12	54860	hgsc.bcm.edu	37	11	60264947	60264947	+	Silent	SNP	C	C	T	rs2298552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:60264947C>T	ENST00000016913.4	+	2	213	c.156C>T	c.(154-156)taC>taT	p.Y52Y	MS4A12_ENST00000525951.1_3'UTR|MS4A12_ENST00000537076.1_Silent_p.Y52Y	NM_017716.2	NP_060186.2	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member 12	52						integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)	17						CTCAGCCCTACGGCATCACAT	0.468													C|||	3082	0.615415	0.6626	0.6599	5008	,	,		18115	0.6607		0.5099	False		,,,				2504	0.5818				p.Y52Y		Atlas-SNP	.											.	MS4A12	44	.	0			c.C156T						PASS	.	C	,	2628,1778	644.3+/-398.0	785,1058,360	83.0	79.0	81.0		156,156	-0.7	0.0	11	dbSNP_100	81	4534,4066	594.6+/-393.3	1209,2116,975	no	coding-synonymous,coding-synonymous	MS4A12	NM_001164470.1,NM_017716.2	,	1994,3174,1335	TT,TC,CC		47.2791,40.3541,44.9331	,	52/222,52/268	60264947	7162,5844	2203	4300	6503	SO:0001819	synonymous_variant	54860	exon2			GCCCTACGGCATC	AK000224	CCDS7988.1, CCDS53638.1	11q12	2008-03-25				ENSG00000071203			13370	protein-coding gene	gene with protein product		606550				11401424, 11486273	Standard	NM_017716		Approved	Ms4a10, FLJ20217	uc001npr.3	Q9NXJ0		ENST00000016913.4:c.156C>T	11.37:g.60264947C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	176	79	0.448864	NM_017716	F5GX98|Q8N6L4	Silent	SNP	ENST00000016913.4	37	CCDS7988.1																																																																																			C|0.427;T|0.573	0.573	strong		0.468	MS4A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383627.1		
CDH23	64072	hgsc.bcm.edu	37	10	73455273	73455273	+	Silent	SNP	T	T	C	rs3752751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:73455273T>C	ENST00000224721.6	+	21	2408	c.2403T>C	c.(2401-2403)gaT>gaC	p.D801D	CDH23_ENST00000299366.7_Silent_p.D841D	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	796	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CAGACTCTGATGTGACCACGG	0.602													C|||	2774	0.553914	0.5038	0.5187	5008	,	,		18162	0.4345		0.7068	False		,,,				2504	0.6125				p.D796D		Atlas-SNP	.											.	CDH23	365	.	0			c.T2388C						PASS	.	C	,,	2281,1855		653,975,440	90.0	96.0	94.0		2388,2388,2388	-4.0	0.9	10	dbSNP_107	94	6124,2296		2222,1680,308	no	coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_022124.5	,,	2875,2655,748	CC,CT,TT		27.2684,44.8501,33.0599	,,	796/1382,796/1062,796/3355	73455273	8405,4151	2068	4210	6278	SO:0001819	synonymous_variant	64072	exon21			CTCTGATGTGACC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.2403T>C	10.37:g.73455273T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				T|0.408;C|0.591	0.591	strong		0.602	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
FLI1	2313	hgsc.bcm.edu	37	11	128651893	128651893	+	Silent	SNP	A	A	G	rs35195224	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:128651893A>G	ENST00000527786.2	+	5	1119	c.630A>G	c.(628-630)caA>caG	p.Q210Q	FLI1_ENST00000534087.2_Silent_p.Q177Q|FLI1_ENST00000281428.8_Silent_p.Q144Q|FLI1_ENST00000344954.6_Silent_p.Q177Q|FLI1_ENST00000525560.1_Silent_p.Q17Q	NM_001271010.1|NM_002017.4	NP_001257939.1|NP_002008.2	Q01543	FLI1_HUMAN	Fli-1 proto-oncogene, ETS transcription factor	210					blood circulation (GO:0008015)|cell differentiation (GO:0030154)|hemostasis (GO:0007599)|megakaryocyte development (GO:0035855)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/FLI1(2569)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(2)	31	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		ACACCGACCAATCCTCACGAT	0.413			T	EWSR1	Ewing sarcoma								A|||	1072	0.214058	0.4576	0.1585	5008	,	,		20960	0.1766		0.0805	False		,,,				2504	0.1002				p.Q210Q		Atlas-SNP	.		Dom	yes		11	11q24	2313	Friend leukemia virus integration 1		M	.	FLI1	72	.	0			c.A630G						PASS	.	A	,	1452,2366		280,892,737	172.0	163.0	165.0		531,630	-3.7	0.9	11	dbSNP_126	165	731,7529		30,671,3429	no	coding-synonymous,coding-synonymous	FLI1	NM_001167681.2,NM_002017.3	,	310,1563,4166	GG,GA,AA		8.8499,38.0304,18.0742	,	177/420,210/453	128651893	2183,9895	1909	4130	6039	SO:0001819	synonymous_variant	2313	exon5			CGACCAATCCTCA	M98833	CCDS44768.1, CCDS53725.1, CCDS59230.1, CCDS59231.1	11q24.1-q24.3	2014-09-17	2013-08-07		ENSG00000151702	ENSG00000151702			3749	protein-coding gene	gene with protein product		193067	"""Friend leukemia virus integration 1"""			1765382	Standard	NM_001167681		Approved	SIC-1, EWSR2	uc010sbu.2	Q01543	OTTHUMG00000165792	ENST00000527786.2:c.630A>G	11.37:g.128651893A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	232	122	0.525862	NM_002017	B2R8H2|B4DFV4|B4DTC6|G3V183|Q14319|Q92480|Q9UE07	Silent	SNP	ENST00000527786.2	37	CCDS44768.1																																																																																			A|0.823;G|0.177	0.177	strong		0.413	FLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386226.2	NM_002017	
FHAD1	114827	hgsc.bcm.edu	37	1	15702130	15702130	+	Silent	SNP	A	A	G	rs17368978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:15702130A>G	ENST00000375998.4	+	26	3543	c.3543A>G	c.(3541-3543)ctA>ctG	p.L1181L	FHAD1_ENST00000417793.1_Silent_p.L1145L|FHAD1_ENST00000375999.3_Silent_p.L1181L|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000314740.8_Silent_p.L434L|FHAD1_ENST00000358897.4_Silent_p.L1181L			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1181										skin(1)|stomach(1)	2						AATCATTTCTAGATTTAAAGA	0.358													A|||	252	0.0503195	0.0847	0.036	5008	,	,		18986	0.001		0.0467	False		,,,				2504	0.0685				p.L1181L		Atlas-SNP	.											.	FHAD1	78	.	0			c.A3543G						PASS	.	A		94,1290		3,88,601	115.0	94.0	100.0		3543	1.4	0.8	1	dbSNP_123	100	187,2995		6,175,1410	no	coding-synonymous	FHAD1	NM_052929.1		9,263,2011	GG,GA,AA		5.8768,6.7919,6.1542		1181/1413	15702130	281,4285	692	1591	2283	SO:0001819	synonymous_variant	114827	exon27			ATTTCTAGATTTA	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.3543A>G	1.37:g.15702130A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	37		96	0.04395604395604396	41	0.08333333333333333	19	0.052486187845303865	0	0.0	36	0.047493403693931395	A	0.392	-0.923114	0.02377	0.067919	0.058768	ENSG00000142621	ENST00000444385	.	.	.	5.08	1.38	0.22167	.	.	.	.	.	.	.	.	.	.	.	0.47441	D	0.999425	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.4267	0.11507	0.6482:0.1692:0.1825:0.0	rs17368978;rs56584101;rs17368978	.	.	.	W	500	.	.	X	+	2	0	FHAD1	15574717	0.627000	0.27129	0.828000	0.32881	0.056000	0.15407	0.299000	0.19138	0.114000	0.18032	-0.250000	0.11733	TAG	A|0.944;G|0.056	0.056	strong		0.358	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
RHOT2	89941	hgsc.bcm.edu	37	16	720986	720986	+	Missense_Mutation	SNP	G	G	A	rs1139897	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:720986G>A	ENST00000315082.4	+	10	848	c.734G>A	c.(733-735)cGg>cAg	p.R245Q		NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	245			R -> Q (in dbSNP:rs1139897). {ECO:0000269|PubMed:12482879}.		cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				CGGGAGGACCGGCTGACCCTG	0.692													G|||	1635	0.326478	0.0393	0.3646	5008	,	,		9342	0.6845		0.2575	False		,,,				2504	0.3896				p.R245Q		Atlas-SNP	.											.	RHOT2	35	.	0			c.G734A						PASS	.	G	GLN/ARG	294,4074		8,278,1898	28.0	29.0	28.0		734	2.1	0.1	16	dbSNP_86	28	1920,6668		209,1502,2583	no	missense	RHOT2	NM_138769.1	43	217,1780,4481	AA,AG,GG		22.3568,6.7308,17.0886	benign	245/619	720986	2214,10742	2184	4294	6478	SO:0001583	missense	89941	exon10			AGGACCGGCTGAC	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"""EF-hand domain containing"""	21169	protein-coding gene	gene with protein product	"""mitochondrial Rho (MIRO) GTPase 2"""	613889	"""chromosome 16 open reading frame 39"", ""ras homolog gene family, member T2"""	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.734G>A	16.37:g.720986G>A	ENSP00000321971:p.Arg245Gln	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	40	23	0.575	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Missense_Mutation	SNP	ENST00000315082.4	37	CCDS10417.1	752	0.3443223443223443	23	0.046747967479674794	130	0.35911602209944754	390	0.6818181818181818	209	0.2757255936675462	G	12.31	1.899957	0.33535	0.067308	0.223568	ENSG00000140983	ENST00000315082	T	0.10477	2.87	5.11	2.08	0.27032	EF hand associated, type-2 (1);EF-hand-like domain (1);	0.209202	0.49305	N	0.000152	T	0.00012	0.0000	N	0.12182	0.205	0.38701	P	0.04701299999999997	B;B	0.34329	0.449;0.027	B;B	0.26864	0.074;0.025	T	0.04165	-1.0972	9	0.66056	D	0.02	-14.1341	9.3233	0.37977	0.2389:0.0:0.7611:0.0	rs1139897;rs3743913;rs11557861;rs61475528;rs1139897	118;245	Q8IXI1-2;Q8IXI1	.;MIRO2_HUMAN	Q	245	ENSP00000321971:R245Q	ENSP00000321971:R245Q	R	+	2	0	RHOT2	660987	0.987000	0.35691	0.114000	0.21550	0.230000	0.25150	3.188000	0.50958	0.189000	0.20188	0.561000	0.74099	CGG	G|0.755;A|0.245	0.245	strong		0.692	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769	
DCLRE1C	64421	hgsc.bcm.edu	37	10	14974905	14974905	+	Missense_Mutation	SNP	T	T	C	rs12768894	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:14974905T>C	ENST00000378278.2	-	9	765	c.728A>G	c.(727-729)cAt>cGt	p.H243R	DCLRE1C_ENST00000396817.2_Missense_Mutation_p.H123R|DCLRE1C_ENST00000357717.2_Missense_Mutation_p.H128R|DCLRE1C_ENST00000378254.1_Missense_Mutation_p.H123R|DCLRE1C_ENST00000453695.2_Missense_Mutation_p.H123R|DCLRE1C_ENST00000378258.1_Missense_Mutation_p.H123R|DCLRE1C_ENST00000378249.1_Missense_Mutation_p.H128R|DCLRE1C_ENST00000378289.4_Missense_Mutation_p.H243R|DCLRE1C_ENST00000378246.2_Missense_Mutation_p.H128R|DCLRE1C_ENST00000378255.1_Missense_Mutation_p.H123R			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	243			H -> R (in dbSNP:rs12768894). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						TGTGAGATGATGAAGGATCTC	0.393								Non-homologous end-joining					T|||	616	0.123003	0.0923	0.2421	5008	,	,		22543	0.0863		0.1481	False		,,,				2504	0.092				p.H243R		Atlas-SNP	.											.	DCLRE1C	136	.	0			c.A728G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	433,3973	208.5+/-229.5	23,387,1793	240.0	196.0	211.0		728,368,368,383	4.2	1.0	10	dbSNP_121	211	1422,7178	274.1+/-291.0	122,1178,3000	yes	missense,missense,missense,missense	DCLRE1C	NM_001033855.1,NM_001033857.1,NM_001033858.1,NM_022487.2	29,29,29,29	145,1565,4793	CC,CT,TT		16.5349,9.8275,14.2626	benign,benign,benign,benign	243/693,123/573,123/573,128/578	14974905	1855,11151	2203	4300	6503	SO:0001583	missense	64421	exon9			AGATGATGAAGGA	BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"""PSO2 homolog (S. cerevisiae)"""	605988	"""severe combined immunodeficiency, type a (Athabascan)"", ""DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"""	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.728A>G	10.37:g.14974905T>C	ENSP00000367527:p.His243Arg	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_001033855	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Missense_Mutation	SNP	ENST00000378278.2	37	CCDS31149.1	284	0.13003663003663005	49	0.09959349593495935	75	0.20718232044198895	46	0.08041958041958042	114	0.1503957783641161	T	8.492	0.862142	0.17178	0.098275	0.165349	ENSG00000152457	ENST00000378289;ENST00000453695;ENST00000378246;ENST00000357717;ENST00000378249;ENST00000396817;ENST00000378255;ENST00000378254;ENST00000378278;ENST00000378258;ENST00000418843	T;T;T;T;T;T;T;T;T;T;T	0.78595	1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;-1.19	5.3	4.15	0.48705	DNA repair metallo-beta-lactamase (1);	0.248373	0.47852	D	0.000220	T	0.00144	0.0004	L	0.46157	1.445	0.42650	P	0.006553000000000031	B;P;B	0.41569	0.005;0.755;0.0	B;P;B	0.44990	0.037;0.466;0.005	T	0.07731	-1.0757	9	0.24483	T	0.36	.	7.1844	0.25791	0.0:0.0724:0.2762:0.6513	rs12768894;rs17851978	243;128;243	Q96SD1-4;Q96SD1-3;Q96SD1	.;.;DCR1C_HUMAN	R	243;123;128;128;128;123;123;123;243;123;97	ENSP00000367538:H243R;ENSP00000400529:H123R;ENSP00000367492:H128R;ENSP00000350349:H128R;ENSP00000367496:H128R;ENSP00000380030:H123R;ENSP00000367503:H123R;ENSP00000367502:H123R;ENSP00000367527:H243R;ENSP00000367506:H123R;ENSP00000391428:H97R	ENSP00000350349:H128R	H	-	2	0	DCLRE1C	15014911	0.996000	0.38824	0.997000	0.53966	0.479000	0.33129	2.273000	0.43381	0.834000	0.34852	-0.321000	0.08615	CAT	T|0.855;C|0.145	0.145	strong		0.393	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487	
KRI1	65095	hgsc.bcm.edu	37	19	10670184	10670184	+	Missense_Mutation	SNP	C	C	G	rs3826709	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10670184C>G	ENST00000312962.6	-	12	1082	c.1063G>C	c.(1063-1065)Gag>Cag	p.E355Q	KRI1_ENST00000361821.5_Missense_Mutation_p.E351Q|KRI1_ENST00000537964.1_5'Flank	NM_023008.3	NP_075384.3	Q8N9T8	KRI1_HUMAN	KRI1 homolog (S. cerevisiae)	349	Glu-rich.					nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			TGCTTGAGCTCTTCCTGCTTC	0.612													C|||	3116	0.622204	0.7247	0.6441	5008	,	,		18769	0.755		0.4523	False		,,,				2504	0.5061				p.E355Q		Atlas-SNP	.											.	KRI1	65	.	0			c.G1063C						PASS	.	C	GLN/GLU	3119,1287	699.4+/-406.5	1110,899,194	104.0	96.0	99.0		1063	5.0	1.0	19	dbSNP_107	99	4117,4483	563.6+/-388.2	963,2191,1146	yes	missense	KRI1	NM_023008.3	29	2073,3090,1340	GG,GC,CC		47.8721,29.2102,44.3641	probably-damaging	355/710	10670184	7236,5770	2203	4300	6503	SO:0001583	missense	65095	exon12			TGAGCTCTTCCTG		CCDS12242.1	19p13.2	2008-02-05			ENSG00000129347	ENSG00000129347			25769	protein-coding gene	gene with protein product						12878157	Standard	NM_023008		Approved	FLJ12949	uc002moy.1	Q8N9T8	OTTHUMG00000150343	ENST00000312962.6:c.1063G>C	19.37:g.10670184C>G	ENSP00000320917:p.Glu355Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	125	51	0.408	NM_023008	Q2M1R5|Q2M1R7|Q7L5J7|Q96G92|Q9BU50|Q9H6I1|Q9H978	Missense_Mutation	SNP	ENST00000312962.6	37	CCDS12242.1	1362	0.6236263736263736	357	0.725609756097561	212	0.585635359116022	439	0.7674825174825175	354	0.46701846965699206	C	12.08	1.831560	0.32329	0.707898	0.478721	ENSG00000129347	ENST00000312962;ENST00000361821;ENST00000541101	T;T	0.37411	1.2;1.2	4.97	4.97	0.65823	.	0.179255	0.48286	D	0.000187	T	0.00012	0.0000	L	0.58583	1.82	0.24477	P	0.99436703	B;B	0.27732	0.187;0.187	B;B	0.26416	0.069;0.069	T	0.22695	-1.0209	9	0.48119	T	0.1	-26.2698	17.0551	0.86531	0.0:1.0:0.0:0.0	rs3826709;rs52823377;rs59047500;rs3826709	355;351	Q8N9T8;D3YTE0	KRI1_HUMAN;.	Q	355;351;355	ENSP00000320917:E355Q;ENSP00000355366:E351Q	ENSP00000320917:E355Q	E	-	1	0	KRI1	10531184	1.000000	0.71417	0.998000	0.56505	0.476000	0.33039	4.333000	0.59285	2.306000	0.77630	0.644000	0.83932	GAG	C|0.425;G|0.575	0.575	strong		0.612	KRI1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317705.1	NM_023008	
RADIL	55698	hgsc.bcm.edu	37	7	4841452	4841452	+	Missense_Mutation	SNP	C	C	G	rs142212641	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:4841452C>G	ENST00000399583.3	-	12	2861	c.2674G>C	c.(2674-2676)Gct>Cct	p.A892P	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.A652P	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	892	Pro-rich.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		GGGGGGCCAGCCTGGGAGCCC	0.731													C|||	45	0.00898562	0.003	0.0086	5008	,	,		13116	0.0		0.0328	False		,,,				2504	0.002				p.A892P		Atlas-SNP	.											RADIL,brain,glioma,0,1	RADIL	110	1	0			c.G2674C						PASS	.	C	PRO/ALA	10,3468		0,10,1729	6.0	8.0	7.0		2674	-1.6	0.0	7	dbSNP_134	7	138,7692		0,138,3777	no	missense	RADIL	NM_018059.4	27	0,148,5506	GG,GC,CC		1.7625,0.2875,1.3088	benign	892/1076	4841452	148,11160	1739	3915	5654	SO:0001583	missense	55698	exon12			GGCCAGCCTGGGA	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2674G>C	7.37:g.4841452C>G	ENSP00000382492:p.Ala892Pro	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	19	0.0086996336996337	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	C	12.81	2.048620	0.36181	0.002875	0.017625	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000538469	T;T	0.07327	3.27;3.2	4.53	-1.56	0.08532	.	1.399110	0.04548	N	0.389347	T	0.02494	0.0076	N	0.20685	0.6	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.41945	-0.9480	10	0.27785	T	0.31	-0.1722	6.1306	0.20203	0.0:0.4756:0.2545:0.2699	.	892;200	Q96JH8;Q75LH2	RADIL_HUMAN;.	P	892;863;652	ENSP00000382492:A892P;ENSP00000442966:A652P	ENSP00000320946:A863P	A	-	1	0	RADIL	4807978	0.000000	0.05858	0.012000	0.15200	0.461000	0.32589	-0.234000	0.09028	-0.212000	0.10109	-0.222000	0.12452	GCT	C|0.991;G|0.009	0.009	strong		0.731	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
NLRC3	197358	hgsc.bcm.edu	37	16	3613126	3613126	+	RNA	SNP	C	C	T	rs12445430	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:3613126C>T	ENST00000301749.7	-	0	2217				NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000359128.5_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGAGGTAGGCCAGGGCAGCGC	0.706													C|||	1118	0.223243	0.2224	0.1916	5008	,	,		14200	0.2708		0.1988	False		,,,				2504	0.2229				p.L604L		Atlas-SNP	.											.	NLRC3	103	.	0			c.G1812A						PASS	.	C		876,3152		102,672,1240	9.0	12.0	11.0		1812	4.1	1.0	16	dbSNP_120	11	1662,6652		192,1278,2687	no	coding-synonymous	NLRC3	NM_178844.2		294,1950,3927	TT,TC,CC		19.9904,21.7478,20.5639		604/1066	3613126	2538,9804	2014	4157	6171			197358	exon5			GTAGGCCAGGGCA	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613126C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	46	32	0.695652	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	37																																																																																				C|0.748;T|0.252	0.252	strong		0.706	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
TEX15	56154	hgsc.bcm.edu	37	8	30700598	30700598	+	Missense_Mutation	SNP	T	T	C	rs61740968	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:30700598T>C	ENST00000256246.2	-	1	6010	c.5936A>G	c.(5935-5937)aAt>aGt	p.N1979S		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1979					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TGCAAGCAAATTACTGTTAAA	0.353													T|||	344	0.0686901	0.0008	0.0807	5008	,	,		17286	0.0992		0.0934	False		,,,				2504	0.0951				p.N1979S		Atlas-SNP	.											TEX15,colon,carcinoma,+1,1	TEX15	350	1	0			c.A5936G						PASS	.	T	SER/ASN	95,4307	73.1+/-111.1	0,95,2106	45.0	48.0	47.0		5936	-0.4	0.0	8	dbSNP_129	47	855,7739	182.6+/-231.0	36,783,3478	yes	missense	TEX15	NM_031271.3	46	36,878,5584	CC,CT,TT		9.9488,2.1581,7.3099	benign	1979/2790	30700598	950,12046	2201	4297	6498	SO:0001583	missense	56154	exon1			AGCAAATTACTGT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.5936A>G	8.37:g.30700598T>C	ENSP00000256246:p.Asn1979Ser	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	172	86	0.5	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	158	0.07234432234432235	1	0.0020325203252032522	22	0.06077348066298342	67	0.11713286713286714	68	0.08970976253298153	T	0.012	-1.682965	0.00745	0.021581	0.099488	ENSG00000133863	ENST00000256246	T	0.09163	3.01	5.73	-0.405	0.12392	.	1.043110	0.07528	N	0.911722	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43327	-0.9398	9	0.87932	D	0	.	2.1003	0.03678	0.139:0.2393:0.3736:0.2481	.	1979	Q9BXT5	TEX15_HUMAN	S	1979	ENSP00000256246:N1979S	ENSP00000256246:N1979S	N	-	2	0	TEX15	30820140	0.066000	0.20996	0.003000	0.11579	0.004000	0.04260	0.075000	0.14686	-0.132000	0.11557	-1.334000	0.01262	AAT	T|0.925;C|0.075	0.075	strong		0.353	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
LIFR	3977	hgsc.bcm.edu	37	5	38486065	38486065	+	Missense_Mutation	SNP	C	C	T	rs3110234	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:38486065C>T	ENST00000263409.4	-	17	2515	c.2353G>A	c.(2353-2355)Gtt>Att	p.V785I	LIFR_ENST00000453190.2_Missense_Mutation_p.V785I	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	785	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs3110234).		cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					ATATTCTTAACTTTTATGTCA	0.403			T	PLAG1	salivary adenoma								C|||	693	0.138379	0.115	0.2666	5008	,	,		9997	0.0218		0.1869	False		,,,				2504	0.1493				p.V785I	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.G2353A						PASS	.	C	ILE/VAL,ILE/VAL	543,3863	242.1+/-252.3	26,491,1686	86.0	81.0	83.0		2353,2353	3.6	0.9	5	dbSNP_103	83	1888,6712	332.1+/-320.0	213,1462,2625	yes	missense,missense	LIFR	NM_001127671.1,NM_002310.5	29,29	239,1953,4311	TT,TC,CC		21.9535,12.3241,18.6914	benign,benign	785/1098,785/1098	38486065	2431,10575	2203	4300	6503	SO:0001583	missense	3977	exon17			TCTTAACTTTTAT	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2353G>A	5.37:g.38486065C>T	ENSP00000263409:p.Val785Ile	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	150	59	0.393333	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	314	0.14377289377289376	53	0.10772357723577236	93	0.2569060773480663	13	0.022727272727272728	155	0.20448548812664907	C	11.42	1.632615	0.29068	0.123241	0.219535	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.56611	0.45;0.45	5.43	3.61	0.41365	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.319101	0.26453	N	0.024293	T	0.00012	0.0000	L	0.34521	1.04	0.39110	P	0.03853799999999996	B	0.34372	0.451	B	0.28991	0.097	T	0.23691	-1.0181	9	0.23891	T	0.37	-14.427	8.5351	0.33357	0.0:0.6167:0.3042:0.0791	rs3110234;rs3729748;rs52830166;rs58101933;rs3110234	785	P42702	LIFR_HUMAN	I	785	ENSP00000263409:V785I;ENSP00000398368:V785I	ENSP00000263409:V785I	V	-	1	0	LIFR	38521822	0.985000	0.35326	0.948000	0.38648	0.836000	0.47400	0.357000	0.20199	0.622000	0.30249	0.563000	0.77884	GTT	C|0.838;T|0.162	0.162	strong		0.403	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
MTMR4	9110	hgsc.bcm.edu	37	17	56585872	56585872	+	Missense_Mutation	SNP	G	G	C	rs3744108	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:56585872G>C	ENST00000323456.5	-	7	632	c.508C>G	c.(508-510)Ctg>Gtg	p.L170V	MTMR4_ENST00000579925.1_Missense_Mutation_p.L170V	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	170	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.		L -> V (in dbSNP:rs3744108). {ECO:0000269|PubMed:11302699, ECO:0000269|PubMed:9734811}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACGTTCTGCAGGTCAAAGCCC	0.527													G|||	1978	0.394968	0.2481	0.5591	5008	,	,		22277	0.5188		0.3648	False		,,,				2504	0.3804				p.L170V		Atlas-SNP	.											.	MTMR4	91	.	0			c.C508G						PASS	.	G	VAL/LEU	1248,3158	427.0+/-341.4	181,886,1136	200.0	153.0	169.0		508	5.1	1.0	17	dbSNP_107	169	3222,5378	485.9+/-371.7	619,1984,1697	yes	missense	MTMR4	NM_004687.4	32	800,2870,2833	CC,CG,GG		37.4651,28.325,34.3688	benign	170/1196	56585872	4470,8536	2203	4300	6503	SO:0001583	missense	9110	exon7			TCTGCAGGTCAAA	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.508C>G	17.37:g.56585872G>C	ENSP00000325285:p.Leu170Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	135	134	0.992593	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Missense_Mutation	SNP	ENST00000323456.5	37	CCDS11608.1	879	0.4024725274725275	111	0.22560975609756098	192	0.5303867403314917	297	0.5192307692307693	279	0.36807387862796836	G	12.30	1.896361	0.33442	0.28325	0.374651	ENSG00000108389	ENST00000323456	D	0.92752	-3.1	6.08	5.11	0.69529	Myotubularin phosphatase domain (1);	0.134831	0.51477	D	0.000086	T	0.00012	0.0000	N	0.21545	0.675	0.22253	P	0.99925004	B	0.29590	0.25	B	0.29267	0.1	T	0.37407	-0.9707	9	0.35671	T	0.21	.	8.4868	0.33076	0.2239:0.0:0.7761:0.0	rs3744108;rs3744108	170	Q9NYA4	MTMR4_HUMAN	V	170	ENSP00000325285:L170V	ENSP00000325285:L170V	L	-	1	2	MTMR4	53940871	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.698000	0.37794	1.585000	0.49928	0.655000	0.94253	CTG	G|0.635;C|0.365	0.365	strong		0.527	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687	
SPINK5	11005	hgsc.bcm.edu	37	5	147499891	147499891	+	Missense_Mutation	SNP	G	G	T	rs2303070	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:147499891G>T	ENST00000256084.7	+	26	2517	c.2475G>T	c.(2473-2475)gaG>gaT	p.E825D	SPINK5_ENST00000359874.3_Missense_Mutation_p.E825D|SPINK5_ENST00000398454.1_Missense_Mutation_p.E825D	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	825	Kazal-like 12. {ECO:0000255|PROSITE- ProRule:PRU00798}.		E -> D (in dbSNP:rs2303070).		anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAAAGAAAGAGGATGAAGACA	0.398													G|||	874	0.174521	0.1195	0.0648	5008	,	,		19681	0.2927		0.0855	False		,,,				2504	0.2965				p.E825D		Atlas-SNP	.											.	SPINK5	245	.	0			c.G2475T						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU	397,3325		13,371,1477	153.0	153.0	153.0		2475,2475,2475	0.6	0.3	5	dbSNP_100	153	779,7417		32,715,3351	yes	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	45,45,45	45,1086,4828	TT,TG,GG		9.5046,10.6663,9.8674	benign,benign,benign	825/1095,825/917,825/1065	147499891	1176,10742	1861	4098	5959	SO:0001583	missense	11005	exon26			GAAAGAGGATGAA	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.2475G>T	5.37:g.147499891G>T	ENSP00000256084:p.Glu825Asp	Somatic	368	1	0.00271739		WXS	Illumina HiSeq	Phase_I	398	186	0.467337	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	302	0.1382783882783883	42	0.08536585365853659	24	0.06629834254143646	169	0.29545454545454547	67	0.08839050131926121	G	12.80	2.045734	0.36085	0.106663	0.095046	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.50548	0.79;0.8;0.95;0.74	4.28	0.564	0.17302	Proteinase inhibitor I1, Kazal (1);	0.260975	0.27164	N	0.020640	T	0.00012	0.0000	L	0.50919	1.6	0.53005	P	3.2000000000032E-5	B;B;B;B	0.26483	0.011;0.128;0.15;0.016	B;B;B;B	0.34931	0.068;0.098;0.192;0.121	T	0.31223	-0.9951	9	0.13108	T	0.6	-23.6059	6.218	0.20665	0.4265:0.0:0.5735:0.0	rs2303070;rs17860506;rs52791568;rs2303070	806;825;825;825	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	D	825;825;806;825	ENSP00000381472:E825D;ENSP00000352936:E825D;ENSP00000421519:E806D;ENSP00000256084:E825D	ENSP00000256084:E825D	E	+	3	2	SPINK5	147480084	0.002000	0.14202	0.294000	0.24946	0.618000	0.37518	-0.614000	0.05604	0.081000	0.16988	0.557000	0.71058	GAG	G|0.858;T|0.142	0.142	strong		0.398	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
NRAP	4892	hgsc.bcm.edu	37	10	115392919	115392919	+	Missense_Mutation	SNP	T	T	A	rs2270182	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:115392919T>A	ENST00000359988.3	-	16	1800	c.1556A>T	c.(1555-1557)aAt>aTt	p.N519I	NRAP_ENST00000369360.3_Missense_Mutation_p.N484I|NRAP_ENST00000369358.4_Missense_Mutation_p.N519I|NRAP_ENST00000360478.3_Missense_Mutation_p.N484I	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		ATTCAACTTATTTTTCTCATA	0.423													T|||	1296	0.258786	0.3336	0.2248	5008	,	,		19373	0.1915		0.2714	False		,,,				2504	0.2382				p.N519I		Atlas-SNP	.											.	NRAP	208	.	0			c.A1556T						PASS	.	T	ILE/ASN,ILE/ASN	1556,2850	488.5+/-361.2	276,1004,923	139.0	118.0	125.0		1451,1556	5.7	1.0	10	dbSNP_100	125	2383,6217	394.7+/-344.8	332,1719,2249	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	149,149	608,2723,3172	AA,AT,TT		27.7093,35.3155,30.286	benign,benign	484/1696,519/1731	115392919	3939,9067	2203	4300	6503	SO:0001583	missense	4892	exon16			AACTTATTTTTCT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.1556A>T	10.37:g.115392919T>A	ENSP00000353078:p.Asn519Ile	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	255	106	0.415686	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	561	0.25686813186813184	152	0.3089430894308943	75	0.20718232044198895	117	0.20454545454545456	217	0.2862796833773087	T	17.26	3.344359	0.61073	0.353155	0.277093	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350;ENST00000369343	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.67	5.67	0.87782	.	0.097718	0.64402	D	0.000002	T	0.00012	0.0000	N	0.17082	0.46	0.32215	P	0.576051	D;P;D	0.53151	0.958;0.889;0.958	P;P;P	0.55749	0.783;0.578;0.783	T	0.38542	-0.9656	9	0.37606	T	0.19	.	11.4347	0.50062	0.0:0.0:0.2723:0.7277	rs2270182;rs60908683;rs2270182	519;484;519	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	I	519;484;519;484;248;248	ENSP00000358365:N519I;ENSP00000358367:N484I;ENSP00000353078:N519I;ENSP00000353666:N484I	ENSP00000353078:N519I	N	-	2	0	NRAP	115382909	1.000000	0.71417	0.959000	0.39883	0.989000	0.77384	2.477000	0.45180	2.159000	0.67721	0.455000	0.32223	AAT	T|0.718;A|0.282	0.282	strong		0.423	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
DIS3	22894	hgsc.bcm.edu	37	13	73343039	73343039	+	Silent	SNP	C	C	T	rs2196979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:73343039C>T	ENST00000377767.4	-	14	1867	c.1767G>A	c.(1765-1767)acG>acA	p.T589T	DIS3_ENST00000377780.4_Silent_p.T559T|DIS3_ENST00000545453.1_Silent_p.T427T	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	589					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		CTTCAGCATACGTCAGAGATG	0.318										Multiple Myeloma(4;0.011)			T|||	3857	0.770168	0.8185	0.7637	5008	,	,		15586	0.748		0.6859	False		,,,				2504	0.819				p.T589T		Atlas-SNP	.											.	DIS3	103	.	0			c.G1767A						PASS	.	T	,	3594,810	318.5+/-295.7	1471,652,79	64.0	64.0	64.0		1677,1767	-9.8	0.4	13	dbSNP_96	64	6122,2470	405.2+/-348.4	2174,1774,348	no	coding-synonymous,coding-synonymous	DIS3	NM_001128226.1,NM_014953.3	,	3645,2426,427	TT,TC,CC		28.7477,18.3924,25.2385	,	559/929,589/959	73343039	9716,3280	2202	4296	6498	SO:0001819	synonymous_variant	22894	exon14			AGCATACGTCAGA	AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"""exosome component 11"""	607533	"""KIAA1008"", ""DIS3 mitotic control homolog (S. cerevisiae)"""	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.1767G>A	13.37:g.73343039C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	161	156	0.968944	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Silent	SNP	ENST00000377767.4	37	CCDS9447.1																																																																																			C|0.244;T|0.756	0.756	strong		0.318	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953	
H1FNT	341567	hgsc.bcm.edu	37	12	48723595	48723595	+	Missense_Mutation	SNP	G	G	A	rs1471997	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48723595G>A	ENST00000335017.1	+	1	833	c.521G>A	c.(520-522)cGg>cAg	p.R174Q		NM_181788.1	NP_861453.1	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	174	Arg-rich.		R -> Q (in a Japanese man; dbSNP:rs1471997). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16533358}.		chromosome condensation (GO:0030261)|multicellular organismal development (GO:0007275)|sperm chromatin condensation (GO:0035092)|spermatid nucleus elongation (GO:0007290)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	13						GTGTGGAGACGGAACGCGAGG	0.711													G|||	807	0.161142	0.09	0.2176	5008	,	,		12981	0.2212		0.2137	False		,,,				2504	0.1012				p.R174Q		Atlas-SNP	.											.	H1FNT	30	.	0			c.G521A						PASS	.	G	GLN/ARG	450,3908		19,412,1748	32.0	29.0	30.0		521	-1.3	0.0	12	dbSNP_88	30	1851,6731		199,1453,2639	yes	missense	H1FNT	NM_181788.1	43	218,1865,4387	AA,AG,GG		21.5684,10.3258,17.7821	benign	174/256	48723595	2301,10639	2179	4291	6470	SO:0001583	missense	341567	exon1			GGAGACGGAACGC	AY302593	CCDS8762.1	12q13.11	2011-01-27				ENSG00000187166		"""Histones / Replication-independent"""	24893	protein-coding gene	gene with protein product						15710904	Standard	NM_181788		Approved	HANP1, H1T2	uc001rrm.3	Q75WM6		ENST00000335017.1:c.521G>A	12.37:g.48723595G>A	ENSP00000334805:p.Arg174Gln	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_181788	Q147U8|Q5GKZ5|Q7Z694	Missense_Mutation	SNP	ENST00000335017.1	37	CCDS8762.1	403	0.18452380952380953	45	0.09146341463414634	82	0.2265193370165746	121	0.21153846153846154	155	0.20448548812664907	G	12.20	1.866692	0.32977	0.103258	0.215684	ENSG00000187166	ENST00000335017	T	0.18960	2.18	4.18	-1.27	0.09347	.	0.299800	0.18034	N	0.153839	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.18968	0.032	B	0.11329	0.006	T	0.32771	-0.9894	9	0.42905	T	0.14	-0.671	1.7845	0.03038	0.2282:0.2568:0.3824:0.1326	rs1471997;rs52803112;rs57038423;rs1471997	174	Q75WM6	H1FNT_HUMAN	Q	174	ENSP00000334805:R174Q	ENSP00000334805:R174Q	R	+	2	0	H1FNT	47009862	0.007000	0.16637	0.001000	0.08648	0.023000	0.10783	0.557000	0.23454	-0.379000	0.07906	-1.367000	0.01198	CGG	G|0.832;A|0.168	0.168	strong		0.711	H1FNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406516.1	NM_181788	
CUX1	1523	hgsc.bcm.edu	37	7	101917521	101917521	+	Missense_Mutation	SNP	G	G	A	rs803064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:101917521G>A	ENST00000437600.4	+	16	1736	c.1384G>A	c.(1384-1386)Gct>Act	p.A462T	CUX1_ENST00000547394.2_Missense_Mutation_p.A448T|CUX1_ENST00000425244.2_Missense_Mutation_p.A418T|CUX1_ENST00000292538.4_Missense_Mutation_p.A464T|CUX1_ENST00000393824.3_Missense_Mutation_p.A425T|CUX1_ENST00000560541.1_3'UTR	NM_181500.2	NP_852477.1	P39880	CUX1_HUMAN	cut-like homeobox 1	0					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						GCAGGGTGCCGCTGAGCACCG	0.607													G|||	2800	0.559105	0.6172	0.5072	5008	,	,		19921	0.498		0.5358	False		,,,				2504	0.6043				p.A464T		Atlas-SNP	.											.	CUX1	253	.	0			c.G1390A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	2609,1797	641.4+/-397.5	776,1057,370	96.0	88.0	90.0		1342,1252,1273,1390,1384	-0.1	0.0	7	dbSNP_86	90	4869,3731	618.5+/-396.8	1369,2131,800	yes	missense,missense,missense,missense,missense	CUX1	NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2	58,58,58,58,58	2145,3188,1170	AA,AG,GG		43.3837,40.7853,42.5035	,,,,	448/663,418/633,425/640,464/679,462/677	101917521	7478,5528	2203	4300	6503	SO:0001583	missense	1523	exon16			GGTGCCGCTGAGC	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000437600.4:c.1384G>A	7.37:g.101917521G>A	ENSP00000414091:p.Ala462Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_001913	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000437600.4	37	CCDS47672.1	1228	0.5622710622710623	321	0.6524390243902439	202	0.5580110497237569	277	0.48426573426573427	428	0.5646437994722955	G	6.651	0.488701	0.12641	0.592147	0.566163	ENSG00000257923	ENST00000292538;ENST00000547394;ENST00000425244;ENST00000437600	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	4.64	-0.106	0.13596	CASP, C-terminal (1);	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B;B;B;B	0.28971	0.127;0.229;0.229;0.001	B;B;B;B	0.24269	0.021;0.052;0.041;0.006	T	0.41070	-0.9529	8	0.12766	T	0.61	.	7.499	0.27507	0.1446:0.0:0.6019:0.2535	rs803064;rs1725585;rs2230106;rs10375045;rs17135114;rs52803548;rs803064	418;448;462;464	B3KV79;G3V1Z6;Q13948-2;Q13948	.;.;.;CASP_HUMAN	T	464;448;418;462	ENSP00000292538:A464T;ENSP00000449371:A448T;ENSP00000409745:A418T;ENSP00000414091:A462T	ENSP00000292538:A464T	A	+	1	0	CUX1	101704241	0.807000	0.29009	0.020000	0.16555	0.029000	0.11900	2.486000	0.45259	0.064000	0.16427	-0.918000	0.02743	GCT	G|0.431;A|0.569	0.569	strong		0.607	CUX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347534.3	NM_001913	
CLDND2	125875	hgsc.bcm.edu	37	19	51871195	51871195	+	Silent	SNP	G	G	A	rs3745403	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51871195G>A	ENST00000291715.1	-	2	680	c.255C>T	c.(253-255)tgC>tgT	p.C85C	CTD-2616J11.11_ENST00000600067.1_Silent_p.C20C|CLDND2_ENST00000601435.1_Silent_p.C85C|CTD-2616J11.10_ENST00000595500.1_RNA|ETFB_ENST00000309244.4_5'Flank	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	85						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CGCCCTCGTCGCACCGAATCC	0.726													G|||	968	0.193291	0.0371	0.2795	5008	,	,		11925	0.1577		0.3897	False		,,,				2504	0.1779				p.C85C		Atlas-SNP	.											.	CLDND2	11	.	0			c.C255T						PASS	.	G		435,3965		25,385,1790	29.0	29.0	29.0		255	1.4	0.0	19	dbSNP_107	29	3464,5130		714,2036,1547	no	coding-synonymous	CLDND2	NM_152353.2		739,2421,3337	AA,AG,GG		40.3072,9.8864,30.0062		85/168	51871195	3899,9095	2200	4297	6497	SO:0001819	synonymous_variant	125875	exon2			CTCGTCGCACCGA	BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.255C>T	19.37:g.51871195G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	64	40	0.625	NM_152353		Silent	SNP	ENST00000291715.1	37	CCDS12829.1																																																																																			G|0.733;A|0.267	0.267	strong		0.726	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353	
BPIFA2	140683	hgsc.bcm.edu	37	20	31761919	31761919	+	Missense_Mutation	SNP	A	A	G	rs17304572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:31761919A>G	ENST00000253362.2	+	4	483	c.337A>G	c.(337-339)Aaa>Gaa	p.K113E	BPIFA2_ENST00000354932.5_Missense_Mutation_p.K113E			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	113			K -> E (in dbSNP:rs17304572).			extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										CCTGGATGTCAAAGCTGAACC	0.507													A|||	36	0.0071885	0.0008	0.0447	5008	,	,		20651	0.0		0.003	False		,,,				2504	0.001				p.K113E		Atlas-SNP	.											.	.	.	.	0			c.A337G						PASS	.	A	GLU/LYS	9,4397	15.5+/-35.6	0,9,2194	190.0	130.0	150.0		337	0.5	0.0	20	dbSNP_123	150	65,8535	39.3+/-95.6	0,65,4235	yes	missense	BPIFA2	NM_080574.2	56	0,74,6429	GG,GA,AA		0.7558,0.2043,0.569	possibly-damaging	113/250	31761919	74,12932	2203	4300	6503	SO:0001583	missense	140683	exon4			GATGTCAAAGCTG	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.337A>G	20.37:g.31761919A>G	ENSP00000253362:p.Lys113Glu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	111	62	0.558559	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	15	0.006868131868131868	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	4	0.005277044854881266	A	14.94	2.685424	0.47991	0.002043	0.007558	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.05580	3.42;3.42	4.11	0.538	0.17150	.	0.626240	0.15043	N	0.283766	T	0.02767	0.0083	L	0.50919	1.6	0.09310	N	1	P	0.41624	0.757	B	0.43728	0.429	T	0.30001	-0.9993	10	0.15952	T	0.53	-20.1787	3.5768	0.07937	0.5707:0.2098:0.2195:0.0	rs17304572;rs52835642;rs56630818;rs17304572	113	Q96DR5	BPIA2_HUMAN	E	113	ENSP00000253362:K113E;ENSP00000347012:K113E	ENSP00000253362:K113E	K	+	1	0	BPIFA2	31225580	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	0.427000	0.21379	0.060000	0.16281	0.459000	0.35465	AAA	A|0.994;G|0.006	0.006	strong		0.507	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	
EFS	10278	hgsc.bcm.edu	37	14	23830042	23830042	+	Splice_Site	SNP	T	T	C	rs2231798	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23830042T>C	ENST00000216733.3	-	2	626	c.19A>G	c.(19-21)Acc>Gcc	p.T7A	EFS_ENST00000429593.2_Intron|EFS_ENST00000351354.3_Intron	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	7	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.		T -> A (in dbSNP:rs2231798).		cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		GCCAGCTGGGTCTGGTTGGGG	0.637													C|||	2282	0.455671	0.8759	0.2478	5008	,	,		16776	0.3046		0.2763	False		,,,				2504	0.3753				p.T7A		Atlas-SNP	.											.	EFS	37	.	0			c.A19G						PASS	.	C	ALA/THR,	3380,1010		1320,740,135	15.0	18.0	17.0		19,	5.0	1.0	14	dbSNP_98	17	2555,6017		413,1729,2144	yes	missense-near-splice,intron	EFS	NM_005864.2,NM_032459.1	58,	1733,2469,2279	CC,CT,TT		29.8063,23.0068,45.7877	benign,	7/562,	23830042	5935,7027	2195	4286	6481	SO:0001630	splice_region_variant	10278	exon2			GCTGGGTCTGGTT	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"""Cas scaffolding proteins"""	16898	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 3"""	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.19-1A>G	14.37:g.23830042T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Missense_Mutation	SNP	ENST00000216733.3	37	CCDS9595.1	930	0.4258241758241758	426	0.8658536585365854	111	0.30662983425414364	186	0.32517482517482516	207	0.27308707124010556	C	5.796	0.331223	0.10956	0.769932	0.298063	ENSG00000100842	ENST00000216733	T	0.55760	0.5	4.99	4.99	0.66335	Src homology-3 domain (2);	0.124031	0.53938	N	0.000051	T	0.00012	0.0000	N	0.21545	0.675	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27331	-1.0077	9	0.11794	T	0.64	-12.5983	11.7333	0.51750	0.0:0.9141:0.0:0.0859	rs2231798;rs57406640;rs2231798	7	O43281	EFS_HUMAN	A	7	ENSP00000216733:T7A	ENSP00000216733:T7A	T	-	1	0	EFS	22899882	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	1.376000	0.34306	1.496000	0.48567	-0.213000	0.12676	ACC	T|0.564;C|0.436	0.436	strong		0.637	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2		Missense_Mutation
SMARCA4	6597	hgsc.bcm.edu	37	19	11145691	11145691	+	Silent	SNP	C	C	T	rs28997582	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11145691C>T	ENST00000429416.3	+	30	4334	c.4053C>T	c.(4051-4053)gaC>gaT	p.D1351D	SMARCA4_ENST00000590574.1_Silent_p.D1318D|SMARCA4_ENST00000358026.2_Silent_p.D1351D|SMARCA4_ENST00000444061.3_Silent_p.D1318D|SMARCA4_ENST00000344626.4_Silent_p.D1351D|SMARCA4_ENST00000538456.3_3'UTR|SMARCA4_ENST00000589677.1_Silent_p.D1318D|SMARCA4_ENST00000541122.2_Silent_p.D1318D|SMARCA4_ENST00000450717.3_Silent_p.D1318D|SMARCA4_ENST00000413806.3_Silent_p.D1318D	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1351					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TCAAGGACGACGCGGAGGTGG	0.672			"""F, N, Mis"""		NSCLC								c|||	236	0.0471246	0.0045	0.0346	5008	,	,		19074	0.0437		0.0666	False		,,,				2504	0.0971				p.D1351D		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	SMARCA4_ENST00000358026,colon,carcinoma,+2,4	SMARCA4	502	4	1	Unknown(1)	lung(1)	c.C4053T						scavenged	.		,,,,,,	57,4349	52.9+/-88.7	1,55,2147	49.0	38.0	42.0		4053,3954,3954,3954,3954,4053,4053	-8.8	0.0	19	dbSNP_125	42	543,8057	146.0+/-201.7	18,507,3775	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SMARCA4	NM_001128844.1,NM_001128845.1,NM_001128846.1,NM_001128847.1,NM_001128848.1,NM_001128849.1,NM_003072.3	,,,,,,	19,562,5922	TT,TC,CC		6.314,1.2937,4.6133	,,,,,,	1351/1648,1318/1618,1318/1617,1318/1615,1318/1614,1351/1680,1351/1648	11145691	600,12406	2203	4300	6503	SO:0001819	synonymous_variant	6597	exon29			GGACGACGCGGAG	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.4053C>T	19.37:g.11145691C>T		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	120	74	0.616667	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	37	CCDS12253.1	86	0.039377289377289376	5	0.01016260162601626	16	0.04419889502762431	15	0.026223776223776224	50	0.06596306068601583	c	2.420	-0.333256	0.05278	0.012937	0.06314	ENSG00000127616	ENST00000538456	.	.	.	4.59	-8.82	0.00810	.	.	.	.	.	T	0.14313	0.0346	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72443	-0.4292	4	.	.	.	-31.1351	19.9771	0.97313	0.0:0.7333:0.0:0.2667	rs28997582;rs28997582	.	.	.	C	88	.	.	R	+	1	0	SMARCA4	11006691	0.000000	0.05858	0.038000	0.18304	0.386000	0.30323	-2.503000	0.00965	-2.813000	0.00347	-2.282000	0.00269	CGC	C|0.956;T|0.044	0.044	strong		0.672	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
OR2T4	127074	hgsc.bcm.edu	37	1	248525330	248525330	+	Missense_Mutation	SNP	A	A	G	rs376643959|rs56721857	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248525330A>G	ENST00000366475.1	+	1	448	c.448A>G	c.(448-450)Atg>Gtg	p.M150V		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCTAGCCACCATGGCCTATGA	0.522													a|||	1358	0.271166	0.2284	0.2637	5008	,	,		19950	0.381		0.1779	False		,,,				2504	0.317				p.M150V		Atlas-SNP	.											.	OR2T4	126	.	0			c.A448G						PASS	.						179.0	174.0	176.0					1																	248525330		2203	4300	6503	SO:0001583	missense	127074	exon1			GCCACCATGGCCT	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.448A>G	1.37:g.248525330A>G	ENSP00000355431:p.Met150Val	Somatic	732	2	0.00273224		WXS	Illumina HiSeq	Phase_I	652	199	0.305215	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.455416	0.63401	.	.	ENSG00000196944	ENST00000366475	T	0.00995	5.46	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000023	T	0.05502	0.0145	M	0.91972	3.26	0.38959	D	0.958507	D	0.61080	0.989	P	0.58721	0.844	T	0.05209	-1.0899	10	0.87932	D	0	.	11.6861	0.51487	1.0:0.0:0.0:0.0	rs56721857	150	Q8NH00	OR2T4_HUMAN	V	150	ENSP00000355431:M150V	ENSP00000355431:M150V	M	+	1	0	OR2T4	246591953	1.000000	0.71417	0.636000	0.29352	0.769000	0.43574	5.832000	0.69337	1.205000	0.43262	0.397000	0.26171	ATG	A|0.878;G|0.122	0.122	strong		0.522	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
FRG2B	441581	hgsc.bcm.edu	37	10	135440203	135440203	+	Missense_Mutation	SNP	A	A	T	rs200661929	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135440203A>T	ENST00000425520.1	-	1	96	c.44T>A	c.(43-45)aTc>aAc	p.I15N	FRG2B_ENST00000443774.1_Missense_Mutation_p.I15N	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	15						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		GGAGCACTGGATGGAGGAGCA	0.507													.|||	867	0.173123	0.1437	0.1254	5008	,	,		19912	0.2411		0.0885	False		,,,				2504	0.2638				p.I15N		Atlas-SNP	.											FRG2B,NS,haematopoietic_neoplasm,0,1	FRG2B	47	1	0			c.T44A						scavenged	.	A	ASN/ILE	303,4103		0,303,1900	227.0	254.0	245.0		44	0.1	0.0	10		245	380,8220		0,380,3920	no	missense	FRG2B	NM_001080998.1	149	0,683,5820	TT,TA,AA		4.4186,6.877,5.2514	benign	15/279	135440203	683,12323	2203	4300	6503	SO:0001583	missense	441581	exon1			CACTGGATGGAGG	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.44T>A	10.37:g.135440203A>T	ENSP00000401310:p.Ile15Asn	Somatic	533	0	0		WXS	Illumina HiSeq	Phase_I	761	164	0.215506	NM_001080998	Q5VSQ1	Missense_Mutation	SNP	ENST00000425520.1	37	CCDS44502.1	.	.	.	.	.	.	.	.	.	.	.	3.902	-0.021862	0.07634	0.06877	0.044186	ENSG00000225899	ENST00000443774;ENST00000425520	T;T	0.44881	0.91;0.91	0.109	0.109	0.14578	.	2.975530	0.01571	N	0.020585	T	0.01905	0.0060	N	0.14661	0.345	0.09310	N	1	B	0.31859	0.343	B	0.24155	0.051	T	0.14227	-1.0480	9	0.87932	D	0	1.8074	.	.	.	.	15	Q96QU4	FRG2B_HUMAN	N	15	ENSP00000408343:I15N;ENSP00000401310:I15N	ENSP00000401310:I15N	I	-	2	0	FRG2B	135290193	0.957000	0.32711	0.030000	0.17652	0.030000	0.12068	0.803000	0.27083	0.156000	0.19299	0.155000	0.16302	ATC	A|0.986;T|0.014	0.014	strong		0.507	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
CPZ	8532	hgsc.bcm.edu	37	4	8594577	8594577	+	Missense_Mutation	SNP	C	C	T	rs34964084	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:8594577C>T	ENST00000360986.4	+	1	191	c.17C>T	c.(16-18)cCg>cTg	p.P6L	CPZ_ENST00000315782.6_Missense_Mutation_p.P6L|CPZ_ENST00000506287.1_3'UTR|CPZ_ENST00000382480.2_5'UTR	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	6			P -> L (in dbSNP:rs34964084). {ECO:0000269|PubMed:9099699}.		proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CCCCCGCTGCCGCTGCTGCTC	0.756													C|||	655	0.130791	0.025	0.1931	5008	,	,		9673	0.1617		0.2366	False		,,,				2504	0.089				p.P6L		Atlas-SNP	.											.	CPZ	95	.	0			c.C17T						PASS	.	C	,LEU/PRO,LEU/PRO	101,2957		1,99,1429	2.0	3.0	3.0		,17,17	-0.6	0.0	4	dbSNP_126	3	811,5659		38,735,2462	no	utr-5,missense,missense	CPZ	NM_001014448.2,NM_003652.3,NM_001014447.2	,98,98	39,834,3891	TT,TC,CC		12.5348,3.3028,9.5718	,benign,benign	,6/642,6/653	8594577	912,8616	1529	3235	4764	SO:0001583	missense	8532	exon1			CGCTGCCGCTGCT	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"""metallocarboxypeptidase Z"""	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.17C>T	4.37:g.8594577C>T	ENSP00000354255:p.Pro6Leu	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	7	5	0.714286	NM_003652	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	352	0.16117216117216118	16	0.032520325203252036	78	0.2154696132596685	77	0.1346153846153846	181	0.23878627968337732	C	0.003	-2.482788	0.00163	0.033028	0.125348	ENSG00000109625	ENST00000360986;ENST00000315782	T;T	0.56776	0.68;0.44	1.87	-0.596	0.11657	.	2.196060	0.02795	N	0.122470	T	0.00012	0.0000	N	0.14661	0.345	0.38383	P	0.054822999999999955	B;B	0.09022	0.002;0.001	B;B	0.01281	0.0;0.0	T	0.06826	-1.0805	9	0.02654	T	1	.	4.365	0.11220	0.0:0.4294:0.0:0.5706	rs34964084	6;6	Q66K79-2;Q66K79	.;CBPZ_HUMAN	L	6	ENSP00000354255:P6L;ENSP00000315074:P6L	ENSP00000315074:P6L	P	+	2	0	CPZ	8645477	0.001000	0.12720	0.014000	0.15608	0.073000	0.16967	0.039000	0.13884	-0.198000	0.10333	-0.379000	0.06801	CCG	C|0.835;T|0.165	0.165	strong		0.756	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
NAV2	89797	hgsc.bcm.edu	37	11	20129311	20129311	+	Missense_Mutation	SNP	G	G	A	rs35891966	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:20129311G>A	ENST00000396087.3	+	39	7219	c.7120G>A	c.(7120-7122)Gtc>Atc	p.V2374I	NAV2_ENST00000349880.4_Missense_Mutation_p.V2315I|NAV2_ENST00000527559.2_Missense_Mutation_p.V2303I|NAV2_ENST00000311043.8_Missense_Mutation_p.V1379I|NAV2_ENST00000360655.4_Missense_Mutation_p.V2251I|NAV2_ENST00000540292.1_Missense_Mutation_p.V2305I|NAV2_ENST00000396085.1_Missense_Mutation_p.V2318I|NAV2_ENST00000533917.1_Missense_Mutation_p.V1379I	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2374			V -> I (in dbSNP:rs35891966). {ECO:0000269|PubMed:14702039}.		glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CCTGGAAGCCGTCAGAGAAGG	0.557													G|||	112	0.0223642	0.0023	0.0187	5008	,	,		20169	0.001		0.0716	False		,,,				2504	0.0235				p.V2374I		Atlas-SNP	.											NAV2,right_upper_lobe,carcinoma,-2,1	NAV2	255	1	0			c.G7120A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	60,4346	58.1+/-94.6	2,56,2145	166.0	155.0	159.0		6751,4135,6943,6952	5.4	1.0	11	dbSNP_126	159	539,8061	149.1+/-204.2	18,503,3779	yes	missense,missense,missense,missense	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	29,29,29,29	20,559,5924	AA,AG,GG		6.2674,1.3618,4.6056	probably-damaging,probably-damaging,probably-damaging,probably-damaging	2251/2366,1379/1494,2315/2430,2318/2433	20129311	599,12407	2203	4300	6503	SO:0001583	missense	89797	exon38			GAAGCCGTCAGAG	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.7120G>A	11.37:g.20129311G>A	ENSP00000379396:p.Val2374Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	93	37	0.397849	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	68	0.031135531135531136	3	0.006097560975609756	8	0.022099447513812154	1	0.0017482517482517483	56	0.07387862796833773	G	26.5	4.741339	0.89573	0.013618	0.062674	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000311043	T;T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98	5.38	5.38	0.77491	.	0.000000	0.53938	D	0.000051	T	0.10078	0.0247	L	0.46157	1.445	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.87578	0.996;0.987;0.998;0.985	T	0.07366	-1.0776	9	.	.	.	.	18.7277	0.91720	0.0:0.0:1.0:0.0	rs35891966;rs61877367	2318;1379;2315;2251	A7E2D6;Q8IVL1-5;Q8IVL1-3;Q8IVL1-4	.;.;.;.	I	2251;2318;2315;2374;2303;2305;1379;1379	ENSP00000353871:V2251I;ENSP00000379394:V2318I;ENSP00000309577:V2315I;ENSP00000379396:V2374I;ENSP00000435395:V2303I;ENSP00000443489:V2305I;ENSP00000437316:V1379I;ENSP00000312169:V1379I	.	V	+	1	0	NAV2	20085887	1.000000	0.71417	0.956000	0.39512	0.698000	0.40448	9.858000	0.99539	2.515000	0.84797	0.462000	0.41574	GTC	G|0.958;A|0.042	0.042	strong		0.557	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
REG1B	5968	hgsc.bcm.edu	37	2	79313990	79313990	+	Missense_Mutation	SNP	C	C	T	rs62640882	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:79313990C>T	ENST00000305089.3	-	3	211	c.131G>A	c.(130-132)cGc>cAc	p.R44H		NM_006507.3	NP_006498.1	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta	44	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell proliferation (GO:0008283)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(40)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	51						GCAGTAGGAGCGATAGGCATT	0.507													C|||	57	0.0113818	0.0	0.0086	5008	,	,		17949	0.0		0.0437	False		,,,				2504	0.0072				p.R44H		Atlas-SNP	.											.	REG1B	83	.	0			c.G131A						PASS	.	C	HIS/ARG	25,4381	31.7+/-61.6	0,25,2178	156.0	152.0	154.0		131	-0.3	0.0	2	dbSNP_129	154	330,8270	115.2+/-175.0	12,306,3982	yes	missense	REG1B	NM_006507.3	29	12,331,6160	TT,TC,CC		3.8372,0.5674,2.7295	benign	44/167	79313990	355,12651	2203	4300	6503	SO:0001583	missense	5968	exon3			TAGGAGCGATAGG		CCDS1963.1	2p12	2008-06-04	2008-06-04		ENSG00000172023	ENSG00000172023			9952	protein-coding gene	gene with protein product	"""lithostathine 1 beta"", ""secretory pancreatic stone protein 2"""	167771	"""regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic thread protein)"""			8110835	Standard	NM_006507		Approved	REGL, PSPS2, REGH, REGI-BETA	uc002sny.2	P48304	OTTHUMG00000130019	ENST00000305089.3:c.131G>A	2.37:g.79313990C>T	ENSP00000303206:p.Arg44His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	159	83	0.522013	NM_006507		Missense_Mutation	SNP	ENST00000305089.3	37	CCDS1963.1	42	0.019230769230769232	0	0.0	5	0.013812154696132596	0	0.0	37	0.048812664907651716	c	10.83	1.459885	0.26248	0.005674	0.038372	ENSG00000172023	ENST00000305089	T	0.08370	3.1	3.74	-0.261	0.12963	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.582077	0.14158	N	0.337555	T	0.00724	0.0024	L	0.45352	1.415	0.09310	N	1	P;P	0.35348	0.496;0.496	B;B	0.15870	0.014;0.014	T	0.37361	-0.9709	10	0.40728	T	0.16	.	3.4587	0.07524	0.0:0.4497:0.1989:0.3515	.	44;44	Q6ICS1;P48304	.;REG1B_HUMAN	H	44	ENSP00000303206:R44H	ENSP00000303206:R44H	R	-	2	0	REG1B	79167498	0.000000	0.05858	0.001000	0.08648	0.778000	0.44026	-0.670000	0.05256	0.044000	0.15775	-0.224000	0.12420	CGC	C|0.975;T|0.025	0.025	strong		0.507	REG1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252292.2	NM_006507	
KIAA1683	80726	hgsc.bcm.edu	37	19	18377496	18377496	+	Missense_Mutation	SNP	C	C	G	rs8104533	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18377496C>G	ENST00000600328.3	-	3	1047	c.854G>C	c.(853-855)aGt>aCt	p.S285T	KIAA1683_ENST00000392413.4_Missense_Mutation_p.S285T|KIAA1683_ENST00000600359.3_Missense_Mutation_p.S239T			Q9H0B3	K1683_HUMAN	KIAA1683	285			S -> T (in dbSNP:rs8104533). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GGTCCGGGCACTTACACGTTT	0.567													G|||	2727	0.544529	0.6929	0.5908	5008	,	,		19158	0.5516		0.4294	False		,,,				2504	0.4223				p.S285T		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G854C						PASS	.	G	THR/SER,THR/SER,THR/SER	2962,1444	464.3+/-353.8	1008,946,249	125.0	131.0	129.0		854,716,854	1.1	0.0	19	dbSNP_116	129	3660,4940	620.9+/-397.1	783,2094,1423	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	58,58,58	1791,3040,1672	GG,GC,CC		42.5581,32.7735,49.085	benign,benign,benign	285/1368,239/1135,285/1181	18377496	6622,6384	2203	4300	6503	SO:0001583	missense	80726	exon3			CGGGCACTTACAC	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.854G>C	19.37:g.18377496C>G	ENSP00000470780:p.Ser285Thr	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	183	72	0.393443	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	1158	0.5302197802197802	340	0.6910569105691057	193	0.5331491712707183	298	0.5209790209790209	327	0.4313984168865435	G	0.010	-1.754861	0.00663	0.672265	0.425581	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000358422	T;T;T	0.02916	4.16;4.18;4.11	3.2	1.08	0.20341	.	0.715954	0.11607	N	0.547205	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25433	-1.0132	9	0.02654	T	1	-2.5511	3.3984	0.07315	0.251:0.2193:0.5297:0.0	rs8104533;rs17655082;rs58108559;rs8104533	285;285	E9PDE0;Q9H0B3	.;K1683_HUMAN	T	285;285;239;284	ENSP00000376213:S285T;ENSP00000352774:S285T;ENSP00000404501:S239T	ENSP00000351198:S284T	S	-	2	0	KIAA1683	18238496	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.129000	0.10515	0.078000	0.16900	-0.352000	0.07741	AGT	C|0.486;G|0.514	0.514	strong		0.567	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
HSPG2	3339	hgsc.bcm.edu	37	1	22168801	22168801	+	Missense_Mutation	SNP	T	T	C	rs2229491	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22168801T>C	ENST00000374695.3	-	68	9062	c.8983A>G	c.(8983-8985)Agc>Ggc	p.S2995G		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2995	Ig-like C2-type 15.		S -> G (in dbSNP:rs2229491). {ECO:0000269|PubMed:1730768}.		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CCTGGGCCGCTGGCTGCACGA	0.642													C|||	444	0.0886581	0.1762	0.0533	5008	,	,		17453	0.0		0.0676	False		,,,				2504	0.1084				p.S2995G		Atlas-SNP	.											.	HSPG2	311	.	0			c.A8983G						PASS	.	C	GLY/SER	799,3607	748.2+/-411.9	73,653,1477	48.0	44.0	46.0		8983	1.0	0.0	1	dbSNP_98	46	660,7940	788.1+/-407.6	26,608,3666	yes	missense	HSPG2	NM_005529.5	56	99,1261,5143	CC,CT,TT		7.6744,18.1344,11.2179	benign	2995/4392	22168801	1459,11547	2203	4300	6503	SO:0001583	missense	3339	exon68			GGCCGCTGGCTGC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.8983A>G	1.37:g.22168801T>C	ENSP00000363827:p.Ser2995Gly	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	170	0.07783882783882784	98	0.1991869918699187	23	0.06353591160220995	0	0.0	49	0.06464379947229551	C	0.020	-1.435149	0.01108	0.181344	0.076744	ENSG00000142798	ENST00000374695	T	0.43688	0.94	4.95	1.0	0.19881	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.192817	0.25411	N	0.030867	T	0.00012	0.0000	N	0.12569	0.235	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23013	-1.0200	9	0.22109	T	0.4	.	1.5458	0.02565	0.1402:0.3054:0.1367:0.4177	rs2229491;rs7528230;rs2229491	935;2995	Q59EG0;P98160	.;PGBM_HUMAN	G	2995	ENSP00000363827:S2995G	ENSP00000363827:S2995G	S	-	1	0	HSPG2	22041388	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.066000	0.11598	-0.063000	0.13065	-1.212000	0.01626	AGC	T|0.899;G|0.000;C|0.101;A|0.000	0.101	strong		0.642	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
OR5W2	390148	hgsc.bcm.edu	37	11	55681375	55681375	+	Silent	SNP	T	T	G	rs17511601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55681375T>G	ENST00000344514.1	-	1	683	c.684A>C	c.(682-684)atA>atC	p.I228I		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CAGCAGAGTGTATCTCCAAGA	0.408													G|||	161	0.0321486	0.0038	0.0331	5008	,	,		17350	0.001		0.0905	False		,,,				2504	0.0419				p.I228I	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.A684C						PASS	.	G		68,4334	818.0+/-416.3	0,68,2133	68.0	76.0	73.0		684	-2.3	0.0	11	dbSNP_123	73	683,7909	787.8+/-407.6	34,615,3647	no	coding-synonymous	OR5W2	NM_001001960.1		34,683,5780	GG,GT,TT		7.9493,1.5448,5.7796		228/311	55681375	751,12243	2201	4296	6497	SO:0001819	synonymous_variant	390148	exon1			AGAGTGTATCTCC	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.684A>C	11.37:g.55681375T>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_001001960		Silent	SNP	ENST00000344514.1	37	CCDS31513.1																																																																																			T|0.952;G|0.048	0.048	strong		0.408	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
PAK7	57144	hgsc.bcm.edu	37	20	9520142	9520142	+	Silent	SNP	G	G	A	rs12329540	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:9520142G>A	ENST00000378429.3	-	11	2673	c.2127C>T	c.(2125-2127)atC>atT	p.I709I	PAK7_ENST00000378423.1_Silent_p.I709I|PAK7_ENST00000353224.5_Silent_p.I709I	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	709					apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TGAGGGGGACGATGCAAGACG	0.493													G|||	215	0.0429313	0.0015	0.0735	5008	,	,		19431	0.0		0.1322	False		,,,				2504	0.0297				p.I709I		Atlas-SNP	.											.	PAK7	194	.	0			c.C2127T						PASS	.	G	,	150,4256	101.2+/-139.8	3,144,2056	241.0	220.0	227.0		2127,2127	-3.4	1.0	20	dbSNP_120	227	1375,7225	267.9+/-287.5	117,1141,3042	no	coding-synonymous,coding-synonymous	PAK7	NM_020341.3,NM_177990.2	,	120,1285,5098	AA,AG,GG		15.9884,3.4044,11.7254	,	709/720,709/720	9520142	1525,11481	2203	4300	6503	SO:0001819	synonymous_variant	57144	exon10			GGGGACGATGCAA	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"""p21(CDKN1A)-activated kinase 7"""			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.2127C>T	20.37:g.9520142G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Silent	SNP	ENST00000378429.3	37	CCDS13107.1																																																																																			G|0.907;A|0.093	0.093	strong		0.493	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1		
PRKCDBP	112464	hgsc.bcm.edu	37	11	6340706	6340706	+	Missense_Mutation	SNP	A	A	G	rs1051992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6340706A>G	ENST00000303927.3	-	2	643	c.473T>C	c.(472-474)cTg>cCg	p.L158P	PRKCDBP_ENST00000530979.1_Missense_Mutation_p.L190P	NM_145040.2	NP_659477.2	Q969G5	PRDBP_HUMAN	protein kinase C, delta binding protein	158			L -> P (in dbSNP:rs1051992).		cortical actin cytoskeleton organization (GO:0030866)|negative regulation of fermentation (GO:1901003)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	caveola (GO:0005901)|protein complex (GO:0043234)				large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TTCGGCCTCCAGCTGCTCTGG	0.677													A|||	2644	0.527955	0.3873	0.4726	5008	,	,		13961	0.623		0.5805	False		,,,				2504	0.6053				p.L158P		Atlas-SNP	.											PRKCDBP,caecum,carcinoma,0,2	PRKCDBP	19	2	0			c.T473C						scavenged	.	A	PRO/LEU	1736,2652		347,1042,805	14.0	17.0	16.0		473	-3.6	0.0	11	dbSNP_86	16	4636,3944		1273,2090,927	yes	missense	PRKCDBP	NM_145040.2	98	1620,3132,1732	GG,GA,AA		45.9674,39.5624,49.1363	benign	158/262	6340706	6372,6596	2194	4290	6484	SO:0001583	missense	112464	exon2			GCCTCCAGCTGCT	AF339881	CCDS7762.1	11p15.4	2011-04-20			ENSG00000170955	ENSG00000170955			9400	protein-coding gene	gene with protein product	"""sdr-related gene product that binds to c-kinase"""					9054438	Standard	NM_145040		Approved	SRBC, HSRBC, MGC20400, cavin-3, CAVIN3	uc001mcu.1	Q969G5	OTTHUMG00000133378	ENST00000303927.3:c.473T>C	11.37:g.6340706A>G	ENSP00000307292:p.Leu158Pro	Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	74	27	0.364865	NM_145040		Missense_Mutation	SNP	ENST00000303927.3	37	CCDS7762.1	1163	0.5325091575091575	196	0.3983739837398374	168	0.46408839779005523	355	0.6206293706293706	444	0.5857519788918206	A	6.291	0.421878	0.11928	0.395624	0.540326	ENSG00000170955	ENST00000303927;ENST00000530979	T;T	0.60171	0.21;0.21	5.08	-3.56	0.04626	.	0.744664	0.13090	N	0.414621	T	0.00012	0.0000	N	0.01576	-0.805	0.48341	P	3.689999999999527E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.44421	-0.9329	9	0.34782	T	0.22	0.097	3.9686	0.09443	0.3954:0.0:0.3447:0.2599	rs1051992;rs3802982;rs17240728;rs58428819;rs1051992	158	Q969G5	PRDBP_HUMAN	P	158;190	ENSP00000307292:L158P;ENSP00000432047:L190P	ENSP00000307292:L158P	L	-	2	0	PRKCDBP	6297282	0.000000	0.05858	0.004000	0.12327	0.432000	0.31715	-1.174000	0.03105	-0.455000	0.07054	-1.559000	0.00887	CTG	A|0.509;G|0.491	0.491	strong		0.677	PRKCDBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257228.2	NM_145040	
DNAJC10	54431	hgsc.bcm.edu	37	2	183584755	183584755	+	Missense_Mutation	SNP	G	G	A	rs6729801	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:183584755G>A	ENST00000264065.7	+	4	641	c.226G>A	c.(226-228)Gat>Aat	p.D76N	DNAJC10_ENST00000469118.1_3'UTR|DNAJC10_ENST00000537515.1_Missense_Mutation_p.D76N	NM_018981.1	NP_061854.1	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	76	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.		D -> N (in dbSNP:rs6729801). {ECO:0000269|PubMed:14587667, ECO:0000269|PubMed:17974005}.		cell redox homeostasis (GO:0045454)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATPase activity (GO:0032781)|protein folding in endoplasmic reticulum (GO:0034975)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|disulfide oxidoreductase activity (GO:0015036)|Hsp70 protein binding (GO:0030544)|misfolded protein binding (GO:0051787)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide oxidoreductase activity (GO:0015035)			breast(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(15)|ovary(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TGCACATGGCGATTTTTTAAA	0.284													G|||	1763	0.352037	0.093	0.3833	5008	,	,		15193	0.2996		0.5586	False		,,,				2504	0.5215				p.D76N	Pancreas(56;860 1183 25669 35822 48585)	Atlas-SNP	.											.	DNAJC10	76	.	0			c.G226A						PASS	.	G	ASN/ASP	771,3635	283.7+/-277.2	67,637,1499	49.0	51.0	50.0		226	5.1	1.0	2	dbSNP_116	50	4894,3706	605.8+/-395.0	1376,2142,782	yes	missense	DNAJC10	NM_018981.1	23	1443,2779,2281	AA,AG,GG		43.093,17.4989,43.5568	benign	76/794	183584755	5665,7341	2203	4300	6503	SO:0001583	missense	54431	exon4			CATGGCGATTTTT		CCDS33345.1, CCDS74613.1	2q32.1	2011-11-23			ENSG00000077232	ENSG00000077232		"""Heat shock proteins / DNAJ (HSP40)"", ""Protein disulfide isomerases"""	24637	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 19"""	607987				12411443, 12446677	Standard	NM_018981		Approved	ERdj5, PDIA19	uc002uow.2	Q8IXB1	OTTHUMG00000154209	ENST00000264065.7:c.226G>A	2.37:g.183584755G>A	ENSP00000264065:p.Asp76Asn	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	50	0.980392	NM_001271581	Q17RJ6|Q3B7W8|Q4ZG06|Q53QT7|Q6UWZ6|Q86T61|Q8NC82|Q8TD87|Q96K38|Q96K44|Q96K54|Q9NSY6	Missense_Mutation	SNP	ENST00000264065.7	37	CCDS33345.1	781	0.3576007326007326	46	0.09349593495934959	157	0.43370165745856354	153	0.2674825174825175	425	0.5606860158311345	G	15.80	2.939858	0.52972	0.174989	0.56907	ENSG00000077232	ENST00000264065;ENST00000392392;ENST00000537410;ENST00000537515	T;T	0.29917	1.55;1.55	5.93	5.05	0.67936	Heat shock protein DnaJ, N-terminal (5);	0.417622	0.28760	N	0.014230	T	0.00012	0.0000	N	0.13098	0.295	0.27389	P	0.9551818	B;B	0.12630	0.002;0.006	B;B	0.04013	0.001;0.001	T	0.46470	-0.9189	9	0.17832	T	0.49	.	5.7114	0.17937	0.2546:0.0:0.7454:0.0	rs6729801;rs52808466;rs6729801	76;76	Q8IXB1-2;Q8IXB1	.;DJC10_HUMAN	N	76	ENSP00000264065:D76N;ENSP00000441560:D76N	ENSP00000264065:D76N	D	+	1	0	DNAJC10	183293000	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.065000	0.64344	2.802000	0.96397	0.563000	0.77884	GAT	G|0.597;A|0.403	0.403	strong		0.284	DNAJC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334418.2	NM_018981	
FUS	2521	hgsc.bcm.edu	37	16	31202291	31202291	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31202291C>T	ENST00000254108.7	+	14	1506	c.1401C>T	c.(1399-1401)aaC>aaT	p.N467N	FUS_ENST00000474990.1_3'UTR|FUS_ENST00000568685.1_Silent_p.N468N|FUS_ENST00000380244.3_Silent_p.N466N	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	467	Arg/Gly-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		TAGGGGGTAACTACGGGGATG	0.592			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""																																p.N467N		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	FUS,NS,carcinoma,0,1	FUS	52	1	0			c.C1401T						scavenged	.						65.0	76.0	72.0					16																	31202291		2196	4300	6496	SO:0001819	synonymous_variant	2521	exon14			GGGTAACTACGGG	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.1401C>T	16.37:g.31202291C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	109	2	0.0183486	NM_004960	Q9H4A8	Silent	SNP	ENST00000254108.7	37	CCDS10707.1																																																																																			.	.	none		0.592	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
IRGQ	126298	hgsc.bcm.edu	37	19	44098963	44098963	+	Silent	SNP	C	C	G	rs304725	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:44098963C>G	ENST00000602269.1	-	1	713	c.528G>C	c.(526-528)cgG>cgC	p.R176R	ZNF576_ENST00000336564.4_5'Flank|ZNF576_ENST00000533118.1_5'Flank|ZNF576_ENST00000525771.1_5'Flank|L34079.2_ENST00000594374.1_5'Flank|SRRM5_ENST00000526798.1_5'Flank|ZNF576_ENST00000391965.2_5'Flank|ZNF576_ENST00000529930.1_5'Flank|SRRM5_ENST00000607544.1_5'Flank|ZNF576_ENST00000528387.1_5'Flank|IRGQ_ENST00000422989.1_Silent_p.R176R|IRGQ_ENST00000601520.1_5'Flank			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	176										endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				GCACTCACCTCCGCAGCGCTT	0.657													C|||	2470	0.493211	0.4017	0.5274	5008	,	,		12894	0.4911		0.5427	False		,,,				2504	0.544				p.R176R		Atlas-SNP	.											.	IRGQ	40	.	0			c.G528C						PASS	.	C		1940,2460		440,1060,700	19.0	22.0	21.0		528	4.8	1.0	19	dbSNP_79	21	4601,3987		1242,2117,935	no	coding-synonymous	IRGQ	NM_001007561.2		1682,3177,1635	GG,GC,CC		46.4252,44.0909,49.6381		176/624	44098963	6541,6447	2200	4294	6494	SO:0001819	synonymous_variant	126298	exon2			TCACCTCCGCAGC	AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"""immunity-related GTPase family, Q1"""	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.528G>C	19.37:g.44098963C>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	32	12	0.375	NM_001007561	B2RNP3	Silent	SNP	ENST00000602269.1	37	CCDS33040.1																																																																																			C|0.497;G|0.503	0.503	strong		0.657	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291188	1291188	+	Silent	SNP	C	C	T	rs17434400	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1291188C>T	ENST00000338844.3	+	3	129	c.96C>T	c.(94-96)gtC>gtT	p.V32V	TPSAB1_ENST00000461509.2_Silent_p.V39V	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	32	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				TGGGCATCGTCGGGGGTCAGG	0.701																																					p.V32V		Atlas-SNP	.											TPSAB1,NS,carcinoma,0,1	TPSAB1	24	1	0			c.C96T						scavenged	.						38.0	38.0	38.0					16																	1291188		2199	4299	6498	SO:0001819	synonymous_variant	7177	exon3			CATCGTCGGGGGT	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.96C>T	16.37:g.1291188C>T		Somatic	132	4	0.030303		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Silent	SNP	ENST00000338844.3	37	CCDS10431.1																																																																																			.	.	weak		0.701	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
SALL4	57167	hgsc.bcm.edu	37	20	50407162	50407162	+	Silent	SNP	T	T	C	rs6021437	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:50407162T>C	ENST00000217086.4	-	2	1971	c.1860A>G	c.(1858-1860)acA>acG	p.T620T	SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000395997.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	620					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCTTAATGGATGTGTTGGTTC	0.527													C|||	1913	0.381989	0.1982	0.3415	5008	,	,		20729	0.6071		0.336	False		,,,				2504	0.4744				p.T620T		Atlas-SNP	.											.	SALL4	168	.	0			c.A1860G						PASS	.	C		962,3444	731.0+/-410.2	105,752,1346	72.0	62.0	66.0		1860	-6.3	0.0	20	dbSNP_114	66	2967,5633	665.6+/-402.3	522,1923,1855	no	coding-synonymous	SALL4	NM_020436.3		627,2675,3201	CC,CT,TT		34.5,21.8339,30.2091		620/1054	50407162	3929,9077	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			AATGGATGTGTTG	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1860A>G	20.37:g.50407162T>C		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	248	102	0.41129	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			T|0.668;C|0.332	0.332	strong		0.527	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
TBXA2R	6915	hgsc.bcm.edu	37	19	3595923	3595923	+	Silent	SNP	G	G	A	rs1131882	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:3595923G>A	ENST00000375190.4	-	3	1188	c.795C>T	c.(793-795)atC>atT	p.I265I	TBXA2R_ENST00000587717.1_5'Flank|TBXA2R_ENST00000411851.3_Silent_p.I265I|TBXA2R_ENST00000589966.1_Missense_Mutation_p.R136C	NM_001060.5|NM_201636.2	NP_001051.1|NP_963998.2	P21731	TA2R_HUMAN	thromboxane A2 receptor	265					blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of vasoconstriction (GO:0045907)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|second-messenger-mediated signaling (GO:0019932)|thromboxane A2 signaling pathway (GO:0038193)	acrosomal vesicle (GO:0001669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|thromboxane A2 receptor activity (GO:0004961)	p.I265I(1)		kidney(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	8		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)	Ridogrel(DB01207)	CTGTCTGGGCGATGAAGACCT	0.697													G|||	1175	0.234625	0.0401	0.2795	5008	,	,		8200	0.5883		0.1471	False		,,,				2504	0.1912				p.I265I		Atlas-SNP	.											TBXA2R,NS,carcinoma,0,1	TBXA2R	31	1	1	Substitution - coding silent(1)	prostate(1)	c.C795T	GRCh37	CM022851	TBXA2R	M	rs1131882	PASS	.	G	,	226,3866		3,220,1823	11.0	12.0	12.0		795,795	-0.8	0.8	19	dbSNP_86	12	1276,7068		105,1066,3001	no	coding-synonymous,coding-synonymous	TBXA2R	NM_001060.5,NM_201636.2	,	108,1286,4824	AA,AG,GG		15.2924,5.523,12.0778	,	265/344,265/408	3595923	1502,10934	2046	4172	6218	SO:0001819	synonymous_variant	6915	exon3			CTGGGCGATGAAG		CCDS42467.1, CCDS54198.1	19p13.3	2014-09-17						"""GPCR / Class A : Prostanoid receptors"""	11608	protein-coding gene	gene with protein product		188070				1825698	Standard	NM_001060		Approved		uc021umv.1	P21731		ENST00000375190.4:c.795C>T	19.37:g.3595923G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_201636	O75228|Q6DK52|Q9UCY1|Q9UCY2	Silent	SNP	ENST00000375190.4	37	CCDS42467.1																																																																																			G|0.733;A|0.267	0.267	strong		0.697	TBXA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453081.2		
EPRS	2058	hgsc.bcm.edu	37	1	220154768	220154768	+	Silent	SNP	C	C	T	rs1061160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:220154768C>T	ENST00000366923.3	-	24	3674	c.3405G>A	c.(3403-3405)caG>caA	p.Q1135Q		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1135	Proline--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	CTCTGTGTGACTGTACCCATT	0.388													C|||	1773	0.354034	0.3986	0.4294	5008	,	,		13799	0.3423		0.3101	False		,,,				2504	0.2975				p.Q1135Q		Atlas-SNP	.											.	EPRS	140	.	0			c.G3405A						PASS	.	C		1649,2757	504.9+/-366.0	329,991,883	143.0	127.0	133.0		3405	4.1	1.0	1	dbSNP_86	133	2938,5662	457.3+/-364.3	523,1892,1885	no	coding-synonymous	EPRS	NM_004446.2		852,2883,2768	TT,TC,CC		34.1628,37.4262,35.2683		1135/1513	220154768	4587,8419	2203	4300	6503	SO:0001819	synonymous_variant	2058	exon24			GTGTGACTGTACC	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"""Aminoacyl tRNA synthetases / Class I"", ""Aminoacyl tRNA synthetases / Class II"""	3418	protein-coding gene	gene with protein product	"""glutamate tRNA ligase"", ""proline tRNA ligase"""	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3405G>A	1.37:g.220154768C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	57	0.57	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Silent	SNP	ENST00000366923.3	37	CCDS31027.1																																																																																			C|0.645;T|0.355	0.355	strong		0.388	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446	
C20orf194	25943	hgsc.bcm.edu	37	20	3362033	3362033	+	Silent	SNP	T	T	C	rs6051818	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3362033T>C	ENST00000252032.9	-	3	343	c.276A>G	c.(274-276)gtA>gtG	p.V92V	U3_ENST00000364476.1_RNA	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	92										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						TACCATCTAGTACTTCTTCAG	0.328													C|||	1190	0.23762	0.3759	0.1873	5008	,	,		18843	0.1657		0.2197	False		,,,				2504	0.1789				p.V92V		Atlas-SNP	.											.	C20orf194	83	.	0			c.A276G						PASS	.	C		1332,2322		243,846,738	81.0	79.0	79.0		276	2.5	1.0	20	dbSNP_114	79	1730,6448		184,1362,2543	no	coding-synonymous	C20orf194	NM_001009984.1		427,2208,3281	CC,CT,TT		21.1543,36.4532,25.879		92/1178	3362033	3062,8770	1827	4089	5916	SO:0001819	synonymous_variant	25943	exon3			ATCTAGTACTTCT	AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.276A>G	20.37:g.3362033T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	101	56	0.554455	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Silent	SNP	ENST00000252032.9	37	CCDS42851.1																																																																																			T|0.757;C|0.243	0.243	strong		0.328	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984	
ABLIM3	22885	hgsc.bcm.edu	37	5	148596546	148596546	+	Missense_Mutation	SNP	A	A	G	rs148615457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:148596546A>G	ENST00000506113.1	+	7	1176	c.694A>G	c.(694-696)Acc>Gcc	p.T232A	ABLIM3_ENST00000508983.1_Missense_Mutation_p.T232A|ABLIM3_ENST00000309868.7_Missense_Mutation_p.T232A|AC012613.2_ENST00000523176.1_RNA|ABLIM3_ENST00000504238.1_Missense_Mutation_p.T232A|ABLIM3_ENST00000356541.3_Missense_Mutation_p.T232A|RP11-331K21.1_ENST00000512647.2_RNA|RP11-331K21.1_ENST00000522685.1_RNA|ABLIM3_ENST00000326685.7_Missense_Mutation_p.T232A			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	232	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTACCACCCAACCTGTGCCAG	0.517																																					p.T232A		Atlas-SNP	.											.	ABLIM3	91	.	0			c.A694G						PASS	.	A	ALA/THR	1,4405	2.1+/-5.4	0,1,2202	94.0	80.0	85.0		694	2.8	1.0	5	dbSNP_134	85	9,8591	7.1+/-27.0	0,9,4291	yes	missense	ABLIM3	NM_014945.2	58	0,10,6493	GG,GA,AA		0.1047,0.0227,0.0769	benign	232/684	148596546	10,12996	2203	4300	6503	SO:0001583	missense	22885	exon8			CACCCAACCTGTG	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.694A>G	5.37:g.148596546A>G	ENSP00000425394:p.Thr232Ala	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	127	68	0.535433	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.710883	0.48517	2.27E-4	0.001047	ENSG00000173210	ENST00000326685;ENST00000356541;ENST00000309868;ENST00000506113;ENST00000504238;ENST00000508983	D;D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18;-2.18	5.49	2.84	0.33178	Zinc finger, LIM-type (5);	0.416904	0.28192	N	0.016242	T	0.80037	0.4550	L	0.38175	1.15	0.26146	N	0.980218	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.11329	0.0;0.0;0.006	T	0.72204	-0.4361	10	0.62326	D	0.03	.	9.5085	0.39062	0.8081:0.0:0.1919:0.0	.	232;232;232	O94929-3;O94929-2;O94929	.;.;ABLM3_HUMAN	A	232	ENSP00000315841:T232A;ENSP00000348938:T232A;ENSP00000310309:T232A;ENSP00000425394:T232A;ENSP00000421183:T232A;ENSP00000420855:T232A	ENSP00000310309:T232A	T	+	1	0	ABLIM3	148576739	0.953000	0.32496	0.990000	0.47175	0.990000	0.78478	3.238000	0.51352	1.013000	0.39391	-0.264000	0.10439	ACC	A|0.999;G|0.001	0.001	strong		0.517	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945	
RBMS3	27303	hgsc.bcm.edu	37	3	30032626	30032626	+	Silent	SNP	C	C	G	rs114278295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:30032626C>G	ENST00000383767.2	+	14	1569	c.1233C>G	c.(1231-1233)acC>acG	p.T411T	RBMS3_ENST00000473799.1_3'UTR|RBMS3_ENST00000452462.1_Silent_p.T395T|RBMS3_ENST00000383766.2_Silent_p.T393T|RBMS3_ENST00000273139.9_Silent_p.T395T|RBMS3_ENST00000396583.3_Silent_p.T408T|RBMS3_ENST00000456853.1_Silent_p.T408T|RBMS3_ENST00000434693.2_Silent_p.T410T			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	411					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				CCCAGGACACCAGTGGTCAGC	0.478													C|||	59	0.0117812	0.0	0.0231	5008	,	,		21432	0.0		0.0278	False		,,,				2504	0.0153				p.T411T		Atlas-SNP	.											.	RBMS3	62	.	0			c.C1233G						PASS	.	C	,,,,	21,4385	29.0+/-57.7	0,21,2182	233.0	178.0	196.0		1179,1233,1185,1224,1185	3.5	1.0	3	dbSNP_132	196	224,8376	93.3+/-155.3	0,224,4076	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RBMS3	NM_001003792.2,NM_001003793.2,NM_001177711.1,NM_001177712.1,NM_014483.3	,,,,	0,245,6258	GG,GC,CC		2.6047,0.4766,1.8837	,,,,	393/420,411/438,395/422,408/434,395/421	30032626	245,12761	2203	4300	6503	SO:0001819	synonymous_variant	27303	exon14			GGACACCAGTGGT	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"""RNA binding motif (RRM) containing"""	13427	protein-coding gene	gene with protein product	"""RNA-binding protein"""	605786	"""RNA binding motif, single stranded interacting protein"""			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.1233C>G	3.37:g.30032626C>G		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	258	140	0.542636	NM_001003793	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Silent	SNP	ENST00000383767.2	37	CCDS33724.1																																																																																			C|0.982;G|0.018	0.018	strong		0.478	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792	
YTHDC2	64848	hgsc.bcm.edu	37	5	112889374	112889374	+	Missense_Mutation	SNP	G	G	A	rs10071816	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:112889374G>A	ENST00000161863.4	+	14	2168	c.1955G>A	c.(1954-1956)aGt>aAt	p.S652N	YTHDC2_ENST00000515883.1_Missense_Mutation_p.S652N	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	652	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		S -> N (in dbSNP:rs10071816).		ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		TTTGCTGACAGTACACATAGG	0.398													A|||	1672	0.333866	0.6172	0.4265	5008	,	,		15678	0.2083		0.1909	False		,,,				2504	0.1616				p.S652N		Atlas-SNP	.											.	YTHDC2	118	.	0			c.G1955A						PASS	.	A	ASN/SER	2532,1872	539.9+/-375.4	746,1040,416	141.0	141.0	141.0		1955	1.6	0.2	5	dbSNP_119	141	1581,7019	743.6+/-407.2	140,1301,2859	yes	missense	YTHDC2	NM_022828.3	46	886,2341,3275	AA,AG,GG		18.3837,42.5068,31.6287	benign	652/1431	112889374	4113,8891	2202	4300	6502	SO:0001583	missense	64848	exon14			CTGACAGTACACA	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.1955G>A	5.37:g.112889374G>A	ENSP00000161863:p.Ser652Asn	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	37	CCDS4113.1	725	0.33195970695970695	324	0.6585365853658537	134	0.3701657458563536	123	0.21503496503496503	144	0.18997361477572558	A	0	-2.651789	0.00109	0.574932	0.183837	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000511372	T;T	0.06933	4.22;3.24	5.38	1.65	0.23941	Helicase, C-terminal (2);	0.343223	0.32836	N	0.005589	T	0.00012	0.0000	N	0.11927	0.2	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.42498	-0.9448	9	0.02654	T	1	.	12.1875	0.54247	0.7907:0.0:0.2093:0.0	rs10071816;rs57240370;rs10071816	652	Q9H6S0	YTDC2_HUMAN	N	652;652;562	ENSP00000161863:S652N;ENSP00000423101:S652N	ENSP00000161863:S652N	S	+	2	0	YTHDC2	112917273	0.970000	0.33590	0.154000	0.22540	0.067000	0.16453	1.347000	0.33975	-0.510000	0.06523	-2.276000	0.00273	AGT	G|0.681;A|0.319	0.319	strong		0.398	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
KCNE3	10008	hgsc.bcm.edu	37	11	74168411	74168411	+	Silent	SNP	A	A	G	rs2270676	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:74168411A>G	ENST00000310128.4	-	3	617	c.198T>C	c.(196-198)ttT>ttC	p.F66F	RP11-702H23.6_ENST00000530510.1_RNA|RP11-702H23.4_ENST00000533008.1_RNA|KCNE3_ENST00000525550.1_Silent_p.F66F	NM_005472.4	NP_005463.1	Q9Y6H6	KCNE3_HUMAN	potassium voltage-gated channel, Isk-related family, member 3	66					regulation of potassium ion transport (GO:0043266)	integral component of membrane (GO:0016021)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			cervix(1)|large_intestine(1)|lung(1)|ovary(1)	4	Breast(11;2.86e-06)					CAGCAAATAGAAACATGACAA	0.542													A|||	707	0.141174	0.1241	0.0879	5008	,	,		19189	0.1627		0.1103	False		,,,				2504	0.2117				p.F66F		Atlas-SNP	.											.	KCNE3	7	.	0			c.T198C	GRCh37	CM057459	KCNE3	M	rs2270676	PASS	.	A		551,3849	246.5+/-255.1	32,487,1681	78.0	68.0	72.0	http://www.ncbi.nlm.nih.gov/pubmed?term	198	1.2	1.0	11	dbSNP_100	72	931,7655	205.6+/-248.0	57,817,3419	no	coding-synonymous	KCNE3	NM_005472.4		89,1304,5100	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	10.8432,12.5227,11.4123		66/104	74168411	1482,11504	2200	4293	6493	SO:0001819	synonymous_variant	10008	exon3			AAATAGAAACATG	AF076531	CCDS8232.1	11q13.4	2014-09-17				ENSG00000175538		"""Potassium channels"""	6243	protein-coding gene	gene with protein product		604433				10219239	Standard	NM_005472		Approved	MiRP2, HOKPP	uc001ovc.3	Q9Y6H6		ENST00000310128.4:c.198T>C	11.37:g.74168411A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	182	73	0.401099	NM_005472		Silent	SNP	ENST00000310128.4	37	CCDS8232.1																																																																																			A|0.881;G|0.119	0.119	strong		0.542	KCNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385531.1	NM_005472	
ZNF571	51276	hgsc.bcm.edu	37	19	38055612	38055612	+	Missense_Mutation	SNP	A	A	T	rs4802029	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:38055612A>T	ENST00000328550.2	-	4	1817	c.1718T>A	c.(1717-1719)cTt>cAt	p.L573H	ZNF571-AS1_ENST00000587121.1_RNA|ZNF571-AS1_ENST00000592392.1_RNA|ZNF571-AS1_ENST00000590838.1_RNA|ZNF571_ENST00000590751.1_Intron|ZNF571_ENST00000358744.3_Missense_Mutation_p.L573H|ZNF571-AS1_ENST00000591430.1_RNA|ZNF571-AS1_ENST00000589802.1_RNA|ZNF540_ENST00000592533.1_Intron|ZNF571-AS1_ENST00000586139.1_RNA|ZNF571-AS1_ENST00000585578.1_RNA|ZNF571_ENST00000593133.1_Missense_Mutation_p.L573H|ZNF571-AS1_ENST00000586013.1_RNA|ZNF571_ENST00000451802.2_Missense_Mutation_p.L573H|ZNF571-AS1_ENST00000589750.1_RNA			Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	573			L -> H (in dbSNP:rs4802029). {ECO:0000269|PubMed:11042152}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	25			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATGCAGAGTAAGTTCTGAGCC	0.438													A|||	1844	0.368211	0.3555	0.2637	5008	,	,		18819	0.6528		0.168	False		,,,				2504	0.3722				p.L573H		Atlas-SNP	.											.	ZNF571	54	.	0			c.T1718A						PASS	.	A	HIS/LEU	1389,3017	457.5+/-351.6	215,959,1029	100.0	92.0	95.0		1718	3.8	0.0	19	dbSNP_111	95	1596,7004	297.4+/-303.4	146,1304,2850	no	missense	ZNF571	NM_016536.3	99	361,2263,3879	TT,TA,AA		18.5581,31.5252,22.9509	probably-damaging	573/610	38055612	2985,10021	2203	4300	6503	SO:0001583	missense	51276	exon4			AGAGTAAGTTCTG	AF161544	CCDS12505.1	19q13.12	2013-09-20			ENSG00000180479	ENSG00000180479		"""Zinc fingers, C2H2-type"", ""-"""	25000	protein-coding gene	gene with protein product						11042152	Standard	XM_005258977		Approved	HSPC059	uc002ogt.3	Q7Z3V5	OTTHUMG00000182016	ENST00000328550.2:c.1718T>A	19.37:g.38055612A>T	ENSP00000333660:p.Leu573His	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	63	41	0.650794	NM_016536	Q2HIY0|Q3ZCU3|Q9NZX7	Missense_Mutation	SNP	ENST00000328550.2	37	CCDS12505.1	792	0.3626373626373626	202	0.4105691056910569	91	0.2513812154696133	372	0.6503496503496503	127	0.16754617414248021	A	17.34	3.363795	0.61513	0.315252	0.185581	ENSG00000180479	ENST00000328550;ENST00000451802;ENST00000358744	T;T;T	0.54071	0.59;0.59;0.59	3.78	3.78	0.43462	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	H	0.97516	4.02	0.43435	P	0.004394000000000009	D	0.89917	1.0	D	0.97110	1.0	T	0.49978	-0.8881	8	0.72032	D	0.01	.	11.5963	0.50975	1.0:0.0:0.0:0.0	rs4802029;rs60357920;rs4802029	573	Q7Z3V5	ZN571_HUMAN	H	573	ENSP00000333660:L573H;ENSP00000392638:L573H;ENSP00000351594:L573H	ENSP00000333660:L573H	L	-	2	0	ZNF571	42747452	0.708000	0.27876	0.044000	0.18714	0.904000	0.53231	4.732000	0.62029	1.556000	0.49512	0.377000	0.23210	CTT	A|0.722;T|0.278	0.278	strong		0.438	ZNF571-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458669.1	NM_016536	
TCERG1	10915	hgsc.bcm.edu	37	5	145838647	145838647	+	Silent	SNP	C	C	T	rs187468589		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:145838647C>T	ENST00000296702.5	+	4	677	c.639C>T	c.(637-639)gcC>gcT	p.A213A	TCERG1_ENST00000394421.2_Silent_p.A213A	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	213	Ala/Gln-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			aggcccaggcccaggcccagg	0.731																																					p.A213A		Atlas-SNP	.											TCERG1,NS,neuroblastoma,0,1	TCERG1	148	1	0			c.C639T						scavenged	.						10.0	14.0	12.0					5																	145838647		2183	4260	6443	SO:0001819	synonymous_variant	10915	exon4			CCAGGCCCAGGCC	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"""transcription factor CA150"", ""co-activator of 150 kDa"", ""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"", ""TATA box-binding protein-associated factor 2S"""	605409	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"""	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.639C>T	5.37:g.145838647C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_006706	Q2NKN2|Q59EA1	Silent	SNP	ENST00000296702.5	37	CCDS4282.1																																																																																			C|0.974;T|0.026	0.026	strong		0.731	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006	
KIAA1377	57562	hgsc.bcm.edu	37	11	101832708	101832708	+	Silent	SNP	A	A	T	rs3740930	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:101832708A>T	ENST00000263468.8	+	6	1212	c.942A>T	c.(940-942)acA>acT	p.T314T	KIAA1377_ENST00000537689.1_Silent_p.T115T	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	314										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		ATTGGCTTACAAATTTAGATG	0.313													A|||	500	0.0998403	0.0121	0.2133	5008	,	,		18796	0.122		0.0278	False		,,,				2504	0.1892				p.T314T		Atlas-SNP	.											.	KIAA1377	111	.	0			c.A942T						PASS	.	A		78,4328	67.6+/-105.2	2,74,2127	53.0	53.0	53.0		942	-0.6	0.6	11	dbSNP_107	53	192,8402	82.6+/-145.2	1,190,4106	no	coding-synonymous	KIAA1377	NM_020802.2		3,264,6233	TT,TA,AA		2.2341,1.7703,2.0769		314/1118	101832708	270,12730	2203	4297	6500	SO:0001819	synonymous_variant	57562	exon6			GCTTACAAATTTA	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.942A>T	11.37:g.101832708A>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	126	121	0.960317	NM_020802	Q4G0U6	Silent	SNP	ENST00000263468.8	37	CCDS31658.1																																																																																			A|0.962;N|0.002	.	strong		0.313	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
PLXNC1	10154	hgsc.bcm.edu	37	12	94645255	94645255	+	Silent	SNP	A	A	G	rs2230757	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:94645255A>G	ENST00000258526.4	+	15	3081	c.2832A>G	c.(2830-2832)acA>acG	p.T944T		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	944					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TTCCTTCCACATGGTATTTTC	0.463													G|||	3048	0.608626	0.5439	0.6974	5008	,	,		19096	0.7411		0.5706	False		,,,				2504	0.5358				p.T944T		Atlas-SNP	.											.	PLXNC1	135	.	0			c.A2832G						PASS	.	G		2538,1868	538.2+/-374.9	717,1104,382	257.0	209.0	225.0		2832	-4.2	0.6	12	dbSNP_98	225	4750,3850	542.1+/-384.1	1278,2194,828	no	coding-synonymous	PLXNC1	NM_005761.2		1995,3298,1210	GG,GA,AA		44.7674,42.3967,43.9643		944/1569	94645255	7288,5718	2203	4300	6503	SO:0001819	synonymous_variant	10154	exon15			TTCCACATGGTAT	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.2832A>G	12.37:g.94645255A>G		Somatic	307	1	0.00325733		WXS	Illumina HiSeq	Phase_I	353	352	0.997167	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			A|0.420;C|0.000;G|0.580;T|0.000	0.580	strong		0.463	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
NOP9	161424	hgsc.bcm.edu	37	14	24771285	24771285	+	Missense_Mutation	SNP	G	G	A	rs4280164	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24771285G>A	ENST00000267425.3	+	4	1016	c.923G>A	c.(922-924)aGt>aAt	p.S308N	NOP9_ENST00000396802.3_Missense_Mutation_p.S308N|DHRS1_ENST00000288111.7_5'Flank|DHRS1_ENST00000396813.1_5'Flank	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	308			S -> N (in dbSNP:rs4280164). {ECO:0000269|PubMed:15489334}.				poly(A) RNA binding (GO:0044822)										GGCTACCTGAGTACTCGCGGT	0.507													G|||	753	0.150359	0.1581	0.3473	5008	,	,		21235	0.004		0.1849	False		,,,				2504	0.1155				p.S308N		Atlas-SNP	.											.	.	.	.	0			c.G923A						PASS	.	G	ASN/SER	736,3670	303.2+/-287.8	63,610,1530	122.0	117.0	118.0		923	5.2	1.0	14	dbSNP_111	118	1783,6817	322.1+/-315.4	189,1405,2706	yes	missense	C14orf21	NM_174913.1	46	252,2015,4236	AA,AG,GG		20.7326,16.7045,19.368	possibly-damaging	308/637	24771285	2519,10487	2203	4300	6503	SO:0001583	missense	161424	exon4			ACCTGAGTACTCG		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.923G>A	14.37:g.24771285G>A	ENSP00000267425:p.Ser308Asn	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	159	75	0.471698	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	37	CCDS9624.1	336	0.15384615384615385	72	0.14634146341463414	108	0.2983425414364641	4	0.006993006993006993	152	0.20052770448548812	G	18.02	3.531149	0.64972	0.167045	0.207326	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.14022	2.54;2.54	5.21	5.21	0.72293	Armadillo-type fold (1);	0.219735	0.45606	D	0.000347	T	0.00012	0.0000	L	0.54323	1.7	0.29261	P	0.871328	P	0.50819	0.939	P	0.50378	0.639	T	0.51458	-0.8703	9	0.17369	T	0.5	-6.0418	13.4219	0.61003	0.0:0.1579:0.8421:0.0	rs4280164;rs17852257;rs52803285;rs56947421;rs4280164	308	Q86U38	CN021_HUMAN	N	308	ENSP00000267425:S308N;ENSP00000380020:S308N	ENSP00000267425:S308N	S	+	2	0	C14orf21	23841125	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	3.940000	0.56599	2.717000	0.92951	0.655000	0.94253	AGT	G|0.835;A|0.165	0.165	strong		0.507	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73932560	73932560	+	Silent	SNP	A	A	G	rs17851629	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:73932560A>G	ENST00000265755.3	+	5	906	c.513A>G	c.(511-513)gaA>gaG	p.E171E	GTF2IRD1_ENST00000424337.2_Silent_p.E171E|GTF2IRD1_ENST00000455841.2_Silent_p.E203E|GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000476977.1_Silent_p.E171E	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	171					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GGCTGCCCGAAGGCCTGGCCT	0.662													G|||	1186	0.236821	0.4682	0.196	5008	,	,		14985	0.0952		0.16	False		,,,				2504	0.1779				p.E203E		Atlas-SNP	.											.	GTF2IRD1	91	.	0			c.A609G						PASS	.	G	,,	1791,2611		358,1075,768	24.0	24.0	24.0		609,513,513	1.6	1.0	7	dbSNP_123	24	1707,6893		165,1377,2758	no	coding-synonymous,coding-synonymous,coding-synonymous	GTF2IRD1	NM_001199207.1,NM_005685.3,NM_016328.2	,,	523,2452,3526	GG,GA,AA		19.8488,40.6861,26.9036	,,	203/977,171/945,171/960	73932560	3498,9504	2201	4300	6501	SO:0001819	synonymous_variant	9569	exon5			GCCCGAAGGCCTG	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.513A>G	7.37:g.73932560A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	NM_001199207	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Silent	SNP	ENST00000265755.3	37	CCDS5571.1																																																																																			A|0.744;G|0.256	0.256	strong		0.662	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328	
PCDH15	65217	hgsc.bcm.edu	37	10	55955444	55955444	+	Splice_Site	SNP	T	T	G	rs4935502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:55955444T>G	ENST00000320301.6	-	11	1698	c.1304A>C	c.(1303-1305)gAt>gCt	p.D435A	PCDH15_ENST00000437009.1_Splice_Site_p.D435A|PCDH15_ENST00000409834.1_Splice_Site_p.D39A|PCDH15_ENST00000373965.2_Splice_Site_p.D435A|PCDH15_ENST00000395430.1_Splice_Site_p.D435A|PCDH15_ENST00000395432.2_Splice_Site_p.D398A|PCDH15_ENST00000414778.1_Splice_Site_p.D440A|PCDH15_ENST00000395438.1_Splice_Site_p.D435A|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395440.1_Splice_Site_p.D435A|PCDH15_ENST00000373955.1_Splice_Site_p.D435A|PCDH15_ENST00000395433.1_Splice_Site_p.D413A|PCDH15_ENST00000373957.3_Splice_Site_p.D413A|PCDH15_ENST00000395445.1_Splice_Site_p.D435A|PCDH15_ENST00000395446.1_Splice_Site_p.D435A|PCDH15_ENST00000361849.3_Splice_Site_p.D435A	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	435	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		D -> A (in dbSNP:rs4935502). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:22815625}.		equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TTAACTTACATCTTCTATGTC	0.373										HNSCC(58;0.16)			T|||	1729	0.345248	0.1346	0.2536	5008	,	,		16771	0.8413		0.1312	False		,,,				2504	0.4039				p.D440A		Atlas-SNP	.											PCDH15_ENST00000417177,colon,carcinoma,-1,12	PCDH15	1715	12	0			c.A1319C						PASS	.	T	ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP	579,3827	256.4+/-261.2	30,519,1654	84.0	79.0	81.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1319,1304,1304,1304,1193,1238,1319,1304,1319,1304,1238,1304	5.1	1.0	10	dbSNP_111	81	1133,7467	234.0+/-267.1	89,955,3256	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	126,126,126,126,126,126,126,126,126,126,126,126	119,1474,4910	GG,GT,TT		13.1744,13.1412,13.1632	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	440/1963,435/1958,435/1887,435/1953,398/1916,413/1936,440/1791,435/1540,440/1683,435/1678,413/1933,435/1956	55955444	1712,11294	2203	4300	6503	SO:0001630	splice_region_variant	65217	exon12			CTTACATCTTCTA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1305+1A>C	10.37:g.55955444T>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	112	61	0.544643	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	736	0.336996336996337	60	0.12195121951219512	89	0.24585635359116023	493	0.8618881118881119	94	0.12401055408970976	T	16.49	3.137493	0.56936	0.131412	0.131744	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58797	0.41;0.69;0.69;0.4;0.35;0.69;0.31;0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.07	5.07	0.68467	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.26555	P	0.9738414	D;D;P;B;D;D;D;P;P;P;P;P;P;P;P	0.64830	0.986;0.975;0.884;0.234;0.994;0.975;0.986;0.866;0.779;0.948;0.727;0.866;0.837;0.866;0.949	D;P;P;B;P;P;D;P;B;P;P;P;B;P;P	0.63033	0.91;0.871;0.719;0.29;0.9;0.871;0.91;0.507;0.392;0.576;0.507;0.507;0.287;0.507;0.796	T	0.12167	-1.0558	8	0.52906	T	0.07	.	14.4836	0.67599	0.0:0.0:0.0:1.0	rs4935502;rs52792713;rs58556608;rs4935502	413;435;435;440;435;398;435;435;435;435;435;440;435;413;435	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	A	435;440;435;435;39;435;435;435;398;435;413;413;435;435;440;435;435	ENSP00000363076:D435A;ENSP00000410304:D440A;ENSP00000378826:D435A;ENSP00000386693:D39A;ENSP00000378832:D435A;ENSP00000378833:D435A;ENSP00000378827:D435A;ENSP00000378820:D398A;ENSP00000354950:D435A;ENSP00000378821:D413A;ENSP00000363068:D413A;ENSP00000322604:D435A;ENSP00000378818:D435A;ENSP00000412628:D435A;ENSP00000363066:D435A	ENSP00000322604:D435A	D	-	2	0	PCDH15	55625450	1.000000	0.71417	0.998000	0.56505	0.877000	0.50540	8.008000	0.88588	1.918000	0.55548	0.482000	0.46254	GAT	G|0.226;N|0.000	0.226	strong		0.373	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	Missense_Mutation
TG	7038	hgsc.bcm.edu	37	8	134108453	134108453	+	Silent	SNP	C	C	T	rs2069568	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:134108453C>T	ENST00000220616.4	+	43	7448	c.7408C>T	c.(7408-7410)Ctg>Ttg	p.L2470L	SLA_ENST00000524345.1_Intron|SLA_ENST00000517648.1_Intron|TG_ENST00000542445.1_Silent_p.L840L|SLA_ENST00000518565.1_Intron|SLA_ENST00000338087.5_Intron|SLA_ENST00000395352.3_Intron|TG_ENST00000377869.1_Silent_p.L2413L|TG_ENST00000519543.1_Silent_p.L603L	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2470					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)		AATGCAGCTCCTGGCCGTGAG	0.493													C|||	1726	0.344649	0.1452	0.3098	5008	,	,		21493	0.4038		0.4791	False		,,,				2504	0.4397				p.L2470L		Atlas-SNP	.											.	TG	416	.	0			c.C7408T						PASS	.	C	,,	905,3501	349.8+/-310.5	92,721,1390	169.0	159.0	163.0		,,7408	4.6	1.0	8	dbSNP_96	163	4022,4578	555.8+/-386.7	940,2142,1218	no	intron,intron,coding-synonymous	SLA,TG	NM_001045556.2,NM_001045557.2,NM_003235.4	,,	1032,2863,2608	TT,TC,CC		46.7674,20.5402,37.8825	,,	,,2470/2769	134108453	4927,8079	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon43			CAGCTCCTGGCCG	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.7408C>T	8.37:g.134108453C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	211	116	0.549763	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	820	0.37545787545787546	93	0.18902439024390244	131	0.36187845303867405	224	0.3916083916083916	372	0.49076517150395776	C	8.661	0.900554	0.17686	0.205402	0.467674	ENSG00000042832	ENST00000519178	.	.	.	5.46	4.58	0.56647	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999972	.	.	.	.	.	.	T	0.52434	-0.8576	3	.	.	.	.	10.5409	0.45033	0.0:0.9081:0.0:0.0919	rs2069568;rs3739265;rs17704072;rs2069568	.	.	.	L	925	.	.	P	+	2	0	TG	134177635	0.995000	0.38212	1.000000	0.80357	0.853000	0.48598	1.553000	0.36255	2.552000	0.86080	0.655000	0.94253	CCT	C|0.629;T|0.371	0.371	strong		0.493	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
ZNF440	126070	hgsc.bcm.edu	37	19	11942615	11942615	+	Silent	SNP	A	A	C	rs394416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11942615A>C	ENST00000304060.5	+	4	788	c.624A>C	c.(622-624)gcA>gcC	p.A208A		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	208					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A208A(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						GTGGGAAAGCATTCCATTGTC	0.363													N|||	2681	0.535343	0.8714	0.4683	5008	,	,		22899	0.4206		0.4036	False		,,,				2504	0.3824				p.A208A		Atlas-SNP	.											ZNF440,NS,carcinoma,0,1	ZNF440	56	1	1	Substitution - coding silent(1)	stomach(1)	c.A624C						PASS	.	C		3520,886	341.0+/-306.5	1415,690,98	104.0	107.0	106.0		624	-2.8	0.0	19	dbSNP_80	106	3674,4924	619.9+/-397.0	771,2132,1396	no	coding-synonymous	ZNF440	NM_152357.2		2186,2822,1494	CC,CA,AA		42.7309,20.1089,44.6786		208/596	11942615	7194,5810	2203	4299	6502	SO:0001819	synonymous_variant	126070	exon4			GAAAGCATTCCAT	AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"""Zinc fingers, C2H2-type"", ""-"""	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.624A>C	19.37:g.11942615A>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	94	37	0.393617	NM_152357	Q8N1R9	Silent	SNP	ENST00000304060.5	37	CCDS42503.1																																																																																			A|0.516;C|0.484	0.484	strong		0.363	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357	
EIF5B	9669	hgsc.bcm.edu	37	2	99992822	99992822	+	Missense_Mutation	SNP	A	A	C	rs7558074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:99992822A>C	ENST00000289371.6	+	10	1767	c.1565A>C	c.(1564-1566)aAa>aCa	p.K522T		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	522			K -> T (in dbSNP:rs7558074). {ECO:0000269|PubMed:10200264, ECO:0000269|PubMed:10432305, ECO:0000269|PubMed:21269460}.		cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GAAGGAAACAAAGTTCATATA	0.343													C|||	2964	0.591853	0.7678	0.7032	5008	,	,		16798	0.3671		0.5686	False		,,,				2504	0.5307				p.K522T	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											.	EIF5B	95	.	0			c.A1565C						PASS	.	C	THR/LYS	2951,933		1154,643,145	8.0	8.0	8.0		1565	5.3	0.5	2	dbSNP_116	8	4651,3555		1372,1907,824	yes	missense	EIF5B	NM_015904.3	78	2526,2550,969	CC,CA,AA		43.322,24.0216,37.1216	benign	522/1221	99992822	7602,4488	1942	4103	6045	SO:0001583	missense	9669	exon10			GAAACAAAGTTCA	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"""translation initiation factor IF2"""	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.1565A>C	2.37:g.99992822A>C	ENSP00000289371:p.Lys522Thr	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Missense_Mutation	SNP	ENST00000289371.6	37	CCDS42721.1	1287	0.5892857142857143	378	0.7682926829268293	254	0.7016574585635359	212	0.3706293706293706	443	0.5844327176781002	C	4.458	0.084868	0.08583	0.759784	0.56678	ENSG00000158417	ENST00000289371	T	0.48522	0.81	6.17	5.29	0.74685	.	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	0.45452	P	0.0015760000000000218	B	0.02656	0.0	B	0.01281	0.0	T	0.28681	-1.0036	7	.	.	.	-4.241	10.7971	0.46466	0.1323:0.7994:0.0:0.0683	rs7558074;rs17856952;rs52796323;rs61100948;rs7558074	522	O60841	IF2P_HUMAN	T	522	ENSP00000289371:K522T	.	K	+	2	0	EIF5B	99359254	0.992000	0.36948	0.545000	0.28153	0.444000	0.32077	2.998000	0.49465	0.933000	0.37291	-0.121000	0.15023	AAA	A|0.436;C|0.564;G|0.000;T|0.000	0.564	strong		0.343	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904	
SMCHD1	23347	hgsc.bcm.edu	37	18	2740714	2740714	+	Silent	SNP	A	A	G	rs12327477	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:2740714A>G	ENST00000320876.6	+	28	3866	c.3528A>G	c.(3526-3528)acA>acG	p.T1176T	SMCHD1_ENST00000261598.8_Silent_p.T1176T|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1176					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TAATAATTACAGATCAGTACG	0.284													G|||	1934	0.386182	0.2685	0.4467	5008	,	,		13651	0.5228		0.2634	False		,,,				2504	0.4877				p.T1176T		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A3528G						PASS	.	G		945,2639		127,691,974	86.0	84.0	85.0		3528	-2.0	1.0	18	dbSNP_120	85	2294,5814		315,1664,2075	no	coding-synonymous	SMCHD1	NM_015295.2		442,2355,3049	GG,GA,AA		28.293,26.3672,27.7027		1176/2006	2740714	3239,8453	1792	4054	5846	SO:0001819	synonymous_variant	23347	exon28			AATTACAGATCAG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.3528A>G	18.37:g.2740714A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			A|0.701;G|0.299	0.299	strong		0.284	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
LRRC4C	57689	hgsc.bcm.edu	37	11	40137543	40137543	+	Silent	SNP	T	T	C	rs2953310	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:40137543T>C	ENST00000278198.2	-	2	2263	c.300A>G	c.(298-300)agA>agG	p.R100R	LRRC4C_ENST00000527150.1_Silent_p.R100R|LRRC4C_ENST00000528697.1_Silent_p.R100R|LRRC4C_ENST00000530763.1_Silent_p.R100R			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	100					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)		p.R100R(1)		NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TTTCCAAGTGTCTCAAGTGCT	0.473													C|||	2501	0.499401	0.7027	0.5058	5008	,	,		19910	0.6052		0.3728	False		,,,				2504	0.2413				p.R100R		Atlas-SNP	.											LRRC4C,NS,carcinoma,0,1	LRRC4C	190	1	1	Substitution - coding silent(1)	stomach(1)	c.A300G						PASS	.	C		2917,1489	477.0+/-357.8	981,955,267	96.0	90.0	92.0		300	3.9	1.0	11	dbSNP_101	92	3562,5038	629.9+/-398.3	730,2102,1468	no	coding-synonymous	LRRC4C	NM_020929.1		1711,3057,1735	CC,CT,TT		41.4186,33.7948,49.8155		100/641	40137543	6479,6527	2203	4300	6503	SO:0001819	synonymous_variant	57689	exon7			CAAGTGTCTCAAG	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.300A>G	11.37:g.40137543T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	211	94	0.445498	NM_001258419	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	37	CCDS31464.1																																																																																			T|0.478;C|0.522	0.522	strong		0.473	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
SART1	9092	hgsc.bcm.edu	37	11	65733393	65733393	+	Silent	SNP	C	C	T	rs688862	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65733393C>T	ENST00000312397.5	+	7	866	c.774C>T	c.(772-774)acC>acT	p.T258T		NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells	258					cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AGGGCCTCACCGTGGAGCATG	0.597													C|||	1885	0.376398	0.2716	0.3228	5008	,	,		19837	0.2183		0.5278	False		,,,				2504	0.5634				p.T258T		Atlas-SNP	.											SART1,NS,carcinoma,0,1	SART1	41	1	0			c.C774T						PASS	.	C		1362,3040	451.6+/-349.7	215,932,1054	106.0	96.0	100.0		774	-9.1	0.3	11	dbSNP_83	100	4462,4130	589.0+/-392.4	1143,2176,977	no	coding-synonymous	SART1	NM_005146.4		1358,3108,2031	TT,TC,CC		48.068,30.9405,44.8207		258/801	65733393	5824,7170	2201	4296	6497	SO:0001819	synonymous_variant	9092	exon7			CCTCACCGTGGAG	AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"""small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"""	605941	"""squamous cell carcinoma antigen recognised by T cells"""			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771	ENST00000312397.5:c.774C>T	11.37:g.65733393C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_005146	A6NDN1|Q53GB5	Silent	SNP	ENST00000312397.5	37	CCDS31611.1																																																																																			C|0.595;T|0.405	0.405	strong		0.597	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1		
PLEKHG2	64857	hgsc.bcm.edu	37	19	39908574	39908574	+	Silent	SNP	C	C	T	rs35466645	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:39908574C>T	ENST00000409794.3	+	9	1762	c.912C>T	c.(910-912)acC>acT	p.T304T	PLEKHG2_ENST00000409797.2_Silent_p.T304T|PLEKHG2_ENST00000378550.1_Silent_p.T304T|PLEKHG2_ENST00000458508.2_Silent_p.T245T|PLEKHG2_ENST00000425673.1_Silent_p.T304T	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	304					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GTGGCTGGACCGGACCAGAGC	0.692													C|||	788	0.157348	0.1762	0.1844	5008	,	,		10187	0.0367		0.1769	False		,,,				2504	0.2168				p.T304T		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C912T						PASS	.	C		677,3487		50,577,1455	16.0	21.0	20.0		912	-9.3	0.4	19	dbSNP_126	20	1233,6895		85,1063,2916	no	coding-synonymous	PLEKHG2	NM_022835.2		135,1640,4371	TT,TC,CC		15.1698,16.2584,15.5386		304/1387	39908574	1910,10382	2082	4064	6146	SO:0001819	synonymous_variant	64857	exon9			CTGGACCGGACCA	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.912C>T	19.37:g.39908574C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	26	11	0.423077	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	333	0.15247252747252749	97	0.19715447154471544	83	0.2292817679558011	14	0.024475524475524476	139	0.18337730870712401	C	1.970	-0.436763	0.04636	0.162584	0.151698	ENSG00000090924	ENST00000205135	.	.	.	4.66	-9.32	0.00643	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999992221	.	.	.	.	.	.	T	0.10245	-1.0638	3	.	.	.	.	12.7222	0.57147	0.0:0.6049:0.2787:0.1164	rs35466645;rs62119735	.	.	.	L	201	.	.	P	+	2	0	PLEKHG2	44600414	0.012000	0.17670	0.371000	0.25978	0.271000	0.26615	-1.138000	0.03216	-2.668000	0.00415	-2.717000	0.00132	CCG	C|0.847;T|0.153	0.153	strong		0.692	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
RARS	5917	hgsc.bcm.edu	37	5	167924260	167924260	+	Silent	SNP	C	C	A	rs11557637	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:167924260C>A	ENST00000231572.3	+	7	783	c.729C>A	c.(727-729)acC>acA	p.T243T	RARS_ENST00000538719.1_Silent_p.T37T|RARS_ENST00000520421.1_3'UTR	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	243					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		ACTGGGGGACCCAGTTTGGCA	0.353													C|||	372	0.0742812	0.0091	0.0908	5008	,	,		17277	0.0645		0.1799	False		,,,				2504	0.0521				p.T243T		Atlas-SNP	.											.	RARS	58	.	0			c.C729A						PASS	.	C		161,4245	105.6+/-144.1	2,157,2044	62.0	63.0	63.0		729	-0.1	1.0	5	dbSNP_120	63	1623,6971	292.0+/-300.6	160,1303,2834	yes	coding-synonymous	RARS	NM_002887.3		162,1460,4878	AA,AC,CC		18.8853,3.6541,13.7231		243/661	167924260	1784,11216	2203	4297	6500	SO:0001819	synonymous_variant	5917	exon7			GGGGACCCAGTTT	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.729C>A	5.37:g.167924260C>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	37	CCDS4367.1																																																																																			C|0.883;A|0.117	0.117	strong		0.353	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
ANO2	57101	hgsc.bcm.edu	37	12	5841701	5841701	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:5841701C>T	ENST00000356134.5	-	16	1604	c.1533G>A	c.(1531-1533)acG>acA	p.T511T	ANO2_ENST00000546188.1_Silent_p.T511T|ANO2_ENST00000538154.1_5'UTR|ANO2_ENST00000327087.8_Silent_p.T510T	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	515					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						CGCCACACTCCGTCGTGTTTG	0.463																																					p.T510T		Atlas-SNP	.											ANO2_ENST00000327087,NS,carcinoma,0,2	ANO2	309	2	0			c.G1530A						PASS	.						110.0	110.0	110.0					12																	5841701		2074	4205	6279	SO:0001819	synonymous_variant	57101	exon15			ACACTCCGTCGTG	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.1533G>A	12.37:g.5841701C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	185	89	0.481081	NM_020373	C4N787|Q9H847	Silent	SNP	ENST00000356134.5	37																																																																																				.	.	none		0.463	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45258284	45258284	+	Missense_Mutation	SNP	G	G	C	rs41278887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:45258284G>C	ENST00000389774.2	+	13	1345	c.1204G>C	c.(1204-1206)Gaa>Caa	p.E402Q	ARHGAP8_ENST00000389773.5_Missense_Mutation_p.E493Q|ARHGAP8_ENST00000336963.4_3'UTR|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.E502Q|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.E581Q|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.E581Q|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.E371Q	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	402	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|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)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CATGTTCACTGAACTGCTGAT	0.587													G|||	16	0.00319489	0.0	0.0058	5008	,	,		19843	0.0		0.001	False		,,,				2504	0.0112				p.E493Q		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.G1477C						PASS	.	G	GLN/GLU,,GLN/GLU,GLN/GLU	1,4405	2.1+/-5.4	0,1,2202	67.0	63.0	64.0		1204,,1477,1111	2.7	0.2	22	dbSNP_127	64	30,8570	21.0+/-64.5	0,30,4270	no	missense,utr-3,missense,missense	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	29,,29,29	0,31,6472	CC,CG,GG		0.3488,0.0227,0.2384	benign,,benign,benign	402/465,,493/556,371/434	45258284	31,12975	2203	4300	6503	SO:0001583	missense	553158	exon15			TTCACTGAACTGC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.1204G>C	22.37:g.45258284G>C	ENSP00000374424:p.Glu402Gln	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	121	67	0.553719	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	9.164	1.019473	0.19355	2.27E-4	0.003488	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000356099	T;T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84;0.84	3.7	2.67	0.31697	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.188373	0.25442	N	0.030642	T	0.37237	0.0996	L	0.41710	1.295	0.22050	N	0.99939	B;D;B;P;B	0.71674	0.129;0.998;0.066;0.808;0.149	B;P;B;B;B	0.56343	0.048;0.796;0.029;0.382;0.053	T	0.19386	-1.0307	10	0.17369	T	0.5	.	7.4445	0.27203	0.2062:0.0:0.7938:0.0	rs41278887	424;407;402;581;502	B7ZMA4;A2RU51;P85298;B1AHC4;B1AHC3	.;.;RHG08_HUMAN;.;.	Q	502;581;581;493;402;371	ENSP00000354732:E502Q;ENSP00000262731:E581Q;ENSP00000429240:E581Q;ENSP00000374423:E493Q;ENSP00000374424:E402Q;ENSP00000348407:E371Q	ENSP00000348407:E371Q	E	+	1	0	PRR5-ARHGAP8;ARHGAP8	43636948	1.000000	0.71417	0.187000	0.23214	0.008000	0.06430	4.561000	0.60809	0.868000	0.35678	0.655000	0.94253	GAA	C|0.002;G|0.998	0.002	strong		0.587	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
HGFAC	3083	hgsc.bcm.edu	37	4	3446091	3446091	+	Missense_Mutation	SNP	G	G	T	rs3748034	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:3446091G>T	ENST00000382774.3	+	6	767	c.652G>T	c.(652-654)Gcc>Tcc	p.A218S	HGFAC_ENST00000511533.1_Missense_Mutation_p.A218S	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	218	Fibronectin type-I. {ECO:0000255|PROSITE- ProRule:PRU00478}.		A -> S (in dbSNP:rs3748034).		proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CGACCGCTGGGCCCGCGTGCG	0.677													G|||	670	0.133786	0.0159	0.1124	5008	,	,		15900	0.3085		0.1362	False		,,,				2504	0.1258				p.A218S		Atlas-SNP	.											.	HGFAC	69	.	0			c.G652T						PASS	.	G	SER/ALA	150,4202		3,144,2029	13.0	15.0	14.0		652	3.7	1.0	4	dbSNP_107	14	1203,7365		78,1047,3159	yes	missense	HGFAC	NM_001528.2	99	81,1191,5188	TT,TG,GG		14.0406,3.4467,10.4721	benign	218/656	3446091	1353,11567	2176	4284	6460	SO:0001583	missense	3083	exon6			CGCTGGGCCCGCG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.652G>T	4.37:g.3446091G>T	ENSP00000372224:p.Ala218Ser	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	37	CCDS3369.1	318	0.14560439560439561	9	0.018292682926829267	40	0.11049723756906077	158	0.2762237762237762	111	0.14643799472295516	G	13.29	2.194105	0.38707	0.034467	0.140406	ENSG00000109758	ENST00000382774;ENST00000511533	T;T	0.21031	2.03;2.03	3.74	3.74	0.42951	Fibronectin, type I (4);	0.144554	0.45867	D	0.000328	T	0.00012	0.0000	L	0.45581	1.43	0.38956	P	0.04154599999999997	P;B	0.39094	0.659;0.417	B;B	0.40534	0.332;0.179	T	0.48525	-0.9028	9	0.23302	T	0.38	.	13.0704	0.59057	0.0:0.0:1.0:0.0	rs3748034;rs3748034	218;218	D6RAR4;Q04756	.;HGFA_HUMAN	S	218	ENSP00000372224:A218S;ENSP00000421801:A218S	ENSP00000372224:A218S	A	+	1	0	HGFAC	3415889	0.998000	0.40836	1.000000	0.80357	0.591000	0.36615	2.000000	0.40816	1.925000	0.55765	0.462000	0.41574	GCC	G|0.878;T|0.122	0.122	strong		0.677	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
MLXIP	22877	hgsc.bcm.edu	37	12	122617989	122617989	+	Missense_Mutation	SNP	A	A	G	rs7978353	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:122617989A>G	ENST00000319080.7	+	9	1319	c.1187A>G	c.(1186-1188)gAg>gGg	p.E396G	MLXIP_ENST00000377037.2_Missense_Mutation_p.E3G|MLXIP_ENST00000538698.1_Missense_Mutation_p.E3G					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		CACATGGATGAGCAGGGCTGT	0.642													G|||	2283	0.455871	0.5113	0.3934	5008	,	,		13429	0.3581		0.4742	False		,,,				2504	0.5072				p.E396G	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											MLXIP,colon,carcinoma,0,2	MLXIP	46	2	0			c.A1187G						scavenged	.	G	GLY/GLU	1981,2079		503,975,552	31.0	35.0	33.0		777	-0.2	0.0	12	dbSNP_116	33	3278,5086		632,2014,1536	yes	missense	MLXIP	NM_014938.3	98	1135,2989,2088	GG,GA,AA		39.1918,48.7931,42.3294	benign	396/920	122617989	5259,7165	2030	4182	6212	SO:0001583	missense	22877	exon9			TGGATGAGCAGGG	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"""Basic helix-loop-helix proteins"""	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.1187A>G	12.37:g.122617989A>G	ENSP00000312834:p.Glu396Gly	Somatic	83	2	0.0240964		WXS	Illumina HiSeq	Phase_I	83	29	0.349398	NM_014938		Missense_Mutation	SNP	ENST00000319080.7	37		936	0.42857142857142855	236	0.4796747967479675	142	0.39226519337016574	209	0.36538461538461536	349	0.4604221635883905	G	4.856	0.159087	0.09236	0.487931	0.391918	ENSG00000175727	ENST00000319080;ENST00000538698;ENST00000539039;ENST00000377037	T;T;T	0.30981	2.51;1.96;1.51	5.04	-0.212	0.13169	.	2.273020	0.01378	N	0.012813	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45454	-0.9260	8	0.13470	T	0.59	0.7027	6.0635	0.19850	0.4415:0.1246:0.4339:0.0	rs7978353;rs60448207;rs7978353	396;396	Q9HAP2-3;Q9HAP2	.;MLXIP_HUMAN	G	396;3;3;3	ENSP00000312834:E396G;ENSP00000440769:E3G;ENSP00000366236:E3G	ENSP00000312834:E396G	E	+	2	0	MLXIP	121183942	0.265000	0.24102	0.000000	0.03702	0.006000	0.05464	0.805000	0.27112	-0.658000	0.05366	-0.898000	0.02899	GAG	A|0.566;G|0.434	0.434	strong		0.642	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938	
MAGEA11	4110	hgsc.bcm.edu	37	X	148798223	148798223	+	Silent	SNP	T	T	C	rs2233050	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:148798223T>C	ENST00000355220.5	+	5	1179	c.1077T>C	c.(1075-1077)ctT>ctC	p.L359L	MAGEA11_ENST00000333104.4_Silent_p.L330L	NM_005366.4	NP_005357.2	P43364	MAGAB_HUMAN	melanoma antigen family A, 11	359	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	9	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					AGAGGCTCCTTACCCAAAATT	0.567													-|||	1917	0.507815	0.6543	0.4914	3775	,	,		15281	0.1776		0.3946	False		,,,				2504	0.138				p.L359L		Atlas-SNP	.											.	MAGEA11	86	.	0			c.T1077C						PASS	.	C	,	3095,740		1059,506,471,67,100	129.0	134.0	132.0		990,1077	-0.1	0.0	X	dbSNP_98	132	3249,3479		585,1168,911,675,961	no	coding-synonymous,coding-synonymous	MAGEA11	NM_001011544.1,NM_005366.4	,	1644,1674,1382,742,1061	CC,CT,C,TT,T		48.2907,19.296,39.9413	,	330/401,359/430	148798223	6344,4219	2203	4300	6503	SO:0001819	synonymous_variant	4110	exon5			GCTCCTTACCCAA		CCDS48180.1	Xq28	2009-03-13			ENSG00000185247	ENSG00000185247			6798	protein-coding gene	gene with protein product	"""MAGE-11 antigen"", ""melanoma-associated antigen 11"", ""cancer/testis antigen family 1, member 11"""	300344		MAGE11		8575766	Standard	NM_001011544		Approved	MAGE-11, MAGEA-11, MGC10511, CT1.11	uc004fdq.3	P43364	OTTHUMG00000022633	ENST00000355220.5:c.1077T>C	X.37:g.148798223T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	123	115	0.934959	NM_005366	Q5ETU4|Q6ZRZ5	Silent	SNP	ENST00000355220.5	37	CCDS48180.1																																																																																			T|0.400;C|0.600	0.600	strong		0.567	MAGEA11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058725.4	NM_005366	
FKBP15	23307	hgsc.bcm.edu	37	9	115941046	115941046	+	Silent	SNP	T	T	C	rs3810912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:115941046T>C	ENST00000238256.3	-	20	2067	c.1950A>G	c.(1948-1950)gcA>gcG	p.A650A		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	650					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GAGAGACCTGTGCAGTGGCCG	0.458													T|||	427	0.0852636	0.0151	0.0836	5008	,	,		18584	0.0546		0.1789	False		,,,				2504	0.1166				p.A650A		Atlas-SNP	.											.	FKBP15	128	.	0			c.A1950G						PASS	.	T		141,3857		1,139,1859	42.0	40.0	41.0		1950	-1.7	1.0	9	dbSNP_107	41	1462,6866		139,1184,2841	no	coding-synonymous	FKBP15	NM_015258.1		140,1323,4700	CC,CT,TT		17.5552,3.5268,13.005		650/1220	115941046	1603,10723	1999	4164	6163	SO:0001819	synonymous_variant	23307	exon20			GACCTGTGCAGTG	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.1950A>G	9.37:g.115941046T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	46	0.638889	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			T|0.885;C|0.115	0.115	strong		0.458	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
ZNF486	90649	hgsc.bcm.edu	37	19	20308149	20308149	+	Nonsense_Mutation	SNP	C	C	G	rs184976796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:20308149C>G	ENST00000335117.8	+	4	687	c.630C>G	c.(628-630)taC>taG	p.Y210*	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	210					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						AGAAACCATACAAATGTGAAG	0.363													C|||	17	0.00339457	0.0	0.0058	5008	,	,		19254	0.0		0.0109	False		,,,				2504	0.002				p.Y210X		Atlas-SNP	.											.	ZNF486	74	.	0			c.C630G						PASS	.	C	stop/TYR	7,4291		0,7,2142	39.0	42.0	41.0		630	0.8	0.1	19		41	54,8492		0,54,4219	no	stop-gained	ZNF486	NM_052852.2		0,61,6361	GG,GC,CC		0.6319,0.1629,0.4749		210/464	20308149	61,12783	2149	4273	6422	SO:0001587	stop_gained	90649	exon4			ACCATACAAATGT	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"""Zinc fingers, C2H2-type"", ""-"""	20807	protein-coding gene	gene with protein product			"""KRAB domain only 2"""	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.630C>G	19.37:g.20308149C>G	ENSP00000335042:p.Tyr210*	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_052852	Q0VG00	Nonsense_Mutation	SNP	ENST00000335117.8	37	CCDS46029.1	8	0.003663003663003663	0	0.0	5	0.013812154696132596	0	0.0	3	0.00395778364116095	c	10.99	1.507634	0.27036	0.001629	0.006319	ENSG00000256229	ENST00000545779;ENST00000335117	.	.	.	0.814	0.814	0.18756	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.9774	0.24683	0.0:1.0:0.0:0.0	.	.	.	.	X	249;210	.	ENSP00000335042:Y210X	Y	+	3	2	ZNF486	20169149	0.000000	0.05858	0.057000	0.19452	0.056000	0.15407	-0.409000	0.07160	0.183000	0.20059	0.186000	0.17326	TAC	C|0.995;G|0.005	0.005	strong		0.363	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
DDX20	11218	hgsc.bcm.edu	37	1	112308953	112308953	+	Missense_Mutation	SNP	T	T	C	rs197412	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:112308953T>C	ENST00000369702.4	+	11	2527	c.1907T>C	c.(1906-1908)aTt>aCt	p.I636T	DDX20_ENST00000475700.1_Missense_Mutation_p.I244T	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	636			I -> T (in dbSNP:rs197412). {ECO:0000269|PubMed:15489334}.		ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATAAAGTTATTGAACAGAGA	0.453													C|||	2376	0.474441	0.7247	0.5072	5008	,	,		19469	0.3403		0.4185	False		,,,				2504	0.3088				p.I636T		Atlas-SNP	.											DDX20,NS,carcinoma,+1,1	DDX20	50	1	0			c.T1907C						PASS	.	C	THR/ILE	2950,1456	465.7+/-354.3	991,968,244	49.0	49.0	49.0		1907	3.9	0.3	1	dbSNP_79	49	3345,5255	640.4+/-399.6	669,2007,1624	yes	missense	DDX20	NM_007204.4	89	1660,2975,1868	CC,CT,TT		38.8953,33.0458,48.4007	benign	636/825	112308953	6295,6711	2203	4300	6503	SO:0001583	missense	11218	exon11			AAGTTATTGAACA	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.1907T>C	1.37:g.112308953T>C	ENSP00000358716:p.Ile636Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	1038	0.47527472527472525	360	0.7317073170731707	162	0.44751381215469616	198	0.34615384615384615	318	0.41952506596306066	C	0.006	-2.070387	0.00379	0.669542	0.388953	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.32023	1.47;1.98	5.72	3.86	0.44501	.	2.200060	0.01328	N	0.011173	T	0.02929	0.0087	N	0.00926	-1.1	0.44899	P	0.0020820000000000283	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33828	-0.9853	8	.	.	.	0.4742	5.1813	0.15161	0.1427:0.6287:0.0:0.2286	rs197412;rs482352;rs17569500;rs17845940;rs17856358;rs17857030;rs17858920;rs52814398;rs60229681;rs197412	244;636	E9PJ60;Q9UHI6	.;DDX20_HUMAN	T	636;244	ENSP00000358716:I636T;ENSP00000435660:I244T	.	I	+	2	0	DDX20	112110476	0.906000	0.30813	0.331000	0.25455	0.101000	0.19017	2.183000	0.42565	0.463000	0.27118	-0.766000	0.03442	ATT	C|0.483;N|0.000	0.483	strong		0.453	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
CALCR	799	hgsc.bcm.edu	37	7	93055753	93055753	+	Missense_Mutation	SNP	A	A	G	rs1801197	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:93055753A>G	ENST00000394441.1	-	13	1655	c.1340T>C	c.(1339-1341)cTg>cCg	p.L447P	CALCR_ENST00000359558.2_Missense_Mutation_p.L481P|CALCR_ENST00000426151.1_Missense_Mutation_p.L447P|CALCR_ENST00000360249.4_Missense_Mutation_p.L463P|CALCR_ENST00000421592.1_Missense_Mutation_p.L463P	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	481					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	TTCATTCCTCAGCTCCTGATG	0.557													G|||	2722	0.54353	0.5408	0.4308	5008	,	,		18060	0.8611		0.3052	False		,,,				2504	0.545				p.L481P		Atlas-SNP	.											CALCR_ENST00000359558,NS,adenoma,0,2	CALCR	200	2	0			c.T1442C	GRCh37	CM980299	CALCR	M	rs1801197	PASS	.	G	PRO/LEU,PRO/LEU,PRO/LEU	2073,2333	606.2+/-390.7	470,1133,600	170.0	158.0	162.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1442,1340,1340	1.3	0.0	7	dbSNP_89	162	2187,6413	712.5+/-405.9	296,1595,2409	yes	missense,missense,missense	CALCR	NM_001164737.1,NM_001164738.1,NM_001742.3	98,98,98	766,2728,3009	GG,GA,AA		25.4302,47.0495,32.7541	benign,benign,benign	481/509,447/475,447/475	93055753	4260,8746	2203	4300	6503	SO:0001583	missense	799	exon16			TTCCTCAGCTCCT	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.1340T>C	7.37:g.93055753A>G	ENSP00000377959:p.Leu447Pro	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	167	76	0.45509	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	37	CCDS5631.1	1154	0.5283882783882784	274	0.556910569105691	157	0.43370165745856354	497	0.8688811188811189	226	0.29815303430079154	G	0.389	-0.924704	0.02377	0.470495	0.254302	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.50001	0.76;0.78;0.78;0.91;0.91	5.11	1.3	0.21679	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53005	P	3.2000000000032E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15521	-1.0434	7	0.28530	T	0.3	.	4.6969	0.12808	0.3355:0.1492:0.5153:0.0	rs1801197;rs3181601;rs10368963;rs11769260;rs17165394;rs58887934;rs1801197	481;447	F5H605;A4D1G6	.;.	P	481;463;463;447;447	ENSP00000352561:L481P;ENSP00000353385:L463P;ENSP00000399552:L463P;ENSP00000377959:L447P;ENSP00000389295:L447P	ENSP00000352561:L481P	L	-	2	0	CALCR	92893689	0.940000	0.31905	0.014000	0.15608	0.178000	0.23041	1.787000	0.38704	-0.050000	0.13356	-0.790000	0.03334	CTG	A|0.561;G|0.439	0.439	strong		0.557	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	
OSBPL5	114879	hgsc.bcm.edu	37	11	3111866	3111866	+	Missense_Mutation	SNP	C	C	T	rs2277301	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:3111866C>T	ENST00000263650.7	-	20	2479	c.2320G>A	c.(2320-2322)Gcc>Acc	p.A774T	OSBPL5_ENST00000478260.1_Missense_Mutation_p.A228T|OSBPL5_ENST00000348039.5_Missense_Mutation_p.A706T|OSBPL5_ENST00000525498.1_Missense_Mutation_p.A685T|OSBPL5_ENST00000542243.1_Missense_Mutation_p.A405T|OSBPL5_ENST00000389989.3_Missense_Mutation_p.A706T	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	774			A -> T (in dbSNP:rs2277301).		cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CTCTCCGTGGCCTGGCTGTGG	0.662													C|||	832	0.166134	0.1634	0.1052	5008	,	,		15699	0.0258		0.2296	False		,,,				2504	0.2924				p.A774T		Atlas-SNP	.											.	OSBPL5	78	.	0			c.G2320A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	683,3719	278.4+/-274.2	57,569,1575	46.0	46.0	46.0		2116,2320,2116	2.7	1.0	11	dbSNP_100	46	1668,6928	301.2+/-305.3	148,1372,2778	yes	missense,missense,missense	OSBPL5	NM_001144063.1,NM_020896.3,NM_145638.2	58,58,58	205,1941,4353	TT,TC,CC		19.4044,15.5157,18.0874	benign,benign,benign	706/812,774/880,706/812	3111866	2351,10647	2201	4298	6499	SO:0001583	missense	114879	exon20			CCGTGGCCTGGCT	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.2320G>A	11.37:g.3111866C>T	ENSP00000263650:p.Ala774Thr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	166	84	0.506024	NM_020896	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Missense_Mutation	SNP	ENST00000263650.7	37	CCDS31344.1	324	0.14835164835164835	76	0.15447154471544716	50	0.13812154696132597	17	0.02972027972027972	181	0.23878627968337732	C	5.445	0.267206	0.10294	0.155157	0.194044	ENSG00000021762	ENST00000478260;ENST00000263650;ENST00000389989;ENST00000534454;ENST00000525498;ENST00000542243;ENST00000348039;ENST00000357352	T;T;T;T;T;T;T	0.44083	0.95;1.54;1.54;0.94;1.54;0.93;1.54	3.81	2.7	0.31948	.	1.830980	0.02719	N	0.113780	T	0.00012	0.0000	N	0.03608	-0.345	0.47994	P	4.3599999999999195E-4	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.22208	-1.0223	9	0.12430	T	0.62	-6.2735	3.7897	0.08715	0.0:0.356:0.0:0.644	rs2277301;rs2277301	685;706;774	B4DVB0;Q8N596;Q9H0X9	.;.;OSBL5_HUMAN	T	228;774;706;327;685;405;706;393	ENSP00000437141:A228T;ENSP00000263650:A774T;ENSP00000374639:A706T;ENSP00000431412:A327T;ENSP00000433342:A685T;ENSP00000441551:A405T;ENSP00000302872:A706T	ENSP00000263650:A774T	A	-	1	0	OSBPL5	3068442	1.000000	0.71417	0.992000	0.48379	0.263000	0.26337	2.242000	0.43106	0.470000	0.27294	0.549000	0.68633	GCC	C|0.835;T|0.165	0.165	strong		0.662	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2		
OR2T4	127074	hgsc.bcm.edu	37	1	248524992	248524992	+	Missense_Mutation	SNP	A	A	G	rs45552134	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248524992A>G	ENST00000366475.1	+	1	110	c.110A>G	c.(109-111)aAc>aGc	p.N37S		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	37						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N37S(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGGATGGCCAACCACACTGGA	0.488																																					p.N37S		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	1	1	Substitution - Missense(1)	liver(1)	c.A110G						scavenged	.	A	SER/ASN	19,4385		2,15,2185	124.0	108.0	113.0		110	0.2	0.1	1	dbSNP_127	113	273,8265		42,189,4038	yes	missense	OR2T4	NM_001004696.1	46	44,204,6223	GG,GA,AA		3.1975,0.4314,2.2562	benign	37/349	248524992	292,12650	2202	4269	6471	SO:0001583	missense	127074	exon1			TGGCCAACCACAC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.110A>G	1.37:g.248524992A>G	ENSP00000355431:p.Asn37Ser	Somatic	745	3	0.00402685		WXS	Illumina HiSeq	Phase_I	515	77	0.149515	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	A	7.617	0.676086	0.14841	0.004314	0.031975	ENSG00000196944	ENST00000366475	T	0.63913	-0.07	1.6	0.248	0.15526	.	0.853037	0.09884	N	0.743276	T	0.34629	0.0904	M	0.78285	2.405	0.44798	P	0.0021959999999999757	B	0.18461	0.028	B	0.20184	0.028	T	0.51865	-0.8651	9	0.72032	D	0.01	.	4.5644	0.12175	0.8044:0.0:0.1956:0.0	rs45552134	37	Q8NH00	OR2T4_HUMAN	S	37	ENSP00000355431:N37S	ENSP00000355431:N37S	N	+	2	0	OR2T4	246591615	0.199000	0.23386	0.064000	0.19789	0.029000	0.11900	3.897000	0.56273	-0.469000	0.06911	-0.956000	0.02647	AAC	A|0.973;G|0.027	0.027	strong		0.488	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
ZNF880	400713	hgsc.bcm.edu	37	19	52887603	52887603	+	Missense_Mutation	SNP	G	G	A	rs78052167|rs148392772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52887603G>A	ENST00000422689.2	+	4	785	c.770G>A	c.(769-771)cGa>cAa	p.R257Q		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	257					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						CTCCTTGCACGACATCAGAGA	0.398													G|||	106	0.0211661	0.0008	0.0288	5008	,	,		11540	0.0536		0.0298	False		,,,				2504	0.001				p.R257Q		Atlas-SNP	.											ZNF880,colon,carcinoma,+1,1	ZNF880	45	1	0			c.G770A						PASS	.						41.0	39.0	39.0					19																	52887603		1568	3582	5150	SO:0001583	missense	400713	exon4			TTGCACGACATCA	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.770G>A	19.37:g.52887603G>A	ENSP00000406318:p.Arg257Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	41	0.018772893772893772	2	0.0040650406504065045	14	0.03867403314917127	0	0.0	25	0.032981530343007916	G	0.973	-0.699584	0.03279	.	.	ENSG00000221923	ENST00000422689	T	0.26223	1.75	1.89	-3.79	0.04320	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02012	0.0063	N	0.13003	0.285	0.09310	N	1	B	0.30763	0.294	B	0.25884	0.064	T	0.26087	-1.0113	8	.	.	.	.	3.169	0.06545	0.2615:0.0:0.2604:0.4781	.	257	Q6PDB4	ZN880_HUMAN	Q	257	ENSP00000406318:R257Q	.	R	+	2	0	ZNF880	57579415	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-7.860000	0.00028	-0.882000	0.03987	-0.404000	0.06349	CGA	G|0.978;A|0.022	0.022	strong		0.398	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
B2M	567	hgsc.bcm.edu	37	15	45003770	45003770	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:45003770T>A	ENST00000558401.1	+	1	96	c.26T>A	c.(25-27)gTg>gAg	p.V9E	B2M_ENST00000559916.1_Missense_Mutation_p.V9E|B2M_ENST00000544417.1_Missense_Mutation_p.V9E|PATL2_ENST00000558573.1_5'Flank	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	9					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GCCTTAGCTGTGCTCGCGCTA	0.617																																					p.V9E		Atlas-SNP	.											.	B2M	99	.	0			c.T26A						PASS	.						132.0	95.0	108.0					15																	45003770		2198	4298	6496	SO:0001583	missense	567	exon1			TAGCTGTGCTCGC	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"""Immunoglobulin superfamily / C1-set domain containing"""	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.26T>A	15.37:g.45003770T>A	ENSP00000452780:p.Val9Glu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	57	52	0.912281	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.499636	0.44455	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01430	4.9	5.35	4.23	0.50019	.	0.532223	0.09808	U	0.753127	T	0.01976	0.0062	L	0.46157	1.445	0.09310	N	1	B;B;B	0.30973	0.302;0.201;0.201	B;B;B	0.26969	0.075;0.073;0.055	T	0.45775	-0.9238	10	0.87932	D	0	.	7.8636	0.29524	0.0:0.0912:0.0:0.9088	.	9;9;9	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	E	9	ENSP00000437604:V9E	ENSP00000340858:V9E	V	+	2	0	B2M	42791062	0.003000	0.15002	0.002000	0.10522	0.005000	0.04900	1.408000	0.34668	1.166000	0.42689	0.533000	0.62120	GTG	.	.	none		0.617	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	
XRRA1	143570	hgsc.bcm.edu	37	11	74559481	74559481	+	Silent	SNP	C	C	T	rs4944961	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:74559481C>T	ENST00000340360.6	-	15	1714	c.1383G>A	c.(1381-1383)ccG>ccA	p.P461P	RN7SL239P_ENST00000490061.2_RNA|XRRA1_ENST00000321448.8_Silent_p.P186P|XRRA1_ENST00000527087.1_Silent_p.P374P	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						GAGGCTGCTTCGGCACCTTTG	0.532													C|||	1400	0.279553	0.0946	0.4957	5008	,	,		19444	0.5089		0.3181	False		,,,				2504	0.1002				p.P461P		Atlas-SNP	.											.	XRRA1	46	.	0			c.G1383A						PASS	.	C		538,3472		48,442,1515	44.0	46.0	45.0		1383	-4.9	1.0	11	dbSNP_111	45	2506,5822		377,1752,2035	no	coding-synonymous	XRRA1	NM_182969.1		425,2194,3550	TT,TC,CC		30.0913,13.4165,24.6717		461/793	74559481	3044,9294	2005	4164	6169	SO:0001819	synonymous_variant	143570	exon15			CTGCTTCGGCACC	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1383G>A	11.37:g.74559481C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_182969		Silent	SNP	ENST00000340360.6	37	CCDS44680.1																																																																																			C|0.687;T|0.313	0.313	strong		0.532	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969	
CCHCR1	54535	hgsc.bcm.edu	37	6	31112737	31112737	+	Missense_Mutation	SNP	C	C	A	rs130079	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31112737C>A	ENST00000376266.5	-	14	1845	c.1723G>T	c.(1723-1725)Ggc>Tgc	p.G575C	CCHCR1_ENST00000396263.2_Missense_Mutation_p.G522C|CCHCR1_ENST00000396268.3_Missense_Mutation_p.G664C|CCHCR1_ENST00000451521.2_Missense_Mutation_p.G628C	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	575			G -> C (in allele HCR*WWCC; associated with psoriasis; dbSNP:rs130079). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:10888604, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						TCCTGCTGGCCCTGGCGTGCT	0.652													C|||	710	0.141773	0.1649	0.1383	5008	,	,		17573	0.0377		0.2018	False		,,,				2504	0.1585				p.G664C		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G1990T						PASS	.	C	CYS/GLY,CYS/GLY,CYS/GLY	835,3571	330.4+/-301.5	89,657,1457	59.0	58.0	59.0		1882,1990,1723	1.5	1.0	6	dbSNP_78	59	2031,6569	351.3+/-328.2	247,1537,2516	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	159,159,159	336,2194,3973	AA,AC,CC		23.6163,18.9514,22.036	benign,benign,benign	628/836,664/872,575/783	31112737	2866,10140	2203	4300	6503	SO:0001583	missense	54535	exon14			GCTGGCCCTGGCG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1723G>T	6.37:g.31112737C>A	ENSP00000365442:p.Gly575Cys	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	329	0.15064102564102563	90	0.18292682926829268	51	0.1408839779005525	26	0.045454545454545456	162	0.21372031662269128	C	12.17	1.857747	0.32791	0.189514	0.236163	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521	T;T;T;T	0.10477	2.87;2.87;2.87;2.87	4.79	1.49	0.22878	.	0.872767	0.09696	N	0.767660	T	0.05502	0.0145	M	0.65975	2.015	0.36574	P	0.12684600000000001	B;B;B;B;B	0.25206	0.077;0.01;0.029;0.12;0.099	B;B;B;B;B	0.29663	0.064;0.015;0.041;0.105;0.064	T	0.24297	-1.0164	9	0.51188	T	0.08	-4.183	7.474	0.27365	0.0:0.6716:0.0:0.3284	rs130079;rs1265077;rs16898850;rs17840016;rs52811991;rs57918849;rs130079	575;575;575;628;664	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	C	664;575;522;575;628	ENSP00000379566:G664C;ENSP00000365442:G575C;ENSP00000379561:G522C;ENSP00000401039:G628C	ENSP00000365442:G575C	G	-	1	0	CCHCR1	31220716	1.000000	0.71417	0.998000	0.56505	0.804000	0.45430	1.297000	0.33400	0.446000	0.26666	0.448000	0.29417	GGC	C|0.801;A|0.199	0.199	strong		0.652	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
NAV3	89795	hgsc.bcm.edu	37	12	78400884	78400884	+	Silent	SNP	G	G	A	rs34276383	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:78400884G>A	ENST00000397909.2	+	8	1739	c.1566G>A	c.(1564-1566)ccG>ccA	p.P522P	NAV3_ENST00000266692.7_Silent_p.P522P|NAV3_ENST00000536525.2_Silent_p.P522P|NAV3_ENST00000228327.6_Silent_p.P522P			Q8IVL0	NAV3_HUMAN	neuron navigator 3	522						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.P522P(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GCTTAATTCCGTCTTCCAGTG	0.448										HNSCC(70;0.22)			A|||	744	0.148562	0.0908	0.1095	5008	,	,		19238	0.2143		0.1322	False		,,,				2504	0.2035				p.P522P		Atlas-SNP	.											NAV3,NS,carcinoma,0,1	NAV3	506	1	1	Substitution - coding silent(1)	stomach(1)	c.G1566A						PASS	.	A		405,3417		31,343,1537	66.0	66.0	66.0		1566	-5.4	0.7	12	dbSNP_126	66	1037,7193		61,915,3139	no	coding-synonymous	NAV3	NM_014903.4		92,1258,4676	AA,AG,GG		12.6002,10.5965,11.9648		522/2364	78400884	1442,10610	1911	4115	6026	SO:0001819	synonymous_variant	89795	exon8			AATTCCGTCTTCC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1566G>A	12.37:g.78400884G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37																																																																																				G|0.867;A|0.133	0.133	strong		0.448	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
PER2	8864	hgsc.bcm.edu	37	2	239165663	239165663	+	Silent	SNP	T	T	C	rs2304669	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:239165663T>C	ENST00000254657.3	-	17	2244	c.1965A>G	c.(1963-1965)gcA>gcG	p.A655A	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	655	CSNK1E binding domain. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		TGCCCGGCAGTGCCAGCGAGG	0.612											OREG0015336	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	471	0.0940495	0.0151	0.147	5008	,	,		16383	0.1399		0.1571	False		,,,				2504	0.0511				p.A655A		Atlas-SNP	.											.	PER2	85	.	0			c.A1965G						PASS	.	T		142,4264	98.5+/-137.1	1,140,2062	81.0	77.0	78.0		1965	-5.3	0.0	2	dbSNP_100	78	1188,7412	242.8+/-272.6	88,1012,3200	no	coding-synonymous	PER2	NM_022817.2		89,1152,5262	CC,CT,TT		13.814,3.2229,10.226		655/1256	239165663	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	8864	exon17			CGGCAGTGCCAGC	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"""period (Drosophila) homolog 2"", ""period homolog 2 (Drosophila)"""			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.1965A>G	2.37:g.239165663T>C		Somatic	70	0	0	2409	WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	37	CCDS2528.1																																																																																			T|0.893;C|0.107	0.107	strong		0.612	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817	
TCOF1	6949	hgsc.bcm.edu	37	5	149759096	149759096	+	Splice_Site	SNP	T	T	C	rs7713638	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149759096T>C	ENST00000504761.2	+	17	2660	c.2660T>C	c.(2659-2661)gTg>gCg	p.V887A	TCOF1_ENST00000439160.2_Splice_Site_p.V887A|TCOF1_ENST00000394269.3_Splice_Site_p.V887A|TCOF1_ENST00000513346.1_Splice_Site_p.V887A|TCOF1_ENST00000377797.3_Splice_Site_p.V887A|TCOF1_ENST00000451292.1_Splice_Site_p.V887A|TCOF1_ENST00000445265.2_Splice_Site_p.V810A|TCOF1_ENST00000506063.1_3'UTR|TCOF1_ENST00000323668.7_Splice_Site_p.V810A			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	887			V -> A (in dbSNP:rs7713638). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15019983, ECO:0000269|PubMed:8563749, ECO:0000269|PubMed:9042910, ECO:0000269|PubMed:9074926, ECO:0000269|PubMed:9096354}.		skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCCTCCAGGTGAAGCCTTCA	0.592													C|||	815	0.16274	0.2534	0.0937	5008	,	,		18970	0.1448		0.1302	False		,,,				2504	0.1411				p.V887A		Atlas-SNP	.											.	TCOF1	154	.	0			c.T2660C						PASS	.	C	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	1125,3281	708.1+/-407.6	134,857,1212	74.0	86.0	82.0		2429,2660,2660,2660,2429,2660	-7.5	0.0	5	dbSNP_116	82	1362,7238	744.5+/-407.2	93,1176,3031	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	64,64,64,64,64,64	227,2033,4243	CC,CT,TT		15.8372,25.5334,19.1219	benign,benign,benign,benign,benign,benign	810/1412,887/959,887/1489,887/1452,810/1413,887/1451	149759096	2487,10519	2203	4300	6503	SO:0001630	splice_region_variant	6949	exon17			TCCAGGTGAAGCC		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.2659-1T>C	5.37:g.149759096T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	318	0.14560439560439561	128	0.2601626016260163	39	0.10773480662983426	57	0.09965034965034965	94	0.12401055408970976	C	9.555	1.116955	0.20795	0.255334	0.158372	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000394269;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04	5.63	-7.47	0.01365	Treacher Collins syndrome, treacle (1);	1.169550	0.06424	N	0.722949	T	0.00012	0.0000	L	0.39020	1.185	0.80722	P	0.0	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.09377	0.004;0.001;0.001;0.001;0.001;0.001;0.001	T	0.04693	-1.0933	9	0.25751	T	0.34	0.6343	13.7244	0.62750	0.0:0.1277:0.0938:0.7784	rs7713638;rs60380481;rs7713638	396;887;810;887;887;810;887	B4DRA2;Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8;Q13428-5	.;.;.;.;TCOF_HUMAN;.;.	A	887;887;810;810;887;887;887;887;887	ENSP00000400939:V887A;ENSP00000367028:V887A;ENSP00000409944:V810A;ENSP00000325223:V810A;ENSP00000406888:V887A;ENSP00000377811:V887A;ENSP00000390717:V887A;ENSP00000421655:V887A;ENSP00000427484:V887A	ENSP00000325223:V810A	V	+	2	0	TCOF1	149739289	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-4.376000	0.00244	-1.851000	0.01168	-0.994000	0.02522	GTG	T|0.836;C|0.164	0.164	strong		0.592	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	Missense_Mutation
RHOQ	23433	hgsc.bcm.edu	37	2	46803354	46803354	+	Silent	SNP	C	C	T	rs41281473	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:46803354C>T	ENST00000238738.4	+	3	649	c.330C>T	c.(328-330)taC>taT	p.Y110Y	RP11-417F21.1_ENST00000506009.2_RNA|RHOQ_ENST00000465198.1_3'UTR	NM_012249.3	NP_036381.2	P17081	RHOQ_HUMAN	ras homolog family member Q	110					cellular response to insulin stimulus (GO:0032869)|cortical actin cytoskeleton organization (GO:0030866)|GTP catabolic process (GO:0006184)|insulin receptor signaling pathway (GO:0008286)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin filament (GO:0005884)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	GBD domain binding (GO:0032427)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|profilin binding (GO:0005522)			skin(2)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			TTAAGGAATACGCACCAAATG	0.413													C|||	31	0.0061901	0.0008	0.0086	5008	,	,		17891	0.0		0.0139	False		,,,				2504	0.0102				p.Y110Y		Atlas-SNP	.											.	RHOQ	22	.	0			c.C330T						PASS	.	C		25,4381	31.7+/-61.6	0,25,2178	81.0	77.0	78.0		330	-8.8	0.6	2	dbSNP_127	78	188,8412	82.9+/-145.4	2,184,4114	no	coding-synonymous	RHOQ	NM_012249.3		2,209,6292	TT,TC,CC		2.186,0.5674,1.6377		110/206	46803354	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	23433	exon3			GGAATACGCACCA	M31470	CCDS33191.1	2p21	2012-02-27	2012-02-27	2004-03-24	ENSG00000119729	ENSG00000119729			17736	protein-coding gene	gene with protein product		605857	"""RAS-like, family 7, member A"", ""ras homolog gene family, member Q"""	RASL7A, ARHQ		2108320	Standard	NM_012249		Approved	TC10	uc002rva.3	P17081	OTTHUMG00000150653	ENST00000238738.4:c.330C>T	2.37:g.46803354C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	211	92	0.436019	NM_012249	D6W5A6|Q0VGN1|Q52LS8|Q53SJ1|Q6NS39|Q6P146|Q7Z480	Silent	SNP	ENST00000238738.4	37	CCDS33191.1																																																																																			C|0.985;T|0.015	0.015	strong		0.413	RHOQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319409.1	NM_012249	
PGR	5241	hgsc.bcm.edu	37	11	100933412	100933412	+	Missense_Mutation	SNP	C	C	A	rs1042838	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:100933412C>A	ENST00000325455.5	-	4	3431	c.1978G>T	c.(1978-1980)Gtg>Ttg	p.V660L	PGR_ENST00000263463.5_Intron|PGR_ENST00000534013.1_Missense_Mutation_p.V66L	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	660			V -> L (in dbSNP:rs1042838). {ECO:0000269|PubMed:12644308, ECO:0000269|PubMed:3551956, ECO:0000269|Ref.3}.		cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	GGAACGCCCACTGGCTGTGGG	0.418													C|||	358	0.0714856	0.0061	0.1369	5008	,	,		15303	0.0099		0.1789	False		,,,				2504	0.0665				p.V660L	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.G1978T	GRCh37	CM043326	PGR	M	rs1042838	PASS	.	C	LEU/VAL,LEU/VAL	132,4274	95.3+/-134.0	1,130,2072	124.0	108.0	113.0		1978,1486	4.5	1.0	11	dbSNP_86	113	1414,7186	272.8+/-290.3	107,1200,2993	yes	missense,missense	PGR	NM_000926.4,NM_001202474.1	32,32	108,1330,5065	AA,AC,CC		16.4419,2.9959,11.8868	benign,benign	660/934,496/770	100933412	1546,11460	2203	4300	6503	SO:0001583	missense	5241	exon4			CGCCCACTGGCTG	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.1978G>T	11.37:g.100933412C>A	ENSP00000325120:p.Val660Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	207	0.09478021978021978	6	0.012195121951219513	54	0.14917127071823205	4	0.006993006993006993	143	0.18865435356200527	C	11.58	1.681111	0.29872	0.029959	0.164419	ENSG00000082175	ENST00000325455;ENST00000534013	D;D	0.86366	-1.67;-2.11	5.41	4.49	0.54785	Nuclear hormone receptor, ligand-binding (1);	0.704963	0.13868	N	0.357217	T	0.00384	0.0012	L	0.43757	1.38	0.09310	P	0.99999999182884	B	0.12630	0.006	B	0.09377	0.004	T	0.23940	-1.0174	9	0.27082	T	0.32	.	5.3111	0.15831	0.1488:0.6304:0.1439:0.077	rs1042838;rs11571223;rs17656622;rs52792239;rs56653495;rs1042838	660	P06401	PRGR_HUMAN	L	660;66	ENSP00000325120:V660L;ENSP00000436561:V66L	ENSP00000325120:V660L	V	-	1	0	PGR	100438622	0.159000	0.22864	0.998000	0.56505	0.714000	0.41099	0.674000	0.25218	2.512000	0.84698	0.591000	0.81541	GTG	C|0.893;A|0.107	0.107	strong		0.418	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
MYH14	79784	hgsc.bcm.edu	37	19	50795617	50795617	+	Silent	SNP	C	C	T	rs147447646	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50795617C>T	ENST00000596571.1	+	34	5104	c.5104C>T	c.(5104-5106)Ctg>Ttg	p.L1702L	MYH14_ENST00000425460.1_Silent_p.L1710L|MYH14_ENST00000601313.1_Silent_p.L1743L|MYH14_ENST00000598205.1_Silent_p.L1710L|MYH14_ENST00000440075.2_Silent_p.L1743L|MYH14_ENST00000376970.2_Silent_p.L1735L|MYH14_ENST00000262269.8_Silent_p.L1743L			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1702					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CCTCAAGGGCCTGGAGGCTGA	0.642													C|||	5	0.000998403	0.0	0.0014	5008	,	,		16103	0.0		0.004	False		,,,				2504	0.0				p.L1743L		Atlas-SNP	.											.	MYH14	261	.	0			c.C5227T						PASS	.	C	,,	4,4008		0,4,2002	14.0	17.0	16.0		5128,5227,5104	1.6	1.0	19	dbSNP_134	16	28,8352		0,28,4162	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	0,32,6164	TT,TC,CC		0.3341,0.0997,0.2582	,,	1710/2004,1743/2037,1702/1996	50795617	32,12360	2006	4190	6196	SO:0001819	synonymous_variant	79784	exon37			AAGGGCCTGGAGG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.5104C>T	19.37:g.50795617C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			C|0.998;T|0.002	0.002	strong		0.642	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
ZDHHC8	29801	hgsc.bcm.edu	37	22	20131121	20131121	+	Silent	SNP	G	G	C	rs145100111	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:20131121G>C	ENST00000334554.7	+	10	2109	c.1968G>C	c.(1966-1968)ccG>ccC	p.P656P	ZDHHC8_ENST00000320602.7_Silent_p.P564P|ZDHHC8_ENST00000405930.3_Silent_p.P656P	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	656					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					GCAACGCCCCGGGGCCCCGGC	0.716													G|||	15	0.00299521	0.0008	0.0043	5008	,	,		14170	0.0		0.0089	False		,,,				2504	0.002				p.P656P		Atlas-SNP	.											.	ZDHHC8	77	.	0			c.G1968C						PASS	.	G	,	13,4351		0,13,2169	15.0	17.0	16.0		1968,1968	-7.4	0.4	22	dbSNP_134	16	93,8485		0,93,4196	no	coding-synonymous,coding-synonymous	ZDHHC8	NM_001185024.1,NM_013373.3	,	0,106,6365	CC,CG,GG		1.0842,0.2979,0.819	,	656/779,656/766	20131121	106,12836	2182	4289	6471	SO:0001819	synonymous_variant	29801	exon10			CGCCCCGGGGCCC	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"""Zinc fingers, DHHC-type"""	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.1968G>C	22.37:g.20131121G>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	37	CCDS13776.1																																																																																			G|0.993;C|0.007	0.007	strong		0.716	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373	
OR5W2	390148	hgsc.bcm.edu	37	11	55681416	55681416	+	Missense_Mutation	SNP	A	A	G	rs17596422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55681416A>G	ENST00000344514.1	-	1	642	c.643T>C	c.(643-645)Ttc>Ctc	p.F215L		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	215			F -> L (in dbSNP:rs17596422).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TAAGAAATGAAAACTCCTGAA	0.418													G|||	165	0.0329473	0.0053	0.0331	5008	,	,		18554	0.003		0.0905	False		,,,				2504	0.0419				p.F215L	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											OR5W2,NS,carcinoma,+2,1	OR5W2	112	1	0			c.T643C						PASS	.	G	LEU/PHE	69,4333	815.7+/-416.2	0,69,2132	56.0	62.0	60.0		643	4.1	0.0	11	dbSNP_123	60	683,7909	786.9+/-407.6	34,615,3647	yes	missense	OR5W2	NM_001001960.1	22	34,684,5779	GG,GA,AA		7.9493,1.5675,5.7873	benign	215/311	55681416	752,12242	2201	4296	6497	SO:0001583	missense	390148	exon1			AAATGAAAACTCC	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.643T>C	11.37:g.55681416A>G	ENSP00000342448:p.Phe215Leu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	77	0.035256410256410256	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	67	0.08839050131926121	G	0.817	-0.750051	0.03041	0.015675	0.079493	ENSG00000187612	ENST00000344514	T	0.00017	9.09	5.0	4.08	0.47627	GPCR, rhodopsin-like superfamily (1);	0.442488	0.16646	N	0.205437	T	0.00012	0.0000	N	0.00131	-2.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37888	-0.9686	10	0.02654	T	1	.	5.0777	0.14640	0.1768:0.0:0.6594:0.1638	rs17596422;rs52792295;rs59501628;rs17596422	215	Q8NH69	OR5W2_HUMAN	L	215	ENSP00000342448:F215L	ENSP00000342448:F215L	F	-	1	0	OR5W2	55437992	0.000000	0.05858	0.004000	0.12327	0.718000	0.41266	-0.530000	0.06179	0.514000	0.28300	-0.263000	0.10527	TTC	A|0.952;G|0.048	0.048	strong		0.418	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
Unknown	0	hgsc.bcm.edu	37	2	97313565	97313565	+	IGR	SNP	G	G	A	rs200413243		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:97313565G>A								KANSL3 (9450 upstream) : FER1L5 (22389 downstream)																							AAACAACCAAGTGAGGTCCTT	0.542																																					p.S94N		Atlas-SNP	.											.	FER1L5	113	.	0			c.G281A						PASS	.		ASN/SER	1,1383		0,1,691	168.0	149.0	155.0		281	-4.4	0.0	2		155	7,3175		0,7,1584	yes	missense	FER1L5	NM_001113382.1	46	0,8,2275	AA,AG,GG		0.22,0.0723,0.1752	benign	94/2094	97313565	8,4558	692	1591	2283	SO:0001628	intergenic_variant	90342	exon4			AACCAAGTGAGGT																													2.37:g.97313565G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	130	51	0.392308	NM_001113382		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	g	0.125	-1.121243	0.01785	7.23E-4	0.0022	ENSG00000214272	ENST00000342152;ENST00000414152;ENST00000436930	.	.	.	4.7	-4.38	0.03622	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	1.475620	0.04180	N	0.326275	T	0.25269	0.0614	N	0.19112	0.55	.	.	.	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.19353	-1.0308	8	0.37606	T	0.19	.	6.2141	0.20646	0.5269:0.2781:0.195:0.0	.	94;24	A0AVI2;A0AVI2-3	FR1L5_HUMAN;.	N	24;94;94	.	ENSP00000441631:S24N	S	+	2	0	FER1L5	96677292	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.186000	0.09670	-0.725000	0.04901	0.457000	0.33378	AGT	.	.	weak	0	0.542								
C9orf78	51759	hgsc.bcm.edu	37	9	132591509	132591509	+	Silent	SNP	A	A	G	rs3818553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:132591509A>G	ENST00000372447.3	-	8	806	c.753T>C	c.(751-753)ggT>ggC	p.G251G	C9orf78_ENST00000461762.1_5'UTR	NM_016520.2	NP_057604.1	Q9NZ63	CI078_HUMAN	chromosome 9 open reading frame 78	251						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.G251G(1)		kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)	13		Ovarian(14;0.00556)				TCTCCGTGTCACCTACTCTCA	0.597													G|||	1190	0.23762	0.2194	0.2147	5008	,	,		17171	0.2143		0.2734	False		,,,				2504	0.2658				p.G251G		Atlas-SNP	.											C9orf78,NS,carcinoma,0,1	C9orf78	26	1	1	Substitution - coding silent(1)	stomach(1)	c.T753C						PASS	.	G		995,3411	730.4+/-410.2	109,777,1317	62.0	60.0	61.0		753	-11.9	0.2	9	dbSNP_107	61	2145,6455	714.0+/-406.0	276,1593,2431	no	coding-synonymous	C9orf78	NM_016520.2		385,2370,3748	GG,GA,AA		24.9419,22.5828,24.1427		251/290	132591509	3140,9866	2203	4300	6503	SO:0001819	synonymous_variant	51759	exon8			CGTGTCACCTACT	BC017570	CCDS6931.1	9q34.2	2012-03-16			ENSG00000136819	ENSG00000136819			24932	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 59"""					11042152, 12097419	Standard	NM_016520		Approved	HSPC220, HCA59	uc004byp.3	Q9NZ63	OTTHUMG00000020796	ENST00000372447.3:c.753T>C	9.37:g.132591509A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_016520	B3KPX8|Q8WVU6|Q9NT39	Silent	SNP	ENST00000372447.3	37	CCDS6931.1	516	0.23626373626373626	95	0.19308943089430894	82	0.2265193370165746	127	0.22202797202797203	212	0.2796833773087071	G	9.641	1.139016	0.21205	0.225828	0.249419	ENSG00000136819	ENST00000435276	.	.	.	5.95	-11.9	0.00025	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999997752	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.5548	0.22454	0.2478:0.2074:0.465:0.0798	rs3818553;rs3818553	.	.	.	R	176	.	.	X	-	1	0	C9orf78	131631330	0.000000	0.05858	0.217000	0.23759	0.854000	0.48673	-2.932000	0.00688	-2.722000	0.00388	-1.140000	0.01884	TGA	A|0.766;G|0.234	0.234	strong		0.597	C9orf78-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054625.1	NM_016520	
PLXNB1	5364	hgsc.bcm.edu	37	3	48456404	48456404	+	Missense_Mutation	SNP	C	C	T	rs149435305	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:48456404C>T	ENST00000358536.4	-	21	4282	c.4013G>A	c.(4012-4014)cGc>cAc	p.R1338H	PLXNB1_ENST00000358459.4_Missense_Mutation_p.R1155H|PLXNB1_ENST00000296440.6_Missense_Mutation_p.R1338H|PLXNB1_ENST00000456774.1_Missense_Mutation_p.R1155H|PLXNB1_ENST00000465117.1_5'UTR|PLXNB1_ENST00000448774.2_Intron	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1338	IPT/TIG 3.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GGCAGGTGTGCGGCACGTGAT	0.582													C|||	3	0.000599042	0.0023	0.0	5008	,	,		18641	0.0		0.0	False		,,,				2504	0.0				p.R1338H		Atlas-SNP	.											PLXNB1,colon,carcinoma,0,1	PLXNB1	150	1	0			c.G4013A						scavenged	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	62.0	69.0	67.0		4013,4013	-0.4	0.7	3	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	PLXNB1	NM_001130082.1,NM_002673.4	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	1338/2136,1338/2136	48456404	1,13005	2203	4300	6503	SO:0001583	missense	5364	exon21			GGTGTGCGGCACG	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"""Plexins"""	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.4013G>A	3.37:g.48456404C>T	ENSP00000351338:p.Arg1338His	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	152	3	0.0197368	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	37	CCDS2765.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	6.067	0.380620	0.11466	0.0	1.16E-4	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06	5.02	-0.387	0.12463	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.652062	0.14279	N	0.329640	T	0.61553	0.2356	L	0.48642	1.525	0.36516	D	0.869899	B;B	0.28419	0.006;0.211	B;B	0.18561	0.007;0.022	T	0.50259	-0.8849	10	0.14656	T	0.56	.	5.2327	0.15430	0.1393:0.3559:0.0:0.5048	.	1338;1155	O43157;O43157-2	PLXB1_HUMAN;.	H	1338;1155;1338;1155	ENSP00000296440:R1338H;ENSP00000351242:R1155H;ENSP00000351338:R1338H;ENSP00000414199:R1155H	ENSP00000296440:R1338H	R	-	2	0	PLXNB1	48431408	0.515000	0.26210	0.729000	0.30791	0.448000	0.32197	0.306000	0.19279	-0.170000	0.10816	-0.126000	0.14955	CGC	C|0.999;T|0.001	0.001	strong		0.582	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	
OR2F1	26211	hgsc.bcm.edu	37	7	143657801	143657801	+	Silent	SNP	A	A	G	rs2072166	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143657801A>G	ENST00000392899.1	+	1	775	c.738A>G	c.(736-738)acA>acG	p.T246T	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	246					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					CTCACCTCACAGTGGTTGCCC	0.488													a|||	2291	0.457468	0.6687	0.415	5008	,	,		22020	0.5744		0.3231	False		,,,				2504	0.2198				p.T246T		Atlas-SNP	.											.	OR2F1	71	.	0			c.A738G						PASS	.	G		2672,1734	519.3+/-369.9	816,1040,347	158.0	130.0	140.0		738	-11.1	0.0	7	dbSNP_96	140	2839,5761	675.2+/-403.2	481,1877,1942	no	coding-synonymous	OR2F1	NM_012369.2		1297,2917,2289	GG,GA,AA		33.0116,39.3554,42.3728		246/318	143657801	5511,7495	2203	4300	6503	SO:0001819	synonymous_variant	26211	exon1			CCTCACAGTGGTT	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"""GPCR / Class A : Olfactory receptors"""	8246	protein-coding gene	gene with protein product		608497	"""olfactory receptor, family 2, subfamily F, member 1"""	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.738A>G	7.37:g.143657801A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	176	94	0.534091	NM_012369	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Silent	SNP	ENST00000392899.1	37	CCDS5887.1																																																																																			A|0.568;G|0.432	0.432	strong		0.488	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1		
PLA2R1	22925	hgsc.bcm.edu	37	2	160879259	160879259	+	Missense_Mutation	SNP	C	C	T	rs33985939	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160879259C>T	ENST00000283243.7	-	7	1417	c.1211G>A	c.(1210-1212)cGt>cAt	p.R404H	PLA2R1_ENST00000392771.1_Missense_Mutation_p.R404H	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	404	C-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00040}.		R -> H (in dbSNP:rs33985939).		cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CTGACAAGAACGCAGAGCCTC	0.458													C|||	186	0.0371406	0.003	0.0303	5008	,	,		16219	0.0179		0.0845	False		,,,				2504	0.0593				p.R404H		Atlas-SNP	.											.	PLA2R1	153	.	0			c.G1211A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	58,4348	57.4+/-93.9	0,58,2145	156.0	143.0	148.0		1211,1211,1211	-3.7	0.8	2	dbSNP_126	148	688,7912	171.0+/-222.0	31,626,3643	yes	missense,missense,missense	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	29,29,29	31,684,5788	TT,TC,CC		8.0,1.3164,5.7358	benign,benign,benign	404/1325,404/1462,404/1464	160879259	746,12260	2203	4300	6503	SO:0001583	missense	22925	exon7			CAAGAACGCAGAG	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.1211G>A	2.37:g.160879259C>T	ENSP00000283243:p.Arg404His	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	198	100	0.50505	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	95	0.043498168498168496	2	0.0040650406504065045	10	0.027624309392265192	12	0.02097902097902098	71	0.09366754617414248	C	0.027	-1.363286	0.01235	0.013164	0.08	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.18338	2.22;2.22	5.19	-3.66	0.04489	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.866082	0.10649	N	0.650092	T	0.00271	0.0008	N	0.05383	-0.06	0.20873	N	0.999832	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.36841	-0.9731	10	0.31617	T	0.26	.	7.2117	0.25937	0.1366:0.4266:0.0:0.4367	rs33985939	404;404;404	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	H	404	ENSP00000283243:R404H;ENSP00000376524:R404H	ENSP00000283243:R404H	R	-	2	0	PLA2R1	160587505	0.355000	0.24921	0.794000	0.32065	0.042000	0.13812	0.003000	0.13083	-0.764000	0.04651	-1.105000	0.02106	CGT	C|0.949;T|0.051	0.051	strong		0.458	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
MAP10	54627	hgsc.bcm.edu	37	1	232943775	232943775	+	Silent	SNP	C	C	T	rs147903928		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:232943775C>T	ENST00000418460.1	+	1	3133	c.3006C>T	c.(3004-3006)tcC>tcT	p.S1002S		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	860					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										CAAATGTGTCCGAACTTAATG	0.378													C|||	1	0.000199681	0.0	0.0	5008	,	,		17059	0.0		0.001	False		,,,				2504	0.0				p.S1002S		Atlas-SNP	.											.	.	.	.	0			c.C3006T						PASS	.	C		0,3776		0,0,1888	133.0	133.0	133.0		3006	-2.9	1.0	1	dbSNP_134	133	10,8194		0,10,4092	no	coding-synonymous	KIAA1383	NM_019090.2		0,10,5980	TT,TC,CC		0.1219,0.0,0.0835		1002/1048	232943775	10,11970	1888	4102	5990	SO:0001819	synonymous_variant	54627	exon1			TGTGTCCGAACTT	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.3006C>T	1.37:g.232943775C>T		Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	294	138	0.469388	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Silent	SNP	ENST00000418460.1	37	CCDS44334.1																																																																																			C|0.999;T|0.001	0.001	strong		0.378	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
UGGT1	56886	hgsc.bcm.edu	37	2	128939799	128939799	+	Silent	SNP	C	C	T	rs17178720	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:128939799C>T	ENST00000259253.6	+	37	4226	c.4179C>T	c.(4177-4179)gaC>gaT	p.D1393D	UGGT1_ENST00000375990.3_Silent_p.D1369D	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1393	Glucosyltransferase. {ECO:0000250}.				'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GAGAAATGGACGGCTACAGGT	0.458													C|||	356	0.0710863	0.0061	0.1427	5008	,	,		18454	0.0		0.1869	False		,,,				2504	0.0624				p.D1393D		Atlas-SNP	.											.	UGGT1	126	.	0			c.C4179T						PASS	.	C		149,4257	104.7+/-143.2	0,149,2054	112.0	114.0	114.0		4179	-3.3	1.0	2	dbSNP_123	114	1622,6978	300.8+/-305.1	146,1330,2824	no	coding-synonymous	UGGT1	NM_020120.3		146,1479,4878	TT,TC,CC		18.8605,3.3818,13.6168		1393/1556	128939799	1771,11235	2203	4300	6503	SO:0001819	synonymous_variant	56886	exon37			AATGGACGGCTAC	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.4179C>T	2.37:g.128939799C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	183	91	0.497268	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																			C|0.882;T|0.118	0.118	strong		0.458	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
TACSTD2	4070	hgsc.bcm.edu	37	1	59042388	59042388	+	Missense_Mutation	SNP	C	C	G	rs1062964	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:59042388C>G	ENST00000371225.2	-	1	778	c.441G>C	c.(439-441)gaG>gaC	p.E147D		NM_002353.2	NP_002344.2	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	147			E -> D (in dbSNP:rs1062964). {ECO:0000269|PubMed:2911574}.		cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell motility (GO:2000146)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of stem cell differentiation (GO:2000738)|regulation of epithelial cell proliferation (GO:0050678)|ureteric bud morphogenesis (GO:0060675)|visual perception (GO:0007601)	basal plasma membrane (GO:0009925)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)					all_cancers(7;6.54e-05)					TGCGCACCAGCTCATCGCAGC	0.682													C|||	189	0.0377396	0.0628	0.0187	5008	,	,		14604	0.0		0.0408	False		,,,				2504	0.0532				p.E147D		Atlas-SNP	.											.	TACSTD2	6	.	0			c.G441C						PASS	.	C	ASP/GLU	307,4091		10,287,1902	29.0	26.0	27.0		441	2.6	1.0	1	dbSNP_86	27	476,8120		16,444,3838	yes	missense	TACSTD2	NM_002353.2	45	26,731,5740	GG,GC,CC		5.5375,6.9804,6.0259	possibly-damaging	147/324	59042388	783,12211	2199	4298	6497	SO:0001583	missense	4070	exon1			CACCAGCTCATCG	X77753	CCDS609.1	1p32	2008-02-05			ENSG00000184292	ENSG00000184292			11530	protein-coding gene	gene with protein product		137290		M1S1		8382772, 11306819	Standard	NM_002353		Approved	TROP2, GA733-1, EGP-1	uc001cyz.4	P09758	OTTHUMG00000010067	ENST00000371225.2:c.441G>C	1.37:g.59042388C>G	ENSP00000360269:p.Glu147Asp	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_002353	Q15658|Q6FG48|Q7Z7Q4|Q96QD2	Missense_Mutation	SNP	ENST00000371225.2	37	CCDS609.1	61	0.027930402930402932	24	0.04878048780487805	7	0.019337016574585635	0	0.0	30	0.0395778364116095	C	14.89	2.669359	0.47677	0.069804	0.055375	ENSG00000184292	ENST00000371225	T	0.63913	-0.07	4.54	2.58	0.30949	Thyroglobulin type-1 (2);	0.120979	0.56097	D	0.000028	T	0.09379	0.0231	M	0.69823	2.125	0.39608	D	0.969847	B	0.14012	0.009	B	0.15052	0.012	T	0.33954	-0.9848	10	0.62326	D	0.03	-26.8598	8.3875	0.32510	0.0:0.6238:0.294:0.0822	rs1062964;rs1062964	147	P09758	TACD2_HUMAN	D	147	ENSP00000360269:E147D	ENSP00000360269:E147D	E	-	3	2	TACSTD2	58814976	0.998000	0.40836	1.000000	0.80357	0.878000	0.50629	0.370000	0.20433	0.472000	0.27344	0.561000	0.74099	GAG	C|0.953;G|0.047	0.047	strong		0.682	TACSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027818.1	NM_002353	
MOV10L1	54456	hgsc.bcm.edu	37	22	50530501	50530501	+	Missense_Mutation	SNP	A	A	T	rs9617066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50530501A>T	ENST00000262794.5	+	2	252	c.169A>T	c.(169-171)Atg>Ttg	p.M57L	MOV10L1_ENST00000475190.1_3'UTR|MOV10L1_ENST00000395843.1_De_novo_Start_InFrame|MOV10L1_ENST00000395858.3_Missense_Mutation_p.M57L|MOV10L1_ENST00000540615.1_Missense_Mutation_p.M37L|MOV10L1_ENST00000545383.1_Missense_Mutation_p.M57L	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	57			M -> L (in dbSNP:rs9617066).		ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.M57L(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GATTGATGATATGATCTACTT	0.428													T|||	1255	0.250599	0.1301	0.3833	5008	,	,		21379	0.255		0.2356	False		,,,				2504	0.3303				p.M57L		Atlas-SNP	.											MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	1	Substitution - Missense(1)	stomach(1)	c.A169T						PASS	.	T	LEU/MET,LEU/MET,LEU/MET	699,3707	760.7+/-413.0	60,579,1564	336.0	276.0	297.0		169,109,169	-1.0	0.1	22	dbSNP_119	297	2048,6552	718.9+/-406.2	247,1554,2499	yes	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	15,15,15	307,2133,4063	TT,TA,AA		23.814,15.8647,21.121	benign,benign,benign	57/1166,37/1166,57/1212	50530501	2747,10259	2203	4300	6503	SO:0001583	missense	54456	exon2			GATGATATGATCT	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.169A>T	22.37:g.50530501A>T	ENSP00000262794:p.Met57Leu	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	230	107	0.465217	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	530	0.24267399267399267	58	0.11788617886178862	121	0.3342541436464088	178	0.3111888111888112	173	0.22823218997361477	T	1.958	-0.439463	0.04636	0.158647	0.23814	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615;ENST00000428564	D;D;T;D	0.83992	-1.6;-1.6;-1.18;-1.79	5.21	-0.971	0.10303	.	0.589282	0.17323	N	0.178429	T	0.00012	0.0000	N	0.00389	-1.56	0.58432	P	4.000000000004E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.11867	-1.0570	9	0.02654	T	1	-6.8196	4.8754	0.13653	0.3029:0.3448:0.0:0.3523	rs9617066;rs17846341;rs17859375;rs52817043;rs9617066	37;37;57;57	F5H403;E7EPK8;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	L	57;57;57;37;37	ENSP00000438978:M57L;ENSP00000262794:M57L;ENSP00000379199:M57L;ENSP00000438542:M37L	ENSP00000262794:M57L	M	+	1	0	MOV10L1	48872628	0.000000	0.05858	0.117000	0.21633	0.988000	0.76386	-1.156000	0.03160	-0.198000	0.10333	-0.265000	0.10407	ATG	A|0.776;T|0.224	0.224	strong		0.428	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
OR1S1	219959	hgsc.bcm.edu	37	11	57982584	57982584	+	Missense_Mutation	SNP	T	T	C	rs1966835	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57982584T>C	ENST00000309433.6	+	1	368	c.368T>C	c.(367-369)aTt>aCt	p.I123T		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	123			I -> T (in dbSNP:rs1966835).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTTGTCGTCATTGACAATTTG	0.448													T|||	2620	0.523163	0.2844	0.5418	5008	,	,		22315	0.8036		0.4225	False		,,,				2504	0.6472				p.I123T		Atlas-SNP	.											.	OR1S1	139	.	0			c.T368C						PASS	.	T	THR/ILE	1323,3079	445.3+/-347.6	197,929,1075	183.0	172.0	176.0		368	-2.6	0.4	11	dbSNP_92	176	3643,4949	524.4+/-380.5	785,2073,1438	no	missense	OR1S1	NM_001004458.1	89	982,3002,2513	CC,CT,TT		42.3999,30.0545,38.2176	benign	123/326	57982584	4966,8028	2201	4296	6497	SO:0001583	missense	219959	exon1			TCGTCATTGACAA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.368T>C	11.37:g.57982584T>C	ENSP00000311688:p.Ile123Thr	Somatic	308	1	0.00324675		WXS	Illumina HiSeq	Phase_I	386	174	0.450777	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1080	0.4945054945054945	147	0.29878048780487804	187	0.5165745856353591	432	0.7552447552447552	314	0.41424802110817943	T	0.360	-0.939776	0.02322	0.300545	0.423999	ENSG00000172774	ENST00000309433	T	0.01685	4.69	3.27	-2.56	0.06268	GPCR, rhodopsin-like superfamily (1);	0.522752	0.16164	N	0.226633	T	0.00012	0.0000	N	0.01515	-0.825	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.16394	-1.0404	9	0.62326	D	0.03	.	1.4226	0.02315	0.1409:0.3037:0.1431:0.4123	rs1966835;rs52810501;rs1966835	123	Q8NH92	OR1S1_HUMAN	T	123	ENSP00000311688:I123T	ENSP00000311688:I123T	I	+	2	0	OR1S1	57739160	0.000000	0.05858	0.354000	0.25760	0.142000	0.21351	-1.070000	0.03440	-0.406000	0.07588	-1.267000	0.01435	ATT	T|0.569;C|0.431	0.431	strong		0.448	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
ALG1L	200810	hgsc.bcm.edu	37	3	125649403	125649403	+	Silent	SNP	C	C	A	rs7615952	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:125649403C>A	ENST00000340333.3	-	5	508	c.345G>T	c.(343-345)ctG>ctT	p.L115L	FAM86JP_ENST00000485843.1_RNA	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like	115							transferase activity, transferring glycosyl groups (GO:0016757)			large_intestine(2)|lung(2)	4						TGGCTACCTGCAGAGCTGCCA	0.577													.|||	1172	0.234026	0.4841	0.1527	5008	,	,		17875	0.1071		0.172	False		,,,				2504	0.1483				p.L135L		Atlas-SNP	.											.	ALG1L	12	.	0			c.G405T						PASS	.	C	,	1082,1666		199,684,491	60.0	56.0	57.0		345,405	0.0	0.8	3	dbSNP_116	57	729,3933		73,583,1675	no	coding-synonymous,coding-synonymous	ALG1L	NM_001015050.2,NM_001195223.1	,	272,1267,2166	AA,AC,CC		15.6371,39.3741,24.4399	,	115/188,135/208	125649403	1811,5599	1374	2331	3705	SO:0001819	synonymous_variant	200810	exon6			TACCTGCAGAGCT	BC073816	CCDS33840.1, CCDS74998.1	3q21.2	2013-02-22	2013-02-22		ENSG00000189366	ENSG00000189366		"""Glycosyltransferase group 1 domain containing"""	33721	protein-coding gene	gene with protein product	"""asparagine-linked glycosylation 1-like 1"""		"""asparagine-linked glycosylation 1-like"""				Standard	NM_001015050		Approved	ALG1L1	uc003eig.2	Q6GMV1	OTTHUMG00000159588	ENST00000340333.3:c.345G>T	3.37:g.125649403C>A		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_001195223	D3DNA5	Silent	SNP	ENST00000340333.3	37	CCDS33840.1																																																																																			.	.	weak		0.577	ALG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356347.1	NM_001015050	
MOV10L1	54456	hgsc.bcm.edu	37	22	50546666	50546666	+	Missense_Mutation	SNP	C	C	T	rs3810971	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50546666C>T	ENST00000262794.5	+	4	627	c.544C>T	c.(544-546)Cgc>Tgc	p.R182C	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Missense_Mutation_p.R182C|MOV10L1_ENST00000540615.1_Missense_Mutation_p.R162C|MOV10L1_ENST00000545383.1_Missense_Mutation_p.R182C	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	182			R -> C (in dbSNP:rs3810971).		ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GAGATACAAGCGCGTGGACAA	0.617													C|||	1236	0.246805	0.1225	0.3833	5008	,	,		18174	0.248		0.2346	False		,,,				2504	0.3292				p.R182C		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C544T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	665,3741	278.7+/-274.4	55,555,1593	51.0	42.0	45.0		544,484,544	4.2	1.0	22	dbSNP_107	45	2052,6548	353.0+/-328.9	248,1556,2496	yes	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	180,180,180	303,2111,4089	TT,TC,CC		23.8605,15.0931,20.8904	probably-damaging,probably-damaging,probably-damaging	182/1166,162/1166,182/1212	50546666	2717,10289	2203	4300	6503	SO:0001583	missense	54456	exon4			TACAAGCGCGTGG	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.544C>T	22.37:g.50546666C>T	ENSP00000262794:p.Arg182Cys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	129	49	0.379845	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	525	0.2403846153846154	54	0.10975609756097561	122	0.3370165745856354	177	0.3094405594405594	172	0.22691292875989447	C	18.20	3.570145	0.65765	0.150931	0.238605	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615;ENST00000428564	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	5.28	4.2	0.49525	.	0.055074	0.64402	D	0.000001	T	0.00012	0.0000	M	0.72894	2.215	0.09310	P	0.9999999999998017	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.68765	0.96;0.938;0.912;0.912	T	0.23762	-1.0179	9	0.87932	D	0	-10.4023	10.4014	0.44231	0.3131:0.6869:0.0:0.0	rs3810971;rs17836603;rs52835906;rs61218086;rs3810971	162;162;182;182	F5H403;E7EPK8;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	C	182;182;182;162;162	ENSP00000438978:R182C;ENSP00000262794:R182C;ENSP00000379199:R182C;ENSP00000438542:R162C	ENSP00000262794:R182C	R	+	1	0	MOV10L1	48888793	1.000000	0.71417	0.951000	0.38953	0.563000	0.35712	2.470000	0.45119	2.480000	0.83734	0.644000	0.83932	CGC	C|0.782;T|0.218	0.218	strong		0.617	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
THAP9	79725	hgsc.bcm.edu	37	4	83838262	83838262	+	Missense_Mutation	SNP	G	G	T	rs897945	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:83838262G>T	ENST00000302236.5	+	5	948	c.897G>T	c.(895-897)ttG>ttT	p.L299F	LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	299			L -> F (in dbSNP:rs897945). {ECO:0000269|PubMed:14702039}.		DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				GTCACAGTTTGCAGGGGTTTA	0.413													G|||	1629	0.32528	0.0651	0.6484	5008	,	,		20952	0.2004		0.5507	False		,,,				2504	0.3446				p.L299F		Atlas-SNP	.											THAP9,colon,carcinoma,+2,1	THAP9	65	1	0			c.G897T						PASS	.	G	PHE/LEU	666,3740	282.2+/-276.4	68,530,1605	136.0	127.0	130.0		897	2.8	1.0	4	dbSNP_86	130	4799,3801	613.2+/-396.1	1359,2081,860	yes	missense	THAP9	NM_024672.4	22	1427,2611,2465	TT,TG,GG		44.1977,15.1158,42.0191	probably-damaging	299/904	83838262	5465,7541	2203	4300	6503	SO:0001583	missense	79725	exon5			CAGTTTGCAGGGG	AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"""THAP (C2CH-type zinc finger) domain containing"""	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.897G>T	4.37:g.83838262G>T	ENSP00000305533:p.Leu299Phe	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_024672	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	37	CCDS3598.1	801	0.36675824175824173	32	0.06504065040650407	220	0.6077348066298343	124	0.21678321678321677	425	0.5606860158311345	G	7.015	0.557611	0.13436	0.151158	0.558023	ENSG00000168152	ENST00000302236;ENST00000536314	T	0.46063	0.88	3.7	2.85	0.33270	.	1.365610	0.05330	N	0.528170	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.999999999612521	P	0.48162	0.906	B	0.38378	0.272	T	0.41251	-0.9519	9	0.20519	T	0.43	-2.6801	9.1917	0.37204	0.104:0.0:0.896:0.0	rs897945;rs17354399;rs52815233;rs59971666;rs897945	299	Q9H5L6	THAP9_HUMAN	F	299	ENSP00000305533:L299F	ENSP00000305533:L299F	L	+	3	2	THAP9	84057286	0.829000	0.29322	0.999000	0.59377	0.224000	0.24922	0.295000	0.19065	1.141000	0.42275	0.650000	0.86243	TTG	G|0.624;T|0.375	0.375	strong		0.413	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672	
CELSR3	1951	hgsc.bcm.edu	37	3	48677895	48677895	+	Silent	SNP	A	A	T	rs1264195	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:48677895A>T	ENST00000164024.4	-	34	9403	c.9123T>A	c.(9121-9123)gcT>gcA	p.A3041A	CELSR3_ENST00000544264.1_Silent_p.A3046A	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	3041					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CAGCTGGCACAGCACGGTGGC	0.637													A|||	70	0.0139776	0.0023	0.0173	5008	,	,		13644	0.0		0.0487	False		,,,				2504	0.0061				p.A3041A		Atlas-SNP	.											.	CELSR3	237	.	0			c.T9123A						PASS	.	A		31,4375		0,31,2172	31.0	34.0	33.0		9123	-8.6	1.0	3	dbSNP_87	33	355,8223		10,335,3944	no	coding-synonymous	CELSR3	NM_001407.2		10,366,6116	TT,TA,AA		4.1385,0.7036,2.9729		3041/3313	48677895	386,12598	2203	4289	6492	SO:0001819	synonymous_variant	1951	exon34			TGGCACAGCACGG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.9123T>A	3.37:g.48677895A>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	248	138	0.556452	NM_001407	O75092	Silent	SNP	ENST00000164024.4	37	CCDS2775.1																																																																																			A|0.976;T|0.024	0.024	strong		0.637	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
IRS4	8471	hgsc.bcm.edu	37	X	107978343	107978343	+	Missense_Mutation	SNP	C	C	T	rs375938401|rs41307415|rs1800993	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:107978343C>T	ENST00000372129.2	-	1	1308	c.1232G>A	c.(1231-1233)cGa>cAa	p.R411Q	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	411					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						CAGTCTTCCTCGCCTGGAGTG	0.642													C|||	171	0.045298	0.0401	0.0562	3775	,	,		13032	0.002		0.0398	False		,,,				2504	0.0378				p.R411Q		Atlas-SNP	.											.	IRS4	253	.	0			c.G1232A						PASS	.	C	GLN/ARG	10,3825		0,0,10,1632,561	49.0	42.0	45.0		1232	2.2	0.0	X	dbSNP_127	45	30,6698		2,1,25,2425,1847	yes	missense	IRS4	NM_003604.2	43	2,1,35,4057,2408	TT,TC,T,CC,C		0.4459,0.2608,0.3787	benign	411/1258	107978343	40,10523	2203	4300	6503	SO:0001583	missense	8471	exon1			CTTCCTCGCCTGG	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1232G>A	X.37:g.107978343C>T	ENSP00000361202:p.Arg411Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	83	80	0.963855	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	66	0.039783001808318265	23	0.046747967479674794	13	0.036931818181818184	0	0.0	17	0.02309782608695652	C	7.661	0.684931	0.14973	0.002608	0.004459	ENSG00000133124	ENST00000372129	T	0.36520	1.25	4.93	2.23	0.28157	.	1.025260	0.07794	N	0.955471	T	0.03959	0.0111	L	0.32530	0.975	0.80722	P	0.0	B	0.29508	0.246	B	0.12837	0.008	T	0.13629	-1.0502	9	0.42905	T	0.14	-0.9947	5.2258	0.15393	0.0:0.4248:0.2889:0.2862	rs41307415	411	O14654	IRS4_HUMAN	Q	411	ENSP00000361202:R411Q	ENSP00000361202:R411Q	R	-	2	0	IRS4	107864999	0.758000	0.28405	0.046000	0.18839	0.146000	0.21551	-0.020000	0.12525	0.157000	0.19338	-0.192000	0.12808	CGA	C|0.950;T|0.050	0.050	strong		0.642	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
DLEC1	9940	hgsc.bcm.edu	37	3	38125705	38125705	+	Silent	SNP	G	G	A	rs7652276	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:38125705G>A	ENST00000308059.6	+	7	1251	c.1230G>A	c.(1228-1230)ccG>ccA	p.P410P	DLEC1_ENST00000346219.3_Silent_p.P410P|DLEC1_ENST00000469151.1_3'UTR|DLEC1_ENST00000452631.2_Silent_p.P410P					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		GAGTCCTCCCGCCTTCCACGC	0.448													g|||	1880	0.375399	0.4145	0.3818	5008	,	,		25644	0.5387		0.3012	False		,,,				2504	0.226				p.P410P		Atlas-SNP	.											.	DLEC1	278	.	0			c.G1230A						PASS	.		,	1644,2520		332,980,770	110.0	120.0	117.0		1230,1230	-10.8	0.0	3	dbSNP_116	117	2535,5901		412,1711,2095	no	coding-synonymous,coding-synonymous	DLEC1	NM_007335.2,NM_007337.2	,	744,2691,2865	AA,AG,GG		30.0498,39.4813,33.1667	,	410/1756,410/1779	38125705	4179,8421	2082	4218	6300	SO:0001819	synonymous_variant	9940	exon7			CCTCCCGCCTTCC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1230G>A	3.37:g.38125705G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	129	52	0.403101	NM_007337		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																			G|0.644;A|0.356	0.356	strong		0.448	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
MUC2	4583	hgsc.bcm.edu	37	11	1080954	1080954	+	Silent	SNP	G	G	A	rs11245929	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1080954G>A	ENST00000441003.2	+	10	1365	c.1338G>A	c.(1336-1338)acG>acA	p.T446T	MUC2_ENST00000359061.5_Silent_p.T446T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	446	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCCTGAAGACGGTGGTGCTGC	0.632													G|||	396	0.0790735	0.1233	0.0519	5008	,	,		15776	0.0506		0.0934	False		,,,				2504	0.0532				p.T446T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.G1338A						PASS	.	G		495,3653		33,429,1612	69.0	80.0	76.0		1338	-7.2	0.7	11	dbSNP_120	76	764,7612		35,694,3459	no	coding-synonymous	MUC2	NM_002457.2		68,1123,5071	AA,AG,GG		9.1213,11.9335,10.0527		446/2813	1080954	1259,11265	2074	4188	6262	SO:0001819	synonymous_variant	4583	exon10			GAAGACGGTGGTG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.1338G>A	11.37:g.1080954G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	200	101	0.505	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				G|0.919;A|0.081	0.081	strong		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CDC16	8881	hgsc.bcm.edu	37	13	115004914	115004914	+	Silent	SNP	C	C	T	rs2296971	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:115004914C>T	ENST00000356221.3	+	5	438	c.330C>T	c.(328-330)gaC>gaT	p.D110D	CDC16_ENST00000375310.1_Silent_p.D16D|CDC16_ENST00000375312.3_Silent_p.D16D|CDC16_ENST00000252458.6_Silent_p.D16D|CDC16_ENST00000252457.5_Silent_p.D109D|CDC16_ENST00000360383.3_Silent_p.D110D|CDC16_ENST00000375308.1_Silent_p.D16D			Q13042	CDC16_HUMAN	cell division cycle 16	110					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			ACTTGAAGGACGAAAGTGGCT	0.453													T|||	2225	0.444289	0.8464	0.3516	5008	,	,		17472	0.2024		0.3191	False		,,,				2504	0.3446				p.D110D		Atlas-SNP	.											.	CDC16	50	.	0			c.C330T						PASS	.	T	,	3299,1107	398.8+/-331.0	1247,805,151	50.0	56.0	54.0		330,330	3.3	1.0	13	dbSNP_100	54	2451,6149	697.3+/-404.9	369,1713,2218	no	coding-synonymous,coding-synonymous	CDC16	NM_001078645.1,NM_003903.3	,	1616,2518,2369	TT,TC,CC		28.5,25.1248,44.2104	,	110/621,110/621	115004914	5750,7256	2203	4300	6503	SO:0001819	synonymous_variant	8881	exon5			GAAGGACGAAAGT	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.330C>T	13.37:g.115004914C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																			C|0.562;T|0.438	0.438	strong		0.453	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	
LAMA1	284217	hgsc.bcm.edu	37	18	6999963	6999963	+	Silent	SNP	G	G	A	rs12970643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:6999963G>A	ENST00000389658.3	-	31	4509	c.4416C>T	c.(4414-4416)caC>caT	p.H1472H		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1472	Laminin EGF-like 16. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AACGGAAATCGTGGTCCCCTT	0.423													G|||	403	0.0804712	0.1604	0.0663	5008	,	,		18721	0.001		0.0905	False		,,,				2504	0.0542				p.H1472H		Atlas-SNP	.											.	LAMA1	458	.	0			c.C4416T						PASS	.	G		663,3743	281.4+/-275.9	46,571,1586	77.0	68.0	71.0		4416	-9.3	0.0	18	dbSNP_121	71	810,7790	188.9+/-235.7	41,728,3531	no	coding-synonymous	LAMA1	NM_005559.3		87,1299,5117	AA,AG,GG		9.4186,15.0477,11.3255		1472/3076	6999963	1473,11533	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon31			GAAATCGTGGTCC	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.4416C>T	18.37:g.6999963G>A		Somatic	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	153	90	0.588235	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.899;A|0.101	0.101	strong		0.423	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
OR4N2	390429	hgsc.bcm.edu	37	14	20296010	20296010	+	Missense_Mutation	SNP	G	G	C	rs17114261	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20296010G>C	ENST00000315947.1	+	1	403	c.403G>C	c.(403-405)Gtc>Ctc	p.V135L	OR4N2_ENST00000568211.1_Missense_Mutation_p.V135L	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	135			V -> L (in dbSNP:rs17114261).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTATCCTACTGTCATGAACCC	0.522																																					p.V135L		Atlas-SNP	.											.	OR4N2	125	.	0			c.G403C						PASS	.	G	LEU/VAL	1121,3285		87,947,1169	209.0	221.0	217.0		403	-0.6	0.4	14	dbSNP_123	217	1852,6748		73,1706,2521	no	missense	OR4N2	NM_001004723.1	32	160,2653,3690	CC,CG,GG		21.5349,25.4426,22.8587	benign	135/308	20296010	2973,10033	2203	4300	6503	SO:0001583	missense	390429	exon1			CCTACTGTCATGA		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.403G>C	14.37:g.20296010G>C	ENSP00000319601:p.Val135Leu	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	218	217	0.995413	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	419	0.19184981684981686	136	0.2764227642276423	62	0.1712707182320442	67	0.11713286713286714	154	0.20316622691292877	.	8.615	0.889998	0.17540	0.254426	0.215349	ENSG00000176294	ENST00000557677;ENST00000315947	T;T	0.01092	5.35;5.35	4.53	-0.609	0.11608	GPCR, rhodopsin-like superfamily (1);	0.151669	0.30800	N	0.008845	T	0.00012	0.0000	N	0.02830	-0.485	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.12156	0.007	T	0.48536	-0.9027	9	0.66056	D	0.02	-16.9757	4.4754	0.11733	0.4631:0.1668:0.3701:0.0	rs17114261	135	Q8NGD1	OR4N2_HUMAN	L	135	ENSP00000452022:V135L;ENSP00000319601:V135L	ENSP00000319601:V135L	V	+	1	0	OR4N2	19365850	0.000000	0.05858	0.387000	0.26183	0.524000	0.34500	-0.609000	0.05635	-0.010000	0.14271	0.591000	0.81541	GTC	G|0.824;C|0.176	0.176	strong		0.522	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
ST20	400410	hgsc.bcm.edu	37	15	80191343	80191343	+	Missense_Mutation	SNP	G	G	A	rs7257	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:80191343G>A	ENST00000478497.1	-	3	849	c.170C>T	c.(169-171)cCa>cTa	p.P57L	ST20_ENST00000485386.1_Missense_Mutation_p.P57L|ST20-MTHFS_ENST00000479961.1_Intron|MTHFS_ENST00000559722.1_5'Flank|ST20_ENST00000562759.1_Missense_Mutation_p.P57L|ST20-MTHFS_ENST00000494999.1_Intron|MTHFS_ENST00000258874.3_5'Flank	NM_001100879.1	NP_001094349.1	Q9HBF5	ST20_HUMAN	suppressor of tumorigenicity 20	57			P -> L (in dbSNP:rs7257). {ECO:0000269|PubMed:11857354}.		extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						TTCACAATATGGAGTGTCCTT	0.383													G|||	2099	0.419129	0.3306	0.4035	5008	,	,		16029	0.3085		0.5179	False		,,,				2504	0.5624				p.P57L		Atlas-SNP	.											.	ST20	9	.	0			c.C170T						PASS	.	G	,LEU/PRO,LEU/PRO,LEU/PRO	1524,2882	479.2+/-358.4	264,996,943	116.0	115.0	115.0		,170,170,170	-0.6	0.0	15	dbSNP_52	115	4789,3811	611.0+/-395.8	1363,2063,874	yes	intron,missense,missense,missense	ST20,ST20-MTHFS	NM_001199760.1,NM_001199757.1,NM_001100880.2,NM_001100879.1	,98,98,98	1627,3059,1817	AA,AG,GG		44.314,34.5892,48.5391	,benign,benign,benign	,57/80,57/80,57/80	80191343	6313,6693	2203	4300	6503	SO:0001583	missense	400410	exon3			CAATATGGAGTGT	AF249277	CCDS42067.1	15q25.1	2007-07-16				ENSG00000180953			33520	protein-coding gene	gene with protein product							Standard	NM_001100879		Approved	HCCS-1		Q9HBF5		ENST00000478497.1:c.170C>T	15.37:g.80191343G>A	ENSP00000453502:p.Pro57Leu	Somatic	389	0	0		WXS	Illumina HiSeq	Phase_I	379	376	0.992084	NM_001199757		Missense_Mutation	SNP	ENST00000478497.1	37	CCDS42067.1	880	0.40293040293040294	152	0.3089430894308943	162	0.44751381215469616	161	0.28146853146853146	405	0.5343007915567283	G	11.35	1.611857	0.28712	0.345892	0.55686	ENSG00000180953	ENST00000322484;ENST00000417278	.	.	.	1.53	-0.622	0.11560	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.13594	0.008	B	0.06405	0.002	T	0.44937	-0.9295	6	0.02654	T	1	.	2.7749	0.05345	0.2087:0.3048:0.4864:0.0	rs7257;rs707187;rs3169168;rs3784763;rs7257	57	Q9HBF5	ST20_HUMAN	L	57	.	ENSP00000319125:P57L	P	-	2	0	ST20	77978398	0.000000	0.05858	0.000000	0.03702	0.730000	0.41778	-0.851000	0.04313	-0.178000	0.10672	0.205000	0.17691	CCA	G|0.590;A|0.410	0.410	strong		0.383	ST20-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416728.2		
DND1	373863	hgsc.bcm.edu	37	5	140050894	140050894	+	Missense_Mutation	SNP	G	G	C	rs201638404		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140050894G>C	ENST00000542735.1	-	4	1089	c.1046C>G	c.(1045-1047)aCc>aGc	p.T349S	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	349					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTAACCATGGTACCTGCCTC	0.602																																					p.T349S		Atlas-SNP	.											DND1,NS,carcinoma,-1,1	DND1	15	1	0			c.C1046G						scavenged	.						75.0	61.0	66.0					5																	140050894		1959	3964	5923	SO:0001583	missense	373863	exon4			ACCATGGTACCTG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1046C>G	5.37:g.140050894G>C	ENSP00000445366:p.Thr349Ser	Somatic	436	1	0.00229358		WXS	Illumina HiSeq	Phase_I	625	57	0.0912	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	G	9.262	1.043394	0.19748	.	.	ENSG00000256453	ENST00000542735	T	0.30182	1.54	4.97	0.117	0.14652	.	1.006470	0.07994	N	0.987573	T	0.16769	0.0403	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29518	-1.0009	10	0.27082	T	0.32	0.0017	3.9136	0.09213	0.3271:0.0:0.5115:0.1614	.	349	Q8IYX4	DND1_HUMAN	S	349	ENSP00000445366:T349S	ENSP00000445366:T349S	T	-	2	0	DND1	140031078	0.002000	0.14202	0.000000	0.03702	0.312000	0.27988	0.583000	0.23849	0.101000	0.17610	0.551000	0.68910	ACC	G|0.979;C|0.021	0.021	strong		0.602	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
VWF	7450	hgsc.bcm.edu	37	12	6167118	6167118	+	Silent	SNP	C	C	T	rs35365059	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6167118C>T	ENST00000261405.5	-	14	1880	c.1626G>A	c.(1624-1626)gcG>gcA	p.A542A		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	542	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CCCGGGGCTCCGCCAGCCCAG	0.662													C|||	412	0.0822684	0.0386	0.0461	5008	,	,		12158	0.1687		0.0696	False		,,,				2504	0.091				p.A542A		Atlas-SNP	.											VWF,colon,carcinoma,0,1	VWF	338	1	0			c.G1626A						PASS	.	C		170,4236	106.0+/-144.5	3,164,2036	56.0	59.0	58.0		1626	-0.3	1.0	12	dbSNP_126	58	739,7861	170.1+/-221.3	34,671,3595	no	coding-synonymous	VWF	NM_000552.3		37,835,5631	TT,TC,CC		8.593,3.8584,6.9891		542/2814	6167118	909,12097	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon14			GGGCTCCGCCAGC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.1626G>A	12.37:g.6167118C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			T|0.074;G|0.000;C|0.925	0.074	strong		0.662	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
RAB11B	9230	hgsc.bcm.edu	37	19	8468322	8468322	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8468322A>G	ENST00000328024.6	+	5	755	c.537A>G	c.(535-537)aaA>aaG	p.K179K		NM_004218.3	NP_004209.2	Q15907	RB11B_HUMAN	RAB11B, member RAS oncogene family	179					cellular response to acidic pH (GO:0071468)|constitutive secretory pathway (GO:0045054)|establishment of protein localization to membrane (GO:0090150)|GTP catabolic process (GO:0006184)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|melanosome transport (GO:0032402)|receptor recycling (GO:0001881)|regulated secretory pathway (GO:0045055)|regulation of anion transport (GO:0044070)|regulation of endocytic recycling (GO:2001135)|regulation of protein localization to cell surface (GO:2000008)|retrograde transport, endosome to plasma membrane (GO:1990126)|small GTPase mediated signal transduction (GO:0007264)|transferrin transport (GO:0033572)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)|synaptic vesicle (GO:0008021)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(1)|ovary(1)	4						TGTCACAGAAACAGATCGCAG	0.657																																					p.K179K		Atlas-SNP	.											.	RAB11B	15	.	0			c.A537G						PASS	.						134.0	109.0	117.0					19																	8468322		2203	4300	6503	SO:0001819	synonymous_variant	9230	exon5			ACAGAAACAGATC	X79780	CCDS12201.1	19p13.2	2012-07-02			ENSG00000185236	ENSG00000185236		"""RAB, member RAS oncogene"""	9761	protein-coding gene	gene with protein product		604198				7811277	Standard	NM_004218		Approved	H-YPT3	uc002mju.4	Q15907		ENST00000328024.6:c.537A>G	19.37:g.8468322A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_004218	A5YM50|B2R7I4|B4DMK0|D6W671|Q2YDT2|Q5U0I1|Q6FHR0|Q6FI42|Q8NI07	Silent	SNP	ENST00000328024.6	37	CCDS12201.1																																																																																			.	.	none		0.657	RAB11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460343.2	NM_004218	
ZNF485	220992	hgsc.bcm.edu	37	10	44104101	44104101	+	Missense_Mutation	SNP	C	C	T	rs45545532	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:44104101C>T	ENST00000361807.3	+	3	258	c.64C>T	c.(64-66)Cgg>Tgg	p.R22W	ZNF485_ENST00000374437.2_Intron|ZNF485_ENST00000374435.3_Missense_Mutation_p.R22W	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	22	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GGCCTTTACCCGGATTGAGTG	0.562													C|||	312	0.0623003	0.056	0.0865	5008	,	,		17332	0.0119		0.1163	False		,,,				2504	0.0501				p.R22W		Atlas-SNP	.											.	ZNF485	102	.	0			c.C64T						PASS	.	C	TRP/ARG	98,1286		5,88,599	171.0	161.0	164.0		64	2.0	0.0	10	dbSNP_127	164	431,2751		33,365,1193	yes	missense	ZNF485	NM_145312.3	101	38,453,1792	TT,TC,CC		13.5449,7.0809,11.5856	possibly-damaging	22/442	44104101	529,4037	692	1591	2283	SO:0001583	missense	220992	exon3			TTTACCCGGATTG	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.64C>T	10.37:g.44104101C>T	ENSP00000354694:p.Arg22Trp	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	288	131	0.454861	NM_145312	B4DSE6|Q96CL0	Missense_Mutation	SNP	ENST00000361807.3	37	CCDS7205.2	165	0.07554945054945054	26	0.052845528455284556	40	0.11049723756906077	8	0.013986013986013986	91	0.12005277044854881	C	13.31	2.199318	0.38806	0.070809	0.135449	ENSG00000198298	ENST00000361807;ENST00000430885;ENST00000374435	T;T;T	0.01887	4.58;4.58;4.58	2.96	2.04	0.26737	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	N	0.04148	-0.265	0.51482	P	7.199999999996098E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.45440	-0.9261	8	0.45353	T	0.12	.	4.2694	0.10778	0.0:0.6208:0.2395:0.1397	rs45545532;rs61729737	22	Q8NCK3	ZN485_HUMAN	W	22	ENSP00000354694:R22W;ENSP00000393570:R22W;ENSP00000363558:R22W	ENSP00000354694:R22W	R	+	1	2	ZNF485	43424107	0.000000	0.05858	0.015000	0.15790	0.921000	0.55340	-0.817000	0.04472	0.567000	0.29293	0.462000	0.41574	CGG	C|0.915;T|0.085	0.085	strong		0.562	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
HLA-C	3107	hgsc.bcm.edu	37	6	31239417	31239417	+	Missense_Mutation	SNP	C	C	T	rs2308557	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239417C>T	ENST00000376228.5	-	2	316	c.302G>A	c.(301-303)aGc>aAc	p.S101N	HLA-C_ENST00000383329.3_Missense_Mutation_p.S101N	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	101	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GTTCCGCAGGCTCACTCGGTC	0.706													c|||	1940	0.38738	0.5408	0.3862	5008	,	,		11155	0.1399		0.4125	False		,,,				2504	0.41				p.S101N		Atlas-SNP	.											.	HLA-C	92	.	0			c.G302A						PASS	.	C	ASN/SER	1619,1403		436,747,328	42.0	43.0	42.0		302	-4.1	0.0	6	dbSNP_126	42	2041,3377		375,1291,1043	yes	missense	HLA-C	NM_002117.5	46	811,2038,1371	TT,TC,CC		37.6707,46.4262,43.3649	benign	101/367	31239417	3660,4780	1511	2709	4220	SO:0001583	missense	3107	exon2			CGCAGGCTCACTC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.302G>A	6.37:g.31239417C>T	ENSP00000365402:p.Ser101Asn	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	196	102	0.520408	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	794	0.36355311355311354	264	0.5365853658536586	141	0.38950276243093923	80	0.13986013986013987	309	0.4076517150395778	N	6.683	0.494653	0.12702	0.535738	0.376707	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00686	5.85;5.85	2.81	-4.12	0.03916	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	2.590310	0.02414	U	0.082017	T	0.00109	0.0003	N	0.01535	-0.81	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.002;0.002;0.001	T	0.43507	-0.9387	9	0.08837	T	0.75	.	4.7356	0.12986	0.0:0.4159:0.166:0.4181	rs2308557;rs3177887;rs17416870	101;101;101;101	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	N	101;101;101;138	ENSP00000365402:S101N;ENSP00000372819:S101N	ENSP00000365402:S101N	S	-	2	0	HLA-C	31347396	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.592000	0.00421	-0.960000	0.03613	-0.727000	0.03589	AGC	T|0.404;G|0.000;C|0.595;A|0.000	0.404	strong		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
BNIPL	149428	hgsc.bcm.edu	37	1	151009208	151009208	+	Missense_Mutation	SNP	A	A	G	rs41266605	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:151009208A>G	ENST00000368931.3	+	1	163	c.7A>G	c.(7-9)Act>Gct	p.T3A	BNIPL_ENST00000295294.7_5'UTR	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	3					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GAAGATGGGAACTATACAAGA	0.468													A|||	71	0.0141773	0.0023	0.0288	5008	,	,		18913	0.0		0.0447	False		,,,				2504	0.0031				p.T3A		Atlas-SNP	.											.	BNIPL	45	.	0			c.A7G						PASS	.	A	,ALA/THR	23,3769		0,23,1873	142.0	138.0	139.0		,7	2.4	0.0	1	dbSNP_127	139	272,7970		2,268,3851	yes	utr-5,missense	BNIPL	NM_001159642.1,NM_138278.3	,58	2,291,5724	GG,GA,AA		3.3002,0.6065,2.4514	,possibly-damaging	,3/358	151009208	295,11739	1896	4121	6017	SO:0001583	missense	149428	exon1			ATGGGAACTATAC	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.7A>G	1.37:g.151009208A>G	ENSP00000357927:p.Thr3Ala	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	108	57	0.527778	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Missense_Mutation	SNP	ENST00000368931.3	37	CCDS978.2	49	0.022435897435897436	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	38	0.05013192612137203	A	13.18	2.160172	0.38119	0.006065	0.033002	ENSG00000163141	ENST00000368931;ENST00000361277	T;T	0.35605	1.31;1.3	4.7	2.4	0.29515	.	0.694155	0.13138	N	0.410913	T	0.16428	0.0395	M	0.67953	2.075	0.09310	N	0.999991	B	0.02656	0.0	B	0.06405	0.002	T	0.31641	-0.9936	10	0.72032	D	0.01	.	6.0234	0.19642	0.7948:0.0:0.2052:0.0	rs41266605	3	Q7Z465	BNIPL_HUMAN	A	3	ENSP00000357927:T3A;ENSP00000355333:T3A	ENSP00000355333:T3A	T	+	1	0	BNIPL	149275832	0.271000	0.24162	0.004000	0.12327	0.336000	0.28762	2.223000	0.42936	0.419000	0.25927	0.524000	0.50904	ACT	A|0.975;G|0.025	0.025	strong		0.468	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279	
HIST1H2AA	221613	hgsc.bcm.edu	37	6	25726675	25726675	+	Silent	SNP	G	G	A	rs9358871	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:25726675G>A	ENST00000297012.3	-	1	115	c.81C>T	c.(79-81)ccC>ccT	p.P27P	HIST1H2BA_ENST00000274764.2_5'Flank	NM_170745.3	NP_734466.1	Q96QV6	H2A1A_HUMAN	histone cluster 1, H2aa	27						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)	13						TCCGGCCTACGGGAAACTGCA	0.547													G|||	1737	0.346845	0.0976	0.4366	5008	,	,		18289	0.6815		0.2922	False		,,,				2504	0.3313				p.P27P		Atlas-SNP	.											.	HIST1H2AA	34	.	0			c.C81T						PASS	.	G		603,3803	264.7+/-266.2	46,511,1646	356.0	271.0	300.0		81	-7.1	0.0	6	dbSNP_119	300	2392,6208	398.3+/-346.1	339,1714,2247	no	coding-synonymous	HIST1H2AA	NM_170745.3		385,2225,3893	AA,AG,GG		27.814,13.6859,23.0278		27/132	25726675	2995,10011	2203	4300	6503	SO:0001819	synonymous_variant	221613	exon1			GCCTACGGGAAAC	AY131982	CCDS4562.1	6p22.2	2011-01-27	2006-10-11		ENSG00000164508	ENSG00000164508		"""Histones / Replication-dependent"""	18729	protein-coding gene	gene with protein product		613499	"""H2A histone family, member R"", ""histone 1, H2aa"""			12408966	Standard	NM_170745		Approved	bA317E16.2, H2AFR	uc003nfc.3	Q96QV6	OTTHUMG00000014407	ENST00000297012.3:c.81C>T	6.37:g.25726675G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_170745		Silent	SNP	ENST00000297012.3	37	CCDS4562.1																																																																																			G|0.717;A|0.283	0.283	strong		0.547	HIST1H2AA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040065.1	NM_170745	
KLHL25	64410	hgsc.bcm.edu	37	15	86312681	86312681	+	Silent	SNP	G	G	A	rs11073537	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86312681G>A	ENST00000337975.5	-	2	635	c.361C>T	c.(361-363)Ctg>Ttg	p.L121L	MIR1276_ENST00000408707.1_RNA|KLHL25_ENST00000536947.1_Silent_p.L121L|KLHL25_ENST00000559131.1_Intron	NM_022480.3	NP_071925.2	Q9H0H3	KLH25_HUMAN	kelch-like family member 25	121					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of translational initiation (GO:0006446)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)				breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	25						CCTGCCTCCAGCAGTGACTCA	0.597													G|||	626	0.125	0.0106	0.2291	5008	,	,		22221	0.0188		0.2883	False		,,,				2504	0.1472				p.L121L		Atlas-SNP	.											.	KLHL25	58	.	0			c.C361T						PASS	.	G		202,4202	126.1+/-163.2	7,188,2007	98.0	89.0	92.0		361	4.8	1.0	15	dbSNP_120	92	2325,6273	390.1+/-343.2	343,1639,2317	no	coding-synonymous	KLHL25	NM_022480.3		350,1827,4324	AA,AG,GG		27.0412,4.5867,19.4355		121/590	86312681	2527,10475	2202	4299	6501	SO:0001819	synonymous_variant	64410	exon2			CCTCCAGCAGTGA		CCDS10339.1	15q25.3	2013-02-22	2013-02-22		ENSG00000183655	ENSG00000183655		"""Kelch-like"", ""BTB/POZ domain containing"""	25732	protein-coding gene	gene with protein product	"""ectodermal-neural cortex 2"""		"""kelch-like 25 (Drosophila)"""				Standard	XM_006720635		Approved	FLJ12587, ENC2, ENC-2	uc002bly.3	Q9H0H3	OTTHUMG00000148672	ENST00000337975.5:c.361C>T	15.37:g.86312681G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_022480	B2RDH2|B3KRT7	Silent	SNP	ENST00000337975.5	37	CCDS10339.1																																																																																			G|0.803;A|0.197	0.197	strong		0.597	KLHL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309023.1	NM_022480	
FAM135A	57579	hgsc.bcm.edu	37	6	71236216	71236216	+	Silent	SNP	C	C	T	rs7740873	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:71236216C>T	ENST00000418814.2	+	15	4043	c.3429C>T	c.(3427-3429)aaC>aaT	p.N1143N	FAM135A_ENST00000361499.3_Silent_p.N947N|FAM135A_ENST00000505868.1_Silent_p.N1143N|FAM135A_ENST00000505769.1_Silent_p.N723N|FAM135A_ENST00000370479.3_Silent_p.N930N|FAM135A_ENST00000457062.2_Silent_p.N930N	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1143										breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						ATGGTATAAACATGCCTACTG	0.363													T|||	1280	0.255591	0.5174	0.2378	5008	,	,		18222	0.0893		0.173	False		,,,				2504	0.1708				p.N1143N		Atlas-SNP	.											.	FAM135A	181	.	0			c.C3429T						PASS	.	T	,,	2098,2308	603.0+/-390.0	525,1048,630	176.0	181.0	179.0		2841,3429,2790	2.4	0.2	6	dbSNP_116	179	1492,7108	748.3+/-407.3	142,1208,2950	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	667,2256,3580	TT,TC,CC		17.3488,47.6169,27.6026	,,	947/1320,1143/1516,930/1303	71236216	3590,9416	2203	4300	6503	SO:0001819	synonymous_variant	57579	exon13			TATAAACATGCCT	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"""KIAA1411"""	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.3429C>T	6.37:g.71236216C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	191	190	0.994764	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			C|0.734;T|0.266	0.266	strong		0.363	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
SON	6651	hgsc.bcm.edu	37	21	34925689	34925689	+	Silent	SNP	G	G	A	rs61739710	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:34925689G>A	ENST00000356577.4	+	3	4627	c.4152G>A	c.(4150-4152)ctG>ctA	p.L1384L	SON_ENST00000300278.4_Silent_p.L1384L|SON_ENST00000290239.6_Silent_p.L1384L|SON_ENST00000381679.4_Silent_p.L1384L|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1384	4 X 8 AA tandem repeats of V-L-E-SS- [AVT]-VT.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						TAACTGTCCTGGAGCCTTCGG	0.567													G|||	881	0.175919	0.0189	0.2421	5008	,	,		20839	0.1637		0.3082	False		,,,				2504	0.2178				p.L1384L		Atlas-SNP	.											.	SON	343	.	0			c.G4152A						PASS	.	G	,	281,4125	156.6+/-189.7	10,261,1932	80.0	72.0	75.0		4152,4152	-5.8	0.0	21	dbSNP_129	75	2385,6215	396.7+/-345.5	322,1741,2237	no	coding-synonymous,coding-synonymous	SON	NM_032195.1,NM_138927.1	,	332,2002,4169	AA,AG,GG		27.7326,6.3777,20.4982	,	1384/2304,1384/2427	34925689	2666,10340	2203	4300	6503	SO:0001819	synonymous_variant	6651	exon3			TGTCCTGGAGCCT	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.4152G>A	21.37:g.34925689G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	204	106	0.519608	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	37	CCDS13629.1	421	0.19276556776556777	14	0.028455284552845527	97	0.26795580110497236	86	0.15034965034965034	224	0.2955145118733509	G	3.643	-0.073046	0.07228	0.063777	0.277326	ENSG00000159140	ENST00000436227	.	.	.	4.95	-5.81	0.02340	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999058328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.1717	0.15114	0.1924:0.0:0.3331:0.4745	rs61739710	.	.	.	X	379	.	.	W	+	2	0	SON	33847559	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.279000	0.02807	-1.193000	0.02688	-1.077000	0.02231	TGG	G|0.792;A|0.208	0.208	strong		0.567	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
SLC4A2	6522	hgsc.bcm.edu	37	7	150768786	150768786	+	Silent	SNP	G	G	A	rs2303937	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:150768786G>A	ENST00000485713.1	+	15	3242	c.2202G>A	c.(2200-2202)acG>acA	p.T734T	SLC4A2_ENST00000461735.1_Silent_p.T720T|SLC4A2_ENST00000392826.2_Silent_p.T725T|SLC4A2_ENST00000310317.5_Silent_p.T652T|SLC4A2_ENST00000413384.2_Silent_p.T734T	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	734	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGAGAAGACGCAGGACCTGA	0.647													G|||	2250	0.449281	0.3381	0.572	5008	,	,		13922	0.4157		0.4294	False		,,,				2504	0.5675				p.T734T		Atlas-SNP	.											.	SLC4A2	98	.	0			c.G2202A						PASS	.	G	,,,	1664,2742	501.3+/-365.0	329,1006,868	58.0	66.0	63.0		2202,2175,2160,2202	-1.7	1.0	7	dbSNP_100	63	3810,4790	534.4+/-382.6	838,2134,1328	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	,,,	1167,3140,2196	AA,AG,GG		44.3023,37.7667,42.0883	,,,	734/1242,725/1233,720/1228,734/1242	150768786	5474,7532	2203	4300	6503	SO:0001819	synonymous_variant	6522	exon15			GAAGACGCAGGAC		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.2202G>A	7.37:g.150768786G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Silent	SNP	ENST00000485713.1	37	CCDS5917.1																																																																																			G|0.581;A|0.419	0.419	strong		0.647	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
SPPL2C	162540	hgsc.bcm.edu	37	17	43923266	43923266	+	Missense_Mutation	SNP	G	G	A	rs62054815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43923266G>A	ENST00000329196.5	+	1	1011	c.994G>A	c.(994-996)Gca>Aca	p.A332T	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	332						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										GAGCCTGTGCGCAACCGTGAT	0.652													A|||	431	0.0860623	0.0151	0.1571	5008	,	,		19554	0.001		0.2396	False		,,,				2504	0.0613				p.A332T		Atlas-SNP	.											.	.	.	.	0			c.G994A						PASS	.	A	THR/ALA	203,4203	805.8+/-415.8	5,193,2005	57.0	50.0	52.0		994	-10.4	0.0	17	dbSNP_129	52	1928,6672	725.8+/-406.6	221,1486,2593	yes	missense	IMP5	NM_175882.2	58	226,1679,4598	AA,AG,GG		22.4186,4.6074,16.3847	benign	332/685	43923266	2131,10875	2203	4300	6503	SO:0001583	missense	162540	exon1			CTGTGCGCAACCG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.994G>A	17.37:g.43923266G>A	ENSP00000332488:p.Ala332Thr	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	A	0.550	-0.850026	0.02651	0.046074	0.224186	ENSG00000185294	ENST00000329196	T	0.16743	2.32	5.18	-10.4	0.00318	.	1.578760	0.03901	N	0.280320	T	0.00012	0.0000	N	0.16166	0.38	0.80722	P	0.0	B	0.24483	0.104	B	0.21708	0.036	T	0.37957	-0.9683	9	0.33141	T	0.24	-8.7503	15.2695	0.73689	0.7025:0.1361:0.1614:0.0	rs62054815	332	Q8IUH8	IMP5_HUMAN	T	332	ENSP00000332488:A332T	ENSP00000332488:A332T	A	+	1	0	AC217771.1	41279046	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.159000	0.01280	-4.847000	0.00029	-3.352000	0.00042	GCA	A|0.120;C|0.240	0.120	strong		0.652	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
RBAK	57786	hgsc.bcm.edu	37	7	5105133	5105133	+	Silent	SNP	C	C	T	rs12334144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:5105133C>T	ENST00000353796.3	+	6	2370	c.2046C>T	c.(2044-2046)aaC>aaT	p.N682N	RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK_ENST00000396912.1_Silent_p.N682N|RBAK-RBAKDN_ENST00000407184.1_Intron	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	682	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		ATGAATGTAACGAGTGTGGGA	0.383													T|||	2884	0.575879	0.7504	0.4193	5008	,	,		19541	0.5526		0.5129	False		,,,				2504	0.5399				p.N682N		Atlas-SNP	.											RBAK_ENST00000396912,colon,carcinoma,0,1	RBAK	82	1	0			c.C2046T						PASS	.	T	,,	3186,1220	420.2+/-338.9	1143,900,160	90.0	99.0	96.0		2046,,2046	-2.8	0.6	7	dbSNP_120	96	4257,4341	577.2+/-390.5	1066,2125,1108	no	coding-synonymous,intron,coding-synonymous	RBAK,RBAK-LOC389458	NM_001204456.1,NM_001204513.1,NM_021163.3	,,	2209,3025,1268	TT,TC,CC		49.5115,27.6895,42.7638	,,	682/715,,682/715	5105133	7443,5561	2203	4299	6502	SO:0001819	synonymous_variant	57786	exon6			ATGTAACGAGTGT	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"""Zinc fingers, C2H2-type"", ""-"""	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.2046C>T	7.37:g.5105133C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_001204456	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Silent	SNP	ENST00000353796.3	37	CCDS5337.1																																																																																			C|0.426;G|0.000;T|0.574	0.574	strong		0.383	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
PTPRO	5800	hgsc.bcm.edu	37	12	15699555	15699555	+	Silent	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:15699555G>C	ENST00000281171.4	+	13	2547	c.2217G>C	c.(2215-2217)gtG>gtC	p.V739V	PTPRO_ENST00000445537.2_5'UTR|PTPRO_ENST00000442921.2_5'UTR|PTPRO_ENST00000542557.1_5'UTR|PTPRO_ENST00000544244.1_5'UTR|PTPRO_ENST00000348962.2_Silent_p.V739V	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	739	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				AGACTTCAGTGACTTTGCTGT	0.393																																					p.V739V		Atlas-SNP	.											.	PTPRO	148	.	0			c.G2217C						PASS	.						98.0	94.0	96.0					12																	15699555		2203	4300	6503	SO:0001819	synonymous_variant	5800	exon13			TTCAGTGACTTTG	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9678	protein-coding gene	gene with protein product	"""osteoclastic transmembrane protein-tyrosine phosphatase"""	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.2217G>C	12.37:g.15699555G>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Silent	SNP	ENST00000281171.4	37	CCDS8675.1																																																																																			.	.	none		0.393	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1		
MYT1L	23040	hgsc.bcm.edu	37	2	1805489	1805489	+	Silent	SNP	A	A	G	rs2288179	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:1805489A>G	ENST00000399161.2	-	23	4002	c.3255T>C	c.(3253-3255)gaT>gaC	p.D1085D	MYT1L_ENST00000428368.2_Silent_p.D1083D|MYT1L_ENST00000407844.1_Silent_p.D81D	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1085					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GTTTAATCATATCGGCTTCCA	0.348													A|||	310	0.061901	0.0136	0.0821	5008	,	,		15974	0.0754		0.0467	False		,,,				2504	0.1145				p.D1083D		Atlas-SNP	.											MYT1L,NS,carcinoma,-2,1	MYT1L	241	1	0			c.T3249C						PASS	.	A		57,3583		0,57,1763	224.0	223.0	223.0		3249	-4.2	0.5	2	dbSNP_100	223	344,7852		4,336,3758	no	coding-synonymous	MYT1L	NM_015025.2		4,393,5521	GG,GA,AA		4.1972,1.5659,3.388		1083/1185	1805489	401,11435	1820	4098	5918	SO:0001819	synonymous_variant	23040	exon23			AATCATATCGGCT	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"""Zinc fingers, C2HC-type containing"""	7623	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 1"""	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.3255T>C	2.37:g.1805489A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	160	87	0.54375	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37																																																																																				A|0.933;C|0.002	.	strong		0.348	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
SPATA6	54558	hgsc.bcm.edu	37	1	48764419	48764419	+	Missense_Mutation	SNP	C	C	T	rs1056042	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:48764419C>T	ENST00000371847.3	-	13	1597	c.1433G>A	c.(1432-1434)tGt>tAt	p.C478Y	SPATA6_ENST00000396199.3_Missense_Mutation_p.C406Y|SPATA6_ENST00000371843.3_Missense_Mutation_p.C462Y	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	478			C -> F (in dbSNP:rs1056042).|C -> S (in dbSNP:rs1056042).|C -> Y (in dbSNP:rs1056042).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)		p.C478Y(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						AGCAGAACTACAGGCCTTTTT	0.423													C|||	1372	0.273962	0.025	0.3329	5008	,	,		16906	0.3492		0.4254	False		,,,				2504	0.3354				p.C478Y		Atlas-SNP	.											SPATA6,NS,carcinoma,0,1	SPATA6	45	1	1	Substitution - Missense(1)	stomach(1)	c.G1433A						PASS	.	C	TYR/CYS	392,4014	195.0+/-219.7	15,362,1826	162.0	159.0	160.0		1433	4.8	1.0	1	dbSNP_86	160	3624,4976	522.3+/-380.1	755,2114,1431	yes	missense	SPATA6	NM_019073.2	194	770,2476,3257	TT,TC,CC		42.1395,8.897,30.8781	probably-damaging	478/489	48764419	4016,8990	2203	4300	6503	SO:0001583	missense	54558	exon13			GAACTACAGGCCT	AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"""spermatogenesis-related factor-1"""	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.1433G>A	1.37:g.48764419C>T	ENSP00000360913:p.Cys478Tyr	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	269	134	0.498141	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	37	CCDS551.1	682	0.31227106227106227	23	0.046747967479674794	125	0.3453038674033149	205	0.3583916083916084	329	0.4340369393139842	C	19.54	3.846395	0.71603	0.08897	0.421395	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199	T;T;T	0.13089	2.64;2.63;2.62	4.78	4.78	0.61160	.	0.064498	0.64402	D	0.000008	T	0.00012	0.0000	N	0.22421	0.69	0.28859	P	0.895616	D;D	0.69078	0.997;0.997	D;D	0.80764	0.994;0.994	T	0.51872	-0.8650	9	0.41790	T	0.15	.	13.1884	0.59695	0.0:1.0:0.0:0.0	rs1056042;rs3196668;rs52835803;rs56856507;rs1056042	462;478	Q9NWH7-2;Q9NWH7	.;SPAT6_HUMAN	Y	478;462;406	ENSP00000360913:C478Y;ENSP00000360909:C462Y;ENSP00000379502:C406Y	ENSP00000360909:C462Y	C	-	2	0	SPATA6	48537006	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.488000	0.35551	2.474000	0.83562	0.563000	0.77884	TGT	T|0.304;C|0.696	0.304	strong		0.423	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073	
BMP2	650	hgsc.bcm.edu	37	20	6751034	6751034	+	Silent	SNP	A	A	G	rs79417223|rs1049007	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:6751034A>G	ENST00000378827.4	+	2	1480	c.261A>G	c.(259-261)tcA>tcG	p.S87S		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	87					activation of MAPK activity (GO:0000187)|atrioventricular valve morphogenesis (GO:0003181)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|bone mineralization (GO:0030282)|bone mineralization involved in bone maturation (GO:0035630)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiocyte differentiation (GO:0035051)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation (GO:0002062)|corticotropin hormone secreting cell differentiation (GO:0060128)|embryo development (GO:0009790)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchyme development (GO:0060485)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of calcium-independent cell-cell adhesion (GO:0051042)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|pericardium development (GO:0060039)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of odontogenesis (GO:0042482)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of Wnt signaling pathway by BMP signaling pathway (GO:0060804)|protein destabilization (GO:0031648)|protein phosphorylation (GO:0006468)|proteoglycan metabolic process (GO:0006029)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP receptor binding (GO:0070700)|phosphatase activator activity (GO:0019211)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)|retinol dehydrogenase activity (GO:0004745)|SMAD binding (GO:0046332)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	13						GCAGGCACTCAGGTCAGCCGG	0.647													G|||	3736	0.746006	0.8964	0.7291	5008	,	,		13556	0.8433		0.6262	False		,,,				2504	0.5777				p.S87S		Atlas-SNP	.											BMP2,NS,carcinoma,0,4	BMP2	45	4	0			c.A261G						scavenged	.	G		3780,622		1632,516,53	22.0	24.0	23.0		261	0.8	0.9	20	dbSNP_86	23	5426,3170		1695,2036,567	no	coding-synonymous	BMP2	NM_001200.2		3327,2552,620	GG,GA,AA		36.8776,14.1299,29.1737		87/397	6751034	9206,3792	2201	4298	6499	SO:0001819	synonymous_variant	650	exon2			GCACTCAGGTCAG		CCDS13099.1	20p12	2014-01-30			ENSG00000125845	ENSG00000125845		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1069	protein-coding gene	gene with protein product		112261		BMP2A		2376592	Standard	NM_001200		Approved		uc002wmu.1	P12643	OTTHUMG00000031833	ENST00000378827.4:c.261A>G	20.37:g.6751034A>G		Somatic	135	3	0.0222222		WXS	Illumina HiSeq	Phase_I	161	76	0.47205	NM_001200		Silent	SNP	ENST00000378827.4	37	CCDS13099.1																																																																																			A|0.276;G|0.724	0.724	strong		0.647	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3		
MLXIP	22877	hgsc.bcm.edu	37	12	122618131	122618131	+	Silent	SNP	A	A	G	rs36045144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:122618131A>G	ENST00000319080.7	+	9	1461	c.1329A>G	c.(1327-1329)ccA>ccG	p.P443P	MLXIP_ENST00000377037.2_Silent_p.P33P|MLXIP_ENST00000538698.1_Silent_p.P50P					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		GCCCCGCCCCACCGCCCATCT	0.652													A|||	1128	0.22524	0.2042	0.1974	5008	,	,		10846	0.2738		0.2306	False		,,,				2504	0.2178				p.P443P	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.A1329G						PASS	.	A		753,3347		82,589,1379	17.0	19.0	19.0		919	-10.0	0.0	12	dbSNP_126	19	1468,6918		136,1196,2861	no	coding-synonymous	MLXIP	NM_014938.3		218,1785,4240	GG,GA,AA		17.5054,18.3659,17.7879		443/920	122618131	2221,10265	2050	4193	6243	SO:0001819	synonymous_variant	22877	exon9			CGCCCCACCGCCC	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"""Basic helix-loop-helix proteins"""	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.1329A>G	12.37:g.122618131A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_014938		Silent	SNP	ENST00000319080.7	37																																																																																				A|0.784;G|0.216;T|0.000	0.216	strong		0.652	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938	
PHACTR4	65979	hgsc.bcm.edu	37	1	28800380	28800380	+	Missense_Mutation	SNP	C	C	A	rs61785974	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:28800380C>A	ENST00000373839.3	+	7	1399	c.1138C>A	c.(1138-1140)Cta>Ata	p.L380I	PHACTR4_ENST00000373836.3_Missense_Mutation_p.L390I|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	380	Pro-rich.				actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		ATCCTTAGATCTACACCAGGA	0.507													C|||	1127	0.22504	0.3048	0.2666	5008	,	,		14282	0.0704		0.3111	False		,,,				2504	0.1585				p.L390I		Atlas-SNP	.											.	PHACTR4	64	.	0			c.C1168A						PASS	.	C	ILE/LEU,ILE/LEU	1153,2617		192,769,924	81.0	81.0	81.0		1138,1168	3.3	0.2	1	dbSNP_129	81	2233,5989		282,1669,2160	yes	missense,missense	PHACTR4	NM_001048183.1,NM_023923.3	5,5	474,2438,3084	AA,AC,CC		27.1588,30.5836,28.2355	possibly-damaging,possibly-damaging	380/703,390/713	28800380	3386,8606	1885	4111	5996	SO:0001583	missense	65979	exon6			TTAGATCTACACC	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"""Phosphatase and actin regulators"""	25793	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 124"""	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1138C>A	1.37:g.28800380C>A	ENSP00000362945:p.Leu380Ile	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	37	CCDS41293.1	560	0.2564102564102564	168	0.34146341463414637	100	0.27624309392265195	54	0.0944055944055944	238	0.31398416886543534	C	5.460	0.270018	0.10349	0.305836	0.271588	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.24908	1.84;1.83	5.22	3.3	0.37823	.	1.100460	0.06835	N	0.794600	T	0.00012	0.0000	L	0.54323	1.7	0.38745	P	0.04601200000000005	B;B	0.31548	0.328;0.22	B;B	0.28011	0.085;0.024	T	0.41980	-0.9478	9	0.19590	T	0.45	-5.1431	5.4783	0.16708	0.1624:0.676:0.0:0.1616	rs61785974	390;380	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	I	380;390;379	ENSP00000362945:L380I;ENSP00000362942:L390I	ENSP00000362942:L390I	L	+	1	2	PHACTR4	28672967	0.235000	0.23794	0.237000	0.24090	0.250000	0.25880	1.307000	0.33516	0.731000	0.32448	0.655000	0.94253	CTA	C|0.726;A|0.274	0.274	strong		0.507	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923	
PDILT	204474	hgsc.bcm.edu	37	16	20410488	20410488	+	Silent	SNP	G	G	A	rs7185940	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20410488G>A	ENST00000302451.4	-	2	383	c.135C>T	c.(133-135)ctC>ctT	p.L45L		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	45					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						TTAGCACTAGGAGACTGCGTT	0.577													G|||	1735	0.346446	0.4644	0.3876	5008	,	,		18405	0.1528		0.3091	False		,,,				2504	0.3957				p.L45L		Atlas-SNP	.											.	PDILT	120	.	0			c.C135T						PASS	.	G		1872,2534	540.5+/-375.5	373,1126,704	149.0	136.0	140.0		135	1.0	0.2	16	dbSNP_116	140	2466,6134	405.8+/-348.6	326,1814,2160	no	coding-synonymous	PDILT	NM_174924.1		699,2940,2864	AA,AG,GG		28.6744,42.4875,33.3538		45/585	20410488	4338,8668	2203	4300	6503	SO:0001819	synonymous_variant	204474	exon2			CACTAGGAGACTG		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"""Protein disulfide isomerases"""	27338	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 7"", ""protein disulfide isomerase-like protein of the testis"""					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.135C>T	16.37:g.20410488G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	118	41	0.347458	NM_174924	Q8IVQ5	Silent	SNP	ENST00000302451.4	37	CCDS10584.1																																																																																			G|0.676;A|0.324	0.324	strong		0.577	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924	
CCDC50	152137	hgsc.bcm.edu	37	3	191075902	191075902	+	Silent	SNP	C	C	T	rs11542549	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:191075902C>T	ENST00000392455.3	+	3	826	c.228C>T	c.(226-228)cgC>cgT	p.R76R	CCDC50_ENST00000392456.3_Silent_p.R76R	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	76						cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		TCCAGAAGCGCTACAAAGACC	0.552													C|||	1339	0.267372	0.2322	0.3156	5008	,	,		17820	0.2579		0.332	False		,,,				2504	0.2239				p.R76R		Atlas-SNP	.											.	CCDC50	39	.	0			c.C228T						PASS	.	C	,	1123,3283	398.3+/-330.8	143,837,1223	105.0	103.0	103.0		228,228	4.4	1.0	3	dbSNP_120	103	2734,5866	435.2+/-358.0	439,1856,2005	no	coding-synonymous,coding-synonymous	CCDC50	NM_174908.3,NM_178335.2	,	582,2693,3228	TT,TC,CC		31.7907,25.488,29.6555	,	76/307,76/483	191075902	3857,9149	2203	4300	6503	SO:0001819	synonymous_variant	152137	exon3			GAAGCGCTACAAA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.228C>T	3.37:g.191075902C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	169	168	0.994083	NM_174908	Q86VH7	Silent	SNP	ENST00000392455.3	37	CCDS33913.1																																																																																			C|0.584;A|0.042	.	strong		0.552	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
TSACC	128229	hgsc.bcm.edu	37	1	156314497	156314497	+	Missense_Mutation	SNP	C	C	T	rs41265043	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156314497C>T	ENST00000368255.3	+	3	521	c.161C>T	c.(160-162)tCg>tTg	p.S54L	TSACC_ENST00000368254.1_Missense_Mutation_p.S54L|TSACC_ENST00000466306.1_Missense_Mutation_p.S54L|TSACC_ENST00000368251.1_Missense_Mutation_p.S54L|TSACC_ENST00000368253.2_Missense_Mutation_p.S54L|TSACC_ENST00000368252.1_Missense_Mutation_p.S54L|TSACC_ENST00000481479.1_Missense_Mutation_p.S54L|TSACC_ENST00000470342.1_Missense_Mutation_p.S54L	NM_144627.3	NP_653228.1	Q96A04	TSACC_HUMAN	TSSK6 activating co-chaperone	54			S -> L (in dbSNP:rs41265043).			cytoplasm (GO:0005737)	chaperone binding (GO:0051087)										AAGCTGCCCTCGGGTAAGGAT	0.507													C|||	40	0.00798722	0.0015	0.0086	5008	,	,		18748	0.0		0.0229	False		,,,				2504	0.0092				p.S54L		Atlas-SNP	.											.	.	.	.	0			c.C161T						PASS	.	C	LEU/SER	21,4385	29.0+/-57.7	0,21,2182	76.0	80.0	79.0		161	4.7	1.0	1	dbSNP_127	79	178,8422	78.9+/-141.6	0,178,4122	yes	missense	C1orf182	NM_144627.3	145	0,199,6304	TT,TC,CC		2.0698,0.4766,1.5301	possibly-damaging	54/126	156314497	199,12807	2203	4300	6503	SO:0001583	missense	128229	exon3			TGCCCTCGGGTAA	AY048672	CCDS1141.1	1q22	2012-08-16	2012-08-16	2012-08-16	ENSG00000163467	ENSG00000163467			30636	protein-coding gene	gene with protein product	"""SSTK-interacting protein"""		"""chromosome 1 open reading frame 182"""	C1orf182		20829357	Standard	NM_144627		Approved	SSTK-IP, SIP	uc001foo.3	Q96A04	OTTHUMG00000024060	ENST00000368255.3:c.161C>T	1.37:g.156314497C>T	ENSP00000357238:p.Ser54Leu	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	30	19	0.633333	NM_144627	D3DVB9	Missense_Mutation	SNP	ENST00000368255.3	37	CCDS1141.1	26	0.011904761904761904	0	0.0	5	0.013812154696132596	0	0.0	21	0.027704485488126648	C	21.1	4.090541	0.76756	0.004766	0.020698	ENSG00000163467	ENST00000368255;ENST00000368254;ENST00000368253;ENST00000368252;ENST00000368251	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	4.71	4.71	0.59529	.	0.432560	0.17252	N	0.181119	T	0.39572	0.1083	L	0.29908	0.895	0.28666	N	0.905879	D	0.76494	0.999	P	0.52710	0.707	T	0.30387	-0.9980	10	0.72032	D	0.01	-0.8916	13.0312	0.58842	0.0:1.0:0.0:0.0	rs41265043	54	Q96A04	CA182_HUMAN	L	54	ENSP00000357238:S54L;ENSP00000357237:S54L;ENSP00000357236:S54L;ENSP00000357235:S54L;ENSP00000357234:S54L	ENSP00000357234:S54L	S	+	2	0	C1orf182	154581121	0.951000	0.32395	0.980000	0.43619	0.886000	0.51366	1.597000	0.36729	2.451000	0.82905	0.561000	0.74099	TCG	C|0.984;T|0.016	0.016	strong		0.507	TSACC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060594.1	NM_144627	
SCRN3	79634	hgsc.bcm.edu	37	2	175263063	175263063	+	Missense_Mutation	SNP	G	G	A	rs10497410	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:175263063G>A	ENST00000272732.6	+	2	134	c.52G>A	c.(52-54)Gat>Aat	p.D18N	CIR1_ENST00000342016.3_5'Flank|SCRN3_ENST00000409673.3_Intron|CIR1_ENST00000362053.5_5'Flank	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	18			D -> N (in dbSNP:rs10497410).				dipeptidase activity (GO:0016805)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			AGCAACAGTCGATAACAGGAT	0.333													G|||	426	0.0850639	0.0121	0.1556	5008	,	,		14445	0.006		0.2127	False		,,,				2504	0.0838				p.D18N		Atlas-SNP	.											.	SCRN3	76	.	0			c.G52A						PASS	.	G	,ASN/ASP	203,4203	117.1+/-155.0	6,191,2006	108.0	115.0	113.0		,52	4.2	0.0	2	dbSNP_119	113	1948,6652	338.3+/-322.7	224,1500,2576	yes	intron,missense	SCRN3	NM_001193528.1,NM_024583.4	,23	230,1691,4582	AA,AG,GG		22.6512,4.6074,16.5385	,benign	,18/425	175263063	2151,10855	2203	4300	6503	SO:0001583	missense	79634	exon2			ACAGTCGATAACA	AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.52G>A	2.37:g.175263063G>A	ENSP00000272732:p.Asp18Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Missense_Mutation	SNP	ENST00000272732.6	37	CCDS2258.1	229	0.10485347985347986	7	0.014227642276422764	61	0.1685082872928177	4	0.006993006993006993	157	0.20712401055408972	G	11.60	1.686750	0.29962	0.046074	0.226512	ENSG00000144306	ENST00000458563;ENST00000272732;ENST00000424069;ENST00000427038;ENST00000548031	T;T;T;T;T	0.29917	2.16;3.01;1.55;1.55;2.16	6.06	4.25	0.50352	.	0.404667	0.31347	N	0.007802	T	0.00012	0.0000	L	0.35723	1.085	0.53005	P	3.2999999999949736E-5	P	0.36249	0.545	B	0.28784	0.094	T	0.28744	-1.0034	9	0.10377	T	0.69	0.007	12.0732	0.53628	0.0657:0.1212:0.8131:0.0	rs10497410;rs17255662;rs52797928;rs57473616;rs10497410	18	Q0VDG4	SCRN3_HUMAN	N	18	ENSP00000396884:D18N;ENSP00000272732:D18N;ENSP00000402086:D18N;ENSP00000408376:D18N;ENSP00000446727:D18N	ENSP00000272732:D18N	D	+	1	0	SCRN3	174971309	1.000000	0.71417	0.024000	0.17045	0.978000	0.69477	6.412000	0.73303	0.881000	0.35993	0.643000	0.83706	GAT	G|0.866;A|0.134	0.134	strong		0.333	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583	
PRB1	5542	hgsc.bcm.edu	37	12	11506288	11506288	+	Missense_Mutation	SNP	T	T	C	rs140825288	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11506288T>C	ENST00000500254.2	-	4	387	c.350A>G	c.(349-351)aAa>aGa	p.K117R	PRB1_ENST00000545626.1_Intron|PRB1_ENST00000546254.1_Missense_Mutation_p.K117R	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1	0	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].		Missing (in allele M).|Missing (in clone CP-4).|Missing (in clone CP-5).			extracellular region (GO:0005576)		p.K117R(2)		NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			ACCTTGAGGTTTGTTGCCTCC	0.612													t|||	39	0.00778754	0.0106	0.0086	5008	,	,		16399	0.0079		0.0099	False		,,,				2504	0.001				p.K117R		Atlas-SNP	.											PRB1,NS,carcinoma,0,2	PRB1	33	2	2	Substitution - Missense(2)	prostate(1)|central_nervous_system(1)	c.A350G						scavenged	.						92.0	112.0	105.0					12																	11506288		2098	4245	6343	SO:0001583	missense	5542	exon4			TGAGGTTTGTTGC		CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.350A>G	12.37:g.11506288T>C	ENSP00000420826:p.Lys117Arg	Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	515	8	0.015534	NM_199353	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Missense_Mutation	SNP	ENST00000500254.2	37	CCDS8642.1	.	.	.	.	.	.	.	.	.	.	.	0.021	-1.431560	0.01108	.	.	ENSG00000251655	ENST00000500254;ENST00000546254	T;T	0.04119	3.7;3.7	1.29	-1.39	0.08997	.	.	.	.	.	T	0.03871	0.0109	L	0.39147	1.195	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.08055	0.002;0.003	T	0.44544	-0.9321	8	.	.	.	.	5.2744	0.15641	0.0:0.2701:0.0:0.7299	.	257;117	Q86YA1;G3V1M9	.;.	R	117	ENSP00000420826:K117R;ENSP00000442127:K117R	.	K	-	2	0	PRB1	11397555	0.003000	0.15002	0.000000	0.03702	0.007000	0.05969	0.188000	0.17018	-0.320000	0.08640	0.113000	0.15668	AAA	.	.	weak		0.612	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039	
ATN1	1822	hgsc.bcm.edu	37	12	7047143	7047143	+	Silent	SNP	C	C	A	rs7969685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7047143C>A	ENST00000356654.4	+	6	2667	c.2430C>A	c.(2428-2430)cgC>cgA	p.R810R	ATN1_ENST00000396684.2_Silent_p.R810R	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	810	Ala/Arg-rich.				cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						CCGAGCAGCGCGCGCGCGAAG	0.692											OREG0021641	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	814	0.16254	0.1059	0.2046	5008	,	,		-128	0.0109		0.3787	False		,,,				2504	0.1431				p.R810R		Atlas-SNP	.											.	ATN1	95	.	0			c.C2430A						PASS	.	C	,	560,3648		48,464,1592	8.0	9.0	9.0		2430,2430	3.0	1.0	12	dbSNP_116	9	2744,5534		492,1760,1887	no	coding-synonymous,coding-synonymous	ATN1	NM_001007026.1,NM_001940.3	,	540,2224,3479	AA,AC,CC		33.1481,13.308,26.4616	,	810/1191,810/1191	7047143	3304,9182	2104	4139	6243	SO:0001819	synonymous_variant	1822	exon6			GCAGCGCGCGCGC	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"""dentatorubral-pallidoluysian atrophy (atrophin-1)"""	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.2430C>A	12.37:g.7047143C>A		Somatic	27	0	0	638	WXS	Illumina HiSeq	Phase_I	39	27	0.692308	NM_001007026	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	37	CCDS31734.1																																																																																			C|0.802;A|0.198	0.198	strong		0.692	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940	
FAM186A	121006	hgsc.bcm.edu	37	12	50727706	50727706	+	Missense_Mutation	SNP	G	G	C	rs6580741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:50727706G>C	ENST00000327337.5	-	5	6683	c.6684C>G	c.(6682-6684)caC>caG	p.H2228Q	FAM186A_ENST00000543111.1_Missense_Mutation_p.H2228Q|FAM186A_ENST00000543096.1_Missense_Mutation_p.H239Q	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2228			H -> Q (in dbSNP:rs6580741). {ECO:0000269|Ref.3}.														GGTTGAATACGTGTATCATTT	0.448													g|||	1739	0.347244	0.3434	0.2565	5008	,	,		21530	0.2569		0.339	False		,,,				2504	0.5184				p.H2228Q	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.C6684G						PASS	.						217.0	171.0	185.0					12																	50727706		692	1591	2283	SO:0001583	missense	121006	exon5			GAATACGTGTATC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.6684C>G	12.37:g.50727706G>C	ENSP00000329995:p.His2228Gln	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	269	119	0.442379	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	685	0.31364468864468864	180	0.36585365853658536	94	0.2596685082872928	160	0.27972027972027974	251	0.3311345646437995	g	2.650	-0.282130	0.05642	.	.	ENSG00000185958	ENST00000543111;ENST00000543096;ENST00000327337	T;T;T	0.40225	1.04;1.04;1.04	4.27	-0.179	0.13299	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.19583	0.037;0.037	B;B	0.20384	0.029;0.029	T	0.45948	-0.9226	8	0.33141	T	0.24	.	7.0351	0.24989	0.2306:0.1377:0.6317:0.0	rs6580741;rs52828511;rs60724480;rs6580741	2228;2228	F5GYN0;A6NE01	.;F186A_HUMAN	Q	2228;239;2228	ENSP00000441337:H2228Q;ENSP00000443703:H239Q;ENSP00000329995:H2228Q	ENSP00000329995:H2228Q	H	-	3	2	FAM186A	49013973	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.315000	0.19451	-0.245000	0.09625	-2.620000	0.00156	CAC	G|0.688;C|0.312	0.312	strong		0.448	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
POLQ	10721	hgsc.bcm.edu	37	3	121208833	121208833	+	Missense_Mutation	SNP	G	G	C	rs3218649	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121208833G>C	ENST00000264233.5	-	16	3073	c.2945C>G	c.(2944-2946)aCa>aGa	p.T982R		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	982				T -> R (in Ref. 2; AAR08421). {ECO:0000305}.	ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		AATGGAACATGTCTGATGTTC	0.353								DNA polymerases (catalytic subunits)					C|||	3488	0.696486	0.5424	0.634	5008	,	,		395	0.876		0.6143	False		,,,				2504	0.8487				p.T982R	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C2945G						PASS	.	C	ARG/THR	2431,1971	528.9+/-372.5	683,1065,453	51.0	53.0	53.0		2945	-3.9	0.0	3	dbSNP_106	53	5405,3193	476.3+/-369.4	1707,1991,601	yes	missense	POLQ	NM_199420.3	71	2390,3056,1054	CC,CG,GG		37.1365,44.7751,39.7231	benign	982/2591	121208833	7836,5164	2201	4299	6500	SO:0001583	missense	10721	exon16			GAACATGTCTGAT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.2945C>G	3.37:g.121208833G>C	ENSP00000264233:p.Thr982Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	1454	0.6657509157509157	257	0.5223577235772358	226	0.6243093922651933	510	0.8916083916083916	461	0.6081794195250659	C	0.020	-1.438016	0.01098	0.552249	0.628635	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.48201	0.82	4.99	-3.86	0.04230	.	1.969910	0.02087	N	0.052835	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26916	-1.0089	9	0.15499	T	0.54	.	8.791	0.34850	0.1538:0.139:0.6117:0.0955	rs3218649;rs3772125;rs52789693;rs59762555;rs3218649	982;154	O75417;O75417-2	DPOLQ_HUMAN;.	R	605;982;1118	ENSP00000264233:T982R	ENSP00000264233:T982R	T	-	2	0	POLQ	122691523	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-2.240000	0.01197	-1.432000	0.01979	-0.986000	0.02555	ACA	G|0.377;C|0.623	0.623	strong		0.353	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
MUC5B	727897	hgsc.bcm.edu	37	11	1263648	1263648	+	Silent	SNP	G	G	A	rs151293115	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1263648G>A	ENST00000529681.1	+	31	5596	c.5538G>A	c.(5536-5538)gtG>gtA	p.V1846V	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.V1849V	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1846	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TCGGGCAGGTGCTGACCTGCA	0.592													g|||	3	0.000599042	0.0	0.0	5008	,	,		19439	0.0		0.003	False		,,,				2504	0.0				p.V1846V		Atlas-SNP	.											.	MUC5B	473	.	0			c.G5538A						PASS	.			0,4334		0,0,2167	59.0	72.0	68.0		5538	-1.6	0.0	11	dbSNP_134	68	28,8486		0,28,4229	no	coding-synonymous	MUC5B	NM_002458.2		0,28,6396	AA,AG,GG		0.3289,0.0,0.2179		1846/5763	1263648	28,12820	2167	4257	6424	SO:0001819	synonymous_variant	727897	exon31			GCAGGTGCTGACC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.5538G>A	11.37:g.1263648G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	129	52	0.403101	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.999;A|0.001	0.001	strong		0.592	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ARMC9	80210	hgsc.bcm.edu	37	2	232156084	232156084	+	Missense_Mutation	SNP	C	C	T	rs148296188	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:232156084C>T	ENST00000349938.4	+	18	1839	c.1645C>T	c.(1645-1647)Cgc>Tgc	p.R549C	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	549						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		AGACATCCTACGCTGCTTCAT	0.398													C|||	15	0.00299521	0.0	0.0014	5008	,	,		20601	0.0		0.0089	False		,,,				2504	0.0051				p.R549C		Atlas-SNP	.											.	ARMC9	129	.	0			c.C1645T						PASS	.	C	CYS/ARG	17,4389	23.3+/-48.9	0,17,2186	160.0	156.0	157.0		1645	4.0	1.0	2	dbSNP_134	157	173,8427	78.9+/-141.6	2,169,4129	yes	missense	ARMC9	NM_025139.3	180	2,186,6315	TT,TC,CC		2.0116,0.3858,1.4609	possibly-damaging	549/666	232156084	190,12816	2203	4300	6503	SO:0001583	missense	80210	exon18			ATCCTACGCTGCT	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"""Armadillo repeat containing"""	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.1645C>T	2.37:g.232156084C>T	ENSP00000258417:p.Arg549Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	37	CCDS2484.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	C	19.02	3.746426	0.69418	0.003858	0.020116	ENSG00000135931	ENST00000349938;ENST00000359743	T	0.19669	2.13	5.74	3.97	0.46021	Armadillo-like helical (1);Armadillo-type fold (1);	0.184961	0.47852	D	0.000212	T	0.09423	0.0232	L	0.60455	1.87	0.80722	D	1	P	0.40875	0.731	B	0.33254	0.16	T	0.01504	-1.1338	10	0.87932	D	0	-7.4763	9.5684	0.39414	0.0:0.7826:0.1415:0.0759	.	549	Q7Z3E5	ARMC9_HUMAN	C	549	ENSP00000258417:R549C	ENSP00000258417:R549C	R	+	1	0	ARMC9	231864328	0.979000	0.34478	0.996000	0.52242	0.996000	0.88848	2.452000	0.44961	0.799000	0.34018	-0.121000	0.15023	CGC	C|0.988;T|0.012	0.012	strong		0.398	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139	
BDP1	55814	hgsc.bcm.edu	37	5	70849021	70849021	+	Silent	SNP	G	G	T	rs469039	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:70849021G>T	ENST00000358731.4	+	35	7337	c.7074G>T	c.(7072-7074)ccG>ccT	p.P2358P	BDP1_ENST00000380675.2_Missense_Mutation_p.R432L	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2358					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		CTAAAAAGCCGCCTGATAATT	0.363													T|||	2167	0.432708	0.385	0.3444	5008	,	,		14870	0.379		0.4911	False		,,,				2504	0.5552				p.P2358P		Atlas-SNP	.											.	BDP1	204	.	0			c.G7074T						PASS	.	T		1348,2264		257,834,715	93.0	85.0	88.0		7074	2.3	0.3	5	dbSNP_80	88	3932,4190		980,1972,1109	no	coding-synonymous	BDP1	NM_018429.2		1237,2806,1824	TT,TG,GG		48.4117,37.32,44.9974		2358/2625	70849021	5280,6454	1806	4061	5867	SO:0001819	synonymous_variant	55814	exon35			AAAGCCGCCTGAT	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.7074G>T	5.37:g.70849021G>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	27	0.346154	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Silent	SNP	ENST00000358731.4	37	CCDS43328.1	911	0.41712454212454214	185	0.37601626016260165	126	0.34806629834254144	223	0.38986013986013984	377	0.4973614775725594	T	0.012	-1.669849	0.00758	0.3732	0.484117	ENSG00000145734	ENST00000380675;ENST00000545546	T	0.50277	0.75	4.94	2.34	0.29019	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.54753	P	1.799999999996249E-5	.	.	.	.	.	.	T	0.45877	-0.9231	5	0.87932	D	0	.	1.6934	0.02856	0.1691:0.0937:0.1759:0.5613	rs469039;rs61337658;rs469039	.	.	.	L	432	ENSP00000370050:R432L	ENSP00000370050:R432L	R	+	2	0	BDP1	70884777	0.021000	0.18746	0.321000	0.25320	0.027000	0.11550	0.510000	0.22723	0.325000	0.23359	-0.256000	0.11100	CGC	G|0.560;T|0.440	0.440	strong		0.363	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
LDLRAD3	143458	hgsc.bcm.edu	37	11	36103228	36103228	+	Silent	SNP	A	A	G	rs1138807	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:36103228A>G	ENST00000315571.5	+	3	240	c.219A>G	c.(217-219)ccA>ccG	p.P73P	LDLRAD3_ENST00000524419.1_Silent_p.P24P|LDLRAD3_ENST00000528989.1_Silent_p.P24P	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	73	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				receptor-mediated endocytosis (GO:0006898)|regulation of protein processing (GO:0070613)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(7)|skin(1)	28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				AATGTGGCCCAACCTTCTTCC	0.512													G|||	1708	0.341054	0.41	0.402	5008	,	,		22683	0.3522		0.3151	False		,,,				2504	0.2198				p.P73P		Atlas-SNP	.											.	LDLRAD3	52	.	0			c.A219G						PASS	.	G		1712,2692	650.4+/-399.0	340,1032,830	163.0	131.0	142.0		219	-4.1	0.4	11	dbSNP_86	142	2899,5697	671.8+/-402.9	471,1957,1870	no	coding-synonymous	LDLRAD3	NM_174902.2		811,2989,2700	GG,GA,AA		33.725,38.8738,35.4692		73/346	36103228	4611,8389	2202	4298	6500	SO:0001819	synonymous_variant	143458	exon3			TGGCCCAACCTTC	AK075546	CCDS31462.1	11p13	2014-06-05			ENSG00000179241	ENSG00000179241			27046	protein-coding gene	gene with protein product						21795536	Standard	NM_174902		Approved	LRAD3	uc001mwk.1	Q86YD5	OTTHUMG00000166313	ENST00000315571.5:c.219A>G	11.37:g.36103228A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_174902	B7Z1U3|B9EG81|Q8NBJ0	Silent	SNP	ENST00000315571.5	37	CCDS31462.1																																																																																			G|0.359;N|0.000	0.359	strong		0.512	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902	
NAV3	89795	hgsc.bcm.edu	37	12	78530991	78530991	+	Silent	SNP	C	C	T	rs61754236	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:78530991C>T	ENST00000397909.2	+	19	4649	c.4476C>T	c.(4474-4476)ccC>ccT	p.P1492P	NAV3_ENST00000266692.7_Silent_p.P1315P|NAV3_ENST00000536525.2_Silent_p.P1492P|NAV3_ENST00000228327.6_Silent_p.P1492P			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1492	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.P1492P(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TTAACCTTCCCGGGCCCAGCA	0.468										HNSCC(70;0.22)			C|||	26	0.00519169	0.0053	0.0043	5008	,	,		17758	0.0		0.0109	False		,,,				2504	0.0051				p.P1492P		Atlas-SNP	.											NAV3,NS,carcinoma,0,1	NAV3	506	1	1	Substitution - coding silent(1)	stomach(1)	c.C4476T						scavenged	.	C		26,3714		0,26,1844	105.0	103.0	104.0		4476	-5.1	0.8	12	dbSNP_129	104	91,8131		3,85,4023	no	coding-synonymous	NAV3	NM_014903.4		3,111,5867	TT,TC,CC		1.1068,0.6952,0.9781		1492/2364	78530991	117,11845	1870	4111	5981	SO:0001819	synonymous_variant	89795	exon19			CCTTCCCGGGCCC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.4476C>T	12.37:g.78530991C>T		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	164	82	0.5	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37		11	0.005036630036630037	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	4.289	0.052786	0.08291	0.006952	0.011068	ENSG00000067798	ENST00000552895	.	.	.	5.76	-5.07	0.02938	.	.	.	.	.	T	0.41673	0.1169	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46569	-0.9182	4	.	.	.	-11.254	7.6438	0.28309	0.0:0.1774:0.4271:0.3955	rs61754236	.	.	.	W	387	.	.	R	+	1	2	NAV3	77055122	0.953000	0.32496	0.848000	0.33437	0.448000	0.32197	-0.014000	0.12656	-1.265000	0.02449	-1.584000	0.00852	CGG	C|0.994;T|0.006	0.006	strong		0.468	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
MS4A14	84689	hgsc.bcm.edu	37	11	60184277	60184277	+	Missense_Mutation	SNP	A	A	C	rs73481226	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:60184277A>C	ENST00000300187.6	+	5	2113	c.1836A>C	c.(1834-1836)caA>caC	p.Q612H	MS4A14_ENST00000531783.1_Missense_Mutation_p.Q645H|MS4A14_ENST00000531787.1_Missense_Mutation_p.Q500H|MS4A14_ENST00000395005.2_Missense_Mutation_p.Q595H	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	612	Gln-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						AGCCGGCCCAAGAGAAGAAAT	0.448													A|||	458	0.0914537	0.0363	0.0389	5008	,	,		20824	0.247		0.0169	False		,,,				2504	0.1196				p.Q645H		Atlas-SNP	.											.	MS4A14	120	.	0			c.A1935C						PASS	.	A	HIS/GLN,HIS/GLN	150,4256	103.4+/-141.9	2,146,2055	52.0	46.0	48.0		1785,1836	1.1	0.0	11	dbSNP_130	48	164,8436	75.4+/-138.0	0,164,4136	yes	missense,missense	MS4A14	NM_001079692.1,NM_032597.3	24,24	2,310,6191	CC,CA,AA		1.907,3.4044,2.4143	possibly-damaging,possibly-damaging	595/663,612/680	60184277	314,12692	2203	4300	6503	SO:0001583	missense	84689	exon6			GGCCCAAGAGAAG	AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"""membrane-spanning 4-domains, subfamily A, member 16"""	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.1836A>C	11.37:g.60184277A>C	ENSP00000300187:p.Gln612His	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	167	0.07646520146520147	10	0.02032520325203252	12	0.03314917127071823	133	0.23251748251748253	12	0.0158311345646438	A	12.64	1.998171	0.35226	0.034044	0.01907	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.35236	1.32;2.54;1.33;2.89	3.52	1.15	0.20763	.	10.332000	0.00166	N	0.000000	T	0.00039	0.0001	L	0.54323	1.7	0.54753	P	1.6000000000016E-5	D;D	0.64830	0.994;0.989	P;P	0.61940	0.896;0.79	T	0.04178	-1.0971	9	0.28530	T	0.3	2.6708	1.8542	0.03175	0.5153:0.0:0.236:0.2487	.	595;612	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	H	500;612;595;645	ENSP00000437222:Q500H;ENSP00000300187:Q612H;ENSP00000378453:Q595H;ENSP00000433761:Q645H	ENSP00000300187:Q612H	Q	+	3	2	MS4A14	59940853	0.016000	0.18221	0.003000	0.11579	0.216000	0.24613	0.380000	0.20602	0.483000	0.27608	0.460000	0.39030	CAA	A|0.960;C|0.040	0.040	strong		0.448	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
ARHGEF40	55701	hgsc.bcm.edu	37	14	21542753	21542753	+	Silent	SNP	G	G	A	rs1243472	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21542753G>A	ENST00000298694.4	+	3	991	c.864G>A	c.(862-864)gcG>gcA	p.A288A	ARHGEF40_ENST00000298693.3_Silent_p.A288A			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	288	Gly-rich.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						GACACCGGGCGTGGATGCACC	0.721													G|||	1212	0.242013	0.1452	0.1369	5008	,	,		16369	0.4762		0.2117	False		,,,				2504	0.2372				p.A288A		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.G864A						PASS	.	G		628,3730		45,538,1596	9.0	12.0	11.0		864	-10.2	0.1	14	dbSNP_87	11	1636,6912		158,1320,2796	no	coding-synonymous	ARHGEF40	NM_018071.3		203,1858,4392	AA,AG,GG		19.139,14.4103,17.5422		288/1520	21542753	2264,10642	2179	4274	6453	SO:0001819	synonymous_variant	55701	exon3			CCGGGCGTGGATG		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.864G>A	14.37:g.21542753G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	30	29	0.966667	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	37	CCDS32041.1																																																																																			G|0.741;A|0.259	0.259	strong		0.721	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
BTBD11	121551	hgsc.bcm.edu	37	12	107937768	107937768	+	Missense_Mutation	SNP	G	G	A	rs1558781	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:107937768G>A	ENST00000280758.5	+	3	1870	c.1342G>A	c.(1342-1344)Ggc>Agc	p.G448S	BTBD11_ENST00000490090.2_Missense_Mutation_p.G448S|BTBD11_ENST00000420571.2_Missense_Mutation_p.G448S	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	448			G -> S (in dbSNP:rs1558781).			integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CAAGCACCACGGCAATGGCAC	0.572													G|||	883	0.176318	0.1891	0.2637	5008	,	,		17911	0.2579		0.1014	False		,,,				2504	0.09				p.G448S		Atlas-SNP	.											BTBD11,NS,carcinoma,-1,2	BTBD11	122	2	0			c.G1342A						PASS	.	G	SER/GLY	897,3509	348.0+/-309.7	109,679,1415	49.0	44.0	46.0		1342	4.9	0.9	12	dbSNP_88	46	1012,7588	217.6+/-256.2	56,900,3344	yes	missense	BTBD11	NM_001018072.1	56	165,1579,4759	AA,AG,GG		11.7674,20.3586,14.6778	benign	448/1105	107937768	1909,11097	2203	4300	6503	SO:0001583	missense	121551	exon3			CACCACGGCAATG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.1342G>A	12.37:g.107937768G>A	ENSP00000280758:p.Gly448Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	396	0.1813186813186813	84	0.17073170731707318	79	0.21823204419889503	158	0.2762237762237762	75	0.09894459102902374	G	15.23	2.771922	0.49680	0.203586	0.117674	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000490090;ENST00000550706;ENST00000415943	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.76	4.87	0.63330	.	0.154372	0.64402	D	0.000017	T	0.00012	0.0000	N	0.16266	0.395	0.09310	P	0.9999999999999999	B;B;P	0.52316	0.179;0.064;0.952	B;B;B	0.39185	0.024;0.007;0.293	T	0.36720	-0.9736	9	0.25106	T	0.35	.	12.0181	0.53326	0.1384:0.0:0.8616:0.0	rs1558781;rs1558781	448;448;448	A6QL63-2;A6QL63;A6QL63-3	.;BTBDB_HUMAN;.	S	448;448;448;79;82	ENSP00000280758:G448S;ENSP00000413889:G448S;ENSP00000447319:G448S;ENSP00000447606:G79S;ENSP00000407416:G82S	ENSP00000280758:G448S	G	+	1	0	BTBD11	106461898	1.000000	0.71417	0.933000	0.37362	0.988000	0.76386	4.346000	0.59367	1.438000	0.47492	-0.137000	0.14449	GGC	G|0.845;A|0.155	0.155	strong		0.572	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1628992	1628992	+	Silent	SNP	G	G	A	rs60210378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1628992G>A	ENST00000399685.1	-	1	701	c.624C>T	c.(622-624)ggC>ggT	p.G208G		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	208	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		atgacccacagcctgaggagc	0.617													g|||	2309	0.461062	0.4939	0.4467	5008	,	,		17035	0.3879		0.5239	False		,,,				2504	0.4376				p.G208G		Atlas-SNP	.											KRTAP5-3,NS,carcinoma,0,1	KRTAP5-3	33	1	0			c.C624T						PASS	.						111.0	121.0	118.0					11																	1628992		2201	4295	6496	SO:0001819	synonymous_variant	387266	exon1			CCCACAGCCTGAG	AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"""Keratin associated proteins"""	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.624C>T	11.37:g.1628992G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	100	97	0.97	NM_001012708	Q6PL44|Q701N3	Silent	SNP	ENST00000399685.1	37	CCDS41591.1																																																																																			G|0.561;A|0.439	0.439	strong		0.617	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1		
OR5P2	120065	hgsc.bcm.edu	37	11	7818165	7818165	+	Missense_Mutation	SNP	C	C	T	rs569926953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7818165C>T	ENST00000329434.2	-	1	355	c.325G>A	c.(325-327)Gtc>Atc	p.V109I	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V109I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GCCAGAAGGACGCATTCGACT	0.483																																					p.V109I		Atlas-SNP	.											OR5P2,brain,glioma,0,2	OR5P2	68	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.G325A						scavenged	.						96.0	111.0	106.0					11																	7818165		2105	4292	6397	SO:0001583	missense	120065	exon1			GAAGGACGCATTC	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.325G>A	11.37:g.7818165C>T	ENSP00000331823:p.Val109Ile	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	60	3	0.05	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	C	6.601	0.479294	0.12581	.	.	ENSG00000183303	ENST00000329434	T	0.01059	5.39	5.5	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	0.172021	0.42172	N	0.000756	T	0.00724	0.0024	N	0.11000	0.08	0.18873	N	0.999981	B	0.02656	0.0	B	0.04013	0.001	T	0.49214	-0.8963	10	0.49607	T	0.09	-40.3172	3.5462	0.07829	0.6539:0.1394:0.0739:0.1327	.	109	Q8WZ92	OR5P2_HUMAN	I	109	ENSP00000331823:V109I	ENSP00000331823:V109I	V	-	1	0	OR5P2	7774741	0.000000	0.05858	0.991000	0.47740	0.012000	0.07955	-0.165000	0.09968	0.161000	0.19458	-1.921000	0.00515	GTC	.	.	none		0.483	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
CCDC116	164592	hgsc.bcm.edu	37	22	21988599	21988599	+	Missense_Mutation	SNP	G	G	A	rs371513	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:21988599G>A	ENST00000292779.3	+	3	522	c.361G>A	c.(361-363)Gga>Aga	p.G121R	CCDC116_ENST00000607942.1_Missense_Mutation_p.G121R	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	121			G -> R (in dbSNP:rs371513).							endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					GCCAAGTGGTGGACGGCGGGC	0.662													G|||	649	0.129593	0.1135	0.1556	5008	,	,		15740	0.0417		0.2018	False		,,,				2504	0.1493				p.G121R		Atlas-SNP	.											.	CCDC116	56	.	0			c.G361A						PASS	.	G	ARG/GLY	478,3928	222.6+/-239.4	25,428,1750	92.0	86.0	88.0		361	-2.9	0.0	22	dbSNP_80	88	1636,6964	297.8+/-303.6	153,1330,2817	yes	missense	CCDC116	NM_152612.2	125	178,1758,4567	AA,AG,GG		19.0233,10.8488,16.254	benign	121/614	21988599	2114,10892	2203	4300	6503	SO:0001583	missense	164592	exon3			AGTGGTGGACGGC	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.361G>A	22.37:g.21988599G>A	ENSP00000292779:p.Gly121Arg	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	41	26	0.634146	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	290	0.13278388278388278	57	0.11585365853658537	65	0.17955801104972377	24	0.04195804195804196	144	0.18997361477572558	G	0.011	-1.717935	0.00706	0.108488	0.190233	ENSG00000161180	ENST00000292779	T	0.21361	2.01	4.42	-2.88	0.05682	.	0.892392	0.09571	N	0.784163	T	0.00012	0.0000	N	0.04959	-0.14	0.80722	P	0.0	B;B	0.20887	0.012;0.049	B;B	0.17433	0.018;0.018	T	0.46062	-0.9218	8	.	.	.	-45.4808	8.7821	0.34798	0.5812:0.0:0.4188:0.0	rs371513;rs60165197;rs371513	121;121	B7Z7H5;Q8IYX3-2	.;.	R	121	ENSP00000292779:G121R	.	G	+	1	0	CCDC116	20318599	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.162000	0.03141	-0.552000	0.06167	-0.658000	0.03865	GGA	G|0.847;A|0.153	0.153	strong		0.662	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
HOXD12	3238	hgsc.bcm.edu	37	2	176965086	176965086	+	Missense_Mutation	SNP	G	G	A	rs35817516	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:176965086G>A	ENST00000406506.2	+	1	629	c.557G>A	c.(556-558)cGa>cAa	p.R186Q	HOXD12_ENST00000404162.2_Missense_Mutation_p.R186Q			P35452	HXD12_HUMAN	homeobox D12	186			R -> Q (in dbSNP:rs35817516).		embryonic digit morphogenesis (GO:0042733)|pattern specification process (GO:0007389)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		TCTTGCCTGCGACCTTCACTG	0.662													G|||	344	0.0686901	0.0106	0.2176	5008	,	,		14242	0.006		0.1223	False		,,,				2504	0.0511				p.R186Q		Atlas-SNP	.											.	HOXD12	25	.	0			c.G557A						PASS	.	G	GLN/ARG	110,3442		1,108,1667	12.0	14.0	13.0		557	4.6	1.0	2	dbSNP_126	13	912,6792		41,830,2981	yes	missense	HOXD12	NM_021193.3	43	42,938,4648	AA,AG,GG		11.838,3.0968,9.0796	benign	186/271	176965086	1022,10234	1776	3852	5628	SO:0001583	missense	3238	exon1			GCCTGCGACCTTC		CCDS46456.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170178	ENSG00000170178		"""Homeoboxes / ANTP class : HOXL subclass"""	5135	protein-coding gene	gene with protein product		142988	"""homeo box D12"""	HOX4H		1675198, 1973146	Standard	NM_021193		Approved		uc010zev.1	P35452	OTTHUMG00000150358	ENST00000406506.2:c.557G>A	2.37:g.176965086G>A	ENSP00000385586:p.Arg186Gln	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	222	110	0.495495	NM_021193	B5MCP0|Q0VAD7|Q0VAD8|Q9NS03	Missense_Mutation	SNP	ENST00000406506.2	37	CCDS46456.1	159	0.07280219780219781	5	0.01016260162601626	65	0.17955801104972377	2	0.0034965034965034965	87	0.11477572559366754	G	16.01	3.000424	0.54147	0.030968	0.11838	ENSG00000170178	ENST00000406506;ENST00000404162	D	0.95588	-3.75	5.46	4.58	0.56647	Homeodomain-like (1);	0.057159	0.64402	D	0.000002	T	0.01765	0.0056	L	0.55103	1.725	0.28197	P	0.9275293	P;P	0.37500	0.597;0.51	B;B	0.23018	0.043;0.025	T	0.47736	-0.9094	9	0.35671	T	0.21	.	12.8047	0.57607	0.0759:0.0:0.9241:0.0	rs35817516;rs62188664;rs35817516	186;186	B5MCD3;P35452	.;HXD12_HUMAN	Q	186	ENSP00000385586:R186Q	ENSP00000385132:R186Q	R	+	2	0	HOXD12	176673332	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.452000	0.66638	1.305000	0.44909	0.655000	0.94253	CGA	G|0.928;A|0.072	0.072	strong		0.662	HOXD12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359253.2	NM_021193	
THUMPD1	55623	hgsc.bcm.edu	37	16	20748331	20748331	+	Missense_Mutation	SNP	C	C	A	rs11074471	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20748331C>A	ENST00000381337.2	-	4	1277	c.933G>T	c.(931-933)gaG>gaT	p.E311D	THUMPD1_ENST00000396083.2_Missense_Mutation_p.E311D|THUMPD1_ENST00000431224.2_Missense_Mutation_p.E397D	NM_017736.3	NP_060206.2	Q9NXG2	THUM1_HUMAN	THUMP domain containing 1	311			E -> D (in dbSNP:rs11074471).				poly(A) RNA binding (GO:0044822)			NS(2)|large_intestine(2)|lung(6)|pancreas(1)|urinary_tract(1)	12						CCTCAGTATTCTCTGGTACCT	0.463													C|||	734	0.146565	0.0961	0.0865	5008	,	,		18190	0.2212		0.1262	False		,,,				2504	0.2014				p.E311D		Atlas-SNP	.											.	THUMPD1	33	.	0			c.G933T						PASS	.	C	ASP/GLU	418,3984	204.1+/-226.4	31,356,1814	179.0	166.0	171.0		933	2.8	0.0	16	dbSNP_120	171	1234,7366	249.2+/-276.5	86,1062,3152	yes	missense	THUMPD1	NM_017736.3	45	117,1418,4966	AA,AC,CC		14.3488,9.4957,12.7057	benign	311/354	20748331	1652,11350	2201	4300	6501	SO:0001583	missense	55623	exon4			AGTATTCTCTGGT	BC000448	CCDS10588.1	16p13.11	2010-06-17			ENSG00000066654	ENSG00000066654			23807	protein-coding gene	gene with protein product							Standard	XM_005255422		Approved	FLJ20274	uc002dho.3	Q9NXG2	OTTHUMG00000131558	ENST00000381337.2:c.933G>T	16.37:g.20748331C>A	ENSP00000370741:p.Glu311Asp	Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	260	127	0.488462	NM_017736	Q9BWC3	Missense_Mutation	SNP	ENST00000381337.2	37	CCDS10588.1	274	0.12545787545787546	36	0.07317073170731707	32	0.08839779005524862	102	0.17832167832167833	104	0.13720316622691292	C	7.688	0.690456	0.15039	0.094957	0.143488	ENSG00000066654	ENST00000381337;ENST00000431224;ENST00000396083	T;T;T	0.50001	0.84;0.76;0.84	5.92	2.77	0.32553	.	0.423294	0.26692	N	0.022994	T	0.00073	0.0002	L	0.54323	1.7	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.09997	-1.0649	9	0.16420	T	0.52	.	5.0688	0.14596	0.0:0.5405:0.1705:0.289	rs11074471;rs61089332;rs11074471	311	Q9NXG2	THUM1_HUMAN	D	311;397;311	ENSP00000370741:E311D;ENSP00000392282:E397D;ENSP00000379392:E311D	ENSP00000370741:E311D	E	-	3	2	THUMPD1	20655832	0.000000	0.05858	0.004000	0.12327	0.026000	0.11368	-0.042000	0.12063	0.769000	0.33313	0.561000	0.74099	GAG	C|0.868;A|0.132	0.132	strong		0.463	THUMPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254420.1	NM_017736	
MUC2	4583	hgsc.bcm.edu	37	11	1081141	1081141	+	Splice_Site	SNP	C	C	T	rs41375149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1081141C>T	ENST00000441003.2	+	11	1464	c.1437C>T	c.(1435-1437)acC>acT	p.T479T	MUC2_ENST00000359061.5_Splice_Site_p.T479T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	479	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCCACGTGACCGGTGAGTTGT	0.657													C|||	283	0.0565096	0.0408	0.0461	5008	,	,		16341	0.0506		0.0934	False		,,,				2504	0.0532				p.T479T		Atlas-SNP	.											.	MUC2	614	.	0			c.C1437T						PASS	.	C		167,3805		4,159,1823	31.0	37.0	35.0		1437	-7.3	0.6	11	dbSNP_127	35	744,7582		33,678,3452	yes	coding-synonymous-near-splice	MUC2	NM_002457.2		37,837,5275	TT,TC,CC		8.9359,4.2044,7.4077		479/2813	1081141	911,11387	1986	4163	6149	SO:0001630	splice_region_variant	4583	exon11			CGTGACCGGTGAG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.1438+1C>T	11.37:g.1081141C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	113	49	0.433628	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.939;T|0.061	0.061	strong		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	Silent
VIPR2	7434	hgsc.bcm.edu	37	7	158827326	158827326	+	Silent	SNP	G	G	A	rs2071624	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:158827326G>A	ENST00000262178.2	-	9	1010	c.825C>T	c.(823-825)aaC>aaT	p.N275N	VIPR2_ENST00000377633.3_Silent_p.N259N|VIPR2_ENST00000402066.1_Silent_p.N416N	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	275					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		CACTGTGGTCGTTTGTATCCC	0.483													G|||	1739	0.347244	0.2383	0.2723	5008	,	,		20595	0.5962		0.2525	False		,,,				2504	0.3885				p.N275N	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.C825T						PASS	.	G		916,3490	348.7+/-310.1	95,726,1382	119.0	107.0	111.0		825	-3.8	0.9	7	dbSNP_96	111	1565,7035	293.8+/-301.5	131,1303,2866	no	coding-synonymous	VIPR2	NM_003382.4		226,2029,4248	AA,AG,GG		18.1977,20.7898,19.0758		275/439	158827326	2481,10525	2203	4300	6503	SO:0001819	synonymous_variant	7434	exon9			GTGGTCGTTTGTA	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12695	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 2"""	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.825C>T	7.37:g.158827326G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	116	63	0.543103	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	37	CCDS5950.1																																																																																			G|0.742;N|0.000	.	strong		0.483	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382	
ZNF831	128611	hgsc.bcm.edu	37	20	57829301	57829301	+	Missense_Mutation	SNP	T	T	C	rs259956	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:57829301T>C	ENST00000371030.2	+	5	4537	c.4537T>C	c.(4537-4539)Tca>Cca	p.S1513P		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1513			S -> P (in dbSNP:rs259956).				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CAGTGCTGAATCACGAGACCA	0.527													C|||	3096	0.618211	0.3116	0.6081	5008	,	,		18876	0.9107		0.5606	False		,,,				2504	0.7975				p.S1513P		Atlas-SNP	.											ZNF831,caecum,carcinoma,0,1	ZNF831	287	1	0			c.T4537C						PASS	.	C	PRO/SER	1427,2813		252,923,945	48.0	52.0	51.0		4537	-3.0	0.0	20	dbSNP_79	51	4568,3926		1251,2066,930	yes	missense	ZNF831	NM_178457.1	74	1503,2989,1875	CC,CT,TT		46.2209,33.6557,47.0787	benign	1513/1678	57829301	5995,6739	2120	4247	6367	SO:0001583	missense	128611	exon5			GCTGAATCACGAG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.4537T>C	20.37:g.57829301T>C	ENSP00000360069:p.Ser1513Pro	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	1304	0.5970695970695971	149	0.30284552845528456	206	0.569060773480663	518	0.9055944055944056	431	0.5686015831134564	C	1.351	-0.591513	0.03799	0.336557	0.537791	ENSG00000124203	ENST00000371030	T	0.04917	3.53	5.6	-2.98	0.05513	.	0.971967	0.08452	N	0.943747	T	0.00012	0.0000	N	0.01003	-1.06	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	9	0.02654	T	1	0.0796	1.5739	0.02621	0.1233:0.2135:0.3263:0.3369	rs259956;rs17829996;rs52820703;rs61110182;rs259956	1513	Q5JPB2	ZN831_HUMAN	P	1513	ENSP00000360069:S1513P	ENSP00000360069:S1513P	S	+	1	0	ZNF831	57262696	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.381000	0.07417	-0.195000	0.10382	-0.197000	0.12766	TCA	T|0.411;C|0.589	0.589	strong		0.527	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
RASGEF1B	153020	hgsc.bcm.edu	37	4	82355804	82355804	+	Missense_Mutation	SNP	C	C	T	rs34211143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:82355804C>T	ENST00000264400.2	-	11	1340	c.1189G>A	c.(1189-1191)Gtc>Atc	p.V397I	RASGEF1B_ENST00000335927.7_Missense_Mutation_p.V355I|RASGEF1B_ENST00000509081.1_Missense_Mutation_p.V396I	NM_152545.1	NP_689758.1	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	397	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	26						TCAAAATTGACATGGCCATTG	0.453													C|||	30	0.00599042	0.0008	0.0159	5008	,	,		17128	0.0		0.0179	False		,,,				2504	0.0				p.V397I		Atlas-SNP	.											RASGEF1B,NS,carcinoma,+2,1	RASGEF1B	44	1	0			c.G1189A						PASS	.	C	ILE/VAL	17,4389	24.3+/-50.5	0,17,2186	74.0	68.0	70.0		1189	3.7	1.0	4	dbSNP_126	70	131,8469	64.9+/-127.2	1,129,4170	yes	missense	RASGEF1B	NM_152545.1	29	1,146,6356	TT,TC,CC		1.5233,0.3858,1.1379	benign	397/474	82355804	148,12858	2203	4300	6503	SO:0001583	missense	153020	exon11			AATTGACATGGCC	AK056257	CCDS34022.1, CCDS75151.1, CCDS75152.1	4q21.21	2013-09-24				ENSG00000138670			24881	protein-coding gene	gene with protein product		614532				12488504	Standard	XM_005262776		Approved	GPIG4, FLJ31695	uc003hmi.1	Q0VAM2		ENST00000264400.2:c.1189G>A	4.37:g.82355804C>T	ENSP00000264400:p.Val397Ile	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_152545	Q0VAM1|Q4W5L7|Q4W5M3|Q96MY8	Missense_Mutation	SNP	ENST00000264400.2	37	CCDS34022.1	18	0.008241758241758242	0	0.0	6	0.016574585635359115	0	0.0	12	0.0158311345646438	C	4.202	0.036168	0.08148	0.003858	0.015233	ENSG00000138670	ENST00000509081;ENST00000264400;ENST00000335927	T;T;T	0.26373	1.74;1.74;1.74	4.62	3.69	0.42338	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine-nucleotide exchange factor, conserved site (1);Ras guanine nucleotide exchange factor, domain (1);	0.122271	0.53938	D	0.000046	T	0.03783	0.0107	N	0.01809	-0.71	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.19063	-1.0317	10	0.02654	T	1	.	12.9491	0.58389	0.0:0.9062:0.0:0.0938	rs34211143	355;396;397	Q0VAM2-2;Q0VAM2-3;Q0VAM2	.;.;RGF1B_HUMAN	I	396;397;355	ENSP00000425393:V396I;ENSP00000264400:V397I;ENSP00000338437:V355I	ENSP00000264400:V397I	V	-	1	0	RASGEF1B	82574828	0.941000	0.31946	0.997000	0.53966	0.997000	0.91878	1.302000	0.33459	2.413000	0.81919	0.585000	0.79938	GTC	C|0.989;T|0.011	0.011	strong		0.453	RASGEF1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362830.1	NM_152545	
MATN1	4146	hgsc.bcm.edu	37	1	31188089	31188089	+	Silent	SNP	C	C	T	rs1065755	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:31188089C>T	ENST00000373765.4	-	6	1310	c.1275G>A	c.(1273-1275)gaG>gaA	p.E425E	MATN1_ENST00000477320.1_5'Flank	NM_002379.3	NP_002370.1	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein	425	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|growth plate cartilage chondrocyte morphogenesis (GO:0003429)|protein complex assembly (GO:0006461)|regulation of bone mineralization (GO:0030500)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)		CTGCCACAGGCTCTGAGGCTA	0.532													C|||	1440	0.28754	0.2564	0.4121	5008	,	,		22606	0.1835		0.3638	False		,,,				2504	0.2699				p.E425E		Atlas-SNP	.											.	MATN1	28	.	0			c.G1275A						PASS	.	C		1282,3124	436.4+/-344.6	173,936,1094	224.0	184.0	198.0		1275	-0.2	0.9	1	dbSNP_86	198	2922,5678	455.2+/-363.7	504,1914,1882	no	coding-synonymous	MATN1	NM_002379.3		677,2850,2976	TT,TC,CC		33.9767,29.0967,32.3235		425/497	31188089	4204,8802	2203	4300	6503	SO:0001819	synonymous_variant	4146	exon6			CACAGGCTCTGAG	M55675	CCDS336.1	1p35	2008-02-05			ENSG00000162510	ENSG00000162510			6907	protein-coding gene	gene with protein product		115437		CRTM, CMP		2246248, 9083061	Standard	NM_002379		Approved		uc001brz.3	P21941	OTTHUMG00000003705	ENST00000373765.4:c.1275G>A	1.37:g.31188089C>T		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	294	153	0.520408	NM_002379	B2R7E3|Q5TBB9	Silent	SNP	ENST00000373765.4	37	CCDS336.1																																																																																			C|0.696;T|0.304	0.304	strong		0.532	MATN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010458.1	NM_002379	
LIPC	3990	hgsc.bcm.edu	37	15	58860963	58860963	+	Silent	SNP	C	C	A	rs6074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:58860963C>A	ENST00000356113.6	+	11	2052	c.1437C>A	c.(1435-1437)acC>acA	p.T479T	LIPC_ENST00000433326.2_Silent_p.T418T|LIPC_ENST00000299022.5_Silent_p.T479T			P11150	LIPC_HUMAN	lipase, hepatic	479	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		TTCGCCCAACCCAGGAAAAAA	0.348													C|||	1009	0.201478	0.0817	0.196	5008	,	,		19374	0.249		0.1561	False		,,,				2504	0.365				p.T479T		Atlas-SNP	.											.	LIPC	56	.	0			c.C1437A						PASS	.	C		432,3952	207.2+/-228.6	27,378,1787	85.0	80.0	81.0		1437	4.6	1.0	15	dbSNP_52	81	1220,7364	244.0+/-273.4	88,1044,3160	no	coding-synonymous	LIPC	NM_000236.2		115,1422,4947	AA,AC,CC		14.2125,9.854,12.739		479/500	58860963	1652,11316	2192	4292	6484	SO:0001819	synonymous_variant	3990	exon9			CCCAACCCAGGAA		CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.1437C>A	15.37:g.58860963C>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_000236	A2RUB4|A8K9B6|O43571|P78529|Q99465	Silent	SNP	ENST00000356113.6	37	CCDS10166.1																																																																																			C|0.856;A|0.144	0.144	strong		0.348	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1		
HFE	3077	hgsc.bcm.edu	37	6	26093141	26093141	+	Missense_Mutation	SNP	G	G	A	rs1800562	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:26093141G>A	ENST00000357618.5	+	4	967	c.845G>A	c.(844-846)tGc>tAc	p.C282Y	HFE_ENST00000352392.4_Intron|HFE_ENST00000461397.1_Missense_Mutation_p.C268Y|HFE_ENST00000309234.6_Missense_Mutation_p.C282Y|HFE_ENST00000488199.1_Missense_Mutation_p.C180Y|HFE_ENST00000349999.4_Missense_Mutation_p.C194Y|HFE_ENST00000336625.8_Missense_Mutation_p.C176Y|HFE_ENST00000397022.3_Missense_Mutation_p.C259Y|HFE_ENST00000470149.1_Missense_Mutation_p.C279Y|HFE_ENST00000353147.5_Missense_Mutation_p.C102Y|HFE_ENST00000317896.7_Missense_Mutation_p.C190Y	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	282	Alpha-3.|Ig-like C1-type.		C -> Y (in HFE1; associated with susceptibility to porphyria cutanea tarda; associated with increased serum transferrin levels; higher frequency in patients with type 2 diabetes than in controls; dbSNP:rs1800562). {ECO:0000269|PubMed:10094552, ECO:0000269|PubMed:10194428, ECO:0000269|PubMed:11069625, ECO:0000269|PubMed:11423500, ECO:0000269|PubMed:12542741, ECO:0000269|PubMed:14633868, ECO:0000269|PubMed:18157833, ECO:0000269|PubMed:8696333, ECO:0000269|PubMed:9024376, ECO:0000269|PubMed:9106528, ECO:0000269|PubMed:9620340, ECO:0000269|Ref.8}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGATATACGTGCCAGGTGGAG	0.547									Hemochromatosis				G|||	63	0.0125799	0.0023	0.0216	5008	,	,		19430	0.0		0.0427	False		,,,				2504	0.002				p.C282Y		Atlas-SNP	.											.	HFE	37	.	0			c.G845A	GRCh37	CM004391|CM960828	HFE	M	rs1800562	PASS	.	G	TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,	67,4339		1,65,2137	84.0	81.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	845,527,569,803,581,539,776,305,	5.3	1.0	6	dbSNP_89	82	551,8049		18,515,3767	yes	missense,missense,missense,missense,missense,missense,missense,missense,intron	HFE	NM_000410.3,NM_139003.2,NM_139004.2,NM_139006.2,NM_139007.2,NM_139008.2,NM_139009.2,NM_139010.2,NM_139011.2	194,194,194,194,194,194,194,194,	19,580,5904	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	6.407,1.5207,4.7517	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,	282/349,176/243,190/257,268/335,194/261,180/247,259/326,102/169,	26093141	618,12388	2203	4300	6503	SO:0001583	missense	3077	exon4	Familial Cancer Database		ATACGTGCCAGGT		CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"""Immunoglobulin superfamily / C1-set domain containing"""	4886	protein-coding gene	gene with protein product	"""high Fe"""	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.845G>A	6.37:g.26093141G>A	ENSP00000417404:p.Cys282Tyr	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	192	87	0.453125	NM_000410	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	ENST00000357618.5	37	CCDS4578.1	43	0.019688644688644688	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	35	0.04617414248021108	.	17.19	3.326013	0.60743	0.015207	0.06407	ENSG00000010704	ENST00000349999;ENST00000397022;ENST00000317896;ENST00000353147;ENST00000357618;ENST00000470149;ENST00000336625;ENST00000461397;ENST00000488199;ENST00000309234	D;D;D;D;D;D;D;D;D;D	0.95342	-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68	5.35	5.35	0.76521	Immunoglobulin/major histocompatibility complex, conserved site (1);Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	D	0.98557	0.9518	H	0.99143	4.445	0.80722	A	1	D;D;D;D;D;P;D;D;D	0.89917	0.982;1.0;1.0;1.0;1.0;0.951;0.996;0.993;0.961	P;D;D;D;D;P;P;D;P	0.91635	0.756;0.999;0.999;0.999;0.999;0.56;0.826;0.917;0.667	D	0.98784	1.0733	9	0.87932	D	0	.	14.7506	0.69522	0.0:0.0:1.0:0.0	rs1800562;rs4134660;rs17530654;rs58044250;rs1800562	279;102;180;190;176;268;194;259;282	Q6B0J5;Q30201-6;Q30201-4;Q30201-7;Q30201-10;Q30201-3;Q30201-2;Q30201-5;Q30201	.;.;.;.;.;.;.;.;HFE_HUMAN	Y	194;259;190;102;282;279;176;268;180;282	ENSP00000259699:C194Y;ENSP00000380217:C259Y;ENSP00000313776:C190Y;ENSP00000312342:C102Y;ENSP00000417404:C282Y;ENSP00000419725:C279Y;ENSP00000337819:C176Y;ENSP00000420802:C268Y;ENSP00000420559:C180Y;ENSP00000311698:C282Y	ENSP00000311698:C282Y	C	+	2	0	HFE	26201120	1.000000	0.71417	0.993000	0.49108	0.351000	0.29236	4.282000	0.58971	2.941000	0.99782	0.655000	0.94253	TGC	G|0.966;A|0.034	0.034	strong		0.547	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1		
N4BP3	23138	hgsc.bcm.edu	37	5	177547519	177547519	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:177547519G>A	ENST00000274605.5	+	3	1030	c.671G>A	c.(670-672)cGg>cAg	p.R224Q		NM_015111.1	NP_055926.1	O15049	N4BP3_HUMAN	NEDD4 binding protein 3	224						cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)				breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCCCTGGACCGGGCCTCTCAA	0.657																																					p.R224Q		Atlas-SNP	.											N4BP3,colon,carcinoma,0,1	N4BP3	25	1	0			c.G671A						scavenged	.						37.0	44.0	42.0					5																	177547519		2201	4297	6498	SO:0001583	missense	23138	exon3			TGGACCGGGCCTC	AB002339	CCDS34307.1	5q35.3	2012-05-17				ENSG00000145911			29852	protein-coding gene	gene with protein product						9205841, 11717310	Standard	XM_006714834		Approved	LZTS4	uc003mik.1	O15049		ENST00000274605.5:c.671G>A	5.37:g.177547519G>A	ENSP00000274605:p.Arg224Gln	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	105	2	0.0190476	NM_015111	B4DIL3|D3DWP3|Q6ZSQ6|Q7Z6I3	Missense_Mutation	SNP	ENST00000274605.5	37	CCDS34307.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.233371	0.79688	.	.	ENSG00000145911	ENST00000274605	T	0.00573	6.48	5.0	5.0	0.66597	.	0.343012	0.30492	N	0.009504	T	0.01592	0.0051	L	0.43152	1.355	0.45567	D	0.998513	D	0.76494	0.999	P	0.61275	0.886	T	0.73981	-0.3811	10	0.54805	T	0.06	-39.489	15.8227	0.78673	0.0:0.0:1.0:0.0	.	224	O15049	N4BP3_HUMAN	Q	224	ENSP00000274605:R224Q	ENSP00000274605:R224Q	R	+	2	0	N4BP3	177480125	1.000000	0.71417	0.990000	0.47175	0.867000	0.49689	5.997000	0.70646	2.600000	0.87896	0.563000	0.77884	CGG	.	.	none		0.657	N4BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373552.2	NM_015111	
PIWIL4	143689	hgsc.bcm.edu	37	11	94337220	94337220	+	Silent	SNP	C	C	T	rs593690	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:94337220C>T	ENST00000299001.6	+	13	1847	c.1636C>T	c.(1636-1638)Ctg>Ttg	p.L546L	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	546	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TGATGTTCAGCTGGTAAGTAC	0.318													T|||	2933	0.585663	0.9085	0.4524	5008	,	,		14671	0.502		0.4145	False		,,,				2504	0.5061				p.L546L		Atlas-SNP	.											.	PIWIL4	70	.	0			c.C1636T						PASS	.	T		3586,810	313.0+/-292.9	1473,640,85	89.0	90.0	90.0		1636	-0.6	1.0	11	dbSNP_83	90	3446,5146	623.1+/-397.4	706,2034,1556	no	coding-synonymous	PIWIL4	NM_152431.2		2179,2674,1641	TT,TC,CC		40.1071,18.4258,45.8577		546/853	94337220	7032,5956	2198	4296	6494	SO:0001819	synonymous_variant	143689	exon13			GTTCAGCTGGTAA	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1636C>T	11.37:g.94337220C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			C|0.455;T|0.545	0.545	strong		0.318	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
H2AFY	9555	hgsc.bcm.edu	37	5	134670765	134670765	+	Silent	SNP	A	A	G	rs3210047	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:134670765A>G	ENST00000511689.1	-	9	1613	c.1020T>C	c.(1018-1020)tcT>tcC	p.S340S	H2AFY_ENST00000512507.1_5'UTR|CTC-349C3.1_ENST00000432382.3_Intron|H2AFY_ENST00000510038.1_Silent_p.S340S|H2AFY_ENST00000423969.2_Silent_p.S168S|H2AFY_ENST00000312469.4_Silent_p.S337S|H2AFY_ENST00000304332.4_Silent_p.S339S	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	340	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGGACATTGTAGACACGAAGT	0.488													G|||	598	0.119409	0.2753	0.0562	5008	,	,		22435	0.0556		0.0626	False		,,,				2504	0.0777				p.S340S		Atlas-SNP	.											.	H2AFY	61	.	0			c.T1020C						PASS	.	G	,,,	1176,3230	711.7+/-408.0	169,838,1196	137.0	125.0	129.0		1017,1017,1011,1020	-2.1	0.8	5	dbSNP_105	129	624,7976	791.2+/-407.6	24,576,3700	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	H2AFY	NM_001040158.1,NM_004893.2,NM_138609.2,NM_138610.2	,,,	193,1414,4896	GG,GA,AA		7.2558,26.6909,13.8398	,,,	339/372,339/372,337/370,340/373	134670765	1800,11206	2203	4300	6503	SO:0001819	synonymous_variant	9555	exon9			CATTGTAGACACG	AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"""Histones / Replication-independent"""	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.1020T>C	5.37:g.134670765A>G		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	302	138	0.456954	NM_138610	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Silent	SNP	ENST00000511689.1	37	CCDS4185.1																																																																																			A|0.875;G|0.125	0.125	strong		0.488	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893	
CLC	1178	hgsc.bcm.edu	37	19	40224986	40224986	+	Silent	SNP	A	A	G	rs384138	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40224986A>G	ENST00000221804.4	-	3	315	c.240T>C	c.(238-240)aaT>aaC	p.N80N		NM_001828.5	NP_001819.2	Q05315	LEG10_HUMAN	Charcot-Leyden crystal galectin	80	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				multicellular organismal development (GO:0007275)|regulation of activated T cell proliferation (GO:0046006)|regulation of T cell anergy (GO:0002667)|regulation of T cell cytokine production (GO:0002724)|T cell apoptotic process (GO:0070231)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)	p.N80N(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(2)|stomach(1)	12	all_cancers(60;2.99e-06)|all_lung(34;4.7e-08)|Lung NSC(34;5.46e-08)|Ovarian(47;0.06)	Renal(1328;0.000147)|Hepatocellular(1079;0.0202)|Myeloproliferative disorder(2;0.0255)	Epithelial(26;6.43e-25)|OV - Ovarian serous cystadenocarcinoma(5;1.07e-24)|all cancers(26;8.38e-23)	GBM - Glioblastoma multiforme(1328;4.97e-06)|STAD - Stomach adenocarcinoma(1328;0.00655)		GAAAGGGCATATTCTTGGATT	0.527													a|||	3051	0.609225	0.7481	0.513	5008	,	,		21859	0.3373		0.6988	False		,,,				2504	0.6779				p.N80N		Atlas-SNP	.											CLC,NS,carcinoma,0,1	CLC	20	1	1	Substitution - coding silent(1)	prostate(1)	c.T240C						PASS	.	A		3361,1045		1281,799,123	205.0	168.0	181.0		240	-2.4	0.0	19	dbSNP_80	181	5734,2866		1883,1968,449	no	coding-synonymous	CLC	NM_001828.4		3164,2767,572	GG,GA,AA		33.3256,23.7177,30.0707		80/143	40224986	9095,3911	2203	4300	6503	SO:0001819	synonymous_variant	1178	exon3			GGGCATATTCTTG	L01664	CCDS33025.1	19q13.1	2013-06-12	2013-06-12		ENSG00000105205	ENSG00000105205		"""Lectins, galactoside-binding"""	2014	protein-coding gene	gene with protein product	"""eosinophil lysophospholipase"", ""lysolecithin acylhydrolase"", ""galectin 10"", ""lectin, galactoside-binding, soluble, 10"""	153310	"""Charcot-Leyden crystal protein"""			1577491, 11834744	Standard	NM_001828		Approved	LGALS10, MGC149659, Gal-10	uc002omh.3	Q05315		ENST00000221804.4:c.240T>C	19.37:g.40224986A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	152	62	0.407895	NM_001828	C5HZ13|C5HZ14|Q0VDE3	Silent	SNP	ENST00000221804.4	37	CCDS33025.1																																																																																			A|0.335;G|0.665	0.665	strong		0.527	CLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465225.1	NM_001828	
PRDM7	11105	hgsc.bcm.edu	37	16	90124871	90124871	+	Missense_Mutation	SNP	G	G	T	rs7206111	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90124871G>T	ENST00000449207.2	-	10	1324	c.1305C>A	c.(1303-1305)aaC>aaA	p.N435K	PRDM7_ENST00000407825.1_Missense_Mutation_p.T135K|PRDM7_ENST00000325921.6_Missense_Mutation_p.T135K	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	435			N -> K (in dbSNP:rs7206111).		regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)	p.T135K(1)		lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		CGTTCCACATGTTGACTGAGA	0.483													.|||	436	0.0870607	0.1225	0.0259	5008	,	,		19923	0.1776		0.0517	False		,,,				2504	0.0256				p.N435K		Atlas-SNP	.											PRDM7,NS,carcinoma,0,1	PRDM7	53	1	1	Substitution - Missense(1)	stomach(1)	c.C1305A						scavenged	.	G	LYS/ASN,LYS/THR	491,3905	229.1+/-243.8	22,447,1729	151.0	143.0	146.0		1305,404	2.7	0.1	16	dbSNP_116	146	512,8088	145.4+/-201.1	13,486,3801	no	missense,missense	PRDM7	NM_001098173.1,NM_052996.2	94,78	35,933,5530	TT,TG,GG		5.9535,11.1692,7.7178	possibly-damaging,possibly-damaging	435/493,135/172	90124871	1003,11993	2198	4300	6498	SO:0001583	missense	11105	exon10			CCACATGTTGACT	AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"""Zinc fingers, C2H2-type"", ""-"""	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.1305C>A	16.37:g.90124871G>T	ENSP00000396732:p.Asn435Lys	Somatic	325	2	0.00615385		WXS	Illumina HiSeq	Phase_I	393	192	0.48855	NM_001098173	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	37	CCDS45557.1	180|180	0.08241758241758242|0.08241758241758242	57|57	0.11585365853658537|0.11585365853658537	11|11	0.03038674033149171|0.03038674033149171	68|68	0.11888111888111888|0.11888111888111888	44|44	0.05804749340369393|0.05804749340369393	G|G	12.21|12.21	1.869148|1.869148	0.32977|0.32977	0.111692|0.111692	0.059535|0.059535	ENSG00000126856|ENSG00000126856	ENST00000449207|ENST00000325921;ENST00000407825	T|T;T	0.12879|0.50277	2.64|0.75;0.75	2.69|2.69	2.69|2.69	0.31865|0.31865	.|.	.|.	.|.	.|.	.|.	T|T	0.01454|0.01454	0.0047|0.0047	.|.	.|.	.|.	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B|D	0.23316|0.76494	0.083|0.999	B|D	0.19391|0.69142	0.025|0.962	T|T	0.32214|0.32214	-0.9915|-0.9915	6|6	.|.	.|.	.|.	0.1464|0.1464	7.4136|7.4136	0.27032|0.27032	0.0:0.0:0.7407:0.2593|0.0:0.0:0.7407:0.2593	rs7206111;rs52835907;rs7206111|rs7206111;rs52835907;rs7206111	435|135	Q9NQW5|Q9NQW5-2	PRDM7_HUMAN|.	K|K	435|135	ENSP00000396732:N435K|ENSP00000315512:T135K;ENSP00000385121:T135K	.|.	N|T	-|-	3|2	2|0	PRDM7|PRDM7	88652372|88652372	0.981000|0.981000	0.34729|0.34729	0.100000|0.100000	0.21137|0.21137	0.502000|0.502000	0.33828|0.33828	3.065000|3.065000	0.49994|0.49994	1.471000|1.471000	0.48121|0.48121	0.467000|0.467000	0.42956|0.42956	AAC|ACA	G|0.923;T|0.077	0.077	strong		0.483	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1		
FBXL4	26235	hgsc.bcm.edu	37	6	99323424	99323424	+	Silent	SNP	C	C	T	rs11537982	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:99323424C>T	ENST00000369244.2	-	9	1997	c.1569G>A	c.(1567-1569)ggG>ggA	p.G523G	FBXL4_ENST00000229971.1_Silent_p.G523G	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	523					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		TGGTGAAGCACCCGGTGCTGC	0.483													C|||	194	0.038738	0.0522	0.0375	5008	,	,		15524	0.002		0.0567	False		,,,				2504	0.0409				p.G523G		Atlas-SNP	.											.	FBXL4	54	.	0			c.G1569A						PASS	.	C		264,4142	150.3+/-184.3	7,250,1946	91.0	87.0	89.0		1569	-4.6	1.0	6	dbSNP_120	89	620,7980	161.1+/-214.1	18,584,3698	no	coding-synonymous	FBXL4	NM_012160.3		25,834,5644	TT,TC,CC		7.2093,5.9918,6.7969		523/622	99323424	884,12122	2203	4300	6503	SO:0001819	synonymous_variant	26235	exon8			GAAGCACCCGGTG	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"""F-boxes / Leucine-rich repeats"""	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.1569G>A	6.37:g.99323424C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	217	105	0.483871	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Silent	SNP	ENST00000369244.2	37	CCDS5041.1																																																																																			T|0.060;G|0.000;C|0.940	0.060	strong		0.483	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2		
NIPAL3	57185	hgsc.bcm.edu	37	1	24785393	24785393	+	Silent	SNP	C	C	T	rs2272935	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24785393C>T	ENST00000374399.4	+	9	1157	c.789C>T	c.(787-789)gcC>gcT	p.A263A	NIPAL3_ENST00000339255.2_Silent_p.A263A|NIPAL3_ENST00000003912.3_Silent_p.A181A	NM_020448.4	NP_065181.1	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3	263						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(1)	14						TGAGTCAAGCCTCACAGATGT	0.463													C|||	1534	0.30631	0.1589	0.4409	5008	,	,		20800	0.4534		0.2773	False		,,,				2504	0.2883				p.A263A		Atlas-SNP	.											NIPAL3,NS,carcinoma,+1,1	NIPAL3	36	1	0			c.C789T						PASS	.	C		704,3702	295.0+/-283.4	49,606,1548	215.0	176.0	189.0		789	1.6	1.0	1	dbSNP_100	189	2253,6347	382.3+/-340.3	281,1691,2328	no	coding-synonymous	NIPAL3	NM_020448.4		330,2297,3876	TT,TC,CC		26.1977,15.9782,22.7357		263/407	24785393	2957,10049	2203	4300	6503	SO:0001819	synonymous_variant	57185	exon9			TCAAGCCTCACAG	BX640883	CCDS30631.1	1p36.12-p35.1	2009-03-24		2009-03-24	ENSG00000001461	ENSG00000001461			25233	protein-coding gene	gene with protein product				NPAL3		8619474, 9110174	Standard	NM_020448		Approved	DJ462O23.2	uc001bjh.3	Q6P499	OTTHUMG00000003299	ENST00000374399.4:c.789C>T	1.37:g.24785393C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	198	97	0.489899	NM_020448	A2A298|Q6MZT9|Q9BVE6	Silent	SNP	ENST00000374399.4	37	CCDS30631.1	697	0.3191391941391941	77	0.1565040650406504	148	0.4088397790055249	260	0.45454545454545453	212	0.2796833773087071	C	16.35	3.098373	0.56183	0.159782	0.261977	ENSG00000001461	ENST00000432012	.	.	.	5.86	1.62	0.23740	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45862	-0.9232	3	.	.	.	-24.4414	1.4986	0.02471	0.2365:0.43:0.1193:0.2142	rs2272935;rs52791624;rs58306533;rs2272935	.	.	.	L	75	.	.	P	+	2	0	NIPAL3	24657980	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.530000	0.23036	0.366000	0.24427	0.563000	0.77884	CCT	C|0.732;T|0.268	0.268	strong		0.463	NIPAL3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276996.1	NM_020448	
OR4C15	81309	hgsc.bcm.edu	37	11	55322539	55322539	+	Missense_Mutation	SNP	G	G	A	rs12790125	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55322539G>A	ENST00000314644.2	+	1	757	c.757G>A	c.(757-759)Gtc>Atc	p.V253I		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						CCTCATGGTGGTCATCAACAG	0.468										HNSCC(20;0.049)			g|||	867	0.173123	0.118	0.2378	5008	,	,		18208	0.1528		0.2107	False		,,,				2504	0.184				p.V253I		Atlas-SNP	.											OR4C15,arm,malignant_melanoma,-2,1	OR4C15	145	1	0			c.G757A						PASS	.	G	ILE/VAL	591,3811	261.0+/-264.0	39,513,1649	172.0	114.0	134.0		757	2.0	0.1	11	dbSNP_121	134	1897,6695	338.2+/-322.6	225,1447,2624	yes	missense	OR4C15	NM_001001920.1	29	264,1960,4273	AA,AG,GG		22.0787,13.4257,19.1473	benign	253/371	55322539	2488,10506	2201	4296	6497	SO:0001583	missense	81309	exon1			ATGGTGGTCATCA	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"""GPCR / Class A : Olfactory receptors"""	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.757G>A	11.37:g.55322539G>A	ENSP00000324958:p.Val253Ile	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	372	371	0.997312	NM_001001920	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	379	0.17353479853479853	35	0.07113821138211382	84	0.23204419889502761	94	0.16433566433566432	166	0.21899736147757257	G	2.293	-0.362064	0.05103	0.134257	0.220787	ENSG00000181939	ENST00000314644	T	0.00076	8.76	5.02	1.98	0.26296	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B	0.17038	0.02	B	0.24269	0.052	T	0.01078	-1.1459	8	0.27785	T	0.31	.	3.4223	0.07398	0.2944:0.0:0.5283:0.1773	rs12790125;rs17496779;rs52792703;rs58731558;rs12790125	199	Q8NGM1	OR4CF_HUMAN	I	253	ENSP00000324958:V253I	ENSP00000324958:V253I	V	+	1	0	OR4C15	55079115	0.000000	0.05858	0.064000	0.19789	0.012000	0.07955	-0.121000	0.10643	0.244000	0.21351	0.385000	0.25706	GTC	G|0.819;A|0.181	0.181	strong		0.468	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920	
CEP131	22994	hgsc.bcm.edu	37	17	79169670	79169670	+	Missense_Mutation	SNP	C	C	T	rs61741549	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79169670C>T	ENST00000269392.4	-	16	2237	c.1990G>A	c.(1990-1992)Gag>Aag	p.E664K	AZI1_ENST00000374782.3_Missense_Mutation_p.E661K|RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000450824.2_Missense_Mutation_p.E661K|AZI1_ENST00000575907.1_Missense_Mutation_p.E664K	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		664					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GCCACACGCTCGGTGCATCTC	0.642													C|||	88	0.0175719	0.0015	0.0086	5008	,	,		18668	0.002		0.0278	False		,,,				2504	0.0511				p.E661K		Atlas-SNP	.											.	AZI1	145	.	0			c.G1981A						PASS	.	C	LYS/GLU,LYS/GLU	15,4389	22.3+/-47.3	0,15,2187	127.0	100.0	109.0		1981,1981	3.0	0.0	17	dbSNP_129	109	212,8388	90.2+/-152.3	5,202,4093	yes	missense,missense	AZI1	NM_001009811.2,NM_014984.2	56,56	5,217,6280	TT,TC,CC		2.4651,0.3406,1.7456	benign,benign	661/1045,661/1081	79169670	227,12777	2202	4300	6502	SO:0001583	missense	22994	exon16			CACGCTCGGTGCA																												ENST00000269392.4:c.1990G>A	17.37:g.79169670C>T	ENSP00000269392:p.Glu664Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	37		25	0.011446886446886446	0	0.0	4	0.011049723756906077	0	0.0	21	0.027704485488126648	C	5.905	0.351152	0.11182	0.003406	0.024651	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.13089	2.62;2.63;2.62	4.11	3.05	0.35203	.	0.529786	0.20181	N	0.097527	T	0.01592	0.0051	N	0.20766	0.605	0.09310	N	1	B;B;B;B	0.27951	0.093;0.04;0.066;0.195	B;B;B;B	0.23018	0.011;0.01;0.007;0.043	T	0.40001	-0.9586	10	0.05620	T	0.96	-3.3514	2.7914	0.05389	0.0:0.4655:0.2646:0.2699	.	661;664;661;661	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	K	661;661;664	ENSP00000393583:E661K;ENSP00000363914:E661K;ENSP00000269392:E664K	ENSP00000269392:E664K	E	-	1	0	AZI1	76784265	0.987000	0.35691	0.004000	0.12327	0.014000	0.08584	2.235000	0.43044	2.120000	0.65058	0.467000	0.42956	GAG	C|0.982;T|0.018	0.018	strong		0.642	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
OR5W2	390148	hgsc.bcm.edu	37	11	55681336	55681336	+	Silent	SNP	G	G	A	rs11231529	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55681336G>A	ENST00000344514.1	-	1	722	c.723C>T	c.(721-723)tgC>tgT	p.C241C		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AGTGGGAAGTGCATGTAGAGA	0.408													G|||	1320	0.263578	0.3434	0.3112	5008	,	,		17093	0.1438		0.329	False		,,,				2504	0.1779				p.C241C	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.C723T						PASS	.	G		1620,2782	497.1+/-363.7	300,1020,881	82.0	93.0	89.0		723	-3.8	0.1	11	dbSNP_120	89	3007,5585	464.8+/-366.3	545,1917,1834	no	coding-synonymous	OR5W2	NM_001001960.1		845,2937,2715	AA,AG,GG		34.9977,36.8015,35.6087		241/311	55681336	4627,8367	2201	4296	6497	SO:0001819	synonymous_variant	390148	exon1			GGAAGTGCATGTA	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.723C>T	11.37:g.55681336G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_001001960		Silent	SNP	ENST00000344514.1	37	CCDS31513.1																																																																																			G|0.677;A|0.323	0.323	strong		0.408	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
HIP1	3092	hgsc.bcm.edu	37	7	75187009	75187009	+	Silent	SNP	T	T	C	rs144294774	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:75187009T>C	ENST00000336926.6	-	16	1556	c.1530A>G	c.(1528-1530)aaA>aaG	p.K510K	HIP1_ENST00000434438.2_Silent_p.K510K	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	510					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CCAGCTCTTTTTTCTCTCGTT	0.537			T	PDGFRB	CMML								T|||	13	0.00259585	0.0098	0.0	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.K510K		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A1530G						PASS	.	T		55,4351	54.2+/-90.2	0,55,2148	160.0	155.0	157.0		1530	-2.0	0.9	7	dbSNP_134	157	0,8600		0,0,4300	no	coding-synonymous	HIP1	NM_005338.5		0,55,6448	CC,CT,TT		0.0,1.2483,0.4229		510/1038	75187009	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	3092	exon16			CTCTTTTTTCTCT	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.1530A>G	7.37:g.75187009T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			T|0.996;C|0.004	0.004	strong		0.537	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
ST3GAL4	6484	hgsc.bcm.edu	37	11	126278203	126278203	+	Splice_Site	SNP	T	T	C	rs2298475	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:126278203T>C	ENST00000526727.1	+	7	813	c.439T>C	c.(439-441)Ttg>Ctg	p.L147L	ST3GAL4_ENST00000530591.1_Splice_Site_p.L143L|ST3GAL4_ENST00000356132.4_Splice_Site_p.L153L|ST3GAL4_ENST00000227495.6_Splice_Site_p.L143L|ST3GAL4_ENST00000534083.1_Splice_Site_p.L147L|ST3GAL4_ENST00000534457.1_Splice_Site_p.L142L|ST3GAL4_ENST00000526756.1_3'UTR|ST3GAL4_ENST00000444328.2_Splice_Site_p.L147L|ST3GAL4_ENST00000532243.1_Splice_Site_p.L146L|ST3GAL4_ENST00000392669.2_Splice_Site_p.L147L|ST3GAL4_ENST00000449406.2_Splice_Site_p.L136L			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	147					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|monosialoganglioside sialyltransferase activity (GO:0047288)	p.L143L(1)		endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)		AACCCCCAGATTGAACAATGC	0.562													T|||	430	0.0858626	0.0129	0.0706	5008	,	,		18899	0.2222		0.0815	False		,,,				2504	0.0593				p.L147L		Atlas-SNP	.											ST3GAL4,NS,carcinoma,0,1	ST3GAL4	25	1	1	Substitution - coding silent(1)	stomach(1)	c.T439C						PASS	.	T		98,4304	78.3+/-116.7	1,96,2104	130.0	113.0	118.0		427	-5.7	0.3	11	dbSNP_100	118	655,7941	165.7+/-217.8	21,613,3664	yes	coding-synonymous-near-splice	ST3GAL4	NM_006278.1		22,709,5768	CC,CT,TT		7.6198,2.2263,5.7932		143/330	126278203	753,12245	2201	4298	6499	SO:0001630	splice_region_variant	6484	exon8			CCCAGATTGAACA	X74570	CCDS8474.1, CCDS58193.1, CCDS58194.1	11q23-q24	2013-03-01	2003-01-14	2005-02-07	ENSG00000110080	ENSG00000110080	2.4.99.4	"""Sialyltransferases"""	10864	protein-coding gene	gene with protein product	"""ST3Gal IV"""	104240	"""sialyltransferase 4C (beta-galactosidase alpha-2,3-sialytransferase)"""	CGS23, SIAT4, NANTA3, SIAT4C		8557707, 8288606	Standard	NM_006278		Approved	STZ, SAT3, FLJ11867	uc001qds.3	Q11206	OTTHUMG00000165830	ENST00000526727.1:c.438-1T>C	11.37:g.126278203T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	172	98	0.569767	NM_001254757	A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	Silent	SNP	ENST00000526727.1	37	CCDS58193.1																																																																																			T|0.925;C|0.075	0.075	strong		0.562	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278	Silent
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43685357	43685357	+	Missense_Mutation	SNP	C	C	A	rs372133350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:43685357C>A	ENST00000377564.3	+	1	456	c.63C>A	c.(61-63)agC>agA	p.S21R	CNTNAP3B_ENST00000276974.6_Missense_Mutation_p.S21R	NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	21					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.S21R(1)		central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						AGACTTGGAGCCCCGTAGGAG	0.522													c|||	1096	0.21885	0.1339	0.3199	5008	,	,		16332	0.1329		0.2863	False		,,,				2504	0.2812				p.S21R		Atlas-SNP	.											CNTNAP3B,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CNTNAP3B	37	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.C63A						scavenged	.																																			SO:0001583	missense	728577	exon1			TTGGAGCCCCGTA	BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.63C>A	9.37:g.43685357C>A	ENSP00000366787:p.Ser21Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	140	41	0.292857	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.685|9.685	1.150274|1.150274	0.21371|0.21371	.|.	.|.	ENSG00000154529|ENSG00000154529	ENST00000377561|ENST00000377564;ENST00000276974;ENST00000341990;ENST00000403166	.|D;D	.|0.95103	.|-2.56;-3.61	1.69|1.69	1.69|1.69	0.24217|0.24217	.|.	.|.	.|.	.|.	.|.	D|D	0.91744|0.91744	0.7389|0.7389	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	D|D	0.89794|0.89794	0.3970|0.3970	4|6	.|0.28530	.|T	.|0.3	.|.	8.2934|8.2934	0.31971|0.31971	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	D|R	70|21	.|ENSP00000366787:S21R;ENSP00000276974:S21R	.|ENSP00000276974:S21R	A|S	+|+	2|3	0|2	CNTNAP3B|CNTNAP3B	43625353|43625353	0.012000|0.012000	0.17670|0.17670	0.004000|0.004000	0.12327|0.12327	0.390000|0.390000	0.30446|0.30446	1.022000|1.022000	0.30052|0.30052	0.914000|0.914000	0.36822|0.36822	0.184000|0.184000	0.17185|0.17185	GCC|AGC	C|0.500;A|0.500	0.500	strong		0.522	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
PARP1	142	hgsc.bcm.edu	37	1	226555302	226555302	+	Missense_Mutation	SNP	A	A	G	rs1136410	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:226555302A>G	ENST00000366794.5	-	17	2428	c.2285T>C	c.(2284-2286)gTg>gCg	p.V762A	PARP1_ENST00000490921.1_5'UTR	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	762	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.		V -> A (in dbSNP:rs1136410). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		AAGCATTTCCACCTTGGCCTG	0.522								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					A|||	986	0.196885	0.0371	0.3516	5008	,	,		22171	0.4365		0.1541	False		,,,				2504	0.1002				p.V762A		Atlas-SNP	.											.	PARP1	100	.	0			c.T2285C	GRCh37	CM042761	PARP1	M	rs1136410	PASS	.	A	ALA/VAL	233,4173	138.8+/-174.5	10,213,1980	106.0	93.0	98.0		2285	5.6	1.0	1	dbSNP_86	98	1371,7229	267.6+/-287.4	125,1121,3054	yes	missense	PARP1	NM_001618.3	64	135,1334,5034	GG,GA,AA		15.9419,5.2882,12.3328	possibly-damaging	762/1015	226555302	1604,11402	2203	4300	6503	SO:0001583	missense	142	exon17			ATTTCCACCTTGG	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.2285T>C	1.37:g.226555302A>G	ENSP00000355759:p.Val762Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	83	51	0.614458	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	37	CCDS1554.1	533	0.24404761904761904	27	0.054878048780487805	119	0.3287292817679558	261	0.4562937062937063	126	0.1662269129287599	A	20.9	4.059621	0.76074	0.052882	0.159419	ENSG00000143799	ENST00000366794	T	0.12361	2.69	5.56	5.56	0.83823	Poly(ADP-ribose) polymerase, regulatory domain (4);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.69358	2.11	0.09310	P	1.0	P	0.40731	0.728	P	0.53649	0.731	T	0.53995	-0.8359	9	0.33141	T	0.24	.	15.7086	0.77606	1.0:0.0:0.0:0.0	rs1136410;rs1805412;rs3199701;rs11541665;rs16845751;rs17853760;rs59953823;rs1136410	762	P09874	PARP1_HUMAN	A	762	ENSP00000355759:V762A	ENSP00000355759:V762A	V	-	2	0	PARP1	224621925	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.957000	0.93082	2.122000	0.65172	0.533000	0.62120	GTG	A|0.827;G|0.173	0.173	strong		0.522	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
DNM2	1785	hgsc.bcm.edu	37	19	10939792	10939792	+	Silent	SNP	T	T	C	rs2229920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10939792T>C	ENST00000355667.6	+	19	2219	c.2139T>C	c.(2137-2139)gcT>gcC	p.A713A	DNM2_ENST00000408974.4_Silent_p.A709A|DNM2_ENST00000585892.1_Silent_p.A713A|DNM2_ENST00000389253.4_Silent_p.A713A|DNM2_ENST00000314646.5_Silent_p.A713A|DNM2_ENST00000359692.6_Silent_p.A709A	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	713	GED. {ECO:0000255|PROSITE- ProRule:PRU00720}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			AGGAGTCGGCTGACCAGGCAC	0.627			"""F, N, Splice, Mis, O"""		ETP ALL								C|||	1694	0.338259	0.2617	0.2695	5008	,	,		19235	0.5595		0.2873	False		,,,				2504	0.3149				p.A713A		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.T2139C						PASS	.	C	,,,,	1148,3258	698.6+/-406.4	143,862,1198	46.0	36.0	39.0		2139,2139,2127,2139,2127	-10.1	0.1	19	dbSNP_98	39	2504,6096	679.1+/-403.5	370,1764,2166	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DNM2	NM_001005360.2,NM_001005361.2,NM_001005362.2,NM_001190716.1,NM_004945.3	,,,,	513,2626,3364	CC,CT,TT		29.1163,26.0554,28.0793	,,,,	713/871,713/871,709/867,713/870,709/867	10939792	3652,9354	2203	4300	6503	SO:0001819	synonymous_variant	1785	exon19			GTCGGCTGACCAG		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"""Pleckstrin homology (PH) domain containing"""	2974	protein-coding gene	gene with protein product	"""dynamin II"", ""cytoskeletal protein"""	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.2139T>C	19.37:g.10939792T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	157	66	0.420382	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Silent	SNP	ENST00000355667.6	37	CCDS45968.1																																																																																			T|0.682;C|0.318	0.318	strong		0.627	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037560	33037560	+	Silent	SNP	G	G	A	rs1042176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33037560G>A	ENST00000419277.1	-	3	333	c.204C>T	c.(202-204)gaC>gaT	p.D68D	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Silent_p.D68D	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	68	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						TCTCCTTCTTGTCCAGATCCA	0.463													.|||	1301	0.259784	0.3971	0.2507	5008	,	,		19428	0.12		0.163	False		,,,				2504	0.3241				p.D68D		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C204T						PASS	.	G	,,	908,2114		141,626,744	67.0	90.0	82.0		204,204,204	2.1	0.9	6	dbSNP_86	82	808,4610		50,708,1951	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	191,1334,2695	AA,AG,GG		14.9133,30.0463,20.3318	,,	68/261,68/261,68/261	33037560	1716,6724	1511	2709	4220	SO:0001819	synonymous_variant	3113	exon2			CTTCTTGTCCAGA	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.204C>T	6.37:g.33037560G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	170	65	0.382353	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1																																																																																			G|0.802;A|0.198	0.198	strong		0.463	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
DNMT1	1786	hgsc.bcm.edu	37	19	10287992	10287992	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10287992G>A	ENST00000340748.4	-	5	732	c.497C>T	c.(496-498)aCc>aTc	p.T166I	DNMT1_ENST00000540357.1_Missense_Mutation_p.T166I|DNMT1_ENST00000359526.4_Missense_Mutation_p.T182I			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	166	Interaction with DNMT3B.|Interaction with PCNA.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	AGATGTGATGGTGGTTTGCCT	0.438																																					p.T182I		Atlas-SNP	.											DNMT1,NS,carcinoma,0,2	DNMT1	148	2	0			c.C545T						scavenged	.						166.0	148.0	154.0					19																	10287992		2203	4300	6503	SO:0001583	missense	1786	exon6			GTGATGGTGGTTT	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.497C>T	19.37:g.10287992G>A	ENSP00000345739:p.Thr166Ile	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	174	3	0.0172414	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	g	14.58	2.577144	0.45902	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.36340	1.26;1.51;1.51	5.26	5.26	0.73747	.	0.058726	0.64402	D	0.000003	T	0.34279	0.0892	L	0.46157	1.445	0.33679	D	0.611906	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.08055	0.003;0.003;0.001	T	0.44406	-0.9330	10	0.62326	D	0.03	.	14.7844	0.69790	0.0:0.0:1.0:0.0	.	166;182;166	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	I	182;166;166;34	ENSP00000352516:T182I;ENSP00000440457:T166I;ENSP00000345739:T166I	ENSP00000345739:T166I	T	-	2	0	DNMT1	10148992	1.000000	0.71417	0.999000	0.59377	0.671000	0.39405	3.174000	0.50847	2.630000	0.89119	0.644000	0.83932	ACC	.	.	none		0.438	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
LRCH3	84859	hgsc.bcm.edu	37	3	197579466	197579466	+	Missense_Mutation	SNP	C	C	T	rs36078463	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:197579466C>T	ENST00000425562.2	+	13	1565	c.1565C>T	c.(1564-1566)cCg>cTg	p.P522L	LRCH3_ENST00000536618.1_Missense_Mutation_p.P117L|LRCH3_ENST00000334859.4_Missense_Mutation_p.P522L|LRCH3_ENST00000441090.2_Missense_Mutation_p.P368L|LRCH3_ENST00000438796.2_Missense_Mutation_p.P522L|LRCH3_ENST00000414675.2_Missense_Mutation_p.P494L			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	522			P -> L (in dbSNP:rs36078463).			cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		AAACAGCACCCGCTCCTAGAT	0.383													C|||	527	0.105232	0.115	0.0447	5008	,	,		16705	0.1835		0.0746	False		,,,				2504	0.0859				p.P522L		Atlas-SNP	.											.	LRCH3	96	.	0			c.C1565T						PASS	.	C	LEU/PRO	471,3935	223.3+/-239.8	20,431,1752	155.0	159.0	158.0		1565	2.7	0.0	3	dbSNP_126	158	633,7967	164.3+/-216.7	21,591,3688	yes	missense	LRCH3	NM_032773.2	98	41,1022,5440	TT,TC,CC		7.3605,10.69,8.4884	benign	522/713	197579466	1104,11902	2203	4300	6503	SO:0001583	missense	84859	exon13			AGCACCCGCTCCT	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1565C>T	3.37:g.197579466C>T	ENSP00000393579:p.Pro522Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	169	93	0.550296	NM_032773	B4E0T7|Q96FP9|Q9NT52	Missense_Mutation	SNP	ENST00000425562.2	37		213	0.09752747252747253	49	0.09959349593495935	17	0.04696132596685083	89	0.1555944055944056	58	0.07651715039577836	C	3.629	-0.076024	0.07184	0.1069	0.073605	ENSG00000186001	ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562;ENST00000536618;ENST00000452660;ENST00000433298	T;T;T;T;T;T;T;T	0.46063	2.13;1.5;2.02;2.38;2.15;0.88;0.95;0.96	5.67	2.74	0.32292	.	0.319926	0.28448	N	0.015311	T	0.00073	0.0002	N	0.17082	0.46	0.80722	P	0.0	B;B;B;B;B	0.14438	0.006;0.005;0.01;0.003;0.005	B;B;B;B;B	0.16289	0.004;0.002;0.015;0.003;0.004	T	0.06972	-1.0797	9	0.48119	T	0.1	0.3333	3.8877	0.09105	0.1691:0.5802:0.1634:0.0873	rs36078463	368;494;522;522;522	E9PD99;B4E0T7;Q96II8-2;Q96II8;Q96II8-3	.;.;.;LRCH3_HUMAN;.	L	522;368;494;522;522;117;33;19	ENSP00000399751:P522L;ENSP00000394609:P368L;ENSP00000394965:P494L;ENSP00000334375:P522L;ENSP00000393579:P522L;ENSP00000439083:P117L;ENSP00000395309:P33L;ENSP00000400164:P19L	ENSP00000334375:P522L	P	+	2	0	LRCH3	199063863	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.499000	0.22546	0.740000	0.32651	0.650000	0.86243	CCG	C|0.913;T|0.087	0.087	strong		0.383	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773	
KRT40	125115	hgsc.bcm.edu	37	17	39137387	39137387	+	Missense_Mutation	SNP	C	C	T	rs2010027	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39137387C>T	ENST00000398486.2	-	6	864	c.704G>A	c.(703-705)cGt>cAt	p.R235H	KRT40_ENST00000377755.4_Missense_Mutation_p.R235H	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	235	Coil 1B.|Rod.		R -> H (in dbSNP:rs2010027).			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				AAGCTGTTCACGAAGCAAGTT	0.502													c|||	1807	0.360823	0.6853	0.2378	5008	,	,		20547	0.1716		0.2684	False		,,,				2504	0.2996				p.R235H		Atlas-SNP	.											.	KRT40	27	.	0			c.G704A						PASS	.	T	HIS/ARG	2370,1684		716,938,373	90.0	97.0	94.0		704	-2.2	0.2	17	dbSNP_92	94	2302,6088		314,1674,2207	yes	missense	KRT40	NM_182497.3	29	1030,2612,2580	TT,TC,CC		27.4374,41.5392,37.5442	benign	235/432	39137387	4672,7772	2027	4195	6222	SO:0001583	missense	125115	exon6			TGTTCACGAAGCA	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.704G>A	17.37:g.39137387C>T	ENSP00000381500:p.Arg235His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	733	0.3356227106227106	338	0.6869918699186992	92	0.2541436464088398	96	0.16783216783216784	207	0.27308707124010556	c	15.14	2.744312	0.49151	0.584608	0.274374	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.89343	-2.5;-2.5	5.4	-2.24	0.06909	Filament (1);	0.507141	0.14933	N	0.289963	T	0.00012	0.0000	M	0.70903	2.155	0.80722	P	0.0	B	0.33266	0.404	B	0.33196	0.159	T	0.40813	-0.9543	9	0.66056	D	0.02	.	6.3188	0.21206	0.1201:0.3779:0.0:0.502	rs2010027;rs17646708	235	Q6A162	K1C40_HUMAN	H	235	ENSP00000366984:R235H;ENSP00000381500:R235H	ENSP00000366984:R235H	R	-	2	0	KRT40	36390913	0.000000	0.05858	0.204000	0.23530	0.385000	0.30292	-0.494000	0.06451	-0.126000	0.11682	-0.119000	0.15052	CGT	C|0.658;T|0.342	0.342	strong		0.502	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240796	39240796	+	Missense_Mutation	SNP	G	G	C	rs553572799|rs199957151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	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,NS,carcinoma,+1,1	KRTAP4-7	49	1	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G338C						scavenged	.																																			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	17.37:g.39240796G>C	ENSP00000375236:p.Ser113Thr	Somatic	28	1	0.0357143		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	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		
USPL1	10208	hgsc.bcm.edu	37	13	31233063	31233063	+	Missense_Mutation	SNP	G	G	A	rs3742302	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:31233063G>A	ENST00000255304.4	+	9	3191	c.2849G>A	c.(2848-2850)aGt>aAt	p.S950N		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	950			S -> N (in dbSNP:rs3742302). {ECO:0000269|PubMed:15489334}.		Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		GATATTGCCAGTGAGTCTGCA	0.413													A|||	2377	0.474641	0.8177	0.3876	5008	,	,		20540	0.1786		0.4006	False		,,,				2504	0.454				p.S950N	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.G2849A						PASS	.	A	ASN/SER	3374,1032	380.2+/-323.6	1295,784,124	151.0	152.0	152.0		2849	3.3	0.0	13	dbSNP_107	152	3532,5068	631.7+/-398.5	722,2088,1490	yes	missense	USPL1	NM_005800.4	46	2017,2872,1614	AA,AG,GG		41.0698,23.4226,46.9014	benign	950/1093	31233063	6906,6100	2203	4300	6503	SO:0001583	missense	10208	exon9			TTGCCAGTGAGTC	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 22"""	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.2849G>A	13.37:g.31233063G>A	ENSP00000255304:p.Ser950Asn	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	148	147	0.993243	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	954	0.4368131868131868	407	0.8272357723577236	153	0.42265193370165743	100	0.17482517482517482	294	0.38786279683377306	A	0	-2.731200	0.00089	0.765774	0.410698	ENSG00000132952	ENST00000255304	T	0.13307	2.6	5.75	3.31	0.37934	.	0.929244	0.09333	N	0.816635	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28681	-1.0036	9	0.14252	T	0.57	-7.2328	12.7153	0.57111	0.7979:0.0:0.2021:0.0	rs3742302;rs17682754;rs17846218;rs17859235;rs52806569;rs60783730;rs3742302	950	Q5W0Q7	USPL1_HUMAN	N	950	ENSP00000255304:S950N	ENSP00000255304:S950N	S	+	2	0	USPL1	30131063	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.530000	0.02221	-0.104000	0.12154	-2.276000	0.00273	AGT	G|0.506;N|0.000	.	strong		0.413	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800	
ANKRD26	22852	hgsc.bcm.edu	37	10	27317840	27317840	+	Missense_Mutation	SNP	C	C	T	rs10829163	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:27317840C>T	ENST00000376087.4	-	27	4078	c.3913G>A	c.(3913-3915)Gtc>Atc	p.V1305I	ANKRD26_ENST00000436985.2_Missense_Mutation_p.V1321I|ANKRD26_ENST00000376070.3_Missense_Mutation_p.V862I	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1304					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TGCTTTTTGACTGTAACTTTT	0.279													T|||	1589	0.317292	0.2352	0.1758	5008	,	,		14382	0.5516		0.1928	False		,,,				2504	0.4151				p.V1305I		Atlas-SNP	.											.	ANKRD26	179	.	0			c.G3913A						PASS	.	T	ILE/VAL	839,2761		96,647,1057	121.0	110.0	114.0		3913	-4.4	0.0	10	dbSNP_120	114	1180,6940		77,1026,2957	yes	missense	ANKRD26	NM_014915.2	29	173,1673,4014	TT,TC,CC		14.532,23.3056,17.227	benign	1305/1711	27317840	2019,9701	1800	4060	5860	SO:0001583	missense	22852	exon27			TTTTGACTGTAAC	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3913G>A	10.37:g.27317840C>T	ENSP00000365255:p.Val1305Ile	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	201	97	0.482587	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	660	0.3021978021978022	109	0.22154471544715448	63	0.17403314917127072	340	0.5944055944055944	148	0.19525065963060687	T	0.013	-1.644536	0.00792	0.233056	0.14532	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.75050	-0.9;-0.9;-0.9	4.9	-4.39	0.03611	.	0.729179	0.11831	N	0.525220	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.24261	-1.0165	9	0.02654	T	1	.	8.0976	0.30837	0.0:0.4553:0.1065:0.4382	rs10829163;rs52823343;rs58305733;rs10829163	1305;1304;1321	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	I	862;1305;1321	ENSP00000365238:V862I;ENSP00000365255:V1305I;ENSP00000405112:V1321I	ENSP00000365238:V862I	V	-	1	0	ANKRD26	27357846	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-1.827000	0.01704	-1.176000	0.02747	-0.308000	0.09152	GTC	C|0.724;T|0.276	0.276	strong		0.279	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
RARS	5917	hgsc.bcm.edu	37	5	167933156	167933156	+	Silent	SNP	A	A	G	rs61744940	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:167933156A>G	ENST00000231572.3	+	10	1242	c.1188A>G	c.(1186-1188)ctA>ctG	p.L396L	RARS_ENST00000538719.1_Silent_p.L190L	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	396					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		AACAAAGACTATTTGAGGAAA	0.348													A|||	190	0.0379393	0.0068	0.0634	5008	,	,		19704	0.001		0.1163	False		,,,				2504	0.0194				p.L396L		Atlas-SNP	.											.	RARS	58	.	0			c.A1188G						PASS	.	A		100,4306		1,98,2104	150.0	146.0	147.0		1188	-9.6	0.0	5	dbSNP_129	147	933,7667		72,789,3439	no	coding-synonymous	RARS	NM_002887.3		73,887,5543	GG,GA,AA		10.8488,2.2696,7.9425		396/661	167933156	1033,11973	2203	4300	6503	SO:0001819	synonymous_variant	5917	exon10			AAGACTATTTGAG	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1188A>G	5.37:g.167933156A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	37	CCDS4367.1																																																																																			A|0.922;G|0.078	0.078	strong		0.348	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
UROC1	131669	hgsc.bcm.edu	37	3	126219627	126219627	+	Silent	SNP	G	G	A	rs34025926	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:126219627G>A	ENST00000290868.2	-	11	1109	c.1056C>T	c.(1054-1056)ggC>ggT	p.G352G	UROC1_ENST00000383579.3_Silent_p.G412G	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	352					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		GGTAGTAGCCGCCATTGAACG	0.612													g|||	1085	0.216653	0.2602	0.2003	5008	,	,		19625	0.005		0.3091	False		,,,				2504	0.2924				p.G412G		Atlas-SNP	.											.	UROC1	150	.	0			c.C1236T						PASS	.		,	1162,3244	410.2+/-335.3	167,828,1208	104.0	98.0	100.0		1236,1056	-9.9	0.6	3	dbSNP_126	100	2684,5916	430.4+/-356.5	409,1866,2025	no	coding-synonymous,coding-synonymous	UROC1	NM_001165974.1,NM_144639.2	,	576,2694,3233	AA,AG,GG		31.2093,26.3731,29.571	,	412/737,352/677	126219627	3846,9160	2203	4300	6503	SO:0001819	synonymous_variant	131669	exon12			GTAGCCGCCATTG	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"""urocanase 1"""	613012	"""urocanase domain containing 1"""			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.1056C>T	3.37:g.126219627G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	NM_001165974	E9PE13|Q14C64|Q68CJ7	Silent	SNP	ENST00000290868.2	37	CCDS3038.1																																																																																			G|0.729;A|0.271	0.271	strong		0.612	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639	
USP32	84669	hgsc.bcm.edu	37	17	58288421	58288421	+	Missense_Mutation	SNP	C	C	T	rs146577219	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:58288421C>T	ENST00000300896.4	-	21	2571	c.2377G>A	c.(2377-2379)Gaa>Aaa	p.E793K	USP32_ENST00000592339.1_Missense_Mutation_p.E463K	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	793	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			CTCCAAAGTTCCTGCACTAAA	0.358																																					p.E793K		Atlas-SNP	.											USP32,NS,carcinoma,0,5	USP32	128	5	0			c.G2377A						scavenged	.						27.0	27.0	27.0					17																	58288421		2203	4296	6499	SO:0001583	missense	84669	exon21			AAAGTTCCTGCAC	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"""Ubiquitin-specific peptidases"", ""EF-hand domain containing"""	19143	protein-coding gene	gene with protein product		607740	"""ubiquitin specific protease 32"""			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.2377G>A	17.37:g.58288421C>T	ENSP00000300896:p.Glu793Lys	Somatic	503	0	0		WXS	Illumina HiSeq	Phase_I	554	107	0.193141	NM_032582	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	C	33	5.220205	0.95139	.	.	ENSG00000170832	ENST00000300896	T	0.29917	1.55	5.26	5.26	0.73747	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.28499	0.0705	N	0.25286	0.73	0.80722	D	1	B	0.30021	0.265	B	0.36959	0.237	T	0.05273	-1.0895	10	0.29301	T	0.29	.	19.2198	0.93791	0.0:1.0:0.0:0.0	.	793	Q8NFA0	UBP32_HUMAN	K	793	ENSP00000300896:E793K	ENSP00000300896:E793K	E	-	1	0	USP32	55643203	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.697000	0.84279	2.615000	0.88500	0.655000	0.94253	GAA	C|0.926;T|0.073	0.073	strong		0.358	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582	
TKT	7086	hgsc.bcm.edu	37	3	53259850	53259850	+	Silent	SNP	C	C	T	rs3163	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:53259850C>T	ENST00000462138.1	-	14	1882	c.1794G>A	c.(1792-1794)ccG>ccA	p.P598P	TKT_ENST00000423525.2_Silent_p.P598P|TKT_ENST00000423516.1_Silent_p.P606P|TKT_ENST00000461139.1_5'UTR|TKT_ENST00000296289.6_Silent_p.P551P			P29401	TKT_HUMAN	transketolase	598					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		GCAGCTCAGCCGGCTTCCCAC	0.587													C|||	606	0.121006	0.0522	0.1354	5008	,	,		17021	0.1091		0.167	False		,,,				2504	0.1687				p.P606P	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.G1818A						PASS	.	C	,	393,4013	196.4+/-220.7	21,351,1831	90.0	75.0	80.0		1794,1794	-5.8	0.0	3	dbSNP_36	80	1650,6950	304.0+/-306.7	158,1334,2808	no	coding-synonymous,coding-synonymous	TKT	NM_001064.3,NM_001135055.2	,	179,1685,4639	TT,TC,CC		19.186,8.9197,15.7081	,	598/624,598/624	53259850	2043,10963	2203	4300	6503	SO:0001819	synonymous_variant	7086	exon15			CTCAGCCGGCTTC		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"""Wernicke-Korsakoff syndrome"""	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.1794G>A	3.37:g.53259850C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Silent	SNP	ENST00000462138.1	37	CCDS2871.1																																																																																			C|0.860;T|0.140	0.140	strong		0.587	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1		
RHBG	57127	hgsc.bcm.edu	37	1	156354367	156354367	+	Silent	SNP	A	A	G	rs6668857	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156354367A>G	ENST00000368249.1	+	9	1322	c.1284A>G	c.(1282-1284)gcA>gcG	p.A428A	RHBG_ENST00000255013.3_Silent_p.A359A|RHBG_ENST00000494874.1_3'UTR|RHBG_ENST00000400992.2_Silent_p.A396A|RHBG_ENST00000368246.2_Missense_Mutation_p.H427R	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	428					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GACTCCCAGCACTACGAGGAC	0.617											OREG0013871	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3671	0.733027	0.8956	0.6686	5008	,	,		18513	0.8978		0.5149	False		,,,				2504	0.6135				p.H428R		Atlas-SNP	.											.	RHBG	133	.	0			c.A1283G						PASS	.	G	ARG/HIS	3441,611		1456,529,41	62.0	75.0	71.0		1284	5.9	1.0	1	dbSNP_116	71	4424,3942		1201,2022,960	no	missense	RHBG	NM_020407.3	29	2657,2551,1001	GG,GA,AA		47.1193,15.079,36.6645	benign	428/459	156354367	7865,4553	2026	4183	6209	SO:0001819	synonymous_variant	57127	exon10			CCCAGCACTACGA	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.1284A>G	1.37:g.156354367A>G		Somatic	99	0	0	1777	WXS	Illumina HiSeq	Phase_I	119	119	1	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		1580	0.7234432234432234	445	0.9044715447154471	238	0.6574585635359116	503	0.8793706293706294	394	0.5197889182058048	G	17.33	3.362164	0.61403	0.84921	0.528807	ENSG00000132677	ENST00000368246	T	0.18174	2.23	5.94	5.94	0.96194	.	.	.	.	.	T	0.20088	0.0483	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.07751	-1.0756	5	0.87932	D	0	-24.589	11.3531	0.49600	0.083:0.0:0.917:0.0	rs6668857;rs17383530;rs17855291;rs59799121;rs6668857	.	.	.	R	427	ENSP00000357229:H427R	ENSP00000357229:H427R	H	+	2	0	RHBG	154620991	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	4.067000	0.57527	1.545000	0.49373	-0.215000	0.12644	CAC	A|0.291;G|0.709	0.709	strong		0.617	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
WBP1L	54838	hgsc.bcm.edu	37	10	104573017	104573017	+	Missense_Mutation	SNP	G	G	T	rs284859	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:104573017G>T	ENST00000369889.4	+	4	1100	c.958G>T	c.(958-960)Gca>Tca	p.A320S	WBP1L_ENST00000448841.1_Missense_Mutation_p.A341S	NM_017787.4	NP_060257.4	Q9NX94	WBP1L_HUMAN	WW domain binding protein 1-like	320			A -> S (in dbSNP:rs284859). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)											ACGGCCGCCCGCATGCCTGCT	0.657													G|||	734	0.146565	0.0431	0.2248	5008	,	,		15672	0.131		0.1909	False		,,,				2504	0.2014				p.A341S		Atlas-SNP	.											.	.	.	.	0			c.G1021T						PASS	.	G	SER/ALA,SER/ALA	268,4132		8,252,1940	20.0	25.0	23.0		1021,958	4.1	0.0	10	dbSNP_79	23	1413,7183		123,1167,3008	yes	missense,missense	C10orf26	NM_001083913.1,NM_017787.4	99,99	131,1419,4948	TT,TG,GG		16.4379,6.0909,12.9347	possibly-damaging,possibly-damaging	341/364,320/343	104573017	1681,11315	2200	4298	6498	SO:0001583	missense	54838	exon4			CCGCCCGCATGCC	AK056285	CCDS7540.1, CCDS44473.1	10q24.33	2012-05-02	2012-05-02	2012-05-02	ENSG00000166272	ENSG00000166272			23510	protein-coding gene	gene with protein product	"""outcome predictor in acute leukemia 1"""	611129	"""chromosome 10 open reading frame 26"""	C10orf26			Standard	NM_017787		Approved	FLJ20154, OPAL1	uc001kwf.4	Q9NX94	OTTHUMG00000018968	ENST00000369889.4:c.958G>T	10.37:g.104573017G>T	ENSP00000358905:p.Ala320Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	62	59	0.951613	NM_001083913	B3KPF4|B7Z6S7|D3DR90|Q1EG70|Q2HIY7|Q5F2G6	Missense_Mutation	SNP	ENST00000369889.4	37	CCDS7540.1	339	0.15521978021978022	17	0.034552845528455285	86	0.23756906077348067	92	0.16083916083916083	144	0.18997361477572558	G	11.44	1.638993	0.29157	0.060909	0.164379	ENSG00000166272	ENST00000448841;ENST00000369889	T;T	0.32272	1.46;1.48	5.94	4.11	0.48088	.	0.483923	0.24752	N	0.035897	T	0.00012	0.0000	L	0.36672	1.1	0.38649	P	0.048190999999999984	B;B	0.30664	0.289;0.191	B;B	0.26693	0.072;0.033	T	0.28933	-1.0028	9	0.31617	T	0.26	-2.2348	12.6473	0.56742	0.1332:0.0:0.8668:0.0	rs284859;rs3740403;rs17723640;rs57211205;rs284859	341;320	Q9NX94-2;Q9NX94	.;OPA1L_HUMAN	S	341;320	ENSP00000414721:A341S;ENSP00000358905:A320S	ENSP00000358905:A320S	A	+	1	0	C10orf26	104563007	0.962000	0.33011	0.027000	0.17364	0.363000	0.29612	3.075000	0.50073	0.870000	0.35726	-0.258000	0.10820	GCA	G|0.855;T|0.137	0.137	strong		0.657	WBP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050100.1	NM_017787	
BRDT	676	hgsc.bcm.edu	37	1	92445257	92445257	+	Missense_Mutation	SNP	C	C	G	rs3088232	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:92445257C>G	ENST00000362005.3	+	9	1648	c.1230C>G	c.(1228-1230)aaC>aaG	p.N410K	BRDT_ENST00000399546.2_Missense_Mutation_p.N410K|BRDT_ENST00000394530.3_Missense_Mutation_p.N364K|BRDT_ENST00000402388.1_Missense_Mutation_p.N410K|BRDT_ENST00000370389.2_Missense_Mutation_p.N337K	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	410			N -> K (in dbSNP:rs3088232). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		CTGAAGGGAACTCTTCTGATG	0.398													C|||	653	0.130391	0.0242	0.2392	5008	,	,		15081	0.0278		0.2167	False		,,,				2504	0.2137				p.N414K		Atlas-SNP	.											.	BRDT	133	.	0			c.C1242G						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN	260,4146	149.9+/-184.0	7,246,1950	110.0	108.0	109.0		1230,1242,1092,1092,1011,1230,1230	3.8	0.9	1	dbSNP_102	109	2137,6463	368.2+/-335.0	259,1619,2422	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	94,94,94,94,94,94,94	266,1865,4372	GG,GC,CC		24.8488,5.901,18.43	benign,benign,benign,benign,benign,benign,benign	410/948,414/952,364/902,364/902,337/875,410/948,410/948	92445257	2397,10609	2203	4300	6503	SO:0001583	missense	676	exon8			AGGGAACTCTTCT	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.1230C>G	1.37:g.92445257C>G	ENSP00000354568:p.Asn410Lys	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	216	121	0.560185	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	293	0.13415750915750915	20	0.04065040650406504	78	0.2154696132596685	18	0.03146853146853147	177	0.23350923482849603	C	8.787	0.929564	0.18131	0.05901	0.248488	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000394530;ENST00000426141;ENST00000402388	T;T;T;T;T;T	0.09255	3.31;3.31;3.31;3.36;3.0;3.31	5.65	3.76	0.43208	.	0.950790	0.08804	N	0.891225	T	0.02304	0.0071	L	0.27053	0.805	0.37695	P	0.07602399999999998	B;B;B;B	0.15473	0.003;0.003;0.013;0.003	B;B;B;B	0.12156	0.002;0.002;0.007;0.002	T	0.44065	-0.9352	9	0.51188	T	0.08	-0.8136	2.5253	0.04689	0.1655:0.5348:0.1407:0.159	rs3088232;rs52821661;rs3088232	364;364;414;410	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	K	410;337;410;410;364;410;410	ENSP00000354568:N410K;ENSP00000359416:N337K;ENSP00000387822:N410K;ENSP00000378038:N364K;ENSP00000404969:N410K;ENSP00000384051:N410K	ENSP00000354568:N410K	N	+	3	2	BRDT	92217845	0.022000	0.18835	0.889000	0.34880	0.201000	0.24016	0.236000	0.17967	0.728000	0.32382	0.655000	0.94253	AAC	C|0.838;G|0.162	0.162	strong		0.398	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
NEIL3	55247	hgsc.bcm.edu	37	4	178231152	178231152	+	Silent	SNP	C	C	A	rs10013040	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:178231152C>A	ENST00000264596.3	+	1	163	c.45C>A	c.(43-45)cgC>cgA	p.R15R		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	15					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		AGAAGATTCGCGCGCGGGTGC	0.677								Base excision repair (BER), DNA glycosylases					C|||	848	0.169329	0.1384	0.1744	5008	,	,		12488	0.1369		0.2177	False		,,,				2504	0.1912				p.R15R		Atlas-SNP	.											.	NEIL3	89	.	0			c.C45A						PASS	.	C		641,3763	266.2+/-267.1	43,555,1604	30.0	33.0	32.0		45	-1.0	0.6	4	dbSNP_119	32	1936,6664	333.4+/-320.5	196,1544,2560	no	coding-synonymous	NEIL3	NM_018248.2		239,2099,4164	AA,AC,CC		22.5116,14.555,19.817		15/606	178231152	2577,10427	2202	4300	6502	SO:0001819	synonymous_variant	55247	exon1			GATTCGCGCGCGG	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.45C>A	4.37:g.178231152C>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	103	43	0.417476	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Silent	SNP	ENST00000264596.3	37	CCDS3828.1																																																																																			C|0.815;A|0.184	0.184	strong		0.677	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
ACTL8	81569	hgsc.bcm.edu	37	1	18149510	18149510	+	Missense_Mutation	SNP	G	G	T	rs694214	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18149510G>T	ENST00000375406.1	+	2	223	c.7G>T	c.(7-9)Gca>Tca	p.A3S		NM_030812.2	NP_110439.2	Q9H568	ACTL8_HUMAN	actin-like 8	3			A -> S (in dbSNP:rs694214). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		epithelial cell differentiation (GO:0030855)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	28		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)		CGCCATGGCTGCAAGAACCGT	0.582													G|||	1531	0.305711	0.143	0.3228	5008	,	,		19268	0.4315		0.4374	False		,,,				2504	0.2485				p.A3S		Atlas-SNP	.											.	ACTL8	58	.	0			c.G7T						PASS	.	G	SER/ALA	892,3514	347.5+/-309.5	98,696,1409	38.0	35.0	36.0		7	-3.4	0.0	1	dbSNP_83	36	3629,4971	520.6+/-379.7	772,2085,1443	yes	missense	ACTL8	NM_030812.2	99	870,2781,2852	TT,TG,GG		42.1977,20.2451,34.7609	possibly-damaging	3/367	18149510	4521,8485	2203	4300	6503	SO:0001583	missense	81569	exon2			ATGGCTGCAAGAA	AK057339	CCDS183.1	1p36.2-p35	2009-03-25			ENSG00000117148	ENSG00000117148			24018	protein-coding gene	gene with protein product	"""cancer/testis antigen 57"""						Standard	NM_030812		Approved	CT57	uc001bat.3	Q9H568	OTTHUMG00000002512	ENST00000375406.1:c.7G>T	1.37:g.18149510G>T	ENSP00000364555:p.Ala3Ser	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_030812	Q13104|Q96M75	Missense_Mutation	SNP	ENST00000375406.1	37	CCDS183.1	758	0.34706959706959706	75	0.1524390243902439	99	0.27348066298342544	233	0.40734265734265734	351	0.4630606860158311	G	12.81	2.048776	0.36181	0.202451	0.421977	ENSG00000117148	ENST00000375406	D	0.94576	-3.46	4.72	-3.42	0.04825	.	1.452380	0.04760	N	0.426156	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.11235	0.004	B	0.12837	0.008	T	0.24083	-1.0170	9	0.87932	D	0	-0.1607	3.7462	0.08549	0.4117:0.0:0.2718:0.3166	rs694214;rs17852618;rs58310046;rs694214	3	Q9H568	ACTL8_HUMAN	S	3	ENSP00000364555:A3S	ENSP00000364555:A3S	A	+	1	0	ACTL8	18022097	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.019000	0.12546	-0.699000	0.05077	-0.274000	0.10170	GCA	G|0.662;T|0.338	0.338	strong		0.582	ACTL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007143.1	NM_030812	
MUC21	394263	hgsc.bcm.edu	37	6	30954335	30954335	+	Missense_Mutation	SNP	C	C	T	rs146461318	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954335C>T	ENST00000376296.3	+	2	624	c.383C>T	c.(382-384)cCc>cTc	p.P128L	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	128	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGCACACCCTCCAGTGGG	0.597													C|||	574	0.114617	0.1263	0.1556	5008	,	,		25093	0.0923		0.1014	False		,,,				2504	0.1063				p.P128L		Atlas-SNP	.											MUC21,NS,carcinoma,+1,1	MUC21	98	1	0			c.C383T						PASS	.						173.0	160.0	164.0					6																	30954335		2203	4300	6503	SO:0001583	missense	394263	exon2			GCACACCCTCCAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.383C>T	6.37:g.30954335C>T	ENSP00000365473:p.Pro128Leu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	153	20	0.130719	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	C	9.866	1.197558	0.22037	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.01767	4.65	3.34	0.415	0.16411	.	.	.	.	.	T	0.00328	0.0010	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.33599	-0.9862	8	.	.	.	.	7.2845	0.26330	0.0:0.6864:0.0:0.3136	.	128	Q5SSG8	MUC21_HUMAN	L	128	ENSP00000365473:P128L	.	P	+	2	0	MUC21	31062314	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	-0.313000	0.08103	-0.043000	0.13513	-0.350000	0.07774	CCC	C|0.983;T|0.016	0.016	strong		0.597	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
LAMA2	3908	hgsc.bcm.edu	37	6	129762112	129762112	+	Silent	SNP	G	G	A	rs2297738	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:129762112G>A	ENST00000421865.2	+	43	6286	c.6237G>A	c.(6235-6237)acG>acA	p.T2079T		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2079	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TCGCCAAAACGAATGCTGTGG	0.418													G|||	914	0.182508	0.1536	0.2334	5008	,	,		21579	0.2202		0.1551	False		,,,				2504	0.1748				p.T2079T		Atlas-SNP	.											.	LAMA2	481	.	0			c.G6237A						PASS	.	G	,	555,3851	250.0+/-257.2	29,497,1677	94.0	83.0	87.0		6237,6237	3.4	1.0	6	dbSNP_100	87	1253,7347	249.9+/-277.0	95,1063,3142	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	124,1560,4819	AA,AG,GG		14.5698,12.5965,13.9013	,	2079/3123,2079/3119	129762112	1808,11198	2203	4300	6503	SO:0001819	synonymous_variant	3908	exon43			CAAAACGAATGCT	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.6237G>A	6.37:g.129762112G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	147	85	0.578231	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			G|0.845;A|0.155	0.155	strong		0.418	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
PICALM	8301	hgsc.bcm.edu	37	11	85725937	85725937	+	Silent	SNP	C	C	T	rs592297	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:85725937C>T	ENST00000393346.3	-	5	670	c.522G>A	c.(520-522)caG>caA	p.Q174Q	PICALM_ENST00000528398.1_Silent_p.Q123Q|PICALM_ENST00000356360.5_Silent_p.Q174Q|PICALM_ENST00000532317.1_Silent_p.Q174Q|PICALM_ENST00000526033.1_Silent_p.Q174Q			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	174					axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				GTGCATCCATCTGATTCTGAA	0.284			T	"""MLLT10, MLL"""	"""TALL, AML, """								T|||	3950	0.788738	0.916	0.7334	5008	,	,		17072	0.6815		0.8171	False		,,,				2504	0.7372				p.Q174Q		Atlas-SNP	.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	.	PICALM	82	.	0			c.G522A						PASS	.	T	,,,	3931,469	216.8+/-235.3	1750,431,19	137.0	129.0	132.0		522,522,369,522	-1.5	1.0	11	dbSNP_83	132	6904,1686	303.6+/-306.5	2775,1354,166	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PICALM	NM_001008660.2,NM_001206946.1,NM_001206947.1,NM_007166.3	,,,	4525,1785,185	TT,TC,CC		19.6275,10.6591,16.5897	,,,	174/611,174/646,123/552,174/653	85725937	10835,2155	2200	4295	6495	SO:0001819	synonymous_variant	8301	exon5			ATCCATCTGATTC	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.522G>A	11.37:g.85725937C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	113	111	0.982301	NM_007166	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Silent	SNP	ENST00000393346.3	37	CCDS8272.1																																																																																			C|0.183;T|0.817	0.817	strong		0.284	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166	
PLXND1	23129	hgsc.bcm.edu	37	3	129308209	129308209	+	Silent	SNP	G	G	A	rs2285373	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129308209G>A	ENST00000324093.4	-	2	1651	c.1473C>T	c.(1471-1473)aaC>aaT	p.N491N	PLXND1_ENST00000393239.1_Silent_p.N491N|RN7SL752P_ENST00000463779.2_RNA	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	491	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.N491N(1)	PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GAAGCCTCCCGTTGACCGTGC	0.672													G|||	672	0.134185	0.0552	0.134	5008	,	,		10757	0.2421		0.0984	False		,,,				2504	0.1667				p.N491N	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											PLXND1,NS,carcinoma,0,1	PLXND1	149	1	1	Substitution - coding silent(1)	stomach(1)	c.C1473T						PASS	.	G		260,4146	147.6+/-182.1	7,246,1950	40.0	36.0	37.0		1473	-8.9	0.0	3	dbSNP_100	37	803,7797	185.9+/-233.5	39,725,3536	no	coding-synonymous	PLXND1	NM_015103.2		46,971,5486	AA,AG,GG		9.3372,5.901,8.1732		491/1926	129308209	1063,11943	2203	4300	6503	SO:0001819	synonymous_variant	23129	exon2			CCTCCCGTTGACC	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.1473C>T	3.37:g.129308209G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	159	77	0.484277	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			G|0.900;A|0.100	0.100	strong		0.672	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
TPSD1	23430	hgsc.bcm.edu	37	16	1306921	1306921	+	Silent	SNP	G	G	A	rs78324915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306921G>A	ENST00000211076.3	+	3	526	c.378G>A	c.(376-378)ggG>ggA	p.G126G	TPSD1_ENST00000397534.2_Silent_p.G119G|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	126	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G126G(2)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TCCAGACCGGGGCGGACATCG	0.647																																					p.G126G		Atlas-SNP	.											TPSD1,NS,carcinoma,0,2	TPSD1	47	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(1)|stomach(1)	c.G378A						PASS	.						77.0	75.0	76.0					16																	1306921		2199	4300	6499	SO:0001819	synonymous_variant	23430	exon3			GACCGGGGCGGAC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.378G>A	16.37:g.1306921G>A		Somatic	421	0	0		WXS	Illumina HiSeq	Phase_I	616	113	0.183442	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			G|0.643;A|0.357	0.357	strong		0.647	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
PTPRD	5789	hgsc.bcm.edu	37	9	8486184	8486184	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:8486184T>C	ENST00000381196.4	-	25	3176	c.2633A>G	c.(2632-2634)gAt>gGt	p.D878G	PTPRD_ENST00000540109.1_Missense_Mutation_p.D878G|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000356435.5_Missense_Mutation_p.D878G|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000360074.4_Missense_Mutation_p.D865G|PTPRD_ENST00000471274.1_5'UTR|PTPRD_ENST00000358503.5_Missense_Mutation_p.D856G|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000486161.1_Intron	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	878	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.D878V(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TGTAAAGTGATCTTCTTTTTC	0.483										TSP Lung(15;0.13)																											p.D878G		Atlas-SNP	.											PTPRD_ENST00000381196,NS,carcinoma,0,2	PTPRD	1348	2	1	Substitution - Missense(1)	lung(1)	c.A2633G						scavenged	.						98.0	94.0	95.0					9																	8486184		2203	4300	6503	SO:0001583	missense	5789	exon28			AAGTGATCTTCTT	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.2633A>G	9.37:g.8486184T>C	ENSP00000370593:p.Asp878Gly	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	182	4	0.021978	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	13.77	2.336468	0.41398	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000540109	T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36	5.78	5.78	0.91487	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.095542	0.64402	D	0.000001	T	0.52484	0.1737	M	0.61703	1.905	0.53688	D	0.999976	B;B;B	0.32031	0.352;0.019;0.238	B;B;B	0.33121	0.138;0.038;0.158	T	0.50092	-0.8868	9	.	.	.	.	16.1138	0.81283	0.0:0.0:0.0:1.0	.	865;878;878	G3XAE2;Q2HXI4;P23468	.;.;PTPRD_HUMAN	G	878;878;865;856;878	ENSP00000370593:D878G;ENSP00000348812:D878G;ENSP00000353187:D865G;ENSP00000351293:D856G;ENSP00000438164:D878G	.	D	-	2	0	PTPRD	8476184	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	8.040000	0.89188	2.220000	0.72140	0.533000	0.62120	GAT	.	.	none		0.483	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
ARMC4	55130	hgsc.bcm.edu	37	10	28257852	28257852	+	Splice_Site	SNP	C	C	T	rs199740026	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:28257852C>T	ENST00000305242.5	-	9	1330	c.1238G>A	c.(1237-1239)cGg>cAg	p.R413Q	ARMC4_ENST00000537576.1_Splice_Site_p.R105Q|ARMC4_ENST00000480504.1_5'UTR|ARMC4_ENST00000239715.3_Splice_Site_p.R270Q|ARMC4_ENST00000545014.1_Intron	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	413					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						AGAAACATACCGAAGTAATTG	0.458													C|||	557	0.111222	0.1884	0.0836	5008	,	,		18036	0.003		0.1213	False		,,,				2504	0.1278				p.R413Q		Atlas-SNP	.											ARMC4,rectum,NS,-1,1	ARMC4	177	1	0			c.G1238A						scavenged	.						4.0	3.0	3.0					10																	28257852		1459	3081	4540	SO:0001630	splice_region_variant	55130	exon9			ACATACCGAAGTA	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1238+1G>A	10.37:g.28257852C>T		Somatic	921	1	0.00108578		WXS	Illumina HiSeq	Phase_I	964	500	0.518672	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	261	0.11950549450549451	136	0.2764227642276423	36	0.09944751381215469	3	0.005244755244755245	86	0.11345646437994723	C	7.770	0.707261	0.15239	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000537573;ENST00000434029;ENST00000239715	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	3.89	2.05	0.26809	.	1.074070	0.07060	N	0.833582	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P	0.35628	0.513	B	0.21360	0.034	T	0.26052	-1.0114	8	.	.	.	-2.5181	6.1142	0.20117	0.0:0.7713:0.0:0.2287	.	413	Q5T2S8	ARMC4_HUMAN	Q	105;413;105;307;270	ENSP00000443208:R105Q;ENSP00000306410:R413Q;ENSP00000398155:R307Q;ENSP00000239715:R270Q	.	R	-	2	0	ARMC4	28297858	0.423000	0.25482	0.063000	0.19743	0.008000	0.06430	0.554000	0.23407	0.620000	0.30215	0.557000	0.71058	CGG	C|0.500;T|0.500	0.500	weak		0.458	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	Missense_Mutation
TEX15	56154	hgsc.bcm.edu	37	8	30701995	30701995	+	Missense_Mutation	SNP	A	A	C	rs61732457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:30701995A>C	ENST00000256246.2	-	1	4613	c.4539T>G	c.(4537-4539)gaT>gaG	p.D1513E		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1513					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TCAGATGGGAATCAATCAAGT	0.348													A|||	190	0.0379393	0.0008	0.0461	5008	,	,		18669	0.0		0.0885	False		,,,				2504	0.0695				p.D1513E		Atlas-SNP	.											.	TEX15	350	.	0			c.T4539G						PASS	.	A	GLU/ASP	81,4325	70.3+/-108.2	0,81,2122	155.0	159.0	158.0		4539	0.0	0.1	8	dbSNP_129	158	809,7789	187.6+/-234.8	31,747,3521	yes	missense	TEX15	NM_031271.3	45	31,828,5643	CC,CA,AA		9.4092,1.8384,6.844	possibly-damaging	1513/2790	30701995	890,12114	2203	4299	6502	SO:0001583	missense	56154	exon1			ATGGGAATCAATC	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.4539T>G	8.37:g.30701995A>C	ENSP00000256246:p.Asp1513Glu	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	195	109	0.558974	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	79	0.036172161172161175	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	65	0.08575197889182058	A	12.51	1.958876	0.34565	0.018384	0.094092	ENSG00000133863	ENST00000256246	T	0.13901	2.55	5.36	0.0242	0.14140	.	0.499340	0.18489	N	0.139686	T	0.00412	0.0013	L	0.55481	1.735	0.09310	N	1	B	0.20052	0.041	B	0.27262	0.078	T	0.29058	-1.0024	10	0.87932	D	0	.	2.4675	0.04556	0.5404:0.2386:0.0897:0.1313	.	1513	Q9BXT5	TEX15_HUMAN	E	1513	ENSP00000256246:D1513E	ENSP00000256246:D1513E	D	-	3	2	TEX15	30821537	0.006000	0.16342	0.137000	0.22149	0.138000	0.21146	0.598000	0.24074	0.111000	0.17947	0.533000	0.62120	GAT	A|0.939;C|0.061	0.061	strong		0.348	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
TMEM217	221468	hgsc.bcm.edu	37	6	37186440	37186440	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:37186440C>T	ENST00000336655.2	-	2	406	c.367G>A	c.(367-369)Gag>Aag	p.E123K	TMEM217_ENST00000356757.2_Missense_Mutation_p.E123K|TMEM217_ENST00000497775.1_Intron	NM_145316.3	NP_660359.2	Q8N7C4	TM217_HUMAN	transmembrane protein 217	123						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(5)|lung(1)	9						ATTCTGACCTCTTTAATGTCA	0.413																																					p.E123K		Atlas-SNP	.											TMEM217,NS,carcinoma,+1,1	TMEM217	24	1	0			c.G367A						scavenged	.						152.0	149.0	150.0					6																	37186440		2203	4300	6503	SO:0001583	missense	221468	exon2			TGACCTCTTTAAT		CCDS4831.1, CCDS69102.1	6p21.31-p21.2	2008-10-20	2008-07-07	2008-07-07	ENSG00000172738	ENSG00000172738			21238	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 128"""	C6orf128			Standard	NM_001162900		Approved	dJ355M6.2	uc010jws.3	Q8N7C4	OTTHUMG00000014618	ENST00000336655.2:c.367G>A	6.37:g.37186440C>T	ENSP00000338164:p.Glu123Lys	Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	142	2	0.0140845	NM_145316	Q8TC54	Missense_Mutation	SNP	ENST00000336655.2	37	CCDS4831.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.691060	0.48097	.	.	ENSG00000172738	ENST00000356757;ENST00000336655	.	.	.	4.54	2.61	0.31194	.	.	.	.	.	T	0.16896	0.0406	L	0.43923	1.385	0.09310	N	1	P;P	0.46912	0.793;0.886	P;P	0.48425	0.478;0.577	T	0.06534	-1.0821	8	0.30078	T	0.28	-0.6609	5.3964	0.16271	0.0:0.6787:0.2035:0.1178	.	123;123	Q8N7C4-2;Q8N7C4	.;TM217_HUMAN	K	123	.	ENSP00000338164:E123K	E	-	1	0	TMEM217	37294418	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	0.333000	0.19768	0.550000	0.28991	0.609000	0.83330	GAG	.	.	none		0.413	TMEM217-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357542.1	NM_145316	
PTPRH	5794	hgsc.bcm.edu	37	19	55715342	55715342	+	Missense_Mutation	SNP	C	C	T	rs55870162	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55715342C>T	ENST00000376350.3	-	5	716	c.694G>A	c.(694-696)Gat>Aat	p.D232N	PTPRH_ENST00000263434.5_Intron|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	232	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		D -> N (in dbSNP:rs55870162).		apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		TCTGTGCCATCGGGGACCTCC	0.542													C|||	90	0.0179712	0.0038	0.0115	5008	,	,		16192	0.001		0.0278	False		,,,				2504	0.0491				p.D232N		Atlas-SNP	.											.	PTPRH	139	.	0			c.G694A						PASS	.	C	,ASN/ASP	41,4365	43.8+/-77.6	0,41,2162	127.0	103.0	111.0		,694	-2.1	0.0	19	dbSNP_129	111	262,8338	101.6+/-162.9	3,256,4041	yes	intron,missense	PTPRH	NM_001161440.1,NM_002842.3	,23	3,297,6203	TT,TC,CC		3.0465,0.9305,2.3297	,benign	,232/1116	55715342	303,12703	2203	4300	6503	SO:0001583	missense	5794	exon5			TGCCATCGGGGAC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.694G>A	19.37:g.55715342C>T	ENSP00000365528:p.Asp232Asn	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	142	62	0.43662	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	27	0.012362637362637362	4	0.008130081300813009	3	0.008287292817679558	0	0.0	20	0.026385224274406333	C	10.62	1.400532	0.25291	0.009305	0.030465	ENSG00000080031	ENST00000376350	T	0.57436	0.4	3.74	-2.09	0.07232	Fibronectin, type III (4);Immunoglobulin-like fold (1);	3.343480	0.01398	N	0.013509	T	0.11965	0.0291	N	0.22421	0.69	0.09310	N	0.999996	B;P	0.37594	0.01;0.601	B;B	0.23852	0.002;0.049	T	0.08472	-1.0720	10	0.23302	T	0.38	.	5.7879	0.18343	0.0:0.5648:0.2178:0.2174	rs55870162	54;232	Q9HD43-2;Q9HD43	.;PTPRH_HUMAN	N	232	ENSP00000365528:D232N	ENSP00000365528:D232N	D	-	1	0	PTPRH	60407154	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.476000	0.02333	-0.264000	0.09365	-0.301000	0.09380	GAT	C|0.980;T|0.020	0.020	strong		0.542	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
DISC1	27185	hgsc.bcm.edu	37	1	231830295	231830295	+	Missense_Mutation	SNP	G	G	A	rs3738401	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:231830295G>A	ENST00000602281.1	+	2	844	c.791G>A	c.(790-792)cGg>cAg	p.R264Q	DISC1_ENST00000366633.3_Missense_Mutation_p.R264Q|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000537876.1_Missense_Mutation_p.R264Q|DISC1_ENST00000366636.4_Missense_Mutation_p.R264Q|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000317586.4_Missense_Mutation_p.R264Q|DISC1_ENST00000539444.1_Missense_Mutation_p.R264Q|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000439617.2_Missense_Mutation_p.R264Q|DISC1_ENST00000535983.1_Missense_Mutation_p.R264Q	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	264	Interaction with MAP1A.		R -> Q (in dbSNP:rs3738401). {ECO:0000269|PubMed:10814723, ECO:0000269|PubMed:12573262, ECO:0000269|PubMed:9455484}.		canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				TGTCTCTCTCGGCCCTTCAGT	0.612													G|||	1163	0.232228	0.1172	0.3329	5008	,	,		19997	0.2173		0.339	False		,,,				2504	0.2219				p.R264Q		Atlas-SNP	.											DISC1_ENST00000366638,NS,carcinoma,+1,3	DISC1	207	3	0			c.G791A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG	648,3758	276.3+/-273.0	54,540,1609	46.0	52.0	50.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,,791	-9.9	0.0	1	dbSNP_107	50	2734,5866	434.7+/-357.8	426,1882,1992	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,intron,missense	DISC1	NM_001012957.1,NM_001012958.1,NM_001012959.1,NM_001164537.1,NM_001164538.1,NM_001164539.1,NM_001164540.1,NM_001164541.1,NM_001164542.1,NM_001164544.1,NM_001164545.1,NM_001164546.1,NM_001164547.1,NM_001164548.1,NM_001164549.1,NM_001164550.1,NM_001164551.1,NM_001164552.1,NM_001164553.1,NM_001164554.1,NM_001164555.1,NM_001164556.1,NM_018662.2	43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,,43	480,2422,3601	AA,AG,GG		31.7907,14.7072,26.0034	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,,benign	264/833,264/370,264/679,264/887,264/804,264/756,264/733,264/696,264/682,264/663,264/580,264/560,264/560,264/552,264/548,264/430,264/424,264/388,264/388,264/376,264/357,,264/855	231830295	3382,9624	2203	4300	6503	SO:0001583	missense	27185	exon2			TCTCTCGGCCCTT	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.791G>A	1.37:g.231830295G>A	ENSP00000473425:p.Arg264Gln	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_001164541	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	37	CCDS59205.1	612	0.2802197802197802	68	0.13821138211382114	142	0.39226519337016574	147	0.256993006993007	255	0.33641160949868076	G	9.745	1.165955	0.21538	0.147072	0.317907	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000317586;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944;ENST00000366632	T;T;T;T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84	4.94	-9.87	0.00470	.	1.746570	0.02520	N	0.092507	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.27559	0.001;0.025;0.068;0.012;0.009;0.181;0.025;0.068;0.009;0.025;0.001;0.004;0.002;0.025;0.026;0.004;0.026;0.026;0.009;0.001	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.12156	0.001;0.007;0.007;0.007;0.004;0.007;0.007;0.007;0.004;0.007;0.0;0.004;0.001;0.007;0.004;0.002;0.004;0.004;0.004;0.0	T	0.32402	-0.9908	9	0.25751	T	0.34	4.3858	1.7516	0.02973	0.1374:0.1906:0.3457:0.3262	rs3738401;rs52831689;rs57749630;rs3738401	264;264;264;264;264;264;264;264;264;264;264;264;264;264;264;264;264;264;264;264	C4P094;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P091;C4P0D2;C4P0D3;C4P0B1;Q5T409;C4P0D0;Q9NRI5-2;Q9NRI5;Q9NRI5-3;Q9NRI5-4	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.;.	Q	264;264;264;264;264;264;264;264;264;264;264;264;115	ENSP00000403888:R264Q;ENSP00000320784:R264Q;ENSP00000355596:R264Q;ENSP00000443996:R264Q;ENSP00000440909:R264Q;ENSP00000355593:R264Q;ENSP00000440953:R264Q;ENSP00000295051:R264Q;ENSP00000441193:R264Q	ENSP00000295051:R264Q	R	+	2	0	DISC1	229896918	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.466000	0.02355	-3.304000	0.00192	-1.288000	0.01363	CGG	G|0.746;A|0.254	0.254	strong		0.612	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052986	33052986	+	Silent	SNP	T	T	C	rs1071597	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33052986T>C	ENST00000418931.2	+	3	740	c.624T>C	c.(622-624)gaT>gaC	p.D208D		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	208	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CCAGCCTGGATAGTCCTGTCA	0.567													.|||	2322	0.463658	0.5976	0.3314	5008	,	,		19701	0.621		0.3151	False		,,,				2504	0.3671				p.D208D		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.T624C						PASS	.	C		1686,1336		460,766,285	75.0	79.0	78.0		624	-0.3	0.4	6	dbSNP_86	78	1606,3810		234,1138,1336	no	coding-synonymous	HLA-DPB1	NM_002121.5		694,1904,1621	CC,CT,TT		29.6529,44.2091,39.014		208/259	33052986	3292,5146	1511	2708	4219	SO:0001819	synonymous_variant	3115	exon3			CCTGGATAGTCCT		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.624T>C	6.37:g.33052986T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	195	77	0.394872	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Silent	SNP	ENST00000418931.2	37	CCDS4765.1	960	0.43956043956043955	290	0.5894308943089431	110	0.30386740331491713	327	0.5716783216783217	233	0.3073878627968338	C	7.716	0.696092	0.15106	0.557909	0.296529	ENSG00000223865	ENST00000416804	.	.	.	4.04	-0.298	0.12814	.	.	.	.	.	T	0.11153	0.0272	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.26292	-1.0107	3	.	.	.	.	2.5941	0.04849	0.1365:0.2507:0.4257:0.1871	rs1071597;rs3179770;rs3181817;rs9277456;rs17409956;rs17851011	.	.	.	T	175	.	.	I	+	2	0	HLA-DPB1	33160964	0.000000	0.05858	0.375000	0.26029	0.969000	0.65631	-0.366000	0.07563	-0.117000	0.11872	-0.262000	0.10625	ATA	T|0.608;C|0.392	0.392	strong		0.567	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
NUGGC	389643	hgsc.bcm.edu	37	8	27903069	27903069	+	Missense_Mutation	SNP	C	C	T	rs13279787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27903069C>T	ENST00000413272.2	-	12	1563	c.1421G>A	c.(1420-1422)aGt>aAt	p.S474N	NUGGC_ENST00000341513.6_Missense_Mutation_p.S474N	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	474			S -> N (in dbSNP:rs13279787). {ECO:0000269|PubMed:15221005}.		cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										GGAGTTGAAACTATCTGTGAG	0.448													C|||	1894	0.378195	0.4304	0.4092	5008	,	,		17688	0.4375		0.2972	False		,,,				2504	0.3078				p.S474N		Atlas-SNP	.											.	.	.	.	0			c.G1421A						PASS	.	C	ASN/SER	1458,2390		292,874,758	120.0	124.0	123.0		1421	2.3	0.6	8	dbSNP_121	123	2321,5933		327,1667,2133	yes	missense	C8orf80	NM_001010906.1	46	619,2541,2891	TT,TC,CC		28.1197,37.8898,31.2262	benign	474/797	27903069	3779,8323	1924	4127	6051	SO:0001583	missense	389643	exon12			TTGAAACTATCTG	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"""speckled-like pattern in the germinal center"""		"""chromosome 8 open reading frame 80"""	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1421G>A	8.37:g.27903069C>T	ENSP00000408697:p.Ser474Asn	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	163	83	0.509202	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	37	CCDS47833.1	833	0.3814102564102564	218	0.44308943089430897	135	0.3729281767955801	256	0.44755244755244755	224	0.2955145118733509	C	7.315	0.615758	0.14129	0.378898	0.281197	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.31510	1.49;1.49	5.31	2.29	0.28610	.	0.348037	0.33180	N	0.005190	T	0.00012	0.0000	N	0.14661	0.345	0.41786	P	0.010159000000000029	B	0.06786	0.001	B	0.04013	0.001	T	0.48768	-0.9006	9	0.22706	T	0.39	-5.1026	6.5726	0.22547	0.0:0.4918:0.4051:0.1031	rs13279787;rs52823771;rs57973781;rs13279787	474	Q68CJ6	SLIP_HUMAN	N	474	ENSP00000408697:S474N;ENSP00000345031:S474N	ENSP00000345031:S474N	S	-	2	0	C8orf80	27958988	0.946000	0.32159	0.643000	0.29450	0.322000	0.28314	0.340000	0.19892	1.181000	0.42912	0.650000	0.86243	AGT	C|0.625;N|0.000	.	strong		0.448	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
MYH11	4629	hgsc.bcm.edu	37	16	15818834	15818834	+	Missense_Mutation	SNP	C	C	T	rs151058774		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15818834C>T	ENST00000300036.5	-	29	3983	c.3874G>A	c.(3874-3876)Gtc>Atc	p.V1292I	NDE1_ENST00000396354.1_3'UTR|NDE1_ENST00000571896.1_3'UTR|NDE1_ENST00000396355.1_3'UTR|NDE1_ENST00000342673.5_3'UTR|AF001548.5_ENST00000574212.1_RNA|MYH11_ENST00000452625.2_Missense_Mutation_p.V1299I|MYH11_ENST00000396324.3_Missense_Mutation_p.V1299I|MYH11_ENST00000576790.2_Missense_Mutation_p.V1292I	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1292					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						ATCCCTGTGACGCTCTCAACT	0.542			T	CBFB	AML																																p.V1299I		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.G3895A						PASS	.						55.0	46.0	49.0					16																	15818834		2197	4300	6497	SO:0001583	missense	4629	exon30			CTGTGACGCTCTC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.3874G>A	16.37:g.15818834C>T	ENSP00000300036:p.Val1292Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.099342	0.56183	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.17	5.17	0.71159	Myosin tail (1);	0.069264	0.56097	D	0.000021	T	0.73164	0.3552	L	0.45470	1.425	0.80722	D	1	B;B;B;B;B	0.28439	0.104;0.212;0.212;0.104;0.212	B;B;B;B;B	0.35312	0.2;0.103;0.103;0.103;0.146	T	0.72714	-0.4210	10	0.52906	T	0.07	.	17.6819	0.88246	0.0:1.0:0.0:0.0	.	1299;1292;1299;1292;1299	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	I	1292;1292;1299;1299;1299	ENSP00000300036:V1292I;ENSP00000345136:V1292I;ENSP00000379616:V1299I;ENSP00000407821:V1299I	ENSP00000300036:V1292I	V	-	1	0	MYH11	15726335	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	7.818000	0.86416	2.409000	0.81822	0.650000	0.86243	GTC	C|0.999;G|0.001	.	alt		0.542	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
PARP4	143	hgsc.bcm.edu	37	13	25033227	25033227	+	Silent	SNP	A	A	G	rs1050107	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25033227A>G	ENST00000381989.3	-	20	2484	c.2379T>C	c.(2377-2379)taT>taC	p.Y793Y	PARP4_ENST00000480576.1_5'UTR	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	793					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		ATTCAATCACATACGGCATCT	0.299													N|||	452	0.0902556	0.1687	0.072	5008	,	,		17890	0.0317		0.0934	False		,,,				2504	0.0542				p.Y793Y		Atlas-SNP	.											.	PARP4	142	.	0			c.T2379C						PASS	.	G		705,3697	754.5+/-412.5	58,589,1554	87.0	86.0	86.0		2379	-5.8	0.0	13	dbSNP_86	86	995,7605	771.9+/-407.7	68,859,3373	no	coding-synonymous	PARP4	NM_006437.3		126,1448,4927	GG,GA,AA		11.5698,16.0154,13.0749		793/1725	25033227	1700,11302	2201	4300	6501	SO:0001819	synonymous_variant	143	exon20			AATCACATACGGC	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2379T>C	13.37:g.25033227A>G		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	262	261	0.996183	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			A|0.887;G|0.113	0.113	strong		0.299	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
ASB2	51676	hgsc.bcm.edu	37	14	94417421	94417421	+	Silent	SNP	G	G	A	rs7147919	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:94417421G>A	ENST00000315988.4	-	4	1148	c.660C>T	c.(658-660)aaC>aaT	p.N220N	MIR4506_ENST00000584693.1_RNA|ASB2_ENST00000555019.1_Silent_p.N268N|ASB2_ENST00000556337.1_Intron	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	220					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		TGCCGTAGGCGTTCTTGGATT	0.602													G|||	2780	0.555112	0.3215	0.4769	5008	,	,		22201	0.7817		0.6541	False		,,,				2504	0.591				p.N268N		Atlas-SNP	.											.	ASB2	71	.	0			c.C804T						PASS	.	G	,	1698,2708	512.6+/-368.1	318,1062,823	132.0	111.0	118.0		804,660	-11.2	0.1	14	dbSNP_116	118	5569,3031	664.1+/-402.1	1806,1957,537	no	coding-synonymous,coding-synonymous	ASB2	NM_001202429.1,NM_016150.4	,	2124,3019,1360	AA,AG,GG		35.2442,38.5384,44.1258	,	268/636,220/588	94417421	7267,5739	2203	4300	6503	SO:0001819	synonymous_variant	51676	exon6			GTAGGCGTTCTTG	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.660C>T	14.37:g.94417421G>A		Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Silent	SNP	ENST00000315988.4	37	CCDS9915.1																																																																																			G|0.432;A|0.568	0.568	strong		0.602	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
NELL1	4745	hgsc.bcm.edu	37	11	20805335	20805335	+	Silent	SNP	C	C	T	rs2280363	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:20805335C>T	ENST00000357134.5	+	3	446	c.294C>T	c.(292-294)tcC>tcT	p.S98S	NELL1_ENST00000532434.1_Silent_p.S98S|NELL1_ENST00000325319.5_Silent_p.S98S|NELL1_ENST00000298925.5_Silent_p.S126S	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	98	Laminin G-like.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						AGAAGCCATCCACTTCAGGAG	0.428													C|||	1374	0.274361	0.4523	0.1513	5008	,	,		20056	0.1607		0.2575	False		,,,				2504	0.2556				p.S98S		Atlas-SNP	.											NELL1,NS,carcinoma,0,1	NELL1	179	1	0			c.C294T						PASS	.	C	,	1934,2472	550.2+/-378.0	418,1098,687	118.0	106.0	110.0		294,294	-11.8	0.0	11	dbSNP_100	110	2072,6528	360.5+/-332.0	253,1566,2481	no	coding-synonymous,coding-synonymous	NELL1	NM_006157.3,NM_201551.1	,	671,2664,3168	TT,TC,CC		24.093,43.8947,30.8012	,	98/811,98/764	20805335	4006,9000	2203	4300	6503	SO:0001819	synonymous_variant	4745	exon3			GCCATCCACTTCA	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.294C>T	11.37:g.20805335C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	110	108	0.981818	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	37	CCDS7855.1																																																																																			C|0.716;T|0.284	0.284	strong		0.428	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
MUC21	394263	hgsc.bcm.edu	37	6	30954439	30954439	+	Missense_Mutation	SNP	A	A	G	rs147266731	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954439A>G	ENST00000376296.3	+	2	728	c.487A>G	c.(487-489)Agc>Ggc	p.S163G	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	163	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CAGTGAGGCCAGCACAGCCAC	0.617																																					p.S163G		Atlas-SNP	.											MUC21,NS,carcinoma,0,3	MUC21	98	3	0			c.A487G						scavenged	.	A	GLY/SER	5,4401	4.2+/-10.8	0,5,2198	145.0	136.0	139.0		487	2.5	0.0	6	dbSNP_134	139	8,8592	3.0+/-9.4	0,8,4292	no	missense	MUC21	NM_001010909.2	56	0,13,6490	GG,GA,AA		0.093,0.1135,0.1	benign	163/567	30954439	13,12993	2203	4300	6503	SO:0001583	missense	394263	exon2			GAGGCCAGCACAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.487A>G	6.37:g.30954439A>G	ENSP00000365473:p.Ser163Gly	Somatic	62	2	0.0322581		WXS	Illumina HiSeq	Phase_I	107	8	0.0747664	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.033332	0.35893	0.001135	9.3E-4	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.03441	3.93	3.76	2.55	0.30701	.	.	.	.	.	T	0.00936	0.0031	N	0.20986	0.625	0.09310	N	1	B	0.27013	0.166	B	0.30782	0.12	T	0.48570	-0.9024	8	.	.	.	-5.3386	7.5189	0.27616	0.8914:0.0:0.1086:0.0	.	163	Q5SSG8	MUC21_HUMAN	G	163	ENSP00000365473:S163G	.	S	+	1	0	MUC21	31062418	0.000000	0.05858	0.006000	0.13384	0.067000	0.16453	1.000000	0.29770	0.599000	0.29845	0.397000	0.26171	AGC	A|0.996;G|0.004	0.004	strong		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
MUC21	394263	hgsc.bcm.edu	37	6	30954594	30954594	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954594G>C	ENST00000376296.3	+	2	883	c.642G>C	c.(640-642)gaG>gaC	p.E214D	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	214	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAACTCTGAGTCCAGAACGA	0.612																																					p.E214D		Atlas-SNP	.											.	MUC21	98	.	0			c.G642C						PASS	.						154.0	152.0	153.0					6																	30954594		2203	4300	6503	SO:0001583	missense	394263	exon2			CTCTGAGTCCAGA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.642G>C	6.37:g.30954594G>C	ENSP00000365473:p.Glu214Asp	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	120	6	0.05	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	3.066	-0.192132	0.06299	.	.	ENSG00000204544	ENST00000376296	T	0.01787	4.64	3.54	-7.08	0.01558	.	.	.	.	.	T	0.00384	0.0012	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.43196	-0.9406	8	.	.	.	.	10.9515	0.47332	0.1259:0.5078:0.3663:0.0	.	214	Q5SSG8	MUC21_HUMAN	D	214	ENSP00000365473:E214D	.	E	+	3	2	MUC21	31062573	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.756000	0.04777	-2.750000	0.00375	-0.349000	0.07799	GAG	.	.	none		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
BCLAF1	9774	hgsc.bcm.edu	37	6	136599885	136599885	+	Missense_Mutation	SNP	C	C	A	rs150873394	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:136599885C>A	ENST00000531224.1	-	4	386	c.134G>T	c.(133-135)aGg>aTg	p.R45M	BCLAF1_ENST00000530767.1_Missense_Mutation_p.R45M|BCLAF1_ENST00000527536.1_Missense_Mutation_p.R45M|BCLAF1_ENST00000353331.4_Missense_Mutation_p.R43M|BCLAF1_ENST00000527759.1_Missense_Mutation_p.R43M|BCLAF1_ENST00000392348.2_Missense_Mutation_p.R43M	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	45					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		ACTACGAGACCTTGAATATGT	0.363																																					p.R45M	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.G134T						PASS	.						47.0	47.0	47.0					6																	136599885		2203	4299	6502	SO:0001583	missense	9774	exon4			CGAGACCTTGAAT	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.134G>T	6.37:g.136599885C>A	ENSP00000435210:p.Arg45Met	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	48	10	0.208333	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	56	0.02564102564102564	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	49	0.06464379947229551	C	16.46	3.130493	0.56828	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T;T	0.18016	2.64;2.53;2.63;2.24;2.55;2.53;2.44	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000004	T	0.29524	0.0736	L	0.42245	1.32	0.80722	D	1	D;D;D;D	0.64830	0.994;0.994;0.994;0.994	D;D;D;D	0.74348	0.983;0.983;0.983;0.983	T	0.01587	-1.1318	10	0.87932	D	0	-9.7833	20.1392	0.98050	0.0:1.0:0.0:0.0	.	43;43;45;45	Q9NYF8-2;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;BCLF1_HUMAN;.	M	45;43;45;45;43;43;45	ENSP00000435210:R45M;ENSP00000229446:R43M;ENSP00000435441:R45M;ENSP00000436501:R45M;ENSP00000434826:R43M;ENSP00000376159:R43M;ENSP00000431734:R45M	ENSP00000229446:R43M	R	-	2	0	BCLAF1	136641578	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.677000	0.68142	2.765000	0.95021	0.557000	0.71058	AGG	C|0.979;A|0.021	0.021	strong		0.363	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	
FAS	355	hgsc.bcm.edu	37	10	90768672	90768672	+	Missense_Mutation	SNP	C	C	T	rs121913078		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:90768672C>T	ENST00000355279.2	+	4	361	c.361C>T	c.(361-363)Cgg>Tgg	p.R121W	FAS_ENST00000357339.2_Missense_Mutation_p.R121W|FAS_ENST00000355740.2_Missense_Mutation_p.R121W|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000352159.4_Missense_Mutation_p.R121W			P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	AAACTGCACCCGGACCCAGAA	0.393																																					p.R121W		Atlas-SNP	.											FAS,caecum,carcinoma,-1,1	FAS	47	1	0			c.C361T	GRCh37	CM971493	FAS	M	rs121913078	PASS	.						247.0	274.0	265.0					10																	90768672		2203	4300	6503	SO:0001583	missense	355	exon4			TGCACCCGGACCC	M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11920	protein-coding gene	gene with protein product	"""TNF receptor superfamily member 6"""	134637	"""tumor necrosis factor receptor superfamily, member 6"", ""Fas (TNF receptor superfamily, member 6)"""	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.361C>T	10.37:g.90768672C>T	ENSP00000347426:p.Arg121Trp	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	71	60	0.84507	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355279.2	37	CCDS7395.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235818	0.39498	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000357339;ENST00000355279;ENST00000371875	D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89	4.2	-2.74	0.05932	TNFR/CD27/30/40/95 cysteine-rich region (3);	2.803120	0.00964	N	0.003143	D	0.94879	0.8345	M	0.68593	2.085	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.971;0.99;0.983	D	0.84814	0.0792	10	0.66056	D	0.02	0.1313	8.0344	0.30484	0.5264:0.2147:0.2589:0.0	.	121;121;121	P25445-6;Q5T9P3;P25445	.;.;TNR6_HUMAN	W	148;121;121;121;121;121	ENSP00000347979:R121W;ENSP00000345601:R121W;ENSP00000349896:R121W;ENSP00000347426:R121W	ENSP00000345601:R121W	R	+	1	2	FAS	90758652	0.000000	0.05858	0.000000	0.03702	0.502000	0.33828	-1.179000	0.03090	-0.519000	0.06444	0.650000	0.86243	CGG	.	.	weak		0.393	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2		
ZFAND2A	90637	hgsc.bcm.edu	37	7	1195215	1195215	+	Silent	SNP	A	A	C	rs1133116	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1195215A>C	ENST00000316495.3	-	4	415	c.156T>G	c.(154-156)gtT>gtG	p.V52V	ZFAND2A_ENST00000401903.1_Silent_p.V52V	NM_182491.2	NP_872297.2	Q8N6M9	ZFN2A_HUMAN	zinc finger, AN1-type domain 2A	52					cellular response to arsenic-containing substance (GO:0071243)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	zinc ion binding (GO:0008270)			lung(2)|ovary(1)	3		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.82e-15)		CTGGGACGTGAACATCCTAAA	0.448													A|||	557	0.111222	0.0749	0.1816	5008	,	,		19995	0.0268		0.1481	False		,,,				2504	0.1595				p.V52V		Atlas-SNP	.											.	ZFAND2A	9	.	0			c.T156G						PASS	.			375,4031	190.9+/-216.7	18,339,1846	146.0	138.0	141.0		156	-8.2	0.1	7	dbSNP_86	141	1527,7073	287.0+/-298.0	131,1265,2904	no	coding-synonymous	ZFAND2A	NM_182491.2		149,1604,4750	CC,CA,AA		17.7558,8.5111,14.624		52/146	1195215	1902,11104	2203	4300	6503	SO:0001819	synonymous_variant	90637	exon4			GACGTGAACATCC	BC029558	CCDS5323.1	7p22.3	2010-04-23			ENSG00000178381	ENSG00000178381		"""Zinc fingers, AN1-type domain containing"""	28073	protein-coding gene	gene with protein product	"""arsenite inducible RNA associated protein"""	610699				20185824	Standard	NM_182491		Approved	AIRAP	uc003skc.3	Q8N6M9	OTTHUMG00000119019	ENST00000316495.3:c.156T>G	7.37:g.1195215A>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_182491	A4D220	Silent	SNP	ENST00000316495.3	37	CCDS5323.1																																																																																			A|0.857;C|0.143	0.143	strong		0.448	ZFAND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239220.2	NM_182491	
BMP1	649	hgsc.bcm.edu	37	8	22049596	22049596	+	Missense_Mutation	SNP	G	G	A	rs145284541	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22049596G>A	ENST00000306385.5	+	9	1782	c.1112G>A	c.(1111-1113)cGc>cAc	p.R371H	BMP1_ENST00000306349.8_Missense_Mutation_p.R371H|BMP1_ENST00000354870.5_3'UTR|BMP1_ENST00000397814.3_Missense_Mutation_p.R371H|BMP1_ENST00000397816.3_Missense_Mutation_p.R371H	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	371	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		GACCTGTACCGCAGCCGCCTG	0.632													G|||	17	0.00339457	0.0008	0.0072	5008	,	,		18169	0.0		0.0109	False		,,,				2504	0.0				p.R371H		Atlas-SNP	.											BMP1_ENST00000306349,NS,carcinoma,+1,2	BMP1	131	2	0			c.G1112A						PASS	.	G	HIS/ARG,HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	179.0	142.0	155.0		1112,1112	5.8	1.0	8	dbSNP_134	155	61,8539	37.8+/-93.5	0,61,4239	yes	missense,missense	BMP1	NM_001199.3,NM_006129.4	29,29	0,67,6436	AA,AG,GG		0.7093,0.1362,0.5151	possibly-damaging,possibly-damaging	371/731,371/987	22049596	67,12939	2203	4300	6503	SO:0001583	missense	649	exon9			TGTACCGCAGCCG		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"""Bone morphogenetic proteins"""	1067	protein-coding gene	gene with protein product	"""procollagen C-endopeptidase"""	112264	"""procollagen C-endopeptidase"""	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.1112G>A	8.37:g.22049596G>A	ENSP00000305714:p.Arg371His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	54	18	0.333333	NM_001199	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Missense_Mutation	SNP	ENST00000306385.5	37	CCDS6026.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	26.4	4.738348	0.89573	0.001362	0.007093	ENSG00000168487	ENST00000306385;ENST00000397816;ENST00000306349;ENST00000397814	T;T;T;T	0.18960	2.18;2.18;2.18;2.18	5.77	5.77	0.91146	CUB (5);	0.000000	0.39274	U	0.001414	T	0.30166	0.0756	L	0.38175	1.15	0.80722	D	1	D;D;D;D	0.89917	0.99;1.0;0.999;0.999	P;D;D;P	0.91635	0.86;0.999;0.949;0.862	T	0.01249	-1.1406	10	0.44086	T	0.13	.	17.4922	0.87707	0.0:0.0:1.0:0.0	.	371;444;371;371	P13497;Q59F71;P13497-2;P13497-6	BMP1_HUMAN;.;.;.	H	371	ENSP00000305714:R371H;ENSP00000380917:R371H;ENSP00000306121:R371H;ENSP00000380915:R371H	ENSP00000306121:R371H	R	+	2	0	BMP1	22105541	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.535000	0.53575	2.724000	0.93272	0.561000	0.74099	CGC	G|0.995;A|0.005	0.005	strong		0.632	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
KIAA1109	84162	hgsc.bcm.edu	37	4	123145751	123145751	+	Silent	SNP	T	T	A	rs7658836	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:123145751T>A	ENST00000264501.4	+	23	3085	c.2712T>A	c.(2710-2712)ccT>ccA	p.P904P	KIAA1109_ENST00000455637.1_Silent_p.P904P|KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000388738.3_Silent_p.P904P			Q2LD37	K1109_HUMAN	KIAA1109	904					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.P904P(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AAGGTCTTCCTTTGGGAAGCG	0.488													T|||	1371	0.273762	0.0408	0.3055	5008	,	,		18022	0.3562		0.2913	False		,,,				2504	0.4632				p.P904P		Atlas-SNP	.											KIAA1109,NS,carcinoma,0,1	KIAA1109	424	1	1	Substitution - coding silent(1)	prostate(1)	c.T2712A						PASS	.	T		335,3591		16,303,1644	107.0	109.0	108.0		2712	3.9	1.0	4	dbSNP_116	108	2508,5788		376,1756,2016	no	coding-synonymous	KIAA1109	NM_015312.3		392,2059,3660	AA,AT,TT		30.2314,8.5329,23.2613		904/5006	123145751	2843,9379	1963	4148	6111	SO:0001819	synonymous_variant	84162	exon21			TCTTCCTTTGGGA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.2712T>A	4.37:g.123145751T>A		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	253	128	0.505929	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	557	0.25503663003663	24	0.04878048780487805	107	0.2955801104972376	197	0.34440559440559443	229	0.3021108179419525	T	9.787	1.176902	0.21787	0.085329	0.302314	ENSG00000138688	ENST00000424425	.	.	.	5.03	3.87	0.44632	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999998	.	.	.	.	.	.	T	0.33445	-0.9868	3	.	.	.	.	9.0195	0.36191	0.0:0.1585:0.0:0.8415	rs7658836;rs7658836	.	.	.	I	736	.	.	F	+	1	0	KIAA1109	123365201	0.905000	0.30787	1.000000	0.80357	0.992000	0.81027	0.023000	0.13533	0.892000	0.36259	0.482000	0.46254	TTT	T|0.727;A|0.273	0.273	strong		0.488	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
ERAP2	64167	hgsc.bcm.edu	37	5	96237326	96237326	+	Silent	SNP	G	G	A	rs2287988	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96237326G>A	ENST00000437043.3	+	11	2400	c.1689G>A	c.(1687-1689)caG>caA	p.Q563Q	CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000515095.1_3'UTR|ERAP2_ENST00000379904.4_Silent_p.Q518Q	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	563					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		GACTGCAACAGGAGCGCTTCC	0.517													G|||	2769	0.552915	0.6021	0.5793	5008	,	,		19464	0.5278		0.5199	False		,,,				2504	0.5276				p.Q563Q		Atlas-SNP	.											.	ERAP2	77	.	0			c.G1689A						PASS	.	G	,	2555,1851	633.8+/-396.1	724,1107,372	59.0	61.0	60.0		1689,1689	1.6	0.4	5	dbSNP_100	60	4484,4116	590.3+/-392.7	1154,2176,970	no	coding-synonymous,coding-synonymous	ERAP2	NM_001130140.1,NM_022350.3	,	1878,3283,1342	AA,AG,GG		47.8605,42.0109,45.8788	,	563/961,563/961	96237326	7039,5967	2203	4300	6503	SO:0001819	synonymous_variant	64167	exon11			GCAACAGGAGCGC	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1689G>A	5.37:g.96237326G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Silent	SNP	ENST00000437043.3	37	CCDS4086.1																																																																																			G|0.454;A|0.546	0.546	strong		0.517	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
COX6A2	1339	hgsc.bcm.edu	37	16	31439170	31439170	+	Silent	SNP	G	G	A	rs12240	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31439170G>A	ENST00000287490.4	-	3	321	c.219C>T	c.(217-219)ccC>ccT	p.P73P		NM_005205.3	NP_005196.1	Q02221	CX6A2_HUMAN	cytochrome c oxidase subunit VIa polypeptide 2	73					generation of precursor metabolites and energy (GO:0006091)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)			endometrium(2)|large_intestine(2)|lung(1)	5						CGTCCCCCCAGGGGTAGGGCT	0.731													G|||	421	0.0840655	0.1036	0.0461	5008	,	,		6488	0.0486		0.0746	False		,,,				2504	0.1309				p.P73P		Atlas-SNP	.											.	COX6A2	7	.	0			c.C219T						PASS	.	G		390,4004	174.4+/-204.0	13,364,1820	36.0	37.0	37.0		219	1.0	0.3	16	dbSNP_52	37	650,7950	148.2+/-203.4	17,616,3667	no	coding-synonymous	COX6A2	NM_005205.3		30,980,5487	AA,AG,GG		7.5581,8.8757,8.0037		73/98	31439170	1040,11954	2197	4300	6497	SO:0001819	synonymous_variant	1339	exon3			CCCCCAGGGGTAG	U66875, M83308	CCDS10712.1	16p11.12	2011-07-04			ENSG00000156885	ENSG00000156885	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2279	protein-coding gene	gene with protein product		602009				1327966, 9177785	Standard	NM_005205		Approved		uc002ebx.2	Q02221	OTTHUMG00000132463	ENST00000287490.4:c.219C>T	16.37:g.31439170G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_005205	O00761|Q6GTW6	Silent	SNP	ENST00000287490.4	37	CCDS10712.1																																																																																			G|0.928;A|0.072	0.072	strong		0.731	COX6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255626.2	NM_005205	
AIFM1	9131	hgsc.bcm.edu	37	X	129283520	129283520	+	Silent	SNP	A	A	G	rs1139851	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:129283520A>G	ENST00000287295.3	-	3	503	c.273T>C	c.(271-273)gaT>gaC	p.D91D	AIFM1_ENST00000319908.3_Silent_p.D87D|AIFM1_ENST00000535724.1_Silent_p.D4D|AIFM1_ENST00000346424.2_Intron	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	91					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	ATCTTTTTTCATCCTCTTTCA	0.383													G|||	1854	0.491126	0.5825	0.3588	3775	,	,		13492	0.1438		0.3171	False		,,,				2504	0.3793				p.D91D		Atlas-SNP	.											.	AIFM1	75	.	0			c.T273C						PASS	.	G	,,,	2712,1121		833,639,407,159,164	208.0	184.0	192.0		273,273,261,	3.7	0.1	X	dbSNP_86	192	2672,4056		387,1157,741,884,1131	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	AIFM1	NM_001130847.3,NM_004208.3,NM_145812.2,NM_145813.2	,,,	1220,1796,1148,1043,1295	GG,GA,G,AA,A		39.7146,29.246,49.02	,,,	91/325,91/614,87/610,	129283520	5384,5177	2202	4300	6502	SO:0001819	synonymous_variant	9131	exon3			TTTTTCATCCTCT	AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"""programmed cell death 8 (apoptosis-inducing factor)"", ""neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"""	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.273T>C	X.37:g.129283520A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	104	97	0.932692	NM_001130847	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Silent	SNP	ENST00000287295.3	37	CCDS14618.1																																																																																			0|0.004;G|0.504	0.504	strong		0.383	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2		
EDNRA	1909	hgsc.bcm.edu	37	4	148461037	148461037	+	Silent	SNP	T	T	C	rs5333	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:148461037T>C	ENST00000324300.5	+	6	1484	c.969T>C	c.(967-969)caT>caC	p.H323H	EDNRA_ENST00000503721.1_3'UTR|EDNRA_ENST00000511804.1_Silent_p.H98H|EDNRA_ENST00000339690.5_3'UTR|EDNRA_ENST00000506066.1_Silent_p.H214H|EDNRA_ENST00000358556.4_Silent_p.H214H	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	323					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|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 ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TCCCTCTTCATTTAAGCCGTA	0.378													T|||	1925	0.384385	0.6498	0.3386	5008	,	,		19262	0.2381		0.2237	False		,,,				2504	0.3742				p.H323H		Atlas-SNP	.											.	EDNRA	48	.	0			c.T969C						PASS	.	T	,	2444,1962	621.4+/-393.7	684,1076,443	193.0	193.0	193.0		642,969	-1.1	1.0	4	dbSNP_52	193	2140,6460	367.5+/-334.7	275,1590,2435	no	coding-synonymous,coding-synonymous	EDNRA	NM_001166055.1,NM_001957.3	,	959,2666,2878	CC,CT,TT		24.8837,44.5302,35.2453	,	214/319,323/428	148461037	4584,8422	2203	4300	6503	SO:0001819	synonymous_variant	1909	exon6			TCTTCATTTAAGC	D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"""GPCR / Class A : Endothelin receptors"""	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.969T>C	4.37:g.148461037T>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	296	133	0.449324	NM_001957	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Silent	SNP	ENST00000324300.5	37	CCDS3769.1																																																																																			T|0.642;C|0.358	0.358	strong		0.378	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13902245	13902245	+	Missense_Mutation	SNP	G	G	C	rs139160176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13902245G>C	ENST00000265104.4	-	13	1751	c.1647C>G	c.(1645-1647)aaC>aaG	p.N549K		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	549	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCCGCAACTCGTTCTAAAACA	0.303									Kartagener syndrome				G|||	34	0.00678914	0.0	0.0144	5008	,	,		17285	0.0		0.0199	False		,,,				2504	0.0041				p.N549K		Atlas-SNP	.											.	DNAH5	868	.	0			c.C1647G						PASS	.	G	LYS/ASN	19,4383	25.3+/-52.1	0,19,2182	40.0	35.0	37.0		1647	-1.1	1.0	5	dbSNP_134	37	136,8444	66.7+/-129.0	1,134,4155	yes	missense	DNAH5	NM_001369.2	94	1,153,6337	CC,CG,GG		1.5851,0.4316,1.194	benign	549/4625	13902245	155,12827	2201	4290	6491	SO:0001583	missense	1767	exon13	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAACTCGTTCTAA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.1647C>G	5.37:g.13902245G>C	ENSP00000265104:p.Asn549Lys	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	20	0.009157509157509158	0	0.0	5	0.013812154696132596	0	0.0	15	0.01978891820580475	G	1.371	-0.586093	0.03827	0.004316	0.015851	ENSG00000039139	ENST00000265104	T	0.55588	0.51	4.84	-1.08	0.09936	Dynein heavy chain, domain-1 (1);	0.580895	0.18719	N	0.133075	T	0.20373	0.0490	L	0.56769	1.78	0.32476	N	0.542092	B	0.02656	0.0	B	0.08055	0.003	T	0.37842	-0.9688	10	0.05959	T	0.93	.	4.0887	0.09960	0.4934:0.0:0.142:0.3645	.	549	Q8TE73	DYH5_HUMAN	K	549	ENSP00000265104:N549K	ENSP00000265104:N549K	N	-	3	2	DNAH5	13955245	0.985000	0.35326	0.988000	0.46212	0.913000	0.54294	0.473000	0.22132	-0.293000	0.08986	-0.290000	0.09829	AAC	G|0.989;C|0.011	0.011	strong		0.303	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
LILRB3	11025	hgsc.bcm.edu	37	19	54726816	54726816	+	Splice_Site	SNP	A	A	T	rs80332440		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54726816A>T	ENST00000391750.1	-	2	169	c.33T>A	c.(31-33)ctT>ctA	p.L11L	LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Splice_Site_p.L11L|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000346401.6_Splice_Site_p.L11L|LILRB3_ENST00000424807.1_Splice_Site_p.L11L|LILRA6_ENST00000391735.3_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	11					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AAATCTCACCAAGGCAGAGCA	0.622																																					p.L11L		Atlas-SNP	.											LILRB3,NS,neuroblastoma,0,1	LILRB3	67	1	0			c.T33A						scavenged	.						33.0	40.0	37.0					19																	54726816		2161	4254	6415	SO:0001630	splice_region_variant	11025	exon1			CTCACCAAGGCAG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.34+1T>A	19.37:g.54726816A>T		Somatic	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	146	84	0.575342	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			.	.	weak		0.622	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	Silent
FAM47E	100129583	hgsc.bcm.edu	37	4	77177415	77177415	+	Silent	SNP	C	C	T	rs61740422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:77177415C>T	ENST00000424749.2	+	2	165	c.159C>T	c.(157-159)gaC>gaT	p.D53D	FAM47E_ENST00000510197.1_Intron|FAM47E_ENST00000515604.1_Silent_p.D53D|FAM47E_ENST00000339906.6_Intron|FAM47E-STBD1_ENST00000539752.1_Intron|FAM47E_ENST00000515589.1_3'UTR	NM_001136570.2	NP_001130042.1	Q6ZV65	FA47E_HUMAN	family with sequence similarity 47, member E	53																	AGGGGCTGGACGACTTCAGGA	0.562													C|||	70	0.0139776	0.0023	0.0216	5008	,	,		17567	0.0		0.0378	False		,,,				2504	0.0143				p.D53D		Atlas-SNP	.											.	.	.	.	0			c.C159T						PASS	.	C		19,1365		0,19,673	49.0	53.0	52.0		159	-2.7	1.0	4	dbSNP_129	52	152,3030		4,144,1443	no	coding-synonymous	FAM47E	NM_001136570.2		4,163,2116	TT,TC,CC		4.7769,1.3728,3.7451		53/394	77177415	171,4395	692	1591	2283	SO:0001819	synonymous_variant	0	exon2			GCTGGACGACTTC	AC034139, AK124936, CR591456, CR627383	CCDS47081.1, CCDS58907.1	4q21.1	2013-04-23			ENSG00000189157	ENSG00000189157			34343	protein-coding gene	gene with protein product	"""similar to genethonin 1"""						Standard	NM_001136570		Approved	FLJ42946, LOC100129583	uc003hjx.3	Q6ZV65	OTTHUMG00000185390	ENST00000424749.2:c.159C>T	4.37:g.77177415C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_001242939	D6R8Y4	Silent	SNP	ENST00000424749.2	37	CCDS47081.1																																																																																			C|0.979;T|0.021	0.021	strong		0.562	FAM47E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362528.2	NM_001136570	
PTPN5	84867	hgsc.bcm.edu	37	11	18764026	18764026	+	Missense_Mutation	SNP	G	G	C	rs4757707	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18764026G>C	ENST00000358540.2	-	7	938	c.508C>G	c.(508-510)Cca>Gca	p.P170A	PTPN5_ENST00000396167.2_Missense_Mutation_p.P138A|PTPN5_ENST00000477854.1_5'UTR|PTPN5_ENST00000396168.1_Missense_Mutation_p.P146A|RP11-1081L13.4_ENST00000527285.1_RNA|PTPN5_ENST00000496201.2_5'UTR|PTPN5_ENST00000396171.4_Missense_Mutation_p.P170A|PTPN5_ENST00000396170.1_Missense_Mutation_p.P138A	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	170			P -> A (in dbSNP:rs4757707). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)	p.P170A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						GGTGGCTCTGGGGGTGTCCTC	0.632													G|||	1489	0.297324	0.0242	0.4899	5008	,	,		16566	0.3194		0.3857	False		,,,				2504	0.4162				p.P170A		Atlas-SNP	.											PTPN5_ENST00000358540,caecum,carcinoma,0,3	PTPN5	163	3	1	Substitution - Missense(1)	skin(1)	c.C508G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO	419,3979	203.5+/-225.9	22,375,1802	41.0	45.0	43.0		412,508,508	1.4	0.8	11	dbSNP_111	43	3372,5214	497.7+/-374.6	674,2024,1595	yes	missense,missense,missense	PTPN5	NM_001039970.1,NM_006906.1,NM_032781.3	27,27,27	696,2399,3397	CC,CG,GG		39.2732,9.5271,29.1975	benign,benign,benign	138/534,170/566,170/566	18764026	3791,9193	2199	4293	6492	SO:0001583	missense	84867	exon7			GCTCTGGGGGTGT	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.508C>G	11.37:g.18764026G>C	ENSP00000351342:p.Pro170Ala	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	41	0.640625	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Missense_Mutation	SNP	ENST00000358540.2	37	CCDS7845.1	679	0.3108974358974359	20	0.04065040650406504	191	0.5276243093922652	173	0.30244755244755245	295	0.3891820580474934	G	11.26	1.587311	0.28268	0.095271	0.392732	ENSG00000110786	ENST00000358540;ENST00000396170;ENST00000396171;ENST00000396167;ENST00000396168	T;T;T;T;T	0.03831	3.79;3.92;3.79;3.92;3.81	4.41	1.4	0.22301	.	0.320871	0.27039	N	0.021226	T	0.00012	0.0000	N	0.24115	0.695	0.40928	P	0.015637000000000012	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.31668	-0.9935	9	0.13108	T	0.6	.	9.4819	0.38906	0.0:0.3185:0.5364:0.1451	rs4757707;rs4757707	170;138	P54829;B3KXG7	PTN5_HUMAN;.	A	170;138;170;138;146	ENSP00000351342:P170A;ENSP00000379473:P138A;ENSP00000379474:P170A;ENSP00000379470:P138A;ENSP00000379471:P146A	ENSP00000351342:P170A	P	-	1	0	PTPN5	18720602	0.979000	0.34478	0.803000	0.32268	0.930000	0.56654	1.786000	0.38694	0.111000	0.17947	0.561000	0.74099	CCA	G|0.702;C|0.298	0.298	strong		0.632	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970	
OR5F1	338674	hgsc.bcm.edu	37	11	55762060	55762060	+	Silent	SNP	T	T	C	rs71490418	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55762060T>C	ENST00000278409.1	-	1	41	c.42A>G	c.(40-42)ctA>ctG	p.L14L		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	14					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					CTAATCCCAATAGGACGAACT	0.348													T|||	673	0.134385	0.0303	0.2089	5008	,	,		18031	0.1419		0.1789	False		,,,				2504	0.1687				p.L14L		Atlas-SNP	.											OR5F1,rectum,carcinoma,-2,2	OR5F1	116	2	0			c.A42G						scavenged	.	T		248,4154	139.2+/-174.8	6,236,1959	59.0	61.0	60.0		42	-2.7	0.3	11	dbSNP_130	60	1660,6932	302.8+/-306.1	180,1300,2816	no	coding-synonymous	OR5F1	NM_003697.1		186,1536,4775	CC,CT,TT		19.3203,5.6338,14.6837		14/315	55762060	1908,11086	2201	4296	6497	SO:0001819	synonymous_variant	338674	exon1			TCCCAATAGGACG	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"""GPCR / Class A : Olfactory receptors"""	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.42A>G	11.37:g.55762060T>C		Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_003697	Q495D1|Q6IFB9	Silent	SNP	ENST00000278409.1	37	CCDS31515.1																																																																																			T|0.844;C|0.156	0.156	strong		0.348	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697	
ANKRD61	100310846	hgsc.bcm.edu	37	7	6071060	6071060	+	Silent	SNP	G	G	A	rs4724769	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:6071060G>A	ENST00000409061.1	+	1	54	c.54G>A	c.(52-54)aaG>aaA	p.K18K	EIF2AK1_ENST00000536084.1_Intron|EIF2AK1_ENST00000199389.6_Intron	NM_001271700.1	NP_001258629.1	A6NGH8	ANR61_HUMAN	ankyrin repeat domain 61	18																	ACAGTGCCAAGTCCCTGGAAG	0.468													G|||	1691	0.33766	0.1679	0.4164	5008	,	,		19742	0.3641		0.4742	False		,,,				2504	0.3436				p.K18K		Atlas-SNP	.											.	.	.	.	0			c.G54A						PASS	.																																			SO:0001819	synonymous_variant	100310846	exon1			TGCCAAGTCCCTG		CCDS64590.1	7p22	2013-01-10			ENSG00000157999	ENSG00000157999		"""Ankyrin repeat domain containing"""	22467	protein-coding gene	gene with protein product							Standard	NM_001271700		Approved		uc031swn.1	A6NGH8	OTTHUMG00000154561	ENST00000409061.1:c.54G>A	7.37:g.6071060G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	155	154	0.993548	NM_001271700		Silent	SNP	ENST00000409061.1	37																																																																																				G|0.600;A|0.400	0.400	strong		0.468	ANKRD61-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000335991.1		
RGAG4	340526	hgsc.bcm.edu	37	X	71350133	71350133	+	Missense_Mutation	SNP	T	T	G	rs6624595	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:71350133T>G	ENST00000545866.1	-	1	1625	c.1258A>C	c.(1258-1260)Agt>Cgt	p.S420R	RGAG4_ENST00000609883.1_Missense_Mutation_p.S420R|NHSL2_ENST00000540800.1_Intron	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	420			S -> R (in dbSNP:rs6624595).							cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					TCATCCTTACTCTCTCCTTCC	0.498													T|||	723	0.191523	0.0091	0.196	3775	,	,		14704	0.3879		0.0646	False		,,,				2504	0.1217				p.S420R		Atlas-SNP	.											.	RGAG4	63	.	0			c.A1258C						PASS	.	T	,ARG/SER	78,3607		2,63,11,1492,560	210.0	197.0	201.0		,1258	1.3	0.0	X	dbSNP_116	201	578,6019		20,386,152,1987,1659	yes	intron,missense	RGAG4,NHSL2	NM_001013627.2,NM_001024455.3	,110	22,449,163,3479,2219	GG,GT,G,TT,T		8.7616,2.1167,6.3801	,benign	,420/570	71350133	656,9626	2128	4204	6332	SO:0001583	missense	340526	exon1			CCTTACTCTCTCC	AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.1258A>C	X.37:g.71350133T>G	ENSP00000441366:p.Ser420Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	144	134	0.930556	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	37	CCDS55446.1	348	0.20976491862567812	8	0.01639344262295082	36	0.11042944785276074	157	0.36682242990654207	43	0.05858310626702997	T	10.15	1.272081	0.23221	0.021167	0.087616	ENSG00000242732	ENST00000545866;ENST00000479991	T;T	0.12569	2.67;2.67	3.71	1.29	0.21616	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.23128	0.08	B	0.17433	0.018	T	0.49254	-0.8959	7	.	.	.	.	6.263	0.20912	0.0:0.2327:0.0:0.7673	rs6624595;rs59381990;rs6624595	420	Q5HYW3	RGAG4_HUMAN	R	420	ENSP00000441366:S420R;ENSP00000418667:S420R	.	S	-	1	0	RGAG4	71266858	0.001000	0.12720	0.000000	0.03702	0.015000	0.08874	0.260000	0.18424	0.153000	0.19213	0.417000	0.27973	AGT	T|0.784;G|0.216	0.216	strong		0.498	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455	
SLC39A4	55630	hgsc.bcm.edu	37	8	145640235	145640235	+	Missense_Mutation	SNP	C	C	T	rs7823979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:145640235C>T	ENST00000301305.3	-	5	955	c.850G>A	c.(850-852)Gaa>Aaa	p.E284K	SLC39A4_ENST00000531013.1_5'Flank|SLC39A4_ENST00000276833.5_Missense_Mutation_p.E259K	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	284			E -> K (in dbSNP:rs7823979).		cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			CCAGCCTGTTCCGACAGTCCA	0.682													C|||	140	0.0279553	0.1014	0.0072	5008	,	,		18311	0.0		0.001	False		,,,				2504	0.0				p.E284K		Atlas-SNP	.											SLC39A4_ENST00000276833,NS,carcinoma,0,2	SLC39A4	54	2	0			c.G850A	GRCh37	CM032675	SLC39A4	M	rs7823979	scavenged	.	C	LYS/GLU,LYS/GLU	392,4014	195.3+/-220.0	11,370,1822	72.0	74.0	73.0		775,850	5.1	0.1	8	dbSNP_116	73	3,8597	1.2+/-3.3	0,3,4297	yes	missense,missense	SLC39A4	NM_017767.2,NM_130849.2	56,56	11,373,6119	TT,TC,CC		0.0349,8.897,3.0371	probably-damaging,probably-damaging	259/623,284/648	145640235	395,12611	2203	4300	6503	SO:0001583	missense	55630	exon5			CCTGTTCCGACAG	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"""Solute carriers"""	17129	protein-coding gene	gene with protein product		607059	"""acrodermatitis enteropathica, zinc-deficiency type"""	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.850G>A	8.37:g.145640235C>T	ENSP00000301305:p.Glu284Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	137	2	0.0145985	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	41	0.018772893772893772	37	0.07520325203252033	4	0.011049723756906077	0	0.0	0	0.0	C	11.76	1.733330	0.30684	0.08897	3.49E-4	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.63580	-0.05;-0.05	5.14	5.14	0.70334	.	0.337781	0.28365	N	0.015607	T	0.05868	0.0153	M	0.62723	1.935	0.09310	N	1	P;P	0.52842	0.9;0.956	B;P	0.47528	0.299;0.549	T	0.12116	-1.0560	10	0.24483	T	0.36	-32.0539	14.1355	0.65284	0.0:1.0:0.0:0.0	rs7823979;rs7823979	284;259	Q6P5W5;A6NDY5	S39A4_HUMAN;.	K	259;284	ENSP00000276833:E259K;ENSP00000301305:E284K	ENSP00000276833:E259K	E	-	1	0	SLC39A4	145611043	0.036000	0.19791	0.064000	0.19789	0.113000	0.19764	2.240000	0.43088	2.429000	0.82318	0.543000	0.68304	GAA	C|0.966;T|0.034	0.034	strong		0.682	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
GSN	2934	hgsc.bcm.edu	37	9	124089692	124089692	+	Missense_Mutation	SNP	C	C	T	rs76463933	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:124089692C>T	ENST00000373818.4	+	13	1916	c.1847C>T	c.(1846-1848)aCg>aTg	p.T616M	GSN_ENST00000373808.2_Missense_Mutation_p.T565M|GSN_ENST00000373807.1_Missense_Mutation_p.T347M|GSN_ENST00000412819.1_Missense_Mutation_p.T565M|GSN_ENST00000436847.1_Missense_Mutation_p.T576M|GSN_ENST00000341272.2_Missense_Mutation_p.T565M|GSN_ENST00000545652.1_Missense_Mutation_p.T573M|GSN_ENST00000394353.2_Missense_Mutation_p.T576M|GSN_ENST00000373806.1_Missense_Mutation_p.T41M|GSN_ENST00000373823.3_Missense_Mutation_p.T565M|GSN_ENST00000449733.1_Missense_Mutation_p.T565M	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	616	Actin-binding, Ca-sensitive. {ECO:0000255}.				actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						GCAGAGAAGACGGGGGCCCAG	0.657													C|||	278	0.0555112	0.1415	0.0303	5008	,	,		14862	0.0		0.0308	False		,,,				2504	0.0399				p.T616M		Atlas-SNP	.											.	GSN	81	.	0			c.C1847T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	558,3848	242.5+/-252.5	32,494,1677	25.0	26.0	26.0		1847,1694,1694,1694,1694,1727,1727,1694	2.2	0.1	9	dbSNP_131	26	288,8310	102.3+/-163.5	5,278,4016	yes	missense,missense,missense,missense,missense,missense,missense,missense	GSN	NM_000177.4,NM_001127662.1,NM_001127663.1,NM_001127664.1,NM_001127665.1,NM_001127666.1,NM_001127667.1,NM_198252.2	81,81,81,81,81,81,81,81	37,772,5693	TT,TC,CC		3.3496,12.6645,6.5057	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	616/783,565/732,565/732,565/732,565/732,576/743,576/743,565/732	124089692	846,12158	2203	4299	6502	SO:0001583	missense	2934	exon13			AGAAGACGGGGGC	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"""amyloidosis, Finnish type"""	137350	"""gelsolin (amyloidosis, Finnish type)"""			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.1847C>T	9.37:g.124089692C>T	ENSP00000362924:p.Thr616Met	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_000177	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Missense_Mutation	SNP	ENST00000373818.4	37	CCDS6828.1	95	0.043498168498168496	59	0.11991869918699187	10	0.027624309392265192	0	0.0	26	0.03430079155672823	C	15.13	2.741830	0.49151	0.126645	0.033496	ENSG00000148180	ENST00000373823;ENST00000436847;ENST00000394353;ENST00000449733;ENST00000412819;ENST00000341272;ENST00000373808;ENST00000394352;ENST00000456109;ENST00000545652;ENST00000373818;ENST00000373807;ENST00000373806;ENST00000373805	T;T;T;T;T;T;T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48;0.48;0.48;0.48;0.48;0.48;0.48	6.16	2.16	0.27623	Gelsolin domain (1);	0.521025	0.23377	N	0.048855	T	0.00440	0.0014	L	0.39898	1.24	0.09310	N	1	P;B;P;P;D	0.54772	0.798;0.41;0.648;0.798;0.968	B;B;B;B;B	0.42995	0.404;0.071;0.212;0.404;0.339	T	0.02333	-1.1175	10	0.72032	D	0.01	-4.3477	4.9696	0.14108	0.2486:0.4454:0.2407:0.0652	.	589;573;576;347;616	B7Z9A0;F5H1A8;B7Z373;Q5T0H9;P06396	.;.;.;.;GELS_HUMAN	M	565;576;576;565;565;565;565;549;539;573;616;347;41;41	ENSP00000362929:T565M;ENSP00000411293:T576M;ENSP00000377882:T576M;ENSP00000409358:T565M;ENSP00000416586:T565M;ENSP00000340888:T565M;ENSP00000362914:T565M;ENSP00000445823:T573M;ENSP00000362924:T616M;ENSP00000362913:T347M;ENSP00000362912:T41M	ENSP00000340888:T565M	T	+	2	0	GSN	123129513	0.070000	0.21116	0.061000	0.19648	0.905000	0.53344	0.669000	0.25142	0.134000	0.18681	0.650000	0.86243	ACG	C|0.940;T|0.060	0.060	strong		0.657	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177	
LILRB3	11025	hgsc.bcm.edu	37	19	54725930	54725930	+	Missense_Mutation	SNP	C	C	T	rs61480095	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54725930C>T	ENST00000391750.1	-	5	564	c.428G>A	c.(427-429)cGa>cAa	p.R143Q	LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.R143Q|LILRB3_ENST00000407860.2_Missense_Mutation_p.R143Q|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000346401.6_Missense_Mutation_p.R143Q|LILRB3_ENST00000424807.1_Missense_Mutation_p.R143Q|LILRA6_ENST00000391735.3_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	143	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.R143Q(11)		endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGAGCCACATCGGAGGGTCAT	0.582													.|||	2249	0.449081	0.2776	0.4769	5008	,	,		13331	0.626		0.4751	False		,,,				2504	0.4519				p.R143Q		Atlas-SNP	.											LILRB3,NS,carcinoma,0,11	LILRB3	67	11	11	Substitution - Missense(11)	kidney(11)	c.G428A						PASS	.						28.0	19.0	22.0					19																	54725930		2090	3824	5914	SO:0001583	missense	11025	exon4			CCACATCGGAGGG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.428G>A	19.37:g.54725930C>T	ENSP00000375630:p.Arg143Gln	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	264	111	0.420455	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	0.024	-1.388513	0.01185	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000445347	T;T;T;T;T;T	0.12774	2.65;2.65;2.65;2.65;2.65;5.75	2.87	-3.69	0.04450	Immunoglobulin-like fold (1);	0.513077	0.18054	N	0.153187	T	0.02047	0.0064	N	0.01109	-1.01	0.80722	P	0.0	B;B;B;B;B	0.25609	0.014;0.007;0.13;0.034;0.037	B;B;B;B;B	0.16722	0.016;0.002;0.003;0.003;0.002	T	0.30563	-0.9974	9	0.02654	T	1	.	1.113	0.01708	0.1765:0.3576:0.1802:0.2857	rs61480095;rs62133096	143;143;143;143;143	B5MCX0;F8WD89;O75022-2;O75022;O75022-3	.;.;.;LIRB3_HUMAN;.	Q	143	ENSP00000375630:R143Q;ENSP00000412771:R143Q;ENSP00000345184:R143Q;ENSP00000245620:R143Q;ENSP00000384274:R143Q;ENSP00000388199:R143Q	ENSP00000245620:R143Q	R	-	2	0	LILRB3	59417742	0.000000	0.05858	0.001000	0.08648	0.033000	0.12548	-6.718000	0.00056	-1.014000	0.03379	-0.350000	0.07774	CGA	.	.	weak		0.582	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
TTN	7273	hgsc.bcm.edu	37	2	179583496	179583496	+	Missense_Mutation	SNP	T	T	G	rs16866465	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179583496T>G	ENST00000591111.1	-	82	23704	c.23480A>C	c.(23479-23481)gAa>gCa	p.E7827A	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.E6900A|TTN_ENST00000589042.1_Missense_Mutation_p.E8144A|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13366	Ig-like 60.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCTCCACTTTCTAATGGCTG	0.453													T|||	1196	0.238818	0.1732	0.183	5008	,	,		20020	0.4375		0.1571	False		,,,				2504	0.2464				p.E8144A		Atlas-SNP	.											.	TTN	18412	.	0			c.A24431C						PASS	.	T	,,,ALA/GLU	590,3382		38,514,1434	75.0	76.0	76.0		,,,20699	6.0	0.5	2	dbSNP_123	76	1266,7082		97,1072,3005	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,107	135,1586,4439	GG,GT,TT		15.1653,14.854,15.0649	,,,benign	,,,6900/33424	179583496	1856,10464	1986	4174	6160	SO:0001583	missense	7273	exon84			CCACTTTCTAATG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.23480A>C	2.37:g.179583496T>G	ENSP00000465570:p.Glu7827Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		500	0.22893772893772893	86	0.17479674796747968	54	0.14917127071823205	244	0.42657342657342656	116	0.15303430079155672	T	7.627	0.678028	0.14841	0.14854	0.151653	ENSG00000155657	ENST00000342992	T	0.67865	-0.29	6.01	6.01	0.97437	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	B	0.10296	0.003	B	0.15870	0.014	T	0.29366	-1.0014	8	0.87932	D	0	.	16.5285	0.84344	0.0:0.0:0.0:1.0	rs16866465;rs52832346;rs16866465	7827	Q8WZ42	TITIN_HUMAN	A	6900	ENSP00000343764:E6900A	ENSP00000343764:E6900A	E	-	2	0	TTN	179291741	1.000000	0.71417	0.490000	0.27465	0.387000	0.30353	5.942000	0.70203	2.307000	0.77673	0.528000	0.53228	GAA	T|0.778;G|0.222	0.222	strong		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17914057	17914057	+	Missense_Mutation	SNP	G	G	A	rs34417109	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17914057G>A	ENST00000361221.3	+	3	299	c.140G>A	c.(139-141)aGc>aAc	p.S47N	ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.S47N|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.S47N|ARHGEF10L_ENST00000375420.3_5'Flank|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.S47N	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	47			S -> N (in dbSNP:rs34417109).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GAGGACACCAGCGCAGCCCTG	0.592													G|||	148	0.0295527	0.0083	0.0303	5008	,	,		17722	0.0		0.0596	False		,,,				2504	0.0573				p.S47N		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.G140A						PASS	.	G	ASN/SER,ASN/SER	66,4340	61.1+/-98.1	0,66,2137	149.0	162.0	157.0		140,140	2.8	0.7	1	dbSNP_126	157	530,8070	148.0+/-203.3	11,508,3781	yes	missense,missense	ARHGEF10L	NM_001011722.2,NM_018125.3	46,46	11,574,5918	AA,AG,GG		6.1628,1.498,4.5825	benign,benign	47/1241,47/1280	17914057	596,12410	2203	4300	6503	SO:0001583	missense	55160	exon3			ACACCAGCGCAGC	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.140G>A	1.37:g.17914057G>A	ENSP00000355060:p.Ser47Asn	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	37	CCDS182.1	65	0.02976190476190476	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	50	0.06596306068601583	G	8.626	0.892561	0.17613	0.01498	0.061628	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415	T;T;T;T	0.58797	0.49;0.35;0.31;0.35	4.7	2.82	0.32997	.	1.191890	0.05940	N	0.636762	T	0.04137	0.0115	N	0.17082	0.46	0.44395	D	0.997308	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.09377	0.004;0.002;0.002;0.002	T	0.16158	-1.0412	10	0.35671	T	0.21	-10.9718	6.4614	0.21958	0.2146:0.0:0.7854:0.0	rs34417109	47;47;47;47	Q9HCE6-5;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;ARGAL_HUMAN	N	47	ENSP00000355060:S47N;ENSP00000399401:S47N;ENSP00000394621:S47N;ENSP00000364564:S47N	ENSP00000355060:S47N	S	+	2	0	ARHGEF10L	17786644	0.334000	0.24739	0.742000	0.31022	0.384000	0.30261	1.201000	0.32259	1.305000	0.44909	0.655000	0.94253	AGC	G|0.956;A|0.044	0.044	strong		0.592	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	
ASB2	51676	hgsc.bcm.edu	37	14	94417586	94417586	+	Silent	SNP	G	G	A	rs4483793	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:94417586G>A	ENST00000315988.4	-	4	983	c.495C>T	c.(493-495)tgC>tgT	p.C165C	MIR4506_ENST00000584693.1_RNA|ASB2_ENST00000555019.1_Silent_p.C213C|ASB2_ENST00000556337.1_Intron	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	165					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		TCTTGCGCTCGCAGGCTGTGC	0.612													G|||	2905	0.580072	0.4107	0.487	5008	,	,		20056	0.7817		0.6541	False		,,,				2504	0.591				p.C213C		Atlas-SNP	.											ASB2,NS,carcinoma,-2,1	ASB2	71	1	0			c.C639T						PASS	.	G	,	2048,2358	563.5+/-381.2	458,1132,613	50.0	45.0	47.0		639,495	1.9	1.0	14	dbSNP_111	47	5573,3027	660.6+/-401.8	1808,1957,535	no	coding-synonymous,coding-synonymous	ASB2	NM_001202429.1,NM_016150.4	,	2266,3089,1148	AA,AG,GG		35.1977,46.4821,41.404	,	213/636,165/588	94417586	7621,5385	2203	4300	6503	SO:0001819	synonymous_variant	51676	exon6			GCGCTCGCAGGCT	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.495C>T	14.37:g.94417586G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Silent	SNP	ENST00000315988.4	37	CCDS9915.1																																																																																			G|0.404;A|0.596	0.596	strong		0.612	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
RTP4	64108	hgsc.bcm.edu	37	3	187088923	187088923	+	Missense_Mutation	SNP	G	G	A	rs35224605	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:187088923G>A	ENST00000259030.2	+	2	613	c.503G>A	c.(502-504)aGc>aAc	p.S168N		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	168			S -> N (in dbSNP:rs35224605).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|protein targeting to membrane (GO:0006612)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		GGCTTAAAAAGCTGCATGACA	0.512													G|||	57	0.0113818	0.0023	0.0274	5008	,	,		5663	0.0		0.0209	False		,,,				2504	0.0143				p.S168N		Atlas-SNP	.											.	RTP4	20	.	0			c.G503A						PASS	.	G	ASN/SER	24,4382	31.7+/-61.6	0,24,2179	65.0	56.0	59.0		503	-0.2	0.0	3	dbSNP_126	59	251,8349	99.7+/-161.2	5,241,4054	yes	missense	RTP4	NM_022147.2	46	5,265,6233	AA,AG,GG		2.9186,0.5447,2.1144	benign	168/247	187088923	275,12731	2203	4300	6503	SO:0001583	missense	64108	exon2			TAAAAAGCTGCAT	BC013161	CCDS33910.1	3q27.3	2014-02-20	2006-11-21		ENSG00000136514	ENSG00000136514		"""Receptor transporter proteins"""	23992	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 4"""	609350	"""receptor transporter protein 4"""			16271481, 15550249, 16720576	Standard	NM_022147		Approved	IFRG28, Z3CXXC4	uc003frm.3	Q96DX8	OTTHUMG00000156459	ENST00000259030.2:c.503G>A	3.37:g.187088923G>A	ENSP00000259030:p.Ser168Asn	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	107	62	0.579439	NM_022147	Q9H4F3	Missense_Mutation	SNP	ENST00000259030.2	37	CCDS33910.1	28	0.01282051282051282	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	15	0.01978891820580475	G	1.338	-0.594773	0.03771	0.005447	0.029186	ENSG00000136514	ENST00000259030	T	0.18174	2.23	4.08	-0.231	0.13086	.	4.744250	0.00166	N	0.000002	T	0.01870	0.0059	N	0.02539	-0.55	0.09310	N	1	B	0.13594	0.008	B	0.04013	0.001	T	0.22941	-1.0202	10	0.14656	T	0.56	0.6097	2.6998	0.05145	0.4786:0.0:0.3026:0.2188	rs35224605	168	Q96DX8	RTP4_HUMAN	N	168	ENSP00000259030:S168N	ENSP00000259030:S168N	S	+	2	0	RTP4	188571617	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.848000	0.04326	-0.045000	0.13468	0.655000	0.94253	AGC	G|0.980;A|0.020	0.020	strong		0.512	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147	
CTBP2	1488	hgsc.bcm.edu	37	10	126715629	126715629	+	Intron	SNP	C	C	T	rs3781409	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:126715629C>T	ENST00000337195.5	-	3	458				CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000309035.6_Missense_Mutation_p.V234M	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		CTGGGGTCCACAACCAGGCAC	0.667													C|||	1010	0.201677	0.0998	0.2651	5008	,	,		17616	0.2431		0.2823	False		,,,				2504	0.1687				p.V234M		Atlas-SNP	.											.	CTBP2	100	.	0			c.G700A						PASS	.	C	,,MET/VAL	541,3865		30,481,1692	40.0	47.0	44.0		,,700	3.6	1.0	10	dbSNP_107	44	2280,6318		321,1638,2340	yes	intron,intron,missense	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,21	351,2119,4032	TT,TC,CC		26.5178,12.2787,21.6933	,,benign	,,234/986	126715629	2821,10183	2203	4299	6502	SO:0001627	intron_variant	1488	exon1			GGTCCACAACCAG	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+11936G>A	10.37:g.126715629C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	226	115	0.50885	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	37	CCDS7643.1	525	0.2403846153846154	42	0.08536585365853659	111	0.30662983425414364	152	0.26573426573426573	220	0.29023746701846964	C	20.6	4.024336	0.75390	0.122787	0.265178	ENSG00000175029	ENST00000309035	D	0.88664	-2.41	4.54	3.64	0.41730	.	0.201012	0.30649	N	0.009162	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B	0.28350	0.208	B	0.30572	0.117	T	0.01909	-1.1249	8	0.59425	D	0.04	.	12.9826	0.58572	0.0:0.9215:0.0:0.0785	rs3781409;rs17710610;rs3781409	234	P56545-2	.	M	234	ENSP00000311825:V234M	ENSP00000311825:V234M	V	-	1	0	CTBP2	126705619	0.997000	0.39634	0.956000	0.39512	0.967000	0.64934	3.490000	0.53245	1.283000	0.44513	0.655000	0.94253	GTG	C|0.782;T|0.218	0.218	strong		0.667	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
CFAP57	149465	hgsc.bcm.edu	37	1	43649336	43649336	+	Silent	SNP	T	T	C	rs75528102	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43649336T>C	ENST00000372492.4	+	4	873	c.549T>C	c.(547-549)gcT>gcC	p.A183A	WDR65_ENST00000528956.1_Silent_p.A183A	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		183			A -> S (in dbSNP:rs6663799).							NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TCCGTTTTGCTGAGGGAACCC	0.473													T|||	640	0.127796	0.0083	0.1888	5008	,	,		19103	0.3175		0.0457	False		,,,				2504	0.135				p.A183A		Atlas-SNP	.											.	WDR65	76	.	0			c.T549C						PASS	.	T	,,	77,4329	68.7+/-106.4	0,77,2126	93.0	95.0	94.0		549,549,549	-5.1	0.1	1	dbSNP_131	94	433,8167	133.3+/-190.8	10,413,3877	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	10,490,6003	CC,CT,TT		5.0349,1.7476,3.9213	,,	183/699,183/699,183/699	43649336	510,12496	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon4			TTTTGCTGAGGGA																												ENST00000372492.4:c.549T>C	1.37:g.43649336T>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				T|0.937;C|0.063	0.063	strong		0.473	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
CSPG4	1464	hgsc.bcm.edu	37	15	75981976	75981976	+	Missense_Mutation	SNP	C	C	T	rs200493777		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75981976C>T	ENST00000308508.5	-	3	1522	c.1430G>A	c.(1429-1431)cGc>cAc	p.R477H		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	477	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.			RH -> HY (in Ref. 1; CAA65529). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.R477H(1)		breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTCGCCATGGCGTGCCCCTCG	0.637																																					p.R477H		Atlas-SNP	.											CSPG4,NS,carcinoma,0,2	CSPG4	175	2	1	Substitution - Missense(1)	kidney(1)	c.G1430A						scavenged	.						67.0	61.0	63.0					15																	75981976		2197	4291	6488	SO:0001583	missense	1464	exon3			CCATGGCGTGCCC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1430G>A	15.37:g.75981976C>T	ENSP00000312506:p.Arg477His	Somatic	158	3	0.0189873		WXS	Illumina HiSeq	Phase_I	223	11	0.0493274	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	9.517	1.107225	0.20714	.	.	ENSG00000173546	ENST00000308508	T	0.19532	2.14	5.12	4.19	0.49359	.	0.096704	0.44483	D	0.000447	T	0.17746	0.0426	L	0.57536	1.79	0.27465	N	0.953023	P	0.35628	0.513	B	0.27380	0.079	T	0.14783	-1.0460	10	0.41790	T	0.15	.	9.3594	0.38186	0.0:0.8315:0.0:0.1685	.	477	Q6UVK1	CSPG4_HUMAN	H	477	ENSP00000312506:R477H	ENSP00000312506:R477H	R	-	2	0	CSPG4	73769031	0.038000	0.19896	0.145000	0.22337	0.035000	0.12851	1.407000	0.34657	2.375000	0.81037	0.555000	0.69702	CGC	C|0.999;T|0.001	0.001	weak		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
EME2	197342	hgsc.bcm.edu	37	16	1825982	1825982	+	Nonsense_Mutation	SNP	C	C	T	rs61753375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1825982C>T	ENST00000568449.1	+	7	985	c.964C>T	c.(964-966)Cag>Tag	p.Q322*	MRPS34_ENST00000177742.3_5'Flank|MRPS34_ENST00000397375.2_5'Flank|EME2_ENST00000307394.7_Nonsense_Mutation_p.Q387*	NM_001257370.1	NP_001244299.1	A4GXA9	EME2_HUMAN	essential meiotic structure-specific endonuclease subunit 2	322					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)			central_nervous_system(1)|kidney(2)|lung(5)|pancreas(1)	9						CCGCCTTCTGCAGCAGGTGGG	0.692								Direct reversal of damage;Homologous recombination					C|||	19	0.00379393	0.0	0.0043	5008	,	,		14562	0.0		0.0159	False		,,,				2504	0.0				p.Q322X		Atlas-SNP	.											.	EME2	40	.	0			c.C964T						PASS	.	C	stop/GLN	16,4344		0,16,2164	17.0	15.0	16.0		1159	2.3	0.9	16	dbSNP_129	16	126,8426		0,126,4150	yes	stop-gained	EME2	NM_001010865.1		0,142,6314	TT,TC,CC		1.4733,0.367,1.0998		387/445	1825982	142,12770	2180	4276	6456	SO:0001587	stop_gained	197342	exon7			CTTCTGCAGCAGG	AK074080	CCDS58404.1	16p13.3	2013-07-03	2013-07-03			ENSG00000197774			27289	protein-coding gene	gene with protein product	"""SLX2 structure-specific endonuclease subunit homolog B (S. cerevisiae)"""	610886	"""essential meiotic endonuclease 1 homolog 2 (S. pombe)"""			12721304	Standard	NM_001257370		Approved	FLJ00151, SLX2B	uc010brw.1	A4GXA9		ENST00000568449.1:c.964C>T	16.37:g.1825982C>T	ENSP00000457353:p.Gln322*	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_001257370	Q8TEP2|Q96RY3	Nonsense_Mutation	SNP	ENST00000568449.1	37	CCDS58404.1	14	0.00641025641025641	0	0.0	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	C	12.42	1.931688	0.34096	0.00367	0.014733	ENSG00000197774	ENST00000307394;ENST00000454910	.	.	.	3.4	2.33	0.28932	.	0.569222	0.15009	N	0.285709	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-21.8279	5.5781	0.17235	0.3465:0.4718:0.1817:0.0	rs61753375	.	.	.	X	387;343	.	ENSP00000303779:Q387X	Q	+	1	0	EME2	1765983	0.997000	0.39634	0.898000	0.35279	0.145000	0.21501	0.645000	0.24782	1.904000	0.55121	0.561000	0.74099	CAG	C|0.992;T|0.008	0.008	strong		0.692	EME2-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433185.2	NM_001010865	
KCNK4	50801	hgsc.bcm.edu	37	11	64066999	64066999	+	Missense_Mutation	SNP	C	C	T	rs953778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64066999C>T	ENST00000539216.1	+	6	1343	c.983C>T	c.(982-984)cCg>cTg	p.P328L	KCNK4_ENST00000422670.2_Missense_Mutation_p.P328L|KCNK4_ENST00000538767.1_Silent_p.A212A|KCNK4_ENST00000394525.2_Missense_Mutation_p.P328L|TEX40_ENST00000539943.1_5'Flank|TEX40_ENST00000328404.6_5'Flank|RP11-783K16.10_ENST00000539086.1_RNA			Q9NYG8	KCNK4_HUMAN	potassium channel, subfamily K, member 4	328			P -> L (in dbSNP:rs953778). {ECO:0000269|Ref.2}.		potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(2)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	10						AAGGCTCAGCCGCCTTCCCCG	0.721													C|||	1406	0.280751	0.2383	0.2939	5008	,	,		12588	0.5437		0.1561	False		,,,				2504	0.1861				p.P328L		Atlas-SNP	.											.	KCNK4	22	.	0			c.C983T						PASS	.	C	LEU/PRO	872,3476		82,708,1384	19.0	23.0	22.0		983	3.3	0.2	11	dbSNP_86	22	1220,7270		96,1028,3121	yes	missense	KCNK4	NM_033310.2	98	178,1736,4505	TT,TC,CC		14.3698,20.0552,16.2954	benign	328/394	64066999	2092,10746	2174	4245	6419	SO:0001583	missense	50801	exon7			CTCAGCCGCCTTC	AF247042	CCDS8067.1	11q13	2012-03-07			ENSG00000182450	ENSG00000182450		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6279	protein-coding gene	gene with protein product		605720				10767409, 16382106	Standard	NM_033310		Approved	K2p4.1, TRAAK	uc001nzk.1	Q9NYG8	OTTHUMG00000168006	ENST00000539216.1:c.983C>T	11.37:g.64066999C>T	ENSP00000444948:p.Pro328Leu	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	15	12	0.8	NM_033310	B5TJL1|Q96T94	Missense_Mutation	SNP	ENST00000539216.1	37	CCDS8067.1	632	0.2893772893772894	115	0.23373983739837398	104	0.287292817679558	300	0.5244755244755245	113	0.14907651715039577	C	10.37	1.330851	0.24167	0.200552	0.143698	ENSG00000182450	ENST00000422670;ENST00000539852;ENST00000394525;ENST00000544845;ENST00000539216	T;T;T	0.14893	2.47;2.47;2.47	4.28	3.34	0.38264	.	1.739010	0.03339	N	0.194476	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B;B	0.19445	0.036;0.003	B;B	0.14023	0.01;0.003	T	0.45175	-0.9279	9	0.62326	D	0.03	.	8.1533	0.31154	0.0:0.8877:0.0:0.1123	rs953778;rs3741401;rs953778	354;328	Q9NYG8-2;Q9NYG8	.;KCNK4_HUMAN	L	328;353;328;390;328	ENSP00000402797:P328L;ENSP00000378033:P328L;ENSP00000444948:P328L	ENSP00000378033:P328L	P	+	2	0	KCNK4	63823575	0.220000	0.23631	0.156000	0.22583	0.206000	0.24218	1.855000	0.39378	2.233000	0.73108	0.561000	0.74099	CCG	C|0.772;T|0.228	0.228	strong		0.721	KCNK4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396430.1	NM_033311	
DIS3	22894	hgsc.bcm.edu	37	13	73350079	73350079	+	Missense_Mutation	SNP	T	T	C	rs4883918	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:73350079T>C	ENST00000377767.4	-	5	906	c.806A>G	c.(805-807)aAt>aGt	p.N269S	DIS3_ENST00000377780.4_Missense_Mutation_p.N239S|DIS3_ENST00000545453.1_Missense_Mutation_p.N107S	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	269			N -> S (in dbSNP:rs4883918). {ECO:0000269|PubMed:11935316, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		ATTTTCTTCATTGTCGCCATG	0.303										Multiple Myeloma(4;0.011)			T|||	1638	0.327077	0.0825	0.4741	5008	,	,		15022	0.4534		0.2634	False		,,,				2504	0.4888				p.N269S		Atlas-SNP	.											.	DIS3	103	.	0			c.A806G						PASS	.	T	SER/ASN,SER/ASN	502,3902	230.7+/-244.8	40,422,1740	74.0	69.0	70.0		716,806	-8.1	0.0	13	dbSNP_111	70	2548,6048	413.0+/-351.0	386,1776,2136	yes	missense,missense	DIS3	NM_001128226.1,NM_014953.3	46,46	426,2198,3876	CC,CT,TT		29.6417,11.3987,23.4615	benign,benign	239/929,269/959	73350079	3050,9950	2202	4298	6500	SO:0001583	missense	22894	exon5			TCTTCATTGTCGC	AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"""exosome component 11"""	607533	"""KIAA1008"", ""DIS3 mitotic control homolog (S. cerevisiae)"""	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.806A>G	13.37:g.73350079T>C	ENSP00000366997:p.Asn269Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	37	CCDS9447.1	697	0.3191391941391941	54	0.10975609756097561	158	0.43646408839779005	278	0.486013986013986	207	0.27308707124010556	T	1.751	-0.489183	0.04352	0.113987	0.296417	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.20200	2.09;2.09;2.09	5.66	-8.07	0.01098	.	1.579370	0.03238	N	0.179867	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43572	-0.9383	9	0.08837	T	0.75	.	14.0915	0.64993	0.0:0.1368:0.2749:0.5883	rs4883918;rs52826006;rs4883918	239;269	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	S	269;239;107	ENSP00000366997:N269S;ENSP00000367011:N239S;ENSP00000440058:N107S	ENSP00000366997:N269S	N	-	2	0	DIS3	72248080	0.000000	0.05858	0.000000	0.03702	0.631000	0.37964	0.585000	0.23879	-1.333000	0.02247	-2.015000	0.00435	AAT	T|0.726;C|0.274	0.274	strong		0.303	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953	
IL1RN	3557	hgsc.bcm.edu	37	2	113887207	113887207	+	Silent	SNP	T	T	C	rs419598	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:113887207T>C	ENST00000409930.3	+	2	235	c.171T>C	c.(169-171)gcT>gcC	p.A57A	IL1RN_ENST00000361779.3_Silent_p.A23A|IL1RN_ENST00000409052.1_Silent_p.A23A|IL1RN_ENST00000259206.5_Silent_p.A60A|IL1RN_ENST00000354115.2_Silent_p.A39A	NM_173842.2	NP_776214.1	P18510	IL1RA_HUMAN	interleukin 1 receptor antagonist	57					acute-phase response (GO:0006953)|carboxylic acid metabolic process (GO:0019752)|chronic inflammatory response to antigenic stimulus (GO:0002439)|female pregnancy (GO:0007565)|fever generation (GO:0001660)|immune response (GO:0006955)|insulin secretion (GO:0030073)|lipid metabolic process (GO:0006629)|memory (GO:0007613)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of membrane potential (GO:0045837)|positive regulation of JUN kinase activity (GO:0043507)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to interleukin-4 (GO:0070670)|response to lipopolysaccharide (GO:0032496)|response to organonitrogen compound (GO:0010243)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	interleukin-1 receptor antagonist activity (GO:0005152)|interleukin-1 receptor binding (GO:0005149)|interleukin-1 Type I receptor antagonist activity (GO:0045352)|interleukin-1 Type II receptor antagonist activity (GO:0045353)|interleukin-1, Type I receptor binding (GO:0005150)|interleukin-1, Type II receptor binding (GO:0005151)			breast(1)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	10					Rilonacept(DB06372)	AACTAGTTGCTGGATACTTGC	0.478									Lichen Sclerosis et Atrophicus, Familial Clustering of				T|||	960	0.191693	0.0333	0.3314	5008	,	,		24639	0.0942		0.2922	False		,,,				2504	0.3037				p.A60A		Atlas-SNP	.											.	IL1RN	30	.	0			c.T180C	GRCh37	CM025329	IL1RN	M	rs419598	PASS	.	T	,,,	283,4123	157.0+/-190.0	6,271,1926	170.0	154.0	159.0		117,180,171,69	-1.5	0.9	2	dbSNP_80	159	2398,6202	397.8+/-345.9	355,1688,2257	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL1RN	NM_000577.4,NM_173841.2,NM_173842.2,NM_173843.2	,,,	361,1959,4183	CC,CT,TT		27.8837,6.4231,20.6136	,,,	39/160,60/181,57/178,23/144	113887207	2681,10325	2203	4300	6503	SO:0001819	synonymous_variant	3557	exon4	Familial Cancer Database	Lichen Sclerosis, Familial	AGTTGCTGGATAC	M55646	CCDS2113.1, CCDS2114.1, CCDS2115.1, CCDS46396.1	2q14.2	2014-09-17			ENSG00000136689	ENSG00000136689		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	6000	protein-coding gene	gene with protein product	"""interleukin-1 receptor antagonist protein"", ""intracellular interleukin-1 receptor antagonist"""	147679				1386337, 8432529	Standard	NM_000577		Approved	IL1RA, ICIL-1RA, IL1F3, IRAP, IL-1RN, MGC10430	uc002tjb.3	P18510	OTTHUMG00000131341	ENST00000409930.3:c.171T>C	2.37:g.113887207T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	161	76	0.47205	NM_173841	A8K4G1|Q14628|Q53SC2|Q7RTZ4|Q96GD6|Q9UPC0	Silent	SNP	ENST00000409930.3	37	CCDS46396.1																																																																																			T|0.816;C|0.184	0.184	strong		0.478	IL1RN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330802.1	NM_173841	
PEX11G	92960	hgsc.bcm.edu	37	19	7542168	7542168	+	Missense_Mutation	SNP	G	G	A	rs11668511	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7542168G>A	ENST00000221480.1	-	5	654	c.646C>T	c.(646-648)Ctc>Ttc	p.L216F	PEX11G_ENST00000593942.1_Missense_Mutation_p.L146F|PEX11G_ENST00000599519.1_5'UTR	NM_001270539.1|NM_080662.3	NP_001257468.1|NP_542393.1	Q96HA9	PX11C_HUMAN	peroxisomal biogenesis factor 11 gamma	216					peroxisome fission (GO:0016559)|regulation of peroxisome size (GO:0044375)	integral component of peroxisomal membrane (GO:0005779)|intrinsic component of peroxisomal membrane (GO:0031231)|peroxisome (GO:0005777)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(1)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	7						GTGCCCATGAGGCCCACTAGC	0.706													G|||	51	0.0101837	0.0008	0.0115	5008	,	,		14100	0.0		0.0358	False		,,,				2504	0.0061				p.L216F		Atlas-SNP	.											.	PEX11G	16	.	0			c.C646T						PASS	.	G	PHE/LEU	25,4313		0,25,2144	12.0	15.0	14.0		646	5.2	1.0	19	dbSNP_120	14	286,8238		4,278,3980	yes	missense	PEX11G	NM_080662.2	22	4,303,6124	AA,AG,GG		3.3552,0.5763,2.418	probably-damaging	216/242	7542168	311,12551	2169	4262	6431	SO:0001583	missense	92960	exon5			CCATGAGGCCCAC	BC008780	CCDS12178.1	19p13.2	2008-02-05				ENSG00000104883			20208	protein-coding gene	gene with protein product		607583				12417726	Standard	NM_080662		Approved		uc002mgk.2	Q96HA9		ENST00000221480.1:c.646C>T	19.37:g.7542168G>A	ENSP00000221480:p.Leu216Phe	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_080662	Q8NDM0	Missense_Mutation	SNP	ENST00000221480.1	37	CCDS12178.1	31	0.014194139194139194	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	25	0.032981530343007916	G	20.6	4.010285	0.75046	0.005763	0.033552	ENSG00000104883	ENST00000221480	T	0.52983	0.64	5.2	5.2	0.72013	.	0.065408	0.64402	D	0.000008	T	0.38321	0.1036	M	0.78223	2.4	0.58432	D	0.999999	D	0.71674	0.998	D	0.63113	0.911	T	0.53301	-0.8458	10	0.28530	T	0.3	-20.3419	9.8052	0.40789	0.094:0.0:0.906:0.0	rs11668511	216	Q96HA9	PX11C_HUMAN	F	216	ENSP00000221480:L216F	ENSP00000221480:L216F	L	-	1	0	PEX11G	7448168	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	4.977000	0.63792	2.405000	0.81733	0.563000	0.77884	CTC	G|0.985;A|0.015	0.015	strong		0.706	PEX11G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458965.1	NM_080662	
PFAS	5198	hgsc.bcm.edu	37	17	8161149	8161149	+	Missense_Mutation	SNP	C	C	T	rs4791641	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:8161149C>T	ENST00000314666.6	+	10	1233	c.1100C>T	c.(1099-1101)cCa>cTa	p.P367L	PFAS_ENST00000545834.1_5'UTR	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	367			P -> L (in dbSNP:rs4791641). {ECO:0000269|PubMed:10548741, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9205841}.		'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	TGGGAGGATCCAAGCTTCCAG	0.537													C|||	1697	0.338858	0.2292	0.3184	5008	,	,		17331	0.2272		0.5288	False		,,,				2504	0.4213				p.P367L		Atlas-SNP	.											.	PFAS	91	.	0			c.C1100T	GRCh37	CM067707	PFAS	M	rs4791641	PASS	.	C	LEU/PRO	1230,3176	424.0+/-340.3	160,910,1133	62.0	61.0	61.0		1100	4.8	0.4	17	dbSNP_111	61	4203,4397	569.3+/-389.2	1039,2125,1136	yes	missense	PFAS	NM_012393.2	98	1199,3035,2269	TT,TC,CC		48.8721,27.9165,41.773	possibly-damaging	367/1339	8161149	5433,7573	2203	4300	6503	SO:0001583	missense	5198	exon10			AGGATCCAAGCTT	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"""FGAR amidotransferase"""	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.1100C>T	17.37:g.8161149C>T	ENSP00000313490:p.Pro367Leu	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	774	0.3543956043956044	107	0.21747967479674796	131	0.36187845303867405	124	0.21678321678321677	412	0.5435356200527705	C	14.18	2.458258	0.43634	0.279165	0.488721	ENSG00000178921	ENST00000314666	T	0.40225	1.04	5.79	4.82	0.62117	PurM, N-terminal-like (1);AIR synthase-related protein (1);	0.260679	0.39407	N	0.001378	T	0.00012	0.0000	L	0.49640	1.575	0.09310	P	0.999999651095	B	0.02656	0.0	B	0.09377	0.004	T	0.43393	-0.9394	9	0.87932	D	0	-4.4143	12.4284	0.55561	0.0:0.9191:0.0:0.0809	rs4791641;rs4791641	367	O15067	PUR4_HUMAN	L	367	ENSP00000313490:P367L	ENSP00000313490:P367L	P	+	2	0	PFAS	8101874	0.006000	0.16342	0.408000	0.26446	0.975000	0.68041	1.652000	0.37313	1.467000	0.48044	0.561000	0.74099	CCA	C|0.624;T|0.376	0.376	strong		0.537	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
TOP3A	7156	hgsc.bcm.edu	37	17	18193941	18193941	+	Silent	SNP	G	G	A	rs2230154	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18193941G>A	ENST00000321105.5	-	13	1741	c.1527C>T	c.(1525-1527)gaC>gaT	p.D509D	TOP3A_ENST00000542570.1_Silent_p.D414D|TOP3A_ENST00000540524.1_Silent_p.D39D	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	509					DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)	p.D509D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						TGGTCTCCCCGTCCACCATCT	0.582													g|||	896	0.178914	0.1611	0.2421	5008	,	,		20534	0.0605		0.3062	False		,,,				2504	0.1493				p.D509D		Atlas-SNP	.											TOP3A,NS,carcinoma,0,1	TOP3A	85	1	1	Substitution - coding silent(1)	stomach(1)	c.C1527T						PASS	.	A		901,3505	348.5+/-309.9	83,735,1385	88.0	62.0	71.0		1527	-6.1	1.0	17	dbSNP_98	71	2600,6000	422.0+/-353.9	383,1834,2083	no	coding-synonymous	TOP3A	NM_004618.3		466,2569,3468	AA,AG,GG		30.2326,20.4494,26.9183		509/1002	18193941	3501,9505	2203	4300	6503	SO:0001819	synonymous_variant	7156	exon13			CTCCCCGTCCACC	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.1527C>T	17.37:g.18193941G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	123	68	0.552846	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Silent	SNP	ENST00000321105.5	37	CCDS11194.1																																																																																			G|0.757;A|0.243	0.243	strong		0.582	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
RASGRP2	10235	hgsc.bcm.edu	37	11	64496357	64496357	+	Silent	SNP	G	G	T	rs2230414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64496357G>T	ENST00000354024.3	-	15	2001	c.1749C>A	c.(1747-1749)ggC>ggA	p.G583G	RASGRP2_ENST00000377494.1_Silent_p.G583G|RASGRP2_ENST00000377497.3_Silent_p.G583G|RASGRP2_ENST00000394432.3_Silent_p.G583G	NM_153819.1	NP_722541.1	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2 (calcium and DAG-regulated)	583					blood coagulation (GO:0007596)|cellular response to calcium ion (GO:0071277)|platelet activation (GO:0030168)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGCCTCGCCTGCCAGGGCGGG	0.642													G|||	931	0.185903	0.118	0.3098	5008	,	,		16741	0.3284		0.0835	False		,,,				2504	0.1483				p.G583G		Atlas-SNP	.											.	RASGRP2	48	.	0			c.C1749A						PASS	.	G	,,	510,3892	233.6+/-246.7	32,446,1723	45.0	42.0	43.0		1749,1749,1749	-0.5	1.0	11	dbSNP_98	43	835,7759	191.4+/-237.6	40,755,3502	yes	coding-synonymous,coding-synonymous,coding-synonymous	RASGRP2	NM_001098670.1,NM_001098671.1,NM_153819.1	,,	72,1201,5225	TT,TG,GG		9.7161,11.5856,10.3493	,,	583/610,583/610,583/610	64496357	1345,11651	2201	4297	6498	SO:0001819	synonymous_variant	10235	exon15			TCGCCTGCCAGGG	U78170	CCDS31598.1	11q13	2014-09-17			ENSG00000068831	ENSG00000068831		"""EF-hand domain containing"""	9879	protein-coding gene	gene with protein product		605577				9789079	Standard	NM_001098670		Approved	CALDAG-GEFI	uc009ypv.3	Q7LDG7	OTTHUMG00000045420	ENST00000354024.3:c.1749C>A	11.37:g.64496357G>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	33	14	0.424242	NM_001098671	A6NDC7|O00538|Q9UL65	Silent	SNP	ENST00000354024.3	37	CCDS31598.1																																																																																			G|0.850;T|0.150	0.150	strong		0.642	RASGRP2-002	NOVEL	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142062.1	NM_153819	
C9orf84	158401	hgsc.bcm.edu	37	9	114484837	114484837	+	Silent	SNP	G	G	T	rs62569959	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:114484837G>T	ENST00000318737.4	-	13	1919	c.1791C>A	c.(1789-1791)ctC>ctA	p.L597L	C9orf84_ENST00000394777.4_Silent_p.L558L|C9orf84_ENST00000374287.3_Silent_p.L597L|C9orf84_ENST00000394779.3_Silent_p.L558L	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	597										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						CTGCTGCTTCGAGGAGGCAAA	0.373													G|||	490	0.0978435	0.0008	0.049	5008	,	,		15793	0.1131		0.1034	False		,,,				2504	0.2423				p.L597L		Atlas-SNP	.											.	C9orf84	207	.	0			c.C1791A						PASS	.	G	,	74,4332	64.1+/-101.4	0,74,2129	94.0	92.0	92.0		1674,1791	2.3	1.0	9	dbSNP_129	92	757,7843	181.5+/-230.2	39,679,3582	no	coding-synonymous,coding-synonymous	C9orf84	NM_001080551.1,NM_173521.3	,	39,753,5711	TT,TG,GG		8.8023,1.6795,6.3894	,	558/1406,597/1445	114484837	831,12175	2203	4300	6503	SO:0001819	synonymous_variant	158401	exon13			TGCTTCGAGGAGG	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.1791C>A	9.37:g.114484837G>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	37	CCDS6781.3																																																																																			G|0.931;T|0.069	0.069	strong		0.373	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
IL32	9235	hgsc.bcm.edu	37	16	3119304	3119304	+	Missense_Mutation	SNP	A	A	G	rs398100042|rs2981599		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:3119304A>G	ENST00000534507.1	+	6	864	c.653A>G	c.(652-654)gAc>gGc	p.D218G	IL32_ENST00000382213.3_Missense_Mutation_p.D163G|IL32_ENST00000529550.1_Missense_Mutation_p.D172G|IL32_ENST00000548652.1_Missense_Mutation_p.D163G|IL32_ENST00000551513.1_Missense_Mutation_p.D209G|IL32_ENST00000530890.1_Missense_Mutation_p.D152G|IL32_ENST00000549213.1_Missense_Mutation_p.D115G|IL32_ENST00000444393.3_Missense_Mutation_p.D172G|IL32_ENST00000533097.2_Missense_Mutation_p.D172G|IL32_ENST00000530538.2_Missense_Mutation_p.D172G|IL32_ENST00000548476.1_Missense_Mutation_p.D218G|IL32_ENST00000552936.1_Missense_Mutation_p.D196G|IL32_ENST00000525643.2_Missense_Mutation_p.D172G|IL32_ENST00000396887.3_Missense_Mutation_p.D115G|IL32_ENST00000548246.1_Missense_Mutation_p.D132G|IL32_ENST00000396890.2_Missense_Mutation_p.D218G|IL32_ENST00000008180.9_Missense_Mutation_p.D152G|IL32_ENST00000552356.1_Missense_Mutation_p.D152G|IL32_ENST00000528163.2_Missense_Mutation_p.D172G|IL32_ENST00000325568.5_Missense_Mutation_p.D172G|IL32_ENST00000529699.1_Missense_Mutation_p.D152G|IL32_ENST00000552664.1_Missense_Mutation_p.D172G|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000551122.1_Missense_Mutation_p.D115G|IL32_ENST00000526464.2_Missense_Mutation_p.D172G|IL32_ENST00000440815.3_Missense_Mutation_p.D172G|IL32_ENST00000531965.1_Missense_Mutation_p.D162G			P24001	IL32_HUMAN	interleukin 32	218					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CCACGGGGGGACAAGGAGGAG	0.577																																					p.D172G		Atlas-SNP	.											IL32,NS,carcinoma,+1,2	IL32	32	2	0			c.A515G						PASS	.						91.0	117.0	108.0					16																	3119304		2197	4300	6497	SO:0001583	missense	9235	exon7			GGGGGGACAAGGA	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.653A>G	16.37:g.3119304A>G	ENSP00000431775:p.Asp218Gly	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	238	106	0.445378	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Missense_Mutation	SNP	ENST00000534507.1	37		.	.	.	.	.	.	.	.	.	.	G	0.809	-0.752764	0.03041	.	.	ENSG00000008517	ENST00000325568;ENST00000534507;ENST00000531965;ENST00000396887;ENST00000529699;ENST00000526464;ENST00000440815;ENST00000529550;ENST00000551122;ENST00000525643;ENST00000548807;ENST00000528163;ENST00000530890;ENST00000444393;ENST00000533097;ENST00000008180;ENST00000396890;ENST00000548652;ENST00000530538;ENST00000549213;ENST00000552936;ENST00000548476;ENST00000552664;ENST00000552356;ENST00000551513;ENST00000382213;ENST00000548246	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.56776	0.45;0.46;0.45;0.44;0.45;0.45;0.45;0.45;0.44;0.45;0.46;0.45;0.45;0.45;0.45;0.45;0.46;0.45;0.45;0.44;0.46;0.46;0.45;0.45;0.46;0.45;0.45	1.26	-2.53	0.06326	.	.	.	.	.	T	0.24736	0.0600	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001;0.0;0.0	T	0.14839	-1.0458	9	0.15952	T	0.53	.	0.7126	0.00926	0.1695:0.1865:0.3513:0.2928	rs2981599	132;152;163;152;218;172;115	B8Q191;C6GKH1;A6NNM0;A8MPX0;P24001;P24001-2;P24001-4	.;.;.;.;IL32_HUMAN;.;.	G	172;218;162;115;152;172;172;172;115;172;218;172;152;172;172;152;218;163;172;115;196;218;172;152;209;163;132	ENSP00000324742:D172G;ENSP00000431775:D218G;ENSP00000433177:D162G;ENSP00000380096:D115G;ENSP00000436937:D152G;ENSP00000450364:D172G;ENSP00000405063:D172G;ENSP00000437020:D172G;ENSP00000447496:D115G;ENSP00000432218:D172G;ENSP00000448354:D218G;ENSP00000432850:D172G;ENSP00000433747:D152G;ENSP00000411958:D172G;ENSP00000432917:D172G;ENSP00000008180:D152G;ENSP00000380099:D218G;ENSP00000446624:D163G;ENSP00000436929:D172G;ENSP00000447812:D115G;ENSP00000447033:D196G;ENSP00000449483:D218G;ENSP00000448683:D172G;ENSP00000446978:D152G;ENSP00000449147:D209G;ENSP00000371648:D163G;ENSP00000447979:D132G	ENSP00000008180:D152G	D	+	2	0	IL32	3059305	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.447000	0.02396	-1.773000	0.01290	-0.245000	0.11935	GAC	.	.	weak		0.577	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
NRP2	8828	hgsc.bcm.edu	37	2	206610502	206610502	+	Silent	SNP	T	T	G	rs849563	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:206610502T>G	ENST00000357785.5	+	10	1705	c.1674T>G	c.(1672-1674)ccT>ccG	p.P558P	NRP2_ENST00000412873.2_Silent_p.P558P|NRP2_ENST00000540178.1_Silent_p.P558P|NRP2_ENST00000360409.3_Silent_p.P558P|NRP2_ENST00000357118.4_Silent_p.P558P|NRP2_ENST00000540841.1_Silent_p.P558P|NRP2_ENST00000272849.3_Silent_p.P558P			Q99435	NELL2_HUMAN	neuropilin 2	0	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						ATGACACCCCTGACATCCGAA	0.607													T|||	1282	0.25599	0.205	0.2176	5008	,	,		18439	0.4593		0.1223	False		,,,				2504	0.2802				p.P558P		Atlas-SNP	.											.	NRP2	179	.	0			c.T1674G	GRCh37	CM073248	NRP2	M	rs849563	PASS	.	T	,,,,	832,3574	329.3+/-301.0	75,682,1446	110.0	89.0	96.0		1674,1674,1674,1674,1674	-11.7	0.1	2	dbSNP_86	96	1216,7384	245.4+/-274.3	82,1052,3166	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRP2	NM_003872.2,NM_018534.3,NM_201266.1,NM_201267.1,NM_201279.1	,,,,	157,1734,4612	GG,GT,TT		14.1395,18.8833,15.7466	,,,,	558/927,558/907,558/932,558/902,558/910	206610502	2048,10958	2203	4300	6503	SO:0001819	synonymous_variant	8828	exon10			CACCCCTGACATC	AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.1674T>G	2.37:g.206610502T>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_201279	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000357785.5	37	CCDS46496.1																																																																																			T|0.802;G|0.198	0.198	strong		0.607	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1		
CDC34	997	hgsc.bcm.edu	37	19	532066	532066	+	Silent	SNP	C	C	T	rs6507	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:532066C>T	ENST00000215574.4	+	1	353	c.135C>T	c.(133-135)atC>atT	p.I45I		NM_004359.1	NP_004350.1	P49427	UB2R1_HUMAN	cell division cycle 34	45					cellular protein modification process (GO:0006464)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of neuron apoptotic process (GO:0043525)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|response to growth factor (GO:0070848)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(1)	2		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGTGGCCATCTTCGGGCCCC	0.692													C|||	516	0.103035	0.0681	0.0389	5008	,	,		9432	0.1181		0.0765	False		,,,				2504	0.2076				p.I45I		Atlas-SNP	.											.	CDC34	5	.	0			c.C135T						PASS	.	C		226,4170		7,212,1979	45.0	42.0	43.0		135	1.9	0.8	19	dbSNP_52	43	696,7896		25,646,3625	yes	coding-synonymous	CDC34	NM_004359.1		32,858,5604	TT,TC,CC		8.1006,5.141,7.0989		45/237	532066	922,12066	2198	4296	6494	SO:0001819	synonymous_variant	997	exon1			GGCCATCTTCGGG	L22005	CCDS12030.1	19p13.3	2013-01-17	2013-01-17					"""Ubiquitin-conjugating enzymes E2"""	1734	protein-coding gene	gene with protein product		116948	"""cell division cycle 34"", ""cell division cycle 34 homolog (S. cerevisiae)"""			8248134, 16210246	Standard	NM_004359		Approved	E2-CDC34, UBE2R1, UBC3	uc002lov.3	P49427		ENST00000215574.4:c.135C>T	19.37:g.532066C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_004359	A8K689	Silent	SNP	ENST00000215574.4	37	CCDS12030.1																																																																																			C|0.920;T|0.080	0.080	strong		0.692	CDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451889.2	NM_004359	
MEF2B	100271849	hgsc.bcm.edu	37	19	19260045	19260045	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19260045T>A	ENST00000602424.2	-	5	974	c.248A>T	c.(247-249)gAc>gTc	p.D83V	MEF2BNB-MEF2B_ENST00000602276.1_5'UTR|MEF2BNB-MEF2B_ENST00000514819.3_Missense_Mutation_p.D100V|MEF2BNB-MEF2B_ENST00000444486.3_Missense_Mutation_p.D83V|MEF2B_ENST00000162023.5_Missense_Mutation_p.D83V|MEF2B_ENST00000410050.1_Missense_Mutation_p.D83V|MEF2B_ENST00000409224.1_Missense_Mutation_p.D83V|MEF2B_ENST00000409447.2_Missense_Mutation_p.D83V|MEF2B_ENST00000424583.2_Missense_Mutation_p.D83V	NM_005919.3	NP_005910.1	Q02080	MEF2B_HUMAN	myocyte enhancer factor 2B	83					muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D83V(11)|p.D83A(2)		breast(1)|haematopoietic_and_lymphoid_tissue(21)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(5;0.00011)|Epithelial(12;0.00412)			CTCGAGGATGTCAGTGTTGGT	0.607																																					p.D83V		Atlas-SNP	.											MEF2BNB-MEF2B,NS,lymphoid_neoplasm,0,15	MEF2BNB-MEF2B	29	15	13	Substitution - Missense(13)	haematopoietic_and_lymphoid_tissue(13)	c.A248T						PASS	.						126.0	63.0	84.0					19																	19260045		2203	4300	6503	SO:0001583	missense	4207	exon5			AGGATGTCAGTGT	X63380	CCDS12394.1, CCDS46024.1	19p13.11	2010-05-12	2007-04-24					"""Myocyte enhancer factors"""	6995	protein-coding gene	gene with protein product		600661				1516833, 8575763	Standard	NM_001145785		Approved	RSRFR2	uc002nll.2	Q02080		ENST00000602424.2:c.248A>T	19.37:g.19260045T>A	ENSP00000473308:p.Asp83Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_005919	A0AV80|B4DVH7|B7ZVY1|G5E9M1	Missense_Mutation	SNP	ENST00000602424.2	37	CCDS12394.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.187318	0.78789	.	.	ENSG00000213999	ENST00000409224;ENST00000424583;ENST00000410050;ENST00000444486;ENST00000409447;ENST00000162023	D;D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77	5.33	5.33	0.75918	Transcription factor, MADS-box (1);	0.000000	0.85682	D	0.000000	D	0.90167	0.6927	M	0.74467	2.265	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.998;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.963;0.92;0.997;0.997;0.998	D	0.91163	0.4962	10	0.72032	D	0.01	-31.0539	13.2359	0.59969	0.0:0.0:0.0:1.0	.	83;130;83;83;83	Q02080;B8ZZJ5;C9J4J4;G5E9M1;B3KQ23	MEF2B_HUMAN;.;.;.;.	V	83;83;83;83;130;83	ENSP00000386480:D83V;ENSP00000402154:D83V;ENSP00000386374:D83V;ENSP00000390762:D83V;ENSP00000162023:D83V	ENSP00000162023:D83V	D	-	2	0	MEF2B	19121045	1.000000	0.71417	0.999000	0.59377	0.518000	0.34316	7.923000	0.87546	2.024000	0.59613	0.459000	0.35465	GAC	.	.	none		0.607	MEF2B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_005919	
SLC44A3	126969	hgsc.bcm.edu	37	1	95294089	95294089	+	Silent	SNP	T	T	C	rs2640065	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:95294089T>C	ENST00000271227.6	+	5	558	c.456T>C	c.(454-456)taT>taC	p.Y152Y	SLC44A3_ENST00000467909.1_Silent_p.Y104Y|SLC44A3_ENST00000527077.1_Silent_p.Y84Y|SLC44A3_ENST00000529450.1_Silent_p.Y120Y|SLC44A3_ENST00000532427.1_Silent_p.Y72Y|SLC44A3_ENST00000446120.2_Silent_p.Y116Y|SLC44A3_ENST00000530397.1_3'UTR	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	152					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Y104Y(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	CCTTCAACTATACCCACAGTC	0.428													C|||	1012	0.202077	0.2466	0.1398	5008	,	,		18783	0.1012		0.2117	False		,,,				2504	0.2802				p.Y152Y		Atlas-SNP	.											SLC44A3,NS,carcinoma,0,1	SLC44A3	109	1	1	Substitution - coding silent(1)	stomach(1)	c.T456C						PASS	.	C	,	1101,3305	720.1+/-409.0	151,799,1253	162.0	151.0	155.0		456,312	-1.5	0.3	1	dbSNP_100	155	1758,6842	734.9+/-406.9	179,1400,2721	no	coding-synonymous,coding-synonymous	SLC44A3	NM_001114106.1,NM_152369.3	,	330,2199,3974	CC,CT,TT		20.4419,24.9887,21.9822	,	152/654,104/606	95294089	2859,10147	2203	4300	6503	SO:0001819	synonymous_variant	126969	exon5			CAACTATACCCAC	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"""Solute carriers"""	28689	protein-coding gene	gene with protein product			"""solute carrier family, member 3"""			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.456T>C	1.37:g.95294089T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Silent	SNP	ENST00000271227.6	37	CCDS44176.1																																																																																			T|0.790;C|0.210	0.210	strong		0.428	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369	
MTRR	4552	hgsc.bcm.edu	37	5	7893005	7893005	+	Silent	SNP	C	C	T	rs34172797	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7893005C>T	ENST00000264668.2	+	11	1647	c.1617C>T	c.(1615-1617)agC>agT	p.S539S	MTRR_ENST00000440940.2_Silent_p.S512S	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	539	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	ATGAAGACAGCGGGAAAGCCC	0.458													C|||	45	0.00898562	0.0045	0.0259	5008	,	,		18337	0.0		0.0189	False		,,,				2504	0.002				p.S539S		Atlas-SNP	.											.	MTRR	74	.	0			c.C1617T						PASS	.	C	,	66,4340	61.7+/-98.7	0,66,2137	84.0	71.0	75.0		1536,1617	0.2	0.0	5	dbSNP_126	75	207,8393	89.4+/-151.6	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,269,6232	TT,TC,CC		2.407,1.498,2.099	,	512/699,539/726	7893005	273,12733	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			AGACAGCGGGAAA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1617C>T	5.37:g.7893005C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			C|0.981;T|0.019	0.019	strong		0.458	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
SOAT2	8435	hgsc.bcm.edu	37	12	53509933	53509933	+	Missense_Mutation	SNP	C	C	T	rs2272296	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53509933C>T	ENST00000301466.3	+	7	821	c.761C>T	c.(760-762)aCc>aTc	p.T254I		NM_003578.3	NP_003569.1	O75908	SOAT2_HUMAN	sterol O-acyltransferase 2	254			T -> I (in dbSNP:rs2272296). {ECO:0000269|PubMed:10846185, ECO:0000269|PubMed:15489334}.		cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|intestinal cholesterol absorption (GO:0030299)|macrophage derived foam cell differentiation (GO:0010742)|very-low-density lipoprotein particle assembly (GO:0034379)	brush border (GO:0005903)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|transferase activity, transferring acyl groups (GO:0016746)			endometrium(5)|kidney(3)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	18					Hesperetin(DB01094)	GTGCCTGGGACCCTTCGTGCC	0.527													C|||	1315	0.26258	0.416	0.2061	5008	,	,		20456	0.3165		0.172	False		,,,				2504	0.1329				p.T254I		Atlas-SNP	.											.	SOAT2	44	.	0			c.C761T						PASS	.	C	ILE/THR	1546,2860	488.0+/-361.1	274,998,931	154.0	133.0	140.0		761	-2.7	0.8	12	dbSNP_100	140	1327,7273	260.1+/-283.0	109,1109,3082	yes	missense	SOAT2	NM_003578.3	89	383,2107,4013	TT,TC,CC		15.4302,35.0885,22.0898	benign	254/523	53509933	2873,10133	2203	4300	6503	SO:0001583	missense	8435	exon7			CTGGGACCCTTCG	AF059203	CCDS8847.1	12q13.13	2012-09-20			ENSG00000167780	ENSG00000167780	2.3.1.26		11178	protein-coding gene	gene with protein product		601311				9756920	Standard	NM_003578		Approved	ACAT2	uc001sbv.3	O75908	OTTHUMG00000169774	ENST00000301466.3:c.761C>T	12.37:g.53509933C>T	ENSP00000301466:p.Thr254Ile	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	160	64	0.4	NM_003578	F5H7W4|I6L9H9|Q4VB99|Q4VBA1|Q96TD4|Q9UNR2	Missense_Mutation	SNP	ENST00000301466.3	37	CCDS8847.1	605	0.27701465201465203	197	0.40040650406504064	71	0.19613259668508287	198	0.34615384615384615	139	0.18337730870712401	C	6.504	0.461214	0.12342	0.350885	0.154302	ENSG00000167780	ENST00000301466	T	0.73897	-0.79	4.96	-2.65	0.06095	.	0.359684	0.24978	N	0.034088	T	0.00012	0.0000	N	0.04820	-0.15	0.40954	P	0.015436000000000005	B	0.09022	0.002	B	0.12156	0.007	T	0.35574	-0.9783	9	0.19147	T	0.46	-6.404	11.847	0.52389	0.0:0.3154:0.0:0.6846	rs2272296;rs58899375;rs2272296	254	O75908	SOAT2_HUMAN	I	254	ENSP00000301466:T254I	ENSP00000301466:T254I	T	+	2	0	SOAT2	51796200	0.002000	0.14202	0.790000	0.31976	0.963000	0.63663	0.383000	0.20651	-0.384000	0.07845	-0.140000	0.14226	ACC	C|0.751;T|0.249	0.249	strong		0.527	SOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405817.1		
ALDH1B1	219	hgsc.bcm.edu	37	9	38395928	38395928	+	Silent	SNP	C	C	T	rs2073477	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:38395928C>T	ENST00000377698.3	+	2	336	c.183C>T	c.(181-183)acC>acT	p.T61T		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	61					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)			NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		ACCCTACCACCGGGGAGGTCA	0.602													C|||	1341	0.267772	0.2292	0.2968	5008	,	,		19392	0.3899		0.1372	False		,,,				2504	0.3078				p.T61T		Atlas-SNP	.											ALDH1B1,NS,carcinoma,0,1	ALDH1B1	50	1	0			c.C183T						scavenged	.	C		1057,3349	387.2+/-326.4	130,797,1276	90.0	85.0	87.0		183	-11.6	0.0	9	dbSNP_96	87	1092,7508	228.3+/-263.4	75,942,3283	no	coding-synonymous	ALDH1B1	NM_000692.4		205,1739,4559	TT,TC,CC		12.6977,23.99,16.5231		61/518	38395928	2149,10857	2203	4300	6503	SO:0001819	synonymous_variant	219	exon2			TACCACCGGGGAG	M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"""Aldehyde dehydrogenases"""	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.183C>T	9.37:g.38395928C>T		Somatic	44	1	0.0227273		WXS	Illumina HiSeq	Phase_I	56	35	0.625	NM_000692	B2R8F0|Q8WX76|Q9BV45	Silent	SNP	ENST00000377698.3	37	CCDS6615.1																																																																																			C|0.796;T|0.204	0.204	strong		0.602	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1		
ACAA2	10449	hgsc.bcm.edu	37	18	47318626	47318626	+	Missense_Mutation	SNP	T	T	C	rs11549285	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:47318626T>C	ENST00000285093.10	-	6	1124	c.649A>G	c.(649-651)Atg>Gtg	p.M217V	ACAA2_ENST00000589432.1_Missense_Mutation_p.M162V|ACAA2_ENST00000587994.1_Missense_Mutation_p.M214V	NM_006111.2	NP_006102.2	P42765	THIM_HUMAN	acetyl-CoA acyltransferase 2	217			M -> V (in dbSNP:rs11549285).		cellular response to hypoxia (GO:0071456)|cholesterol biosynthetic process (GO:0006695)|fatty acid metabolic process (GO:0006631)|negative regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902109)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	acetyl-CoA C-acyltransferase activity (GO:0003988)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(7)|ovary(1)	10						TCTACCTGCATTGTCTGTTTT	0.423													T|||	300	0.0599042	0.0015	0.0375	5008	,	,		16355	0.1885		0.0268	False		,,,				2504	0.0562				p.M217V		Atlas-SNP	.											.	ACAA2	29	.	0			c.A649G						PASS	.	T	VAL/MET	13,4393	17.9+/-39.9	0,13,2190	172.0	144.0	153.0		649	1.8	0.7	18	dbSNP_120	153	191,8409	84.5+/-147.0	6,179,4115	yes	missense	ACAA2	NM_006111.2	21	6,192,6305	CC,CT,TT		2.2209,0.2951,1.5685	benign	217/398	47318626	204,12802	2203	4300	6503	SO:0001583	missense	10449	exon6			CCTGCATTGTCTG	D16294	CCDS11939.1	18q21	2010-04-30	2010-04-30		ENSG00000167315	ENSG00000167315	2.3.1.16		83	protein-coding gene	gene with protein product	"""mitochondrial 3-oxoacyl-Coenzyme A thiolase"""	604770	"""acetyl-Coenzyme A acyltransferase 2"""			8241273	Standard	NM_006111		Approved	DSAEC	uc002ldw.4	P42765	OTTHUMG00000132667	ENST00000285093.10:c.649A>G	18.37:g.47318626T>C	ENSP00000285093:p.Met217Val	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	211	102	0.483412	NM_006111	Q9BUT6	Missense_Mutation	SNP	ENST00000285093.10	37	CCDS11939.1	126	0.057692307692307696	2	0.0040650406504065045	14	0.03867403314917127	91	0.1590909090909091	19	0.025065963060686015	T	2.008	-0.427751	0.04701	0.002951	0.022209	ENSG00000167315	ENST00000285093	D	0.87334	-2.24	5.49	1.75	0.24633	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.104157	0.85682	N	0.000000	T	0.00440	0.0014	N	0.01464	-0.85	0.20074	P	0.999936946	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.002	T	0.05550	-1.0878	9	0.15499	T	0.54	-15.6312	9.3216	0.37968	0.0:0.2745:0.0:0.7255	rs11549285;rs52835379;rs11549285	217;217	B2RB23;P42765	.;THIM_HUMAN	V	217	ENSP00000285093:M217V	ENSP00000285093:M217V	M	-	1	0	ACAA2	45572624	0.963000	0.33076	0.699000	0.30290	0.306000	0.27790	1.674000	0.37544	0.063000	0.16370	-0.269000	0.10298	ATG	T|0.970;C|0.030	0.030	strong		0.423	ACAA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255921.2	NM_006111	
KLHL26	55295	hgsc.bcm.edu	37	19	18775077	18775077	+	Silent	SNP	C	C	T	rs1076235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18775077C>T	ENST00000300976.4	+	2	180	c.90C>T	c.(88-90)gcC>gcT	p.A30A	KLHL26_ENST00000596843.1_3'UTR|KLHL26_ENST00000599006.1_Silent_p.A30A|KLHL26_ENST00000595182.1_Silent_p.A30A	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	30										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						GCAGCACGGCCGACAAGAACG	0.622													C|||	2193	0.437899	0.5136	0.4251	5008	,	,		13998	0.4365		0.3091	False		,,,				2504	0.4785				p.A30A		Atlas-SNP	.											KLHL26,NS,carcinoma,0,1	KLHL26	43	1	0			c.C90T						PASS	.	C		2177,2229	580.5+/-385.1	553,1071,579	87.0	101.0	96.0		90	-8.3	0.0	19	dbSNP_86	96	2460,6140	404.2+/-348.1	333,1794,2173	no	coding-synonymous	KLHL26	NM_018316.1		886,2865,2752	TT,TC,CC		28.6047,49.4099,35.6528		30/616	18775077	4637,8369	2203	4300	6503	SO:0001819	synonymous_variant	55295	exon2			CACGGCCGACAAG		CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"""Kelch-like"", ""BTB/POZ domain containing"""	25623	protein-coding gene	gene with protein product			"""kelch-like 26 (Drosophila)"""				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.90C>T	19.37:g.18775077C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.625;T|0.375	0.375	strong		0.622	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316	
H6PD	9563	hgsc.bcm.edu	37	1	9307138	9307138	+	Silent	SNP	T	T	C	rs11121350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:9307138T>C	ENST00000377403.2	+	3	1043	c.741T>C	c.(739-741)gcT>gcC	p.A247A	H6PD_ENST00000602477.1_Silent_p.A258A	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	247	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		CCGTGGATGCTGAAGGTGTGT	0.622													C|||	1381	0.275759	0.2867	0.281	5008	,	,		17664	0.4196		0.2445	False		,,,				2504	0.1411				p.A247A		Atlas-SNP	.											.	H6PD	71	.	0			c.T741C						PASS	.	C		1335,3071	694.1+/-405.8	200,935,1068	105.0	98.0	101.0		741	-10.1	0.0	1	dbSNP_120	101	2060,6540	719.2+/-406.3	240,1580,2480	no	coding-synonymous	H6PD	NM_004285.3		440,2515,3548	CC,CT,TT		23.9535,30.2996,26.1033		247/792	9307138	3395,9611	2203	4300	6503	SO:0001819	synonymous_variant	9563	exon3			GGATGCTGAAGGT	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"""glucose dehyrogenase"""	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.741T>C	1.37:g.9307138T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	171	81	0.473684	NM_004285	Q4TT33|Q66I35|Q68DT3	Silent	SNP	ENST00000377403.2	37	CCDS101.1																																																																																			T|0.725;C|0.275	0.275	strong		0.622	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
TELO2	9894	hgsc.bcm.edu	37	16	1544302	1544302	+	Missense_Mutation	SNP	A	A	G	rs2667661|rs35400877	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1544302A>G	ENST00000262319.6	+	2	299	c.20A>G	c.(19-21)gAg>gGg	p.E7G		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	7			E -> G (in dbSNP:rs2667661).|E -> Q (in dbSNP:rs2667660).	E -> R (in Ref. 1; BAA31658). {ECO:0000305}.	regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				GCACCCTCAGAGGTTCGACTC	0.607											OREG0023547	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1441	0.28774	0.2345	0.196	5008	,	,		16358	0.5119		0.2416	False		,,,				2504	0.2413				p.E7G		Atlas-SNP	.											TELO2,NS,carcinoma,-1,1	TELO2	44	1	0			c.A20G						PASS	.	G	GLY/GLU	66,4332		27,12,2160	59.0	57.0	57.0		20	-7.1	0.0	16	dbSNP_100	57	113,8487		37,39,4224	yes	missense	TELO2	NM_016111.3	98	64,51,6384	GG,GA,AA		1.314,1.5007,1.3771	benign	7/838	1544302	179,12819	2199	4300	6499	SO:0001583	missense	9894	exon2			CCTCAGAGGTTCG	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"""TEL2, telomere maintenance 2, homolog (S. cerevisiae)"""			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.20A>G	16.37:g.1544302A>G	ENSP00000262319:p.Glu7Gly	Somatic	48	0	0	596	WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	576	0.26373626373626374	83	0.16869918699186992	61	0.1685082872928177	273	0.4772727272727273	159	0.20976253298153033	G	10.18	1.278700	0.23307	0.015007	0.01314	ENSG00000100726	ENST00000262319	T	0.15487	2.42	4.69	-7.1	0.01547	.	1.140400	0.06530	N	0.741364	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48328	-0.9045	9	0.22706	T	0.39	-0.28	3.1741	0.06562	0.4976:0.2557:0.0974:0.1493	rs2667661;rs3752929;rs61439070;rs2667661	7	Q9Y4R8	TELO2_HUMAN	G	7	ENSP00000262319:E7G	ENSP00000262319:E7G	E	+	2	0	TELO2	1484303	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.276000	0.08514	-1.371000	0.02141	-3.517000	0.00032	GAG	A|0.738;G|0.262	0.262	strong		0.607	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
SMO	6608	hgsc.bcm.edu	37	7	128843263	128843263	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:128843263C>A	ENST00000249373.3	+	2	650	c.370C>A	c.(370-372)Ccc>Acc	p.P124T		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	124	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	AGTGATCCAGCCCCTGCTGTG	0.652			Mis		skin basal cell																																p.P124T		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	SMO	145	.	0			c.C370A						PASS	.						22.0	18.0	19.0					7																	128843263		2178	4271	6449	SO:0001583	missense	6608	exon2			ATCCAGCCCCTGC	U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"""GPCR / Class F : Frizzled receptors"""	11119	protein-coding gene	gene with protein product	"""frizzled family member 11"""	601500	"""smoothened (Drosophila) homolog"", ""smoothened homolog (Drosophila)"", ""smoothened, seven transmembrane spanning receptor"", ""smoothened, frizzled family receptor"""	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.370C>A	7.37:g.128843263C>A	ENSP00000249373:p.Pro124Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_005631	A4D1K5	Missense_Mutation	SNP	ENST00000249373.3	37	CCDS5811.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.690771	0.88735	.	.	ENSG00000128602	ENST00000249373	T	0.79554	-1.28	5.5	5.5	0.81552	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.90321	0.6972	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90922	0.4784	10	0.56958	D	0.05	.	16.9188	0.86158	0.0:1.0:0.0:0.0	.	124	Q99835	SMO_HUMAN	T	124	ENSP00000249373:P124T	ENSP00000249373:P124T	P	+	1	0	SMO	128630499	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.695000	0.84257	2.584000	0.87258	0.563000	0.77884	CCC	.	.	none		0.652	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631	
NMT2	9397	hgsc.bcm.edu	37	10	15175336	15175336	+	Missense_Mutation	SNP	T	T	C	rs145950604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:15175336T>C	ENST00000378165.4	-	4	498	c.418A>G	c.(418-420)Att>Gtt	p.I140V	RPP38_ENST00000451677.1_Intron|NMT2_ENST00000378150.1_Missense_Mutation_p.I127V|NMT2_ENST00000540259.1_5'UTR|NMT2_ENST00000535341.1_Missense_Mutation_p.I127V	NM_004808.2	NP_004799.1	O60551	NMT2_HUMAN	N-myristoyltransferase 2	140					intracellular transport of virus (GO:0075733)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(3)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(3)	21						TCTGGTTCAATTGCACCATGA	0.403													T|||	5	0.000998403	0.0	0.0029	5008	,	,		20277	0.0		0.001	False		,,,				2504	0.002				p.I140V	Melanoma(117;1345 1645 4130 12688 30625)	Atlas-SNP	.											.	NMT2	44	.	0			c.A418G						PASS	.	T	VAL/ILE	5,4401	9.9+/-24.2	0,5,2198	166.0	161.0	163.0		418	4.7	0.6	10	dbSNP_134	163	40,8560	26.8+/-75.7	0,40,4260	yes	missense	NMT2	NM_004808.2	29	0,45,6458	CC,CT,TT		0.4651,0.1135,0.346	benign	140/499	15175336	45,12961	2203	4300	6503	SO:0001583	missense	9397	exon4			GTTCAATTGCACC	AF043325	CCDS7109.1	10p13	2006-07-11			ENSG00000152465	ENSG00000152465			7858	protein-coding gene	gene with protein product		603801				9506952	Standard	NM_004808		Approved		uc001inz.1	O60551	OTTHUMG00000017723	ENST00000378165.4:c.418A>G	10.37:g.15175336T>C	ENSP00000367407:p.Ile140Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	159	71	0.446541	NM_004808	B0YJ49|Q53Y38|Q5VUC8|Q9BRB4	Missense_Mutation	SNP	ENST00000378165.4	37	CCDS7109.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	16.26	3.073085	0.55646	0.001135	0.004651	ENSG00000152465	ENST00000378165;ENST00000378150;ENST00000378143;ENST00000535341	T	0.52983	0.64	5.81	4.68	0.58851	Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.49695	0.1572	M	0.79614	2.46	0.80722	D	1	B;B;B	0.22604	0.018;0.072;0.018	B;B;B	0.25140	0.034;0.058;0.034	T	0.45934	-0.9227	10	0.39692	T	0.17	-22.8035	11.5325	0.50618	0.0:0.0697:0.0:0.9303	.	140;127;140	B2RCF3;Q5VUC6;O60551	.;.;NMT2_HUMAN	V	140;127;171;127	ENSP00000367407:I140V	ENSP00000367385:I171V	I	-	1	0	NMT2	15215342	1.000000	0.71417	0.623000	0.29173	0.940000	0.58332	6.239000	0.72356	1.027000	0.39758	0.533000	0.62120	ATT	T|0.997;C|0.003	0.003	strong		0.403	NMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046958.2	NM_004808	
TAPBPL	55080	hgsc.bcm.edu	37	12	6562823	6562823	+	Missense_Mutation	SNP	C	C	T	rs2041387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6562823C>T	ENST00000266556.7	+	3	671	c.506C>T	c.(505-507)gCg>gTg	p.A169V	CD27-AS1_ENST00000545339.1_RNA|TAPBPL_ENST00000544021.1_Missense_Mutation_p.A92V|CD27-AS1_ENST00000399492.2_RNA|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	169			A -> V (in dbSNP:rs2041387). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						AAGAATGAGGCGCTCTGGCAC	0.572													C|||	1293	0.258187	0.1846	0.1744	5008	,	,		18472	0.3224		0.3042	False		,,,				2504	0.3037				p.A169V		Atlas-SNP	.											.	TAPBPL	21	.	0			c.C506T						PASS	.	C	VAL/ALA	825,3581	324.8+/-298.8	84,657,1462	37.0	35.0	36.0		506	4.6	0.0	12	dbSNP_94	36	2622,5978	419.4+/-353.1	407,1808,2085	yes	missense	TAPBPL	NM_018009.4	64	491,2465,3547	TT,TC,CC		30.4884,18.7245,26.5032	benign	169/469	6562823	3447,9559	2203	4300	6503	SO:0001583	missense	55080	exon3			ATGAGGCGCTCTG	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.506C>T	12.37:g.6562823C>T	ENSP00000266556:p.Ala169Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	119	50	0.420168	NM_018009	Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	37	CCDS8546.1	562	0.2573260073260073	88	0.17886178861788618	63	0.17403314917127072	188	0.32867132867132864	223	0.2941952506596306	C	9.385	1.073965	0.20147	0.187245	0.304884	ENSG00000139192	ENST00000544021;ENST00000266556	T;T	0.48201	0.82;3.02	4.56	4.56	0.56223	.	0.481446	0.23317	N	0.049484	T	0.00012	0.0000	L	0.56769	1.78	0.58432	P	2.9999999999752447E-6	B	0.10296	0.003	B	0.08055	0.003	T	0.25012	-1.0144	9	0.21014	T	0.42	-5.8199	12.8579	0.57897	0.0:1.0:0.0:0.0	rs2041387;rs3168617;rs16932609;rs17196801;rs17845451;rs17858324;rs57407101;rs2041387	169	Q9BX59	TPSNR_HUMAN	V	92;169	ENSP00000445341:A92V;ENSP00000266556:A169V	ENSP00000266556:A169V	A	+	2	0	TAPBPL	6433084	0.179000	0.23135	0.022000	0.16811	0.002000	0.02628	1.069000	0.30641	2.097000	0.63578	0.609000	0.83330	GCG	C|0.744;N|0.000	.	strong		0.572	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
TTYH2	94015	hgsc.bcm.edu	37	17	72249229	72249229	+	Missense_Mutation	SNP	C	C	A	rs9899862	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72249229C>A	ENST00000269346.4	+	12	1343	c.1269C>A	c.(1267-1269)gaC>gaA	p.D423E	TTYH2_ENST00000529107.1_Missense_Mutation_p.D402E|TTYH2_ENST00000441391.2_Missense_Mutation_p.D102E	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	423	Poly-Asp.		D -> E (in dbSNP:rs9899862). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						GAAACAGAGACTACGATGACA	0.572													C|||	920	0.183706	0.2337	0.1369	5008	,	,		20455	0.0466		0.2147	False		,,,				2504	0.2587				p.D423E		Atlas-SNP	.											.	TTYH2	63	.	0			c.C1269A						PASS	.	C	GLU/ASP,GLU/ASP	994,3412	371.5+/-320.0	123,748,1332	132.0	129.0	130.0		1269,306	3.5	1.0	17	dbSNP_119	130	2161,6439	371.5+/-336.3	266,1629,2405	yes	missense,missense	TTYH2	NM_032646.5,NM_052869.1	45,45	389,2377,3737	AA,AC,CC		25.1279,22.5601,24.258	benign,benign	423/535,102/214	72249229	3155,9851	2203	4300	6503	SO:0001583	missense	94015	exon12			CAGAGACTACGAT		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.1269C>A	17.37:g.72249229C>A	ENSP00000269346:p.Asp423Glu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	377	0.17261904761904762	121	0.2459349593495935	56	0.15469613259668508	30	0.05244755244755245	170	0.22427440633245382	C	10.92	1.486385	0.26686	0.225601	0.251279	ENSG00000141540	ENST00000269346;ENST00000529107;ENST00000441391	T;T;T	0.12569	2.67;2.67;2.67	4.51	3.51	0.40186	.	0.179999	0.45606	D	0.000348	T	0.00012	0.0000	L	0.58669	1.825	0.20764	P	0.999859506	B;B	0.14805	0.007;0.011	B;B	0.22880	0.015;0.042	T	0.35001	-0.9806	9	0.30078	T	0.28	-30.422	4.3371	0.11092	0.1796:0.631:0.0:0.1893	rs9899862;rs59462156;rs9899862	402;423	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	E	423;402;102	ENSP00000269346:D423E;ENSP00000433089:D402E;ENSP00000394576:D102E	ENSP00000269346:D423E	D	+	3	2	TTYH2	69760824	0.997000	0.39634	0.997000	0.53966	0.851000	0.48451	0.568000	0.23623	1.065000	0.40693	0.561000	0.74099	GAC	C|0.793;A|0.207	0.207	strong		0.572	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
PBLD	64081	hgsc.bcm.edu	37	10	70044031	70044031	+	Missense_Mutation	SNP	T	T	C	rs4142048	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70044031T>C	ENST00000358769.2	-	10	972	c.770A>G	c.(769-771)cAc>cGc	p.H257R	PBLD_ENST00000309049.4_Missense_Mutation_p.H257R|PBLD_ENST00000336578.1_Missense_Mutation_p.H224R	NM_022129.3	NP_071412.2	P30039	PBLD_HUMAN	phenazine biosynthesis-like protein domain containing	257			H -> R (in dbSNP:rs4142048). {ECO:0000269|PubMed:15806103}.		biosynthetic process (GO:0009058)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein import into nucleus (GO:0060392)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	isomerase activity (GO:0016853)			endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21						TCCTCCTCGGTGGGAACACTG	0.418													C|||	1499	0.299321	0.3275	0.3847	5008	,	,		19313	0.2946		0.1968	False		,,,				2504	0.3108				p.H257R		Atlas-SNP	.											.	PBLD	53	.	0			c.A770G						PASS	.	C	ARG/HIS	1394,3012	688.1+/-404.9	224,946,1033	129.0	112.0	118.0		770	-3.4	0.0	10	dbSNP_110	118	1656,6944	740.9+/-407.1	155,1346,2799	yes	missense	PBLD	NM_022129.3	29	379,2292,3832	CC,CT,TT		19.2558,31.6387,23.4507	benign	257/289	70044031	3050,9956	2203	4300	6503	SO:0001583	missense	64081	exon10			CCTCGGTGGGAAC	AK027673	CCDS7277.2, CCDS44413.1	10q21.3	2006-11-27			ENSG00000108187	ENSG00000108187			23301	protein-coding gene	gene with protein product	MAWD binding protein	612189				11355021	Standard	XM_005270028		Approved	MAWBP, MAWDBP, FLJ14767	uc001jns.1	P30039	OTTHUMG00000073949	ENST00000358769.2:c.770A>G	10.37:g.70044031T>C	ENSP00000351619:p.His257Arg	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_022129	A8MZJ3|C9JIM0|Q9HCC2	Missense_Mutation	SNP	ENST00000358769.2	37	CCDS7277.2	600	0.27472527472527475	153	0.31097560975609756	119	0.3287292817679558	175	0.30594405594405594	153	0.20184696569920843	C	0.014	-1.582466	0.00879	0.316387	0.192558	ENSG00000108187	ENST00000336578;ENST00000358769;ENST00000309049	T;T;T	0.27890	1.64;1.64;1.64	5.76	-3.42	0.04825	.	0.876636	0.10093	N	0.716886	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42832	-0.9428	9	0.13470	T	0.59	19.1478	8.1479	0.31124	0.0:0.3771:0.2466:0.3763	rs4142048;rs52827340;rs59287186;rs4142048	257	P30039	PBLD_HUMAN	R	224;257;257	ENSP00000338041:H224R;ENSP00000351619:H257R;ENSP00000308466:H257R	ENSP00000308466:H257R	H	-	2	0	PBLD	69714037	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-4.606000	0.00209	-1.970000	0.01003	-2.815000	0.00110	CAC	T|0.753;C|0.247	0.247	strong		0.418	PBLD-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048314.1	NM_022129	
C4BPA	722	hgsc.bcm.edu	37	1	207304900	207304900	+	Missense_Mutation	SNP	T	T	C	rs4844573	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207304900T>C	ENST00000367070.3	+	8	1093	c.899T>C	c.(898-900)aTt>aCt	p.I300T		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	300	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.		I -> T (in dbSNP:rs4844573).		complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						GATAGTTGTATTAATTTACCA	0.433													C|||	2453	0.489816	0.8374	0.4625	5008	,	,		19901	0.2679		0.3767	False		,,,				2504	0.3845				p.I300T		Atlas-SNP	.											.	C4BPA	70	.	0			c.T899C						PASS	.	C	THR/ILE	3316,1090	394.2+/-329.2	1254,808,141	99.0	74.0	83.0		899	-8.9	0.0	1	dbSNP_111	83	2980,5620	665.4+/-402.3	534,1912,1854	no	missense	C4BPA	NM_000715.3	89	1788,2720,1995	CC,CT,TT		34.6512,24.739,48.4084	benign	300/598	207304900	6296,6710	2203	4300	6503	SO:0001583	missense	722	exon8			GTTGTATTAATTT	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"""complement component 4-binding protein, alpha"""	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.899T>C	1.37:g.207304900T>C	ENSP00000356037:p.Ile300Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_000715	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	1022	0.46794871794871795	401	0.8150406504065041	156	0.430939226519337	187	0.3269230769230769	278	0.36675461741424803	C	0.513	-0.865722	0.02590	0.75261	0.346512	ENSG00000123838	ENST00000367070	T	0.62498	0.02	4.51	-8.9	0.00782	Complement control module (2);Sushi/SCR/CCP (3);	1.917680	0.02627	N	0.103873	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.39702	-0.9601	9	0.08599	T	0.76	.	16.2134	0.82186	0.0:0.6809:0.0:0.3191	rs4844573;rs17258788;rs56540637;rs58565781;rs4844573	300	P04003	C4BPA_HUMAN	T	300	ENSP00000356037:I300T	ENSP00000356037:I300T	I	+	2	0	C4BPA	205371523	0.000000	0.05858	0.000000	0.03702	0.394000	0.30568	-2.583000	0.00904	-2.717000	0.00390	-0.119000	0.15052	ATT	T|0.519;C|0.481	0.481	strong		0.433	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		
EXOSC3	51010	hgsc.bcm.edu	37	9	37780831	37780831	+	Missense_Mutation	SNP	A	A	G	rs3208406	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:37780831A>G	ENST00000327304.5	-	4	685	c.673T>C	c.(673-675)Tat>Cat	p.Y225H	EXOSC3_ENST00000490516.1_5'UTR|EXOSC3_ENST00000396521.3_3'UTR|RP11-613M10.9_ENST00000540557.1_Intron	NM_016042.3	NP_057126.2	Q9NQT5	EXOS3_HUMAN	exosome component 3	225			Y -> H (in dbSNP:rs3208406).		CUT catabolic process (GO:0071034)|DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|isotype switching (GO:0045190)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of isotype switching (GO:0045830)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(1)	4				GBM - Glioblastoma multiforme(29;0.00771)|Lung(182;0.221)		TCCAGTGGATAGAGTTTTCCC	0.383													A|||	179	0.0357428	0.0015	0.049	5008	,	,		20262	0.003		0.1113	False		,,,				2504	0.0286				p.Y225H		Atlas-SNP	.											.	EXOSC3	8	.	0			c.T673C						PASS	.	A	,HIS/TYR	89,4317	73.6+/-111.7	1,87,2115	85.0	78.0	80.0		,673	5.7	1.0	9	dbSNP_105	80	848,7752	193.5+/-239.2	44,760,3496	yes	utr-3,missense	EXOSC3	NM_001002269.1,NM_016042.2	,83	45,847,5611	GG,GA,AA		9.8605,2.02,7.2044	,possibly-damaging	,225/276	37780831	937,12069	2203	4300	6503	SO:0001583	missense	51010	exon4			GTGGATAGAGTTT	BC002437	CCDS35016.1, CCDS43805.1	9p11	2009-01-20			ENSG00000107371	ENSG00000107371			17944	protein-coding gene	gene with protein product	"""exosome component Rrp40"", ""CGI-102 protein"""	606489				10810093, 11110791	Standard	NM_016042		Approved	hRrp40p, Rrp40p, RRP40, CGI-102, p10, hRrp-40	uc004aal.3	Q9NQT5	OTTHUMG00000019932	ENST00000327304.5:c.673T>C	9.37:g.37780831A>G	ENSP00000323046:p.Tyr225His	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	127	52	0.409449	NM_016042	A8K0K6|Q5QP85|Q9Y3A8	Missense_Mutation	SNP	ENST00000327304.5	37	CCDS35016.1	100	0.045787545787545784	2	0.0040650406504065045	20	0.055248618784530384	1	0.0017482517482517483	77	0.10158311345646438	A	21.0	4.074761	0.76415	0.0202	0.098605	ENSG00000107371	ENST00000327304	T	0.16897	2.31	5.66	5.66	0.87406	.	0.167853	0.52532	D	0.000074	T	0.00936	0.0031	M	0.66939	2.045	0.09310	P	1.0	D	0.65815	0.995	P	0.61201	0.885	T	0.06862	-1.0803	9	0.15499	T	0.54	-10.691	14.1342	0.65276	1.0:0.0:0.0:0.0	rs3208406;rs17586551;rs52820434;rs59118498;rs3208406	225	Q9NQT5	EXOS3_HUMAN	H	225	ENSP00000323046:Y225H	ENSP00000323046:Y225H	Y	-	1	0	EXOSC3	37770831	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.782000	0.75073	2.270000	0.75569	0.533000	0.62120	TAT	A|0.941;G|0.059	0.059	strong		0.383	EXOSC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052478.3	NM_016042	
WEE1	7465	hgsc.bcm.edu	37	11	9607032	9607032	+	Silent	SNP	A	A	G	rs10770042	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:9607032A>G	ENST00000450114.2	+	8	1681	c.1428A>G	c.(1426-1428)gaA>gaG	p.E476E	WEE1_ENST00000299613.6_Silent_p.E262E	NM_003390.3	NP_003381.1	P30291	WEE1_HUMAN	WEE1 G2 checkpoint kinase	476	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|establishment of cell polarity (GO:0030010)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neuron projection morphogenesis (GO:0048812)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	23				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		CACAAGTTGAAGAGGGCGATA	0.368													A|||	759	0.151558	0.1172	0.1787	5008	,	,		18585	0.1815		0.175	False		,,,				2504	0.1237				p.E476E		Atlas-SNP	.											.	WEE1	54	.	0			c.A1428G						PASS	.	A	,	550,3852	250.6+/-257.6	34,482,1685	202.0	196.0	198.0		786,1428	3.0	1.0	11	dbSNP_120	198	1283,7305	255.1+/-280.1	81,1121,3092	no	coding-synonymous,coding-synonymous	WEE1	NM_001143976.1,NM_003390.3	,	115,1603,4777	GG,GA,AA		14.9395,12.4943,14.1109	,	262/433,476/647	9607032	1833,11157	2201	4294	6495	SO:0001819	synonymous_variant	7465	exon8			AGTTGAAGAGGGC	X62048	CCDS7800.1, CCDS44536.1	11p15.4	2013-10-21	2013-10-21		ENSG00000166483	ENSG00000166483			12761	protein-coding gene	gene with protein product		193525	"""wee1+ (S. pombe) homolog"", ""WEE1 homolog (S. pombe)"""			1840647	Standard	NM_003390		Approved		uc001mhs.3	P30291	OTTHUMG00000165863	ENST00000450114.2:c.1428A>G	11.37:g.9607032A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_003390	B3KVE1|D3DQV0	Silent	SNP	ENST00000450114.2	37	CCDS7800.1																																																																																			A|0.852;G|0.148	0.148	strong		0.368	WEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386757.1	NM_003390	
HLA-C	3107	hgsc.bcm.edu	37	6	31237991	31237991	+	Missense_Mutation	SNP	G	G	T	rs2308628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31237991G>T	ENST00000376228.5	-	4	905	c.891C>A	c.(889-891)agC>agA	p.S297R	HLA-C_ENST00000383329.3_Missense_Mutation_p.S297R	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	297	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CCTTACCCCAGCTCAGGGTGA	0.597													T|||	3754	0.749601	0.7602	0.7925	5008	,	,		12752	0.7917		0.7107	False		,,,				2504	0.7014				p.S297R		Atlas-SNP	.											.	HLA-C	92	.	0			c.C891A						PASS	.						21.0	30.0	27.0					6																	31237991		2043	4078	6121	SO:0001583	missense	3107	exon4			ACCCCAGCTCAGG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.891C>A	6.37:g.31237991G>T	ENSP00000365402:p.Ser297Arg	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	36	34	0.944444	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1291	0.5911172161172161	299	0.6077235772357723	233	0.643646408839779	355	0.6206293706293706	404	0.5329815303430079	.	1.551	-0.539218	0.04053	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.13657	2.57;2.57	2.67	2.67	0.31697	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.560998	0.14149	N	0.338152	T	0.01222	0.0040	.	.	.	0.58432	P	5.999999999950489E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.48222	-0.9054	8	0.02654	T	1	.	5.9273	0.19120	0.0:0.0:0.2721:0.7279	rs2308628;rs9264630	297;297;297;297	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	R	297;297;297;334	ENSP00000365402:S297R;ENSP00000372819:S297R	ENSP00000365402:S297R	S	-	3	2	HLA-C	31345970	0.009000	0.17119	1.000000	0.80357	0.066000	0.16364	-0.618000	0.05578	0.447000	0.26695	-0.904000	0.02843	AGC	G|0.408;T|0.592	0.592	strong		0.597	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
SMPD2	6610	hgsc.bcm.edu	37	6	109764535	109764535	+	Missense_Mutation	SNP	G	G	T	rs1476387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:109764535G>T	ENST00000258052.3	+	9	1154	c.795G>T	c.(793-795)agG>agT	p.R265S	PPIL6_ENST00000521072.2_5'Flank|PPIL6_ENST00000424445.2_5'Flank|PPIL6_ENST00000440797.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	265			R -> S (in dbSNP:rs1476387). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9520418}.		apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		ACCCTCACAGGGGCACCCCCC	0.527													T|||	2769	0.552915	0.7549	0.4928	5008	,	,		15276	0.4534		0.4314	False		,,,				2504	0.5501				p.R265S		Atlas-SNP	.											SMPD2,NS,carcinoma,0,1	SMPD2	25	1	0			c.G795T						scavenged	.	T	SER/ARG	3071,1335	447.9+/-348.5	1072,927,204	82.0	87.0	85.0		795	-7.3	0.0	6	dbSNP_88	85	3627,4973	626.0+/-397.8	757,2113,1430	yes	missense	SMPD2	NM_003080.2	110	1829,3040,1634	TT,TG,GG		42.1744,30.2996,48.5007	benign	265/424	109764535	6698,6308	2203	4300	6503	SO:0001583	missense	6610	exon9			TCACAGGGGCACC	AJ222801	CCDS5075.1	6q21	2009-10-23			ENSG00000135587	ENSG00000135587	3.1.4.12		11121	protein-coding gene	gene with protein product		603498				9520418	Standard	XM_005267109		Approved	nSMase, ISC1	uc003pti.3	O60906	OTTHUMG00000015348	ENST00000258052.3:c.795G>T	6.37:g.109764535G>T	ENSP00000258052:p.Arg265Ser	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	216	102	0.472222	NM_003080	Q5TED1|Q9BWR3	Missense_Mutation	SNP	ENST00000258052.3	37	CCDS5075.1	1165|1165	0.5334249084249084|0.5334249084249084	369|369	0.75|0.75	176|176	0.4861878453038674|0.4861878453038674	292|292	0.5104895104895105|0.5104895104895105	328|328	0.43271767810026385|0.43271767810026385	T|T	0.004|0.004	-2.274012|-2.274012	0.00257|0.00257	0.697004|0.697004	0.421744|0.421744	ENSG00000135587|ENSG00000135587	ENST00000458487|ENST00000258052	.|T	.|0.80393	.|-1.37	5.95|5.95	-7.33|-7.33	0.01431|0.01431	.|Endonuclease/exonuclease/phosphatase (2);	.|1.368040	.|0.03834	.|N	.|0.269560	T|T	0.29458|0.29458	0.0734|0.0734	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.28618|0.28618	-1.0038|-1.0038	4|9	.|0.07325	.|T	.|0.83	1.5163|1.5163	3.582|3.582	0.07957|0.07957	0.1863:0.4025:0.0883:0.3229|0.1863:0.4025:0.0883:0.3229	rs1476387;rs17855992;rs60625554;rs1476387|rs1476387;rs17855992;rs60625554;rs1476387	.|265	.|O60906	.|NSMA_HUMAN	V|S	162|265	.|ENSP00000258052:R265S	.|ENSP00000258052:R265S	G|R	+|+	2|3	0|2	SMPD2|SMPD2	109871228|109871228	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.013000|0.013000	0.08279|0.08279	-0.424000|-0.424000	0.07025|0.07025	-1.675000|-1.675000	0.01459|0.01459	-3.969000|-3.969000	0.00014|0.00014	GGG|AGG	A|0.000;G|0.469;T|0.531	0.531	strong		0.527	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1		
IGSF3	3321	hgsc.bcm.edu	37	1	117122288	117122288	+	Missense_Mutation	SNP	G	G	C	rs56982445|rs647711	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:117122288G>C	ENST00000369486.3	-	10	3825	c.3060C>G	c.(3058-3060)gaC>gaG	p.D1020E	IGSF3_ENST00000369483.1_Missense_Mutation_p.D1040E|IGSF3_ENST00000318837.6_Missense_Mutation_p.D1040E	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1020	Ig-like C2-type 8.		D -> E (in dbSNP:rs647711). {ECO:0000269|PubMed:9790749}.		lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		cgtcgtcgtcgtcctcctcct	0.632													G|||	1310	0.261581	0.1732	0.3141	5008	,	,		18340	0.1101		0.4324	False		,,,				2504	0.3241				p.D1040E		Atlas-SNP	.											IGSF3_ENST00000369483,caecum,carcinoma,0,2	IGSF3	294	2	0			c.C3120G						scavenged	.	-	GLU/ASP,GLU/ASP	592,3814		65,462,1676	28.0	28.0	28.0		3060,3120	-5.3	0.0	1	dbSNP_83	28	2480,6120		528,1424,2348	no	missense,missense	IGSF3	NM_001007237.1,NM_001542.2	45,45	593,1886,4024	CC,CG,GG		28.8372,13.4362,23.6199	benign,benign	1020/1195,1040/1215	117122288	3072,9934	2203	4300	6503	SO:0001583	missense	3321	exon11			GTCGTCGTCCTCC	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3060C>G	1.37:g.117122288G>C	ENSP00000358498:p.Asp1020Glu	Somatic	82	3	0.0365854		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	608	0.2783882783882784	94	0.1910569105691057	113	0.31215469613259667	77	0.1346153846153846	324	0.42744063324538256	G	0.003	-2.465162	0.00169	0.134362	0.288372	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.03386	4.08;3.95;3.95	2.68	-5.35	0.02697	Immunoglobulin subtype (1);Immunoglobulin-like (1);	1.228830	0.05945	N	0.637693	T	0.00440	0.0014	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48570	-0.9024	9	0.07325	T	0.83	-2.1932	7.1155	0.25414	0.0:0.1943:0.4957:0.3101	rs647711;rs797616;rs57801380	1020;1040	O75054;A6NJZ6	IGSF3_HUMAN;.	E	1020;1040;1040	ENSP00000358498:D1020E;ENSP00000358495:D1040E;ENSP00000321184:D1040E	ENSP00000321184:D1040E	D	-	3	2	IGSF3	116923811	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-1.686000	0.01929	-2.572000	0.00467	-1.748000	0.00681	GAC	G|0.692;C|0.308	0.308	strong		0.632	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
WDR90	197335	hgsc.bcm.edu	37	16	711905	711905	+	Silent	SNP	A	A	G	rs2301426	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:711905A>G	ENST00000293879.4	+	32	3879	c.3879A>G	c.(3877-3879)ccA>ccG	p.P1293P	WDR90_ENST00000549091.1_Silent_p.P1293P			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1293										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GTCGAGAGCCAGTCCCAGAGG	0.637													G|||	3501	0.699081	0.8896	0.5951	5008	,	,		16926	0.9841		0.3708	False		,,,				2504	0.5593				p.P1293P		Atlas-SNP	.											WDR90,NS,carcinoma,0,1	WDR90	107	1	0			c.A3879G						scavenged	.	G		3157,973		1218,721,126	81.0	106.0	98.0		3879	-7.3	0.0	16	dbSNP_100	98	2959,5457		538,1883,1787	yes	coding-synonymous	WDR90	NM_145294.4		1756,2604,1913	GG,GA,AA		35.1592,23.5593,48.7486		1293/1749	711905	6116,6430	2065	4208	6273	SO:0001819	synonymous_variant	197335	exon32			AGAGCCAGTCCCA	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.3879A>G	16.37:g.711905A>G		Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			A|0.387;G|0.613	0.613	strong		0.637	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
CFTR	1080	hgsc.bcm.edu	37	7	117199533	117199533	+	Missense_Mutation	SNP	G	G	A	rs213950|rs397508204	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:117199533G>A	ENST00000003084.6	+	11	1540	c.1408G>A	c.(1408-1410)Gtg>Atg	p.V470M	CFTR_ENST00000454343.1_Missense_Mutation_p.V409M|AC000111.3_ENST00000441019.1_RNA	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	470	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		V -> M (in dbSNP:rs213950). {ECO:0000269|PubMed:10651488, ECO:0000269|PubMed:1710598, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:2475911, ECO:0000269|Ref.3}.		cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	ACTTCTAATGGTGATTATGGG	0.393									Cystic Fibrosis				A|||	2915	0.582069	0.9349	0.513	5008	,	,		17643	0.3869		0.4384	False		,,,				2504	0.5031				p.V470M		Atlas-SNP	.											.	CFTR	171	.	0			c.G1408A	GRCh37	CM034388	CFTR	M	rs213950	PASS	.	A	MET/VAL	3747,659		1586,575,42	102.0	111.0	108.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1408	3.0	1.0	7	dbSNP_79	108	4026,4574		1025,1976,1299	yes	missense	CFTR	NM_000492.3	21	2611,2551,1341	AA,AG,GG		46.814,14.9569,40.2353	benign	470/1481	117199533	7773,5233	2203	4300	6503	SO:0001583	missense	1080	exon11	Familial Cancer Database	CF	CTAATGGTGATTA	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.1408G>A	7.37:g.117199533G>A	ENSP00000003084:p.Val470Met	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	1180	0.5402930402930403	449	0.9126016260162602	192	0.5303867403314917	202	0.3531468531468531	337	0.4445910290237467	A	2.095	-0.407418	0.04832	0.850431	0.46814	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.94280	-3.39;-3.39;-3.39	5.47	3.05	0.35203	ABC transporter, transmembrane domain, type 1 (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.113641	0.85682	N	0.000000	T	0.00012	0.0000	N	0.11341	0.13	0.46279	P	0.0010339999999999794	B	0.02656	0.0	B	0.06405	0.002	T	0.42032	-0.9475	9	0.16420	T	0.52	-17.102	2.8388	0.05523	0.5314:0.1098:0.0703:0.2886	rs213950;rs10360044;rs34570734;rs52833540;rs57055567;rs213950	470	P13569	CFTR_HUMAN	M	470;409;440	ENSP00000003084:V470M;ENSP00000403677:V409M;ENSP00000389119:V440M	ENSP00000003084:V470M	V	+	1	0	CFTR	116986769	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.608000	0.46308	0.103000	0.17682	-0.269000	0.10298	GTG	G|0.436;A|0.564	0.564	strong		0.393	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68249499	68249499	+	Missense_Mutation	SNP	C	C	T	rs2235967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:68249499C>T	ENST00000347230.4	-	21	4508	c.4370G>A	c.(4369-4371)tGt>tAt	p.C1457Y	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.C1457Y	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1457			C -> Y (in dbSNP:rs2235967). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9205841}.		cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CTGCTCACCACATGCCACAGC	0.473													C|||	802	0.160144	0.0318	0.2089	5008	,	,		20789	0.0278		0.3748	False		,,,				2504	0.2147				p.C1457Y		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.G4370A						PASS	.	C	TYR/CYS	385,4021	194.0+/-219.0	20,345,1838	201.0	201.0	201.0		4370	2.5	0.1	14	dbSNP_98	201	3042,5558	467.3+/-367.0	558,1926,1816	yes	missense	ZFYVE26	NM_015346.3	194	578,2271,3654	TT,TC,CC		35.3721,8.7381,26.3494	benign	1457/2540	68249499	3427,9579	2203	4300	6503	SO:0001583	missense	23503	exon21			TCACCACATGCCA	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.4370G>A	14.37:g.68249499C>T	ENSP00000251119:p.Cys1457Tyr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	412	0.18864468864468864	25	0.0508130081300813	83	0.2292817679558011	15	0.026223776223776224	289	0.3812664907651715	C	0.095	-1.161394	0.01673	0.087381	0.353721	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.26660	1.86;1.72	5.5	2.54	0.30619	.	0.636029	0.16951	N	0.192905	T	0.00012	0.0000	L	0.31294	0.92	0.53005	P	3.2999999999949736E-5	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.47129	-0.9141	9	0.20519	T	0.43	-4.5647	5.2322	0.15428	0.0:0.5103:0.0:0.4897	rs2235967;rs17782931;rs57145995;rs2235967	1457;1457	G3V2D8;Q68DK2	.;ZFY26_HUMAN	Y	1457;1436;1457	ENSP00000251119:C1457Y;ENSP00000450603:C1457Y	ENSP00000251119:C1457Y	C	-	2	0	ZFYVE26	67319252	0.497000	0.26067	0.078000	0.20375	0.975000	0.68041	2.529000	0.45632	0.898000	0.36418	0.655000	0.94253	TGT	C|0.785;N|0.000	.	strong		0.473	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
C2orf54	79919	hgsc.bcm.edu	37	2	241835379	241835379	+	Silent	SNP	G	G	A	rs12105122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241835379G>A	ENST00000388934.4	-	1	194	c.36C>T	c.(34-36)gcC>gcT	p.A12A		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	12										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		GCACCTGCACGGCCATGGCTG	0.697													G|||	2624	0.523962	0.7685	0.3487	5008	,	,		17050	0.4415		0.5159	False		,,,				2504	0.411				p.A12A		Atlas-SNP	.											C2orf54,rectum,carcinoma,0,1	C2orf54	14	1	0			c.C36T						PASS	.	G		2920,1058		1120,680,189	5.0	6.0	6.0		36	-10.5	0.0	2	dbSNP_120	6	4133,4053		1141,1851,1101	no	coding-synonymous	C2orf54	NM_001085437.1		2261,2531,1290	AA,AG,GG		49.5114,26.5963,42.0174		12/448	241835379	7053,5111	1989	4093	6082	SO:0001819	synonymous_variant	79919	exon1			CTGCACGGCCATG	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.36C>T	2.37:g.241835379G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	26	25	0.961538	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	37	CCDS42839.1																																																																																			G|0.494;A|0.506	0.506	strong		0.697	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
HLA-B	3106	hgsc.bcm.edu	37	6	31324666	31324666	+	Missense_Mutation	SNP	A	A	T	rs713031	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324666A>T	ENST00000412585.2	-	2	170	c.142T>A	c.(142-144)Tca>Aca	p.S48T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	48	Alpha-1.		S -> A (in dbSNP:rs713031).|S -> P (in dbSNP:rs713031).|S -> T (in dbSNP:rs713031).		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TAGCCCACTGAGATGAAGCGG	0.692									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	989	0.197484	0.1172	0.1945	5008	,	,		9910	0.245		0.2584	False		,,,				2504	0.1963				p.S48T		Atlas-SNP	.											.	HLA-B	54	.	0			c.T142A						PASS	.						28.0	22.0	24.0					6																	31324666		2121	4117	6238	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CCACTGAGATGAA	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.142T>A	6.37:g.31324666A>T	ENSP00000399168:p.Ser48Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	0.014	-1.590854	0.00864	.	.	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00009	9.46;9.46	3.2	-6.41	0.01938	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	2.396650	0.02953	N	0.141997	T	0.00039	0.0001	L	0.43152	1.355	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.001;0.001;0.005	T	0.15150	-1.0447	10	0.30078	T	0.28	.	7.9313	0.29904	0.5944:0.243:0.0:0.1626	rs713031;rs1050436;rs3175289;rs3177889;rs3190747;rs9266185;rs16896254;rs17883097	48;48;23	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	T	48;59	ENSP00000399168:S48T;ENSP00000405931:S59T	ENSP00000399168:S48T	S	-	1	0	HLA-B	31432645	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.308000	0.01131	-2.734000	0.00382	-3.242000	0.00051	TCA	T|0.021;C|0.549;A|0.429	0.021	strong		0.692	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
GPNMB	10457	hgsc.bcm.edu	37	7	23313171	23313171	+	Silent	SNP	T	T	C	rs2268748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:23313171T>C	ENST00000381990.2	+	10	1658	c.1497T>C	c.(1495-1497)agT>agC	p.S499S	GPNMB_ENST00000478451.1_3'UTR|GPNMB_ENST00000453162.2_Silent_p.S441S|GPNMB_ENST00000539136.1_Silent_p.S388S|GPNMB_ENST00000258733.4_Silent_p.S487S	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	499					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			TGGCAAACAGTGCCCTGATCT	0.448													T|||	693	0.138379	0.0045	0.2291	5008	,	,		19558	0.3641		0.0417	False		,,,				2504	0.1217				p.S499S		Atlas-SNP	.											.	GPNMB	88	.	0			c.T1497C						PASS	.	T	,	54,4352	53.6+/-89.4	0,54,2149	220.0	168.0	185.0		1497,1461	-0.8	0.0	7	dbSNP_100	185	337,8263	116.6+/-176.3	8,321,3971	no	coding-synonymous,coding-synonymous	GPNMB	NM_001005340.1,NM_002510.2	,	8,375,6120	CC,CT,TT		3.9186,1.2256,3.0063	,	499/573,487/561	23313171	391,12615	2203	4300	6503	SO:0001819	synonymous_variant	10457	exon10			AAACAGTGCCCTG	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1497T>C	7.37:g.23313171T>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	186	99	0.532258	NM_001005340	A4D155|Q6UVX1|Q8N1A1	Silent	SNP	ENST00000381990.2	37	CCDS34610.1																																																																																			T|0.909;G|0.000	.	strong		0.448	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340	
ZNF557	79230	hgsc.bcm.edu	37	19	7083629	7083629	+	Silent	SNP	A	A	G	rs966591	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7083629A>G	ENST00000439035.2	+	8	1386	c.1146A>G	c.(1144-1146)tcA>tcG	p.S382S	ZNF557_ENST00000414706.1_Silent_p.S389S|ZNF557_ENST00000252840.6_Silent_p.S389S			Q8N988	ZN557_HUMAN	zinc finger protein 557	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17				Lung(535;0.179)		ATGTTCTCTCATCCGTTAAGA	0.368													G|||	2232	0.445687	0.5227	0.438	5008	,	,		20778	0.5218		0.3777	False		,,,				2504	0.3384				p.S389S		Atlas-SNP	.											.	ZNF557	40	.	0			c.A1167G						PASS	.	G	,,	2150,2118		547,1056,531	65.0	68.0	67.0		1167,1146,1167	-2.6	0.0	19	dbSNP_86	67	3306,5234		675,1956,1639	yes	coding-synonymous,coding-synonymous,coding-synonymous	ZNF557	NM_001044387.1,NM_001044388.1,NM_024341.2	,,	1222,3012,2170	GG,GA,AA		38.7119,49.6251,42.5984	,,	389/431,382/424,389/431	7083629	5456,7352	2134	4270	6404	SO:0001819	synonymous_variant	79230	exon8			TCTCTCATCCGTT	AK095524	CCDS42485.1, CCDS45945.1	19p13.2	2013-09-20			ENSG00000130544	ENSG00000130544		"""Zinc fingers, C2H2-type"", ""-"""	28632	protein-coding gene	gene with protein product						12477932	Standard	NM_024341		Approved	MGC4054	uc002mgc.3	Q8N988	OTTHUMG00000181977	ENST00000439035.2:c.1146A>G	19.37:g.7083629A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_001044387	Q6PEJ3|Q9BTZ1	Silent	SNP	ENST00000439035.2	37	CCDS45945.1																																																																																			G|0.431;N|0.000	0.431	strong		0.368	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	NM_024341	
SSTR3	6753	hgsc.bcm.edu	37	22	37603021	37603021	+	Silent	SNP	G	G	A	rs2071710	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:37603021G>A	ENST00000328544.3	-	2	1355	c.822C>T	c.(820-822)taC>taT	p.Y274Y	SSTR3_ENST00000402501.1_Silent_p.Y274Y	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	274					cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	TGTTGAGCACGTAGAAGGGCA	0.662													g|||	1564	0.3123	0.2005	0.3069	5008	,	,		15542	0.5863		0.2197	False		,,,				2504	0.2802				p.Y274Y		Atlas-SNP	.											.	SSTR3	42	.	0			c.C822T						PASS	.	A		812,3594	319.3+/-296.1	77,658,1468	95.0	71.0	79.0		822	-2.2	1.0	22	dbSNP_96	79	1741,6859	310.4+/-309.8	178,1385,2737	no	coding-synonymous	SSTR3	NM_001051.2		255,2043,4205	AA,AG,GG		20.2442,18.4294,19.6294		274/419	37603021	2553,10453	2203	4300	6503	SO:0001819	synonymous_variant	6753	exon2			GAGCACGTAGAAG		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"""GPCR / Class A : Somatostatin receptors"""	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.822C>T	22.37:g.37603021G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	49	0.569767	NM_001051	A8K550|Q53ZR7	Silent	SNP	ENST00000328544.3	37	CCDS13944.1																																																																																			G|0.742;A|0.258	0.258	strong		0.662	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1		
FNDC1	84624	hgsc.bcm.edu	37	6	159672542	159672542	+	Silent	SNP	C	C	T	rs550443	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:159672542C>T	ENST00000297267.9	+	17	5243	c.5043C>T	c.(5041-5043)gcC>gcT	p.A1681A	FNDC1_ENST00000340366.6_Silent_p.A1618A	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1681	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		GGGACAAAGCCACCCCAGGAG	0.527													C|||	1100	0.219649	0.1899	0.1772	5008	,	,		22776	0.3353		0.1382	False		,,,				2504	0.2546				p.A1681A		Atlas-SNP	.											.	FNDC1	250	.	0			c.C5043T						PASS	.	C		735,3337		54,627,1355	51.0	49.0	50.0		5043	0.6	0.4	6	dbSNP_83	50	1091,7281		78,935,3173	no	coding-synonymous	FNDC1	NM_032532.2		132,1562,4528	TT,TC,CC		13.0315,18.0501,14.6737		1681/1895	159672542	1826,10618	2036	4186	6222	SO:0001819	synonymous_variant	84624	exon17			CAAAGCCACCCCA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.5043C>T	6.37:g.159672542C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	476	0.21794871794871795	115	0.23373983739837398	59	0.16298342541436464	202	0.3531468531468531	100	0.13192612137203166	C	9.638	1.138209	0.21123	0.180501	0.130315	ENSG00000164694	ENST00000329629	.	.	.	5.51	0.589	0.17452	.	.	.	.	.	T	0.14743	0.0356	.	.	.	0.09310	P	0.9999999799344	.	.	.	.	.	.	T	0.17623	-1.0363	3	.	.	.	-19.5874	4.8442	0.13505	0.1405:0.4502:0.0:0.4093	rs550443;rs3814447;rs59986709;rs550443	.	.	.	Y	1577	.	.	H	+	1	0	FNDC1	159592532	0.008000	0.16893	0.405000	0.26409	0.997000	0.91878	0.181000	0.16880	0.028000	0.15324	0.585000	0.79938	CAC	C|0.789;T|0.211	0.211	strong		0.527	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
MYO3B	140469	hgsc.bcm.edu	37	2	171242761	171242761	+	Silent	SNP	G	G	A	rs17497636	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:171242761G>A	ENST00000408978.4	+	13	1496	c.1353G>A	c.(1351-1353)caG>caA	p.Q451Q	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Silent_p.Q460Q|MYO3B_ENST00000409044.3_Silent_p.Q451Q	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	451	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TGATTGTTCAGCATTTGACTT	0.433													G|||	569	0.113618	0.0461	0.0965	5008	,	,		20758	0.0794		0.162	False		,,,				2504	0.2025				p.Q451Q		Atlas-SNP	.											.	MYO3B	320	.	0			c.G1353A						PASS	.	G	,,	227,3659		8,211,1724	128.0	125.0	126.0		1353,1353,1353	1.1	1.0	2	dbSNP_123	126	1424,6866		112,1200,2833	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	120,1411,4557	AA,AG,GG		17.1773,5.8415,13.5595	,,	451/1315,451/1276,451/1342	171242761	1651,10525	1943	4145	6088	SO:0001819	synonymous_variant	140469	exon13			TGTTCAGCATTTG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1353G>A	2.37:g.171242761G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	238	107	0.44958	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																			G|0.891;A|0.109	0.109	strong		0.433	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
PEBP4	157310	hgsc.bcm.edu	37	8	22785159	22785159	+	Silent	SNP	G	G	A	rs2175192	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22785159G>A	ENST00000256404.6	-	2	160	c.69C>T	c.(67-69)gaC>gaT	p.D23D	PEBP4_ENST00000521284.1_5'UTR	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	23						extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)				breast(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|stomach(2)	10		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		TCTCATCCTCGTCTCCAGTGA	0.577													G|||	850	0.169728	0.0847	0.1455	5008	,	,		20299	0.1984		0.1889	False		,,,				2504	0.2526				p.D23D		Atlas-SNP	.											.	PEBP4	23	.	0			c.C69T						PASS	.	G		399,3803		23,353,1725	110.0	116.0	114.0		69	-4.8	0.0	8	dbSNP_96	114	1646,6824		179,1288,2768	no	coding-synonymous	PEBP4	NM_144962.2		202,1641,4493	AA,AG,GG		19.4333,9.4955,16.1379		23/228	22785159	2045,10627	2101	4235	6336	SO:0001819	synonymous_variant	157310	exon2			ATCCTCGTCTCCA	BC020779	CCDS43724.1	8p21.3	2009-08-13			ENSG00000134020	ENSG00000134020			28319	protein-coding gene	gene with protein product	"""cousin-of-RKIP 1 protein"""	612473				15302887, 16865237	Standard	NM_144962		Approved	MGC22776, CORK1, hPEBP4	uc003xcn.1	Q96S96	OTTHUMG00000163749	ENST00000256404.6:c.69C>T	8.37:g.22785159G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_144962	Q5EVA1|Q8WW74	Silent	SNP	ENST00000256404.6	37	CCDS43724.1																																																																																			G|0.830;A|0.170	0.170	strong		0.577	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
SMYD1	150572	hgsc.bcm.edu	37	2	88396174	88396174	+	Silent	SNP	T	T	C	rs2919881	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:88396174T>C	ENST00000419482.2	+	6	844	c.759T>C	c.(757-759)atT>atC	p.I253I	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.I240I	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	253	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						TGTCCTATATTGACTTCCTCA	0.483													C|||	1572	0.313898	0.4244	0.2579	5008	,	,		22653	0.1627		0.3559	False		,,,				2504	0.317				p.I253I		Atlas-SNP	.											.	SMYD1	95	.	0			c.T759C						PASS	.	C		1789,2617	641.1+/-397.4	357,1075,771	111.0	105.0	107.0		759	-3.6	0.9	2	dbSNP_101	107	3139,5461	656.5+/-401.4	570,1999,1731	no	coding-synonymous	SMYD1	NM_198274.3		927,3074,2502	CC,CT,TT		36.5,40.6037,37.8902		253/491	88396174	4928,8078	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon6			CTATATTGACTTC	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.759T>C	2.37:g.88396174T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			T|0.654;C|0.346	0.346	strong		0.483	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
NPSR1	387129	hgsc.bcm.edu	37	7	34889222	34889222	+	Silent	SNP	T	T	C	rs10275028	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:34889222T>C	ENST00000360581.1	+	9	1199	c.1071T>C	c.(1069-1071)acT>acC	p.T357T	NPSR1_ENST00000359791.1_Intron|NPSR1_ENST00000531252.1_Intron|NPSR1_ENST00000381539.3_Nonstop_Mutation_p.*391R|NPSR1_ENST00000381542.1_Silent_p.T291T	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	357						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	GGGAGAGAACTGAGAGGCATG	0.493													C|||	1338	0.267173	0.4047	0.2349	5008	,	,		21395	0.1508		0.3549	False		,,,				2504	0.1339				p.T357T		Atlas-SNP	.											.	NPSR1	134	.	0			c.T1071C						PASS	.	C	,	1725,2681	649.9+/-399.0	330,1065,808	136.0	123.0	127.0		1071,	-10.5	0.0	7	dbSNP_119	127	3003,5597	665.5+/-402.3	499,2005,1796	no	coding-synonymous,intron	NPSR1	NM_207172.1,NM_207173.1	,	829,3070,2604	CC,CT,TT		34.9186,39.1512,36.3525	,	357/372,	34889222	4728,8278	2203	4300	6503	SO:0001819	synonymous_variant	387129	exon9			GAGAACTGAGAGG	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.1071T>C	7.37:g.34889222T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	216	103	0.476852	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Silent	SNP	ENST00000360581.1	37	CCDS5444.1	660	0.3021978021978022	202	0.4105691056910569	103	0.2845303867403315	92	0.16083916083916083	263	0.3469656992084433	C	0.005	-2.234893	0.00277	0.391512	0.349186	ENSG00000187258	ENST00000381539	.	.	.	5.24	-10.5	0.00291	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.4057	0.11407	0.1771:0.4488:0.1298:0.2442	rs10275028;rs10486658;rs56862582;rs10275028	.	.	.	R	391	.	.	X	+	1	0	NPSR1	34855747	0.000000	0.05858	0.001000	0.08648	0.031000	0.12232	-4.665000	0.00201	-3.287000	0.00195	-2.157000	0.00329	TGA	T|0.710;C|0.290	0.290	strong		0.493	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173	
IRF2BP2	359948	hgsc.bcm.edu	37	1	234744250	234744250	+	Silent	SNP	G	G	A	rs8722	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:234744250G>A	ENST00000366609.3	-	1	1021	c.991C>T	c.(991-993)Ctg>Ttg	p.L331L	IRF2BP2_ENST00000366610.3_Silent_p.L331L|IRF2BP2_ENST00000491430.1_5'Flank|RP4-781K5.2_ENST00000436039.1_RNA	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	331					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			CCTGCAGTCAGGGCCGGCTCC	0.642													G|||	680	0.135783	0.0129	0.1398	5008	,	,		14867	0.2034		0.2455	False		,,,				2504	0.1166				p.L331L		Atlas-SNP	.											.	IRF2BP2	37	.	0			c.C991T						PASS	.	G	,	199,4203		5,189,2007	22.0	21.0	22.0		991,991	4.8	1.0	1	dbSNP_52	22	1983,6617		240,1503,2557	no	coding-synonymous,coding-synonymous	IRF2BP2	NM_001077397.1,NM_182972.2	,	245,1692,4564	AA,AG,GG		23.0581,4.5207,16.782	,	331/572,331/588	234744250	2182,10820	2201	4300	6501	SO:0001819	synonymous_variant	359948	exon1			CAGTCAGGGCCGG	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.991C>T	1.37:g.234744250G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	37	CCDS1602.1																																																																																			G|0.834;A|0.166	0.166	strong		0.642	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972	
KIAA1549L	25758	hgsc.bcm.edu	37	11	33604885	33604885	+	Splice_Site	SNP	C	C	T	rs2273117	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:33604885C>T	ENST00000321505.4	+	10	3693	c.3513C>T	c.(3511-3513)ccC>ccT	p.P1171P	KIAA1549L_ENST00000265654.5_Splice_Site_p.P1177P|KIAA1549L_ENST00000389726.3_Splice_Site_p.P1177P			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1171						integral component of membrane (GO:0016021)											TTCCCACAGCCGTGGTGAAGA	0.577													C|||	973	0.194289	0.0764	0.2378	5008	,	,		20548	0.3591		0.2197	False		,,,				2504	0.1268				p.P1171P		Atlas-SNP	.											.	.	.	.	0			c.C3513T						PASS	.	C		374,3764		16,342,1711	32.0	35.0	34.0		3513	-2.6	1.0	11	dbSNP_100	34	1961,6495		225,1511,2492	yes	coding-synonymous-near-splice	C11orf41	NM_012194.2		241,1853,4203	TT,TC,CC		23.1906,9.0382,18.5406		1171/1850	33604885	2335,10259	2069	4228	6297	SO:0001630	splice_region_variant	25758	exon10			CACAGCCGTGGTG	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"""chromosome 11 open reading frame 69"", ""chromosome 11 open reading frame 41"""	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.3512-1C>T	11.37:g.33604885C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2	492	0.22527472527472528	36	0.07317073170731707	80	0.22099447513812154	206	0.36013986013986016	170	0.22427440633245382	C	10.63	1.402903	0.25291	0.090382	0.231906	ENSG00000110427	ENST00000526400	.	.	.	5.57	-2.59	0.06209	.	0.049055	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.34551	-0.9824	5	0.87932	D	0	.	9.6103	0.39659	0.0:0.1407:0.1313:0.728	rs2273117;rs2273117	.	.	.	L	569	.	ENSP00000433481:P569L	P	+	2	0	C11orf41	33561461	0.953000	0.32496	0.994000	0.49952	0.963000	0.63663	0.040000	0.13905	-0.235000	0.09767	0.561000	0.74099	CCG	C|0.789;T|0.211	0.211	strong		0.577	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	Silent
MAGEB6	158809	hgsc.bcm.edu	37	X	26212334	26212334	+	Missense_Mutation	SNP	A	A	C	rs143802048	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:26212334A>C	ENST00000379034.1	+	2	520	c.371A>C	c.(370-372)tAt>tCt	p.Y124S		NM_173523.2	NP_775794.2	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	124	Ser-rich.									breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(18)|ovary(3)|prostate(2)	33						GGCTCAAAATATGATGTGGCT	0.552													.|||	342	0.090596	0.0242	0.0706	3775	,	,		12620	0.0794		0.0646	False		,,,				2504	0.1186				p.Y124S		Atlas-SNP	.											.	MAGEB6	91	.	0			c.A371C						PASS	.	C	SER/TYR	21,3809		1,4,15,1626,553	85.0	77.0	80.0		371	-1.5	0.0	X	dbSNP_134	80	81,6624		6,7,62,2414,1789	no	missense	MAGEB6	NM_173523.2	144	7,11,77,4040,2342	CC,CA,C,AA,A		1.2081,0.5483,0.9682	benign	124/408	26212334	102,10433	2199	4278	6477	SO:0001583	missense	158809	exon2			CAAAATATGATGT	AF320514	CCDS14217.1	Xp22.12	2009-03-17			ENSG00000176746	ENSG00000176746			23796	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 4"""	300467				10861452	Standard	NM_173523		Approved	FLJ40242, MAGE-B6, MAGEB6A, CT3.4	uc004dbr.3	Q8N7X4	OTTHUMG00000021285	ENST00000379034.1:c.371A>C	X.37:g.26212334A>C	ENSP00000368320:p.Tyr124Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_173523	Q6GS19|Q9H219	Missense_Mutation	SNP	ENST00000379034.1	37	CCDS14217.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.460724	0.00171	0.005483	0.012081	ENSG00000176746	ENST00000379034	T	0.01629	4.72	1.23	-1.47	0.08772	.	.	.	.	.	T	0.00468	0.0015	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42292	-0.9460	9	0.02654	T	1	.	2.6776	0.05084	0.2703:0.469:0.0:0.2607	.	124	Q8N7X4	MAGB6_HUMAN	S	124	ENSP00000368320:Y124S	ENSP00000368320:Y124S	Y	+	2	0	MAGEB6	26122255	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.070000	0.03440	-1.353000	0.02191	-2.567000	0.00172	TAT	A|0.980;C|0.020	0.020	strong		0.552	MAGEB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056123.1	NM_173523	
GLYR1	84656	hgsc.bcm.edu	37	16	4855279	4855279	+	Silent	SNP	A	A	G	rs8064024	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:4855279A>G	ENST00000321919.9	-	16	1696	c.1620T>C	c.(1618-1620)tcT>tcC	p.S540S	GLYR1_ENST00000591451.1_Silent_p.S534S|GLYR1_ENST00000436648.5_Silent_p.S459S|ROGDI_ENST00000322048.7_5'Flank|GLYR1_ENST00000381983.3_Silent_p.S523S	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	540					pentose-phosphate shunt (GO:0006098)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	19						TATCGTTGTCAGACTGGTCCA	0.562													G|||	2888	0.576677	0.7973	0.6484	5008	,	,		15442	0.3244		0.5199	False		,,,				2504	0.546				p.S540S		Atlas-SNP	.											.	GLYR1	49	.	0			c.T1620C						PASS	.	G		3321,1073	389.3+/-327.3	1257,807,133	114.0	96.0	102.0		1620	1.3	1.0	16	dbSNP_116	102	4162,4438	588.1+/-392.3	1037,2088,1175	no	coding-synonymous	GLYR1	NM_032569.3		2294,2895,1308	GG,GA,AA		48.3953,24.4197,42.4119		540/554	4855279	7483,5511	2197	4300	6497	SO:0001819	synonymous_variant	84656	exon16			GTTGTCAGACTGG	AF244907	CCDS10524.1	16p13.3	2010-02-17			ENSG00000140632	ENSG00000140632			24434	protein-coding gene	gene with protein product	"""nuclear protein 60kDa"""	610660				16352664	Standard	NM_032569		Approved	BM045, HIBDL, NP60, N-PAC	uc002cxx.4	Q49A26	OTTHUMG00000129530	ENST00000321919.9:c.1620T>C	16.37:g.4855279A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_032569	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	Silent	SNP	ENST00000321919.9	37	CCDS10524.1																																																																																			A|0.434;G|0.566	0.566	strong		0.562	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251717.2	NM_032569	
MEF2D	4209	hgsc.bcm.edu	37	1	156446903	156446903	+	Silent	SNP	T	T	C	rs2274317	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156446903T>C	ENST00000348159.4	-	7	1236	c.756A>G	c.(754-756)ccA>ccG	p.P252P	MEF2D_ENST00000340875.5_Silent_p.P251P|MEF2D_ENST00000464356.2_Silent_p.P251P|MEF2D_ENST00000353795.3_Silent_p.P206P|MEF2D_ENST00000368240.2_Silent_p.P252P|MEF2D_ENST00000360595.3_Silent_p.P252P	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	252	Poly-Pro.				adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TAGGTGGGGGTGGAGACTTGG	0.612													T|||	2863	0.571685	0.2368	0.5951	5008	,	,		16626	0.756		0.672	False		,,,				2504	0.7147				p.P252P		Atlas-SNP	.											MEF2D,colon,adenoma,-1,1	MEF2D	43	1	0			c.A756G						scavenged	.	T		1389,3017	458.6+/-352.0	238,913,1052	82.0	75.0	77.0		756	-8.0	0.9	1	dbSNP_100	77	5651,2949	668.0+/-402.5	1850,1951,499	no	coding-synonymous	MEF2D	NM_005920.2		2088,2864,1551	CC,CT,TT		34.2907,31.5252,45.8711		252/522	156446903	7040,5966	2203	4300	6503	SO:0001819	synonymous_variant	4209	exon7			TGGGGGTGGAGAC	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"""Myocyte enhancer factors"""	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.756A>G	1.37:g.156446903T>C		Somatic	137	2	0.0145985		WXS	Illumina HiSeq	Phase_I	116	113	0.974138	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Silent	SNP	ENST00000348159.4	37	CCDS1143.1																																																																																			A|0.000;C|0.551;T|0.449	0.551	strong		0.612	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920	
ULK1	8408	hgsc.bcm.edu	37	12	132401566	132401566	+	Missense_Mutation	SNP	C	C	T	rs11546871	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:132401566C>T	ENST00000321867.4	+	21	2492	c.2141C>T	c.(2140-2142)cCg>cTg	p.P714L	ULK1_ENST00000540647.1_5'Flank	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	714			P -> L (in dbSNP:rs11546871). {ECO:0000269|PubMed:17344846}.		autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)	p.P714L(1)		breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		GCCCCGGACCCGGGCAGCACG	0.672													c|||	1020	0.203674	0.0877	0.2651	5008	,	,		9562	0.0377		0.326	False		,,,				2504	0.362				p.P714L		Atlas-SNP	.											ULK1,NS,carcinoma,0,2	ULK1	92	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2141T						PASS	.		LEU/PRO	449,3933	198.7+/-222.5	15,419,1757	32.0	42.0	39.0		2141	4.2	0.3	12	dbSNP_120	39	2658,5922	403.8+/-347.9	403,1852,2035	yes	missense	ULK1	NM_003565.2	98	418,2271,3792	TT,TC,CC		30.979,10.2465,23.9701	benign	714/1051	132401566	3107,9855	2191	4290	6481	SO:0001583	missense	8408	exon21			CGGACCCGGGCAG	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"""ATG1 autophagy related 1 homolog (S. cerevisiae)"""	603168	"""unc-51 (C. elegans)-like kinase 1"", ""unc-51-like kinase 1 (C. elegans)"""			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.2141C>T	12.37:g.132401566C>T	ENSP00000324560:p.Pro714Leu	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	227	110	0.484582	NM_003565	Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	37	CCDS9274.1	407	0.18635531135531136	44	0.08943089430894309	108	0.2983425414364641	19	0.033216783216783216	236	0.3113456464379947	c	6.883	0.532418	0.13127	0.102465	0.30979	ENSG00000177169	ENST00000321867;ENST00000541761	T;T	0.28454	1.61;1.61	5.06	4.16	0.48862	.	0.806381	0.11335	N	0.574590	T	0.00012	0.0000	N	0.08118	0	0.35606	P	0.19176400000000005	B	0.13145	0.007	B	0.06405	0.002	T	0.41875	-0.9484	9	0.10902	T	0.67	-6.2137	9.0411	0.36319	0.0:0.7578:0.1633:0.079	rs11546871	714	O75385	ULK1_HUMAN	L	714;62	ENSP00000324560:P714L;ENSP00000444298:P62L	ENSP00000324560:P714L	P	+	2	0	ULK1	130967519	0.590000	0.26815	0.345000	0.25642	0.033000	0.12548	2.192000	0.42649	1.226000	0.43582	0.556000	0.70494	CCG	C|0.780;T|0.220	0.220	strong		0.672	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3		
GFER	2671	hgsc.bcm.edu	37	16	2035999	2035999	+	Silent	SNP	C	C	T	rs1802834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2035999C>T	ENST00000248114.6	+	3	594	c.588C>T	c.(586-588)cgC>cgT	p.R196R	AC005606.14_ENST00000564438.1_lincRNA|GFER_ENST00000567719.1_Silent_p.R121R|GFER_ENST00000569451.1_3'UTR	NM_005262.2	NP_005253.3	P55789	ALR_HUMAN	growth factor, augmenter of liver regeneration	196					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|protein disulfide oxidoreductase activity (GO:0015035)|thiol oxidase activity (GO:0016972)			endometrium(1)|large_intestine(1)|lung(3)	5					Flavin adenine dinucleotide(DB03147)	AGCGCTGGCGCGACGGCTGGA	0.582													C|||	167	0.0333466	0.0106	0.0548	5008	,	,		22184	0.0		0.0944	False		,,,				2504	0.0204				p.R196R		Atlas-SNP	.											.	GFER	8	.	0			c.C588T						PASS	.	C		91,4305	73.1+/-111.1	1,89,2108	74.0	69.0	71.0		588	-8.9	0.3	16	dbSNP_89	71	780,7820	183.2+/-231.5	43,694,3563	no	coding-synonymous	GFER	NM_005262.2		44,783,5671	TT,TC,CC		9.0698,2.0701,6.7021		196/206	2035999	871,12125	2198	4300	6498	SO:0001819	synonymous_variant	2671	exon3			CTGGCGCGACGGC	BC002429	CCDS32368.1	16p13.3-p13.12	2011-06-22	2008-08-01		ENSG00000127554	ENSG00000127554			4236	protein-coding gene	gene with protein product	"""ERV1 homolog (S. cerevisiae)"""	600924	"""growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)"""			8575761	Standard	NM_005262		Approved	HSS, ERV1, ALR, HERV1, HPO1, HPO2	uc002cob.3	P55789		ENST00000248114.6:c.588C>T	16.37:g.2035999C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_005262	Q53YM6|Q8TAH6|Q9H290|Q9UK40	Silent	SNP	ENST00000248114.6	37	CCDS32368.1																																																																																			C|0.939;T|0.061	0.061	strong		0.582	GFER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434243.1	NM_005262	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751465	19751465	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:19751465C>T	ENST00000400113.3	-	4	762	c.658G>A	c.(658-660)Gag>Aag	p.E220K		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	220					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		GTGGGACGCTCGATGTCCAGG	0.562																																					p.E220K		Atlas-SNP	.											TUBA3C,NS,carcinoma,0,1	TUBA3C	166	1	0			c.G658A						scavenged	.						230.0	192.0	205.0					13																	19751465		2203	4300	6503	SO:0001583	missense	7278	exon4			GACGCTCGATGTC	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.658G>A	13.37:g.19751465C>T	ENSP00000382982:p.Glu220Lys	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	300	5	0.0166667	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000400113.3	37	CCDS9284.1	.	.	.	.	.	.	.	.	.	.	c	6.970	0.548898	0.13312	.	.	ENSG00000198033	ENST00000400113;ENST00000360801	T	0.69685	-0.42	1.21	0.297	0.15762	.	0.000000	0.47455	U	0.000235	T	0.66867	0.2833	.	.	.	0.38473	D	0.947519	.	.	.	.	.	.	T	0.65857	-0.6066	7	0.87932	D	0	.	5.6914	0.17831	0.0:0.7927:0.0:0.2073	.	.	.	.	K	220	ENSP00000382982:E220K	ENSP00000354037:E220K	E	-	1	0	TUBA3C	18649465	1.000000	0.71417	0.977000	0.42913	0.465000	0.32709	4.655000	0.61476	0.076000	0.16826	0.184000	0.17185	GAG	.	.	none		0.562	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
CEP19	84984	hgsc.bcm.edu	37	3	196435534	196435534	+	Missense_Mutation	SNP	T	T	C	rs6776064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:196435534T>C	ENST00000409690.3	-	2	429	c.7A>G	c.(7-9)Atg>Gtg	p.M3V	RNU6-646P_ENST00000364571.1_RNA|CEP19_ENST00000399942.4_Intron	NM_032898.3	NP_116287.2	Q96LK0	CEP19_HUMAN	centrosomal protein 19kDa	0						centriole (GO:0005814)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	10						ATCATTCCCATGTACATGTCC	0.408													C|||	2194	0.438099	0.4319	0.3184	5008	,	,		19510	0.5952		0.3459	False		,,,				2504	0.4642				p.M3V		Atlas-SNP	.											.	CEP19	22	.	0			c.A7G						PASS	.	C	VAL/MET	1516,2322		306,904,709	95.0	88.0	90.0		7	2.9	0.0	3	dbSNP_116	90	2935,5349		493,1949,1700	yes	missense	CEP19	NM_032898.3	21	799,2853,2409	CC,CT,TT		35.4297,39.4997,36.7184		3/168	196435534	4451,7671	1919	4142	6061	SO:0001583	missense	84984	exon2			TTCCCATGTACAT	BC007827	CCDS43193.2	3q29	2014-02-20	2011-05-06	2011-05-06	ENSG00000174007	ENSG00000174007			28209	protein-coding gene	gene with protein product		615586	"""chromosome 3 open reading frame 34"""	C3orf34		21399614	Standard	XM_005269370		Approved	MGC14126	uc011btw.2	Q96LK0	OTTHUMG00000153933	ENST00000409690.3:c.7A>G	3.37:g.196435534T>C	ENSP00000387209:p.Met3Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_032898	B2RA74|Q96I48	Missense_Mutation	SNP	ENST00000409690.3	37	CCDS43193.2	950	0.434981684981685	217	0.4410569105691057	115	0.31767955801104975	347	0.6066433566433567	271	0.3575197889182058	C	0.005	-2.165644	0.00318	0.394997	0.354297	ENSG00000174007	ENST00000409690	.	.	.	4.99	2.89	0.33648	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.44128	-0.9348	4	0.05525	T	0.97	.	7.3183	0.26513	0.0:0.5696:0.0:0.4304	rs6776064;rs56846764;rs6776064	.	.	.	V	3	.	ENSP00000387209:M3V	M	-	1	0	CEP19	197919931	0.000000	0.05858	0.007000	0.13788	0.318000	0.28184	-0.082000	0.11304	0.535000	0.28714	-0.128000	0.14901	ATG	T|0.571;C|0.429	0.429	strong		0.408	CEP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333080.2	NM_032898	
SLC28A1	9154	hgsc.bcm.edu	37	15	85448875	85448875	+	Missense_Mutation	SNP	C	C	A	rs8187758	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:85448875C>A	ENST00000286749.3	+	7	799	c.709C>A	c.(709-711)Cag>Aag	p.Q237K	SLC28A1_ENST00000394573.1_Missense_Mutation_p.Q237K|SLC28A1_ENST00000537703.1_Missense_Mutation_p.Q159K|SLC28A1_ENST00000538177.1_Missense_Mutation_p.Q237K|SLC28A1_ENST00000537216.1_Missense_Mutation_p.Q237K|SLC28A1_ENST00000537624.1_Missense_Mutation_p.Q237K			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	237			Q -> K (in dbSNP:rs8187758).		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GCTGGGCGAGCAGATCCGGGT	0.572													C|||	1505	0.300519	0.1573	0.3646	5008	,	,		16768	0.3075		0.2366	False		,,,				2504	0.5072				p.Q237K		Atlas-SNP	.											.	SLC28A1	118	.	0			c.C709A						PASS	.	C	LYS/GLN	752,3654	308.0+/-290.3	65,622,1516	139.0	112.0	121.0		709	4.0	1.0	15	dbSNP_123	121	1926,6672	341.8+/-324.2	210,1506,2583	yes	missense	SLC28A1	NM_004213.3	53	275,2128,4099	AA,AC,CC		22.4006,17.0676,20.5937	benign	237/650	85448875	2678,10326	2203	4299	6502	SO:0001583	missense	9154	exon8			GGCGAGCAGATCC	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.709C>A	15.37:g.85448875C>A	ENSP00000286749:p.Gln237Lys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	549	0.25137362637362637	78	0.15853658536585366	125	0.3453038674033149	163	0.28496503496503495	183	0.24142480211081793	C	10.23	1.292038	0.23564	0.170676	0.224006	ENSG00000156222	ENST00000537216;ENST00000538177;ENST00000537624;ENST00000286749;ENST00000394573;ENST00000537703	T;T;T;T;T;T	0.13307	2.6;2.6;2.6;2.6;2.6;2.6	4.03	4.03	0.46877	Na dependent nucleoside transporter (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.46885	1.475	0.09310	P	0.99999771651	P;B;D;B;P	0.76494	0.927;0.094;0.999;0.115;0.927	P;B;D;B;P	0.91635	0.679;0.155;0.999;0.241;0.679	T	0.49370	-0.8947	9	0.22706	T	0.39	-5.2491	11.8824	0.52583	0.0:1.0:0.0:0.0	rs8187758;rs17222323;rs52791431;rs60871224;rs8187758	237;237;237;159;237	B7Z533;F5H560;B7Z3L6;B7Z3M4;O00337	.;.;.;.;S28A1_HUMAN	K	237;237;237;237;237;159	ENSP00000440546:Q237K;ENSP00000443752:Q237K;ENSP00000444700:Q237K;ENSP00000286749:Q237K;ENSP00000378074:Q237K;ENSP00000443764:Q159K	ENSP00000286749:Q237K	Q	+	1	0	SLC28A1	83249879	1.000000	0.71417	0.974000	0.42286	0.561000	0.35649	5.575000	0.67430	2.240000	0.73641	0.557000	0.71058	CAG	C|0.768;A|0.232	0.232	strong		0.572	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
PDE6C	5146	hgsc.bcm.edu	37	10	95389041	95389041	+	Silent	SNP	G	G	A	rs714550	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:95389041G>A	ENST00000371447.3	+	8	1236	c.1098G>A	c.(1096-1098)gcG>gcA	p.A366A		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	366	GAF 2.				phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	ATGCCCCTGCGGATGAATACT	0.507													G|||	1982	0.395767	0.4493	0.389	5008	,	,		21297	0.4792		0.3459	False		,,,				2504	0.2935				p.A366A		Atlas-SNP	.											.	PDE6C	97	.	0			c.G1098A						PASS	.	G		1894,2512	544.9+/-376.7	426,1042,735	175.0	153.0	160.0		1098	-8.3	0.7	10	dbSNP_86	160	2870,5730	451.3+/-362.6	474,1922,1904	no	coding-synonymous	PDE6C	NM_006204.3		900,2964,2639	AA,AG,GG		33.3721,42.9868,36.6292		366/859	95389041	4764,8242	2203	4300	6503	SO:0001819	synonymous_variant	5146	exon8			CCCTGCGGATGAA	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.1098G>A	10.37:g.95389041G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	123	6	0.0487805	NM_006204	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	37	CCDS7429.1																																																																																			G|0.622;A|0.378	0.378	strong		0.507	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
DMKN	93099	hgsc.bcm.edu	37	19	35998362	35998362	+	Intron	SNP	T	T	G	rs4254439	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:35998362T>G	ENST00000339686.3	-	8	1215				DMKN_ENST00000480502.1_Intron|DMKN_ENST00000419602.1_Silent_p.R315R|DMKN_ENST00000418261.1_Intron|DMKN_ENST00000458071.1_Intron|DMKN_ENST00000467637.1_Intron|DMKN_ENST00000451297.2_Intron|DMKN_ENST00000472252.2_Intron|DMKN_ENST00000474928.1_Intron|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000392206.2_Intron|DMKN_ENST00000402589.2_Intron|DMKN_ENST00000461300.1_Intron|DMKN_ENST00000488892.1_Intron|DMKN_ENST00000602781.1_Intron|DMKN_ENST00000424570.2_Intron|DMKN_ENST00000443640.1_Silent_p.R89R|DMKN_ENST00000447113.2_Silent_p.R376R|DMKN_ENST00000462126.1_Intron|DMKN_ENST00000440396.1_Silent_p.R376R|DMKN_ENST00000414866.2_Intron|DMKN_ENST00000492341.2_Intron|DMKN_ENST00000436012.1_Intron	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine							extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			AGGCTCACCCTATAATTGTCT	0.507													G|||	1927	0.384784	0.4455	0.3184	5008	,	,		18711	0.4425		0.3022	False		,,,				2504	0.3753				p.R376R		Atlas-SNP	.											.	DMKN	116	.	0			c.A1126C						PASS	.						94.0	84.0	87.0					19																	35998362		692	1591	2283	SO:0001627	intron_variant	93099	exon9			TCACCCTATAATT	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.1039-1474A>C	19.37:g.35998362T>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_001190348	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1	837	0.38324175824175827	224	0.45528455284552843	108	0.2983425414364641	269	0.47027972027972026	236	0.3113456464379947	G	8.948	0.967522	0.18659	.	.	ENSG00000161249	ENST00000434389	.	.	.	3.66	3.66	0.41972	.	.	.	.	.	.	.	.	.	.	.	0.20074	P	0.9999308811	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.7274	0.34478	0.0:0.0:0.7736:0.2264	rs4254439;rs59459723	.	.	.	S	56	.	.	X	-	2	0	DMKN	40690202	0.932000	0.31603	0.543000	0.28128	0.000000	0.00434	1.913000	0.39956	1.133000	0.42147	-0.121000	0.15023	TAG	G|0.367;N|0.002	0.367	strong		0.507	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
YTHDC2	64848	hgsc.bcm.edu	37	5	112917278	112917278	+	Silent	SNP	T	T	G	rs11748794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:112917278T>G	ENST00000161863.4	+	25	3732	c.3519T>G	c.(3517-3519)tcT>tcG	p.S1173S		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1173					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		AACAACCATCTGGGATTGGCC	0.423													T|||	1031	0.205871	0.2799	0.3818	5008	,	,		15677	0.1002		0.166	False		,,,				2504	0.1309				p.S1173S		Atlas-SNP	.											.	YTHDC2	118	.	0			c.T3519G						PASS	.	T		1280,3124	432.2+/-343.2	194,892,1116	61.0	61.0	61.0		3519	-0.6	1.0	5	dbSNP_120	61	1378,7222	265.3+/-286.1	102,1174,3024	no	coding-synonymous	YTHDC2	NM_022828.3		296,2066,4140	GG,GT,TT		16.0233,29.0645,20.4399		1173/1431	112917278	2658,10346	2202	4300	6502	SO:0001819	synonymous_variant	64848	exon25			ACCATCTGGGATT	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.3519T>G	5.37:g.112917278T>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																			G|0.200;N|0.000	0.200	strong		0.423	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
FCGBP	8857	hgsc.bcm.edu	37	19	40376811	40376811	+	Missense_Mutation	SNP	C	C	T	rs4802062	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40376811C>T	ENST00000221347.6	-	24	11618	c.11611G>A	c.(11611-11613)Ggg>Agg	p.G3871R	FCGBP_ENST00000595713.1_5'Flank	NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3871	VWFD 9. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GACAGTGGCCCTGTGGGGCTG	0.602																																					p.G3871R		Atlas-SNP	.											FCGBP,NS,carcinoma,+2,1	FCGBP	416	1	0			c.G11611A						scavenged	.						9.0	14.0	12.0					19																	40376811		2097	4111	6208	SO:0001583	missense	8857	exon24			GTGGCCCTGTGGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.11611G>A	19.37:g.40376811C>T	ENSP00000221347:p.Gly3871Arg	Somatic	618	1	0.00161812		WXS	Illumina HiSeq	Phase_I	785	145	0.184713	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	c	19.42	3.823259	0.71143	.	.	ENSG00000090920	ENST00000221347	T	0.19806	2.12	3.75	3.75	0.43078	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.55049	0.1896	M	0.92649	3.33	0.43485	D	0.995715	D	0.89917	1.0	D	0.97110	1.0	T	0.69038	-0.5251	9	0.72032	D	0.01	.	14.6972	0.69132	0.0:1.0:0.0:0.0	rs4802062	3871	Q9Y6R7	FCGBP_HUMAN	R	3871	ENSP00000221347:G3871R	ENSP00000221347:G3871R	G	-	1	0	FCGBP	45068651	0.998000	0.40836	0.523000	0.27875	0.621000	0.37620	3.885000	0.56182	1.792000	0.52537	0.313000	0.20887	GGG	C|0.962;T|0.038	0.038	strong		0.602	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
KIF19	124602	hgsc.bcm.edu	37	17	72349067	72349067	+	Silent	SNP	C	C	T	rs2280108	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72349067C>T	ENST00000389916.4	+	15	2226	c.2088C>T	c.(2086-2088)agC>agT	p.S696S	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	696					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						TGCAGAACAGCGCCCTCCCTC	0.607													C|||	1655	0.330471	0.0287	0.4409	5008	,	,		17871	0.3988		0.5109	False		,,,				2504	0.4039				p.S696S		Atlas-SNP	.											.	KIF19	102	.	0			c.C2088T						PASS	.	C		424,3614		31,362,1626	69.0	75.0	73.0		2088	3.0	0.1	17	dbSNP_100	73	4254,4102		1065,2124,989	no	coding-synonymous	KIF19	NM_153209.3		1096,2486,2615	TT,TC,CC		49.0905,10.5002,37.7441		696/999	72349067	4678,7716	2019	4178	6197	SO:0001819	synonymous_variant	124602	exon15			GAACAGCGCCCTC	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2088C>T	17.37:g.72349067C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			C|0.641;T|0.359	0.359	strong		0.607	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
POLR1A	25885	hgsc.bcm.edu	37	2	86297186	86297186	+	Silent	SNP	C	C	T	rs76924572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:86297186C>T	ENST00000263857.6	-	13	2199	c.1821G>A	c.(1819-1821)gaG>gaA	p.E607E	POLR1A_ENST00000409681.1_Silent_p.E607E			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	607					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						GGACGTAGGCCTCGGCCCGGC	0.567													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20627	0.0		0.002	False		,,,				2504	0.0				p.E607E		Atlas-SNP	.											.	POLR1A	137	.	0			c.G1821A						PASS	.	C		1,4069		0,1,2034	40.0	42.0	41.0		1821	2.5	1.0	2	dbSNP_133	41	32,8304		0,32,4136	no	coding-synonymous	POLR1A	NM_015425.3		0,33,6170	TT,TC,CC		0.3839,0.0246,0.266		607/1721	86297186	33,12373	2035	4168	6203	SO:0001819	synonymous_variant	25885	exon13			GTAGGCCTCGGCC	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1821G>A	2.37:g.86297186C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Silent	SNP	ENST00000263857.6	37	CCDS42706.1																																																																																			C|0.999;T|0.001	0.001	strong		0.567	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
TTN	7273	hgsc.bcm.edu	37	2	179447848	179447848	+	Silent	SNP	T	T	C	rs4894029	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179447848T>C	ENST00000591111.1	-	263	60983	c.60759A>G	c.(60757-60759)acA>acG	p.T20253T	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Silent_p.T12829T|TTN_ENST00000342992.6_Silent_p.T19326T|TTN_ENST00000589042.1_Silent_p.T21894T|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Silent_p.T12954T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.T13021T|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20253	Ig-like 111.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCAAGAAACTGTTGGCATCG	0.458													C|||	2573	0.513778	0.5749	0.4078	5008	,	,		18418	0.7202		0.2555	False		,,,				2504	0.5593				p.T21894T		Atlas-SNP	.											.	TTN	18412	.	0			c.A65682G						PASS	.	C	,,,	2050,1812		558,934,439	63.0	60.0	61.0		38487,57978,38862,39063	-6.8	0.4	2	dbSNP_111	61	1860,6430		195,1470,2480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	753,2404,2919	CC,CT,TT		22.4367,46.9187,32.1758	,,,	12829/26927,19326/33424,12954/27052,13021/27119	179447848	3910,8242	1931	4145	6076	SO:0001819	synonymous_variant	7273	exon313			AGAAACTGTTGGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.60759A>G	2.37:g.179447848T>C		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	236	107	0.45339	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.555;C|0.445	0.445	strong		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
EXD3	54932	hgsc.bcm.edu	37	9	140262424	140262424	+	Silent	SNP	C	C	T	rs11507683	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140262424C>T	ENST00000340951.4	-	6	675	c.480G>A	c.(478-480)gcG>gcA	p.A160A	EXD3_ENST00000479452.1_Silent_p.A160A|EXD3_ENST00000342129.4_5'UTR|EXD3_ENST00000475006.1_5'UTR	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						GCTTCAACGTCGCGCCCAGCG	0.557													C|||	433	0.0864617	0.1475	0.0749	5008	,	,		21032	0.0288		0.1382	False		,,,				2504	0.0184				p.A160A		Atlas-SNP	.											EXD3_ENST00000340951,colon,carcinoma,-2,2	EXD3	86	2	0			c.G480A						PASS	.	C		555,3429		50,455,1487	38.0	38.0	38.0		480	-3.0	0.1	9	dbSNP_120	38	972,7372		65,842,3265	no	coding-synonymous	EXD3	NM_017820.3		115,1297,4752	TT,TC,CC		11.6491,13.9307,12.3864		160/877	140262424	1527,10801	1992	4172	6164	SO:0001819	synonymous_variant	54932	exon6			CAACGTCGCGCCC		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.480G>A	9.37:g.140262424C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_017820	Q6P1M1|Q8IXT8	Silent	SNP	ENST00000340951.4	37	CCDS48066.1																																																																																			C|0.899;T|0.101	0.101	strong		0.557	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
DNAH6	1768	hgsc.bcm.edu	37	2	84921433	84921433	+	Silent	SNP	A	A	G	rs1192295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:84921433A>G	ENST00000237449.6	+	45	7361	c.7353A>G	c.(7351-7353)acA>acG	p.T2451T	DNAH6_ENST00000398278.2_Silent_p.T2402T|DNAH6_ENST00000389394.3_Silent_p.T2451T|DNAH6_ENST00000602588.1_Silent_p.T423T			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2451	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TAGGAGGCACAGGAAAGCAGT	0.443													A|||	498	0.0994409	0.2602	0.0432	5008	,	,		21203	0.002		0.0646	False		,,,				2504	0.0583				p.T2451T		Atlas-SNP	.											.	DNAH6	194	.	0			c.A7353G						PASS	.	A		306,1078		31,244,417	153.0	136.0	141.0		7353	-6.6	0.9	2	dbSNP_87	141	173,3009		4,165,1422	no	coding-synonymous	DNAH6	NM_001370.1		35,409,1839	GG,GA,AA		5.4368,22.1098,10.4906		2451/4159	84921433	479,4087	692	1591	2283	SO:0001819	synonymous_variant	1768	exon46			AGGCACAGGAAAG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7353A>G	2.37:g.84921433A>G		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	215	116	0.539535	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			A|0.904;G|0.096	0.096	strong		0.443	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
Unknown	0	hgsc.bcm.edu	37	11	124096275	124096275	+	IGR	SNP	T	T	C	rs2512268	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124096275T>C								OR10D3 (39323 upstream) : OR8G1 (24147 downstream)																							TTTTATACTATTGTTGTGCCC	0.448													N|||	504	0.100639	0.0174	0.1585	5008	,	,		20278	0.131		0.1441	False		,,,				2504	0.0961				p.I293T		Atlas-SNP	.											.	.	.	.	0			c.T878C						PASS	.	C	THR/ILE	136,3726		3,130,1798	73.0	67.0	69.0		878	-4.1	0.0	11	dbSNP_100	69	1122,7182		95,932,3125	no	missense	OR8G2	NM_001007249.1	89	98,1062,4923	CC,CT,TT		13.5116,3.5215,10.3403	benign	293/305	124096275	1258,10908	1931	4152	6083	SO:0001628	intergenic_variant	26492	exon1			ATACTATTGTTGT																													11.37:g.124096275T>C		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	182	86	0.472527	NM_001007249		Missense_Mutation	SNP		37																																																																																				T|0.891;C|0.109	0.109	strong	0	0.448								
MAPT	4137	hgsc.bcm.edu	37	17	44061023	44061023	+	Missense_Mutation	SNP	G	G	A	rs62063786	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44061023G>A	ENST00000571987.1	+	5	853	c.853G>A	c.(853-855)Gac>Aac	p.D285N	MAPT_ENST00000576518.1_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.D285N|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.D285N|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.D285N|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	285			D -> N (risk factor for PSNP1; dbSNP:rs62063786). {ECO:0000269|PubMed:10534245, ECO:0000269|PubMed:9629852}.		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	CTCAGAGCCCGACGGGCCCAG	0.622													G|||	439	0.0876597	0.0204	0.1571	5008	,	,		15639	0.001		0.2406	False		,,,				2504	0.0613				p.D285N		Atlas-SNP	.											.	MAPT	135	.	0			c.G853A						PASS	.	G	ASN/ASP,,,,,,ASN/ASP,	228,4178	130.6+/-167.2	8,212,1983	39.0	44.0	42.0		853,,,,,,853,	-3.2	0.0	17	dbSNP_129	42	1928,6672	327.6+/-317.9	221,1486,2593	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	23,,,,,,23,	229,1698,4576	AA,AG,GG		22.4186,5.1748,16.577	benign,,,,,,benign,	285/777,,,,,,285/759,	44061023	2156,10850	2203	4300	6503	SO:0001583	missense	4137	exon6			GAGCCCGACGGGC	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.853G>A	17.37:g.44061023G>A	ENSP00000458742:p.Asp285Asn	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	13.42	2.230841	0.39399	0.051748	0.224186	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.12147	2.72;2.71;2.72	4.94	-3.22	0.05125	.	2.226750	0.01871	N	0.037217	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B;B	0.26363	0.117;0.147	B;B	0.21546	0.035;0.023	T	0.37731	-0.9693	9	0.28530	T	0.3	4.184	6.1584	0.20350	0.5145:0.1459:0.3396:0.0	rs62063786	285;285	P10636-9;P10636	.;TAU_HUMAN	N	285	ENSP00000340820:D285N;ENSP00000262410:D285N;ENSP00000410838:D285N	ENSP00000262410:D285N	D	+	1	0	MAPT	41416860	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.030000	0.13688	-0.440000	0.07211	0.561000	0.74099	GAC	A|0.118;C|0.246	0.118	strong		0.622	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
KLK10	5655	hgsc.bcm.edu	37	19	51519346	51519346	+	Silent	SNP	G	G	C	rs1061368	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51519346G>C	ENST00000309958.3	-	4	554	c.336C>G	c.(334-336)acC>acG	p.T112T	CTC-518B2.12_ENST00000596286.1_RNA|KLK10_ENST00000358789.3_Silent_p.T112T|KLK10_ENST00000391805.1_Silent_p.T112T	NM_002776.4	NP_002767.2	O43240	KLK10_HUMAN	kallikrein-related peptidase 10	112	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		CAGAGCGAGTGGTCCGGCGGA	0.617													G|||	1698	0.339058	0.4402	0.4078	5008	,	,		15934	0.252		0.34	False		,,,				2504	0.2423				p.T112T		Atlas-SNP	.											.	KLK10	32	.	0			c.C336G						PASS	.	G	,,	1800,2598		357,1086,756	44.0	37.0	39.0		336,336,336	-0.5	0.2	19	dbSNP_86	39	2799,5791		479,1841,1975	no	coding-synonymous,coding-synonymous,coding-synonymous	KLK10	NM_001077500.1,NM_002776.4,NM_145888.2	,,	836,2927,2731	CC,CG,GG		32.5844,40.9277,35.4096	,,	112/277,112/277,112/277	51519346	4599,8389	2199	4295	6494	SO:0001819	synonymous_variant	5655	exon4			GCGAGTGGTCCGG	AF024605	CCDS12817.1	19q13	2011-03-07	2006-10-27			ENSG00000129451		"""Kallikreins"""	6358	protein-coding gene	gene with protein product		602673	"""kallikrein 10"""	PRSSL1		8764136, 9533035, 16800724, 16800723, 10675891	Standard	NM_145888		Approved	NES1	uc002pva.3	O43240		ENST00000309958.3:c.336C>G	19.37:g.51519346G>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_145888	A6NC12|Q53YL3|Q99920|Q9GZW9	Silent	SNP	ENST00000309958.3	37	CCDS12817.1																																																																																			G|0.655;C|0.345	0.345	strong		0.617	KLK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464337.2	NM_002776	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50659025	50659025	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50659025G>T	ENST00000248846.5	-	16	3867	c.3763C>A	c.(3763-3765)Cct>Act	p.P1255T	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_Missense_Mutation_p.P1255T			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1255	9 X 27 AA tandem repeats.				G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TCCGACACAGGCTCCCCCAAG	0.637																																					p.P1255T		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.C3763A						PASS	.						68.0	53.0	58.0					22																	50659025		2203	4300	6503	SO:0001583	missense	85378	exon16			ACACAGGCTCCCC	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.3763C>A	22.37:g.50659025G>T	ENSP00000248846:p.Pro1255Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	.	.	.	.	.	.	.	.	.	.	g	6.032	0.374231	0.11409	.	.	ENSG00000128159	ENST00000248846;ENST00000439308	T;T	0.11063	3.19;2.81	3.02	-0.545	0.11843	.	2.098260	0.03949	U	0.288172	T	0.05456	0.0144	N	0.08118	0	0.09310	N	1	B;B;B	0.16166	0.016;0.004;0.012	B;B;B	0.18561	0.013;0.013;0.022	T	0.36890	-0.9729	10	0.07644	T	0.81	.	8.0715	0.30691	0.0:0.0962:0.5704:0.3334	.	1247;1255;1255	B2RWN4;Q96RT7;Q96RT7-3	.;GCP6_HUMAN;.	T	1255	ENSP00000248846:P1255T;ENSP00000397387:P1255T	ENSP00000248846:P1255T	P	-	1	0	TUBGCP6	49001152	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-0.481000	0.06552	-0.178000	0.10672	-0.578000	0.04140	CCT	.	.	none		0.637	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
CD44	960	hgsc.bcm.edu	37	11	35229673	35229673	+	Missense_Mutation	SNP	T	T	C	rs1467558	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:35229673T>C	ENST00000428726.2	+	12	1559	c.1436T>C	c.(1435-1437)aTa>aCa	p.I479T	CD44_ENST00000526669.2_Intron|CD44_ENST00000433354.2_Missense_Mutation_p.I480T|CD44_ENST00000360158.4_Missense_Mutation_p.I230T|CD44_ENST00000278386.6_Intron|CD44_ENST00000449691.2_Missense_Mutation_p.I436T|CD44_ENST00000352818.4_Intron|CD44_ENST00000437706.2_Missense_Mutation_p.I479T|RP1-68D18.4_ENST00000528869.1_RNA|CD44_ENST00000434472.2_Intron|CD44_ENST00000433892.2_Missense_Mutation_p.I230T|CD44_ENST00000263398.6_Intron|CD44_ENST00000415148.2_Missense_Mutation_p.I436T	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	479	Stem.		I -> T (in dbSNP:rs1467558). {ECO:0000269|PubMed:1281868, ECO:0000269|PubMed:1465456, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1991450, ECO:0000269|PubMed:2007624, ECO:0000269|PubMed:2056274, ECO:0000269|PubMed:7508842, ECO:0000269|PubMed:8352881, ECO:0000269|Ref.11}.		blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	AGTCATAGTATAACGCTTCAG	0.423													C|||	4703	0.939097	0.9939	0.8919	5008	,	,		22348	0.999		0.8141	False		,,,				2504	0.9652				p.I479T		Atlas-SNP	.											.	CD44	48	.	0			c.T1436C						PASS	.	C	THR/ILE,THR/ILE,THR/ILE,,,,,	4228,176	114.6+/-152.6	2029,170,3	129.0	115.0	120.0		1436,1307,689,,,,,	6.2	0.6	11	dbSNP_88	120	6994,1602	298.2+/-303.8	2844,1306,148	yes	missense,missense,missense,intron,intron,intron,intron,intron	CD44	NM_000610.3,NM_001001389.1,NM_001001390.1,NM_001001391.1,NM_001001392.1,NM_001202555.1,NM_001202556.1,NM_001202557.1	89,89,89,,,,,	4873,1476,151	CC,CT,TT		18.6366,3.9964,13.6769	benign,benign,benign,,,,,	479/743,436/700,230/494,,,,,	35229673	11222,1778	2202	4298	6500	SO:0001583	missense	960	exon12			ATAGTATAACGCT	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.1436T>C	11.37:g.35229673T>C	ENSP00000398632:p.Ile479Thr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Missense_Mutation	SNP	ENST00000428726.2	37	CCDS7897.1	2002|2002	0.9166666666666666|0.9166666666666666	486|486	0.9878048780487805|0.9878048780487805	317|317	0.8756906077348067|0.8756906077348067	572|572	1.0|1.0	627|627	0.8271767810026385|0.8271767810026385	C|C	0.086|0.086	-1.175163|-1.175163	0.01646|0.01646	0.960036|0.960036	0.813634|0.813634	ENSG00000026508|ENSG00000026508	ENST00000415148;ENST00000433354;ENST00000449691;ENST00000437706;ENST00000360158;ENST00000428726;ENST00000433892;ENST00000531110;ENST00000278385;ENST00000533222;ENST00000528672|ENST00000527889;ENST00000525685	T;T;T;T;T;T;T;T;T;T;T|.	0.28666|.	1.6;1.6;1.6;1.6;3.03;1.6;2.5;1.6;2.5;1.6;1.6|.	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	0.208531|.	0.34223|.	N|.	0.004150|.	T|.	0.00012|.	0.0000|.	N|N	0.00104|0.00104	-2.125|-2.125	0.58432|0.58432	P|P	2.9999999999752447E-6|2.9999999999752447E-6	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|.	0.42015|.	-0.9476|.	9|.	0.11485|.	T|.	0.65|.	-21.1811|-21.1811	11.8073|11.8073	0.52163|0.52163	0.0:0.9202:0.0:0.0798|0.0:0.9202:0.0:0.0798	rs1467558;rs17375486;rs17856114;rs52835516;rs56467545;rs61254354;rs1467558|rs1467558;rs17375486;rs17856114;rs52835516;rs56467545;rs61254354;rs1467558	230;436;479|.	P16070-10;P16070-4;P16070|.	.;.;CD44_HUMAN|.	T|Q	436;480;436;479;230;479;230;191;66;105;87|155;183	ENSP00000389830:I436T;ENSP00000414567:I480T;ENSP00000391008:I436T;ENSP00000403990:I479T;ENSP00000353280:I230T;ENSP00000398632:I479T;ENSP00000392331:I230T;ENSP00000436549:I191T;ENSP00000278385:I66T;ENSP00000435321:I105T;ENSP00000431860:I87T|.	ENSP00000278385:I66T|.	I|X	+|+	2|1	0|0	CD44|CD44	35186249|35186249	0.889000|0.889000	0.30405|0.30405	0.601000|0.601000	0.28877|0.28877	0.012000|0.012000	0.07955|0.07955	2.089000|2.089000	0.41672|0.41672	1.638000|1.638000	0.50547|0.50547	-0.128000|-0.128000	0.14901|0.14901	ATA|TAA	T|0.086;C|0.914	0.914	strong		0.423	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
SLC9A7	84679	hgsc.bcm.edu	37	X	46618321	46618321	+	Silent	SNP	C	C	G	rs1056846	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:46618321C>G	ENST00000328306.4	-	1	169	c.144G>C	c.(142-144)gcG>gcC	p.A48A		NM_001257291.1|NM_032591.2	NP_001244220.1|NP_115980.1	Q96T83	SL9A7_HUMAN	solute carrier family 9, subfamily A (NHE7, cation proton antiporter 7), member 7	48					ion transport (GO:0006811)|potassium ion transmembrane transport (GO:0071805)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)	potassium:proton antiporter activity (GO:0015386)|protein homodimerization activity (GO:0042803)|sodium:proton antiporter activity (GO:0015385)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|skin(1)	21						TGCTGTCCTCCGCCGCCGCCC	0.731													G|||	2895	0.766887	0.7428	0.5101	3775	,	,		6012	0.6538		0.3549	False		,,,				2504	0.5552				p.A48A	Pancreas(118;454 1696 1930 13865 39976)	Atlas-SNP	.											.	SLC9A7	73	.	0			c.G144C						PASS	.	G		3476,346		1364,241,507,24,57	13.0	11.0	12.0		144	-7.6	0.3	X	dbSNP_86	12	2995,3723		473,1165,884,789,980	no	coding-synonymous	SLC9A7	NM_032591.1		1837,1406,1391,813,1037	GG,GC,G,CC,C		44.5817,9.0529,38.6053		48/726	46618321	6471,4069	2193	4291	6484	SO:0001819	synonymous_variant	84679	exon1			GTCCTCCGCCGCC	AF298591	CCDS14269.1, CCDS75967.1	Xp11.3	2013-05-22	2012-03-22		ENSG00000065923	ENSG00000065923		"""Solute carriers"""	17123	protein-coding gene	gene with protein product		300368	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 7"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 7"""			11279194	Standard	NM_001257291		Approved	NHE7	uc004dgv.2	Q96T83	OTTHUMG00000021428	ENST00000328306.4:c.144G>C	X.37:g.46618321C>G		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_001257291	O75827|Q5JXP9	Silent	SNP	ENST00000328306.4	37	CCDS14269.1																																																																																			C|0.279;G|0.721	0.721	strong		0.731	SLC9A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056370.1	NM_032591	
AKR1C3	8644	hgsc.bcm.edu	37	10	5141619	5141619	+	Missense_Mutation	SNP	A	A	G	rs61730879	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:5141619A>G	ENST00000380554.3	+	5	1200	c.548A>G	c.(547-549)aAg>aGg	p.K183R	AKR1C3_ENST00000605149.1_Missense_Mutation_p.K160R|AKR1C3_ENST00000439082.2_Missense_Mutation_p.K64R	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	183					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	CCAGGACTCAAGTACAAGCCT	0.512													A|||	7	0.00139776	0.0008	0.0029	5008	,	,		17607	0.0		0.004	False		,,,				2504	0.0				p.K183R		Atlas-SNP	.											.	AKR1C3	21	.	0			c.A548G						PASS	.						145.0	130.0	135.0					10																	5141619		2203	4300	6503	SO:0001583	missense	8644	exon5			GACTCAAGTACAA	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"""Aldo-keto reductases"""	386	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase X"", ""prostaglandin F synthase"", ""3-alpha hydroxysteroid dehydrogenase, type II"""	603966	"""hydroxysteroid (17-beta) dehydrogenase 5"", ""aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"""	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.548A>G	10.37:g.5141619A>G	ENSP00000369927:p.Lys183Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	123	65	0.528455	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	14.92	2.680782	0.47886	.	.	ENSG00000196139	ENST00000439082;ENST00000380554	T;T	0.25414	1.8;1.8	2.67	2.67	0.31697	NADP-dependent oxidoreductase domain (3);	0.000000	0.64402	D	0.000003	T	0.23846	0.0577	L	0.36672	1.1	0.42266	D	0.992032	B;B;B	0.22480	0.002;0.07;0.07	B;B;B	0.37239	0.018;0.244;0.244	T	0.08513	-1.0718	10	0.44086	T	0.13	.	8.7963	0.34881	1.0:0.0:0.0:0.0	.	64;183;183	B4DL37;P42330;Q2XPP3	.;AK1C3_HUMAN;.	R	64;183	ENSP00000401327:K64R;ENSP00000369927:K183R	ENSP00000369927:K183R	K	+	2	0	AKR1C3	5131619	1.000000	0.71417	0.997000	0.53966	0.929000	0.56500	5.877000	0.69675	0.992000	0.38840	0.402000	0.26972	AAG	A|0.997;G|0.001;T|0.002	0.001	strong		0.512	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
RSPH14	27156	hgsc.bcm.edu	37	22	23482483	23482483	+	Missense_Mutation	SNP	G	G	A	rs35211242	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:23482483G>A	ENST00000216036.4	-	2	321	c.125C>T	c.(124-126)aCg>aTg	p.T42M	RTDR1_ENST00000406876.1_Missense_Mutation_p.T42M	NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN		42			T -> M (in dbSNP:rs35211242). {ECO:0000269|PubMed:10607907}.							breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		TTTCTGCCTCGTCTGGAGGTC	0.562													G|||	413	0.0824681	0.0182	0.0879	5008	,	,		18478	0.0387		0.1471	False		,,,				2504	0.1442				p.T42M		Atlas-SNP	.											.	RTDR1	39	.	0			c.C125T						PASS	.	G	MET/THR	159,4247	107.3+/-145.7	4,151,2048	159.0	121.0	134.0		125	3.9	0.1	22	dbSNP_126	134	1340,7260	262.1+/-284.2	99,1142,3059	yes	missense	RTDR1	NM_014433.2	81	103,1293,5107	AA,AG,GG		15.5814,3.6087,11.5254	probably-damaging	42/349	23482483	1499,11507	2203	4300	6503	SO:0001583	missense	27156	exon2			TGCCTCGTCTGGA																												ENST00000216036.4:c.125C>T	22.37:g.23482483G>A	ENSP00000216036:p.Thr42Met	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_014433		Missense_Mutation	SNP	ENST00000216036.4	37	CCDS13803.1	174	0.07967032967032966	6	0.012195121951219513	32	0.08839779005524862	24	0.04195804195804196	112	0.14775725593667546	G	13.37	2.218034	0.39201	0.036087	0.155814	ENSG00000100218	ENST00000216036;ENST00000452757;ENST00000406876	T;T;T	0.52754	2.19;0.65;2.19	4.91	3.89	0.44902	Armadillo-like helical (1);Armadillo-type fold (1);	0.202525	0.40302	N	0.001127	T	0.00496	0.0016	M	0.78801	2.425	0.23923	P	0.99645841	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.21109	-1.0255	9	0.49607	T	0.09	-11.896	10.8955	0.47021	0.0924:0.0:0.9076:0.0	rs35211242;rs62220915	63;42	B7Z5X4;Q9UHP6	.;RTDR1_HUMAN	M	42;2;42	ENSP00000216036:T42M;ENSP00000391552:T2M;ENSP00000385567:T42M	ENSP00000216036:T42M	T	-	2	0	RTDR1	21812483	0.994000	0.37717	0.054000	0.19295	0.039000	0.13416	2.293000	0.43558	1.214000	0.43395	0.561000	0.74099	ACG	G|0.894;A|0.106	0.106	strong		0.562	RTDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319049.1		
C1QTNF6	114904	hgsc.bcm.edu	37	22	37581383	37581383	+	Missense_Mutation	SNP	C	C	T	rs7290488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:37581383C>T	ENST00000337843.2	-	2	239	c.164G>A	c.(163-165)gGc>gAc	p.G55D	C1QTNF6_ENST00000397110.2_Missense_Mutation_p.G55D|RP1-151B14.6_ENST00000419128.1_RNA|C1QTNF6_ENST00000470655.1_5'UTR|C1QTNF6_ENST00000255836.6_5'Flank	NM_031910.3	NP_114116.3	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	36					protein heterotrimerization (GO:0070208)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(1)|large_intestine(2)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)	11						CCGTTGGCAGCCGCTGGCCAC	0.642													C|||	394	0.0786741	0.062	0.1138	5008	,	,		18212	0.0		0.1958	False		,,,				2504	0.0368				p.G55D		Atlas-SNP	.											.	C1QTNF6	32	.	0			c.G164A						PASS	.	C	ASP/GLY,ASP/GLY	367,4039	178.7+/-207.4	20,327,1856	34.0	34.0	34.0		164,164	1.0	0.0	22	dbSNP_116	34	1518,7082	283.1+/-295.9	128,1262,2910	yes	missense,missense	C1QTNF6	NM_031910.3,NM_182486.1	94,94	148,1589,4766	TT,TC,CC		17.6512,8.3296,14.4933	benign,benign	55/279,55/279	37581383	1885,11121	2203	4300	6503	SO:0001583	missense	114904	exon2			TGGCAGCCGCTGG	AF329842	CCDS13943.1	22q13.1	2014-02-21			ENSG00000133466	ENSG00000133466			14343	protein-coding gene	gene with protein product		614910				12975309	Standard	NM_031910		Approved	CTRP6, ZACRP6	uc003aqy.1	Q9BXI9	OTTHUMG00000150538	ENST00000337843.2:c.164G>A	22.37:g.37581383C>T	ENSP00000338812:p.Gly55Asp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_182486	Q5H9G8|Q6ZRM7	Missense_Mutation	SNP	ENST00000337843.2	37	CCDS13943.1	210	0.09615384615384616	23	0.046747967479674794	48	0.13259668508287292	0	0.0	139	0.18337730870712401	C	8.652	0.898587	0.17686	0.083296	0.176512	ENSG00000133466	ENST00000397110;ENST00000337843	T;T	0.36340	1.26;1.26	4.49	1.05	0.20165	.	2.480080	0.02106	N	0.054378	T	0.00073	0.0002	L	0.51422	1.61	0.53005	P	4.0000000000040004E-5	P;B	0.35944	0.529;0.394	B;B	0.36666	0.23;0.115	T	0.03910	-1.0993	9	0.28530	T	0.3	.	1.764	0.02998	0.1574:0.4793:0.1624:0.2009	rs7290488;rs17812729;rs59032796;rs7290488	55;36	Q9BXI9-2;Q9BXI9	.;C1QT6_HUMAN	D	55	ENSP00000380299:G55D;ENSP00000338812:G55D	ENSP00000338812:G55D	G	-	2	0	C1QTNF6	35911329	0.002000	0.14202	0.004000	0.12327	0.406000	0.30931	0.303000	0.19210	-0.035000	0.13691	0.491000	0.48974	GGC	C|0.884;T|0.116	0.116	strong		0.642	C1QTNF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318807.1	NM_182486	
LACC1	144811	hgsc.bcm.edu	37	13	44457925	44457925	+	Missense_Mutation	SNP	A	A	G	rs3764147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:44457925A>G	ENST00000441843.1	+	4	1245	c.760A>G	c.(760-762)Atc>Gtc	p.I254V	LACC1_ENST00000325686.6_Missense_Mutation_p.I254V	NM_001128303.1	NP_001121775.1	Q8IV20	LACC1_HUMAN	laccase (multicopper oxidoreductase) domain containing 1	254			I -> V (in dbSNP:rs3764147). {ECO:0000269|PubMed:14702039}.														TTCCAATGACATCTGGATTAT	0.378													A|||	1532	0.305911	0.3048	0.3646	5008	,	,		15919	0.3472		0.2266	False		,,,				2504	0.3047				p.I254V		Atlas-SNP	.											.	.	.	.	0			c.A760G						PASS	.	A	VAL/ILE,VAL/ILE	1297,3109	437.2+/-344.9	200,897,1106	88.0	85.0	86.0	http://omim.org/entry/613407|http://www.ncbi.nlm.nih.gov/pubmed?term	760,760	1.9	0.8	13	dbSNP_107	86	1981,6619	347.4+/-326.6	236,1509,2555	yes	missense,missense	LACC1	NM_001128303.1,NM_153218.2	29,29	436,2406,3661	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	23.0349,29.4371,25.2038	benign,benign	254/431,254/431	44457925	3278,9728	2203	4300	6503	SO:0001583	missense	144811	exon4			AATGACATCTGGA	AK096044	CCDS9391.1	13q14.11	2012-05-11	2011-08-09	2011-08-09	ENSG00000179630	ENSG00000179630			26789	protein-coding gene	gene with protein product		613409	"""chromosome 13 open reading frame 31"""	C13orf31		16740638, 22504414	Standard	NM_153218		Approved	FLJ38725	uc010acg.3	Q8IV20	OTTHUMG00000016826	ENST00000441843.1:c.760A>G	13.37:g.44457925A>G	ENSP00000391747:p.Ile254Val	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	88	83	0.943182	NM_001128303	A2A3Z6|Q8N8X5	Missense_Mutation	SNP	ENST00000441843.1	37	CCDS9391.1	660	0.3021978021978022	161	0.32723577235772355	134	0.3701657458563536	184	0.32167832167832167	181	0.23878627968337732	A	1.113	-0.657608	0.03454	0.294371	0.230349	ENSG00000179630	ENST00000441843;ENST00000325686	T;T	0.33216	1.42;1.42	5.7	1.94	0.25998	.	0.235834	0.42548	N	0.000690	T	0.00012	0.0000	N	0.01257	-0.925	0.39694	P	0.028919999999999946	B	0.06786	0.001	B	0.04013	0.001	T	0.47156	-0.9139	9	0.02654	T	1	-11.666	8.8558	0.35227	0.3187:0.0:0.6813:0.0	rs3764147;rs61264110;rs3764147	254	Q8IV20	LACC1_HUMAN	V	254	ENSP00000391747:I254V;ENSP00000317619:I254V	ENSP00000317619:I254V	I	+	1	0	LACC1	43355925	1.000000	0.71417	0.815000	0.32552	0.795000	0.44927	2.664000	0.46783	0.041000	0.15688	-0.242000	0.12053	ATC	A|0.722;G|0.278	0.278	strong		0.378	LACC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044726.3	NM_153218	
C2CD3	26005	hgsc.bcm.edu	37	11	73785326	73785326	+	Silent	SNP	T	T	C	rs4453265	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:73785326T>C	ENST00000334126.7	-	24	5149	c.4923A>G	c.(4921-4923)gtA>gtG	p.V1641V	C2CD3_ENST00000313663.7_Silent_p.V1641V			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1641	C2 2.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TTGCTCTTTCTACTAGGATGC	0.532													T|||	2259	0.451078	0.4312	0.4798	5008	,	,		20957	0.4425		0.4692	False		,,,				2504	0.4479				p.V1641V		Atlas-SNP	.											.	C2CD3	288	.	0			c.A4923G						PASS	.	T		1833,2567	534.0+/-373.9	369,1095,736	106.0	89.0	95.0		4923	1.6	1.0	11	dbSNP_111	95	4033,4553	555.8+/-386.7	982,2069,1242	yes	coding-synonymous	C2CD3	NM_015531.4		1351,3164,1978	CC,CT,TT		46.9718,41.6591,45.1717		1641/1964	73785326	5866,7120	2200	4293	6493	SO:0001819	synonymous_variant	26005	exon24			TCTTTCTACTAGG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.4923A>G	11.37:g.73785326T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	185	185	1	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Silent	SNP	ENST00000334126.7	37																																																																																				T|0.543;C|0.457	0.457	strong		0.532	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
POLR2A	5430	hgsc.bcm.edu	37	17	7399866	7399866	+	Silent	SNP	G	G	A	rs2301609	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7399866G>A	ENST00000322644.6	+	4	870	c.471G>A	c.(469-471)ggG>ggA	p.G157G	POLR2A_ENST00000572844.1_Silent_p.G157G	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	157					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				GCGAGGGTGGGGAGGAGATGG	0.532													G|||	859	0.171526	0.2186	0.0994	5008	,	,		19352	0.0278		0.1849	False		,,,				2504	0.2935				p.G157G		Atlas-SNP	.											.	POLR2A	157	.	0			c.G471A						PASS	.	G		913,3493	352.8+/-311.9	90,733,1380	143.0	148.0	146.0		471	-0.5	1.0	17	dbSNP_100	146	1798,6802	323.7+/-316.1	221,1356,2723	no	coding-synonymous	POLR2A	NM_000937.4		311,2089,4103	AA,AG,GG		20.907,20.7217,20.8442		157/1971	7399866	2711,10295	2203	4300	6503	SO:0001819	synonymous_variant	5430	exon4			GGGTGGGGAGGAG			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.471G>A	17.37:g.7399866G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	121	57	0.471074	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			G|0.810;A|0.190	0.190	strong		0.532	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
OR1L1	26737	hgsc.bcm.edu	37	9	125424507	125424507	+	Silent	SNP	A	A	C	rs70156	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:125424507A>C	ENST00000373686.1	+	1	663	c.663A>C	c.(661-663)tcA>tcC	p.S221S	OR1L1_ENST00000309623.1_Silent_p.S171S			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17						TCTGTGCCTCAAATGTCATCC	0.438													.|||	2253	0.44988	0.7292	0.3213	5008	,	,		25158	0.5089		0.2147	False		,,,				2504	0.3446				p.S171S		Atlas-SNP	.											.	OR1L1	54	.	0			c.A513C						PASS	.	C		2877,1529	484.2+/-360.0	940,997,266	315.0	287.0	297.0		513	-1.0	0.0	9	dbSNP_79	297	1710,6890	737.8+/-407.0	179,1352,2769	no	coding-synonymous	OR1L1	NM_001005236.3		1119,2349,3035	CC,CA,AA		19.8837,34.7027,35.2683		171/311	125424507	4587,8419	2203	4300	6503	SO:0001819	synonymous_variant	26737	exon1			TGCCTCAAATGTC		CCDS35127.1, CCDS35127.2	9q33.2	2013-09-20			ENSG00000173679	ENSG00000173679		"""GPCR / Class A : Olfactory receptors"""	8213	protein-coding gene	gene with protein product				OR1L2			Standard	NM_001005236		Approved	OR9-C	uc022bmz.1	Q8NH94	OTTHUMG00000020618	ENST00000373686.1:c.663A>C	9.37:g.125424507A>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	198	100	0.50505	NM_001005236	Q5T7Z3|Q6IFN2	Silent	SNP	ENST00000373686.1	37																																																																																				A|0.606;C|0.394	0.394	strong		0.438	OR1L1-201	KNOWN	basic	protein_coding	protein_coding			
ETV3L	440695	hgsc.bcm.edu	37	1	157062739	157062739	+	Missense_Mutation	SNP	C	C	G	rs12136960	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:157062739C>G	ENST00000454449.2	-	5	1072	c.788G>C	c.(787-789)gGg>gCg	p.G263A		NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	263	Pro-rich.		G -> A (in dbSNP:rs12136960).		cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Hepatocellular(266;0.158)	Prostate(1639;0.184)				CTTAAAAGCCCCTGGGAGCTG	0.657													C|||	767	0.153155	0.1044	0.1311	5008	,	,		15435	0.2133		0.2048	False		,,,				2504	0.1196				p.G263A		Atlas-SNP	.											.	ETV3L	73	.	0			c.G788C						PASS	.	C	ALA/GLY	501,3903		31,439,1732	21.0	25.0	24.0		788	0.9	0.0	1	dbSNP_120	24	1694,6902		199,1296,2803	yes	missense	ETV3L	NM_001004341.2	60	230,1735,4535	GG,GC,CC		19.7068,11.376,16.8846	possibly-damaging	263/362	157062739	2195,10805	2202	4298	6500	SO:0001583	missense	440695	exon5			AAAGCCCCTGGGA	AK131392	CCDS30893.1	1q23.1	2013-09-24	2008-09-12		ENSG00000253831	ENSG00000253831			33834	protein-coding gene	gene with protein product			"""ets variant gene 3-like"""				Standard	NM_001004341		Approved	FLJ16478	uc001fqq.2	Q6ZN32	OTTHUMG00000041325	ENST00000454449.2:c.788G>C	1.37:g.157062739C>G	ENSP00000430271:p.Gly263Ala	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	77	32	0.415584	NM_001004341		Missense_Mutation	SNP	ENST00000454449.2	37	CCDS30893.1	400	0.18315018315018314	50	0.1016260162601626	57	0.1574585635359116	133	0.23251748251748253	160	0.21108179419525067	C	11.23	1.577096	0.28092	0.11376	0.197068	ENSG00000253831	ENST00000454449	T	0.35789	1.29	3.96	0.879	0.19155	.	.	.	.	.	T	0.08670	0.0215	L	0.29908	0.895	0.80722	P	0.0	P	0.40970	0.734	B	0.34652	0.187	T	0.14476	-1.0471	8	0.32370	T	0.25	.	6.7402	0.23431	0.0:0.5821:0.0:0.4179	rs12136960;rs12136960	263	Q6ZN32	ETV3L_HUMAN	A	263	ENSP00000430271:G263A	ENSP00000430271:G263A	G	-	2	0	ETV3L	155329363	0.002000	0.14202	0.001000	0.08648	0.046000	0.14306	1.049000	0.30392	0.316000	0.23135	0.491000	0.48974	GGG	C|0.828;G|0.172	0.172	strong		0.657	ETV3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099024.2	NM_001004341	
ZNF248	57209	hgsc.bcm.edu	37	10	38120642	38120642	+	Silent	SNP	C	C	T	rs1208731	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:38120642C>T	ENST00000395867.3	-	6	2191	c.1641G>A	c.(1639-1641)ccG>ccA	p.P547P	ZNF248_ENST00000494133.1_Intron|AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000357328.4_Silent_p.P547P	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	547					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TACACTCATACGGCTTCTCCC	0.438													C|||	160	0.0319489	0.0023	0.0648	5008	,	,		18392	0.0		0.1034	False		,,,				2504	0.0082				p.P547P		Atlas-SNP	.											.	ZNF248	61	.	0			c.G1641A						PASS	.	C		80,4326	69.8+/-107.6	1,78,2124	125.0	113.0	117.0		1641	0.5	1.0	10	dbSNP_87	117	758,7842	181.6+/-230.3	32,694,3574	no	coding-synonymous	ZNF248	NM_021045.1		33,772,5698	TT,TC,CC		8.814,1.8157,6.4432		547/580	38120642	838,12168	2203	4300	6503	SO:0001819	synonymous_variant	57209	exon6			CTCATACGGCTTC	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"""Zinc fingers, C2H2-type"", ""-"""	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.1641G>A	10.37:g.38120642C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_001267597	Q8NDV8|Q9UMP3	Silent	SNP	ENST00000395867.3	37	CCDS7194.1																																																																																			C|0.936;T|0.064	0.064	strong		0.438	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045	
NAA15	80155	hgsc.bcm.edu	37	4	140278638	140278638	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:140278638T>G	ENST00000296543.5	+	11	1509	c.1186T>G	c.(1186-1188)Tac>Gac	p.Y396D	NAA15_ENST00000398947.1_Missense_Mutation_p.Y396D	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	396					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)	p.Y396H(1)		NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TGCTTTGGAGTACATAAATAC	0.338																																					p.Y396D		Atlas-SNP	.											NAA15,NS,carcinoma,0,1	NAA15	88	1	1	Substitution - Missense(1)	endometrium(1)	c.T1186G						PASS	.						83.0	76.0	78.0					4																	140278638		1854	4087	5941	SO:0001583	missense	80155	exon11			TTGGAGTACATAA	AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"""N(alpha)-acetyltransferase subunits"""	30782	protein-coding gene	gene with protein product		608000	"""NMDA receptor regulated 1"""	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.1186T>G	4.37:g.140278638T>G	ENSP00000296543:p.Tyr396Asp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	133	55	0.413534	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Missense_Mutation	SNP	ENST00000296543.5	37	CCDS43270.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.795402	0.90453	.	.	ENSG00000164134	ENST00000296543;ENST00000544077;ENST00000398947	T;T	0.49720	0.77;0.77	5.71	5.71	0.89125	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.72518	0.3470	M	0.90082	3.085	0.80722	D	1	P	0.46220	0.874	P	0.59889	0.865	T	0.77327	-0.2629	10	0.54805	T	0.06	-6.2825	15.994	0.80228	0.0:0.0:0.0:1.0	.	396	Q9BXJ9	NAA15_HUMAN	D	396;270;396	ENSP00000296543:Y396D;ENSP00000381920:Y396D	ENSP00000296543:Y396D	Y	+	1	0	NAA15	140498088	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	5.959000	0.70339	2.168000	0.68352	0.528000	0.53228	TAC	.	.	none		0.338	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175	
MOV10L1	54456	hgsc.bcm.edu	37	22	50572473	50572473	+	Missense_Mutation	SNP	G	G	A	rs2340601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50572473G>A	ENST00000262794.5	+	14	2031	c.1948G>A	c.(1948-1950)Gtc>Atc	p.V650I	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Missense_Mutation_p.V650I|MOV10L1_ENST00000540615.1_Missense_Mutation_p.V630I|MOV10L1_ENST00000545383.1_Missense_Mutation_p.V650I	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	650			V -> I (in dbSNP:rs2340601).		ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.V650I(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		ACTTGAACACGTCATCCACTT	0.338													G|||	1242	0.248003	0.1218	0.3847	5008	,	,		16603	0.254		0.2356	False		,,,				2504	0.3282				p.V650I		Atlas-SNP	.											MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	1	Substitution - Missense(1)	stomach(1)	c.G1948A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	667,3739	284.0+/-277.4	55,557,1591	118.0	106.0	110.0		1948,1888,1948	5.8	0.0	22	dbSNP_100	110	2049,6551	358.1+/-331.0	246,1557,2497	yes	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	29,29,29	301,2114,4088	AA,AG,GG		23.8256,15.1384,20.8827	possibly-damaging,possibly-damaging,possibly-damaging	650/1166,630/1166,650/1212	50572473	2716,10290	2203	4300	6503	SO:0001583	missense	54456	exon14			GAACACGTCATCC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1948G>A	22.37:g.50572473G>A	ENSP00000262794:p.Val650Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	133	77	0.578947	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	530	0.24267399267399267	54	0.10975609756097561	123	0.3397790055248619	181	0.31643356643356646	172	0.22691292875989447	G	14.38	2.518497	0.44763	0.151384	0.238256	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;T;D	0.85411	-1.79;-1.79;-1.38;-1.98	5.78	5.78	0.91487	.	0.317187	0.38326	N	0.001735	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.999999999875443	P;P;P	0.47962	0.903;0.743;0.619	B;B;B	0.36766	0.232;0.117;0.117	T	0.04178	-1.0971	9	0.30854	T	0.27	-27.556	19.6307	0.95700	0.0:0.0:1.0:0.0	rs2340601;rs3736687;rs17248063;rs52826881;rs61128514;rs2340601	630;650;650	F5H403;A8MXC6;Q9BXT6	.;.;M10L1_HUMAN	I	650;650;650;630	ENSP00000438978:V650I;ENSP00000262794:V650I;ENSP00000379199:V650I;ENSP00000438542:V630I	ENSP00000262794:V650I	V	+	1	0	MOV10L1	48914600	0.645000	0.27286	0.011000	0.14972	0.979000	0.70002	4.303000	0.59098	2.730000	0.93505	0.655000	0.94253	GTC	G|0.776;A|0.224	0.224	strong		0.338	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
ATF7	11016	hgsc.bcm.edu	37	12	53925573	53925573	+	Silent	SNP	C	C	T	rs139241958	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53925573C>T	ENST00000548446.2	-	9	1027	c.915G>A	c.(913-915)caG>caA	p.Q305Q	ATF7_ENST00000420353.2_Silent_p.Q294Q|ATF7_ENST00000415113.1_Silent_p.Q273Q|RP11-793H13.10_ENST00000591834.1_Silent_p.Q294Q|ATF7_ENST00000328463.7_Silent_p.Q305Q|ATF7_ENST00000456903.4_Silent_p.Q294Q			P17544	ATF7_HUMAN	activating transcription factor 7	305					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9					Pseudoephedrine(DB00852)	GGATGAGAATCTGGCTCTGCT	0.517													C|||	27	0.00539137	0.0008	0.0144	5008	,	,		14364	0.0		0.0149	False		,,,				2504	0.001				p.Q294Q		Atlas-SNP	.											.	ATF7	51	.	0			c.G882A						PASS	.	C	,,	14,4046		0,14,2016	68.0	76.0	73.0		915,819,882	5.4	1.0	12	dbSNP_134	73	131,8225		2,127,4049	no	coding-synonymous,coding-synonymous,coding-synonymous	ATF7	NM_001130059.1,NM_001130060.1,NM_006856.2	,,	2,141,6065	TT,TC,CC		1.5677,0.3448,1.1678	,,	305/495,273/463,294/484	53925573	145,12271	2030	4178	6208	SO:0001819	synonymous_variant	11016	exon9			GAGAATCTGGCTC	X52943	CCDS44906.1, CCDS58238.1	12q13	2013-01-10				ENSG00000170653		"""basic leucine zipper proteins"""	792	protein-coding gene	gene with protein product		606371				1694576, 11278933	Standard	NM_006856		Approved	ATFA	uc001sdz.3	P17544	OTTHUMG00000169776	ENST00000548446.2:c.915G>A	12.37:g.53925573C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_006856	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Silent	SNP	ENST00000548446.2	37																																																																																				C|0.991;T|0.009	0.009	strong		0.517	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059	
FAM66B	100128890	hgsc.bcm.edu	37	8	7190935	7190935	+	lincRNA	SNP	G	G	A	rs117479685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:7190935G>A	ENST00000606573.1	-	0	703									family with sequence similarity 66, member B																		CAAAGCTCAAGAAGTCCAGTG	0.483													g|||	16	0.00319489	0.0008	0.0029	5008	,	,		18653	0.001		0.005	False		,,,				2504	0.0072				p.E343K		Atlas-SNP	.											.	.	.	.	0			c.G1027A						PASS	.																																					401447	exon1			GCTCAAGAAGTCC			8p23.1	2013-07-05			ENSG00000215374	ENSG00000215374		"""Long non-coding RNAs"""	28890	non-coding RNA	RNA, long non-coding							Standard	NR_027423		Approved				OTTHUMG00000165383		8.37:g.7190935G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	169	88	0.52071	NM_001256873		Missense_Mutation	SNP	ENST00000606573.1	37																																																																																				G|0.996;A|0.004	0.004	strong		0.483	FAM66B-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470344.1	NR_027423	
PLCG2	5336	hgsc.bcm.edu	37	16	81942028	81942028	+	Missense_Mutation	SNP	C	C	G	rs72824905	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81942028C>G	ENST00000359376.3	+	17	1779	c.1565C>G	c.(1564-1566)cCc>cGc	p.P522R		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	522					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						CAGGATATACCCCCTACAGAA	0.537													C|||	14	0.00279553	0.0	0.0029	5008	,	,		20275	0.0		0.0109	False		,,,				2504	0.001				p.P522R		Atlas-SNP	.											.	PLCG2	276	.	0			c.C1565G						PASS	.	C	ARG/PRO	3,3799		0,3,1898	56.0	56.0	56.0		1565	4.8	1.0	16	dbSNP_130	56	73,8147		0,73,4037	yes	missense	PLCG2	NM_002661.3	103	0,76,5935	GG,GC,CC		0.8881,0.0789,0.6322	benign	522/1266	81942028	76,11946	1901	4110	6011	SO:0001583	missense	5336	exon17			ATATACCCCCTAC		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1565C>G	16.37:g.81942028C>G	ENSP00000352336:p.Pro522Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	61	21	0.344262	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	6.031	0.373996	0.11409	7.89E-4	0.008881	ENSG00000197943	ENST00000359376	T	0.65364	-0.15	4.85	4.85	0.62838	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);SH2 motif (1);	0.750593	0.12934	N	0.427117	T	0.36248	0.0960	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.25710	-1.0124	10	0.49607	T	0.09	.	11.0904	0.48113	0.2379:0.7621:0.0:0.0	.	389;522	B4E3H3;P16885	.;PLCG2_HUMAN	R	522	ENSP00000352336:P522R	ENSP00000352336:P522R	P	+	2	0	PLCG2	80499529	0.014000	0.17966	0.979000	0.43373	0.335000	0.28730	2.624000	0.46444	2.249000	0.74217	0.655000	0.94253	CCC	C|0.993;G|0.007	0.007	strong		0.537	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
FRY	10129	hgsc.bcm.edu	37	13	32785086	32785086	+	Silent	SNP	G	G	A	rs798981	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:32785086G>A	ENST00000380250.3	+	34	5002	c.4506G>A	c.(4504-4506)gaG>gaA	p.E1502E		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1502						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		AGCAGACAGAGCCCGTGAACC	0.502													G|||	1731	0.345647	0.4191	0.4409	5008	,	,		18738	0.1657		0.4404	False		,,,				2504	0.2669				p.E1502E		Atlas-SNP	.											FRY,NS,carcinoma,0,1	FRY	312	1	0			c.G4506A						PASS	.	G		1620,2314		350,920,697	78.0	83.0	81.0		4506	2.9	1.0	13	dbSNP_86	81	3414,4924		695,2024,1450	no	coding-synonymous	FRY	NM_023037.2		1045,2944,2147	AA,AG,GG		40.9451,41.1795,41.0202		1502/3014	32785086	5034,7238	1967	4169	6136	SO:0001819	synonymous_variant	10129	exon34			GACAGAGCCCGTG	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.4506G>A	13.37:g.32785086G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	52	48	0.923077	NM_023037	Q9Y3N6	Silent	SNP	ENST00000380250.3	37	CCDS41875.1																																																																																			G|0.632;A|0.368	0.368	strong		0.502	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
IRAK4	51135	hgsc.bcm.edu	37	12	44180295	44180295	+	Missense_Mutation	SNP	G	G	A	rs4251545	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:44180295G>A	ENST00000448290.2	+	11	1353	c.1282G>A	c.(1282-1284)Gct>Act	p.A428T	IRAK4_ENST00000551736.1_Missense_Mutation_p.A428T|IRAK4_ENST00000431837.1_Missense_Mutation_p.A304T|IRAK4_ENST00000440781.2_Missense_Mutation_p.A304T	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	428	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in dbSNP:rs4251545). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.5}.		cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		TTCAGTTGAAGCTATGTACTC	0.284													g|||	854	0.170527	0.3169	0.1455	5008	,	,		13391	0.127		0.0865	False		,,,				2504	0.1217				p.A428T		Atlas-SNP	.											.	IRAK4	77	.	0			c.G1282A						PASS	.	A	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	1200,3206	407.8+/-334.4	154,892,1157	68.0	79.0	75.0		1282,910,910,910,1282	-0.3	0.1	12	dbSNP_111	75	847,7743	190.8+/-237.2	35,777,3483	yes	missense,missense,missense,missense,missense	IRAK4	NM_001114182.2,NM_001145256.1,NM_001145257.1,NM_001145258.1,NM_016123.3	58,58,58,58,58	189,1669,4640	AA,AG,GG		9.8603,27.2356,15.751	benign,benign,benign,benign,benign	428/461,304/337,304/337,304/337,428/461	44180295	2047,10949	2203	4295	6498	SO:0001583	missense	51135	exon11			GTTGAAGCTATGT	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		ENST00000448290.2:c.1282G>A	12.37:g.44180295G>A	ENSP00000390651:p.Ala428Thr	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	161	85	0.52795	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	37	CCDS8744.1	328	0.15018315018315018	160	0.3252032520325203	51	0.1408839779005525	55	0.09615384615384616	62	0.08179419525065963	g	8.196	0.797029	0.16327	0.272356	0.098603	ENSG00000198001	ENST00000440781;ENST00000431837;ENST00000448290;ENST00000551736	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	6.02	-0.286	0.12862	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.615280	0.18370	N	0.143300	T	0.00012	0.0000	L	0.37630	1.12	0.54753	P	1.2000000000012001E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.24333	-1.0163	9	0.35671	T	0.21	-0.8847	7.4103	0.27014	0.6553:0.1054:0.2393:0.0	rs4251545;rs52833385;rs57239220;rs4251545	428	Q9NWZ3	IRAK4_HUMAN	T	304;304;428;428	ENSP00000408734:A304T;ENSP00000390327:A304T;ENSP00000390651:A428T;ENSP00000446490:A428T	ENSP00000390327:A304T	A	+	1	0	IRAK4	42466562	0.972000	0.33761	0.062000	0.19696	0.991000	0.79684	0.757000	0.26433	-0.274000	0.09232	-0.127000	0.14921	GCT	G|0.843;A|0.157	0.157	strong		0.284	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1		
PPIC	5480	hgsc.bcm.edu	37	5	122364538	122364538	+	Missense_Mutation	SNP	T	T	C	rs34341374	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:122364538T>C	ENST00000306442.4	-	3	372	c.257A>G	c.(256-258)aAg>aGg	p.K86R		NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)	86	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.		K -> R (in dbSNP:rs34341374). {ECO:0000269|Ref.2}.		protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	ACGATGAAACTTGCTTCCTTT	0.383													C|||	153	0.0305511	0.0492	0.0231	5008	,	,		20464	0.002		0.0368	False		,,,				2504	0.0337				p.K86R	Ovarian(99;690 1502 20765 45543 49568)	Atlas-SNP	.											.	PPIC	18	.	0			c.A257G						PASS	.	C	ARG/LYS	198,4208	808.3+/-415.9	5,188,2010	146.0	115.0	126.0		257	-10.4	0.0	5	dbSNP_126	126	154,8446	812.4+/-407.1	2,150,4148	yes	missense	PPIC	NM_000943.4	26	7,338,6158	CC,CT,TT		1.7907,4.4939,2.7064	benign	86/213	122364538	352,12654	2203	4300	6503	SO:0001583	missense	5480	exon3			TGAAACTTGCTTC	S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.257A>G	5.37:g.122364538T>C	ENSP00000303057:p.Lys86Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	145	61	0.42069	NM_000943	A4LBB5	Missense_Mutation	SNP	ENST00000306442.4	37	CCDS4133.1	63	0.028846153846153848	22	0.044715447154471545	12	0.03314917127071823	3	0.005244755244755245	26	0.03430079155672823	C	11.84	1.760030	0.31137	0.044939	0.017907	ENSG00000168938	ENST00000306442	T	0.22945	1.93	5.22	-10.4	0.00318	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);Peptidyl-prolyl cis-trans isomerase, cyclophilin-type, conserved site (1);	0.684498	0.15758	N	0.246077	T	0.01730	0.0055	N	0.11870	0.19	0.21762	N	0.999551	B	0.09022	0.002	B	0.11329	0.006	T	0.06197	-1.0840	10	0.23302	T	0.38	.	6.4392	0.21841	0.0767:0.262:0.4504:0.2108	rs34341374	86	P45877	PPIC_HUMAN	R	86	ENSP00000303057:K86R	ENSP00000303057:K86R	K	-	2	0	PPIC	122392437	0.218000	0.23608	0.006000	0.13384	0.812000	0.45895	-0.415000	0.07106	-3.724000	0.00115	-2.872000	0.00099	AAG	T|0.971;C|0.029	0.029	strong		0.383	PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250898.2	NM_000943	
ATRNL1	26033	hgsc.bcm.edu	37	10	117486763	117486763	+	Silent	SNP	G	G	T	rs2254619	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:117486763G>T	ENST00000355044.3	+	27	3927	c.3801G>T	c.(3799-3801)ctG>ctT	p.L1267L	ATRNL1_ENST00000423111.2_Silent_p.L318L|ATRNL1_ENST00000303745.7_Silent_p.L60L	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1267					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TCCAGCAACTGCTTCGAGAAC	0.428													G|||	1007	0.201078	0.0983	0.2565	5008	,	,		17727	0.0387		0.4195	False		,,,				2504	0.2434				p.L1267L		Atlas-SNP	.											.	ATRNL1	219	.	0			c.G3801T						PASS	.	G		610,3796	268.9+/-268.7	38,534,1631	46.0	44.0	45.0		3801	2.9	1.0	10	dbSNP_100	45	3538,5062	514.7+/-378.5	709,2120,1471	no	coding-synonymous	ATRNL1	NM_207303.2		747,2654,3102	TT,TG,GG		41.1395,13.8448,31.893		1267/1380	117486763	4148,8858	2203	4300	6503	SO:0001819	synonymous_variant	26033	exon27			GCAACTGCTTCGA	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3801G>T	10.37:g.117486763G>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1																																																																																			G|0.735;T|0.265	0.265	strong		0.428	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	
LONRF2	164832	hgsc.bcm.edu	37	2	100916315	100916315	+	Silent	SNP	A	A	G	rs11123823	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:100916315A>G	ENST00000393437.3	-	5	1770	c.1131T>C	c.(1129-1131)ggT>ggC	p.G377G	LONRF2_ENST00000409647.1_Silent_p.G134G	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	377							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)	p.G377G(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						CAAAGTGTAGACCCAGTATAA	0.408													A|||	1456	0.290735	0.028	0.2392	5008	,	,		13944	0.4851		0.4851	False		,,,				2504	0.2822				p.G377G		Atlas-SNP	.											LONRF2,NS,carcinoma,0,1	LONRF2	62	1	1	Substitution - coding silent(1)	stomach(1)	c.T1131C						PASS	.	A		472,3934	222.6+/-239.4	26,420,1757	64.0	63.0	63.0		1131	0.6	0.0	2	dbSNP_120	63	3989,4611	555.0+/-386.6	941,2107,1252	no	coding-synonymous	LONRF2	NM_198461.3		967,2527,3009	GG,GA,AA		46.3837,10.7127,34.2996		377/755	100916315	4461,8545	2203	4300	6503	SO:0001819	synonymous_variant	164832	exon5			GTGTAGACCCAGT	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"""RING-type (C3HC4) zinc fingers"""	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1131T>C	2.37:g.100916315A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	127	50	0.393701	NM_198461	B9A006|Q6ZSR4	Silent	SNP	ENST00000393437.3	37	CCDS2046.2																																																																																			A|0.664;G|0.336	0.336	strong		0.408	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461	
ERAP1	51752	hgsc.bcm.edu	37	5	96117555	96117555	+	Silent	SNP	C	C	T	rs61745685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96117555C>T	ENST00000443439.2	-	16	2355	c.2289G>A	c.(2287-2289)ctG>ctA	p.L763L	ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000512856.1_RNA|ERAP1_ENST00000296754.3_Silent_p.L763L	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	763					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		CGTCGACAGGCAGGCTATAGA	0.458													C|||	261	0.0521166	0.0605	0.0605	5008	,	,		17353	0.003		0.0924	False		,,,				2504	0.044				p.L763L		Atlas-SNP	.											.	ERAP1	59	.	0			c.G2289A						PASS	.	C	,,	310,4096	168.0+/-198.9	10,290,1903	49.0	50.0	49.0		2289,2289,2289	-0.5	0.5	5	dbSNP_129	49	727,7873	177.2+/-226.9	34,659,3607	no	coding-synonymous,coding-synonymous,coding-synonymous	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	,,	44,949,5510	TT,TC,CC		8.4535,7.0359,7.9732	,,	763/942,763/942,763/949	96117555	1037,11969	2203	4300	6503	SO:0001819	synonymous_variant	51752	exon16			GACAGGCAGGCTA	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.2289G>A	5.37:g.96117555C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Silent	SNP	ENST00000443439.2	37	CCDS47250.1																																																																																			C|0.923;T|0.077	0.077	strong		0.458	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
HDGF	3068	hgsc.bcm.edu	37	1	156713558	156713558	+	Missense_Mutation	SNP	G	G	A	rs4399146	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156713558G>A	ENST00000357325.5	-	5	916	c.602C>T	c.(601-603)cCc>cTc	p.P201L	HDGF_ENST00000368209.5_Missense_Mutation_p.P194L|HDGF_ENST00000416666.2_Missense_Mutation_p.P169L|MRPL24_ENST00000368211.4_5'Flank|HDGF_ENST00000537739.1_Missense_Mutation_p.P201L|HDGF_ENST00000465180.1_5'UTR|HDGF_ENST00000368206.5_Missense_Mutation_p.P217L|MRPL24_ENST00000361531.2_5'Flank	NM_004494.2	NP_004485.1	P51858	HDGF_HUMAN	hepatoma-derived growth factor	201	Glu-rich.		P -> L (in dbSNP:rs4399146). {ECO:0000269|PubMed:14702039}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription corepressor binding (GO:0001222)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)		GGGCTCAGAGGGGGTGCTATT	0.602													G|||	962	0.192093	0.0666	0.2219	5008	,	,		17389	0.125		0.334	False		,,,				2504	0.2638				p.P217L		Atlas-SNP	.											.	HDGF	60	.	0			c.C650T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	499,3907	224.6+/-240.7	31,437,1735	36.0	38.0	37.0		650,581,602	1.7	1.0	1	dbSNP_111	37	2966,5634	436.8+/-358.4	533,1900,1867	yes	missense,missense,missense	HDGF	NM_001126050.1,NM_001126051.1,NM_004494.2	98,98,98	564,2337,3602	AA,AG,GG		34.4884,11.3255,26.6416	benign,benign,benign	217/257,194/234,201/241	156713558	3465,9541	2203	4300	6503	SO:0001583	missense	3068	exon5			TCAGAGGGGGTGC	D16431	CCDS1156.1, CCDS44247.1, CCDS44248.1	1q23.1	2013-10-14	2010-03-19		ENSG00000143321	ENSG00000143321			4856	protein-coding gene	gene with protein product	"""high-mobility group protein 1-like"""	600339	"""hepatoma-derived growth factor (high-mobility group protein 1-like)"""			8833162	Standard	NM_004494		Approved	HMG1L2	uc001fpy.4	P51858	OTTHUMG00000041295	ENST00000357325.5:c.602C>T	1.37:g.156713558G>A	ENSP00000349878:p.Pro201Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_001126050	B3KU21|D3DVC9|Q5SZ07|Q5SZ08|Q5SZ09	Missense_Mutation	SNP	ENST00000357325.5	37	CCDS1156.1	449	0.20558608058608058	26	0.052845528455284556	99	0.27348066298342544	73	0.12762237762237763	251	0.3311345646437995	G	10.57	1.385885	0.25031	0.113255	0.344884	ENSG00000143321	ENST00000357325;ENST00000368209;ENST00000537739;ENST00000416666;ENST00000368206;ENST00000406805	T;T;T;T;T	0.39406	1.67;1.15;1.67;1.22;1.08	4.67	1.7	0.24286	.	0.957193	0.08579	U	0.924918	T	0.17534	0.0421	L	0.50333	1.59	0.31954	P	0.609266	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.16512	-1.0400	9	0.52906	T	0.07	-1.8131	6.7766	0.23622	0.0948:0.343:0.5621:0.0	rs4399146;rs4399146	176;217;194;201	B7Z958;Q5SZ07;Q5SZ08;P51858	.;.;.;HDGF_HUMAN	L	201;194;201;169;217;224	ENSP00000349878:P201L;ENSP00000357192:P194L;ENSP00000443120:P201L;ENSP00000416752:P169L;ENSP00000357189:P217L	ENSP00000349878:P201L	P	-	2	0	HDGF	154980182	0.750000	0.28316	0.985000	0.45067	0.759000	0.43091	0.827000	0.27421	0.192000	0.20272	-0.366000	0.07423	CCC	G|0.790;A|0.210	0.210	strong		0.602	HDGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098946.1	NM_004494	
RGS17	26575	hgsc.bcm.edu	37	6	153365100	153365100	+	Silent	SNP	A	A	C	rs2295230	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:153365100A>C	ENST00000367225.2	-	1	78	c.54T>G	c.(52-54)gcT>gcG	p.A18A	RGS17_ENST00000206262.1_Silent_p.A18A			Q9UGC6	RGS17_HUMAN	regulator of G-protein signaling 17	18					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(2)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	14		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)		GGTTTCCAGGAGCTTGAGACA	0.488													C|||	2495	0.498203	0.6051	0.379	5008	,	,		16658	0.6319		0.2932	False		,,,				2504	0.5112				p.A18A	Esophageal Squamous(78;500 1236 6775 24364 49058)	Atlas-SNP	.											.	RGS17	32	.	0			c.T54G						PASS	.	C		2424,1982	556.0+/-379.4	646,1132,425	175.0	174.0	174.0		54	-10.6	0.1	6	dbSNP_100	174	2561,6039	691.2+/-404.5	376,1809,2115	no	coding-synonymous	RGS17	NM_012419.4		1022,2941,2540	CC,CA,AA		29.7791,44.9841,38.3285		18/211	153365100	4985,8021	2203	4300	6503	SO:0001819	synonymous_variant	26575	exon2			TCCAGGAGCTTGA	AF202257	CCDS5244.1	6q25-q26	2009-05-29	2007-08-14		ENSG00000091844	ENSG00000091844		"""Regulators of G-protein signaling"""	14088	protein-coding gene	gene with protein product		607191	"""regulator of G-protein signalling 17"""			10419452	Standard	NM_012419		Approved	RGSZ2, RGS-17	uc003qpm.3	Q9UGC6	OTTHUMG00000015858	ENST00000367225.2:c.54T>G	6.37:g.153365100A>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	132	129	0.977273	NM_012419	Q5TF49|Q8TD61|Q9UJS8	Silent	SNP	ENST00000367225.2	37	CCDS5244.1																																																																																			A|0.590;C|0.409;T|0.000	0.409	strong		0.488	RGS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042773.2		
CMBL	134147	hgsc.bcm.edu	37	5	10282396	10282396	+	Silent	SNP	A	A	G	rs10067744	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:10282396A>G	ENST00000296658.3	-	5	891	c.471T>C	c.(469-471)atT>atC	p.I157I	CMBL_ENST00000510532.1_Intron	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	157						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)	p.I157I(1)		endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						AATCCTTGACAATGCCTGAAA	0.453													G|||	2153	0.429912	0.4811	0.4366	5008	,	,		17088	0.0754		0.7197	False		,,,				2504	0.4233				p.I157I		Atlas-SNP	.											CMBL,NS,carcinoma,0,1	CMBL	24	1	1	Substitution - coding silent(1)	stomach(1)	c.T471C						PASS	.	G		2190,2216	590.6+/-387.4	557,1076,570	81.0	81.0	81.0		471	-5.4	0.0	5	dbSNP_119	81	6039,2561	417.1+/-352.3	2107,1825,368	no	coding-synonymous	CMBL	NM_138809.3		2664,2901,938	GG,GA,AA		29.7791,49.7049,36.7292		157/246	10282396	8229,4777	2203	4300	6503	SO:0001819	synonymous_variant	134147	exon5			CTTGACAATGCCT		CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	"""carboxymethylenebutenolidase-like (Pseudomonas)"""			3804974, 20177059	Standard	NM_138809		Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.471T>C	5.37:g.10282396A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	174	82	0.471264	NM_138809	D3DTC7|Q8TED6	Silent	SNP	ENST00000296658.3	37	CCDS3878.1																																																																																			A|0.476;G|0.524	0.524	strong		0.453	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253689.1	NM_138809	
OR51Q1	390061	hgsc.bcm.edu	37	11	5444353	5444353	+	Missense_Mutation	SNP	T	T	C	rs2647573	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5444353T>C	ENST00000300778.4	+	1	1013	c.923T>C	c.(922-924)tTc>tCc	p.F308S	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	308			F -> S (in dbSNP:rs2647573).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGTTAAATTTCCTTTCCCTC	0.393													T|||	2272	0.453674	0.2799	0.3991	5008	,	,		20869	0.7024		0.3986	False		,,,				2504	0.5276				p.F308S		Atlas-SNP	.											.	OR51Q1	79	.	0			c.T923C						PASS	.	T	SER/PHE	1324,3078		204,916,1081	43.0	42.0	43.0		923	5.0	0.0	11	dbSNP_100	43	3352,5242		675,2002,1620	yes	missense	OR51Q1	NM_001004757.2	155	879,2918,2701	CC,CT,TT		39.004,30.0772,35.9803	benign	308/318	5444353	4676,8320	2201	4297	6498	SO:0001583	missense	390061	exon1			TAAATTTCCTTTC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.923T>C	11.37:g.5444353T>C	ENSP00000300778:p.Phe308Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_001004757	B2RNN1	Missense_Mutation	SNP	ENST00000300778.4	37	CCDS31381.1	960	0.43956043956043955	139	0.28252032520325204	147	0.40607734806629836	391	0.6835664335664335	283	0.3733509234828496	T	12.00	1.807088	0.31961	0.300772	0.39004	ENSG00000167360	ENST00000300778	T	0.37235	1.21	5.0	5.0	0.66597	.	0.335344	0.20267	N	0.095752	T	0.00012	0.0000	N	0.20483	0.58	0.80722	P	0.0	B	0.23937	0.094	B	0.20767	0.031	T	0.33240	-0.9876	9	0.59425	D	0.04	.	12.3207	0.54983	0.0:0.0:0.0:1.0	rs2647573;rs52795273;rs57515914;rs2647573	308	Q8NH59	O51Q1_HUMAN	S	308	ENSP00000300778:F308S	ENSP00000300778:F308S	F	+	2	0	OR51Q1	5400929	0.005000	0.15991	0.006000	0.13384	0.035000	0.12851	1.616000	0.36933	2.133000	0.65898	0.311000	0.20440	TTC	T|0.608;C|0.392	0.392	strong		0.393	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
MICAL3	57553	hgsc.bcm.edu	37	22	18301693	18301693	+	Missense_Mutation	SNP	T	T	C	rs8135914	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:18301693T>C	ENST00000441493.2	-	26	4086	c.3734A>G	c.(3733-3735)cAg>cGg	p.Q1245R		NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1245	Pro-rich.			Q -> R (in Ref. 5; BAA74842). {ECO:0000305}.	actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		CACGGGTGGCTGGGGCTGCGG	0.682													C|||	1277	0.254992	0.3812	0.2161	5008	,	,		12128	0.0893		0.331	False		,,,				2504	0.2045				p.Q1245R		Atlas-SNP	.											.	MICAL3	53	.	0			c.A3734G						PASS	.	C	ARG/GLN	1292,2596		229,834,881	11.0	15.0	14.0		3734	-4.2	0.0	22	dbSNP_116	14	2684,5550		476,1732,1909	yes	missense	MICAL3	NM_015241.2	43	705,2566,2790	CC,CT,TT		32.5966,33.2305,32.7999	benign	1245/2003	18301693	3976,8146	1944	4117	6061	SO:0001583	missense	57553	exon26			GGTGGCTGGGGCT	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.3734A>G	22.37:g.18301693T>C	ENSP00000416015:p.Gln1245Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	37	CCDS46659.1	548|548	0.2509157509157509|0.2509157509157509	180|180	0.36585365853658536|0.36585365853658536	86|86	0.23756906077348067|0.23756906077348067	45|45	0.07867132867132867|0.07867132867132867	237|237	0.31266490765171506|0.31266490765171506	C|C	5.042|5.042	0.193465|0.193465	0.09599|0.09599	0.332305|0.332305	0.325966|0.325966	ENSG00000093100|ENSG00000093100	ENST00000441493|ENST00000252134	T|.	0.62232|.	0.04|.	4.73|4.73	-4.25|-4.25	0.03766|0.03766	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.41822|0.41822	-0.9487|-0.9487	8|4	0.10902|.	T|.	0.67|.	.|.	6.364|6.364	0.21445|0.21445	0.1275:0.3101:0.463:0.0994|0.1275:0.3101:0.463:0.0994	rs8135914;rs61587067|rs8135914;rs61587067	1245|.	Q7RTP6|.	MICA3_HUMAN|.	R|G	1245|227	ENSP00000416015:Q1245R|.	ENSP00000416015:Q1245R|.	Q|S	-|-	2|1	0|0	XXbac-B461K10.4|XXbac-B461K10.4	16681693|16681693	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.645000|-1.645000	0.02000|0.02000	-1.684000|-1.684000	0.01443|0.01443	-2.475000|-2.475000	0.00201|0.00201	CAG|AGC	T|0.774;C|0.226	0.226	strong		0.682	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
OR14I1	401994	hgsc.bcm.edu	37	1	248845356	248845356	+	Missense_Mutation	SNP	G	G	T	rs41311583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248845356G>T	ENST00000342623.3	-	1	273	c.250C>A	c.(250-252)Ctg>Atg	p.L84M		NM_001004734.1	NP_001004734.1	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I, member 1	84			L -> M (in dbSNP:rs41311583).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L84M(1)		NS(1)|breast(4)|large_intestine(2)|lung(24)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	35						CTGCGAGTCAGGGAGTTACGG	0.478													T|||	659	0.131589	0.1649	0.0951	5008	,	,		22143	0.128		0.1113	False		,,,				2504	0.137				p.L84M		Atlas-SNP	.											OR14I1,NS,carcinoma,0,1	OR14I1	64	1	1	Substitution - Missense(1)	stomach(1)	c.C250A						scavenged	.	T	MET/LEU	673,3733		44,585,1574	123.0	105.0	112.0		250	-2.5	0.0	1	dbSNP_127	112	962,7638		55,852,3393	yes	missense	OR14I1	NM_001004734.1	15	99,1437,4967	TT,TG,GG		11.186,15.2746,12.5711	possibly-damaging	84/312	248845356	1635,11371	2203	4300	6503	SO:0001583	missense	401994	exon1			GAGTCAGGGAGTT		CCDS31125.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000189181	ENSG00000189181		"""GPCR / Class A : Olfactory receptors"""	19575	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BU, member 1"""	OR5BU1P, OR5BU1			Standard	NM_001004734		Approved		uc001ieu.1	A6ND48	OTTHUMG00000040378	ENST00000342623.3:c.250C>A	1.37:g.248845356G>T	ENSP00000339726:p.Leu84Met	Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	193	95	0.492228	NM_001004734		Missense_Mutation	SNP	ENST00000342623.3	37	CCDS31125.1	285	0.1304945054945055	86	0.17479674796747968	38	0.10497237569060773	73	0.12762237762237763	88	0.11609498680738786	.	12.84	2.059125	0.36373	0.152746	0.11186	ENSG00000189181	ENST00000342623	T	0.01422	4.91	3.48	-2.55	0.06288	GPCR, rhodopsin-like superfamily (1);	0.205916	0.23414	N	0.048434	T	0.00012	0.0000	M	0.78049	2.395	0.80722	P	0.0	P	0.47545	0.897	P	0.51324	0.666	T	0.25187	-1.0139	9	0.66056	D	0.02	.	6.1146	0.20120	0.1323:0.0:0.3002:0.5675	rs41311583;rs61834347	84	A6ND48	O14I1_HUMAN	M	84	ENSP00000339726:L84M	ENSP00000339726:L84M	L	-	1	2	OR14I1	246911979	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-6.278000	0.00072	-0.723000	0.04915	-1.751000	0.00678	CTG	G|0.876;T|0.124	0.124	strong		0.478	OR14I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097128.1	NM_001004734	
DSCC1	79075	hgsc.bcm.edu	37	8	120850521	120850521	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:120850521C>T	ENST00000313655.4	-	8	1265	c.1051G>A	c.(1051-1053)Gaa>Aaa	p.E351K		NM_024094.2	NP_076999.2	Q9BVC3	DCC1_HUMAN	DNA replication and sister chromatid cohesion 1	351					DNA replication (GO:0006260)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			NS(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|pancreas(1)	9	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GCAATATCTTCTTCTGTCCAC	0.338																																					p.E351K		Atlas-SNP	.											.	DSCC1	40	.	0			c.G1051A						PASS	.						82.0	86.0	85.0					8																	120850521		2203	4300	6503	SO:0001583	missense	79075	exon8			TATCTTCTTCTGT		CCDS6330.1	8q24.12	2013-05-24	2013-05-24		ENSG00000136982	ENSG00000136982			24453	protein-coding gene	gene with protein product	"""defective in sister chromatid cohesion homolog 1 (S. cerevisiae)"""	613203	"""defective in sister chromatid cohesion 1 homolog (S. cerevisiae)"""			12766176, 20826785	Standard	NM_024094		Approved	DCC1, hDCC1, MGC5528	uc003yov.3	Q9BVC3	OTTHUMG00000165010	ENST00000313655.4:c.1051G>A	8.37:g.120850521C>T	ENSP00000322180:p.Glu351Lys	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	127	16	0.125984	NM_024094	Q969N5	Missense_Mutation	SNP	ENST00000313655.4	37	CCDS6330.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.870756	0.72065	.	.	ENSG00000136982	ENST00000313655	T	0.46819	0.86	4.82	4.82	0.62117	.	0.212150	0.48767	D	0.000170	T	0.38321	0.1036	L	0.41079	1.255	0.50039	D	0.99984	P	0.35468	0.503	B	0.30029	0.11	T	0.19976	-1.0289	10	0.19590	T	0.45	-21.7187	18.2534	0.90011	0.0:1.0:0.0:0.0	.	351	Q9BVC3	DCC1_HUMAN	K	351	ENSP00000322180:E351K	ENSP00000322180:E351K	E	-	1	0	DSCC1	120919702	1.000000	0.71417	0.999000	0.59377	0.880000	0.50808	5.923000	0.70045	2.372000	0.80975	0.563000	0.77884	GAA	.	.	none		0.338	DSCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381443.1	NM_024094	
HOXC9	3225	hgsc.bcm.edu	37	12	54394497	54394497	+	Silent	SNP	C	C	T	rs2241820	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:54394497C>T	ENST00000303450.4	+	1	595	c.525C>T	c.(523-525)gcC>gcT	p.A175A	HOXC-AS1_ENST00000512427.1_RNA|HOXC-AS1_ENST00000505700.1_RNA|RP11-834C11.12_ENST00000513209.1_Intron|HOXC9_ENST00000504557.1_Intron|HOXC9_ENST00000508190.1_Silent_p.A175A	NM_006897.1	NP_008828.1	P31274	HXC9_HUMAN	homeobox C9	175					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(3)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14						AGGAGAAGGCCGACCTGGACC	0.692													C|||	2895	0.578075	0.4667	0.5346	5008	,	,		12030	0.7609		0.6014	False		,,,				2504	0.547				p.A175A		Atlas-SNP	.											.	HOXC9	25	.	0			c.C525T						PASS	.	C		1809,1381		539,731,325	6.0	7.0	7.0		525	1.1	1.0	12	dbSNP_98	7	4221,2551		1360,1501,525	no	coding-synonymous	HOXC9	NM_006897.1		1899,2232,850	TT,TC,CC		37.6698,43.2915,39.47		175/261	54394497	6030,3932	1595	3386	4981	SO:0001819	synonymous_variant	3225	exon1			GAAGGCCGACCTG		CCDS8869.1	12q13.13	2011-06-20	2005-12-22			ENSG00000180806		"""Homeoboxes / ANTP class : HOXL subclass"""	5130	protein-coding gene	gene with protein product		142971	"""homeo box C9"""	HOX3, HOX3B		1973146	Standard	NM_006897		Approved		uc001seq.3	P31274		ENST00000303450.4:c.525C>T	12.37:g.54394497C>T		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_006897	B2RCN7|Q9H1I0	Silent	SNP	ENST00000303450.4	37	CCDS8869.1																																																																																			C|0.388;T|0.612	0.612	strong		0.692	HOXC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358958.1		
APBA3	9546	hgsc.bcm.edu	37	19	3752515	3752515	+	Silent	SNP	G	G	A	rs61735536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:3752515G>A	ENST00000316757.3	-	8	1586	c.1386C>T	c.(1384-1386)gcC>gcT	p.A462A	AC005954.3_ENST00000591962.1_RNA|AC005954.4_ENST00000586503.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	462	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		CGCGGACAGCGGCCTGGCACG	0.716													G|||	861	0.171925	0.0613	0.2104	5008	,	,		14902	0.1825		0.1421	False		,,,				2504	0.3139				p.A462A		Atlas-SNP	.											APBA3,NS,carcinoma,0,1	APBA3	28	1	0			c.C1386T						PASS	.	G		238,4008		3,232,1888	6.0	8.0	7.0		1386	-8.4	0.0	19	dbSNP_129	7	869,7349		28,813,3268	no	coding-synonymous	APBA3	NM_004886.3		31,1045,5156	AA,AG,GG		10.5743,5.6053,8.8816		462/576	3752515	1107,11357	2123	4109	6232	SO:0001819	synonymous_variant	9546	exon8			GACAGCGGCCTGG	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.1386C>T	19.37:g.3752515G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			G|0.844;A|0.156	0.156	strong		0.716	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552717	43552717	+	Silent	SNP	G	G	C	rs147243132	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43552717G>C	ENST00000430334.3	-	4	805	c.672C>G	c.(670-672)tcC>tcG	p.S224S	PLEKHM1_ENST00000421073.2_Silent_p.S135S	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	224					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CTGAAGAATGGGAAATGGAAT	0.562													G|||	412	0.0822684	0.0378	0.1556	5008	,	,		21763	0.001		0.1958	False		,,,				2504	0.0573				p.S224S		Atlas-SNP	.											PLEKHM1,caecum,carcinoma,-1,1	PLEKHM1	69	1	0			c.C672G						PASS	.						25.0	23.0	24.0					17																	43552717		2202	4294	6496	SO:0001819	synonymous_variant	9842	exon4			AGAATGGGAAATG	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.672C>G	17.37:g.43552717G>C		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	274	109	0.39781	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			G|0.873;C|0.127	0.127	strong		0.562	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
EMR3	84658	hgsc.bcm.edu	37	19	14758168	14758168	+	Missense_Mutation	SNP	G	G	A	rs34226397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14758168G>A	ENST00000253673.5	-	8	807	c.707C>T	c.(706-708)gCc>gTc	p.A236V	EMR3_ENST00000599900.1_Missense_Mutation_p.A21V|EMR3_ENST00000443157.2_Missense_Mutation_p.A110V|EMR3_ENST00000344373.4_Missense_Mutation_p.A184V	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	236			A -> V (in dbSNP:rs34226397).		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						AAAGGCAATGGCACTGGGACC	0.353													G|||	1493	0.298123	0.3691	0.2104	5008	,	,		21054	0.2738		0.3091	False		,,,				2504	0.2781				p.A236V		Atlas-SNP	.											.	EMR3	99	.	0			c.C707T						PASS	.	G	VAL/ALA	1628,2778	501.8+/-365.1	298,1032,873	70.0	68.0	69.0		707	3.9	0.1	19	dbSNP_126	69	2623,5977	423.5+/-354.4	410,1803,2087	yes	missense	EMR3	NM_032571.3	64	708,2835,2960	AA,AG,GG		30.5,36.9496,32.6849	benign	236/653	14758168	4251,8755	2203	4300	6503	SO:0001583	missense	84658	exon8			GCAATGGCACTGG	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"""-"", ""GPCR / Class B : Orphans"""	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.707C>T	19.37:g.14758168G>A	ENSP00000253673:p.Ala236Val	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	123	68	0.552846	NM_032571		Missense_Mutation	SNP	ENST00000253673.5	37	CCDS12315.1	647	0.29624542124542125	196	0.3983739837398374	88	0.2430939226519337	141	0.2465034965034965	222	0.2928759894459103	G	0.010	-1.771288	0.00645	0.369496	0.305	ENSG00000131355	ENST00000443157;ENST00000253673;ENST00000344373	T;T;T	0.42900	0.96;3.23;3.23	3.94	3.94	0.45596	.	.	.	.	.	T	0.00012	0.0000	L	0.48986	1.54	0.80722	P	0.0	B;B;B	0.23854	0.092;0.028;0.023	B;B;B	0.22753	0.017;0.015;0.041	T	0.40739	-0.9547	8	0.27082	T	0.32	.	11.5753	0.50858	0.0:0.0:1.0:0.0	rs34226397	110;184;236	E7EW83;Q9BY15-2;Q9BY15	.;.;EMR3_HUMAN	V	110;236;184	ENSP00000396208:A110V;ENSP00000253673:A236V;ENSP00000340758:A184V	ENSP00000253673:A236V	A	-	2	0	EMR3	14619168	0.148000	0.22702	0.108000	0.21378	0.026000	0.11368	2.331000	0.43894	1.753000	0.51906	0.644000	0.83932	GCC	G|0.679;A|0.321	0.321	strong		0.353	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571	
USP45	85015	hgsc.bcm.edu	37	6	99956560	99956560	+	Missense_Mutation	SNP	T	T	C	rs7744845	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:99956560T>C	ENST00000327681.6	-	3	731	c.199A>G	c.(199-201)Aaa>Gaa	p.K67E	USP45_ENST00000369233.2_Missense_Mutation_p.K67E|USP45_ENST00000392738.2_5'UTR|USP45_ENST00000500704.2_Missense_Mutation_p.K67E|USP45_ENST00000369231.3_Missense_Mutation_p.K67E|USP45_ENST00000369232.2_5'UTR|USP45_ENST00000329966.6_Missense_Mutation_p.K67E|USP45_ENST00000472914.2_Missense_Mutation_p.K67E	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	67			K -> E (in dbSNP:rs7744845). {ECO:0000269|PubMed:15489334}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.K67E(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		CTTCTTTCTTTTAAACATTCT	0.373													T|||	1652	0.329872	0.0635	0.3501	5008	,	,		18487	0.5546		0.327	False		,,,				2504	0.4468				p.K67E		Atlas-SNP	.											USP45,NS,carcinoma,0,1	USP45	56	1	1	Substitution - Missense(1)	stomach(1)	c.A199G						PASS	.	T	GLU/LYS	483,3921	223.6+/-240.1	33,417,1752	96.0	92.0	93.0		199	5.3	1.0	6	dbSNP_116	93	2502,6098	410.3+/-350.1	365,1772,2163	yes	missense	USP45	NM_001080481.1	56	398,2189,3915	CC,CT,TT		29.093,10.9673,22.9545	possibly-damaging	67/815	99956560	2985,10019	2202	4300	6502	SO:0001583	missense	85015	exon3			TTTCTTTTAAACA	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"""Ubiquitin-specific peptidases"""	20080	protein-coding gene	gene with protein product			"""ubiquitin specific protease 45"""			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.199A>G	6.37:g.99956560T>C	ENSP00000333376:p.Lys67Glu	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	115	69	0.6	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	37	CCDS34501.1	687	0.31456043956043955	39	0.07926829268292683	108	0.2983425414364641	291	0.5087412587412588	249	0.32849604221635886	T	24.0	4.478488	0.84747	0.109673	0.29093	ENSG00000123552	ENST00000500704;ENST00000327681;ENST00000369233;ENST00000329966;ENST00000472914;ENST00000369231	T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99	5.35	5.35	0.76521	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (2);	0.150538	0.56097	D	0.000024	T	0.58736	0.2143	M	0.86651	2.83	0.19775	P	0.9999570881	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.62324	-0.6878	9	0.22109	T	0.4	.	14.9824	0.71321	0.0:0.0:0.0:1.0	rs7744845;rs17845068;rs17857850;rs60315569;rs7744845	67;67	D6RBV3;Q70EL2	.;UBP45_HUMAN	E	67	ENSP00000424372:K67E;ENSP00000333376:K67E;ENSP00000358236:K67E;ENSP00000330540:K67E;ENSP00000423993:K67E;ENSP00000358234:K67E	ENSP00000333376:K67E	K	-	1	0	USP45	100063281	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.207000	0.77899	2.036000	0.60181	0.402000	0.26972	AAA	T|0.734;C|0.266	0.266	strong		0.373	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929	
TBC1D32	221322	hgsc.bcm.edu	37	6	121625945	121625945	+	Missense_Mutation	SNP	A	A	G	rs79040695	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:121625945A>G	ENST00000398212.2	-	6	774	c.725T>C	c.(724-726)tTg>tCg	p.L242S	TBC1D32_ENST00000275159.6_Missense_Mutation_p.L242S	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	242					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TGGAGAAAGCAAAAATGTCTG	0.303													G|||	273	0.0545128	0.034	0.1196	5008	,	,		16158	0.124		0.0109	False		,,,				2504	0.0092				p.L242S		Atlas-SNP	.											.	C6orf170	146	.	0			c.T725C						PASS	.	G	SER/LEU	107,3489		3,101,1694	68.0	68.0	68.0		725	4.9	0.8	6	dbSNP_131	68	95,8033		0,95,3969	yes	missense	C6orf170	NM_152730.4	145	3,196,5663	GG,GA,AA		1.1688,2.9755,1.723	benign	242/1258	121625945	202,11522	1798	4064	5862	SO:0001583	missense	221322	exon6			GAAAGCAAAAATG	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.725T>C	6.37:g.121625945A>G	ENSP00000381270:p.Leu242Ser	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	300	149	0.496667	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	143	0.06547619047619048	24	0.04878048780487805	34	0.09392265193370165	75	0.13111888111888112	10	0.013192612137203167	G	1.750	-0.489592	0.04352	0.029755	0.011688	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.13901	2.55;2.55	4.93	4.93	0.64822	.	0.285462	0.33813	N	0.004535	T	0.00998	0.0033	N	0.00554	-1.385	0.52501	P	4.899999999996574E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43426	-0.9392	9	0.02654	T	1	-9.7811	13.545	0.61697	0.0757:0.0:0.9243:0.0	.	242	Q96NH3	BROMI_HUMAN	S	242	ENSP00000275159:L242S;ENSP00000381270:L242S	ENSP00000275159:L242S	L	-	2	0	C6orf170	121667644	1.000000	0.71417	0.838000	0.33150	0.388000	0.30384	5.087000	0.64480	1.077000	0.40990	-0.134000	0.14843	TTG	A|0.954;G|0.046	0.046	strong		0.303	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
UBP1	7342	hgsc.bcm.edu	37	3	33458266	33458266	+	Missense_Mutation	SNP	T	T	C	rs3736563	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33458266T>C	ENST00000283629.3	-	3	855	c.326A>G	c.(325-327)aAt>aGt	p.N109S	UBP1_ENST00000283628.5_Missense_Mutation_p.N109S|UBP1_ENST00000447368.2_Missense_Mutation_p.N109S|RNU7-110P_ENST00000516891.1_RNA	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	109			N -> S (in dbSNP:rs3736563). {ECO:0000269|PubMed:8114710}.		angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						TAATTTTCCATTGATCTCAGG	0.294													C|||	2399	0.479034	0.5333	0.5605	5008	,	,		18916	0.6091		0.3141	False		,,,				2504	0.3834				p.N109S		Atlas-SNP	.											.	UBP1	42	.	0			c.A326G						PASS	.	C	SER/ASN,SER/ASN,SER/ASN	2363,2043	566.7+/-382.0	610,1143,450	104.0	107.0	106.0		326,326,326	4.0	1.0	3	dbSNP_107	106	2423,6175	697.0+/-404.9	332,1759,2208	yes	missense,missense,missense	UBP1	NM_001128160.1,NM_001128161.1,NM_014517.4	46,46,46	942,2902,2658	CC,CT,TT		28.181,46.3686,36.8041	benign,benign,benign	109/505,109/541,109/541	33458266	4786,8218	2203	4299	6502	SO:0001583	missense	7342	exon3			TTTCCATTGATCT	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.326A>G	3.37:g.33458266T>C	ENSP00000283629:p.Asn109Ser	Somatic	487	0	0		WXS	Illumina HiSeq	Phase_I	454	238	0.524229	NM_001128160	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	37	CCDS2659.1	993	0.45467032967032966	253	0.5142276422764228	182	0.5027624309392266	309	0.5402097902097902	249	0.32849604221635886	C	2.681	-0.275386	0.05679	0.536314	0.28181	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628;ENST00000456378	T;T;T;T	0.16324	2.35;2.35;2.35;2.35	5.73	3.95	0.45737	CP2 transcription factor (1);	0.144057	0.64402	N	0.000005	T	0.00012	0.0000	N	0.03608	-0.345	0.44247	P	0.002905999999999964	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.44590	-0.9318	9	0.07325	T	0.83	-11.4831	2.3834	0.04360	0.113:0.4797:0.1756:0.2318	rs3736563;rs57275094;rs3736563	109;109	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	S	109	ENSP00000283629:N109S;ENSP00000395558:N109S;ENSP00000283628:N109S;ENSP00000401614:N109S	ENSP00000283628:N109S	N	-	2	0	UBP1	33433270	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	1.041000	0.30291	0.464000	0.27142	-0.119000	0.15052	AAT	T|0.585;C|0.415	0.415	strong		0.294	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517	
EXOSC8	11340	hgsc.bcm.edu	37	13	37580139	37580139	+	Silent	SNP	G	G	A	rs1127446	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:37580139G>A	ENST00000389704.3	+	6	586	c.321G>A	c.(319-321)caG>caA	p.Q107Q	EXOSC8_ENST00000489088.1_3'UTR	NM_181503.2	NP_852480.1	Q96B26	EXOS8_HUMAN	exosome component 8	107					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)			biliary_tract(1)|breast(1)|kidney(2)|pancreas(1)|prostate(1)|skin(1)	7		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)		TGGCTAGCCAGTTCATTGCAG	0.413													G|||	2071	0.413538	0.0817	0.4236	5008	,	,		14507	0.7232		0.3797	False		,,,				2504	0.5706				p.Q107Q		Atlas-SNP	.											.	EXOSC8	16	.	0			c.G321A						PASS	.	G		624,3782	268.6+/-268.5	47,530,1626	92.0	87.0	89.0		321	4.2	1.0	13	dbSNP_86	89	3428,5172	505.0+/-376.3	692,2044,1564	no	coding-synonymous	EXOSC8	NM_181503.2		739,2574,3190	AA,AG,GG		39.8605,14.1625,31.1549		107/277	37580139	4052,8954	2203	4300	6503	SO:0001819	synonymous_variant	11340	exon6			TAGCCAGTTCATT	AF025438	CCDS31958.1	13q13.1	2010-05-07			ENSG00000120699	ENSG00000120699	3.1.13.-		17035	protein-coding gene	gene with protein product	"""CBP-interacting protein 3"", ""Opa interacting protein 2"""	606019				9466265, 11929972	Standard	NM_181503		Approved	OIP2, RRP43, bA421P11.3, Rrp43p, EAP2, p9, CIP3	uc001uwa.3	Q96B26	OTTHUMG00000016742	ENST00000389704.3:c.321G>A	13.37:g.37580139G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	87	82	0.942529	NM_181503	O43480|Q5TBA5	Silent	SNP	ENST00000389704.3	37	CCDS31958.1																																																																																			G|0.659;A|0.341	0.341	strong		0.413	EXOSC8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044535.2	NM_181503	
ERC2	26059	hgsc.bcm.edu	37	3	56114861	56114861	+	Missense_Mutation	SNP	T	T	C	rs12488237	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:56114861T>C	ENST00000288221.6	-	7	1880	c.1625A>G	c.(1624-1626)aAt>aGt	p.N542S		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	542			N -> S (in dbSNP:rs12488237).			cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		CTGAAGAACATTGATTTTTCT	0.378													T|||	270	0.0539137	0.0023	0.1715	5008	,	,		19603	0.0764		0.0437	False		,,,				2504	0.0276				p.N542S		Atlas-SNP	.											.	ERC2	221	.	0			c.A1625G						PASS	.	T	SER/ASN	44,3718		1,42,1838	163.0	148.0	153.0		1625	5.8	1.0	3	dbSNP_120	153	456,7748		10,436,3656	yes	missense	ERC2	NM_015576.1	46	11,478,5494	CC,CT,TT		5.5583,1.1696,4.1785	possibly-damaging	542/958	56114861	500,11466	1881	4102	5983	SO:0001583	missense	26059	exon7			AGAACATTGATTT	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.1625A>G	3.37:g.56114861T>C	ENSP00000288221:p.Asn542Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	37	CCDS46851.1	119|119	0.05448717948717949|0.05448717948717949	3|3	0.006097560975609756|0.006097560975609756	38|38	0.10497237569060773|0.10497237569060773	45|45	0.07867132867132867|0.07867132867132867	33|33	0.04353562005277045|0.04353562005277045	T|T	17.29|17.29	3.352024|3.352024	0.61183|0.61183	0.011696|0.011696	0.055583|0.055583	ENSG00000187672|ENSG00000187672	ENST00000492584|ENST00000288221	.|T	.|0.43294	.|0.95	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.02455|0.02455	0.0075|0.0075	L|L	0.43598|0.43598	1.365|1.365	0.19945|0.19945	P|P	0.9999419556|0.9999419556	.|D	.|0.57257	.|0.979	.|D	.|0.71414	.|0.973	T|T	0.02004|0.02004	-1.1231|-1.1231	4|9	.|0.21540	.|T	.|0.41	-23.3184|-23.3184	16.1581|16.1581	0.81680|0.81680	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs12488237;rs17216538;rs52792613;rs58091640;rs12488237|rs12488237;rs17216538;rs52792613;rs58091640;rs12488237	.|542	.|O15083	.|ERC2_HUMAN	V|S	181|542	.|ENSP00000288221:N542S	.|ENSP00000288221:N542S	M|N	-|-	1|2	0|0	ERC2|ERC2	56089901|56089901	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.201000|6.201000	0.72124|0.72124	2.220000|2.220000	0.72140|0.72140	0.477000|0.477000	0.44152|0.44152	ATG|AAT	T|0.944;C|0.056	0.056	strong		0.378	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576	
ZNF23	7571	hgsc.bcm.edu	37	16	71487952	71487952	+	Silent	SNP	G	G	T	rs11641967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:71487952G>T	ENST00000393539.2	-	4	840	c.27C>A	c.(25-27)gcC>gcA	p.A9A	ZNF23_ENST00000564528.1_5'Flank|ZNF23_ENST00000357254.4_Silent_p.A9A|ZNF23_ENST00000428724.2_5'UTR|AC010547.9_ENST00000561908.1_3'UTR|ZNF23_ENST00000358700.2_Silent_p.A9A|ZNF23_ENST00000497160.1_Silent_p.A9A|ZNF23_ENST00000417828.1_Silent_p.A9A|ZNF23_ENST00000539742.1_Intron	NM_145911.1	NP_666016.1	P17027	ZNF23_HUMAN	zinc finger protein 23	9	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(14)|stomach(1)|urinary_tract(1)	29		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		TACCCAGGGAGGCCACATTCC	0.552													G|||	438	0.0874601	0.0098	0.0706	5008	,	,		19013	0.0516		0.162	False		,,,				2504	0.1646				p.A9A		Atlas-SNP	.											.	ZNF23	65	.	0			c.C27A						PASS	.	G		157,4239	107.8+/-146.2	5,147,2046	151.0	122.0	132.0		27	1.5	1.0	16	dbSNP_120	132	1480,7120	281.3+/-295.0	138,1204,2958	no	coding-synonymous	ZNF23	NM_145911.1		143,1351,5004	TT,TG,GG		17.2093,3.5714,12.5962		9/644	71487952	1637,11359	2198	4300	6498	SO:0001819	synonymous_variant	7571	exon4			CAGGGAGGCCACA	X52347	CCDS10900.1	16q22.2	2013-03-28	2012-07-12		ENSG00000167377	ENSG00000167377		"""Zinc fingers, C2H2-type"""	13023	protein-coding gene	gene with protein product		194527	"""zinc finger protein 359"""	ZNF359			Standard	NM_145911		Approved	KOX16, Zfp612, ZNF612	uc002faf.3	P17027	OTTHUMG00000176797	ENST00000393539.2:c.27C>A	16.37:g.71487952G>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	86	50	0.581395	NM_145911	Q8NDP5|Q96IT3|Q9UG42	Silent	SNP	ENST00000393539.2	37	CCDS10900.1																																																																																			G|0.883;T|0.117	0.117	strong		0.552	ZNF23-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268985.23	NM_145911	
LY75	4065	hgsc.bcm.edu	37	2	160673526	160673526	+	Missense_Mutation	SNP	A	A	G	rs2059696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160673526A>G	ENST00000263636.4	-	30	4198	c.4171T>C	c.(4171-4173)Tat>Cat	p.Y1391H	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.Y1391H|LY75_ENST00000553424.1_Missense_Mutation_p.Y1391H|LY75_ENST00000554112.1_Missense_Mutation_p.Y1391H|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.Y1391H	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1391			Y -> H (in dbSNP:rs2059696).		endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.Y1391H(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GTAGTATTATATTCTTCTTTG	0.284													A|||	1030	0.205671	0.0287	0.4827	5008	,	,		18449	0.2212		0.327	False		,,,				2504	0.1074				p.Y1391H		Atlas-SNP	.											LY75,NS,carcinoma,0,1	LY75	151	1	1	Substitution - Missense(1)	stomach(1)	c.T4171C						PASS	.	A	HIS/TYR,HIS/TYR,HIS/TYR	307,4099	165.4+/-196.9	9,289,1905	75.0	75.0	75.0		4171,4171,4171	2.0	1.0	2	dbSNP_94	75	2652,5948	423.7+/-354.4	411,1830,2059	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	83,83,83	420,2119,3964	GG,GA,AA		30.8372,6.9678,22.751	benign,benign,benign	1391/1874,1391/1818,1391/1723	160673526	2959,10047	2203	4300	6503	SO:0001583	missense	4065	exon30			TATTATATTCTTC	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.4171T>C	2.37:g.160673526A>G	ENSP00000263636:p.Tyr1391His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	543	0.24862637362637363	16	0.032520325203252036	156	0.430939226519337	122	0.21328671328671328	249	0.32849604221635886	A	9.660	1.143804	0.21205	0.069678	0.308372	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	5.65	1.99	0.26369	.	0.269362	0.19663	N	0.108922	T	0.00012	0.0000	L	0.27053	0.805	0.40886	P	0.015965000000000007	B;B;B	0.14438	0.003;0.003;0.01	B;B;B	0.15484	0.013;0.004;0.01	T	0.48833	-0.9000	9	0.15952	T	0.53	-6.7853	5.9111	0.19029	0.5812:0.1296:0.2892:0.0	rs2059696;rs17230537;rs2059696	1391;1391;1391	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	H	1391	ENSP00000451511:Y1391H;ENSP00000451446:Y1391H;ENSP00000263636:Y1391H;ENSP00000423463:Y1391H;ENSP00000421035:Y1391H	ENSP00000423463:Y1391H	Y	-	1	0	LY75;LY75-CD302	160381772	0.991000	0.36638	0.995000	0.50966	0.994000	0.84299	0.893000	0.28336	0.166000	0.19597	0.528000	0.53228	TAT	A|0.775;G|0.225	0.225	strong		0.284	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
DDX11	1663	hgsc.bcm.edu	37	12	31256905	31256905	+	Missense_Mutation	SNP	T	T	C	rs1046458	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:31256905T>C	ENST00000407793.2	+	27	3102	c.2851T>C	c.(2851-2853)Tgc>Cgc	p.C951R	DDX11_ENST00000545668.1_Missense_Mutation_p.C951R|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000228264.6_3'UTR|DDX11_ENST00000350437.4_3'UTR	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	951			C -> R (in dbSNP:rs1046458).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GAGTCCAGAGTGCTGCCAGGA	0.592										Multiple Myeloma(12;0.14)			C|||	3197	0.638379	0.708	0.6153	5008	,	,		16557	0.8105		0.4553	False		,,,				2504	0.5716				p.C951R		Atlas-SNP	.											.	DDX11	188	.	0			c.T2851C						PASS	.						19.0	32.0	27.0					12																	31256905		1309	2289	3598	SO:0001583	missense	1663	exon27			CCAGAGTGCTGCC	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.2851T>C	12.37:g.31256905T>C	ENSP00000384703:p.Cys951Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_001257144	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	1181	0.5407509157509157	301	0.6117886178861789	189	0.5220994475138122	420	0.7342657342657343	271	0.3575197889182058	C	0.031	-1.335212	0.01287	.	.	ENSG00000013573	ENST00000407793;ENST00000545668	T;T	0.72725	-0.68;-0.68	1.38	-2.53	0.06326	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.53005	P	3.900000000001125E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.39292	-0.9621	7	.	.	.	.	4.767	0.13137	0.0:0.1951:0.2372:0.5677	rs1046458;rs3175510;rs4031272;rs60595330	951	Q96FC9	DDX11_HUMAN	R	951	ENSP00000384703:C951R;ENSP00000440402:C951R	.	C	+	1	0	DDX11	31148172	0.000000	0.05858	0.011000	0.14972	0.005000	0.04900	-0.876000	0.04201	-1.616000	0.01572	-1.518000	0.00936	TGC	T|0.458;C|0.542	0.542	strong		0.592	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
KTI12	112970	hgsc.bcm.edu	37	1	52498370	52498370	+	Silent	SNP	C	C	T	rs2809917	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:52498370C>T	ENST00000371614.1	-	1	1118	c.1064G>A	c.(1063-1065)tGa>tAa	p.*355*	TXNDC12_ENST00000371626.4_Intron|RP11-91A18.4_ENST00000425802.1_RNA	NM_138417.2	NP_612426.1	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated (S. cerevisiae)	0							ATP binding (GO:0005524)	p.*355*(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						CTCCTCTGGTCAGTGCAGGCT	0.488													T|||	1102	0.220048	0.4092	0.1354	5008	,	,		20525	0.1786		0.0855	False		,,,				2504	0.2055				p.X355X		Atlas-SNP	.											KTI12,NS,carcinoma,0,1	KTI12	30	1	1	Substitution - coding silent(1)	stomach(1)	c.G1064A						PASS	.	T	,	1580,2826	652.5+/-399.4	302,976,925	46.0	50.0	48.0		,1064	0.9	0.1	1	dbSNP_100	48	971,7629	757.0+/-407.5	46,879,3375	no	intron,coding-synonymous	TXNDC12,KTI12	NM_015913.2,NM_138417.2	,	348,1855,4300	TT,TC,CC		11.2907,35.8602,19.614	,	,355/355	52498370	2551,10455	2203	4300	6503	SO:0001819	synonymous_variant	112970	exon1			TCTGGTCAGTGCA		CCDS562.1	1p32.3	2008-02-05			ENSG00000198841	ENSG00000198841			25160	protein-coding gene	gene with protein product						11929532	Standard	NM_138417		Approved	TOT4, MGC20419, SBBI81	uc001ctj.1	Q96EK9	OTTHUMG00000008630	ENST00000371614.1:c.1064G>A	1.37:g.52498370C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_138417		Silent	SNP	ENST00000371614.1	37	CCDS562.1																																																																																			C|0.799;T|0.201	0.201	strong		0.488	KTI12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023821.1	NM_138417	
CAGE1	285782	hgsc.bcm.edu	37	6	7374207	7374207	+	Missense_Mutation	SNP	T	T	G	rs2876098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:7374207T>G	ENST00000512086.1	-	5	1047	c.845A>C	c.(844-846)gAg>gCg	p.E282A	CAGE1_ENST00000338150.4_Missense_Mutation_p.E282A|CAGE1_ENST00000296742.7_Missense_Mutation_p.E146A|CAGE1_ENST00000379918.4_Missense_Mutation_p.E282A|CAGE1_ENST00000509324.1_5'UTR|CAGE1_ENST00000502583.1_Missense_Mutation_p.E282A			Q8TC20	CAGE1_HUMAN	cancer antigen 1	282			E -> A (in dbSNP:rs2876098).							breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					CTCACAGTTCTCCCGACATGC	0.458													T|||	513	0.102436	0.0703	0.1455	5008	,	,		19557	0.1062		0.1491	False		,,,				2504	0.0634				p.E282A		Atlas-SNP	.											.	CAGE1	165	.	0			c.A845C						PASS	.	T	ALA/GLU,ALA/GLU,ALA/GLU	360,3568		13,334,1617	99.0	96.0	97.0		845,845,437	3.2	0.0	6	dbSNP_101	97	1179,7115		106,967,3074	yes	missense,missense,missense	CAGE1	NM_001170692.1,NM_001170693.1,NM_205864.2	107,107,107	119,1301,4691	GG,GT,TT		14.2151,9.165,12.592	possibly-damaging,possibly-damaging,possibly-damaging	282/840,282/825,146/642	7374207	1539,10683	1964	4147	6111	SO:0001583	missense	285782	exon5			CAGTTCTCCCGAC	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"""cancer/testis antigen 95"""	608304	"""cancer/testis antigen 3"""	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.845A>C	6.37:g.7374207T>G	ENSP00000427583:p.Glu282Ala	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	172	146	0.848837	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Missense_Mutation	SNP	ENST00000512086.1	37		276	0.12637362637362637	42	0.08536585365853659	53	0.1464088397790055	63	0.11013986013986014	118	0.15567282321899736	T	16.25	3.071426	0.55646	0.09165	0.142151	ENSG00000164304	ENST00000541116;ENST00000379918;ENST00000502583;ENST00000296742;ENST00000512086;ENST00000338150;ENST00000542431;ENST00000512691	T;T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33;1.33	5.66	3.23	0.37069	.	0.542419	0.18024	N	0.154151	T	0.19446	0.0467	L	0.55481	1.735	0.80722	P	0.0	P;P;P	0.48294	0.908;0.775;0.86	B;B;P	0.44561	0.436;0.356;0.453	T	0.04635	-1.0937	9	0.54805	T	0.06	-0.3094	7.542	0.27744	0.0:0.1713:0.0:0.8287	rs2876098;rs17673083;rs60779509;rs2876098	282;282;282	Q8TC20-3;D6RCT9;Q8TC20	.;.;CAGE1_HUMAN	A	282;282;282;146;282;282;282;294	ENSP00000369250:E282A;ENSP00000425493:E282A;ENSP00000296742:E146A;ENSP00000427583:E282A;ENSP00000338107:E282A;ENSP00000423789:E294A	ENSP00000296742:E146A	E	-	2	0	CAGE1	7319206	0.008000	0.16893	0.001000	0.08648	0.005000	0.04900	0.785000	0.26830	0.410000	0.25675	0.482000	0.46254	GAG	T|0.882;G|0.118	0.118	strong		0.458	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745	
OR4D6	219983	hgsc.bcm.edu	37	11	59224608	59224608	+	Missense_Mutation	SNP	A	A	G	rs1453544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:59224608A>G	ENST00000300127.2	+	1	198	c.175A>G	c.(175-177)Atg>Gtg	p.M59V		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	59			M -> V (in dbSNP:rs1453544).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						ACACACTCCTATGTACTTTCT	0.448													A|||	627	0.1252	0.0197	0.1326	5008	,	,		20337	0.1141		0.2525	False		,,,				2504	0.1431				p.M59V		Atlas-SNP	.											OR4D6,NS,adenoma,0,1	OR4D6	65	1	0			c.A175G						PASS	.	A	VAL/MET	244,4158	143.8+/-178.8	10,224,1967	145.0	122.0	130.0		175	4.9	0.9	11	dbSNP_88	130	2264,6326	383.5+/-340.8	283,1698,2314	yes	missense	OR4D6	NM_001004708.1	21	293,1922,4281	GG,GA,AA		26.3562,5.5429,19.3042	probably-damaging	59/315	59224608	2508,10484	2201	4295	6496	SO:0001583	missense	219983	exon1			ACTCCTATGTACT	AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"""GPCR / Class A : Olfactory receptors"""	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.175A>G	11.37:g.59224608A>G	ENSP00000300127:p.Met59Val	Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	318	148	0.465409	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	349	0.15979853479853479	18	0.036585365853658534	59	0.16298342541436464	71	0.12412587412587413	201	0.26517150395778366	A	13.29	2.192610	0.38707	0.055429	0.263562	ENSG00000166884	ENST00000300127	T	0.09350	2.99	6.01	4.88	0.63580	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.00012	0.0000	M	0.91406	3.205	0.32048	P	0.5973200000000001	P	0.50819	0.939	P	0.54759	0.76	T	0.10989	-1.0606	9	0.87932	D	0	-29.9948	11.1494	0.48449	0.9274:0.0:0.0726:0.0	rs1453544;rs52794667;rs57726108;rs1453544	59	Q8NGJ1	OR4D6_HUMAN	V	59	ENSP00000300127:M59V	ENSP00000300127:M59V	M	+	1	0	OR4D6	58981184	1.000000	0.71417	0.862000	0.33874	0.497000	0.33675	7.516000	0.81772	1.088000	0.41272	0.533000	0.62120	ATG	A|0.815;G|0.185	0.185	strong		0.448	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708	
LRRD1	401387	hgsc.bcm.edu	37	7	91779971	91779971	+	Missense_Mutation	SNP	T	T	G	rs6465353	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:91779971T>G	ENST00000458448.1	-	4	2355	c.2155A>C	c.(2155-2157)Att>Ctt	p.I719L	LRRD1_ENST00000422722.1_5'UTR|LRRD1_ENST00000430130.2_Missense_Mutation_p.I719L|CTB-161K23.1_ENST00000453068.1_RNA|LRRD1_ENST00000454089.2_Missense_Mutation_p.I70L|LRRD1_ENST00000343318.5_Missense_Mutation_p.I70L			A4D1F6	LRRD1_HUMAN	leucine-rich repeats and death domain containing 1	719					signal transduction (GO:0007165)					breast(4)|endometrium(1)	5						AGTGAAAAAATATTGTAGATA	0.323													G|||	2086	0.416534	0.6717	0.3732	5008	,	,		15605	0.1885		0.3926	False		,,,				2504	0.362				p.I719L		Atlas-SNP	.											.	LRRD1	35	.	0			c.A2155C						PASS	.						97.0	79.0	84.0					7																	91779971		692	1591	2283	SO:0001583	missense	401387	exon3			AAAAAATATTGTA	BC026112	CCDS55124.1	7q21.2	2011-05-23			ENSG00000240720	ENSG00000240720			34300	protein-coding gene	gene with protein product							Standard	NM_001161528		Approved	IMAGE:4798971	uc011khp.1	A4D1F6	OTTHUMG00000155861	ENST00000458448.1:c.2155A>C	7.37:g.91779971T>G	ENSP00000405987:p.Ile719Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	112	61	0.544643	NM_001161528	B7ZMM9|Q49AT9	Missense_Mutation	SNP	ENST00000458448.1	37	CCDS55124.1	899	0.4116300366300366	342	0.6951219512195121	144	0.39779005524861877	114	0.1993006993006993	299	0.3944591029023747	G	5.515	0.279899	0.10458	.	.	ENSG00000240720	ENST00000343318;ENST00000458448;ENST00000430130;ENST00000454089	T;T;T;T	0.17054	2.62;2.3;2.3;2.62	5.61	5.61	0.85477	.	.	.	.	.	T	0.00012	0.0000	N	0.00068	-2.285	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	8	0.02654	T	1	.	15.7556	0.78021	0.0:0.0:0.8621:0.1379	rs6465353;rs59146464;rs6465353	719	A4D1F6	LRRD1_HUMAN	L	70;719;719;70	ENSP00000339642:I70L;ENSP00000405987:I719L;ENSP00000411568:I719L;ENSP00000392112:I70L	ENSP00000339642:I70L	I	-	1	0	LRRD1	91617907	1.000000	0.71417	0.510000	0.27712	0.523000	0.34469	4.909000	0.63314	1.386000	0.46466	-0.121000	0.15023	ATT	T|0.575;G|0.425	0.425	strong		0.323	LRRD1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342027.2	NM_001045475	
CAPN14	440854	hgsc.bcm.edu	37	2	31410653	31410653	+	Missense_Mutation	SNP	C	C	T	rs7422120	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:31410653C>T	ENST00000403897.3	-	15	1699	c.1558G>A	c.(1558-1560)Gat>Aat	p.D520N	CAPN14_ENST00000444918.2_Missense_Mutation_p.D520N	NM_001145122.1	NP_001138594.1	A8MX76	CAN14_HUMAN	calpain 14	520	Domain IV.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|endometrium(2)|prostate(1)|skin(1)|stomach(2)	7						AAGAATTCATCCTGCCTTTCA	0.423													T|||	1644	0.328275	0.5908	0.389	5008	,	,		17909	0.1558		0.1899	False		,,,				2504	0.2505				p.D520N		Atlas-SNP	.											.	CAPN14	36	.	0			c.G1558A						PASS	.	T	ASN/ASP	716,668		183,350,159	121.0	121.0	121.0		1558	-0.2	0.0	2	dbSNP_116	121	530,2652		50,430,1111	yes	missense	CAPN14	NM_001145122.1	23	233,780,1270	TT,TC,CC		16.6562,48.2659,27.2887	benign	520/685	31410653	1246,3320	692	1591	2283	SO:0001583	missense	440854	exon15			ATTCATCCTGCCT	AC015980	CCDS46254.1	2p23.1-p21	2013-01-10			ENSG00000214711	ENSG00000214711		"""EF-hand domain containing"""	16664	protein-coding gene	gene with protein product		610229				11675017	Standard	NM_001145122		Approved		uc010yms.2	A8MX76	OTTHUMG00000152039	ENST00000403897.3:c.1558G>A	2.37:g.31410653C>T	ENSP00000385247:p.Asp520Asn	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_001145122	B3KRU9	Missense_Mutation	SNP	ENST00000403897.3	37	CCDS46254.1	648	0.2967032967032967	273	0.5548780487804879	131	0.36187845303867405	94	0.16433566433566432	150	0.19788918205804748	T	0.077	-1.191270	0.01607	0.517341	0.166562	ENSG00000214711	ENST00000444918;ENST00000403897	T;T	0.28895	1.59;1.59	3.54	-0.241	0.13043	EF-hand-like domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.46527	-0.9185	8	0.40728	T	0.16	.	11.185	0.48650	0.0:0.6894:0.0:0.3106	rs7422120;rs52813309;rs7422120	520;344	A8MX76;A8MX76-2	CAN14_HUMAN;.	N	520	ENSP00000398670:D520N;ENSP00000385247:D520N	ENSP00000385247:D520N	D	-	1	0	CAPN14	31264157	0.461000	0.25783	0.001000	0.08648	0.007000	0.05969	-0.095000	0.11077	-1.004000	0.03421	-2.680000	0.00142	GAT	C|0.732;T|0.268	0.268	strong		0.423	CAPN14-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325010.1	NM_001145122	
PHKG1	5260	hgsc.bcm.edu	37	7	56149362	56149362	+	Silent	SNP	C	C	T	rs11238393	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:56149362C>T	ENST00000297373.2	-	9	1073	c.879G>A	c.(877-879)gtG>gtA	p.V293V	PHKG1_ENST00000489604.1_5'Flank|PHKG1_ENST00000452681.2_Silent_p.V325V|PHKG1_ENST00000537360.1_Silent_p.V239V	NM_001258460.1|NM_006213.4	NP_001245389.1|NP_006204.1	Q16816	PHKG1_HUMAN	phosphorylase kinase, gamma 1 (muscle)	293					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|tau-protein kinase activity (GO:0050321)			endometrium(1)|large_intestine(1)|lung(5)	7	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GCACTTCCTCCACCAAGTACT	0.607													C|||	749	0.149561	0.0613	0.2147	5008	,	,		17366	0.0714		0.2237	False		,,,				2504	0.227				p.V325V	Melanoma(184;580 2064 5329 24177 35303)	Atlas-SNP	.											.	PHKG1	38	.	0			c.G975A						PASS	.	C		350,4056	180.1+/-208.5	18,314,1871	37.0	39.0	38.0		879	-1.4	1.0	7	dbSNP_120	38	1921,6679	332.8+/-320.3	208,1505,2587	no	coding-synonymous	PHKG1	NM_006213.3		226,1819,4458	TT,TC,CC		22.3372,7.9437,17.4612		293/388	56149362	2271,10735	2203	4300	6503	SO:0001819	synonymous_variant	5260	exon10			TTCCTCCACCAAG	X80590	CCDS5525.1, CCDS59057.1	7p11.2	2009-07-10			ENSG00000164776	ENSG00000164776	2.7.11.19		8930	protein-coding gene	gene with protein product		172470		PHKG		8530014	Standard	NM_001258459		Approved		uc011kdb.2	Q16816	OTTHUMG00000023869	ENST00000297373.2:c.879G>A	7.37:g.56149362C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	72	27	0.375	NM_001258459	B7Z1D0|F5H2S1|Q75LP5	Silent	SNP	ENST00000297373.2	37	CCDS5525.1																																																																																			C|0.839;T|0.161	0.161	strong		0.607	PHKG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251587.1	NM_006213	
SAMM50	25813	hgsc.bcm.edu	37	22	44368122	44368122	+	Missense_Mutation	SNP	A	A	G	rs3761472	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:44368122A>G	ENST00000350028.4	+	5	486	c.329A>G	c.(328-330)gAc>gGc	p.D110G	SAMM50_ENST00000396202.3_Intron|SAMM50_ENST00000493161.1_3'UTR	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	110			D -> G (in dbSNP:rs3761472). {ECO:0000269|PubMed:14702039}.		cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)		p.D110G(1)		endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				TTAGGTGATGACGCACTTCCA	0.363													A|||	1223	0.244209	0.171	0.2968	5008	,	,		17374	0.371		0.1879	False		,,,				2504	0.2331				p.D110G		Atlas-SNP	.											SAMM50,NS,carcinoma,0,1	SAMM50	30	1	1	Substitution - Missense(1)	stomach(1)	c.A329G						PASS	.	A	GLY/ASP	786,3620	318.5+/-295.7	88,610,1505	123.0	113.0	116.0		329	4.8	0.9	22	dbSNP_107	116	1339,7261	263.0+/-284.7	107,1125,3068	yes	missense	SAMM50	NM_015380.4	94	195,1735,4573	GG,GA,AA		15.5698,17.8393,16.3386	benign	110/470	44368122	2125,10881	2203	4300	6503	SO:0001583	missense	25813	exon5			GTGATGACGCACT	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"""sorting and assembly machinery component 50 homolog (S. cerevisiae)"""			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.329A>G	22.37:g.44368122A>G	ENSP00000345445:p.Asp110Gly	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Missense_Mutation	SNP	ENST00000350028.4	37	CCDS14055.1	554	0.25366300366300365	86	0.17479674796747968	96	0.26519337016574585	232	0.40559440559440557	140	0.18469656992084432	A	14.99	2.701189	0.48307	0.178393	0.155698	ENSG00000100347	ENST00000350028	T	0.54279	0.58	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.53249	1.67	0.09310	P	1.0	B	0.14438	0.01	B	0.17722	0.019	T	0.33574	-0.9863	9	0.48119	T	0.1	-28.447	13.7811	0.63084	1.0:0.0:0.0:0.0	rs3761472;rs11547246;rs52828379;rs57886466;rs3761472	110	Q9Y512	SAM50_HUMAN	G	110	ENSP00000345445:D110G	ENSP00000345445:D110G	D	+	2	0	SAMM50	42699455	0.998000	0.40836	0.898000	0.35279	0.991000	0.79684	3.639000	0.54339	1.916000	0.55485	0.533000	0.62120	GAC	A|0.790;G|0.210	0.210	strong		0.363	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
ASPRV1	151516	hgsc.bcm.edu	37	2	70188676	70188676	+	Missense_Mutation	SNP	T	T	C	rs3796097	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:70188676T>C	ENST00000320256.4	-	1	721	c.145A>G	c.(145-147)Act>Gct	p.T49A	PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000596259.1_RNA|PCBP1-AS1_ENST00000419542.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA	NM_152792.2	NP_690005.2			aspartic peptidase, retroviral-like 1											endometrium(3)|large_intestine(4)|lung(6)|ovary(1)	14						CGAAGCAGAGTGGGGATGACT	0.637													C|||	3496	0.698083	0.9145	0.7421	5008	,	,		17996	0.6815		0.503	False		,,,				2504	0.592				p.T49A		Atlas-SNP	.											.	ASPRV1	41	.	0			c.A145G						PASS	.	C	ALA/THR	3733,673	283.1+/-276.9	1585,563,55	45.0	46.0	46.0		145	-4.7	0.0	2	dbSNP_107	46	4480,4120	560.7+/-387.6	1171,2138,991	yes	missense	ASPRV1	NM_152792.2	58	2756,2701,1046	CC,CT,TT		47.907,15.2746,36.8522	benign	49/344	70188676	8213,4793	2203	4300	6503	SO:0001583	missense	151516	exon1			GCAGAGTGGGGAT	AK055994	CCDS1897.1	2p13.3	2008-02-20			ENSG00000244617	ENSG00000244617			26321	protein-coding gene	gene with protein product	"""Skin ASpartic Protease"""	611765				16098038, 16565508	Standard	NM_152792		Approved	Taps, SASPase, FLJ25084	uc002sfz.4	Q53RT3	OTTHUMG00000129647	ENST00000320256.4:c.145A>G	2.37:g.70188676T>C	ENSP00000315383:p.Thr49Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	164	160	0.97561	NM_152792		Missense_Mutation	SNP	ENST00000320256.4	37	CCDS1897.1	1456	0.6666666666666666	450	0.9146341463414634	255	0.7044198895027625	370	0.6468531468531469	381	0.5026385224274407	C	2.190	-0.385484	0.04966	0.847254	0.52093	ENSG00000244617	ENST00000320256	T	0.43294	0.95	3.88	-4.7	0.03288	.	1.015840	0.07926	N	0.976770	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.23868	-1.0176	9	0.27082	T	0.32	.	11.8715	0.52523	0.0:0.5647:0.0:0.4353	rs3796097;rs13025324;rs3796097	49	Q53RT3	APRV1_HUMAN	A	49	ENSP00000315383:T49A	ENSP00000315383:T49A	T	-	1	0	ASPRV1	70042180	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.869000	0.04232	-1.206000	0.02641	-1.088000	0.02184	ACT	T|0.345;C|0.655	0.655	strong		0.637	ASPRV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334161.1	NM_152792	
SAGE1	55511	hgsc.bcm.edu	37	X	134978425	134978425	+	Silent	SNP	G	G	A	rs5930805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:134978425G>A	ENST00000370709.3	+	1	24	c.24G>A	c.(22-24)acG>acA	p.T8T	SAGE1_ENST00000324447.3_Silent_p.T8T|SAGE1_ENST00000537770.1_Silent_p.T8T|SAGE1_ENST00000535938.1_Silent_p.T8T			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	8						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					CACTTCAAACGAGTCAACCAA	0.403													g|||	611	0.161854	0.0673	0.1614	3775	,	,		11604	0.1012		0.2058	False		,,,				2504	0.1033				p.T8T		Atlas-SNP	.											.	SAGE1	160	.	0			c.G24A						PASS	.	G		545,3290		29,416,71,1187,500	108.0	88.0	95.0		24	0.8	0.0	X	dbSNP_114	95	1753,4975		188,923,454,1317,1418	no	coding-synonymous	SAGE1	NM_018666.2		217,1339,525,2504,1918	AA,AG,A,GG,G		26.0553,14.2112,21.7552		8/905	134978425	2298,8265	2203	4300	6503	SO:0001819	synonymous_variant	55511	exon2			TCAAACGAGTCAA	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.24G>A	X.37:g.134978425G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	311	17	0.0546624	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			G|0.792;A|0.208	0.208	strong		0.403	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
TUBB8	347688	hgsc.bcm.edu	37	10	94026	94026	+	Silent	SNP	G	G	A	rs10904032	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:94026G>A	ENST00000309812.4	-	4	368	c.306C>T	c.(304-306)gcC>gcT	p.A102A	TUBB8_ENST00000447903.2_Silent_p.A30A|TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000332708.5_Missense_Mutation_p.P66L	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	102					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		AGTGTCCCTTGGCCCAGTTGT	0.572																																					p.A102A	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.C306T						PASS	.	G		693,3713		18,657,1528	68.0	56.0	60.0		306		0.4	10	dbSNP_120	60	3519,5081		504,2511,1285	no	coding-synonymous	TUBB8	NM_177987.2		522,3168,2813	AA,AG,GG		40.9186,15.7286,32.3851		102/445	94026	4212,8794	2203	4300	6503	SO:0001819	synonymous_variant	347688	exon4			TCCCTTGGCCCAG	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.306C>T	10.37:g.94026G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	224	86	0.383929	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1	587	0.26877289377289376	72	0.14634146341463414	129	0.356353591160221	89	0.1555944055944056	297	0.391820580474934	G	10.07	1.248892	0.22880	0.157286	0.409186	ENSG00000173876	ENST00000309812;ENST00000332708	.	.	.	.	.	.	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40997	-0.9533	3	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	rs10904032;rs59810031	.	.	.	L	110;66	.	ENSP00000311042:P110L	P	-	2	0	RP11-631M21.2	84026	0.240000	0.23847	0.361000	0.25849	0.365000	0.29674	-3.811000	0.00360	0.119000	0.18210	0.121000	0.15741	CCA	G|0.731;A|0.269	0.269	strong		0.572	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
RPAP3	79657	hgsc.bcm.edu	37	12	48090118	48090118	+	Silent	SNP	G	G	A	rs12368459	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48090118G>A	ENST00000005386.3	-	5	601	c.486C>T	c.(484-486)gcC>gcT	p.A162A	RPAP3_ENST00000380650.4_Silent_p.A162A|RPAP3_ENST00000432584.3_Silent_p.A3A	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	162										endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					TATATGGATCGGCATCCATGC	0.353													G|||	50	0.00998403	0.0	0.013	5008	,	,		18197	0.001		0.0338	False		,,,				2504	0.0061				p.A162A		Atlas-SNP	.											.	RPAP3	45	.	0			c.C486T						PASS	.	G	,,	31,4375	36.0+/-67.5	0,31,2172	159.0	141.0	147.0		486,9,486	-6.7	0.9	12	dbSNP_120	147	312,8288	112.0+/-172.2	4,304,3992	no	coding-synonymous,coding-synonymous,coding-synonymous	RPAP3	NM_001146075.1,NM_001146076.1,NM_024604.2	,,	4,335,6164	AA,AG,GG		3.6279,0.7036,2.6372	,,	162/632,3/507,162/666	48090118	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	79657	exon5			TGGATCGGCATCC	AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"""Tetratricopeptide (TTC) repeat domain containing"""	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.486C>T	12.37:g.48090118G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_024604	B4DRW9|Q6PHR5	Silent	SNP	ENST00000005386.3	37	CCDS8753.1																																																																																			G|0.977;A|0.023	0.023	strong		0.353	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604	
SYK	6850	hgsc.bcm.edu	37	9	93641175	93641175	+	Silent	SNP	C	C	T	rs2306041	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:93641175C>T	ENST00000375754.4	+	11	1669	c.1521C>T	c.(1519-1521)taC>taT	p.Y507Y	SYK_ENST00000375747.1_Silent_p.Y484Y|SYK_ENST00000375751.4_Silent_p.Y484Y|SYK_ENST00000375746.1_Silent_p.Y507Y	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	507	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						CCCAACATTACGCCAAGATCA	0.438			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								C|||	993	0.198283	0.2179	0.366	5008	,	,		20099	0.2321		0.1362	False		,,,				2504	0.0818				p.Y507Y		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.C1521T						PASS	.	C	,,,	968,3438	365.4+/-317.4	102,764,1337	181.0	158.0	166.0		1452,1521,1452,1521	-3.4	1.0	9	dbSNP_100	166	1215,7385	245.3+/-274.2	88,1039,3173	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	190,1803,4510	TT,TC,CC		14.1279,21.97,16.7846	,,,	484/613,507/636,484/613,507/636	93641175	2183,10823	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon11			ACATTACGCCAAG	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1521C>T	9.37:g.93641175C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	184	88	0.478261	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			C|0.822;T|0.178	0.178	strong		0.438	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
TTC7A	57217	hgsc.bcm.edu	37	2	47278901	47278901	+	Silent	SNP	G	G	A	rs3739100	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:47278901G>A	ENST00000319190.5	+	18	2402	c.2034G>A	c.(2032-2034)tcG>tcA	p.S678S	TTC7A_ENST00000394850.2_Silent_p.S702S|TTC7A_ENST00000263737.6_Silent_p.S324S|TTC7A_ENST00000409245.1_Silent_p.S644S	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	678					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GGCGGGCTTCGTCCATCGCCG	0.657													G|||	921	0.183906	0.1566	0.1398	5008	,	,		16415	0.4435		0.0378	False		,,,				2504	0.135				p.S678S		Atlas-SNP	.											.	TTC7A	80	.	0			c.G2034A						PASS	.	G		691,3693		63,565,1564	45.0	47.0	47.0		2034	-10.4	0.1	2	dbSNP_107	47	261,8305		4,253,4026	no	coding-synonymous	TTC7A	NM_020458.2		67,818,5590	AA,AG,GG		3.0469,15.7619,7.3514		678/859	47278901	952,11998	2192	4283	6475	SO:0001819	synonymous_variant	57217	exon18			GGCTTCGTCCATC	AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"""Tetratricopeptide (TTC) repeat domain containing"""	19750	protein-coding gene	gene with protein product		609332	"""tetratricopeptide repeat domain 7"""	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.2034G>A	2.37:g.47278901G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																			G|0.870;A|0.130	0.130	strong		0.657	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
LCP2	3937	hgsc.bcm.edu	37	5	169695446	169695446	+	Silent	SNP	C	C	T	rs2292254	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:169695446C>T	ENST00000046794.5	-	8	1179	c.564G>A	c.(562-564)gtG>gtA	p.V188V	LCP2_ENST00000521416.1_5'Flank	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	188					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TCTGGGGGGGCACAGGAGGCT	0.627											OREG0017023	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2279	0.455072	0.2927	0.4856	5008	,	,		6718	0.6538		0.4245	False		,,,				2504	0.4796				p.V188V		Atlas-SNP	.											LCP2_ENST00000046794,NS,carcinoma,0,2	LCP2	133	2	0			c.G564A						scavenged	.	C		775,2241		158,459,891	2.0	3.0	2.0		564	3.3	0.8	5	dbSNP_100	2	2547,4561		602,1343,1609	no	coding-synonymous	LCP2	NM_005565.3		760,1802,2500	TT,TC,CC		35.8329,25.6963,32.8131		188/534	169695446	3322,6802	1508	3554	5062	SO:0001819	synonymous_variant	3937	exon8			GGGGGGCACAGGA		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.564G>A	5.37:g.169695446C>T		Somatic	5	1	0.2	1879	WXS	Illumina HiSeq	Phase_I	9	5	0.555556	NM_005565	A8KA25|Q53XV4	Silent	SNP	ENST00000046794.5	37	CCDS47339.1																																																																																			C|0.530;T|0.470	0.470	strong		0.627	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
FRG2B	441581	hgsc.bcm.edu	37	10	135438955	135438955	+	Missense_Mutation	SNP	C	C	T	rs201563622		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135438955C>T	ENST00000425520.1	-	4	537	c.485G>A	c.(484-486)cGg>cAg	p.R162Q	FRG2B_ENST00000443774.1_Missense_Mutation_p.R163Q	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	162						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TCCTAGGGCCCGAGACCTATG	0.562																																					p.R162Q		Atlas-SNP	.											.	FRG2B	47	.	0			c.G485A						PASS	.						119.0	143.0	135.0					10																	135438955		2195	4295	6490	SO:0001583	missense	441581	exon4			AGGGCCCGAGACC	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.485G>A	10.37:g.135438955C>T	ENSP00000401310:p.Arg162Gln	Somatic	367	1	0.0027248		WXS	Illumina HiSeq	Phase_I	355	132	0.371831	NM_001080998	Q5VSQ1	Missense_Mutation	SNP	ENST00000425520.1	37	CCDS44502.1	.	.	.	.	.	.	.	.	.	.	.	9.163	1.019099	0.19355	.	.	ENSG00000225899	ENST00000443774;ENST00000425520	T;T	0.51574	0.7;0.7	.	.	.	.	2.176020	0.02470	N	0.087405	T	0.34279	0.0892	L	0.27053	0.805	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.19386	-1.0307	8	0.39692	T	0.17	-0.4106	.	.	.	.	162	Q96QU4	FRG2B_HUMAN	Q	163;162	ENSP00000408343:R163Q;ENSP00000401310:R162Q	ENSP00000401310:R162Q	R	-	2	0	FRG2B	135288945	0.004000	0.15560	0.161000	0.22692	0.162000	0.22319	-0.834000	0.04391	0.119000	0.18210	0.121000	0.15741	CGG	.	.	weak		0.562	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
C9orf57	138240	hgsc.bcm.edu	37	9	74671719	74671719	+	Silent	SNP	T	T	C	rs13295099	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:74671719T>C	ENST00000377024.3	-	3	299	c.204A>G	c.(202-204)aaA>aaG	p.K68K	C9orf57_ENST00000424431.2_Silent_p.K34K	NM_001128618.1	NP_001122090.1	Q5W0N0	CI057_HUMAN	chromosome 9 open reading frame 57	68						integral component of membrane (GO:0016021)				endometrium(1)	1						GGACCTCTTCTTTCCAGTACT	0.368													T|||	1334	0.266374	0.1566	0.3228	5008	,	,		17668	0.0774		0.5467	False		,,,				2504	0.2812				p.K68K		Atlas-SNP	.											.	C9orf57	16	.	0			c.A204G						PASS	.	T		304,1080		30,244,418	94.0	75.0	80.0		204	-0.4	0.0	9	dbSNP_121	80	1785,1397		499,787,305	no	coding-synonymous	C9orf57	NM_001128618.1		529,1031,723	CC,CT,TT		43.9032,21.9653,45.7512		68/162	74671719	2089,2477	692	1591	2283	SO:0001819	synonymous_variant	138240	exon3			CTCTTCTTTCCAG	BC036255	CCDS47980.1	9q21.2	2012-03-15			ENSG00000204669	ENSG00000204669			27037	protein-coding gene	gene with protein product						12477932	Standard	NM_001128618		Approved		uc004aip.3	Q5W0N0	OTTHUMG00000020003	ENST00000377024.3:c.204A>G	9.37:g.74671719T>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	33	20	0.606061	NM_001128618	A1L456	Silent	SNP	ENST00000377024.3	37	CCDS47980.1																																																																																			.	.	alt		0.368	C9orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052631.1	NM_001128618	
LHCGR	3973	hgsc.bcm.edu	37	2	48921375	48921375	+	Missense_Mutation	SNP	T	T	C	rs2293275	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:48921375T>C	ENST00000294954.7	-	10	956	c.935A>G	c.(934-936)aAt>aGt	p.N312S	STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000344775.3_Missense_Mutation_p.N250S|LHCGR_ENST00000405626.1_Intron|LHCGR_ENST00000401907.1_Missense_Mutation_p.N312S|LHCGR_ENST00000403273.1_Missense_Mutation_p.N312S	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	312			N -> S (in dbSNP:rs2293275). {ECO:0000269|PubMed:2244890, ECO:0000269|PubMed:7556872}.	Missing (in Ref. 3; AAA70231). {ECO:0000305}.	activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	TGTTTTGTTATTCACTTTCCT	0.323													T|||	2960	0.591054	0.2352	0.6657	5008	,	,		18928	0.9276		0.6402	False		,,,				2504	0.6217				p.N312S		Atlas-SNP	.											.	LHCGR	154	.	0			c.A935G						PASS	.	T	SER/ASN,	1307,3093	429.3+/-342.2	203,901,1096	137.0	102.0	114.0		935,	3.9	0.8	2	dbSNP_100	114	5074,3516	612.9+/-396.0	1492,2090,713	yes	missense,intron	LHCGR,STON1-GTF2A1L	NM_000233.3,NM_001198593.1	46,	1695,2991,1809	CC,CT,TT		40.9313,29.7045,49.1224	benign,	312/700,	48921375	6381,6609	2200	4295	6495	SO:0001583	missense	3973	exon10			TTGTTATTCACTT		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"""GPCR / Class A : Gonadotropin and TSH receptors"""	6585	protein-coding gene	gene with protein product		152790	"""hypergonadotropic hypogonadism"""	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.935A>G	2.37:g.48921375T>C	ENSP00000294954:p.Asn312Ser	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	247	125	0.506073	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	37	CCDS1842.1	1387	0.63507326007326	125	0.2540650406504065	262	0.7237569060773481	529	0.9248251748251748	471	0.6213720316622692	T	4.051	0.007198	0.07866	0.297045	0.590687	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000403273;ENST00000401907	T;T;T;T	0.78003	-0.95;-0.77;-1.14;-0.97	5.09	3.9	0.45041	.	0.636684	0.17257	N	0.180938	T	0.00012	0.0000	N	0.17564	0.495	0.35412	P	0.20750199999999996	B	0.11235	0.004	B	0.08055	0.003	T	0.34030	-0.9845	8	.	.	.	.	9.9216	0.41468	0.0:0.0:0.3586:0.6414	rs2293275;rs17398177;rs52807977;rs60456102;rs2293275	312	P22888	LSHR_HUMAN	S	250;312;312;312	ENSP00000344301:N250S;ENSP00000294954:N312S;ENSP00000385847:N312S;ENSP00000385406:N312S	.	N	-	2	0	LHCGR	48774879	0.889000	0.30405	0.794000	0.32065	0.151000	0.21798	1.185000	0.32065	0.848000	0.35191	0.460000	0.39030	AAT	T|0.446;C|0.554	0.554	strong		0.323	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3	
GLTSCR1	29998	hgsc.bcm.edu	37	19	48182787	48182787	+	Silent	SNP	C	C	T	rs4802382	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48182787C>T	ENST00000396720.3	+	6	554	c.360C>T	c.(358-360)gcC>gcT	p.A120A	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	120										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		CGCTGGAGGCCGAGGCTGAGC	0.736													c|||	1700	0.339457	0.4576	0.3127	5008	,	,		12558	0.3254		0.2485	False		,,,				2504	0.3067				p.A120A		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.C360T						PASS	.						14.0	17.0	16.0					19																	48182787		689	1587	2276	SO:0001819	synonymous_variant	29998	exon6			GGAGGCCGAGGCT	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.360C>T	19.37:g.48182787C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	37	CCDS46134.1																																																																																			C|0.688;T|0.312	0.312	strong		0.736	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711	
ISX	91464	hgsc.bcm.edu	37	22	35481493	35481493	+	Missense_Mutation	SNP	C	C	T	rs61735502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:35481493C>T	ENST00000308700.6	+	4	1497	c.545C>T	c.(544-546)aCg>aTg	p.T182M	ISX_ENST00000404699.2_Missense_Mutation_p.T182M	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	182					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						GCTCCTCCCACGAGCTGTTGT	0.617													C|||	328	0.0654952	0.0507	0.049	5008	,	,		19609	0.0129		0.0994	False		,,,				2504	0.1166				p.T182M		Atlas-SNP	.											ISX,NS,carcinoma,-1,1	ISX	62	1	0			c.C545T						PASS	.	C	MET/THR	262,4144	149.5+/-183.7	7,248,1948	138.0	118.0	125.0		545	-9.1	0.0	22	dbSNP_129	125	801,7799	187.0+/-234.4	38,725,3537	yes	missense	ISX	NM_001008494.1	81	45,973,5485	TT,TC,CC		9.314,5.9464,8.1732	benign	182/246	35481493	1063,11943	2203	4300	6503	SO:0001583	missense	91464	exon4			CTCCCACGAGCTG	AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"""Homeoboxes / PRD class"""	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.545C>T	22.37:g.35481493C>T	ENSP00000311492:p.Thr182Met	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	189	87	0.460317	NM_001008494	Q68DJ5	Missense_Mutation	SNP	ENST00000308700.6	37	CCDS33640.1	115	0.052655677655677656	17	0.034552845528455285	19	0.052486187845303865	4	0.006993006993006993	75	0.09894459102902374	C	10.91	1.484734	0.26598	0.059464	0.09314	ENSG00000175329	ENST00000308700;ENST00000404699	D;D	0.90444	-2.67;-2.67	5.14	-9.08	0.00720	.	1.074000	0.07246	N	0.865135	T	0.10895	0.0266	L	0.28115	0.83	0.80722	P	0.0	B	0.13145	0.007	B	0.08055	0.003	T	0.48502	-0.9030	9	0.33940	T	0.23	.	9.3624	0.38203	0.0:0.2592:0.1077:0.6331	rs61735502	182	Q2M1V0	ISX_HUMAN	M	182	ENSP00000311492:T182M;ENSP00000386037:T182M	ENSP00000311492:T182M	T	+	2	0	ISX	33811493	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.783000	0.01770	-1.704000	0.01407	-0.982000	0.02568	ACG	C|0.926;T|0.074	0.074	strong		0.617	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494	
TM9SF1	10548	hgsc.bcm.edu	37	14	24662296	24662296	+	Missense_Mutation	SNP	T	T	C	rs62621251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24662296T>C	ENST00000261789.4	-	3	883	c.525A>G	c.(523-525)atA>atG	p.I175M	TM9SF1_ENST00000528669.1_Missense_Mutation_p.I175M|TM9SF1_ENST00000524835.1_Missense_Mutation_p.I88M|TM9SF1_ENST00000556387.1_Missense_Mutation_p.I384M|TM9SF1_ENST00000530611.1_Missense_Mutation_p.I384M|TM9SF1_ENST00000396854.4_Missense_Mutation_p.I175M|RP11-468E2.2_ENST00000561419.1_5'Flank	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	175					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		CATTGGCAAATATAATTCGGT	0.522													T|||	19	0.00379393	0.0	0.0086	5008	,	,		20446	0.0		0.0129	False		,,,				2504	0.0				p.I175M		Atlas-SNP	.											.	TM9SF1	58	.	0			c.A525G						PASS	.	T	MET/ILE,MET/ILE	9,4397	16.8+/-37.8	0,9,2194	103.0	99.0	100.0		525,525	3.9	1.0	14	dbSNP_129	100	87,8513	49.4+/-109.1	0,87,4213	yes	missense,missense	TM9SF1	NM_001014842.1,NM_006405.5	10,10	0,96,6407	CC,CT,TT		1.0116,0.2043,0.7381	possibly-damaging,possibly-damaging	175/490,175/607	24662296	96,12910	2203	4300	6503	SO:0001583	missense	10548	exon3			GGCAAATATAATT	U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.525A>G	14.37:g.24662296T>C	ENSP00000261789:p.Ile175Met	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	180	82	0.455556	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	37	CCDS9617.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	17.64	3.439673	0.63067	0.002043	0.010116	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000528895;ENST00000530563;ENST00000530468;ENST00000525592;ENST00000528010;ENST00000530611	T;T;T;T;T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.1	3.94	0.45596	.	0.052007	0.64402	D	0.000001	T	0.54498	0.1862	M	0.65320	2	0.58432	D	0.999998	P;P;B	0.51791	0.948;0.494;0.016	P;B;B	0.59643	0.861;0.297;0.101	T	0.62765	-0.6785	10	0.72032	D	0.01	-10.9909	9.0359	0.36287	0.0:0.0:0.2919:0.7081	rs62621251	175;175;175	E9PJM1;Q86SZ6;O15321	.;.;TM9S1_HUMAN	M	175;175;384;88;175;175;88;175;175;175;384	ENSP00000261789:I175M;ENSP00000432997:I175M;ENSP00000451949:I384M;ENSP00000434387:I88M;ENSP00000380063:I175M;ENSP00000431447:I175M;ENSP00000437127:I88M;ENSP00000435857:I175M;ENSP00000432435:I175M;ENSP00000433792:I175M;ENSP00000433967:I384M	ENSP00000433967:I384M	I	-	3	3	TM9SF1;RP11-468E2.1	23732136	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.136000	0.50554	2.137000	0.66172	0.533000	0.62120	ATA	T|0.994;C|0.006	0.006	strong		0.522	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405	
DYSF	8291	hgsc.bcm.edu	37	2	71838597	71838597	+	Silent	SNP	C	C	A	rs2303606	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:71838597C>A	ENST00000258104.3	+	38	4285	c.4008C>A	c.(4006-4008)atC>atA	p.I1336I	DYSF_ENST00000409582.3_Silent_p.I1353I|DYSF_ENST00000429174.2_Silent_p.I1336I|DYSF_ENST00000409762.1_Silent_p.I1353I|DYSF_ENST00000409366.1_Silent_p.I1337I|DYSF_ENST00000409651.1_Silent_p.I1368I|DYSF_ENST00000410020.3_Silent_p.I1354I|DYSF_ENST00000410041.1_Silent_p.I1354I|DYSF_ENST00000394120.2_Silent_p.I1337I|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000413539.2_Silent_p.I1367I|DYSF_ENST00000409744.1_Silent_p.I1323I	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1336	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GTGCTTAGATCCTGGCATGGG	0.647													C|||	2251	0.449481	0.3585	0.5331	5008	,	,		17324	0.4792		0.5378	False		,,,				2504	0.3916				p.I1368I		Atlas-SNP	.											.	DYSF	536	.	0			c.C4104A						PASS	.	C	,,,,,,,,,,,,,	1741,2665	514.2+/-368.6	338,1065,800	53.0	51.0	52.0		4011,3966,3966,4008,4101,4059,4059,4104,4011,3969,4062,3969,4062,4008	2.8	1.0	2	dbSNP_100	52	4392,4208	577.1+/-390.5	1120,2152,1028	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	1458,3217,1828	AA,AC,CC		48.9302,39.5143,47.1552	,,,,,,,,,,,,,	1337/2082,1322/2067,1322/2088,1336/2102,1367/2112,1353/2098,1353/2119,1368/2113,1337/2103,1323/2089,1354/2099,1323/2068,1354/2120,1336/2081	71838597	6133,6873	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon39			TTAGATCCTGGCA	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4008C>A	2.37:g.71838597C>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	81	58	0.716049	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			C|0.529;A|0.471	0.471	strong		0.647	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
OR5D16	390144	hgsc.bcm.edu	37	11	55607057	55607057	+	Missense_Mutation	SNP	C	C	T	rs61896326	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55607057C>T	ENST00000378396.1	+	1	830	c.830C>T	c.(829-831)tCt>tTt	p.S277F		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				AAAGTGGCCTCTGTGTTTTAC	0.458													-|||	160	0.0319489	0.003	0.0331	5008	,	,		18104	0.001		0.0905	False		,,,				2504	0.0419				p.S277F		Atlas-SNP	.											OR5D16,NS,carcinoma,0,1	OR5D16	94	1	0			c.C830T						PASS	.	C	PHE/SER	57,4345		0,57,2144	85.0	79.0	81.0		830	0.5	0.0	11	dbSNP_129	81	682,7910		34,614,3648	no	missense	OR5D16	NM_001005496.1	155	34,671,5792	TT,TC,CC		7.9376,1.2949,5.6872	benign	277/329	55607057	739,12255	2201	4296	6497	SO:0001583	missense	390144	exon1			TGGCCTCTGTGTT	AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"""GPCR / Class A : Olfactory receptors"""	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.830C>T	11.37:g.55607057C>T	ENSP00000367649:p.Ser277Phe	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	137	68	0.49635	NM_001005496	Q6IF65|Q96RB4	Missense_Mutation	SNP	ENST00000378396.1	37	CCDS31512.1	77	0.035256410256410256	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	67	0.08839050131926121	.	10.78	1.446491	0.25987	0.012949	0.079376	ENSG00000205029	ENST00000378396	T	0.00274	8.35	4.43	0.459	0.16678	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	M	0.93420	3.415	0.09310	N	1	D	0.53885	0.963	D	0.71184	0.972	T	0.44847	-0.9301	9	0.87932	D	0	-40.4071	5.5736	0.17210	0.0:0.615:0.1533:0.2317	rs61896326	277	Q8NGK9	OR5DG_HUMAN	F	277	ENSP00000367649:S277F	ENSP00000367649:S277F	S	+	2	0	OR5D16	55363633	0.000000	0.05858	0.000000	0.03702	0.105000	0.19272	0.674000	0.25218	-0.011000	0.14247	0.537000	0.68136	TCT	C|0.951;T|0.049	0.049	strong		0.458	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496	
ADSSL1	122622	hgsc.bcm.edu	37	14	105196235	105196235	+	Silent	SNP	G	G	A	rs34672588|rs386781068	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105196235G>A	ENST00000332972.5	+	1	165	c.6G>A	c.(4-6)gtG>gtA	p.V2V	ADSSL1_ENST00000330877.2_Intron	NM_199165.1	NP_954634.1			adenylosuccinate synthase like 1											central_nervous_system(1)|cervix(1)|kidney(1)|lung(5)|ovary(2)|prostate(1)	11		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)		tcggcatggtggggaggagct	0.721													g|||	2676	0.534345	0.5514	0.4813	5008	,	,		11282	0.6042		0.4334	False		,,,				2504	0.5808				p.V2V		Atlas-SNP	.											.	ADSSL1	37	.	0			c.G6A						PASS	.	A	,	2238,1912		650,938,487	20.0	19.0	19.0		,6	-0.3	0.1	14	dbSNP_126	19	3395,4597		809,1777,1410	no	intron,coding-synonymous	ADSSL1	NM_152328.3,NM_199165.1	,	1459,2715,1897	AA,AG,GG		42.48,46.0723,46.3927	,	,2/501	105196235	5633,6509	2075	3996	6071	SO:0001819	synonymous_variant	122622	exon1			CATGGTGGGGAGG	AK095921	CCDS9990.1, CCDS9991.1	14q32.33	2010-08-05			ENSG00000185100	ENSG00000185100			20093	protein-coding gene	gene with protein product		612498					Standard	NM_199165		Approved	FLJ38602	uc001ype.3	Q8N142		ENST00000332972.5:c.6G>A	14.37:g.105196235G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	26	17	0.653846	NM_199165		Silent	SNP	ENST00000332972.5	37	CCDS9991.1																																																																																			G|0.490;A|0.510	0.510	strong		0.721	ADSSL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410531.1		
MKI67	4288	hgsc.bcm.edu	37	10	129921195	129921195	+	Silent	SNP	A	A	T	rs1063536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:129921195A>T	ENST00000368654.3	-	4	612	c.237T>A	c.(235-237)ccT>ccA	p.P79P	MKI67_ENST00000368653.3_Silent_p.P79P	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	79					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.P79P(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTAGCCGTACAGGCTCATCAA	0.353													A|||	619	0.123602	0.1641	0.1441	5008	,	,		20270	0.122		0.0875	False		,,,				2504	0.093				p.P79P		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - coding silent(1)	stomach(1)	c.T237A						PASS	.	A	,	647,3759	277.2+/-273.6	42,563,1598	144.0	135.0	138.0		237,237	-5.6	0.0	10	dbSNP_86	138	669,7931	169.3+/-220.7	28,613,3659	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	70,1176,5257	TT,TA,AA		7.7791,14.6845,10.1184	,	79/2897,79/3257	129921195	1316,11690	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon4			CCGTACAGGCTCA	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.237T>A	10.37:g.129921195A>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	220	101	0.459091	NM_001145966	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			A|0.894;T|0.106	0.106	strong		0.353	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
STAB2	55576	hgsc.bcm.edu	37	12	104048454	104048454	+	Missense_Mutation	SNP	C	C	A	rs1609860	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:104048454C>A	ENST00000388887.2	+	13	1733	c.1529C>A	c.(1528-1530)cCc>cAc	p.P510H	RP11-341G23.2_ENST00000551905.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						AAGTTAGAACCCACATTTGAG	0.458													C|||	432	0.086262	0.0045	0.0965	5008	,	,		21239	0.1091		0.0964	False		,,,				2504	0.1554				p.P510H		Atlas-SNP	.											.	STAB2	370	.	0			c.C1529A						PASS	.	C	HIS/PRO	76,4330	67.6+/-105.2	0,76,2127	105.0	94.0	98.0		1529	5.8	1.0	12	dbSNP_88	98	694,7906	172.3+/-223.0	25,644,3631	yes	missense	STAB2	NM_017564.9	77	25,720,5758	AA,AC,CC		8.0698,1.7249,5.9203	probably-damaging	510/2552	104048454	770,12236	2203	4300	6503	SO:0001583	missense	55576	exon13			TAGAACCCACATT	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.1529C>A	12.37:g.104048454C>A	ENSP00000373539:p.Pro510His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	176	0.08058608058608059	5	0.01016260162601626	32	0.08839779005524862	66	0.11538461538461539	73	0.09630606860158311	C	16.67	3.188134	0.57909	0.017249	0.080698	ENSG00000136011	ENST00000388887	T	0.65549	-0.16	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.05640	0.0148	M	0.81942	2.565	0.22266	P	0.999242006	D	0.89917	1.0	D	0.91635	0.999	T	0.49476	-0.8936	9	0.52906	T	0.07	.	19.6797	0.95957	0.0:1.0:0.0:0.0	rs1609860;rs17034278;rs52796344;rs57169136;rs1609860	510	Q8WWQ8	STAB2_HUMAN	H	510	ENSP00000373539:P510H	ENSP00000373539:P510H	P	+	2	0	STAB2	102572584	1.000000	0.71417	0.976000	0.42696	0.017000	0.09413	6.154000	0.71826	2.758000	0.94735	0.563000	0.77884	CCC	A|0.068;C|0.932;G|0.000	0.068	strong		0.458	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
ZNF335	63925	hgsc.bcm.edu	37	20	44582435	44582435	+	Missense_Mutation	SNP	G	G	T	rs41280276	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:44582435G>T	ENST00000322927.2	-	18	2695	c.2595C>A	c.(2593-2595)gaC>gaA	p.D865E	ZNF335_ENST00000426788.1_Missense_Mutation_p.D710E	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	865					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				TCTGCGGTAGGTCAGGAGGGC	0.647													G|||	114	0.0227636	0.0023	0.0216	5008	,	,		18480	0.0		0.0606	False		,,,				2504	0.0358				p.D865E		Atlas-SNP	.											.	ZNF335	115	.	0			c.C2595A						PASS	.	G	GLU/ASP	60,4346	56.2+/-92.4	2,56,2145	88.0	74.0	79.0		2595	0.6	1.0	20	dbSNP_127	79	560,8040	152.5+/-207.1	19,522,3759	yes	missense	ZNF335	NM_022095.3	45	21,578,5904	TT,TG,GG		6.5116,1.3618,4.767	benign	865/1343	44582435	620,12386	2203	4300	6503	SO:0001583	missense	63925	exon18			CGGTAGGTCAGGA	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.2595C>A	20.37:g.44582435G>T	ENSP00000325326:p.Asp865Glu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	37	CCDS13389.1	61	0.027930402930402932	0	0.0	8	0.022099447513812154	0	0.0	53	0.06992084432717678	G	6.762	0.509469	0.12883	0.013618	0.065116	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	T;T	0.07688	3.28;3.17	4.97	0.553	0.17235	.	0.262935	0.37761	N	0.001951	T	0.00552	0.0018	N	0.11560	0.145	0.25408	N	0.988386	B;D	0.58970	0.0;0.984	B;D	0.70016	0.004;0.967	T	0.29731	-1.0002	10	0.22706	T	0.39	-12.6612	2.2555	0.04054	0.1527:0.2867:0.4124:0.1482	rs41280276;rs61751048	710;865	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	E	865;642;710	ENSP00000325326:D865E;ENSP00000397098:D710E	ENSP00000243961:D642E	D	-	3	2	ZNF335	44015842	1.000000	0.71417	0.961000	0.40146	0.115000	0.19883	0.619000	0.24388	-0.021000	0.14009	-0.274000	0.10170	GAC	G|0.959;T|0.041	0.041	strong		0.647	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
OR7A10	390892	hgsc.bcm.edu	37	19	14952017	14952017	+	Missense_Mutation	SNP	T	T	A	rs11880955	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14952017T>A	ENST00000248058.1	-	1	672	c.673A>T	c.(673-675)Ata>Tta	p.I225L		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	225			I -> L (in dbSNP:rs11880955).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					ATTGCACGTATGGAGGAAACT	0.463													.|||	725	0.144768	0.2179	0.1297	5008	,	,		22434	0.0903		0.1551	False		,,,				2504	0.1022				p.I225L		Atlas-SNP	.											.	OR7A10	33	.	0			c.A673T						PASS	.	T	LEU/ILE	1043,3363	382.5+/-324.5	129,785,1289	75.0	67.0	70.0		673	2.8	0.8	19	dbSNP_120	70	1462,7138	278.3+/-293.3	141,1180,2979	no	missense	OR7A10	NM_001005190.1	5	270,1965,4268	AA,AT,TT		17.0,23.6723,19.2603	benign	225/310	14952017	2505,10501	2203	4300	6503	SO:0001583	missense	390892	exon1			CACGTATGGAGGA		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.673A>T	19.37:g.14952017T>A	ENSP00000248058:p.Ile225Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	37	0.649123	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	301	0.13782051282051283	106	0.21544715447154472	52	0.143646408839779	27	0.0472027972027972	116	0.15303430079155672	t	9.153	1.016847	0.19355	0.236723	0.17	ENSG00000127515	ENST00000248058	T	0.00227	8.5	2.75	2.75	0.32379	GPCR, rhodopsin-like superfamily (1);	0.174607	0.25645	U	0.029254	T	0.00012	0.0000	M	0.84683	2.71	0.80722	P	0.0	B	0.33612	0.419	B	0.42738	0.396	T	0.11743	-1.0575	9	0.46703	T	0.11	.	9.0825	0.36561	0.0:0.0:0.0:1.0	rs11880955;rs41345444;rs11880955	225	O76100	OR7AA_HUMAN	L	225	ENSP00000248058:I225L	ENSP00000248058:I225L	I	-	1	0	OR7A10	14813017	0.000000	0.05858	0.843000	0.33291	0.558000	0.35554	-0.384000	0.07389	1.301000	0.44836	0.113000	0.15668	ATA	T|0.831;A|0.169	0.169	strong		0.463	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
PHLDB2	90102	hgsc.bcm.edu	37	3	111672825	111672825	+	Missense_Mutation	SNP	C	C	T	rs3749298	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:111672825C>T	ENST00000431670.2	+	12	3232	c.2821C>T	c.(2821-2823)Ccc>Tcc	p.P941S	PHLDB2_ENST00000393925.3_Missense_Mutation_p.P941S|PHLDB2_ENST00000495180.1_Missense_Mutation_p.P432S|PHLDB2_ENST00000481953.1_Missense_Mutation_p.P898S|PHLDB2_ENST00000412622.1_Missense_Mutation_p.P898S|PHLDB2_ENST00000393923.3_Missense_Mutation_p.P925S	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	941			P -> S (in dbSNP:rs3749298). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)		p.P898S(1)		breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						TGTGCTCCCTCCCTCACTGGC	0.527													C|||	475	0.0948482	0.0582	0.1268	5008	,	,		19095	0.1587		0.0865	False		,,,				2504	0.0644				p.P941S		Atlas-SNP	.											PHLDB2,NS,carcinoma,0,1	PHLDB2	449	1	1	Substitution - Missense(1)	stomach(1)	c.C2821T						scavenged	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	199,4207	124.9+/-162.1	5,189,2009	94.0	79.0	84.0		2773,2821,2821,2692	5.5	0.9	3	dbSNP_107	84	681,7919	169.6+/-220.9	25,631,3644	yes	missense,missense,missense,missense	PHLDB2	NM_001134437.1,NM_001134438.1,NM_001134439.1,NM_145753.2	74,74,74,74	30,820,5653	TT,TC,CC		7.9186,4.5166,6.7661	benign,benign,benign,benign	925/1238,941/1254,941/1254,898/1211	111672825	880,12126	2203	4300	6503	SO:0001583	missense	90102	exon12			CTCCCTCCCTCAC		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"""Pleckstrin homology (PH) domain containing"""	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.2821C>T	3.37:g.111672825C>T	ENSP00000405405:p.Pro941Ser	Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_001134439	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Missense_Mutation	SNP	ENST00000431670.2	37	CCDS46886.1	239	0.10943223443223443	34	0.06910569105691057	44	0.12154696132596685	96	0.16783216783216784	65	0.08575197889182058	C	16.99	3.274672	0.59649	0.045166	0.079186	ENSG00000144824	ENST00000393923;ENST00000431670;ENST00000412622;ENST00000498699;ENST00000393925;ENST00000481953;ENST00000495180	T;T;T;T;T;T;T	0.41758	1.61;1.61;1.61;1.62;1.61;1.61;0.99	5.46	5.46	0.80206	.	0.196219	0.46442	D	0.000293	T	0.00073	0.0002	N	0.14661	0.345	0.39172	P	0.037394999999999956	B;B;B;B	0.18310	0.008;0.002;0.027;0.027	B;B;B;B	0.20577	0.012;0.004;0.018;0.03	T	0.04128	-1.0975	9	0.42905	T	0.14	.	16.5746	0.84633	0.0:1.0:0.0:0.0	rs3749298;rs52820841;rs60913710;rs3749298	432;941;898;925	E9PGF6;Q86SQ0;Q86SQ0-2;Q86SQ0-3	.;PHLB2_HUMAN;.;.	S	925;941;898;898;941;898;432	ENSP00000377500:P925S;ENSP00000405405:P941S;ENSP00000405292:P898S;ENSP00000418296:P898S;ENSP00000377502:P941S;ENSP00000418319:P898S;ENSP00000420303:P432S	ENSP00000377500:P925S	P	+	1	0	PHLDB2	113155515	0.992000	0.36948	0.947000	0.38551	0.976000	0.68499	3.235000	0.51328	2.721000	0.93114	0.655000	0.94253	CCC	C|0.912;T|0.088	0.088	strong		0.527	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753	
MT-ND4	4538	hgsc.bcm.edu	37	M	11869	11869	+	Silent	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:11869C>A	ENST00000361381.2	+	1	1110	c.1110C>A	c.(1108-1110)ccC>ccA	p.P370P	MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	370					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						CTCGCCTTACCCCCCACTATT	0.448																																					p.P370P		Atlas-SNP	.											.	.	.	.	0			c.C1110A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CTTACCCCCCACT			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1110C>A	M.37:g.11869C>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.448	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74206481	74206481	+	Silent	SNP	T	T	C	rs758774	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:74206481T>C	ENST00000286523.5	-	2	1013	c.231A>G	c.(229-231)gtA>gtG	p.V77V	ELMSAN1_ENST00000394071.2_Silent_p.V77V|ELMSAN1_ENST00000486739.1_5'Flank	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	77					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										CAGGCCCATATACCACAGAGT	0.652													C|||	4319	0.86242	0.9728	0.8213	5008	,	,		18743	0.9325		0.7654	False		,,,				2504	0.7699				p.V77V		Atlas-SNP	.											.	.	.	.	0			c.A231G						PASS	.	C	,	4136,270		1941,254,8	35.0	36.0	35.0		231,231	-1.2	0.9	14	dbSNP_86	35	6574,2014		2528,1518,248	no	coding-synonymous,coding-synonymous	C14orf43	NM_001043318.1,NM_194278.3	,	4469,1772,256	CC,CT,TT		23.4513,6.128,17.5773	,	77/1046,77/1046	74206481	10710,2284	2203	4294	6497	SO:0001819	synonymous_variant	91748	exon2			CCCATATACCACA	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.231A>G	14.37:g.74206481T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	183	181	0.989071	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Silent	SNP	ENST00000286523.5	37	CCDS9819.1																																																																																			T|0.148;C|0.852	0.852	strong		0.652	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278	
OSBPL11	114885	hgsc.bcm.edu	37	3	125266387	125266387	+	Silent	SNP	G	G	A	rs35535572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:125266387G>A	ENST00000296220.5	-	10	1993	c.1704C>T	c.(1702-1704)ccC>ccT	p.P568P		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	568					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						CATATGCACAGGGTAGAGAAA	0.418													A|||	216	0.043131	0.0076	0.098	5008	,	,		18181	0.0347		0.0716	False		,,,				2504	0.0317				p.P568P		Atlas-SNP	.											OSBPL11,NS,malignant_melanoma,-2,1	OSBPL11	64	1	0			c.C1704T						PASS	.	A		112,4294	816.4+/-416.2	4,104,2095	125.0	112.0	116.0		1704	2.3	1.0	3	dbSNP_126	116	867,7733	779.4+/-407.7	50,767,3483	no	coding-synonymous	OSBPL11	NM_022776.4		54,871,5578	AA,AG,GG		10.0814,2.542,7.5273		568/748	125266387	979,12027	2203	4300	6503	SO:0001819	synonymous_variant	114885	exon10			TGCACAGGGTAGA	AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.1704C>T	3.37:g.125266387G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	116	38	0.327586	NM_022776	A8K9I7	Silent	SNP	ENST00000296220.5	37	CCDS3033.1																																																																																			G|0.930;A|0.070	0.070	strong		0.418	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776	
GPR111	222611	hgsc.bcm.edu	37	6	47649573	47649573	+	Silent	SNP	C	C	T	rs10807371|rs71538333	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:47649573C>T	ENST00000296862.1	+	6	1278	c.1278C>T	c.(1276-1278)agC>agT	p.S426S	GPR111_ENST00000507065.1_Silent_p.S358S|GPR111_ENST00000398742.2_Silent_p.S358S			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	426	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						GTAGGCCAAGCAAATTGTTTA	0.438													C|||	2551	0.509385	0.4448	0.4323	5008	,	,		22594	0.3085		0.6272	False		,,,				2504	0.7372				p.S358S		Atlas-SNP	.											.	GPR111	123	.	0			c.C1074T						PASS	.	C		1753,2103		395,963,570	138.0	131.0	133.0		1074	3.7	0.6	6	dbSNP_120	133	5324,2930		1737,1850,540	yes	coding-synonymous	GPR111	NM_153839.6		2132,2813,1110	TT,TC,CC		35.4979,45.4616,41.5607		358/643	47649573	7077,5033	1928	4127	6055	SO:0001819	synonymous_variant	222611	exon7			GCCAAGCAAATTG	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.1278C>T	6.37:g.47649573C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Silent	SNP	ENST00000296862.1	37																																																																																				CA|0.500;TG|0.500	.	alt		0.438	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
COPA	1314	hgsc.bcm.edu	37	1	160303416	160303416	+	Silent	SNP	G	G	A	rs1802778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:160303416G>A	ENST00000241704.7	-	5	592	c.363C>T	c.(361-363)aaC>aaT	p.N121N	COPA_ENST00000368069.3_Silent_p.N121N	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	121					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)	p.N121N(1)		central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TAGATTGCCAGTTCCACACTC	0.408													A|||	3319	0.66274	0.91	0.5922	5008	,	,		18939	0.4395		0.5517	False		,,,				2504	0.7229				p.N121N		Atlas-SNP	.											COPA,NS,carcinoma,0,1	COPA	181	1	1	Substitution - coding silent(1)	stomach(1)	c.C363T						PASS	.	A	,	3761,645	277.2+/-273.6	1602,557,44	70.0	70.0	70.0		363,363	2.3	1.0	1	dbSNP_89	70	4624,3976	552.2+/-386.1	1251,2122,927	no	coding-synonymous,coding-synonymous	COPA	NM_001098398.1,NM_004371.3	,	2853,2679,971	AA,AG,GG		46.2326,14.6391,35.5298	,	121/1234,121/1225	160303416	8385,4621	2203	4300	6503	SO:0001819	synonymous_variant	1314	exon5			TTGCCAGTTCCAC	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"""WD repeat domain containing"", ""Endogenous ligands"""	2230	protein-coding gene	gene with protein product	"""proxenin"", ""xenin"""	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.363C>T	1.37:g.160303416G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_001098398	Q5T201|Q8IXZ9	Silent	SNP	ENST00000241704.7	37	CCDS1202.1																																																																																			G|0.356;A|0.644	0.644	strong		0.408	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371	
MPDU1	9526	hgsc.bcm.edu	37	17	7490810	7490810	+	Missense_Mutation	SNP	G	G	A	rs10852891	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7490810G>A	ENST00000250124.6	+	7	901	c.685G>A	c.(685-687)Gcc>Acc	p.A229T	MPDU1_ENST00000423172.2_Intron|MPDU1_ENST00000396501.4_3'UTR	NM_004870.3	NP_004861.2	O75352	MPU1_HUMAN	mannose-P-dolichol utilization defect 1	229			A -> T (in dbSNP:rs10852891). {ECO:0000269|PubMed:15489334}.		dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|oligosaccharide biosynthetic process (GO:0009312)|protein folding (GO:0006457)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)				central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(1)	7						CCTCATCGCCGCCCAGCTGCT	0.562													G|||	782	0.15615	0.1611	0.121	5008	,	,		17180	0.1567		0.159	False		,,,				2504	0.1708				p.A229T		Atlas-SNP	.											.	MPDU1	14	.	0			c.G685A						PASS	.	G	THR/ALA	778,3628	316.9+/-294.8	68,642,1493	98.0	97.0	97.0		685	2.1	1.0	17	dbSNP_120	97	1439,7161	277.1+/-292.7	135,1169,2996	yes	missense	MPDU1	NM_004870.3	58	203,1811,4489	AA,AG,GG		16.7326,17.6577,17.046	benign	229/248	7490810	2217,10789	2203	4300	6503	SO:0001583	missense	9526	exon7			ATCGCCGCCCAGC	AF038961	CCDS11115.1	17p13.1-p12	2008-07-03			ENSG00000129255	ENSG00000129255			7207	protein-coding gene	gene with protein product		604041				8663248, 9653160, 11733564	Standard	NM_004870		Approved	SL15, Lec35, PQLC5, CDGIf	uc002ghw.3	O75352	OTTHUMG00000108147	ENST00000250124.6:c.685G>A	17.37:g.7490810G>A	ENSP00000250124:p.Ala229Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	NM_004870	B3KQP1|B4DT74|Q9BUU8	Missense_Mutation	SNP	ENST00000250124.6	37	CCDS11115.1	350|350	0.16025641025641027|0.16025641025641027	82|82	0.16666666666666666|0.16666666666666666	43|43	0.11878453038674033|0.11878453038674033	104|104	0.18181818181818182|0.18181818181818182	121|121	0.15963060686015831|0.15963060686015831	G|G	15.61|15.61	2.885117|2.885117	0.51908|0.51908	0.176577|0.176577	0.167326|0.167326	ENSG00000129255|ENSG00000129255	ENST00000250124|ENST00000359822	T|.	0.75154|.	-0.91|.	5.38|5.38	2.12|2.12	0.27331|0.27331	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.00144|0.00144	0.0004|0.0004	M|M	0.64404|0.64404	1.975|1.975	0.09310|0.09310	P|P	0.9999999739491|0.9999999739491	P|.	0.37612|.	0.602|.	B|.	0.23018|.	0.043|.	T|T	0.05162|0.05162	-1.0902|-1.0902	8|6	0.36615|0.46703	T|T	0.2|0.11	0.0031|0.0031	5.5505|5.5505	0.17087|0.17087	0.0927:0.0:0.5297:0.3776|0.0927:0.0:0.5297:0.3776	rs10852891;rs17710846;rs17844933;rs17857663;rs10852891|rs10852891;rs17710846;rs17844933;rs17857663;rs10852891	229|.	O75352|.	MPU1_HUMAN|.	T|H	229|228	ENSP00000250124:A229T|.	ENSP00000250124:A229T|ENSP00000352876:R228H	A|R	+|+	1|2	0|0	MPDU1|MPDU1	7431534|7431534	0.035000|0.035000	0.19736|0.19736	0.968000|0.968000	0.41197|0.41197	0.960000|0.960000	0.62799|0.62799	0.870000|0.870000	0.28010|0.28010	0.827000|0.827000	0.34685|0.34685	0.655000|0.655000	0.94253|0.94253	GCC|CGC	G|0.828;A|0.172	0.172	strong		0.562	MPDU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226950.4		
TCF20	6942	hgsc.bcm.edu	37	22	42609148	42609148	+	Missense_Mutation	SNP	T	T	C	rs5758651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:42609148T>C	ENST00000359486.3	-	1	2300	c.2164A>G	c.(2164-2166)Agt>Ggt	p.S722G	TCF20_ENST00000335626.4_Missense_Mutation_p.S722G|TCF20_ENST00000404876.1_5'Flank	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	722			S -> G (in dbSNP:rs5758651).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						GGAAAGCCACTGACATTTCGT	0.498													T|||	995	0.198682	0.1384	0.1412	5008	,	,		20108	0.377		0.1958	False		,,,				2504	0.1401				p.S722G		Atlas-SNP	.											.	TCF20	164	.	0			c.A2164G						PASS	.	T	GLY/SER,GLY/SER	582,3824	256.7+/-261.4	38,506,1659	159.0	152.0	155.0		2164,2164	2.0	1.0	22	dbSNP_114	155	1797,6803	322.9+/-315.8	186,1425,2689	yes	missense,missense	TCF20	NM_005650.1,NM_181492.1	56,56	224,1931,4348	CC,CT,TT		20.8953,13.2093,18.2916	benign,benign	722/1961,722/1939	42609148	2379,10627	2203	4300	6503	SO:0001583	missense	6942	exon1			AGCCACTGACATT	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.2164A>G	22.37:g.42609148T>C	ENSP00000352463:p.Ser722Gly	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	37	CCDS14033.1	439	0.20100732600732601	56	0.11382113821138211	57	0.1574585635359116	175	0.30594405594405594	151	0.19920844327176782	T	5.754	0.323545	0.10900	0.132093	0.208953	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.56941	0.44;0.43	5.66	1.98	0.26296	.	0.277554	0.36665	N	0.002461	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.9999999999987778	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35724	-0.9777	9	0.29301	T	0.29	-5.7344	7.1169	0.25421	0.0:0.4771:0.0:0.5229	rs5758651;rs52815222;rs56780310;rs5758651	722;722	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	G	722	ENSP00000352463:S722G;ENSP00000335561:S722G	ENSP00000335561:S722G	S	-	1	0	TCF20	40939092	0.941000	0.31946	0.999000	0.59377	0.998000	0.95712	0.277000	0.18734	0.393000	0.25203	0.533000	0.62120	AGT	T|0.812;C|0.188	0.188	strong		0.498	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
TTN	7273	hgsc.bcm.edu	37	2	179455207	179455207	+	Silent	SNP	T	T	C	rs2163009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179455207T>C	ENST00000591111.1	-	254	56546	c.56322A>G	c.(56320-56322)acA>acG	p.T18774T	TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000460472.2_Silent_p.T11350T|TTN_ENST00000342992.6_Silent_p.T17847T|TTN_ENST00000589042.1_Silent_p.T20415T|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Silent_p.T11475T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.T11542T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18774	Fibronectin type-III 36. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCATTGTGCTGTGCCAGGTT	0.433													t|||	2566	0.51238	0.5688	0.4078	5008	,	,		22493	0.7232		0.2545	False		,,,				2504	0.5583				p.T20415T		Atlas-SNP	.											.	TTN	18412	.	0			c.A61245G						PASS	.	C	,,,	2033,1861		544,945,458	109.0	110.0	110.0		34050,53541,34425,34626	-12.2	0.0	2	dbSNP_96	110	1857,6427		195,1467,2480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	739,2412,2938	CC,CT,TT		22.4167,47.7915,31.9428	,,,	11350/26927,17847/33424,11475/27052,11542/27119	179455207	3890,8288	1947	4142	6089	SO:0001819	synonymous_variant	7273	exon304			TTGTGCTGTGCCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.56322A>G	2.37:g.179455207T>C		Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	356	177	0.497191	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.557;C|0.443	0.443	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
STEAP1B	256227	hgsc.bcm.edu	37	7	22533397	22533397	+	Splice_Site	SNP	T	T	C	rs16881810	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:22533397T>C	ENST00000406890.2	-	3	180	c.86A>G	c.(85-87)cAa>cGa	p.Q29R	STEAP1B_ENST00000404369.4_Missense_Mutation_p.Q48R	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	29			Q -> R (in dbSNP:rs16881810).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						ATGGGCTGTTTGCTGCAAATG	0.423													t|||	256	0.0511182	0.0968	0.0504	5008	,	,		18580	0.0		0.0666	False		,,,				2504	0.0266				p.Q48R		Atlas-SNP	.											.	STEAP1B	22	.	0			c.A143G						PASS	.	T	ARG/GLN,ARG/GLN	127,1257		8,111,573	79.0	59.0	65.0		143,86	1.1	0.5	7	dbSNP_123	65	290,2892		14,262,1315	no	missense,missense-near-splice	STEAP1B	NM_001164460.1,NM_207342.2	43,43	22,373,1888	CC,CT,TT		9.1138,9.1763,9.1327	possibly-damaging,possibly-damaging	48/343,29/246	22533397	417,4149	692	1591	2283	SO:0001630	splice_region_variant	256227	exon3			GCTGTTTGCTGCA		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.85-1A>G	7.37:g.22533397T>C		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	268	105	0.391791	NM_001164460	B5MCI2	Missense_Mutation	SNP	ENST00000406890.2	37	CCDS55094.1	112	0.05128205128205128	44	0.08943089430894309	17	0.04696132596685083	0	0.0	51	0.06728232189973615	t	9.268	1.045026	0.19748	0.091763	0.091138	ENSG00000105889	ENST00000406890;ENST00000404369;ENST00000424363;ENST00000439708	T;T;T;T	0.12465	2.73;2.79;2.89;2.68	1.06	1.06	0.20224	.	0.000000	0.31051	U	0.008349	T	0.00496	0.0016	M	0.73962	2.25	0.58432	P	9.99999999995449E-6	B;B	0.10296	0.003;0.0	B;B	0.09377	0.004;0.001	T	0.03514	-1.1029	9	0.45353	T	0.12	-0.1098	6.3811	0.21536	0.0:0.0:0.0:1.0	rs16881810;rs16881810	48;29	B5MCI2;Q6NZ63	.;STEAL_HUMAN	R	29;48;48;48	ENSP00000385239:Q29R;ENSP00000384370:Q48R;ENSP00000416608:Q48R;ENSP00000408954:Q48R	ENSP00000384370:Q48R	Q	-	2	0	STEAP1B	22499922	0.486000	0.25980	0.500000	0.27589	0.077000	0.17291	0.226000	0.17776	0.759000	0.33084	0.102000	0.15555	CAA	T|0.946;C|0.054	0.054	strong		0.423	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		Missense_Mutation
PROKR1	10887	hgsc.bcm.edu	37	2	68882468	68882468	+	Silent	SNP	T	T	C	rs6722313	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:68882468T>C	ENST00000303786.3	+	3	1362	c.942T>C	c.(940-942)ttT>ttC	p.F314F	PROKR1_ENST00000394342.2_Silent_p.F314F			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	314					negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			endometrium(3)|kidney(2)|large_intestine(14)|lung(9)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CCACCGTGTTTGTGAAGGAGA	0.562													C|||	2265	0.452276	0.6823	0.3055	5008	,	,		22858	0.3919		0.3171	False		,,,				2504	0.4468				p.F314F		Atlas-SNP	.											.	PROKR1	69	.	0			c.T942C						PASS	.	C		2684,1722	516.3+/-369.1	817,1050,336	180.0	130.0	147.0		942	0.8	1.0	2	dbSNP_116	147	2415,6185	699.9+/-405.1	333,1749,2218	no	coding-synonymous	PROKR1	NM_138964.2		1150,2799,2554	CC,CT,TT		28.0814,39.0831,39.205		314/394	68882468	5099,7907	2203	4300	6503	SO:0001819	synonymous_variant	10887	exon2			CGTGTTTGTGAAG	AF506287	CCDS1889.1	2p14	2012-08-08	2006-02-15	2006-02-15	ENSG00000169618	ENSG00000169618		"""GPCR / Class A : Prokineticin receptors"""	4524	protein-coding gene	gene with protein product		607122	"""G protein-coupled receptor 73"""	GPR73		10760605	Standard	NM_138964		Approved	PKR1, ZAQ, GPR73a	uc010yqj.2	Q8TCW9	OTTHUMG00000129567	ENST00000303786.3:c.942T>C	2.37:g.68882468T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	277	86	0.310469	NM_138964	A5JUU2|Q53QT9|Q8NFJ7	Silent	SNP	ENST00000303786.3	37	CCDS1889.1																																																																																			T|0.606;C|0.394	0.394	strong		0.562	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2		
MACROD1	28992	hgsc.bcm.edu	37	11	63767186	63767186	+	Silent	SNP	A	A	G	rs709594	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:63767186A>G	ENST00000255681.6	-	6	780	c.714T>C	c.(712-714)agT>agC	p.S238S	OTUB1_ENST00000535715.1_Intron	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1	238	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						CGGCAGCCTGACTGGCGCTGG	0.726													G|||	2143	0.427915	0.736	0.2493	5008	,	,		10778	0.1379		0.4463	False		,,,				2504	0.4182				p.S238S		Atlas-SNP	.											.	MACROD1	17	.	0			c.T714C						PASS	.	G		2959,1321		1069,821,250	10.0	13.0	12.0		714	3.8	1.0	11	dbSNP_86	12	3770,4672		906,1958,1357	no	coding-synonymous	MACROD1	NM_014067.3		1975,2779,1607	GG,GA,AA		44.6577,30.8645,47.1074		238/326	63767186	6729,5993	2140	4221	6361	SO:0001819	synonymous_variant	28992	exon6			AGCCTGACTGGCG	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.714T>C	11.37:g.63767186A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_014067	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			A|0.619;G|0.381	0.381	strong		0.726	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
TENM4	26011	hgsc.bcm.edu	37	11	78399121	78399121	+	Silent	SNP	G	G	A	rs1792148	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:78399121G>A	ENST00000278550.7	-	29	5700	c.5238C>T	c.(5236-5238)ggC>ggT	p.G1746G		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1746					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										TGTAGAAGGCGCCTGAGGCAG	0.542													A|||	662	0.132188	0.3222	0.1023	5008	,	,		18874	0.002		0.1342	False		,,,				2504	0.0286				p.G1746G		Atlas-SNP	.											ODZ4_ENST00000278550,colon,carcinoma,-2,1	.	.	1	0			c.C5238T						PASS	.	A		1085,3021		145,795,1113	159.0	163.0	162.0		5238	2.5	1.0	11	dbSNP_89	162	889,7415		45,799,3308	no	coding-synonymous	ODZ4	NM_001098816.2		190,1594,4421	AA,AG,GG		10.7057,26.4247,15.9065		1746/2770	78399121	1974,10436	2053	4152	6205	SO:0001819	synonymous_variant	26011	exon29			GAAGGCGCCTGAG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5238C>T	11.37:g.78399121G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	130	63	0.484615	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			G|0.864;A|0.136	0.136	strong		0.542	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
CYP27C1	339761	hgsc.bcm.edu	37	2	127953054	127953054	+	Silent	SNP	A	A	C	rs7568070	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:127953054A>C	ENST00000335247.7	-	5	706	c.576T>G	c.(574-576)acT>acG	p.T192T	CYP27C1_ENST00000409327.1_Silent_p.T192T	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	192						membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.T192T(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		GGAGGTACACAGTCCAAGACA	0.542													C|||	1399	0.279353	0.4644	0.1499	5008	,	,		17596	0.1141		0.2664	False		,,,				2504	0.3047				p.T192T		Atlas-SNP	.											CYP27C1,NS,carcinoma,0,1	CYP27C1	52	1	1	Substitution - coding silent(1)	stomach(1)	c.T576G						scavenged	.	C		1929,2477	624.5+/-394.3	419,1091,693	87.0	74.0	79.0		576	-8.9	0.2	2	dbSNP_116	79	2374,6226	701.5+/-405.2	334,1706,2260	no	coding-synonymous	CYP27C1	NM_001001665.3		753,2797,2953	CC,CA,AA		27.6047,43.7812,33.0847		192/373	127953054	4303,8703	2203	4300	6503	SO:0001819	synonymous_variant	339761	exon5			GTACACAGTCCAA	AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684		"""Cytochrome P450s"""	33480	protein-coding gene	gene with protein product							Standard	NM_001001665		Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.576T>G	2.37:g.127953054A>C		Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	173	76	0.439306	NM_001001665	Q6ZNI7	Silent	SNP	ENST00000335247.7	37	CCDS33285.1																																																																																			A|0.696;C|0.304	0.304	strong		0.542	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665	
RHOT2	89941	hgsc.bcm.edu	37	16	720960	720960	+	Silent	SNP	C	C	T	rs3743912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:720960C>T	ENST00000315082.4	+	10	822	c.708C>T	c.(706-708)aaC>aaT	p.N236N		NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	236					cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				TGTGCAGGAACGTGGCGGGCG	0.692													C|||	1070	0.213658	0.3124	0.1614	5008	,	,		8514	0.3036		0.1054	False		,,,				2504	0.136				p.N236N		Atlas-SNP	.											.	RHOT2	35	.	0			c.C708T						PASS	.	C		1159,3225	371.0+/-319.8	154,851,1187	27.0	30.0	29.0		708	-7.7	0.4	16	dbSNP_107	29	1030,7552	205.5+/-247.9	54,922,3315	no	coding-synonymous	RHOT2	NM_138769.1		208,1773,4502	TT,TC,CC		12.0019,26.437,16.8826		236/619	720960	2189,10777	2192	4291	6483	SO:0001819	synonymous_variant	89941	exon10			CAGGAACGTGGCG	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"""EF-hand domain containing"""	21169	protein-coding gene	gene with protein product	"""mitochondrial Rho (MIRO) GTPase 2"""	613889	"""chromosome 16 open reading frame 39"", ""ras homolog gene family, member T2"""	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.708C>T	16.37:g.720960C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Silent	SNP	ENST00000315082.4	37	CCDS10417.1																																																																																			C|0.824;T|0.176	0.176	strong		0.692	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769	
NLRP14	338323	hgsc.bcm.edu	37	11	7079038	7079038	+	Missense_Mutation	SNP	G	G	A	rs10839708	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7079038G>A	ENST00000299481.4	+	7	2768	c.2422G>A	c.(2422-2424)Gag>Aag	p.E808K		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	808			E -> K (in dbSNP:rs10839708). {ECO:0000269|PubMed:16931801}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GCTTTTGTGTGAGGCCTTAAG	0.383													G|||	2834	0.565895	0.3502	0.6124	5008	,	,		21400	0.7063		0.6024	False		,,,				2504	0.6421				p.E808K		Atlas-SNP	.											.	NLRP14	187	.	0			c.G2422A						PASS	.	G	LYS/GLU	1588,2814	492.5+/-362.4	294,1000,907	239.0	213.0	222.0		2422	4.0	1.0	11	dbSNP_120	222	5055,3537	630.7+/-398.4	1502,2051,743	yes	missense	NLRP14	NM_176822.3	56	1796,3051,1650	AA,AG,GG		41.1662,36.0745,48.8764	benign	808/1094	7079038	6643,6351	2201	4296	6497	SO:0001583	missense	338323	exon7			TTGTGTGAGGCCT	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.2422G>A	11.37:g.7079038G>A	ENSP00000299481:p.Glu808Lys	Somatic	446	1	0.00224215		WXS	Illumina HiSeq	Phase_I	485	238	0.490722	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	1230	0.5631868131868132	173	0.3516260162601626	214	0.5911602209944752	386	0.6748251748251748	457	0.6029023746701847	G	22.4	4.278511	0.80692	0.360745	0.588338	ENSG00000158077	ENST00000299481	T	0.41400	1.0	4.89	3.98	0.46160	.	0.000000	0.44483	D	0.000452	T	0.00012	0.0000	L	0.49699	1.58	0.30466	P	0.773848	P	0.52692	0.955	P	0.53224	0.721	T	0.38520	-0.9657	9	0.28530	T	0.3	.	9.4719	0.38847	0.0996:0.0:0.9004:0.0	rs10839708;rs17280430;rs52825881;rs59059579;rs10839708	808	Q86W24	NAL14_HUMAN	K	808	ENSP00000299481:E808K	ENSP00000299481:E808K	E	+	1	0	NLRP14	7035614	1.000000	0.71417	0.977000	0.42913	0.959000	0.62525	3.157000	0.50716	1.205000	0.43262	0.585000	0.79938	GAG	G|0.472;A|0.528	0.528	strong		0.383	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
NALCN	259232	hgsc.bcm.edu	37	13	101881777	101881777	+	Silent	SNP	G	G	A	rs3916906	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:101881777G>A	ENST00000251127.6	-	13	1674	c.1593C>T	c.(1591-1593)gtC>gtT	p.V531V	NALCN_ENST00000376196.3_Silent_p.V531V|NALCN_ENST00000470333.1_5'UTR	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	531					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.V531V(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CCAGTTCTTCGACAAAGCAGA	0.343													G|||	963	0.192292	0.1029	0.1888	5008	,	,		15730	0.0417		0.3519	False		,,,				2504	0.3067				p.V531V		Atlas-SNP	.											NALCN,NS,carcinoma,0,1	NALCN	431	1	1	Substitution - coding silent(1)	stomach(1)	c.C1593T						PASS	.	G		589,3817	260.4+/-263.7	35,519,1649	100.0	104.0	103.0		1593	-10.4	0.5	13	dbSNP_108	103	3091,5509	471.9+/-368.2	534,2023,1743	no	coding-synonymous	NALCN	NM_052867.2		569,2542,3392	AA,AG,GG		35.9419,13.3681,28.2946		531/1739	101881777	3680,9326	2203	4300	6503	SO:0001819	synonymous_variant	259232	exon13			TTCTTCGACAAAG	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1593C>T	13.37:g.101881777G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	93	33	0.354839	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																			G|0.766;N|0.000	.	strong		0.343	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
TRPM3	80036	hgsc.bcm.edu	37	9	73461337	73461337	+	Silent	SNP	T	T	A	rs7862440	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:73461337T>A	ENST00000377111.2	-	4	876	c.633A>T	c.(631-633)gcA>gcT	p.A211A	TRPM3_ENST00000377105.1_Silent_p.A58A|TRPM3_ENST00000396280.5_Silent_p.A58A|TRPM3_ENST00000377101.1_Silent_p.A58A|TRPM3_ENST00000358082.3_Silent_p.A58A|TRPM3_ENST00000396292.4_Silent_p.A58A|TRPM3_ENST00000377097.3_Silent_p.A58A|TRPM3_ENST00000396283.1_Silent_p.A58A|TRPM3_ENST00000377110.3_Silent_p.A211A|TRPM3_ENST00000408909.2_Silent_p.A58A|TRPM3_ENST00000357533.2_Silent_p.A213A|TRPM3_ENST00000361823.5_Silent_p.A58A|TRPM3_ENST00000396285.1_Silent_p.A58A|TRPM3_ENST00000423814.3_Silent_p.A213A|TRPM3_ENST00000360823.2_Silent_p.A58A|TRPM3_ENST00000377106.1_Silent_p.A58A	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	211					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						CAGTTGTCATTGCTGCTTTGA	0.483													A|||	2607	0.520567	0.5885	0.5591	5008	,	,		17392	0.2728		0.5835	False		,,,				2504	0.592				p.A211A		Atlas-SNP	.											.	TRPM3	700	.	0			c.A633T						PASS	.	A	,,,,,,,,	2473,1933	550.0+/-377.9	707,1059,437	221.0	213.0	215.0		174,633,174,174,174,174,174,174,174	2.6	1.0	9	dbSNP_116	215	5069,3531	515.0+/-378.5	1482,2105,713	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPM3	NM_001007470.1,NM_001007471.2,NM_020952.4,NM_024971.5,NM_206944.3,NM_206945.3,NM_206946.3,NM_206947.3,NM_206948.2	,,,,,,,,	2189,3164,1150	AA,AT,TT		41.0581,43.872,42.0114	,,,,,,,,	58/256,211/1708,58/1555,58/1567,58/1545,58/1557,58/1580,58/1570,58/231	73461337	7542,5464	2203	4300	6503	SO:0001819	synonymous_variant	80036	exon4			TGTCATTGCTGCT	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.633A>T	9.37:g.73461337T>A		Somatic	408	0	0		WXS	Illumina HiSeq	Phase_I	509	256	0.502947	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377111.2	37		1074|1074	0.49175824175824173|0.49175824175824173	280|280	0.5691056910569106|0.5691056910569106	214|214	0.5911602209944752|0.5911602209944752	139|139	0.243006993006993|0.243006993006993	441|441	0.5817941952506597|0.5817941952506597	A|A	10.70|10.70	1.423613|1.423613	0.25639|0.25639	0.56128|0.56128	0.589419|0.589419	ENSG00000083067|ENSG00000083067	ENST00000396280|ENST00000377097	.|.	.|.	.|.	5.54|5.54	2.61|2.61	0.31194|0.31194	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43589|0.43589	-0.9382|-0.9382	3|3	.|.	.|.	.|.	-20.3858|-20.3858	2.883|2.883	0.05653|0.05653	0.1967:0.2206:0.4692:0.1136|0.1967:0.2206:0.4692:0.1136	rs7862440;rs17845693;rs17858635;rs7862440|rs7862440;rs17845693;rs17858635;rs7862440	.|.	.|.	.|.	Y|L	58|101	.|.	.|.	N|Q	-|-	1|2	0|0	TRPM3|TRPM3	72651157|72651157	0.994000|0.994000	0.37717|0.37717	0.998000|0.998000	0.56505|0.56505	0.974000|0.974000	0.67602|0.67602	0.268000|0.268000	0.18571|0.18571	0.020000|0.020000	0.15106|0.15106	-1.003000|-1.003000	0.02500|0.02500	AAT|CAA	T|0.455;A|0.545	0.545	strong		0.483	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945	
TULP3	7289	hgsc.bcm.edu	37	12	3046802	3046802	+	Silent	SNP	A	A	G	rs33973716	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:3046802A>G	ENST00000448120.2	+	9	981	c.930A>G	c.(928-930)acA>acG	p.T310T	TULP3_ENST00000397132.2_Silent_p.T310T	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	310					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			TCCAGGAAACAAACGTACTTG	0.378													a|||	1108	0.221246	0.2163	0.1801	5008	,	,		18091	0.2083		0.2048	False		,,,				2504	0.2873				p.T310T		Atlas-SNP	.											.	TULP3	45	.	0			c.A930G						PASS	.		,	899,3505	341.8+/-306.9	91,717,1394	48.0	44.0	45.0		930,930	-1.2	1.0	12	dbSNP_126	45	1784,6816	319.9+/-314.4	168,1448,2684	no	coding-synonymous,coding-synonymous	TULP3	NM_001160408.1,NM_003324.4	,	259,2165,4078	GG,GA,AA		20.7442,20.4133,20.6321	,	310/502,310/443	3046802	2683,10321	2202	4300	6502	SO:0001819	synonymous_variant	7289	exon9			GGAAACAAACGTA	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.930A>G	12.37:g.3046802A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	230	227	0.986957	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Silent	SNP	ENST00000448120.2	37	CCDS8519.1																																																																																			A|0.796;G|0.204	0.204	strong		0.378	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
ADCK4	79934	hgsc.bcm.edu	37	19	41211056	41211056	+	Missense_Mutation	SNP	T	T	C	rs3865452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:41211056T>C	ENST00000324464.3	-	7	822	c.521A>G	c.(520-522)cAc>cGc	p.H174R	ADCK4_ENST00000450541.1_Missense_Mutation_p.H133R|ADCK4_ENST00000243583.6_Missense_Mutation_p.H133R|RNU6-195P_ENST00000411352.1_RNA	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	174			H -> R (in dbSNP:rs3865452). {ECO:0000269|PubMed:17344846}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)	p.H174R(2)		NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CTCAAAGATGTGCTGCAGCTG	0.622													C|||	2391	0.477436	0.3381	0.6441	5008	,	,		20444	0.4782		0.4901	False		,,,				2504	0.5337				p.H174R		Atlas-SNP	.											ADCK4_ENST00000324464,NS,carcinoma,0,4	ADCK4	92	4	2	Substitution - Missense(2)	stomach(2)	c.A521G						PASS	.	C	ARG/HIS,ARG/HIS	1636,2770	651.5+/-399.2	317,1002,884	39.0	36.0	37.0		398,521	2.9	1.0	19	dbSNP_108	37	4249,4351	575.6+/-390.2	1051,2147,1102	yes	missense,missense	ADCK4	NM_001142555.2,NM_024876.3	29,29	1368,3149,1986	CC,CT,TT		49.407,37.1312,45.2483	benign,benign	133/504,174/545	41211056	5885,7121	2203	4300	6503	SO:0001583	missense	79934	exon7			AAGATGTGCTGCA	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.521A>G	19.37:g.41211056T>C	ENSP00000315118:p.His174Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	NM_024876	Q8TAJ1|Q9HA52	Missense_Mutation	SNP	ENST00000324464.3	37	CCDS12562.1	1009	0.461996336996337	147	0.29878048780487804	218	0.6022099447513812	269	0.47027972027972026	375	0.4947229551451187	C	3.325	-0.137935	0.06711	0.371312	0.49407	ENSG00000123815	ENST00000324464;ENST00000450541;ENST00000243583	T;T;T	0.73047	-0.71;-0.32;-0.32	5.04	2.89	0.33648	.	0.120557	0.53938	N	0.000041	T	0.00012	0.0000	N	0.00413	-1.525	0.54753	P	1.6000000000016E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46610	-0.9179	9	0.15066	T	0.55	-6.3523	8.2791	0.31889	0.0:0.6747:0.0:0.3253	rs3865452;rs52828684;rs61182676;rs3865452	174;133	Q96D53;Q96D53-2	ADCK4_HUMAN;.	R	174;133;133	ENSP00000315118:H174R;ENSP00000412839:H133R;ENSP00000243583:H133R	ENSP00000243583:H133R	H	-	2	0	ADCK4	45902896	0.996000	0.38824	0.995000	0.50966	0.293000	0.27360	0.735000	0.26115	0.544000	0.28883	-0.215000	0.12644	CAC	T|0.557;C|0.443	0.443	strong		0.622	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
NRAP	4892	hgsc.bcm.edu	37	10	115412793	115412793	+	Silent	SNP	A	A	G	rs3737322	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:115412793A>G	ENST00000359988.3	-	6	715	c.471T>C	c.(469-471)taT>taC	p.Y157Y	NRAP_ENST00000369360.3_Silent_p.Y157Y|NRAP_ENST00000369358.4_Silent_p.Y157Y|NRAP_ENST00000360478.3_Silent_p.Y157Y	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		AGTCTTCTGTATATTCCTGTT	0.443													A|||	1543	0.308107	0.4887	0.2378	5008	,	,		16745	0.2173		0.2664	False		,,,				2504	0.2505				p.Y157Y		Atlas-SNP	.											.	NRAP	208	.	0			c.T471C						PASS	.	A	,	1969,2435		499,971,732	157.0	139.0	145.0		471,471	-1.3	0.2	10	dbSNP_107	145	2390,6210		336,1718,2246	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	835,2689,2978	GG,GA,AA		27.7907,44.7094,33.5205	,	157/1696,157/1731	115412793	4359,8645	2202	4300	6502	SO:0001819	synonymous_variant	4892	exon6			TTCTGTATATTCC		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.471T>C	10.37:g.115412793A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			A|0.676;G|0.324	0.324	strong		0.443	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
AIF1L	83543	hgsc.bcm.edu	37	9	133995669	133995669	+	Missense_Mutation	SNP	T	T	C	rs112778089	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:133995669T>C	ENST00000247291.3	+	6	501	c.413T>C	c.(412-414)gTt>gCt	p.V138A	AIF1L_ENST00000372297.2_3'UTR|AIF1L_ENST00000372312.3_Missense_Mutation_p.V143A|AIF1L_ENST00000372300.1_3'UTR|AIF1L_ENST00000372298.1_Intron|AIF1L_ENST00000372309.3_Missense_Mutation_p.V164A|AIF1L_ENST00000372301.2_Missense_Mutation_p.V82A|AIF1L_ENST00000372302.1_Missense_Mutation_p.V130A	NM_031426.3	NP_113614.1	Q9BQI0	AIF1L_HUMAN	allograft inflammatory factor 1-like	138						actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			lung(2)	2						CCCAAGCCAGTTGGCCCCCCT	0.542													T|||	3	0.000599042	0.0	0.0014	5008	,	,		14018	0.0		0.002	False		,,,				2504	0.0				p.V164A	Esophageal Squamous(95;611 1423 5044 34794 42333)	Atlas-SNP	.											.	AIF1L	15	.	0			c.T491C						PASS	.	T	ALA/VAL,,ALA/VAL	0,4406		0,0,2203	64.0	66.0	65.0		491,,413	-9.0	0.0	9	dbSNP_132	65	23,8577	16.6+/-54.9	0,23,4277	yes	missense,utr-3,missense	AIF1L	NM_001185095.1,NM_001185096.1,NM_031426.3	64,,64	0,23,6480	CC,CT,TT		0.2674,0.0,0.1768	benign,,benign	164/177,,138/151	133995669	23,12983	2203	4300	6503	SO:0001583	missense	83543	exon7			AGCCAGTTGGCCC	AL136566	CCDS6939.1, CCDS55348.1, CCDS55349.1	9q34.13-q34.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000126878	ENSG00000126878		"""EF-hand domain containing"""	28904	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 58"""	C9orf58		11230166	Standard	NM_001185095		Approved	IBA2, FLJ12783	uc004cad.2	Q9BQI0	OTTHUMG00000020817	ENST00000247291.3:c.413T>C	9.37:g.133995669T>C	ENSP00000247291:p.Val138Ala	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	181	99	0.546961	NM_001185095	B2RBC4|Q6ZR40|Q8NAX7|Q8WU47|Q9H9G0	Missense_Mutation	SNP	ENST00000247291.3	37	CCDS6939.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	6.283	0.420255	0.11928	0.0	0.002674	ENSG00000126878	ENST00000372309;ENST00000247291;ENST00000372302;ENST00000372312;ENST00000372301	T;T;T;T;T	0.61040	0.46;0.3;0.6;0.14;0.44	5.72	-9.04	0.00734	.	1.715750	0.03111	N	0.162504	T	0.34250	0.0891	N	0.25890	0.77	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.21177	-1.0253	10	0.08599	T	0.76	-0.9621	6.5492	0.22423	0.1036:0.5225:0.2109:0.1631	.	143;164;138	F5GYC9;Q9BQI0-2;Q9BQI0	.;.;AIF1L_HUMAN	A	164;138;130;143;82	ENSP00000361383:V164A;ENSP00000247291:V138A;ENSP00000361376:V130A;ENSP00000361386:V143A;ENSP00000361375:V82A	ENSP00000247291:V138A	V	+	2	0	AIF1L	132985490	0.000000	0.05858	0.001000	0.08648	0.925000	0.55904	-0.339000	0.07832	-1.647000	0.01511	-2.617000	0.00157	GTT	T|0.998;C|0.002	0.002	strong		0.542	AIF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054703.2	NM_031426	
OR2T3	343173	hgsc.bcm.edu	37	1	248637391	248637391	+	Missense_Mutation	SNP	C	C	T	rs150934113	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248637391C>T	ENST00000359594.2	+	1	765	c.740C>T	c.(739-741)tCc>tTc	p.S247F		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	247						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCCACCTGCTCCTCCCACATG	0.562																																					p.S247F		Atlas-SNP	.											OR2T3,colon,carcinoma,0,1	OR2T3	79	1	0			c.C740T						scavenged	.						208.0	180.0	190.0					1																	248637391		2203	4300	6503	SO:0001583	missense	343173	exon1			CCTGCTCCTCCCA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.740C>T	1.37:g.248637391C>T	ENSP00000352604:p.Ser247Phe	Somatic	581	1	0.00172117		WXS	Illumina HiSeq	Phase_I	584	77	0.131849	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	133	0.060897435897435896	67	0.13617886178861788	13	0.03591160220994475	22	0.038461538461538464	31	0.040897097625329816	c	12.69	2.015045	0.35511	.	.	ENSG00000196539	ENST00000359594	T	0.37058	1.22	2.37	-0.0991	0.13625	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00637	0.0021	M	0.93197	3.39	0.09310	N	1	P	0.46912	0.886	P	0.55087	0.768	T	0.01018	-1.1479	9	0.72032	D	0.01	.	5.0305	0.14407	0.0:0.4862:0.3582:0.1556	.	247	Q8NH03	OR2T3_HUMAN	F	247	ENSP00000352604:S247F	ENSP00000352604:S247F	S	+	2	0	OR2T3	246704014	0.000000	0.05858	0.014000	0.15608	0.232000	0.25224	-0.547000	0.06055	0.112000	0.17975	0.186000	0.17326	TCC	C|0.956;T|0.044	0.044	strong		0.562	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
OR51Q1	390061	hgsc.bcm.edu	37	11	5443442	5443442	+	Silent	SNP	G	G	C	rs2736590	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5443442G>C	ENST00000300778.4	+	1	102	c.12G>C	c.(10-12)gtG>gtC	p.V4V	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTCCCAGGTGACTAACACCA	0.453													G|||	2382	0.475639	0.3623	0.4006	5008	,	,		22376	0.7024		0.3986	False		,,,				2504	0.5276				p.V4V		Atlas-SNP	.											.	OR51Q1	79	.	0			c.G12C						PASS	.	G		1585,2817	495.5+/-363.3	287,1011,903	199.0	150.0	167.0		12	-1.0	0.0	11	dbSNP_100	167	3379,5215	500.2+/-375.2	680,2019,1598	no	coding-synonymous	OR51Q1	NM_001004757.2		967,3030,2501	CC,CG,GG		39.3181,36.0064,38.1964		4/318	5443442	4964,8032	2201	4297	6498	SO:0001819	synonymous_variant	390061	exon1			CCAGGTGACTAAC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.12G>C	11.37:g.5443442G>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	182	90	0.494505	NM_001004757	B2RNN1	Silent	SNP	ENST00000300778.4	37	CCDS31381.1																																																																																			G|0.587;C|0.413	0.413	strong		0.453	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
RANGAP1	5905	hgsc.bcm.edu	37	22	41652250	41652250	+	Silent	SNP	C	C	T	rs2066780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:41652250C>T	ENST00000455915.2	-	8	2402	c.933G>A	c.(931-933)ctG>ctA	p.L311L	RANGAP1_ENST00000356244.3_Silent_p.L311L|RANGAP1_ENST00000407260.4_Silent_p.L256L|RANGAP1_ENST00000405486.1_Silent_p.L311L			P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	311					mitotic cell cycle (GO:0000278)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear pore (GO:0005643)|perinuclear region of cytoplasm (GO:0048471)	Ran GTPase activator activity (GO:0005098)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CAGCAACAGCCAGGGCAGCAT	0.572													C|||	27	0.00539137	0.0008	0.0101	5008	,	,		18905	0.001		0.0119	False		,,,				2504	0.0061				p.L311L		Atlas-SNP	.											.	RANGAP1	47	.	0			c.G933A						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	102.0	93.0	96.0		933	4.3	0.9	22	dbSNP_94	96	110,8490	59.1+/-120.7	1,108,4191	no	coding-synonymous	RANGAP1	NM_002883.2		1,117,6385	TT,TC,CC		1.2791,0.2043,0.915		311/588	41652250	119,12887	2203	4300	6503	SO:0001819	synonymous_variant	5905	exon9			AACAGCCAGGGCA	X82260	CCDS14012.1	22q13	2013-01-17			ENSG00000100401	ENSG00000100401			9854	protein-coding gene	gene with protein product		602362	"""segregation distorter homolog (Drosophila)"""	SD		7878053	Standard	NM_002883		Approved	Fug1, KIAA1835	uc003azu.3	P46060	OTTHUMG00000150940	ENST00000455915.2:c.933G>A	22.37:g.41652250C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	162	78	0.481481	NM_002883	Q96JJ2	Silent	SNP	ENST00000455915.2	37	CCDS14012.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	9.239	1.037783	0.19669	0.002043	0.012791	ENSG00000100401	ENST00000446258	.	.	.	5.36	4.35	0.52113	.	.	.	.	.	T	0.62708	0.2450	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66110	-0.6005	4	.	.	.	-1.5858	13.9631	0.64193	0.0:0.9271:0.0:0.0729	rs2066780	.	.	.	S	207	.	.	G	-	1	0	RANGAP1	39982196	0.936000	0.31750	0.899000	0.35326	0.875000	0.50365	1.640000	0.37186	1.259000	0.44117	0.462000	0.41574	GGC	C|0.992;T|0.008	0.008	strong		0.572	RANGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320606.1	NM_002883	
TMCO4	255104	hgsc.bcm.edu	37	1	20097941	20097941	+	Missense_Mutation	SNP	G	G	T	rs10917536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:20097941G>T	ENST00000294543.6	-	5	455	c.214C>A	c.(214-216)Cag>Aag	p.Q72K	TMCO4_ENST00000375122.2_Missense_Mutation_p.Q72K|TMCO4_ENST00000375127.1_Missense_Mutation_p.Q72K	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	72			Q -> K (in dbSNP:rs10917536).			integral component of membrane (GO:0016021)				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		TCCAGCCACTGCACCAGGCCT	0.527													T|||	1898	0.378994	0.3918	0.3833	5008	,	,		16802	0.4315		0.3698	False		,,,				2504	0.3139				p.Q72K		Atlas-SNP	.											.	TMCO4	46	.	0			c.C214A						PASS	.	T	LYS/GLN	1802,2604	632.0+/-395.8	360,1082,761	44.0	42.0	42.0		214	4.2	1.0	1	dbSNP_120	42	2965,5635	659.3+/-401.7	506,1953,1841	yes	missense	TMCO4	NM_181719.4	53	866,3035,2602	TT,TG,GG		34.4767,40.8988,36.6523	benign	72/635	20097941	4767,8239	2203	4300	6503	SO:0001583	missense	255104	exon5			GCCACTGCACCAG		CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.214C>A	1.37:g.20097941G>T	ENSP00000294543:p.Gln72Lys	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	17	0.354167	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Missense_Mutation	SNP	ENST00000294543.6	37	CCDS198.1	810	0.3708791208791209	183	0.3719512195121951	119	0.3287292817679558	224	0.3916083916083916	284	0.37467018469656993	T	0.492	-0.875000	0.02550	0.408988	0.344767	ENSG00000162542	ENST00000294543;ENST00000375127;ENST00000375122	T;T;T	0.26660	1.76;1.73;1.72	5.39	4.25	0.50352	.	0.410133	0.29348	N	0.012415	T	0.00012	0.0000	N	0.00554	-1.385	0.46167	P	0.0010989999999999611	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47328	-0.9126	9	0.02654	T	1	-12.1827	6.5726	0.22547	0.0:0.0759:0.3019:0.6222	rs10917536;rs52824630;rs58395459;rs10917536	72;72	Q5TGY1;Q5TGY1-2	TMCO4_HUMAN;.	K	72	ENSP00000294543:Q72K;ENSP00000364269:Q72K;ENSP00000364264:Q72K	ENSP00000294543:Q72K	Q	-	1	0	TMCO4	19970528	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	1.487000	0.35540	0.349000	0.23975	-1.597000	0.00832	CAG	G|0.637;T|0.363	0.363	strong		0.527	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719	
PLXNB3	5365	hgsc.bcm.edu	37	X	153039502	153039502	+	Missense_Mutation	SNP	G	G	C	rs6643791	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153039502G>C	ENST00000361971.5	+	20	3582	c.3468G>C	c.(3466-3468)gaG>gaC	p.E1156D	PLXNB3_ENST00000538966.1_Missense_Mutation_p.E1179D|PLXNB3_ENST00000538776.1_Missense_Mutation_p.E809D|SRPK3_ENST00000489426.1_5'Flank|PLXNB3_ENST00000538282.1_Missense_Mutation_p.E766D	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1156			E -> D (in dbSNP:rs6643791). {ECO:0000269|PubMed:14702039}.		axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					TCAGCCGCGAGGGGCCTGCCC	0.687													G|||	2923	0.774305	0.5083	0.6254	3775	,	,		10389	0.5893		0.6103	False		,,,				2504	0.6227				p.E1179D		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G3537C						PASS	.	G	ASP/GLU,ASP/GLU	2559,1169		777,648,357,172,177	12.0	13.0	13.0		3537,3468	-0.6	0.0	X	dbSNP_116	13	5170,1385		1513,761,1383,119,386	no	missense,missense	PLXNB3	NM_001163257.1,NM_005393.2	45,45	2290,1409,1740,291,563	CC,CG,C,GG,G		21.1289,31.3573,24.8371	benign,benign	1179/1933,1156/1910	153039502	7729,2554	2131	4162	6293	SO:0001583	missense	5365	exon21			CCGCGAGGGGCCT	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.3468G>C	X.37:g.153039502G>C	ENSP00000355378:p.Glu1156Asp	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	1295	0.7805907172995781	193	0.6069182389937107	149	0.7028301886792453	226	0.6174863387978142	323	0.684322033898305	G	4.265	0.048215	0.08243	0.686427	0.788711	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.69561	5.2;5.16;4.57;-0.41	4.98	-0.654	0.11443	.	0.271361	0.40385	N	0.001117	T	0.00012	0.0000	L	0.33792	1.035	0.47994	P	4.309999999999592E-4	B;B;B	0.12013	0.001;0.005;0.001	B;B;B	0.17433	0.005;0.018;0.005	T	0.29274	-1.0017	9	0.33940	T	0.23	.	0.874	0.01220	0.1971:0.3293:0.2277:0.2458	rs6643791	809;1179;1156	B7Z3H9;F5H773;Q9ULL4	.;.;PLXB3_HUMAN	D	1179;1156;809;766	ENSP00000442736:E1179D;ENSP00000355378:E1156D;ENSP00000445569:E809D;ENSP00000441919:E766D	ENSP00000355378:E1156D	E	+	3	2	PLXNB3	152692696	0.142000	0.22610	0.008000	0.14137	0.112000	0.19704	-0.444000	0.06854	-0.245000	0.09625	0.468000	0.43344	GAG	G|0.218;C|0.782	0.782	strong		0.687	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
MATN2	4147	hgsc.bcm.edu	37	8	99006736	99006736	+	Silent	SNP	C	C	T	rs11559202	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:99006736C>T	ENST00000520016.1	+	6	1234	c.1110C>T	c.(1108-1110)caC>caT	p.H370H	MATN2_ENST00000521689.1_Silent_p.H370H|MATN2_ENST00000254898.5_Silent_p.H370H|MATN2_ENST00000524308.1_Intron|MATN2_ENST00000522025.2_Silent_p.H86H			O00339	MATN2_HUMAN	matrilin 2	370	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			CATCTAATCACGGATGTCAGC	0.428													C|||	609	0.121605	0.1505	0.1052	5008	,	,		18994	0.0774		0.1471	False		,,,				2504	0.1135				p.H370H		Atlas-SNP	.											.	MATN2	165	.	0			c.C1110T						PASS	.	C	,	518,3370		29,460,1455	194.0	189.0	190.0		1110,1110	-11.5	0.0	8	dbSNP_120	190	1435,6851		126,1183,2834	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	155,1643,4289	TT,TC,CC		17.3184,13.323,16.0424	,	370/957,370/938	99006736	1953,10221	1944	4143	6087	SO:0001819	synonymous_variant	4147	exon7			TAATCACGGATGT	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1110C>T	8.37:g.99006736C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	263	0.12042124542124542	74	0.15040650406504066	42	0.11602209944751381	37	0.06468531468531469	110	0.14511873350923482	C	2.388	-0.340579	0.05243	0.13323	0.173184	ENSG00000132561	ENST00000518154;ENST00000521041	.	.	.	5.73	-11.5	0.00074	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.20926	P	0.999823375	.	.	.	.	.	.	T	0.19160	-1.0314	3	.	.	.	-19.9164	13.3653	0.60680	0.0779:0.5461:0.0:0.376	rs11559202;rs17850659;rs11559202	.	.	.	W	153;125	.	.	R	+	1	2	MATN2	99075912	0.001000	0.12720	0.006000	0.13384	0.489000	0.33432	-2.225000	0.01212	-3.033000	0.00265	-1.740000	0.00687	CGG	C|0.872;T|0.128	0.128	strong		0.428	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
FLVCR2	55640	hgsc.bcm.edu	37	14	76045858	76045858	+	Silent	SNP	G	G	A	rs2287016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:76045858G>A	ENST00000238667.4	+	1	899	c.543G>A	c.(541-543)gtG>gtA	p.V181V	AC007182.6_ENST00000455232.1_RNA	NM_017791.2	NP_060261.2	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular receptor family, member 2	181					heme transport (GO:0015886)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	heme binding (GO:0020037)|heme transporter activity (GO:0015232)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15				BRCA - Breast invasive adenocarcinoma(234;0.029)		CGGTCACCGTGGTGGGCCAGC	0.627													g|||	2371	0.473442	0.7186	0.3501	5008	,	,		19556	0.5685		0.2137	False		,,,				2504	0.3988				p.V181V		Atlas-SNP	.											.	FLVCR2	39	.	0			c.G543A						PASS	.	A		2920,1486	670.9+/-402.4	974,972,257	50.0	54.0	53.0		543	0.6	0.1	14	dbSNP_100	53	1938,6662	337.1+/-322.1	219,1500,2581	no	coding-synonymous	FLVCR2	NM_017791.2		1193,2472,2838	AA,AG,GG		22.5349,33.7267,37.352		181/527	76045858	4858,8148	2203	4300	6503	SO:0001819	synonymous_variant	55640	exon1			CACCGTGGTGGGC	AK000378	CCDS9844.1, CCDS55933.1	14q24.3	2013-05-22	2007-05-01	2007-05-01	ENSG00000119686	ENSG00000119686		"""Solute carriers"""	20105	protein-coding gene	gene with protein product		610865	"""chromosome 14 open reading frame 58"", ""feline leukemia virus subgroup C cellular receptor 2"""	C14orf58		16439531, 20206334	Standard	NM_017791		Approved	FLJ20371, MFSD7C	uc001xrs.2	Q9UPI3	OTTHUMG00000171487	ENST00000238667.4:c.543G>A	14.37:g.76045858G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_017791	B7Z485|Q53ZT9|Q96JY3|Q9NX90	Silent	SNP	ENST00000238667.4	37	CCDS9844.1																																																																																			G|0.599;A|0.401	0.401	strong		0.627	FLVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413672.1	NM_017791	
SLC6A15	55117	hgsc.bcm.edu	37	12	85277608	85277608	+	Intron	SNP	C	C	T	rs17183612	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:85277608C>T	ENST00000266682.5	-	5	1298				SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000552192.1_Intron|SLC6A15_ENST00000450363.3_Silent_p.L262L	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15						amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						TGGTGATTAGCAGAATGAGGA	0.408													C|||	552	0.110224	0.0076	0.2219	5008	,	,		17451	0.002		0.3042	False		,,,				2504	0.0818				p.L262L		Atlas-SNP	.											.	SLC6A15	159	.	0			c.G786A						PASS	.	C	,,	274,4132	154.8+/-188.1	13,248,1942	83.0	75.0	78.0		,786,	-1.3	0.0	12	dbSNP_123	78	2570,6030	418.1+/-352.7	411,1748,2141	no	intron,coding-synonymous,intron	SLC6A15	NM_001146335.1,NM_018057.5,NM_182767.4	,,	424,1996,4083	TT,TC,CC		29.8837,6.2188,21.8668	,,	,262/290,	85277608	2844,10162	2203	4300	6503	SO:0001627	intron_variant	55117	exon5			GATTAGCAGAATG	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"""Solute carriers"""	13621	protein-coding gene	gene with protein product	"""homolog of rat orphan transporter v7-3"", ""sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"""	607971	"""solute carrier family 6 (neurotransmitter transporter), member 15"""			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.756+29G>A	12.37:g.85277608C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	167	165	0.988024	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Silent	SNP	ENST00000266682.5	37	CCDS9026.1																																																																																			C|0.801;T|0.199	0.199	strong		0.408	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
UPK3BL	100134938	hgsc.bcm.edu	37	7	102279621	102279621	+	Missense_Mutation	SNP	C	C	T	rs56365279	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:102279621C>T	ENST00000340457.8	-	4	560	c.511G>A	c.(511-513)Gaa>Aaa	p.E171K	RP11-514P8.6_ENST00000519541.1_Missense_Mutation_p.E171K|POLR2J2_ENST00000591000.1_3'UTR|POLR2J2_ENST00000476151.1_3'UTR	NM_001114403.2	NP_001107875.1	B0FP48	UPK3L_HUMAN	uroplakin 3B-like	171						integral component of membrane (GO:0016021)		p.E171K(1)		kidney(2)|stomach(1)	3						ACGGGTCCTTCGTCATTCATC	0.612																																					p.E171K		Atlas-SNP	.											UPK3BL,NS,carcinoma,0,4	UPK3BL	6	4	1	Substitution - Missense(1)	stomach(1)	c.G511A						PASS	.						85.0	57.0	66.0					7																	102279621		691	1584	2275	SO:0001583	missense	100134938	exon4			GTCCTTCGTCATT	EU341824	CCDS47675.1	7q22.1	2014-02-12	2010-03-03		ENSG00000267368	ENSG00000267368			37278	protein-coding gene	gene with protein product	"""uroplakin-like protein"""						Standard	NM_001114403		Approved	UPLP		B0FP48	OTTHUMG00000165036	ENST00000340457.8:c.511G>A	7.37:g.102279621C>T	ENSP00000342938:p.Glu171Lys	Somatic	514	0	0		WXS	Illumina HiSeq	Phase_I	793	109	0.137453	NM_001114403		Missense_Mutation	SNP	ENST00000340457.8	37	CCDS47675.1	.	.	.	.	.	.	.	.	.	.	c	0.114	-1.134744	0.01742	.	.	ENSG00000205236	ENST00000519541;ENST00000340457	T;T	0.62232	0.04;0.04	1.82	-0.237	0.13061	.	.	.	.	.	T	0.28896	0.0717	N	0.04508	-0.205	0.09310	N	1	.	.	.	.	.	.	T	0.20773	-1.0265	7	0.06891	T	0.86	-0.3179	3.8141	0.08808	0.0:0.4273:0.0:0.5727	rs4729821;rs9648930;rs11557253;rs17358649	.	.	.	K	171	ENSP00000429397:E171K;ENSP00000342938:E171K	ENSP00000342938:E171K	E	-	1	0	UPK3BL	102066857	0.000000	0.05858	0.168000	0.22838	0.095000	0.18619	-0.872000	0.04219	-0.225000	0.09913	0.186000	0.17326	GAA	.	.	weak		0.612	UPK3BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381510.1	NM_001114403	
ACSBG1	23205	hgsc.bcm.edu	37	15	78471954	78471954	+	Silent	SNP	G	G	A	rs17479031	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:78471954G>A	ENST00000258873.4	-	10	1627	c.1422C>T	c.(1420-1422)taC>taT	p.Y474Y	ACSBG1_ENST00000541759.1_Silent_p.Y232Y|ACSBG1_ENST00000560817.1_Silent_p.Y232Y	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	474					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						CACTGAGGCCGTAGCCCGCAT	0.567													G|||	445	0.0888578	0.0832	0.0418	5008	,	,		18281	0.0327		0.0696	False		,,,				2504	0.2076				p.Y474Y		Atlas-SNP	.											.	ACSBG1	79	.	0			c.C1422T						PASS	.	G	,	316,4076	170.1+/-200.6	13,290,1893	72.0	66.0	68.0		1410,1422	-10.1	0.6	15	dbSNP_123	68	576,8010	155.1+/-209.2	19,538,3736	no	coding-synonymous,coding-synonymous	ACSBG1	NM_001199377.1,NM_015162.4	,	32,828,5629	AA,AG,GG		6.7086,7.1949,6.8732	,	470/721,474/725	78471954	892,12086	2196	4293	6489	SO:0001819	synonymous_variant	23205	exon10			GAGGCCGTAGCCC	AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"""Acyl-CoA synthetase family"""	29567	protein-coding gene	gene with protein product	"""bubblegum"", ""very long-chain acyl-CoA synthetase"", ""lipidosin"""	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.1422C>T	15.37:g.78471954G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_015162	B2RB61|O75126|Q76N27|Q9HC26	Silent	SNP	ENST00000258873.4	37	CCDS10298.1																																																																																			G|0.936;A|0.064	0.064	strong		0.567	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162	
PKP3	11187	hgsc.bcm.edu	37	11	403980	403980	+	Silent	SNP	G	G	A	rs11748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:403980G>A	ENST00000331563.2	+	11	2191	c.2115G>A	c.(2113-2115)ccG>ccA	p.P705P		NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	705					desmosome assembly (GO:0002159)|establishment of protein localization to plasma membrane (GO:0090002)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|desmosome (GO:0030057)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)			breast(1)|central_nervous_system(1)|endometrium(3)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGAAGCTGCCGGGCAGCGTGG	0.672													g|||	2559	0.510982	0.5212	0.6066	5008	,	,		17443	0.3651		0.5606	False		,,,				2504	0.5286				p.P705P		Atlas-SNP	.											.	PKP3	36	.	0			c.G2115A						PASS	.	G		2320,2030	583.5+/-385.8	626,1068,481	30.0	34.0	33.0		2115	-7.9	0.8	11	dbSNP_52	33	4812,3748	599.7+/-394.1	1358,2096,826	no	coding-synonymous	PKP3	NM_007183.2		1984,3164,1307	AA,AG,GG		43.785,46.6667,44.756		705/798	403980	7132,5778	2175	4280	6455	SO:0001819	synonymous_variant	11187	exon11			GCTGCCGGGCAGC	Z98265	CCDS7695.1	11p15	2013-02-14			ENSG00000184363	ENSG00000184363		"""Armadillo repeat containing"""	9025	protein-coding gene	gene with protein product		605561				10374265	Standard	XM_005252760		Approved		uc001lpc.3	Q9Y446	OTTHUMG00000119068	ENST00000331563.2:c.2115G>A	11.37:g.403980G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	94	57	0.606383	NM_007183	F8J390|Q53EX8	Silent	SNP	ENST00000331563.2	37	CCDS7695.1																																																																																			G|0.467;A|0.533	0.533	strong		0.672	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183	
OR6S1	341799	hgsc.bcm.edu	37	14	21109141	21109141	+	Missense_Mutation	SNP	C	C	T	rs17277522	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21109141C>T	ENST00000320704.3	-	1	709	c.710G>A	c.(709-711)cGt>cAt	p.R237H		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	237			R -> H (in dbSNP:rs17277522).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		GGCCTTCTGACGGCCTGAAGC	0.542													c|||	2662	0.53155	0.4493	0.4539	5008	,	,		21653	0.749		0.4662	False		,,,				2504	0.5409				p.R237H		Atlas-SNP	.											.	OR6S1	49	.	0			c.G710A						PASS	.	T	HIS/ARG	1924,2482	549.6+/-377.8	395,1134,674	96.0	90.0	92.0		710	4.7	1.0	14	dbSNP_123	92	3813,4787	539.4+/-383.6	848,2117,1335	yes	missense	OR6S1	NM_001001968.1	29	1243,3251,2009	TT,TC,CC		44.3372,43.6677,44.1104	probably-damaging	237/332	21109141	5737,7269	2203	4300	6503	SO:0001583	missense	341799	exon1			TTCTGACGGCCTG	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.710G>A	14.37:g.21109141C>T	ENSP00000313110:p.Arg237His	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	37	CCDS32038.1	1149	0.5260989010989011	232	0.4715447154471545	149	0.4116022099447514	415	0.7255244755244755	353	0.4656992084432718	c	19.17	3.775961	0.70107	0.436677	0.443372	ENSG00000181803	ENST00000320704	T	0.00333	8.07	5.62	4.74	0.60224	GPCR, rhodopsin-like superfamily (1);	0.135832	0.34314	N	0.004065	T	0.00012	0.0000	M	0.83774	2.66	0.41849	P	0.009839000000000042	D	0.63880	0.993	P	0.57371	0.819	T	0.00011	-1.2439	9	0.72032	D	0.01	-6.6056	12.5829	0.56399	0.0:0.9195:0.0:0.0805	rs17277522;rs52796102;rs58862668;rs17277522	237	Q8NH40	OR6S1_HUMAN	H	237	ENSP00000313110:R237H	ENSP00000313110:R237H	R	-	2	0	OR6S1	20178981	0.000000	0.05858	0.995000	0.50966	0.963000	0.63663	0.104000	0.15313	1.377000	0.46286	-0.119000	0.15052	CGT	C|0.523;N|0.000	.	strong		0.542	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
ATHL1	80162	hgsc.bcm.edu	37	11	290888	290888	+	Silent	SNP	G	G	A	rs150075556	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:290888G>A	ENST00000409548.2	+	4	796	c.681G>A	c.(679-681)ctG>ctA	p.L227L	RP11-326C3.2_ENST00000525217.1_RNA|ATHL1_ENST00000409479.1_Silent_p.L227L|ATHL1_ENST00000409655.1_Silent_p.L50L|RP11-326C3.2_ENST00000534742.1_RNA|RP11-326C3.2_ENST00000533924.1_RNA	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	227					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		GGGGAGCTCTGTATACGGCTC	0.682													G|||	26	0.00519169	0.0	0.0144	5008	,	,		19309	0.003		0.005	False		,,,				2504	0.0082				p.L227L		Atlas-SNP	.											.	ATHL1	88	.	0			c.G681A						PASS	.	G		5,4401		0,5,2198	45.0	49.0	48.0		681	2.8	0.6	11	dbSNP_134	48	26,8574	7.1+/-27.0	0,26,4274	no	coding-synonymous	ATHL1	NM_025092.4		0,31,6472	AA,AG,GG		0.3023,0.1135,0.2384		227/738	290888	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	80162	exon4			AGCTCTGTATACG	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.681G>A	11.37:g.290888G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	162	91	0.561728	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																			G|0.995;A|0.005	0.005	strong		0.682	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
ABLIM3	22885	hgsc.bcm.edu	37	5	148630930	148630930	+	Silent	SNP	C	C	T	rs150543954		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:148630930C>T	ENST00000506113.1	+	20	2279	c.1797C>T	c.(1795-1797)agC>agT	p.S599S	ABLIM3_ENST00000508983.1_Silent_p.S566S|ABLIM3_ENST00000309868.7_Silent_p.S599S|AC012613.2_ENST00000523176.1_RNA|ABLIM3_ENST00000504238.1_Silent_p.S488S|ABLIM3_ENST00000517451.1_Silent_p.S85S|ABLIM3_ENST00000356541.3_Silent_p.S488S|RP11-331K21.1_ENST00000512647.2_RNA|RP11-331K21.1_ENST00000522685.1_RNA|ABLIM3_ENST00000326685.7_Silent_p.S504S			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	599					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGACACCCAGCGCAGACCTCT	0.597																																					p.S599S		Atlas-SNP	.											ABLIM3,NS,carcinoma,0,1	ABLIM3	91	1	0			c.C1797T						scavenged	.	C		1,4405	2.1+/-5.4	0,1,2202	92.0	63.0	73.0		1797	-0.0	1.0	5	dbSNP_134	73	0,8600		0,0,4300	no	coding-synonymous	ABLIM3	NM_014945.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		599/684	148630930	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	22885	exon21			ACCCAGCGCAGAC	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.1797C>T	5.37:g.148630930C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	199	2	0.0100503	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Silent	SNP	ENST00000506113.1	37	CCDS4294.1																																																																																			C|1.000;T|0.000	0.000	weak		0.597	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945	
AHNAK	79026	hgsc.bcm.edu	37	11	62287828	62287828	+	Silent	SNP	T	T	C	rs12292433	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62287828T>C	ENST00000378024.4	-	5	14335	c.14061A>G	c.(14059-14061)aaA>aaG	p.K4687K	AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4687					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CAACGTCCACTTTGGGTCCTG	0.502													C|||	224	0.0447284	0.1067	0.0303	5008	,	,		21713	0.0119		0.0258	False		,,,				2504	0.0245				p.K4687K		Atlas-SNP	.											AHNAK,caecum,carcinoma,0,1	AHNAK	532	1	0			c.A14061G						PASS	.	C	,	428,3976	786.1+/-414.8	18,392,1792	239.0	244.0	242.0		14061,	0.1	1.0	11	dbSNP_120	242	222,8376	809.2+/-407.2	4,214,4081	no	coding-synonymous,intron	AHNAK	NM_001620.1,NM_024060.2	,	22,606,5873	CC,CT,TT		2.582,9.7184,4.9992	,	4687/5891,	62287828	650,12352	2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			GTCCACTTTGGGT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.14061A>G	11.37:g.62287828T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																			T|0.949;C|0.051	0.051	strong		0.502	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
IL7R	3575	hgsc.bcm.edu	37	5	35874575	35874575	+	Missense_Mutation	SNP	C	C	T	rs6897932	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:35874575C>T	ENST00000303115.3	+	6	860	c.731C>T	c.(730-732)aCc>aTc	p.T244I	IL7R_ENST00000506850.1_Intron|IL7R_ENST00000343305.4_Intron	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	244			T -> I (in dbSNP:rs6897932). {ECO:0000269|PubMed:17660817, ECO:0000269|PubMed:9843216, ECO:0000269|Ref.5}.		B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)	p.T244_I245insPPVCSVT(2)|p.T244I(2)|p.T244>NECS(1)|p.T244>KKCTN(1)|p.L243_T244insMCP(1)|p.T244_I245insRPCG(1)|p.P240_T244>RFCPH(1)|p.T244_I245insCPT(1)|p.L243_T244insMPEQDCP(1)|p.T244_I245insLPCVY(1)|p.L243_T244>PIYRCVL(1)|p.L242_S246>PQGGC(1)|p.P240_S246>LKC(1)|p.L242_T243>CGIREI(1)|p.L243_T244>PCPL(1)|p.P240_S246>LQSC(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			ATCTTACTAACCATCAGCATT	0.443			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency						C|||	864	0.172524	0.0658	0.183	5008	,	,		20099	0.1687		0.2714	False		,,,				2504	0.2117				p.T244I		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	IL7R,NS,carcinoma,-1,3	IL7R	200	3	18	Insertion - In frame(7)|Complex - insertion inframe(5)|Substitution - Missense(2)|Complex - deletion inframe(2)|Complex - compound substitution(2)	haematopoietic_and_lymphoid_tissue(17)|stomach(1)	c.C731T	GRCh37	CM074279	IL7R	M	rs6897932	PASS	.	C	ILE/THR	484,3922	227.5+/-242.7	28,428,1747	251.0	218.0	229.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	731	-2.5	0.0	5	dbSNP_116	229	2300,6300	386.4+/-341.8	296,1708,2296	yes	missense	IL7R	NM_002185.2	89	324,2136,4043	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	26.7442,10.985,21.4055	benign	244/460	35874575	2784,10222	2203	4300	6503	SO:0001583	missense	3575	exon6			TACTAACCATCAG	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.731C>T	5.37:g.35874575C>T	ENSP00000306157:p.Thr244Ile	Somatic	425	0	0		WXS	Illumina HiSeq	Phase_I	453	218	0.481236	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	37	CCDS3911.1	417	0.19093406593406592	32	0.06504065040650407	72	0.19889502762430938	102	0.17832167832167833	211	0.2783641160949868	C	7.247	0.602421	0.13939	0.10985	0.267442	ENSG00000168685	ENST00000303115	D	0.96104	-3.91	5.97	-2.49	0.06403	.	1.508970	0.03292	N	0.187788	T	0.00039	0.0001	N	0.20766	0.605	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.55964	-0.8057	9	0.06757	T	0.87	-26.1859	7.3691	0.26792	0.0:0.3863:0.1198:0.4939	rs6897932;rs57894527;rs6897932	244	P16871	IL7RA_HUMAN	I	244	ENSP00000306157:T244I	ENSP00000306157:T244I	T	+	2	0	IL7R	35910332	0.000000	0.05858	0.000000	0.03702	0.889000	0.51656	-0.450000	0.06803	-0.378000	0.07918	0.655000	0.94253	ACC	C|0.810;T|0.190	0.190	strong		0.443	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2		
HECW1	23072	hgsc.bcm.edu	37	7	43484310	43484310	+	Silent	SNP	T	T	C	rs73098706	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:43484310T>C	ENST00000395891.2	+	11	2144	c.1539T>C	c.(1537-1539)tcT>tcC	p.S513S	HECW1_ENST00000453890.1_Silent_p.S513S	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	513	Glu-rich.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						GAGATGTGTCTACCCTGGAGC	0.632													T|||	1478	0.295128	0.2307	0.2839	5008	,	,		18387	0.1508		0.4155	False		,,,				2504	0.4151				p.S513S		Atlas-SNP	.											.	HECW1	540	.	0			c.T1539C						PASS	.	T		1038,3216		138,762,1227	26.0	33.0	31.0		1539	-5.1	0.0	7	dbSNP_130	31	3277,5169		673,1931,1619	no	coding-synonymous	HECW1	NM_015052.3		811,2693,2846	CC,CT,TT		38.7994,24.4006,33.9764		513/1607	43484310	4315,8385	2127	4223	6350	SO:0001819	synonymous_variant	23072	exon11			TGTGTCTACCCTG	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.1539T>C	7.37:g.43484310T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			T|0.710;C|0.290	0.290	strong		0.632	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
PLXND1	23129	hgsc.bcm.edu	37	3	129286413	129286413	+	Silent	SNP	G	G	C	rs2245285	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129286413G>C	ENST00000324093.4	-	22	4186	c.4008C>G	c.(4006-4008)ctC>ctG	p.L1336L	PLXND1_ENST00000393239.1_Silent_p.L1336L	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1336					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GCTCCTTGGTGAGATCTGTCA	0.622													C|||	2594	0.517971	0.6044	0.379	5008	,	,		18165	0.7431		0.3519	False		,,,				2504	0.4387				p.L1336L	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C4008G						PASS	.	C		2429,1977	549.3+/-377.7	655,1119,429	71.0	55.0	60.0		4008	3.5	1.0	3	dbSNP_100	60	2783,5817	668.9+/-402.6	459,1865,1976	no	coding-synonymous	PLXND1	NM_015103.2		1114,2984,2405	CC,CG,GG		32.3605,44.8706,40.0738		1336/1926	129286413	5212,7794	2203	4300	6503	SO:0001819	synonymous_variant	23129	exon22			CTTGGTGAGATCT	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.4008C>G	3.37:g.129286413G>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	123	71	0.577236	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			G|0.549;C|0.451	0.451	strong		0.622	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
ZNF407	55628	hgsc.bcm.edu	37	18	72344553	72344553	+	Silent	SNP	G	G	A	rs7227391	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:72344553G>A	ENST00000299687.5	+	1	1578	c.1578G>A	c.(1576-1578)acG>acA	p.T526T	ZNF407_ENST00000582337.1_Silent_p.T526T|ZNF407_ENST00000577538.1_Silent_p.T526T|ZNF407_ENST00000309902.6_Silent_p.T526T	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	526					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GCTCTCAGACGTTGTGTGCTT	0.542													G|||	341	0.0680911	0.112	0.0663	5008	,	,		19719	0.003		0.1064	False		,,,				2504	0.0378				p.T526T		Atlas-SNP	.											.	ZNF407	231	.	0			c.G1578A						PASS	.	G	,,	401,3607		17,367,1620	138.0	147.0	144.0		1578,1578,1578	3.0	0.0	18	dbSNP_116	144	1159,7179		87,985,3097	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	104,1352,4717	AA,AG,GG		13.9002,10.005,12.6357	,,	526/1816,526/1661,526/2249	72344553	1560,10786	2004	4169	6173	SO:0001819	synonymous_variant	55628	exon1			TCAGACGTTGTGT	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1578G>A	18.37:g.72344553G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	153	67	0.437909	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			G|0.907;A|0.093	0.093	strong		0.542	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
SMPD4	55627	hgsc.bcm.edu	37	2	130912720	130912720	+	Nonsense_Mutation	SNP	G	G	A	rs80067546	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:130912720G>A	ENST00000409031.1	-	15	2667	c.1519C>T	c.(1519-1521)Cga>Tga	p.R507*	SMPD4_ENST00000426662.2_Nonsense_Mutation_p.R143*|SMPD4_ENST00000453750.1_Nonsense_Mutation_p.R256*|SMPD4_ENST00000431183.2_Nonsense_Mutation_p.R405*|SMPD4_ENST00000351288.6_Nonsense_Mutation_p.R478*|SMPD4_ENST00000443958.2_Nonsense_Mutation_p.R171*|SMPD4_ENST00000473720.1_5'Flank|SMPD4_ENST00000452225.2_Nonsense_Mutation_p.R248*|SMPD4_ENST00000339679.7_Nonsense_Mutation_p.R365*	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	468					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	TTGGCCACTCGGAACACCATG	0.587																																					p.R507X		Atlas-SNP	.											.	SMPD4	67	.	0			c.C1519T						PASS	.						81.0	79.0	80.0					2																	130912720		2203	4300	6503	SO:0001587	stop_gained	55627	exon15			CCACTCGGAACAC	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.1519C>T	2.37:g.130912720G>A	ENSP00000386531:p.Arg507*	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	136	20	0.147059	NM_017951	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Nonsense_Mutation	SNP	ENST00000409031.1	37	CCDS42751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	38|38	7.004215|7.004215	0.97994|0.97994	.|.	.|.	ENSG00000136699|ENSG00000136699	ENST00000430682|ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750;ENST00000443958;ENST00000339679;ENST00000452225;ENST00000426662;ENST00000457039;ENST00000449159;ENST00000451542	.|.	.|.	.|.	4.24|4.24	3.32|3.32	0.38043|0.38043	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.23451|.	0.0567|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.33317|.	-0.9873|.	3|.	.|0.02654	.|T	.|1	.|.	9.2033|9.2033	0.37272|0.37272	0.0:0.0:0.568:0.432|0.0:0.0:0.568:0.432	.|.	.|.	.|.	.|.	L|X	188|478;507;405;256;171;365;248;143;104;43;249	.|.	.|ENSP00000339721:R365X	P|R	-|-	2|1	0|2	SMPD4|SMPD4	130629190|130629190	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.874000|0.874000	0.50279|0.50279	2.350000|2.350000	0.44063|0.44063	0.680000|0.680000	0.31366|0.31366	0.305000|0.305000	0.20034|0.20034	CCG|CGA	G|0.984;A|0.016	0.016	strong		0.587	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751	
MYH6	4624	hgsc.bcm.edu	37	14	23861811	23861811	+	Missense_Mutation	SNP	A	A	G	rs365990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23861811A>G	ENST00000356287.3	-	24	3331	c.3302T>C	c.(3301-3303)gTg>gCg	p.V1101A	MYH6_ENST00000405093.3_Missense_Mutation_p.V1101A			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1101			V -> A (in dbSNP:rs365990). {ECO:0000269|PubMed:1776652}.		adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		AAGGGCCAGCACCTGCTCATC	0.502													G|||	1877	0.3748	0.6437	0.2925	5008	,	,		19097	0.1597		0.3489	False		,,,				2504	0.318				p.V1101A		Atlas-SNP	.											.	MYH6	274	.	0			c.T3302C						PASS	.	G	ALA/VAL	2712,1694	513.2+/-368.3	859,994,350	197.0	191.0	193.0	http://www.ncbi.nlm.nih.gov/pubmed?term	3302	4.7	1.0	14	dbSNP_80	193	3214,5386	652.0+/-400.9	613,1988,1699	yes	missense	MYH6	NM_002471.3	64	1472,2982,2049	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	37.3721,38.4476,45.5636	benign	1101/1940	23861811	5926,7080	2203	4300	6503	SO:0001583	missense	4624	exon25			GCCAGCACCTGCT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.3302T>C	14.37:g.23861811A>G	ENSP00000348634:p.Val1101Ala	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	236	108	0.457627	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	786	0.3598901098901099	310	0.6300813008130082	123	0.3397790055248619	91	0.1590909090909091	262	0.34564643799472294	g	3.060	-0.193522	0.06259	0.615524	0.373721	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.75589	-0.95;-0.95	4.69	4.69	0.59074	Myosin tail (1);	.	.	.	.	T	0.00012	0.0000	N	0.01242	-0.935	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.41805	-0.9488	8	0.02654	T	1	.	9.4753	0.38867	0.1653:0.0:0.8347:0.0	rs365990;rs2071633;rs17199121;rs52814774;rs59057410;rs365990	1101	P13533	MYH6_HUMAN	A	1101	ENSP00000386041:V1101A;ENSP00000348634:V1101A	ENSP00000348634:V1101A	V	-	2	0	MYH6	22931651	0.072000	0.21174	0.996000	0.52242	0.607000	0.37147	2.250000	0.43178	1.118000	0.41863	-0.374000	0.07098	GTG	A|0.576;G|0.424	0.424	strong		0.502	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
PCDHAC2	56134	hgsc.bcm.edu	37	5	140347902	140347902	+	Silent	SNP	A	A	T	rs144335538	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140347902A>T	ENST00000289269.5	+	1	2083	c.1551A>T	c.(1549-1551)ccA>ccT	p.P517P	PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	517	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGGGCTGCCAGTCACCTCCT	0.507													A|||	11	0.00219649	0.0015	0.0014	5008	,	,		22726	0.0		0.008	False		,,,				2504	0.0				p.P517P	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.A1551T						PASS	.	A	,,,,,,,,,,,,,,,,,,	15,4391	21.2+/-45.6	0,15,2188	92.0	88.0	89.0		,1551,,,,,,,,,,,,,,,,,1551	3.6	1.0	5	dbSNP_134	89	94,8506	54.0+/-114.7	1,92,4207	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	1,107,6395	TT,TA,AA		1.093,0.3404,0.8381	,,,,,,,,,,,,,,,,,,	,517/1008,,,,,,,,,,,,,,,,,517/885	140347902	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			GCTGCCAGTCACC	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1551A>T	5.37:g.140347902A>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	167	86	0.51497	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			A|0.993;T|0.007	0.007	strong		0.507	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
RFPL4A	342931	hgsc.bcm.edu	37	19	56273285	56273285	+	Missense_Mutation	SNP	A	A	G	rs200422093	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56273285A>G	ENST00000434937.2	+	2	290	c.119A>G	c.(118-120)aAg>aGg	p.K40R		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	40							zinc ion binding (GO:0008270)	p.K40R(1)		haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						TCACTCCAGAAGGAGCCCGAT	0.502																																					p.K40R		Atlas-SNP	.											ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	1	Substitution - Missense(1)	stomach(1)	c.A119G						scavenged	.						3.0	2.0	2.0					19																	56273285		554	1274	1828	SO:0001583	missense	342931	exon2			TCCAGAAGGAGCC		CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638		"""RING-type (C3HC4) zinc fingers"""	16449	protein-coding gene	gene with protein product		612601	"""ret finger protein-like 4"""	RFPL4		11850190	Standard	NM_001145014		Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.119A>G	19.37:g.56273285A>G	ENSP00000392936:p.Lys40Arg	Somatic	590	1	0.00169492		WXS	Illumina HiSeq	Phase_I	671	116	0.172876	NM_001145014		Missense_Mutation	SNP	ENST00000434937.2	37	CCDS46201.1	.	.	.	.	.	.	.	.	.	.	A	8.702	0.909908	0.17833	.	.	ENSG00000223638	ENST00000434937	T	0.10005	2.92	3.31	-0.759	0.11045	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);RDM domain, Ret finger protein-like (1);	.	.	.	.	T	0.12305	0.0299	M	0.72118	2.19	0.09310	N	1	B	0.32467	0.372	B	0.39531	0.302	T	0.35748	-0.9776	9	0.32370	T	0.25	-37.9873	0.4858	0.00555	0.4389:0.2097:0.1467:0.2047	.	40	A6NLU0	RFPLA_HUMAN	R	40	ENSP00000392936:K40R	ENSP00000392936:K40R	K	+	2	0	RFPL4A	60965097	0.000000	0.05858	0.000000	0.03702	0.144000	0.21451	-0.924000	0.03996	-0.357000	0.08175	0.383000	0.25322	AAG	.	.	weak		0.502	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384184.1	XM_292796	
CSF2RA	1438	hgsc.bcm.edu	37	X	1413300	1413300	+	Silent	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:1413300C>A	ENST00000381524.3	+	8	912	c.726C>A	c.(724-726)acC>acA	p.T242T	CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000381500.1_Silent_p.T242T|CSF2RA_ENST00000355432.3_Silent_p.T242T|MIR3690_ENST00000580266.1_RNA|CSF2RA_ENST00000498153.1_3'UTR|CSF2RA_ENST00000432318.2_Silent_p.T242T|CSF2RA_ENST00000501036.2_Silent_p.T109T|CSF2RA_ENST00000381509.3_Silent_p.T242T|BX649553.1_ENST00000583047.1_RNA|BX649553.2_ENST00000578699.1_RNA|CSF2RA_ENST00000361536.3_Silent_p.T242T|CSF2RA_ENST00000355805.2_Intron|CSF2RA_ENST00000417535.2_Silent_p.T242T|CSF2RA_ENST00000381529.3_Silent_p.T242T|BX649553.3_ENST00000581137.1_RNA|BX649553.4_ENST00000580687.1_RNA			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	242	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	AGCCCAGGACCTATCAGAAGC	0.597																																					p.T242T	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.C726A						PASS	.						330.0	265.0	287.0					X																	1413300		2203	4296	6499	SO:0001819	synonymous_variant	1438	exon6			CAGGACCTATCAG	M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"""CD molecules"", ""Pseudoautosomal regions / PAR1"""	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.726C>A	X.37:g.1413300C>A		Somatic	464	0	0		WXS	Illumina HiSeq	Phase_I	263	13	0.0494297	NM_172247	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Silent	SNP	ENST00000381524.3	37	CCDS35191.1																																																																																			.	.	none		0.597	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2		
ROR2	4920	hgsc.bcm.edu	37	9	94495608	94495608	+	Missense_Mutation	SNP	T	T	C	rs10820900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:94495608T>C	ENST00000375708.3	-	6	931	c.733A>G	c.(733-735)Aca>Gca	p.T245A	ROR2_ENST00000375715.1_Missense_Mutation_p.T105A|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	245	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.		T -> A (in dbSNP:rs10820900). {ECO:0000269|PubMed:10700182, ECO:0000269|PubMed:10986040, ECO:0000269|PubMed:1334494, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.3}.		cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GGCTTGGGTGTCCGGGAGCGC	0.647													C|||	3230	0.644968	0.7587	0.5159	5008	,	,		11431	0.5268		0.659	False		,,,				2504	0.6902				p.T245A		Atlas-SNP	.											ROR2,rectum,carcinoma,0,1	ROR2	167	1	0			c.A733G						PASS	.	C	ALA/THR	3275,1131	391.0+/-327.9	1215,845,143	41.0	39.0	39.0		733	3.5	1.0	9	dbSNP_120	39	5554,3046	459.5+/-364.9	1804,1946,550	yes	missense	ROR2	NM_004560.3	58	3019,2791,693	CC,CT,TT		35.4186,25.6695,32.1159	benign	245/944	94495608	8829,4177	2203	4300	6503	SO:0001583	missense	4920	exon6			TGGGTGTCCGGGA	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.733A>G	9.37:g.94495608T>C	ENSP00000364860:p.Thr245Ala	Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	CCDS6691.1	1366	0.6254578754578755	384	0.7804878048780488	192	0.5303867403314917	291	0.5087412587412588	499	0.658311345646438	C	5.817	0.334936	0.11013	0.743305	0.645814	ENSG00000169071	ENST00000375715;ENST00000375708	T;T	0.74947	-0.89;-0.89	4.44	3.45	0.39498	Frizzled domain (2);Kringle (1);	0.182670	0.26334	N	0.024971	T	0.00012	0.0000	N	0.16656	0.425	0.52501	P	4.300000000001525E-5	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.45542	-0.9254	9	0.02654	T	1	.	4.1846	0.10392	0.0:0.5303:0.0:0.4697	rs10820900;rs10820900	245;105	Q01974;B1APY4	ROR2_HUMAN;.	A	105;245	ENSP00000364867:T105A;ENSP00000364860:T245A	ENSP00000364860:T245A	T	-	1	0	ROR2	93535429	0.000000	0.05858	0.998000	0.56505	0.714000	0.41099	0.861000	0.27885	1.109000	0.41680	-0.215000	0.12644	ACA	T|0.340;C|0.660	0.660	strong		0.647	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
DNASE1L2	1775	hgsc.bcm.edu	37	16	2287294	2287294	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2287294C>T	ENST00000564065.1	+	3	1310	c.309C>T	c.(307-309)ttC>ttT	p.F103F	RP11-304L19.12_ENST00000564055.1_lincRNA|DNASE1L2_ENST00000382437.4_Silent_p.F103F|DNASE1L2_ENST00000320700.5_Silent_p.F103F|DNASE1L2_ENST00000567494.1_Silent_p.F103F			Q92874	DNSL2_HUMAN	deoxyribonuclease I-like 2	103					corneocyte development (GO:0003335)|DNA metabolic process (GO:0006259)|hair follicle development (GO:0001942)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			endometrium(1)|prostate(1)|skin(2)	4						TGTACCTGTTCGTGTACAGGT	0.692																																					p.F103F		Atlas-SNP	.											.	DNASE1L2	14	.	0			c.C309T						PASS	.						13.0	16.0	15.0					16																	2287294		1860	4078	5938	SO:0001819	synonymous_variant	1775	exon4			CCTGTTCGTGTAC	U62647	CCDS42105.1	16p13.3	2008-02-05				ENSG00000167968			2958	protein-coding gene	gene with protein product		602622				9205125, 1577479	Standard	NM_001374		Approved	DNAS1L2	uc002cpp.3	Q92874		ENST00000564065.1:c.309C>T	16.37:g.2287294C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	17	6	0.352941	NM_001374	E9PBY4|Q6JVM2|Q6JVM3	Silent	SNP	ENST00000564065.1	37	CCDS42105.1																																																																																			.	.	none		0.692	DNASE1L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435236.1	NM_001374	
FAM161B	145483	hgsc.bcm.edu	37	14	74402693	74402693	+	Silent	SNP	C	C	T	rs17182699	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:74402693C>T	ENST00000534936.1	-	8	1869	c.1764G>A	c.(1762-1764)cgG>cgA	p.R588R	RP5-1021I20.5_ENST00000555916.1_RNA|FAM161B_ENST00000286544.3_Silent_p.R651R			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	588										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						CTTGAACAGCCCGGGTGCCTT	0.468													C|||	219	0.04373	0.0083	0.0648	5008	,	,		18871	0.0		0.1123	False		,,,				2504	0.0511				p.R651R		Atlas-SNP	.											.	FAM161B	67	.	0			c.G1953A						PASS	.	C		96,4310	78.3+/-116.7	2,92,2109	144.0	133.0	137.0		1953	-4.7	0.0	14	dbSNP_123	137	887,7713	199.4+/-243.5	56,775,3469	no	coding-synonymous	FAM161B	NM_152445.2		58,867,5578	TT,TC,CC		10.314,2.1788,7.5581		651/711	74402693	983,12023	2203	4300	6503	SO:0001819	synonymous_variant	145483	exon8			AACAGCCCGGGTG	AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 44"""	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.1764G>A	14.37:g.74402693C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	179	92	0.513967	NM_152445	B7Z882|J3KNA2	Silent	SNP	ENST00000534936.1	37		119	0.05448717948717949	1	0.0020325203252032522	29	0.08011049723756906	0	0.0	89	0.11741424802110818	C	3.048	-0.196076	0.06259	0.021788	0.10314	ENSG00000156050	ENST00000556794	.	.	.	4.86	-4.65	0.03339	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.22487	-1.0215	3	.	.	.	20.474	1.6237	0.02719	0.2691:0.1841:0.099:0.4477	rs17182699;rs60311174;rs17182699	.	.	.	S	116	.	.	G	-	1	0	FAM161B	73472446	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.111000	0.01333	-0.712000	0.04988	-0.768000	0.03414	GGC	C|0.935;T|0.065	0.065	strong		0.468	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445	
CCP110	9738	hgsc.bcm.edu	37	16	19548740	19548740	+	Silent	SNP	A	A	G	rs17227190	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:19548740A>G	ENST00000381396.5	+	4	1996	c.1749A>G	c.(1747-1749)aaA>aaG	p.K583K	CCP110_ENST00000396212.2_Silent_p.K583K|CCP110_ENST00000396208.2_Silent_p.K583K	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	583					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						GTTTTGAGAAAGTTAAACGGA	0.368													A|||	362	0.0722843	0.0023	0.1153	5008	,	,		20175	0.1458		0.0577	False		,,,				2504	0.0757				p.K583K		Atlas-SNP	.											.	CCP110	57	.	0			c.A1749G						PASS	.	A	,	83,4311	70.3+/-108.2	3,77,2117	98.0	104.0	102.0		1749,1749	4.4	1.0	16	dbSNP_123	102	603,7997	158.2+/-211.7	20,563,3717	no	coding-synonymous,coding-synonymous	CCP110	NM_001199022.1,NM_014711.4	,	23,640,5834	GG,GA,AA		7.0116,1.8889,5.2794	,	583/1013,583/992	19548740	686,12308	2197	4300	6497	SO:0001819	synonymous_variant	9738	exon4			TGAGAAAGTTAAA	AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.1749A>G	16.37:g.19548740A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	224	114	0.508929	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Silent	SNP	ENST00000381396.5	37	CCDS55992.1																																																																																			A|0.938;G|0.062;T|0.000	0.062	strong		0.368	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
COL1A2	1278	hgsc.bcm.edu	37	7	94030899	94030899	+	Silent	SNP	T	T	C	rs1800222|rs74315131	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:94030899T>C	ENST00000297268.6	+	6	717	c.246T>C	c.(244-246)gaT>gaC	p.D82D		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	82			Missing (in EDS7B). {ECO:0000269|PubMed:1577745, ECO:0000269|PubMed:2394758, ECO:0000269|PubMed:3680255}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CTCAGTATGATGGAAAAGGAG	0.279										HNSCC(75;0.22)			T|||	1524	0.304313	0.5741	0.1729	5008	,	,		9153	0.3948		0.1491	False		,,,				2504	0.0992				p.D82D		Atlas-SNP	.											.	COL1A2	240	.	0			c.T246C						PASS	.	T		2218,2188	589.6+/-387.2	560,1098,545	108.0	113.0	112.0		246	3.3	0.5	7	dbSNP_89	112	1060,7540	222.7+/-259.7	70,920,3310	no	coding-synonymous	COL1A2	NM_000089.3		630,2018,3855	CC,CT,TT		12.3256,49.6596,25.2038		82/1367	94030899	3278,9728	2203	4300	6503	SO:0001819	synonymous_variant	1278	exon6			GTATGATGGAAAA	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.246T>C	7.37:g.94030899T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	144	75	0.520833	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	37	CCDS34682.1																																																																																			T|0.716;C|0.284	0.284	strong		0.279	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
NACA	4666	hgsc.bcm.edu	37	12	57108203	57108203	+	Silent	SNP	A	A	G	rs4902	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57108203A>G	ENST00000454682.1	-	5	6047	c.5766T>C	c.(5764-5766)atT>atC	p.I1922I	NACA_ENST00000546392.1_Silent_p.I59I|NACA_ENST00000356769.3_Silent_p.I59I|NACA_ENST00000393891.4_Silent_p.I59I|NACA_ENST00000550952.1_Silent_p.I769I|NACA_ENST00000548563.1_5'UTR|NACA_ENST00000552540.1_Silent_p.I59I|NACA_ENST00000551793.1_5'UTR	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1922					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.I59I(1)|p.I1922I(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GTTCTTCATCAATTTCAGCTG	0.398			T	BCL6	NHL								A|||	3043	0.607628	0.3343	0.6657	5008	,	,		20870	0.7401		0.6252	False		,,,				2504	0.7812				p.I769I		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	NACA_ENST00000454682,NS,carcinoma,0,2	NACA	131	2	2	Substitution - coding silent(2)	prostate(2)	c.T2307C						PASS	.	A	,,,	1820,2586	533.6+/-373.7	369,1082,752	99.0	89.0	93.0		177,177,2307,177	-0.8	1.0	12	dbSNP_52	93	5345,3255	649.4+/-400.6	1667,2011,622	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NACA	NM_001113201.1,NM_001113202.1,NM_001113203.2,NM_005594.4	,,,	2036,3093,1374	GG,GA,AA		37.8488,41.3073,44.91	,,,	59/216,59/216,769/926,59/216	57108203	7165,5841	2203	4300	6503	SO:0001819	synonymous_variant	4666	exon7			TTCATCAATTTCA	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.5766T>C	12.37:g.57108203A>G		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	199	95	0.477387	NM_001113203		Silent	SNP	ENST00000454682.1	37																																																																																				T|0.000;G|0.576;C|0.000;A|0.424	0.576	strong		0.398	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
IGSF10	285313	hgsc.bcm.edu	37	3	151161330	151161330	+	Missense_Mutation	SNP	T	T	A	rs35736581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:151161330T>A	ENST00000282466.3	-	5	5404	c.5405A>T	c.(5404-5406)gAc>gTc	p.D1802V	IGSF10_ENST00000495443.1_5'Flank	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1802	Ig-like C2-type 4.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CAATGTTCCGTCAACCGTCAC	0.493													T|||	5	0.000998403	0.0	0.0014	5008	,	,		20951	0.0		0.004	False		,,,				2504	0.0				p.D1802V		Atlas-SNP	.											.	IGSF10	279	.	0			c.A5405T						PASS	.	T	VAL/ASP	9,4397	15.5+/-35.6	0,9,2194	93.0	83.0	87.0		5405	5.3	0.1	3	dbSNP_126	87	44,8556	29.0+/-79.6	0,44,4256	yes	missense	IGSF10	NM_178822.4	152	0,53,6450	AA,AT,TT		0.5116,0.2043,0.4075	probably-damaging	1802/2624	151161330	53,12953	2203	4300	6503	SO:0001583	missense	285313	exon5			GTTCCGTCAACCG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5405A>T	3.37:g.151161330T>A	ENSP00000282466:p.Asp1802Val	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	238	128	0.537815	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	11.28	1.592435	0.28357	0.002043	0.005116	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.79653	-1.29	5.26	5.26	0.73747	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.128349	0.34291	N	0.004098	D	0.84456	0.5476	M	0.79475	2.455	0.80722	D	1	P	0.50943	0.94	P	0.62885	0.908	D	0.86437	0.1764	9	.	.	.	.	12.3129	0.54938	0.0:0.0:0.1409:0.8591	rs35736581	1802	Q6WRI0	IGS10_HUMAN	V	1802;429	ENSP00000282466:D1802V	.	D	-	2	0	IGSF10	152644020	0.991000	0.36638	0.052000	0.19188	0.038000	0.13279	2.679000	0.46909	1.993000	0.58246	0.482000	0.46254	GAC	T|0.996;A|0.004	0.004	strong		0.493	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
GRID2IP	392862	hgsc.bcm.edu	37	7	6591041	6591041	+	Silent	SNP	C	C	G	rs4724818	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:6591041C>G	ENST00000457091.2	-	1	26	c.27G>C	c.(25-27)acG>acC	p.T9T		NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	9	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						AGCCCTGGTTCGTGGCCGGCG	0.637													G|||	1518	0.303115	0.2557	0.3703	5008	,	,		12344	0.2173		0.5249	False		,,,				2504	0.18				p.T9T		Atlas-SNP	.											.	GRID2IP	82	.	0			c.G27C						PASS	.						6.0	8.0	8.0					7																	6591041		684	1581	2265	SO:0001819	synonymous_variant	392862	exon1			CTGGTTCGTGGCC		CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045			18464	protein-coding gene	gene with protein product		610639	"""glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1"""			14612983	Standard	NM_001145118		Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.27G>C	7.37:g.6591041C>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_001145118		Silent	SNP	ENST00000457091.2	37	CCDS47537.1																																																																																			C|0.635;G|0.365	0.365	strong		0.637	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
PKD1L1	168507	hgsc.bcm.edu	37	7	47852837	47852837	+	Missense_Mutation	SNP	C	C	T	rs2290386	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:47852837C>T	ENST00000289672.2	-	49	7278	c.7228G>A	c.(7228-7230)Gaa>Aaa	p.E2410K	C7orf69_ENST00000258776.4_Intron|C7orf69_ENST00000418326.2_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2410			E -> K (in dbSNP:rs2290386).		detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CCTCCAACTTCGGGACTACAT	0.527													C|||	754	0.150559	0.0174	0.2133	5008	,	,		20794	0.2153		0.1799	False		,,,				2504	0.1892				p.E2410K		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G7228A						PASS	.	C	,LYS/GLU	226,4180	134.1+/-170.4	5,216,1982	103.0	106.0	105.0		,7228	-9.8	0.0	7	dbSNP_100	105	1369,7231	266.5+/-286.8	101,1167,3032	yes	intron,missense	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,56	106,1383,5014	TT,TC,CC		15.9186,5.1294,12.2636	,possibly-damaging	,2410/2850	47852837	1595,11411	2203	4300	6503	SO:0001583	missense	168507	exon49			CAACTTCGGGACT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.7228G>A	7.37:g.47852837C>T	ENSP00000289672:p.Glu2410Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	158	77	0.487342	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	342	0.1565934065934066	12	0.024390243902439025	85	0.23480662983425415	111	0.19405594405594406	134	0.17678100263852242	C	5.314	0.243209	0.10077	0.051294	0.159186	ENSG00000158683	ENST00000289672	T	0.19806	2.12	4.89	-9.77	0.00500	.	1.624130	0.03305	N	0.189679	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.15719	0.014	B	0.06405	0.002	T	0.25745	-1.0123	9	0.06757	T	0.87	0.0	7.6032	0.28087	0.0:0.2043:0.4057:0.3901	rs2290386;rs17545543;rs57785392;rs2290386	2410	Q8TDX9	PK1L1_HUMAN	K	2410	ENSP00000289672:E2410K	ENSP00000289672:E2410K	E	-	1	0	PKD1L1	47819362	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.669000	0.00398	-1.502000	0.01814	-0.819000	0.03115	GAA	C|0.865;T|0.135	0.135	strong		0.527	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
TSHZ1	10194	hgsc.bcm.edu	37	18	72997677	72997677	+	Silent	SNP	C	C	T	rs3826609	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:72997677C>T	ENST00000580243.1	+	2	663	c.315C>T	c.(313-315)agC>agT	p.S105S	TSHZ1_ENST00000322038.5_Silent_p.S60S			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	105	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		GTCCCGACAGCGTCTCGTACC	0.557													C|||	926	0.184904	0.0295	0.2997	5008	,	,		13935	0.1498		0.329	False		,,,				2504	0.2014				p.S60S		Atlas-SNP	.											.	TSHZ1	104	.	0			c.C180T						PASS	.	C		374,4032	191.6+/-217.2	16,342,1845	97.0	80.0	86.0		180	-1.2	0.0	18	dbSNP_107	86	2667,5933	429.2+/-356.1	418,1831,2051	yes	coding-synonymous	TSHZ1	NM_005786.4		434,2173,3896	TT,TC,CC		31.0116,8.4884,23.3815		60/1033	72997677	3041,9965	2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			CGACAGCGTCTCG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.315C>T	18.37:g.72997677C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				C|0.779;T|0.221	0.221	strong		0.557	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
TECPR1	25851	hgsc.bcm.edu	37	7	97847040	97847040	+	Silent	SNP	G	G	A	rs2279676	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:97847040G>A	ENST00000447648.2	-	25	3647	c.3348C>T	c.(3346-3348)caC>caT	p.H1116H	TECPR1_ENST00000379795.3_Silent_p.H1118H			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	1116					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCTTGGGCTCGTGAGGCTGCA	0.667													G|||	1040	0.207668	0.2156	0.2882	5008	,	,		16670	0.2589		0.1879	False		,,,				2504	0.1074				p.H1116H		Atlas-SNP	.											TECPR1,colon,carcinoma,0,1	TECPR1	77	1	0			c.C3348T						PASS	.	G		632,3406		41,550,1428	12.0	16.0	15.0		3348	-9.1	0.0	7	dbSNP_100	15	1048,6808		57,934,2937	no	coding-synonymous	TECPR1	NM_015395.1		98,1484,4365	AA,AG,GG		13.3401,15.6513,14.1248		1116/1166	97847040	1680,10214	2019	3928	5947	SO:0001819	synonymous_variant	25851	exon25			GGGCTCGTGAGGC		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.3348C>T	7.37:g.97847040G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	37	CCDS47648.1																																																																																			G|0.772;A|0.228	0.228	strong		0.667	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
FBXO34	55030	hgsc.bcm.edu	37	14	55817708	55817708	+	Silent	SNP	T	T	C	rs10144418	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:55817708T>C	ENST00000313833.4	+	2	845	c.600T>C	c.(598-600)taT>taC	p.Y200Y	FBXO34_ENST00000440021.1_Silent_p.Y200Y	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	200								p.Y200Y(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						ATGGAGTCTATGCTGGGAGGC	0.502													T|||	1597	0.31889	0.2073	0.3012	5008	,	,		22020	0.3185		0.4155	False		,,,				2504	0.3834				p.Y200Y		Atlas-SNP	.											FBXO34,NS,carcinoma,0,1	FBXO34	61	1	1	Substitution - coding silent(1)	stomach(1)	c.T600C						PASS	.	T	,	1078,3328	392.1+/-328.4	130,818,1255	103.0	90.0	95.0		600,600	-3.2	0.0	14	dbSNP_119	95	3534,5066	514.5+/-378.4	751,2032,1517	no	coding-synonymous,coding-synonymous	FBXO34	NM_017943.3,NM_152231.1	,	881,2850,2772	CC,CT,TT		41.093,24.4666,35.4606	,	200/712,200/712	55817708	4612,8394	2203	4300	6503	SO:0001819	synonymous_variant	55030	exon2			AGTCTATGCTGGG	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.600T>C	14.37:g.55817708T>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	225	104	0.462222	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Silent	SNP	ENST00000313833.4	37	CCDS32086.1																																																																																			T|0.655;C|0.345	0.345	strong		0.502	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
NLRP9	338321	hgsc.bcm.edu	37	19	56249672	56249672	+	Silent	SNP	A	A	G	rs56211941	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56249672A>G	ENST00000332836.2	-	1	96	c.69T>C	c.(67-69)ttT>ttC	p.F23F	RN7SKP109_ENST00000410592.1_RNA	NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	23	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		TAAATTTCCAAAACTCTTCCT	0.448													A|||	953	0.190296	0.0121	0.2349	5008	,	,		15384	0.1786		0.2068	False		,,,				2504	0.3947				p.F23F		Atlas-SNP	.											NLRP9,colon,carcinoma,0,1	NLRP9	163	1	0			c.T69C						PASS	.	A		162,4244	106.5+/-144.9	0,162,2041	120.0	128.0	125.0		69	0.5	0.4	19	dbSNP_129	125	1760,6840	316.8+/-312.9	191,1378,2731	no	coding-synonymous	NLRP9	NM_176820.2		191,1540,4772	GG,GA,AA		20.4651,3.6768,14.7778		23/992	56249672	1922,11084	2203	4300	6503	SO:0001819	synonymous_variant	338321	exon1			TTTCCAAAACTCT	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22941	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"""	609663	"""NACHT, leucine rich repeat and PYD containing 9"""	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.69T>C	19.37:g.56249672A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	173	86	0.49711	NM_176820	B2RN12|Q86W27	Silent	SNP	ENST00000332836.2	37	CCDS12934.1																																																																																			A|0.852;G|0.148	0.148	strong		0.448	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820	
GPR128	84873	hgsc.bcm.edu	37	3	100354524	100354524	+	Missense_Mutation	SNP	A	A	G	rs1144122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:100354524A>G	ENST00000273352.3	+	5	719	c.451A>G	c.(451-453)Aag>Gag	p.K151E	GPR128_ENST00000475887.1_5'UTR	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	151			K -> E (in dbSNP:rs1144122). {ECO:0000269|PubMed:14702039}.		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						AAAACAGGTAAAGGATGTCAC	0.368													A|||	762	0.152157	0.1097	0.1758	5008	,	,		19132	0.0159		0.3598	False		,,,				2504	0.1196				p.K151E	Pancreas(87;185 1975 7223 18722)	Atlas-SNP	.											.	GPR128	126	.	0			c.A451G						PASS	.	A	GLU/LYS	738,3668	302.1+/-287.2	62,614,1527	107.0	107.0	107.0		451	-1.4	0.0	3	dbSNP_87	107	2954,5646	458.0+/-364.5	501,1952,1847	yes	missense	GPR128	NM_032787.2	56	563,2566,3374	GG,GA,AA		34.3488,16.7499,28.3869	benign	151/798	100354524	3692,9314	2203	4300	6503	SO:0001583	missense	84873	exon5			CAGGTAAAGGATG	AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"""-"", ""GPCR / Class B : Orphans"""	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.451A>G	3.37:g.100354524A>G	ENSP00000273352:p.Lys151Glu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	198	93	0.469697	NM_032787	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	37	CCDS2938.1	399	0.18269230769230768	53	0.10772357723577236	67	0.1850828729281768	5	0.008741258741258742	274	0.36147757255936674	A	0.464	-0.887513	0.02511	0.167499	0.343488	ENSG00000144820	ENST00000273352	T	0.37915	1.17	5.63	-1.43	0.08884	.	1.779360	0.02534	N	0.093883	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.29058	-1.0024	9	0.05620	T	0.96	.	5.6426	0.17572	0.4414:0.1339:0.4247:0.0	rs1144122;rs17280945;rs52835550;rs60319073;rs1144122	151	Q96K78	GP128_HUMAN	E	151	ENSP00000273352:K151E	ENSP00000273352:K151E	K	+	1	0	GPR128	101837214	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.015000	0.01447	-0.594000	0.05836	-0.177000	0.13119	AAG	A|0.772;G|0.228	0.228	strong		0.368	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1		
RFC4	5984	hgsc.bcm.edu	37	3	186509517	186509517	+	Silent	SNP	G	G	A	rs187868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:186509517G>A	ENST00000392481.2	-	8	1079	c.798C>T	c.(796-798)gcC>gcT	p.A266A	RFC4_ENST00000433496.1_Silent_p.A266A|RFC4_ENST00000296273.2_Silent_p.A266A	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	266					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		CTCTTACCCCGGCAATGTCTG	0.388													A|||	2423	0.483826	0.4402	0.4942	5008	,	,		17459	0.5		0.494	False		,,,				2504	0.5082				p.A266A		Atlas-SNP	.											RFC4,colon,carcinoma,0,1	RFC4	54	1	0			c.C798T						PASS	.	A	,	2040,2366	609.3+/-391.3	467,1106,630	124.0	123.0	123.0		798,798	4.6	1.0	3	dbSNP_79	123	4135,4465	588.7+/-392.4	1011,2113,1176	no	coding-synonymous,coding-synonymous	RFC4	NM_002916.3,NM_181573.2	,	1478,3219,1806	AA,AG,GG		48.0814,46.3005,47.4781	,	266/364,266/364	186509517	6175,6831	2203	4300	6503	SO:0001819	synonymous_variant	5984	exon8			TACCCCGGCAATG		CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"""ATPases / AAA-type"""	9972	protein-coding gene	gene with protein product	"""A1 37 kDa subunit"", ""activator 1 37 kDa subunit"", ""RFC 37 kDa subunit"""	102577	"""replication factor C (activator 1) 4 (37kD)"""			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.798C>T	3.37:g.186509517G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_181573	B4DM41|D3DNV2|Q6FHX7	Silent	SNP	ENST00000392481.2	37	CCDS3283.1																																																																																			G|0.516;A|0.484	0.484	strong		0.388	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916	
ESPNL	339768	hgsc.bcm.edu	37	2	239039779	239039779	+	Silent	SNP	G	G	A	rs73102306	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:239039779G>A	ENST00000343063.3	+	9	2687	c.2424G>A	c.(2422-2424)ctG>ctA	p.L808L	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Silent_p.L440L|ESPNL_ENST00000409169.1_Silent_p.L764L	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	808										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		CCCACCTGCTGGGCAACTGGA	0.756													G|||	435	0.086861	0.0968	0.0634	5008	,	,		12580	0.0536		0.0915	False		,,,				2504	0.1196				p.L808L		Atlas-SNP	.											.	ESPNL	63	.	0			c.G2424A						PASS	.	G		281,3529		10,261,1634	3.0	3.0	3.0		2424	2.7	1.0	2	dbSNP_130	3	539,6963		9,521,3221	no	coding-synonymous	ESPNL	NM_194312.2		19,782,4855	AA,AG,GG		7.1848,7.3753,7.2489		808/1006	239039779	820,10492	1905	3751	5656	SO:0001819	synonymous_variant	339768	exon9			CCTGCTGGGCAAC	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2424G>A	2.37:g.239039779G>A		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	6	4	0.666667	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			G|0.922;A|0.078	0.078	strong		0.756	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
PIGN	23556	hgsc.bcm.edu	37	18	59768375	59768375	+	Silent	SNP	A	A	G	rs17714063	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:59768375A>G	ENST00000357637.5	-	22	2425	c.2010T>C	c.(2008-2010)acT>acC	p.T670T	PIGN_ENST00000400334.3_Silent_p.T670T	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	670					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				GACTACTCTGAGTGCTATACA	0.413													G|||	479	0.095647	0.0144	0.1239	5008	,	,		17793	0.0069		0.2694	False		,,,				2504	0.0982				p.T670T		Atlas-SNP	.											.	PIGN	62	.	0			c.T2010C						PASS	.	G	,	216,3574		5,206,1684	99.0	89.0	92.0		2010,2010	-0.1	0.5	18	dbSNP_123	92	2056,6194		246,1564,2315	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	251,1770,3999	GG,GA,AA		24.9212,5.6992,18.8704	,	670/932,670/932	59768375	2272,9768	1895	4125	6020	SO:0001819	synonymous_variant	23556	exon22			ACTCTGAGTGCTA	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.2010T>C	18.37:g.59768375A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			A|0.851;G|0.149	0.149	strong		0.413	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
RAI14	26064	hgsc.bcm.edu	37	5	34824555	34824555	+	Missense_Mutation	SNP	G	G	T	rs1048944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:34824555G>T	ENST00000265109.3	+	15	2895	c.2608G>T	c.(2608-2610)Gct>Tct	p.A870S	RAI14_ENST00000397449.1_Missense_Mutation_p.A863S|RAI14_ENST00000428746.2_Missense_Mutation_p.A870S|RAI14_ENST00000512629.1_Missense_Mutation_p.A841S|RAI14_ENST00000515799.1_Missense_Mutation_p.A873S|RAI14_ENST00000506376.1_Missense_Mutation_p.A862S|RAI14_ENST00000503673.1_Missense_Mutation_p.A870S	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	870			A -> S (in dbSNP:rs1048944). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GAAAAGATACGCTGAGAGCTC	0.368													T|||	2186	0.436502	0.2859	0.5879	5008	,	,		19028	0.369		0.4891	False		,,,				2504	0.5481				p.A873S		Atlas-SNP	.											.	RAI14	100	.	0			c.G2617T						PASS	.	T	SER/ALA,SER/ALA,SER/ALA,SER/ALA,SER/ALA,SER/ALA	1385,3015		252,881,1067	29.0	30.0	29.0		2608,2608,2521,2584,2617,2608	4.4	0.1	5	dbSNP_86	29	4233,4355		1061,2111,1122	yes	missense,missense,missense,missense,missense,missense	RAI14	NM_001145520.1,NM_001145521.1,NM_001145522.1,NM_001145523.1,NM_001145525.1,NM_015577.2	99,99,99,99,99,99	1313,2992,2189	TT,TG,GG		49.2897,31.4773,43.2553	benign,benign,benign,benign,benign,benign	870/981,870/981,841/952,862/973,873/984,870/981	34824555	5618,7370	2200	4294	6494	SO:0001583	missense	26064	exon17			AGATACGCTGAGA	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.2608G>T	5.37:g.34824555G>T	ENSP00000265109:p.Ala870Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	928	0.4249084249084249	149	0.30284552845528456	212	0.585635359116022	198	0.34615384615384615	369	0.4868073878627968	T	9.574	1.121851	0.20877	0.314773	0.492897	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02;2.02	5.63	4.43	0.53597	.	.	.	.	.	T	0.00012	0.0000	N	0.00670	-1.27	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.39961	-0.9588	8	0.10111	T	0.7	-2.7917	8.8112	0.34967	0.1267:0.0:0.133:0.7403	rs1048944;rs3189001;rs52791950;rs60733664	862;841;873;870	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	S	870;841;870;870;873;862;863	ENSP00000265109:A870S;ENSP00000422377:A841S;ENSP00000388725:A870S;ENSP00000422942:A870S;ENSP00000427123:A873S;ENSP00000423854:A862S;ENSP00000380591:A863S	ENSP00000265109:A870S	A	+	1	0	RAI14	34860312	0.249000	0.23941	0.132000	0.22025	0.973000	0.67179	0.620000	0.24403	0.385000	0.24970	-0.375000	0.07067	GCT	A|0.004;C|0.007	.	strong		0.368	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
KLK1	3816	hgsc.bcm.edu	37	19	51323232	51323232	+	Missense_Mutation	SNP	T	T	C	rs5517	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51323232T>C	ENST00000301420.2	-	4	591	c.556A>G	c.(556-558)Aaa>Gaa	p.K186E	CTD-2568A17.5_ENST00000326989.5_lincRNA|KLK1_ENST00000448701.2_Missense_Mutation_p.K84E	NM_002257.2	NP_002248.1	P06870	KLK1_HUMAN	kallikrein 1	186	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		K -> E (in dbSNP:rs5517). {ECO:0000269|PubMed:3004571, ECO:0000269|PubMed:3853975, ECO:0000269|Ref.7}.			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			breast(1)|large_intestine(4)|lung(7)|urinary_tract(1)	13		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00399)	Aprotinin(DB06692)	TGGGCTTTTTTGCACTCATCA	0.557													t|||	1700	0.339457	0.1815	0.4568	5008	,	,		19193	0.5972		0.2674	False		,,,				2504	0.2781				p.K186E		Atlas-SNP	.											.	KLK1	27	.	0			c.A556G	GRCh37	CM074309	KLK1	M	rs5517	PASS	.		GLU/LYS	865,3541		80,705,1418	109.0	86.0	94.0		556	-0.6	0.0	19	dbSNP_52	94	2310,6290		313,1684,2303	yes	missense	KLK1	NM_002257.2	56	393,2389,3721	CC,CT,TT		26.8605,19.6323,24.4118	benign	186/263	51323232	3175,9831	2203	4300	6503	SO:0001583	missense	3816	exon4			CTTTTTTGCACTC	L10038	CCDS12804.1	19q13.3	2008-02-05	2006-10-27			ENSG00000167748	3.4.21.35	"""Kallikreins"""	6357	protein-coding gene	gene with protein product		147910	"""kallikrein 1, renal/pancreas/salivary"""			1684954, 16800724, 16800723	Standard	NM_002257		Approved	Klk6	uc002ptk.1	P06870		ENST00000301420.2:c.556A>G	19.37:g.51323232T>C	ENSP00000301420:p.Lys186Glu	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	237	117	0.493671	NM_002257	Q66US9|Q86U61|Q8TCV8|Q9BS53|Q9NQU4|Q9UD19|Q9UMJ1	Missense_Mutation	SNP	ENST00000301420.2	37	CCDS12804.1	791	0.36217948717948717	94	0.1910569105691057	151	0.4171270718232044	336	0.5874125874125874	210	0.2770448548812665	N	0.052	-1.247545	0.01469	0.196323	0.268605	ENSG00000167748	ENST00000301420;ENST00000448701	D;D	0.88664	-2.41;-2.41	2.89	-0.553	0.11815	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B	0.14805	0.011	B	0.19391	0.025	T	0.26503	-1.0101	8	0.02654	T	1	.	6.4041	0.21654	0.0:0.5048:0.0:0.4952	rs5517;rs3195245;rs3819318;rs17800555;rs61327587;rs5517	186	P06870	KLK1_HUMAN	E	186;84	ENSP00000301420:K186E;ENSP00000400994:K84E	ENSP00000301420:K186E	K	-	1	0	KLK1	56015044	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.665000	0.01965	-0.281000	0.09141	-0.747000	0.03512	AAA	T|0.707;C|0.293	0.293	strong		0.557	KLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464135.2	NM_002257	
HR	55806	hgsc.bcm.edu	37	8	21976710	21976710	+	Missense_Mutation	SNP	T	T	C	rs7014851	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21976710T>C	ENST00000381418.4	-	15	4544	c.3064A>G	c.(3064-3066)Aca>Gca	p.T1022A	HR_ENST00000312841.8_Missense_Mutation_p.T1022A	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	1022	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.		T -> A (in ALUNC; dbSNP:rs7014851). {ECO:0000269|PubMed:9445480}.		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		GGCAGTGGTGTGTCGGCATGC	0.642													C|||	392	0.0782748	0.261	0.0418	5008	,	,		15589	0.0		0.0159	False		,,,				2504	0.002				p.T1022A		Atlas-SNP	.											.	HR	71	.	0			c.A3064G	GRCh37	CM983990	HR	M	rs7014851	PASS	.	C	ALA/THR,ALA/THR	1101,3305	718.9+/-408.9	131,839,1233	64.0	59.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3064,3064	4.3	0.0	8	dbSNP_116	61	138,8462	812.3+/-407.1	1,136,4163	yes	missense,missense	HR	NM_005144.4,NM_018411.4	58,58	132,975,5396	CC,CT,TT		1.6047,24.9887,9.5264	benign,benign	1022/1190,1022/1135	21976710	1239,11767	2203	4300	6503	SO:0001583	missense	55806	exon15			GTGGTGTGTCGGC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.3064A>G	8.37:g.21976710T>C	ENSP00000370826:p.Thr1022Ala	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	164	0.07509157509157509	140	0.2845528455284553	15	0.04143646408839779	0	0.0	9	0.011873350923482849	C	0.021	-1.420024	0.01136	0.249887	0.016047	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.69806	-0.43;-0.43	5.18	4.29	0.51040	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.56097	N	0.000034	T	0.00012	0.0000	N	0.00210	-1.845	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16129	-1.0413	9	0.17832	T	0.49	-2.4672	7.2891	0.26356	0.0:0.7386:0.1695:0.0919	rs7014851;rs7014851	1022;1022	O43593-2;O43593	.;HAIR_HUMAN	A	1022	ENSP00000370826:T1022A;ENSP00000326765:T1022A	ENSP00000326765:T1022A	T	-	1	0	HR	22032655	0.965000	0.33210	0.010000	0.14722	0.026000	0.11368	1.953000	0.40352	0.571000	0.29365	-0.642000	0.03964	ACA	T|0.909;C|0.091	0.091	strong		0.642	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
WDR66	144406	hgsc.bcm.edu	37	12	122405912	122405912	+	Splice_Site	SNP	G	G	T	rs1169081	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:122405912G>T	ENST00000288912.4	+	17	3462	c.2608G>T	c.(2608-2610)Gtg>Ttg	p.V870L	WDR66_ENST00000545752.1_3'UTR|WDR66_ENST00000397454.2_Splice_Site_p.V870L	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	870				V -> L (in Ref. 2; AAH28421 and 4; CAD38786). {ECO:0000305}.			calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		TCCTTTCTAGGTGGGACTTCA	0.527													G|||	1474	0.294329	0.0877	0.3631	5008	,	,		21223	0.4702		0.3121	False		,,,				2504	0.3252				p.V870L	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.G2608T						PASS	.	G	LEU/VAL,LEU/VAL	429,3459		32,365,1547	101.0	99.0	100.0		2608,2608	5.2	1.0	12	dbSNP_87	100	2488,5778		383,1722,2028	yes	missense-near-splice,missense-near-splice	WDR66	NM_001178003.1,NM_144668.5	32,32	415,2087,3575	TT,TG,GG		30.0992,11.034,24.0003	possibly-damaging,possibly-damaging	870/942,870/1150	122405912	2917,9237	1944	4133	6077	SO:0001630	splice_region_variant	144406	exon17			TTCTAGGTGGGAC	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.2608-1G>T	12.37:g.122405912G>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	85	30	0.352941	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	686	0.3141025641025641	46	0.09349593495934959	123	0.3397790055248619	277	0.48426573426573427	240	0.316622691292876	G	17.08	3.298504	0.60195	0.11034	0.300992	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.54479	0.57;1.31	5.19	5.19	0.71726	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.139333	0.47455	D	0.000222	T	0.00012	0.0000	L	0.55743	1.74	0.20703	P	0.999862575	P	0.35745	0.518	B	0.37091	0.241	T	0.47484	-0.9114	8	.	.	.	.	18.7082	0.91646	0.0:0.0:1.0:0.0	rs1169081;rs1720054;rs17298029;rs60986192;rs1169081	870	Q8TBY9	WDR66_HUMAN	L	870	ENSP00000288912:V870L;ENSP00000380595:V870L	.	V	+	1	0	WDR66	120890295	1.000000	0.71417	1.000000	0.80357	0.345000	0.29048	5.134000	0.64770	2.420000	0.82092	0.561000	0.74099	GTG	G|0.708;T|0.292	0.292	strong		0.527	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	Missense_Mutation
DNAH14	127602	hgsc.bcm.edu	37	1	225495168	225495168	+	Missense_Mutation	SNP	G	G	A	rs112172758	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225495168G>A	ENST00000445597.2	+	39	6773	c.6773G>A	c.(6772-6774)cGc>cAc	p.R2258H	DNAH14_ENST00000439375.2_Missense_Mutation_p.R2911H|DNAH14_ENST00000430092.1_Missense_Mutation_p.R2911H			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2258					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TTCAGGGATCGCTTCCATATG	0.338													G|||	115	0.0229633	0.003	0.0231	5008	,	,		16445	0.0		0.0507	False		,,,				2504	0.045				p.R2911H		Atlas-SNP	.											.	DNAH14	300	.	0			c.G8732A						PASS	.	G	HIS/ARG	10,1374		0,10,682	104.0	84.0	90.0		8732	-0.2	0.0	1	dbSNP_132	90	159,3023		2,155,1434	yes	missense	DNAH14	NM_001373.1	29	2,165,2116	AA,AG,GG		4.9969,0.7225,3.7013	benign	2911/4516	225495168	169,4397	692	1591	2283	SO:0001583	missense	127602	exon57			GGGATCGCTTCCA	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.6773G>A	1.37:g.225495168G>A	ENSP00000409472:p.Arg2258His	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		46	0.021062271062271064	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	36	0.047493403693931395	G	10.89	1.479593	0.26511	0.007225	0.049969	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.80994	-1.44;-1.44;-1.44	5.04	-0.22	0.13130	.	0.262219	0.20313	N	0.094786	T	0.40932	0.1137	M	0.86097	2.795	0.09310	N	1	B	0.29232	0.238	B	0.22601	0.04	T	0.58736	-0.7584	10	0.49607	T	0.09	.	8.715	0.34405	0.4004:0.0:0.5996:0.0	.	2911	Q0VDD8-4	.	H	2258;2911;2911	ENSP00000409472:R2258H;ENSP00000414402:R2911H;ENSP00000392061:R2911H	ENSP00000414402:R2911H	R	+	2	0	DNAH14	223561791	0.034000	0.19679	0.000000	0.03702	0.019000	0.09904	0.307000	0.19296	-0.218000	0.10018	-0.362000	0.07510	CGC	G|0.972;A|0.028	0.028	strong		0.338	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
LRRC2	79442	hgsc.bcm.edu	37	3	46580591	46580591	+	Missense_Mutation	SNP	G	G	T	rs17078944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:46580591G>T	ENST00000395905.3	-	4	826	c.434C>A	c.(433-435)gCg>gAg	p.A145E	LRRC2_ENST00000296144.3_Missense_Mutation_p.A145E	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	145			A -> E (in dbSNP:rs17078944). {ECO:0000269|PubMed:11896456}.							breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		AATTCTCATCGCTTGAAATAA	0.423													G|||	1435	0.286542	0.1195	0.2622	5008	,	,		22068	0.2768		0.3718	False		,,,				2504	0.4519				p.A145E		Atlas-SNP	.											.	LRRC2	37	.	0			c.C434A						PASS	.	G	GLU/ALA	656,3750	281.1+/-275.7	42,572,1589	147.0	134.0	139.0		434	1.8	0.2	3	dbSNP_123	139	2894,5706	453.3+/-363.2	481,1932,1887	yes	missense	LRRC2	NM_024512.4	107	523,2504,3476	TT,TG,GG		33.6512,14.8888,27.2951	benign	145/372	46580591	3550,9456	2203	4300	6503	SO:0001583	missense	79442	exon4			CTCATCGCTTGAA	AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"""leucine-rich repeat-containing 2"""			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.434C>A	3.37:g.46580591G>T	ENSP00000379241:p.Ala145Glu	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	174	173	0.994253	NM_024512	B2RDQ7|Q96LT5	Missense_Mutation	SNP	ENST00000395905.3	37	CCDS2741.1	601	0.2751831501831502	74	0.15040650406504066	87	0.24033149171270718	158	0.2762237762237762	282	0.3720316622691293	G	2.344	-0.350518	0.05173	0.148888	0.336512	ENSG00000163827	ENST00000395905;ENST00000296144	T;T	0.42900	0.96;0.96	5.09	1.79	0.24919	.	0.636520	0.15631	N	0.252392	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.45862	-0.9232	9	0.17832	T	0.49	.	6.0349	0.19702	0.0946:0.0:0.4145:0.4909	rs17078944;rs52823125;rs17078944	145	Q9BYS8	LRRC2_HUMAN	E	145	ENSP00000379241:A145E;ENSP00000296144:A145E	ENSP00000296144:A145E	A	-	2	0	LRRC2	46555595	0.969000	0.33509	0.221000	0.23827	0.806000	0.45545	2.517000	0.45529	0.654000	0.30846	0.650000	0.86243	GCG	G|0.726;T|0.274	0.274	strong		0.423	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2		
UBN1	29855	hgsc.bcm.edu	37	16	4930100	4930100	+	Silent	SNP	C	C	T	rs1876359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:4930100C>T	ENST00000396658.4	+	17	4075	c.3372C>T	c.(3370-3372)caC>caT	p.H1124H	UBN1_ENST00000590769.1_Silent_p.H1094H|UBN1_ENST00000262376.6_Silent_p.H1124H|UBN1_ENST00000545171.1_Silent_p.H1094H	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	1124					chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						CTCAGCTTCACGGGAAAGGGC	0.488													C|||	1901	0.379593	0.2852	0.4582	5008	,	,		21591	0.3343		0.3767	False		,,,				2504	0.501				p.H1124H		Atlas-SNP	.											.	UBN1	88	.	0			c.C3372T						PASS	.	C	,	1305,3089	442.0+/-346.6	167,971,1059	132.0	129.0	130.0		3372,3372	-3.0	1.0	16	dbSNP_92	130	3073,5527	470.7+/-367.9	547,1979,1774	no	coding-synonymous,coding-synonymous	UBN1	NM_001079514.1,NM_016936.3	,	714,2950,2833	TT,TC,CC		35.7326,29.6996,33.6925	,	1124/1135,1124/1135	4930100	4378,8616	2197	4300	6497	SO:0001819	synonymous_variant	29855	exon18			GCTTCACGGGAAA	AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.3372C>T	16.37:g.4930100C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	174	81	0.465517	NM_001079514	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Silent	SNP	ENST00000396658.4	37	CCDS10525.1																																																																																			C|0.650;T|0.350	0.350	strong		0.488	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936	
FAM208A	23272	hgsc.bcm.edu	37	3	56703746	56703746	+	Silent	SNP	A	A	C	rs13094666	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:56703746A>C	ENST00000493960.2	-	5	727	c.717T>G	c.(715-717)gtT>gtG	p.V239V	FAM208A_ENST00000355628.5_Silent_p.V239V	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	239							poly(A) RNA binding (GO:0044822)	p.V239V(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						TTTTAAAAATAACAACATCAC	0.318													A|||	1864	0.372204	0.3964	0.4885	5008	,	,		16006	0.4613		0.2803	False		,,,				2504	0.2597				p.V239V		Atlas-SNP	.											FAM208A,NS,carcinoma,0,1	FAM208A	113	1	1	Substitution - coding silent(1)	kidney(1)	c.T717G						PASS	.	A		536,848		109,318,265	60.0	55.0	57.0		717	4.1	1.0	3	dbSNP_121	57	931,2249		136,659,795	no	coding-synonymous	FAM208A	NM_001112736.1		245,977,1060	CC,CA,AA		29.2767,38.7283,32.1429		239/1513	56703746	1467,3097	692	1590	2282	SO:0001819	synonymous_variant	23272	exon5			AAAAATAACAACA	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.717T>G	3.37:g.56703746A>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	145	86	0.593103	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Silent	SNP	ENST00000493960.2	37	CCDS46853.1																																																																																			A|0.623;C|0.377	0.377	strong		0.318	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
BRCA2	675	hgsc.bcm.edu	37	13	32906980	32906980	+	Silent	SNP	A	A	G	rs397507583|rs1801439	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:32906980A>G	ENST00000380152.3	+	10	1598	c.1365A>G	c.(1363-1365)tcA>tcG	p.S455S	BRCA2_ENST00000544455.1_Silent_p.S455S			P51587	BRCA2_HUMAN	breast cancer 2, early onset	455					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TACCAAAATCAGAGAAGCCAT	0.353			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			A|||	369	0.0736821	0.0325	0.0922	5008	,	,		19193	0.0962		0.0348	False		,,,				2504	0.1329				p.S455S	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.A1365G						PASS	.	A		87,4315	66.4+/-103.9	0,87,2114	55.0	65.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1365	2.1	0.3	13	dbSNP_89	61	316,8278	110.2+/-170.6	8,300,3989	no	coding-synonymous	BRCA2	NM_000059.3		8,387,6103	GG,GA,AA		3.677,1.9764,3.101		455/3419	32906980	403,12593	2201	4297	6498	SO:0001819	synonymous_variant	675	exon10	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	AAAATCAGAGAAG	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.1365A>G	13.37:g.32906980A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	45	42	0.933333	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																			A|0.955;G|0.045	0.045	strong		0.353	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
APOBR	55911	hgsc.bcm.edu	37	16	28509509	28509509	+	Silent	SNP	G	G	A	rs61738759	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28509509G>A	ENST00000431282.1	+	4	3046	c.3036G>A	c.(3034-3036)ccG>ccA	p.P1012P	CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000328423.5_Silent_p.P1012P|APOBR_ENST00000564831.1_Silent_p.P1021P|CLN3_ENST00000569430.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	1012					cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						GTCGGACTCCGGCCTGGGAGC	0.672													G|||	64	0.0127796	0.0015	0.0101	5008	,	,		15790	0.0		0.0467	False		,,,				2504	0.0082				p.P1021P		Atlas-SNP	.											.	APOBR	89	.	0			c.G3063A						PASS	.	G		55,4119		1,53,2033	12.0	15.0	14.0		3036	-9.3	0.0	16	dbSNP_129	14	486,7960		15,456,3752	no	coding-synonymous	APOBR	NM_018690.3		16,509,5785	AA,AG,GG		5.7542,1.3177,4.2868		1012/1089	28509509	541,12079	2087	4223	6310	SO:0001819	synonymous_variant	55911	exon3			GACTCCGGCCTGG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.3036G>A	16.37:g.28509509G>A		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	37																																																																																				G|0.972;A|0.028	0.028	strong		0.672	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
CARD14	79092	hgsc.bcm.edu	37	17	78178916	78178916	+	Silent	SNP	C	C	T	rs61757652	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78178916C>T	ENST00000573882.1	+	20	3017	c.2481C>T	c.(2479-2481)ccC>ccT	p.P827P	RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000576824.1_RNA|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|CARD14_ENST00000344227.2_Silent_p.P827P|RP11-334C17.5_ENST00000573346.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	827	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CCGCCCGGCCCCGGCCTGTGC	0.652													C|||	501	0.10004	0.0492	0.1369	5008	,	,		14544	0.1042		0.0746	False		,,,				2504	0.1646				p.P827P		Atlas-SNP	.											.	CARD14	98	.	0			c.C2481T						PASS	.	C		192,4214	114.2+/-152.2	7,178,2018	53.0	53.0	53.0		2481	-1.5	0.9	17	dbSNP_129	53	660,7940	165.8+/-217.9	26,608,3666	yes	coding-synonymous	CARD14	NM_024110.3		33,786,5684	TT,TC,CC		7.6744,4.3577,6.5508		827/1005	78178916	852,12154	2203	4300	6503	SO:0001819	synonymous_variant	79092	exon18			CCGGCCCCGGCCT	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2481C>T	17.37:g.78178916C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	87	55	0.632184	NM_024110	B8QQJ3|Q9BVB5	Silent	SNP	ENST00000573882.1	37	CCDS11768.1																																																																																			C|0.928;T|0.072	0.072	strong		0.652	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
UGDH	7358	hgsc.bcm.edu	37	4	39512347	39512347	+	Silent	SNP	T	T	C	rs11544855	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:39512347T>C	ENST00000316423.6	-	4	741	c.399A>G	c.(397-399)ccA>ccG	p.P133P	UGDH_ENST00000507089.1_Silent_p.P36P|UGDH_ENST00000506179.1_Silent_p.P133P|UGDH_ENST00000515398.1_5'Flank|UGDH_ENST00000501493.2_Intron	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	133					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)			breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						CTGCCCGCACTGGAACTGTGC	0.408													T|||	311	0.0621006	0.0121	0.0735	5008	,	,		18962	0.0268		0.1551	False		,,,				2504	0.0624				p.P133P		Atlas-SNP	.											UGDH,caecum,carcinoma,-2,1	UGDH	52	1	0			c.A399G						PASS	.	T	,,	149,4257	102.1+/-140.7	5,139,2059	182.0	174.0	176.0		,108,399	-8.9	0.7	4	dbSNP_120	176	1222,7378	246.4+/-274.8	83,1056,3161	no	intron,coding-synonymous,coding-synonymous	UGDH	NM_001184700.1,NM_001184701.1,NM_003359.3	,,	88,1195,5220	CC,CT,TT		14.2093,3.3818,10.5413	,,	,36/398,133/495	39512347	1371,11635	2203	4300	6503	SO:0001819	synonymous_variant	7358	exon4			CCGCACTGGAACT	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"""UDP-glucose dehydrogenase"""			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.399A>G	4.37:g.39512347T>C		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	278	136	0.489209	NM_003359	B3KUU2|B4DN25|O60589	Silent	SNP	ENST00000316423.6	37	CCDS3455.1																																																																																			T|0.904;C|0.096	0.096	strong		0.408	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359	
OR8H1	219469	hgsc.bcm.edu	37	11	56057898	56057898	+	Missense_Mutation	SNP	G	G	A	rs61888286	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56057898G>A	ENST00000313022.2	-	1	668	c.641C>T	c.(640-642)tCt>tTt	p.S214F		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					ATAGGATGCAGATATTGTGAT	0.423													g|||	195	0.0389377	0.0121	0.0447	5008	,	,		20185	0.001		0.0924	False		,,,				2504	0.0552				p.S214F		Atlas-SNP	.											.	OR8H1	89	.	0			c.C641T						PASS	.	G	PHE/SER	96,4306	77.3+/-115.6	0,96,2105	154.0	139.0	144.0		641	-1.7	0.0	11	dbSNP_129	144	685,7907	170.1+/-221.3	33,619,3644	yes	missense	OR8H1	NM_001005199.1	155	33,715,5749	AA,AG,GG		7.9725,2.1808,6.0105	possibly-damaging	214/312	56057898	781,12213	2201	4296	6497	SO:0001583	missense	219469	exon1			GATGCAGATATTG	AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"""GPCR / Class A : Olfactory receptors"""	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.641C>T	11.37:g.56057898G>A	ENSP00000323595:p.Ser214Phe	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	208	92	0.442308	NM_001005199	B2RNI7|Q6IFC5	Missense_Mutation	SNP	ENST00000313022.2	37	CCDS31526.1	87	0.03983516483516483	4	0.008130081300813009	14	0.03867403314917127	0	0.0	69	0.09102902374670185	G	4.343	0.063115	0.08388	0.021808	0.079725	ENSG00000181693	ENST00000313022;ENST00000395186	T	0.00054	8.8	3.81	-1.71	0.08133	GPCR, rhodopsin-like superfamily (1);	0.703730	0.13027	N	0.419599	T	0.00012	0.0000	N	0.13003	0.285	0.09310	N	1	B	0.09022	0.002	B	0.18561	0.022	T	0.01345	-1.1379	10	0.18710	T	0.47	.	4.6672	0.12671	0.56:0.182:0.258:0.0	rs61888286	214	Q8NGG4	OR8H1_HUMAN	F	214;210	ENSP00000323595:S214F	ENSP00000323595:S214F	S	-	2	0	OR8H1	55814474	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	1.742000	0.38248	-0.227000	0.09884	-0.242000	0.12053	TCT	G|0.948;A|0.052	0.052	strong		0.423	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199	
SVIL	6840	hgsc.bcm.edu	37	10	29822159	29822159	+	Silent	SNP	T	T	C	rs7076239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:29822159T>C	ENST00000355867.4	-	8	1889	c.1137A>G	c.(1135-1137)ctA>ctG	p.L379L	SVIL_ENST00000375400.3_Intron|SVIL_ENST00000375398.2_Silent_p.L379L	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	379					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CTGGCGTCACTAGCTTGGCGG	0.562													C|||	1556	0.310703	0.3502	0.3862	5008	,	,		18887	0.0823		0.4274	False		,,,				2504	0.319				p.L379L		Atlas-SNP	.											SVIL,caecum,carcinoma,-2,1	SVIL	226	1	0			c.A1137G						PASS	.	C	,	1599,2807	665.1+/-401.5	298,1003,902	88.0	75.0	79.0		,1137	3.7	0.3	10	dbSNP_116	79	3839,4761	610.3+/-395.7	858,2123,1319	no	intron,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	1156,3126,2221	CC,CT,TT		44.6395,36.2914,41.8115	,	,379/2215	29822159	5438,7568	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon8			CGTCACTAGCTTG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1137A>G	10.37:g.29822159T>C		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	244	121	0.495902	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			T|0.634;C|0.366	0.366	strong		0.562	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
KCNK10	54207	hgsc.bcm.edu	37	14	88652389	88652389	+	Silent	SNP	C	C	T	rs3742692	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:88652389C>T	ENST00000340700.5	-	7	1558	c.1107G>A	c.(1105-1107)gcG>gcA	p.A369A	KCNK10_ENST00000312350.5_Silent_p.A374A|KCNK10_ENST00000319231.5_Silent_p.A374A	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	369					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	47						GGATGGTGGCCGCCCGCTGCA	0.667													C|||	1091	0.217851	0.028	0.1614	5008	,	,		15139	0.3681		0.2744	False		,,,				2504	0.3016				p.A374A		Atlas-SNP	.											KCNK10_ENST00000319231,NS,carcinoma,0,3	KCNK10	273	3	0			c.G1122A						PASS	.	C	,,	294,4094		19,256,1919	26.0	25.0	26.0		1107,1122,1122	-7.6	0.3	14	dbSNP_107	26	2384,6188		363,1658,2265	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNK10	NM_021161.4,NM_138317.2,NM_138318.2	,,	382,1914,4184	TT,TC,CC		27.8115,6.7001,20.6636	,,	369/539,374/544,374/544	88652389	2678,10282	2194	4286	6480	SO:0001819	synonymous_variant	54207	exon7			GGTGGCCGCCCGC	AF279890	CCDS9880.1, CCDS9881.1, CCDS9882.1	14q31	2014-06-12						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6273	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 97"""	605873				10880510, 16382106	Standard	NM_021161		Approved	K2p10.1, TREK-2, TREK2, PPP1R97	uc001xwn.3	P57789		ENST00000340700.5:c.1107G>A	14.37:g.88652389C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	89	57	0.640449	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Silent	SNP	ENST00000340700.5	37	CCDS9880.1																																																																																			C|0.786;T|0.214	0.214	strong		0.667	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161	
MUL1	79594	hgsc.bcm.edu	37	1	20827216	20827216	+	Silent	SNP	C	C	T	rs595980	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:20827216C>T	ENST00000264198.3	-	4	1162	c.1026G>A	c.(1024-1026)gcG>gcA	p.A342A		NM_024544.2	NP_078820.2	Q969V5	MUL1_HUMAN	mitochondrial E3 ubiquitin protein ligase 1	342					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|cellular response to exogenous dsRNA (GO:0071360)|mitochondrial fission (GO:0000266)|mitochondrion localization (GO:0051646)|negative regulation of cell growth (GO:0030308)|negative regulation of chemokine (C-C motif) ligand 5 production (GO:0071650)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of innate immune response (GO:0045824)|negative regulation of mitochondrial fusion (GO:0010637)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein sumoylation (GO:0033235)|protein stabilization (GO:0050821)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)	cytoplasm (GO:0005737)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(5)	11		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00748)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000137)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CCCGGGTGATCGCCTGTCTGC	0.557													C|||	357	0.0712859	0.0272	0.1023	5008	,	,		19030	0.001		0.1988	False		,,,				2504	0.0501				p.A342A		Atlas-SNP	.											MUL1,colon,carcinoma,-1,1	MUL1	34	1	0			c.G1026A						PASS	.	C		280,4126	154.4+/-187.8	12,256,1935	71.0	71.0	71.0		1026	-0.7	0.7	1	dbSNP_83	71	1750,6850	315.0+/-312.1	164,1422,2714	no	coding-synonymous	MUL1	NM_024544.2		176,1678,4649	TT,TC,CC		20.3488,6.355,15.6082		342/353	20827216	2030,10976	2203	4300	6503	SO:0001819	synonymous_variant	79594	exon4			GGTGATCGCCTGT	BC014010	CCDS208.1	1p36.12	2013-01-11	2010-09-17	2008-03-26	ENSG00000090432	ENSG00000090432		"""RING-type (C3HC4) zinc fingers"""	25762	protein-coding gene	gene with protein product	"""ring finger protein 218"", ""mitochondria-anchored protein ligase"", ""growth inhibition and death E3 ligase"", ""mitochondrial ubiquitin ligase activator of NFKB 1"""	612037	"""chromosome 1 open reading frame 166"""	C1orf166		18591963, 12761501, 18213395, 18207745	Standard	NM_024544		Approved	FLJ12875, MULAN, RNF218, MAPL, GIDE	uc001bdi.4	Q969V5	OTTHUMG00000002838	ENST00000264198.3:c.1026G>A	1.37:g.20827216C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_024544	B5M497|Q7Z431|Q9H9B5	Silent	SNP	ENST00000264198.3	37	CCDS208.1																																																																																			C|0.864;T|0.136	0.136	strong		0.557	MUL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007951.1	NM_024544	
MOV10L1	54456	hgsc.bcm.edu	37	22	50599466	50599466	+	Missense_Mutation	SNP	C	C	A	rs2272843	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50599466C>A	ENST00000262794.5	+	26	3619	c.3536C>A	c.(3535-3537)gCa>gAa	p.A1179E	MOV10L1_ENST00000545383.1_Missense_Mutation_p.A1179E|MOV10L1_ENST00000395858.3_Missense_Mutation_p.A1133E|MOV10L1_ENST00000540615.1_Intron|MOV10L1_ENST00000395852.1_Missense_Mutation_p.A306E	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	1179			A -> E (in dbSNP:rs2272843). {ECO:0000269|PubMed:17974005}.		ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TTACCTCCTGCACTGCAGTCT	0.522													A|||	624	0.124601	0.031	0.2017	5008	,	,		20039	0.1488		0.1372	False		,,,				2504	0.1585				p.A1179E		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C3536A						PASS	.	A	GLU/ALA,,GLU/ALA,GLU/ALA	245,4161		9,227,1967	223.0	207.0	212.0		3398,,917,3536	5.1	0.2	22	dbSNP_100	212	1276,7324		93,1090,3117	yes	missense,intron,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_001164106.1,NM_018995.2	107,,107,107	102,1317,5084	AA,AC,CC		14.8372,5.5606,11.6946	benign,,benign,benign	1133/1166,,306/339,1179/1212	50599466	1521,11485	2203	4300	6503	SO:0001583	missense	54456	exon26			CTCCTGCACTGCA	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.3536C>A	22.37:g.50599466C>A	ENSP00000262794:p.Ala1179Glu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	138	74	0.536232	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	289	0.13232600732600733	15	0.03048780487804878	63	0.17403314917127072	108	0.1888111888111888	103	0.1358839050131926	.	0.005	-2.223352	0.00283	0.055606	0.148372	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000395852	D;D;T;D	0.92348	-1.72;-1.72;-1.22;-3.02	5.14	5.14	0.70334	.	0.228388	0.45361	N	0.000368	T	0.00241	0.0007	N	0.01048	-1.04	0.49130	P	2.4199999999996447E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.40136	-0.9579	9	0.02654	T	1	-29.185	5.4416	0.16511	0.7323:0.1784:0.0892:0.0	rs2272843;rs3188620;rs17412558;rs17836649;rs52811465;rs61473516;rs2272843	306;1133;1179	Q9BXT6-2;A8MXC6;Q9BXT6	.;.;M10L1_HUMAN	E	1179;1179;1133;306	ENSP00000438978:A1179E;ENSP00000262794:A1179E;ENSP00000379199:A1133E;ENSP00000379193:A306E	ENSP00000262794:A1179E	A	+	2	0	MOV10L1	48941593	0.833000	0.29383	0.241000	0.24154	0.060000	0.15804	2.379000	0.44318	0.804000	0.34136	-0.471000	0.05019	GCA	C|0.878;A|0.122	0.122	strong		0.522	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
SYK	6850	hgsc.bcm.edu	37	9	93639973	93639973	+	Silent	SNP	G	G	C	rs2290888	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:93639973G>C	ENST00000375754.4	+	10	1450	c.1302G>C	c.(1300-1302)cgG>cgC	p.R434R	SYK_ENST00000375747.1_Silent_p.R411R|SYK_ENST00000375751.4_Silent_p.R411R|SYK_ENST00000375746.1_Silent_p.R434R	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	434	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						ACATCGTGCGGATGATCGGGA	0.483			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								C|||	984	0.196486	0.211	0.366	5008	,	,		21474	0.2321		0.1362	False		,,,				2504	0.0818				p.R434R		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.G1302C						PASS	.	C	,,,	935,3471	737.2+/-410.9	93,749,1361	132.0	115.0	121.0		1233,1302,1233,1302	-1.8	1.0	9	dbSNP_100	121	1214,7386	763.0+/-407.6	87,1040,3173	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	180,1789,4534	CC,CG,GG		14.1163,21.2211,16.5231	,,,	411/613,434/636,411/613,434/636	93639973	2149,10857	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon10			CGTGCGGATGATC	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1302G>C	9.37:g.93639973G>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	181	98	0.541436	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			G|0.789;C|0.211	0.211	strong		0.483	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
WDR5	11091	hgsc.bcm.edu	37	9	137005023	137005023	+	Silent	SNP	C	C	T	rs11556390	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:137005023C>T	ENST00000358625.3	+	2	195	c.24C>T	c.(22-24)ccC>ccT	p.P8P	WDR5_ENST00000425041.1_Silent_p.P8P	NM_017588.2	NP_060058.1	P61964	WDR5_HUMAN	WD repeat domain 5	8					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|histone H3-K4 methylation (GO:0051568)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|positive regulation of gluconeogenesis (GO:0045722)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|histone acetyltransferase complex (GO:0000123)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)				endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123)		Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154)		AGAAGAAGCCCGAGACCGAGG	0.647													C|||	1600	0.319489	0.1982	0.438	5008	,	,		12500	0.3562		0.4185	False		,,,				2504	0.2597				p.P8P		Atlas-SNP	.											.	WDR5	29	.	0			c.C24T						PASS	.	C	,	941,3465	340.7+/-306.4	103,735,1365	57.0	53.0	55.0		24,24	-8.8	0.2	9	dbSNP_120	55	3809,4791	523.5+/-380.3	869,2071,1360	yes	coding-synonymous,coding-synonymous	WDR5	NM_017588.2,NM_052821.3	,	972,2806,2725	TT,TC,CC		44.2907,21.3572,36.5216	,	8/335,8/335	137005023	4750,8256	2203	4300	6503	SO:0001819	synonymous_variant	11091	exon1			GAAGCCCGAGACC	AJ011376	CCDS6981.1	9q34	2014-09-03			ENSG00000196363	ENSG00000196363		"""WD repeat domain containing"""	12757	protein-coding gene	gene with protein product	"""SWD3, Set1c WD40 repeat protein, homolog (S. cerevisiae)"", ""cilia and flagella associated protein 89"""	609012				11551928	Standard	XM_005272163		Approved	SWD3, CFAP89	uc004cey.3	P61964	OTTHUMG00000131707	ENST00000358625.3:c.24C>T	9.37:g.137005023C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_052821	Q91VA5|Q9NWX7|Q9UGP9	Silent	SNP	ENST00000358625.3	37	CCDS6981.1																																																																																			C|0.632;T|0.368	0.368	strong		0.647	WDR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254621.1	NM_052821	
RHPN2	85415	hgsc.bcm.edu	37	19	33490564	33490564	+	Missense_Mutation	SNP	G	G	T	rs147870656	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:33490564G>T	ENST00000254260.3	-	10	1188	c.1153C>A	c.(1153-1155)Ctc>Atc	p.L385I	RHPN2_ENST00000400226.4_Missense_Mutation_p.L234I	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	385	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.L385I(1)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TGGTCGTAGAGCTGGGACAGG	0.602													G|||	20	0.00399361	0.0	0.0072	5008	,	,		29445	0.0		0.007	False		,,,				2504	0.0082				p.L385I		Atlas-SNP	.											RHPN2,NS,carcinoma,0,1	RHPN2	107	1	1	Substitution - Missense(1)	prostate(1)	c.C1153A						scavenged	.						81.0	65.0	70.0					19																	33490564		2203	4300	6503	SO:0001583	missense	85415	exon10			CGTAGAGCTGGGA	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1153C>A	19.37:g.33490564G>T	ENSP00000254260:p.Leu385Ile	Somatic	628	0	0		WXS	Illumina HiSeq	Phase_I	640	61	0.0953125	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.059746	0.76074	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.17213	2.29;2.29	4.72	4.72	0.59763	BRO1 domain (2);	0.064498	0.64402	D	0.000006	T	0.34745	0.0908	M	0.71581	2.175	0.52501	D	0.999957	D	0.58970	0.984	P	0.54815	0.761	T	0.09862	-1.0655	10	0.36615	T	0.2	0.0099	17.6847	0.88253	0.0:0.0:1.0:0.0	.	385	Q8IUC4	RHPN2_HUMAN	I	385;115;234	ENSP00000254260:L385I;ENSP00000402244:L234I	ENSP00000254260:L385I	L	-	1	0	RHPN2	38182404	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.145000	0.42207	2.174000	0.68829	0.484000	0.47621	CTC	G|0.999;T|0.001	0.001	weak		0.602	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
GFAP	2670	hgsc.bcm.edu	37	17	42987523	42987523	+	Intron	SNP	G	G	A	rs9908084|rs386797323	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:42987523G>A	ENST00000253408.5	-	7	1237				GFAP_ENST00000435360.2_Missense_Mutation_p.T426M|GFAP_ENST00000588735.1_Intron	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein						astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				AGCCGGCGGCGTTCCATTTAC	0.537													G|||	529	0.105631	0.1021	0.1081	5008	,	,		18163	0.005		0.167	False		,,,				2504	0.1493				p.T426M		Atlas-SNP	.											.	GFAP	88	.	0			c.C1277T						PASS	.	G	MET/THR,,	299,2837		12,275,1281	215.0	191.0	198.0		1277,,	3.8	0.9	17	dbSNP_119	198	1196,5968		93,1010,2479	no	missense,utr-3,intron	GFAP	NM_001131019.2,NM_001242376.1,NM_002055.4	81,,	105,1285,3760	AA,AG,GG		16.6946,9.5344,14.5146	,,	426/432,,	42987523	1495,8805	1568	3582	5150	SO:0001627	intron_variant	2670	exon8			GGCGGCGTTCCAT	S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"""Intermediate filaments type III"""	4235	protein-coding gene	gene with protein product	"""intermediate filament protein"""	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.1171+459C>T	17.37:g.42987523G>A		Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	402	200	0.497512	NM_001131019	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Missense_Mutation	SNP	ENST00000253408.5	37	CCDS11491.1	179	0.08195970695970696	36	0.07317073170731707	46	0.1270718232044199	2	0.0034965034965034965	95	0.12532981530343007	G	13.54	2.267411	0.40095	0.095344	0.166946	ENSG00000131095	ENST00000435360	D	0.84730	-1.89	4.79	3.8	0.43715	.	.	.	.	.	T	0.00440	0.0014	N	0.08118	0	0.09310	P	0.999999999608325	B	0.13145	0.007	B	0.04013	0.001	T	0.32877	-0.9890	8	0.72032	D	0.01	.	9.5131	0.39089	0.0951:0.0:0.9049:0.0	rs9908084;rs9908084	426	E9PAX3	.	M	426	ENSP00000403962:T426M	ENSP00000403962:T426M	T	-	2	0	GFAP	40343049	1.000000	0.71417	0.910000	0.35882	0.158000	0.22134	1.941000	0.40233	1.599000	0.50093	0.655000	0.94253	ACG	G|0.911;A|0.089	0.089	strong		0.537	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055	
SH3GLB1	51100	hgsc.bcm.edu	37	1	87170606	87170606	+	Silent	SNP	G	G	A	rs150324653	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:87170606G>A	ENST00000370558.4	+	1	348	c.24G>A	c.(22-24)gtG>gtA	p.V8V	SH3GLB1_ENST00000535010.1_5'UTR|SH3GLB1_ENST00000482504.1_Silent_p.V8V|RP4-612B15.3_ENST00000565575.1_RNA	NM_001206651.1|NM_001206653.1|NM_016009.4	NP_001193580.1|NP_001193582.1|NP_057093.1	Q9Y371	SHLB1_HUMAN	SH3-domain GRB2-like endophilin B1	8	Membrane-binding amphipathic helix.				'de novo' posttranslational protein folding (GO:0051084)|apoptotic process (GO:0006915)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|protein complex (GO:0043234)	fatty acid binding (GO:0005504)|identical protein binding (GO:0042802)|lysophosphatidic acid acyltransferase activity (GO:0042171)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|stomach(1)	11		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)		ACTTCAACGTGAAGAAGCTGG	0.716													G|||	28	0.00559105	0.0008	0.0058	5008	,	,		12901	0.0		0.0179	False		,,,				2504	0.0051				p.V8V		Atlas-SNP	.											.	SH3GLB1	57	.	0			c.G24A						PASS	.	G	,,,	10,4384		0,10,2187	13.0	16.0	15.0		24,24,,24	1.6	1.0	1	dbSNP_134	15	87,8499		0,87,4206	no	coding-synonymous,coding-synonymous,utr-5,coding-synonymous	SH3GLB1	NM_001206651.1,NM_001206652.1,NM_001206653.1,NM_016009.4	,,,	0,97,6393	AA,AG,GG		1.0133,0.2276,0.7473	,,,	8/395,8/387,,8/366	87170606	97,12883	2197	4293	6490	SO:0001819	synonymous_variant	51100	exon1			CAACGTGAAGAAG	AF263293	CCDS710.1, CCDS55612.1, CCDS55613.1, CCDS72819.1	1p22.3	2012-04-17	2001-12-04		ENSG00000097033	ENSG00000097033		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	10833	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 70"""	609287	"""SH3-domain, GRB2-like, endophilin B1"""			11161816, 11259440	Standard	NM_016009		Approved	CGI-61, KIAA0491, Bif-1, PPP1R70	uc001dly.3	Q9Y371	OTTHUMG00000010257	ENST00000370558.4:c.24G>A	1.37:g.87170606G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_001206652	B4E182|Q5H8U5|Q9H3Z0|Q9NR47|Q9NYA9	Silent	SNP	ENST00000370558.4	37	CCDS710.1																																																																																			G|0.993;A|0.007	0.007	strong		0.716	SH3GLB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028287.2	NM_016009	
EPRS	2058	hgsc.bcm.edu	37	1	220156729	220156729	+	Silent	SNP	C	C	T	rs5030754	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:220156729C>T	ENST00000366923.3	-	22	3371	c.3102G>A	c.(3100-3102)aaG>aaA	p.K1034K		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1034	Proline--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	TCATTTCTGACTTTGTGATGA	0.348													C|||	567	0.113219	0.2428	0.0591	5008	,	,		18032	0.0526		0.0984	False		,,,				2504	0.0542				p.K1034K		Atlas-SNP	.											.	EPRS	140	.	0			c.G3102A						PASS	.	C		947,3459	351.3+/-311.2	110,727,1366	46.0	48.0	47.0		3102	2.6	1.0	1	dbSNP_113	47	701,7899	170.1+/-221.3	33,635,3632	no	coding-synonymous	EPRS	NM_004446.2		143,1362,4998	TT,TC,CC		8.1512,21.4934,12.6711		1034/1513	220156729	1648,11358	2203	4300	6503	SO:0001819	synonymous_variant	2058	exon22			TTCTGACTTTGTG	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"""Aminoacyl tRNA synthetases / Class I"", ""Aminoacyl tRNA synthetases / Class II"""	3418	protein-coding gene	gene with protein product	"""glutamate tRNA ligase"", ""proline tRNA ligase"""	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3102G>A	1.37:g.220156729C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	190	80	0.421053	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Silent	SNP	ENST00000366923.3	37	CCDS31027.1																																																																																			C|0.883;T|0.117	0.117	strong		0.348	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446	
PDZD2	23037	hgsc.bcm.edu	37	5	32074509	32074509	+	Silent	SNP	G	G	A	rs2291113	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:32074509G>A	ENST00000438447.1	+	18	3685	c.3297G>A	c.(3295-3297)acG>acA	p.T1099T	PDZD2_ENST00000282493.3_Silent_p.T1099T			O15018	PDZD2_HUMAN	PDZ domain containing 2	1099					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						AGAGTCCGACGAACACTGGGA	0.592													G|||	494	0.0986422	0.0318	0.1066	5008	,	,		19596	0.2232		0.0507	False		,,,				2504	0.1043				p.T1099T		Atlas-SNP	.											.	PDZD2	306	.	0			c.G3297A						PASS	.	G		202,4204	126.6+/-163.6	2,198,2003	80.0	90.0	86.0		3297	3.6	0.0	5	dbSNP_100	86	587,8013	157.5+/-211.1	23,541,3736	no	coding-synonymous	PDZD2	NM_178140.2		25,739,5739	AA,AG,GG		6.8256,4.5847,6.0664		1099/2840	32074509	789,12217	2203	4300	6503	SO:0001819	synonymous_variant	23037	exon17			TCCGACGAACACT	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3297G>A	5.37:g.32074509G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	91	50	0.549451	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			G|0.922;A|0.078	0.078	strong		0.592	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
TUBB8	347688	hgsc.bcm.edu	37	10	95169	95169	+	Missense_Mutation	SNP	T	T	G	rs199817418	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:95169T>G	ENST00000309812.4	-	1	72	c.10A>C	c.(10-12)Atc>Ctc	p.I4L	TUBB8_ENST00000447903.2_Intron|TUBB8_ENST00000413237.3_Intron|TUBB8_ENST00000332708.5_Missense_Mutation_p.I4L	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	4					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		GTGAGCACGATCTCCCTCATG	0.667																																					p.I4L	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,colon,carcinoma,0,2	TUBB8	62	2	0			c.A10C						scavenged	.						18.0	17.0	17.0					10																	95169		2196	4294	6490	SO:0001583	missense	347688	exon1			GCACGATCTCCCT	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.10A>C	10.37:g.95169T>G	ENSP00000311042:p.Ile4Leu	Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	118	9	0.0762712	NM_177987	Q5SQX9|Q8WZ78	Missense_Mutation	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	T	7.968	0.748352	0.15710	.	.	ENSG00000173876	ENST00000440680;ENST00000328974;ENST00000309812;ENST00000332708	T;T	0.75704	-0.96;-0.76	0.109	0.109	0.14578	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.64402	U	0.000017	T	0.73938	0.3651	M	0.88450	2.955	0.80722	D	1	B;B	0.09022	0.0;0.002	B;B	0.27608	0.001;0.081	T	0.68334	-0.5436	10	0.87932	D	0	.	4.6217	0.12455	0.0:4.0E-4:0.0:0.9996	.	4;4	C9JAA5;Q3ZCM7	.;TBB8_HUMAN	L	4	ENSP00000311042:I4L;ENSP00000371071:I4L	ENSP00000311042:I4L	I	-	1	0	RP11-631M21.2	85169	1.000000	0.71417	0.020000	0.16555	0.020000	0.10135	2.326000	0.43849	0.156000	0.19299	0.155000	0.16302	ATC	T|0.980;G|0.020	0.020	strong		0.667	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
FMN2	56776	hgsc.bcm.edu	37	1	240370941	240370941	+	Silent	SNP	T	T	C	rs71170718|rs4997329|rs562038978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:240370941T>C	ENST00000319653.9	+	5	3059	c.2829T>C	c.(2827-2829)ccT>ccC	p.P943P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	943	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGGAATACCTCCTCCGCCCC	0.697													C|||	1375	0.274561	0.357	0.1902	5008	,	,		7400	0.3105		0.2286	False		,,,				2504	0.2331				p.P943P		Atlas-SNP	.											FMN2,caecum,carcinoma,0,1	FMN2	451	1	0			c.T2829C						scavenged	.	C		371,3909		68,235,1837	23.0	29.0	27.0		2829	-8.0	0.0	1	dbSNP_113	27	396,8032		78,240,3896	no	coding-synonymous	FMN2	NM_020066.4		146,475,5733	CC,CT,TT		4.6986,8.6682,6.0356		943/1723	240370941	767,11941	2140	4214	6354	SO:0001819	synonymous_variant	56776	exon5			AATACCTCCTCCG	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2829T>C	1.37:g.240370941T>C		Somatic	101	3	0.029703		WXS	Illumina HiSeq	Phase_I	116	42	0.362069	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			T|0.863;C|0.137	0.137	strong		0.697	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
DTX2	113878	hgsc.bcm.edu	37	7	76131644	76131644	+	Silent	SNP	C	C	T	rs141587206	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:76131644C>T	ENST00000324432.5	+	9	1770	c.1260C>T	c.(1258-1260)tcC>tcT	p.S420S	DTX2_ENST00000446820.2_Silent_p.S373S|DTX2_ENST00000307569.8_Silent_p.S373S|DTX2_ENST00000446600.1_Silent_p.S329S|DTX2_ENST00000430490.2_Silent_p.S420S|DTX2_ENST00000413936.2_Silent_p.S420S	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	420					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.S420S(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						AGAAGCTGTCCACAGCGTCTG	0.582													.|||	206	0.0411342	0.0961	0.0202	5008	,	,		17191	0.0089		0.0328	False		,,,				2504	0.0235				p.S420S		Atlas-SNP	.											DTX2,rectum,carcinoma,0,1	DTX2	64	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C1260T						scavenged	.						77.0	61.0	66.0					7																	76131644		2199	4295	6494	SO:0001819	synonymous_variant	113878	exon8			GCTGTCCACAGCG		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.1260C>T	7.37:g.76131644C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	155	6	0.0387097	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			.	.	weak		0.582	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
TRPM3	80036	hgsc.bcm.edu	37	9	73150918	73150918	+	Missense_Mutation	SNP	C	C	T	rs41287373	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:73150918C>T	ENST00000377110.3	-	25	5318	c.5075G>A	c.(5074-5076)aGa>aAa	p.R1692K	TRPM3_ENST00000377105.1_Missense_Mutation_p.R1551K|TRPM3_ENST00000396280.5_Missense_Mutation_p.R1541K|TRPM3_ENST00000358082.3_Missense_Mutation_p.R1554K|TRPM3_ENST00000396292.4_Missense_Mutation_p.R1564K|TRPM3_ENST00000408909.2_Missense_Mutation_p.R1551K|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000357533.2_Missense_Mutation_p.R1696K|TRPM3_ENST00000396285.1_Missense_Mutation_p.R1551K|TRPM3_ENST00000423814.3_Missense_Mutation_p.R1719K|TRPM3_ENST00000360823.2_Missense_Mutation_p.R1554K|TRPM3_ENST00000377106.1_Missense_Mutation_p.R1564K			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1717					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TCTGGACAGTCTCCTCATGGA	0.517													C|||	1040	0.207668	0.0681	0.3228	5008	,	,		21340	0.1766		0.2803	False		,,,				2504	0.272				p.R1692K		Atlas-SNP	.											.	TRPM3	700	.	0			c.G5075A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	438,3968	209.2+/-230.0	32,374,1797	125.0	125.0	125.0		5075,4616,4652,4586,4622,4691,4661	5.6	1.0	9	dbSNP_127	125	2597,6003	422.5+/-354.0	414,1769,2117	yes	missense,missense,missense,missense,missense,missense,missense	TRPM3	NM_001007471.2,NM_020952.4,NM_024971.5,NM_206944.3,NM_206945.3,NM_206946.3,NM_206947.3	26,26,26,26,26,26,26	446,2143,3914	TT,TC,CC		30.1977,9.941,23.3354	benign,benign,benign,benign,benign,benign,benign	1692/1708,1539/1555,1551/1567,1529/1545,1541/1557,1564/1580,1554/1570	73150918	3035,9971	2203	4300	6503	SO:0001583	missense	80036	exon25			GACAGTCTCCTCA	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.5075G>A	9.37:g.73150918C>T	ENSP00000366314:p.Arg1692Lys	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	168	69	0.410714	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377110.3	37	CCDS43835.1	458	0.2097069597069597	30	0.06097560975609756	126	0.34806629834254144	98	0.17132867132867133	204	0.2691292875989446	C	13.32	2.202198	0.38905	0.09941	0.301977	ENSG00000083067	ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	T;T;T;T;T;T;T;T;T;T	0.51574	0.73;0.73;0.73;0.7;0.74;0.7;0.73;0.73;0.73;0.73	5.57	5.57	0.84162	.	0.104908	0.64402	D	0.000004	T	0.00012	0.0000	N	0.12182	0.205	0.26598	P	0.9730724	B;B;B;B;B;B;B	0.06786	0.001;0.001;0.0;0.0;0.001;0.001;0.0	B;B;B;B;B;B;B	0.06405	0.002;0.001;0.0;0.0;0.001;0.001;0.0	T	0.37314	-0.9711	9	0.23302	T	0.38	-18.1855	19.5403	0.95271	0.0:1.0:0.0:0.0	rs41287373;rs62543232	1692;1682;1696;1554;1551;1664;1551	Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.;.;.;.;.;.;.	K	1692;1564;1554;1551;1696;1551;1551;1564;1554;1719	ENSP00000366314:R1692K;ENSP00000366310:R1564K;ENSP00000354066:R1554K;ENSP00000366309:R1551K;ENSP00000350140:R1696K;ENSP00000386127:R1551K;ENSP00000379581:R1551K;ENSP00000379587:R1564K;ENSP00000350791:R1554K;ENSP00000389542:R1719K	ENSP00000350140:R1696K	R	-	2	0	TRPM3	72340738	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.745000	0.68672	2.619000	0.88677	0.655000	0.94253	AGA	C|0.770;T|0.230	0.230	strong		0.517	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945	
R3HCC1L	27291	hgsc.bcm.edu	37	10	99969475	99969475	+	Missense_Mutation	SNP	A	A	C	rs34494334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:99969475A>C	ENST00000298999.3	+	5	1907	c.1604A>C	c.(1603-1605)gAc>gCc	p.D535A	R3HCC1L_ENST00000370584.3_Missense_Mutation_p.D535A|R3HCC1L_ENST00000314594.5_5'UTR|R3HCC1L_ENST00000370586.2_Intron	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	535			D -> A (in dbSNP:rs34494334).				nucleotide binding (GO:0000166)										GAGCAAGATGACTCAGGGAGT	0.438													A|||	680	0.135783	0.1664	0.1499	5008	,	,		20094	0.0298		0.2217	False		,,,				2504	0.1053				p.D535A		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.A1604C						PASS	.	A	ALA/ASP	806,3600	320.4+/-296.6	84,638,1481	133.0	124.0	127.0		1604	-0.5	1.0	10	dbSNP_126	127	1857,6743	332.1+/-320.0	195,1467,2638	yes	missense	C10orf28	NM_014472.4	126	279,2105,4119	CC,CA,AA		21.593,18.2932,20.4752	benign	535/779	99969475	2663,10343	2203	4300	6503	SO:0001583	missense	27291	exon4			AAGATGACTCAGG	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 28"""	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1604A>C	10.37:g.99969475A>C	ENSP00000298999:p.Asp535Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	43	8	0.186047	NM_001256620	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	37	CCDS31267.1	353	0.16163003663003664	104	0.21138211382113822	63	0.17403314917127072	19	0.033216783216783216	167	0.22031662269129287	A	5.598	0.295168	0.10622	0.182932	0.21593	ENSG00000166024	ENST00000370584;ENST00000298999	T;T	0.07216	3.21;3.21	5.15	-0.501	0.12008	.	0.693696	0.13424	N	0.388881	T	0.00012	0.0000	L	0.38838	1.175	0.09310	P	0.999999999439986	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.003	T	0.45338	-0.9268	8	.	.	.	0.4892	4.5381	0.12043	0.4801:0.0:0.0844:0.4355	rs34494334	535;535	Q7Z5L2;Q7Z5L2-2	GIDRP_HUMAN;.	A	535	ENSP00000359616:D535A;ENSP00000298999:D535A	.	D	+	2	0	C10orf28	99959465	0.992000	0.36948	0.987000	0.45799	0.581000	0.36288	0.319000	0.19522	-0.020000	0.14032	-0.501000	0.04562	GAC	A|0.813;C|0.187	0.187	strong		0.438	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	
CFH	3075	hgsc.bcm.edu	37	1	196654324	196654324	+	Silent	SNP	A	A	C	rs1061147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:196654324A>C	ENST00000359637.2	+	6	791	c.729A>C	c.(727-729)gcA>gcC	p.A243A	CFH_ENST00000367429.4_Silent_p.A307A|CFH_ENST00000439155.2_Silent_p.A307A			P08603	CFAH_HUMAN	complement factor H	307	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						GAAATACAGCAAAATGCACAA	0.393													A|||	3571	0.713059	0.5688	0.7565	5008	,	,		15542	0.9504		0.6382	False		,,,				2504	0.7096				p.A307A		Atlas-SNP	.											.	CFH	251	.	0			c.A921C	GRCh37	CM057396	CFH	M	rs1061147	PASS	.	A	,	2601,1805	636.9+/-396.7	770,1061,372	119.0	108.0	112.0		921,921	-0.8	0.0	1	dbSNP_86	112	5308,3292	645.1+/-400.1	1648,2012,640	no	coding-synonymous,coding-synonymous	CFH	NM_000186.3,NM_001014975.2	,	2418,3073,1012	CC,CA,AA		38.2791,40.9669,39.1896	,	307/1232,307/450	196654324	7909,5097	2203	4300	6503	SO:0001819	synonymous_variant	3075	exon7			TACAGCAAAATGC	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000359637.2:c.729A>C	1.37:g.196654324A>C		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	248	111	0.447581	NM_001014975	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000359637.2	37																																																																																				A|0.352;C|0.648	0.648	strong		0.393	CFH-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000087502.1	NM_000186	
BAZ1B	9031	hgsc.bcm.edu	37	7	72892705	72892705	+	Silent	SNP	A	A	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:72892705A>T	ENST00000339594.4	-	7	1424	c.1086T>A	c.(1084-1086)ccT>ccA	p.P362P	BAZ1B_ENST00000404251.1_Silent_p.P362P	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	362	Lys-rich.				cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				GATGTTCTTCAGGAGATTTGG	0.423																																					p.P362P	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											BAZ1B,arm,malignant_melanoma,-2,1	BAZ1B	147	1	0			c.T1086A						scavenged	.						104.0	92.0	96.0					7																	72892705		2203	4300	6503	SO:0001819	synonymous_variant	9031	exon7			TTCTTCAGGAGAT	AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.1086T>A	7.37:g.72892705A>T		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	276	3	0.0108696	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Silent	SNP	ENST00000339594.4	37	CCDS5549.1																																																																																			.	.	none		0.423	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17914122	17914122	+	Missense_Mutation	SNP	G	G	A	rs35497285	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17914122G>A	ENST00000361221.3	+	3	364	c.205G>A	c.(205-207)Gac>Aac	p.D69N	ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.D69N|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.D69N|ARHGEF10L_ENST00000375420.3_5'Flank|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.D69N	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	69			D -> N (in dbSNP:rs35497285).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GATCCACTTGGACTCCATCCC	0.587													G|||	464	0.0926518	0.0038	0.1225	5008	,	,		17367	0.2044		0.0835	False		,,,				2504	0.0859				p.D69N		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.G205A						PASS	.	G	ASN/ASP,ASN/ASP	79,4327	69.2+/-107.0	1,77,2125	130.0	142.0	138.0		205,205	5.3	0.4	1	dbSNP_126	138	727,7873	177.5+/-227.1	44,639,3617	yes	missense,missense	ARHGEF10L	NM_001011722.2,NM_018125.3	23,23	45,716,5742	AA,AG,GG		8.4535,1.793,6.1971	benign,benign	69/1241,69/1280	17914122	806,12200	2203	4300	6503	SO:0001583	missense	55160	exon3			CACTTGGACTCCA	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.205G>A	1.37:g.17914122G>A	ENSP00000355060:p.Asp69Asn	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	37	CCDS182.1	221	0.10119047619047619	1	0.0020325203252032522	44	0.12154696132596685	115	0.20104895104895104	61	0.08047493403693931	G	19.11	3.764533	0.69878	0.01793	0.084535	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415	T;T;T;T	0.61274	0.3;0.3;0.12;0.3	5.3	5.3	0.74995	.	0.181464	0.37348	N	0.002128	T	0.00109	0.0003	L	0.27053	0.805	0.09310	P	0.9999999999970101	D;D;D;D	0.69078	0.996;0.969;0.969;0.997	P;P;P;D	0.73380	0.889;0.829;0.766;0.98	T	0.01720	-1.1288	9	0.16420	T	0.52	-37.9281	14.7973	0.69886	0.0:0.0:1.0:0.0	rs35497285;rs61749342	69;69;69;69	Q9HCE6-5;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;ARGAL_HUMAN	N	69	ENSP00000355060:D69N;ENSP00000399401:D69N;ENSP00000394621:D69N;ENSP00000364564:D69N	ENSP00000355060:D69N	D	+	1	0	ARHGEF10L	17786709	0.334000	0.24739	0.387000	0.26183	0.004000	0.04260	2.057000	0.41365	2.649000	0.89929	0.561000	0.74099	GAC	G|0.929;A|0.071	0.071	strong		0.587	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	
PLEKHO2	80301	hgsc.bcm.edu	37	15	65153690	65153690	+	Silent	SNP	G	G	A	rs12595292	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:65153690G>A	ENST00000323544.4	+	5	527	c.399G>A	c.(397-399)aaG>aaA	p.K133K	AC069368.3_ENST00000437723.1_Silent_p.K133K	NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	133										NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						AGGTGGACAAGAGCTGCGCCC	0.667													G|||	1404	0.280351	0.1082	0.2925	5008	,	,		17190	0.747		0.1451	False		,,,				2504	0.1626				p.K133K		Atlas-SNP	.											.	PLEKHO2	50	.	0			c.G399A						PASS	.	G	,	512,3882		32,448,1717	28.0	24.0	25.0	http://www.ncbi.nlm.nih.gov/pubmed?term	249,399	4.8	1.0	15	dbSNP_120	25	1285,7313		97,1091,3111	yes	coding-synonymous,coding-synonymous	PLEKHO2	NM_001195059.1,NM_025201.4	,	129,1539,4828	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.9453,11.6523,13.8316	,	83/441,133/491	65153690	1797,11195	2197	4299	6496	SO:0001819	synonymous_variant	80301	exon5			GGACAAGAGCTGC	AF318373	CCDS10196.1, CCDS73739.1	15q22.31	2013-01-10	2007-12-14	2007-12-14	ENSG00000241839	ENSG00000241839		"""Pleckstrin homology (PH) domain containing"""	30026	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family Q member 1"""	PLEKHQ1		12477932	Standard	NM_025201		Approved	DKFZp761K2312, PP1628, pp9099	uc002anv.3	Q8TD55	OTTHUMG00000133050	ENST00000323544.4:c.399G>A	15.37:g.65153690G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_025201	Q7L4H4|Q8WYS8	Silent	SNP	ENST00000323544.4	37	CCDS10196.1																																																																																			G|0.776;A|0.224	0.224	strong		0.667	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1	NM_025201	
AKAP13	11214	hgsc.bcm.edu	37	15	86123019	86123019	+	Missense_Mutation	SNP	C	C	T	rs2061824	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86123019C>T	ENST00000394518.2	+	7	1815	c.1720C>T	c.(1720-1722)Cgt>Tgt	p.R574C	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.R574C	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	574			R -> C (in dbSNP:rs2061824). {ECO:0000269|PubMed:11696353, ECO:0000269|Ref.3}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						TTCACGAAGTCGTGAGGAGAG	0.428													C|||	2920	0.583067	0.5507	0.6182	5008	,	,		21349	0.5784		0.6153	False		,,,				2504	0.5736				p.R574C	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C1720T						PASS	.	C	CYS/ARG,CYS/ARG	2612,1792	634.2+/-396.2	784,1044,374	77.0	79.0	79.0		1720,1720	-6.6	0.0	15	dbSNP_94	79	5537,3061	647.3+/-400.4	1798,1941,560	yes	missense,missense	AKAP13	NM_006738.4,NM_007200.3	180,180	2582,2985,934	TT,TC,CC		35.6013,40.6903,37.325	benign,benign	574/2818,574/2814	86123019	8149,4853	2202	4299	6501	SO:0001583	missense	11214	exon7			CGAAGTCGTGAGG	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.1720C>T	15.37:g.86123019C>T	ENSP00000378026:p.Arg574Cys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	1278	0.5851648351648352	262	0.532520325203252	221	0.6104972375690608	334	0.583916083916084	461	0.6081794195250659	C	8.845	0.943177	0.18281	0.593097	0.643987	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.11385	2.78;2.8	5.76	-6.59	0.01830	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42515	-0.9447	8	0.24483	T	0.36	.	1.1663	0.01816	0.359:0.3087:0.1226:0.2097	rs2061824;rs52800734;rs58232423;rs2061824	574;574	Q12802;Q12802-2	AKP13_HUMAN;.	C	574;574;573;573	ENSP00000354718:R574C;ENSP00000378026:R574C	ENSP00000354718:R574C	R	+	1	0	AKAP13	83924023	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.839000	0.04368	-0.658000	0.05366	-0.290000	0.09829	CGT	C|0.388;T|0.612	0.612	strong		0.428	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
RMI2	116028	hgsc.bcm.edu	37	16	11444572	11444572	+	Silent	SNP	A	A	C	rs7204628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:11444572A>C	ENST00000312499.5	+	2	410	c.369A>C	c.(367-369)acA>acC	p.T123T	RMI2_ENST00000572173.1_Silent_p.T60T|RMI2_ENST00000381820.2_Silent_p.T60T|RP11-485G7.6_ENST00000574681.1_RNA|AC009121.1_ENST00000458885.1_RNA|RMI2_ENST00000576027.1_3'UTR	NM_152308.1	NP_689521.1	Q96E14	RMI2_HUMAN	RecQ mediated genome instability 2	123					DNA replication (GO:0006260)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|kidney(1)|ovary(1)	3						TGAAGATGACAGACCTTTCTG	0.443													A|||	892	0.178115	0.2549	0.1599	5008	,	,		19442	0.001		0.2565	False		,,,				2504	0.1892				p.T123T		Atlas-SNP	.											.	RMI2	11	.	0			c.A369C						PASS	.	A		1067,3327	387.7+/-326.6	133,801,1263	116.0	113.0	114.0		369	-1.1	0.8	16	dbSNP_116	114	2121,6479	364.6+/-333.6	261,1599,2440	no	coding-synonymous	RMI2	NM_152308.1		394,2400,3703	CC,CA,AA		24.6628,24.2831,24.5344		123/148	11444572	3188,9806	2197	4300	6497	SO:0001819	synonymous_variant	116028	exon2			GATGACAGACCTT	AK123764	CCDS10548.1	16p13.13	2013-06-10	2013-06-10	2011-06-09	ENSG00000175643	ENSG00000175643			28349	protein-coding gene	gene with protein product		612426	"""chromosome 16 open reading frame 75"", ""RMI2, RecQ mediated genome instability 2, homolog (S. cerevisiae)"""	C16orf75		18923083, 20826341	Standard	NM_152308		Approved	MGC24665, BLAP18	uc002daw.1	Q96E14	OTTHUMG00000129793	ENST00000312499.5:c.369A>C	16.37:g.11444572A>C		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	119	117	0.983193	NM_152308	B3KVZ6|Q49AE2|Q8TBL0	Silent	SNP	ENST00000312499.5	37	CCDS10548.1																																																																																			A|0.786;C|0.214	0.214	strong		0.443	RMI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252019.1	NM_152308	
TMEM169	92691	hgsc.bcm.edu	37	2	216965010	216965010	+	Silent	SNP	C	C	T	rs61732363	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:216965010C>T	ENST00000295658.4	+	3	846	c.639C>T	c.(637-639)ttC>ttT	p.F213F	TMEM169_ENST00000437356.2_Silent_p.F213F|TMEM169_ENST00000406027.2_Silent_p.F213F|TMEM169_ENST00000454545.1_Silent_p.F213F	NM_001142311.1|NM_001142312.1|NM_138390.3	NP_001135783.1|NP_001135784.1|NP_612399.1	Q96HH4	TM169_HUMAN	transmembrane protein 169	213						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(2)	13		Renal(323;0.0651)		Epithelial(149;6.44e-06)|all cancers(144;0.000398)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCGTTCTCTTCTATCCAGTGC	0.547													C|||	61	0.0121805	0.0	0.0058	5008	,	,		21755	0.0		0.0119	False		,,,				2504	0.046				p.F213F		Atlas-SNP	.											.	TMEM169	46	.	0			c.C639T						PASS	.	C	,,,	12,4394	19.1+/-41.9	0,12,2191	350.0	271.0	298.0		639,639,639,639	3.8	1.0	2	dbSNP_129	298	131,8469	68.0+/-130.5	0,131,4169	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TMEM169	NM_001142310.1,NM_001142311.1,NM_001142312.1,NM_138390.3	,,,	0,143,6360	TT,TC,CC		1.5233,0.2724,1.0995	,,,	213/298,213/298,213/298,213/298	216965010	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	92691	exon4			TCTCTTCTATCCA	AK091582	CCDS2401.1	2q35	2008-02-05			ENSG00000163449	ENSG00000163449			25130	protein-coding gene	gene with protein product						12477932	Standard	NM_001142310		Approved	FLJ34263	uc002vfv.4	Q96HH4	OTTHUMG00000133053	ENST00000295658.4:c.639C>T	2.37:g.216965010C>T		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	211	91	0.43128	NM_001142310	B2R8W6	Silent	SNP	ENST00000295658.4	37	CCDS2401.1																																																																																			C|0.990;T|0.010	0.010	strong		0.547	TMEM169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256666.2	NM_138390	
DNAH14	127602	hgsc.bcm.edu	37	1	225328440	225328440	+	Intron	SNP	T	T	G	rs75827633|rs138066581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225328440T>G	ENST00000445597.2	+	17	3051				DNAH14_ENST00000439375.2_Missense_Mutation_p.Y1392D|DNAH14_ENST00000430092.1_Missense_Mutation_p.Y1392D			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.Y1392D(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TAGAGAGAGATATATATATAA	0.239													T|||	321	0.0640974	0.1384	0.0418	5008	,	,		13956	0.0		0.0696	False		,,,				2504	0.0399				p.Y1392D		Atlas-SNP	.											DNAH14_ENST00000430092,NS,carcinoma,0,1	DNAH14	300	1	1	Substitution - Missense(1)	endometrium(1)	c.T4174G						scavenged	.						9.0	7.0	8.0					1																	225328440		688	1555	2243	SO:0001627	intron_variant	127602	exon27			GAGAGATATATAT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.3052-30T>G	1.37:g.225328440T>G		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	19	13	0.684211	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		132	0.06043956043956044	55	0.11178861788617886	18	0.049723756906077346	4	0.006993006993006993	55	0.07255936675461741	T	10.21	1.288261	0.23478	.	.	ENSG00000185842	ENST00000430092;ENST00000439375	T;T	0.31247	1.5;1.5	5.29	-3.14	0.05250	.	.	.	.	.	T	0.00815	0.0027	M	0.93720	3.45	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30995	-0.9959	8	0.54805	T	0.06	.	6.4099	0.21686	0.0:0.1916:0.3392:0.4692	.	1392	Q0VDD8-4	.	D	1392	ENSP00000414402:Y1392D;ENSP00000392061:Y1392D	ENSP00000414402:Y1392D	Y	+	1	0	DNAH14	223395063	0.001000	0.12720	0.000000	0.03702	0.017000	0.09413	0.655000	0.24933	-0.306000	0.08818	0.491000	0.48974	TAT	T|0.939;G|0.061	0.061	strong		0.239	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
SLC25A47	283600	hgsc.bcm.edu	37	14	100793603	100793603	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100793603C>T	ENST00000361529.3	+	4	301	c.223C>T	c.(223-225)Cgc>Tgc	p.R75C	SLC25A47_ENST00000557052.1_5'UTR	NM_207117.2	NP_997000.2	Q6Q0C1	S2547_HUMAN	solute carrier family 25, member 47	75					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	13						TGGCACCTACCGCCACTGCCT	0.657																																					p.R75C	GBM(11;1289 1351)	Atlas-SNP	.											.	SLC25A47	36	.	0			c.C223T						PASS	.						102.0	101.0	101.0					14																	100793603		2203	4300	6503	SO:0001583	missense	283600	exon4			ACCTACCGCCACT		CCDS9959.1	14q32.2	2013-05-22	2010-07-19	2010-07-19	ENSG00000140107	ENSG00000140107		"""Solute carriers"""	20115	protein-coding gene	gene with protein product		609911	"""chromosome 14 open reading frame 68"""	C14orf68			Standard	NM_207117		Approved		uc001yhc.3	Q6Q0C1	OTTHUMG00000171571	ENST00000361529.3:c.223C>T	14.37:g.100793603C>T	ENSP00000354886:p.Arg75Cys	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_207117	B2RP39|Q68CL2|Q6PZD8|Q86U14	Missense_Mutation	SNP	ENST00000361529.3	37	CCDS9959.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.821452	0.50633	.	.	ENSG00000140107	ENST00000361529	T	0.79352	-1.26	4.7	3.73	0.42828	Mitochondrial carrier domain (2);	0.267820	0.33959	N	0.004392	T	0.78065	0.4225	M	0.85197	2.74	0.80722	D	1	B	0.20052	0.041	B	0.21546	0.035	T	0.78725	-0.2092	10	0.59425	D	0.04	2.8807	9.8376	0.40980	0.3148:0.6851:0.0:0.0	.	75	Q6Q0C1	S2547_HUMAN	C	75	ENSP00000354886:R75C	ENSP00000354886:R75C	R	+	1	0	SLC25A47	99863356	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.291000	0.33330	2.465000	0.83290	0.485000	0.47835	CGC	.	.	none		0.657	SLC25A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414231.1		
OR8H2	390151	hgsc.bcm.edu	37	11	55873026	55873026	+	Missense_Mutation	SNP	G	G	T	rs61734396|rs386753744	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55873026G>T	ENST00000313503.1	+	1	508	c.508G>T	c.(508-510)Gac>Tac	p.D170Y		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	170						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					GCATTTCTACGACTCAAACGT	0.423										HNSCC(53;0.14)			g|||	195	0.0389377	0.0121	0.0447	5008	,	,		21027	0.001		0.0944	False		,,,				2504	0.0532				p.D170Y		Atlas-SNP	.											.	OR8H2	117	.	0			c.G508T						PASS	.	G	TYR/ASP	97,4305	73.1+/-111.1	0,97,2104	257.0	231.0	240.0		508	-7.2	0.0	11	dbSNP_129	240	686,7906	156.6+/-210.4	34,618,3644	no	missense	OR8H2	NM_001005200.1	160	34,715,5748	TT,TG,GG		7.9842,2.2035,6.0259	possibly-damaging	170/313	55873026	783,12211	2201	4296	6497	SO:0001583	missense	390151	exon1			TTCTACGACTCAA	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.508G>T	11.37:g.55873026G>T	ENSP00000323982:p.Asp170Tyr	Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	293	138	0.47099	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	86	0.039377289377289376	4	0.008130081300813009	14	0.03867403314917127	0	0.0	68	0.08970976253298153	g	9.675	1.147702	0.21288	0.022035	0.079842	ENSG00000181767	ENST00000313503	T	0.33865	1.39	3.58	-7.16	0.01516	GPCR, rhodopsin-like superfamily (1);	0.996321	0.08137	N	0.992280	T	0.00815	0.0027	L	0.41824	1.3	0.09310	N	1	B	0.16166	0.016	B	0.21917	0.037	T	0.30416	-0.9979	10	0.72032	D	0.01	.	4.277	0.10813	0.4686:0.0929:0.3448:0.0938	rs61734396	170	Q8N162	OR8H2_HUMAN	Y	170	ENSP00000323982:D170Y	ENSP00000323982:D170Y	D	+	1	0	OR8H2	55629602	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.721000	0.04963	-1.824000	0.01209	-0.760000	0.03462	GAC	G|0.948;T|0.052	0.052	strong		0.423	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
OR5M10	390167	hgsc.bcm.edu	37	11	56344260	56344260	+	Missense_Mutation	SNP	A	A	G	rs10896488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56344260A>G	ENST00000526812.2	-	1	1003	c.938T>C	c.(937-939)aTt>aCt	p.I313T		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	313			I -> T (in dbSNP:rs10896488).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						CTAAACTGCAATTTTACAAAA	0.378													a|||	630	0.125799	0.0287	0.098	5008	,	,		16005	0.1597		0.2018	False		,,,				2504	0.1636				p.I313T		Atlas-SNP	.											.	OR5M10	56	.	0			c.T938C						PASS	.	G	THR/ILE	242,3404		8,226,1589	124.0	124.0	124.0		938	-1.9	0.0	11	dbSNP_120	124	1787,6371		207,1373,2499	yes	missense	OR5M10	NM_001004741.1	89	215,1599,4088	GG,GA,AA		21.9049,6.6374,17.1891	benign	313/316	56344260	2029,9775	1823	4079	5902	SO:0001583	missense	390167	exon1			ACTGCAATTTTAC	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"""GPCR / Class A : Olfactory receptors"""	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.938T>C	11.37:g.56344260A>G	ENSP00000436004:p.Ile313Thr	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	261	138	0.528736	NM_001004741	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	37	CCDS53630.1	319	0.14606227106227107	18	0.036585365853658534	47	0.1298342541436464	101	0.17657342657342656	153	0.20184696569920843	a	5.891	0.348452	0.11126	0.066374	0.219049	ENSG00000254834	ENST00000526812	T	0.03386	3.95	4.02	-1.86	0.07760	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47315	-0.9127	8	0.17832	T	0.49	.	5.819	0.18516	0.594:0.1347:0.2713:0.0	rs10896488;rs52792721;rs10896488	313	Q6IEU7	OR5MA_HUMAN	T	313	ENSP00000436004:I313T	ENSP00000436004:I313T	I	-	2	0	OR5M10	56100836	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.269000	0.02834	-0.745000	0.04772	-1.650000	0.00758	ATT	A|0.849;G|0.151	0.151	strong		0.378	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741	
MFI2	4241	hgsc.bcm.edu	37	3	196746629	196746629	+	Intron	SNP	T	T	C	rs1056664	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:196746629T>C	ENST00000296350.5	-	6	826				MFI2_ENST00000296351.4_Silent_p.E252E	NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5						cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of plasminogen activation (GO:0010756)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ferric iron binding (GO:0008199)|iron ion binding (GO:0005506)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(1)	20	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		ACTCGCCTTCTTCCTCCTCAG	0.488													C|||	1334	0.266374	0.2844	0.3444	5008	,	,		20384	0.2847		0.2266	False		,,,				2504	0.2086				p.E252E		Atlas-SNP	.											.	MFI2	88	.	0			c.A756G						PASS	.	C	,	1202,3204	708.8+/-407.7	167,868,1168	112.0	87.0	96.0		,756	-2.4	0.0	3	dbSNP_86	96	1912,6688	726.6+/-406.6	216,1480,2604	no	intron,coding-synonymous	MFI2	NM_005929.5,NM_033316.3	,	383,2348,3772	CC,CT,TT		22.2326,27.281,23.9428	,	,252/303	196746629	3114,9892	2203	4300	6503	SO:0001627	intron_variant	4241	exon7			GCCTTCTTCCTCC		CCDS3325.1, CCDS3326.1	3q28-q29	2012-10-02			ENSG00000163975	ENSG00000163975		"""CD molecules"""	7037	protein-coding gene	gene with protein product	"""melanotransferrin"", ""membrane-bound transferrin-like protein"""	155750					Standard	NM_033316		Approved	CD228, FLJ38863, MAP97, MGC4856, MTF1	uc003fxk.4	P08582	OTTHUMG00000155518	ENST00000296350.5:c.712+1645A>G	3.37:g.196746629T>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	166	84	0.506024	NM_033316	Q9BQE2	Silent	SNP	ENST00000296350.5	37	CCDS3325.1																																																																																			T|0.742;C|0.258	0.258	strong		0.488	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1		
CFAP58	159686	hgsc.bcm.edu	37	10	106214272	106214272	+	Missense_Mutation	SNP	C	C	A	rs74741614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:106214272C>A	ENST00000369704.3	+	18	2737	c.2603C>A	c.(2602-2604)aCc>aAc	p.T868N		NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		868						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		CTCAGGTCAACCAAAATGACG	0.458													C|||	26	0.00519169	0.0068	0.0144	5008	,	,		18670	0.0		0.007	False		,,,				2504	0.0				p.T868N		Atlas-SNP	.											.	CCDC147	137	.	0			c.C2603A						PASS	.	C	ASN/THR	36,4370	40.0+/-72.8	2,32,2169	130.0	122.0	124.0		2603	-0.6	0.0	10	dbSNP_131	124	122,8478	62.8+/-124.8	0,122,4178	yes	missense	CCDC147	NM_001008723.1	65	2,154,6347	AA,AC,CC		1.4186,0.8171,1.2148	benign	868/873	106214272	158,12848	2203	4300	6503	SO:0001583	missense	159686	exon18			GGTCAACCAAAAT																												ENST00000369704.3:c.2603C>A	10.37:g.106214272C>A	ENSP00000358718:p.Thr868Asn	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	87	7	0.0804598	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	37	CCDS31282.1	18	0.008241758241758242	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	5	0.006596306068601583	C	1.808	-0.475500	0.04414	0.008171	0.014186	ENSG00000120051	ENST00000369704	T	0.31769	1.48	5.47	-0.581	0.11713	.	1.145310	0.06302	N	0.701091	T	0.05090	0.0136	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24225	-1.0166	10	0.41790	T	0.15	6.1358	1.4035	0.02276	0.2731:0.4062:0.1339:0.1869	.	868	Q5T655	CC147_HUMAN	N	868	ENSP00000358718:T868N	ENSP00000358718:T868N	T	+	2	0	CCDC147	106204262	0.083000	0.21467	0.000000	0.03702	0.006000	0.05464	0.730000	0.26043	0.002000	0.14630	0.650000	0.86243	ACC	C|0.989;A|0.011	0.011	strong		0.458	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1		
ZNF773	374928	hgsc.bcm.edu	37	19	58018618	58018618	+	Silent	SNP	A	A	G	rs2074064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58018618A>G	ENST00000282292.4	+	4	1295	c.1155A>G	c.(1153-1155)aaA>aaG	p.K385K	ZNF773_ENST00000598770.1_Silent_p.K384K|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)		CTGGAGAAAAACCTTTTAAGT	0.428													G|||	860	0.171725	0.2716	0.1484	5008	,	,		21099	0.1012		0.2018	False		,,,				2504	0.0951				p.K385K		Atlas-SNP	.											.	ZNF773	62	.	0			c.A1155G						PASS	.	G		1160,3246	707.2+/-407.5	167,826,1210	107.0	111.0	109.0		1155	1.1	1.0	19	dbSNP_96	109	1701,6899	735.9+/-407.0	153,1395,2752	no	coding-synonymous	ZNF773	NM_198542.1		320,2221,3962	GG,GA,AA		19.7791,26.3277,21.9975		385/443	58018618	2861,10145	2203	4300	6503	SO:0001819	synonymous_variant	374928	exon4			AGAAAAACCTTTT	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"""Zinc fingers, C2H2-type"", ""-"""	30487	protein-coding gene	gene with protein product			"""zinc finger protein 419B"""	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.1155A>G	19.37:g.58018618A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	67	27	0.402985	NM_198542	Q96DL8	Silent	SNP	ENST00000282292.4	37	CCDS33134.1																																																																																			A|0.791;G|0.209	0.209	strong		0.428	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542	
YPEL1	29799	hgsc.bcm.edu	37	22	22049783	22049783	+	IGR	SNP	C	C	T	rs12484060	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:22049783C>T	ENST00000339468.3	-	0	4329				PPIL2_ENST00000406385.1_3'UTR|PPIL2_ENST00000412327.1_Silent_p.S521S|PPIL2_ENST00000335025.8_3'UTR|PPIL2_ENST00000446951.1_3'UTR|PPIL2_ENST00000398831.3_3'UTR|PPIL2_ENST00000456792.2_Missense_Mutation_p.A467V|PPIL2_ENST00000492445.2_3'UTR	NM_013313.3	NP_037445.1	O60688	YPEL1_HUMAN	yippee-like 1 (Drosophila)							nucleus (GO:0005634)				breast(1)|large_intestine(1)|lung(1)	3	Colorectal(54;0.105)					CTGGTAGCAGCAGGTTGGCCG	0.607													C|||	1832	0.365815	0.4032	0.3473	5008	,	,		17350	0.4425		0.3211	False		,,,				2504	0.2955				p.S521S		Atlas-SNP	.											.	PPIL2	38	.	0			c.C1563T						PASS	.	C	,,	1675,2723		325,1025,849	24.0	22.0	23.0		,,1563	0.9	0.1	22	dbSNP_120	23	2935,5665		512,1911,1877	no	utr-3,utr-3,coding-synonymous	PPIL2	NM_014337.3,NM_148175.2,NM_148176.2	,,	837,2936,2726	TT,TC,CC		34.1279,38.0855,35.467	,,	,,521/528	22049783	4610,8388	2199	4300	6499	SO:0001628	intergenic_variant	23759	exon20			TAGCAGCAGGTTG	AF060862	CCDS13794.1	22q11.2	2008-02-04	2001-11-28		ENSG00000100027	ENSG00000100027			12845	protein-coding gene	gene with protein product		608082	"""yippee (Drosophila) homolog-like 1"""			11473580	Standard	NM_013313		Approved		uc002zvl.3	O60688	OTTHUMG00000150830		22.37:g.22049783C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	188	89	0.473404	NM_148176	Q65ZA1|Q6GLI6	Silent	SNP	ENST00000339468.3	37	CCDS13794.1	846	0.3873626373626374	206	0.4186991869918699	133	0.3674033149171271	263	0.4597902097902098	244	0.32189973614775724	C	15.10	2.732309	0.48939	0.380855	0.341279	ENSG00000100023	ENST00000456792	T	0.25085	1.82	3.28	0.931	0.19460	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.39086	P	0.038999000000000006	B	0.26935	0.164	B	0.17433	0.018	T	0.47032	-0.9148	7	0.37606	T	0.19	.	11.6688	0.51389	0.0:0.6561:0.3439:0.0	rs12484060;rs12484060	467	E7EW80	.	V	467	ENSP00000396228:A467V	ENSP00000396228:A467V	A	+	2	0	PPIL2	20379783	0.015000	0.18098	0.080000	0.20451	0.572000	0.35998	0.725000	0.25970	0.196000	0.20367	0.558000	0.71614	GCA	C|0.616;T|0.384	0.384	strong		0.607	YPEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320245.1	NM_013313	
R3HCC1	203069	hgsc.bcm.edu	37	8	23150878	23150878	+	Missense_Mutation	SNP	T	T	G	rs13530	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:23150878T>G	ENST00000411463.1	+	7	1208	c.1208T>G	c.(1207-1209)cTg>cGg	p.L403R	R3HCC1_ENST00000265806.6_Missense_Mutation_p.L176R|R3HCC1_ENST00000518454.1_Missense_Mutation_p.L176R|R3HCC1_ENST00000522012.1_3'UTR			Q9Y3T6	R3HC1_HUMAN	R3H domain and coiled-coil containing 1	403			L -> R (in dbSNP:rs13530).				nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)			central_nervous_system(1)|skin(2)	3						TTTCCCTGCCTGGCCTCAGGT	0.607													T|||	2768	0.552716	0.4289	0.4553	5008	,	,		18639	0.7996		0.5398	False		,,,				2504	0.5481				p.L176R		Atlas-SNP	.											.	R3HCC1	11	.	0			c.T527G						PASS	.						41.0	36.0	38.0					8																	23150878		692	1591	2283	SO:0001583	missense	203069	exon6			CCTGCCTGGCCTC		CCDS47826.1	8p21.3	2012-05-23		2005-11-20	ENSG00000104679	ENSG00000104679			27329	protein-coding gene	gene with protein product						12477932	Standard	XM_005273427		Approved	DKFZp564N123	uc003xdf.3	Q9Y3T6	OTTHUMG00000163786	ENST00000411463.1:c.1208T>G	8.37:g.23150878T>G	ENSP00000397555:p.Leu403Arg	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_001136108	B7ZLI1	Missense_Mutation	SNP	ENST00000411463.1	37		1277	0.5847069597069597	219	0.4451219512195122	178	0.49171270718232046	459	0.8024475524475524	421	0.5554089709762533	T	12.75	2.032237	0.35893	.	.	ENSG00000104679	ENST00000518454;ENST00000265806;ENST00000411463;ENST00000520480	T;T;T;T	0.41065	1.01;1.01;2.21;1.01	5.83	3.48	0.39840	Nucleotide-binding, alpha-beta plait (1);	0.400244	0.26525	N	0.023881	T	0.00012	0.0000	L	0.54323	1.7	0.09310	P	1.0	D	0.54397	0.966	P	0.52159	0.691	T	0.27191	-1.0081	9	0.15952	T	0.53	-1.5068	7.6633	0.28415	0.0:0.1695:0.0:0.8305	rs13530;rs1128916;rs3186283;rs11135721;rs17296698;rs17357785;rs56792131;rs11135721	403	Q9Y3T6	R3HC1_HUMAN	R	176;176;403;98	ENSP00000430607:L176R;ENSP00000265806:L176R;ENSP00000397555:L403R;ENSP00000430339:L98R	ENSP00000265806:L176R	L	+	2	0	R3HCC1	23206823	0.255000	0.24002	0.992000	0.48379	0.986000	0.74619	0.384000	0.20668	0.489000	0.27749	0.533000	0.62120	CTG	T|0.219;G|0.311	0.311	strong		0.607	R3HCC1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001136108	
PIGN	23556	hgsc.bcm.edu	37	18	59781800	59781800	+	Silent	SNP	A	A	G	rs13381627	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:59781800A>G	ENST00000357637.5	-	15	1660	c.1245T>C	c.(1243-1245)gaT>gaC	p.D415D	PIGN_ENST00000400334.3_Silent_p.D415D	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	415					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				TTACCACTTCATCAAACTTTC	0.338													G|||	479	0.095647	0.0144	0.1239	5008	,	,		15310	0.0069		0.2694	False		,,,				2504	0.0982				p.D415D		Atlas-SNP	.											.	PIGN	62	.	0			c.T1245C						PASS	.	G	,	165,3269		4,157,1556	75.0	65.0	68.0		1245,1245	-2.8	0.8	18	dbSNP_121	68	1611,6081		152,1307,2387	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	156,1464,3943	GG,GA,AA		20.9438,4.8049,15.9626	,	415/932,415/932	59781800	1776,9350	1717	3846	5563	SO:0001819	synonymous_variant	23556	exon15			CACTTCATCAAAC	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.1245T>C	18.37:g.59781800A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			A|0.876;G|0.124	0.124	strong		0.338	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
CLEC17A	388512	hgsc.bcm.edu	37	19	14705574	14705574	+	Missense_Mutation	SNP	T	T	C	rs78269670	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14705574T>C	ENST00000417570.1	+	7	403	c.365T>C	c.(364-366)cTg>cCg	p.L122P	CLEC17A_ENST00000397439.2_Missense_Mutation_p.L105P|CLEC17A_ENST00000547437.1_Missense_Mutation_p.L122P	NM_001204118.1	NP_001191047.1	Q6ZS10	CL17A_HUMAN	C-type lectin domain family 17, member A	122						cell surface (GO:0009986)|integral component of membrane (GO:0016021)	fucose binding (GO:0042806)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)										CTTCTAGGCCTGGACCTCGCC	0.532													N|||	417	0.0832668	0.174	0.036	5008	,	,		18213	0.004		0.0676	False		,,,				2504	0.092				p.L122P		Atlas-SNP	.											.	CLEC17A	27	.	0			c.T365C						PASS	.		PRO/LEU,PRO/LEU	571,3429		39,493,1468	79.0	81.0	81.0		365,365	-0.2	0.0	19	dbSNP_131	81	555,7781		21,513,3634	yes	missense,missense	CLEC17A	NM_207390.3,NM_001204118.1	98,98	60,1006,5102	CC,CT,TT		6.6579,14.275,9.1278	benign,benign	122/307,122/379	14705574	1126,11210	2000	4168	6168	SO:0001583	missense	388512	exon7			TAGGCCTGGACCT	AK127809	CCDS46002.1, CCDS46002.2, CCDS56087.1	19p13.12	2009-06-26			ENSG00000187912	ENSG00000187912		"""C-type lectin domain containing"""	34520	protein-coding gene	gene with protein product	"""prolectin"""					19419970	Standard	NM_207390		Approved	FLJ45910	uc010dzn.2	Q6ZS10		ENST00000417570.1:c.365T>C	19.37:g.14705574T>C	ENSP00000393719:p.Leu122Pro	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	NM_207390	A8MX68|B2RTX0|B7ZMM4	Missense_Mutation	SNP	ENST00000417570.1	37	CCDS56087.1	122	0.055860805860805864	59	0.11991869918699187	13	0.03591160220994475	3	0.005244755244755245	47	0.06200527704485488	t	12.58	1.982059	0.34942	0.14275	0.066579	ENSG00000187912	ENST00000547437;ENST00000397439;ENST00000417570	T;T;T	0.63255	-0.03;1.28;-0.03	3.42	-0.168	0.13343	.	2.549380	0.02249	N	0.066442	T	0.00440	0.0014	L	0.27053	0.805	0.19575	N	0.999962	B;B;B;B	0.21309	0.041;0.023;0.054;0.015	B;B;B;B	0.17722	0.019;0.01;0.014;0.011	T	0.08493	-1.0719	10	0.66056	D	0.02	-19.8414	2.8523	0.05561	0.1885:0.2354:0.0:0.5761	.	122;122;122;122	Q6ZS10-2;Q6ZS10-3;Q6ZS10;F8W1T8	.;.;CL17A_HUMAN;.	P	122;105;122	ENSP00000450065:L122P;ENSP00000380581:L105P;ENSP00000393719:L122P	ENSP00000341620:L122P	L	+	2	0	CLEC17A	14566574	0.484000	0.25964	0.013000	0.15412	0.011000	0.07611	1.094000	0.30951	-0.251000	0.09542	-0.560000	0.04181	CTG	T|0.943;C|0.057	0.057	strong		0.532	CLEC17A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403400.1	NM_207390	
BTNL2	56244	hgsc.bcm.edu	37	6	32370794	32370794	+	Silent	SNP	C	C	T	rs60036207	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32370794C>T	ENST00000374993.1	-	3	626	c.627G>A	c.(625-627)agG>agA	p.R209R	BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000454136.3_Silent_p.R209R|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000374995.3_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	209	Ig-like V-type 2.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CAGAGGCGTTCCTGACCACCA	0.582													C|||	672	0.134185	0.1369	0.1369	5008	,	,		18686	0.1984		0.0974	False		,,,				2504	0.1002				p.R209R		Atlas-SNP	.											.	BTNL2	50	.	0			c.G627A						PASS	.	C		339,2681		12,315,1183	94.0	80.0	85.0		627	-0.7	0.0	6	dbSNP_129	85	427,4989		15,397,2296	no	coding-synonymous	BTNL2	NM_019602.1		27,712,3479	TT,TC,CC		7.884,11.2252,9.0801		209/456	32370794	766,7670	1510	2708	4218	SO:0001819	synonymous_variant	56244	exon3			GGCGTTCCTGACC	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.627G>A	6.37:g.32370794C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	202	99	0.490099	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Silent	SNP	ENST00000374993.1	37																																																																																				C|0.898;T|0.102	0.102	strong		0.582	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
DHRS1	115817	hgsc.bcm.edu	37	14	24760808	24760808	+	Silent	SNP	C	C	T	rs1131941	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24760808C>T	ENST00000288111.7	-	7	954	c.678G>A	c.(676-678)gcG>gcA	p.A226A	DHRS1_ENST00000559088.1_5'UTR|DHRS1_ENST00000396813.1_Silent_p.A226A	NM_001136050.2	NP_001129522.1	Q96LJ7	DHRS1_HUMAN	dehydrogenase/reductase (SDR family) member 1	226						endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	6				GBM - Glioblastoma multiforme(265;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(311;0.0442)		CTGTGGTTTCCGCAGATGAGA	0.498													C|||	746	0.148962	0.1513	0.3473	5008	,	,		22102	0.004		0.1869	False		,,,				2504	0.1155				p.A226A		Atlas-SNP	.											.	DHRS1	21	.	0			c.G678A						PASS	.	C	,	728,3678	301.0+/-286.6	62,604,1537	196.0	192.0	193.0		678,678	-7.2	0.0	14	dbSNP_86	193	1783,6817	322.1+/-315.4	189,1405,2706	no	coding-synonymous,coding-synonymous	DHRS1	NM_001136050.2,NM_138452.2	,	251,2009,4243	TT,TC,CC		20.7326,16.5229,19.3065	,	226/314,226/314	24760808	2511,10495	2203	4300	6503	SO:0001819	synonymous_variant	115817	exon7			GGTTTCCGCAGAT	AK058159	CCDS9623.1	14q11.2	2011-09-14			ENSG00000157379	ENSG00000157379	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16445	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 19C, member 1"""	610410				12153138, 19027726	Standard	NM_138452		Approved	FLJ25430, MGC20204, SDR19C1	uc001wok.3	Q96LJ7	OTTHUMG00000029333	ENST00000288111.7:c.678G>A	14.37:g.24760808C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_138452	D3DS71|Q8NDG3|Q96B59|Q96CQ5	Silent	SNP	ENST00000288111.7	37	CCDS9623.1																																																																																			C|0.827;T|0.173	0.173	strong		0.498	DHRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073168.4	NM_138452	
SPTB	6710	hgsc.bcm.edu	37	14	65249066	65249066	+	Missense_Mutation	SNP	C	C	T	rs17180350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:65249066C>T	ENST00000389721.5	-	19	4240	c.4208G>A	c.(4207-4209)cGg>cAg	p.R1403Q	SPTB_ENST00000542895.1_Missense_Mutation_p.R1403Q|SPTB_ENST00000389722.3_Missense_Mutation_p.R1403Q|SPTB_ENST00000389720.3_Missense_Mutation_p.R1403Q|SPTB_ENST00000556626.1_Missense_Mutation_p.R1403Q	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1403			R -> Q (in dbSNP:rs17180350).		actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GTCGTCTGACCGCAGCTGGTC	0.587													C|||	164	0.0327476	0.0045	0.0432	5008	,	,		19629	0.0238		0.0845	False		,,,				2504	0.0194				p.R1403Q		Atlas-SNP	.											.	SPTB	378	.	0			c.G4208A						PASS	.	C	GLN/ARG,GLN/ARG	65,4341	60.5+/-97.4	1,63,2139	110.0	97.0	102.0		4208,4208	4.5	1.0	14	dbSNP_123	102	697,7903	173.3+/-223.8	30,637,3633	yes	missense,missense	SPTB	NM_000347.5,NM_001024858.2	43,43	31,700,5772	TT,TC,CC		8.1047,1.4753,5.8588	benign,benign	1403/2138,1403/2329	65249066	762,12244	2203	4300	6503	SO:0001583	missense	6710	exon19			TCTGACCGCAGCT		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4208G>A	14.37:g.65249066C>T	ENSP00000374371:p.Arg1403Gln	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	158	65	0.411392	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	97	0.044413919413919416	5	0.01016260162601626	18	0.049723756906077346	10	0.017482517482517484	64	0.08443271767810026	C	7.218	0.596855	0.13875	0.014753	0.081047	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000553938;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83	5.36	4.47	0.54385	.	0.124654	0.56097	N	0.000026	T	0.01124	0.0037	N	0.12182	0.205	0.36617	D	0.875519	B;B;B	0.13145	0.007;0.0;0.0	B;B;B	0.08055	0.003;0.002;0.003	T	0.07790	-1.0754	10	0.02654	T	1	.	7.7187	0.28719	0.0:0.7518:0.0:0.2482	rs17180350;rs52807358;rs17180350	187;1403;1407	E7EV95;P11277;Q59FP5	.;SPTB1_HUMAN;.	Q	1407;1403;187;68;1403;1403;1403;1403	ENSP00000374372:R1403Q;ENSP00000451324:R68Q;ENSP00000451752:R1403Q;ENSP00000374371:R1403Q;ENSP00000443882:R1403Q;ENSP00000374370:R1403Q	ENSP00000334218:R187Q	R	-	2	0	SPTB	64318819	0.467000	0.25831	0.994000	0.49952	0.973000	0.67179	0.978000	0.29488	1.411000	0.46957	0.462000	0.41574	CGG	C|0.947;N|0.000	.	strong		0.587	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
OR51Q1	390061	hgsc.bcm.edu	37	11	5443887	5443887	+	Missense_Mutation	SNP	T	T	C	rs10838093	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5443887T>C	ENST00000300778.4	+	1	547	c.457T>C	c.(457-459)Tgc>Cgc	p.C153R	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	153			C -> R (in dbSNP:rs10838093).	CCV -> RCI (in Ref. 3; BAC05778). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATCATTTGCTGCTGTGTTCT	0.512													C|||	2272	0.453674	0.2799	0.3991	5008	,	,		21029	0.7024		0.3986	False		,,,				2504	0.5276				p.C153R		Atlas-SNP	.											OR51Q1,colon,carcinoma,-1,1	OR51Q1	79	1	0			c.T457C						scavenged	.	C	ARG/CYS	1316,3086	694.4+/-405.8	202,912,1087	261.0	224.0	236.0		457	3.1	1.0	11	dbSNP_120	236	3370,5224	641.7+/-399.7	675,2020,1602	yes	missense	OR51Q1	NM_001004757.2	180	877,2932,2689	CC,CT,TT		39.2134,29.8955,36.0572	benign	153/318	5443887	4686,8310	2201	4297	6498	SO:0001583	missense	390061	exon1			ATTTGCTGCTGTG	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.457T>C	11.37:g.5443887T>C	ENSP00000300778:p.Cys153Arg	Somatic	257	2	0.0077821		WXS	Illumina HiSeq	Phase_I	249	115	0.461847	NM_001004757	B2RNN1	Missense_Mutation	SNP	ENST00000300778.4	37	CCDS31381.1	966	0.4423076923076923	139	0.28252032520325204	148	0.4088397790055249	395	0.6905594405594405	284	0.37467018469656993	C	0.004	-2.346301	0.00219	0.298955	0.392134	ENSG00000167360	ENST00000300778	T	0.36520	1.25	5.0	3.09	0.35607	GPCR, rhodopsin-like superfamily (1);	0.102173	0.44097	N	0.000496	T	0.00012	0.0000	N	0.00008	-3.13	0.52099	P	5.900000000003125E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.44390	-0.9331	9	0.02654	T	1	.	6.8803	0.24168	0.1413:0.7052:0.0:0.1535	rs10838093;rs52801150;rs57444579;rs10838093	153	Q8NH59	O51Q1_HUMAN	R	153	ENSP00000300778:C153R	ENSP00000300778:C153R	C	+	1	0	OR51Q1	5400463	0.000000	0.05858	0.991000	0.47740	0.181000	0.23173	-1.070000	0.03440	0.308000	0.22923	-1.239000	0.01543	TGC	C|0.398;N|0.001	0.398	strong		0.512	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
TP53BP2	7159	hgsc.bcm.edu	37	1	223980207	223980207	+	Silent	SNP	G	G	C	rs1153936	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:223980207G>C	ENST00000343537.7	-	15	3171	c.2880C>G	c.(2878-2880)ctC>ctG	p.L960L	TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391879.2_Silent_p.L193L|TP53BP2_ENST00000391878.2_Silent_p.L831L	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	954	Mediates interaction with APC2.				cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		CATCATTGGGGAGGCTTGGGT	0.458													C|||	1071	0.213858	0.4198	0.2133	5008	,	,		18960	0.1935		0.0944	False		,,,				2504	0.0798				p.L960L		Atlas-SNP	.											.	TP53BP2	144	.	0			c.C2880G						PASS	.	C	,	1553,2853	668.9+/-402.1	260,1033,910	87.0	81.0	83.0		2880,2493	3.4	1.0	1	dbSNP_87	83	596,8004	792.5+/-407.5	28,540,3732	yes	coding-synonymous,coding-synonymous	TP53BP2	NM_001031685.2,NM_005426.2	,	288,1573,4642	CC,CG,GG		6.9302,35.2474,16.5231	,	960/1135,831/1006	223980207	2149,10857	2203	4300	6503	SO:0001819	synonymous_variant	7159	exon15			ATTGGGGAGGCTT	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	12000	protein-coding gene	gene with protein product		602143	"""tumor protein p53-binding protein, 2"""			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.2880C>G	1.37:g.223980207G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Silent	SNP	ENST00000343537.7	37	CCDS44319.1																																																																																			G|0.824;C|0.176	0.176	strong		0.458	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240790	39240790	+	Missense_Mutation	SNP	G	G	A	rs11650261|rs553572799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240790G>A	ENST00000391417.4	+	1	332	c.332G>A	c.(331-333)cGc>cAc	p.R111H		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	136	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						acctgctgccgccccagctgc	0.657													g|||	343	0.0684904	0.0272	0.1196	5008	,	,		10689	0.0685		0.1153	False		,,,				2504	0.0399				p.R111H		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,3	KRTAP4-7	49	3	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G332A						scavenged	.						11.0	13.0	12.0					17																	39240790		682	1579	2261	SO:0001583	missense	100132476	exon1			GCTGCCGCCCCAG	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.332G>A	17.37:g.39240790G>A	ENSP00000375236:p.Arg111His	Somatic	29	1	0.0344828		WXS	Illumina HiSeq	Phase_I	33	5	0.151515	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	148	0.06776556776556776	22	0.044715447154471545	32	0.08839779005524862	22	0.038461538461538464	72	0.09498680738786279	.	6.498	0.460116	0.12342	.	.	ENSG00000240871	ENST00000391417	T	0.00612	6.22	3.95	-0.91	0.10511	.	8.977930	0.00616	U	0.000420	T	0.00039	0.0001	.	.	.	0.09310	N	1	D	0.60575	0.988	P	0.46389	0.515	T	0.44050	-0.9353	9	0.48119	T	0.1	.	3.4362	0.07446	0.2202:0.0:0.299:0.4808	rs11650261	166	Q9BYR0	KRA47_HUMAN	H	111	ENSP00000375236:R111H	ENSP00000375236:R111H	R	+	2	0	KRTAP4-7	36494316	0.000000	0.05858	0.005000	0.12908	0.119000	0.20118	0.218000	0.17622	0.230000	0.21059	-0.391000	0.06502	CGC	G|0.932;A|0.068	0.068	strong		0.657	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
PDIA2	64714	hgsc.bcm.edu	37	16	334543	334543	+	Missense_Mutation	SNP	C	C	G	rs45614840	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:334543C>G	ENST00000219406.6	+	2	374	c.356C>G	c.(355-357)aCg>aGg	p.T119R	PDIA2_ENST00000404312.1_Missense_Mutation_p.T119R	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	119	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.		T -> R (in dbSNP:rs45614840).		cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GAGTACCCTACGCTCAAGTTC	0.677													c|||	240	0.0479233	0.0045	0.0749	5008	,	,		16618	0.0		0.1421	False		,,,				2504	0.0399				p.T119R		Atlas-SNP	.											.	PDIA2	51	.	0			c.C356G						PASS	.	C	ARG/THR	110,4208		2,106,2051	55.0	62.0	59.0		356	3.2	0.8	16	dbSNP_127	59	1147,7363		69,1009,3177	yes	missense	PDIA2	NM_006849.2	71	71,1115,5228	GG,GC,CC		13.4783,2.5475,9.7989	probably-damaging	119/526	334543	1257,11571	2159	4255	6414	SO:0001583	missense	64714	exon2			ACCCTACGCTCAA	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"""Protein disulfide isomerases"""	14180	protein-coding gene	gene with protein product		608012	"""protein disulfide isomerase, pancreatic"", ""protein disulfide isomerase-associated 2"""	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.356C>G	16.37:g.334543C>G	ENSP00000219406:p.Thr119Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	137|137	0.06272893772893773|0.06272893772893773	3|3	0.006097560975609756|0.006097560975609756	31|31	0.0856353591160221|0.0856353591160221	0|0	0.0|0.0	103|103	0.1358839050131926|0.1358839050131926	c|c	13.79|13.79	2.341804|2.341804	0.41498|0.41498	0.025475|0.025475	0.134783|0.134783	ENSG00000185615|ENSG00000185615	ENST00000456379|ENST00000219406;ENST00000455994;ENST00000404312	.|T;T	.|0.05258	.|3.47;3.47	4.14|4.14	3.17|3.17	0.36434|0.36434	.|Thioredoxin domain (1);Thioredoxin-like fold (3);	.|0.273073	.|0.32578	.|N	.|0.005912	T|T	0.00271|0.00271	0.0008|0.0008	H|H	0.95151|0.95151	3.63|3.63	0.24811|0.24811	P|P	0.99264751|0.99264751	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	T|T	0.13575|0.13575	-1.0504|-1.0504	4|9	.|0.87932	.|D	.|0	.|.	11.2461|11.2461	0.48998|0.48998	0.0:0.9043:0.0:0.0957|0.0:0.9043:0.0:0.0957	rs45614840|rs45614840	.|119	.|Q13087	.|PDIA2_HUMAN	G|R	116|119;88;119	.|ENSP00000219406:T119R;ENSP00000384410:T119R	.|ENSP00000219406:T119R	R|T	+|+	1|2	0|0	PDIA2|PDIA2	274544|274544	0.053000|0.053000	0.20554|0.20554	0.797000|0.797000	0.32132|0.32132	0.182000|0.182000	0.23217|0.23217	1.869000|1.869000	0.39519|0.39519	1.873000|1.873000	0.54277|0.54277	0.550000|0.550000	0.68814|0.68814	CGC|ACG	C|0.922;G|0.078	0.078	strong		0.677	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
PDCD6IP	10015	hgsc.bcm.edu	37	3	33887008	33887008	+	Silent	SNP	G	G	A	rs112754416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33887008G>A	ENST00000307296.3	+	12	1946	c.1569G>A	c.(1567-1569)ttG>ttA	p.L523L	PDCD6IP_ENST00000457054.2_Silent_p.L528L			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	523	Interaction with EIAV p9.|Self-association.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						TCGTGCTTTTGTGTAAGCCAG	0.473													G|||	140	0.0279553	0.0098	0.0173	5008	,	,		17462	0.002		0.0437	False		,,,				2504	0.0706				p.L528L		Atlas-SNP	.											PDCD6IP,NS,carcinoma,0,1	PDCD6IP	62	1	0			c.G1584A						PASS	.	G	,	75,4331	67.6+/-105.2	0,75,2128	120.0	97.0	105.0		1584,1569	-3.5	1.0	3	dbSNP_132	105	482,8118	139.5+/-196.2	17,448,3835	no	coding-synonymous,coding-synonymous	PDCD6IP	NM_001162429.1,NM_013374.4	,	17,523,5963	AA,AG,GG		5.6047,1.7022,4.2826	,	528/874,523/869	33887008	557,12449	2203	4300	6503	SO:0001819	synonymous_variant	10015	exon12			GCTTTTGTGTAAG	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.1569G>A	3.37:g.33887008G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	196	99	0.505102	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Silent	SNP	ENST00000307296.3	37	CCDS2660.1																																																																																			G|0.962;A|0.038	0.038	strong		0.473	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
GGCX	2677	hgsc.bcm.edu	37	2	85783341	85783341	+	Silent	SNP	G	G	A	rs76767923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:85783341G>A	ENST00000233838.4	-	5	662	c.582C>T	c.(580-582)caC>caT	p.H194H	GGCX_ENST00000473665.1_5'Flank|GGCX_ENST00000430215.3_Silent_p.H137H	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	194					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	AAAGGGGCACGTGGGCATTCC	0.557													G|||	7	0.00139776	0.0	0.0014	5008	,	,		14470	0.0		0.006	False		,,,				2504	0.0				p.H194H		Atlas-SNP	.											.	GGCX	44	.	0			c.C582T						PASS	.	G	,	7,4399	11.4+/-27.6	0,7,2196	127.0	93.0	104.0		582,411	-11.9	0.5	2	dbSNP_131	104	43,8557	27.9+/-77.7	0,43,4257	no	coding-synonymous,coding-synonymous	GGCX	NM_000821.5,NM_001142269.2	,	0,50,6453	AA,AG,GG		0.5,0.1589,0.3844	,	194/759,137/702	85783341	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	2677	exon5			GGGCACGTGGGCA		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.582C>T	2.37:g.85783341G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Silent	SNP	ENST00000233838.4	37	CCDS1978.1																																																																																			G|0.996;A|0.004	0.004	strong		0.557	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
SCN10A	6336	hgsc.bcm.edu	37	3	38748833	38748833	+	Silent	SNP	T	T	C	rs6790627	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:38748833T>C	ENST00000449082.2	-	25	4322	c.4323A>G	c.(4321-4323)aaA>aaG	p.K1441K		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1441					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.K1441K(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CATTGTAGTATTTCTTCTGCT	0.542													C|||	1214	0.242412	0.3578	0.2104	5008	,	,		19164	0.3115		0.1571	False		,,,				2504	0.1258				p.K1441K		Atlas-SNP	.											SCN10A,NS,carcinoma,0,1	SCN10A	359	1	1	Substitution - coding silent(1)	stomach(1)	c.A4323G						PASS	.	C		1500,2906	676.4+/-403.2	263,974,966	131.0	139.0	136.0		4323	1.7	1.0	3	dbSNP_116	136	1230,7370	762.2+/-407.6	75,1080,3145	no	coding-synonymous	SCN10A	NM_006514.2		338,2054,4111	CC,CT,TT		14.3023,34.0445,20.9903		1441/1957	38748833	2730,10276	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon25			GTAGTATTTCTTC	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4323A>G	3.37:g.38748833T>C		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	301	155	0.51495	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			T|0.796;C|0.204	0.204	strong		0.542	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
FUT8	2530	hgsc.bcm.edu	37	14	66028446	66028446	+	Silent	SNP	A	A	G	rs2229677	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:66028446A>G	ENST00000360689.5	+	3	1892	c.165A>G	c.(163-165)caA>caG	p.Q55Q	FUT8_ENST00000394586.2_Silent_p.Q55Q|FUT8_ENST00000394585.1_Silent_p.Q55Q|FUT8_ENST00000557164.1_Intron|FUT8_ENST00000358307.2_Intron	NM_004480.4|NM_178155.2	NP_004471.4|NP_835368.1	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	55					cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		GCTTAAAACAACAGAATGAAG	0.408													G|||	3790	0.756789	0.7579	0.6729	5008	,	,		19620	0.9048		0.6352	False		,,,				2504	0.7873				p.Q55Q		Atlas-SNP	.											.	FUT8	101	.	0			c.A165G						PASS	.	G	,,	3236,1170	410.9+/-335.5	1178,880,145	75.0	73.0	74.0		,165,165	0.2	1.0	14	dbSNP_107	74	5860,2738	436.4+/-358.3	2012,1836,451	no	intron,coding-synonymous,coding-synonymous	FUT8	NM_004480.4,NM_178155.2,NM_178156.2	,,	3190,2716,596	GG,GA,AA		31.8446,26.5547,30.0523	,,	,55/576,55/576	66028446	9096,3908	2203	4299	6502	SO:0001819	synonymous_variant	2530	exon3			AAAACAACAGAAT	AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170		"""Fucosyltransferases"""	4019	protein-coding gene	gene with protein product		602589				9368041	Standard	NM_178155		Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	ENST00000360689.5:c.165A>G	14.37:g.66028446A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	58	0.467742	NM_178155	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	Silent	SNP	ENST00000360689.5	37	CCDS9775.1																																																																																			A|0.277;G|0.723	0.723	strong		0.408	FUT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286406.1	NM_004480	
MYEOV2	150678	hgsc.bcm.edu	37	2	241066179	241066179	+	Missense_Mutation	SNP	C	C	A	rs140948790		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241066179C>A	ENST00000307266.3	-	5	559	c.560G>T	c.(559-561)cGg>cTg	p.R187L		NM_138336.1	NP_612209.1	Q8WXC6	MYOV2_HUMAN	myeloma overexpressed 2	0										breast(1)|lung(5)|pancreas(1)	7		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)		TTGGTTCTTCCGTAAACTGTT	0.483																																					p.R187L		Atlas-SNP	.											MYEOV2,NS,carcinoma,0,1	MYEOV2	20	1	0			c.G560T						scavenged	.						252.0	249.0	250.0					2																	241066179		2203	4300	6503	SO:0001583	missense	150678	exon5			TTCTTCCGTAAAC	AF453951	CCDS2532.1, CCDS63183.1	2q37.3	2008-02-05			ENSG00000172428	ENSG00000172428			21314	protein-coding gene	gene with protein product							Standard	NM_138336		Approved		uc002vyu.1	Q8WXC6	OTTHUMG00000133352	ENST00000307266.3:c.560G>T	2.37:g.241066179C>A	ENSP00000304147:p.Arg187Leu	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	280	4	0.0142857	NM_138336	Q8N110	Missense_Mutation	SNP	ENST00000307266.3	37	CCDS2532.1	.	.	.	.	.	.	.	.	.	.	C	7.984	0.751831	0.15778	.	.	ENSG00000172428	ENST00000307266	.	.	.	1.94	-2.27	0.06846	.	.	.	.	.	T	0.29093	0.0723	.	.	.	0.09310	N	1	B	0.17667	0.023	B	0.17433	0.018	T	0.30031	-0.9992	7	0.87932	D	0	.	5.9522	0.19253	0.0:0.508:0.0:0.492	.	187	Q8WXC6-1	.	L	187	.	ENSP00000304147:R187L	R	-	2	0	MYEOV2	240714852	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.337000	0.02657	-0.577000	0.05967	-0.474000	0.04947	CGG	C|1.000;T|0.000	.	alt		0.483	MYEOV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257182.2	NM_138336	
DAAM1	23002	hgsc.bcm.edu	37	14	59797373	59797373	+	Silent	SNP	G	G	A	rs28927674	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:59797373G>A	ENST00000395125.1	+	12	1550	c.1527G>A	c.(1525-1527)gcG>gcA	p.A509A	DAAM1_ENST00000360909.3_Silent_p.A509A|DAAM1_ENST00000351081.1_Silent_p.A509A	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	509					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AGCAGGTGGCGGACCTCACAG	0.522													G|||	153	0.0305511	0.0053	0.0375	5008	,	,		19108	0.0109		0.0924	False		,,,				2504	0.0164				p.A509A		Atlas-SNP	.											DAAM1,colon,carcinoma,+1,1	DAAM1	95	1	0			c.G1527A						scavenged	.	G		70,4336	66.4+/-103.9	0,70,2133	71.0	71.0	71.0		1527	-12.0	0.4	14	dbSNP_125	71	814,7786	188.9+/-235.7	33,748,3519	no	coding-synonymous	DAAM1	NM_014992.1		33,818,5652	AA,AG,GG		9.4651,1.5887,6.7969		509/1079	59797373	884,12122	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon13			GGTGGCGGACCTC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.1527G>A	14.37:g.59797373G>A		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	183	82	0.448087	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.939;A|0.061	0.061	strong		0.522	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
OR8S1	341568	hgsc.bcm.edu	37	12	48919659	48919659	+	Missense_Mutation	SNP	T	T	C	rs4075258|rs71439450	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48919659T>C	ENST00000310194.1	+	1	245	c.245T>C	c.(244-246)cTg>cCg	p.L82P	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	82			L -> P (in dbSNP:rs4075258).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						CCCAAGATGCTGGAGAACCTC	0.488													T|||	2896	0.578275	0.4849	0.6599	5008	,	,		21421	0.6905		0.5139	False		,,,				2504	0.5971				p.L82P		Atlas-SNP	.											.	OR8S1	47	.	0			c.T245C						PASS	.	T	PRO/LEU	2183,2223	585.8+/-386.3	519,1145,539	136.0	129.0	132.0		245	5.0	0.2	12	dbSNP_108	132	4566,4034	596.6+/-393.6	1210,2146,944	yes	missense	OR8S1	NM_001005203.2	98	1729,3291,1483	CC,CT,TT		46.907,49.5461,48.1086	probably-damaging	82/360	48919659	6749,6257	2203	4300	6503	SO:0001583	missense	341568	exon1			AGATGCTGGAGAA		CCDS31789.1	12q13.2	2012-08-09				ENSG00000197376		"""GPCR / Class A : Olfactory receptors"""	19628	protein-coding gene	gene with protein product							Standard	NM_001005203		Approved		uc010slu.2	Q8NH09		ENST00000310194.1:c.245T>C	12.37:g.48919659T>C	ENSP00000310632:p.Leu82Pro	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	184	90	0.48913	NM_001005203		Missense_Mutation	SNP	ENST00000310194.1	37	CCDS31789.1	1183	0.5416666666666666	224	0.45528455284552843	223	0.6160220994475138	405	0.708041958041958	331	0.4366754617414248	T	19.46	3.831371	0.71258	0.495461	0.53093	ENSG00000197376	ENST00000310194	T	0.00441	7.41	5.03	5.03	0.67393	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32503	N	0.006015	T	0.00012	0.0000	H	0.96805	3.885	0.18873	P	0.9999875511	D	0.89917	1.0	D	0.79108	0.992	T	0.04140	-1.0974	9	0.87932	D	0	-22.5349	12.7618	0.57370	0.0:0.0:0.0:1.0	rs4075258;rs4590919;rs59443622;rs4075258	82	Q8NH09	OR8S1_HUMAN	P	82	ENSP00000310632:L82P	ENSP00000310632:L82P	L	+	2	0	OR8S1	47205926	0.688000	0.27680	0.192000	0.23308	0.928000	0.56348	4.302000	0.59092	2.105000	0.64084	0.533000	0.62120	CTG	CA|0.500;TG|0.500	.	alt		0.488	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1		
WDR11	55717	hgsc.bcm.edu	37	10	122668181	122668181	+	Silent	SNP	T	T	C	rs34567350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122668181T>C	ENST00000263461.6	+	29	3877	c.3631T>C	c.(3631-3633)Ttg>Ctg	p.L1211L	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				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						CAAAGACTTATTGAATGAGCT	0.488													t|||	57	0.0113818	0.0408	0.0043	5008	,	,		18032	0.0		0.0	False		,,,				2504	0.0				p.L1211L		Atlas-SNP	.											.	WDR11	95	.	0			c.T3631C						PASS	.	C		143,4263	101.2+/-139.8	3,137,2063	99.0	101.0	100.0		3631	-7.0	0.0	10	dbSNP_126	100	0,8600		0,0,4300	no	coding-synonymous	WDR11	NM_018117.11		3,137,6363	CC,CT,TT		0.0,3.2456,1.0995		1211/1225	122668181	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon29			GACTTATTGAATG	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.3631T>C	10.37:g.122668181T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	153	73	0.477124	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			T|0.990;C|0.010	0.010	strong		0.488	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
MT-ND1	4535	hgsc.bcm.edu	37	M	3480	3480	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:3480A>G	ENST00000361390.2	+	1	174	c.174A>G	c.(172-174)aaA>aaG	p.K58K	MT-TC_ENST00000387405.1_RNA|MT-TF_ENST00000387314.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-RNR2_ENST00000387347.2_RNA|MT-TN_ENST00000387400.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-TY_ENST00000387409.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TW_ENST00000387382.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	58					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CTCTTCACCAAAGAGCCCCTA	0.522																																					p.K58K		Atlas-SNP	.											.	.	.	.	0			c.A174G						PASS	.																																			SO:0001819	synonymous_variant	10625	exon1			CACCAAAGAGCCC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.174A>G	M.37:g.3480A>G		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	23	22	0.956522	ENST00000361390	C0JKH6|Q37523	Silent	SNP	ENST00000361390.2	37																																																																																				.	.	none		0.522	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
ZNF99	7652	hgsc.bcm.edu	37	19	22942325	22942325	+	Missense_Mutation	SNP	G	G	C	rs7255780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:22942325G>C	ENST00000596209.1	-	4	476	c.386C>G	c.(385-387)gCt>gGt	p.A129G	ZNF99_ENST00000397104.3_Missense_Mutation_p.A150G	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	129			A -> G (in dbSNP:rs7255780).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTTATTATAAGCTTCTTCGTG	0.299													C|||	1840	0.367412	0.5386	0.3256	5008	,	,		16402	0.3462		0.2783	False		,,,				2504	0.2791				p.A129G		Atlas-SNP	.											.	ZNF99	273	.	0			c.C386G						PASS	.	C	GLY/ALA	1869,1871		455,959,456	101.0	98.0	99.0		449	-0.8	0.0	19	dbSNP_116	99	2332,5862		324,1684,2089	yes	missense	ZNF99	NM_001080409.2	60	779,2643,2545	CC,CG,GG		28.4598,49.9733,35.2019	benign	150/912	22942325	4201,7733	1870	4097	5967	SO:0001583	missense	7652	exon4			TTATAAGCTTCTT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.386C>G	19.37:g.22942325G>C	ENSP00000472969:p.Ala129Gly	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	802	0.36721611721611724	266	0.540650406504065	120	0.3314917127071823	207	0.3618881118881119	209	0.2757255936675462	N	0.175	-1.068074	0.01934	0.499733	0.284598	ENSG00000213973	ENST00000397104	T	0.06294	3.32	1.18	-0.806	0.10875	.	.	.	.	.	T	0.00012	0.0000	N	0.00057	-2.36	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31308	-0.9948	8	0.02654	T	1	.	4.3885	0.11328	0.2323:0.3046:0.4631:0.0	rs7255780;rs57975939;rs7255780	150	A8MXY4	ZNF99_HUMAN	G	150	ENSP00000380293:A150G	ENSP00000380293:A150G	A	-	2	0	ZNF99	22734165	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.658000	0.05329	-1.903000	0.01093	-1.120000	0.02017	GCT	G|0.635;C|0.364	0.364	strong		0.299	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
C1orf109	54955	hgsc.bcm.edu	37	1	38149076	38149076	+	Silent	SNP	G	G	A	rs34250208	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:38149076G>A	ENST00000358011.4	-	4	678	c.489C>T	c.(487-489)atC>atT	p.I163I	C1orf109_ENST00000609516.1_5'UTR|C1orf109_ENST00000464085.1_Silent_p.I163I	NM_017850.1	NP_060320.1	Q9NX04	CA109_HUMAN	chromosome 1 open reading frame 109	163										lung(2)|prostate(2)	4		Myeloproliferative disorder(586;0.0393)				CTCCCCACTGGATAGACGAAA	0.428													G|||	260	0.0519169	0.0061	0.0663	5008	,	,		21770	0.001		0.1183	False		,,,				2504	0.0879				p.I163I		Atlas-SNP	.											.	C1orf109	13	.	0			c.C489T						PASS	.	G		119,4287	90.2+/-128.9	3,113,2087	133.0	130.0	131.0		489	4.4	0.6	1	dbSNP_126	131	1132,7468	232.8+/-266.3	88,956,3256	no	coding-synonymous	C1orf109	NM_017850.1		91,1069,5343	AA,AG,GG		13.1628,2.7009,9.6186		163/204	38149076	1251,11755	2203	4300	6503	SO:0001819	synonymous_variant	54955	exon4			CCACTGGATAGAC	AK000515	CCDS423.1	1p34.3	2012-06-21			ENSG00000116922	ENSG00000116922			26039	protein-coding gene	gene with protein product		614799				22548824	Standard	XM_005270979		Approved	FLJ20508	uc001cbp.3	Q9NX04	OTTHUMG00000004323	ENST00000358011.4:c.489C>T	1.37:g.38149076G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_017850	D3DPT1|Q8WVD1	Silent	SNP	ENST00000358011.4	37	CCDS423.1																																																																																			G|0.913;A|0.087	0.087	strong		0.428	C1orf109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012486.1	NM_017850	
NRG3	10718	hgsc.bcm.edu	37	10	84744926	84744926	+	Missense_Mutation	SNP	C	C	A	rs17101193	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:84744926C>A	ENST00000404547.1	+	10	1728	c.1728C>A	c.(1726-1728)aaC>aaA	p.N576K	NRG3_ENST00000545131.1_Missense_Mutation_p.N202K|NRG3_ENST00000404576.2_Missense_Mutation_p.N356K|NRG3_ENST00000372142.2_Missense_Mutation_p.N355K|NRG3_ENST00000537893.1_Missense_Mutation_p.N202K|NRG3_ENST00000556918.1_Missense_Mutation_p.N382K|NRG3_ENST00000372141.2_Missense_Mutation_p.N552K			P56975	NRG3_HUMAN	neuregulin 3	576					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		GAGAGACAAACCCCTATTTTA	0.423													C|||	477	0.0952476	0.1732	0.1571	5008	,	,		18705	0.0109		0.0567	False		,,,				2504	0.0726				p.N552K		Atlas-SNP	.											.	NRG3	301	.	0			c.C1656A						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN	682,3724	279.3+/-274.7	56,570,1577	145.0	163.0	157.0		1656,1653,1065	2.7	1.0	10	dbSNP_123	157	499,8101	142.0+/-198.3	15,469,3816	yes	missense,missense,missense	NRG3	NM_001010848.3,NM_001165972.1,NM_001165973.1	94,94,94	71,1039,5393	AA,AC,CC		5.8023,15.4789,9.0804	benign,benign,benign	552/697,551/696,355/500	84744926	1181,11825	2203	4300	6503	SO:0001583	missense	10718	exon9			GACAAACCCCTAT	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1728C>A	10.37:g.84744926C>A	ENSP00000384796:p.Asn576Lys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_001010848	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	37	CCDS31233.1	189	0.08653846153846154	92	0.18699186991869918	51	0.1408839779005525	9	0.015734265734265736	37	0.048812664907651716	C	7.793	0.712044	0.15306	0.154789	0.058023	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287;ENST00000372142;ENST00000404576;ENST00000556918;ENST00000545131;ENST00000537893	T;T;T;T;T;T;T	0.53857	1.6;1.57;1.57;0.6;0.6;0.6;0.6	5.95	2.74	0.32292	.	0.280347	0.33875	N	0.004474	T	0.00039	0.0001	N	0.14661	0.345	0.39742	P	0.028237999999999985	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.09377	0.002;0.001;0.004;0.003	T	0.06180	-1.0841	9	0.39692	T	0.17	-37.4496	4.4692	0.11704	0.2732:0.533:0.0:0.1938	rs17101193;rs52798772;rs17101193	551;576;355;552	B9EGV5;P56975;P56975-3;P56975-4	.;NRG3_HUMAN;.;.	K	552;576;551;355;356;382;202;202	ENSP00000361214:N552K;ENSP00000384796:N576K;ENSP00000361215:N355K;ENSP00000385804:N356K;ENSP00000451376:N382K;ENSP00000441201:N202K;ENSP00000440377:N202K	ENSP00000361214:N552K	N	+	3	2	NRG3	84734906	0.867000	0.29959	1.000000	0.80357	0.983000	0.72400	-0.264000	0.08658	0.788000	0.33755	0.650000	0.86243	AAC	C|0.910;A|0.090	0.090	strong		0.423	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086	
MAN2B1	4125	hgsc.bcm.edu	37	19	12772090	12772090	+	Missense_Mutation	SNP	C	C	T	rs1133330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12772090C>T	ENST00000456935.2	-	7	1050	c.1010G>A	c.(1009-1011)cGg>cAg	p.R337Q	MAN2B1_ENST00000221363.4_Missense_Mutation_p.R337Q|MAN2B1_ENST00000495617.1_5'Flank	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	337			R -> Q (in dbSNP:rs1133330). {ECO:0000269|PubMed:22161967, ECO:0000269|PubMed:9915946}.		cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						ATTTACCAGCCGGATGAGCTT	0.552													C|||	1244	0.248403	0.3086	0.255	5008	,	,		20976	0.0615		0.3926	False		,,,				2504	0.2065				p.R337Q		Atlas-SNP	.											MAN2B1,NS,meningioma,0,1	MAN2B1	91	1	0			c.G1010A						PASS	.	C	GLN/ARG,GLN/ARG	1379,3027	455.9+/-351.1	215,949,1039	221.0	174.0	190.0		1010,1010	-5.3	0.3	19	dbSNP_86	190	3431,5169	504.3+/-376.1	668,2095,1537	yes	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	43,43	883,3044,2576	TT,TC,CC		39.8953,31.2982,36.9829	benign,benign	337/1012,337/1011	12772090	4810,8196	2203	4300	6503	SO:0001583	missense	4125	exon7			ACCAGCCGGATGA		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.1010G>A	19.37:g.12772090C>T	ENSP00000395473:p.Arg337Gln	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	161	70	0.434783	NM_001173498	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	566	0.2591575091575092	140	0.2845528455284553	106	0.292817679558011	30	0.05244755244755245	290	0.38258575197889183	C	12.08	1.830324	0.32329	0.312982	0.398953	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	T;T	0.79454	-1.27;-1.27	5.51	-5.32	0.02722	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	1.735930	0.03031	N	0.152116	T	0.00012	0.0000	N	0.05510	-0.035	0.46849	P	7.770000000000277E-4	B;B	0.20550	0.022;0.046	B;B	0.15052	0.007;0.012	T	0.03840	-1.0999	9	0.29301	T	0.29	-13.1141	13.4528	0.61180	0.0:0.3494:0.0:0.6506	rs1133330;rs2070087;rs3195023;rs17421598;rs56909861;rs1133330	337;337	G5E928;O00754	.;MA2B1_HUMAN	Q	337;276;337	ENSP00000395473:R337Q;ENSP00000221363:R337Q	ENSP00000221363:R337Q	R	-	2	0	MAN2B1	12633090	0.013000	0.17824	0.311000	0.25182	0.842000	0.47809	-0.041000	0.12084	-0.929000	0.03757	-0.291000	0.09656	CGG	C|0.675;T|0.325	0.325	strong		0.552	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
DIDO1	11083	hgsc.bcm.edu	37	20	61510849	61510849	+	Silent	SNP	C	C	T	rs373321839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:61510849C>T	ENST00000266070.4	-	16	6784	c.6459G>A	c.(6457-6459)agG>agA	p.R2153R	DIDO1_ENST00000395343.1_Silent_p.R2153R	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	2153	Arg-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GGTTGGCGCTCCTCTcccggt	0.726													C|||	4	0.000798722	0.0008	0.0014	5008	,	,		12926	0.0		0.002	False		,,,				2504	0.0				p.R2153R	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.G6459A						PASS	.	C	,	1,4315		0,1,2157	17.0	14.0	15.0		6459,6459	-0.3	0.0	20		15	5,8397		0,5,4196	no	coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_033081.2	,	0,6,6353	TT,TC,CC		0.0595,0.0232,0.0472	,	2153/2241,2153/2241	61510849	6,12712	2158	4201	6359	SO:0001819	synonymous_variant	11083	exon16			GGCGCTCCTCTCC	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.6459G>A	20.37:g.61510849C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	13	5	0.384615	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			.	.	weak		0.726	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102493761	102493761	+	Silent	SNP	A	A	G	rs8010870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102493761A>G	ENST00000360184.4	+	46	9092	c.8928A>G	c.(8926-8928)ctA>ctG	p.L2976L		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2976	AAA 4. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ATGAAGATCTACGGACAGTGT	0.418													A|||	975	0.194688	0.2504	0.1484	5008	,	,		23531	0.248		0.0895	False		,,,				2504	0.2055				p.L2976L		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A8928G						PASS	.	A		976,3430	366.4+/-317.8	117,742,1344	118.0	111.0	113.0		8928	-12.1	0.0	14	dbSNP_116	113	942,7658	206.9+/-248.8	54,834,3412	no	coding-synonymous	DYNC1H1	NM_001376.4		171,1576,4756	GG,GA,AA		10.9535,22.1516,14.747		2976/4647	102493761	1918,11088	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon46			AGATCTACGGACA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.8928A>G	14.37:g.102493761A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	126	68	0.539683	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			A|0.835;G|0.165;T|0.000	0.165	strong		0.418	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036999	33036999	+	Missense_Mutation	SNP	T	T	C	rs1042190	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33036999T>C	ENST00000419277.1	-	4	554	c.425A>G	c.(424-426)aAg>aGg	p.K142R	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.K142R	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	142	Alpha-2.|Ig-like C1-type.		K -> R (in allele DPA1*02:01 and allele DPA1*02:02; dbSNP:rs1042190).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						TGGGAAGAACTTGTCAATGTG	0.592													.|||	2158	0.430911	0.5772	0.2824	5008	,	,		19467	0.6508		0.1889	False		,,,				2504	0.3609				p.K142R		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.A425G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	1386,1632		317,752,440	115.0	137.0	129.0		425,425,425	0.8	0.9	6	dbSNP_86	129	954,4460		70,814,1823	yes	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	26,26,26	387,1566,2263	CC,CT,TT		17.621,45.9245,27.7514	benign,benign,benign	142/261,142/261,142/261	33036999	2340,6092	1509	2707	4216	SO:0001583	missense	3113	exon3			AAGAACTTGTCAA	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.425A>G	6.37:g.33036999T>C	ENSP00000393566:p.Lys142Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	117	50	0.42735	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	847	0.38782051282051283	272	0.5528455284552846	89	0.24585635359116023	356	0.6223776223776224	130	0.17150395778364116	T	13.63	2.295035	0.40594	0.459245	0.17621	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.08546	6.24;6.24;3.08	3.4	0.821	0.18799	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.154150	0.43919	U	0.000507	T	0.03263	0.0095	L	0.56280	1.765	0.40470	P	0.01966800000000002	B	0.21821	0.061	B	0.29440	0.102	T	0.23297	-1.0192	9	0.66056	D	0.02	.	6.4481	0.21887	0.0:0.2451:0.0:0.7549	rs1042190;rs2308926;rs45518435;rs52798036;rs1042190	142	P20036	DPA1_HUMAN	R	142;142;109;142	ENSP00000393566:K142R;ENSP00000402872:K142R;ENSP00000390929:K142R	ENSP00000393566:K142R	K	-	2	0	HLA-DPA1	33144977	0.919000	0.31177	0.935000	0.37517	0.984000	0.73092	0.797000	0.26999	0.038000	0.15604	0.523000	0.50628	AAG	.	.	weak		0.592	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
FCER2	2208	hgsc.bcm.edu	37	19	7763248	7763248	+	Missense_Mutation	SNP	G	G	A	rs2228137	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7763248G>A	ENST00000346664.5	-	4	396	c.184C>T	c.(184-186)Cgg>Tgg	p.R62W	FCER2_ENST00000597921.1_Missense_Mutation_p.R62W|FCER2_ENST00000360067.4_Missense_Mutation_p.R61W	NM_001220500.1|NM_002002.4	NP_001207429.1|NP_001993.2	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor for (CD23)	62			R -> W (in dbSNP:rs2228137).		Notch signaling pathway (GO:0007219)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	10						ATACCGTTCCGGGCAGCCCTC	0.622													G|||	1020	0.203674	0.3411	0.0879	5008	,	,		13883	0.0813		0.1421	False		,,,				2504	0.2894				p.R62W		Atlas-SNP	.											.	FCER2	19	.	0			c.C184T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	1324,3082	445.3+/-347.6	201,922,1080	94.0	72.0	79.0		181,184,184	3.2	0.0	19	dbSNP_98	79	1214,7386	245.0+/-274.0	81,1052,3167	yes	missense,missense,missense	FCER2	NM_001207019.2,NM_001220500.1,NM_002002.4	101,101,101	282,1974,4247	AA,AG,GG		14.1163,30.0499,19.5141	probably-damaging,probably-damaging,probably-damaging	61/321,62/322,62/322	7763248	2538,10468	2203	4300	6503	SO:0001583	missense	2208	exon4			CGTTCCGGGCAGC	M15059	CCDS12184.1	19p13.3	2011-08-30	2006-03-09			ENSG00000104921		"""C-type lectin domain containing"", ""CD molecules"""	3612	protein-coding gene	gene with protein product		151445	"""Fc fragment of IgE, low affinity II, receptor for (CD23A)"""	CD23A, FCE2			Standard	NM_002002		Approved	CLEC4J, CD23	uc002mhm.2	P06734		ENST00000346664.5:c.184C>T	19.37:g.7763248G>A	ENSP00000264072:p.Arg62Trp	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	224	111	0.495536	NM_002002		Missense_Mutation	SNP	ENST00000346664.5	37	CCDS12184.1	357	0.16346153846153846	168	0.34146341463414637	28	0.07734806629834254	48	0.08391608391608392	113	0.14907651715039577	G	14.50	2.553764	0.45487	0.300499	0.141163	ENSG00000104921	ENST00000346664;ENST00000360067	T;T	0.02812	4.15;4.15	4.24	3.19	0.36642	.	1.265470	0.06051	N	0.656637	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D;D	0.59767	0.986;0.975	P;B	0.50270	0.636;0.432	T	0.55755	-0.8091	9	0.72032	D	0.01	.	9.5199	0.39129	0.0:0.0:0.7898:0.2101	rs2228137;rs4804773;rs61348850;rs2228137	61;62	P06734-2;P06734	.;FCER2_HUMAN	W	62;61	ENSP00000264072:R62W;ENSP00000353178:R61W	ENSP00000264072:R62W	R	-	1	2	FCER2	7669248	0.005000	0.15991	0.003000	0.11579	0.016000	0.09150	1.486000	0.35530	1.357000	0.45904	0.655000	0.94253	CGG	G|0.809;N|0.000	.	strong		0.622	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002	
SPPL2C	162540	hgsc.bcm.edu	37	17	43923934	43923934	+	Silent	SNP	T	T	C	rs11079725	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43923934T>C	ENST00000329196.5	+	1	1679	c.1662T>C	c.(1660-1662)gaT>gaC	p.D554D	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	554						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										GCGCAGCAGATGCCCACACAG	0.597													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		17960	0.001		0.2396	False		,,,				2504	0.0613				p.D554D		Atlas-SNP	.											.	.	.	.	0			c.T1662C						PASS	.	C		201,4205	806.3+/-415.8	5,191,2007	49.0	48.0	48.0		1662	-9.4	0.0	17	dbSNP_120	48	1926,6674	725.4+/-406.5	221,1484,2595	no	coding-synonymous	IMP5	NM_175882.2		226,1675,4602	CC,CT,TT		22.3953,4.562,16.354		554/685	43923934	2127,10879	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			AGCAGATGCCCAC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1662T>C	17.37:g.43923934T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	81	46	0.567901	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			T|0.854;C|0.146	0.146	strong		0.597	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
TMA16	55319	hgsc.bcm.edu	37	4	164440581	164440581	+	Missense_Mutation	SNP	T	T	C	rs1561736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:164440581T>C	ENST00000358572.5	+	7	868	c.527T>C	c.(526-528)aTt>aCt	p.I176T	TMA16_ENST00000513134.1_Intron|TMA16_ENST00000513272.1_3'UTR	NM_018352.2	NP_060822.2	Q96EY4	TMA16_HUMAN	translation machinery associated 16 homolog (S. cerevisiae)	176			I -> T (in dbSNP:rs1561736). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)		p.I176T(1)									AGGAAAACTATTATAACTGTA	0.373													T|||	1916	0.382588	0.2526	0.6052	5008	,	,		18042	0.3423		0.4742	False		,,,				2504	0.3476				p.I176T		Atlas-SNP	.											C4orf43,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.T527C						PASS	.	T	THR/ILE	1026,2688		147,732,978	53.0	53.0	53.0		527	-0.5	0.0	4	dbSNP_88	53	3916,4252		965,1986,1133	no	missense	C4orf43	NM_018352.2	89	1112,2718,2111	CC,CT,TT		47.9432,27.6252,41.5923	benign	176/204	164440581	4942,6940	1857	4084	5941	SO:0001583	missense	55319	exon7			AAACTATTATAAC		CCDS43278.1	4q32.3	2012-03-02	2012-03-02	2012-03-02	ENSG00000198498	ENSG00000198498			25638	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 43"""	C4orf43		12477932	Standard	NM_018352		Approved	FLJ11184	uc003iqq.4	Q96EY4	OTTHUMG00000161528	ENST00000358572.5:c.527T>C	4.37:g.164440581T>C	ENSP00000351380:p.Ile176Thr	Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	278	123	0.442446	NM_018352	Q0P6E4|Q0P6J1|Q9NUR7	Missense_Mutation	SNP	ENST00000358572.5	37	CCDS43278.1	901	0.4125457875457875	124	0.25203252032520324	216	0.5966850828729282	197	0.34440559440559443	364	0.48021108179419525	T	2.009	-0.427555	0.04701	0.276252	0.479432	ENSG00000198498	ENST00000358572	T	0.21734	1.99	5.05	-0.516	0.11950	.	1.344700	0.04600	N	0.398357	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45041	-0.9288	9	0.07990	T	0.79	3.0277	3.462	0.07536	0.3859:0.1705:0.0:0.4436	rs1561736;rs3207217;rs17043749;rs17845311;rs17858149;rs1561736	176	Q96EY4	CD043_HUMAN	T	176	ENSP00000351380:I176T	ENSP00000351380:I176T	I	+	2	0	C4orf43	164660031	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.439000	0.06897	-0.127000	0.11661	0.533000	0.62120	ATT	T|0.582;C|0.418	0.418	strong		0.373	TMA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365208.1	NM_018352	
DNAH6	1768	hgsc.bcm.edu	37	2	84880445	84880445	+	Missense_Mutation	SNP	G	G	C	rs28375417	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:84880445G>C	ENST00000237449.6	+	33	5089	c.5081G>C	c.(5080-5082)gGa>gCa	p.G1694A	DNAH6_ENST00000398278.2_Missense_Mutation_p.G1694A|DNAH6_ENST00000389394.3_Missense_Mutation_p.G1694A			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1694					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTTGACAGTGGAATCATATCT	0.303													G|||	497	0.0992412	0.0703	0.0994	5008	,	,		18517	0.0724		0.1402	False		,,,				2504	0.1237				p.G1694A		Atlas-SNP	.											.	DNAH6	194	.	0			c.G5081C						PASS	.	G	ALA/GLY	103,1281		0,103,589	30.0	27.0	28.0		5081	5.0	1.0	2	dbSNP_125	28	425,2755		30,365,1195	yes	missense	DNAH6	NM_001370.1	60	30,468,1784	CC,CG,GG		13.3648,7.4422,11.5688	possibly-damaging	1694/4159	84880445	528,4036	692	1590	2282	SO:0001583	missense	1768	exon34			ACAGTGGAATCAT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.5081G>C	2.37:g.84880445G>C	ENSP00000237449:p.Gly1694Ala	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	203	0.09294871794871795	25	0.0508130081300813	42	0.11602209944751381	35	0.06118881118881119	101	0.13324538258575197	G	8.710	0.911836	0.17907	0.074422	0.133648	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.38887	1.11;1.11;1.11	5.03	5.03	0.67393	.	.	.	.	.	T	0.00384	0.0012	L	0.35249	1.045	0.20196	P	0.9999220701	B	0.26635	0.155	B	0.28011	0.085	T	0.06935	-1.0799	8	0.22706	T	0.39	.	17.1312	0.86727	0.0:0.0:1.0:0.0	rs28375417;rs61140001	1694	Q9C0G6	DYH6_HUMAN	A	1694	ENSP00000374045:G1694A;ENSP00000381326:G1694A;ENSP00000237449:G1694A	ENSP00000237449:G1694A	G	+	2	0	DNAH6	84733956	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	6.876000	0.75556	2.332000	0.79248	0.544000	0.68410	GGA	G|0.896;C|0.104	0.104	strong		0.303	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
SCN7A	6332	hgsc.bcm.edu	37	2	167262169	167262169	+	Missense_Mutation	SNP	T	T	C	rs35344714	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:167262169T>C	ENST00000409855.1	-	25	5096	c.4970A>G	c.(4969-4971)gAc>gGc	p.D1657G		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1657			D -> G (in dbSNP:rs35344714).		membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	AACATCTCTGTCACCATCTAT	0.378													T|||	266	0.053115	0.031	0.0288	5008	,	,		19281	0.0129		0.0775	False		,,,				2504	0.1166				p.D1657G		Atlas-SNP	.											.	SCN7A	410	.	0			c.A4970G						PASS	.	T	GLY/ASP	158,3554		3,152,1701	256.0	240.0	245.0		4970	0.9	0.0	2	dbSNP_126	245	807,7383		38,731,3326	yes	missense	SCN7A	NM_002976.3	94	41,883,5027	CC,CT,TT		9.8535,4.2565,8.1079	benign	1657/1683	167262169	965,10937	1856	4095	5951	SO:0001583	missense	6332	exon25			TCTCTGTCACCAT	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.4970A>G	2.37:g.167262169T>C	ENSP00000386796:p.Asp1657Gly	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	268	142	0.529851	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	87	0.03983516483516483	9	0.018292682926829267	10	0.027624309392265192	12	0.02097902097902098	56	0.07387862796833773	T	6.169	0.399411	0.11696	0.042565	0.098535	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.96802	-4.13	4.62	0.936	0.19488	.	0.625902	0.14359	N	0.324601	T	0.21801	0.0525	N	0.13235	0.315	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.64892	-0.6300	9	0.06891	T	0.86	.	6.3668	0.21459	0.0:0.3025:0.0:0.6975	rs35344714	1657	Q01118	SCN7A_HUMAN	G	1657	ENSP00000386796:D1657G	ENSP00000259060:D1657G	D	-	2	0	SCN7A	166970415	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.973000	0.29422	0.074000	0.16767	0.459000	0.35465	GAC	T|0.949;C|0.051	0.051	strong		0.378	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
SLC1A6	6511	hgsc.bcm.edu	37	19	15083693	15083693	+	Silent	SNP	C	C	A	rs3746295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:15083693C>A	ENST00000221742.3	-	1	37	c.30G>T	c.(28-30)ctG>ctT	p.L10L	SLC1A6_ENST00000600144.1_Silent_p.L10L|SLC1A6_ENST00000598504.1_Silent_p.L10L|SLC1A6_ENST00000544886.2_Silent_p.L10L|SLC1A6_ENST00000430939.2_Missense_Mutation_p.A15S	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	10					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						CGCTCTCCCGCAGGAACAGGC	0.682													C|||	2765	0.552117	0.5091	0.4697	5008	,	,		15275	0.6567		0.5199	False		,,,				2504	0.5941				p.L10L		Atlas-SNP	.											SLC1A6,NS,carcinoma,0,2	SLC1A6	111	2	0			c.G30T						PASS	.	C		2182,2006		634,914,546	6.0	7.0	7.0		30	4.4	1.0	19	dbSNP_107	7	4397,3857		1268,1861,998	no	coding-synonymous	SLC1A6	NM_005071.1		1902,2775,1544	AA,AC,CC		46.7289,47.8988,47.1226		10/565	15083693	6579,5863	2094	4127	6221	SO:0001819	synonymous_variant	6511	exon4			CTCCCGCAGGAAC		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.30G>T	19.37:g.15083693C>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_001272087	Q8N753	Silent	SNP	ENST00000221742.3	37	CCDS12321.1	1207	0.5526556776556777	249	0.5060975609756098	186	0.5138121546961326	377	0.6590909090909091	395	0.521108179419525	C	13.75	2.329945	0.41297	0.521012	0.532711	ENSG00000105143	ENST00000430939	T	0.74002	-0.8	4.41	4.41	0.53225	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B	0.16603	0.018	B	0.14578	0.011	T	0.48387	-0.9040	7	0.87932	D	0	-12.2133	12.3616	0.55207	0.0:1.0:0.0:0.0	rs3746295;rs57060104;rs3746295	15	E7EV13	.	S	15	ENSP00000409386:A15S	ENSP00000409386:A15S	A	-	1	0	SLC1A6	14944693	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.323000	0.33701	2.278000	0.76064	0.313000	0.20887	GCG	C|0.450;A|0.550	0.550	strong		0.682	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
CYP2A13	1553	hgsc.bcm.edu	37	19	41596013	41596013	+	Silent	SNP	A	A	G	rs199984436		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:41596013A>G	ENST00000330436.3	+	3	405	c.405A>G	c.(403-405)ctA>ctG	p.L135L		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	135					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	TCGCCACCCTAAGGGGTTTTG	0.692																																					p.L135L		Atlas-SNP	.											CYP2A13,colon,carcinoma,0,1	CYP2A13	90	1	0			c.A405G						scavenged	.						23.0	24.0	24.0					19																	41596013		2201	4294	6495	SO:0001819	synonymous_variant	1553	exon3			CACCCTAAGGGGT	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"""Cytochrome P450s"""	2608	protein-coding gene	gene with protein product		608055	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"""			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.405A>G	19.37:g.41596013A>G		Somatic	104	2	0.0192308		WXS	Illumina HiSeq	Phase_I	82	6	0.0731707	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Silent	SNP	ENST00000330436.3	37	CCDS12571.1																																																																																			A|0.999;G|0.001	0.001	weak		0.692	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766	
LAMA3	3909	hgsc.bcm.edu	37	18	21513768	21513768	+	Silent	SNP	C	C	T	rs1131521	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:21513768C>T	ENST00000313654.9	+	67	8972	c.8731C>T	c.(8731-8733)Cta>Tta	p.L2911L	LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000587184.1_Silent_p.L1246L|LAMA3_ENST00000269217.6_Silent_p.L1302L|LAMA3_ENST00000399516.3_Silent_p.L2855L	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2911	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TCCTGAAGTCCTAGATTTGAC	0.443													C|||	743	0.148363	0.0113	0.1628	5008	,	,		21876	0.1815		0.2058	False		,,,				2504	0.2301				p.L2911L		Atlas-SNP	.											.	LAMA3	397	.	0			c.C8731T						PASS	.	C	,,,	190,4216	121.7+/-159.2	8,174,2021	101.0	89.0	93.0		3904,8563,3736,8731	2.5	0.2	18	dbSNP_86	93	1707,6893	311.6+/-310.4	160,1387,2753	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	168,1561,4774	TT,TC,CC		19.8488,4.3123,14.5856	,,,	1302/1725,2855/3278,1246/1669,2911/3334	21513768	1897,11109	2203	4300	6503	SO:0001819	synonymous_variant	3909	exon67			GAAGTCCTAGATT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.8731C>T	18.37:g.21513768C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	167	85	0.508982	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.853;T|0.147	0.147	strong		0.443	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
NEFM	4741	hgsc.bcm.edu	37	8	24775457	24775457	+	Missense_Mutation	SNP	G	G	C	rs59726684	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:24775457G>C	ENST00000221166.5	+	3	2871	c.2089G>C	c.(2089-2091)Ggg>Cgg	p.G697R	NEFM_ENST00000521540.1_Intron|NEFM_ENST00000518131.1_Intron|NEFM_ENST00000437366.2_Missense_Mutation_p.G658R|NEFM_ENST00000433454.2_Missense_Mutation_p.G321R			P07197	NFM_HUMAN	neurofilament, medium polypeptide	697	Tail.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		agcagaagtggggaaaggtga	0.453													G|||	15	0.00299521	0.0	0.0043	5008	,	,		21230	0.0		0.0119	False		,,,				2504	0.0				p.G697R		Atlas-SNP	.											NEFM,uveal_tract,malignant_melanoma,0,1	NEFM	115	1	0			c.G2089C						PASS	.	G	ARG/GLY,ARG/GLY	14,4392	21.2+/-45.6	0,14,2189	57.0	62.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	961,2089	-0.9	0.0	8	dbSNP_129	60	113,8487	59.5+/-121.1	3,107,4190	yes	missense,missense	NEFM	NM_001105541.1,NM_005382.2	125,125	3,121,6379	CC,CG,GG		1.314,0.3177,0.9765	probably-damaging,probably-damaging	321/541,697/917	24775457	127,12879	2203	4300	6503	SO:0001583	missense	4741	exon3			GAAGTGGGGAAAG	BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"""Intermediate filaments type IV"""	7734	protein-coding gene	gene with protein product		162250	"""neurofilament, medium polypeptide 150kDa"""	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.2089G>C	8.37:g.24775457G>C	ENSP00000221166:p.Gly697Arg	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_005382	B4DGN2|E9PBF7|Q4QRK6	Missense_Mutation	SNP	ENST00000221166.5	37	CCDS6046.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	G	2.862	-0.235919	0.05944	0.003177	0.01314	ENSG00000104722	ENST00000221166;ENST00000437366;ENST00000433454	D;D;D	0.93906	-1.74;-1.6;-3.31	3.31	-0.908	0.10517	.	1.331490	0.05366	N	0.534543	T	0.80555	0.4645	N	0.19112	0.55	0.09310	N	1	B	0.15141	0.012	B	0.10450	0.005	T	0.69105	-0.5233	10	0.10111	T	0.7	.	4.7715	0.13158	0.4719:0.1587:0.3695:0.0	rs59726684;rs62636219	697	P07197	NFM_HUMAN	R	697;658;321	ENSP00000221166:G697R;ENSP00000410137:G658R;ENSP00000412295:G321R	ENSP00000221166:G697R	G	+	1	0	NEFM	24831362	0.000000	0.05858	0.000000	0.03702	0.649000	0.38597	-0.320000	0.08028	-0.615000	0.05679	0.205000	0.17691	GGG	G|0.993;C|0.007	0.007	strong		0.453	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382	
IL27	246778	hgsc.bcm.edu	37	16	28513403	28513403	+	Missense_Mutation	SNP	A	A	G	rs181206	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28513403A>G	ENST00000356897.1	-	4	378	c.356T>C	c.(355-357)cTg>cCg	p.L119P		NM_145659.3	NP_663634.2	Q8TAD2	IL17D_HUMAN	interleukin 27	0					inflammatory response (GO:0006954)	extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	10						CCCTCCCAGCAGGGCATGGAA	0.657													A|||	801	0.159944	0.0151	0.3501	5008	,	,		20164	0.0833		0.2873	False		,,,				2504	0.1687				p.L119P		Atlas-SNP	.											.	IL27	27	.	0			c.T356C						PASS	.	A	PRO/LEU	320,4074	163.3+/-195.1	14,292,1891	53.0	54.0	54.0		356	3.0	0.9	16	dbSNP_79	54	2753,5847	419.4+/-353.1	453,1847,2000	yes	missense	IL27	NM_145659.3	98	467,2139,3891	GG,GA,AA		32.0116,7.2827,23.6494	possibly-damaging	119/244	28513403	3073,9921	2197	4300	6497	SO:0001583	missense	246778	exon4			CCCAGCAGGGCAT	AY099296	CCDS10633.1	16p11	2011-07-21	2003-12-17	2003-12-19	ENSG00000197272	ENSG00000197272		"""Interleukins and interleukin receptors"""	19157	protein-coding gene	gene with protein product		608273	"""interleukin 30"""	IL30		12121660	Standard	NM_145659		Approved	IL-27, p28, IL27p28, IL-27A, IL27A, MGC71873	uc002dqc.3	Q8NEV9	OTTHUMG00000097023	ENST00000356897.1:c.356T>C	16.37:g.28513403A>G	ENSP00000349365:p.Leu119Pro	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	NM_145659	B1AM69	Missense_Mutation	SNP	ENST00000356897.1	37	CCDS10633.1	397	0.18177655677655677	10	0.02032520325203252	99	0.27348066298342544	59	0.10314685314685315	229	0.3021108179419525	A	14.22	2.471119	0.43942	0.072827	0.320116	ENSG00000197272	ENST00000356897	T	0.38560	1.13	4.33	2.97	0.34412	.	0.556457	0.13501	N	0.383273	T	0.00012	0.0000	L	0.40543	1.245	0.54753	P	1.2000000000012001E-5	D	0.61697	0.99	P	0.58266	0.836	T	0.25082	-1.0142	9	0.72032	D	0.01	-0.6238	6.3931	0.21597	0.8633:0.0:0.1366:0.0	rs181206;rs181206	119	Q8NEV9	IL27A_HUMAN	P	119	ENSP00000349365:L119P	ENSP00000349365:L119P	L	-	2	0	IL27	28420904	0.769000	0.28531	0.877000	0.34402	0.768000	0.43524	1.753000	0.38359	1.600000	0.50102	0.358000	0.22013	CTG	A|0.798;G|0.202	0.202	strong		0.657	IL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214114.1	NM_145659	
ITGA9	3680	hgsc.bcm.edu	37	3	37536056	37536056	+	Silent	SNP	C	C	T	rs2507941	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:37536056C>T	ENST00000264741.5	+	5	865	c.609C>T	c.(607-609)acC>acT	p.T203T	ITGA9_ENST00000422441.1_Silent_p.T203T	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	203					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GCTTCTTCACCGAGGTGGGTG	0.517													C|||	235	0.0469249	0.0068	0.0749	5008	,	,		20842	0.0774		0.0537	False		,,,				2504	0.0429				p.T203T		Atlas-SNP	.											.	ITGA9	98	.	0			c.C609T						PASS	.	C		77,4329	66.4+/-103.9	0,77,2126	178.0	181.0	180.0		609	-6.6	0.9	3	dbSNP_100	180	488,8112	141.1+/-197.5	14,460,3826	yes	coding-synonymous	ITGA9	NM_002207.2		14,537,5952	TT,TC,CC		5.6744,1.7476,4.3441		203/1036	37536056	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	3680	exon5			CTTCACCGAGGTG	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.609C>T	3.37:g.37536056C>T		Somatic	378	0	0		WXS	Illumina HiSeq	Phase_I	362	181	0.5	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																			C|0.959;T|0.041	0.041	strong		0.517	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
ZNF341	84905	hgsc.bcm.edu	37	20	32376748	32376748	+	Silent	SNP	C	C	T	rs34260449	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32376748C>T	ENST00000375200.1	+	13	2297	c.1932C>T	c.(1930-1932)caC>caT	p.H644H	RP4-553F4.6_ENST00000423074.1_RNA|ZNF341_ENST00000342427.2_Silent_p.H637H|RP4-553F4.6_ENST00000439444.1_RNA|RP4-553F4.6_ENST00000443171.1_RNA	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	644					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						TGTTGATCCACGAGCCCTTCA	0.552													C|||	60	0.0119808	0.0	0.0159	5008	,	,		17759	0.001		0.0318	False		,,,				2504	0.0164				p.H637H		Atlas-SNP	.											.	ZNF341	73	.	0			c.C1911T						PASS	.	C		17,4389	25.3+/-52.1	0,17,2186	121.0	99.0	106.0		1911	-4.3	1.0	20	dbSNP_126	106	180,8420	82.6+/-145.2	2,176,4122	no	coding-synonymous	ZNF341	NM_032819.3		2,193,6308	TT,TC,CC		2.093,0.3858,1.5147		637/848	32376748	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	84905	exon13			GATCCACGAGCCC	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"""Zinc fingers, C2H2-type"""	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.1932C>T	20.37:g.32376748C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	210	105	0.5	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	37																																																																																				C|0.985;T|0.015	0.015	strong		0.552	ZNF341-201	KNOWN	basic	protein_coding	protein_coding			
OR5T2	219464	hgsc.bcm.edu	37	11	56000581	56000581	+	Silent	SNP	G	G	A	rs76457874	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56000581G>A	ENST00000313264.4	-	1	156	c.81C>T	c.(79-81)aaC>aaT	p.N27N		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	27						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TAAAGTTACAGTTCATATTAT	0.343													g|||	194	0.038738	0.0091	0.0447	5008	,	,		15438	0.001		0.0944	False		,,,				2504	0.0562				p.N27N		Atlas-SNP	.											.	OR5T2	107	.	0			c.C81T						PASS	.	G		86,4316	71.4+/-109.4	0,86,2115	96.0	89.0	92.0		81	0.9	0.0	11	dbSNP_131	92	689,7903	169.1+/-220.5	33,623,3640	no	coding-synonymous	OR5T2	NM_001004746.1		33,709,5755	AA,AG,GG		8.0191,1.9537,5.9643		27/360	56000581	775,12219	2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			GTTACAGTTCATA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.81C>T	11.37:g.56000581G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	37	CCDS31523.1																																																																																			G|0.949;A|0.051	0.051	strong		0.343	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
ULK4	54986	hgsc.bcm.edu	37	3	41952838	41952838	+	Silent	SNP	A	A	G	rs9877875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:41952838A>G	ENST00000301831.4	-	11	1518	c.1056T>C	c.(1054-1056)ggT>ggC	p.G352G	ULK4_ENST00000420927.1_Silent_p.G352G	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	352					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CATTCAATTGACCCTCAAGAG	0.348													A|||	297	0.0593051	0.1241	0.0375	5008	,	,		20404	0.0327		0.0159	False		,,,				2504	0.0593				p.G352G		Atlas-SNP	.											.	ULK4	150	.	0			c.T1056C						PASS	.	A		443,3217		24,395,1411	92.0	86.0	88.0		1056	1.4	0.4	3	dbSNP_119	88	139,8019		2,135,3942	no	coding-synonymous	ULK4	NM_017886.2		26,530,5353	GG,GA,AA		1.7038,12.1038,4.9247		352/1276	41952838	582,11236	1830	4079	5909	SO:0001819	synonymous_variant	54986	exon11			CAATTGACCCTCA	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1056T>C	3.37:g.41952838A>G		Somatic	323	1	0.00309598		WXS	Illumina HiSeq	Phase_I	320	153	0.478125	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Silent	SNP	ENST00000301831.4	37	CCDS43071.1																																																																																			A|0.948;G|0.052	0.052	strong		0.348	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
OR2T3	343173	hgsc.bcm.edu	37	1	248637447	248637447	+	Missense_Mutation	SNP	C	C	T	rs369769145		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248637447C>T	ENST00000359594.2	+	1	821	c.796C>T	c.(796-798)Ctc>Ttc	p.L266F		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACCTACATGCTCCCGAGTTC	0.547																																					p.L266F		Atlas-SNP	.											.	OR2T3	79	.	0			c.C796T						PASS	.	C	PHE/LEU	0,4406		0,0,2203	363.0	338.0	347.0		796	1.4	0.0	1		347	1,8599	1.2+/-3.3	0,1,4299	no	missense	OR2T3	NM_001005495.1	22	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	266/319	248637447	1,13005	2203	4300	6503	SO:0001583	missense	343173	exon1			TACATGCTCCCGA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.796C>T	1.37:g.248637447C>T	ENSP00000352604:p.Leu266Phe	Somatic	856	0	0		WXS	Illumina HiSeq	Phase_I	957	292	0.30512	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	c	11.19	1.565845	0.27915	0.0	1.16E-4	ENSG00000196539	ENST00000359594	T	0.37235	1.21	2.37	1.42	0.22433	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.31638	0.0803	L	0.33189	0.99	0.09310	N	1	P	0.41848	0.763	P	0.51016	0.656	T	0.17837	-1.0356	9	0.16420	T	0.52	.	3.9402	0.09323	0.0:0.593:0.2477:0.1593	.	266	Q8NH03	OR2T3_HUMAN	F	266	ENSP00000352604:L266F	ENSP00000352604:L266F	L	+	1	0	OR2T3	246704070	0.000000	0.05858	0.011000	0.14972	0.280000	0.26924	-1.065000	0.03458	0.109000	0.17891	0.186000	0.17326	CTC	.	.	none		0.547	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
ALPP	250	hgsc.bcm.edu	37	2	233243793	233243793	+	Silent	SNP	C	C	T	rs1130337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233243793C>T	ENST00000392027.2	+	2	458	c.189C>T	c.(187-189)ggC>ggT	p.G63G	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	63					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		TCTTCCTGGGCGATGGTGAGT	0.677													C|||	57	0.0113818	0.0008	0.0101	5008	,	,		17685	0.0		0.0249	False		,,,				2504	0.0245				p.G63G		Atlas-SNP	.											.	ALPP	53	.	0			c.C189T						PASS	.	T		10,4396		0,10,2193	71.0	79.0	76.0		189	-5.0	0.0	2	dbSNP_86	76	137,8463		3,131,4166	no	coding-synonymous	ALPP	NM_001632.3		3,141,6359	TT,TC,CC		1.593,0.227,1.1302		63/536	233243793	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	250	exon2			CCTGGGCGATGGT	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.189C>T	2.37:g.233243793C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	88	36	0.409091	NM_001632	P05188|P06861|Q53S78|Q96DB7	Silent	SNP	ENST00000392027.2	37	CCDS2490.1																																																																																			C|0.996;G|0.001;T|0.003	0.003	strong		0.677	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
PCDHA4	56144	hgsc.bcm.edu	37	5	140187102	140187102	+	Silent	SNP	A	A	G	rs3822347	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140187102A>G	ENST00000530339.1	+	1	330	c.330A>G	c.(328-330)gtA>gtG	p.V110V	PCDHA4_ENST00000356878.4_Silent_p.V110V|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Silent_p.V110V	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	110	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGTGATCGTAGACAGGCCGC	0.562																																					p.V110V		Atlas-SNP	.											.	PCDHA4	419	.	0			c.A330G						PASS	.						71.0	78.0	75.0					5																	140187102		2203	4298	6501	SO:0001819	synonymous_variant	56144	exon1			GATCGTAGACAGG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.330A>G	5.37:g.140187102A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	113	41	0.362832	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	weak		0.562	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
KIF3C	3797	hgsc.bcm.edu	37	2	26177198	26177198	+	Silent	SNP	A	A	G	rs17047211	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:26177198A>G	ENST00000264712.3	-	4	2406	c.1827T>C	c.(1825-1827)taT>taC	p.Y609Y	KIF3C_ENST00000496378.1_5'Flank|KIF3C_ENST00000405914.1_Silent_p.Y609Y	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	609					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCACGCGGATATACTCATCAT	0.627													G|||	703	0.140375	0.2685	0.121	5008	,	,		17832	0.001		0.1481	False		,,,				2504	0.1166				p.Y609Y		Atlas-SNP	.											.	KIF3C	79	.	0			c.T1827C						PASS	.	G		1108,3298	718.5+/-408.8	137,834,1232	91.0	70.0	77.0		1827	4.1	1.0	2	dbSNP_123	77	1347,7253	756.2+/-407.5	112,1123,3065	no	coding-synonymous	KIF3C	NM_002254.6		249,1957,4297	GG,GA,AA		15.6628,25.1475,18.8759		609/794	26177198	2455,10551	2203	4300	6503	SO:0001819	synonymous_variant	3797	exon4			GCGGATATACTCA		CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731		"""Kinesins"""	6321	protein-coding gene	gene with protein product		602845				9480755	Standard	NM_002254		Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000264712.3:c.1827T>C	2.37:g.26177198A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_002254	O43544|Q4ZG18|Q53SX5|Q562F7	Silent	SNP	ENST00000264712.3	37	CCDS1719.1																																																																																			A|0.828;G|0.172	0.172	strong		0.627	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31238931	31238931	+	Silent	SNP	G	G	A	rs697743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238931G>A	ENST00000376228.5	-	3	552	c.538C>T	c.(538-540)Ctg>Ttg	p.L180L	HLA-C_ENST00000383329.3_Silent_p.L180L	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	180	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)	p.L180L(2)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TAGGCTCTCAGCTGCTCCGCC	0.682													g|||	595	0.11881	0.0749	0.0634	5008	,	,		11367	0.0853		0.1342	False		,,,				2504	0.2362				p.L180L		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,4	HLA-C	92	4	2	Substitution - coding silent(2)	prostate(2)	c.C538T						scavenged	.						43.0	30.0	34.0					6																	31238931		2197	4291	6488	SO:0001819	synonymous_variant	3107	exon3			CTCTCAGCTGCTC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.538C>T	6.37:g.31238931G>A		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	182	32	0.175824	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	4.195	0.034910	0.08101	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	-5.62	0.02481	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.20638	N	0.999871	.	.	.	.	.	.	T	0.03566	-1.1024	4	.	.	.	.	2.8574	0.05576	0.25:0.4691:0.1066:0.1744	rs697743;rs2308591;rs3176036;rs3179868;rs3200237;rs3204480;rs12721958;rs17839941;rs28732104	.	.	.	V	179	.	.	A	-	2	0	HLA-C	31346910	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-12.042000	0.00002	-4.714000	0.00035	-1.872000	0.00552	GCT	G|0.777;C|0.108;A|0.115	0.115	strong		0.682	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
PRDM9	56979	hgsc.bcm.edu	37	5	23527323	23527323	+	Missense_Mutation	SNP	C	C	G	rs200539936	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:23527323C>G	ENST00000296682.3	+	11	2308	c.2126C>G	c.(2125-2127)aCt>aGt	p.T709S		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	709					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GTCCTCCTCACTCACCAGAGG	0.587										HNSCC(3;0.000094)			c|||	492	0.0982428	0.2398	0.0893	5008	,	,		21450	0.0387		0.0298	False		,,,				2504	0.045				p.T709S		Atlas-SNP	.											PRDM9,NS,carcinoma,0,1	PRDM9	344	1	0			c.C2126G						scavenged	.						16.0	15.0	15.0					5																	23527323		1825	3640	5465	SO:0001583	missense	56979	exon11			TCCTCACTCACCA	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2126C>G	5.37:g.23527323C>G	ENSP00000296682:p.Thr709Ser	Somatic	56	6	0.107143		WXS	Illumina HiSeq	Phase_I	79	14	0.177215	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	c	0.001	-4.409211	0.00000	.	.	ENSG00000164256	ENST00000296682	T	0.17370	2.28	2.57	-5.13	0.02884	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	3.203060	0.01089	N	0.005146	T	0.07999	0.0200	N	0.12920	0.275	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32771	-0.9894	10	0.10111	T	0.7	.	1.0864	0.01654	0.2843:0.3342:0.1048:0.2768	.	709	Q9NQV7	PRDM9_HUMAN	S	709	ENSP00000296682:T709S	ENSP00000296682:T709S	T	+	2	0	PRDM9	23563080	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-20.000000	0.00000	-6.649000	0.00003	-6.748000	0.00000	ACT	C|0.934;G|0.066	0.066	strong		0.587	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
MYO3A	53904	hgsc.bcm.edu	37	10	26462790	26462790	+	Silent	SNP	G	G	A	rs3740232	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:26462790G>A	ENST00000265944.5	+	30	3763	c.3597G>A	c.(3595-3597)gaG>gaA	p.E1199E	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1199					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E1199E(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ATGAGGAAGAGGTTAAGCAAG	0.418													G|||	1648	0.329073	0.2262	0.317	5008	,	,		19882	0.3532		0.3429	False		,,,				2504	0.4376				p.E1199E		Atlas-SNP	.											MYO3A,colon,carcinoma,0,2	MYO3A	371	2	1	Substitution - coding silent(1)	stomach(1)	c.G3597A						scavenged	.	G		1105,3301	396.7+/-330.2	139,827,1237	87.0	86.0	86.0		3597	0.0	0.0	10	dbSNP_107	86	2884,5716	452.0+/-362.8	486,1912,1902	no	coding-synonymous	MYO3A	NM_017433.4		625,2739,3139	AA,AG,GG		33.5349,25.0794,30.6705		1199/1617	26462790	3989,9017	2203	4300	6503	SO:0001819	synonymous_variant	53904	exon30			GGAAGAGGTTAAG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3597G>A	10.37:g.26462790G>A		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																			G|0.681;A|0.319	0.319	strong		0.418	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
POMGNT2	84892	hgsc.bcm.edu	37	3	43122702	43122702	+	Silent	SNP	G	G	A	rs141040291		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:43122702G>A	ENST00000344697.2	-	2	567	c.222C>T	c.(220-222)caC>caT	p.H74H	POMGNT2_ENST00000441964.1_Silent_p.H74H	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	74					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)										TGCGGTCTGTGTGCGTGCGGC	0.607																																					p.H74H		Atlas-SNP	.											.	.	.	.	0			c.C222T						PASS	.	G		0,4406		0,0,2203	83.0	73.0	76.0		222	4.9	1.0	3	dbSNP_134	76	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	C3orf39	NM_032806.4		0,3,6500	AA,AG,GG		0.0349,0.0,0.0231		74/581	43122702	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	84892	exon2			GTCTGTGTGCGTG	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"""chromosome 3 open reading frame 39"", ""glycosyltransferase-like domain containing 2"""	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.222C>T	3.37:g.43122702G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	NM_032806	B3KWC3|Q96SY3	Silent	SNP	ENST00000344697.2	37	CCDS2709.1																																																																																			G|1.000;A|0.000	0.000	weak		0.607	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806	
OR5H2	79310	hgsc.bcm.edu	37	3	98002527	98002527	+	Missense_Mutation	SNP	C	C	T	rs17787561	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:98002527C>T	ENST00000355273.2	+	1	796	c.796C>T	c.(796-798)Cgc>Tgc	p.R266C	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	266			R -> C (in dbSNP:rs17787561).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						CATGTATTTGCGCCCTGCATC	0.398													C|||	19	0.00379393	0.0	0.0058	5008	,	,		17042	0.0		0.0089	False		,,,				2504	0.0061				p.R266C		Atlas-SNP	.											.	OR5H2	63	.	0			c.C796T						PASS	.	C	CYS/ARG	6,4400	9.9+/-24.2	0,6,2197	87.0	83.0	84.0		796	-1.1	0.0	3	dbSNP_123	84	80,8520	47.2+/-106.3	1,78,4221	yes	missense	OR5H2	NM_001005482.1	180	1,84,6418	TT,TC,CC		0.9302,0.1362,0.6612	benign	266/315	98002527	86,12920	2203	4300	6503	SO:0001583	missense	79310	exon1			TATTTGCGCCCTG		CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"""GPCR / Class A : Olfactory receptors"""	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.796C>T	3.37:g.98002527C>T	ENSP00000347418:p.Arg266Cys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	141	69	0.489362	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	0.635	-0.815604	0.02776	0.001362	0.009302	ENSG00000197938	ENST00000355273	T	0.35789	1.29	3.03	-1.07	0.09968	GPCR, rhodopsin-like superfamily (1);	0.410613	0.17855	U	0.159738	T	0.22742	0.0549	M	0.69523	2.12	0.09310	N	1	B	0.21688	0.059	B	0.19148	0.024	T	0.24728	-1.0152	10	0.62326	D	0.03	.	3.5217	0.07744	0.1797:0.3604:0.0:0.4599	rs17787561;rs52823927;rs17787561	266	Q8NGV7	OR5H2_HUMAN	C	266	ENSP00000347418:R266C	ENSP00000347418:R266C	R	+	1	0	OR5H2	99485217	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	-0.227000	0.09126	-0.440000	0.07211	-0.495000	0.04643	CGC	C|0.993;T|0.007	0.007	strong		0.398	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2		
CSNK2B	1460	hgsc.bcm.edu	37	6	31635710	31635710	+	Silent	SNP	T	T	C	rs14365	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31635710T>C	ENST00000375882.2	+	3	294	c.138T>C	c.(136-138)taT>taC	p.Y46Y	GPANK1_ENST00000375900.4_5'Flank|GPANK1_ENST00000375893.2_5'Flank|GPANK1_ENST00000375906.1_5'Flank|LY6G5B_ENST00000375864.4_5'Flank|GPANK1_ENST00000375896.4_5'Flank|CSNK2B_ENST00000375866.2_Silent_p.Y46Y|CSNK2B-LY6G5B-1181_ENST00000375880.2_Silent_p.Y46Y|CSNK2B_ENST00000375885.4_Silent_p.Y65Y|GPANK1_ENST00000375895.2_5'Flank|CSNK2B_ENST00000375865.2_Silent_p.Y46Y|LY6G5B_ENST00000409525.1_5'Flank	NM_001282385.1|NM_001320.5	NP_001269314.1|NP_001311.3	P67870	CSK2B_HUMAN	casein kinase 2, beta polypeptide	46					adiponectin-activated signaling pathway (GO:0033211)|axon guidance (GO:0007411)|cellular protein complex assembly (GO:0043623)|endothelial tube morphogenesis (GO:0061154)|mitotic cell cycle (GO:0000278)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell proliferation (GO:0008285)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|protein phosphorylation (GO:0006468)|regulation of DNA binding (GO:0051101)|regulation of protein kinase activity (GO:0045859)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein kinase CK2 complex (GO:0005956)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein kinase regulator activity (GO:0019887)|receptor binding (GO:0005102)|transcription factor binding (GO:0008134)			central_nervous_system(5)|endometrium(1)|large_intestine(2)|liver(1)|urinary_tract(1)	10						TCCCTCACTATCGACAAGCTC	0.468													T|||	1520	0.303514	0.4312	0.3501	5008	,	,		20497	0.2976		0.2237	False		,,,				2504	0.1861				p.Y46Y		Atlas-SNP	.											.	CSNK2B	15	.	0			c.T138C						PASS	.	T		1747,2659	521.1+/-370.4	342,1063,798	136.0	124.0	128.0		138	4.6	1.0	6	dbSNP_52	128	1656,6944	304.6+/-307.0	153,1350,2797	yes	coding-synonymous	CSNK2B	NM_001320.5		495,2413,3595	CC,CT,TT		19.2558,39.6505,26.1648		46/216	31635710	3403,9603	2203	4300	6503	SO:0001819	synonymous_variant	1460	exon3			TCACTATCGACAA	M30448	CCDS4712.1	6p21.33	2013-01-17			ENSG00000204435	ENSG00000204435	2.7.11.1		2460	protein-coding gene	gene with protein product		115441				2276748, 9503014	Standard	NM_001320		Approved		uc003nvr.1	P67870	OTTHUMG00000177888	ENST00000375882.2:c.138T>C	6.37:g.31635710T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_001320	B0UXA9|P07312|P13862|Q4VX47	Silent	SNP	ENST00000375882.2	37	CCDS4712.1																																																																																			T|0.720;C|0.280	0.280	strong		0.468	CSNK2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076063.8	NM_001320	
PIGR	5284	hgsc.bcm.edu	37	1	207106444	207106444	+	Silent	SNP	A	A	G	rs172361	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207106444A>G	ENST00000356495.4	-	7	1956	c.1773T>C	c.(1771-1773)ttT>ttC	p.F591F	PIGR_ENST00000487208.1_5'Flank	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	591					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)	p.F591F(1)		central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CAATCTCCCGAAAACCAGAGT	0.552													A|||	1304	0.260383	0.7398	0.1916	5008	,	,		20444	0.121		0.0258	False		,,,				2504	0.046				p.F591F		Atlas-SNP	.											PIGR,NS,carcinoma,0,1	PIGR	98	1	1	Substitution - coding silent(1)	stomach(1)	c.T1773C						scavenged	.	A		2791,1615	662.4+/-401.0	915,961,327	84.0	84.0	84.0		1773	0.4	0.0	1	dbSNP_79	84	251,8349	98.1+/-159.7	7,237,4056	no	coding-synonymous	PIGR	NM_002644.3		922,1198,4383	GG,GA,AA		2.9186,36.6546,23.3892		591/765	207106444	3042,9964	2203	4300	6503	SO:0001819	synonymous_variant	5284	exon7			CTCCCGAAAACCA		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"""Immunoglobulin superfamily / V-set domain containing"""	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1773T>C	1.37:g.207106444A>G		Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	117	66	0.564103	NM_002644	Q68D81|Q8IZY7	Silent	SNP	ENST00000356495.4	37	CCDS1474.1																																																																																			A|0.773;G|0.227	0.227	strong		0.552	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644	
NOD2	64127	hgsc.bcm.edu	37	16	50745199	50745199	+	Silent	SNP	C	C	T	rs2066843	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:50745199C>T	ENST00000300589.2	+	4	1482	c.1377C>T	c.(1375-1377)cgC>cgT	p.R459R	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	459	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				TGAGGAAGCGCCATCATGAGC	0.617													C|||	539	0.107628	0.0477	0.1671	5008	,	,		17950	0.0079		0.2475	False		,,,				2504	0.1053				p.R459R		Atlas-SNP	.											.	NOD2	118	.	0			c.C1377T						PASS	.	C		294,4102	153.3+/-186.9	13,268,1917	68.0	72.0	70.0		1377	0.9	0.7	16	dbSNP_94	70	2330,6268	370.2+/-335.8	328,1674,2297	no	coding-synonymous	NOD2	NM_022162.1		341,1942,4214	TT,TC,CC		27.0993,6.6879,20.1939		459/1041	50745199	2624,10370	2198	4299	6497	SO:0001819	synonymous_variant	64127	exon4			GAAGCGCCATCAT	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.1377C>T	16.37:g.50745199C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	79	46	0.582278	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Silent	SNP	ENST00000300589.2	37	CCDS10746.1																																																																																			C|0.831;T|0.169	0.169	strong		0.617	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
R3HDM2	22864	hgsc.bcm.edu	37	12	57648772	57648772	+	Silent	SNP	C	C	A	rs73120051	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57648772C>A	ENST00000347140.3	-	24	3105	c.2715G>T	c.(2713-2715)ggG>ggT	p.G905G	RP11-123K3.4_ENST00000548184.1_Intron|R3HDM2_ENST00000403821.2_Silent_p.G939G|R3HDM2_ENST00000358907.2_Silent_p.G905G|R3HDM2_ENST00000441731.2_Silent_p.G600G|R3HDM2_ENST00000402412.1_Silent_p.G919G|R3HDM2_ENST00000413953.2_Intron			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	905						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						CTCCAGGCAGCCCCTGAGCAT	0.627													C|||	28	0.00559105	0.0	0.0072	5008	,	,		15280	0.0		0.0159	False		,,,				2504	0.0072				p.G905G		Atlas-SNP	.											.	R3HDM2	125	.	0			c.G2715T						PASS	.	C		14,4392	22.3+/-47.3	0,14,2189	55.0	52.0	53.0		2715	5.2	1.0	12	dbSNP_130	53	168,8432	78.6+/-141.3	3,162,4135	no	coding-synonymous	R3HDM2	NM_014925.3		3,176,6324	AA,AC,CC		1.9535,0.3177,1.3994		905/977	57648772	182,12824	2203	4300	6503	SO:0001819	synonymous_variant	22864	exon22			AGGCAGCCCCTGA	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.2715G>T	12.37:g.57648772C>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_014925	Q2M1T9|Q3ZCT5	Silent	SNP	ENST00000347140.3	37	CCDS8937.2																																																																																			C|0.989;A|0.011	0.011	strong		0.627	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925	
ZNF418	147686	hgsc.bcm.edu	37	19	58437629	58437629	+	Silent	SNP	T	T	A	rs147202003	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58437629T>A	ENST00000396147.1	-	4	2211	c.1920A>T	c.(1918-1920)gtA>gtT	p.V640V	ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000595830.1_Silent_p.V640V|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599852.1_Silent_p.V555V|ZNF418_ENST00000425570.3_Silent_p.V661V	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	640					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		CTCCAGTGTGTACTCTCCTGT	0.438																																					p.V640V		Atlas-SNP	.											.	ZNF418	76	.	0			c.A1920T						PASS	.	A		11,4393		0,11,2191	120.0	122.0	121.0		1920	-3.1	0.0	19	dbSNP_134	121	120,8480		1,118,4181	no	coding-synonymous	ZNF418	NM_133460.1		1,129,6372	AA,AT,TT		1.3953,0.2498,1.0074		640/677	58437629	131,12873	2202	4300	6502	SO:0001819	synonymous_variant	147686	exon4			AGTGTGTACTCTC	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1920A>T	19.37:g.58437629T>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	88	13	0.147727	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			T|0.993;A|0.007	0.007	strong		0.438	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183191	11183191	+	Silent	SNP	T	T	C	rs116737741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11183191T>C	ENST00000390675.2	-	1	815	c.744A>G	c.(742-744)tcA>tcG	p.S248S	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	248					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						AACTCCAAACTGATATCATTA	0.408													.|||	414	0.0826677	0.0847	0.085	5008	,	,		20364	0.002		0.1203	False		,,,				2504	0.1227				p.S248S		Atlas-SNP	.											.	TAS2R31	24	.	0			c.A744G						PASS	.	T		457,3929		30,397,1766	198.0	206.0	203.0		744	-2.6	0.0	12	dbSNP_132	203	1314,7276		119,1076,3100	no	coding-synonymous	TAS2R31	NM_176885.2		149,1473,4866	CC,CT,TT		15.2969,10.4195,13.6483		248/310	11183191	1771,11205	2193	4295	6488	SO:0001819	synonymous_variant	259290	exon1			CCAAACTGATATC	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.744A>G	12.37:g.11183191T>C		Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	323	172	0.532508	NM_176885	P59547|Q17R84|Q645X5	Silent	SNP	ENST00000390675.2	37	CCDS53747.1																																																																																			T|0.912;C|0.088	0.088	strong		0.408	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
DLGAP5	9787	hgsc.bcm.edu	37	14	55619311	55619311	+	Silent	SNP	A	A	G	rs15870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:55619311A>G	ENST00000247191.2	-	16	2334	c.2118T>C	c.(2116-2118)aaT>aaC	p.N706N	DLGAP5_ENST00000395425.2_Silent_p.N706N	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	706					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TACTTACATGATTTTCTTCAA	0.338													G|||	1693	0.338059	0.4145	0.2911	5008	,	,		21438	0.1895		0.4085	False		,,,				2504	0.3487				p.N706N		Atlas-SNP	.											.	DLGAP5	84	.	0			c.T2118C						PASS	.	G	,	1849,2557	630.4+/-395.5	390,1069,744	104.0	103.0	104.0		2118,2118	-1.9	0.0	14	dbSNP_52	104	3465,5135	631.3+/-398.5	727,2011,1562	no	coding-synonymous,coding-synonymous	DLGAP5	NM_001146015.1,NM_014750.4	,	1117,3080,2306	GG,GA,AA		40.2907,41.9655,40.8581	,	706/843,706/847	55619311	5314,7692	2203	4300	6503	SO:0001819	synonymous_variant	9787	exon16			TACATGATTTTCT	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"""discs, large homolog 7 (Drosophila)"""	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.2118T>C	14.37:g.55619311A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	70	26	0.371429	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Silent	SNP	ENST00000247191.2	37	CCDS9723.1																																																																																			A|0.621;G|0.379	0.379	strong		0.338	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	
CFAP46	54777	hgsc.bcm.edu	37	10	134682855	134682855	+	Silent	SNP	C	C	T	rs7908950	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:134682855C>T	ENST00000368586.5	-	33	4633	c.4533G>A	c.(4531-4533)gaG>gaA	p.E1511E		NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TCAGCTTCAGCTCGGAGCACG	0.657													C|||	1568	0.313099	0.1256	0.5173	5008	,	,		14842	0.2649		0.3877	False		,,,				2504	0.3947				p.E1511E		Atlas-SNP	.											.	TTC40	100	.	0			c.G4533A						PASS	.																																			SO:0001819	synonymous_variant	54777	exon33			CTTCAGCTCGGAG																												ENST00000368586.5:c.4533G>A	10.37:g.134682855C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	50	47	0.94	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			C|0.713;T|0.287	0.287	strong		0.657	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
KCNA7	3743	hgsc.bcm.edu	37	19	49575304	49575304	+	Missense_Mutation	SNP	G	G	A	rs77059600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49575304G>A	ENST00000221444.1	-	1	894	c.539C>T	c.(538-540)gCa>gTa	p.A180V		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	180				A -> V (in Ref. 3; AAX11186). {ECO:0000305}.	protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	GGCTGCGGCTGCAGCAGCAAG	0.687													A|||	709	0.141573	0.2837	0.1398	5008	,	,		8486	0.0486		0.0885	False		,,,				2504	0.1012				p.A180V	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											KCNA7,rectum,carcinoma,0,1	KCNA7	30	1	0			c.C539T						scavenged	.	A	VAL/ALA	883,3133		82,719,1207	7.0	9.0	8.0		539	1.8	0.0	19	dbSNP_131	8	658,7272		33,592,3340	no	missense	KCNA7	NM_031886.2	64	115,1311,4547	AA,AG,GG		8.2976,21.9871,12.8997	benign	180/457	49575304	1541,10405	2008	3965	5973	SO:0001583	missense	3743	exon1			GCGGCTGCAGCAG	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.539C>T	19.37:g.49575304G>A	ENSP00000221444:p.Ala180Val	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_031886	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	37	CCDS12755.1	322	0.14743589743589744	158	0.32113821138211385	62	0.1712707182320442	34	0.05944055944055944	68	0.08970976253298153	A	9.871	1.198847	0.22121	0.219871	0.082976	ENSG00000104848	ENST00000221444	D	0.97620	-4.46	4.28	1.79	0.24919	.	3.155100	0.01167	N	0.006767	T	0.00012	0.0000	N	0.03224	-0.385	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.55503	-0.8131	9	0.27785	T	0.31	.	4.3707	0.11246	0.4332:0.237:0.3298:0.0	.	180	Q96RP8	KCNA7_HUMAN	V	180	ENSP00000221444:A180V	ENSP00000221444:A180V	A	-	2	0	KCNA7	54267116	0.034000	0.19679	0.006000	0.13384	0.002000	0.02628	-0.536000	0.06135	0.175000	0.19841	-0.504000	0.04507	GCA	G|0.847;A|0.153	0.153	strong		0.687	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886	
PLXND1	23129	hgsc.bcm.edu	37	3	129290087	129290087	+	Silent	SNP	G	G	A	rs2285366	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129290087G>A	ENST00000324093.4	-	18	3574	c.3396C>T	c.(3394-3396)aaC>aaT	p.N1132N	PLXND1_ENST00000393239.1_Silent_p.N1132N	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1132	IPT/TIG 3.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GCGCTGATGCGTTGCTCAGGG	0.662													G|||	472	0.0942492	0.0182	0.0965	5008	,	,		17586	0.2341		0.005	False		,,,				2504	0.1431				p.N1132N	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C3396T						PASS	.	G		52,4354	48.9+/-83.8	0,52,2151	38.0	44.0	42.0		3396	-4.8	0.1	3	dbSNP_100	42	88,8512	48.1+/-107.5	0,88,4212	no	coding-synonymous	PLXND1	NM_015103.2		0,140,6363	AA,AG,GG		1.0233,1.1802,1.0764		1132/1926	129290087	140,12866	2203	4300	6503	SO:0001819	synonymous_variant	23129	exon18			TGATGCGTTGCTC	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.3396C>T	3.37:g.129290087G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	171	88	0.51462	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			G|0.961;A|0.039	0.039	strong		0.662	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
TXLNB	167838	hgsc.bcm.edu	37	6	139564167	139564167	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:139564167C>T	ENST00000358430.3	-	10	1783	c.1551G>A	c.(1549-1551)ccG>ccA	p.P517P	RP1-225E12.3_ENST00000585874.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	517						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		TGGACTGGTGCGGGGTTGACT	0.527																																					p.P517P		Atlas-SNP	.											TXLNB,NS,carcinoma,-1,1	TXLNB	96	1	0			c.G1551A						scavenged	.						122.0	130.0	127.0					6																	139564167		2203	4300	6503	SO:0001819	synonymous_variant	167838	exon10			CTGGTGCGGGGTT		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"""chromosome 6 open reading frame 198"""	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.1551G>A	6.37:g.139564167C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	240	3	0.0125	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Silent	SNP	ENST00000358430.3	37	CCDS34545.1																																																																																			.	.	none		0.527	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235	
TPSD1	23430	hgsc.bcm.edu	37	16	1306355	1306355	+	Missense_Mutation	SNP	T	T	C	rs1800984	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306355T>C	ENST00000211076.3	+	1	222	c.74T>C	c.(73-75)gTg>gCg	p.V25A	TPSD1_ENST00000397534.2_Missense_Mutation_p.V18A|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	25			V -> A (in dbSNP:rs1800984).	V -> G (in Ref. 1; AAD17861). {ECO:0000305}.		extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CCGGCCTACGTGGCCCCTGGT	0.721													-|||	3599	0.71865	0.7564	0.6542	5008	,	,		14753	0.9484		0.5577	False		,,,				2504	0.6421				p.V25A		Atlas-SNP	.											TPSD1,rectum,NS,0,1	TPSD1	47	1	0			c.T74C						PASS	.	T	ALA/VAL	3121,1271		1094,933,169	29.0	37.0	34.0		74	-3.1	0.0	16	dbSNP_89	34	4690,3906		1125,2440,733	no	missense	TPSD1	NM_012217.2	64	2219,3373,902	CC,CT,TT		45.4397,28.939,39.8599	benign	25/243	1306355	7811,5177	2196	4298	6494	SO:0001583	missense	23430	exon1			CCTACGTGGCCCC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.74T>C	16.37:g.1306355T>C	ENSP00000211076:p.Val25Ala	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	1558	0.7133699633699634	388	0.7886178861788617	208	0.574585635359116	556	0.972027972027972	406	0.5356200527704486	-	0.855	-0.737258	0.03111	0.71061	0.545603	ENSG00000095917	ENST00000397534;ENST00000211076	T;T	0.81247	-1.47;-1.47	2.55	-3.13	0.05266	.	0.813971	0.10635	N	0.651704	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35076	-0.9803	9	0.02654	T	1	.	3.4489	0.07491	0.0:0.375:0.2043:0.4206	rs1800984;rs3865206;rs4083416	25	Q9BZJ3	TRYD_HUMAN	A	18;25	ENSP00000380668:V18A;ENSP00000211076:V25A	ENSP00000211076:V25A	V	+	2	0	TPSD1	1246356	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.814000	0.01723	-0.826000	0.04284	-1.137000	0.01932	GTG	T|0.347;C|0.653	0.653	strong		0.721	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
HHLA2	11148	hgsc.bcm.edu	37	3	108081277	108081277	+	Missense_Mutation	SNP	C	C	A	rs6779094	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:108081277C>A	ENST00000357759.5	+	7	1506	c.1092C>A	c.(1090-1092)agC>agA	p.S364R	HHLA2_ENST00000467761.1_Missense_Mutation_p.S364R|HHLA2_ENST00000491820.1_Missense_Mutation_p.S364R|HHLA2_ENST00000467562.1_Missense_Mutation_p.S300R|HHLA2_ENST00000489514.2_Missense_Mutation_p.S364R	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	364			S -> R (in dbSNP:rs6779094).		positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						TGATTTGGAGCGTAAAATGTT	0.413													A|||	546	0.109026	0.0809	0.1571	5008	,	,		17658	0.001		0.2336	False		,,,				2504	0.0961				p.S364R		Atlas-SNP	.											.	HHLA2	95	.	0			c.C1092A						PASS	.	A	ARG/SER	456,3216		30,396,1410	111.0	99.0	103.0		1092	-8.0	0.0	3	dbSNP_116	103	1906,6284		237,1432,2426	yes	missense	HHLA2	NM_007072.2	110	267,1828,3836	AA,AC,CC		23.2723,12.4183,19.9123	possibly-damaging	364/415	108081277	2362,9500	1836	4095	5931	SO:0001583	missense	11148	exon7			TTGGAGCGTAAAA	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.1092C>A	3.37:g.108081277C>A	ENSP00000350402:p.Ser364Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Missense_Mutation	SNP	ENST00000357759.5	37	CCDS46883.1	299|299	0.13690476190476192|0.13690476190476192	44|44	0.08943089430894309|0.08943089430894309	66|66	0.18232044198895028|0.18232044198895028	0|0	0.0|0.0	189|189	0.24934036939313983|0.24934036939313983	A|A	0.596|0.596	-0.830853|-0.830853	0.02713|0.02713	0.124183|0.124183	0.232723|0.232723	ENSG00000114455|ENSG00000114455	ENST00000482099|ENST00000491820;ENST00000467562;ENST00000357759;ENST00000467761;ENST00000489514	.|T;T;T;T;T	.|0.10382	.|5.08;2.88;5.05;5.05;5.05	3.98|3.98	-7.96|-7.96	0.01144|0.01144	.|.	.|8.316520	.|0.00166	.|N	.|0.000010	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.30851|0.30851	-0.9964|-0.9964	4|9	.|0.72032	.|D	.|0.01	-18.4602|-18.4602	5.9093|5.9093	0.19018|0.19018	0.1377:0.0963:0.5385:0.2274|0.1377:0.0963:0.5385:0.2274	rs6779094;rs17242385;rs52829163;rs59044069;rs6779094|rs6779094;rs17242385;rs52829163;rs59044069;rs6779094	.|300;364;364	.|B4DKN2;C9J7D0;Q9UM44	.|.;.;HHLA2_HUMAN	S|R	267|364;300;364;364;364	.|ENSP00000418284:S364R;ENSP00000418345:S300R;ENSP00000350402:S364R;ENSP00000419207:S364R;ENSP00000417856:S364R	.|ENSP00000350402:S364R	R|S	+|+	1|3	0|2	HHLA2|HHLA2	109563967|109563967	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.012000|0.012000	0.07955|0.07955	-2.044000|-2.044000	0.01411|0.01411	-3.721000|-3.721000	0.00115|0.00115	-1.066000|-1.066000	0.02275|0.02275	CGT|AGC	C|0.868;A|0.132	0.132	strong		0.413	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072	
SNX19	399979	hgsc.bcm.edu	37	11	130784707	130784707	+	Silent	SNP	C	C	T	rs61736752	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130784707C>T	ENST00000265909.4	-	1	1697	c.1128G>A	c.(1126-1128)ccG>ccA	p.P376P	SNX19_ENST00000533318.1_Intron|SNX19_ENST00000533214.1_Silent_p.P376P|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000530356.1_Intron|SNX19_ENST00000539184.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	376					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GTTCAGACAGCGGAGACTCCA	0.488													C|||	639	0.127596	0.0492	0.0893	5008	,	,		20287	0.1538		0.1988	False		,,,				2504	0.1605				p.P376P		Atlas-SNP	.											.	SNX19	84	.	0			c.G1128A						PASS	.	C		315,4087	168.3+/-199.2	14,287,1900	66.0	66.0	66.0		1128	-11.2	0.0	11	dbSNP_129	66	1787,6807	323.5+/-316.1	173,1441,2683	no	coding-synonymous	SNX19	NM_014758.2		187,1728,4583	TT,TC,CC		20.7936,7.1558,16.1742		376/993	130784707	2102,10894	2201	4297	6498	SO:0001819	synonymous_variant	399979	exon1			AGACAGCGGAGAC	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1128G>A	11.37:g.130784707C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_014758	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	37	CCDS31721.1																																																																																			C|0.844;T|0.156	0.156	strong		0.488	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
LIAS	11019	hgsc.bcm.edu	37	4	39466779	39466779	+	Silent	SNP	A	A	G	rs35086467	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:39466779A>G	ENST00000261434.3	+	5	625	c.507A>G	c.(505-507)gaA>gaG	p.E169E	LIAS_ENST00000381846.1_Silent_p.E169E|LIAS_ENST00000513731.1_Intron|LIAS_ENST00000340169.2_Silent_p.E169E|LIAS_ENST00000515061.1_3'UTR	NM_006859.2	NP_006850.2			lipoic acid synthetase											breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)|ovary(2)	12						CAATTGCAGAATGGGGTCTGG	0.453													A|||	139	0.0277556	0.0008	0.0317	5008	,	,		19401	0.0		0.0765	False		,,,				2504	0.0399				p.E169E		Atlas-SNP	.											.	LIAS	26	.	0			c.A507G						PASS	.	A	,	85,4321	70.9+/-108.8	0,85,2118	212.0	199.0	203.0		507,507	4.2	1.0	4	dbSNP_126	203	840,7760	193.5+/-239.2	46,748,3506	no	coding-synonymous,coding-synonymous	LIAS	NM_006859.2,NM_194451.1	,	46,833,5624	GG,GA,AA		9.7674,1.9292,7.1121	,	169/373,169/323	39466779	925,12081	2203	4300	6503	SO:0001819	synonymous_variant	11019	exon5			TGCAGAATGGGGT	AJ224162	CCDS3453.1, CCDS3454.1, CCDS63950.1	4p14	2008-02-05			ENSG00000121897	ENSG00000121897			16429	protein-coding gene	gene with protein product		607031				11124703	Standard	NM_006859		Approved	LAS	uc003guf.3	O43766	OTTHUMG00000099369	ENST00000261434.3:c.507A>G	4.37:g.39466779A>G		Somatic	277	1	0.00361011		WXS	Illumina HiSeq	Phase_I	273	133	0.487179	NM_194451		Silent	SNP	ENST00000261434.3	37	CCDS3453.1																																																																																			A|0.938;G|0.062	0.062	strong		0.453	LIAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216815.1	NM_194451	
HLA-C	3107	hgsc.bcm.edu	37	6	31238230	31238230	+	Missense_Mutation	SNP	G	G	C	rs1050716	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238230G>C	ENST00000376228.5	-	4	666	c.652C>G	c.(652-654)Ctc>Gtc	p.L218V	HLA-C_ENST00000383329.3_Missense_Mutation_p.L218V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	218	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TGGTCAGAGAGGGGGTGGTGG	0.602													N|||	3923	0.783347	0.8109	0.8156	5008	,	,		18139	0.8135		0.7276	False		,,,				2504	0.7495				p.L218V		Atlas-SNP	.											.	HLA-C	92	.	0			c.C652G						PASS	.	C	VAL/LEU	3476,930		1379,718,106	47.0	52.0	51.0		652	-5.3	0.0	6	dbSNP_86	51	5820,2778		1997,1826,476	no	missense	HLA-C	NM_002117.5	32	3376,2544,582	CC,CG,GG		32.3098,21.1076,28.5143	benign	218/367	31238230	9296,3708	2203	4299	6502	SO:0001583	missense	3107	exon4			CAGAGAGGGGGTG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.652C>G	6.37:g.31238230G>C	ENSP00000365402:p.Leu218Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	121	119	0.983471	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1691|1691	0.7742673992673993|0.7742673992673993	396|396	0.8048780487804879|0.8048780487804879	290|290	0.8011049723756906|0.8011049723756906	459|459	0.8024475524475524|0.8024475524475524	546|546	0.7203166226912929|0.7203166226912929	.|.	0.706|0.706	-0.788894|-0.788894	0.02884|0.02884	0.788924|0.788924	0.676902|0.676902	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|T	0.14766|0.00760	2.48;2.48|5.73	2.65|2.65	-5.3|-5.3	0.02738|0.02738	Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	1.852760|.	0.03982|.	N|.	0.293400|.	T|T	0.00300|0.00300	0.0009|0.0009	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.08055|.	0.003;0.0;0.003;0.0|.	T|T	0.33343|0.33343	-0.9872|-0.9872	8|5	0.02654|0.87932	T|D	1|0	.|.	4.2716|4.2716	0.10789|0.10789	0.1371:0.5216:0.1388:0.2025|0.1371:0.5216:0.1388:0.2025	rs1050716;rs1059566;rs2308611;rs3190635;rs3191069;rs3200296;rs9264634|rs1050716;rs1059566;rs2308611;rs3190635;rs3191069;rs3200296;rs9264634	218;218;218;218|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	V|R	218;218;218;255|217	ENSP00000365402:L218V;ENSP00000372819:L218V|ENSP00000400410:P217R	ENSP00000365402:L218V|ENSP00000400410:P217R	L|P	-|-	1|2	0|0	HLA-C|HLA-C	31346209|31346209	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.010000|0.010000	0.07245|0.07245	-5.189000|-5.189000	0.00143|0.00143	-2.567000|-2.567000	0.00470|0.00470	-3.009000|-3.009000	0.00075|0.00075	CTC|CCT	G|0.265;C|0.735	0.735	strong		0.602	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
TBC1D32	221322	hgsc.bcm.edu	37	6	121638666	121638666	+	Missense_Mutation	SNP	G	G	A	rs75747353	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:121638666G>A	ENST00000398212.2	-	3	519	c.470C>T	c.(469-471)tCt>tTt	p.S157F	TBC1D32_ENST00000275159.6_Missense_Mutation_p.S157F	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	157					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.S157F(1)									ATCACTATCAGAGCAATTGTC	0.318													G|||	273	0.0545128	0.034	0.1196	5008	,	,		15308	0.124		0.0109	False		,,,				2504	0.0092				p.S157F		Atlas-SNP	.											C6orf170,colon,carcinoma,-1,6	C6orf170	146	6	1	Substitution - Missense(1)	central_nervous_system(1)	c.C470T						PASS	.	G	PHE/SER	109,3615		3,103,1756	294.0	267.0	276.0		470	5.0	1.0	6	dbSNP_131	276	98,8084		0,98,3993	yes	missense	C6orf170	NM_152730.4	155	3,201,5749	AA,AG,GG		1.1978,2.927,1.7386	probably-damaging	157/1258	121638666	207,11699	1862	4091	5953	SO:0001583	missense	221322	exon3			CTATCAGAGCAAT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.470C>T	6.37:g.121638666G>A	ENSP00000381270:p.Ser157Phe	Somatic	458	0	0		WXS	Illumina HiSeq	Phase_I	480	198	0.4125	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	143	0.06547619047619048	24	0.04878048780487805	34	0.09392265193370165	75	0.13111888111888112	10	0.013192612137203167	G	22.8	4.332774	0.81801	0.02927	0.011978	ENSG00000146350	ENST00000275159;ENST00000398212;ENST00000422369	T;T;T	0.25579	1.79;1.79;1.79	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.46229	0.1382	M	0.74258	2.255	0.09310	P	0.99999893982	D	0.89917	1.0	D	0.80764	0.994	T	0.49588	-0.8924	9	0.66056	D	0.02	-0.0535	18.7354	0.91751	0.0:0.0:1.0:0.0	.	157	Q96NH3	BROMI_HUMAN	F	157	ENSP00000275159:S157F;ENSP00000381270:S157F;ENSP00000397993:S157F	ENSP00000275159:S157F	S	-	2	0	C6orf170	121680365	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.507000	0.90522	2.485000	0.83878	0.655000	0.94253	TCT	G|0.954;A|0.046	0.046	strong		0.318	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
MTMR7	9108	hgsc.bcm.edu	37	8	17157605	17157605	+	Missense_Mutation	SNP	A	A	C	rs145244130	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:17157605A>C	ENST00000180173.5	-	14	1783	c.1749T>G	c.(1747-1749)agT>agG	p.S583R	VPS37A_ENST00000521162.1_3'UTR|MTMR7_ENST00000398099.3_Missense_Mutation_p.S174R	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	583					inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		TCATATTCCCACTGTAATCCT	0.453													A|||	6	0.00119808	0.0	0.0	5008	,	,		17679	0.0		0.003	False		,,,				2504	0.0031				p.S583R		Atlas-SNP	.											.	MTMR7	75	.	0			c.T1749G						PASS	.	A	ARG/SER	4,4402	8.1+/-20.4	0,4,2199	193.0	193.0	193.0		1749	-2.7	0.9	8	dbSNP_134	193	36,8564	24.6+/-71.5	1,34,4265	yes	missense	MTMR7	NM_004686.4	110	1,38,6464	CC,CA,AA		0.4186,0.0908,0.3076	possibly-damaging	583/661	17157605	40,12966	2203	4300	6503	SO:0001583	missense	9108	exon14			ATTCCCACTGTAA	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1749T>G	8.37:g.17157605A>C	ENSP00000180173:p.Ser583Arg	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	286	141	0.493007	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	37	CCDS34851.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	12.24	1.877751	0.33162	9.08E-4	0.004186	ENSG00000003987	ENST00000180173;ENST00000398099	D;T	0.92965	-3.14;-1.07	5.32	-2.65	0.06095	.	0.377447	0.33127	N	0.005259	T	0.79476	0.4452	L	0.36672	1.1	0.39153	D	0.96225	B	0.28128	0.201	B	0.19391	0.025	T	0.68507	-0.5390	10	0.15499	T	0.54	.	13.1914	0.59713	0.4371:0.0:0.5629:0.0	.	583	Q9Y216	MTMR7_HUMAN	R	583;174	ENSP00000180173:S583R;ENSP00000381171:S174R	ENSP00000180173:S583R	S	-	3	2	MTMR7	17201976	0.516000	0.26218	0.932000	0.37286	0.971000	0.66376	-0.103000	0.10940	-0.380000	0.07894	-0.326000	0.08463	AGT	A|0.997;C|0.003	0.003	strong		0.453	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
GALNS	2588	hgsc.bcm.edu	37	16	88893122	88893122	+	Missense_Mutation	SNP	C	C	T	rs150734270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:88893122C>T	ENST00000268695.5	-	10	1215	c.1127G>A	c.(1126-1128)cGg>cAg	p.R376Q	GALNS_ENST00000542788.1_Missense_Mutation_p.R301Q|AC092384.1_ENST00000593752.1_5'Flank	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	376	Catalytic domain.		R -> Q (in MPS4A; severe form; dbSNP:rs150734270). {ECO:0000269|PubMed:9521421}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		GTCCATCAGCCGGCCCTGCAG	0.662													C|||	7	0.00139776	0.0	0.0029	5008	,	,		14448	0.0		0.005	False		,,,				2504	0.0				p.R376Q	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											GALNS,bladder,carcinoma,0,1	GALNS	37	1	0			c.G1127A	GRCh37	CM980820	GALNS	M	rs150734270	PASS	.	C	GLN/ARG	1,4393	2.1+/-5.4	0,1,2196	28.0	29.0	28.0		1127	-2.8	0.2	16	dbSNP_134	28	16,8584	10.5+/-38.8	0,16,4284	yes	missense	GALNS	NM_000512.4	43	0,17,6480	TT,TC,CC		0.186,0.0228,0.1308	benign	376/523	88893122	17,12977	2197	4300	6497	SO:0001583	missense	2588	exon10			ATCAGCCGGCCCT	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"""Arylsulfatase family"""	4122	protein-coding gene	gene with protein product	"""Morquio syndrome"", ""mucopolysaccharidosis type IVA"""	612222	"""galactosamine (N-acetyl)-6-sulfate sulfatase"""			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.1127G>A	16.37:g.88893122C>T	ENSP00000268695:p.Arg376Gln	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_000512	Q86VK3	Missense_Mutation	SNP	ENST00000268695.5	37	CCDS10970.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	6.207	0.406403	0.11754	2.28E-4	0.00186	ENSG00000141012	ENST00000268695;ENST00000542788	D;D	0.93488	-3.23;-3.23	5.43	-2.81	0.05805	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.908483	0.09491	N	0.794912	T	0.80358	0.4608	N	0.12853	0.265	0.09310	N	1	B;B	0.18310	0.007;0.027	B;B	0.08055	0.003;0.003	T	0.66064	-0.6016	10	0.31617	T	0.26	.	12.0153	0.53311	0.0:0.2983:0.0:0.7017	.	376;376	B2R6P1;P34059	.;GALNS_HUMAN	Q	376;301	ENSP00000268695:R376Q;ENSP00000438197:R301Q	ENSP00000268695:R376Q	R	-	2	0	GALNS	87420623	0.004000	0.15560	0.161000	0.22692	0.072000	0.16883	-0.448000	0.06820	-0.733000	0.04850	-0.755000	0.03482	CGG	C|0.999;T|0.001	0.001	strong		0.662	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1		
MUC16	94025	hgsc.bcm.edu	37	19	9083143	9083143	+	Missense_Mutation	SNP	G	G	A	rs7245949	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9083143G>A	ENST00000397910.4	-	1	8875	c.8672C>T	c.(8671-8673)aCa>aTa	p.T2891I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2892	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAACTCAAATGTCAAGGTAGA	0.517													G|||	1134	0.226438	0.27	0.2983	5008	,	,		21087	0.0228		0.3111	False		,,,				2504	0.2393				p.T2891I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C8672T						PASS	.	G	ILE/THR	1009,2791		143,723,1034	69.0	64.0	66.0		8672	0.8	0.0	19	dbSNP_116	66	2724,5530		461,1802,1864	yes	missense	MUC16	NM_024690.2	89	604,2525,2898	AA,AG,GG		33.0022,26.5526,30.969	probably-damaging	2891/14508	9083143	3733,8321	1900	4127	6027	SO:0001583	missense	94025	exon1			TCAAATGTCAAGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8672C>T	19.37:g.9083143G>A	ENSP00000381008:p.Thr2891Ile	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	198	198	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	490	0.22435897435897437	127	0.258130081300813	111	0.30662983425414364	14	0.024475524475524476	238	0.31398416886543534	g	1.396	-0.579371	0.03854	0.265526	0.330022	ENSG00000181143	ENST00000397910	T	0.02472	4.28	0.773	0.773	0.18516	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	D	0.62365	0.991	D	0.65323	0.934	T	0.55049	-0.8201	8	0.87932	D	0	.	4.823	0.13400	0.0:0.0:1.0:0.0	rs7245949;rs56689992;rs7245949	2891	B5ME49	.	I	2891	ENSP00000381008:T2891I	ENSP00000381008:T2891I	T	-	2	0	MUC16	8944143	0.016000	0.18221	0.002000	0.10522	0.009000	0.06853	1.193000	0.32162	0.680000	0.31366	0.313000	0.20887	ACA	G|0.771;A|0.229	0.229	strong		0.517	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
EFHD1	80303	hgsc.bcm.edu	37	2	233537125	233537125	+	Missense_Mutation	SNP	A	A	G	rs11550699	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233537125A>G	ENST00000264059.3	+	3	1034	c.557A>G	c.(556-558)aAa>aGa	p.K186R	EFHD1_ENST00000409708.1_Missense_Mutation_p.K74R|EFHD1_ENST00000410095.1_Missense_Mutation_p.K74R|EFHD1_ENST00000409613.1_Missense_Mutation_p.K90R	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	186			K -> R (in dbSNP:rs11550699). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		neuron projection development (GO:0031175)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|large_intestine(2)|lung(3)	7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		GAGGGTGTCAAAGGTGCCAAG	0.577													A|||	1735	0.346446	0.1483	0.464	5008	,	,		18935	0.4891		0.3469	False		,,,				2504	0.3834				p.K186R		Atlas-SNP	.											.	EFHD1	28	.	0			c.A557G						PASS	.	A	ARG/LYS	810,3596	324.8+/-298.8	83,644,1476	132.0	129.0	130.0		557	-0.4	0.9	2	dbSNP_120	130	3173,5427	482.0+/-370.8	597,1979,1724	yes	missense	EFHD1	NM_025202.3	26	680,2623,3200	GG,GA,AA		36.8953,18.384,30.6243	benign	186/240	233537125	3983,9023	2203	4300	6503	SO:0001583	missense	80303	exon3			GTGTCAAAGGTGC		CCDS2497.1, CCDS58755.1	2q37.1	2014-07-01	2005-01-25		ENSG00000115468	ENSG00000115468		"""EF-hand domain containing"""	29556	protein-coding gene	gene with protein product	"""swiprosin-2"""	611617	"""EF hand domain containing 1"""			21244694	Standard	NM_025202		Approved	FLJ13612	uc002vtc.3	Q9BUP0	OTTHUMG00000133263	ENST00000264059.3:c.557A>G	2.37:g.233537125A>G	ENSP00000264059:p.Lys186Arg	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	138	66	0.478261	NM_025202	B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	Missense_Mutation	SNP	ENST00000264059.3	37	CCDS2497.1	754	0.34523809523809523	73	0.1483739837398374	152	0.4198895027624309	272	0.4755244755244755	257	0.3390501319261214	A	9.677	1.148271	0.21288	0.18384	0.368953	ENSG00000115468	ENST00000409613;ENST00000264059;ENST00000540187;ENST00000409708;ENST00000427698;ENST00000410095	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	4.96	-0.41	0.12374	.	0.207888	0.48767	N	0.000164	T	0.00012	0.0000	L	0.53780	1.695	0.32928	P	0.48319999999999996	B;B	0.17268	0.002;0.021	B;B	0.15484	0.001;0.013	T	0.44513	-0.9323	9	0.30854	T	0.27	-1.3083	4.7049	0.12844	0.5494:0.1545:0.2961:0.0	rs11550699;rs17844998;rs17857759;rs52815265;rs59739742;rs11550699	90;186	E9PFH3;Q9BUP0	.;EFHD1_HUMAN	R	90;186;89;74;74;74	ENSP00000386556:K90R;ENSP00000264059:K186R;ENSP00000386243:K74R;ENSP00000401073:K74R;ENSP00000386685:K74R	ENSP00000264059:K186R	K	+	2	0	EFHD1	233245369	0.388000	0.25197	0.930000	0.37139	0.370000	0.29829	0.160000	0.16462	-0.331000	0.08501	-0.379000	0.06801	AAA	A|0.685;G|0.315	0.315	strong		0.577	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202	
RAD1	5810	hgsc.bcm.edu	37	5	34908988	34908988	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:34908988C>T	ENST00000382038.2	-	6	2150	c.731G>A	c.(730-732)cGg>cAg	p.R244Q	RAD1_ENST00000341754.4_Missense_Mutation_p.R244Q	NM_002853.3	NP_002844.1	O60671	RAD1_HUMAN	RAD1 checkpoint DNA exonuclease	244					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|meiotic recombination checkpoint (GO:0051598)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|substantia nigra development (GO:0021762)	chromosome (GO:0005694)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|damaged DNA binding (GO:0003684)|exodeoxyribonuclease III activity (GO:0008853)	p.R244L(1)		endometrium(3)|large_intestine(1)|lung(5)|urinary_tract(1)	10	all_lung(31;0.000107)	Lung NSC(810;5.19e-05)|Ovarian(839;0.0448)|Breast(839;0.198)	COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			GTTATCTGTCCGAATAGATAC	0.343								Other conserved DNA damage response genes																													p.R244Q		Atlas-SNP	.											RAD1,NS,carcinoma,-1,2	RAD1	17	2	1	Substitution - Missense(1)	lung(1)	c.G731A						scavenged	.						93.0	97.0	96.0					5																	34908988		2203	4297	6500	SO:0001583	missense	5810	exon6			TCTGTCCGAATAG	AF074717	CCDS3905.1	5p13	2014-08-08	2014-08-08		ENSG00000113456	ENSG00000113456	3.1.11.2		9806	protein-coding gene	gene with protein product	"""exonuclease homolog RAD1"", ""checkpoint control protein HRAD1"", ""cell cycle checkpoint protein Hrad1"", ""Rad1-like DNA damage checkpoint"", ""DNA repair exonuclease REC1"""	603153	"""RAD1 (S. pombe) homolog"", ""RAD1 homolog (S. pombe)"""			9716408, 9828137	Standard	NR_026591		Approved	HRAD1, REC1	uc003jix.3	O60671	OTTHUMG00000090783	ENST00000382038.2:c.731G>A	5.37:g.34908988C>T	ENSP00000371469:p.Arg244Gln	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	335	4	0.0119403	NM_002853	O75572|O95304|Q1W161|Q5KSM0|Q5KSM1|Q9UEP1	Missense_Mutation	SNP	ENST00000382038.2	37	CCDS3905.1	.	.	.	.	.	.	.	.	.	.	C	36	5.728166	0.96856	.	.	ENSG00000113456	ENST00000382038;ENST00000341754;ENST00000542494	T;T	0.27104	1.69;1.69	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.56485	0.1988	M	0.85859	2.78	0.80722	D	1	D	0.89917	1.0	D	0.64595	0.927	T	0.59273	-0.7485	10	0.52906	T	0.07	.	19.8841	0.96908	0.0:1.0:0.0:0.0	.	244	O60671	RAD1_HUMAN	Q	244;244;208	ENSP00000371469:R244Q;ENSP00000340879:R244Q	ENSP00000340879:R244Q	R	-	2	0	RAD1	34944745	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	7.365000	0.79537	2.713000	0.92767	0.655000	0.94253	CGG	.	.	none		0.343	RAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207567.1	NM_002853	
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709691	31709691	+	Missense_Mutation	SNP	G	G	A	rs2244485	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:31709691G>A	ENST00000382835.2	-	1	321	c.296C>T	c.(295-297)gCg>gTg	p.A99V		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	99			A -> V (in dbSNP:rs2244485).			intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						TGATTGGCACGCTGTCCTTTC	0.502													G|||	1609	0.321286	0.1793	0.3473	5008	,	,		20460	0.2639		0.4503	False		,,,				2504	0.4213				p.A99V		Atlas-SNP	.											KRTAP27-1,NS,carcinoma,-1,1	KRTAP27-1	53	1	0			c.C296T						scavenged	.	G	VAL/ALA	979,3427	367.8+/-318.4	108,763,1332	133.0	133.0	133.0		296	0.3	0.0	21	dbSNP_100	133	4174,4426	568.2+/-389.0	1012,2150,1138	yes	missense	KRTAP27-1	NM_001077711.1	64	1120,2913,2470	AA,AG,GG		48.5349,22.2197,39.6202	benign	99/208	31709691	5153,7853	2203	4300	6503	SO:0001583	missense	643812	exon1			TGGCACGCTGTCC	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"""Keratin associated proteins"""	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.296C>T	21.37:g.31709691G>A	ENSP00000372286:p.Ala99Val	Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	266	121	0.454887	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	37	CCDS33532.1	674	0.3086080586080586	81	0.16463414634146342	127	0.35082872928176795	126	0.2202797202797203	340	0.44854881266490765	G	5.791	0.330292	0.10956	0.222197	0.485349	ENSG00000206107	ENST00000382835	T	0.03301	3.98	4.44	0.262	0.15597	.	2.953730	0.01681	N	0.026127	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P	0.40032	0.699	B	0.32677	0.15	T	0.44019	-0.9355	9	0.34782	T	0.22	2.1633	4.478	0.11753	0.2144:0.3548:0.4308:0.0	rs2244485;rs17593215;rs56539537;rs2244485	99	Q3LI81	KR271_HUMAN	V	99	ENSP00000372286:A99V	ENSP00000372286:A99V	A	-	2	0	KRTAP27-1	30631562	0.003000	0.15002	0.000000	0.03702	0.007000	0.05969	0.536000	0.23129	0.039000	0.15632	0.591000	0.81541	GCG	G|0.654;A|0.346	0.346	strong		0.502	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711	
PTPRE	5791	hgsc.bcm.edu	37	10	129871690	129871690	+	Silent	SNP	A	A	G	rs2275803	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:129871690A>G	ENST00000254667.3	+	17	1833	c.1554A>G	c.(1552-1554)aaA>aaG	p.K518K	PTPRE_ENST00000419012.2_Silent_p.K518K|PTPRE_ENST00000306042.5_Silent_p.K460K	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	518	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.K518K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	GGGAATGGAAATCCCACACTA	0.597													A|||	1296	0.258786	0.2829	0.2435	5008	,	,		20991	0.2599		0.2018	False		,,,				2504	0.2945				p.K518K	Colon(52;977 1184 20575 41685)	Atlas-SNP	.											PTPRE,NS,carcinoma,0,1	PTPRE	132	1	1	Substitution - coding silent(1)	stomach(1)	c.A1554G						PASS	.	A	,	1176,3230	415.2+/-337.1	153,870,1180	119.0	101.0	107.0		1554,1380	1.5	1.0	10	dbSNP_100	107	1752,6848	317.9+/-313.4	185,1382,2733	no	coding-synonymous,coding-synonymous	PTPRE	NM_006504.4,NM_130435.3	,	338,2252,3913	GG,GA,AA		20.3721,26.6909,22.5127	,	518/701,460/643	129871690	2928,10078	2203	4300	6503	SO:0001819	synonymous_variant	5791	exon17			ATGGAAATCCCAC	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.1554A>G	10.37:g.129871690A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	122	63	0.516393	NM_006504	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Silent	SNP	ENST00000254667.3	37	CCDS7657.1																																																																																			G|0.223;N|0.000	0.223	strong		0.597	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1		
CST9L	128821	hgsc.bcm.edu	37	20	23546639	23546639	+	Missense_Mutation	SNP	T	T	G	rs2295564	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:23546639T>G	ENST00000376979.3	-	2	624	c.326A>C	c.(325-327)cAt>cCt	p.H109P		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	109			H -> P (in dbSNP:rs2295564).			extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.H109P(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					TTCTTGGAAATGGCAGTTGTC	0.502													G|||	1882	0.375799	0.1899	0.4049	5008	,	,		22065	0.5417		0.3877	False		,,,				2504	0.4233				p.H109P		Atlas-SNP	.											CST9L,NS,carcinoma,0,1	CST9L	25	1	1	Substitution - Missense(1)	prostate(1)	c.A326C						PASS	.	G	PRO/HIS	997,3409	730.4+/-410.2	128,741,1334	285.0	228.0	247.0		326	1.9	0.2	20	dbSNP_100	247	3511,5089	633.0+/-398.7	710,2091,1499	yes	missense	CST9L	NM_080610.2	77	838,2832,2833	GG,GT,TT		40.8256,22.6282,34.6609	benign	109/148	23546639	4508,8498	2203	4300	6503	SO:0001583	missense	128821	exon2			TGGAAATGGCAGT		CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"""cystatin 9 (mouse)-like"""			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.326A>C	20.37:g.23546639T>G	ENSP00000366178:p.His109Pro	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	293	131	0.447099	NM_080610	B2R5A1	Missense_Mutation	SNP	ENST00000376979.3	37	CCDS13157.1	839	0.3841575091575092	89	0.18089430894308944	153	0.42265193370165743	305	0.5332167832167832	292	0.38522427440633245	G	0.007	-1.937714	0.00484	0.226282	0.408256	ENSG00000101435	ENST00000376979	T	0.24350	1.86	1.92	1.92	0.25849	Proteinase inhibitor I25, cystatin (2);	0.000000	0.37261	N	0.002175	T	0.00012	0.0000	N	0.00016	-2.85	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45220	-0.9276	9	0.02654	T	1	.	5.6793	0.17765	0.0:0.0:0.6787:0.3213	rs2295564;rs17231619;rs52819629;rs2295564	109	Q9H4G1	CST9L_HUMAN	P	109	ENSP00000366178:H109P	ENSP00000366178:H109P	H	-	2	0	CST9L	23494639	0.711000	0.27906	0.202000	0.23494	0.040000	0.13550	0.460000	0.21924	0.363000	0.24346	-0.323000	0.08544	CAT	T|0.629;G|0.371	0.371	strong		0.502	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610	
GALK2	2585	hgsc.bcm.edu	37	15	49620200	49620200	+	Silent	SNP	C	C	T	rs1055254	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:49620200C>T	ENST00000560031.1	+	10	1528	c.1221C>T	c.(1219-1221)tgC>tgT	p.C407C	GALK2_ENST00000544523.1_Silent_p.C383C|GALK2_ENST00000327171.3_Silent_p.C396C|GALK2_ENST00000396509.2_Silent_p.C383C|GALK2_ENST00000559454.1_Silent_p.C383C|GALK2_ENST00000543495.1_3'UTR			Q01415	GALK2_HUMAN	galactokinase 2	407					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		GGGGAGGCTGCACAGTATCAA	0.458													C|||	1012	0.202077	0.2428	0.1873	5008	,	,		17677	0.0466		0.2575	False		,,,				2504	0.2607				p.C407C		Atlas-SNP	.											.	GALK2	78	.	0			c.C1221T						PASS	.	C	,	1090,3302	393.5+/-328.9	140,810,1246	99.0	99.0	99.0		1188,1221	2.6	1.0	15	dbSNP_86	99	1905,6685	339.4+/-323.1	215,1475,2605	no	coding-synonymous,coding-synonymous	GALK2	NM_001001556.1,NM_002044.2	,	355,2285,3851	TT,TC,CC		22.1769,24.8179,23.0704	,	396/448,407/459	49620200	2995,9987	2196	4295	6491	SO:0001819	synonymous_variant	2585	exon10			AGGCTGCACAGTA		CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.1221C>T	15.37:g.49620200C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_002044	Q7Z4Q4	Silent	SNP	ENST00000560031.1	37	CCDS42034.1																																																																																			C|0.783;T|0.217	0.217	strong		0.458	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1		
KIAA1462	57608	hgsc.bcm.edu	37	10	30318345	30318345	+	Silent	SNP	C	C	T	rs11813359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:30318345C>T	ENST00000375377.1	-	3	833	c.732G>A	c.(730-732)acG>acA	p.T244T		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	244					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						TGGGAATTTCCGTGCAACTCA	0.453													C|||	20	0.00399361	0.0023	0.0029	5008	,	,		21995	0.0		0.0139	False		,,,				2504	0.001				p.T244T		Atlas-SNP	.											KIAA1462,NS,carcinoma,-2,1	KIAA1462	162	1	0			c.G732A						scavenged	.	C		12,3910		0,12,1949	136.0	139.0	138.0		732	0.8	0.0	10	dbSNP_120	138	113,8169		0,113,4028	no	coding-synonymous	KIAA1462	NM_020848.2		0,125,5977	TT,TC,CC		1.3644,0.306,1.0243		244/1360	30318345	125,12079	1961	4141	6102	SO:0001819	synonymous_variant	57608	exon3			AATTTCCGTGCAA	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.732G>A	10.37:g.30318345C>T		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	175	75	0.428571	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																			C|0.994;T|0.006	0.006	strong		0.453	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
ABCB10	23456	hgsc.bcm.edu	37	1	229654053	229654053	+	Missense_Mutation	SNP	T	T	C	rs115488729	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:229654053T>C	ENST00000344517.4	-	13	2132	c.2090A>G	c.(2089-2091)aAt>aGt	p.N697S	ABCB10_ENST00000498158.1_5'UTR	NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	697	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				CATATTAGCATTCTTAATGGT	0.393													T|||	73	0.0145767	0.0023	0.0216	5008	,	,		20530	0.0		0.0537	False		,,,				2504	0.001				p.N697S		Atlas-SNP	.											.	ABCB10	71	.	0			c.A2090G						PASS	.	T	SER/ASN	27,4379	34.3+/-65.2	0,27,2176	92.0	88.0	89.0		2090	4.1	1.0	1	dbSNP_132	89	272,8328	103.6+/-164.7	4,264,4032	yes	missense	ABCB10	NM_012089.2	46	4,291,6208	CC,CT,TT		3.1628,0.6128,2.2989	benign	697/739	229654053	299,12707	2203	4300	6503	SO:0001583	missense	23456	exon13			TTAGCATTCTTAA	U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"""ATP binding cassette transporters / subfamily B"""	41	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family B member 10, mitochondrial"", ""ATP-binding cassette transporter 10"", ""ABC transporter 10 protein"", ""mitochondrial ATP-binding cassette 2"""	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.2090A>G	1.37:g.229654053T>C	ENSP00000355637:p.Asn697Ser	Somatic	400	0	0		WXS	Illumina HiSeq	Phase_I	415	200	0.481928	NM_012089	Q13040|Q6P1Q8|Q9H3V0	Missense_Mutation	SNP	ENST00000344517.4	37	CCDS1580.1	52	0.023809523809523808	3	0.006097560975609756	13	0.03591160220994475	0	0.0	36	0.047493403693931395	T	6.860	0.528004	0.13127	0.006128	0.031628	ENSG00000135776	ENST00000344517	T	0.77358	-1.09	5.18	4.05	0.47172	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.089199	0.85682	D	0.000000	T	0.25568	0.0622	L	0.31476	0.935	0.43808	D	0.996363	B	0.09022	0.002	B	0.04013	0.001	T	0.42447	-0.9451	10	0.33940	T	0.23	-12.485	11.1415	0.48404	0.0:0.0732:0.0:0.9268	.	697	Q9NRK6	ABCBA_HUMAN	S	697	ENSP00000355637:N697S	ENSP00000355637:N697S	N	-	2	0	ABCB10	227720676	1.000000	0.71417	0.963000	0.40424	0.056000	0.15407	3.992000	0.56980	0.918000	0.36919	0.533000	0.62120	AAT	T|0.976;C|0.024	0.024	strong		0.393	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089	
OR5M9	390162	hgsc.bcm.edu	37	11	56230328	56230328	+	Missense_Mutation	SNP	G	G	T	rs61902869	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56230328G>T	ENST00000279791.1	-	1	549	c.550C>A	c.(550-552)Cag>Aag	p.Q184K		NM_001004743.1	NP_001004743.1	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M, member 9	184						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	36	Esophageal squamous(21;0.00448)					CAGGCAATCTGGATGAGAGGG	0.418													t|||	326	0.0650958	0.112	0.0432	5008	,	,		22544	0.001		0.0934	False		,,,				2504	0.0542				p.Q184K		Atlas-SNP	.											.	OR5M9	75	.	0			c.C550A						PASS	.	T	LYS/GLN	426,3976	786.1+/-414.8	19,388,1794	82.0	87.0	85.0		550	3.2	1.0	11	dbSNP_129	85	694,7898	787.3+/-407.6	35,624,3637	yes	missense	OR5M9	NM_001004743.1	53	54,1012,5431	TT,TG,GG		8.0773,9.6774,8.6194	benign	184/311	56230328	1120,11874	2201	4296	6497	SO:0001583	missense	390162	exon1			CAATCTGGATGAG	AB065747	CCDS31531.1	11q11	2012-08-09			ENSG00000150269	ENSG00000150269		"""GPCR / Class A : Olfactory receptors"""	15294	protein-coding gene	gene with protein product							Standard	NM_001004743		Approved		uc010rjj.2	Q8NGP3	OTTHUMG00000166874	ENST00000279791.1:c.550C>A	11.37:g.56230328G>T	ENSP00000279791:p.Gln184Lys	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	165	79	0.478788	NM_001004743	Q6IEW5|Q96RB9	Missense_Mutation	SNP	ENST00000279791.1	37	CCDS31531.1	155	0.07097069597069597	72	0.14634146341463414	13	0.03591160220994475	0	0.0	70	0.09234828496042216	T	1.058	-0.673770	0.03403	0.096774	0.080773	ENSG00000150269	ENST00000279791	T	0.00016	9.12	4.39	3.25	0.37280	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	N	0.000288	T	0.00012	0.0000	N	0.00298	-1.69	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.01484	-1.1343	9	0.11485	T	0.65	-9.0552	3.397	0.07310	0.0:0.1949:0.2099:0.5952	rs61902869	184	Q8NGP3	OR5M9_HUMAN	K	184	ENSP00000279791:Q184K	ENSP00000279791:Q184K	Q	-	1	0	OR5M9	55986904	0.000000	0.05858	1.000000	0.80357	0.830000	0.47004	-0.367000	0.07553	0.653000	0.30826	-0.407000	0.06327	CAG	G|0.922;T|0.078	0.078	strong		0.418	OR5M9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391638.1	NM_001004743	
SYTL2	54843	hgsc.bcm.edu	37	11	85436500	85436500	+	Intron	SNP	T	T	C	rs580459	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:85436500T>C	ENST00000528231.1	-	7	1737				SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000359152.5_Missense_Mutation_p.M858V|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000525423.1_Missense_Mutation_p.M334V|SYTL2_ENST00000354566.3_Missense_Mutation_p.M334V	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TCTGCAGCCATCTGAATCAAA	0.463													T|||	3338	0.666534	0.8812	0.5706	5008	,	,		19951	0.6012		0.6551	False		,,,				2504	0.5235				p.M334V		Atlas-SNP	.											.	SYTL2	231	.	0			c.A1000G						PASS	.	T	,,,VAL/MET,VAL/MET	3631,775	753.6+/-412.4	1499,633,71	95.0	96.0	96.0		,,,1000,1000	1.7	0.0	11	dbSNP_83	96	5650,2948	668.6+/-402.6	1881,1888,530	yes	intron,intron,intron,missense,missense	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,21,21	3380,2521,601	CC,CT,TT		34.287,17.5897,28.6297	,,,benign,benign	,,,334/1273,334/1257	85436500	9281,3723	2203	4299	6502	SO:0001627	intron_variant	54843	exon1			CAGCCATCTGAAT	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2438A>G	11.37:g.85436500T>C		Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	1480	0.6776556776556777	428	0.8699186991869918	223	0.6160220994475138	326	0.5699300699300699	503	0.6635883905013192	T	7.460	0.644420	0.14451	0.824103	0.65713	ENSG00000137501	ENST00000359152;ENST00000354566;ENST00000525423	T;T;T	0.26660	1.72;1.73;1.73	5.43	1.74	0.24563	.	0.842935	0.10717	N	0.642187	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.16802	0.019;0.019;0.019	B;B;B	0.12156	0.007;0.007;0.007	T	0.15292	-1.0442	8	.	.	.	-0.0784	3.4297	0.07424	0.1717:0.2449:0.0:0.5834	rs580459;rs17810970;rs52803235;rs59688999;rs580459	334;334;334	Q9HCH5-11;Q9HCH5-7;Q9HCH5-8	.;.;.	V	858;334;334	ENSP00000352065:M858V;ENSP00000346576:M334V;ENSP00000432694:M334V	.	M	-	1	0	SYTL2	85114148	0.000000	0.05858	0.030000	0.17652	0.963000	0.63663	-2.079000	0.01369	0.490000	0.27771	0.533000	0.62120	ATG	T|0.304;C|0.696	0.696	strong		0.463	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
AARS2	57505	hgsc.bcm.edu	37	6	44270870	44270870	+	Missense_Mutation	SNP	C	C	T	rs35623954	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:44270870C>T	ENST00000244571.4	-	16	2190	c.2188G>A	c.(2188-2190)Gtg>Atg	p.V730M	RP11-444E17.6_ENST00000505802.1_Intron|AARS2_ENST00000491573.1_5'Flank|TMEM151B_ENST00000438774.2_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GCATGGGCCACGGGCACCCCC	0.612													C|||	65	0.0129792	0.0	0.0101	5008	,	,		17970	0.001		0.0507	False		,,,				2504	0.0061				p.V730M		Atlas-SNP	.											.	AARS2	77	.	0			c.G2188A						PASS	.	C	MET/VAL	42,4364	45.3+/-79.5	0,42,2161	57.0	60.0	59.0		2188	5.3	1.0	6	dbSNP_126	59	360,8240	120.6+/-179.8	9,342,3949	yes	missense	AARS2	NM_020745.2	21	9,384,6110	TT,TC,CC		4.186,0.9532,3.0909	probably-damaging	730/986	44270870	402,12604	2203	4300	6503	SO:0001583	missense	57505	exon16			GGGCCACGGGCAC	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	21022	protein-coding gene	gene with protein product	"""alanine tRNA ligase 2, mitochondrial"""	612035	"""alanyl-tRNA synthetase like"", ""alanyl-tRNA synthetase 2, mitochondrial (putative)"""	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.2188G>A	6.37:g.44270870C>T	ENSP00000244571:p.Val730Met	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	37	CCDS34464.1	40	0.018315018315018316	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	34	0.044854881266490766	C	17.17	3.320587	0.60634	0.009532	0.04186	ENSG00000124608	ENST00000244571	T	0.67171	-0.25	5.26	5.26	0.73747	Threonyl/alanyl tRNA synthetase, SAD (2);Alanyl-tRNA synthetase, class IIc, core domain (1);Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.060246	0.64402	D	0.000003	T	0.79569	0.4468	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82210	-0.0570	10	0.87932	D	0	-23.4327	12.3948	0.55378	0.0:0.9239:0.0:0.0761	rs35623954	730	Q5JTZ9	SYAM_HUMAN	M	730	ENSP00000244571:V730M	ENSP00000244571:V730M	V	-	1	0	AARS2	44378848	1.000000	0.71417	0.954000	0.39281	0.175000	0.22909	4.489000	0.60309	2.733000	0.93635	0.655000	0.94253	GTG	C|0.975;T|0.025	0.025	strong		0.612	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745	
CCDC170	80129	hgsc.bcm.edu	37	6	151894340	151894340	+	Missense_Mutation	SNP	C	C	T	rs12205837	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:151894340C>T	ENST00000239374.7	+	6	905	c.806C>T	c.(805-807)gCt>gTt	p.A269V	CCDC170_ENST00000367290.5_Missense_Mutation_p.A269V	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	269			A -> V (in dbSNP:rs12205837).														GCAAAAGAAGCTCTTGAAAGG	0.458													C|||	384	0.0766773	0.0787	0.0865	5008	,	,		19899	0.0704		0.0795	False		,,,				2504	0.0706				p.A269V		Atlas-SNP	.											.	.	.	.	0			c.C806T						PASS	.	C	VAL/ALA	272,3478		9,254,1612	57.0	56.0	56.0		806	2.3	0.8	6	dbSNP_120	56	888,7352		40,808,3272	yes	missense	C6orf97	NM_025059.3	64	49,1062,4884	TT,TC,CC		10.7767,7.2533,9.6747	benign	269/716	151894340	1160,10830	1875	4120	5995	SO:0001583	missense	80129	exon6			AAGAAGCTCTTGA	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.806C>T	6.37:g.151894340C>T	ENSP00000239374:p.Ala269Val	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	179	87	0.486034	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	182	0.08333333333333333	60	0.12195121951219512	32	0.08839779005524862	30	0.05244755244755245	60	0.079155672823219	C	13.23	2.174854	0.38413	0.072533	0.107767	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.08634	3.1;3.07	5.35	2.34	0.29019	.	0.441618	0.24532	N	0.037710	T	0.02571	0.0078	L	0.41027	1.25	0.40540	P	0.018985999999999947	B	0.15930	0.015	B	0.16289	0.015	T	0.33240	-0.9876	9	0.33940	T	0.23	-9.5343	9.0511	0.36376	0.1324:0.419:0.4486:0.0	rs12205837;rs52799427;rs12205837	269	Q8IYT3	CF097_HUMAN	V	269	ENSP00000239374:A269V;ENSP00000356259:A269V	ENSP00000239374:A269V	A	+	2	0	C6orf97	151936033	0.730000	0.28100	0.825000	0.32803	0.813000	0.45954	0.908000	0.28545	1.317000	0.45149	0.643000	0.83706	GCT	C|0.911;T|0.089	0.089	strong		0.458	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
SLC36A3	285641	hgsc.bcm.edu	37	5	150667016	150667016	+	Missense_Mutation	SNP	T	T	C	rs978012	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150667016T>C	ENST00000335230.3	-	6	910	c.499A>G	c.(499-501)Aaa>Gaa	p.K167E	SLC36A3_ENST00000377713.3_Missense_Mutation_p.K208E	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	167			K -> E (in dbSNP:rs978012). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.			integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACGTGGGCTTTTTCCACCATC	0.458													C|||	2884	0.575879	0.7723	0.5749	5008	,	,		20597	0.5337		0.3996	False		,,,				2504	0.5358				p.K208E		Atlas-SNP	.											.	SLC36A3	54	.	0			c.A622G						PASS	.	C	GLU/LYS,GLU/LYS	3134,1272	431.4+/-342.9	1130,874,199	102.0	95.0	98.0		622,499	2.8	1.0	5	dbSNP_86	98	3277,5323	645.3+/-400.1	618,2041,1641	yes	missense,missense	SLC36A3	NM_001145017.1,NM_181774.3	56,56	1748,2915,1840	CC,CT,TT		38.1047,28.8697,49.2926	benign,benign	208/512,167/471	150667016	6411,6595	2203	4300	6503	SO:0001583	missense	285641	exon7			GGGCTTTTTCCAC	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"""Solute carriers"""	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.499A>G	5.37:g.150667016T>C	ENSP00000334750:p.Lys167Glu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	145	61	0.42069	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Missense_Mutation	SNP	ENST00000335230.3	37	CCDS4314.1	1169	0.5352564102564102	395	0.8028455284552846	190	0.5248618784530387	283	0.49475524475524474	301	0.3970976253298153	C	10.86	1.471187	0.26423	0.711303	0.381047	ENSG00000186334	ENST00000335230;ENST00000377713	T;T	0.02216	4.39;4.39	4.56	2.76	0.32466	.	0.111229	0.64402	N	0.000015	T	0.00012	0.0000	N	0.00335	-1.625	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.04140	-1.0974	9	0.27082	T	0.32	.	10.6464	0.45623	0.0:0.7721:0.0:0.2279	rs978012;rs17729135;rs978012	208;167;152	Q495N2-3;Q495N2;Q495N2-2	.;S36A3_HUMAN;.	E	167;208	ENSP00000334750:K167E;ENSP00000366942:K208E	ENSP00000334750:K167E	K	-	1	0	SLC36A3	150647209	1.000000	0.71417	0.995000	0.50966	0.971000	0.66376	1.917000	0.39996	0.665000	0.31066	-0.119000	0.15052	AAA	T|0.484;C|0.515	0.515	strong		0.458	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90572435	90572435	+	RNA	SNP	A	A	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:90572435A>C	ENST00000551025.1	+	0	2444									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		AGTCGAGTAGACTCTCAAAGT	0.348																																					p.D336A	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.A1007C						PASS	.																																					9994	exon7			GAGTAGACTCTCA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90572435A>C		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																				.	.	none		0.348	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
ICAM1	3383	hgsc.bcm.edu	37	19	10395683	10395683	+	Missense_Mutation	SNP	A	A	G	rs5498	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10395683A>G	ENST00000264832.3	+	6	1730	c.1405A>G	c.(1405-1407)Aag>Gag	p.K469E	CTD-2369P2.8_ENST00000589379.1_RNA|ICAM1_ENST00000423829.2_Missense_Mutation_p.K247E|ICAM4_ENST00000393717.2_5'Flank|ICAM4_ENST00000340992.4_5'Flank|CTD-2369P2.5_ENST00000592893.1_RNA|ICAM4_ENST00000380770.3_5'Flank	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	469			K -> E (in dbSNP:rs5498). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:15572059, ECO:0000269|PubMed:1680919, ECO:0000269|PubMed:3340213, ECO:0000269|PubMed:3349522, ECO:0000269|PubMed:7525451}.		adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	GGTCACCCGCAAGGTGACCGT	0.612													a|||	1797	0.358826	0.1354	0.5548	5008	,	,		17106	0.2788		0.4662	False		,,,				2504	0.4939				p.K469E		Atlas-SNP	.											.	ICAM1	32	.	0			c.A1405G	GRCh37	CM003891	ICAM1	M	rs5498	PASS	.	A	GLU/LYS	849,3557	332.3+/-302.4	78,693,1432	58.0	57.0	57.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1405	-2.6	0.0	19	dbSNP_52	57	3708,4892	529.2+/-381.5	825,2058,1417	yes	missense	ICAM1	NM_000201.2	56	903,2751,2849	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	43.1163,19.2692,35.0377	benign	469/533	10395683	4557,8449	2203	4300	6503	SO:0001583	missense	3383	exon6			ACCCGCAAGGTGA		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	5344	protein-coding gene	gene with protein product	"""human rhinovirus receptor"""	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.1405A>G	19.37:g.10395683A>G	ENSP00000264832:p.Lys469Glu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_000201	B2R6M3|Q5NKV7|Q96B50	Missense_Mutation	SNP	ENST00000264832.3	37	CCDS12231.1	763	0.34935897435897434	59	0.11991869918699187	185	0.511049723756906	174	0.3041958041958042	345	0.4551451187335092	a	0.754	-0.771911	0.02951	0.192692	0.431163	ENSG00000090339	ENST00000264832;ENST00000423829	T;T	0.12039	2.72;2.72	4.61	-2.57	0.06248	Immunoglobulin-like fold (1);	1.925990	0.02941	N	0.140416	T	0.00012	0.0000	N	0.00525	-1.395	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46133	-0.9213	9	0.02654	T	1	-1.9773	5.4083	0.16335	0.3754:0.1751:0.4495:0.0	rs5498;rs1135683;rs1801713;rs2228118;rs3198540;rs5030382;rs17000453;rs58198099;rs5498	247;469	E7ESS4;P05362	.;ICAM1_HUMAN	E	469;247	ENSP00000264832:K469E;ENSP00000413124:K247E	ENSP00000264832:K469E	K	+	1	0	ICAM1	10256683	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.132000	0.15891	-0.217000	0.10033	-0.244000	0.11960	AAG	A|0.656;G|0.344	0.344	strong		0.612	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1		
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1605983	1605983	+	Missense_Mutation	SNP	G	G	C	rs59007122		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1605983G>C	ENST00000382171.2	-	1	530	c.497C>G	c.(496-498)gCc>gGc	p.A166G	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	166	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AGAACCACAGGCCCCCTTGGA	0.657																																					p.A166G		Atlas-SNP	.											KRTAP5-1,caecum,carcinoma,0,3	KRTAP5-1	74	3	0			c.C497G						scavenged	.																																			SO:0001583	missense	387264	exon1			CCACAGGCCCCCT	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.497C>G	11.37:g.1605983G>C	ENSP00000371606:p.Ala166Gly	Somatic	115	5	0.0434783		WXS	Illumina HiSeq	Phase_I	116	23	0.198276	NM_001005922		Missense_Mutation	SNP	ENST00000382171.2	37	CCDS31330.1	.	.	.	.	.	.	.	.	.	.	-	0.306	-0.971005	0.02232	.	.	ENSG00000205869	ENST00000382171	T	0.03860	3.78	3.47	2.54	0.30619	.	.	.	.	.	T	0.01189	0.0039	N	0.00134	-2.025	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.44817	-0.9303	9	0.39692	T	0.17	.	5.0286	0.14398	0.0:0.6557:0.2202:0.1241	rs59007122	166	Q6L8H4	KRA51_HUMAN	G	166	ENSP00000371606:A166G	ENSP00000371606:A166G	A	-	2	0	KRTAP5-1	1562559	0.000000	0.05858	0.726000	0.30738	0.031000	0.12232	-0.388000	0.07352	0.444000	0.26612	-0.803000	0.03203	GCC	G|0.500;C|0.500	0.500	weak		0.657	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
FANCA	2175	hgsc.bcm.edu	37	16	89809319	89809319	+	Silent	SNP	T	T	C	rs1800358	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89809319T>C	ENST00000389301.3	-	37	3684	c.3654A>G	c.(3652-3654)ccA>ccG	p.P1218P	FANCA_ENST00000568369.1_Silent_p.P1218P	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1218					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GGTTGGGTGCTGGGGAGGCAG	0.542			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	789	0.157548	0.2216	0.0389	5008	,	,		18197	0.2629		0.0765	False		,,,				2504	0.1299				p.P1218P		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.A3654G						PASS	.	C		924,3472	736.3+/-410.8	87,750,1361	71.0	71.0	71.0		3654	-9.7	0.0	16	dbSNP_89	71	791,7809	783.2+/-407.6	36,719,3545	no	coding-synonymous	FANCA	NM_000135.2		123,1469,4906	CC,CT,TT		9.1977,21.0191,13.1964		1218/1456	89809319	1715,11281	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon37	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGGTGCTGGGGAG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3654A>G	16.37:g.89809319T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			T|0.874;C|0.126	0.126	strong		0.542	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
CD86	942	hgsc.bcm.edu	37	3	121838319	121838319	+	Missense_Mutation	SNP	G	G	A	rs1129055	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121838319G>A	ENST00000330540.2	+	7	1044	c.928G>A	c.(928-930)Gcc>Acc	p.A310T	CD86_ENST00000493101.1_Missense_Mutation_p.A198T|CD86_ENST00000393627.2_Missense_Mutation_p.A304T|CD86_ENST00000264468.5_Missense_Mutation_p.A97T|CD86_ENST00000469710.1_Missense_Mutation_p.A228T	NM_175862.4	NP_787058	P42081	CD86_HUMAN	CD86 molecule	310			A -> T (in dbSNP:rs1129055). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		aging (GO:0007568)|B cell activation (GO:0042113)|cell-cell signaling (GO:0007267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to metal ion (GO:0071248)|defense response to virus (GO:0051607)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|immune response (GO:0006955)|innate immune response (GO:0045087)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of T cell anergy (GO:0002668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of lymphotoxin A biosynthetic process (GO:0043017)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|response to interferon-gamma (GO:0034341)|response to yeast (GO:0001878)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell proliferation involved in immune response (GO:0002309)|toll-like receptor signaling pathway (GO:0002224)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|kidney(1)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	23				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)|Antithymocyte globulin(DB00098)|Belatacept(DB06681)	ATCTGATGAAGCCCAGCGTGT	0.313													G|||	1716	0.342652	0.1611	0.2133	5008	,	,		19584	0.5972		0.2823	False		,,,				2504	0.4796				p.A310T	GBM(67;1379 1389 36064 39806)	Atlas-SNP	.											.	CD86	43	.	0			c.G928A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	756,3650	298.7+/-285.4	69,618,1516	73.0	74.0	74.0		592,682,910,928,766	3.2	0.0	3	dbSNP_86	74	2235,6365	378.2+/-338.8	295,1645,2360	yes	missense,missense,missense,missense,missense	CD86	NM_001206924.1,NM_001206925.1,NM_006889.4,NM_175862.4,NM_176892.1	58,58,58,58,58	364,2263,3876	AA,AG,GG		25.9884,17.1584,22.9971	benign,benign,benign,benign,benign	198/218,228/248,304/324,310/330,256/276	121838319	2991,10015	2203	4300	6503	SO:0001583	missense	942	exon7			GATGAAGCCCAGC		CCDS3009.1, CCDS43138.1, CCDS56272.1, CCDS56273.1, CCDS74991.1	3q21	2013-01-29	2006-03-28		ENSG00000114013	ENSG00000114013		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1705	protein-coding gene	gene with protein product	"""B-lymphocyte antigen B7-2"""	601020	"""CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)"""	CD28LG2		7513726	Standard	NM_006889		Approved	B7.2, B7-2	uc003eet.3	P42081	OTTHUMG00000159482	ENST00000330540.2:c.928G>A	3.37:g.121838319G>A	ENSP00000332049:p.Ala310Thr	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	231	100	0.4329	NM_175862	A0N0P0|B7Z2F3|B7Z702|E7ETN5|E9PC27|Q13655|Q6FHB1|Q6GTS4|Q7M4L5	Missense_Mutation	SNP	ENST00000330540.2	37	CCDS3009.1	725|725	0.33195970695970695|0.33195970695970695	76|76	0.15447154471544716|0.15447154471544716	77|77	0.212707182320442|0.212707182320442	354|354	0.6188811188811189|0.6188811188811189	218|218	0.287598944591029|0.287598944591029	G|G	11.90|11.90	1.776513|1.776513	0.31411|0.31411	0.171584|0.171584	0.259884|0.259884	ENSG00000114013|ENSG00000114013	ENST00000469710;ENST00000493101;ENST00000330540;ENST00000264468;ENST00000393627|ENST00000478741	T;T;T;T;T|.	0.45276|.	3.01;2.06;4.34;0.9;4.35|.	4.07|4.07	3.2|3.2	0.36748|0.36748	.|.	0.895791|.	0.09201|.	N|.	0.834660|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.39898|0.39898	1.24|1.24	0.80722|0.80722	P|P	0.0|0.0	P;B|.	0.50156|.	0.932;0.006|.	P;B|.	0.50352|.	0.638;0.005|.	T|T	0.46091|0.46091	-0.9216|-0.9216	9|4	0.42905|.	T|.	0.14|.	2.7254|2.7254	7.8408|7.8408	0.29397|0.29397	0.1125:0.0:0.8875:0.0|0.1125:0.0:0.8875:0.0	rs1129055;rs1801727;rs3186539;rs17281988;rs17857215;rs52796615;rs58681419;rs1129055|rs1129055;rs1801727;rs3186539;rs17281988;rs17857215;rs52796615;rs58681419;rs1129055	198;310|.	E9PC27;P42081|.	.;CD86_HUMAN|.	T|N	228;198;310;97;304|257	ENSP00000418988:A228T;ENSP00000420230:A198T;ENSP00000332049:A310T;ENSP00000264468:A97T;ENSP00000377248:A304T|.	ENSP00000264468:A97T|.	A|S	+|+	1|2	0|0	CD86|CD86	123321009|123321009	0.657000|0.657000	0.27393|0.27393	0.027000|0.027000	0.17364|0.17364	0.099000|0.099000	0.18886|0.18886	0.767000|0.767000	0.26575|0.26575	1.301000|1.301000	0.44836|0.44836	0.563000|0.563000	0.77884|0.77884	GCC|AGC	G|0.642;A|0.358	0.358	strong		0.313	CD86-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355671.1	NM_006889	
NEFH	4744	hgsc.bcm.edu	37	22	29885016	29885016	+	Missense_Mutation	SNP	G	G	A	rs59371099	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29885016G>A	ENST00000310624.6	+	4	1420	c.1387G>A	c.(1387-1389)Gag>Aag	p.E463K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	463	Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						ACAGACAGAGGAGACCCaagt	0.493													G|||	147	0.029353	0.0053	0.0519	5008	,	,		21774	0.0		0.0855	False		,,,				2504	0.0184				p.E463K		Atlas-SNP	.											.	NEFH	178	.	0			c.G1387A						PASS	.	G	LYS/GLU	69,4337	62.9+/-100.1	1,67,2135	67.0	64.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1387	5.8	1.0	22	dbSNP_129	65	844,7756	193.1+/-238.9	45,754,3501	no	missense	NEFH	NM_021076.3	56	46,821,5636	AA,AG,GG		9.814,1.566,7.0198	probably-damaging	463/1021	29885016	913,12093	2203	4300	6503	SO:0001583	missense	4744	exon4			ACAGAGGAGACCC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1387G>A	22.37:g.29885016G>A	ENSP00000311997:p.Glu463Lys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	86	0.039377289377289376	5	0.01016260162601626	18	0.049723756906077346	0	0.0	63	0.08311345646437995	G	24.9	4.578565	0.86645	0.01566	0.09814	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.83837	-1.77	5.79	5.79	0.91817	.	0.000000	0.52532	D	0.000069	T	0.25531	0.0621	L	0.51422	1.61	0.09310	P	0.9999999874095	D	0.89917	1.0	D	0.74674	0.984	T	0.69187	-0.5211	9	0.87932	D	0	.	20.0313	0.97540	0.0:0.0:1.0:0.0	rs59371099;rs61742192	463	P12036	NFH_HUMAN	K	463	ENSP00000311997:E463K	ENSP00000311997:E463K	E	+	1	0	NEFH	28215016	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.354000	0.73036	2.746000	0.94184	0.655000	0.94253	GAG	G|0.941;A|0.059	0.059	strong		0.493	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
WASL	8976	hgsc.bcm.edu	37	7	123332793	123332793	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:123332793T>A	ENST00000223023.4	-	9	1287	c.955A>T	c.(955-957)Aca>Tca	p.T319S		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	319	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGTGCAGCTGTGGGAGCTCTT	0.642																																					p.T319S		Atlas-SNP	.											.	WASL	70	.	0			c.A955T						PASS	.						78.0	76.0	77.0					7																	123332793		2203	4300	6503	SO:0001583	missense	8976	exon9			CAGCTGTGGGAGC	D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.955A>T	7.37:g.123332793T>A	ENSP00000223023:p.Thr319Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	73	5	0.0684932	NM_003941	A1JUI9|Q7Z746	Missense_Mutation	SNP	ENST00000223023.4	37	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	T	8.371	0.835392	0.16820	.	.	ENSG00000106299	ENST00000223023	D	0.91180	-2.8	5.39	2.92	0.33932	.	0.235349	0.41938	N	0.000787	T	0.80352	0.4607	N	0.20881	0.62	0.44067	D	0.996816	B	0.06786	0.001	B	0.04013	0.001	T	0.67197	-0.5731	10	0.06625	T	0.88	-12.2313	10.6239	0.45495	0.2563:0.0:0.0:0.7437	.	319	O00401	WASL_HUMAN	S	319	ENSP00000223023:T319S	ENSP00000223023:T319S	T	-	1	0	WASL	123120029	0.958000	0.32768	0.997000	0.53966	0.999000	0.98932	1.689000	0.37700	0.315000	0.23110	0.524000	0.50904	ACA	.	.	none		0.642	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941	
AHNAK	79026	hgsc.bcm.edu	37	11	62299945	62299945	+	Silent	SNP	A	A	C	rs11231130	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62299945A>C	ENST00000378024.4	-	5	2218	c.1944T>G	c.(1942-1944)gtT>gtG	p.V648V	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	648					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GAGTCATATGAACATCTGGAC	0.502													a|||	422	0.0842652	0.2534	0.036	5008	,	,		19386	0.0119		0.0258	False		,,,				2504	0.0245				p.V648V		Atlas-SNP	.											.	AHNAK	532	.	0			c.T1944G						PASS	.	C	,	948,3456	735.5+/-410.7	102,744,1356	128.0	125.0	126.0		1944,	-3.5	0.0	11	dbSNP_120	126	226,8372	809.2+/-407.2	4,218,4077	no	coding-synonymous,intron	AHNAK	NM_001620.1,NM_024060.2	,	106,962,5433	CC,CA,AA		2.6285,21.5259,9.0294	,	648/5891,	62299945	1174,11828	2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			CATATGAACATCT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.1944T>G	11.37:g.62299945A>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																			A|0.906;C|0.094	0.094	strong		0.502	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
BACH1	571	hgsc.bcm.edu	37	21	30699557	30699557	+	Missense_Mutation	SNP	G	G	C	rs35766001	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:30699557G>C	ENST00000399921.1	+	3	1655	c.1412G>C	c.(1411-1413)gGc>gCc	p.G471A	BACH1_ENST00000286800.3_Missense_Mutation_p.G471A	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0					DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						AGTACTGAAGGCTGTTCAAGC	0.423													G|||	40	0.00798722	0.0015	0.0173	5008	,	,		20941	0.0		0.0119	False		,,,				2504	0.0143				p.G471A		Atlas-SNP	.											.	BACH1	66	.	0			c.G1412C						PASS	.	G	ALA/GLY,ALA/GLY	20,4386	26.2+/-53.5	0,20,2183	124.0	119.0	121.0		1412,1412	2.2	1.0	21	dbSNP_126	121	141,8459	71.0+/-133.6	1,139,4160	yes	missense,missense	BACH1	NM_001186.2,NM_206866.1	60,60	1,159,6343	CC,CG,GG		1.6395,0.4539,1.2379	benign,benign	471/737,471/737	30699557	161,12845	2203	4300	6503	SO:0001583	missense	571	exon3			CTGAAGGCTGTTC	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.1412G>C	21.37:g.30699557G>C	ENSP00000382805:p.Gly471Ala	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	190	98	0.515789	NM_206866	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000399921.1	37	CCDS13585.1	17|17	0.007783882783882784|0.007783882783882784	0|0	0.0|0.0	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	G|G	12.49|12.49	1.952889|1.952889	0.34471|0.34471	0.004539|0.004539	0.016395|0.016395	ENSG00000156273|ENSG00000156273	ENST00000286800;ENST00000399921|ENST00000422809	T;T|.	0.71461|.	-0.57;-0.57|.	5.48|5.48	2.16|2.16	0.27623|0.27623	.|.	0.249525|.	0.34853|.	N|.	0.003632|.	T|T	0.38931|0.38931	0.1059|0.1059	L|L	0.44542|0.44542	1.39|1.39	0.40301|0.40301	D|D	0.978604|0.978604	B|.	0.20052|.	0.041|.	B|.	0.15052|.	0.012|.	T|T	0.41161|0.41161	-0.9524|-0.9524	10|5	0.05436|.	T|.	0.98|.	-16.108|-16.108	10.9423|10.9423	0.47281|0.47281	0.0764:0.2453:0.6782:0.0|0.0764:0.2453:0.6782:0.0	rs35766001|rs35766001	471|.	O14867|.	BACH1_HUMAN|.	A|S	471|36	ENSP00000286800:G471A;ENSP00000382805:G471A|.	ENSP00000286800:G471A|.	G|R	+|+	2|3	0|2	BACH1|BACH1	29621428|29621428	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.990000|0.990000	0.78478|0.78478	1.712000|1.712000	0.37940|0.37940	0.648000|0.648000	0.30732|0.30732	-0.176000|-0.176000	0.13171|0.13171	GGC|AGG	G|0.989;C|0.011	0.011	strong		0.423	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866	
LILRB3	11025	hgsc.bcm.edu	37	19	54726241	54726241	+	Missense_Mutation	SNP	C	C	T	rs77279742	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54726241C>T	ENST00000391750.1	-	4	400	c.264G>A	c.(262-264)atG>atA	p.M88I	LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.M88I|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000346401.6_Missense_Mutation_p.M88I|LILRB3_ENST00000424807.1_Missense_Mutation_p.M88I|LILRA6_ENST00000391735.3_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	88	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGTGCTCTGTCATGGATGGGA	0.562													.|||	2272	0.453674	0.5325	0.4265	5008	,	,		12679	0.4871		0.4046	False		,,,				2504	0.3824				p.M88I		Atlas-SNP	.											LILRB3,NS,haematopoietic_neoplasm,0,2	LILRB3	67	2	0			c.G264A						PASS	.	C	ILE/MET,ILE/MET	2307,1735		841,625,555	85.0	121.0	109.0		264,264	0.8	0.0	19	dbSNP_131	109	3530,4528		697,2136,1196	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	10,10	1538,2761,1751	TT,TC,CC		43.8074,42.9243,48.2397	benign,benign	88/633,88/632	54726241	5837,6263	2021	4029	6050	SO:0001583	missense	11025	exon3			CTCTGTCATGGAT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.264G>A	19.37:g.54726241C>T	ENSP00000375630:p.Met88Ile	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	424	179	0.42217	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	930	0.4258241758241758	254	0.516260162601626	141	0.38950276243093923	263	0.4597902097902098	272	0.35883905013192613	C	4.046	0.006136	0.07866	0.570757	0.438074	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000445347	T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88	3.08	0.77	0.18497	Immunoglobulin-like fold (1);	0.442058	0.21614	N	0.071749	T	0.00012	0.0000	M	0.75884	2.315	0.80722	P	0.0	P;B	0.43352	0.804;0.06	B;B	0.35655	0.087;0.207	T	0.38993	-0.9635	9	0.23891	T	0.37	.	8.9029	0.35505	0.0:0.5451:0.4549:0.0	.	88;88	O75022;O75022-3	LIRB3_HUMAN;.	I	88	ENSP00000375630:M88I;ENSP00000412771:M88I;ENSP00000345184:M88I;ENSP00000245620:M88I;ENSP00000388199:M88I	ENSP00000245620:M88I	M	-	3	0	LILRB3	59418053	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.092000	0.15066	0.300000	0.22699	0.573000	0.79308	ATG	C|0.581;T|0.419	0.419	strong		0.562	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
RANBP2	5903	hgsc.bcm.edu	37	2	109367844	109367844	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:109367844T>G	ENST00000283195.6	+	10	1524	c.1398T>G	c.(1396-1398)caT>caG	p.H466Q		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	466					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.H466Q(6)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						ATTTGCCCCATGAAACCTCAA	0.358																																					p.H466Q		Atlas-SNP	.											RANBP2_ENST00000283195,NS,carcinoma,0,6	RANBP2	488	6	6	Substitution - Missense(6)	endometrium(6)	c.T1398G						scavenged	.						69.0	78.0	75.0					2																	109367844		1510	2703	4213	SO:0001583	missense	5903	exon10			GCCCCATGAAACC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.1398T>G	2.37:g.109367844T>G	ENSP00000283195:p.His466Gln	Somatic	1235	11	0.00890688		WXS	Illumina HiSeq	Phase_I	1255	18	0.0143426	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	G	2.180	-0.387877	0.04932	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	D	0.82526	-1.62	5.25	2.44	0.29823	.	.	.	.	.	T	0.43545	0.1252	N	0.00197	-1.87	0.20563	N	0.999888	B	0.02656	0.0	B	0.01281	0.0	T	0.50039	-0.8874	9	0.02654	T	1	-0.0972	5.4961	0.16804	0.3195:0.0:0.5396:0.1409	.	466	P49792	RBP2_HUMAN	Q	466	ENSP00000283195:H466Q	ENSP00000283195:H466Q	H	+	3	2	RANBP2	108734276	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.307000	0.43682	0.319000	0.23209	-0.127000	0.14921	CAT	.	.	weak		0.358	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
ABCA12	26154	hgsc.bcm.edu	37	2	215820013	215820013	+	Silent	SNP	G	G	A	rs10498027	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:215820013G>A	ENST00000272895.7	-	43	6525	c.6306C>T	c.(6304-6306)taC>taT	p.Y2102Y	ABCA12_ENST00000389661.4_Silent_p.Y1784Y|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2102					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TGACACAGACGTAAGTGATGA	0.408													A|||	1753	0.35004	0.3018	0.3905	5008	,	,		19189	0.2341		0.3956	False		,,,				2504	0.4591				p.Y2102Y	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C6306T						PASS	.	A	,	1389,3017	688.5+/-405.0	221,947,1035	99.0	87.0	91.0		5352,6306	-3.9	0.9	2	dbSNP_119	91	3582,5018	627.9+/-398.0	762,2058,1480	no	coding-synonymous,coding-synonymous	ABCA12	NM_015657.3,NM_173076.2	,	983,3005,2515	AA,AG,GG		41.6512,31.5252,38.2208	,	1784/2278,2102/2596	215820013	4971,8035	2203	4300	6503	SO:0001819	synonymous_variant	26154	exon43			ACAGACGTAAGTG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.6306C>T	2.37:g.215820013G>A		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	292	134	0.458904	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																			G|0.660;A|0.340	0.340	strong		0.408	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
FAM78A	286336	hgsc.bcm.edu	37	9	134136248	134136248	+	Silent	SNP	G	G	A	rs9966	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:134136248G>A	ENST00000372271.3	-	2	1180	c.813C>T	c.(811-813)taC>taT	p.Y271Y	FAM78A_ENST00000372269.3_Silent_p.Y268Y|FAM78A_ENST00000247295.4_5'UTR	NM_033387.3	NP_203745.2	Q5JUQ0	FA78A_HUMAN	family with sequence similarity 78, member A	271										NS(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.15e-05)|Epithelial(140;0.000267)		GCGGCTGCCCGTACTTGGGCC	0.582													G|||	434	0.0866613	0.0182	0.0951	5008	,	,		15398	0.0129		0.1879	False		,,,				2504	0.1452				p.Y271Y		Atlas-SNP	.											.	FAM78A	28	.	0			c.C813T						PASS	.	G		246,4160	135.7+/-171.8	9,228,1966	69.0	75.0	73.0		813	1.2	1.0	9	dbSNP_52	73	1859,6741	324.6+/-316.5	204,1451,2645	no	coding-synonymous	FAM78A	NM_033387.3		213,1679,4611	AA,AG,GG		21.6163,5.5833,16.1848		271/284	134136248	2105,10901	2203	4300	6503	SO:0001819	synonymous_variant	286336	exon2			CTGCCCGTACTTG	AK095423	CCDS6941.2	9q34	2008-02-05	2005-07-18	2005-07-18	ENSG00000126882	ENSG00000126882			25465	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 59"""	C9orf59		11214971	Standard	NM_033387		Approved	FLJ00024	uc004cak.3	Q5JUQ0	OTTHUMG00000020821	ENST00000372271.3:c.813C>T	9.37:g.134136248G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_033387	Q86VQ9|Q9H7P4	Silent	SNP	ENST00000372271.3	37	CCDS6941.2																																																																																			G|0.872;A|0.128	0.128	strong		0.582	FAM78A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054720.1	NM_033387	
GATA4	2626	hgsc.bcm.edu	37	8	11606438	11606438	+	Silent	SNP	C	C	T	rs192122549	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11606438C>T	ENST00000335135.4	+	3	1185	c.627C>T	c.(625-627)gaC>gaT	p.D209D	GATA4_ENST00000528712.1_Silent_p.D3D|GATA4_ENST00000532059.1_Silent_p.D210D	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	209					atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		ATATGTTTGACGACTTCTCAG	0.517													C|||	2	0.000399361	0.0	0.0	5008	,	,		20917	0.0		0.002	False		,,,				2504	0.0				p.D209D		Atlas-SNP	.											.	GATA4	29	.	0			c.C627T						PASS	.	C		0,4406		0,0,2203	134.0	134.0	134.0		627	-10.2	0.2	8		134	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GATA4	NM_002052.3		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		209/443	11606438	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	2626	exon3			GTTTGACGACTTC	AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574		"""GATA zinc finger domain containing"""	4173	protein-coding gene	gene with protein product		600576	"""GATA-binding protein 4"""			7665171	Standard	NM_002052		Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.627C>T	8.37:g.11606438C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	224	105	0.46875	NM_002052	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	Silent	SNP	ENST00000335135.4	37	CCDS5983.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207587.2	NM_002052	
OR2A2	442361	hgsc.bcm.edu	37	7	143807518	143807518	+	Silent	SNP	T	T	C	rs2951315	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143807518T>C	ENST00000408979.2	+	1	912	c.843T>C	c.(841-843)aaT>aaC	p.N281N		NM_001005480.2	NP_001005480.2	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A, member 2	281						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)|skin(4)	22	Melanoma(164;0.0783)					GTGTCTTTAATCCAATGCTGA	0.502													-|||	2503	0.4998	0.3525	0.6095	5008	,	,		17300	0.7391		0.3191	False		,,,				2504	0.5603				p.N281N		Atlas-SNP	.											.	OR2A2	48	.	0			c.T843C						PASS	.	T		1319,2615		227,865,875	154.0	148.0	150.0		843	-1.7	0.0	7	dbSNP_101	150	2681,5669		449,1783,1943	no	coding-synonymous	OR2A2	NM_001005480.2		676,2648,2818	CC,CT,TT		32.1078,33.5282,32.5627		281/319	143807518	4000,8284	1967	4175	6142	SO:0001819	synonymous_variant	442361	exon1			CTTTAATCCAATG		CCDS43671.1	7q35	2013-09-20		2004-03-10	ENSG00000221989	ENSG00000221989		"""GPCR / Class A : Olfactory receptors"""	8230	protein-coding gene	gene with protein product				OR2A2P, OR2A17P			Standard	NM_001005480		Approved	OST008	uc011ktz.2	Q6IF42	OTTHUMG00000158001	ENST00000408979.2:c.843T>C	7.37:g.143807518T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	128	56	0.4375	NM_001005480	B2RN85|Q8NGT6	Silent	SNP	ENST00000408979.2	37	CCDS43671.1																																																																																			T|0.585;C|0.415	0.415	strong		0.502	OR2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349978.1		
ASMTL	8623	hgsc.bcm.edu	37	X	1531687	1531687	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:1531687T>C	ENST00000381317.3	-	12	1615	c.1583A>G	c.(1582-1584)cAt>cGt	p.H528R	ASMTL_ENST00000381333.4_Missense_Mutation_p.H512R|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL_ENST00000416733.2_Missense_Mutation_p.H452R|ASMTL-AS1_ENST00000425740.2_RNA|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL_ENST00000534940.1_Missense_Mutation_p.H470R|ASMTL-AS1_ENST00000602357.1_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	528	ASMT-like.					cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGGCCAGTCATGCAGGATCCG	0.542													t|||	69	0.013778	0.0053	0.0101	5008	,	,		17057	0.0		0.0537	False		,,,				2504	0.001				p.H528R		Atlas-SNP	.											.	ASMTL	56	.	0			c.A1583G						PASS	.		ARG/HIS,ARG/HIS,ARG/HIS	65,4009		1,63,1973	178.0	189.0	186.0		1409,1535,1583	1.4	0.1	X	dbSNP_134	186	651,7731		26,599,3566	no	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	29,29,29	27,662,5539	CC,CT,TT		7.7666,1.5955,5.7482	probably-damaging,probably-damaging,probably-damaging	470/564,512/606,528/622	1531687	716,11740	2037	4191	6228	SO:0001583	missense	8623	exon12			CAGTCATGCAGGA	Y15521	CCDS43917.1, CCDS55362.1, CCDS55363.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000169093	ENSG00000169093		"""Pseudoautosomal regions / PAR1"""	751	protein-coding gene	gene with protein product		300162, 400011				9736779	Standard	NM_004192		Approved		uc004cpx.2	O95671	OTTHUMG00000021057	ENST00000381317.3:c.1583A>G	X.37:g.1531687T>C	ENSP00000370718:p.His528Arg	Somatic	453	0	0		WXS	Illumina HiSeq	Phase_I	285	261	0.915789	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	52	0.023809523809523808	0	0.0	4	0.011049723756906077	0	0.0	48	0.0633245382585752	N	9.505	1.104249	0.20632	0.015955	0.077666	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	1.43	1.43	0.22495	O-methyltransferase, family 2 (1);	0.218384	0.37437	U	0.002092	T	0.05731	0.0150	M	0.88775	2.98	0.34823	D	0.738929	D;D;D	0.89917	1.0;0.994;0.995	D;P;P	0.81914	0.995;0.836;0.898	T	0.48559	-0.9025	10	0.87932	D	0	.	8.1988	0.31413	0.0:0.0:0.0:1.0	.	452;512;528	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	R	452;470;512;528	ENSP00000410578:H452R;ENSP00000446410:H470R;ENSP00000370734:H512R;ENSP00000370718:H528R	ENSP00000370718:H528R	H	-	2	0	ASMTL	1491687	1.000000	0.71417	0.077000	0.20336	0.000000	0.00434	3.601000	0.54059	0.431000	0.26258	0.000000	0.15137	CAT	T|0.962;C|0.038	0.038	strong		0.542	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
TWSG1	57045	hgsc.bcm.edu	37	18	9359990	9359990	+	Silent	SNP	G	G	A	rs142770364	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:9359990G>A	ENST00000262120.5	+	3	335	c.144G>A	c.(142-144)ccG>ccA	p.P48P	TWSG1_ENST00000581641.1_Silent_p.P48P	NM_020648.5	NP_065699.1	Q9GZX9	TWSG1_HUMAN	twisted gastrulation BMP signaling modulator 1	48	Cys-rich.				BMP signaling pathway (GO:0030509)|camera-type eye development (GO:0043010)|cell differentiation (GO:0030154)|forebrain development (GO:0030900)|hemopoiesis (GO:0030097)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of BMP signaling pathway (GO:0030513)|salivary gland morphogenesis (GO:0007435)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.P48P(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|pancreas(2)	10						AGTGCCGGCCGGGAGAAGGCA	0.458													G|||	9	0.00179712	0.0	0.0043	5008	,	,		15709	0.0		0.006	False		,,,				2504	0.0				p.P48P		Atlas-SNP	.											TWSG1,NS,carcinoma,0,1	TWSG1	23	1	1	Substitution - coding silent(1)	pancreas(1)	c.G144A						PASS	.	G		5,4401	8.1+/-20.4	0,5,2198	102.0	97.0	99.0		144	-8.9	0.2	18	dbSNP_134	99	67,8533	40.8+/-97.7	0,67,4233	no	coding-synonymous	TWSG1	NM_020648.5		0,72,6431	AA,AG,GG		0.7791,0.1135,0.5536		48/224	9359990	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	57045	exon3			CCGGCCGGGAGAA	AA486291	CCDS11844.1	18p11.3	2013-10-03	2013-10-03		ENSG00000128791	ENSG00000128791			12429	protein-coding gene	gene with protein product		605049	"""twisted gastrulation homolog 1 (Drosophila)"""			11260715	Standard	NM_020648		Approved	TSG	uc002knz.3	Q9GZX9	OTTHUMG00000131597	ENST00000262120.5:c.144G>A	18.37:g.9359990G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_020648	B2RE08|D3DUH9|Q8NBI7|Q96K46	Silent	SNP	ENST00000262120.5	37	CCDS11844.1																																																																																			G|0.995;A|0.005	0.005	strong		0.458	TWSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254480.2		
CHSY1	22856	hgsc.bcm.edu	37	15	101717888	101717888	+	Missense_Mutation	SNP	C	C	T	rs62621399	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:101717888C>T	ENST00000254190.3	-	3	2589	c.2114G>A	c.(2113-2115)cGa>cAa	p.R705Q	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	705					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GCCACCCACTCGGACAAGATC	0.478													C|||	262	0.0523163	0.0061	0.0663	5008	,	,		19215	0.002		0.1561	False		,,,				2504	0.0501				p.R705Q		Atlas-SNP	.											CHSY1,colon,carcinoma,-1,1	CHSY1	60	1	0			c.G2114A						PASS	.	C	GLN/ARG	121,4285	90.6+/-129.3	1,119,2083	103.0	113.0	109.0		2114	4.7	0.9	15	dbSNP_129	109	1221,7379	246.0+/-274.6	96,1029,3175	yes	missense	CHSY1	NM_014918.4	43	97,1148,5258	TT,TC,CC		14.1977,2.7463,10.3183	benign	705/803	101717888	1342,11664	2203	4300	6503	SO:0001583	missense	22856	exon3			CCCACTCGGACAA	AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	17198	protein-coding gene	gene with protein product		608183	"""carbohydrate (chondroitin) synthase 1"""			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.2114G>A	15.37:g.101717888C>T	ENSP00000254190:p.Arg705Gln	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	160	77	0.48125	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Missense_Mutation	SNP	ENST00000254190.3	37	CCDS10390.1	154	0.07051282051282051	5	0.01016260162601626	29	0.08011049723756906	1	0.0017482517482517483	119	0.15699208443271767	C	11.62	1.693241	0.30052	0.027463	0.141977	ENSG00000131873	ENST00000254190;ENST00000543813	T	0.35048	1.33	5.6	4.69	0.59074	.	0.069705	0.56097	D	0.000021	T	0.00109	0.0003	N	0.25647	0.755	0.21147	P	0.999773402	P	0.48016	0.904	B	0.39771	0.309	T	0.12502	-1.0545	9	0.12103	T	0.63	-20.3917	14.5886	0.68347	0.0:0.9297:0.0:0.0703	rs62621399	705	Q86X52	CHSS1_HUMAN	Q	705;433	ENSP00000254190:R705Q	ENSP00000254190:R705Q	R	-	2	0	CHSY1	99535411	0.939000	0.31865	0.923000	0.36655	0.963000	0.63663	1.711000	0.37930	1.365000	0.46057	0.561000	0.74099	CGA	C|0.907;G|0.000;T|0.093	0.093	strong		0.478	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918	
FLVCR1	28982	hgsc.bcm.edu	37	1	213061308	213061308	+	Silent	SNP	T	T	C	rs17677416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:213061308T>C	ENST00000366971.4	+	6	1470	c.1272T>C	c.(1270-1272)taT>taC	p.Y424Y	FLVCR1_ENST00000483790.1_Intron	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	424					blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	heme transporter activity (GO:0015232)|transporter activity (GO:0005215)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2)	12				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		ACCTTAGATATATTATCATCG	0.328													T|||	60	0.0119808	0.0038	0.0216	5008	,	,		16709	0.001		0.0358	False		,,,				2504	0.0031				p.Y424Y	Esophageal Squamous(199;2235 2952 19233 26256)	Atlas-SNP	.											.	FLVCR1	31	.	0			c.T1272C						PASS	.	T		46,4360	48.2+/-83.0	1,44,2158	169.0	167.0	168.0		1272	4.7	0.5	1	dbSNP_123	168	351,8249	118.1+/-177.6	7,337,3956	no	coding-synonymous	FLVCR1	NM_014053.3		8,381,6114	CC,CT,TT		4.0814,1.044,3.0524		424/556	213061308	397,12609	2203	4300	6503	SO:0001819	synonymous_variant	28982	exon6			TAGATATATTATC	AF118637	CCDS1510.1	1q32.3	2014-05-30			ENSG00000162769	ENSG00000162769		"""Solute carriers"""	24682	protein-coding gene	gene with protein product		609144	"""ataxia, posterior column 1, with retinitis pigmentosa"""	AXPC1		10400745, 10648427, 21070897	Standard	NM_014053		Approved	FLVCR, MFSD7B, PCA	uc001hjt.3	Q9Y5Y0	OTTHUMG00000036924	ENST00000366971.4:c.1272T>C	1.37:g.213061308T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Silent	SNP	ENST00000366971.4	37	CCDS1510.1	32	0.014652014652014652	3	0.006097560975609756	9	0.024861878453038673	1	0.0017482517482517483	19	0.025065963060686015	T	0.732	-0.779740	0.02929	0.01044	0.040814	ENSG00000162769	ENST00000419102	.	.	.	5.57	4.67	0.58626	.	.	.	.	.	T	0.38983	0.1061	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57808	-0.7747	4	.	.	.	-29.414	14.4351	0.67274	0.0:0.9282:0.0:0.0718	rs17677416;rs17854550;rs17677416	.	.	.	T	223	.	.	I	+	2	0	FLVCR1	211127931	1.000000	0.71417	0.522000	0.27862	0.114000	0.19823	2.954000	0.49113	1.358000	0.45922	-0.146000	0.13790	ATA	T|0.974;C|0.026	0.026	strong		0.328	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053	
CPNE6	9362	hgsc.bcm.edu	37	14	24545375	24545375	+	Silent	SNP	C	C	T	rs2070341	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24545375C>T	ENST00000397016.2	+	12	1253	c.942C>T	c.(940-942)acC>acT	p.T314T	CPNE6_ENST00000537691.1_Silent_p.T369T|CPNE6_ENST00000216775.2_Silent_p.T314T	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	314	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		TTGACTTCACCGCCTCCAATG	0.632													C|||	1972	0.39377	0.0787	0.4625	5008	,	,		16188	0.5337		0.6193	False		,,,				2504	0.3947				p.T314T		Atlas-SNP	.											.	CPNE6	40	.	0			c.C942T						PASS	.	C		750,3656	305.2+/-288.9	63,624,1516	47.0	45.0	46.0		942	-9.8	0.4	14	dbSNP_96	46	5306,3294	643.9+/-400.0	1631,2044,625	no	coding-synonymous	CPNE6	NM_006032.2		1694,2668,2141	TT,TC,CC		38.3023,17.0222,46.5631		314/558	24545375	6056,6950	2203	4300	6503	SO:0001819	synonymous_variant	9362	exon11			CTTCACCGCCTCC	AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.942C>T	14.37:g.24545375C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	144	141	0.979167	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Silent	SNP	ENST00000397016.2	37	CCDS9607.1																																																																																			C|0.525;T|0.475	0.475	strong		0.632	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5		
MPP2	4355	hgsc.bcm.edu	37	17	41955315	41955315	+	Missense_Mutation	SNP	G	G	A	rs118165424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:41955315G>A	ENST00000461854.1	-	14	1676	c.1591C>T	c.(1591-1593)Cgc>Tgc	p.R531C	MPP2_ENST00000269095.4_Missense_Mutation_p.R507C|MPP2_ENST00000520305.1_Missense_Mutation_p.R368C|MPP2_ENST00000523501.1_Missense_Mutation_p.R496C|MPP2_ENST00000377184.3_Missense_Mutation_p.R524C|MPP2_ENST00000518766.1_Missense_Mutation_p.R552C|MPP2_ENST00000536246.1_Missense_Mutation_p.R496C			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	531	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.			R -> C (in Ref. 3; BAG57760). {ECO:0000305}.	nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(4)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		CGCTGGATGCGGCTGCTCTCC	0.622													G|||	18	0.00359425	0.0008	0.0043	5008	,	,		18030	0.0		0.0139	False		,,,				2504	0.0				p.R507C		Atlas-SNP	.											MPP2,NS,carcinoma,+1,1	MPP2	67	1	0			c.C1519T						PASS	.	G	CYS/ARG	15,4391	22.3+/-47.3	0,15,2188	68.0	55.0	60.0		1519	4.2	1.0	17	dbSNP_132	60	129,8471	66.0+/-128.3	3,123,4174	yes	missense	MPP2	NM_005374.3	180	3,138,6362	AA,AG,GG		1.5,0.3404,1.1072	probably-damaging	507/553	41955315	144,12862	2203	4300	6503	SO:0001583	missense	4355	exon13			GGATGCGGCTGCT		CCDS11471.1, CCDS62206.1, CCDS62207.1, CCDS62208.1, CCDS62209.1, CCDS62210.1	17q12-q21	2008-07-18			ENSG00000108852	ENSG00000108852			7220	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 2"", ""discs large, homolog 2"""	600723		DLG2		7590743	Standard	NM_001278370		Approved	DKFZp761D0712	uc002ieo.1	Q14168	OTTHUMG00000133840	ENST00000461854.1:c.1591C>T	17.37:g.41955315G>A	ENSP00000428286:p.Arg531Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	96	59	0.614583	NM_005374	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000461854.1	37		13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	g	15.76	2.928029	0.52759	0.003404	0.015	ENSG00000108852	ENST00000377184;ENST00000269095;ENST00000461854;ENST00000520305;ENST00000523501;ENST00000536246;ENST00000518766	T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93	5.21	4.23	0.50019	.	.	.	.	.	T	0.37376	0.1001	M	0.79475	2.455	0.80722	D	1	P;P	0.42039	0.766;0.769	B;B	0.41271	0.288;0.352	T	0.39643	-0.9604	9	0.37606	T	0.19	.	11.8021	0.52133	0.0858:0.0:0.9142:0.0	.	552;524	E7EV80;Q14168-3	.;.	C	524;507;531;368;496;496;552	ENSP00000366389:R524C;ENSP00000269095:R507C;ENSP00000428286:R531C;ENSP00000428136:R368C;ENSP00000430540:R496C;ENSP00000438012:R496C;ENSP00000428182:R552C	ENSP00000269095:R507C	R	-	1	0	MPP2	39310841	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.339000	0.65953	1.203000	0.43233	0.555000	0.69702	CGC	G|0.991;A|0.009	0.009	strong		0.622	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374	
DBH	1621	hgsc.bcm.edu	37	9	136522274	136522274	+	Missense_Mutation	SNP	C	C	T	rs6271	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:136522274C>T	ENST00000393056.2	+	11	1657	c.1645C>T	c.(1645-1647)Cgc>Tgc	p.R549C	DBH-AS1_ENST00000425189.1_RNA	NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	549			R -> C (in dbSNP:rs6271). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:3443096}.		behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	CTCCTTCAACCGCGACGTACT	0.612													C|||	104	0.0207668	0.0053	0.0447	5008	,	,		16323	0.0		0.0606	False		,,,				2504	0.0051				p.R549C		Atlas-SNP	.											.	DBH	86	.	0			c.C1645T	GRCh37	CM054656	DBH	M	rs6271	PASS	.	C	CYS/ARG	57,4349	56.2+/-92.4	0,57,2146	166.0	120.0	136.0		1645	4.2	0.0	9	dbSNP_52	136	656,7944	166.4+/-218.3	25,606,3669	yes	missense	DBH	NM_000787.3	180	25,663,5815	TT,TC,CC		7.6279,1.2937,5.4821	possibly-damaging	549/618	136522274	713,12293	2203	4300	6503	SO:0001583	missense	1621	exon11			TTCAACCGCGACG	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.1645C>T	9.37:g.136522274C>T	ENSP00000376776:p.Arg549Cys	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	215	111	0.516279	NM_000787	Q5T381|Q96AG2	Missense_Mutation	SNP	ENST00000393056.2	37	CCDS6977.2	71	0.03250915750915751	1	0.0020325203252032522	26	0.0718232044198895	0	0.0	44	0.05804749340369393	C	10.61	1.397932	0.25205	0.012937	0.076279	ENSG00000123454	ENST00000393056	T	0.49432	0.78	5.07	4.16	0.48862	.	0.346260	0.30492	N	0.009514	T	0.04815	0.0130	M	0.78223	2.4	0.19300	N	0.99997	D	0.57899	0.981	P	0.47162	0.54	T	0.07888	-1.0749	10	0.54805	T	0.06	-26.8568	8.555	0.33476	0.3682:0.5038:0.128:0.0	rs6271;rs6271	549	P09172	DOPO_HUMAN	C	549	ENSP00000376776:R549C	ENSP00000376776:R549C	R	+	1	0	DBH	135512095	0.996000	0.38824	0.028000	0.17463	0.046000	0.14306	3.394000	0.52551	1.109000	0.41680	-0.500000	0.04577	CGC	C|0.956;T|0.044	0.044	strong		0.612	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
USP35	57558	hgsc.bcm.edu	37	11	77909014	77909014	+	Missense_Mutation	SNP	G	G	A	rs2510044	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:77909014G>A	ENST00000529308.1	+	3	967	c.706G>A	c.(706-708)Gtg>Atg	p.V236M	USP35_ENST00000530267.1_Intron|USP35_ENST00000530535.1_Intron|USP35_ENST00000441408.2_5'UTR|USP35_ENST00000526425.1_5'Flank	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	236			V -> M (in dbSNP:rs2510044).		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			CCTGGCCAGCGTGGTCCAGCA	0.612													G|||	1022	0.204073	0.0325	0.2968	5008	,	,		21718	0.3591		0.1561	False		,,,				2504	0.2597				p.V236M		Atlas-SNP	.											.	USP35	179	.	0			c.G706A						PASS	.	G	MET/VAL	179,4141		7,165,1988	64.0	69.0	67.0		706	4.8	1.0	11	dbSNP_100	67	1165,7347		80,1005,3171	yes	missense	USP35	NM_020798.2	21	87,1170,5159	AA,AG,GG		13.6866,4.1435,10.4738	probably-damaging	236/1019	77909014	1344,11488	2160	4256	6416	SO:0001583	missense	57558	exon3			GCCAGCGTGGTCC	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.706G>A	11.37:g.77909014G>A	ENSP00000431876:p.Val236Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	442	0.20238095238095238	21	0.042682926829268296	88	0.2430939226519337	209	0.36538461538461536	124	0.16358839050131926	G	11.80	1.745434	0.30955	0.041435	0.136866	ENSG00000118369	ENST00000529308	T	0.46451	0.87	4.82	4.82	0.62117	Armadillo-like helical (1);	0.311212	0.22400	N	0.060547	T	0.00012	0.0000	L	0.48642	1.525	0.09310	P	1.0	D	0.76494	0.999	P	0.59703	0.862	T	0.26815	-1.0092	9	0.72032	D	0.01	-35.837	18.1059	0.89520	0.0:0.0:1.0:0.0	rs2510044;rs58071390;rs2510044	236	Q9P2H5	UBP35_HUMAN	M	236	ENSP00000431876:V236M	ENSP00000431876:V236M	V	+	1	0	USP35	77586662	1.000000	0.71417	0.992000	0.48379	0.090000	0.18270	5.378000	0.66190	2.506000	0.84524	0.561000	0.74099	GTG	G|0.802;A|0.198	0.198	strong		0.612	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
NCKAP5	344148	hgsc.bcm.edu	37	2	133538703	133538703	+	Silent	SNP	G	G	A	rs61742426	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:133538703G>A	ENST00000409261.1	-	15	5344	c.4971C>T	c.(4969-4971)ggC>ggT	p.G1657G	NCKAP5_ENST00000317721.6_Silent_p.G1657G|NCKAP5_ENST00000473859.1_5'UTR|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1657										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TGATAGAGCTGCCGATGAGAC	0.458													G|||	8	0.00159744	0.0	0.0	5008	,	,		17507	0.0		0.008	False		,,,				2504	0.0				p.G1657G		Atlas-SNP	.											.	NCKAP5	322	.	0			c.C4971T						PASS	.	G	,	5,3821		0,5,1908	94.0	97.0	96.0		4971,	5.3	0.0	2	dbSNP_129	96	55,8203		1,53,4075	no	coding-synonymous,intron	NCKAP5	NM_207363.2,NM_207481.3	,	1,58,5983	AA,AG,GG		0.666,0.1307,0.4965	,	1657/1910,	133538703	60,12024	1913	4129	6042	SO:0001819	synonymous_variant	344148	exon15			AGAGCTGCCGATG	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.4971C>T	2.37:g.133538703G>A		Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	434	219	0.504608	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			G|0.996;A|0.004	0.004	strong		0.458	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
ADAMTS17	170691	hgsc.bcm.edu	37	15	100801698	100801698	+	Silent	SNP	G	G	A	rs4965613	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:100801698G>A	ENST00000268070.4	-	6	1122	c.1017C>T	c.(1015-1017)gcC>gcT	p.A339A	ADAMTS17_ENST00000559976.1_5'UTR	NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	339	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		TCACAAACACGGCAGCATCCA	0.537													A|||	3466	0.692093	0.7027	0.7061	5008	,	,		20936	0.622		0.6948	False		,,,				2504	0.7372				p.A339A		Atlas-SNP	.											ADAMTS17,NS,carcinoma,-1,1	ADAMTS17	127	1	0			c.C1017T						PASS	.	A		3039,1367	453.8+/-350.4	1059,921,223	75.0	64.0	68.0		1017	-1.2	0.6	15	dbSNP_111	68	5727,2873	450.1+/-362.3	1913,1901,486	no	coding-synonymous	ADAMTS17	NM_139057.2		2972,2822,709	AA,AG,GG		33.407,31.0259,32.6003		339/1096	100801698	8766,4240	2203	4300	6503	SO:0001819	synonymous_variant	170691	exon6			AAACACGGCAGCA	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.1017C>T	15.37:g.100801698G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_139057	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	37	CCDS10383.1																																																																																			G|0.331;A|0.669	0.669	strong		0.537	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
USP2	9099	hgsc.bcm.edu	37	11	119243670	119243670	+	Missense_Mutation	SNP	C	C	T	rs33929148	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:119243670C>T	ENST00000260187.2	-	2	815	c.521G>A	c.(520-522)cGg>cAg	p.R174Q	RP11-334E6.3_ENST00000530918.2_RNA|USP2_ENST00000455332.2_Intron	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	174	Necessary for interaction with MDM4.		R -> Q (in dbSNP:rs33929148).		cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		CTTGCGCGTCCGGGCCAGCAT	0.632													C|||	97	0.019369	0.003	0.0259	5008	,	,		16368	0.001		0.0596	False		,,,				2504	0.0143				p.R174Q		Atlas-SNP	.											.	USP2	71	.	0			c.G521A						PASS	.	C	GLN/ARG	60,4338	58.1+/-94.6	1,58,2140	55.0	60.0	59.0		521	5.5	1.0	11	dbSNP_126	59	573,8017	151.2+/-206.0	22,529,3744	yes	missense	USP2	NM_004205.4	43	23,587,5884	TT,TC,CC		6.6705,1.3643,4.8737	benign	174/606	119243670	633,12355	2199	4295	6494	SO:0001583	missense	9099	exon2			CGCGTCCGGGCCA	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.521G>A	11.37:g.119243670C>T	ENSP00000260187:p.Arg174Gln	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Missense_Mutation	SNP	ENST00000260187.2	37	CCDS8422.1	61	0.027930402930402932	2	0.0040650406504065045	15	0.04143646408839779	3	0.005244755244755245	41	0.05408970976253298	C	15.75	2.925239	0.52759	0.013643	0.066705	ENSG00000036672	ENST00000260187;ENST00000530918	T	0.18174	2.23	5.52	5.52	0.82312	.	6.086370	0.00357	N	0.000022	T	0.01489	0.0048	N	0.14661	0.345	0.80722	D	1	D	0.76494	0.999	P	0.50314	0.637	T	0.09037	-1.0693	10	0.35671	T	0.21	-6.1444	12.9227	0.58241	0.0:0.8245:0.1755:0.0	rs33929148	174	O75604	UBP2_HUMAN	Q	174;144	ENSP00000260187:R174Q	ENSP00000260187:R174Q	R	-	2	0	USP2	118748880	0.431000	0.25546	1.000000	0.80357	0.840000	0.47671	0.733000	0.26087	2.578000	0.87016	0.655000	0.94253	CGG	C|0.963;T|0.037	0.037	strong		0.632	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997	
LPHN1	22859	hgsc.bcm.edu	37	19	14273641	14273641	+	Silent	SNP	A	A	G	rs3745462	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14273641A>G	ENST00000340736.6	-	6	1284	c.987T>C	c.(985-987)cgT>cgC	p.R329R	LPHN1_ENST00000591528.1_5'Flank|CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000592086.1_RNA|LPHN1_ENST00000361434.3_Silent_p.R324R	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	329	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CGTACACGGAACGCAGGACGT	0.612													G|||	1098	0.219249	0.4319	0.3026	5008	,	,		19441	0.0774		0.1322	False		,,,				2504	0.1084				p.R329R		Atlas-SNP	.											.	LPHN1	107	.	0			c.T987C						PASS	.	G	,	1772,2634	643.2+/-397.8	372,1028,803	130.0	88.0	102.0		987,972	0.2	1.0	19	dbSNP_107	102	1099,7501	768.0+/-407.6	86,927,3287	no	coding-synonymous,coding-synonymous	LPHN1	NM_001008701.2,NM_014921.4	,	458,1955,4090	GG,GA,AA		12.7791,40.2179,22.0744	,	329/1475,324/1470	14273641	2871,10135	2203	4300	6503	SO:0001819	synonymous_variant	22859	exon6			CACGGAACGCAGG	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.987T>C	19.37:g.14273641A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	37	CCDS32928.1																																																																																			A|0.784;G|0.216	0.216	strong		0.612	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921	
SPATA21	374955	hgsc.bcm.edu	37	1	16748432	16748432	+	Silent	SNP	C	C	T	rs114456729	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:16748432C>T	ENST00000335496.1	-	4	551	c.69G>A	c.(67-69)acG>acA	p.T23T	SPATA21_ENST00000540400.1_Intron|SPATA21_ENST00000466212.1_5'UTR	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	23							calcium ion binding (GO:0005509)	p.T23T(1)		breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		TAGGTCCAGGCGTGGATGGCA	0.562													C|||	122	0.024361	0.0015	0.036	5008	,	,		19316	0.001		0.0726	False		,,,				2504	0.0215				p.T23T		Atlas-SNP	.											SPATA21,NS,carcinoma,-1,2	SPATA21	47	2	1	Substitution - coding silent(1)	pancreas(1)	c.G69A						PASS	.	C		57,4349	54.9+/-90.9	0,57,2146	219.0	207.0	211.0		69	-2.2	0.0	1	dbSNP_132	211	600,8000	158.9+/-212.3	23,554,3723	no	coding-synonymous	SPATA21	NM_198546.1		23,611,5869	TT,TC,CC		6.9767,1.2937,5.0515		23/470	16748432	657,12349	2203	4300	6503	SO:0001819	synonymous_variant	374955	exon4			TCCAGGCGTGGAT		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"""EF-hand domain containing"""	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.69G>A	1.37:g.16748432C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	129	73	0.565891	NM_198546	B9EK40|F5GXP5	Silent	SNP	ENST00000335496.1	37	CCDS172.1																																																																																			C|0.954;T|0.046	0.046	strong		0.562	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
PLEC	5339	hgsc.bcm.edu	37	8	144995494	144995494	+	Missense_Mutation	SNP	C	C	T	rs6558407	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144995494C>T	ENST00000322810.4	-	32	9075	c.8906G>A	c.(8905-8907)cGc>cAc	p.R2969H	PLEC_ENST00000398774.2_Missense_Mutation_p.R2800H|PLEC_ENST00000345136.3_Missense_Mutation_p.R2832H|PLEC_ENST00000354589.3_Missense_Mutation_p.R2832H|PLEC_ENST00000354958.2_Missense_Mutation_p.R2810H|PLEC_ENST00000436759.2_Missense_Mutation_p.R2859H|PLEC_ENST00000527096.1_Missense_Mutation_p.R2855H|PLEC_ENST00000356346.3_Missense_Mutation_p.R2818H|PLEC_ENST00000357649.2_Missense_Mutation_p.R2836H	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2969	Globular 2.		R -> H (in dbSNP:rs6558407).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GAAGTAGCCGCGCCGGTAGGC	0.682													C|||	1155	0.230631	0.028	0.2939	5008	,	,		19137	0.1419		0.4294	False		,,,				2504	0.3466				p.R2969H		Atlas-SNP	.											.	PLEC	1144	.	0			c.G8906A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	368,3618		24,320,1649	60.0	66.0	64.0		8576,8453,8429,8906,8399,8495,8507,8495	2.1	1.0	8	dbSNP_116	64	3412,4876		720,1972,1452	no	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	29,29,29,29,29,29,29,29	744,2292,3101	TT,TC,CC		41.168,9.2323,30.7968	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	2859/4575,2818/4534,2810/4526,2969/4685,2800/4516,2832/4548,2836/4552,2832/4548	144995494	3780,8494	1993	4144	6137	SO:0001583	missense	5339	exon32			TAGCCGCGCCGGT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8906G>A	8.37:g.144995494C>T	ENSP00000323856:p.Arg2969His	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	538	0.24633699633699635	15	0.03048780487804878	108	0.2983425414364641	94	0.16433566433566432	321	0.4234828496042216	C	9.838	1.190145	0.21954	0.092323	0.41168	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25;-1.25;-1.25;-1.25;-1.25	4.95	2.11	0.27256	.	0.205118	0.33591	U	0.004744	T	0.00012	0.0000	M	0.92412	3.305	0.30565	P	0.76412	B;B;B;B;B;B;B;B	0.25007	0.095;0.095;0.095;0.116;0.095;0.095;0.095;0.095	B;B;B;B;B;B;B;B	0.14023	0.006;0.006;0.006;0.01;0.006;0.006;0.006;0.006	T	0.09015	-1.0694	9	0.54805	T	0.06	.	7.3802	0.26851	0.1365:0.7151:0.0:0.1483	rs6558407;rs6558407	2859;2818;2810;2969;2800;2832;2836;2832	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	H	2832;2836;2832;2800;2969;2810;2818;2859;2855	ENSP00000344848:R2832H;ENSP00000350277:R2836H;ENSP00000346602:R2832H;ENSP00000381756:R2800H;ENSP00000323856:R2969H;ENSP00000347044:R2810H;ENSP00000348702:R2818H;ENSP00000388180:R2859H;ENSP00000434583:R2855H	ENSP00000323856:R2969H	R	-	2	0	PLEC	145067482	0.993000	0.37304	0.985000	0.45067	0.496000	0.33645	2.910000	0.48766	0.222000	0.20900	-0.538000	0.04264	CGC	.	.	weak		0.682	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
PSMC5	5705	hgsc.bcm.edu	37	17	61908271	61908271	+	Silent	SNP	C	C	T	rs968719	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:61908271C>T	ENST00000310144.6	+	7	963	c.655C>T	c.(655-657)Ctg>Ttg	p.L219L	PSMC5_ENST00000580864.1_Silent_p.L211L|PSMC5_ENST00000375812.4_Silent_p.L211L|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000581882.1_Silent_p.L211L	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	219	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						TGGCTCTGAACTGGTACAGAA	0.507													T|||	3669	0.732628	0.9788	0.6816	5008	,	,		19973	0.5556		0.5984	False		,,,				2504	0.7566				p.L219L		Atlas-SNP	.											.	PSMC5	41	.	0			c.C655T						PASS	.	T	,	4014,392	196.0+/-220.5	1829,356,18	90.0	88.0	89.0		631,655	-3.3	0.5	17	dbSNP_86	89	5215,3385	501.6+/-375.5	1599,2017,684	no	coding-synonymous,coding-synonymous	PSMC5	NM_001199163.1,NM_002805.5	,	3428,2373,702	TT,TC,CC		39.3605,8.897,29.0404	,	211/399,219/407	61908271	9229,3777	2203	4300	6503	SO:0001819	synonymous_variant	5705	exon7			TCTGAACTGGTAC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.655C>T	17.37:g.61908271C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	134	69	0.514925	NM_002805	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Silent	SNP	ENST00000310144.6	37	CCDS11645.1																																																																																			T|0.696;G|0.002	0.696	strong		0.507	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
SLC22A18	5002	hgsc.bcm.edu	37	11	2924610	2924610	+	Missense_Mutation	SNP	G	G	A	rs1048047	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:2924610G>A	ENST00000380574.1	+	2	466	c.35G>A	c.(34-36)cGg>cAg	p.R12Q	SLC22A18AS_ENST00000455942.2_Intron|SLC22A18_ENST00000449793.2_Missense_Mutation_p.R12Q|SLC22A18AS_ENST00000533594.1_Intron|SLC22A18_ENST00000312221.5_Missense_Mutation_p.R12Q|SLC22A18_ENST00000347936.2_Missense_Mutation_p.R12Q			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	12			R -> Q (in dbSNP:rs1048047). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9520460, ECO:0000269|PubMed:9570947, ECO:0000269|Ref.6}.		drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		GACCAGGGCCGGTCCCCCGGC	0.657													A|||	3043	0.607628	0.4516	0.5908	5008	,	,		17020	0.7579		0.6014	False		,,,				2504	0.682				p.R12Q		Atlas-SNP	.											.	SLC22A18	20	.	0			c.G35A						PASS	.	A	GLN/ARG,,GLN/ARG	2107,2297	597.3+/-388.8	505,1097,600	58.0	58.0	58.0		35,,35	-1.5	0.0	11	dbSNP_86	58	4948,3650	521.1+/-379.8	1422,2104,773	yes	missense,intron,missense	SLC22A18,SLC22A18AS	NM_002555.5,NM_007105.2,NM_183233.2	43,,43	1927,3201,1373	AA,AG,GG		42.4517,47.8429,45.7391	benign,,benign	12/425,,12/425	2924610	7055,5947	2202	4299	6501	SO:0001583	missense	5002	exon2			AGGGCCGGTCCCC	AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"""Solute carriers"""	10964	protein-coding gene	gene with protein product		602631	"""solute carrier family 22 (organic cation transporter), member 1-like"""	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.35G>A	11.37:g.2924610G>A	ENSP00000369948:p.Arg12Gln	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	198	196	0.989899	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	1325	0.6066849816849816	218	0.44308943089430897	226	0.6243093922651933	422	0.7377622377622378	459	0.6055408970976254	A	1.533	-0.543878	0.04053	0.478429	0.575483	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574;ENST00000485423	T;T;T;T;T	0.54675	0.56;0.56;2.32;0.56;1.56	2.98	-1.5	0.08691	.	2.386420	0.02278	N	0.069164	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.39881	-0.9592	9	0.02654	T	1	-17.8276	3.9699	0.09449	0.3951:0.3697:0.2352:0.0	rs1048047;rs3168333;rs17845466;rs17858344;rs60355993	12;12	E9PRM7;Q96BI1	.;S22AI_HUMAN	Q	12	ENSP00000307859:R12Q;ENSP00000311139:R12Q;ENSP00000392072:R12Q;ENSP00000369948:R12Q;ENSP00000433019:R12Q	ENSP00000311139:R12Q	R	+	2	0	SLC22A18	2881186	0.007000	0.16637	0.009000	0.14445	0.079000	0.17450	0.041000	0.13927	-0.929000	0.03757	-0.521000	0.04368	CGG	G|0.425;A|0.575	0.575	strong		0.657	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233	
SLC9A8	23315	hgsc.bcm.edu	37	20	48491258	48491258	+	Silent	SNP	T	T	G	rs542234	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:48491258T>G	ENST00000361573.2	+	11	1017	c.975T>G	c.(973-975)ctT>ctG	p.L325L	SLC9A8_ENST00000417961.1_Silent_p.L341L|SLC9A8_ENST00000539601.1_Silent_p.L106L|SLC9A8_ENST00000541138.1_Silent_p.L25L			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	325					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			TGGCCATCCTTTTCTCAGGCA	0.562													G|||	4121	0.822883	0.8033	0.8256	5008	,	,		18879	0.8373		0.7952	False		,,,				2504	0.8609				p.L341L		Atlas-SNP	.											.	SLC9A8	63	.	0			c.T1023G						PASS	.	G		3476,930	355.6+/-313.1	1363,750,90	250.0	173.0	199.0		975	3.8	1.0	20	dbSNP_83	199	6819,1781	321.2+/-315.0	2705,1409,186	no	coding-synonymous	SLC9A8	NM_015266.1		4068,2159,276	GG,GT,TT		20.7093,21.1076,20.8442		325/582	48491258	10295,2711	2203	4300	6503	SO:0001819	synonymous_variant	23315	exon11			CATCCTTTTCTCA	AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"""Solute carriers"""	20728	protein-coding gene	gene with protein product		612730	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 8"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 8"""			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.975T>G	20.37:g.48491258T>G		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	255	255	1	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																			T|0.200;G|0.800	0.800	strong		0.562	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524	
CEP164	22897	hgsc.bcm.edu	37	11	117222592	117222592	+	Missense_Mutation	SNP	G	G	A	rs490262	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:117222592G>A	ENST00000278935.3	+	5	428	c.281G>A	c.(280-282)aGc>aAc	p.S94N		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	94	Interaction with ATRIP.		S -> N (in dbSNP:rs490262).		cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		CACTATCGGAGCTTGGTGATC	0.493													A|||	1053	0.210264	0.2595	0.2594	5008	,	,		17920	0.1151		0.174	False		,,,				2504	0.2444				p.S94N		Atlas-SNP	.											.	CEP164	121	.	0			c.G281A						PASS	.	A	ASN/SER	1211,3191	707.2+/-407.5	173,865,1163	102.0	90.0	94.0		281	3.7	1.0	11	dbSNP_83	94	1718,6874	737.1+/-407.0	170,1378,2748	yes	missense	CEP164	NM_014956.4	46	343,2243,3911	AA,AG,GG		19.9953,27.5102,22.5412	benign	94/1461	117222592	2929,10065	2201	4296	6497	SO:0001583	missense	22897	exon4			ATCGGAGCTTGGT	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.281G>A	11.37:g.117222592G>A	ENSP00000278935:p.Ser94Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	421	0.19276556776556777	141	0.2865853658536585	93	0.2569060773480663	63	0.11013986013986014	124	0.16358839050131926	A	8.664	0.901215	0.17760	0.275102	0.199953	ENSG00000110274	ENST00000525734;ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000527609;ENST00000533570;ENST00000529538	T;T;T;T;T;T	0.61510	0.1;0.1;0.1;0.1;0.1;0.1	5.95	3.69	0.42338	.	0.226336	0.31113	N	0.008222	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.27673	-1.0067	9	0.02654	T	1	-16.7382	9.0374	0.36296	0.7919:0.0:0.2081:0.0	rs490262;rs11565214;rs17120632;rs52807120;rs58774828;rs490262	94;48;94;94	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	N	94;48;94;48;48;94;94;94	ENSP00000436609:S94N;ENSP00000436034:S48N;ENSP00000278935:S94N;ENSP00000435759:S48N;ENSP00000436351:S94N;ENSP00000431302:S94N	ENSP00000278935:S94N	S	+	2	0	CEP164	116727802	0.000000	0.05858	0.991000	0.47740	0.996000	0.88848	0.872000	0.28037	0.527000	0.28560	-0.254000	0.11334	AGC	G|0.799;A|0.201	0.201	strong		0.493	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
RPS6KA1	6195	hgsc.bcm.edu	37	1	26887592	26887592	+	Silent	SNP	T	T	C	rs1064196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26887592T>C	ENST00000374168.2	+	16	1552	c.1398T>C	c.(1396-1398)taT>taC	p.Y466Y	RPS6KA1_ENST00000374166.4_Silent_p.Y455Y|RPS6KA1_ENST00000374162.2_Silent_p.Y374Y|RPS6KA1_ENST00000526792.1_Silent_p.Y374Y|RPS6KA1_ENST00000531382.1_Silent_p.Y475Y|RPS6KA1_ENST00000530003.1_Silent_p.Y450Y	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	466	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		TTCTGCGGTATGGCCAGCACC	0.517													C|||	2556	0.510383	0.5068	0.3646	5008	,	,		20757	0.756		0.2903	False		,,,				2504	0.592				p.Y475Y		Atlas-SNP	.											.	RPS6KA1	65	.	0			c.T1425C						PASS	.	C	,	2037,2369	610.8+/-391.6	467,1103,633	76.0	77.0	77.0		1425,1398	-6.2	0.7	1	dbSNP_86	77	2263,6337	707.5+/-405.6	299,1665,2336	no	coding-synonymous,coding-synonymous	RPS6KA1	NM_001006665.1,NM_002953.3	,	766,2768,2969	CC,CT,TT		26.314,46.2324,33.0617	,	475/745,466/736	26887592	4300,8706	2203	4300	6503	SO:0001819	synonymous_variant	6195	exon15			GCGGTATGGCCAG	BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"""ribosomal protein S6 kinase, 90kD, polypeptide 1"""			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.1398T>C	1.37:g.26887592T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_001006665	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Silent	SNP	ENST00000374168.2	37	CCDS284.1																																																																																			T|0.604;C|0.396	0.396	strong		0.517	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011431.1	NM_002953	
NEU4	129807	hgsc.bcm.edu	37	2	242758326	242758326	+	Silent	SNP	G	G	A	rs2293761	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242758326G>A	ENST00000391969.2	+	5	2118	c.1407G>A	c.(1405-1407)aaG>aaA	p.K469K	NEU4_ENST00000405370.1_Silent_p.K469K|NEU4_ENST00000325935.6_Silent_p.K482K|NEU4_ENST00000404257.1_Silent_p.K481K|NEU4_ENST00000407683.1_Silent_p.K469K	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	469					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		CCAGCCCCAAGCCGCCCAACC	0.657													G|||	2224	0.444089	0.4864	0.3458	5008	,	,		12711	0.4216		0.3847	False		,,,				2504	0.5409				p.K482K		Atlas-SNP	.											NEU4,rectum,carcinoma,0,1	NEU4	39	1	0			c.G1446A						PASS	.		,,,,	1448,1946		319,810,568	12.0	14.0	13.0		1446,1407,1407,1407,1443	3.7	0.0	2	dbSNP_100	13	2170,4686		383,1404,1641	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	,,,,	702,2214,2209	AA,AG,GG		31.6511,42.6635,35.2976	,,,,	482/498,469/485,469/485,469/485,481/497	242758326	3618,6632	1697	3428	5125	SO:0001819	synonymous_variant	129807	exon4			CCCCAAGCCGCCC	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.1407G>A	2.37:g.242758326G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001167599	A8K056|J3KNJ5|Q96D64	Silent	SNP	ENST00000391969.2	37	CCDS54442.1																																																																																			G|0.618;A|0.382	0.382	strong		0.657	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
UGT2B11	10720	hgsc.bcm.edu	37	4	70066306	70066306	+	Missense_Mutation	SNP	T	T	C	rs200852364	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:70066306T>C	ENST00000446444.1	-	6	1450	c.1442A>G	c.(1441-1443)cAt>cGt	p.H481R	RP11-704M14.1_ENST00000505646.1_RNA|RP11-704M14.1_ENST00000504301.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	481					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						GGTGAGGTCATGGGCTGCAAC	0.463																																					p.H481R		Atlas-SNP	.											.	UGT2B11	92	.	0			c.A1442G						PASS	.						128.0	123.0	124.0					4																	70066306		2203	4300	6503	SO:0001583	missense	10720	exon6			AGGTCATGGGCTG	AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.1442A>G	4.37:g.70066306T>C	ENSP00000387683:p.His481Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	154	16	0.103896	NM_001073	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	.	.	.	.	.	.	.	.	.	.	-	2.143	-0.396340	0.04899	.	.	ENSG00000213759	ENST00000446444	T	0.61859	0.07	1.27	-0.615	0.11587	.	0.080367	0.49305	N	0.000142	T	0.52419	0.1733	M	0.73598	2.24	0.18873	N	0.999981	B	0.23185	0.081	B	0.28638	0.092	T	0.51220	-0.8733	10	0.66056	D	0.02	.	6.3349	0.21291	0.0:0.1865:0.0:0.8135	.	481	O75310	UDB11_HUMAN	R	481	ENSP00000387683:H481R	ENSP00000387683:H481R	H	-	2	0	UGT2B11	70100895	0.998000	0.40836	0.158000	0.22627	0.020000	0.10135	3.239000	0.51360	-0.460000	0.07003	-2.767000	0.00120	CAT	T|0.967;C|0.032	0.032	strong		0.463	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
TEK	7010	hgsc.bcm.edu	37	9	27213580	27213580	+	Silent	SNP	T	T	C	rs3737188	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:27213580T>C	ENST00000380036.4	+	18	3418	c.2976T>C	c.(2974-2976)taT>taC	p.Y992Y	TEK_ENST00000406359.4_Silent_p.Y949Y|TEK_ENST00000519097.1_Silent_p.Y844Y	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	992	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	AAGAGGTGTATGTGAAAAAGA	0.458													T|||	770	0.153754	0.0651	0.1787	5008	,	,		19621	0.1925		0.2008	False		,,,				2504	0.1677				p.Y992Y		Atlas-SNP	.											.	TEK	250	.	0			c.T2976C						PASS	.	T		453,3953	215.5+/-234.4	27,399,1777	125.0	121.0	122.0		2976	0.6	1.0	9	dbSNP_107	122	1873,6727	335.0+/-321.2	190,1493,2617	no	coding-synonymous	TEK	NM_000459.3		217,1892,4394	CC,CT,TT		21.7791,10.2814,17.8841		992/1125	27213580	2326,10680	2203	4300	6503	SO:0001819	synonymous_variant	7010	exon18			GGTGTATGTGAAA	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2976T>C	9.37:g.27213580T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																			T|0.835;C|0.165	0.165	strong		0.458	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
TNFRSF9	3604	hgsc.bcm.edu	37	1	7995152	7995152	+	Silent	SNP	G	G	A	rs373859958		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:7995152G>A	ENST00000377507.3	-	6	631	c.465C>T	c.(463-465)gaC>gaT	p.D155D		NM_001561.5	NP_001552.2	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily, member 9	155					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		CACAGACCACGTCCCTCTCCT	0.502																																					p.D155D		Atlas-SNP	.											.	TNFRSF9	50	.	0			c.C465T						PASS	.						105.0	88.0	94.0					1																	7995152		2203	4300	6503	SO:0001819	synonymous_variant	3604	exon7			GACCACGTCCCTC	L12964	CCDS92.1	1p36	2008-02-05			ENSG00000049249	ENSG00000049249		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11924	protein-coding gene	gene with protein product		602250		ILA		8262389, 8639902	Standard	NM_001561		Approved	CD137, 4-1BB	uc001aot.3	Q07011	OTTHUMG00000001223	ENST00000377507.3:c.465C>T	1.37:g.7995152G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	130	56	0.430769	NM_001561		Silent	SNP	ENST00000377507.3	37	CCDS92.1																																																																																			.	.	none		0.502	TNFRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003622.1		
LRWD1	222229	hgsc.bcm.edu	37	7	102113226	102113226	+	Missense_Mutation	SNP	C	C	T	rs148981077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:102113226C>T	ENST00000292616.5	+	14	1930	c.1778C>T	c.(1777-1779)cCg>cTg	p.P593L	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	593					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						CCCCTGCTGCCGGCAGCCCTG	0.657													C|||	91	0.0181709	0.0008	0.0202	5008	,	,		15520	0.0		0.0417	False		,,,				2504	0.0348				p.P593L		Atlas-SNP	.											.	LRWD1	41	.	0			c.C1778T						PASS	.	C	LEU/PRO	49,4355	49.6+/-84.7	0,49,2153	27.0	29.0	28.0		1778	-3.2	0.0	7	dbSNP_134	28	397,8203	124.4+/-183.2	11,375,3914	yes	missense	LRWD1	NM_152892.1	98	11,424,6067	TT,TC,CC		4.6163,1.1126,3.4297	benign	593/648	102113226	446,12558	2202	4300	6502	SO:0001583	missense	222229	exon14			TGCTGCCGGCAGC	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"""WD repeat domain containing"""	21769	protein-coding gene	gene with protein product	"""origin recognition complex associated"", ""centromere protein 33"""	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.1778C>T	7.37:g.102113226C>T	ENSP00000292616:p.Pro593Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Missense_Mutation	SNP	ENST00000292616.5	37	CCDS34715.1	41|41	0.018772893772893772|0.018772893772893772	0|0	0.0|0.0	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	34|34	0.044854881266490766|0.044854881266490766	C|C	10.41|10.41	1.343116|1.343116	0.24339|0.24339	0.011126|0.011126	0.046163|0.046163	ENSG00000161036|ENSG00000161036	ENST00000292616|ENST00000488689;ENST00000468175	T|.	0.61158|.	0.13|.	4.84|4.84	-3.22|-3.22	0.05125|0.05125	.|.	1.243750|.	0.05070|.	N|.	0.481534|.	T|T	0.01421|0.01421	0.0046|0.0046	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.23476|0.23476	-1.0187|-1.0187	10|5	0.26408|.	T|.	0.33|.	-8.2538|-8.2538	1.2114|1.2114	0.01905|0.01905	0.4387:0.2221:0.1196:0.2197|0.4387:0.2221:0.1196:0.2197	.|.	593|.	Q9UFC0|.	LRWD1_HUMAN|.	L|W	593|204;179	ENSP00000292616:P593L|.	ENSP00000292616:P593L|.	P|R	+|+	2|1	0|2	LRWD1|LRWD1	101900231|101900231	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.026000|0.026000	0.11368|0.11368	-2.426000|-2.426000	0.01027|0.01027	-0.794000|-0.794000	0.04468|0.04468	0.555000|0.555000	0.69702|0.69702	CCG|CGG	C|0.972;T|0.028	0.028	strong		0.657	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
CYP2D6	1565	hgsc.bcm.edu	37	22	42526694	42526694	+	Missense_Mutation	SNP	G	G	A	rs1065852	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:42526694G>A	ENST00000360608.5	-	1	214	c.100C>T	c.(100-102)Cca>Tca	p.P34S	CYP2D6_ENST00000389970.3_Missense_Mutation_p.P34S|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.P34S|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000608288.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	34			P -> S (in allele CYP2D6*10 and allele CYP2D6*14; poor debrisquone metabolism; dbSNP:rs1065852). {ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:8287064}.		alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GGGCCTGGTGGGTAGCGTGCA	0.642													G|||	1192	0.238019	0.1127	0.1484	5008	,	,		19317	0.5714		0.2018	False		,,,				2504	0.1646				p.P34S		Atlas-SNP	.											.	CYP2D6	104	.	0			c.C100T	GRCh37	CM900081	CYP2D6	M	rs1065852	PASS	.	G	SER/PRO,SER/PRO	525,3867	221.0+/-238.3	63,399,1734	48.0	38.0	41.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	100,100	3.5	0.9	22	dbSNP_86	41	1924,6674	321.5+/-315.1	249,1426,2624	no	missense,missense	CYP2D6	NM_000106.4,NM_001025161.1	74,74	312,1825,4358	AA,AG,GG		22.3773,11.9536,18.853	benign,benign	34/498,34/447	42526694	2449,10541	2196	4299	6495	SO:0001583	missense	1565	exon1			CTGGTGGGTAGCG	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.100C>T	22.37:g.42526694G>A	ENSP00000353820:p.Pro34Ser	Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	672	471	0.700893	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	557	0.25503663003663	44	0.08943089430894309	62	0.1712707182320442	296	0.5174825174825175	155	0.20448548812664907	g	18.34	3.602268	0.66445	0.119536	0.223773	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000359033;ENST00000542856	D;D;D	0.83837	-1.77;-1.77;-1.77	3.46	3.46	0.39613	.	0.000000	0.64402	D	0.000011	T	0.00012	0.0000	H	0.97829	4.085	0.09310	P	0.9999999475737	D;P	0.89917	1.0;0.946	D;P	0.97110	1.0;0.571	T	0.01648	-1.1304	9	0.66056	D	0.02	.	14.6963	0.69124	0.0:0.0:1.0:0.0	rs1065852;rs58862176	34;34	Q6NXU8;Q6NWU0	.;.	S	34	ENSP00000353820:P34S;ENSP00000374620:P34S;ENSP00000351927:P34S	ENSP00000351927:P34S	P	-	1	0	CYP2D6	40856638	1.000000	0.71417	0.928000	0.36995	0.499000	0.33736	7.106000	0.77039	2.218000	0.71995	0.484000	0.47621	CCA	G|0.753;A|0.247	0.247	strong		0.642	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
EDN1	1906	hgsc.bcm.edu	37	6	12296255	12296255	+	Missense_Mutation	SNP	G	G	T	rs5370	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:12296255G>T	ENST00000379375.5	+	5	861	c.594G>T	c.(592-594)aaG>aaT	p.K198N		NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	198			K -> N (polymorphism associated with HDL cholesterol levels is some populations and in a sex-specific manner; dbSNP:rs5370). {ECO:0000269|PubMed:10334806, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17357073, ECO:0000269|PubMed:18288492, ECO:0000269|Ref.5}.		artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|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 endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)	p.K198N(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				TGAAAGGCAAGCCCTCCAGAG	0.483													G|||	1239	0.247404	0.1619	0.147	5008	,	,		18203	0.2857		0.2127	False		,,,				2504	0.4305				p.K198N		Atlas-SNP	.											EDN1,NS,carcinoma,0,1	EDN1	23	1	1	Substitution - Missense(1)	stomach(1)	c.G594T	GRCh37	CM993569	EDN1	M	rs5370	PASS	.	G	ASN/LYS,ASN/LYS	865,3541	337.0+/-304.7	98,669,1436	158.0	150.0	152.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	591,594	2.2	0.1	6	dbSNP_52	152	1817,6783	326.9+/-317.6	185,1447,2668	yes	missense,missense	EDN1	NM_001168319.1,NM_001955.4	94,94	283,2116,4104	TT,TG,GG		21.1279,19.6323,20.6213	benign,benign	197/212,198/213	12296255	2682,10324	2203	4300	6503	SO:0001583	missense	1906	exon5			AGGCAAGCCCTCC	S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401		"""Endogenous ligands"""	3176	protein-coding gene	gene with protein product		131240					Standard	NM_001168319		Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.594G>T	6.37:g.12296255G>T	ENSP00000368683:p.Lys198Asn	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_001955	Q96DA1	Missense_Mutation	SNP	ENST00000379375.5	37	CCDS4522.1	449	0.20558608058608058	68	0.13821138211382114	63	0.17403314917127072	158	0.2762237762237762	160	0.21108179419525067	G	7.695	0.691892	0.15039	0.196323	0.211279	ENSG00000078401	ENST00000379375	D	0.84589	-1.87	5.93	2.18	0.27775	.	0.551151	0.21002	N	0.081852	T	0.60894	0.2304	L	0.38175	1.15	0.45452	P	0.001570999999999989	P;P	0.34462	0.454;0.454	B;B	0.26614	0.071;0.071	T	0.49532	-0.8930	9	0.51188	T	0.08	-14.7064	9.471	0.38842	0.276:0.0:0.724:0.0	rs5370;rs2229566;rs17845238;rs17858054;rs57072783;rs5370	198;198	Q6FH53;P05305	.;EDN1_HUMAN	N	198	ENSP00000368683:K198N	ENSP00000368683:K198N	K	+	3	2	EDN1	12404241	0.001000	0.12720	0.141000	0.22245	0.005000	0.04900	0.049000	0.14099	0.116000	0.18110	0.655000	0.94253	AAG	G|0.787;T|0.213	0.213	strong		0.483	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039872.1	NM_001955	
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1605996	1605996	+	Missense_Mutation	SNP	A	A	C	rs576032555	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1605996A>C	ENST00000382171.2	-	1	517	c.484T>G	c.(484-486)Tgc>Ggc	p.C162G	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	162	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCTTGGAGCACCCACAGGAG	0.652													a|||	20	0.00399361	0.0015	0.0014	5008	,	,		7787	0.002		0.002	False		,,,				2504	0.0133				p.C162G		Atlas-SNP	.											KRTAP5-1,NS,carcinoma,0,2	KRTAP5-1	74	2	0			c.T484G						scavenged	.						73.0	89.0	83.0					11																	1605996		2202	4299	6501	SO:0001583	missense	387264	exon1			TGGAGCACCCACA	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.484T>G	11.37:g.1605996A>C	ENSP00000371606:p.Cys162Gly	Somatic	119	9	0.0756303		WXS	Illumina HiSeq	Phase_I	116	14	0.12069	NM_001005922		Missense_Mutation	SNP	ENST00000382171.2	37	CCDS31330.1	.	.	.	.	.	.	.	.	.	.	-	0.664	-0.804452	0.02819	.	.	ENSG00000205869	ENST00000382171	T	0.03772	3.81	3.45	-0.721	0.11189	.	.	.	.	.	T	0.01940	0.0061	N	0.01505	-0.83	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45205	-0.9277	9	0.72032	D	0.01	.	7.1539	0.25626	0.6345:0.2696:0.0:0.0958	.	162	Q6L8H4	KRA51_HUMAN	G	162	ENSP00000371606:C162G	ENSP00000371606:C162G	C	-	1	0	KRTAP5-1	1562572	0.000000	0.05858	0.033000	0.17914	0.010000	0.07245	-0.881000	0.04179	-0.557000	0.06126	-3.103000	0.00063	TGC	.	.	none		0.652	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
CUL7	9820	hgsc.bcm.edu	37	6	43008298	43008298	+	Silent	SNP	C	C	T	rs2273917	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:43008298C>T	ENST00000265348.3	-	21	4078	c.3993G>A	c.(3991-3993)ctG>ctA	p.L1331L	CUL7_ENST00000535468.1_Silent_p.L1415L			Q14999	CUL7_HUMAN	cullin 7	1331					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CCTCCAGCTTCAGGAGTTCCT	0.567													T|||	1628	0.32508	0.6377	0.2406	5008	,	,		21471	0.2202		0.1203	False		,,,				2504	0.2812				p.L1415L		Atlas-SNP	.											.	CUL7	133	.	0			c.G4245A						PASS	.	T	,	2540,1866	539.1+/-375.2	732,1076,395	146.0	160.0	155.0		4245,3993	3.5	1.0	6	dbSNP_100	155	1136,7464	765.8+/-407.6	74,988,3238	no	coding-synonymous,coding-synonymous	CUL7	NM_001168370.1,NM_014780.4	,	806,2064,3633	TT,TC,CC		13.2093,42.3513,28.2639	,	1415/1783,1331/1699	43008298	3676,9330	2203	4300	6503	SO:0001819	synonymous_variant	9820	exon21			CAGCTTCAGGAGT	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.3993G>A	6.37:g.43008298C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Silent	SNP	ENST00000265348.3	37	CCDS4881.1																																																																																			C|0.709;T|0.291	0.291	strong		0.567	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
MARCH3	115123	hgsc.bcm.edu	37	5	126250812	126250812	+	Missense_Mutation	SNP	C	C	T	rs34821177	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:126250812C>T	ENST00000308660.5	-	3	717	c.203G>A	c.(202-204)cGg>cAg	p.R68Q	MARCH3_ENST00000502289.1_5'UTR|MARCH3_ENST00000515241.1_Missense_Mutation_p.R68Q	NM_178450.3	NP_848545.1	Q86UD3	MARH3_HUMAN	membrane-associated ring finger (C3HC4) 3, E3 ubiquitin protein ligase	68			R -> Q (in dbSNP:rs34821177). {ECO:0000269|PubMed:14702039}.		endocytosis (GO:0006897)|protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.074)|OV - Ovarian serous cystadenocarcinoma(64;0.0793)		GCACATCGGCCGGTCATTGAA	0.592													C|||	49	0.00978435	0.0015	0.0101	5008	,	,		14359	0.0		0.0378	False		,,,				2504	0.002				p.R68Q		Atlas-SNP	.											.	MARCH3	14	.	0			c.G203A						PASS	.	C	GLN/ARG	20,4386	28.1+/-56.4	0,20,2183	43.0	41.0	41.0		203	4.6	1.0	5	dbSNP_126	41	238,8362	95.9+/-157.7	5,228,4067	yes	missense	MARCH3	NM_178450.3	43	5,248,6250	TT,TC,CC		2.7674,0.4539,1.9837	benign	68/254	126250812	258,12748	2203	4300	6503	SO:0001583	missense	115123	exon3			ATCGGCCGGTCAT	AF055007	CCDS4141.1	5q23.2	2013-01-09	2012-02-23		ENSG00000173926	ENSG00000173926		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	28728	protein-coding gene	gene with protein product		613333	"""membrane-associated ring finger (C3HC4) 3"""			14722266, 8619474	Standard	NM_178450		Approved	MGC48332, MARCH-III, RNF173	uc003kuf.4	Q86UD3	OTTHUMG00000128968	ENST00000308660.5:c.203G>A	5.37:g.126250812C>T	ENSP00000309141:p.Arg68Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_178450	A8K264|B9EJE7	Missense_Mutation	SNP	ENST00000308660.5	37	CCDS4141.1	40	0.018315018315018316	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	31	0.040897097625329816	C	14.87	2.664876	0.47572	0.004539	0.027674	ENSG00000173926	ENST00000308660;ENST00000515241	T;T	0.28895	1.59;1.59	4.63	4.63	0.57726	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-CH-type (1);	0.000000	0.64402	D	0.000002	T	0.05227	0.0139	L	0.29908	0.895	0.44677	D	0.997664	B;B	0.31730	0.337;0.123	B;B	0.23716	0.048;0.021	T	0.04153	-1.0973	10	0.12430	T	0.62	-14.4337	18.8146	0.92072	0.0:1.0:0.0:0.0	rs34821177	68;68	B9EJE7;Q86UD3	.;MARH3_HUMAN	Q	68	ENSP00000309141:R68Q;ENSP00000421979:R68Q	ENSP00000309141:R68Q	R	-	2	0	MARCH3	126278711	0.993000	0.37304	1.000000	0.80357	1.000000	0.99986	3.118000	0.50414	2.865000	0.98341	0.655000	0.94253	CGG	C|0.978;T|0.022	0.022	strong		0.592	MARCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250955.2	NM_178450	
FANCD2	2177	hgsc.bcm.edu	37	3	10085536	10085536	+	Silent	SNP	A	A	G	rs34046352	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:10085536A>G	ENST00000419585.1	+	14	1283	c.1122A>G	c.(1120-1122)gtA>gtG	p.V374V	FANCD2_ENST00000383807.1_Silent_p.V374V|FANCD2_ENST00000383806.1_Silent_p.V374V|FANCD2_ENST00000287647.3_Silent_p.V374V			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	374					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CTGCCTCAGTATCTGAACACA	0.393			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.V374V		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	.	FANCD2	253	.	0			c.A1122G						PASS	.						82.0	76.0	78.0					3																	10085536		2202	4298	6500	SO:0001819	synonymous_variant	2177	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTCAGTATCTGAA	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1122A>G	3.37:g.10085536A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	146	49	0.335616	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																			A|0.876;G|0.124	0.124	strong		0.393	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
AMICA1	120425	hgsc.bcm.edu	37	11	118081345	118081345	+	Missense_Mutation	SNP	A	A	T	rs17121881	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:118081345A>T	ENST00000356289.5	-	4	454	c.281T>A	c.(280-282)aTc>aAc	p.I94N	AMICA1_ENST00000533261.1_Missense_Mutation_p.I94N|AMICA1_ENST00000292067.7_Missense_Mutation_p.I84N|AMICA1_ENST00000526620.1_Missense_Mutation_p.I55N	NM_001098526.1	NP_001091996.1	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen 1	94	Ig-like V-type 1.		I -> N (in dbSNP:rs17121881). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.		blood coagulation (GO:0007596)|gamma-delta T cell activation (GO:0046629)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte migration (GO:0050900)|monocyte extravasation (GO:0035696)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein homodimerization activity (GO:0042803)	p.I84N(1)		central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|stomach(2)	20	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		ATTGCATAAGATGTCCCCCAT	0.502													A|||	2341	0.467452	0.1346	0.487	5008	,	,		18947	0.5387		0.5298	False		,,,				2504	0.7658				p.I94N		Atlas-SNP	.											AMICA1,caecum,carcinoma,0,2	AMICA1	49	2	1	Substitution - Missense(1)	stomach(1)	c.T281A						PASS	.	A	ASN/ILE,ASN/ILE	902,3498	347.5+/-309.5	92,718,1390	143.0	127.0	132.0		281,251	4.0	0.1	11	dbSNP_123	132	4910,3682	621.3+/-397.2	1406,2098,792	yes	missense,missense	AMICA1	NM_001098526.1,NM_153206.2	149,149	1498,2816,2182	TT,TA,AA		42.8538,20.5,44.7352	possibly-damaging,possibly-damaging	94/395,84/385	118081345	5812,7180	2200	4296	6496	SO:0001583	missense	120425	exon4			CATAAGATGTCCC	AY138965, AY358362	CCDS8391.1, CCDS41723.1, CCDS66240.1	11q23.3	2013-01-11				ENSG00000160593		"""Immunoglobulin superfamily / V-set domain containing"""	19084	protein-coding gene	gene with protein product		609770				12975309	Standard	NM_001098526		Approved	Gm638, AMICA	uc001psk.2	Q86YT9		ENST00000356289.5:c.281T>A	11.37:g.118081345A>T	ENSP00000348635:p.Ile94Asn	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	211	101	0.478673	NM_001098526	B0YIV1|B0YIV2|Q496M1|Q5DTC6|Q7Z499|Q8N9I7|Q8NF70	Missense_Mutation	SNP	ENST00000356289.5	37	CCDS41723.1	985	0.451007326007326	74	0.15040650406504066	173	0.47790055248618785	325	0.5681818181818182	413	0.5448548812664907	A	9.598	1.127979	0.20959	0.205	0.571462	ENSG00000160593	ENST00000356289;ENST00000292067;ENST00000533261;ENST00000526620;ENST00000537867;ENST00000524477;ENST00000525565	T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	5.14	3.98	0.46160	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.691620	0.13216	N	0.404776	T	0.00012	0.0000	M	0.63843	1.955	0.80722	P	0.0	B;P;P;D	0.63880	0.237;0.952;0.952;0.993	B;P;P;P	0.54238	0.1;0.695;0.695;0.746	T	0.49476	-0.8936	9	0.33141	T	0.24	-8.4456	7.8888	0.29665	0.9063:0.0:0.0937:0.0	rs17121881;rs17121881	55;94;94;84	E9PKK2;Q86YT9;E9PR26;Q86YT9-2	.;JAML1_HUMAN;.;.	N	94;84;94;55;55;55;94	ENSP00000348635:I94N;ENSP00000292067:I84N;ENSP00000436117:I94N;ENSP00000431218:I55N;ENSP00000432769:I55N;ENSP00000431791:I94N	ENSP00000292067:I84N	I	-	2	0	AMICA1	117586555	0.008000	0.16893	0.073000	0.20177	0.011000	0.07611	1.514000	0.35834	0.925000	0.37094	0.533000	0.62120	ATC	A|0.546;N|0.000	.	strong		0.502	AMICA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392105.2	NM_153206	
SAMD15	161394	hgsc.bcm.edu	37	14	77844592	77844592	+	Silent	SNP	T	T	A	rs10133824	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77844592T>A	ENST00000216471.4	+	1	1117	c.831T>A	c.(829-831)ggT>ggA	p.G277G	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	277										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						AGGAGGCAGGTCTAGAGCCTC	0.502													T|||	760	0.151757	0.0968	0.2666	5008	,	,		18706	0.0159		0.2038	False		,,,				2504	0.2311				p.G277G		Atlas-SNP	.											.	SAMD15	60	.	0			c.T831A						PASS	.	T		558,3848	242.1+/-252.3	32,494,1677	67.0	71.0	70.0		831	-0.7	0.0	14	dbSNP_119	70	1685,6915	300.8+/-305.1	182,1321,2797	no	coding-synonymous	SAMD15	NM_001010860.1		214,1815,4474	AA,AT,TT		19.593,12.6645,17.2459		277/675	77844592	2243,10763	2203	4300	6503	SO:0001819	synonymous_variant	161394	exon1			GGCAGGTCTAGAG	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.831T>A	14.37:g.77844592T>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_001010860	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																			T|0.848;A|0.152	0.152	strong		0.502	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
ST6GALNAC1	55808	hgsc.bcm.edu	37	17	74625686	74625686	+	Missense_Mutation	SNP	A	A	G	rs8077382	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:74625686A>G	ENST00000156626.7	-	2	438	c.239T>C	c.(238-240)gTg>gCg	p.V80A	ST6GALNAC1_ENST00000590878.1_5'UTR	NM_018414.3	NP_060884.1	Q9NSC7	SIA7A_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	80			V -> A (in dbSNP:rs8077382). {ECO:0000269|PubMed:12975309}.		oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	22						GTTCTCTGGCACTGGCTCTGC	0.577													G|||	398	0.0794728	0.1392	0.062	5008	,	,		18833	0.001		0.0924	False		,,,				2504	0.0787				p.V80A		Atlas-SNP	.											.	ST6GALNAC1	42	.	0			c.T239C						PASS	.	G	ALA/VAL	600,3806	770.8+/-413.8	41,518,1644	165.0	146.0	152.0		239	-7.4	0.0	17	dbSNP_116	152	856,7744	780.5+/-407.7	39,778,3483	yes	missense	ST6GALNAC1	NM_018414.3	64	80,1296,5127	GG,GA,AA		9.9535,13.6178,11.1948	benign	80/601	74625686	1456,11550	2203	4300	6503	SO:0001583	missense	55808	exon2			TCTGGCACTGGCT	Y11339	CCDS11748.1	17q25.3	2013-03-01	2005-02-07	2005-02-07	ENSG00000070526	ENSG00000070526		"""Sialyltransferases"""	23614	protein-coding gene	gene with protein product		610138	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) A"""	SIAT7A			Standard	NM_001289107		Approved	ST6GalNAcI	uc002jsh.3	Q9NSC7	OTTHUMG00000180369	ENST00000156626.7:c.239T>C	17.37:g.74625686A>G	ENSP00000156626:p.Val80Ala	Somatic	395	0	0		WXS	Illumina HiSeq	Phase_I	445	223	0.501124	NM_018414	Q6UW90|Q9NSC6	Missense_Mutation	SNP	ENST00000156626.7	37	CCDS11748.1	156	0.07142857142857142	55	0.11178861788617886	26	0.0718232044198895	0	0.0	75	0.09894459102902374	G	0.015	-1.552182	0.00918	0.136178	0.099535	ENSG00000070526	ENST00000156626;ENST00000359088	T;T	0.23147	1.96;1.92	3.72	-7.44	0.01379	.	.	.	.	.	T	0.00039	0.0001	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.19128	-1.0315	8	0.07325	T	0.83	0.9285	3.5529	0.07853	0.3065:0.1162:0.4618:0.1155	rs8077382;rs52828162;rs60500971;rs8077382	80	Q9NSC7	SIA7A_HUMAN	A	80	ENSP00000156626:V80A;ENSP00000351991:V80A	ENSP00000156626:V80A	V	-	2	0	ST6GALNAC1	72137281	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-4.894000	0.00173	-2.119000	0.00827	-3.716000	0.00023	GTG	A|0.898;G|0.102	0.102	strong		0.577	ST6GALNAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450974.1	NM_018414	
LRIT3	345193	hgsc.bcm.edu	37	4	110791290	110791290	+	Missense_Mutation	SNP	C	C	T	rs201097191		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:110791290C>T	ENST00000594814.1	+	4	1385	c.1385C>T	c.(1384-1386)cCt>cTt	p.P462L	LRIT3_ENST00000409621.2_Missense_Mutation_p.P279L|LRIT3_ENST00000327908.3_Missense_Mutation_p.P279L|LRIT3_ENST00000379920.3_Missense_Mutation_p.P417L	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	462					regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		AGTAAGCTTCCTCCAGCCAGC	0.468													C|||	1	0.000199681	0.0	0.0	5008	,	,		22471	0.0		0.001	False		,,,				2504	0.0				p.P462L		Atlas-SNP	.											.	LRIT3	107	.	0			c.C1385T						PASS	.						67.0	68.0	68.0					4																	110791290		2203	4300	6503	SO:0001583	missense	345193	exon4			AGCTTCCTCCAGC	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1385C>T	4.37:g.110791290C>T	ENSP00000469759:p.Pro462Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	121	61	0.504132	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.59	1.982265	0.34942	.	.	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.57752	0.38;0.55;0.38	5.06	4.22	0.49857	.	0.662798	0.13364	N	0.393444	T	0.42630	0.1211	L	0.43152	1.355	0.42468	D	0.992817	B;B	0.17667	0.006;0.023	B;B	0.16722	0.005;0.016	T	0.28996	-1.0026	10	0.36615	T	0.2	.	6.7454	0.23458	0.223:0.686:0.0:0.091	.	417;279	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	L	279;417;279	ENSP00000328222:P279L;ENSP00000369252:P417L;ENSP00000386734:P279L	ENSP00000328222:P279L	P	+	2	0	LRIT3	111010739	0.070000	0.21116	0.179000	0.23059	0.105000	0.19272	3.151000	0.50670	1.121000	0.41925	0.655000	0.94253	CCT	C|1.000;T|0.000	0.000	strong		0.468	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
PNPLA3	80339	hgsc.bcm.edu	37	22	44324730	44324730	+	Silent	SNP	C	C	T	rs738408	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:44324730C>T	ENST00000216180.3	+	3	620	c.447C>T	c.(445-447)ccC>ccT	p.P149P	PNPLA3_ENST00000423180.2_Silent_p.P145P|PNPLA3_ENST00000478713.1_3'UTR	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	149	Patatin.				acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)	p.P149P(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				GCTTCATCCCCTTCTACAGTG	0.502													T|||	1313	0.262181	0.118	0.4841	5008	,	,		20434	0.3502		0.2256	False		,,,				2504	0.2464				p.P149P		Atlas-SNP	.											PNPLA3,NS,carcinoma,0,1	PNPLA3	53	1	1	Substitution - coding silent(1)	stomach(1)	c.C447T						PASS	.	T		637,3769	764.4+/-413.3	57,523,1623	303.0	254.0	271.0		447	-4.8	0.0	22	dbSNP_86	271	1890,6710	723.2+/-406.4	208,1474,2618	no	coding-synonymous	PNPLA3	NM_025225.2		265,1997,4241	TT,TC,CC		21.9767,14.4576,19.4295		149/482	44324730	2527,10479	2203	4300	6503	SO:0001819	synonymous_variant	80339	exon3			CATCCCCTTCTAC		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"""Patatin-like phospholipase domain containing"""	18590	protein-coding gene	gene with protein product		609567	"""chromosome 22 open reading frame 20"", ""adiponutrin"""	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.447C>T	22.37:g.44324730C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	90	35	0.388889	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Silent	SNP	ENST00000216180.3	37	CCDS14054.1																																																																																			C|0.802;T|0.198	0.198	strong		0.502	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225	
SPINK5	11005	hgsc.bcm.edu	37	5	147469113	147469113	+	Silent	SNP	G	G	A	rs35121983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:147469113G>A	ENST00000256084.7	+	7	573	c.531G>A	c.(529-531)agG>agA	p.R177R	SPINK5_ENST00000359874.3_Silent_p.R177R|SPINK5_ENST00000398454.1_Silent_p.R177R	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	177	Kazal-like 3. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R177R(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATGCACAAGGGAAAATGATC	0.448													G|||	235	0.0469249	0.0605	0.0144	5008	,	,		19926	0.0337		0.0239	False		,,,				2504	0.089				p.R177R		Atlas-SNP	.											SPINK5,NS,carcinoma,0,1	SPINK5	245	1	1	Substitution - coding silent(1)	stomach(1)	c.G531A						PASS	.	G	,,	182,3916		4,174,1871	268.0	251.0	256.0		531,531,531	1.5	1.0	5	dbSNP_126	256	167,8217		2,163,4027	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	,,	6,337,5898	AA,AG,GG		1.9919,4.4412,2.796	,,	177/1095,177/917,177/1065	147469113	349,12133	2049	4192	6241	SO:0001819	synonymous_variant	11005	exon7			CACAAGGGAAAAT	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.531G>A	5.37:g.147469113G>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	226	114	0.504425	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			G|0.976;A|0.024	0.024	strong		0.448	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
SMG7	9887	hgsc.bcm.edu	37	1	183515428	183515428	+	Missense_Mutation	SNP	G	G	A	rs2298083	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:183515428G>A	ENST00000347615.2	+	17	2817	c.2698G>A	c.(2698-2700)Gtc>Atc	p.V900I	SMG7_ENST00000508461.1_Missense_Mutation_p.V858I|SMG7_ENST00000367537.3_Missense_Mutation_p.V883I|SMG7_ENST00000507469.1_Missense_Mutation_p.V854I|SMG7_ENST00000456731.2_Missense_Mutation_p.V812I|SMG7_ENST00000515829.2_Missense_Mutation_p.V854I	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	900			V -> I (in dbSNP:rs2298083). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9039502}.		gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						GTCACCAGGAGTCTTCCGTCC	0.502													G|||	829	0.165535	0.2935	0.2233	5008	,	,		19170	0.1052		0.0984	False		,,,				2504	0.0828				p.V900I		Atlas-SNP	.											.	SMG7	165	.	0			c.G2698A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1128,3278	404.0+/-332.9	147,834,1222	86.0	92.0	90.0		2572,2698,2560,2560	5.7	1.0	1	dbSNP_100	90	942,7658	207.9+/-249.5	51,840,3409	yes	missense,missense,missense,missense	SMG7	NM_001174061.1,NM_173156.2,NM_201568.2,NM_201569.2	29,29,29,29	198,1674,4631	AA,AG,GG		10.9535,25.6015,15.9157	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	858/1146,900/1138,854/1092,854/1179	183515428	2070,10936	2203	4300	6503	SO:0001583	missense	9887	exon17			CCAGGAGTCTTCC	D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog C (S. cerevisiae)"""	610964	"""chromosome 1 open reading frame 16"", ""smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.2698G>A	1.37:g.183515428G>A	ENSP00000340766:p.Val900Ile	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	190	100	0.526316	NM_173156	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	362	0.16575091575091574	154	0.3130081300813008	64	0.17679558011049723	61	0.10664335664335664	83	0.10949868073878628	G	19.08	3.758164	0.69763	0.256015	0.109535	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	5.72	5.72	0.89469	.	1.036620	0.07582	N	0.920575	T	0.00012	0.0000	N	0.24115	0.695	0.22127	P	0.999341797	B;B;B;B;B;B	0.29716	0.255;0.118;0.255;0.187;0.255;0.247	B;B;B;B;B;B	0.29716	0.071;0.049;0.071;0.106;0.071;0.075	T	0.30909	-0.9962	9	0.38643	T	0.18	-1.2894	19.8968	0.96969	0.0:0.0:1.0:0.0	rs2298083;rs56498132;rs60312482;rs2298083	858;883;812;854;900;854	E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;.;SMG7_HUMAN;.	I	812;883;858;900;854;854	ENSP00000407629:V812I;ENSP00000356507:V883I;ENSP00000426915:V858I;ENSP00000340766:V900I;ENSP00000425133:V854I;ENSP00000421358:V854I	ENSP00000340766:V900I	V	+	1	0	SMG7	181782051	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.505000	0.66981	2.691000	0.91804	0.655000	0.94253	GTC	G|0.837;A|0.162	0.162	strong		0.502	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837	
MGARP	84709	hgsc.bcm.edu	37	4	140188094	140188094	+	Missense_Mutation	SNP	C	C	T	rs3208941	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:140188094C>T	ENST00000398955.1	-	4	561	c.382G>A	c.(382-384)Gct>Act	p.A128T		NM_032623.3	NP_116012.2	Q8TDB4	HUMMR_HUMAN	mitochondria-localized glutamic acid-rich protein	128			A -> T (in dbSNP:rs3208941).		anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cellular response to gonadotropin-releasing hormone (GO:0097211)|cellular response to hypoxia (GO:0071456)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of mitochondrion organization (GO:0010822)|protein targeting to mitochondrion (GO:0006626)|retrograde axon cargo transport (GO:0008090)	integral component of mitochondrial outer membrane (GO:0031307)|mitochondrion (GO:0005739)											ACAACTGTAGCACTGGGACTT	0.517													C|||	261	0.0521166	0.0318	0.0476	5008	,	,		17941	0.1052		0.0507	False		,,,				2504	0.0297				p.A128T		Atlas-SNP	.											.	.	.	.	0			c.G382A						PASS	.	C	THR/ALA	175,3857		4,167,1845	166.0	159.0	161.0		382	5.3	0.0	4	dbSNP_105	161	567,7815		15,537,3639	yes	missense	C4orf49	NM_032623.3	58	19,704,5484	TT,TC,CC		6.7645,4.3403,5.9771	possibly-damaging	128/241	140188094	742,11672	2016	4191	6207	SO:0001583	missense	84709	exon4			CTGTAGCACTGGG	AF484960	CCDS43269.1	4q31.1	2014-02-19	2014-02-19	2012-04-17	ENSG00000137463	ENSG00000137463			29969	protein-coding gene	gene with protein product	"""ovary-specific acidic protein"", ""corneal endothelium-specific protein 1"", ""hypoxia up-regulated mitochondrial movement regulator"""		"""chromosome 4 open reading frame 49"""	C4orf49			Standard	NM_032623		Approved	OSAP, CESP-1, HUMMR	uc003ihr.1	Q8TDB4	OTTHUMG00000161325	ENST00000398955.1:c.382G>A	4.37:g.140188094C>T	ENSP00000381928:p.Ala128Thr	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	188	87	0.462766	NM_032623	Q9BZC3	Missense_Mutation	SNP	ENST00000398955.1	37	CCDS43269.1	110	0.05036630036630037	17	0.034552845528455285	10	0.027624309392265192	49	0.08566433566433566	34	0.044854881266490766	C	14.42	2.528927	0.44969	0.043403	0.067645	ENSG00000137463	ENST00000398955	T	0.49432	0.78	5.31	5.31	0.75309	.	0.559675	0.18543	N	0.138136	T	0.02047	0.0064	L	0.41710	1.295	0.80722	D	1	P	0.35745	0.518	B	0.36504	0.226	T	0.02059	-1.1221	10	0.87932	D	0	-11.2069	14.4853	0.67614	0.0:1.0:0.0:0.0	rs3208941;rs52834247;rs3208941	128	Q8TDB4	CD049_HUMAN	T	128	ENSP00000381928:A128T	ENSP00000381928:A128T	A	-	1	0	C4orf49	140407544	0.000000	0.05858	0.020000	0.16555	0.004000	0.04260	0.517000	0.22832	2.481000	0.83766	0.467000	0.42956	GCT	C|0.944;T|0.056	0.056	strong		0.517	MGARP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364536.1	NM_032623	
FPR1	2357	hgsc.bcm.edu	37	19	52249672	52249672	+	Silent	SNP	A	A	G	rs1042229	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52249672A>G	ENST00000595042.1	-	3	717	c.576T>C	c.(574-576)aaT>aaC	p.N192N	FPR1_ENST00000304748.4_Silent_p.N192N	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	192			N -> K (in dbSNP:rs1042229). {ECO:0000269|PubMed:1612600, ECO:0000269|Ref.7}.		activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)	p.N192N(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	CAACGGCCACATTTATCCTCT	0.498													C|||	662	0.132188	0.0779	0.0764	5008	,	,		21616	0.2192		0.1153	False		,,,				2504	0.1728				p.N192N		Atlas-SNP	.											FPR1,NS,carcinoma,0,1	FPR1	64	1	1	Substitution - coding silent(1)	stomach(1)	c.T576C						PASS	.						118.0	109.0	112.0					19																	52249672		2203	4300	6503	SO:0001819	synonymous_variant	2357	exon3			GGCCACATTTATC	M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"""GPCR / Class A : Formyl peptide receptors"""	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.576T>C	19.37:g.52249672A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Silent	SNP	ENST00000595042.1	37	CCDS12839.1																																																																																			G|0.018;C|0.428;A|0.554	0.018	strong		0.498	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029	
NLRP4	147945	hgsc.bcm.edu	37	19	56390237	56390237	+	Missense_Mutation	SNP	A	A	T	rs302453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56390237A>T	ENST00000301295.6	+	9	3196	c.2774A>T	c.(2773-2775)cAg>cTg	p.Q925L	NLRP4_ENST00000587891.1_Missense_Mutation_p.Q850L|NLRP4_ENST00000346986.5_Missense_Mutation_p.Q869L	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	925			Q -> L (in dbSNP:rs302453). {ECO:0000269|PubMed:15489334}.		inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		ACCCTGCAGCAGCTCAACCTG	0.542													A|||	680	0.135783	0.0189	0.2089	5008	,	,		21691	0.1637		0.2187	False		,,,				2504	0.1278				p.Q925L		Atlas-SNP	.											.	NLRP4	331	.	0			c.A2774T						PASS	.	A	LEU/GLN	237,4169	139.2+/-174.8	8,221,1974	109.0	88.0	95.0		2774	-7.2	0.0	19	dbSNP_79	95	2281,6319	384.6+/-341.2	286,1709,2305	yes	missense	NLRP4	NM_134444.4	113	294,1930,4279	TT,TA,AA		26.5233,5.379,19.3603	benign	925/995	56390237	2518,10488	2203	4300	6503	SO:0001583	missense	147945	exon9			TGCAGCAGCTCAA	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.2774A>T	19.37:g.56390237A>T	ENSP00000301295:p.Gln925Leu	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	271	133	0.490775	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	349	0.15979853479853479	15	0.03048780487804878	76	0.20994475138121546	85	0.1486013986013986	173	0.22823218997361477	A	7.734	0.699873	0.15106	0.05379	0.265233	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.42513	0.97;0.97	3.92	-7.21	0.01490	.	.	.	.	.	T	0.00012	0.0000	N	0.10874	0.06	0.80722	P	0.0	B;B;B	0.13594	0.0;0.008;0.0	B;B;B	0.10450	0.0;0.005;0.0	T	0.31779	-0.9931	8	0.25751	T	0.34	.	3.4525	0.07503	0.384:0.0:0.2435:0.3724	rs302453;rs17854611;rs302453	869;850;925	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	L	925;869	ENSP00000301295:Q925L;ENSP00000344787:Q869L	ENSP00000301295:Q925L	Q	+	2	0	NLRP4	61082049	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.723000	0.04952	-1.354000	0.02188	-0.672000	0.03802	CAG	A|0.823;T|0.177	0.177	strong		0.542	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
TCIRG1	10312	hgsc.bcm.edu	37	11	67809268	67809268	+	Missense_Mutation	SNP	C	C	T	rs36027301	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:67809268C>T	ENST00000265686.3	+	3	274	c.166C>T	c.(166-168)Cgg>Tgg	p.R56W	TCIRG1_ENST00000532635.1_5'Flank	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	56			R -> W (in dbSNP:rs36027301).		ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						GGTTGATGTTCGGCGCTGTGA	0.602													C|||	85	0.0169728	0.0038	0.0216	5008	,	,		18487	0.0		0.0497	False		,,,				2504	0.0153				p.R56W		Atlas-SNP	.											.	TCIRG1	40	.	0			c.C166T						PASS	.	C	TRP/ARG	44,4356	44.6+/-78.6	0,44,2156	92.0	69.0	77.0		166	3.7	1.0	11	dbSNP_126	77	547,8039	146.6+/-202.2	23,501,3769	yes	missense	TCIRG1	NM_006019.3	101	23,545,5925	TT,TC,CC		6.3708,1.0,4.5511	probably-damaging	56/831	67809268	591,12395	2200	4293	6493	SO:0001583	missense	10312	exon3			GATGTTCGGCGCT	AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"""ATPases / V-type"""	11647	protein-coding gene	gene with protein product	"""T-cell immune response cDNA 7"""	604592	"""T-cell, immune regulator 1"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"""			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.166C>T	11.37:g.67809268C>T	ENSP00000265686:p.Arg56Trp	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	107	59	0.551402	NM_006019	O75877|Q8WVC5	Missense_Mutation	SNP	ENST00000265686.3	37	CCDS8177.1	49	0.022435897435897436	4	0.008130081300813009	5	0.013812154696132596	0	0.0	40	0.052770448548812667	C	21.7	4.193773	0.78902	0.01	0.063708	ENSG00000110719	ENST00000265686;ENST00000524598;ENST00000529657	D;D;D	0.88354	-2.37;-2.37;-2.37	3.72	3.72	0.42706	.	0.000000	0.85682	D	0.000000	T	0.77909	0.4201	H	0.94620	3.56	0.80722	D	1	D	0.76494	0.999	D	0.70016	0.967	D	0.84506	0.0619	10	0.87932	D	0	-46.7811	12.7234	0.57154	0.0:1.0:0.0:0.0	rs36027301;rs61749183;rs36027301	56	Q13488	VPP3_HUMAN	W	56;42;56	ENSP00000265686:R56W;ENSP00000432846:R42W;ENSP00000435023:R56W	ENSP00000265686:R56W	R	+	1	2	TCIRG1	67565844	0.989000	0.36119	0.980000	0.43619	0.920000	0.55202	4.169000	0.58223	2.090000	0.63153	0.462000	0.41574	CGG	C|0.964;T|0.036	0.036	strong		0.602	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019	
PREX1	57580	hgsc.bcm.edu	37	20	47307618	47307618	+	Silent	SNP	G	G	A	rs3746820	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:47307618G>A	ENST00000371941.3	-	9	1075	c.1053C>T	c.(1051-1053)aaC>aaT	p.N351N	PREX1_ENST00000396220.1_Silent_p.N351N	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	351	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.N351N(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CGGTATAGCCGTTGCTATGGT	0.582													g|||	1428	0.285144	0.5764	0.1816	5008	,	,		20171	0.0962		0.2028	False		,,,				2504	0.2444				p.N351N		Atlas-SNP	.											PREX1,NS,carcinoma,0,1	PREX1	441	1	1	Substitution - coding silent(1)	stomach(1)	c.C1053T						PASS	.	A		2199,2207	588.0+/-386.8	565,1069,569	140.0	108.0	119.0		1053	-2.9	1.0	20	dbSNP_107	119	1554,7046	291.2+/-300.2	161,1232,2907	no	coding-synonymous	PREX1	NM_020820.3		726,2301,3476	AA,AG,GG		18.0698,49.9092,28.8559		351/1660	47307618	3753,9253	2203	4300	6503	SO:0001819	synonymous_variant	57580	exon9			ATAGCCGTTGCTA	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1053C>T	20.37:g.47307618G>A		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	269	137	0.509294	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			G|0.717;A|0.283	0.283	strong		0.582	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
COPE	11316	hgsc.bcm.edu	37	19	19017862	19017862	+	Missense_Mutation	SNP	G	G	A	rs10330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19017862G>A	ENST00000262812.4	-	4	398	c.350C>T	c.(349-351)aCc>aTc	p.T117I	COPE_ENST00000349893.4_Missense_Mutation_p.T117I|COPE_ENST00000351079.4_Intron|COPE_ENST00000598969.1_Intron|AC002985.3_ENST00000596918.1_3'UTR|COPE_ENST00000600932.1_Missense_Mutation_p.T117I	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	117			T -> I (in dbSNP:rs10330). {ECO:0000269|PubMed:10469566, ECO:0000269|PubMed:14702039}.		COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						CAGGAAGGTGGTGTTGGTCAC	0.647													G|||	1041	0.207867	0.413	0.1239	5008	,	,		18826	0.0754		0.1332	False		,,,				2504	0.2035				p.T117I		Atlas-SNP	.											.	COPE	26	.	0			c.C350T						PASS	.	G	ILE/THR,,ILE/THR	1575,2829	456.9+/-351.5	267,1041,894	130.0	72.0	92.0		350,,350	4.8	1.0	19	dbSNP_52	92	1004,7594	203.2+/-246.3	60,884,3355	yes	missense,intron,missense	COPE	NM_007263.3,NM_199442.1,NM_199444.1	89,,89	327,1925,4249	AA,AG,GG		11.6771,35.7629,19.8354	benign,,benign	117/309,,117/257	19017862	2579,10423	2202	4299	6501	SO:0001583	missense	11316	exon4			AAGGTGGTGTTGG	AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669			2234	protein-coding gene	gene with protein product		606942				10469566	Standard	NM_007263		Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.350C>T	19.37:g.19017862G>A	ENSP00000262812:p.Thr117Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	109	54	0.495413	NM_007263	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	Missense_Mutation	SNP	ENST00000262812.4	37	CCDS12387.1	400	0.18315018315018314	194	0.3943089430894309	52	0.143646408839779	57	0.09965034965034965	97	0.1279683377308707	G	14.17	2.455055	0.43634	0.357629	0.116771	ENSG00000105669	ENST00000262812;ENST00000349893;ENST00000538245	T;T	0.44881	0.91;2.33	4.76	4.76	0.60689	Tetratricopeptide-like helical (1);	0.050875	0.85682	D	0.000000	T	0.00012	0.0000	L	0.57536	1.79	0.09310	P	0.99999572547	B;B;P	0.36660	0.408;0.31;0.564	B;B;B	0.32090	0.09;0.14;0.09	T	0.45145	-0.9281	9	0.30854	T	0.27	-56.6019	16.3456	0.83132	0.0:0.0:1.0:0.0	rs10330;rs1044168;rs3177139;rs59201994;rs10330	117;117;117	Q53HJ6;A6NE29;O14579	.;.;COPE_HUMAN	I	117;117;116	ENSP00000262812:T117I;ENSP00000343134:T117I	ENSP00000262812:T117I	T	-	2	0	COPE	18878862	1.000000	0.71417	1.000000	0.80357	0.741000	0.42261	5.207000	0.65197	2.190000	0.69967	0.561000	0.74099	ACC	G|0.804;A|0.196	0.196	strong		0.647	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464801.1	NM_007263	
MUC7	4589	hgsc.bcm.edu	37	4	71347050	71347050	+	Missense_Mutation	SNP	G	G	A	rs144679944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:71347050G>A	ENST00000304887.5	+	3	779	c.589G>A	c.(589-591)Gca>Aca	p.A197T	MUC7_ENST00000413702.1_Missense_Mutation_p.A197T|MUC7_ENST00000456088.1_Missense_Mutation_p.A197T	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	197	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			CACACCTTCTGCAACTACACA	0.592													G|||	7	0.00139776	0.0	0.0	5008	,	,		20060	0.0		0.007	False		,,,				2504	0.0				p.A197T		Atlas-SNP	.											.	MUC7	91	.	0			c.G589A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	428.0	344.0	372.0		589,589,589	-4.1	0.0	4	dbSNP_134	372	48,8552	31.2+/-83.2	0,48,4252	no	missense,missense,missense	MUC7	NM_152291.2,NM_001145007.1,NM_001145006.1	58,58,58	0,51,6452	AA,AG,GG		0.5581,0.0681,0.3921	benign,benign,benign	197/378,197/378,197/378	71347050	51,12955	2203	4300	6503	SO:0001583	missense	4589	exon4			CCTTCTGCAACTA	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"""Mucins"""	7518	protein-coding gene	gene with protein product		158375	"""mucin 7, salivary"""			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.589G>A	4.37:g.71347050G>A	ENSP00000302021:p.Ala197Thr	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	359	149	0.415042	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	5.104	0.204826	0.09704	6.81E-4	0.005581	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.48836	0.8;0.8;0.8	2.05	-4.1	0.03940	.	.	.	.	.	T	0.19565	0.0470	L	0.27053	0.805	0.09310	N	1	B	0.16396	0.017	B	0.12837	0.008	T	0.14337	-1.0476	8	.	.	.	-1.511	4.8329	0.13449	0.4757:0.3088:0.2155:0.0	.	197	Q8TAX7	MUC7_HUMAN	T	197	ENSP00000407422:A197T;ENSP00000400585:A197T;ENSP00000302021:A197T	.	A	+	1	0	MUC7	71381639	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-6.631000	0.00059	-1.559000	0.01688	-0.136000	0.14681	GCA	G|0.996;A|0.004	0.004	strong		0.592	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
COL6A3	1293	hgsc.bcm.edu	37	2	238257013	238257013	+	Silent	SNP	G	G	A	rs2646265	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:238257013G>A	ENST00000295550.4	-	30	7397	c.6945C>T	c.(6943-6945)ttC>ttT	p.F2315F	COL6A3_ENST00000409809.1_Silent_p.F2109F|COL6A3_ENST00000472056.1_Silent_p.F1708F|COL6A3_ENST00000353578.4_Silent_p.F2109F|COL6A3_ENST00000346358.4_Silent_p.F2115F|COL6A3_ENST00000347401.3_Silent_p.F2114F	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2315	Collagen-like 5.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GGTATCCAGGGAATCCTCTTT	0.358													G|||	533	0.10643	0.0817	0.1729	5008	,	,		17771	0.0516		0.1302	False		,,,				2504	0.1247				p.F2315F		Atlas-SNP	.											.	COL6A3	608	.	0			c.C6945T						PASS	.	G	,,	360,4046	158.1+/-190.9	15,330,1858	90.0	92.0	91.0		6945,5124,6327	3.1	1.0	2	dbSNP_100	91	911,7689	193.2+/-239.0	57,797,3446	yes	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	72,1127,5304	AA,AG,GG		10.593,8.1707,9.7724	,,	2315/3178,1708/2571,2109/2972	238257013	1271,11735	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon30			TCCAGGGAATCCT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.6945C>T	2.37:g.238257013G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.901;A|0.099	0.099	strong		0.358	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
LPHN1	22859	hgsc.bcm.edu	37	19	14261853	14261853	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14261853G>A	ENST00000340736.6	-	24	4554	c.4257C>T	c.(4255-4257)ccC>ccT	p.P1419P	CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000588658.1_RNA|LPHN1_ENST00000361434.3_Silent_p.P1414P	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1419	Poly-Pro.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AGATTTCGGGGGGGCCGGGGG	0.731																																					p.P1419P		Atlas-SNP	.											.	LPHN1	107	.	0			c.C4257T						PASS	.						2.0	3.0	3.0					19																	14261853		1382	3162	4544	SO:0001819	synonymous_variant	22859	exon24			TTCGGGGGGGCCG	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.4257C>T	19.37:g.14261853G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	33	23	0.69697	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	37	CCDS32928.1																																																																																			.	.	none		0.731	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921	
PLXNB3	5365	hgsc.bcm.edu	37	X	153035798	153035798	+	Missense_Mutation	SNP	G	G	A	rs2266879	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153035798G>A	ENST00000361971.5	+	9	1906	c.1792G>A	c.(1792-1794)Gtc>Atc	p.V598I	PLXNB3_ENST00000538966.1_Missense_Mutation_p.V621I|PLXNB3_ENST00000538776.1_Missense_Mutation_p.V251I|PLXNB3_ENST00000538543.1_Missense_Mutation_p.V148I|PLXNB3_ENST00000538282.1_Missense_Mutation_p.V208I	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	598			V -> I (in dbSNP:rs2266879). {ECO:0000269|PubMed:14702039}.		axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCAGACCACGTCACTGTGCC	0.642													G|||	1137	0.301192	0.177	0.2378	3775	,	,		13509	0.0804		0.4791	False		,,,				2504	0.1789				p.V621I		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G1861A						PASS	.		ILE/VAL,ILE/VAL	1017,2810		131,607,148,892,419	76.0	50.0	59.0		1861,1792	-2.9	0.0	X	dbSNP_100	59	4336,2389		1034,1079,1189,315,680	yes	missense,missense	PLXNB3	NM_001163257.1,NM_005393.2	29,29	1165,1686,1337,1207,1099	AA,AG,A,GG,G		35.5242,26.5743,49.2703	benign,benign	621/1933,598/1910	153035798	5353,5199	2197	4297	6494	SO:0001583	missense	5365	exon10			GACCACGTCACTG	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.1792G>A	X.37:g.153035798G>A	ENSP00000355378:p.Val598Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	336	202	0.60119	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	610	0.3676913803496082	78	0.18055555555555555	66	0.2185430463576159	31	0.05719557195571956	253	0.4755639097744361	g	5.719	0.317087	0.10845	0.265743	0.644758	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538543;ENST00000538282	T;T;T;T;T	0.70164	5.1;5.06;4.51;1.75;-0.46	4.78	-2.94	0.05581	.	1.088280	0.07055	N	0.832721	T	0.00012	0.0000	N	0.25245	0.725	0.52501	P	4.999999999999449E-5	B;P;B;B	0.44776	0.018;0.843;0.055;0.018	B;B;B;B	0.33295	0.007;0.161;0.026;0.012	T	0.36480	-0.9746	9	0.30078	T	0.28	.	11.2095	0.48790	0.5531:0.0:0.4469:0.0	rs2266879	251;148;621;598	B7Z3H9;F5GZZ4;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	I	621;598;251;148;208	ENSP00000442736:V621I;ENSP00000355378:V598I;ENSP00000445569:V251I;ENSP00000444086:V148I;ENSP00000441919:V208I	ENSP00000355378:V598I	V	+	1	0	PLXNB3	152688992	0.000000	0.05858	0.037000	0.18230	0.021000	0.10359	-0.430000	0.06973	-1.033000	0.03299	-0.303000	0.09236	GTC	G|0.542;A|0.458	0.458	strong		0.642	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
ZBTB38	253461	hgsc.bcm.edu	37	3	141163705	141163705	+	Silent	SNP	G	G	A	rs3732868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:141163705G>A	ENST00000514251.1	+	4	2754	c.2475G>A	c.(2473-2475)ccG>ccA	p.P825P	ZBTB38_ENST00000441582.2_Silent_p.P825P|ZBTB38_ENST00000321464.5_Silent_p.P826P					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						CTGCTCTGCCGGGAACCTCCA	0.408													G|||	119	0.023762	0.0461	0.0014	5008	,	,		21124	0.0298		0.003	False		,,,				2504	0.0245				p.P825P		Atlas-SNP	.											.	ZBTB38	92	.	0			c.G2475A						PASS	.	G		187,3519		7,173,1673	61.0	58.0	59.0		2475	-11.1	0.0	3	dbSNP_107	59	23,8155		0,23,4066	no	coding-synonymous	ZBTB38	NM_001080412.2		7,196,5739	AA,AG,GG		0.2812,5.0459,1.7671		825/1196	141163705	210,11674	1853	4089	5942	SO:0001819	synonymous_variant	253461	exon8			TCTGCCGGGAACC	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.2475G>A	3.37:g.141163705G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	180	78	0.433333	NM_001080412		Silent	SNP	ENST00000514251.1	37	CCDS43157.1																																																																																			G|0.980;A|0.020	0.020	strong		0.408	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
RIN2	54453	hgsc.bcm.edu	37	20	19915770	19915770	+	Missense_Mutation	SNP	G	G	A	rs78648341	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:19915770G>A	ENST00000255006.6	+	3	381	c.232G>A	c.(232-234)Gga>Aga	p.G78R	RIN2_ENST00000440354.2_Missense_Mutation_p.G29R|RIN2_ENST00000484638.1_3'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	29					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						CTCGGAGATCGGAGAACTGAA	0.532													G|||	37	0.00738818	0.0008	0.0101	5008	,	,		17562	0.0		0.0278	False		,,,				2504	0.001				p.G78R		Atlas-SNP	.											.	RIN2	126	.	0			c.G232A						PASS	.	G	ARG/GLY,ARG/GLY	4,3954		0,4,1975	70.0	68.0	69.0		232,85	5.7	1.0	20	dbSNP_131	69	99,8211		1,97,4057	yes	missense,missense	RIN2	NM_001242581.1,NM_018993.3	125,125	1,101,6032	AA,AG,GG		1.1913,0.1011,0.8396	probably-damaging,probably-damaging	78/945,29/896	19915770	103,12165	1979	4155	6134	SO:0001583	missense	54453	exon3			GAGATCGGAGAAC	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.232G>A	20.37:g.19915770G>A	ENSP00000255006:p.Gly78Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	37	CCDS56182.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	G	27.9	4.876983	0.91664	0.001011	0.011913	ENSG00000132669	ENST00000255006;ENST00000440354	T;T	0.06933	3.24;3.24	5.71	5.71	0.89125	.	0.059318	0.64402	D	0.000003	T	0.08846	0.0219	L	0.47716	1.5	0.33565	D	0.597839	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00834	-1.1547	9	.	.	.	-14.9319	18.6285	0.91350	0.0:0.0:1.0:0.0	.	29;29	E7EPJ1;Q8WYP3	.;RIN2_HUMAN	R	78;29	ENSP00000255006:G78R;ENSP00000391239:G29R	.	G	+	1	0	RIN2	19863770	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.995000	0.76257	2.703000	0.92315	0.655000	0.94253	GGA	G|0.987;A|0.013	0.013	strong		0.532	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
CLIP4	79745	hgsc.bcm.edu	37	2	29356567	29356567	+	Silent	SNP	G	G	C	rs17749904	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29356567G>C	ENST00000320081.5	+	5	669	c.414G>C	c.(412-414)ctG>ctC	p.L138L	CLIP4_ENST00000404424.1_Silent_p.L138L|CLIP4_ENST00000401617.2_Silent_p.L31L|CLIP4_ENST00000401605.1_Silent_p.L138L	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	138										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					TTATTGACCTGGGAGCAGACA	0.353													G|||	625	0.1248	0.0681	0.1326	5008	,	,		17197	0.0149		0.2008	False		,,,				2504	0.2311				p.L138L		Atlas-SNP	.											.	CLIP4	69	.	0			c.G414C						PASS	.	G		395,4011	196.7+/-221.0	16,363,1824	111.0	104.0	106.0		414	4.7	1.0	2	dbSNP_123	106	1947,6653	341.2+/-323.9	209,1529,2562	no	coding-synonymous	CLIP4	NM_024692.4		225,1892,4386	CC,CG,GG		22.6395,8.965,18.0071		138/706	29356567	2342,10664	2203	4300	6503	SO:0001819	synonymous_variant	79745	exon5			TGACCTGGGAGCA	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"""Ankyrin repeat domain containing"""	26108	protein-coding gene	gene with protein product			"""restin-like 2"""	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.414G>C	2.37:g.29356567G>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	140	55	0.392857	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Silent	SNP	ENST00000320081.5	37	CCDS1770.1																																																																																			G|0.838;C|0.162	0.162	strong		0.353	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692	
FGF20	26281	hgsc.bcm.edu	37	8	16859440	16859440	+	Silent	SNP	C	C	T	rs17514894	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:16859440C>T	ENST00000180166.5	-	1	250	c.102G>A	c.(100-102)ccG>ccA	p.P34P		NM_019851.2	NP_062825.1	Q9NP95	FGF20_HUMAN	fibroblast growth factor 20	34					cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of cardiac muscle cell proliferation (GO:0060043)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	11				Colorectal(111;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		CCAGCAGCGGCGGCCGCTCCC	0.766													C|||	373	0.0744808	0.0439	0.072	5008	,	,		7842	0.004		0.1541	False		,,,				2504	0.1084				p.P34P		Atlas-SNP	.											.	FGF20	16	.	0			c.G102A						PASS	.	C		124,1958		2,120,919	1.0	2.0	1.0		102	0.8	0.0	8	dbSNP_123	1	761,4477		44,673,1902	no	coding-synonymous	FGF20	NM_019851.2		46,793,2821	TT,TC,CC		14.5284,5.9558,12.0902		34/212	16859440	885,6435	1041	2619	3660	SO:0001819	synonymous_variant	26281	exon1			CAGCGGCGGCCGC	AB030648	CCDS5998.1	8p22	2008-05-15			ENSG00000078579	ENSG00000078579			3677	protein-coding gene	gene with protein product		605558				10913340	Standard	NM_019851		Approved		uc003wxc.1	Q9NP95	OTTHUMG00000096964	ENST00000180166.5:c.102G>A	8.37:g.16859440C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_019851	B2RPH5	Silent	SNP	ENST00000180166.5	37	CCDS5998.1																																																																																			C|0.916;T|0.084	0.084	strong		0.766	FGF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214030.1		
GGTLC2	91227	hgsc.bcm.edu	37	22	22989270	22989270	+	Missense_Mutation	SNP	G	G	A	rs2330126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:22989270G>A	ENST00000480559.1	+	2	223	c.223G>A	c.(223-225)Gat>Aat	p.D75N	POM121L1P_ENST00000402027.1_RNA|GGTLC2_ENST00000448514.1_Missense_Mutation_p.D75N	NM_199127.2	NP_954578.2	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase light chain 2	75			D -> N (in dbSNP:rs2330126).		glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)	gamma-glutamyltransferase activity (GO:0003840)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)		CCTGTTCAATGATGAAATGGA	0.597													.|||	846	0.16893	0.056	0.1066	5008	,	,		9615	0.2123		0.2296	False		,,,				2504	0.2587				p.D75N		Atlas-SNP	.											.	GGTLC2	20	.	0			c.G223A						PASS	.						93.0	95.0	94.0					22																	22989270		2203	4294	6497	SO:0001583	missense	91227	exon2			TTCAATGATGAAA	X98922	CCDS13802.2	22q11.21	2008-03-25	2008-03-10	2008-03-10	ENSG00000100121	ENSG00000100121		"""Gamma-glutamyltransferases"""	18596	protein-coding gene	gene with protein product		612339	"""gamma-glutamyltransferase-like 4"""	GGTL4		9074928, 18357469	Standard	NM_199127		Approved		uc010gtt.2	Q14390	OTTHUMG00000151177	ENST00000480559.1:c.223G>A	22.37:g.22989270G>A	ENSP00000419751:p.Asp75Asn	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	24	8	0.333333	NM_199127	A1A516|A2VCM9|Q5NV76|Q6ISH0	Missense_Mutation	SNP	ENST00000480559.1	37	CCDS13802.2	244	0.11172161172161173	14	0.028455284552845527	26	0.0718232044198895	87	0.1520979020979021	117	0.15435356200527706	g	0.017	-1.492819	0.01009	.	.	ENSG00000100121	ENST00000480559;ENST00000448514	T;T	0.03951	3.75;3.75	.	.	.	.	0.166570	0.50627	N	0.000104	T	0.00012	0.0000	N	0.11201	0.11	0.34013	D	0.651672	B;B	0.06786	0.0;0.001	B;B	0.12156	0.007;0.003	T	0.49504	-0.8933	9	0.02654	T	1	-16.3779	5.8178	0.18506	0.001:0.0:0.999:0.0	rs2330126;rs2330126	75;75	Q14390;B7WND7	GGTL2_HUMAN;.	N	75	ENSP00000419751:D75N;ENSP00000415676:D75N	ENSP00000415676:D75N	D	+	1	0	GGTLC2	21319270	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	1.893000	0.39758	-0.000000	0.14550	0.000000	0.15137	GAT	G|0.899;A|0.101	0.101	strong		0.597	GGTLC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321662.1	NM_199127	
POMC	5443	hgsc.bcm.edu	37	2	25387535	25387535	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:25387535T>C	ENST00000405623.1	-	2	562	c.107A>G	c.(106-108)gAc>gGc	p.D36G	POMC_ENST00000395826.2_Missense_Mutation_p.D36G|POMC_ENST00000380794.1_Missense_Mutation_p.D36G|POMC_ENST00000264708.3_Missense_Mutation_p.D36G			P01189	COLI_HUMAN	proopiomelanocortin	36					cell-cell signaling (GO:0007267)|cellular pigmentation (GO:0033059)|cellular protein metabolic process (GO:0044267)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|negative regulation of tumor necrosis factor production (GO:0032720)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of appetite (GO:0032098)|regulation of blood pressure (GO:0008217)|regulation of corticosterone secretion (GO:2000852)|regulation of glycogen metabolic process (GO:0070873)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|peroxisomal matrix (GO:0005782)|secretory granule (GO:0030141)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|hormone activity (GO:0005179)|receptor binding (GO:0005102)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)	12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Loperamide(DB00836)	CGTGGTGAGGTCCTGACACTG	0.592																																					p.D36G	Colon(110;1515 1566 8452 10082 43216)	Atlas-SNP	.											POMC,NS,carcinoma,-1,1	POMC	33	1	0			c.A107G						scavenged	.						82.0	80.0	81.0					2																	25387535		2203	4300	6503	SO:0001583	missense	5443	exon3			GTGAGGTCCTGAC		CCDS1717.1	2p23	2013-02-25	2008-07-31		ENSG00000115138	ENSG00000115138		"""Endogenous ligands"""	9201	protein-coding gene	gene with protein product	"""adrenocorticotropin"", ""beta-lipotropin"", ""alpha-melanocyte stimulating hormone"", ""beta-melanocyte stimulating hormone"", ""beta-endorphin"", ""adrenocorticotropic hormone"", ""opiomelanocortin prepropeptide"""	176830				6254047, 9620771	Standard	NM_001035256		Approved	MSH, POC, CLIP, ACTH, NPP, LPH	uc002rfz.1	P01189	OTTHUMG00000094764	ENST00000405623.1:c.107A>G	2.37:g.25387535T>C	ENSP00000384092:p.Asp36Gly	Somatic	233	5	0.0214592		WXS	Illumina HiSeq	Phase_I	300	5	0.0166667	NM_001035256	P78442|Q53T23|Q9UD39|Q9UD40	Missense_Mutation	SNP	ENST00000405623.1	37	CCDS1717.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.540371	0.85917	.	.	ENSG00000115138	ENST00000380794;ENST00000405623;ENST00000264708;ENST00000395826;ENST00000449220	T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13	5.34	5.34	0.76211	Pro-opiomelanocortin N-terminal (1);	0.154870	0.56097	D	0.000032	D	0.86632	0.5979	M	0.75447	2.3	0.80722	D	1	D	0.63046	0.992	D	0.66196	0.942	D	0.88329	0.2967	10	0.87932	D	0	-10.6078	14.4351	0.67274	0.0:0.0:0.0:1.0	.	36	P01189	COLI_HUMAN	G	36	ENSP00000370171:D36G;ENSP00000384092:D36G;ENSP00000264708:D36G;ENSP00000379170:D36G;ENSP00000387993:D36G	ENSP00000264708:D36G	D	-	2	0	POMC	25241039	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.387000	0.66243	2.146000	0.66826	0.379000	0.24179	GAC	.	.	none		0.592	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211573.3	NM_001035256	
AFMID	125061	hgsc.bcm.edu	37	17	76200965	76200965	+	Missense_Mutation	SNP	C	C	T	rs72897843	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:76200965C>T	ENST00000327898.5	+	6	460	c.451C>T	c.(451-453)Cgg>Tgg	p.R151W	AFMID_ENST00000589664.1_3'UTR|AFMID_ENST00000591952.1_Intron|AFMID_ENST00000409257.5_Missense_Mutation_p.R151W|AFMID_ENST00000588800.1_Intron					arylformamidase											autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|skin(1)	19			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.134)			TGTCCAGAAGCGGTATCCAAG	0.552													C|||	196	0.0391374	0.0068	0.0533	5008	,	,		21238	0.001		0.0835	False		,,,				2504	0.0665				p.R151W		Atlas-SNP	.											.	AFMID	38	.	0			c.C451T						PASS	.	C	TRP/ARG,TRP/ARG	95,4311	78.8+/-117.2	2,91,2110	120.0	110.0	113.0		451,451	3.9	0.0	17	dbSNP_130	113	846,7754	193.7+/-239.3	49,748,3503	yes	missense,missense	AFMID	NM_001010982.4,NM_001145526.2	101,101	51,839,5613	TT,TC,CC		9.8372,2.1562,7.2351	probably-damaging,probably-damaging	151/304,151/309	76200965	941,12065	2203	4300	6503	SO:0001583	missense	125061	exon6			CAGAAGCGGTATC	BX648442	CCDS32750.2, CCDS45801.1	17q25.3	2005-11-09			ENSG00000183077	ENSG00000183077	3.5.1.9		20910	protein-coding gene	gene with protein product							Standard	NR_027083		Approved	DKFZp686F03259, KF	uc002juz.3	Q63HM1	OTTHUMG00000153957	ENST00000327898.5:c.451C>T	17.37:g.76200965C>T	ENSP00000328938:p.Arg151Trp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	170	82	0.482353	NM_001145526		Missense_Mutation	SNP	ENST00000327898.5	37	CCDS45801.1	105	0.04807692307692308	4	0.008130081300813009	27	0.07458563535911603	1	0.0017482517482517483	73	0.09630606860158311	C	18.23	3.578450	0.65878	0.021562	0.098372	ENSG00000183077	ENST00000409257;ENST00000327898	T;T	0.12255	2.7;2.7	4.89	3.89	0.44902	Alpha/beta hydrolase fold-3 (1);	0.723244	0.13872	N	0.356932	T	0.00936	0.0031	M	0.75264	2.295	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.60609	0.877;0.804	T	0.00039	-1.2241	10	0.66056	D	0.02	-9.5486	12.4906	0.55897	0.1675:0.8325:0.0:0.0	.	151;151	Q63HM1;Q63HM1-2	AFMID_HUMAN;.	W	151	ENSP00000386890:R151W;ENSP00000328938:R151W	ENSP00000328938:R151W	R	+	1	2	AFMID	73712560	1.000000	0.71417	0.032000	0.17829	0.006000	0.05464	4.622000	0.61240	1.224000	0.43551	0.655000	0.94253	CGG	C|0.933;T|0.067	0.067	strong		0.552	AFMID-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333203.1	XM_058889	
FBXL16	146330	hgsc.bcm.edu	37	16	746914	746914	+	Silent	SNP	G	G	A	rs4984915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:746914G>A	ENST00000397621.1	-	2	823	c.492C>T	c.(490-492)gcC>gcT	p.A164A	FBXL16_ENST00000562585.1_5'Flank|FBXL16_ENST00000324361.5_Silent_p.A164A|FBXL16_ENST00000562563.1_5'Flank	NM_153350.3	NP_699181.2	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	164										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)	10		Hepatocellular(780;0.0218)				AGCCTCTGGCGGCAAAACCCT	0.587													G|||	1919	0.383187	0.208	0.3833	5008	,	,		8377	0.7123		0.2535	False		,,,				2504	0.4141				p.A164A		Atlas-SNP	.											FBXL16,NS,carcinoma,0,1	FBXL16	25	1	0			c.C492T						PASS	.	G		837,3563	328.0+/-300.3	86,665,1449	80.0	71.0	74.0		492	-8.3	0.0	16	dbSNP_111	74	1906,6692	337.4+/-322.3	205,1496,2598	no	coding-synonymous	FBXL16	NM_153350.3		291,2161,4047	AA,AG,GG		22.1679,19.0227,21.1032		164/480	746914	2743,10255	2200	4299	6499	SO:0001819	synonymous_variant	146330	exon2			TCTGGCGGCAAAA	BC036680	CCDS10421.1	16p13.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000127585	ENSG00000127585		"""F-boxes / Leucine-rich repeats"""	14150	protein-coding gene	gene with protein product		609082	"""chromosome 16 open reading frame 22"""	C16orf22		11157797	Standard	NM_153350		Approved	MGC33974, Fbl16	uc021taa.1	Q8N461	OTTHUMG00000090420	ENST00000397621.1:c.492C>T	16.37:g.746914G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_153350	B3KR59|D3DU60|Q2MHR2|Q96S14|Q9UJI0	Silent	SNP	ENST00000397621.1	37	CCDS10421.1																																																																																			G|0.718;A|0.282	0.282	strong		0.587	FBXL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206851.2	NM_153350	
CCDC91	55297	hgsc.bcm.edu	37	12	28412372	28412372	+	Missense_Mutation	SNP	G	G	A	rs11049488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:28412372G>A	ENST00000545336.1	+	6	525	c.106G>A	c.(106-108)Gca>Aca	p.A36T	CCDC91_ENST00000381259.1_Missense_Mutation_p.A36T|CCDC91_ENST00000539107.1_Missense_Mutation_p.A36T|CCDC91_ENST00000381256.1_Missense_Mutation_p.A36T			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	36				A -> T (in Ref. 1; AAP42284). {ECO:0000305}.	protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					TGCCTTTCCTGCAGGTATTGG	0.388													A|||	624	0.124601	0.0182	0.1239	5008	,	,		14041	0.0427		0.2972	False		,,,				2504	0.1759				p.A36T		Atlas-SNP	.											.	CCDC91	63	.	0			c.G106A						PASS	.	A	THR/ALA	243,4163	803.2+/-415.7	8,227,1968	112.0	93.0	100.0		106	-0.5	1.0	12	dbSNP_120	100	2641,5957	685.6+/-404.1	403,1835,2061	yes	missense	CCDC91	NM_018318.3	58	411,2062,4029	AA,AG,GG		30.7164,5.5152,22.1778	benign	36/442	28412372	2884,10120	2203	4299	6502	SO:0001583	missense	55297	exon2			TTTCCTGCAGGTA	AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"""GGA binding partner"""					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.106G>A	12.37:g.28412372G>A	ENSP00000438040:p.Ala36Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	136	130	0.955882	NM_018318	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Missense_Mutation	SNP	ENST00000545336.1	37	CCDS8716.1	331	0.15155677655677655	16	0.032520325203252036	50	0.13812154696132597	31	0.05419580419580419	234	0.3087071240105541	A	5.392	0.257578	0.10239	0.055152	0.307164	ENSG00000123106	ENST00000538586;ENST00000539107;ENST00000536442;ENST00000545336;ENST00000543534;ENST00000545737;ENST00000381259;ENST00000381256	T;T;T;T;T;T	0.30448	1.56;1.53;1.54;1.53;1.54;1.56	5.57	-0.515	0.11954	.	0.204155	0.34268	N	0.004109	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.9999999999920092	B	0.02656	0.0	B	0.08055	0.003	T	0.38373	-0.9664	9	0.09843	T	0.71	-2.8834	1.3506	0.02172	0.4348:0.1422:0.2856:0.1374	rs11049488;rs52814885;rs58237387;rs11049488	36	Q7Z6B0	CCD91_HUMAN	T	36	ENSP00000440513:A36T;ENSP00000445660:A36T;ENSP00000438040:A36T;ENSP00000442544:A36T;ENSP00000370658:A36T;ENSP00000370655:A36T	ENSP00000370655:A36T	A	+	1	0	CCDC91	28303639	0.388000	0.25197	0.992000	0.48379	0.931000	0.56810	-0.115000	0.10741	-0.272000	0.09259	-0.254000	0.11334	GCA	G|0.816;A|0.184	0.184	strong		0.388	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1	NM_018318	
PTPRG	5793	hgsc.bcm.edu	37	3	62189189	62189189	+	Missense_Mutation	SNP	G	G	A	rs2292245	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:62189189G>A	ENST00000474889.1	+	12	2097	c.1720G>A	c.(1720-1722)Ggc>Agc	p.G574S	PTPRG_ENST00000295874.10_Missense_Mutation_p.G574S	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	574			G -> S (in dbSNP:rs2292245).		brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		AACCAAGGACGGCGAGGGCAC	0.617													A|||	1089	0.217452	0.1543	0.1124	5008	,	,		16506	0.3581		0.159	False		,,,				2504	0.2924				p.G574S		Atlas-SNP	.											.	PTPRG	153	.	0			c.G1720A						PASS	.	A	SER/GLY	586,3754		42,502,1626	59.0	37.0	44.0		1720	-5.6	0.4	3	dbSNP_100	44	1350,7154		105,1140,3007	yes	missense	PTPRG	NM_002841.3	56	147,1642,4633	AA,AG,GG		15.8749,13.5023,15.0732	benign	574/1446	62189189	1936,10908	2170	4252	6422	SO:0001583	missense	5793	exon12			AAGGACGGCGAGG	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.1720G>A	3.37:g.62189189G>A	ENSP00000418112:p.Gly574Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	393	0.17994505494505494	55	0.11178861788617886	48	0.13259668508287292	166	0.2902097902097902	124	0.16358839050131926	A	8.693	0.907841	0.17833	0.135023	0.158749	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.51574	0.7;0.73	4.39	-5.58	0.02512	.	0.953046	0.08810	N	0.890407	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B;B	0.24132	0.098;0.059	B;B	0.14578	0.011;0.003	T	0.29088	-1.0023	9	0.02654	T	1	.	14.1478	0.65362	0.592:0.0:0.408:0.0	rs2292245;rs52793348;rs58550740;rs2292245	574;574	P23470-2;P23470	.;PTPRG_HUMAN	S	574	ENSP00000418112:G574S;ENSP00000295874:G574S	ENSP00000295874:G574S	G	+	1	0	PTPRG	62164229	0.000000	0.05858	0.357000	0.25798	0.616000	0.37450	-1.794000	0.01753	-1.665000	0.01477	-0.332000	0.08345	GGC	G|0.820;A|0.180	0.180	strong		0.617	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
DOCK5	80005	hgsc.bcm.edu	37	8	25230168	25230168	+	Silent	SNP	C	C	T	rs2271108	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:25230168C>T	ENST00000276440.7	+	35	3662	c.3618C>T	c.(3616-3618)gaC>gaT	p.D1206D		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1206					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.D1206D(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		ACCTGCTGGACTATAGAACCA	0.537													C|||	2194	0.438099	0.382	0.464	5008	,	,		20146	0.3968		0.508	False		,,,				2504	0.4663				p.D1206D	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											DOCK5,NS,carcinoma,0,1	DOCK5	167	1	1	Substitution - coding silent(1)	stomach(1)	c.C3618T						PASS	.	C		1669,2737	507.8+/-366.8	322,1025,856	93.0	79.0	83.0		3618	3.5	1.0	8	dbSNP_100	83	4219,4381	570.7+/-389.4	1030,2159,1111	no	coding-synonymous	DOCK5	NM_024940.6		1352,3184,1967	TT,TC,CC		49.0581,37.8802,45.2714		1206/1871	25230168	5888,7118	2203	4300	6503	SO:0001819	synonymous_variant	80005	exon35			GCTGGACTATAGA		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.3618C>T	8.37:g.25230168C>T		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1																																																																																			C|0.562;T|0.438	0.438	strong		0.537	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
PIP	5304	hgsc.bcm.edu	37	7	142836203	142836203	+	Missense_Mutation	SNP	A	A	T	rs73170678	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:142836203A>T	ENST00000291009.3	+	3	277	c.237A>T	c.(235-237)caA>caT	p.Q79H		NM_002652.2	NP_002643.1	P12273	PIP_HUMAN	prolactin-induced protein	79					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of gene expression (GO:0010628)|proteolysis (GO:0006508)|regulation of immune system process (GO:0002682)|retina homeostasis (GO:0001895)	apical plasma membrane (GO:0016324)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	actin binding (GO:0003779)|aspartic-type endopeptidase activity (GO:0004190)|glycoprotein binding (GO:0001948)|IgG binding (GO:0019864)|protein dimerization activity (GO:0046983)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	18	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)		TCCCTCTACAAGGTGCATTTA	0.428													A|||	233	0.0465256	0.0197	0.0605	5008	,	,		19261	0.002		0.1431	False		,,,				2504	0.0194				p.Q79H		Atlas-SNP	.											.	PIP	34	.	0			c.A237T						PASS	.	A	HIS/GLN	137,4269	98.5+/-137.1	2,133,2068	129.0	113.0	119.0		237	-8.4	0.0	7	dbSNP_130	119	1208,7390	244.2+/-273.5	98,1012,3189	yes	missense	PIP	NM_002652.2	24	100,1145,5257	TT,TA,AA		14.0498,3.1094,10.343	benign	79/147	142836203	1345,11659	2203	4299	6502	SO:0001583	missense	5304	exon3			TCTACAAGGTGCA		CCDS34768.1	7q34	2013-09-19			ENSG00000159763	ENSG00000159763			8993	protein-coding gene	gene with protein product	"""prolactin-inducible protein"""	176720				2727805, 1955075	Standard	NM_002652		Approved	GCDFP-15, GCDFP15, GPIP4	uc003wcf.1	P12273	OTTHUMG00000152635	ENST00000291009.3:c.237A>T	7.37:g.142836203A>T	ENSP00000291009:p.Gln79His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	190	98	0.515789	NM_002652	A0A963|A0A9C3|A0A9F3|A4D2I1	Missense_Mutation	SNP	ENST00000291009.3	37	CCDS34768.1	150	0.06868131868131869	14	0.028455284552845527	25	0.06906077348066299	0	0.0	111	0.14643799472295516	A	7.950	0.744750	0.15710	0.031094	0.140498	ENSG00000159763	ENST00000291009	T	0.14516	2.5	4.18	-8.36	0.00980	.	2.263620	0.01312	N	0.010651	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.28964	-1.0027	9	0.72032	D	0.01	.	11.9753	0.53087	0.1343:0.093:0.0:0.7727	.	79	P12273	PIP_HUMAN	H	79	ENSP00000291009:Q79H	ENSP00000291009:Q79H	Q	+	3	2	PIP	142546325	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.469000	0.00992	-3.599000	0.00134	-1.437000	0.01076	CAA	A|0.904;T|0.096	0.096	strong		0.428	PIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327089.1	NM_002652	
CYP4A22	284541	hgsc.bcm.edu	37	1	47607785	47607785	+	Missense_Mutation	SNP	G	G	A	rs2056900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:47607785G>A	ENST00000371891.3	+	4	419	c.388G>A	c.(388-390)Ggc>Agc	p.G130S	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000294337.3_Missense_Mutation_p.G130S|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000371890.3_Missense_Mutation_p.G130S	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	130			G -> S (in allele CYP4A22*4, allele CYP4A22*10, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs2056900). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTTAGGGTACGGCTTGCTCCT	0.537													G|||	1684	0.336262	0.2073	0.232	5008	,	,		22904	0.5546		0.1928	False		,,,				2504	0.5072				p.G130S	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.G388A						PASS	.	G	SER/GLY	1005,3401	374.2+/-321.1	104,797,1302	100.0	83.0	89.0		388	0.7	0.1	1	dbSNP_94	89	1733,6867	316.6+/-312.8	183,1367,2750	yes	missense	CYP4A22	NM_001010969.2	56	287,2164,4052	AA,AG,GG		20.1512,22.8098,21.0518	probably-damaging	130/520	47607785	2738,10268	2203	4300	6503	SO:0001583	missense	284541	exon4			GGGTACGGCTTGC		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.388G>A	1.37:g.47607785G>A	ENSP00000360958:p.Gly130Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	640	0.29304029304029305	98	0.1991869918699187	86	0.23756906077348067	315	0.5506993006993007	141	0.18601583113456466	g	18.98	3.738385	0.69304	0.228098	0.201512	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.72394	-0.65;-0.65;-0.65	1.7	0.679	0.17975	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.87328	2.875	0.22811	P	0.99870156	P;D	0.69078	0.935;0.997	B;P	0.61722	0.38;0.893	T	0.45716	-0.9242	9	0.72032	D	0.01	.	8.2754	0.31868	0.1313:0.0:0.8687:0.0	rs2056900;rs52794745;rs2056900	130;130	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	S	130	ENSP00000360957:G130S;ENSP00000360958:G130S;ENSP00000294337:G130S	ENSP00000294337:G130S	G	+	1	0	CYP4A22	47380372	1.000000	0.71417	0.118000	0.21660	0.682000	0.39822	3.218000	0.51192	0.034000	0.15491	0.195000	0.17529	GGC	G|0.768;A|0.232	0.232	strong		0.537	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
CASC5	57082	hgsc.bcm.edu	37	15	40903684	40903684	+	Missense_Mutation	SNP	A	A	G	rs12911738	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:40903684A>G	ENST00000346991.5	+	8	727	c.337A>G	c.(337-339)Aca>Gca	p.T113A	CASC5_ENST00000527044.1_Missense_Mutation_p.T85A|CASC5_ENST00000399668.2_Missense_Mutation_p.T87A			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	113	Interaction with BUB1 and BUB1B.		T -> A (in dbSNP:rs12911738). {ECO:0000269|PubMed:12087463}.		acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		aGAAACAGAAACAGGAGAAAA	0.249													G|||	3532	0.705272	0.9213	0.6225	5008	,	,		12055	0.3532		0.8559	False		,,,				2504	0.68				p.T113A		Atlas-SNP	.											CASC5_ENST00000346991,NS,carcinoma,0,2	CASC5	269	2	0			c.A337G						PASS	.						12.0	10.0	11.0					15																	40903684		899	2049	2948	SO:0001583	missense	57082	exon8			ACAGAAACAGGAG	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.337A>G	15.37:g.40903684A>G	ENSP00000335463:p.Thr113Ala	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	1531	0.701007326007326	451	0.9166666666666666	243	0.6712707182320442	183	0.31993006993006995	654	0.862796833773087	G	4.886	0.164667	0.09287	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000527044;ENST00000399668	T;T;T	0.47869	3.5;1.72;0.83	3.8	3.8	0.43715	.	0.597985	0.12673	N	0.448590	T	0.00012	0.0000	N	0.00926	-1.1	0.51012	P	9.499999999995623E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33007	-0.9885	9	0.07482	T	0.82	.	7.6321	0.28245	0.1166:0.0:0.8834:0.0	rs12911738;rs52797035;rs12911738	87;113;87	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	A	113;87;85;87	ENSP00000335463:T113A;ENSP00000432654:T85A;ENSP00000382576:T87A	ENSP00000260369:T87A	T	+	1	0	CASC5	38690976	0.445000	0.25657	0.997000	0.53966	0.630000	0.37929	0.544000	0.23253	1.180000	0.42898	-0.119000	0.15052	ACA	A|0.319;G|0.681	0.681	strong		0.249	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
MOB3B	79817	hgsc.bcm.edu	37	9	27455135	27455135	+	Silent	SNP	G	G	A	rs34959338	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:27455135G>A	ENST00000262244.5	-	2	838	c.414C>T	c.(412-414)tgC>tgT	p.C138C		NM_024761.4	NP_079037.3	Q86TA1	MOB3B_HUMAN	MOB kinase activator 3B	138							metal ion binding (GO:0046872)										ACTTACCCACGCATGTTGGAA	0.438													G|||	364	0.0726837	0.0537	0.0879	5008	,	,		20257	0.0		0.1879	False		,,,				2504	0.044				p.C138C		Atlas-SNP	.											.	.	.	.	0			c.C414T						PASS	.	G		301,4105	162.9+/-194.8	13,275,1915	95.0	88.0	90.0		414	-7.9	0.1	9	dbSNP_126	90	1603,6997	298.7+/-304.1	154,1295,2851	no	coding-synonymous	MOB3B	NM_024761.4		167,1570,4766	AA,AG,GG		18.6395,6.8316,14.6394		138/217	27455135	1904,11102	2203	4300	6503	SO:0001819	synonymous_variant	79817	exon2			ACCCACGCATGTT	AK023266	CCDS6520.1	9p21.1	2012-07-05	2011-09-28	2011-09-28	ENSG00000120162	ENSG00000120162		"""MOB kinase activators"""	23825	protein-coding gene	gene with protein product	"""monopolar spindle 1 binding, MOB1, domain containing"""		"""MOB1, Mps One Binder kinase activator-like 2B (yeast)"", ""chromosome 9 open reading frame 35"""	MOBKL2B, C9orf35		12477932	Standard	NM_024761		Approved	MOB1D, FLJ13204	uc003zqn.3	Q86TA1	OTTHUMG00000019717	ENST00000262244.5:c.414C>T	9.37:g.27455135G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	149	80	0.536913	NM_024761	Q8NEB4|Q9H8V4	Silent	SNP	ENST00000262244.5	37	CCDS6520.1																																																																																			G|0.872;A|0.128	0.128	strong		0.438	MOB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051974.2	NM_024761	
RBM12B	389677	hgsc.bcm.edu	37	8	94747496	94747496	+	Missense_Mutation	SNP	A	A	C	rs111589624	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:94747496A>C	ENST00000399300.2	-	3	1356	c.1143T>G	c.(1141-1143)gaT>gaG	p.D381E	RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000520961.1_Intron|RBM12B_ENST00000517700.1_Missense_Mutation_p.D381E	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	381							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			GTCCGGGCCTATCTCTCTCTA	0.363													A|||	29	0.00579073	0.0	0.0144	5008	,	,		19764	0.001		0.0179	False		,,,				2504	0.0				p.D381E		Atlas-SNP	.											.	RBM12B	78	.	0			c.T1143G						PASS	.	A	GLU/ASP	12,3674		0,12,1831	117.0	115.0	116.0		1143	0.2	0.9	8	dbSNP_132	116	178,7982		1,176,3903	yes	missense	RBM12B	NM_203390.2	45	1,188,5734	CC,CA,AA		2.1814,0.3256,1.6039	benign	381/1002	94747496	190,11656	1843	4080	5923	SO:0001583	missense	389677	exon3			GGGCCTATCTCTC		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.1143T>G	8.37:g.94747496A>C	ENSP00000382239:p.Asp381Glu	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	183	85	0.464481	NM_203390	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	37	CCDS43755.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	0.004	-2.307298	0.00240	0.003256	0.021814	ENSG00000183808	ENST00000399300;ENST00000517700	T;T	0.07327	3.2;3.22	5.26	0.157	0.14915	.	0.298288	0.29218	N	0.012782	T	0.00936	0.0031	N	0.01874	-0.695	0.18873	N	0.999986	B	0.02656	0.0	B	0.01281	0.0	T	0.40365	-0.9567	10	0.07482	T	0.82	-12.6752	2.1343	0.03758	0.2692:0.306:0.288:0.1368	.	381	Q8IXT5	RB12B_HUMAN	E	381	ENSP00000382239:D381E;ENSP00000427729:D381E	ENSP00000382239:D381E	D	-	3	2	RBM12B	94816672	0.003000	0.15002	0.895000	0.35142	0.446000	0.32137	-0.638000	0.05452	-0.182000	0.10602	-1.433000	0.01084	GAT	A|0.987;C|0.013	0.013	strong		0.363	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390	
EML4	27436	hgsc.bcm.edu	37	2	42515437	42515437	+	Missense_Mutation	SNP	A	A	G	rs28651764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:42515437A>G	ENST00000318522.5	+	11	1455	c.1193A>G	c.(1192-1194)aAg>aGg	p.K398R	EML4_ENST00000401738.3_Missense_Mutation_p.K409R|EML4_ENST00000402711.2_Missense_Mutation_p.K340R	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	398			K -> R (in dbSNP:rs28651764). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						GACTGGCAGAAGAAAGCAAAA	0.333			T	ALK	NSCLC								A|||	1365	0.272564	0.1679	0.1657	5008	,	,		17440	0.5784		0.3131	False		,,,				2504	0.1329				p.K398R		Atlas-SNP	.		Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	EML4_ENST00000318522,NS,carcinoma,-1,2	EML4	92	2	0			c.A1193G						PASS	.	A	ARG/LYS,ARG/LYS	765,3641	306.6+/-289.6	80,605,1518	128.0	133.0	131.0		1019,1193	1.8	1.0	2	dbSNP_125	131	2649,5951	425.5+/-355.0	406,1837,2057	yes	missense,missense	EML4	NM_001145076.1,NM_019063.3	26,26	486,2442,3575	GG,GA,AA		30.8023,17.3627,26.2494	benign,benign	340/924,398/982	42515437	3414,9592	2203	4300	6503	SO:0001583	missense	27436	exon11			GGCAGAAGAAAGC	AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924		"""WD repeat domain containing"""	1316	protein-coding gene	gene with protein product		607442		C2orf2			Standard	NM_019063		Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.1193A>G	2.37:g.42515437A>G	ENSP00000320663:p.Lys398Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_019063	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	Missense_Mutation	SNP	ENST00000318522.5	37	CCDS1807.1	716	0.32783882783882784	83	0.16869918699186992	74	0.20441988950276244	310	0.541958041958042	249	0.32849604221635886	A	13.48	2.249720	0.39797	0.173627	0.308023	ENSG00000143924	ENST00000318522;ENST00000402711;ENST00000401738	T;T;T	0.56941	0.43;0.43;0.43	5.43	1.76	0.24704	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.100460	0.64402	N	0.000003	T	0.00012	0.0000	N	0.13168	0.305	0.09310	P	0.9999999999936345	B;B;B	0.10296	0.003;0.003;0.002	B;B;B	0.13407	0.005;0.009;0.006	T	0.48502	-0.9030	9	0.20519	T	0.43	-9.7437	9.4373	0.38646	0.7214:0.0:0.2786:0.0	rs28651764	340;409;398	B5MCW9;B5MBZ0;Q9HC35	.;.;EMAL4_HUMAN	R	398;340;409	ENSP00000320663:K398R;ENSP00000385059:K340R;ENSP00000384939:K409R	ENSP00000320663:K398R	K	+	2	0	EML4	42368941	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	3.107000	0.50329	0.352000	0.24053	0.482000	0.46254	AAG	A|0.717;G|0.283	0.283	strong		0.333	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250463.3	NM_019063	
KIAA1107	23285	hgsc.bcm.edu	37	1	92647636	92647636	+	Missense_Mutation	SNP	T	T	G	rs17578364	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:92647636T>G	ENST00000370378.4	+	8	3180	c.3082T>G	c.(3082-3084)Ttt>Gtt	p.F1028V	KIAA1107_ENST00000409154.4_Missense_Mutation_p.F1083V	NM_015237.2	NP_056052.2	Q9UPP5	K1107_HUMAN	KIAA1107	1083										breast(4)|central_nervous_system(1)|endometrium(3)|kidney(2)|prostate(1)|skin(3)	14						TGTAGATTCTTTTTCACCTTC	0.378													T|||	158	0.0315495	0.0045	0.0692	5008	,	,		19351	0.001		0.0497	False		,,,				2504	0.0542				p.F1028V		Atlas-SNP	.											.	KIAA1107	60	.	0			c.T3082G						PASS	.	T	VAL/PHE	22,1362		1,20,671	84.0	79.0	81.0		3082	4.2	0.0	1	dbSNP_123	81	194,2988		8,178,1405	yes	missense	KIAA1107	NM_015237.2	50	9,198,2076	GG,GT,TT		6.0968,1.5896,4.7306	benign	1028/1355	92647636	216,4350	692	1591	2283	SO:0001583	missense	23285	exon8			GATTCTTTTTCAC	AB029030	CCDS44172.1	1p22.1	2008-02-05			ENSG00000069712	ENSG00000069712			29192	protein-coding gene	gene with protein product						10470851	Standard	NM_015237		Approved		uc010otd.2	Q9UPP5	OTTHUMG00000010292	ENST00000370378.4:c.3082T>G	1.37:g.92647636T>G	ENSP00000359404:p.Phe1028Val	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	144	73	0.506944	NM_015237	O14767|Q8N3X7	Missense_Mutation	SNP	ENST00000370378.4	37	CCDS44172.1	69	0.03159340659340659	3	0.006097560975609756	27	0.07458563535911603	0	0.0	39	0.051451187335092345	T	2.763	-0.257332	0.05791	0.015896	0.060968	ENSG00000069712	ENST00000409154;ENST00000370378	T;T	0.04119	3.7;3.7	6.06	4.15	0.48705	.	0.536093	0.19981	N	0.101775	T	0.00637	0.0021	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.47824	-0.9087	10	0.20046	T	0.44	.	6.2572	0.20879	0.0:0.5601:0.2791:0.1608	rs17578364;rs52832623;rs17578364	1028	E9PEZ5	.	V	1083;1028	ENSP00000386957:F1083V;ENSP00000359404:F1028V	ENSP00000359404:F1028V	F	+	1	0	KIAA1107	92420224	0.000000	0.05858	0.013000	0.15412	0.415000	0.31203	0.038000	0.13862	0.835000	0.34877	0.533000	0.62120	TTT	T|0.969;G|0.031	0.031	strong		0.378	KIAA1107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028375.3	XM_034086	
GRHL2	79977	hgsc.bcm.edu	37	8	102585965	102585965	+	Silent	SNP	C	C	T	rs55682875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:102585965C>T	ENST00000251808.3	+	6	1142	c.804C>T	c.(802-804)acC>acT	p.T268T	GRHL2_ENST00000395927.1_Silent_p.T252T	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	268					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			GCCCCATGACCTACCTCAACA	0.527													C|||	3	0.000599042	0.0	0.0014	5008	,	,		19445	0.0		0.002	False		,,,				2504	0.0				p.T268T		Atlas-SNP	.											.	GRHL2	68	.	0			c.C804T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	84.0	70.0	75.0		804	4.0	1.0	8	dbSNP_129	75	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	GRHL2	NM_024915.3		0,12,6491	TT,TC,CC		0.1163,0.0454,0.0923		268/626	102585965	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	79977	exon6			CATGACCTACCTC	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"""deafness, autosomal dominant 28"", ""transcription factor CP2-like 3"""	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.804C>T	8.37:g.102585965C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_024915	A1L303|Q6NT03|Q9H8B8	Silent	SNP	ENST00000251808.3	37	CCDS34931.1																																																																																			C|0.999;T|0.001	0.001	strong		0.527	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915	
NXPE1	120400	hgsc.bcm.edu	37	11	114401283	114401283	+	Silent	SNP	C	C	T	rs7941923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:114401283C>T	ENST00000424269.1	-	2	446	c.447G>A	c.(445-447)acG>acA	p.T149T	NXPE1_ENST00000536312.1_Silent_p.T149T|NXPE1_ENST00000251921.2_Silent_p.T7T|NXPE1_ENST00000536271.1_5'Flank			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	149						extracellular region (GO:0005576)											AAGCACCTGCCGTCAGTGCTG	0.572													C|||	1204	0.240415	0.5061	0.2421	5008	,	,		19321	0.0		0.1332	False		,,,				2504	0.2382				p.T7T		Atlas-SNP	.											.	NXPE1	8	.	0			c.G21A						PASS	.	C		1901,2501	543.6+/-376.3	407,1087,707	77.0	80.0	79.0		21	2.6	0.7	11	dbSNP_116	79	1188,7404	240.6+/-271.2	97,994,3205	no	coding-synonymous	FAM55A	NM_152315.2		504,2081,3912	TT,TC,CC		13.8268,43.1849,23.7725		7/406	114401283	3089,9905	2201	4296	6497	SO:0001819	synonymous_variant	120400	exon3			ACCTGCCGTCAGT	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member A"""	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.447G>A	11.37:g.114401283C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	166	91	0.548193	NM_152315	B0YJ13	Silent	SNP	ENST00000424269.1	37																																																																																				C|0.779;T|0.221	0.221	strong		0.572	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315	
RAB40A	142684	hgsc.bcm.edu	37	X	102755551	102755551	+	Missense_Mutation	SNP	T	T	A	rs1180895	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:102755551T>A	ENST00000372633.1	-	1	2252	c.134A>T	c.(133-135)cAt>cTt	p.H45L	LL0XNC01-250H12.3_ENST00000445990.1_RNA|RAB40A_ENST00000304236.1_Missense_Mutation_p.H45L			Q8WXH6	RB40A_HUMAN	RAB40A, member RAS oncogene family	45			H -> L (in dbSNP:rs1180895).		protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	12						CCCCCCGAGATGGCTGTACGG	0.602													.|||	362	0.095894	0.0348	0.1009	3775	,	,		11652	0.005		0.1879	False		,,,				2504	0.0532				p.H45L		Atlas-SNP	.											.	RAB40A	30	.	0			c.A134T						PASS	.	T	LEU/HIS	305,3530		14,234,43,1384,528	133.0	116.0	122.0		134	0.2	0.0	X	dbSNP_87	122	1828,4900		197,921,513,1310,1359	yes	missense	RAB40A	NM_080879.2	99	211,1155,556,2694,1887	AA,AT,A,TT,T		27.17,7.9531,20.1931	benign	45/278	102755551	2133,8430	2203	4300	6503	SO:0001583	missense	142684	exon3			CCGAGATGGCTGT	AF132748	CCDS35357.1	Xq22.1	2009-08-25			ENSG00000172476	ENSG00000172476		"""RAB, member RAS oncogene"""	18283	protein-coding gene	gene with protein product						11697911	Standard	NM_080879		Approved	RAR2A, Rar-2	uc004ekk.3	Q8WXH6	OTTHUMG00000022100	ENST00000372633.1:c.134A>T	X.37:g.102755551T>A	ENSP00000361716:p.His45Leu	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	247	15	0.0607287	NM_080879	O00407|Q17RQ5|Q6DK06|Q8TF06	Missense_Mutation	SNP	ENST00000372633.1	37	CCDS35357.1	210	0.12658227848101267	14	0.029166666666666667	32	0.0963855421686747	0	0.0	89	0.13692307692307693	.	3.010	-0.204171	0.06180	0.079531	0.2717	ENSG00000172476	ENST00000372633;ENST00000304236	T;T	0.78707	-1.2;-1.2	0.225	0.225	0.15325	Small GTP-binding protein domain (1);	0.136669	0.30193	U	0.010194	T	0.00012	0.0000	N	0.17474	0.49	0.31075	P	0.712591	B	0.12013	0.005	B	0.18871	0.023	T	0.06409	-1.0828	9	0.72032	D	0.01	.	4.7556	0.13082	0.0:3.0E-4:0.0:0.9997	rs1180895	45	Q8WXH6	RB40A_HUMAN	L	45	ENSP00000361716:H45L;ENSP00000305648:H45L	ENSP00000305648:H45L	H	-	2	0	RAB40A	102642207	0.984000	0.35163	0.006000	0.13384	0.003000	0.03518	1.850000	0.39328	0.238000	0.21222	0.235000	0.17854	CAT	T|0.816;A|0.184	0.184	strong		0.602	RAB40A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057714.1		
WDR90	197335	hgsc.bcm.edu	37	16	700644	700644	+	Missense_Mutation	SNP	G	G	C	rs13337278	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:700644G>C	ENST00000293879.4	+	5	494	c.494G>C	c.(493-495)aGc>aCc	p.S165T	WDR90_ENST00000549091.1_Missense_Mutation_p.S165T|AL022341.3_ENST00000455294.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	165			S -> T (in dbSNP:rs13337278). {ECO:0000269|PubMed:11572484, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CATCTCAAGAGCATCAGGCTG	0.627													G|||	1280	0.255591	0.4599	0.1772	5008	,	,		20326	0.2996		0.1103	False		,,,				2504	0.1391				p.S165T		Atlas-SNP	.											.	WDR90	107	.	0			c.G494C						PASS	.	G	THR/SER	1509,2569		286,937,816	46.0	54.0	51.0		494	5.1	0.2	16	dbSNP_121	51	1031,7345		55,921,3212	yes	missense	WDR90	NM_145294.4	58	341,1858,4028	CC,CG,GG		12.309,37.0034,20.3951	probably-damaging	165/1749	700644	2540,9914	2039	4188	6227	SO:0001583	missense	197335	exon5			TCAAGAGCATCAG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.494G>C	16.37:g.700644G>C	ENSP00000293879:p.Ser165Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	493	0.22573260073260074	204	0.4146341463414634	45	0.12430939226519337	173	0.30244755244755245	71	0.09366754617414248	G	15.88	2.963881	0.53507	0.370034	0.12309	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.21734	1.99;1.99	5.05	5.05	0.67936	.	0.000000	0.85682	U	0.000000	T	0.00012	0.0000	M	0.78637	2.42	0.09310	P	1.0	D;D;D	0.63046	0.992;0.969;0.961	P;P;P	0.62382	0.901;0.795;0.756	T	0.43491	-0.9388	9	0.72032	D	0.01	.	14.666	0.68907	0.0:0.1457:0.8543:0.0	rs13337278;rs61246473;rs13337278	165;165;165	Q96KV7;C9JMK1;Q96KV7-3	WDR90_HUMAN;.;.	T	165	ENSP00000448122:S165T;ENSP00000293879:S165T	ENSP00000293879:S165T	S	+	2	0	WDR90	640645	1.000000	0.71417	0.227000	0.23927	0.064000	0.16182	4.994000	0.63901	2.356000	0.79943	0.462000	0.41574	AGC	G|0.797;C|0.203	0.203	strong		0.627	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
SARDH	1757	hgsc.bcm.edu	37	9	136536679	136536679	+	Silent	SNP	G	G	A	rs129932	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:136536679G>A	ENST00000371872.4	-	18	2561	c.2304C>T	c.(2302-2304)atC>atT	p.I768I	SARDH_ENST00000371868.1_Silent_p.I196I|SARDH_ENST00000439388.1_Silent_p.I768I|SARDH_ENST00000422262.2_Silent_p.I600I	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	768					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		TCAGGGAGTCGATGGCGCGGT	0.677													G|||	2921	0.583267	0.6483	0.5879	5008	,	,		16133	0.7569		0.4523	False		,,,				2504	0.4479				p.I768I		Atlas-SNP	.											.	SARDH	112	.	0			c.C2304T						PASS	.	G	,	2540,1858		742,1056,401	38.0	31.0	33.0		2304,2304	-0.1	1.0	9	dbSNP_78	33	3712,4876		793,2126,1375	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	1535,3182,1776	AA,AG,GG		43.2231,42.2465,48.1442	,	768/919,768/919	136536679	6252,6734	2199	4294	6493	SO:0001819	synonymous_variant	1757	exon18			GGAGTCGATGGCG		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.2304C>T	9.37:g.136536679G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	259	124	0.478764	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			G|0.464;A|0.536	0.536	strong		0.677	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
STPG2	285555	hgsc.bcm.edu	37	4	99027137	99027137	+	Silent	SNP	T	T	C	rs2865979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:99027137T>C	ENST00000295268.3	-	5	668	c.579A>G	c.(577-579)ctA>ctG	p.L193L		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	193																	TTATTTCATATAGTCGTGGGA	0.274													T|||	1880	0.375399	0.4425	0.2882	5008	,	,		15184	0.2758		0.4026	False		,,,				2504	0.4213				p.L193L		Atlas-SNP	.											.	.	.	.	0			c.A579G						PASS	.	T		1962,2436	542.8+/-376.1	451,1060,688	85.0	88.0	87.0		579	1.1	0.9	4	dbSNP_101	87	3402,5194	491.9+/-373.2	692,2018,1588	no	coding-synonymous	C4orf37	NM_174952.2		1143,3078,2276	CC,CT,TT		39.5765,44.6112,41.2806		193/460	99027137	5364,7630	2199	4298	6497	SO:0001819	synonymous_variant	285555	exon5			TTCATATAGTCGT	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.579A>G	4.37:g.99027137T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_174952		Silent	SNP	ENST00000295268.3	37	CCDS3645.1																																																																																			T|0.607;C|0.393	0.393	strong		0.274	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
LMOD3	56203	hgsc.bcm.edu	37	3	69167851	69167851	+	Splice_Site	SNP	G	G	T	rs145387235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:69167851G>T	ENST00000420581.2	-	2	1834	c.1655C>A	c.(1654-1656)cCt>cAt	p.P552H	LMOD3_ENST00000475434.1_Splice_Site_p.P552H|LMOD3_ENST00000489031.1_Splice_Site_p.P552H	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	552	WH2.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		TCTACTTACAGGTTTAAGATA	0.473													G|||	37	0.00738818	0.0008	0.0187	5008	,	,		19795	0.0		0.0219	False		,,,				2504	0.001				p.P552H		Atlas-SNP	.											.	LMOD3	92	.	0			c.C1655A						PASS	.	G	HIS/PRO	18,3888		0,18,1935	63.0	62.0	63.0		1655	5.8	1.0	3	dbSNP_134	63	140,8154		2,136,4009	yes	missense-near-splice	LMOD3	NM_198271.3	77	2,154,5944	TT,TG,GG		1.688,0.4608,1.2951	probably-damaging	552/561	69167851	158,12042	1953	4147	6100	SO:0001630	splice_region_variant	56203	exon2			CTTACAGGTTTAA	AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.1656+1C>A	3.37:g.69167851G>T		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	252	115	0.456349	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Missense_Mutation	SNP	ENST00000420581.2	37	CCDS46862.1	21	0.009615384615384616	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	13	0.017150395778364115	G	22.1	4.238686	0.79800	0.004608	0.01688	ENSG00000163380	ENST00000420581;ENST00000489031;ENST00000475434	T;T;T	0.12361	2.69;2.69;2.69	5.84	5.84	0.93424	.	0.171431	0.56097	D	0.000032	T	0.21509	0.0518	M	0.63428	1.95	0.49582	D	0.999808	D	0.76494	0.999	D	0.65573	0.936	T	0.00293	-1.1841	10	0.62326	D	0.03	-12.4636	20.1466	0.98079	0.0:0.0:1.0:0.0	.	552	Q0VAK6	LMOD3_HUMAN	H	552	ENSP00000414670:P552H;ENSP00000417210:P552H;ENSP00000418645:P552H	ENSP00000414670:P552H	P	-	2	0	LMOD3	69250541	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.341000	0.97041	2.779000	0.95612	0.591000	0.81541	CCT	G|0.988;T|0.012	0.012	strong		0.473	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529	Missense_Mutation
CCDC102B	79839	hgsc.bcm.edu	37	18	66504351	66504351	+	Silent	SNP	G	G	A	rs637051	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:66504351G>A	ENST00000360242.5	+	2	468	c.351G>A	c.(349-351)agG>agA	p.R117R	CCDC102B_ENST00000584156.1_Silent_p.R117R|CCDC102B_ENST00000319445.6_Silent_p.R117R|CCDC102B_ENST00000358653.5_Silent_p.R117R|CCDC102B_ENST00000577772.1_3'UTR	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	117										breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				ACAGTGCCAGGGAGGAAGGAA	0.468													G|||	1033	0.20627	0.1929	0.2839	5008	,	,		19812	0.006		0.4165	False		,,,				2504	0.1595				p.R117R		Atlas-SNP	.											CCDC102B,NS,carcinoma,+1,1	CCDC102B	92	1	0			c.G351A						PASS	.	G	,	841,3021		88,665,1178	90.0	88.0	89.0		351,351	1.3	1.0	18	dbSNP_83	89	3363,4903		679,2005,1449	no	coding-synonymous,coding-synonymous	CCDC102B	NM_001093729.1,NM_024781.2	,	767,2670,2627	AA,AG,GG		40.6847,21.7763,34.6636	,	117/514,117/514	66504351	4204,7924	1931	4133	6064	SO:0001819	synonymous_variant	79839	exon4			TGCCAGGGAGGAA	AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 14"", ""aminoacylase 1-like"""	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.351G>A	18.37:g.66504351G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	154	84	0.545455	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Silent	SNP	ENST00000360242.5	37	CCDS11996.2																																																																																			G|0.744;A|0.256	0.256	strong		0.468	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52132325	52132325	+	Silent	SNP	A	A	T	rs2305372	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52132325A>T	ENST00000534261.2	-	5	1104	c.705T>A	c.(703-705)gcT>gcA	p.A235A	SIGLEC5_ENST00000222107.4_Silent_p.A235A|SIGLEC5_ENST00000429354.3_Silent_p.A235A|SIGLEC5_ENST00000599649.1_Silent_p.A235A|SIGLEC5_ENST00000570106.2_Silent_p.A235A			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	235					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		TGGTCTGTGGAGCATCTGGGA	0.527													A|||	710	0.141773	0.0197	0.0865	5008	,	,		18981	0.4921		0.0358	False		,,,				2504	0.0941				p.A235A		Atlas-SNP	.											.	SIGLEC5	67	.	0			c.T705A						PASS	.	A		139,4267	98.9+/-137.6	2,135,2066	183.0	162.0	169.0		705	-1.9	0.1	19	dbSNP_100	169	266,8334	101.2+/-162.5	3,260,4037	no	coding-synonymous	SIGLEC5	NM_003830.2		5,395,6103	TT,TA,AA		3.093,3.1548,3.1139		235/552	52132325	405,12601	2203	4300	6503	SO:0001819	synonymous_variant	8778	exon4			CTGTGGAGCATCT	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.705T>A	19.37:g.52132325A>T		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	297	137	0.461279	NM_003830		Silent	SNP	ENST00000534261.2	37	CCDS33088.1																																																																																			A|0.938;T|0.062	0.062	strong		0.527	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
PCDHGB1	56104	hgsc.bcm.edu	37	5	140731022	140731022	+	Missense_Mutation	SNP	A	A	G	rs77250251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140731022A>G	ENST00000523390.1	+	1	1195	c.1195A>G	c.(1195-1197)Aag>Gag	p.K399E	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	399	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAATTATTACAAGCTGGTGAT	0.478													.|||	118	0.0235623	0.0356	0.0288	5008	,	,		20579	0.001		0.0298	False		,,,				2504	0.0204				p.K399E		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.A1195G						PASS	.	A	,,,GLU/LYS,GLU/LYS	120,3818		2,116,1851	54.0	57.0	56.0		,,,1195,1195	3.0	0.6	5	dbSNP_132	56	243,8063		3,237,3913	yes	intron,intron,intron,missense,missense	PCDHGB1,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018922.2,NM_032095.1	,,,56,56	5,353,5764	GG,GA,AA		2.9256,3.0472,2.9647	,,,,	,,,399/928,399/811	140731022	363,11881	1969	4153	6122	SO:0001583	missense	56104	exon1			TATTACAAGCTGG	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1195A>G	5.37:g.140731022A>G	ENSP00000429273:p.Lys399Glu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	37	CCDS54923.1	53	0.024267399267399268	16	0.032520325203252036	16	0.04419889502762431	0	0.0	21	0.027704485488126648	.	10.77	1.444408	0.25987	0.030472	0.029256	ENSG00000254221	ENST00000523390	T	0.01705	4.68	5.49	2.97	0.34412	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01156	0.0038	M	0.69463	2.115	0.19300	N	0.999972	P;P	0.48998	0.918;0.835	P;P	0.51385	0.668;0.612	T	0.20273	-1.0280	9	0.66056	D	0.02	.	12.1998	0.54319	0.7302:0.2698:0.0:0.0	.	399;399	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	E	399	ENSP00000429273:K399E	ENSP00000429273:K399E	K	+	1	0	PCDHGB1	140711206	0.000000	0.05858	0.646000	0.29493	0.241000	0.25554	0.720000	0.25896	0.406000	0.25560	0.460000	0.39030	AAG	A|0.975;G|0.025	0.025	strong		0.478	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
IRS4	8471	hgsc.bcm.edu	37	X	107979512	107979512	+	Silent	SNP	C	C	T	rs2073114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:107979512C>T	ENST00000372129.2	-	1	139	c.63G>A	c.(61-63)gcG>gcA	p.A21A	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	21	Poly-Ala.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						CTGCCGCTGCCGCCGCTGCTG	0.612													c|||	2048	0.542517	0.5446	0.4236	3775	,	,		9782	0.5298		0.174	False		,,,				2504	0.3323				p.A21A		Atlas-SNP	.											.	IRS4	253	.	0			c.G63A						PASS	.			2473,1362		695,713,370,224,201	30.0	33.0	32.0		63	-4.9	0.0	X	dbSNP_96	32	1403,5319		108,798,389,1522,1477	no	coding-synonymous	IRS4	NM_003604.2		803,1511,759,1746,1678	TT,TC,T,CC,C		20.8718,35.515,36.715		21/1258	107979512	3876,6681	2203	4294	6497	SO:0001819	synonymous_variant	8471	exon1			CGCTGCCGCCGCT	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.63G>A	X.37:g.107979512C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	121	115	0.950413	NM_003604		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																			C|0.562;T|0.438	0.438	strong		0.612	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
PKD2L1	9033	hgsc.bcm.edu	37	10	102089663	102089663	+	Silent	SNP	C	C	T	rs569511	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:102089663C>T	ENST00000318222.3	-	1	580	c.198G>A	c.(196-198)gtG>gtA	p.V66V	PKD2L1_ENST00000353274.3_Silent_p.V66V|PKD2L1_ENST00000338519.3_Silent_p.V66V	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	66					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)			NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		AGCAGCTGGACACCTGGGTCC	0.557													C|||	685	0.136781	0.1021	0.085	5008	,	,		13499	0.0337		0.1153	False		,,,				2504	0.3487				p.C12Y		Atlas-SNP	.											.	PKD2L1	103	.	0			c.G35A						PASS	.	C		485,3921	226.2+/-241.8	30,425,1748	78.0	80.0	79.0		198	0.3	0.4	10	dbSNP_83	79	1145,7455	234.4+/-267.4	76,993,3231	no	coding-synonymous	PKD2L1	NM_016112.2		106,1418,4979	TT,TC,CC		13.314,11.0077,12.5327		66/806	102089663	1630,11376	2203	4300	6503	SO:0001819	synonymous_variant	9033	exon1			GCTGGACACCTGG	AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9011	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 3"""	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.198G>A	10.37:g.102089663C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	122	12	0.0983607	NM_001253837	O75972|Q5W039|Q9UP35|Q9UPA2	Missense_Mutation	SNP	ENST00000318222.3	37	CCDS7492.1	203	0.09294871794871795	56	0.11382113821138211	32	0.08839779005524862	22	0.038461538461538464	93	0.12269129287598944	C	2.201	-0.383055	0.04966	0.110077	0.13314	ENSG00000107593	ENST00000465680	T	0.55930	0.49	5.57	0.255	0.15561	.	0.558636	0.17756	N	0.163041	T	0.00524	0.0017	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.08351	-1.0726	6	0.54805	T	0.06	-2.5227	2.1951	0.03909	0.1367:0.4921:0.1331:0.238	rs569511	.	.	.	I	23	ENSP00000434019:V23I	ENSP00000434019:V23I	V	-	1	0	PKD2L1	102079653	0.010000	0.17322	0.355000	0.25773	0.134000	0.20937	-0.344000	0.07780	0.325000	0.23359	-0.143000	0.13931	GTC	C|0.882;T|0.118	0.118	strong		0.557	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112	
POTEC	388468	hgsc.bcm.edu	37	18	14543034	14543034	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:14543034T>C	ENST00000358970.5	-	1	111	c.112A>G	c.(112-114)Agc>Ggc	p.S38G	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	38										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						CTCTTGCCGCTCCCCTTGCAG	0.562																																					p.S38G		Atlas-SNP	.											POTEC,NS,carcinoma,+2,1	POTEC	129	1	0			c.A112G						scavenged	.						108.0	92.0	97.0					18																	14543034		692	1591	2283	SO:0001583	missense	388468	exon1			TGCCGCTCCCCTT	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.112A>G	18.37:g.14543034T>C	ENSP00000351856:p.Ser38Gly	Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	242	5	0.0206612	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	.	.	.	.	.	.	.	.	.	.	t	8.514	0.867213	0.17250	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.36157	1.27	0.722	-1.44	0.08856	.	.	.	.	.	T	0.26159	0.0638	L	0.43152	1.355	0.09310	N	1	B	0.31910	0.346	B	0.32289	0.143	T	0.24083	-1.0170	8	0.72032	D	0.01	.	.	.	.	.	38	B2RU33	POTEC_HUMAN	G	38	ENSP00000351856:S38G	ENSP00000351856:S38G	S	-	1	0	POTEC	14533034	0.000000	0.05858	0.005000	0.12908	0.171000	0.22731	-0.710000	0.05024	-0.428000	0.07339	0.156000	0.16432	AGC	.	.	none		0.562	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
DSE	29940	hgsc.bcm.edu	37	6	116752290	116752290	+	Missense_Mutation	SNP	A	A	G	rs34994230	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:116752290A>G	ENST00000331677.3	+	5	1288	c.844A>G	c.(844-846)Atc>Gtc	p.I282V	DSE_ENST00000452085.3_Missense_Mutation_p.I282V|DSE_ENST00000359564.2_Missense_Mutation_p.I282V|DSE_ENST00000537543.1_Missense_Mutation_p.I301V			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	282			I -> V (in dbSNP:rs34994230).		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		GCACTTCAACATCAACCACTT	0.458													A|||	69	0.013778	0.0038	0.0159	5008	,	,		18296	0.0		0.0348	False		,,,				2504	0.0184				p.I282V		Atlas-SNP	.											.	DSE	98	.	0			c.A844G						PASS	.	A	VAL/ILE,VAL/ILE	52,4354	52.3+/-87.9	0,52,2151	174.0	139.0	151.0		844,844	5.0	1.0	6	dbSNP_126	151	344,8256	117.9+/-177.5	11,322,3967	yes	missense,missense	DSE	NM_001080976.1,NM_013352.2	29,29	11,374,6118	GG,GA,AA		4.0,1.1802,3.0447	possibly-damaging,possibly-damaging	282/959,282/959	116752290	396,12610	2203	4300	6503	SO:0001583	missense	29940	exon4			TTCAACATCAACC	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"""squamous cell carcinoma antigen recognized by T cells 2"""	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.844A>G	6.37:g.116752290A>G	ENSP00000332151:p.Ile282Val	Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	237	234	0.987342	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	36	0.016483516483516484	3	0.006097560975609756	6	0.016574585635359115	0	0.0	27	0.03562005277044855	A	25.6	4.654420	0.88056	0.011802	0.04	ENSG00000111817	ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T	0.36340	1.26;1.26;1.26;1.26	6.17	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.21062	0.0507	M	0.62723	1.935	0.80722	D	1	B;B	0.18166	0.026;0.026	B;B	0.20184	0.028;0.028	T	0.04413	-1.0953	10	0.35671	T	0.21	-21.3292	12.297	0.54854	0.9345:0.0:0.0655:0.0	rs34994230	301;282	B7Z765;Q9UL01	.;DSE_HUMAN	V	282;301;282;282	ENSP00000404049:I282V;ENSP00000441152:I301V;ENSP00000332151:I282V;ENSP00000352567:I282V	ENSP00000332151:I282V	I	+	1	0	DSE	116858983	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	9.339000	0.96797	1.158000	0.42547	0.533000	0.62120	ATC	A|0.973;G|0.027	0.027	strong		0.458	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
USP15	9958	hgsc.bcm.edu	37	12	62798067	62798067	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:62798067C>G	ENST00000280377.5	+	22	2916	c.2858C>G	c.(2857-2859)gCt>gGt	p.A953G	USP15_ENST00000353364.3_Missense_Mutation_p.A924G|USP15_ENST00000393654.3_Missense_Mutation_p.A928G	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	953					BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		GGTGCTTCAGCTGCCACTGGC	0.398																																					p.A953G	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.C2858G						PASS	.						95.0	99.0	98.0					12																	62798067		2203	4300	6503	SO:0001583	missense	9958	exon22			CTTCAGCTGCCAC	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2858C>G	12.37:g.62798067C>G	ENSP00000280377:p.Ala953Gly	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	140	76	0.542857	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Missense_Mutation	SNP	ENST00000280377.5	37	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.640463	0.29157	.	.	ENSG00000135655	ENST00000353364;ENST00000280377;ENST00000393654	T;T;T	0.20200	2.09;2.09;2.09	5.69	5.69	0.88448	.	0.143143	0.47852	D	0.000211	T	0.12092	0.0294	N	0.08118	0	0.46376	D	0.999012	B;B	0.32620	0.378;0.206	B;B	0.26864	0.074;0.058	T	0.19679	-1.0298	9	.	.	.	-10.7833	19.8183	0.96579	0.0:1.0:0.0:0.0	.	953;924	Q9Y4E8;Q9Y4E8-2	UBP15_HUMAN;.	G	924;953;928	ENSP00000258123:A924G;ENSP00000280377:A953G;ENSP00000377264:A928G	.	A	+	2	0	USP15	61084334	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.544000	0.53640	2.691000	0.91804	0.650000	0.86243	GCT	.	.	none		0.398	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
COQ3	51805	hgsc.bcm.edu	37	6	99825348	99825348	+	Missense_Mutation	SNP	T	T	C	rs11548336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:99825348T>C	ENST00000254759.3	-	4	424	c.400A>G	c.(400-402)Aaa>Gaa	p.K134E	COQ3_ENST00000369242.1_5'UTR|COQ3_ENST00000369240.1_5'Flank|COQ3_ENST00000479163.1_5'UTR	NM_017421.3	NP_059117.3	Q9NZJ6	COQ3_HUMAN	coenzyme Q3 methyltransferase	134			K -> E (in dbSNP:rs11548336). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		glycerol metabolic process (GO:0006071)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0008425)|3-demethylubiquinone-9 3-O-methyltransferase activity (GO:0008689)|hexaprenyldihydroxybenzoate methyltransferase activity (GO:0004395)|O-methyltransferase activity (GO:0008171)			cervix(1)|lung(5)|upper_aerodigestive_tract(2)	8		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)		GGAATTGTTTTCAGAAGATTG	0.348													T|||	1594	0.318291	0.2428	0.2017	5008	,	,		12394	0.496		0.3151	False		,,,				2504	0.3231				p.K134E		Atlas-SNP	.											.	COQ3	19	.	0			c.A400G						PASS	.	T	GLU/LYS	1205,3201	401.9+/-332.2	174,857,1172	76.0	67.0	70.0		400	5.6	1.0	6	dbSNP_120	70	2586,6014	400.1+/-346.7	406,1774,2120	yes	missense	COQ3	NM_017421.3	56	580,2631,3292	CC,CT,TT		30.0698,27.3491,29.1481	benign	134/370	99825348	3791,9215	2203	4300	6503	SO:0001583	missense	51805	exon4			TTGTTTTCAGAAG	AF193016	CCDS5042.1	6q21	2013-05-01	2013-05-01		ENSG00000132423	ENSG00000132423	2.1.1.114		18175	protein-coding gene	gene with protein product	"""polyprenyldihydroxybenzoate methyltransferase"""	605196	"""coenzyme Q3 homolog, methyltransferase (yeast)"", ""coenzyme Q3 homolog, methyltransferase (S. cerevisiae)"""			10777520	Standard	NM_017421		Approved	bA9819.1	uc003ppk.3	Q9NZJ6	OTTHUMG00000015264	ENST00000254759.3:c.400A>G	6.37:g.99825348T>C	ENSP00000254759:p.Lys134Glu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	61	35	0.57377	NM_017421	B3KPX0|Q5T061|Q6P4F0|Q8IXG6|Q96BG1|Q9H0N1	Missense_Mutation	SNP	ENST00000254759.3	37	CCDS5042.1	704	0.32234432234432236	122	0.24796747967479674	79	0.21823204419889503	253	0.4423076923076923	250	0.32981530343007914	T	15.33	2.802452	0.50315	0.273491	0.300698	ENSG00000132423	ENST00000254759	T	0.13420	2.59	5.61	5.61	0.85477	.	0.196194	0.51477	D	0.000085	T	0.04137	0.0115	N	0.21617	0.685	0.09310	P	1.0	B	0.21821	0.061	B	0.20184	0.028	T	0.34925	-0.9809	9	0.22109	T	0.4	-30.8554	14.3797	0.66902	0.0:0.0:0.0:1.0	rs11548336;rs17355554;rs45447894;rs58257605	134	Q9NZJ6	COQ3_HUMAN	E	134	ENSP00000254759:K134E	ENSP00000254759:K134E	K	-	1	0	COQ3	99932069	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.681000	0.74523	2.147000	0.66899	0.477000	0.44152	AAA	T|0.701;C|0.299	0.299	strong		0.348	COQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041602.1	NM_017421	
APOBR	55911	hgsc.bcm.edu	37	16	28508004	28508004	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28508004G>A	ENST00000431282.1	+	3	1625	c.1615G>A	c.(1615-1617)Ggc>Agc	p.G539S	CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000328423.5_Missense_Mutation_p.G539S|APOBR_ENST00000564831.1_Missense_Mutation_p.G548S|CLN3_ENST00000569430.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	539	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						TGGCCTACTGGGCGTGGAATG	0.637																																					p.G548S		Atlas-SNP	.											APOBR,NS,carcinoma,-2,1	APOBR	89	1	0			c.G1642A						scavenged	.						12.0	14.0	13.0					16																	28508004		2048	4186	6234	SO:0001583	missense	55911	exon2			CTACTGGGCGTGG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1615G>A	16.37:g.28508004G>A	ENSP00000416094:p.Gly539Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	144	3	0.0208333	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	37		.	.	.	.	.	.	.	.	.	.	G	15.62	2.887100	0.52014	.	.	ENSG00000184730	ENST00000328423;ENST00000431282	T;T	0.61392	0.11;0.11	4.99	-2.0	0.07433	.	.	.	.	.	T	0.37265	0.0997	L	0.27053	0.805	0.09310	N	1	B;B	0.28128	0.201;0.112	B;B	0.30105	0.111;0.111	T	0.26189	-1.0110	9	0.25751	T	0.34	-3.6768	4.8597	0.13577	0.4799:0.3094:0.2108:0.0	.	539;539	Q0VD83;Q9NS13	APOBR_HUMAN;.	S	539	ENSP00000327669:G539S;ENSP00000416094:G539S	ENSP00000327669:G539S	G	+	1	0	APOBR	28415505	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.112000	0.10791	-0.053000	0.13289	-0.224000	0.12420	GGC	.	.	none		0.637	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
PSD4	23550	hgsc.bcm.edu	37	2	113956371	113956371	+	Silent	SNP	G	G	C	rs2276561	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:113956371G>C	ENST00000245796.6	+	15	2874	c.2679G>C	c.(2677-2679)acG>acC	p.T893T	PSD4_ENST00000441564.3_Silent_p.T864T	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	893					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTGCGGCCACGCACTCCGCGC	0.706													G|||	2211	0.441494	0.1838	0.5288	5008	,	,		10664	0.6498		0.4692	False		,,,				2504	0.4847				p.T893T		Atlas-SNP	.											.	PSD4	74	.	0			c.G2679C						PASS	.	G		931,3401		105,721,1340	22.0	19.0	20.0		2679	-4.7	0.9	2	dbSNP_100	20	3876,4582		947,1982,1300	no	coding-synonymous	PSD4	NM_012455.2		1052,2703,2640	CC,CG,GG		45.8264,21.4912,37.5841		893/1057	113956371	4807,7983	2166	4229	6395	SO:0001819	synonymous_variant	23550	exon15			GGCCACGCACTCC	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.2679G>C	2.37:g.113956371G>C		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Silent	SNP	ENST00000245796.6	37	CCDS33276.1																																																																																			G|0.597;C|0.403	0.403	strong		0.706	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
PGA5	5222	hgsc.bcm.edu	37	11	61018729	61018729	+	Silent	SNP	G	G	A	rs150783741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61018729G>A	ENST00000312403.5	+	9	1328	c.1143G>A	c.(1141-1143)caG>caA	p.Q381Q	PGA5_ENST00000451616.2_Silent_p.Q227Q|CTD-2331C18.5_ENST00000537594.1_RNA|PGA5_ENST00000541528.1_Silent_p.Q121Q|PGA4_ENST00000422676.2_Silent_p.Q381Q	NM_014224.2	NP_055039.1	P0DJD9	PEPA5_HUMAN	pepsinogen 5, group I (pepsinogen A)	381					digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			large_intestine(1)|skin(1)	2						CAAACAACCAGGTCGGCCTGG	0.547													g|||	28	0.00559105	0.0	0.0029	5008	,	,		19442	0.0		0.002	False		,,,				2504	0.0245				p.Q381Q		Atlas-SNP	.											.	PGA5	20	.	0			c.G1143A						PASS	.	G		3,4401	6.2+/-15.9	1,1,2200	151.0	148.0	149.0		1143	1.9	0.0	11	dbSNP_134	149	55,8543	34.3+/-88.2	1,53,4245	no	coding-synonymous	PGA5	NM_014224.2		2,54,6445	AA,AG,GG		0.6397,0.0681,0.4461		381/389	61018729	58,12944	2202	4299	6501	SO:0001819	synonymous_variant	5222	exon9			CAACCAGGTCGGC	BC029055	CCDS8001.1	11q13	2012-10-02			ENSG00000256713	ENSG00000256713	3.4.23.1		8887	protein-coding gene	gene with protein product		169730					Standard	NM_014224		Approved		uc001nqz.3	P0DJD9	OTTHUMG00000168075	ENST00000312403.5:c.1143G>A	11.37:g.61018729G>A		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	329	167	0.507599	NM_014224	A8K749|B7ZW62|B7ZW75|P00790|Q7M4R0|Q8N1E3	Silent	SNP	ENST00000312403.5	37	CCDS8001.1																																																																																			G|0.995;A|0.005	0.005	strong		0.547	PGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397972.1	NM_014224	
TTN	7273	hgsc.bcm.edu	37	2	179400869	179400869	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179400869T>C	ENST00000591111.1	-	307	95906	c.95682A>G	c.(95680-95682)gaA>gaG	p.E31894E	TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Silent_p.E24470E|TTN_ENST00000342992.6_Silent_p.E30967E|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000589042.1_Silent_p.E33535E|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Silent_p.E24595E|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.E24662E|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588804.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31894	Ig-like 141.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGCAATGATTTCTTTGCCTT	0.403																																					p.E33535E		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,-2,4	TTN	18412	4	0			c.A100605G						scavenged	.						130.0	115.0	120.0					2																	179400869		1876	4111	5987	SO:0001819	synonymous_variant	7273	exon357			AATGATTTCTTTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.95682A>G	2.37:g.179400869T>C		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	257	5	0.0194553	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.	.	none		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CATSPER4	378807	hgsc.bcm.edu	37	1	26517267	26517267	+	Missense_Mutation	SNP	A	A	G	rs41284333	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26517267A>G	ENST00000456354.2	+	1	216	c.149A>G	c.(148-150)cAc>cGc	p.H50R		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	50					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		AGTACCATTCACGAGTCCTAC	0.632													A|||	617	0.123203	0.2269	0.0908	5008	,	,		15690	0.0089		0.1879	False		,,,				2504	0.0573				p.H50R		Atlas-SNP	.											CATSPER4,NS,carcinoma,0,1	CATSPER4	59	1	0			c.A149G						PASS	.	A	ARG/HIS	980,3426	356.6+/-313.6	123,734,1346	37.0	41.0	40.0		149	1.2	0.0	1	dbSNP_127	40	1629,6971	294.4+/-301.9	152,1325,2823	yes	missense	CATSPER4	NM_198137.1	29	275,2059,4169	GG,GA,AA		18.9419,22.2424,20.06	benign	50/473	26517267	2609,10397	2203	4300	6503	SO:0001583	missense	378807	exon1			CCATTCACGAGTC	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.149A>G	1.37:g.26517267A>G	ENSP00000390423:p.His50Arg	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_198137	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	300	0.13736263736263737	114	0.23170731707317074	38	0.10497237569060773	7	0.012237762237762238	141	0.18601583113456466	A	10.33	1.319305	0.23994	0.222424	0.189419	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.97256	-4.31;-4.29	5.05	1.19	0.21007	.	1.497430	0.04299	N	0.347079	T	0.00468	0.0015	L	0.43152	1.355	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.56920	-0.7899	9	0.49607	T	0.09	-0.57	1.9246	0.03314	0.5768:0.169:0.0915:0.1627	rs41284333;rs61776646	50	Q7RTX7	CTSR4_HUMAN	R	50	ENSP00000341006:H50R;ENSP00000390423:H50R	ENSP00000341006:H50R	H	+	2	0	CATSPER4	26389854	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.742000	0.26216	0.354000	0.24105	-0.461000	0.05368	CAC	A|0.826;G|0.174	0.174	strong		0.632	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
SERPINB2	5055	hgsc.bcm.edu	37	18	61565062	61565062	+	Silent	SNP	C	C	G	rs6105	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:61565062C>G	ENST00000299502.4	+	5	599	c.519C>G	c.(517-519)gtC>gtG	p.V173V	SERPINB2_ENST00000482254.1_3'UTR|SERPINB2_ENST00000457692.1_Silent_p.V173V	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	173					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	ATTCCTGGGTCAAGACTCAAA	0.353													C|||	287	0.0573083	0.0545	0.0216	5008	,	,		19008	0.0526		0.0408	False		,,,				2504	0.1084				p.V173V		Atlas-SNP	.											.	SERPINB2	63	.	0			c.C519G						PASS	.	C	,	234,4172	135.7+/-171.8	5,224,1974	48.0	51.0	50.0		519,519	-4.7	0.1	18	dbSNP_52	50	341,8259	117.4+/-177.0	7,327,3966	no	coding-synonymous,coding-synonymous	SERPINB2	NM_001143818.1,NM_002575.2	,	12,551,5940	GG,GC,CC		3.9651,5.3109,4.421	,	173/416,173/416	61565062	575,12431	2203	4300	6503	SO:0001819	synonymous_variant	5055	exon5			CTGGGTCAAGACT	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.519C>G	18.37:g.61565062C>G		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	213	108	0.507042	NM_002575	Q96E96	Silent	SNP	ENST00000299502.4	37	CCDS11989.1	104	0.047619047619047616	32	0.06504065040650407	10	0.027624309392265192	31	0.05419580419580419	31	0.040897097625329816	C	6.549	0.469485	0.12461	0.053109	0.039651	ENSG00000242550	ENST00000397996;ENST00000418725	.	.	.	5.6	-4.72	0.03269	.	.	.	.	.	T	0.03739	0.0106	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27571	-1.0070	4	.	.	.	.	3.0445	0.06149	0.2086:0.1606:0.1024:0.5284	rs6105;rs6105	.	.	.	E	50	.	.	Q	+	1	0	SERPINB10	59716042	0.017000	0.18338	0.126000	0.21872	0.966000	0.64601	-1.314000	0.02715	-0.594000	0.05836	-0.175000	0.13238	CAA	C|0.956;G|0.044	0.044	strong		0.353	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
BRD2	6046	hgsc.bcm.edu	37	6	32948426	32948426	+	Silent	SNP	C	C	T	rs2071876	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32948426C>T	ENST00000374825.4	+	13	4038	c.2337C>T	c.(2335-2337)tcC>tcT	p.S779S	BRD2_ENST00000443797.2_Silent_p.S659S|BRD2_ENST00000395287.1_Silent_p.S814S|BRD2_ENST00000374831.4_Silent_p.S779S|BRD2_ENST00000449085.2_Silent_p.S732S|BRD2_ENST00000395289.2_Silent_p.S814S	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	779	Poly-Ser.|Ser-rich.				chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						CTTCCAGCTCCAGCTCAGATT	0.527													C|||	303	0.0605032	0.028	0.0591	5008	,	,		18054	0.0397		0.0805	False		,,,				2504	0.1063				p.S814S		Atlas-SNP	.											.	BRD2	70	.	0			c.C2442T						PASS	.	C	,,,	103,2919		1,101,1409	110.0	90.0	97.0		2337,2442,2196,2337	4.3	1.0	6	dbSNP_96	97	432,4986		12,408,2289	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BRD2	NM_001113182.2,NM_001199455.1,NM_001199456.1,NM_005104.3	,,,	13,509,3698	TT,TC,CC		7.9734,3.4083,6.3389	,,,	779/802,814/837,732/755,779/802	32948426	535,7905	1511	2709	4220	SO:0001819	synonymous_variant	6046	exon13			CAGCTCCAGCTCA	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.2337C>T	6.37:g.32948426C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_001199455	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	122	0.055860805860805864	8	0.016260162601626018	22	0.06077348066298342	30	0.05244755244755245	62	0.08179419525065963	C	10.64	1.405612	0.25378	0.034083	0.079734	ENSG00000204256	ENST00000449025	.	.	.	6.15	4.34	0.51931	.	.	.	.	.	T	0.50429	0.1615	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50242	-0.8851	4	.	.	.	-14.4569	11.7392	0.51784	0.1385:0.7281:0.1333:0.0	rs2071876;rs17430814;rs2071876	.	.	.	L	785	.	.	P	+	2	0	BRD2	33056404	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.126000	0.50477	0.871000	0.35750	0.643000	0.83706	CCA	T|0.061;G|0.000;C|0.938	0.061	strong		0.527	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
OVGP1	5016	hgsc.bcm.edu	37	1	111957583	111957583	+	Missense_Mutation	SNP	A	A	G	rs1126656|rs376377993	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111957583A>G	ENST00000369732.3	-	11	1595	c.1540T>C	c.(1540-1542)Tat>Cat	p.Y514H		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	514			Y -> H (in dbSNP:rs1126656). {ECO:0000269|Ref.2}.		binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		ACAGACTGATAACCCACAGAG	0.562																																					p.Y514H		Atlas-SNP	.											.	OVGP1	177	.	0			c.T1540C						PASS	.						61.0	57.0	58.0					1																	111957583		2194	4298	6492	SO:0001583	missense	5016	exon11			ACTGATAACCCAC	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1540T>C	1.37:g.111957583A>G	ENSP00000358747:p.Tyr514His	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	173	60	0.346821	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	409	0.18727106227106227	107	0.21747967479674796	67	0.1850828729281768	72	0.1258741258741259	163	0.21503957783641162	a	1.263	-0.615397	0.03663	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.03717	3.83	2.88	-5.76	0.02376	.	.	.	.	.	T	0.00241	0.0007	N	0.00729	-1.24	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43845	-0.9366	8	0.18710	T	0.47	.	1.6984	0.02867	0.1807:0.1255:0.4461:0.2478	rs1126656	514;578	Q12889;Q59HH5	OVGP1_HUMAN;.	H	514;578;322	ENSP00000358747:Y514H	ENSP00000358743:Y578H	Y	-	1	0	OVGP1	111759106	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-2.105000	0.01339	-3.042000	0.00263	-0.386000	0.06593	TAT	A|0.800;G|0.200	0.200	strong		0.562	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
KRT71	112802	hgsc.bcm.edu	37	12	52946498	52946498	+	Missense_Mutation	SNP	C	C	T	rs665470	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:52946498C>T	ENST00000267119.5	-	1	433	c.364G>A	c.(364-366)Gag>Aag	p.E122K		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	122	Head.		E -> K (in dbSNP:rs665470).		hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		TTCTGGATCTCGGGGTCCAGC	0.607													C|||	1017	0.203075	0.3351	0.1556	5008	,	,		18005	0.0208		0.2286	False		,,,				2504	0.2198				p.E122K		Atlas-SNP	.											.	KRT71	70	.	0			c.G364A						PASS	.	C	LYS/GLU	1322,3084	445.5+/-347.7	196,930,1077	107.0	102.0	104.0		364	4.8	1.0	12	dbSNP_83	104	2038,6562	355.1+/-329.8	250,1538,2512	yes	missense	KRT71	NM_033448.2	56	446,2468,3589	TT,TC,CC		23.6977,30.0045,25.8342	benign	122/524	52946498	3360,9646	2203	4300	6503	SO:0001583	missense	112802	exon1			GGATCTCGGGGTC	AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.364G>A	12.37:g.52946498C>T	ENSP00000267119:p.Glu122Lys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	228	108	0.473684	NM_033448	B3KVC1|Q3SY85|Q96DU2	Missense_Mutation	SNP	ENST00000267119.5	37	CCDS8831.1	383	0.17536630036630035	143	0.29065040650406504	60	0.16574585635359115	10	0.017482517482517484	170	0.22427440633245382	C	15.01	2.706774	0.48412	0.300045	0.236977	ENSG00000139648	ENST00000267119	T	0.75477	-0.94	4.82	4.82	0.62117	.	0.000000	0.45606	D	0.000344	T	0.00012	0.0000	M	0.88640	2.97	0.35215	P	0.22447700000000004	P	0.40107	0.703	B	0.27796	0.083	T	0.28902	-1.0029	9	0.51188	T	0.08	.	7.977	0.30161	0.0:0.6938:0.2167:0.0895	rs665470;rs1618791;rs17662526;rs665470	122	Q3SY84	K2C71_HUMAN	K	122	ENSP00000267119:E122K	ENSP00000267119:E122K	E	-	1	0	KRT71	51232765	0.000000	0.05858	0.956000	0.39512	0.941000	0.58515	-0.127000	0.10547	2.398000	0.81561	0.561000	0.74099	GAG	C|0.774;N|0.000	.	strong		0.607	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448	
GPR39	2863	hgsc.bcm.edu	37	2	133174999	133174999	+	Silent	SNP	A	A	G	rs2241763	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:133174999A>G	ENST00000329321.3	+	1	853	c.384A>G	c.(382-384)acA>acG	p.T128T		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	128					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACGTGCTGACACTCAGCTTTG	0.582													G|||	1947	0.388778	0.5825	0.3444	5008	,	,		21679	0.2321		0.327	False		,,,				2504	0.3834				p.T128T		Atlas-SNP	.											.	GPR39	60	.	0			c.A384G						PASS	.	G		2351,2055	566.7+/-382.0	618,1115,470	121.0	106.0	111.0		384	-0.9	1.0	2	dbSNP_98	111	2814,5786	676.3+/-403.3	478,1858,1964	no	coding-synonymous	GPR39	NM_001508.2		1096,2973,2434	GG,GA,AA		32.7209,46.6409,39.7124		128/454	133174999	5165,7841	2203	4300	6503	SO:0001819	synonymous_variant	2863	exon1			GCTGACACTCAGC	AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.384A>G	2.37:g.133174999A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	264	138	0.522727	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	Silent	SNP	ENST00000329321.3	37	CCDS2170.1																																																																																			A|0.608;G|0.392	0.392	strong		0.582	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1		
OR4C16	219428	hgsc.bcm.edu	37	11	55339702	55339702	+	Silent	SNP	C	C	T	rs34100491	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55339702C>T	ENST00000314634.3	+	1	99	c.99C>T	c.(97-99)taC>taT	p.Y33Y		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				TGCGTCTCTACTTGGGAACAC	0.368													c|||	874	0.174521	0.1188	0.2392	5008	,	,		19090	0.1528		0.2117	False		,,,				2504	0.1881				p.Y33Y		Atlas-SNP	.											.	OR4C16	104	.	0			c.C99T						PASS	.	C		591,3811	261.0+/-264.0	39,513,1649	199.0	187.0	191.0		99	-6.9	0.0	11	dbSNP_126	191	1891,6701	337.4+/-322.3	227,1437,2632	no	coding-synonymous	OR4C16	NM_001004701.2		266,1950,4281	TT,TC,CC		22.0088,13.4257,19.1011		33/311	55339702	2482,10512	2201	4296	6497	SO:0001819	synonymous_variant	219428	exon1			TCTCTACTTGGGA	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.99C>T	11.37:g.55339702C>T		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	179	178	0.994413	NM_001004701	Q6IEV8	Silent	SNP	ENST00000314634.3	37	CCDS31502.1																																																																																			C|0.816;T|0.184	0.184	strong		0.368	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
FAM209B	388799	hgsc.bcm.edu	37	20	55108617	55108617	+	Missense_Mutation	SNP	C	C	A	rs3209183	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:55108617C>A	ENST00000371325.1	+	1	316	c.220C>A	c.(220-222)Cag>Aag	p.Q74K		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	74			Q -> K (in dbSNP:rs3209183). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TGTGATACTGCAGTGTCAAAG	0.463													A|||	3329	0.664736	0.9713	0.5086	5008	,	,		20058	0.5456		0.6243	False		,,,				2504	0.5256				p.Q74K		Atlas-SNP	.											.	.	.	.	0			c.C220A						PASS	.	A	LYS/GLN	4023,383	193.0+/-218.2	1843,337,23	150.0	135.0	140.0		220	2.8	0.1	20	dbSNP_105	140	5243,3357	498.0+/-374.7	1589,2065,646	yes	missense	C20orf107	NM_001013646.2	53	3432,2402,669	AA,AC,CC		39.0349,8.6927,28.756	benign	74/172	55108617	9266,3740	2203	4300	6503	SO:0001583	missense	388799	exon1			ATACTGCAGTGTC	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 107"""	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.220C>A	20.37:g.55108617C>A	ENSP00000360376:p.Gln74Lys	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	236	116	0.491525	NM_001013646	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	37	CCDS33494.1	1446	0.6620879120879121	472	0.959349593495935	203	0.5607734806629834	297	0.5192307692307693	474	0.6253298153034301	A	0.001	-2.951362	0.00051	0.913073	0.609651	ENSG00000213714	ENST00000371325	T	0.05447	3.44	2.8	2.8	0.32819	.	0.123818	0.35903	N	0.002909	T	0.00012	0.0000	N	0.01009	-1.055	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27806	-1.0063	9	0.02654	T	1	-23.1828	5.9871	0.19440	0.7302:0.2698:0.0:0.0	rs3209183;rs6423447;rs57187066;rs3209183	74	Q5JX69	CT107_HUMAN	K	74	ENSP00000360376:Q74K	ENSP00000360376:Q74K	Q	+	1	0	C20orf107	54542024	0.975000	0.34042	0.101000	0.21167	0.023000	0.10783	2.038000	0.41184	0.297000	0.22615	-0.769000	0.03391	CAG	C|0.297;A|0.703	0.703	strong		0.463	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
NBEAL2	23218	hgsc.bcm.edu	37	3	47045739	47045739	+	Silent	SNP	C	C	G	rs1079276	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:47045739C>G	ENST00000450053.3	+	37	6233	c.6054C>G	c.(6052-6054)ccC>ccG	p.P2018P	NBEAL2_ENST00000292309.5_Silent_p.P1834P|NBEAL2_ENST00000383740.2_Silent_p.P297P	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2018					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		GCCAGACTCCCAGACCCCAGC	0.592													C|||	2364	0.472045	0.2383	0.5245	5008	,	,		16261	0.5387		0.5865	False		,,,				2504	0.5644				p.P2018P		Atlas-SNP	.											.	NBEAL2	267	.	0			c.C6054G						PASS	.	C		1130,2916		177,776,1070	119.0	123.0	122.0		6054	3.5	0.4	3	dbSNP_86	122	4708,3612		1330,2048,782	no	coding-synonymous	NBEAL2	NM_015175.1		1507,2824,1852	GG,GC,CC		43.4135,27.9288,47.2101		2018/2755	47045739	5838,6528	2023	4160	6183	SO:0001819	synonymous_variant	23218	exon37			GACTCCCAGACCC	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.6054C>G	3.37:g.47045739C>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1	1089|1089	0.49862637362637363|0.49862637362637363	143|143	0.29065040650406504|0.29065040650406504	197|197	0.5441988950276243|0.5441988950276243	305|305	0.5332167832167832|0.5332167832167832	444|444	0.5857519788918206|0.5857519788918206	C|C	0.021|0.021	-1.429707|-1.429707	0.01117|0.01117	0.279288|0.279288	0.565865|0.565865	ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000443829	T|.	0.58358|.	0.34|.	4.5|4.5	3.54|3.54	0.40534|0.40534	.|.	0.778268|.	0.11528|.	N|.	0.555013|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.54753|0.54753	P|P	1.2000000000012001E-5|1.2000000000012001E-5	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.50709|0.50709	-0.8796|-0.8796	6|3	0.44086|.	T|.	0.13|.	.|.	12.1995|12.1995	0.54317|0.54317	0.0:0.7822:0.2178:0.0|0.0:0.7822:0.2178:0.0	rs1079276;rs2305636;rs17223787;rs1079276|rs1079276;rs2305636;rs17223787;rs1079276	.|.	.|.	.|.	R|E	1306|387	ENSP00000410405:P1306R|.	ENSP00000410405:P1306R|.	P|Q	+|+	2|1	0|0	NBEAL2|NBEAL2	47020743|47020743	0.000000|0.000000	0.05858|0.05858	0.428000|0.428000	0.26697|0.26697	0.093000|0.093000	0.18481|0.18481	0.120000|0.120000	0.15647|0.15647	1.242000|1.242000	0.43836|0.43836	0.491000|0.491000	0.48974|0.48974	CCA|CAG	C|0.500;G|0.500	0.500	strong		0.592	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
KIAA1211	57482	hgsc.bcm.edu	37	4	57190356	57190356	+	Silent	SNP	G	G	A	rs7695701	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:57190356G>A	ENST00000504228.1	+	8	3570	c.3465G>A	c.(3463-3465)agG>agA	p.R1155R	KIAA1211_ENST00000541073.1_Silent_p.R1148R|KIAA1211_ENST00000264229.6_Silent_p.R1155R			Q6ZU35	K1211_HUMAN	KIAA1211	1155								p.R1155R(1)		endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					AAGAGAAGAGGCCCGAGACTG	0.567													G|||	1129	0.225439	0.0968	0.268	5008	,	,		20625	0.0704		0.4135	False		,,,				2504	0.3354				p.R1155R		Atlas-SNP	.											KIAA1211,NS,carcinoma,0,2	KIAA1211	178	2	1	Substitution - coding silent(1)	prostate(1)	c.G3465A						scavenged	.	G		555,3675		28,499,1588	59.0	66.0	63.0		3465	4.5	1.0	4	dbSNP_116	63	3519,4971		712,2095,1438	no	coding-synonymous	KIAA1211	NM_020722.1		740,2594,3026	AA,AG,GG		41.4488,13.1206,32.0283		1155/1234	57190356	4074,8646	2115	4245	6360	SO:0001819	synonymous_variant	57482	exon10			GAAGAGGCCCGAG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.3465G>A	4.37:g.57190356G>A		Somatic	337	3	0.00890208		WXS	Illumina HiSeq	Phase_I	321	314	0.978193	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																			G|0.741;A|0.259	0.259	strong		0.567	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
AS3MT	57412	hgsc.bcm.edu	37	10	104638211	104638211	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:104638211G>A	ENST00000369880.3	+	8	763	c.686G>A	c.(685-687)cGt>cAt	p.R229H	C10orf32-ASMT_ENST00000299353.6_3'UTR	NM_020682.3	NP_065733.2	Q9HBK9	AS3MT_HUMAN	arsenite methyltransferase	229					arsonoacetate metabolic process (GO:0018872)|toxin metabolic process (GO:0009404)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	arsenite methyltransferase activity (GO:0030791)|methylarsonite methyltransferase activity (GO:0030792)			large_intestine(1)|lung(6)	7		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)		TGCCCTCCACGTTTGGTCACT	0.403																																					p.R229H		Atlas-SNP	.											.	AS3MT	17	.	0			c.G686A						PASS	.						181.0	173.0	176.0					10																	104638211		1886	4134	6020	SO:0001583	missense	57412	exon8			CTCCACGTTTGGT	AF226730	CCDS41567.1	10q24.33	2014-05-09	2014-05-09		ENSG00000214435	ENSG00000214435	2.1.1.137		17452	protein-coding gene	gene with protein product		611806	"""arsenic (+3 oxidation state) methyltransferase"""			11790780	Standard	NM_020682		Approved	CYT19	uc001kwk.3	Q9HBK9	OTTHUMG00000018972	ENST00000369880.3:c.686G>A	10.37:g.104638211G>A	ENSP00000358896:p.Arg229His	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	40	38	0.95	NM_020682	A6NP79|Q0VDK3|Q0VDK4|Q5PZ02	Missense_Mutation	SNP	ENST00000369880.3	37	CCDS41567.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376179	0.82682	.	.	ENSG00000214435	ENST00000369880	T	0.22945	1.93	5.48	3.61	0.41365	.	0.053428	0.64402	D	0.000001	T	0.41994	0.1183	M	0.74881	2.28	0.35290	D	0.782117	D;D;D	0.65815	0.965;0.995;0.995	P;P;P	0.56398	0.548;0.797;0.797	T	0.58042	-0.7706	9	0.40728	T	0.16	-15.267	11.7063	0.51599	0.1505:0.0:0.8495:0.0	.	229;229;229	Q0VDK3;Q9HBK9;Q0VDK4	.;AS3MT_HUMAN;.	H	229	ENSP00000358896:R229H	ENSP00000358896:R229H	R	+	2	0	AS3MT	104628201	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.613000	0.67688	1.314000	0.45095	-0.254000	0.11334	CGT	.	.	none		0.403	AS3MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050107.1	NM_020682	
C15orf53	400359	hgsc.bcm.edu	37	15	38988815	38988815	+	Missense_Mutation	SNP	C	C	G	rs7165988	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:38988815C>G	ENST00000318792.1	+	1	17	c.7C>G	c.(7-9)Cta>Gta	p.L3V		NM_207444.2	NP_997327.1	Q8NAA6	CO053_HUMAN	chromosome 15 open reading frame 53	3			L -> V (in dbSNP:rs7165988).					p.L3V(1)		endometrium(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	6		all_cancers(109;1.75e-13)|all_epithelial(112;1.02e-11)|Lung NSC(122;1.9e-09)|all_lung(180;4.04e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;8.39e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0321)		TGATATGGAGCTACAAGGGGC	0.557													C|||	972	0.194089	0.1755	0.2536	5008	,	,		19831	0.0992		0.2624	False		,,,				2504	0.2045				p.L3V		Atlas-SNP	.											C15orf53,NS,carcinoma,0,1	C15orf53	12	1	1	Substitution - Missense(1)	stomach(1)	c.C7G						PASS	.	C	VAL/LEU	917,3483	351.3+/-311.2	93,731,1376	91.0	85.0	87.0		7	-0.6	0.0	15	dbSNP_116	87	2604,5990	421.4+/-353.7	376,1852,2069	yes	missense	C15orf53	NM_207444.2	32	469,2583,3445	GG,GC,CC		30.3002,20.8409,27.0971	possibly-damaging	3/180	38988815	3521,9473	2200	4297	6497	SO:0001583	missense	400359	exon1			ATGGAGCTACAAG		CCDS10048.1	15q14	2007-11-21			ENSG00000175779	ENSG00000175779			33796	protein-coding gene	gene with protein product							Standard	NM_207444		Approved	FLJ35695	uc001zkf.1	Q8NAA6	OTTHUMG00000129841	ENST00000318792.1:c.7C>G	15.37:g.38988815C>G	ENSP00000325144:p.Leu3Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	123	48	0.390244	NM_207444		Missense_Mutation	SNP	ENST00000318792.1	37	CCDS10048.1	441	0.20192307692307693	94	0.1910569105691057	98	0.27071823204419887	57	0.09965034965034965	192	0.2532981530343008	C	6.416	0.444857	0.12164	0.208409	0.303002	ENSG00000175779	ENST00000318792	T	0.39229	1.09	3.36	-0.565	0.11771	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.54964	0.969	P	0.51945	0.685	T	0.30238	-0.9985	8	0.87932	D	0	.	5.8987	0.18953	0.0:0.3748:0.0:0.6252	rs7165988;rs52800519;rs7165988	3	Q8NAA6	CO053_HUMAN	V	3	ENSP00000325144:L3V	ENSP00000325144:L3V	L	+	1	2	C15orf53	36776107	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.638000	0.05452	-0.065000	0.13021	-0.459000	0.05422	CTA	C|0.752;G|0.248	0.248	strong		0.557	C15orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252081.1	NM_207444	
PARP4	143	hgsc.bcm.edu	37	13	25021154	25021154	+	Splice_Site	SNP	C	C	T	rs61947037	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25021154C>T	ENST00000381989.3	-	26	3390	c.3285G>A	c.(3283-3285)caG>caA	p.Q1095Q		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1095					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GTCTTCTTACCTGTGTGCAGT	0.468													c|||	2480	0.495208	0.1967	0.5951	5008	,	,		15400	0.6062		0.5278	False		,,,				2504	0.68				p.Q1095Q		Atlas-SNP	.											.	PARP4	142	.	0			c.G3285A						PASS	.	C		694,3710		139,416,1647	81.0	65.0	71.0		3285	3.8	1.0	13	dbSNP_129	71	4242,4352		1312,1618,1367	no	coding-synonymous-near-splice	PARP4	NM_006437.3		1451,2034,3014	TT,TC,CC		49.36,15.7584,37.9751		1095/1725	25021154	4936,8062	2202	4297	6499	SO:0001630	splice_region_variant	143	exon26			TCTTACCTGTGTG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3285+1G>A	13.37:g.25021154C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	132	114	0.863636	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			C|0.555;T|0.445	0.445	strong		0.468	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	Silent
C16orf62	57020	hgsc.bcm.edu	37	16	19680546	19680546	+	Silent	SNP	T	T	C	rs957676	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:19680546T>C	ENST00000251143.5	+	27	2298	c.2286T>C	c.(2284-2286)gaT>gaC	p.D762D	C16orf62_ENST00000543152.1_Silent_p.D511D|C16orf62_ENST00000542263.1_Silent_p.D758D|C16orf62_ENST00000438132.3_Silent_p.D851D|C16orf62_ENST00000417362.2_Silent_p.D669D|C16orf62_ENST00000448695.1_Silent_p.D612D			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	762						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						TTAATATTGATGGGAAGATGC	0.408													C|||	1627	0.32488	0.3729	0.3098	5008	,	,		19645	0.2887		0.34	False		,,,				2504	0.2924				p.D851D		Atlas-SNP	.											.	C16orf62	164	.	0			c.T2553C						PASS	.	C		1628,2764	659.7+/-400.6	290,1048,858	118.0	117.0	118.0		2553	-2.5	0.6	16	dbSNP_86	118	2851,5749	674.3+/-403.1	467,1917,1916	no	coding-synonymous	C16orf62	NM_020314.5		757,2965,2774	CC,CT,TT		33.1512,37.0674,34.4751		851/1053	19680546	4479,8513	2196	4300	6496	SO:0001819	synonymous_variant	57020	exon27			TATTGATGGGAAG		CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.2286T>C	16.37:g.19680546T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Silent	SNP	ENST00000251143.5	37																																																																																				T|0.656;C|0.344	0.344	strong		0.408	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314	
MUC16	94025	hgsc.bcm.edu	37	19	9049396	9049396	+	Silent	SNP	C	C	G	rs10425044	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9049396C>G	ENST00000397910.4	-	5	32438	c.32235G>C	c.(32233-32235)ggG>ggC	p.G10745G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10747	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCTGTCTGTCCCAGAACTAG	0.478													C|||	939	0.1875	0.1566	0.2637	5008	,	,		22460	0.0258		0.2823	False		,,,				2504	0.2444				p.G10745G		Atlas-SNP	.											.	MUC16	4315	.	0			c.G32235C						PASS	.			624,3188		47,530,1329	173.0	156.0	161.0		32235	-1.9	0.0	19	dbSNP_119	161	2503,5737		402,1699,2019	no	coding-synonymous	MUC16	NM_024690.2		449,2229,3348	GG,GC,CC		30.3762,16.3694,25.9459		10745/14508	9049396	3127,8925	1906	4120	6026	SO:0001819	synonymous_variant	94025	exon5			GTCTGTCCCAGAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.32235G>C	19.37:g.9049396C>G		Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	265	265	1	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.781;G|0.219	0.219	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NRG3	10718	hgsc.bcm.edu	37	10	84745040	84745040	+	Silent	SNP	A	A	G	rs17101196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:84745040A>G	ENST00000404547.1	+	10	1842	c.1842A>G	c.(1840-1842)ccA>ccG	p.P614P	NRG3_ENST00000545131.1_Silent_p.P240P|NRG3_ENST00000404576.2_Silent_p.P394P|NRG3_ENST00000372142.2_Silent_p.P393P|NRG3_ENST00000537893.1_Silent_p.P240P|NRG3_ENST00000556918.1_Silent_p.P420P|NRG3_ENST00000372141.2_Silent_p.P590P			P56975	NRG3_HUMAN	neuregulin 3	614					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		TGCAAATGCCAGGGATTTCTG	0.473													A|||	477	0.0952476	0.1732	0.1571	5008	,	,		19753	0.0109		0.0567	False		,,,				2504	0.0726				p.P590P		Atlas-SNP	.											.	NRG3	301	.	0			c.A1770G						PASS	.	A	,,	686,3720	289.5+/-280.5	58,570,1575	97.0	98.0	98.0		1770,1767,1179	4.8	1.0	10	dbSNP_123	98	502,8098	144.8+/-200.6	15,472,3813	no	coding-synonymous,coding-synonymous,coding-synonymous	NRG3	NM_001010848.3,NM_001165972.1,NM_001165973.1	,,	73,1042,5388	GG,GA,AA		5.8372,15.5697,9.1342	,,	590/697,589/696,393/500	84745040	1188,11818	2203	4300	6503	SO:0001819	synonymous_variant	10718	exon9			AATGCCAGGGATT	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1842A>G	10.37:g.84745040A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	160	74	0.4625	NM_001010848	A4D7U1|Q0PEH2|Q5VYH3	Silent	SNP	ENST00000404547.1	37	CCDS31233.1																																																																																			A|0.911;G|0.089	0.089	strong		0.473	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086	
CD4	920	hgsc.bcm.edu	37	12	6928075	6928075	+	Silent	SNP	T	T	C	rs12821756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6928075T>C	ENST00000011653.4	+	9	1599	c.1341T>C	c.(1339-1341)tgT>tgC	p.C447C	GPR162_ENST00000428545.2_5'Flank|GPR162_ENST00000311268.3_5'Flank|GPR162_ENST00000382315.3_5'Flank	NM_000616.4|NM_001195015.2|NM_001195016.2|NM_001195017.2	NP_000607.1|NP_001181944.1|NP_001181945.1|NP_001181946.1	P01730	CD4_HUMAN	CD4 molecule	447	HIV-1 Vpu-susceptibility domain.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cytokine production (GO:0001816)|defense response to Gram-negative bacterium (GO:0050829)|entry into host cell (GO:0030260)|enzyme linked receptor protein signaling pathway (GO:0007167)|immune response (GO:0006955)|induction by virus of host cell-cell fusion (GO:0006948)|innate immune response (GO:0045087)|maintenance of protein location in cell (GO:0032507)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase activity (GO:0045860)|protein palmitoleylation (GO:0045234)|regulation of defense response to virus by virus (GO:0050690)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|T cell selection (GO:0045058)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|enzyme binding (GO:0019899)|extracellular matrix structural constituent (GO:0005201)|glycoprotein binding (GO:0001948)|MHC class II protein binding (GO:0042289)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	23		Myeloproliferative disorder(1001;0.0122)			Antithymocyte globulin(DB00098)	CCTGCCAGTGTCCTCAGTAAG	0.597													C|||	3787	0.75619	0.8245	0.6758	5008	,	,		-128	0.9117		0.5686	False		,,,				2504	0.7536				p.C447C		Atlas-SNP	.											.	CD4	47	.	0			c.T1341C						PASS	.	C	,,,,	3399,1001		1320,759,121	33.0	31.0	31.0		1341,804,522,522,522	-2.0	0.1	12	dbSNP_121	31	4661,3935		1289,2083,926	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD4	NM_000616.4,NM_001195014.2,NM_001195015.2,NM_001195016.2,NM_001195017.2	,,,,	2609,2842,1047	CC,CT,TT		45.7771,22.75,37.9809	,,,,	447/459,268/280,174/186,174/186,174/186	6928075	8060,4936	2200	4298	6498	SO:0001819	synonymous_variant	920	exon9			CCAGTGTCCTCAG	M35160	CCDS8562.1	12p13.31	2013-01-11	2006-03-28		ENSG00000010610	ENSG00000010610		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1678	protein-coding gene	gene with protein product		186940	"""CD4 antigen (p55)"", ""T-cell surface glycoprotein CD4"""				Standard	NM_000616		Approved		uc001qqv.2	P01730	OTTHUMG00000168514	ENST00000011653.4:c.1341T>C	12.37:g.6928075T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	145	54	0.372414	NM_000616	B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5	Silent	SNP	ENST00000011653.4	37	CCDS8562.1																																																																																			T|0.352;C|0.648	0.648	strong		0.597	CD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399978.1	NM_000616	
HIST1H2BA	255626	hgsc.bcm.edu	37	6	25727265	25727265	+	Silent	SNP	C	C	T	rs4712960	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:25727265C>T	ENST00000274764.2	+	1	129	c.129C>T	c.(127-129)atC>atT	p.I43I	HIST1H2AA_ENST00000297012.3_5'Flank	NM_170610.2	NP_733759.1	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	43					cellular response to acid chemical (GO:0071229)|chromatin organization (GO:0006325)|inflammatory response (GO:0006954)|mononuclear cell migration (GO:0071674)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|plasminogen activation (GO:0031639)|positive regulation of binding (GO:0051099)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	extrinsic component of plasma membrane (GO:0019897)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)	2						CTATTTACATCTACAAAGTGC	0.433													C|||	1738	0.347045	0.0976	0.4366	5008	,	,		22101	0.6825		0.2922	False		,,,				2504	0.3313				p.I43I		Atlas-SNP	.											.	HIST1H2BA	25	.	0			c.C129T						PASS	.	C		605,3801	265.3+/-266.6	47,511,1645	351.0	287.0	308.0		129	-2.3	0.1	6	dbSNP_111	308	2391,6209	398.2+/-346.0	339,1713,2248	no	coding-synonymous	HIST1H2BA	NM_170610.2		386,2224,3893	TT,TC,CC		27.8023,13.7313,23.0355		43/128	25727265	2996,10010	2203	4300	6503	SO:0001819	synonymous_variant	255626	exon1			TTACATCTACAAA	AF397301	CCDS4563.1	6p22.2	2011-01-27	2006-10-11		ENSG00000146047	ENSG00000146047		"""Histones / Replication-dependent"""	18730	protein-coding gene	gene with protein product		609904	"""H2B histone family, member U, (testis-specific)"", ""histone 1, H2ba"""			12408966, 12213818	Standard	NM_170610		Approved	bA317E16.3, STBP, TSH2B, H2BFU	uc003nfd.3	Q96A08	OTTHUMG00000014408	ENST00000274764.2:c.129C>T	6.37:g.25727265C>T		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_170610	B2R544|Q6NZ98|Q6NZA0|Q6NZA1	Silent	SNP	ENST00000274764.2	37	CCDS4563.1																																																																																			C|0.714;T|0.286	0.286	strong		0.433	HIST1H2BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040066.1	NM_170610	
LAMB3	3914	hgsc.bcm.edu	37	1	209811886	209811886	+	Silent	SNP	T	T	G	rs2076356	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:209811886T>G	ENST00000356082.4	-	4	425	c.291A>C	c.(289-291)tcA>tcC	p.S97S	LAMB3_ENST00000391911.1_Silent_p.S97S|LAMB3_ENST00000367030.3_Silent_p.S97S	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	97	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.S97S(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		CACCATTCTGTGACTGCCACC	0.532													T|||	2166	0.432508	0.3517	0.4582	5008	,	,		18725	0.2847		0.6412	False		,,,				2504	0.4611				p.S97S		Atlas-SNP	.											LAMB3,NS,carcinoma,0,1	LAMB3	136	1	1	Substitution - coding silent(1)	stomach(1)	c.A291C						scavenged	.	T	,,	1917,2489	547.6+/-377.3	408,1101,694	96.0	75.0	82.0		291,291,291	-7.7	0.9	1	dbSNP_96	82	5556,3044	661.4+/-401.9	1792,1972,536	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	2200,3073,1230	GG,GT,TT		35.3953,43.5089,42.5419	,,	97/1173,97/1173,97/1173	209811886	7473,5533	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon4			ATTCTGTGACTGC	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.291A>C	1.37:g.209811886T>G		Somatic	138	4	0.0289855		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			T|0.476;G|0.524	0.524	strong		0.532	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
PCMTD1	115294	hgsc.bcm.edu	37	8	52733196	52733196	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:52733196C>A	ENST00000360540.5	-	7	1195	c.789G>T	c.(787-789)atG>atT	p.M263I	PCMTD1_ENST00000544451.1_Missense_Mutation_p.M187I|PCMTD1_ENST00000522514.1_Missense_Mutation_p.M263I|PCMTD1_ENST00000519559.1_5'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	263						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				CCTTGGCCTGCATCTCATCAT	0.398																																					p.M263I		Atlas-SNP	.											PCMTD1,NS,carcinoma,0,1	PCMTD1	73	1	0			c.G789T						scavenged	.						96.0	100.0	99.0					8																	52733196		2203	4297	6500	SO:0001583	missense	115294	exon6			GGCCTGCATCTCA		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.789G>T	8.37:g.52733196C>A	ENSP00000353739:p.Met263Ile	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	214	6	0.0280374	NM_052937	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	C	9.598	1.127945	0.20959	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.39787	1.06;1.06;1.06	5.77	4.9	0.64082	.	0.368613	0.35870	N	0.002934	T	0.33962	0.0881	L	0.36672	1.1	0.41234	D	0.986591	B;B;B	0.15141	0.012;0.005;0.009	B;B;B	0.17722	0.01;0.004;0.019	T	0.09796	-1.0658	10	0.21014	T	0.42	-17.22	14.5538	0.68086	0.0:0.9301:0.0:0.0699	.	133;187;263	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	I	263;187;263	ENSP00000353739:M263I;ENSP00000444026:M187I;ENSP00000428099:M263I	ENSP00000353739:M263I	M	-	3	0	PCMTD1	52895749	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.889000	0.39718	1.442000	0.47568	0.655000	0.94253	ATG	.	.	none		0.398	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
MIIP	60672	hgsc.bcm.edu	37	1	12082461	12082461	+	Missense_Mutation	SNP	C	C	T	rs11588712	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:12082461C>T	ENST00000235332.4	+	3	593	c.424C>T	c.(424-426)Ccg>Tcg	p.P142S	MIIP_ENST00000436478.2_Missense_Mutation_p.P142S|MIIP_ENST00000466860.1_3'UTR|Y_RNA_ENST00000365591.1_RNA	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein	142			P -> S (in dbSNP:rs11588712). {ECO:0000269|PubMed:15867349}.							autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						GGCACAGACCCCGAGGTCCAT	0.632													C|||	419	0.0836661	0.0242	0.0893	5008	,	,		19449	0.0675		0.159	False		,,,				2504	0.0992				p.P142S		Atlas-SNP	.											MIIP,NS,carcinoma,0,1	MIIP	34	1	0			c.C424T						PASS	.	C	SER/PRO	202,4200		5,192,2004	23.0	22.0	23.0		424	2.5	0.0	1	dbSNP_120	23	1295,7301		102,1091,3105	yes	missense	MIIP	NM_021933.3	74	107,1283,5109	TT,TC,CC		15.0651,4.5888,11.5172	benign	142/389	12082461	1497,11501	2201	4298	6499	SO:0001583	missense	60672	exon3			CAGACCCCGAGGT	AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"""invasion inhibitory protein 45"""	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.424C>T	1.37:g.12082461C>T	ENSP00000235332:p.Pro142Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	144	75	0.520833	NM_021933	C0KL22|Q96HU6|Q9H839|Q9HA00	Missense_Mutation	SNP	ENST00000235332.4	37	CCDS143.1	173	0.07921245421245421	8	0.016260162601626018	25	0.06906077348066299	21	0.03671328671328671	119	0.15699208443271767	C	11.55	1.671371	0.29693	0.045888	0.150651	ENSG00000116691	ENST00000235332;ENST00000436478	T;T	0.18174	2.23;2.23	4.42	2.51	0.30379	.	2.687200	0.01449	N	0.015426	T	0.00073	0.0002	L	0.47716	1.5	0.80722	P	0.0	P	0.35272	0.493	B	0.36845	0.234	T	0.21586	-1.0241	9	0.19590	T	0.45	2.1469	5.7764	0.18281	0.1928:0.7043:0.0:0.103	rs11588712;rs17856240;rs52816027;rs11588712	142	Q5JXC2	MIIP_HUMAN	S	142	ENSP00000235332:P142S;ENSP00000392417:P142S	ENSP00000235332:P142S	P	+	1	0	MIIP	12005048	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.286000	0.18902	0.550000	0.28991	0.591000	0.81541	CCG	C|0.911;T|0.089	0.089	strong		0.632	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933	
CDC37L1	55664	hgsc.bcm.edu	37	9	4685008	4685008	+	Silent	SNP	C	C	T	rs2295967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:4685008C>T	ENST00000381854.3	+	2	466	c.264C>T	c.(262-264)tcC>tcT	p.S88S	CDC37L1_ENST00000479095.1_3'UTR|CDC37L1_ENST00000381858.1_Silent_p.S88S	NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	88	Self-association.					cytoplasm (GO:0005737)				breast(1)|kidney(1)|lung(2)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		ATTCTGAGTCCTTGGATCAGG	0.453													C|||	899	0.179513	0.0333	0.111	5008	,	,		19935	0.376		0.0865	False		,,,				2504	0.319				p.S88S		Atlas-SNP	.											.	CDC37L1	19	.	0			c.C264T						PASS	.	C		216,4190	133.3+/-169.7	6,204,1993	143.0	137.0	139.0		264	5.7	1.0	9	dbSNP_100	139	784,7816	185.0+/-232.9	35,714,3551	no	coding-synonymous	CDC37L1	NM_017913.2		41,918,5544	TT,TC,CC		9.1163,4.9024,7.6888		88/338	4685008	1000,12006	2203	4300	6503	SO:0001819	synonymous_variant	55664	exon2			TGAGTCCTTGGAT	AK000497	CCDS6454.1	9p24.1	2013-01-17	2013-01-17		ENSG00000106993	ENSG00000106993			17179	protein-coding gene	gene with protein product		610346	"""CDC37 cell division cycle 37 homolog (S. cerevisiae)-like 1"", ""cell division cycle 37 homolog (S. cerevisiae)-like 1"""				Standard	NM_017913		Approved	HARC, FLJ20639, CDC37B	uc003zio.3	Q7L3B6	OTTHUMG00000019465	ENST00000381854.3:c.264C>T	9.37:g.4685008C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	181	97	0.535912	NM_017913	B1AL70|Q9NWS3|Q9NX16	Silent	SNP	ENST00000381854.3	37	CCDS6454.1																																																																																			C|0.893;T|0.107	0.107	strong		0.453	CDC37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051564.1	NM_017913	
MAP9	79884	hgsc.bcm.edu	37	4	156273768	156273768	+	Missense_Mutation	SNP	T	T	C	rs2305050	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:156273768T>C	ENST00000311277.4	-	13	2064	c.1801A>G	c.(1801-1803)Aat>Gat	p.N601D	MAP9_ENST00000515654.1_Missense_Mutation_p.N577D|AC097467.2_ENST00000609486.1_RNA|AC097467.2_ENST00000608463.1_RNA|AC097467.2_ENST00000610249.1_RNA|AC097467.2_ENST00000609254.1_RNA|AC097467.2_ENST00000598252.1_RNA|AC097467.2_ENST00000599555.2_RNA|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000608092.1_RNA|AC097467.2_ENST00000601977.1_RNA|AC097467.2_ENST00000417474.1_RNA|AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000597939.1_RNA|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000593387.2_RNA|AC097467.2_ENST00000595229.1_RNA|AC097467.2_ENST00000608544.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	601			N -> D (in dbSNP:rs2305050). {ECO:0000269|PubMed:17974005}.		cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		TCATATTCATTAATAGCTTGT	0.294													C|||	3276	0.654153	0.7844	0.5346	5008	,	,		16630	0.7946		0.5557	False		,,,				2504	0.5194				p.N601D		Atlas-SNP	.											.	MAP9	79	.	0			c.A1801G						PASS	.	C	ASP/ASN	3191,1213	419.6+/-338.7	1166,859,177	181.0	183.0	182.0		1801	0.3	0.8	4	dbSNP_100	182	4536,4064	556.5+/-386.9	1205,2126,969	yes	missense	MAP9	NM_001039580.1	23	2371,2985,1146	CC,CT,TT		47.2558,27.5431,40.5798	benign	601/648	156273768	7727,5277	2202	4300	6502	SO:0001583	missense	79884	exon13			ATTCATTAATAGC	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"""aster-associated protein"""	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.1801A>G	4.37:g.156273768T>C	ENSP00000310593:p.Asn601Asp	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	195	90	0.461538	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	37	CCDS35493.1	1466	0.6712454212454212	384	0.7804878048780488	193	0.5331491712707183	456	0.7972027972027972	433	0.5712401055408971	C	2.934	-0.220339	0.06061	0.724569	0.527442	ENSG00000164114	ENST00000311277;ENST00000515654	T;T	0.16457	2.36;2.34	5.15	0.287	0.15714	.	0.823090	0.11196	N	0.589371	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	0.999999725776	B	0.02656	0.0	B	0.04013	0.001	T	0.25433	-1.0132	9	0.07325	T	0.83	-0.0073	9.4433	0.38681	0.0:0.5786:0.0:0.4214	rs2305050;rs13127917;rs17377512;rs59632960;rs2305050	601	Q49MG5	MAP9_HUMAN	D	601;577	ENSP00000310593:N601D;ENSP00000427402:N577D	ENSP00000310593:N601D	N	-	1	0	MAP9	156493218	0.002000	0.14202	0.818000	0.32626	0.961000	0.63080	0.139000	0.16036	-0.088000	0.12506	-1.427000	0.01099	AAT	T|0.372;C|0.628	0.628	strong		0.294	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	
PCDHB5	26167	hgsc.bcm.edu	37	5	140517034	140517034	+	Missense_Mutation	SNP	C	C	G	rs139801121	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140517034C>G	ENST00000231134.5	+	1	2235	c.2018C>G	c.(2017-2019)cCg>cGg	p.P673R		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	673					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGCCGCTGCCGGAGGCGGCC	0.692													C|||	46	0.0091853	0.0008	0.0159	5008	,	,		14307	0.0		0.0318	False		,,,				2504	0.002				p.P673R		Atlas-SNP	.											.	PCDHB5	184	.	0			c.C2018G						PASS	.	C	ARG/PRO	11,4325		0,11,2157	53.0	60.0	58.0		2018	4.7	0.1	5	dbSNP_134	58	155,8307		1,153,4077	no	missense	PCDHB5	NM_015669.2	103	1,164,6234	GG,GC,CC		1.8317,0.2537,1.2971	possibly-damaging	673/796	140517034	166,12632	2168	4231	6399	SO:0001583	missense	26167	exon1			CGCTGCCGGAGGC	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"""Cadherins / Protocadherins : Clustered"""	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.2018C>G	5.37:g.140517034C>G	ENSP00000231134:p.Pro673Arg	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_015669	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	37	CCDS4247.1	40	0.018315018315018316	4	0.008130081300813009	11	0.03038674033149171	0	0.0	25	0.032981530343007916	C	14.58	2.579289	0.46006	0.002537	0.018317	ENSG00000113209	ENST00000231134	T	0.50277	0.75	4.71	4.71	0.59529	.	.	.	.	.	T	0.48589	0.1508	M	0.86028	2.79	0.09310	N	1	D	0.67145	0.996	D	0.69654	0.965	T	0.56902	-0.7902	9	0.72032	D	0.01	.	15.1203	0.72438	0.0:0.7833:0.2167:0.0	.	673	Q9Y5E4	PCDB5_HUMAN	R	673	ENSP00000231134:P673R	ENSP00000231134:P673R	P	+	2	0	PCDHB5	140497218	0.000000	0.05858	0.064000	0.19789	0.138000	0.21146	0.604000	0.24164	2.337000	0.79520	0.430000	0.28490	CCG	C|0.986;G|0.014	0.014	strong		0.692	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669	
TAP2	6891	hgsc.bcm.edu	37	6	32797297	32797297	+	Silent	SNP	T	T	C	rs241441	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32797297T>C	ENST00000452392.2	-	11	1985	c.1812A>G	c.(1810-1812)ggA>ggG	p.G604G	TAP2_ENST00000485701.1_5'Flank|TAP2_ENST00000374899.4_Silent_p.G604G|TAP2_ENST00000374897.2_Silent_p.G604G			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)									Vitamin E(DB00163)	CCAGCTGGCTTCCCTTCTCCC	0.552													C|||	1498	0.299121	0.1551	0.304	5008	,	,		20092	0.3621		0.2783	False		,,,				2504	0.4468				p.G604G		Atlas-SNP	.											.	TAP2	98	.	0			c.A1812G						PASS	.	C	,	815,3591	317.7+/-295.3	77,661,1465	70.0	72.0	71.0		1812,1812	-2.5	0.1	6	dbSNP_79	71	2259,6341	376.1+/-338.0	292,1675,2333	no	coding-synonymous,coding-synonymous	TAP2	NM_000544.3,NM_018833.2	,	369,2336,3798	CC,CT,TT		26.2674,18.4975,23.6352	,	604/704,604/654	32797297	3074,9932	2203	4300	6503	SO:0001819	synonymous_variant	6891	exon11			CTGGCTTCCCTTC	M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1812A>G	6.37:g.32797297T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Silent	SNP	ENST00000452392.2	37																																																																																				T|0.748;C|0.252	0.252	strong		0.552	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
POLQ	10721	hgsc.bcm.edu	37	3	121154974	121154974	+	Missense_Mutation	SNP	T	T	C	rs1381057	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121154974T>C	ENST00000264233.5	-	28	7666	c.7538A>G	c.(7537-7539)cAa>cGa	p.Q2513R		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2513				Q -> R (in Ref. 1; AAC33565 and 2; AAR08421). {ECO:0000305}.	ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CAAACCTGTTTGGTCACTTTG	0.368								DNA polymerases (catalytic subunits)					C|||	3732	0.745208	0.6309	0.6945	5008	,	,		20710	0.877		0.668	False		,,,				2504	0.8793				p.Q2513R	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A7538G						PASS	.	C	ARG/GLN	2840,1566	490.3+/-361.7	924,992,287	190.0	171.0	177.0		7538	-0.3	0.0	3	dbSNP_88	177	5869,2731	436.2+/-358.2	2002,1865,433	yes	missense	POLQ	NM_199420.3	43	2926,2857,720	CC,CT,TT		31.7558,35.5424,33.0386	benign	2513/2591	121154974	8709,4297	2203	4300	6503	SO:0001583	missense	10721	exon28			CCTGTTTGGTCAC	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.7538A>G	3.37:g.121154974T>C	ENSP00000264233:p.Gln2513Arg	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	239	125	0.523013	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	1562	0.7152014652014652	300	0.6097560975609756	250	0.6906077348066298	511	0.8933566433566433	501	0.6609498680738787	C	1.151	-0.646621	0.03531	0.644576	0.682442	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.47177	0.85	5.81	-0.307	0.12777	DNA-directed DNA polymerase, family A, palm domain (2);	0.799731	0.11667	N	0.541194	T	0.00012	0.0000	N	0.04959	-0.14	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.38607	-0.9653	9	0.02654	T	1	.	7.6272	0.28218	0.0:0.4356:0.1049:0.4595	rs1381057;rs17481360;rs52804123;rs1381057	2513;1685	O75417;O75417-2	DPOLQ_HUMAN;.	R	2136;2513;2649	ENSP00000264233:Q2513R	ENSP00000264233:Q2513R	Q	-	2	0	POLQ	122637664	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-0.473000	0.06615	-0.673000	0.05259	-0.941000	0.02677	CAA	T|0.298;C|0.702	0.702	strong		0.368	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
SAMD15	161394	hgsc.bcm.edu	37	14	77843971	77843971	+	Silent	SNP	C	C	T	rs45540040	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77843971C>T	ENST00000216471.4	+	1	496	c.210C>T	c.(208-210)gaC>gaT	p.D70D	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	70										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GGGAGCCAGACAGTGCTAAGA	0.547													c|||	709	0.141573	0.059	0.2651	5008	,	,		18232	0.0159		0.2038	False		,,,				2504	0.2311				p.D70D		Atlas-SNP	.											.	SAMD15	60	.	0			c.C210T						PASS	.	G		409,3997	201.8+/-224.7	16,377,1810	97.0	93.0	94.0		210	-2.1	0.0	14	dbSNP_127	94	1685,6915	307.2+/-308.3	182,1321,2797	no	coding-synonymous	SAMD15	NM_001010860.1		198,1698,4607	TT,TC,CC		19.593,9.2828,16.1003		70/675	77843971	2094,10912	2203	4300	6503	SO:0001819	synonymous_variant	161394	exon1			GCCAGACAGTGCT	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.210C>T	14.37:g.77843971C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_001010860	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																			C|0.848;T|0.152	0.152	strong		0.547	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
AKAP13	11214	hgsc.bcm.edu	37	15	86278309	86278309	+	Missense_Mutation	SNP	G	G	A	rs2241268	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86278309G>A	ENST00000394518.2	+	31	7464	c.7369G>A	c.(7369-7371)Ggt>Agt	p.G2457S	AKAP13_ENST00000361243.2_Missense_Mutation_p.G2461S|AKAP13_ENST00000394510.2_Missense_Mutation_p.G702S|AKAP13_ENST00000560579.1_3'UTR	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2457	Interaction with ESR1.		G -> S (in dbSNP:rs2241268). {ECO:0000269|PubMed:11546812, ECO:0000269|PubMed:11696353, ECO:0000269|PubMed:9627117, ECO:0000269|Ref.10}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						AGATGTGGTCGGTCCCGTTTC	0.502													G|||	684	0.136581	0.0098	0.2248	5008	,	,		18633	0.0486		0.2793	False		,,,				2504	0.1892				p.G2461S	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G7381A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	198,4206	124.1+/-161.4	7,184,2011	198.0	197.0	198.0		7381,7369,2104	4.9	0.9	15	dbSNP_98	198	2292,6306	386.4+/-341.8	327,1638,2334	yes	missense,missense,missense	AKAP13	NM_006738.4,NM_007200.3,NM_144767.3	56,56,56	334,1822,4345	AA,AG,GG		26.6574,4.4959,19.1509	possibly-damaging,possibly-damaging,possibly-damaging	2461/2818,2457/2814,702/1059	86278309	2490,10512	2202	4299	6501	SO:0001583	missense	11214	exon31			GTGGTCGGTCCCG	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.7369G>A	15.37:g.86278309G>A	ENSP00000378026:p.Gly2457Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	185	183	0.989189	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	340	0.15567765567765568	5	0.01016260162601626	85	0.23480662983425415	35	0.06118881118881119	215	0.2836411609498681	G	17.55	3.418288	0.62622	0.044959	0.266574	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	T;T;T	0.19532	2.14;2.14;2.14	5.77	4.86	0.63082	.	.	.	.	.	T	0.00012	0.0000	L	0.35593	1.075	0.22737	P	0.99879801	D;D	0.76494	0.999;0.999	D;D	0.69654	0.924;0.965	T	0.29971	-0.9994	8	0.45353	T	0.12	.	14.2	0.65696	0.0715:0.0:0.9285:0.0	rs2241268;rs17638162;rs52827429;rs58056875;rs2241268	2457;2461	Q12802;Q12802-2	AKP13_HUMAN;.	S	2461;2457;2460;2436;702	ENSP00000354718:G2461S;ENSP00000378026:G2457S;ENSP00000378018:G702S	ENSP00000354718:G2461S	G	+	1	0	AKAP13	84079313	1.000000	0.71417	0.860000	0.33809	0.062000	0.15995	2.615000	0.46368	1.458000	0.47871	-0.363000	0.07495	GGT	G|0.820;A|0.180	0.180	strong		0.502	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
HDX	139324	hgsc.bcm.edu	37	X	83591866	83591866	+	Silent	SNP	C	C	T	rs5922966	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:83591866C>T	ENST00000297977.5	-	7	1794	c.1683G>A	c.(1681-1683)ccG>ccA	p.P561P	HDX_ENST00000506585.2_Silent_p.P503P|HDX_ENST00000373177.2_Silent_p.P561P	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	561						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TTGCATCATTCGGAACAACTT	0.343													C|||	239	0.0633113	0.0061	0.1124	3775	,	,		12668	0.001		0.1322	False		,,,				2504	0.0194				p.P561P	Pancreas(53;231 1169 36156 43751 51139)	Atlas-SNP	.											.	HDX	124	.	0			c.G1683A						PASS	.	C	,,	143,3690		4,122,13,1505,558	99.0	81.0	87.0		1509,1683,1683	1.1	0.8	X	dbSNP_114	87	1356,5369		96,788,376,1543,1495	no	coding-synonymous,coding-synonymous,coding-synonymous	HDX	NM_001177478.1,NM_001177479.1,NM_144657.4	,,	100,910,389,3048,2053	TT,TC,T,CC,C		20.1636,3.7308,14.1978	,,	503/633,561/691,561/691	83591866	1499,9059	2202	4298	6500	SO:0001819	synonymous_variant	139324	exon7			ATCATTCGGAACA	BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"""Homeoboxes / POU class"""	26411	protein-coding gene	gene with protein product			"""chromosome X open reading frame 43"""	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.1683G>A	X.37:g.83591866C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	51	49	0.960784	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Silent	SNP	ENST00000297977.5	37	CCDS35342.1																																																																																			C|0.875;0|0.014	.	strong		0.343	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	140636	140636	+	Missense_Mutation	SNP	G	G	A	rs12523402	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140636G>A	ENST00000283426.6	+	1	264	c.214G>A	c.(214-216)Gct>Act	p.A72T	CTD-2231H16.1_ENST00000512035.1_lincRNA	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	72			A -> T (in dbSNP:rs12523402).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		AGGTCCAGGAGCTGCAGGGCG	0.662													G|||	163	0.0325479	0.0121	0.0346	5008	,	,		10641	0.0		0.0964	False		,,,				2504	0.0266				p.A72T		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.G214A						PASS	.		THR/ALA	104,4238		2,100,2069	16.0	21.0	19.0		214	1.4	0.0	5	dbSNP_120	19	729,7815		33,663,3576	yes	missense	PLEKHG4B	NM_052909.3	58	35,763,5645	AA,AG,GG		8.5323,2.3952,6.4644	possibly-damaging	72/1272	140636	833,12053	2171	4272	6443	SO:0001583	missense	153478	exon1			CCAGGAGCTGCAG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.214G>A	5.37:g.140636G>A	ENSP00000283426:p.Ala72Thr	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	277	141	0.509025	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	94	0.04304029304029304	4	0.008130081300813009	13	0.03591160220994475	0	0.0	77	0.10158311345646438	.	8.993	0.978293	0.18812	0.023952	0.085323	ENSG00000153404	ENST00000283426	T	0.21932	1.98	2.59	1.43	0.22495	.	.	.	.	.	T	0.00271	0.0008	N	0.14661	0.345	0.09310	N	1	B	0.24721	0.11	B	0.19666	0.026	T	0.37291	-0.9712	9	0.13853	T	0.58	.	7.0407	0.25019	0.0:0.0:0.7104:0.2896	rs12523402;rs12523402	72	Q96PX9	PKH4B_HUMAN	T	72	ENSP00000283426:A72T	ENSP00000283426:A72T	A	+	1	0	PLEKHG4B	193636	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	-0.123000	0.10611	0.963000	0.38082	0.298000	0.19748	GCT	G|0.950;A|0.050	0.050	strong		0.662	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
CMTM5	116173	hgsc.bcm.edu	37	14	23848311	23848311	+	Silent	SNP	C	C	T	rs723840	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23848311C>T	ENST00000339180.4	+	4	768	c.552C>T	c.(550-552)gaC>gaT	p.D184D	CMTM5_ENST00000397227.3_Silent_p.D66D|CMTM5_ENST00000555731.1_Silent_p.D79D|CMTM5_ENST00000342473.4_Intron|CMTM5_ENST00000359320.3_Silent_p.D117D|CMTM5_ENST00000382809.2_Intron			Q96DZ9	CKLF5_HUMAN	CKLF-like MARVEL transmembrane domain containing 5	184	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.D117D(1)		endometrium(1)|large_intestine(1)|lung(4)|prostate(1)|stomach(1)	8	all_cancers(95;2e-05)			GBM - Glioblastoma multiforme(265;0.0064)|READ - Rectum adenocarcinoma(4;0.0276)|Colorectal(4;0.0382)		CCTCCCGGGACGGAGCTGCCA	0.582													T|||	2551	0.509385	0.848	0.3674	5008	,	,		18254	0.256		0.4742	False		,,,				2504	0.4499				p.D117D		Atlas-SNP	.											CMTM5,NS,carcinoma,0,1	CMTM5	38	1	1	Substitution - coding silent(1)	stomach(1)	c.C351T						PASS	.	T	,	3420,986	367.3+/-318.2	1322,776,105	88.0	75.0	79.0		,351	-1.4	1.0	14	dbSNP_86	79	4046,4554	596.3+/-393.6	955,2136,1209	no	intron,coding-synonymous	CMTM5	NM_001037288.1,NM_138460.2	,	2277,2912,1314	TT,TC,CC		47.0465,22.3786,42.5957	,	,117/157	23848311	7466,5540	2203	4300	6503	SO:0001819	synonymous_variant	116173	exon3			CCGGGACGGAGCT	BC013109	CCDS9598.1, CCDS32050.1, CCDS73617.1, CCDS73618.1, CCDS73619.1	14q11.2	2005-11-08	2005-11-08	2005-11-08	ENSG00000166091	ENSG00000166091			19176	protein-coding gene	gene with protein product		607888	"""chemokine-like factor super family 5"", ""chemokine-like factor superfamily 5"""	CKLFSF5			Standard	NM_138460		Approved	FLJ37521	uc001wjs.3	Q96DZ9	OTTHUMG00000028751	ENST00000339180.4:c.552C>T	14.37:g.23848311C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	137	136	0.992701	NM_138460	E9PH91|Q5PY48	Silent	SNP	ENST00000339180.4	37																																																																																				C|0.454;T|0.546	0.546	strong		0.582	CMTM5-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000133708.2		
TREML2	79865	hgsc.bcm.edu	37	6	41166021	41166021	+	Missense_Mutation	SNP	C	C	T	rs386700523|rs61736679	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41166021C>T	ENST00000483722.1	-	2	387	c.202G>A	c.(202-204)Gcc>Acc	p.A68T		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	68	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					CAGACTCGGGCAAAGCCAGGC	0.572																																					p.A68T		Atlas-SNP	.											TREML2,caecum,carcinoma,0,1	TREML2	41	1	0			c.G202A						scavenged	.						133.0	131.0	132.0					6																	41166021		2203	4300	6503	SO:0001583	missense	79865	exon2			CTCGGGCAAAGCC	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.202G>A	6.37:g.41166021C>T	ENSP00000418767:p.Ala68Thr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	104	7	0.0673077	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	0.011	-1.711493	0.00712	.	.	ENSG00000112195	ENST00000483722	T	0.67865	-0.29	4.75	0.472	0.16758	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.870478	0.09855	N	0.747087	T	0.06508	0.0167	N	0.00263	-1.745	0.21256	N	0.999743	B	0.10296	0.003	B	0.04013	0.001	T	0.39121	-0.9629	10	0.02654	T	1	-2.4265	5.3045	0.15795	0.0:0.0954:0.3459:0.5587	.	68	Q5T2D2	TRML2_HUMAN	T	68	ENSP00000418767:A68T	ENSP00000418767:A68T	A	-	1	0	TREML2	41273999	0.082000	0.21442	0.327000	0.25402	0.012000	0.07955	-0.620000	0.05565	-0.041000	0.13558	-0.440000	0.05779	GCC	C|0.989;T|0.011	0.011	strong		0.572	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
PRAM1	84106	hgsc.bcm.edu	37	19	8567475	8567475	+	Start_Codon_SNP	SNP	T	T	C	rs968502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8567475T>C	ENST00000423345.4	-	1	521	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	PRAM1_ENST00000255612.3_Start_Codon_SNP_p.M1V			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	1					integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						TGATGGGCCATGGGATGAGTG	0.627													C|||	1562	0.311901	0.6626	0.2032	5008	,	,		7435	0.1815		0.1998	False		,,,				2504	0.1646				p.M1V		Atlas-SNP	.											.	PRAM1	53	.	0			c.A1G						PASS	.	C	VAL/MET	2055,1891		555,945,473	16.0	17.0	16.0		1	1.1	0.0	19	dbSNP_86	16	1396,6726		130,1136,2795	yes	missense	PRAM1	NM_032152.4	21	685,2081,3268	CC,CT,TT		17.1879,47.9219,28.5963	benign	1/671	8567475	3451,8617	1973	4061	6034	SO:0001582	initiator_codon_variant	84106	exon1			GGGCCATGGGATG	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.1A>G	19.37:g.8567475T>C	ENSP00000408342:p.Met1Val	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	645	0.29532967032967034	331	0.6727642276422764	68	0.1878453038674033	97	0.16958041958041958	149	0.19656992084432717	C	0.001	-2.997294	0.00044	0.520781	0.171879	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.13538	2.58;2.58	3.35	1.06	0.20224	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53688	P	2.6999999999999247E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41034	-0.9531	7	0.02654	T	1	.	1.9836	0.03432	0.206:0.4762:0.2003:0.1175	rs968502;rs17160538;rs60284359;rs968502	1;1	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	V	1	ENSP00000255612:M1V;ENSP00000408342:M1V	ENSP00000255612:M1V	M	-	1	0	PRAM1	8473475	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-0.509000	0.06336	0.070000	0.16634	-0.355000	0.07637	ATG	T|0.672;C|0.328	0.328	strong		0.627	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152	Missense_Mutation
TTC3	7267	hgsc.bcm.edu	37	21	38512956	38512956	+	Silent	SNP	A	A	G	rs1133001	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:38512956A>G	ENST00000399017.2	+	20	4502	c.1755A>G	c.(1753-1755)gtA>gtG	p.V585V	TTC3_ENST00000355666.1_Silent_p.V585V|TTC3_ENST00000354749.2_Silent_p.V585V|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000540756.1_Silent_p.V275V	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	585					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TTGGAAAAGTATATTTGAAAA	0.358													A|||	2964	0.591853	0.6445	0.6282	5008	,	,		15700	0.6032		0.4642	False		,,,				2504	0.6145				p.V585V	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	1	Unknown(1)	skin(1)	c.A1755G						PASS	.	A	,	2766,1640	657.1+/-400.2	869,1028,306	92.0	91.0	91.0		1755,1755	-6.1	1.0	21	dbSNP_86	91	3848,4752	540.8+/-383.9	896,2056,1348	no	coding-synonymous,coding-synonymous	TTC3	NM_001001894.1,NM_003316.3	,	1765,3084,1654	GG,GA,AA		44.7442,37.222,49.1465	,	585/2026,585/2026	38512956	6614,6392	2203	4300	6503	SO:0001819	synonymous_variant	7267	exon20			AAAAGTATATTTG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.1755A>G	21.37:g.38512956A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1																																																																																			A|0.475;G|0.525	0.525	strong		0.358	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
MATN3	4148	hgsc.bcm.edu	37	2	20202930	20202930	+	Missense_Mutation	SNP	G	G	A	rs77245812	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:20202930G>A	ENST00000407540.3	-	3	970	c.908C>T	c.(907-909)aCg>aTg	p.T303M	MATN3_ENST00000421259.2_Intron|AC079145.4_ENST00000416575.1_RNA	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	303	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.		T -> M (in dbSNP:rs28939676). {ECO:0000269|PubMed:12736871, ECO:0000269|PubMed:14729835, ECO:0000269|PubMed:15459972}.		extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACCTGAACACGTTTTCTTGTC	0.527													G|||	70	0.0139776	0.0	0.0101	5008	,	,		18855	0.001		0.0159	False		,,,				2504	0.047				p.T303M		Atlas-SNP	.											.	MATN3	28	.	0			c.C908T	GRCh37	CM031237	MATN3	M	rs77245812	PASS	.	G	MET/THR	20,4030		0,20,2005	127.0	118.0	121.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	908	5.5	0.4	2	dbSNP_131	121	122,8220		0,122,4049	yes	missense	MATN3	NM_002381.4	81	0,142,6054	AA,AG,GG		1.4625,0.4938,1.1459	probably-damaging	303/487	20202930	142,12250	2025	4171	6196	SO:0001583	missense	4148	exon3			GAACACGTTTTCT	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.908C>T	2.37:g.20202930G>A	ENSP00000383894:p.Thr303Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	171	65	0.380117	NM_002381	B2CPU0|Q4ZG02	Missense_Mutation	SNP	ENST00000407540.3	37	CCDS46226.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	0	0.0	12	0.0158311345646438	G	22.5	4.298303	0.81025	0.004938	0.014625	ENSG00000132031	ENST00000407540	D	0.88201	-2.35	5.5	5.5	0.81552	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.93106	0.7805	H	0.95539	3.685	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93432	0.6786	10	0.72032	D	0.01	-21.4112	16.1448	0.81559	0.0:0.0:1.0:0.0	rs28939676;rs52790166	303	O15232	MATN3_HUMAN	M	303	ENSP00000383894:T303M	ENSP00000383894:T303M	T	-	2	0	MATN3	20066411	1.000000	0.71417	0.415000	0.26534	0.782000	0.44232	8.518000	0.90559	2.596000	0.87737	0.650000	0.86243	ACG	G|0.990;A|0.010	0.010	strong		0.527	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381	
ETAA1	54465	hgsc.bcm.edu	37	2	67630980	67630980	+	Missense_Mutation	SNP	G	G	A	rs3770657	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:67630980G>A	ENST00000272342.5	+	5	1296	c.1166G>A	c.(1165-1167)aGt>aAt	p.S389N	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	389			S -> N (in dbSNP:rs3770657). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)		p.S389N(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						TTACTAGGTAGTGAACCTTTT	0.353													A|||	3670	0.732827	0.8699	0.719	5008	,	,		19009	0.5685		0.7296	False		,,,				2504	0.7301				p.S389N		Atlas-SNP	.											ETAA1,NS,carcinoma,+1,2	ETAA1	88	2	1	Substitution - Missense(1)	stomach(1)	c.G1166A						PASS	.	A	ASN/SER	3752,654	274.9+/-272.2	1602,548,53	93.0	98.0	96.0		1166	3.4	0.6	2	dbSNP_107	96	6148,2446	403.5+/-347.8	2213,1722,362	yes	missense	ETAA1	NM_019002.3	46	3815,2270,415	AA,AG,GG		28.4617,14.8434,23.8462	benign	389/927	67630980	9900,3100	2203	4297	6500	SO:0001583	missense	54465	exon5			TAGGTAGTGAACC	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1166G>A	2.37:g.67630980G>A	ENSP00000272342:p.Ser389Asn	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	320	94	0.29375	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	1572	0.7197802197802198	430	0.8739837398373984	265	0.7320441988950276	325	0.5681818181818182	552	0.7282321899736148	A	0.005	-2.185214	0.00305	0.851566	0.715383	ENSG00000143971	ENST00000272342	T	0.14516	2.5	5.77	3.4	0.38934	.	0.289310	0.38111	N	0.001815	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35151	-0.9800	9	0.02654	T	1	-33.7308	8.8244	0.35045	0.7808:0.0:0.2192:0.0	rs3770657;rs56442704;rs59377126;rs3770657	389	Q9NY74	ETAA1_HUMAN	N	389	ENSP00000272342:S389N	ENSP00000272342:S389N	S	+	2	0	ETAA1	67484484	1.000000	0.71417	0.567000	0.28434	0.043000	0.13939	2.213000	0.42844	0.125000	0.18397	-0.254000	0.11334	AGT	G|0.257;N|0.000	.	strong		0.353	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002	
CATSPER4	378807	hgsc.bcm.edu	37	1	26527951	26527951	+	Missense_Mutation	SNP	G	G	A	rs6657616	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26527951G>A	ENST00000456354.2	+	9	1373	c.1306G>A	c.(1306-1308)Gac>Aac	p.D436N		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	436			D -> N (in dbSNP:rs6657616).		calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		GTCATCCAAGGACATCCGCCA	0.577													G|||	1053	0.210264	0.3744	0.1657	5008	,	,		17952	0.0218		0.2654	False		,,,				2504	0.1575				p.D436N		Atlas-SNP	.											.	CATSPER4	59	.	0			c.G1306A						PASS	.	G	ASN/ASP	1510,2896	481.7+/-359.2	272,966,965	124.0	108.0	114.0		1306	3.1	0.0	1	dbSNP_116	114	2216,6384	375.4+/-337.8	287,1642,2371	yes	missense	CATSPER4	NM_198137.1	23	559,2608,3336	AA,AG,GG		25.7674,34.2714,28.6483	benign	436/473	26527951	3726,9280	2203	4300	6503	SO:0001583	missense	378807	exon9			TCCAAGGACATCC	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.1306G>A	1.37:g.26527951G>A	ENSP00000390423:p.Asp436Asn	Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	392	185	0.471939	NM_198137	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	467	0.21382783882783882	175	0.3556910569105691	69	0.19060773480662985	11	0.019230769230769232	212	0.2796833773087071	G	18.48	3.633953	0.67130	0.342714	0.257674	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.97455	-4.39;-4.36	5.1	3.1	0.35709	.	0.271285	0.25695	N	0.028916	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	P	0.42409	0.779	B	0.37480	0.251	T	0.00224	-1.1902	9	0.45353	T	0.12	-17.8632	5.74	0.18087	0.1085:0.2169:0.6746:0.0	rs6657616;rs52798453;rs60006559;rs6657616	436	Q7RTX7	CTSR4_HUMAN	N	436	ENSP00000341006:D436N;ENSP00000390423:D436N	ENSP00000341006:D436N	D	+	1	0	CATSPER4	26400538	0.025000	0.19082	0.018000	0.16275	0.149000	0.21700	1.622000	0.36997	2.393000	0.81446	0.313000	0.20887	GAC	G|0.743;A|0.257	0.257	strong		0.577	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
ATP11A	23250	hgsc.bcm.edu	37	13	113530199	113530199	+	Missense_Mutation	SNP	G	G	A	rs11616795	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:113530199G>A	ENST00000487903.1	+	28	3359	c.3271G>A	c.(3271-3273)Gtc>Atc	p.V1091I	ATP11A_ENST00000375630.2_Missense_Mutation_p.V1091I|ATP11A_ENST00000283558.8_Missense_Mutation_p.V1091I|ATP11A_ENST00000375645.3_Missense_Mutation_p.V1091I			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	1091			V -> I (in dbSNP:rs11616795).		phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				CCTTCCCGACGTCCTCAAGAA	0.637													G|||	411	0.0820687	0.0129	0.098	5008	,	,		18273	0.0853		0.1272	False		,,,				2504	0.1145				p.V1091I		Atlas-SNP	.											.	ATP11A	225	.	0			c.G3271A						PASS	.	G	ILE/VAL,ILE/VAL	107,4299	83.4+/-121.9	1,105,2097	56.0	52.0	53.0		3271,3271	1.6	0.4	13	dbSNP_120	53	912,7688	203.0+/-246.1	51,810,3439	yes	missense,missense	ATP11A	NM_015205.2,NM_032189.3	29,29	52,915,5536	AA,AG,GG		10.6047,2.4285,7.8348	benign,benign	1091/1135,1091/1192	113530199	1019,11987	2203	4300	6503	SO:0001583	missense	23250	exon28			CCCGACGTCCTCA	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.3271G>A	13.37:g.113530199G>A	ENSP00000420387:p.Val1091Ile	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	37	CCDS32011.1	167|167	0.07646520146520147|0.07646520146520147	11|11	0.022357723577235773|0.022357723577235773	38|38	0.10497237569060773|0.10497237569060773	42|42	0.07342657342657342|0.07342657342657342	76|76	0.10026385224274406|0.10026385224274406	G|G	7.790|7.790	0.711346|0.711346	0.15239|0.15239	0.024285|0.024285	0.106047|0.106047	ENSG00000068650|ENSG00000068650	ENST00000415301|ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558;ENST00000419631	.|T;T;T;T;T	.|0.59083	.|0.29;0.29;0.29;0.29;0.29	4.79|4.79	1.59|1.59	0.23543|0.23543	.|.	.|0.059905	.|0.64402	.|D	.|0.000003	T|T	0.00815|0.00815	0.0027|0.0027	N|N	0.25332|0.25332	0.735|0.735	0.22541|0.22541	P|P	0.999006184|0.999006184	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.06405	.|0.002;0.001	T|T	0.10291|0.10291	-1.0636|-1.0636	4|9	.|0.15952	.|T	.|0.53	.|.	10.9244|10.9244	0.47184|0.47184	0.247:0.0:0.753:0.0|0.247:0.0:0.753:0.0	rs11616795;rs11616795|rs11616795;rs11616795	.|1091;1091	.|E9PEJ6;P98196	.|.;AT11A_HUMAN	H|I	26|1091;1091;1091;1091;83	.|ENSP00000420387:V1091I;ENSP00000364781:V1091I;ENSP00000364796:V1091I;ENSP00000283558:V1091I;ENSP00000410824:V83I	.|ENSP00000283558:V1091I	R|V	+|+	2|1	0|0	ATP11A|ATP11A	112578200|112578200	1.000000|1.000000	0.71417|0.71417	0.358000|0.358000	0.25811|0.25811	0.004000|0.004000	0.04260|0.04260	4.185000|4.185000	0.58330|0.58330	0.446000|0.446000	0.26666|0.26666	-0.258000|-0.258000	0.10820|0.10820	CGT|GTC	G|0.920;A|0.080	0.080	strong		0.637	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
SIX5	147912	hgsc.bcm.edu	37	19	46269076	46269076	+	Missense_Mutation	SNP	G	G	A	rs2014576	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:46269076G>A	ENST00000317578.6	-	3	2284	c.1903C>T	c.(1903-1905)Ccc>Tcc	p.P635S	AC074212.6_ENST00000590076.1_RNA|AC074212.5_ENST00000592217.2_RNA|AC074212.5_ENST00000559756.1_RNA|SIX5_ENST00000560168.1_3'UTR	NM_175875.4	NP_787071	Q8N196	SIX5_HUMAN	SIX homeobox 5	635			P -> S (in dbSNP:rs2014576).		lens development in camera-type eye (GO:0002088)|negative regulation of cell proliferation (GO:0008285)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)		GGGGAGAAGGGCAGGCTGGTG	0.711													G|||	2509	0.500998	0.3192	0.621	5008	,	,		14771	0.6111		0.4523	False		,,,				2504	0.5982				p.P635S		Atlas-SNP	.											.	SIX5	35	.	0			c.C1903T						PASS	.	G	SER/PRO	1510,2866		283,944,961	14.0	17.0	16.0		1903	-0.8	1.0	19	dbSNP_92	16	3703,4851		853,1997,1427	no	missense	SIX5	NM_175875.4	74	1136,2941,2388	AA,AG,GG		43.2897,34.5064,40.3171	possibly-damaging	635/740	46269076	5213,7717	2188	4277	6465	SO:0001583	missense	147912	exon3			AGAAGGGCAGGCT	L08835	CCDS12673.1	19q13.32	2011-06-20	2007-07-13			ENSG00000177045		"""Homeoboxes / SINE class"""	10891	protein-coding gene	gene with protein product		600963	"""sine oculis homeobox (Drosophila) homolog 5"", ""sine oculis homeobox homolog 5 (Drosophila)"""	DMAHP		8595416	Standard	NM_175875		Approved		uc002pdb.3	Q8N196		ENST00000317578.6:c.1903C>T	19.37:g.46269076G>A	ENSP00000316842:p.Pro635Ser	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_175875		Missense_Mutation	SNP	ENST00000317578.6	37	CCDS12673.1	1119	0.5123626373626373	173	0.3516260162601626	211	0.5828729281767956	386	0.6748251748251748	349	0.4604221635883905	g	12.37	1.919029	0.33908	0.345064	0.432897	ENSG00000177045	ENST00000317578	D	0.88896	-2.44	4.2	-0.76	0.11041	.	1.194610	0.05919	N	0.633071	T	0.00012	0.0000	N	0.14661	0.345	0.49582	P	1.9499999999994522E-4	B	0.11235	0.004	B	0.06405	0.002	T	0.40850	-0.9541	9	0.33940	T	0.23	-6.713	1.8982	0.03262	0.1077:0.1739:0.3629:0.3556	rs2014576;rs52791013;rs2014576	635	Q8N196	SIX5_HUMAN	S	635	ENSP00000316842:P635S	ENSP00000316842:P635S	P	-	1	0	SIX5	50960916	0.011000	0.17503	0.983000	0.44433	0.942000	0.58702	-0.164000	0.09983	0.388000	0.25054	0.555000	0.69702	CCC	G|0.543;A|0.457	0.457	strong		0.711	SIX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417341.3	NM_175875	
PARP4	143	hgsc.bcm.edu	37	13	25060313	25060313	+	Silent	SNP	A	A	G	rs73154350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25060313A>G	ENST00000381989.3	-	11	1450	c.1345T>C	c.(1345-1347)Ttg>Ctg	p.L449L		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	449	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TACCGACACAAGATTCCCACG	0.373													.|||	194	0.038738	0.0083	0.0591	5008	,	,		17531	0.002		0.0934	False		,,,				2504	0.047				p.L449L		Atlas-SNP	.											.	PARP4	142	.	0			c.T1345C						PASS	.	A		115,4291	87.3+/-125.9	4,107,2092	97.0	85.0	89.0		1345	2.6	1.0	13	dbSNP_131	89	978,7622	212.1+/-252.5	65,848,3387	no	coding-synonymous	PARP4	NM_006437.3		69,955,5479	GG,GA,AA		11.3721,2.6101,8.4038		449/1725	25060313	1093,11913	2203	4300	6503	SO:0001819	synonymous_variant	143	exon11			GACACAAGATTCC	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1345T>C	13.37:g.25060313A>G		Somatic	499	1	0.00200401		WXS	Illumina HiSeq	Phase_I	567	563	0.992945	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			A|0.924;G|0.076	0.076	strong		0.373	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
OR8I2	120586	hgsc.bcm.edu	37	11	55861153	55861153	+	Missense_Mutation	SNP	A	A	G	rs17603011	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55861153A>G	ENST00000302124.2	+	1	401	c.370A>G	c.(370-372)Ata>Gta	p.I124V		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	124			I -> V (in dbSNP:rs17603011).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					CAATCGCTACATAGCAATCTG	0.433													G|||	195	0.0389377	0.0121	0.0447	5008	,	,		21616	0.001		0.0944	False		,,,				2504	0.0532				p.I124V		Atlas-SNP	.											.	OR8I2	119	.	0			c.A370G						PASS	.	G	VAL/ILE	98,4304	817.2+/-416.3	0,98,2103	155.0	138.0	144.0		370	4.5	0.7	11	dbSNP_123	144	693,7899	787.9+/-407.6	34,625,3637	yes	missense	OR8I2	NM_001003750.1	29	34,723,5740	GG,GA,AA		8.0656,2.2263,6.0874	benign	124/311	55861153	791,12203	2201	4296	6497	SO:0001583	missense	120586	exon1			CGCTACATAGCAA	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.370A>G	11.37:g.55861153A>G	ENSP00000303864:p.Ile124Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	149	68	0.456376	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	37	CCDS31517.1	86	0.039377289377289376	4	0.008130081300813009	14	0.03867403314917127	0	0.0	68	0.08970976253298153	G	0.004	-2.307026	0.00240	0.022263	0.080656	ENSG00000172154	ENST00000302124	T	0.02158	4.42	4.5	4.5	0.54988	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36482	N	0.002580	T	0.00039	0.0001	N	0.00403	-1.54	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46965	-0.9153	10	0.02654	T	1	-5.479	6.5633	0.22499	0.1699:0.1479:0.6822:0.0	rs17603011;rs52829267;rs17603011	124	Q8N0Y5	OR8I2_HUMAN	V	124	ENSP00000303864:I124V	ENSP00000303864:I124V	I	+	1	0	OR8I2	55617729	0.001000	0.12720	0.745000	0.31077	0.007000	0.05969	0.147000	0.16202	1.027000	0.39758	-0.440000	0.05779	ATA	A|0.950;G|0.050	0.050	strong		0.433	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
PCSK5	5125	hgsc.bcm.edu	37	9	78937974	78937974	+	Missense_Mutation	SNP	C	C	T	rs3001772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:78937974C>T	ENST00000545128.1	+	31	4566	c.4028C>T	c.(4027-4029)aCg>aTg	p.T1343M		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1343	CRM (Cys-rich motif).				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						CCAGAGTGCACGCCTGAGTTC	0.552													T|||	2451	0.489417	0.6846	0.4337	5008	,	,		18793	0.2093		0.5487	False		,,,				2504	0.4928				p.T1343M		Atlas-SNP	.											.	PCSK5	329	.	0			c.C4028T						PASS	.	T	MET/THR	1139,613		375,389,112	21.0	18.0	19.0		4028	5.7	1.0	9	dbSNP_101	19	2170,1812		603,964,424	yes	missense	PCSK5	NM_001190482.1	81	978,1353,536	TT,TC,CC		45.5048,34.9886,42.2916	benign	1343/1861	78937974	3309,2425	876	1991	2867	SO:0001583	missense	5125	exon31			AGTGCACGCCTGA		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.4028C>T	9.37:g.78937974C>T	ENSP00000446280:p.Thr1343Met	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	1020	0.46703296703296704	326	0.6626016260162602	164	0.4530386740331492	110	0.19230769230769232	420	0.554089709762533	T	10.28	1.305791	0.23736	0.650114	0.544952	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.30714	1.54;1.52	5.65	5.65	0.86999	.	0.444025	0.27340	N	0.019810	T	0.00012	0.0000	N	0.03071	-0.42	0.58432	P	6.999999999979245E-6	.	.	.	.	.	.	T	0.10019	-1.0648	7	0.40728	T	0.16	-8.0846	10.9166	0.47139	0.0:0.0746:0.0:0.9254	rs3001772;rs58696668	.	.	.	M	1343;1073;1043	ENSP00000446280:T1343M;ENSP00000411654:T1043M	ENSP00000365945:T1073M	T	+	2	0	PCSK5	78127794	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	1.767000	0.38501	0.976000	0.38417	-0.269000	0.10298	ACG	C|0.517;T|0.483	0.483	strong		0.552	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FAM220A	84792	hgsc.bcm.edu	37	7	6370317	6370317	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:6370317G>A	ENST00000313324.4	-	2	936	c.469C>T	c.(469-471)Cgc>Tgc	p.R157C	FAM220A_ENST00000533877.1_5'Flank	NM_001037163.1	NP_001032240.1	Q7Z4H9	F220A_HUMAN	family with sequence similarity 220, member A	157						nucleus (GO:0005634)											TTTTGATGGCGTGGCAGTCGT	0.617																																					p.R157C		Atlas-SNP	.											C7orf70,colon,carcinoma,+1,1	.	.	1	0			c.C469T						scavenged	.						46.0	54.0	51.0					7																	6370317		2203	4300	6503	SO:0001583	missense	84792	exon2			GATGGCGTGGCAG	BC006110	CCDS34599.1	7p22.1	2012-03-19	2012-03-19	2012-03-19	ENSG00000178397	ENSG00000178397			22422	protein-coding gene	gene with protein product	"""STAT3-interacting protein as a repressor"""		"""chromosome 7 open reading frame 70"""	C7orf70			Standard	NM_001037163		Approved	SIPAR, MGC12966	uc003spu.3	Q7Z4H9	OTTHUMG00000122091	ENST00000313324.4:c.469C>T	7.37:g.6370317G>A	ENSP00000317289:p.Arg157Cys	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	127	2	0.015748	NM_001037163	Q75ML2|Q8NA52|Q9BRR7	Missense_Mutation	SNP	ENST00000313324.4	37	CCDS34599.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.476137	0.26511	.	.	ENSG00000178397	ENST00000313324	T	0.07444	3.19	5.42	-3.96	0.04106	.	1.224330	0.06033	N	0.653410	T	0.02380	0.0073	N	0.00583	-1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47749	-0.9093	10	0.37606	T	0.19	3.0244	8.9684	0.35890	0.376:0.4775:0.1466:0.0	.	157	Q7Z4H9	SIPAR_HUMAN	C	157	ENSP00000317289:R157C	ENSP00000317289:R157C	R	-	1	0	C7orf70	6336842	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.232000	0.09055	-1.055000	0.03209	-1.110000	0.02074	CGC	.	.	none		0.617	FAM220A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000242853.2	NM_001037163	
SPATA7	55812	hgsc.bcm.edu	37	14	88862529	88862529	+	Missense_Mutation	SNP	G	G	A	rs3179969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:88862529G>A	ENST00000393545.4	+	4	509	c.220G>A	c.(220-222)Gtg>Atg	p.V74M	SPATA7_ENST00000045347.7_Missense_Mutation_p.V74M|SPATA7_ENST00000556553.1_Missense_Mutation_p.V42M|SPATA7_ENST00000554102.1_3'UTR|SPATA7_ENST00000356583.5_Missense_Mutation_p.V42M	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	74			V -> M (in dbSNP:rs3179969). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12736779}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						TCCAGTAAGCGTGAGTACCAG	0.289													A|||	2041	0.407548	0.5749	0.281	5008	,	,		18207	0.3621		0.3002	False		,,,				2504	0.4284				p.V74M		Atlas-SNP	.											.	SPATA7	58	.	0			c.G220A						PASS	.	A	MET/VAL,MET/VAL	2396,2010	558.6+/-380.0	648,1100,455	60.0	63.0	62.0		124,220	2.5	0.8	14	dbSNP_105	62	2948,5650	665.7+/-402.3	492,1964,1843	yes	missense,missense	SPATA7	NM_001040428.3,NM_018418.4	21,21	1140,3064,2298	AA,AG,GG		34.287,45.6196,41.095	benign,benign	42/568,74/600	88862529	5344,7660	2203	4299	6502	SO:0001583	missense	55812	exon4			GTAAGCGTGAGTA	AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"""Leber congenital amaurosis 3"""	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.220G>A	14.37:g.88862529G>A	ENSP00000377176:p.Val74Met	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Missense_Mutation	SNP	ENST00000393545.4	37	CCDS9883.1	822	0.37637362637362637	287	0.5833333333333334	106	0.292817679558011	191	0.3339160839160839	238	0.31398416886543534	A	9.944	1.218398	0.22373	0.543804	0.34287	ENSG00000042317	ENST00000556553;ENST00000393545;ENST00000356583;ENST00000555401;ENST00000553885;ENST00000045347	T;T;T;T;T;T	0.36878	2.34;2.34;2.34;2.34;1.23;2.34	5.36	2.45	0.29901	.	0.708733	0.13894	N	0.355375	T	0.00012	0.0000	N	0.01742	-0.745	0.58432	P	5.999999999950489E-6	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.46775	-0.9167	9	0.02654	T	1	-0.2599	3.8224	0.08841	0.6321:0.0:0.2162:0.1517	rs3179969;rs58922179;rs3179969	42;74	Q9P0W8-2;Q9P0W8	.;SPAT7_HUMAN	M	42;74;42;17;42;74	ENSP00000451128:V42M;ENSP00000377176:V74M;ENSP00000348991:V42M;ENSP00000452435:V17M;ENSP00000450606:V42M;ENSP00000045347:V74M	ENSP00000045347:V74M	V	+	1	0	SPATA7	87932282	1.000000	0.71417	0.769000	0.31535	0.374000	0.29953	1.184000	0.32053	-0.020000	0.14032	-0.521000	0.04368	GTG	G|0.599;A|0.401	0.401	strong		0.289	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1		
DMPK	1760	hgsc.bcm.edu	37	19	46275976	46275976	+	Missense_Mutation	SNP	G	G	C	rs527221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:46275976G>C	ENST00000291270.4	-	10	1392	c.1267C>G	c.(1267-1269)Ctg>Gtg	p.L423V	AC074212.6_ENST00000591530.1_RNA|DMPK_ENST00000447742.2_Missense_Mutation_p.L418V|AC074212.6_ENST00000590076.1_RNA|AC074212.5_ENST00000592217.2_RNA|AC074212.6_ENST00000586251.1_RNA|DMPK_ENST00000458663.2_Missense_Mutation_p.L418V|DMPK_ENST00000600757.1_Missense_Mutation_p.L428V|DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000343373.4_Missense_Mutation_p.L433V|DMPK_ENST00000354227.5_Missense_Mutation_p.L418V|AC074212.6_ENST00000586498.1_RNA	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	423			L -> V (in dbSNP:rs527221). {ECO:0000269|PubMed:1310900, ECO:0000269|PubMed:7905855, ECO:0000269|PubMed:8469976, ECO:0000269|PubMed:8499920}.		cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		TCGGCCTCCAGTTCCATGGGT	0.627													G|||	727	0.145168	0.053	0.1902	5008	,	,		18162	0.1796		0.1113	False		,,,				2504	0.2372				p.L433V	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-SNP	.											DMPK_ENST00000343373,NS,carcinoma,0,2	DMPK	74	2	0			c.C1297G						scavenged	.	G	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	296,4110	160.0+/-192.4	4,288,1911	42.0	43.0	43.0		1252,1252,1297,1267	3.9	1.0	19	dbSNP_83	43	971,7629	208.4+/-249.9	58,855,3387	yes	missense,missense,missense,missense	DMPK	NM_001081560.1,NM_001081562.1,NM_001081563.1,NM_004409.3	32,32,32,32	62,1143,5298	CC,CG,GG		11.2907,6.7181,9.7417	benign,benign,benign,benign	418/625,418/626,433/640,423/630	46275976	1267,11739	2203	4300	6503	SO:0001583	missense	1760	exon9			CCTCCAGTTCCAT	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"""dystrophia myotonica 1"", ""DM protein kinase"", ""myotonin protein kinase A"", ""myotonic dystrophy associated protein kinase"", ""thymopoietin homolog"""	605377	"""dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"""	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.1267C>G	19.37:g.46275976G>C	ENSP00000291270:p.Leu423Val	Somatic	60	1	0.0166667		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_001081563	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	37	CCDS12674.1	268	0.1227106227106227	28	0.056910569105691054	56	0.15469613259668508	98	0.17132867132867133	86	0.11345646437994723	g	14.92	2.680756	0.47886	0.067181	0.112907	ENSG00000104936	ENST00000458663;ENST00000342805;ENST00000291270;ENST00000447742;ENST00000377750;ENST00000343373;ENST00000348168;ENST00000354227	T;T;T;T;T	0.67865	-0.29;-0.23;-0.26;-0.24;-0.18	3.87	3.87	0.44632	AGC-kinase, C-terminal (1);	0.000000	0.33854	N	0.004494	T	0.00496	0.0016	L	0.55481	1.735	0.09310	P	1.0	B;D;D;D;D;D;D;D	0.76494	0.34;0.998;0.999;0.999;0.996;0.999;0.997;0.999	B;D;D;D;P;D;P;D	0.71414	0.108;0.913;0.973;0.918;0.82;0.94;0.906;0.945	T	0.29518	-1.0009	9	0.13108	T	0.6	.	11.5239	0.50569	0.0:0.0:1.0:0.0	rs527221;rs1042156;rs3170161;rs17423419;rs527221	418;423;449;418;418;423;465;433	Q09013-12;Q09013-16;G5E982;E5KR07;E5KR05;Q09013;Q59FU6;E5KR08	.;.;.;.;.;DMPK_HUMAN;.;.	V	418;449;423;418;418;433;433;418	ENSP00000401753:L418V;ENSP00000291270:L423V;ENSP00000413417:L418V;ENSP00000345997:L433V;ENSP00000346168:L418V	ENSP00000291270:L423V	L	-	1	2	DMPK	50967816	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.365000	0.59486	2.157000	0.67596	0.561000	0.74099	CTG	G|0.900;C|0.100	0.100	strong		0.627	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409	
KRT81	3887	hgsc.bcm.edu	37	12	52681416	52681416	+	Silent	SNP	T	T	C	rs7300801	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:52681416T>C	ENST00000327741.5	-	6	1058	c.990A>G	c.(988-990)caA>caG	p.Q330Q	KRT86_ENST00000423955.2_Intron|KRT86_ENST00000544024.1_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	330	Coil 2.|Rod.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCGTCAGCCTTTGGATCATGC	0.592													.|||	2106	0.420527	0.5688	0.3761	5008	,	,		19889	0.1577		0.5169	False		,,,				2504	0.4233				p.Q330Q		Atlas-SNP	.											.	KRT81	46	.	0			c.A990G						PASS	.	C		2429,1977		770,889,544	94.0	83.0	86.0		990	3.8	1.0	12	dbSNP_116	86	4253,4347		1121,2011,1168	no	coding-synonymous	KRT81	NM_002281.3		1891,2900,1712	CC,CT,TT		49.4535,44.8706,48.6237		330/506	52681416	6682,6324	2203	4300	6503	SO:0001819	synonymous_variant	3887	exon6			CAGCCTTTGGATC	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6458	protein-coding gene	gene with protein product	"""hard keratin type II 1"""	602153	"""keratin, hair, basic, 1"""	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.990A>G	12.37:g.52681416T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	130	57	0.438462	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Silent	SNP	ENST00000327741.5	37	CCDS31805.1																																																																																			T|0.642;C|0.358	0.358	strong		0.592	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281	
ZNF540	163255	hgsc.bcm.edu	37	19	38091932	38091932	+	Missense_Mutation	SNP	A	A	T	rs1975937	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:38091932A>T	ENST00000592533.1	+	4	490	c.158A>T	c.(157-159)gAt>gTt	p.D53V	ZNF540_ENST00000587220.1_3'UTR|ZNF540_ENST00000316433.4_Missense_Mutation_p.D53V|ZNF540_ENST00000343599.5_Missense_Mutation_p.D53V|ZNF540_ENST00000589117.1_Intron|ZNF540_ENST00000586792.1_Intron	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	53	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		D -> V (in dbSNP:rs1975937). {ECO:0000269|PubMed:14702039}.		negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCAAAGCCAGATGTGATTACC	0.423													A|||	1840	0.367412	0.3563	0.2651	5008	,	,		18762	0.6528		0.167	False		,,,				2504	0.3671				p.D53V		Atlas-SNP	.											ZNF540,NS,carcinoma,0,1	ZNF540	75	1	0			c.A158T						PASS	.	A	VAL/ASP,,VAL/ASP	1355,3051		208,939,1056	55.0	47.0	49.0		158,,158	-0.9	0.4	19	dbSNP_92	49	1524,7074		134,1256,2909	yes	missense,intron,missense	ZNF540	NM_001172225.1,NM_001172226.1,NM_152606.3	152,,152	342,2195,3965	TT,TA,AA		17.7251,30.7535,22.1393	possibly-damaging,,possibly-damaging	53/661,,53/661	38091932	2879,10125	2203	4299	6502	SO:0001583	missense	163255	exon4			AGCCAGATGTGAT	AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"""Zinc fingers, C2H2-type"", ""-"""	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.158A>T	19.37:g.38091932A>T	ENSP00000466274:p.Asp53Val	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_152606	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Missense_Mutation	SNP	ENST00000592533.1	37	CCDS12506.1	791	0.36217948717948717	202	0.4105691056910569	92	0.2541436464088398	372	0.6503496503496503	125	0.16490765171503957	A	15.83	2.949743	0.53186	0.307535	0.177251	ENSG00000171817	ENST00000316433	T	0.00976	5.48	1.66	-0.9	0.10544	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	M	0.71871	2.18	0.35010	P	0.24318099999999998	B	0.24721	0.11	B	0.12837	0.008	T	0.14200	-1.0481	8	0.72032	D	0.01	.	2.3341	0.04243	0.4861:0.3053:0.2086:0.0	rs1975937;rs52836732;rs60025228;rs1975937	53	Q8NDQ6	ZN540_HUMAN	V	53	ENSP00000324598:D53V	ENSP00000324598:D53V	D	+	2	0	ZNF540	42783772	0.032000	0.19561	0.357000	0.25798	0.773000	0.43773	0.083000	0.14871	-0.326000	0.08564	0.254000	0.18369	GAT	A|0.726;N|0.000	.	strong		0.423	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606	
STOX1	219736	hgsc.bcm.edu	37	10	70641860	70641860	+	Missense_Mutation	SNP	T	T	C	rs1341667	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70641860T>C	ENST00000298596.6	+	2	540	c.457T>C	c.(457-459)Tac>Cac	p.Y153H	STOX1_ENST00000399165.4_Missense_Mutation_p.Y153H|STOX1_ENST00000399169.4_Missense_Mutation_p.Y153H|STOX1_ENST00000399162.2_Missense_Mutation_p.Y153H|STOX1_ENST00000421961.2_Missense_Mutation_p.Y43H	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	153			Y -> H (in PEE4; dbSNP:rs1341667). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15806103}.			cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						GATGAAACATTACCCAGGTAG	0.353													T|||	3067	0.61242	0.3835	0.6081	5008	,	,		16049	0.9008		0.6412	False		,,,				2504	0.5982				p.Y153H		Atlas-SNP	.											.	STOX1	75	.	0			c.T457C	GRCh37	CM057373	STOX1	M	rs1341667	PASS	.	T	HIS/TYR,HIS/TYR,HIS/TYR,HIS/TYR,HIS/TYR	1532,2148		321,890,629	109.0	98.0	102.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	457,457,457,127,457	4.4	1.0	10	dbSNP_88	102	5240,2926		1685,1870,528	yes	missense,missense,missense,missense,missense	STOX1	NM_001130159.2,NM_001130160.2,NM_001130161.2,NM_001130162.2,NM_152709.4	83,83,83,83,83	2006,2760,1157	CC,CT,TT		35.8315,41.6304,42.833	benign,benign,benign,benign,benign	153/228,153/170,153/990,43/880,153/990	70641860	6772,5074	1840	4083	5923	SO:0001583	missense	219736	exon2			AAACATTACCCAG	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.457T>C	10.37:g.70641860T>C	ENSP00000298596:p.Tyr153His	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	172	170	0.988372	NM_001130160	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	1379	0.6314102564102564	172	0.34959349593495936	199	0.5497237569060773	515	0.9003496503496503	493	0.6503957783641161	T	12.38	1.919961	0.33908	0.416304	0.641685	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000399165;ENST00000399162;ENST00000421961	T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03	5.57	4.44	0.53790	Storkhead-box protein, winged-helix domain (1);	0.076403	0.53938	U	0.000056	T	0.00012	0.0000	L	0.32530	0.975	0.28283	P	0.9238804	P;P;B	0.39759	0.687;0.467;0.339	B;B;B	0.36719	0.135;0.231;0.135	T	0.32025	-0.9922	9	0.29301	T	0.29	.	11.6046	0.51024	0.0:0.07:0.0:0.93	rs1341667;rs58396100;rs1341667	153;153;153	Q6ZVD7-3;Q6ZVD7;Q6ZVD7-2	.;STOX1_HUMAN;.	H	153;153;153;153;43	ENSP00000382121:Y153H;ENSP00000298596:Y153H;ENSP00000382118:Y153H;ENSP00000382115:Y153H;ENSP00000394509:Y43H	ENSP00000298596:Y153H	Y	+	1	0	STOX1	70311866	0.997000	0.39634	0.990000	0.47175	0.981000	0.71138	3.031000	0.49728	1.055000	0.40461	0.482000	0.46254	TAC	T|0.384;C|0.616	0.616	strong		0.353	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
BAIAP3	8938	hgsc.bcm.edu	37	16	1397815	1397815	+	Silent	SNP	C	C	T	rs1132358	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1397815C>T	ENST00000324385.5	+	31	3281	c.3123C>T	c.(3121-3123)gaC>gaT	p.D1041D	BAIAP3_ENST00000421665.2_Silent_p.D970D|BAIAP3_ENST00000568887.1_Silent_p.D978D|BAIAP3_ENST00000426824.3_Silent_p.D1006D|BAIAP3_ENST00000562208.1_Silent_p.D983D|BAIAP3_ENST00000397489.1_Silent_p.D1023D|BAIAP3_ENST00000397488.2_Silent_p.D1023D	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	1041	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				TCCCCCTGGACGCCAACGGTG	0.677													C|||	1691	0.33766	0.1868	0.5879	5008	,	,		12493	0.2222		0.4592	False		,,,				2504	0.3579				p.D1041D		Atlas-SNP	.											BAIAP3,NS,carcinoma,0,1	BAIAP3	88	1	0			c.C3123T						PASS	.	C	,,,,	957,3393		114,729,1332	16.0	20.0	19.0		2910,3018,2949,2934,3123	-6.9	0.9	16	dbSNP_86	19	3804,4722		880,2044,1339	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAIAP3	NM_001199096.1,NM_001199097.1,NM_001199098.1,NM_001199099.1,NM_003933.4	,,,,	994,2773,2671	TT,TC,CC		44.6165,22.0,36.9758	,,,,	970/1117,1006/1153,983/1130,978/1125,1041/1188	1397815	4761,8115	2175	4263	6438	SO:0001819	synonymous_variant	8938	exon31			CCTGGACGCCAAC	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.3123C>T	16.37:g.1397815C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Silent	SNP	ENST00000324385.5	37	CCDS10434.1																																																																																			C|0.656;T|0.344	0.344	strong		0.677	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
BCAR1	9564	hgsc.bcm.edu	37	16	75269534	75269534	+	Silent	SNP	C	C	T	rs3743613	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:75269534C>T	ENST00000162330.5	-	5	1389	c.1263G>A	c.(1261-1263)ccG>ccA	p.P421P	BCAR1_ENST00000542031.2_Silent_p.P419P|BCAR1_ENST00000538440.2_Silent_p.P421P|BCAR1_ENST00000535626.2_Silent_p.P273P|BCAR1_ENST00000420641.3_Silent_p.P439P|BCAR1_ENST00000393422.2_Silent_p.P439P|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000393420.6_Silent_p.P439P|BCAR1_ENST00000418647.3_Silent_p.P467P|BCAR1_ENST00000546196.1_Silent_p.P392P	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	421					actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		TGCCCTCTGCCGGGGCTTCAC	0.687													C|||	2363	0.471845	0.3056	0.3703	5008	,	,		14951	0.8512		0.3171	False		,,,				2504	0.5368				p.P467P		Atlas-SNP	.											.	BCAR1	184	.	0			c.G1401A						PASS	.	C	,,,,,,,,	1323,3071		196,931,1070	20.0	25.0	23.0		1401,1317,1317,1317,1263,1257,819,633,1263	-3.8	0.0	16	dbSNP_107	23	2633,5963		413,1807,2078	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCAR1	NM_001170714.1,NM_001170715.1,NM_001170716.1,NM_001170717.1,NM_001170718.1,NM_001170719.1,NM_001170720.1,NM_001170721.1,NM_014567.3	,,,,,,,,	609,2738,3148	TT,TC,CC		30.6305,30.1092,30.4542	,,,,,,,,	467/917,439/889,439/889,439/889,421/871,419/869,273/723,211/661,421/871	75269534	3956,9034	2197	4298	6495	SO:0001819	synonymous_variant	9564	exon6			CTCTGCCGGGGCT	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.1263G>A	16.37:g.75269534C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Silent	SNP	ENST00000162330.5	37	CCDS10915.1																																																																																			C|0.603;T|0.397	0.397	strong		0.687	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
OR51Q1	390061	hgsc.bcm.edu	37	11	5444136	5444136	+	Nonsense_Mutation	SNP	C	C	T	rs2647574	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5444136C>T	ENST00000300778.4	+	1	796	c.706C>T	c.(706-708)Cga>Tga	p.R236*	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGGGCTGAGCGACTCCGTGC	0.483													C|||	2273	0.453874	0.2799	0.4006	5008	,	,		20965	0.7024		0.3986	False		,,,				2504	0.5276				p.R236X		Atlas-SNP	.											.	OR51Q1	79	.	0			c.C706T						PASS	.	C	stop/ARG	1332,3070	447.3+/-348.3	203,926,1072	135.0	114.0	121.0		706	-10.0	0.0	11	dbSNP_100	121	3372,5222	499.5+/-375.0	676,2020,1601	yes	stop-gained	OR51Q1	NM_001004757.2		879,2946,2673	TT,TC,CC		39.2367,30.259,36.1958		236/318	5444136	4704,8292	2201	4297	6498	SO:0001587	stop_gained	390061	exon1			GCTGAGCGACTCC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.706C>T	11.37:g.5444136C>T	ENSP00000300778:p.Arg236*	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	210	91	0.433333	NM_001004757	B2RNN1	Nonsense_Mutation	SNP	ENST00000300778.4	37	CCDS31381.1	966	0.4423076923076923	139	0.28252032520325204	148	0.4088397790055249	395	0.6905594405594405	284	0.37467018469656993	C	9.017	0.983956	0.18889	0.30259	0.392367	ENSG00000167360	ENST00000300778	.	.	.	5.0	-9.99	0.00435	.	0.244803	0.27388	N	0.019593	.	.	.	.	.	.	0.09310	P	0.99999999896276	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	26.1186	0.99996	0.1626:0.8374:0.0:0.0	rs2647574;rs52806938;rs58830716;rs2647574	.	.	.	X	236	.	ENSP00000300778:R236X	R	+	1	2	OR51Q1	5400712	0.000000	0.05858	0.000000	0.03702	0.120000	0.20174	-6.681000	0.00057	-1.753000	0.01323	-1.378000	0.01179	CGA	C|0.603;T|0.397	0.397	strong		0.483	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052950	33052950	+	Silent	SNP	T	T	C	rs1042331	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33052950T>C	ENST00000418931.2	+	3	704	c.588T>C	c.(586-588)gaT>gaC	p.D196D		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	196	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						AGCAGGGAGATGTCTACACCT	0.567													.|||	2312	0.461661	0.5976	0.3314	5008	,	,		18696	0.6171		0.3151	False		,,,				2504	0.3609				p.D196D		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.T588C						PASS	.	C		1684,1338		458,768,285	96.0	95.0	95.0		588	-5.4	0.0	6	dbSNP_86	95	1605,3813		234,1137,1338	no	coding-synonymous	HLA-DPB1	NM_002121.5		692,1905,1623	CC,CT,TT		29.6235,44.2753,38.9692		196/259	33052950	3289,5151	1511	2709	4220	SO:0001819	synonymous_variant	3115	exon3			GGGAGATGTCTAC		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.588T>C	6.37:g.33052950T>C		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	266	117	0.43985	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Silent	SNP	ENST00000418931.2	37	CCDS4765.1	960	0.43956043956043955	290	0.5894308943089431	110	0.30386740331491713	327	0.5716783216783217	233	0.3073878627968338	C	7.596	0.671728	0.14776	0.557247	0.296235	ENSG00000223865	ENST00000416804	.	.	.	4.04	-5.42	0.02640	.	.	.	.	.	T	0.11922	0.0290	.	.	.	0.26806	P	0.9691072	.	.	.	.	.	.	T	0.17137	-1.0379	3	.	.	.	.	7.1415	0.25558	0.0:0.2951:0.2066:0.4983	rs1042331;rs3173288;rs16868630;rs17845373;rs17858226	.	.	.	T	163	.	.	M	+	2	0	HLA-DPB1	33160928	0.000000	0.05858	0.007000	0.13788	0.925000	0.55904	-3.721000	0.00384	-1.636000	0.01533	-1.096000	0.02151	ATG	T|0.609;C|0.391	0.391	strong		0.567	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
HS3ST1	9957	hgsc.bcm.edu	37	4	11401012	11401012	+	Silent	SNP	A	A	G	rs1047385	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:11401012A>G	ENST00000002596.5	-	2	1792	c.618T>C	c.(616-618)ttT>ttC	p.F206F		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	206					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						GCAGCGGGAAAAAGCGCAGCC	0.602													G|||	1251	0.2498	0.3192	0.1945	5008	,	,		17747	0.1796		0.1978	False		,,,				2504	0.3211				p.F206F		Atlas-SNP	.											.	HS3ST1	41	.	0			c.T618C						PASS	.	G		1288,3118	699.4+/-406.5	196,896,1111	48.0	46.0	47.0		618	3.5	1.0	4	dbSNP_86	47	1817,6783	730.2+/-406.8	188,1441,2671	no	coding-synonymous	HS3ST1	NM_005114.2		384,2337,3782	GG,GA,AA		21.1279,29.2329,23.8736		206/308	11401012	3105,9901	2203	4300	6503	SO:0001819	synonymous_variant	9957	exon2			CGGGAAAAAGCGC	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.618T>C	4.37:g.11401012A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_005114	B3KUA6|Q6PEY8	Silent	SNP	ENST00000002596.5	37	CCDS3408.1																																																																																			G|0.240;N|0.000	0.240	strong		0.602	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114	
BTNL9	153579	hgsc.bcm.edu	37	5	180472513	180472513	+	Silent	SNP	A	A	G	rs6894087	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:180472513A>G	ENST00000327705.9	+	2	255	c.24A>G	c.(22-24)ccA>ccG	p.P8P	BTNL9_ENST00000376842.3_Silent_p.P8P|BTNL9_ENST00000515271.1_Intron|BTNL9_ENST00000376841.2_Silent_p.P8P	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	8						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGTCTCCCCAGACTCCTTGA	0.602													G|||	2530	0.505192	0.6596	0.5245	5008	,	,		17341	0.3919		0.5189	False		,,,				2504	0.3855				p.P8P		Atlas-SNP	.											.	BTNL9	58	.	0			c.A24G						PASS	.	G		2806,1598	496.2+/-363.5	899,1008,295	108.0	93.0	98.0		24	1.9	0.0	5	dbSNP_116	98	4501,4097	561.7+/-387.8	1170,2161,968	no	coding-synonymous	BTNL9	NM_152547.4		2069,3169,1263	GG,GA,AA		47.6506,36.2852,43.801		8/536	180472513	7307,5695	2202	4299	6501	SO:0001819	synonymous_variant	153579	exon2			CTCCCCAGACTCC	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.24A>G	5.37:g.180472513A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_152547	A6NL42|Q6P660|Q96DM5	Silent	SNP	ENST00000327705.9	37	CCDS4460.2																																																																																			A|0.458;G|0.542	0.542	strong		0.602	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547	
TEAD1	7003	hgsc.bcm.edu	37	11	12903443	12903443	+	Splice_Site	SNP	C	C	T	rs2304733	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:12903443C>T	ENST00000526600.1	+	3	448	c.225C>T	c.(223-225)gaC>gaT	p.D75D	TEAD1_ENST00000361905.4_Splice_Site_p.D156D|TEAD1_ENST00000334310.6_Splice_Site_p.D160D|TEAD1_ENST00000527575.1_Splice_Site_p.D171D|TEAD1_ENST00000527636.1_Splice_Site_p.D171D|TEAD1_ENST00000361985.2_Splice_Site_p.D171D			P28347	TEAD1_HUMAN	TEA domain family member 1 (SV40 transcriptional enhancer factor)	171					gene expression (GO:0010467)|hippo signaling (GO:0035329)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)	17				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CTGTTCCCAGCGTCAAGCCTT	0.592													C|||	2172	0.433706	0.2973	0.2925	5008	,	,		20550	0.8393		0.4195	False		,,,				2504	0.3149				p.D171D		Atlas-SNP	.											.	TEAD1	40	.	0			c.C513T						PASS	.	C		1390,3010	457.1+/-351.5	218,954,1028	134.0	119.0	124.0		513	0.2	1.0	11	dbSNP_100	124	3536,5052	514.2+/-378.3	732,2072,1490	yes	coding-synonymous-near-splice	TEAD1	NM_021961.5		950,3026,2518	TT,TC,CC		41.1737,31.5909,37.9273		171/427	12903443	4926,8062	2200	4294	6494	SO:0001630	splice_region_variant	7003	exon8			TCCCAGCGTCAAG	X84839	CCDS7810.1, CCDS7810.2	11p15.4	2008-11-12				ENSG00000187079			11714	protein-coding gene	gene with protein product		189967	"""atrophia areata, peripapillary chorioretinal degeneration"""	TCF13, AA		1851669, 9889009, 15016762	Standard	NM_021961		Approved	TEF-1	uc021qdx.1	P28347		ENST00000526600.1:c.225-1C>T	11.37:g.12903443C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	146	68	0.465753	NM_021961	A4FUP2|E7EV65	Silent	SNP	ENST00000526600.1	37																																																																																				C|0.574;T|0.426	0.426	strong		0.592	TEAD1-007	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000387220.1	NM_021961	Silent
C19orf48	84798	hgsc.bcm.edu	37	19	51301395	51301395	+	Missense_Mutation	SNP	C	C	T	rs4801853	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51301395C>T	ENST00000598463.1	-	5	1409	c.311G>A	c.(310-312)gGg>gAg	p.G104E	C19orf48_ENST00000595794.1_5'Flank|SNORD88A_ENST00000408314.1_RNA|C19orf48_ENST00000345523.4_Missense_Mutation_p.G104E|C19orf48_ENST00000596655.1_Missense_Mutation_p.G104E|C19orf48_ENST00000391812.1_Missense_Mutation_p.G104E|SNORD88B_ENST00000408454.1_RNA			Q6RUI8	CS048_HUMAN	chromosome 19 open reading frame 48	104			G -> E (in dbSNP:rs4801853).							endometrium(1)|kidney(1)|lung(1)|ovary(1)	4		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		CTGCTTCACCCCTGGAGCACC	0.617													c|||	1652	0.329872	0.1309	0.2161	5008	,	,		21442	0.6538		0.3012	False		,,,				2504	0.3753				p.G104E		Atlas-SNP	.											.	C19orf48	11	.	0			c.G311A						PASS	.	T	GLU/GLY,GLU/GLY	680,3726	290.4+/-280.9	45,590,1568	87.0	89.0	88.0		311,311	-2.2	0.0	19	dbSNP_111	88	2413,6187	397.0+/-345.6	350,1713,2237	yes	missense,missense	C19orf48	NM_199249.1,NM_199250.1	98,98	395,2303,3805	TT,TC,CC		28.0581,15.4335,23.7813	probably-damaging,probably-damaging	104/118,104/118	51301395	3093,9913	2203	4300	6503	SO:0001583	missense	84798	exon5			TTCACCCCTGGAG	BC037227	CCDS12803.1	19q13.33	2012-10-26			ENSG00000167747	ENSG00000167747			29667	protein-coding gene	gene with protein product	"""multidrug resistance-related protein"""					12452007	Standard	NM_001290154		Approved	MGC13170	uc002ptg.3	Q6RUI8		ENST00000598463.1:c.311G>A	19.37:g.51301395C>T	ENSP00000471463:p.Gly104Glu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_199249		Missense_Mutation	SNP	ENST00000598463.1	37	CCDS12803.1	769	0.35210622710622713	71	0.1443089430894309	80	0.22099447513812154	383	0.6695804195804196	235	0.3100263852242744	c	3.466	-0.108946	0.06924	0.154335	0.280581	ENSG00000167747	ENST00000391812;ENST00000345523	T;T	0.35048	1.33;1.33	1.67	-2.21	0.06973	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.55172	0.97	B	0.41332	0.354	T	0.41645	-0.9497	8	0.87932	D	0	.	2.7674	0.05324	0.0:0.4002:0.2503:0.3495	rs4801853;rs17657787;rs58154692;rs4801853	104	Q6RUI8	CS048_HUMAN	E	104	ENSP00000375688:G104E;ENSP00000301419:G104E	ENSP00000301419:G104E	G	-	2	0	C19orf48	55993207	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.508000	0.06344	-0.483000	0.06772	-0.215000	0.12644	GGG	C|0.714;N|0.001	.	strong		0.617	C19orf48-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464107.1	NM_032712	
SMR3A	26952	hgsc.bcm.edu	37	4	71227877	71227877	+	Silent	SNP	G	G	A	rs62322478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:71227877G>A	ENST00000226460.4	+	2	141	c.45G>A	c.(43-45)gcG>gcA	p.A15A		NM_012390.3	NP_036522.3	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3A	15						extracellular region (GO:0005576)		p.A15A(1)		endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)	15		all_hematologic(202;0.196)				CTCTTGCAGCGTGTTTCACAG	0.353													G|||	642	0.128195	0.3321	0.0807	5008	,	,		18065	0.0		0.1143	False		,,,				2504	0.0327				p.A15A		Atlas-SNP	.											SMR3A,NS,carcinoma,0,1	SMR3A	35	1	1	Substitution - coding silent(1)	ovary(1)	c.G45A						PASS	.	G		1339,3067	428.5+/-341.9	175,989,1039	210.0	188.0	196.0		45	-5.1	0.0	4	dbSNP_129	196	913,7687	201.0+/-244.6	37,839,3424	no	coding-synonymous	SMR3A	NM_012390.3		212,1828,4463	AA,AG,GG		10.6163,30.3904,17.3151		15/135	71227877	2252,10754	2203	4300	6503	SO:0001819	synonymous_variant	26952	exon2			TGCAGCGTGTTTC	D89501	CCDS34000.1	4q13.3	2009-04-17	2008-02-27	2005-02-07	ENSG00000109208	ENSG00000109208			19216	protein-coding gene	gene with protein product			"""proline rich 5 (salivary)"", ""submaxillary gland androgen regulated protein 3 homolog A (mouse)"""	PROL5		9354371, 17512016	Standard	NM_012390		Approved	PBI, PRL5	uc003hfg.1	Q99954	OTTHUMG00000160839	ENST00000226460.4:c.45G>A	4.37:g.71227877G>A		Somatic	610	0	0		WXS	Illumina HiSeq	Phase_I	616	201	0.326299	NM_012390		Silent	SNP	ENST00000226460.4	37	CCDS34000.1																																																																																			G|0.881;A|0.119	0.119	strong		0.353	SMR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362574.1	NM_012390	
B3GNTL1	146712	hgsc.bcm.edu	37	17	81006629	81006629	+	Silent	SNP	C	C	T	rs7406119	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:81006629C>T	ENST00000320865.3	-	2	106	c.93G>A	c.(91-93)ccG>ccA	p.P31P	B3GNTL1_ENST00000576599.1_De_novo_Start_OutOfFrame|B3GNTL1_ENST00000571954.1_5'UTR	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	31							transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			CGTCCAGCCACGGTTCAGCGT	0.423													C|||	968	0.193291	0.2194	0.1628	5008	,	,		21632	0.2073		0.2177	False		,,,				2504	0.1401				p.P31P		Atlas-SNP	.											.	B3GNTL1	40	.	0			c.G93A						PASS	.	C		881,3525	343.8+/-307.8	90,701,1412	91.0	91.0	91.0		93	-8.3	0.0	17	dbSNP_116	91	2081,6519	359.5+/-331.6	256,1569,2475	no	coding-synonymous	B3GNTL1	NM_001009905.1		346,2270,3887	TT,TC,CC		24.1977,19.9955,22.7741		31/362	81006629	2962,10044	2203	4300	6503	SO:0001819	synonymous_variant	146712	exon2			CAGCCACGGTTCA	AY634364	CCDS32778.1	17q25.3	2013-02-22	2004-01-13	2004-01-14	ENSG00000175711	ENSG00000175711		"""Glycosyltransferase family 2 domain containing"""	21727	protein-coding gene	gene with protein product		615337					Standard	NM_001009905		Approved	B3GNT8	uc002kgg.1	Q67FW5	OTTHUMG00000177788	ENST00000320865.3:c.93G>A	17.37:g.81006629C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	216	112	0.518519	NM_001009905	Q6GV30|Q8WUT3	Silent	SNP	ENST00000320865.3	37	CCDS32778.1																																																																																			C|0.782;T|0.218	0.218	strong		0.423	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905	
GSN	2934	hgsc.bcm.edu	37	9	124088908	124088908	+	Missense_Mutation	SNP	C	C	G	rs77681311	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:124088908C>G	ENST00000373818.4	+	12	1757	c.1688C>G	c.(1687-1689)aCc>aGc	p.T563S	GSN_ENST00000373808.2_Missense_Mutation_p.T512S|GSN_ENST00000373807.1_Missense_Mutation_p.T294S|GSN_ENST00000412819.1_Missense_Mutation_p.T512S|GSN_ENST00000436847.1_Missense_Mutation_p.T523S|GSN_ENST00000341272.2_Missense_Mutation_p.T512S|GSN_ENST00000545652.1_Missense_Mutation_p.T520S|GSN_ENST00000394353.2_Missense_Mutation_p.T523S|GSN_ENST00000373806.1_5'UTR|GSN_ENST00000373823.3_Missense_Mutation_p.T512S|GSN_ENST00000449733.1_Missense_Mutation_p.T512S	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	563	Actin-binding, Ca-sensitive. {ECO:0000255}.				actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						CCTGCCAGCACCCGCCTCTTC	0.642													C|||	119	0.023762	0.0265	0.0202	5008	,	,		17479	0.0		0.0308	False		,,,				2504	0.0399				p.T563S		Atlas-SNP	.											.	GSN	81	.	0			c.C1688G						PASS	.	C	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	141,4261		3,135,2063	17.0	18.0	18.0		1688,1535,1535,1535,1535,1568,1568,1535	4.2	1.0	9	dbSNP_131	18	270,8320		5,260,4030	no	missense,missense,missense,missense,missense,missense,missense,missense	GSN	NM_000177.4,NM_001127662.1,NM_001127663.1,NM_001127664.1,NM_001127665.1,NM_001127666.1,NM_001127667.1,NM_198252.2	58,58,58,58,58,58,58,58	8,395,6093	GG,GC,CC		3.1432,3.2031,3.1635	benign,benign,benign,benign,benign,benign,benign,benign	563/783,512/732,512/732,512/732,512/732,523/743,523/743,512/732	124088908	411,12581	2201	4295	6496	SO:0001583	missense	2934	exon12			CCAGCACCCGCCT	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"""amyloidosis, Finnish type"""	137350	"""gelsolin (amyloidosis, Finnish type)"""			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.1688C>G	9.37:g.124088908C>G	ENSP00000362924:p.Thr563Ser	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_000177	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Missense_Mutation	SNP	ENST00000373818.4	37	CCDS6828.1	45	0.020604395604395604	12	0.024390243902439025	7	0.019337016574585635	0	0.0	26	0.03430079155672823	C	16.12	3.032917	0.54790	0.032031	0.031432	ENSG00000148180	ENST00000373823;ENST00000436847;ENST00000394353;ENST00000449733;ENST00000412819;ENST00000341272;ENST00000373808;ENST00000394352;ENST00000456109;ENST00000545652;ENST00000373818;ENST00000373807	T;T;T;T;T;T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89	5.13	4.22	0.49857	.	0.154614	0.64402	D	0.000019	T	0.14184	0.0343	M	0.86953	2.85	0.42695	D	0.993598	B;P;B;B;B	0.34826	0.42;0.471;0.043;0.009;0.087	B;B;B;B;B	0.36534	0.227;0.149;0.069;0.021;0.086	T	0.04427	-1.0952	10	0.40728	T	0.16	-23.1495	9.5322	0.39200	0.0:0.8376:0.0:0.1624	.	536;520;523;294;563	B7Z9A0;F5H1A8;B7Z373;Q5T0H9;P06396	.;.;.;.;GELS_HUMAN	S	512;523;523;512;512;512;512;496;486;520;563;294	ENSP00000362929:T512S;ENSP00000411293:T523S;ENSP00000377882:T523S;ENSP00000409358:T512S;ENSP00000416586:T512S;ENSP00000340888:T512S;ENSP00000362914:T512S;ENSP00000445823:T520S;ENSP00000362924:T563S;ENSP00000362913:T294S	ENSP00000340888:T512S	T	+	2	0	GSN	123128729	0.990000	0.36364	0.970000	0.41538	0.966000	0.64601	2.987000	0.49378	1.119000	0.41883	0.655000	0.94253	ACC	C|0.969;G|0.031	0.031	strong		0.642	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177	
APBA3	9546	hgsc.bcm.edu	37	19	3754020	3754020	+	Silent	SNP	G	G	C	rs61731066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:3754020G>C	ENST00000316757.3	-	5	1046	c.846C>G	c.(844-846)tcC>tcG	p.S282S	AC005954.3_ENST00000591962.1_RNA|AC005954.4_ENST00000586503.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	282	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCGTACCTGGGAGTCCGCTG	0.706													G|||	86	0.0171725	0.0091	0.036	5008	,	,		12207	0.0		0.0308	False		,,,				2504	0.0184				p.S282S		Atlas-SNP	.											.	APBA3	28	.	0			c.C846G						PASS	.	G		41,4365	35.2+/-66.4	0,41,2162	27.0	25.0	26.0		846	1.7	1.0	19	dbSNP_129	26	286,8314	97.2+/-158.9	4,278,4018	no	coding-synonymous	APBA3	NM_004886.3		4,319,6180	CC,CG,GG		3.3256,0.9305,2.5142		282/576	3754020	327,12679	2203	4300	6503	SO:0001819	synonymous_variant	9546	exon5			TACCTGGGAGTCC	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.846C>G	19.37:g.3754020G>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			G|0.968;C|0.032	0.032	strong		0.706	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
NFASC	23114	hgsc.bcm.edu	37	1	204951138	204951138	+	Silent	SNP	C	C	T	rs61741829	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:204951138C>T	ENST00000401399.1	+	20	2659	c.2460C>T	c.(2458-2460)tcC>tcT	p.S820S	NFASC_ENST00000338586.6_Silent_p.S820S|NFASC_ENST00000539706.1_Silent_p.S816S|NFASC_ENST00000367169.4_Silent_p.S820S|NFASC_ENST00000367170.4_Silent_p.S820S|NFASC_ENST00000404076.1_Silent_p.S799S|NFASC_ENST00000513543.1_Silent_p.S816S|NFASC_ENST00000367171.4_Silent_p.S805S|NFASC_ENST00000367172.4_Silent_p.S820S|NFASC_ENST00000360049.4_Silent_p.S816S|NFASC_ENST00000404907.1_Silent_p.S816S|NFASC_ENST00000338515.6_Silent_p.S820S|NFASC_ENST00000339876.6_Silent_p.S820S			O94856	NFASC_HUMAN	neurofascin	820	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TCGGTTACTCCGGAGAAGATT	0.612													C|||	75	0.014976	0.0008	0.0259	5008	,	,		17738	0.0		0.0159	False		,,,				2504	0.0409				p.S831S		Atlas-SNP	.											.	NFASC	396	.	0			c.C2493T						PASS	.	C	,,,	20,4386	25.3+/-52.1	0,20,2183	49.0	47.0	48.0		2460,2493,2448,2448	-10.2	0.7	1	dbSNP_129	48	282,8318	102.9+/-164.1	3,276,4021	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFASC	NM_001005388.2,NM_001160331.1,NM_001160332.1,NM_015090.3	,,,	3,296,6204	TT,TC,CC		3.2791,0.4539,2.322	,,,	820/1241,831/1190,816/1175,816/1170	204951138	302,12704	2203	4300	6503	SO:0001819	synonymous_variant	23114	exon19			TTACTCCGGAGAA	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.2460C>T	1.37:g.204951138C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_001160331	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	19	0.0086996336996337	0	0.0	8	0.022099447513812154	0	0.0	11	0.014511873350923483	C	9.292	1.050979	0.19827	0.004539	0.032791	ENSG00000163531	ENST00000367173;ENST00000425360	.	.	.	5.55	-10.2	0.00374	.	.	.	.	.	T	0.12433	0.0302	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38972	-0.9636	4	.	.	.	.	1.3537	0.02178	0.1796:0.1563:0.2987:0.3654	rs61741829	.	.	.	L	790;52	.	.	P	+	2	0	NFASC	203217761	0.000000	0.05858	0.717000	0.30585	0.914000	0.54420	-6.623000	0.00059	-1.512000	0.01791	0.563000	0.77884	CCG	C|0.985;T|0.015	0.015	strong		0.612	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
CEBPZ	10153	hgsc.bcm.edu	37	2	37438993	37438993	+	Silent	SNP	G	G	A	rs1137437	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:37438993G>A	ENST00000234170.5	-	12	2938	c.2793C>T	c.(2791-2793)agC>agT	p.S931S	RP11-423P10.2_ENST00000606229.1_RNA|AC007390.5_ENST00000397064.2_Intron	NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	931					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				TACCTGGAACGCTCTCACTTT	0.353													G|||	1600	0.319489	0.2579	0.3674	5008	,	,		20249	0.3462		0.4264	False		,,,				2504	0.2311				p.S931S		Atlas-SNP	.											.	CEBPZ	68	.	0			c.C2793T						PASS	.	G		1242,3162	426.6+/-341.2	165,912,1125	124.0	109.0	114.0		2793	-0.0	0.0	2	dbSNP_86	114	3454,5144	506.3+/-376.6	708,2038,1553	no	coding-synonymous	CEBPZ	NM_005760.2		873,2950,2678	AA,AG,GG		40.1721,28.2016,36.1175		931/1055	37438993	4696,8306	2202	4299	6501	SO:0001819	synonymous_variant	10153	exon12			TGGAACGCTCTCA	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.2793C>T	2.37:g.37438993G>A		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	199	198	0.994975	NM_005760	Q8NE75	Silent	SNP	ENST00000234170.5	37	CCDS1787.1																																																																																			G|0.635;A|0.365	0.365	strong		0.353	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760	
RBMXL1	494115	hgsc.bcm.edu	37	1	89448608	89448608	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89448608G>A	ENST00000321792.5	-	2	1329	c.902C>T	c.(901-903)cCg>cTg	p.P301L	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.P301L|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000413769.1_5'Flank|CCBL2_ENST00000370491.3_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	301	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										ATAAGATGGCGGGGGCCCTCG	0.483																																					p.P301L		Atlas-SNP	.											CCBL2,caecum,carcinoma,+1,1	.	.	1	0			c.C902T						scavenged	.						172.0	172.0	172.0					1																	89448608		2203	4300	6503	SO:0001583	missense	494115	exon3			GATGGCGGGGGCC	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.902C>T	1.37:g.89448608G>A	ENSP00000318415:p.Pro301Leu	Somatic	182	6	0.032967		WXS	Illumina HiSeq	Phase_I	242	19	0.0785124	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.022446	0.35701	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.78126	-1.15;-1.15	1.41	0.0579	0.14325	.	0.060058	0.64402	D	0.000002	T	0.52629	0.1746	M	0.66939	2.045	0.46725	D	0.999174	B	0.34255	0.445	B	0.20577	0.03	T	0.56341	-0.7995	10	0.52906	T	0.07	-2.8526	6.2127	0.20638	0.0:0.0:0.7093:0.2907	.	301	Q96E39	RBMXL_HUMAN	L	301	ENSP00000318415:P301L;ENSP00000446099:P301L	ENSP00000318415:P301L	P	-	2	0	RBMXL1	89221196	1.000000	0.71417	0.993000	0.49108	0.967000	0.64934	6.229000	0.72294	0.760000	0.33108	0.306000	0.20318	CCG	.	.	none		0.483	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
C3orf35	339883	hgsc.bcm.edu	37	3	37458758	37458758	+	Start_Codon_SNP	SNP	A	A	C	rs113724034	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:37458758A>C	ENST00000328376.5	+	5	980	c.1A>C	c.(1-3)Atg>Ctg	p.M1L	C3orf35_ENST00000425932.1_Start_Codon_SNP_p.M1L|C3orf35_ENST00000481400.1_Intron|C3orf35_ENST00000452017.2_Start_Codon_SNP_p.M1L|C3orf35_ENST00000425564.2_Start_Codon_SNP_p.M1L|C3orf35_ENST00000426078.1_Start_Codon_SNP_p.M1L	NM_178339.2	NP_848029.2	Q8IVJ8	APRG1_HUMAN	chromosome 3 open reading frame 35	1						integral component of membrane (GO:0016021)		p.M1L(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	11						CTGAATCCACATGAAAACAAT	0.358													A|||	59	0.0117812	0.0008	0.0202	5008	,	,		20657	0.0		0.0318	False		,,,				2504	0.0123				p.M1L		Atlas-SNP	.											C3orf35,NS,carcinoma,0,1	C3orf35	21	1	1	Substitution - Missense(1)	pancreas(1)	c.A1C						PASS	.	A	LEU/MET,LEU/MET	30,3622		0,30,1796	65.0	63.0	63.0		1,1	2.8	0.6	3	dbSNP_132	63	360,7792		7,346,3723	yes	missense,missense	C3orf35	NM_178339.2,NM_178342.2	15,15	7,376,5519	CC,CA,AA		4.4161,0.8215,3.304	benign,benign	1/171,1/120	37458758	390,11414	1826	4076	5902	SO:0001582	initiator_codon_variant	339883	exon5			ATCCACATGAAAA	AJ493599	CCDS43065.1, CCDS46792.1	3p22.3	2014-05-22			ENSG00000198590	ENSG00000198590			24082	protein-coding gene	gene with protein product	"""AP20 region protein"", ""APRG1 tumor suppressor candidate"""	611429				12543795	Standard	NM_178342		Approved	APRG1	uc003cha.4	Q8IVJ8	OTTHUMG00000155923	ENST00000328376.5:c.1A>C	3.37:g.37458758A>C	ENSP00000331625:p.Met1Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_178342	B7ZMA0|Q8IVJ5|Q8IVJ9	Missense_Mutation	SNP	ENST00000328376.5	37	CCDS43065.1	31	0.014194139194139194	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	22	0.029023746701846966	A	6.436	0.448663	0.12223	0.008215	0.044161	ENSG00000198590	ENST00000425932;ENST00000328376;ENST00000452017;ENST00000426078;ENST00000425564	T	0.44083	0.93	4.04	2.84	0.33178	.	.	.	.	.	T	0.08891	0.0220	.	.	.	0.09310	N	0.999999	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.002	T	0.13818	-1.0495	8	0.87932	D	0	.	7.5	0.27511	0.7799:0.2201:0.0:0.0	.	1;1	Q8IVJ8-3;Q8IVJ8	.;APRG1_HUMAN	L	1	ENSP00000331625:M1L	ENSP00000331625:M1L	M	+	1	0	C3orf35	37433762	0.509000	0.26163	0.625000	0.29200	0.611000	0.37282	0.529000	0.23019	0.861000	0.35504	0.460000	0.39030	ATG	A|0.976;C|0.024	0.024	strong		0.358	C3orf35-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342344.2	NM_178338	Missense_Mutation
SCYL2	55681	hgsc.bcm.edu	37	12	100709420	100709420	+	Silent	SNP	C	C	T	rs10860577	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:100709420C>T	ENST00000360820.2	+	9	1617	c.1180C>T	c.(1180-1182)Cta>Tta	p.L394L		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	394					endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						GCCCAATGTTCTACTTATTGC	0.398													C|||	553	0.110423	0.1263	0.1239	5008	,	,		15891	0.003		0.1998	False		,,,				2504	0.0982				p.L394L		Atlas-SNP	.											SCYL2,colon,carcinoma,-1,1	SCYL2	99	1	0			c.C1180T						PASS	.	C		536,3870	242.1+/-252.3	39,458,1706	110.0	102.0	105.0		1180	2.4	1.0	12	dbSNP_120	105	1541,7059	289.8+/-299.5	135,1271,2894	no	coding-synonymous	SCYL2	NM_017988.4		174,1729,4600	TT,TC,CC		17.9186,12.1652,15.9696		394/930	100709420	2077,10929	2203	4300	6503	SO:0001819	synonymous_variant	55681	exon9			AATGTTCTACTTA	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.1180C>T	12.37:g.100709420C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	174	87	0.5	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Silent	SNP	ENST00000360820.2	37	CCDS9076.1																																																																																			C|0.853;T|0.147	0.147	strong		0.398	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988	
GPR111	222611	hgsc.bcm.edu	37	6	47654742	47654742	+	Silent	SNP	A	A	T	rs9296573	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:47654742A>T	ENST00000398742.2	+	6	1927	c.1878A>T	c.(1876-1878)ctA>ctT	p.L626L	GPR115_ENST00000371220.1_Intron			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	0					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						TCTTCATCCTAGTGTTTGGAA	0.368													A|||	2590	0.517173	0.4637	0.4337	5008	,	,		18601	0.3085		0.6262	False		,,,				2504	0.7515				p.L626L		Atlas-SNP	.											.	GPR111	123	.	0			c.A1878T						PASS	.	A		1711,1961		390,931,515	233.0	210.0	217.0		1878	3.1	1.0	6	dbSNP_119	217	5276,2888		1714,1848,520	no	coding-synonymous	GPR111	NM_153839.6		2104,2779,1035	TT,TA,AA		35.3748,46.5959,40.9682		626/643	47654742	6987,4849	1836	4082	5918	SO:0001819	synonymous_variant	222611	exon8			CATCCTAGTGTTT	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000398742.2:c.1878A>T	6.37:g.47654742A>T		Somatic	381	1	0.00262467		WXS	Illumina HiSeq	Phase_I	375	188	0.501333	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Silent	SNP	ENST00000398742.2	37																																																																																				A|0.464;T|0.536	0.536	strong		0.368	GPR111-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153839	
ZCCHC14	23174	hgsc.bcm.edu	37	16	87445363	87445363	+	Silent	SNP	G	G	A	rs1050846	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:87445363G>A	ENST00000268616.4	-	12	2770	c.2553C>T	c.(2551-2553)caC>caT	p.H851H		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	851							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		TGTAAGGGGCGTGCACGACGG	0.657													G|||	738	0.147364	0.0545	0.2161	5008	,	,		12294	0.002		0.4453	False		,,,				2504	0.0675				p.H851H		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.C2553T						PASS	.	G		528,3868	229.1+/-243.8	24,480,1694	35.0	32.0	33.0		2553	-0.1	0.2	16	dbSNP_86	33	3787,4813	522.4+/-380.1	828,2131,1341	no	coding-synonymous	ZCCHC14	NM_015144.2		852,2611,3035	AA,AG,GG		44.0349,12.0109,33.2025		851/950	87445363	4315,8681	2198	4300	6498	SO:0001819	synonymous_variant	23174	exon12			AGGGGCGTGCACG	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2553C>T	16.37:g.87445363G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Silent	SNP	ENST00000268616.4	37	CCDS10961.1																																																																																			G|0.719;A|0.281	0.281	strong		0.657	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
CSPG4	1464	hgsc.bcm.edu	37	15	75980112	75980112	+	Silent	SNP	A	A	G	rs4414463	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75980112A>G	ENST00000308508.5	-	3	3386	c.3294T>C	c.(3292-3294)gcT>gcC	p.A1098A		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1098	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						AGCCACGGTCAGCCCCTGAGT	0.647													G|||	2210	0.441294	0.4024	0.5548	5008	,	,		19871	0.3145		0.5229	False		,,,				2504	0.4601				p.A1098A		Atlas-SNP	.											.	CSPG4	175	.	0			c.T3294C						PASS	.	G		1868,2526		388,1092,717	62.0	60.0	61.0		3294	-7.1	0.5	15	dbSNP_111	61	4735,3849		1329,2077,886	no	coding-synonymous	CSPG4	NM_001897.4		1717,3169,1603	GG,GA,AA		44.8392,42.5125,49.1216		1098/2323	75980112	6603,6375	2197	4292	6489	SO:0001819	synonymous_variant	1464	exon3			ACGGTCAGCCCCT	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.3294T>C	15.37:g.75980112A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	193	191	0.989637	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			A|0.524;G|0.476	0.476	strong		0.647	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
LILRB2	10288	hgsc.bcm.edu	37	19	54780769	54780769	+	Missense_Mutation	SNP	G	G	C	rs139961541		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54780769G>C	ENST00000391749.4	-	10	1646	c.1375C>G	c.(1375-1377)Ctg>Gtg	p.L459V	LILRB2_ENST00000314446.5_Missense_Mutation_p.L458V|LILRB2_ENST00000391746.1_Missense_Mutation_p.L459V|LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000391748.1_Missense_Mutation_p.L458V|LILRB2_ENST00000434421.1_Missense_Mutation_p.L343V	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	459					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)	p.L459V(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACAACCCCCAGGTGCCTTCCC	0.572																																					p.L459V		Atlas-SNP	.											LILRB2,right_upper_lobe,carcinoma,+2,1	LILRB2	94	1	1	Substitution - Missense(1)	lung(1)	c.C1375G						scavenged	.						160.0	108.0	126.0					19																	54780769		2203	4300	6503	SO:0001583	missense	10288	exon10			CCCCCAGGTGCCT	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.1375C>G	19.37:g.54780769G>C	ENSP00000375629:p.Leu459Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	120	17	0.141667	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	.	.	.	.	.	.	.	.	.	.	G	5.506	0.278355	0.10403	.	.	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00507	7.04;7.04;7.05;6.92;6.95	1.5	1.5	0.22942	.	23.978700	0.00481	U	0.000134	T	0.00524	0.0017	L	0.43757	1.38	0.09310	N	1	B;B;B	0.21606	0.058;0.01;0.004	B;B;B	0.19391	0.025;0.014;0.004	T	0.48536	-0.9027	10	0.34782	T	0.22	.	6.574	0.22555	0.0:0.0:1.0:0.0	.	459;475;459	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	V	458;458;459;459;343	ENSP00000375628:L458V;ENSP00000319960:L458V;ENSP00000375629:L459V;ENSP00000375626:L459V;ENSP00000410117:L343V	ENSP00000319960:L458V	L	-	1	2	LILRB2	59472581	0.038000	0.19896	0.026000	0.17262	0.110000	0.19582	1.230000	0.32612	1.185000	0.42971	0.297000	0.19635	CTG	G|0.919;C|0.081	0.081	strong		0.572	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
LILRB4	11006	hgsc.bcm.edu	37	19	55174498	55174498	+	Missense_Mutation	SNP	T	T	C	rs28366008	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55174498T>C	ENST00000391736.1	+	3	328	c.13T>C	c.(13-15)Ttc>Ctc	p.F5L	LILRB4_ENST00000430952.2_Missense_Mutation_p.F5L|LILRB4_ENST00000391734.3_Missense_Mutation_p.F5L|LILRB4_ENST00000391733.3_Missense_Mutation_p.F5L|LILRB4_ENST00000270452.2_Missense_Mutation_p.F5L	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	5			F -> L (in dbSNP:rs28366008). {ECO:0000269|PubMed:10941837}.		immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)	p.F5L(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		GATCCCCACCTTCACGGCTCT	0.602											OREG0003670	type=REGULATORY REGION|Gene=LILRB4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	1525	0.304513	0.4955	0.2334	5008	,	,		14806	0.2331		0.2386	False		,,,				2504	0.2382				p.F5L		Atlas-SNP	.											LILRB4,NS,carcinoma,0,1	LILRB4	86	1	1	Substitution - Missense(1)	stomach(1)	c.T13C						PASS	.	C	LEU/PHE,LEU/PHE	1861,2545	627.9+/-395.0	392,1077,734	52.0	55.0	54.0		13,13	0.5	0.0	19	dbSNP_125	54	2156,6444	711.8+/-405.9	282,1592,2426	yes	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	22,22	674,2669,3160	CC,CT,TT		25.0698,42.2379,30.8857	benign,benign	5/448,5/449	55174498	4017,8989	2203	4300	6503	SO:0001583	missense	11006	exon1			CCCACCTTCACGG	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.13T>C	19.37:g.55174498T>C	ENSP00000375616:p.Phe5Leu	Somatic	47	0	0	1005	WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	641	0.2934981684981685	244	0.4959349593495935	84	0.23204419889502761	127	0.22202797202797203	186	0.24538258575197888	C	0.070	-1.203873	0.01581	0.422379	0.250698	ENSG00000186818	ENST00000420271;ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00438	7.44;7.44;7.44;7.43;7.46;7.42	2.87	0.476	0.16779	.	.	.	.	.	T	0.00012	0.0000	N	0.00029	-2.625	0.80722	P	0.0	B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B	0.06405	0.002;0.001;0.001;0.001;0.0;0.0	T	0.34675	-0.9819	8	0.02654	T	1	.	3.4403	0.07461	0.0:0.5078:0.2147:0.2775	rs28366008;rs36220281	5;5;5;5;5;46	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6;C9JHA6	.;.;.;.;LIRB4_HUMAN;.	L	46;5;5;5;5;5;5	ENSP00000375616:F5L;ENSP00000270452:F5L;ENSP00000408995:F5L;ENSP00000375614:F5L;ENSP00000375613:F5L;ENSP00000401962:F5L	ENSP00000270452:F5L	F	+	1	0	LILRB4	59866310	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	-0.282000	0.08445	-0.466000	0.06943	-0.479000	0.04858	TTC	T|0.700;C|0.300	0.300	strong		0.602	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
COG1	9382	hgsc.bcm.edu	37	17	71197323	71197323	+	Missense_Mutation	SNP	G	G	C	rs62621249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:71197323G>C	ENST00000299886.4	+	7	1437	c.1357G>C	c.(1357-1359)Gaa>Caa	p.E453Q		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	453					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			GCAGGAACTTGAAAGCAGCAC	0.468													G|||	252	0.0503195	0.0295	0.0663	5008	,	,		21462	0.0		0.0885	False		,,,				2504	0.0798				p.E453Q		Atlas-SNP	.											.	COG1	46	.	0			c.G1357C						PASS	.	G	GLN/GLU	153,4253	106.9+/-145.3	2,149,2052	121.0	117.0	118.0		1357	5.3	0.1	17	dbSNP_129	118	726,7874	176.5+/-226.3	38,650,3612	yes	missense	COG1	NM_018714.2	29	40,799,5664	CC,CG,GG		8.4419,3.4725,6.7584	possibly-damaging	453/981	71197323	879,12127	2203	4300	6503	SO:0001583	missense	9382	exon7			GAACTTGAAAGCA		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1357G>C	17.37:g.71197323G>C	ENSP00000299886:p.Glu453Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	118	71	0.601695	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	37	CCDS11692.1	121	0.0554029304029304	19	0.03861788617886179	33	0.09116022099447514	0	0.0	69	0.09102902374670185	G	10.37	1.331855	0.24167	0.034725	0.084419	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.24151	1.87;1.88	5.28	5.28	0.74379	.	0.098849	0.64402	D	0.000002	T	0.00998	0.0033	M	0.61703	1.905	0.09310	P	0.99999866012	P;P;P	0.44478	0.836;0.539;0.836	B;B;B	0.37267	0.245;0.135;0.245	T	0.12218	-1.0556	9	0.17369	T	0.5	-22.1809	19.2788	0.94042	0.0:0.0:1.0:0.0	rs62621249	453;453;453	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	Q	453	ENSP00000400111:E453Q;ENSP00000299886:E453Q	ENSP00000299886:E453Q	E	+	1	0	COG1	68708918	1.000000	0.71417	0.066000	0.19879	0.655000	0.38815	4.140000	0.58031	2.624000	0.88883	0.655000	0.94253	GAA	G|0.935;C|0.065	0.065	strong		0.468	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
ABCA4	24	hgsc.bcm.edu	37	1	94564483	94564483	+	Missense_Mutation	SNP	C	C	T	rs6657239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:94564483C>T	ENST00000370225.3	-	6	721	c.635G>A	c.(634-636)cGc>cAc	p.R212H	ABCA4_ENST00000535735.1_Missense_Mutation_p.R212H	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	212			R -> C (in STGD1 and CORD3; common mutation in southern Europe; reduced ATP- binding capacity). {ECO:0000269|PubMed:10711710, ECO:0000269|PubMed:10958761, ECO:0000269|PubMed:10958763, ECO:0000269|PubMed:11385708, ECO:0000269|PubMed:18977788, ECO:0000269|PubMed:9503029, ECO:0000269|PubMed:9781034}.|R -> H (in dbSNP:rs6657239). {ECO:0000269|PubMed:10711710, ECO:0000269|PubMed:10958763, ECO:0000269|PubMed:11379881, ECO:0000269|PubMed:11384574, ECO:0000269|PubMed:11527935}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GATGATGAAGCGCTCCAGGAG	0.602													C|||	267	0.0533147	0.0832	0.0375	5008	,	,		18327	0.0595		0.0517	False		,,,				2504	0.0194				p.R212H		Atlas-SNP	.											.	ABCA4	275	.	0			c.G635A	GRCh37	CM020912	ABCA4	M	rs6657239	PASS	.	C	HIS/ARG	311,4095	168.3+/-199.2	6,299,1898	55.0	53.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	635	4.0	1.0	1	dbSNP_116	54	293,8307	108.2+/-168.9	7,279,4014	no	missense	ABCA4	NM_000350.2	29	13,578,5912	TT,TC,CC		3.407,7.0586,4.644	probably-damaging	212/2274	94564483	604,12402	2203	4300	6503	SO:0001583	missense	24	exon6			ATGAAGCGCTCCA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.635G>A	1.37:g.94564483C>T	ENSP00000359245:p.Arg212His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	92	52	0.565217	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	112	0.05128205128205128	36	0.07317073170731707	11	0.03038674033149171	27	0.0472027972027972	38	0.05013192612137203	C	24.1	4.495284	0.85069	0.070586	0.03407	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.91792	-2.79;-2.91	5.83	3.98	0.46160	.	0.071424	0.56097	D	0.000023	D	0.93828	0.8026	M	0.78049	2.395	0.23215	P	0.99810284	D;D	0.89917	0.972;1.0	P;D	0.72338	0.576;0.977	D	0.94093	0.7355	9	0.66056	D	0.02	.	10.8655	0.46853	0.0:0.8525:0.0:0.1475	rs6657239;rs6657239	212;212	F5H6E5;P78363	.;ABCA4_HUMAN	H	212	ENSP00000359245:R212H;ENSP00000437682:R212H	ENSP00000359245:R212H	R	-	2	0	ABCA4	94337071	1.000000	0.71417	0.995000	0.50966	0.930000	0.56654	3.776000	0.55356	0.823000	0.34589	-0.244000	0.11960	CGC	C|0.954;T|0.046	0.046	strong		0.602	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
FAT2	2196	hgsc.bcm.edu	37	5	150947162	150947162	+	Missense_Mutation	SNP	A	A	G	rs114337863	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150947162A>G	ENST00000261800.5	-	1	1343	c.1331T>C	c.(1330-1332)gTg>gCg	p.V444A		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	444	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTCAATGACCACCACGGTGGA	0.542													A|||	39	0.00778754	0.0	0.0187	5008	,	,		18868	0.0		0.0209	False		,,,				2504	0.0051				p.V444A		Atlas-SNP	.											.	FAT2	465	.	0			c.T1331C						PASS	.	A	ALA/VAL	24,4382	31.7+/-61.6	0,24,2179	138.0	134.0	135.0		1331	5.7	0.1	5	dbSNP_132	135	222,8378	91.9+/-153.9	5,212,4083	yes	missense	FAT2	NM_001447.2	64	5,236,6262	GG,GA,AA		2.5814,0.5447,1.8914	probably-damaging	444/4350	150947162	246,12760	2203	4300	6503	SO:0001583	missense	2196	exon1			ATGACCACCACGG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.1331T>C	5.37:g.150947162A>G	ENSP00000261800:p.Val444Ala	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	213	90	0.422535	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	23	0.010531135531135532	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	15	0.01978891820580475	A	15.30	2.791763	0.50102	0.005447	0.025814	ENSG00000086570	ENST00000261800	T	0.69435	-0.4	5.72	5.72	0.89469	Cadherin (3);Cadherin-like (1);	0.000000	0.56097	D	0.000024	T	0.62171	0.2406	M	0.82132	2.575	0.58432	D	0.999999	D	0.67145	0.996	P	0.60473	0.875	T	0.76911	-0.2784	10	0.62326	D	0.03	.	16.0156	0.80439	1.0:0.0:0.0:0.0	.	444	Q9NYQ8	FAT2_HUMAN	A	444	ENSP00000261800:V444A	ENSP00000261800:V444A	V	-	2	0	FAT2	150927355	1.000000	0.71417	0.116000	0.21606	0.171000	0.22731	9.262000	0.95591	2.189000	0.69895	0.533000	0.62120	GTG	A|0.983;G|0.017	0.017	strong		0.542	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
AKAP9	10142	hgsc.bcm.edu	37	7	91715662	91715662	+	Silent	SNP	C	C	T	rs28927678	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:91715662C>T	ENST00000359028.2	+	37	9382	c.9157C>T	c.(9157-9159)Ctg>Ttg	p.L3053L	AKAP9_ENST00000356239.3_Silent_p.L3049L|AKAP9_ENST00000358100.2_Silent_p.L2999L			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3053					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TCGGACGGAGCTGACAGCTCT	0.403			T	BRAF	papillary thyroid								C|||	1481	0.295727	0.2201	0.3458	5008	,	,		14480	0.1617		0.3837	False		,,,				2504	0.41				p.L3049L		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C9145T						PASS	.	C	,	1175,3231	412.8+/-336.2	165,845,1193	209.0	206.0	207.0		9145,9121	1.4	1.0	7	dbSNP_125	207	3451,5149	508.6+/-377.1	670,2111,1519	no	coding-synonymous,coding-synonymous	AKAP9	NM_005751.4,NM_147185.2	,	835,2956,2712	TT,TC,CC		40.1279,26.6682,35.5682	,	3049/3908,3041/3900	91715662	4626,8380	2203	4300	6503	SO:0001819	synonymous_variant	10142	exon37			ACGGAGCTGACAG	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.9157C>T	7.37:g.91715662C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	207	88	0.425121	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				C|0.656;T|0.344	0.344	strong		0.403	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
KRT40	125115	hgsc.bcm.edu	37	17	39137154	39137154	+	Missense_Mutation	SNP	C	C	G	rs721958	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39137154C>G	ENST00000398486.2	-	7	1018	c.858G>C	c.(856-858)gaG>gaC	p.E286D	KRT40_ENST00000377755.4_Missense_Mutation_p.E286D	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	286	Coil 2.|Rod.		E -> D (in dbSNP:rs721958).			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				GCTGATTCAGCTCTTCTGTCT	0.493													C|||	1808	0.361022	0.6861	0.2378	5008	,	,		21239	0.1716		0.2684	False		,,,				2504	0.2996				p.E286D		Atlas-SNP	.											.	KRT40	27	.	0			c.G858C						PASS	.	C	ASP/GLU	2314,1614		691,932,341	97.0	99.0	98.0		858	0.6	1.0	17	dbSNP_86	98	2293,6057		313,1667,2195	yes	missense	KRT40	NM_182497.3	45	1004,2599,2536	GG,GC,CC		27.4611,41.0896,37.5224	possibly-damaging	286/432	39137154	4607,7671	1964	4175	6139	SO:0001583	missense	125115	exon7			ATTCAGCTCTTCT	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.858G>C	17.37:g.39137154C>G	ENSP00000381500:p.Glu286Asp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	105	40	0.380952	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	733	0.3356227106227106	338	0.6869918699186992	92	0.2541436464088398	96	0.16783216783216784	207	0.27308707124010556	C	18.09	3.546022	0.65198	0.589104	0.274611	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.89343	-2.5;-2.5	5.4	0.634	0.17718	Filament (1);	0.000000	0.34067	N	0.004287	T	0.00012	0.0000	L	0.45698	1.435	0.37677	P	0.07666300000000004	P	0.45672	0.864	P	0.57371	0.819	T	0.47058	-0.9146	9	0.56958	D	0.05	.	5.6359	0.17536	0.0:0.4478:0.1375:0.4147	rs721958;rs17714313	286	Q6A162	K1C40_HUMAN	D	286	ENSP00000366984:E286D;ENSP00000381500:E286D	ENSP00000366984:E286D	E	-	3	2	KRT40	36390680	0.015000	0.18098	1.000000	0.80357	0.963000	0.63663	-0.680000	0.05197	0.356000	0.24157	0.655000	0.94253	GAG	C|0.656;G|0.344	0.344	strong		0.493	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
FLNB	2317	hgsc.bcm.edu	37	3	58081888	58081888	+	Silent	SNP	T	T	C	rs1522384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:58081888T>C	ENST00000295956.4	+	6	1092	c.927T>C	c.(925-927)agT>agC	p.S309S	FLNB_ENST00000490882.1_Silent_p.S309S|FLNB_ENST00000358537.3_Silent_p.S309S|FLNB_ENST00000493452.1_Silent_p.S140S|FLNB_ENST00000348383.5_Silent_p.S309S|FLNB_ENST00000419752.2_Silent_p.S140S|FLNB_ENST00000429972.2_Silent_p.S309S|FLNB_ENST00000357272.4_Silent_p.S309S	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	309					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CCCCTGACAGTGACAAGAACA	0.552													C|||	3215	0.641973	0.5825	0.5821	5008	,	,		19936	0.9772		0.3668	False		,,,				2504	0.7025				p.S309S		Atlas-SNP	.											.	FLNB	430	.	0			c.T927C						PASS	.	C	,,,	2349,2057	566.4+/-381.9	621,1107,475	97.0	79.0	85.0		927,927,927,927	-2.9	0.3	3	dbSNP_88	85	2790,5810	677.4+/-403.4	463,1864,1973	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	1084,2971,2448	CC,CT,TT		32.4419,46.6863,39.5125	,,,	309/2634,309/2592,309/2579,309/2603	58081888	5139,7867	2203	4300	6503	SO:0001819	synonymous_variant	2317	exon6			TGACAGTGACAAG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.927T>C	3.37:g.58081888T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																			T|0.536;C|0.464	0.464	strong		0.552	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
PTPRF	5792	hgsc.bcm.edu	37	1	44072066	44072066	+	Silent	SNP	C	C	T	rs10890266	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:44072066C>T	ENST00000359947.4	+	20	3979	c.3639C>T	c.(3637-3639)ccC>ccT	p.P1213P	PTPRF_ENST00000372414.3_Silent_p.P1213P|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000438120.1_Silent_p.P1204P|PTPRF_ENST00000422171.2_Silent_p.P561P|PTPRF_ENST00000372413.3_Silent_p.P1204P	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1213					cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ACAACCGGCCCCTGTCTCCGG	0.572													C|||	1408	0.28115	0.0303	0.2752	5008	,	,		15878	0.4702		0.3648	False		,,,				2504	0.3436				p.P1213P		Atlas-SNP	.											.	PTPRF	172	.	0			c.C3639T						PASS	.	C	,	413,3993	202.8+/-225.5	21,371,1811	137.0	148.0	144.0		3639,3612	-0.5	1.0	1	dbSNP_120	144	3111,5489	475.5+/-369.1	574,1963,1763	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	595,2334,3574	TT,TC,CC		36.1744,9.3736,27.0952	,	1213/1908,1204/1899	44072066	3524,9482	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon20			CCGGCCCCTGTCT	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.3639C>T	1.37:g.44072066C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	636|636	0.29120879120879123|0.29120879120879123	19|19	0.03861788617886179|0.03861788617886179	113|113	0.31215469613259667|0.31215469613259667	229|229	0.40034965034965037|0.40034965034965037	275|275	0.3627968337730871|0.3627968337730871	C|C	9.612|9.612	1.131657|1.131657	0.21041|0.21041	0.093736|0.093736	0.361744|0.361744	ENSG00000142949|ENSG00000142949	ENST00000429895|ENST00000412568;ENST00000414879	T|T;T	0.25414|0.38077	1.8|1.17;1.16	5.2|5.2	-0.529|-0.529	0.11901|0.11901	.|.	0.000000|0.000000	0.34002|0.34002	N|N	0.004350|0.004350	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999843067|0.999999843067	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.39121|0.39121	-0.9629|-0.9629	6|6	0.51188|0.56958	T|D	0.08|0.05	.|.	1.5715|1.5715	0.02616|0.02616	0.1907:0.2989:0.3086:0.2018|0.1907:0.2989:0.3086:0.2018	rs10890266;rs59351132;rs10890266|rs10890266;rs59351132;rs10890266	.|.	.|.	.|.	L|S	859|586;627	ENSP00000408952:P859L|ENSP00000391764:P586S;ENSP00000416343:P627S	ENSP00000408952:P859L|ENSP00000361484:P536S	P|P	+|+	2|1	0|0	PTPRF|PTPRF	43844653|43844653	0.007000|0.007000	0.16637|0.16637	0.998000|0.998000	0.56505|0.56505	0.993000|0.993000	0.82548|0.82548	-1.265000|-1.265000	0.02844|0.02844	0.019000|0.019000	0.15079|0.15079	0.561000|0.561000	0.74099|0.74099	CCC|CCT	C|0.727;N|0.000	.	strong		0.572	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
KRT77	374454	hgsc.bcm.edu	37	12	53088484	53088484	+	Missense_Mutation	SNP	C	C	T	rs10783528	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53088484C>T	ENST00000341809.3	-	5	1034	c.1006G>A	c.(1006-1008)Gat>Aat	p.D336N	KRT77_ENST00000537195.1_Missense_Mutation_p.D103N|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	336	Coil 2.|Rod.			D -> N (in Ref. 1; CAD91892). {ECO:0000305}.		cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CGCACTGCATCGATGATGCTG	0.587													C|||	1594	0.318291	0.1377	0.281	5008	,	,		19567	0.5813		0.3559	False		,,,				2504	0.2791				p.D336N		Atlas-SNP	.											.	KRT77	58	.	0			c.G1006A						PASS	.	C	ASN/ASP	875,3531	342.8+/-307.3	90,695,1418	139.0	97.0	111.0		1006	0.5	0.0	12	dbSNP_120	111	2918,5682	456.7+/-364.1	504,1910,1886	yes	missense	KRT77	NM_175078.2	23	594,2605,3304	TT,TC,CC		33.9302,19.8593,29.1635	benign	336/579	53088484	3793,9213	2203	4300	6503	SO:0001583	missense	374454	exon5			CTGCATCGATGAT	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20411	protein-coding gene	gene with protein product		611158	"""keratin 1B"""	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.1006G>A	12.37:g.53088484C>T	ENSP00000342710:p.Asp336Asn	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	36	0.428571	NM_175078	Q7RTS8	Missense_Mutation	SNP	ENST00000341809.3	37	CCDS8837.1	801	0.36675824175824173	65	0.13211382113821138	114	0.3149171270718232	345	0.6031468531468531	277	0.3654353562005277	C	10.17	1.275491	0.23307	0.198593	0.339302	ENSG00000189182	ENST00000341809;ENST00000537195	T;T	0.78816	-1.21;-1.07	4.94	0.542	0.17174	Filament (1);	.	.	.	.	T	0.00012	0.0000	N	0.16903	0.455	0.80722	P	0.0	B	0.32731	0.382	B	0.22386	0.039	T	0.46638	-0.9177	8	0.66056	D	0.02	.	8.2491	0.31706	0.0:0.515:0.3418:0.1432	rs10783528;rs52810493;rs58359758;rs10783528	336	Q7Z794	K2C1B_HUMAN	N	336;103	ENSP00000342710:D336N;ENSP00000440803:D103N	ENSP00000342710:D336N	D	-	1	0	KRT77	51374751	0.000000	0.05858	0.004000	0.12327	0.187000	0.23431	-0.031000	0.12287	0.188000	0.20168	0.555000	0.69702	GAT	C|0.676;T|0.324	0.324	strong		0.587	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651161	1651161	+	Missense_Mutation	SNP	T	T	C	rs71454094	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1651161T>C	ENST00000399676.2	+	1	129	c.91T>C	c.(91-93)Tgt>Cgt	p.C31R		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	31				C -> R (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ctgtggaggctgtggctctgg	0.716													t|||	1915	0.382388	0.4319	0.379	5008	,	,		7894	0.2976		0.3966	False		,,,				2504	0.3906				p.C31R		Atlas-SNP	.											KRTAP5-5,colon,carcinoma,0,1	KRTAP5-5	86	1	0			c.T91C						scavenged	.						23.0	34.0	30.0					11																	1651161		2084	4164	6248	SO:0001583	missense	439915	exon1			GGAGGCTGTGGCT	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.91T>C	11.37:g.1651161T>C	ENSP00000382584:p.Cys31Arg	Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	37	24	0.648649	NM_001001480	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	735	0.33653846153846156	187	0.3800813008130081	124	0.3425414364640884	158	0.2762237762237762	266	0.35092348284960423	T	1.810	-0.474941	0.04414	.	.	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.02067	4.47	2.25	0.968	0.19680	.	.	.	.	.	T	0.00012	0.0000	M	0.84773	2.715	0.45899	P	0.0012569999999999526	P	0.34699	0.464	B	0.32864	0.154	T	0.37842	-0.9688	8	0.49607	T	0.09	.	4.9279	0.13903	0.0:0.0:0.3203:0.6797	.	31	Q701N2	KRA55_HUMAN	R	31;29	ENSP00000382584:C31R	ENSP00000382584:C31R	C	+	1	0	KRTAP5-5	1607737	0.998000	0.40836	0.001000	0.08648	0.093000	0.18481	1.786000	0.38694	0.251000	0.21505	0.368000	0.22195	TGT	T|0.663;C|0.337	0.337	strong		0.716	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
LINS	55180	hgsc.bcm.edu	37	15	101120963	101120963	+	Missense_Mutation	SNP	T	T	C	rs11247226	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:101120963T>C	ENST00000314742.8	-	2	307	c.85A>G	c.(85-87)Atc>Gtc	p.I29V	LINS_ENST00000559149.1_5'UTR|LINS_ENST00000561308.1_Missense_Mutation_p.I29V|LINS_ENST00000560133.1_Intron	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	29			I -> V (in dbSNP:rs11247226). {ECO:0000269|PubMed:14702039}.							central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						AGATAAAAGATGTAATCATGG	0.413													T|||	1495	0.298522	0.1861	0.2464	5008	,	,		19384	0.246		0.4523	False		,,,				2504	0.3834				p.I29V		Atlas-SNP	.											.	LINS	62	.	0			c.A85G						PASS	.	T	VAL/ILE	1008,3398	373.4+/-320.8	105,798,1300	65.0	60.0	62.0		85	-4.7	0.0	15	dbSNP_120	62	4039,4561	556.0+/-386.8	960,2119,1221	yes	missense	LINS	NM_001040616.2	29	1065,2917,2521	CC,CT,TT		46.9651,22.8779,38.8052	benign	29/758	101120963	5047,7959	2203	4300	6503	SO:0001583	missense	55180	exon2			AAAAGATGTAATC	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"""lines homolog 1 (Drosophila)"""	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.85A>G	15.37:g.101120963T>C	ENSP00000318423:p.Ile29Val	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	212	108	0.509434	NM_001040616	Q96FW2|Q9NVQ3	Missense_Mutation	SNP	ENST00000314742.8	37	CCDS10385.1	690	0.3159340659340659	95	0.19308943089430894	102	0.281767955801105	142	0.24825174825174826	351	0.4630606860158311	T	5.107	0.205418	0.09704	0.228779	0.469651	ENSG00000140471	ENST00000314742	T	0.24723	1.84	5.63	-4.72	0.03269	.	1.128080	0.06487	N	0.733828	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.12013	0.005;0.001	B;B	0.10450	0.002;0.005	T	0.46830	-0.9163	9	0.06891	T	0.86	0.0042	10.8854	0.46964	0.0992:0.5941:0.0:0.3068	rs11247226;rs17845256;rs17858082;rs57524614;rs11247226	29;29	Q8NG48-2;Q8NG48	.;LINES_HUMAN	V	29	ENSP00000318423:I29V	ENSP00000318423:I29V	I	-	1	0	LINS	98938486	0.000000	0.05858	0.001000	0.08648	0.571000	0.35966	-2.670000	0.00844	-0.798000	0.04444	0.528000	0.53228	ATC	T|0.653;C|0.347	0.347	strong		0.413	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148	
UBR2	23304	hgsc.bcm.edu	37	6	42585064	42585064	+	Silent	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:42585064C>A	ENST00000372899.1	+	11	1527	c.1269C>A	c.(1267-1269)acC>acA	p.T423T	UBR2_ENST00000372903.2_Intron|UBR2_ENST00000372883.3_Intron|UBR2_ENST00000372901.1_Intron	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	423					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			AGTTCTTCACCGCACCTACTC	0.458																																					p.T423T		Atlas-SNP	.											UBR2,NS,carcinoma,0,1	UBR2	134	1	0			c.C1269A						scavenged	.						137.0	121.0	127.0					6																	42585064		2203	4300	6503	SO:0001819	synonymous_variant	23304	exon11			CTTCACCGCACCT	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.1269C>A	6.37:g.42585064C>A		Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	189	6	0.031746	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			.	.	none		0.458	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
ATR	545	hgsc.bcm.edu	37	3	142277536	142277536	+	Silent	SNP	A	A	G	rs2227929	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:142277536A>G	ENST00000350721.4	-	8	1936	c.1815T>C	c.(1813-1815)gaT>gaC	p.D605D	ATR_ENST00000383101.3_Silent_p.D541D	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	605					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TTAAACAGCCATCATCAGAAT	0.368								Other conserved DNA damage response genes					A|||	1556	0.310703	0.2042	0.3516	5008	,	,		12160	0.3552		0.3867	False		,,,				2504	0.3016				p.D605D		Atlas-SNP	.											.	ATR	285	.	0			c.T1815C						PASS	.	A		937,3469	357.4+/-313.9	96,745,1362	258.0	265.0	263.0		1815	0.0	0.1	3	dbSNP_98	263	3560,5040	516.4+/-378.8	740,2080,1480	no	coding-synonymous	ATR	NM_001184.3		836,2825,2842	GG,GA,AA		41.3953,21.2665,34.5763		605/2645	142277536	4497,8509	2203	4300	6503	SO:0001819	synonymous_variant	545	exon8			ACAGCCATCATCA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.1815T>C	3.37:g.142277536A>G		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	262	259	0.98855	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1																																																																																			A|0.656;G|0.344	0.344	strong		0.368	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
RBMX	27316	hgsc.bcm.edu	37	X	135956467	135956467	+	Missense_Mutation	SNP	C	C	T	rs35899675		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:135956467C>T	ENST00000320676.7	-	9	1164	c.1010G>A	c.(1009-1011)aGt>aAt	p.S337N	RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000496459.2_5'Flank|RBMX_ENST00000565438.1_Missense_Mutation_p.S209N|RBMX_ENST00000570135.1_Missense_Mutation_p.S202N	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	337	Necessary for RNA-binding.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.S337N(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					ATCACGACCACTTGAGTAGAG	0.527																																					p.S337N		Atlas-SNP	.											.	RBMX	149	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1010A						PASS	.						126.0	116.0	119.0					X																	135956467		2203	4300	6503	SO:0001583	missense	27316	exon9			CGACCACTTGAGT		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.1010G>A	X.37:g.135956467C>T	ENSP00000359645:p.Ser337Asn	Somatic	348	1	0.00287356		WXS	Illumina HiSeq	Phase_I	537	267	0.497207	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	14.40	2.523817	0.44866	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.77229	-1.08	5.4	5.4	0.78164	.	0.134440	0.49916	U	0.000121	D	0.83959	0.5367	L	0.43152	1.355	0.23661	P	0.99717437	D	0.57899	0.981	D	0.67900	0.954	D	0.83628	0.0143	9	0.44086	T	0.13	.	18.4308	0.90624	0.0:1.0:0.0:0.0	rs55701431	337	P38159	HNRPG_HUMAN	N	337;324	ENSP00000359645:S337N	ENSP00000359645:S337N	S	-	2	0	RBMX	135784133	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.933000	0.63484	2.380000	0.81148	0.600000	0.82982	AGT	.	.	weak		0.527	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
ZNF268	10795	hgsc.bcm.edu	37	12	133768553	133768553	+	Missense_Mutation	SNP	A	A	T	rs61960670	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133768553A>T	ENST00000536435.2	+	5	751	c.421A>T	c.(421-423)Atg>Ttg	p.M141L	ZNF268_ENST00000542711.2_Silent_p.V31V|ZNF268_ENST00000592241.1_Missense_Mutation_p.M74L|ZNF268_ENST00000228289.5_Missense_Mutation_p.M141L|ZNF268_ENST00000537565.1_Intron|ZNF268_ENST00000542986.2_Missense_Mutation_p.M126L|CTD-2140B24.4_ENST00000540096.2_Missense_Mutation_p.M306L|ZNF268_ENST00000539248.2_Intron|ZNF268_ENST00000541009.2_Missense_Mutation_p.M141L|ZNF268_ENST00000541211.2_Silent_p.V98V|ZNF268_ENST00000416488.1_Missense_Mutation_p.M306L|ZNF268_ENST00000536899.2_Intron	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	141	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		AGAGCTGTGTATGGTGCAGGC	0.398													A|||	722	0.144169	0.0083	0.1571	5008	,	,		18153	0.1121		0.2396	False		,,,				2504	0.2536				p.M141L		Atlas-SNP	.											.	ZNF268	71	.	0			c.A421T						PASS	.	A	LEU/MET,LEU/MET,,,,,LEU/MET,LEU/MET,LEU/MET	194,3686		6,182,1752	150.0	145.0	146.0		421,172,,,294,93,220,421,421	-2.5	0.1	12	dbSNP_129	146	2209,6109		302,1605,2252	yes	missense,missense,intron,intron,coding-synonymous,coding-synonymous,missense,missense,missense	ZNF268	NM_001165881.2,NM_001165882.2,NM_001165883.1,NM_001165884.2,NM_001165885.1,NM_001165886.1,NM_001165887.1,NM_003415.2,NM_152943.2	15,15,,,,,15,15,15	308,1787,4004	TT,TA,AA		26.5569,5.0,19.7	benign,benign,,,,,benign,benign,benign	141/948,58/865,,,98/168,31/101,74/127,141/948,141/194	133768553	2403,9795	1940	4159	6099	SO:0001583	missense	10795	exon5			CTGTGTATGGTGC	X78926	CCDS45012.1, CCDS53851.1, CCDS53852.1, CCDS53853.1, CCDS53854.1, CCDS59239.1, CCDS59240.1	12q24.33	2013-01-08				ENSG00000090612		"""Zinc fingers, C2H2-type"", ""-"""	13061	protein-coding gene	gene with protein product		604753				7865130	Standard	NM_003415		Approved	HZF3	uc010tcf.2	Q14587	OTTHUMG00000167946	ENST00000536435.2:c.421A>T	12.37:g.133768553A>T	ENSP00000444412:p.Met141Leu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_152943	Q8TDG8|Q96RH4|Q9BZJ9	Missense_Mutation	SNP	ENST00000536435.2	37	CCDS45012.1	309	0.14148351648351648	6	0.012195121951219513	61	0.1685082872928177	61	0.10664335664335664	181	0.23878627968337732	A	0.076	-1.193631	0.01594	0.05	0.265569	ENSG00000090612	ENST00000416488;ENST00000541009;ENST00000542986;ENST00000228289;ENST00000534953	T;T;T	0.07327	5.93;5.44;3.2	3.38	-2.54	0.06307	Krueppel-associated box (2);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48854	-0.8998	6	.	.	.	.	5.1496	0.15002	0.5528:0.1507:0.2964:0.0	rs61960670	141	Q14587	ZN268_HUMAN	L	306;141;74;141;65	ENSP00000409295:M306L;ENSP00000439539:M141L;ENSP00000228289:M141L	.	M	+	1	0	ZNF268	132278626	0.008000	0.16893	0.097000	0.21041	0.064000	0.16182	-0.439000	0.06897	-0.679000	0.05217	-1.964000	0.00472	ATG	A|0.835;T|0.165	0.165	strong		0.398	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943	
HLA-B	3106	hgsc.bcm.edu	37	6	31324643	31324643	+	Silent	SNP	G	G	C	rs1050517	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324643G>C	ENST00000412585.2	-	2	193	c.165C>G	c.(163-165)acC>acG	p.T55T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	55	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TCACGAACTGGGTGTCGTCCA	0.672									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	1882	0.375799	0.3283	0.4323	5008	,	,		9531	0.3631		0.4732	False		,,,				2504	0.3129				p.T55T		Atlas-SNP	.											.	HLA-B	54	.	0			c.C165G						PASS	.	C		1189,3113		329,531,1291	38.0	30.0	33.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	165	1.4	1.0	6	dbSNP_86	33	3132,5168		1013,1106,2031	no	coding-synonymous	HLA-B	NM_005514.6		1342,1637,3322	CC,CG,GG		37.7349,27.6383,34.2882		55/363	31324643	4321,8281	2151	4150	6301	SO:0001819	synonymous_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	GAACTGGGTGTCG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.165C>G	6.37:g.31324643G>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			G|0.584;C|0.416	0.416	strong		0.672	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
RBM19	9904	hgsc.bcm.edu	37	12	114383651	114383651	+	Silent	SNP	C	C	T	rs12321179	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:114383651C>T	ENST00000545145.2	-	13	1686	c.1608G>A	c.(1606-1608)aaG>aaA	p.K536K	RBM19_ENST00000261741.5_Silent_p.K536K|RBM19_ENST00000392561.3_Silent_p.K536K	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	536					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K536K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					ACACTTGACTCTTGGTGGCGT	0.552													C|||	994	0.198482	0.3472	0.0764	5008	,	,		22010	0.1885		0.1133	False		,,,				2504	0.182				p.K536K		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - coding silent(1)	stomach(1)	c.G1608A						PASS	.	C	,,	1440,2966	466.0+/-354.4	254,932,1017	161.0	119.0	133.0		1608,1608,1608	3.8	1.0	12	dbSNP_120	133	887,7713	199.4+/-243.5	39,809,3452	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	293,1741,4469	TT,TC,CC		10.314,32.6827,17.8917	,,	536/961,536/961,536/961	114383651	2327,10679	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon13			TTGACTCTTGGTG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1608G>A	12.37:g.114383651C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	181	100	0.552486	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			C|0.823;T|0.177	0.177	strong		0.552	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
SPATA3	130560	hgsc.bcm.edu	37	2	231865090	231865090	+	Missense_Mutation	SNP	T	T	C	rs2271376	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:231865090T>C	ENST00000452881.1	+	2	419	c.311T>C	c.(310-312)aTt>aCt	p.I104T	SPATA3_ENST00000409956.1_Intron|SPATA3_ENST00000433428.2_Missense_Mutation_p.I104T|SPATA3_ENST00000424440.1_Missense_Mutation_p.I104T|SPATA3_ENST00000455816.1_Missense_Mutation_p.I104T			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	104				I -> T (in Ref. 4; AAH47704). {ECO:0000305}.						endometrium(2)|lung(1)	3						GGGCCTCTGATTCGCGCCGGC	0.657													C|||	2248	0.448882	0.4644	0.3617	5008	,	,		17108	0.4742		0.4095	False		,,,				2504	0.5041				p.I104T		Atlas-SNP	.											.	SPATA3	52	.	0			c.T311C						PASS	.	C	THR/ILE	637,747		147,343,202	39.0	38.0	38.0		311	-0.7	0.0	2	dbSNP_100	38	1228,1954		215,798,578	yes	missense	SPATA3	NM_139073.3	89	362,1141,780	CC,CT,TT		38.5921,46.026,40.8454	benign	104/193	231865090	1865,2701	692	1591	2283	SO:0001583	missense	130560	exon2			CTCTGATTCGCGC	AY032925	CCDS2481.1	2q37.1	2008-02-05			ENSG00000173699	ENSG00000173699			17884	protein-coding gene	gene with protein product							Standard	NM_139073		Approved	TSARG1	uc010zmd.2	Q8NHX4	OTTHUMG00000133221	ENST00000452881.1:c.311T>C	2.37:g.231865090T>C	ENSP00000388895:p.Ile104Thr	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	219	217	0.990868	NM_139073	Q86WX5|Q8N9Y6	Missense_Mutation	SNP	ENST00000452881.1	37	CCDS2481.1	935	0.4281135531135531	240	0.4878048780487805	132	0.36464088397790057	244	0.42657342657342656	319	0.420844327176781	C	0.016	-1.514670	0.00975	0.46026	0.385921	ENSG00000173699	ENST00000424440;ENST00000452881;ENST00000433428;ENST00000455816;ENST00000355662	.	.	.	4.25	-0.717	0.11208	.	1.005100	0.08013	N	0.990612	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43814	-0.9368	8	0.02654	T	1	-2.041	4.8384	0.13476	0.0:0.3588:0.1618:0.4794	rs2271376;rs17857338;rs60977521;rs2271376	95	Q8NHX4	SPTA3_HUMAN	T	104;104;104;104;95	.	ENSP00000347884:I95T	I	+	2	0	SPATA3	231573334	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.835000	0.04386	-0.390000	0.07774	-0.733000	0.03571	ATT	T|0.565;C|0.435	0.435	strong		0.657	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
CST9	128822	hgsc.bcm.edu	37	20	23586360	23586360	+	Missense_Mutation	SNP	G	G	A	rs2983640	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:23586360G>A	ENST00000376971.3	-	1	153	c.142C>T	c.(142-144)Ctc>Ttc	p.L48F		NM_001008693.2	NP_001008693.2	Q5W186	CST9_HUMAN	cystatin 9 (testatin)	48			L -> F (in dbSNP:rs2983640). {ECO:0000269|PubMed:12535658}.			extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			central_nervous_system(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Colorectal(13;0.0993)					ACTGTGGCGAGGAACATAGGA	0.507													G|||	2279	0.455072	0.0915	0.6182	5008	,	,		21096	0.6796		0.6302	False		,,,				2504	0.4192				p.L48F		Atlas-SNP	.											.	CST9	26	.	0			c.C142T						PASS	.	G	PHE/LEU	711,3695	293.8+/-282.8	64,583,1556	267.0	223.0	238.0		142	-1.9	0.0	20	dbSNP_101	238	5219,3381	641.7+/-399.7	1610,1999,691	yes	missense	CST9	NM_001008693.2	22	1674,2582,2247	AA,AG,GG		39.314,16.1371,45.5943	probably-damaging	48/160	23586360	5930,7076	2203	4300	6503	SO:0001583	missense	128822	exon1			TGGCGAGGAACAT	AF494536	CCDS33450.1	20p11.21	2012-08-14			ENSG00000173335	ENSG00000173335			13261	protein-coding gene	gene with protein product						20565543	Standard	NM_001008693		Approved	CLM, CTES7A	uc002wtl.3	Q5W186	OTTHUMG00000032076	ENST00000376971.3:c.142C>T	20.37:g.23586360G>A	ENSP00000366170:p.Leu48Phe	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001008693	B2RP76|Q8TD53	Missense_Mutation	SNP	ENST00000376971.3	37	CCDS33450.1	1133	0.5187728937728938	45	0.09146341463414634	223	0.6160220994475138	375	0.6555944055944056	490	0.6464379947229552	G	5.925	0.354650	0.11239	0.161371	0.60686	ENSG00000173335	ENST00000376971	T	0.26223	1.75	2.66	-1.91	0.07641	Proteinase inhibitor I25, cystatin (1);	1.320590	0.05565	N	0.570071	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D	0.61080	0.989	P	0.60173	0.87	T	0.48514	-0.9029	9	0.09590	T	0.72	.	2.6821	0.05096	0.405:0.0:0.3833:0.2117	rs2983640;rs17684648;rs52834245;rs59793432;rs2983640	48	Q5W186	CST9_HUMAN	F	48	ENSP00000366170:L48F	ENSP00000366170:L48F	L	-	1	0	CST9	23534360	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.154000	0.10130	-0.396000	0.07703	-0.225000	0.12378	CTC	G|0.526;A|0.474	0.474	strong		0.507	CST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078341.1	NM_001008693.1	
ACSM5	54988	hgsc.bcm.edu	37	16	20442613	20442613	+	Silent	SNP	T	T	C	rs77351186	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20442613T>C	ENST00000331849.4	+	10	1425	c.1278T>C	c.(1276-1278)acT>acC	p.T426T		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	426					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						TCAGACCCACTCGGCCCTTCT	0.498																																					p.T426T		Atlas-SNP	.											ACSM5,NS,carcinoma,0,1	ACSM5	101	1	0			c.T1278C						scavenged	.						171.0	145.0	154.0					16																	20442613		2203	4300	6503	SO:0001819	synonymous_variant	54988	exon10			ACCCACTCGGCCC		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1278T>C	16.37:g.20442613T>C		Somatic	130	2	0.0153846		WXS	Illumina HiSeq	Phase_I	166	44	0.26506	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Silent	SNP	ENST00000331849.4	37	CCDS10585.1																																																																																			T|0.997;C|0.003	0.003	strong		0.498	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
FREM1	158326	hgsc.bcm.edu	37	9	14770658	14770658	+	Silent	SNP	G	G	T	rs17219005	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:14770658G>T	ENST00000380880.3	-	26	5787	c.5004C>A	c.(5002-5004)atC>atA	p.I1668I	FREM1_ENST00000422223.2_Silent_p.I1668I|FREM1_ENST00000380881.4_Silent_p.I1669I|FREM1_ENST00000486223.1_5'UTR|FREM1_ENST00000380894.1_Silent_p.I204I			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1668					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TTTTAAAGATGATCTGATCGT	0.458													G|||	1273	0.254193	0.2723	0.2723	5008	,	,		18061	0.0813		0.4056	False		,,,				2504	0.2393				p.I1668I		Atlas-SNP	.											.	FREM1	261	.	0			c.C5004A						PASS	.	G	,	1096,2778		157,782,998	135.0	126.0	129.0		612,5004	1.0	1.0	9	dbSNP_123	129	3316,4980		648,2020,1480	no	coding-synonymous,coding-synonymous	FREM1	NM_001177704.1,NM_144966.5	,	805,2802,2478	TT,TG,GG		39.9711,28.2912,36.2531	,	204/716,1668/2180	14770658	4412,7758	1937	4148	6085	SO:0001819	synonymous_variant	158326	exon27			AAAGATGATCTGA	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.5004C>A	9.37:g.14770658G>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	146	77	0.527397	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			G|0.749;T|0.251	0.251	strong		0.458	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
PCSK7	9159	hgsc.bcm.edu	37	11	117096652	117096652	+	Silent	SNP	G	G	A	rs2277287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:117096652G>A	ENST00000320934.3	-	6	1485	c.855C>T	c.(853-855)agC>agT	p.S285S	PCSK7_ENST00000540028.1_5'Flank	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	285	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CTCACCTGCAGCTGTAGATGT	0.552			T	IGH@	MLCLS						OREG0021371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1249	0.249401	0.3381	0.2666	5008	,	,		17158	0.1508		0.1928	False		,,,				2504	0.2771				p.S285S		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.C855T						PASS	.	G		1333,3069	445.7+/-347.8	189,955,1057	127.0	90.0	102.0		855	2.7	1.0	11	dbSNP_100	102	1788,6804	323.2+/-315.9	181,1426,2689	no	coding-synonymous	PCSK7	NM_004716.2		370,2381,3746	AA,AG,GG		20.8101,30.2817,24.0188		285/786	117096652	3121,9873	2201	4296	6497	SO:0001819	synonymous_variant	9159	exon6			CCTGCAGCTGTAG	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.855C>T	11.37:g.117096652G>A		Somatic	86	0	0	1478	WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			G|0.759;A|0.241	0.241	strong		0.552	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
SMPD4	55627	hgsc.bcm.edu	37	2	130931167	130931167	+	Missense_Mutation	SNP	G	G	A	rs41269839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:130931167G>A	ENST00000339679.7	-	4	297	c.43C>T	c.(43-45)Cgt>Tgt	p.R15C	SMPD4_ENST00000426662.2_Intron|SMPD4_ENST00000453750.1_Intron|SMPD4_ENST00000431183.2_Intron|SMPD4_ENST00000351288.6_Silent_p.L102L|SMPD4_ENST00000409031.1_Silent_p.L102L|SMPD4_ENST00000443958.2_Intron|SMPD4_ENST00000473720.1_Intron|SMPD4_ENST00000452225.2_Intron			Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	0					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	TCCAGCCAACGAGGACACCAT	0.562													.|||	21	0.00419329	0.0015	0.0086	5008	,	,		18638	0.001		0.005	False		,,,				2504	0.0072				p.L102L		Atlas-SNP	.											.	SMPD4	67	.	0			c.C306T						PASS	.	G	,,	5,4401	9.9+/-24.2	0,5,2198	57.0	50.0	53.0		,306,306	-4.0	0.0	2	dbSNP_127	53	70,8530	41.2+/-98.3	0,70,4230	no	intron,coding-synonymous,coding-synonymous	SMPD4	NM_001171083.2,NM_017751.4,NM_017951.4	,,	0,75,6428	AA,AG,GG		0.814,0.1135,0.5767	,,	,102/838,102/867	130931167	75,12931	2203	4300	6503	SO:0001583	missense	55627	exon4			GCCAACGAGGACA	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000339679.7:c.43C>T	2.37:g.130931167G>A	ENSP00000339721:p.Arg15Cys	Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	256	128	0.5	NM_017751	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Silent	SNP	ENST00000339679.7	37		13	0.005952380952380952	5	0.01016260162601626	4	0.011049723756906077	1	0.0017482517482517483	3	0.00395778364116095	g	1.344	-0.593348	0.03771	0.001135	0.00814	ENSG00000136699	ENST00000339679	.	.	.	3.57	-3.95	0.04118	.	.	.	.	.	T	0.16769	0.0403	.	.	.	0.18873	N	0.999988	B	0.06786	0.001	B	0.01281	0.0	T	0.22138	-1.0225	7	0.51188	T	0.08	.	1.3972	0.02263	0.4039:0.2904:0.1726:0.1332	rs41269839	15	B4E0T5	.	C	15	.	ENSP00000339721:R15C	R	-	1	0	SMPD4	130647637	0.000000	0.05858	0.021000	0.16686	0.069000	0.16628	-0.875000	0.04205	-0.661000	0.05345	0.455000	0.32223	CGT	G|0.994;A|0.006	0.006	strong		0.562	SMPD4-201	KNOWN	basic	protein_coding	protein_coding		NM_017751	
OLFML1	283298	hgsc.bcm.edu	37	11	7507174	7507174	+	Missense_Mutation	SNP	C	C	T	rs80215761	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7507174C>T	ENST00000329293.3	+	1	462	c.68C>T	c.(67-69)cCg>cTg	p.P23L	CTD-2516F10.2_ENST00000530201.1_RNA|OLFML1_ENST00000528758.1_Missense_Mutation_p.P23L|OLFML1_ENST00000530135.1_Missense_Mutation_p.P23L	NM_198474.3	NP_940876.2	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1	23						extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(3)|prostate(2)	24				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		CTGCCCCCGCCGCAGTGTACC	0.537													C|||	30	0.00599042	0.0015	0.0058	5008	,	,		18647	0.0		0.0219	False		,,,				2504	0.002				p.P23L		Atlas-SNP	.											.	OLFML1	54	.	0			c.C68T						PASS	.	C	LEU/PRO	30,4372	35.2+/-66.4	0,30,2171	126.0	113.0	117.0		68	4.7	0.0	11	dbSNP_132	117	283,8309	105.4+/-166.3	4,275,4017	yes	missense	OLFML1	NM_198474.3	98	4,305,6188	TT,TC,CC		3.2938,0.6815,2.4088	benign	23/403	7507174	313,12681	2201	4296	6497	SO:0001583	missense	283298	exon1			CCCCGCCGCAGTG	AY358591	CCDS7779.1	11p15	2008-02-05			ENSG00000183801	ENSG00000183801			24473	protein-coding gene	gene with protein product							Standard	NM_198474		Approved	UNQ564	uc001mfi.3	Q6UWY5	OTTHUMG00000165527	ENST00000329293.3:c.68C>T	11.37:g.7507174C>T	ENSP00000332511:p.Pro23Leu	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	243	128	0.526749	NM_198474	B4DP03|Q569G4	Missense_Mutation	SNP	ENST00000329293.3	37	CCDS7779.1	22	0.010073260073260074	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	17	0.022427440633245383	C	12.53	1.966877	0.34659	0.006815	0.032938	ENSG00000183801	ENST00000530135;ENST00000329293;ENST00000534244;ENST00000528758	D;D	0.86956	-2.19;-2.19	5.59	4.67	0.58626	.	0.427258	0.22758	N	0.055984	T	0.55386	0.1917	L	0.33485	1.01	0.09310	N	0.999999	B;B	0.24317	0.008;0.101	B;B	0.17722	0.005;0.019	T	0.52480	-0.8570	10	0.02654	T	1	.	10.8203	0.46601	0.0:0.9115:0.0:0.0885	.	23;23	Q6UWY5;Q5HYE3	OLFL1_HUMAN;.	L	23	ENSP00000433455:P23L;ENSP00000332511:P23L	ENSP00000332511:P23L	P	+	2	0	OLFML1	7463750	0.022000	0.18835	0.041000	0.18516	0.645000	0.38454	1.839000	0.39220	1.332000	0.45431	0.591000	0.81541	CCG	C|0.983;T|0.017	0.017	strong		0.537	OLFML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384656.1	NM_198474	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595183	140595183	+	Silent	SNP	G	G	T	rs2910330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140595183G>T	ENST00000341948.4	+	1	1675	c.1488G>T	c.(1486-1488)ccG>ccT	p.P496P		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	496	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCAGGACCCGCACCTGCCCC	0.657													G|||	602	0.120208	0.1036	0.0937	5008	,	,		15894	0.0933		0.1421	False		,,,				2504	0.1667				p.P496P		Atlas-SNP	.											.	PCDHB13	142	.	0			c.G1488T						PASS	.	G		522,3884		34,454,1715	101.0	108.0	105.0		1488	0.3	0.0	5	dbSNP_101	105	1410,7190		133,1144,3023	no	coding-synonymous	PCDHB13	NM_018933.2		167,1598,4738	TT,TG,GG		16.3953,11.8475,14.8547		496/799	140595183	1932,11074	2203	4300	6503	SO:0001819	synonymous_variant	56123	exon1			GGACCCGCACCTG	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"""Cadherins / Protocadherins : Clustered"""	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.1488G>T	5.37:g.140595183G>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	161	68	0.42236	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			A|0.000;G|0.862;T|0.138	0.138	strong		0.657	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
GBP4	115361	hgsc.bcm.edu	37	1	89652102	89652102	+	Missense_Mutation	SNP	A	A	T	rs655260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89652102A>T	ENST00000355754.6	-	10	1718	c.1621T>A	c.(1621-1623)Tac>Aac	p.Y541N	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	541			Y -> N (in dbSNP:rs655260).	YM -> NI (in Ref. 1; AAL02054 and 3; BAC85144). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		TGGGCCATGTATTCCTGGAAG	0.488													A|||	1801	0.359625	0.1445	0.3141	5008	,	,		18800	0.3998		0.4891	False		,,,				2504	0.5082				p.Y541N		Atlas-SNP	.											.	GBP4	89	.	0			c.T1621A						PASS	.	A	ASN/TYR	435,3971		120,195,1888	167.0	106.0	127.0		1621	0.4	0.0	1	dbSNP_83	127	2958,5642		1090,778,2432	no	missense	GBP4	NM_052941.4	143	1210,973,4320	TT,TA,AA		34.3953,9.8729,26.088	benign	541/641	89652102	3393,9613	2203	4300	6503	SO:0001583	missense	115361	exon10			CCATGTATTCCTG	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1621T>A	1.37:g.89652102A>T	ENSP00000359490:p.Tyr541Asn	Somatic	357	1	0.00280112		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	630	0.28846153846153844	39	0.07926829268292683	115	0.31767955801104975	184	0.32167832167832167	292	0.38522427440633245	A	0.009	-1.824350	0.00589	0.098729	0.343953	ENSG00000162654	ENST00000355754	T	0.01804	4.63	4.29	0.417	0.16421	Guanylate-binding protein, C-terminal (3);	0.451332	0.23175	N	0.051084	T	0.00073	0.0002	N	0.00010	-3.05	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13737	-1.0498	9	0.02654	T	1	.	6.8128	0.23814	0.1531:0.0:0.4653:0.3816	rs655260;rs1142885;rs3180071;rs3206367;rs655260	541	Q96PP9	GBP4_HUMAN	N	541	ENSP00000359490:Y541N	ENSP00000359490:Y541N	Y	-	1	0	GBP4	89424690	0.025000	0.19082	0.002000	0.10522	0.043000	0.13939	0.002000	0.13061	-0.033000	0.13736	-2.024000	0.00429	TAC	A|0.677;T|0.323	0.323	strong		0.488	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
FSCN1	6624	hgsc.bcm.edu	37	7	5643145	5643145	+	Silent	SNP	T	T	C	rs1640233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:5643145T>C	ENST00000382361.3	+	3	1122	c.1008T>C	c.(1006-1008)ttT>ttC	p.F336F	FSCN1_ENST00000340250.6_Silent_p.F315F	NM_003088.3	NP_003079.1	Q16658	FSCN1_HUMAN	fascin actin-bundling protein 1	336					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|cell motility (GO:0048870)|cell proliferation (GO:0008283)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|invadopodium (GO:0071437)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|drug binding (GO:0008144)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)		GCTGCTACTTTGACATCGAGT	0.642													C|||	1193	0.238219	0.32	0.2176	5008	,	,		18061	0.1766		0.165	False		,,,				2504	0.2812				p.F336F		Atlas-SNP	.											.	FSCN1	29	.	0			c.T1008C						PASS	.	C		1262,3144	428.3+/-341.8	184,894,1125	68.0	69.0	68.0		1008	-1.1	1.0	7	dbSNP_89	68	1553,7047	290.3+/-299.7	148,1257,2895	no	coding-synonymous	FSCN1	NM_003088.3		332,2151,4020	CC,CT,TT		18.0581,28.6428,21.6439		336/494	5643145	2815,10191	2203	4300	6503	SO:0001819	synonymous_variant	6624	exon3			CTACTTTGACATC	U03057	CCDS5342.1	7p22	2014-02-03	2014-02-03	2002-09-20	ENSG00000075618	ENSG00000075618		"""Fascins"""	11148	protein-coding gene	gene with protein product	"""Singed, drosophila, homolog-like"", ""actin bundling protein"""	602689	"""singed (Drosophila)-like (sea urchin fascin homolog like)"", ""fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus)"""	SNL		8068206, 10783262	Standard	NM_003088		Approved	p55, FLJ38511	uc003sou.3	Q16658	OTTHUMG00000090599	ENST00000382361.3:c.1008T>C	7.37:g.5643145T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	127	61	0.480315	NM_003088	A6NI89|B2RE97|Q96IC5|Q96IH1|Q9BRF1	Silent	SNP	ENST00000382361.3	37	CCDS5342.1																																																																																			T|0.793;C|0.207	0.207	strong		0.642	FSCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207153.3	NM_003088	
NR3C1	2908	hgsc.bcm.edu	37	5	142661490	142661490	+	Silent	SNP	A	A	G	rs6196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:142661490A>G	ENST00000343796.2	-	9	3291	c.2298T>C	c.(2296-2298)aaT>aaC	p.N766N	NR3C1_ENST00000231509.3_Silent_p.N767N|NR3C1_ENST00000503201.1_Silent_p.N766N|NR3C1_ENST00000415690.2_Intron|NR3C1_ENST00000504572.1_Silent_p.N767N|NR3C1_ENST00000394464.2_Silent_p.N766N|NR3C1_ENST00000424646.2_Silent_p.N740N|NR3C1_ENST00000416954.2_Silent_p.N369N|NR3C1_ENST00000394466.2_Silent_p.N767N	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	766	Interaction with CLOCK.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	TGATATTTCCATTTGAATATT	0.303													A|||	595	0.11881	0.1929	0.1066	5008	,	,		18489	0.0873		0.1491	False		,,,				2504	0.0286				p.N767N		Atlas-SNP	.											.	NR3C1	124	.	0			c.T2301C	GRCh37	CS044090	NR3C1	S	rs6196	PASS	.	A	,,,,,,,,,,,,,	826,3580	324.2+/-298.5	80,666,1457	98.0	99.0	99.0		2298,2298,2298,2298,2298,,2301,2220,2043,2031,2007,1353,1308,1293	3.6	1.0	5	dbSNP_52	99	1320,7280	258.6+/-282.2	116,1088,3096	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NR3C1	NM_000176.2,NM_001018074.1,NM_001018075.1,NM_001018076.1,NM_001018077.1,NM_001020825.1,NM_001024094.1,NM_001204258.1,NM_001204259.1,NM_001204260.1,NM_001204261.1,NM_001204262.1,NM_001204263.1,NM_001204264.1	,,,,,,,,,,,,,	196,1754,4553	GG,GA,AA		15.3488,18.7472,16.5001	,,,,,,,,,,,,,	766/778,766/778,766/778,766/778,766/778,,767/779,740/752,681/693,677/689,669/681,451/463,436/448,431/443	142661490	2146,10860	2203	4300	6503	SO:0001819	synonymous_variant	2908	exon9			ATTTCCATTTGAA	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"""Nuclear hormone receptors"""	7978	protein-coding gene	gene with protein product		138040	"""nuclear receptor subfamily 3, group C, member 1"""	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.2298T>C	5.37:g.142661490A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	216	105	0.486111	NM_001024094	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Silent	SNP	ENST00000343796.2	37	CCDS4278.1																																																																																			A|0.852;G|0.148	0.148	strong		0.303	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1		
NPY4R	5540	hgsc.bcm.edu	37	10	47086915	47086915	+	Silent	SNP	C	C	T	rs59974223	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:47086915C>T	ENST00000395716.1	+	2	217	c.132C>T	c.(130-132)atC>atT	p.I44I	NPY4R_ENST00000374312.1_Silent_p.I44I			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	44					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										TGGTCTTCATCGTCACTTCCT	0.522																																					p.I44I		Atlas-SNP	.											.	PPYR1	54	.	0			c.C132T						PASS	.	C		589,3817		0,589,1614	238.0	209.0	219.0		132	0.5	0.5	10	dbSNP_129	219	922,7678		0,922,3378	no	coding-synonymous	PPYR1	NM_005972.4		0,1511,4992	TT,TC,CC		10.7209,13.3681,11.6177		44/376	47086915	1511,11495	2203	4300	6503	SO:0001819	synonymous_variant	5540	exon3			CTTCATCGTCACT		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"""GPCR / Class A : Neuropeptide receptors : Y"""	9329	protein-coding gene	gene with protein product		601790	"""pancreatic polypeptide receptor 1"""	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.132C>T	10.37:g.47086915C>T		Somatic	333	0	0		WXS	Illumina HiSeq	Phase_I	379	179	0.472296	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Silent	SNP	ENST00000395716.1	37	CCDS31193.1																																																																																			C|0.835;T|0.165	0.165	strong		0.522	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
LPPR2	64748	hgsc.bcm.edu	37	19	11471990	11471990	+	Silent	SNP	C	C	T	rs143046204	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11471990C>T	ENST00000251473.5	+	6	865	c.489C>T	c.(487-489)cgC>cgT	p.R163R	DKFZP761J1410_ENST00000591608.1_Silent_p.R138R	NM_001170635.1|NM_022737.2	NP_001164106.1|NP_073574.2																					CCGTGTGCCGCCCCAACTACA	0.667													c|||	31	0.0061901	0.0	0.0086	5008	,	,		15461	0.0		0.0109	False		,,,				2504	0.0143				p.R163R		Atlas-SNP	.											.	LPPR2	21	.	0			c.C489T						PASS	.		,	15,4391	23.3+/-48.9	0,15,2188	67.0	52.0	57.0		414,489	3.0	1.0	19	dbSNP_134	57	144,8454	70.7+/-133.2	0,144,4155	no	coding-synonymous,coding-synonymous	LPPR2	NM_001170635.1,NM_022737.2	,	0,159,6343	TT,TC,CC		1.6748,0.3404,1.2227	,	138/428,163/344	11471990	159,12845	2203	4299	6502	SO:0001819	synonymous_variant	0	exon6			GTGCCGCCCCAAC																												ENST00000251473.5:c.489C>T	19.37:g.11471990C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	128	50	0.390625	NM_022737		Silent	SNP	ENST00000251473.5	37	CCDS12258.1																																																																																			C|0.989;T|0.011	0.011	strong		0.667	DKFZP761J1410-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458779.1		
GTF3C6	112495	hgsc.bcm.edu	37	6	111288941	111288941	+	Missense_Mutation	SNP	T	T	C	rs41289884	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:111288941T>C	ENST00000329970.7	+	6	800	c.590T>C	c.(589-591)aTa>aCa	p.I197T	AL357515.1_ENST00000583422.1_RNA|GTF3C6_ENST00000480191.1_3'UTR	NM_138408.3	NP_612417.1	Q969F1	TF3C6_HUMAN	general transcription factor IIIC, polypeptide 6, alpha 35kDa	197					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			NS(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(87;0.00328)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|Colorectal(196;0.0466)|all_epithelial(87;0.0575)		OV - Ovarian serous cystadenocarcinoma(136;0.105)|all cancers(137;0.179)|Epithelial(106;0.186)		CTTATTGATATACCTTCTGAG	0.368													T|||	168	0.0335463	0.0008	0.0202	5008	,	,		17242	0.0119		0.0298	False		,,,				2504	0.1135				p.I197T		Atlas-SNP	.											.	GTF3C6	14	.	0			c.T590C						PASS	.	T	THR/ILE	40,4366	42.3+/-75.8	1,38,2164	93.0	96.0	95.0		590	0.0	0.0	6	dbSNP_127	95	326,8274	114.8+/-174.7	2,322,3976	yes	missense	GTF3C6	NM_138408.3	89	3,360,6140	CC,CT,TT		3.7907,0.9079,2.8141	benign	197/214	111288941	366,12640	2203	4300	6503	SO:0001583	missense	112495	exon6			TTGATATACCTTC	AK057977	CCDS5087.1	6q21	2010-03-23	2007-07-26	2007-07-26	ENSG00000155115	ENSG00000155115		"""General transcription factors"""	20872	protein-coding gene	gene with protein product		611784	"""chromosome 6 open reading frame 51"""	C6orf51		17409385	Standard	NM_138408		Approved	bA397G5.3, TFIIIC35	uc003pum.3	Q969F1	OTTHUMG00000015370	ENST00000329970.7:c.590T>C	6.37:g.111288941T>C	ENSP00000357863:p.Ile197Thr	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	238	105	0.441176	NM_138408	Q5VXN2	Missense_Mutation	SNP	ENST00000329970.7	37	CCDS5087.1	38	0.0173992673992674	2	0.0040650406504065045	6	0.016574585635359115	9	0.015734265734265736	21	0.027704485488126648	t	1.594	-0.528260	0.04112	0.009079	0.037907	ENSG00000155115	ENST00000329970	.	.	.	5.01	0.00227	0.14049	.	1.036740	0.07541	N	0.913832	T	0.05135	0.0137	N	0.17674	0.51	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35400	-0.9790	9	0.02654	T	1	-21.1238	5.3285	0.15920	0.0:0.2684:0.2183:0.5134	rs41289884;rs61733790	197	Q969F1	TF3C6_HUMAN	T	197	.	ENSP00000357863:I197T	I	+	2	0	GTF3C6	111395634	0.001000	0.12720	0.014000	0.15608	0.762000	0.43233	0.357000	0.20199	0.188000	0.20168	0.402000	0.26972	ATA	T|0.976;C|0.024	0.024	strong		0.368	GTF3C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041820.1	NM_138408	
WDR17	116966	hgsc.bcm.edu	37	4	177095773	177095773	+	Missense_Mutation	SNP	G	G	A	rs72706355	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:177095773G>A	ENST00000280190.4	+	28	3626	c.3470G>A	c.(3469-3471)cGa>cAa	p.R1157Q	WDR17_ENST00000393643.2_Missense_Mutation_p.R1133Q|WDR17_ENST00000507824.2_Missense_Mutation_p.R1132Q|WDR17_ENST00000508596.1_Missense_Mutation_p.R1118Q			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1157										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		TTTAGAGCTCGAAATGAGTTG	0.328													G|||	82	0.0163738	0.0023	0.013	5008	,	,		16285	0.002		0.0169	False		,,,				2504	0.0521				p.R1157Q		Atlas-SNP	.											WDR17,NS,carcinoma,+1,1	WDR17	198	1	0			c.G3470A						PASS	.	G	GLN/ARG,GLN/ARG	31,4375	36.8+/-68.6	0,31,2172	113.0	107.0	109.0		3470,3353	5.1	1.0	4	dbSNP_130	109	190,8410	83.1+/-145.7	3,184,4113	yes	missense,missense	WDR17	NM_170710.4,NM_181265.3	43,43	3,215,6285	AA,AG,GG		2.2093,0.7036,1.6992	probably-damaging,probably-damaging	1157/1323,1118/1284	177095773	221,12785	2203	4300	6503	SO:0001583	missense	116966	exon28			GAGCTCGAAATGA	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"""WD repeat domain containing"""	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3470G>A	4.37:g.177095773G>A	ENSP00000280190:p.Arg1157Gln	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	146	74	0.506849	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	11	0.014511873350923483	G	33	5.194203	0.94960	0.007036	0.022093	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.59364	0.27;0.27;0.27	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000002	T	0.64283	0.2584	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.99;0.99	T	0.75671	-0.3237	10	0.87932	D	0	-11.1687	18.9538	0.92650	0.0:0.0:1.0:0.0	.	1133;1118;1157	E7EP77;E7EQX0;Q8IZU2	.;.;WDR17_HUMAN	Q	1118;1133;1157;1133	ENSP00000422763:R1118Q;ENSP00000377258:R1133Q;ENSP00000280190:R1157Q	ENSP00000280190:R1157Q	R	+	2	0	WDR17	177332767	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	9.376000	0.97181	2.562000	0.86427	0.591000	0.81541	CGA	G|0.985;A|0.015	0.015	strong		0.328	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
UPF3A	65110	hgsc.bcm.edu	37	13	115067328	115067328	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:115067328G>T	ENST00000375299.3	+	9	1186	c.1130G>T	c.(1129-1131)cGg>cTg	p.R377L	UPF3A_ENST00000475218.2_3'UTR|UPF3A_ENST00000351487.5_Missense_Mutation_p.R344L	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	377					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleocytoplasmic transport (GO:0006913)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	16	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		GAGCCTGAACGGCTTTCCAGA	0.582																																					p.R377L		Atlas-SNP	.											UPF3A,colon,carcinoma,0,1	UPF3A	47	1	0			c.G1130T						scavenged	.						44.0	37.0	39.0					13																	115067328		2203	4300	6503	SO:0001583	missense	65110	exon9			CTGAACGGCTTTC	AF318575	CCDS9543.1, CCDS9544.1	13q34	2010-04-30			ENSG00000169062	ENSG00000169062			20332	protein-coding gene	gene with protein product		605530				11113196, 11163187	Standard	NM_023011		Approved	RENT3A, UPF3, HUPF3A	uc001vup.3	Q9H1J1	OTTHUMG00000017403	ENST00000375299.3:c.1130G>T	13.37:g.115067328G>T	ENSP00000364448:p.Arg377Leu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	123	2	0.0162602	NM_023011	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Missense_Mutation	SNP	ENST00000375299.3	37	CCDS9543.1	.	.	.	.	.	.	.	.	.	.	G	9.886	1.203037	0.22121	.	.	ENSG00000169062	ENST00000375299;ENST00000351487	T;T	0.80738	-1.41;1.57	5.03	-3.85	0.04243	.	0.466178	0.24666	N	0.036599	T	0.67268	0.2875	L	0.57536	1.79	0.09310	N	1	B;B	0.28713	0.082;0.22	B;B	0.22601	0.04;0.04	T	0.53697	-0.8402	9	.	.	.	-0.0311	5.6512	0.17616	0.4985:0.2406:0.2609:0.0	.	344;377	Q9H1J1-2;Q9H1J1	.;REN3A_HUMAN	L	377;344	ENSP00000364448:R377L;ENSP00000329592:R344L	.	R	+	2	0	UPF3A	114085430	0.887000	0.30362	0.000000	0.03702	0.001000	0.01503	0.590000	0.23954	-0.888000	0.03956	0.655000	0.94253	CGG	.	.	none		0.582	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2		
RIC8A	60626	hgsc.bcm.edu	37	11	210660	210660	+	Missense_Mutation	SNP	C	C	G	rs34925440	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:210660C>G	ENST00000526104.1	+	4	2160	c.816C>G	c.(814-816)caC>caG	p.H272Q	RIC8A_ENST00000325207.5_Missense_Mutation_p.H272Q|RIC8A_ENST00000527696.1_Missense_Mutation_p.H266Q			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	272					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGGAGTTCCACGGGTGAGAAT	0.587													C|||	30	0.00599042	0.0	0.0144	5008	,	,		19929	0.0		0.0159	False		,,,				2504	0.0041				p.H272Q		Atlas-SNP	.											.	RIC8A	45	.	0			c.C816G						PASS	.	C	GLN/HIS	7,4399	11.4+/-27.6	0,7,2196	81.0	78.0	79.0		816	-5.6	0.9	11	dbSNP_126	79	144,8456	68.4+/-130.8	2,140,4158	yes	missense	RIC8A	NM_021932.4	24	2,147,6354	GG,GC,CC		1.6744,0.1589,1.161	probably-damaging	272/538	210660	151,12855	2203	4300	6503	SO:0001583	missense	60626	exon4			GTTCCACGGGTGA	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"""resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"""			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069	ENST00000526104.1:c.816C>G	11.37:g.210660C>G	ENSP00000432008:p.His272Gln	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	125	70	0.56	NM_021932	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Missense_Mutation	SNP	ENST00000526104.1	37		21|21	0.009615384615384616|0.009615384615384616	0|0	0.0|0.0	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	15|15	0.01978891820580475|0.01978891820580475	C|C	16.14|16.14	3.038516|3.038516	0.55003|0.55003	0.001589|0.001589	0.016744|0.016744	ENSG00000177963|ENSG00000177963	ENST00000526104;ENST00000325207;ENST00000527696|ENST00000527728	T;T;T|.	0.42513|.	0.97;0.97;0.97|.	4.47|4.47	-5.57|-5.57	0.02521|0.02521	Armadillo-type fold (1);|.	0.047726|.	0.85682|.	N|.	0.000000|.	T|T	0.35624|0.35624	0.0938|0.0938	L|L	0.51853|0.51853	1.615|1.615	0.54753|0.54753	D|D	0.999985|0.999985	P;D;D|.	0.89917|.	0.548;1.0;1.0|.	B;D;D|.	0.97110|.	0.283;1.0;1.0|.	T|T	0.50866|0.50866	-0.8777|-0.8777	10|5	0.26408|.	T|.	0.33|.	-18.6535|-18.6535	8.7496|8.7496	0.34607|0.34607	0.0:0.5309:0.099:0.3701|0.0:0.5309:0.099:0.3701	rs34925440|rs34925440	266;272;272|.	Q9NPQ8-2;Q9NPQ8;Q9NPQ8-3|.	.;RIC8A_HUMAN;.|.	Q|R	272;272;266|167	ENSP00000432008:H272Q;ENSP00000325941:H272Q;ENSP00000434833:H266Q|.	ENSP00000325941:H272Q|.	H|T	+|+	3|2	2|0	RIC8A|RIC8A	200660|200660	0.002000|0.002000	0.14202|0.14202	0.872000|0.872000	0.34217|0.34217	0.678000|0.678000	0.39670|0.39670	-1.433000|-1.433000	0.02428|0.02428	-1.247000|-1.247000	0.02507|0.02507	-1.201000|-1.201000	0.01664|0.01664	CAC|ACG	C|0.988;G|0.012	0.012	strong		0.587	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932	
THRB	7068	hgsc.bcm.edu	37	3	24164510	24164510	+	Silent	SNP	A	A	G	rs13081063	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:24164510A>G	ENST00000356447.4	-	10	1535	c.1251T>C	c.(1249-1251)ttT>ttC	p.F417F	THRB_ENST00000416420.1_Silent_p.F417F|THRB_ENST00000396671.2_Silent_p.F417F|THRB_ENST00000280696.5_Silent_p.F432F	NM_000461.4|NM_001128177.1	NP_000452.2|NP_001121649.1	P10828	THB_HUMAN	thyroid hormone receptor, beta	417	Interaction with NR2F6.|Ligand-binding.				female courtship behavior (GO:0008050)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of female receptivity (GO:0007621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|sensory perception of sound (GO:0007605)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(2)|prostate(1)|skin(3)	19					Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	GTTTTGGCCAAAAGTGTGTCA	0.493													A|||	57	0.0113818	0.0	0.0029	5008	,	,		17842	0.0		0.0398	False		,,,				2504	0.0153				p.F417F	Melanoma(21;896 1043 15021 37958)	Atlas-SNP	.											.	THRB	52	.	0			c.T1251C						PASS	.	A	,,	37,4369	40.8+/-73.8	0,37,2166	171.0	177.0	175.0		1251,1251,1251	5.9	1.0	3	dbSNP_121	175	279,8321	105.4+/-166.3	5,269,4026	no	coding-synonymous,coding-synonymous,coding-synonymous	THRB	NM_000461.4,NM_001128176.1,NM_001128177.1	,,	5,306,6192	GG,GA,AA		3.2442,0.8398,2.4296	,,	417/462,417/462,417/462	24164510	316,12690	2203	4300	6503	SO:0001819	synonymous_variant	7068	exon10			TGGCCAAAAGTGT		CCDS2641.1	3p24.2	2013-01-16	2011-05-19		ENSG00000151090	ENSG00000151090		"""Nuclear hormone receptors"""	11799	protein-coding gene	gene with protein product	"""avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2"", ""oncogene ERBA2"", ""generalized resistance to thyroid hormone"", ""thyroid hormone receptor beta 1"""	190160	"""thyroid hormone receptor, beta (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2)"", ""pituitary resistance to thyroid hormone"", ""thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)"""	ERBA2, PRTH		1973914, 8040303	Standard	NM_000461		Approved	THRB1, THRB2, NR1A2, THR1, ERBA-BETA, GRTH	uc003ccy.4	P10828	OTTHUMG00000130478	ENST00000356447.4:c.1251T>C	3.37:g.24164510A>G		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	297	156	0.525253	NM_000461	B3KU79|P37243|Q13986|Q3KP35|Q6WGL2|Q9UD41	Silent	SNP	ENST00000356447.4	37	CCDS2641.1																																																																																			A|0.977;G|0.023	0.023	strong		0.493	THRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252877.3	NM_000461	
P2RX6	9127	hgsc.bcm.edu	37	22	21377301	21377301	+	Silent	SNP	C	C	A	rs1548411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:21377301C>A	ENST00000413302.2	+	5	682	c.534C>A	c.(532-534)ccC>ccA	p.P178P	P2RX6_ENST00000402329.3_3'UTR|P2RX6_ENST00000336296.2_Silent_p.P168P|P2RX6_ENST00000443995.3_Silent_p.P125P|P2RX6_ENST00000401443.1_Silent_p.P152P			O15547	P2RX6_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 6	178					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|channel activity (GO:0015267)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)										GTTGGTGCCCCGTGGAGAGTG	0.577													A|||	3157	0.630391	0.7587	0.67	5008	,	,		18740	0.6349		0.5358	False		,,,				2504	0.5215				p.P178P		Atlas-SNP	.											.	.	.	.	0			c.C534A						PASS	.	A	,	3215,1191	418.3+/-338.2	1193,829,181	163.0	162.0	162.0		456,534	-10.6	0.3	22	dbSNP_88	162	4505,4095	561.9+/-387.9	1201,2103,996	no	coding-synonymous,coding-synonymous	P2RX6	NM_001159554.1,NM_005446.3	,	2394,2932,1177	AA,AC,CC		47.6163,27.0313,40.6428	,	152/416,178/442	21377301	7720,5286	2203	4300	6503	SO:0001819	synonymous_variant	9127	exon5			GTGCCCCGTGGAG		CCDS13788.2, CCDS54504.1	22q11.21	2012-01-17	2008-03-28	2008-03-28	ENSG00000099957	ENSG00000099957		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8538	protein-coding gene	gene with protein product		608077	"""purinergic receptor P2X-like 1, orphan receptor"""	P2RXL1		9242461, 10591208, 8786426	Standard	NM_005446		Approved	P2XM, MGC129625, P2X6	uc010gsu.1	O15547	OTTHUMG00000150689	ENST00000413302.2:c.534C>A	22.37:g.21377301C>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	183	84	0.459016	NM_005446	F6V3D7|Q32MB6|Q58F04|Q6IC33|Q9UL50	Silent	SNP	ENST00000413302.2	37	CCDS13788.2																																																																																			C|0.383;A|0.617	0.617	strong		0.577	P2RX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319625.2	NM_005446	
FAM187B	148109	hgsc.bcm.edu	37	19	35718891	35718891	+	Nonsense_Mutation	SNP	C	C	T	rs35001809	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:35718891C>T	ENST00000324675.3	-	1	741	c.693G>A	c.(691-693)tgG>tgA	p.W231*		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	231						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						GACAGTCGAGCCACACAAATT	0.507													C|||	86	0.0171725	0.0	0.0115	5008	,	,		19197	0.001		0.0398	False		,,,				2504	0.0378				p.W231X		Atlas-SNP	.											.	FAM187B	28	.	0			c.G693A						PASS	.	C	stop/TRP	41,4365	44.6+/-78.6	0,41,2162	82.0	68.0	73.0		693	3.8	0.8	19	dbSNP_126	73	252,8348	98.6+/-160.1	3,246,4051	yes	stop-gained	FAM187B	NM_152481.1		3,287,6213	TT,TC,CC		2.9302,0.9305,2.2528		231/370	35718891	293,12713	2203	4300	6503	SO:0001587	stop_gained	148109	exon1			GTCGAGCCACACA	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558			26366	protein-coding gene	gene with protein product			"""transmembrane protein 162"""	TMEM162			Standard	NM_152481		Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.693G>A	19.37:g.35718891C>T	ENSP00000323355:p.Trp231*	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	202	85	0.420792	NM_152481	Q8N7G6	Nonsense_Mutation	SNP	ENST00000324675.3	37	CCDS12448.1	33	0.01510989010989011	1	0.0020325203252032522	2	0.0055248618784530384	1	0.0017482517482517483	29	0.03825857519788918	C	15.73	2.918681	0.52546	0.009305	0.029302	ENSG00000177558	ENST00000324675	.	.	.	4.91	3.85	0.44370	.	0.693744	0.12668	N	0.449031	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-6.6331	10.6862	0.45843	0.1915:0.8085:0.0:0.0	rs35001809;rs61744928	.	.	.	X	231	.	ENSP00000323355:W231X	W	-	3	0	FAM187B	40410731	0.905000	0.30787	0.764000	0.31436	0.016000	0.09150	1.334000	0.33827	1.142000	0.42291	0.655000	0.94253	TGG	C|0.978;T|0.022	0.022	strong		0.507	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481	
CATSPERG	57828	hgsc.bcm.edu	37	19	38861333	38861333	+	Silent	SNP	G	G	A	rs1052375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:38861333G>A	ENST00000409235.3	+	29	3496	c.3381G>A	c.(3379-3381)ccG>ccA	p.P1127P	CATSPERG_ENST00000410018.1_Silent_p.P1087P|CATSPERG_ENST00000215069.4_3'UTR	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	1127					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						CGAGCATGCCGTCTCTGAGAC	0.537													G|||	1351	0.269768	0.0363	0.3228	5008	,	,		20493	0.2262		0.5249	False		,,,				2504	0.3303				p.P1127P		Atlas-SNP	.											.	CATSPERG	121	.	0			c.G3381A						PASS	.	G		525,3881	239.6+/-250.7	33,459,1711	155.0	139.0	144.0		3381	-7.6	0.0	19	dbSNP_86	144	4545,4055	594.8+/-393.4	1210,2125,965	no	coding-synonymous	CATSPERG	NM_021185.4		1243,2584,2676	AA,AG,GG		47.1512,11.9156,38.982		1127/1160	38861333	5070,7936	2203	4300	6503	SO:0001819	synonymous_variant	57828	exon29			CATGCCGTCTCTG	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"""chromosome 19 open reading frame 15"", ""cation channel, sperm-associated, gamma"""	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.3381G>A	19.37:g.38861333G>A		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	178	176	0.988764	NM_021185	A6NEG6|Q659E1	Silent	SNP	ENST00000409235.3	37	CCDS12514.2																																																																																			G|0.657;A|0.343	0.343	strong		0.537	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185	
TDGF1	6997	hgsc.bcm.edu	37	3	46622629	46622629	+	Silent	SNP	T	T	C	rs112928637	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:46622629T>C	ENST00000296145.5	+	6	1189	c.456T>C	c.(454-456)ctT>ctC	p.L152L	LRRC2_ENST00000296144.3_5'Flank|TDGF1_ENST00000542931.1_Silent_p.L136L	NM_003212.3	NP_003203.1	P13385	TDGF1_HUMAN	teratocarcinoma-derived growth factor 1	152					activation of MAPK activity (GO:0000187)|anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle cell differentiation (GO:0055007)|cell differentiation (GO:0030154)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-6 (GO:0071354)|cellular response to tumor necrosis factor (GO:0071356)|embryo development (GO:0009790)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of signal transduction (GO:0009966)|vasculogenesis (GO:0001570)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	growth factor activity (GO:0008083)|receptor binding (GO:0005102)			cervix(2)|endometrium(1)|kidney(1)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0173)|Kidney(197;0.0204)		CAGATGGCCTTGTGATGGATG	0.483													T|||	90	0.0179712	0.0083	0.0187	5008	,	,		21615	0.0278		0.0298	False		,,,				2504	0.0082				p.L152L		Atlas-SNP	.											.	TDGF1	17	.	0			c.T456C						PASS	.	T	,	94,4312	76.8+/-115.0	0,94,2109	109.0	91.0	97.0		408,456	-2.5	0.4	3	dbSNP_132	97	229,8371	93.5+/-155.5	9,211,4080	no	coding-synonymous,coding-synonymous	TDGF1	NM_001174136.1,NM_003212.3	,	9,305,6189	CC,CT,TT		2.6628,2.1335,2.4835	,	136/173,152/189	46622629	323,12683	2203	4300	6503	SO:0001819	synonymous_variant	6997	exon6			TGGCCTTGTGATG	M96955	CCDS2742.1, CCDS54575.1	3p21.31	2012-10-03			ENSG00000241186	ENSG00000241186			11701	protein-coding gene	gene with protein product		187395				1882841, 10393436	Standard	NM_003212		Approved	CRIPTO, CR, Cripto-1	uc021wxd.1	P13385	OTTHUMG00000133482	ENST00000296145.5:c.456T>C	3.37:g.46622629T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_003212	Q8TCC1	Silent	SNP	ENST00000296145.5	37	CCDS2742.1																																																																																			T|0.972;C|0.028	0.028	strong		0.483	TDGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257378.2	NM_003212	
CDH17	1015	hgsc.bcm.edu	37	8	95158259	95158259	+	Silent	SNP	G	G	A	rs2251734	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:95158259G>A	ENST00000027335.3	-	15	2188	c.2064C>T	c.(2062-2064)ttC>ttT	p.F688F	CDH17_ENST00000450165.2_Silent_p.F688F|CDH17_ENST00000441892.2_Silent_p.F474F	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	688	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			CAGTAGCCTCGAAAATGAGAC	0.483													G|||	1563	0.312101	0.4523	0.3804	5008	,	,		18213	0.1597		0.2604	False		,,,				2504	0.2843				p.F688F		Atlas-SNP	.											.	CDH17	119	.	0			c.C2064T						PASS	.	G	,	1847,2559	537.1+/-374.7	390,1067,746	102.0	90.0	94.0		2064,2064	-11.7	0.0	8	dbSNP_100	94	2410,6190	398.7+/-346.2	358,1694,2248	no	coding-synonymous,coding-synonymous	CDH17	NM_001144663.1,NM_004063.3	,	748,2761,2994	AA,AG,GG		28.0233,41.9201,32.731	,	688/833,688/833	95158259	4257,8749	2203	4300	6503	SO:0001819	synonymous_variant	1015	exon15			AGCCTCGAAAATG	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.2064C>T	8.37:g.95158259G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	255	137	0.537255	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			G|0.692;A|0.308	0.308	strong		0.483	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
IFT88	8100	hgsc.bcm.edu	37	13	21189941	21189941	+	Missense_Mutation	SNP	G	G	A	rs2442455	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:21189941G>A	ENST00000319980.6	+	16	1476	c.1149G>A	c.(1147-1149)atG>atA	p.M383I	IFT88_ENST00000537103.1_Missense_Mutation_p.M355I|IFT88_ENST00000351808.5_Missense_Mutation_p.M374I|IFT88_ENST00000382778.4_Missense_Mutation_p.M383I|IFT88_ENST00000461115.1_3'UTR	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	383			M -> I (in dbSNP:rs2442455). {ECO:0000269|PubMed:15489334}.		anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		GGAAAGCCATGGCAGAAAAAT	0.289													G|||	651	0.129992	0.2776	0.134	5008	,	,		15594	0.0		0.1382	False		,,,				2504	0.0532				p.M383I		Atlas-SNP	.											.	IFT88	83	.	0			c.G1149A						PASS	.	G	ILE/MET,ILE/MET	1094,3312	386.3+/-326.1	130,834,1239	79.0	89.0	85.0		1122,1149	4.7	1.0	13	dbSNP_100	85	1264,7328	250.1+/-277.1	95,1074,3127	yes	missense,missense	IFT88	NM_006531.3,NM_175605.3	10,10	225,1908,4366	AA,AG,GG		14.7114,24.8298,18.1413	benign,benign	374/825,383/834	21189941	2358,10640	2203	4296	6499	SO:0001583	missense	8100	exon16			AGCCATGGCAGAA	AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"""Intraflagellar transport homologs"", ""Tetratricopeptide (TTC) repeat domain containing"""	20606	protein-coding gene	gene with protein product	"""polaris homolog"""	600595	"""tetratricopeptide repeat domain 10"", ""intraflagellar transport 88 homolog (Chlamydomonas)"""	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.1149G>A	13.37:g.21189941G>A	ENSP00000323580:p.Met383Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	56	20	0.357143	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Missense_Mutation	SNP	ENST00000319980.6	37	CCDS31944.1	289	0.13232600732600733	136	0.2764227642276423	54	0.14917127071823205	0	0.0	99	0.13060686015831136	G	14.05	2.419414	0.42918	0.248298	0.147114	ENSG00000032742	ENST00000382778;ENST00000389374;ENST00000351808;ENST00000319980;ENST00000537103	T;T;T;T	0.28895	1.59;1.59;1.59;1.6	5.59	4.74	0.60224	.	0.243577	0.43110	D	0.000611	T	0.00012	0.0000	N	0.19112	0.55	0.28726	P	0.9027585	B;B;B;B	0.17667	0.001;0.002;0.0;0.023	B;B;B;B	0.11329	0.001;0.003;0.0;0.006	T	0.24728	-1.0152	9	0.35671	T	0.21	-20.9649	9.7533	0.40490	0.1501:0.0:0.8499:0.0	rs2442455;rs17852821;rs52832974;rs58218357;rs2442455	355;383;181;383	F5H6C2;E7EW86;Q6MZX0;Q13099	.;.;.;IFT88_HUMAN	I	383;246;374;383;355	ENSP00000372228:M383I;ENSP00000261632:M374I;ENSP00000323580:M383I;ENSP00000437719:M355I	ENSP00000323580:M383I	M	+	3	0	IFT88	20087941	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.179000	0.50887	2.625000	0.88918	0.650000	0.86243	ATG	G|0.837;A|0.163	0.163	strong		0.289	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531	
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194878	18194878	+	Missense_Mutation	SNP	T	T	G	rs2445180	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18194878T>G	ENST00000314254.3	+	1	495	c.75T>G	c.(73-75)aaT>aaG	p.N25K	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	25			N -> K (in dbSNP:rs2445180). {ECO:0000269|PubMed:11850634}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CTTGCTACAATCAGACCCTGA	0.562													T|||	1654	0.330272	0.2557	0.3415	5008	,	,		20734	0.4375		0.3072	False		,,,				2504	0.3364				p.N25K		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.T75G						PASS	.	T	LYS/ASN	1082,3316	391.2+/-328.0	130,822,1247	177.0	163.0	167.0		75	-4.8	0.0	11	dbSNP_100	167	2448,6138	405.3+/-348.4	338,1772,2183	no	missense	MRGPRX4	NM_054032.3	94	468,2594,3430	GG,GT,TT		28.5115,24.6021,27.1873	benign	25/323	18194878	3530,9454	2199	4293	6492	SO:0001583	missense	117196	exon1			CTACAATCAGACC	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.75T>G	11.37:g.18194878T>G	ENSP00000314042:p.Asn25Lys	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	188	92	0.489362	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	37	CCDS7831.1	749	0.34294871794871795	114	0.23170731707317074	120	0.3314917127071823	274	0.479020979020979	241	0.3179419525065963	T	0.005	-2.225888	0.00283	0.246021	0.285115	ENSG00000179817	ENST00000314254	T	0.64085	-0.08	2.41	-4.82	0.03171	.	4.447680	0.00424	N	0.000078	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22661	-1.0210	9	0.05833	T	0.94	.	4.5651	0.12180	0.5502:0.0:0.1701:0.2797	rs2445180;rs2445180	25	Q96LA9	MRGX4_HUMAN	K	25	ENSP00000314042:N25K	ENSP00000314042:N25K	N	+	3	2	MRGPRX4	18151454	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.930000	0.03972	-2.245000	0.00705	-1.338000	0.01255	AAT	T|0.706;G|0.294	0.294	strong		0.562	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
TRABD2A	129293	hgsc.bcm.edu	37	2	85097590	85097590	+	Missense_Mutation	SNP	C	C	T	rs1863772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:85097590C>T	ENST00000409520.2	-	2	470	c.428G>A	c.(427-429)cGc>cAc	p.R143H	TRABD2A_ENST00000409133.1_Missense_Mutation_p.R143H|TRABD2A_ENST00000335459.5_Missense_Mutation_p.R143H	NM_001277053.1	NP_001263982.1	Q86V40	TIKI1_HUMAN	TraB domain containing 2A	143			R -> H (in dbSNP:rs1863772). {ECO:0000269|PubMed:15489334}.		head development (GO:0060322)|metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|Wnt-protein binding (GO:0017147)										CCCCTTGCCGCGCTGGTCTGG	0.577													C|||	123	0.0245607	0.0045	0.013	5008	,	,		20287	0.003		0.0527	False		,,,				2504	0.0532				p.S143Y		Atlas-SNP	.											C2orf89_ENST00000335459,bladder,carcinoma,+1,2	.	.	2	0			c.C428A						scavenged	.	C	HIS/ARG	32,4278		1,30,2124	70.0	75.0	73.0		428	2.5	0.2	2	dbSNP_92	73	340,8178		5,330,3924	yes	missense	C2orf89	NM_001080824.1	29	6,360,6048	TT,TC,CC		3.9915,0.7425,2.8999	probably-damaging	143/457	85097590	372,12456	2155	4259	6414	SO:0001583	missense	129293	exon2			TTGCCGCGCTGGT	BC049209	CCDS46349.1, CCDS62946.1	2p11.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000186854	ENSG00000186854			27013	protein-coding gene	gene with protein product		614912	"""chromosome 2 open reading frame 89"""	C2orf89		12477932	Standard	NM_001080824		Approved		uc010ysl.3	Q86V40	OTTHUMG00000152922	ENST00000409520.2:c.428G>A	2.37:g.85097590C>T	ENSP00000387075:p.Arg143His	Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_001080824	B4DKK8|I6UMB9	Missense_Mutation	SNP	ENST00000409520.2	37		43	0.019688644688644688	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	37	0.048812664907651716	C	17.63	3.437203	0.62955	0.007425	0.039915	ENSG00000186854	ENST00000335459;ENST00000409520;ENST00000409133	T;T;T	0.15256	2.44;2.44;2.44	3.43	2.55	0.30701	.	0.094831	0.41500	D	0.000875	T	0.07728	0.0194	.	.	.	0.36341	D	0.859492	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.987;0.996	T	0.09015	-1.0694	9	0.72032	D	0.01	.	8.3407	0.32241	0.0:0.8776:0.0:0.1224	rs1863772;rs52806347;rs1863772	143;143;143	Q86V40;C9IYB5;Q86V40-2	CB089_HUMAN;.;.	H	143	ENSP00000335004:R143H;ENSP00000387075:R143H;ENSP00000387183:R143H	ENSP00000335004:R143H	R	-	2	0	C2orf89	84951101	0.968000	0.33430	0.249000	0.24280	0.730000	0.41778	3.457000	0.53007	0.660000	0.30964	0.462000	0.41574	CGC	C|0.979;T|0.021	0.021	strong		0.577	TRABD2A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001080824	
ATP8B3	148229	hgsc.bcm.edu	37	19	1796166	1796166	+	Missense_Mutation	SNP	C	C	T	rs8100856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1796166C>T	ENST00000310127.6	-	17	2090	c.1852G>A	c.(1852-1854)Gtc>Atc	p.V618I	ATP8B3_ENST00000539485.1_Missense_Mutation_p.V618I|ATP8B3_ENST00000525591.1_Missense_Mutation_p.V571I	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	618			V -> I (in dbSNP:rs8100856).		binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGATCGTGACGGTGTCCTGG	0.652											OREG0025127	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	1334	0.266374	0.1362	0.3617	5008	,	,		15906	0.5784		0.1451	False		,,,				2504	0.1779				p.V618I		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G1852A						PASS	.	T	ILE/VAL,ILE/VAL	553,3517		34,485,1516	48.0	51.0	50.0		1711,1852	3.8	1.0	19	dbSNP_116	50	1261,7117		104,1053,3032	yes	missense,missense	ATP8B3	NM_001178002.1,NM_138813.2	29,29	138,1538,4548	TT,TC,CC		15.0513,13.5872,14.5726	benign,benign	571/1264,618/1301	1796166	1814,10634	2035	4189	6224	SO:0001583	missense	148229	exon17			TCGTGACGGTGTC	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.1852G>A	19.37:g.1796166C>T	ENSP00000311336:p.Val618Ile	Somatic	139	0	0	598	WXS	Illumina HiSeq	Phase_I	158	91	0.575949	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	631	0.2889194139194139	67	0.13617886178861788	116	0.32044198895027626	328	0.5734265734265734	120	0.158311345646438	T	1.184	-0.637173	0.03557	0.135872	0.150513	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.56776	0.44;0.44;0.44	4.8	3.77	0.43336	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.182934	0.48286	N	0.000190	T	0.00012	0.0000	N	0.00966	-1.09	0.45899	P	0.0012569999999999526	B;B	0.09022	0.001;0.002	B;B	0.10450	0.0;0.005	T	0.47995	-0.9073	9	0.02654	T	1	.	8.725	0.34463	0.0:0.1598:0.0:0.8402	rs8100856;rs57162774;rs8100856	618;571	O60423;Q7Z485	AT8B3_HUMAN;.	I	618;618;571	ENSP00000311336:V618I;ENSP00000443574:V618I;ENSP00000437115:V571I	ENSP00000311336:V618I	V	-	1	0	ATP8B3	1747166	1.000000	0.71417	0.980000	0.43619	0.260000	0.26232	1.856000	0.39389	0.281000	0.22233	-0.361000	0.07541	GTC	C|0.735;N|0.000	.	strong		0.652	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
EMID1	129080	hgsc.bcm.edu	37	22	29629605	29629605	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29629605C>T	ENST00000404820.3	+	10	1043	c.916C>T	c.(916-918)Ccc>Tcc	p.P306S	EMID1_ENST00000404755.3_Missense_Mutation_p.P306S|EMID1_ENST00000334018.6_Missense_Mutation_p.P306S|EMID1_ENST00000484039.1_3'UTR			Q96A84	EMID1_HUMAN	EMI domain containing 1	304	Collagen-like.					collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)|skin(3)	12						TTTTCCAGGTCCCCCTGGGCC	0.542																																					p.P306S		Atlas-SNP	.											EMID1,NS,malignant_melanoma,0,1	EMID1	33	1	0			c.C916T						scavenged	.						135.0	117.0	123.0					22																	29629605		2203	4300	6503	SO:0001583	missense	129080	exon10			CCAGGTCCCCCTG	AJ416090	CCDS33630.1	22q12.2	2009-08-04			ENSG00000186998	ENSG00000186998		"""EMI domain containing"""	18036	protein-coding gene	gene with protein product	"""emilin and multimerin-domain containing protein 1"", ""putative emu1"""	608926				12221002	Standard	NM_001267895		Approved	EMU1, hEmu1, EMI5	uc003aem.4	Q96A84	OTTHUMG00000151013	ENST00000404820.3:c.916C>T	22.37:g.29629605C>T	ENSP00000384452:p.Pro306Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	195	3	0.0153846	NM_133455	B0QYK6|Q6ICG1|Q86SS7	Missense_Mutation	SNP	ENST00000404820.3	37		.	.	.	.	.	.	.	.	.	.	C	22.5	4.299261	0.81025	.	.	ENSG00000186998	ENST00000334018;ENST00000404755;ENST00000404820	D;D;D	0.96587	-3.83;-3.83;-4.06	5.12	5.12	0.69794	.	0.392300	0.19128	N	0.121997	D	0.97062	0.9040	M	0.64404	1.975	0.54753	D	0.999989	P;D;P;P	0.89917	0.939;1.0;0.939;0.925	P;D;P;P	0.72982	0.666;0.979;0.666;0.536	D	0.95364	0.8458	10	0.14656	T	0.56	-6.5843	14.0162	0.64525	0.0:1.0:0.0:0.0	.	306;306;304;306	B0QYK4;B0QYK5;Q96A84;Q96A84-3	.;.;EMID1_HUMAN;.	S	306	ENSP00000335481:P306S;ENSP00000385414:P306S;ENSP00000384452:P306S	ENSP00000335481:P306S	P	+	1	0	EMID1	27959605	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.984000	0.63838	2.390000	0.81377	0.561000	0.74099	CCC	.	.	none		0.542	EMID1-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321075.1	NM_133455	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735106	55735106	+	Silent	SNP	A	A	G	rs61896163	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55735106A>G	ENST00000312345.2	-	1	884	c.834T>C	c.(832-834)ccT>ccC	p.P278P		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					TATATATAATAGGATTCAAAG	0.338													G|||	191	0.038139	0.0129	0.0389	5008	,	,		18514	0.001		0.0934	False		,,,				2504	0.0532				p.P278P		Atlas-SNP	.											OR10AG1,NS,carcinoma,-2,1	OR10AG1	100	1	0			c.T834C						PASS	.	G		107,4295	809.1+/-416.0	3,101,2097	56.0	62.0	60.0		834	-4.3	0.0	11	dbSNP_129	60	691,7901	785.0+/-407.6	34,623,3639	no	coding-synonymous	OR10AG1	NM_001005491.1		37,724,5736	GG,GA,AA		8.0424,2.4307,6.1413		278/302	55735106	798,12196	2201	4296	6497	SO:0001819	synonymous_variant	282770	exon1			TATAATAGGATTC	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.834T>C	11.37:g.55735106A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	187	91	0.486631	NM_001005491	B2RNH4|Q6IEU3	Silent	SNP	ENST00000312345.2	37	CCDS31514.1																																																																																			A|0.948;G|0.052	0.052	strong		0.338	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
GPR173	54328	hgsc.bcm.edu	37	X	53106865	53106865	+	Silent	SNP	C	C	T	rs11091720	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:53106865C>T	ENST00000332582.4	+	2	1553	c.1062C>T	c.(1060-1062)caC>caT	p.H354H		NM_018969.5	NP_061842.1	Q9NS66	GP173_HUMAN	G protein-coupled receptor 173	354					negative regulation of neuron migration (GO:2001223)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|gonadotropin-releasing hormone receptor activity (GO:0004968)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)	16						TGAGGACTCACGCCCCCTGCT	0.602													C|||	1132	0.299868	0.4281	0.1167	3775	,	,		14293	0.1518		0.159	False		,,,				2504	0.1759				p.H354H		Atlas-SNP	.											.	GPR173	66	.	0			c.C1062T						PASS	.	C		1912,1922		414,788,296,430,274	41.0	36.0	38.0		1062	-5.3	0.1	X	dbSNP_120	38	1283,5443		93,717,380,1618,1490	no	coding-synonymous	GPR173	NM_018969.5		507,1505,676,2048,1764	TT,TC,T,CC,C		19.0752,49.8696,30.2557		354/374	53106865	3195,7365	2202	4298	6500	SO:0001819	synonymous_variant	54328	exon2			GACTCACGCCCCC	AB040801	CCDS14349.1	Xp11	2012-08-21	2006-02-15		ENSG00000184194	ENSG00000184194		"""GPCR / Class A : Orphans"""	18186	protein-coding gene	gene with protein product		300253	"""G-protein coupled receptor 173"", ""G protein coupled receptor 173"""			10833454	Standard	NM_018969		Approved	SREB3	uc004dru.3	Q9NS66	OTTHUMG00000021596	ENST00000332582.4:c.1062C>T	X.37:g.53106865C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	88	58	0.659091	NM_018969	B1B0A5	Silent	SNP	ENST00000332582.4	37	CCDS14349.1																																																																																			C|0.687;T|0.313	0.313	strong		0.602	GPR173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056717.2	NM_018969	
RTL1	388015	hgsc.bcm.edu	37	14	101348584	101348584	+	Missense_Mutation	SNP	C	C	G	rs11623267	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:101348584C>G	ENST00000534062.1	-	1	2600	c.2542G>C	c.(2542-2544)Gag>Cag	p.E848Q	MIR136_ENST00000385207.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	848			E -> Q (in dbSNP:rs11623267).		multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TCTTGCTCCTCGACTCCCCAG	0.612													C|||	1006	0.200879	0.0915	0.1455	5008	,	,		17756	0.3482		0.2654	False		,,,				2504	0.1697				p.E848Q		Atlas-SNP	.											RTL1,NS,carcinoma,0,1	RTL1	120	1	0			c.G2542C						PASS	.						27.0	27.0	27.0					14																	101348584		692	1591	2283	SO:0001583	missense	388015	exon1			GCTCCTCGACTCC		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.2542G>C	14.37:g.101348584C>G	ENSP00000435342:p.Glu848Gln	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	37	CCDS53910.1	519	0.23763736263736263	42	0.08536585365853659	62	0.1712707182320442	205	0.3583916083916084	210	0.2770448548812665	C	11.41	1.629661	0.28978	.	.	ENSG00000254656	ENST00000534062	T	0.52526	0.66	3.33	3.33	0.38152	.	0.294433	0.19232	N	0.119389	T	0.00012	0.0000	L	0.56340	1.77	0.34432	P	0.30138699999999996	D	0.57571	0.98	P	0.53912	0.737	T	0.37888	-0.9686	9	0.34782	T	0.22	.	12.9629	0.58468	0.0:1.0:0.0:0.0	rs11623267;rs58725312;rs11623267	848	E9PKS8	.	Q	848	ENSP00000435342:E848Q	ENSP00000435342:E848Q	E	-	1	0	RTL1	100418337	0.992000	0.36948	0.816000	0.32577	0.297000	0.27493	3.624000	0.54231	2.180000	0.69256	0.561000	0.74099	GAG	C|0.751;G|0.249	0.249	strong		0.612	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
STAB2	55576	hgsc.bcm.edu	37	12	104100617	104100617	+	Silent	SNP	C	C	T	rs697212	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:104100617C>T	ENST00000388887.2	+	38	4248	c.4044C>T	c.(4042-4044)tgC>tgT	p.C1348C		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GCCAGCCCTGCCCAGGGAATG	0.547													C|||	2158	0.430911	0.1203	0.3256	5008	,	,		20375	0.747		0.504	False		,,,				2504	0.5245				p.C1348C		Atlas-SNP	.											.	STAB2	370	.	0			c.C4044T						PASS	.	C		862,3544	338.1+/-305.1	88,686,1429	126.0	117.0	120.0		4044	3.5	1.0	12	dbSNP_86	120	4234,4366	573.2+/-389.8	1044,2146,1110	no	coding-synonymous	STAB2	NM_017564.9		1132,2832,2539	TT,TC,CC		49.2326,19.5642,39.1819		1348/2552	104100617	5096,7910	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon38			GCCCTGCCCAGGG	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.4044C>T	12.37:g.104100617C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	232	230	0.991379	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			T|0.403;G|0.003	0.403	strong		0.547	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
PKD1L1	168507	hgsc.bcm.edu	37	7	47920345	47920345	+	Silent	SNP	G	G	A	rs62447081	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:47920345G>A	ENST00000289672.2	-	21	3551	c.3501C>T	c.(3499-3501)taC>taT	p.Y1167Y		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1167	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CTTGCAGGACGTACGTCTCTC	0.463													g|||	1703	0.340056	0.59	0.3429	5008	,	,		19115	0.0952		0.2932	False		,,,				2504	0.3006				p.Y1167Y		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C3501T						PASS	.	A		2416,1990	616.4+/-392.8	651,1114,438	214.0	165.0	182.0		3501	-5.1	0.0	7	dbSNP_129	182	2442,6158	403.4+/-347.8	342,1758,2200	no	coding-synonymous	PKD1L1	NM_138295.3		993,2872,2638	AA,AG,GG		28.3953,45.1657,37.352		1167/2850	47920345	4858,8148	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon21			CAGGACGTACGTC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.3501C>T	7.37:g.47920345G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	124	58	0.467742	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			G|0.645;A|0.355	0.355	strong		0.463	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
SLC38A1	81539	hgsc.bcm.edu	37	12	46622959	46622959	+	Silent	SNP	T	T	C	rs61928115	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:46622959T>C	ENST00000398637.5	-	5	985	c.291A>G	c.(289-291)gcA>gcG	p.A97A	SLC38A1_ENST00000552197.1_Silent_p.A97A|SLC38A1_ENST00000546893.1_Silent_p.A97A|SLC38A1_ENST00000439706.1_Silent_p.A97A|SLC38A1_ENST00000549633.1_5'UTR|SLC38A1_ENST00000549049.1_Silent_p.A97A	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	97					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)			NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			TTCCAGTGTTTGCCAGGGCAA	0.408													T|||	42	0.00838658	0.0023	0.0101	5008	,	,		16884	0.0		0.0278	False		,,,				2504	0.0041				p.A97A		Atlas-SNP	.											.	SLC38A1	58	.	0			c.A291G						PASS	.	T	,	15,3751		0,15,1868	57.0	52.0	54.0		291,291	-1.7	1.0	12	dbSNP_129	54	215,7997		2,211,3893	no	coding-synonymous,coding-synonymous	SLC38A1	NM_001077484.1,NM_030674.3	,	2,226,5761	CC,CT,TT		2.6181,0.3983,1.9202	,	97/488,97/488	46622959	230,11748	1883	4106	5989	SO:0001819	synonymous_variant	81539	exon5			AGTGTTTGCCAGG	AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"""Solute carriers"""	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.291A>G	12.37:g.46622959T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_030674	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Silent	SNP	ENST00000398637.5	37	CCDS41774.1																																																																																			T|0.985;C|0.015	0.015	strong		0.408	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2		
PRUNE2	158471	hgsc.bcm.edu	37	9	79318367	79318367	+	Missense_Mutation	SNP	T	T	C	rs4745571	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:79318367T>C	ENST00000376718.3	-	9	8285	c.8162A>G	c.(8161-8163)aAt>aGt	p.N2721S	PRUNE2_ENST00000428286.1_Missense_Mutation_p.N2362S	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2721				N -> S (in Ref. 4; BAD93351 and 6; BAA20822). {ECO:0000305}.	apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TTCCCATTCATTGTCATGGGT	0.527													T|||	659	0.131589	0.0333	0.2666	5008	,	,		14803	0.1716		0.166	False		,,,				2504	0.092				p.N2721S		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A8162G						PASS	.	T	SER/ASN	180,2956		5,170,1393	110.0	89.0	96.0		8162	0.6	1.0	9	dbSNP_111	96	1217,5947		105,1007,2470	yes	missense	PRUNE2	NM_015225.2	46	110,1177,3863	CC,CT,TT		16.9877,5.7398,13.5631	benign	2721/3089	79318367	1397,8903	1568	3582	5150	SO:0001583	missense	158471	exon9			CATTCATTGTCAT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.8162A>G	9.37:g.79318367T>C	ENSP00000365908:p.Asn2721Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	348	0.15934065934065933	16	0.032520325203252036	91	0.2513812154696133	114	0.1993006993006993	127	0.16754617414248021	T	11.11	1.542186	0.27563	0.057398	0.169877	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.53857	0.6;0.62	5.6	0.607	0.17564	.	0.313274	0.27782	N	0.017863	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	0.999999999046641	B;P	0.34864	0.42;0.473	B;B	0.29077	0.098;0.091	T	0.18085	-1.0348	9	0.18710	T	0.47	-8.8714	9.364	0.38212	0.0:0.4701:0.0:0.5299	rs4745571;rs57277953;rs4745571	2721;2721	Q8WUY3-3;Q8WUY3	.;PRUN2_HUMAN	S	2721;2362;2720	ENSP00000365908:N2721S;ENSP00000397425:N2362S	ENSP00000365908:N2721S	N	-	2	0	PRUNE2	78508187	0.997000	0.39634	0.996000	0.52242	0.619000	0.37552	0.440000	0.21592	-0.121000	0.11787	-0.342000	0.07992	AAT	T|0.854;C|0.146	0.146	strong		0.527	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
C2orf54	79919	hgsc.bcm.edu	37	2	241834944	241834944	+	Silent	SNP	T	T	C	rs4468809	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241834944T>C	ENST00000388934.4	-	1	629	c.471A>G	c.(469-471)gtA>gtG	p.V157V		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	157										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		CGATGGCTGCTACCAGCAGGT	0.607													C|||	2640	0.527157	0.7806	0.3473	5008	,	,		23599	0.4405		0.5179	False		,,,				2504	0.411				p.V157V		Atlas-SNP	.											.	C2orf54	14	.	0			c.A471G						PASS	.	C		3201,1197		1185,831,183	21.0	24.0	23.0		471	3.5	1.0	2	dbSNP_111	23	4222,4364		1072,2078,1143	no	coding-synonymous	C2orf54	NM_001085437.1		2257,2909,1326	CC,CT,TT		49.1731,27.2169,42.8296		157/448	241834944	7423,5561	2199	4293	6492	SO:0001819	synonymous_variant	79919	exon1			GGCTGCTACCAGC	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.471A>G	2.37:g.241834944T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	37	CCDS42839.1																																																																																			T|0.497;C|0.503	0.503	strong		0.607	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
PTPRO	5800	hgsc.bcm.edu	37	12	15679120	15679120	+	Silent	SNP	C	C	A	rs6488782	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:15679120C>A	ENST00000281171.4	+	12	2418	c.2088C>A	c.(2086-2088)ggC>ggA	p.G696G	PTPRO_ENST00000348962.2_Silent_p.G696G	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	696	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				TGCCTCCAGGCGACATCTATA	0.443													C|||	2019	0.403155	0.5635	0.5086	5008	,	,		19039	0.127		0.4235	False		,,,				2504	0.3753				p.G696G		Atlas-SNP	.											.	PTPRO	148	.	0			c.C2088A						PASS	.	C	,	2332,2074	605.2+/-390.5	603,1126,474	142.0	128.0	133.0		2088,2088	1.2	1.0	12	dbSNP_116	133	3465,5135	508.5+/-377.1	690,2085,1525	no	coding-synonymous,coding-synonymous	PTPRO	NM_002848.3,NM_030667.2	,	1293,3211,1999	AA,AC,CC		40.2907,47.0722,44.5717	,	696/1189,696/1217	15679120	5797,7209	2203	4300	6503	SO:0001819	synonymous_variant	5800	exon12			TCCAGGCGACATC	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9678	protein-coding gene	gene with protein product	"""osteoclastic transmembrane protein-tyrosine phosphatase"""	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.2088C>A	12.37:g.15679120C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Silent	SNP	ENST00000281171.4	37	CCDS8675.1																																																																																			C|0.579;A|0.421	0.421	strong		0.443	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1		
GCC2	9648	hgsc.bcm.edu	37	2	109106381	109106381	+	Silent	SNP	A	A	G	rs12104502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:109106381A>G	ENST00000309863.6	+	18	4854	c.4140A>G	c.(4138-4140)caA>caG	p.Q1380Q		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	1380					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						CTGAACTTCAAACATTGCAGT	0.383													A|||	2286	0.45647	0.1679	0.5879	5008	,	,		17454	0.8899		0.3757	False		,,,				2504	0.3896				p.Q1380Q		Atlas-SNP	.											.	GCC2	129	.	0			c.A4140G						PASS	.	A		970,3436	362.6+/-316.2	101,768,1334	66.0	60.0	62.0		4140	-2.3	0.0	2	dbSNP_120	62	3495,5105	510.0+/-377.4	714,2067,1519	no	coding-synonymous	GCC2	NM_181453.3		815,2835,2853	GG,GA,AA		40.6395,22.0154,34.3303		1380/1685	109106381	4465,8541	2203	4300	6503	SO:0001819	synonymous_variant	9648	exon18			ACTTCAAACATTG	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.4140A>G	2.37:g.109106381A>G		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	232	112	0.482759	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Silent	SNP	ENST00000309863.6	37	CCDS33268.1																																																																																			A|0.618;G|0.382	0.382	strong		0.383	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635	
MARCH7	64844	hgsc.bcm.edu	37	2	160599717	160599717	+	Missense_Mutation	SNP	C	C	G	rs17813964	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160599717C>G	ENST00000259050.4	+	3	421	c.299C>G	c.(298-300)aCt>aGt	p.T100S	MARCH7_ENST00000539065.1_Missense_Mutation_p.T100S|MARCH7_ENST00000473749.1_3'UTR|MARCH7_ENST00000409175.1_Missense_Mutation_p.T100S|MARCH7_ENST00000409591.1_Missense_Mutation_p.T62S	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	100	Ser-rich.		T -> S (in dbSNP:rs17813964).		protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						ACAAACTGTACTACCTCAGCT	0.403													C|||	192	0.0383387	0.0038	0.0447	5008	,	,		20371	0.0238		0.0865	False		,,,				2504	0.046				p.T100S		Atlas-SNP	.											.	MARCH7	48	.	0			c.C299G						PASS	.	C	SER/THR	70,4336	64.1+/-101.4	0,70,2133	131.0	126.0	127.0		299	5.5	1.0	2	dbSNP_123	127	730,7870	177.8+/-227.3	30,670,3600	yes	missense	MARCH7	NM_022826.2	58	30,740,5733	GG,GC,CC		8.4884,1.5887,6.151	benign	100/705	160599717	800,12206	2203	4300	6503	SO:0001583	missense	64844	exon3			ACTGTACTACCTC	AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	17393	protein-coding gene	gene with protein product		613334	"""axotrophin"", ""membrane-associated ring finger (C3HC4) 7"""	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.299C>G	2.37:g.160599717C>G	ENSP00000259050:p.Thr100Ser	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	324	150	0.462963	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	105	0.04807692307692308	3	0.006097560975609756	17	0.04696132596685083	14	0.024475524475524476	71	0.09366754617414248	C	14.19	2.462449	0.43736	0.015887	0.084884	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000421037;ENST00000409591	T;T;T;T;T	0.50277	2.73;2.68;2.73;0.75;2.72	5.54	5.54	0.83059	.	0.496290	0.22512	N	0.059089	T	0.04272	0.0118	L	0.41236	1.265	0.27891	N	0.939314	D;B;B	0.67145	0.996;0.441;0.307	D;B;B	0.73380	0.98;0.138;0.138	T	0.13710	-1.0499	10	0.10902	T	0.67	-3.1194	17.6728	0.88223	0.0:1.0:0.0:0.0	rs17813964;rs52819098;rs17813964	100;62;100	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	S	100;100;100;100;62	ENSP00000386830:T100S;ENSP00000442992:T100S;ENSP00000259050:T100S;ENSP00000392862:T100S;ENSP00000387238:T62S	ENSP00000259050:T100S	T	+	2	0	MARCH7	160307963	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.019000	0.64060	2.607000	0.88179	0.650000	0.86243	ACT	C|0.945;G|0.055	0.055	strong		0.403	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
NAGLU	4669	hgsc.bcm.edu	37	17	40695462	40695462	+	Missense_Mutation	SNP	G	G	A	rs147293270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:40695462G>A	ENST00000225927.2	+	6	1539	c.1438G>A	c.(1438-1440)Gcc>Acc	p.A480T	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	480					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	CAGCTTTGCCGCCCGGCGGTA	0.652													G|||	2	0.000399361	0.0008	0.0	5008	,	,		17281	0.0		0.001	False		,,,				2504	0.0				p.A480T		Atlas-SNP	.											.	NAGLU	36	.	0			c.G1438A						PASS	.	G	THR/ALA	3,4401		0,3,2199	21.0	19.0	19.0		1438	-0.8	0.0	17	dbSNP_134	19	13,8581		0,13,4284	yes	missense	NAGLU	NM_000263.3	58	0,16,6483	AA,AG,GG		0.1513,0.0681,0.1231	benign	480/744	40695462	16,12982	2202	4297	6499	SO:0001583	missense	4669	exon6			TTTGCCGCCCGGC		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"""Sanfilippo disease IIIB"""	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.1438G>A	17.37:g.40695462G>A	ENSP00000225927:p.Ala480Thr	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.721599	0.00700	6.81E-4	0.001513	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.98550	-4.99	4.37	-0.768	0.11013	Alpha-N-acetylglucosaminidase, C-terminal (1);	2.129420	0.01419	N	0.014306	D	0.94152	0.8124	N	0.25957	0.775	0.09310	N	1	B	0.19706	0.038	B	0.15870	0.014	D	0.89959	0.4085	10	0.08381	T	0.77	0.3738	4.8095	0.13337	0.3302:0.1519:0.518:0.0	.	480	P54802	ANAG_HUMAN	T	480;156	ENSP00000225927:A480T	ENSP00000225927:A480T	A	+	1	0	NAGLU	37948988	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	0.114000	0.15520	-0.174000	0.10743	0.205000	0.17691	GCC	G|0.999;A|0.001	0.001	strong		0.652	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263	
MACC1	346389	hgsc.bcm.edu	37	7	20201395	20201395	+	Missense_Mutation	SNP	G	G	C	rs4721888	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:20201395G>C	ENST00000400331.5	-	4	399	c.91C>G	c.(91-93)Ctc>Gtc	p.L31V	MACC1_ENST00000332878.4_Missense_Mutation_p.L31V|MACC1_ENST00000589011.1_Missense_Mutation_p.L31V|MACC1_ENST00000471019.1_5'Flank	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	31			L -> V (in dbSNP:rs4721888). {ECO:0000269|PubMed:14702039}.		positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						CTTTTTGAGAGTTTTCCAGCT	0.333													G|||	575	0.114816	0.0053	0.0476	5008	,	,		16230	0.2917		0.0845	False		,,,				2504	0.1595				p.L31V		Atlas-SNP	.											.	MACC1	99	.	0			c.C91G						PASS	.	G	VAL/LEU	92,4312	74.7+/-112.8	3,86,2113	135.0	135.0	135.0		91	-6.7	0.0	7	dbSNP_111	135	680,7916	169.4+/-220.8	31,618,3649	yes	missense	MACC1	NM_182762.3	32	34,704,5762	CC,CG,GG		7.9107,2.089,5.9385	benign	31/853	20201395	772,12228	2202	4298	6500	SO:0001583	missense	346389	exon4			TTGAGAGTTTTCC		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.91C>G	7.37:g.20201395G>C	ENSP00000383185:p.Leu31Val	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	213	99	0.464789	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	239	0.10943223443223443	4	0.008130081300813009	20	0.055248618784530384	149	0.26048951048951047	66	0.0870712401055409	G	0.022	-1.406190	0.01155	0.02089	0.079107	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.09255	3.0;3.0	5.51	-6.67	0.01783	.	1.245410	0.05400	N	0.540615	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.20887	0.049	B	0.19666	0.026	T	0.43718	-0.9374	9	0.02654	T	1	4.8931	7.7931	0.29131	0.4927:0.2859:0.2214:0.0	rs4721888;rs4721888	31	Q6ZN28	MACC1_HUMAN	V	31	ENSP00000383185:L31V;ENSP00000328410:L31V	ENSP00000328410:L31V	L	-	1	0	MACC1	20167920	0.018000	0.18449	0.000000	0.03702	0.003000	0.03518	-0.088000	0.11198	-1.306000	0.02324	-0.140000	0.14226	CTC	G|0.907;C|0.093	0.093	strong		0.333	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762	
TMEM63A	9725	hgsc.bcm.edu	37	1	226040404	226040404	+	Missense_Mutation	SNP	C	C	T	rs1009668	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:226040404C>T	ENST00000366835.3	-	20	2134	c.1864G>A	c.(1864-1866)Gtg>Atg	p.V622M		NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	622			V -> M (in dbSNP:rs1009668).		ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					CTGTAGGCCACGATGACAGTG	0.557													C|||	367	0.0732827	0.0045	0.1844	5008	,	,		22110	0.0933		0.1113	False		,,,				2504	0.0276				p.V622M		Atlas-SNP	.											.	TMEM63A	75	.	0			c.G1864A						PASS	.	C	MET/VAL	108,4298	83.4+/-121.9	1,106,2096	194.0	124.0	147.0		1864	1.6	1.0	1	dbSNP_86	147	847,7753	194.2+/-239.7	39,769,3492	yes	missense	TMEM63A	NM_014698.2	21	40,875,5588	TT,TC,CC		9.8488,2.4512,7.3428	benign	622/808	226040404	955,12051	2203	4300	6503	SO:0001583	missense	9725	exon20			AGGCCACGATGAC		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.1864G>A	1.37:g.226040404C>T	ENSP00000355800:p.Val622Met	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	138	76	0.550725	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	37	CCDS31042.1	219	0.10027472527472528	4	0.008130081300813009	66	0.18232044198895028	55	0.09615384615384616	94	0.12401055408970976	C	3.663	-0.069188	0.07228	0.024512	0.098488	ENSG00000196187	ENST00000366835	T	0.28666	1.6	5.27	1.6	0.23607	Domain of unknown function DUF221 (1);	0.107487	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00069	-2.28	0.09310	P	1.0	B	0.09022	0.002	B	0.08055	0.003	T	0.33266	-0.9875	9	0.12430	T	0.62	-24.5043	9.5115	0.39080	0.0:0.2061:0.0:0.7939	rs1009668;rs52835276;rs58918745;rs1009668	622	O94886	TM63A_HUMAN	M	622	ENSP00000355800:V622M	ENSP00000355800:V622M	V	-	1	0	TMEM63A	224107027	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	3.404000	0.52623	0.010000	0.14839	-0.414000	0.06135	GTG	C|0.918;T|0.082	0.082	strong		0.557	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
NFATC4	4776	hgsc.bcm.edu	37	14	24839165	24839165	+	Silent	SNP	C	C	T	rs2228233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24839165C>T	ENST00000250373.4	+	2	702	c.561C>T	c.(559-561)gaC>gaT	p.D187D	NFATC4_ENST00000555453.1_Silent_p.D175D|NFATC4_ENST00000554661.1_Silent_p.D117D|NFATC4_ENST00000557451.1_Silent_p.D117D|NFATC4_ENST00000553879.1_Silent_p.D117D|NFATC4_ENST00000554344.1_Silent_p.D117D|NFATC4_ENST00000539237.2_Silent_p.D219D|NFATC4_ENST00000556279.1_Silent_p.D219D|NFATC4_ENST00000422617.3_Silent_p.D175D|NFATC4_ENST00000554050.1_Silent_p.D187D|NFATC4_ENST00000553469.1_Silent_p.D219D|NFATC4_ENST00000440487.2_3'UTR|NFATC4_ENST00000553708.1_Silent_p.D187D|NFATC4_ENST00000556759.1_5'Flank|NFATC4_ENST00000554591.1_Silent_p.D250D|NFATC4_ENST00000556169.1_Silent_p.D175D|NFATC4_ENST00000424781.2_Silent_p.D200D|NFATC4_ENST00000555590.1_Silent_p.D200D|NFATC4_ENST00000413692.2_Silent_p.D250D|NFATC4_ENST00000554473.1_5'Flank|NFATC4_ENST00000555167.1_5'Flank|NFATC4_ENST00000554966.1_Silent_p.D200D	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	187	Pro-rich.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		ATGCCTCTGACGAGGCAGCCC	0.677													C|||	2004	0.40016	0.3986	0.4323	5008	,	,		13805	0.4692		0.2644	False		,,,				2504	0.4479				p.D250D		Atlas-SNP	.											.	NFATC4	115	.	0			c.C750T						PASS	.	C	,,,,	1539,2789		287,965,912	23.0	25.0	24.0		750,561,351,750,561	-7.2	0.2	14	dbSNP_98	24	2264,6272		323,1618,2327	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFATC4	NM_001136022.1,NM_001198965.1,NM_001198966.1,NM_001198967.1,NM_004554.4	,,,,	610,2583,3239	TT,TC,CC		26.523,35.5591,29.5631	,,,,	250/965,187/795,117/833,250/858,187/903	24839165	3803,9061	2164	4268	6432	SO:0001819	synonymous_variant	4776	exon3			CTCTGACGAGGCA	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"""Nuclear factor of activated T-cells"""	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.561C>T	14.37:g.24839165C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Silent	SNP	ENST00000250373.4	37	CCDS9629.1																																																																																			C|0.667;T|0.333	0.333	strong		0.677	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554	
ABLIM1	3983	hgsc.bcm.edu	37	10	116335246	116335246	+	Silent	SNP	G	G	A	rs985273	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:116335246G>A	ENST00000277895.5	-	3	589	c.492C>T	c.(490-492)ttC>ttT	p.F164F	ABLIM1_ENST00000369252.4_Silent_p.F104F|ABLIM1_ENST00000533213.2_Silent_p.F104F	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	164	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)	p.F104F(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		CGCCCTCCACGAACTCCCCAC	0.537													G|||	1525	0.304513	0.475	0.3602	5008	,	,		19474	0.2321		0.2078	False		,,,				2504	0.2086				p.F164F		Atlas-SNP	.											ABLIM1,NS,carcinoma,0,1	ABLIM1	131	1	1	Substitution - coding silent(1)	stomach(1)	c.C492T						scavenged	.	G	,,	1935,2471	549.1+/-377.7	436,1063,704	141.0	113.0	122.0		312,312,492	-3.2	1.0	10	dbSNP_86	122	1537,7063	289.4+/-299.3	147,1243,2910	no	coding-synonymous,coding-synonymous,coding-synonymous	ABLIM1	NM_001003407.1,NM_001003408.1,NM_002313.5	,,	583,2306,3614	AA,AG,GG		17.8721,43.9174,26.6954	,,	104/719,104/747,164/779	116335246	3472,9534	2203	4300	6503	SO:0001819	synonymous_variant	3983	exon3			CTCCACGAACTCC	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.492C>T	10.37:g.116335246G>A		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Silent	SNP	ENST00000277895.5	37	CCDS7590.1																																																																																			G|0.719;A|0.281	0.281	strong		0.537	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3		
ITPR3	3710	hgsc.bcm.edu	37	6	33643558	33643558	+	Silent	SNP	G	G	A	rs2229637	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33643558G>A	ENST00000374316.5	+	26	4267	c.3207G>A	c.(3205-3207)ccG>ccA	p.P1069P	ITPR3_ENST00000605930.1_Silent_p.P1069P			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1069					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	ACTATGCGCCGCTGGTCTCGG	0.647													G|||	890	0.177716	0.1906	0.245	5008	,	,		21343	0.0704		0.2843	False		,,,				2504	0.1135				p.P1069P		Atlas-SNP	.											ITPR3_ENST00000374316,NS,carcinoma,0,2	ITPR3	409	2	0			c.G3207A						PASS	.	G		862,3544	317.4+/-295.1	75,712,1416	40.0	30.0	34.0		3207	-11.3	0.0	6	dbSNP_98	34	2451,6149	382.4+/-340.4	357,1737,2206	no	coding-synonymous	ITPR3	NM_002224.3		432,2449,3622	AA,AG,GG		28.5,19.5642,25.4729		1069/2672	33643558	3313,9693	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon25			TGCGCCGCTGGTC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.3207G>A	6.37:g.33643558G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	192	91	0.473958	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			G|0.786;A|0.214	0.214	strong		0.647	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
LRP5	4041	hgsc.bcm.edu	37	11	68115631	68115631	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:68115631C>A	ENST00000294304.7	+	2	514	c.408C>A	c.(406-408)aaC>aaA	p.N136K		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	136	Beta-propeller 1.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGGTGGCCAACCTCAATGGCA	0.642																																					p.N136K		Atlas-SNP	.											.	LRP5	136	.	0			c.C408A						PASS	.						97.0	93.0	94.0					11																	68115631		2200	4294	6494	SO:0001583	missense	4041	exon2			GGCCAACCTCAAT	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.408C>A	11.37:g.68115631C>A	ENSP00000294304:p.Asn136Lys	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	52	22	0.423077	NM_002335	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	12.31	1.900963	0.33535	.	.	ENSG00000162337	ENST00000294304	D	0.83506	-1.73	3.71	2.78	0.32641	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.52532	U	0.000075	T	0.77772	0.4180	L	0.42632	1.34	0.50313	D	0.999863	P	0.45672	0.864	P	0.47376	0.545	T	0.71718	-0.4508	10	0.27785	T	0.31	.	7.2059	0.25907	0.0:0.7283:0.0:0.2717	.	136	O75197	LRP5_HUMAN	K	136	ENSP00000294304:N136K	ENSP00000294304:N136K	N	+	3	2	LRP5	67872207	0.792000	0.28813	0.998000	0.56505	0.307000	0.27823	-0.168000	0.09925	0.888000	0.36160	0.561000	0.74099	AAC	.	.	none		0.642	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335	
TTN	7273	hgsc.bcm.edu	37	2	179427186	179427186	+	Silent	SNP	A	A	G	rs2366751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179427186A>G	ENST00000591111.1	-	276	78974	c.78750T>C	c.(78748-78750)ggT>ggC	p.G26250G	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Silent_p.G18826G|TTN_ENST00000342992.6_Silent_p.G25323G|TTN_ENST00000589042.1_Silent_p.G27891G|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Silent_p.G18951G|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.G19018G|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26250	Fibronectin type-III 91. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTTGCTGCCACCATCACTTT	0.433													G|||	2548	0.508786	0.5673	0.4078	5008	,	,		21523	0.7153		0.2535	False		,,,				2504	0.5511				p.G27891G		Atlas-SNP	.											.	TTN	18412	.	0			c.T83673C						PASS	.	G	,,,	2019,1847		546,927,460	65.0	67.0	67.0		56478,75969,56853,57054	-1.6	1.0	2	dbSNP_100	67	1847,6443		193,1461,2491	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	739,2388,2951	GG,GA,AA		22.2799,47.7755,31.8032	,,,	18826/26927,25323/33424,18951/27052,19018/27119	179427186	3866,8290	1933	4145	6078	SO:0001819	synonymous_variant	7273	exon326			GCTGCCACCATCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.78750T>C	2.37:g.179427186A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	213	113	0.530516	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.562;G|0.438	0.438	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ITGA9	3680	hgsc.bcm.edu	37	3	37523079	37523079	+	Silent	SNP	G	G	A	rs17227748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:37523079G>A	ENST00000264741.5	+	4	781	c.525G>A	c.(523-525)acG>acA	p.T175T	ITGA9_ENST00000422441.1_Silent_p.T175T	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	175					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.T175T(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		AAGGCAGGACGCTGATCCCTT	0.552													G|||	408	0.0814696	0.031	0.0994	5008	,	,		20890	0.0863		0.1332	False		,,,				2504	0.0787				p.T175T		Atlas-SNP	.											ITGA9,NS,carcinoma,0,1	ITGA9	98	1	1	Substitution - coding silent(1)	stomach(1)	c.G525A						PASS	.	G		184,4222	118.8+/-156.5	4,176,2023	223.0	184.0	197.0		525	0.3	0.9	3	dbSNP_123	197	1219,7381	246.1+/-274.7	80,1059,3161	no	coding-synonymous	ITGA9	NM_002207.2		84,1235,5184	AA,AG,GG		14.1744,4.1761,10.7873		175/1036	37523079	1403,11603	2203	4300	6503	SO:0001819	synonymous_variant	3680	exon4			CAGGACGCTGATC	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.525G>A	3.37:g.37523079G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																			G|0.892;A|0.108	0.108	strong		0.552	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
CEP170	9859	hgsc.bcm.edu	37	1	243333027	243333027	+	Silent	SNP	A	A	G	rs200644784		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:243333027A>G	ENST00000366542.1	-	12	1797	c.1746T>C	c.(1744-1746)cgT>cgC	p.R582R	RP11-261C10.4_ENST00000422938.1_RNA|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Silent_p.R484R|CEP170_ENST00000366544.1_Silent_p.R484R	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	582						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.R582R(3)		NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GTGAAACCCAACGTTTGCTTC	0.398																																					p.R582R		Atlas-SNP	.											CEP170_ENST00000366543,NS,carcinoma,0,6	CEP170	153	6	3	Substitution - coding silent(3)	kidney(3)	c.T1746C						scavenged	.						103.0	92.0	95.0					1																	243333027		1878	4106	5984	SO:0001819	synonymous_variant	9859	exon12			AACCCAACGTTTG	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.1746T>C	1.37:g.243333027A>G		Somatic	538	5	0.00929368		WXS	Illumina HiSeq	Phase_I	628	12	0.0191083	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Silent	SNP	ENST00000366542.1	37	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	A	9.754	1.168273	0.21621	.	.	ENSG00000143702	ENST00000336415	.	.	.	4.66	-6.75	0.01738	.	.	.	.	.	T	0.46833	0.1413	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51576	-0.8688	4	.	.	.	-8.1159	6.5973	0.22681	0.3246:0.0:0.4436:0.2317	.	.	.	.	A	546	.	.	V	-	2	0	CEP170	241399650	0.846000	0.29590	0.974000	0.42286	0.957000	0.61999	-0.087000	0.11215	-0.781000	0.04548	-0.555000	0.04198	GTT	.	.	weak		0.398	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
PLA2G4E	123745	hgsc.bcm.edu	37	15	42287578	42287578	+	Silent	SNP	G	G	A	rs1668586	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:42287578G>A	ENST00000399518.3	-	12	1713	c.1227C>T	c.(1225-1227)acC>acT	p.T409T	CTD-2382E5.1_ENST00000499478.2_RNA|PLA2G4E_ENST00000413860.2_Silent_p.T380T	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	397	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		CTGATAGACCGGTGATGTAGC	0.602													A|||	3297	0.658347	0.5083	0.6816	5008	,	,		18768	0.5704		0.8479	False		,,,				2504	0.7403				p.T409T		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.C1227T						PASS	.	A		2384,1682		718,948,367	59.0	60.0	60.0		1227	-9.8	0.8	15	dbSNP_89	60	7344,1066		3214,916,75	no	coding-synonymous	PLA2G4E	NM_001206670.1		3932,1864,442	AA,AG,GG		12.6754,41.3674,22.0263		409/869	42287578	9728,2748	2033	4205	6238	SO:0001819	synonymous_variant	123745	exon12			TAGACCGGTGATG		CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.1227C>T	15.37:g.42287578G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_001206670	Q6ZSC0	Silent	SNP	ENST00000399518.3	37	CCDS55962.1																																																																																			G|0.328;A|0.672	0.672	strong		0.602	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442	
AGRN	375790	hgsc.bcm.edu	37	1	989207	989207	+	Missense_Mutation	SNP	G	G	C	rs74685771	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:989207G>C	ENST00000379370.2	+	34	5776	c.5726G>C	c.(5725-5727)aGt>aCt	p.S1909T	RP11-54O7.14_ENST00000418300.1_RNA	NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1931	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)		GTGCTCTGGAGTGGCAAGGCC	0.652													G|||	45	0.00898562	0.0	0.0519	5008	,	,		19298	0.0089		0.0	False		,,,				2504	0.0				p.S1909T		Atlas-SNP	.											.	AGRN	110	.	0			c.G5726C						PASS	.	G	THR/SER	7,4393	9.9+/-24.2	0,7,2193	44.0	36.0	39.0		5726	-0.8	0.2	1	dbSNP_132	39	5,8587	5.0+/-18.6	0,5,4291	yes	missense	AGRN	NM_198576.3	58	0,12,6484	CC,CG,GG		0.0582,0.1591,0.0924	benign	1909/2046	989207	12,12980	2200	4296	6496	SO:0001583	missense	375790	exon34			TCTGGAGTGGCAA	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.5726G>C	1.37:g.989207G>C	ENSP00000368678:p.Ser1909Thr	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	237	123	0.518987	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	19|19	0.0086996336996337|0.0086996336996337	0|0	0.0|0.0	13|13	0.03591160220994475|0.03591160220994475	6|6	0.01048951048951049|0.01048951048951049	0|0	0.0|0.0	G|G	1.487|1.487	-0.555666|-0.555666	0.03967|0.03967	0.001591|0.001591	5.82E-4|5.82E-4	ENSG00000188157|ENSG00000188157	ENST00000419249|ENST00000379370;ENST00000379364	.|T	.|0.78595	.|-1.19	3.95|3.95	-0.779|-0.779	0.10973|0.10973	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	.|0.141330	.|0.44902	.|D	.|0.000411	T|T	0.43166|0.43166	0.1235|0.1235	L|L	0.45285|0.45285	1.41|1.41	0.40815|0.40815	D|D	0.98345|0.98345	.|B	.|0.22346	.|0.068	.|B	.|0.42422	.|0.387	T|T	0.49495|0.49495	-0.8934|-0.8934	5|10	.|0.09338	.|T	.|0.73	-3.2936|-3.2936	12.7066|12.7066	0.57063|0.57063	0.0:0.0:0.4308:0.5692|0.0:0.0:0.4308:0.5692	.|.	.|1909	.|O00468	.|AGRIN_HUMAN	D|T	230|1909;271	.|ENSP00000368678:S1909T	.|ENSP00000368671:S271T	E|S	+|+	3|2	2|0	AGRN|AGRN	979070|979070	1.000000|1.000000	0.71417|0.71417	0.215000|0.215000	0.23724|0.23724	0.135000|0.135000	0.20990|0.20990	4.270000|4.270000	0.58896|0.58896	-0.358000|-0.358000	0.08162|0.08162	-0.521000|-0.521000	0.04368|0.04368	GAG|AGT	G|0.997;C|0.003	0.003	strong		0.652	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
RNF17	56163	hgsc.bcm.edu	37	13	25367301	25367301	+	Silent	SNP	C	C	T	rs1158061	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25367301C>T	ENST00000255324.5	+	10	1109	c.1057C>T	c.(1057-1059)Cta>Tta	p.L353L	RNF17_ENST00000255326.4_3'UTR|RNF17_ENST00000381921.1_Silent_p.L353L|RNF17_ENST00000255325.6_Silent_p.L353L	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	353					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		CATGTCTGTCCTAACCAGTGA	0.383													C|||	1255	0.250599	0.1074	0.3228	5008	,	,		20278	0.3542		0.2097	False		,,,				2504	0.3282				p.L353L		Atlas-SNP	.											.	RNF17	259	.	0			c.C1057T						PASS	.	C	,	476,3930	224.6+/-240.7	28,420,1755	192.0	180.0	184.0		1057,1057	1.3	0.0	13	dbSNP_87	184	2106,6494	364.4+/-333.5	243,1620,2437	no	coding-synonymous,coding-synonymous	RNF17	NM_001184993.1,NM_031277.2	,	271,2040,4192	TT,TC,CC		24.4884,10.8034,19.8524	,	353/1620,353/1624	25367301	2582,10424	2203	4300	6503	SO:0001819	synonymous_variant	56163	exon10			TCTGTCCTAACCA	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"""RING-type (C3HC4) zinc fingers"", ""Tudor domain containing"""	10060	protein-coding gene	gene with protein product	"""spermatogenesis associated 23"""	605793	"""tudor domain containing 4"""	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.1057C>T	13.37:g.25367301C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	37	CCDS9308.2																																																																																			C|0.771;T|0.229	0.229	strong		0.383	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
SHANK3	85358	hgsc.bcm.edu	37	22	51117580	51117580	+	Missense_Mutation	SNP	T	T	C	rs9616915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:51117580T>C	ENST00000414786.2	+	6	961	c.734T>C	c.(733-735)aTc>aCc	p.I245T	SHANK3_ENST00000445220.2_Missense_Mutation_p.I245T|SHANK3_ENST00000262795.3_Missense_Mutation_p.I245T			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	245			I -> T (in dbSNP:rs9616915). {ECO:0000269|PubMed:20385823}.		adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CAGCTGGGGATCACCGACGAG	0.667													C|||	1719	0.343251	0.4077	0.353	5008	,	,		16829	0.0754		0.5089	False		,,,				2504	0.3548				p.I245T		Atlas-SNP	.											SHANK3_ENST00000262795,NS,carcinoma,0,1	SHANK3	96	1	0			c.T734C						PASS	.		THR/ILE	1655,2437		344,967,735	16.0	19.0	18.0		734	4.7	1.0	22	dbSNP_119	18	4315,4031		1167,1981,1025	yes	missense	SHANK3	NM_001080420.1	89	1511,2948,1760	CC,CT,TT		48.2986,40.4448,47.9981	benign	245/1748	51117580	5970,6468	2046	4173	6219	SO:0001583	missense	85358	exon6			TGGGGATCACCGA	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.734T>C	22.37:g.51117580T>C	ENSP00000464552:p.Ile245Thr	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	37		784	0.358974358974359	198	0.4024390243902439	141	0.38950276243093923	55	0.09615384615384616	390	0.5145118733509235	C	10.19	1.281994	0.23392	0.404448	0.517014	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.20463	2.07;2.07	4.65	4.65	0.58169	.	.	.	.	.	T	0.00012	0.0000	N	0.25992	0.78	0.46631	P	8.610000000000007E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.44050	-0.9353	8	0.16896	T	0.51	.	6.7166	0.23306	0.0:0.7264:0.1781:0.0955	rs9616915;rs9616915	245	F2Z3L0	.	T	245	ENSP00000442518:I245T;ENSP00000446078:I245T	ENSP00000442518:I245T	I	+	2	0	SHANK3	49464446	0.997000	0.39634	0.997000	0.53966	0.979000	0.70002	1.469000	0.35343	1.190000	0.43042	-0.142000	0.14014	ATC	T|0.638;C|0.362	0.362	strong		0.667	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
KLK4	9622	hgsc.bcm.edu	37	19	51412668	51412668	+	Missense_Mutation	SNP	A	A	C	rs1654551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51412668A>C	ENST00000324041.1	-	2	63	c.64T>G	c.(64-66)Tcg>Gcg	p.S22A	KLK4_ENST00000431178.2_5'Flank|KLK4_ENST00000597441.1_5'Flank	NM_004917.3	NP_004908.3	Q9Y5K2	KLK4_HUMAN	kallikrein-related peptidase 4	22			S -> A (in dbSNP:rs1654551). {ECO:0000269|PubMed:15235027}.		amelogenesis (GO:0097186)|extracellular matrix disassembly (GO:0022617)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(8)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00624)|GBM - Glioblastoma multiforme(134;0.00878)		GAGACGAGCGATCCTGAGGGC	0.637													A|||	644	0.128594	0.2678	0.0605	5008	,	,		11795	0.0873		0.0736	False		,,,				2504	0.0879				p.S22A		Atlas-SNP	.											KLK4,colon,carcinoma,+2,2	KLK4	46	2	0			c.T64G						scavenged	.	A	ALA/SER	933,3473	342.8+/-307.3	106,721,1376	86.0	96.0	92.0		64	-7.0	0.0	19	dbSNP_89	92	616,7984	157.5+/-211.1	24,568,3708	no	missense	KLK4	NM_004917.3	99	130,1289,5084	CC,CA,AA		7.1628,21.1757,11.9099	benign	22/255	51412668	1549,11457	2203	4300	6503	SO:0001583	missense	9622	exon2			CGAGCGATCCTGA	AF113141	CCDS12809.1	19q13.41	2014-09-04	2006-10-27		ENSG00000167749	ENSG00000167749		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6365	protein-coding gene	gene with protein product		603767	"""kallikrein 4 (prostase, enamel matrix, prostate)"""	PRSS17		10077646, 10438493, 16800724, 10863090, 9465170	Standard	XM_005259441		Approved	EMSP, EMSP1, PSTS, KLK-L1	uc002pua.1	Q9Y5K2	OTTHUMG00000182964	ENST00000324041.1:c.64T>G	19.37:g.51412668A>C	ENSP00000326159:p.Ser22Ala	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	134	56	0.41791	NM_004917	Q4VB16|Q96RU5|Q9GZL6|Q9UBJ6	Missense_Mutation	SNP	ENST00000324041.1	37	CCDS12809.1	270	0.12362637362637363	129	0.2621951219512195	24	0.06629834254143646	59	0.10314685314685315	58	0.07651715039577836	a	4.871	0.161905	0.09287	0.211757	0.071628	ENSG00000167749	ENST00000324041	D	0.92647	-3.08	3.63	-7.01	0.01594	.	1.425490	0.05046	N	0.477318	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.45934	-0.9227	9	0.02654	T	1	.	9.8336	0.40956	0.2057:0.6849:0.1094:0.0	rs1654551	22	Q9Y5K2	KLK4_HUMAN	A	22	ENSP00000326159:S22A	ENSP00000326159:S22A	S	-	1	0	KLK4	56104480	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.150000	0.01290	-1.157000	0.02815	-0.488000	0.04728	TCG	A|0.875;C|0.125	0.125	strong		0.637	KLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464449.1	NM_004917	
FRY	10129	hgsc.bcm.edu	37	13	32811607	32811607	+	Missense_Mutation	SNP	G	G	A	rs2806639	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:32811607G>A	ENST00000380250.3	+	44	6398	c.5902G>A	c.(5902-5904)Ggc>Agc	p.G1968S		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1968			G -> S (in dbSNP:rs2806639).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		AACCACCAGCGGCAACACCGC	0.532													G|||	1081	0.215855	0.3487	0.2392	5008	,	,		17080	0.004		0.3091	False		,,,				2504	0.1421				p.G1968S		Atlas-SNP	.											.	FRY	312	.	0			c.G5902A						PASS	.	G	SER/GLY	1295,2733		197,901,916	61.0	69.0	66.0		5902	6.2	1.0	13	dbSNP_100	66	2626,5758		412,1802,1978	yes	missense	FRY	NM_023037.2	56	609,2703,2894	AA,AG,GG		31.3216,32.15,31.5904	benign	1968/3014	32811607	3921,8491	2014	4192	6206	SO:0001583	missense	10129	exon44			ACCAGCGGCAACA	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.5902G>A	13.37:g.32811607G>A	ENSP00000369600:p.Gly1968Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	28	27	0.964286	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	492	0.22527472527472528	155	0.3150406504065041	89	0.24585635359116023	4	0.006993006993006993	244	0.32189973614775724	G	4.136	0.023614	0.08006	0.3215	0.313216	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.21361	2.01	6.17	6.17	0.99709	.	0.227868	0.40554	N	0.001075	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46735	-0.9170	9	0.18710	T	0.47	.	15.9457	0.79792	0.0657:0.0:0.9343:0.0	rs2806639;rs52798355;rs61692237;rs2806639	1968	Q5TBA9	FRY_HUMAN	S	1968;805	ENSP00000369600:G1968S	ENSP00000369600:G1968S	G	+	1	0	FRY	31709607	0.986000	0.35501	0.993000	0.49108	0.081000	0.17604	1.858000	0.39408	2.941000	0.99782	0.655000	0.94253	GGC	G|0.755;A|0.245	0.245	strong		0.532	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
LGI4	163175	hgsc.bcm.edu	37	19	35617270	35617270	+	Silent	SNP	T	T	C	rs1319969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:35617270T>C	ENST00000310123.3	-	8	1722	c.1203A>G	c.(1201-1203)acA>acG	p.T401T	LGI4_ENST00000392225.3_Missense_Mutation_p.Q427R|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	401					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CGGGGATGTCTGTGCGTCTCT	0.667													T|||	1835	0.366414	0.3359	0.2493	5008	,	,		13875	0.2669		0.3708	False		,,,				2504	0.589				p.T401T		Atlas-SNP	.											LGI4,NS,carcinoma,0,1	LGI4	32	1	0			c.A1203G						PASS	.	T		1566,2840	452.0+/-349.9	280,1006,917	29.0	28.0	28.0		1203	-9.0	0.3	19	dbSNP_88	28	3066,5534	438.8+/-359.0	529,2008,1763	no	coding-synonymous	LGI4	NM_139284.2		809,3014,2680	CC,CT,TT		35.6512,35.5424,35.6143		401/538	35617270	4632,8374	2203	4300	6503	SO:0001819	synonymous_variant	163175	exon8			GATGTCTGTGCGT	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.1203A>G	19.37:g.35617270T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_139284	B2RN53|B9EGS7|Q5M8T1	Silent	SNP	ENST00000310123.3	37	CCDS12444.1	694	0.31776556776556775	183	0.3719512195121951	85	0.23480662983425415	136	0.23776223776223776	290	0.38258575197889183	T	8.894	0.954608	0.18431	0.355424	0.356512	ENSG00000153902	ENST00000392225	T	0.65732	-0.17	4.51	-9.02	0.00741	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999394594	.	.	.	.	.	.	T	0.39292	-0.9621	5	0.87932	D	0	.	10.368	0.44035	0.0:0.126:0.3738:0.5002	rs1319969;rs3810442;rs17656168;rs61511650	.	.	.	R	427	ENSP00000376059:Q427R	ENSP00000376059:Q427R	Q	-	2	0	LGI4	40309110	0.000000	0.05858	0.336000	0.25522	0.936000	0.57629	-4.585000	0.00212	-2.941000	0.00297	-1.540000	0.00911	CAG	T|0.660;C|0.340	0.340	strong		0.667	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1		
KARS	3735	hgsc.bcm.edu	37	16	75675609	75675609	+	Silent	SNP	T	T	C	rs5030748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:75675609T>C	ENST00000302445.3	-	2	114	c.75A>G	c.(73-75)agA>agG	p.R25R	KARS_ENST00000319410.5_Silent_p.R53R|KARS_ENST00000568378.1_Intron	NM_005548.2	NP_005539.1	Q15046	SYK_HUMAN	lysyl-tRNA synthetase	25					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|lysyl-tRNA aminoacylation (GO:0006430)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)|viral process (GO:0016032)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|microtubule cytoskeleton (GO:0015630)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid binding (GO:0016597)|ATP binding (GO:0005524)|lysine-tRNA ligase activity (GO:0004824)|metal ion binding (GO:0046872)|tRNA binding (GO:0000049)			kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18					L-Lysine(DB00123)	CTTTCAGGCGTCTCTTCAGCT	0.473													T|||	149	0.0297524	0.0053	0.0403	5008	,	,		21087	0.0		0.0964	False		,,,				2504	0.0174				p.R53R		Atlas-SNP	.											.	KARS	77	.	0			c.A159G						PASS	.	T	,	114,4282	85.8+/-124.5	1,112,2085	136.0	121.0	126.0		159,75	2.4	1.0	16	dbSNP_113	126	942,7658	206.8+/-248.7	60,822,3418	no	coding-synonymous,coding-synonymous	KARS	NM_001130089.1,NM_005548.2	,	61,934,5503	CC,CT,TT		10.9535,2.5933,8.1256	,	53/626,25/598	75675609	1056,11940	2198	4300	6498	SO:0001819	synonymous_variant	3735	exon3			CAGGCGTCTCTTC	AF285758	CCDS10923.1, CCDS45532.1	16q23.1	2014-09-17			ENSG00000065427	ENSG00000065427	6.1.1.6	"""Aminoacyl tRNA synthetases / Class II"""	6215	protein-coding gene	gene with protein product	"""lysine tRNA ligase"""	601421	"""deafness, autosomal recessive 89"""	DFNB89		8812440, 9278442, 23768514	Standard	NM_005548		Approved	KARS2, KARS1	uc002fer.3	Q15046	OTTHUMG00000137609	ENST00000302445.3:c.75A>G	16.37:g.75675609T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_001130089	A8MSK1|D3DUK4|O14946|Q96J25|Q9HB23	Silent	SNP	ENST00000302445.3	37	CCDS10923.1																																																																																			T|0.933;C|0.067	0.067	strong		0.473	KARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269023.1	NM_005548	
FBN2	2201	hgsc.bcm.edu	37	5	127645675	127645675	+	Splice_Site	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:127645675C>T	ENST00000508053.1	-	46	6174	c.5200G>A	c.(5200-5202)Gac>Aac	p.D1734N	FBN2_ENST00000262464.4_Splice_Site_p.D1734N			P35556	FBN2_HUMAN	fibrillin 2	1734					anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CTTTACCTACCCATGCAGTTG	0.453																																					p.D1734N		Atlas-SNP	.											FBN2_ENST00000508053,colon,carcinoma,0,2	FBN2	858	2	0			c.G5200A						scavenged	.						98.0	91.0	93.0					5																	127645675		2203	4300	6503	SO:0001630	splice_region_variant	2201	exon40			ACCTACCCATGCA	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.5200+1G>A	5.37:g.127645675C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	207	3	0.0144928	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	35	5.590431	0.96590	.	.	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.94184	-3.37;-3.37	5.32	5.32	0.75619	Matrix fibril-associated (2);	0.000000	0.64402	D	0.000010	D	0.95856	0.8651	L	0.57536	1.79	0.80722	D	1	D	0.63880	0.993	D	0.74674	0.984	D	0.94825	0.7990	9	.	.	.	.	19.1954	0.93686	0.0:1.0:0.0:0.0	.	1734	P35556	FBN2_HUMAN	N	1734	ENSP00000262464:D1734N;ENSP00000424571:D1734N	.	D	-	1	0	FBN2	127673574	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.651000	0.83577	2.772000	0.95346	0.650000	0.86243	GAC	.	.	none		0.453	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	Missense_Mutation
NPY4R	5540	hgsc.bcm.edu	37	10	47086978	47086978	+	Silent	SNP	G	G	A	rs3740294	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:47086978G>A	ENST00000395716.1	+	2	280	c.195G>A	c.(193-195)gtG>gtA	p.V65V	NPY4R_ENST00000374312.1_Silent_p.V65V			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	65					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										TGATGTGTGTGACTGTGAGGC	0.557													G|||	871	0.173922	0.1029	0.1369	5008	,	,		43421	0.3264		0.1521	False		,,,				2504	0.1616				p.V65V		Atlas-SNP	.											.	PPYR1	54	.	0			c.G195A						PASS	.	G		302,4104		0,302,1901	234.0	210.0	218.0		195	1.0	0.0	10	dbSNP_107	218	974,7626		0,974,3326	no	coding-synonymous	PPYR1	NM_005972.4		0,1276,5227	AA,AG,GG		11.3256,6.8543,9.8109		65/376	47086978	1276,11730	2203	4300	6503	SO:0001819	synonymous_variant	5540	exon3			GTGTGTGACTGTG		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"""GPCR / Class A : Neuropeptide receptors : Y"""	9329	protein-coding gene	gene with protein product		601790	"""pancreatic polypeptide receptor 1"""	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.195G>A	10.37:g.47086978G>A		Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	301	153	0.508306	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Silent	SNP	ENST00000395716.1	37	CCDS31193.1																																																																																			G|0.852;A|0.148	0.148	strong		0.557	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
CTDP1	9150	hgsc.bcm.edu	37	18	77475455	77475455	+	Silent	SNP	G	G	A	rs11549119	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:77475455G>A	ENST00000299543.7	+	8	2142	c.1995G>A	c.(1993-1995)gcG>gcA	p.A665A	CTDP1_ENST00000075430.7_Silent_p.A665A	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	665	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		CGCTGGGAGCGAAGATCCTCA	0.647													G|||	293	0.0585064	0.0197	0.0303	5008	,	,		16470	0.0377		0.0318	False		,,,				2504	0.18				p.A665A		Atlas-SNP	.											.	CTDP1	67	.	0			c.G1995A						PASS	.	G	,,	100,4302		0,100,2101	24.0	21.0	22.0		1638,1995,1995	-2.5	0.0	18	dbSNP_120	22	426,8166		14,398,3884	no	coding-synonymous,coding-synonymous,coding-synonymous	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	,,	14,498,5985	AA,AG,GG		4.9581,2.2717,4.048	,,	546/843,665/962,665/868	77475455	526,12468	2201	4296	6497	SO:0001819	synonymous_variant	9150	exon8			GGGAGCGAAGATC	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.1995G>A	18.37:g.77475455G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Silent	SNP	ENST00000299543.7	37	CCDS12017.1																																																																																			G|0.969;A|0.031	0.031	strong		0.647	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
INTS2	57508	hgsc.bcm.edu	37	17	59969000	59969000	+	Silent	SNP	T	T	C	rs753765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:59969000T>C	ENST00000444766.3	-	14	1848	c.1773A>G	c.(1771-1773)caA>caG	p.Q591Q	INTS2_ENST00000251334.6_Silent_p.Q583Q	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	591					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						AAGGAAGTAATTGAGGATGAA	0.368													T|||	669	0.133586	0.0136	0.0504	5008	,	,		15194	0.2381		0.0646	False		,,,				2504	0.318				p.Q591Q		Atlas-SNP	.											INTS2,NS,carcinoma,0,1	INTS2	89	1	0			c.A1773G						PASS	.	T		63,3675		1,61,1807	100.0	97.0	98.0		1773	-7.1	0.4	17	dbSNP_86	98	507,7695		20,467,3614	no	coding-synonymous	INTS2	NM_020748.2		21,528,5421	CC,CT,TT		6.1814,1.6854,4.7739		591/1205	59969000	570,11370	1869	4101	5970	SO:0001819	synonymous_variant	57508	exon14			AAGTAATTGAGGA	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"""KIAA1287"""	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.1773A>G	17.37:g.59969000T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	119	51	0.428571	NM_020748	Q9ULD3	Silent	SNP	ENST00000444766.3	37	CCDS45750.1																																																																																			T|0.903;C|0.097	0.097	strong		0.368	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748	
LATS2	26524	hgsc.bcm.edu	37	13	21562948	21562948	+	Missense_Mutation	SNP	G	G	A	rs558614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:21562948G>A	ENST00000382592.4	-	4	1376	c.971C>T	c.(970-972)gCg>gTg	p.A324V	LATS2_ENST00000472754.1_5'Flank|LATS2_ENST00000542899.1_Missense_Mutation_p.A324V	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CTGGTGGGCCGCGGGACCGGC	0.726													G|||	3153	0.629593	0.5129	0.6888	5008	,	,		11971	0.5387		0.7972	False		,,,				2504	0.6667				p.A324V		Atlas-SNP	.											LATS2_ENST00000382592,NS,carcinoma,0,2	LATS2	176	2	0			c.C971T						PASS	.	G	VAL/ALA	2514,1854		739,1036,409	17.0	20.0	19.0		971	2.7	0.0	13	dbSNP_83	19	6953,1567		2835,1283,142	no	missense	LATS2	NM_014572.2	64	3574,2319,551	AA,AG,GG		18.392,42.4451,26.5441	benign	324/1089	21562948	9467,3421	2184	4260	6444	SO:0001583	missense	26524	exon4			TGGGCCGCGGGAC	AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"""LATS (large tumor suppressor, Drosophila) homolog 2"", ""LATS, large tumor suppressor, homolog 2 (Drosophila)"""			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.971C>T	13.37:g.21562948G>A	ENSP00000372035:p.Ala324Val	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	1424	0.652014652014652	248	0.5040650406504065	266	0.7348066298342542	315	0.5506993006993007	595	0.7849604221635884	G	6.803	0.517276	0.13005	0.575549	0.81608	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.59083	0.29;0.29	3.57	2.72	0.32119	.	0.947577	0.08664	N	0.911940	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.28584	0.216	B	0.20184	0.028	T	0.37979	-0.9682	9	0.25751	T	0.34	.	12.1462	0.54024	0.0:0.2164:0.7836:0.0	rs558614;rs3742219;rs57107378;rs558614	324	Q9NRM7	LATS2_HUMAN	V	324	ENSP00000372035:A324V;ENSP00000441817:A324V	ENSP00000372035:A324V	A	-	2	0	LATS2	20460948	1.000000	0.71417	0.001000	0.08648	0.251000	0.25915	6.231000	0.72307	0.682000	0.31407	0.485000	0.47835	GCG	G|0.298;A|0.702	0.702	strong		0.726	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1		
FCGBP	8857	hgsc.bcm.edu	37	19	40368520	40368520	+	Silent	SNP	G	G	C	rs36079378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40368520G>C	ENST00000221347.6	-	28	12835	c.12828C>G	c.(12826-12828)ggC>ggG	p.G4276G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4276	VWFD 10. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.G4276G(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGAAGCCAGGGCCCTCGTACT	0.652													G|||	2378	0.47484	0.5643	0.3026	5008	,	,		15152	0.5853		0.3698	False		,,,				2504	0.4703				p.G4276G		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - coding silent(1)	stomach(1)	c.C12828G						scavenged	.						49.0	51.0	51.0					19																	40368520		2203	4295	6498	SO:0001819	synonymous_variant	8857	exon28			GCCAGGGCCCTCG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12828C>G	19.37:g.40368520G>C		Somatic	146	2	0.0136986		WXS	Illumina HiSeq	Phase_I	288	102	0.354167	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.500;C|0.500	0.500	strong		0.652	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ST8SIA2	8128	hgsc.bcm.edu	37	15	92987938	92987938	+	Silent	SNP	C	C	G	rs2305561	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:92987938C>G	ENST00000268164.3	+	5	858	c.621C>G	c.(619-621)ccC>ccG	p.P207P	ST8SIA2_ENST00000539113.1_Silent_p.P186P	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	207					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			CCATGAACCCCTCGGTCATCC	0.592													C|||	1121	0.223842	0.5968	0.1297	5008	,	,		18692	0.0258		0.1054	False		,,,				2504	0.1125				p.P207P		Atlas-SNP	.											.	ST8SIA2	41	.	0			c.C621G						PASS	.	C		2271,2125	597.1+/-388.8	587,1097,514	69.0	70.0	70.0		621	-0.2	1.0	15	dbSNP_100	70	1159,7437	236.8+/-268.9	83,993,3222	no	coding-synonymous	ST8SIA2	NM_006011.3		670,2090,3736	GG,GC,CC		13.483,48.3394,26.4009		207/376	92987938	3430,9562	2198	4298	6496	SO:0001819	synonymous_variant	8128	exon5			GAACCCCTCGGTC	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"""Sialyltransferases"""	10870	protein-coding gene	gene with protein product		602546	"""sialyltransferase 8 (alpha-2, 8-sialytransferase) B"""	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.621C>G	15.37:g.92987938C>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	131	57	0.435115	NM_006011	Q4VAZ0|Q92470|Q92746	Silent	SNP	ENST00000268164.3	37	CCDS10372.1																																																																																			C|0.758;G|0.242	0.242	strong		0.592	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011	
OR10Z1	128368	hgsc.bcm.edu	37	1	158577109	158577109	+	Missense_Mutation	SNP	A	A	C	rs857685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:158577109A>C	ENST00000361284.1	+	1	881	c.881A>C	c.(880-882)aAt>aCt	p.N294T		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	294			N -> T (in dbSNP:rs857685). {ECO:0000269|Ref.3}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					AGTCTAAGGAATAGGGCTATA	0.468													A|||	1213	0.242212	0.0658	0.2983	5008	,	,		21019	0.495		0.2634	False		,,,				2504	0.1585				p.N294T		Atlas-SNP	.											.	OR10Z1	99	.	0			c.A881C						PASS	.	A	THR/ASN	432,3974	210.2+/-230.7	16,400,1787	181.0	183.0	182.0		881	5.2	0.9	1	dbSNP_86	182	2170,6430	370.0+/-335.7	290,1590,2420	yes	missense	OR10Z1	NM_001004478.1	65	306,1990,4207	CC,CA,AA		25.2326,9.8048,20.0062	probably-damaging	294/314	158577109	2602,10404	2203	4300	6503	SO:0001583	missense	128368	exon1			TAAGGAATAGGGC	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"""GPCR / Class A : Olfactory receptors"""	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.881A>C	1.37:g.158577109A>C	ENSP00000354707:p.Asn294Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	145	72	0.496552	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	595	0.2724358974358974	38	0.07723577235772358	101	0.27900552486187846	252	0.4405594405594406	204	0.2691292875989446	A	12.87	2.067421	0.36470	0.098048	0.252326	ENSG00000198967	ENST00000361284	T	0.47528	0.84	5.19	5.19	0.71726	.	0.000000	0.40818	N	0.001014	T	0.48607	0.1509	L	0.34521	1.04	0.53688	P	2.6999999999999247E-5	D	0.89917	1.0	D	0.78314	0.991	T	0.57382	-0.7821	9	0.87932	D	0	.	14.1654	0.65473	1.0:0.0:0.0:0.0	rs857685;rs52811497;rs857685	294	Q8NGY1	O10Z1_HUMAN	T	294	ENSP00000354707:N294T	ENSP00000354707:N294T	N	+	2	0	OR10Z1	156843733	1.000000	0.71417	0.901000	0.35422	0.564000	0.35744	5.936000	0.70153	2.170000	0.68504	0.528000	0.53228	AAT	A|0.766;C|0.234	0.234	strong		0.468	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478	
APOL5	80831	hgsc.bcm.edu	37	22	36122517	36122517	+	Silent	SNP	T	T	C	rs17723764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:36122517T>C	ENST00000249044.2	+	3	402	c.402T>C	c.(400-402)ctT>ctC	p.L134L		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	134					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|skin(2)|urinary_tract(1)	19						ACGAGTTGCTTACCAAGACCA	0.507													C|||	1080	0.215655	0.115	0.2565	5008	,	,		19182	0.1389		0.3419	False		,,,				2504	0.272				p.L134L		Atlas-SNP	.											.	APOL5	45	.	0			c.T402C						PASS	.	C		632,3774	768.3+/-413.6	42,548,1613	73.0	74.0	74.0		402	-0.1	0.0	22	dbSNP_123	74	2924,5676	669.4+/-402.7	504,1916,1880	no	coding-synonymous	APOL5	NM_030642.1		546,2464,3493	CC,CT,TT		34.0,14.3441,27.3412		134/434	36122517	3556,9450	2203	4300	6503	SO:0001819	synonymous_variant	80831	exon3			GTTGCTTACCAAG	AY014878	CCDS13920.1	22q12.3	2013-01-24			ENSG00000128313	ENSG00000128313		"""Apolipoproteins"""	14869	protein-coding gene	gene with protein product		607255				11374903	Standard	NM_030642		Approved	APOLV	uc003aof.3	Q9BWW9	OTTHUMG00000150588	ENST00000249044.2:c.402T>C	22.37:g.36122517T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	141	76	0.539007	NM_030642	Q5TFL9|Q9UGW5	Silent	SNP	ENST00000249044.2	37	CCDS13920.1																																																																																			C|0.262;N|0.000	0.262	strong		0.507	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
OR56A4	120793	hgsc.bcm.edu	37	11	6023581	6023581	+	Silent	SNP	A	A	G	rs11040248	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6023581A>G	ENST00000330728.4	-	1	843	c.798T>C	c.(796-798)ctT>ctC	p.L266L		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAATAAGGATAAGATCAGAGC	0.468													.|||	813	0.16234	0.0582	0.1945	5008	,	,		20590	0.0794		0.2694	False		,,,				2504	0.2556				p.L266L		Atlas-SNP	.											.	OR56A4	66	.	0			c.T798C						PASS	.	A		475,3927	222.6+/-239.4	30,415,1756	35.0	36.0	35.0		798	-0.8	0.2	11	dbSNP_120	35	2563,6029	415.9+/-351.9	399,1765,2132	no	coding-synonymous	OR56A4	NM_001005179.2		429,2180,3888	GG,GA,AA		29.8301,10.7905,23.38		266/366	6023581	3038,9956	2201	4296	6497	SO:0001819	synonymous_variant	120793	exon1			AAGGATAAGATCA	BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"""GPCR / Class A : Olfactory receptors"""	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.798T>C	11.37:g.6023581A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_001005179	B9EH17	Silent	SNP	ENST00000330728.4	37	CCDS31404.1																																																																																			A|0.799;G|0.201	0.201	strong		0.468	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179	
AMTN	401138	hgsc.bcm.edu	37	4	71384537	71384537	+	Missense_Mutation	SNP	C	C	T	rs35286445	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:71384537C>T	ENST00000339336.4	+	2	173	c.43C>T	c.(43-45)Cgg>Tgg	p.R15W	AMTN_ENST00000504451.1_Missense_Mutation_p.R15W	NM_212557.2	NP_997722.1	Q6UX39	AMTN_HUMAN	amelotin	15					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|odontogenesis of dentin-containing tooth (GO:0042475)	basal lamina (GO:0005605)|cell-cell junction (GO:0005911)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)|skin(1)	19			Lung(101;0.235)			AGGATCAACTCGGTCATTACC	0.393													C|||	571	0.114018	0.0068	0.1052	5008	,	,		19467	0.1875		0.164	False		,,,				2504	0.138				p.R15W		Atlas-SNP	.											.	AMTN	28	.	0			c.C43T						PASS	.	C	TRP/ARG	139,4267	99.4+/-138.0	2,135,2066	243.0	223.0	230.0		43	4.9	1.0	4	dbSNP_126	230	1198,7402	242.2+/-272.3	86,1026,3188	yes	missense	AMTN	NM_212557.2	101	88,1161,5254	TT,TC,CC		13.9302,3.1548,10.2799	possibly-damaging	15/210	71384537	1337,11669	2203	4300	6503	SO:0001583	missense	401138	exon2			TCAACTCGGTCAT	AY358528	CCDS3542.1, CCDS68716.1	4q13.3	2006-12-12			ENSG00000187689	ENSG00000187689			33188	protein-coding gene	gene with protein product		610912				16304441	Standard	NM_001286731		Approved	UNQ689, RSTI689	uc003hfk.1	Q6UX39	OTTHUMG00000129906	ENST00000339336.4:c.43C>T	4.37:g.71384537C>T	ENSP00000341013:p.Arg15Trp	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	143	60	0.41958	NM_212557	Q0P503|Q0P506	Missense_Mutation	SNP	ENST00000339336.4	37	CCDS3542.1	254	0.1163003663003663	3	0.006097560975609756	38	0.10497237569060773	105	0.18356643356643357	108	0.1424802110817942	C	13.10	2.137570	0.37728	0.031548	0.139302	ENSG00000187689	ENST00000339336;ENST00000504451	T;T	0.33654	1.41;1.4	5.76	4.91	0.64330	.	0.589854	0.15252	N	0.272246	T	0.00039	0.0001	N	0.08118	0	0.50813	P	1.0500000000002174E-4	P;P	0.49447	0.924;0.924	B;B	0.39152	0.292;0.292	T	0.08513	-1.0718	9	0.54805	T	0.06	0.2352	12.1289	0.53932	0.1714:0.8286:0.0:0.0	rs35286445	15;15	Q6UX39-2;Q6UX39	.;AMTN_HUMAN	W	15	ENSP00000341013:R15W;ENSP00000422452:R15W	ENSP00000341013:R15W	R	+	1	2	AMTN	71419126	1.000000	0.71417	0.997000	0.53966	0.687000	0.40016	2.234000	0.43035	1.423000	0.47198	0.655000	0.94253	CGG	C|0.887;T|0.113	0.113	strong		0.393	AMTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252157.1	NM_212557	
ARFGAP3	26286	hgsc.bcm.edu	37	22	43206950	43206950	+	Splice_Site	SNP	A	A	C	rs1018448	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:43206950A>C	ENST00000263245.5	-	12	1284	c.1065T>G	c.(1063-1065)agT>agG	p.S355R	ARFGAP3_ENST00000429508.2_Splice_Site_p.S283R|ARFGAP3_ENST00000437119.2_Splice_Site_p.S311R	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	355	Ser-rich.		S -> R (in dbSNP:rs1018448). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15592455}.		intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						CGTCAAAGTAACTGTAGGAGC	0.468													C|||	3515	0.701877	0.9206	0.7378	5008	,	,		18594	0.6399		0.5417	False		,,,				2504	0.6094				p.S355R	GBM(58;544 1030 21460 27159 48838)	Atlas-SNP	.											.	ARFGAP3	48	.	0			c.T1065G						PASS	.	C	ARG/SER,ARG/SER	3808,598	253.0+/-259.1	1654,500,49	76.0	73.0	74.0		933,1065	4.2	1.0	22	dbSNP_86	74	4689,3911	536.4+/-383.0	1292,2105,903	yes	missense-near-splice,missense-near-splice	ARFGAP3	NM_001142293.1,NM_014570.4	110,110	2946,2605,952	CC,CA,AA		45.4767,13.5724,34.6686	benign,benign	311/473,355/517	43206950	8497,4509	2203	4300	6503	SO:0001630	splice_region_variant	26286	exon12			AAAGTAACTGTAG	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"""ADP-ribosylation factor GTPase activating proteins"""	661	protein-coding gene	gene with protein product		612439	"""ADP-ribosylation factor GTPase activating protein 1"""	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.1065-1T>G	22.37:g.43206950A>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_014570	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Missense_Mutation	SNP	ENST00000263245.5	37	CCDS14042.1	1480	0.6776556776556777	443	0.9004065040650406	264	0.7292817679558011	375	0.6555944055944056	398	0.525065963060686	C	2.837	-0.241382	0.05906	0.864276	0.545233	ENSG00000242247	ENST00000263245;ENST00000429508;ENST00000437119	T;T;T	0.06218	3.48;3.33;3.46	5.22	4.2	0.49525	.	0.262548	0.36002	N	0.002850	T	0.00012	0.0000	N	0.01109	-1.01	0.39798	P	0.027474	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.29088	-1.0023	9	0.05833	T	0.94	.	4.3541	0.11169	0.1978:0.6411:0.0:0.1611	rs1128010	311;355	E9PB03;Q9NP61	.;ARFG3_HUMAN	R	355;283;311	ENSP00000263245:S355R;ENSP00000393959:S283R;ENSP00000388791:S311R	ENSP00000263245:S355R	S	-	3	2	ARFGAP3	41536894	1.000000	0.71417	0.998000	0.56505	0.227000	0.25037	1.294000	0.33365	1.192000	0.43071	-0.121000	0.15023	AGT	A|0.326;C|0.674	0.674	strong		0.468	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570	Missense_Mutation
FSTL5	56884	hgsc.bcm.edu	37	4	162307060	162307060	+	Silent	SNP	G	G	T	rs17040984	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:162307060G>T	ENST00000306100.5	-	16	2819	c.2383C>A	c.(2383-2385)Cgg>Agg	p.R795R	FSTL5_ENST00000427802.2_Silent_p.R785R|FSTL5_ENST00000536695.1_Silent_p.R794R|FSTL5_ENST00000379164.4_Silent_p.R794R|RP11-234O6.2_ENST00000508189.1_RNA	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	795						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		CTGTTTTTCCGGTTCCAAGGC	0.458													G|||	912	0.182109	0.0416	0.1657	5008	,	,		18093	0.3175		0.2256	False		,,,				2504	0.1994				p.R795R		Atlas-SNP	.											FSTL5,NS,carcinoma,+2,1	FSTL5	207	1	0			c.C2383A						PASS	.	G	,,	323,4083	171.6+/-201.8	12,299,1892	225.0	201.0	209.0		2380,2353,2383	1.6	0.0	4	dbSNP_123	209	2173,6427	372.0+/-336.5	273,1627,2400	no	coding-synonymous,coding-synonymous,coding-synonymous	FSTL5	NM_001128427.1,NM_001128428.1,NM_020116.3	,,	285,1926,4292	TT,TG,GG		25.2674,7.3309,19.1911	,,	794/847,785/838,795/848	162307060	2496,10510	2203	4300	6503	SO:0001819	synonymous_variant	56884	exon16			TTTTCCGGTTCCA	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.2383C>A	4.37:g.162307060G>T		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	274	135	0.492701	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	37	CCDS3802.1																																																																																			G|0.805;T|0.195	0.195	strong		0.458	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
USP47	55031	hgsc.bcm.edu	37	11	11941793	11941793	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:11941793C>T	ENST00000399455.2	+	10	1240	c.1120C>T	c.(1120-1122)Cgg>Tgg	p.R374W	USP47_ENST00000527733.1_Missense_Mutation_p.R354W|USP47_ENST00000539466.1_5'UTR|USP47_ENST00000339865.5_Missense_Mutation_p.R286W	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	374	USP.				base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		GTGTGATGCACGGAAGGTAAA	0.373																																					p.R286W		Atlas-SNP	.											USP47,rectum,carcinoma,-2,5	USP47	91	5	0			c.C856T						scavenged	.						118.0	108.0	111.0					11																	11941793		1840	4074	5914	SO:0001583	missense	55031	exon8			GATGCACGGAAGG	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"""Ubiquitin-specific peptidases"""	20076	protein-coding gene	gene with protein product		614460	"""Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)"", ""ubiquitin specific protease 47"""			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.1120C>T	11.37:g.11941793C>T	ENSP00000382382:p.Arg374Trp	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	188	3	0.0159574	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	37		.	.	.	.	.	.	.	.	.	.	C	20.4	3.978509	0.74360	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455;ENST00000535588	T;T;T	0.05786	3.39;3.39;3.39	5.38	4.45	0.53987	.	0.000000	0.85682	D	0.000000	T	0.18635	0.0447	L	0.49126	1.545	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.74348	0.983;0.972	T	0.00325	-1.1816	10	0.66056	D	0.02	.	13.1306	0.59380	0.3468:0.6532:0.0:0.0	.	354;286	E9PM46;Q96K76-2	.;.	W	286;354;374;374	ENSP00000339957:R286W;ENSP00000433146:R354W;ENSP00000382382:R374W	ENSP00000339957:R286W	R	+	1	2	USP47	11898369	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.831000	0.62752	1.234000	0.43709	0.563000	0.77884	CGG	.	.	none		0.373	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944	
FCGR2A	2212	hgsc.bcm.edu	37	1	161487914	161487914	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:161487914C>T	ENST00000271450.6	+	7	968	c.930C>T	c.(928-930)aaC>aaT	p.N310N	RP11-25K21.6_ENST00000537821.2_RNA|FCGR2A_ENST00000367972.4_Silent_p.N309N|FCGR2A_ENST00000486608.1_3'UTR	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	310					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TTCCTCCCAACGACCATGTCA	0.448																																					p.N310N		Atlas-SNP	.											FCGR2A,colon,carcinoma,0,1	FCGR2A	38	1	0			c.C930T						scavenged	.						77.0	77.0	77.0					1																	161487914		2203	4297	6500	SO:0001819	synonymous_variant	2212	exon7			TCCCAACGACCAT	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3616	protein-coding gene	gene with protein product	"""Immunoglobulin G Fc receptor II"""	146790	"""Fc fragment of IgG, low affinity IIa, receptor for (CD32)"""	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.930C>T	1.37:g.161487914C>T		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	330	16	0.0484848	NM_001136219	Q8WUN1|Q8WW64	Silent	SNP	ENST00000271450.6	37	CCDS44264.1																																																																																			C|0.250;T|0.750	0.750	weak		0.448	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642	
KIF3C	3797	hgsc.bcm.edu	37	2	26174744	26174744	+	Silent	SNP	C	C	T	rs71441005	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:26174744C>T	ENST00000264712.3	-	5	2499	c.1920G>A	c.(1918-1920)ccG>ccA	p.P640P	KIF3C_ENST00000496378.1_5'UTR|KIF3C_ENST00000405914.1_Silent_p.P640P	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	640	Globular. {ECO:0000255}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTTCTCCTCCGGCGGGATGA	0.552													C|||	171	0.0341454	0.0968	0.0101	5008	,	,		19309	0.001		0.008	False		,,,				2504	0.0276				p.P640P		Atlas-SNP	.											.	KIF3C	79	.	0			c.G1920A						PASS	.	C		313,4093	169.1+/-199.8	12,289,1902	126.0	109.0	115.0		1920	-12.1	0.2	2	dbSNP_130	115	76,8524	44.5+/-102.8	1,74,4225	no	coding-synonymous	KIF3C	NM_002254.6		13,363,6127	TT,TC,CC		0.8837,7.1039,2.9909		640/794	26174744	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	3797	exon5			CTCCTCCGGCGGG		CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731		"""Kinesins"""	6321	protein-coding gene	gene with protein product		602845				9480755	Standard	NM_002254		Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000264712.3:c.1920G>A	2.37:g.26174744C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_002254	O43544|Q4ZG18|Q53SX5|Q562F7	Silent	SNP	ENST00000264712.3	37	CCDS1719.1																																																																																			C|0.971;T|0.029	0.029	strong		0.552	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1		
EVL	51466	hgsc.bcm.edu	37	14	100613197	100613197	+	IGR	SNP	G	G	A	rs140696950	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100613197G>A	ENST00000402714.2	+	0	2353				DEGS2_ENST00000305631.5_Silent_p.H291H|DEGS2_ENST00000553834.1_Missense_Mutation_p.L44F|DEGS2_ENST00000557117.1_5'Flank			Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin filament organization (GO:0007015)|actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of stress fiber assembly (GO:0051496)|protein homotetramerization (GO:0051289)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	profilin binding (GO:0005522)|SH3 domain binding (GO:0017124)			cervix(1)|large_intestine(5)|lung(3)|ovary(3)|urinary_tract(2)	14		Melanoma(154;0.152)				TCACCCAGGAGTGGTGCTGCG	0.637													G|||	14	0.00279553	0.0008	0.0058	5008	,	,		18492	0.0		0.004	False		,,,				2504	0.0051				p.H291H		Atlas-SNP	.											.	DEGS2	25	.	0			c.C873T						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	119.0	114.0	116.0		873	3.8	1.0	14	dbSNP_134	116	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous	DEGS2	NM_206918.2		0,22,6481	AA,AG,GG		0.2093,0.0908,0.1692		291/324	100613197	22,12984	2203	4300	6503	SO:0001628	intergenic_variant	123099	exon3			CCAGGAGTGGTGC	AF112209	CCDS9955.1	14q32.2	2014-08-13			ENSG00000196405	ENSG00000196405			20234	protein-coding gene	gene with protein product						10945997, 10993894	Standard	NM_016337		Approved	RNB6	uc001ygu.3	Q9UI08	OTTHUMG00000171530		14.37:g.100613197G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_206918	A8K105|O95884|Q7Z522|Q8TBV1|Q9UF25|Q9UIC2	Silent	SNP	ENST00000402714.2	37		3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	14.12	2.441563	0.43326	9.08E-4	0.002093	ENSG00000168350	ENST00000553834	T	0.58210	0.35	4.86	3.75	0.43078	.	.	.	.	.	T	0.37183	0.0994	.	.	.	0.23519	N	0.997508	.	.	.	.	.	.	T	0.22906	-1.0203	5	.	.	.	-28.8619	8.174	0.31270	0.1037:0.2977:0.5986:0.0	.	.	.	.	F	44	ENSP00000450637:L44F	.	L	-	1	0	DEGS2	99682950	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	0.611000	0.24268	2.251000	0.74343	0.561000	0.74099	CTC	G|0.998;A|0.002	0.002	strong		0.637	EVL-006	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000413958.1		
SLC6A6	6533	hgsc.bcm.edu	37	3	14518802	14518802	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:14518802C>T	ENST00000454876.2	+	11	1628	c.1299C>T	c.(1297-1299)gcC>gcT	p.A433A	SLC6A6_ENST00000360861.3_Silent_p.A433A			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	433					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|taurine transport (GO:0015734)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|taurine binding (GO:0030977)|taurine:sodium symporter activity (GO:0005369)	p.A433A(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)	28						TCTTCATCGCCTTCGTGTGTA	0.532																																					p.A433A		Atlas-SNP	.											SLC6A6,NS,carcinoma,+2,2	SLC6A6	58	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C1299T						scavenged	.						167.0	137.0	147.0					3																	14518802		2203	4300	6503	SO:0001819	synonymous_variant	6533	exon11			CATCGCCTTCGTG		CCDS33705.1, CCDS46765.1	3p25.1	2013-07-19	2013-07-19		ENSG00000131389	ENSG00000131389		"""Solute carriers"""	11052	protein-coding gene	gene with protein product	"""taurine transporter"""	186854	"""solute carrier family 6 (neurotransmitter transporter, taurine), member 6"""			8010975, 8382624	Standard	XM_006713307		Approved	TAUT	uc010heg.4	P31641	OTTHUMG00000155525	ENST00000454876.2:c.1299C>T	3.37:g.14518802C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	174	3	0.0172414	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Silent	SNP	ENST00000454876.2	37	CCDS33705.1																																																																																			.	.	none		0.532	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043	
SYTL2	54843	hgsc.bcm.edu	37	11	85436868	85436868	+	Intron	SNP	G	G	C	rs597480	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:85436868G>C	ENST00000528231.1	-	7	1737				SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000359152.5_Missense_Mutation_p.A735G|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000525423.1_Missense_Mutation_p.A211G|SYTL2_ENST00000354566.3_Missense_Mutation_p.A211G	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CTCAGTATCAGCAAAATCTGT	0.398													G|||	2613	0.521765	0.4077	0.4986	5008	,	,		21672	0.5972		0.6282	False		,,,				2504	0.5051				p.A211G		Atlas-SNP	.											.	SYTL2	231	.	0			c.C632G						PASS	.	G	,,,GLY/ALA,GLY/ALA	1927,2479	547.8+/-377.4	436,1055,712	147.0	133.0	138.0		,,,632,632	3.0	0.0	11	dbSNP_83	138	5436,3162	655.2+/-401.2	1734,1968,597	yes	intron,intron,intron,missense,missense	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,60,60	2170,3023,1309	CC,CG,GG		36.776,43.7358,43.379	,,,possibly-damaging,possibly-damaging	,,,211/1273,211/1257	85436868	7363,5641	2203	4299	6502	SO:0001627	intron_variant	54843	exon1			GTATCAGCAAAAT	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2070C>G	11.37:g.85436868G>C		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	242	242	1	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	1202	0.5503663003663004	207	0.42073170731707316	195	0.5386740331491713	323	0.5646853146853147	477	0.6292875989445911	G	11.68	1.709859	0.30322	0.437358	0.63224	ENSG00000137501	ENST00000359152;ENST00000354566;ENST00000525423	T;T;T	0.33654	1.4;1.41;1.41	6.03	2.97	0.34412	.	0.135236	0.33792	N	0.004544	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;P;P	0.37370	0.592;0.592;0.592	B;B;B	0.40199	0.322;0.322;0.322	T	0.37337	-0.9710	8	.	.	.	-0.2866	5.1608	0.15060	0.2405:0.1501:0.6094:0.0	rs597480;rs17810982;rs56612956;rs597480	211;211;211	Q9HCH5-11;Q9HCH5-7;Q9HCH5-8	.;.;.	G	735;211;211	ENSP00000352065:A735G;ENSP00000346576:A211G;ENSP00000432694:A211G	.	A	-	2	0	SYTL2	85114516	0.000000	0.05858	0.009000	0.14445	0.899000	0.52679	0.469000	0.22067	0.849000	0.35215	0.655000	0.94253	GCT	G|0.491;C|0.509	0.509	strong		0.398	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240805	39240805	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240805G>T	ENST00000391417.4	+	1	347	c.347G>T	c.(346-348)cGc>cTc	p.R116L		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	141	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)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						agctgctgccgcccctgctgc	0.672																																					p.R116L		Atlas-SNP	.											KRTAP4-7,caecum,carcinoma,+1,1	KRTAP4-7	49	1	0			c.G347T						scavenged	.						18.0	18.0	18.0					17																	39240805		692	1587	2279	SO:0001583	missense	100132476	exon1			GCTGCCGCCCCTG	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.347G>T	17.37:g.39240805G>T	ENSP00000375236:p.Arg116Leu	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	59	9	0.152542	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	6.805	0.517638	0.13005	.	.	ENSG00000240871	ENST00000391417	T	0.00606	6.26	3.15	2.13	0.27403	.	0.163808	0.19966	U	0.102091	T	0.00496	0.0016	.	.	.	0.09310	N	1	B	0.18461	0.028	B	0.15052	0.012	T	0.45804	-0.9236	9	0.28530	T	0.3	.	9.2621	0.37619	0.0:0.0:0.7821:0.2179	.	171	Q9BYR0	KRA47_HUMAN	L	116	ENSP00000375236:R116L	ENSP00000375236:R116L	R	+	2	0	KRTAP4-7	36494331	0.000000	0.05858	0.028000	0.17463	0.502000	0.33828	-0.081000	0.11321	0.603000	0.29913	0.289000	0.19496	CGC	.	.	none		0.672	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
KDM3B	51780	hgsc.bcm.edu	37	5	137766066	137766066	+	Silent	SNP	G	G	A	rs61749634	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:137766066G>A	ENST00000314358.5	+	22	5222	c.5022G>A	c.(5020-5022)gtG>gtA	p.V1674V	KDM3B_ENST00000394866.1_Silent_p.V1330V|KDM3B_ENST00000542866.1_Silent_p.V706V	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1674	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						GGGCTATTGTGCAGTTCCTAG	0.532																																					p.V1674V		Atlas-SNP	.											.	KDM3B	177	.	0			c.G5022A						PASS	.	G		242,4164	143.1+/-178.2	8,226,1969	161.0	147.0	152.0		5022	3.9	1.0	5	dbSNP_129	152	279,8321	104.8+/-165.8	4,271,4025	yes	coding-synonymous	KDM3B	NM_016604.3		12,497,5994	AA,AG,GG		3.2442,5.4925,4.0058		1674/1762	137766066	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	51780	exon22			TATTGTGCAGTTC	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"""Chromatin-modifying enzymes / K-demethylases"""	1337	protein-coding gene	gene with protein product		609373	"""chromosome 5 open reading frame 7"", ""jumonji domain containing 1B"""	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.5022G>A	5.37:g.137766066G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	184	95	0.516304	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	37	CCDS34242.1																																																																																			A|0.040;C|0.000;G|0.960;T|0.000	0.040	strong		0.532	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
TPSD1	23430	hgsc.bcm.edu	37	16	1306817	1306817	+	Missense_Mutation	SNP	G	G	A	rs3993983		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306817G>A	ENST00000211076.3	+	3	422	c.274G>A	c.(274-276)Gcc>Acc	p.A92T	TPSD1_ENST00000397534.2_Missense_Mutation_p.A85T|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	92	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.A92T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				GGATCTGGCCGCCCTCAGGGT	0.652																																					p.A92T		Atlas-SNP	.											TPSD1,trunk,malignant_melanoma,0,1	TPSD1	47	1	1	Substitution - Missense(1)	skin(1)	c.G274A						PASS	.						42.0	48.0	46.0					16																	1306817		2199	4300	6499	SO:0001583	missense	23430	exon3			CTGGCCGCCCTCA	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.274G>A	16.37:g.1306817G>A	ENSP00000211076:p.Ala92Thr	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	424	56	0.132075	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	.	.	.	.	.	.	.	.	.	.	-	0.599	-0.829982	0.02734	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.88975	-2.45;-2.45	2.55	-5.1	0.02911	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.840310	0.02910	N	0.136553	T	0.73442	0.3587	N	0.12920	0.275	0.09310	N	1	B	0.20459	0.045	B	0.11329	0.006	T	0.65977	-0.6037	10	0.10111	T	0.7	.	2.4616	0.04542	0.3598:0.0:0.2688:0.3714	rs3993983	92	Q9BZJ3	TRYD_HUMAN	T	85;92	ENSP00000380668:A85T;ENSP00000211076:A92T	ENSP00000211076:A92T	A	+	1	0	TPSD1	1246818	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.726000	0.01861	-1.446000	0.01945	0.185000	0.17295	GCC	G|0.999;A|0.001	0.001	weak		0.652	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
USP10	9100	hgsc.bcm.edu	37	16	84808824	84808824	+	Silent	SNP	C	C	G	rs774298	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84808824C>G	ENST00000219473.7	+	13	2315	c.2202C>G	c.(2200-2202)ctC>ctG	p.L734L	USP10_ENST00000570191.1_Silent_p.L738L	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	734	USP.				autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.L734L(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						CCTATCGGCTCTTTGCAGGTG	0.398													c|||	2179	0.435104	0.3079	0.3818	5008	,	,		20790	0.506		0.6163	False		,,,				2504	0.3855				p.L738L		Atlas-SNP	.											USP10,NS,carcinoma,0,1	USP10	51	1	1	Substitution - coding silent(1)	stomach(1)	c.C2214G						PASS	.	C		1235,2437		217,801,818	74.0	71.0	72.0		2202	-9.5	0.8	16	dbSNP_86	72	5013,3165		1528,1957,604	no	coding-synonymous	USP10	NM_005153.2		1745,2758,1422	GG,GC,CC		38.7014,33.6329,47.2743		734/799	84808824	6248,5602	1836	4089	5925	SO:0001819	synonymous_variant	9100	exon14			TCGGCTCTTTGCA	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.2202C>G	16.37:g.84808824C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	31	0.3875	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			A|0.004;C|0.853;G|0.143	0.143	strong		0.398	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
DRC1	92749	hgsc.bcm.edu	37	2	26679362	26679362	+	Missense_Mutation	SNP	G	G	A	rs35313480	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:26679362G>A	ENST00000288710.2	+	17	2274	c.2200G>A	c.(2200-2202)Gtg>Atg	p.V734M		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	734			V -> M (in dbSNP:rs35313480).		axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											TCCCACTCAGGTGTTGCGGGT	0.542													G|||	109	0.0217652	0.0023	0.0519	5008	,	,		19088	0.0		0.0497	False		,,,				2504	0.0204				p.V734M		Atlas-SNP	.											.	CCDC164	84	.	0			c.G2200A						PASS	.	G	MET/VAL	41,4365	43.1+/-76.7	0,41,2162	105.0	99.0	101.0		2200	4.8	0.9	2	dbSNP_126	101	550,8050	151.3+/-206.1	13,524,3763	yes	missense	CCDC164	NM_145038.2	21	13,565,5925	AA,AG,GG		6.3953,0.9305,4.5441	benign	734/741	26679362	591,12415	2203	4300	6503	SO:0001583	missense	92749	exon17			ACTCAGGTGTTGC	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"""chromosome 2 open reading frame 39"", ""coiled-coil domain containing 164"", ""dynein regulatory complex subunit 1 homolog (Chlamydomonas)"""	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.2200G>A	2.37:g.26679362G>A	ENSP00000288710:p.Val734Met	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	223	105	0.470852	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	37	CCDS1723.1	64	0.029304029304029304	2	0.0040650406504065045	24	0.06629834254143646	0	0.0	38	0.05013192612137203	G	12.28	1.890752	0.33348	0.009305	0.063953	ENSG00000157856	ENST00000288710	T	0.15952	2.38	4.84	4.84	0.62591	.	0.917959	0.09241	N	0.829194	T	0.01489	0.0048	L	0.49513	1.565	0.23972	N	0.996305	B	0.22003	0.063	B	0.21917	0.037	T	0.04128	-1.0975	10	0.46703	T	0.11	-10.2951	13.8055	0.63227	0.0:0.0:1.0:0.0	rs35313480;rs61746007	734	Q96MC2	CC164_HUMAN	M	734	ENSP00000288710:V734M	ENSP00000288710:V734M	V	+	1	0	CCDC164	26532866	1.000000	0.71417	0.914000	0.36105	0.515000	0.34225	2.445000	0.44899	2.398000	0.81561	0.563000	0.77884	GTG	G|0.960;A|0.040	0.040	strong		0.542	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038	
HSPA12B	116835	hgsc.bcm.edu	37	20	3732633	3732633	+	Silent	SNP	C	C	T	rs541760	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3732633C>T	ENST00000254963.2	+	13	2026	c.1881C>T	c.(1879-1881)tgC>tgT	p.C627C	HSPA12B_ENST00000542646.1_Silent_p.C461C	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	627							ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						TGCGCAAATGCGGCGCGCTCA	0.736													C|||	2954	0.589856	0.528	0.6499	5008	,	,		10207	0.6121		0.5626	False		,,,				2504	0.636				p.C627C		Atlas-SNP	.											.	HSPA12B	43	.	0			c.C1881T						PASS	.	C	,	2234,1612		690,854,379	5.0	5.0	5.0		1878,1881	-1.2	1.0	20	dbSNP_83	5	4676,2784		1549,1578,603	no	coding-synonymous,coding-synonymous	HSPA12B	NM_001197327.1,NM_052970.4	,	2239,2432,982	TT,TC,CC		37.319,41.9137,38.882	,	626/686,627/687	3732633	6910,4396	1923	3730	5653	SO:0001819	synonymous_variant	116835	exon13			CAAATGCGGCGCG	AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"""Heat shock proteins / HSP70"""	16193	protein-coding gene	gene with protein product		610702	"""chromosome 20 open reading frame 60"""	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.1881C>T	20.37:g.3732633C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	NM_052970	D3DVX7|Q2TAK3|Q9BR52	Silent	SNP	ENST00000254963.2	37	CCDS13061.1																																																																																			C|0.439;T|0.561	0.561	strong		0.736	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970	
DCST1	149095	hgsc.bcm.edu	37	1	155006999	155006999	+	Silent	SNP	C	C	T	rs6680600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:155006999C>T	ENST00000295542.1	+	3	246	c.150C>T	c.(148-150)ctC>ctT	p.L50L	DCST1_ENST00000368419.2_Silent_p.L50L|DCST2_ENST00000295536.5_5'Flank|DCST2_ENST00000368424.3_5'Flank|DCST1_ENST00000423025.2_Silent_p.L50L|DCST1_ENST00000392480.1_Silent_p.L50L	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	50						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			TCACTGCTCTCCTGCTGGGGG	0.652													C|||	2833	0.565695	0.4266	0.5922	5008	,	,		16607	0.8819		0.3579	False		,,,				2504	0.6227				p.L50L		Atlas-SNP	.											.	DCST1	69	.	0			c.C150T						PASS	.	C	,	1897,2509	533.7+/-373.8	383,1131,689	64.0	76.0	72.0		150,150	4.3	1.0	1	dbSNP_116	72	2962,5638	451.6+/-362.7	512,1938,1850	no	coding-synonymous,coding-synonymous	DCST1	NM_001143687.2,NM_152494.3	,	895,3069,2539	TT,TC,CC		34.4419,43.0549,37.3597	,	50/682,50/707	155006999	4859,8147	2203	4300	6503	SO:0001819	synonymous_variant	149095	exon3			TGCTCTCCTGCTG	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.150C>T	1.37:g.155006999C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Silent	SNP	ENST00000295542.1	37	CCDS1083.1																																																																																			C|0.550;T|0.450	0.450	strong		0.652	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494	
CR2	1380	hgsc.bcm.edu	37	1	207646462	207646462	+	Missense_Mutation	SNP	G	G	A	rs17615	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207646462G>A	ENST00000367058.3	+	10	2105	c.1916G>A	c.(1915-1917)aGt>aAt	p.S639N	CR2_ENST00000367057.3_Missense_Mutation_p.S639N|CR2_ENST00000367059.3_Missense_Mutation_p.S639N|CR2_ENST00000458541.2_Missense_Mutation_p.S612N	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	639	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.		S -> N (in dbSNP:rs17615). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17360460}.		B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						TTGAAGGGCAGTAGTCAGATT	0.388													G|||	1294	0.258387	0.4251	0.2017	5008	,	,		20652	0.1071		0.2913	False		,,,				2504	0.1953				p.S639N		Atlas-SNP	.											.	CR2	164	.	0			c.G1916A						PASS	.	G	ASN/SER,ASN/SER	1674,2732	508.8+/-367.0	334,1006,863	93.0	92.0	92.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1916,1916	4.8	1.0	1	dbSNP_63	92	2714,5886	433.7+/-357.5	422,1870,2008	yes	missense,missense	CR2	NM_001006658.2,NM_001877.4	46,46	756,2876,2871	AA,AG,GG		31.5581,37.9936,33.7383	probably-damaging,probably-damaging	639/1093,639/1034	207646462	4388,8618	2203	4300	6503	SO:0001583	missense	1380	exon10			AGGGCAGTAGTCA	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1916G>A	1.37:g.207646462G>A	ENSP00000356025:p.Ser639Asn	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	586	0.2683150183150183	206	0.4186991869918699	90	0.24861878453038674	65	0.11363636363636363	225	0.29683377308707126	G	19.15	3.772477	0.69992	0.379936	0.315581	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.77	4.8	0.61643	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	L	0.52823	1.66	0.30327	P	0.786987	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.83275	0.995;0.982;0.996;0.986	T	0.38415	-0.9662	8	0.41790	T	0.15	.	11.2876	0.49230	0.0:0.0:0.8184:0.1816	rs17615;rs2274565;rs17045200;rs57858208;rs17615	639;639;639;639	C9JHD2;Q5SR47;P20023;P20023-3	.;.;CR2_HUMAN;.	N	639;639;639;612	ENSP00000356025:S639N;ENSP00000356024:S639N;ENSP00000356026:S639N;ENSP00000404222:S612N	ENSP00000356024:S639N	S	+	2	0	CR2	205713085	0.056000	0.20664	0.971000	0.41717	0.994000	0.84299	0.504000	0.22626	2.723000	0.93209	0.655000	0.94253	AGT	G|0.702;A|0.298	0.298	strong		0.388	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
NHSL2	340527	hgsc.bcm.edu	37	X	71359555	71359555	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:71359555G>A	ENST00000373677.1	+	2	2321	c.1059G>A	c.(1057-1059)tcG>tcA	p.S353S	NHSL2_ENST00000510661.1_Silent_p.S488S|NHSL2_ENST00000540800.1_Silent_p.S719S|NHSL2_ENST00000535692.1_Silent_p.S353S			Q5HYW2	NHSL2_HUMAN	NHS-like 2	353	Ser-rich.									NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					CCAGCCAGTCGGAAACACCAA	0.592																																					p.S719S		Atlas-SNP	.											.	NHSL2	148	.	0			c.G2157A						PASS	.						70.0	52.0	58.0					X																	71359555		2203	4300	6503	SO:0001819	synonymous_variant	340527	exon6			CCAGTCGGAAACA			Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.1059G>A	X.37:g.71359555G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	84	6	0.0714286	NM_001013627	B2RN94	Silent	SNP	ENST00000373677.1	37																																																																																				.	.	none		0.592	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627	
IQGAP3	128239	hgsc.bcm.edu	37	1	156518379	156518379	+	Missense_Mutation	SNP	G	G	A	rs744224	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156518379G>A	ENST00000361170.2	-	17	1997	c.1987C>T	c.(1987-1989)Cgt>Tgt	p.R663C		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	663			R -> C (in dbSNP:rs744224). {ECO:0000269|Ref.1, ECO:0000269|Ref.2}.		activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTACCTGGACGCTGTTTCTTT	0.607													G|||	2039	0.407149	0.2958	0.3646	5008	,	,		19167	0.5724		0.2575	False		,,,				2504	0.5716				p.R663C		Atlas-SNP	.											IQGAP3,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	IQGAP3	146	1	0			c.C1987T						scavenged	.	G	CYS/ARG	1316,3090	443.9+/-347.2	196,924,1083	143.0	101.0	115.0		1987	1.9	0.0	1	dbSNP_86	115	2370,6230	394.8+/-344.8	341,1688,2271	yes	missense	IQGAP3	NM_178229.4	180	537,2612,3354	AA,AG,GG		27.5581,29.8684,28.3408	benign	663/1632	156518379	3686,9320	2203	4300	6503	SO:0001583	missense	128239	exon17			CTGGACGCTGTTT	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.1987C>T	1.37:g.156518379G>A	ENSP00000354451:p.Arg663Cys	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	141	77	0.546099	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	758	0.34706959706959706	134	0.27235772357723576	123	0.3397790055248619	311	0.5437062937062938	190	0.25065963060686014	G	3.973	-0.007916	0.07773	0.298684	0.275581	ENSG00000183856	ENST00000361170	T	0.06849	3.25	4.85	1.89	0.25635	.	1.156880	0.06169	N	0.677301	T	0.02455	0.0075	L	0.29908	0.895	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.42085	-0.9472	9	0.48119	T	0.1	2.333	9.5002	0.39013	0.2415:0.0:0.7585:0.0	rs744224;rs1774954;rs17391814;rs57842273;rs744224	663	Q86VI3	IQGA3_HUMAN	C	663	ENSP00000354451:R663C	ENSP00000354451:R663C	R	-	1	0	IQGAP3	154785003	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.029000	0.12329	0.108000	0.17862	-0.258000	0.10820	CGT	G|0.683;A|0.317	0.317	strong		0.607	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
FMO3	2328	hgsc.bcm.edu	37	1	171076935	171076935	+	Silent	SNP	C	C	T	rs1800822	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:171076935C>T	ENST00000367755.4	+	4	552	c.441C>T	c.(439-441)tcC>tcT	p.S147S	FMO3_ENST00000392085.2_Silent_p.S147S|FMO3_ENST00000542847.1_Silent_p.S127S|FMO3_ENST00000538429.1_Silent_p.S84S	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	147					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)	p.S147S(1)		endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	TGGTTTGTTCCGGACATCATG	0.403													C|||	709	0.141573	0.0651	0.2334	5008	,	,		15135	0.1944		0.0636	False		,,,				2504	0.2055				p.S147S		Atlas-SNP	.											FMO3,NS,carcinoma,0,1	FMO3	73	1	1	Substitution - coding silent(1)	stomach(1)	c.C441T						PASS	.	C	,	355,4051	182.6+/-210.3	17,321,1865	151.0	152.0	152.0		441,441	-1.4	1.0	1	dbSNP_89	152	486,8114	141.4+/-197.7	8,470,3822	no	coding-synonymous,coding-synonymous	FMO3	NM_001002294.2,NM_006894.5	,	25,791,5687	TT,TC,CC		5.6512,8.0572,6.4662	,	147/533,147/533	171076935	841,12165	2203	4300	6503	SO:0001819	synonymous_variant	2328	exon4			TTGTTCCGGACAT	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.441C>T	1.37:g.171076935C>T		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	188	98	0.521277	NM_006894	B2R816|Q14854|Q8N5N5	Silent	SNP	ENST00000367755.4	37	CCDS1292.1																																																																																			C|0.898;T|0.102	0.102	strong		0.403	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	
LILRB1	10859	hgsc.bcm.edu	37	19	55146139	55146139	+	Missense_Mutation	SNP	A	A	G	rs1061683	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55146139A>G	ENST00000396331.1	+	11	1765	c.1408A>G	c.(1408-1410)Atc>Gtc	p.I470V	LILRB1_ENST00000434867.2_Missense_Mutation_p.I470V|LILRB1_ENST00000396321.2_Missense_Mutation_p.I470V|LILRB1_ENST00000418536.2_Missense_Mutation_p.I454V|LILRB1_ENST00000396315.1_Missense_Mutation_p.I471V|LILRB1_ENST00000448689.1_Missense_Mutation_p.I470V|LILRB1_ENST00000396332.4_Missense_Mutation_p.I470V|LILRB1_ENST00000427581.2_Missense_Mutation_p.I520V|LILRB1_ENST00000324602.7_Missense_Mutation_p.I471V|LILRB1_ENST00000396317.1_Missense_Mutation_p.I454V|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000396327.3_Missense_Mutation_p.I471V	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	470					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		GGTGGCCGTCAtcctactgct	0.577										HNSCC(37;0.09)			N|||	612	0.122204	0.2035	0.0648	5008	,	,		17091	0.0198		0.1213	False		,,,				2504	0.1595				p.I471V		Atlas-SNP	.											.	LILRB1	140	.	0			c.A1411G						PASS	.						169.0	134.0	146.0					19																	55146139		2203	4300	6503	SO:0001583	missense	10859	exon10			GCCGTCATCCTAC	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1408A>G	19.37:g.55146139A>G	ENSP00000379622:p.Ile470Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	82	33	0.402439	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	218	0.09981684981684982	97	0.19715447154471544	18	0.049723756906077346	9	0.015734265734265736	94	0.12401055408970976	G	0.003	-2.450950	0.00175	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.00500	7.05;7.18;6.96;7.05;7.12;7.12;7.05;7.05;7.16;7.18;7.12	1.81	-3.61	0.04556	.	3.910550	0.01107	N	0.005490	T	0.00012	0.0000	N	0.11756	0.17	0.80722	P	0.0	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.09377	0.0;0.0;0.004;0.001;0.001;0.0	T	0.42799	-0.9430	9	0.02654	T	1	.	3.3522	0.07156	0.3863:0.0:0.3819:0.2318	rs1061683;rs3202775;rs17435121	454;470;471;470;471;470	A8MVE2;D9IDM5;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;.;LIRB1_HUMAN	V	470;454;470;470;471;471;470;470;520;454;471	ENSP00000379614:I470V;ENSP00000391514:I454V;ENSP00000409968:I470V;ENSP00000379622:I470V;ENSP00000379618:I471V;ENSP00000315997:I471V;ENSP00000405243:I470V;ENSP00000379623:I470V;ENSP00000395004:I520V;ENSP00000379610:I454V;ENSP00000379608:I471V	ENSP00000315997:I471V	I	+	1	0	LILRB1	59837951	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-5.617000	0.00109	-2.140000	0.00806	-0.971000	0.02607	ATC	A|0.898;G|0.102	0.102	strong		0.577	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
DMRTA1	63951	hgsc.bcm.edu	37	9	22447655	22447655	+	Silent	SNP	T	T	A	rs558612	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:22447655T>A	ENST00000325870.2	+	1	816	c.591T>A	c.(589-591)ggT>ggA	p.G197G		NM_022160.2	NP_071443.2	Q5VZB9	DMRTA_HUMAN	DMRT-like family A1	197					male mating behavior (GO:0060179)|ovarian follicle development (GO:0001541)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(5;4.09e-243)|Acute lymphoblastic leukemia(3;8.25e-150)|all_hematologic(3;4.25e-147)|Esophageal squamous(3;2.32e-09)|Renal(3;1.71e-07)|Breast(3;2.07e-06)|Hepatocellular(5;0.00563)		GBM - Glioblastoma multiforme(1;5.12e-278)|Lung(24;8.2e-52)|LUSC - Lung squamous cell carcinoma(38;1.46e-37)|OV - Ovarian serous cystadenocarcinoma(39;0.0517)		TGGGACTGGGTGCCTTGAGAC	0.632													T|||	1561	0.311701	0.3669	0.3963	5008	,	,		11356	0.2331		0.3022	False		,,,				2504	0.2679				p.G197G		Atlas-SNP	.											.	DMRTA1	29	.	0			c.T591A						PASS	.	T		1435,2893		253,929,982	14.0	17.0	16.0		591	-8.7	0.0	9	dbSNP_83	16	2418,6140		347,1724,2208	no	coding-synonymous	DMRTA1	NM_022160.2		600,2653,3190	AA,AT,TT		28.2543,33.1562,29.9007		197/505	22447655	3853,9033	2164	4279	6443	SO:0001819	synonymous_variant	63951	exon1			ACTGGGTGCCTTG	AJ290954	CCDS6514.1	9p21.3	2008-05-15			ENSG00000176399	ENSG00000176399			13826	protein-coding gene	gene with protein product		614803					Standard	NM_022160		Approved		uc003zpp.1	Q5VZB9	OTTHUMG00000019693	ENST00000325870.2:c.591T>A	9.37:g.22447655T>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_022160	A1L481|Q8N8Y9|Q9H4B9	Silent	SNP	ENST00000325870.2	37	CCDS6514.1																																																																																			T|0.705;A|0.295	0.295	strong		0.632	DMRTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051935.2		
HEPHL1	341208	hgsc.bcm.edu	37	11	93839219	93839219	+	Missense_Mutation	SNP	A	A	C	rs200078708		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:93839219A>C	ENST00000315765.9	+	17	2976	c.2968A>C	c.(2968-2970)Aac>Cac	p.N990H		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	990	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TACAATGACAAACTGGTATTT	0.348																																					p.N990H		Atlas-SNP	.											.	HEPHL1	144	.	0			c.A2968C						PASS	.	A	HIS/ASN	0,3770		0,0,1885	127.0	125.0	126.0		2968	4.8	1.0	11		126	5,8207		0,5,4101	yes	missense	HEPHL1	NM_001098672.1	68	0,5,5986	CC,CA,AA		0.0609,0.0,0.0417	possibly-damaging	990/1160	93839219	5,11977	1885	4106	5991	SO:0001583	missense	341208	exon17			ATGACAAACTGGT	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.2968A>C	11.37:g.93839219A>C	ENSP00000313699:p.Asn990His	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	203	122	0.600985	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.088343	0.55968	0.0	6.09E-4	ENSG00000181333	ENST00000315765	D	0.99660	-6.32	5.95	4.84	0.62591	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.232485	0.50627	D	0.000102	D	0.99055	0.9676	L	0.38649	1.16	0.29801	N	0.832439	D	0.56968	0.978	D	0.64687	0.928	D	0.97256	0.9901	10	0.37606	T	0.19	-8.3966	11.4972	0.50415	0.9307:0.0:0.0693:0.0	.	990	Q6MZM0	HPHL1_HUMAN	H	990	ENSP00000313699:N990H	ENSP00000313699:N990H	N	+	1	0	HEPHL1	93478867	0.993000	0.37304	1.000000	0.80357	0.982000	0.71751	2.852000	0.48310	2.279000	0.76181	0.533000	0.62120	AAC	.	.	weak		0.348	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
ECI2	10455	hgsc.bcm.edu	37	6	4116262	4116262	+	Splice_Site	SNP	G	G	A	rs7166	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:4116262G>A	ENST00000380118.3	-	10	1067	c.1031C>T	c.(1030-1032)gCc>gTc	p.A344V	ECI2_ENST00000413766.2_Splice_Site_p.A177V|C6orf201_ENST00000380175.4_Intron|ECI2_ENST00000465828.1_Splice_Site_p.A314V|C6orf201_ENST00000430835.2_Intron|ECI2_ENST00000380125.2_Splice_Site_p.A314V|C6orf201_ENST00000333388.5_Intron|ECI2_ENST00000361538.2_Splice_Site_p.A314V			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	344			A -> V (in dbSNP:rs7166). {ECO:0000269|PubMed:10354522, ECO:0000269|PubMed:12097419}.		fatty acid catabolic process (GO:0009062)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|fatty-acyl-CoA binding (GO:0000062)|receptor binding (GO:0005102)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	11						AATTCTCAAGGCCTGGAAAAA	0.463													G|||	1543	0.308107	0.292	0.3573	5008	,	,		20514	0.3581		0.332	False		,,,				2504	0.2188				p.A344V		Atlas-SNP	.											.	ECI2	59	.	0			c.C1031T						PASS	.	G	,VAL/ALA,VAL/ALA,VAL/ALA	1254,3152	429.5+/-342.2	186,882,1135	72.0	67.0	69.0		,941,941,1031	3.6	0.8	6	dbSNP_52	69	2616,5984	421.7+/-353.8	394,1828,2078	yes	intron,missense-near-splice,missense-near-splice,missense-near-splice	ECI2,C6orf201	NM_001085401.1,NM_001166010.1,NM_006117.2,NM_206836.2	,64,64,64	580,2710,3213	AA,AG,GG		30.4186,28.4612,29.7555	,benign,benign,benign	,314/365,314/365,344/395	4116262	3870,9136	2203	4300	6503	SO:0001630	splice_region_variant	10455	exon10			CTCAAGGCCTGGA	AF069301	CCDS4490.1, CCDS43420.1, CCDS43420.2	6p24.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000198721	ENSG00000198721			14601	protein-coding gene	gene with protein product	"""acyl-Coenzyme A binding domain containing 2"", "" Hepatocellular carcinoma-associated antigen 88"""	608024	"""peroxisomal D3,D2-enoyl-CoA isomerase"""	PECI		10419495	Standard	NM_206836		Approved	ACBD2, DRS1, HCA88	uc003mwf.3	O75521	OTTHUMG00000014158	ENST00000380118.3:c.1030-1C>T	6.37:g.4116262G>A		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	144	144	1	NM_206836	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Missense_Mutation	SNP	ENST00000380118.3	37	CCDS43420.2	736	0.336996336996337	138	0.2804878048780488	128	0.35359116022099446	210	0.36713286713286714	260	0.34300791556728233	G	15.37	2.814243	0.50527	0.284612	0.304186	ENSG00000198721	ENST00000380118;ENST00000380125;ENST00000413766;ENST00000361538;ENST00000465828	T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68	5.44	3.6	0.41247	.	0.517099	0.23282	N	0.049892	T	0.23054	0.0557	L	0.48362	1.52	0.38998	P	0.04071899999999995	B	0.14438	0.01	B	0.14578	0.011	T	0.11792	-1.0573	9	0.48119	T	0.1	.	10.1077	0.42544	0.0759:0.1368:0.7872:0.0	rs7166;rs605312;rs1128188;rs3184842;rs13209353;rs17294765;rs17349268;rs17734713;rs7166	344	O75521	ECI2_HUMAN	V	344;314;177;314;314	ENSP00000369461:A344V;ENSP00000369468:A314V;ENSP00000406969:A177V;ENSP00000354737:A314V;ENSP00000420309:A314V	ENSP00000354737:A314V	A	-	2	0	ECI2	4061261	0.994000	0.37717	0.820000	0.32676	0.830000	0.47004	4.146000	0.58072	1.293000	0.44690	0.655000	0.94253	GCC	G|0.699;A|0.301	0.301	strong		0.463	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117	Missense_Mutation
CRISP3	10321	hgsc.bcm.edu	37	6	49701523	49701523	+	Missense_Mutation	SNP	A	A	G	rs495335	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:49701523A>G	ENST00000393666.1	-	4	322	c.316T>C	c.(316-318)Tcc>Ccc	p.S106P	CRISP3_ENST00000263045.4_Missense_Mutation_p.S119P|CRISP3_ENST00000371159.4_Missense_Mutation_p.S137P|CRISP3_ENST00000423399.2_Missense_Mutation_p.S16P|CRISP3_ENST00000433368.2_Missense_Mutation_p.S129P			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	106	SCP.		S -> P (in dbSNP:rs495335). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		defense response (GO:0006952)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|specific granule (GO:0042581)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|skin(6)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			CATGAGCTGGAGGCACTTGAC	0.433													G|||	3381	0.67512	0.7383	0.7594	5008	,	,		18918	0.5476		0.6948	False		,,,				2504	0.6411				p.S129P		Atlas-SNP	.											.	CRISP3	67	.	0			c.T385C						PASS	.	G	PRO/SER,PRO/SER	3280,1126	401.5+/-332.0	1205,870,128	149.0	139.0	142.0		385,355	5.1	0.0	6	dbSNP_83	142	5784,2816	445.5+/-361.0	1947,1890,463	yes	missense,missense	CRISP3	NM_001190986.1,NM_006061.2	74,74	3152,2760,591	GG,GA,AA		32.7442,25.5561,30.3091	benign,benign	129/269,119/259	49701523	9064,3942	2203	4300	6503	SO:0001583	missense	10321	exon5			AGCTGGAGGCACT	X94323	CCDS4929.1, CCDS4929.2, CCDS55019.1	6p12.3	2008-02-05			ENSG00000096006	ENSG00000096006			16904	protein-coding gene	gene with protein product						8665901, 12223513	Standard	NM_006061		Approved	SGP28, CRISP-3, CRS3, dJ442L6.3, Aeg2	uc003ozs.3	P54108	OTTHUMG00000014823	ENST00000393666.1:c.316T>C	6.37:g.49701523A>G	ENSP00000377274:p.Ser106Pro	Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_001190986	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Missense_Mutation	SNP	ENST00000393666.1	37		1478	0.6767399267399268	372	0.7560975609756098	273	0.7541436464088398	310	0.541958041958042	523	0.6899736147757256	G	1.963	-0.438361	0.04636	0.744439	0.672558	ENSG00000096006	ENST00000263045;ENST00000433368;ENST00000393666;ENST00000423399;ENST00000371159;ENST00000354620	T;T;T;T;T;T	0.44881	3.06;3.06;3.06;0.91;3.06;3.06	5.1	5.1	0.69264	CAP domain (3);	0.182430	0.34291	N	0.004100	T	0.03305	0.0096	N	0.00500	-1.43	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35101	-0.9802	9	0.02654	T	1	.	9.8183	0.40867	0.0963:0.0:0.9037:0.0	rs495335;rs1771237;rs13192493;rs16879714;rs52821725;rs495335	106	P54108	CRIS3_HUMAN	P	119;129;106;16;137;129	ENSP00000263045:S119P;ENSP00000389026:S129P;ENSP00000377274:S106P;ENSP00000410469:S16P;ENSP00000360201:S137P;ENSP00000346636:S129P	ENSP00000263045:S119P	S	-	1	0	CRISP3	49809482	0.021000	0.18746	0.003000	0.11579	0.001000	0.01503	1.944000	0.40263	1.156000	0.42514	-0.197000	0.12766	TCC	A|0.322;G|0.678	0.678	strong		0.433	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061	
SCYL2	55681	hgsc.bcm.edu	37	12	100732822	100732822	+	Missense_Mutation	SNP	G	G	A	rs117356610	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:100732822G>A	ENST00000360820.2	+	18	3099	c.2662G>A	c.(2662-2664)Gtg>Atg	p.V888M		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	888	Necessary for interaction with AP2 complex and clathrin, interaction with clathrin is necessary for its targeting to the TGN and endosomal membranes.				endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						ACAGATGAACGTGATAGGACA	0.438													G|||	6	0.00119808	0.0	0.0	5008	,	,		20321	0.001		0.004	False		,,,				2504	0.001				p.V888M		Atlas-SNP	.											SCYL2,NS,carcinoma,-2,1	SCYL2	99	1	0			c.G2662A						PASS	.	G	MET/VAL	4,4402	8.1+/-20.4	0,4,2199	185.0	178.0	181.0		2662	-7.1	0.4	12	dbSNP_132	181	38,8562	26.3+/-74.7	0,38,4262	yes	missense	SCYL2	NM_017988.4	21	0,42,6461	AA,AG,GG		0.4419,0.0908,0.3229	benign	888/930	100732822	42,12964	2203	4300	6503	SO:0001583	missense	55681	exon18			ATGAACGTGATAG	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.2662G>A	12.37:g.100732822G>A	ENSP00000354061:p.Val888Met	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	184	79	0.429348	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	37	CCDS9076.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	3.958	-0.010846	0.07727	9.08E-4	0.004419	ENSG00000136021	ENST00000360820	T	0.28454	1.61	5.8	-7.11	0.01542	.	0.675157	0.16660	N	0.204822	T	0.08891	0.0220	N	0.02916	-0.46	0.23314	N	0.99793	B	0.02656	0.0	B	0.01281	0.0	T	0.15983	-1.0418	10	0.30078	T	0.28	0.0271	7.2695	0.26248	0.3732:0.0:0.4283:0.1985	.	888	Q6P3W7	SCYL2_HUMAN	M	888	ENSP00000354061:V888M	ENSP00000354061:V888M	V	+	1	0	SCYL2	99256953	0.922000	0.31269	0.385000	0.26158	0.940000	0.58332	0.731000	0.26058	-1.435000	0.01972	-0.300000	0.09419	GTG	G|0.997;A|0.003	0.003	strong		0.438	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988	
HYOU1	10525	hgsc.bcm.edu	37	11	118925341	118925341	+	Silent	SNP	G	G	A	rs538478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:118925341G>A	ENST00000404233.3	-	7	667	c.543C>T	c.(541-543)aaC>aaT	p.N181N	HYOU1_ENST00000543287.1_Silent_p.N94N|HYOU1_ENST00000525859.1_Silent_p.N181N|HYOU1_ENST00000529972.1_Silent_p.N181N	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	181					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		GCTCGGCCTGGTTGAAGAAGA	0.577													G|||	2165	0.432308	0.1868	0.2954	5008	,	,		18893	0.7192		0.4821	False		,,,				2504	0.5143				p.N181N		Atlas-SNP	.											HYOU1,NS,carcinoma,-1,1	HYOU1	88	1	0			c.C543T						PASS	.	G	,	1028,3372	377.1+/-322.3	137,754,1309	69.0	63.0	65.0		543,543	2.3	1.0	11	dbSNP_83	65	3815,4775	538.2+/-383.4	857,2101,1337	no	coding-synonymous,coding-synonymous	HYOU1	NM_001130991.1,NM_006389.3	,	994,2855,2646	AA,AG,GG		44.4121,23.3636,37.2825	,	181/1000,181/1000	118925341	4843,8147	2200	4295	6495	SO:0001819	synonymous_variant	10525	exon7			GGCCTGGTTGAAG	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.543C>T	11.37:g.118925341G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Silent	SNP	ENST00000404233.3	37	CCDS8408.1																																																																																			G|0.585;A|0.415	0.415	strong		0.577	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	
CEACAM20	125931	hgsc.bcm.edu	37	19	45021210	45021210	+	RNA	SNP	G	G	A	rs10414398	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:45021210G>A	ENST00000454753.1	-	0	1384							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				GGTCAGGCTGGAGTTGAGCTC	0.567													G|||	938	0.1873	0.3033	0.2608	5008	,	,		19063	0.1369		0.0746	False		,,,				2504	0.1462				p.S369F		Atlas-SNP	.											.	CEACAM20	31	.	0			c.C1106T						PASS	.	G	PHE/SER,,,PHE/SER	966,3270		117,732,1269	75.0	73.0	74.0		1106,,,1106	2.4	0.0	19	dbSNP_119	74	699,7777		29,641,3568	yes	missense,intron,intron,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	155,,,155	146,1373,4837	AA,AG,GG		8.2468,22.8045,13.0979	probably-damaging,,,probably-damaging	369/597,,,369/585	45021210	1665,11047	2118	4238	6356			125931	exon6			AGGCTGGAGTTGA	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45021210G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				G|0.836;A|0.164	0.164	strong		0.567	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
RP1L1	94137	hgsc.bcm.edu	37	8	10466482	10466482	+	Missense_Mutation	SNP	G	G	A	rs13267180	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:10466482G>A	ENST00000382483.3	-	4	5349	c.5126C>T	c.(5125-5127)gCc>gTc	p.A1709V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1789					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CTTGCCAGGGGCCACCTCTGC	0.647													G|||	1556	0.310703	0.4009	0.33	5008	,	,		14848	0.0208		0.499	False		,,,				2504	0.2802				p.A1709V		Atlas-SNP	.											RP1L1,colon,carcinoma,-1,1	RP1L1	453	1	0			c.C5126T						PASS	.	G	VAL/ALA	1604,2440		316,972,734	79.0	88.0	85.0		5126	0.7	0.0	8	dbSNP_121	85	3972,4380		959,2054,1163	yes	missense	RP1L1	NM_178857.5	64	1275,3026,1897	AA,AG,GG		47.5575,39.6637,44.9823	benign	1709/2401	10466482	5576,6820	2022	4176	6198	SO:0001583	missense	94137	exon4			CCAGGGGCCACCT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5126C>T	8.37:g.10466482G>A	ENSP00000371923:p.Ala1709Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	727	0.33287545787545786	210	0.4268292682926829	128	0.35359116022099446	13	0.022727272727272728	376	0.49604221635883905	G	13.50	2.255844	0.39896	0.396637	0.475575	ENSG00000183638	ENST00000382483	T	0.05855	3.38	4.54	0.695	0.18070	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.29862	0.259	B	0.22386	0.039	T	0.38001	-0.9681	8	0.33940	T	0.23	0.0686	8.0577	0.30614	0.4262:0.0:0.5738:0.0	rs13267180;rs58866563;rs13267180	1709	A6NKC6	.	V	1709	ENSP00000371923:A1709V	ENSP00000371923:A1709V	A	-	2	0	RP1L1	10503892	0.000000	0.05858	0.000000	0.03702	0.101000	0.19017	-0.304000	0.08199	-0.059000	0.13154	0.462000	0.41574	GCC	G|0.614;A|0.386	0.386	strong		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
SRRM1	10250	hgsc.bcm.edu	37	1	24993386	24993386	+	Missense_Mutation	SNP	G	G	T	rs78787676		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24993386G>T	ENST00000323848.9	+	13	2024	c.1709G>T	c.(1708-1710)cGc>cTc	p.R570L	SRRM1_ENST00000537199.1_3'UTR|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000374389.4_Missense_Mutation_p.R579L|SRRM1_ENST00000447431.2_Missense_Mutation_p.R582L|SRRM1_ENST00000479034.1_3'UTR	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	570	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R570L(2)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CCTCGACGGCGCAGGACTCCC	0.557																																					p.R570L	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											SRRM1,bladder,carcinoma,0,2	SRRM1	81	2	2	Substitution - Missense(2)	urinary_tract(1)|central_nervous_system(1)	c.G1709T						scavenged	.						54.0	45.0	48.0					1																	24993386		2203	4300	6503	SO:0001583	missense	10250	exon13			GACGGCGCAGGAC	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1709G>T	1.37:g.24993386G>T	ENSP00000326261:p.Arg570Leu	Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	135	4	0.0296296	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.693027	0.88735	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.34667	1.35;1.35;1.35	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000007	T	0.58104	0.2099	L	0.54323	1.7	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.76575	0.988;0.972	T	0.57318	-0.7832	10	0.62326	D	0.03	-1.2563	19.3453	0.94361	0.0:0.0:1.0:0.0	.	582;570	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	L	570;582;579	ENSP00000326261:R570L;ENSP00000391430:R582L;ENSP00000363510:R579L	ENSP00000326261:R570L	R	+	2	0	SRRM1	24865973	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.773000	0.85462	2.654000	0.90174	0.650000	0.86243	CGC	G|0.999;A|0.001	.	alt		0.557	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
UMODL1	89766	hgsc.bcm.edu	37	21	43543193	43543193	+	Missense_Mutation	SNP	G	G	A	rs150611312	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:43543193G>A	ENST00000408910.2	+	17	3080	c.3080G>A	c.(3079-3081)aGc>aAc	p.S1027N	UMODL1_ENST00000408989.2_Missense_Mutation_p.S1155N|UMODL1_ENST00000400424.2_Missense_Mutation_p.S955N|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400427.1_Missense_Mutation_p.S1083N	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1027	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		S -> N (in dbSNP:rs150611312). {ECO:0000269|PubMed:16026467}.		adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						TGCAACGTGAGCCACAGCAAT	0.607													G|||	19	0.00379393	0.0	0.0029	5008	,	,		21514	0.0		0.0149	False		,,,				2504	0.002				p.S1155N	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											UMODL1_ENST00000408989,NS,haematopoietic_neoplasm,0,2	UMODL1	186	2	0			c.G3464A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER	7,4317		0,7,2155	64.0	67.0	66.0		3080,3248,2864,3464	3.1	0.9	21	dbSNP_134	66	114,8362		1,112,4125	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	46,46,46,46	1,119,6280	AA,AG,GG		1.345,0.1619,0.9453	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1027/1319,1083/1375,955/1247,1155/1447	43543193	121,12679	2162	4238	6400	SO:0001583	missense	89766	exon16			ACGTGAGCCACAG		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.3080G>A	21.37:g.43543193G>A	ENSP00000386147:p.Ser1027Asn	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	G	17.79	3.475678	0.63737	0.001619	0.01345	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62	3.13	3.13	0.36017	Zona pellucida sperm-binding protein (3);	0.116173	0.37304	N	0.002159	D	0.83450	0.5257	L	0.50919	1.6	0.37860	D	0.929673	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.972	D	0.86025	0.1509	9	.	.	.	-19.0186	13.6342	0.62213	0.0:0.0:1.0:0.0	.	1155;1027	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	N	1083;955;1155;1027	ENSP00000383279:S1083N;ENSP00000383276:S955N;ENSP00000386126:S1155N;ENSP00000386147:S1027N	.	S	+	2	0	UMODL1	42416262	1.000000	0.71417	0.901000	0.35422	0.724000	0.41520	3.829000	0.55760	2.060000	0.61445	0.313000	0.20887	AGC	G|0.993;A|0.007	0.007	strong		0.607	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
DCHS2	54798	hgsc.bcm.edu	37	4	155264637	155264637	+	Missense_Mutation	SNP	G	G	A	rs62331892	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:155264637G>A	ENST00000357232.4	-	7	961	c.962C>T	c.(961-963)gCt>gTt	p.A321V	DCHS2_ENST00000507542.1_Intron|DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	321	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		aagaatcttagctagatttgc	0.393													G|||	128	0.0255591	0.0	0.0317	5008	,	,		21148	0.001		0.0467	False		,,,				2504	0.0593				p.A321V		Atlas-SNP	.											.	DCHS2	594	.	0			c.C962T						PASS	.	G	,VAL/ALA	23,2631		0,23,1304	115.0	115.0	115.0		,962	-0.6	0.0	4	dbSNP_129	115	228,4390		6,216,2087	no	intron,missense	DCHS2	NM_001142552.1,NM_017639.3	,64	6,239,3391	AA,AG,GG		4.9372,0.8666,3.4516	,benign	,321/2917	155264637	251,7021	1327	2309	3636	SO:0001583	missense	54798	exon7			ATCTTAGCTAGAT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.962C>T	4.37:g.155264637G>A	ENSP00000349768:p.Ala321Val	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	30	20	0.666667	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	52	0.023809523809523808	0	0.0	18	0.049723756906077346	0	0.0	34	0.044854881266490766	G	0.034	-1.315950	0.01331	0.008666	0.049372	ENSG00000197410	ENST00000357232	T	0.54675	0.56	0.593	-0.554	0.11811	Cadherin (1);	.	.	.	.	T	0.05044	0.0135	N	0.14661	0.345	0.09310	N	1	B	0.17465	0.022	B	0.08055	0.003	T	0.07328	-1.0778	8	0.27082	T	0.32	.	.	.	.	rs62331892	321	Q6V1P9	PCD23_HUMAN	V	321	ENSP00000349768:A321V	ENSP00000349768:A321V	A	-	2	0	DCHS2	155484087	0.023000	0.18921	0.006000	0.13384	0.006000	0.05464	0.529000	0.23019	-0.291000	0.09012	-0.291000	0.09656	GCT	G|0.976;A|0.024	0.024	strong		0.393	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
SPEN	23013	hgsc.bcm.edu	37	1	16255799	16255799	+	Missense_Mutation	SNP	G	G	A	rs115566585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:16255799G>A	ENST00000375759.3	+	11	3268	c.3064G>A	c.(3064-3066)Gtg>Atg	p.V1022M		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1022					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GCAGCCTGACGTGTCCTCTAG	0.423													G|||	12	0.00239617	0.0	0.0115	5008	,	,		20147	0.0		0.004	False		,,,				2504	0.0				p.V1022M		Atlas-SNP	.											.	SPEN	374	.	0			c.G3064A						PASS	.	G	MET/VAL	2,4404	2.1+/-5.4	0,2,2201	46.0	53.0	51.0		3064	-5.8	0.0	1	dbSNP_132	51	31,8569	18.5+/-59.3	0,31,4269	yes	missense	SPEN	NM_015001.2	21	0,33,6470	AA,AG,GG		0.3605,0.0454,0.2537	benign	1022/3665	16255799	33,12973	2203	4300	6503	SO:0001583	missense	23013	exon11			CCTGACGTGTCCT		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.3064G>A	1.37:g.16255799G>A	ENSP00000364912:p.Val1022Met	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	5	0.0022893772893772895	0	0.0	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	0.012	-1.676123	0.00751	4.54E-4	0.003605	ENSG00000065526	ENST00000375759	T	0.09445	2.98	5.13	-5.85	0.02311	.	.	.	.	.	T	0.02304	0.0071	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.41233	-0.9520	9	0.42905	T	0.14	6.4781	3.6799	0.08306	0.2371:0.3302:0.3421:0.0907	.	1022	Q96T58	MINT_HUMAN	M	1022	ENSP00000364912:V1022M	ENSP00000364912:V1022M	V	+	1	0	SPEN	16128386	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-1.308000	0.02730	-0.807000	0.04393	-0.150000	0.13652	GTG	G|0.998;A|0.002	0.002	strong		0.423	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
MYOM1	8736	hgsc.bcm.edu	37	18	3126811	3126811	+	Missense_Mutation	SNP	A	A	G	rs1071600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:3126811A>G	ENST00000356443.4	-	19	3212	c.2879T>C	c.(2878-2880)aTt>aCt	p.I960T	MYOM1_ENST00000400569.3_Missense_Mutation_p.I960T|MYOM1_ENST00000582016.1_5'UTR|MYOM1_ENST00000261606.7_Missense_Mutation_p.I864T	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	960	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> T (in dbSNP:rs1071600). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7505783, ECO:0000269|Ref.1}.		muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.I960T(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TGCCCCTCCAATCTTATCTGG	0.453													A|||	1274	0.254393	0.3177	0.1988	5008	,	,		20132	0.3204		0.1571	False		,,,				2504	0.2403				p.I960T		Atlas-SNP	.											MYOM1,NS,carcinoma,0,1	MYOM1	192	1	1	Substitution - Missense(1)	stomach(1)	c.T2879C						PASS	.	A	THR/ILE,THR/ILE	1017,2887		125,767,1060	98.0	89.0	92.0		2879,2591	1.4	1.0	18	dbSNP_86	92	1175,7127		78,1019,3054	yes	missense,missense	MYOM1	NM_003803.3,NM_019856.1	89,89	203,1786,4114	GG,GA,AA		14.1532,26.0502,17.9584	benign,benign	960/1686,864/1590	3126811	2192,10014	1952	4151	6103	SO:0001583	missense	8736	exon19			CCTCCAATCTTAT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2879T>C	18.37:g.3126811A>G	ENSP00000348821:p.Ile960Thr	Somatic	368	1	0.00271739		WXS	Illumina HiSeq	Phase_I	381	375	0.984252	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	562	0.2573260073260073	169	0.3434959349593496	65	0.17955801104972377	207	0.3618881118881119	121	0.15963060686015831	A	0.202	-1.044108	0.01997	0.260502	0.141532	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.54479	0.57;0.57;0.57	5.46	1.43	0.22495	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.317474	0.37857	N	0.001914	T	0.00012	0.0000	N	0.01086	-1.025	0.51767	P	6.700000000003925E-5	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.41858	-0.9485	9	0.12103	T	0.63	.	7.3969	0.26942	0.1872:0.3443:0.4685:0.0	rs1071600;rs52834060;rs60947648;rs1071600	864;960	P52179-2;P52179	.;MYOM1_HUMAN	T	960;960;864	ENSP00000348821:I960T;ENSP00000383413:I960T;ENSP00000261606:I864T	ENSP00000261606:I864T	I	-	2	0	MYOM1	3116811	0.006000	0.16342	0.972000	0.41901	0.926000	0.56050	0.450000	0.21762	-0.028000	0.13850	-0.242000	0.12053	ATT	A|0.744;G|0.256	0.256	strong		0.453	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
IQCE	23288	hgsc.bcm.edu	37	7	2613062	2613062	+	Silent	SNP	T	T	C	rs61739566	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:2613062T>C	ENST00000402050.2	+	6	589	c.405T>C	c.(403-405)ccT>ccC	p.P135P	IQCE_ENST00000325979.7_Silent_p.P70P|IQCE_ENST00000438376.2_Silent_p.P119P|IQCE_ENST00000404984.1_Silent_p.P84P	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	135						mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		GTCATGTCCCTGGGACTCCTG	0.348													T|||	483	0.0964457	0.1263	0.0994	5008	,	,		21532	0.001		0.1421	False		,,,				2504	0.1053				p.P135P		Atlas-SNP	.											.	IQCE	66	.	0			c.T405C						PASS	.	T	,	485,3185		35,415,1385	154.0	138.0	143.0		357,405	-10.9	0.0	7	dbSNP_129	143	1321,6845		107,1107,2869	no	coding-synonymous,coding-synonymous	IQCE	NM_001100390.1,NM_152558.3	,	142,1522,4254	CC,CT,TT		16.1768,13.2153,15.2585	,	119/680,135/696	2613062	1806,10030	1835	4083	5918	SO:0001819	synonymous_variant	23288	exon6			TGTCCCTGGGACT	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.405T>C	7.37:g.2613062T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	133	55	0.413534	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	37	CCDS43542.1																																																																																			T|0.884;C|0.116	0.116	strong		0.348	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
AKR7A3	22977	hgsc.bcm.edu	37	1	19612477	19612477	+	Missense_Mutation	SNP	C	C	T	rs2231198	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:19612477C>T	ENST00000361640.4	-	3	952	c.412G>A	c.(412-414)Gtg>Atg	p.V138M		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	138			V -> M (in dbSNP:rs2231198). {ECO:0000269|PubMed:10383892, ECO:0000269|PubMed:15489334}.		cellular aldehyde metabolic process (GO:0006081)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)	13		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CCAAGCTCCACGAACTTGCCC	0.612													C|||	2320	0.463259	0.3646	0.5432	5008	,	,		19169	0.6905		0.3817	False		,,,				2504	0.3896				p.V138M		Atlas-SNP	.											.	AKR7A3	30	.	0			c.G412A						PASS	.	C	MET/VAL	1614,2784		319,976,904	58.0	54.0	55.0		412	3.0	1.0	1	dbSNP_98	55	3110,5490		564,1982,1754	no	missense	AKR7A3	NM_012067.2	21	883,2958,2658	TT,TC,CC		36.1628,36.6985,36.3441	benign	138/332	19612477	4724,8274	2199	4300	6499	SO:0001583	missense	22977	exon3			GCTCCACGAACTT	AF040639	CCDS193.1	1p36.13	2008-05-14			ENSG00000162482	ENSG00000162482		"""Aldo-keto reductases"""	390	protein-coding gene	gene with protein product		608477				10383892	Standard	NM_012067		Approved		uc001bbv.1	O95154	OTTHUMG00000002523	ENST00000361640.4:c.412G>A	1.37:g.19612477C>T	ENSP00000355377:p.Val138Met	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	165	73	0.442424	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Missense_Mutation	SNP	ENST00000361640.4	37	CCDS193.1	1072	0.4908424908424908	187	0.3800813008130081	194	0.5359116022099447	411	0.7185314685314685	280	0.36939313984168864	.	6.831	0.522560	0.13066	0.366985	0.361628	ENSG00000162482	ENST00000361640	T	0.23348	1.91	3.04	3.04	0.35103	NADP-dependent oxidoreductase domain (3);	0.240515	0.40640	N	0.001046	T	0.00012	0.0000	M	0.82823	2.61	0.41505	P	0.011692999999999953	B	0.32543	0.375	B	0.24974	0.057	T	0.34453	-0.9828	9	0.41790	T	0.15	.	5.9087	0.19016	0.0:0.8521:0.0:0.1479	rs2231198;rs11539611;rs13374777;rs17852954;rs59246333	138	O95154	ARK73_HUMAN	M	138	ENSP00000355377:V138M	ENSP00000355377:V138M	V	-	1	0	AKR7A3	19485064	1.000000	0.71417	1.000000	0.80357	0.263000	0.26337	2.346000	0.44027	1.542000	0.49330	0.194000	0.17425	GTG	C|0.603;T|0.397	0.397	strong		0.612	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067	
MYPN	84665	hgsc.bcm.edu	37	10	69934258	69934258	+	Missense_Mutation	SNP	C	C	G	rs3814182	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:69934258C>G	ENST00000358913.5	+	11	2897	c.2409C>G	c.(2407-2409)agC>agG	p.S803R	MYPN_ENST00000540630.1_Missense_Mutation_p.S803R|MYPN_ENST00000354393.2_Missense_Mutation_p.S528R	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	803	Pro-rich.		S -> R (in dbSNP:rs3814182). {ECO:0000269|PubMed:11309420, ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						CCATCCCCAGCGGAAACCAGT	0.542													C|||	2361	0.471446	0.447	0.4597	5008	,	,		18659	0.3512		0.5666	False		,,,				2504	0.5389				p.S803R		Atlas-SNP	.											.	MYPN	189	.	0			c.C2409G						PASS	.	C	ARG/SER	2064,2342	568.8+/-382.5	495,1074,634	111.0	98.0	103.0		2409	-9.6	0.3	10	dbSNP_107	103	4738,3862	609.4+/-395.5	1314,2110,876	yes	missense	MYPN	NM_032578.2	110	1809,3184,1510	GG,GC,CC		44.907,46.8452,47.7011	benign	803/1321	69934258	6802,6204	2203	4300	6503	SO:0001583	missense	84665	exon11			CCCCAGCGGAAAC	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2409C>G	10.37:g.69934258C>G	ENSP00000351790:p.Ser803Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	1046	0.47893772893772896	240	0.4878048780487805	182	0.5027624309392266	195	0.3409090909090909	429	0.5659630606860159	C	12.78	2.039690	0.35989	0.468452	0.55093	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.58506	0.33;0.38;0.36	5.8	-9.63	0.00544	.	0.277370	0.41823	D	0.000815	T	0.00012	0.0000	L	0.46157	1.445	0.38615	P	0.04899699999999996	P;P;P	0.46512	0.879;0.773;0.664	B;B;B	0.43360	0.397;0.417;0.12	T	0.08269	-1.0730	8	.	.	.	.	19.5953	0.95535	0.0:0.7212:0.0:0.2788	rs3814182;rs59227755;rs3814182	803;528;803	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	R	528;528;803;803	ENSP00000346369:S528R;ENSP00000351790:S803R;ENSP00000441668:S803R	.	S	+	3	2	MYPN	69604264	0.000000	0.05858	0.265000	0.24526	0.876000	0.50452	-3.502000	0.00449	-1.913000	0.01079	-0.136000	0.14681	AGC	C|0.500;G|0.500	0.500	strong		0.542	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
BAZ1A	11177	hgsc.bcm.edu	37	14	35263983	35263983	+	Silent	SNP	T	T	C	rs17102745	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:35263983T>C	ENST00000382422.2	-	10	1662	c.1335A>G	c.(1333-1335)caA>caG	p.Q445Q	BAZ1A_ENST00000360310.1_Silent_p.Q445Q|BAZ1A_ENST00000358716.4_Silent_p.Q445Q			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	445	DDT. {ECO:0000255|PROSITE- ProRule:PRU00063}.				chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		GAAACTCATCTTGAAGATCAA	0.378													T|||	580	0.115815	0.118	0.0749	5008	,	,		18705	0.0377		0.1044	False		,,,				2504	0.2342				p.Q445Q		Atlas-SNP	.											.	BAZ1A	128	.	0			c.A1335G						PASS	.	T	,	471,3935	223.6+/-240.1	22,427,1754	92.0	89.0	90.0		1335,1335	2.3	1.0	14	dbSNP_123	90	840,7760	193.2+/-239.0	36,768,3496	no	coding-synonymous,coding-synonymous	BAZ1A	NM_013448.2,NM_182648.1	,	58,1195,5250	CC,CT,TT		9.7674,10.69,10.08	,	445/1557,445/1525	35263983	1311,11695	2203	4300	6503	SO:0001819	synonymous_variant	11177	exon11			CTCATCTTGAAGA	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.1335A>G	14.37:g.35263983T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_182648	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1																																																																																			T|0.899;C|0.101	0.101	strong		0.378	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
CWC22	57703	hgsc.bcm.edu	37	2	180835443	180835443	+	Missense_Mutation	SNP	C	C	G	rs143785942	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:180835443C>G	ENST00000410053.3	-	10	1380	c.1081G>C	c.(1081-1083)Gaa>Caa	p.E361Q	CWC22_ENST00000295749.6_Missense_Mutation_p.E361Q	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	361					mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						TCATCTTCTTCCACCAAATCA	0.403													C|||	4	0.000798722	0.0	0.0014	5008	,	,		14767	0.0		0.001	False		,,,				2504	0.002				p.E361Q		Atlas-SNP	.											.	CWC22	62	.	0			c.G1081C						PASS	.	C	GLN/GLU	0,3776		0,0,1888	96.0	91.0	92.0		1081	5.9	1.0	2	dbSNP_134	92	10,8210		0,10,4100	yes	missense	CWC22	NM_020943.2	29	0,10,5988	GG,GC,CC		0.1217,0.0,0.0834	possibly-damaging	361/909	180835443	10,11986	1888	4110	5998	SO:0001583	missense	57703	exon10			CTTCTTCCACCAA		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein b"""	615186	"""CWC22 spliceosome-associated protein homolog (S. cerevisiae)"""			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.1081G>C	2.37:g.180835443C>G	ENSP00000387006:p.Glu361Gln	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	161	76	0.47205	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	37	CCDS46465.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	27.9	4.873213	0.91664	0.0	0.001217	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.30448	1.78;1.77;1.53	5.95	5.95	0.96441	Armadillo-type fold (1);	0.047002	0.85682	D	0.000000	T	0.62392	0.2424	M	0.88570	2.965	0.80722	D	1	D	0.76494	0.999	P	0.62649	0.905	T	0.67825	-0.5570	10	0.72032	D	0.01	-23.3839	19.3813	0.94536	0.0:1.0:0.0:0.0	.	361	Q9HCG8	CWC22_HUMAN	Q	361	ENSP00000387006:E361Q;ENSP00000295749:E361Q;ENSP00000384159:E361Q	ENSP00000295749:E361Q	E	-	1	0	CWC22	180543688	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	GAA	C|1.000;G|0.000	0.000	strong		0.403	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943	
ZNF471	57573	hgsc.bcm.edu	37	19	57036678	57036678	+	Silent	SNP	G	G	A	rs3752177	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57036678G>A	ENST00000308031.5	+	5	1375	c.1242G>A	c.(1240-1242)tcG>tcA	p.S414S	ZNF471_ENST00000591537.1_3'UTR|ZNF471_ENST00000593197.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	414					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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		CCTTCAGCTCGGGTTCATCCC	0.413													T|||	969	0.19349	0.1793	0.1816	5008	,	,		21284	0.1766		0.2078	False		,,,				2504	0.2239				p.S414S	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.G1242A						PASS	.	T		911,3495		98,715,1390	83.0	82.0	82.0		1242	-2.0	0.0	19	dbSNP_107	82	1855,6745		193,1469,2638	no	coding-synonymous	ZNF471	NM_020813.2		291,2184,4028	AA,AG,GG		21.5698,20.6764,21.2671		414/627	57036678	2766,10240	2203	4300	6503	SO:0001819	synonymous_variant	57573	exon5			CAGCTCGGGTTCA	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"""Zinc fingers, C2H2-type"", ""-"""	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1242G>A	19.37:g.57036678G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Silent	SNP	ENST00000308031.5	37	CCDS12945.1																																																																																			A|0.209;G|0.791	0.209	strong		0.413	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813	
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97933601	97933601	+	Silent	SNP	C	C	T	rs1045916	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:97933601C>T	ENST00000005260.8	-	12	1544	c.1329G>A	c.(1327-1329)ttG>ttA	p.L443L		NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	443					filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			CCCCCATGGACAAGCATTCCA	0.577													C|||	2783	0.555711	0.3253	0.6787	5008	,	,		18035	0.6915		0.7485	False		,,,				2504	0.4417				p.L443L		Atlas-SNP	.											.	BAIAP2L1	61	.	0			c.G1329A						PASS	.	C		1705,2701	512.7+/-368.2	340,1025,838	84.0	72.0	76.0		1329	3.9	0.0	7	dbSNP_86	76	6389,2211	710.1+/-405.8	2367,1655,278	no	coding-synonymous	BAIAP2L1	NM_018842.4		2707,2680,1116	TT,TC,CC		25.7093,38.6972,37.7672		443/512	97933601	8094,4912	2203	4300	6503	SO:0001819	synonymous_variant	55971	exon12			CATGGACAAGCAT	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.1329G>A	7.37:g.97933601C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	102	100	0.980392	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	37	CCDS34687.1																																																																																			C|0.383;T|0.617	0.617	strong		0.577	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842	
AGFG1	3267	hgsc.bcm.edu	37	2	228388545	228388545	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:228388545C>T	ENST00000310078.8	+	4	704	c.444C>T	c.(442-444)gcC>gcT	p.A148A	AGFG1_ENST00000373671.3_Silent_p.A148A|AGFG1_ENST00000486932.1_3'UTR|AGFG1_ENST00000409979.2_Silent_p.A148A|AGFG1_ENST00000409315.1_Silent_p.A148A|AGFG1_ENST00000409171.1_Silent_p.A148A	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	148					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						GGTCCTCTGCCAGTAGCACAA	0.438																																					p.A148A		Atlas-SNP	.											AGFG1_ENST00000409979,colon,carcinoma,+1,2	AGFG1	80	2	0			c.C444T						scavenged	.						127.0	117.0	120.0					2																	228388545		2203	4300	6503	SO:0001819	synonymous_variant	3267	exon4			CTCTGCCAGTAGC		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"""ADP-ribosylation factor GTPase activating proteins"""	5175	protein-coding gene	gene with protein product		600862	"""HIV-1 Rev binding protein"""	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.444C>T	2.37:g.228388545C>T		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	252	3	0.0119048	NM_004504	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Silent	SNP	ENST00000310078.8	37	CCDS2467.1																																																																																			.	.	none		0.438	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504	
C12orf43	64897	hgsc.bcm.edu	37	12	121442199	121442199	+	Silent	SNP	T	T	A	rs3751151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:121442199T>A	ENST00000288757.3	-	6	568	c.546A>T	c.(544-546)acA>acT	p.T182T	C12orf43_ENST00000536407.2_Intron|C12orf43_ENST00000445832.3_Silent_p.T152T|C12orf43_ENST00000366211.2_Silent_p.T141T|C12orf43_ENST00000537817.1_Silent_p.T183T|C12orf43_ENST00000539736.1_Silent_p.T172T	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	182										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCTTCTCCACTGTTCCAGGGC	0.602													.|||	1295	0.258586	0.3101	0.196	5008	,	,		19038	0.2748		0.3241	False		,,,				2504	0.1493				p.T182T		Atlas-SNP	.											C12orf43,NS,adenoma,0,1	C12orf43	30	1	0			c.A546T						PASS	.	T		1398,3008	457.3+/-351.6	222,954,1027	120.0	136.0	131.0		546	-8.9	0.0	12	dbSNP_107	131	2693,5907	431.5+/-356.8	426,1841,2033	no	coding-synonymous	C12orf43	NM_022895.1		648,2795,3060	AA,AT,TT		31.314,31.7295,31.4547		182/263	121442199	4091,8915	2203	4300	6503	SO:0001819	synonymous_variant	64897	exon6			CTCCACTGTTCCA	AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.546A>T	12.37:g.121442199T>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	161	80	0.496894	NM_022895	Q53HF0|Q9H9Z7	Silent	SNP	ENST00000288757.3	37	CCDS9210.1	612	0.2802197802197802	158	0.32113821138211385	74	0.20441988950276244	135	0.23601398601398602	245	0.3232189973614776	T	5.337	0.247414	0.10130	0.317295	0.31314	ENSG00000157895	ENST00000546272	.	.	.	5.28	-8.94	0.00768	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.38845	-0.9642	3	.	.	.	12.9924	1.7231	0.02916	0.1567:0.269:0.3073:0.267	rs3751151;rs17845433;rs17858305;rs3751151	.	.	.	L	136	.	.	Q	-	2	0	C12orf43	119926582	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.286000	0.02788	-1.292000	0.02366	-1.715000	0.00711	CAG	T|0.704;A|0.296	0.296	strong		0.602	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
RNF5	6048	hgsc.bcm.edu	37	6	32147696	32147696	+	Silent	SNP	G	G	A	rs3130349	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32147696G>A	ENST00000375094.3	+	4	473	c.315G>A	c.(313-315)ccG>ccA	p.P105P	AGPAT1_ENST00000336984.6_5'Flank|AGPAT1_ENST00000395497.1_5'Flank|AGPAT1_ENST00000395499.1_5'Flank|AGPAT1_ENST00000375104.2_5'Flank|RNF5_ENST00000427134.2_Silent_p.P105P|AGPAT1_ENST00000490711.1_5'Flank	NM_006913.3	NP_008844.1	Q99942	RNF5_HUMAN	ring finger protein 5, E3 ubiquitin protein ligase	105					cellular protein catabolic process (GO:0044257)|ER-associated misfolded protein catabolic process (GO:0071712)|negative regulation of autophagy (GO:0010507)|protein destabilization (GO:0031648)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|regulation of autophagic vacuole assembly (GO:2000785)|response to bacterium (GO:0009617)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|lung(7)|urinary_tract(2)	10						GACCAGCTCCGGAGAGCAGAG	0.542													A|||	667	0.133187	0.1241	0.0865	5008	,	,		18422	0.0933		0.159	False		,,,				2504	0.1933				p.P105P		Atlas-SNP	.											.	RNF5	16	.	0			c.G315A						PASS	.	A		500,3906	773.7+/-414.0	29,442,1732	92.0	107.0	102.0		315	-10.3	0.3	6	dbSNP_103	102	1568,7032	742.8+/-407.2	140,1288,2872	yes	coding-synonymous	RNF5	NM_006913.3		169,1730,4604	AA,AG,GG		18.2326,11.3482,15.9004		105/181	32147696	2068,10938	2203	4300	6503	SO:0001819	synonymous_variant	6048	exon4			AGCTCCGGAGAGC	U89336	CCDS4745.1	6p21.31	2013-01-09	2012-02-23			ENSG00000204308		"""RING-type (C3HC4) zinc fingers"""	10068	protein-coding gene	gene with protein product		602677	"""ring finger protein 5"""			9533025	Standard	NM_006913		Approved	NG2, G16, RING5, RMA1	uc031snv.1	Q99942	OTTHUMG00000031093	ENST00000375094.3:c.315G>A	6.37:g.32147696G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	232	121	0.521552	NM_006913	A2BFI6|B2R4K3|Q0VDB7|Q9UMQ2	Silent	SNP	ENST00000375094.3	37	CCDS4745.1																																																																																			G|0.863;A|0.137	0.137	strong		0.542	RNF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076133.2	NM_006913	
CSMD1	64478	hgsc.bcm.edu	37	8	3076959	3076959	+	Missense_Mutation	SNP	T	T	C	rs28455997	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:3076959T>C	ENST00000520002.1	-	30	5048	c.4493A>G	c.(4492-4494)aAc>aGc	p.N1498S	CSMD1_ENST00000602723.1_Missense_Mutation_p.N1498S|CSMD1_ENST00000537824.1_Missense_Mutation_p.N1497S|CSMD1_ENST00000602557.1_Missense_Mutation_p.N1498S|CSMD1_ENST00000400186.3_Missense_Mutation_p.N1498S|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000542608.1_Missense_Mutation_p.N1497S|CSMD1_ENST00000539096.1_Missense_Mutation_p.N1497S			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1498	CUB 9. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GGGCTCCATGTTGAAACTAAA	0.423													T|||	398	0.0794728	0.0045	0.1772	5008	,	,		16601	0.0605		0.1342	False		,,,				2504	0.0746				p.N1497S		Atlas-SNP	.											CSMD1_ENST00000537824,colon,carcinoma,-1,2	CSMD1	1469	2	0			c.A4490G						PASS	.	T	SER/ASN	96,3552		3,90,1731	29.0	29.0	29.0		4490	3.0	1.0	8	dbSNP_125	29	1058,7114		72,914,3100	yes	missense	CSMD1	NM_033225.5	46	75,1004,4831	CC,CT,TT		12.9466,2.6316,9.7631	benign	1497/3565	3076959	1154,10666	1824	4086	5910	SO:0001583	missense	64478	exon29			TCCATGTTGAAAC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4493A>G	8.37:g.3076959T>C	ENSP00000430733:p.Asn1498Ser	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		214	0.09798534798534798	5	0.01016260162601626	63	0.17403314917127072	42	0.07342657342657342	104	0.13720316622691292	T	5.619	0.298944	0.10622	0.026316	0.129466	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.19105	2.17;2.17;2.17;2.17;2.17	5.39	3.02	0.34903	CUB (5);	0.058200	0.64402	N	0.000003	T	0.00012	0.0000	N	0.01631	-0.79	0.23936	P	0.99641553	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.16289	0.003;0.015;0.009	T	0.37572	-0.9700	9	0.07482	T	0.82	.	9.2185	0.37362	0.0:0.1503:0.0:0.8497	rs28455997	1498;1498;1498	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	S	1498;1498;1360;1497;1497;1497	ENSP00000383047:N1498S;ENSP00000430733:N1498S;ENSP00000441462:N1497S;ENSP00000446243:N1497S;ENSP00000441675:N1497S	ENSP00000320445:N1360S	N	-	2	0	CSMD1	3064366	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.629000	0.46485	0.445000	0.26639	0.454000	0.30748	AAC	T|0.897;C|0.103	0.103	strong		0.423	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
OR10A2	341276	hgsc.bcm.edu	37	11	6891385	6891385	+	Missense_Mutation	SNP	G	G	A	rs2741764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6891385G>A	ENST00000307322.4	+	1	462	c.400G>A	c.(400-402)Gcc>Acc	p.A134T		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	134			A -> T (in dbSNP:rs2741764). {ECO:0000269|PubMed:11416212, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		ACTGGCTGCTGCCTCCTGGTT	0.532													-|||	1140	0.227636	0.087	0.3069	5008	,	,		21689	0.2798		0.3141	False		,,,				2504	0.2188				p.A134T		Atlas-SNP	.											.	OR10A2	55	.	0			c.G400A						PASS	.	G	THR/ALA	550,3852	245.9+/-254.7	39,472,1690	151.0	143.0	146.0		400	2.1	0.0	11	dbSNP_100	146	2901,5691	454.7+/-363.6	502,1897,1897	no	missense	OR10A2	NM_001004460.1	58	541,2369,3587	AA,AG,GG		33.764,12.4943,26.5584	possibly-damaging	134/304	6891385	3451,9543	2201	4296	6497	SO:0001583	missense	341276	exon1			GCTGCTGCCTCCT	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"""GPCR / Class A : Olfactory receptors"""	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.400G>A	11.37:g.6891385G>A	ENSP00000303862:p.Ala134Thr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	166	76	0.457831	NM_001004460	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	37	CCDS31415.1	602	0.27564102564102566	52	0.10569105691056911	122	0.3370165745856354	190	0.3321678321678322	238	0.31398416886543534	g	12.17	1.856251	0.32791	0.124943	0.33764	ENSG00000170790	ENST00000307322	T	0.01414	4.92	3.99	2.09	0.27110	GPCR, rhodopsin-like superfamily (1);	0.444913	0.21217	N	0.078217	T	0.00012	0.0000	L	0.31157	0.91	0.80722	P	0.0	B	0.34349	0.45	B	0.43658	0.426	T	0.51020	-0.8758	9	0.41790	T	0.15	.	8.2209	0.31541	0.2026:0.0:0.7974:0.0	rs2741764;rs52835088;rs60213581;rs2741764	134	Q9H208	O10A2_HUMAN	T	134	ENSP00000303862:A134T	ENSP00000303862:A134T	A	+	1	0	OR10A2	6847961	0.000000	0.05858	0.034000	0.17996	0.578000	0.36192	0.835000	0.27531	0.457000	0.26962	0.650000	0.86243	GCC	G|0.725;A|0.275	0.275	strong		0.532	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460	
QSOX2	169714	hgsc.bcm.edu	37	9	139110654	139110654	+	Splice_Site	SNP	C	C	T	rs12684650	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139110654C>T	ENST00000358701.5	-	8	994	c.957G>A	c.(955-957)aaG>aaA	p.K319K		NM_181701.3	NP_859052.3	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2	319					cell redox homeostasis (GO:0045454)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	thiol oxidase activity (GO:0016972)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)		ACAGCTTCGACCTAGGACGGG	0.647													C|||	767	0.153155	0.0098	0.2075	5008	,	,		16290	0.121		0.2873	False		,,,				2504	0.2035				p.K319K		Atlas-SNP	.											.	QSOX2	63	.	0			c.G957A						PASS	.	C		277,4129	154.4+/-187.8	10,257,1936	78.0	63.0	68.0		957	4.0	0.5	9	dbSNP_120	68	2552,6048	415.6+/-351.9	362,1828,2110	yes	coding-synonymous-near-splice	QSOX2	NM_181701.3		372,2085,4046	TT,TC,CC		29.6744,6.2869,21.7515		319/699	139110654	2829,10177	2203	4300	6503	SO:0001630	splice_region_variant	169714	exon8			CTTCGACCTAGGA	AJ318051	CCDS35178.1	9q34.3	2008-02-05	2007-04-23	2007-04-23	ENSG00000165661	ENSG00000165661			30249	protein-coding gene	gene with protein product		612860	"""quiescin Q6-like 1"""	QSCN6L1		12176051	Standard	NM_181701		Approved	SOXN, DKFZp762A2013	uc010nbi.2	Q6ZRP7	OTTHUMG00000020923	ENST00000358701.5:c.957-1G>A	9.37:g.139110654C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_181701	A2CEE0|A6NLB0|Q5TB37|Q7Z7B6|Q86VV7|Q8N3G2	Silent	SNP	ENST00000358701.5	37	CCDS35178.1	379	0.17353479853479853	8	0.016260162601626018	75	0.20718232044198895	75	0.13111888111888112	221	0.29155672823219	C	5.417	0.262043	0.10239	0.062869	0.296744	ENSG00000165661	ENST00000455222	.	.	.	4.86	3.96	0.45880	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.19353	-1.0308	3	.	.	.	.	10.2325	0.43264	0.0:0.832:0.0:0.168	rs12684650;rs17602333;rs12684650	.	.	.	I	87	.	.	V	-	1	0	QSOX2	138250475	1.000000	0.71417	0.519000	0.27824	0.049000	0.14656	1.654000	0.37334	1.032000	0.39892	0.436000	0.28706	GTC	C|0.803;N|0.000	.	strong		0.647	QSOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055046.2	NM_181701	Silent
CACNA1F	778	hgsc.bcm.edu	37	X	49081291	49081291	+	Silent	SNP	G	G	A	rs2235127	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:49081291G>A	ENST00000376265.2	-	14	1903	c.1842C>T	c.(1840-1842)ggC>ggT	p.G614G	CACNA1F_ENST00000323022.5_Silent_p.G603G|CACNA1F_ENST00000480889.1_5'Flank|CACNA1F_ENST00000376251.1_Silent_p.G549G	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	614					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GCTGCATGGCGCCCACCTCCA	0.582													g|||	1663	0.44053	0.3585	0.366	3775	,	,		13422	0.5188		0.2028	False		,,,				2504	0.2127				p.G614G		Atlas-SNP	.											.	CACNA1F	218	.	0			c.C1842T						PASS	.			1651,2184		306,806,233,520,338	74.0	47.0	56.0		1842	-6.8	0.9	X	dbSNP_98	56	1874,4853		193,968,520,1267,1351	no	coding-synonymous	CACNA1F	NM_005183.2		499,1774,753,1787,1689	AA,AG,A,GG,G		27.8579,43.0508,33.3744		614/1978	49081291	3525,7037	2203	4299	6502	SO:0001819	synonymous_variant	778	exon14			CATGGCGCCCACC	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.1842C>T	X.37:g.49081291G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	94	92	0.978723	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	37	CCDS35253.1																																																																																			G|0.623;A|0.377	0.377	strong		0.582	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
OR52E4	390081	hgsc.bcm.edu	37	11	5906143	5906143	+	Silent	SNP	T	T	C	rs11823809	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5906143T>C	ENST00000316987.2	+	1	643	c.621T>C	c.(619-621)taT>taC	p.Y207Y		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	207						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGATTTCTTATATTATTGTGG	0.448													T|||	1792	0.357827	0.3222	0.402	5008	,	,		21992	0.3641		0.4085	False		,,,				2504	0.316				p.Y207Y		Atlas-SNP	.											.	OR52E4	65	.	0			c.T621C						PASS	.	T		1502,2900	477.5+/-357.9	262,978,961	298.0	257.0	271.0		621	-0.4	0.9	11	dbSNP_120	271	3625,4967	522.8+/-380.2	780,2065,1451	no	coding-synonymous	OR52E4	NM_001005165.1		1042,3043,2412	CC,CT,TT		42.1904,34.1209,39.4567		207/313	5906143	5127,7867	2201	4296	6497	SO:0001819	synonymous_variant	390081	exon1			TTCTTATATTATT	AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"""GPCR / Class A : Olfactory receptors"""	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.621T>C	11.37:g.5906143T>C		Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	417	194	0.465228	NM_001005165	Q6IFG0	Silent	SNP	ENST00000316987.2	37	CCDS31401.1																																																																																			T|0.611;C|0.389	0.389	strong		0.448	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165	
SRGAP2	23380	hgsc.bcm.edu	37	1	206566195	206566195	+	Silent	SNP	C	C	T	rs12090039	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:206566195C>T	ENST00000414007.1	+	2	216	c.216C>T	c.(214-216)aaC>aaT	p.N72N	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	212	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.N72N(1)		NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					CCACGGCCAACGTTCGCATTG	0.532																																					p.N59N		Atlas-SNP	.											SRGAP2_ENST00000414007,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	prostate(1)	c.C177T						scavenged	.						82.0	80.0	80.0					1																	206566195		2170	4280	6450	SO:0001819	synonymous_variant	100996712	exon2			GGCCAACGTTCGC	AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028		"""Rho GTPase activating proteins"""	19751	protein-coding gene	gene with protein product		606524	"""formin binding protein 2"""	FNBP2		15046868, 11672528	Standard	XM_005277510		Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.216C>T	1.37:g.206566195C>T		Somatic	960	1	0.00104167		WXS	Illumina HiSeq	Phase_I	1298	172	0.132512	NM_001271887		Silent	SNP	ENST00000414007.1	37		.	.	.	.	.	.	.	.	.	.	C	8.707	0.911068	0.17833	.	.	ENSG00000163486	ENST00000295713	.	.	.	5.36	-10.7	0.00240	.	.	.	.	.	T	0.55847	0.1946	.	.	.	0.30974	N	0.7227589999999999	.	.	.	.	.	.	T	0.63642	-0.6591	3	.	.	.	.	19.6945	0.96019	0.0:0.164:0.0:0.836	.	.	.	.	C	126	.	.	R	+	1	0	SRGAP2	204632818	0.146000	0.22672	0.630000	0.29268	0.787000	0.44495	-0.403000	0.07214	-2.202000	0.00745	-0.384000	0.06662	CGT	C|0.875;T|0.125	0.125	strong		0.532	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326	
DLGAP5	9787	hgsc.bcm.edu	37	14	55655692	55655692	+	Missense_Mutation	SNP	C	C	T	rs2274271	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:55655692C>T	ENST00000247191.2	-	2	422	c.206G>A	c.(205-207)gGg>gAg	p.G69E	DLGAP5_ENST00000395425.2_Missense_Mutation_p.G69E	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	69			G -> E (in dbSNP:rs2274271). {ECO:0000269|PubMed:12527899}.		cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TGGAACAAGCCCTTGAGATGT	0.348													T|||	1814	0.36222	0.854	0.2003	5008	,	,		16635	0.2411		0.1034	False		,,,				2504	0.2035				p.G69E		Atlas-SNP	.											.	DLGAP5	84	.	0			c.G206A						PASS	.	T	GLU/GLY,GLU/GLY	3234,1172	409.1+/-334.9	1200,834,169	112.0	110.0	111.0		206,206	3.2	0.5	14	dbSNP_100	111	852,7746	780.2+/-407.7	37,778,3484	yes	missense,missense	DLGAP5	NM_001146015.1,NM_014750.4	98,98	1237,1612,3653	TT,TC,CC		9.9093,26.6001,31.4211	benign,benign	69/843,69/847	55655692	4086,8918	2203	4299	6502	SO:0001583	missense	9787	exon2			ACAAGCCCTTGAG	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"""discs, large homolog 7 (Drosophila)"""	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.206G>A	14.37:g.55655692C>T	ENSP00000247191:p.Gly69Glu	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	190	101	0.531579	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	37	CCDS9723.1	695	0.3182234432234432	399	0.8109756097560976	84	0.23204419889502761	146	0.25524475524475526	66	0.0870712401055409	T	0.007	-1.936758	0.00484	0.733999	0.099093	ENSG00000126787	ENST00000395425;ENST00000247191;ENST00000557645;ENST00000554067	T;T;T;T	0.38560	2.15;2.15;2.15;1.13	5.71	3.15	0.36227	.	1.015010	0.07848	N	0.964172	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39542	-0.9609	9	0.02654	T	1	.	6.4107	0.21690	0.0:0.1517:0.3878:0.4604	rs2274271;rs52794975;rs2274271	69;69	A8MTM6;Q15398	.;DLGP5_HUMAN	E	69	ENSP00000378815:G69E;ENSP00000247191:G69E;ENSP00000451747:G69E;ENSP00000452168:G69E	ENSP00000247191:G69E	G	-	2	0	DLGAP5	54725445	0.000000	0.05858	0.461000	0.27105	0.187000	0.23431	-0.080000	0.11339	0.494000	0.27859	-0.254000	0.11334	GGG	C|0.668;T|0.332	0.332	strong		0.348	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	
ZNF839	55778	hgsc.bcm.edu	37	14	102792386	102792386	+	Missense_Mutation	SNP	T	T	C	rs7158731	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102792386T>C	ENST00000558850.1	+	2	355	c.5T>C	c.(4-6)cTc>cCc	p.L2P	ZNF839_ENST00000442396.2_Missense_Mutation_p.L118P|ZNF839_ENST00000559185.1_Missense_Mutation_p.L2P|ZNF839_ENST00000262236.5_Missense_Mutation_p.L2P	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	2							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AGGCCAATGCTCCTACCGACC	0.522													C|||	2096	0.41853	0.73	0.4179	5008	,	,		17991	0.3403		0.171	False		,,,				2504	0.3333				p.L118P		Atlas-SNP	.											.	ZNF839	41	.	0			c.T353C						PASS	.	C	PRO/LEU	2401,1441		734,933,254	36.0	42.0	40.0		353	4.2	0.0	14	dbSNP_116	40	1417,6883		129,1159,2862	yes	missense	ZNF839	NM_018335.3	98	863,2092,3116	CC,CT,TT		17.0723,37.5065,31.4446	benign	118/928	102792386	3818,8324	1921	4150	6071	SO:0001583	missense	55778	exon2			CAATGCTCCTACC	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.5T>C	14.37:g.102792386T>C	ENSP00000453363:p.Leu2Pro	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Missense_Mutation	SNP	ENST00000558850.1	37	CCDS58336.1	813	0.37225274725274726	348	0.7073170731707317	152	0.4198895027624309	200	0.34965034965034963	113	0.14907651715039577	C	4.460	0.085278	0.08583	0.624935	0.170723	ENSG00000022976	ENST00000442396;ENST00000262236	T;T	0.22539	2.37;1.95	5.05	4.15	0.48705	.	.	.	.	.	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.40794	-0.9544	8	0.02654	T	1	.	8.822	0.35032	0.1473:0.7766:0.0:0.0762	rs7158731;rs52836998;rs57254003;rs7158731	118;2;2	A8K0R7-5;A8K0R7-2;A8K0R7	.;.;ZN839_HUMAN	P	118;2	ENSP00000399863:L118P;ENSP00000262236:L2P	ENSP00000262236:L2P	L	+	2	0	ZNF839	101862139	0.003000	0.15002	0.003000	0.11579	0.011000	0.07611	1.518000	0.35877	0.549000	0.28973	-0.234000	0.12200	CTC	T|0.626;C|0.374	0.374	strong		0.522	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
CLEC4G	339390	hgsc.bcm.edu	37	19	7795955	7795955	+	Silent	SNP	C	C	A	rs8112382	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7795955C>A	ENST00000328853.5	-	4	308	c.240G>T	c.(238-240)gcG>gcT	p.A80A	CLEC4G_ENST00000598081.1_5'UTR	NM_001244856.1|NM_198492.3	NP_001231785.1|NP_940894.1	Q6UXB4	CLC4G_HUMAN	C-type lectin domain family 4, member G	80						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(1)|large_intestine(1)|lung(1)	6						GGGCACCCAGCGCCGCCGTCT	0.697													N|||	408	0.0814696	0.2557	0.0432	5008	,	,		9941	0.0		0.005	False		,,,				2504	0.0358				p.A80A	Esophageal Squamous(146;540 1807 3349 19438 30853)	Atlas-SNP	.											.	CLEC4G	18	.	0			c.G240T						PASS	.	C		909,3493		87,735,1379	18.0	21.0	20.0		240	-2.9	0.0	19	dbSNP_116	20	50,8534		0,50,4242	no	coding-synonymous	CLEC4G	NM_198492.3		87,785,5621	AA,AC,CC		0.5825,20.6497,7.3849		80/294	7795955	959,12027	2201	4292	6493	SO:0001819	synonymous_variant	339390	exon4			ACCCAGCGCCGCC	AY358431	CCDS12185.1	19p13.2	2010-04-27	2008-11-04			ENSG00000182566		"""C-type lectin domain containing"""	24591	protein-coding gene	gene with protein product			"""C-type lectin superfamily 4, member G"""			12975309	Standard	NM_198492		Approved	UNQ431, LSECtin	uc002mhp.4	Q6UXB4		ENST00000328853.5:c.240G>T	19.37:g.7795955C>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_198492		Silent	SNP	ENST00000328853.5	37	CCDS12185.1																																																																																			C|0.917;A|0.083	0.083	strong		0.697	CLEC4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461989.1	NM_198492	
BTNL9	153579	hgsc.bcm.edu	37	5	180472498	180472498	+	Silent	SNP	C	C	T	rs28677846	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:180472498C>T	ENST00000327705.9	+	2	240	c.9C>T	c.(7-9)gaC>gaT	p.D3D	BTNL9_ENST00000376842.3_Silent_p.D3D|BTNL9_ENST00000515271.1_Intron|BTNL9_ENST00000376841.2_Silent_p.D3D	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	3						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGATGGTGGACCTCTCAGTCT	0.602													T|||	2495	0.498203	0.6422	0.5216	5008	,	,		17239	0.3909		0.5189	False		,,,				2504	0.3763				p.D3D		Atlas-SNP	.											.	BTNL9	58	.	0			c.C9T						PASS	.	T		2716,1688	510.1+/-367.4	842,1032,328	95.0	83.0	87.0		9	-5.5	0.0	5	dbSNP_125	87	4498,4100	561.5+/-387.8	1168,2162,969	no	coding-synonymous	BTNL9	NM_152547.4		2010,3194,1297	TT,TC,CC		47.6855,38.3288,44.5162		3/536	180472498	7214,5788	2202	4299	6501	SO:0001819	synonymous_variant	153579	exon2			GGTGGACCTCTCA	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.9C>T	5.37:g.180472498C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_152547	A6NL42|Q6P660|Q96DM5	Silent	SNP	ENST00000327705.9	37	CCDS4460.2																																																																																			C|0.460;G|0.000;T|0.539	0.539	strong		0.602	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547	
PSG2	5670	hgsc.bcm.edu	37	19	43585325	43585325	+	Silent	SNP	G	G	A	rs7248878	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:43585325G>A	ENST00000406487.1	-	2	236	c.138C>T	c.(136-138)tcC>tcT	p.S46S	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	46	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				CCTTCCCCTCGGAAACTTTTG	0.478													G|||	460	0.091853	0.0628	0.196	5008	,	,		21569	0.003		0.1034	False		,,,				2504	0.137				p.S46S		Atlas-SNP	.											.	PSG2	84	.	0			c.C138T						PASS	.	G		313,4093		15,283,1905	156.0	154.0	155.0		138	-1.1	0.0	19	dbSNP_116	155	936,7660		39,858,3401	no	coding-synonymous	PSG2	NM_031246.3		54,1141,5306	AA,AG,GG		10.8888,7.1039,9.6062		46/336	43585325	1249,11753	2203	4298	6501	SO:0001819	synonymous_variant	5670	exon2			CCCCTCGGAAACT		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.138C>T	19.37:g.43585325G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	192	75	0.390625	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			.	.	weak		0.478	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
SLCO1B3	28234	hgsc.bcm.edu	37	12	21036411	21036411	+	Silent	SNP	A	A	G	rs2053098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:21036411A>G	ENST00000381545.3	+	13	1776	c.1557A>G	c.(1555-1557)gcA>gcG	p.A519A	LST3_ENST00000540229.1_Silent_p.A519A|SLCO1B3_ENST00000553473.1_Silent_p.A519A|SLCO1B3_ENST00000261196.2_Silent_p.A519A|LST3_ENST00000381541.3_Intron|SLCO1B7_ENST00000554957.1_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	519					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	ATTACTCAGCACACTTGGGTG	0.338													.|||	3520	0.702875	0.3578	0.8357	5008	,	,		14809	0.6974		0.8648	False		,,,				2504	0.9141				p.A519A		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.A1557G						PASS	.	G		1977,2429		468,1041,694	94.0	96.0	95.0		1557	-7.2	0.0	12	dbSNP_94	95	7427,1173		3209,1009,82	no	coding-synonymous	SLCO1B3	NM_019844.2		3677,2050,776	GG,GA,AA		13.6395,44.8706,27.6949		519/703	21036411	9404,3602	2203	4300	6503	SO:0001819	synonymous_variant	28234	exon13			CTCAGCACACTTG		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1557A>G	12.37:g.21036411A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_019844	E7EMT8|Q5JAR4	Silent	SNP	ENST00000381545.3	37	CCDS8684.1																																																																																			A|0.284;G|0.716	0.716	strong		0.338	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
LLGL1	3996	hgsc.bcm.edu	37	17	18137141	18137141	+	Missense_Mutation	SNP	A	A	G	rs2290505	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18137141A>G	ENST00000316843.4	+	5	538	c.442A>G	c.(442-444)Agc>Ggc	p.S148G		NM_004140.3	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1 (Drosophila)	148			S -> G (in dbSNP:rs2290505). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7542763, ECO:0000269|PubMed:8565641}.		axonogenesis (GO:0007409)|cortical actin cytoskeleton organization (GO:0030866)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|maintenance of apical/basal cell polarity (GO:0035090)|positive regulation of Rab GTPase activity (GO:0032851)|protein complex assembly (GO:0006461)	cell projection (GO:0042995)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome membrane (GO:0031901)|Golgi cis cisterna (GO:0000137)|myelin sheath abaxonal region (GO:0035748)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)|structural molecule activity (GO:0005198)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_neural(463;0.228)					GGTGGCTGCCAGCGACATAGC	0.632													G|||	3918	0.782348	0.848	0.7493	5008	,	,		11652	0.6786		0.7614	False		,,,				2504	0.8456				p.S148G		Atlas-SNP	.											LLGL1,rectum,carcinoma,0,1	LLGL1	61	1	0			c.A442G						scavenged	.	G	GLY/SER	3690,716	298.1+/-285.1	1556,578,69	89.0	80.0	83.0		442	2.6	0.0	17	dbSNP_100	83	6459,2141	365.6+/-334.0	2422,1615,263	yes	missense	LLGL1	NM_004140.3	56	3978,2193,332	GG,GA,AA		24.8953,16.2506,21.9668	benign	148/1065	18137141	10149,2857	2203	4300	6503	SO:0001583	missense	3996	exon5			GCTGCCAGCGACA		CCDS32586.1	17p11.2	2013-01-10	2001-11-28		ENSG00000131899	ENSG00000131899		"""WD repeat domain containing"""	6628	protein-coding gene	gene with protein product		600966	"""lethal giant larvae (Drosophila) homolog 1"""	DLG4, LLGL, HUGL, HUGL-1		7542763, 8565641	Standard	XM_005256643		Approved		uc002gsp.3	Q15334	OTTHUMG00000059396	ENST00000316843.4:c.442A>G	17.37:g.18137141A>G	ENSP00000321537:p.Ser148Gly	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_004140	A7MBM7|O00188|Q58F11|Q86UK6	Missense_Mutation	SNP	ENST00000316843.4	37	CCDS32586.1	1650	0.7554945054945055	406	0.8252032520325203	274	0.7569060773480663	402	0.7027972027972028	568	0.7493403693931399	G	0.008	-1.867144	0.00547	0.837494	0.751047	ENSG00000131899	ENST00000316843	T	0.05139	3.49	5.87	2.63	0.31362	WD40 repeat-like-containing domain (1);	0.357650	0.36444	N	0.002589	T	0.00012	0.0000	N	0.11341	0.13	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07673	-1.0760	9	0.16896	T	0.51	-8.2838	7.0524	0.25081	0.2156:0.0:0.6055:0.1788	rs2290505;rs58954283;rs2290505	148	Q15334	L2GL1_HUMAN	G	148	ENSP00000321537:S148G	ENSP00000321537:S148G	S	+	1	0	LLGL1	18077866	0.002000	0.14202	0.001000	0.08648	0.033000	0.12548	-0.023000	0.12456	0.428000	0.26173	-0.748000	0.03510	AGC	A|0.229;G|0.771	0.771	strong		0.632	LLGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132067.3		
TXLNG	55787	hgsc.bcm.edu	37	X	16859628	16859628	+	Silent	SNP	G	G	A	rs5924530	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:16859628G>A	ENST00000380122.5	+	10	1387	c.1326G>A	c.(1324-1326)caG>caA	p.Q442Q	TXLNG_ENST00000485153.1_3'UTR|TXLNG_ENST00000398155.4_Silent_p.Q310Q	NM_018360.2	NP_060830.2	Q9NUQ3	TXLNG_HUMAN	taxilin gamma	442					cell cycle (GO:0007049)|regulation of bone mineralization (GO:0030500)|regulation of cell cycle (GO:0051726)|regulation of cell cycle process (GO:0010564)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)	protein heterodimerization activity (GO:0046982)			breast(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	15						GGGCTCTTCAGACAGAAAGGA	0.453													A|||	2434	0.644768	0.6483	0.4957	3775	,	,		13006	0.6538		0.2962	False		,,,				2504	0.2822				p.Q442Q		Atlas-SNP	.											.	TXLNG	40	.	0			c.G1326A						PASS	.	A	,	3100,735		1071,496,462,65,109	68.0	61.0	63.0		930,1326	0.7	0.7	X	dbSNP_114	63	2624,4104		384,1142,714,902,1158	no	coding-synonymous,coding-synonymous	TXLNG	NM_001168683.1,NM_018360.2	,	1455,1638,1176,967,1267	AA,AG,A,GG,G		39.0012,19.1656,45.8108	,	310/397,442/529	16859628	5724,4839	2203	4300	6503	SO:0001819	synonymous_variant	55787	exon10			TCTTCAGACAGAA	AK002071	CCDS14178.1, CCDS55373.1	Xp22.2	2014-05-07	2010-04-20	2010-04-20	ENSG00000086712	ENSG00000086712			18578	protein-coding gene	gene with protein product	"""lipopolysaccharide specific response-5 protein"", ""factor inhibiting activating transcription factor 4 (ATF4)-mediated transcription"""	300677	"""chromosome X open reading frame 15"""	CXorf15		15911876, 15184072, 16831913	Standard	NM_018360		Approved	FLJ11209, LSR5, FIAT, MGC126621, MGC126625, TXLNGX	uc004cxq.2	Q9NUQ3	OTTHUMG00000021196	ENST00000380122.5:c.1326G>A	X.37:g.16859628G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	182	8	0.043956	NM_018360	Q2KQ75|Q5JNZ7|Q9P0X1	Silent	SNP	ENST00000380122.5	37	CCDS14178.1																																																																																			0|0.012;A|0.602	0.602	strong		0.453	TXLNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055912.1	NM_018360	
NT5E	4907	hgsc.bcm.edu	37	6	86199243	86199243	+	Missense_Mutation	SNP	T	T	C	rs2229524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:86199243T>C	ENST00000257770.3	+	6	1185	c.1136T>C	c.(1135-1137)aTg>aCg	p.M379T	NT5E_ENST00000369651.3_Missense_Mutation_p.M379T	NM_002526.3	NP_002517.1	P21589	5NTD_HUMAN	5'-nucleotidase, ecto (CD73)	379			M -> T (in dbSNP:rs2229524).		adenosine biosynthetic process (GO:0046086)|AMP catabolic process (GO:0006196)|dephosphorylation (GO:0016311)|DNA metabolic process (GO:0006259)|negative regulation of inflammatory response (GO:0050728)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Cytarabine(DB00987)|Pentoxifylline(DB00806)	ACGGATGAAATGTTCTGGAAC	0.473													T|||	780	0.155751	0.407	0.0576	5008	,	,		21001	0.0516		0.0537	False		,,,				2504	0.0982				p.M379T	Melanoma(140;797 1765 2035 2752 18208)	Atlas-SNP	.											.	NT5E	56	.	0			c.T1136C						PASS	.	T	THR/MET,THR/MET	1603,2803	498.6+/-364.2	294,1015,894	143.0	120.0	128.0		1136,1136	-0.3	0.9	6	dbSNP_98	128	589,8011	156.1+/-210.0	20,549,3731	yes	missense,missense	NT5E	NM_001204813.1,NM_002526.3	81,81	314,1564,4625	CC,CT,TT		6.8488,36.3822,16.8538	benign,benign	379/525,379/575	86199243	2192,10814	2203	4300	6503	SO:0001583	missense	4907	exon6			ATGAAATGTTCTG	X55740	CCDS5002.1, CCDS56439.1	6q14-q21	2013-08-28	2002-04-18	2002-04-19	ENSG00000135318	ENSG00000135318	3.1.3.5	"""CD molecules"""	8021	protein-coding gene	gene with protein product		129190	"""5' nucleotidase (CD73)"""	NT5			Standard	NM_002526		Approved	CD73, eN, eNT, CALJA	uc003pko.4	P21589	OTTHUMG00000015139	ENST00000257770.3:c.1136T>C	6.37:g.86199243T>C	ENSP00000257770:p.Met379Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	33	0.340206	NM_001204813	B3KQI8|O75520|Q5W116	Missense_Mutation	SNP	ENST00000257770.3	37	CCDS5002.1	282|282	0.12912087912087913|0.12912087912087913	187|187	0.3800813008130081|0.3800813008130081	21|21	0.058011049723756904|0.058011049723756904	32|32	0.055944055944055944|0.055944055944055944	42|42	0.055408970976253295|0.055408970976253295	T|T	2.618|2.618	-0.289306|-0.289306	0.05605|0.05605	0.363822|0.363822	0.068488|0.068488	ENSG00000135318|ENSG00000135318	ENST00000416334;ENST00000437581|ENST00000369647;ENST00000257770;ENST00000369651	.|T;T	.|0.54071	.|0.59;0.59	5.21|5.21	-0.33|-0.33	0.12683|0.12683	.|5&apos (3);-Nucleotidase, C-terminal (3);	.|0.825447	.|0.11656	.|N	.|0.542338	T|T	0.04907|0.04907	0.0132|0.0132	N|N	0.01352|0.01352	-0.895|-0.895	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.10450	.|0.005;0.005	T|T	0.29274|0.29274	-1.0017|-1.0017	4|9	.|0.12430	.|T	.|0.62	-2.4118|-2.4118	0.9741|0.9741	0.01422|0.01422	0.2381:0.2036:0.0989:0.4594|0.2381:0.2036:0.0989:0.4594	rs2229524;rs10081139;rs52794129;rs10081139|rs2229524;rs10081139;rs52794129;rs10081139	.|379;379	.|B3KQI8;P21589	.|.;5NTD_HUMAN	R|T	144;75|155;379;379	.|ENSP00000257770:M379T;ENSP00000358665:M379T	.|ENSP00000257770:M379T	C|M	+|+	1|2	0|0	NT5E|NT5E	86255962|86255962	0.005000|0.005000	0.15991|0.15991	0.886000|0.886000	0.34754|0.34754	0.800000|0.800000	0.45204|0.45204	0.677000|0.677000	0.25262|0.25262	0.017000|0.017000	0.15025|0.15025	0.379000|0.379000	0.24179|0.24179	TGT|ATG	A|0.000;C|0.157;G|0.000;T|0.843	0.157	strong		0.473	NT5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041388.1		
FAHD2B	151313	hgsc.bcm.edu	37	2	97749730	97749730	+	Silent	SNP	G	G	T	rs113222096	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:97749730G>T	ENST00000414820.1	-	8	1107	c.837C>A	c.(835-837)acC>acA	p.T279T	FAHD2B_ENST00000272610.3_Silent_p.T279T|FAHD2B_ENST00000440566.2_Silent_p.T279T|FAHD2B_ENST00000468548.1_5'Flank			Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing 2B	279							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			kidney(5)|large_intestine(2)|lung(3)|skin(2)	12						CACCTGGGGGGGTCCCAGTTA	0.557													g|||	25	0.00499201	0.0	0.0014	5008	,	,		21137	0.0		0.0209	False		,,,				2504	0.0031				p.T279T		Atlas-SNP	.											.	FAHD2B	34	.	0			c.C837A						PASS	.	G		22,4384	26.2+/-53.5	0,22,2181	31.0	32.0	32.0		837	-2.4	1.0	2	dbSNP_132	32	159,8437	73.8+/-136.5	0,159,4139	no	coding-synonymous	FAHD2B	NM_199336.1		0,181,6320	TT,TG,GG		1.8497,0.4993,1.3921		279/315	97749730	181,12821	2203	4298	6501	SO:0001819	synonymous_variant	151313	exon7			TGGGGGGGTCCCA		CCDS2030.1	2q11.2	2012-06-29			ENSG00000144199	ENSG00000144199			25318	protein-coding gene	gene with protein product							Standard	NM_199336		Approved	DKFZp434N062	uc002sxm.3	Q6P2I3	OTTHUMG00000130533	ENST00000414820.1:c.837C>A	2.37:g.97749730G>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	162	74	0.45679	NM_199336	D3DXH7|Q8NDK1	Silent	SNP	ENST00000414820.1	37	CCDS2030.1																																																																																			G|0.987;T|0.013	0.013	strong		0.557	FAHD2B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339482.1	NM_199336	
GPIHBP1	338328	hgsc.bcm.edu	37	8	144295782	144295782	+	Silent	SNP	G	G	T	rs11538388	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144295782G>T	ENST00000330824.2	+	2	213	c.138G>T	c.(136-138)gtG>gtT	p.V46V		NM_178172.3	NP_835466.1	Q8IV16	HDBP1_HUMAN	glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1	46	Poly-Glu.				cholesterol homeostasis (GO:0042632)|intracellular protein transport (GO:0006886)|positive regulation of chylomicron remnant clearance (GO:0090321)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein import (GO:0017038)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|protein transmembrane transport (GO:0071806)|response to heparin (GO:0071503)|transcytosis (GO:0045056)|triglyceride homeostasis (GO:0070328)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|external side of plasma membrane (GO:0009897)|high-density lipoprotein particle (GO:0034364)	chylomicron binding (GO:0035478)|lipase binding (GO:0035473)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|protein transmembrane transporter activity (GO:0008320)			lung(2)	2	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					aggatgaggtggaagaggagg	0.632													G|||	1797	0.358826	0.2231	0.4265	5008	,	,		17689	0.4296		0.4473	False		,,,				2504	0.3303				p.V46V		Atlas-SNP	.											.	GPIHBP1	12	.	0			c.G138T						PASS	.	G		999,3329		148,703,1313	181.0	109.0	133.0		138	1.3	0.7	8	dbSNP_120	133	3590,4850		814,1962,1444	no	coding-synonymous	GPIHBP1	NM_178172.3		962,2665,2757	TT,TG,GG		42.5355,23.0823,35.9414		46/185	144295782	4589,8179	2164	4220	6384	SO:0001819	synonymous_variant	338328	exon2			TGAGGTGGAAGAG	AF088057	CCDS34954.1	8q24.3	2014-07-14	2008-02-07						24945	protein-coding gene	gene with protein product	"""endothelial cell LPL transporter"""	612757	"""GPI anchored high density lipoprotein binding protein 1"""			12496272, 17883852, 17620854, 17403372	Standard	NM_178172		Approved	LOC338328, GPI-HBP1	uc003yxu.2	Q8IV16		ENST00000330824.2:c.138G>T	8.37:g.144295782G>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	40	0.412371	NM_178172	Q6P3T2|Q86W15	Silent	SNP	ENST00000330824.2	37	CCDS34954.1																																																																																			G|0.641;T|0.359	0.359	strong		0.632	GPIHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381113.1	NM_178172	
NOX3	50508	hgsc.bcm.edu	37	6	155774608	155774608	+	Silent	SNP	C	C	T	rs34960420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:155774608C>T	ENST00000159060.2	-	4	372	c.270G>A	c.(268-270)ccG>ccA	p.P90P		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	90	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		GCCTCCTCCACGGTCCTCTGC	0.378													C|||	638	0.127396	0.1059	0.2291	5008	,	,		19963	0.1121		0.1044	False		,,,				2504	0.1237				p.P90P		Atlas-SNP	.											.	NOX3	93	.	0			c.G270A						PASS	.	C		471,3935	221.7+/-238.7	29,413,1761	203.0	209.0	207.0		270	-5.3	0.8	6	dbSNP_126	207	968,7632	210.8+/-251.6	57,854,3389	no	coding-synonymous	NOX3	NM_015718.2		86,1267,5150	TT,TC,CC		11.2558,10.69,11.0641		90/569	155774608	1439,11567	2203	4300	6503	SO:0001819	synonymous_variant	50508	exon4			CCTCCACGGTCCT	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.270G>A	6.37:g.155774608C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	194	104	0.536082	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	37	CCDS5250.1																																																																																			C|0.888;T|0.112	0.112	strong		0.378	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
VPS53	55275	hgsc.bcm.edu	37	17	465775	465775	+	Silent	SNP	G	G	A	rs2075443	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:465775G>A	ENST00000571805.1	-	14	1660	c.1524C>T	c.(1522-1524)taC>taT	p.Y508Y	VPS53_ENST00000446250.2_Silent_p.Y310Y|VPS53_ENST00000437048.2_Silent_p.Y508Y|VPS53_ENST00000401468.3_Silent_p.Y231Y|VPS53_ENST00000291074.5_Silent_p.Y479Y|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000576149.1_5'UTR			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	508					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		TTTTCCAGGCGTATTCTCGGA	0.483													g|||	1746	0.348642	0.6021	0.4207	5008	,	,		19160	0.2163		0.2247	False		,,,				2504	0.2188				p.Y508Y		Atlas-SNP	.											.	VPS53	109	.	0			c.C1524T						PASS	.	A	,	2369,2037	611.2+/-391.7	669,1031,503	83.0	79.0	81.0		1524,1437	-12.1	0.3	17	dbSNP_96	81	1978,6622	347.3+/-326.5	239,1500,2561	no	coding-synonymous,coding-synonymous	VPS53	NM_001128159.2,NM_018289.3	,	908,2531,3064	AA,AG,GG		23.0,46.2324,33.423	,	508/833,479/671	465775	4347,8659	2203	4300	6503	SO:0001819	synonymous_variant	55275	exon14			CCAGGCGTATTCT		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"""vacuolar protein sorting 53 (yeast)"""			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.1524C>T	17.37:g.465775G>A		Somatic	316	1	0.00316456		WXS	Illumina HiSeq	Phase_I	291	289	0.993127	NM_001128159	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Silent	SNP	ENST00000571805.1	37																																																																																				G|0.681;A|0.319	0.319	strong		0.483	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289	
WDFY4	57705	hgsc.bcm.edu	37	10	50034833	50034833	+	Missense_Mutation	SNP	G	G	A	rs6537579	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50034833G>A	ENST00000325239.5	+	35	6127	c.6100G>A	c.(6100-6102)Ggc>Agc	p.G2034S	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	2034						integral component of membrane (GO:0016021)		p.G2034S(1)		NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CGAATGCCTCGGCCTTCTCAG	0.488													A|||	1005	0.200679	0.4039	0.1729	5008	,	,		20229	0.1012		0.1243	False		,,,				2504	0.1268				p.G2034S		Atlas-SNP	.											WDFY4,NS,carcinoma,0,1	WDFY4	205	1	1	Substitution - Missense(1)	stomach(1)	c.G6100A						scavenged	.	A	SER/GLY	522,862		96,330,266	112.0	93.0	99.0		6100	-4.3	0.3	10	dbSNP_116	99	342,2840		19,304,1268	yes	missense	WDFY4	NM_020945.1	56	115,634,1534	AA,AG,GG		10.748,37.7168,18.9225	benign	2034/3185	50034833	864,3702	692	1591	2283	SO:0001583	missense	57705	exon36			TGCCTCGGCCTTC	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.6100G>A	10.37:g.50034833G>A	ENSP00000320563:p.Gly2034Ser	Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	220	116	0.527273	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	394|394	0.1804029304029304|0.1804029304029304	177|177	0.3597560975609756|0.3597560975609756	55|55	0.15193370165745856|0.15193370165745856	70|70	0.12237762237762238|0.12237762237762238	92|92	0.12137203166226913|0.12137203166226913	A|A	3.158|3.158	-0.172780|-0.172780	0.06421|0.06421	0.377168|0.377168	0.10748|0.10748	ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239|ENST00000312002	T|.	0.51071|.	0.72|.	5.62|5.62	-4.33|-4.33	0.03677|0.03677	.|.	0.801903|.	0.11711|.	N|.	0.536877|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02315|0.02315	-0.6|-0.6	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.32981|0.32981	-0.9886|-0.9886	8|4	.|.	.|.	.|.	.|.	15.8609|15.8609	0.79019|0.79019	0.4631:0.0:0.5369:0.0|0.4631:0.0:0.5369:0.0	rs6537579;rs52795837;rs61660295;rs6537579|rs6537579;rs52795837;rs61660295;rs6537579	2034|.	Q6ZS81|.	WDFY4_HUMAN|.	S|Q	2034|1124	ENSP00000320563:G2034S|.	.|.	G|R	+|+	1|2	0|0	WDFY4|WDFY4	49704839|49704839	0.000000|0.000000	0.05858|0.05858	0.266000|0.266000	0.24541|0.24541	0.867000|0.867000	0.49689|0.49689	0.486000|0.486000	0.22340|0.22340	-1.105000|-1.105000	0.03011|0.03011	-1.062000|-1.062000	0.02293|0.02293	GGC|CGG	G|0.801;A|0.199	0.199	strong		0.488	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
GPR155	151556	hgsc.bcm.edu	37	2	175300997	175300997	+	Silent	SNP	G	G	A	rs6757461	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:175300997G>A	ENST00000392552.2	-	16	2698	c.2460C>T	c.(2458-2460)aaC>aaT	p.N820N	GPR155_ENST00000392551.2_Silent_p.N820N|GPR155_ENST00000459996.1_5'Flank|GPR155_ENST00000295500.4_Silent_p.N820N	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	820	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						ATTCATACTCGTTGGTAATAT	0.463													G|||	1070	0.213658	0.0825	0.1974	5008	,	,		20403	0.2143		0.3827	False		,,,				2504	0.228				p.N820N		Atlas-SNP	.											GPR155,NS,carcinoma,-1,1	GPR155	76	1	0			c.C2460T						PASS	.	G	,	544,3862	247.2+/-255.5	37,470,1696	162.0	160.0	161.0		2460,2460	-2.2	0.9	2	dbSNP_116	161	2944,5656	459.0+/-364.8	521,1902,1877	no	coding-synonymous,coding-synonymous	GPR155	NM_001033045.2,NM_152529.5	,	558,2372,3573	AA,AG,GG		34.2326,12.3468,26.8184	,	820/871,820/871	175300997	3488,9518	2203	4300	6503	SO:0001819	synonymous_variant	151556	exon17			ATACTCGTTGGTA	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.2460C>T	2.37:g.175300997G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	163	77	0.472393	NM_001033045	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Silent	SNP	ENST00000392552.2	37	CCDS2259.1																																																																																			G|0.734;A|0.266	0.266	strong		0.463	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529	
KIAA1462	57608	hgsc.bcm.edu	37	10	30316872	30316872	+	Silent	SNP	T	T	C	rs3739996	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:30316872T>C	ENST00000375377.1	-	3	2306	c.2205A>G	c.(2203-2205)gcA>gcG	p.A735A		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	735					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						CGGTAGGGAATGCTGTGTGCG	0.577													T|||	1058	0.211262	0.1127	0.2406	5008	,	,		20585	0.2242		0.3897	False		,,,				2504	0.1268				p.A735A		Atlas-SNP	.											.	KIAA1462	162	.	0			c.A2205G						PASS	.	T		556,3696		45,466,1615	54.0	57.0	56.0		2205	-11.2	0.0	10	dbSNP_107	56	3196,5302		593,2010,1646	no	coding-synonymous	KIAA1462	NM_020848.2		638,2476,3261	CC,CT,TT		37.6088,13.0762,29.4275		735/1360	30316872	3752,8998	2126	4249	6375	SO:0001819	synonymous_variant	57608	exon3			AGGGAATGCTGTG	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.2205A>G	10.37:g.30316872T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	191	99	0.518325	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																			T|0.732;C|0.268	0.268	strong		0.577	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
SLC2A8	29988	hgsc.bcm.edu	37	9	130165995	130165995	+	Silent	SNP	C	C	T	rs1138740	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:130165995C>T	ENST00000373371.3	+	6	869	c.780C>T	c.(778-780)ggC>ggT	p.G260G	SLC2A8_ENST00000373360.3_Silent_p.G260G|SLC2A8_ENST00000373352.1_5'UTR	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	260					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|male meiosis I (GO:0007141)|response to hypoxia (GO:0001666)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	glucose binding (GO:0005536)|glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	11						TCATCATCGGCGTCTCCCTGA	0.577													C|||	521	0.104034	0.0091	0.2147	5008	,	,		19449	0.0089		0.2326	False		,,,				2504	0.1196				p.G260G		Atlas-SNP	.											.	SLC2A8	27	.	0			c.C780T						PASS	.	C		190,4216	120.0+/-157.7	4,182,2017	57.0	56.0	56.0		780	0.9	0.3	9	dbSNP_86	56	1795,6805	323.2+/-315.9	197,1401,2702	no	coding-synonymous	SLC2A8	NM_014580.3		201,1583,4719	TT,TC,CC		20.8721,4.3123,15.2622		260/478	130165995	1985,11021	2203	4300	6503	SO:0001819	synonymous_variant	29988	exon6			CATCGGCGTCTCC	AJ245937	CCDS6870.1, CCDS65138.1, CCDS75903.1	9q33.3	2013-05-22	2008-09-02		ENSG00000136856	ENSG00000136856		"""Solute carriers"""	13812	protein-coding gene	gene with protein product		605245	"""solute carrier family 2 (facilitated glucose transporter) member 8"""			10671487, 10821868	Standard	NM_014580		Approved	GLUTX1, GLUT8	uc004bqu.4	Q9NY64	OTTHUMG00000020702	ENST00000373371.3:c.780C>T	9.37:g.130165995C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	118	80	0.677966	NM_014580	Q8WUZ9|Q9NSC4	Silent	SNP	ENST00000373371.3	37	CCDS6870.1																																																																																			C|0.860;T|0.140	0.140	strong		0.577	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580	
SNX29	92017	hgsc.bcm.edu	37	16	12662420	12662420	+	Silent	SNP	C	C	T	rs2288423	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:12662420C>T	ENST00000566228.1	+	21	2445	c.2376C>T	c.(2374-2376)ttC>ttT	p.F792F	CTD-3037G24.3_ENST00000564505.1_RNA|SNX29_ENST00000306030.3_Silent_p.F407F	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	792						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						CTTCCCGCTTCCCCAAACTGT	0.642													C|||	1634	0.326278	0.41	0.2017	5008	,	,		15444	0.4524		0.2306	False		,,,				2504	0.2699				p.F792F		Atlas-SNP	.											.	SNX29	60	.	0			c.C2376T						PASS	.	C		1327,2603		227,873,865	31.0	39.0	36.0		1221	5.1	1.0	16	dbSNP_100	36	1854,6514		196,1462,2526	no	coding-synonymous	SNX29	NM_001080530.2		423,2335,3391	TT,TC,CC		22.1558,33.7659,25.866		407/429	12662420	3181,9117	1965	4184	6149	SO:0001819	synonymous_variant	92017	exon21			CCGCTTCCCCAAA	AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"""Sorting nexins"""	30542	protein-coding gene	gene with protein product			"""RUN domain containing 2A"""	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.2376C>T	16.37:g.12662420C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Silent	SNP	ENST00000566228.1	37	CCDS10553.2																																																																																			C|0.684;T|0.316	0.316	strong		0.642	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
PKD1L2	114780	hgsc.bcm.edu	37	16	81241100	81241100	+	RNA	SNP	G	G	C	rs386792899|rs11150370	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81241100G>C	ENST00000525539.1	-	0	900				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TACCTCGGCGGGTTGTAGGGA	0.453													G|||	2372	0.473642	0.177	0.4784	5008	,	,		18125	0.8661		0.4384	False		,,,				2504	0.5031				p.P301A		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C901G						PASS	.	G	ALA/PRO,ALA/PRO	788,3012		102,584,1214	97.0	96.0	96.0		901,901	4.9	1.0	16	dbSNP_120	96	3522,4718		826,1870,1424	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	27,27	928,2454,2638	CC,CG,GG		42.7427,20.7368,35.7973	probably-damaging,probably-damaging	301/992,301/2460	81241100	4310,7730	1900	4120	6020			114780	exon5			TCGGCGGGTTGTA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81241100G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1108	0.5073260073260073	107	0.21747967479674796	172	0.47513812154696133	482	0.8426573426573427	347	0.4577836411609499	G	15.13	2.741991	0.49151	0.207368	0.427427	ENSG00000166473	ENST00000337114	T	0.66280	-0.2	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.33489	P	0.411547	P;D	0.89917	0.951;1.0	P;D	0.72338	0.639;0.977	T	0.36432	-0.9748	8	0.62326	D	0.03	-15.1939	18.1543	0.89686	0.0:0.0:1.0:0.0	rs11150370;rs11150370	301;301	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	A	301	ENSP00000337397:P301A	ENSP00000337397:P301A	P	-	1	0	PKD1L2	79798601	1.000000	0.71417	0.976000	0.42696	0.032000	0.12392	6.049000	0.71053	2.277000	0.76020	0.563000	0.77884	CCG	G|0.506;C|0.494	0.494	strong		0.453	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
WDR61	80349	hgsc.bcm.edu	37	15	78585106	78585106	+	Silent	SNP	C	C	T	rs2280364	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:78585106C>T	ENST00000267973.2	-	5	442	c.171G>A	c.(169-171)caG>caA	p.Q57Q	WDR61_ENST00000558459.1_Intron|WDR61_ENST00000558311.1_Silent_p.Q57Q|RP11-762H8.1_ENST00000560057.1_RNA			Q9GZS3	WDR61_HUMAN	WD repeat domain 61	57					histone H3-K4 trimethylation (GO:0080182)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9						CCAGACTCCACTGTAGGTCCA	0.512													C|||	461	0.0920527	0.0567	0.0706	5008	,	,		17709	0.121		0.0865	False		,,,				2504	0.1309				p.Q57Q		Atlas-SNP	.											.	WDR61	26	.	0			c.G171A						PASS	.	C		287,4105	159.6+/-192.1	12,263,1921	64.0	59.0	61.0		171	3.9	1.0	15	dbSNP_100	61	882,7704	200.0+/-243.9	45,792,3456	no	coding-synonymous	WDR61	NM_025234.1		57,1055,5377	TT,TC,CC		10.2725,6.5346,9.0076		57/306	78585106	1169,11809	2196	4293	6489	SO:0001819	synonymous_variant	80349	exon5			ACTCCACTGTAGG		CCDS10300.1	15q25.1	2013-01-09			ENSG00000140395	ENSG00000140395		"""WD repeat domain containing"""	30300	protein-coding gene	gene with protein product		609540				12477932	Standard	NM_025234		Approved	REC14	uc002bdn.3	Q9GZS3	OTTHUMG00000143735	ENST00000267973.2:c.171G>A	15.37:g.78585106C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_025234	D3DW84|Q6IA22|Q7Z4X4	Silent	SNP	ENST00000267973.2	37	CCDS10300.1																																																																																			C|0.910;T|0.090	0.090	strong		0.512	WDR61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289803.3	NM_025234	
OR4N2	390429	hgsc.bcm.edu	37	14	20296004	20296004	+	Missense_Mutation	SNP	C	C	T	rs2318279	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20296004C>T	ENST00000315947.1	+	1	397	c.397C>T	c.(397-399)Cct>Tct	p.P133S	OR4N2_ENST00000568211.1_Missense_Mutation_p.P133S	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	133			P -> S (in dbSNP:rs2318279).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P133S(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCTGCACTATCCTACTGTCAT	0.522																																					p.P133S		Atlas-SNP	.											OR4N2,NS,carcinoma,0,1	OR4N2	125	1	1	Substitution - Missense(1)	stomach(1)	c.C397T						PASS	.	T	SER/PRO	1656,2750		218,1220,765	205.0	218.0	214.0		397	-1.6	0.0	14	dbSNP_100	214	2205,6395		148,1909,2243	yes	missense	OR4N2	NM_001004723.1	74	366,3129,3008	TT,TC,CC		25.6395,37.5851,29.6863	benign	133/308	20296004	3861,9145	2203	4300	6503	SO:0001583	missense	390429	exon1			CACTATCCTACTG		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.397C>T	14.37:g.20296004C>T	ENSP00000319601:p.Pro133Ser	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	211	210	0.995261	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	569	0.26053113553113555	215	0.4369918699186992	77	0.212707182320442	69	0.12062937062937062	208	0.27440633245382584	.	0.188	-1.055704	0.01965	0.375851	0.256395	ENSG00000176294	ENST00000557677;ENST00000315947	T;T	0.00995	5.46;5.46	4.53	-1.58	0.08479	GPCR, rhodopsin-like superfamily (1);	0.174373	0.27976	N	0.017092	T	0.00012	0.0000	N	0.21373	0.66	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41556	-0.9502	9	0.40728	T	0.16	-1.2504	2.051	0.03571	0.2302:0.0877:0.3897:0.2924	rs2318279;rs52793006;rs2318279	133	Q8NGD1	OR4N2_HUMAN	S	133	ENSP00000452022:P133S;ENSP00000319601:P133S	ENSP00000319601:P133S	P	+	1	0	OR4N2	19365844	0.000000	0.05858	0.006000	0.13384	0.292000	0.27327	-1.373000	0.02568	-0.283000	0.09115	-0.332000	0.08345	CCT	C|0.753;T|0.247	0.247	strong		0.522	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
DSPP	1834	hgsc.bcm.edu	37	4	88537268	88537268	+	Missense_Mutation	SNP	G	G	A	rs62651555	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:88537268G>A	ENST00000282478.7	+	4	3487	c.3454G>A	c.(3454-3456)Gac>Aac	p.D1152N	DSPP_ENST00000399271.1_Missense_Mutation_p.D1152N|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1152	Asp/Ser-rich.			D -> N (in Ref. 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgaaagcagcgacagcagtga	0.557													G|||	745	0.148762	0.0144	0.3372	5008	,	,		27589	0.1776		0.2147	False		,,,				2504	0.0992				p.D1152N		Atlas-SNP	.											.	DSPP	174	.	0			c.G3454A						PASS	.	G	ASN/ASP	162,3000		5,152,1424	46.0	60.0	55.0		3454	1.5	0.4	4	dbSNP_134	55	1296,4426		118,1060,1683	no	missense	DSPP	NM_014208.3	23	123,1212,3107	AA,AG,GG		22.6494,5.1233,16.4115	probably-damaging	1152/1302	88537268	1458,7426	1581	2861	4442	SO:0001583	missense	1834	exon5			AGCAGCGACAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3454G>A	4.37:g.88537268G>A	ENSP00000282478:p.Asp1152Asn	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	107	58	0.542056	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	G	2.285	-0.363699	0.05103	0.051233	0.226494	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.90444	-2.67;-2.67	1.52	1.52	0.23074	.	0.483859	0.15263	N	0.271667	T	0.00271	0.0008	L	0.29908	0.895	0.52501	P	4.199999999998649E-5	D	0.89917	1.0	D	0.74348	0.983	T	0.09640	-1.0665	9	0.44086	T	0.13	.	6.5429	0.22390	0.0:0.0:1.0:0.0	rs62651555	1152	Q9NZW4	DSPP_HUMAN	N	1152	ENSP00000382213:D1152N;ENSP00000282478:D1152N	ENSP00000282478:D1152N	D	+	1	0	DSPP	88756292	0.924000	0.31332	0.365000	0.25901	0.010000	0.07245	1.465000	0.35299	1.179000	0.42884	0.298000	0.19748	GAC	.	.	weak		0.557	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
OR51S1	119692	hgsc.bcm.edu	37	11	4870261	4870261	+	Missense_Mutation	SNP	G	G	C	rs11602499	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:4870261G>C	ENST00000322101.2	-	1	253	c.178C>G	c.(178-180)Cag>Gag	p.Q60E	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	60			Q -> E (in dbSNP:rs11602499).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGGGCGGGCTGCAGGGCAATG	0.567													C|||	1373	0.274161	0.2352	0.2579	5008	,	,		20052	0.0675		0.4066	False		,,,				2504	0.4151				p.Q60E		Atlas-SNP	.											.	OR51S1	83	.	0			c.C178G						PASS	.	C	GLU/GLN	1237,3165	705.5+/-407.3	183,871,1147	109.0	88.0	95.0		178	4.8	0.2	11	dbSNP_120	95	3700,4896	619.9+/-397.0	805,2090,1403	yes	missense	OR51S1	NM_001004758.1	29	988,2961,2550	CC,CG,GG		43.0433,28.1009,37.9828	benign	60/324	4870261	4937,8061	2201	4298	6499	SO:0001583	missense	119692	exon1			CGGGCTGCAGGGC	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"""GPCR / Class A : Olfactory receptors"""	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.178C>G	11.37:g.4870261G>C	ENSP00000322754:p.Gln60Glu	Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	230	228	0.991304	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	573	0.2623626373626374	121	0.2459349593495935	118	0.3259668508287293	32	0.055944055944055944	302	0.39841688654353563	C	0.003	-2.537173	0.00143	0.281009	0.430433	ENSG00000176922	ENST00000322101	T	0.02709	4.19	4.85	4.85	0.62838	GPCR, rhodopsin-like superfamily (1);	0.173223	0.27460	N	0.019276	T	0.00012	0.0000	N	0.00157	-1.96	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42447	-0.9451	9	0.02654	T	1	-1.7637	14.1463	0.65353	0.0:0.8486:0.1514:0.0	rs11602499;rs17328866;rs61047571;rs11602499	60	Q8NGJ8	O51S1_HUMAN	E	60	ENSP00000322754:Q60E	ENSP00000322754:Q60E	Q	-	1	0	OR51S1	4826837	0.000000	0.05858	0.205000	0.23548	0.102000	0.19082	0.343000	0.19944	1.277000	0.44412	-0.215000	0.12644	CAG	G|0.673;C|0.327	0.327	strong		0.567	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
RTKN	6242	hgsc.bcm.edu	37	2	74657782	74657782	+	Missense_Mutation	SNP	C	C	T	rs145310583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:74657782C>T	ENST00000233330.6	-	3	501	c.184G>A	c.(184-186)Gct>Act	p.A62T	RTKN_ENST00000272430.5_Missense_Mutation_p.A112T|RTKN_ENST00000484453.1_5'Flank|RTKN_ENST00000305557.5_Missense_Mutation_p.A99T	NM_001015056.1	NP_001015056.1			rhotekin											endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						GAGCGCTCAGCGGGCGGGCCA	0.632													C|||	14	0.00279553	0.0	0.0	5008	,	,		16318	0.0		0.0139	False		,,,				2504	0.0				p.A112T		Atlas-SNP	.											.	RTKN	80	.	0			c.G334A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	6,4400	8.1+/-20.4	1,4,2198	33.0	40.0	38.0		334,184,295	-0.4	0.3	2	dbSNP_134	38	42,8556	26.8+/-75.7	0,42,4257	yes	missense,missense,missense	RTKN	NM_001015055.1,NM_001015056.1,NM_033046.2	58,58,58	1,46,6455	TT,TC,CC		0.4885,0.1362,0.3691	benign,benign,benign	112/564,62/514,99/551	74657782	48,12956	2203	4299	6502	SO:0001583	missense	6242	exon3			GCTCAGCGGGCGG	AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"""Pleckstrin homology (PH) domain containing"""	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000233330.6:c.184G>A	2.37:g.74657782C>T	ENSP00000233330:p.Ala62Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	97	62	0.639175	NM_001015055		Missense_Mutation	SNP	ENST00000233330.6	37	CCDS42699.1	10	0.004578754578754579	0	0.0	0	0.0	0	0.0	10	0.013192612137203167	C	9.293	1.051164	0.19827	0.001362	0.004885	ENSG00000114993	ENST00000305557;ENST00000272430;ENST00000233330	T;T;T	0.31510	1.49;1.49;1.49	4.81	-0.392	0.12442	.	0.520712	0.20647	N	0.088294	T	0.11196	0.0273	L	0.29908	0.895	0.21105	N	0.999781	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.21484	-1.0244	10	0.16420	T	0.52	.	5.1099	0.14804	0.0:0.4777:0.2819:0.2405	.	112;99	Q9BST9;Q9BST9-2	RTKN_HUMAN;.	T	99;112;62	ENSP00000305298:A99T;ENSP00000272430:A112T;ENSP00000233330:A62T	ENSP00000233330:A62T	A	-	1	0	RTKN	74511290	0.001000	0.12720	0.253000	0.24343	0.590000	0.36582	-0.409000	0.07160	-0.026000	0.13895	0.655000	0.94253	GCT	C|0.997;T|0.003	0.003	strong		0.632	RTKN-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328236.3	NM_001015055	
SOHLH2	54937	hgsc.bcm.edu	37	13	36744910	36744910	+	Missense_Mutation	SNP	C	C	T	rs2296968	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:36744910C>T	ENST00000379881.3	-	10	1103	c.1015G>A	c.(1015-1017)Gcc>Acc	p.A339T	SOHLH2_ENST00000554962.1_Missense_Mutation_p.A416T|CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.A416T	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	339			A -> T (in dbSNP:rs2296968).		multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		TTCTCTGAGGCGGAGCTTGAT	0.393													T|||	1317	0.262979	0.1324	0.3559	5008	,	,		19622	0.4911		0.1769	False		,,,				2504	0.227				p.A416T		Atlas-SNP	.											.	.	.	.	0			c.G1246A						PASS	.	T	THR/ALA,THR/ALA	663,3743	764.4+/-413.3	50,563,1590	100.0	98.0	99.0		1246,1015	-3.6	0.0	13	dbSNP_100	99	1693,6907	738.3+/-407.0	188,1317,2795	yes	missense,missense	SOHLH2,CCDC169-SOHLH2	NM_001198910.1,NM_017826.2	58,58	238,1880,4385	TT,TC,CC		19.686,15.0477,18.1147	benign,benign	416/503,339/426	36744910	2356,10650	2203	4300	6503	SO:0001583	missense	100526761	exon15			CTGAGGCGGAGCT	AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"""Basic helix-loop-helix proteins"""	26026	protein-coding gene	gene with protein product	"""spermatogenesis associated 28"""					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.1015G>A	13.37:g.36744910C>T	ENSP00000369210:p.Ala339Thr	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	95	87	0.915789	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Missense_Mutation	SNP	ENST00000379881.3	37	CCDS9355.1	609	0.27884615384615385	67	0.13617886178861788	112	0.30939226519337015	283	0.49475524475524474	147	0.19393139841688653	T	0.007	-1.961100	0.00465	0.150477	0.19686	ENSG00000120669;ENSG00000120669;ENSG00000250709	ENST00000379881;ENST00000554962;ENST00000511166	T;T;T	0.28255	1.62;1.62;1.62	5.14	-3.58	0.04597	.	0.813735	0.10856	N	0.626583	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39418	-0.9615	9	0.02654	T	1	0.1824	8.8556	0.35225	0.0:0.5597:0.1434:0.2969	rs2296968;rs52824331;rs58809693;rs2296968	416;339	B4DX90;Q9NX45	.;SOLH2_HUMAN	T	339;416;416	ENSP00000369210:A339T;ENSP00000451542:A416T;ENSP00000421868:A416T	ENSP00000421868:A416T	A	-	1	0	CCDC169-SOHLH2;SOHLH2	35642910	0.178000	0.23122	0.045000	0.18777	0.017000	0.09413	-0.316000	0.08071	-1.047000	0.03242	-0.972000	0.02603	GCC	C|0.773;T|0.227	0.227	strong		0.393	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826	
CEP164	22897	hgsc.bcm.edu	37	11	117252437	117252437	+	Missense_Mutation	SNP	A	A	G	rs117083334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:117252437A>G	ENST00000278935.3	+	13	1577	c.1430A>G	c.(1429-1431)cAc>cGc	p.H477R	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	477	Glu-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		CCACTTCCACACGAGGAGCGG	0.652													A|||	69	0.013778	0.0045	0.0259	5008	,	,		15364	0.0		0.0398	False		,,,				2504	0.0051				p.H480R		Atlas-SNP	.											CEP164,NS,carcinoma,+1,1	CEP164	121	1	0			c.A1439G						scavenged	.	A	ARG/HIS	29,4369		0,29,2170	12.0	14.0	13.0		1430	-7.6	0.0	11	dbSNP_132	13	289,8291		3,283,4004	yes	missense	CEP164	NM_014956.4	29	3,312,6174	GG,GA,AA		3.3683,0.6594,2.4503	benign	477/1461	117252437	318,12660	2199	4290	6489	SO:0001583	missense	22897	exon12			TTCCACACGAGGA	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.1430A>G	11.37:g.117252437A>G	ENSP00000278935:p.His477Arg	Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	40	0.018315018315018316	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	28	0.036939313984168866	A	1.866	-0.461349	0.04508	0.006594	0.033683	ENSG00000110274	ENST00000278935;ENST00000529538;ENST00000375253	T	0.56444	0.46	5.04	-7.58	0.01313	.	1.878760	0.02525	N	0.092962	T	0.06600	0.0169	N	0.16478	0.41	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.18209	-1.0344	10	0.06625	T	0.88	3.6794	3.6757	0.08291	0.1701:0.3914:0.3296:0.1089	.	451;477;480	E9PI34;Q9UPV0;Q9UPV0-2	.;CE164_HUMAN;.	R	477;451;407	ENSP00000278935:H477R	ENSP00000278935:H477R	H	+	2	0	CEP164	116757647	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.333000	0.01108	-1.341000	0.02225	-0.441000	0.05720	CAC	A|0.979;G|0.021	0.021	strong		0.652	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
AKNA	80709	hgsc.bcm.edu	37	9	117124731	117124731	+	Missense_Mutation	SNP	G	G	A	rs3748176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:117124731G>A	ENST00000307564.4	-	8	2032	c.1871C>T	c.(1870-1872)cCg>cTg	p.P624L	AKNA_ENST00000374088.3_Missense_Mutation_p.P624L|AKNA_ENST00000312033.3_Missense_Mutation_p.P624L|AKNA_ENST00000223791.3_Missense_Mutation_p.P84L|AKNA_ENST00000374075.5_Missense_Mutation_p.P543L	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	624			P -> L (in dbSNP:rs3748176). {ECO:0000269|PubMed:11853319, ECO:0000269|PubMed:14702039}.		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.P624L(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GCCGGCAAGCGGCTGGGCAGG	0.657													g|||	1924	0.384185	0.115	0.4798	5008	,	,		16480	0.3869		0.506	False		,,,				2504	0.5521				p.P624L		Atlas-SNP	.											AKNA,NS,carcinoma,0,1	AKNA	119	1	1	Substitution - Missense(1)	stomach(1)	c.C1871T						PASS	.		LEU/PRO	828,3578	320.2+/-296.5	83,662,1458	30.0	35.0	33.0		1871	-0.4	0.0	9	dbSNP_107	33	4570,4030	582.2+/-391.4	1195,2180,925	yes	missense	AKNA	NM_030767.4	98	1278,2842,2383	AA,AG,GG		46.8605,18.7926,41.5039	possibly-damaging	624/1440	117124731	5398,7608	2203	4300	6503	SO:0001583	missense	80709	exon8			GCAAGCGGCTGGG	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.1871C>T	9.37:g.117124731G>A	ENSP00000303769:p.Pro624Leu	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	833	0.3814102564102564	55	0.11178861788617886	179	0.494475138121547	218	0.3811188811188811	381	0.5026385224274407	g	10.14	1.267287	0.23136	0.187926	0.531395	ENSG00000106948	ENST00000307564;ENST00000394582;ENST00000374088;ENST00000223791;ENST00000374075;ENST00000312033	T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47	4.7	-0.371	0.12525	.	0.691128	0.12739	N	0.443148	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	P;B	0.38110	0.618;0.072	B;B	0.31946	0.138;0.009	T	0.44847	-0.9301	9	0.07990	T	0.79	-4.3767	4.4668	0.11692	0.0:0.1894:0.3545:0.4561	rs3748176;rs3748176	624;543	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	L	624;465;624;84;543;624	ENSP00000303769:P624L;ENSP00000363201:P624L;ENSP00000223791:P84L;ENSP00000363188:P543L;ENSP00000309222:P624L	ENSP00000223791:P84L	P	-	2	0	AKNA	116164552	0.048000	0.20356	0.001000	0.08648	0.003000	0.03518	0.347000	0.20014	-0.219000	0.10003	-0.422000	0.05995	CCG	G|0.599;A|0.401	0.401	strong		0.657	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
MUC16	94025	hgsc.bcm.edu	37	19	9047267	9047267	+	Missense_Mutation	SNP	C	C	T	rs10410169	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9047267C>T	ENST00000397910.4	-	5	34567	c.34364G>A	c.(34363-34365)gGt>gAt	p.G11455D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11457	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTTTGATGCACCAGGGGAGAC	0.493													C|||	949	0.189497	0.1982	0.1988	5008	,	,		24195	0.0258		0.2823	False		,,,				2504	0.2444				p.G11455D		Atlas-SNP	.											.	MUC16	4315	.	0			c.G34364A						PASS	.		ASP/GLY	754,3276		70,614,1331	173.0	169.0	170.0		34364	0.9	0.0	19	dbSNP_119	170	2524,5826		402,1720,2053	yes	missense	MUC16	NM_024690.2	94	472,2334,3384	TT,TC,CC		30.2275,18.7097,26.4782	possibly-damaging	11455/14508	9047267	3278,9102	2015	4175	6190	SO:0001583	missense	94025	exon5			GATGCACCAGGGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.34364G>A	19.37:g.9047267C>T	ENSP00000381008:p.Gly11455Asp	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	408	0.18681318681318682	103	0.20934959349593496	76	0.20994475138121546	11	0.019230769230769232	218	0.287598944591029	c	7.617	0.676019	0.14841	0.187097	0.302275	ENSG00000181143	ENST00000397910	T	0.04862	3.54	3.05	0.877	0.19145	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	.	.	.	P	0.36086	0.536	B	0.39339	0.297	T	0.49234	-0.8961	8	0.87932	D	0	.	5.0244	0.14378	0.0:0.7109:0.0:0.2891	rs10410169;rs52822154;rs58775557;rs10410169	11455	B5ME49	.	D	11455	ENSP00000381008:G11455D	ENSP00000381008:G11455D	G	-	2	0	MUC16	8908267	0.000000	0.05858	0.001000	0.08648	0.182000	0.23217	-1.197000	0.03038	0.307000	0.22880	0.306000	0.20318	GGT	C|0.788;T|0.212	0.212	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GRM6	2916	hgsc.bcm.edu	37	5	178416063	178416063	+	Silent	SNP	G	G	A	rs2645339	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:178416063G>A	ENST00000517717.1	-	7	1265	c.1227C>T	c.(1225-1227)taC>taT	p.Y409Y	GRM6_ENST00000231188.5_Silent_p.Y409Y|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	409					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		GGGCAATGGCGTACACCGCAT	0.637																																					p.Y409Y		Atlas-SNP	.											GRM6,NS,adenoma,0,1	GRM6	149	1	0			c.C1227T	GRCh37	CM061056	GRM6	M	rs2645339	PASS	.	G		1757,2649	523.5+/-371.1	361,1035,807	143.0	123.0	129.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1227	-0.9	1.0	5	dbSNP_100	129	4593,4007	596.8+/-393.7	1177,2239,884	no	coding-synonymous	GRM6	NM_000843.3		1538,3274,1691	AA,AG,GG		46.593,39.8774,48.8236		409/878	178416063	6350,6656	2203	4300	6503	SO:0001819	synonymous_variant	2916	exon6			AATGGCGTACACC	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1227C>T	5.37:g.178416063G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	222	119	0.536036	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																			G|0.502;A|0.498	0.498	strong		0.637	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
HS3ST4	9951	hgsc.bcm.edu	37	16	25704441	25704441	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:25704441A>G	ENST00000331351.5	+	1	1095	c.703A>G	c.(703-705)Agg>Ggg	p.R235G		NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	235	Substrate binding. {ECO:0000250}.				heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		CTTCTTCGACAGGAACTACGA	0.677																																					p.R235G		Atlas-SNP	.											.	HS3ST4	120	.	0			c.A703G						PASS	.						21.0	24.0	23.0					16																	25704441		1999	4138	6137	SO:0001583	missense	9951	exon1			TTCGACAGGAACT	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.703A>G	16.37:g.25704441A>G	ENSP00000330606:p.Arg235Gly	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_006040	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	37	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	.	22.4	4.279999	0.80692	.	.	ENSG00000182601	ENST00000331351	T	0.54866	0.55	4.29	4.29	0.51040	Sulfotransferase domain (1);	0.103409	0.56097	D	0.000029	T	0.72526	0.3471	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.76299	-0.3010	10	0.72032	D	0.01	.	10.165	0.42875	0.8331:0.1669:0.0:0.0	.	235	Q9Y661	HS3S4_HUMAN	G	235	ENSP00000330606:R235G	ENSP00000330606:R235G	R	+	1	2	HS3ST4	25611942	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.496000	0.45346	1.560000	0.49568	0.460000	0.39030	AGG	.	.	none		0.677	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040	
CTSH	1512	hgsc.bcm.edu	37	15	79224747	79224747	+	Silent	SNP	C	C	T	rs13345	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:79224747C>T	ENST00000220166.5	-	6	568	c.459G>A	c.(457-459)gcG>gcA	p.A153A	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	153					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						CGATGGCGATCGCAGACTCCA	0.637													C|||	1517	0.302915	0.5166	0.2219	5008	,	,		17877	0.3214		0.1909	False		,,,				2504	0.1677				p.A153A		Atlas-SNP	.											CTSH,NS,carcinoma,0,1	CTSH	23	1	0			c.G459A						PASS	.	C		1976,2416	557.6+/-379.8	458,1060,678	70.0	71.0	71.0		459	-9.4	0.0	15	dbSNP_52	71	1635,6951	303.4+/-306.4	157,1321,2815	no	coding-synonymous	CTSH	NM_004390.3		615,2381,3493	TT,TC,CC		19.0426,44.9909,27.824		153/336	79224747	3611,9367	2196	4293	6489	SO:0001819	synonymous_variant	1512	exon6			GGCGATCGCAGAC	X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.459G>A	15.37:g.79224747C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Silent	SNP	ENST00000220166.5	37	CCDS10308.1																																																																																			C|0.720;T|0.280	0.280	strong		0.637	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
TPSD1	23430	hgsc.bcm.edu	37	16	1306918	1306918	+	Silent	SNP	C	C	T	rs74470113		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306918C>T	ENST00000211076.3	+	3	523	c.375C>T	c.(373-375)acC>acT	p.T125T	TPSD1_ENST00000397534.2_Silent_p.T118T|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	125	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.T125T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TCATCCAGACCGGGGCGGACA	0.652																																					p.T125T		Atlas-SNP	.											TPSD1,pharynx,carcinoma,0,1	TPSD1	47	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C375T						scavenged	.						77.0	75.0	76.0					16																	1306918		2199	4300	6499	SO:0001819	synonymous_variant	23430	exon3			CCAGACCGGGGCG	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.375C>T	16.37:g.1306918C>T		Somatic	428	1	0.00233645		WXS	Illumina HiSeq	Phase_I	636	112	0.176101	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			C|0.644;T|0.356	0.356	strong		0.652	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
PI4KA	5297	hgsc.bcm.edu	37	22	21167787	21167787	+	Silent	SNP	G	G	A	rs165854	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:21167787G>A	ENST00000572273.1	-	8	920	c.690C>T	c.(688-690)tgC>tgT	p.C230C	PI4KA_ENST00000255882.6_Silent_p.C288C			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	230					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)	p.C230C(1)		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)			CATCGGGCAAGCAGGAGGCTG	0.522													G|||	2461	0.491414	0.6036	0.5144	5008	,	,		16352	0.5486		0.4254	False		,,,				2504	0.3323				p.C288C	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,0,1	PI4KA	313	1	1	Substitution - coding silent(1)	stomach(1)	c.C864T						PASS	.	G		2509,1897	628.1+/-395.0	717,1075,411	58.0	60.0	59.0		690	5.3	0.1	22	dbSNP_79	59	3494,5106	510.8+/-377.6	718,2058,1524	no	coding-synonymous	PI4KA	NM_058004.3		1435,3133,1935	AA,AG,GG		40.6279,43.0549,46.1556		230/2045	21167787	6003,7003	2203	4300	6503	SO:0001819	synonymous_variant	5297	exon8			GGGCAAGCAGGAG	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.690C>T	22.37:g.21167787G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				G|0.526;A|0.474	0.474	strong		0.522	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
CSN3	1448	hgsc.bcm.edu	37	4	71115152	71115152	+	Silent	SNP	T	T	C	rs3775738	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:71115152T>C	ENST00000304954.3	+	4	611	c.525T>C	c.(523-525)gtT>gtC	p.V175V		NM_005212.2	NP_005203.2	Q9UNS2	CSN3_HUMAN	casein kappa	0					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)		p.V175V(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						CAACCACAGTTGCAGTTACTC	0.448													C|||	1575	0.314497	0.1899	0.4006	5008	,	,		19405	0.3175		0.3946	False		,,,				2504	0.3364				p.V175V		Atlas-SNP	.											CSN3,NS,carcinoma,0,1	CSN3	43	1	1	Substitution - coding silent(1)	prostate(1)	c.T525C						scavenged	.	C		997,3409	729.2+/-410.0	124,749,1330	56.0	56.0	56.0		525	0.2	0.0	4	dbSNP_107	56	3385,5215	639.8+/-399.5	646,2093,1561	no	coding-synonymous	CSN3	NM_005212.2		770,2842,2891	CC,CT,TT		39.3605,22.6282,33.6921		175/183	71115152	4382,8624	2203	4300	6503	SO:0001819	synonymous_variant	1448	exon4			CACAGTTGCAGTT	U51899	CCDS3538.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000171209	ENSG00000171209			2446	protein-coding gene	gene with protein product		601695	"""casein, kappa"""	CSN10		8863730, 9050925	Standard	NM_005212		Approved		uc003hfe.4	P07498	OTTHUMG00000129399	ENST00000304954.3:c.525T>C	4.37:g.71115152T>C		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_005212	B2R683|B4DY81|O43191|Q7LDR6	Silent	SNP	ENST00000304954.3	37	CCDS3538.1																																																																																			T|0.682;C|0.318	0.318	strong		0.448	CSN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251555.1	NM_005212	
THADA	63892	hgsc.bcm.edu	37	2	43625184	43625184	+	Missense_Mutation	SNP	T	T	A	rs33979934	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:43625184T>A	ENST00000405006.4	-	29	4504	c.4153A>T	c.(4153-4155)Act>Tct	p.T1385S	THADA_ENST00000405975.2_Missense_Mutation_p.T1385S|THADA_ENST00000485353.1_5'UTR|THADA_ENST00000415080.2_Missense_Mutation_p.T1066S|THADA_ENST00000330266.7_Intron	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1385			T -> S (in dbSNP:rs33979934). {ECO:0000269|PubMed:15489334}.					p.T1385S(1)		breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				GACAACAGAGTTCGAATGGTA	0.493													T|||	1068	0.213259	0.2723	0.1412	5008	,	,		19775	0.0327		0.2704	False		,,,				2504	0.3119				p.T1385S		Atlas-SNP	.											THADA,NS,carcinoma,0,1	THADA	131	1	1	Substitution - Missense(1)	stomach(1)	c.A4153T						scavenged	.	T	SER/THR,SER/THR	981,3127		126,729,1199	158.0	161.0	160.0		4153,4153	-10.3	0.0	2	dbSNP_126	160	2088,6336		268,1552,2392	yes	missense,missense	THADA	NM_001083953.1,NM_022065.4	58,58	394,2281,3591	AA,AT,TT		24.7863,23.8802,24.4893	benign,benign	1385/1954,1385/1954	43625184	3069,9463	2054	4212	6266	SO:0001583	missense	63892	exon29			ACAGAGTTCGAAT	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.4153A>T	2.37:g.43625184T>A	ENSP00000385995:p.Thr1385Ser	Somatic	118	2	0.0169492		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	421|421	0.19276556776556777|0.19276556776556777	128|128	0.2601626016260163|0.2601626016260163	54|54	0.14917127071823205|0.14917127071823205	26|26	0.045454545454545456|0.045454545454545456	213|213	0.28100263852242746|0.28100263852242746	T|T	3.520|3.520	-0.097927|-0.097927	0.07010|0.07010	0.238802|0.238802	0.247863|0.247863	ENSG00000115970|ENSG00000115970	ENST00000407351|ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006	.|T;T;T	.|0.64803	.|-0.12;-0.12;-0.12	5.17|5.17	-10.3|-10.3	0.00346|0.00346	.|Armadillo-type fold (1);	.|0.961987	.|0.08558	.|N	.|0.927958	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01576|0.01576	-0.805|-0.805	0.45762|0.45762	P|P	0.0013440000000000119|0.0013440000000000119	.|B;B;B;B	.|0.18968	.|0.004;0.032;0.002;0.001	.|B;B;B;B	.|0.20767	.|0.007;0.031;0.002;0.001	T|T	0.16988|0.16988	-1.0384|-1.0384	4|9	.|0.18710	.|T	.|0.47	.|.	8.8731|8.8731	0.35327|0.35327	0.236:0.5274:0.0:0.2366|0.236:0.5274:0.0:0.2366	rs33979934;rs61143339|rs33979934;rs61143339	.|1064;1312;1066;1385	.|Q6YHU6-2;B6ZDQ0;C9JJB1;Q6YHU6	.|.;.;.;THADA_HUMAN	D|S	624|1385;1312;1066;1385	.|ENSP00000386088:T1385S;ENSP00000416048:T1066S;ENSP00000385995:T1385S	.|ENSP00000349464:T1312S	E|T	-|-	3|1	2|0	THADA|THADA	43478688|43478688	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.014000|0.014000	0.08584|0.08584	-0.358000|-0.358000	0.07641|0.07641	-1.592000|-1.592000	0.01619|0.01619	-0.248000|-0.248000	0.11899|0.11899	GAA|ACT	A|0.209;T|0.791	0.209	strong		0.493	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
SNX19	399979	hgsc.bcm.edu	37	11	130777886	130777886	+	Silent	SNP	G	G	A	rs2276098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130777886G>A	ENST00000265909.4	-	5	2696	c.2127C>T	c.(2125-2127)acC>acT	p.T709T	SNX19_ENST00000533318.1_Intron|SNX19_ENST00000545537.1_Intron|SNX19_ENST00000533214.1_Silent_p.T709T|SNX19_ENST00000528555.1_Silent_p.T89T|SNX19_ENST00000534726.1_5'UTR|SNX19_ENST00000530356.1_Silent_p.T89T|SNX19_ENST00000539184.1_Silent_p.T152T	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	709					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GCTTGCTTTCGGTCTCGGCCT	0.562													G|||	649	0.129593	0.0492	0.0893	5008	,	,		18593	0.1637		0.1988	False		,,,				2504	0.1605				p.T709T		Atlas-SNP	.											.	SNX19	84	.	0			c.C2127T						PASS	.	G		315,4087	168.7+/-199.5	15,285,1901	191.0	164.0	173.0		2127	-1.9	1.0	11	dbSNP_100	173	1789,6805	324.2+/-316.4	175,1439,2683	no	coding-synonymous	SNX19	NM_014758.2		190,1724,4584	AA,AG,GG		20.8168,7.1558,16.1896		709/993	130777886	2104,10892	2201	4297	6498	SO:0001819	synonymous_variant	399979	exon5			GCTTTCGGTCTCG	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.2127C>T	11.37:g.130777886G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_014758	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	37	CCDS31721.1																																																																																			G|0.842;A|0.158	0.158	strong		0.562	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
DCHS2	54798	hgsc.bcm.edu	37	4	155256177	155256177	+	Silent	SNP	A	A	G	rs6858157	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:155256177A>G	ENST00000357232.4	-	8	1058	c.1059T>C	c.(1057-1059)ggT>ggC	p.G353G	DCHS2_ENST00000507542.1_5'UTR|DCHS2_ENST00000339452.1_Silent_p.G852G	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	353	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G353G(2)|p.G852G(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CTGTGAGCCCACCACCGTCTT	0.423													A|||	1746	0.348642	0.3396	0.3242	5008	,	,		19216	0.3899		0.3101	False		,,,				2504	0.3753				p.G852G		Atlas-SNP	.											DCHS2_ENST00000339452,NS,carcinoma,0,3	DCHS2	594	3	3	Substitution - coding silent(3)	prostate(2)|stomach(1)	c.T2556C						PASS	.	A	,	1460,2946	471.8+/-356.2	258,944,1001	103.0	105.0	104.0		2556,1059	-4.3	0.9	4	dbSNP_116	104	2827,5773	446.7+/-361.3	467,1893,1940	no	coding-synonymous,coding-synonymous	DCHS2	NM_001142552.1,NM_017639.3	,	725,2837,2941	GG,GA,AA		32.8721,33.1366,32.9617	,	852/1370,353/2917	155256177	4287,8719	2203	4300	6503	SO:0001819	synonymous_variant	54798	exon4			GAGCCCACCACCG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.1059T>C	4.37:g.155256177A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			A|0.668;G|0.332	0.332	strong		0.423	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
CSAG1	158511	hgsc.bcm.edu	37	X	151908844	151908844	+	Missense_Mutation	SNP	A	A	T	rs1894359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:151908844A>T	ENST00000370287.3	+	4	411	c.83A>T	c.(82-84)tAc>tTc	p.Y28F	CSAG1_ENST00000452779.2_Missense_Mutation_p.Y28F|CSAG1_ENST00000370291.2_Missense_Mutation_p.Y28F	NM_153478.1	NP_705611.1	Q6PB30	CSAG1_HUMAN	chondrosarcoma associated gene 1	28			Y -> F (in dbSNP:rs1894359).	Y -> C (in Ref. 1; AF195880). {ECO:0000305}.						central_nervous_system(1)|kidney(1)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)					AGTAGACTGTACAGAGACACT	0.532													.|||	377	0.0998675	0.0802	0.0533	3775	,	,		11916	0.0238		0.1531	False		,,,				2504	0.0573				p.Y28F		Atlas-SNP	.											.	CSAG1	27	.	0			c.A83T						PASS	.	T	PHE/TYR,PHE/TYR	314,3521		19,223,53,1390,518	232.0	210.0	217.0		83,83	0.8	0.0	X	dbSNP_92	217	1051,5677		80,546,345,1802,1527	no	missense,missense	CSAG1	NM_001102576.1,NM_153478.1	22,22	99,769,398,3192,2045	TT,TA,T,AA,A		15.6213,8.1877,12.9225	benign,benign	28/79,28/79	151908844	1365,9198	2203	4300	6503	SO:0001583	missense	158511	exon4			GACTGTACAGAGA	AF268419	CCDS76047.1	Xq28	2009-08-07			ENSG00000198930	ENSG00000198930			24294	protein-coding gene	gene with protein product	"""cancer/testis antigen family 24, member 1"""					12039054	Standard	XM_006724810		Approved	CSAGE, CT24.1	uc004fgf.3	Q6PB30	OTTHUMG00000022648	ENST00000370287.3:c.83A>T	X.37:g.151908844A>T	ENSP00000359310:p.Tyr28Phe	Somatic	385	1	0.0025974		WXS	Illumina HiSeq	Phase_I	851	490	0.575793	NM_153478	A6NE22	Missense_Mutation	SNP	ENST00000370287.3	37	CCDS14711.1	146	0.08800482218203737	18	0.0375	16	0.04519774011299435	5	0.008896797153024912	67	0.09544159544159544	T	2.436	-0.329767	0.05314	0.081877	0.156213	ENSG00000198930	ENST00000370287;ENST00000452779;ENST00000370291	T;T;T	0.49432	1.39;1.39;0.78	0.837	0.837	0.18896	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06481	-1.0824	6	0.51188	T	0.08	.	.	.	.	rs1894359;rs52815057;rs61405848;rs1894359	28	Q6PB30	CSAG1_HUMAN	F	28	ENSP00000359310:Y28F;ENSP00000396520:Y28F;ENSP00000359314:Y28F	ENSP00000359310:Y28F	Y	+	2	0	CSAG1	151659500	0.002000	0.14202	0.001000	0.08648	0.003000	0.03518	-0.150000	0.10189	-0.223000	0.09943	-1.340000	0.01251	TAC	.	.	alt		0.532	CSAG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058760.2	NM_153479	
TMEM190	147744	hgsc.bcm.edu	37	19	55889451	55889451	+	Silent	SNP	G	G	A	rs77912983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55889451G>A	ENST00000291934.3	+	5	432	c.414G>A	c.(412-414)acG>acA	p.T138T	CTD-2105E13.15_ENST00000595064.1_RNA	NM_139172.1	NP_631911.1	Q8WZ59	TM190_HUMAN	transmembrane protein 190	138					hematopoietic progenitor cell differentiation (GO:0002244)	inner acrosomal membrane (GO:0002079)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	5	Breast(117;0.191)		BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CCAAGAAGACGCCGTCCACGG	0.657													G|||	243	0.0485224	0.0643	0.0908	5008	,	,		12250	0.0		0.0716	False		,,,				2504	0.0235				p.T138T		Atlas-SNP	.											.	TMEM190	17	.	0			c.G414A						PASS	.	G		284,4120	149.9+/-184.0	8,268,1926	36.0	34.0	35.0		414	-3.8	0.0	19	dbSNP_132	35	592,8008	150.9+/-205.7	28,536,3736	no	coding-synonymous	TMEM190	NM_139172.1		36,804,5662	AA,AG,GG		6.8837,6.4487,6.7364		138/178	55889451	876,12128	2202	4300	6502	SO:0001819	synonymous_variant	147744	exon5			GAAGACGCCGTCC	AF442729	CCDS33113.1	19q13.42	2011-09-28				ENSG00000160472			29632	protein-coding gene	gene with protein product						21273369	Standard	NM_139172		Approved	MDAC1	uc002qkt.1	Q8WZ59		ENST00000291934.3:c.414G>A	19.37:g.55889451G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_139172	A6NJL5	Silent	SNP	ENST00000291934.3	37	CCDS33113.1																																																																																			G|0.937;A|0.063	0.063	strong		0.657	TMEM190-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453042.1	NM_139172	
TMEM132B	114795	hgsc.bcm.edu	37	12	126137060	126137060	+	Missense_Mutation	SNP	C	C	T	rs61021440	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:126137060C>T	ENST00000299308.3	+	8	1981	c.1973C>T	c.(1972-1974)gCg>gTg	p.A658V	TMEM132B_ENST00000535886.1_Missense_Mutation_p.A170V	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	658			A -> V (in dbSNP:rs16919359). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		GTCACCATCGCGGAGCTGGGA	0.587													C|||	1715	0.342452	0.5008	0.451	5008	,	,		21676	0.2768		0.2505	False		,,,				2504	0.2137				p.A658V		Atlas-SNP	.											TMEM132B,NS,carcinoma,-1,1	TMEM132B	207	1	0			c.C1973T						PASS	.						47.0	51.0	50.0					12																	126137060		2106	4242	6348	SO:0001583	missense	114795	exon8			CCATCGCGGAGCT	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.1973C>T	12.37:g.126137060C>T	ENSP00000299308:p.Ala658Val	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	236	108	0.457627	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	613	0.2806776556776557	182	0.3699186991869919	135	0.3729281767955801	121	0.21153846153846154	175	0.23087071240105542	C	12.01	1.810105	0.32053	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.46063	0.88;0.88	5.53	4.64	0.57946	.	0.589970	0.16854	N	0.196801	T	0.00012	0.0000	N	0.12746	0.255	0.39908	P	0.02601500000000001	B	0.09022	0.002	B	0.06405	0.002	T	0.38134	-0.9675	9	0.40728	T	0.16	.	10.7695	0.46314	0.0:0.8542:0.0:0.1458	rs61021440;rs61748700	658	Q14DG7	T132B_HUMAN	V	658;170	ENSP00000299308:A658V;ENSP00000440436:A170V	ENSP00000299308:A658V	A	+	2	0	TMEM132B	124703013	0.003000	0.15002	0.256000	0.24389	0.132000	0.20833	1.919000	0.40015	1.317000	0.45149	0.655000	0.94253	GCG	C|0.759;T|0.241	0.241	strong		0.587	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
ROBO4	54538	hgsc.bcm.edu	37	11	124766128	124766128	+	Silent	SNP	A	A	G	rs4078313	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124766128A>G	ENST00000306534.3	-	4	1130	c.645T>C	c.(643-645)caT>caC	p.H215H	ROBO4_ENST00000533054.1_Silent_p.H70H|ROBO4_ENST00000526899.1_5'UTR	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	215	Ig-like C2-type 2.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GGCTCTCCCTATGTCCTGCGC	0.627													G|||	2483	0.495807	0.8162	0.2853	5008	,	,		16460	0.4534		0.334	False		,,,				2504	0.4223				p.H215H		Atlas-SNP	.											.	ROBO4	130	.	0			c.T645C						PASS	.	G		3161,1241	427.4+/-341.5	1151,859,191	85.0	84.0	84.0		645	0.2	0.0	11	dbSNP_108	84	2684,5914	684.3+/-404.0	433,1818,2048	no	coding-synonymous	ROBO4	NM_019055.5		1584,2677,2239	GG,GA,AA		31.2166,28.1917,44.9615		215/1008	124766128	5845,7155	2201	4299	6500	SO:0001819	synonymous_variant	54538	exon4			CTCCCTATGTCCT	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.645T>C	11.37:g.124766128A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	155	154	0.993548	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			A|0.539;G|0.461	0.461	strong		0.627	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
ZFHX3	463	hgsc.bcm.edu	37	16	72992547	72992547	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992547C>A	ENST00000268489.5	-	2	2170	c.1498G>T	c.(1498-1500)Gat>Tat	p.D500Y	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	500					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				AGTTCCTCATCCAACTCGCTT	0.552																																					p.D500Y		Atlas-SNP	.											ZFHX3,NS,carcinoma,+1,1	ZFHX3	404	1	0			c.G1498T						PASS	.						82.0	87.0	85.0					16																	72992547		2198	4300	6498	SO:0001583	missense	463	exon2			CCTCATCCAACTC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1498G>T	16.37:g.72992547C>A	ENSP00000268489:p.Asp500Tyr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	5.812	0.334030	0.11013	.	.	ENSG00000140836	ENST00000268489	T	0.78246	-1.16	5.01	5.01	0.66863	.	0.250248	0.27513	N	0.019037	T	0.60728	0.2291	N	0.08118	0	0.80722	D	1	P	0.34462	0.454	B	0.24974	0.057	T	0.67432	-0.5672	10	0.72032	D	0.01	.	18.6828	0.91553	0.0:1.0:0.0:0.0	.	500	Q15911	ZFHX3_HUMAN	Y	500	ENSP00000268489:D500Y	ENSP00000268489:D500Y	D	-	1	0	ZFHX3	71550048	1.000000	0.71417	0.991000	0.47740	0.641000	0.38312	1.580000	0.36547	2.487000	0.83934	0.650000	0.86243	GAT	.	.	none		0.552	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
OR4N2	390429	hgsc.bcm.edu	37	14	20295779	20295779	+	Missense_Mutation	SNP	C	C	G	rs11621884	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20295779C>G	ENST00000315947.1	+	1	172	c.172C>G	c.(172-174)Ccc>Gcc	p.P58A	OR4N2_ENST00000568211.1_Missense_Mutation_p.P58A	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	58						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GCTCACAGCCCCCCTCTATTT	0.473													.|||	1039	0.207468	0.2663	0.1657	5008	,	,		25877	0.1161		0.2107	False		,,,				2504	0.2485				p.P58A		Atlas-SNP	.											OR4N2,NS,carcinoma,-2,1	OR4N2	125	1	0			c.C172G						PASS	.	C	ALA/PRO	76,4330		24,28,2151	178.0	213.0	201.0		172	4.3	0.2	14	dbSNP_120	201	114,8482		37,40,4221	no	missense	OR4N2	NM_001004723.1	27	61,68,6372	GG,GC,CC		1.3262,1.7249,1.4613	probably-damaging	58/308	20295779	190,12812	2203	4298	6501	SO:0001583	missense	390429	exon1			ACAGCCCCCCTCT		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.172C>G	14.37:g.20295779C>G	ENSP00000319601:p.Pro58Ala	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	205	200	0.97561	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	266	0.12179487179487179	80	0.16260162601626016	41	0.1132596685082873	49	0.08566433566433566	96	0.1266490765171504	.	16.18	3.050174	0.55218	0.017249	0.013262	ENSG00000176294	ENST00000557677;ENST00000315947	T;T	0.02015	4.5;4.5	4.3	4.3	0.51218	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000189	T	0.00073	0.0002	M	0.93550	3.43	0.24376	P	0.99481913	D	0.89917	1.0	D	0.97110	1.0	T	0.01549	-1.1327	9	0.72032	D	0.01	-18.589	14.6285	0.68640	0.0:1.0:0.0:0.0	rs11621884	58	Q8NGD1	OR4N2_HUMAN	A	58	ENSP00000452022:P58A;ENSP00000319601:P58A	ENSP00000319601:P58A	P	+	1	0	OR4N2	19365619	0.998000	0.40836	0.248000	0.24265	0.439000	0.31926	4.629000	0.61290	2.374000	0.81015	0.591000	0.81541	CCC	C|0.886;G|0.114	0.114	strong		0.473	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
TTN	7273	hgsc.bcm.edu	37	2	179605180	179605180	+	Silent	SNP	C	C	T	rs746578	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179605180C>T	ENST00000591111.1	-	46	12053	c.11829G>A	c.(11827-11829)gcG>gcA	p.A3943A	TTN_ENST00000460472.2_Silent_p.A3897A|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Silent_p.A4260A|TTN_ENST00000359218.5_Silent_p.A4022A|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Silent_p.A4089A|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAAGATGAGCGCACTTTGTG	0.483													C|||	1196	0.238818	0.1846	0.1585	5008	,	,		20859	0.4702		0.1382	False		,,,				2504	0.2342				p.A4260A		Atlas-SNP	.											TTN_ENST00000359218,colon,carcinoma,-1,1	TTN	18412	1	0			c.G12780A						PASS	.	C	,,,	585,3313		44,497,1408	106.0	99.0	101.0		11691,,12066,12267	-1.9	0.0	2	dbSNP_86	101	1064,7228		80,904,3162	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	124,1401,4570	TT,TC,CC		12.8316,15.0077,13.5275	,,,	3897/26927,,4022/27052,4089/27119	179605180	1649,10541	1949	4146	6095	SO:0001819	synonymous_variant	7273	exon48			GATGAGCGCACTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.11829G>A	2.37:g.179605180C>T		Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	235	134	0.570213	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.233;C|0.757;A|0.010	0.233	strong		0.483	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
HLA-B	3106	hgsc.bcm.edu	37	6	31324145	31324145	+	Missense_Mutation	SNP	A	A	C	rs9266150	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324145A>C	ENST00000412585.2	-	3	446	c.418T>G	c.(418-420)Tac>Gac	p.Y140D		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	140	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TCGTAGGCGTACTGGTCATGC	0.706									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.Y140D		Atlas-SNP	.											HLA-B,colon,carcinoma,+1,1	HLA-B	54	1	0			c.T418G						PASS	.	A	ASP/TYR	318,3856		18,282,1787	26.0	21.0	22.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	418	-6.4	0.0	6	dbSNP_118	22	1185,7191		77,1031,3080	no	missense	HLA-B	NM_005514.6	160	95,1313,4867	CC,CA,AA		14.1476,7.6186,11.9761		140/363	31324145	1503,11047	2087	4188	6275	SO:0001583	missense	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	AGGCGTACTGGTC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.418T>G	6.37:g.31324145A>C	ENSP00000399168:p.Tyr140Asp	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	3.928	-0.016793	0.07681	0.076186	0.141476	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.00012	9.31;9.31	3.18	-6.36	0.01969	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	1.609830	0.05070	U	0.481455	T	0.00012	0.0000	N	0.02368	-0.58	0.80722	P	0.0	B;B	0.23377	0.084;0.01	B;B	0.26094	0.066;0.058	T	0.02138	-1.1207	9	0.10636	T	0.68	.	2.0837	0.03640	0.2816:0.3839:0.0845:0.25	rs9266150	140;140	P30480;P01889	1B42_HUMAN;1B07_HUMAN	D	140;19;19;151	ENSP00000399168:Y140D;ENSP00000405931:Y151D	ENSP00000399168:Y140D	Y	-	1	0	HLA-B	31432124	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.243000	0.01194	-2.056000	0.00898	-2.701000	0.00136	TAC	A|0.886;C|0.114	0.114	strong		0.706	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
BRD2	6046	hgsc.bcm.edu	37	6	32948462	32948462	+	Silent	SNP	G	G	A	rs3918140	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32948462G>A	ENST00000374825.4	+	13	4074	c.2373G>A	c.(2371-2373)tcG>tcA	p.S791S	BRD2_ENST00000443797.2_Silent_p.S671S|BRD2_ENST00000395287.1_Silent_p.S826S|BRD2_ENST00000374831.4_Silent_p.S791S|BRD2_ENST00000449085.2_Silent_p.S744S|BRD2_ENST00000395289.2_Silent_p.S826S	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	791	Poly-Ser.|Ser-rich.				chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						CCTCGTCGTCGTCTTCAGACA	0.587													G|||	439	0.0876597	0.0015	0.1297	5008	,	,		16554	0.1915		0.0338	False		,,,				2504	0.1227				p.S826S		Atlas-SNP	.											.	BRD2	70	.	0			c.G2478A						PASS	.	G	,,,	27,2993		1,25,1484	103.0	88.0	94.0		2373,2478,2232,2373	-12.3	0.1	6	dbSNP_108	94	177,5239		2,173,2533	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BRD2	NM_001113182.2,NM_001199455.1,NM_001199456.1,NM_005104.3	,,,	3,198,4017	AA,AG,GG		3.2681,0.894,2.4182	,,,	791/802,826/837,744/755,791/802	32948462	204,8232	1510	2708	4218	SO:0001819	synonymous_variant	6046	exon13			GTCGTCGTCTTCA	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.2373G>A	6.37:g.32948462G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_001199455	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	159	0.07280219780219781	2	0.0040650406504065045	33	0.09116022099447514	103	0.18006993006993008	21	0.027704485488126648	G	5.310	0.242488	0.10077	0.00894	0.032681	ENSG00000204256	ENST00000449025	.	.	.	6.15	-12.3	0.00002	.	.	.	.	.	T	0.09113	0.0225	.	.	.	0.09310	P	0.999999898225	.	.	.	.	.	.	T	0.13202	-1.0518	3	.	.	.	-14.1245	9.7307	0.40359	0.0:0.2116:0.3529:0.4355	rs3918140;rs3918140	.	.	.	H	797	.	.	R	+	2	0	BRD2	33056440	0.000000	0.05858	0.114000	0.21550	0.615000	0.37417	-5.485000	0.00118	-2.846000	0.00333	-2.081000	0.00379	CGT	G|0.953;A|0.047	0.047	strong		0.587	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
ITGAM	3684	hgsc.bcm.edu	37	16	31289396	31289396	+	Missense_Mutation	SNP	T	T	C	rs1143680	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31289396T>C	ENST00000287497.8	+	12	1397	c.1322T>C	c.(1321-1323)aTg>aCg	p.M441T	ITGAM_ENST00000544665.3_Missense_Mutation_p.M441T			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	441			M -> T (in dbSNP:rs11861251). {ECO:0000269|PubMed:15489334}.		activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						AACACTGGCATGTGGGAGTCC	0.572													T|||	466	0.0930511	0.1876	0.0692	5008	,	,		17377	0.003		0.1302	False		,,,				2504	0.0368				p.M441T		Atlas-SNP	.											.	ITGAM	137	.	0			c.T1322C						PASS	.	T	THR/MET,THR/MET	728,3420		65,598,1411	53.0	54.0	54.0		1322,1322	-0.1	0.0	16	dbSNP_120	54	1270,7150		97,1076,3037	yes	missense,missense	ITGAM	NM_000632.3,NM_001145808.1	81,81	162,1674,4448	CC,CT,TT		15.0831,17.5506,15.8975	benign,benign	441/1153,441/1154	31289396	1998,10570	2074	4210	6284	SO:0001583	missense	3684	exon12			CTGGCATGTGGGA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.1322T>C	16.37:g.31289396T>C	ENSP00000287497:p.Met441Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	194	98	0.505155	NM_000632	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	228	0.1043956043956044	104	0.21138211382113822	26	0.0718232044198895	1	0.0017482517482517483	97	0.1279683377308707	T	0.426	-0.905663	0.02453	0.175506	0.150831	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.10860	2.83;2.83	4.44	-0.0783	0.13715	.	.	.	.	.	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45731	-0.9241	8	0.12103	T	0.63	.	3.7061	0.08401	0.0:0.4606:0.1859:0.3535	rs11861251;rs52822161;rs58631826;rs11861251	441;441	Q4VAK1;P11215	.;ITAM_HUMAN	T	441	ENSP00000441691:M441T;ENSP00000287497:M441T	ENSP00000287497:M441T	M	+	2	0	ITGAM	31196897	0.000000	0.05858	0.017000	0.16124	0.066000	0.16364	-1.014000	0.03641	-0.078000	0.12730	-0.366000	0.07423	ATG	T|0.871;C|0.129	0.129	strong		0.572	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632	
SLC2A6	11182	hgsc.bcm.edu	37	9	136337168	136337168	+	Missense_Mutation	SNP	G	G	A	rs3094378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:136337168G>A	ENST00000371899.4	-	10	1576	c.1499C>T	c.(1498-1500)aCg>aTg	p.T500M	SLC2A6_ENST00000485978.1_5'UTR|SLC2A6_ENST00000371897.4_Missense_Mutation_p.T438M	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	500			T -> M (in dbSNP:rs3094378). {ECO:0000269|PubMed:10970791, ECO:0000269|Ref.2}.		glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		CCTTCTCCCCGTGCGGAAGAA	0.632													G|||	167	0.0333466	0.0121	0.0562	5008	,	,		19068	0.002		0.0924	False		,,,				2504	0.0174				p.T500M		Atlas-SNP	.											.	SLC2A6	31	.	0			c.C1499T						PASS	.	G	MET/THR,MET/THR	69,4337	63.5+/-100.7	2,65,2136	101.0	87.0	92.0		1313,1499	1.8	0.0	9	dbSNP_103	92	779,7821	183.0+/-231.3	38,703,3559	yes	missense,missense	SLC2A6	NM_001145099.1,NM_017585.3	81,81	40,768,5695	AA,AG,GG		9.0581,1.566,6.5201	probably-damaging,probably-damaging	438/446,500/508	136337168	848,12158	2203	4300	6503	SO:0001583	missense	11182	exon10			CTCCCCGTGCGGA	AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"""Solute carriers"""	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.1499C>T	9.37:g.136337168G>A	ENSP00000360966:p.Thr500Met	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	37	CCDS6975.1	104	0.047619047619047616	9	0.018292682926829267	24	0.06629834254143646	0	0.0	71	0.09366754617414248	G	10.78	1.447376	0.25987	0.01566	0.090581	ENSG00000160326	ENST00000371897;ENST00000371899	D;D	0.82344	-1.53;-1.6	4.78	1.84	0.25277	.	0.208551	0.49305	D	0.000157	T	0.19967	0.0480	N	0.17764	0.52	0.28480	N	0.914992	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.914	T	0.63409	-0.6644	10	0.62326	D	0.03	.	13.8686	0.63603	0.0:0.4442:0.5558:0.0	rs3094378;rs52832403;rs57165600;rs3094378	438;500	Q9UGQ3-2;Q9UGQ3	.;GTR6_HUMAN	M	438;500	ENSP00000360964:T438M;ENSP00000360966:T500M	ENSP00000360964:T438M	T	-	2	0	SLC2A6	135326989	1.000000	0.71417	0.011000	0.14972	0.011000	0.07611	3.728000	0.54991	0.224000	0.20940	-0.182000	0.12963	ACG	G|0.943;A|0.057	0.057	strong		0.632	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585	
SPAG5	10615	hgsc.bcm.edu	37	17	26911204	26911204	+	Silent	SNP	C	C	T	rs117510770	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:26911204C>T	ENST00000321765.5	-	13	2708	c.2376G>A	c.(2374-2376)ctG>ctA	p.L792L		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	792	Interaction with KNSTRN.				chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					CCTCTTTGGCCAGGACAGCTT	0.507													C|||	20	0.00399361	0.0008	0.0043	5008	,	,		23516	0.0		0.0159	False		,,,				2504	0.0				p.L792L		Atlas-SNP	.											.	SPAG5	92	.	0			c.G2376A						PASS	.	C		14,4392	22.3+/-47.3	0,14,2189	207.0	176.0	186.0		2376	3.8	1.0	17	dbSNP_132	186	132,8468	67.0+/-129.4	2,128,4170	no	coding-synonymous	SPAG5	NM_006461.3		2,142,6359	TT,TC,CC		1.5349,0.3177,1.1226		792/1194	26911204	146,12860	2203	4300	6503	SO:0001819	synonymous_variant	10615	exon13			TTTGGCCAGGACA	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"""mitotic spindle coiled-coil related protein"", ""astrin"", ""mitotic spindle associated protein p126"""	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.2376G>A	17.37:g.26911204C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Silent	SNP	ENST00000321765.5	37	CCDS32594.1																																																																																			C|0.991;T|0.009	0.009	strong		0.507	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461	
CC2D2A	57545	hgsc.bcm.edu	37	4	15569018	15569018	+	Silent	SNP	G	G	A	rs73125627	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:15569018G>A	ENST00000503292.1	+	26	3381	c.3201G>A	c.(3199-3201)tcG>tcA	p.S1067S	CC2D2A_ENST00000389652.5_Silent_p.S1018S|CC2D2A_ENST00000424120.1_Silent_p.S1067S|CC2D2A_ENST00000413206.1_Silent_p.S1067S	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	1067	C2.				cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)		p.S1018S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						AGCAGCCGTCGAGGTCTTCAA	0.433													G|||	760	0.151757	0.1051	0.1873	5008	,	,		19807	0.0724		0.2475	False		,,,				2504	0.1728				p.S1067S		Atlas-SNP	.											CC2D2A,NS,carcinoma,0,1	CC2D2A	158	1	1	Substitution - coding silent(1)	prostate(1)	c.G3201A						PASS	.	G		483,3519		27,429,1545	63.0	61.0	62.0		3201	-10.8	0.0	4	dbSNP_130	62	2063,6275		267,1529,2373	no	coding-synonymous	CC2D2A	NM_001080522.2		294,1958,3918	AA,AG,GG		24.7421,12.069,20.6321		1067/1621	15569018	2546,9794	2001	4169	6170	SO:0001819	synonymous_variant	57545	exon26			GCCGTCGAGGTCT	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"""Meckel syndrome, type 6"""	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.3201G>A	4.37:g.15569018G>A		Somatic	380	1	0.00263158		WXS	Illumina HiSeq	Phase_I	411	408	0.992701	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	37	CCDS47026.1																																																																																			G|0.819;A|0.181	0.181	strong		0.433	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522	
KCNA7	3743	hgsc.bcm.edu	37	19	49573518	49573518	+	Silent	SNP	G	G	A	rs3810188	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49573518G>A	ENST00000221444.1	-	2	1528	c.1173C>T	c.(1171-1173)ccC>ccT	p.P391P		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	391					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	AGACAATGACGGGCACTGGCA	0.567													G|||	723	0.144369	0.2988	0.1354	5008	,	,		19724	0.0476		0.0875	False		,,,				2504	0.1002				p.P391P	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											.	KCNA7	30	.	0			c.C1173T						PASS	.	G		1129,3277	403.7+/-332.8	128,873,1202	74.0	66.0	69.0		1173	-9.3	0.1	19	dbSNP_107	69	806,7794	188.0+/-235.1	42,722,3536	no	coding-synonymous	KCNA7	NM_031886.2		170,1595,4738	AA,AG,GG		9.3721,25.6241,14.8777		391/457	49573518	1935,11071	2203	4300	6503	SO:0001819	synonymous_variant	3743	exon2			AATGACGGGCACT	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.1173C>T	19.37:g.49573518G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_031886	A1KYX7|Q9BYS4	Silent	SNP	ENST00000221444.1	37	CCDS12755.1																																																																																			G|0.856;A|0.144	0.144	strong		0.567	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886	
ZNF468	90333	hgsc.bcm.edu	37	19	53344118	53344118	+	Missense_Mutation	SNP	C	C	G	rs10419826	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53344118C>G	ENST00000595646.1	-	4	1549	c.1429G>C	c.(1429-1431)Ggt>Cgt	p.G477R	ZNF468_ENST00000243639.4_3'UTR|ZNF468_ENST00000390651.4_Missense_Mutation_p.G424R|ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000396409.4_Missense_Mutation_p.G424R			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	477			G -> R (in dbSNP:rs10419826).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G477R(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		GATGTCTGACCGAAGGTCTTG	0.453													-|||	2904	0.579872	0.8041	0.6326	5008	,	,		21287	0.3254		0.4135	False		,,,				2504	0.6728				p.G477R		Atlas-SNP	.											ZNF468,NS,carcinoma,0,1	ZNF468	46	1	1	Substitution - Missense(1)	stomach(1)	c.G1429C						scavenged	.	G	ARG/GLY,ARG/GLY	3208,1198		1214,780,209	109.0	138.0	128.0		1429,1270	0.9	0.0	19	dbSNP_119	128	3625,4963		836,1953,1505	no	missense,missense	ZNF468	NM_001008801.1,NM_199132.1	125,125	2050,2733,1714	GG,GC,CC		42.2101,27.1902,47.4142	benign,benign	477/523,424/470	53344118	6833,6161	2203	4294	6497	SO:0001583	missense	90333	exon4			TCTGACCGAAGGT	AK023558	CCDS33094.1, CCDS62781.1	19q13.41	2013-01-08				ENSG00000204604		"""Zinc fingers, C2H2-type"", ""-"""	33105	protein-coding gene	gene with protein product						16144304	Standard	NM_001277120		Approved		uc002qaf.3	Q5VIY5		ENST00000595646.1:c.1429G>C	19.37:g.53344118C>G	ENSP00000470381:p.Gly477Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Missense_Mutation	SNP	ENST00000595646.1	37	CCDS33094.1	983	0.4500915750915751	320	0.6504065040650406	191	0.5276243093922652	194	0.33916083916083917	278	0.36675461741424803	-	1.040	-0.679015	0.03378	0.728098	0.422101	ENSG00000204604	ENST00000243639;ENST00000396409;ENST00000390651	T;T	0.07327	3.2;3.2	1.99	0.854	0.19007	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04320	-0.23	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06197	-1.0840	8	0.23891	T	0.37	.	4.2223	0.10563	0.0:0.1304:0.2093:0.6602	rs10419826;rs57381965	477	Q5VIY5	ZN468_HUMAN	R	477;424;424	ENSP00000379690:G424R;ENSP00000445669:G424R	ENSP00000243639:G477R	G	-	1	0	ZNF468	58035930	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.884000	0.01622	-0.405000	0.07599	-2.606000	0.00160	GGT	C|0.485;G|0.515	0.515	strong		0.453	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801	
IL12RB2	3595	hgsc.bcm.edu	37	1	67852335	67852335	+	Silent	SNP	G	G	A	rs2228420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:67852335G>A	ENST00000262345.1	+	14	2569	c.1929G>A	c.(1927-1929)acG>acA	p.T643T	IL12RB2_ENST00000544434.1_Silent_p.T557T|IL12RB2_ENST00000371000.1_Silent_p.T643T|IL12RB2_ENST00000541374.1_Silent_p.T643T|IL12RB2_ENST00000465396.1_3'UTR	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	643					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						TTTTCTCAACGCATTACTTCC	0.428													G|||	2071	0.413538	0.1989	0.4697	5008	,	,		16651	0.3442		0.5845	False		,,,				2504	0.5593				p.T643T		Atlas-SNP	.											.	IL12RB2	94	.	0			c.G1929A						PASS	.	G		1023,3383	377.8+/-322.6	127,769,1307	210.0	178.0	189.0		1929	-3.9	0.0	1	dbSNP_111	189	4908,3692	621.0+/-397.1	1405,2098,797	no	coding-synonymous	IL12RB2	NM_001559.2		1532,2867,2104	AA,AG,GG		42.9302,23.2183,45.602		643/863	67852335	5931,7075	2203	4300	6503	SO:0001819	synonymous_variant	3595	exon14			CTCAACGCATTAC	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.1929G>A	1.37:g.67852335G>A		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	241	112	0.46473	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Silent	SNP	ENST00000262345.1	37	CCDS638.1																																																																																			G|0.567;A|0.433	0.433	strong		0.428	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	
PSMB6	5694	hgsc.bcm.edu	37	17	4699552	4699552	+	Silent	SNP	G	G	A	rs3169950	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4699552G>A	ENST00000270586.3	+	1	114	c.63G>A	c.(61-63)gcG>gcA	p.A21A		NM_001270481.1|NM_002798.2	NP_001257410.1|NP_002789.1	P28072	PSB6_HUMAN	proteasome (prosome, macropain) subunit, beta type, 6	21					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	endopeptidase activity (GO:0004175)|threonine-type endopeptidase activity (GO:0004298)			endometrium(3)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11						GGCCGGAGGCGTTCACTCCAG	0.592													C|||	1348	0.269169	0.2368	0.4078	5008	,	,		14486	0.0982		0.4125	False		,,,				2504	0.2434				p.A21A		Atlas-SNP	.											.	PSMB6	20	.	0			c.G63A						PASS	.	C		1344,3042		215,914,1064	22.0	21.0	22.0		63	-5.4	0.0	17	dbSNP_105	22	3771,4819		847,2077,1371	no	coding-synonymous	PSMB6	NM_002798.1		1062,2991,2435	AA,AG,GG		43.8999,30.643,39.4189		21/240	4699552	5115,7861	2193	4295	6488	SO:0001819	synonymous_variant	5694	exon1			GGAGGCGTTCACT	BC000835	CCDS11056.1, CCDS73944.1	17p13	2004-02-18			ENSG00000142507	ENSG00000142507		"""Proteasome (prosome, macropain) subunits"""	9543	protein-coding gene	gene with protein product		600307				8066462, 1888762	Standard	NM_002798		Approved	Y, DELTA	uc002fzb.4	P28072	OTTHUMG00000090777	ENST00000270586.3:c.63G>A	17.37:g.4699552G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_002798	Q96J55	Silent	SNP	ENST00000270586.3	37	CCDS11056.1																																																																																			A|0.322;C|0.010;G|0.668;T|0.000	0.322	strong		0.592	PSMB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207559.2	NM_002798	
CCDC88B	283234	hgsc.bcm.edu	37	11	64110683	64110683	+	Silent	SNP	G	G	C	rs479552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64110683G>C	ENST00000356786.5	+	11	1139	c.1095G>C	c.(1093-1095)gcG>gcC	p.A365A	CCDC88B_ENST00000301897.4_5'Flank|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	365						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TGCTGGAGGCGTCCAAGGCGC	0.706													C|||	1761	0.351637	0.3366	0.3991	5008	,	,		10651	0.248		0.3718	False		,,,				2504	0.4243				p.A365A		Atlas-SNP	.											CCDC88B,NS,carcinoma,0,1	CCDC88B	89	1	0			c.G1095C						PASS	.	C		1282,2854		246,790,1032	10.0	9.0	9.0		1095	1.9	1.0	11	dbSNP_83	9	2672,5414		532,1608,1903	no	coding-synonymous	CCDC88B	NM_032251.5		778,2398,2935	CC,CG,GG		33.0448,30.9961,32.3515		365/1477	64110683	3954,8268	2068	4043	6111	SO:0001819	synonymous_variant	283234	exon11			GGAGGCGTCCAAG	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.1095G>C	11.37:g.64110683G>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			G|0.651;C|0.349	0.349	strong		0.706	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
NPAP1	23742	hgsc.bcm.edu	37	15	24921468	24921468	+	Missense_Mutation	SNP	T	T	C	rs35870568	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:24921468T>C	ENST00000329468.2	+	1	928	c.454T>C	c.(454-456)Tgg>Cgg	p.W152R		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	152			W -> R (in dbSNP:rs35870568).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											GACCGAGGTGTGGGCCCAAGA	0.617													C|||	71	0.0141773	0.0023	0.0259	5008	,	,		15056	0.0		0.0318	False		,,,				2504	0.0184				p.W152R		Atlas-SNP	.											C15orf2,NS,meningioma,0,1	.	.	1	0			c.T454C						PASS	.	C	ARG/TRP	42,4364		0,42,2161	34.0	34.0	34.0		454	1.0	0.0	15	dbSNP_126	34	322,8268		9,304,3982	yes	missense	C15orf2	NM_018958.2	101	9,346,6143	CC,CT,TT		3.7485,0.9532,2.8009	benign	152/1157	24921468	364,12632	2203	4295	6498	SO:0001583	missense	23742	exon1			GAGGTGTGGGCCC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.454T>C	15.37:g.24921468T>C	ENSP00000333735:p.Trp152Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	40	0.018315018315018316	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	29	0.03825857519788918	.	0.059	-1.229991	0.01518	0.009532	0.037485	ENSG00000185823	ENST00000329468	T	0.04706	3.57	2.12	0.958	0.19619	.	2.511100	0.01927	N	0.040905	T	0.00468	0.0015	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39702	-0.9601	10	0.07030	T	0.85	.	2.8379	0.05520	0.4758:0.284:0.0:0.2403	rs35870568	152	Q9NZP6	CO002_HUMAN	R	152	ENSP00000333735:W152R	ENSP00000333735:W152R	W	+	1	0	C15orf2	22472561	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.899000	0.04101	-0.099000	0.12263	-1.535000	0.00915	TGG	T|0.977;C|0.023	0.023	strong		0.617	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
SAMD15	161394	hgsc.bcm.edu	37	14	77844265	77844265	+	Missense_Mutation	SNP	G	G	A	rs45527334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77844265G>A	ENST00000216471.4	+	1	790	c.504G>A	c.(502-504)atG>atA	p.M168I	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	168			M -> I (in dbSNP:rs45527334).							breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CGGAAACCATGTCTGAGGTTT	0.488													G|||	709	0.141573	0.059	0.2651	5008	,	,		18678	0.0159		0.2038	False		,,,				2504	0.2311				p.M168I		Atlas-SNP	.											.	SAMD15	60	.	0			c.G504A						PASS	.	G	ILE/MET	404,4002	194.0+/-219.0	16,372,1815	86.0	94.0	92.0		504	-1.5	0.0	14	dbSNP_127	92	1681,6919	298.1+/-303.7	182,1317,2801	yes	missense	SAMD15	NM_001010860.1	10	198,1689,4616	AA,AG,GG		19.5465,9.1693,16.0311	possibly-damaging	168/675	77844265	2085,10921	2203	4300	6503	SO:0001583	missense	161394	exon1			AACCATGTCTGAG	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.504G>A	14.37:g.77844265G>A	ENSP00000216471:p.Met168Ile	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_001010860	Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	37	CCDS32126.1	289	0.13232600732600733	31	0.06300813008130081	104	0.287292817679558	8	0.013986013986013986	146	0.19261213720316622	G	11.61	1.688514	0.29962	0.091693	0.195465	ENSG00000100583	ENST00000216471	T	0.18657	2.2	4.45	-1.46	0.08800	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44667	-0.9313	8	0.42905	T	0.14	5.3758	4.6975	0.12811	0.5573:0.1817:0.261:0.0	rs45527334;rs57688204;rs61729328	168	Q9P1V8	SAM15_HUMAN	I	168	ENSP00000216471:M168I	ENSP00000216471:M168I	M	+	3	0	SAMD15	76914018	0.000000	0.05858	0.000000	0.03702	0.359000	0.29487	-0.322000	0.08007	0.034000	0.15491	0.484000	0.47621	ATG	G|0.848;A|0.152	0.152	strong		0.488	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048461	33048461	+	Missense_Mutation	SNP	T	T	A	rs1126509|rs386699868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33048461T>A	ENST00000418931.2	+	2	229	c.113T>A	c.(112-114)tTc>tAc	p.F38Y	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPA1_ENST00000419277.1_5'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.F38Y	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	38	Beta-1.		F -> D (in allele DPB1*70:01; requires 2 nucleotide substitutions).|F -> H (in allele DPB1*09:01, allele DPB1*10:01, allele DPB1*14:01, allele DPB1*16:02, allele DPB1*17:01, allele DPB1*22:02, allele DPB1*30:01, allele DPB1*35:01, allele DPB1*45:01, allele DPB1*54:01, allele DPB1*55:01, allele DPB1*58:01, allele DPB1*66:01, allele DPB1*67:01, allele DPB1*76:01, allele DPB1*86:01, allele DPB1*91:01 and allele DPB1*98:01; requires 2 nucleotide substitutions).|F -> L (in dbSNP:rs12722013).|F -> Y (in allele DPB1*01:01, allele DPB1*03:01, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*09:02, allele DPB1*11:01, allele DPB1*11:02, allele DPB1*13:01, allele DPB1*13:02, allele DPB1*14:02, allele DPB1*15:01, allele DPB1*17:02, allele DPB1*18:01, allele DPB1*20:02, allele DPB1*21:01, allele DPB1*21:02, allele DPB1*20:01, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*27:01, allele DPB1*29:01, allele DPB1*36:01, allele DPB1*37:01, allele DPB1*44:01, allele DPB1*50:01, allele DPB1*52:01, allele DPB1*56:01, allele DPB1*69:01, allele DPB1*74:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*85:01, allele DPB1*87:01, allele DPB1*88:01, allele DPB1*89:01, allele DPB1*90:01, allele DPB1*92:01 and allele DPB1*93:01; dbSNP:rs1126509).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						AATTACCTTTTCCAGGGACGG	0.552													.|||	1999	0.399161	0.6641	0.3357	5008	,	,		15143	0.2351		0.2992	False		,,,				2504	0.3579				p.F38Y		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.T113A						PASS	.	A	,,TYR/PHE	1572,1444		521,530,457	46.0	52.0	50.0		,,113	-6.8	0.0	6	dbSNP_86	50	925,4479		180,565,1957	no	utr-5,utr-5,missense	HLA-DPA1,HLA-DPB1	NM_001242524.1,NM_001242525.1,NM_002121.5	,,22	701,1095,2414	AA,AT,TT		17.117,47.878,29.6556	,,benign	,,38/259	33048461	2497,5923	1508	2702	4210	SO:0001583	missense	3115	exon2			ACCTTTTCCAGGG		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.113T>A	6.37:g.33048461T>A	ENSP00000408146:p.Phe38Tyr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	60	20	0.333333	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	709|709	0.32463369963369965|0.32463369963369965	301|301	0.6117886178861789|0.6117886178861789	97|97	0.26795580110497236|0.26795580110497236	114|114	0.1993006993006993|0.1993006993006993	197|197	0.2598944591029024|0.2598944591029024	A|A	0.251|0.251	-1.006668|-1.006668	0.02112|0.02112	0.52122|0.52122	0.17117|0.17117	ENSG00000223865|ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942|ENST00000416804	T;T|.	0.02579|.	4.24;4.24|.	3.4|3.4	-6.79|-6.79	0.01715|0.01715	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);|.	0.702565|.	0.11117|.	N|.	0.597882|.	T|T	0.02649|0.02649	0.0080|0.0080	N|N	0.02345|0.02345	-0.59|-0.59	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.20706|0.20706	-1.0267|-1.0267	9|4	0.02654|.	T|.	1|.	.|.	8.1577|8.1577	0.31178|0.31178	0.241:0.0:0.0883:0.6708|0.241:0.0:0.0883:0.6708	rs1126509;rs3176936;rs3181578;rs9277345;rs17214706;rs17418788|rs1126509;rs3176936;rs3181578;rs9277345;rs17214706;rs17418788	48;38|.	Q59GY1;P04440|.	.;DPB1_HUMAN|.	Y|T	38|5	ENSP00000408146:F38Y;ENSP00000439674:F38Y|.	ENSP00000389210:F38Y|.	F|S	+|+	2|1	0|0	HLA-DPB1|HLA-DPB1	33156439|33156439	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-3.263000|-3.263000	0.00535|0.00535	-3.679000|-3.679000	0.00122|0.00122	-4.666000|-4.666000	0.00003|0.00003	TTC|TCC	T|0.694;A|0.306	0.306	strong		0.552	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
FAM188B	84182	hgsc.bcm.edu	37	7	30831082	30831082	+	Missense_Mutation	SNP	C	C	T	rs12701034	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:30831082C>T	ENST00000265299.6	+	5	1042	c.965C>T	c.(964-966)aCg>aTg	p.T322M	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	322			T -> M (in dbSNP:rs12701034). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.							endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGCACAGACACGGACAGGATG	0.642													C|||	2519	0.502995	0.8048	0.4424	5008	,	,		19011	0.1627		0.4801	False		,,,				2504	0.5123				p.T322M		Atlas-SNP	.											.	FAM188B	62	.	0			c.C965T						PASS	.	C	MET/THR	3149,973		1214,721,126	52.0	65.0	61.0		965	-2.8	0.0	7	dbSNP_121	61	4220,4176		1067,2086,1045	yes	missense	FAM188B	NM_032222.2	81	2281,2807,1171	TT,TC,CC		49.738,23.605,41.1328	benign	322/758	30831082	7369,5149	2061	4198	6259	SO:0001583	missense	84182	exon5			CAGACACGGACAG	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.965C>T	7.37:g.30831082C>T	ENSP00000265299:p.Thr322Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_032222	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	37	CCDS43565.1	994	0.4551282051282051	368	0.7479674796747967	166	0.4585635359116022	95	0.1660839160839161	365	0.4815303430079156	C	7.655	0.683653	0.14907	0.76395	0.50262	ENSG00000106125	ENST00000265299	T	0.02944	4.1	4.25	-2.83	0.05769	.	1.399050	0.04297	N	0.346702	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15141	0.012	B	0.08055	0.003	T	0.20706	-1.0267	9	0.87932	D	0	-17.7019	1.0409	0.01559	0.2474:0.3729:0.122:0.2577	rs12701034;rs12701034	322	Q4G0A6	F188B_HUMAN	M	322	ENSP00000265299:T322M	ENSP00000265299:T322M	T	+	2	0	FAM188B	30797607	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.912000	0.01582	-0.654000	0.05394	-1.151000	0.01829	ACG	C|0.515;T|0.485	0.485	strong		0.642	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
BAG6	7917	hgsc.bcm.edu	37	6	31612353	31612353	+	Missense_Mutation	SNP	G	G	C	rs143499629	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31612353G>C	ENST00000375964.6	-	11	1727	c.1414C>G	c.(1414-1416)Ccg>Gcg	p.P472A	BAG6_ENST00000211379.5_Missense_Mutation_p.P466A|BAG6_ENST00000439687.2_Missense_Mutation_p.P466A|BAG6_ENST00000470875.1_5'Flank|BAG6_ENST00000375976.4_Missense_Mutation_p.P466A|BAG6_ENST00000362049.6_Missense_Mutation_p.P466A|BAG6_ENST00000404765.2_Missense_Mutation_p.P466A	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	472	4 X 29 AA approximate repeats.|Pro-rich.				brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						GGAGCACTCGGAACACCACCA	0.602																																					p.P472A		Atlas-SNP	.											.	BAG6	73	.	0			c.C1414G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	0,3020		0,0,1510	52.0	39.0	44.0		1396,1396,1396,1414,1396,1396	4.8	1.0	6	dbSNP_134	44	3,5413		0,3,2705	yes	missense,missense,missense,missense,missense,missense	BAG6	NM_001098534.1,NM_001199697.1,NM_001199698.1,NM_004639.3,NM_080702.2,NM_080703.2	27,27,27,27,27,27	0,3,4215	CC,CG,GG		0.0554,0.0,0.0356	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	466/1127,466/904,466/1078,472/1133,466/1127,466/1127	31612353	3,8433	1510	2708	4218	SO:0001583	missense	7917	exon11			CACTCGGAACACC	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"""HLA-B associated transcript 3"""	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.1414C>G	6.37:g.31612353G>C	ENSP00000365131:p.Pro472Ala	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Missense_Mutation	SNP	ENST00000375964.6	37	CCDS47403.1	.	.	.	.	.	.	.	.	.	.	g	13.78	2.339423	0.41398	0.0	5.54E-4	ENSG00000204463	ENST00000375976;ENST00000375964;ENST00000211379;ENST00000404765;ENST00000439687;ENST00000362049;ENST00000437771;ENST00000438149;ENST00000436214;ENST00000435080	T;T;T;T;T;T;T;T	0.47528	1.58;1.57;1.58;1.47;1.01;1.56;0.87;0.84	4.8	4.8	0.61643	.	0.204155	0.42053	D	0.000772	T	0.43366	0.1244	N	0.24115	0.695	0.40063	D	0.975923	D;D;B;B;B	0.60575	0.98;0.988;0.059;0.019;0.033	D;D;B;B;B	0.73708	0.956;0.981;0.023;0.009;0.014	T	0.40289	-0.9571	10	0.42905	T	0.14	.	13.3019	0.60330	0.0:0.0:1.0:0.0	.	466;466;466;472;466	E7EMZ4;F8VXY4;B0UX85;P46379;P46379-2	.;.;.;BAG6_HUMAN;.	A	466;472;466;466;466;466;466;60;80;466	ENSP00000365143:P466A;ENSP00000365131:P472A;ENSP00000211379:P466A;ENSP00000384494:P466A;ENSP00000402856:P466A;ENSP00000354875:P466A;ENSP00000397978:P466A;ENSP00000410280:P60A	ENSP00000211379:P466A	P	-	1	0	BAG6	31720332	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.066000	0.50002	2.497000	0.84241	0.645000	0.84053	CCG	G|0.999;C|0.001	0.001	strong		0.602	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703	
DEPTOR	64798	hgsc.bcm.edu	37	8	121061879	121061879	+	Missense_Mutation	SNP	G	G	A	rs4871827	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:121061879G>A	ENST00000286234.5	+	9	1296	c.1166G>A	c.(1165-1167)aGc>aAc	p.S389N	DEPTOR_ENST00000523492.1_Missense_Mutation_p.S288N	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	389	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.		S -> N (in dbSNP:rs4871827). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						CGGACCGTGAGCAATCTGATT	0.527													G|||	1500	0.299521	0.1241	0.4784	5008	,	,		16804	0.5526		0.331	False		,,,				2504	0.1166				p.S389N		Atlas-SNP	.											.	DEPTOR	41	.	0			c.G1166A						PASS	.	G	ASN/SER	657,3749	280.8+/-275.6	51,555,1597	180.0	155.0	164.0		1166	6.0	1.0	8	dbSNP_111	164	2726,5874	435.9+/-358.1	426,1874,2000	yes	missense	DEPTOR	NM_022783.2	46	477,2429,3597	AA,AG,GG		31.6977,14.9115,26.0111	possibly-damaging	389/410	121061879	3383,9623	2203	4300	6503	SO:0001583	missense	64798	exon9			CCGTGAGCAATCT		CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792			22953	protein-coding gene	gene with protein product		612974	"""DEP domain containing 6"""	DEPDC6		19446321	Standard	NM_022783		Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.1166G>A	8.37:g.121061879G>A	ENSP00000286234:p.Ser389Asn	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	242	104	0.429752	NM_022783	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	Missense_Mutation	SNP	ENST00000286234.5	37	CCDS6331.1	816	0.37362637362637363	65	0.13211382113821138	174	0.48066298342541436	326	0.5699300699300699	251	0.3311345646437995	G	17.16	3.319471	0.60524	0.149115	0.316977	ENSG00000155792	ENST00000523492;ENST00000286234	T;T	0.30182	1.54;1.54	6.01	6.01	0.97437	PDZ/DHR/GLGF (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.52011	1.625	0.09310	P	0.999999999649191	B;B	0.24721	0.11;0.013	B;B	0.21917	0.037;0.008	T	0.48559	-0.9025	9	0.52906	T	0.07	-33.6104	20.1162	0.97934	0.0:0.0:1.0:0.0	rs4871827;rs17850843;rs52808957;rs59755806;rs4871827	288;389	E7EV87;Q8TB45	.;DPTOR_HUMAN	N	288;389	ENSP00000430457:S288N;ENSP00000286234:S389N	ENSP00000286234:S389N	S	+	2	0	DEPTOR	121131060	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	8.997000	0.93544	2.861000	0.98227	0.650000	0.86243	AGC	G|0.693;A|0.307	0.307	strong		0.527	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381601.1	NM_022783	
ANKRD24	170961	hgsc.bcm.edu	37	19	4200156	4200156	+	Missense_Mutation	SNP	G	G	A	rs2052191	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:4200156G>A	ENST00000600132.1	+	5	607	c.331G>A	c.(331-333)Gcg>Acg	p.A111T	ANKRD24_ENST00000318934.4_Missense_Mutation_p.A111T|ANKRD24_ENST00000262970.5_Missense_Mutation_p.A201T	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	111			A -> T (in dbSNP:rs2052191). {ECO:0000269|PubMed:11853319}.							endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		TGTCATGAGCGCGGACGGGGC	0.657													A|||	2035	0.40635	0.5454	0.3228	5008	,	,		16174	0.3234		0.4632	False		,,,				2504	0.3047				p.A111T		Atlas-SNP	.											.	ANKRD24	180	.	0			c.G331A						PASS	.	A	THR/ALA	2003,1899		519,965,467	20.0	22.0	21.0		331	2.0	0.2	19	dbSNP_94	21	3515,4749		775,1965,1392	no	missense	ANKRD24	NM_133475.1	58	1294,2930,1859	AA,AG,GG		42.5339,48.6674,45.3559	benign	111/1147	4200156	5518,6648	1951	4132	6083	SO:0001583	missense	170961	exon5			ATGAGCGCGGACG	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.331G>A	19.37:g.4200156G>A	ENSP00000471252:p.Ala111Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	889	0.40705128205128205	248	0.5040650406504065	114	0.3149171270718232	189	0.3304195804195804	338	0.44591029023746703	A	0.005	-2.235948	0.00277	0.513326	0.425339	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.28895	1.59;1.59	4.17	2.01	0.26516	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.00012	0.0000	N	0.17838	0.53	0.80722	P	0.0	B;B	0.13145	0.0;0.007	B;B	0.01281	0.0;0.0	T	0.47861	-0.9084	8	0.05525	T	0.97	-9.5245	6.9181	0.24371	0.7004:0.0:0.2996:0.0	rs2052191;rs57740215;rs2052191	111;201	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	T	111;201	ENSP00000321731:A111T;ENSP00000262970:A201T	ENSP00000262970:A201T	A	+	1	0	ANKRD24	4151156	0.552000	0.26505	0.241000	0.24154	0.046000	0.14306	1.923000	0.40055	-0.245000	0.09625	-0.817000	0.03123	GCG	G|0.591;A|0.409	0.409	strong		0.657	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
ERICH3	127254	hgsc.bcm.edu	37	1	75037385	75037385	+	Missense_Mutation	SNP	C	C	T	rs200080388		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:75037385C>T	ENST00000326665.5	-	14	4227	c.4009G>A	c.(4009-4011)Gtt>Att	p.V1337I	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1337	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						ACAGCCACAACCCTTCCTCCT	0.562																																					p.V1337I		Atlas-SNP	.											.	C1orf173	380	.	0			c.G4009A						PASS	.	C	ILE/VAL	0,4406		0,0,2203	254.0	238.0	243.0		4009	2.1	0.0	1		243	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C1orf173	NM_001002912.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1337/1531	75037385	1,13005	2203	4300	6503	SO:0001583	missense	127254	exon14			CCACAACCCTTCC																												ENST00000326665.5:c.4009G>A	1.37:g.75037385C>T	ENSP00000322609:p.Val1337Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	134	72	0.537313	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.771644	0.31320	0.0	1.16E-4	ENSG00000178965	ENST00000326665	T	0.13901	2.55	4.1	2.14	0.27477	.	.	.	.	.	T	0.02727	0.0082	N	0.19112	0.55	0.09310	N	0.999999	P	0.36535	0.557	B	0.35971	0.215	T	0.42068	-0.9473	9	0.38643	T	0.18	.	7.5396	0.27731	0.0:0.734:0.1688:0.0972	.	1337	Q5RHP9	CA173_HUMAN	I	1337	ENSP00000322609:V1337I	ENSP00000322609:V1337I	V	-	1	0	C1orf173	74809973	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.090000	0.15025	0.187000	0.20147	0.462000	0.41574	GTT	.	.	weak		0.562	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
KANSL1	284058	hgsc.bcm.edu	37	17	44249096	44249096	+	Silent	SNP	A	A	C	rs571568457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44249096A>C	ENST00000262419.6	-	2	884	c.414T>G	c.(412-414)ctT>ctG	p.L138L	KANSL1_ENST00000574590.1_Silent_p.L138L|KANSL1_ENST00000575318.1_Silent_p.L138L|KANSL1_ENST00000572904.1_Silent_p.L138L|KANSL1_ENST00000432791.1_Silent_p.L138L|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000393476.3_5'UTR	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	138					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TCATGGTTCTAAGATTTTCTA	0.428													A|||	364	0.0726837	0.0113	0.1398	5008	,	,		24050	0.001		0.1998	False		,,,				2504	0.0511				p.L138L		Atlas-SNP	.											.	.	.	.	0			c.T414G						PASS	.	A	,,	169,4237		0,169,2034	140.0	201.0	180.0		414,414,414	0.8	1.0	17	dbSNP_123	180	1588,7012		0,1588,2712	yes	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	0,1757,4746	CC,CA,AA		18.4651,3.8357,13.5091	,,	138/1105,138/1106,138/1106	44249096	1757,11249	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon2			GGTTCTAAGATTT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.414T>G	17.37:g.44249096A>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	103	29	0.281553	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.888;C|0.112	0.112	strong		0.428	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
CDHR4	389118	hgsc.bcm.edu	37	3	49830032	49830032	+	Silent	SNP	C	C	T	rs61745903	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49830032C>T	ENST00000412678.2	-	15	2015	c.2007G>A	c.(2005-2007)acG>acA	p.T669T	CDHR4_ENST00000462108.1_Intron	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	669	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						TGGGTGTCATCGTTGAGGGCA	0.592													C|||	108	0.0215655	0.0068	0.0259	5008	,	,		20425	0.006		0.0686	False		,,,				2504	0.0061				p.T669T		Atlas-SNP	.											.	CDHR4	37	.	0			c.G2007A						PASS	.	C		10,1374		0,10,682	119.0	123.0	121.0		2007	-0.1	0.1	3	dbSNP_129	121	178,3004		6,166,1419	no	coding-synonymous	CDHR4	NM_001007540.2		6,176,2101	TT,TC,CC		5.594,0.7225,4.1174		669/789	49830032	188,4378	692	1591	2283	SO:0001819	synonymous_variant	389118	exon15			TGTCATCGTTGAG		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"""Cadherins / Cadherin-related"""	34527	protein-coding gene	gene with protein product			"""cadherin-like 29"""	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.2007G>A	3.37:g.49830032C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_001007540	Q6UXT0	Silent	SNP	ENST00000412678.2	37	CCDS46829.1	79	0.036172161172161175	5	0.01016260162601626	16	0.04419889502762431	3	0.005244755244755245	55	0.07255936675461741	C	0.228	-1.023004	0.02061	0.007225	0.05594	ENSG00000187492	ENST00000487666	.	.	.	5.48	-0.057	0.13803	.	.	.	.	.	T	0.03011	0.0089	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.10706	-1.0618	4	.	.	.	.	9.6427	0.39848	0.0:0.5567:0.0:0.4433	.	.	.	.	N	31	.	.	D	-	1	0	CDHR4	49805036	0.105000	0.21958	0.076000	0.20297	0.376000	0.30014	0.105000	0.15333	0.102000	0.17638	-0.898000	0.02899	GAT	C|0.964;T|0.036	0.036	strong		0.592	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	
CCDC9	26093	hgsc.bcm.edu	37	19	47774572	47774572	+	Silent	SNP	C	C	T	rs60930438	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:47774572C>T	ENST00000221922.6	+	12	1455	c.1233C>T	c.(1231-1233)gaC>gaT	p.D411D		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	411	Glu-rich.						poly(A) RNA binding (GO:0044822)	p.N416_E420delNEGEE(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		CTCCTgaagacgagggggaag	0.607													C|||	2566	0.51238	0.3411	0.5836	5008	,	,		18840	0.6825		0.4304	False		,,,				2504	0.6022				p.D411D		Atlas-SNP	.											.	CCDC9	37	.	1	Deletion - In frame(1)	ovary(1)	c.C1233T						PASS	.	C		1400,3006		233,934,1036	51.0	49.0	50.0		1233	-0.9	0.9	19	dbSNP_129	50	3755,4843		833,2089,1377	no	coding-synonymous	CCDC9	NM_015603.2		1066,3023,2413	TT,TC,CC		43.6729,31.7749,39.6416		411/532	47774572	5155,7849	2203	4299	6502	SO:0001819	synonymous_variant	26093	exon12			TGAAGACGAGGGG	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1233C>T	19.37:g.47774572C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_015603		Silent	SNP	ENST00000221922.6	37	CCDS12698.1																																																																																			C|0.569;G|0.000;T|0.431	0.431	strong		0.607	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189485	11189485	+	Silent	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11189485G>T	ENST00000382435.4	+	1	1089	c.870G>T	c.(868-870)gtG>gtT	p.V290V		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	290	EamA 2.					integral component of membrane (GO:0016021)											ATTCCGAGGTGGTTGTGGCCC	0.572																																					p.V290V		Atlas-SNP	.											AMAC1L2,NS,carcinoma,+1,1	.	.	1	0			c.G870T						scavenged	.						131.0	119.0	123.0					8																	11189485		2203	4299	6502	SO:0001819	synonymous_variant	83650	exon1			CGAGGTGGTTGTG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.870G>T	8.37:g.11189485G>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	199	4	0.0201005	NM_054028	A2RRL6	Silent	SNP	ENST00000382435.4	37	CCDS5980.1																																																																																			.	.	none		0.572	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
KRT40	125115	hgsc.bcm.edu	37	17	39134455	39134455	+	Silent	SNP	G	G	A	rs2271277	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39134455G>A	ENST00000398486.2	-	9	1450	c.1290C>T	c.(1288-1290)tgC>tgT	p.C430C	AC004231.2_ENST00000418393.1_RNA|KRT40_ENST00000377755.4_Silent_p.C430C	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	430	Tail.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				ACATTCACAAGCAGCAGTTTT	0.507													A|||	2419	0.483027	0.8737	0.3617	5008	,	,		19718	0.3353		0.2952	False		,,,				2504	0.3865				p.C430C		Atlas-SNP	.											.	KRT40	27	.	0			c.C1290T						PASS	.	A		2967,1017		1123,721,148	94.0	103.0	100.0		1290	2.7	0.3	17	dbSNP_100	100	2444,5906		359,1726,2090	no	coding-synonymous	KRT40	NM_182497.3		1482,2447,2238	AA,AG,GG		29.2695,25.5271,43.8706		430/432	39134455	5411,6923	1992	4175	6167	SO:0001819	synonymous_variant	125115	exon9			TCACAAGCAGCAG	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.1290C>T	17.37:g.39134455G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_182497	Q6IFU5	Silent	SNP	ENST00000398486.2	37	CCDS42320.1																																																																																			G|0.549;A|0.451	0.451	strong		0.507	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
OVCH2	341277	hgsc.bcm.edu	37	11	7727886	7727886	+	lincRNA	SNP	C	C	T	rs7927138	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7727886C>T	ENST00000527565.1	-	0	542				RP11-35J10.4_ENST00000527443.1_RNA|OVCH2_ENST00000534193.2_RNA|OVCH2_ENST00000454689.1_RNA																							AGATTTACCTCGTTCAAAAAA	0.378													C|||	2019	0.403155	0.205	0.5144	5008	,	,		19440	0.4157		0.3728	False		,,,				2504	0.6104				p.R19Q		Atlas-SNP	.											OVCH2,NS,carcinoma,0,2	OVCH2	47	2	0			c.G56A						PASS	.	C	GLN/ARG	892,2764		108,676,1044	96.0	90.0	92.0		56	0.0	0.2	11	dbSNP_116	92	2993,5169		562,1869,1650	yes	missense	OVCH2	NM_198185.2	43	670,2545,2694	TT,TC,CC		36.6699,24.3982,32.8736	benign	19/565	7727886	3885,7933	1828	4081	5909			341277	exon1			TTACCTCGTTCAA																													11.37:g.7727886C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	48	0.585366	NM_198185		Missense_Mutation	SNP	ENST00000527565.1	37		818	0.37454212454212454	96	0.1951219512195122	175	0.48342541436464087	247	0.4318181818181818	300	0.39577836411609496	C	0.005	-2.187034	0.00305	0.243982	0.366699	ENSG00000183378	ENST00000454689	D	0.92752	-3.1	5.03	0.0262	0.14149	.	0.808373	0.10434	N	0.675164	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29458	-1.0011	9	0.09843	T	0.71	-4.9541	1.9492	0.03363	0.1568:0.0899:0.3253:0.4281	rs7927138;rs17232885;rs7927138	19	Q7RTZ1	OVCH2_HUMAN	Q	19	ENSP00000407158:R19Q	ENSP00000407158:R19Q	R	-	2	0	OVCH2	7684462	0.020000	0.18652	0.179000	0.23059	0.001000	0.01503	0.179000	0.16840	0.413000	0.25759	-1.225000	0.01585	CGA	C|0.636;T|0.364	0.364	strong		0.378	RP11-35J10.5-001	KNOWN	basic|readthrough_transcript	lincRNA	lincRNA	OTTHUMT00000385692.1		
OR5I1	10798	hgsc.bcm.edu	37	11	55703766	55703766	+	Silent	SNP	A	A	G	rs17597589	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55703766A>G	ENST00000301532.3	-	1	110	c.111T>C	c.(109-111)taT>taC	p.Y37Y		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	37					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GAATTATAGCATACAATGTCA	0.398													A|||	175	0.0349441	0.0136	0.0346	5008	,	,		16126	0.001		0.0905	False		,,,				2504	0.0419				p.Y37Y		Atlas-SNP	.											.	OR5I1	110	.	0			c.T111C						PASS	.	A		107,4291	82.4+/-120.9	3,101,2095	66.0	64.0	65.0		111	-7.1	0.0	11	dbSNP_123	65	684,7906	169.1+/-220.5	34,616,3645	no	coding-synonymous	OR5I1	NM_006637.1		37,717,5740	GG,GA,AA		7.9627,2.4329,6.0902		37/315	55703766	791,12197	2199	4295	6494	SO:0001819	synonymous_variant	10798	exon1			TATAGCATACAAT	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.111T>C	11.37:g.55703766A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	151	73	0.483444	NM_006637	Q6IEU4	Silent	SNP	ENST00000301532.3	37	CCDS7949.1																																																																																			A|0.951;G|0.049	0.049	strong		0.398	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
NCKIPSD	51517	hgsc.bcm.edu	37	3	48716537	48716537	+	Silent	SNP	C	C	A	rs76815705	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:48716537C>A	ENST00000294129.2	-	10	1769	c.1650G>T	c.(1648-1650)ctG>ctT	p.L550L	NCKIPSD_ENST00000341520.4_Silent_p.L550L|NCKIPSD_ENST00000416649.2_Silent_p.L543L	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	550	Leu-rich.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AGAGGTCCGGCAGCTGCTCTG	0.652													C|||	26	0.00519169	0.0	0.0029	5008	,	,		17050	0.0		0.0139	False		,,,				2504	0.0102				p.L550L		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.G1650T						PASS	.	C	,	16,4390	22.3+/-47.3	0,16,2187	53.0	54.0	54.0		1650,1629	4.5	1.0	3	dbSNP_132	54	112,8488	52.3+/-112.8	0,112,4188	no	coding-synonymous,coding-synonymous	NCKIPSD	NM_016453.2,NM_184231.1	,	0,128,6375	AA,AC,CC		1.3023,0.3631,0.9842	,	550/723,543/716	48716537	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	51517	exon10			GTCCGGCAGCTGC	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"""dia interacting protein"", ""diaphanous protein interacting protein"", ""SH3 protein interacting with Nck, 90 kDa"""	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.1650G>T	3.37:g.48716537C>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	153	73	0.477124	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Silent	SNP	ENST00000294129.2	37	CCDS2776.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	C	7.195	0.592354	0.13812	0.003631	0.013023	ENSG00000213672	ENST00000415281	.	.	.	5.37	4.49	0.54785	.	.	.	.	.	T	0.47728	0.1461	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50406	-0.8832	4	.	.	.	.	6.1236	0.20167	0.1406:0.6518:0.1354:0.0721	.	.	.	.	S	259	.	.	A	-	1	0	NCKIPSD	48691541	0.999000	0.42202	1.000000	0.80357	0.841000	0.47740	0.710000	0.25748	1.236000	0.43740	0.650000	0.86243	GCC	C|0.989;A|0.011	0.011	strong		0.652	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453	
TSPO	706	hgsc.bcm.edu	37	22	43558972	43558972	+	Silent	SNP	G	G	A	rs41371752|rs6972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:43558972G>A	ENST00000396265.3	+	3	379	c.204G>A	c.(202-204)gcG>gcA	p.A68A	TSPO_ENST00000329563.4_Missense_Mutation_p.R162H|TSPO_ENST00000337554.3_Missense_Mutation_p.R162H|TSPO_ENST00000583777.1_Missense_Mutation_p.R58H			B1AH88	TSPOB_HUMAN	translocator protein (18kDa)	68					adrenal gland development (GO:0030325)|aging (GO:0007568)|behavioral response to pain (GO:0048266)|cellular hypotonic response (GO:0071476)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to zinc ion (GO:0071294)|chloride transport (GO:0006821)|contact inhibition (GO:0060242)|glial cell migration (GO:0008347)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of tumor necrosis factor production (GO:0032720)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of necrotic cell death (GO:0010940)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of steroid biosynthetic process (GO:0050810)|response to drug (GO:0042493)|response to manganese ion (GO:0010042)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to vitamin B1 (GO:0010266)|steroid biosynthetic process (GO:0006694)	mitochondrial outer membrane (GO:0005741)	androgen binding (GO:0005497)|benzodiazepine receptor activity (GO:0008503)			endometrium(1)|prostate(1)	2		Ovarian(80;0.0694)				CATGGCTGGCGTGGGGGACGG	0.672													G|||	1015	0.202676	0.0552	0.1556	5008	,	,		13994	0.2411		0.2575	False		,,,				2504	0.3395				p.R162H		Atlas-SNP	.											.	TSPO	6	.	0			c.G485A	GRCh37	CM060884	TSPO	M	rs6972	PASS	.	G	HIS/ARG,	373,3999		16,341,1829	27.0	21.0	23.0		485,204	3.3	0.0	22	dbSNP_52	23	2008,6552		244,1520,2516	yes	missense,coding-synonymous	TSPO	NM_000714.4,NM_007311.3	29,	260,1861,4345	AA,AG,GG		23.4579,8.5316,18.4117	benign,	162/170,68/103	43558972	2381,10551	2186	4280	6466	SO:0001819	synonymous_variant	706	exon4			GCTGGCGTGGGGG	AF075589	CCDS33661.1	22q13.3	2006-07-12	2006-07-12	2006-07-12	ENSG00000100300	ENSG00000100300			1158	protein-coding gene	gene with protein product	"""peripheral-type benzodiazepine receptor/recognition site"""	109610	"""benzodiazapine receptor (peripheral)"""	BZRP		1326278, 1847678, 16822554	Standard	NM_000714		Approved	PBR, MBR, PKBS, mDRC, DBI, IBP, pk18	uc003bdo.4	B1AH88	OTTHUMG00000150573	ENST00000396265.3:c.204G>A	22.37:g.43558972G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_001256531	Q13849|Q6IAZ7	Missense_Mutation	SNP	ENST00000396265.3	37		443	0.20283882783882784	39	0.07926829268292683	59	0.16298342541436464	131	0.229020979020979	214	0.28232189973614774	G	11.96	1.794907	0.31777	0.085316	0.234579	ENSG00000100300	ENST00000337554;ENST00000329563	T;T	0.23950	1.88;1.88	4.38	3.33	0.38152	.	0.339156	0.29192	N	0.012880	T	0.00012	0.0000	L	0.54323	1.7	0.51233	P	8.699999999994823E-5	B	0.16802	0.019	B	0.09377	0.004	T	0.27054	-1.0085	9	0.38643	T	0.18	-12.9691	12.1528	0.54059	0.0:0.1743:0.8257:0.0	rs6972;rs3171720;rs17844888;rs17857605;rs6972	162	P30536	TSPOA_HUMAN	H	162	ENSP00000338004:R162H;ENSP00000328973:R162H	ENSP00000328973:R162H	R	+	2	0	TSPO	41888916	0.386000	0.25180	0.025000	0.17156	0.073000	0.16967	2.623000	0.46435	1.147000	0.42369	0.655000	0.94253	CGT	G|0.812;A|0.188	0.188	strong		0.672	TSPO-201	KNOWN	basic	protein_coding	protein_coding		NM_007311	
SENP1	29843	hgsc.bcm.edu	37	12	48477422	48477422	+	Silent	SNP	A	A	G	rs886588	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48477422A>G	ENST00000004980.5	-	6	982	c.504T>C	c.(502-504)ctT>ctC	p.L168L	SENP1_ENST00000339976.6_3'UTR|SENP1_ENST00000549518.1_Silent_p.L168L|RNU6-1203P_ENST00000410703.1_RNA|SENP1_ENST00000549595.1_Silent_p.L168L|SENP1_ENST00000551330.1_Silent_p.L168L|SENP1_ENST00000547886.1_5'UTR|SENP1_ENST00000448372.1_Silent_p.L168L			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	168	Ser-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)	p.L168L(1)		large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				TGGGGCTCAAAAGACTTCGAC	0.408													A|||	803	0.160343	0.053	0.1744	5008	,	,		18083	0.2371		0.2177	False		,,,				2504	0.1575				p.L168L		Atlas-SNP	.											SENP1,NS,carcinoma,0,1	SENP1	44	1	1	Substitution - coding silent(1)	stomach(1)	c.T504C						PASS	.	A		253,3463		11,231,1616	120.0	111.0	114.0		504	1.8	1.0	12	dbSNP_86	114	1803,6381		192,1419,2481	no	coding-synonymous	SENP1	NM_014554.2		203,1650,4097	GG,GA,AA		22.0308,6.8084,17.2773		168/644	48477422	2056,9844	1858	4092	5950	SO:0001819	synonymous_variant	29843	exon6			GCTCAAAAGACTT	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"""SUMO1/sentrin specific protease 1"""			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.504T>C	12.37:g.48477422A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	192	92	0.479167	NM_001267594	A8K7P5|Q86XC8	Silent	SNP	ENST00000004980.5	37	CCDS44868.2																																																																																			A|0.817;G|0.183	0.183	strong		0.408	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554	
TACR2	6865	hgsc.bcm.edu	37	10	71176012	71176012	+	Missense_Mutation	SNP	A	A	G	rs5030920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:71176012A>G	ENST00000373306.4	-	1	611	c.68T>C	c.(67-69)aTc>aCc	p.I23T		NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	23			I -> T (in dbSNP:rs5030920). {ECO:0000269|PubMed:1659297, ECO:0000269|PubMed:1710456}.		excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						GAAGGCTGTGATGCCCGTGGT	0.597													G|||	1220	0.24361	0.4002	0.1758	5008	,	,		20717	0.0546		0.2356	False		,,,				2504	0.2832				p.I23T		Atlas-SNP	.											TACR2,colon,carcinoma,0,1	TACR2	37	1	0			c.T68C						PASS	.	G	THR/ILE	1649,2757	659.5+/-400.6	320,1009,874	71.0	69.0	70.0		68	2.8	0.4	10	dbSNP_113	70	1930,6670	725.9+/-406.6	220,1490,2590	yes	missense	TACR2	NM_001057.2	89	540,2499,3464	GG,GA,AA		22.4419,37.4262,27.5181	benign	23/399	71176012	3579,9427	2203	4300	6503	SO:0001583	missense	6865	exon1			GCTGTGATGCCCG		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"""GPCR / Class A : Tachykinin receptors"""	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.68T>C	10.37:g.71176012A>G	ENSP00000362403:p.Ile23Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	129	55	0.426357	NM_001057	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Missense_Mutation	SNP	ENST00000373306.4	37	CCDS7293.1	475	0.2174908424908425	196	0.3983739837398374	69	0.19060773480662985	27	0.0472027972027972	183	0.24142480211081793	G	1.368	-0.586835	0.03827	0.374262	0.224419	ENSG00000075073	ENST00000373306	T	0.36878	1.23	5.31	2.83	0.33086	.	0.651620	0.14923	N	0.290532	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47182	-0.9137	9	0.17832	T	0.49	.	7.3299	0.26575	0.6881:0.1194:0.1924:0.0	rs5030920;rs59892825;rs5030920	23	P21452	NK2R_HUMAN	T	23	ENSP00000362403:I23T	ENSP00000362403:I23T	I	-	2	0	TACR2	70846018	0.000000	0.05858	0.369000	0.25952	0.119000	0.20118	0.208000	0.17415	0.431000	0.26258	-1.073000	0.02249	ATC	A|0.748;G|0.252	0.252	strong		0.597	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1		
ZNF662	389114	hgsc.bcm.edu	37	3	42956694	42956694	+	Nonsense_Mutation	SNP	C	C	T	rs201163995		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:42956694C>T	ENST00000541208.1	+	5	1498	c.1129C>T	c.(1129-1131)Cga>Tga	p.R377*	ZNF662_ENST00000440367.2_Nonsense_Mutation_p.R377*|ZNF662_ENST00000422021.1_Intron|KRBOX1_ENST00000426937.1_Intron|ZNF662_ENST00000328199.6_Nonsense_Mutation_p.R403*			Q6ZS27	ZN662_HUMAN	zinc finger protein 662	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.217)		ACATCTTATTCGACATCAAAG	0.458													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20898	0.0		0.0	False		,,,				2504	0.0				p.R403X		Atlas-SNP	.											ZNF662_ENST00000328199,NS,carcinoma,-1,4	ZNF662	112	4	0			c.C1207T						scavenged	.						81.0	81.0	81.0					3																	42956694		2203	4300	6503	SO:0001587	stop_gained	389114	exon4			CTTATTCGACATC	AK127779	CCDS2708.1, CCDS46807.1	3p22.1	2013-01-08			ENSG00000182983	ENSG00000182983		"""Zinc fingers, C2H2-type"", ""-"""	31930	protein-coding gene	gene with protein product							Standard	NM_207404		Approved	FLJ45880	uc003cmk.2	Q6ZS27	OTTHUMG00000133041	ENST00000541208.1:c.1129C>T	3.37:g.42956694C>T	ENSP00000446208:p.Arg377*	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	113	2	0.0176991	NM_001134656	A1A4T9|F8W7S8|Q6ZNF8|Q6ZQW8	Nonsense_Mutation	SNP	ENST00000541208.1	37	CCDS2708.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999424	0.74818	.	.	ENSG00000182983	ENST00000440367;ENST00000328199;ENST00000541208	.	.	.	2.71	-0.0708	0.13746	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	6.6881	0.23156	0.0:0.6352:0.0:0.3648	.	.	.	.	X	377;403;377	.	ENSP00000329264:R403X	R	+	1	2	ZNF662	42931698	0.000000	0.05858	0.820000	0.32676	0.884000	0.51177	-2.178000	0.01260	-0.033000	0.13736	-0.143000	0.13931	CGA	.	.	weak		0.458	ZNF662-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256646.4	NM_207404	
C11orf16	56673	hgsc.bcm.edu	37	11	8947179	8947179	+	Silent	SNP	G	G	A	rs2568077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:8947179G>A	ENST00000326053.5	-	5	1141	c.1035C>T	c.(1033-1035)gaC>gaT	p.D345D	C11orf16_ENST00000528998.1_5'Flank|C11orf16_ENST00000525780.1_Silent_p.D345D	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	345								p.D345D(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	22				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		TCTCCACACCGTCTTGTTCAC	0.527													G|||	1349	0.269369	0.1067	0.2507	5008	,	,		22559	0.2232		0.3549	False		,,,				2504	0.4622				p.D345D		Atlas-SNP	.											C11orf16,NS,carcinoma,0,1	C11orf16	43	1	1	Substitution - coding silent(1)	stomach(1)	c.C1035T						PASS	.	G		586,3816	259.5+/-263.1	41,504,1656	109.0	95.0	99.0		1035	-10.2	0.0	11	dbSNP_100	99	3050,5542	469.2+/-367.5	544,1962,1790	no	coding-synonymous	C11orf16	NM_020643.2		585,2466,3446	AA,AG,GG		35.4981,13.3121,27.9821		345/468	8947179	3636,9358	2201	4296	6497	SO:0001819	synonymous_variant	56673	exon5			CACACCGTCTTGT	AJ400877	CCDS7794.1	11p15.3	2008-06-25			ENSG00000176029	ENSG00000176029			1169	protein-coding gene	gene with protein product						11528127	Standard	NM_020643		Approved		uc001mhb.4	Q9NQ32	OTTHUMG00000165654	ENST00000326053.5:c.1035C>T	11.37:g.8947179G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_020643	Q53FB2|Q8N6Y9	Silent	SNP	ENST00000326053.5	37	CCDS7794.1																																																																																			G|0.717;A|0.283	0.283	strong		0.527	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643	
KRTAP10-5	386680	hgsc.bcm.edu	37	21	45999653	45999653	+	Missense_Mutation	SNP	C	C	G	rs464391	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:45999653C>G	ENST00000400372.1	-	1	828	c.803G>C	c.(802-804)cGc>cCc	p.R268P	TSPEAR_ENST00000323084.4_Intron	NM_198694.2	NP_941967.2	P60370	KR105_HUMAN	keratin associated protein 10-5	268			R -> P (in dbSNP:rs464391). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				endometrium(2)|kidney(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	14						GCAGGCCAGGCGGGAGCACGC	0.697													.|||	512	0.102236	0.09	0.0519	5008	,	,		18751	0.1964		0.0378	False		,,,				2504	0.1237				p.R268P		Atlas-SNP	.											KRTAP10-5,NS,carcinoma,0,1	KRTAP10-5	43	1	0			c.G803C						PASS	.	C	,PRO/ARG	329,4009		11,307,1851	25.0	32.0	30.0		,803	3.7	0.0	21	dbSNP_80	30	195,8295		3,189,4053	no	intron,missense	TSPEAR,KRTAP10-5	NM_144991.2,NM_198694.2	,103	14,496,5904	GG,GC,CC		2.2968,7.5841,4.0848	,probably-damaging	,268/272	45999653	524,12304	2169	4245	6414	SO:0001583	missense	386680	exon1			GCCAGGCGGGAGC	AJ566384	CCDS42958.1	21q22.3	2007-10-05			ENSG00000241123	ENSG00000241123		"""Keratin associated proteins"""	22969	protein-coding gene	gene with protein product				KRTAP18-5			Standard	NM_198694		Approved	KAP10.5, KAP18.5	uc002zfl.1	P60370	OTTHUMG00000057638	ENST00000400372.1:c.803G>C	21.37:g.45999653C>G	ENSP00000383223:p.Arg268Pro	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	12	9	0.75	NM_198694	Q0VAR7|Q0VAR8|Q70LJ3	Missense_Mutation	SNP	ENST00000400372.1	37	CCDS42958.1	195	0.08928571428571429	36	0.07317073170731707	19	0.052486187845303865	119	0.20804195804195805	21	0.027704485488126648	c	11.55	1.670676	0.29693	0.075841	0.022968	ENSG00000241123	ENST00000400372	T	0.00824	5.65	3.68	3.68	0.42216	.	.	.	.	.	T	0.00012	0.0000	M	0.82630	2.6	0.80722	P	0.0	D	0.76494	0.999	D	0.81914	0.995	T	0.42882	-0.9425	8	0.72032	D	0.01	.	13.2517	0.60055	0.0:1.0:0.0:0.0	rs464391	268	P60370	KR105_HUMAN	P	268	ENSP00000383223:R268P	ENSP00000383223:R268P	R	-	2	0	KRTAP10-5	44824081	0.010000	0.17322	0.041000	0.18516	0.096000	0.18686	1.292000	0.33342	2.027000	0.59764	0.455000	0.32223	CGC	C|0.932;G|0.068	0.068	strong		0.697	KRTAP10-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128042.1		
AK9	221264	hgsc.bcm.edu	37	6	109885475	109885475	+	Missense_Mutation	SNP	G	G	A	rs10499052	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:109885475G>A	ENST00000424296.2	-	23	2519	c.2443C>T	c.(2443-2445)Cct>Tct	p.P815S	AK9_ENST00000341338.6_5'UTR	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	815					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										GGAAACTCAGGTAGTACAACT	0.363													G|||	809	0.161542	0.0295	0.1844	5008	,	,		15711	0.1637		0.3002	False		,,,				2504	0.1789				p.P815S		Atlas-SNP	.											.	AKD1	223	.	0			c.C2443T						PASS	.	G	SER/PRO	88,1296		4,80,608	81.0	65.0	70.0		2443	5.9	1.0	6	dbSNP_119	70	910,2272		134,642,815	yes	missense	AKD1	NM_001145128.2	74	138,722,1423	AA,AG,GG		28.5984,6.3584,21.8572	possibly-damaging	815/1912	109885475	998,3568	692	1591	2283	SO:0001583	missense	221264	exon23			ACTCAGGTAGTAC	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.2443C>T	6.37:g.109885475G>A	ENSP00000410186:p.Pro815Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	37	CCDS55048.1	428	0.19597069597069597	18	0.036585365853658534	74	0.20441988950276244	114	0.1993006993006993	222	0.2928759894459103	G	24.2	4.505146	0.85282	0.063584	0.285984	ENSG00000155085	ENST00000424296	T	0.67171	-0.25	5.92	5.92	0.95590	.	.	.	.	.	T	0.65790	0.2725	N	0.19112	0.55	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.63404	-0.6645	7	.	.	.	.	19.9123	0.97029	0.0:0.0:1.0:0.0	rs10499052;rs57834410;rs10499052	815	Q5TCS8	AKD1_HUMAN	S	815	ENSP00000410186:P815S	.	P	-	1	0	AKD1	109992168	1.000000	0.71417	0.965000	0.40720	0.881000	0.50899	6.309000	0.72825	2.801000	0.96364	0.650000	0.86243	CCT	G|0.809;A|0.191	0.191	strong		0.363	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
YTHDC2	64848	hgsc.bcm.edu	37	5	112868693	112868693	+	Silent	SNP	C	C	A	rs6594732	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:112868693C>A	ENST00000161863.4	+	5	1006	c.793C>A	c.(793-795)Cgg>Agg	p.R265R	YTHDC2_ENST00000515883.1_Silent_p.R265R	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	265	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		CGCAGAGAGACGGGAAAGGAT	0.398													A|||	1668	0.333067	0.5802	0.4524	5008	,	,		17308	0.2093		0.2107	False		,,,				2504	0.1677				p.R265R		Atlas-SNP	.											.	YTHDC2	118	.	0			c.C793A						PASS	.	A		2362,2042	565.4+/-381.7	660,1042,500	94.0	99.0	97.0		793	4.4	1.0	5	dbSNP_116	97	1816,6784	733.0+/-406.9	187,1442,2671	no	coding-synonymous	YTHDC2	NM_022828.3		847,2484,3171	AA,AC,CC		21.1163,46.3669,32.1286		265/1431	112868693	4178,8826	2202	4300	6502	SO:0001819	synonymous_variant	64848	exon5			GAGAGACGGGAAA	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.793C>A	5.37:g.112868693C>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																			C|0.678;A|0.322	0.322	strong		0.398	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
IL17B	27190	hgsc.bcm.edu	37	5	148754153	148754153	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:148754153C>T	ENST00000261796.3	-	3	372	c.322G>A	c.(322-324)Gac>Aac	p.D108N	RP11-394O4.3_ENST00000521756.1_RNA|IL17B_ENST00000505432.1_5'UTR	NM_014443.2	NP_055258.1	Q9UHF5	IL17B_HUMAN	interleukin 17B	108					cell-cell signaling (GO:0007267)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|urinary_tract(1)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCTGGGGTCGTGGTTGATG	0.607																																					p.D108N		Atlas-SNP	.											.	IL17B	15	.	0			c.G322A						PASS	.						23.0	23.0	23.0					5																	148754153		2197	4291	6488	SO:0001583	missense	27190	exon3			TGGGGTCGTGGTT	AF184969	CCDS4297.1	5q33.1	2011-07-14			ENSG00000127743	ENSG00000127743		"""Interleukins and interleukin receptors"""	5982	protein-coding gene	gene with protein product	"""neuronal interleukin-17-related factor"""	604627				10639155	Standard	NM_014443		Approved	IL-17B, ZCYTO7, IL-20, MGC138900, MGC138901, NIRF	uc003lqo.3	Q9UHF5	OTTHUMG00000130051	ENST00000261796.3:c.322G>A	5.37:g.148754153C>T	ENSP00000261796:p.Asp108Asn	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_014443	Q14CE5	Missense_Mutation	SNP	ENST00000261796.3	37	CCDS4297.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.231424	0.58777	.	.	ENSG00000127743	ENST00000261796	T	0.64260	-0.09	4.68	4.68	0.58851	.	0.159823	0.42420	D	0.000720	T	0.76659	0.4018	L	0.58583	1.82	0.50813	D	0.999891	D	0.89917	1.0	D	0.91635	0.999	T	0.78851	-0.2041	10	0.62326	D	0.03	-20.8315	17.807	0.88604	0.0:1.0:0.0:0.0	.	108	Q9UHF5	IL17B_HUMAN	N	108	ENSP00000261796:D108N	ENSP00000261796:D108N	D	-	1	0	IL17B	148734346	1.000000	0.71417	1.000000	0.80357	0.092000	0.18411	5.794000	0.69067	2.423000	0.82170	0.561000	0.74099	GAC	.	.	none		0.607	IL17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252330.1	NM_014443	
ZNF100	163227	hgsc.bcm.edu	37	19	21910451	21910451	+	Silent	SNP	A	A	C	rs35587380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:21910451A>C	ENST00000358296.6	-	5	861	c.663T>G	c.(661-663)acT>acG	p.T221T	ZNF100_ENST00000305570.6_Silent_p.T157T	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						TTTTATGTTGAGTTAGGTGTA	0.318													N|||	514	0.102636	0.1369	0.0533	5008	,	,		19858	0.0218		0.0596	False		,,,				2504	0.2188				p.T221T		Atlas-SNP	.											.	ZNF100	62	.	0			c.T663G						PASS	.	A		621,3465		51,519,1473	53.0	55.0	55.0		663	1.0	0.0	19	dbSNP_126	55	631,7821		23,585,3618	no	coding-synonymous	ZNF100	NM_173531.3		74,1104,5091	CC,CA,AA		7.4657,15.1982,9.9856		221/543	21910451	1252,11286	2043	4226	6269	SO:0001819	synonymous_variant	163227	exon5			ATGTTGAGTTAGG	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"""Zinc fingers, C2H2-type"", ""-"""	12880	protein-coding gene	gene with protein product		603982	"""zinc finger protein 100 (Y1)"""			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.663T>G	19.37:g.21910451A>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			.	.	weak		0.318	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
EVA1A	84141	hgsc.bcm.edu	37	2	75720664	75720664	+	Silent	SNP	G	G	A	rs6741778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:75720664G>A	ENST00000233712.1	-	4	594	c.157C>T	c.(157-159)Ctg>Ttg	p.L53L	EVA1A_ENST00000410071.1_Silent_p.L53L|EVA1A_ENST00000410113.1_Silent_p.L53L|EVA1A_ENST00000393913.3_Silent_p.L53L|EVA1A_ENST00000490746.1_Intron|EVA1A_ENST00000410010.1_Silent_p.L41L	NM_032181.2	NP_115557.1	Q9H8M9	EVA1A_HUMAN	eva-1 homolog A (C. elegans)	53	Necessary for the localization and biological activity.				apoptotic process (GO:0006915)|autophagy (GO:0006914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|plasma membrane (GO:0005886)											CTTATCACCAGAGCAGCCAGG	0.572													A|||	1155	0.230631	0.4576	0.1599	5008	,	,		17088	0.0298		0.2078	False		,,,				2504	0.2045				p.L53L		Atlas-SNP	.											.	.	.	.	0			c.C157T						PASS	.	A	,	1810,2596	638.3+/-396.9	376,1058,769	41.0	39.0	40.0		157,157	-8.4	0.0	2	dbSNP_116	40	1801,6799	732.1+/-406.8	198,1405,2697	no	coding-synonymous,coding-synonymous	FAM176A	NM_001135032.1,NM_032181.2	,	574,2463,3466	AA,AG,GG		20.9419,41.0803,27.7641	,	53/153,53/153	75720664	3611,9395	2203	4300	6503	SO:0001819	synonymous_variant	84141	exon4			TCACCAGAGCAGC	BC016157	CCDS1959.1	2p12	2012-11-05	2012-11-05	2012-11-05	ENSG00000115363	ENSG00000115363			25816	protein-coding gene	gene with protein product			"""transmembrane protein 166"", ""family with sequence similarity 176, member A"""	TMEM166, FAM176A		12477932	Standard	NM_001135032		Approved	FLJ13391	uc002sni.2	Q9H8M9	OTTHUMG00000129991	ENST00000233712.1:c.157C>T	2.37:g.75720664G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	67	41	0.61194	NM_032181	D6W5J3|Q9HC41	Silent	SNP	ENST00000233712.1	37	CCDS1959.1																																																																																			G|0.745;A|0.255	0.255	strong		0.572	EVA1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328707.1	NM_032181	
RNF175	285533	hgsc.bcm.edu	37	4	154631587	154631587	+	Missense_Mutation	SNP	C	C	G	rs1337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:154631587C>G	ENST00000347063.4	-	9	1293	c.921G>C	c.(919-921)ttG>ttC	p.L307F		NM_173662.2	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	307			L -> F (in dbSNP:rs1337).			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	13	all_hematologic(180;0.093)	Renal(120;0.118)				GCCAGGCCACCAAATAACGAA	0.458													C|||	399	0.0796725	0.0053	0.147	5008	,	,		16752	0.004		0.1889	False		,,,				2504	0.0982				p.L307F		Atlas-SNP	.											.	RNF175	40	.	0			c.G921C						PASS	.	C	PHE/LEU	142,3706		3,136,1785	83.0	75.0	78.0		921	2.5	1.0	4	dbSNP_36	78	1648,6620		155,1338,2641	yes	missense	RNF175	NM_173662.2	22	158,1474,4426	GG,GC,CC		19.9323,3.6902,14.7739	probably-damaging	307/329	154631587	1790,10326	1924	4134	6058	SO:0001583	missense	285533	exon9			GGCCACCAAATAA	BC034385	CCDS47149.1	4q31.3	2008-02-05			ENSG00000145428	ENSG00000145428		"""RING-type (C3HC4) zinc fingers"""	27735	protein-coding gene	gene with protein product							Standard	NM_173662		Approved	FLJ34190	uc003int.3	Q8N4F7	OTTHUMG00000161557	ENST00000347063.4:c.921G>C	4.37:g.154631587C>G	ENSP00000340979:p.Leu307Phe	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_173662	C9JL66|Q8NB61	Missense_Mutation	SNP	ENST00000347063.4	37	CCDS47149.1	213	0.09752747252747253	1	0.0020325203252032522	54	0.14917127071823205	1	0.0017482517482517483	157	0.20712401055408972	C	17.39	3.378453	0.61735	0.036902	0.199323	ENSG00000145428	ENST00000347063	T	0.30182	1.54	4.26	2.52	0.30459	.	0.103637	0.39146	N	0.001441	T	0.00039	0.0001	M	0.82193	2.58	0.09310	P	0.9999999999999867	D	0.59357	0.985	P	0.53518	0.728	T	0.04103	-1.0977	9	0.39692	T	0.17	-16.9333	3.9719	0.09457	0.1867:0.6155:0.0:0.1978	rs1337;rs17370770;rs1337	307	Q8N4F7	RN175_HUMAN	F	307	ENSP00000340979:L307F	ENSP00000340979:L307F	L	-	3	2	RNF175	154851037	1.000000	0.71417	0.963000	0.40424	0.988000	0.76386	1.070000	0.30653	0.720000	0.32209	0.655000	0.94253	TTG	C|0.896;G|0.104	0.104	strong		0.458	RNF175-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365286.1	NM_173662	
TSC22D2	9819	hgsc.bcm.edu	37	3	150128484	150128484	+	Silent	SNP	C	C	A	rs3749400	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:150128484C>A	ENST00000361875.3	+	1	2363	c.1347C>A	c.(1345-1347)gtC>gtA	p.V449V	TSC22D2_ENST00000361136.2_Silent_p.V449V	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	449					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GCGGGCAGGTCGCGCCTTGTC	0.731													C|||	635	0.126797	0.1921	0.1052	5008	,	,		13898	0.0317		0.173	False		,,,				2504	0.1043				p.V449V		Atlas-SNP	.											.	TSC22D2	42	.	0			c.C1347A						PASS	.	C		826,3416		95,636,1390	5.0	7.0	6.0		1347	-5.9	0.1	3	dbSNP_107	6	1577,6731		174,1229,2751	no	coding-synonymous	TSC22D2	NM_014779.2		269,1865,4141	AA,AC,CC		18.9817,19.4719,19.1474		449/781	150128484	2403,10147	2121	4154	6275	SO:0001819	synonymous_variant	9819	exon1			GCAGGTCGCGCCT	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.1347C>A	3.37:g.150128484C>A		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Silent	SNP	ENST00000361875.3	37	CCDS3149.1																																																																																			C|0.879;A|0.121	0.121	strong		0.731	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779	
AKAP13	11214	hgsc.bcm.edu	37	15	86122779	86122779	+	Missense_Mutation	SNP	T	T	C	rs2061822	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86122779T>C	ENST00000394518.2	+	7	1575	c.1480T>C	c.(1480-1482)Tgg>Cgg	p.W494R	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.W494R	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	494	RII-binding.		W -> R (in dbSNP:rs2061822). {ECO:0000269|Ref.3}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						TGCCACTGTTTGGAAGAATGT	0.493													t|||	2986	0.596246	0.5545	0.6499	5008	,	,		20993	0.5794		0.6511	False		,,,				2504	0.5757				p.W494R	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											AKAP13_ENST00000394518,right_upper_lobe,carcinoma,-1,2	AKAP13	394	2	0			c.T1480C						PASS	.	T	ARG/TRP,ARG/TRP	2636,1768	643.2+/-397.8	793,1050,359	71.0	77.0	75.0		1480,1480	2.2	0.0	15	dbSNP_94	75	5803,2795	676.8+/-403.3	1973,1857,469	yes	missense,missense	AKAP13	NM_006738.4,NM_007200.3	101,101	2766,2907,828	CC,CT,TT		32.5076,40.1453,35.0946	benign,benign	494/2818,494/2814	86122779	8439,4563	2202	4299	6501	SO:0001583	missense	11214	exon7			ACTGTTTGGAAGA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.1480T>C	15.37:g.86122779T>C	ENSP00000378026:p.Trp494Arg	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	206	205	0.995146	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	1325	0.6066849816849816	266	0.540650406504065	238	0.6574585635359116	334	0.583916083916084	487	0.6424802110817942	t	8.469	0.857011	0.17106	0.598547	0.674924	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.08896	3.04;3.05	5.15	2.25	0.28309	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18524	-1.0334	8	0.10636	T	0.68	.	4.5676	0.12195	0.1551:0.6128:0.1496:0.0826	rs2061822;rs52836073;rs58319762;rs2061822	494;494	Q12802;Q12802-2	AKP13_HUMAN;.	R	494;494;493;493	ENSP00000354718:W494R;ENSP00000378026:W494R	ENSP00000354718:W494R	W	+	1	0	AKAP13	83923783	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.087000	0.11215	0.414000	0.25790	-0.838000	0.03060	TGG	T|0.368;C|0.632	0.632	strong		0.493	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
KIAA2018	205717	hgsc.bcm.edu	37	3	113376113	113376113	+	Silent	SNP	C	C	T	rs62265537|rs59601191|rs112313093|rs59990801|rs397990842|rs10606566		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:113376113C>T	ENST00000478658.1	-	5	4433	c.4416G>A	c.(4414-4416)caG>caA	p.Q1472Q	KIAA2018_ENST00000316407.4_Silent_p.Q1472Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1472	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgctgttgctgctgctgct	0.502																																					p.Q1472Q		Atlas-SNP	.											KIAA2018,rectum,carcinoma,0,1	KIAA2018	180	1	0			c.G4416A						scavenged	.						68.0	71.0	70.0					3																	113376113		2188	4274	6462	SO:0001819	synonymous_variant	205717	exon7			CTGTTGCTGCTGC	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4416G>A	3.37:g.113376113C>T		Somatic	45	1	0.0222222		WXS	Illumina HiSeq	Phase_I	104	24	0.230769	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.	.	weak		0.502	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
ZFHX3	463	hgsc.bcm.edu	37	16	72992629	72992629	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992629C>T	ENST00000268489.5	-	2	2088	c.1416G>A	c.(1414-1416)gcG>gcA	p.A472A	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	472	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cctcctcctccgcctcttcct	0.572																																					p.A472A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G1416A						PASS	.						39.0	43.0	42.0					16																	72992629		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCCTCCGCCTCT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1416G>A	16.37:g.72992629C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	53	5	0.0943396	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	none		0.572	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
MUC2	4583	hgsc.bcm.edu	37	11	1088835	1088835	+	Missense_Mutation	SNP	C	C	T	rs41389046	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1088835C>T	ENST00000441003.2	+	26	3647	c.3620C>T	c.(3619-3621)aCc>aTc	p.T1207I	MUC2_ENST00000359061.5_Missense_Mutation_p.T1207I	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1207					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACCGAGGAGACCTGCAAGTCC	0.572													T|||	326	0.0650958	0.053	0.0591	5008	,	,		23089	0.0556		0.0974	False		,,,				2504	0.0624				p.T1207I		Atlas-SNP	.											MUC2_ENST00000441003,colon,carcinoma,0,2	MUC2	614	2	0			c.C3620T						PASS	.	T	ILE/THR	227,3961		5,217,1872	51.0	53.0	52.0		3620	-7.2	0.0	11	dbSNP_127	52	782,7632		36,710,3461	yes	missense	MUC2	NM_002457.2	89	41,927,5333	TT,TC,CC		9.294,5.4202,8.0067	benign	1207/2813	1088835	1009,11593	2094	4207	6301	SO:0001583	missense	4583	exon26			AGGAGACCTGCAA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3620C>T	11.37:g.1088835C>T	ENSP00000415183:p.Thr1207Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		136	0.06227106227106227	21	0.042682926829268296	18	0.049723756906077346	28	0.04895104895104895	69	0.09102902374670185	T	4.811	0.150695	0.09185	0.054202	0.09294	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13196	2.67;2.61	3.61	-7.21	0.01490	.	8.859210	0.01114	N	0.005658	T	0.00178	0.0005	N	0.00742	-1.23	0.58432	P	2.9999999999752447E-6	B	0.14805	0.011	B	0.15870	0.014	T	0.38735	-0.9647	9	0.39692	T	0.17	.	8.0296	0.30457	0.5745:0.2881:0.0:0.1374	rs41389046;rs61732138	1207	E7EUV1	.	I	1207	ENSP00000415183:T1207I;ENSP00000351956:T1207I	ENSP00000351956:T1207I	T	+	2	0	MUC2	1078835	0.002000	0.14202	0.000000	0.03702	0.068000	0.16541	-0.083000	0.11286	-3.281000	0.00197	-0.847000	0.03039	ACC	C|0.932;T|0.068	0.068	strong		0.572	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
PDE6A	5145	hgsc.bcm.edu	37	5	149264117	149264117	+	Missense_Mutation	SNP	T	T	C	rs149380104	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149264117T>C	ENST00000255266.5	-	16	2071	c.1952A>G	c.(1951-1953)aAt>aGt	p.N651S		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	651					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CTGTCGACGATTGAGGTTTTG	0.438													T|||	5	0.000998403	0.0	0.0029	5008	,	,		14804	0.0		0.0	False		,,,				2504	0.0031				p.N651S		Atlas-SNP	.											.	PDE6A	98	.	0			c.A1952G						PASS	.	T	SER/ASN	0,4406		0,0,2203	96.0	96.0	96.0		1952	4.6	1.0	5	dbSNP_134	96	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PDE6A	NM_000440.2	46	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	benign	651/861	149264117	3,13003	2203	4300	6503	SO:0001583	missense	5145	exon16			CGACGATTGAGGT		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.1952A>G	5.37:g.149264117T>C	ENSP00000255266:p.Asn651Ser	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	227	161	0.709251	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	37	CCDS4299.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	11.92	1.781228	0.31502	0.0	3.49E-4	ENSG00000132915	ENST00000255266	T	0.74737	-0.87	5.72	4.56	0.56223	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.096275	0.64402	N	0.000002	T	0.57257	0.2041	N	0.20328	0.56	0.44079	D	0.996839	P	0.36438	0.553	B	0.40782	0.34	T	0.55604	-0.8115	10	0.02654	T	1	.	9.7477	0.40457	0.0:0.0815:0.0:0.9185	.	651	P16499	PDE6A_HUMAN	S	651	ENSP00000255266:N651S	ENSP00000255266:N651S	N	-	2	0	PDE6A	149244310	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	3.597000	0.54031	1.011000	0.39340	0.455000	0.32223	AAT	T|1.000;C|0.000	0.000	strong		0.438	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
ARHGAP10	79658	hgsc.bcm.edu	37	4	148834245	148834245	+	Missense_Mutation	SNP	G	G	A	rs115753644	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:148834245G>A	ENST00000336498.3	+	13	1422	c.1183G>A	c.(1183-1185)Ggg>Agg	p.G395R	ARHGAP10_ENST00000414545.2_Missense_Mutation_p.G44R	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		GGATAAGATGGGGTTCACAAT	0.299													G|||	3	0.000599042	0.0	0.0	5008	,	,		18290	0.0		0.003	False		,,,				2504	0.0				p.G395R		Atlas-SNP	.											ARHGAP10,NS,carcinoma,-2,1	ARHGAP10	92	1	0			c.G1183A						PASS	.	G	ARG/GLY	0,4406		0,0,2203	110.0	104.0	106.0		1183	5.6	1.0	4	dbSNP_133	106	7,8589	5.7+/-21.5	0,7,4291	yes	missense	ARHGAP10	NM_024605.3	125	0,7,6494	AA,AG,GG		0.0814,0.0,0.0538	probably-damaging	395/787	148834245	7,12995	2203	4298	6501	SO:0001583	missense	79658	exon13			AAGATGGGGTTCA	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"""Rho GTPase activating proteins"""	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.1183G>A	4.37:g.148834245G>A	ENSP00000336923:p.Gly395Arg	Somatic	348	0	0		WXS	Illumina HiSeq	Phase_I	333	161	0.483483	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	37	CCDS34075.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	G|G	22.7|22.7	4.327623|4.327623	0.81690|0.81690	0.0|0.0	8.14E-4|8.14E-4	ENSG00000071205|ENSG00000071205	ENST00000507661|ENST00000336498;ENST00000414545	.|T;T	.|0.12569	.|2.91;2.67	5.64|5.64	5.64|5.64	0.86602|0.86602	.|Rho GTPase-activating protein domain (2);Rho GTPase activation protein (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.50497|0.50497	0.1619|0.1619	H|H	0.94423|0.94423	3.535|3.535	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.989	T|T	0.63699|0.63699	-0.6578|-0.6578	6|10	.|0.87932	.|D	.|0	.|.	16.6148|16.6148	0.84904|0.84904	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|44;395	.|E7EUW5;A1A4S6	.|.;RHG10_HUMAN	E|R	72|395;44	.|ENSP00000336923:G395R;ENSP00000406624:G44R	.|ENSP00000336923:G395R	G|G	+|+	2|1	0|0	ARHGAP10|ARHGAP10	149053695|149053695	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	5.905000|5.905000	0.69893|0.69893	2.665000|2.665000	0.90641|0.90641	0.557000|0.557000	0.71058|0.71058	GGG|GGG	G|0.999;A|0.001	0.001	strong		0.299	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605	
BLM	641	hgsc.bcm.edu	37	15	91346923	91346923	+	Silent	SNP	C	C	A	rs2227934	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91346923C>A	ENST00000355112.3	+	18	3649	c.3531C>A	c.(3529-3531)gcC>gcA	p.A1177A	BLM_ENST00000560509.1_Intron|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1177					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			GAAATAAAGCCCAAACTGTAC	0.313			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome				C|||	667	0.133187	0.1309	0.1052	5008	,	,		18805	0.1875		0.165	False		,,,				2504	0.0675				p.A1177A		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.C3531A						PASS	.	C		546,3850	246.2+/-254.9	28,490,1680	88.0	86.0	87.0		3531	1.2	0.3	15	dbSNP_98	87	1568,7028	291.1+/-300.1	142,1284,2872	no	coding-synonymous	BLM	NM_000057.2		170,1774,4552	AA,AC,CC		18.241,12.4204,16.2716		1177/1418	91346923	2114,10878	2198	4298	6496	SO:0001819	synonymous_variant	641	exon18	Familial Cancer Database		TAAAGCCCAAACT	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3531C>A	15.37:g.91346923C>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	37	CCDS10363.1																																																																																			C|0.848;A|0.152	0.152	strong		0.313	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
DYNC1H1	1778	hgsc.bcm.edu	37	14	102453073	102453073	+	Silent	SNP	A	A	G	rs17512054	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102453073A>G	ENST00000360184.4	+	8	2675	c.2511A>G	c.(2509-2511)gcA>gcG	p.A837A		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	837	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						AGCGCTTAGCAGAGACTGTCT	0.478													A|||	43	0.00858626	0.0008	0.0086	5008	,	,		23475	0.0		0.008	False		,,,				2504	0.0286				p.A837A		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A2511G						PASS	.	A		11,4395	17.9+/-39.9	0,11,2192	99.0	92.0	94.0		2511	-6.3	0.7	14	dbSNP_123	94	90,8510	51.5+/-111.7	0,90,4210	no	coding-synonymous	DYNC1H1	NM_001376.4		0,101,6402	GG,GA,AA		1.0465,0.2497,0.7766		837/4647	102453073	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon8			CTTAGCAGAGACT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.2511A>G	14.37:g.102453073A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	171	91	0.532164	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			A|0.993;G|0.007	0.007	strong		0.478	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
SPRY2	10253	hgsc.bcm.edu	37	13	80911525	80911525	+	Missense_Mutation	SNP	G	G	A	rs504122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:80911525G>A	ENST00000377102.1	-	2	1293	c.316C>T	c.(316-318)Cct>Tct	p.P106S	SPRY2_ENST00000377104.3_Missense_Mutation_p.P106S|SPRY2_ENST00000540649.1_Missense_Mutation_p.P106S			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	106			P -> S (in dbSNP:rs504122).		bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of mitotic spindle orientation (GO:0000132)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inner ear morphogenesis (GO:0042472)|lung growth (GO:0060437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|sensory perception of sound (GO:0007605)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase inhibitor activity (GO:0030291)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	12	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		CTGGACAGAGGGGCTCGTGCA	0.597													G|||	1436	0.286741	0.0182	0.4539	5008	,	,		20149	0.4345		0.3529	False		,,,				2504	0.3108				p.P106S		Atlas-SNP	.											.	SPRY2	28	.	0			c.C316T						PASS	.	G	SER/PRO	354,4052	180.8+/-209.0	13,328,1862	92.0	87.0	89.0		316	0.6	0.1	13	dbSNP_83	89	3087,5513	469.1+/-367.5	550,1987,1763	yes	missense	SPRY2	NM_005842.2	74	563,2315,3625	AA,AG,GG		35.8953,8.0345,26.457	benign	106/316	80911525	3441,9565	2203	4300	6503	SO:0001583	missense	10253	exon2			ACAGAGGGGCTCG	AF039843	CCDS9463.1	13q31.1	2008-05-14	2001-11-28		ENSG00000136158	ENSG00000136158			11270	protein-coding gene	gene with protein product		602466	"""sprouty (Drosophila) homolog 2"""			9458049	Standard	NM_005842		Approved	hSPRY2	uc001vlj.3	O43597	OTTHUMG00000017140	ENST00000377102.1:c.316C>T	13.37:g.80911525G>A	ENSP00000366306:p.Pro106Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_005842	B2R9J9|Q5T6Z7	Missense_Mutation	SNP	ENST00000377102.1	37	CCDS9463.1	674	0.3086080586080586	14	0.028455284552845527	148	0.4088397790055249	245	0.42832167832167833	267	0.35224274406332456	G	9.125	1.009882	0.19277	0.080345	0.358953	ENSG00000136158	ENST00000377104;ENST00000377102;ENST00000541655;ENST00000540649	T;T;T	0.57107	0.42;0.42;0.42	5.48	0.638	0.17742	.	0.226724	0.45867	N	0.000333	T	0.00012	0.0000	M	0.66939	2.045	0.44175	P	0.0030120000000000147	B	0.02656	0.0	B	0.04013	0.001	T	0.36720	-0.9736	9	0.36615	T	0.2	.	4.6416	0.12552	0.1252:0.2223:0.5371:0.1154	rs504122;rs3825414;rs17845004;rs17857765;rs57585481;rs504122	106	O43597	SPY2_HUMAN	S	106	ENSP00000366308:P106S;ENSP00000366306:P106S;ENSP00000439027:P106S	ENSP00000366306:P106S	P	-	1	0	SPRY2	79809526	0.534000	0.26362	0.051000	0.19133	0.952000	0.60782	0.958000	0.29227	-0.211000	0.10124	0.655000	0.94253	CCT	G|0.726;N|0.000	.	strong		0.597	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1		
KIAA1279	26128	hgsc.bcm.edu	37	10	70775959	70775959	+	Silent	SNP	C	C	T	rs35893997	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70775959C>T	ENST00000361983.4	+	7	1755	c.1653C>T	c.(1651-1653)gcC>gcT	p.A551A		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	551					cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						TTCGAGTTGCCCGTCTCTATG	0.408													C|||	134	0.0267572	0.0045	0.0648	5008	,	,		21021	0.0		0.0666	False		,,,				2504	0.0164				p.A551A		Atlas-SNP	.											.	KIAA1279	35	.	0			c.C1653T						PASS	.	C		53,4353	52.3+/-87.9	0,53,2150	104.0	98.0	100.0		1653	-0.2	1.0	10	dbSNP_126	100	653,7947	166.4+/-218.3	26,601,3673	no	coding-synonymous	KIAA1279	NM_015634.3		26,654,5823	TT,TC,CC		7.593,1.2029,5.4283		551/622	70775959	706,12300	2203	4300	6503	SO:0001819	synonymous_variant	26128	exon7			AGTTGCCCGTCTC	BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954			23419	protein-coding gene	gene with protein product		609367					Standard	NM_015634		Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.1653C>T	10.37:g.70775959C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	144	66	0.458333	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Silent	SNP	ENST00000361983.4	37	CCDS7284.1																																																																																			C|0.954;T|0.046	0.046	strong		0.408	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634	
SPTB	6710	hgsc.bcm.edu	37	14	65270391	65270391	+	Silent	SNP	G	G	A	rs11623956	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:65270391G>A	ENST00000389721.5	-	3	440	c.408C>T	c.(406-408)caC>caT	p.H136H	SPTB_ENST00000542895.1_Silent_p.H136H|SPTB_ENST00000389722.3_Silent_p.H136H|SPTB_ENST00000389720.3_Silent_p.H136H|SPTB_ENST00000556626.1_Silent_p.H136H	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	136	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CTACAATGTCGTGGGAGCCCA	0.597													G|||	136	0.0271565	0.0045	0.0331	5008	,	,		20126	0.003		0.0855	False		,,,				2504	0.0184				p.H136H		Atlas-SNP	.											.	SPTB	378	.	0			c.C408T						PASS	.	G	,	65,4341	60.5+/-97.4	1,63,2139	115.0	100.0	105.0		408,408	-3.8	0.8	14	dbSNP_120	105	707,7893	174.9+/-225.1	31,645,3624	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	32,708,5763	AA,AG,GG		8.2209,1.4753,5.9357	,	136/2138,136/2329	65270391	772,12234	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon3			AATGTCGTGGGAG		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.408C>T	14.37:g.65270391G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	201	94	0.467662	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			G|0.945;A|0.055	0.055	strong		0.597	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
MUM1	84939	hgsc.bcm.edu	37	19	1370675	1370675	+	Silent	SNP	C	C	G	rs12608765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1370675C>G	ENST00000415183.3	+	11	1613	c.1587C>G	c.(1585-1587)gtC>gtG	p.V529V	MUM1_ENST00000591806.1_Silent_p.V529V|MUM1_ENST00000344663.3_Silent_p.V529V|MUM1_ENST00000311401.5_Silent_p.V460V			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	528					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCAGGACGTCTTGGGGACCA	0.652													C|||	1644	0.328275	0.0582	0.3963	5008	,	,		14823	0.369		0.496	False		,,,				2504	0.4305				p.V529V		Atlas-SNP	.											MUM1,NS,carcinoma,0,2	MUM1	54	2	0			c.C1587G						PASS	.	C		560,3610		61,438,1586	13.0	12.0	12.0		1587	-9.4	0.0	19	dbSNP_120	12	3891,4325		1023,1845,1240	no	coding-synonymous	MUM1	NM_032853.3		1084,2283,2826	GG,GC,CC		47.3588,13.4293,35.9357		529/712	1370675	4451,7935	2085	4108	6193	SO:0001819	synonymous_variant	84939	exon12			GGACGTCTTGGGG	AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.1587C>G	19.37:g.1370675C>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	165	164	0.993939	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Silent	SNP	ENST00000415183.3	37																																																																																				C|0.666;G|0.334	0.334	strong		0.652	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853	
FHAD1	114827	hgsc.bcm.edu	37	1	15687059	15687059	+	Missense_Mutation	SNP	A	A	G	rs4661330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:15687059A>G	ENST00000375998.4	+	20	2756	c.2756A>G	c.(2755-2757)gAa>gGa	p.E919G	FHAD1_ENST00000417793.1_Missense_Mutation_p.E883G|FHAD1_ENST00000375999.3_Missense_Mutation_p.E919G|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000314740.8_Missense_Mutation_p.E172G|FHAD1_ENST00000358897.4_Missense_Mutation_p.E919G			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	919										skin(1)|stomach(1)	2						CACGGGTTTGAAGAAGAGATC	0.473													A|||	1267	0.252995	0.2579	0.2147	5008	,	,		19740	0.2887		0.2853	False		,,,				2504	0.2035				p.E919G		Atlas-SNP	.											.	FHAD1	78	.	0			c.A2756G						PASS	.	A	GLY/GLU	361,1023		52,257,383	117.0	108.0	111.0		2756	5.3	0.1	1	dbSNP_111	111	901,2281		137,627,827	yes	missense	FHAD1	NM_052929.1	98	189,884,1210	GG,GA,AA		28.3155,26.0838,27.6391	benign	919/1413	15687059	1262,3304	692	1591	2283	SO:0001583	missense	114827	exon21			GGTTTGAAGAAGA	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.2756A>G	1.37:g.15687059A>G	ENSP00000365166:p.Glu919Gly	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	111	43	0.387387	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		562|562	0.2573260073260073|0.2573260073260073	134|134	0.27235772357723576|0.27235772357723576	80|80	0.22099447513812154|0.22099447513812154	140|140	0.24475524475524477|0.24475524475524477	208|208	0.27440633245382584|0.27440633245382584	A|A	18.07|18.07	3.540762|3.540762	0.65085|0.65085	0.260838|0.260838	0.283155|0.283155	ENSG00000142621|ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998;ENST00000529606;ENST00000314740;ENST00000314668|ENST00000444385	T;T;T;T;T;T;T|.	0.43688|.	0.94;0.94;0.94;0.94;1.72;1.72;1.72|.	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.70595|0.70595	2.14|2.14	0.80722|0.80722	P|P	0.0|0.0	D;D;B|.	0.89917|.	1.0;0.999;0.033|.	D;D;B|.	0.85130|.	0.997;0.989;0.009|.	T|T	0.06661|0.06661	-1.0814|-1.0814	8|4	0.66056|.	D|.	0.02|.	.|.	11.7335|11.7335	0.51752|0.51752	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs4661330;rs52808175;rs61608267;rs4661330|rs4661330;rs52808175;rs61608267;rs4661330	172;919;919|.	B7WPP2;B1AJZ9-3;B1AJZ9|.	.;.;FHAD1_HUMAN|.	G|E	919;883;919;919;190;172;154|238	ENSP00000351770:E919G;ENSP00000407615:E883G;ENSP00000365167:E919G;ENSP00000365166:E919G;ENSP00000434909:E190G;ENSP00000322979:E172G;ENSP00000318812:E154G|.	ENSP00000318812:E154G|.	E|K	+|+	2|1	0|0	FHAD1|FHAD1	15559646|15559646	0.983000|0.983000	0.35010|0.35010	0.119000|0.119000	0.21687|0.21687	0.012000|0.012000	0.07955|0.07955	3.610000|3.610000	0.54125|0.54125	2.034000|2.034000	0.60081|0.60081	0.460000|0.460000	0.39030|0.39030	GAA|AAG	A|0.740;G|0.260	0.260	strong		0.473	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
GEMIN4	50628	hgsc.bcm.edu	37	17	649232	649232	+	Missense_Mutation	SNP	C	C	T	rs3744741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:649232C>T	ENST00000319004.5	-	2	2169	c.2051G>A	c.(2050-2052)cGa>cAa	p.R684Q	GEMIN4_ENST00000576778.1_Missense_Mutation_p.R673Q	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	684			R -> Q (in dbSNP:rs3744741).		gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GTATTCCTCTCGGCACGCGTT	0.527													C|||	1387	0.276957	0.3449	0.3055	5008	,	,		19971	0.3571		0.1412	False		,,,				2504	0.2219				p.R684Q		Atlas-SNP	.											.	GEMIN4	116	.	0			c.G2051A						PASS	.	C	GLN/ARG	1197,2743		208,781,981	36.0	38.0	37.0		2051	0.4	0.0	17	dbSNP_107	37	1049,7247		71,907,3170	yes	missense	GEMIN4	NM_015721.2	43	279,1688,4151	TT,TC,CC		12.6446,30.3807,18.3557	benign	684/1059	649232	2246,9990	1970	4148	6118	SO:0001583	missense	50628	exon2			TCCTCTCGGCACG	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.2051G>A	17.37:g.649232C>T	ENSP00000321706:p.Arg684Gln	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	28	0.622222	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	540	0.24725274725274726	162	0.32926829268292684	97	0.26795580110497236	171	0.29895104895104896	110	0.14511873350923482	C	0.022	-1.409509	0.01155	0.303807	0.126446	ENSG00000179409	ENST00000319004	T	0.05258	3.47	5.57	0.423	0.16463	.	0.981010	0.08322	N	0.963658	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.32425	0.371	B	0.23419	0.046	T	0.45833	-0.9234	9	0.14252	T	0.57	-1.6698	1.934	0.03333	0.4363:0.3151:0.1026:0.1461	rs3744741;rs56482056;rs59343482;rs3744741	684	P57678	GEMI4_HUMAN	Q	684	ENSP00000321706:R684Q	ENSP00000321706:R684Q	R	-	2	0	GEMIN4	595982	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	0.224000	0.17738	0.402000	0.25451	-1.114000	0.02060	CGA	C|0.765;T|0.235	0.235	strong		0.527	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
EVC2	132884	hgsc.bcm.edu	37	4	5624670	5624670	+	Missense_Mutation	SNP	T	T	C	rs730469	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:5624670T>C	ENST00000344408.5	-	14	2148	c.2095A>G	c.(2095-2097)Acg>Gcg	p.T699A	EVC2_ENST00000310917.2_Missense_Mutation_p.T619A|EVC2_ENST00000344938.1_Missense_Mutation_p.T699A	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	699			T -> A (in dbSNP:rs730469).		smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TCCTCAACCGTTCGGAAGGCC	0.632													C|||	2592	0.517572	0.8775	0.3963	5008	,	,		15234	0.62		0.2555	False		,,,				2504	0.2812				p.T699A		Atlas-SNP	.											EVC2,colon,carcinoma,+2,1	EVC2	202	1	0			c.A2095G						PASS	.	C	ALA/THR,ALA/THR	3407,999		1328,751,124	49.0	55.0	53.0		1855,2095	0.4	0.0	4	dbSNP_86	53	2393,6207		340,1713,2247	yes	missense,missense	EVC2	NM_001166136.1,NM_147127.4	58,58	1668,2464,2371	CC,CT,TT		27.8256,22.6736,44.5948	benign,benign	619/1229,699/1309	5624670	5800,7206	2203	4300	6503	SO:0001583	missense	132884	exon14			CAACCGTTCGGAA	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2095A>G	4.37:g.5624670T>C	ENSP00000342144:p.Thr699Ala	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	158	79	0.5	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	1097	0.5022893772893773	421	0.8556910569105691	141	0.38950276243093923	334	0.583916083916084	201	0.26517150395778366	C	0.004	-2.288290	0.00248	0.773264	0.278256	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.73897	-0.79;-0.78;-0.79	5.0	0.373	0.16178	.	0.802333	0.11785	N	0.529747	T	0.00012	0.0000	N	0.04297	-0.235	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39603	-0.9606	9	0.06757	T	0.87	-0.5273	1.4581	0.02390	0.1583:0.1958:0.1568:0.489	rs730469;rs58423551;rs730469	699	Q86UK5	LBN_HUMAN	A	699;619;699	ENSP00000339954:T699A;ENSP00000311683:T619A;ENSP00000342144:T699A	ENSP00000311683:T619A	T	-	1	0	EVC2	5675571	0.205000	0.23458	0.000000	0.03702	0.003000	0.03518	1.480000	0.35464	-0.092000	0.12417	-0.642000	0.03964	ACG	T|0.515;C|0.485	0.485	strong		0.632	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
PLCH1	23007	hgsc.bcm.edu	37	3	155199598	155199598	+	Missense_Mutation	SNP	C	C	T	rs150381264	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:155199598C>T	ENST00000340059.7	-	23	4240	c.4241G>A	c.(4240-4242)cGc>cAc	p.R1414H	PLCH1_ENST00000414191.1_Missense_Mutation_p.R1376H|PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000334686.6_Missense_Mutation_p.R1376H|PLCH1_ENST00000460012.1_Missense_Mutation_p.R1376H|PLCH1_ENST00000494598.1_Intron	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1414					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.R1376L(1)		NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GACAGAAGGGCGGAGGGTCTC	0.398													C|||	8	0.00159744	0.0008	0.0043	5008	,	,		20288	0.0		0.004	False		,,,				2504	0.0				p.R1414H		Atlas-SNP	.											PLCH1,NS,carcinoma,0,1	PLCH1	406	1	1	Substitution - Missense(1)	prostate(1)	c.G4241A						PASS	.	C	HIS/ARG,,HIS/ARG	8,4398	14.3+/-33.2	0,8,2195	89.0	91.0	90.0		4241,,4127	-5.8	0.0	3	dbSNP_134	90	28,8572	19.8+/-62.0	0,28,4272	yes	missense,utr-3,missense	PLCH1	NM_001130960.1,NM_001130961.1,NM_014996.2	29,,29	0,36,6467	TT,TC,CC		0.3256,0.1816,0.2768	benign,,benign	1414/1694,,1376/1656	155199598	36,12970	2203	4300	6503	SO:0001583	missense	23007	exon23			GAAGGGCGGAGGG	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.4241G>A	3.37:g.155199598C>T	ENSP00000345988:p.Arg1414His	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	197	93	0.472081	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	0.170	-1.072366	0.01918	0.001816	0.003256	ENSG00000114805	ENST00000460012;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88	5.32	-5.8	0.02347	.	2.124280	0.01545	N	0.019395	T	0.35624	0.0938	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33471	-0.9867	10	0.13470	T	0.59	.	1.5657	0.02604	0.1272:0.2019:0.3066:0.3643	.	1376;1414	Q4KWH8-2;Q4KWH8	.;PLCH1_HUMAN	H	1376;1414;1376;1376	ENSP00000417502:R1376H;ENSP00000345988:R1414H;ENSP00000335469:R1376H;ENSP00000412977:R1376H	ENSP00000335469:R1376H	R	-	2	0	PLCH1	156682292	0.000000	0.05858	0.000000	0.03702	0.191000	0.23601	-0.326000	0.07965	-0.784000	0.04528	-0.385000	0.06624	CGC	C|0.997;T|0.003	0.003	strong		0.398	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
ZNF99	7652	hgsc.bcm.edu	37	19	22941191	22941191	+	Missense_Mutation	SNP	T	T	A	rs11667397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:22941191T>A	ENST00000596209.1	-	4	1610	c.1520A>T	c.(1519-1521)aAa>aTa	p.K507I	ZNF99_ENST00000397104.3_Missense_Mutation_p.K416I	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	507					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTTGCAAGGTTTCTCTTCCAT	0.348													T|||	749	0.149561	0.118	0.1931	5008	,	,		19973	0.1716		0.1421	False		,,,				2504	0.1462				p.K507I		Atlas-SNP	.											.	ZNF99	273	.	0			c.A1520T						PASS	.	T	ILE/LYS	504,3640		26,452,1594	43.0	45.0	44.0		1247	-0.1	0.0	19	dbSNP_120	44	1372,7068		93,1186,2941	no	missense	ZNF99	NM_001080409.2	102	119,1638,4535	AA,AT,TT		16.2559,12.1622,14.9078	probably-damaging	416/912	22941191	1876,10708	2072	4220	6292	SO:0001583	missense	7652	exon4			CAAGGTTTCTCTT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1520A>T	19.37:g.22941191T>A	ENSP00000472969:p.Lys507Ile	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	344	0.1575091575091575	62	0.12601626016260162	65	0.17955801104972377	103	0.18006993006993008	114	0.1503957783641161	-	11.30	1.596585	0.28445	0.121622	0.162559	ENSG00000213973	ENST00000397104	T	0.33654	1.4	1.16	-0.143	0.13444	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00144	0.0004	H	0.94734	3.575	0.39932	P	0.025704999999999978	P	0.45902	0.868	P	0.46452	0.517	T	0.04115	-1.0976	8	0.87932	D	0	.	5.0822	0.14663	0.0:0.1911:0.0:0.8089	rs11667397;rs35159026	416	A8MXY4	ZNF99_HUMAN	I	416	ENSP00000380293:K416I	ENSP00000380293:K416I	K	-	2	0	ZNF99	22733031	0.001000	0.12720	0.004000	0.12327	0.075000	0.17131	-0.278000	0.08490	-0.345000	0.08325	0.163000	0.16589	AAA	T|0.834;A|0.166	0.166	strong		0.348	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
PCDHGB6	56100	hgsc.bcm.edu	37	5	140787850	140787850	+	Silent	SNP	C	C	G	rs62378453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140787850C>G	ENST00000520790.1	+	1	81	c.81C>G	c.(79-81)ccC>ccG	p.P27P	PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA9_ENST00000573521.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	27					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P27P(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTTCTACCCCACCCTGAGTG	0.647											OREG0016861	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	506	0.101038	0.2065	0.0576	5008	,	,		15227	0.0407		0.0815	False		,,,				2504	0.0716				p.P27P		Atlas-SNP	.											PCDHGB6,NS,carcinoma,0,1	PCDHGB6	120	1	1	Substitution - coding silent(1)	stomach(1)	c.C81G						PASS	.	C	,,,,,,,,,,,,,,,	682,3112		59,564,1274	37.0	40.0	39.0		,,,,,,,,,,,,,81,,81	2.4	1.0	5	dbSNP_129	39	741,7503		32,677,3413	no	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032100.1	,,,,,,,,,,,,,,,	91,1241,4687	GG,GC,CC		8.9884,17.9758,11.8209	,,,,,,,,,,,,,,,	,,,,,,,,,,,,,27/931,,27/821	140787850	1423,10615	1897	4122	6019	SO:0001819	synonymous_variant	56100	exon1			CTACCCCACCCTG	AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"""Cadherins / Protocadherins : Clustered"""	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.81C>G	5.37:g.140787850C>G		Somatic	186	0	0	1659	WXS	Illumina HiSeq	Phase_I	211	95	0.450237	NM_032100	Q9Y5C5	Silent	SNP	ENST00000520790.1	37	CCDS54929.1																																																																																			C|0.906;G|0.094	0.094	strong		0.647	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926	
WASL	8976	hgsc.bcm.edu	37	7	123349251	123349251	+	Silent	SNP	T	T	C	rs3195229	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:123349251T>C	ENST00000223023.4	-	2	476	c.144A>G	c.(142-144)ttA>ttG	p.L48L		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	48	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTGCTGCATATAACTGCACCA	0.368													T|||	4	0.000798722	0.0	0.0014	5008	,	,		16453	0.0		0.002	False		,,,				2504	0.001				p.L48L		Atlas-SNP	.											.	WASL	70	.	0			c.A144G						PASS	.	T		5,4401	11.4+/-27.6	0,5,2198	76.0	70.0	72.0		144	1.8	1.0	7	dbSNP_105	72	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous	WASL	NM_003941.2		0,39,6464	CC,CT,TT		0.3953,0.1135,0.2999		48/506	123349251	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	8976	exon2			TGCATATAACTGC	D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.144A>G	7.37:g.123349251T>C		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	322	143	0.444099	NM_003941	A1JUI9|Q7Z746	Silent	SNP	ENST00000223023.4	37	CCDS34743.1																																																																																			T|0.998;C|0.002	0.002	strong		0.368	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941	
SPPL2C	162540	hgsc.bcm.edu	37	17	43924231	43924231	+	Silent	SNP	G	G	A	rs12373140	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43924231G>A	ENST00000329196.5	+	1	1976	c.1959G>A	c.(1957-1959)caG>caA	p.Q653Q	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	653						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										TCCATGCCCAGGCCCAGGCCC	0.627													G|||	431	0.0860623	0.0151	0.1571	5008	,	,		18478	0.001		0.2396	False		,,,				2504	0.0613				p.Q653Q		Atlas-SNP	.											.	.	.	.	0			c.G1959A						PASS	.	G		202,4204	120.0+/-157.7	5,192,2006	35.0	37.0	37.0		1959	3.0	0.9	17	dbSNP_120	37	1921,6679	320.1+/-314.5	221,1479,2600	no	coding-synonymous	IMP5	NM_175882.2		226,1671,4606	AA,AG,GG		22.3372,4.5847,16.3232		653/685	43924231	2123,10883	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			TGCCCAGGCCCAG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1959G>A	17.37:g.43924231G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			C|0.852;T|0.148	.	strong		0.627	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
KLHDC8A	55220	hgsc.bcm.edu	37	1	205308335	205308335	+	Silent	SNP	G	G	A	rs1105385	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:205308335G>A	ENST00000367156.3	-	7	1560	c.744C>T	c.(742-744)ttC>ttT	p.F248F	KLHDC8A_ENST00000539253.1_Silent_p.F248F|KLHDC8A_ENST00000367155.3_Silent_p.F248F|KLHDC8A_ENST00000537168.1_Silent_p.F135F|KLHDC8A_ENST00000460687.1_Silent_p.F114F	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	248										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GTTCCATGTCGAACACGTCCA	0.612													G|||	918	0.183307	0.2247	0.1354	5008	,	,		18148	0.0317		0.2942	False		,,,				2504	0.2035				p.F248F		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.C744T						PASS	.	G		987,3419	369.1+/-318.9	109,769,1325	47.0	41.0	43.0		744	-6.8	0.8	1	dbSNP_86	43	2613,5987	420.9+/-353.5	364,1885,2051	no	coding-synonymous	KLHDC8A	NM_018203.1		473,2654,3376	AA,AG,GG		30.3837,22.4013,27.6795		248/351	205308335	3600,9406	2203	4300	6503	SO:0001819	synonymous_variant	55220	exon4			CATGTCGAACACG		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.744C>T	1.37:g.205308335G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_018203	B3KU70|Q9NVG5	Silent	SNP	ENST00000367156.3	37	CCDS30985.1																																																																																			A|0.232;C|0.004	0.232	strong		0.612	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203	
CDH15	1013	hgsc.bcm.edu	37	16	89245890	89245890	+	Missense_Mutation	SNP	G	G	T	rs2287359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89245890G>T	ENST00000289746.2	+	2	174	c.109G>T	c.(109-111)Gcg>Tcg	p.A37S	CDH15_ENST00000521087.1_3'UTR	NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	37					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		CTGGCGCCGGGCGCCTGCCCT	0.657													G|||	845	0.16873	0.0461	0.0677	5008	,	,		15134	0.4444		0.0567	False		,,,				2504	0.2372				p.A37S		Atlas-SNP	.											.	CDH15	54	.	0			c.G109T						PASS	.	G	SER/ALA	222,4174	132.9+/-169.3	4,214,1980	83.0	82.0	82.0		109	-9.1	0.0	16	dbSNP_100	82	543,8057	149.5+/-204.6	13,517,3770	no	missense	CDH15	NM_004933.2	99	17,731,5750	TT,TG,GG		6.314,5.05,5.8864	benign	37/815	89245890	765,12231	2198	4300	6498	SO:0001583	missense	1013	exon2			CGCCGGGCGCCTG	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"""Cadherins / Major cadherins"""	1754	protein-coding gene	gene with protein product		114019	"""cadherin 15, M-cadherin (myotubule)"""	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.109G>T	16.37:g.89245890G>T	ENSP00000289746:p.Ala37Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	143	80	0.559441	NM_004933		Missense_Mutation	SNP	ENST00000289746.2	37	CCDS10976.1	347	0.15888278388278387	33	0.06707317073170732	26	0.0718232044198895	246	0.43006993006993005	42	0.055408970976253295	G	5.716	0.316650	0.10845	0.0505	0.06314	ENSG00000129910	ENST00000289746	T	0.56103	0.48	4.58	-9.15	0.00698	.	0.762345	0.11336	N	0.574538	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.12630	0.006	B	0.10450	0.005	T	0.30909	-0.9962	9	0.02654	T	1	.	9.8338	0.40958	0.264:0.5899:0.146:0.0	rs2287359	37	P55291	CAD15_HUMAN	S	37	ENSP00000289746:A37S	ENSP00000289746:A37S	A	+	1	0	CDH15	87773391	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-0.447000	0.06828	-1.239000	0.02532	-0.693000	0.03709	GCG	G|0.915;T|0.085	0.085	strong		0.657	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933	
SIGLEC11	114132	hgsc.bcm.edu	37	19	50462298	50462298	+	Missense_Mutation	SNP	G	G	C	rs62113133	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50462298G>C	ENST00000447370.2	-	6	1184	c.1094C>G	c.(1093-1095)gCa>gGa	p.A365G	CTC-326K19.6_ENST00000451973.1_5'Flank|SIGLEC11_ENST00000426971.2_Missense_Mutation_p.A365G	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	365	Ig-like C2-type 3.			A -> G (in Ref. 3; AAQ88502). {ECO:0000305}.	cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		TGTCCTGTTTGCTTGGGAAAC	0.587													G|||	1017	0.203075	0.1006	0.196	5008	,	,		17088	0.255		0.2416	False		,,,				2504	0.2536				p.A365G		Atlas-SNP	.											.	SIGLEC11	70	.	0			c.C1094G						PASS	.						75.0	77.0	76.0					19																	50462298		2203	4297	6500	SO:0001583	missense	114132	exon6			CTGTTTGCTTGGG	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.1094C>G	19.37:g.50462298G>C	ENSP00000412361:p.Ala365Gly	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	143	49	0.342657	NM_052884		Missense_Mutation	SNP	ENST00000447370.2	37	CCDS12790.2	462|462	0.21153846153846154|0.21153846153846154	49|49	0.09959349593495935|0.09959349593495935	84|84	0.23204419889502761|0.23204419889502761	147|147	0.256993006993007|0.256993006993007	182|182	0.24010554089709762|0.24010554089709762	G|G	11.88|11.88	1.770505|1.770505	0.31320|0.31320	.|.	.|.	ENSG00000161640|ENSG00000161640	ENST00000447370;ENST00000458019|ENST00000426971	T|.	0.55052|.	0.54|.	2.52|2.52	-1.51|-1.51	0.08664|0.08664	Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.896444|.	0.09326|.	N|.	0.817572|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.16016|0.16016	0.355|0.355	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.27013|.	0.166;0.125|.	B;B|.	0.33750|.	0.169;0.143|.	T|T	0.40308|0.40308	-0.9570|-0.9570	9|4	0.13853|.	T|.	0.58|.	.|.	2.9208|2.9208	0.05768|0.05768	0.158:0.0:0.3593:0.4827|0.158:0.0:0.3593:0.4827	rs62113133|rs62113133	365;365|.	Q96RL6-2;Q96RL6|.	.;SIG11_HUMAN|.	G|E	365|355	ENSP00000412361:A365G|.	ENSP00000412361:A365G|.	A|Q	-|-	2|1	0|0	SIGLEC11|SIGLEC11	55154110|55154110	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.933000|0.933000	0.57130|0.57130	-0.724000|-0.724000	0.04947|0.04947	-0.090000|-0.090000	0.12462|0.12462	0.556000|0.556000	0.70494|0.70494	GCA|CAA	G|0.826;C|0.174	0.174	strong		0.587	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884	
TRIOBP	11078	hgsc.bcm.edu	37	22	38120343	38120343	+	Missense_Mutation	SNP	A	A	G	rs71317067		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38120343A>G	ENST00000406386.3	+	7	2035	c.1780A>G	c.(1780-1782)Aca>Gca	p.T594A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	594					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.T594A(5)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAATAGAGCTACACGAGACAA	0.572																																					p.T594A		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,5	TRIOBP	262	5	5	Substitution - Missense(5)	skin(2)|large_intestine(1)|NS(1)|prostate(1)	c.A1780G						scavenged	.						112.0	164.0	147.0					22																	38120343		1955	4165	6120	SO:0001583	missense	11078	exon7			AGAGCTACACGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1780A>G	22.37:g.38120343A>G	ENSP00000384312:p.Thr594Ala	Somatic	302	7	0.0231788		WXS	Illumina HiSeq	Phase_I	450	16	0.0355556	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	-	7.079	0.569772	0.13560	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.20738	2.05	2.6	0.164	0.14990	.	.	.	.	.	T	0.11879	0.0289	L	0.28115	0.83	0.09310	N	0.999998	B	0.21381	0.055	B	0.12837	0.008	T	0.32745	-0.9895	9	0.26408	T	0.33	.	5.3198	0.15876	0.5376:0.0:0.0:0.4624	.	594	Q9H2D6	TARA_HUMAN	A	594	ENSP00000384312:T594A	ENSP00000384312:T594A	T	+	1	0	TRIOBP	36450289	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.521000	0.06245	-0.162000	0.10964	-1.765000	0.00666	ACA	A|0.500;G|0.500	0.500	weak		0.572	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
CLCA1	1179	hgsc.bcm.edu	37	1	86961245	86961245	+	Missense_Mutation	SNP	C	C	T	rs150256560		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:86961245C>T	ENST00000234701.3	+	13	2351	c.2000C>T	c.(1999-2001)aCg>aTg	p.T667M	CLCA1_ENST00000394711.1_Missense_Mutation_p.T667M			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	667					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		ACTTATGACACGAATGGTAGA	0.468													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20832	0.0		0.0	False		,,,				2504	0.0				p.T667M		Atlas-SNP	.											CLCA1,NS,carcinoma,0,1	CLCA1	109	1	0			c.C2000T						scavenged	.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	105.0	101.0	102.0		2000	2.4	0.9	1	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CLCA1	NM_001285.3	81	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging	667/915	86961245	2,13004	2203	4300	6503	SO:0001583	missense	1179	exon12			ATGACACGAATGG		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"""chloride channel, calcium activated, family member 1"", ""chloride channel regulator 1"""			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.2000C>T	1.37:g.86961245C>T	ENSP00000234701:p.Thr667Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	156	3	0.0192308	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	37	CCDS709.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.55	2.270723	0.40194	2.27E-4	1.16E-4	ENSG00000016490	ENST00000234701;ENST00000394711	T;T	0.02890	4.12;4.12	5.69	2.43	0.29744	.	0.776603	0.12300	N	0.481207	T	0.01254	0.0041	L	0.54323	1.7	0.09310	N	0.999999	P	0.43701	0.815	B	0.40782	0.34	T	0.48896	-0.8994	10	0.49607	T	0.09	-0.7528	2.935	0.05811	0.2989:0.3344:0.2831:0.0836	.	667	A8K7I4	CLCA1_HUMAN	M	667	ENSP00000234701:T667M;ENSP00000378200:T667M	ENSP00000234701:T667M	T	+	2	0	CLCA1	86733833	0.001000	0.12720	0.856000	0.33681	0.906000	0.53458	0.288000	0.18939	1.363000	0.46019	0.655000	0.94253	ACG	C|1.000;T|0.000	0.000	strong		0.468	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103052558	103052558	+	Silent	SNP	T	T	C	rs11225584	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:103052558T>C	ENST00000375735.2	+	40	6564	c.6420T>C	c.(6418-6420)aaT>aaC	p.N2140N	DYNC2H1_ENST00000398093.3_Silent_p.N2140N|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2140	AAA 2. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		ATAGAAATAATCTTGAAAATT	0.299													T|||	672	0.134185	0.0726	0.0922	5008	,	,		15505	0.2312		0.1123	False		,,,				2504	0.1697				p.N2140N		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T6420C						PASS	.	T	,	268,3292		12,244,1524	30.0	30.0	30.0		6420,6420	4.3	1.0	11	dbSNP_120	30	861,7229		55,751,3239	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	67,995,4763	CC,CT,TT		10.6428,7.5281,9.691	,	2140/4315,2140/4308	103052558	1129,10521	1780	4045	5825	SO:0001819	synonymous_variant	79659	exon40			AAATAATCTTGAA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.6420T>C	11.37:g.103052558T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			T|0.871;C|0.129	0.129	strong		0.299	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37499386	37499386	+	Silent	SNP	C	C	T	rs11704654	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:37499386C>T	ENST00000346753.3	-	2	215	c.99G>A	c.(97-99)ccG>ccA	p.P33P	TMPRSS6_ENST00000406725.1_Silent_p.P24P|TMPRSS6_ENST00000381792.2_Silent_p.P24P|TMPRSS6_ENST00000442782.2_Silent_p.P33P|TMPRSS6_ENST00000406856.1_Silent_p.P24P	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	33					angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						ACATCCCCTCCGGCTCCGCTT	0.662													C|||	759	0.151558	0.1528	0.1124	5008	,	,		17102	0.131		0.1879	False		,,,				2504	0.1616				p.P33P		Atlas-SNP	.											TMPRSS6,NS,carcinoma,-2,2	TMPRSS6	99	2	0			c.G99A						PASS	.	C		653,3753	276.6+/-273.2	45,563,1595	87.0	94.0	91.0		99	-8.1	0.8	22	dbSNP_120	91	1671,6929	307.4+/-308.4	164,1343,2793	no	coding-synonymous	TMPRSS6	NM_153609.2		209,1906,4388	TT,TC,CC		19.4302,14.8207,17.8687		33/812	37499386	2324,10682	2203	4300	6503	SO:0001819	synonymous_variant	164656	exon2			CCCCTCCGGCTCC	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.99G>A	22.37:g.37499386C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	37	CCDS13941.1																																																																																			C|0.825;T|0.175	0.175	strong		0.662	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
ITGAX	3687	hgsc.bcm.edu	37	16	31367318	31367318	+	Splice_Site	SNP	T	T	C	rs2230424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31367318T>C	ENST00000268296.4	+	2	263	c.142T>C	c.(142-144)Tgg>Cgg	p.W48R	ITGAX_ENST00000562522.1_Splice_Site_p.W48R|ITGAX_ENST00000562918.1_3'UTR	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	48			W -> R (in dbSNP:rs2230424).		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						TGCCAACTCCTGGTGAGGCCC	0.592													T|||	178	0.0355431	0.0098	0.0403	5008	,	,		17148	0.0		0.1193	False		,,,				2504	0.0174				p.W48R		Atlas-SNP	.											.	ITGAX	198	.	0			c.T142C						PASS	.	T	ARG/TRP	109,4285	84.8+/-123.5	4,101,2092	96.0	92.0	93.0		142	-2.8	0.2	16	dbSNP_98	93	1203,7397	244.7+/-273.8	83,1037,3180	yes	missense-near-splice	ITGAX	NM_000887.3	101	87,1138,5272	CC,CT,TT		13.9884,2.4807,10.097	benign	48/1164	31367318	1312,11682	2197	4300	6497	SO:0001630	splice_region_variant	3687	exon2			AACTCCTGGTGAG	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.143+1T>C	16.37:g.31367318T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	110	0.05036630036630037	5	0.01016260162601626	16	0.04419889502762431	0	0.0	89	0.11741424802110818	T	5.021	0.189531	0.09547	0.024807	0.139884	ENSG00000140678	ENST00000268296	T	0.71461	-0.57	4.33	-2.77	0.05877	.	.	.	.	.	T	0.00356	0.0011	N	0.10645	0.015	0.50632	P	1.1499999999997623E-4	B;B	0.17465	0.022;0.006	B;B	0.15484	0.013;0.003	T	0.04885	-1.0920	8	0.14656	T	0.56	.	5.054	0.14524	0.6206:0.0972:0.0:0.2822	rs2230424;rs11574633;rs52822365;rs11574633	48;48	B4DKQ1;P20702	.;ITAX_HUMAN	R	48	ENSP00000268296:W48R	ENSP00000268296:W48R	W	+	1	0	ITGAX	31274819	0.045000	0.20229	0.197000	0.23402	0.706000	0.40770	-0.013000	0.12678	-0.379000	0.07906	0.397000	0.26171	TGG	T|0.924;C|0.076	0.076	strong		0.592	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	Missense_Mutation
APOB	338	hgsc.bcm.edu	37	2	21231524	21231524	+	Missense_Mutation	SNP	G	G	A	rs676210	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:21231524G>A	ENST00000233242.1	-	26	8343	c.8216C>T	c.(8215-8217)cCa>cTa	p.P2739L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2739			P -> L (in dbSNP:rs676210). {ECO:0000269|PubMed:22095935, ECO:0000269|PubMed:2216805, ECO:0000269|PubMed:9490296}.		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGGAATTCTGGTATGTGAAG	0.398													G|||	1834	0.366214	0.1241	0.2493	5008	,	,		21164	0.7192		0.2177	False		,,,				2504	0.5654				p.P2739L		Atlas-SNP	.											.	APOB	761	.	0			c.C8216T	GRCh37	CM980093	APOB	M	rs676210	PASS	.	G	LEU/PRO	694,3712	289.5+/-280.5	52,590,1561	185.0	186.0	186.0		8216	5.2	1.0	2	dbSNP_83	186	1862,6738	331.8+/-319.8	227,1408,2665	yes	missense	APOB	NM_000384.2	98	279,1998,4226	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	21.6512,15.7512,19.6525	probably-damaging	2739/4564	21231524	2556,10450	2203	4300	6503	SO:0001583	missense	338	exon26			AATTCTGGTATGT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8216C>T	2.37:g.21231524G>A	ENSP00000233242:p.Pro2739Leu	Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	323	149	0.4613	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	737	0.3374542124542125	77	0.1565040650406504	79	0.21823204419889503	406	0.7097902097902098	175	0.23087071240105542	G	24.9	4.580663	0.86748	0.157512	0.216512	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01185	5.21	5.22	5.22	0.72569	.	0.000000	0.52532	D	0.000061	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.08597	-1.0714	9	0.87932	D	0	.	18.7715	0.91893	0.0:0.0:1.0:0.0	rs676210;rs17240903;rs52830519;rs60113879;rs676210	2739	P04114	APOB_HUMAN	L	2739	ENSP00000233242:P2739L	ENSP00000233242:P2739L	P	-	2	0	APOB	21085029	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.803000	0.99136	2.437000	0.82529	0.561000	0.74099	CCA	G|0.731;A|0.269	0.269	strong		0.398	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
MUC6	4588	hgsc.bcm.edu	37	11	1017773	1017773	+	Silent	SNP	G	G	A	rs57384288	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1017773G>A	ENST00000421673.2	-	31	5078	c.5028C>T	c.(5026-5028)agC>agT	p.S1676S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1676	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.S1676S(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGCTGGTCCCGCTGGTGGTCA	0.557													A|||	1486	0.296725	0.3298	0.1542	5008	,	,		31162	0.3165		0.2505	False		,,,				2504	0.3804				p.S1676S		Atlas-SNP	.											MUC6,NS,carcinoma,0,1	MUC6	408	1	1	Substitution - coding silent(1)	ovary(1)	c.C5028T						scavenged	.						688.0	686.0	687.0					11																	1017773		2198	4294	6492	SO:0001819	synonymous_variant	4588	exon31			GGTCCCGCTGGTG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5028C>T	11.37:g.1017773G>A		Somatic	577	34	0.0589255		WXS	Illumina HiSeq	Phase_I	837	146	0.174433	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			G|0.500;A|0.500	0.500	strong		0.557	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
CHAT	1103	hgsc.bcm.edu	37	10	50830171	50830171	+	Missense_Mutation	SNP	C	C	T	rs8178990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50830171C>T	ENST00000337653.2	+	5	880	c.727C>T	c.(727-729)Ctc>Ttc	p.L243F	CHAT_ENST00000455728.2_Missense_Mutation_p.L125F|CHAT_ENST00000395559.2_Missense_Mutation_p.L125F|CHAT_ENST00000460699.1_3'UTR|CHAT_ENST00000351556.3_Missense_Mutation_p.L125F|CHAT_ENST00000395562.2_Missense_Mutation_p.L161F|CHAT_ENST00000339797.1_Missense_Mutation_p.L125F	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	243			L -> F (in dbSNP:rs8178990).		adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	CTCTGGTGTACTCAGCTACAA	0.622													C|||	126	0.0251597	0.0015	0.0202	5008	,	,		15265	0.0		0.0944	False		,,,				2504	0.0153				p.L243F		Atlas-SNP	.											.	CHAT	162	.	0			c.C727T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	49,4357	50.2+/-85.5	1,47,2155	216.0	167.0	184.0		373,481,373,727,373,373,373	4.7	1.0	10	dbSNP_117	184	546,8054	150.3+/-205.2	29,488,3783	yes	missense,missense,missense,missense,missense,missense,missense	CHAT	NM_001142929.1,NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3,NM_020985.3,NM_020986.3	22,22,22,22,22,22,22	30,535,5938	TT,TC,CC		6.3488,1.1121,4.5748	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	125/631,161/667,125/631,243/749,125/631,125/631,125/631	50830171	595,12411	2203	4300	6503	SO:0001583	missense	1103	exon5			GGTGTACTCAGCT	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.727C>T	10.37:g.50830171C>T	ENSP00000337103:p.Leu243Phe	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	80	46	0.575	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	80	0.03663003663003663	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	72	0.09498680738786279	C	21.3	4.121133	0.77436	0.011121	0.063488	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	D;D;D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76;-2.76;-2.76	4.74	4.74	0.60224	.	0.245457	0.35096	N	0.003446	T	0.58104	0.2099	M	0.84156	2.68	0.43688	D	0.996133	P;D	0.67145	0.858;0.996	P;D	0.74348	0.637;0.983	T	0.76542	-0.2921	10	0.87932	D	0	-13.929	17.7116	0.88323	0.0:1.0:0.0:0.0	rs8178990;rs61678759;rs8178990	125;243	F8W8I2;P28329	.;CLAT_HUMAN	F	125;125;125;243;161;125	ENSP00000343486:L125F;ENSP00000345878:L125F;ENSP00000378926:L125F;ENSP00000337103:L243F;ENSP00000378929:L161F;ENSP00000390521:L125F	ENSP00000337103:L243F	L	+	1	0	CHAT	50500177	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.979000	0.56888	2.161000	0.67846	0.561000	0.74099	CTC	C|0.955;T|0.045	0.045	strong		0.622	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100820663	100820663	+	Missense_Mutation	SNP	G	G	A	rs17647207	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:100820663G>A	ENST00000298815.8	+	12	1141	c.1138G>A	c.(1138-1140)Gcc>Acc	p.A380T	ARHGAP42_ENST00000524892.2_Missense_Mutation_p.A346T	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	380	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TACTCTGCCTGCCATTATAAG	0.294													G|||	156	0.0311502	0.0023	0.0346	5008	,	,		15251	0.0		0.0994	False		,,,				2504	0.0297				p.A380T		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.G1138A						PASS	.	G	THR/ALA	30,1354		4,22,666	140.0	138.0	139.0		1138	5.2	1.0	11	dbSNP_123	139	304,2878		18,268,1305	yes	missense	ARHGAP42	NM_152432.2	58	22,290,1971	AA,AG,GG		9.5537,2.1676,7.3149	benign	380/875	100820663	334,4232	692	1591	2283	SO:0001583	missense	143872	exon12			CTGCCTGCCATTA			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.1138G>A	11.37:g.100820663G>A	ENSP00000298815:p.Ala380Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_152432	Q96M56	Missense_Mutation	SNP	ENST00000298815.8	37		91	0.041666666666666664	1	0.0020325203252032522	15	0.04143646408839779	0	0.0	75	0.09894459102902374	G	16.75	3.209747	0.58343	0.021676	0.095537	ENSG00000165895	ENST00000524892;ENST00000298815	T;T	0.07114	3.22;3.31	5.23	5.23	0.72850	Rho GTPase-activating protein domain (1);	1.291020	0.06034	N	0.653550	T	0.00300	0.0009	L	0.33485	1.01	0.09310	P	0.999999897393	B	0.16396	0.017	B	0.20184	0.028	T	0.28138	-1.0053	9	0.25106	T	0.35	.	16.6609	0.85240	0.0:0.0:1.0:0.0	rs17647207;rs52820744;rs60330976;rs17647207	380	A6NI28	RHG42_HUMAN	T	346;380	ENSP00000431776:A346T;ENSP00000298815:A380T	ENSP00000298815:A380T	A	+	1	0	ARHGAP42	100325873	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.371000	0.73119	2.596000	0.87737	0.491000	0.48974	GCC	G|0.949;A|0.051	0.051	strong		0.294	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
ABCA13	154664	hgsc.bcm.edu	37	7	48559696	48559696	+	Silent	SNP	T	T	C	rs61378229	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:48559696T>C	ENST00000435803.1	+	53	13881	c.13857T>C	c.(13855-13857)tgT>tgC	p.C4619C	ABCA13_ENST00000544596.1_Silent_p.C349C	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4619					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTCAATTCTGTCTTGGTCAAG	0.363													C|||	430	0.0858626	0.1793	0.0375	5008	,	,		19047	0.003		0.0308	False		,,,				2504	0.136				p.C4619C		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T13857C						PASS	.	C		592,3118		46,500,1309	119.0	108.0	111.0		13857	2.5	1.0	7	dbSNP_129	111	322,7860		6,310,3775	no	coding-synonymous	ABCA13	NM_152701.3		52,810,5084	CC,CT,TT		3.9355,15.9569,7.6858		4619/5059	48559696	914,10978	1855	4091	5946	SO:0001819	synonymous_variant	154664	exon53			ATTCTGTCTTGGT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.13857T>C	7.37:g.48559696T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	156	73	0.467949	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1	119	0.05448717948717949	79	0.16056910569105692	14	0.03867403314917127	2	0.0034965034965034965	24	0.0316622691292876	C	9.441	1.088018	0.20390	0.159569	0.039355	ENSG00000179869	ENST00000435451	.	.	.	5.35	2.45	0.29901	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	P	0.9999999999976537	.	.	.	.	.	.	T	0.08269	-1.0730	3	.	.	.	.	7.7027	0.28632	0.0:0.6482:0.0:0.3518	rs61378229;rs62447310	.	.	.	P	140	.	.	S	+	1	0	ABCA13	48530242	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	0.908000	0.28545	-0.017000	0.14103	-0.755000	0.03482	TCT	T|0.945;C|0.055	0.055	strong		0.363	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
FLNB	2317	hgsc.bcm.edu	37	3	58112488	58112488	+	Splice_Site	SNP	C	C	T	rs2362904	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:58112488C>T	ENST00000295956.4	+	24	4386	c.4221C>T	c.(4219-4221)ccC>ccT	p.P1407P	FLNB_ENST00000490882.1_Splice_Site_p.P1407P|FLNB_ENST00000358537.3_Splice_Site_p.P1407P|FLNB_ENST00000493452.1_Splice_Site_p.P1238P|FLNB_ENST00000348383.5_Splice_Site_p.P1407P|FLNB_ENST00000419752.2_Splice_Site_p.P1238P|FLNB_ENST00000429972.2_Splice_Site_p.P1407P|FLNB_ENST00000357272.4_Splice_Site_p.P1407P	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1407	Interaction with FBLP1.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CCCACATCCCCGGTGAGCTAT	0.458													T|||	3248	0.648562	0.7852	0.4942	5008	,	,		19177	0.9712		0.2833	False		,,,				2504	0.6166				p.P1407P		Atlas-SNP	.											.	FLNB	430	.	0			c.C4221T						PASS	.	T	,,,	3123,1283	436.4+/-344.6	1098,927,178	50.0	51.0	50.0		4221,4221,4221,4221	3.5	1.0	3	dbSNP_100	50	2111,6489	715.9+/-406.1	268,1575,2457	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	1366,2502,2635	TT,TC,CC		24.5465,29.1194,40.243	,,,	1407/2634,1407/2592,1407/2579,1407/2603	58112488	5234,7772	2203	4300	6503	SO:0001630	splice_region_variant	2317	exon24			CATCCCCGGTGAG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.4222+1C>T	3.37:g.58112488C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	130	71	0.546154	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																			C|0.489;T|0.511	0.511	strong		0.458	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	Silent
PPFIA4	8497	hgsc.bcm.edu	37	1	203028371	203028371	+	Missense_Mutation	SNP	G	G	T	rs61732315	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:203028371G>T	ENST00000447715.2	+	25	2848	c.2407G>T	c.(2407-2409)Gca>Tca	p.A803S	PPFIA4_ENST00000414050.2_Missense_Mutation_p.A532S|PPFIA4_ENST00000367240.2_Missense_Mutation_p.A804S|PPFIA4_ENST00000295706.4_Missense_Mutation_p.A319S|PPFIA4_ENST00000599966.1_Missense_Mutation_p.A319S|PPFIA4_ENST00000272198.6_Missense_Mutation_p.A319S			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	803				A -> S (in Ref. 3; AAI44263). {ECO:0000305}.	cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						GGGGACCCAGGCAGAGAAGGA	0.602													G|||	610	0.121805	0.0129	0.1196	5008	,	,		18586	0.1577		0.1759	False		,,,				2504	0.1779				p.A319S		Atlas-SNP	.											.	PPFIA4	139	.	0			c.G955T						PASS	.	G	SER/ALA	150,3658		5,140,1759	18.0	20.0	19.0		955	4.8	1.0	1	dbSNP_129	19	1379,6841		122,1135,2853	yes	missense	PPFIA4	NM_015053.1	99	127,1275,4612	TT,TG,GG		16.7762,3.9391,12.712	possibly-damaging	319/702	203028371	1529,10499	1904	4110	6014	SO:0001583	missense	8497	exon7			ACCCAGGCAGAGA	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2407G>T	1.37:g.203028371G>T	ENSP00000402576:p.Ala803Ser	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	240	237	0.9875	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		257	0.11767399267399267	11	0.022357723577235773	37	0.10220994475138122	68	0.11888111888111888	141	0.18601583113456466	G	19.80	3.894080	0.72639	0.039391	0.167762	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.25085	2.17;1.85;1.82;1.84;1.82	4.83	4.83	0.62350	.	0.000000	0.45126	D	0.000395	T	0.00073	0.0002	M	0.66939	2.045	0.09310	P	0.999999060264	B;B;P;P	0.48089	0.011;0.011;0.905;0.665	B;B;P;P	0.57720	0.01;0.054;0.826;0.563	T	0.02417	-1.1162	9	0.48119	T	0.1	-10.7022	11.5666	0.50809	0.0813:0.0:0.9187:0.0	rs61732315	803;14;319;319	B1N949;B3KN22;O75335-2;O75335	.;.;.;LIPA4_HUMAN	S	804;803;319;532;319	ENSP00000356209:A804S;ENSP00000402576:A803S;ENSP00000295706:A319S;ENSP00000400379:A532S;ENSP00000272198:A319S	ENSP00000272198:A319S	A	+	1	0	PPFIA4	201294994	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.834000	0.86773	2.495000	0.84180	0.462000	0.41574	GCA	G|0.878;T|0.122	0.122	strong		0.602	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
DNAH3	55567	hgsc.bcm.edu	37	16	21008690	21008690	+	Silent	SNP	T	T	C	rs3115446	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:21008690T>C	ENST00000261383.3	-	44	6515	c.6516A>G	c.(6514-6516)aaA>aaG	p.K2172K	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2172	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TTGTGTCTTTTTTGTCAAACC	0.562													C|||	2705	0.540136	0.5976	0.5259	5008	,	,		20850	0.4851		0.4543	False		,,,				2504	0.6176				p.K2172K		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A6516G						PASS	.	C		2605,1797	528.4+/-372.4	773,1059,369	128.0	118.0	122.0		6516	2.2	1.0	16	dbSNP_103	122	3841,4759	609.9+/-395.6	857,2127,1316	no	coding-synonymous	DNAH3	NM_017539.1		1630,3186,1685	CC,CT,TT		44.6628,40.8224,49.577		2172/4117	21008690	6446,6556	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon44			GTCTTTTTTGTCA	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.6516A>G	16.37:g.21008690T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	180	92	0.511111	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			C|0.498;N|0.000	0.498	strong		0.562	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
COL14A1	7373	hgsc.bcm.edu	37	8	121298156	121298156	+	Missense_Mutation	SNP	G	G	C	rs17833992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:121298156G>C	ENST00000297848.3	+	33	4294	c.4024G>C	c.(4024-4026)Gtt>Ctt	p.V1342L	COL14A1_ENST00000309791.4_Missense_Mutation_p.V1342L|COL14A1_ENST00000247781.3_Missense_Mutation_p.V1247L	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			TTTTCAAACTGTTACTTTCGA	0.284													G|||	489	0.0976438	0.1263	0.0922	5008	,	,		16555	0.0317		0.1561	False		,,,				2504	0.0706				p.V1342L		Atlas-SNP	.											.	COL14A1	292	.	0			c.G4024C						PASS	.	G	LEU/VAL	538,3866	235.8+/-248.2	36,466,1700	59.0	62.0	61.0		4024	3.2	1.0	8	dbSNP_123	61	1491,7105	279.7+/-294.1	139,1213,2946	yes	missense	COL14A1	NM_021110.1	32	175,1679,4646	CC,CG,GG		17.3453,12.2162,15.6077	possibly-damaging	1342/1797	121298156	2029,10971	2202	4298	6500	SO:0001583	missense	7373	exon33			CAAACTGTTACTT		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4024G>C	8.37:g.121298156G>C	ENSP00000297848:p.Val1342Leu	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	192	81	0.421875	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	234	0.10714285714285714	60	0.12195121951219512	39	0.10773480662983426	17	0.02972027972027972	118	0.15567282321899736	G	14.71	2.615181	0.46631	0.122162	0.173453	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781	T;T;T	0.20069	2.1;2.1;2.1	4.99	3.17	0.36434	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.367370	0.30732	N	0.008998	T	0.00073	0.0002	M	0.61703	1.905	0.09310	P	0.9999999999974227	B	0.19073	0.033	B	0.14023	0.01	T	0.06232	-1.0838	9	0.54805	T	0.06	.	8.535	0.33357	0.2369:0.0:0.7631:0.0	rs17833992;rs17851220;rs52814456;rs17833992	1342	Q05707	COEA1_HUMAN	L	1342;1342;1247	ENSP00000311809:V1342L;ENSP00000297848:V1342L;ENSP00000247781:V1247L	ENSP00000247781:V1247L	V	+	1	0	COL14A1	121367337	1.000000	0.71417	0.963000	0.40424	0.908000	0.53690	4.859000	0.62954	1.240000	0.43803	0.555000	0.69702	GTT	G|0.870;C|0.130	0.130	strong		0.284	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382950	24382950	+	IGR	SNP	G	G	A	rs16982979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:24382950G>A								AC004552.1 (15927 upstream) : PDK3 (100387 downstream)																							AGGTTCCGCAGGGCTCGGCGG	0.627													G|||	622	0.164768	0.2988	0.1282	3775	,	,		13040	0.0615		0.0378	False		,,,				2504	0.0389				p.Q691Q		Atlas-SNP	.											.	.	.	.	0			c.G2073A						PASS	.	G		844,1783		115,464,150,480,359	51.0	50.0	50.0		2073	-7.6	0.0	X	dbSNP_123	50	290,5208		4,197,85,1715,1581	no	coding-synonymous	FAM48B1	NM_001136234.1		119,661,235,2195,1940	AA,AG,A,GG,G		5.2746,32.1279,13.9569		691/888	24382950	1134,6991	1568	3582	5150	SO:0001628	intergenic_variant	100130302	exon1			TCCGCAGGGCTCG																													X.37:g.24382950G>A		Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	186	175	0.94086	NM_001136234		Silent	SNP		37																																																																																				0|0.011;A|0.158	0.158	strong	0	0.627								
SLC38A8	146167	hgsc.bcm.edu	37	16	84070500	84070500	+	Silent	SNP	C	C	G	rs1317524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84070500C>G	ENST00000299709.3	-	2	194	c.195G>C	c.(193-195)tcG>tcC	p.S65S		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	65					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						GGAAGACCAACGAGACCTGCG	0.657													G|||	2209	0.441094	0.5416	0.3646	5008	,	,		11922	0.5863		0.33	False		,,,				2504	0.3241				p.S65S		Atlas-SNP	.											.	SLC38A8	60	.	0			c.G195C						PASS	.	G		2096,2304	585.5+/-386.3	484,1128,588	47.0	40.0	42.0		195	2.0	1.0	16	dbSNP_88	42	2718,5882	667.3+/-402.5	448,1822,2030	no	coding-synonymous	SLC38A8	NM_001080442.1		932,2950,2618	GG,GC,CC		31.6047,47.6364,37.0308		65/436	84070500	4814,8186	2200	4300	6500	SO:0001819	synonymous_variant	146167	exon2			GACCAACGAGACC		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.195G>C	16.37:g.84070500C>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_001080442		Silent	SNP	ENST00000299709.3	37	CCDS32495.1																																																																																			C|0.617;G|0.383	0.383	strong		0.657	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
DAGLB	221955	hgsc.bcm.edu	37	7	6476104	6476104	+	Missense_Mutation	SNP	G	G	A	rs117103601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:6476104G>A	ENST00000297056.6	-	3	477	c.308C>T	c.(307-309)gCg>gTg	p.A103V	DAGLB_ENST00000479922.2_5'UTR|DAGLB_ENST00000425398.2_Missense_Mutation_p.A103V|DAGLB_ENST00000436575.1_Missense_Mutation_p.A62V|DAGLB_ENST00000428902.2_Intron|DAGLB_ENST00000421761.2_Intron	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	103					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		AAAAAACAGCGCCAGGCGGAT	0.527													G|||	78	0.0155751	0.0	0.0317	5008	,	,		17687	0.0		0.0398	False		,,,				2504	0.0164				p.A103V		Atlas-SNP	.											DAGLB,NS,haematopoietic_neoplasm,0,1	DAGLB	74	1	0			c.C308T						PASS	.	G	VAL/ALA,VAL/ALA	26,4380	33.5+/-64.1	1,24,2178	89.0	92.0	91.0		308,308	5.0	0.2	7	dbSNP_132	91	301,8299	109.0+/-169.6	4,293,4003	yes	missense,missense	DAGLB	NM_001142936.1,NM_139179.3	64,64	5,317,6181	AA,AG,GG		3.5,0.5901,2.5142	benign,benign	103/544,103/673	6476104	327,12679	2203	4300	6503	SO:0001583	missense	221955	exon3			AACAGCGCCAGGC	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.308C>T	7.37:g.6476104G>A	ENSP00000297056:p.Ala103Val	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	143	65	0.454545	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Missense_Mutation	SNP	ENST00000297056.6	37	CCDS5350.1	46	0.021062271062271064	0	0.0	16	0.04419889502762431	0	0.0	30	0.0395778364116095	G	6.078	0.382635	0.11524	0.005901	0.035	ENSG00000164535	ENST00000297056;ENST00000425398;ENST00000436575;ENST00000471132;ENST00000432248	T;T;T	0.45668	0.94;0.89;0.9	5.87	5.0	0.66597	.	0.323228	0.31221	N	0.008026	T	0.06600	0.0169	L	0.44542	1.39	0.21897	N	0.999487	B;B	0.30605	0.287;0.013	B;B	0.22601	0.04;0.003	T	0.20174	-1.0283	10	0.02654	T	1	-17.2141	7.9535	0.30029	0.1505:0.1348:0.7147:0.0	.	103;103	B4DQU0;Q8NCG7	.;DGLB_HUMAN	V	103;103;62;103;103	ENSP00000297056:A103V;ENSP00000391171:A103V;ENSP00000404785:A62V	ENSP00000297056:A103V	A	-	2	0	DAGLB	6442629	0.025000	0.19082	0.248000	0.24265	0.440000	0.31957	2.356000	0.44116	1.635000	0.50512	0.655000	0.94253	GCG	G|0.976;A|0.024	0.024	strong		0.527	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
TGS1	96764	hgsc.bcm.edu	37	8	56698365	56698365	+	Missense_Mutation	SNP	G	G	A	rs61753685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:56698365G>A	ENST00000260129.5	+	3	731	c.254G>A	c.(253-255)aGt>aAt	p.S85N		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	85					7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			CTGGATGAAAGTGAACTTGAT	0.418													G|||	7	0.00139776	0.0	0.0043	5008	,	,		17006	0.0		0.003	False		,,,				2504	0.001				p.S85N	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.G254A						PASS	.	G	ASN/SER	5,4401	11.4+/-27.6	0,5,2198	153.0	140.0	145.0		254	1.6	1.0	8	dbSNP_129	145	55,8545	34.8+/-89.0	1,53,4246	yes	missense	TGS1	NM_024831.6	46	1,58,6444	AA,AG,GG		0.6395,0.1135,0.4613	benign	85/854	56698365	60,12946	2203	4300	6503	SO:0001583	missense	96764	exon3			ATGAAAGTGAACT	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"""nuclear receptor coactivator 6 interacting protein"", ""trimethylguanosine synthase homolog (S. cerevisiae)"""	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.254G>A	8.37:g.56698365G>A	ENSP00000260129:p.Ser85Asn	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	226	112	0.495575	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	0.835	-0.743908	0.03088	0.001135	0.006395	ENSG00000137574	ENST00000260129	T	0.18338	2.22	5.8	1.61	0.23674	.	0.520508	0.22306	N	0.061787	T	0.06188	0.0160	N	0.25647	0.755	0.27538	N	0.950872	B	0.02656	0.0	B	0.01281	0.0	T	0.34850	-0.9812	10	0.13853	T	0.58	-5.7431	5.868	0.18786	0.3053:0.0:0.5326:0.1621	rs61753685	85	Q96RS0	TGS1_HUMAN	N	85	ENSP00000260129:S85N	ENSP00000260129:S85N	S	+	2	0	TGS1	56860919	0.976000	0.34144	0.996000	0.52242	0.006000	0.05464	0.183000	0.16919	0.382000	0.24878	-0.880000	0.02959	AGT	G|0.995;A|0.005	0.005	strong		0.418	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831	
GSTO1	9446	hgsc.bcm.edu	37	10	106022789	106022789	+	Missense_Mutation	SNP	C	C	A	rs4925	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:106022789C>A	ENST00000369713.5	+	4	613	c.419C>A	c.(418-420)gCt>gAt	p.A140D	GSTO1_ENST00000369710.4_Intron|GSTO1_ENST00000493946.1_3'UTR|GSTO1_ENST00000539281.1_Missense_Mutation_p.A112D	NM_004832.2	NP_004823.1	P78417	GSTO1_HUMAN	glutathione S-transferase omega 1	140	GST C-terminal.		A -> D (in allele GSTO1*C; no effect on protein stability; dbSNP:rs4925). {ECO:0000269|PubMed:12618591, ECO:0000269|PubMed:12928150}.		cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014810)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)	p.A140D(1)		large_intestine(1)|lung(1)|stomach(1)	3		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)|Vitamin E(DB00163)	GAAGACTATGCTGGCCTAAAA	0.353													C|||	888	0.177316	0.0696	0.2075	5008	,	,		18895	0.13		0.337	False		,,,				2504	0.1861				p.A140D		Atlas-SNP	.											GSTO1,NS,carcinoma,0,1	GSTO1	14	1	1	Substitution - Missense(1)	stomach(1)	c.C419A	GRCh37	CM061795	GSTO1	M	rs4925	PASS	.	C	,ASP/ALA,ASP/ALA	481,3925	226.2+/-241.8	25,431,1747	88.0	85.0	86.0		,335,419	3.9	0.0	10	dbSNP_52	86	2665,5935	427.8+/-355.7	415,1835,2050	yes	intron,missense,missense	GSTO1	NM_001191002.1,NM_001191003.1,NM_004832.2	,126,126	440,2266,3797	AA,AC,CC		30.9884,10.9169,24.1888	,benign,benign	,112/214,140/242	106022789	3146,9860	2203	4300	6503	SO:0001583	missense	9446	exon4			ACTATGCTGGCCT	AF212303	CCDS7555.1, CCDS53572.1, CCDS53573.1	10q25.1	2012-06-21			ENSG00000148834	ENSG00000148834	2.5.1.18, 1.8.5.1, 1.20.4.2	"""Glutathione S-transferases / Soluble"""	13312	protein-coding gene	gene with protein product		605482				10783391, 12618591	Standard	NM_004832		Approved	GSTTLp28, P28	uc001kya.3	P78417	OTTHUMG00000019001	ENST00000369713.5:c.419C>A	10.37:g.106022789C>A	ENSP00000358727:p.Ala140Asp	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	57	4	0.0701754	NM_004832	D3DRA3|F5H7H0|Q5TA03|Q7Z3T2	Missense_Mutation	SNP	ENST00000369713.5	37	CCDS7555.1	459	0.21016483516483517	32	0.06504065040650407	87	0.24033149171270718	86	0.15034965034965034	254	0.33509234828496043	C	13.32	2.201635	0.38905	0.109169	0.309884	ENSG00000148834	ENST00000539281;ENST00000369713;ENST00000445155	T;T;T	0.13196	2.61;2.61;2.61	4.83	3.93	0.45458	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.523772	0.23569	N	0.046768	T	0.00012	0.0000	N	0.02158	-0.66	0.50467	P	1.2500000000004174E-4	B	0.29136	0.234	B	0.29716	0.106	T	0.48103	-0.9064	9	0.25106	T	0.35	-0.2439	11.8844	0.52594	0.0:0.915:0.0:0.085	rs4925;rs3184686;rs3740467;rs17825384;rs17880534;rs56435924;rs56733715;rs4925	140	P78417	GSTO1_HUMAN	D	112;140;112	ENSP00000441488:A112D;ENSP00000358727:A140D;ENSP00000406708:A112D	ENSP00000358727:A140D	A	+	2	0	GSTO1	106012779	0.016000	0.18221	0.046000	0.18839	0.099000	0.18886	0.831000	0.27476	1.389000	0.46526	0.655000	0.94253	GCT	C|0.778;A|0.222	0.222	strong		0.353	GSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050193.1	NM_004832	
OSER1	51526	hgsc.bcm.edu	37	20	42826379	42826379	+	Splice_Site	SNP	C	C	T	rs11274	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:42826379C>T	ENST00000372970.2	-	6	372	c.192G>A	c.(190-192)ggG>ggA	p.G64G	OSER1_ENST00000255174.2_Splice_Site_p.G64G			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	64					cellular response to hydrogen peroxide (GO:0070301)												TCCTTGTAGACCTAAAGAGGA	0.408													C|||	1916	0.382588	0.6346	0.1571	5008	,	,		22340	0.4782		0.1561	False		,,,				2504	0.3364				p.G64G		Atlas-SNP	.											.	C20orf111	28	.	0			c.G192A						PASS	.	C		2370,2036	589.2+/-387.1	648,1074,481	36.0	36.0	36.0		192	2.0	1.0	20	dbSNP_52	36	1276,7324	243.8+/-273.2	90,1096,3114	yes	coding-synonymous-near-splice	C20orf111	NM_016470.7		738,2170,3595	TT,TC,CC		14.8372,46.2097,28.0332		64/293	42826379	3646,9360	2203	4300	6503	SO:0001630	splice_region_variant	51526	exon4			TGTAGACCTAAAG	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"""peroxide-inducible transcript 1"", ""oxidative stress-responsive 1"""		"""chromosome 20 open reading frame 111"""	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.192-1G>A	20.37:g.42826379C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Silent	SNP	ENST00000372970.2	37	CCDS13327.1																																																																																			C|0.685;N|0.000	.	strong		0.408	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470	Silent
AHNAK	79026	hgsc.bcm.edu	37	11	62295361	62295361	+	Missense_Mutation	SNP	C	C	A	rs145871196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62295361C>A	ENST00000378024.4	-	5	6802	c.6528G>T	c.(6526-6528)gaG>gaT	p.E2176D	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2176					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGAAGTGCATCTCAGGCATCT	0.493													C|||	132	0.0263578	0.0386	0.0274	5008	,	,		22032	0.0119		0.0258	False		,,,				2504	0.0245				p.E2176D		Atlas-SNP	.											.	AHNAK	532	.	0			c.G6528T						PASS	.	C	ASP/GLU,	200,4204	124.5+/-161.8	3,194,2005	204.0	214.0	211.0		6528,	-8.1	0.0	11	dbSNP_134	211	219,8379	92.3+/-154.4	4,211,4084	no	missense,intron	AHNAK	NM_001620.1,NM_024060.2	45,	7,405,6089	AA,AC,CC		2.5471,4.5413,3.2226	benign,	2176/5891,	62295361	419,12583	2202	4299	6501	SO:0001583	missense	79026	exon5			GTGCATCTCAGGC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.6528G>T	11.37:g.62295361C>A	ENSP00000367263:p.Glu2176Asp	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	113	48	0.424779	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	57	0.0260989010989011	20	0.04065040650406504	13	0.03591160220994475	7	0.012237762237762238	17	0.022427440633245383	C	0.005	-2.194808	0.00299	0.045413	0.025471	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.00966	5.49	4.03	-8.05	0.01106	.	0.826573	0.09781	N	0.756617	T	0.00144	0.0004	N	0.11756	0.17	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.46541	-0.9184	10	0.12430	T	0.62	.	16.9464	0.86231	0.0:0.1777:0.6967:0.1255	.	2176	Q09666	AHNK_HUMAN	D	265;2176	ENSP00000367263:E2176D	ENSP00000244934:E265D	E	-	3	2	AHNAK	62051937	0.984000	0.35163	0.043000	0.18650	0.089000	0.18198	-0.265000	0.08644	-2.469000	0.00531	-1.158000	0.01797	GAG	C|0.968;A|0.032	0.032	strong		0.493	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
CALR3	125972	hgsc.bcm.edu	37	19	16593318	16593318	+	Silent	SNP	C	C	T	rs118131979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:16593318C>T	ENST00000269881.3	-	7	923	c.861G>A	c.(859-861)acG>acA	p.T287T	CTD-3222D19.2_ENST00000409035.1_3'UTR|CALR3_ENST00000602234.1_5'UTR	NM_145046.4	NP_659483.2	Q96L12	CALR3_HUMAN	calreticulin 3	287	P-domain.				cell differentiation (GO:0030154)|protein folding (GO:0006457)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|prostate(1)|skin(1)	15						GGTCATACTGCGTCAAATAGT	0.423													C|||	27	0.00539137	0.0008	0.0029	5008	,	,		21729	0.0		0.0189	False		,,,				2504	0.0051				p.T287T		Atlas-SNP	.											.	CALR3	41	.	0			c.G861A						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	207.0	184.0	192.0		861	-10.5	0.0	19	dbSNP_132	192	144,8456	70.3+/-132.9	2,140,4158	no	coding-synonymous	CALR3	NM_145046.3		2,154,6347	TT,TC,CC		1.6744,0.3177,1.2148		287/385	16593318	158,12848	2203	4300	6503	SO:0001819	synonymous_variant	125972	exon7			ATACTGCGTCAAA	AK058084	CCDS12344.1	19p13.11	2014-09-17				ENSG00000269058			20407	protein-coding gene	gene with protein product	"""cancer/testis antigen 93"", ""calsperin"""	611414				12384296	Standard	NM_145046		Approved	CRT2, FLJ25355, MGC26577, CT93	uc002ned.3	Q96L12		ENST00000269881.3:c.861G>A	19.37:g.16593318C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_145046	D9N574|Q96LN3	Silent	SNP	ENST00000269881.3	37	CCDS12344.1																																																																																			C|0.990;T|0.010	0.010	strong		0.423	CALR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461089.1	NM_145046	
MKL1	57591	hgsc.bcm.edu	37	22	40814500	40814500	+	Missense_Mutation	SNP	T	T	C	rs878756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:40814500T>C	ENST00000355630.3	-	12	2532	c.1942A>G	c.(1942-1944)Agc>Ggc	p.S648G	MKL1_ENST00000402042.1_Missense_Mutation_p.S598G|MKL1_ENST00000407029.1_Missense_Mutation_p.S648G|MKL1_ENST00000396617.3_Missense_Mutation_p.S648G	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	648	Pro-rich.		S -> G (in dbSNP:rs878756). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:17974005}.		negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.S648G(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						TTGATGAGGCTGGGGCCCTGA	0.677			T	RBM15	acute megakaryocytic leukemia								C|||	2420	0.483227	0.9448	0.2839	5008	,	,		11023	0.1111		0.3797	False		,,,				2504	0.4908				p.S648G		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	MKL1,NS,carcinoma,0,1	MKL1	69	1	1	Substitution - Missense(1)	stomach(1)	c.A1942G						PASS	.	C	GLY/SER	3792,614	258.0+/-262.2	1646,500,57	55.0	58.0	57.0		1942	-8.5	0.0	22	dbSNP_86	57	3414,5186	622.5+/-397.3	705,2004,1591	yes	missense	MKL1	NM_020831.3	56	2351,2504,1648	CC,CT,TT		39.6977,13.9355,44.5948	benign	648/932	40814500	7206,5800	2203	4300	6503	SO:0001583	missense	57591	exon12			TGAGGCTGGGGCC	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.1942A>G	22.37:g.40814500T>C	ENSP00000347847:p.Ser648Gly	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	190	90	0.473684	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	CCDS14003.1	917	0.4198717948717949	459	0.9329268292682927	109	0.3011049723756906	66	0.11538461538461539	283	0.3733509234828496	C	0.261	-0.999638	0.02128	0.860645	0.396977	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	4.45	-8.52	0.00920	.	1.024570	0.07702	N	0.940646	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.29941	-0.9995	9	0.14252	T	0.57	-1.3436	18.4959	0.90865	0.0:0.5986:0.0:0.4014	rs878756;rs17424984;rs58451515;rs878756	598;648;648	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	G	648;648;598;648	ENSP00000347847:S648G;ENSP00000379861:S648G;ENSP00000385584:S598G;ENSP00000385835:S648G	ENSP00000347847:S648G	S	-	1	0	MKL1	39144446	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-2.523000	0.00949	-2.402000	0.00577	-2.030000	0.00424	AGC	T|0.474;C|0.526	0.526	strong		0.677	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831	
APOBR	55911	hgsc.bcm.edu	37	16	28508069	28508069	+	Silent	SNP	C	C	T	rs151174	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28508069C>T	ENST00000431282.1	+	3	1690	c.1680C>T	c.(1678-1680)ggC>ggT	p.G560G	CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000328423.5_Silent_p.G560G|APOBR_ENST00000564831.1_Silent_p.G569G|CLN3_ENST00000569430.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	560	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						TGATGGGGGGCGCCCAGACCC	0.637													C|||	1194	0.238419	0.2156	0.4135	5008	,	,		17870	0.0933		0.3469	False		,,,				2504	0.183				p.G569G		Atlas-SNP	.											.	APOBR	89	.	0			c.C1707T						PASS	.	C		977,3027		149,679,1174	8.0	9.0	9.0		1680	-9.6	0.0	16	dbSNP_79	9	3211,5119		667,1877,1621	no	coding-synonymous	APOBR	NM_018690.3		816,2556,2795	TT,TC,CC		38.5474,24.4006,33.9549		560/1089	28508069	4188,8146	2002	4165	6167	SO:0001819	synonymous_variant	55911	exon2			GGGGGGCGCCCAG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1680C>T	16.37:g.28508069C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	153	71	0.464052	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	37																																																																																				C|0.747;T|0.253	0.253	strong		0.637	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
CDH15	1013	hgsc.bcm.edu	37	16	89246670	89246670	+	Silent	SNP	T	T	C	rs59865771	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89246670T>C	ENST00000289746.2	+	3	329	c.264T>C	c.(262-264)gaT>gaC	p.D88D	CDH15_ENST00000521087.1_Intron	NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	88	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		CCGGCGTGGATGAGGAGCCCC	0.602													C|||	2158	0.430911	0.3003	0.3141	5008	,	,		19591	0.8224		0.2813	False		,,,				2504	0.4407				p.D88D		Atlas-SNP	.											.	CDH15	54	.	0			c.T264C						PASS	.	C		1268,3124	675.8+/-403.1	177,914,1105	47.0	43.0	45.0		264	-6.6	0.7	16	dbSNP_129	45	2213,6387	690.5+/-404.4	303,1607,2390	no	coding-synonymous	CDH15	NM_004933.2		480,2521,3495	CC,CT,TT		25.7326,28.8707,26.7934		88/815	89246670	3481,9511	2196	4300	6496	SO:0001819	synonymous_variant	1013	exon3			CGTGGATGAGGAG	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"""Cadherins / Major cadherins"""	1754	protein-coding gene	gene with protein product		114019	"""cadherin 15, M-cadherin (myotubule)"""	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.264T>C	16.37:g.89246670T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	NM_004933		Silent	SNP	ENST00000289746.2	37	CCDS10976.1																																																																																			T|0.694;C|0.306	0.306	strong		0.602	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933	
THNSL2	55258	hgsc.bcm.edu	37	2	88474256	88474256	+	Missense_Mutation	SNP	G	G	A	rs35541720	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:88474256G>A	ENST00000324166.5	+	2	2013	c.322G>A	c.(322-324)Gtc>Atc	p.V108I	THNSL2_ENST00000377254.3_Missense_Mutation_p.V108I|THNSL2_ENST00000358591.2_Missense_Mutation_p.V108I|THNSL2_ENST00000402102.1_Missense_Mutation_p.V108I|THNSL2_ENST00000449349.1_Missense_Mutation_p.V76I|THNSL2_ENST00000343544.4_Missense_Mutation_p.V108I	NM_018271.4	NP_060741.3	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2 (S. cerevisiae)	108			V -> I (in dbSNP:rs35541720).		2-oxobutyrate biosynthetic process (GO:0046360)|dephosphorylation (GO:0016311)|serine family amino acid catabolic process (GO:0009071)	extracellular space (GO:0005615)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|serine binding (GO:0070905)			breast(4)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	27						GTGGCATGGCGTCACATATGC	0.527													G|||	24	0.00479233	0.0	0.0	5008	,	,		21977	0.0		0.0209	False		,,,				2504	0.0031				p.V108I		Atlas-SNP	.											.	THNSL2	66	.	0			c.G322A						PASS	.	G	ILE/VAL	18,4388	24.3+/-50.5	0,18,2185	248.0	181.0	203.0		322	-0.8	0.0	2	dbSNP_126	203	102,8498	57.2+/-118.5	2,98,4200	yes	missense	THNSL2	NM_018271.4	29	2,116,6385	AA,AG,GG		1.186,0.4085,0.9227	benign	108/485	88474256	120,12886	2203	4300	6503	SO:0001583	missense	55258	exon2			CATGGCGTCACAT		CCDS2002.2, CCDS58718.1, CCDS74539.1	2p11.2	2007-06-20			ENSG00000144115	ENSG00000144115			25602	protein-coding gene	gene with protein product		611261				17034760	Standard	NM_018271		Approved	FLJ10916	uc021vkr.1	Q86YJ6	OTTHUMG00000130314	ENST00000324166.5:c.322G>A	2.37:g.88474256G>A	ENSP00000327323:p.Val108Ile	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	190	98	0.515789	NM_018271	B3KTB1|B5MDX8|B7WPF8|D9ZZB8|Q6P2M7|Q6PI27|Q9NV54	Missense_Mutation	SNP	ENST00000324166.5	37	CCDS2002.2	19	0.0086996336996337	0	0.0	0	0.0	0	0.0	19	0.025065963060686015	G	12.48	1.950290	0.34377	0.004085	0.01186	ENSG00000144115	ENST00000358591;ENST00000377254;ENST00000402102;ENST00000419759;ENST00000449349;ENST00000343544;ENST00000324166	T;T;T;T;T;T;T	0.11385	2.78;2.78;2.78;2.78;2.78;2.78;2.78	5.63	-0.798	0.10905	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.665977	0.14906	N	0.291503	T	0.01940	0.0061	L	0.27053	0.805	0.09310	N	1	B;B;B	0.27498	0.102;0.18;0.15	B;B;B	0.17098	0.012;0.017;0.007	T	0.28776	-1.0033	10	0.87932	D	0	.	7.2691	0.26246	0.1944:0.3339:0.4717:0.0	rs35541720	108;76;108	Q86YJ6;C9JU10;Q86YJ6-2	THNS2_HUMAN;.;.	I	108;108;108;108;76;108;108	ENSP00000351402:V108I;ENSP00000366464:V108I;ENSP00000384475:V108I;ENSP00000391300:V108I;ENSP00000407553:V76I;ENSP00000339563:V108I;ENSP00000327323:V108I	ENSP00000327323:V108I	V	+	1	0	THNSL2	88255371	0.046000	0.20272	0.000000	0.03702	0.799000	0.45148	1.335000	0.33839	-0.183000	0.10585	0.561000	0.74099	GTC	G|0.988;A|0.012	0.012	strong		0.527	THNSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252662.1	NM_018271	
TMCO4	255104	hgsc.bcm.edu	37	1	20097822	20097822	+	Silent	SNP	G	G	A	rs11551819	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:20097822G>A	ENST00000294543.6	-	5	574	c.333C>T	c.(331-333)gaC>gaT	p.D111D	TMCO4_ENST00000375122.2_Silent_p.D111D|TMCO4_ENST00000375127.1_Silent_p.D111D	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	111						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		CCGTCGGGTCGTCCTTCAAGA	0.483													G|||	440	0.0878594	0.1089	0.0648	5008	,	,		18313	0.001		0.1382	False		,,,				2504	0.1135				p.D111D		Atlas-SNP	.											.	TMCO4	46	.	0			c.C333T						PASS	.	G		543,3863	246.5+/-255.1	32,479,1692	129.0	131.0	131.0		333	-6.7	0.0	1	dbSNP_120	131	1112,7488	231.4+/-265.4	69,974,3257	no	coding-synonymous	TMCO4	NM_181719.4		101,1453,4949	AA,AG,GG		12.9302,12.3241,12.7249		111/635	20097822	1655,11351	2203	4300	6503	SO:0001819	synonymous_variant	255104	exon5			CGGGTCGTCCTTC		CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.333C>T	1.37:g.20097822G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Silent	SNP	ENST00000294543.6	37	CCDS198.1																																																																																			G|0.888;A|0.112	0.112	strong		0.483	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719	
CRTAC1	55118	hgsc.bcm.edu	37	10	99696003	99696003	+	Silent	SNP	G	G	A	rs35027739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:99696003G>A	ENST00000370597.3	-	3	700	c.345C>T	c.(343-345)atC>atT	p.I115I	CRTAC1_ENST00000298819.4_Silent_p.I115I|CRTAC1_ENST00000370591.2_Silent_p.I115I	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	115						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		CTGTGACCCCGATGGCGTTCC	0.632													G|||	538	0.107428	0.0613	0.0893	5008	,	,		17709	0.0208		0.166	False		,,,				2504	0.2117				p.I115I		Atlas-SNP	.											.	CRTAC1	86	.	0			c.C345T						PASS	.	G	,	342,4064	177.3+/-206.3	19,304,1880	73.0	57.0	63.0		345,345	-3.0	1.0	10	dbSNP_126	63	1713,6887	314.7+/-311.9	179,1355,2766	no	coding-synonymous,coding-synonymous	CRTAC1	NM_001206528.2,NM_018058.6	,	198,1659,4646	AA,AG,GG		19.9186,7.7621,15.8004	,	115/646,115/662	99696003	2055,10951	2203	4300	6503	SO:0001819	synonymous_variant	55118	exon3			GACCCCGATGGCG	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.345C>T	10.37:g.99696003G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Silent	SNP	ENST00000370597.3	37	CCDS31266.1																																																																																			G|0.861;A|0.139	0.139	strong		0.632	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
PAXIP1	22976	hgsc.bcm.edu	37	7	154760369	154760369	+	Silent	SNP	A	A	G	rs935037	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:154760369A>G	ENST00000404141.1	-	7	1696	c.1542T>C	c.(1540-1542)ctT>ctC	p.L514L	PAXIP1_ENST00000397192.1_Silent_p.L514L|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	514	Gln-rich.			Missing (in Ref. 4; AAB91434). {ECO:0000305}.	adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		ggagctgggcaagctgctgct	0.637													G|||	3082	0.615415	0.5454	0.7262	5008	,	,		16041	0.6071		0.6292	False		,,,				2504	0.6258				p.L514L		Atlas-SNP	.											.	PAXIP1	150	.	0			c.T1542C						PASS	.	G		1990,1564		577,836,364	16.0	17.0	17.0		1542	-3.0	0.2	7	dbSNP_86	17	4087,2557		1271,1545,506	no	coding-synonymous	PAXIP1	NM_007349.3		1848,2381,870	GG,GA,AA		38.4859,44.0068,40.4099		514/1070	154760369	6077,4121	1777	3322	5099	SO:0001819	synonymous_variant	22976	exon7			CTGGGCAAGCTGC	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1542T>C	7.37:g.154760369A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Silent	SNP	ENST00000404141.1	37	CCDS47753.1																																																																																			A|0.380;G|0.620	0.620	strong		0.637	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349	
CSTA	1475	hgsc.bcm.edu	37	3	122060404	122060404	+	Missense_Mutation	SNP	C	C	T	rs34173813	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:122060404C>T	ENST00000264474.3	+	3	336	c.287C>T	c.(286-288)aCg>aTg	p.T96M		NM_005213.3	NP_005204.1	P01040	CYTA_HUMAN	cystatin A (stefin A)	96			T -> M (in dbSNP:rs34173813).		keratinocyte differentiation (GO:0030216)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|peptide cross-linking (GO:0018149)|single organismal cell-cell adhesion (GO:0016337)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			large_intestine(2)|lung(2)	4				GBM - Glioblastoma multiforme(114;0.155)		GACGAGCTGACGGGCTTTTAG	0.398													C|||	474	0.0946486	0.0189	0.1124	5008	,	,		18573	0.0407		0.1561	False		,,,				2504	0.1769				p.T96M	Pancreas(26;157 1503 12440)	Atlas-SNP	.											.	CSTA	11	.	0			c.C287T	GRCh37	CM076131	CSTA	M	rs34173813	PASS	.	C	MET/THR	212,4194	129.0+/-165.8	1,210,1992	119.0	117.0	118.0		287	-7.3	0.0	3	dbSNP_126	118	1277,7323	255.2+/-280.2	110,1057,3133	yes	missense	CSTA	NM_005213.3	81	111,1267,5125	TT,TC,CC		14.8488,4.8116,11.4486	probably-damaging	96/99	122060404	1489,11517	2203	4300	6503	SO:0001583	missense	1475	exon3			AGCTGACGGGCTT		CCDS3011.1	3q21	2008-04-15			ENSG00000121552	ENSG00000121552			2481	protein-coding gene	gene with protein product		184600		STF1, STFA		1674139	Standard	NM_005213		Approved		uc003eex.3	P01040	OTTHUMG00000159488	ENST00000264474.3:c.287C>T	3.37:g.122060404C>T	ENSP00000264474:p.Thr96Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	NM_005213	Q6IB90	Missense_Mutation	SNP	ENST00000264474.3	37	CCDS3011.1	168	0.07692307692307693	3	0.006097560975609756	50	0.13812154696132597	8	0.013986013986013986	107	0.14116094986807387	C	13.20	2.165243	0.38217	0.048116	0.148488	ENSG00000121552	ENST00000264474	T	0.78126	-1.15	5.34	-7.34	0.01427	Proteinase inhibitor I25, cystatin (1);	1.232960	0.05253	N	0.514252	T	0.00468	0.0015	.	.	.	0.80722	P	0.0	P	0.45715	0.865	B	0.36504	0.226	T	0.33137	-0.9880	8	0.72032	D	0.01	0.7508	2.1125	0.03706	0.5059:0.1369:0.1003:0.2569	rs34173813	96	P01040	CYTA_HUMAN	M	96	ENSP00000264474:T96M	ENSP00000264474:T96M	T	+	2	0	CSTA	123543094	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.161000	0.01278	-1.034000	0.03295	0.655000	0.94253	ACG	T|0.104;G|0.000;C|0.895	0.104	strong		0.398	CSTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355751.1	NM_005213	
C17orf58	284018	hgsc.bcm.edu	37	17	65988049	65988049	+	Missense_Mutation	SNP	T	T	C	rs9891146	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:65988049T>C	ENST00000449250.2	-	3	463	c.274A>G	c.(274-276)Att>Gtt	p.I92V	RP11-855A2.5_ENST00000580729.1_lincRNA|C17orf58_ENST00000334461.7_3'UTR|C17orf58_ENST00000536693.1_3'UTR			Q2M2W7	CQ058_HUMAN	chromosome 17 open reading frame 58	92			I -> V (in dbSNP:rs9891146). {ECO:0000269|PubMed:15489334}.					p.I92V(1)		lung(2)	2	all_cancers(12;4.57e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGGGTATGAATTGCACCTTGA	0.493													T|||	2439	0.487021	0.3094	0.6455	5008	,	,		19703	0.2659		0.7286	False		,,,				2504	0.5941				p.I92V		Atlas-SNP	.											C17orf58_ENST00000449250,NS,carcinoma,0,1	C17orf58	15	1	1	Substitution - Missense(1)	stomach(1)	c.A274G						PASS	.	T	VAL/ILE,	1570,2386		337,896,745	162.0	150.0	154.0		274,	-4.6	0.0	17	dbSNP_119	154	6062,2248		2220,1622,313	yes	missense,utr-3	C17orf58	NM_181655.2,NM_181656.3	29,	2557,2518,1058	CC,CT,TT		27.0517,39.6866,37.7792	benign,	92/98,	65988049	7632,4634	1978	4155	6133	SO:0001583	missense	284018	exon3			TATGAATTGCACC	AK026583	CCDS42375.1, CCDS45765.1	17q24.2	2012-10-11			ENSG00000186665	ENSG00000186665			27568	protein-coding gene	gene with protein product						12477932	Standard	NM_181656		Approved		uc002jgi.4	Q2M2W7	OTTHUMG00000179782	ENST00000449250.2:c.274A>G	17.37:g.65988049T>C	ENSP00000402020:p.Ile92Val	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	242	117	0.483471	NM_181655	A8MQV2	Missense_Mutation	SNP	ENST00000449250.2	37	CCDS45765.1	1111	0.5086996336996337	158	0.32113821138211385	231	0.638121546961326	170	0.2972027972027972	552	0.7282321899736148	T	0.887	-0.726655	0.03158	0.396866	0.729483	ENSG00000186665	ENST00000449250	T	0.28895	1.59	4.35	-4.59	0.03400	Tissue inhibitor of metalloproteinases-like, OB-fold (1);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37526	-0.9702	7	0.02654	T	1	-0.2988	10.9844	0.47514	0.11:0.7678:0.0:0.1222	rs9891146;rs52818390;rs60913504;rs9891146	92	Q2M2W7	CQ058_HUMAN	V	92	ENSP00000402020:I92V	ENSP00000402020:I92V	I	-	1	0	C17orf58	63418511	0.000000	0.05858	0.000000	0.03702	0.224000	0.24922	-0.340000	0.07821	-1.060000	0.03189	-0.388000	0.06559	ATT	T|0.487;C|0.513	0.513	strong		0.493	C17orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448104.1	NM_181656	
C1orf94	84970	hgsc.bcm.edu	37	1	34663180	34663180	+	Silent	SNP	G	G	A	rs3795412	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:34663180G>A	ENST00000488417.1	+	2	795	c.675G>A	c.(673-675)agG>agA	p.R225R	C1orf94_ENST00000373374.3_Silent_p.R35R	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	225										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				CAGAGGACAGGGGCCGCATCC	0.547													G|||	576	0.115016	0.1346	0.1124	5008	,	,		20597	0.0575		0.164	False		,,,				2504	0.0992				p.R225R		Atlas-SNP	.											.	C1orf94	156	.	0			c.G675A						PASS	.	G	,	694,3712	292.7+/-282.2	47,600,1556	87.0	76.0	80.0		675,105	0.7	0.0	1	dbSNP_107	80	1680,6920	307.8+/-308.6	170,1340,2790	yes	coding-synonymous,coding-synonymous	C1orf94	NM_001134734.1,NM_032884.3	,	217,1940,4346	AA,AG,GG		19.5349,15.7512,18.2531	,	225/599,35/409	34663180	2374,10632	2203	4300	6503	SO:0001819	synonymous_variant	84970	exon2			GGACAGGGGCCGC	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.675G>A	1.37:g.34663180G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	111	59	0.531532	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	37	CCDS44108.1																																																																																			G|0.833;A|0.167	0.167	strong		0.547	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
SMOX	54498	hgsc.bcm.edu	37	20	4158164	4158164	+	Silent	SNP	C	C	A	rs11552911	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:4158164C>A	ENST00000305958.4	+	3	600	c.375C>A	c.(373-375)acC>acA	p.T125T	SMOX_ENST00000484515.1_3'UTR|SMOX_ENST00000346595.2_Silent_p.T125T|SMOX_ENST00000379460.2_Silent_p.T125T|SMOX_ENST00000278795.3_Silent_p.T125T|SMOX_ENST00000339123.6_Silent_p.T125T	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	125					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	GCTACCTTACCAACCACGGCC	0.577													C|||	240	0.0479233	0.0045	0.0288	5008	,	,		17218	0.0268		0.0775	False		,,,				2504	0.1115				p.T125T		Atlas-SNP	.											.	SMOX	119	.	0			c.C375A						PASS	.	C	,,,	57,4349		0,57,2146	57.0	48.0	51.0		375,375,375,375	5.3	1.0	20	dbSNP_120	51	642,7956		17,608,3674	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SMOX	NM_175839.1,NM_175840.1,NM_175841.1,NM_175842.1	,,,	17,665,5820	AA,AC,CC		7.4669,1.2937,5.3753	,,,	125/556,125/503,125/191,125/533	4158164	699,12305	2203	4299	6502	SO:0001819	synonymous_variant	54498	exon3			CCTTACCAACCAC	AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"""chromosome 20 open reading frame 16"""	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.375C>A	20.37:g.4158164C>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_175839	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Silent	SNP	ENST00000305958.4	37	CCDS13075.1																																																																																			C|0.950;A|0.050	0.050	strong		0.577	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842	
SYCE1	93426	hgsc.bcm.edu	37	10	135370633	135370633	+	Silent	SNP	C	C	T	rs8181356	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135370633C>T	ENST00000343131.5	-	7	506	c.402G>A	c.(400-402)aaG>aaA	p.K134K	SYCE1_ENST00000432597.2_Silent_p.K98K|SPRN_ENST00000541506.1_Intron|SYCE1_ENST00000368517.3_Silent_p.K98K	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	134					synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.K134K(1)|p.K98K(1)		breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		AAATTCTCTCCTTGCACTCCT	0.552													C|||	775	0.154752	0.0454	0.1715	5008	,	,		21865	0.2698		0.1093	False		,,,				2504	0.2188				p.K134K		Atlas-SNP	.											SYCE1_ENST00000343131,NS,carcinoma,0,2	SYCE1	81	2	2	Substitution - coding silent(2)	stomach(2)	c.G402A						scavenged	.	C	,,	260,4146	142.7+/-177.9	6,248,1949	274.0	260.0	264.0		402,402,294	0.3	1.0	10	dbSNP_117	264	815,7785	186.2+/-233.7	45,725,3530	no	coding-synonymous,coding-synonymous,coding-synonymous	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	,,	51,973,5479	TT,TC,CC		9.4767,5.901,8.2654	,,	134/319,134/352,98/283	135370633	1075,11931	2203	4300	6503	SO:0001819	synonymous_variant	93426	exon7			TCTCTCCTTGCAC	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.402G>A	10.37:g.135370633C>T		Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	246	73	0.296748	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Silent	SNP	ENST00000343131.5	37	CCDS44501.1																																																																																			C|0.889;T|0.111	0.111	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
CEPT1	10390	hgsc.bcm.edu	37	1	111726869	111726869	+	Silent	SNP	G	G	A	rs3795823	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111726869G>A	ENST00000545121.1	+	9	1396	c.1188G>A	c.(1186-1188)gcG>gcA	p.A396A	RP5-1180E21.5_ENST00000610049.1_RNA|RP5-1180E21.4_ENST00000607951.1_RNA|CEPT1_ENST00000467362.1_3'UTR|CEPT1_ENST00000357172.4_Silent_p.A396A	NM_001007794.1	NP_001007795.1	Q9Y6K0	CEPT1_HUMAN	choline/ethanolamine phosphotransferase 1	396					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	diacylglycerol cholinephosphotransferase activity (GO:0004142)|ethanolaminephosphotransferase activity (GO:0004307)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	8		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)	ATCAGATTGCGTCTCACCTGC	0.403													G|||	948	0.189297	0.0257	0.1787	5008	,	,		18778	0.3294		0.2823	False		,,,				2504	0.1779				p.A396A		Atlas-SNP	.											CEPT1,colon,carcinoma,+1,1	CEPT1	25	1	0			c.G1188A						PASS	.	G	,	323,4083	171.2+/-201.5	12,299,1892	183.0	171.0	175.0		1188,1188	-11.5	0.2	1	dbSNP_107	175	2363,6237	395.1+/-345.0	335,1693,2272	no	coding-synonymous,coding-synonymous	CEPT1	NM_001007794.1,NM_006090.3	,	347,1992,4164	AA,AG,GG		27.4767,7.3309,20.652	,	396/417,396/417	111726869	2686,10320	2203	4300	6503	SO:0001819	synonymous_variant	10390	exon9			GATTGCGTCTCAC	AF068302	CCDS830.1	1p13	2010-07-08			ENSG00000134255	ENSG00000134255	2.7.8.1, 2.7.8.2		24289	protein-coding gene	gene with protein product						10191259, 12216837	Standard	XM_005270353		Approved		uc001eah.1	Q9Y6K0	OTTHUMG00000012357	ENST00000545121.1:c.1188G>A	1.37:g.111726869G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	224	95	0.424107	NM_006090	Q69YJ9|Q9P0Y8	Silent	SNP	ENST00000545121.1	37	CCDS830.1																																																																																			G|0.797;N|0.000	.	strong		0.403	CEPT1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034462.2	NM_006090	
KCNS3	3790	hgsc.bcm.edu	37	2	18113623	18113623	+	Missense_Mutation	SNP	A	A	G	rs4832524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:18113623A>G	ENST00000403915.1	+	3	1799	c.1348A>G	c.(1348-1350)Acc>Gcc	p.T450A	KCNS3_ENST00000465292.1_Intron|KCNS3_ENST00000304101.4_Missense_Mutation_p.T450A	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	450			T -> A (in dbSNP:rs4832524). {ECO:0000269|PubMed:10484328, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GCGGATGCACACCTTCATTAC	0.453													G|||	3987	0.796126	0.7383	0.8098	5008	,	,		21769	0.9831		0.6074	False		,,,				2504	0.8661				p.T450A		Atlas-SNP	.											.	KCNS3	85	.	0			c.A1348G						PASS	.	G	ALA/THR	3183,1223	424.0+/-340.3	1142,899,162	161.0	145.0	150.0		1348	3.9	0.7	2	dbSNP_111	150	5477,3123	477.4+/-369.6	1747,1983,570	yes	missense	KCNS3	NM_002252.3	58	2889,2882,732	GG,GA,AA		36.314,27.7576,33.4153	benign	450/492	18113623	8660,4346	2203	4300	6503	SO:0001583	missense	3790	exon3			ATGCACACCTTCA	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.1348A>G	2.37:g.18113623A>G	ENSP00000385968:p.Thr450Ala	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	37	CCDS1692.1	1655	0.7577838827838828	355	0.7215447154471545	275	0.7596685082872928	558	0.9755244755244755	467	0.6160949868073878	G	0.060	-1.226797	0.01518	0.722424	0.63686	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.96830	-4.14;-4.14	5.86	3.9	0.45041	.	0.399617	0.27710	N	0.018168	T	0.00012	0.0000	N	0.02011	-0.69	0.51767	P	6.399999999995298E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.44190	-0.9344	9	0.02654	T	1	.	5.3245	0.15898	0.174:0.0:0.4937:0.3322	rs4832524;rs17316360;rs17856098;rs17856121;rs17856499;rs52813731;rs58131892;rs4832524	450	Q9BQ31	KCNS3_HUMAN	A	450	ENSP00000385968:T450A;ENSP00000305824:T450A	ENSP00000305824:T450A	T	+	1	0	KCNS3	17977104	1.000000	0.71417	0.730000	0.30809	0.870000	0.49936	3.596000	0.54024	0.835000	0.34877	-0.119000	0.15052	ACC	A|0.284;G|0.716	0.716	strong		0.453	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252	
OR51M1	390059	hgsc.bcm.edu	37	11	5411398	5411398	+	Missense_Mutation	SNP	T	T	G	rs2736531	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5411398T>G	ENST00000328611.3	+	1	792	c.770T>G	c.(769-771)cTc>cGc	p.L257R	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004756.2	NP_001004756.2	Q9H341	O51M1_HUMAN	olfactory receptor, family 51, subfamily M, member 1	257			L -> R (in dbSNP:rs2736531). {ECO:0000269|PubMed:11121057}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|upper_aerodigestive_tract(1)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.98e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCGCTCCTCTCTGTGCTGTG	0.562													T|||	1805	0.360423	0.3419	0.3228	5008	,	,		20493	0.3145		0.3767	False		,,,				2504	0.4427				p.L257R		Atlas-SNP	.											.	OR51M1	60	.	0			c.T770G						PASS	.	T	ARG/LEU	1355,2769		217,921,924	99.0	92.0	94.0		770	5.2	1.0	11	dbSNP_100	94	3136,5260		601,1934,1663	yes	missense	OR51M1	NM_001004756.2	102	818,2855,2587	GG,GT,TT		37.3511,32.8565,35.8706	benign	257/327	5411398	4491,8029	2062	4198	6260	SO:0001583	missense	390059	exon1			CTCCTCTCTGTGC	BK004382	CCDS53596.1	11p15.4	2012-08-09			ENSG00000184698	ENSG00000184698		"""GPCR / Class A : Olfactory receptors"""	14847	protein-coding gene	gene with protein product							Standard	NM_001004756		Approved		uc010qzc.2	Q9H341	OTTHUMG00000066680	ENST00000328611.3:c.770T>G	11.37:g.5411398T>G	ENSP00000333196:p.Leu257Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	NM_001004756	Q6IF80	Missense_Mutation	SNP	ENST00000328611.3	37	CCDS53596.1	721	0.3301282051282051	157	0.31910569105691056	127	0.35082872928176795	174	0.3041958041958042	263	0.3469656992084433	T	18.57	3.653476	0.67472	0.328565	0.373511	ENSG00000184698	ENST00000328611	T	0.51325	0.71	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.288076	0.18688	U	0.133956	T	0.00012	0.0000	M	0.68952	2.095	0.27897	P	0.939105	P	0.49307	0.922	P	0.59948	0.866	T	0.21314	-1.0249	9	0.87932	D	0	.	14.0973	0.65032	0.0:0.0:0.0:1.0	rs2736531;rs52814371;rs2736531	246	Q9H341	O51M1_HUMAN	R	257	ENSP00000333196:L257R	ENSP00000333196:L257R	L	+	2	0	OR51M1	5367974	0.569000	0.26643	1.000000	0.80357	0.790000	0.44656	4.461000	0.60115	2.207000	0.71202	0.533000	0.62120	CTC	T|0.663;G|0.337	0.337	strong		0.562	OR51M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142981.1	NM_001004756	
TUBA1A	7846	hgsc.bcm.edu	37	12	49580180	49580180	+	Silent	SNP	T	T	C	rs1056875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:49580180T>C	ENST00000295766.5	-	3	767	c.288A>G	c.(286-288)aaA>aaG	p.K96K	TUBA1A_ENST00000301071.7_Silent_p.K96K|TUBA1A_ENST00000546918.1_Missense_Mutation_p.K147R|TUBA1A_ENST00000550767.1_Silent_p.K61K	NM_001270399.1	NP_001257328.1	Q71U36	TBA1A_HUMAN	tubulin, alpha 1a	96					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			stomach(1)|upper_aerodigestive_tract(1)	2					Albendazole(DB00518)|Mebendazole(DB00643)|Vinblastine(DB00570)	CAGCATCTTCTTTGCCTGTGA	0.527													C|||	2786	0.55631	0.6952	0.366	5008	,	,		16133	0.6925		0.3439	False		,,,				2504	0.5818				p.K96K	Pancreas(111;782 2307 24613 44561)|NSCLC(165;1667 2752 9496 39006)|Ovarian(19;24 776 10875 37451)	Atlas-SNP	.											.	TUBA1A	32	.	0			c.A288G						PASS	.	C		2911,1495	469.2+/-355.4	980,951,272	118.0	123.0	121.0		288	3.4	1.0	12	dbSNP_86	121	2838,5762	670.9+/-402.8	483,1872,1945	no	coding-synonymous	TUBA1A	NM_006009.2		1463,2823,2217	CC,CT,TT		33.0,33.931,44.2027		96/452	49580180	5749,7257	2203	4300	6503	SO:0001819	synonymous_variant	7846	exon3			ATCTTCTTTGCCT	AF141347	CCDS8781.1, CCDS58226.1, CCDS58227.1	12q13.12	2007-02-07						"""Tubulins"""	20766	protein-coding gene	gene with protein product	"""tubulin, alpha, brain-specific"""	602529				11504633, 3839072	Standard	NM_006009		Approved	TUBA3, B-ALPHA-1, FLJ25113	uc010smg.1	Q71U36	OTTHUMG00000169511	ENST00000295766.5:c.288A>G	12.37:g.49580180T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_001270399	A8K0B8|G3V1U9|P04687|P05209	Silent	SNP	ENST00000295766.5	37	CCDS58227.1	1060	0.48534798534798534	298	0.6056910569105691	129	0.356353591160221	393	0.6870629370629371	240	0.316622691292876	C	9.806	1.181768	0.21787	0.66069	0.33	ENSG00000167552	ENST00000546918	T	0.62498	0.02	5.22	3.41	0.39046	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.37549	P	0.08137399999999995	.	.	.	.	.	.	T	0.46119	-0.9214	6	0.87932	D	0	.	9.4202	0.38546	0.0:0.7154:0.0:0.2846	rs1056875;rs3741682;rs6580704;rs17255319;rs17846464;rs17859518	.	.	.	R	147	ENSP00000446613:K147R	ENSP00000446613:K147R	K	-	2	0	TUBA1A	47866447	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.876000	0.28092	0.327000	0.23409	-0.215000	0.12644	AAG	T|0.550;C|0.450	0.450	strong		0.527	TUBA1A-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404547.2	NM_006009	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3679928	3679928	+	Silent	SNP	G	G	A	rs74423567	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3679928G>A	ENST00000344754.4	-	7	1706	c.1707C>T	c.(1705-1707)gaC>gaT	p.D569D	SIGLEC1_ENST00000202578.4_Silent_p.D569D	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	569	Ig-like C2-type 5.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						ATGAGCCGGCGTCAGTGCTGG	0.677													G|||	86	0.0171725	0.0015	0.0259	5008	,	,		14064	0.0		0.0547	False		,,,				2504	0.0112				p.D569D		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C1707T						PASS	.	G		54,4348		0,54,2147	20.0	19.0	19.0		1707	-9.4	0.0	20	dbSNP_132	19	544,8048		19,506,3771	no	coding-synonymous	SIGLEC1	NM_023068.3		19,560,5918	AA,AG,GG		6.3315,1.2267,4.6021		569/1710	3679928	598,12396	2201	4296	6497	SO:0001819	synonymous_variant	6614	exon7			GCCGGCGTCAGTG	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.1707C>T	20.37:g.3679928G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	52	0.619048	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1																																																																																			G|0.966;A|0.034	0.034	strong		0.677	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
STT3A	3703	hgsc.bcm.edu	37	11	125479363	125479363	+	Silent	SNP	G	G	A	rs2241502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:125479363G>A	ENST00000529196.1	+	11	1202	c.996G>A	c.(994-996)tcG>tcA	p.S332S	STT3A_ENST00000531491.1_Silent_p.S240S|STT3A_ENST00000392708.4_Silent_p.S332S			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	332					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		GTTTCTACTCGCTGCTGGATC	0.453													A|||	2100	0.419329	0.5227	0.2752	5008	,	,		19315	0.4335		0.3787	False		,,,				2504	0.409				p.S332S		Atlas-SNP	.											STT3A,NS,carcinoma,+1,1	STT3A	52	1	0			c.G996A						PASS	.	A		2208,2194	588.4+/-386.9	570,1068,563	200.0	189.0	193.0		996	-4.4	0.9	11	dbSNP_98	193	3157,5441	655.5+/-401.3	583,1991,1725	no	coding-synonymous	STT3A	NM_152713.3		1153,3059,2288	AA,AG,GG		36.7178,49.841,41.2692		332/706	125479363	5365,7635	2201	4299	6500	SO:0001819	synonymous_variant	3703	exon10			CTACTCGCTGCTG	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"""dolichyl-diphosphooligosaccharide protein glycotransferase"""	601134	"""integral membrane protein 1"", ""STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)"", ""STT3A, cataylic subunit of the oligosaccharyltransferase complex"""	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.996G>A	11.37:g.125479363G>A		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	257	139	0.540856	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	37	CCDS8458.1	893	0.4088827838827839	280	0.5691056910569106	114	0.3149171270718232	220	0.38461538461538464	279	0.36807387862796836	A	20.3	3.961505	0.74016	0.50159	0.367178	ENSG00000134910	ENST00000526726	.	.	.	5.4	-4.43	0.03568	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47484	-0.9114	3	.	.	.	-7.8117	0.9414	0.01356	0.2588:0.3186:0.2101:0.2125	rs2241502;rs17720009;rs59721461;rs2241502	.	.	.	T	75	.	.	A	+	1	0	STT3A	124984573	0.016000	0.18221	0.950000	0.38849	0.919000	0.55068	-0.694000	0.05115	-0.923000	0.03785	-1.905000	0.00526	GCT	G|0.582;A|0.418	0.418	strong		0.453	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
NOTCH4	4855	hgsc.bcm.edu	37	6	32188640	32188640	+	Missense_Mutation	SNP	T	T	C	rs71556915|rs520692	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32188640T>C	ENST00000375023.3	-	5	953	c.815A>G	c.(814-816)gAc>gGc	p.D272G		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	272	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.		D -> G (in dbSNP:rs520692).		cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CACCTCACAGTCTGGGCCTAT	0.612													T|||	1341	0.267772	0.208	0.2594	5008	,	,		18615	0.1935		0.3519	False		,,,				2504	0.3446				p.D272G		Atlas-SNP	.											NOTCH4,NS,carcinoma,-1,1	NOTCH4	201	1	0			c.A815G						PASS	.	T	GLY/ASP	937,3469	350.8+/-311.0	90,757,1356	95.0	86.0	89.0		815	3.6	0.6	6	dbSNP_83	89	2742,5858	430.3+/-356.5	449,1844,2007	yes	missense	NOTCH4	NM_004557.3	94	539,2601,3363	CC,CT,TT		31.8837,21.2665,28.2869	benign	272/2004	32188640	3679,9327	2203	4300	6503	SO:0001583	missense	4855	exon5			TCACAGTCTGGGC		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.815A>G	6.37:g.32188640T>C	ENSP00000364163:p.Asp272Gly	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	582	0.2664835164835165	106	0.21544715447154472	107	0.2955801104972376	109	0.19055944055944055	260	0.34300791556728233	T	5.652	0.304853	0.10678	0.212665	0.318837	ENSG00000204301	ENST00000375023	D	0.91464	-2.85	4.74	3.6	0.41247	Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	1.257480	0.05700	N	0.593812	T	0.73194	0.3556	L	0.31578	0.945	0.09310	P	1.0	B;B	0.06786	0.001;0.001	B;B	0.17979	0.02;0.005	T	0.56739	-0.7929	9	0.25106	T	0.35	.	6.6914	0.23174	0.0:0.1285:0.0:0.8715	rs520692;rs16869856;rs17846655;rs17859751;rs61001202;rs520692	272;272	Q6P3V5;Q99466	.;NOTC4_HUMAN	G	272	ENSP00000364163:D272G	ENSP00000364163:D272G	D	-	2	0	NOTCH4	32296618	0.995000	0.38212	0.633000	0.29310	0.292000	0.27327	2.466000	0.45084	0.865000	0.35603	0.402000	0.26972	GAC	CCC|0.500;TCT|0.500	.	alt		0.612	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
DLEC1	9940	hgsc.bcm.edu	37	3	38081031	38081031	+	Silent	SNP	A	A	T	rs7616776	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:38081031A>T	ENST00000308059.6	+	1	336	c.315A>T	c.(313-315)tcA>tcT	p.S105S	DLEC1_ENST00000346219.3_Silent_p.S105S|DLEC1_ENST00000452631.2_Silent_p.S105S					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		ACTTGTACTCAGCCGAGGTCA	0.632													g|||	1715	0.342452	0.2927	0.3429	5008	,	,		19111	0.5546		0.3032	False		,,,				2504	0.2311				p.S105S		Atlas-SNP	.											DLEC1_ENST00000346219,NS,carcinoma,0,2	DLEC1	278	2	0			c.A315T						PASS	.	G	,	1240,2908		182,876,1016	55.0	59.0	58.0		315,315	-6.2	0.0	3	dbSNP_116	58	2475,5941		387,1701,2120	no	coding-synonymous,coding-synonymous	DLEC1	NM_007335.2,NM_007337.2	,	569,2577,3136	TT,TA,AA		29.4083,29.8939,29.5686	,	105/1756,105/1779	38081031	3715,8849	2074	4208	6282	SO:0001819	synonymous_variant	9940	exon1			GTACTCAGCCGAG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.315A>T	3.37:g.38081031A>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	32	0.415584	NM_007337		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																			A|0.652;T|0.348	0.348	strong		0.632	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
AMZ1	155185	hgsc.bcm.edu	37	7	2748758	2748758	+	Silent	SNP	G	G	C	rs59438885	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:2748758G>C	ENST00000312371.4	+	5	1019	c.651G>C	c.(649-651)tcG>tcC	p.S217S	AMZ1_ENST00000407112.1_Intron|AMZ1_ENST00000489665.1_Intron	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	217							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		TCCCGAAGTCGGGGCCCAGCG	0.677													G|||	1284	0.25639	0.1974	0.1124	5008	,	,		15442	0.5754		0.1123	False		,,,				2504	0.2577				p.S217S		Atlas-SNP	.											.	AMZ1	41	.	0			c.G651C						PASS	.	G		775,3619		75,625,1497	18.0	22.0	21.0		651	-2.4	0.0	7	dbSNP_129	21	1053,7545		61,931,3307	no	coding-synonymous	AMZ1	NM_133463.1		136,1556,4804	CC,CG,GG		12.247,17.6377,14.0702		217/499	2748758	1828,11164	2197	4299	6496	SO:0001819	synonymous_variant	155185	exon5			GAAGTCGGGGCCC	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.651G>C	7.37:g.2748758G>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	194	92	0.474227	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	37	CCDS34589.1																																																																																			A|0.000;C|0.164;G|0.836	0.164	strong		0.677	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
MAML3	55534	hgsc.bcm.edu	37	4	140811081	140811081	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:140811081C>T	ENST00000509479.2	-	2	2365	c.1509G>A	c.(1507-1509)caG>caA	p.Q503Q	MAML3_ENST00000327122.5_Silent_p.Q347Q|MAML3_ENST00000398940.1_Intron	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.527																																					p.Q503Q		Atlas-SNP	.											MAML3_ENST00000509479,NS,carcinoma,0,2	MAML3	192	2	0			c.G1509A						scavenged	.						23.0	31.0	29.0					4																	140811081		2165	4290	6455	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1509G>A	4.37:g.140811081C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	98	3	0.0306122	NM_018717		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																			.	.	none		0.527	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
TENM2	57451	hgsc.bcm.edu	37	5	167674472	167674472	+	Silent	SNP	G	G	A	rs17070023	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:167674472G>A	ENST00000518659.1	+	27	6567	c.6528G>A	c.(6526-6528)acG>acA	p.T2176T	TENM2_ENST00000519204.1_Silent_p.T2055T|TENM2_ENST00000545108.1_Silent_p.T2175T|TENM2_ENST00000520394.1_Silent_p.T1937T|TENM2_ENST00000403607.2_Silent_p.T2000T	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2176					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										ACTGGATGACGGTGCAATATG	0.547													G|||	532	0.10623	0.1815	0.0634	5008	,	,		21125	0.004		0.0825	False		,,,				2504	0.1646				p.T2167T		Atlas-SNP	.											ODZ2_ENST00000519204,NS,carcinoma,+1,6	.	.	6	0			c.G6501A						PASS	.	G		616,3524		45,526,1499	108.0	103.0	105.0		6501	-11.0	0.2	5	dbSNP_123	105	764,7646		32,700,3473	no	coding-synonymous	ODZ2	NM_001122679.1		77,1226,4972	AA,AG,GG		9.0844,14.8792,10.996		2167/2766	167674472	1380,11170	2070	4205	6275	SO:0001819	synonymous_variant	57451	exon27			GATGACGGTGCAA	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.6528G>A	5.37:g.167674472G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	160	160	1	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				G|0.910;A|0.090	0.090	strong		0.547	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
CCDC129	223075	hgsc.bcm.edu	37	7	31594508	31594508	+	Silent	SNP	C	C	T	rs2286711	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:31594508C>T	ENST00000407970.3	+	4	287	c.249C>T	c.(247-249)gaC>gaT	p.D83D	CCDC129_ENST00000409210.1_5'UTR|CCDC129_ENST00000451887.2_Silent_p.D109D|CCDC129_ENST00000319386.3_Silent_p.D83D|CCDC129_ENST00000482748.1_3'UTR	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	83										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AAGTCATTGACCGCACTGGTA	0.318													C|||	1146	0.228834	0.1551	0.1671	5008	,	,		17987	0.3313		0.2435	False		,,,				2504	0.2515				p.D109D		Atlas-SNP	.											.	CCDC129	127	.	0			c.C327T						PASS	.	C		788,3618		83,622,1498	49.0	45.0	46.0		249	3.2	0.1	7	dbSNP_100	46	2031,6567		263,1505,2531	no	coding-synonymous	CCDC129	NM_194300.2		346,2127,4029	TT,TC,CC		23.6218,17.8847,21.6779		83/1045	31594508	2819,10185	2203	4299	6502	SO:0001819	synonymous_variant	223075	exon4			CATTGACCGCACT	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.249C>T	7.37:g.31594508C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	160	78	0.4875	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Silent	SNP	ENST00000407970.3	37	CCDS5435.2																																																																																			C|0.772;T|0.228	0.228	strong		0.318	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
FRRS1	391059	hgsc.bcm.edu	37	1	100182997	100182997	+	Missense_Mutation	SNP	G	G	C	rs149801998		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:100182997G>C	ENST00000414213.1	-	11	1806	c.1205C>G	c.(1204-1206)gCt>gGt	p.A402G	FRRS1_ENST00000287474.5_Missense_Mutation_p.A402G|FRRS1_ENST00000492943.1_5'Flank			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	402	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		AAGCAAGAAAGCTTTTGACCA	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		22156	0.0		0.001	False		,,,				2504	0.0				p.A402G		Atlas-SNP	.											.	FRRS1	50	.	0			c.C1205G						PASS	.	G	GLY/ALA	0,4406		0,0,2203	163.0	157.0	159.0		1205	3.2	0.6	1	dbSNP_134	159	12,8588	9.1+/-34.3	0,12,4288	yes	missense	FRRS1	NM_001013660.2	60	0,12,6491	CC,CG,GG		0.1395,0.0,0.0923	benign	402/627	100182997	12,12994	2203	4300	6503	SO:0001583	missense	391059	exon11			AAGAAAGCTTTTG	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"""stromal cell derived factor receptor 2 homolog (mouse)"""	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.1205C>G	1.37:g.100182997G>C	ENSP00000393884:p.Ala402Gly	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_001013660	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	G	11.14	1.550414	0.27739	0.0	0.001395	ENSG00000156869	ENST00000414213;ENST00000287474	.	.	.	5.03	3.16	0.36331	.	0.744958	0.13319	N	0.396864	T	0.23054	0.0557	L	0.54323	1.7	0.09310	N	0.99999	B	0.15930	0.015	B	0.19666	0.026	T	0.26538	-1.0100	9	0.40728	T	0.16	-1.6172	9.3248	0.37986	0.2357:0.0:0.7643:0.0	.	402	Q6ZNA5-2	.	G	402	.	ENSP00000287474:A402G	A	-	2	0	FRRS1	99955585	0.017000	0.18338	0.612000	0.29024	0.767000	0.43475	1.388000	0.34442	0.633000	0.30452	0.561000	0.74099	GCT	G|0.999;C|0.001	0.001	strong		0.398	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
PLEC	5339	hgsc.bcm.edu	37	8	144993377	144993377	+	Silent	SNP	A	A	G	rs6992333	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144993377A>G	ENST00000322810.4	-	32	11192	c.11023T>C	c.(11023-11025)Ttg>Ctg	p.L3675L	PLEC_ENST00000398774.2_Silent_p.L3506L|PLEC_ENST00000345136.3_Silent_p.L3538L|PLEC_ENST00000354589.3_Silent_p.L3538L|PLEC_ENST00000354958.2_Silent_p.L3516L|PLEC_ENST00000436759.2_Silent_p.L3565L|PLEC_ENST00000527096.1_Silent_p.L3561L|PLEC_ENST00000356346.3_Silent_p.L3524L|PLEC_ENST00000357649.2_Silent_p.L3542L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3675	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						AGAAGGCGCAAGCCCGTCTCG	0.607													G|||	2363	0.471845	0.8918	0.3746	5008	,	,		16831	0.1438		0.4324	False		,,,				2504	0.3517				p.L3675L		Atlas-SNP	.											.	PLEC	1144	.	0			c.T11023C						PASS	.	G	,,,,,,,	3429,675		1444,541,67	73.0	89.0	84.0		10693,10570,10546,11023,10516,10612,10624,10612	2.9	0.8	8	dbSNP_116	84	3601,4801		800,2001,1400	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	2244,2542,1467	GG,GA,AA		42.8588,16.4474,43.787	,,,,,,,	3565/4575,3524/4534,3516/4526,3675/4685,3506/4516,3538/4548,3542/4552,3538/4548	144993377	7030,5476	2052	4201	6253	SO:0001819	synonymous_variant	5339	exon32			GGCGCAAGCCCGT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.11023T>C	8.37:g.144993377A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	107	46	0.429907	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			A|0.544;G|0.456	0.456	strong		0.607	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
COL16A1	1307	hgsc.bcm.edu	37	1	32165495	32165495	+	Missense_Mutation	SNP	G	G	T	rs2228552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32165495G>T	ENST00000373672.3	-	4	701	c.185C>A	c.(184-186)aCg>aAg	p.T62K	COL16A1_ENST00000271069.6_Missense_Mutation_p.T62K|COL16A1_ENST00000373668.3_Missense_Mutation_p.T62K	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	62	Laminin G-like.		T -> K (in dbSNP:rs2228552). {ECO:0000269|PubMed:1631157}.		cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		GATGGCAGACGTCTTCATGAG	0.607													g|||	2140	0.427316	0.261	0.4553	5008	,	,		18858	0.2708		0.6481	False		,,,				2504	0.5665				p.T62K	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											COL16A1,colon,carcinoma,0,1	COL16A1	137	1	0			c.C185A						PASS	.		LYS/THR	1393,2625		248,897,864	103.0	102.0	103.0		185	-2.4	0.1	1	dbSNP_98	103	5284,3044		1698,1888,578	yes	missense	COL16A1	NM_001856.3	78	1946,2785,1442	TT,TG,GG		36.5514,34.669,45.9177	benign	62/1605	32165495	6677,5669	2009	4164	6173	SO:0001583	missense	1307	exon4			GCAGACGTCTTCA	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.185C>A	1.37:g.32165495G>T	ENSP00000362776:p.Thr62Lys	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	37	CCDS41297.1	936	0.42857142857142855	125	0.2540650406504065	183	0.505524861878453	135	0.23601398601398602	493	0.6503957783641161	g	11.33	1.607805	0.28623	0.34669	0.634486	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668	T;T;T	0.24538	1.85;1.85;1.85	4.63	-2.4	0.06583	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.848291	0.10321	N	0.688765	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	D;B	0.54964	0.969;0.047	P;B	0.45195	0.473;0.045	T	0.37888	-0.9686	9	0.38643	T	0.18	.	8.0524	0.30585	0.4022:0.1013:0.4966:0.0	rs2228552;rs2297673;rs10798885;rs17498623;rs52810622;rs56583694;rs58033914;rs2228552	62;62	A6NCT7;Q07092	.;COGA1_HUMAN	K	62	ENSP00000362776:T62K;ENSP00000271069:T62K;ENSP00000362772:T62K	ENSP00000271069:T62K	T	-	2	0	COL16A1	31938082	0.000000	0.05858	0.076000	0.20297	0.704000	0.40688	-0.788000	0.04614	-1.129000	0.02918	-2.101000	0.00361	ACG	G|0.551;T|0.449	0.449	strong		0.607	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
TTN	7273	hgsc.bcm.edu	37	2	179395560	179395560	+	Missense_Mutation	SNP	G	G	A	rs16866380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179395560G>A	ENST00000591111.1	-	308	101083	c.100859C>T	c.(100858-100860)cCg>cTg	p.P33620L	TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P26196L|TTN_ENST00000342992.6_Missense_Mutation_p.P32693L|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P35261L|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P26321L|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P26388L|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000588804.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33620			P -> L. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACGGCTTTCGGGTGAGAAGG	0.498													G|||	397	0.0792732	0.0885	0.0403	5008	,	,		17438	0.1716		0.0318	False		,,,				2504	0.0481				p.P35261L		Atlas-SNP	.											.	TTN	18412	.	0			c.C105782T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	260,3546		9,242,1652	126.0	126.0	126.0		79163,78962,98078,78587	5.0	0.9	2	dbSNP_123	126	171,8049		4,163,3943	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	98,98,98,98	13,405,5595	AA,AG,GG		2.0803,6.8313,3.5839	benign,benign,benign,benign	26388/27119,26321/27052,32693/33424,26196/26927	179395560	431,11595	1903	4110	6013	SO:0001583	missense	7273	exon358			GCTTTCGGGTGAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.100859C>T	2.37:g.179395560G>A	ENSP00000465570:p.Pro33620Leu	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	366	191	0.521858	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		178	0.0815018315018315	41	0.08333333333333333	15	0.04143646408839779	100	0.17482517482517482	22	0.029023746701846966	G	14.57	2.573687	0.45902	0.068313	0.020803	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.69175	-0.38;-0.12;-0.14;-0.13	4.99	4.99	0.66335	Ribonuclease H-like (1);	.	.	.	.	T	0.00241	0.0007	L	0.32530	0.975	0.20764	P	0.999855559	B;B;B;B	0.32731	0.382;0.382;0.382;0.382	B;B;B;B	0.17098	0.017;0.017;0.017;0.017	T	0.17776	-1.0358	8	0.87932	D	0	.	18.2867	0.90117	0.0:0.0:1.0:0.0	rs16866380;rs52806480;rs16866380	26196;26321;26388;33620	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	32693;26196;26388;26321;26193	ENSP00000343764:P32693L;ENSP00000434586:P26196L;ENSP00000340554:P26388L;ENSP00000352154:P26321L	ENSP00000340554:P26388L	P	-	2	0	TTN	179103806	0.891000	0.30450	0.934000	0.37439	0.694000	0.40290	5.487000	0.66863	2.321000	0.78463	0.455000	0.32223	CCG	G|0.921;A|0.079	0.079	strong		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DOPEY1	23033	hgsc.bcm.edu	37	6	83880167	83880167	+	IGR	SNP	C	C	T	rs473267	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:83880167C>T	ENST00000349129.2	+	0	8210				PGM3_ENST00000283977.4_Missense_Mutation_p.D385N|PGM3_ENST00000513973.1_Missense_Mutation_p.D466N|PGM3_ENST00000512866.1_Missense_Mutation_p.D466N|PGM3_ENST00000506587.1_Missense_Mutation_p.D494N|DOPEY1_ENST00000484282.1_3'UTR	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1						protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CTTTCAGCATCGGTAGTGCTA	0.438													T|||	1778	0.355032	0.5877	0.2795	5008	,	,		17766	0.2877		0.2952	False		,,,				2504	0.2249				p.D494N		Atlas-SNP	.											.	PGM3	39	.	0			c.G1480A						PASS	.	T	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	2414,1992	557.4+/-379.7	645,1124,434	170.0	155.0	160.0		1480,1153,1396,1396	3.8	0.4	6	dbSNP_83	160	2174,6426	712.7+/-405.9	287,1600,2413	yes	missense,missense,missense,missense	PGM3	NM_001199917.1,NM_001199918.1,NM_001199919.1,NM_015599.2	23,23,23,23	932,2724,2847	TT,TC,CC		25.2791,45.2111,35.276	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	494/571,385/442,466/567,466/543	83880167	4588,8418	2203	4300	6503	SO:0001628	intergenic_variant	5238	exon13			CAGCATCGGTAGT	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365		6.37:g.83880167C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	200	198	0.99	NM_001199917	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	810	0.3708791208791209	299	0.6077235772357723	104	0.287292817679558	183	0.31993006993006995	224	0.2955145118733509	T	13.34	2.208459	0.39003	0.547889	0.252791	ENSG00000013375	ENST00000513973;ENST00000512866;ENST00000283977;ENST00000506587;ENST00000509219	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.6	3.8	0.43715	.	0.085352	0.85682	N	0.000000	T	0.17789	0.0427	L	0.43598	1.365	0.21553	P	0.999645667	B;B;B	0.34349	0.45;0.038;0.243	B;B;B	0.34385	0.181;0.045;0.061	T	0.03630	-1.1018	9	0.28530	T	0.3	-45.2701	11.7024	0.51579	0.0:0.79:0.0:0.21	rs473267;rs1058809;rs1741359;rs3173065;rs17856040;rs59744941;rs473267	494;494;466	E9PF86;B4DX94;O95394	.;.;AGM1_HUMAN	N	466;466;385;494;97	ENSP00000424874:D466N;ENSP00000421565:D466N;ENSP00000283977:D385N;ENSP00000425809:D494N;ENSP00000423389:D97N	ENSP00000283977:D385N	D	-	1	0	PGM3	83936886	0.997000	0.39634	0.412000	0.26496	0.001000	0.01503	3.562000	0.53777	0.400000	0.25396	-1.014000	0.02459	GAT	C|0.638;N|0.000	.	strong		0.438	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
KCNU1	157855	hgsc.bcm.edu	37	8	36767024	36767024	+	Missense_Mutation	SNP	T	T	C	rs28608091	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:36767024T>C	ENST00000399881.3	+	21	2339	c.2302T>C	c.(2302-2304)Tgg>Cgg	p.W768R		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	768			W -> R (in dbSNP:rs28608091).		multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		GCGATTTCTCTGGAATTTTCC	0.363													C|||	1902	0.379792	0.3268	0.4827	5008	,	,		16997	0.376		0.4006	False		,,,				2504	0.3609				p.W768R		Atlas-SNP	.											.	KCNU1	359	.	0			c.T2302C						PASS	.	C	ARG/TRP	1230,2436		205,820,808	115.0	114.0	114.0		2302	2.6	1.0	8	dbSNP_125	114	3255,4909		659,1937,1486	yes	missense	KCNU1	NM_001031836.2	101	864,2757,2294	CC,CT,TT		39.8702,33.5516,37.9121	benign	768/1150	36767024	4485,7345	1833	4082	5915	SO:0001583	missense	157855	exon21			TTTCTCTGGAATT	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2302T>C	8.37:g.36767024T>C	ENSP00000382770:p.Trp768Arg	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	140	69	0.492857	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	811	0.37133699633699635	144	0.2926829268292683	169	0.46685082872928174	203	0.3548951048951049	295	0.3891820580474934	C	0.875	-0.730645	0.03135	0.335516	0.398702	ENSG00000215262	ENST00000399881	T	0.39787	1.06	5.8	2.64	0.31445	.	0.229234	0.21687	N	0.070624	T	0.00012	0.0000	N	0.01267	-0.92	0.09310	P	0.99999999579857	B	0.02656	0.0	B	0.01281	0.0	T	0.46484	-0.9188	9	0.06494	T	0.89	-4.8224	8.6358	0.33948	0.2308:0.6384:0.0:0.1308	rs28608091	768	A8MYU2	KCNU1_HUMAN	R	768	ENSP00000382770:W768R	ENSP00000382770:W768R	W	+	1	0	KCNU1	36886182	0.670000	0.27512	0.979000	0.43373	0.017000	0.09413	1.370000	0.34238	0.356000	0.24157	-0.119000	0.15052	TGG	T|0.627;C|0.373	0.373	strong		0.363	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
RNF113B	140432	hgsc.bcm.edu	37	13	98829217	98829217	+	Missense_Mutation	SNP	C	C	T	rs16955011	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:98829217C>T	ENST00000267291.6	-	1	302	c.274G>A	c.(274-276)Gtg>Atg	p.V92M	FARP1_ENST00000595437.1_Intron|FARP1_ENST00000319562.6_Intron|FARP1_ENST00000376586.2_Intron|FARP1_ENST00000376581.5_Intron	NM_178861.4	NP_849192.1	Q8IZP6	R113B_HUMAN	ring finger protein 113B	92			V -> M (in dbSNP:rs16955011).				zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.13)			CTGTACACCACGTCGAGGCTC	0.721													C|||	571	0.114018	0.1959	0.1153	5008	,	,		13867	0.0635		0.0696	False		,,,				2504	0.1002				p.V92M		Atlas-SNP	.											.	RNF113B	41	.	0			c.G274A						PASS	.	C	,,MET/VAL	703,3703	291.5+/-281.6	63,577,1563	39.0	39.0	39.0		,,274	0.2	0.0	13	dbSNP_123	39	497,8101	141.9+/-198.1	18,461,3820	yes	intron,intron,missense	FARP1,RNF113B	NM_001001715.2,NM_005766.2,NM_178861.4	,,21	81,1038,5383	TT,TC,CC		5.7804,15.9555,9.2279	,,possibly-damaging	,,92/323	98829217	1200,11804	2203	4299	6502	SO:0001583	missense	140432	exon1			ACACCACGTCGAG	AF539427	CCDS9486.1	13q32.2	2006-08-22	2005-03-22	2005-03-22	ENSG00000139797	ENSG00000139797		"""RING-type (C3HC4) zinc fingers"""	17267	protein-coding gene	gene with protein product			"""zinc finger protein 183-like 1"""	ZNF183L1			Standard	NM_178861		Approved	RNF161	uc001vnk.3	Q8IZP6	OTTHUMG00000017245	ENST00000267291.6:c.274G>A	13.37:g.98829217C>T	ENSP00000267291:p.Val92Met	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	41	23	0.560976	NM_178861	Q8WWF9|Q96QY9	Missense_Mutation	SNP	ENST00000267291.6	37	CCDS9486.1	226	0.10347985347985347	90	0.18292682926829268	45	0.12430939226519337	40	0.06993006993006994	51	0.06728232189973615	C	10.89	1.477709	0.26511	0.159555	0.057804	ENSG00000139797	ENST00000267291	T	0.34667	1.35	1.16	0.21	0.15231	.	0.075401	0.52532	U	0.000073	T	0.00109	0.0003	M	0.90814	3.15	0.80722	P	0.0	D	0.58268	0.982	P	0.47402	0.546	T	0.04885	-1.0920	9	0.72032	D	0.01	.	6.2308	0.20734	0.0:0.7862:0.0:0.2138	rs16955011;rs16955011	92	Q8IZP6	R113B_HUMAN	M	92	ENSP00000267291:V92M	ENSP00000267291:V92M	V	-	1	0	RNF113B	97627218	0.014000	0.17966	0.017000	0.16124	0.002000	0.02628	0.490000	0.22403	-0.377000	0.07930	-1.626000	0.00786	GTG	C|0.904;T|0.096	0.096	strong		0.721	RNF113B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045536.3	NM_178861	
CAPN10	11132	hgsc.bcm.edu	37	2	241533345	241533345	+	Silent	SNP	C	C	T	rs13007017	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241533345C>T	ENST00000391984.2	+	5	907	c.711C>T	c.(709-711)ttC>ttT	p.F237F	CAPN10_ENST00000404753.3_Silent_p.F237F|CAPN10_ENST00000391982.2_Silent_p.F237F|CAPN10_ENST00000270364.7_Intron|CAPN10_ENST00000354082.4_Silent_p.F237F|CAPN10_ENST00000352879.4_Intron	NM_023083.3	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10	237	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				actin cytoskeleton reorganization (GO:0031532)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to insulin stimulus (GO:0032869)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin secretion (GO:0032024)|positive regulation of intracellular transport (GO:0032388)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteolysis (GO:0006508)|type B pancreatic cell apoptotic process (GO:0097050)	cell (GO:0005623)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cytoskeletal protein binding (GO:0008092)|SNARE binding (GO:0000149)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|urinary_tract(1)	27		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)		TGGGGGAGTTCCATGCCTTCA	0.662													C|||	85	0.0169728	0.0008	0.0231	5008	,	,		17992	0.0		0.0666	False		,,,				2504	0.001				p.F237F		Atlas-SNP	.											.	CAPN10	105	.	0			c.C711T						PASS	.	C	,	41,4365	42.3+/-75.8	0,41,2162	118.0	119.0	119.0		711,711	-1.9	0.9	2	dbSNP_121	119	451,8149	133.8+/-191.2	10,431,3859	no	coding-synonymous,coding-synonymous	CAPN10	NM_023083.3,NM_023085.3	,	10,472,6021	TT,TC,CC		5.2442,0.9305,3.7829	,	237/673,237/518	241533345	492,12514	2203	4300	6503	SO:0001819	synonymous_variant	11132	exon5			GGAGTTCCATGCC	AF089088	CCDS33420.1, CCDS42838.1	2q37.3	2008-05-22			ENSG00000142330	ENSG00000142330			1477	protein-coding gene	gene with protein product		605286				11017071, 11018080	Standard	NM_023083		Approved		uc002vzk.2	Q9HC96	OTTHUMG00000133358	ENST00000391984.2:c.711C>T	2.37:g.241533345C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	169	76	0.449704	NM_023085	A8MVS7|Q4ZFV1|Q8NCD4|Q96IG4|Q96JI2|Q9HC89|Q9HC90|Q9HC91|Q9HC92|Q9HC93|Q9HC94|Q9HC95	Silent	SNP	ENST00000391984.2	37	CCDS42838.1																																																																																			C|0.961;T|0.039	0.039	strong		0.662	CAPN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257191.3	NM_023083	
ABCA3	21	hgsc.bcm.edu	37	16	2367336	2367336	+	Silent	SNP	G	G	A	rs13332514	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2367336G>A	ENST00000301732.5	-	10	1759	c.1059C>T	c.(1057-1059)ttC>ttT	p.F353F	ABCA3_ENST00000382381.3_Silent_p.F353F	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	353					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	TAGAGATGGCGAAGCACAGCA	0.622													G|||	965	0.192692	0.0764	0.3228	5008	,	,		21181	0.372		0.0934	False		,,,				2504	0.1748				p.F353F		Atlas-SNP	.											.	ABCA3	176	.	0			c.C1059T						PASS	.	G		383,4013	192.3+/-217.7	17,349,1832	125.0	110.0	115.0		1059	-1.1	0.8	16	dbSNP_121	115	847,7753	193.1+/-238.9	36,775,3489	no	coding-synonymous	ABCA3	NM_001089.2		53,1124,5321	AA,AG,GG		9.8488,8.7125,9.4645		353/1705	2367336	1230,11766	2198	4300	6498	SO:0001819	synonymous_variant	21	exon10			GATGGCGAAGCAC	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"""ATP binding cassette transporters / subfamily A"""	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.1059C>T	16.37:g.2367336G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			G|0.869;A|0.131	0.131	strong		0.622	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
KRT40	125115	hgsc.bcm.edu	37	17	39139370	39139370	+	Missense_Mutation	SNP	G	G	A	rs9908304	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39139370G>A	ENST00000398486.2	-	4	618	c.458C>T	c.(457-459)aCg>aTg	p.T153M	KRT40_ENST00000377755.4_Missense_Mutation_p.T153M	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	153	Coil 1B.|Rod.		T -> M (in dbSNP:rs9908304).			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				CTCTGCTTTCGTGCATAAGAT	0.338													G|||	1809	0.361222	0.6861	0.2378	5008	,	,		15802	0.1716		0.2684	False		,,,				2504	0.3006				p.T153M		Atlas-SNP	.											.	KRT40	27	.	0			c.C458T						PASS	.	G	MET/THR	2217,1477		676,865,306	155.0	153.0	154.0		458	4.7	0.9	17	dbSNP_119	154	2256,5930		305,1646,2142	yes	missense	KRT40	NM_182497.3	81	981,2511,2448	AA,AG,GG		27.5592,39.9838,37.6515	probably-damaging	153/432	39139370	4473,7407	1847	4093	5940	SO:0001583	missense	125115	exon4			GCTTTCGTGCATA	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.458C>T	17.37:g.39139370G>A	ENSP00000381500:p.Thr153Met	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	733	0.3356227106227106	338	0.6869918699186992	92	0.2541436464088398	96	0.16783216783216784	207	0.27308707124010556	G	18.40	3.615102	0.66672	0.600162	0.275592	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.89123	-2.47;-2.47	5.72	4.72	0.59763	Filament (1);	.	.	.	.	T	0.00012	0.0000	M	0.68317	2.08	0.31417	P	0.6747449999999999	D	0.71674	0.998	D	0.74674	0.984	T	0.49331	-0.8951	8	0.87932	D	0	.	13.2977	0.60307	0.0792:0.0:0.9208:0.0	rs9908304;rs17646931;rs9908304	153	Q6A162	K1C40_HUMAN	M	153	ENSP00000366984:T153M;ENSP00000381500:T153M	ENSP00000366984:T153M	T	-	2	0	KRT40	36392896	0.443000	0.25641	0.908000	0.35775	0.786000	0.44442	2.736000	0.47385	1.490000	0.48466	0.591000	0.81541	ACG	G|0.630;A|0.370	0.370	strong		0.338	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
TAS2R5	54429	hgsc.bcm.edu	37	7	141490325	141490325	+	Missense_Mutation	SNP	G	G	A	rs147887777		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:141490325G>A	ENST00000247883.4	+	1	309	c.164G>A	c.(163-165)cGa>cAa	p.R55Q		NM_018980.2	NP_061853.1	Q9NYW4	TA2R5_HUMAN	taste receptor, type 2, member 5	55					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.R55Q(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9	Melanoma(164;0.0171)					GCTGGCTGCCGATTTCTCCTG	0.468													g|||	1	0.000199681	0.0	0.0014	5008	,	,		19581	0.0		0.0	False		,,,				2504	0.0				p.R55Q		Atlas-SNP	.											TAS2R5,colon,carcinoma,0,1	TAS2R5	33	1	1	Substitution - Missense(1)	large_intestine(1)	c.G164A						PASS	.	G	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	112.0	107.0	109.0		164	1.7	0.0	7	dbSNP_134	109	17,8583	12.6+/-44.7	0,17,4283	yes	missense	TAS2R5	NM_018980.2	43	0,20,6483	AA,AG,GG		0.1977,0.0681,0.1538	probably-damaging	55/300	141490325	20,12986	2203	4300	6503	SO:0001583	missense	54429	exon1			GCTGCCGATTTCT	AF227132	CCDS5869.1	7q31.3-q32	2012-08-22			ENSG00000127366	ENSG00000127366		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14912	protein-coding gene	gene with protein product		605062					Standard	NM_018980		Approved	T2R5	uc003vwr.1	Q9NYW4	OTTHUMG00000157632	ENST00000247883.4:c.164G>A	7.37:g.141490325G>A	ENSP00000247883:p.Arg55Gln	Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	236	135	0.572034	NM_018980	Q645W0|Q75MV7	Missense_Mutation	SNP	ENST00000247883.4	37	CCDS5869.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	12.07	1.828778	0.32329	6.81E-4	0.001977	ENSG00000127366	ENST00000247883	T	0.37058	1.22	4.46	1.67	0.24075	.	.	.	.	.	T	0.57989	0.2091	M	0.84683	2.71	0.09310	N	1	D	0.76494	0.999	D	0.70716	0.97	T	0.45249	-0.9274	9	0.87932	D	0	.	6.4583	0.21942	0.3113:0.0:0.6887:0.0	.	55	Q9NYW4	TA2R5_HUMAN	Q	55	ENSP00000247883:R55Q	ENSP00000247883:R55Q	R	+	2	0	TAS2R5	141136794	0.130000	0.22417	0.009000	0.14445	0.033000	0.12548	1.820000	0.39032	0.162000	0.19483	0.561000	0.74099	CGA	G|0.999;A|0.001	0.001	strong		0.468	TAS2R5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349283.1		
GLRA3	8001	hgsc.bcm.edu	37	4	175688141	175688141	+	Silent	SNP	G	G	A	rs12651268|rs201682361	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:175688141G>A	ENST00000274093.3	-	3	742	c.240C>T	c.(238-240)agC>agT	p.S80S	GLRA3_ENST00000340217.5_Silent_p.S80S	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	80					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)|Ivermectin(DB00602)|Lindane(DB00431)	TAGAGCCAAAGCTGTTGATGA	0.353													G|||	1696	0.338658	0.1142	0.3242	5008	,	,		16006	0.5198		0.3708	False		,,,				2504	0.4325				p.S80S		Atlas-SNP	.											.	GLRA3	76	.	0			c.C240T						PASS	.	G	,	53,4353		24,5,2174	168.0	160.0	163.0		240,240	4.8	1.0	4	dbSNP_120	163	621,7979		243,135,3922	no	coding-synonymous,coding-synonymous	GLRA3	NM_001042543.1,NM_006529.2	,	267,140,6096	AA,AG,GG		7.2209,1.2029,5.1822	,	80/450,80/465	175688141	674,12332	2203	4300	6503	SO:0001819	synonymous_variant	8001	exon3			GCCAAAGCTGTTG	AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"""Ligand-gated ion channels / Glycine receptors"""	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.240C>T	4.37:g.175688141G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_001042543	D3DP44|O75816|Q5D0E3	Silent	SNP	ENST00000274093.3	37	CCDS3822.1																																																																																			G|0.704;A|0.296	0.296	strong		0.353	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1		
MYBPH	4608	hgsc.bcm.edu	37	1	203143725	203143725	+	Splice_Site	SNP	G	G	C	rs2642531	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:203143725G>C	ENST00000255416.4	-	3	398	c.341C>G	c.(340-342)gCc>gGc	p.A114G		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H	114	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		A -> G (in dbSNP:rs2642531).		cell adhesion (GO:0007155)|regulation of striated muscle contraction (GO:0006942)	myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			endometrium(5)|large_intestine(6)|lung(7)|skin(1)|urinary_tract(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.153)	Colorectal(1306;0.0306)		CCACTCCGAGGCTGAGGGGAT	0.612													g|||	1271	0.253794	0.528	0.2522	5008	,	,		17735	0.1468		0.1352	False		,,,				2504	0.1166				p.A114G	NSCLC(32;174 1025 14462 23899 42933)	Atlas-SNP	.											.	MYBPH	41	.	0			c.C341G						PASS	.	C	GLY/ALA	2143,2263		534,1075,594	28.0	23.0	25.0		341	4.6	1.0	1	dbSNP_100	25	1124,7476		86,952,3262	yes	missense-near-splice	MYBPH	NM_004997.2	60	620,2027,3856	CC,CG,GG		13.0698,48.6382,25.1192	benign	114/478	203143725	3267,9739	2203	4300	6503	SO:0001630	splice_region_variant	4608	exon3			TCCGAGGCTGAGG	BC044226	CCDS30975.1	1q32.1	2013-02-11	2001-11-28		ENSG00000133055	ENSG00000133055		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7552	protein-coding gene	gene with protein product		160795	"""myosin-binding protein H"""			8486381	Standard	NM_004997		Approved		uc001gzh.1	Q13203	OTTHUMG00000042121	ENST00000255416.4:c.341-1C>G	1.37:g.203143725G>C		Somatic	316	1	0.00316456		WXS	Illumina HiSeq	Phase_I	389	174	0.447301	NM_004997	Q16886|Q86YC5	Missense_Mutation	SNP	ENST00000255416.4	37	CCDS30975.1	536	0.2454212454212454	263	0.5345528455284553	85	0.23480662983425415	91	0.1590909090909091	97	0.1279683377308707	g	10.09	1.255596	0.22965	0.486382	0.130698	ENSG00000133055	ENST00000255416	T	0.54866	0.55	5.53	4.62	0.57501	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.133482	0.34245	N	0.004140	T	0.00012	0.0000	N	0.17872	0.535	0.30470	P	0.773413	B	0.20780	0.048	B	0.25614	0.062	T	0.45600	-0.9250	9	0.45353	T	0.12	.	12.5921	0.56449	0.0:0.1669:0.8331:0.0	rs2642531;rs3820146;rs59912116;rs2642531	114	Q13203	MYBPH_HUMAN	G	114	ENSP00000255416:A114G	ENSP00000255416:A114G	A	-	2	0	MYBPH	201410348	0.997000	0.39634	1.000000	0.80357	0.037000	0.13140	1.982000	0.40638	1.346000	0.45694	-0.121000	0.15023	GCC	G|0.736;C|0.264	0.264	strong		0.612	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	NM_004997	Missense_Mutation
EVA1C	59271	hgsc.bcm.edu	37	21	33830006	33830006	+	Silent	SNP	G	G	A	rs55878843	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:33830006G>A	ENST00000300255.2	+	3	932	c.459G>A	c.(457-459)ctG>ctA	p.L153L	EVA1C_ENST00000401402.3_Silent_p.L153L|EVA1C_ENST00000382699.3_Silent_p.L153L	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	153	SUEL-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00260}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										AATACCTCCTGGTCTCCTTTA	0.517													G|||	147	0.029353	0.0023	0.0187	5008	,	,		18558	0.001		0.0785	False		,,,				2504	0.0521				p.L153L		Atlas-SNP	.											.	.	.	.	0			c.G459A						PASS	.	G		77,4329	69.2+/-107.0	2,73,2128	97.0	82.0	87.0		459	4.9	1.0	21	dbSNP_129	87	684,7916	170.0+/-221.2	38,608,3654	no	coding-synonymous	C21orf63	NM_058187.3		40,681,5782	AA,AG,GG		7.9535,1.7476,5.8511		153/442	33830006	761,12245	2203	4300	6503	SO:0001819	synonymous_variant	59271	exon3			CCTCCTGGTCTCC	AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 64"", ""chromosome 21 open reading frame 63"", ""family with sequence similarity 176, member C"""	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.459G>A	21.37:g.33830006G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	163	75	0.460123	NM_058187	A6ND58|Q8IXZ0	Silent	SNP	ENST00000300255.2	37	CCDS13614.1																																																																																			G|0.948;A|0.052	0.052	strong		0.517	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187	
PROM2	150696	hgsc.bcm.edu	37	2	95947099	95947099	+	Missense_Mutation	SNP	G	G	A	rs72819488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:95947099G>A	ENST00000317620.9	+	12	1670	c.1537G>A	c.(1537-1539)Ggc>Agc	p.G513S	PROM2_ENST00000542147.1_Missense_Mutation_p.G513S|PROM2_ENST00000403131.2_Missense_Mutation_p.G513S|PROM2_ENST00000317668.4_Missense_Mutation_p.G513S	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	513				G -> S (in Ref. 3; BAC03657). {ECO:0000305}.	negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						CTGGGAGAACGGCGAGCTCTT	0.637													G|||	504	0.100639	0.003	0.0879	5008	,	,		14390	0.2004		0.1382	False		,,,				2504	0.1002				p.G513S		Atlas-SNP	.											.	PROM2	78	.	0			c.G1537A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	126,4280	92.5+/-131.2	0,126,2077	62.0	60.0	61.0		1537,1537,1537	1.6	0.1	2	dbSNP_130	61	1215,7385	246.5+/-274.9	85,1045,3170	yes	missense,missense,missense	PROM2	NM_001165977.1,NM_001165978.1,NM_144707.2	56,56,56	85,1171,5247	AA,AG,GG		14.1279,2.8597,10.3106	possibly-damaging,possibly-damaging,possibly-damaging	513/835,513/835,513/835	95947099	1341,11665	2203	4300	6503	SO:0001583	missense	150696	exon12			GAGAACGGCGAGC	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.1537G>A	2.37:g.95947099G>A	ENSP00000318270:p.Gly513Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_001165977	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Missense_Mutation	SNP	ENST00000317620.9	37	CCDS2012.1	253	0.11584249084249085	2	0.0040650406504065045	24	0.06629834254143646	114	0.1993006993006993	113	0.14907651715039577	G	12.21	1.869411	0.32977	0.028597	0.141279	ENSG00000155066	ENST00000403131;ENST00000317668;ENST00000317620;ENST00000542147	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.07	1.65	0.23941	.	0.772089	0.11975	N	0.511351	T	0.00039	0.0001	M	0.68952	2.095	0.80722	P	0.0	D	0.58970	0.984	P	0.51918	0.684	T	0.12785	-1.0534	9	0.10377	T	0.69	-7.9994	4.4445	0.11591	0.2656:0.2336:0.5007:0.0	.	513	Q8N271	PROM2_HUMAN	S	513	ENSP00000385716:G513S;ENSP00000318520:G513S;ENSP00000318270:G513S;ENSP00000442542:G513S	ENSP00000318270:G513S	G	+	1	0	PROM2	95310826	0.044000	0.20184	0.062000	0.19696	0.034000	0.12701	0.897000	0.28390	0.357000	0.24183	0.561000	0.74099	GGC	G|0.895;A|0.105	0.105	strong		0.637	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707	
DSG4	147409	hgsc.bcm.edu	37	18	28968371	28968371	+	Silent	SNP	G	G	A	rs16959856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:28968371G>A	ENST00000308128.4	+	4	393	c.258G>A	c.(256-258)cgG>cgA	p.R86R	DSG4_ENST00000359747.4_Silent_p.R86R|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	86	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TAACATACCGGATTTCTGGAG	0.403													A|||	3609	0.720647	0.5257	0.8617	5008	,	,		19285	0.8839		0.7644	False		,,,				2504	0.6708				p.R86R		Atlas-SNP	.											DSG4_ENST00000359747,NS,malignant_melanoma,+1,4	DSG4	343	4	0			c.G258A						PASS	.	A	,	2472,1934	549.4+/-377.8	703,1066,434	110.0	97.0	101.0		258,258	-4.6	0.7	18	dbSNP_123	101	6557,2041	355.0+/-329.7	2500,1557,242	no	coding-synonymous,coding-synonymous	DSG4	NM_001134453.1,NM_177986.3	,	3203,2623,676	AA,AG,GG		23.7381,43.8947,30.5675	,	86/1060,86/1041	28968371	9029,3975	2203	4299	6502	SO:0001819	synonymous_variant	147409	exon4			ATACCGGATTTCT	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.258G>A	18.37:g.28968371G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Silent	SNP	ENST00000308128.4	37	CCDS11897.1																																																																																			G|0.274;A|0.726	0.726	strong		0.403	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
ABCF2	10061	hgsc.bcm.edu	37	7	150916228	150916228	+	Silent	SNP	G	G	A	rs6949587	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:150916228G>A	ENST00000287844.2	-	8	1048	c.939C>T	c.(937-939)taC>taT	p.Y313Y	ABCF2_ENST00000473874.1_5'UTR|ABCF2_ENST00000222388.2_Silent_p.Y313Y	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	313	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCGTCTTCACGTACTGATCAT	0.498													G|||	2100	0.419329	0.2095	0.4107	5008	,	,		19404	0.7202		0.4563	False		,,,				2504	0.3609				p.Y313Y		Atlas-SNP	.											.	ABCF2	54	.	0			c.C939T						PASS	.	G	,	992,3414	368.8+/-318.8	111,770,1322	173.0	151.0	158.0		939,939	0.3	1.0	7	dbSNP_116	158	3537,5063	514.7+/-378.4	717,2103,1480	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	828,2873,2802	AA,AG,GG		41.1279,22.5148,34.8224	,	313/635,313/624	150916228	4529,8477	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon8			CTTCACGTACTGA	AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"""ATP binding cassette transporters / subfamily F"""	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.939C>T	7.37:g.150916228G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	119	63	0.529412	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			G|0.611;A|0.389	0.389	strong		0.498	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
KIAA1671	85379	hgsc.bcm.edu	37	22	25570273	25570273	+	Silent	SNP	G	G	A	rs5760891	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25570273G>A	ENST00000406486.4	+	9	5103	c.4716G>A	c.(4714-4716)ttG>ttA	p.L1572L	KIAA1671_ENST00000358431.3_Silent_p.L1572L|KIAA1671_ENST00000401395.1_Silent_p.L79L			Q9BY89	K1671_HUMAN	KIAA1671	1572										autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						GCAGCCGTTTGTCTTCTCTGT	0.592													G|||	447	0.0892572	0.0499	0.0994	5008	,	,		18016	0.1567		0.0666	False		,,,				2504	0.089				p.L1572L		Atlas-SNP	.											.	KIAA1671	28	.	0			c.G4716A						PASS	.	G		78,1306		0,78,614	28.0	32.0	31.0		4716	2.6	0.1	22	dbSNP_114	31	174,3008		6,162,1423	no	coding-synonymous	KIAA1671	NM_001145206.1		6,240,2037	AA,AG,GG		5.4683,5.6358,5.5191		1572/1807	25570273	252,4314	692	1591	2283	SO:0001819	synonymous_variant	85379	exon6			CCGTTTGTCTTCT		CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077			29345	protein-coding gene	gene with protein product						15289310	Standard	NM_001145206		Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.4716G>A	22.37:g.25570273G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	147	71	0.482993	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			G|0.898;A|0.102	0.102	strong		0.592	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	
KANSL1	284058	hgsc.bcm.edu	37	17	44248769	44248769	+	Silent	SNP	T	T	C	rs566672630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44248769T>C	ENST00000262419.6	-	2	1211	c.741A>G	c.(739-741)agA>agG	p.R247R	KANSL1_ENST00000574590.1_Silent_p.R247R|KANSL1_ENST00000575318.1_Silent_p.R247R|KANSL1_ENST00000572904.1_Silent_p.R247R|KANSL1_ENST00000432791.1_Silent_p.R247R|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000393476.3_5'UTR	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	247					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CAGGTGATAATCTACTGCTTC	0.438													C|||	437	0.0872604	0.0182	0.1571	5008	,	,		24930	0.001		0.2406	False		,,,				2504	0.0624				p.R247R		Atlas-SNP	.											.	.	.	.	0			c.A741G						PASS	.	C	,,	226,4180	805.7+/-415.8	6,214,1983	92.0	118.0	109.0		741,741,741	5.0	1.0	17	dbSNP_92	109	1936,6664	725.7+/-406.6	220,1496,2584	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	226,1710,4567	CC,CT,TT		22.5116,5.1294,16.6231	,,	247/1105,247/1106,247/1106	44248769	2162,10844	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon2			TGATAATCTACTG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.741A>G	17.37:g.44248769T>C		Somatic	431	1	0.00232019		WXS	Illumina HiSeq	Phase_I	528	222	0.420455	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			T|0.841;C|0.159	0.159	strong		0.438	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
TPSD1	23430	hgsc.bcm.edu	37	16	1306671	1306671	+	Silent	SNP	G	G	A	rs1141966	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306671G>A	ENST00000211076.3	+	2	385	c.237G>A	c.(235-237)gcG>gcA	p.A79A	TPSD1_ENST00000397534.2_Silent_p.A72A|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	79	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TGCTAACCGCGGCGCACTGCG	0.701													-|||	2225	0.444289	0.3351	0.3012	5008	,	,		17135	0.7946		0.3211	False		,,,				2504	0.4591				p.A79A		Atlas-SNP	.											.	TPSD1	47	.	0			c.G237A						PASS	.	G		1420,2978		209,1002,988	43.0	52.0	49.0		237	-6.0	0.0	16	dbSNP_86	49	2535,6061		359,1817,2122	no	coding-synonymous	TPSD1	NM_012217.2		568,2819,3110	AA,AG,GG		29.4905,32.2874,30.4371		79/243	1306671	3955,9039	2199	4298	6497	SO:0001819	synonymous_variant	23430	exon2			AACCGCGGCGCAC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.237G>A	16.37:g.1306671G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	173	88	0.508671	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			G|1.000;|0.000	.	weak		0.701	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
TTN	7273	hgsc.bcm.edu	37	2	179582327	179582327	+	Missense_Mutation	SNP	C	C	T	rs13390491	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179582327C>T	ENST00000591111.1	-	85	24547	c.24323G>A	c.(24322-24324)aGc>aAc	p.S8108N	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.S7181N|TTN_ENST00000589042.1_Missense_Mutation_p.S8425N|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12299	Ig-like 63.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCCTATGTGGCTCTGGTCAGT	0.423													C|||	1221	0.24381	0.1936	0.183	5008	,	,		21045	0.4355		0.1571	False		,,,				2504	0.2464				p.S8425N		Atlas-SNP	.											.	TTN	18412	.	0			c.G25274A						PASS	.	C	,,,ASN/SER	613,3149		46,521,1314	76.0	78.0	77.0		,,,21542	5.5	1.0	2	dbSNP_121	77	1242,6996		96,1050,2973	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,46	142,1571,4287	TT,TC,CC		15.0765,16.2945,15.4583	,,,benign	,,,7181/33424	179582327	1855,10145	1881	4119	6000	SO:0001583	missense	7273	exon87			ATGTGGCTCTGGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.24323G>A	2.37:g.179582327C>T	ENSP00000465570:p.Ser8108Asn	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	349	183	0.524355	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		512	0.23443223443223443	98	0.1991869918699187	55	0.15193370165745856	243	0.42482517482517484	116	0.15303430079155672	C	8.404	0.842666	0.16963	0.162945	0.150765	ENSG00000155657	ENST00000342992	T	0.68903	-0.36	5.51	5.51	0.81932	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.61036	1.89	0.19945	P	0.999942837	B	0.26602	0.154	B	0.22753	0.041	T	0.31613	-0.9937	8	0.87932	D	0	.	10.3596	0.43984	0.0:0.7257:0.2009:0.0734	rs13390491;rs52812757;rs58114390;rs13390491	8108	Q8WZ42	TITIN_HUMAN	N	7181	ENSP00000343764:S7181N	ENSP00000343764:S7181N	S	-	2	0	TTN	179290572	0.357000	0.24938	1.000000	0.80357	0.939000	0.58152	0.935000	0.28924	2.738000	0.93877	0.655000	0.94253	AGC	C|0.774;T|0.226	0.226	strong		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DPY19L2	283417	hgsc.bcm.edu	37	12	63954304	63954304	+	Silent	SNP	T	T	C	rs1054891	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:63954304T>C	ENST00000324472.4	-	22	2448	c.2265A>G	c.(2263-2265)ttA>ttG	p.L755L	DPY19L2_ENST00000413230.2_Silent_p.L202L	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	755					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		AGTTAACCTTTAATACTCTGT	0.418													N|||	2174	0.434105	0.7057	0.4568	5008	,	,		16369	0.2857		0.4245	False		,,,				2504	0.2137				p.L755L		Atlas-SNP	.											DPY19L2,colon,carcinoma,0,1	DPY19L2	97	1	0			c.A2265G						PASS	.	C		2776,1630	500.0+/-364.6	884,1008,311	85.0	80.0	82.0		2265	-1.3	0.3	12	dbSNP_86	82	3491,5109	633.6+/-398.7	694,2103,1503	no	coding-synonymous	DPY19L2	NM_173812.4		1578,3111,1814	CC,CT,TT		40.593,36.995,48.1855		755/759	63954304	6267,6739	2203	4300	6503	SO:0001819	synonymous_variant	283417	exon22			AACCTTTAATACT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.2265A>G	12.37:g.63954304T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	201	102	0.507463	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Silent	SNP	ENST00000324472.4	37	CCDS31851.1																																																																																			T|0.532;C|0.468	0.468	strong		0.418	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
PKP1	5317	hgsc.bcm.edu	37	1	201282573	201282573	+	Missense_Mutation	SNP	A	A	G	rs35507614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:201282573A>G	ENST00000352845.3	+	3	586	c.586A>G	c.(586-588)Ata>Gta	p.I196V	PKP1_ENST00000367324.3_Missense_Mutation_p.I196V|PKP1_ENST00000263946.3_Missense_Mutation_p.I196V			Q13835	PKP1_HUMAN	plakophilin 1	196			I -> V (in dbSNP:rs35507614).		apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						TCAGAAGGCCATAAAGAAGTG	0.617													A|||	520	0.103834	0.2814	0.0677	5008	,	,		17311	0.0		0.0616	False		,,,				2504	0.0399				p.I196V		Atlas-SNP	.											.	PKP1	127	.	0			c.A586G						PASS	.	A	VAL/ILE,VAL/ILE	1022,3384	352.8+/-311.9	120,782,1301	52.0	53.0	52.0		586,586	-4.2	0.0	1	dbSNP_126	52	501,8099	138.7+/-195.5	11,479,3810	yes	missense,missense	PKP1	NM_000299.3,NM_001005337.2	29,29	131,1261,5111	GG,GA,AA		5.8256,23.1956,11.71	benign,benign	196/748,196/727	201282573	1523,11483	2203	4300	6503	SO:0001583	missense	5317	exon3			AAGGCCATAAAGA	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"""Armadillo repeat containing"""	9023	protein-coding gene	gene with protein product	"""ectodermal dysplasia/skin fragility syndrome"""	601975	"""plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"""			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.586A>G	1.37:g.201282573A>G	ENSP00000295597:p.Ile196Val	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	296	142	0.47973	NM_001005337	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	37	CCDS30966.1	218	0.09981684981684982	143	0.29065040650406504	29	0.08011049723756906	0	0.0	46	0.06068601583113457	A	0.006	-2.037916	0.00402	0.231956	0.058256	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.72615	-0.67;-0.55;-0.55	4.13	-4.2	0.03823	.	2.434390	0.01442	N	0.015125	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.11036	-1.0604	9	0.11794	T	0.64	-10.7048	14.7395	0.69442	0.8255:0.0:0.1745:0.0	rs35507614	196;196	Q13835-2;Q13835	.;PKP1_HUMAN	V	196	ENSP00000356293:I196V;ENSP00000263946:I196V;ENSP00000295597:I196V	ENSP00000263946:I196V	I	+	1	0	PKP1	199549196	0.000000	0.05858	0.002000	0.10522	0.483000	0.33249	-0.092000	0.11129	-1.103000	0.03019	-0.344000	0.07964	ATA	A|0.887;G|0.113	0.113	strong		0.617	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
LLGL2	3993	hgsc.bcm.edu	37	17	73567846	73567846	+	Missense_Mutation	SNP	C	C	T	rs1661715	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73567846C>T	ENST00000392550.3	+	18	2392	c.2275C>T	c.(2275-2277)Cct>Tct	p.P759S	LLGL2_ENST00000167462.5_Missense_Mutation_p.P759S|LLGL2_ENST00000577200.1_Missense_Mutation_p.P759S	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	759			P -> S (in dbSNP:rs1661715). {ECO:0000269|PubMed:15489334}.		cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			AATGGATGAGCCTGTGCGGGC	0.697													C|||	1552	0.309904	0.5915	0.2435	5008	,	,		17459	0.1508		0.2823	False		,,,				2504	0.1687				p.P759S		Atlas-SNP	.											LLGL2_ENST00000167462,rectum,carcinoma,0,6	LLGL2	155	6	0			c.C2275T						PASS	.	C	SER/PRO,SER/PRO	2440,1962		693,1054,454	29.0	31.0	30.0		2275,2275	4.4	0.8	17	dbSNP_89	30	2542,6054		397,1748,2153	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	74,74	1090,2802,2607	TT,TC,CC		29.5719,44.5706,38.329	benign,benign	759/1021,759/1016	73567846	4982,8016	2201	4298	6499	SO:0001583	missense	3993	exon18			GATGAGCCTGTGC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2275C>T	17.37:g.73567846C>T	ENSP00000376333:p.Pro759Ser	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	711	0.32554945054945056	322	0.6544715447154471	87	0.24033149171270718	81	0.14160839160839161	221	0.29155672823219	C	12.78	2.039977	0.35989	0.554294	0.295719	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.08008	3.14;3.26	5.4	4.41	0.53225	.	0.209202	0.51477	D	0.000100	T	0.00012	0.0000	L	0.57536	1.79	0.27633	P	0.947969	B;P;B;B	0.36789	0.434;0.57;0.01;0.003	B;B;B;B	0.39904	0.166;0.313;0.015;0.004	T	0.06516	-1.0822	9	0.33141	T	0.24	-0.6264	10.9596	0.47376	0.1462:0.713:0.1408:0.0	rs1661715;rs17855941;rs60583153;rs1661715	748;748;759;759	B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;L2GL2_HUMAN	S	759;759;748	ENSP00000167462:P759S;ENSP00000376333:P759S	ENSP00000167462:P759S	P	+	1	0	LLGL2	71079441	0.854000	0.29725	0.840000	0.33206	0.932000	0.56968	2.448000	0.44926	1.245000	0.43885	0.549000	0.68633	CCT	C|0.622;T|0.378	0.378	strong		0.697	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
KCNK10	54207	hgsc.bcm.edu	37	14	88693725	88693725	+	Silent	SNP	G	G	C	rs2277524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:88693725G>C	ENST00000340700.5	-	4	1111	c.660C>G	c.(658-660)gtC>gtG	p.V220V	KCNK10_ENST00000312350.5_Silent_p.V225V|KCNK10_ENST00000319231.5_Silent_p.V225V	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	220					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	47						TCACTCGAAAGACCTTCTCCA	0.448													G|||	1713	0.342053	0.4501	0.2032	5008	,	,		18025	0.4405		0.2187	False		,,,				2504	0.32				p.V225V		Atlas-SNP	.											.	KCNK10	273	.	0			c.C675G						PASS	.	G	,,	1783,2623	526.8+/-372.0	353,1077,773	118.0	114.0	115.0		660,675,675	3.3	1.0	14	dbSNP_100	115	2049,6551	356.4+/-330.3	254,1541,2505	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNK10	NM_021161.4,NM_138317.2,NM_138318.2	,,	607,2618,3278	CC,CG,GG		23.8256,40.4675,29.4633	,,	220/539,225/544,225/544	88693725	3832,9174	2203	4300	6503	SO:0001819	synonymous_variant	54207	exon4			TCGAAAGACCTTC	AF279890	CCDS9880.1, CCDS9881.1, CCDS9882.1	14q31	2014-06-12						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6273	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 97"""	605873				10880510, 16382106	Standard	NM_021161		Approved	K2p10.1, TREK-2, TREK2, PPP1R97	uc001xwn.3	P57789		ENST00000340700.5:c.660C>G	14.37:g.88693725G>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Silent	SNP	ENST00000340700.5	37	CCDS9880.1																																																																																			G|0.690;C|0.310	0.310	strong		0.448	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161	
ATP8B2	57198	hgsc.bcm.edu	37	1	154317153	154317153	+	Silent	SNP	C	C	T	rs1194587	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:154317153C>T	ENST00000368489.3	+	21	2277	c.2277C>T	c.(2275-2277)tcC>tcT	p.S759S		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	745					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CATCCCGCTCCGTAGGCAACG	0.547											OREG0013835	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2103	0.419928	0.1203	0.4899	5008	,	,		19944	0.624		0.4523	False		,,,				2504	0.5317				p.S759S		Atlas-SNP	.											.	ATP8B2	158	.	0			c.C2277T						PASS	.	C		789,3617	317.7+/-295.3	68,653,1482	133.0	126.0	128.0		2277	-11.5	0.0	1	dbSNP_87	128	4064,4536	559.9+/-387.5	964,2136,1200	no	coding-synonymous	ATP8B2	NM_020452.3		1032,2789,2682	TT,TC,CC		47.2558,17.9074,37.3135		759/1224	154317153	4853,8153	2203	4300	6503	SO:0001819	synonymous_variant	57198	exon21			CCGCTCCGTAGGC	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"""ATPases / P-type"""	13534	protein-coding gene	gene with protein product		605867	"""ATPase, class I, type 8B, member 2"""			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.2277C>T	1.37:g.154317153C>T		Somatic	114	0	0	1762	WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Silent	SNP	ENST00000368489.3	37	CCDS1066.1																																																																																			C|0.608;T|0.392	0.392	strong		0.547	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452	
ABCF1	23	hgsc.bcm.edu	37	6	30545879	30545879	+	Silent	SNP	A	A	G	rs113473909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30545879A>G	ENST00000326195.8	+	4	355	c.243A>G	c.(241-243)aaA>aaG	p.K81K	ABCF1_ENST00000376545.3_Silent_p.K81K|ABCF1_ENST00000396515.4_Silent_p.K81K	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	81					inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						ATACCCGAAAAGGCAGGCGGA	0.493													A|||	37	0.00738818	0.0	0.0043	5008	,	,		19009	0.006		0.004	False		,,,				2504	0.0245				p.K81K		Atlas-SNP	.											.	ABCF1	61	.	0			c.A243G						PASS	.	A	,	8,4398	14.3+/-33.2	0,8,2195	88.0	93.0	91.0		243,243	3.2	1.0	6	dbSNP_132	91	90,8510	42.6+/-100.3	1,88,4211	no	coding-synonymous,coding-synonymous	ABCF1	NM_001025091.1,NM_001090.2	,	1,96,6406	GG,GA,AA		1.0465,0.1816,0.7535	,	81/846,81/808	30545879	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	23	exon4			CCGAAAAGGCAGG	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"""ATP binding cassette transporters / subfamily F"""	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.243A>G	6.37:g.30545879A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_001090	A2BF75|O14897|Q69YP6	Silent	SNP	ENST00000326195.8	37	CCDS34380.1																																																																																			A|0.993;G|0.007	0.007	strong		0.493	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3		
IRS2	8660	hgsc.bcm.edu	37	13	110436232	110436232	+	Silent	SNP	G	G	A	rs3742210	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:110436232G>A	ENST00000375856.3	-	1	2683	c.2169C>T	c.(2167-2169)agC>agT	p.S723S		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	723					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			AGCCGCCCCCGCTCGCCGGGA	0.741													.|||	2802	0.559505	0.5794	0.7104	5008	,	,		8930	0.4514		0.5875	False		,,,				2504	0.5082				p.S723S	Melanoma(100;613 2409 40847)	Atlas-SNP	.											.	IRS2	44	.	0			c.C2169T						PASS	.	A		2185,1205		746,693,256	9.0	5.0	6.0		2169	-3.3	0.0	13	dbSNP_107	6	4433,2525		1525,1383,571	no	coding-synonymous	IRS2	NM_003749.2		2271,2076,827	AA,AG,GG		36.2892,35.5457,36.0456		723/1339	110436232	6618,3730	1695	3479	5174	SO:0001819	synonymous_variant	8660	exon1			GCCCCCGCTCGCC	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"""Pleckstrin homology (PH) domain containing"""	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.2169C>T	13.37:g.110436232G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	25	14	0.56	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Silent	SNP	ENST00000375856.3	37	CCDS9510.1																																																																																			G|0.422;A|0.578	0.578	strong		0.741	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749	
C17orf98	388381	hgsc.bcm.edu	37	17	36997503	36997503	+	Missense_Mutation	SNP	T	T	C	rs61752602	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:36997503T>C	ENST00000398575.4	-	1	205	c.140A>G	c.(139-141)cAg>cGg	p.Q47R		NM_001080465.2	NP_001073934.1	A8MV24	CQ098_HUMAN	chromosome 17 open reading frame 98	47								p.Q47R(1)		endometrium(5)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(3)	14						GTGGTAGTCCTGCTGCGCGTT	0.617													T|||	64	0.0127796	0.0023	0.0144	5008	,	,		12922	0.0		0.0437	False		,,,				2504	0.0072				p.Q47R		Atlas-SNP	.											C17orf98,NS,carcinoma,0,1	C17orf98	34	1	1	Substitution - Missense(1)	pancreas(1)	c.A140G						PASS	.	T	ARG/GLN	25,3925		0,25,1950	55.0	55.0	55.0		140	1.4	1.0	17	dbSNP_129	55	343,7973		7,329,3822	yes	missense	C17orf98	NM_001080465.2	43	7,354,5772	CC,CT,TT		4.1246,0.6329,3.0002	benign	47/155	36997503	368,11898	1975	4158	6133	SO:0001583	missense	388381	exon1			TAGTCCTGCTGCG	AC006449, DY654789	CCDS42310.1	17q12	2014-05-06			ENSG00000214556	ENSG00000275489			34492	protein-coding gene	gene with protein product						16625196	Standard	NM_001080465		Approved	LOC388381	uc002hqv.2	A8MV24	OTTHUMG00000188506	ENST00000398575.4:c.140A>G	17.37:g.36997503T>C	ENSP00000381580:p.Gln47Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_001080465		Missense_Mutation	SNP	ENST00000398575.4	37	CCDS42310.1	38	0.0173992673992674	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	31	0.040897097625329816	T	8.259	0.810759	0.16537	0.006329	0.041246	ENSG00000214556	ENST00000398575	T	0.43294	0.95	5.16	1.35	0.21983	.	1.362360	0.06396	U	0.717920	T	0.05364	0.0142	N	0.16790	0.44	0.23704	N	0.997064	B	0.12013	0.005	B	0.13407	0.009	T	0.16070	-1.0415	10	0.07175	T	0.84	-11.8449	4.455	0.11639	0.518:0.0925:0.0:0.3895	.	47	A8MV24	CQ098_HUMAN	R	47	ENSP00000381580:Q47R	ENSP00000381580:Q47R	Q	-	2	0	C17orf98	34251029	0.913000	0.31002	1.000000	0.80357	0.893000	0.52053	0.142000	0.16096	0.376000	0.24707	0.379000	0.24179	CAG	T|0.971;C|0.029	0.029	strong		0.617	C17orf98-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255469.2	NM_001080465	
H2AFV	94239	hgsc.bcm.edu	37	7	44874113	44874113	+	Missense_Mutation	SNP	T	T	C	rs1802437		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:44874113T>C	ENST00000308153.4	-	5	465	c.374A>G	c.(373-375)cAg>cGg	p.Q125R	H2AFV_ENST00000222690.6_Intron|H2AFV_ENST00000350771.3_Missense_Mutation_p.Q99R|H2AFV_ENST00000349299.3_Missense_Mutation_p.Q87R|H2AFV_ENST00000437072.1_Intron|H2AFV_ENST00000521529.1_3'UTR|H2AFV_ENST00000381124.5_3'UTR	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	125			Q -> R (in dbSNP:rs1802437).			extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						AGCAGTTTTCTGCTGTCCCTT	0.373																																					p.Q125R		Atlas-SNP	.											.	H2AFV	14	.	0			c.A374G						PASS	.						90.0	79.0	83.0					7																	44874113		2203	4300	6503	SO:0001583	missense	94239	exon5			GTTTTCTGCTGTC	AF081192	CCDS5495.1, CCDS5496.1, CCDS5497.1, CCDS5498.1, CCDS47581.1	7p13	2011-01-27		2004-03-26	ENSG00000105968	ENSG00000105968		"""Histones / Replication-independent"""	20664	protein-coding gene	gene with protein product				H2AV			Standard	NM_012412		Approved	MGC10170, MGC10831, MGC1947	uc003tma.2	Q71UI9	OTTHUMG00000129217	ENST00000308153.4:c.374A>G	7.37:g.44874113T>C	ENSP00000308405:p.Gln125Arg	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	167	11	0.0658683	NM_012412	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	Missense_Mutation	SNP	ENST00000308153.4	37	CCDS5496.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461982	0.63513	.	.	ENSG00000105968	ENST00000349299;ENST00000308153;ENST00000350771	T;D;T	0.82619	0.93;-1.63;0.94	5.91	5.91	0.95273	Histone-fold (1);Histone H2A (1);	.	.	.	.	T	0.71600	0.3359	N	0.17474	0.49	0.80722	D	1	B;B;P	0.41673	0.0;0.029;0.759	B;B;B	0.37267	0.001;0.009;0.245	T	0.76405	-0.2971	9	0.59425	D	0.04	-19.8855	14.2973	0.66321	0.0:0.0:0.0:1.0	rs1802437	99;87;125	A6NKY0;A6NFA8;Q71UI9	.;.;H2AV_HUMAN	R	87;125;99	ENSP00000342714:Q87R;ENSP00000308405:Q125R;ENSP00000340708:Q99R	ENSP00000308405:Q125R	Q	-	2	0	H2AFV	44840638	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.465000	0.80898	2.261000	0.74972	0.533000	0.62120	CAG	T|0.999;C|0.001	0.001	weak		0.373	H2AFV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251305.1	NM_012412	
CGNL1	84952	hgsc.bcm.edu	37	15	57835903	57835903	+	Missense_Mutation	SNP	T	T	G	rs1620402	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:57835903T>G	ENST00000281282.5	+	15	3379	c.3301T>G	c.(3301-3303)Ttg>Gtg	p.L1101V		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	1101			L -> V (in dbSNP:rs1620402). {ECO:0000269|PubMed:11214970}.			myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		GATGGAGCAGTTGAGGAATGA	0.507													G|||	1393	0.278155	0.4652	0.2925	5008	,	,		18980	0.1141		0.2376	False		,,,				2504	0.226				p.L1101V		Atlas-SNP	.											.	CGNL1	125	.	0			c.T3301G						PASS	.	G	VAL/LEU	1886,2498	628.0+/-395.0	420,1046,726	112.0	91.0	99.0		3301	3.3	1.0	15	dbSNP_89	99	2192,6392	710.8+/-405.8	295,1602,2395	yes	missense	CGNL1	NM_032866.3	32	715,2648,3121	GG,GT,TT		25.5359,43.0201,31.4466	benign	1101/1303	57835903	4078,8890	2192	4292	6484	SO:0001583	missense	84952	exon15			GAGCAGTTGAGGA	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.3301T>G	15.37:g.57835903T>G	ENSP00000281282:p.Leu1101Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	159	70	0.440252	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	582	0.2664835164835165	234	0.47560975609756095	105	0.2900552486187845	66	0.11538461538461539	177	0.23350923482849603	G	12.23	1.876811	0.33162	0.430201	0.255359	ENSG00000128849	ENST00000281282	T	0.81415	-1.49	5.58	3.26	0.37387	Myosin tail (1);	0.483073	0.20708	N	0.087153	T	0.00012	0.0000	L	0.50333	1.59	0.58432	P	1.0000000000287557E-6	B	0.13145	0.007	B	0.22601	0.04	T	0.33214	-0.9877	9	0.51188	T	0.08	-14.6373	4.7461	0.13038	0.7176:0.0:0.1465:0.1359	rs1620402;rs61066618;rs1620402	1101	Q0VF96	CGNL1_HUMAN	V	1101	ENSP00000281282:L1101V	ENSP00000281282:L1101V	L	+	1	2	CGNL1	55623195	1.000000	0.71417	0.997000	0.53966	0.669000	0.39330	1.532000	0.36029	0.090000	0.17273	-0.121000	0.15023	TTG	A|0.000;G|0.296;T|0.704	0.296	strong		0.507	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	
TCEANC	170082	hgsc.bcm.edu	37	X	13681679	13681679	+	Missense_Mutation	SNP	G	G	T	rs5935650	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:13681679G>T	ENST00000380600.1	+	2	1139	c.1052G>T	c.(1051-1053)tGg>tTg	p.W351L	TCEANC_ENST00000544987.1_Missense_Mutation_p.W351L|TCEANC_ENST00000545566.1_Missense_Mutation_p.W351L|TCEANC_ENST00000314720.4_Missense_Mutation_p.W381L|TCEANC_ENST00000490617.1_3'UTR			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	351					regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						TGGGTGTGCTGGTAACTGTAA	0.408													T|||	2235	0.592053	0.379	0.4424	3775	,	,		16443	0.5109		0.3917	False		,,,				2504	0.5297				p.W381L		Atlas-SNP	.											.	TCEANC	29	.	0			c.G1142T						PASS	.	T	LEU/TRP	1713,1639		381,670,281,351,267	58.0	48.0	51.0		1142	4.1	0.2	X	dbSNP_114	51	3494,2920		715,1139,925,483,815	yes	missense	TCEANC	NM_152634.2	61	1096,1809,1206,834,1082	TT,TG,T,GG,G		45.5254,48.8962,46.6824	benign	381/382	13681679	5207,4559	1950	4077	6027	SO:0001583	missense	170082	exon4			TGTGCTGGTAACT		CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.1052G>T	X.37:g.13681679G>T	ENSP00000369974:p.Trp351Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	118	7	0.059322	NM_152634	A6NI06|B2RDM3	Missense_Mutation	SNP	ENST00000380600.1	37		943	0.568414707655214	135	0.3515625	121	0.47265625	182	0.4918918918918919	196	0.35251798561151076	T	7.416	0.635682	0.14322	0.511038	0.544746	ENSG00000176896	ENST00000545566;ENST00000544987;ENST00000314720;ENST00000380600	T;T;T;T	0.39997	1.08;1.08;1.05;1.08	5.32	4.13	0.48395	.	0.220091	0.27971	N	0.017109	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43940	-0.9360	9	0.37606	T	0.19	.	7.8224	0.29294	0.0:0.074:0.1355:0.7905	rs5935650;rs6633182;rs12862235;rs52796379;rs5935650	381;351	Q8N8B7-2;Q8N8B7	.;TEANC_HUMAN	L	351;351;381;351	ENSP00000438952:W351L;ENSP00000440038:W351L;ENSP00000313886:W381L;ENSP00000369974:W351L	ENSP00000313886:W381L	W	+	2	0	TCEANC	13591600	0.809000	0.29036	0.172000	0.22920	0.045000	0.14185	1.941000	0.40233	0.685000	0.31468	-0.394000	0.06481	TGG	G|0.415;0|0.026	.	strong		0.408	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055796.1	NM_152634	
PADI1	29943	hgsc.bcm.edu	37	1	17555508	17555508	+	Silent	SNP	G	G	T	rs2977234	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17555508G>T	ENST00000375471.4	+	8	983	c.891G>T	c.(889-891)acG>acT	p.T297T		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	297					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	GGATCATGACGCCCAACACTC	0.622													G|||	1074	0.214457	0.1831	0.1902	5008	,	,		15507	0.0585		0.3539	False		,,,				2504	0.2914				p.T297T	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											PADI1,NS,carcinoma,0,1	PADI1	77	1	0			c.G891T						PASS	.	G		921,3483		95,731,1376	40.0	31.0	34.0		891	-0.3	1.0	1	dbSNP_101	34	2761,5839		451,1859,1990	no	coding-synonymous	PADI1	NM_013358.2		546,2590,3366	TT,TG,GG		32.1047,20.9128,28.3144		297/664	17555508	3682,9322	2202	4300	6502	SO:0001819	synonymous_variant	29943	exon8			CATGACGCCCAAC	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"""Peptidyl arginine deiminases"""	18367	protein-coding gene	gene with protein product	"""peptidylarginine deiminase type I"", ""protein-arginine deiminase type-1"", ""hPAD-colony 10"""	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.891G>T	1.37:g.17555508G>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_013358	A1L4K6|Q70SX6	Silent	SNP	ENST00000375471.4	37	CCDS178.1																																																																																			G|0.762;T|0.238	0.238	strong		0.622	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358	
KCNG4	93107	hgsc.bcm.edu	37	16	84256422	84256422	+	Missense_Mutation	SNP	C	C	T	rs4782905	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84256422C>T	ENST00000308251.4	-	3	1029	c.961G>A	c.(961-963)Gag>Aag	p.E321K		NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	321			E -> K (in dbSNP:rs4782905).		protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						CTCGGCCTCTCGCCGTCCTCC	0.657													C|||	252	0.0503195	0.0219	0.036	5008	,	,		17438	0.0317		0.0835	False		,,,				2504	0.0838				p.E321K		Atlas-SNP	.											.	KCNG4	71	.	0			c.G961A						PASS	.	C	LYS/GLU	106,4294	80.4+/-118.8	0,106,2094	33.0	37.0	36.0		961	4.7	0.0	16	dbSNP_111	36	621,7977	157.7+/-211.4	19,583,3697	yes	missense	KCNG4	NM_172347.2	56	19,689,5791	TT,TC,CC		7.2226,2.4091,5.5932	benign	321/520	84256422	727,12271	2200	4299	6499	SO:0001583	missense	93107	exon3			GCCTCTCGCCGTC	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.961G>A	16.37:g.84256422C>T	ENSP00000312129:p.Glu321Lys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	115	0.052655677655677656	10	0.02032520325203252	19	0.052486187845303865	23	0.04020979020979021	63	0.08311345646437995	C	10.47	1.357950	0.24598	0.024091	0.072226	ENSG00000168418	ENST00000308251	D	0.96459	-4.02	5.61	4.66	0.58398	Ion transport (1);	1.828760	0.02581	N	0.098884	T	0.48077	0.1480	N	0.05230	-0.09	0.80722	D	1	B	0.23316	0.083	B	0.21708	0.036	T	0.55211	-0.8176	10	0.12103	T	0.63	.	13.7582	0.62950	0.0:0.9263:0.0:0.0737	rs4782905;rs59381780;rs4782905	321	Q8TDN1	KCNG4_HUMAN	K	321	ENSP00000312129:E321K	ENSP00000312129:E321K	E	-	1	0	KCNG4	82813923	0.000000	0.05858	0.049000	0.19019	0.018000	0.09664	0.458000	0.21892	1.362000	0.46000	0.655000	0.94253	GAG	C|0.945;T|0.055	0.055	strong		0.657	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
MCCD1	401250	hgsc.bcm.edu	37	6	31496949	31496949	+	Missense_Mutation	SNP	C	C	T	rs78957773	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31496949C>T	ENST00000376191.2	+	1	456	c.158C>T	c.(157-159)aCg>aTg	p.T53M	DDX39B_ENST00000462421.1_5'Flank	NM_001011700.2	NP_001011700.2	P59942	MCCD1_HUMAN	mitochondrial coiled-coil domain 1	53			T -> M (in dbSNP:rs78957773). {ECO:0000269|PubMed:14527716}.			mitochondrion (GO:0005739)				skin(1)	1						GGGAAGATGACGTCCCCTCCC	0.562													t|||	79	0.0157748	0.0212	0.0504	5008	,	,		12082	0.0		0.0159	False		,,,				2504	0.0				p.T53M		Atlas-SNP	.											.	MCCD1	3	.	0			c.C158T						PASS	.	C	MET/THR	77,2941		0,77,1432	92.0	81.0	85.0		158	-4.1	0.0	6	dbSNP_132	85	143,5275		5,133,2571	yes	missense	MCCD1	NM_001011700.2	81	5,210,4003	TT,TC,CC		2.6394,2.5514,2.6079	possibly-damaging	53/120	31496949	220,8216	1509	2709	4218	SO:0001583	missense	401250	exon1			AGATGACGTCCCC		CCDS34396.1	6p21.3	2003-10-17				ENSG00000204511			20668	protein-coding gene	gene with protein product		609624				14527716	Standard	NM_001011700		Approved		uc003ntp.1	P59942		ENST00000376191.2:c.158C>T	6.37:g.31496949C>T	ENSP00000365362:p.Thr53Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_001011700	A2AB29|A2RUP7|B0UZB2|Q7RTY2	Missense_Mutation	SNP	ENST00000376191.2	37	CCDS34396.1	44	0.020146520146520148	10	0.02032520325203252	21	0.058011049723756904	0	0.0	13	0.017150395778364115	-	5.728	0.318810	0.10845	0.025514	0.026394	ENSG00000204511	ENST00000376191	T	0.23552	1.9	3.65	-4.09	0.03951	.	1.010190	0.07963	N	0.982703	T	0.02807	0.0084	N	0.08118	0	0.09310	N	1	B	0.20887	0.049	B	0.09377	0.004	T	0.40001	-0.9586	10	0.45353	T	0.12	.	2.2155	0.03958	0.1008:0.273:0.1986:0.4276	.	53	P59942	MCCD1_HUMAN	M	53	ENSP00000365362:T53M	ENSP00000365362:T53M	T	+	2	0	MCCD1	31604928	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.018000	0.03626	-0.616000	0.05671	-2.186000	0.00314	ACG	C|0.973;T|0.027	0.027	strong		0.562	MCCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259099.1		
VN1R1	57191	hgsc.bcm.edu	37	19	57967049	57967049	+	Missense_Mutation	SNP	G	G	T	rs61744949	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57967049G>T	ENST00000321039.3	-	1	805	c.806C>A	c.(805-807)gCc>gAc	p.A269D	AC004076.9_ENST00000596831.1_Missense_Mutation_p.P107T|AC004076.9_ENST00000415705.3_5'UTR	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	269			A -> D (in allele VN1R1*3; dbSNP:rs61744949). {ECO:0000269|PubMed:10973240, ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		TGTGGCTCTGGCTTCCTGGGA	0.488													G|||	2070	0.413339	0.3109	0.451	5008	,	,		18776	0.5913		0.2783	False		,,,				2504	0.4806				p.A269D		Atlas-SNP	.											.	VN1R1	48	.	0			c.C806A						PASS	.	G	ASP/ALA	1342,3064	450.2+/-349.3	188,966,1049	126.0	88.0	101.0		806	-0.9	0.0	19	dbSNP_129	101	2454,6146	404.0+/-348.0	330,1794,2176	yes	missense	VN1R1	NM_020633.3	126	518,2760,3225	TT,TG,GG		28.5349,30.4585,29.1865	possibly-damaging	269/354	57967049	3796,9210	2203	4300	6503	SO:0001583	missense	57191	exon1			GCTCTGGCTTCCT	AF255342	CCDS12951.1	19q13.4	2012-08-22	2003-01-15		ENSG00000178201	ENSG00000178201		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	13548	protein-coding gene	gene with protein product		605234	"""vomeronasal olfactory receptor, (chromosome 19) subtype I, member 1"""	VNR19I1		10973240	Standard	NM_020633		Approved	V1RL1, ZVNR1, ZVNH1	uc002qos.2	Q9GZP7		ENST00000321039.3:c.806C>A	19.37:g.57967049G>T	ENSP00000322339:p.Ala269Asp	Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	307	135	0.439739	NM_020633	B3KSV5|Q7Z5H8|Q7Z5H9	Missense_Mutation	SNP	ENST00000321039.3	37	CCDS12951.1	877	0.4015567765567766	149	0.30284552845528456	135	0.3729281767955801	368	0.6433566433566433	225	0.29683377308707126	G	10.04	1.242857	0.22796	0.304585	0.285349	ENSG00000178201	ENST00000321039	T	0.09255	3.0	4.17	-0.913	0.10500	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.25060	0.705	0.80722	P	0.0	B	0.25609	0.13	B	0.31016	0.123	T	0.24621	-1.0155	8	0.56958	D	0.05	.	4.0826	0.09932	0.3162:0.3379:0.3459:0.0	rs61744949	269	Q9GZP7	VN1R1_HUMAN	D	269	ENSP00000322339:A269D	ENSP00000322339:A269D	A	-	2	0	VN1R1	62658861	0.996000	0.38824	0.000000	0.03702	0.015000	0.08874	0.517000	0.22832	-0.140000	0.11394	0.650000	0.86243	GCC	G|0.675;T|0.325	0.325	strong		0.488	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466464.1	NM_020633	
BSN	8927	hgsc.bcm.edu	37	3	49701983	49701983	+	Silent	SNP	G	G	A	rs9858542	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49701983G>A	ENST00000296452.4	+	9	11850	c.11736G>A	c.(11734-11736)acG>acA	p.T3912T		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3912					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GCAAACTGACGGAAGGTATGC	0.637													G|||	978	0.195288	0.2171	0.17	5008	,	,		17930	0.0516		0.3241	False		,,,				2504	0.1994				p.T3912T		Atlas-SNP	.											BSN,NS,carcinoma,+1,1	BSN	272	1	0			c.G11736A						PASS	.	G		1044,3362	379.7+/-323.4	120,804,1279	48.0	54.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	11736	-10.1	0.6	3	dbSNP_119	52	2577,6023	416.5+/-352.1	402,1773,2125	yes	coding-synonymous	BSN	NM_003458.3		522,2577,3404	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	29.9651,23.695,27.841		3912/3927	49701983	3621,9385	2203	4300	6503	SO:0001819	synonymous_variant	8927	exon9			ACTGACGGAAGGT	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.11736G>A	3.37:g.49701983G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	37	14	0.378378	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			G|0.749;A|0.251	0.251	strong		0.637	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3672240	3672240	+	Silent	SNP	G	G	A	rs111969446	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3672240G>A	ENST00000344754.4	-	17	4337	c.4338C>T	c.(4336-4338)cgC>cgT	p.R1446R	SIGLEC1_ENST00000202578.4_Silent_p.R1446R	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1446	Ig-like C2-type 15.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CTGCCACCACGCGTGCACCTG	0.667													G|||	53	0.0105831	0.0023	0.0029	5008	,	,		17190	0.001		0.0268	False		,,,				2504	0.0204				p.R1446R		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C4338T						PASS	.	G		18,4388		0,18,2185	29.0	33.0	32.0		4338	-1.5	0.2	20	dbSNP_132	32	210,8384		3,204,4090	no	coding-synonymous	SIGLEC1	NM_023068.3		3,222,6275	AA,AG,GG		2.4436,0.4085,1.7538		1446/1710	3672240	228,12772	2203	4297	6500	SO:0001819	synonymous_variant	6614	exon17			CACCACGCGTGCA	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.4338C>T	20.37:g.3672240G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	32	0.615385	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1	22	0.010073260073260074	0	0.0	0	0.0	0	0.0	22	0.029023746701846966	G	0.070	-1.204057	0.01581	0.004085	0.024436	ENSG00000088827	ENST00000419548	T	0.11821	2.74	5.34	-1.48	0.08745	.	1.124510	0.06783	N	0.785547	T	0.04497	0.0123	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.41520	-0.9504	7	0.66056	D	0.02	.	5.4318	0.16458	0.3977:0.1713:0.4311:0.0	.	.	.	.	C	260	ENSP00000395778:R260C	ENSP00000395778:R260C	R	-	1	0	SIGLEC1	3620240	0.000000	0.05858	0.200000	0.23457	0.014000	0.08584	-1.386000	0.02537	0.048000	0.15891	-0.345000	0.07892	CGT	G|0.985;A|0.015	0.015	strong		0.667	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
GLB1L2	89944	hgsc.bcm.edu	37	11	134244123	134244123	+	Silent	SNP	C	C	G	rs3741097	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:134244123C>G	ENST00000535456.2	+	17	1868	c.1680C>G	c.(1678-1680)acC>acG	p.T560T	GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Silent_p.T560T|GLB1L2_ENST00000389881.3_Silent_p.T560T	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	560					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		TCAGCTCCACCCCTTGTGACA	0.552													C|||	1333	0.266174	0.0877	0.1527	5008	,	,		19376	0.5089		0.2097	False		,,,				2504	0.3957				p.T560T		Atlas-SNP	.											.	GLB1L2	79	.	0			c.C1680G						PASS	.	C		467,3935	219.7+/-237.4	27,413,1761	225.0	188.0	200.0		1680	-2.1	0.0	11	dbSNP_107	200	1752,6842	317.8+/-313.4	167,1418,2712	no	coding-synonymous	GLB1L2	NM_138342.3		194,1831,4473	GG,GC,CC		20.3863,10.6088,17.0745		560/637	134244123	2219,10777	2201	4297	6498	SO:0001819	synonymous_variant	89944	exon17			CTCCACCCCTTGT		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.1680C>G	11.37:g.134244123C>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	183	88	0.480874	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Silent	SNP	ENST00000535456.2	37	CCDS31724.1	552	0.25274725274725274	43	0.08739837398373984	56	0.15469613259668508	294	0.513986013986014	159	0.20976253298153033	C	3.526	-0.096667	0.07010	0.106088	0.203863	ENSG00000149328	ENST00000525089	.	.	.	5.56	-2.06	0.07298	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.43164	P	0.005040999999999962	.	.	.	.	.	.	T	0.47433	-0.9118	3	.	.	.	-11.6576	0.8726	0.01217	0.1675:0.3217:0.1904:0.3204	rs3741097;rs3741097	.	.	.	A	499	.	.	P	+	1	0	GLB1L2	133749333	0.054000	0.20591	0.013000	0.15412	0.035000	0.12851	0.246000	0.18160	-0.202000	0.10268	-0.885000	0.02943	CCC	C|0.793;G|0.207	0.207	strong		0.552	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	
HEATR4	399671	hgsc.bcm.edu	37	14	73961982	73961982	+	Missense_Mutation	SNP	C	C	T	rs76429074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:73961982C>T	ENST00000553558.1	-	16	3056	c.2735G>A	c.(2734-2736)gGa>gAa	p.G912E	HEATR4_ENST00000334988.2_Missense_Mutation_p.G912E|C14orf169_ENST00000531973.1_RNA|HEATR4_ENST00000560393.1_Missense_Mutation_p.G865E	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	912										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		TCCTTGTTCTCCTTTGGGTTT	0.443													C|||	46	0.0091853	0.0015	0.0101	5008	,	,		18401	0.0		0.0258	False		,,,				2504	0.0112				p.G912E		Atlas-SNP	.											.	HEATR4	126	.	0			c.G2735A						PASS	.	C	GLU/GLY,GLU/GLY	24,4382	30.8+/-60.4	0,24,2179	235.0	195.0	209.0		2735,2735	1.1	0.0	14	dbSNP_131	209	254,8346	99.9+/-161.4	9,236,4055	yes	missense,missense	HEATR4	NM_001220484.1,NM_203309.2	98,98	9,260,6234	TT,TC,CC		2.9535,0.5447,2.1375	probably-damaging,probably-damaging	912/1027,912/1027	73961982	278,12728	2203	4300	6503	SO:0001583	missense	399671	exon15			TGTTCTCCTTTGG	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2735G>A	14.37:g.73961982C>T	ENSP00000450444:p.Gly912Glu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	153	66	0.431373	NM_203309	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2	27	0.012362637362637362	0	0.0	6	0.016574585635359115	0	0.0	21	0.027704485488126648	C	0.004	-2.369551	0.00209	0.005447	0.029535	ENSG00000187105	ENST00000553558;ENST00000334988	T	0.20332	2.08	4.96	1.12	0.20585	.	0.699661	0.12884	N	0.431159	T	0.01730	0.0055	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38308	-0.9667	10	0.02654	T	1	-2.6044	5.0448	0.14477	0.0:0.0995:0.3604:0.5401	.	912	Q86WZ0	HEAT4_HUMAN	E	912;865	ENSP00000450444:G912E	ENSP00000335447:G865E	G	-	2	0	HEATR4	73031735	0.000000	0.05858	0.045000	0.18777	0.010000	0.07245	-0.069000	0.11542	0.027000	0.15297	-0.302000	0.09304	GGA	C|0.982;T|0.018	0.018	strong		0.443	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309	
PHACTR2	9749	hgsc.bcm.edu	37	6	144081609	144081609	+	Missense_Mutation	SNP	C	C	T	rs2073214	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:144081609C>T	ENST00000427704.2	+	5	623	c.493C>T	c.(493-495)Ccc>Tcc	p.P165S	PHACTR2_ENST00000440869.2_Missense_Mutation_p.P176S|PHACTR2_ENST00000367582.3_Intron|PHACTR2_ENST00000367584.4_Intron|PHACTR2_ENST00000305766.6_Intron	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	165			P -> S (in dbSNP:rs2073214). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.				protein phosphatase inhibitor activity (GO:0004864)			NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		TAAGCCTAGACCCAAACCTAA	0.488													C|||	1002	0.20008	0.2943	0.2378	5008	,	,		18421	0.1409		0.174	False		,,,				2504	0.1339				p.P176S	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)	Atlas-SNP	.											.	PHACTR2	99	.	0			c.C526T						PASS	.	C	SER/PRO,,,SER/PRO	1084,2756		139,806,975	53.0	58.0	57.0		526,,,493	4.3	1.0	6	dbSNP_96	57	1194,7046		76,1042,3002	yes	missense,intron,intron,missense	PHACTR2	NM_001100164.1,NM_001100165.1,NM_001100166.1,NM_014721.2	74,,,74	215,1848,3977	TT,TC,CC		14.4903,28.2292,18.8576	probably-damaging,,,probably-damaging	176/646,,,165/635	144081609	2278,9802	1920	4120	6040	SO:0001583	missense	9749	exon5			CCTAGACCCAAAC	AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"""Phosphatase and actin regulators"""	20956	protein-coding gene	gene with protein product		608724	"""chromosome 6 open reading frame 56"""	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.493C>T	6.37:g.144081609C>T	ENSP00000391763:p.Pro165Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001100164	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Missense_Mutation	SNP	ENST00000427704.2	37	CCDS47492.1	429	0.19642857142857142	147	0.29878048780487804	87	0.24033149171270718	77	0.1346153846153846	118	0.15567282321899736	C	10.78	1.445776	0.25987	0.282292	0.144903	ENSG00000112419	ENST00000427704;ENST00000440869	T;T	0.23348	1.91;1.91	6.08	4.31	0.51392	.	0.430763	0.28442	N	0.015325	T	0.07098	0.0180	L	0.41236	1.265	0.09310	P	0.999999999960581	B;B	0.12630	0.006;0.004	B;B	0.15052	0.012;0.005	T	0.22695	-1.0209	9	0.12103	T	0.63	.	9.3236	0.37980	0.0:0.7284:0.0:0.2716	rs2073214;rs52819078;rs58994387;rs2073214	176;165	O75167-4;O75167	.;PHAR2_HUMAN	S	165;176	ENSP00000391763:P165S;ENSP00000417038:P176S	ENSP00000391763:P165S	P	+	1	0	PHACTR2	144123302	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.774000	0.26675	0.912000	0.36772	0.655000	0.94253	CCC	C|0.801;T|0.199	0.199	strong		0.488	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721	
MIS18BP1	55320	hgsc.bcm.edu	37	14	45700409	45700409	+	Missense_Mutation	SNP	C	C	T	rs61741592	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:45700409C>T	ENST00000310806.4	-	8	1987	c.1529G>A	c.(1528-1530)cGa>cAa	p.R510Q		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	510				R -> Q (in Ref. 1; BAB67796). {ECO:0000305}.	CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R510Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						TTGGTTTTCTCGTGCATCATT	0.378													C|||	185	0.0369409	0.0015	0.0893	5008	,	,		17067	0.0		0.1153	False		,,,				2504	0.0051				p.R510Q		Atlas-SNP	.											MIS18BP1,NS,carcinoma,0,1	MIS18BP1	92	1	1	Substitution - Missense(1)	pancreas(1)	c.G1529A						PASS	.	C	GLN/ARG	99,4307	79.9+/-118.3	1,97,2105	248.0	197.0	214.0		1529	-4.4	0.0	14	dbSNP_129	214	969,7631	211.7+/-252.2	48,873,3379	yes	missense	MIS18BP1	NM_018353.4	43	49,970,5484	TT,TC,CC		11.2674,2.2469,8.2116	benign	510/1133	45700409	1068,11938	2203	4300	6503	SO:0001583	missense	55320	exon8			TTTTCTCGTGCAT	AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"""kinetochore null 2 homolog (C. elegans)"""		"""chromosome 14 open reading frame 106"""	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.1529G>A	14.37:g.45700409C>T	ENSP00000309790:p.Arg510Gln	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	333	152	0.456456	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	120	0.054945054945054944	1	0.0020325203252032522	38	0.10497237569060773	0	0.0	81	0.10686015831134564	C	0.477	-0.881862	0.02530	0.022469	0.112674	ENSG00000129534	ENST00000310806	T	0.17370	2.28	4.77	-4.37	0.03633	.	1.756370	0.02378	N	0.078591	T	0.00210	0.0006	N	0.19112	0.55	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.29579	-1.0007	9	0.13853	T	0.58	1.4088	11.3146	0.49383	0.0:0.3454:0.0:0.6546	.	510	Q6P0N0	M18BP_HUMAN	Q	510	ENSP00000309790:R510Q	ENSP00000309790:R510Q	R	-	2	0	MIS18BP1	44770159	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.815000	0.04481	-0.708000	0.05015	-1.314000	0.01303	CGA	C|0.929;T|0.071	0.071	strong		0.378	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2		
BDP1	55814	hgsc.bcm.edu	37	5	70806649	70806649	+	Missense_Mutation	SNP	T	T	A	rs1961760	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:70806649T>A	ENST00000358731.4	+	17	3993	c.3730T>A	c.(3730-3732)Ttc>Atc	p.F1244I	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	1244	9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.		F -> I (in dbSNP:rs1961760). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:15489334}.		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.F1244I(1)		NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		GCTAGCAGAGTTCAGTGCTAT	0.403													A|||	2203	0.439896	0.4107	0.3444	5008	,	,		19893	0.379		0.492	False		,,,				2504	0.5562				p.F1244I		Atlas-SNP	.											BDP1,NS,carcinoma,0,2	BDP1	204	2	1	Substitution - Missense(1)	prostate(1)	c.T3730A						PASS	.	A	ILE/PHE	1415,2243		280,855,694	117.0	117.0	117.0		3730	-4.5	0.0	5	dbSNP_92	117	3943,4213		979,1985,1114	yes	missense	BDP1	NM_018429.2	21	1259,2840,1808	AA,AT,TT		48.3448,38.6823,45.353	benign	1244/2625	70806649	5358,6456	1829	4078	5907	SO:0001583	missense	55814	exon17			GCAGAGTTCAGTG	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.3730T>A	5.37:g.70806649T>A	ENSP00000351575:p.Phe1244Ile	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	922	0.42216117216117216	195	0.39634146341463417	127	0.35082872928176795	223	0.38986013986013984	377	0.4973614775725594	A	0.512	-0.865930	0.02590	0.386823	0.483448	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.10763	2.84	3.7	-4.49	0.03504	.	2.205680	0.02179	N	0.060365	T	0.00012	0.0000	N	0.00347	-1.61	0.58432	P	5.000000000032756E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.46555	-0.9183	9	0.33940	T	0.23	.	3.2644	0.06860	0.2201:0.1396:0.5027:0.1376	rs1961760;rs52799834;rs1961760	1244;1244;1244	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	I	1244;824	ENSP00000351575:F1244I	ENSP00000351575:F1244I	F	+	1	0	BDP1	70842405	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-0.869000	0.04232	-1.348000	0.02205	-0.827000	0.03088	TTC	T|0.561;A|0.439	0.439	strong		0.403	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
GAS8	2622	hgsc.bcm.edu	37	16	90095620	90095620	+	Intron	SNP	A	A	G	rs61740023	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90095620A>G	ENST00000268699.4	+	2	212				GAS8_ENST00000536122.1_Intron|GAS8_ENST00000540721.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.V44A	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		ggggcaggctacggggcaggc	0.672																																					p.V44A		Atlas-SNP	.											.	C16orf3	14	.	0			c.T131C						PASS	.						25.0	29.0	27.0					16																	90095620		2197	4298	6495	SO:0001627	intron_variant	750	exon1			CAGGCTACGGGGC	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1490A>G	16.37:g.90095620A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	70	10	0.142857	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	A	1.744	-0.491041	0.04322	.	.	ENSG00000221819	ENST00000408886	T	0.48836	0.8	.	.	.	.	.	.	.	.	T	0.22322	0.0538	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.21965	-1.0230	4	.	.	.	.	.	.	.	.	.	.	.	A	44	ENSP00000386218:V44A	.	V	-	2	0	C16orf3	88623121	.	.	0.004000	0.12327	0.042000	0.13812	.	.	0.064000	0.16427	0.063000	0.15292	GTA	A|0.970;G|0.030	0.030	strong		0.672	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
TMEM207	131920	hgsc.bcm.edu	37	3	190167533	190167533	+	Silent	SNP	C	C	T	rs10513852	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:190167533C>T	ENST00000354905.2	-	1	132	c.66G>A	c.(64-66)ccG>ccA	p.P22P		NM_207316.1	NP_997199.1	Q6UWW9	TM207_HUMAN	transmembrane protein 207	22						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(4)	7	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)		CCTGGAATAGCGGCAAACACA	0.413													C|||	281	0.0561102	0.0166	0.1052	5008	,	,		20602	0.0198		0.1441	False		,,,				2504	0.0215				p.P22P		Atlas-SNP	.											.	TMEM207	19	.	0			c.G66A						PASS	.	C		186,4220	118.8+/-156.5	6,174,2023	155.0	129.0	138.0		66	-5.4	0.0	3	dbSNP_119	138	1194,7406	242.1+/-272.2	96,1002,3202	no	coding-synonymous	TMEM207	NM_207316.1		102,1176,5225	TT,TC,CC		13.8837,4.2215,10.6105		22/147	190167533	1380,11626	2203	4300	6503	SO:0001819	synonymous_variant	131920	exon1			GAATAGCGGCAAA	BC071780	CCDS3297.1	3q28	2008-02-18			ENSG00000198398	ENSG00000198398			33705	protein-coding gene	gene with protein product		614786					Standard	NM_207316		Approved		uc003fsj.2	Q6UWW9	OTTHUMG00000156213	ENST00000354905.2:c.66G>A	3.37:g.190167533C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	139	73	0.52518	NM_207316		Silent	SNP	ENST00000354905.2	37	CCDS3297.1																																																																																			C|0.917;T|0.083	0.083	strong		0.413	TMEM207-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343515.1	NM_207316	
DPP6	1804	hgsc.bcm.edu	37	7	154672646	154672646	+	Silent	SNP	T	T	C	rs3817522	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:154672646T>C	ENST00000377770.3	+	21	2268	c.2127T>C	c.(2125-2127)ttT>ttC	p.F709F	DPP6_ENST00000427557.1_Silent_p.F602F|DPP6_ENST00000332007.3_Silent_p.F647F|DPP6_ENST00000404039.1_Silent_p.F645F			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	709					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TGGCCGTGTTTGGGAAGGTGA	0.552													t|||	1327	0.264976	0.4902	0.3963	5008	,	,		16029	0.1002		0.1879	False		,,,				2504	0.1166				p.F709F	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.T2127C						PASS	.	T	,,	1773,2469		377,1019,725	99.0	109.0	106.0		1581,1500,1500	-2.1	1.0	7	dbSNP_107	106	1514,6950		133,1248,2851	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	510,2267,3576	CC,CT,TT		17.8875,41.7963,25.8697	,,	527/684,500/657,500/657	154672646	3287,9419	2121	4232	6353	SO:0001819	synonymous_variant	1804	exon21			CGTGTTTGGGAAG	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"""dipeptidylpeptidase VI"", ""dipeptidylpeptidase 6"""			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.2127T>C	7.37:g.154672646T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	111	44	0.396396	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				T|0.742;C|0.258	0.258	strong		0.552	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
RABEPK	10244	hgsc.bcm.edu	37	9	127975654	127975654	+	Missense_Mutation	SNP	C	C	T	rs1128362	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:127975654C>T	ENST00000373538.3	+	4	527	c.217C>T	c.(217-219)Cac>Tac	p.H73Y	RABEPK_ENST00000394125.4_Missense_Mutation_p.H73Y|RABEPK_ENST00000394124.4_Missense_Mutation_p.H73Y|RABEPK_ENST00000373544.1_Missense_Mutation_p.H73Y|RABEPK_ENST00000259460.8_Intron	NM_005833.3	NP_005824.2	Q7Z6M1	RABEK_HUMAN	Rab9 effector protein with kelch motifs	73			H -> Y (in dbSNP:rs16927965). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		receptor-mediated endocytosis (GO:0006898)|vesicle docking involved in exocytosis (GO:0006904)	endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15						TCCAGGAAAACACCAGTGGGA	0.493													C|||	483	0.0964457	0.118	0.0879	5008	,	,		18384	0.005		0.1362	False		,,,				2504	0.1268				p.H73Y		Atlas-SNP	.											.	RABEPK	46	.	0			c.C217T						PASS	.	C	TYR/HIS,,TYR/HIS	593,3813	259.5+/-263.1	41,511,1651	116.0	110.0	112.0		217,,217	3.6	1.0	9	dbSNP_123	112	1219,7381	246.7+/-275.0	94,1031,3175	yes	missense,intron,missense	RABEPK	NM_001174152.1,NM_001174153.1,NM_005833.3	83,,83	135,1542,4826	TT,TC,CC		14.1744,13.4589,13.932	probably-damaging,,probably-damaging	73/373,,73/373	127975654	1812,11194	2203	4300	6503	SO:0001583	missense	10244	exon4			GGAAAACACCAGT	BC000503	CCDS6862.1, CCDS55341.1	9q33.1-q33.3	2010-04-19			ENSG00000136933	ENSG00000136933			16896	protein-coding gene	gene with protein product		605962				9230071	Standard	NM_005833		Approved	RAB9P40, bA65N13.1	uc004bpi.3	Q7Z6M1	OTTHUMG00000020674	ENST00000373538.3:c.217C>T	9.37:g.127975654C>T	ENSP00000362639:p.His73Tyr	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_005833	A8K403|O00568|Q69YR2|Q6FHA4|Q6IBG7|Q6P092|Q86Y76|Q9BWB1	Missense_Mutation	SNP	ENST00000373538.3	37	CCDS6862.1	200	0.09157509157509157	58	0.11788617886178862	40	0.11049723756906077	0	0.0	102	0.1345646437994723	C	11.28	1.592552	0.28357	0.134589	0.141744	ENSG00000136933	ENST00000394125;ENST00000373544;ENST00000394124;ENST00000373538;ENST00000416065	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	5.47	3.63	0.41609	Galactose oxidase, beta-propeller (1);	0.099119	0.64402	D	0.000002	T	0.00178	0.0005	L	0.47716	1.5	0.23425	P	0.99770432	B;P	0.50369	0.014;0.934	B;P	0.50708	0.017;0.648	T	0.07712	-1.0758	9	0.09590	T	0.72	-13.4768	9.2746	0.37692	0.0:0.8267:0.0:0.1733	rs16927965;rs17252930;rs17849327;rs52838209;rs16927965	73;73	Q7Z6M1;Q5T1S4	RABEK_HUMAN;.	Y	73;73;73;73;156	ENSP00000377683:H73Y;ENSP00000362645:H73Y;ENSP00000377682:H73Y;ENSP00000362639:H73Y;ENSP00000402234:H156Y	ENSP00000362639:H73Y	H	+	1	0	RABEPK	127015475	0.968000	0.33430	1.000000	0.80357	0.890000	0.51754	2.254000	0.43214	1.330000	0.45394	-0.218000	0.12543	CAC	C|0.880;T|0.120	0.120	strong		0.493	RABEPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054064.1	NM_005833	
ABL1	25	hgsc.bcm.edu	37	9	133759686	133759686	+	Missense_Mutation	SNP	A	A	G	rs61746126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:133759686A>G	ENST00000318560.5	+	11	2390	c.2009A>G	c.(2008-2010)aAt>aGt	p.N670S		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	670					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GGGGTCCCCAATGGAGCCCTC	0.672			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								A|||	2	0.000399361	0.0008	0.0	5008	,	,		15138	0.0		0.001	False		,,,				2504	0.0				p.N689S		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.A2066G						PASS	.	A	SER/ASN,SER/ASN	0,4366		0,0,2183	17.0	21.0	19.0		2009,2066	5.6	1.0	9	dbSNP_129	19	2,8516		0,2,4257	no	missense,missense	ABL1	NM_005157.4,NM_007313.2	46,46	0,2,6440	GG,GA,AA		0.0235,0.0,0.0155	possibly-damaging,possibly-damaging	670/1131,689/1150	133759686	2,12882	2183	4259	6442	SO:0001583	missense	25	exon11			TCCCCAATGGAGC	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2009A>G	9.37:g.133759686A>G	ENSP00000323315:p.Asn670Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	28	19	0.678571	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	A	12.12	1.842721	0.32606	0.0	2.35E-4	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.12774	2.65;2.65	5.57	5.57	0.84162	.	0.093032	0.64402	D	0.000001	T	0.11495	0.0280	L	0.42245	1.32	0.54753	D	0.999987	B;B	0.33212	0.402;0.402	B;B	0.26864	0.074;0.074	T	0.10428	-1.0630	10	0.11182	T	0.66	.	14.9117	0.70761	1.0:0.0:0.0:0.0	rs61746126	670;707	P00519;Q59FK4	ABL1_HUMAN;.	S	485;689;670	ENSP00000361423:N689S;ENSP00000323315:N670S	ENSP00000323315:N670S	N	+	2	0	ABL1	132749507	0.999000	0.42202	0.997000	0.53966	0.985000	0.73830	4.109000	0.57824	2.117000	0.64856	0.459000	0.35465	AAT	A|0.999;G|0.001	0.001	strong		0.672	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
MMP1	4312	hgsc.bcm.edu	37	11	102668022	102668022	+	Silent	SNP	C	C	T	rs10488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:102668022C>T	ENST00000315274.6	-	2	382	c.315G>A	c.(313-315)ggG>ggA	p.G105G	WTAPP1_ENST00000525739.2_RNA	NM_001145938.1|NM_002421.3	NP_001139410.1|NP_002412.1	P03956	MMP1_HUMAN	matrix metallopeptidase 1 (interstitial collagenase)	105	Metalloprotease.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|proteolysis (GO:0006508)|viral process (GO:0016032)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)	Marimastat(DB00786)	AGCGAGGGTTCCCCTCAGTGA	0.532													C|||	362	0.0722843	0.1626	0.0461	5008	,	,		20019	0.0188		0.0676	False		,,,				2504	0.0286				p.G105G		Atlas-SNP	.											.	MMP1	74	.	0			c.G315A						PASS	.	C	,	606,3800	266.5+/-267.3	44,518,1641	117.0	93.0	101.0		117,315	1.2	0.0	11	dbSNP_52	101	475,8123	139.8+/-196.4	9,457,3833	no	coding-synonymous,coding-synonymous	MMP1	NM_001145938.1,NM_002421.3	,	53,975,5474	TT,TC,CC		5.5245,13.754,8.3128	,	39/404,105/470	102668022	1081,11923	2203	4299	6502	SO:0001819	synonymous_variant	4312	exon2			AGGGTTCCCCTCA	X54925	CCDS8322.1	11q21-q22	2014-01-30	2005-08-08		ENSG00000196611	ENSG00000196611	3.4.24.7	"""Endogenous ligands"""	7155	protein-coding gene	gene with protein product		120353	"""matrix metalloproteinase 1 (interstitial collagenase)"""	CLG			Standard	NM_002421		Approved		uc001phi.2	P03956	OTTHUMG00000048192	ENST00000315274.6:c.315G>A	11.37:g.102668022C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	157	74	0.471338	NM_002421	P08156	Silent	SNP	ENST00000315274.6	37	CCDS8322.1																																																																																			C|0.924;T|0.076	0.076	strong		0.532	MMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109632.1	NM_002421	
TMEM150A	129303	hgsc.bcm.edu	37	2	85826721	85826721	+	Silent	SNP	G	G	A	rs11891495	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:85826721G>A	ENST00000409668.1	-	6	968	c.501C>T	c.(499-501)acC>acT	p.T167T	TMEM150A_ENST00000306353.3_Silent_p.T114T|TMEM150A_ENST00000334462.5_Silent_p.T167T			Q86TG1	T150A_HUMAN	transmembrane protein 150A	167					catabolic process (GO:0009056)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|lung(1)|skin(1)	7						CCAGCGGGGCGGTGGCCCCTT	0.617													G|||	880	0.175719	0.1369	0.1801	5008	,	,		20935	0.0823		0.2535	False		,,,				2504	0.2413				p.T167T		Atlas-SNP	.											.	TMEM150A	15	.	0			c.C501T						PASS	.	G		645,3761	274.9+/-272.2	42,561,1600	70.0	67.0	68.0		501	-10.2	0.1	2	dbSNP_120	68	2184,6416	372.2+/-336.6	267,1650,2383	no	coding-synonymous	TMEM150A	NM_001031738.2		309,2211,3983	AA,AG,GG		25.3953,14.6391,21.7515		167/272	85826721	2829,10177	2203	4300	6503	SO:0001819	synonymous_variant	129303	exon7			CGGGGCGGTGGCC	AK098152	CCDS33233.1	2p11.2	2009-06-12	2009-06-12	2009-06-12	ENSG00000168890	ENSG00000168890			24677	protein-coding gene	gene with protein product			"""transmembrane protein 150"""	TMEM150		10858565	Standard	NM_001031738		Approved	TM6P1, FLJ90024	uc002spy.2	Q86TG1	OTTHUMG00000130168	ENST00000409668.1:c.501C>T	2.37:g.85826721G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	268	142	0.529851	NM_001031738	A8K764|B7WPQ9|D6W5L2|Q8N2R6	Silent	SNP	ENST00000409668.1	37	CCDS33233.1																																																																																			G|0.810;A|0.190	0.190	strong		0.617	TMEM150A-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329474.1	NM_153342	
KY	339855	hgsc.bcm.edu	37	3	134322877	134322877	+	Silent	SNP	G	G	A	rs35316983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:134322877G>A	ENST00000423778.2	-	11	1591	c.1530C>T	c.(1528-1530)cgC>cgT	p.R510R	KY_ENST00000503669.1_3'UTR|KY_ENST00000508956.1_Silent_p.R489R	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	510					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGAAGATGTAGCGCCGCTGTG	0.592													G|||	25	0.00499201	0.0	0.0058	5008	,	,		19389	0.0		0.0209	False		,,,				2504	0.0				p.R510R		Atlas-SNP	.											KY_ENST00000423778,NS,carcinoma,-2,2	KY	92	2	0			c.C1530T						PASS	.	G		14,4172		0,14,2079	48.0	51.0	50.0		1530	4.6	1.0	3	dbSNP_126	50	191,8247		3,185,4031	yes	coding-synonymous	KY	NM_178554.4		3,199,6110	AA,AG,GG		2.2636,0.3344,1.6239		510/662	134322877	205,12419	2093	4219	6312	SO:0001819	synonymous_variant	339855	exon11			GATGTAGCGCCGC	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.1530C>T	3.37:g.134322877G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			G|0.989;A|0.011	0.011	strong		0.592	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
CCR6	1235	hgsc.bcm.edu	37	6	167549775	167549775	+	Silent	SNP	T	T	C	rs3093007	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:167549775T>C	ENST00000341935.5	+	3	609	c.57T>C	c.(55-57)ttT>ttC	p.F19F	RP11-517H2.6_ENST00000609590.1_RNA|CCR6_ENST00000349984.4_Silent_p.F19F|CCR6_ENST00000400926.2_Silent_p.F19F	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	19					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|humoral immune response (GO:0006959)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	14		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		AAGATTATTTTGTGTCAGTCA	0.418													T|||	655	0.130791	0.1778	0.1167	5008	,	,		22549	0.0476		0.1759	False		,,,				2504	0.1166				p.F19F		Atlas-SNP	.											.	CCR6	36	.	0			c.T57C						PASS	.	T	,	777,3629	315.8+/-294.3	79,619,1505	149.0	147.0	148.0		57,57	-3.2	0.0	6	dbSNP_103	148	1594,7006	297.5+/-303.5	149,1296,2855	no	coding-synonymous,coding-synonymous	CCR6	NM_004367.5,NM_031409.3	,	228,1915,4360	CC,CT,TT		18.5349,17.635,18.23	,	19/375,19/375	167549775	2371,10635	2203	4300	6503	SO:0001819	synonymous_variant	1235	exon3			TTATTTTGTGTCA	U68030	CCDS5298.1	6q27	2012-08-08			ENSG00000112486	ENSG00000112486		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1607	protein-coding gene	gene with protein product		601835		STRL22		8886020	Standard	NM_031409		Approved	CKR-L3, GPR-CY4, CMKBR6, GPR29, DRY-6, DCR2, BN-1, CD196	uc010kkm.3	P51684	OTTHUMG00000016015	ENST00000341935.5:c.57T>C	6.37:g.167549775T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_004367	E1P5C6|P78553|Q92846	Silent	SNP	ENST00000341935.5	37	CCDS5298.1																																																																																			T|0.835;C|0.165	0.165	strong		0.418	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043118.1		
ACAT1	38	hgsc.bcm.edu	37	11	107992346	107992346	+	Missense_Mutation	SNP	G	G	C	rs11540420|rs3741056	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:107992346G>C	ENST00000265838.4	+	1	104	c.13G>C	c.(13-15)Gcg>Ccg	p.A5P	RP11-144G7.2_ENST00000525548.1_RNA|ACAT1_ENST00000299355.6_Missense_Mutation_p.A5P	NM_000019.3	NP_000010.1	P24752	THIL_HUMAN	acetyl-CoA acetyltransferase 1	5			A -> P (in dbSNP:rs3741056).		adipose tissue development (GO:0060612)|brain development (GO:0007420)|branched-chain amino acid catabolic process (GO:0009083)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular nitrogen compound metabolic process (GO:0034641)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|metanephric proximal convoluted tubule development (GO:0072229)|protein homooligomerization (GO:0051260)|response to hormone (GO:0009725)|response to organic cyclic compound (GO:0014070)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acetyl-CoA C-acetyltransferase activity (GO:0003985)|coenzyme binding (GO:0050662)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|prostate(2)	10		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	GGCTGTGCTGGCGGCACTTCT	0.726													G|||	1662	0.331869	0.1293	0.4222	5008	,	,		13418	0.3601		0.3419	False		,,,				2504	0.502				p.A5P		Atlas-SNP	.											.	ACAT1	35	.	0			c.G13C						PASS	.	G	PRO/ALA	498,3570		40,418,1576	7.0	7.0	7.0		13	0.2	0.0	11	dbSNP_107	7	2021,5923		259,1503,2210	yes	missense	ACAT1	NM_000019.3	27	299,1921,3786	CC,CG,GG		25.4406,12.2419,20.9707	possibly-damaging	5/428	107992346	2519,9493	2034	3972	6006	SO:0001583	missense	38	exon1			GTGCTGGCGGCAC	D90228	CCDS8339.1	11q22.3	2010-04-30	2010-04-30		ENSG00000075239	ENSG00000075239	2.3.1.9		93	protein-coding gene	gene with protein product	"""acetoacetyl Coenzyme A thiolase"""	607809	"""acetyl-Coenzyme A acetyltransferase 1"""	ACAT		1979337	Standard	NM_000019		Approved	THIL	uc001pjy.3	P24752	OTTHUMG00000166381	ENST00000265838.4:c.13G>C	11.37:g.107992346G>C	ENSP00000265838:p.Ala5Pro	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	41	13	0.317073	NM_000019	B2R6H1|G3XAB4|Q96FG8	Missense_Mutation	SNP	ENST00000265838.4	37	CCDS8339.1	677	0.309981684981685	73	0.1483739837398374	142	0.39226519337016574	210	0.36713286713286714	252	0.3324538258575198	G	16.39	3.111218	0.56398	0.122419	0.254406	ENSG00000075239	ENST00000265838;ENST00000299355	D;D	0.93906	-3.13;-3.31	3.31	0.195	0.15151	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P	0.37864	0.61;0.514	B;B	0.35688	0.103;0.208	T	0.11792	-1.0573	8	0.66056	D	0.02	-1.264	2.6303	0.04942	0.2756:0.0:0.4998:0.2246	rs3741056;rs17800684;rs17845275;rs17858107;rs3741056	5;5	P24752;G3XAB4	THIL_HUMAN;.	P	5	ENSP00000265838:A5P;ENSP00000299355:A5P	ENSP00000265838:A5P	A	+	1	0	ACAT1	107497556	0.001000	0.12720	0.002000	0.10522	0.760000	0.43138	-0.118000	0.10692	0.050000	0.15949	-0.475000	0.04921	GCG	G|0.710;C|0.290	0.290	strong		0.726	ACAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389474.1	NM_000019	
APOL5	80831	hgsc.bcm.edu	37	22	36123083	36123083	+	Missense_Mutation	SNP	C	C	T	rs2076672	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:36123083C>T	ENST00000249044.2	+	3	968	c.968C>T	c.(967-969)aCg>aTg	p.T323M		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	323			T -> M (in dbSNP:rs2076672).		lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|skin(2)|urinary_tract(1)	19						GGGGCAAGGACGGAGACAGCA	0.612													C|||	744	0.148562	0.0923	0.2032	5008	,	,		18198	0.0804		0.2545	False		,,,				2504	0.1472				p.T323M		Atlas-SNP	.											.	APOL5	45	.	0			c.C968T						PASS	.	C	MET/THR	523,3883	234.2+/-247.1	28,467,1708	43.0	43.0	43.0		968	1.8	0.0	22	dbSNP_96	43	2264,6336	376.9+/-338.3	292,1680,2328	yes	missense	APOL5	NM_030642.1	81	320,2147,4036	TT,TC,CC		26.3256,11.8702,21.4286	probably-damaging	323/434	36123083	2787,10219	2203	4300	6503	SO:0001583	missense	80831	exon3			CAAGGACGGAGAC	AY014878	CCDS13920.1	22q12.3	2013-01-24			ENSG00000128313	ENSG00000128313		"""Apolipoproteins"""	14869	protein-coding gene	gene with protein product		607255				11374903	Standard	NM_030642		Approved	APOLV	uc003aof.3	Q9BWW9	OTTHUMG00000150588	ENST00000249044.2:c.968C>T	22.37:g.36123083C>T	ENSP00000249044:p.Thr323Met	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_030642	Q5TFL9|Q9UGW5	Missense_Mutation	SNP	ENST00000249044.2	37	CCDS13920.1	386	0.17673992673992675	55	0.11178861788617886	88	0.2430939226519337	38	0.06643356643356643	205	0.2704485488126649	C	13.49	2.253235	0.39797	0.118702	0.263256	ENSG00000128313	ENST00000249044	T	0.04119	3.7	3.9	1.78	0.24846	.	0.611094	0.13858	U	0.357864	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	D	0.71674	0.998	P	0.58331	0.837	T	0.47142	-0.9140	9	0.87932	D	0	.	7.0387	0.25008	0.0:0.7788:0.0:0.2212	rs2076672;rs52809043;rs60873045;rs2076672	323	Q9BWW9	APOL5_HUMAN	M	323	ENSP00000249044:T323M	ENSP00000249044:T323M	T	+	2	0	APOL5	34453029	0.001000	0.12720	0.000000	0.03702	0.065000	0.16274	0.985000	0.29578	0.174000	0.19809	0.655000	0.94253	ACG	C|0.812;T|0.188	0.188	strong		0.612	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
OR7A10	390892	hgsc.bcm.edu	37	19	14952238	14952238	+	Missense_Mutation	SNP	A	A	G	rs12972670	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14952238A>G	ENST00000248058.1	-	1	451	c.452T>C	c.(451-453)aTg>aCg	p.M151T		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	151			M -> T (in dbSNP:rs12972670).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					CAGAACACTCATGATCCAGGA	0.453													.|||	617	0.123203	0.1422	0.1196	5008	,	,		21909	0.0903		0.1541	False		,,,				2504	0.1022				p.M151T		Atlas-SNP	.											OR7A10,colon,carcinoma,0,1	OR7A10	33	1	0			c.T452C						PASS	.	A	THR/MET	678,3728	286.0+/-278.5	58,562,1583	74.0	71.0	72.0		452	2.8	0.0	19	dbSNP_121	72	1457,7143	278.6+/-293.5	139,1179,2982	yes	missense	OR7A10	NM_001005190.1	81	197,1741,4565	GG,GA,AA		16.9419,15.3881,16.4155	benign	151/310	14952238	2135,10871	2203	4300	6503	SO:0001583	missense	390892	exon1			ACACTCATGATCC		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.452T>C	19.37:g.14952238A>G	ENSP00000248058:p.Met151Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	165	90	0.545455	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	260	0.11904761904761904	69	0.1402439024390244	48	0.13259668508287292	27	0.0472027972027972	116	0.15303430079155672	a	0.596	-0.830989	0.02713	0.153881	0.169419	ENSG00000127515	ENST00000248058	T	0.00441	7.41	2.75	2.75	0.32379	GPCR, rhodopsin-like superfamily (1);	0.862066	0.09618	N	0.777980	T	0.00012	0.0000	N	0.21324	0.655	0.80722	P	0.0	B	0.10296	0.003	B	0.19666	0.026	T	0.19031	-1.0318	9	0.49607	T	0.09	.	9.0825	0.36561	1.0:0.0:0.0:0.0	rs12972670;rs16979967;rs58275244;rs12972670	151	O76100	OR7AA_HUMAN	T	151	ENSP00000248058:M151T	ENSP00000248058:M151T	M	-	2	0	OR7A10	14813238	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	-0.724000	0.04947	1.301000	0.44836	0.113000	0.15668	ATG	A|0.860;G|0.140	0.140	strong		0.453	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189184	11189184	+	Missense_Mutation	SNP	C	C	T	rs115295428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11189184C>T	ENST00000382435.4	+	1	788	c.569C>T	c.(568-570)aCc>aTc	p.T190I		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	190						integral component of membrane (GO:0016021)		p.T190I(1)									GTCTACACCACCCTGGGCTAT	0.587																																					p.T190I		Atlas-SNP	.											AMAC1L2,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.C569T						scavenged	.						145.0	143.0	143.0					8																	11189184		2203	4300	6503	SO:0001583	missense	83650	exon1			ACACCACCCTGGG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.569C>T	8.37:g.11189184C>T	ENSP00000371872:p.Thr190Ile	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	175	29	0.165714	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	C	6.076	0.382330	0.11524	.	.	ENSG00000177710	ENST00000382435	T	0.24151	1.87	.	.	.	.	0.138504	0.32287	N	0.006302	T	0.10937	0.0267	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28106	-1.0054	8	0.18276	T	0.48	-0.7964	.	.	.	.	190	Q96KT7	S35G5_HUMAN	I	190	ENSP00000371872:T190I	ENSP00000371872:T190I	T	+	2	0	SLC35G5	11226594	0.778000	0.28640	0.080000	0.20451	0.075000	0.17131	0.362000	0.20284	0.088000	0.17205	0.089000	0.15464	ACC	C|0.978;T|0.022	0.022	strong		0.587	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
KIAA0825	285600	hgsc.bcm.edu	37	5	93753017	93753017	+	Missense_Mutation	SNP	C	C	T	rs29910	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:93753017C>T	ENST00000513200.3	-	14	2623	c.2551G>A	c.(2551-2553)Gcc>Acc	p.A851T	KIAA0825_ENST00000427991.2_Missense_Mutation_p.A851T|KIAA0825_ENST00000312498.7_Missense_Mutation_p.A856T	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	851								p.A851T(1)|p.A856T(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TTAAAGATGGCTTCCATCAAG	0.353													C|||	921	0.183906	0.1293	0.1715	5008	,	,		18183	0.0784		0.2863	False		,,,				2504	0.2699				p.A851T		Atlas-SNP	.											KIAA0825_ENST00000513200,NS,carcinoma,0,2	KIAA0825	172	2	2	Substitution - Missense(2)	kidney(2)	c.G2551A						scavenged	.	C	THR/ALA	205,1179		23,159,510	207.0	172.0	183.0		2551	3.6	1.0	5	dbSNP_76	183	940,2242		144,652,795	yes	missense	KIAA0825	NM_001145678.1	58	167,811,1305	TT,TC,CC		29.5412,14.8121,25.0767	benign	851/1276	93753017	1145,3421	692	1591	2283	SO:0001583	missense	285600	exon15			AGATGGCTTCCAT	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 36"""	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.2551G>A	5.37:g.93753017C>T	ENSP00000424618:p.Ala851Thr	Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	174	83	0.477012	NM_001145678	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000513200.3	37		386	0.17673992673992675	50	0.1016260162601626	72	0.19889502762430938	37	0.06468531468531469	227	0.2994722955145119	C	12.22	1.873335	0.33069	0.148121	0.295412	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498	T;T;T	0.49432	0.79;0.79;0.78	5.39	3.57	0.40892	.	0.000000	0.64402	D	0.000010	T	0.00012	0.0000	L	0.34521	1.04	0.35559	P	0.19545800000000002	B	0.29988	0.264	B	0.31290	0.127	T	0.22730	-1.0208	9	0.06494	T	0.89	.	8.2205	0.31539	0.1549:0.7637:0.0:0.0814	rs29910;rs17378492;rs56725943;rs29910	851	Q8IV33	K0825_HUMAN	T	851;851;856	ENSP00000424618:A851T;ENSP00000400288:A851T;ENSP00000312205:A856T	ENSP00000312205:A856T	A	-	1	0	KIAA0825	93778773	0.994000	0.37717	0.989000	0.46669	0.868000	0.49771	0.084000	0.14891	0.608000	0.30000	0.557000	0.71058	GCC	C|0.811;T|0.189	0.189	strong		0.353	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665	
METTL21A	151194	hgsc.bcm.edu	37	2	208477852	208477852	+	Missense_Mutation	SNP	G	G	A	rs2551949	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:208477852G>A	ENST00000411432.1	-	4	791	c.575C>T	c.(574-576)aCt>aTt	p.T192I	METTL21A_ENST00000448007.2_Missense_Mutation_p.T192I|METTL21A_ENST00000272839.3_Missense_Mutation_p.T210I|METTL21A_ENST00000426075.1_Missense_Mutation_p.T192I|METTL21A_ENST00000448823.2_3'UTR|METTL21A_ENST00000477919.1_5'Flank|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000406927.2_Missense_Mutation_p.T192I|METTL21A_ENST00000432416.1_Intron|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000442521.1_Missense_Mutation_p.T192I	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	192			T -> I (in dbSNP:rs2551949). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						CTTTCTCACAGTAAATTGCCT	0.388													G|||	4528	0.904153	0.8646	0.879	5008	,	,		21589	0.998		0.831	False		,,,				2504	0.954				p.T192I		Atlas-SNP	.											.	METTL21A	24	.	0			c.C575T						PASS	.	G	ILE/THR,ILE/THR	3826,580	771.5+/-413.8	1661,504,38	154.0	154.0	154.0		575,575	2.9	1.0	2	dbSNP_100	154	7025,1575	744.2+/-407.2	2855,1315,130	yes	missense,missense	METTL21A	NM_001127395.1,NM_145280.4	89,89	4516,1819,168	AA,AG,GG		18.314,13.1639,16.5693	possibly-damaging,possibly-damaging	192/219,192/219	208477852	10851,2155	2203	4300	6503	SO:0001583	missense	151194	exon4			CTCACAGTAAATT	AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 557b"", ""heat shock protein 70kDa lysine (K) methyltransferase"""	615257	"""family with sequence similarity 119, member A"""	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.575C>T	2.37:g.208477852G>A	ENSP00000415115:p.Thr192Ile	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	207	205	0.990338	NM_145280	Q53RV0|Q8N1Z9|Q96GH6	Missense_Mutation	SNP	ENST00000411432.1	37	CCDS2376.1	1943	0.8896520146520146	435	0.8841463414634146	311	0.8591160220994475	572	1.0	625	0.8245382585751979	G	9.518	1.107586	0.20714	0.868361	0.81686	ENSG00000144401	ENST00000411432;ENST00000448007;ENST00000272839;ENST00000406927;ENST00000426075;ENST00000442521	T;T;T;T;T;T	0.16196	2.36;2.36;2.36;2.36;2.36;2.36	4.76	2.88	0.33553	.	0.688774	0.15486	N	0.259817	T	0.00012	0.0000	L	0.46157	1.445	0.33695	P	0.38621300000000003	B	0.20671	0.047	B	0.17979	0.02	T	0.31308	-0.9948	9	0.44086	T	0.13	-7.5229	11.4516	0.50156	0.0:0.1366:0.7213:0.1421	rs2551949;rs17846056;rs17859049;rs59049071;rs2551949	192	Q8WXB1	MT21A_HUMAN	I	192;192;210;192;192;192	ENSP00000415115:T192I;ENSP00000407622:T192I;ENSP00000272839:T210I;ENSP00000385481:T192I;ENSP00000403317:T192I;ENSP00000392062:T192I	ENSP00000272839:T210I	T	-	2	0	METTL21A	208186097	0.999000	0.42202	0.993000	0.49108	0.945000	0.59286	3.042000	0.49815	0.678000	0.31325	0.561000	0.74099	ACT	G|0.142;A|0.858	0.858	strong		0.388	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280	
BRCA1	672	hgsc.bcm.edu	37	17	41244936	41244936	+	Missense_Mutation	SNP	G	G	A	rs397508986|rs799917|rs80357962	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:41244936G>A	ENST00000357654.3	-	10	2730	c.2612C>T	c.(2611-2613)cCg>cTg	p.P871L	BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.P871L|BRCA1_ENST00000471181.2_Missense_Mutation_p.P871L|BRCA1_ENST00000309486.4_Missense_Mutation_p.P575L|BRCA1_ENST00000354071.3_Missense_Mutation_p.P871L|BRCA1_ENST00000493795.1_Missense_Mutation_p.P824L|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	871			P -> L (common polymorphism; dbSNP:rs799917). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:12442274, ECO:0000269|PubMed:15365993, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P871L(1)		NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		ATTTGAAAACGGAGCAAATGA	0.408			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			A|||	2724	0.54393	0.885	0.428	5008	,	,		21773	0.371		0.3628	False		,,,				2504	0.5297				p.P871L		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	BRCA1,NS,carcinoma,+1,2	BRCA1	304	2	1	Substitution - Missense(1)	stomach(1)	c.C2612T	GRCh37	CD982488	BRCA1	D	rs799917	PASS	.	A	LEU/PRO,LEU/PRO,,,LEU/PRO	3525,881	342.5+/-307.2	1419,687,97	102.0	101.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2612,2471,,,2612	5.0	1.0	17	dbSNP_86	101	2889,5711	670.0+/-402.7	470,1949,1881	yes	missense,missense,intron,intron,missense	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	98,98,,,98	1889,2636,1978	AA,AG,GG		33.593,19.9955,49.3157	benign,benign,,,benign	871/1864,824/1817,,,871/1885	41244936	6414,6592	2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		GAAAACGGAGCAA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.2612C>T	17.37:g.41244936G>A	ENSP00000350283:p.Pro871Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	172	81	0.47093	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	1055	0.48305860805860806	425	0.8638211382113821	164	0.4530386740331492	189	0.3304195804195804	277	0.3654353562005277	A	2.240	-0.374065	0.05034	0.800045	0.33593	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	5.04	5.04	0.67666	.	0.000000	0.39544	N	0.001340	T	0.00012	0.0000	N	0.00004	-3.395	0.43771	P	0.003703000000000012	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.43829	-0.9367	9	0.02654	T	1	.	9.647	0.39875	0.9207:0.0:0.0793:0.0	rs799917;rs52820477;rs56917575;rs799917	871;830;871;871;871;871	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	L	871;871;871;871;575;871;824	ENSP00000350283:P871L;ENSP00000326002:P871L;ENSP00000246907:P871L;ENSP00000310938:P575L;ENSP00000418960:P871L;ENSP00000418775:P824L	ENSP00000310938:P575L	P	-	2	0	BRCA1	38498462	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	4.246000	0.58740	0.938000	0.37419	-0.524000	0.04348	CCG	G|0.499;A|0.501	0.501	strong		0.408	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
POLG	5428	hgsc.bcm.edu	37	15	89862237	89862237	+	Silent	SNP	C	C	T	rs61752780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:89862237C>T	ENST00000268124.5	-	20	3531	c.3198G>A	c.(3196-3198)acG>acA	p.T1066T	POLG_ENST00000442287.2_Silent_p.T1066T	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	1066					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			GTATGTCAGACGTAGCAATGC	0.567								DNA polymerases (catalytic subunits)					C|||	29	0.00579073	0.0008	0.0043	5008	,	,		19589	0.0		0.0089	False		,,,				2504	0.0164				p.T1066T	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.G3198A						PASS	.	C	,	13,4387	20.2+/-43.8	0,13,2187	120.0	105.0	110.0		3198,3198	-0.2	0.0	15	dbSNP_129	110	67,8531	40.8+/-97.7	0,67,4232	no	coding-synonymous,coding-synonymous	POLG	NM_001126131.1,NM_002693.2	,	0,80,6419	TT,TC,CC		0.7793,0.2955,0.6155	,	1066/1240,1066/1240	89862237	80,12918	2200	4299	6499	SO:0001819	synonymous_variant	5428	exon20			GTCAGACGTAGCA	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.3198G>A	15.37:g.89862237C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_002693	Q8NFM2|Q92515	Silent	SNP	ENST00000268124.5	37	CCDS10350.1																																																																																			C|0.994;T|0.006	0.006	strong		0.567	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693	
C2orf54	79919	hgsc.bcm.edu	37	2	241830969	241830969	+	Silent	SNP	G	G	A	rs10171067	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241830969G>A	ENST00000388934.4	-	2	884	c.726C>T	c.(724-726)agC>agT	p.S242S	C2orf54_ENST00000307486.8_Silent_p.S93S|C2orf54_ENST00000402775.2_Silent_p.S74S	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	242										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		AGAGCTGGGCGCTGGCCGGCA	0.692													G|||	2640	0.527157	0.7799	0.3473	5008	,	,		17745	0.4415		0.5179	False		,,,				2504	0.411				p.S242S		Atlas-SNP	.											.	C2orf54	14	.	0			c.C726T						PASS	.	G	,	2960,1022		1120,720,151	46.0	54.0	51.0		726,222	-2.7	0.0	2	dbSNP_119	51	4114,4174		1043,2028,1073	no	coding-synonymous,coding-synonymous	C2orf54	NM_001085437.1,NM_024861.2	,	2163,2748,1224	AA,AG,GG		49.638,25.6655,42.3472	,	242/448,74/280	241830969	7074,5196	1991	4144	6135	SO:0001819	synonymous_variant	79919	exon2			CTGGGCGCTGGCC	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.726C>T	2.37:g.241830969G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	37	CCDS42839.1																																																																																			G|0.490;A|0.510	0.510	strong		0.692	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
ZNF512B	57473	hgsc.bcm.edu	37	20	62595990	62595990	+	Missense_Mutation	SNP	T	T	C	rs817326	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62595990T>C	ENST00000450537.1	-	6	1174	c.1114A>G	c.(1114-1116)Atg>Gtg	p.M372V	ZNF512B_ENST00000369888.1_Missense_Mutation_p.M372V|ZNF512B_ENST00000217130.3_Missense_Mutation_p.M372V			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	372			M -> V (in dbSNP:rs817326).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.M372V(1)		NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTCTGGCCCATGGAGGAGGGG	0.667													T|||	473	0.0944489	0.056	0.1225	5008	,	,		16621	0.0149		0.2207	False		,,,				2504	0.0787				p.M372V		Atlas-SNP	.											ZNF512B,NS,carcinoma,0,3	ZNF512B	72	3	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1114G						PASS	.	T	VAL/MET	397,4009	195.0+/-219.7	17,363,1823	61.0	55.0	57.0		1114	-11.0	0.0	20	dbSNP_86	57	1814,6786	325.8+/-317.1	202,1410,2688	yes	missense	ZNF512B	NM_020713.1	21	219,1773,4511	CC,CT,TT		21.093,9.0104,16.9998	benign	372/893	62595990	2211,10795	2203	4300	6503	SO:0001583	missense	57473	exon6			GGCCCATGGAGGA	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.1114A>G	20.37:g.62595990T>C	ENSP00000393795:p.Met372Val	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	158	57	0.360759	NM_020713	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	37	CCDS13548.1	256	0.11721611721611722	30	0.06097560975609756	49	0.13535911602209943	11	0.019230769230769232	166	0.21899736147757257	T	2.059	-0.415806	0.04766	0.090104	0.21093	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.21031	2.03;2.03;2.03	5.55	-11.0	0.00169	.	1.065800	0.07256	N	0.866716	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26395	-1.0104	9	0.09590	T	0.72	0.0763	8.2355	0.31622	0.0:0.3128:0.4162:0.271	rs817326;rs817326	372	Q96KM6	Z512B_HUMAN	V	372	ENSP00000358904:M372V;ENSP00000393795:M372V;ENSP00000217130:M372V	ENSP00000217130:M372V	M	-	1	0	ZNF512B	62066434	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.146000	0.01294	-2.664000	0.00417	-1.627000	0.00785	ATG	T|0.852;C|0.148	0.148	strong		0.667	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
DPCR1	135656	hgsc.bcm.edu	37	6	30917482	30917482	+	Missense_Mutation	SNP	C	C	T	rs112148530	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30917482C>T	ENST00000462446.1	+	2	1269	c.1241C>T	c.(1240-1242)aCa>aTa	p.T414I	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	319	Thr-rich.					integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						GACAAAACCACATCATCCTCA	0.498													-|||	243	0.0485224	0.0582	0.072	5008	,	,		25939	0.0476		0.0348	False		,,,				2504	0.0337				p.T414I		Atlas-SNP	.											.	DPCR1	99	.	0			c.C1241T						PASS	.	C	ILE/THR	82,1302		1,80,611	153.0	147.0	149.0		1241	2.4	0.0	6	dbSNP_132	149	105,3077		2,101,1488	no	missense	DPCR1	NM_080870.3	89	3,181,2099	TT,TC,CC		3.2998,5.9249,4.0955	possibly-damaging	414/1394	30917482	187,4379	692	1591	2283	SO:0001583	missense	135656	exon2			AAACCACATCATC	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.1241C>T	6.37:g.30917482C>T	ENSP00000417182:p.Thr414Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	122	0.055860805860805864	30	0.06097560975609756	33	0.09116022099447514	33	0.057692307692307696	26	0.03430079155672823	-	12.86	2.065209	0.36470	0.059249	0.032998	ENSG00000168631	ENST00000462446	T	0.51574	0.7	2.36	2.36	0.29203	.	.	.	.	.	T	0.47764	0.1463	M	0.62723	1.935	0.20196	N	0.999921	D	0.71674	0.998	D	0.72075	0.976	T	0.13072	-1.0523	9	0.39692	T	0.17	.	8.5353	0.33360	0.0:1.0:0.0:0.0	.	414	E9PEI6	.	I	414	ENSP00000417182:T414I	ENSP00000417182:T414I	T	+	2	0	DPCR1	31025461	0.040000	0.19996	0.047000	0.18901	0.029000	0.11900	1.917000	0.39996	1.683000	0.51011	0.525000	0.51046	ACA	C|0.944;T|0.056	0.056	strong		0.498	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
CD68	968	hgsc.bcm.edu	37	17	7484101	7484101	+	Splice_Site	SNP	C	C	A	rs25679|rs9901673	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7484101C>A	ENST00000250092.6	+	4	971	c.760C>A	c.(760-762)Cag>Aag	p.Q254K	AC113189.5_ENST00000572046.1_RNA|AC113189.5_ENST00000573187.1_RNA|MPDU1_ENST00000582151.1_5'Flank|AC113189.5_ENST00000417897.1_RNA|AC113189.5_ENST00000415124.1_RNA|CD68_ENST00000380498.6_Splice_Site_p.Q227K|SENP3-EIF4A1_ENST00000579777.1_RNA|SNORA67_ENST00000384423.1_RNA|MPDU1_ENST00000250124.6_5'Flank	NM_001251.2	NP_001242.2	P34810	CD68_HUMAN	CD68 molecule	254			Q -> K (in dbSNP:rs25679). {ECO:0000269|PubMed:7680921}.		cellular response to organic substance (GO:0071310)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				endometrium(1)|lung(1)|skin(1)	3						CCACGCAGCACGTAAGTAACC	0.572													C|||	789	0.157548	0.1657	0.121	5008	,	,		19669	0.1567		0.16	False		,,,				2504	0.1708				p.Q254K		Atlas-SNP	.											.	CD68	17	.	0			c.C760A						PASS	.	C	LYS/GLN,LYS/GLN	787,3619	318.8+/-295.8	68,651,1484	103.0	85.0	91.0		679,760	2.0	0.3	17	dbSNP_119	91	1443,7157	277.9+/-293.1	136,1171,2993	yes	missense-near-splice,missense-near-splice	CD68	NM_001040059.1,NM_001251.2	53,53	204,1822,4477	AA,AC,CC		16.7791,17.862,17.1459	possibly-damaging,possibly-damaging	227/328,254/355	7484101	2230,10776	2203	4300	6503	SO:0001630	splice_region_variant	968	exon4			GCAGCACGTAAGT	S57235	CCDS11114.1, CCDS58512.1	17p13	2011-11-24	2006-03-28		ENSG00000129226	ENSG00000129226		"""CD molecules"""	1693	protein-coding gene	gene with protein product	"""scavenger receptor class D, member 1"", ""CD68 antigen"", ""macrophage antigen CD68"""	153634	"""CD68 antigen"""			9790779	Standard	NM_001251		Approved	SCARD1, macrosialin, GP110, DKFZp686M18236, LAMP4	uc002ghv.3	P34810	OTTHUMG00000108146	ENST00000250092.6:c.760+1C>A	17.37:g.7484101C>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	155	77	0.496774	NM_001251	B4DVT4|Q53HR6|Q53XI3|Q96BI7	Missense_Mutation	SNP	ENST00000250092.6	37	CCDS11114.1	352	0.16117216117216118	83	0.16869918699186992	43	0.11878453038674033	104	0.18181818181818182	122	0.16094986807387862	C	10.69	1.422540	0.25639	0.17862	0.167791	ENSG00000129226	ENST00000250092;ENST00000380498	T	0.31769	1.48	5.16	1.97	0.26223	.	0.397176	0.21802	N	0.068903	T	0.00073	0.0002	M	0.72479	2.2	0.36687	P	0.12062600000000001	B;B	0.15141	0.012;0.012	B;B	0.18871	0.009;0.023	T	0.05305	-1.0893	9	0.42905	T	0.14	-1.8387	8.4898	0.33093	0.1656:0.5142:0.3201:0.0	rs9901673;rs60414741;rs9901673	254;227	P34810;B4DVT4	CD68_HUMAN;.	K	254;197	ENSP00000250092:Q254K	ENSP00000250092:Q254K	Q	+	1	0	CD68	7424825	0.565000	0.26610	0.295000	0.24960	0.028000	0.11728	0.685000	0.25378	0.294000	0.22547	-0.176000	0.13171	CAG	C|0.830;A|0.170	0.170	strong		0.572	CD68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226949.3	NM_001251	Missense_Mutation
CNTRL	11064	hgsc.bcm.edu	37	9	123929770	123929770	+	Silent	SNP	C	C	T	rs61745682	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:123929770C>T	ENST00000373855.1	+	37	5919	c.5659C>T	c.(5659-5661)Ctg>Ttg	p.L1887L	CNTRL_ENST00000238341.5_Silent_p.L1887L|CNTRL_ENST00000373850.1_Silent_p.L1335L|CNTRL_ENST00000373845.2_3'UTR			Q7Z7A1	CNTRL_HUMAN	centriolin	1887					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						CCTAAAGGACCTGCTTCACAC	0.453													C|||	637	0.127196	0.0174	0.1945	5008	,	,		19467	0.1746		0.1431	False		,,,				2504	0.1626				p.L1887L		Atlas-SNP	.											.	CNTRL	161	.	0			c.C5659T						PASS	.	C		160,4246	107.3+/-145.7	1,158,2044	60.0	48.0	52.0		5659	4.2	0.9	9	dbSNP_129	52	1234,7366	244.3+/-273.6	91,1052,3157	no	coding-synonymous	CNTRL	NM_007018.4		92,1210,5201	TT,TC,CC		14.3488,3.6314,10.7181		1887/2326	123929770	1394,11612	2203	4300	6503	SO:0001819	synonymous_variant	11064	exon35			AAGGACCTGCTTC	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.5659C>T	9.37:g.123929770C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	205	93	0.453659	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Silent	SNP	ENST00000373855.1	37	CCDS35118.1																																																																																			C|0.881;T|0.119	0.119	strong		0.453	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
RP1L1	94137	hgsc.bcm.edu	37	8	10470148	10470148	+	Missense_Mutation	SNP	G	G	A	rs74400517	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:10470148G>A	ENST00000382483.3	-	4	1683	c.1460C>T	c.(1459-1461)gCc>gTc	p.A487V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	487			A -> V.		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CCCTATCTGGGCAGAGGGGCT	0.716													G|||	191	0.038139	0.0076	0.0562	5008	,	,		15070	0.001		0.1054	False		,,,				2504	0.0358				p.A487V		Atlas-SNP	.											.	RP1L1	453	.	0			c.C1460T						PASS	.	G	VAL/ALA	80,3728		1,78,1825	25.0	29.0	28.0		1460	3.0	0.0	8	dbSNP_131	28	827,7389		41,745,3322	yes	missense	RP1L1	NM_178857.5	64	42,823,5147	AA,AG,GG		10.0657,2.1008,7.5432	benign	487/2401	10470148	907,11117	1904	4108	6012	SO:0001583	missense	94137	exon4			ATCTGGGCAGAGG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1460C>T	8.37:g.10470148G>A	ENSP00000371923:p.Ala487Val	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	51	35	0.686275	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	111	0.050824175824175824	8	0.016260162601626018	18	0.049723756906077346	0	0.0	85	0.11213720316622691	G	13.67	2.307532	0.40795	0.021008	0.100657	ENSG00000183638	ENST00000382483	T	0.04454	3.62	3.89	3.0	0.34707	.	1.900250	0.03515	U	0.220195	T	0.00073	0.0002	N	0.14661	0.345	0.80722	P	0.0	B	0.33904	0.431	B	0.24155	0.051	T	0.38585	-0.9654	9	0.49607	T	0.09	.	7.4371	0.27162	0.1227:0.0:0.8773:0.0	.	487	A6NKC6	.	V	487	ENSP00000371923:A487V	ENSP00000371923:A487V	A	-	2	0	RP1L1	10507558	0.005000	0.15991	0.003000	0.11579	0.166000	0.22503	1.202000	0.32271	0.973000	0.38340	0.561000	0.74099	GCC	G|0.934;A|0.066	0.066	strong		0.716	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
PDE4A	5141	hgsc.bcm.edu	37	19	10570141	10570141	+	Silent	SNP	C	C	T	rs141286487	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10570141C>T	ENST00000352831.6	+	9	1277	c.1167C>T	c.(1165-1167)cgC>cgT	p.R389R	PDE4A_ENST00000440014.2_Silent_p.R328R|PDE4A_ENST00000380702.2_Silent_p.R367R|PDE4A_ENST00000592685.1_Silent_p.R367R|PDE4A_ENST00000293683.5_Silent_p.R363R|PDE4A_ENST00000344979.3_Silent_p.R150R	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	389	Catalytic.				cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Caffeine(DB00201)|Dipyridamole(DB00975)|Drotaverine(DB06751)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theophylline(DB00277)|Tofisopam(DB08811)	CTGGAGGCCGCTCACTCACCT	0.607													C|||	13	0.00259585	0.0	0.0043	5008	,	,		19910	0.0		0.0099	False		,,,				2504	0.0				p.R389R		Atlas-SNP	.											PDE4A_ENST00000440014,NS,carcinoma,+1,4	PDE4A	236	4	0			c.C1167T						PASS	.	C	,,,	7,4399	11.4+/-27.6	0,7,2196	78.0	69.0	72.0		1167,1089,984,450	-4.0	0.8	19	dbSNP_134	72	59,8541	36.9+/-92.0	0,59,4241	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE4A	NM_001111307.1,NM_001111308.1,NM_001111309.1,NM_006202.2	,,,	0,66,6437	TT,TC,CC		0.686,0.1589,0.5075	,,,	389/887,363/861,328/826,150/648	10570141	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	5141	exon9			AGGCCGCTCACTC		CCDS12238.1, CCDS45961.1, CCDS45962.1, CCDS45963.1, CCDS58649.1	19p13.2	2010-06-24	2010-06-24			ENSG00000065989	3.1.4.17	"""Phosphodiesterases"""	8780	protein-coding gene	gene with protein product	"""phosphodiesterase E2 dunce homolog (Drosophila)"""	600126	"""phosphodiesterase 4A, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E2)"""	DPDE2		8009369	Standard	NM_006202		Approved		uc002moj.2	P27815		ENST00000352831.6:c.1167C>T	19.37:g.10570141C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Silent	SNP	ENST00000352831.6	37	CCDS45961.1																																																																																			C|0.995;T|0.005	0.005	strong		0.607	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1		
LRRC14B	389257	hgsc.bcm.edu	37	5	195318	195318	+	Silent	SNP	T	T	C	rs6886707	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:195318T>C	ENST00000328278.3	+	2	1423	c.1395T>C	c.(1393-1395)gcT>gcC	p.A465A	CTD-2083E4.7_ENST00000563761.1_RNA	NM_001080478.1	NP_001073947.1	A6NHZ5	LR14B_HUMAN	leucine rich repeat containing 14B	465										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	10						TGCTGCGGGCTGACCGAGAGG	0.552													C|||	945	0.188698	0.4955	0.1354	5008	,	,		18137	0.005		0.1352	False		,,,				2504	0.0562				p.A465A		Atlas-SNP	.											.	LRRC14B	30	.	0			c.T1395C						PASS	.	C		1805,2549		382,1041,754	111.0	122.0	119.0		1395	-4.5	0.0	5	dbSNP_116	119	1015,7543		74,867,3338	no	coding-synonymous	LRRC14B	NM_001080478.1		456,1908,4092	CC,CT,TT		11.8602,41.4561,21.8401		465/515	195318	2820,10092	2177	4279	6456	SO:0001819	synonymous_variant	389257	exon2			GCGGGCTGACCGA		CCDS47184.1	5p15.33	2010-02-17			ENSG00000185028	ENSG00000185028			37268	protein-coding gene	gene with protein product							Standard	NM_001080478		Approved		uc003jal.1	A6NHZ5	OTTHUMG00000161578	ENST00000328278.3:c.1395T>C	5.37:g.195318T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_001080478		Silent	SNP	ENST00000328278.3	37	CCDS47184.1																																																																																			T|0.847;C|0.153	0.153	strong		0.552	LRRC14B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000365393.2	NM_001080478	
FCRLB	127943	hgsc.bcm.edu	37	1	161697319	161697319	+	Missense_Mutation	SNP	G	G	A	rs34868416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:161697319G>A	ENST00000367948.2	+	8	1363	c.1148G>A	c.(1147-1149)gGc>gAc	p.G383D	FCRLB_ENST00000336830.5_3'UTR|FCRLB_ENST00000367944.3_3'UTR|FCRLB_ENST00000495397.1_3'UTR|FCRLB_ENST00000367946.3_3'UTR|FCRLB_ENST00000392158.1_Missense_Mutation_p.G383D|FCRLB_ENST00000367945.1_3'UTR			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	383					negative regulation of immune response (GO:0050777)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|skin(1)	17	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			CTGCTCAAAGGCCTTCTGAGC	0.652													G|||	290	0.0579073	0.0061	0.0735	5008	,	,		14050	0.0883		0.0944	False		,,,				2504	0.0481				p.G383D		Atlas-SNP	.											.	FCRLB	35	.	0			c.G1148A						PASS	.	G	ASP/GLY	71,4335	58.7+/-95.3	2,67,2134	40.0	45.0	43.0		1148	2.4	0.7	1	dbSNP_126	43	759,7841	170.6+/-221.7	33,693,3574	yes	missense	FCRLB	NM_001002901.2	94	35,760,5708	AA,AG,GG		8.8256,1.6114,6.3817	possibly-damaging	383/427	161697319	830,12176	2203	4300	6503	SO:0001583	missense	127943	exon6			TCAAAGGCCTTCT	AY670683	CCDS30927.1, CCDS72962.1, CCDS72963.1, CCDS72964.1, CCDS72965.1	1q23.3	2013-01-11	2006-09-26	2006-09-26	ENSG00000162746	ENSG00000162746		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26431	protein-coding gene	gene with protein product		609251	"""Fc receptor-like and mucin-like 2"""	FCRLM2		15676285	Standard	NM_001288829		Approved	FLJ31052, FCRL2, FREB-2, FCRLY	uc001gbi.3	Q6BAA4	OTTHUMG00000133629	ENST00000367948.2:c.1148G>A	1.37:g.161697319G>A	ENSP00000356925:p.Gly383Asp	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Missense_Mutation	SNP	ENST00000367948.2	37	CCDS30927.1	143	0.06547619047619048	4	0.008130081300813009	31	0.0856353591160221	37	0.06468531468531469	71	0.09366754617414248	G	18.27	3.586607	0.66105	0.016114	0.088256	ENSG00000162746	ENST00000367948;ENST00000392158	T;T	0.01495	4.83;4.83	4.27	2.39	0.29439	.	0.447792	0.19012	N	0.125045	T	0.01029	0.0034	L	0.54323	1.7	0.34815	P	0.2619	D	0.54047	0.964	P	0.44811	0.461	T	0.55528	-0.8127	9	0.51188	T	0.08	.	6.4599	0.21950	0.2233:0.0:0.7767:0.0	rs34868416	383	Q6BAA4	FCRLB_HUMAN	D	383	ENSP00000356925:G383D;ENSP00000375999:G383D	ENSP00000356925:G383D	G	+	2	0	FCRLB	159963943	1.000000	0.71417	0.719000	0.30619	0.892000	0.51952	1.789000	0.38724	0.442000	0.26555	0.455000	0.32223	GGC	G|0.940;A|0.060	0.060	strong		0.652	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378	
NME8	51314	hgsc.bcm.edu	37	7	37936530	37936530	+	Silent	SNP	T	T	C	rs3213975	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:37936530T>C	ENST00000199447.4	+	17	1975	c.1603T>C	c.(1603-1605)Ttg>Ctg	p.L535L	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Silent_p.L535L	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	535	NDK 3.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										ATGGAGACGATTGATGGGCCC	0.463													T|||	1034	0.20647	0.1672	0.2017	5008	,	,		16821	0.2292		0.2396	False		,,,				2504	0.2055				p.L535L		Atlas-SNP	.											.	.	.	.	0			c.T1603C						PASS	.	T		907,3499	348.2+/-309.8	94,719,1390	116.0	111.0	113.0		1603	-4.0	0.8	7	dbSNP_106	113	2077,6523	359.8+/-331.7	256,1565,2479	no	coding-synonymous	TXNDC3	NM_016616.4		350,2284,3869	CC,CT,TT		24.1512,20.5856,22.9433		535/589	37936530	2984,10022	2203	4300	6503	SO:0001819	synonymous_variant	51314	exon17			AGACGATTGATGG	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.1603T>C	7.37:g.37936530T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_016616	Q9NZH1	Silent	SNP	ENST00000199447.4	37	CCDS5452.1																																																																																			T|0.770;C|0.230	0.230	strong		0.463	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
CPA1	1357	hgsc.bcm.edu	37	7	130022041	130022041	+	Silent	SNP	C	C	T	rs968404	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:130022041C>T	ENST00000011292.3	+	4	624	c.474C>T	c.(472-474)taC>taT	p.Y158Y	CPA1_ENST00000484324.1_Silent_p.Y70Y	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	158					proteolysis (GO:0006508)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(18;0.0435)					GTCCCATTTACGTGCTGAAGG	0.557													C|||	477	0.0952476	0.1286	0.0706	5008	,	,		22263	0.0069		0.1362	False		,,,				2504	0.1166				p.Y158Y		Atlas-SNP	.											.	CPA1	73	.	0			c.C474T						PASS	.	C		564,3842	252.7+/-259.0	35,494,1674	119.0	92.0	102.0		474	-6.8	0.0	7	dbSNP_86	102	1321,7279	260.3+/-283.2	105,1111,3084	yes	coding-synonymous	CPA1	NM_001868.2		140,1605,4758	TT,TC,CC		15.3605,12.8007,14.4933		158/420	130022041	1885,11121	2203	4300	6503	SO:0001819	synonymous_variant	1357	exon4			CATTTACGTGCTG		CCDS5820.1	7q32	2012-02-10			ENSG00000091704	ENSG00000091704	3.4.17.1		2296	protein-coding gene	gene with protein product	"""pancreatic carboxypeptidase A"""	114850		CPA			Standard	NM_001868		Approved		uc003vpx.3	P15085	OTTHUMG00000157826	ENST00000011292.3:c.474C>T	7.37:g.130022041C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_001868	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	Silent	SNP	ENST00000011292.3	37	CCDS5820.1																																																																																			C|0.875;T|0.125	0.125	strong		0.557	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868	
SERPINA9	327657	hgsc.bcm.edu	37	14	94936110	94936110	+	Missense_Mutation	SNP	G	G	A	rs45438398	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:94936110G>A	ENST00000380365.3	-	2	146	c.68C>T	c.(67-69)cCg>cTg	p.P23L	SERPINA9_ENST00000298845.7_Missense_Mutation_p.P41L|SERPINA9_ENST00000337425.5_Missense_Mutation_p.P41L|SERPINA9_ENST00000424550.2_Intron|SERPINA9_ENST00000448305.2_Intron|SERPINA9_ENST00000539349.1_5'UTR|SERPINA9_ENST00000546329.1_Intron			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	23				P -> L (in Ref. 1; AAO65242/AAO65243 and 3; AAQ89063). {ECO:0000305}.	negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		GGCATTGGCCGGGGACACACA	0.517													G|||	293	0.0585064	0.0219	0.0865	5008	,	,		18535	0.0188		0.0974	False		,,,				2504	0.089				p.P41L		Atlas-SNP	.											.	SERPINA9	105	.	0			c.C122T						PASS	.	G	LEU/PRO,LEU/PRO	143,3863		1,141,1861	87.0	87.0	87.0		122,122	-1.2	0.0	14	dbSNP_127	87	991,7343		51,889,3227	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	98,98	52,1030,5088	AA,AG,GG		11.891,3.5696,9.1896	possibly-damaging,possibly-damaging	41/336,41/436	94936110	1134,11206	2003	4167	6170	SO:0001583	missense	327657	exon2			TTGGCCGGGGACA	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.68C>T	14.37:g.94936110G>A	ENSP00000369723:p.Pro23Leu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	162	85	0.524691	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		121	0.0554029304029304	15	0.03048780487804878	30	0.08287292817679558	14	0.024475524475524476	62	0.08179419525065963	G	11.58	1.680823	0.29872	0.035696	0.11891	ENSG00000170054	ENST00000298845;ENST00000337425;ENST00000380365	D;D;D	0.88046	-2.33;-2.33;-2.33	3.99	-1.2	0.09554	Serpin domain (1);	2.666900	0.01664	U	0.025291	T	0.02610	0.0079	N	0.08118	0	0.80722	P	0.0	B;B;B	0.19817	0.024;0.039;0.012	B;B;B	0.14023	0.003;0.01;0.002	T	0.43861	-0.9365	9	0.30078	T	0.28	.	0.6265	0.00787	0.3019:0.2479:0.2904:0.1597	rs45438398;rs61757458	23;41;41	Q86WD7;Q86WD7-7;Q86WD7-2	SPA9_HUMAN;.;.	L	41;41;23	ENSP00000298845:P41L;ENSP00000337133:P41L;ENSP00000369723:P23L	ENSP00000298845:P41L	P	-	2	0	SERPINA9	94005863	0.000000	0.05858	0.001000	0.08648	0.101000	0.19017	0.074000	0.14662	0.123000	0.18342	0.313000	0.20887	CCG	G|0.920;A|0.080	0.080	strong		0.517	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
ADSSL1	122622	hgsc.bcm.edu	37	14	105196230	105196230	+	Start_Codon_SNP	SNP	A	A	C	rs386781068|rs80097179	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105196230A>C	ENST00000332972.5	+	1	160	c.1A>C	c.(1-3)Atg>Ctg	p.M1L	ADSSL1_ENST00000330877.2_Intron	NM_199165.1	NP_954634.1			adenylosuccinate synthase like 1											central_nervous_system(1)|cervix(1)|kidney(1)|lung(5)|ovary(2)|prostate(1)	11		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)		tggcgtcggcatggtggggag	0.721													a|||	1884	0.376198	0.1914	0.3646	5008	,	,		11381	0.5774		0.3241	False		,,,				2504	0.4806				p.M1L		Atlas-SNP	.											.	ADSSL1	37	.	0			c.A1C						PASS	.	A	,LEU/MET	863,3221		99,665,1278	19.0	18.0	18.0		,1	-0.3	0.0	14	dbSNP_131	18	2369,5543		361,1647,1948	no	intron,missense	ADSSL1	NM_152328.3,NM_199165.1	,15	460,2312,3226	CC,CA,AA		29.9419,21.1312,26.9423	,benign	,1/501	105196230	3232,8764	2042	3956	5998	SO:0001582	initiator_codon_variant	122622	exon1			GTCGGCATGGTGG	AK095921	CCDS9990.1, CCDS9991.1	14q32.33	2010-08-05			ENSG00000185100	ENSG00000185100			20093	protein-coding gene	gene with protein product		612498					Standard	NM_199165		Approved	FLJ38602	uc001ype.3	Q8N142		ENST00000332972.5:c.1A>C	14.37:g.105196230A>C	ENSP00000333019:p.Met1Leu	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	25	16	0.64	NM_199165		Missense_Mutation	SNP	ENST00000332972.5	37	CCDS9991.1	784	0.358974358974359	97	0.19715447154471544	132	0.36464088397790057	317	0.5541958041958042	238	0.31398416886543534	a	2.920	-0.223509	0.06061	0.211312	0.299419	ENSG00000185100	ENST00000332972	T	0.39229	1.09	0.158	-0.317	0.12736	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	8.000000000008E-6	B	0.10296	0.003	B	0.01281	0.0	T	0.43523	-0.9386	6	0.87932	D	0	-24.6368	.	.	.	.	1	Q8N142-2	.	L	1	ENSP00000333019:M1L	ENSP00000333019:M1L	M	+	1	0	ADSSL1	104267275	0.222000	0.23652	0.018000	0.16275	0.006000	0.05464	-2.212000	0.01225	-1.178000	0.02741	-1.194000	0.01681	ATG	A|0.640;C|0.360	0.360	strong		0.721	ADSSL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410531.1		Missense_Mutation
IFT122	55764	hgsc.bcm.edu	37	3	129214369	129214369	+	Silent	SNP	C	C	T	rs73204231		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129214369C>T	ENST00000348417.2	+	18	2204	c.2127C>T	c.(2125-2127)gcC>gcT	p.A709A	IFT122_ENST00000440957.2_Silent_p.A500A|IFT122_ENST00000504021.1_Silent_p.A585A|IFT122_ENST00000431818.2_Silent_p.A559A|IFT122_ENST00000513932.1_3'UTR|IFT122_ENST00000349441.2_Silent_p.A598A|IFT122_ENST00000296266.3_Silent_p.A760A|IFT122_ENST00000347300.2_Silent_p.A650A|IFT122_ENST00000507564.1_Silent_p.A701A	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	709					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						TCCATGAGGCCGCCAAACTGT	0.507																																					p.A760A		Atlas-SNP	.											IFT122,colon,carcinoma,0,3	IFT122	117	3	0			c.C2280T						scavenged	.						109.0	94.0	99.0					3																	129214369		2203	4300	6503	SO:0001819	synonymous_variant	55764	exon19			TGAGGCCGCCAAA	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.2127C>T	3.37:g.129214369C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	142	2	0.0140845	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Silent	SNP	ENST00000348417.2	37	CCDS3061.1																																																																																			.	.	strong		0.507	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
PCNT	5116	hgsc.bcm.edu	37	21	47841989	47841989	+	Missense_Mutation	SNP	C	C	T	rs61735814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47841989C>T	ENST00000359568.5	+	32	7237	c.7130C>T	c.(7129-7131)cCg>cTg	p.P2377L	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2377					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AGGTTTCAGCCGCTGCCGGAA	0.627													C|||	94	0.01877	0.0008	0.0259	5008	,	,		16400	0.001		0.0676	False		,,,				2504	0.0061				p.P2377L		Atlas-SNP	.											PCNT,NS,carcinoma,+1,1	PCNT	283	1	0			c.C7130T						PASS	.	C	LEU/PRO	61,4345	57.4+/-93.9	1,59,2143	55.0	56.0	56.0		7130	-7.7	0.0	21	dbSNP_129	56	524,8076	147.1+/-202.6	11,502,3787	yes	missense	PCNT	NM_006031.5	98	12,561,5930	TT,TC,CC		6.093,1.3845,4.4979	benign	2377/3337	47841989	585,12421	2203	4300	6503	SO:0001583	missense	5116	exon32			TTCAGCCGCTGCC	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7130C>T	21.37:g.47841989C>T	ENSP00000352572:p.Pro2377Leu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	72	0.03296703296703297	2	0.0040650406504065045	13	0.03591160220994475	1	0.0017482517482517483	56	0.07387862796833773	C	10.31	1.315395	0.23908	0.013845	0.06093	ENSG00000160299	ENST00000359568	T	0.01464	4.86	4.05	-7.69	0.01263	.	.	.	.	.	T	0.00109	0.0003	L	0.40543	1.245	0.09310	N	1	B;P	0.41848	0.0;0.763	B;B	0.24155	0.001;0.051	T	0.45101	-0.9284	9	0.25751	T	0.34	.	0.2513	0.00206	0.3263:0.2474:0.2047:0.2216	rs61735814	2259;2377	O95613-2;O95613	.;PCNT_HUMAN	L	2377	ENSP00000352572:P2377L	ENSP00000352572:P2377L	P	+	2	0	PCNT	46666417	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.156000	0.03160	-1.441000	0.01958	-0.397000	0.06425	CCG	C|0.960;T|0.040	0.040	strong		0.627	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
HELZ2	85441	hgsc.bcm.edu	37	20	62193019	62193019	+	Silent	SNP	C	C	T	rs11551684	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62193019C>T	ENST00000467148.1	-	12	6840	c.6771G>A	c.(6769-6771)ccG>ccA	p.P2257P	HELZ2_ENST00000427522.2_Silent_p.P1688P	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2257	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P2257P(1)									TGCCCACACGCGGCACTGGGA	0.652													C|||	1096	0.21885	0.0068	0.085	5008	,	,		15633	0.5734		0.166	False		,,,				2504	0.2894				p.P2257P		Atlas-SNP	.											PRIC285,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	prostate(1)	c.G6771A						PASS	.	C	,	169,4237	106.5+/-144.9	2,165,2036	40.0	45.0	43.0		6771,5064	-9.0	0.0	20	dbSNP_120	43	1371,7229	253.3+/-279.0	110,1151,3039	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	112,1316,5075	TT,TC,CC		15.9419,3.8357,11.8407	,	2257/2650,1688/2081	62193019	1540,11466	2203	4300	6503	SO:0001819	synonymous_variant	85441	exon13			CACACGCGGCACT	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.6771G>A	20.37:g.62193019C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			C|0.849;T|0.151	0.151	strong		0.652	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
TWF1	5756	hgsc.bcm.edu	37	12	44191625	44191625	+	Silent	SNP	G	G	A	rs12829856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:44191625G>A	ENST00000395510.2	-	6	624	c.495C>T	c.(493-495)gaC>gaT	p.D165D	TWF1_ENST00000548315.1_Silent_p.D172D|TWF1_ENST00000552521.1_Silent_p.D67D|TWF1_ENST00000325127.4_Silent_p.D199D	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	165					barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		CCACACCCACGTCAGTCTGTA	0.378													G|||	491	0.0980431	0.1687	0.0677	5008	,	,		17574	0.0863		0.0964	False		,,,				2504	0.0378				p.D172D		Atlas-SNP	.											.	TWF1	37	.	0			c.C516T						PASS	.	G	,	607,3799	265.3+/-266.6	32,543,1628	99.0	95.0	96.0		516,495	-3.5	1.0	12	dbSNP_121	96	802,7798	188.0+/-235.1	26,750,3524	yes	coding-synonymous,coding-synonymous	TWF1	NM_001242397.1,NM_002822.4	,	58,1293,5152	AA,AG,GG		9.3256,13.7767,10.8335	,	172/358,165/351	44191625	1409,11597	2203	4300	6503	SO:0001819	synonymous_variant	5756	exon7			ACCCACGTCAGTC	U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"""protein tyrosine kinase 9"", ""PTK9 protein tyrosine kinase 9"", ""twinfilin, actin-binding protein, homolog 1 (Drosophila)"""	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.495C>T	12.37:g.44191625G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_001242397	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Silent	SNP	ENST00000395510.2	37	CCDS31780.2																																																																																			G|0.896;A|0.104	0.104	strong		0.378	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702688	27702688	+	Silent	SNP	C	C	T	rs7087552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:27702688C>T	ENST00000438700.3	-	1	609	c.492G>A	c.(490-492)gaG>gaA	p.E164E		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	164					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						CTAGGTCTTCCTCTTCGTCCT	0.652													C|||	993	0.198283	0.3805	0.2839	5008	,	,		14646	0.0129		0.2137	False		,,,				2504	0.0665				p.E164E		Atlas-SNP	.											.	PTCHD3	140	.	0			c.G492A						PASS	.	C		1586,2820	485.3+/-360.3	282,1022,899	90.0	100.0	96.0		492	-5.0	0.0	10	dbSNP_116	96	1936,6664	332.3+/-320.0	234,1468,2598	no	coding-synonymous	PTCHD3	NM_001034842.3		516,2490,3497	TT,TC,CC		22.5116,35.9964,27.0798		164/768	27702688	3522,9484	2203	4300	6503	SO:0001819	synonymous_variant	374308	exon1			GTCTTCCTCTTCG	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.492G>A	10.37:g.27702688C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	124	56	0.451613	NM_001034842	I3L499|Q6ZU28	Silent	SNP	ENST00000438700.3	37	CCDS31173.1																																																																																			C|0.764;T|0.236	0.236	strong		0.652	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
TTN	7273	hgsc.bcm.edu	37	2	179582853	179582853	+	Missense_Mutation	SNP	T	T	C	rs72648982	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179582853T>C	ENST00000591111.1	-	84	24153	c.23929A>G	c.(23929-23931)Aga>Gga	p.R7977G	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.R7050G|TTN_ENST00000589042.1_Missense_Mutation_p.R8294G|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12168	Ig-like 62.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAAGAAATTCTAATTTCTGGA	0.378													T|||	61	0.0121805	0.0023	0.013	5008	,	,		21179	0.001		0.0278	False		,,,				2504	0.0204				p.R8294G		Atlas-SNP	.											.	TTN	18412	.	0			c.A24880G						PASS	.	T	,,,GLY/ARG	21,3687		0,21,1833	118.0	109.0	112.0		,,,21148	5.0	1.0	2	dbSNP_130	112	253,7959		2,249,3855	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,125	2,270,5688	CC,CT,TT		3.0809,0.5663,2.2987	,,,benign	,,,7050/33424	179582853	274,11646	1854	4106	5960	SO:0001583	missense	7273	exon86			AAATTCTAATTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.23929A>G	2.37:g.179582853T>C	ENSP00000465570:p.Arg7977Gly	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	30	0.6	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		28	0.01282051282051282	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	20	0.026385224274406333	T	9.326	1.059350	0.19987	0.005663	0.030809	ENSG00000155657	ENST00000342992	T	0.67523	-0.27	6.16	4.99	0.66335	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.42539	0.1207	M	0.70595	2.14	0.58432	D	0.999996	B	0.26577	0.153	B	0.24394	0.053	T	0.58725	-0.7586	9	0.87932	D	0	.	13.6119	0.62083	0.0:0.0:0.1293:0.8707	.	7977	Q8WZ42	TITIN_HUMAN	G	7050	ENSP00000343764:R7050G	ENSP00000343764:R7050G	R	-	1	2	TTN	179291098	0.010000	0.17322	0.992000	0.48379	0.963000	0.63663	1.356000	0.34079	1.113000	0.41760	0.528000	0.53228	AGA	T|0.981;C|0.019	0.019	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RNF123	63891	hgsc.bcm.edu	37	3	49737954	49737954	+	Missense_Mutation	SNP	G	G	A	rs35620248	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49737954G>A	ENST00000327697.6	+	14	1304	c.1160G>A	c.(1159-1161)cGg>cAg	p.R387Q	RNF123_ENST00000432042.1_Missense_Mutation_p.R241Q	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	387			R -> Q (in dbSNP:rs35620248).		protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		TCTCTGCTTCGGCTGTACCGA	0.587													G|||	112	0.0223642	0.0068	0.0259	5008	,	,		19470	0.006		0.0716	False		,,,				2504	0.0072				p.R387Q		Atlas-SNP	.											.	RNF123	100	.	0			c.G1160A						PASS	.	G	GLN/ARG	43,4363	44.6+/-78.6	0,43,2160	104.0	96.0	99.0		1160	5.4	1.0	3	dbSNP_126	99	521,8079	146.9+/-202.4	15,491,3794	yes	missense	RNF123	NM_022064.2	43	15,534,5954	AA,AG,GG		6.0581,0.9759,4.3365	probably-damaging	387/1315	49737954	564,12442	2203	4300	6503	SO:0001583	missense	63891	exon14			TGCTTCGGCTGTA	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1160G>A	3.37:g.49737954G>A	ENSP00000328287:p.Arg387Gln	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	194	84	0.43299	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	79	0.036172161172161175	5	0.01016260162601626	16	0.04419889502762431	3	0.005244755244755245	55	0.07255936675461741	G	21.1	4.095435	0.76870	0.009759	0.060581	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.75260	-0.63;-0.92	5.4	5.4	0.78164	.	0.192451	0.43919	D	0.000518	T	0.25754	0.0627	N	0.24115	0.695	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.72625	0.978;0.968	T	0.61879	-0.6972	10	0.33940	T	0.23	-25.9688	18.1469	0.89661	0.0:0.0:1.0:0.0	rs35620248	241;387	C9J266;Q5XPI4	.;RN123_HUMAN	Q	387;387;241	ENSP00000328287:R387Q;ENSP00000392443:R241Q	ENSP00000328287:R387Q	R	+	2	0	RNF123	49712958	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.053000	0.93860	2.529000	0.85273	0.655000	0.94253	CGG	G|0.956;A|0.044	0.044	strong		0.587	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242194	81242194	+	RNA	SNP	T	T	C	rs6564838	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81242194T>C	ENST00000525539.1	-	0	661				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TGACTGTAGCTCCTGGCACTG	0.547													C|||	3667	0.732228	0.5749	0.745	5008	,	,		20530	0.8839		0.8469	False		,,,				2504	0.6616				p.E221G		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A662G						PASS	.	C	GLY/GLU,GLY/GLU	2645,1567		845,955,306	68.0	66.0	67.0		662,662	4.3	1.0	16	dbSNP_116	67	7120,1322		3003,1114,104	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	98,98	3848,2069,410	CC,CT,TT		15.6598,37.2032,22.8307	benign,benign	221/992,221/2460	81242194	9765,2889	2106	4221	6327			114780	exon4			TGTAGCTCCTGGC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242194T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1714	0.7847985347985348	282	0.573170731707317	289	0.7983425414364641	495	0.8653846153846154	648	0.8548812664907651	C	2.293	-0.362040	0.05103	0.627968	0.843402	ENSG00000166473	ENST00000337114	T	0.14144	2.53	4.31	4.31	0.51392	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.070422	0.56097	N	0.000031	T	0.00012	0.0000	.	.	.	0.39873	P	0.026468000000000047	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36504	-0.9745	8	0.02654	T	1	-11.4682	11.9836	0.53133	0.0:0.9136:0.0:0.0864	rs6564838;rs59152870;rs6564838	221;221	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	G	221	ENSP00000337397:E221G	ENSP00000337397:E221G	E	-	2	0	PKD1L2	79799695	0.999000	0.42202	1.000000	0.80357	0.451000	0.32288	4.255000	0.58804	0.824000	0.34613	-0.642000	0.03964	GAG	T|0.231;C|0.769	0.769	strong		0.547	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
IL12RB2	3595	hgsc.bcm.edu	37	1	67861520	67861520	+	Silent	SNP	C	C	A	rs2229546	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:67861520C>A	ENST00000262345.1	+	16	2977	c.2337C>A	c.(2335-2337)ccC>ccA	p.P779P	IL12RB2_ENST00000544434.1_Silent_p.P693P|IL12RB2_ENST00000371000.1_3'UTR	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	779					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						ACCCAAAGCCCGAAAACCCAG	0.592													A|||	2780	0.555112	0.5106	0.5879	5008	,	,		19161	0.3829		0.675	False		,,,				2504	0.6462				p.P779P		Atlas-SNP	.											.	IL12RB2	94	.	0			c.C2337A						PASS	.	A		2235,2171	584.6+/-386.1	564,1107,532	118.0	116.0	117.0		2337	-10.0	0.0	1	dbSNP_98	117	5737,2863	450.0+/-362.3	1910,1917,473	no	coding-synonymous	IL12RB2	NM_001559.2		2474,3024,1005	AA,AC,CC		33.2907,49.2737,38.7052		779/863	67861520	7972,5034	2203	4300	6503	SO:0001819	synonymous_variant	3595	exon16			AAAGCCCGAAAAC	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.2337C>A	1.37:g.67861520C>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Silent	SNP	ENST00000262345.1	37	CCDS638.1																																																																																			C|0.418;A|0.582	0.582	strong		0.592	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	
RHAG	6005	hgsc.bcm.edu	37	6	49580194	49580194	+	Silent	SNP	C	C	T	rs10485291	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:49580194C>T	ENST00000371175.4	-	6	887	c.861G>A	c.(859-861)gcG>gcA	p.A287A	RHAG_ENST00000229810.7_Silent_p.A287A	NM_000324.2	NP_000315.2	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	287					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|carbon dioxide transport (GO:0015670)|cellular ion homeostasis (GO:0006873)|erythrocyte development (GO:0048821)|multicellular organismal iron ion homeostasis (GO:0060586)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	39	Lung NSC(77;0.0255)					TTGCCATATCCGCACAAGTGC	0.478													C|||	352	0.0702875	0.0809	0.036	5008	,	,		17597	0.0655		0.0189	False		,,,				2504	0.138				p.A287A	Ovarian(176;476 2003 7720 43408 44749)	Atlas-SNP	.											.	RHAG	85	.	0			c.G861A						PASS	.	C		296,4110	162.5+/-194.5	8,280,1915	116.0	96.0	103.0		861	-11.1	0.4	6	dbSNP_119	103	233,8367	94.2+/-156.2	1,231,4068	no	coding-synonymous	RHAG	NM_000324.2		9,511,5983	TT,TC,CC		2.7093,6.7181,4.0674		287/410	49580194	529,12477	2203	4300	6503	SO:0001819	synonymous_variant	6005	exon6			CATATCCGCACAA		CCDS4927.1	6p12.3	2014-07-19	2006-02-23		ENSG00000112077	ENSG00000112077		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	10006	protein-coding gene	gene with protein product		180297	"""Rhesus blood group-associated glycoprotein"""			9479501	Standard	NM_000324		Approved	RH50A, CD241, SLC42A1	uc003ozk.4	Q02094	OTTHUMG00000016377	ENST00000371175.4:c.861G>A	6.37:g.49580194C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	206	85	0.412621	NM_000324	B2R8T8|O43514|O43515|Q7L8L3|Q9H454	Silent	SNP	ENST00000371175.4	37	CCDS4927.1																																																																																			C|0.945;T|0.055	0.055	strong		0.478	RHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043806.1		
TMEM161B	153396	hgsc.bcm.edu	37	5	87498849	87498849	+	Silent	SNP	G	G	A	rs3097146	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:87498849G>A	ENST00000296595.6	-	9	968	c.844C>T	c.(844-846)Ctg>Ttg	p.L282L	TMEM161B_ENST00000506536.1_Silent_p.L100L|TMEM161B_ENST00000512429.1_Silent_p.L271L|TMEM161B_ENST00000511218.1_Silent_p.L100L|TMEM161B_ENST00000514135.1_Silent_p.L282L|TMEM161B_ENST00000509387.1_Silent_p.L155L	NM_153354.3	NP_699185.1	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	282						integral component of membrane (GO:0016021)				endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		ACCCAGAGCAGAACCATAAAT	0.358													G|||	2409	0.48103	0.1036	0.6095	5008	,	,		17516	0.7897		0.5875	False		,,,				2504	0.4724				p.L282L		Atlas-SNP	.											.	TMEM161B	46	.	0			c.C844T						PASS	.	G		845,3561	331.0+/-301.8	92,661,1450	153.0	142.0	146.0		844	4.9	1.0	5	dbSNP_103	146	5208,3392	639.6+/-399.5	1576,2056,668	no	coding-synonymous	TMEM161B	NM_153354.3		1668,2717,2118	AA,AG,GG		39.4419,19.1784,46.5401		282/488	87498849	6053,6953	2203	4300	6503	SO:0001819	synonymous_variant	153396	exon9			AGAGCAGAACCAT	BC037287	CCDS4065.1, CCDS75269.1, CCDS75270.1	5q14.3	2008-02-05			ENSG00000164180	ENSG00000164180			28483	protein-coding gene	gene with protein product						12477932	Standard	NM_001289008		Approved	MGC33214	uc003kjc.3	Q8NDZ6	OTTHUMG00000131323	ENST00000296595.6:c.844C>T	5.37:g.87498849G>A		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	252	114	0.452381	NM_153354	Q5CZH7|Q6UWQ6	Silent	SNP	ENST00000296595.6	37	CCDS4065.1																																																																																			G|0.530;A|0.470	0.470	strong		0.358	TMEM161B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254094.1	NM_153354	
ARHGAP21	57584	hgsc.bcm.edu	37	10	24873369	24873369	+	Missense_Mutation	SNP	C	C	G	rs1127893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:24873369C>G	ENST00000396432.2	-	26	6335	c.5849G>C	c.(5848-5850)aGt>aCt	p.S1950T		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1949					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						CTCTGCTTTACTGCCTGGGGT	0.428													C|||	2467	0.492612	0.388	0.5461	5008	,	,		15418	0.5883		0.5109	False		,,,				2504	0.4785				p.S1950T		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.G5849C						PASS	.	C	THR/SER	1836,2570	534.7+/-374.0	391,1054,758	111.0	106.0	108.0		5849	-11.0	0.0	10	dbSNP_86	108	4582,4018	597.7+/-393.8	1230,2122,948	no	missense	ARHGAP21	NM_020824.3	58	1621,3176,1706	GG,GC,CC		46.7209,41.6704,49.3465	benign	1950/1959	24873369	6418,6588	2203	4300	6503	SO:0001583	missense	57584	exon26			GCTTTACTGCCTG	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.5849G>C	10.37:g.24873369C>G	ENSP00000379709:p.Ser1950Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	1081	0.49496336996337	189	0.38414634146341464	187	0.5165745856353591	321	0.5611888111888111	384	0.5065963060686016	C	0.747	-0.774062	0.02951	0.416704	0.532791	ENSG00000107863	ENST00000396432;ENST00000447364	T	0.09255	3.0	5.52	-11.0	0.00169	.	1.947540	0.02232	N	0.064948	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40534	-0.9558	9	0.02654	T	1	.	8.6155	0.33829	0.1217:0.5515:0.23:0.0967	rs1127893;rs3184290;rs10828676;rs58137164;rs1127893	1949	Q5T5U3	RHG21_HUMAN	T	1950;1399	ENSP00000379709:S1950T	ENSP00000379709:S1950T	S	-	2	0	ARHGAP21	24913375	0.000000	0.05858	0.000000	0.03702	0.550000	0.35303	0.032000	0.13732	-3.011000	0.00272	-1.149000	0.01842	AGT	C|0.500;G|0.500	0.500	strong		0.428	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824	
FAM184A	79632	hgsc.bcm.edu	37	6	119341211	119341211	+	Missense_Mutation	SNP	C	C	T	rs41292560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:119341211C>T	ENST00000338891.7	-	4	1707	c.1264G>A	c.(1264-1266)Gct>Act	p.A422T	FAM184A_ENST00000368475.4_Missense_Mutation_p.A302T|FAM184A_ENST00000521531.1_Missense_Mutation_p.A422T|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000352896.5_Missense_Mutation_p.A302T|FAM184A_ENST00000522284.1_Missense_Mutation_p.A302T	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	422						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						CGCAAAAAAGCTCTTTCCTCT	0.398													C|||	20	0.00399361	0.0	0.0029	5008	,	,		15929	0.0		0.0169	False		,,,				2504	0.001				p.A422T		Atlas-SNP	.											.	FAM184A	109	.	0			c.G1264A						PASS	.	C	THR/ALA,THR/ALA	11,3663		0,11,1826	156.0	142.0	146.0		904,1264	2.7	1.0	6	dbSNP_127	146	96,8068		1,94,3987	yes	missense,missense	FAM184A	NM_001100411.1,NM_024581.4	58,58	1,105,5813	TT,TC,CC		1.1759,0.2994,0.9039	benign,benign	302/972,422/1141	119341211	107,11731	1837	4082	5919	SO:0001583	missense	79632	exon4			AAAAAGCTCTTTC	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 60"""	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1264G>A	6.37:g.119341211C>T	ENSP00000342604:p.Ala422Thr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	224	113	0.504464	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	15	0.006868131868131868	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	C	12.19	1.862249	0.32884	0.002994	0.011759	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284	T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48	5.85	2.69	0.31865	.	0.416381	0.27831	N	0.017672	T	0.05960	0.0155	L	0.36672	1.1	0.27593	N	0.949223	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.11329	0.004;0.002;0.006	T	0.33471	-0.9867	10	0.15066	T	0.55	-3.7601	1.9962	0.03457	0.2501:0.3672:0.0:0.3827	rs41292560	422;302;422	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	T	422;302;302;422;302	ENSP00000342604:A422T;ENSP00000326608:A302T;ENSP00000357460:A302T;ENSP00000430442:A422T;ENSP00000429826:A302T	ENSP00000342604:A422T	A	-	1	0	FAM184A	119382910	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.652000	0.46682	0.788000	0.33755	0.557000	0.71058	GCT	C|0.992;T|0.008	0.008	strong		0.398	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581	
ATR	545	hgsc.bcm.edu	37	3	142222284	142222284	+	Silent	SNP	A	A	G	rs2227931	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:142222284A>G	ENST00000350721.4	-	30	5329	c.5208T>C	c.(5206-5208)taT>taC	p.Y1736Y	ATR_ENST00000383101.3_Silent_p.Y1672Y	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1736	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CTACACCATGATAATGAATGA	0.299								Other conserved DNA damage response genes					A|||	1565	0.3125	0.2073	0.353	5008	,	,		14160	0.3542		0.3917	False		,,,				2504	0.3016				p.Y1736Y		Atlas-SNP	.											.	ATR	285	.	0			c.T5208C						PASS	.	A		945,3461	352.3+/-311.7	97,751,1355	43.0	41.0	42.0		5208	-0.1	1.0	3	dbSNP_98	42	3598,4992	511.5+/-377.7	763,2072,1460	no	coding-synonymous	ATR	NM_001184.3		860,2823,2815	GG,GA,AA		41.8859,21.448,34.9569		1736/2645	142222284	4543,8453	2203	4295	6498	SO:0001819	synonymous_variant	545	exon30			ACCATGATAATGA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5208T>C	3.37:g.142222284A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1																																																																																			T|0.124;G|0.289	0.289	strong		0.299	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
OR5M3	219482	hgsc.bcm.edu	37	11	56237564	56237564	+	Missense_Mutation	SNP	A	A	T	rs61902880		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56237564A>T	ENST00000312240.2	-	1	450	c.410T>A	c.(409-411)gTt>gAt	p.V137D		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	137						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					AATACAGACAACCCTTGACAT	0.403																																					p.V137D		Atlas-SNP	.											OR5M3,NS,meningioma,0,1	OR5M3	103	1	0			c.T410A						PASS	.						98.0	91.0	94.0					11																	56237564		2201	4294	6495	SO:0001583	missense	219482	exon1			CAGACAACCCTTG	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"""GPCR / Class A : Olfactory receptors"""	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.410T>A	11.37:g.56237564A>T	ENSP00000312208:p.Val137Asp	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	113	18	0.159292	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	37	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	A	5.338	0.247608	0.10130	.	.	ENSG00000174937	ENST00000312240	T	0.37411	1.2	4.98	-2.14	0.07123	GPCR, rhodopsin-like superfamily (1);	2.278830	0.01880	N	0.037797	T	0.21468	0.0517	N	0.08118	0	0.09310	N	1	B	0.19935	0.04	B	0.29440	0.102	T	0.25257	-1.0137	10	0.33141	T	0.24	-1.4382	6.6958	0.23197	0.3341:0.0:0.5207:0.1452	rs61902880	137	Q8NGP4	OR5M3_HUMAN	D	137	ENSP00000312208:V137D	ENSP00000312208:V137D	V	-	2	0	OR5M3	55994140	0.000000	0.05858	0.082000	0.20525	0.847000	0.48162	-5.994000	0.00086	-0.034000	0.13713	0.391000	0.25812	GTT	A|0.999;T|0.001	0.001	weak		0.403	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742	
SCLY	51540	hgsc.bcm.edu	37	2	238999883	238999883	+	Silent	SNP	T	T	C	rs1128552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:238999883T>C	ENST00000555827.1	+	8	973	c.909T>C	c.(907-909)gcT>gcC	p.A303A	SCLY_ENST00000409736.2_Silent_p.A303A|SCLY_ENST00000422984.2_Silent_p.A209A|SCLY_ENST00000373332.3_Silent_p.A221A|SCLY_ENST00000254663.6_Silent_p.A311A|SCLY_ENST00000429612.2_Intron			Q96I15	SCLY_HUMAN	selenocysteine lyase	303					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)	p.A303A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		CAATGATTGCTGGCCTTGGGA	0.478													C|||	1074	0.214457	0.1838	0.2349	5008	,	,		18815	0.0704		0.2177	False		,,,				2504	0.3865				p.A311A	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	Atlas-SNP	.											SCLY,NS,carcinoma,0,1	SCLY	51	1	1	Substitution - coding silent(1)	stomach(1)	c.T933C						PASS	.	C		866,3540	744.4+/-411.6	86,694,1423	252.0	236.0	242.0		933	-3.9	1.0	2	dbSNP_86	242	1927,6673	726.6+/-406.6	222,1483,2595	no	coding-synonymous	SCLY	NM_016510.5		308,2177,4018	CC,CT,TT		22.407,19.655,21.4747		311/454	238999883	2793,10213	2203	4300	6503	SO:0001819	synonymous_variant	51540	exon8			GATTGCTGGCCTT	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.909T>C	2.37:g.238999883T>C		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	313	164	0.523962	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Silent	SNP	ENST00000555827.1	37		389|389	0.17811355311355312|0.17811355311355312	104|104	0.21138211382113822|0.21138211382113822	81|81	0.22375690607734808|0.22375690607734808	29|29	0.050699300699300696|0.050699300699300696	175|175	0.23087071240105542|0.23087071240105542	C|C	10.29|10.29	1.309196|1.309196	0.23821|0.23821	0.19655|0.19655	0.22407|0.22407	ENSG00000132330|ENSG00000132330	ENST00000440143;ENST00000433750|ENST00000437134	.|.	.|.	.|.	5.48|5.48	-3.93|-3.93	0.04143|0.04143	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24621|0.24621	-1.0155|-1.0155	3|3	.|.	.|.	.|.	-27.6118|-27.6118	10.8593|10.8593	0.46817|0.46817	0.0:0.1559:0.1139:0.7302|0.0:0.1559:0.1139:0.7302	rs1128552;rs3185626;rs1128552|rs1128552;rs3185626;rs1128552	.|.	.|.	.|.	P|R	45|147	.|.	.|.	L|W	+|+	2|1	0|0	SCLY|SCLY	238664622|238664622	0.000000|0.000000	0.05858|0.05858	0.959000|0.959000	0.39883|0.39883	0.838000|0.838000	0.47535|0.47535	-3.358000|-3.358000	0.00499|0.00499	-0.637000|-0.637000	0.05516|0.05516	-1.651000|-1.651000	0.00758|0.00758	CTG|TGG	T|0.801;C|0.199	0.199	strong		0.478	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
ATP13A4	84239	hgsc.bcm.edu	37	3	193183817	193183817	+	Silent	SNP	A	A	G	rs3796181	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:193183817A>G	ENST00000342695.4	-	11	1591	c.1269T>C	c.(1267-1269)agT>agC	p.S423S	ATP13A4_ENST00000392443.3_Intron|ATP13A4_ENST00000295548.3_Silent_p.S423S	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	423						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		AGCTTACCCCACTAAGCACAT	0.423													G|||	2775	0.554113	0.6838	0.5288	5008	,	,		16612	0.5387		0.4503	False		,,,				2504	0.5194				p.S423S		Atlas-SNP	.											.	ATP13A4	154	.	0			c.T1269C						PASS	.	G		2811,1595	496.0+/-363.4	883,1045,275	169.0	152.0	158.0		1269	-2.9	0.9	3	dbSNP_107	158	3828,4772	611.5+/-395.8	876,2076,1348	no	coding-synonymous	ATP13A4	NM_032279.2		1759,3121,1623	GG,GA,AA		44.5116,36.2006,48.9543		423/1197	193183817	6639,6367	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon11			TACCCCACTAAGC	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.1269T>C	3.37:g.193183817A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	98	96	0.979592	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			A|0.474;G|0.526	0.526	strong		0.423	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31106459	31106459	+	Missense_Mutation	SNP	C	C	A	rs1265097	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31106459C>A	ENST00000259881.9	+	5	359	c.70C>A	c.(70-72)Ccc>Acc	p.P24T	PSORS1C1_ENST00000547221.1_5'UTR|PSORS1C2_ENST00000259845.4_Intron|PSORS1C1_ENST00000481450.2_Intron	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	24			P -> T (in dbSNP:rs1265097). {ECO:0000269|PubMed:12930300}.							kidney(1)|ovary(2)|prostate(1)|skin(1)	5						TTTACAAGGACCCCAGCTCCT	0.572													C|||	561	0.112021	0.1293	0.1974	5008	,	,		15727	0.0357		0.1312	False		,,,				2504	0.0869				p.P24T		Atlas-SNP	.											.	PSORS1C1	11	.	0			c.C70A						PASS	.	C	THR/PRO,	362,2660		17,328,1166	136.0	139.0	138.0		70,	-0.4	0.0	6	dbSNP_87	138	609,4809		37,535,2137	yes	missense,intron	PSORS1C1,PSORS1C2	NM_014068.2,NM_014069.2	38,	54,863,3303	AA,AC,CC		11.2403,11.9788,11.5047	benign,	24/153,	31106459	971,7469	1511	2709	4220	SO:0001583	missense	170679	exon5			CAAGGACCCCAGC	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.70C>A	6.37:g.31106459C>A	ENSP00000259881:p.Pro24Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	261	0.11950549450549451	60	0.12195121951219512	78	0.2154696132596685	23	0.04020979020979021	100	0.13192612137203166	C	10.76	1.440615	0.25900	0.119788	0.112403	ENSG00000204540	ENST00000259881	T	0.16324	2.35	3.91	-0.431	0.12295	.	.	.	.	.	T	0.02230	0.0069	N	0.08118	0	0.80722	P	0.0	B	0.28713	0.22	B	0.27076	0.076	T	0.41945	-0.9480	8	0.87932	D	0	.	3.3895	0.07283	0.346:0.4424:0.0:0.2116	rs1265097;rs52820852;rs1265097	24	Q9UIG5	PS1C1_HUMAN	T	24	ENSP00000259881:P24T	ENSP00000259881:P24T	P	+	1	0	PSORS1C1	31214438	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-0.724000	0.04947	-0.232000	0.09811	0.478000	0.44815	CCC	C|0.883;A|0.117	0.117	strong		0.572	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
OR8D4	338662	hgsc.bcm.edu	37	11	123777861	123777861	+	Silent	SNP	T	T	C	rs61748875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:123777861T>C	ENST00000321355.2	+	1	753	c.723T>C	c.(721-723)tgT>tgC	p.C241C		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C241C(1)		large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		TTAGCACCTGTAGCTCCCACC	0.458													T|||	818	0.163339	0.2005	0.1398	5008	,	,		18173	0.0933		0.1819	False		,,,				2504	0.183				p.C241C		Atlas-SNP	.											OR8D4,NS,carcinoma,0,1	OR8D4	62	1	1	Substitution - coding silent(1)	stomach(1)	c.T723C						PASS	.	T		857,3547	336.5+/-304.4	88,681,1433	114.0	114.0	114.0		723	3.6	1.0	11	dbSNP_129	114	1634,6964	303.0+/-306.2	164,1306,2829	no	coding-synonymous	OR8D4	NM_001005197.1		252,1987,4262	CC,CT,TT		19.0044,19.4596,19.1586		241/315	123777861	2491,10511	2202	4299	6501	SO:0001819	synonymous_variant	338662	exon1			CACCTGTAGCTCC	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"""GPCR / Class A : Olfactory receptors"""	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.723T>C	11.37:g.123777861T>C		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	300	141	0.47	NM_001005197	Q6IFE9	Silent	SNP	ENST00000321355.2	37	CCDS31698.1																																																																																			T|0.815;C|0.185	0.185	strong		0.458	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197	
NAA20	51126	hgsc.bcm.edu	37	20	20006368	20006368	+	Silent	SNP	T	T	C	rs7263	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:20006368T>C	ENST00000334982.4	+	3	407	c.126T>C	c.(124-126)taT>taC	p.Y42Y	NAA20_ENST00000398602.2_Silent_p.Y30Y|NAA20_ENST00000484480.1_3'UTR|NAA20_ENST00000310450.4_Silent_p.Y42Y	NM_016100.4	NP_057184.1	P61599	NAA20_HUMAN	N(alpha)-acetyltransferase 20, NatB catalytic subunit	42	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.					cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	peptide alpha-N-acetyltransferase activity (GO:0004596)			endometrium(3)|lung(2)|prostate(1)	6						GGCCAGAGTATTTCATTGTTG	0.373													T|||	485	0.096845	0.0756	0.121	5008	,	,		16707	0.131		0.0736	False		,,,				2504	0.0971				p.Y42Y		Atlas-SNP	.											.	NAA20	15	.	0			c.T126C						PASS	.	T	,,	297,4109	163.3+/-195.1	11,275,1917	136.0	136.0	136.0		126,90,126	-1.9	1.0	20	dbSNP_52	136	546,8054	150.9+/-205.7	20,506,3774	yes	coding-synonymous,coding-synonymous,coding-synonymous	NAA20	NM_016100.4,NM_181527.3,NM_181528.3	,,	31,781,5691	CC,CT,TT		6.3488,6.7408,6.4816	,,	42/179,30/167,42/112	20006368	843,12163	2203	4300	6503	SO:0001819	synonymous_variant	51126	exon3			AGAGTATTTCATT	AF085355	CCDS13141.1, CCDS13142.1, CCDS42854.1	20p11.23	2010-05-07	2010-01-14	2010-01-14	ENSG00000173418	ENSG00000173418	2.3.1.88	"""N(alpha)-acetyltransferase subunits"""	15908	protein-coding gene	gene with protein product	"""N-acetyltransferase 3 homolog (S. cerevisiae)"""	610833	"""N-acetyltransferase 5, ARD1 subunit (arrest-defective 1, S. cerevisiae, homolog)"", ""N-acetyltransferase 5 (ARD1 homolog, S. cerevisiae)"", ""N-acetyltransferase 5"", ""N-acetyltransferase 5 (GCN5-related, putative)"""	NAT5		12888564, 19660095	Standard	NM_016100		Approved	dJ1002M8.1, NAT3	uc002wrp.3	P61599	OTTHUMG00000031998	ENST00000334982.4:c.126T>C	20.37:g.20006368T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_181528	A6NHA3|B2R4G4|Q5TFT7|Q9D7H8|Q9H0Y4|Q9NQH6|Q9Y6D2	Silent	SNP	ENST00000334982.4	37	CCDS13141.1																																																																																			T|0.924;C|0.076	0.076	strong		0.373	NAA20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078217.2	NM_016100	
KIAA1614	57710	hgsc.bcm.edu	37	1	180905352	180905352	+	Silent	SNP	C	C	T	rs3795505	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:180905352C>T	ENST00000367588.4	+	5	2362	c.2307C>T	c.(2305-2307)agC>agT	p.S769S	KIAA1614_ENST00000367587.1_Silent_p.S390S	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	769										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						TTACAGAAAGCCACGAGTCCC	0.602													C|||	1665	0.332468	0.1536	0.4006	5008	,	,		18104	0.2599		0.4245	False		,,,				2504	0.5061				p.S769S		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C2307T						PASS	.	C		775,3357		80,615,1371	84.0	90.0	88.0		2307	0.8	0.0	1	dbSNP_107	88	3455,4929		703,2049,1440	no	coding-synonymous	KIAA1614	NM_020950.1		783,2664,2811	TT,TC,CC		41.2094,18.7561,33.7967		769/1191	180905352	4230,8286	2066	4192	6258	SO:0001819	synonymous_variant	57710	exon5			AGAAAGCCACGAG	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2307C>T	1.37:g.180905352C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_020950	Q5VZ45|Q9HCF8	Silent	SNP	ENST00000367588.4	37	CCDS41442.1																																																																																			C|0.668;T|0.332	0.332	strong		0.602	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
NOL8	55035	hgsc.bcm.edu	37	9	95077289	95077289	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:95077289G>A	ENST00000535387.1	-	6	1617	c.1618C>T	c.(1618-1620)Cgt>Tgt	p.R540C	NOL8_ENST00000358855.4_Missense_Mutation_p.R472C|NOL8_ENST00000545558.1_Missense_Mutation_p.R540C|NOL8_ENST00000442668.2_Missense_Mutation_p.R540C|NOL8_ENST00000542053.1_Missense_Mutation_p.R472C					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TCCGCAGGACGAATACACTGT	0.498																																					p.R540C		Atlas-SNP	.											.	NOL8	118	.	0			c.C1618T						PASS	.						74.0	70.0	71.0					9																	95077289		1855	4090	5945	SO:0001583	missense	55035	exon7			CAGGACGAATACA	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.1618C>T	9.37:g.95077289G>A	ENSP00000441300:p.Arg540Cys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	139	66	0.47482	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	.	.	.	.	.	.	.	.	.	.	G	6.026	0.373204	0.11409	.	.	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	5.69	-5.16	0.02857	.	1.619260	0.02753	N	0.117648	T	0.20659	0.0497	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11591	-1.0581	10	0.40728	T	0.16	1.0458	2.1033	0.03685	0.3083:0.0914:0.1236:0.4767	.	540	Q76FK4	NOL8_HUMAN	C	540;542;472;540;540;472;540	ENSP00000401177:R540C;ENSP00000351723:R472C;ENSP00000441140:R540C;ENSP00000441300:R540C;ENSP00000440709:R472C;ENSP00000414112:R540C	ENSP00000351723:R472C	R	-	1	0	NOL8	94117110	0.000000	0.05858	0.004000	0.12327	0.118000	0.20060	-1.388000	0.02533	-0.487000	0.06735	-0.136000	0.14681	CGT	.	.	none		0.498	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
AMBN	258	hgsc.bcm.edu	37	4	71468985	71468985	+	Silent	SNP	A	A	G	rs35266919	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:71468985A>G	ENST00000322937.6	+	10	760	c.657A>G	c.(655-657)caA>caG	p.Q219Q	AMBN_ENST00000449493.2_Silent_p.Q204Q	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	219					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|odontogenesis of dentin-containing tooth (GO:0042475)	proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|structural constituent of tooth enamel (GO:0030345)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29			Lung(101;0.235)			AGATTTTCCAAATAGCCCGTT	0.323													A|||	381	0.0760783	0.0363	0.1225	5008	,	,		14127	0.003		0.1938	False		,,,				2504	0.0511				p.Q219Q		Atlas-SNP	.											.	AMBN	73	.	0			c.A657G						PASS	.	A		296,4108	154.4+/-187.8	14,268,1920	73.0	70.0	71.0		657	-0.9	0.9	4	dbSNP_126	71	1920,6674	334.6+/-321.1	194,1532,2571	no	coding-synonymous	AMBN	NM_016519.5		208,1800,4491	GG,GA,AA		22.3412,6.7212,17.0488		219/448	71468985	2216,10782	2202	4297	6499	SO:0001819	synonymous_variant	258	exon10			TTTCCAAATAGCC	AF209780	CCDS3543.1	4q21	2006-11-28	2006-04-27		ENSG00000178522	ENSG00000178522			452	protein-coding gene	gene with protein product		601259	"""ameloblastin, enamel matrix protein"""			9126491	Standard	NM_016519		Approved		uc003hfl.3	Q9NP70	OTTHUMG00000129913	ENST00000322937.6:c.657A>G	4.37:g.71468985A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	163	85	0.521472	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Silent	SNP	ENST00000322937.6	37	CCDS3543.1																																																																																			A|0.853;G|0.147	0.147	strong		0.323	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519	
NEU4	129807	hgsc.bcm.edu	37	2	242758179	242758179	+	Silent	SNP	C	C	T	rs2293764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242758179C>T	ENST00000391969.2	+	5	1971	c.1260C>T	c.(1258-1260)tcC>tcT	p.S420S	NEU4_ENST00000405370.1_Silent_p.S420S|NEU4_ENST00000325935.6_Silent_p.S433S|NEU4_ENST00000404257.1_Silent_p.S432S|NEU4_ENST00000407683.1_Silent_p.S420S	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	420					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		GCGGCTACTCCGACCTGGCGT	0.652													C|||	1081	0.215855	0.3306	0.1715	5008	,	,		12562	0.1994		0.161	False		,,,				2504	0.1656				p.S433S		Atlas-SNP	.											.	NEU4	39	.	0			c.C1299T						PASS	.		,,,,	1025,3263		106,813,1225	10.0	13.0	12.0		1299,1260,1260,1260,1296	-8.5	0.7	2	dbSNP_100	12	987,7445		66,855,3295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	,,,,	172,1668,4520	TT,TC,CC		11.7054,23.9039,15.8176	,,,,	433/498,420/485,420/485,420/485,432/497	242758179	2012,10708	2144	4216	6360	SO:0001819	synonymous_variant	129807	exon4			CTACTCCGACCTG	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.1260C>T	2.37:g.242758179C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	95	38	0.4	NM_001167599	A8K056|J3KNJ5|Q96D64	Silent	SNP	ENST00000391969.2	37	CCDS54442.1																																																																																			C|0.819;T|0.181	0.181	strong		0.652	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
CYFIP2	26999	hgsc.bcm.edu	37	5	156753257	156753257	+	Silent	SNP	C	C	T	rs11551374	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:156753257C>T	ENST00000521420.1	+	17	2074	c.1983C>T	c.(1981-1983)taC>taT	p.Y661Y	CYFIP2_ENST00000318218.6_Silent_p.Y712Y|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000522463.1_Silent_p.Y491Y|CYFIP2_ENST00000541131.1_Silent_p.Y612Y|CYFIP2_ENST00000377576.3_Silent_p.Y687Y|CYFIP2_ENST00000435847.2_Silent_p.Y386Y|CYFIP2_ENST00000347377.6_Silent_p.Y687Y|CYFIP2_ENST00000520960.1_3'UTR					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AGTTCCTGTACGATGAGATAG	0.438													C|||	323	0.0644968	0.0083	0.085	5008	,	,		21965	0.0308		0.1093	False		,,,				2504	0.1145				p.Y687Y		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C2061T						PASS	.	C	,,	87,3829		0,87,1871	167.0	164.0	164.0		2061,2061,2061	-9.6	0.6	5	dbSNP_120	164	869,7417		49,771,3323	no	coding-synonymous,coding-synonymous,coding-synonymous	CYFIP2	NM_001037332.2,NM_001037333.1,NM_014376.2	,,	49,858,5194	TT,TC,CC		10.4876,2.2217,7.8348	,,	687/1254,687/1254,687/1254	156753257	956,11246	1958	4143	6101	SO:0001819	synonymous_variant	26999	exon18			CCTGTACGATGAG	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.1983C>T	5.37:g.156753257C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	178	84	0.47191	NM_001037332		Silent	SNP	ENST00000521420.1	37																																																																																				C|0.936;G|0.000;T|0.064	0.064	strong		0.438	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
MET	4233	hgsc.bcm.edu	37	7	116435768	116435768	+	Silent	SNP	C	C	T	rs41736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116435768C>T	ENST00000318493.6	+	20	4099	c.3912C>T	c.(3910-3912)gaC>gaT	p.D1304D	MET_ENST00000397752.3_Silent_p.D1286D|MET_ENST00000539704.1_Silent_p.D156D			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.D1304D(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CTTATCCTGACGTAAACACCT	0.473			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)		OREG0003446	type=REGULATORY REGION|Gene=MET|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	c|||	1764	0.352236	0.034	0.464	5008	,	,		18610	0.4673		0.4414	False		,,,				2504	0.4928				p.D1304D		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.C3912T						scavenged	.	T	,	393,3383		15,363,1510	245.0	238.0	240.0		3858,3912	-10.9	0.0	7	dbSNP_76	240	3487,4731		756,1975,1378	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	771,2338,2888	TT,TC,CC		42.4312,10.4078,32.3495	,	1286/1391,1304/1409	116435768	3880,8114	1888	4109	5997	SO:0001819	synonymous_variant	4233	exon20	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TCCTGACGTAAAC	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3912C>T	7.37:g.116435768C>T		Somatic	143	1	0.00699301	1473	WXS	Illumina HiSeq	Phase_I	147	79	0.537415	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.624;T|0.376	0.376	strong		0.473	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
MRGPRX4	117196	hgsc.bcm.edu	37	11	18195448	18195448	+	Silent	SNP	C	C	T	rs4630269	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18195448C>T	ENST00000314254.3	+	1	1065	c.645C>T	c.(643-645)taC>taT	p.Y215Y	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CCAGGCTGTACGTGACCATCC	0.552													C|||	1653	0.330072	0.2542	0.3415	5008	,	,		20894	0.4415		0.3032	False		,,,				2504	0.3374				p.Y215Y		Atlas-SNP	.											MRGPRX4,NS,adenoma,0,1	MRGPRX4	68	1	0			c.C645T						PASS	.	C		1077,3321	389.8+/-327.4	131,815,1253	112.0	102.0	105.0		645	-4.1	0.0	11	dbSNP_111	105	2447,6139	404.8+/-348.3	336,1775,2182	no	coding-synonymous	MRGPRX4	NM_054032.3		467,2590,3435	TT,TC,CC		28.4999,24.4884,27.1411		215/323	18195448	3524,9460	2199	4293	6492	SO:0001819	synonymous_variant	117196	exon1			GCTGTACGTGACC	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.645C>T	11.37:g.18195448C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	127	49	0.385827	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Silent	SNP	ENST00000314254.3	37	CCDS7831.1																																																																																			C|0.710;T|0.290	0.290	strong		0.552	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
APEH	327	hgsc.bcm.edu	37	3	49721798	49721798	+	IGR	SNP	C	C	A	rs13085791	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49721798C>A	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Silent_p.R655R	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TCTCACTCTCCCGCACACGTC	0.597													C|||	1046	0.208866	0.2632	0.1729	5008	,	,		21198	0.0565		0.3241	False		,,,				2504	0.1994				p.R655R		Atlas-SNP	.											.	MST1	84	.	0			c.G1965T						PASS	.	C		1184,3222	408.9+/-334.8	153,878,1172	55.0	57.0	56.0		1965	-6.0	0.0	3	dbSNP_121	56	2576,6024	406.4+/-348.8	399,1778,2123	no	coding-synonymous	MST1	NM_020998.3		552,2656,3295	AA,AC,CC		29.9535,26.8724,28.9097		655/726	49721798	3760,9246	2203	4300	6503	SO:0001628	intergenic_variant	4485	exon17			ACTCTCCCGCACA	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49721798C>A		Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	311	171	0.549839	NM_020998	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	37	CCDS2801.1	515	0.2358058608058608	148	0.3008130081300813	83	0.2292817679558011	37	0.06468531468531469	247	0.3258575197889182	C	5.900	0.350100	0.11182	0.268724	0.299535	ENSG00000173531	ENST00000448220	.	.	.	5.59	-5.99	0.02213	.	.	.	.	.	.	.	.	.	.	.	0.23023	P	0.99841852	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.6906	0.02851	0.1818:0.3582:0.266:0.194	rs13085791;rs13085791	.	.	.	X	125	.	.	G	-	1	0	MST1	49696802	0.000000	0.05858	0.001000	0.08648	0.939000	0.58152	-1.124000	0.03260	-1.376000	0.02126	0.655000	0.94253	GGA	C|0.725;A|0.275	0.275	strong		0.597	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
KDM4B	23030	hgsc.bcm.edu	37	19	5144411	5144411	+	Silent	SNP	T	T	C	rs10408767|rs57489512		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:5144411T>C	ENST00000159111.4	+	20	3107	c.2889T>C	c.(2887-2889)ccT>ccC	p.P963P	KDM4B_ENST00000536461.1_Silent_p.P997P	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	963	Tudor 1.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						ACCTGTACCCTGAGAGCATCA	0.642																																					p.P963P		Atlas-SNP	.											KDM4B,rectum,carcinoma,0,6	KDM4B	120	6	0			c.T2889C						PASS	.						20.0	16.0	17.0					19																	5144411		2173	4262	6435	SO:0001819	synonymous_variant	23030	exon20			GTACCCTGAGAGC	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.2889T>C	19.37:g.5144411T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	72	9	0.125	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Silent	SNP	ENST00000159111.4	37	CCDS12138.1																																																																																			T|1.000;|0.000	.	weak		0.642	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015	
RP1L1	94137	hgsc.bcm.edu	37	8	10465097	10465097	+	Missense_Mutation	SNP	C	C	T	rs4354268	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:10465097C>T	ENST00000382483.3	-	4	6734	c.6511G>A	c.(6511-6513)Gag>Aag	p.E2171K		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2251	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].		E -> K (in dbSNP:rs4354268).		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGGGCCTCCTCTTCAGCCTCC	0.612													C|||	1563	0.312101	0.4228	0.3184	5008	,	,		17645	0.0208		0.4891	False		,,,				2504	0.2761				p.E2171K		Atlas-SNP	.											.	RP1L1	453	.	0			c.G6511A						PASS	.	C	LYS/GLU	1526,2284		304,918,683	166.0	180.0	176.0		6511	1.2	0.0	8	dbSNP_111	176	3835,4373		908,2019,1177	yes	missense	RP1L1	NM_178857.5	56	1212,2937,1860	TT,TC,CC		46.7227,40.0525,44.6081	benign	2171/2401	10465097	5361,6657	1905	4104	6009	SO:0001583	missense	94137	exon4			CCTCCTCTTCAGC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.6511G>A	8.37:g.10465097C>T	ENSP00000371923:p.Glu2171Lys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	721	0.3301282051282051	217	0.4410569105691057	124	0.3425414364640884	13	0.022727272727272728	367	0.4841688654353562	C	9.516	1.107149	0.20714	0.400525	0.467227	ENSG00000183638	ENST00000382483	T	0.07688	3.17	2.18	1.25	0.21368	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.13145	0.007	B	0.08055	0.003	T	0.45086	-0.9285	8	0.05436	T	0.98	.	4.3001	0.10920	0.0:0.5052:0.2282:0.2665	rs4354268;rs17188537	2171	A6NKC6	.	K	2171	ENSP00000371923:E2171K	ENSP00000371923:E2171K	E	-	1	0	RP1L1	10502507	0.000000	0.05858	0.011000	0.14972	0.030000	0.12068	0.037000	0.13840	0.184000	0.20083	0.430000	0.28490	GAG	C|0.615;T|0.385	0.385	strong		0.612	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
TMCC3	57458	hgsc.bcm.edu	37	12	94975799	94975799	+	Silent	SNP	G	G	A	rs3747553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:94975799G>A	ENST00000261226.4	-	2	725	c.594C>T	c.(592-594)ttC>ttT	p.F198F	TMCC3_ENST00000551457.1_Silent_p.F167F	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	198						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						TATTGAAAACGAACACAGGTG	0.493													A|||	3441	0.687101	0.8979	0.5965	5008	,	,		19714	0.5972		0.5746	False		,,,				2504	0.6748				p.F198F		Atlas-SNP	.											.	TMCC3	63	.	0			c.C594T						PASS	.	A		3696,710	295.6+/-283.7	1560,576,67	77.0	84.0	81.0		594	-2.6	0.9	12	dbSNP_107	81	4813,3787	534.8+/-382.7	1370,2073,857	no	coding-synonymous	TMCC3	NM_020698.2		2930,2649,924	AA,AG,GG		44.0349,16.1144,34.5763		198/478	94975799	8509,4497	2203	4300	6503	SO:0001819	synonymous_variant	57458	exon2			GAAAACGAACACA	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"""Transmembrane and coiled-coil domain containing"""	29199	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 3"""			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.594C>T	12.37:g.94975799G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	173	172	0.99422	NM_020698	Q8IWB2	Silent	SNP	ENST00000261226.4	37	CCDS31877.1																																																																																			G|0.345;A|0.655	0.655	strong		0.493	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
LMTK2	22853	hgsc.bcm.edu	37	7	97821855	97821855	+	Missense_Mutation	SNP	T	T	C	rs56204700	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:97821855T>C	ENST00000297293.5	+	11	2371	c.2078T>C	c.(2077-2079)aTt>aCt	p.I693T		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	693			I -> T (in dbSNP:rs56204700). {ECO:0000269|PubMed:17344846}.		early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					CCCCGTAAGATTTTTGACAGT	0.378													T|||	642	0.128195	0.0197	0.1931	5008	,	,		16935	0.374		0.0427	False		,,,				2504	0.0634				p.I693T		Atlas-SNP	.											.	LMTK2	228	.	0			c.T2078C						PASS	.	T	THR/ILE	94,4310		2,90,2110	69.0	80.0	76.0		2078	5.7	0.8	7	dbSNP_129	76	162,8432		0,162,4135	yes	missense	LMTK2	NM_014916.3	89	2,252,6245	CC,CT,TT		1.885,2.1344,1.9695	benign	693/1504	97821855	256,12742	2202	4297	6499	SO:0001583	missense	22853	exon11			GTAAGATTTTTGA	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.2078T>C	7.37:g.97821855T>C	ENSP00000297293:p.Ile693Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_014916	A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	37	CCDS5654.1	303	0.13873626373626374	8	0.016260162601626018	73	0.20165745856353592	186	0.32517482517482516	36	0.047493403693931395	T	10.64	1.406816	0.25378	0.021344	0.01885	ENSG00000164715	ENST00000297293	T	0.78246	-1.16	5.7	5.7	0.88788	.	0.695881	0.14714	N	0.302746	T	0.00012	0.0000	N	0.19112	0.55	0.51482	P	7.40000000000185E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.07443	-1.0772	9	0.29301	T	0.29	.	7.4353	0.27152	0.0:0.0753:0.1452:0.7795	rs56204700;rs61734174	693	Q8IWU2	LMTK2_HUMAN	T	693	ENSP00000297293:I693T	ENSP00000297293:I693T	I	+	2	0	LMTK2	97659791	0.122000	0.22280	0.755000	0.31263	0.454000	0.32378	0.901000	0.28445	2.161000	0.67846	0.533000	0.62120	ATT	T|0.944;C|0.056	0.056	strong		0.378	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
TUBGCP2	10844	hgsc.bcm.edu	37	10	135106550	135106550	+	Silent	SNP	G	G	A	rs141042122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135106550G>A	ENST00000252936.3	-	6	1056	c.1017C>T	c.(1015-1017)gcC>gcT	p.A339A	TUBGCP2_ENST00000368563.2_Silent_p.A339A|TUBGCP2_ENST00000543663.1_Silent_p.A367A|TUBGCP2_ENST00000368562.1_5'Flank|TUBGCP2_ENST00000417178.2_Silent_p.A209A|RP11-122K13.12_ENST00000424450.1_RNA			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	339					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		CACCGAGGGAGGCCAGGATGT	0.652													G|||	5	0.000998403	0.0	0.0014	5008	,	,		17939	0.0		0.002	False		,,,				2504	0.002				p.A367A		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.C1101T						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	45.0	45.0	45.0		1017	1.6	1.0	10	dbSNP_134	45	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous	TUBGCP2	NM_006659.2		0,36,6467	AA,AG,GG		0.3721,0.0908,0.2768		339/903	135106550	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	10844	exon8			GAGGGAGGCCAGG	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.1017C>T	10.37:g.135106550G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	130	67	0.515385	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	37	CCDS7676.1																																																																																			G|0.997;A|0.003	0.003	strong		0.652	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1		
LRRC16B	90668	hgsc.bcm.edu	37	14	24534916	24534916	+	Missense_Mutation	SNP	G	G	T	rs79328356	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24534916G>T	ENST00000342740.5	+	34	3636	c.3482G>T	c.(3481-3483)gGg>gTg	p.G1161V	LRRC16B_ENST00000334420.7_Intron	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1161						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		GCCCTTCCCGGGTTGGAAAGA	0.617													G|||	98	0.0195687	0.003	0.0245	5008	,	,		17823	0.003		0.0616	False		,,,				2504	0.0123				p.G1161V		Atlas-SNP	.											LRRC16B,NS,carcinoma,+1,1	LRRC16B	120	1	0			c.G3482T						PASS	.	G	VAL/GLY	63,4343	58.7+/-95.3	1,61,2141	123.0	109.0	114.0		3482	4.5	1.0	14	dbSNP_131	114	574,8026	154.6+/-208.8	26,522,3752	yes	missense	LRRC16B	NM_138360.3	109	27,583,5893	TT,TG,GG		6.6744,1.4299,4.8977	probably-damaging	1161/1373	24534916	637,12369	2203	4300	6503	SO:0001583	missense	90668	exon34			TTCCCGGGTTGGA	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.3482G>T	14.37:g.24534916G>T	ENSP00000340467:p.Gly1161Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	60	0.027472527472527472	2	0.0040650406504065045	10	0.027624309392265192	1	0.0017482517482517483	47	0.06200527704485488	G	18.54	3.645209	0.67358	0.014299	0.066744	ENSG00000186648	ENST00000342740	T	0.17854	2.25	5.4	4.51	0.55191	.	0.141061	0.33161	N	0.005214	T	0.01835	0.0058	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00950	-1.1503	10	0.72032	D	0.01	-15.7681	9.7564	0.40506	0.0947:0.0:0.9053:0.0	.	1161	Q8ND23	LR16B_HUMAN	V	1161	ENSP00000340467:G1161V	ENSP00000340467:G1161V	G	+	2	0	LRRC16B	23604756	0.964000	0.33143	0.972000	0.41901	0.867000	0.49689	1.806000	0.38892	1.272000	0.44329	0.655000	0.94253	GGG	G|0.958;T|0.042	0.042	strong		0.617	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
ARSB	411	hgsc.bcm.edu	37	5	78181423	78181423	+	Missense_Mutation	SNP	C	C	T	rs1071598	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:78181423C>T	ENST00000264914.4	-	5	1662	c.1126G>A	c.(1126-1128)Gtg>Atg	p.V376M	ARSB_ENST00000396151.3_Missense_Mutation_p.V376M|ARSB_ENST00000565165.1_Missense_Mutation_p.V376M|ARSB_ENST00000521800.1_5'UTR	NM_000046.3	NP_000037.2	P15848	ARSB_HUMAN	arylsulfatase B	376			V -> M (in dbSNP:rs17220759). {ECO:0000269|PubMed:14974081, ECO:0000269|PubMed:1718978}.		autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|lysosomal transport (GO:0007041)|lysosome organization (GO:0007040)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|rough endoplasmic reticulum (GO:0005791)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		GTTTTCCACACGTCGAAGCCA	0.532													C|||	544	0.108626	0.0469	0.196	5008	,	,		15642	0.0149		0.1461	False		,,,				2504	0.1881				p.V376M	Melanoma(169;563 1968 25780 26156 52266)	Atlas-SNP	.											.	ARSB	47	.	0			c.G1126A						PASS	.	C	MET/VAL,MET/VAL	309,4097	166.9+/-198.0	10,289,1904	119.0	108.0	112.0		1126,1126	0.6	1.0	5	dbSNP_123	112	1473,7127	281.7+/-295.2	136,1201,2963	yes	missense,missense	ARSB	NM_000046.3,NM_198709.2	21,21	146,1490,4867	TT,TC,CC		17.1279,7.0132,13.7014	benign,benign	376/534,376/414	78181423	1782,11224	2203	4300	6503	SO:0001583	missense	411	exon6			TCCACACGTCGAA	M32373	CCDS4043.1, CCDS43334.1	5q14.1	2013-02-14			ENSG00000113273	ENSG00000113273	3.1.6.1	"""Arylsulfatase family"""	714	protein-coding gene	gene with protein product		611542				2303452	Standard	NM_000046		Approved		uc003kfq.3	P15848	OTTHUMG00000108129	ENST00000264914.4:c.1126G>A	5.37:g.78181423C>T	ENSP00000264914:p.Val376Met	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_198709	B2RC20|Q8N322|Q9UDI9	Missense_Mutation	SNP	ENST00000264914.4	37	CCDS4043.1	208	0.09523809523809523	20	0.04065040650406504	70	0.19337016574585636	6	0.01048951048951049	112	0.14775725593667546	C	14.04	2.417132	0.42918	0.070132	0.171279	ENSG00000113273	ENST00000264914;ENST00000396151	D;D	0.96365	-3.99;-3.99	5.46	0.601	0.17529	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.324515	0.32884	N	0.005530	T	0.00875	0.0029	N	0.26162	0.8	0.24694	P	0.99329924	P;P	0.44281	0.779;0.831	B;B	0.32928	0.131;0.155	T	0.47032	-0.9148	9	0.33940	T	0.23	.	9.6382	0.39822	0.0:0.6519:0.0:0.3481	rs17220759;rs17220759	376;376	Q8N322;P15848	.;ARSB_HUMAN	M	376	ENSP00000264914:V376M;ENSP00000379455:V376M	ENSP00000264914:V376M	V	-	1	0	ARSB	78217179	0.977000	0.34250	0.962000	0.40283	0.898000	0.52572	2.189000	0.42621	-0.194000	0.10399	-0.254000	0.11334	GTG	C|0.884;T|0.116	0.116	strong		0.532	ARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226932.2	NM_000046	
ZNF485	220992	hgsc.bcm.edu	37	10	44112763	44112763	+	Silent	SNP	C	C	G	rs7069748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:44112763C>G	ENST00000361807.3	+	5	1466	c.1272C>G	c.(1270-1272)gcC>gcG	p.A424A	ZNF485_ENST00000374437.2_Silent_p.A333A|ZNF485_ENST00000374435.3_Silent_p.A424A	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	424					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GAAGTTCAGCCCTTAAGCAAC	0.393													C|||	236	0.0471246	0.0393	0.0432	5008	,	,		19676	0.002		0.0696	False		,,,				2504	0.0838				p.A424A		Atlas-SNP	.											.	ZNF485	102	.	0			c.C1272G						PASS	.	C		235,4171	125.3+/-162.5	9,217,1977	39.0	43.0	41.0		1272	0.1	0.0	10	dbSNP_116	41	655,7945	161.1+/-214.1	32,591,3677	no	coding-synonymous	ZNF485	NM_145312.3		41,808,5654	GG,GC,CC		7.6163,5.3336,6.843		424/442	44112763	890,12116	2203	4300	6503	SO:0001819	synonymous_variant	220992	exon5			TTCAGCCCTTAAG	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.1272C>G	10.37:g.44112763C>G		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_145312	B4DSE6|Q96CL0	Silent	SNP	ENST00000361807.3	37	CCDS7205.2																																																																																			C|0.938;G|0.062	0.062	strong		0.393	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
BTNL2	56244	hgsc.bcm.edu	37	6	32370986	32370986	+	Silent	SNP	C	C	A	rs57116766	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32370986C>A	ENST00000374993.1	-	3	434	c.435G>T	c.(433-435)ggG>ggT	p.G145G	BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000454136.3_Silent_p.G145G|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000374995.3_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	145	Ig-like V-type 2.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						TAGGGGCAGACCCCAGACCTG	0.607													C|||	672	0.134185	0.1369	0.1369	5008	,	,		17688	0.1984		0.0974	False		,,,				2504	0.1002				p.G145G		Atlas-SNP	.											.	BTNL2	50	.	0			c.G435T						PASS	.	C		327,2689		12,303,1193	19.0	18.0	19.0		435	-8.8	0.1	6	dbSNP_129	19	381,5037		13,355,2341	no	coding-synonymous	BTNL2	NM_019602.1		25,658,3534	AA,AC,CC		7.0321,10.8422,8.3946		145/456	32370986	708,7726	1508	2709	4217	SO:0001819	synonymous_variant	56244	exon3			GGCAGACCCCAGA	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.435G>T	6.37:g.32370986C>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Silent	SNP	ENST00000374993.1	37																																																																																				C|0.904;A|0.096	0.096	strong		0.607	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
TRIML2	205860	hgsc.bcm.edu	37	4	189018486	189018486	+	Silent	SNP	A	A	G	rs17883789	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:189018486A>G	ENST00000512729.1	-	5	860	c.486T>C	c.(484-486)tcT>tcC	p.S162S	TRIML2_ENST00000326754.3_Silent_p.S187S	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	162					protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)			central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		ACCTTTCTAAAGAGTATTTTG	0.383													A|||	709	0.141573	0.093	0.2176	5008	,	,		19757	0.1935		0.1392	False		,,,				2504	0.1022				p.S162S		Atlas-SNP	.											.	TRIML2	80	.	0			c.T486C						PASS	.	A		530,3876	238.4+/-249.8	24,482,1697	158.0	168.0	165.0		486	1.5	0.1	4	dbSNP_124	165	1154,7446	236.8+/-268.9	83,988,3229	no	coding-synonymous	TRIML2	NM_173553.1		107,1470,4926	GG,GA,AA		13.4186,12.0291,12.9479		162/388	189018486	1684,11322	2203	4300	6503	SO:0001819	synonymous_variant	205860	exon5			TTCTAAAGAGTAT	AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"""SPRY domain containing 6"""						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.486T>C	4.37:g.189018486A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_173553	B7Z6J6	Silent	SNP	ENST00000512729.1	37	CCDS3850.1																																																																																			A|0.866;G|0.134	0.134	strong		0.383	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553	
OVCH1	341350	hgsc.bcm.edu	37	12	29617550	29617550	+	Missense_Mutation	SNP	G	G	A	rs11050243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:29617550G>A	ENST00000318184.5	-	18	2014	c.2015C>T	c.(2014-2016)tCt>tTt	p.S672F	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	672	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.		S -> F (in dbSNP:rs11050243).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.S672F(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					CTCCAGAGGAGAGCTTAGTTG	0.493													G|||	912	0.182109	0.3585	0.1023	5008	,	,		18329	0.0853		0.1352	False		,,,				2504	0.1483				p.S672F		Atlas-SNP	.											OVCH1,NS,carcinoma,0,1	OVCH1	195	1	1	Substitution - Missense(1)	stomach(1)	c.C2015T						PASS	.	G	PHE/SER	1315,2565		217,881,842	125.0	125.0	125.0		2015	2.7	0.6	12	dbSNP_120	125	1174,7148		90,994,3077	yes	missense	OVCH1	NM_183378.2	155	307,1875,3919	AA,AG,GG		14.1072,33.8918,20.3983	probably-damaging	672/1135	29617550	2489,9713	1940	4161	6101	SO:0001583	missense	341350	exon18			AGAGGAGAGCTTA	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.2015C>T	12.37:g.29617550G>A	ENSP00000326708:p.Ser672Phe	Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	248	130	0.524194	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		355	0.16254578754578755	164	0.3333333333333333	29	0.08011049723756906	59	0.10314685314685315	103	0.1358839050131926	G	16.70	3.194855	0.58017	0.338918	0.141072	ENSG00000187950	ENST00000318184	T	0.61859	0.07	2.73	2.73	0.32206	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	M	0.71920	2.185	0.41092	P	0.014395999999999964	D	0.89917	1.0	D	0.81914	0.995	T	0.13818	-1.0495	8	0.45353	T	0.12	.	7.0766	0.25207	0.0:0.0:0.7311:0.2689	rs11050243;rs60892337;rs11050243	672	Q7RTY7	OVCH1_HUMAN	F	672	ENSP00000326708:S672F	ENSP00000326708:S672F	S	-	2	0	OVCH1	29508817	0.587000	0.26791	0.559000	0.28332	0.394000	0.30568	1.776000	0.38594	1.836000	0.53414	0.655000	0.94253	TCT	G|0.825;A|0.175	0.175	strong		0.493	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
C3orf30	152405	hgsc.bcm.edu	37	3	118866376	118866376	+	Missense_Mutation	SNP	C	C	T	rs56317615	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:118866376C>T	ENST00000295622.1	+	1	1380	c.1340C>T	c.(1339-1341)tCa>tTa	p.S447L	RP11-484M3.5_ENST00000490594.1_Missense_Mutation_p.S52L|IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	447			S -> L (in dbSNP:rs56317615). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		CCCTCCATCTCATCCAAATTG	0.433													C|||	903	0.180312	0.0166	0.2435	5008	,	,		19119	0.2431		0.3221	False		,,,				2504	0.1462				p.S447L		Atlas-SNP	.											.	C3orf30	64	.	0			c.C1340T						PASS	.	C	LEU/SER	295,4111	161.4+/-193.6	8,279,1916	84.0	86.0	86.0		1340	3.6	0.0	3	dbSNP_129	86	2650,5950	427.4+/-355.6	416,1818,2066	yes	missense	C3orf30	NM_152539.2	145	424,2097,3982	TT,TC,CC		30.814,6.6954,22.6434	probably-damaging	447/537	118866376	2945,10061	2203	4300	6503	SO:0001583	missense	152405	exon1			CCATCTCATCCAA	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.1340C>T	3.37:g.118866376C>T	ENSP00000295622:p.Ser447Leu	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	176	85	0.482955	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	481	0.22023809523809523	8	0.016260162601626018	98	0.27071823204419887	145	0.2534965034965035	230	0.3034300791556728	C	8.567	0.879199	0.17395	0.066954	0.30814	ENSG00000163424;ENSG00000163424;ENSG00000251012	ENST00000295622;ENST00000470341;ENST00000490594	T;T	0.51071	2.58;0.72	4.49	3.62	0.41486	.	0.470495	0.17918	N	0.157611	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	D;P	0.61697	0.99;0.873	P;P	0.56865	0.808;0.461	T	0.16305	-1.0407	9	0.72032	D	0.01	-0.5483	8.4037	0.32601	0.0:0.8961:0.0:0.1039	rs56317615	447;447	E9PFE5;Q96M34	.;CC030_HUMAN	L	447;447;52	ENSP00000295622:S447L;ENSP00000424708:S52L	ENSP00000295622:S447L	S	+	2	0	C3orf30;RP11-484M3.5	120349066	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	0.556000	0.23438	1.500000	0.48636	0.655000	0.94253	TCA	C|0.766;T|0.234	0.234	strong		0.433	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
STAG3	10734	hgsc.bcm.edu	37	7	99796146	99796146	+	Silent	SNP	A	A	C	rs3735241	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99796146A>C	ENST00000426455.1	+	13	1700	c.1293A>C	c.(1291-1293)ccA>ccC	p.P431P	STAG3_ENST00000394018.2_Silent_p.P373P|STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000543273.1_RNA|STAG3_ENST00000317296.5_Silent_p.P431P	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	431					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCGTCTACCCAGTTGTGTATG	0.522													C|||	2504	0.5	0.3654	0.6254	5008	,	,		19600	0.6815		0.498	False		,,,				2504	0.408				p.P431P		Atlas-SNP	.											.	STAG3	121	.	0			c.A1293C						PASS	.	C		1816,2590		363,1090,750	142.0	123.0	130.0		1293	-6.2	0.1	7	dbSNP_107	130	4281,4319		1082,2117,1101	no	coding-synonymous	STAG3	NM_012447.2		1445,3207,1851	CC,CA,AA		49.7791,41.2165,46.8784		431/1226	99796146	6097,6909	2203	4300	6503	SO:0001819	synonymous_variant	10734	exon13			CTACCCAGTTGTG	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.1293A>C	7.37:g.99796146A>C		Somatic	295	1	0.00338983		WXS	Illumina HiSeq	Phase_I	325	179	0.550769	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Silent	SNP	ENST00000426455.1	37	CCDS34703.1																																																																																			C|0.482;N|0.000	0.482	strong		0.522	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
TRIM22	10346	hgsc.bcm.edu	37	11	5719750	5719750	+	Missense_Mutation	SNP	G	G	C	rs1063303	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5719750G>C	ENST00000379965.3	+	4	1002	c.725G>C	c.(724-726)aGg>aCg	p.R242T	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	242			R -> T (in dbSNP:rs1063303). {ECO:0000269|PubMed:7797467}.		defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R242T(1)		kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		CGGAGGTTGAGGGGATCGTCA	0.547													G|||	2138	0.426917	0.3722	0.4553	5008	,	,		19187	0.2054		0.5398	False		,,,				2504	0.593				p.R242T	GBM(104;491 2336 5222)	Atlas-SNP	.											TRIM22,NS,carcinoma,0,1	TRIM22	66	1	1	Substitution - Missense(1)	stomach(1)	c.G725C						PASS	.	G	THR/ARG,THR/ARG	1598,2444		337,924,760	54.0	59.0	57.0		713,725	-2.2	0.0	11	dbSNP_86	57	4787,3611		1395,1997,807	yes	missense,missense	TRIM22	NM_001199573.1,NM_006074.4	71,71	1732,2921,1567	CC,CG,GG		42.9983,39.5349,48.6736	benign,benign	238/495,242/499	5719750	6385,6055	2021	4199	6220	SO:0001583	missense	10346	exon4			GGTTGAGGGGATC	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16379	protein-coding gene	gene with protein product		606559	"""tripartite motif-containing 22"""			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.725G>C	11.37:g.5719750G>C	ENSP00000369299:p.Arg242Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	154	75	0.487013	NM_006074	Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	37	CCDS41612.1	848	0.3882783882783883	198	0.4024390243902439	149	0.4116022099447514	90	0.15734265734265734	411	0.5422163588390502	G	10.42	1.345247	0.24426	0.395349	0.570017	ENSG00000132274	ENST00000379965;ENST00000545338;ENST00000454828;ENST00000455293	T;T	0.05025	3.51;3.51	3.53	-2.15	0.07102	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B;B;B;B	0.14012	0.009;0.0;0.001;0.001	B;B;B;B	0.16722	0.016;0.0;0.009;0.003	T	0.35919	-0.9769	8	0.54805	T	0.06	.	8.0653	0.30657	0.4386:0.0:0.5614:0.0	rs1063303;rs3204345;rs59613853;rs1063303	164;210;238;242	F8WAP8;C9JWC5;Q8IYM9-2;Q8IYM9	.;.;.;TRI22_HUMAN	T	242;53;210;164	ENSP00000369299:R242T;ENSP00000393250:R210T	ENSP00000369299:R242T	R	+	2	0	TRIM22	5676326	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.177000	0.09796	-0.378000	0.07918	-0.384000	0.06662	AGG	G|0.570;C|0.430	0.430	strong		0.547	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
F13A1	2162	hgsc.bcm.edu	37	6	6174866	6174866	+	Missense_Mutation	SNP	G	G	A	rs5982	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:6174866G>A	ENST00000264870.3	-	12	1959	c.1694C>T	c.(1693-1695)cCg>cTg	p.P565L		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	565			P -> L (in allele F13A*1A, allele F13A*2A and allele F13*(2)A; dbSNP:rs5982). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:2901091, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.P565L(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TTCTGCCTTCGGGACCCCGGT	0.522													G|||	1204	0.240415	0.1452	0.1009	5008	,	,		18278	0.3581		0.2107	False		,,,				2504	0.3773				p.P565L		Atlas-SNP	.											F13A1,NS,malignant_melanoma,-1,2	F13A1	135	2	1	Substitution - Missense(1)	breast(1)	c.C1694T						PASS	.	G	LEU/PRO	697,3709	292.4+/-282.0	58,581,1564	300.0	255.0	271.0		1694	5.8	0.2	6	dbSNP_52	271	1807,6793	325.6+/-317.0	205,1397,2698	yes	missense	F13A1	NM_000129.3	98	263,1978,4262	AA,AG,GG		21.0116,15.8193,19.2527	benign	565/733	6174866	2504,10502	2203	4300	6503	SO:0001583	missense	2162	exon12			GCCTTCGGGACCC	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1694C>T	6.37:g.6174866G>A	ENSP00000264870:p.Pro565Leu	Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	396	199	0.502525	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	CCDS4496.1	467	0.21382783882783882	82	0.16666666666666666	45	0.12430939226519337	176	0.3076923076923077	164	0.21635883905013192	G	0.427	-0.905523	0.02453	0.158193	0.210116	ENSG00000124491	ENST00000264870;ENST00000441301	T	0.63744	-0.06	5.78	5.78	0.91487	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.568490	0.18516	N	0.138901	T	0.16557	0.0398	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.10296	0.001;0.003	B;B	0.06405	0.001;0.002	T	0.06752	-1.0809	9	0.09084	T	0.74	.	12.3343	0.55058	0.0763:0.0:0.9237:0.0	rs5982;rs3191129;rs3818482;rs17375117;rs57528694;rs5982	502;565	F5H080;P00488	.;F13A_HUMAN	L	565;502	ENSP00000264870:P565L	ENSP00000264870:P565L	P	-	2	0	F13A1	6119865	0.586000	0.26782	0.164000	0.22755	0.127000	0.20565	2.506000	0.45433	2.726000	0.93360	0.643000	0.83706	CCG	G|0.798;A|0.202	0.202	strong		0.522	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
CASC5	57082	hgsc.bcm.edu	37	15	40914772	40914772	+	Silent	SNP	C	C	T	rs11855334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:40914772C>T	ENST00000346991.5	+	11	2778	c.2388C>T	c.(2386-2388)gtC>gtT	p.V796V	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Silent_p.V770V			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	796					acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.V796V(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GCCACACTGTCGTCATTGGAT	0.388													T|||	1757	0.350839	0.348	0.3285	5008	,	,		21039	0.254		0.3986	False		,,,				2504	0.4213				p.V796V		Atlas-SNP	.											CASC5,NS,carcinoma,0,1	CASC5	269	1	1	Substitution - coding silent(1)	stomach(1)	c.C2388T						PASS	.	T	,	1367,2429		266,835,797	75.0	67.0	69.0		2310,2388	3.6	0.8	15	dbSNP_120	69	3321,4907		682,1957,1475	no	coding-synonymous,coding-synonymous	CASC5	NM_144508.3,NM_170589.3	,	948,2792,2272	TT,TC,CC		40.3622,36.0116,38.9887	,	770/2317,796/2343	40914772	4688,7336	1898	4114	6012	SO:0001819	synonymous_variant	57082	exon11			CACTGTCGTCATT	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.2388C>T	15.37:g.40914772C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	113	6	0.0530973	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Silent	SNP	ENST00000346991.5	37	CCDS42023.1																																																																																			C|0.633;T|0.367	0.367	strong		0.388	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
TTN	7273	hgsc.bcm.edu	37	2	179590329	179590329	+	Missense_Mutation	SNP	C	C	T	rs17355460	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179590329C>T	ENST00000591111.1	-	69	19875	c.19651G>A	c.(19651-19653)Gga>Aga	p.G6551R	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.G5624R|TTN_ENST00000589042.1_Missense_Mutation_p.G6868R|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.1_ENST00000590024.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12154	Ig-like 47.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCAGGCTCTCCGGCTACAACA	0.433													C|||	33	0.00658946	0.0008	0.0086	5008	,	,		20718	0.0		0.0209	False		,,,				2504	0.0051				p.G6868R		Atlas-SNP	.											.	TTN	18412	.	0			c.G20602A						PASS	.	C	ARG/GLY,,,	13,3713		0,13,1850	88.0	80.0	83.0		16870,,,	5.9	1.0	2	dbSNP_123	83	142,8056		2,138,3959	yes	missense,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	125,,,	2,151,5809	TT,TC,CC		1.7321,0.3489,1.2999	probably-damaging,,,	5624/33424,,,	179590329	155,11769	1863	4099	5962	SO:0001583	missense	7273	exon71			GCTCTCCGGCTAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.19651G>A	2.37:g.179590329C>T	ENSP00000465570:p.Gly6551Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	150	65	0.433333	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	C	13.86	2.363340	0.41902	0.003489	0.017321	ENSG00000155657	ENST00000342992	T	0.81330	-1.48	5.86	5.86	0.93980	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89515	0.6737	H	0.96748	3.875	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.92012	0.5619	9	0.87932	D	0	.	20.5632	0.99335	0.0:1.0:0.0:0.0	rs17355460;rs52829777;rs17355460	6551	Q8WZ42	TITIN_HUMAN	R	5624	ENSP00000343764:G5624R	ENSP00000343764:G5624R	G	-	1	0	TTN	179298574	0.989000	0.36119	0.998000	0.56505	0.450000	0.32258	3.002000	0.49496	2.937000	0.99478	0.650000	0.86243	GGA	C|0.991;T|0.009	0.009	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FNDC1	84624	hgsc.bcm.edu	37	6	159650978	159650978	+	Missense_Mutation	SNP	A	A	G	rs509648	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:159650978A>G	ENST00000297267.9	+	10	1512	c.1312A>G	c.(1312-1314)Aca>Gca	p.T438A	FNDC1_ENST00000340366.6_Intron	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	438	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> A (in dbSNP:rs509648). {ECO:0000269|PubMed:15489334}.		cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AATCCGGGCCACAAACAGGAG	0.507													G|||	2547	0.508586	0.7194	0.3458	5008	,	,		16618	0.7232		0.2276	False		,,,				2504	0.407				p.T438A		Atlas-SNP	.											.	FNDC1	250	.	0			c.A1312G						PASS	.	G	ALA/THR	2489,1467		791,907,280	161.0	177.0	172.0		1312	0.9	0.7	6	dbSNP_83	172	1889,6415		202,1485,2465	yes	missense	FNDC1	NM_032532.2	58	993,2392,2745	GG,GA,AA		22.7481,37.0829,35.7096	benign	438/1895	159650978	4378,7882	1978	4152	6130	SO:0001583	missense	84624	exon10			CGGGCCACAAACA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.1312A>G	6.37:g.159650978A>G	ENSP00000297267:p.Thr438Ala	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	1039	0.4757326007326007	344	0.6991869918699187	111	0.30662983425414364	421	0.736013986013986	163	0.21503957783641162	G	2.627	-0.287136	0.05605	0.629171	0.227481	ENSG00000164694	ENST00000297267	T	0.56275	0.47	5.5	0.856	0.19019	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.173617	0.50627	N	0.000110	T	0.04363	0.0120	N	0.00583	-1.355	0.09310	P	0.9999999999999734	B	0.02656	0.0	B	0.06405	0.002	T	0.34054	-0.9844	9	0.11485	T	0.65	-2.9046	5.6533	0.17629	0.165:0.0:0.4552:0.3797	rs509648;rs57028228;rs509648	438	Q4ZHG4	FNDC1_HUMAN	A	438	ENSP00000297267:T438A	ENSP00000297267:T438A	T	+	1	0	FNDC1	159570966	0.999000	0.42202	0.659000	0.29680	0.862000	0.49288	2.806000	0.47947	-0.411000	0.07530	-0.825000	0.03093	ACA	A|0.529;G|0.471	0.471	strong		0.507	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
VCX3A	51481	hgsc.bcm.edu	37	X	6451872	6451872	+	Missense_Mutation	SNP	C	C	G	rs77148209	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:6451872C>G	ENST00000381089.3	-	3	781	c.475G>C	c.(475-477)Gag>Cag	p.E159Q	VCX3A_ENST00000398729.1_Missense_Mutation_p.E139Q	NM_016379.3	NP_057463.2	Q9NNX9	VCX3_HUMAN	variable charge, X-linked 3A	159	8 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				brain development (GO:0007420)	nucleolus (GO:0005730)|nucleus (GO:0005634)		p.E159Q(1)		NS(1)|lung(2)|pancreas(1)	4						TCCTCCACCTCGCTCTCCTGA	0.582													c|||	748	0.198146	0.2935	0.0562	3775	,	,		12584	0.1508		0.0984	False		,,,				2504	0.0716				p.E159Q		Atlas-SNP	.											.	VCX3A	17	.	1	Substitution - Missense(1)	NS(1)	c.G475C						PASS	.	C	GLN/GLU	761,3006		16,603,126,994,415	62.0	66.0	64.0		475	-1.0	0.0	X	dbSNP_134	64	289,6328		0,233,56,2178,1739	no	missense	VCX3A	NM_016379.3	29	16,836,182,3172,2154	GG,GC,G,CC,C		4.3675,20.2018,10.1117	benign	159/187	6451872	1050,9334	2154	4206	6360	SO:0001583	missense	51481	exon3			CCACCTCGCTCTC	AF159128	CCDS35199.1	Xp22.31	2008-02-05	2005-01-11	2005-01-12	ENSG00000169059	ENSG00000169059			18159	protein-coding gene	gene with protein product		300533	"""variable charge, X-linked 3"""	VCX3		10607842	Standard	NM_016379		Approved	VCX-8r, VCX-8R, VCX-A	uc004crs.3	Q9NNX9	OTTHUMG00000021097	ENST00000381089.3:c.475G>C	X.37:g.6451872C>G	ENSP00000370479:p.Glu159Gln	Somatic	429	1	0.002331		WXS	Illumina HiSeq	Phase_I	474	133	0.280591	NM_016379	Q9P0H4	Missense_Mutation	SNP	ENST00000381089.3	37	CCDS35199.1	.	.	.	.	.	.	.	.	.	.	-	0.009	-1.855340	0.00558	0.202018	0.043675	ENSG00000169059	ENST00000381089;ENST00000398729	T;T	0.15952	2.38;2.38	0.511	-1.02	0.10135	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.18166	0.026	B	0.09377	0.004	T	0.40079	-0.9582	8	0.13470	T	0.59	.	3.3799	0.07251	0.0:0.4906:0.2639:0.2455	.	159	Q9NNX9	VCX3_HUMAN	Q	159;139	ENSP00000370479:E159Q;ENSP00000381713:E139Q	ENSP00000370479:E159Q	E	-	1	0	VCX3A	6461872	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.770000	0.04705	-1.689000	0.01434	-1.304000	0.01323	GAG	C|0.901;G|0.099	0.099	strong		0.582	VCX3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055679.1	NM_016379	
COA7	65260	hgsc.bcm.edu	37	1	53153432	53153432	+	Missense_Mutation	SNP	T	T	C	rs443751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:53153432T>C	ENST00000371538.3	-	3	695	c.656A>G	c.(655-657)aAa>aGa	p.K219R	SELRC1_ENST00000486918.1_5'UTR	NM_023077.2	NP_075565.2												p.K219R(1)		breast(1)|lung(3)|prostate(1)|urinary_tract(1)	6						CTGCTGTTCTTTGTGTAGCTG	0.532													T|||	1056	0.210863	0.1611	0.2205	5008	,	,		19949	0.0139		0.3658	False		,,,				2504	0.3149				p.K219R		Atlas-SNP	.											SELRC1,NS,carcinoma,0,1	SELRC1	11	1	1	Substitution - Missense(1)	prostate(1)	c.A656G						PASS	.	T	ARG/LYS	879,3527	341.8+/-306.9	80,719,1404	165.0	144.0	152.0		656	5.6	1.0	1	dbSNP_80	152	3053,5547	468.3+/-367.3	539,1975,1786	yes	missense	SELRC1	NM_023077.2	26	619,2694,3190	CC,CT,TT		35.5,19.9501,30.2322	benign	219/232	53153432	3932,9074	2203	4300	6503	SO:0001583	missense	65260	exon3			TGTTCTTTGTGTA																												ENST00000371538.3:c.656A>G	1.37:g.53153432T>C	ENSP00000360593:p.Lys219Arg	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	211	99	0.469194	NM_023077		Missense_Mutation	SNP	ENST00000371538.3	37	CCDS570.1	447	0.20467032967032966	68	0.13821138211382114	94	0.2596685082872928	7	0.012237762237762238	278	0.36675461741424803	T	10.92	1.485729	0.26686	0.199501	0.355	ENSG00000162377	ENST00000371538	T	0.44482	0.92	5.55	5.55	0.83447	.	0.269500	0.43260	N	0.000598	T	0.00012	0.0000	L	0.29908	0.895	0.28440	P	0.9168529	B	0.12630	0.006	B	0.08055	0.003	T	0.40646	-0.9552	9	0.18276	T	0.48	-22.7937	8.2315	0.31601	0.0:0.1487:0.0:0.8513	rs443751;rs3174551;rs17845459;rs17858336;rs52795029;rs60837595;rs443751	219	Q96BR5	SELR1_HUMAN	R	219	ENSP00000360593:K219R	ENSP00000360593:K219R	K	-	2	0	SELRC1	52926020	.	.	1.000000	0.80357	0.608000	0.37181	.	.	2.123000	0.65237	0.449000	0.29647	AAA	T|0.745;C|0.255	0.255	strong		0.532	SELRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023462.1		
TUBGCP6	85378	hgsc.bcm.edu	37	22	50660137	50660137	+	Missense_Mutation	SNP	G	G	A	rs34455105	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50660137G>A	ENST00000248846.5	-	16	2755	c.2651C>T	c.(2650-2652)gCg>gTg	p.A884V	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_Missense_Mutation_p.A884V			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	884			A -> V (in dbSNP:rs34455105).		G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GGCCCCCTCCGCCTGCTGCAG	0.672													G|||	132	0.0263578	0.0053	0.0432	5008	,	,		16222	0.0		0.0696	False		,,,				2504	0.0256				p.A884V		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.C2651T						PASS	.	G	VAL/ALA	56,4348	52.3+/-87.9	0,56,2146	35.0	37.0	36.0		2651	-1.6	0.0	22	dbSNP_126	36	560,8038	147.3+/-202.7	14,532,3753	yes	missense	TUBGCP6	NM_020461.3	64	14,588,5899	AA,AG,GG		6.5131,1.2716,4.7377	benign	884/1820	50660137	616,12386	2202	4299	6501	SO:0001583	missense	85378	exon16			CCCTCCGCCTGCT	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.2651C>T	22.37:g.50660137G>A	ENSP00000248846:p.Ala884Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	208	100	0.480769	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	75	0.034340659340659344	3	0.006097560975609756	18	0.049723756906077346	1	0.0017482517482517483	53	0.06992084432717678	G	7.374	0.627376	0.14257	0.012716	0.065131	ENSG00000128159	ENST00000248846;ENST00000439308	T;T	0.12465	3.08;2.68	2.35	-1.64	0.08318	.	3.676470	0.00974	N	0.003295	T	0.00496	0.0016	N	0.04880	-0.145	0.09310	N	1	B;B	0.21309	0.054;0.054	B;B	0.21546	0.035;0.023	T	0.29058	-1.0024	10	0.33141	T	0.24	.	3.8471	0.08939	0.3208:0.2085:0.4707:0.0	rs34455105	876;884	B2RWN4;Q96RT7	.;GCP6_HUMAN	V	884	ENSP00000248846:A884V;ENSP00000397387:A884V	ENSP00000248846:A884V	A	-	2	0	TUBGCP6	49002264	0.000000	0.05858	0.008000	0.14137	0.004000	0.04260	-0.232000	0.09055	-0.160000	0.11002	-1.099000	0.02127	GCG	G|0.956;A|0.044	0.044	strong		0.672	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
ANKRD18A	253650	hgsc.bcm.edu	37	9	38615698	38615698	+	Missense_Mutation	SNP	C	C	T	rs1832313	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:38615698C>T	ENST00000399703.5	-	3	762	c.388G>A	c.(388-390)Gag>Aag	p.E130K		NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	130			E -> K (in dbSNP:rs1832313). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.							NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						TAGATATCCTCAATGTTTGGA	0.438													.|||	2112	0.421725	0.4539	0.4265	5008	,	,		16313	0.5109		0.4264	False		,,,				2504	0.2781				p.E130K		Atlas-SNP	.											.	ANKRD18A	49	.	0			c.G388A						PASS	.	T	LYS/GLU	620,764		145,330,217	93.0	75.0	80.0		388	0.2	0.0	9	dbSNP_92	80	1297,1885		272,753,566	yes	missense	ANKRD18A	NM_147195.2	56	417,1083,783	TT,TC,CC		40.7605,44.7977,41.9842	benign	130/993	38615698	1917,2649	692	1591	2283	SO:0001583	missense	253650	exon3			TATCCTCAATGTT	AB095935	CCDS55311.1	9p13.1	2013-01-10			ENSG00000180071	ENSG00000180071		"""Ankyrin repeat domain containing"""	23643	protein-coding gene	gene with protein product							Standard	NM_147195		Approved	KIAA2015, FLJ35740	uc004abg.4	Q8IVF6	OTTHUMG00000019950	ENST00000399703.5:c.388G>A	9.37:g.38615698C>T	ENSP00000382610:p.Glu130Lys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_147195	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	Missense_Mutation	SNP	ENST00000399703.5	37	CCDS55311.1	996	0.45604395604395603	243	0.49390243902439024	165	0.4558011049723757	280	0.48951048951048953	308	0.40633245382585753	T	0.020	-1.439439	0.01098	0.447977	0.407605	ENSG00000180071	ENST00000399703	T	0.61510	0.1	1.4	0.224	0.15297	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41466	-0.9507	7	0.02654	T	1	.	5.9244	0.19101	0.0:0.5856:0.0:0.4144	rs1832313;rs59901375	130	Q8IVF6	AN18A_HUMAN	K	130	ENSP00000382610:E130K	ENSP00000382610:E130K	E	-	1	0	ANKRD18A	38605698	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	0.393000	0.20817	-0.357000	0.08175	-1.220000	0.01600	GAG	C|0.550;T|0.450	0.450	strong		0.438	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052506.3		
LAMA5	3911	hgsc.bcm.edu	37	20	60898889	60898889	+	Missense_Mutation	SNP	C	C	T	rs372008452		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60898889C>T	ENST00000252999.3	-	44	5858	c.5792G>A	c.(5791-5793)cGa>cAa	p.R1931Q		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1931	Laminin EGF-like 18. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCGGCCGCCTCGCAGGACACA	0.692																																					p.R1931Q		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5792A						PASS	.	C	GLN/ARG	1,4365		0,1,2182	22.0	24.0	23.0		5792	1.2	0.1	20		23	1,8575		0,1,4287	no	missense	LAMA5	NM_005560.3	43	0,2,6469	TT,TC,CC		0.0117,0.0229,0.0155	probably-damaging	1931/3696	60898889	2,12940	2183	4288	6471	SO:0001583	missense	3911	exon44			CCGCCTCGCAGGA	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.5792G>A	20.37:g.60898889C>T	ENSP00000252999:p.Arg1931Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	41	0.569444	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.842202	0.32513	2.29E-4	1.17E-4	ENSG00000130702	ENST00000252999	T	0.63096	-0.02	3.63	1.17	0.20885	EGF-like, laminin (3);	0.328525	0.30101	U	0.010416	T	0.38241	0.1033	L	0.42008	1.315	0.09310	N	1	P	0.42993	0.797	B	0.32022	0.139	T	0.22906	-1.0203	10	0.15952	T	0.53	.	3.2772	0.06902	0.0:0.4524:0.2687:0.2789	.	1931	O15230	LAMA5_HUMAN	Q	1931	ENSP00000252999:R1931Q	ENSP00000252999:R1931Q	R	-	2	0	LAMA5	60332284	0.012000	0.17670	0.069000	0.20011	0.382000	0.30200	0.755000	0.26405	0.466000	0.27193	0.297000	0.19635	CGA	.	.	weak		0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SYNE4	163183	hgsc.bcm.edu	37	19	36499173	36499173	+	Silent	SNP	C	C	T	rs2285424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:36499173C>T	ENST00000324444.3	-	2	336	c.225G>A	c.(223-225)ccG>ccA	p.P75P	ALKBH6_ENST00000495116.2_5'Flank|AC002116.8_ENST00000473572.2_RNA|SYNE4_ENST00000340477.5_Silent_p.P75P	NM_001039876.1	NP_001034965.1	Q8N205	SYNE4_HUMAN	spectrin repeat containing, nuclear envelope family member 4	75					establishment of epithelial cell apical/basal polarity (GO:0045198)	integral component of nuclear outer membrane (GO:0031309)											TTGACCATCTCGGGGGGTGAG	0.652													T|||	1616	0.322684	0.6112	0.4006	5008	,	,		16536	0.2153		0.159	False		,,,				2504	0.1564				p.P75P		Atlas-SNP	.											.	.	.	.	0			c.G225A						PASS	.	T		2041,1845		535,971,437	50.0	57.0	54.0		225	-2.1	0.0	19	dbSNP_100	54	1391,6881		108,1175,2853	no	coding-synonymous	C19orf46	NM_001039876.1		643,2146,3290	TT,TC,CC		16.8158,47.4781,28.2283		75/405	36499173	3432,8726	1943	4136	6079	SO:0001819	synonymous_variant	163183	exon2			CCATCTCGGGGGG	BC038360	CCDS42553.1	19q13.12	2014-01-28	2012-05-31	2012-05-31	ENSG00000181392	ENSG00000181392			26703	protein-coding gene	gene with protein product		615535	"""chromosome 19 open reading frame 46"", ""deafness, autosomal recessive 76"""	C19orf46, DFNB76		23348741	Standard	XM_005258597		Approved	FLJ36445, Nesprin-4, Nesp4	uc002ocq.1	Q8N205	OTTHUMG00000048135	ENST00000324444.3:c.225G>A	19.37:g.36499173C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	146	59	0.40411	NM_001039876	A8MRS0|A8MYE3|Q7Z7L3	Silent	SNP	ENST00000324444.3	37	CCDS42553.1	664	0.304029304029304	291	0.5914634146341463	114	0.3149171270718232	138	0.24125874125874125	121	0.15963060686015831	T	6.092	0.385312	0.11524	0.525219	0.168158	ENSG00000181392	ENST00000503121	.	.	.	4.22	-2.1	0.07210	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	9.99999999995449E-6	.	.	.	.	.	.	T	0.44997	-0.9291	3	.	.	.	-12.4381	7.6711	0.28460	0.0:0.1916:0.4832:0.3252	rs2285424;rs2285424	.	.	.	Q	63	.	.	R	-	2	0	C19orf46	41191013	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-0.306000	0.08178	-0.673000	0.05259	-1.006000	0.02489	CGA	C|0.707;T|0.293	0.293	strong		0.652	SYNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109525.3	NM_001039876	
CALU	813	hgsc.bcm.edu	37	7	128388648	128388648	+	Missense_Mutation	SNP	G	G	A	rs2290228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:128388648G>A	ENST00000249364.4	+	2	113	c.11G>A	c.(10-12)cGa>cAa	p.R4Q	CALU_ENST00000535623.1_Missense_Mutation_p.R12Q|CALU_ENST00000449187.2_Missense_Mutation_p.R4Q|CALU_ENST00000479257.1_Missense_Mutation_p.R12Q|CALU_ENST00000538546.1_Intron|CALU_ENST00000542996.2_Missense_Mutation_p.R12Q|CALU_ENST00000535011.2_Missense_Mutation_p.R4Q	NM_001219.4	NP_001210.1	O43852	CALU_HUMAN	calumenin	4			R -> Q (in dbSNP:rs2290228). {ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)			kidney(2)|large_intestine(3)|lung(5)	10						ATGGACCTGCGACAGTTTCTT	0.418													G|||	855	0.170727	0.0961	0.1859	5008	,	,		19745	0.1974		0.159	False		,,,				2504	0.2454				p.R12Q		Atlas-SNP	.											.	CALU	42	.	0			c.G35A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG	485,3921	225.9+/-241.6	29,427,1747	84.0	81.0	82.0		11,35,35,11,,11	5.9	1.0	7	dbSNP_100	82	1415,7185	273.1+/-290.5	115,1185,3000	yes	missense,missense,missense,missense,intron,missense	CALU	NM_001130674.2,NM_001199671.1,NM_001199672.1,NM_001199673.1,NM_001199674.1,NM_001219.4	43,43,43,43,,43	144,1612,4747	AA,AG,GG		16.4535,11.0077,14.6086	benign,benign,benign,benign,,benign	4/316,12/324,12/324,4/225,,4/316	128388648	1900,11106	2203	4300	6503	SO:0001583	missense	813	exon3			ACCTGCGACAGTT	AF013759	CCDS5805.1, CCDS47703.1, CCDS56506.1, CCDS56507.1, CCDS56508.1	7q32	2013-01-10			ENSG00000128595	ENSG00000128595		"""EF-hand domain containing"""	1458	protein-coding gene	gene with protein product		603420				9598325	Standard	NM_001219		Approved		uc003vnq.3	O43852	OTTHUMG00000158274	ENST00000249364.4:c.11G>A	7.37:g.128388648G>A	ENSP00000249364:p.Arg4Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	114	48	0.421053	NM_001199671	B3KPG9|D6QS48|D6QS49|D6QS50|D6QS51|D6QS52|D6QS53|D6QS54|D6QS55|D6QS56|D6QS57|D6QS58|D6QS59|F5H1Q9|F5H879|O60456|Q6FHB9|Q96RL3|Q9NR43	Missense_Mutation	SNP	ENST00000249364.4	37	CCDS5805.1	345	0.15796703296703296	46	0.09349593495934959	60	0.16574585635359115	116	0.20279720279720279	123	0.16226912928759896	G	17.69	3.452475	0.63290	0.110077	0.164535	ENSG00000128595	ENST00000542996;ENST00000535623;ENST00000538394;ENST00000537667;ENST00000535011;ENST00000537014;ENST00000249364;ENST00000449187;ENST00000342367;ENST00000479257	T;T;T;T;T;T	0.61510	2.71;0.1;2.5;2.74;2.74;2.71	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	M	0.68593	2.085	0.09310	P	1.0	B;B	0.20368	0.044;0.003	B;B	0.09377	0.004;0.001	T	0.06899	-1.0801	9	0.18710	T	0.47	-2.4555	17.8434	0.88721	0.0:0.0:1.0:0.0	rs2290228;rs10399443;rs11545532;rs61408000;rs2290228	12;4	D6QS48;O43852	.;CALU_HUMAN	Q	12;12;4;4;4;4;4;4;4;12	ENSP00000438248:R12Q;ENSP00000439139:R12Q;ENSP00000442110:R4Q;ENSP00000249364:R4Q;ENSP00000408838:R4Q;ENSP00000420381:R12Q	ENSP00000249364:R4Q	R	+	2	0	CALU	128175884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.343000	0.52167	2.814000	0.96858	0.591000	0.81541	CGA	G|0.841;A|0.159	0.159	strong		0.418	CALU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350533.1	NM_001219	
HIPK1	204851	hgsc.bcm.edu	37	1	114515717	114515717	+	Silent	SNP	G	G	A	rs2358996	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:114515717G>A	ENST00000369558.1	+	16	3448	c.3216G>A	c.(3214-3216)gcG>gcA	p.A1072A	HIPK1_ENST00000426820.2_Silent_p.A1072A|HIPK1_ENST00000340480.4_Silent_p.A698A|HIPK1_ENST00000369561.4_Silent_p.A1038A|HIPK1_ENST00000369554.2_Silent_p.A1027A|HIPK1_ENST00000369553.1_Silent_p.A678A|HIPK1_ENST00000406344.1_Silent_p.A678A|HIPK1_ENST00000369555.2_Silent_p.A1027A			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	1072	Interaction with TP53.				anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGCAGCAGGCGTTTGTGGCCC	0.632													G|||	2435	0.486222	0.5469	0.4366	5008	,	,		14415	0.5238		0.4314	False		,,,				2504	0.4571				p.A1072A		Atlas-SNP	.											.	HIPK1	195	.	0			c.G3216A						PASS	.	G	,,	2246,2160	593.3+/-388.0	575,1096,532	87.0	97.0	93.0		2034,3216,2094	-0.0	1.0	1	dbSNP_100	93	3576,5024	518.0+/-379.2	764,2048,1488	yes	coding-synonymous,coding-synonymous,coding-synonymous	HIPK1	NM_181358.2,NM_198268.2,NM_198269.2	,,	1339,3144,2020	AA,AG,GG		41.5814,49.0241,44.764	,,	678/817,1072/1211,698/837	114515717	5822,7184	2203	4300	6503	SO:0001819	synonymous_variant	204851	exon16			GCAGGCGTTTGTG	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.3216G>A	1.37:g.114515717G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Silent	SNP	ENST00000369558.1	37	CCDS867.1	1065	0.4876373626373626	282	0.573170731707317	156	0.430939226519337	302	0.527972027972028	325	0.4287598944591029	G	7.551	0.662757	0.14645	0.509759	0.415814	ENSG00000163349	ENST00000361587	.	.	.	5.82	-0.0111	0.13994	.	.	.	.	.	T	0.07413	0.0187	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33085	-0.9882	3	.	.	.	.	0.4926	0.00566	0.3222:0.1962:0.2944:0.1872	rs2358996;rs57274379;rs2358996	.	.	.	I	353	.	.	V	+	1	0	HIPK1	114317240	0.393000	0.25237	0.998000	0.56505	0.993000	0.82548	-0.289000	0.08365	-0.012000	0.14223	-0.175000	0.13238	GTT	G|0.519;A|0.481	0.481	strong		0.632	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268	
DND1	373863	hgsc.bcm.edu	37	5	140050940	140050940	+	Missense_Mutation	SNP	C	C	T	rs77880328	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140050940C>T	ENST00000542735.1	-	4	1043	c.1000G>A	c.(1000-1002)Gag>Aag	p.E334K	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	334					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCCCAGACTCACTGAGTGCC	0.592																																					p.E334K		Atlas-SNP	.											DND1,NS,carcinoma,0,1	DND1	15	1	0			c.G1000A						scavenged	.						67.0	61.0	63.0					5																	140050940		2008	4046	6054	SO:0001583	missense	373863	exon4			CAGACTCACTGAG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1000G>A	5.37:g.140050940C>T	ENSP00000445366:p.Glu334Lys	Somatic	440	1	0.00227273		WXS	Illumina HiSeq	Phase_I	797	72	0.0903388	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.984700	0.35036	.	.	ENSG00000256453	ENST00000542735	T	0.32988	1.43	5.3	3.53	0.40419	.	0.429652	0.22940	N	0.053797	T	0.16769	0.0403	L	0.27053	0.805	0.27535	N	0.950973	B	0.02656	0.0	B	0.06405	0.002	T	0.29792	-1.0000	10	0.05620	T	0.96	-17.9422	9.0835	0.36567	0.0:0.7627:0.0:0.2373	.	334	Q8IYX4	DND1_HUMAN	K	334	ENSP00000445366:E334K	ENSP00000445366:E334K	E	-	1	0	DND1	140031124	0.995000	0.38212	0.998000	0.56505	0.721000	0.41392	1.914000	0.39966	0.821000	0.34540	0.551000	0.68910	GAG	A|0.029;G|0.971	.	alt		0.592	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
USP40	55230	hgsc.bcm.edu	37	2	234433190	234433190	+	Missense_Mutation	SNP	C	C	G	rs200068889		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:234433190C>G	ENST00000427112.2	-	14	1861	c.1826G>C	c.(1825-1827)tGt>tCt	p.C609S	USP40_ENST00000251722.6_Missense_Mutation_p.C609S|USP40_ENST00000450966.1_Missense_Mutation_p.C621S			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	609					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		TTCAGTTTCACACAGTGTCAG	0.378																																					p.C621S		Atlas-SNP	.											.	USP40	174	.	0			c.G1862C						PASS	.	C	SER/CYS	1,3723		0,1,1861	84.0	78.0	80.0		1862	2.4	0.1	2		80	2,8252		0,2,4125	yes	missense	USP40	NM_018218.2	112	0,3,5986	GG,GC,CC		0.0242,0.0269,0.025	benign	621/1248	234433190	3,11975	1862	4127	5989	SO:0001583	missense	55230	exon14			GTTTCACACAGTG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1826G>C	2.37:g.234433190C>G	ENSP00000387898:p.Cys609Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	131	60	0.458015	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	C	6.767	0.510490	0.12883	2.69E-4	2.42E-4	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.41065	1.01;1.01;1.01	5.68	2.38	0.29361	.	2.175690	0.01523	N	0.018456	T	0.31606	0.0802	L	0.27053	0.805	0.09310	N	0.999999	B;B	0.11235	0.002;0.004	B;B	0.11329	0.002;0.006	T	0.14254	-1.0479	10	0.21014	T	0.42	.	6.3009	0.21111	0.1483:0.6338:0.0:0.2179	.	609;621	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	S	621;609;609	ENSP00000415434:C621S;ENSP00000251722:C609S;ENSP00000387898:C609S	ENSP00000251722:C609S	C	-	2	0	USP40	234097929	0.190000	0.23276	0.056000	0.19401	0.988000	0.76386	0.707000	0.25704	0.709000	0.31976	0.563000	0.77884	TGT	.	.	weak		0.378	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
TFAP2C	7022	hgsc.bcm.edu	37	20	55209257	55209257	+	Silent	SNP	T	T	C	rs35023929	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:55209257T>C	ENST00000201031.2	+	5	1098	c.855T>C	c.(853-855)atT>atC	p.I285I	TFAP2C_ENST00000544508.1_Silent_p.I116I	NM_003222.3	NP_003213.1	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma)	285					cell-cell signaling (GO:0007267)|cerebral cortex development (GO:0021987)|dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis (GO:0060598)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|forebrain neuron fate commitment (GO:0021877)|germ-line stem cell maintenance (GO:0030718)|hair follicle development (GO:0001942)|keratinocyte development (GO:0003334)|male gonad development (GO:0008584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermis development (GO:0045682)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sebaceous gland development (GO:0048733)|somatic stem cell maintenance (GO:0035019)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			Colorectal(105;0.229)			TGGACAAGATTGGGTTGAATC	0.463													T|||	312	0.0623003	0.0068	0.072	5008	,	,		16001	0.001		0.17	False		,,,				2504	0.0828				p.I285I		Atlas-SNP	.											.	TFAP2C	51	.	0			c.T855C						PASS	.	T		134,4272	96.7+/-135.4	1,132,2070	77.0	79.0	78.0		855	-3.4	0.4	20	dbSNP_126	78	1474,7126	281.3+/-295.0	123,1228,2949	no	coding-synonymous	TFAP2C	NM_003222.3		124,1360,5019	CC,CT,TT		17.1395,3.0413,12.3635		285/451	55209257	1608,11398	2203	4300	6503	SO:0001819	synonymous_variant	7022	exon5			CAAGATTGGGTTG		CCDS13454.1	20q13.2	2008-07-17	2001-11-28		ENSG00000087510	ENSG00000087510			11744	protein-coding gene	gene with protein product	"""estrogen receptor factor 1"""	601602	"""transcription factor AP-2 gamma (activating enhancer-binding protein 2 gamma)"""			8661133	Standard	NM_003222		Approved	AP2-GAMMA, ERF1, TFAP2G, hAP-2g	uc002xya.3	Q92754	OTTHUMG00000032805	ENST00000201031.2:c.855T>C	20.37:g.55209257T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_003222	B4DWK3|O00685|O00730|Q86V30|Q8IVB6|Q9P1X2	Silent	SNP	ENST00000201031.2	37	CCDS13454.1																																																																																			T|0.892;C|0.108	0.108	strong		0.463	TFAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079823.2	NM_003222	
FBXW12	285231	hgsc.bcm.edu	37	3	48419897	48419897	+	Missense_Mutation	SNP	C	C	T	rs6442117	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:48419897C>T	ENST00000296438.5	+	6	682	c.496C>T	c.(496-498)Cgg>Tgg	p.R166W	FBXW12_ENST00000415155.1_Intron|FBXW12_ENST00000436231.1_Missense_Mutation_p.R9W|FBXW12_ENST00000445170.1_Missense_Mutation_p.R147W|RN7SL321P_ENST00000581742.1_RNA	NM_207102.2	NP_996985.2	Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	166			R -> W (in dbSNP:rs6442117).							breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CACTATGGATCGGAAAAAAAC	0.488													C|||	3102	0.619409	0.6021	0.6225	5008	,	,		20116	0.6597		0.5298	False		,,,				2504	0.6912				p.R166W		Atlas-SNP	.											.	FBXW12	44	.	0			c.C496T						PASS	.	C	,TRP/ARG,TRP/ARG	2643,1763	645.1+/-398.1	786,1071,346	94.0	81.0	86.0		,439,496	-8.5	0.0	3	dbSNP_116	86	4534,4066	595.2+/-393.4	1199,2136,965	yes	intron,missense,missense	FBXW12	NM_001159927.1,NM_001159929.1,NM_207102.2	,101,101	1985,3207,1311	TT,TC,CC		47.2791,40.0136,44.8178	,possibly-damaging,possibly-damaging	,147/446,166/465	48419897	7177,5829	2203	4300	6503	SO:0001583	missense	285231	exon6			ATGGATCGGAAAA	AK097594, AY247969	CCDS2764.1, CCDS54577.1, CCDS54578.1	3p21.31	2011-07-01	2007-02-08	2004-07-21	ENSG00000164049	ENSG00000164049		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	20729	protein-coding gene	gene with protein product		609075	"""F-box only protein 35"", ""F-box and WD-40 domain protein 12"""	FBXO35		15040455	Standard	NM_207102		Approved	Fbw12	uc010hjv.3	Q6X9E4	OTTHUMG00000133530	ENST00000296438.5:c.496C>T	3.37:g.48419897C>T	ENSP00000296438:p.Arg166Trp	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	155	75	0.483871	NM_207102	E9PG36|Q494Y9|Q494Z0	Missense_Mutation	SNP	ENST00000296438.5	37	CCDS2764.1	1344	0.6153846153846154	322	0.6544715447154471	225	0.6215469613259669	386	0.6748251748251748	411	0.5422163588390502	C	10.03	1.240004	0.22711	0.599864	0.527209	ENSG00000164049	ENST00000458736;ENST00000296438;ENST00000436231;ENST00000445170	T;T;T	0.63580	1.51;-0.05;1.51	4.23	-8.47	0.00939	WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);	5.234690	0.00424	N	0.000067	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P;P	0.38048	0.616;0.616;0.482	B;B;B	0.14578	0.011;0.007;0.005	T	0.42716	-0.9435	9	0.62326	D	0.03	-0.4377	0.4543	0.00506	0.2707:0.2517:0.2584:0.2192	rs6442117;rs52832609;rs58987429;rs6442117	65;147;166	E9PCA2;E9PG36;Q6X9E4	.;.;FBW12_HUMAN	W	65;166;9;147	ENSP00000296438:R166W;ENSP00000413866:R9W;ENSP00000406139:R147W	ENSP00000296438:R166W	R	+	1	2	FBXW12	48394901	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.945000	0.01537	-3.246000	0.00205	-2.084000	0.00378	CGG	C|0.418;T|0.582	0.582	strong		0.488	FBXW12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257505.1	NM_207102	
ZBTB46	140685	hgsc.bcm.edu	37	20	62378364	62378364	+	Silent	SNP	C	C	T	rs12625387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62378364C>T	ENST00000245663.4	-	5	1839	c.1689G>A	c.(1687-1689)gcG>gcA	p.A563A	ZBTB46_ENST00000302995.2_Silent_p.A563A|RP4-583P15.10_ENST00000447343.2_RNA|RP4-583P15.10_ENST00000433905.2_RNA|ZBTB46_ENST00000395104.1_Silent_p.A563A	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	563					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					CCTTGTCGTCCGCCAACAGCG	0.721													C|||	1350	0.269569	0.1392	0.3804	5008	,	,		10252	0.3452		0.3499	False		,,,				2504	0.2065				p.A563A		Atlas-SNP	.											ZBTB46,rectum,carcinoma,0,1	ZBTB46	72	1	0			c.G1689A						PASS	.	C		746,3652		73,600,1526	30.0	29.0	29.0		1689	-0.2	0.3	20	dbSNP_120	29	2911,5675		480,1951,1862	no	coding-synonymous	ZBTB46	NM_025224.3		553,2551,3388	TT,TC,CC		33.904,16.9623,28.1654		563/590	62378364	3657,9327	2199	4293	6492	SO:0001819	synonymous_variant	140685	exon5			GTCGTCCGCCAAC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1689G>A	20.37:g.62378364C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			C|0.724;T|0.276	0.276	strong		0.721	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
GALNT4	8693	hgsc.bcm.edu	37	12	89916811	89916811	+	Missense_Mutation	SNP	C	C	T	rs2230283	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:89916811C>T	ENST00000529983.2	-	1	1772	c.1516G>A	c.(1516-1518)Gta>Ata	p.V506I	GALNT4_ENST00000413530.1_Missense_Mutation_p.V334I|POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000549504.1_Intron|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.V503I|POC1B_ENST00000549035.1_Intron|POC1B_ENST00000313546.3_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000393179.4_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	506	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.		V -> I (in dbSNP:rs2230283). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9804815}.		carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.V506I(1)		endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						TGCTCAGGTACCTCTGCACAT	0.363													C|||	1028	0.205272	0.1536	0.2435	5008	,	,		19332	0.1369		0.3529	False		,,,				2504	0.1667				p.V506I		Atlas-SNP	.											GALNT4,NS,carcinoma,0,1	GALNT4	38	1	1	Substitution - Missense(1)	prostate(1)	c.G1516A						PASS	.	C	,ILE/VAL,ILE/VAL,ILE/VAL,	657,3021		60,537,1242	61.0	57.0	59.0		,1507,1000,1516,	5.9	0.2	12	dbSNP_98	59	2808,5382		474,1860,1761	yes	intron,missense,missense,missense,intron	GALNT4,POC1B,POC1B-GALNT4	NM_001199777.1,NM_001199781.1,NM_001199782.1,NM_003774.4,NM_172240.2	,29,29,29,	534,2397,3003	TT,TC,CC		34.2857,17.863,29.1962	,benign,benign,benign,	,503/576,334/407,506/579,	89916811	3465,8403	1839	4095	5934	SO:0001583	missense	8693	exon1			CAGGTACCTCTGC	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.1516G>A	12.37:g.89916811C>T	ENSP00000436604:p.Val506Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	37	CCDS53817.1	530	0.24267399267399267	88	0.17886178861788618	84	0.23204419889502761	83	0.1451048951048951	275	0.3627968337730871	C	23.6	4.430637	0.83776	0.17863	0.342857	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;T;T	0.33438	1.41;1.41;1.41	5.93	5.93	0.95920	Ricin B-related lectin (1);Ricin B lectin (3);	.	.	.	.	T	0.00012	0.0000	L	0.61036	1.89	0.21256	P	0.999749278	P;P	0.46578	0.855;0.88	P;P	0.56216	0.753;0.794	T	0.09773	-1.0659	8	0.54805	T	0.06	.	19.3377	0.94326	0.0:1.0:0.0:0.0	rs2230283;rs17464272;rs52822348;rs57746596;rs2230283	503;506	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	I	503;334;506	ENSP00000447852:V503I;ENSP00000389686:V334I;ENSP00000436604:V506I	ENSP00000436604:V506I	V	-	1	0	GALNT4;RP11-1109F11.4	88440942	1.000000	0.71417	0.220000	0.23810	0.991000	0.79684	7.429000	0.80309	2.814000	0.96858	0.591000	0.81541	GTA	C|0.758;T|0.242	0.242	strong		0.363	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
MYH6	4624	hgsc.bcm.edu	37	14	23855569	23855569	+	Silent	SNP	A	A	G	rs178640	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23855569A>G	ENST00000356287.3	-	32	4943	c.4914T>C	c.(4912-4914)gcT>gcC	p.A1638A	MIR208A_ENST00000362287.1_RNA|MYH6_ENST00000405093.3_Silent_p.A1638A			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1638					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		GGGCCTCGGCAGCCATGCGGT	0.607													G|||	2468	0.492812	0.7579	0.3718	5008	,	,		18793	0.2569		0.4891	False		,,,				2504	0.4673				p.A1638A		Atlas-SNP	.											.	MYH6	274	.	0			c.T4914C						PASS	.	G		3020,1386	442.5+/-346.7	1066,888,249	82.0	79.0	80.0		4914	-5.1	0.0	14	dbSNP_79	80	4175,4425	580.0+/-391.0	1030,2115,1155	no	coding-synonymous	MYH6	NM_002471.3		2096,3003,1404	GG,GA,AA		48.5465,31.4571,44.6794		1638/1940	23855569	7195,5811	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon33			CTCGGCAGCCATG	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.4914T>C	14.37:g.23855569A>G		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	172	172	1	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			.	.	weak		0.607	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
SPHKAP	80309	hgsc.bcm.edu	37	2	228855866	228855866	+	Missense_Mutation	SNP	G	G	C	rs16824283	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:228855866G>C	ENST00000392056.3	-	11	4855	c.4809C>G	c.(4807-4809)agC>agG	p.S1603R	SPHKAP_ENST00000344657.5_Missense_Mutation_p.S1574R	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1603			S -> R (in dbSNP:rs16824283).			extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCCTCTGGGGGCTGGCTGTTC	0.577													G|||	879	0.175519	0.0303	0.1931	5008	,	,		14524	0.2282		0.3022	False		,,,				2504	0.1748				p.S1603R		Atlas-SNP	.											SPHKAP_ENST00000392056,colon,carcinoma,0,2	SPHKAP	750	2	0			c.C4809G						scavenged	.	G	ARG/SER,ARG/SER	296,4110	158.9+/-191.5	11,274,1918	43.0	45.0	44.0		4809,4722	-2.2	0.0	2	dbSNP_123	44	2318,6282	381.5+/-340.0	321,1676,2303	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	110,110	332,1950,4221	CC,CG,GG		26.9535,6.7181,20.0984	probably-damaging,probably-damaging	1603/1701,1574/1672	228855866	2614,10392	2203	4300	6503	SO:0001583	missense	80309	exon11			CTGGGGGCTGGCT		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4809C>G	2.37:g.228855866G>C	ENSP00000375909:p.Ser1603Arg	Somatic	136	2	0.0147059		WXS	Illumina HiSeq	Phase_I	147	65	0.442177	NM_001142644	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	435	0.19917582417582416	17	0.034552845528455285	77	0.212707182320442	120	0.2097902097902098	221	0.29155672823219	G	11.64	1.699048	0.30142	0.067181	0.269535	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.06608	3.28;3.28	6.17	-2.19	0.07015	A-kinase anchor 110kDa, C-terminal (1);	0.300797	0.43919	D	0.000501	T	0.00012	0.0000	L	0.48362	1.52	0.80722	P	0.0	D;P	0.54397	0.966;0.935	P;P	0.55923	0.787;0.613	T	0.19614	-1.0300	9	0.59425	D	0.04	.	13.8991	0.63792	0.6506:0.0:0.3494:0.0	rs16824283;rs16824283	1603;1574	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	R	1603;1574	ENSP00000375909:S1603R;ENSP00000339886:S1574R	ENSP00000339886:S1574R	S	-	3	2	SPHKAP	228564110	0.088000	0.21588	0.000000	0.03702	0.090000	0.18270	0.210000	0.17455	-0.511000	0.06514	-0.137000	0.14449	AGC	G|0.803;C|0.197	0.197	strong		0.577	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
PNPLA5	150379	hgsc.bcm.edu	37	22	44287062	44287062	+	Silent	SNP	A	A	G	rs2071884	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:44287062A>G	ENST00000597664.1	-	2	435	c.306T>C	c.(304-306)gaT>gaC	p.D102D	PNPLA5_ENST00000593866.1_Intron|PNPLA5_ENST00000216177.4_Silent_p.D102D|PNPLA5_ENST00000381198.2_Intron			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	102	Patatin.				lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				GGGGCAGAGCATCCTGCAGCT	0.667													G|||	1773	0.354034	0.2027	0.3242	5008	,	,		14974	0.4335		0.3877	False		,,,				2504	0.4632				p.D102D		Atlas-SNP	.											PNPLA5,NS,carcinoma,0,3	PNPLA5	46	3	0			c.T306C						scavenged	.	G	,	1103,3301	695.5+/-405.9	142,819,1241	37.0	33.0	34.0		,306	-0.3	0.0	22	dbSNP_96	34	3271,5329	628.6+/-398.1	610,2051,1639	no	intron,coding-synonymous	PNPLA5	NM_001177675.1,NM_138814.3	,	752,2870,2880	GG,GA,AA		38.0349,25.0454,33.6358	,	,102/430	44287062	4374,8630	2202	4300	6502	SO:0001819	synonymous_variant	150379	exon2			CAGAGCATCCTGC	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.306T>C	22.37:g.44287062A>G		Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	166	69	0.415663	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Silent	SNP	ENST00000597664.1	37																																																																																				A|0.657;G|0.343	0.343	strong		0.667	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
NTRK3	4916	hgsc.bcm.edu	37	15	88576185	88576185	+	Silent	SNP	G	G	C	rs2229910	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:88576185G>C	ENST00000360948.2	-	13	1649	c.1488C>G	c.(1486-1488)gcC>gcG	p.A496A	NTRK3_ENST00000357724.2_Silent_p.A488A|NTRK3_ENST00000542733.2_Silent_p.A398A|NTRK3_ENST00000317501.3_Silent_p.A496A|NTRK3_ENST00000557856.1_Silent_p.A488A|NTRK3_ENST00000540489.2_Silent_p.A496A|NTRK3_ENST00000355254.2_Silent_p.A496A|NTRK3_ENST00000558676.1_Silent_p.A488A|NTRK3_ENST00000394480.2_Silent_p.A496A|NTRK3_ENST00000558306.1_5'UTR	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	496					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.A496A(1)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			TGTCGGGCCCGGCATCCAGTG	0.602			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)			G|||	1753	0.35004	0.4395	0.3746	5008	,	,		11027	0.2083		0.3171	False		,,,				2504	0.3916				p.A496A		Atlas-SNP	.		Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	NTRK3_ENST00000360948,NS,carcinoma,-1,4	NTRK3	587	4	1	Substitution - coding silent(1)	stomach(1)	c.C1488G						scavenged	.	G	,,	1782,2620	525.1+/-371.5	378,1026,797	96.0	63.0	74.0		1488,1488,1488	-5.5	0.0	15	dbSNP_129	74	3053,5545	464.4+/-366.2	548,1957,1794	no	coding-synonymous,coding-synonymous,coding-synonymous	NTRK3	NM_001007156.2,NM_001012338.2,NM_002530.3	,,	926,2983,2591	CC,CG,GG		35.5083,40.4816,37.1923	,,	496/613,496/840,496/826	88576185	4835,8165	2201	4299	6500	SO:0001819	synonymous_variant	4916	exon14			GGGCCCGGCATCC	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1488C>G	15.37:g.88576185G>C		Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	ENST00000360948.2	37	CCDS32322.1																																																																																			G|0.647;C|0.353	0.353	strong		0.602	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
ZNF214	7761	hgsc.bcm.edu	37	11	7022038	7022038	+	Silent	SNP	A	A	G	rs12575236	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7022038A>G	ENST00000278314.4	-	3	1191	c.876T>C	c.(874-876)ttT>ttC	p.F292F	ZNF214_ENST00000536068.1_Silent_p.F292F|ZNF214_ENST00000531083.1_5'Flank	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	292					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		CTCTCTGATGAAAGTGAACTC	0.433													A|||	1003	0.20028	0.0121	0.3055	5008	,	,		19229	0.2431		0.2266	False		,,,				2504	0.3088				p.F292F	Ovarian(22;251 657 736 21522 46864)	Atlas-SNP	.											.	ZNF214	65	.	0			c.T876C						PASS	.	A		211,4189	126.6+/-163.6	4,203,1993	132.0	131.0	131.0		876	1.3	0.7	11	dbSNP_120	131	2038,6550	353.5+/-329.1	241,1556,2497	no	coding-synonymous	ZNF214	NM_013249.2		245,1759,4490	GG,GA,AA		23.7308,4.7955,17.316		292/607	7022038	2249,10739	2200	4294	6494	SO:0001819	synonymous_variant	7761	exon3			CTGATGAAAGTGA	AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"""Zinc fingers, C2H2-type"", ""-"""	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.876T>C	11.37:g.7022038A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_013249	B2R8Q1	Silent	SNP	ENST00000278314.4	37	CCDS31418.1																																																																																			A|0.816;G|0.184	0.184	strong		0.433	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1		
SLC22A7	10864	hgsc.bcm.edu	37	6	43270151	43270151	+	Splice_Site	SNP	C	C	T	rs2270860	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:43270151C>T	ENST00000372585.5	+	8	1370	c.1275C>T	c.(1273-1275)tcC>tcT	p.S425S	SLC22A7_ENST00000372574.3_Splice_Site_p.S423S|SLC22A7_ENST00000372589.3_Splice_Site_p.S423S	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	425					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	TAGTGTCCTCCGGTGAGCCCA	0.667													C|||	2319	0.463059	0.7156	0.3804	5008	,	,		16841	0.369		0.3439	False		,,,				2504	0.3998				p.S425S		Atlas-SNP	.											.	SLC22A7	69	.	0			c.C1275T						PASS	.	C	,	2894,1510		964,966,272	26.0	25.0	25.0		1269,1275	-10.5	0.0	6	dbSNP_100	25	2676,5918		395,1886,2016	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	SLC22A7	NM_006672.3,NM_153320.2	,	1359,2852,2288	TT,TC,CC		31.138,34.287,42.8527	,	423/547,425/549	43270151	5570,7428	2202	4297	6499	SO:0001630	splice_region_variant	10864	exon7			GTCCTCCGGTGAG	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"""Solute carriers"""	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.1276+1C>T	6.37:g.43270151C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_153320	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Silent	SNP	ENST00000372585.5	37	CCDS4893.2																																																																																			C|0.562;T|0.436	0.436	strong		0.667	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1		Silent
KIF1B	23095	hgsc.bcm.edu	37	1	10421878	10421878	+	Silent	SNP	A	A	G	rs12125492	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:10421878A>G	ENST00000377086.1	+	40	4501	c.4299A>G	c.(4297-4299)ccA>ccG	p.P1433P	KIF1B_ENST00000263934.6_Silent_p.P1387P|KIF1B_ENST00000465635.1_3'UTR|KIF1B_ENST00000377081.1_Silent_p.P1433P			O60333	KIF1B_HUMAN	kinesin family member 1B	1433					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CAAAGTCACCAGATTCGTAAG	0.468													A|||	402	0.0802716	0.0045	0.0922	5008	,	,		21563	0.0129		0.1223	False		,,,				2504	0.2004				p.P1387P		Atlas-SNP	.											.	KIF1B	242	.	0			c.A4161G						PASS	.	A		92,4314	77.3+/-115.6	1,90,2112	129.0	113.0	118.0		4161	-4.5	0.9	1	dbSNP_120	118	1083,7517	227.9+/-263.1	69,945,3286	no	coding-synonymous	KIF1B	NM_015074.3		70,1035,5398	GG,GA,AA		12.593,2.0881,9.0343		1387/1771	10421878	1175,11831	2203	4300	6503	SO:0001819	synonymous_variant	23095	exon38			GTCACCAGATTCG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.4299A>G	1.37:g.10421878A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	37																																																																																				A|0.914;G|0.086	0.086	strong		0.468	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
LMNA	4000	hgsc.bcm.edu	37	1	156106185	156106185	+	Silent	SNP	T	T	C	rs505058	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156106185T>C	ENST00000368300.4	+	7	1550	c.1338T>C	c.(1336-1338)gaT>gaC	p.D446D	LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000347559.2_Silent_p.D446D|LMNA_ENST00000368297.1_Silent_p.D365D|LMNA_ENST00000361308.4_Silent_p.D446D|LMNA_ENST00000368301.2_Silent_p.D446D|LMNA_ENST00000392353.3_Silent_p.D365D|LMNA_ENST00000473598.2_Silent_p.D347D|LMNA_ENST00000368299.3_Silent_p.D446D|LMNA_ENST00000448611.2_Silent_p.D334D	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	446	LTD.|Tail.		D -> V (in EDMD2). {ECO:0000269|PubMed:14684700}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					AGGAGGTGGATGAGGAGGGCA	0.602									Werner syndrome;Hutchinson-Gilford Progeria Syndrome				C|||	1248	0.249201	0.7247	0.098	5008	,	,		20622	0.0228		0.0865	False		,,,				2504	0.1145				p.D446D		Atlas-SNP	.											.	LMNA	31	.	0			c.T1338C						PASS	.	C	,,	2650,1756	492.7+/-362.5	782,1086,335	47.0	53.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1338,1338,1338	-5.0	0.9	1	dbSNP_83	51	653,7939	763.3+/-407.6	21,611,3664	yes	coding-synonymous,coding-synonymous,coding-synonymous	LMNA	NM_005572.3,NM_170707.2,NM_170708.2	,,	803,1697,3999	CC,CT,TT		7.6001,39.8547,25.4116	,,	446/573,446/665,446/635	156106185	3303,9695	2203	4296	6499	SO:0001819	synonymous_variant	4000	exon7	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	GGTGGATGAGGAG	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"""Intermediate filaments type V, lamins"""	6636	protein-coding gene	gene with protein product		150330	"""cardiomyopathy, dilated 1A (autosomal dominant)"", ""limb girdle muscular dystrophy 1B (autosomal dominant)"", ""progeria 1 (Hutchinson-Gilford type)"", ""lamin A/C-like 1"""	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1338T>C	1.37:g.156106185T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	37	CCDS1129.1	469	0.21474358974358973	347	0.7052845528455285	44	0.12154696132596685	10	0.017482517482517484	68	0.08970976253298153	C	10.16	1.275065	0.23307	0.601453	0.076001	ENSG00000160789	ENST00000292302	.	.	.	5.74	-5.0	0.03001	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4921	0.84205	0.0:0.2176:0.0:0.7824	rs505058;rs17847243;rs58351647;rs505058	.	.	.	.	-1	.	.	.	+	.	.	LMNA	154372809	0.110000	0.22057	0.908000	0.35775	0.984000	0.73092	-0.362000	0.07602	-1.095000	0.03050	-0.733000	0.03571	.	T|0.729;G|0.001	.	strong		0.602	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	
TRGC1	6966	hgsc.bcm.edu	37	7	38305142	38305142	+	RNA	SNP	G	G	C	rs113809137	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:38305142G>C	ENST00000443402.2	-	0	137					NM_001003799.1|NM_001003806.1	NP_001003799.1|NP_001003806.1	P0CF51	TRGC1_HUMAN	T cell receptor gamma constant 1							integral component of membrane (GO:0016021)											TTCTTTTCTTGCCAATGTATC	0.398													g|||	1036	0.206869	0.1596	0.1686	5008	,	,		17640	0.1944		0.2515	False		,,,				2504	0.2648				p.G42G		Atlas-SNP	.											.	.	.	.	0			c.C126G						PASS	.	G	,	601,3039		80,441,1299	167.0	173.0	171.0		126,	3.3	0.9	7	dbSNP_132	171	1903,6245		234,1435,2405	no	coding-synonymous,utr-5	TARP	NM_001003799.1,NM_001003806.1	,	314,1876,3704	CC,CG,GG		23.3554,16.511,21.2419	,	42/59,	38305142	2504,9284	1820	4074	5894			0	exon2			TTTCTTGCCAATG	M14996		7p14	2012-02-07			ENSG00000211689	ENSG00000211689		"""T cell receptors / TRG locus"""	12275	other	T cell receptor gene	"""T-cell receptor, gamma, constant region C1"""	186970		TCRGC1		2879283	Standard	NG_001336		Approved	C1		P0CF51	OTTHUMG00000155219		7.37:g.38305142G>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	239	118	0.493724	NM_001003799		Silent	SNP	ENST00000443402.2	37																																																																																				G|0.805;C|0.195	0.195	strong		0.398	TRGC1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	TR_C_gene	TR_C_gene	OTTHUMT00000338825.3	NG_001336	
SLFN13	146857	hgsc.bcm.edu	37	17	33768381	33768381	+	Missense_Mutation	SNP	T	T	C	rs115402160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:33768381T>C	ENST00000285013.6	-	6	2202	c.1927A>G	c.(1927-1929)Aga>Gga	p.R643G	SLFN13_ENST00000526861.1_Missense_Mutation_p.R643G|SLFN13_ENST00000533791.1_Missense_Mutation_p.R643G|SLFN13_ENST00000360502.2_Missense_Mutation_p.R325G|SLFN13_ENST00000542635.1_Missense_Mutation_p.R643G|SLFN13_ENST00000534689.1_Missense_Mutation_p.R325G	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	643						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CAGATATTTCTATCACTGTAA	0.383													T|||	33	0.00658946	0.0015	0.013	5008	,	,		17174	0.0		0.0119	False		,,,				2504	0.0102				p.R643G		Atlas-SNP	.											SLFN13,NS,carcinoma,+1,1	SLFN13	79	1	0			c.A1927G						PASS	.	T	GLY/ARG	12,4108		0,12,2048	38.0	45.0	43.0		1927	2.1	0.0	17	dbSNP_132	43	93,8417		1,91,4163	yes	missense	SLFN13	NM_144682.5	125	1,103,6211	CC,CT,TT		1.0928,0.2913,0.8314	benign	643/898	33768381	105,12525	2060	4255	6315	SO:0001583	missense	146857	exon6			TATTTCTATCACT	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.1927A>G	17.37:g.33768381T>C	ENSP00000285013:p.Arg643Gly	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	15	0.006868131868131868	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	8	0.010554089709762533	t	9.680	1.148994	0.21288	0.002913	0.010928	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16	3.29	2.07	0.26955	Domain of unknown function DUF2075 (1);	0.253739	0.28031	N	0.016877	T	0.65626	0.2709	L	0.36672	1.1	0.09310	N	1	B;B	0.26708	0.099;0.157	B;B	0.26969	0.075;0.042	T	0.66814	-0.5828	10	0.72032	D	0.01	.	5.9539	0.19263	0.0:0.0:0.2705:0.7295	.	325;643	Q68D06-2;Q68D06	.;SLN13_HUMAN	G	643;325;643;643;325	ENSP00000285013:R643G;ENSP00000353692:R325G;ENSP00000434439:R643G;ENSP00000444016:R643G;ENSP00000435442:R325G	ENSP00000285013:R643G	R	-	1	2	SLFN13	30792494	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-0.012000	0.12699	1.489000	0.48450	0.172000	0.16884	AGA	T|0.989;C|0.011	0.011	strong		0.383	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
ABCC3	8714	hgsc.bcm.edu	37	17	48765038	48765038	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48765038C>T	ENST00000285238.8	+	30	4502	c.4422C>T	c.(4420-4422)acC>acT	p.T1474T		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1474	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	AGTTTGATACCTGCACTGTCC	0.577																																					p.T1474T		Atlas-SNP	.											ABCC3,colon,carcinoma,0,1	ABCC3	138	1	0			c.C4422T						scavenged	.						180.0	132.0	148.0					17																	48765038		2203	4300	6503	SO:0001819	synonymous_variant	8714	exon30			TGATACCTGCACT	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.4422C>T	17.37:g.48765038C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	122	2	0.0163934	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			.	.	none		0.577	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10525230	10525230	+	Silent	SNP	T	T	C	rs34404959	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:10525230T>C	ENST00000396560.2	+	3	980	c.753T>C	c.(751-753)acT>acC	p.T251T	ATF7IP2_ENST00000324570.5_Silent_p.T251T|ATF7IP2_ENST00000356427.2_Silent_p.T251T|ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Silent_p.T251T	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	251					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						TTTTGAAAACTGATGAGTGTA	0.358													C|||	1214	0.242412	0.4713	0.2219	5008	,	,		20902	0.1577		0.1034	False		,,,				2504	0.1779				p.T251T		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.T753C						PASS	.	C		1806,2588	629.4+/-395.3	381,1044,772	73.0	72.0	72.0		753	-2.1	0.0	16	dbSNP_126	72	1010,7590	770.9+/-407.7	59,892,3349	no	coding-synonymous	ATF7IP2	NM_024997.2		440,1936,4121	CC,CT,TT		11.7442,41.1015,21.6715		251/683	10525230	2816,10178	2197	4300	6497	SO:0001819	synonymous_variant	80063	exon3			GAAAACTGATGAG	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.753T>C	16.37:g.10525230T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	212	112	0.528302	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Silent	SNP	ENST00000396560.2	37	CCDS10540.1																																																																																			T|0.795;C|0.205	0.205	strong		0.358	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
UIMC1	51720	hgsc.bcm.edu	37	5	176382995	176382995	+	Missense_Mutation	SNP	G	G	A	rs3733876	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:176382995G>A	ENST00000377227.4	-	8	1436	c.1304C>T	c.(1303-1305)cCa>cTa	p.P435L	UIMC1_ENST00000511320.1_Missense_Mutation_p.P435L|UIMC1_ENST00000503273.1_5'UTR|UIMC1_ENST00000506128.1_Missense_Mutation_p.P269L|UIMC1_ENST00000377219.2_Missense_Mutation_p.P435L			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	435	Necessary for interaction with NR6A1 C- terminus.		P -> L (common polymorphism not associated with susceptibility to breast cancer; dbSNP:rs3733876). {ECO:0000269|PubMed:18695986}.		double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGAACTCTCTGGCATAAGGAC	0.378													G|||	514	0.102636	0.0189	0.0879	5008	,	,		20269	0.1944		0.1571	False		,,,				2504	0.0757				p.P435L		Atlas-SNP	.											.	UIMC1	55	.	0			c.C1304T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	192,4214	121.7+/-159.2	4,184,2015	111.0	105.0	107.0		1304,1304,1304	5.5	1.0	5	dbSNP_107	107	1496,7104	284.7+/-296.8	142,1212,2946	yes	missense,missense,missense	UIMC1	NM_001199297.1,NM_001199298.1,NM_016290.4	98,98,98	146,1396,4961	AA,AG,GG		17.3953,4.3577,12.9786	probably-damaging,probably-damaging,probably-damaging	435/720,435/720,435/720	176382995	1688,11318	2203	4300	6503	SO:0001583	missense	51720	exon8			CTCTCTGGCATAA	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"""receptor associated protein 80"""	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.1304C>T	5.37:g.176382995G>A	ENSP00000366434:p.Pro435Leu	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	252	248	0.984127	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Missense_Mutation	SNP	ENST00000377227.4	37	CCDS4408.1	279	0.12774725274725274	14	0.028455284552845527	38	0.10497237569060773	99	0.17307692307692307	128	0.16886543535620052	G	12.80	2.047947	0.36085	0.043577	0.173953	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000506128;ENST00000377220;ENST00000323774	T;T;T;T	0.13901	2.58;2.58;2.58;2.55	5.53	5.53	0.82687	.	0.106427	0.40818	N	0.001018	T	0.00073	0.0002	L	0.43152	1.355	0.22034	P	0.999408074	D;D;D;D;P	0.89917	0.96;1.0;0.986;0.977;0.928	P;D;P;P;P	0.91635	0.55;0.999;0.775;0.73;0.494	T	0.00657	-1.1623	9	0.59425	D	0.04	.	15.1875	0.73016	0.0:0.1397:0.8603:0.0	rs3733876;rs52809311;rs56465845;rs58246171;rs3733876	435;154;269;65;357	Q96RL1;D6RCF3;C9JR12;Q96RL1-4;Q96RL1-3	UIMC1_HUMAN;.;.;.;.	L	435;435;435;269;357;65	ENSP00000366434:P435L;ENSP00000366425:P435L;ENSP00000421926:P435L;ENSP00000427480:P269L	ENSP00000314909:P65L	P	-	2	0	UIMC1	176315601	1.000000	0.71417	0.990000	0.47175	0.754000	0.42855	2.389000	0.44407	2.775000	0.95449	0.650000	0.86243	CCA	G|0.879;A|0.121	0.121	strong		0.378	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290	
BTBD11	121551	hgsc.bcm.edu	37	12	108035903	108035903	+	Silent	SNP	T	T	C	rs9919712	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:108035903T>C	ENST00000280758.5	+	14	3405	c.2877T>C	c.(2875-2877)gaT>gaC	p.D959D	BTBD11_ENST00000490090.2_Silent_p.D959D|BTBD11_ENST00000494235.2_Silent_p.D38D|BTBD11_ENST00000357167.4_Silent_p.D496D|BTBD11_ENST00000420571.2_Silent_p.D840D	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	959	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CGACAAATGATGGCACCTGCA	0.478													t|||	980	0.195687	0.3835	0.1383	5008	,	,		19176	0.003		0.1948	False		,,,				2504	0.182				p.D959D		Atlas-SNP	.											.	BTBD11	122	.	0			c.T2877C						PASS	.	T	,	1441,2965	468.1+/-355.0	215,1011,977	159.0	148.0	152.0		1488,2877	2.0	1.0	12	dbSNP_119	152	1624,6976	302.0+/-305.7	146,1332,2822	no	coding-synonymous,coding-synonymous	BTBD11	NM_001017523.1,NM_001018072.1	,	361,2343,3799	CC,CT,TT		18.8837,32.7054,23.566	,	496/642,959/1105	108035903	3065,9941	2203	4300	6503	SO:0001819	synonymous_variant	121551	exon14			AAATGATGGCACC	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2877T>C	12.37:g.108035903T>C		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	203	91	0.448276	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	37	CCDS31893.1																																																																																			T|0.779;C|0.221	0.221	strong		0.478	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
DOK7	285489	hgsc.bcm.edu	37	4	3494898	3494898	+	Silent	SNP	C	C	T	rs6850908	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:3494898C>T	ENST00000340083.5	+	7	1250	c.1185C>T	c.(1183-1185)taC>taT	p.Y395Y	DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR|DOK7_ENST00000389653.2_Silent_p.Y395Y	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	395					neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CAGTCGAGTACCAGGTGCCCA	0.692													.|||	1100	0.219649	0.0386	0.1441	5008	,	,		14813	0.502		0.2237	False		,,,				2504	0.2229				p.Y395Y		Atlas-SNP	.											DOK7,NS,carcinoma,0,1	DOK7	44	1	0			c.C1185T						PASS	.	C	,	291,4089		15,261,1914	15.0	15.0	15.0		,1185	2.8	1.0	4	dbSNP_116	15	1780,6802		194,1392,2705	yes	utr-3,coding-synonymous	DOK7	NM_001164673.1,NM_173660.4	,	209,1653,4619	TT,TC,CC		20.7411,6.6438,15.9775	,	,395/505	3494898	2071,10891	2190	4291	6481	SO:0001819	synonymous_variant	285489	exon7			CGAGTACCAGGTG	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.1185C>T	4.37:g.3494898C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_173660	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Silent	SNP	ENST00000340083.5	37	CCDS3370.2																																																																																			C|0.794;T|0.206	0.206	strong		0.692	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
TCOF1	6949	hgsc.bcm.edu	37	5	149754991	149754991	+	Silent	SNP	C	C	T	rs2071238	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149754991C>T	ENST00000504761.2	+	11	1578	c.1578C>T	c.(1576-1578)ccC>ccT	p.P526P	TCOF1_ENST00000439160.2_Silent_p.P526P|TCOF1_ENST00000394269.3_Silent_p.P526P|TCOF1_ENST00000513346.1_Silent_p.P526P|TCOF1_ENST00000377797.3_Silent_p.P526P|TCOF1_ENST00000451292.1_Silent_p.P526P|TCOF1_ENST00000445265.2_Silent_p.P449P|TCOF1_ENST00000323668.7_Silent_p.P449P			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	526					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAGTGCCACCCGGGAAGGTGG	0.642													T|||	795	0.158746	0.2383	0.0922	5008	,	,		17107	0.1448		0.1292	False		,,,				2504	0.1431				p.P526P		Atlas-SNP	.											.	TCOF1	154	.	0			c.C1578T						PASS	.	T	,,,,,	1034,3372	713.5+/-408.2	112,810,1281	46.0	52.0	50.0		1347,1578,1578,1578,1347,1578	0.8	0.0	5	dbSNP_96	50	1351,7249	746.9+/-407.3	90,1171,3039	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	,,,,,	202,1981,4320	TT,TC,CC		15.7093,23.468,18.3377	,,,,,	449/1412,526/959,526/1489,526/1452,449/1413,526/1451	149754991	2385,10621	2203	4300	6503	SO:0001819	synonymous_variant	6949	exon11			GCCACCCGGGAAG		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.1578C>T	5.37:g.149754991C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Silent	SNP	ENST00000504761.2	37	CCDS54936.1																																																																																			C|0.836;T|0.164	0.164	strong		0.642	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
OMA1	115209	hgsc.bcm.edu	37	1	58999651	58999651	+	Missense_Mutation	SNP	T	T	G	rs17117678	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:58999651T>G	ENST00000371226.3	-	5	1098	c.985A>C	c.(985-987)Ata>Cta	p.I329L	OMA1_ENST00000358603.2_Missense_Mutation_p.I329L|OMA1_ENST00000467063.1_5'Flank|DAB1_ENST00000485760.1_Intron	NM_145243.3	NP_660286.1	Q96E52	OMA1_HUMAN	OMA1 zinc metallopeptidase	329			I -> L (in dbSNP:rs17117678). {ECO:0000269|PubMed:21220648}.		cristae formation (GO:0042407)|diet induced thermogenesis (GO:0002024)|energy homeostasis (GO:0097009)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrial protein processing (GO:0034982)|negative regulation of mitochondrial fusion (GO:0010637)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(1)|large_intestine(6)|liver(2)|lung(6)|prostate(1)|skin(1)	18	all_cancers(7;6.54e-05)					GCATGTGCTATTTCATGGCCC	0.338													T|||	512	0.102236	0.2224	0.0908	5008	,	,		16634	0.004		0.1103	False		,,,				2504	0.0409				p.I329L		Atlas-SNP	.											.	OMA1	50	.	0			c.A985C						PASS	.	T	LEU/ILE	761,3645	309.1+/-290.9	62,637,1504	104.0	104.0	104.0		985	2.4	1.0	1	dbSNP_123	104	942,7658	207.2+/-249.0	48,846,3406	yes	missense	OMA1	NM_145243.3	5	110,1483,4910	GG,GT,TT		10.9535,17.2719,13.094	benign	329/525	58999651	1703,11303	2203	4300	6503	SO:0001583	missense	115209	exon5			GTGCTATTTCATG	AK091101	CCDS608.1	1p32.2-p32.1	2013-05-03	2013-05-03		ENSG00000162600	ENSG00000162600			29661	protein-coding gene	gene with protein product	"""overlapping activity with M-AAA protease"", ""zinc metallopeptidase OMA1"""		"""OMA1 zinc metallopeptidase homolog (S. cerevisiae)"""			12477932	Standard	NM_145243		Approved	MPRP-1, YKR087C, ZMPOMA1, FLJ33782	uc001cyy.3	Q96E52	OTTHUMG00000010068	ENST00000371226.3:c.985A>C	1.37:g.58999651T>G	ENSP00000360270:p.Ile329Leu	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	178	95	0.533708	NM_145243	D3DQ54|Q5T3G6|Q5T3G7|Q5T3G8|Q5T3G9|Q5T3H0|Q8NBB3	Missense_Mutation	SNP	ENST00000371226.3	37	CCDS608.1	219|219	0.10027472527472528|0.10027472527472528	101|101	0.20528455284552846|0.20528455284552846	40|40	0.11049723756906077|0.11049723756906077	0|0	0.0|0.0	78|78	0.10290237467018469|0.10290237467018469	T|T	13.86|13.86	2.362500|2.362500	0.41902|0.41902	0.172719|0.172719	0.109535|0.109535	ENSG00000162600|ENSG00000162600	ENST00000358603;ENST00000371226|ENST00000421528	T;T|.	0.72725|.	-0.68;-0.68|.	4.84|4.84	2.43|2.43	0.29744|0.29744	.|.	0.151018|.	0.64402|.	D|.	0.000017|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.49640|0.49640	1.575|1.575	0.09310|0.09310	P|P	0.9999999999999997|0.9999999999999997	B;B|.	0.33448|.	0.412;0.194|.	B;B|.	0.34301|.	0.179;0.143|.	T|T	0.11591|0.11591	-1.0581|-1.0581	9|4	0.62326|.	D|.	0.03|.	-14.64|-14.64	3.2378|3.2378	0.06771|0.06771	0.137:0.0757:0.1426:0.6448|0.137:0.0757:0.1426:0.6448	rs17117678;rs17117678|rs17117678;rs17117678	329;329|.	Q96E52;Q96E52-2|.	OMA1_HUMAN;.|.	L|T	329|170	ENSP00000351417:I329L;ENSP00000360270:I329L|.	ENSP00000351417:I329L|.	I|N	-|-	1|2	0|0	OMA1|OMA1	58772239|58772239	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	3.313000|3.313000	0.51935|0.51935	0.862000|0.862000	0.35528|0.35528	-0.460000|-0.460000	0.05396|0.05396	ATA|AAT	T|0.883;G|0.117	0.117	strong		0.338	OMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027819.1	NM_145243	
WLS	79971	hgsc.bcm.edu	37	1	68614320	68614320	+	Silent	SNP	G	G	A	rs17130529	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:68614320G>A	ENST00000262348.4	-	7	1249	c.996C>T	c.(994-996)atC>atT	p.I332I	WLS_ENST00000370976.3_Silent_p.I241I|GNG12-AS1_ENST00000420587.1_RNA|WLS_ENST00000491811.1_5'UTR|GNG12-AS1_ENST00000413628.1_RNA|WLS_ENST00000354777.2_Silent_p.I330I|WLS_ENST00000540432.1_Silent_p.I332I	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	332					anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						AATACCCTGCGATGTGGTTCC	0.507													A|||	301	0.0601038	0.0847	0.0461	5008	,	,		21430	0.0625		0.0477	False		,,,				2504	0.047				p.I332I		Atlas-SNP	.											.	WLS	97	.	0			c.C996T						PASS	.	A	,,	377,4029	791.7+/-415.1	18,341,1844	137.0	91.0	106.0		990,723,996	-3.5	0.9	1	dbSNP_123	106	380,8220	802.1+/-407.4	6,368,3926	yes	coding-synonymous,coding-synonymous,coding-synonymous	WLS	NM_001002292.3,NM_001193334.1,NM_024911.6	,,	24,709,5770	AA,AG,GG		4.4186,8.5565,5.8204	,,	330/544,241/451,332/542	68614320	757,12249	2203	4300	6503	SO:0001819	synonymous_variant	79971	exon7			CCCTGCGATGTGG	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"""wntless homolog"""	611514	"""chromosome 1 open reading frame 139"", ""G protein-coupled receptor 177"", ""wntless homolog (Drosophila)"""	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.996C>T	1.37:g.68614320G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	99	61	0.616162	NM_024911	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Silent	SNP	ENST00000262348.4	37	CCDS642.1																																																																																			G|0.937;A|0.063	0.063	strong		0.507	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911	
DAAM1	23002	hgsc.bcm.edu	37	14	59792755	59792755	+	Silent	SNP	G	G	A	rs61755642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:59792755G>A	ENST00000395125.1	+	9	1157	c.1134G>A	c.(1132-1134)ccG>ccA	p.P378P	DAAM1_ENST00000360909.3_Silent_p.P378P|DAAM1_ENST00000351081.1_Silent_p.P378P	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	378	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AAGCTTACCCGCATTTCATGT	0.443													G|||	9	0.00179712	0.0	0.0014	5008	,	,		19975	0.0		0.007	False		,,,				2504	0.001				p.P378P		Atlas-SNP	.											.	DAAM1	95	.	0			c.G1134A						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	161.0	122.0	135.0		1134	-0.9	1.0	14	dbSNP_129	135	54,8546	35.3+/-89.8	0,54,4246	no	coding-synonymous	DAAM1	NM_014992.1		0,59,6444	AA,AG,GG		0.6279,0.1135,0.4536		378/1079	59792755	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon10			TTACCCGCATTTC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.1134G>A	14.37:g.59792755G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	192	101	0.526042	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.995;A|0.005	0.005	strong		0.443	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
PSEN2	5664	hgsc.bcm.edu	37	1	227069737	227069737	+	Silent	SNP	C	C	T	rs6759	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:227069737C>T	ENST00000366783.3	+	4	565	c.129C>T	c.(127-129)aaC>aaT	p.N43N	PSEN2_ENST00000366782.1_Silent_p.N76N|PSEN2_ENST00000391872.2_Silent_p.N76N|PSEN2_ENST00000340188.4_Silent_p.N43N|PSEN2_ENST00000422240.2_Silent_p.N43N|PSEN2_ENST00000472139.2_5'Flank	NM_000447.2|NM_012486.2	NP_000438.2|NP_036618.2	P49810	PSN2_HUMAN	presenilin 2	43					amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|brain morphogenesis (GO:0048854)|calcium ion transport (GO:0006816)|cardiac muscle contraction (GO:0060048)|cell fate specification (GO:0001708)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|forebrain development (GO:0030900)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|locomotion (GO:0040011)|lung alveolus development (GO:0048286)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|memory (GO:0007613)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of protein phosphorylation (GO:0001933)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of synaptic plasticity (GO:0048167)|response to hypoxia (GO:0001666)|somitogenesis (GO:0001756)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear inner membrane (GO:0005637)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|urinary_tract(1)	20		Prostate(94;0.0771)				ATGGAGAGAACACTGCCCAGT	0.597													C|||	2220	0.443291	0.3646	0.4827	5008	,	,		19385	0.3859		0.5934	False		,,,				2504	0.4264				p.N43N		Atlas-SNP	.											.	PSEN2	55	.	0			c.C129T						PASS	.	C	,	1733,2673	506.2+/-366.3	342,1049,812	34.0	35.0	35.0		129,129	-6.8	0.0	1	dbSNP_52	35	4633,3965	585.4+/-391.9	1271,2091,937	no	coding-synonymous,coding-synonymous	PSEN2	NM_000447.2,NM_012486.2	,	1613,3140,1749	TT,TC,CC		46.1154,39.3327,48.9542	,	43/449,43/448	227069737	6366,6638	2203	4299	6502	SO:0001819	synonymous_variant	5664	exon4			AGAGAACACTGCC	BC006365	CCDS1556.1, CCDS44324.1	1q42.13	2014-09-17	2014-02-24		ENSG00000143801	ENSG00000143801			9509	protein-coding gene	gene with protein product		600759	"""Alzheimer disease 4"""	AD4		7638621	Standard	NM_000447		Approved	AD3L, STM2, PS2	uc009xeo.1	P49810	OTTHUMG00000037563	ENST00000366783.3:c.129C>T	1.37:g.227069737C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	86	83	0.965116	NM_012486	A8K8D4|B1AP21|Q96P32	Silent	SNP	ENST00000366783.3	37	CCDS1556.1																																																																																			C|0.520;T|0.480	0.480	strong		0.597	PSEN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091539.1	NM_000447	
OR5K2	402135	hgsc.bcm.edu	37	3	98217178	98217178	+	Nonsense_Mutation	SNP	T	T	A	rs55639376	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:98217178T>A	ENST00000427338.1	+	1	731	c.654T>A	c.(652-654)taT>taA	p.Y218*	CLDND1_ENST00000502288.1_Intron	NM_001004737.1	NP_001004737.1	Q8NHB8	OR5K2_HUMAN	olfactory receptor, family 5, subfamily K, member 2	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TAATATCTTATCTCTATATTC	0.368													T|||	620	0.123802	0.1422	0.1412	5008	,	,		19030	0.0526		0.16	False		,,,				2504	0.1227				p.Y218X		Atlas-SNP	.											.	OR5K2	56	.	0			c.T654A						PASS	.	T	stop/TYR	596,3810	260.7+/-263.8	42,512,1649	132.0	131.0	131.0		654	-2.8	0.0	3	dbSNP_129	131	1581,7017	293.4+/-301.3	156,1269,2874	no	stop-gained	OR5K2	NM_001004737.1		198,1781,4523	AA,AT,TT		18.388,13.527,16.741		218/317	98217178	2177,10827	2203	4299	6502	SO:0001587	stop_gained	402135	exon1			ATCTTATCTCTAT	AC021660	CCDS33804.1	3q11.2	2013-09-23			ENSG00000231861	ENSG00000231861		"""GPCR / Class A : Olfactory receptors"""	14774	protein-coding gene	gene with protein product							Standard	NM_001004737		Approved		uc011bgx.2	Q8NHB8	OTTHUMG00000160049	ENST00000427338.1:c.654T>A	3.37:g.98217178T>A	ENSP00000393889:p.Tyr218*	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	219	109	0.497717	NM_001004737	B2RN70|Q6IF47	Nonsense_Mutation	SNP	ENST00000427338.1	37	CCDS33804.1	278	0.12728937728937728	66	0.13414634146341464	62	0.1712707182320442	39	0.06818181818181818	111	0.14643799472295516	T	10.46	1.356721	0.24598	0.13527	0.18388	ENSG00000231861	ENST00000427338	.	.	.	2.82	-2.78	0.05859	.	0.000000	0.38959	N	0.001505	.	.	.	.	.	.	0.39546	P	0.031106999999999996	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.3632	9.4431	0.38681	0.0:0.6126:0.0:0.3874	rs55639376;rs61750892	.	.	.	X	218	.	ENSP00000393889:Y218X	Y	+	3	2	OR5K2	99699868	0.000000	0.05858	0.002000	0.10522	0.203000	0.24098	-2.229000	0.01208	-0.629000	0.05575	0.260000	0.18958	TAT	T|0.847;A|0.153	0.153	strong		0.368	OR5K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359020.2		
PCK1	5105	hgsc.bcm.edu	37	20	56137184	56137184	+	Silent	SNP	C	C	T	rs6070157	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:56137184C>T	ENST00000319441.4	+	3	446	c.282C>T	c.(280-282)atC>atT	p.I94I	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Intron	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	94					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			AGACGGTTATCGTCACCCAAG	0.547													C|||	612	0.122204	0.1483	0.1167	5008	,	,		19900	0.0159		0.174	False		,,,				2504	0.1472				p.I94I		Atlas-SNP	.											.	PCK1	95	.	0			c.C282T						PASS	.	C		588,3818	256.1+/-261.0	37,514,1652	102.0	89.0	94.0		282	2.5	0.2	20	dbSNP_114	94	1686,6914	309.6+/-309.4	176,1334,2790	no	coding-synonymous	PCK1	NM_002591.3		213,1848,4442	TT,TC,CC		19.6047,13.3454,17.4842		94/623	56137184	2274,10732	2203	4300	6503	SO:0001819	synonymous_variant	5105	exon3			GGTTATCGTCACC		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.282C>T	20.37:g.56137184C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			C|0.851;T|0.149	0.149	strong		0.547	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
ZFYVE28	57732	hgsc.bcm.edu	37	4	2341194	2341194	+	Silent	SNP	T	T	C	rs2071680	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:2341194T>C	ENST00000290974.2	-	4	846	c.507A>G	c.(505-507)gcA>gcG	p.A169A	ZFYVE28_ENST00000509171.1_Silent_p.A122A|ZFYVE28_ENST00000511071.1_Silent_p.A169A|ZFYVE28_ENST00000515312.1_Silent_p.A99A|ZFYVE28_ENST00000503000.1_Silent_p.A169A|ZFYVE28_ENST00000515169.1_Silent_p.A99A	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	169					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						GCTCAAACTCTGCGAACAGGA	0.622													c|||	3216	0.642173	0.6944	0.7075	5008	,	,		18243	0.6994		0.5815	False		,,,				2504	0.5286				p.A169A		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.A507G						PASS	.	C	,,,,,	2989,1417	461.5+/-352.9	1012,965,226	87.0	68.0	74.0		507,507,366,297,297,507	-9.0	0.0	4	dbSNP_96	74	4916,3684	524.1+/-380.5	1407,2102,791	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZFYVE28	NM_001172656.1,NM_001172657.1,NM_001172658.1,NM_001172659.1,NM_001172660.1,NM_020972.2	,,,,,	2419,3067,1017	CC,CT,TT		42.8372,32.1607,39.2204	,,,,,	169/858,169/288,122/173,99/818,99/164,169/888	2341194	7905,5101	2203	4300	6503	SO:0001819	synonymous_variant	57732	exon4			AAACTCTGCGAAC	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"""Zinc fingers, FYVE domain containing"""	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.507A>G	4.37:g.2341194T>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	179	82	0.458101	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Silent	SNP	ENST00000290974.2	37	CCDS33942.1																																																																																			T|0.375;C|0.625	0.625	strong		0.622	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2929392	2929392	+	Silent	SNP	G	G	A	rs55904912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:2929392G>A	ENST00000254695.8	+	20	1932	c.1842G>A	c.(1840-1842)ccG>ccA	p.P614P	RAP1GAP2_ENST00000540393.2_Silent_p.P595P|RAP1GAP2_ENST00000542807.1_Silent_p.P614P|RAP1GAP2_ENST00000366401.4_Silent_p.P599P	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	614	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)	p.P614P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CCAGCTCTCCGGAAATCTGCC	0.577													G|||	2146	0.428514	0.2451	0.4986	5008	,	,		16508	0.5466		0.4066	False		,,,				2504	0.5276				p.P614P		Atlas-SNP	.											RAP1GAP2_ENST00000254695,NS,carcinoma,0,2	RAP1GAP2	90	2	1	Substitution - coding silent(1)	stomach(1)	c.G1842A						PASS	.	G	,	1082,2966		152,778,1094	45.0	48.0	47.0		1797,1842	-7.4	1.0	17	dbSNP_129	47	3415,4945		687,2041,1452	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	839,2819,2546	AA,AG,GG		40.8493,26.7292,36.2427	,	599/716,614/731	2929392	4497,7911	2024	4180	6204	SO:0001819	synonymous_variant	23108	exon20			CTCTCCGGAAATC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1842G>A	17.37:g.2929392G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	262	119	0.454198	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			G|0.579;A|0.421	0.421	strong		0.577	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
EPSTI1	94240	hgsc.bcm.edu	37	13	43462422	43462422	+	IGR	SNP	A	A	T	rs1044856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:43462422A>T	ENST00000398762.3	-	0	957				EPSTI1_ENST00000313624.7_3'UTR|EPSTI1_ENST00000313640.7_Missense_Mutation_p.N399K			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)											endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		GGCAGTAGAGATTAAATATGA	0.423													A|||	788	0.157348	0.0182	0.2003	5008	,	,		17038	0.126		0.3419	False		,,,				2504	0.1575				p.N399K		Atlas-SNP	.											.	EPSTI1	47	.	0			c.T1197A						PASS	.	A	LYS/ASN,	290,4116	159.2+/-191.8	15,260,1928	87.0	87.0	87.0		1197,	-0.1	0.0	13	dbSNP_86	87	2934,5666	456.7+/-364.1	503,1928,1869	yes	missense,utr-3	EPSTI1	NM_001002264.1,NM_033255.2	94,	518,2188,3797	TT,TA,AA		34.1163,6.5819,24.7886	probably-damaging,	399/411,	43462422	3224,9782	2203	4300	6503	SO:0001628	intergenic_variant	94240	exon13			GTAGAGATTAAAT	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"""epithelial stromal interaction protein 1"""	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814		13.37:g.43462422A>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	133	10	0.075188	NM_001002264	Q8IVC7|Q8NDQ7	Missense_Mutation	SNP	ENST00000398762.3	37	CCDS9387.1	407	0.18635531135531136	12	0.024390243902439025	82	0.2265193370165746	62	0.10839160839160839	251	0.3311345646437995	A	16.66	3.184624	0.57909	0.065819	0.341163	ENSG00000133106	ENST00000313640	.	.	.	5.2	-0.0576	0.13800	.	0.505521	0.16647	N	0.205374	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999421063	D	0.63046	0.992	P	0.60541	0.876	T	0.15780	-1.0425	7	0.87932	D	0	-3.571	7.6816	0.28518	0.621:0.0:0.379:0.0	rs1044856;rs3184675;rs56461472;rs1044856	399	Q96J88-3	.	K	399	.	ENSP00000318982:N399K	N	-	3	2	EPSTI1	42360422	1.000000	0.71417	0.028000	0.17463	0.596000	0.36781	1.479000	0.35453	-0.144000	0.11314	0.533000	0.62120	AAT	A|0.789;T|0.211	0.211	strong		0.423	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264	
ALG1	56052	hgsc.bcm.edu	37	16	5128817	5128817	+	Missense_Mutation	SNP	G	G	A	rs17849848	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:5128817G>A	ENST00000262374.5	+	7	831	c.800G>A	c.(799-801)aGc>aAc	p.S267N	ALG1_ENST00000588623.1_Missense_Mutation_p.S156N|ALG1_ENST00000544428.1_Missense_Mutation_p.S156N	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	267			S -> N (in dbSNP:rs17849848). {ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				GATGCTGGGAGCGGGCTGGTG	0.642													G|||	364	0.0726837	0.0061	0.1571	5008	,	,		16094	0.128		0.0815	False		,,,				2504	0.0368				p.S267N		Atlas-SNP	.											ALG1,NS,haematopoietic_neoplasm,-1,1	ALG1	35	1	0			c.G800A						PASS	.	G	ASN/SER	60,4334		1,58,2138	29.0	31.0	30.0		800	3.3	0.0	16	dbSNP_123	30	733,7863		38,657,3603	no	missense	ALG1	NM_019109.4	46	39,715,5741	AA,AG,GG		8.5272,1.3655,6.1047	benign	267/465	5128817	793,12197	2197	4298	6495	SO:0001583	missense	56052	exon7			CTGGGAGCGGGCT	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.800G>A	16.37:g.5128817G>A	ENSP00000262374:p.Ser267Asn	Somatic	370	0	0		WXS	Illumina HiSeq	Phase_I	366	183	0.5	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	210	0.09615384615384616	6	0.012195121951219513	52	0.143646408839779	79	0.1381118881118881	73	0.09630606860158311	G	8.409	0.843640	0.16963	0.013655	0.085272	ENSG00000033011	ENST00000262374;ENST00000544428	T;T	0.77229	-1.08;-1.07	5.32	3.29	0.37713	.	0.411911	0.31554	N	0.007450	T	0.00845	0.0028	L	0.45051	1.395	0.80722	P	0.0	B;B	0.10296	0.003;0.002	B;B	0.12156	0.002;0.007	T	0.14980	-1.0453	9	0.09338	T	0.73	-15.871	7.5941	0.28037	0.0858:0.3124:0.6018:0.0	rs17849848;rs60659731	156;267	B4DP08;Q9BT22	.;ALG1_HUMAN	N	267;156	ENSP00000262374:S267N;ENSP00000440019:S156N	ENSP00000262374:S267N	S	+	2	0	ALG1	5068818	0.041000	0.20044	0.006000	0.13384	0.004000	0.04260	0.415000	0.21181	0.585000	0.29608	0.555000	0.69702	AGC	G|0.925;A|0.075	0.075	strong		0.642	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
RAI1	10743	hgsc.bcm.edu	37	17	17697102	17697102	+	Silent	SNP	G	G	A	rs398124422|rs34083643|rs398124421|rs587780431		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17697102G>A	ENST00000353383.1	+	3	1309	c.840G>A	c.(838-840)caG>caA	p.Q280Q	RAI1_ENST00000261641.6_Silent_p.Q280Q	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	280	Gln-rich.|Poly-Gln.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)	p.Q280fs*84(1)		breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ACcagcagcagcagcagcagc	0.627																																					p.Q280Q		Atlas-SNP	.											RAI1,colon,carcinoma,0,3	RAI1	121	3	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.G840A						scavenged	.						20.0	25.0	23.0					17																	17697102		2038	4033	6071	SO:0001819	synonymous_variant	10743	exon3			GCAGCAGCAGCAG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.840G>A	17.37:g.17697102G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	92	5	0.0543478	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			.	.	none		0.627	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
EXPH5	23086	hgsc.bcm.edu	37	11	108409784	108409784	+	Missense_Mutation	SNP	T	T	A	rs2640785	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:108409784T>A	ENST00000265843.4	-	3	520	c.410A>T	c.(409-411)gAg>gTg	p.E137V	EXPH5_ENST00000428840.1_Missense_Mutation_p.E61V|EXPH5_ENST00000525344.1_Missense_Mutation_p.E130V|EXPH5_ENST00000443411.1_5'Flank|EXPH5_ENST00000524840.1_5'Flank	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	137			E -> V (in dbSNP:rs2640785).		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTTTGAAGTCTCCTTTCCAGA	0.433													T|||	1264	0.252396	0.0393	0.3501	5008	,	,		17701	0.5804		0.17	False		,,,				2504	0.2178				p.E137V		Atlas-SNP	.											.	EXPH5	193	.	0			c.A410T						PASS	.	T	VAL/GLU	281,4121	156.6+/-189.7	4,273,1924	144.0	141.0	142.0		410	5.0	0.8	11	dbSNP_100	142	1462,7134	279.8+/-294.2	141,1180,2977	yes	missense	EXPH5	NM_015065.2	121	145,1453,4901	AA,AT,TT		17.0079,6.3835,13.4098	probably-damaging	137/1990	108409784	1743,11255	2201	4298	6499	SO:0001583	missense	23086	exon3			GAAGTCTCCTTTC		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.410A>T	11.37:g.108409784T>A	ENSP00000265843:p.Glu137Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	124	65	0.524194	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	638	0.29212454212454214	31	0.06300813008130081	111	0.30662983425414364	356	0.6223776223776224	140	0.18469656992084432	T	22.7	4.322784	0.81580	0.063835	0.170079	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000525344;ENST00000526312;ENST00000531386	T;T;T;T;T	0.40756	3.92;3.84;3.92;3.74;1.02	4.99	4.99	0.66335	.	0.347910	0.24755	N	0.035872	T	0.00012	0.0000	M	0.69823	2.125	0.09310	P	1.0	D	0.61080	0.989	P	0.58266	0.836	T	0.50013	-0.8877	9	0.87932	D	0	-6.9937	11.3852	0.49780	0.0:0.0:0.0:1.0	rs2640785;rs3741047;rs52819845;rs2640785	137	Q8NEV8	EXPH5_HUMAN	V	137;61;130;61;61	ENSP00000265843:E137V;ENSP00000391966:E61V;ENSP00000432546:E130V;ENSP00000432683:E61V;ENSP00000433909:E61V	ENSP00000265843:E137V	E	-	2	0	EXPH5	107914994	0.997000	0.39634	0.799000	0.32177	0.948000	0.59901	4.094000	0.57721	2.012000	0.59069	0.528000	0.53228	GAG	T|0.797;A|0.203	0.203	strong		0.433	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
ABCB5	340273	hgsc.bcm.edu	37	7	20762646	20762646	+	Missense_Mutation	SNP	G	G	T	rs62453384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:20762646G>T	ENST00000404938.2	+	21	3081	c.2429G>T	c.(2428-2430)gGt>gTt	p.G810V	ABCB5_ENST00000258738.6_Missense_Mutation_p.G365V	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	810	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						TAGGCAACAGGTTCCAGGATT	0.353													G|||	1163	0.232228	0.1142	0.1945	5008	,	,		16136	0.1855		0.3608	False		,,,				2504	0.3344				p.G810V		Atlas-SNP	.											ABCB5,NS,carcinoma,+1,1	ABCB5	357	1	0			c.G2429T						scavenged	.	G	VAL/GLY,VAL/GLY	621,3785	268.0+/-268.2	47,527,1629	142.0	138.0	140.0		2429,1094	3.8	1.0	7	dbSNP_129	140	3269,5331	489.7+/-372.7	606,2057,1637	yes	missense,missense	ABCB5	NM_001163941.1,NM_178559.5	109,109	653,2584,3266	TT,TG,GG		38.0116,14.0944,29.9093	possibly-damaging,possibly-damaging	810/1258,365/813	20762646	3890,9116	2203	4300	6503	SO:0001583	missense	340273	exon21			CAACAGGTTCCAG	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"""ATP binding cassette transporters / subfamily B"""	46	protein-coding gene	gene with protein product	"""P-glycoprotein ABCB5"", ""ATP-binding cassette protein"""	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.2429G>T	7.37:g.20762646G>T	ENSP00000384881:p.Gly810Val	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	113	48	0.424779	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	515	0.2358058608058608	56	0.11382113821138211	84	0.23204419889502761	116	0.20279720279720279	259	0.341688654353562	G	17.37	3.371456	0.61624	0.140944	0.380116	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.90900	-2.75;-2.75	4.75	3.84	0.44239	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.224289	0.30401	N	0.009703	T	0.00012	0.0000	M	0.91300	3.195	0.09310	P	0.9999999509414	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.992	T	0.00000	-1.5246	9	0.87932	D	0	.	12.6345	0.56675	0.0:0.1751:0.8249:0.0	rs62453384	810;365	A7BKA4;Q2M3G0	.;ABCB5_HUMAN	V	810;365	ENSP00000384881:G810V;ENSP00000258738:G365V	ENSP00000258738:G365V	G	+	2	0	ABCB5	20729171	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	3.961000	0.56759	1.318000	0.45170	0.655000	0.94253	GGT	G|0.714;T|0.286	0.286	strong		0.353	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
FAT2	2196	hgsc.bcm.edu	37	5	150942969	150942969	+	Missense_Mutation	SNP	G	G	A	rs2304053	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150942969G>A	ENST00000261800.5	-	2	3503	c.3491C>T	c.(3490-3492)cCa>cTa	p.P1164L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1164	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> L (in dbSNP:rs2304053).		epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCTGGAGTCTGGGTCCCAGGC	0.527													G|||	1821	0.363618	0.2965	0.4308	5008	,	,		19033	0.3135		0.4851	False		,,,				2504	0.3333				p.P1164L		Atlas-SNP	.											.	FAT2	465	.	0			c.C3491T						PASS	.	G	LEU/PRO	1455,2951	471.7+/-356.1	262,931,1010	111.0	107.0	108.0		3491	2.1	1.0	5	dbSNP_100	108	4426,4174	587.5+/-392.2	1146,2134,1020	yes	missense	FAT2	NM_001447.2	98	1408,3065,2030	AA,AG,GG		48.5349,33.0232,45.2176	benign	1164/4350	150942969	5881,7125	2203	4300	6503	SO:0001583	missense	2196	exon2			GAGTCTGGGTCCC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3491C>T	5.37:g.150942969G>A	ENSP00000261800:p.Pro1164Leu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	173	170	0.982659	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	851	0.38965201465201466	159	0.3231707317073171	151	0.4171270718232044	176	0.3076923076923077	365	0.4815303430079156	G	13.52	2.262454	0.39995	0.330232	0.514651	ENSG00000086570	ENST00000261800	T	0.60672	0.17	5.03	2.07	0.26955	Cadherin (4);Cadherin-like (1);	0.204986	0.34652	N	0.003789	T	0.00012	0.0000	L	0.41961	1.31	0.20764	P	0.999852395	P	0.41498	0.752	B	0.41764	0.366	T	0.49418	-0.8942	9	0.25751	T	0.34	.	7.4677	0.27330	0.1455:0.0:0.7199:0.1346	rs2304053;rs17661383;rs52833409;rs58031114;rs2304053	1164	Q9NYQ8	FAT2_HUMAN	L	1164	ENSP00000261800:P1164L	ENSP00000261800:P1164L	P	-	2	0	FAT2	150923162	0.992000	0.36948	0.998000	0.56505	0.876000	0.50452	2.295000	0.43576	0.646000	0.30693	0.561000	0.74099	CCA	G|0.578;A|0.422	0.422	strong		0.527	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
IRAK1	3654	hgsc.bcm.edu	37	X	153278829	153278829	+	Missense_Mutation	SNP	G	G	A	rs1059703	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153278829G>A	ENST00000369980.3	-	12	1762	c.1595C>T	c.(1594-1596)tCg>tTg	p.S532L	IRAK1_ENST00000393682.1_Intron|IRAK1_ENST00000477274.1_Intron|IRAK1_ENST00000393687.2_Intron|IRAK1_ENST00000429936.2_Intron|IRAK1_ENST00000369974.2_Missense_Mutation_p.S453L	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	532			S -> L (in dbSNP:rs1059703). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8599092}.		activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGCGGCCTCCGAATGCCCGGG	0.657													G|||	1951	0.516821	0.4622	0.3991	3775	,	,		10774	0.1597		0.6421	False		,,,				2504	0.2618				p.S532L		Atlas-SNP	.											.	IRAK1	107	.	0			c.C1595T	GRCh37	CM082902	IRAK1	M	rs1059703	PASS	.	G	,LEU/SER,LEU/SER	2477,1324		716,708,337,199,218	18.0	22.0	21.0		,1358,1595	-0.9	0.0	X	dbSNP_86	21	5660,977		1770,581,1539,58,280	yes	intron,missense,missense	IRAK1	NM_001025242.1,NM_001025243.1,NM_001569.3	,145,145	2486,1289,1876,257,498	AA,AG,A,GG,G		14.7205,34.8329,22.0445	,benign,benign	,453/634,532/713	153278829	8137,2301	2178	4228	6406	SO:0001583	missense	3654	exon12			GCCTCCGAATGCC	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.1595C>T	X.37:g.153278829G>A	ENSP00000358997:p.Ser532Leu	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	65	41	0.630769	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Missense_Mutation	SNP	ENST00000369980.3	37	CCDS14740.1	947	0.5708257986738999	182	0.5055555555555555	103	0.412	53	0.10433070866141732	340	0.6995884773662552	G	8.776	0.927074	0.18056	0.651671	0.852795	ENSG00000184216	ENST00000369980;ENST00000369974	T;T	0.73258	-0.73;-0.71	4.69	-0.873	0.10635	Protein kinase-like domain (1);	2.089680	0.01994	N	0.045764	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41610	-0.9499	9	0.23302	T	0.38	0.3135	1.7514	0.02973	0.2892:0.1313:0.4329:0.1467	rs1059703;rs3200493;rs17332589;rs17856472;rs1059703	453;532	P51617-4;P51617	.;IRAK1_HUMAN	L	532;453	ENSP00000358997:S532L;ENSP00000358991:S453L	ENSP00000358991:S453L	S	-	2	0	IRAK1	152932023	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.171000	0.09883	-0.378000	0.07918	-0.905000	0.02835	TCG	G|0.335;0|0.010	.	strong		0.657	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3		
KIAA0430	9665	hgsc.bcm.edu	37	16	15711335	15711335	+	Silent	SNP	G	G	A	rs62036917	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15711335G>A	ENST00000396368.3	-	14	2984	c.2778C>T	c.(2776-2778)atC>atT	p.I926I	KIAA0430_ENST00000551742.1_Silent_p.I926I|KIAA0430_ENST00000540441.2_Silent_p.I761I|KIAA0430_ENST00000548025.1_Silent_p.I923I|KIAA0430_ENST00000602337.1_Silent_p.I923I|KIAA0430_ENST00000344181.3_Silent_p.I568I	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	926	HTH OST-type 1. {ECO:0000255|PROSITE- ProRule:PRU00975}.				double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						CTTGTTCACGGATTGCGACCG	0.512													G|||	177	0.0353435	0.0045	0.049	5008	,	,		16675	0.0387		0.0686	False		,,,				2504	0.0297				p.I926I		Atlas-SNP	.											.	KIAA0430	154	.	0			c.C2778T						PASS	.	G	,,	54,3806		0,54,1876	52.0	55.0	54.0		2778,2769,2778	4.3	1.0	16	dbSNP_129	54	574,7694		15,544,3575	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA0430	NM_001184998.1,NM_001184999.1,NM_014647.3	,,	15,598,5451	AA,AG,GG		6.9424,1.399,5.1781	,,	926/1743,923/1740,926/1743	15711335	628,11500	1930	4134	6064	SO:0001819	synonymous_variant	9665	exon14			TTCACGGATTGCG	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29562	protein-coding gene	gene with protein product	"""limkain b1"", ""protein phosphatase 1, regulatory subunit 34"", ""meiosis arrest female 1"""	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.2778C>T	16.37:g.15711335G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_001184998	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Silent	SNP	ENST00000396368.3	37	CCDS10562.2																																																																																			G|0.948;A|0.052	0.052	strong		0.512	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647	
TOMM40	10452	hgsc.bcm.edu	37	19	45396144	45396144	+	Silent	SNP	C	C	T	rs11556505	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:45396144C>T	ENST00000426677.2	+	3	573	c.393C>T	c.(391-393)ttC>ttT	p.F131F	CTB-129P6.4_ENST00000585408.1_RNA|TOMM40_ENST00000252487.5_Silent_p.F131F|TOMM40_ENST00000405636.2_Silent_p.F131F|TOMM40_ENST00000592434.1_Silent_p.F131F	NM_001128917.1	NP_001122389.1	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)	131					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)		ACTACCACTTCGGGGTCACAT	0.488													C|||	571	0.114018	0.1112	0.1052	5008	,	,		22184	0.0962		0.1312	False		,,,				2504	0.1247				p.F131F		Atlas-SNP	.											.	TOMM40	13	.	0			c.C393T						PASS	.	C	,,	516,3890	238.0+/-249.6	46,424,1733	90.0	75.0	80.0		393,393,393	-3.0	1.0	19	dbSNP_120	80	1134,7466	234.6+/-267.5	81,972,3247	no	coding-synonymous,coding-synonymous,coding-synonymous	TOMM40	NM_001128916.1,NM_001128917.1,NM_006114.2	,,	127,1396,4980	TT,TC,CC		13.186,11.7113,12.6865	,,	131/362,131/362,131/362	45396144	1650,11356	2203	4300	6503	SO:0001819	synonymous_variant	10452	exon3			CCACTTCGGGGTC	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.393C>T	19.37:g.45396144C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	220	111	0.504545	NM_001128917	Q86VW4|Q8WY09|Q8WY10|Q8WY11|Q9BR95	Silent	SNP	ENST00000426677.2	37	CCDS12646.1																																																																																			C|0.866;T|0.134	0.134	strong		0.488	TOMM40-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453241.1		
RAD54B	25788	hgsc.bcm.edu	37	8	95470507	95470507	+	Missense_Mutation	SNP	G	G	A	rs148525625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:95470507G>A	ENST00000336148.5	-	3	417	c.293C>T	c.(292-294)cCa>cTa	p.P98L	RAD54B_ENST00000297592.5_Missense_Mutation_p.P98L	NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	98					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			TGTATGAGGTGGATCTAATGT	0.308								Direct reversal of damage;Homologous recombination																													p.P98L		Atlas-SNP	.											RAD54B,NS,carcinoma,+1,1	RAD54B	88	1	0			c.C293T						PASS	.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	163.0	154.0	157.0		293,293	1.4	0.0	8	dbSNP_134	157	2,8594	2.2+/-6.3	0,2,4296	no	missense,missense	RAD54B	NM_001205262.1,NM_012415.3	98,98	0,2,6499	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	98/118,98/911	95470507	2,13000	2203	4298	6501	SO:0001583	missense	25788	exon3			TGAGGTGGATCTA	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.293C>T	8.37:g.95470507G>A	ENSP00000336606:p.Pro98Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	148	73	0.493243	NM_001205262	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	37	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989826	0.54041	0.0	2.33E-4	ENSG00000197275	ENST00000336148;ENST00000523839;ENST00000297592	D;T;T	0.87966	-2.32;1.57;1.54	5.44	1.42	0.22433	.	1.455470	0.03871	N	0.275599	D	0.82435	0.5036	L	0.48642	1.525	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.11329	0.006;0.001	T	0.60321	-0.7286	10	0.15066	T	0.55	-28.8344	7.8043	0.29193	0.366:0.0:0.634:0.0	.	98;98	F6WBS8;Q9Y620	.;RA54B_HUMAN	L	98	ENSP00000336606:P98L;ENSP00000428554:P98L;ENSP00000430153:P98L	ENSP00000430153:P98L	P	-	2	0	RAD54B	95539683	0.000000	0.05858	0.000000	0.03702	0.525000	0.34531	-0.063000	0.11655	0.123000	0.18342	0.650000	0.86243	CCA	G|1.000;A|0.000	0.000	strong		0.308	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
FANCA	2175	hgsc.bcm.edu	37	16	89836323	89836323	+	Missense_Mutation	SNP	C	C	T	rs7195066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89836323C>T	ENST00000389301.3	-	26	2456	c.2426G>A	c.(2425-2427)gGt>gAt	p.G809D	FANCA_ENST00000568369.1_Missense_Mutation_p.G809D|FANCA_ENST00000567284.2_5'Flank	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	809			G -> D (common polymorphism; dbSNP:rs7195066). {ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:9371798, ECO:0000269|PubMed:9399890, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		AAGGCCAGCACCAGGTGCAGG	0.617			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				T|||	3339	0.666733	0.7398	0.5821	5008	,	,		17886	0.9881		0.3221	False		,,,				2504	0.6513				p.G809D		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,NS,carcinoma,0,1	FANCA	99	1	0			c.G2426A						PASS	.	T	ASP/GLY	2895,1501	476.3+/-357.6	953,989,256	92.0	68.0	76.0		2426	-0.2	0.0	16	dbSNP_116	76	2702,5898	682.3+/-403.8	438,1826,2036	yes	missense	FANCA	NM_000135.2	94	1391,2815,2292	TT,TC,CC		31.4186,34.1447,43.0671	benign	809/1456	89836323	5597,7399	2198	4300	6498	SO:0001583	missense	2175	exon26	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CCAGCACCAGGTG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.2426G>A	16.37:g.89836323C>T	ENSP00000373952:p.Gly809Asp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	1344	0.6153846153846154	348	0.7073170731707317	190	0.5248618784530387	565	0.9877622377622378	241	0.3179419525065963	T	3.507	-0.100499	0.06967	0.658553	0.314186	ENSG00000187741	ENST00000389301	D	0.84442	-1.85	3.13	-0.167	0.13347	.	0.597657	0.15671	N	0.250384	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27054	-1.0085	9	0.18710	T	0.47	-0.0117	2.3692	0.04326	0.1117:0.3478:0.3548:0.1856	rs7195066;rs17233043;rs60022722;rs7195066	809;809	B4DRI7;O15360	.;FANCA_HUMAN	D	809	ENSP00000373952:G809D	ENSP00000373952:G809D	G	-	2	0	FANCA	88363824	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.305000	0.19254	-0.200000	0.10300	-1.562000	0.00884	GGT	C|0.485;T|0.515	0.515	strong		0.617	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
CLLU1	574028	hgsc.bcm.edu	37	12	92818786	92818786	+	Silent	SNP	A	A	G	rs1515565	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:92818786A>G	ENST00000378485.1	+	1	1052	c.330A>G	c.(328-330)aaA>aaG	p.K110K	CLLU1_ENST00000472839.2_Intron|CLLU1OS_ENST00000378487.2_Intron|RP11-693J15.4_ENST00000508671.1_RNA|CLLU1OS_ENST00000538965.1_Intron	NM_001025233.1	NP_001020404.1	Q5K131	CLLU1_HUMAN	chronic lymphocytic leukemia up-regulated 1	110						cytoplasm (GO:0005737)				NS(1)|breast(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	7						TTTTGTCCAAAAATTTTAAAT	0.318													G|||	3458	0.690495	0.9357	0.536	5008	,	,		18609	0.6766		0.5199	False		,,,				2504	0.6585				p.K110K		Atlas-SNP	.											.	CLLU1	12	.	0			c.A330G						PASS	.	G	,	3128,490		1360,408,41	38.0	38.0	38.0		,330	-4.5	0.0	12	dbSNP_88	38	4248,3866		1123,2002,932	no	intron,coding-synonymous	CLLU1OS,CLLU1	NM_001025232.1,NM_001025233.1	,	2483,2410,973	GG,GA,AA		47.646,13.5434,37.1292	,	,110/122	92818786	7376,4356	1809	4057	5866	SO:0001819	synonymous_variant	574028	exon1			GTCCAAAAATTTT	AJ845162		12q22	2012-04-19			ENSG00000257127	ENSG00000257127			29841	protein-coding gene	gene with protein product						19726446	Standard	NR_027932		Approved		uc001tcg.1	Q5K131	OTTHUMG00000170103	ENST00000378485.1:c.330A>G	12.37:g.92818786A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	96	31	0.322917	NM_001025233		Silent	SNP	ENST00000378485.1	37																																																																																				A|0.334;G|0.666	0.666	strong		0.318	CLLU1-003	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000366643.1	NM_001025233	
ZC3H3	23144	hgsc.bcm.edu	37	8	144522387	144522387	+	Nonsense_Mutation	SNP	G	G	T	rs2272754	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144522387G>T	ENST00000262577.5	-	11	2670	c.2639C>A	c.(2638-2640)tCa>tAa	p.S880*		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	880	Poly-Ser.				mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			Gggaggggatgaggaggagga	0.652													G|||	560	0.111821	0.0363	0.1167	5008	,	,		17078	0.2431		0.1461	False		,,,				2504	0.0399				p.S880X		Atlas-SNP	.											.	ZC3H3	75	.	0			c.C2639A						PASS	.	G	stop/SER	220,4186		8,204,1991	29.0	28.0	29.0		2639	1.1	0.0	8	dbSNP_100	29	943,7655		116,711,3472	yes	stop-gained	ZC3H3	NM_015117.2		124,915,5463	TT,TG,GG		10.9677,4.9932,8.9434		880/949	144522387	1163,11841	2203	4299	6502	SO:0001587	stop_gained	23144	exon11			GGGGATGAGGAGG	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"""Zinc fingers, CCCH-type domain containing"""	28972	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 3"""	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.2639C>A	8.37:g.144522387G>T	ENSP00000262577:p.Ser880*	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_015117	Q14163|Q8N4E2|Q9BUS4	Nonsense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	273	0.125	25	0.0508130081300813	42	0.11602209944751381	122	0.21328671328671328	84	0.11081794195250659	G	27.7	4.854259	0.91355	0.049932	0.109677	ENSG00000014164	ENST00000262577	.	.	.	4.25	1.07	0.20283	.	2.759650	0.01499	N	0.017425	.	.	.	.	.	.	0.09310	P	0.9999999999699166	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	2.0487	8.7374	0.34537	0.0967:0.5505:0.3527:0.0	rs2272754	.	.	.	X	880	.	ENSP00000262577:S880X	S	-	2	0	ZC3H3	144593530	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.528000	0.06193	-0.133000	0.11537	-0.444000	0.05651	TCA	G|0.879;T|0.121	0.121	strong		0.652	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
RBFA	79863	hgsc.bcm.edu	37	18	77805949	77805949	+	Missense_Mutation	SNP	A	A	C	rs3744873	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:77805949A>C	ENST00000306735.5	+	7	964	c.826A>C	c.(826-828)Aaa>Caa	p.K276Q	RP11-795F19.5_ENST00000569722.1_Intron|RBFA_ENST00000262197.7_3'UTR|RP11-795F19.5_ENST00000564012.1_Intron	NM_024805.2	NP_079081.2	Q8N0V3	RBFA_HUMAN	ribosome binding factor A (putative)	276			K -> Q (in dbSNP:rs3744873). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		rRNA processing (GO:0006364)	mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						AACGCAGATGAAAAAGGGAAG	0.577													A|||	1022	0.204073	0.1936	0.1801	5008	,	,		18207	0.1696		0.339	False		,,,				2504	0.1319				p.K276Q		Atlas-SNP	.											.	RBFA	27	.	0			c.A826C						PASS	.	A	,GLN/LYS	1092,3314	394.0+/-329.1	146,800,1257	72.0	75.0	74.0		,826	2.0	0.0	18	dbSNP_107	74	3042,5558	466.8+/-366.9	561,1920,1819	yes	utr-3,missense	RBFA	NM_001171967.1,NM_024805.2	,53	707,2720,3076	CC,CA,AA		35.3721,24.7844,31.7853	,possibly-damaging	,276/344	77805949	4134,8872	2203	4300	6503	SO:0001583	missense	79863	exon7			CAGATGAAAAAGG	BC014195	CCDS12021.1, CCDS54194.1	18q23	2010-10-21	2010-10-21	2010-10-21	ENSG00000101546	ENSG00000101546			26120	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 22"""	C18orf22		12477932	Standard	NM_024805		Approved	FLJ21172, HsT169	uc002lns.3	Q8N0V3	OTTHUMG00000132923	ENST00000306735.5:c.826A>C	18.37:g.77805949A>C	ENSP00000305696:p.Lys276Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	80	29	0.3625	NM_024805	Q6PF07|Q8WZ65|Q9H776	Missense_Mutation	SNP	ENST00000306735.5	37	CCDS12021.1	506	0.2316849816849817	85	0.17276422764227642	76	0.20994475138121546	84	0.14685314685314685	261	0.34432717678100266	A	12.37	1.916400	0.33815	0.247844	0.353721	ENSG00000101546	ENST00000306735	T	0.25085	1.82	4.53	2.03	0.26663	.	1.311440	0.05065	N	0.480480	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	P	0.40476	0.718	B	0.39299	0.296	T	0.35895	-0.9770	9	0.54805	T	0.06	-3.6476	5.5151	0.16902	0.7224:0.1815:0.096:0.0	rs3744873;rs17249619;rs17856451;rs59441886;rs3744873	276	Q8N0V3	RBFA_HUMAN	Q	276	ENSP00000305696:K276Q	ENSP00000305696:K276Q	K	+	1	0	RBFA	75906937	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.697000	0.25556	0.198000	0.20407	-0.290000	0.09829	AAA	A|0.722;C|0.278	0.278	strong		0.577	RBFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256436.2	NM_024805	
WRNIP1	56897	hgsc.bcm.edu	37	6	2784571	2784571	+	Silent	SNP	G	G	A	rs160703	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:2784571G>A	ENST00000380773.4	+	6	1865	c.1656G>A	c.(1654-1656)ccG>ccA	p.P552P	WRNIP1_ENST00000380764.1_Silent_p.P168P|WRNIP1_ENST00000380769.4_Silent_p.P332P|WRNIP1_ENST00000380771.4_Silent_p.P527P	NM_020135.2	NP_064520.2			Werner helicase interacting protein 1											breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				TGGCAGACCCGTCTGCGTTAA	0.502													G|||	1052	0.210064	0.0968	0.2147	5008	,	,		20281	0.256		0.1968	False		,,,				2504	0.3262				p.P552P		Atlas-SNP	.											.	WRNIP1	39	.	0			c.G1656A						PASS	.	G	,	464,3942	219.1+/-236.9	32,400,1771	113.0	88.0	96.0		1656,1581	-11.1	0.1	6	dbSNP_79	96	1689,6911	308.8+/-309.1	169,1351,2780	no	coding-synonymous,coding-synonymous	WRNIP1	NM_020135.2,NM_130395.1	,	201,1751,4551	AA,AG,GG		19.6395,10.5311,16.5539	,	552/666,527/641	2784571	2153,10853	2203	4300	6503	SO:0001819	synonymous_variant	56897	exon6			AGACCCGTCTGCG	AB056152	CCDS4475.1, CCDS4476.1	6p25.2	2010-04-21			ENSG00000124535	ENSG00000124535		"""ATPases / AAA-type"""	20876	protein-coding gene	gene with protein product		608196				11301316	Standard	NM_020135		Approved	WHIP, FLJ22526, bA420G6.2	uc003mtz.3	Q96S55	OTTHUMG00000014126	ENST00000380773.4:c.1656G>A	6.37:g.2784571G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_020135		Silent	SNP	ENST00000380773.4	37	CCDS4475.1																																																																																			G|0.824;A|0.176	0.176	strong		0.502	WRNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039641.1	NM_130395	
TCFL5	10732	hgsc.bcm.edu	37	20	61488785	61488785	+	Silent	SNP	T	T	C	rs2294996	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:61488785T>C	ENST00000335351.3	-	4	1292	c.1200A>G	c.(1198-1200)caA>caG	p.Q400Q	TCFL5_ENST00000217162.5_Silent_p.Q352Q	NM_006602.2	NP_006593.2	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 (basic helix-loop-helix)	400	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|urinary_tract(1)	9	Breast(26;5.68e-08)					TCTCCCTACGTTGAGACCTTC	0.537													C|||	1139	0.227436	0.27	0.196	5008	,	,		19544	0.1597		0.2763	False		,,,				2504	0.2117				p.Q400Q		Atlas-SNP	.											.	TCFL5	43	.	0			c.A1200G						PASS	.	C		1244,3162	704.4+/-407.1	164,916,1123	198.0	169.0	179.0		1200	4.7	1.0	20	dbSNP_100	179	2379,6221	701.2+/-405.2	314,1751,2235	no	coding-synonymous	TCFL5	NM_006602.2		478,2667,3358	CC,CT,TT		27.6628,28.2342,27.8564		400/501	61488785	3623,9383	2203	4300	6503	SO:0001819	synonymous_variant	10732	exon4			CCTACGTTGAGAC	AB012124	CCDS13506.1	20q13.33	2013-09-19			ENSG00000101190	ENSG00000101190		"""Basic helix-loop-helix proteins"""	11646	protein-coding gene	gene with protein product	"""HPV-16 E2 binding protein 1"""	604745				9763657	Standard	XM_005260185		Approved	Figlb, E2BP-1, CHA, bHLHe82	uc002ydp.3	Q9UL49	OTTHUMG00000032939	ENST00000335351.3:c.1200A>G	20.37:g.61488785T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_006602	O94771|Q9BYW0	Silent	SNP	ENST00000335351.3	37	CCDS13506.1																																																																																			A|0.005;C|0.255	0.255	strong		0.537	TCFL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080079.2	NM_006602	
SNX19	399979	hgsc.bcm.edu	37	11	130784396	130784396	+	Missense_Mutation	SNP	G	G	A	rs62621284	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130784396G>A	ENST00000265909.4	-	1	2008	c.1439C>T	c.(1438-1440)cCg>cTg	p.P480L	SNX19_ENST00000533318.1_Intron|SNX19_ENST00000533214.1_Missense_Mutation_p.P480L|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000530356.1_Intron|SNX19_ENST00000539184.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	480					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		TAAGCATGACGGCCGTGAGGG	0.522													G|||	639	0.127596	0.0492	0.0893	5008	,	,		21233	0.1538		0.1988	False		,,,				2504	0.1605				p.P480L		Atlas-SNP	.											SNX19,NS,carcinoma,+1,1	SNX19	84	1	0			c.C1439T						scavenged	.	G	LEU/PRO	315,4087	168.7+/-199.5	15,285,1901	111.0	101.0	105.0		1439	5.6	0.2	11	dbSNP_129	105	1788,6806	324.1+/-316.3	174,1440,2683	yes	missense	SNX19	NM_014758.2	98	189,1725,4584	AA,AG,GG		20.8052,7.1558,16.1819	possibly-damaging	480/993	130784396	2103,10893	2201	4297	6498	SO:0001583	missense	399979	exon1			CATGACGGCCGTG	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1439C>T	11.37:g.130784396G>A	ENSP00000265909:p.Pro480Leu	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	161	70	0.434783	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	37	CCDS31721.1	314	0.14377289377289376	25	0.0508130081300813	35	0.09668508287292818	99	0.17307692307692307	155	0.20448548812664907	G	16.15	3.041915	0.55003	0.071558	0.208052	ENSG00000120451	ENST00000265909;ENST00000533214	T;T	0.20200	2.51;2.09	5.63	5.63	0.86233	.	0.440036	0.26919	N	0.021828	T	0.00039	0.0001	M	0.67953	2.075	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.72625	0.978;0.978	T	0.00645	-1.1629	9	0.23891	T	0.37	-22.5694	17.8541	0.88756	0.0:0.0:1.0:0.0	.	480;480	E9PKB9;Q92543	.;SNX19_HUMAN	L	480	ENSP00000265909:P480L;ENSP00000435390:P480L	ENSP00000265909:P480L	P	-	2	0	SNX19	130289606	1.000000	0.71417	0.214000	0.23707	0.201000	0.24016	6.284000	0.72652	2.660000	0.90430	0.650000	0.86243	CCG	G|0.842;A|0.158	0.158	strong		0.522	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
IL17RC	84818	hgsc.bcm.edu	37	3	9960070	9960070	+	Missense_Mutation	SNP	C	C	T	rs708567	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9960070C>T	ENST00000295981.3	+	4	763	c.545C>T	c.(544-546)tCa>tTa	p.S182L	RNU6-882P_ENST00000391025.1_RNA|IL17RC_ENST00000413608.1_Missense_Mutation_p.S111L|IL17RC_ENST00000403601.3_Missense_Mutation_p.S111L|IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000416074.2_Intron|IL17RC_ENST00000383812.4_Missense_Mutation_p.S111L|IL17RC_ENST00000455057.1_Missense_Mutation_p.S111L	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	182			S -> L (in dbSNP:rs708567). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1}.		cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GCAGCTGACTCAGGGGTGGAG	0.642													C|||	1938	0.386981	0.4955	0.4683	5008	,	,		17282	0.0933		0.5437	False		,,,				2504	0.3241				p.S182L		Atlas-SNP	.											.	IL17RC	55	.	0			c.C545T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER	2150,2254	558.2+/-379.9	533,1084,585	60.0	65.0	64.0		332,332,332,332,332,545	-0.3	0.0	3	dbSNP_86	64	4574,4026	572.6+/-389.7	1199,2176,925	yes	missense,missense,missense,missense,missense,missense	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	145,145,145,145,145,145	1732,3260,1510	TT,TC,CC		46.814,48.8193,48.2928	benign,benign,benign,benign,benign,benign	111/708,111/691,111/689,111/706,111/721,182/792	9960070	6724,6280	2202	4300	6502	SO:0001583	missense	84818	exon4			CTGACTCAGGGGT	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.545C>T	3.37:g.9960070C>T	ENSP00000295981:p.Ser182Leu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	37	CCDS2590.1	856	0.39194139194139194	239	0.48577235772357724	170	0.4696132596685083	38	0.06643356643356643	409	0.5395778364116095	C	3.436	-0.115044	0.06881	0.488193	0.53186	ENSG00000163702	ENST00000383812;ENST00000295981;ENST00000403601;ENST00000455057;ENST00000413608	T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27	5.07	-0.28	0.12886	.	0.950409	0.08755	N	0.898547	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B;B;B;B	0.23937	0.0;0.0;0.0;0.025;0.0;0.094;0.043	B;B;B;B;B;B;B	0.20767	0.0;0.0;0.0;0.014;0.001;0.014;0.031	T	0.43572	-0.9383	9	0.36615	T	0.2	0.7799	4.0234	0.09677	0.301:0.4467:0.0:0.2523	rs708567;rs1695435;rs11546398;rs17775675;rs61446752;rs708567	111;111;111;111;111;182;111	Q8NAC3-4;E9PHG1;A8BWD5;E9PHJ6;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;I17RC_HUMAN;.	L	111;182;111;111;111	ENSP00000373323:S111L;ENSP00000295981:S182L;ENSP00000384969:S111L;ENSP00000407894:S111L;ENSP00000396064:S111L	ENSP00000295981:S182L	S	+	2	0	IL17RC	9935070	0.000000	0.05858	0.005000	0.12908	0.015000	0.08874	-0.564000	0.05936	0.232000	0.21100	-0.397000	0.06425	TCA	T|0.437;G|0.004	0.437	strong		0.642	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
PMF1	11243	hgsc.bcm.edu	37	1	156202173	156202173	+	Missense_Mutation	SNP	A	A	G	rs1052053	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156202173A>G	ENST00000368277.3	+	2	233	c.224A>G	c.(223-225)cAa>cGa	p.Q75R	PMF1-BGLAP_ENST00000490491.1_Missense_Mutation_p.Q75R|PMF1-BGLAP_ENST00000320139.5_Missense_Mutation_p.Q75R|PMF1_ENST00000567140.1_Missense_Mutation_p.Q75R|PMF1_ENST00000368273.4_Intron|PMF1_ENST00000565805.1_Missense_Mutation_p.Q75R|PMF1-BGLAP_ENST00000368276.4_Missense_Mutation_p.Q75R|PMF1_ENST00000368279.3_Missense_Mutation_p.Q75R	NM_007221.3	NP_009152.2			polyamine-modulated factor 1											kidney(1)|large_intestine(2)|lung(3)	6	Hepatocellular(266;0.158)					ATGACACAGCAAATCTATGAC	0.522													G|||	2240	0.447284	0.7065	0.366	5008	,	,		20911	0.3313		0.3708	False		,,,				2504	0.3528				p.Q75R	Pancreas(32;764 914 7316 34504 37150)|Ovarian(64;846 1195 21996 34382 40415)	Atlas-SNP	.											.	PMF1	12	.	0			c.A224G						PASS	.	G	ARG/GLN,,ARG/GLN,ARG/GLN,ARG/GLN,,ARG/GLN	2971,1435	467.4+/-354.8	1006,959,238	190.0	191.0	191.0		224,,224,224,224,,224	4.7	0.0	1	dbSNP_86	191	3134,5466	657.1+/-401.4	573,1988,1739	yes	missense,intron,missense,missense,missense,intron,missense	PMF1,PMF1-BGLAP	NM_001199653.1,NM_001199654.1,NM_001199661.1,NM_001199662.1,NM_001199663.1,NM_001199664.1,NM_007221.3	43,,43,43,43,,43	1579,2947,1977	GG,GA,AA		36.4419,32.5692,46.9399	benign,,benign,benign,benign,,benign	75/181,,75/221,75/212,75/176,,75/206	156202173	6105,6901	2203	4300	6503	SO:0001583	missense	11243	exon2			CACAGCAAATCTA	AF141310	CCDS30886.1, CCDS55648.1, CCDS55649.1	1q22	2013-07-03			ENSG00000160783	ENSG00000160783			9112	protein-coding gene	gene with protein product		609176				10419538	Standard	NM_007221		Approved			Q6P1K2	OTTHUMG00000177123	ENST00000368277.3:c.224A>G	1.37:g.156202173A>G	ENSP00000357260:p.Gln75Arg	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	186	85	0.456989	NM_001199653		Missense_Mutation	SNP	ENST00000368277.3	37	CCDS30886.1	957	0.4381868131868132	349	0.709349593495935	131	0.36187845303867405	191	0.3339160839160839	286	0.37730870712401055	G	0.077	-1.191101	0.01607	0.674308	0.364419	ENSG00000160783	ENST00000368279;ENST00000368277;ENST00000368276;ENST00000320139	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	5.68	4.69	0.59074	.	0.352984	0.25478	N	0.030393	T	0.01870	0.0059	N	0.00436	-1.5	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42982	-0.9419	9	0.02654	T	1	-2.0422	8.2179	0.31524	0.0875:0.0:0.7472:0.1653	rs1052053;rs3192457;rs17855947;rs17856982;rs59642561;rs1052053	75;75;75	Q6P1K2-3;Q5TCK1;Q6P1K2	.;.;PMF1_HUMAN	R	75	ENSP00000357262:Q75R;ENSP00000357260:Q75R;ENSP00000357259:Q75R;ENSP00000324909:Q75R	ENSP00000324909:Q75R	Q	+	2	0	PMF1	154468797	0.576000	0.26700	0.027000	0.17364	0.444000	0.32077	2.569000	0.45973	1.429000	0.47314	-0.119000	0.15052	CAA	A|0.544;C|0.003	.	strong		0.522	PMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040860.1	NM_007221	
GPR63	81491	hgsc.bcm.edu	37	6	97247566	97247566	+	Silent	SNP	T	T	A	rs392127	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:97247566T>A	ENST00000229955.3	-	2	387	c.42A>T	c.(40-42)acA>acT	p.T14T	GPR63_ENST00000417980.1_Silent_p.T14T	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		TTGTGTTGGATGTCCCGGTAT	0.448													T|||	349	0.0696885	0.031	0.0893	5008	,	,		21021	0.002		0.1352	False		,,,				2504	0.1104				p.T14T		Atlas-SNP	.											.	GPR63	60	.	0			c.A42T						PASS	.	T	,	233,4173	137.7+/-173.5	4,225,1974	127.0	115.0	119.0		42,42	-2.3	0.5	6	dbSNP_80	119	1161,7439	238.2+/-269.8	76,1009,3215	no	coding-synonymous,coding-synonymous	GPR63	NM_001143957.1,NM_030784.2	,	80,1234,5189	AA,AT,TT		13.5,5.2882,10.7181	,	14/420,14/420	97247566	1394,11612	2203	4300	6503	SO:0001819	synonymous_variant	81491	exon2			GTTGGATGTCCCG	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"""GPCR / Class A : Orphans"""	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.42A>T	6.37:g.97247566T>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_030784	Q9UJH3	Silent	SNP	ENST00000229955.3	37	CCDS5036.1																																																																																			T|0.909;A|0.091	0.091	strong		0.448	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2		
RGPD3	653489	hgsc.bcm.edu	37	2	107040564	107040564	+	Missense_Mutation	SNP	C	C	T	rs55993306	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:107040564C>T	ENST00000409886.3	-	20	3946	c.3859G>A	c.(3859-3861)Gag>Aag	p.E1287K	RGPD3_ENST00000304514.7_Missense_Mutation_p.E1287K	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1287					protein targeting to Golgi (GO:0000042)			p.E1287K(2)		breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						GTTGTTGACTCATCAAAGTGG	0.408													.|||	714	0.142572	0.1021	0.1095	5008	,	,		15360	0.0724		0.2227	False		,,,				2504	0.2106				p.E1287K		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	2	2	Substitution - Missense(2)	kidney(2)	c.G3859A						scavenged	.	C	LYS/GLU	162,1158		31,100,529	162.0	121.0	134.0		3859	2.3	1.0	2	dbSNP_129	134	736,2294		196,344,975	no	missense	RGPD3	NM_001144013.1	56	227,444,1504	TT,TC,CC		24.2904,12.2727,20.6437	possibly-damaging	1287/1759	107040564	898,3452	660	1515	2175	SO:0001583	missense	653489	exon20			TTGACTCATCAAA		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.3859G>A	2.37:g.107040564C>T	ENSP00000386588:p.Glu1287Lys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	854	419	0.490632	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	326	0.14926739926739926	69	0.1402439024390244	41	0.1132596685082873	37	0.06468531468531469	179	0.23614775725593667	.	9.178	1.022948	0.19433	0.122727	0.242904	ENSG00000153165	ENST00000409886;ENST00000304514	T;T	0.40756	1.03;1.02	2.35	2.35	0.29111	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.30981	P	0.722513	D	0.54772	0.968	P	0.50405	0.64	T	0.03433	-1.1037	8	0.06236	T	0.91	-28.1101	10.4115	0.44296	0.0:1.0:0.0:0.0	rs55993306	1287	A6NKT7	RGPD3_HUMAN	K	1287	ENSP00000386588:E1287K;ENSP00000303659:E1287K	ENSP00000303659:E1287K	E	-	1	0	RGPD3	106406996	1.000000	0.71417	0.997000	0.53966	0.035000	0.12851	7.578000	0.82498	1.314000	0.45095	0.186000	0.17326	GAG	C|0.847;T|0.153	0.153	strong		0.408	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
DGCR6	8214	hgsc.bcm.edu	37	22	18900750	18900750	+	IGR	SNP	G	G	A	rs372055	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:18900750G>A	ENST00000331444.6	+	0	1214				PRODH_ENST00000357068.6_Silent_p.L581L|PRODH_ENST00000334029.2_Silent_p.L473L|PRODH_ENST00000420436.1_Silent_p.L473L	NM_005675.4	NP_005666.2	Q14129	DGCR6_HUMAN	DiGeorge syndrome critical region gene 6						cell adhesion (GO:0007155)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|upper_aerodigestive_tract(1)	3						AGCCACAGCAGCTGCCGCTCC	0.667													.|||	3823	0.763379	0.615	0.8156	5008	,	,		15331	0.8224		0.7932	False		,,,				2504	0.8354				p.L581L		Atlas-SNP	.											.	PRODH	42	.	0			c.C1741T						PASS	.	G	,	2837,1479		935,967,256	24.0	20.0	21.0		1417,1741	4.4	1.0	22	dbSNP_80	21	6865,1605		2778,1309,148	no	coding-synonymous,coding-synonymous	PRODH	NM_001195226.1,NM_016335.4	,	3713,2276,404	AA,AG,GG		18.9492,34.2678,24.1201	,	473/493,581/601	18900750	9702,3084	2158	4235	6393	SO:0001628	intergenic_variant	5625	exon15			ACAGCAGCTGCCG	X96484	CCDS13753.1	22q11.21	2008-06-12			ENSG00000183628	ENSG00000183628			2846	protein-coding gene	gene with protein product		601279				8733130	Standard	NM_005675		Approved		uc002zoh.4	Q14129	OTTHUMG00000150162		22.37:g.18900750G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	173	172	0.99422	NM_016335	B2RCH5|D3DX15|G5E9J8|Q9BY28	Silent	SNP	ENST00000331444.6	37	CCDS13753.1																																																																																			G|0.253;A|0.747	0.747	strong		0.667	DGCR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316631.2	NM_005675	
RXRG	6258	hgsc.bcm.edu	37	1	165389129	165389129	+	Silent	SNP	G	G	A	rs1128977	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:165389129G>A	ENST00000359842.5	-	3	722	c.420C>T	c.(418-420)gcC>gcT	p.A140A	RXRG_ENST00000470566.1_5'UTR	NM_001256570.1|NM_006917.4	NP_001243499.1|NP_008848.1	P48443	RXRG_HUMAN	retinoid X receptor, gamma	140					gene expression (GO:0010467)|heart development (GO:0007507)|neuron differentiation (GO:0030182)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|skeletal muscle tissue development (GO:0007519)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	9-cis retinoic acid receptor activity (GO:0004886)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(3)|large_intestine(6)|lung(22)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	38	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tretinoin(DB00755)	CTCCACAGATGGCACAGATGT	0.527													G|||	1139	0.227436	0.0719	0.2637	5008	,	,		17790	0.122		0.3996	False		,,,				2504	0.3436				p.A140A		Atlas-SNP	.											.	RXRG	91	.	0			c.C420T						PASS	.	G		537,3869	242.5+/-252.5	33,471,1699	143.0	131.0	135.0		420	4.3	1.0	1	dbSNP_86	135	3324,5276	495.8+/-374.1	646,2032,1622	no	coding-synonymous	RXRG	NM_006917.4		679,2503,3321	AA,AG,GG		38.6512,12.1879,29.6863		140/464	165389129	3861,9145	2203	4300	6503	SO:0001819	synonymous_variant	6258	exon3			ACAGATGGCACAG	U38480	CCDS1248.1, CCDS72970.1	1q22-q23	2013-01-16			ENSG00000143171	ENSG00000143171		"""Nuclear hormone receptors"""	10479	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 3"""	180247				8034312	Standard	NR_033824		Approved	NR2B3	uc001gda.3	P48443	OTTHUMG00000034626	ENST00000359842.5:c.420C>T	1.37:g.165389129G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	133	69	0.518797	NM_006917	A6NIP1|Q6IBU7	Silent	SNP	ENST00000359842.5	37	CCDS1248.1																																																																																			G|0.737;A|0.263	0.263	strong		0.527	RXRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083794.2	NM_006917	
ADIPOR2	79602	hgsc.bcm.edu	37	12	1890199	1890199	+	Silent	SNP	G	G	A	rs16928751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:1890199G>A	ENST00000357103.4	+	6	1046	c.795G>A	c.(793-795)caG>caA	p.Q265Q		NM_024551.2	NP_078827.2	Q86V24	ADR2_HUMAN	adiponectin receptor 2	265					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|female pregnancy (GO:0007565)|heart development (GO:0007507)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of cell growth (GO:0030308)|positive regulation of glucose import (GO:0046326)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|receptor activity (GO:0004872)			endometrium(1)|large_intestine(3)|lung(7)|stomach(1)	12	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			TAGTCTCCCAGTGGGACATGT	0.438													G|||	532	0.10623	0.208	0.0663	5008	,	,		18929	0.0258		0.1252	False		,,,				2504	0.0603				p.Q265Q		Atlas-SNP	.											.	ADIPOR2	30	.	0			c.G795A						PASS	.	G		895,3511	345.1+/-308.4	98,699,1406	119.0	115.0	116.0		795	4.8	1.0	12	dbSNP_123	116	1048,7552	221.5+/-258.9	58,932,3310	no	coding-synonymous	ADIPOR2	NM_024551.2		156,1631,4716	AA,AG,GG		12.186,20.3132,14.9393		265/387	1890199	1943,11063	2203	4300	6503	SO:0001819	synonymous_variant	79602	exon6			CTCCCAGTGGGAC	AY424280	CCDS8511.1	12p13	2012-08-22			ENSG00000006831	ENSG00000006831		"""GPCR / Unclassified : Adiponectin receptors"""	24041	protein-coding gene	gene with protein product		607946				12802337	Standard	NM_024551		Approved	PAQR2, ACDCR2	uc001qjm.3	Q86V24	OTTHUMG00000130139	ENST00000357103.4:c.795G>A	12.37:g.1890199G>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	225	98	0.435556	NM_024551	Q53YY5|Q9H737	Silent	SNP	ENST00000357103.4	37	CCDS8511.1																																																																																			G|0.876;A|0.124	0.124	strong		0.438	ADIPOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252447.2	NM_024551	
LMTK2	22853	hgsc.bcm.edu	37	7	97823125	97823125	+	Silent	SNP	G	G	A	rs3801296	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:97823125G>A	ENST00000297293.5	+	11	3641	c.3348G>A	c.(3346-3348)agG>agA	p.R1116R		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1116					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					CCGAGAAAAGGTCTGAGGAGG	0.607													G|||	639	0.127596	0.0325	0.196	5008	,	,		15924	0.3552		0.0427	False		,,,				2504	0.0603				p.R1116R		Atlas-SNP	.											.	LMTK2	228	.	0			c.G3348A						PASS	.	G		166,4240	108.6+/-147.0	4,158,2041	64.0	63.0	63.0		3348	3.2	0.1	7	dbSNP_107	63	166,8434	76.6+/-139.3	0,166,4134	no	coding-synonymous	LMTK2	NM_014916.3		4,324,6175	AA,AG,GG		1.9302,3.7676,2.5527		1116/1504	97823125	332,12674	2203	4300	6503	SO:0001819	synonymous_variant	22853	exon11			GAAAAGGTCTGAG	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.3348G>A	7.37:g.97823125G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_014916	A4D272|Q75MG7|Q9UPS3	Silent	SNP	ENST00000297293.5	37	CCDS5654.1																																																																																			G|0.925;A|0.075	0.075	strong		0.607	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
KIAA1328	57536	hgsc.bcm.edu	37	18	34647176	34647176	+	Silent	SNP	T	T	C	rs3747895	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:34647176T>C	ENST00000280020.5	+	7	922	c.900T>C	c.(898-900)ccT>ccC	p.P300P	KIAA1328_ENST00000586135.1_Silent_p.P16P|KIAA1328_ENST00000543923.1_Silent_p.P192P|KIAA1328_ENST00000591619.1_Silent_p.P296P|KIAA1328_ENST00000435985.2_Silent_p.P16P|KIAA1328_ENST00000586501.1_Silent_p.P16P	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	300										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		ATCTTAAGCCTACTCCTAGTC	0.443													T|||	1297	0.258986	0.643	0.1311	5008	,	,		21398	0.1101		0.1292	False		,,,				2504	0.1176				p.P300P		Atlas-SNP	.											.	KIAA1328	39	.	0			c.T900C						PASS	.	T		2272,1844		625,1022,411	104.0	98.0	100.0		900	0.1	0.0	18	dbSNP_107	100	1148,7264		78,992,3136	no	coding-synonymous	KIAA1328	NM_020776.1		703,2014,3547	CC,CT,TT		13.6472,44.8008,27.2989		300/578	34647176	3420,9108	2058	4206	6264	SO:0001819	synonymous_variant	57536	exon7			TAAGCCTACTCCT	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.900T>C	18.37:g.34647176T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	208	103	0.495192	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Silent	SNP	ENST00000280020.5	37	CCDS45855.1																																																																																			T|0.749;C|0.251	0.251	strong		0.443	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776	
GNA14	9630	hgsc.bcm.edu	37	9	80049298	80049298	+	Silent	SNP	C	C	T	rs1801258	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:80049298C>T	ENST00000341700.6	-	3	963	c.450G>A	c.(448-450)tcG>tcA	p.S150S	GNA14_ENST00000464095.1_5'Flank	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	150					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						TGGCAGAGTCCGACAGCTGGT	0.587											OREG0019263	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1793	0.358027	0.5091	0.33	5008	,	,		18433	0.3512		0.2942	False		,,,				2504	0.2464				p.S150S		Atlas-SNP	.											.	GNA14	50	.	0			c.G450A						PASS	.	C		2127,2279	577.3+/-384.4	493,1141,569	106.0	83.0	91.0		450	-10.4	0.2	9	dbSNP_89	91	2443,6157	403.5+/-347.8	336,1771,2193	no	coding-synonymous	GNA14	NM_004297.3		829,2912,2762	TT,TC,CC		28.407,48.2751,35.1376		150/356	80049298	4570,8436	2203	4300	6503	SO:0001819	synonymous_variant	9630	exon3			AGAGTCCGACAGC	AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.450G>A	9.37:g.80049298C>T		Somatic	98	0	0	1195	WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_004297	B1ALW3	Silent	SNP	ENST00000341700.6	37	CCDS6657.1																																																																																			T|0.356;C|0.644;N|0.000	0.356	strong		0.587	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1		
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058986	79058986	+	Silent	SNP	C	C	T	rs150434082	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:79058986C>T	ENST00000388820.4	-	19	3477	c.3267G>A	c.(3265-3267)gcG>gcA	p.A1089A	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1089					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CCCCTGTCCCCGCCAGGTCTA	0.627													c|||	4	0.000798722	0.0	0.0	5008	,	,		14692	0.0		0.004	False		,,,				2504	0.0				p.A1089A		Atlas-SNP	.											ADAMTS7,NS,carcinoma,-1,1	ADAMTS7	142	1	0			c.G3267A						PASS	.	C		5,4369		0,5,2182	18.0	24.0	22.0		3267	-4.2	0.0	15	dbSNP_134	22	48,8500		1,46,4227	no	coding-synonymous	ADAMTS7	NM_014272.3		1,51,6409	TT,TC,CC		0.5615,0.1143,0.4102		1089/1687	79058986	53,12869	2187	4274	6461	SO:0001819	synonymous_variant	11173	exon19			TGTCCCCGCCAGG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3267G>A	15.37:g.79058986C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	106	63	0.59434	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			C|0.996;T|0.004	0.004	strong		0.627	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
GNA14	9630	hgsc.bcm.edu	37	9	80040628	80040628	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:80040628G>A	ENST00000341700.6	-	6	1240	c.727C>T	c.(727-729)Cgc>Tgc	p.R243C	GNA14_ENST00000464095.1_5'UTR	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	243					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						TCTTCCATGCGATTCTAAGTG	0.418																																					p.R243C		Atlas-SNP	.											GNA14,NS,carcinoma,0,2	GNA14	50	2	0			c.C727T						scavenged	.						83.0	83.0	83.0					9																	80040628		2203	4300	6503	SO:0001583	missense	9630	exon6			CCATGCGATTCTA	AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.727C>T	9.37:g.80040628G>A	ENSP00000365807:p.Arg243Cys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	154	4	0.025974	NM_004297	B1ALW3	Missense_Mutation	SNP	ENST00000341700.6	37	CCDS6657.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.456634	0.84317	.	.	ENSG00000156049	ENST00000341700	D	0.92348	-3.02	5.79	4.9	0.64082	.	0.050910	0.85682	D	0.000000	D	0.97087	0.9048	H	0.95079	3.62	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.97797	1.0242	10	0.87932	D	0	.	13.024	0.58804	0.0752:0.0:0.9248:0.0	.	243	O95837	GNA14_HUMAN	C	243	ENSP00000365807:R243C	ENSP00000365807:R243C	R	-	1	0	GNA14	79230448	1.000000	0.71417	0.999000	0.59377	0.910000	0.53928	9.869000	0.99810	1.447000	0.47661	0.650000	0.86243	CGC	.	.	none		0.418	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1		
PCDHGB2	56103	hgsc.bcm.edu	37	5	140741738	140741738	+	Missense_Mutation	SNP	G	G	C	rs62378417	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140741738G>C	ENST00000522605.1	+	1	2036	c.2036G>C	c.(2035-2037)cGg>cCg	p.R679P	PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	679					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R679P(2)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCGACCGCCGGGAGCCCTCT	0.597													.|||	651	0.129992	0.3124	0.0692	5008	,	,		18420	0.0407		0.0885	False		,,,				2504	0.0613				p.R679P		Atlas-SNP	.											PCDHGB2_ENST00000522605,NS,carcinoma,0,3	PCDHGB2	196	3	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.G2036C						PASS	.	C	,,,,,PRO/ARG,PRO/ARG	1054,2978		127,800,1089	60.0	64.0	63.0		,,,,,2036,2036	3.2	0.0	5	dbSNP_129	63	750,7600		29,692,3454	yes	intron,intron,intron,intron,intron,missense,missense	PCDHGB2,PCDHGB1,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018922.2,NM_018923.2,NM_032096.1	,,,,,103,103	156,1492,4543	CC,CG,GG		8.982,26.1409,14.5695	,,,,,,	,,,,,679/932,679/812	140741738	1804,10578	2016	4175	6191	SO:0001583	missense	56103	exon1			ACCGCCGGGAGCC	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"""Cadherins / Protocadherins : Clustered"""	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.2036G>C	5.37:g.140741738G>C	ENSP00000429018:p.Arg679Pro	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	37	CCDS54924.1	271	0.12408424908424909	153	0.31097560975609756	28	0.07734806629834254	20	0.03496503496503497	70	0.09234828496042216	.	7.189	0.591232	0.13812	0.261409	0.08982	ENSG00000253910	ENST00000522605	T	0.49139	0.79	4.95	3.16	0.36331	.	.	.	.	.	T	0.00012	0.0000	N	0.00133	-2.03	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38222	-0.9671	8	0.02654	T	1	.	6.3059	0.21139	0.1375:0.6554:0.1326:0.0744	rs62378417	679;679	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	P	679	ENSP00000429018:R679P	ENSP00000429018:R679P	R	+	2	0	PCDHGB2	140721922	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.827000	0.27421	0.233000	0.21120	-1.266000	0.01441	CGG	G|0.882;C|0.118	0.118	strong		0.597	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923	
STK17B	9262	hgsc.bcm.edu	37	2	197021372	197021372	+	Silent	SNP	T	T	A	rs12478353	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:197021372T>A	ENST00000263955.4	-	3	412	c.126A>T	c.(124-126)ggA>ggT	p.G42G	RP11-347P5.1_ENST00000606818.1_RNA|STK17B_ENST00000409228.1_Silent_p.G42G	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	42	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(10)	15			OV - Ovarian serous cystadenocarcinoma(117;0.141)			CAGCAAATTTTCCTCTGGGGG	0.348													T|||	3256	0.65016	0.4266	0.7003	5008	,	,		16560	0.9028		0.6243	False		,,,				2504	0.683				p.G42G		Atlas-SNP	.											.	STK17B	28	.	0			c.A126T						PASS	.	T		2049,2357	536.4+/-374.5	476,1097,630	70.0	74.0	73.0		126	5.1	1.0	2	dbSNP_120	73	5085,3515	615.3+/-396.4	1500,2085,715	no	coding-synonymous	STK17B	NM_004226.3		1976,3182,1345	AA,AT,TT		40.8721,46.5048,45.1484		42/373	197021372	7134,5872	2203	4300	6503	SO:0001819	synonymous_variant	9262	exon3			AAATTTTCCTCTG	AB011421	CCDS2315.1	2q33.1	2008-02-05	2007-02-12		ENSG00000081320	ENSG00000081320			11396	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 2"""	604727	"""serine/threonine kinase 17b (apoptosis-inducing)"""			9786912	Standard	NM_004226		Approved	DRAK2	uc002utk.3	O94768	OTTHUMG00000132735	ENST00000263955.4:c.126A>T	2.37:g.197021372T>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_004226		Silent	SNP	ENST00000263955.4	37	CCDS2315.1																																																																																			T|0.406;A|0.594	0.594	strong		0.348	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2		
CCDC38	120935	hgsc.bcm.edu	37	12	96292170	96292170	+	Missense_Mutation	SNP	C	C	G	rs75959092	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:96292170C>G	ENST00000344280.3	-	7	1164	c.607G>C	c.(607-609)Gtg>Ctg	p.V203L	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	203										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CACCTTTTCACTGCTTGTACC	0.428													C|||	282	0.0563099	0.0045	0.0706	5008	,	,		19368	0.0278		0.1342	False		,,,				2504	0.0654				p.V203L		Atlas-SNP	.											.	CCDC38	45	.	0			c.G607C						PASS	.	C	LEU/VAL	102,4304	80.9+/-119.3	2,98,2103	346.0	261.0	290.0		607	0.7	0.1	12	dbSNP_132	290	1073,7527	225.1+/-261.3	70,933,3297	yes	missense	CCDC38	NM_182496.2	32	72,1031,5400	GG,GC,CC		12.4767,2.315,9.0343	benign	203/564	96292170	1175,11831	2203	4300	6503	SO:0001583	missense	120935	exon7			TTTTCACTGCTTG	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.607G>C	12.37:g.96292170C>G	ENSP00000345470:p.Val203Leu	Somatic	424	1	0.00235849		WXS	Illumina HiSeq	Phase_I	470	218	0.46383	NM_182496	Q8N835	Missense_Mutation	SNP	ENST00000344280.3	37	CCDS9056.1	139	0.06364468864468864	6	0.012195121951219513	24	0.06629834254143646	10	0.017482517482517484	99	0.13060686015831136	C	5.900	0.350137	0.11182	0.02315	0.124767	ENSG00000165972	ENST00000344280	T	0.07688	3.17	5.4	0.671	0.17929	.	0.361234	0.28062	N	0.016743	T	0.00039	0.0001	L	0.28556	0.865	0.42212	P	0.008184999999999998	B	0.23128	0.08	B	0.23419	0.046	T	0.42749	-0.9433	9	0.07325	T	0.83	-3.5442	4.7641	0.13123	0.0:0.3797:0.1564:0.4638	.	203	Q502W7	CCD38_HUMAN	L	203	ENSP00000345470:V203L	ENSP00000345470:V203L	V	-	1	0	CCDC38	94816301	0.010000	0.17322	0.129000	0.21949	0.024000	0.10985	-0.125000	0.10579	0.055000	0.16094	-0.424000	0.05967	GTG	C|0.917;G|0.083	0.083	strong		0.428	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
SLC4A7	9497	hgsc.bcm.edu	37	3	27473066	27473066	+	Silent	SNP	A	A	G	rs13077400	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:27473066A>G	ENST00000295736.5	-	7	916	c.846T>C	c.(844-846)ctT>ctC	p.L282L	SLC4A7_ENST00000440156.1_Silent_p.L278L|SLC4A7_ENST00000428386.1_Intron|SLC4A7_ENST00000445684.1_Silent_p.L278L|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000454389.1_Silent_p.L291L|SLC4A7_ENST00000425128.2_Silent_p.L274L|SLC4A7_ENST00000446700.1_Silent_p.L274L|SLC4A7_ENST00000435667.2_Intron|SLC4A7_ENST00000455077.1_Intron|SLC4A7_ENST00000437179.1_Intron	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	282					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	GAAGATGACCAAGAAGAAGAG	0.522													G|||	823	0.164337	0.1702	0.1772	5008	,	,		17626	0.0575		0.2276	False		,,,				2504	0.1922				p.L282L		Atlas-SNP	.											.	SLC4A7	119	.	0			c.T846C						PASS	.	G		833,3573	747.4+/-411.8	77,679,1447	89.0	97.0	94.0		846	6.0	1.0	3	dbSNP_121	94	2165,6435	713.6+/-406.0	271,1623,2406	no	coding-synonymous	SLC4A7	NM_003615.3		348,2302,3853	GG,GA,AA		25.1744,18.906,23.0509		282/1215	27473066	2998,10008	2203	4300	6503	SO:0001819	synonymous_variant	9497	exon7			ATGACCAAGAAGA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.846T>C	3.37:g.27473066A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			A|0.800;G|0.200	0.200	strong		0.522	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
HTR1D	3352	hgsc.bcm.edu	37	1	23519633	23519633	+	Silent	SNP	A	A	G	rs6300	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:23519633A>G	ENST00000374619.1	-	1	1589	c.1080T>C	c.(1078-1080)aaT>aaC	p.N360N	HTR1D_ENST00000314113.3_Silent_p.N360N	NM_000864.4	NP_000855.1	P28221	5HT1D_HUMAN	5-hydroxytryptamine (serotonin) receptor 1D, G protein-coupled	360					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intestine smooth muscle contraction (GO:0014827)|regulation of behavior (GO:0050795)|regulation of locomotion (GO:0040012)|response to toxic substance (GO:0009636)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000779)|all_lung(284;0.00135)|Breast(348;0.0385)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0561)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;4.69e-27)|Colorectal(126;4.86e-08)|COAD - Colon adenocarcinoma(152;2.86e-06)|GBM - Glioblastoma multiforme(114;0.00012)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(1967;0.00122)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.083)|LUSC - Lung squamous cell carcinoma(448;0.185)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Naratriptan(DB00952)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GAAACTCTTCATTAAACACAG	0.463													A|||	1033	0.20627	0.1581	0.2709	5008	,	,		14943	0.1845		0.0934	False		,,,				2504	0.364				p.N360N		Atlas-SNP	.											.	HTR1D	36	.	0			c.T1080C						PASS	.	A		786,3620	311.1+/-291.9	74,638,1491	62.0	67.0	65.0		1080	-6.8	0.8	1	dbSNP_52	65	903,7697	199.0+/-243.2	45,813,3442	no	coding-synonymous	HTR1D	NM_000864.4		119,1451,4933	GG,GA,AA		10.5,17.8393,12.9863		360/378	23519633	1689,11317	2203	4300	6503	SO:0001819	synonymous_variant	3352	exon1			CTCTTCATTAAAC	M89955	CCDS231.1	1p36.3-p34.3	2012-08-08	2012-02-03		ENSG00000179546	ENSG00000179546		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5289	protein-coding gene	gene with protein product		182133	"""5-hydroxytryptamine (serotonin) receptor 1D"""	HTRL		2541503, 1662665	Standard	NM_000864		Approved	RDC4, HT1DA, 5-HT1D	uc001bgn.3	P28221	OTTHUMG00000003235	ENST00000374619.1:c.1080T>C	1.37:g.23519633A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_000864		Silent	SNP	ENST00000374619.1	37	CCDS231.1																																																																																			A|0.854;G|0.146	0.146	strong		0.463	HTR1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008924.1	NM_000864	
TMPRSS3	64699	hgsc.bcm.edu	37	21	43809092	43809092	+	Missense_Mutation	SNP	C	C	T	rs45598239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:43809092C>T	ENST00000291532.3	-	4	1223	c.268G>A	c.(268-270)Gct>Act	p.A90T	TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000433957.2_Missense_Mutation_p.A90T|TMPRSS3_ENST00000398405.1_Missense_Mutation_p.A88T|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.A90T|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.A174T	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	90	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.			A -> T (in Ref. 1; AAG37012). {ECO:0000305}.	cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						TCACATCGAGCTATCAGCTCG	0.527													C|||	51	0.0101837	0.0038	0.0086	5008	,	,		21045	0.0		0.0358	False		,,,				2504	0.0041				p.A90T		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.G268A	GRCh37	CM054156	TMPRSS3	M	rs45598239	PASS	.	C	THR/ALA,THR/ALA	40,4366	43.8+/-77.6	0,40,2163	93.0	79.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	268,268	5.2	0.1	21	dbSNP_127	83	415,8185	130.3+/-188.3	8,399,3893	yes	missense,missense	TMPRSS3	NM_024022.2,NM_032405.1	58,58	8,439,6056	TT,TC,CC		4.8256,0.9079,3.4984	probably-damaging,probably-damaging	90/455,90/345	43809092	455,12551	2203	4300	6503	SO:0001583	missense	64699	exon4			ATCGAGCTATCAG	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.268G>A	21.37:g.43809092C>T	ENSP00000291532:p.Ala90Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	37	CCDS13686.1	36	0.016483516483516484	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	28	0.036939313984168866	C	14.53	2.562692	0.45694	0.009079	0.048256	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	D;D;D;D;D	0.95412	-3.7;-3.7;-3.7;-3.7;-3.7	5.23	5.23	0.72850	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.138905	0.48286	D	0.000189	D	0.87529	0.6200	M	0.75447	2.3	0.38709	D	0.953168	D;D;D	0.56746	0.967;0.977;0.96	P;P;P	0.57244	0.765;0.787;0.816	D	0.87660	0.2534	9	.	.	.	.	18.8283	0.92127	0.0:1.0:0.0:0.0	rs45598239	90;90;90	P57727-3;P57727-5;P57727	.;.;TMPS3_HUMAN	T	90;90;88;174;90	ENSP00000291532:A90T;ENSP00000411013:A90T;ENSP00000381442:A88T;ENSP00000369762:A174T;ENSP00000381434:A90T	.	A	-	1	0	TMPRSS3	42682161	0.992000	0.36948	0.079000	0.20413	0.008000	0.06430	4.157000	0.58144	2.443000	0.82685	0.561000	0.74099	GCT	C|0.969;T|0.031	0.031	strong		0.527	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		
CCDC125	202243	hgsc.bcm.edu	37	5	68616331	68616331	+	Missense_Mutation	SNP	C	C	T	rs10471774	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:68616331C>T	ENST00000396496.2	-	2	144	c.37G>A	c.(37-39)Gtg>Atg	p.V13M	CCDC125_ENST00000383374.2_Missense_Mutation_p.V13M|CCDC125_ENST00000460090.1_5'UTR|CCDC125_ENST00000511257.1_De_novo_Start_OutOfFrame|CCDC125_ENST00000396499.1_Missense_Mutation_p.V13M			Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	13			V -> M (in dbSNP:rs10471774). {ECO:0000269|PubMed:19787194}.			cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|urinary_tract(1)	19		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)		CAGAGCTGCACGTCTGACTCA	0.423													c|||	1305	0.260583	0.062	0.2968	5008	,	,		21831	0.2837		0.4543	False		,,,				2504	0.2802				p.V13M		Atlas-SNP	.											.	CCDC125	41	.	0			c.G37A						PASS	.	C	MET/VAL	578,3828	257.4+/-261.8	41,496,1666	113.0	107.0	109.0		37	4.0	0.0	5	dbSNP_119	109	3811,4789	538.9+/-383.5	864,2083,1353	yes	missense	CCDC125	NM_176816.3	21	905,2579,3019	TT,TC,CC		44.314,13.1185,33.746	possibly-damaging	13/512	68616331	4389,8617	2203	4300	6503	SO:0001583	missense	202243	exon1			GCTGCACGTCTGA	AB024691	CCDS4000.1, CCDS75255.1	5q13.2	2008-02-05			ENSG00000183323	ENSG00000183323			28924	protein-coding gene	gene with protein product		613781					Standard	XM_005248461		Approved	KENAE	uc003jvv.1	Q86Z20	OTTHUMG00000131259	ENST00000396496.2:c.37G>A	5.37:g.68616331C>T	ENSP00000379754:p.Val13Met	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_176816	Q86Z19	Missense_Mutation	SNP	ENST00000396496.2	37	CCDS4000.1	673	0.30815018315018317	28	0.056910569105691054	135	0.3729281767955801	157	0.2744755244755245	353	0.4656992084432718	c	15.98	2.992915	0.54041	0.131185	0.44314	ENSG00000183323	ENST00000396496;ENST00000396499;ENST00000383374	T;T;T	0.46819	0.91;0.91;0.86	4.92	4.02	0.46733	.	0.793398	0.10812	N	0.631478	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	D;D	0.64830	0.994;0.994	P;P	0.50754	0.649;0.482	T	0.47169	-0.9138	9	0.46703	T	0.11	-20.8152	11.3743	0.49719	0.0:0.8163:0.1837:0.0	rs10471774;rs52811895;rs56777974;rs10471774	13;13	F8W912;Q86Z20	.;CC125_HUMAN	M	13	ENSP00000379754:V13M;ENSP00000379756:V13M;ENSP00000372865:V13M	ENSP00000372865:V13M	V	-	1	0	CCDC125	68652087	0.051000	0.20477	0.003000	0.11579	0.201000	0.24016	2.597000	0.46214	1.170000	0.42753	0.457000	0.33378	GTG	C|0.689;T|0.311	0.311	strong		0.423	CCDC125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254027.4	NM_176816	
TENM1	10178	hgsc.bcm.edu	37	X	123554646	123554646	+	Silent	SNP	T	T	C	rs12013090	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:123554646T>C	ENST00000371130.3	-	24	4539	c.4476A>G	c.(4474-4476)gcA>gcG	p.A1492A	TENM1_ENST00000422452.2_Silent_p.A1499A|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1492					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CTTTCATCTTTGCATCTTTGG	0.453													T|||	795	0.210596	0.2557	0.0591	3775	,	,		16029	0.0813		0.0865	False		,,,				2504	0.2526				p.A1499A		Atlas-SNP	.											.	.	.	.	0			c.A4497G						PASS	.	T	,,	1149,2686		156,668,169,808,402	106.0	93.0	98.0		4497,4494,4476	-3.0	1.0	X	dbSNP_120	98	870,5858		42,519,267,1867,1605	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	198,1187,436,2675,2007	CC,CT,C,TT,T		12.931,29.9609,19.1139	,,	1499/2733,1498/2732,1492/2726	123554646	2019,8544	2203	4300	6503	SO:0001819	synonymous_variant	10178	exon25			CATCTTTGCATCT	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.4476A>G	X.37:g.123554646T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	211	130	0.616114	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			T|0.812;C|0.188	0.188	strong		0.453	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
KANSL1	284058	hgsc.bcm.edu	37	17	44108906	44108906	+	Missense_Mutation	SNP	A	A	G	rs34579536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44108906A>G	ENST00000262419.6	-	15	3724	c.3254T>C	c.(3253-3255)aTt>aCt	p.I1085T	KANSL1_ENST00000574590.1_Missense_Mutation_p.I1085T|KANSL1_ENST00000575318.1_Missense_Mutation_p.I1021T|KANSL1_ENST00000572904.1_Missense_Mutation_p.I1085T|KANSL1_ENST00000432791.1_Missense_Mutation_p.I1085T|KANSL1_ENST00000393476.3_Missense_Mutation_p.I379T	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	1085	Sufficient for interaction with KAT8.		I -> T (in dbSNP:rs34579536).		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GAGGGGGACAATGGGAGGCGA	0.627													G|||	432	0.086262	0.0151	0.1571	5008	,	,		15744	0.001		0.2406	False		,,,				2504	0.0613				p.I1085T		Atlas-SNP	.											KIAA1267,colon,carcinoma,0,1	.	.	1	0			c.T3254C						PASS	.	G	THR/ILE,THR/ILE,THR/ILE	203,4203	780.9+/-414.5	6,191,2006	29.0	26.0	27.0		3251,3254,3254	2.3	0.0	17	dbSNP_126	27	1914,6686	697.4+/-404.9	220,1474,2606	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	89,89,89	226,1665,4612	GG,GA,AA		22.2558,4.6074,16.2771	benign,benign,benign	1084/1105,1085/1106,1085/1106	44108906	2117,10889	2203	4300	6503	SO:0001583	missense	284058	exon15			GGGACAATGGGAG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.3254T>C	17.37:g.44108906A>G	ENSP00000262419:p.Ile1085Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	3.452	-0.111802	0.06881	0.046074	0.222558	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.25085	2.63;2.63;1.82	5.72	2.34	0.29019	.	1.538450	0.03719	N	0.251449	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37979	-0.9682	9	0.12766	T	0.61	3.041	9.2051	0.37285	0.7644:0.0:0.2356:0.0	rs34579536	416;1085	Q7Z3B3-2;Q7Z3B3	.;K1267_HUMAN	T	1085;1085;379	ENSP00000262419:I1085T;ENSP00000387393:I1085T;ENSP00000377117:I379T	ENSP00000262419:I1085T	I	-	2	0	KIAA1267	41464753	0.000000	0.05858	0.001000	0.08648	0.426000	0.31534	0.910000	0.28571	-0.087000	0.12528	-1.163000	0.01768	ATT	A|0.860;G|0.140	0.140	strong		0.627	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46012259	46012259	+	Missense_Mutation	SNP	T	T	G	rs201362069	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:46012259T>G	ENST00000400368.1	-	1	127	c.107A>C	c.(106-108)gAc>gCc	p.D36A	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	36						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CTCTGGGCAGTCGTCCACCTG	0.687													.|||	62	0.0123802	0.0295	0.0029	5008	,	,		14636	0.002		0.0109	False		,,,				2504	0.0082				p.D36A		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.A107C						PASS	.	T	ALA/ASP,	103,3931		1,101,1915	46.0	45.0	45.0		107,	2.2	1.0	21		45	117,8165		2,113,4026	no	missense,intron	TSPEAR,KRTAP10-6	NM_198688.2,NM_144991.2	126,	3,214,5941	GG,GT,TT		1.4127,2.5533,1.7863	possibly-damaging,	36/366,	46012259	220,12096	2017	4141	6158	SO:0001583	missense	386674	exon1			GGGCAGTCGTCCA	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.107A>C	21.37:g.46012259T>G	ENSP00000383219:p.Asp36Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	80	23	0.2875	NM_198688		Missense_Mutation	SNP	ENST00000400368.1	37	CCDS42959.1	23	0.010531135531135532	13	0.026422764227642278	3	0.008287292817679558	1	0.0017482517482517483	6	0.0079155672823219	t	10.71	1.425617	0.25639	0.025533	0.014127	ENSG00000188155	ENST00000400368	T	0.14893	2.47	3.49	2.18	0.27775	.	.	.	.	.	T	0.05640	0.0148	M	0.63843	1.955	0.26990	N	0.965169	P	0.51791	0.948	B	0.41332	0.354	T	0.09729	-1.0661	9	0.38643	T	0.18	.	7.2248	0.26010	0.0:0.0:0.4041:0.5959	.	36	P60371	KR106_HUMAN	A	36	ENSP00000383219:D36A	ENSP00000383219:D36A	D	-	2	0	KRTAP10-6	44836687	0.979000	0.34478	0.997000	0.53966	0.407000	0.30961	1.226000	0.32563	1.354000	0.45846	0.334000	0.21626	GAC	T|0.993;G|0.007	0.007	strong		0.687	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
OR8H3	390152	hgsc.bcm.edu	37	11	55890726	55890726	+	Missense_Mutation	SNP	G	G	T	rs61747871	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55890726G>T	ENST00000313472.3	+	1	878	c.878G>T	c.(877-879)aGa>aTa	p.R293I		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TATAGTCTTAGAAACAGAGAA	0.368													G|||	191	0.038139	0.0091	0.0447	5008	,	,		17921	0.001		0.0944	False		,,,				2504	0.0532				p.R293I		Atlas-SNP	.											.	OR8H3	92	.	0			c.G878T						PASS	.	G	ILE/ARG	86,4316	68.7+/-106.4	0,86,2115	94.0	99.0	97.0		878	3.6	0.9	11	dbSNP_129	97	690,7898	169.4+/-220.8	33,624,3637	no	missense	OR8H3	NM_001005201.1	97	33,710,5752	TT,TG,GG		8.0345,1.9537,5.9738	probably-damaging	293/313	55890726	776,12214	2201	4294	6495	SO:0001583	missense	390152	exon1			GTCTTAGAAACAG	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.878G>T	11.37:g.55890726G>T	ENSP00000323928:p.Arg293Ile	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	211	78	0.369668	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	86	0.039377289377289376	3	0.006097560975609756	14	0.03867403314917127	0	0.0	69	0.09102902374670185	G	16.34	3.096665	0.56075	0.019537	0.080345	ENSG00000181761	ENST00000313472	T	0.39056	1.1	3.62	3.62	0.41486	.	0.000000	0.64402	D	0.000019	T	0.12135	0.0295	H	0.98178	4.165	0.44477	D	0.997412	D	0.89917	1.0	D	0.73380	0.98	T	0.70706	-0.4798	10	0.87932	D	0	.	15.6872	0.77421	0.0:0.0:1.0:0.0	rs61747871	293	Q8N146	OR8H3_HUMAN	I	293	ENSP00000323928:R293I	ENSP00000323928:R293I	R	+	2	0	OR8H3	55647302	0.463000	0.25799	0.948000	0.38648	0.649000	0.38597	2.810000	0.47979	1.734000	0.51633	0.173000	0.16961	AGA	G|0.948;T|0.052	0.052	strong		0.368	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
HIF3A	64344	hgsc.bcm.edu	37	19	46823751	46823751	+	Silent	SNP	C	C	T	rs3764610	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:46823751C>T	ENST00000377670.4	+	9	1108	c.1077C>T	c.(1075-1077)caC>caT	p.H359H	HIF3A_ENST00000244303.6_Silent_p.H290H|HIF3A_ENST00000472815.1_Silent_p.H290H|HIF3A_ENST00000300862.3_Silent_p.H357H|HIF3A_ENST00000420102.2_Silent_p.H308H|HIF3A_ENST00000339613.2_Silent_p.H303H|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000600383.1_Silent_p.H290H	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	359					cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		CGGAGCAACACTCTCGCAGAC	0.652													C|||	1004	0.200479	0.0393	0.268	5008	,	,		16562	0.3224		0.1511	False		,,,				2504	0.2955				p.H359H		Atlas-SNP	.											HIF3A_ENST00000377670,NS,carcinoma,+1,2	HIF3A	154	2	0			c.C1077T						PASS	.	C	,,,	305,4101	166.2+/-197.5	10,285,1908	93.0	85.0	88.0		870,1071,1077,870	-4.1	1.0	19	dbSNP_107	88	1452,7148	278.2+/-293.3	134,1184,2982	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HIF3A	NM_022462.4,NM_152794.3,NM_152795.3,NM_152796.2	,,,	144,1469,4890	TT,TC,CC		16.8837,6.9224,13.5091	,,,	290/601,357/668,359/670,290/451	46823751	1757,11249	2203	4300	6503	SO:0001819	synonymous_variant	64344	exon9			GCAACACTCTCGC	AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"""Basic helix-loop-helix proteins"""	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1077C>T	19.37:g.46823751C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Silent	SNP	ENST00000377670.4	37	CCDS12681.2	429	0.19642857142857142	19	0.03861788617886179	81	0.22375690607734808	207	0.3618881118881119	122	0.16094986807387862	C	5.700	0.313625	0.10789	0.069224	0.168837	ENSG00000124440	ENST00000472815	.	.	.	4.47	-4.12	0.03916	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.35830	P	0.174763	.	.	.	.	.	.	T	0.43343	-0.9397	3	.	.	.	.	5.1733	0.15122	0.1579:0.2628:0.0:0.5793	rs3764610;rs60081426;rs3764610	.	.	.	F	332	.	.	L	+	1	0	HIF3A	51515591	0.464000	0.25807	0.961000	0.40146	0.668000	0.39293	-0.201000	0.09464	-0.393000	0.07739	-0.254000	0.11334	CTC	C|0.840;N|0.000	.	strong		0.652	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3		
FBXL16	146330	hgsc.bcm.edu	37	16	746884	746884	+	Silent	SNP	A	A	C	rs4984683	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:746884A>C	ENST00000397621.1	-	2	853	c.522T>G	c.(520-522)gtT>gtG	p.V174V	FBXL16_ENST00000562585.1_5'Flank|FBXL16_ENST00000324361.5_Silent_p.V174V|FBXL16_ENST00000562563.1_5'Flank	NM_153350.3	NP_699181.2	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	174										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)	10		Hepatocellular(780;0.0218)				CGGAGACGCCAACCAGGCAGA	0.577													A|||	1924	0.384185	0.2095	0.3833	5008	,	,		8611	0.7123		0.2565	False		,,,				2504	0.4141				p.V174V		Atlas-SNP	.											.	FBXL16	25	.	0			c.T522G						PASS	.	A		842,3558	328.5+/-300.6	87,668,1445	88.0	77.0	80.0		522	-7.7	0.2	16	dbSNP_111	80	1907,6691	337.1+/-322.1	205,1497,2597	no	coding-synonymous	FBXL16	NM_153350.3		292,2165,4042	CC,CA,AA		22.1796,19.1364,21.1494		174/480	746884	2749,10249	2200	4299	6499	SO:0001819	synonymous_variant	146330	exon2			GACGCCAACCAGG	BC036680	CCDS10421.1	16p13.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000127585	ENSG00000127585		"""F-boxes / Leucine-rich repeats"""	14150	protein-coding gene	gene with protein product		609082	"""chromosome 16 open reading frame 22"""	C16orf22		11157797	Standard	NM_153350		Approved	MGC33974, Fbl16	uc021taa.1	Q8N461	OTTHUMG00000090420	ENST00000397621.1:c.522T>G	16.37:g.746884A>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_153350	B3KR59|D3DU60|Q2MHR2|Q96S14|Q9UJI0	Silent	SNP	ENST00000397621.1	37	CCDS10421.1																																																																																			A|0.718;C|0.282	0.282	strong		0.577	FBXL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206851.2	NM_153350	
KCNT2	343450	hgsc.bcm.edu	37	1	196309523	196309523	+	Silent	SNP	C	C	T	rs142546287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:196309523C>T	ENST00000294725.9	-	16	2646	c.1731G>A	c.(1729-1731)tcG>tcA	p.S577S	KCNT2_ENST00000367433.5_Silent_p.S577S|KCNT2_ENST00000451324.2_Silent_p.S188S|KCNT2_ENST00000367431.4_Silent_p.S527S|KCNT2_ENST00000609185.1_Silent_p.S527S|KCNT2_ENST00000498426.1_5'UTR			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	577					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						CATGATAAAACGACCTGGACA	0.303													T|||	113	0.0225639	0.0008	0.0259	5008	,	,		14172	0.0218		0.0606	False		,,,				2504	0.0112				p.S577S		Atlas-SNP	.											.	KCNT2	243	.	0			c.G1731A						PASS	.	T		54,4352	820.8+/-416.4	0,54,2149	114.0	108.0	110.0		1731	-2.1	0.9	1	dbSNP_134	110	581,8019	791.9+/-407.5	17,547,3736	no	coding-synonymous	KCNT2	NM_198503.2		17,601,5885	TT,TC,CC		6.7558,1.2256,4.8824		577/1136	196309523	635,12371	2203	4300	6503	SO:0001819	synonymous_variant	343450	exon16			ATAAAACGACCTG	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.1731G>A	1.37:g.196309523C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	37	CCDS1384.1																																																																																			C|0.956;T|0.044	0.044	strong		0.303	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102504838	102504838	+	Silent	SNP	C	C	T	rs17541505	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102504838C>T	ENST00000360184.4	+	58	11114	c.10950C>T	c.(10948-10950)aaC>aaT	p.N3650N	RP11-1017G21.4_ENST00000557551.1_RNA|RP11-1017G21.4_ENST00000557242.1_RNA|RP11-1017G21.4_ENST00000553701.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	3650	AAA 5. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						CGGTGCTGAACCGTGAAGTGC	0.542													C|||	311	0.0621006	0.0461	0.0576	5008	,	,		18878	0.005		0.0666	False		,,,				2504	0.1411				p.N3650N		Atlas-SNP	.											DYNC1H1,NS,carcinoma,+1,1	DYNC1H1	395	1	0			c.C10950T						PASS	.	C		183,4223	117.5+/-155.4	5,173,2025	87.0	81.0	83.0		10950	3.8	1.0	14	dbSNP_123	83	608,7992	159.8+/-213.0	27,554,3719	no	coding-synonymous	DYNC1H1	NM_001376.4		32,727,5744	TT,TC,CC		7.0698,4.1534,6.0818		3650/4647	102504838	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon58			GCTGAACCGTGAA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.10950C>T	14.37:g.102504838C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	54	32	0.592593	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			C|0.948;T|0.052	0.052	strong		0.542	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
OR5W2	390148	hgsc.bcm.edu	37	11	55681942	55681942	+	Missense_Mutation	SNP	G	G	T	rs17511797	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55681942G>T	ENST00000344514.1	-	1	116	c.117C>A	c.(115-117)ttC>ttA	p.F39L		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	39			F -> L (in dbSNP:rs17511797).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GATTTGCTGAGAAATTAATGA	0.358													G|||	161	0.0321486	0.0038	0.0331	5008	,	,		20131	0.001		0.0905	False		,,,				2504	0.0419				p.F39L	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.C117A						PASS	.	G	LEU/PHE	68,4334	61.1+/-98.1	0,68,2133	71.0	74.0	73.0		117	-10.0	0.0	11	dbSNP_123	73	685,7907	170.3+/-221.5	34,617,3645	yes	missense	OR5W2	NM_001001960.1	22	34,685,5778	TT,TG,GG		7.9725,1.5448,5.795	benign	39/311	55681942	753,12241	2201	4296	6497	SO:0001583	missense	390148	exon1			TGCTGAGAAATTA	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.117C>A	11.37:g.55681942G>T	ENSP00000342448:p.Phe39Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	112	46	0.410714	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	77	0.035256410256410256	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	67	0.08839050131926121	G	0.019	-1.448949	0.01080	0.015448	0.079725	ENSG00000187612	ENST00000344514	T	0.00293	8.26	5.01	-10.0	0.00425	.	1.403840	0.05284	N	0.519912	T	0.00012	0.0000	N	0.00059	-2.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47302	-0.9128	10	0.02654	T	1	.	3.8009	0.08758	0.1404:0.2722:0.407:0.1804	rs17511797;rs52834620;rs60974682;rs17511797	39	Q8NH69	OR5W2_HUMAN	L	39	ENSP00000342448:F39L	ENSP00000342448:F39L	F	-	3	2	OR5W2	55438518	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.651000	0.01989	-3.259000	0.00202	-2.839000	0.00105	TTC	G|0.951;T|0.049	0.049	strong		0.358	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
LYZL6	57151	hgsc.bcm.edu	37	17	34264859	34264859	+	Silent	SNP	A	A	G	rs2280783	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:34264859A>G	ENST00000585556.1	-	3	535	c.201T>C	c.(199-201)gaT>gaC	p.D67D	LYZL6_ENST00000492340.2_5'UTR|LYZL6_ENST00000394523.3_Silent_p.D67D|LYZL6_ENST00000293274.4_Silent_p.D67D			O75951	LYZL6_HUMAN	lysozyme-like 6	67					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)	p.D67D(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	12				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CAAAGCTTCCATCTGCATTTT	0.448													A|||	647	0.129193	0.2247	0.0994	5008	,	,		23330	0.0972		0.1302	False		,,,				2504	0.0532				p.D67D		Atlas-SNP	.											LYZL6,NS,carcinoma,0,1	LYZL6	18	1	1	Substitution - coding silent(1)	stomach(1)	c.T201C						PASS	.	A	,	894,3512	346.9+/-309.2	92,710,1401	103.0	101.0	101.0		201,201	-3.1	0.3	17	dbSNP_100	101	1144,7456	235.8+/-268.3	71,1002,3227	no	coding-synonymous,coding-synonymous	LYZL6	NM_001199951.1,NM_020426.2	,	163,1712,4628	GG,GA,AA		13.3023,20.2905,15.6697	,	67/149,67/149	34264859	2038,10968	2203	4300	6503	SO:0001819	synonymous_variant	57151	exon2			GCTTCCATCTGCA	AF088219, AY742214	CCDS11302.1	17q11.2	2014-04-10			ENSG00000161572	ENSG00000275722			29614	protein-coding gene	gene with protein product		612751				10213461	Standard	NM_020426		Approved	LYC1, PRO1485, TKAL754	uc002hkj.2	O75951	OTTHUMG00000188400	ENST00000585556.1:c.201T>C	17.37:g.34264859A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	175	89	0.508571	NM_020426	Q6UW30	Silent	SNP	ENST00000585556.1	37	CCDS11302.1																																																																																			A|0.847;G|0.153	0.153	strong		0.448	LYZL6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256578.2	NM_020426	
CARD11	84433	hgsc.bcm.edu	37	7	2976767	2976767	+	Silent	SNP	G	G	A	rs6945582	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:2976767G>A	ENST00000396946.4	-	9	1648	c.1245C>T	c.(1243-1245)gaC>gaT	p.D415D		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	415					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TCCTCATCTCGTCGTTCTTCT	0.577			Mis		DLBCL								G|||	454	0.090655	0.0424	0.1556	5008	,	,		22008	0.0109		0.2078	False		,,,				2504	0.0716				p.D415D		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.C1245T						PASS	.	G		309,4097	166.5+/-197.7	10,289,1904	179.0	145.0	156.0		1245	-0.6	1.0	7	dbSNP_116	156	1622,6978	301.8+/-305.6	159,1304,2837	no	coding-synonymous	CARD11	NM_032415.4		169,1593,4741	AA,AG,GG		18.8605,7.0132,14.847		415/1155	2976767	1931,11075	2203	4300	6503	SO:0001819	synonymous_variant	84433	exon9			CATCTCGTCGTTC	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1245C>T	7.37:g.2976767G>A		Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	167	167	1	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																			G|0.868;A|0.132	0.132	strong		0.577	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48606537	48606537	+	Missense_Mutation	SNP	C	C	G	rs1133818	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48606537C>G	ENST00000323776.5	+	18	3003	c.2841C>G	c.(2839-2841)agC>agG	p.S947R	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.S910R	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			ACACCCAGAGCCTGCACAGTG	0.542													G|||	4057	0.810104	0.9153	0.6988	5008	,	,		17926	0.8819		0.7336	False		,,,				2504	0.7515				p.S947R		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.C2841G						PASS	.	G	ARG/SER	3922,484	221.7+/-238.7	1753,416,34	37.0	41.0	39.0		2841	5.3	0.6	17	dbSNP_86	39	6269,2331	387.7+/-342.3	2297,1675,328	yes	missense	MYCBPAP	NM_032133.4	110	4050,2091,362	GG,GC,CC		27.1047,10.985,21.6439	possibly-damaging	947/985	48606537	10191,2815	2203	4300	6503	SO:0001583	missense	84073	exon18			CCAGAGCCTGCAC	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.2841C>G	17.37:g.48606537C>G	ENSP00000323184:p.Ser947Arg	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	1777	0.8136446886446886	456	0.926829268292683	258	0.712707182320442	507	0.8863636363636364	556	0.7335092348284961	G	3.009	-0.204353	0.06180	0.89015	0.728953	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.20200	2.09;2.09	5.26	5.26	0.73747	.	0.198671	0.43110	N	0.000611	T	0.00012	0.0000	N	0.00099	-2.14	0.54753	P	1.2000000000012001E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.38067	-0.9678	9	0.02654	T	1	-23.3303	13.166	0.59571	0.0:0.1604:0.8396:0.0	rs1133818;rs3178519;rs3195892;rs11559079;rs17421945;rs17642482;rs17856810;rs52811849;rs58726894;rs1133818	910	Q8TBZ2	MYBPP_HUMAN	R	947;910	ENSP00000323184:S947R;ENSP00000397209:S910R	ENSP00000323184:S947R	S	+	3	2	MYCBPAP	45961536	1.000000	0.71417	0.610000	0.28997	0.752000	0.42762	0.855000	0.27805	1.239000	0.43787	-0.120000	0.15030	AGC	C|0.198;G|0.802	0.802	strong		0.542	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
ATP4B	496	hgsc.bcm.edu	37	13	114309226	114309226	+	Silent	SNP	G	G	A	rs11164142	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:114309226G>A	ENST00000335288.4	-	2	185	c.144C>T	c.(142-144)taC>taT	p.Y48Y		NM_000705.3	NP_000696.1	P51164	ATP4B_HUMAN	ATPase, H+/K+ exchanging, beta polypeptide	48					cell adhesion (GO:0007155)|hydrogen ion transmembrane transport (GO:1902600)|ion transmembrane transport (GO:0034220)|response to lipopolysaccharide (GO:0032496)|response to organonitrogen compound (GO:0010243)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	hydrogen:potassium-exchanging ATPase activity (GO:0008900)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.00696)|all_epithelial(44;0.00347)|all_lung(25;0.0221)|Breast(118;0.0411)|Lung NSC(25;0.0839)	all cancers(43;0.171)			TCATCACCACGTAGAAGGCCA	0.542													G|||	2370	0.473243	0.32	0.4438	5008	,	,		17342	0.6032		0.4592	False		,,,				2504	0.5818				p.Y48Y		Atlas-SNP	.											.	ATP4B	35	.	0			c.C144T						PASS	.	G		1313,3093	442.5+/-346.7	194,925,1084	185.0	131.0	149.0		144	0.5	1.0	13	dbSNP_120	149	3763,4837	533.8+/-382.5	849,2065,1386	no	coding-synonymous	ATP4B	NM_000705.3		1043,2990,2470	AA,AG,GG		43.7558,29.8003,39.0281		48/292	114309226	5076,7930	2203	4300	6503	SO:0001819	synonymous_variant	496	exon2			CACCACGTAGAAG		CCDS9539.1	13q34	2011-08-01			ENSG00000186009	ENSG00000186009	3.6.3.10	"""ATPases / P-type"""	820	protein-coding gene	gene with protein product		137217				1330887, 15057823	Standard	NM_000705		Approved	ATP6B	uc001vtz.3	P51164	OTTHUMG00000140234	ENST00000335288.4:c.144C>T	13.37:g.114309226G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	135	72	0.533333	NM_000705	B1B0N8	Silent	SNP	ENST00000335288.4	37	CCDS9539.1																																																																																			G|0.586;A|0.414	0.414	strong		0.542	ATP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276703.2	NM_000705	
MTR	4548	hgsc.bcm.edu	37	1	237058828	237058828	+	Silent	SNP	C	C	T	rs1131449	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:237058828C>T	ENST00000366577.5	+	31	3970	c.3576C>T	c.(3574-3576)ctC>ctT	p.L1192L	MTR_ENST00000535889.1_Silent_p.L1141L|MTR_ENST00000470570.1_3'UTR	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	1192	AdoMet activation. {ECO:0000255|PROSITE- ProRule:PRU00346}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	TGTGGAGACTCGCAGACATCG	0.592													C|||	2650	0.529153	0.4342	0.5922	5008	,	,		17413	0.5198		0.5358	False		,,,				2504	0.6155				p.L1192L		Atlas-SNP	.											MTR,NS,carcinoma,0,2	MTR	127	2	0			c.C3576T						scavenged	.	C		2051,2349		475,1101,624	19.0	18.0	19.0		3576	-11.3	0.0	1	dbSNP_86	19	5038,3544		1496,2046,749	no	coding-synonymous	MTR	NM_000254.2		1971,3147,1373	TT,TC,CC		41.2957,46.6136,45.3936		1192/1266	237058828	7089,5893	2200	4291	6491	SO:0001819	synonymous_variant	4548	exon31			GAGACTCGCAGAC	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.3576C>T	1.37:g.237058828C>T		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	172	79	0.459302	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Silent	SNP	ENST00000366577.5	37	CCDS1614.1																																																																																			C|0.456;G|0.000;T|0.544	0.544	strong		0.592	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	
DNASE1L3	1776	hgsc.bcm.edu	37	3	58191266	58191266	+	Silent	SNP	C	C	T	rs2070117	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:58191266C>T	ENST00000394549.2	-	3	568	c.252G>A	c.(250-252)acG>acA	p.T84T	DNASE1L3_ENST00000486455.1_Intron|DNASE1L3_ENST00000318316.3_Silent_p.T84T|DNASE1L3_ENST00000483681.1_Silent_p.T84T	NM_004944.3	NP_004935.1	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3	84					apoptotic DNA fragmentation (GO:0006309)|developmental programmed cell death (GO:0010623)|DNA metabolic process (GO:0006259)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			breast(2)|large_intestine(4)|lung(6)	12				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)		CATAGTTGTACGTTATGCCTC	0.388													C|||	1812	0.361821	0.1664	0.2997	5008	,	,		22701	0.6429		0.2237	False		,,,				2504	0.5225				p.T84T	Esophageal Squamous(96;1069 1424 4841 43466 52325)	Atlas-SNP	.											.	DNASE1L3	36	.	0			c.G252A						PASS	.	C		728,3676	300.4+/-286.3	54,620,1528	186.0	182.0	183.0		252	3.4	0.2	3	dbSNP_96	183	1709,6891	313.0+/-311.1	166,1377,2757	no	coding-synonymous	DNASE1L3	NM_004944.2		220,1997,4285	TT,TC,CC		19.8721,16.5304,18.7404		84/306	58191266	2437,10567	2202	4300	6502	SO:0001819	synonymous_variant	1776	exon3			GTTGTACGTTATG	AF047354	CCDS2886.1, CCDS58836.1	3p14.3	2008-05-15			ENSG00000163687	ENSG00000163687			2959	protein-coding gene	gene with protein product	"""DNase gamma"""	602244				9205125, 9714828, 14646506	Standard	NM_004944		Approved	DNAS1L3, LSD	uc003djo.2	Q13609	OTTHUMG00000159153	ENST00000394549.2:c.252G>A	3.37:g.58191266C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	142	79	0.556338	NM_004944	B2R8B1|B7Z707|O75803	Silent	SNP	ENST00000394549.2	37	CCDS2886.1																																																																																			C|0.747;T|0.253	0.253	strong		0.388	DNASE1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353533.1	NM_004944	
PIGN	23556	hgsc.bcm.edu	37	18	59770033	59770033	+	Silent	SNP	C	C	T	rs12326381	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:59770033C>T	ENST00000357637.5	-	21	2377	c.1962G>A	c.(1960-1962)ctG>ctA	p.L654L	PIGN_ENST00000400334.3_Silent_p.L654L	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	654					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				TGACCTGTAACAGATGTACCA	0.333													T|||	478	0.0954473	0.0144	0.1239	5008	,	,		17245	0.0069		0.2684	False		,,,				2504	0.0982				p.L654L		Atlas-SNP	.											.	PIGN	62	.	0			c.G1962A						PASS	.	T	,	210,3464		6,198,1633	61.0	59.0	59.0		1962,1962	-6.9	0.0	18	dbSNP_120	59	1996,6176		231,1534,2321	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	237,1732,3954	TT,TC,CC		24.4249,5.7158,18.6223	,	654/932,654/932	59770033	2206,9640	1837	4086	5923	SO:0001819	synonymous_variant	23556	exon21			CTGTAACAGATGT	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.1962G>A	18.37:g.59770033C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			C|0.880;T|0.120	0.120	strong		0.333	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
MYSM1	114803	hgsc.bcm.edu	37	1	59148118	59148118	+	Missense_Mutation	SNP	A	A	T	rs17118103	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:59148118A>T	ENST00000472487.1	-	8	637	c.598T>A	c.(598-600)Tgt>Agt	p.C200S	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	200			C -> S (in dbSNP:rs17118103).		chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.C200S(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					CCCCTTAAACATGATGGTGTC	0.408													A|||	780	0.155751	0.0076	0.1527	5008	,	,		16491	0.2143		0.1859	False		,,,				2504	0.2669				p.C200S		Atlas-SNP	.											MYSM1,NS,carcinoma,0,1	MYSM1	50	1	1	Substitution - Missense(1)	stomach(1)	c.T598A						PASS	.	A	SER/CYS	117,3651		2,113,1769	102.0	92.0	95.0		598	0.2	0.1	1	dbSNP_123	95	1235,6969		101,1033,2968	yes	missense	MYSM1	NM_001085487.2	112	103,1146,4737	TT,TA,AA		15.0536,3.1051,11.293	benign	200/829	59148118	1352,10620	1884	4102	5986	SO:0001583	missense	114803	exon8			TTAAACATGATGG	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.598T>A	1.37:g.59148118A>T	ENSP00000418734:p.Cys200Ser	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	236	116	0.491525	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Missense_Mutation	SNP	ENST00000472487.1	37	CCDS41343.1	311	0.1423992673992674	5	0.01016260162601626	51	0.1408839779005525	111	0.19405594405594406	144	0.18997361477572558	A	7.056	0.565341	0.13498	0.031051	0.150536	ENSG00000162601	ENST00000472487	T	0.19806	2.12	5.03	0.157	0.14915	.	1.182020	0.05605	N	0.577165	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	9	0.08179	T	0.78	0.5257	1.2295	0.01941	0.2009:0.2532:0.1083:0.4376	rs17118103;rs52792942;rs17118103	200	Q5VVJ2	MYSM1_HUMAN	S	200	ENSP00000418734:C200S	ENSP00000418734:C200S	C	-	1	0	MYSM1	58920706	0.000000	0.05858	0.060000	0.19600	0.938000	0.57974	-0.148000	0.10219	0.099000	0.17552	0.528000	0.53228	TGT	A|0.854;T|0.146	0.146	strong		0.408	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481	
CPSF4	10898	hgsc.bcm.edu	37	7	99047978	99047978	+	Silent	SNP	T	T	C	rs883403	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99047978T>C	ENST00000292476.5	+	4	397	c.387T>C	c.(385-387)cgT>cgC	p.R129R	CPSF4_ENST00000441580.1_Silent_p.R76R|ATP5J2-PTCD1_ENST00000437572.1_Intron|ATP5J2_ENST00000466753.1_Intron|CPSF4_ENST00000436336.2_Silent_p.R129R|CPSF4_ENST00000451876.1_Intron|ATP5J2-PTCD1_ENST00000413834.1_Intron|PTCD1_ENST00000555673.1_Intron|CPSF4_ENST00000471455.1_3'UTR			O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4, 30kDa	129					modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA processing (GO:0006397)|viral life cycle (GO:0019058)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(5)	14	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					GGTATGACCGTGGCTTCTGCA	0.617													C|||	2277	0.454673	0.9054	0.2824	5008	,	,		19251	0.3403		0.165	False		,,,				2504	0.3834				p.R129R		Atlas-SNP	.											.	CPSF4	24	.	0			c.T387C						PASS	.	C	,,	3396,1010	375.1+/-321.5	1304,788,111	69.0	59.0	62.0		387,,387	-11.7	0.3	7	dbSNP_86	62	1238,7362	761.7+/-407.6	102,1034,3164	no	coding-synonymous,intron,coding-synonymous	CPSF4,ATP5J2-PTCD1	NM_001081559.1,NM_001198879.1,NM_006693.2	,,	1406,1822,3275	CC,CT,TT		14.3953,22.9233,35.6297	,,	129/245,,129/270	99047978	4634,8372	2203	4300	6503	SO:0001819	synonymous_variant	10898	exon4			TGACCGTGGCTTC		CCDS5664.1, CCDS47652.1	7q22	2007-10-18	2002-08-29		ENSG00000160917	ENSG00000160917			2327	protein-coding gene	gene with protein product		603052	"""cleavage and polyadenylation specific factor 4, 30kD subunit"""			9651582, 9224719	Standard	NM_006693		Approved	NAR, CPSF30	uc003uqj.3	O95639	OTTHUMG00000154599	ENST00000292476.5:c.387T>C	7.37:g.99047978T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	147	70	0.47619	NM_001081559	D6W5S8|Q6FGE6|Q86TF8|Q9BTW6	Silent	SNP	ENST00000292476.5	37	CCDS5664.1	858	0.39285714285714285	428	0.8699186991869918	112	0.30939226519337015	192	0.3356643356643357	126	0.1662269129287599	C	9.966	1.224022	0.22457	0.770767	0.143953	ENSG00000160917	ENST00000440514	.	.	.	5.93	-11.7	0.00046	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999811	.	.	.	.	.	.	T	0.23190	-1.0195	3	.	.	.	-8.6058	5.2076	0.15299	0.1613:0.3878:0.0609:0.39	rs883403;rs11539768;rs17854666;rs57853370;rs883403	.	.	.	R	11	.	.	W	+	1	0	CPSF4	98885914	0.000000	0.05858	0.280000	0.24747	0.974000	0.67602	-1.672000	0.01952	-2.308000	0.00652	-0.733000	0.03571	TGG	T|0.639;C|0.361	0.361	strong		0.617	CPSF4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336254.1		
ROR2	4920	hgsc.bcm.edu	37	9	94486321	94486321	+	Missense_Mutation	SNP	C	C	T	rs10761129	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:94486321C>T	ENST00000375708.3	-	9	2653	c.2455G>A	c.(2455-2457)Gtc>Atc	p.V819I	ROR2_ENST00000375715.1_Intron|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	819	Pro-rich.		V -> I (in dbSNP:rs10761129). {ECO:0000269|PubMed:10700182, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.3}.		cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						TTGACGGGGACGTAGAGCTGC	0.672													T|||	3746	0.748003	0.7776	0.7723	5008	,	,		14910	0.9137		0.6879	False		,,,				2504	0.5818				p.V819I		Atlas-SNP	.											.	ROR2	167	.	0			c.G2455A						PASS	.	T	ILE/VAL	3350,1056		1276,798,129	38.0	47.0	44.0		2455	3.4	1.0	9	dbSNP_120	44	5761,2835		1914,1933,451	yes	missense	ROR2	NM_004560.3	29	3190,2731,580	TT,TC,CC		32.9805,23.9673,29.9262	benign	819/944	94486321	9111,3891	2203	4298	6501	SO:0001583	missense	4920	exon9			CGGGGACGTAGAG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.2455G>A	9.37:g.94486321C>T	ENSP00000364860:p.Val819Ile	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	CCDS6691.1	1712	0.7838827838827839	383	0.7784552845528455	267	0.7375690607734806	531	0.9283216783216783	531	0.7005277044854882	T	0.024	-1.385455	0.01194	0.760327	0.670195	ENSG00000169071	ENST00000375708	T	0.75477	-0.94	4.52	3.39	0.38822	.	0.000000	0.42548	N	0.000696	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43475	-0.9389	9	0.02654	T	1	.	8.9652	0.35872	0.0:0.1524:0.0:0.8476	rs10761129;rs10761129	819	Q01974	ROR2_HUMAN	I	819	ENSP00000364860:V819I	ENSP00000364860:V819I	V	-	1	0	ROR2	93526142	1.000000	0.71417	1.000000	0.80357	0.407000	0.30961	4.807000	0.62576	0.273000	0.22049	-1.677000	0.00738	GTC	C|0.262;T|0.738	0.738	strong		0.672	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
ATP13A2	23400	hgsc.bcm.edu	37	1	17312592	17312592	+	3'UTR	SNP	G	G	A	rs15786	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17312592G>A	ENST00000326735.8	-	0	3700				ATP13A2_ENST00000452699.1_3'UTR|ATP13A2_ENST00000341676.5_Missense_Mutation_p.P1122L|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2						cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		TCTCGGGGGAGGAGTGTAGAC	0.652													G|||	66	0.0131789	0.0008	0.0187	5008	,	,		15289	0.001		0.0437	False		,,,				2504	0.0072				p.P1122L		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C3365T						PASS	.	G	,LEU/PRO,	16,1368		0,16,676	62.0	66.0	64.0		,3365,	0.6	0.0	1	dbSNP_52	64	181,3001		7,167,1417	yes	utr-3,missense,utr-3	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,98,	7,183,2093	AA,AG,GG		5.6882,1.1561,4.3145	,,	,1122/1159,	17312592	197,4369	692	1591	2283	SO:0001624	3_prime_UTR_variant	23400	exon27			GGGGGAGGAGTGT	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.*124C>T	1.37:g.17312592G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	148	76	0.513514	NM_001141974	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	37	CCDS175.1	41	0.018772893772893772	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	32	0.04221635883905013	G	17.03	3.283848	0.59867	0.011561	0.056882	ENSG00000159363	ENST00000341676;ENST00000502418	D;D	0.97209	-3.28;-4.29	4.91	0.624	0.17659	.	.	.	.	.	T	0.57344	0.2047	N	0.08118	0	0.41991	D	0.990841	B	0.24186	0.099	B	0.16722	0.016	T	0.70718	-0.4795	9	0.48119	T	0.1	.	4.2628	0.10749	0.0855:0.1361:0.5832:0.1952	rs15786;rs3195757;rs52834367;rs59275127;rs15786	1122	Q5JXY1	.	L	1122;362	ENSP00000341115:P1122L;ENSP00000423065:P362L	ENSP00000341115:P1122L	P	-	2	0	ATP13A2	17185179	0.007000	0.16637	0.001000	0.08648	0.457000	0.32468	0.471000	0.22100	-0.064000	0.13043	0.467000	0.42956	CCT	G|0.979;A|0.021	0.021	strong		0.652	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
FER1L5	90342	hgsc.bcm.edu	37	2	97351840	97351840	+	RNA	SNP	A	A	G	rs7599598	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:97351840A>G	ENST00000457909.1	+	0	598							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						CCGCCTCAACACCGTGCTCCC	0.667													G|||	2528	0.504792	0.8926	0.3357	5008	,	,		19684	0.4524		0.4324	False		,,,				2504	0.229				p.T682A		Atlas-SNP	.											.	FER1L5	113	.	0			c.A2044G						PASS	.	G	ALA/THR	1136,248		467,202,23	70.0	85.0	80.0		2044	1.5	0.0	2	dbSNP_116	80	1288,1894		252,784,555	yes	missense	FER1L5	NM_001113382.1	58	719,986,578	GG,GA,AA		40.4777,17.9191,46.912	benign	682/2094	97351840	2424,2142	692	1591	2283			90342	exon21			CTCAACACCGTGC	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"""fer-1-like 5 (C. elegans)"""				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		2.37:g.97351840A>G		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	163	162	0.993865	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	37		1124	0.5146520146520146	429	0.8719512195121951	120	0.3314917127071823	243	0.42482517482517484	332	0.43799472295514513	G	12.09	1.834794	0.32421	0.820809	0.404777	ENSG00000214272	ENST00000414152;ENST00000436930	.	.	.	5.59	1.53	0.23141	.	.	.	.	.	T	0.00012	0.0000	N	0.01109	-1.01	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.34204	-0.9838	7	0.02654	T	1	-0.4898	3.8475	0.08940	0.2503:0.0:0.4341:0.3156	rs7599598;rs61161537;rs7599598	682	A0AVI2	FR1L5_HUMAN	A	682;675	.	ENSP00000444148:T682A	T	+	1	0	FER1L5	96715567	0.000000	0.05858	0.001000	0.08648	0.787000	0.44495	-0.134000	0.10436	-0.218000	0.10018	-0.119000	0.15052	ACC	A|0.465;G|0.535	0.535	strong		0.667	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400	
ADAM7	8756	hgsc.bcm.edu	37	8	24359068	24359068	+	Silent	SNP	G	G	A	rs13277171	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:24359068G>A	ENST00000175238.6	+	20	2270	c.2187G>A	c.(2185-2187)ctG>ctA	p.L729L	RP11-624C23.1_ENST00000523578.1_RNA|RP11-561E1.1_ENST00000519364.1_RNA|ADAM7_ENST00000520720.1_Silent_p.L501L|ADAM7_ENST00000380789.1_Silent_p.L729L|RP11-624C23.1_ENST00000519689.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	729						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		AGCCAATCCTGCCAGAAATTC	0.378													G|||	1326	0.264776	0.1006	0.428	5008	,	,		15229	0.1885		0.3042	False		,,,				2504	0.409				p.L729L		Atlas-SNP	.											ADAM7,colon,carcinoma,0,1	ADAM7	165	1	0			c.G2187A						PASS	.	G		558,3848	250.3+/-257.4	38,482,1683	77.0	78.0	78.0		2187	-2.7	0.0	8	dbSNP_121	78	2858,5742	449.2+/-362.0	482,1894,1924	no	coding-synonymous	ADAM7	NM_003817.2		520,2376,3607	AA,AG,GG		33.2326,12.6645,26.2648		729/755	24359068	3416,9590	2203	4300	6503	SO:0001819	synonymous_variant	8756	exon20			AATCCTGCCAGAA	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.2187G>A	8.37:g.24359068G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_003817	A8K8X7|O75959|Q6PEJ6	Silent	SNP	ENST00000175238.6	37	CCDS6045.1																																																																																			G|0.743;A|0.257	0.257	strong		0.378	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	182291	182291	+	Silent	SNP	A	A	G	rs11747660	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:182291A>G	ENST00000283426.6	+	18	3719	c.3669A>G	c.(3667-3669)ctA>ctG	p.L1223L		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	1223	Ser-rich.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		ACCCGGGCCTATGGAGCCCTG	0.632													A|||	270	0.0539137	0.0076	0.0879	5008	,	,		17635	0.002		0.1292	False		,,,				2504	0.0685				p.L1223L		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.A3669G						PASS	.	A		121,4285	88.7+/-127.4	2,117,2084	50.0	53.0	52.0		3669	1.9	0.0	5	dbSNP_120	52	992,7608	211.4+/-252.0	67,858,3375	no	coding-synonymous	PLEKHG4B	NM_052909.3		69,975,5459	GG,GA,AA		11.5349,2.7463,8.5576		1223/1272	182291	1113,11893	2203	4300	6503	SO:0001819	synonymous_variant	153478	exon18			GGGCCTATGGAGC	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.3669A>G	5.37:g.182291A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	154	70	0.454545	NM_052909		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																			A|0.923;G|0.077	0.077	strong		0.632	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
USP24	23358	hgsc.bcm.edu	37	1	55563349	55563349	+	Silent	SNP	G	G	A	rs75297697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:55563349G>A	ENST00000294383.6	-	48	5636	c.5637C>T	c.(5635-5637)agC>agT	p.S1879S	USP24_ENST00000407756.1_Silent_p.S1719S	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1879	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						TTACCAAGACGCTAGGTAAAG	0.333													G|||	10	0.00199681	0.0045	0.0029	5008	,	,		17063	0.0		0.002	False		,,,				2504	0.0				p.S1879S		Atlas-SNP	.											.	USP24	323	.	0			c.C5637T						PASS	.	G		27,3571		0,27,1772	38.0	34.0	35.0		5637	-2.3	1.0	1	dbSNP_132	35	18,8108		0,18,4045	no	coding-synonymous	USP24	NM_015306.2		0,45,5817	AA,AG,GG		0.2215,0.7504,0.3838		1879/2621	55563349	45,11679	1799	4063	5862	SO:0001819	synonymous_variant	23358	exon48			CAAGACGCTAGGT	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.5637C>T	1.37:g.55563349G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																			G|0.997;A|0.003	0.003	strong		0.333	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
TULP3	7289	hgsc.bcm.edu	37	12	3049698	3049698	+	3'UTR	SNP	T	T	C	rs998814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:3049698T>C	ENST00000448120.2	+	0	2468				TULP3_ENST00000397132.2_Missense_Mutation_p.C438R	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3						anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CTTCCCAGAATGTATCCAAAC	0.498													C|||	1389	0.277356	0.4085	0.2046	5008	,	,		20215	0.2183		0.2058	False		,,,				2504	0.2863				p.C438R		Atlas-SNP	.											.	TULP3	45	.	0			c.T1312C						PASS	.	C	,ARG/CYS	517,867		96,325,271	49.0	44.0	46.0		,1312	-0.3	0.0	12	dbSNP_86	46	691,2491		69,553,969	yes	utr-3,missense	TULP3	NM_003324.4,NM_001160408.1	,180	165,878,1240	CC,CT,TT		21.7159,37.3555,26.4564	,benign	,438/502	3049698	1208,3358	692	1591	2283	SO:0001624	3_prime_UTR_variant	7289	exon12			CCAGAATGTATCC	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.*1088T>C	12.37:g.3049698T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_001160408	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	37	CCDS8519.1	537	0.24587912087912087	186	0.3780487804878049	75	0.20718232044198895	110	0.19230769230769232	166	0.21899736147757257	C	0.107	-1.143619	0.01728	0.373555	0.217159	ENSG00000078246	ENST00000397132	D	0.91351	-2.83	3.48	-0.313	0.12754	.	.	.	.	.	T	0.00012	0.0000	N	0.04090	-0.28	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10314	-1.0635	8	0.46703	T	0.11	.	4.1363	0.10172	0.0:0.2335:0.1803:0.5862	rs998814;rs3210448;rs998814	438	F8WBZ9	.	R	438	ENSP00000380321:C438R	ENSP00000380321:C438R	C	+	1	0	TULP3	2919959	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.057000	0.03486	-0.212000	0.10109	-1.259000	0.01468	TGT	A|0.008;C|0.256	0.256	strong		0.498	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
PCDHB10	56126	hgsc.bcm.edu	37	5	140572763	140572763	+	Missense_Mutation	SNP	C	C	G	rs2907323	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140572763C>G	ENST00000239446.4	+	1	822	c.638C>G	c.(637-639)aCa>aGa	p.T213R		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	213	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTAACCCTCACAGCGCTGGAT	0.532													C|||	485	0.096845	0.0166	0.0879	5008	,	,		17115	0.0933		0.1431	False		,,,				2504	0.1677				p.T213R		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C638G						PASS	.	C	ARG/THR	213,4193	130.6+/-167.2	6,201,1996	94.0	103.0	100.0		638	3.4	1.0	5	dbSNP_101	100	1405,7195	272.2+/-289.9	132,1141,3027	no	missense	PCDHB10	NM_018930.3	71	138,1342,5023	GG,GC,CC		16.3372,4.8343,12.4404	possibly-damaging	213/801	140572763	1618,11388	2203	4300	6503	SO:0001583	missense	56126	exon1			CCCTCACAGCGCT	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.638C>G	5.37:g.140572763C>G	ENSP00000239446:p.Thr213Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	182	94	0.516484	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	222	0.10164835164835165	12	0.024390243902439025	40	0.11049723756906077	53	0.09265734265734266	117	0.15435356200527706	C	13.91	2.378234	0.42207	0.048343	0.163372	ENSG00000120324	ENST00000239446	T	0.02944	4.1	3.41	3.41	0.39046	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00039	0.0001	M	0.81614	2.55	0.30500	P	0.770458	D	0.56746	0.977	D	0.65323	0.934	T	0.05886	-1.0858	8	0.87932	D	0	.	6.8307	0.23909	0.0:0.7129:0.1825:0.1045	rs61730160	213	Q9UN67	PCDBA_HUMAN	R	213	ENSP00000239446:T213R	ENSP00000239446:T213R	T	+	2	0	PCDHB10	140552947	0.000000	0.05858	0.991000	0.47740	0.786000	0.44442	-0.561000	0.05957	1.930000	0.55929	0.556000	0.70494	ACA	C|0.881;G|0.119	0.119	strong		0.532	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
CD4	920	hgsc.bcm.edu	37	12	6924109	6924109	+	Silent	SNP	C	C	T	rs11575099	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6924109C>T	ENST00000011653.4	+	5	816	c.558C>T	c.(556-558)gtC>gtT	p.V186V	CD4_ENST00000541982.1_Silent_p.V131V|CD4_ENST00000538827.1_3'UTR	NM_000616.4|NM_001195015.2|NM_001195016.2|NM_001195017.2	NP_000607.1|NP_001181944.1|NP_001181945.1|NP_001181946.1	P01730	CD4_HUMAN	CD4 molecule	186	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cytokine production (GO:0001816)|defense response to Gram-negative bacterium (GO:0050829)|entry into host cell (GO:0030260)|enzyme linked receptor protein signaling pathway (GO:0007167)|immune response (GO:0006955)|induction by virus of host cell-cell fusion (GO:0006948)|innate immune response (GO:0045087)|maintenance of protein location in cell (GO:0032507)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase activity (GO:0045860)|protein palmitoleylation (GO:0045234)|regulation of defense response to virus by virus (GO:0050690)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|T cell selection (GO:0045058)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|enzyme binding (GO:0019899)|extracellular matrix structural constituent (GO:0005201)|glycoprotein binding (GO:0001948)|MHC class II protein binding (GO:0042289)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	23		Myeloproliferative disorder(1001;0.0122)			Antithymocyte globulin(DB00098)	CATGCACTGTCTTGCAGAACC	0.557													C|||	65	0.0129792	0.0189	0.0101	5008	,	,		-128	0.0		0.0288	False		,,,				2504	0.0041				p.V186V		Atlas-SNP	.											.	CD4	47	.	0			c.C558T						PASS	.	C	,,,,	73,4333	65.3+/-102.7	0,73,2130	86.0	70.0	75.0		558,,,,	0.7	0.0	12	dbSNP_120	75	236,8364	96.6+/-158.3	3,230,4067	no	coding-synonymous,utr-5,utr-5,utr-5,utr-5	CD4	NM_000616.4,NM_001195014.2,NM_001195015.2,NM_001195016.2,NM_001195017.2	,,,,	3,303,6197	TT,TC,CC		2.7442,1.6568,2.3758	,,,,	186/459,,,,	6924109	309,12697	2203	4300	6503	SO:0001819	synonymous_variant	920	exon5			CACTGTCTTGCAG	M35160	CCDS8562.1	12p13.31	2013-01-11	2006-03-28		ENSG00000010610	ENSG00000010610		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1678	protein-coding gene	gene with protein product		186940	"""CD4 antigen (p55)"", ""T-cell surface glycoprotein CD4"""				Standard	NM_000616		Approved		uc001qqv.2	P01730	OTTHUMG00000168514	ENST00000011653.4:c.558C>T	12.37:g.6924109C>T		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	235	129	0.548936	NM_000616	B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5	Silent	SNP	ENST00000011653.4	37	CCDS8562.1																																																																																			C|0.979;T|0.021	0.021	strong		0.557	CD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399978.1	NM_000616	
PTPRQ	374462	hgsc.bcm.edu	37	12	80936082	80936082	+	Silent	SNP	C	C	T	rs11114503	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:80936082C>T	ENST00000266688.5	+	27	3648	c.3648C>T	c.(3646-3648)gcC>gcT	p.A1216A				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1262	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						TTTTTGCTGCCGCAAGAACTA	0.333													T|||	1993	0.397963	0.7988	0.3069	5008	,	,		15962	0.2192		0.2783	False		,,,				2504	0.228				p.A1048A		Atlas-SNP	.											.	PTPRQ	119	.	0			c.C3144T						PASS	.	T		982,402		347,288,57	62.0	53.0	56.0		3206	-2.7	1.0	12	dbSNP_120	56	878,2302		135,608,847	no	coding-synonymous	PTPRQ	NM_001145026.1		482,896,904	TT,TC,CC		27.6101,29.0462,40.7537		1220/2300	80936082	1860,2704	692	1590	2282	SO:0001819	synonymous_variant	374462	exon19			TGCTGCCGCAAGA	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.3648C>T	12.37:g.80936082C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	NM_001145026		Silent	SNP	ENST00000266688.5	37		839	0.3841575091575092	375	0.7621951219512195	132	0.36464088397790057	135	0.23601398601398602	197	0.2598944591029024	T	7.971	0.749000	0.15710	0.709538	0.276101	ENSG00000139304	ENST00000532722	.	.	.	5.59	-2.67	0.06059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999797	.	.	.	.	.	.	T	0.32929	-0.9888	3	.	.	.	.	1.3022	0.02081	0.1985:0.2312:0.1025:0.4678	rs11114503;rs17713244;rs59001378;rs11114503	.	.	.	L	917	.	.	P	+	2	0	PTPRQ	79460213	0.997000	0.39634	0.989000	0.46669	0.981000	0.71138	0.137000	0.15995	-0.504000	0.06577	-1.120000	0.02017	CCG	C|0.585;T|0.415	0.415	strong		0.333	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
ELMOD3	84173	hgsc.bcm.edu	37	2	85595818	85595818	+	Missense_Mutation	SNP	C	C	T	rs955592	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:85595818C>T	ENST00000409890.2	+	7	876	c.209C>T	c.(208-210)aCa>aTa	p.T70I	RN7SL113P_ENST00000497900.2_RNA|ELMOD3_ENST00000409013.3_Missense_Mutation_p.T70I|ELMOD3_ENST00000409344.3_Missense_Mutation_p.T70I|Y_RNA_ENST00000365512.1_RNA|ELMOD3_ENST00000315658.7_Missense_Mutation_p.T70I|ELMOD3_ENST00000490508.1_3'UTR|ELMOD3_ENST00000393852.4_Missense_Mutation_p.T70I|ELMOD3_ENST00000428955.2_Missense_Mutation_p.T70I			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3	70			T -> I (in dbSNP:rs955592).		phagocytosis (GO:0006909)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	12						GTTGTGAGTACAGAGGTGGTC	0.552													C|||	158	0.0315495	0.0219	0.036	5008	,	,		18926	0.0099		0.0547	False		,,,				2504	0.0399				p.T70I		Atlas-SNP	.											.	ELMOD3	53	.	0			c.C209T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR,ILE/THR	140,4266	97.1+/-135.8	2,136,2065	131.0	110.0	117.0		209,209,209,209	2.2	0.1	2	dbSNP_86	117	616,7984	160.5+/-213.6	21,574,3705	yes	missense,missense,missense,missense	ELMOD3	NM_001135021.1,NM_001135022.1,NM_001135023.1,NM_032213.4	89,89,89,89	23,710,5770	TT,TC,CC		7.1628,3.1775,5.8127	benign,benign,benign,benign	70/382,70/382,70/382,70/392	85595818	756,12250	2203	4300	6503	SO:0001583	missense	84173	exon7			TGAGTACAGAGGT	AF258573	CCDS1973.1, CCDS46352.1	2p11.2	2014-01-28	2008-08-14	2008-08-14	ENSG00000115459	ENSG00000115459		"""RNA binding motif (RRM) containing"""	26158	protein-coding gene	gene with protein product		615427	"""RNA binding motif protein 29"", ""RNA binding motif and ELMO/CED-12 domain 1"", ""deafness, autosomal recessive 88"""	RBM29, RBED1, DFNB88		24039609	Standard	NM_032213		Approved	FLJ21977	uc010ysn.2	Q96FG2	OTTHUMG00000130170	ENST00000409890.2:c.209C>T	2.37:g.85595818C>T	ENSP00000386304:p.Thr70Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_001135022	B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Missense_Mutation	SNP	ENST00000409890.2	37	CCDS46352.1	74	0.03388278388278388	14	0.028455284552845527	15	0.04143646408839779	3	0.005244755244755245	42	0.055408970976253295	C	11.80	1.747127	0.30955	0.031775	0.071628	ENSG00000115459	ENST00000409331;ENST00000409013;ENST00000409890;ENST00000409344;ENST00000393852;ENST00000428955;ENST00000315658;ENST00000418268	T;T;T;T;T;T;T;T	0.31510	1.56;1.54;1.54;1.54;1.54;1.53;1.49;1.53	5.08	2.22	0.28083	.	1.501900	0.03555	N	0.226185	T	0.02012	0.0063	L	0.40543	1.245	0.09310	N	1	B;B	0.20671	0.02;0.047	B;B	0.18871	0.023;0.01	T	0.11891	-1.0569	10	0.45353	T	0.12	1.7855	5.1075	0.14793	0.1642:0.6568:0.0:0.1789	rs955592;rs17735041;rs57387558;rs955592	70;70	Q96FG2-6;Q96FG2	.;ELMD3_HUMAN	I	70	ENSP00000386257:T70I;ENSP00000387139:T70I;ENSP00000386304:T70I;ENSP00000386248:T70I;ENSP00000377434:T70I;ENSP00000412692:T70I;ENSP00000318264:T70I;ENSP00000393443:T70I	ENSP00000318264:T70I	T	+	2	0	ELMOD3	85449329	0.000000	0.05858	0.125000	0.21846	0.769000	0.43574	0.327000	0.19663	0.705000	0.31890	0.455000	0.32223	ACA	C|0.951;T|0.049	0.049	strong		0.552	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213	
ZNF229	7772	hgsc.bcm.edu	37	19	44933504	44933504	+	Silent	SNP	G	G	A	rs59505617	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:44933504G>A	ENST00000588931.1	-	6	1885	c.1452C>T	c.(1450-1452)acC>acT	p.T484T	ZNF229_ENST00000291187.4_Silent_p.T478T|CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	484					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)	p.T484T(1)		breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				GCCTCTCGCCGGTGTGTGTCT	0.542													G|||	795	0.158746	0.1899	0.3184	5008	,	,		19986	0.1498		0.0984	False		,,,				2504	0.0746				p.T484T		Atlas-SNP	.											ZNF229,NS,carcinoma,0,2	ZNF229	123	2	1	Substitution - coding silent(1)	stomach(1)	c.C1452T						PASS	.	G		697,3577		56,585,1496	102.0	110.0	107.0		1452	-7.5	0.0	19	dbSNP_129	107	903,7639		53,797,3421	no	coding-synonymous	ZNF229	NM_014518.2		109,1382,4917	AA,AG,GG		10.5713,16.3079,12.4844		484/826	44933504	1600,11216	2137	4271	6408	SO:0001819	synonymous_variant	7772	exon6			CTCGCCGGTGTGT	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1452C>T	19.37:g.44933504G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_014518	B2RWN3|Q59FV2|Q86WL9	Silent	SNP	ENST00000588931.1	37	CCDS42574.1																																																																																			G|0.852;A|0.148	0.148	strong		0.542	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
TRIM4	89122	hgsc.bcm.edu	37	7	99500911	99500911	+	Silent	SNP	A	A	G	rs2247761	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99500911A>G	ENST00000355947.2	-	6	978	c.849T>C	c.(847-849)tcT>tcC	p.S283S	TRIM4_ENST00000354241.5_Silent_p.S257S|TRIM4_ENST00000349062.2_Silent_p.S257S	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	283					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				CAGCTTCAAGAGAATAGTTCA	0.478													G|||	2898	0.578674	0.9039	0.4597	5008	,	,		21033	0.2976		0.5338	False		,,,				2504	0.5593				p.S283S		Atlas-SNP	.											.	TRIM4	33	.	0			c.T849C						PASS	.	G	,	3721,685	286.6+/-278.8	1574,573,56	126.0	120.0	122.0		849,771	1.2	0.0	7	dbSNP_100	122	5016,3584	518.2+/-379.2	1452,2112,736	no	coding-synonymous,coding-synonymous	TRIM4	NM_033017.3,NM_033091.2	,	3026,2685,792	GG,GA,AA		41.6744,15.547,32.8233	,	283/501,257/475	99500911	8737,4269	2203	4300	6503	SO:0001819	synonymous_variant	89122	exon6			TTCAAGAGAATAG	AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16275	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM4"", ""tripartite motif protein 4"""		"""tripartite motif-containing 4"""			11331580	Standard	NM_033017		Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.849T>C	7.37:g.99500911A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Silent	SNP	ENST00000355947.2	37	CCDS5679.1	1194	0.5467032967032966	440	0.8943089430894309	181	0.5	158	0.2762237762237762	415	0.5474934036939314	G	0.012	-1.669101	0.00765	0.84453	0.583256	ENSG00000146833	ENST00000447480	T	0.03358	3.96	2.16	1.25	0.21368	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.29058	-1.0024	5	0.02654	T	1	.	8.2152	0.31507	0.1842:0.0:0.8158:0.0	rs2247761;rs10386374;rs17212140;rs2247761	.	.	.	P	159	ENSP00000396229:S159P	ENSP00000396229:S159P	S	-	1	0	TRIM4	99338847	0.002000	0.14202	0.001000	0.08648	0.000000	0.00434	-0.126000	0.10563	-0.206000	0.10203	-1.820000	0.00599	TCT	A|0.383;G|0.617	0.617	strong		0.478	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017	
F5	2153	hgsc.bcm.edu	37	1	169484767	169484767	+	Missense_Mutation	SNP	A	A	G	rs9332701	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:169484767A>G	ENST00000367797.3	-	24	6644	c.6443T>C	c.(6442-6444)aTg>aCg	p.M2148T	F5_ENST00000367796.3_Missense_Mutation_p.M2153T	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	2148	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.		M -> T (in dbSNP:rs9332701). {ECO:0000269|Ref.3}.		blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	CTTTACATACATTTCAGAGGA	0.438													A|||	57	0.0113818	0.0023	0.0115	5008	,	,		18651	0.0		0.0328	False		,,,				2504	0.0133				p.M2148T		Atlas-SNP	.											.	F5	301	.	0			c.T6443C						PASS	.	A	THR/MET	46,4360	48.2+/-83.0	1,44,2158	182.0	170.0	174.0		6443	5.6	1.0	1	dbSNP_119	174	384,8216	125.5+/-184.1	10,364,3926	yes	missense	F5	NM_000130.4	81	11,408,6084	GG,GA,AA		4.4651,1.044,3.3062	probably-damaging	2148/2225	169484767	430,12576	2203	4300	6503	SO:0001583	missense	2153	exon24			ACATACATTTCAG	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.6443T>C	1.37:g.169484767A>G	ENSP00000356771:p.Met2148Thr	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	199	92	0.462312	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	26	0.011904761904761904	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	20	0.026385224274406333	A	17.28	3.350086	0.61183	0.01044	0.044651	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.98135	-4.74;-4.74	5.61	5.61	0.85477	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.079729	0.85682	D	0.000000	D	0.97632	0.9224	L	0.54965	1.715	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.98720	1.0708	10	0.87932	D	0	-23.2154	11.4589	0.50197	0.8651:0.0:0.0:0.1349	rs9332701;rs52800373;rs9332701	2148	P12259	FA5_HUMAN	T	2148;2153	ENSP00000356771:M2148T;ENSP00000356770:M2153T	ENSP00000356770:M2153T	M	-	2	0	F5	167751391	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.613000	0.54152	2.128000	0.65567	0.383000	0.25322	ATG	A|0.974;G|0.026	0.026	strong		0.438	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
DPP7	29952	hgsc.bcm.edu	37	9	140006202	140006202	+	Silent	SNP	G	G	A	rs13631	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140006202G>A	ENST00000371579.2	-	11	1216	c.1212C>T	c.(1210-1212)ctC>ctT	p.L404L		NM_013379.2	NP_037511.2	Q9UHL4	DPP2_HUMAN	dipeptidyl-peptidase 7	404						cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;4.25e-05)|Epithelial(140;0.000633)		TGGCGGCTCTGAGATCTGCAA	0.637													G|||	2578	0.514776	0.5325	0.4971	5008	,	,		12322	0.6776		0.3946	False		,,,				2504	0.4591				p.L404L		Atlas-SNP	.											.	DPP7	22	.	0			c.C1212T						PASS	.	G		2278,2128	597.5+/-388.9	593,1092,518	52.0	56.0	55.0		1212	3.2	0.9	9	dbSNP_52	55	3302,5298	491.7+/-373.2	638,2026,1636	no	coding-synonymous	DPP7	NM_013379.2		1231,3118,2154	AA,AG,GG		38.3953,48.2978,42.9033		404/493	140006202	5580,7426	2203	4300	6503	SO:0001819	synonymous_variant	29952	exon11			GGCTCTGAGATCT	AF154502	CCDS7030.1	9q34.3	2008-02-05	2006-01-12		ENSG00000176978	ENSG00000176978			14892	protein-coding gene	gene with protein product		610537	"""dipeptidylpeptidase 7"""			10477574, 11139392	Standard	XM_005266075		Approved	DPPII	uc004clh.3	Q9UHL4	OTTHUMG00000020977	ENST00000371579.2:c.1212C>T	9.37:g.140006202G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_013379	A8K7U7|Q5VSF1|Q969X4	Silent	SNP	ENST00000371579.2	37	CCDS7030.1																																																																																			G|0.539;A|0.461	0.461	strong		0.637	DPP7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055279.1	NM_013379	
ATP11A	23250	hgsc.bcm.edu	37	13	113481026	113481026	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:113481026G>A	ENST00000487903.1	+	12	1130	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N	ATP11A_ENST00000375630.2_Missense_Mutation_p.D348N|ATP11A_ENST00000283558.8_Missense_Mutation_p.D348N|ATP11A_ENST00000375645.3_Missense_Mutation_p.D348N			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	348					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				GGCATTCACGGACTTCCTGGC	0.547																																					p.D348N		Atlas-SNP	.											.	ATP11A	225	.	0			c.G1042A						PASS	.						118.0	104.0	109.0					13																	113481026		2203	4300	6503	SO:0001583	missense	23250	exon12			TTCACGGACTTCC	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.1042G>A	13.37:g.113481026G>A	ENSP00000420387:p.Asp348Asn	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	259	132	0.509652	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	37	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.006318	0.74932	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558	D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7	5.05	5.05	0.67936	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.93048	0.7787	L	0.45744	1.44	0.80722	D	1	D;P;B	0.89917	1.0;0.887;0.217	D;P;B	0.97110	1.0;0.733;0.444	D	0.90323	0.4346	10	0.15499	T	0.54	.	18.4296	0.90620	0.0:0.0:1.0:0.0	.	348;348;348	E9PCW5;E9PEJ6;P98196	.;.;AT11A_HUMAN	N	348	ENSP00000420387:D348N;ENSP00000364781:D348N;ENSP00000364796:D348N;ENSP00000283558:D348N	ENSP00000283558:D348N	D	+	1	0	ATP11A	112529027	1.000000	0.71417	0.933000	0.37362	0.121000	0.20230	9.445000	0.97587	2.341000	0.79615	0.557000	0.71058	GAC	.	.	none		0.547	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
TXLNB	167838	hgsc.bcm.edu	37	6	139564101	139564101	+	Silent	SNP	C	C	T	rs12529180	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:139564101C>T	ENST00000358430.3	-	10	1849	c.1617G>A	c.(1615-1617)aaG>aaA	p.K539K	RP1-225E12.3_ENST00000585874.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	539						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		GCTCTGGCTCCTTGAGAGCGG	0.557													C|||	272	0.0543131	0.0825	0.0533	5008	,	,		17514	0.001		0.0984	False		,,,				2504	0.0266				p.K539K		Atlas-SNP	.											.	TXLNB	96	.	0			c.G1617A						PASS	.	C		395,4011	178.7+/-207.4	21,353,1829	68.0	75.0	73.0		1617	1.5	0.0	6	dbSNP_120	73	873,7727	180.8+/-229.6	48,777,3475	no	coding-synonymous	TXLNB	NM_153235.3		69,1130,5304	TT,TC,CC		10.1512,8.965,9.7493		539/685	139564101	1268,11738	2203	4300	6503	SO:0001819	synonymous_variant	167838	exon10			TGGCTCCTTGAGA		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"""chromosome 6 open reading frame 198"""	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.1617G>A	6.37:g.139564101C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	137	52	0.379562	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Silent	SNP	ENST00000358430.3	37	CCDS34545.1																																																																																			C|0.908;T|0.092	0.092	strong		0.557	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235	
RB1CC1	9821	hgsc.bcm.edu	37	8	53555069	53555069	+	Silent	SNP	A	A	G	rs2305427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:53555069A>G	ENST00000025008.5	-	18	4702	c.4179T>C	c.(4177-4179)cgT>cgC	p.R1393R	RB1CC1_ENST00000435644.2_Silent_p.R1393R|RB1CC1_ENST00000539297.1_Silent_p.R1393R|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1393					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				AACTGCTACTACGCAACTTAC	0.438													A|||	1440	0.28754	0.0885	0.3199	5008	,	,		17931	0.6548		0.2048	False		,,,				2504	0.2403				p.R1393R	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.T4179C						PASS	.	A	,	401,4005	198.7+/-222.5	12,377,1814	125.0	117.0	120.0		4179,4179	-9.3	0.0	8	dbSNP_100	120	1429,7171	274.3+/-291.2	121,1187,2992	no	coding-synonymous,coding-synonymous	RB1CC1	NM_001083617.1,NM_014781.4	,	133,1564,4806	GG,GA,AA		16.6163,9.1012,14.0704	,	1393/1592,1393/1595	53555069	1830,11176	2203	4300	6503	SO:0001819	synonymous_variant	9821	exon18			GCTACTACGCAAC	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.4179T>C	8.37:g.53555069A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	194	81	0.417526	NM_001083617	Q86YR4|Q8WVU9|Q92601	Silent	SNP	ENST00000025008.5	37	CCDS34892.1																																																																																			A|0.779;G|0.221	0.221	strong		0.438	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	
KIAA1551	55196	hgsc.bcm.edu	37	12	32134207	32134207	+	Missense_Mutation	SNP	C	C	A	rs2388981	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:32134207C>A	ENST00000312561.4	+	4	732	c.318C>A	c.(316-318)caC>caA	p.H106Q	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	106			H -> Q (in dbSNP:rs2388981).														AACTAACTCACAATTTGCAGA	0.393													C|||	680	0.135783	0.0681	0.1254	5008	,	,		23821	0.0843		0.1859	False		,,,				2504	0.2362				p.H106Q		Atlas-SNP	.											.	.	.	.	0			c.C318A						PASS	.	C	GLN/HIS	350,4056	180.5+/-208.7	12,326,1865	86.0	80.0	82.0		318	-11.2	0.0	12	dbSNP_100	82	1726,6874	313.9+/-311.6	168,1390,2742	yes	missense	C12orf35	NM_018169.3	24	180,1716,4607	AA,AC,CC		20.0698,7.9437,15.9619	benign	106/1748	32134207	2076,10930	2203	4300	6503	SO:0001583	missense	55196	exon4			AACTCACAATTTG	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.318C>A	12.37:g.32134207C>A	ENSP00000310338:p.His106Gln	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	202	100	0.49505	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	282	0.12912087912087913	40	0.08130081300813008	47	0.1298342541436464	58	0.10139860139860139	137	0.18073878627968337	C	8.274	0.814058	0.16537	0.079437	0.200698	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.06933	3.24;3.24	5.59	-11.2	0.00127	.	0.459276	0.20637	N	0.088474	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.21586	-1.0241	8	.	.	.	.	3.0339	0.06116	0.2278:0.1376:0.1066:0.528	rs2388981;rs17511064;rs2388981	106	Q9HCM1	CL035_HUMAN	Q	106	ENSP00000310338:H106Q;ENSP00000370442:H106Q	.	H	+	3	2	C12orf35	32025474	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.821000	0.00749	-2.883000	0.00318	-1.734000	0.00692	CAC	C|0.850;A|0.150	0.150	strong		0.393	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
ZNF30	90075	hgsc.bcm.edu	37	19	35434448	35434448	+	Missense_Mutation	SNP	A	A	G	rs62122088	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:35434448A>G	ENST00000601142.1	+	5	815	c.578A>G	c.(577-579)aAg>aGg	p.K193R	ZNF30_ENST00000439785.1_Missense_Mutation_p.K194R|ZNF30_ENST00000303586.7_Missense_Mutation_p.K194R|ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000426813.2_Missense_Mutation_p.K112R			P17039	ZNF30_HUMAN	zinc finger protein 30	193				K -> R (in Ref. 2; CAE45802). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		GCCTTTGTTAAGCATGGGAGA	0.398													A|||	427	0.0852636	0.0628	0.0403	5008	,	,		19724	0.0635		0.1551	False		,,,				2504	0.0982				p.K194R		Atlas-SNP	.											.	ZNF30	44	.	0			c.A581G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	309,3769		11,287,1741	39.0	42.0	41.0		581,581,578	-0.0	0.0	19	dbSNP_129	41	1266,7172		91,1084,3044	yes	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	26,26,26	102,1371,4785	GG,GA,AA		15.0036,7.5772,12.5839	benign,benign,benign	194/625,194/625,193/624	35434448	1575,10941	2039	4219	6258	SO:0001583	missense	90075	exon5			TTGTTAAGCATGG	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.578A>G	19.37:g.35434448A>G	ENSP00000469954:p.Lys193Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	198	0.09065934065934066	30	0.06097560975609756	18	0.049723756906077346	30	0.05244755244755245	120	0.158311345646438	A	0.019	-1.464275	0.01053	0.075772	0.150036	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813	T;T	0.13657	2.57;2.57	2.4	-0.0256	0.13934	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04373	-0.215	0.80722	P	0.0	B;B	0.15473	0.005;0.013	B;B	0.13407	0.009;0.007	T	0.44651	-0.9314	8	0.10377	T	0.69	.	2.7105	0.05174	0.5563:0.2742:0.1695:0.0	rs62122088	194;193	P17039-2;P17039	.;ZNF30_HUMAN	R	194;193;112	ENSP00000403441:K194R;ENSP00000416457:K112R	ENSP00000303889:K193R	K	+	2	0	ZNF30	40126288	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.896000	0.00706	-0.220000	0.09988	-0.487000	0.04747	AAG	A|0.892;G|0.108	0.108	strong		0.398	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
WWC1	23286	hgsc.bcm.edu	37	5	167858434	167858434	+	Silent	SNP	T	T	C	rs3822658	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:167858434T>C	ENST00000265293.4	+	15	2767	c.2265T>C	c.(2263-2265)caT>caC	p.H755H	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Silent_p.H755H	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	755	C2.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		ACAGGAGCCATCTGGAAGAGT	0.572													T|||	84	0.0167732	0.0	0.0014	5008	,	,		14554	0.0556		0.0179	False		,,,				2504	0.0092				p.H755H		Atlas-SNP	.											.	WWC1	98	.	0			c.T2265C						PASS	.	T	,,	6,4400	11.4+/-27.6	0,6,2197	41.0	38.0	39.0		2265,2265,2265	-7.2	0.0	5	dbSNP_107	39	66,8534	37.8+/-93.5	0,66,4234	no	coding-synonymous,coding-synonymous,coding-synonymous	WWC1	NM_001161661.1,NM_001161662.1,NM_015238.2	,,	0,72,6431	CC,CT,TT		0.7674,0.1362,0.5536	,,	755/1120,755/1119,755/1114	167858434	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	23286	exon15			GAGCCATCTGGAA	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"""WW, C2 and coiled-coil domain containing"""	29435	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 168"""	610533	"""WW, C2 and coiled-coil domain containing 1"""			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2265T>C	5.37:g.167858434T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Silent	SNP	ENST00000265293.4	37	CCDS4366.1	39	0.017857142857142856	0	0.0	0	0.0	23	0.04020979020979021	16	0.021108179419525065	T	5.524	0.281662	0.10458	0.001362	0.007674	ENSG00000113645	ENST00000393895;ENST00000524228	.	.	.	5.24	-7.21	0.01490	.	.	.	.	.	T	0.05777	0.0151	.	.	.	0.20307	N	0.999911	.	.	.	.	.	.	T	0.19943	-1.0290	4	.	.	.	.	5.7589	0.18188	0.0973:0.4751:0.0983:0.3293	rs3822658;rs3822658	.	.	.	P	717;532	.	.	S	+	1	0	WWC1	167791012	0.000000	0.05858	0.000000	0.03702	0.800000	0.45204	-0.315000	0.08081	-1.361000	0.02169	-0.290000	0.09829	TCT	T|0.990;C|0.010	0.010	strong		0.572	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	
DRC7	84229	hgsc.bcm.edu	37	16	57762401	57762401	+	Missense_Mutation	SNP	T	T	C	rs2923147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:57762401T>C	ENST00000360716.3	+	17	2517	c.2296T>C	c.(2296-2298)Tgc>Cgc	p.C766R	CCDC135_ENST00000394337.4_Missense_Mutation_p.C766R|CCDC135_ENST00000336825.8_Missense_Mutation_p.C701R			Q8IY82	CC135_HUMAN		766			C -> R (in dbSNP:rs2923147). {ECO:0000269|PubMed:11230166}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						GAAACTAACATGCTGGCAGGC	0.622													c|||	1976	0.394569	0.7133	0.2954	5008	,	,		16930	0.3839		0.2256	False		,,,				2504	0.2188				p.C766R		Atlas-SNP	.											CCDC135,NS,carcinoma,0,1	CCDC135	97	1	0			c.T2296C						PASS	.	C	ARG/CYS	2798,1594	487.6+/-361.0	900,998,298	46.0	51.0	49.0		2296	4.2	0.8	16	dbSNP_101	49	1710,6882	732.0+/-406.8	169,1372,2755	yes	missense	CCDC135	NM_032269.5	180	1069,2370,3053	CC,CT,TT		19.9022,36.2933,34.7197	benign	766/875	57762401	4508,8476	2196	4296	6492	SO:0001583	missense	84229	exon16			CTAACATGCTGGC																												ENST00000360716.3:c.2296T>C	16.37:g.57762401T>C	ENSP00000353942:p.Cys766Arg	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	247	118	0.477733	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	843	0.385989010989011	344	0.6991869918699187	109	0.3011049723756906	218	0.3811188811188811	172	0.22691292875989447	c	0.059	-1.228281	0.01518	0.637067	0.199022	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.35973	1.28;1.28;1.28	5.15	4.16	0.48862	.	0.215200	0.37304	N	0.002154	T	0.00012	0.0000	N	0.00067	-2.295	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43180	-0.9407	9	0.02654	T	1	-14.2278	8.0328	0.30476	0.2595:0.6617:0.0:0.0788	rs2923147;rs3803595;rs57995451;rs2923147	701;766	Q8IY82-2;Q8IY82	.;CC135_HUMAN	R	766;701;766	ENSP00000377869:C766R;ENSP00000338938:C701R;ENSP00000353942:C766R	ENSP00000338938:C701R	C	+	1	0	CCDC135	56319902	0.054000	0.20591	0.822000	0.32727	0.661000	0.39034	1.019000	0.30014	1.184000	0.42957	-0.320000	0.08662	TGC	T|0.627;C|0.373	0.373	strong		0.622	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
ERAP2	64167	hgsc.bcm.edu	37	5	96245343	96245343	+	Silent	SNP	C	C	T	rs2549796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96245343C>T	ENST00000437043.3	+	15	2940	c.2229C>T	c.(2227-2229)ggC>ggT	p.G743G	CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000379904.4_Silent_p.G698G	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	743					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		GTGACAAGGGCTCAGTCTGGG	0.488													C|||	2527	0.504593	0.4395	0.5692	5008	,	,		19251	0.5278		0.5189	False		,,,				2504	0.5082				p.G743G		Atlas-SNP	.											.	ERAP2	77	.	0			c.C2229T						PASS	.	C	,	1906,2500	546.3+/-377.0	395,1116,692	121.0	113.0	116.0		2229,2229	3.7	1.0	5	dbSNP_100	116	4484,4116	590.4+/-392.7	1154,2176,970	no	coding-synonymous,coding-synonymous	ERAP2	NM_001130140.1,NM_022350.3	,	1549,3292,1662	TT,TC,CC		47.8605,43.2592,49.1312	,	743/961,743/961	96245343	6390,6616	2203	4300	6503	SO:0001819	synonymous_variant	64167	exon15			CAAGGGCTCAGTC	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.2229C>T	5.37:g.96245343C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	228	112	0.491228	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Silent	SNP	ENST00000437043.3	37	CCDS4086.1																																																																																			C|0.500;T|0.500	0.500	strong		0.488	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
RGS11	8786	hgsc.bcm.edu	37	16	319511	319511	+	Missense_Mutation	SNP	A	A	G	rs739999	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:319511A>G	ENST00000397770.3	-	16	1297	c.1280T>C	c.(1279-1281)aTg>aCg	p.M427T	ARHGDIG_ENST00000464609.1_Intron|ITFG3_ENST00000600536.1_Intron|ITFG3_ENST00000442458.2_Intron|RGS11_ENST00000359740.5_Missense_Mutation_p.M416T|RGS11_ENST00000316163.5_Missense_Mutation_p.M406T			O94810	RGS11_HUMAN	regulator of G-protein signaling 11	427			M -> T (in dbSNP:rs739999).		G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)	8		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				CCGTCTCTTCATCTCCAGCGG	0.657													G|||	1547	0.308906	0.6415	0.2493	5008	,	,		17262	0.3194		0.0785	False		,,,				2504	0.1278				p.M427T		Atlas-SNP	.											RGS11,colon,carcinoma,0,1	RGS11	29	1	0			c.T1280C						scavenged	.	G	THR/MET,THR/MET	2422,1982	554.5+/-379.0	673,1076,453	57.0	55.0	55.0		1217,1280	3.5	0.0	16	dbSNP_86	55	769,7831	782.9+/-407.6	45,679,3576	yes	missense,missense	RGS11	NM_003834.1,NM_183337.1	81,81	718,1755,4029	GG,GA,AA		8.9419,45.0045,24.5386	benign,benign	406/447,427/468	319511	3191,9813	2202	4300	6502	SO:0001583	missense	8786	exon16			CTCTTCATCTCCA	AF035153	CCDS10403.1, CCDS42088.1, CCDS66884.1	16p13.3	2008-07-28	2007-08-14		ENSG00000076344	ENSG00000076344		"""Regulators of G-protein signaling"""	9993	protein-coding gene	gene with protein product		603895	"""regulator of G-protein signalling 11"""			9789084	Standard	NM_001286486		Approved		uc002cgj.1	O94810	OTTHUMG00000064893	ENST00000397770.3:c.1280T>C	16.37:g.319511A>G	ENSP00000380876:p.Met427Thr	Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	154	62	0.402597	NM_183337	O75883|Q4TT71|Q4TT72	Missense_Mutation	SNP	ENST00000397770.3	37	CCDS42088.1	644	0.2948717948717949	304	0.6178861788617886	87	0.24033149171270718	195	0.3409090909090909	58	0.07651715039577836	G	4.184	0.032829	0.08101	0.549955	0.089419	ENSG00000076344	ENST00000397770;ENST00000316163;ENST00000359740	T;T;T	0.24538	1.86;1.85;1.86	4.42	3.46	0.39613	.	0.327034	0.31821	N	0.007020	T	0.00012	0.0000	N	0.00152	-1.975	0.09310	P	0.999999999866987	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44697	-0.9311	9	0.05959	T	0.93	-12.3827	9.475	0.38867	0.1772:0.0:0.8228:0.0	rs739999;rs57130699;rs739999	416;427;427	O94810-2;Q4TT70;O94810	.;.;RGS11_HUMAN	T	427;406;416	ENSP00000380876:M427T;ENSP00000319069:M406T;ENSP00000352778:M416T	ENSP00000319069:M406T	M	-	2	0	RGS11	259512	1.000000	0.71417	0.046000	0.18839	0.044000	0.14063	4.897000	0.63231	0.341000	0.23771	-1.212000	0.01626	ATG	A|0.720;G|0.280	0.280	strong		0.657	RGS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139325.2		
HLA-B	3106	hgsc.bcm.edu	37	6	31323286	31323286	+	Missense_Mutation	SNP	C	C	T	rs146555925		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323286C>T	ENST00000412585.2	-	4	731	c.703G>A	c.(703-705)Gcg>Acg	p.A235T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	235	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GTGATCTCCGCAGGGTAGAAA	0.592									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.A235T		Atlas-SNP	.											.	HLA-B	54	.	0			c.G703A						PASS	.						83.0	81.0	82.0					6																	31323286		2203	4298	6501	SO:0001583	missense	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	TCTCCGCAGGGTA	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.703G>A	6.37:g.31323286C>T	ENSP00000399168:p.Ala235Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	162	10	0.0617284	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	11.65	1.701624	0.30142	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.14766	2.48;2.48	3.06	-1.02	0.10135	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.402479	0.17716	U	0.164428	T	0.16727	0.0402	H	0.95780	3.72	0.09310	N	1	B	0.28820	0.224	B	0.41619	0.361	T	0.25847	-1.0120	10	0.87932	D	0	.	6.9863	0.24731	0.0:0.3733:0.0:0.6267	rs1050335;rs3190627	235	P01889	1B07_HUMAN	T	235;114;114;246	ENSP00000399168:A235T;ENSP00000405931:A246T	ENSP00000399168:A235T	A	-	1	0	HLA-B	31431265	0.000000	0.05858	0.023000	0.16930	0.855000	0.48748	-0.862000	0.04263	-0.113000	0.11958	0.442000	0.29010	GCG	C|0.999;T|0.001	0.001	weak		0.592	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
SREBF2	6721	hgsc.bcm.edu	37	22	42276742	42276742	+	Missense_Mutation	SNP	G	G	C	rs2228314	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:42276742G>C	ENST00000361204.4	+	10	1950	c.1784G>C	c.(1783-1785)gGc>gCc	p.G595A		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	595			G -> A (in dbSNP:rs2228314). {ECO:0000269|PubMed:7903453}.		cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						GCTGCTGCCGGCAACCTACAA	0.557													C|||	2032	0.405751	0.6165	0.5893	5008	,	,		16039	0.2004		0.2316	False		,,,				2504	0.3814				p.G595A		Atlas-SNP	.											SREBF2,NS,carcinoma,+1,1	SREBF2	99	1	0			c.G1784C						scavenged	.	C	ALA/GLY	2515,1891	535.8+/-374.3	739,1037,427	66.0	76.0	72.0		1784	4.9	0.9	22	dbSNP_98	72	2288,6312	697.2+/-404.9	328,1632,2340	yes	missense	SREBF2	NM_004599.2	60	1067,2669,2767	CC,CG,GG		26.6047,42.9187,36.9291	benign	595/1142	42276742	4803,8203	2203	4300	6503	SO:0001583	missense	6721	exon10			CTGCCGGCAACCT	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.1784G>C	22.37:g.42276742G>C	ENSP00000354476:p.Gly595Ala	Somatic	196	3	0.0153061		WXS	Illumina HiSeq	Phase_I	230	121	0.526087	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	37	CCDS14023.1	800	0.3663003663003663	303	0.6158536585365854	197	0.5441988950276243	130	0.22727272727272727	170	0.22427440633245382	C	5.347	0.249403	0.10130	0.570813	0.266047	ENSG00000198911	ENST00000361204;ENST00000457567	T	0.18016	2.24	4.95	4.95	0.65309	.	0.513362	0.22633	N	0.057556	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38045	-0.9679	9	0.06625	T	0.88	-8.3867	6.5586	0.22474	0.0:0.6932:0.1526:0.1542	rs2228314;rs4822063;rs11547819;rs4822063	595	Q12772	SRBP2_HUMAN	A	595	ENSP00000354476:G595A	ENSP00000354476:G595A	G	+	2	0	SREBF2	40606688	0.687000	0.27671	0.866000	0.34008	0.887000	0.51463	1.148000	0.31614	1.094000	0.41399	-0.345000	0.07892	GGC	G|0.627;C|0.373	0.373	strong		0.557	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	
PSG4	5672	hgsc.bcm.edu	37	19	43709637	43709637	+	Missense_Mutation	SNP	C	C	G	rs141508635	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:43709637C>G	ENST00000405312.3	-	1	289	c.52G>C	c.(52-54)Gtc>Ctc	p.V18L	PSG4_ENST00000244295.9_Missense_Mutation_p.V18L|PSG4_ENST00000433626.2_Missense_Mutation_p.V18L	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	18				V -> L (in Ref. 4; AAA60195). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)		p.V18L(3)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				GTGAGCAGGACCCCCTTCCAG	0.582													G|||	582	0.116214	0.0219	0.2478	5008	,	,		13900	0.0843		0.163	False		,,,				2504	0.135				p.L18L		Atlas-SNP	.											PSG4_ENST00000405312,NS,carcinoma,0,3	PSG4	129	3	3	Substitution - Missense(3)	pancreas(3)	c.C52C						PASS	.	G	LEU/VAL,LEU/VAL	163,4211		16,131,2040	60.0	58.0	59.0		52,52	0.2	0.0	19	dbSNP_134	59	1364,7180		199,966,3107	no	missense,missense	PSG4	NM_002780.3,NM_213633.1	32,32	215,1097,5147	GG,GC,CC		15.9644,3.7266,11.8207	,	18/420,18/327	43709637	1527,11391	2187	4272	6459	SO:0001583	missense	5672	exon1			GCAGGACCCCCTT		CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9521	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1-glycoprotein 4"""	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.52G>C	19.37:g.43709637C>G	ENSP00000384770:p.Val18Leu	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Silent	SNP	ENST00000405312.3	37	CCDS46093.1	217	0.09935897435897435	18	0.036585365853658534	68	0.1878453038674033	34	0.05944055944055944	97	0.1279683377308707	-	0.008	-1.892871	0.00522	0.037266	0.159644	ENSG00000243137	ENST00000244295;ENST00000405312;ENST00000433626	T;T;T	0.43688	1.35;0.94;2.07	2.55	0.165	0.14995	.	.	.	.	.	T	0.00012	0.0000	N	0.00166	-1.94	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.28870	-1.0030	8	0.02654	T	1	.	3.4088	0.07351	0.2854:0.2215:0.4931:0.0	.	18;18;18	E7EX79;Q00888-2;Q00888	.;.;PSG4_HUMAN	L	18	ENSP00000244295:V18L;ENSP00000384770:V18L;ENSP00000387864:V18L	ENSP00000244295:V18L	V	-	1	0	PSG4	48401477	0.048000	0.20356	0.001000	0.08648	0.002000	0.02628	-0.096000	0.11059	-0.081000	0.12662	-1.092000	0.02172	GTC	C|0.889;G|0.111	0.111	strong		0.582	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
Unknown	0	hgsc.bcm.edu	37	11	124096247	124096247	+	IGR	SNP	G	G	A	rs2466613	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124096247G>A								OR10D3 (39295 upstream) : OR8G1 (24175 downstream)																							CATGGACCAGGGGAAAGTGTC	0.458																																					p.G284R		Atlas-SNP	.											.	.	.	.	0			c.G850A						PASS	.						72.0	72.0	72.0					11																	124096247		1971	4186	6157	SO:0001628	intergenic_variant	26492	exon1			GACCAGGGGAAAG																													11.37:g.124096247G>A		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	198	185	0.934343	NM_001007249		Missense_Mutation	SNP		37																																																																																				G|0.495;A|0.505	0.505	strong	0	0.458								
KY	339855	hgsc.bcm.edu	37	3	134369716	134369716	+	Silent	SNP	C	C	A	rs13060869	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:134369716C>A	ENST00000423778.2	-	1	148	c.87G>T	c.(85-87)acG>acT	p.T29T	KY_ENST00000503669.1_Silent_p.T29T|KY_ENST00000508956.1_Silent_p.T29T	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	29					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGTCTGAGAGCGTACCCTGTG	0.662													C|||	711	0.141973	0.1097	0.1758	5008	,	,		13584	0.0208		0.2863	False		,,,				2504	0.138				p.T29T		Atlas-SNP	.											.	KY	92	.	0			c.G87T						PASS	.	C		507,3631		29,449,1591	39.0	44.0	43.0		87	2.8	0.6	3	dbSNP_121	43	2394,6006		339,1716,2145	no	coding-synonymous	KY	NM_178554.4		368,2165,3736	AA,AC,CC		28.5,12.2523,23.1377		29/662	134369716	2901,9637	2069	4200	6269	SO:0001819	synonymous_variant	339855	exon1			TGAGAGCGTACCC	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.87G>T	3.37:g.134369716C>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			C|0.832;A|0.168	0.168	strong		0.662	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
MAGEB16	139604	hgsc.bcm.edu	37	X	35821056	35821056	+	Missense_Mutation	SNP	T	T	A	rs4829391|rs370444095	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:35821056T>A	ENST00000399989.1	+	2	1022	c.743T>A	c.(742-744)aTg>aAg	p.M248K	MAGEB16_ENST00000399992.1_Missense_Mutation_p.M280K|MAGEB16_ENST00000399985.1_Missense_Mutation_p.M248K|MAGEB16_ENST00000399987.1_Missense_Mutation_p.M248K|MAGEB16_ENST00000399988.1_Missense_Mutation_p.M248K	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	248	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		M -> K (in dbSNP:rs4829391).|M -> V (in dbSNP:rs4829390).							breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						GAGCCCAGAATGCTCATCACC	0.502													A|||	2343	0.620662	0.4478	0.4121	3775	,	,		15958	0.5694		0.4205	False		,,,				2504	0.4785				p.M248K		Atlas-SNP	.											.	MAGEB16	64	.	0			c.T743A						PASS	.	A	LYS/MET	396,3363		64,150,118,1380,453	44.0	44.0	44.0		743	3.1	0.0	X	dbSNP_111	44	749,5958		102,225,320,2095,1543	yes	missense	MAGEB16	NM_001099921.1	95	166,375,438,3475,1996	AA,AT,A,TT,T		11.1674,10.5347,10.9402	benign	248/325	35821056	1145,9321	2165	4285	6450	SO:0001583	missense	139604	exon2			CCAGAATGCTCAT		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.743T>A	X.37:g.35821056T>A	ENSP00000382871:p.Met248Lys	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	124	10	0.0806452	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	895	0.5394816154309825	145	0.3835978835978836	92	0.36220472440944884	192	0.4948453608247423	202	0.33554817275747506	A	0.014	-1.583330	0.00872	0.105347	0.111674	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.03580	3.88;3.88;3.88;3.88;3.88	3.06	3.06	0.35304	.	0.726440	0.13630	N	0.373788	T	0.00012	0.0000	N	0.00002	-3.54	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.41305	-0.9516	9	0.02654	T	1	.	5.0116	0.14315	0.7301:0.0:0.0:0.2699	rs4829391;rs4829391	248	A2A368	MAGBG_HUMAN	K	248;280;248;248;248	ENSP00000382870:M248K;ENSP00000382874:M280K;ENSP00000382869:M248K;ENSP00000382871:M248K;ENSP00000382867:M248K	ENSP00000382867:M248K	M	+	2	0	MAGEB16	35730977	0.038000	0.19896	0.000000	0.03702	0.002000	0.02628	1.366000	0.34193	0.445000	0.26639	-0.541000	0.04245	ATG	T|0.434;A|0.566	0.566	strong		0.502	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
OR51Q1	390061	hgsc.bcm.edu	37	11	5443963	5443963	+	Missense_Mutation	SNP	G	G	A	rs10838095	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5443963G>A	ENST00000300778.4	+	1	623	c.533G>A	c.(532-534)cGc>cAc	p.R178H	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	178			R -> H (in dbSNP:rs10838095). {ECO:0000269|Ref.3}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTTCTCTCTCGCTCCTATTGC	0.512													A|||	2271	0.453474	0.2799	0.3991	5008	,	,		21098	0.7024		0.3976	False		,,,				2504	0.5276				p.R178H		Atlas-SNP	.											.	OR51Q1	79	.	0			c.G533A						PASS	.	A	HIS/ARG	1332,3070	694.1+/-405.8	203,926,1072	190.0	180.0	184.0		533	5.0	1.0	11	dbSNP_120	184	3371,5223	642.0+/-399.8	675,2021,1601	yes	missense	OR51Q1	NM_001004757.2	29	878,2947,2673	AA,AG,GG		39.225,30.259,36.1881	benign	178/318	5443963	4703,8293	2201	4297	6498	SO:0001583	missense	390061	exon1			TCTCTCGCTCCTA	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.533G>A	11.37:g.5443963G>A	ENSP00000300778:p.Arg178His	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	250	121	0.484	NM_001004757	B2RNN1	Missense_Mutation	SNP	ENST00000300778.4	37	CCDS31381.1	965	0.44184981684981683	139	0.28252032520325204	148	0.4088397790055249	395	0.6905594405594405	283	0.3733509234828496	A	0.013	-1.632241	0.00806	0.30259	0.39225	ENSG00000167360	ENST00000300778	T	0.00032	8.88	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000008	T	0.00012	0.0000	N	0.00003	-3.43	0.53688	P	2.2999999999995246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.32851	-0.9891	9	0.02654	T	1	.	9.9808	0.41813	0.9193:0.0:0.0807:0.0	rs10838095;rs52808857;rs59301431;rs10838095	178	Q8NH59	O51Q1_HUMAN	H	178	ENSP00000300778:R178H	ENSP00000300778:R178H	R	+	2	0	OR51Q1	5400539	0.924000	0.31332	1.000000	0.80357	0.088000	0.18126	3.515000	0.53429	0.960000	0.38005	-1.540000	0.00911	CGC	G|0.605;A|0.395	0.395	strong		0.512	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
ALX1	8092	hgsc.bcm.edu	37	12	85674221	85674221	+	Missense_Mutation	SNP	A	A	G	rs115440539	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:85674221A>G	ENST00000316824.3	+	1	337	c.182A>G	c.(181-183)cAt>cGt	p.H61R		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	61					anterior/posterior pattern specification (GO:0009952)|brain development (GO:0007420)|cartilage condensation (GO:0001502)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|mesenchymal cell development (GO:0014031)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1)	26				GBM - Glioblastoma multiforme(134;0.134)		CGCGCCGAGCATCACGTGCGC	0.637													A|||	24	0.00479233	0.0	0.0043	5008	,	,		14543	0.0		0.0169	False		,,,				2504	0.0041				p.H61R		Atlas-SNP	.											.	ALX1	61	.	0			c.A182G						PASS	.	A	ARG/HIS	10,4396	16.8+/-37.8	0,10,2193	34.0	36.0	35.0		182	5.5	1.0	12	dbSNP_132	35	95,8505	51.5+/-111.7	1,93,4206	yes	missense	ALX1	NM_006982.2	29	1,103,6399	GG,GA,AA		1.1047,0.227,0.8073	benign	61/327	85674221	105,12901	2203	4300	6503	SO:0001583	missense	8092	exon1			CCGAGCATCACGT	U31986	CCDS9028.1	12q21.31	2011-06-20	2007-07-26	2007-07-26		ENSG00000180318		"""Homeoboxes / PRD class"""	1494	protein-coding gene	gene with protein product		601527	"""cartilage paired-class homeoprotein 1"""	CART1		8756334, 7592751	Standard	NM_006982		Approved		uc001tae.4	Q15699	OTTHUMG00000169820	ENST00000316824.3:c.182A>G	12.37:g.85674221A>G	ENSP00000315417:p.His61Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_006982	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	37	CCDS9028.1	16	0.007326007326007326	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	A	16.30	3.084377	0.55861	0.00227	0.011047	ENSG00000180318	ENST00000316824	D	0.91686	-2.89	5.47	5.47	0.80525	.	0.165804	0.53938	D	0.000051	T	0.75642	0.3877	N	0.19112	0.55	0.50467	D	0.999873	B	0.24186	0.099	B	0.19946	0.027	T	0.77474	-0.2574	10	0.31617	T	0.26	.	12.1271	0.53922	0.8569:0.143:0.0:0.0	.	61	Q15699	ALX1_HUMAN	R	61	ENSP00000315417:H61R	ENSP00000315417:H61R	H	+	2	0	ALX1	84198352	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.410000	0.52664	2.069000	0.61940	0.528000	0.53228	CAT	A|0.991;G|0.009	0.009	strong		0.637	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982	
CITED2	10370	hgsc.bcm.edu	37	6	139695061	139695061	+	Silent	SNP	G	G	T	rs1131400	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:139695061G>T	ENST00000367651.2	-	2	236	c.21C>A	c.(19-21)gcC>gcA	p.A7A	CITED2_ENST00000536159.1_Silent_p.A7A|CITED2_ENST00000537332.1_Silent_p.A7A	NM_006079.4	NP_006070.2	Q99967	CITE2_HUMAN	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	7					adrenal cortex formation (GO:0035802)|bone morphogenesis (GO:0060349)|cardiac neural crest cell development involved in heart development (GO:0061308)|cell aging (GO:0007569)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|cranial nerve morphogenesis (GO:0021602)|decidualization (GO:0046697)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endocardial cushion development (GO:0003197)|erythrocyte development (GO:0048821)|granulocyte differentiation (GO:0030851)|heart development (GO:0007507)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|left/right axis specification (GO:0070986)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|peripheral nervous system development (GO:0007422)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of gene expression (GO:0010628)|positive regulation of male gonad development (GO:2000020)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|pulmonary artery morphogenesis (GO:0061156)|regulation of organ formation (GO:0003156)|regulation of RNA biosynthetic process (GO:2001141)|response to estrogen (GO:0043627)|response to fluid shear stress (GO:0034405)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sex determination (GO:0007530)|skeletal muscle cell differentiation (GO:0035914)|spleen development (GO:0048536)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|LBD domain binding (GO:0050693)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(4)	5	Breast(32;0.226)			GBM - Glioblastoma multiforme(68;0.000171)|OV - Ovarian serous cystadenocarcinoma(155;0.00134)		CGTGGTTCATGGCCATCATAT	0.627													G|||	625	0.1248	0.1112	0.1571	5008	,	,		17475	0.0317		0.1918	False		,,,				2504	0.1472				p.A12A	NSCLC(98;1219 1550 33720 43229 49330)	Atlas-SNP	.											.	CITED2	16	.	0			c.C36A						PASS	.	G	,,	651,3755	271.0+/-269.9	56,539,1608	33.0	30.0	31.0		21,21,21	3.9	1.0	6	dbSNP_86	31	1655,6945	295.5+/-302.4	148,1359,2793	no	coding-synonymous,coding-synonymous,coding-synonymous	CITED2	NM_001168388.1,NM_001168389.1,NM_006079.3	,,	204,1898,4401	TT,TG,GG		19.2442,14.7753,17.7303	,,	7/271,7/271,7/271	139695061	2306,10700	2203	4300	6503	SO:0001819	synonymous_variant	10370	exon2			GTTCATGGCCATC	U65093	CCDS5195.1, CCDS75530.1	6q23.3	2008-08-29			ENSG00000164442	ENSG00000164442			1987	protein-coding gene	gene with protein product		602937				8901575, 10552932	Standard	NM_006079		Approved	MRG1	uc021zfz.2	Q99967	OTTHUMG00000015691	ENST00000367651.2:c.21C>A	6.37:g.139695061G>T		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_001168389	O95426|Q5VTF4	Silent	SNP	ENST00000367651.2	37	CCDS5195.1																																																																																			G|0.852;T|0.148	0.148	strong		0.627	CITED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042463.1		
NAP1L5	266812	hgsc.bcm.edu	37	4	89618837	89618837	+	Silent	SNP	T	T	C	rs710834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:89618837T>C	ENST00000323061.5	-	1	549	c.69A>G	c.(67-69)gcA>gcG	p.A23A	HERC3_ENST00000264345.3_Intron|HERC3_ENST00000543130.1_Intron|HERC3_ENST00000402738.1_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	23	Poly-Ala.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(123;0.000181)		ttacctcctctgccgctgcct	0.682													C|||	2787	0.55651	0.7292	0.3588	5008	,	,		11493	0.5516		0.3678	False		,,,				2504	0.6626				p.A23A		Atlas-SNP	.											.	NAP1L5	23	.	0			c.A69G						PASS	.	C	,	2661,1617		892,877,370	13.0	17.0	16.0		,69	-1.3	0.0	4	dbSNP_86	16	2912,5504		568,1776,1864	no	intron,coding-synonymous	HERC3,NAP1L5	NM_014606.1,NM_153757.2	,	1460,2653,2234	CC,CT,TT		34.6008,37.798,43.9026	,	,23/183	89618837	5573,7121	2139	4208	6347	SO:0001819	synonymous_variant	266812	exon1			CTCCTCTGCCGCT	NM_153757	CCDS3632.1	4q21-q22	2006-04-12			ENSG00000177432	ENSG00000177432			19968	protein-coding gene	gene with protein product		612203				12383514	Standard	NM_153757		Approved	DRLM	uc003hrx.3	Q96NT1	OTTHUMG00000130950	ENST00000323061.5:c.69A>G	4.37:g.89618837T>C		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_153757		Silent	SNP	ENST00000323061.5	37	CCDS3632.1																																																																																			T|0.512;C|0.488	0.488	strong		0.682	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757	
SPOCK3	50859	hgsc.bcm.edu	37	4	167656073	167656073	+	Silent	SNP	C	C	T	rs1057377	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:167656073C>T	ENST00000357154.3	-	12	1447	c.1310G>A	c.(1309-1311)tGa>tAa	p.*437*	SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Silent_p.*434*|SPOCK3_ENST00000510741.1_Silent_p.*394*|SPOCK3_ENST00000534949.1_Silent_p.*341*|SPOCK3_ENST00000506886.1_Silent_p.*437*|SPOCK3_ENST00000535728.1_Silent_p.*305*|SPOCK3_ENST00000511269.1_Silent_p.*434*|SPOCK3_ENST00000541637.1_Silent_p.*339*|SPOCK3_ENST00000541354.1_Silent_p.*317*|SPOCK3_ENST00000511531.1_Silent_p.*437*|SPOCK3_ENST00000512681.1_Silent_p.*339*|SPOCK3_ENST00000504953.1_Silent_p.*434*|SPOCK3_ENST00000502330.1_Silent_p.*437*|SPOCK3_ENST00000421836.2_Silent_p.*386*	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	0					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		tgtcatcaatcaaatgtatac	0.294													C|||	646	0.128994	0.0113	0.1167	5008	,	,		14599	0.001		0.2565	False		,,,				2504	0.2975				p.X437X		Atlas-SNP	.											.	SPOCK3	90	.	0			c.G1310A						PASS	.	C	,,,,,,,	179,4227	113.8+/-151.8	6,167,2030	134.0	129.0	130.0		1301,1157,950,1034,1022,1181,1181,1310	5.0	0.8	4	dbSNP_86	130	2290,6310	379.2+/-339.2	309,1672,2319	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPOCK3	NM_001040159.1,NM_001204352.1,NM_001204353.1,NM_001204354.1,NM_001204355.1,NM_001204356.1,NM_001204357.1,NM_016950.2	,,,,,,,	315,1839,4349	TT,TC,CC		26.6279,4.0626,18.9835	,,,,,,,	434/434,386/386,317/317,345/345,341/341,394/394,394/394,437/437	167656073	2469,10537	2203	4300	6503	SO:0001819	synonymous_variant	50859	exon12			ATCAATCAAATGT	AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1310G>A	4.37:g.167656073C>T		Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	301	164	0.54485	NM_016950	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Silent	SNP	ENST00000357154.3	37	CCDS54817.1																																																																																			C|0.843;T|0.157	0.157	strong		0.294	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1		
PREX2	80243	hgsc.bcm.edu	37	8	68968166	68968166	+	Silent	SNP	C	C	A	rs1434774	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:68968166C>A	ENST00000288368.4	+	10	1472	c.1195C>A	c.(1195-1197)Cga>Aga	p.R399R	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	399	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						GATCAAAGACCGAAAGAGAAA	0.398													A|||	2813	0.561701	0.8865	0.4755	5008	,	,		18944	0.2688		0.5239	False		,,,				2504	0.5245				p.R399R		Atlas-SNP	.											PREX2_ENST00000354677,NS,malignant_melanoma,-1,2	PREX2	614	2	0			c.C1195A						PASS	.	A	,	3625,781	314.7+/-293.7	1503,619,81	117.0	128.0	124.0		1195,1195	3.2	1.0	8	dbSNP_88	124	4214,4386	583.1+/-391.5	1038,2138,1124	no	coding-synonymous,coding-synonymous	PREX2	NM_024870.2,NM_025170.4	,	2541,2757,1205	AA,AC,CC		49.0,17.7258,39.7278	,	399/1607,399/980	68968166	7839,5167	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon10			AAAGACCGAAAGA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1195C>A	8.37:g.68968166C>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			C|0.420;A|0.580	0.580	strong		0.398	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
CEACAM20	125931	hgsc.bcm.edu	37	19	45029208	45029208	+	RNA	SNP	G	G	A	rs10408247	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:45029208G>A	ENST00000454753.1	-	0	400							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				ACTTTGGGTGGCATCAAGTGG	0.567													G|||	1455	0.290535	0.6445	0.2911	5008	,	,		18869	0.1815		0.0765	False		,,,				2504	0.1442				p.A41V		Atlas-SNP	.											.	CEACAM20	31	.	0			c.C122T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	2132,2024		560,1012,506	115.0	123.0	120.0		122,122,122,122	0.0	0.0	19	dbSNP_119	120	731,7695		31,669,3513	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	64,64,64,64	591,1681,4019	AA,AG,GG		8.6755,48.7007,22.7547	benign,benign,benign,benign	41/597,41/492,41/504,41/585	45029208	2863,9719	2078	4213	6291			125931	exon2			TGGGTGGCATCAA	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45029208G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	169	75	0.443787	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				G|0.725;A|0.275	0.275	strong		0.567	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
FARP1	10160	hgsc.bcm.edu	37	13	99100547	99100547	+	Silent	SNP	T	T	C	rs12261	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:99100547T>C	ENST00000319562.6	+	27	3379	c.3114T>C	c.(3112-3114)agT>agC	p.S1038S	FARP1_ENST00000595437.1_Silent_p.S1069S|FARP1_ENST00000376586.2_Silent_p.S1069S	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	1038					dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			ACGTGTTGAGTCACAAAGAGT	0.527											OREG0022475	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2516	0.502396	0.4637	0.438	5008	,	,		21272	0.5625		0.5905	False		,,,				2504	0.4479				p.S1038S		Atlas-SNP	.											.	FARP1	207	.	0			c.T3114C						PASS	.	C		2144,2262	597.3+/-388.8	524,1096,583	209.0	163.0	179.0		3114	1.2	0.9	13	dbSNP_52	179	4991,3609	521.6+/-379.9	1441,2109,750	no	coding-synonymous	FARP1	NM_005766.2		1965,3205,1333	CC,CT,TT		41.9651,48.6609,45.1407		1038/1046	99100547	7135,5871	2203	4300	6503	SO:0001819	synonymous_variant	10160	exon27			GTTGAGTCACAAA	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"""Rho guanine nucleotide exchange factors"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Pleckstrin homology (PH) domain containing"""	3591	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 75"""	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.3114T>C	13.37:g.99100547T>C		Somatic	277	0	0	1341	WXS	Illumina HiSeq	Phase_I	270	268	0.992593	NM_005766	Q5JVI9|Q6IQ29	Silent	SNP	ENST00000319562.6	37	CCDS9487.1																																																																																			T|0.458;C|0.542	0.542	strong		0.527	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	
FARP2	9855	hgsc.bcm.edu	37	2	242407588	242407588	+	Missense_Mutation	SNP	G	G	A	rs41342147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242407588G>A	ENST00000264042.3	+	18	2097	c.1927G>A	c.(1927-1929)Gtc>Atc	p.V643I		NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	643	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		V -> I (in dbSNP:rs41342147).		actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		ACATGACGAGGTCCTAACAGA	0.522													G|||	422	0.0842652	0.0938	0.0893	5008	,	,		20182	0.0258		0.1153	False		,,,				2504	0.0961				p.V643I		Atlas-SNP	.											FARP2,rectum,carcinoma,-2,1	FARP2	92	1	0			c.G1927A						PASS	.	G	ILE/VAL	376,4030	188.1+/-214.6	19,338,1846	167.0	169.0	169.0		1927	5.0	1.0	2	dbSNP_127	169	1140,7460	235.3+/-267.9	72,996,3232	yes	missense	FARP2	NM_014808.2	29	91,1334,5078	AA,AG,GG		13.2558,8.5338,11.6562	probably-damaging	643/1055	242407588	1516,11490	2203	4300	6503	SO:0001583	missense	9855	exon18			GACGAGGTCCTAA	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.1927G>A	2.37:g.242407588G>A	ENSP00000264042:p.Val643Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	185	0.08470695970695971	43	0.08739837398373984	28	0.07734806629834254	21	0.03671328671328671	93	0.12269129287598944	G	21.3	4.129199	0.77549	0.085338	0.132558	ENSG00000006607	ENST00000264042	T	0.63417	-0.04	4.96	4.96	0.65561	Dbl homology (DH) domain (5);	0.000000	0.64402	D	0.000001	T	0.01523	0.0049	L	0.31804	0.96	0.09310	P	1.0	D	0.76494	0.999	D	0.85130	0.997	T	0.13229	-1.0517	9	0.12766	T	0.61	.	18.2382	0.89957	0.0:0.0:1.0:0.0	rs41342147;rs61752501;rs41342147	643	O94887	FARP2_HUMAN	I	643	ENSP00000264042:V643I	ENSP00000264042:V643I	V	+	1	0	FARP2	242056261	1.000000	0.71417	0.975000	0.42487	0.898000	0.52572	9.096000	0.94182	2.290000	0.77057	0.655000	0.94253	GTC	G|0.892;A|0.108	0.108	strong		0.522	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
RNFT1	51136	hgsc.bcm.edu	37	17	58031412	58031412	+	Silent	SNP	A	A	G	rs11368	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:58031412A>G	ENST00000305783.8	-	8	1222	c.1167T>C	c.(1165-1167)atT>atC	p.I389I	RNFT1_ENST00000442346.2_3'UTR|RP11-178C3.1_ENST00000591035.1_Intron	NM_016125.3	NP_057209.3	Q5M7Z0	RNFT1_HUMAN	ring finger protein, transmembrane 1	389						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	all_cancers(5;1.58e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;7.95e-12)|all cancers(12;1.34e-10)			TTACCTGACAAATGAGAAGAA	0.328													G|||	2901	0.579273	0.8797	0.5	5008	,	,		19138	0.5764		0.4195	False		,,,				2504	0.3967				p.I389I		Atlas-SNP	.											.	RNFT1	30	.	0			c.T1167C						PASS	.	G		2953,719		1192,569,75	51.0	50.0	50.0		1167	0.9	1.0	17	dbSNP_52	50	3587,4589		816,1955,1317	no	coding-synonymous	RNFT1	NM_016125.3		2008,2524,1392	GG,GA,AA		43.8723,19.5806,44.8008		389/436	58031412	6540,5308	1836	4088	5924	SO:0001819	synonymous_variant	51136	exon8			CTGACAAATGAGA	BC006971	CCDS11622.2	17q23.2	2013-01-09			ENSG00000189050	ENSG00000189050		"""RING-type (C3HC4) zinc fingers"""	30206	protein-coding gene	gene with protein product		615172				12477932	Standard	NM_016125		Approved	PTD016	uc002iya.3	Q5M7Z0	OTTHUMG00000148658	ENST00000305783.8:c.1167T>C	17.37:g.58031412A>G		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	248	120	0.483871	NM_016125	Q8N7D0|Q96IZ9|Q9Y686	Silent	SNP	ENST00000305783.8	37	CCDS11622.2																																																																																			A|0.499;G|0.501	0.501	strong		0.328	RNFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308958.1	NM_016125	
GRHL3	57822	hgsc.bcm.edu	37	1	24663184	24663184	+	Missense_Mutation	SNP	T	T	C	rs34637004	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24663184T>C	ENST00000350501.5	+	4	606	c.479T>C	c.(478-480)gTg>gCg	p.V160A	GRHL3_ENST00000530984.1_3'UTR|GRHL3_ENST00000342072.4_Missense_Mutation_p.V67A|GRHL3_ENST00000356046.2_Missense_Mutation_p.V114A|GRHL3_ENST00000236255.4_Missense_Mutation_p.V165A|GRHL3_ENST00000361548.4_Missense_Mutation_p.V160A	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	160			V -> A (in dbSNP:rs34637004).		central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		GCCGGCTCTGTGGACAGCTAC	0.592													T|||	88	0.0175719	0.0008	0.0231	5008	,	,		18592	0.0		0.0567	False		,,,				2504	0.0143				p.V165A		Atlas-SNP	.											.	GRHL3	69	.	0			c.T494C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	38,4368	40.0+/-72.8	0,38,2165	82.0	90.0	87.0		479,479,494,341	3.7	1.0	1	dbSNP_126	87	387,8213	125.0+/-183.6	9,369,3922	yes	missense,missense,missense,missense	GRHL3	NM_198174.2,NM_198173.2,NM_021180.3,NM_001195010.1	64,64,64,64	9,407,6087	CC,CT,TT		4.5,0.8625,3.2677	benign,benign,benign,benign	160/627,160/603,165/608,114/557	24663184	425,12581	2203	4300	6503	SO:0001583	missense	57822	exon4			GCTCTGTGGACAG	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"""transcription factor CP2-like 4"""	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.479T>C	1.37:g.24663184T>C	ENSP00000288955:p.Val160Ala	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_021180	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	51	0.023351648351648352	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	41	0.05408970976253298	T	6.967	0.548347	0.13312	0.008625	0.045	ENSG00000158055	ENST00000361548;ENST00000342072;ENST00000350501;ENST00000356046;ENST00000236255	T;T;T;T;T	0.10860	3.03;2.83;3.01;3.03;3.02	6.02	3.72	0.42706	.	0.567833	0.18141	N	0.150415	T	0.00695	0.0023	N	0.12182	0.205	0.20873	N	0.999832	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42275	-0.9461	10	0.16896	T	0.51	-22.8389	2.5509	0.04749	0.197:0.2286:0.0:0.5743	rs34637004	114;165;160	A2A297;Q8TE85-2;G3XAF0	.;.;.	A	160;67;160;114;165	ENSP00000354943:V160A;ENSP00000340543:V67A;ENSP00000288955:V160A;ENSP00000348333:V114A;ENSP00000236255:V165A	ENSP00000236255:V165A	V	+	2	0	GRHL3	24535771	0.997000	0.39634	1.000000	0.80357	0.856000	0.48823	0.403000	0.20982	1.116000	0.41820	0.533000	0.62120	GTG	T|0.971;C|0.029	0.029	strong		0.592	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
JPH2	57158	hgsc.bcm.edu	37	20	42747247	42747247	+	Missense_Mutation	SNP	C	C	T	rs3810510	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:42747247C>T	ENST00000372980.3	-	3	2058	c.1186G>A	c.(1186-1188)Gcc>Acc	p.A396T		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	396	Ala-rich.		A -> T (in dbSNP:rs3810510).		calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			TCAGCTTTGGCCTTGGCGTGG	0.592													C|||	1354	0.270367	0.3933	0.1009	5008	,	,		19145	0.3571		0.1163	False		,,,				2504	0.2935				p.A396T		Atlas-SNP	.											JPH2,caecum,carcinoma,0,1	JPH2	86	1	0			c.G1186A						PASS	.	C	THR/ALA	1455,2951	470.0+/-355.6	249,957,997	90.0	91.0	90.0		1186	3.8	1.0	20	dbSNP_107	90	1109,7491	231.1+/-265.2	78,953,3269	yes	missense	JPH2	NM_020433.4	58	327,1910,4266	TT,TC,CC		12.8953,33.0232,19.714	probably-damaging	396/697	42747247	2564,10442	2203	4300	6503	SO:0001583	missense	57158	exon3			CTTTGGCCTTGGC	AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.1186G>A	20.37:g.42747247C>T	ENSP00000362071:p.Ala396Thr	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_020433	E1P5X1|O95913|Q5JY74|Q9UJN4	Missense_Mutation	SNP	ENST00000372980.3	37	CCDS13325.1	527	0.2413003663003663	185	0.37601626016260165	39	0.10773480662983426	217	0.3793706293706294	86	0.11345646437994723	C	21.7	4.194721	0.78902	0.330232	0.128953	ENSG00000149596	ENST00000372980	T	0.61980	0.06	4.78	3.84	0.44239	.	0.516515	0.20203	N	0.097052	T	0.00012	0.0000	L	0.48877	1.53	0.09310	P	1.0	D	0.54601	0.967	P	0.49276	0.605	T	0.29640	-1.0005	9	0.37606	T	0.19	.	11.654	0.51306	0.0:0.9117:0.0:0.0883	rs3810510;rs60986665;rs3810510	396	Q9BR39	JPH2_HUMAN	T	396	ENSP00000362071:A396T	ENSP00000362071:A396T	A	-	1	0	JPH2	42180661	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	4.050000	0.57404	1.005000	0.39183	0.561000	0.74099	GCC	C|0.772;T|0.228	0.228	strong		0.592	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1		
CPZ	8532	hgsc.bcm.edu	37	4	8621167	8621167	+	Silent	SNP	G	G	A	rs9342	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:8621167G>A	ENST00000360986.4	+	11	1956	c.1782G>A	c.(1780-1782)ggG>ggA	p.G594G	CPZ_ENST00000315782.6_Silent_p.G583G|CPZ_ENST00000429646.2_Silent_p.G202G|CPZ_ENST00000382480.2_Silent_p.G457G	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	594					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TTATTCATGGGCTGCGGAGGA	0.652													G|||	300	0.0599042	0.1354	0.0331	5008	,	,		14230	0.0288		0.0507	False		,,,				2504	0.0184				p.G594G		Atlas-SNP	.											.	CPZ	95	.	0			c.G1782A						PASS	.	G	,,	498,3908	230.4+/-244.6	36,426,1741	49.0	50.0	49.0		1782,1371,1749	-0.6	0.0	4	dbSNP_52	49	413,8187	129.8+/-187.9	8,397,3895	no	coding-synonymous,coding-synonymous,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	44,823,5636	AA,AG,GG		4.8023,11.3028,7.0045	,,	594/653,457/516,583/642	8621167	911,12095	2203	4300	6503	SO:0001819	synonymous_variant	8532	exon11			TCATGGGCTGCGG	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"""metallocarboxypeptidase Z"""	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.1782G>A	4.37:g.8621167G>A		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	255	136	0.533333	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			G|0.936;A|0.064	0.064	strong		0.652	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
FRAS1	80144	hgsc.bcm.edu	37	4	79403682	79403682	+	Silent	SNP	C	C	T	rs41327848	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:79403682C>T	ENST00000264895.6	+	58	9185	c.8745C>T	c.(8743-8745)ttC>ttT	p.F2915F		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2911	Calx-beta 4.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ATGACACATTCCAAGATGGTA	0.413													C|||	806	0.160942	0.3449	0.1383	5008	,	,		21952	0.005		0.1938	False		,,,				2504	0.0552				p.F2915F		Atlas-SNP	.											.	FRAS1	779	.	0			c.C8745T						PASS	.	C		1237,2561		207,823,869	115.0	114.0	114.0		8745	3.9	1.0	4	dbSNP_127	114	1749,6499		192,1365,2567	no	coding-synonymous	FRAS1	NM_025074.6		399,2188,3436	TT,TC,CC		21.2051,32.5698,24.7883		2915/4013	79403682	2986,9060	1899	4124	6023	SO:0001819	synonymous_variant	80144	exon58			CACATTCCAAGAT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.8745C>T	4.37:g.79403682C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	121	43	0.355372	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	374	0.17124542124542125	173	0.3516260162601626	54	0.14917127071823205	2	0.0034965034965034965	145	0.19129287598944592	C	9.445	1.089100	0.20390	0.325698	0.212051	ENSG00000138759	ENST00000512123	.	.	.	5.9	3.86	0.44501	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.27123	-1.0083	3	.	.	.	.	12.2097	0.54373	0.0:0.7952:0.0:0.2048	rs56181015;rs56526896;rs57256258	.	.	.	S	1144	.	.	P	+	1	0	FRAS1	79622706	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.199000	0.32235	1.503000	0.48686	0.585000	0.79938	CCA	C|0.828;T|0.172	0.172	strong		0.413	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MUC21	394263	hgsc.bcm.edu	37	6	30954334	30954334	+	Missense_Mutation	SNP	C	C	A	rs143481246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954334C>A	ENST00000376296.3	+	2	623	c.382C>A	c.(382-384)Ccc>Acc	p.P128T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	128	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GTCCAGCACACCCTCCAGTGG	0.597													A|||	105	0.0209665	0.0189	0.0418	5008	,	,		24356	0.0198		0.0219	False		,,,				2504	0.0092				p.P128T		Atlas-SNP	.											MUC21,NS,carcinoma,0,1	MUC21	98	1	0			c.C382A						scavenged	.						173.0	161.0	165.0					6																	30954334		2203	4300	6503	SO:0001583	missense	394263	exon2			AGCACACCCTCCA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.382C>A	6.37:g.30954334C>A	ENSP00000365473:p.Pro128Thr	Somatic	94	3	0.0319149		WXS	Illumina HiSeq	Phase_I	151	18	0.119205	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	A	0.015	-1.544929	0.00934	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.00570	6.51	3.34	-5.44	0.02624	.	.	.	.	.	T	0.00039	0.0001	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17561	-1.0365	8	.	.	.	.	1.1104	0.01703	0.3821:0.2781:0.2052:0.1346	.	128	Q5SSG8	MUC21_HUMAN	T	128	ENSP00000365473:P128T	.	P	+	1	0	MUC21	31062313	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.006000	0.13152	-1.189000	0.02702	-1.983000	0.00453	CCC	C|0.994;A|0.006	0.006	strong		0.597	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
MKI67	4288	hgsc.bcm.edu	37	10	129910475	129910475	+	Missense_Mutation	SNP	T	T	G	rs997983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:129910475T>G	ENST00000368654.3	-	9	2266	c.1891A>C	c.(1891-1893)Atc>Ctc	p.I631L	MKI67_ENST00000368653.3_Missense_Mutation_p.I271L|MKI67_ENST00000484853.1_5'UTR	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	631			I -> L (in dbSNP:rs997983).		cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.I631V(1)|p.I631L(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTTCGGCTGATAGACACTCTC	0.443													T|||	553	0.110423	0.093	0.1585	5008	,	,		20495	0.1359		0.0795	False		,,,				2504	0.1053				p.I631L		Atlas-SNP	.											MKI67,rectum,carcinoma,0,2	MKI67	363	2	2	Substitution - Missense(2)	large_intestine(1)|stomach(1)	c.A1891C						PASS	.	T	LEU/ILE,LEU/ILE	412,3994	203.5+/-225.9	22,368,1813	112.0	100.0	104.0		811,1891	-8.1	0.0	10	dbSNP_86	104	777,7823	184.6+/-232.5	39,699,3562	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	5,5	61,1067,5375	GG,GT,TT		9.0349,9.3509,9.1419	benign,benign	271/2897,631/3257	129910475	1189,11817	2203	4300	6503	SO:0001583	missense	4288	exon9			GGCTGATAGACAC	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.1891A>C	10.37:g.129910475T>G	ENSP00000357643:p.Ile631Leu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	153	68	0.444444	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	220	0.10073260073260074	43	0.08739837398373984	40	0.11049723756906077	79	0.1381118881118881	58	0.07651715039577836	T	7.470	0.646557	0.14451	0.093509	0.090349	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01246	5.14;5.11	4.03	-8.06	0.01102	.	0.788319	0.11269	N	0.581682	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B;B;B	0.11235	0.004;0.002;0.001	B;B;B	0.11329	0.006;0.004;0.002	T	0.44726	-0.9309	9	0.25106	T	0.35	.	1.3818	0.02232	0.1695:0.3373:0.2008:0.2923	rs997983;rs17731527;rs52826393;rs58983470;rs997983	630;271;631	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	L	631;271;630;206	ENSP00000357643:I631L;ENSP00000357642:I271L	ENSP00000357641:I206L	I	-	1	0	MKI67	129800465	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.743000	0.04845	-2.155000	0.00791	-0.291000	0.09656	ATC	T|0.906;G|0.094	0.094	strong		0.443	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
MAGEB16	139604	hgsc.bcm.edu	37	X	35820696	35820696	+	Missense_Mutation	SNP	G	G	A	rs1410962	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:35820696G>A	ENST00000399989.1	+	2	662	c.383G>A	c.(382-384)tGt>tAt	p.C128Y	MAGEB16_ENST00000399992.1_Missense_Mutation_p.C160Y|MAGEB16_ENST00000399985.1_Missense_Mutation_p.C128Y|MAGEB16_ENST00000399987.1_Missense_Mutation_p.C128Y|MAGEB16_ENST00000399988.1_Missense_Mutation_p.C128Y	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	128	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		C -> Y (in dbSNP:rs1410962).							breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						CTGCACAAGTGTCAGATGAAA	0.458													A|||	2341	0.620132	0.4478	0.4121	3775	,	,		17188	0.5694		0.4185	False		,,,				2504	0.4785				p.C128Y		Atlas-SNP	.											.	MAGEB16	64	.	0			c.G383A						PASS	.	A	TYR/CYS	1943,1385		494,648,307,237,263	59.0	56.0	57.0		383	3.1	0.0	X	dbSNP_88	57	3485,3016		688,1158,951,505,848	yes	missense	MAGEB16	NM_001099921.1	194	1182,1806,1258,742,1111	AA,AG,A,GG,G		46.3929,41.6166,44.7757	benign	128/325	35820696	5428,4401	1949	4150	6099	SO:0001583	missense	139604	exon2			ACAAGTGTCAGAT		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.383G>A	X.37:g.35820696G>A	ENSP00000382871:p.Cys128Tyr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	100	6	0.06	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	1014	0.6112115732368897	151	0.4415204678362573	102	0.4146341463414634	212	0.5792349726775956	230	0.3885135135135135	A	0.007	-1.966782	0.00461	0.583834	0.536071	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04275	3.66;3.66;3.66;3.66;3.66	3.13	3.13	0.36017	.	0.108202	0.64402	N	0.000013	T	0.00012	0.0000	N	0.00009	-3.09	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37009	-0.9724	9	0.02654	T	1	.	4.6321	0.12507	0.8483:0.0:0.1517:0.0	rs1410962;rs17311179;rs61142141;rs1410962	128	A2A368	MAGBG_HUMAN	Y	128;160;128;128;128	ENSP00000382870:C128Y;ENSP00000382874:C160Y;ENSP00000382869:C128Y;ENSP00000382871:C128Y;ENSP00000382867:C128Y	ENSP00000382867:C128Y	C	+	2	0	MAGEB16	35730617	0.327000	0.24678	0.008000	0.14137	0.001000	0.01503	1.389000	0.34453	0.466000	0.27193	-0.426000	0.05927	TGT	0|0.006;A|0.623	0.623	strong		0.458	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
AIFM2	84883	hgsc.bcm.edu	37	10	71880858	71880858	+	Missense_Mutation	SNP	A	A	G	rs10999147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:71880858A>G	ENST00000307864.1	-	4	617	c.404T>C	c.(403-405)aTg>aCg	p.M135T	AIFM2_ENST00000482166.1_5'Flank|AIFM2_ENST00000373248.1_Missense_Mutation_p.M135T	NM_001198696.1|NM_032797.5	NP_001185625.1|NP_116186.1	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 2	135			M -> T (in dbSNP:rs10999147).		apoptotic mitochondrial changes (GO:0008637)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|urinary_tract(2)	16						CTGCCTCACCATGTCCTCATA	0.617													A|||	465	0.0928514	0.0129	0.0576	5008	,	,		15284	0.1637		0.0835	False		,,,				2504	0.1626				p.M135T		Atlas-SNP	.											.	AIFM2	33	.	0			c.T404C						PASS	.	A	THR/MET,THR/MET	110,4296	83.9+/-122.4	1,108,2094	92.0	84.0	87.0		404,404	6.2	1.0	10	dbSNP_120	87	756,7844	180.0+/-229.1	29,698,3573	yes	missense,missense	AIFM2	NM_001198696.1,NM_032797.5	81,81	30,806,5667	GG,GA,AA		8.7907,2.4966,6.6585	benign,benign	135/374,135/374	71880858	866,12140	2203	4300	6503	SO:0001583	missense	84883	exon4			CTCACCATGTCCT	AK027403	CCDS7297.1	10q22.2	2006-11-16	2006-11-16	2006-11-16	ENSG00000042286	ENSG00000042286			21411	protein-coding gene	gene with protein product		605159	"""apoptosis-inducing factor (AIF)-like mitochondrion-associated inducer of death"""	AMID		12135761, 11980907, 15958387	Standard	NM_001198696		Approved	FLJ14497, PRG3	uc001jqp.2	Q9BRQ8	OTTHUMG00000018398	ENST00000307864.1:c.404T>C	10.37:g.71880858A>G	ENSP00000312370:p.Met135Thr	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	48	29	0.604167	NM_001198696	B3KXI0|Q63Z39	Missense_Mutation	SNP	ENST00000307864.1	37	CCDS7297.1	179	0.08195970695970696	7	0.014227642276422764	23	0.06353591160220995	88	0.15384615384615385	61	0.08047493403693931	A	17.46	3.394955	0.62066	0.024966	0.087907	ENSG00000042286	ENST00000373248;ENST00000307864	T;T	0.44881	0.91;0.91	6.17	6.17	0.99709	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.213826	0.51477	D	0.000096	T	0.00241	0.0007	L	0.39397	1.21	0.22127	P	0.99934758	B	0.25235	0.121	B	0.29942	0.109	T	0.06917	-1.0800	9	0.22109	T	0.4	-38.7414	16.4957	0.84242	1.0:0.0:0.0:0.0	rs10999147;rs52808584;rs57546560;rs10999147	135	Q9BRQ8	AIFM2_HUMAN	T	135	ENSP00000362345:M135T;ENSP00000312370:M135T	ENSP00000312370:M135T	M	-	2	0	AIFM2	71550864	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.930000	0.87610	2.371000	0.80710	0.533000	0.62120	ATG	A|0.920;G|0.080	0.080	strong		0.617	AIFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048487.1	NM_032797	
FMN2	56776	hgsc.bcm.edu	37	1	240370934	240370934	+	Missense_Mutation	SNP	G	G	C	rs71170718|rs4997328|rs562038978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:240370934G>C	ENST00000319653.9	+	5	3052	c.2822G>C	c.(2821-2823)gGa>gCa	p.G941A		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	941	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCCGGAGCGGGAATACCTCCT	0.706													G|||	1385	0.276558	0.3616	0.1902	5008	,	,		7542	0.3115		0.2276	False		,,,				2504	0.2372				p.G941A		Atlas-SNP	.											FMN2,NS,carcinoma,0,3	FMN2	451	3	0			c.G2822C						scavenged	.						25.0	31.0	29.0					1																	240370934		2135	4205	6340	SO:0001583	missense	56776	exon5			GAGCGGGAATACC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2822G>C	1.37:g.240370934G>C	ENSP00000318884:p.Gly941Ala	Somatic	102	2	0.0196078		WXS	Illumina HiSeq	Phase_I	123	29	0.235772	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	510	0.23351648351648352	149	0.30284552845528456	59	0.16298342541436464	154	0.2692307692307692	148	0.19525065963060687	G	6.179	0.401283	0.11696	.	.	ENSG00000155816	ENST00000319653	T	0.51574	0.7	3.52	2.6	0.31112	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.28291	0.206	B	0.31869	0.137	T	0.28618	-1.0038	7	.	.	.	.	8.7591	0.34663	0.0:0.2724:0.5786:0.149	rs4997328	941	Q9NZ56	FMN2_HUMAN	A	941	ENSP00000318884:G941A	.	G	+	2	0	FMN2	238437557	0.024000	0.19004	0.019000	0.16419	0.001000	0.01503	0.529000	0.23019	1.071000	0.40834	-0.415000	0.06103	GGA	G|0.781;C|0.219	0.219	strong		0.706	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
HLA-C	3107	hgsc.bcm.edu	37	6	31237162	31237162	+	Splice_Site	SNP	C	C	G	rs1130863|rs35708511	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31237162C>G	ENST00000376228.5	-	7	1063	c.1049G>C	c.(1048-1050)tGc>tCc	p.C350S	HLA-C_ENST00000383329.3_Splice_Site_p.C356S	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	356					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACTGTTGCTGCCTGGGGTAGA	0.562													G|||	3934	0.785543	0.8139	0.8184	5008	,	,		16610	0.8135		0.7276	False		,,,				2504	0.7546				p.C350S		Atlas-SNP	.											.	HLA-C	92	.	0			c.G1049C						PASS	.	G	SER/CYS	2395,627		954,487,70	38.0	45.0	42.0		1049	-1.8	0.0	6	dbSNP_126	42	3722,1696		1281,1160,268	yes	missense-near-splice	HLA-C	NM_002117.5	112	2235,1647,338	GG,GC,CC		31.3031,20.7478,27.5237	benign	350/367	31237162	6117,2323	1511	2709	4220	SO:0001630	splice_region_variant	3107	exon7			TTGCTGCCTGGGG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.1049-1G>C	6.37:g.31237162C>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	138	136	0.985507	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1702|1702	0.7793040293040293|0.7793040293040293	401|401	0.8150406504065041|0.8150406504065041	291|291	0.8038674033149171|0.8038674033149171	461|461	0.8059440559440559|0.8059440559440559	549|549	0.7242744063324539|0.7242744063324539	.|.	0.156|0.156	-1.086412|-1.086412	0.01873|0.01873	0.792522|0.792522	0.686969|0.686969	ENSG00000204525|ENSG00000204525	ENST00000396254|ENST00000376228;ENST00000383329;ENST00000539307	.|T;T	.|0.01145	.|5.27;5.27	2.51|2.51	-1.82|-1.82	0.07857|0.07857	.|MHC class I, alpha chain, C-terminal (1);	.|.	.|.	.|.	.|.	T|T	0.00178|0.00178	0.0005|0.0005	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B|B;B	0.02656|0.02656	0.0|0.0;0.0	B|B;B	0.04013|0.06405	0.001|0.001;0.002	T|T	0.30357|0.30357	-0.9981|-0.9981	6|7	0.62326|0.02654	D|T	0.03|1	.|.	6.4696|6.4696	0.22001|0.22001	0.0:0.317:0.5566:0.1264|0.0:0.317:0.5566:0.1264	rs35708511;rs41543417;rs52825850|rs35708511;rs41543417;rs52825850	349|356;350	A2AEA4|A2AEA2;P10321	.|.;1C07_HUMAN	P|S	349|350;356;387	.|ENSP00000365402:C350S;ENSP00000372819:C356S	ENSP00000379553:A349P|ENSP00000365402:C350S	A|C	-|-	1|2	0|0	HLA-C|HLA-C	31345141|31345141	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.054000|0.054000	0.15201|0.15201	-1.016000|-1.016000	0.03633|0.03633	-0.461000|-0.461000	0.06993|0.06993	-3.595000|-3.595000	0.00028|0.00028	GCA|TGC	C|0.266;G|0.734	0.734	strong		0.562	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	Missense_Mutation
OR2T4	127074	hgsc.bcm.edu	37	1	248525146	248525146	+	Silent	SNP	C	C	T	rs28482938	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248525146C>T	ENST00000366475.1	+	1	264	c.264C>T	c.(262-264)caC>caT	p.H88H		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCCACCTCCACACCCCCATGT	0.488																																					p.H88H		Atlas-SNP	.											.	OR2T4	126	.	0			c.C264T						PASS	.	C		852,3554		12,828,1363	490.0	328.0	383.0		264	-2.4	0.5	1	dbSNP_125	383	1323,7277		51,1221,3028	no	coding-synonymous	OR2T4	NM_001004696.1		63,2049,4391	TT,TC,CC		15.3837,19.3373,16.7231		88/349	248525146	2175,10831	2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			CCTCCACACCCCC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.264C>T	1.37:g.248525146C>T		Somatic	710	0	0		WXS	Illumina HiSeq	Phase_I	853	245	0.287222	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			C|0.863;T|0.137	0.137	strong		0.488	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
DNMBP	23268	hgsc.bcm.edu	37	10	101645498	101645498	+	Silent	SNP	T	T	C	rs2490763	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:101645498T>C	ENST00000324109.4	-	14	3835	c.3744A>G	c.(3742-3744)ccA>ccG	p.P1248P	DNMBP_ENST00000540316.1_Silent_p.P184P|DNMBP_ENST00000342239.3_Silent_p.P1272P|DNMBP_ENST00000472036.1_5'Flank|DNMBP_ENST00000543621.1_Silent_p.P494P	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1248					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TCCTCTCAAATGGCTTCTTGG	0.542													C|||	2397	0.478634	0.587	0.4827	5008	,	,		16751	0.2698		0.5388	False		,,,				2504	0.4826				p.P1248P		Atlas-SNP	.											.	DNMBP	173	.	0			c.A3744G						PASS	.			2570,1836		765,1040,398	33.0	29.0	30.0		3744	-10.9	0.0	10	dbSNP_100	30	4502,4098		1188,2126,986	no	coding-synonymous	DNMBP	NM_015221.2		1953,3166,1384	CC,CT,TT		47.6512,41.6704,45.6251		1248/1578	101645498	7072,5934	2203	4300	6503	SO:0001819	synonymous_variant	23268	exon14			CTCAAATGGCTTC	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.3744A>G	10.37:g.101645498T>C		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	107	97	0.906542	NM_015221	Q8IVY3|Q9Y2L3	Silent	SNP	ENST00000324109.4	37	CCDS7485.1																																																																																			T|0.492;C|0.508	0.508	strong		0.542	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
SCLT1	132320	hgsc.bcm.edu	37	4	129864289	129864289	+	Silent	SNP	T	T	C	rs144333168	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:129864289T>C	ENST00000281142.5	-	17	1997	c.1494A>G	c.(1492-1494)gtA>gtG	p.V498V	SCLT1_ENST00000439369.2_Intron|SCLT1_ENST00000502495.1_5'UTR|SCLT1_ENST00000434680.1_Intron|SCLT1_ENST00000503215.1_Intron	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	498					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						CAGACTCCAATACATTTTGAA	0.348													T|||	3	0.000599042	0.0	0.0	5008	,	,		17091	0.0		0.002	False		,,,				2504	0.001				p.V498V		Atlas-SNP	.											.	SCLT1	136	.	0			c.A1494G						PASS	.	T		2,4402	4.2+/-10.8	0,2,2200	79.0	75.0	76.0		1494	-10.6	0.0	4	dbSNP_134	76	22,8574	16.0+/-53.3	0,22,4276	no	coding-synonymous	SCLT1	NM_144643.2		0,24,6476	CC,CT,TT		0.2559,0.0454,0.1846		498/689	129864289	24,12976	2202	4298	6500	SO:0001819	synonymous_variant	132320	exon17			CTCCAATACATTT	AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.1494A>G	4.37:g.129864289T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_144643	A4QN04|Q0VAH2|Q6P2M4	Silent	SNP	ENST00000281142.5	37	CCDS3740.1																																																																																			T|0.999;C|0.001	0.001	strong		0.348	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643	
SALL2	6297	hgsc.bcm.edu	37	14	21993638	21993638	+	Missense_Mutation	SNP	G	G	C	rs2242527	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21993638G>C	ENST00000327430.3	-	2	518	c.224C>G	c.(223-225)tCt>tGt	p.S75C	SALL2_ENST00000450879.2_Missense_Mutation_p.S73C|SALL2_ENST00000317492.5_Missense_Mutation_p.S75C|SALL2_ENST00000538754.1_Missense_Mutation_p.S73C|AE000658.22_ENST00000535893.1_RNA	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	75			S -> C (in dbSNP:rs2242527).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		GGAGGCCGAAGAGTTGTTGGG	0.557													G|||	368	0.0734824	0.118	0.0576	5008	,	,		12336	0.0069		0.1153	False		,,,				2504	0.0501				p.S75C		Atlas-SNP	.											.	SALL2	95	.	0			c.C224G						PASS	.	G	CYS/SER	492,3914	229.1+/-243.8	31,430,1742	86.0	84.0	85.0		224	4.4	1.0	14	dbSNP_98	85	959,7641	209.4+/-250.6	47,865,3388	yes	missense	SALL2	NM_005407.1	112	78,1295,5130	CC,CG,GG		11.1512,11.1666,11.1564	probably-damaging	75/1008	21993638	1451,11555	2203	4300	6503	SO:0001583	missense	6297	exon2			GCCGAAGAGTTGT	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"""Zinc fingers, C2H2-type"""	10526	protein-coding gene	gene with protein product		602219	"""sal (Drosophila)-like 2"", ""sal-like 2 (Drosophila)"""			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.224C>G	14.37:g.21993638G>C	ENSP00000333537:p.Ser75Cys	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	301	127	0.421927	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Missense_Mutation	SNP	ENST00000327430.3	37	CCDS32045.1	172|172	0.07875457875457875|0.07875457875457875	52|52	0.10569105691056911|0.10569105691056911	24|24	0.06629834254143646|0.06629834254143646	4|4	0.006993006993006993|0.006993006993006993	92|92	0.12137203166226913|0.12137203166226913	G|G	14.69|14.69	2.610559|2.610559	0.46527|0.46527	0.111666|0.111666	0.111512|0.111512	ENSG00000165821|ENSG00000165821	ENST00000546363|ENST00000327430;ENST00000317492;ENST00000538754;ENST00000450879;ENST00000541876;ENST00000537235;ENST00000541965	.|T;T;T;T;T;T	.|0.44083	.|3.55;1.3;1.16;3.36;1.23;0.93	4.36|4.36	4.36|4.36	0.52297|0.52297	.|.	.|0.000000	.|0.38548	.|N	.|0.001650	T|T	0.01124|0.01124	0.0037|0.0037	L|L	0.55481|0.55481	1.735|1.735	0.45378|0.45378	P|P	0.0016359999999999708|0.0016359999999999708	.|D;D;D;D;D;D	.|0.89917	.|0.999;0.999;0.999;0.999;1.0;0.997	.|P;P;P;D;D;P	.|0.81914	.|0.908;0.908;0.908;0.995;0.991;0.887	T|T	0.33033|0.33033	-0.9884|-0.9884	4|9	.|0.66056	.|D	.|0.02	-13.033|-13.033	8.149|8.149	0.31130|0.31130	0.1078:0.0:0.8922:0.0|0.1078:0.0:0.8922:0.0	rs2242527;rs52815753;rs2242527|rs2242527;rs52815753;rs2242527	.|73;73;73;75;73;75	.|B4DK65;E7EW59;B4DFD9;F5GY43;Q8N656;Q9Y467	.|.;.;.;.;.;SALL2_HUMAN	V|C	69|75;75;73;73;75;73;13	.|ENSP00000333537:S75C;ENSP00000320536:S75C;ENSP00000445916:S73C;ENSP00000396773:S73C;ENSP00000438493:S73C;ENSP00000439654:S13C	.|ENSP00000320536:S75C	L|S	-|-	1|2	0|0	SALL2|SALL2	21063478|21063478	0.456000|0.456000	0.25744|0.25744	0.992000|0.992000	0.48379|0.48379	0.785000|0.785000	0.44390|0.44390	2.781000|2.781000	0.47750|0.47750	2.296000|2.296000	0.77279|0.77279	0.558000|0.558000	0.71614|0.71614	CTT|TCT	G|0.901;C|0.099	0.099	strong		0.557	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407	
OR2T34	127068	hgsc.bcm.edu	37	1	248737319	248737319	+	Missense_Mutation	SNP	G	G	A	rs77940099	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248737319G>A	ENST00000328782.2	-	1	761	c.740C>T	c.(739-741)tCc>tTc	p.S247F		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	247						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S247F(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATGTGGGAGGAGCAGGTGGC	0.562																																					p.S247F		Atlas-SNP	.											OR2T34,NS,carcinoma,0,1	OR2T34	72	1	1	Substitution - Missense(1)	stomach(1)	c.C740T						PASS	.	G	PHE/SER	1234,3114		180,874,1120	90.0	101.0	98.0		740	1.1	1.0	1	dbSNP_131	98	912,7688		3,906,3391	no	missense	OR2T34	NM_001001821.1	155	183,1780,4511	AA,AG,GG		10.6047,28.3809,16.574	possibly-damaging	247/319	248737319	2146,10802	2174	4300	6474	SO:0001583	missense	127068	exon1			TGGGAGGAGCAGG	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.740C>T	1.37:g.248737319G>A	ENSP00000330904:p.Ser247Phe	Somatic	293	1	0.00341297		WXS	Illumina HiSeq	Phase_I	358	131	0.365922	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	342	0.1565934065934066	151	0.30691056910569103	49	0.13535911602209943	54	0.0944055944055944	88	0.11609498680738786	.	10.47	1.358825	0.24598	0.283809	0.106047	ENSG00000183310	ENST00000328782	T	0.37058	1.22	2.22	1.14	0.20703	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.92169	3.28	0.49299	P	2.2599999999994846E-4	D	0.56287	0.975	P	0.61940	0.896	T	0.04467	-1.0949	8	0.72032	D	0.01	.	4.6375	0.12531	0.1478:0.4341:0.418:0.0	.	247	Q8NGX1	O2T34_HUMAN	F	247	ENSP00000330904:S247F	ENSP00000330904:S247F	S	-	2	0	OR2T34	246803942	0.000000	0.05858	0.989000	0.46669	0.333000	0.28666	-0.317000	0.08060	1.083000	0.41159	0.123000	0.15791	TCC	G|0.841;A|0.159	0.159	strong		0.562	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
RAB3GAP1	22930	hgsc.bcm.edu	37	2	135893372	135893372	+	Missense_Mutation	SNP	A	A	G	rs10445686	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:135893372A>G	ENST00000264158.8	+	17	1836	c.1793A>G	c.(1792-1794)aAt>aGt	p.N598S	RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.N598S|SNORA40_ENST00000385573.1_RNA|ZRANB3_ENST00000412849.1_5'Flank|RAB3GAP1_ENST00000487003.1_3'UTR|RAB3GAP1_ENST00000539493.1_Missense_Mutation_p.N554S	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	598			N -> S (in dbSNP:rs10445686). {ECO:0000269|PubMed:15489334}.		brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		CTTAAAGGAAATGGACAAGAG	0.433													A|||	1074	0.214457	0.0204	0.2003	5008	,	,		18540	0.3859		0.1909	False		,,,				2504	0.3344				p.N598S		Atlas-SNP	.											.	RAB3GAP1	87	.	0			c.A1793G						PASS	.	A	SER/ASN,SER/ASN	138,4268	98.9+/-137.6	3,132,2068	84.0	84.0	84.0		1793,1793	4.3	1.0	2	dbSNP_119	84	1324,7276	260.2+/-283.1	134,1056,3110	yes	missense,missense	RAB3GAP1	NM_001172435.1,NM_012233.2	46,46	137,1188,5178	GG,GA,AA		15.3953,3.1321,11.241	benign,benign	598/989,598/982	135893372	1462,11544	2203	4300	6503	SO:0001583	missense	22930	exon17			AAGGAAATGGACA	D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.1793A>G	2.37:g.135893372A>G	ENSP00000264158:p.Asn598Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	148	74	0.5	NM_001172435	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	37	CCDS33294.1	470	0.21520146520146521	13	0.026422764227642278	73	0.20165745856353592	242	0.4230769230769231	142	0.18733509234828497	A	11.59	1.682973	0.29872	0.031321	0.153953	ENSG00000115839	ENST00000264158;ENST00000539493;ENST00000442034	T;T;T	0.42900	0.96;0.96;0.96	5.4	4.26	0.50523	.	0.301526	0.39274	N	0.001405	T	0.00012	0.0000	N	0.11560	0.145	0.33124	P	0.45778300000000005	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.40251	-0.9573	9	0.07813	T	0.8	-25.553	8.0603	0.30629	0.8474:0.0:0.1526:0.0	rs10445686;rs17845714;rs17858662;rs52816789;rs59620553;rs10445686	598;598	C9J837;Q15042	.;RB3GP_HUMAN	S	598;554;598	ENSP00000264158:N598S;ENSP00000444306:N554S;ENSP00000411418:N598S	ENSP00000264158:N598S	N	+	2	0	RAB3GAP1	135609842	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.026000	0.64103	2.051000	0.60960	0.482000	0.46254	AAT	A|0.834;G|0.166	0.166	strong		0.433	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233	
SSTR3	6753	hgsc.bcm.edu	37	22	37603744	37603744	+	Silent	SNP	C	C	T	rs86583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:37603744C>T	ENST00000328544.3	-	2	632	c.99G>A	c.(97-99)gcG>gcA	p.A33A	SSTR3_ENST00000402501.1_Silent_p.A33A	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	33			A -> V (in dbSNP:rs4988466).		cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	GGCTTGGGCCCGCCGACACGT	0.647													C|||	2043	0.407947	0.5461	0.3343	5008	,	,		17335	0.5863		0.2247	False		,,,				2504	0.2781				p.A33A		Atlas-SNP	.											SSTR3,NS,carcinoma,-1,1	SSTR3	42	1	0			c.G99A						scavenged	.	C		2134,2270	550.2+/-378.0	503,1128,571	45.0	47.0	46.0		99	-7.8	0.0	22	dbSNP_79	46	1779,6821	309.2+/-309.3	185,1409,2706	no	coding-synonymous	SSTR3	NM_001051.2		688,2537,3277	TT,TC,CC		20.686,48.4559,30.0907		33/419	37603744	3913,9091	2202	4300	6502	SO:0001819	synonymous_variant	6753	exon2			TGGGCCCGCCGAC		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"""GPCR / Class A : Somatostatin receptors"""	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.99G>A	22.37:g.37603744C>T		Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_001051	A8K550|Q53ZR7	Silent	SNP	ENST00000328544.3	37	CCDS13944.1																																																																																			C|0.664;T|0.336	0.336	strong		0.647	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1		
PRPF8	10594	hgsc.bcm.edu	37	17	1580929	1580929	+	Silent	SNP	G	G	C	rs11078565	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1580929G>C	ENST00000572621.1	-	13	2179	c.1914C>G	c.(1912-1914)ctC>ctG	p.L638L	PRPF8_ENST00000304992.6_Silent_p.L638L			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	638					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GCATGAAAAAGAGCCAGACTC	0.532													C|||	1364	0.272364	0.6324	0.147	5008	,	,		16152	0.0903		0.1948	False		,,,				2504	0.1421				p.L638L		Atlas-SNP	.											.	PRPF8	169	.	0			c.C1914G						PASS	.	C		2450,1956	552.3+/-378.5	681,1088,434	85.0	87.0	87.0		1914	1.7	1.0	17	dbSNP_120	87	1824,6776	732.1+/-406.8	190,1444,2666	no	coding-synonymous	PRPF8	NM_006445.3		871,2532,3100	CC,CG,GG		21.2093,44.394,32.8618		638/2336	1580929	4274,8732	2203	4300	6503	SO:0001819	synonymous_variant	10594	exon14			GAAAAAGAGCCAG	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.1914C>G	17.37:g.1580929G>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	NM_006445	O14547|O75965	Silent	SNP	ENST00000572621.1	37	CCDS11010.1																																																																																			G|0.698;C|0.302	0.302	strong		0.532	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
SENP3	26168	hgsc.bcm.edu	37	17	7474729	7474729	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7474729C>T	ENST00000429205.2	+	12	1702	c.1653C>T	c.(1651-1653)ttC>ttT	p.F551F	EIF4A1_ENST00000582746.1_5'Flank|EIF4A1_ENST00000380512.5_5'Flank|EIF4A1_ENST00000577269.1_5'Flank|SENP3_ENST00000578868.1_3'UTR|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000293831.8_5'Flank|SENP3_ENST00000321337.7_Silent_p.F550F			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	551						cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				CATTCAGCTTCACCCAGCAGG	0.542																																					p.F551F		Atlas-SNP	.											.	SENP3	18	.	0			c.C1653T						PASS	.						101.0	101.0	101.0					17																	7474729		1991	4189	6180	SO:0001819	synonymous_variant	26168	exon12			CAGCTTCACCCAG	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.1653C>T	17.37:g.7474729C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	37																																																																																				.	.	none		0.542	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	
ZFYVE19	84936	hgsc.bcm.edu	37	15	41105942	41105942	+	Missense_Mutation	SNP	G	G	A	rs34516375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:41105942G>A	ENST00000355341.4	+	9	1643	c.1142G>A	c.(1141-1143)aGt>aAt	p.S381N	ZFYVE19_ENST00000299173.10_Missense_Mutation_p.S313N|ZFYVE19_ENST00000564258.1_Missense_Mutation_p.S206N|ZFYVE19_ENST00000570108.1_Missense_Mutation_p.S358N|ZFYVE19_ENST00000336455.5_Missense_Mutation_p.S371N	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	381					abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		GATGAGGCAAGTGGCTTTAAC	0.597													G|||	7	0.00139776	0.0	0.0	5008	,	,		20274	0.0		0.006	False		,,,				2504	0.001				p.S381N		Atlas-SNP	.											.	ZFYVE19	31	.	0			c.G1142A						PASS	.	G	ASN/SER	2,4120		0,2,2059	50.0	56.0	54.0		1142	5.3	1.0	15	dbSNP_126	54	32,8382		0,32,4175	yes	missense	ZFYVE19	NM_001077268.1	46	0,34,6234	AA,AG,GG		0.3803,0.0485,0.2712	possibly-damaging	381/472	41105942	34,12502	2061	4207	6268	SO:0001583	missense	84936	exon9			AGGCAAGTGGCTT	AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"""Zinc fingers, FYVE domain containing"""	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.1142G>A	15.37:g.41105942G>A	ENSP00000347498:p.Ser381Asn	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_001077268	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Missense_Mutation	SNP	ENST00000355341.4	37	CCDS42025.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	32	5.125010	0.94429	4.85E-4	0.003803	ENSG00000166140	ENST00000355341;ENST00000299173;ENST00000336455	T;T;T	0.35048	1.33;1.33;1.33	5.27	5.27	0.74061	.	0.078430	0.85682	D	0.000000	T	0.51890	0.1701	M	0.72894	2.215	0.49389	D	0.999784	D;D;P	0.89917	1.0;0.981;0.753	D;P;B	0.87578	0.998;0.725;0.352	T	0.52631	-0.8550	10	0.36615	T	0.2	-14.0194	17.8147	0.88628	0.0:0.0:1.0:0.0	rs34516375	371;313;381	Q96K21-2;Q96K21-3;Q96K21	.;.;ZFY19_HUMAN	N	381;313;371	ENSP00000347498:S381N;ENSP00000299173:S313N;ENSP00000337824:S371N	ENSP00000299173:S313N	S	+	2	0	ZFYVE19	38893234	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.753000	0.91637	2.742000	0.94016	0.455000	0.32223	AGT	G|0.997;A|0.003	0.003	strong		0.597	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850	
PRR25	388199	hgsc.bcm.edu	37	16	855717	855717	+	Missense_Mutation	SNP	C	C	G	rs1005190	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:855717C>G	ENST00000301698.1	+	1	275	c.275C>G	c.(274-276)aCc>aGc	p.T92S		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	92			T -> S (in dbSNP:rs1005190).							large_intestine(1)|lung(1)|skin(1)	3						GAGCTCCCAACCAGCTCAGGA	0.647													A|||	2821	0.563299	0.8525	0.4726	5008	,	,		17560	0.4494		0.2833	False		,,,				2504	0.6421				p.T92S		Atlas-SNP	.											PRR25,rectum,carcinoma,0,1	PRR25	27	1	0			c.C275G						PASS	.	A	SER/THR	2833,1047		1053,727,160	21.0	29.0	27.0		275	0.4	0.0	16	dbSNP_86	27	2410,5858		335,1740,2059	yes	missense	PRR25	NM_001013638.1	58	1388,2467,2219	GG,GC,CC		29.1485,26.9845,43.1594	benign	92/403	855717	5243,6905	1940	4134	6074	SO:0001583	missense	388199	exon1			TCCCAACCAGCTC	BC156145	CCDS45372.1	16p13.3	2009-09-11			ENSG00000167945	ENSG00000167945			37230	protein-coding gene	gene with protein product						11157797	Standard	NM_001013638		Approved	gs64	uc010uut.2	Q96S07		ENST00000301698.1:c.275C>G	16.37:g.855717C>G	ENSP00000301698:p.Thr92Ser	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	94	53	0.56383	NM_001013638		Missense_Mutation	SNP	ENST00000301698.1	37	CCDS45372.1	1043	0.4775641025641026	417	0.8475609756097561	159	0.43922651933701656	268	0.46853146853146854	199	0.262532981530343	A	0	-2.773183	0.00081	0.730155	0.291485	ENSG00000167945	ENST00000301698	T	0.36157	1.27	0.364	0.364	0.16124	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14309	-1.0477	8	0.87932	D	0	.	5.1656	0.15084	0.3575:0.6424:0.0:0.0	rs1005190;rs59369772;rs1005190	92	Q96S07	PRR25_HUMAN	S	92	ENSP00000301698:T92S	ENSP00000301698:T92S	T	+	2	0	PRR25	795718	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.151000	0.03175	-0.656000	0.05380	-0.694000	0.03704	ACC	C|0.548;G|0.452	0.452	strong		0.647	PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638	
ACSM3	6296	hgsc.bcm.edu	37	16	20796387	20796387	+	Missense_Mutation	SNP	G	G	C	rs5716	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20796387G>C	ENST00000289416.5	+	8	1576	c.1101G>C	c.(1099-1101)aaG>aaC	p.K367N	ERI2_ENST00000300005.3_Intron|ACSM3_ENST00000450120.2_Missense_Mutation_p.K359N|ACSM3_ENST00000440284.2_Missense_Mutation_p.K367N|ACSM3_ENST00000567387.1_3'UTR|RNU6-944P_ENST00000364023.1_RNA	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3	367			K -> N (in dbSNP:rs5716). {ECO:0000269|PubMed:17278971, ECO:0000269|Ref.4}.		cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						GGAGAAACAAGACGGGCCTGG	0.418													G|||	465	0.0928514	0.0151	0.0519	5008	,	,		16439	0.2202		0.0706	False		,,,				2504	0.1186				p.K367N		Atlas-SNP	.											.	ACSM3	113	.	0			c.G1101C	GRCh37	CM070002	ACSM3	M	rs5716	PASS	.	G	ASN/LYS,,ASN/LYS	136,4266	97.6+/-136.3	4,128,2069	134.0	122.0	126.0		1101,,1101	2.1	0.1	16	dbSNP_52	126	772,7828	184.2+/-232.2	28,716,3556	yes	missense,intron,missense	ACSM3,ERI2	NM_005622.3,NM_080663.2,NM_202000.2	94,,94	32,844,5625	CC,CG,GG		8.9767,3.0895,6.9835	benign,,benign	367/587,,367/439	20796387	908,12094	2201	4300	6501	SO:0001583	missense	6296	exon8			AAACAAGACGGGC	D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"""Acyl-CoA synthetase family"""	10522	protein-coding gene	gene with protein product		145505	"""SA (rat hypertension-associated) homolog"", ""SA hypertension-associated homolog (rat)"""	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.1101G>C	16.37:g.20796387G>C	ENSP00000289416:p.Lys367Asn	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_202000	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Missense_Mutation	SNP	ENST00000289416.5	37	CCDS10589.1	182	0.08333333333333333	9	0.018292682926829267	12	0.03314917127071823	102	0.17832167832167833	59	0.07783641160949868	G	9.858	1.195592	0.22037	0.030895	0.089767	ENSG00000005187	ENST00000289416;ENST00000440284;ENST00000450120	T;T;T	0.42900	0.96;0.96;0.96	5.34	2.11	0.27256	AMP-dependent synthetase/ligase (1);	0.803410	0.11646	N	0.543268	T	0.00073	0.0002	L	0.31578	0.945	0.09310	P	0.9999999477389	B;B;B	0.33612	0.336;0.166;0.419	B;B;B	0.33121	0.158;0.102;0.133	T	0.15178	-1.0446	9	0.28530	T	0.3	-12.9705	6.8068	0.23782	0.2151:0.1283:0.6567:0.0	rs5716;rs52821460;rs56500245;rs5716	359;367;367	E7ETR5;Q53FZ2;Q53FZ2-2	.;ACSM3_HUMAN;.	N	367;367;359	ENSP00000289416:K367N;ENSP00000394565:K367N;ENSP00000395297:K359N	ENSP00000289416:K367N	K	+	3	2	ACSM3	20703888	0.006000	0.16342	0.127000	0.21898	0.854000	0.48673	0.010000	0.13242	0.747000	0.32809	0.655000	0.94253	AAG	G|0.919;C|0.081	0.081	strong		0.418	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622	
CCDC141	285025	hgsc.bcm.edu	37	2	179732845	179732845	+	Missense_Mutation	SNP	G	G	A	rs12988301	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179732845G>A	ENST00000420890.2	-	16	2599	c.2482C>T	c.(2482-2484)Cgg>Tgg	p.R828W	CCDC141_ENST00000295723.5_Missense_Mutation_p.R253W	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	828			R -> W (reduced affinity for MRLC and impairs cortical migration; dbSNP:rs1298830).							NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TGAGAGCACCGGAGGTGAATC	0.522													G|||	600	0.119808	0.1876	0.0706	5008	,	,		16434	0.1607		0.0706	False		,,,				2504	0.0716				p.R828W		Atlas-SNP	.											.	CCDC141	362	.	0			c.C2482T						PASS	.	G	TRP/ARG	733,3673	301.0+/-286.6	54,625,1524	129.0	111.0	117.0		2482	-11.0	0.0	2	dbSNP_121	117	600,8000	159.1+/-212.4	24,552,3724	yes	missense	CCDC141	NM_173648.3	101	78,1177,5248	AA,AG,GG		6.9767,16.6364,10.2491	benign	828/1531	179732845	1333,11673	2203	4300	6503	SO:0001583	missense	285025	exon16			AGCACCGGAGGTG	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26821	protein-coding gene	gene with protein product	"""coiled-coil protein associated with myosin II and DISC1"""					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.2482C>T	2.37:g.179732845G>A	ENSP00000395995:p.Arg828Trp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	37		278	0.12728937728937728	105	0.21341463414634146	30	0.08287292817679558	89	0.1555944055944056	54	0.0712401055408971	G	13.03	2.114663	0.37339	0.166364	0.069767	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723;ENST00000443758	T;T;T;T	0.50548	0.74;1.37;1.37;1.35	5.5	-11.0	0.00169	.	1.486400	0.03654	N	0.241424	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.08371	-1.0725	9	0.54805	T	0.06	0.8235	6.5786	0.22581	0.0861:0.176:0.528:0.2098	rs12988301;rs52829504;rs57427600;rs12988301	253	Q6ZP82	CC141_HUMAN	W	828;272;253;828	ENSP00000395995:R828W;ENSP00000344627:R272W;ENSP00000295723:R253W;ENSP00000390190:R828W	ENSP00000295723:R253W	R	-	1	2	CCDC141	179441090	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.972000	0.01502	-2.276000	0.00678	-3.619000	0.00027	CGG	G|0.885;A|0.115	0.115	strong		0.522	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648	
PECR	55825	hgsc.bcm.edu	37	2	216904019	216904019	+	Missense_Mutation	SNP	A	A	T	rs9288513	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:216904019A>T	ENST00000265322.7	-	8	965	c.891T>A	c.(889-891)ttT>ttA	p.F297L		NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	297			F -> L (in dbSNP:rs9288513).		fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	CTTTCTCCTTAAAGGTCTCCT	0.453													A|||	908	0.18131	0.2398	0.1225	5008	,	,		16415	0.1855		0.0964	False		,,,				2504	0.227				p.F297L		Atlas-SNP	.											.	PECR	22	.	0			c.T891A						PASS	.	A	LEU/PHE	994,3412	372.0+/-320.2	104,786,1313	150.0	147.0	148.0		891	-8.6	0.0	2	dbSNP_119	148	861,7739	196.1+/-241.1	50,761,3489	yes	missense	PECR	NM_018441.5	22	154,1547,4802	TT,TA,AA		10.0116,22.5601,14.2626	benign	297/304	216904019	1855,11151	2203	4300	6503	SO:0001583	missense	55825	exon8			CTCCTTAAAGGTC	AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18281	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 29C, member 1"""	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.891T>A	2.37:g.216904019A>T	ENSP00000265322:p.Phe297Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_018441	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	Missense_Mutation	SNP	ENST00000265322.7	37	CCDS33375.1	360	0.16483516483516483	116	0.23577235772357724	41	0.1132596685082873	136	0.23776223776223776	67	0.08839050131926121	A	12.70	2.015222	0.35511	0.225601	0.100116	ENSG00000115425	ENST00000265322	D	0.82167	-1.58	4.59	-8.63	0.00878	.	1.476780	0.03295	N	0.188134	T	0.00039	0.0001	N	0.17082	0.46	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.09773	-1.0659	9	0.11485	T	0.65	.	1.8223	0.03113	0.259:0.2499:0.3508:0.1402	rs9288513;rs52814596;rs9288513	297;151	Q9BY49;Q9BY49-2	PECR_HUMAN;.	L	297	ENSP00000265322:F297L	ENSP00000265322:F297L	F	-	3	2	PECR	216612264	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.640000	0.02009	-1.639000	0.01527	-0.466000	0.05196	TTT	A|0.844;T|0.156	0.156	strong		0.453	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441	
ANO7	50636	hgsc.bcm.edu	37	2	242149010	242149010	+	Missense_Mutation	SNP	C	C	T	rs57677160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242149010C>T	ENST00000274979.8	+	13	1584	c.1481C>T	c.(1480-1482)gCg>gTg	p.A494V	ANO7_ENST00000402430.3_Missense_Mutation_p.A493V	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	494					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						AGGAGCCGCGCGCGCCGCATG	0.682													C|||	616	0.123003	0.0998	0.1571	5008	,	,		15793	0.0159		0.2565	False		,,,				2504	0.1033				p.A494V		Atlas-SNP	.											ANO7,NS,carcinoma,+2,1	ANO7	136	1	0			c.C1481T						PASS	.	C	VAL/ALA	556,3850	245.9+/-254.7	34,488,1681	46.0	49.0	48.0		1481	-0.2	0.0	2	dbSNP_129	48	2203,6397	371.3+/-336.2	288,1627,2385	yes	missense	ANO7	NM_001001891.3	64	322,2115,4066	TT,TC,CC		25.6163,12.6192,21.2133	benign	494/934	242149010	2759,10247	2203	4300	6503	SO:0001583	missense	50636	exon13			GCCGCGCGCGCCG	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.1481C>T	2.37:g.242149010C>T	ENSP00000274979:p.Ala494Val	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	267	132	0.494382	NM_001001891	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	308	0.14102564102564102	52	0.10569105691056911	58	0.16022099447513813	5	0.008741258741258742	193	0.2546174142480211	C	1.607	-0.525135	0.04141	0.126192	0.256163	ENSG00000146205	ENST00000274979;ENST00000402430	T;T	0.63096	-0.02;-0.02	3.09	-0.242	0.13039	.	5.980880	0.00465	N	0.000112	T	0.00012	0.0000	N	0.04297	-0.235	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.06734	-1.0810	9	0.09084	T	0.74	.	7.1853	0.25797	0.0:0.1983:0.0:0.8017	rs57677160	494	Q6IWH7	ANO7_HUMAN	V	494;493	ENSP00000274979:A494V;ENSP00000385418:A493V	ENSP00000274979:A494V	A	+	2	0	ANO7	241797683	0.072000	0.21174	0.005000	0.12908	0.282000	0.26991	2.903000	0.48711	-0.078000	0.12730	0.306000	0.20318	GCG	C|0.812;T|0.188	0.188	strong		0.682	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
TPSD1	23430	hgsc.bcm.edu	37	16	1306681	1306681	+	Missense_Mutation	SNP	G	G	A	rs1141967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306681G>A	ENST00000211076.3	+	2	395	c.247G>A	c.(247-249)Gtg>Atg	p.V83M	TPSD1_ENST00000397534.2_Missense_Mutation_p.V76M|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	83	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		V -> M (in dbSNP:rs3993987). {ECO:0000269|PubMed:12391231, ECO:0000269|PubMed:18854315, ECO:0000269|PubMed:9920877}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				GGCGCACTGCGTGGAACCGTG	0.706													-|||	2212	0.441693	0.326	0.2983	5008	,	,		17934	0.7946		0.3221	False		,,,				2504	0.4591				p.V83M		Atlas-SNP	.											.	TPSD1	47	.	0			c.G247A						PASS	.	C	MET/VAL	1411,2987		210,991,998	39.0	47.0	44.0		247	-2.4	0.0	16	dbSNP_86	44	2540,6056		362,1816,2120	yes	missense	TPSD1	NM_012217.2	21	572,2807,3118	AA,AG,GG		29.5486,32.0828,30.4063	possibly-damaging	83/243	1306681	3951,9043	2199	4298	6497	SO:0001583	missense	23430	exon2			CACTGCGTGGAAC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.247G>A	16.37:g.1306681G>A	ENSP00000211076:p.Val83Met	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	179	90	0.502793	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	974	0.445970695970696	160	0.3252032520325203	98	0.27071823204419887	470	0.8216783216783217	246	0.3245382585751979	-	12.51	1.959770	0.34565	0.320828	0.295486	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.83992	-1.79;-1.79	2.89	-2.38	0.06622	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.525008	0.15921	N	0.238116	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	D;D	0.64830	0.994;0.991	P;P	0.58454	0.839;0.731	T	0.48581	-0.9023	9	0.66056	D	0.02	.	1.0121	0.01499	0.2287:0.3302:0.2737:0.1674	rs3993987;rs58194992	76;83	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	M	76;83	ENSP00000380668:V76M;ENSP00000211076:V83M	ENSP00000211076:V83M	V	+	1	0	TPSD1	1246682	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	-0.832000	0.04400	-0.652000	0.05408	-1.097000	0.02148	GTG	C|1.000;|0.000	.	alt		0.706	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
GGTLC1	92086	hgsc.bcm.edu	37	20	23965995	23965995	+	Missense_Mutation	SNP	A	A	T	rs150377656	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:23965995A>T	ENST00000335694.4	-	6	740	c.536T>A	c.(535-537)gTg>gAg	p.V179E	GGTLC1_ENST00000286890.4_Missense_Mutation_p.V179E|GGTLC1_ENST00000278765.4_Missense_Mutation_p.V179E	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	179					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						GGCTGCAGTCACTTCCTGGGG	0.632													.|||	92	0.0183706	0.0	0.0288	5008	,	,		18863	0.0		0.0656	False		,,,				2504	0.0061				p.V179E		Atlas-SNP	.											.	GGTLC1	37	.	0			c.T536A						PASS	.	A	GLU/VAL,GLU/VAL	47,4355		1,45,2155	65.0	69.0	68.0		536,536	0.8	0.4	20	dbSNP_134	68	433,8153		8,417,3868	no	missense,missense	GGTLC1	NM_178311.2,NM_178312.2	121,121	9,462,6023	TT,TA,AA		5.0431,1.0677,3.6957	probably-damaging,probably-damaging	179/226,179/226	23965995	480,12508	2201	4293	6494	SO:0001583	missense	92086	exon6			GCAGTCACTTCCT	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"""Gamma-glutamyltransferases"""	16437	protein-coding gene	gene with protein product		612338	"""gamma-glutamyltransferase-like activity 4"", ""gamma-glutamyltransferase-like activity 3"""	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.536T>A	20.37:g.23965995A>T	ENSP00000337587:p.Val179Glu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	184	99	0.538043	NM_178311	D3DW43|Q08246	Missense_Mutation	SNP	ENST00000335694.4	37	CCDS13163.1	61	0.027930402930402932	0	0.0	12	0.03314917127071823	0	0.0	49	0.06464379947229551	a	13.62	2.291493	0.40494	0.010677	0.050431	ENSG00000149435	ENST00000286890;ENST00000278765;ENST00000335694	T;T;T	0.09255	3.0;3.0;3.0	0.844	0.844	0.18943	.	0.141960	0.45867	D	0.000324	T	0.02727	0.0082	M	0.81341	2.54	0.29453	N	0.858351	D	0.58970	0.984	D	0.65010	0.931	T	0.01819	-1.1267	10	0.87932	D	0	-23.1385	4.1373	0.10178	1.0:0.0:0.0:0.0	.	179	Q9BX51	GGTL1_HUMAN	E	179	ENSP00000286890:V179E;ENSP00000278765:V179E;ENSP00000337587:V179E	ENSP00000278765:V179E	V	-	2	0	GGTLC1	23913995	0.073000	0.21202	0.390000	0.26220	0.393000	0.30537	1.957000	0.40392	0.077000	0.16863	0.076000	0.15429	GTG	A|0.967;T|0.033	0.033	strong		0.632	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2	
ZNF598	90850	hgsc.bcm.edu	37	16	2048826	2048826	+	Silent	SNP	C	C	G	rs2240691	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2048826C>G	ENST00000563630.1	-	11	2315	c.2073G>C	c.(2071-2073)gcG>gcC	p.A691A	ZNF598_ENST00000562103.1_Silent_p.A691A|ZNF598_ENST00000431526.1_Silent_p.A746A|AC005606.15_ENST00000567515.1_lincRNA			Q86UK7	ZN598_HUMAN	zinc finger protein 598	746	Pro-rich.						poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GGACTAGGTACGCCCGTGGGG	0.617													G|||	2287	0.456669	0.6785	0.4193	5008	,	,		13272	0.369		0.4026	False		,,,				2504	0.3292				p.A746A		Atlas-SNP	.											.	ZNF598	55	.	0			c.G2238C						PASS	.	G		2346,1544		718,910,317	25.0	29.0	28.0		2240	4.3	1.0	16	dbSNP_98	28	3160,5116		597,1966,1575	yes	coding-synonymous	ZNF598	NM_178167.2		1315,2876,1892	GG,GC,CC		38.1827,39.6915,45.2573		746/905	2048826	5506,6660	1945	4138	6083	SO:0001819	synonymous_variant	90850	exon13			TAGGTACGCCCGT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.2073G>C	16.37:g.2048826C>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Silent	SNP	ENST00000563630.1	37																																																																																				C|0.564;G|0.436	0.436	strong		0.617	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
DFFA	1676	hgsc.bcm.edu	37	1	10529326	10529326	+	Missense_Mutation	SNP	A	A	G	rs138842024	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:10529326A>G	ENST00000377038.3	-	2	273	c.206T>C	c.(205-207)aTa>aCa	p.I69T	DFFA_ENST00000377036.2_Missense_Mutation_p.I69T	NM_004401.2	NP_004392.1	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha polypeptide	69	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|negative regulation of apoptotic DNA fragmentation (GO:1902511)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of apoptotic process (GO:0043065)|thymocyte apoptotic process (GO:0070242)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				large_intestine(3)|lung(2)	5	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		ATCATCCACTATGGTGCCATC	0.423													A|||	11	0.00219649	0.0	0.0043	5008	,	,		21849	0.0		0.006	False		,,,				2504	0.002				p.I69T		Atlas-SNP	.											.	DFFA	24	.	0			c.T206C						PASS	.	A	THR/ILE,THR/ILE	5,4401	9.9+/-24.2	0,5,2198	152.0	132.0	139.0		206,206	5.5	1.0	1	dbSNP_134	139	38,8562	25.7+/-73.6	0,38,4262	yes	missense,missense	DFFA	NM_004401.2,NM_213566.1	89,89	0,43,6460	GG,GA,AA		0.4419,0.1135,0.3306	probably-damaging,probably-damaging	69/332,69/269	10529326	43,12963	2203	4300	6503	SO:0001583	missense	1676	exon2			TCCACTATGGTGC	AF087573	CCDS118.1, CCDS119.1	1p36.3-p36.2	2008-07-18	2002-08-29		ENSG00000160049	ENSG00000160049			2772	protein-coding gene	gene with protein product	"""DNA fragmentation factor, 45 kD, alpha subunit"""	601882	"""DNA fragmentation factor, 45 kD, alpha polypeptide"""			9605855, 9108473	Standard	NM_004401		Approved	DFF-45, DFF45, ICAD, DFF1	uc001arj.3	O00273	OTTHUMG00000001909	ENST00000377038.3:c.206T>C	1.37:g.10529326A>G	ENSP00000366237:p.Ile69Thr	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	272	135	0.496324	NM_004401	Q5T6G5|Q5T6G6|Q96I97|Q9Y6C6	Missense_Mutation	SNP	ENST00000377038.3	37	CCDS118.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	19.98	3.927190	0.73327	0.001135	0.004419	ENSG00000160049	ENST00000377038;ENST00000377036	.	.	.	5.49	5.49	0.81192	Caspase-activated nuclease CIDE-N (3);	0.000000	0.85682	D	0.000000	T	0.66752	0.2821	L	0.48362	1.52	0.58432	D	0.999998	D;D	0.89917	0.999;1.0	D;D	0.97110	0.991;1.0	T	0.69639	-0.5091	9	0.37606	T	0.19	-14.8227	15.6132	0.76744	1.0:0.0:0.0:0.0	.	69;69	O00273-2;O00273	.;DFFA_HUMAN	T	69	.	ENSP00000366235:I69T	I	-	2	0	DFFA	10451913	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.677000	0.84024	2.076000	0.62316	0.533000	0.62120	ATA	A|0.997;G|0.003	0.003	strong		0.423	DFFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005418.1	NM_004401	
ACACB	32	hgsc.bcm.edu	37	12	109577344	109577344	+	Missense_Mutation	SNP	A	A	G	rs139767464	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:109577344A>G	ENST00000338432.7	+	2	253	c.134A>G	c.(133-135)cAg>cGg	p.Q45R	ACACB_ENST00000377854.5_Missense_Mutation_p.Q45R|ACACB_ENST00000377848.3_Missense_Mutation_p.Q45R			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	45					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	ATCCCGAGCCAGGAGCCCTTT	0.557													A|||	3	0.000599042	0.0	0.0014	5008	,	,		15671	0.0		0.002	False		,,,				2504	0.0				p.Q45R		Atlas-SNP	.											.	ACACB	330	.	0			c.A134G						PASS	.	A	ARG/GLN	4,4402	6.2+/-15.9	0,4,2199	76.0	80.0	79.0		134	0.2	0.9	12	dbSNP_134	79	23,8577	17.3+/-56.4	0,23,4277	yes	missense	ACACB	NM_001093.3	43	0,27,6476	GG,GA,AA		0.2674,0.0908,0.2076	benign	45/2459	109577344	27,12979	2203	4300	6503	SO:0001583	missense	32	exon1			CGAGCCAGGAGCC	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.134A>G	12.37:g.109577344A>G	ENSP00000341044:p.Gln45Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	9.803	1.181034	0.21787	9.08E-4	0.002674	ENSG00000076555	ENST00000338432;ENST00000539864;ENST00000377848;ENST00000377854	D;D;D	0.95307	-3.67;-3.67;-3.67	5.53	0.147	0.14838	.	0.427648	0.19984	N	0.101719	D	0.83737	0.5319	N	0.14661	0.345	0.44579	D	0.997548	B	0.02656	0.0	B	0.04013	0.001	T	0.69172	-0.5215	10	0.15499	T	0.54	.	4.3681	0.11233	0.4845:0.3353:0.1802:0.0	.	45	O00763	ACACB_HUMAN	R	45;20;45;45	ENSP00000341044:Q45R;ENSP00000367079:Q45R;ENSP00000367085:Q45R	ENSP00000341044:Q45R	Q	+	2	0	ACACB	108061727	0.310000	0.24527	0.936000	0.37596	0.137000	0.21094	0.076000	0.14712	0.361000	0.24292	0.528000	0.53228	CAG	A|0.998;G|0.002	0.002	strong		0.557	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
MANBA	4126	hgsc.bcm.edu	37	4	103557077	103557077	+	Missense_Mutation	SNP	G	G	A	rs2866413	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:103557077G>A	ENST00000226578.4	-	15	2201	c.2102C>T	c.(2101-2103)aCg>aTg	p.T701M	MANBA_ENST00000505239.1_Missense_Mutation_p.T644M	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	701			T -> M (in dbSNP:rs2866413). {ECO:0000269|PubMed:15489334}.		cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)			cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		GATATAGAACGTGTTTTCATT	0.378													G|||	2750	0.549121	0.6626	0.6542	5008	,	,		21434	0.5159		0.493	False		,,,				2504	0.4131				p.T701M		Atlas-SNP	.											MANBA,NS,adenoma,0,1	MANBA	78	1	0			c.C2102T						PASS	.	G	MET/THR	2720,1686	654.3+/-399.7	850,1020,333	100.0	96.0	97.0		2102	2.8	0.0	4	dbSNP_101	97	4413,4187	585.7+/-391.9	1120,2173,1007	yes	missense	MANBA	NM_005908.3	81	1970,3193,1340	AA,AG,GG		48.686,38.266,45.1561	benign	701/880	103557077	7133,5873	2203	4300	6503	SO:0001583	missense	4126	exon15			TAGAACGTGTTTT		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.2102C>T	4.37:g.103557077G>A	ENSP00000226578:p.Thr701Met	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	1205	0.5517399267399268	311	0.6321138211382114	225	0.6215469613259669	295	0.5157342657342657	374	0.49340369393139843	G	9.422	1.083279	0.20309	0.61734	0.51314	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.58060	0.36;0.36	5.42	2.83	0.33086	.	0.610170	0.17652	N	0.166653	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B	0.21753	0.054;0.06	B;B	0.14578	0.004;0.011	T	0.42155	-0.9468	9	0.46703	T	0.11	-0.6633	8.7571	0.34652	0.8361:0.0:0.1639:0.0	rs2866413;rs3733203;rs17851324;rs52825236;rs57086295;rs2866413	644;701	E9PFW2;O00462	.;MANBA_HUMAN	M	701;644	ENSP00000226578:T701M;ENSP00000427322:T644M	ENSP00000226578:T701M	T	-	2	0	MANBA	103776125	0.002000	0.14202	0.000000	0.03702	0.017000	0.09413	1.802000	0.38853	0.344000	0.23847	-0.290000	0.09829	ACG	G|0.448;A|0.552	0.552	strong		0.378	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
UBXN10	127733	hgsc.bcm.edu	37	1	20517187	20517187	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:20517187C>T	ENST00000375099.3	+	2	217	c.133C>T	c.(133-135)Cgg>Tgg	p.R45W		NM_152376.3	NP_689589.1	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	45								p.R45W(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|skin(2)	14						CGCCAAGGGACGGACAAGACC	0.537																																					p.R45W		Atlas-SNP	.											UBXN10,NS,carcinoma,0,3	UBXN10	29	3	1	Substitution - Missense(1)	kidney(1)	c.C133T						scavenged	.						98.0	85.0	89.0					1																	20517187		2203	4300	6503	SO:0001583	missense	127733	exon2			AAGGGACGGACAA	AK058158	CCDS205.1	1p36.13	2008-07-25	2008-07-25	2008-07-25	ENSG00000162543	ENSG00000162543		"""UBX domain containing"""	26354	protein-coding gene	gene with protein product			"""UBX domain containing 3"""	UBXD3		12477932	Standard	NM_152376		Approved	FLJ25429	uc001bdb.3	Q96LJ8	OTTHUMG00000002708	ENST00000375099.3:c.133C>T	1.37:g.20517187C>T	ENSP00000364240:p.Arg45Trp	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	175	4	0.0228571	NM_152376	Q5R386	Missense_Mutation	SNP	ENST00000375099.3	37	CCDS205.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.913432	0.72983	.	.	ENSG00000162543	ENST00000375099	.	.	.	5.23	5.23	0.72850	.	0.000000	0.64402	D	0.000015	T	0.78910	0.4358	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81335	-0.0979	9	0.87932	D	0	-18.0001	17.361	0.87350	0.0:1.0:0.0:0.0	.	45	Q96LJ8	UBX10_HUMAN	W	45	.	ENSP00000364240:R45W	R	+	1	2	UBXN10	20389774	1.000000	0.71417	0.879000	0.34478	0.443000	0.32047	5.162000	0.64942	2.444000	0.82710	0.655000	0.94253	CGG	.	.	none		0.537	UBXN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007693.1	NM_152376	
ANKRD44	91526	hgsc.bcm.edu	37	2	197946392	197946392	+	Silent	SNP	C	C	T	rs35272229	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:197946392C>T	ENST00000328737.2	-	15	1516	c.1440G>A	c.(1438-1440)gaG>gaA	p.E480E	ANKRD44_ENST00000337207.5_Silent_p.E480E|ANKRD44_ENST00000539527.1_Silent_p.E433E|ANKRD44_ENST00000450567.1_Silent_p.E480E|ANKRD44_ENST00000409153.1_Silent_p.E505E|ANKRD44_ENST00000477852.1_5'Flank|ANKRD44_ENST00000282272.8_Silent_p.E497E			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	505										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TTTCCTTCAGCTCCCTGGCTC	0.393													C|||	129	0.0257588	0.0212	0.0317	5008	,	,		19848	0.0		0.0537	False		,,,				2504	0.0256				p.E505E		Atlas-SNP	.											.	ANKRD44	281	.	0			c.G1515A						PASS	.	C		82,4324	70.3+/-108.2	1,80,2122	215.0	215.0	215.0		1515	1.5	1.0	2	dbSNP_126	215	471,8129	139.2+/-195.9	9,453,3838	no	coding-synonymous	ANKRD44	NM_001195144.1		10,533,5960	TT,TC,CC		5.4767,1.8611,4.2519		505/994	197946392	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	91526	exon15			CTTCAGCTCCCTG	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1440G>A	2.37:g.197946392C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	174	78	0.448276	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	37																																																																																				C|0.957;T|0.043	0.043	strong		0.393	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	
HLA-C	3107	hgsc.bcm.edu	37	6	31238029	31238029	+	Missense_Mutation	SNP	T	T	C	rs2308622	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238029T>C	ENST00000376228.5	-	4	867	c.853A>G	c.(853-855)Atg>Gtg	p.M285V	HLA-C_ENST00000383329.3_Missense_Mutation_p.M285V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	285	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TCGTGCTGCATATGGCACGTG	0.577													C|||	3860	0.770767	0.7912	0.8084	5008	,	,		14620	0.8006		0.7177	False		,,,				2504	0.7403				p.M285V		Atlas-SNP	.											.	HLA-C	92	.	0			c.A853G						PASS	.						31.0	33.0	32.0					6																	31238029		2185	4274	6459	SO:0001583	missense	3107	exon4			GCTGCATATGGCA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.853A>G	6.37:g.31238029T>C	ENSP00000365402:p.Met285Val	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1473|1473	0.6744505494505495|0.6744505494505495	340|340	0.6910569105691057|0.6910569105691057	265|265	0.7320441988950276|0.7320441988950276	407|407	0.7115384615384616|0.7115384615384616	461|461	0.6081794195250659|0.6081794195250659	.|.	0.041|0.041	-1.283503|-1.283503	0.01398|0.01398	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.00753	.|5.74;5.74	2.67|2.67	2.67|2.67	0.31697|0.31697	.|Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	.|0.000000	.|0.37530	.|N	.|0.002056	T|T	0.00109|0.00109	0.0003|0.0003	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.04013	.|0.001;0.0;0.001;0.0	T|T	0.30327|0.30327	-0.9982|-0.9982	3|8	.|0.02654	.|T	.|1	.|.	5.8147|5.8147	0.18486|0.18486	0.0:0.8464:0.0:0.1536|0.0:0.8464:0.0:0.1536	rs2308622;rs9264632;rs17413443|rs2308622;rs9264632;rs17413443	.|285;285;285;285	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	M|V	248|285;285;285;322	.|ENSP00000365402:M285V;ENSP00000372819:M285V	.|ENSP00000365402:M285V	I|M	-|-	3|1	3|0	HLA-C|HLA-C	31346008|31346008	0.911000|0.911000	0.30947|0.30947	0.078000|0.078000	0.20375|0.20375	0.054000|0.054000	0.15201|0.15201	2.199000|2.199000	0.42715|0.42715	0.710000|0.710000	0.31997|0.31997	-0.711000|-0.711000	0.03637|0.03637	ATA|ATG	T|0.324;C|0.676	0.676	strong		0.577	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
HGFAC	3083	hgsc.bcm.edu	37	4	3444592	3444592	+	Missense_Mutation	SNP	C	C	G	rs149401735	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:3444592C>G	ENST00000382774.3	+	2	366	c.251C>G	c.(250-252)cCg>cGg	p.P84R	HGFAC_ENST00000511533.1_Missense_Mutation_p.P84R	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	84					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGGGGGCTCCCGCCCCCGCCC	0.672													C|||	9	0.00179712	0.0	0.0072	5008	,	,		15436	0.0		0.003	False		,,,				2504	0.001				p.P84R		Atlas-SNP	.											HGFAC,NS,carcinoma,-1,1	HGFAC	69	1	0			c.C251G						PASS	.	C	ARG/PRO	6,4396	4.2+/-10.8	0,6,2195	45.0	53.0	51.0		251	-2.5	0.0	4	dbSNP_134	51	53,8545	29.0+/-79.6	0,53,4246	yes	missense	HGFAC	NM_001528.2	103	0,59,6441	GG,GC,CC		0.6164,0.1363,0.4538	benign	84/656	3444592	59,12941	2201	4299	6500	SO:0001583	missense	3083	exon2			GGCTCCCGCCCCC	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.251C>G	4.37:g.3444592C>G	ENSP00000372224:p.Pro84Arg	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	133	59	0.443609	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	37	CCDS3369.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	5.950	0.359220	0.11239	0.001363	0.006164	ENSG00000109758	ENST00000382774;ENST00000511533	D;D	0.88509	-2.39;-2.37	2.01	-2.48	0.06423	.	17.007900	0.01301	U	0.010281	T	0.70395	0.3219	N	0.14661	0.345	0.09310	N	1	B;B	0.34015	0.435;0.435	B;B	0.31016	0.123;0.123	T	0.65397	-0.6178	10	0.27082	T	0.32	.	3.8805	0.09076	0.0:0.3454:0.3762:0.2783	.	84;84	D6RAR4;Q04756	.;HGFA_HUMAN	R	84	ENSP00000372224:P84R;ENSP00000421801:P84R	ENSP00000372224:P84R	P	+	2	0	HGFAC	3414390	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.289000	0.00525	-0.825000	0.04290	-0.676000	0.03789	CCG	C|0.997;G|0.003	0.003	strong		0.672	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
PIWIL4	143689	hgsc.bcm.edu	37	11	94326765	94326765	+	Missense_Mutation	SNP	G	G	C	rs57607909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:94326765G>C	ENST00000299001.6	+	9	1319	c.1108G>C	c.(1108-1110)Gct>Cct	p.A370P	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	370	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.		A -> P (in dbSNP:rs57607909). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CAACAGTGAGGCTCAGCTCGC	0.438													G|||	1151	0.229832	0.3071	0.1686	5008	,	,		18030	0.2649		0.2286	False		,,,				2504	0.1339				p.A370P		Atlas-SNP	.											.	PIWIL4	70	.	0			c.G1108C						PASS	.	G	PRO/ALA	1234,3168	426.6+/-341.2	163,908,1130	149.0	148.0	148.0		1108	-1.1	0.0	11	dbSNP_129	148	1922,6674	340.9+/-323.8	225,1472,2601	yes	missense	PIWIL4	NM_152431.2	27	388,2380,3731	CC,CG,GG		22.3592,28.0327,24.2807	benign	370/853	94326765	3156,9842	2201	4298	6499	SO:0001583	missense	143689	exon9			AGTGAGGCTCAGC	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1108G>C	11.37:g.94326765G>C	ENSP00000299001:p.Ala370Pro	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	509	0.23305860805860806	135	0.27439024390243905	69	0.19060773480662985	136	0.23776223776223776	169	0.22295514511873352	G	0.011	-1.692544	0.00731	0.280327	0.223592	ENSG00000134627	ENST00000299001	T	0.09073	3.02	4.77	-1.1	0.09872	Argonaute/Dicer protein, PAZ (4);	0.585427	0.15970	N	0.235824	T	0.00012	0.0000	N	0.13043	0.29	0.54753	P	1.8999999999991246E-5	B	0.02656	0.0	B	0.09377	0.004	T	0.46830	-0.9163	9	0.30078	T	0.28	-0.0363	13.5706	0.61845	0.0775:0.6422:0.2803:0.0	rs57607909	370	Q7Z3Z4	PIWL4_HUMAN	P	370	ENSP00000299001:A370P	ENSP00000299001:A370P	A	+	1	0	PIWIL4	93966413	0.488000	0.25996	0.005000	0.12908	0.009000	0.06853	0.106000	0.15354	-0.073000	0.12842	-0.379000	0.06801	GCT	G|0.768;C|0.232	0.232	strong		0.438	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
ZNF554	115196	hgsc.bcm.edu	37	19	2833943	2833943	+	Missense_Mutation	SNP	G	G	A	rs34753687	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:2833943G>A	ENST00000317243.5	+	5	908	c.710G>A	c.(709-711)gGa>gAa	p.G237E	ZNF554_ENST00000591265.1_3'UTR	NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	237					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTATCACAGGGAAGCTCTAAA	0.498													G|||	31	0.0061901	0.0	0.0101	5008	,	,		19762	0.0		0.0239	False		,,,				2504	0.0				p.G237E		Atlas-SNP	.											.	ZNF554	47	.	0			c.G710A						PASS	.	G	GLU/GLY	13,3779		0,13,1883	105.0	105.0	105.0		710	2.9	0.0	19	dbSNP_126	105	196,8026		5,186,3920	yes	missense	ZNF554	NM_001102651.1	98	5,199,5803	AA,AG,GG		2.3838,0.3428,1.7396	probably-damaging	237/539	2833943	209,11805	1896	4111	6007	SO:0001583	missense	115196	exon5			CACAGGGAAGCTC	AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"""Zinc fingers, C2H2-type"", ""-"""	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.710G>A	19.37:g.2833943G>A	ENSP00000321132:p.Gly237Glu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_001102651	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	23	0.010531135531135532	0	0.0	5	0.013812154696132596	0	0.0	18	0.023746701846965697	G	4.844	0.156867	0.09236	0.003428	0.023838	ENSG00000172006	ENST00000317243	T	0.06142	3.34	2.86	2.86	0.33363	.	.	.	.	.	T	0.02418	0.0074	L	0.29908	0.895	0.09310	N	0.999999	B	0.15141	0.012	B	0.15870	0.014	T	0.29610	-1.0006	9	0.45353	T	0.12	.	7.936	0.29931	0.0:0.2557:0.7442:0.0	rs34753687	237	Q86TJ5	ZN554_HUMAN	E	237	ENSP00000321132:G237E	ENSP00000321132:G237E	G	+	2	0	ZNF554	2784943	0.031000	0.19500	0.009000	0.14445	0.022000	0.10575	1.124000	0.31320	1.615000	0.50252	0.643000	0.83706	GGA	G|0.986;A|0.014	0.014	strong		0.498	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303	
OR1K1	392392	hgsc.bcm.edu	37	9	125562651	125562651	+	Missense_Mutation	SNP	G	G	A	rs55961642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:125562651G>A	ENST00000277309.2	+	1	282	c.250G>A	c.(250-252)Gcc>Acc	p.A84T		NM_080859.1	NP_543135.1	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K, member 1	84						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(8)|lung(2)|ovary(1)|skin(4)|stomach(1)	17						CAAGATGTTGGCCAACTTGTT	0.577													G|||	102	0.0203674	0.0	0.0807	5008	,	,		22147	0.0		0.0328	False		,,,				2504	0.0133				p.A84T		Atlas-SNP	.											.	OR1K1	34	.	0			c.G250A						PASS	.	G	THR/ALA	26,4380	33.5+/-64.1	0,26,2177	166.0	119.0	135.0		250	3.7	0.9	9	dbSNP_129	135	241,8359	96.3+/-158.1	3,235,4062	yes	missense	OR1K1	NM_080859.1	58	3,261,6239	AA,AG,GG		2.8023,0.5901,2.0529	benign	84/317	125562651	267,12739	2203	4300	6503	SO:0001583	missense	392392	exon1			ATGTTGGCCAACT	AL359512	CCDS35132.1	9q33	2013-09-20			ENSG00000165204	ENSG00000165204		"""GPCR / Class A : Olfactory receptors"""	8212	protein-coding gene	gene with protein product							Standard	NM_080859		Approved	hg99, MNAB	uc011lze.2	Q8NGR3	OTTHUMG00000020625	ENST00000277309.2:c.250G>A	9.37:g.125562651G>A	ENSP00000277309:p.Ala84Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	111	62	0.558559	NM_080859	B9EH41|Q4VXB7|Q96R23	Missense_Mutation	SNP	ENST00000277309.2	37	CCDS35132.1	59	0.027014652014652016	4	0.008130081300813009	20	0.055248618784530384	0	0.0	35	0.04617414248021108	G	10.13	1.266463	0.23136	0.005901	0.028023	ENSG00000165204	ENST00000277309	T	0.00397	7.57	4.61	3.72	0.42706	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38663	U	0.001609	T	0.00039	0.0001	L	0.45228	1.405	0.21553	N	0.999649	B	0.29571	0.249	B	0.30646	0.118	T	0.45977	-0.9224	10	0.59425	D	0.04	.	7.6529	0.28358	0.0903:0.1659:0.7438:0.0	rs55961642	84	Q8NGR3	OR1K1_HUMAN	T	84	ENSP00000277309:A84T	ENSP00000277309:A84T	A	+	1	0	OR1K1	124602472	0.000000	0.05858	0.945000	0.38365	0.308000	0.27856	0.162000	0.16501	1.162000	0.42619	0.655000	0.94253	GCC	G|0.979;A|0.021	0.021	strong		0.577	OR1K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053958.1		
ATN1	1822	hgsc.bcm.edu	37	12	7046077	7046077	+	Silent	SNP	G	G	A	rs11547602	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7046077G>A	ENST00000356654.4	+	5	1884	c.1647G>A	c.(1645-1647)ctG>ctA	p.L549L	ATN1_ENST00000396684.2_Silent_p.L549L	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	549	Involved in binding BAIAP2.				cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						CAGCACACCTGCCCCCACCTC	0.637													g|||	57	0.0113818	0.0015	0.0231	5008	,	,		-128	0.001		0.0328	False		,,,				2504	0.0051				p.L549L		Atlas-SNP	.											.	ATN1	95	.	0			c.G1647A						PASS	.	G	,	46,4360	48.2+/-83.0	0,46,2157	111.0	92.0	98.0		1647,1647	2.6	1.0	12	dbSNP_120	98	360,8240	120.8+/-180.0	11,338,3951	no	coding-synonymous,coding-synonymous	ATN1	NM_001007026.1,NM_001940.3	,	11,384,6108	AA,AG,GG		4.186,1.044,3.1216	,	549/1191,549/1191	7046077	406,12600	2203	4300	6503	SO:0001819	synonymous_variant	1822	exon5			ACACCTGCCCCCA	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"""dentatorubral-pallidoluysian atrophy (atrophin-1)"""	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.1647G>A	12.37:g.7046077G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	168	82	0.488095	NM_001007026	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	37	CCDS31734.1																																																																																			G|0.970;A|0.030	0.030	strong		0.637	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940	
CPAMD8	27151	hgsc.bcm.edu	37	19	17108094	17108094	+	Missense_Mutation	SNP	C	C	T	rs143454938	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17108094C>T	ENST00000443236.1	-	11	1094	c.1063G>A	c.(1063-1065)Gtc>Atc	p.V355I	CPAMD8_ENST00000388925.4_Missense_Mutation_p.V308I	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	308						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.V355I(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						TGCTCAGGGACGTCCGCTGGG	0.637													c|||	122	0.024361	0.0023	0.036	5008	,	,		19517	0.0		0.0487	False		,,,				2504	0.046				p.V355I		Atlas-SNP	.											CPAMD8,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CPAMD8	192	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.G1063A						PASS	.	C	ILE/VAL	26,3838		0,26,1906	14.0	16.0	15.0		1063	1.9	0.2	19	dbSNP_134	15	343,7903		8,327,3788	no	missense	CPAMD8	NM_015692.2	29	8,353,5694	TT,TC,CC		4.1596,0.6729,3.0471	possibly-damaging	355/1933	17108094	369,11741	1932	4123	6055	SO:0001583	missense	27151	exon11			CAGGGACGTCCGC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1063G>A	19.37:g.17108094C>T	ENSP00000402505:p.Val355Ile	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	177	77	0.435028	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	53	0.024267399267399268	3	0.006097560975609756	10	0.027624309392265192	0	0.0	40	0.052770448548812667	c	6.014	0.370965	0.11409	0.006729	0.041596	ENSG00000160111	ENST00000291440;ENST00000388925	T;T	0.52983	0.64;0.66	3.0	1.94	0.25998	.	0.967515	0.08382	N	0.954315	T	0.09423	0.0232	M	0.75447	2.3	0.32844	D	0.505707	P	0.34662	0.462	B	0.17433	0.018	T	0.36768	-0.9734	10	0.49607	T	0.09	.	5.6238	0.17470	0.1927:0.7012:0.0:0.1061	.	308	Q8IZJ3	CPMD8_HUMAN	I	355;308	ENSP00000291440:V355I;ENSP00000373577:V308I	ENSP00000291440:V355I	V	-	1	0	CPAMD8	16969094	0.992000	0.36948	0.198000	0.23420	0.159000	0.22180	2.780000	0.47742	0.397000	0.25310	0.555000	0.69702	GTC	C|0.909;T|0.091	0.091	strong		0.637	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
LRRC48	83450	hgsc.bcm.edu	37	17	17919414	17919414	+	Missense_Mutation	SNP	G	G	A	rs200381151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17919414G>A	ENST00000399187.1	+	13	1581	c.1363G>A	c.(1363-1365)Ggg>Agg	p.G455R	ATPAF2_ENST00000469327.1_5'Flank|LRRC48_ENST00000313838.8_Missense_Mutation_p.G455R|LRRC48_ENST00000583995.1_3'UTR	NM_031294.3	NP_112584.3	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48	455						cytoplasm (GO:0005737)				breast(1)|large_intestine(2)|lung(2)|pancreas(1)|urinary_tract(1)	7	all_neural(463;0.228)					TAATGCTGTCGGGGCATCGCA	0.443													G|||	14	0.00279553	0.0038	0.0043	5008	,	,		21102	0.0		0.004	False		,,,				2504	0.002				p.G455R		Atlas-SNP	.											.	LRRC48	49	.	0			c.G1363A						PASS	.	G	ARG/GLY,ARG/GLY	28,3894		0,28,1933	153.0	145.0	147.0		1363,1363	5.5	0.9	17		147	67,8235		0,67,4084	yes	missense,missense	LRRC48	NM_001130090.1,NM_031294.3	125,125	0,95,6017	AA,AG,GG		0.807,0.7139,0.7772	,	455/524,455/524	17919414	95,12129	1961	4151	6112	SO:0001583	missense	83450	exon13			GCTGTCGGGGCAT	AK093317	CCDS45622.1, CCDS45623.1	17p11.2	2014-07-18			ENSG00000171962	ENSG00000171962			25384	protein-coding gene	gene with protein product						11997338, 23354437	Standard	NM_001130090		Approved	DKFZP586M1120	uc021trk.1	Q9H069	OTTHUMG00000059355	ENST00000399187.1:c.1363G>A	17.37:g.17919414G>A	ENSP00000382140:p.Gly455Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	100	41	0.41	NM_031294	A8KAE6|Q86SF9|Q86W73|Q8IWG0	Missense_Mutation	SNP	ENST00000399187.1	37	CCDS45622.1	4	0.0018315018315018315	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	0	0.0	G	20.0	3.931107	0.73327	0.007139	0.00807	ENSG00000171962	ENST00000313838;ENST00000448396;ENST00000399187;ENST00000399185	T;T	0.52526	0.66;0.66	5.47	5.47	0.80525	.	0.412797	0.28724	N	0.014349	T	0.47581	0.1453	M	0.63428	1.95	0.80722	D	1	D	0.71674	0.998	P	0.55871	0.786	T	0.53380	-0.8447	10	0.45353	T	0.12	-51.1913	8.5414	0.33395	0.1643:0.0:0.8357:0.0	.	455	Q9H069	LRC48_HUMAN	R	455	ENSP00000326870:G455R;ENSP00000382140:G455R	ENSP00000326870:G455R	G	+	1	0	LRRC48	17860139	0.998000	0.40836	0.932000	0.37286	0.749000	0.42624	3.102000	0.50291	2.557000	0.86248	0.563000	0.77884	GGG	G|0.997;A|0.003	0.003	strong		0.443	LRRC48-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131945.3	NM_031294	
OR5M3	219482	hgsc.bcm.edu	37	11	56237728	56237728	+	Silent	SNP	G	G	A	rs79240946	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56237728G>A	ENST00000312240.2	-	1	286	c.246C>T	c.(244-246)aaC>aaT	p.N82N		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					CTGATAACAGGTTTTCCAACA	0.368													g|||	182	0.0363419	0.003	0.0432	5008	,	,		19752	0.001		0.0934	False		,,,				2504	0.0542				p.N82N		Atlas-SNP	.											.	OR5M3	103	.	0			c.C246T						PASS	.	G		55,4347	53.6+/-89.4	0,55,2146	95.0	85.0	88.0		246	-2.8	0.0	11	dbSNP_131	88	683,7907	166.2+/-218.2	35,613,3647	no	coding-synonymous	OR5M3	NM_001004742.2		35,668,5793	AA,AG,GG		7.9511,1.2494,5.6804		82/308	56237728	738,12254	2201	4295	6496	SO:0001819	synonymous_variant	219482	exon1			TAACAGGTTTTCC	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"""GPCR / Class A : Olfactory receptors"""	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.246C>T	11.37:g.56237728G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	149	65	0.436242	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Silent	SNP	ENST00000312240.2	37	CCDS31532.1																																																																																			G|0.951;A|0.049	0.049	strong		0.368	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742	
HSP90AB1	3326	hgsc.bcm.edu	37	6	44221316	44221316	+	Missense_Mutation	SNP	G	G	A	rs76772157	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:44221316G>A	ENST00000371554.1	+	12	2370	c.2156G>A	c.(2155-2157)cGc>cAc	p.R719H	SLC35B2_ENST00000495706.1_5'Flank|MIR4647_ENST00000583964.1_RNA|HSP90AB1_ENST00000371646.5_Missense_Mutation_p.R719H|HSP90AB1_ENST00000353801.3_Missense_Mutation_p.R719H			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	719					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)	p.R719H(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GATGCGTCTCGCATGGAAGAA	0.522											OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R719H		Atlas-SNP	.											HSP90AB1,extremity,malignant_melanoma,0,1	HSP90AB1	83	1	1	Substitution - Missense(1)	skin(1)	c.G2156A						scavenged	.						72.0	75.0	74.0					6																	44221316		2203	4300	6503	SO:0001583	missense	3326	exon12			CGTCTCGCATGGA	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2156G>A	6.37:g.44221316G>A	ENSP00000360609:p.Arg719His	Somatic	192	1	0.00520833	922	WXS	Illumina HiSeq	Phase_I	220	29	0.131818	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Missense_Mutation	SNP	ENST00000371554.1	37	CCDS4909.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099702	0.56183	.	.	ENSG00000096384	ENST00000371646;ENST00000353801;ENST00000371554	T;T;T	0.09723	2.95;2.95;2.95	3.91	3.91	0.45181	.	0.000000	0.64402	U	0.000001	T	0.06554	0.0168	M	0.61703	1.905	0.80722	D	1	B;B;B	0.30584	0.004;0.286;0.002	B;B;B	0.30029	0.11;0.092;0.013	T	0.06499	-1.0823	10	0.44086	T	0.13	-1.7567	12.0789	0.53659	0.0881:0.0:0.9119:0.0	.	681;709;719	B4DMA2;B4DGL0;P08238	.;.;HS90B_HUMAN	H	719	ENSP00000360709:R719H;ENSP00000325875:R719H;ENSP00000360609:R719H	ENSP00000325875:R719H	R	+	2	0	HSP90AB1	44329294	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	5.571000	0.67404	2.188000	0.69820	0.609000	0.83330	CGC	G|0.986;A|0.014	0.014	strong		0.522	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355	
PSMA6	5687	hgsc.bcm.edu	37	14	35783656	35783656	+	Silent	SNP	A	A	G	rs13393	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:35783656A>G	ENST00000261479.4	+	6	798	c.678A>G	c.(676-678)aaA>aaG	p.K226K	KIAA0391_ENST00000557565.1_3'UTR|PSMA6_ENST00000555764.1_Silent_p.K147K|PSMA6_ENST00000553809.1_Silent_p.K232K|PSMA6_ENST00000540871.1_Silent_p.K207K|PSMA6_ENST00000556506.1_Intron	NM_002791.1	NP_002782.1	P60900	PSA6_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 6	226					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of inflammatory response (GO:0050727)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|myofibril (GO:0030016)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysome (GO:0005844)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)|sarcomere (GO:0030017)	endopeptidase activity (GO:0004175)|NF-kappaB binding (GO:0051059)|purine ribonucleoside triphosphate binding (GO:0035639)|RNA binding (GO:0003723)|threonine-type endopeptidase activity (GO:0004298)			kidney(2)|large_intestine(1)|lung(5)|prostate(1)|urinary_tract(1)	10	Breast(36;0.0519)|Hepatocellular(127;0.158)		Lung(238;3.81e-05)|LUAD - Lung adenocarcinoma(48;5.59e-05)|Epithelial(34;0.00342)|all cancers(34;0.00973)	GBM - Glioblastoma multiforme(112;0.0234)		AAAATCCTAAATTCAGGTGAG	0.393													A|||	210	0.0419329	0.0847	0.0144	5008	,	,		17374	0.001		0.0258	False		,,,				2504	0.0624				p.K226K		Atlas-SNP	.											.	PSMA6	18	.	0			c.A678G						PASS	.	A		419,3987	201.8+/-224.7	26,367,1810	56.0	51.0	53.0		678	1.9	1.0	14	dbSNP_52	53	242,8358	96.3+/-158.1	1,240,4059	no	coding-synonymous	PSMA6	NM_002791.1		27,607,5869	GG,GA,AA		2.814,9.5098,5.0823		226/247	35783656	661,12345	2203	4300	6503	SO:0001819	synonymous_variant	5687	exon6			TCCTAAATTCAGG	X59417	CCDS9655.1, CCDS61437.1, CCDS61438.1	14q13	2003-03-12			ENSG00000100902	ENSG00000100902		"""Proteasome (prosome, macropain) subunits"""	9535	protein-coding gene	gene with protein product		602855				1888762, 8811196	Standard	NM_002791		Approved	IOTA, PROS27, p27K, MGC22756, MGC2333, MGC23846	uc001wtd.3	P60900	OTTHUMG00000140221	ENST00000261479.4:c.678A>G	14.37:g.35783656A>G		Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	301	136	0.451827	NM_002791	B2R7J9|B4DQR4|B4DXJ9|P34062|Q6IB60	Silent	SNP	ENST00000261479.4	37	CCDS9655.1	65	0.02976190476190476	42	0.08536585365853659	6	0.016574585635359115	0	0.0	17	0.022427440633245383	A	9.601	1.128795	0.21041	0.095098	0.02814	ENSG00000100902	ENST00000556221	.	.	.	5.55	1.88	0.25563	.	.	.	.	.	T	0.02888	0.0086	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00822	-1.1552	4	.	.	.	-11.0995	9.9144	0.41425	0.7254:0.0:0.2746:0.0	rs13393;rs17586;rs28600041	.	.	.	S	65	.	.	N	+	2	0	PSMA6	34853407	0.978000	0.34361	1.000000	0.80357	0.994000	0.84299	0.408000	0.21065	0.480000	0.27534	0.528000	0.53228	AAT	A|0.955;G|0.045	0.045	strong		0.393	PSMA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276684.1		
ERAP1	51752	hgsc.bcm.edu	37	5	96118866	96118866	+	Missense_Mutation	SNP	C	C	T	rs17482078	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96118866C>T	ENST00000443439.2	-	15	2240	c.2174G>A	c.(2173-2175)cGa>cAa	p.R725Q	ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000512856.1_RNA|ERAP1_ENST00000296754.3_Missense_Mutation_p.R725Q|CTD-2260A17.1_ENST00000602972.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	725			R -> Q (in dbSNP:rs17482078). {ECO:0000269|PubMed:11481040, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:9628581}.		angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		CCGCAGCATTCGCTCTGAGAC	0.532													C|||	504	0.100639	0.0537	0.1239	5008	,	,		18856	0.0575		0.2237	False		,,,				2504	0.0654				p.R725Q		Atlas-SNP	.											.	ERAP1	59	.	0			c.G2174A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	422,3984	205.8+/-227.6	22,378,1803	184.0	156.0	165.0		2174,2174,2174	5.8	1.0	5	dbSNP_123	165	1762,6838	319.9+/-314.4	191,1380,2729	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	43,43,43	213,1758,4532	TT,TC,CC		20.4884,9.5778,16.7922	probably-damaging,probably-damaging,probably-damaging	725/942,725/942,725/949	96118866	2184,10822	2203	4300	6503	SO:0001583	missense	51752	exon15			AGCATTCGCTCTG	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.2174G>A	5.37:g.96118866C>T	ENSP00000406304:p.Arg725Gln	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	184	82	0.445652	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	285	0.1304945054945055	28	0.056910569105691054	48	0.13259668508287292	40	0.06993006993006994	169	0.22295514511873352	C	18.63	3.664349	0.67700	0.095778	0.204884	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.05258	3.47;3.47	5.78	5.78	0.91487	.	0.065264	0.64402	D	0.000020	T	0.00012	0.0000	M	0.76838	2.35	0.09310	P	0.999999367196	B;P;P	0.41673	0.272;0.587;0.759	B;B;B	0.28305	0.027;0.04;0.088	T	0.52373	-0.8584	9	0.30854	T	0.27	.	19.6088	0.95594	0.0:1.0:0.0:0.0	rs17482078;rs17482078	725;725;725	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	Q	725	ENSP00000296754:R725Q;ENSP00000406304:R725Q	ENSP00000296754:R725Q	R	-	2	0	ERAP1	96144622	1.000000	0.71417	0.990000	0.47175	0.504000	0.33889	4.515000	0.60489	2.734000	0.93682	0.563000	0.77884	CGA	C|0.859;T|0.141	0.141	strong		0.532	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
LIPN	643418	hgsc.bcm.edu	37	10	90537942	90537942	+	Silent	SNP	C	C	T	rs11202851	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:90537942C>T	ENST00000404459.1	+	9	1140	c.1140C>T	c.(1138-1140)ctC>ctT	p.L380L		NM_001102469.1	NP_001095939.1	Q5VXI9	LIPN_HUMAN	lipase, family member N	380					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	9		Colorectal(252;0.0161)		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)		TCTGGGGCCTCGATGCCCCTC	0.418													C|||	629	0.125599	0.0038	0.1455	5008	,	,		22386	0.2679		0.0547	False		,,,				2504	0.2025				p.L380L		Atlas-SNP	.											.	LIPN	28	.	0			c.C1140T						PASS	.	C		61,3695		1,59,1818	79.0	74.0	75.0		1140	-10.4	0.0	10	dbSNP_120	75	489,7711		17,455,3628	no	coding-synonymous	LIPN	NM_001102469.1		18,514,5446	TT,TC,CC		5.9634,1.6241,4.6002		380/399	90537942	550,11406	1878	4100	5978	SO:0001819	synonymous_variant	643418	exon9			GGGCCTCGATGCC		CCDS44456.1	10q23.31	2013-09-20	2007-02-27	2007-02-27	ENSG00000204020	ENSG00000204020			23452	protein-coding gene	gene with protein product		613924	"""lipase-like, ab-hydrolase domain containing 4"""	LIPL4			Standard	NM_001102469		Approved	bA186O14.3	uc010qmw.2	Q5VXI9	OTTHUMG00000018694	ENST00000404459.1:c.1140C>T	10.37:g.90537942C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	96	89	0.927083	NM_001102469	A7KIH9	Silent	SNP	ENST00000404459.1	37	CCDS44456.1																																																																																			C|0.901;T|0.099	0.099	strong		0.418	LIPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049254.2	XM_926751	
SNRNP48	154007	hgsc.bcm.edu	37	6	7602857	7602857	+	Splice_Site	SNP	C	C	T	rs9502622	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:7602857C>T	ENST00000342415.5	+	6	656	c.597C>T	c.(595-597)gaC>gaT	p.D199D		NM_152551.3	NP_689764.3	Q6IEG0	SNR48_HUMAN	small nuclear ribonucleoprotein 48kDa (U11/U12)	199					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)			kidney(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						TTTCATTAGACAATAGTCGAA	0.289													T|||	631	0.125998	0.3517	0.0706	5008	,	,		15641	0.001		0.0964	False		,,,				2504	0.0194				p.D199D		Atlas-SNP	.											.	SNRNP48	32	.	0			c.C597T						PASS	.	T		1329,3075	669.4+/-402.2	210,909,1083	41.0	45.0	44.0		597	3.7	1.0	6	dbSNP_119	44	799,7799	776.5+/-407.7	50,699,3550	yes	coding-synonymous-near-splice	SNRNP48	NM_152551.3		260,1608,4633	TT,TC,CC		9.2929,30.1771,16.3667		199/340	7602857	2128,10874	2202	4299	6501	SO:0001630	splice_region_variant	154007	exon6			ATTAGACAATAGT	AK056796	CCDS4502.1	6p24.3	2011-10-11	2008-10-29	2008-10-29	ENSG00000168566	ENSG00000168566			21368	protein-coding gene	gene with protein product	"""U11/U12 snRNP 48K"""		"""chromosome 6 open reading frame 151"""	C6orf151		15146077	Standard	XR_427825		Approved	FLJ32234, dJ512B11.2, dJ336K20B.1	uc003mxr.3	Q6IEG0	OTTHUMG00000014213	ENST00000342415.5:c.596-1C>T	6.37:g.7602857C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_152551	A8K8P4|Q14C91|Q5T339|Q5THM1|Q5THM2|Q96MK1	Silent	SNP	ENST00000342415.5	37	CCDS4502.1																																																																																			C|0.857;T|0.143	0.143	strong		0.289	SNRNP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039787.3	NM_152551	Silent
MUC21	394263	hgsc.bcm.edu	37	6	30954963	30954963	+	Silent	SNP	G	G	A	rs55956203	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954963G>A	ENST00000376296.3	+	2	1252	c.1011G>A	c.(1009-1011)acG>acA	p.T337T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	337	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T337T(1)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AGTCCAGCACGACCTCCAGTG	0.627																																					p.T337T		Atlas-SNP	.											MUC21,NS,carcinoma,0,1	MUC21	98	1	1	Substitution - coding silent(1)	prostate(1)	c.G1011A						scavenged	.						135.0	136.0	136.0					6																	30954963		2203	4296	6499	SO:0001819	synonymous_variant	394263	exon2			CAGCACGACCTCC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1011G>A	6.37:g.30954963G>A		Somatic	78	2	0.025641		WXS	Illumina HiSeq	Phase_I	132	37	0.280303	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			G|0.932;A|0.068	0.068	strong		0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
HLA-C	3107	hgsc.bcm.edu	37	6	31239050	31239050	+	Missense_Mutation	SNP	G	G	A	rs713032	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239050G>A	ENST00000376228.5	-	3	433	c.419C>T	c.(418-420)tCc>tTc	p.S140F	HLA-C_ENST00000383329.3_Missense_Mutation_p.S140F	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	140	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GTCGTAGGCGGACTGGTCATA	0.706													t|||	1632	0.325879	0.4115	0.3746	5008	,	,		12716	0.2242		0.3062	False		,,,				2504	0.3006				p.S140F		Atlas-SNP	.											.	HLA-C	92	.	0			c.C419T						PASS	.	T	PHE/SER	1653,2703		220,1213,745	34.0	26.0	29.0		419	-5.2	0.0	6	dbSNP_86	29	2775,5727		449,1877,1925	no	missense	HLA-C	NM_002117.5	155	669,3090,2670	AA,AG,GG		32.6394,37.9477,34.4377	benign	140/367	31239050	4428,8430	2178	4251	6429	SO:0001583	missense	3107	exon3			TAGGCGGACTGGT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.419C>T	6.37:g.31239050G>A	ENSP00000365402:p.Ser140Phe	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	188	111	0.590426	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	782	0.35805860805860806	218	0.44308943089430897	155	0.4281767955801105	157	0.2744755244755245	252	0.3324538258575198	.	1.018	-0.685805	0.03328	0.379477	0.326394	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00007	9.66;9.66	2.59	-5.18	0.02840	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.604250	0.05088	N	0.484814	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B;B	0.15473	0.009;0.003;0.003;0.013	B;B;B;B	0.23275	0.045;0.024;0.024;0.024	T	0.47058	-0.9146	8	0.09590	T	0.72	.	2.3892	0.04374	0.4981:0.0781:0.2076:0.2163	rs713032;rs1050374;rs2308577;rs3176000;rs3176035;rs3177879	140;140;140;140	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	F	140;140;140;177	ENSP00000365402:S140F;ENSP00000372819:S140F	ENSP00000365402:S140F	S	-	2	0	HLA-C	31347029	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-14.540000	0.00000	-6.427000	0.00004	-4.240000	0.00008	TCC	G|0.583;A|0.417	0.417	strong		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
MYPN	84665	hgsc.bcm.edu	37	10	69926334	69926334	+	Missense_Mutation	SNP	C	C	G	rs10823148	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:69926334C>G	ENST00000358913.5	+	10	2372	c.1884C>G	c.(1882-1884)ttC>ttG	p.F628L	MYPN_ENST00000540630.1_Missense_Mutation_p.F628L|MYPN_ENST00000354393.2_Missense_Mutation_p.F353L	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	628			F -> L (in dbSNP:rs10823148). {ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						CCGATTCTTTCCAGGAGAGGT	0.537													C|||	1585	0.316494	0.1104	0.4049	5008	,	,		16523	0.2163		0.5099	False		,,,				2504	0.4366				p.F628L		Atlas-SNP	.											.	MYPN	189	.	0			c.C1884G						PASS	.	C	LEU/PHE	768,3638	311.9+/-292.3	73,622,1508	71.0	66.0	68.0		1884	4.3	1.0	10	dbSNP_120	68	4382,4218	582.8+/-391.5	1167,2048,1085	yes	missense	MYPN	NM_032578.2	22	1240,2670,2593	GG,GC,CC		49.0465,17.4308,39.5971	benign	628/1321	69926334	5150,7856	2203	4300	6503	SO:0001583	missense	84665	exon10			TTCTTTCCAGGAG	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1884C>G	10.37:g.69926334C>G	ENSP00000351790:p.Phe628Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	736	0.336996336996337	64	0.13008130081300814	157	0.43370165745856354	128	0.22377622377622378	387	0.5105540897097626	C	0.738	-0.777515	0.02929	0.174308	0.509535	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.55588	0.51;0.57;0.55	5.29	4.3	0.51218	.	0.087877	0.49305	D	0.000149	T	0.00012	0.0000	N	0.22421	0.69	0.29149	P	0.878514	B;B;B	0.12013	0.005;0.002;0.001	B;B;B	0.13407	0.009;0.006;0.003	T	0.45071	-0.9286	8	.	.	.	.	7.6139	0.28145	0.129:0.6838:0.1132:0.0741	rs10823148;rs17457985;rs52812887;rs10823148	628;353;628	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	L	353;353;628;628	ENSP00000346369:F353L;ENSP00000351790:F628L;ENSP00000441668:F628L	.	F	+	3	2	MYPN	69596340	1.000000	0.71417	0.994000	0.49952	0.087000	0.18053	2.051000	0.41307	2.455000	0.83008	0.655000	0.94253	TTC	C|0.625;G|0.374	0.374	strong		0.537	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
GBP1	2633	hgsc.bcm.edu	37	1	89522646	89522646	+	Missense_Mutation	SNP	G	G	C	rs1048425	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89522646G>C	ENST00000370473.4	-	7	1265	c.1046C>G	c.(1045-1047)aCc>aGc	p.T349S	GBP1_ENST00000484970.1_5'Flank	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	349			T -> S (in dbSNP:rs1048425). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1715024, ECO:0000269|Ref.2}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		CTCCTGGAGGGTTTCTGTGGG	0.527													.|||	3597	0.718251	0.7958	0.6138	5008	,	,		18570	0.5595		0.7654	False		,,,				2504	0.8027				p.T349S		Atlas-SNP	.											GBP1,colon,carcinoma,0,2	GBP1	68	2	0			c.C1046G						PASS	.	C	SER/THR	3581,825	326.9+/-299.8	1457,667,79	96.0	93.0	94.0		1046	3.9	1.0	1	dbSNP_86	94	6746,1854	331.4+/-319.6	2626,1494,180	no	missense	GBP1	NM_002053.2	58	4083,2161,259	CC,CG,GG		21.5581,18.7245,20.5982	benign	349/593	89522646	10327,2679	2203	4300	6503	SO:0001583	missense	2633	exon7			TGGAGGGTTTCTG	BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"""guanylate binding protein 1, interferon-inducible, 67kDa"""			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.1046C>G	1.37:g.89522646G>C	ENSP00000359504:p.Thr349Ser	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	244	243	0.995902	NM_002053	D3DT26|Q5T8M1	Missense_Mutation	SNP	ENST00000370473.4	37	CCDS718.1	1523	0.6973443223443223	386	0.7845528455284553	247	0.6823204419889503	311	0.5437062937062938	579	0.7638522427440633	C	12.80	2.046072	0.36085	0.812755	0.784419	ENSG00000117228	ENST00000370473;ENST00000542693	T	0.03468	3.92	4.8	3.89	0.44902	Guanylate-binding protein, C-terminal (3);	0.115624	0.64402	N	0.000018	T	0.07954	0.0199	M	0.90145	3.09	0.53005	P	3.900000000001125E-5	B	0.29671	0.254	B	0.43990	0.438	T	0.00276	-1.1855	9	0.54805	T	0.06	.	12.9599	0.58451	0.0:0.1645:0.8355:0.0	rs1048425;rs17856068	349	P32455	GBP1_HUMAN	S	349;312	ENSP00000359504:T349S	ENSP00000359504:T349S	T	-	2	0	GBP1	89295234	0.527000	0.26306	0.995000	0.50966	0.510000	0.34073	2.002000	0.40835	1.026000	0.39733	-0.323000	0.08544	ACC	G|0.240;C|0.760	0.760	strong		0.527	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053	
LILRA6	79168	hgsc.bcm.edu	37	19	54744358	54744358	+	Nonsense_Mutation	SNP	A	A	C	rs1052992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54744358A>C	ENST00000396365.2	-	6	1089	c.1050T>G	c.(1048-1050)taT>taG	p.Y350*	LILRA6_ENST00000245621.5_Nonsense_Mutation_p.Y350*|LILRA6_ENST00000419410.2_Nonsense_Mutation_p.Y350*|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	350	Ig-like C2-type 2.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.Y350*(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AAGTGTCAAAATAACCCCGTG	0.557													.|||	381	0.0760783	0.0749	0.0303	5008	,	,		17493	0.2163		0.0239	False		,,,				2504	0.0194				p.Y350X		Atlas-SNP	.											LILRA6,NS,carcinoma,0,1	LILRA6	75	1	1	Substitution - Nonsense(1)	ovary(1)	c.T1050G						scavenged	.						72.0	100.0	90.0					19																	54744358		2084	4248	6332	SO:0001587	stop_gained	79168	exon6			GTCAAAATAACCC	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.1050T>G	19.37:g.54744358A>C	ENSP00000379651:p.Tyr350*	Somatic	296	8	0.027027		WXS	Illumina HiSeq	Phase_I	205	24	0.117073	NM_024318		Nonsense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	a	15.47	2.843898	0.51164	.	.	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	.	.	.	1.86	-2.86	0.05717	.	6.418410	0.00397	N	0.000047	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	0.8525	0.01175	0.3877:0.2736:0.192:0.1467	rs1052992;rs2361803;rs3193476	.	.	.	X	350	.	ENSP00000245621:Y350X	Y	-	3	2	LILRA6	59436170	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.095000	0.00152	-1.064000	0.03172	-1.043000	0.02367	TAT	A|1.000;|0.000	.	weak		0.557	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735280	55735280	+	Silent	SNP	T	T	A	rs61896164	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55735280T>A	ENST00000312345.2	-	1	710	c.660A>T	c.(658-660)tcA>tcT	p.S220S		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					CTCTGGCTGATGACAATTTCA	0.403													T|||	191	0.038139	0.0129	0.0389	5008	,	,		20186	0.001		0.0934	False		,,,				2504	0.0532				p.S220S		Atlas-SNP	.											.	OR10AG1	100	.	0			c.A660T						PASS	.	T		108,4294	83.4+/-121.9	3,102,2096	67.0	65.0	66.0		660	-2.3	0.3	11	dbSNP_129	66	692,7900	170.6+/-221.7	34,624,3638	no	coding-synonymous	OR10AG1	NM_001005491.1		37,726,5734	AA,AT,TT		8.054,2.4534,6.1567		220/302	55735280	800,12194	2201	4296	6497	SO:0001819	synonymous_variant	282770	exon1			GGCTGATGACAAT	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.660A>T	11.37:g.55735280T>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	196	96	0.489796	NM_001005491	B2RNH4|Q6IEU3	Silent	SNP	ENST00000312345.2	37	CCDS31514.1																																																																																			T|0.948;A|0.052	0.052	strong		0.403	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
POM121	9883	hgsc.bcm.edu	37	7	72413423	72413423	+	Missense_Mutation	SNP	C	C	T	rs71554686	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:72413423C>T	ENST00000434423.2	+	11	2891	c.2891C>T	c.(2890-2892)cCg>cTg	p.P964L	POM121_ENST00000446813.1_Missense_Mutation_p.P699L|POM121_ENST00000257622.4_Missense_Mutation_p.P699L|POM121_ENST00000395270.1_Missense_Mutation_p.P699L|POM121_ENST00000358357.3_Missense_Mutation_p.P699L			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	964	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.P699L(1)		NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CCATCATATCCGGGAGCCAAC	0.647																																					p.P699L		Atlas-SNP	.											POM121,rectum,carcinoma,0,1	POM121	131	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2096T						scavenged	.						9.0	12.0	11.0					7																	72413423		1897	3928	5825	SO:0001583	missense	9883	exon11			CATATCCGGGAGC	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.2891C>T	7.37:g.72413423C>T	ENSP00000405562:p.Pro964Leu	Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	290	78	0.268966	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		.	.	.	.	.	.	.	.	.	.	C	11.06	1.528404	0.27299	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.06371	3.31;3.34;3.31;3.34;3.52	2.33	2.33	0.28932	.	0.532332	0.14207	N	0.334357	T	0.16938	0.0407	L	0.55481	1.735	0.30006	P	0.815588	D;P	0.89917	1.0;0.839	D;B	0.91635	0.999;0.287	T	0.16778	-1.0391	9	0.28530	T	0.3	.	10.1668	0.42886	0.0:1.0:0.0:0.0	.	699;964	A8MXF9;Q96HA1	.;P121A_HUMAN	L	699;699;699;699;964	ENSP00000393020:P699L;ENSP00000257622:P699L;ENSP00000378687:P699L;ENSP00000351124:P699L;ENSP00000405562:P964L	ENSP00000257622:P699L	P	+	2	0	POM121	72051359	0.041000	0.20044	0.365000	0.25901	0.077000	0.17291	2.433000	0.44793	1.309000	0.44985	0.173000	0.16961	CCG	C|0.500;T|0.500	0.500	weak		0.647	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
SLC25A40	55972	hgsc.bcm.edu	37	7	87483585	87483585	+	Silent	SNP	T	T	A	rs150511221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:87483585T>A	ENST00000341119.5	-	5	544	c.198A>T	c.(196-198)ctA>ctT	p.L66L		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40	66					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	17	Esophageal squamous(14;0.00202)					CACAGACACATAGATGATCCA	0.343													T|||	36	0.0071885	0.0015	0.0375	5008	,	,		16226	0.0		0.005	False		,,,				2504	0.0031				p.L66L		Atlas-SNP	.											.	SLC25A40	32	.	0			c.A198T						PASS	.	T		7,4399	14.3+/-33.2	0,7,2196	161.0	150.0	154.0		198	-7.1	0.1	7	dbSNP_134	154	106,8494	56.8+/-118.0	0,106,4194	no	coding-synonymous	SLC25A40	NM_018843.3		0,113,6390	AA,AT,TT		1.2326,0.1589,0.8688		66/339	87483585	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	55972	exon5			GACACATAGATGA	AF125531	CCDS5610.1	7q21.12	2013-05-22			ENSG00000075303	ENSG00000075303		"""Solute carriers"""	29680	protein-coding gene	gene with protein product		610821				16949250	Standard	NM_018843		Approved	MCFP	uc003uje.3	Q8TBP6	OTTHUMG00000131033	ENST00000341119.5:c.198A>T	7.37:g.87483585T>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_018843	A8K483|D6W5P6|Q53GB1|Q9UHR1	Silent	SNP	ENST00000341119.5	37	CCDS5610.1																																																																																			T|0.994;A|0.006	0.006	strong		0.343	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	NM_018843	
PRDM2	7799	hgsc.bcm.edu	37	1	14105139	14105139	+	Missense_Mutation	SNP	T	T	A	rs2076324|rs369010172	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14105139T>A	ENST00000235372.7	+	8	1705	c.849T>A	c.(847-849)gaT>gaA	p.D283E	PRDM2_ENST00000343137.4_Missense_Mutation_p.D82E|PRDM2_ENST00000311066.5_Missense_Mutation_p.D283E|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.D82E	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	283	Asp/Glu-rich (acidic).		D -> E (in dbSNP:rs2076324).	EDEEEEEDDDDDELEDEG -> VGGGGGVVVVVSWKARGE (in Ref. 6; AAA87023). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		aagaagaagatgatgatgatg	0.483													A|||	1859	0.371206	0.208	0.5375	5008	,	,		20316	0.3988		0.327	False		,,,				2504	0.4908				p.D283E		Atlas-SNP	.											.	PRDM2	147	.	0			c.T849A						PASS	.	A	GLU/ASP,,GLU/ASP,GLU/ASP	1104,3302	717.2+/-408.7	142,820,1241	63.0	64.0	63.0		246,,849,849	-3.6	0.5	1	dbSNP_96	63	3066,5534	652.7+/-401.0	525,2016,1759	yes	missense,intron,missense,missense	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	45,,45,45	667,2836,3000	AA,AT,TT		35.6512,25.0567,32.0621	benign,,benign,benign	82/1482,,283/1719,283/1683	14105139	4170,8836	2203	4300	6503	SO:0001583	missense	7799	exon8			AGAAGATGATGAT	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.849T>A	1.37:g.14105139T>A	ENSP00000235372:p.Asp283Glu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	771	0.35302197802197804	99	0.20121951219512196	186	0.5138121546961326	243	0.42482517482517484	243	0.32058047493403696	A	0.003	-2.513786	0.00151	0.250567	0.356512	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.01446	4.98;4.88;4.91;4.91	2.02	-3.62	0.04543	.	0.430301	0.17431	N	0.174473	T	0.00012	0.0000	N	0.00742	-1.23	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.12013	0.003;0.0;0.003;0.005	B;B;B;B	0.06405	0.001;0.0;0.001;0.002	T	0.11743	-1.0575	9	0.02654	T	1	.	3.3022	0.06987	0.2462:0.0:0.158:0.5958	rs62648362	283;141;283;283	A8MW16;Q5THJ0;Q13029;Q13029-2	.;.;PRDM2_HUMAN;.	E	283;283;283;82;82	ENSP00000235372:D283E;ENSP00000312352:D283E;ENSP00000411103:D82E;ENSP00000341621:D82E	ENSP00000235372:D283E	D	+	3	2	PRDM2	13977726	0.931000	0.31567	0.455000	0.27031	0.122000	0.20287	-0.258000	0.08733	-1.465000	0.01899	-0.376000	0.06991	GAT	T|0.662;A|0.338	0.338	strong		0.483	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
MAGEC1	9947	hgsc.bcm.edu	37	X	140995712	140995712	+	Missense_Mutation	SNP	G	G	T	rs41299076	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:140995712G>T	ENST00000285879.4	+	4	2808	c.2522G>T	c.(2521-2523)aGt>aTt	p.S841I	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	841										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					ACTTCATCGAGTCTTTCCAAG	0.547										HNSCC(15;0.026)			G|||	16	0.00423841	0.0	0.0043	3775	,	,		12688	0.0		0.0129	False		,,,				2504	0.0				p.S841I		Atlas-SNP	.											.	MAGEC1	317	.	0			c.G2522T						PASS	.	G	ILE/SER	10,3825		0,10,0,1622,571	126.0	131.0	129.0		2522	0.1	0.0	X	dbSNP_127	129	107,6621		1,83,22,2344,1850	yes	missense	MAGEC1	NM_005462.4	142	1,93,22,3966,2421	TT,TG,T,GG,G		1.5904,0.2608,1.1076	probably-damaging	841/1143	140995712	117,10446	2203	4300	6503	SO:0001583	missense	9947	exon4			CATCGAGTCTTTC	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.2522G>T	X.37:g.140995712G>T	ENSP00000285879:p.Ser841Ile	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	95	88	0.926316	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	8	0.004822182037371911	0	0.0	1	0.002777777777777778	0	0.0	3	0.003989361702127659	-	10.73	1.432840	0.25813	0.002608	0.015904	ENSG00000155495	ENST00000285879	T	0.02258	4.37	0.109	0.109	0.14578	.	.	.	.	.	T	0.01156	0.0038	N	0.14661	0.345	0.32301	N	0.565025	D	0.54964	0.969	P	0.52598	0.703	T	0.51926	-0.8643	9	0.66056	D	0.02	.	5.9735	0.19365	6.0E-4:0.0:0.9994:0.0	rs41299076	841	O60732	MAGC1_HUMAN	I	841	ENSP00000285879:S841I	ENSP00000285879:S841I	S	+	2	0	MAGEC1	140823378	0.000000	0.05858	0.032000	0.17829	0.073000	0.16967	-1.338000	0.02655	0.168000	0.19655	0.171000	0.16805	AGT	G|0.992;T|0.008	0.008	strong		0.547	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
VCAN	1462	hgsc.bcm.edu	37	5	82837631	82837631	+	Missense_Mutation	SNP	G	G	T	rs160277	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:82837631G>T	ENST00000265077.3	+	8	9374	c.8809G>T	c.(8809-8811)Gat>Tat	p.D2937Y	VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.D1950Y|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2937	GAG-beta.		D -> Y (in dbSNP:rs160277).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AAACAAAACCGATGGTCAAGT	0.398													G|||	1806	0.360623	0.357	0.4597	5008	,	,		18764	0.3234		0.4254	False		,,,				2504	0.2669				p.D2937Y		Atlas-SNP	.											.	VCAN	498	.	0			c.G8809T						PASS	.	G	,TYR/ASP,,TYR/ASP	1625,2781	482.4+/-359.4	296,1033,874	80.0	85.0	83.0		,5848,,8809	0.8	0.0	5	dbSNP_79	83	3433,5167	503.3+/-375.9	700,2033,1567	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,160,,160	996,3066,2441	TT,TG,GG		39.9186,36.8815,38.8897	,possibly-damaging,,possibly-damaging	,1950/2410,,2937/3397	82837631	5058,7948	2203	4300	6503	SO:0001583	missense	1462	exon8			AAAACCGATGGTC	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.8809G>T	5.37:g.82837631G>T	ENSP00000265077:p.Asp2937Tyr	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	837	0.38324175824175827	145	0.29471544715447157	168	0.46408839779005523	203	0.3548951048951049	321	0.4234828496042216	G	12.91	2.079124	0.36662	0.368815	0.399186	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.18338	2.22;2.22	5.99	0.819	0.18785	.	1.042050	0.07483	N	0.904317	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D;D	0.60160	0.987;0.979	P;P	0.52672	0.706;0.607	T	0.46748	-0.9169	9	0.59425	D	0.04	.	2.3966	0.04391	0.5352:0.1193:0.2293:0.1161	rs160277;rs310482;rs496670;rs3734093;rs52794243;rs60765899;rs160277	1950;2937	P13611-2;P13611	.;CSPG2_HUMAN	Y	2937;1950	ENSP00000265077:D2937Y;ENSP00000340062:D1950Y	ENSP00000265077:D2937Y	D	+	1	0	VCAN	82873387	0.001000	0.12720	0.001000	0.08648	0.083000	0.17756	0.638000	0.24674	0.540000	0.28808	-0.312000	0.09012	GAT	G|0.618;T|0.382	0.382	strong		0.398	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
KIAA0141	9812	hgsc.bcm.edu	37	5	141307833	141307833	+	Missense_Mutation	SNP	T	T	C	rs10036567	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:141307833T>C	ENST00000432126.2	+	4	516	c.382T>C	c.(382-384)Ttc>Ctc	p.F128L	KIAA0141_ENST00000194118.4_Missense_Mutation_p.F128L	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	128			F -> L (in dbSNP:rs10036567).		extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACCGTTTCTTCTCATCTCC	0.627													C|||	789	0.157548	0.3835	0.0749	5008	,	,		18906	0.0099		0.0865	False		,,,				2504	0.136				p.F128L		Atlas-SNP	.											.	KIAA0141	44	.	0			c.T382C						PASS	.	C	LEU/PHE,LEU/PHE	1445,2961	682.2+/-404.1	235,975,993	104.0	98.0	100.0		382,382	4.8	0.8	5	dbSNP_119	100	722,7878	786.4+/-407.6	26,670,3604	yes	missense,missense	KIAA0141	NM_001142603.1,NM_014773.3	22,22	261,1645,4597	CC,CT,TT		8.3953,32.7962,16.6615	benign,benign	128/516,128/516	141307833	2167,10839	2203	4300	6503	SO:0001583	missense	9812	exon4			CGTTTCTTCTCAT	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.382T>C	5.37:g.141307833T>C	ENSP00000396225:p.Phe128Leu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	186	89	0.478495	NM_001142603	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	290	0.13278388278388278	191	0.3882113821138211	32	0.08839779005524862	7	0.012237762237762238	60	0.079155672823219	C	2.862	-0.235939	0.05944	0.327962	0.083953	ENSG00000081791	ENST00000432126;ENST00000194118;ENST00000508751	T;T;T	0.14766	2.96;2.96;2.48	5.62	4.75	0.60458	.	0.352416	0.26297	N	0.025200	T	0.00012	0.0000	N	0.00170	-1.935	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45293	-0.9271	9	0.02654	T	1	-7.1069	9.4807	0.38900	0.0:0.8348:0.0:0.1652	rs10036567;rs52831480;rs56547810;rs59311928;rs10036567	128	Q14154	DELE_HUMAN	L	128	ENSP00000396225:F128L;ENSP00000194118:F128L;ENSP00000422686:F128L	ENSP00000194118:F128L	F	+	1	0	KIAA0141	141288017	0.924000	0.31332	0.756000	0.31282	0.471000	0.32888	1.118000	0.31246	0.856000	0.35383	-0.227000	0.12334	TTC	T|0.836;C|0.164	0.164	strong		0.627	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
SMC5	23137	hgsc.bcm.edu	37	9	72912914	72912914	+	Silent	SNP	G	G	A	rs61752954	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:72912914G>A	ENST00000361138.5	+	9	1144	c.1086G>A	c.(1084-1086)aaG>aaA	p.K362K		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	362					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						TAATAGTAAAGCAAAATGAAG	0.368													G|||	92	0.0183706	0.0121	0.0403	5008	,	,		17855	0.0		0.0467	False		,,,				2504	0.001				p.K362K		Atlas-SNP	.											.	SMC5	96	.	0			c.G1086A						PASS	.	G		58,4348	56.8+/-93.2	0,58,2145	97.0	100.0	99.0		1086	1.0	1.0	9	dbSNP_129	99	492,8106	140.1+/-196.7	12,468,3819	no	coding-synonymous	SMC5	NM_015110.3		12,526,5964	AA,AG,GG		5.7223,1.3164,4.2295		362/1102	72912914	550,12454	2203	4299	6502	SO:0001819	synonymous_variant	23137	exon9			AGTAAAGCAAAAT	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.1086G>A	9.37:g.72912914G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Silent	SNP	ENST00000361138.5	37	CCDS6632.1																																																																																			G|0.964;A|0.036	0.036	strong		0.368	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	
FAM90A1	55138	hgsc.bcm.edu	37	12	8374812	8374812	+	Missense_Mutation	SNP	G	G	A	rs17855656	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:8374812G>A	ENST00000538603.1	-	7	1559	c.1001C>T	c.(1000-1002)cCg>cTg	p.P334L	FAM90A1_ENST00000307435.6_Missense_Mutation_p.P334L	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	334			P -> L (in dbSNP:rs17855656). {ECO:0000269|PubMed:15489334}.				nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TGCGGCTGGCGGAGGTTGGAG	0.652													.|||	1132	0.226038	0.0983	0.1801	5008	,	,		14308	0.4087		0.1829	False		,,,				2504	0.2873				p.P334L		Atlas-SNP	.											FAM90A1,caecum,carcinoma,0,1	FAM90A1	68	1	0			c.C1001T						PASS	.	G	LEU/PRO	380,3994		13,354,1820	17.0	17.0	17.0		1001	-1.4	0.0	12	dbSNP_123	17	1279,7285		88,1103,3091	no	missense	FAM90A1	NM_018088.3	98	101,1457,4911	AA,AG,GG		14.9346,8.6877,12.8227	benign	334/465	8374812	1659,11279	2187	4282	6469	SO:0001583	missense	55138	exon7			GCTGGCGGAGGTT	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.1001C>T	12.37:g.8374812G>A	ENSP00000445418:p.Pro334Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	102	63	0.617647	NM_018088	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	457	0.20924908424908426	44	0.08943089430894309	68	0.1878453038674033	217	0.3793706293706294	128	0.16886543535620052	.	0.006	-2.030824	0.00410	0.086877	0.149346	ENSG00000171847	ENST00000307435;ENST00000538603	T;T	0.15372	2.43;2.43	1.02	-1.44	0.08856	.	.	.	.	.	T	0.00012	0.0000	L	0.31476	0.935	0.80722	P	0.0	B	0.17667	0.023	B	0.15870	0.014	T	0.47699	-0.9097	8	0.34782	T	0.22	1.633	4.0479	0.09781	0.4969:0.0:0.5031:0.0	rs17855656	334	Q86YD7	F90A1_HUMAN	L	334	ENSP00000307798:P334L;ENSP00000445418:P334L	ENSP00000307798:P334L	P	-	2	0	FAM90A1	8266079	0.004000	0.15560	0.006000	0.13384	0.073000	0.16967	-0.651000	0.05372	-0.509000	0.06532	0.194000	0.17425	CCG	G|0.833;A|0.167	0.167	strong		0.652	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
SAMD9	54809	hgsc.bcm.edu	37	7	92734983	92734983	+	Missense_Mutation	SNP	A	A	G	rs6969691	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:92734983A>G	ENST00000379958.2	-	3	697	c.428T>C	c.(427-429)aTa>aCa	p.I143T		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	143			I -> T (in dbSNP:rs6969691).			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TTTATCTTCTATGAGCTCAAC	0.358													A|||	764	0.152556	0.2905	0.1268	5008	,	,		20645	0.1359		0.1292	False		,,,				2504	0.0256				p.I143T		Atlas-SNP	.											.	SAMD9	239	.	0			c.T428C						PASS	.	A	THR/ILE,THR/ILE	1183,3223	414.6+/-336.9	164,855,1184	123.0	134.0	130.0		428,428	-4.0	0.0	7	dbSNP_116	130	1116,7484	230.1+/-264.6	84,948,3268	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	89,89	248,1803,4452	GG,GA,AA		12.9767,26.8498,17.6765	benign,benign	143/1590,143/1590	92734983	2299,10707	2203	4300	6503	SO:0001583	missense	54809	exon2			TCTTCTATGAGCT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.428T>C	7.37:g.92734983A>G	ENSP00000369292:p.Ile143Thr	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	205	89	0.434146	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	382	0.1749084249084249	146	0.2967479674796748	51	0.1408839779005525	94	0.16433566433566432	91	0.12005277044854881	A	4.275	0.050167	0.08243	0.268498	0.129767	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.13089	2.62;2.62	4.32	-4.02	0.04034	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47560	-0.9108	8	0.11182	T	0.66	.	5.2975	0.15760	0.367:0.0:0.397:0.2361	rs6969691;rs10363606;rs60909665;rs6969691	143	Q5K651	SAMD9_HUMAN	T	143	ENSP00000369292:I143T;ENSP00000414529:I143T	ENSP00000369292:I143T	I	-	2	0	SAMD9	92572919	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.406000	0.07187	-0.592000	0.05851	-0.322000	0.08575	ATA	A|0.818;G|0.182	0.182	strong		0.358	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
FANCI	55215	hgsc.bcm.edu	37	15	89838318	89838318	+	Missense_Mutation	SNP	A	A	T	rs35875311	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:89838318A>T	ENST00000310775.7	+	24	2715	c.2629A>T	c.(2629-2631)Ata>Tta	p.I877L	FANCI_ENST00000300027.8_Intron	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	877				I -> L (in Ref. 6; BAB47423). {ECO:0000305}.	cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CCTCTGTGACATAACTCGGTA	0.478								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				A|||	298	0.0595048	0.0038	0.072	5008	,	,		19029	0.0595		0.0924	False		,,,				2504	0.092				p.I877L		Atlas-SNP	.											.	FANCI	129	.	0			c.A2629T						PASS	.	A	LEU/ILE,	29,1349		1,27,661	117.0	105.0	108.0		2629,	6.0	1.0	15	dbSNP_126	108	349,2831		17,315,1258	yes	missense,intron	FANCI	NM_001113378.1,NM_018193.2	5,	18,342,1919	TT,TA,AA		10.9748,2.1045,8.2931	benign,	877/1329,	89838318	378,4180	689	1590	2279	SO:0001583	missense	55215	exon24	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGTGACATAACTC	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.2629A>T	15.37:g.89838318A>T	ENSP00000310842:p.Ile877Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	37	CCDS45346.1	140	0.0641025641025641	2	0.0040650406504065045	25	0.06906077348066299	37	0.06468531468531469	76	0.10026385224274406	A	19.13	3.766935	0.69878	0.021045	0.109748	ENSG00000140525	ENST00000310775	T	0.73897	-0.79	5.98	5.98	0.97165	.	0.101413	0.36409	U	0.002613	T	0.03348	0.0097	L	0.48362	1.52	0.80722	D	1	B	0.22604	0.072	B	0.25140	0.058	T	0.36578	-0.9742	10	0.13108	T	0.6	-2.4301	16.4696	0.84102	1.0:0.0:0.0:0.0	rs35875311	877	Q9NVI1	FANCI_HUMAN	L	877	ENSP00000310842:I877L	ENSP00000310842:I877L	I	+	1	0	FANCI	87639322	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.129000	0.57957	2.289000	0.77006	0.482000	0.46254	ATA	A|0.931;T|0.069	0.069	strong		0.478	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
TMEM17	200728	hgsc.bcm.edu	37	2	62729653	62729653	+	Silent	SNP	A	A	G	rs6713096	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:62729653A>G	ENST00000335390.5	-	3	448	c.237T>C	c.(235-237)atT>atC	p.I79I		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	79					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			CAGTGATCACAATGAATTTGT	0.333													A|||	349	0.0696885	0.1225	0.0418	5008	,	,		19818	0.0079		0.0676	False		,,,				2504	0.0838				p.I79I		Atlas-SNP	.											.	TMEM17	19	.	0			c.T237C						PASS	.	A		524,3882	238.0+/-249.6	36,452,1715	93.0	92.0	92.0		237	3.6	1.0	2	dbSNP_116	92	713,7887	175.0+/-225.2	34,645,3621	no	coding-synonymous	TMEM17	NM_198276.2		70,1097,5336	GG,GA,AA		8.2907,11.8929,9.511		79/199	62729653	1237,11769	2203	4300	6503	SO:0001819	synonymous_variant	200728	exon3			GATCACAATGAAT		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.237T>C	2.37:g.62729653A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	67	0.626168	NM_198276	Q53QP7|Q53R98	Silent	SNP	ENST00000335390.5	37	CCDS1871.1																																																																																			A|0.922;G|0.078	0.078	strong		0.333	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
FAT2	2196	hgsc.bcm.edu	37	5	150947719	150947719	+	Silent	SNP	C	C	T	rs3734060	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150947719C>T	ENST00000261800.5	-	1	786	c.774G>A	c.(772-774)tcG>tcA	p.S258S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	258					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCACCACCACCGAAGCAATGG	0.557																																					p.S258S		Atlas-SNP	.											FAT2,colon,carcinoma,0,2	FAT2	465	2	0			c.G774A						PASS	.	C		1956,2450	549.1+/-377.7	420,1116,667	43.0	42.0	43.0		774	-10.1	0.0	5	dbSNP_107	43	4496,4104	585.4+/-391.9	1181,2134,985	no	coding-synonymous	FAT2	NM_001447.2		1601,3250,1652	TT,TC,CC		47.7209,44.394,49.6079		258/4350	150947719	6452,6554	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			CACCACCGAAGCA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.774G>A	5.37:g.150947719C>T		Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			C|0.527;T|0.473	0.473	strong		0.557	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
SOWAHB	345079	hgsc.bcm.edu	37	4	77818548	77818548	+	Missense_Mutation	SNP	T	T	C	rs2703129	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:77818548T>C	ENST00000334306.2	-	1	454	c.455A>G	c.(454-456)gAc>gGc	p.D152G		NM_001029870.1	NP_001025041.1	A6NEL2	SWAHB_HUMAN	sosondowah ankyrin repeat domain family member B	152	Ala-rich.		D -> G (in dbSNP:rs2703129).														CCTACGGGAGTCGCTGCCCGG	0.756													C|||	1672	0.333866	0.4924	0.2392	5008	,	,		10127	0.2272		0.332	False		,,,				2504	0.2986				p.D152G		Atlas-SNP	.											.	.	.	.	0			c.A455G						PASS	.	C	GLY/ASP	673,1997		83,507,745	2.0	2.0	2.0		455	4.1	0.0	4	dbSNP_100	2	1078,4958		96,886,2036	yes	missense	ANKRD56	NM_001029870.1	94	179,1393,2781	CC,CT,TT		17.8595,25.206,20.1126	benign	152/794	77818548	1751,6955	1335	3018	4353	SO:0001583	missense	345079	exon1			CGGGAGTCGCTGC		CCDS34017.1	4q21.1	2013-01-10	2012-01-12	2012-01-12	ENSG00000186212	ENSG00000186212		"""Ankyrin repeat domain containing"""	32958	protein-coding gene	gene with protein product			"""ankyrin repeat domain 56"""	ANKRD56		22234889	Standard	NM_001029870		Approved		uc003hki.3	A6NEL2	OTTHUMG00000160876	ENST00000334306.2:c.455A>G	4.37:g.77818548T>C	ENSP00000334879:p.Asp152Gly	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	11	7	0.636364	NM_001029870	B2RP29	Missense_Mutation	SNP	ENST00000334306.2	37	CCDS34017.1	679	0.3108974358974359	233	0.4735772357723577	96	0.26519337016574585	102	0.17832167832167833	248	0.32717678100263853	C	3.384	-0.125815	0.06795	0.25206	0.178595	ENSG00000186212	ENST00000334306	T	0.04119	3.7	4.06	4.06	0.47325	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32929	-0.9888	8	0.07990	T	0.79	-0.9909	10.9322	0.47224	0.0:0.9059:0.0:0.0941	rs2703129	152	A6NEL2	ANR56_HUMAN	G	152	ENSP00000334879:D152G	ENSP00000334879:D152G	D	-	2	0	ANKRD56	78037572	0.204000	0.23447	0.003000	0.11579	0.006000	0.05464	0.000000	0.12993	0.941000	0.37499	-0.186000	0.12905	GAC	T|0.689;C|0.311	0.311	strong		0.756	SOWAHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362762.1	NM_001029870	
C15orf27	123591	hgsc.bcm.edu	37	15	76496340	76496340	+	Missense_Mutation	SNP	C	C	T	rs937733	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:76496340C>T	ENST00000388942.3	+	11	1556	c.1280C>T	c.(1279-1281)cCg>cTg	p.P427L		NM_152335.2	NP_689548.2	Q2M3C6	CO027_HUMAN	chromosome 15 open reading frame 27	427			P -> L (in dbSNP:rs937733). {ECO:0000269|PubMed:14702039}.		calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|membrane depolarization during action potential (GO:0086010)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|large_intestine(1)|lung(10)|pancreas(1)	13						CCTTCTCCCCCGCCGCTGCCA	0.697													T|||	1871	0.373602	0.2269	0.3256	5008	,	,		15096	0.5794		0.2674	False		,,,				2504	0.5031				p.P427L		Atlas-SNP	.											.	C15orf27	32	.	0			c.C1280T						PASS	.	T	LEU/PRO	1018,3366		107,804,1281	15.0	17.0	16.0		1280	-3.3	0.2	15	dbSNP_86	16	2162,6418		287,1588,2415	no	missense	C15orf27	NM_152335.2	98	394,2392,3696	TT,TC,CC		25.1981,23.2208,24.5295	benign	427/532	76496340	3180,9784	2192	4290	6482	SO:0001583	missense	123591	exon11			CTCCCCCGCCGCT	AK095509	CCDS10289.2	15q23-q24.1	2012-09-27			ENSG00000169758	ENSG00000169758			26763	protein-coding gene	gene with protein product						14702039, 22020278	Standard	NM_152335		Approved	FLJ38190	uc002bbq.3	Q2M3C6	OTTHUMG00000142918	ENST00000388942.3:c.1280C>T	15.37:g.76496340C>T	ENSP00000373594:p.Pro427Leu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	42	24	0.571429	NM_152335	Q8N993|Q96LL5	Missense_Mutation	SNP	ENST00000388942.3	37	CCDS10289.2	759	0.3475274725274725	118	0.23983739837398374	124	0.3425414364640884	316	0.5524475524475524	201	0.26517150395778366	T	2.116	-0.402548	0.04865	0.232208	0.251981	ENSG00000169758	ENST00000388942	T	0.30714	1.52	4.31	-3.27	0.05048	.	0.669305	0.15393	N	0.264739	T	0.00012	0.0000	N	0.12182	0.205	0.51233	P	8.699999999994823E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42965	-0.9420	9	0.06494	T	0.89	-13.482	0.4214	0.00456	0.2841:0.2834:0.1451:0.2874	rs937733;rs57604304	391;427	Q2M3C6-2;Q2M3C6	.;CO027_HUMAN	L	427	ENSP00000373594:P427L	ENSP00000373594:P427L	P	+	2	0	C15orf27	74283395	0.122000	0.22280	0.194000	0.23346	0.242000	0.25591	0.130000	0.15850	-0.611000	0.05709	-0.775000	0.03384	CCG	C|0.712;T|0.288	0.288	strong		0.697	C15orf27-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286637.2	NM_152335	
LILRB3	11025	hgsc.bcm.edu	37	19	54721012	54721012	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54721012C>T	ENST00000391750.1	-	14	1982	c.1846G>A	c.(1846-1848)Ggg>Agg	p.G616R	LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.G617R|LILRB3_ENST00000245620.9_Missense_Mutation_p.G617R|LILRB3_ENST00000407860.2_Missense_Mutation_p.G633R|LILRA6_ENST00000440558.2_Missense_Mutation_p.G616R|LILRA6_ENST00000270464.5_Missense_Mutation_p.G617R|LILRB3_ENST00000346401.6_Missense_Mutation_p.G628R|LILRB3_ENST00000424807.1_Missense_Mutation_p.G616R|LILRA6_ENST00000391735.3_3'UTR			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	616					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGAGGTTCCCCTTCCTGGGAT	0.622																																					p.G617R		Atlas-SNP	.											LILRB3,colon,carcinoma,+1,2	LILRB3	67	2	0			c.G1849A						scavenged	.						114.0	111.0	112.0					19																	54721012		2202	4300	6502	SO:0001583	missense	11025	exon13			GTTCCCCTTCCTG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1846G>A	19.37:g.54721012C>T	ENSP00000375630:p.Gly616Arg	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	247	4	0.0161943	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	7.211	0.595402	0.13875	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00514	6.89;6.89;6.89;6.91;6.91;6.88;6.89;6.92	2.81	-0.661	0.11417	.	.	.	.	.	T	0.00328	0.0010	N	0.20401	0.57	0.09310	N	1	B;B;B;B;B;B;B	0.33583	0.034;0.033;0.002;0.041;0.418;0.001;0.004	B;B;B;B;B;B;B	0.37731	0.022;0.034;0.004;0.014;0.257;0.004;0.017	T	0.39981	-0.9587	9	0.42905	T	0.14	.	1.6031	0.02679	0.2167:0.4446:0.2111:0.1276	.	633;616;617;628;633;616;617	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	R	616;616;628;617;633;616;617;617	ENSP00000375630:G616R;ENSP00000412771:G616R;ENSP00000345184:G628R;ENSP00000245620:G617R;ENSP00000384274:G633R;ENSP00000390120:G616R;ENSP00000270464:G617R;ENSP00000411227:G617R	ENSP00000270464:G617R	G	-	1	0	LILRB3;LILRA6	59412824	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.104000	0.15313	-0.017000	0.14103	-0.389000	0.06534	GGG	.	.	none		0.622	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
HLA-C	3107	hgsc.bcm.edu	37	6	31238053	31238053	+	Missense_Mutation	SNP	G	G	C	rs707908	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238053G>C	ENST00000376228.5	-	4	843	c.829C>G	c.(829-831)Caa>Gaa	p.Q277E	HLA-C_ENST00000383329.3_Missense_Mutation_p.Q277E	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	277	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CTCTGCTCTTGTCCAGAAGGC	0.602																																					p.Q277E		Atlas-SNP	.											.	HLA-C	92	.	0			c.C829G						PASS	.						39.0	36.0	37.0					6																	31238053		2202	4296	6498	SO:0001583	missense	3107	exon4			GCTCTTGTCCAGA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.829C>G	6.37:g.31238053G>C	ENSP00000365402:p.Gln277Glu	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1431|1431	0.6552197802197802|0.6552197802197802	280|280	0.5691056910569106|0.5691056910569106	261|261	0.7209944751381215|0.7209944751381215	424|424	0.7412587412587412|0.7412587412587412	466|466	0.6147757255936676|0.6147757255936676	.|.	0.060|0.060	-1.226779|-1.226779	0.01518|0.01518	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.02606	.|4.23;4.23	2.67|2.67	-1.85|-1.85	0.07784|0.07784	.|Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	.|0.354393	.|0.19535	.|N	.|0.111955	T|T	0.00356|0.00356	0.0011|0.0011	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.08055	.|0.001;0.0;0.003;0.0	T|T	0.38156|0.38156	-0.9674|-0.9674	3|8	.|0.02654	.|T	.|1	.|.	7.6102|7.6102	0.28126|0.28126	0.0:0.342:0.54:0.118|0.0:0.342:0.54:0.118	rs707908;rs1050261;rs2308620;rs3175287;rs3177861;rs3190554;rs9264633;rs17839908;rs52795260|rs707908;rs1050261;rs2308620;rs3175287;rs3177861;rs3190554;rs9264633;rs17839908;rs52795260	.|277;277;277;277	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	E|E	240|277;277;277;314	.|ENSP00000365402:Q277E;ENSP00000372819:Q277E	.|ENSP00000365402:Q277E	D|Q	-|-	3|1	2|0	HLA-C|HLA-C	31346032|31346032	0.000000|0.000000	0.05858|0.05858	0.674000|0.674000	0.29902|0.29902	0.069000|0.069000	0.16628|0.16628	-0.829000|-0.829000	0.04415|0.04415	-0.860000|-0.860000	0.04099|0.04099	-2.716000|-2.716000	0.00133|0.00133	GAC|CAA	G|0.328;C|0.672	0.672	strong		0.602	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
HK2	3099	hgsc.bcm.edu	37	2	75101454	75101454	+	Silent	SNP	T	T	C	rs2229622	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:75101454T>C	ENST00000290573.2	+	7	1353	c.753T>C	c.(751-753)gaT>gaC	p.D251D	HK2_ENST00000409174.1_Silent_p.D223D	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	251	Hexokinase type-2 1.|Regulatory.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						TGGAAGGCGATGAGGGGCGGA	0.587													C|||	1581	0.315695	0.6112	0.1888	5008	,	,		17571	0.2817		0.1869	False		,,,				2504	0.1738				p.D251D		Atlas-SNP	.											.	HK2	85	.	0			c.T753C						PASS	.	C		2329,2077	570.5+/-382.9	627,1075,501	61.0	60.0	60.0		753	-2.9	0.1	2	dbSNP_98	60	1693,6907	738.5+/-407.1	155,1383,2762	no	coding-synonymous	HK2	NM_000189.4		782,2458,3263	CC,CT,TT		19.686,47.1403,30.9242		251/918	75101454	4022,8984	2203	4300	6503	SO:0001819	synonymous_variant	3099	exon7			AGGCGATGAGGGG		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.753T>C	2.37:g.75101454T>C		Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	459	279	0.607843	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	37	CCDS1956.1																																																																																			T|0.680;C|0.320	0.320	strong		0.587	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
SLC35B2	347734	hgsc.bcm.edu	37	6	44223010	44223010	+	Silent	SNP	G	G	T	rs1875324	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:44223010G>T	ENST00000393812.3	-	4	875	c.732C>A	c.(730-732)acC>acA	p.T244T	SLC35B2_ENST00000495706.1_5'UTR|SLC35B2_ENST00000538577.1_Silent_p.T151T|SLC35B2_ENST00000537814.1_Silent_p.T111T|MIR4647_ENST00000583964.1_RNA|SLC35B2_ENST00000393810.1_3'UTR	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	244					3'-phospho-5'-adenylyl sulfate transmembrane transport (GO:1902559)|3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|3'-phosphoadenosine 5'-phosphosulfate transport (GO:0046963)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity (GO:0046964)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	15	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGGAGATGAGGGTGGCTGTCA	0.592													g|||	1012	0.202077	0.0076	0.1945	5008	,	,		19124	0.3899		0.1958	False		,,,				2504	0.2832				p.T244T		Atlas-SNP	.											.	SLC35B2	40	.	0			c.C732A						PASS	.	G		170,4236	111.6+/-149.8	1,168,2034	74.0	72.0	73.0		732	2.5	1.0	6	dbSNP_92	73	1696,6904	309.4+/-309.4	149,1398,2753	no	coding-synonymous	SLC35B2	NM_178148.2		150,1566,4787	TT,TG,GG		19.7209,3.8584,14.3472		244/433	44223010	1866,11140	2203	4300	6503	SO:0001819	synonymous_variant	347734	exon4			GATGAGGGTGGCT	AK075456	CCDS34462.1, CCDS69127.1, CCDS75462.1, CCDS75463.1	6p12.1-p11.21	2013-07-17	2013-07-17		ENSG00000157593	ENSG00000157593		"""Solute carriers"""	16872	protein-coding gene	gene with protein product		610788	"""solute carrier family 35, member B2"""				Standard	NM_001286517		Approved	UGTrel4	uc003oxd.3	Q8TB61	OTTHUMG00000014760	ENST00000393812.3:c.732C>A	6.37:g.44223010G>T		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	252	125	0.496032	NM_178148	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Silent	SNP	ENST00000393812.3	37	CCDS34462.1																																																																																			G|0.829;T|0.171	0.171	strong		0.592	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2		
ITPKB	3707	hgsc.bcm.edu	37	1	226924642	226924642	+	Missense_Mutation	SNP	C	C	T	rs3754415	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:226924642C>T	ENST00000272117.3	-	1	517	c.518G>A	c.(517-519)cGc>cAc	p.R173H	ITPKB_ENST00000429204.1_Missense_Mutation_p.R173H|ITPKB_ENST00000366784.1_Missense_Mutation_p.R173H			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	173				R -> H (in Ref. 2; CAC40650 and 4; AAH15009). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				GGAGGGCGAGCGAGCCCTGCC	0.672													C|||	1137	0.227037	0.1694	0.2032	5008	,	,		15203	0.3393		0.2127	False		,,,				2504	0.2209				p.R173H	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	0			c.G518A						PASS	.	C	HIS/ARG	773,3615		65,643,1486	48.0	54.0	52.0		518	4.6	1.0	1	dbSNP_107	52	1557,7003		156,1245,2879	yes	missense	ITPKB	NM_002221.3	29	221,1888,4365	TT,TC,CC		18.1893,17.6162,17.9951	probably-damaging	173/947	226924642	2330,10618	2194	4280	6474	SO:0001583	missense	3707	exon2			GGCGAGCGAGCCC	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.518G>A	1.37:g.226924642C>T	ENSP00000272117:p.Arg173His	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	521	0.23855311355311357	88	0.17886178861788618	80	0.22099447513812154	186	0.32517482517482516	167	0.22031662269129287	C	20.6	4.025053	0.75390	0.176162	0.181893	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.37752	1.24;1.24;1.18	4.6	4.6	0.57074	.	0.000000	0.53938	D	0.000055	T	0.00012	0.0000	L	0.27053	0.805	0.32169	P	0.581978	P	0.51537	0.946	B	0.36418	0.224	T	0.40040	-0.9584	9	0.54805	T	0.06	.	9.1902	0.37195	0.0:0.8609:0.0:0.1391	rs3754415;rs17851263	173	P27987	IP3KB_HUMAN	H	173	ENSP00000272117:R173H;ENSP00000411152:R173H;ENSP00000355748:R173H	ENSP00000272117:R173H	R	-	2	0	ITPKB	224991265	0.985000	0.35326	0.998000	0.56505	0.888000	0.51559	2.942000	0.49018	2.374000	0.81015	0.561000	0.74099	CGC	C|0.795;T|0.205	0.205	strong		0.672	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197593	39197593	+	Silent	SNP	G	G	T	rs145621540		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39197593G>T	ENST00000306271.4	-	1	120	c.57C>A	c.(55-57)acC>acA	p.T19T		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	19			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)				NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGAGCCGCAGGTCCCACTGG	0.607																																					p.T19T		Atlas-SNP	.											KRTAP1-1,NS,carcinoma,0,1	KRTAP1-1	23	1	0			c.C57A						scavenged	.						41.0	52.0	48.0					17																	39197593		1960	4168	6128	SO:0001819	synonymous_variant	81851	exon1			GCCGCAGGTCCCA	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.57C>A	17.37:g.39197593G>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	189	22	0.116402	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			G|0.983;A|0.017	.	strong		0.607	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
LRRK1	79705	hgsc.bcm.edu	37	15	101464915	101464915	+	Silent	SNP	T	T	C	rs11630691	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:101464915T>C	ENST00000388948.3	+	2	437	c.78T>C	c.(76-78)cgT>cgC	p.R26R	LRRK1_ENST00000284395.5_5'UTR|LRRK1_ENST00000532029.2_Silent_p.R26R	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1									p.R26R(1)		breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GTCCAGAACGTGCCATGGAGA	0.577													C|||	1709	0.341254	0.6891	0.1772	5008	,	,		17664	0.1339		0.2435	False		,,,				2504	0.3016				p.R26R		Atlas-SNP	.											LRRK1_ENST00000388948,NS,carcinoma,0,1	LRRK1	310	1	1	Substitution - coding silent(1)	prostate(1)	c.T78C						PASS	.	C		2680,1726	514.7+/-368.7	824,1032,347	121.0	141.0	134.0		78	-1.9	0.0	15	dbSNP_120	134	2245,6355	704.9+/-405.4	288,1669,2343	no	coding-synonymous	LRRK1	NM_024652.3		1112,2701,2690	CC,CT,TT		26.1047,39.1739,37.8671		26/2016	101464915	4925,8081	2203	4300	6503	SO:0001819	synonymous_variant	79705	exon2			AGAACGTGCCATG	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.78T>C	15.37:g.101464915T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	139	60	0.431655	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			T|0.682;C|0.318	0.318	strong		0.577	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
ZNF618	114991	hgsc.bcm.edu	37	9	116764283	116764283	+	Silent	SNP	C	C	T	rs4978561	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:116764283C>T	ENST00000374126.5	+	5	540	c.441C>T	c.(439-441)taC>taT	p.Y147Y	ZNF618_ENST00000288466.7_Silent_p.Y115Y			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	147					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						CAGGGTCTTACGAATGCGGAA	0.562													T|||	1654	0.330272	0.1293	0.2882	5008	,	,		21788	0.6022		0.3489	False		,,,				2504	0.3323				p.Y115Y		Atlas-SNP	.											.	ZNF618	184	.	0			c.C345T						PASS	.	T		611,3365		37,537,1414	131.0	134.0	133.0		345	-3.8	1.0	9	dbSNP_111	133	2760,5542		468,1824,1859	no	coding-synonymous	ZNF618	NM_133374.2		505,2361,3273	TT,TC,CC		33.245,15.3672,27.4556		115/862	116764283	3371,8907	1988	4151	6139	SO:0001819	synonymous_variant	114991	exon4			GTCTTACGAATGC	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.441C>T	9.37:g.116764283C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				C|0.645;T|0.355	0.355	strong		0.562	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
PLEC	5339	hgsc.bcm.edu	37	8	145008560	145008560	+	Silent	SNP	A	A	G	rs11783799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:145008560A>G	ENST00000322810.4	-	11	1675	c.1506T>C	c.(1504-1506)gaT>gaC	p.D502D	PLEC_ENST00000398774.2_Silent_p.D333D|PLEC_ENST00000345136.3_Silent_p.D365D|PLEC_ENST00000354589.3_Silent_p.D365D|PLEC_ENST00000354958.2_Silent_p.D343D|PLEC_ENST00000436759.2_Silent_p.D392D|PLEC_ENST00000527096.1_Silent_p.D388D|PLEC_ENST00000356346.3_Silent_p.D351D|PLEC_ENST00000357649.2_Silent_p.D369D	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	502	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CCTTCTCCACATCCAGCGGGT	0.677													G|||	1159	0.23143	0.0613	0.2867	5008	,	,		16296	0.1409		0.4066	False		,,,				2504	0.3354				p.D502D		Atlas-SNP	.											.	PLEC	1144	.	0			c.T1506C						PASS	.	G	,,,,,,,	440,3688		26,388,1650	32.0	36.0	35.0		1176,1053,1029,1506,999,1095,1107,1095	-5.7	0.6	8	dbSNP_120	35	3220,5166		612,1996,1585	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	638,2384,3235	GG,GA,AA		38.3973,10.6589,29.2472	,,,,,,,	392/4575,351/4534,343/4526,502/4685,333/4516,365/4548,369/4552,365/4548	145008560	3660,8854	2064	4193	6257	SO:0001819	synonymous_variant	5339	exon11			CTCCACATCCAGC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.1506T>C	8.37:g.145008560A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	155	62	0.4	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			A|0.702;G|0.298	0.298	strong		0.677	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
PNPLA5	150379	hgsc.bcm.edu	37	22	44287629	44287629	+	Silent	SNP	G	G	A	rs74445350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:44287629G>A	ENST00000597664.1	-	1	261	c.132C>T	c.(130-132)cgC>cgT	p.R44R	PNPLA5_ENST00000593866.1_Silent_p.R44R|PNPLA5_ENST00000216177.4_Silent_p.R44R|PNPLA5_ENST00000381198.2_Silent_p.R44R			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	44	Patatin.				lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				AACCGTAGATGCGGCGGGCGC	0.726													G|||	667	0.133187	0.0053	0.1297	5008	,	,		12691	0.248		0.1034	False		,,,				2504	0.2209				p.R44R		Atlas-SNP	.											.	PNPLA5	46	.	0			c.C132T						PASS	.	G	,	70,3548		0,70,1739	5.0	5.0	5.0		132,132	-3.6	0.1	22	dbSNP_131	5	524,6092		14,496,2798	no	coding-synonymous,coding-synonymous	PNPLA5	NM_001177675.1,NM_138814.3	,	14,566,4537	AA,AG,GG		7.9202,1.9348,5.8042	,	44/316,44/430	44287629	594,9640	1809	3308	5117	SO:0001819	synonymous_variant	150379	exon1			GTAGATGCGGCGG	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.132C>T	22.37:g.44287629G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Silent	SNP	ENST00000597664.1	37																																																																																				G|0.878;A|0.122	0.122	strong		0.726	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
COL5A1	1289	hgsc.bcm.edu	37	9	137707834	137707834	+	Splice_Site	SNP	G	G	A	rs3827848	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:137707834G>A	ENST00000371817.3	+	52	4536	c.4122G>A	c.(4120-4122)acG>acA	p.T1374T		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1374	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.T1374T(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCGGGCAGACGGTGAGTCCAC	0.552													G|||	650	0.129792	0.1014	0.0994	5008	,	,		20008	0.1696		0.1392	False		,,,				2504	0.1391				p.T1374T		Atlas-SNP	.											COL5A1,NS,carcinoma,0,2	COL5A1	323	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.G4122A						scavenged	.	G		486,3920	228.1+/-243.1	34,418,1751	143.0	131.0	135.0		4122	3.2	1.0	9	dbSNP_107	135	1358,7242	264.8+/-285.7	114,1130,3056	yes	coding-synonymous-near-splice	COL5A1	NM_000093.3		148,1548,4807	AA,AG,GG		15.7907,11.0304,14.1781		1374/1839	137707834	1844,11162	2203	4300	6503	SO:0001630	splice_region_variant	1289	exon52			GCAGACGGTGAGT	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4122+1G>A	9.37:g.137707834G>A		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	225	105	0.466667	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			G|0.865;A|0.135	0.135	strong		0.552	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Silent
PLEKHN1	84069	hgsc.bcm.edu	37	1	909242	909242	+	Silent	SNP	A	A	G	rs3829739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:909242A>G	ENST00000379409.2	+	13	1650	c.1620A>G	c.(1618-1620)ggA>ggG	p.G540G	PLEKHN1_ENST00000379410.3_Silent_p.G488G|PLEKHN1_ENST00000379407.3_Silent_p.G453G			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	540										central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	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;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		GTGCACGTGGACCCACGCCCT	0.687													A|||	660	0.131789	0.2723	0.1225	5008	,	,		14987	0.1637		0.0189	False		,,,				2504	0.0317				p.G488G		Atlas-SNP	.											.	PLEKHN1	49	.	0			c.A1464G						PASS	.	A	,	944,3450	328.5+/-300.6	100,744,1353	28.0	34.0	32.0		1359,1464	0.6	0.2	1	dbSNP_107	32	143,8445	67.0+/-129.4	0,143,4151	no	coding-synonymous,coding-synonymous	PLEKHN1	NM_001160184.1,NM_032129.2	,	100,887,5504	GG,GA,AA		1.6651,21.4838,8.3731	,	453/577,488/612	909242	1087,11895	2197	4294	6491	SO:0001819	synonymous_variant	84069	exon14			ACGTGGACCCACG	AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"""Pleckstrin homology (PH) domain containing"""	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.1620A>G	1.37:g.909242A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_032129	Q494U2|Q5SV98|Q9H0M7	Silent	SNP	ENST00000379409.2	37																																																																																				A|0.902;G|0.098	0.098	strong		0.687	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129	
Unknown	0	hgsc.bcm.edu	37	14	20181502	20181502	+	IGR	SNP	C	C	T	rs201024081		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20181502C>T								RP11-597A11.2 (28604 upstream) : OR4Q3 (34084 downstream)																							TCACACACAACATGGTCAATA	0.443																																					p.V192I		Atlas-SNP	.											.	.	.	.	0			c.G574A						PASS	.																																			SO:0001628	intergenic_variant	79334	exon2			ACACAACATGGTC																													14.37:g.20181502C>T		Somatic	440	0	0		WXS	Illumina HiSeq	Phase_I	494	346	0.700405	NM_001197287		Missense_Mutation	SNP		37																																																																																				.	.	weak	0	0.443								
PTPRQ	374462	hgsc.bcm.edu	37	12	80900348	80900348	+	Splice_Site	SNP	T	T	G	rs7965277	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:80900348T>G	ENST00000266688.5	+	21	2444	c.2444T>G	c.(2443-2445)gTa>gGa	p.V815G				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	861	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)	p.V815G(1)		breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						TTCTCTTTAGTACTGAAGAAA	0.353													G|||	1462	0.291933	0.5719	0.2767	5008	,	,		17606	0.0516		0.2724	False		,,,				2504	0.1922				p.V647G		Atlas-SNP	.											PTPRQ,NS,carcinoma,0,1	PTPRQ	119	1	1	Substitution - Missense(1)	kidney(1)	c.T1940G						PASS	.	G	GLY/VAL	696,688		178,340,174	92.0	82.0	85.0		2002	4.4	1.0	12	dbSNP_116	85	868,2310		134,600,855	yes	missense-near-splice	PTPRQ	NM_001145026.1	109	312,940,1029	GG,GT,TT		27.3128,49.711,34.2832	benign	819/2300	80900348	1564,2998	692	1589	2281	SO:0001630	splice_region_variant	374462	exon13			CTTTAGTACTGAA	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.2444-1T>G	12.37:g.80900348T>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	37		649|649	0.29716117216117216|0.29716117216117216	297|297	0.6036585365853658|0.6036585365853658	117|117	0.32320441988950277|0.32320441988950277	39|39	0.06818181818181818|0.06818181818181818	196|196	0.25857519788918204|0.25857519788918204	G|G	8.428|8.428	0.847930|0.847930	0.17034|0.17034	0.50289|0.50289	0.273128|0.273128	ENSG00000139304|ENSG00000139304	ENST00000266688|ENST00000532722	T|.	0.47177|.	0.85|.	5.3|5.3	4.41|4.41	0.53225|0.53225	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.30637|0.30637	P|P	0.756892|0.756892	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.49093|0.49093	-0.8975|-0.8975	6|3	.|.	.|.	.|.	.|.	10.1713|10.1713	0.42911|0.42911	0.0716:0.0:0.791:0.1374|0.0716:0.0:0.791:0.1374	rs7965277;rs60159653;rs7965277|rs7965277;rs60159653;rs7965277	861|.	Q9UMZ3|.	PTPRQ_HUMAN|.	G|D	815|516	ENSP00000266688:V815G|.	.|.	V|Y	+|+	2|1	0|0	PTPRQ|PTPRQ	79424479|79424479	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.244000|0.244000	0.25665|0.25665	2.385000|2.385000	0.44371|0.44371	0.732000|0.732000	0.32470|0.32470	-0.187000|-0.187000	0.12897|0.12897	GTA|TAC	T|0.686;G|0.314	0.314	strong		0.353	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	Missense_Mutation
CDKL5	6792	hgsc.bcm.edu	37	X	18664128	18664128	+	Splice_Site	SNP	C	C	T	rs201714912		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:18664128C>T	ENST00000379989.3	+	20	3000	c.2715C>T	c.(2713-2715)gaC>gaT	p.D905D	RS1_ENST00000476595.1_Intron|CDKL5_ENST00000379996.3_Splice_Site_p.D905D|RS1_ENST00000379984.3_Intron	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	905					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)	p.D905D(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					actaactagacggtggatgtg	0.493													A|||	1	0.000264901	0.0	0.0	3775	,	,		14324	0.0		0.001	False		,,,				2504	0.0				p.D905D		Atlas-SNP	.											.	CDKL5	124	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C2715T						PASS	.	A	,,	1,3834		0,1,1631,571	140.0	112.0	122.0		,2715,2715	0.6	0.1	X		122	0,6728		0,0,2428,1872	no	intron,coding-synonymous-near-splice,coding-synonymous-near-splice	RS1,CDKL5	NM_000330.3,NM_001037343.1,NM_003159.2	,,	0,1,4059,2443	TT,TC,CC,C		0.0,0.0261,0.0095	,,	,905/1031,905/1031	18664128	1,10562	2203	4300	6503	SO:0001630	splice_region_variant	6792	exon19			ACTAGACGGTGGA	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"""Cyclin-dependent kinases"""	11411	protein-coding gene	gene with protein product		300203	"""serine/threonine kinase 9"""	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.2714-1C>T	X.37:g.18664128C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	49	5	0.102041	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Silent	SNP	ENST00000379989.3	37	CCDS14186.1																																																																																			C|0.999;T|0.001	0.001	strong		0.493	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	Silent
STARD3	10948	hgsc.bcm.edu	37	17	37815305	37815305	+	Splice_Site	SNP	G	G	A	rs144713925		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:37815305G>A	ENST00000336308.5	+	8	866	c.648G>A	c.(646-648)ggG>ggA	p.G216G	STARD3_ENST00000578232.1_3'UTR|STARD3_ENST00000544210.2_Splice_Site_p.G216G|STARD3_ENST00000580611.1_Splice_Site_p.G190G|STARD3_ENST00000394250.4_Splice_Site_p.G198G	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	216	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.		G -> A (in dbSNP:rs11556624). {ECO:0000269|PubMed:15489334}.		cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TTTCTGCAGGGTCTGACAATG	0.527													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16693	0.0		0.0	False		,,,				2504	0.0				p.G216G		Atlas-SNP	.											.	STARD3	33	.	0			c.G648A						PASS	.	G	,,	1,4405		0,1,2202	221.0	216.0	218.0		648,594,648	2.7	1.0	17	dbSNP_134	218	10,8590	3.7+/-12.6	0,10,4290	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	STARD3	NM_001165937.1,NM_001165938.1,NM_006804.3	,,	0,11,6492	AA,AG,GG		0.1163,0.0227,0.0846	,,	216/446,198/428,216/446	37815305	11,12995	2203	4300	6503	SO:0001630	splice_region_variant	10948	exon8			TGCAGGGTCTGAC		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"""StAR-related lipid transfer (START) domain containing"""	17579	protein-coding gene	gene with protein product		607048	"""START domain containing 3"""				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.647-1G>A	17.37:g.37815305G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	203	92	0.453202	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Silent	SNP	ENST00000336308.5	37	CCDS11341.1																																																																																			G|0.999;A|0.001	0.001	strong		0.527	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1		Silent
ADSSL1	122622	hgsc.bcm.edu	37	14	105196365	105196365	+	Silent	SNP	T	T	C	rs33958252	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105196365T>C	ENST00000332972.5	+	1	295	c.136T>C	c.(136-138)Tta>Cta	p.L46L	ADSSL1_ENST00000330877.2_Intron	NM_199165.1	NP_954634.1			adenylosuccinate synthase like 1											central_nervous_system(1)|cervix(1)|kidney(1)|lung(5)|ovary(2)|prostate(1)	11		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)		GAGTCTCCAGTTACTGAGTGG	0.662													C|||	3051	0.609225	0.7927	0.5058	5008	,	,		12559	0.6111		0.4453	False		,,,				2504	0.6012				p.L46L		Atlas-SNP	.											.	ADSSL1	37	.	0			c.T136C						PASS	.	C	,	3224,1142		1212,800,171	35.0	30.0	32.0		,136	-0.8	0.0	14	dbSNP_126	32	3913,4671		926,2061,1305	no	intron,coding-synonymous	ADSSL1	NM_152328.3,NM_199165.1	,	2138,2861,1476	CC,CT,TT		45.5848,26.1567,44.888	,	,46/501	105196365	7137,5813	2183	4292	6475	SO:0001819	synonymous_variant	122622	exon1			CTCCAGTTACTGA	AK095921	CCDS9990.1, CCDS9991.1	14q32.33	2010-08-05			ENSG00000185100	ENSG00000185100			20093	protein-coding gene	gene with protein product		612498					Standard	NM_199165		Approved	FLJ38602	uc001ype.3	Q8N142		ENST00000332972.5:c.136T>C	14.37:g.105196365T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_199165		Silent	SNP	ENST00000332972.5	37	CCDS9991.1																																																																																			T|0.432;C|0.568	0.568	strong		0.662	ADSSL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410531.1		
ICE2	79664	hgsc.bcm.edu	37	15	60734697	60734697	+	Silent	SNP	A	A	G	rs1063100	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:60734697A>G	ENST00000261520.4	-	12	2577	c.2343T>C	c.(2341-2343)taT>taC	p.Y781Y	NARG2_ENST00000439632.1_Silent_p.Y644Y	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						CTTCAACTCCATAACAAGCTT	0.323													A|||	2978	0.594649	0.2534	0.6513	5008	,	,		18942	0.8244		0.5726	False		,,,				2504	0.8016				p.Y781Y		Atlas-SNP	.											.	NARG2	82	.	0			c.T2343C						PASS	.	A	,	1267,3139	430.4+/-342.5	187,893,1123	89.0	79.0	82.0		1932,2343	-7.4	0.9	15	dbSNP_86	82	4931,3667	621.5+/-397.2	1431,2069,799	no	coding-synonymous,coding-synonymous	NARG2	NM_001018089.1,NM_024611.4	,	1618,2962,1922	GG,GA,AA		42.6495,28.7562,47.6623	,	644/846,781/983	60734697	6198,6806	2203	4299	6502	SO:0001819	synonymous_variant	79664	exon12			AACTCCATAACAA																												ENST00000261520.4:c.2343T>C	15.37:g.60734697A>G		Somatic	539	1	0.00185529		WXS	Illumina HiSeq	Phase_I	522	517	0.990421	NM_024611		Silent	SNP	ENST00000261520.4	37	CCDS10176.1																																																																																			.	.	weak		0.323	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1		
FAM186A	121006	hgsc.bcm.edu	37	12	50727811	50727811	+	Missense_Mutation	SNP	C	C	T	rs6580742	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:50727811C>T	ENST00000327337.5	-	5	6578	c.6579G>A	c.(6577-6579)atG>atA	p.M2193I	FAM186A_ENST00000543111.1_Missense_Mutation_p.M2193I|FAM186A_ENST00000543096.1_Missense_Mutation_p.M204I	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2193			M -> I (in dbSNP:rs6580742).														GTCTGCTCAGCATCATGTGGA	0.423													C|||	340	0.0678914	0.0113	0.1066	5008	,	,		21742	0.001		0.163	False		,,,				2504	0.0879				p.M2193I	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.G6579A						PASS	.	C	ILE/MET	41,1343		1,39,652	277.0	224.0	240.0		6579	3.5	1.0	12	dbSNP_116	240	527,2655		58,411,1122	yes	missense	FAM186A	NM_001145475.1	10	59,450,1774	TT,TC,CC		16.5619,2.9624,12.4398	possibly-damaging	2193/2352	50727811	568,3998	692	1591	2283	SO:0001583	missense	121006	exon5			GCTCAGCATCATG		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.6579G>A	12.37:g.50727811C>T	ENSP00000329995:p.Met2193Ile	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	262	132	0.503817	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	169	0.07738095238095238	7	0.014227642276422764	40	0.11049723756906077	2	0.0034965034965034965	120	0.158311345646438	C	9.768	1.171981	0.21704	0.029624	0.165619	ENSG00000185958	ENST00000543111;ENST00000543096;ENST00000327337	T;T;T	0.31247	1.5;1.5;1.5	4.39	3.51	0.40186	.	.	.	.	.	T	0.00144	0.0004	L	0.36672	1.1	0.41050	P	0.014708000000000054	D;D	0.71674	0.998;0.982	D;P	0.69479	0.964;0.873	T	0.05750	-1.0866	8	0.72032	D	0.01	.	8.5972	0.33723	0.0:0.8973:0.0:0.1027	rs6580742;rs17413065;rs52828310;rs58453917;rs6580742	2193;2193	F5GYN0;A6NE01	.;F186A_HUMAN	I	2193;204;2193	ENSP00000441337:M2193I;ENSP00000443703:M204I;ENSP00000329995:M2193I	ENSP00000329995:M2193I	M	-	3	0	FAM186A	49014078	0.996000	0.38824	0.981000	0.43875	0.046000	0.14306	0.791000	0.26915	1.448000	0.47680	-0.150000	0.13652	ATG	C|0.920;T|0.080	0.080	strong		0.423	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
DNAJC21	134218	hgsc.bcm.edu	37	5	34945122	34945122	+	Silent	SNP	A	A	G	rs17304200	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:34945122A>G	ENST00000342382.4	+	8	1361	c.1134A>G	c.(1132-1134)ccA>ccG	p.P378P	DNAJC21_ENST00000303525.7_Silent_p.P378P|DNAJC21_ENST00000382021.2_Silent_p.P378P			Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21	378					protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			AAGATGCACCAAAACAAAAGT	0.318													A|||	249	0.0497204	0.003	0.0432	5008	,	,		18965	0.0367		0.0676	False		,,,				2504	0.1125				p.P378P		Atlas-SNP	.											.	DNAJC21	54	.	0			c.A1134G						PASS	.	A	,	66,4340	56.8+/-93.2	2,62,2139	77.0	84.0	81.0		1134,1134	-2.3	0.6	5	dbSNP_123	81	720,7880	174.2+/-224.5	33,654,3613	no	coding-synonymous,coding-synonymous	DNAJC21	NM_001012339.2,NM_194283.3	,	35,716,5752	GG,GA,AA		8.3721,1.498,6.0434	,	378/532,378/577	34945122	786,12220	2203	4300	6503	SO:0001819	synonymous_variant	134218	exon8			TGCACCAAAACAA		CCDS3907.2, CCDS34144.1	5p13-p12	2012-10-05			ENSG00000168724	ENSG00000168724		"""Heat shock proteins / DNAJ (HSP40)"""	27030	protein-coding gene	gene with protein product	"""JJJ1 DnaJ domain protein homolog (S. cerevisiae)"""					15067379	Standard	XM_005248250		Approved	GS3, DNAJA5, JJJ1	uc003jjc.3	Q5F1R6	OTTHUMG00000074103	ENST00000342382.4:c.1134A>G	5.37:g.34945122A>G		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	222	113	0.509009	NM_001012339	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	Silent	SNP	ENST00000342382.4	37	CCDS34144.1																																																																																			A|0.950;G|0.050	0.050	strong		0.318	DNAJC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157337.1	NM_194283	
PIWIL1	9271	hgsc.bcm.edu	37	12	130841638	130841638	+	Missense_Mutation	SNP	G	G	A	rs1106042	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:130841638G>A	ENST00000245255.3	+	13	1852	c.1580G>A	c.(1579-1581)aGa>aAa	p.R527K		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	527			R -> K (in dbSNP:rs1106042). {ECO:0000269|PubMed:15489334}.		gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		ATGCAAATGAGAAAAGCAATA	0.363													A|||	442	0.0882588	0.0189	0.0245	5008	,	,		20859	0.119		0.0596	False		,,,				2504	0.2249				p.R527K		Atlas-SNP	.											.	PIWIL1	157	.	0			c.G1580A						PASS	.	A	LYS/ARG,LYS/ARG	128,4278	788.0+/-414.9	5,118,2080	48.0	48.0	48.0		1580,1580	4.2	1.0	12	dbSNP_86	48	491,8109	792.1+/-407.5	10,471,3819	yes	missense,missense	PIWIL1	NM_001190971.1,NM_004764.4	26,26	15,589,5899	AA,AG,GG		5.7093,2.9051,4.7593	benign,benign	527/830,527/862	130841638	619,12387	2203	4300	6503	SO:0001583	missense	9271	exon13			AAATGAGAAAAGC	AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"""Argonaute/PIWI family"""	9007	protein-coding gene	gene with protein product		605571	"""piwi (Drosophila)-like 1"", ""piwi-like 1 (Drosophila)"""			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.1580G>A	12.37:g.130841638G>A	ENSP00000245255:p.Arg527Lys	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	37	CCDS9268.1	132	0.06043956043956044	7	0.014227642276422764	11	0.03038674033149171	68	0.11888111888111888	46	0.06068601583113457	A	7.073	0.568697	0.13560	0.029051	0.057093	ENSG00000125207	ENST00000245255	T	0.13538	2.58	5.41	4.25	0.50352	Ribonuclease H-like (1);	0.139746	0.64402	N	0.000003	T	0.00073	0.0002	N	0.02916	-0.46	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34229	-0.9837	9	0.02654	T	1	-14.5403	9.5597	0.39362	0.8532:0.0:0.1468:0.0	rs1106042;rs2242365;rs17856813;rs52797056;rs60950081;rs1106042	527;527	Q96J94;Q96J94-2	PIWL1_HUMAN;.	K	527	ENSP00000245255:R527K	ENSP00000245255:R527K	R	+	2	0	PIWIL1	129407591	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	4.313000	0.59160	0.879000	0.35944	-0.254000	0.11334	AGA	G|0.943;A|0.057	0.057	strong		0.363	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1		
WDR11	55717	hgsc.bcm.edu	37	10	122645376	122645376	+	Silent	SNP	A	A	T	rs7899928	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122645376A>T	ENST00000263461.6	+	15	2145	c.1899A>T	c.(1897-1899)gcA>gcT	p.A633A	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					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)	p.A633A(1)		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						AGCAACTTGCAACTCGAGAGG	0.473													T|||	1981	0.395567	0.4297	0.4366	5008	,	,		18356	0.4177		0.334	False		,,,				2504	0.3609				p.A633A		Atlas-SNP	.											WDR11,NS,carcinoma,0,1	WDR11	95	1	1	Substitution - coding silent(1)	stomach(1)	c.A1899T						PASS	.	T		1846,2560	635.2+/-396.3	392,1062,749	138.0	133.0	135.0		1899	-5.2	0.9	10	dbSNP_116	135	2894,5706	671.5+/-402.8	471,1952,1877	no	coding-synonymous	WDR11	NM_018117.11		863,3014,2626	TT,TA,AA		33.6512,41.8974,36.4447		633/1225	122645376	4740,8266	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon15			ACTTGCAACTCGA	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.1899A>T	10.37:g.122645376A>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			A|0.640;T|0.360	0.360	strong		0.473	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
METTL11B	149281	hgsc.bcm.edu	37	1	170136787	170136787	+	Silent	SNP	C	C	T	rs12075997	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:170136787C>T	ENST00000439373.2	+	4	848	c.741C>T	c.(739-741)agC>agT	p.S247S		NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	247			S -> R (in dbSNP:rs12735494).			nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						TCCTCCGGAGCCTAATAAGGA	0.557													C|||	293	0.0585064	0.1067	0.0562	5008	,	,		18583	0.004		0.0915	False		,,,				2504	0.0174				p.S247S		Atlas-SNP	.											.	METTL11B	18	.	0			c.C741T						PASS	.	C		157,1227		14,129,549	53.0	52.0	53.0		741	1.2	0.3	1	dbSNP_120	53	213,2969		6,201,1384	no	coding-synonymous	METTL11B	NM_001136107.1		20,330,1933	TT,TC,CC		6.6939,11.3439,8.1034		247/284	170136787	370,4196	692	1591	2283	SO:0001819	synonymous_variant	149281	exon4			CCGGAGCCTAATA	AL445203, CAH72139	CCDS44275.1	1q24.2	2012-11-05	2008-06-11	2008-06-11	ENSG00000203740	ENSG00000203740			31932	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 184"""	C1orf184			Standard	NM_001136107		Approved	HOMT1B	uc009wvv.1	Q5VVY1	OTTHUMG00000035959	ENST00000439373.2:c.741C>T	1.37:g.170136787C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	128	124	0.96875	NM_001136107	B2RXI0	Silent	SNP	ENST00000439373.2	37	CCDS44275.1																																																																																			C|0.930;T|0.070	0.070	strong		0.557	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
KLHL24	54800	hgsc.bcm.edu	37	3	183368216	183368216	+	Silent	SNP	A	A	T	rs3755648	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:183368216A>T	ENST00000454652.2	+	4	458	c.72A>T	c.(70-72)cgA>cgT	p.R24R	KLHL24_ENST00000242810.6_Silent_p.R24R|KLHL24_ENST00000476808.1_Silent_p.R24R	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24	24						cell projection (GO:0042995)|cytoplasm (GO:0005737)		p.R24R(1)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			CAACTAAGCGAAAAGTTTTTG	0.403													T|||	1755	0.350439	0.5144	0.2795	5008	,	,		17517	0.4355		0.2654	False		,,,				2504	0.1789				p.R24R		Atlas-SNP	.											KLHL24,caecum,carcinoma,+1,2	KLHL24	56	2	1	Substitution - coding silent(1)	stomach(1)	c.A72T						PASS	.	T		2126,2280	578.7+/-384.7	527,1072,604	63.0	67.0	66.0		72	-3.2	1.0	3	dbSNP_107	66	2370,6230	697.6+/-405.0	339,1692,2269	no	coding-synonymous	KLHL24	NM_017644.3		866,2764,2873	TT,TA,AA		27.5581,48.2524,34.5687		24/601	183368216	4496,8510	2203	4300	6503	SO:0001819	synonymous_variant	54800	exon3			TAAGCGAAAAGTT		CCDS3246.1	3q27.1	2013-02-22	2013-02-22		ENSG00000114796	ENSG00000114796		"""Kelch-like"", ""BTB/POZ domain containing"""	25947	protein-coding gene	gene with protein product		611295	"""kelch-like 24 (Drosophila)"""				Standard	XM_005247552		Approved	DRE1, FLJ20059	uc003flv.3	Q6TFL4	OTTHUMG00000156911	ENST00000454652.2:c.72A>T	3.37:g.183368216A>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	219	109	0.497717	NM_017644	A5PLN8|Q9H620|Q9NXT9	Silent	SNP	ENST00000454652.2	37	CCDS3246.1																																																																																			A|0.647;T|0.353	0.353	strong		0.403	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	NM_017644	
RIMBP2	23504	hgsc.bcm.edu	37	12	130941150	130941150	+	Silent	SNP	G	G	C	rs2277361	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:130941150G>C	ENST00000261655.4	-	4	361	c.198C>G	c.(196-198)ggC>ggG	p.G66G	RIMBP2_ENST00000536002.1_5'UTR|RIMBP2_ENST00000535703.1_5'UTR	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	66					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		GGTCAATCTTGCCAGCGTGCT	0.612													C|||	1853	0.370008	0.3714	0.2622	5008	,	,		18755	0.377		0.4374	False		,,,				2504	0.3681				p.G66G		Atlas-SNP	.											.	RIMBP2	220	.	0			c.C198G						PASS	.	C		1747,2659	644.0+/-397.9	313,1121,769	47.0	38.0	41.0		198	-1.9	0.0	12	dbSNP_100	41	3913,4687	603.2+/-394.6	879,2155,1266	no	coding-synonymous	RIMBP2	NM_015347.4		1192,3276,2035	CC,CG,GG		45.5,39.6505,43.5184		66/1053	130941150	5660,7346	2203	4300	6503	SO:0001819	synonymous_variant	23504	exon4			AATCTTGCCAGCG	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.198C>G	12.37:g.130941150G>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_015347	Q96ID2	Silent	SNP	ENST00000261655.4	37	CCDS31925.1																																																																																			G|0.590;C|0.410	0.410	strong		0.612	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
MUC16	94025	hgsc.bcm.edu	37	19	9072296	9072296	+	Silent	SNP	G	G	T	rs7254970	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9072296G>T	ENST00000397910.4	-	3	15353	c.15150C>A	c.(15148-15150)acC>acA	p.T5050T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5052	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGAAGGTGTGGTCATTGCAG	0.468													G|||	844	0.16853	0.171	0.1844	5008	,	,		20301	0.0089		0.2634	False		,,,				2504	0.2209				p.T5050T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C15150A						PASS	.			664,3246		60,544,1351	91.0	86.0	88.0		15150	0.5	0.0	19	dbSNP_116	88	2428,5862		370,1688,2087	no	coding-synonymous	MUC16	NM_024690.2		430,2232,3438	TT,TG,GG		29.2883,16.9821,25.3443		5050/14508	9072296	3092,9108	1955	4145	6100	SO:0001819	synonymous_variant	94025	exon3			AGGTGTGGTCATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15150C>A	19.37:g.9072296G>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	113	112	0.99115	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.815;T|0.185	0.185	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
EIF4G1	1981	hgsc.bcm.edu	37	3	184046470	184046470	+	Silent	SNP	C	C	T	rs2230571	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:184046470C>T	ENST00000346169.2	+	27	4276	c.4005C>T	c.(4003-4005)caC>caT	p.H1335H	EIF4G1_ENST00000319274.6_Silent_p.H1335H|EIF4G1_ENST00000342981.4_Silent_p.H1336H|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000414031.1_Silent_p.H1295H|EIF4G1_ENST00000427845.1_Silent_p.H1249H|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000382330.3_Silent_p.H1342H|EIF4G1_ENST00000350481.5_Silent_p.H1171H|EIF4G1_ENST00000411531.1_Silent_p.H1296H|EIF4G1_ENST00000424196.1_Silent_p.H1342H|EIF4G1_ENST00000441154.1_Silent_p.H1172H|EIF4G1_ENST00000392537.2_Silent_p.H1248H|EIF4G1_ENST00000435046.2_Silent_p.H1139H|EIF4G1_ENST00000352767.3_Silent_p.H1342H|EIF4G1_ENST00000434061.2_Silent_p.H1140H	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1335	MI. {ECO:0000255|PROSITE- ProRule:PRU00698}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACATCCCCCACGTGTGGCTCT	0.532													C|||	672	0.134185	0.0219	0.1354	5008	,	,		19260	0.0506		0.2346	False		,,,				2504	0.2679				p.H1342H		Atlas-SNP	.											EIF4G1,NS,adenoma,0,1	EIF4G1	151	1	0			c.C4026T						PASS	.	C	,,,,,,	252,4154	146.1+/-180.8	11,230,1962	149.0	149.0	149.0		4026,4026,3420,4008,4005,3513,3744	-4.2	1.0	3	dbSNP_98	149	2115,6485	365.1+/-333.8	282,1551,2467	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	,,,,,,	293,1781,4429	TT,TC,CC		24.593,5.7195,18.1993	,,,,,,	1342/1607,1342/1607,1140/1405,1336/1601,1335/1600,1171/1436,1248/1513	184046470	2367,10639	2203	4300	6503	SO:0001819	synonymous_variant	1981	exon28			CCCCCACGTGTGG	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.4005C>T	3.37:g.184046470C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	111	59	0.531532	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																			C|0.850;T|0.150	0.150	strong		0.532	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
ATP8B2	57198	hgsc.bcm.edu	37	1	154310048	154310048	+	Silent	SNP	C	C	G	rs1760795	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:154310048C>G	ENST00000368487.3	+	12	1249	c.1062C>G	c.(1060-1062)ctC>ctG	p.L354L	ATP8B2_ENST00000426445.1_Intron|RNU7-57P_ENST00000459540.1_RNA|ATP8B2_ENST00000341822.2_Intron|ATP8B2_ENST00000368489.3_Intron	NM_001005855.1	NP_001005855.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	372					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CCTGGGGTCTCTCCAGGGAGT	0.468													C|||	2153	0.429912	0.1551	0.4957	5008	,	,		20687	0.624		0.4523	False		,,,				2504	0.5317				p.L354L		Atlas-SNP	.											.	ATP8B2	158	.	0			c.C1062G						PASS	.	C	,	933,3473	355.1+/-312.9	92,749,1362	214.0	201.0	206.0		1062,	2.4	0.0	1	dbSNP_89	206	4062,4538	559.7+/-387.5	963,2136,1201	no	coding-synonymous,intron	ATP8B2	NM_001005855.1,NM_020452.3	,	1055,2885,2563	GG,GC,CC		47.2326,21.1757,38.4054	,	354/388,	154310048	4995,8011	2203	4300	6503	SO:0001819	synonymous_variant	57198	exon12			GGGTCTCTCCAGG	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"""ATPases / P-type"""	13534	protein-coding gene	gene with protein product		605867	"""ATPase, class I, type 8B, member 2"""			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368487.3:c.1062C>G	1.37:g.154310048C>G		Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	259	127	0.490348	NM_001005855	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Silent	SNP	ENST00000368487.3	37	CCDS41405.1																																																																																			C|0.542;G|0.458	0.458	strong		0.468	ATP8B2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087903.2	NM_020452	
ARVCF	421	hgsc.bcm.edu	37	22	19958829	19958829	+	Silent	SNP	G	G	A	rs5993890	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:19958829G>A	ENST00000263207.3	-	19	3102	c.2811C>T	c.(2809-2811)ccC>ccT	p.P937P	ARVCF_ENST00000344269.3_Silent_p.P874P|ARVCF_ENST00000401994.1_Silent_p.P874P|ARVCF_ENST00000406259.1_Silent_p.P931P|ARVCF_ENST00000406522.1_Silent_p.P868P	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	937					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					TGCTGGGCCCGGGGGGAGGGG	0.657											OREG0026306	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	447	0.0892572	0.1679	0.0634	5008	,	,		18048	0.0278		0.0467	False		,,,				2504	0.1084				p.P937P		Atlas-SNP	.											.	ARVCF	54	.	0			c.C2811T						PASS	.			531,3751		40,451,1650	38.0	28.0	32.0		2811	-5.7	0.8	22	dbSNP_114	32	412,8054		17,378,3838	no	coding-synonymous	ARVCF	NM_001670.2		57,829,5488	AA,AG,GG		4.8665,12.4007,7.3972		937/963	19958829	943,11805	2141	4233	6374	SO:0001819	synonymous_variant	421	exon19			GGGCCCGGGGGGA		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"""Armadillo repeat containing"""	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.2811C>T	22.37:g.19958829G>A		Somatic	28	0	0	737	WXS	Illumina HiSeq	Phase_I	32	21	0.65625	NM_001670	B7WNV2	Silent	SNP	ENST00000263207.3	37	CCDS13771.1																																																																																			G|0.916;A|0.084	0.084	strong		0.657	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
PRCP	5547	hgsc.bcm.edu	37	11	82535963	82535963	+	Silent	SNP	C	C	T	rs4759	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:82535963C>T	ENST00000313010.3	-	9	1670	c.1476G>A	c.(1474-1476)gcG>gcA	p.A492A	PRCP_ENST00000393399.2_Silent_p.A513A|PRCP_ENST00000535099.1_Silent_p.A387A|PRCP_ENST00000525772.1_5'Flank	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	492					angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						GCTGCTTTCCCGCACTGTCAT	0.403													C|||	984	0.196486	0.0272	0.1124	5008	,	,		20304	0.5496		0.0726	False		,,,				2504	0.2485				p.A513A		Atlas-SNP	.											.	PRCP	69	.	0			c.G1539A						PASS	.	C	,	145,4261	100.7+/-139.4	2,141,2060	60.0	58.0	59.0		1476,1539	-10.5	0.0	11	dbSNP_52	59	699,7901	172.9+/-223.5	38,623,3639	no	coding-synonymous,coding-synonymous	PRCP	NM_005040.2,NM_199418.2	,	40,764,5699	TT,TC,CC		8.1279,3.291,6.4893	,	492/497,513/518	82535963	844,12162	2203	4300	6503	SO:0001819	synonymous_variant	5547	exon10			CTTTCCCGCACTG	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.1476G>A	11.37:g.82535963C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_199418	A8MU24|B2R7B7|B3KRK5|B5BU34	Silent	SNP	ENST00000313010.3	37	CCDS8262.1																																																																																			C|0.873;T|0.127	0.127	strong		0.403	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040	
TRPA1	8989	hgsc.bcm.edu	37	8	72948588	72948588	+	Silent	SNP	C	C	T	rs13280644	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:72948588C>T	ENST00000262209.4	-	21	2697	c.2490G>A	c.(2488-2490)ctG>ctA	p.L830L	TRPA1_ENST00000519720.1_5'UTR|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	830					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	ATTGCCACTGCAGATGAGCTG	0.353													C|||	251	0.0501198	0.0045	0.0634	5008	,	,		17025	0.003		0.0924	False		,,,				2504	0.1074				p.L830L		Atlas-SNP	.											.	TRPA1	256	.	0			c.G2490A						PASS	.	C		78,4328	69.8+/-107.6	0,78,2125	67.0	66.0	67.0		2490	0.2	0.6	8	dbSNP_121	67	841,7759	193.7+/-239.3	46,749,3505	no	coding-synonymous	TRPA1	NM_007332.2		46,827,5630	TT,TC,CC		9.7791,1.7703,7.066		830/1120	72948588	919,12087	2203	4300	6503	SO:0001819	synonymous_variant	8989	exon21			CCACTGCAGATGA	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.2490G>A	8.37:g.72948588C>T		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	322	175	0.543478	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																			C|0.934;T|0.066	0.066	strong		0.353	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
CDH23	64072	hgsc.bcm.edu	37	10	73537614	73537614	+	Missense_Mutation	SNP	G	G	A	rs17712523	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:73537614G>A	ENST00000224721.6	+	38	5043	c.5038G>A	c.(5038-5040)Gtc>Atc	p.V1680I		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1675	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.V1680I(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CTATGCCATCGTCGCAGGCAA	0.582													G|||	662	0.132188	0.0083	0.1225	5008	,	,		22375	0.1518		0.2177	False		,,,				2504	0.1984				p.V1675I		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - Missense(1)	stomach(1)	c.G5023A						PASS	.	G	ILE/VAL	171,4215	98.9+/-137.6	7,157,2029	87.0	80.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5023	-1.2	0.0	10	dbSNP_123	82	1654,6906	296.7+/-303.1	168,1318,2794	yes	missense	CDH23	NM_022124.5	29	175,1475,4823	AA,AG,GG		19.3224,3.8988,14.097	benign	1675/3355	73537614	1825,11121	2193	4280	6473	SO:0001583	missense	64072	exon37			GCCATCGTCGCAG	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.5038G>A	10.37:g.73537614G>A	ENSP00000224721:p.Val1680Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	146	75	0.513699	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		318	0.14560439560439561	8	0.016260162601626018	52	0.143646408839779	79	0.1381118881118881	179	0.23614775725593667	G	11.11	1.542382	0.27563	0.038988	0.193224	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	5.76	-1.2	0.09554	Cadherin (4);Cadherin-like (1);	0.734425	0.13151	N	0.409894	T	0.00012	0.0000	N	0.20845	0.615	0.41555	P	0.01140399999999997	B	0.06786	0.001	B	0.06405	0.002	T	0.26710	-1.0095	8	0.27785	T	0.31	.	6.2351	0.20758	0.6383:0.0:0.2126:0.1492	rs17712523;rs52808163;rs56502918;rs17712523	1675	Q9H251	CAD23_HUMAN	I	1680;1675;1678	.	ENSP00000224721:V1680I	V	+	1	0	CDH23	73207620	0.003000	0.15002	0.028000	0.17463	0.800000	0.45204	0.102000	0.15272	-0.097000	0.12307	-0.140000	0.14226	GTC	G|0.857;A|0.143	0.143	strong		0.582	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
STAP1	26228	hgsc.bcm.edu	37	4	68447040	68447040	+	Silent	SNP	C	C	T	rs11556615	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:68447040C>T	ENST00000265404.2	+	5	463	c.381C>T	c.(379-381)aaC>aaT	p.N127N	STAP1_ENST00000396225.1_Silent_p.N127N	NM_012108.2	NP_036240.1	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	127					intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	12						TTCCCCAAAACGTGTCACTCC	0.423													T|||	631	0.125998	0.1135	0.1628	5008	,	,		20180	0.005		0.2475	False		,,,				2504	0.1166				p.N127N		Atlas-SNP	.											.	STAP1	46	.	0			c.C381T						PASS	.	T		624,3782	768.4+/-413.6	47,530,1626	131.0	123.0	126.0		381	-2.2	0.7	4	dbSNP_120	126	2294,6306	705.6+/-405.5	282,1730,2288	no	coding-synonymous	STAP1	NM_012108.2		329,2260,3914	TT,TC,CC		26.6744,14.1625,22.4358		127/296	68447040	2918,10088	2203	4300	6503	SO:0001819	synonymous_variant	26228	exon5			CCAAAACGTGTCA	AB023483	CCDS3515.1	4q13.2	2013-02-14	2007-08-09		ENSG00000035720	ENSG00000035720		"""SH2 domain containing"""	24133	protein-coding gene	gene with protein product	"""BCR downstream signaling 1"""	604298				10518561, 10679268	Standard	NM_012108		Approved	STAP-1, BRDG1	uc003hde.4	Q9ULZ2	OTTHUMG00000129304	ENST00000265404.2:c.381C>T	4.37:g.68447040C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	108	59	0.546296	NM_012108	B2R980	Silent	SNP	ENST00000265404.2	37	CCDS3515.1																																																																																			T|0.162;G|0.138;C|0.673;A|0.027	0.162	strong		0.423	STAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251434.1	NM_012108	
WDR64	128025	hgsc.bcm.edu	37	1	241951329	241951329	+	Missense_Mutation	SNP	C	C	T	rs12074374	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:241951329C>T	ENST00000366552.2	+	23	3061	c.2854C>T	c.(2854-2856)Cgg>Tgg	p.R952W	WDR64_ENST00000437684.2_Missense_Mutation_p.R785W	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	952			R -> W (in dbSNP:rs12074374).							breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GATATTTGACCGGGAAAAGTA	0.363													C|||	563	0.11242	0.2186	0.1254	5008	,	,		20463	0.005		0.16	False		,,,				2504	0.0215				p.R952W		Atlas-SNP	.											WDR64_ENST00000366552,NS,carcinoma,-1,2	WDR64	234	2	0			c.C2854T						PASS	.	C	TRP/ARG	944,3462	354.6+/-312.7	92,760,1351	53.0	53.0	53.0		2854	2.8	0.9	1	dbSNP_120	53	1450,7150	275.4+/-291.8	134,1182,2984	yes	missense	WDR64	NM_144625.4	101	226,1942,4335	TT,TC,CC		16.8605,21.4253,18.4069	probably-damaging	952/1082	241951329	2394,10612	2203	4300	6503	SO:0001583	missense	128025	exon23			TTTGACCGGGAAA	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"""WD repeat domain containing"""	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.2854C>T	1.37:g.241951329C>T	ENSP00000355510:p.Arg952Trp	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	115	113	0.982609	NM_144625	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	37		275	0.1259157509157509	104	0.21138211382113822	53	0.1464088397790055	2	0.0034965034965034965	116	0.15303430079155672	C	16.98	3.271363	0.59649	0.214253	0.168605	ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635	T;T;T	0.42131	1.17;0.98;0.99	5.69	2.8	0.32819	.	0.363501	0.23589	N	0.046575	T	0.00073	0.0002	L	0.60455	1.87	0.45791	P	0.0013250000000000206	D;D	0.89917	0.999;1.0	P;D	0.64687	0.874;0.928	T	0.05007	-1.0912	9	0.87932	D	0	-2.9469	9.3749	0.38277	0.417:0.4484:0.1345:0.0	rs12074374;rs52791125;rs56770384;rs12074374	952;505	B1ANS9;D1MPS4	WDR64_HUMAN;.	W	952;785;556	ENSP00000355510:R952W;ENSP00000402446:R785W;ENSP00000406656:R556W	ENSP00000355510:R952W	R	+	1	2	WDR64	240017952	0.148000	0.22702	0.856000	0.33681	0.989000	0.77384	0.373000	0.20484	0.339000	0.23719	-0.134000	0.14843	CGG	C|0.837;T|0.163	0.163	strong		0.363	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625	
RNF157	114804	hgsc.bcm.edu	37	17	74152366	74152366	+	Silent	SNP	A	A	G	rs881502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:74152366A>G	ENST00000269391.6	-	14	1582	c.1450T>C	c.(1450-1452)Ttg>Ctg	p.L484L	RNF157-AS1_ENST00000585542.1_RNA|RNF157-AS1_ENST00000590137.1_RNA|RNF157-AS1_ENST00000586661.1_RNA|RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000592748.1_RNA|RNF157_ENST00000319945.6_Silent_p.L484L	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	484	Ser-rich.						zinc ion binding (GO:0008270)	p.L1087L(1)		breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			GATGACGACAAGGTGAGATTC	0.557													A|||	1558	0.311102	0.2572	0.3977	5008	,	,		22760	0.2163		0.3767	False		,,,				2504	0.3528				p.L484L	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											RNF157,NS,carcinoma,0,1	RNF157	66	1	1	Substitution - coding silent(1)	stomach(1)	c.T1450C						PASS	.	A		1180,3226	415.9+/-337.4	164,852,1187	126.0	109.0	115.0		1450	-8.4	0.2	17	dbSNP_86	115	3098,5502	473.0+/-368.5	575,1948,1777	no	coding-synonymous	RNF157	NM_052916.2		739,2800,2964	GG,GA,AA		36.0233,26.7817,32.8925		484/680	74152366	4278,8728	2203	4300	6503	SO:0001819	synonymous_variant	114804	exon14			ACGACAAGGTGAG	AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"""RING-type (C3HC4) zinc fingers"""	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.1450T>C	17.37:g.74152366A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_052916	Q8NB72|Q96N56	Silent	SNP	ENST00000269391.6	37	CCDS32740.1																																																																																			A|0.685;G|0.315	0.315	strong		0.557	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732	
TREML2	79865	hgsc.bcm.edu	37	6	41166017	41166017	+	Missense_Mutation	SNP	C	C	T	rs77093113	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41166017C>T	ENST00000483722.1	-	2	391	c.206G>A	c.(205-207)cGa>cAa	p.R69Q		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	69	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					CACCCAGACTCGGGCAAAGCC	0.572																																					p.R69Q		Atlas-SNP	.											TREML2,caecum,carcinoma,0,2	TREML2	41	2	0			c.G206A						scavenged	.						126.0	124.0	125.0					6																	41166017		2203	4300	6503	SO:0001583	missense	79865	exon2			CAGACTCGGGCAA	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.206G>A	6.37:g.41166017C>T	ENSP00000418767:p.Arg69Gln	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	104	7	0.0673077	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	15.90	2.968589	0.53614	.	.	ENSG00000112195	ENST00000483722	T	0.64991	-0.13	4.75	4.75	0.60458	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.129603	0.32563	N	0.005924	T	0.66567	0.2802	L	0.60455	1.87	0.26861	N	0.967955	D	0.89917	1.0	D	0.91635	0.999	T	0.60352	-0.7280	10	0.48119	T	0.1	-23.6018	13.6225	0.62144	0.0:1.0:0.0:0.0	.	69	Q5T2D2	TRML2_HUMAN	Q	69	ENSP00000418767:R69Q	ENSP00000418767:R69Q	R	-	2	0	TREML2	41273995	0.203000	0.23435	0.325000	0.25375	0.013000	0.08279	3.388000	0.52509	2.344000	0.79699	0.563000	0.77884	CGA	C|0.995;T|0.005	0.005	strong		0.572	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
RARS	5917	hgsc.bcm.edu	37	5	167919726	167919726	+	Silent	SNP	A	A	G	rs2305727	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:167919726A>G	ENST00000231572.3	+	3	297	c.243A>G	c.(241-243)caA>caG	p.Q81Q	RARS_ENST00000538719.1_5'UTR	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	81					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		GCCGCCTACAAGAGGTCTTTG	0.408													A|||	372	0.0742812	0.0091	0.0908	5008	,	,		18589	0.0645		0.1799	False		,,,				2504	0.0521				p.Q81Q		Atlas-SNP	.											RARS,NS,carcinoma,+1,1	RARS	58	1	0			c.A243G						PASS	.	A		160,4246	108.2+/-146.6	2,156,2045	117.0	117.0	117.0		243	-4.8	0.0	5	dbSNP_100	117	1627,6973	300.5+/-305.0	162,1303,2835	no	coding-synonymous	RARS	NM_002887.3		164,1459,4880	GG,GA,AA		18.9186,3.6314,13.7398		81/661	167919726	1787,11219	2203	4300	6503	SO:0001819	synonymous_variant	5917	exon3			CCTACAAGAGGTC	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.243A>G	5.37:g.167919726A>G		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	177	174	0.983051	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	37	CCDS4367.1																																																																																			A|0.881;G|0.119	0.119	strong		0.408	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
C1orf94	84970	hgsc.bcm.edu	37	1	34663208	34663208	+	Missense_Mutation	SNP	C	C	G	rs1382602	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:34663208C>G	ENST00000488417.1	+	2	823	c.703C>G	c.(703-705)Caa>Gaa	p.Q235E	C1orf94_ENST00000373374.3_Missense_Mutation_p.Q45E	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	235			Q -> E (in dbSNP:rs1382602). {ECO:0000269|PubMed:15489334}.							central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				CTCCAACTTGCAAGTCAGCAA	0.542													G|||	1903	0.379992	0.7632	0.3617	5008	,	,		20334	0.1409		0.2376	False		,,,				2504	0.2679				p.Q235E		Atlas-SNP	.											.	C1orf94	156	.	0			c.C703G						PASS	.	G	GLU/GLN,GLU/GLN	2938,1468	470.7+/-355.8	991,956,256	85.0	76.0	79.0		703,133	3.1	0.5	1	dbSNP_88	79	2284,6316	707.0+/-405.6	317,1650,2333	yes	missense,missense	C1orf94	NM_001134734.1,NM_032884.3	29,29	1308,2606,2589	GG,GC,CC		26.5581,33.3182,40.1507	benign,benign	235/599,45/409	34663208	5222,7784	2203	4300	6503	SO:0001583	missense	84970	exon2			AACTTGCAAGTCA	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.703C>G	1.37:g.34663208C>G	ENSP00000435634:p.Gln235Glu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	108	60	0.555556	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	37	CCDS44108.1	752	0.3443223443223443	378	0.7682926829268293	128	0.35359116022099446	72	0.1258741258741259	174	0.22955145118733508	G	0.004	-2.343661	0.00222	0.666818	0.265581	ENSG00000142698	ENST00000373374;ENST00000488417	T;T	0.17528	2.27;2.27	4.98	3.09	0.35607	.	0.320719	0.26979	N	0.021522	T	0.00012	0.0000	N	0.00210	-1.845	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33650	-0.9860	9	0.02654	T	1	-10.8271	4.6061	0.12378	0.1965:0.1836:0.6199:0.0	rs1382602;rs3795413;rs17845123;rs17857923;rs52817485;rs61292196;rs1382602	235	Q6P1W5	CA094_HUMAN	E	45;235	ENSP00000362472:Q45E;ENSP00000435634:Q235E	ENSP00000362472:Q45E	Q	+	1	0	C1orf94	34435795	0.977000	0.34250	0.525000	0.27900	0.047000	0.14425	1.778000	0.38614	0.516000	0.28340	-0.215000	0.12644	CAA	C|0.612;G|0.387	0.387	strong		0.542	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
RPA4	29935	hgsc.bcm.edu	37	X	96139406	96139406	+	Missense_Mutation	SNP	G	G	A	rs2642219	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:96139406G>A	ENST00000373040.3	+	1	500	c.97G>A	c.(97-99)Gct>Act	p.A33T	DIAPH2_ENST00000373054.4_Intron|DIAPH2_ENST00000355827.4_Intron|DIAPH2_ENST00000373061.3_Intron|DIAPH2_ENST00000373049.4_Intron|DIAPH2_ENST00000324765.8_Intron	NM_013347.4	NP_037479.1	Q13156	RFA4_HUMAN	replication protein A4, 30kDa	33			A -> T (in dbSNP:rs2642219). {ECO:0000269|Ref.3}.		DNA damage checkpoint (GO:0000077)|DNA recombination (GO:0006310)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)	DNA replication factor A complex (GO:0005662)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	13						TGCAACTCCTGCTATTAAGAC	0.493								Other identified genes with known or suspected DNA repair function					G|||	1517	0.401854	0.5076	0.2896	3775	,	,		14948	0.2837		0.2087	False		,,,				2504	0.1524				p.A33T		Atlas-SNP	.											.	RPA4	29	.	0			c.G97A	GRCh37	CM076485	RPA4	M	rs2642219	PASS	.	G	,,THR/ALA	2440,1395		657,774,352,201,219	141.0	113.0	122.0		,,97	1.3	0.0	X	dbSNP_100	122	2002,4726		212,1019,559,1197,1313	yes	intron,intron,missense	DIAPH2,RPA4	NM_006729.4,NM_007309.3,NM_013347.4	,,58	869,1793,911,1398,1532	AA,AG,A,GG,G		29.7562,36.3755,42.0524	,,benign	,,33/262	96139406	4442,6121	2203	4300	6503	SO:0001583	missense	29935	exon1			ACTCCTGCTATTA	U24186	CCDS35345.1	Xq21	2010-04-09	2010-04-09		ENSG00000204086	ENSG00000204086			30305	protein-coding gene	gene with protein product		300767	"""replication protein A4, 34kDa"""			7760808	Standard	NM_013347		Approved	HSU24186	uc004efv.4	Q13156	OTTHUMG00000021987	ENST00000373040.3:c.97G>A	X.37:g.96139406G>A	ENSP00000362131:p.Ala33Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	121	9	0.0743802	NM_013347	Q3SY03	Missense_Mutation	SNP	ENST00000373040.3	37	CCDS35345.1	723	0.4358047016274864	183	0.5319767441860465	70	0.2517985611510791	123	0.2942583732057416	105	0.1590909090909091	G	5.102	0.204401	0.09704	0.636245	0.297562	ENSG00000204086	ENST00000373040	T	0.18502	2.21	3.17	1.31	0.21738	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.27498	0.18	B	0.21546	0.035	T	0.28427	-1.0044	8	0.62326	D	0.03	-14.3524	3.8015	0.08760	0.1496:0.2501:0.6003:0.0	rs2642219;rs3747348;rs17328529;rs52816515;rs57433190;rs2642219	33	Q13156	RFA4_HUMAN	T	33	ENSP00000362131:A33T	ENSP00000362131:A33T	A	+	1	0	RPA4	96026062	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.878000	0.28126	0.213000	0.20722	-0.191000	0.12829	GCT	G|0.556;0|0.014	.	strong		0.493	RPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057464.1	NM_013347	
HELZ2	85441	hgsc.bcm.edu	37	20	62196182	62196182	+	Silent	SNP	G	G	C	rs3810488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62196182G>C	ENST00000467148.1	-	8	4062	c.3993C>G	c.(3991-3993)gcC>gcG	p.A1331A	HELZ2_ENST00000427522.2_Silent_p.A762A	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1331					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CTCGGCGGCCGGCAACCCGGC	0.657													G|||	1052	0.210064	0.0068	0.085	5008	,	,		15542	0.5288		0.1759	False		,,,				2504	0.2802				p.A1331A		Atlas-SNP	.											PRIC285,NS,carcinoma,0,1	.	.	1	0			c.C3993G						PASS	.	G	,	191,4211		6,179,2016	30.0	34.0	33.0		3993,2286	-8.9	0.0	20	dbSNP_107	33	1448,7140		123,1202,2969	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	129,1381,4985	CC,CG,GG		16.8607,4.3389,12.6174	,	1331/2650,762/2081	62196182	1639,11351	2201	4294	6495	SO:0001819	synonymous_variant	85441	exon9			GCGGCCGGCAACC	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.3993C>G	20.37:g.62196182G>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	159	79	0.496855	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			A|0.001;C|0.168;G|0.831	0.168	strong		0.657	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
TNRC6A	27327	hgsc.bcm.edu	37	16	24801737	24801737	+	Missense_Mutation	SNP	G	G	A	rs6497759	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:24801737G>A	ENST00000395799.3	+	6	1903	c.1774G>A	c.(1774-1776)Gca>Aca	p.A592T	TNRC6A_ENST00000315183.7_Missense_Mutation_p.A592T	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	592	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.|Sufficient for interaction with AGO2.		A -> T (in dbSNP:rs6497759).		cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		TGGAAATGGCGCAAATTCTGG	0.483													G|||	800	0.159744	0.1974	0.1455	5008	,	,		21893	0.126		0.162	False		,,,				2504	0.1513				p.A592T		Atlas-SNP	.											.	TNRC6A	171	.	0			c.G1774A						PASS	.	G	THR/ALA	819,3575	325.9+/-299.3	73,673,1451	95.0	94.0	94.0		1774	1.2	0.6	16	dbSNP_116	94	1643,6957	302.5+/-306.0	156,1331,2813	yes	missense	TNRC6A	NM_014494.2	58	229,2004,4264	AA,AG,GG		19.1047,18.6391,18.9472	benign	592/1963	24801737	2462,10532	2197	4300	6497	SO:0001583	missense	27327	exon6			AATGGCGCAAATT	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.1774G>A	16.37:g.24801737G>A	ENSP00000379144:p.Ala592Thr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	176	92	0.522727	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	304	0.1391941391941392	80	0.16260162601626016	55	0.15193370165745856	59	0.10314685314685315	110	0.14511873350923482	G	0.006	-2.114307	0.00349	0.186391	0.191047	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.11169	2.8;2.8	5.66	1.22	0.21188	.	0.346332	0.32134	N	0.006527	T	0.00012	0.0000	N	0.11427	0.14	0.41321	P	0.012826000000000004	P;P;P	0.42871	0.709;0.792;0.688	B;B;B	0.24974	0.057;0.043;0.028	T	0.48614	-0.9020	9	0.12103	T	0.63	-2.3485	6.1035	0.20061	0.0692:0.2501:0.5514:0.1293	rs6497759;rs52832662;rs59562937;rs6497759	339;592;592	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	T	592	ENSP00000326900:A592T;ENSP00000379144:A592T	ENSP00000326900:A592T	A	+	1	0	TNRC6A	24709238	0.997000	0.39634	0.630000	0.29268	0.014000	0.08584	3.886000	0.56190	0.314000	0.23086	-0.499000	0.04595	GCA	G|0.839;A|0.161	0.161	strong		0.483	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
TNRC6B	23112	hgsc.bcm.edu	37	22	40552119	40552119	+	Splice_Site	SNP	G	G	A	rs9611280	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:40552119G>A	ENST00000301923.9	+	4	348	c.46G>A	c.(46-48)Gtg>Atg	p.V16M	TNRC6B_ENST00000402203.1_Splice_Site_p.V16M	NM_001024843.1	NP_001020014.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	0	Interaction with argonaute proteins.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|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)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						GCCTTTGCAGGTGGAACAGGA	0.493													G|||	173	0.0345447	0.0068	0.0476	5008	,	,		21118	0.0		0.0934	False		,,,				2504	0.0378				p.V16M		Atlas-SNP	.											TNRC6B_ENST00000301923,lymph_node,lymphoid_neoplasm,0,1	TNRC6B	195	1	0			c.G46A						PASS	.	G	MET/VAL	78,4016		1,76,1970	67.0	67.0	67.0		46	3.4	1.0	22	dbSNP_119	67	875,7515		39,797,3359	yes	missense-near-splice	TNRC6B	NM_001024843.1	21	40,873,5329	AA,AG,GG		10.4291,1.9052,7.6338		16/1030	40552119	953,11531	2047	4195	6242	SO:0001630	splice_region_variant	23112	exon4			TTGCAGGTGGAAC	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"""Trinucleotide (CAG) repeat containing"""	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000301923.9:c.46-1G>A	22.37:g.40552119G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_001024843	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Missense_Mutation	SNP	ENST00000301923.9	37	CCDS46712.1	105	0.04807692307692308	5	0.01016260162601626	21	0.058011049723756904	0	0.0	79	0.10422163588390501	G	14.63	2.593253	0.46214	0.019052	0.104291	ENSG00000100354	ENST00000441751;ENST00000301923;ENST00000402203	T;T	0.36878	1.23;1.23	5.52	3.44	0.39384	.	0.812716	0.09400	U	0.807347	T	0.00552	0.0018	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13737	-1.0498	8	.	.	.	.	5.8592	0.18736	0.3051:0.0:0.6949:0.0	rs9611280;rs52808489;rs61442552;rs9611280	16	Q9UPQ9-2	.	M	16	ENSP00000306759:V16M;ENSP00000384795:V16M	.	V	+	1	0	TNRC6B	38882065	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.007000	0.49536	1.340000	0.45581	0.650000	0.86243	GTG	G|0.943;A|0.057	0.057	strong		0.493	TNRC6B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321393.1		Missense_Mutation
TNS1	7145	hgsc.bcm.edu	37	2	218762616	218762616	+	Missense_Mutation	SNP	C	C	T	rs41272679	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:218762616C>T	ENST00000171887.4	-	6	525	c.73G>A	c.(73-75)Gtc>Atc	p.V25I	TNS1_ENST00000430930.1_Missense_Mutation_p.V25I|TNS1_ENST00000419504.1_Missense_Mutation_p.V25I|TNS1_ENST00000310858.6_Missense_Mutation_p.V56I	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	25	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GGGAAGGAGACAGCGATGATC	0.577													C|||	75	0.014976	0.0015	0.013	5008	,	,		22420	0.0		0.0517	False		,,,				2504	0.0123				p.V25I		Atlas-SNP	.											.	TNS1	251	.	0			c.G73A						PASS	.	C	ILE/VAL	26,4380	32.6+/-62.9	0,26,2177	180.0	136.0	151.0		73	5.4	1.0	2	dbSNP_127	151	320,8280	113.9+/-173.9	7,306,3987	yes	missense	TNS1	NM_022648.4	29	7,332,6164	TT,TC,CC		3.7209,0.5901,2.6603	possibly-damaging	25/1736	218762616	346,12660	2203	4300	6503	SO:0001583	missense	7145	exon6			AGGAGACAGCGAT	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.73G>A	2.37:g.218762616C>T	ENSP00000171887:p.Val25Ile	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	176	80	0.454545	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	43	0.019688644688644688	0	0.0	5	0.013812154696132596	0	0.0	38	0.05013192612137203	C	20.6	4.020220	0.75275	0.005901	0.037209	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554;ENST00000310858;ENST00000413280;ENST00000439083;ENST00000423413	D;D;D;D;D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.68	5.42	5.42	0.78866	Phosphatase tensin type (1);	0.061386	0.64402	D	0.000004	D	0.91968	0.7456	L	0.54965	1.715	0.54753	D	0.999985	P;B;P;D;P;P	0.57257	0.894;0.391;0.879;0.979;0.894;0.894	B;B;P;P;B;B	0.57776	0.437;0.28;0.688;0.827;0.437;0.437	D	0.88401	0.3015	10	0.54805	T	0.06	.	19.4123	0.94679	0.0:1.0:0.0:0.0	rs41272679	25;79;56;25;25;25	B2RU35;A1L0S7;Q6IPI5;Q9HBL0;E9PGF5;E9PF55	.;.;.;TENS1_HUMAN;.;.	I	25;25;25;150;93;56;25;25;90	ENSP00000171887:V25I;ENSP00000408724:V25I;ENSP00000406016:V25I;ENSP00000405460:V150I;ENSP00000400383:V93I;ENSP00000308321:V56I;ENSP00000395615:V25I;ENSP00000404477:V25I;ENSP00000411349:V90I	ENSP00000171887:V25I	V	-	1	0	TNS1	218470861	0.998000	0.40836	1.000000	0.80357	0.858000	0.48976	3.830000	0.55768	2.819000	0.97034	0.655000	0.94253	GTC	C|0.975;G|0.000;T|0.025	0.025	strong		0.577	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
TPSB2	64499	hgsc.bcm.edu	37	16	1279714	1279714	+	RNA	SNP	A	A	G	rs192643610	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1279714A>G	ENST00000339687.6	-	0	108				TPSB2_ENST00000445910.1_RNA|TPSB2_ENST00000430512.2_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				AACGATGCCCACTCGCTGCAG	0.711																																					p.V29A		Atlas-SNP	.											TPSB2,rectum,carcinoma,0,1	TPSB2	8	1	0			c.T86C						scavenged	.						25.0	32.0	29.0					16																	1279714		2180	4295	6475			64499	exon3			ATGCCCACTCGCT	AF099143		16p13.3	2009-11-20	2009-11-18		ENSG00000197253	ENSG00000197253			14120	protein-coding gene	gene with protein product	"""tryptase beta II"", ""tryptase beta III"""	191081	"""tryptase beta 2"""			19748655	Standard	NM_024164		Approved		uc002cky.3	P20231	OTTHUMG00000155926		16.37:g.1279714A>G		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	74	25	0.337838	NM_024164	D2E6S0|D2E6S2|O95827|Q15664|Q9UQI6|Q9UQI7	Missense_Mutation	SNP	ENST00000339687.6	37		171	0.0782967032967033	39	0.07926829268292683	28	0.07734806629834254	44	0.07692307692307693	60	0.079155672823219	a	8.603	0.887339	0.17540	.	.	ENSG00000197253	ENST00000430512	T	0.81078	-1.45	4.02	-8.04	0.01110	.	1.382050	0.04868	N	0.445430	T	0.05090	0.0136	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32375	-0.9909	9	0.07644	T	0.81	.	3.7543	0.08579	0.5801:0.1008:0.1165:0.2027	.	29	P20231	TRYB2_HUMAN	A	29	ENSP00000412409:V29A	ENSP00000412409:V29A	V	-	2	0	TPSB2	1219715	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.520000	0.00221	-2.364000	0.00607	-1.306000	0.01317	GTG	A|0.924;G|0.076	0.076	strong		0.711	TPSB2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000342364.1	NM_024164	
PPEF2	5470	hgsc.bcm.edu	37	4	76805745	76805745	+	Splice_Site	SNP	A	A	G	rs17220803	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:76805745A>G	ENST00000286719.7	-	8	1103		c.e8+1			NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2						detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TTTGACTTGTACCGTAAGTTC	0.348													A|||	92	0.0183706	0.0023	0.0317	5008	,	,		19043	0.0		0.0547	False		,,,				2504	0.0123				.	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.746+2T>C						PASS	.	A		43,4363	45.3+/-79.5	1,41,2161	159.0	163.0	161.0			4.8	1.0	4	dbSNP_123	161	372,8228	122.7+/-181.7	5,362,3933	yes	splice-5	PPEF2	NM_006239.2		6,403,6094	GG,GA,AA		4.3256,0.9759,3.1908			76805745	415,12591	2203	4300	6503	SO:0001630	splice_region_variant	5470	exon9			ACTTGTACCGTAA	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""EF-hand domain containing"""	9244	protein-coding gene	gene with protein product	"""protein phosphatase 7, catalytic subunit, beta isozyme"""	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.746+1T>C	4.37:g.76805745A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_006239	O14831	Splice_Site	SNP	ENST00000286719.7	37	CCDS34013.1	52	0.023809523809523808	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	37	0.048812664907651716	A	17.72	3.459889	0.63401	0.009759	0.043256	ENSG00000156194	ENST00000286719;ENST00000337500	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4445	0.55643	1.0:0.0:0.0:0.0	rs17220803;rs17220803	.	.	.	.	-1	.	.	.	-	.	.	PPEF2	77024769	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	8.370000	0.90120	2.034000	0.60081	0.533000	0.62120	.	A|0.967;G|0.033	0.033	strong		0.348	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239	Intron
RPS16	6217	hgsc.bcm.edu	37	19	39923952	39923952	+	Silent	SNP	G	G	A	rs17627	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:39923952G>A	ENST00000251453.3	-	5	454	c.402C>T	c.(400-402)ggC>ggT	p.G134G	RPS16_ENST00000599539.1_3'UTR|RPS16_ENST00000339471.4_3'UTR|RPS16_ENST00000601655.1_Silent_p.G117G	NM_001020.4	NP_001011.1	P62249	RS16_HUMAN	ribosomal protein S16	134					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|large_intestine(2)|lung(2)|skin(2)	7	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;4.14e-26)|all cancers(26;2.68e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GGGCACCAGGGCCTCCAAACT	0.488													G|||	1206	0.240815	0.4501	0.1801	5008	,	,		18656	0.0764		0.1839	False		,,,				2504	0.229				p.G134G		Atlas-SNP	.											.	RPS16	12	.	0			c.C402T						PASS	.	G		1752,2654	513.4+/-368.3	341,1070,792	60.0	63.0	62.0		402	-4.5	0.9	19	dbSNP_63	62	1605,6995	294.8+/-302.1	160,1285,2855	no	coding-synonymous	RPS16	NM_001020.4		501,2355,3647	AA,AG,GG		18.6628,39.764,25.8112		134/147	39923952	3357,9649	2203	4300	6503	SO:0001819	synonymous_variant	6217	exon5			ACCAGGGCCTCCA	M60854	CCDS12535.1	19q13.1	2011-04-05				ENSG00000105193		"""S ribosomal proteins"""	10396	protein-coding gene	gene with protein product	"""40S ribosomal protein S16"""	603675				2016298, 9582194	Standard	XM_005259137		Approved	S16	uc002olk.3	P62249		ENST00000251453.3:c.402C>T	19.37:g.39923952G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	153	65	0.424837	NM_001020	B2RDD5|P17008	Silent	SNP	ENST00000251453.3	37	CCDS12535.1																																																																																			G|0.758;A|0.242	0.242	strong		0.488	RPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464511.1	NM_001020	
OR5M11	219487	hgsc.bcm.edu	37	11	56310356	56310356	+	Nonsense_Mutation	SNP	A	A	T	rs17547284	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56310356A>T	ENST00000528616.2	-	1	401	c.378T>A	c.(376-378)taT>taA	p.Y126*		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)	18						GCAGAGGGTCATATATGGCCA	0.483													A|||	214	0.0427316	0.0144	0.0504	5008	,	,		22419	0.001		0.0974	False		,,,				2504	0.0624				p.Y126X		Atlas-SNP	.											OR5M11,NS,carcinoma,-2,1	OR5M11	60	1	0			c.T378A						PASS	.	A	stop/TYR	122,4262	80.9+/-119.3	2,118,2072	57.0	60.0	59.0		378	-0.6	0.3	11	dbSNP_123	59	708,7876	170.3+/-221.5	35,638,3619	yes	stop-gained	OR5M11	NM_001005245.1		37,756,5691	TT,TA,AA		8.2479,2.7828,6.4004		126/306	56310356	830,12138	2192	4292	6484	SO:0001587	stop_gained	219487	exon1			AGGGTCATATATG	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"""GPCR / Class A : Olfactory receptors"""	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.378T>A	11.37:g.56310356A>T	ENSP00000432417:p.Tyr126*	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_001005245	B2RNL5|B2RNL7	Nonsense_Mutation	SNP	ENST00000528616.2	37	CCDS53629.1	94	0.04304029304029304	7	0.014227642276422764	16	0.04419889502762431	0	0.0	71	0.09366754617414248	A	10.48	1.360980	0.24684	0.027828	0.082479	ENSG00000255223	ENST00000528616	.	.	.	5.1	-0.628	0.11537	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	9.2036	0.37275	0.436:0.0:0.564:0.0	rs17547284;rs52832495;rs17547284	.	.	.	X	126	.	ENSP00000432417:Y126X	Y	-	3	2	OR5M11	56066932	0.000000	0.05858	0.294000	0.24946	0.247000	0.25773	-0.620000	0.05565	-0.268000	0.09312	-0.463000	0.05309	TAT	A|0.952;T|0.048	0.048	strong		0.483	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245	
ALPK3	57538	hgsc.bcm.edu	37	15	85382307	85382307	+	Missense_Mutation	SNP	G	G	A	rs34407151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:85382307G>A	ENST00000258888.5	+	4	1174	c.1007G>A	c.(1006-1008)cGc>cAc	p.R336H		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	336	Ig-like 1.		R -> H (in dbSNP:rs34407151). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CAGGGCAACCGCCACACACTG	0.582													G|||	27	0.00539137	0.0015	0.0058	5008	,	,		16839	0.0		0.0129	False		,,,				2504	0.0082				p.R336H		Atlas-SNP	.											.	ALPK3	289	.	0			c.G1007A						PASS	.	G	HIS/ARG	17,4389	22.3+/-47.3	0,17,2186	49.0	39.0	42.0		1007	4.9	1.0	15	dbSNP_126	42	120,8478	62.4+/-124.4	1,118,4180	yes	missense	ALPK3	NM_020778.4	29	1,135,6366	AA,AG,GG		1.3957,0.3858,1.0535	probably-damaging	336/1908	85382307	137,12867	2203	4299	6502	SO:0001583	missense	57538	exon4			GCAACCGCCACAC	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.1007G>A	15.37:g.85382307G>A	ENSP00000258888:p.Arg336His	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	15	0.006868131868131868	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	10	0.013192612137203167	G	18.96	3.732990	0.69189	0.003858	0.013957	ENSG00000136383	ENST00000258888	T	0.68025	-0.3	4.89	4.89	0.63831	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.308968	0.31438	N	0.007658	T	0.68513	0.3009	L	0.45228	1.405	0.32666	N	0.517502	D	0.89917	1.0	D	0.67231	0.95	T	0.78770	-0.2074	10	0.56958	D	0.05	-8.4768	15.5548	0.76184	0.0:0.0:1.0:0.0	rs34407151	336	Q96L96	ALPK3_HUMAN	H	336	ENSP00000258888:R336H	ENSP00000258888:R336H	R	+	2	0	ALPK3	83183311	0.443000	0.25641	0.990000	0.47175	0.998000	0.95712	2.146000	0.42216	2.266000	0.75297	0.491000	0.48974	CGC	G|0.990;A|0.010	0.010	strong		0.582	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
FAM86B1	85002	hgsc.bcm.edu	37	8	12044010	12044010	+	Missense_Mutation	SNP	C	C	T	rs201876260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:12044010C>T	ENST00000448228.2	-	5	540	c.491G>A	c.(490-492)cGa>cAa	p.R164Q	FAM86B1_ENST00000534520.1_Intron|FAM86B1_ENST00000321602.8_Intron|FAM86B1_ENST00000533513.1_3'UTR|FAM86B1_ENST00000533852.2_Missense_Mutation_p.R198Q	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	164										kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		GACATTCCCTCGGAGCTGCTC	0.617																																					p.R164Q		Atlas-SNP	.											FAM86B1,NS,carcinoma,0,1	FAM86B1	7	1	0			c.G491A						scavenged	.						39.0	43.0	42.0					8																	12044010		1489	2646	4135	SO:0001583	missense	85002	exon5			TTCCCTCGGAGCT	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.491G>A	8.37:g.12044010C>T	ENSP00000407067:p.Arg164Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	114	20	0.175439	NM_001083537		Missense_Mutation	SNP	ENST00000448228.2	37	CCDS59512.1	.	.	.	.	.	.	.	.	.	.	-	11.09	1.537041	0.27475	.	.	ENSG00000186523	ENST00000431227;ENST00000448228;ENST00000526708	T	0.20881	2.04	1.17	1.17	0.20885	.	.	.	.	.	T	0.12689	0.0308	L	0.33624	1.015	0.80722	D	1	B;B	0.32573	0.376;0.123	B;B	0.28385	0.089;0.046	T	0.13124	-1.0521	9	0.24483	T	0.36	.	8.2654	0.31810	0.0:1.0:0.0:0.0	.	164;198	Q8N7N1;E9PN63	F86B1_HUMAN;.	Q	198;164;198	ENSP00000407067:R164Q	ENSP00000444227:R198Q	R	-	2	0	FAM86B1	12081419	0.000000	0.05858	0.202000	0.23494	0.276000	0.26787	-0.432000	0.06956	0.950000	0.37743	0.173000	0.16961	CGA	C|0.983;T|0.016	0.016	strong		0.617	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916	
NEU4	129807	hgsc.bcm.edu	37	2	242758203	242758203	+	Silent	SNP	T	T	C	rs2293763	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242758203T>C	ENST00000391969.2	+	5	1995	c.1284T>C	c.(1282-1284)gcT>gcC	p.A428A	NEU4_ENST00000405370.1_Silent_p.A428A|NEU4_ENST00000325935.6_Silent_p.A441A|NEU4_ENST00000404257.1_Silent_p.A440A|NEU4_ENST00000407683.1_Silent_p.A428A	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	428					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		TCGGGCCGGCTCCTGAGGGGG	0.652													C|||	2229	0.445088	0.4887	0.3458	5008	,	,		12581	0.4187		0.3847	False		,,,				2504	0.546				p.A441A		Atlas-SNP	.											NEU4,NS,carcinoma,0,1	NEU4	39	1	0			c.T1323C						scavenged	.		,,,,	1780,2412		436,908,752	11.0	15.0	14.0		1323,1284,1284,1284,1320	-6.6	0.0	2	dbSNP_100	14	2654,5640		489,1676,1982	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	,,,,	925,2584,2734	CC,CT,TT		31.999,42.4618,35.5118	,,,,	441/498,428/485,428/485,428/485,440/497	242758203	4434,8052	2096	4147	6243	SO:0001819	synonymous_variant	129807	exon4			GCCGGCTCCTGAG	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.1284T>C	2.37:g.242758203T>C		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	122	54	0.442623	NM_001167599	A8K056|J3KNJ5|Q96D64	Silent	SNP	ENST00000391969.2	37	CCDS54442.1																																																																																			T|0.640;C|0.360	0.360	strong		0.652	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
R3HCC1	203069	hgsc.bcm.edu	37	8	23148978	23148978	+	Silent	SNP	G	G	T	rs2272760	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:23148978G>T	ENST00000411463.1	+	6	1077	c.1077G>T	c.(1075-1077)gtG>gtT	p.V359V	R3HCC1_ENST00000265806.6_Silent_p.V132V|R3HCC1_ENST00000518454.1_Silent_p.V132V|R3HCC1_ENST00000522012.1_3'UTR			Q9Y3T6	R3HC1_HUMAN	R3H domain and coiled-coil containing 1	359							nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)			central_nervous_system(1)|skin(2)	3						TTGCCCACGTGGTAGAGATCT	0.537													G|||	629	0.125599	0.0295	0.2133	5008	,	,		21083	0.0536		0.2803	False		,,,				2504	0.1084				p.V132V		Atlas-SNP	.											.	R3HCC1	11	.	0			c.G396T						PASS	.	G		89,1295		6,77,609	127.0	114.0	118.0		396	5.9	1.0	8	dbSNP_100	118	884,2298		116,652,823	no	coding-synonymous	R3HCC1	NM_001136108.1		122,729,1432	TT,TG,GG		27.7813,6.4306,21.3097		132/254	23148978	973,3593	692	1591	2283	SO:0001819	synonymous_variant	203069	exon5			CCACGTGGTAGAG		CCDS47826.1	8p21.3	2012-05-23		2005-11-20	ENSG00000104679	ENSG00000104679			27329	protein-coding gene	gene with protein product						12477932	Standard	XM_005273427		Approved	DKFZp564N123	uc003xdf.3	Q9Y3T6	OTTHUMG00000163786	ENST00000411463.1:c.1077G>T	8.37:g.23148978G>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	129	59	0.457364	NM_001136108	B7ZLI1	Silent	SNP	ENST00000411463.1	37																																																																																				G|0.820;T|0.180	0.180	strong		0.537	R3HCC1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001136108	
TGOLN2	10618	hgsc.bcm.edu	37	2	85549874	85549874	+	Missense_Mutation	SNP	A	A	G	rs3637	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:85549874A>G	ENST00000409232.3	-	4	1377	c.1316T>C	c.(1315-1317)tTt>tCt	p.F439S	TGOLN2_ENST00000398263.2_Intron|TGOLN2_ENST00000377386.3_Intron|TGOLN2_ENST00000409015.1_Missense_Mutation_p.F453L|TGOLN2_ENST00000282120.2_Intron			O43493	TGON2_HUMAN	trans-golgi network protein 2	444						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											ACTTAGGGGAAAAAAGATCTT	0.378													A|||	1944	0.388179	0.1188	0.5951	5008	,	,		18679	0.504		0.3817	False		,,,				2504	0.4928				p.F439S		Atlas-SNP	.											.	TGOLN2	32	.	0			c.T1316C						PASS	.	A	LEU/PHE,SER/PHE,,	553,3199		50,453,1373	61.0	59.0	59.0		1357,1316,,	-8.3	0.0	2	dbSNP_36	59	3146,5052		612,1922,1565	yes	missense,missense,intron,intron	TGOLN2	NM_001206840.1,NM_001206841.1,NM_001206844.1,NM_006464.3	22,155,,	662,2375,2938	GG,GA,AA		38.3752,14.7388,30.954	,,,	453/481,439/454,,	85549874	3699,8251	1876	4099	5975	SO:0001583	missense	10618	exon4			AGGGGAAAAAAGA	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"""trans-Golgi network protein (46, 48, 51kD isoforms)"""	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.1316T>C	2.37:g.85549874A>G	ENSP00000386443:p.Phe439Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Missense_Mutation	SNP	ENST00000409232.3	37	CCDS56126.1	793|793	0.3630952380952381|0.3630952380952381	49|49	0.09959349593495935|0.09959349593495935	190|190	0.5248618784530387|0.5248618784530387	278|278	0.486013986013986|0.486013986013986	276|276	0.3641160949868074|0.3641160949868074	A|A	9.461|9.461	1.093162|1.093162	0.20471|0.20471	0.147388|0.147388	0.383752|0.383752	ENSG00000152291|ENSG00000152291	ENST00000409015|ENST00000409232	T|T	0.05786|0.11385	3.39|2.78	4.17|4.17	-8.34|-8.34	0.00988|0.00988	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.37337|0.37337	-0.9710|-0.9710	5|5	0.02654|0.07482	T|T	1|0.82	.|.	0.9547|0.9547	0.01383|0.01383	0.1483:0.2996:0.2248:0.3273|0.1483:0.2996:0.2248:0.3273	rs3637;rs1578987;rs3637|rs3637;rs1578987;rs3637	.|.	.|.	.|.	L|S	453|439	ENSP00000387035:F453L|ENSP00000386443:F439S	ENSP00000387035:F453L|ENSP00000386443:F439S	F|F	-|-	1|2	0|0	TGOLN2|TGOLN2	85403385|85403385	.|.	.|.	0.000000|0.000000	0.03702|0.03702	0.208000|0.208000	0.24298|0.24298	.|.	.|.	-4.149000|-4.149000	0.00069|0.00069	0.533000|0.533000	0.62120|0.62120	TTC|TTT	A|0.637;G|0.363	0.363	strong		0.378	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464	
RASA4	10156	hgsc.bcm.edu	37	7	102246311	102246311	+	Missense_Mutation	SNP	T	T	C	rs11547189		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:102246311T>C	ENST00000262940.7	-	5	489	c.422A>G	c.(421-423)gAg>gGg	p.E141G	RP11-514P8.6_ENST00000519541.1_3'UTR|RASA4_ENST00000449970.2_Missense_Mutation_p.E141G|RASA4_ENST00000462172.1_Missense_Mutation_p.E69G|AC105052.1_ENST00000411396.1_RNA|RASA4_ENST00000461209.1_Missense_Mutation_p.E69G	NM_006989.5	NP_008920.5	O43374	RASL2_HUMAN	RAS p21 protein activator 4	141	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cellular response to calcium ion (GO:0071277)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			lung(1)|prostate(1)|urinary_tract(1)	3						TCACCTGGCCTCCAGCACAGA	0.687																																					p.E141G		Atlas-SNP	.											RASA4_ENST00000262940,NS,carcinoid-endocrine_tumour,0,2	RASA4	7	2	0			c.A422G						scavenged	.						5.0	4.0	5.0					7																	102246311		1956	3444	5400	SO:0001583	missense	10156	exon5			CTGGCCTCCAGCA	AB011110	CCDS5725.1, CCDS47674.1	7q22-q31.1	2008-12-05			ENSG00000105808	ENSG00000105808			23181	protein-coding gene	gene with protein product		607943				11448776	Standard	NM_001079877		Approved	KIAA0538, CAPRI, GAPL	uc003vae.3	O43374	OTTHUMG00000150383	ENST00000262940.7:c.422A>G	7.37:g.102246311T>C	ENSP00000262940:p.Glu141Gly	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	133	32	0.240602	NM_006989	O60286|Q14CQ4|Q86UW3|Q96QU0	Missense_Mutation	SNP	ENST00000262940.7	37	CCDS5725.1	.	.	.	.	.	.	.	.	.	.	t	18.93	3.728286	0.69074	.	.	ENSG00000105808	ENST00000262940;ENST00000461209;ENST00000449970;ENST00000541884;ENST00000462172;ENST00000522801;ENST00000520042	T;T;T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32	2.66	2.66	0.31614	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	3.132260	0.01073	N	0.004851	D	0.87791	0.6266	L	0.52905	1.665	0.43959	D	0.996631	D;D	0.69078	0.996;0.997	D;D	0.69824	0.922;0.966	T	0.77327	-0.2629	10	0.72032	D	0.01	.	9.2448	0.37518	0.0:0.0:0.0:1.0	.	141;141	O43374-2;O43374	.;RASL2_HUMAN	G	141;69;141;69;69;122;69	ENSP00000262940:E141G;ENSP00000420352:E69G;ENSP00000412876:E141G;ENSP00000438250:E69G;ENSP00000417395:E69G;ENSP00000430418:E122G;ENSP00000428732:E69G	ENSP00000262940:E141G	E	-	2	0	RASA4	102033379	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	6.241000	0.72369	1.503000	0.48686	0.423000	0.28283	GAG	.	.	weak		0.687	RASA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317900.3	NM_006989	
SOAT2	8435	hgsc.bcm.edu	37	12	53516993	53516993	+	Silent	SNP	C	C	T	rs35335316	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53516993C>T	ENST00000301466.3	+	13	1425	c.1365C>T	c.(1363-1365)gtC>gtT	p.V455V		NM_003578.3	NP_003569.1	O75908	SOAT2_HUMAN	sterol O-acyltransferase 2	455					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|intestinal cholesterol absorption (GO:0030299)|macrophage derived foam cell differentiation (GO:0010742)|very-low-density lipoprotein particle assembly (GO:0034379)	brush border (GO:0005903)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|transferase activity, transferring acyl groups (GO:0016746)			endometrium(5)|kidney(3)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	18					Hesperetin(DB01094)	TCTTCCTTGTCATTGGAGGTG	0.577													C|||	16	0.00319489	0.0008	0.0101	5008	,	,		17201	0.0		0.007	False		,,,				2504	0.001				p.V455V		Atlas-SNP	.											.	SOAT2	44	.	0			c.C1365T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	209.0	164.0	179.0		1365	1.6	0.1	12	dbSNP_126	179	70,8530	42.2+/-99.7	1,68,4231	no	coding-synonymous	SOAT2	NM_003578.3		1,72,6430	TT,TC,CC		0.814,0.0908,0.569		455/523	53516993	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	8435	exon13			CCTTGTCATTGGA	AF059203	CCDS8847.1	12q13.13	2012-09-20			ENSG00000167780	ENSG00000167780	2.3.1.26		11178	protein-coding gene	gene with protein product		601311				9756920	Standard	NM_003578		Approved	ACAT2	uc001sbv.3	O75908	OTTHUMG00000169774	ENST00000301466.3:c.1365C>T	12.37:g.53516993C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	202	96	0.475248	NM_003578	F5H7W4|I6L9H9|Q4VB99|Q4VBA1|Q96TD4|Q9UNR2	Silent	SNP	ENST00000301466.3	37	CCDS8847.1																																																																																			C|0.993;T|0.007	0.007	strong		0.577	SOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405817.1		
OR1S1	219959	hgsc.bcm.edu	37	11	57983194	57983194	+	Splice_Site	SNP	A	A	G	rs7103033	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57983194A>G	ENST00000309433.6	+	1	978	c.978A>G	c.(976-978)tgA>tgG	p.*326W		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	0						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				CTTCCCTTTGATGCCCTGGAC	0.413													A|||	2171	0.433506	0.2224	0.428	5008	,	,		20118	0.7619		0.3141	False		,,,				2504	0.5072				p.X326W		Atlas-SNP	.											.	OR1S1	139	.	0			c.A978G						PASS	.	A	TRP/stop	1064,3338	386.5+/-326.1	126,812,1263	132.0	132.0	132.0		978	2.6	0.0	11	dbSNP_116	132	2806,5784	442.8+/-360.2	476,1854,1965	no	stop-lost	OR1S1	NM_001004458.1		602,2666,3228	GG,GA,AA		32.6659,24.1708,29.7876		326/326	57983194	3870,9122	2201	4295	6496	SO:0001630	splice_region_variant	219959	exon1			CCTTTGATGCCCT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.975+1A>G	11.37:g.57983194A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	105	41	0.390476	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	903	0.41346153846153844	104	0.21138211382113822	150	0.4143646408839779	412	0.7202797202797203	237	0.31266490765171506	A	9.164	1.019495	0.19355	0.241708	0.326659	ENSG00000172774	ENST00000309433	.	.	.	2.61	2.61	0.31194	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.0192	0.24904	1.0:0.0:0.0:0.0	rs7103033;rs7103033	.	.	.	W	326	.	.	X	+	3	0	OR1S1	57739770	0.001000	0.12720	0.014000	0.15608	0.012000	0.07955	0.032000	0.13732	1.200000	0.43188	0.392000	0.25879	TGA	A|0.672;G|0.328	0.328	strong		0.413	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	Nonstop_Mutation
TBC1D32	221322	hgsc.bcm.edu	37	6	121642916	121642916	+	Silent	SNP	C	C	T	rs75082736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:121642916C>T	ENST00000398212.2	-	2	229	c.180G>A	c.(178-180)agG>agA	p.R60R	TBC1D32_ENST00000275159.6_Silent_p.R60R	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	60					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										CTATATGCTGCCTGAGGTATT	0.343													T|||	368	0.0734824	0.1021	0.1268	5008	,	,		18910	0.124		0.0109	False		,,,				2504	0.0092				p.R60R		Atlas-SNP	.											.	C6orf170	146	.	0			c.G180A						PASS	.	T		305,3359		13,279,1540	132.0	118.0	122.0		180	4.3	1.0	6	dbSNP_131	122	104,8102		0,104,3999	no	coding-synonymous	C6orf170	NM_152730.4		13,383,5539	TT,TC,CC		1.2674,8.3242,3.4457		60/1258	121642916	409,11461	1832	4103	5935	SO:0001819	synonymous_variant	221322	exon2			ATGCTGCCTGAGG	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.180G>A	6.37:g.121642916C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	152	82	0.539474	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																			C|0.944;T|0.056	0.056	strong		0.343	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
DNAJC17	55192	hgsc.bcm.edu	37	15	41068771	41068771	+	Missense_Mutation	SNP	T	T	G	rs79709714	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:41068771T>G	ENST00000220496.4	-	5	380	c.350A>C	c.(349-351)gAg>gCg	p.E117A		NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	117	Poly-Glu.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)		nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|skin(1)	6		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GCTCCGGCTCTCCTCTTCCTC	0.622													T|||	42	0.00838658	0.0	0.0173	5008	,	,		14514	0.0		0.0258	False		,,,				2504	0.0041				p.E117A		Atlas-SNP	.											.	DNAJC17	18	.	0			c.A350C						PASS	.	T	ALA/GLU	26,4380	34.3+/-65.2	1,24,2178	156.0	128.0	138.0		350	4.5	1.0	15	dbSNP_131	138	239,8361	95.9+/-157.7	1,237,4062	yes	missense	DNAJC17	NM_018163.2	107	2,261,6240	GG,GT,TT		2.7791,0.5901,2.0375	benign	117/305	41068771	265,12741	2203	4300	6503	SO:0001583	missense	55192	exon5			CGGCTCTCCTCTT	AK001496	CCDS10065.1	15q15.1	2014-02-12			ENSG00000104129	ENSG00000104129		"""Heat shock proteins / DNAJ (HSP40)"", ""RNA binding motif (RRM) containing"""	25556	protein-coding gene	gene with protein product						12477932	Standard	NM_018163		Approved	FLJ10634	uc001zms.2	Q9NVM6	OTTHUMG00000130065	ENST00000220496.4:c.350A>C	15.37:g.41068771T>G	ENSP00000220496:p.Glu117Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	69	57	0.826087	NM_018163		Missense_Mutation	SNP	ENST00000220496.4	37	CCDS10065.1	30	0.013736263736263736	0	0.0	6	0.016574585635359115	0	0.0	24	0.0316622691292876	T	10.51	1.369675	0.24771	0.005901	0.027791	ENSG00000104129	ENST00000220496	T	0.21191	2.02	4.46	4.46	0.54185	.	0.262954	0.42548	D	0.000681	T	0.06096	0.0158	L	0.55481	1.735	0.39777	D	0.972244	B	0.12630	0.006	B	0.10450	0.005	T	0.05550	-1.0878	10	0.10377	T	0.69	.	10.0697	0.42325	0.0:0.0:0.0:1.0	.	117	Q9NVM6	DJC17_HUMAN	A	117	ENSP00000220496:E117A	ENSP00000220496:E117A	E	-	2	0	DNAJC17	38856063	1.000000	0.71417	0.964000	0.40570	0.954000	0.61252	6.100000	0.71473	1.889000	0.54706	0.459000	0.35465	GAG	T|0.984;G|0.016	0.016	strong		0.622	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163	
NOTCH4	4855	hgsc.bcm.edu	37	6	32163799	32163799	+	Silent	SNP	T	T	C	rs8192579	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32163799T>C	ENST00000375023.3	-	30	5565	c.5427A>G	c.(5425-5427)caA>caG	p.Q1809Q	NOTCH4_ENST00000443903.2_Missense_Mutation_p.T186A|GPSM3_ENST00000375043.3_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1809					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						AGTGGTTACGTTGGTGAGCGA	0.716													T|||	422	0.0842652	0.0946	0.049	5008	,	,		14647	0.0556		0.0696	False		,,,				2504	0.1401				p.Q1809Q		Atlas-SNP	.											NOTCH4,rectum,carcinoma,0,3	NOTCH4	201	3	0			c.A5427G						PASS	.	T		213,2587		10,193,1197	10.0	12.0	11.0		5427	2.7	1.0	6	dbSNP_117	11	283,4995		7,269,2363	no	coding-synonymous	NOTCH4	NM_004557.3		17,462,3560	CC,CT,TT		5.3619,7.6071,6.1401		1809/2004	32163799	496,7582	1400	2639	4039	SO:0001819	synonymous_variant	4855	exon30			GTTACGTTGGTGA		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.5427A>G	6.37:g.32163799T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	37	14	0.378378	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1	157	0.07188644688644688	49	0.09959349593495935	19	0.052486187845303865	33	0.057692307692307696	56	0.07387862796833773	T	11.85	1.761797	0.31228	0.076071	0.053619	ENSG00000204301	ENST00000443903	T	0.69435	-0.4	4.71	2.66	0.31614	.	.	.	.	.	T	0.37489	0.1005	.	.	.	0.50313	P	1.3799999999997148E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.19257	-1.0311	7	0.66056	D	0.02	.	8.6674	0.34130	0.0:0.785:0.0:0.215	rs8192579;rs59212197;rs8192579	186	B4DFM3	.	A	186	ENSP00000398123:T186A	ENSP00000398123:T186A	T	-	1	0	NOTCH4	32271777	0.419000	0.25449	0.997000	0.53966	0.064000	0.16182	-0.336000	0.07863	0.539000	0.28788	-0.468000	0.05107	ACG	T|0.930;C|0.070	0.070	strong		0.716	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
DACT1	51339	hgsc.bcm.edu	37	14	59105188	59105188	+	Silent	SNP	C	C	T	rs2003021	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:59105188C>T	ENST00000335867.4	+	1	292	c.268C>T	c.(268-270)Ctg>Ttg	p.L90L	DACT1_ENST00000556859.1_Intron|DACT1_ENST00000395153.3_Silent_p.L90L|DACT1_ENST00000541264.2_5'Flank|DACT1_ENST00000555845.1_Intron			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	90					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						TGGGGAGCTACTGGGGGAGGC	0.687													C|||	2808	0.560703	0.7012	0.5576	5008	,	,		11899	0.4246		0.5378	False		,,,				2504	0.5368				p.L90L		Atlas-SNP	.											.	DACT1	119	.	0			c.C268T						PASS	.	C	,	2402,1206		810,782,212	16.0	17.0	17.0		268,268	2.5	1.0	14	dbSNP_92	17	4400,3684		1208,1984,850	no	coding-synonymous,coding-synonymous	DACT1	NM_001079520.1,NM_016651.5	,	2018,2766,1062	TT,TC,CC		45.5715,33.4257,41.8235	,	90/800,90/837	59105188	6802,4890	1804	4042	5846	SO:0001819	synonymous_variant	51339	exon1			GAGCTACTGGGGG	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.268C>T	14.37:g.59105188C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_016651	A8MYJ2|Q86TY0	Silent	SNP	ENST00000335867.4	37	CCDS9736.1																																																																																			C|0.454;T|0.546	0.546	strong		0.687	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
COX10	1352	hgsc.bcm.edu	37	17	13980350	13980350	+	Missense_Mutation	SNP	G	G	A	rs2072279	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:13980350G>A	ENST00000261643.3	+	3	553	c.476G>A	c.(475-477)cGa>cAa	p.R159Q	COX10_ENST00000537334.1_Intron|COX10_ENST00000429152.2_Missense_Mutation_p.R159Q|COX10_ENST00000536205.1_Missense_Mutation_p.D9N	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	159			R -> Q (in dbSNP:rs8077302). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8078902, ECO:0000269|PubMed:9177788, ECO:0000269|Ref.4}.		aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		ATTTTGGCTCGACTATCCAAA	0.343													G|||	2323	0.463858	0.4433	0.536	5008	,	,		17734	0.375		0.506	False		,,,				2504	0.4888				p.R159Q		Atlas-SNP	.											.	COX10	36	.	0			c.G476A						PASS	.	G	GLN/ARG	1944,2462	548.8+/-377.6	447,1050,706	73.0	78.0	76.0		476	5.5	0.6	17	dbSNP_116	76	4434,4166	585.3+/-391.9	1149,2136,1015	yes	missense	COX10	NM_001303.3	43	1596,3186,1721	AA,AG,GG		48.4419,44.1217,49.0389	benign	159/444	13980350	6378,6628	2203	4300	6503	SO:0001583	missense	1352	exon3			TGGCTCGACTATC	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"""Mitochondrial respiratory chain complex assembly factors"""	2260	protein-coding gene	gene with protein product	"""heme A: farnesyltransferase"", ""protoheme IX farnesyltransferase, mitochondrial"", ""heme O synthase"""	602125	"""COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)"", ""COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"""			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.476G>A	17.37:g.13980350G>A	ENSP00000261643:p.Arg159Gln	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	37	CCDS11166.1	1065|1065	0.4876373626373626|0.4876373626373626	229|229	0.4654471544715447|0.4654471544715447	183|183	0.505524861878453|0.505524861878453	259|259	0.4527972027972028|0.4527972027972028	394|394	0.5197889182058048|0.5197889182058048	G|G	16.81|16.81	3.226566|3.226566	0.58668|0.58668	0.441217|0.441217	0.515581|0.515581	ENSG00000006695|ENSG00000006695	ENST00000536205|ENST00000261643	T|T	0.71579|0.65549	-0.58|-0.16	5.49|5.49	5.49|5.49	0.81192|0.81192	.|.	.|0.201022	.|0.40818	.|N	.|0.001002	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.76328|0.76328	2.33|2.33	0.09310|0.09310	P|P	1.0|1.0	B|B	0.27416|0.14805	0.178|0.011	B|B	0.19391|0.12837	0.025|0.008	T|T	0.44513|0.44513	-0.9323|-0.9323	8|9	0.72032|0.10902	D|T	0.01|0.67	-11.5042|-11.5042	17.9318|17.9318	0.88999|0.88999	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs8077302;rs52823178;rs59945391;rs8077302|rs8077302;rs52823178;rs59945391;rs8077302	9|159	B4DJ50|Q12887	.|COX10_HUMAN	N|Q	9|159	ENSP00000439494:D9N|ENSP00000261643:R159Q	ENSP00000439494:D9N|ENSP00000261643:R159Q	D|R	+|+	1|2	0|0	COX10|COX10	13921075|13921075	1.000000|1.000000	0.71417|0.71417	0.605000|0.605000	0.28930|0.28930	0.996000|0.996000	0.88848|0.88848	7.163000|7.163000	0.77524|0.77524	2.741000|2.741000	0.93983|0.93983	0.655000|0.655000	0.94253|0.94253	GAC|CGA	G|0.515;A|0.485	0.485	strong		0.343	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303	
GRM6	2916	hgsc.bcm.edu	37	5	178416288	178416288	+	Silent	SNP	G	G	A	rs2071246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:178416288G>A	ENST00000517717.1	-	6	1169	c.1131C>T	c.(1129-1131)gaC>gaT	p.D377D	GRM6_ENST00000231188.5_Silent_p.D377D|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	377					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		GGGTGGAATCGTCTGACTGGG	0.607													G|||	3614	0.721645	0.7791	0.6772	5008	,	,		9752	0.6974		0.7455	False		,,,				2504	0.6759				p.D377D		Atlas-SNP	.											.	GRM6	149	.	0			c.C1131T						PASS	.	G		3300,1106	720.2+/-409.0	1260,780,163	79.0	76.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1131	-10.3	0.0	5	dbSNP_96	77	6294,2306	705.3+/-405.5	2276,1742,282	no	coding-synonymous	GRM6	NM_000843.3		3536,2522,445	AA,AG,GG		26.814,25.1021,26.234		377/878	178416288	9594,3412	2203	4300	6503	SO:0001819	synonymous_variant	2916	exon5			GGAATCGTCTGAC	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1131C>T	5.37:g.178416288G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	186	86	0.462366	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																			G|0.261;A|0.739	0.739	strong		0.607	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
CSMD1	64478	hgsc.bcm.edu	37	8	3253768	3253768	+	Silent	SNP	C	C	T	rs3802303	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:3253768C>T	ENST00000520002.1	-	18	3099	c.2544G>A	c.(2542-2544)ctG>ctA	p.L848L	CSMD1_ENST00000602723.1_Silent_p.L848L|CSMD1_ENST00000537824.1_Silent_p.L847L|CSMD1_ENST00000602557.1_Silent_p.L848L|CSMD1_ENST00000400186.3_Silent_p.L848L|CSMD1_ENST00000542608.1_Silent_p.L847L|CSMD1_ENST00000539096.1_Silent_p.L847L			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	848	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CAGTGGTGAACAGCAGGTACA	0.597													T|||	1501	0.29972	0.3472	0.3386	5008	,	,		15559	0.0972		0.4235	False		,,,				2504	0.2894				p.L847L		Atlas-SNP	.											CSMD1_ENST00000537824,colon,carcinoma,0,2	CSMD1	1469	2	0			c.G2541A						PASS	.	T		1459,2877		278,903,987	34.0	45.0	42.0		2541	-9.9	0.0	8	dbSNP_107	42	3475,5079		732,2011,1534	no	coding-synonymous	CSMD1	NM_033225.5		1010,2914,2521	TT,TC,CC		40.6243,33.6485,38.2777		847/3565	3253768	4934,7956	2168	4277	6445	SO:0001819	synonymous_variant	64478	exon17			GGTGAACAGCAGG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.2544G>A	8.37:g.3253768C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	160	158	0.9875	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		687	0.31456043956043955	168	0.34146341463414637	133	0.3674033149171271	67	0.11713286713286714	319	0.420844327176781	T	0.026	-1.367594	0.01225	0.336485	0.406243	ENSG00000183117	ENST00000335551	.	.	.	4.93	-9.86	0.00473	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999776374	.	.	.	.	.	.	T	0.07065	-1.0792	3	.	.	.	.	5.1615	0.15064	0.136:0.4309:0.1698:0.2633	rs3802303;rs3802303	.	.	.	I	328	.	.	V	-	1	0	CSMD1	3241175	0.000000	0.05858	0.035000	0.18076	0.032000	0.12392	-3.102000	0.00603	-4.229000	0.00063	-4.636000	0.00004	GTT	C|0.663;T|0.337	0.337	strong		0.597	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
PDE6C	5146	hgsc.bcm.edu	37	10	95372734	95372734	+	Silent	SNP	G	G	A	rs1131978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:95372734G>A	ENST00000371447.3	+	1	390	c.252G>A	c.(250-252)ctG>ctA	p.L84L		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	84	GAF 1.				phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	ACAGGGCCCTGCAGAGGCTGG	0.662													G|||	823	0.164337	0.2421	0.1643	5008	,	,		18058	0.1131		0.167	False		,,,				2504	0.1094				p.L84L		Atlas-SNP	.											.	PDE6C	97	.	0			c.G252A						PASS	.	G		1058,3348	379.7+/-323.4	136,786,1281	31.0	33.0	32.0		252	4.3	1.0	10	dbSNP_86	32	1472,7128	277.4+/-292.8	135,1202,2963	no	coding-synonymous	PDE6C	NM_006204.3		271,1988,4244	AA,AG,GG		17.1163,24.0127,19.4526		84/859	95372734	2530,10476	2203	4300	6503	SO:0001819	synonymous_variant	5146	exon1			GGCCCTGCAGAGG	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.252G>A	10.37:g.95372734G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_006204	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	37	CCDS7429.1																																																																																			A|0.180;G|0.820;T|0.000	0.180	strong		0.662	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
OR12D2	26529	hgsc.bcm.edu	37	6	29364951	29364951	+	Missense_Mutation	SNP	G	G	A	rs2073151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29364951G>A	ENST00000383555.2	+	1	536	c.475G>A	c.(475-477)Gta>Ata	p.V159I	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	159			V -> I (in dbSNP:rs2073151).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						GCTGCACTCCGTAATGACTTC	0.483													G|||	1598	0.319089	0.1921	0.3473	5008	,	,		22625	0.3641		0.4523	False		,,,				2504	0.2873				p.V159I		Atlas-SNP	.											.	OR12D2	42	.	0			c.G475A						PASS	.	G	ILE/VAL	670,2352		75,520,916	164.0	159.0	160.0		475	-3.1	0.0	6	dbSNP_96	160	2412,3006		536,1340,833	yes	missense	OR12D2	NM_013936.3	29	611,1860,1749	AA,AG,GG		44.5183,22.1707,36.5166	benign	159/308	29364951	3082,5358	1511	2709	4220	SO:0001583	missense	26529	exon1			CACTCCGTAATGA		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.475G>A	6.37:g.29364951G>A	ENSP00000373047:p.Val159Ile	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	208	92	0.442308	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	787	0.36034798534798534	101	0.20528455284552846	123	0.3397790055248619	208	0.36363636363636365	355	0.4683377308707124	G	0.020	-1.445958	0.01089	0.221707	0.445183	ENSG00000168787	ENST00000383555	T	0.37058	1.22	3.94	-3.14	0.05250	GPCR, rhodopsin-like superfamily (1);	0.634583	0.15162	N	0.277100	T	0.05364	0.0142	N	0.17082	0.46	0.80722	P	0.0	B	0.17268	0.021	B	0.24006	0.05	T	0.38845	-0.9642	9	0.06494	T	0.89	.	9.2814	0.37731	0.2203:0.1535:0.6262:0.0	rs2073151;rs56462678;rs60511171;rs2073151	159	P58182	O12D2_HUMAN	I	159	ENSP00000373047:V159I	ENSP00000373047:V159I	V	+	1	0	OR12D2	29472930	0.000000	0.05858	0.000000	0.03702	0.237000	0.25408	-3.504000	0.00449	-0.890000	0.03945	0.205000	0.17691	GTA	G|0.639;A|0.361	0.361	strong		0.483	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
VPS52	6293	hgsc.bcm.edu	37	6	33235755	33235755	+	Silent	SNP	G	G	A	rs213199	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33235755G>A	ENST00000445902.2	-	9	1038	c.820C>T	c.(820-822)Ctg>Ttg	p.L274L	VPS52_ENST00000482399.1_3'UTR|VPS52_ENST00000436044.2_Silent_p.L149L|VPS52_ENST00000478934.1_5'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	274					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						TCATTGCCCAGCAGAAACTGA	0.507													G|||	2227	0.444688	0.4501	0.3761	5008	,	,		19882	0.5823		0.3847	False		,,,				2504	0.4059				p.L274L		Atlas-SNP	.											.	VPS52	56	.	0			c.C820T						PASS	.	G		1291,1731		266,759,486	153.0	160.0	158.0		820	3.1	1.0	6	dbSNP_79	158	1948,3470		348,1252,1109	yes	coding-synonymous	VPS52	NM_022553.4		614,2011,1595	AA,AG,GG		35.9542,42.7201,38.3768		274/724	33235755	3239,5201	1511	2709	4220	SO:0001819	synonymous_variant	6293	exon9			TGCCCAGCAGAAA	AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"""SAC2 suppressor of actin mutations 2-like (yeast)"", ""vacuolar protein sorting 52 (yeast)"""	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.820C>T	6.37:g.33235755G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																			G|0.576;A|0.424	0.424	strong		0.507	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553	
DDX20	11218	hgsc.bcm.edu	37	1	112308972	112308972	+	Silent	SNP	G	G	A	rs197413	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:112308972G>A	ENST00000369702.4	+	11	2546	c.1926G>A	c.(1924-1926)gtG>gtA	p.V642V	DDX20_ENST00000475700.1_Silent_p.V250V	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	642					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAGTCCCTGTGTTGGCAAGTA	0.443													A|||	2403	0.479832	0.7428	0.5115	5008	,	,		19455	0.3403		0.4185	False		,,,				2504	0.3088				p.V642V		Atlas-SNP	.											.	DDX20	50	.	0			c.G1926A						PASS	.	A		2992,1414	455.7+/-351.1	1018,956,229	47.0	48.0	48.0		1926	-2.6	0.0	1	dbSNP_79	48	3349,5251	639.0+/-399.4	671,2007,1622	no	coding-synonymous	DDX20	NM_007204.4		1689,2963,1851	AA,AG,GG		38.9419,32.0926,48.7544		642/825	112308972	6341,6665	2203	4300	6503	SO:0001819	synonymous_variant	11218	exon11			CCCTGTGTTGGCA	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.1926G>A	1.37:g.112308972G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Silent	SNP	ENST00000369702.4	37	CCDS842.1																																																																																			G|0.512;A|0.488	0.488	strong		0.443	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
KCNK18	338567	hgsc.bcm.edu	37	10	118957027	118957027	+	Missense_Mutation	SNP	A	A	G	rs67346047	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:118957027A>G	ENST00000334549.1	+	1	28	c.28A>G	c.(28-30)Agg>Ggg	p.R10G		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	10					cellular response to pH (GO:0071467)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41		Colorectal(252;0.19)		all cancers(201;0.0211)		CCCCCAGGCCAGGAGATGCTG	0.632													a|||	444	0.0886581	0.0023	0.1398	5008	,	,		18186	0.1627		0.0537	False		,,,				2504	0.1288				p.R10G		Atlas-SNP	.											.	KCNK18	70	.	0			c.A28G						PASS	.	G	GLY/ARG	65,4341	58.1+/-94.6	1,63,2139	65.0	63.0	64.0		28	-5.4	0.0	10	dbSNP_130	64	634,7966	162.5+/-215.2	14,606,3680	yes	missense	KCNK18	NM_181840.1	125	15,669,5819	GG,GA,AA		7.3721,1.4753,5.3744	benign	10/385	118957027	699,12307	2203	4300	6503	SO:0001583	missense	338567	exon1			CAGGCCAGGAGAT	AB087138	CCDS7598.1	10q26.11	2012-03-07			ENSG00000186795	ENSG00000186795		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	19439	protein-coding gene	gene with protein product	"""TWIK related spinal cord K+ channel"""	613655				16382106	Standard	NM_181840		Approved	K2p18.1, TRESK-2, TRESK2, TRESK, TRIK	uc010qsr.2	Q7Z418	OTTHUMG00000019120	ENST00000334549.1:c.28A>G	10.37:g.118957027A>G	ENSP00000334650:p.Arg10Gly	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	91	35	0.384615	NM_181840	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	37	CCDS7598.1	166	0.076007326007326	2	0.0040650406504065045	45	0.12430939226519337	78	0.13636363636363635	41	0.05408970976253298	a	2.206	-0.381730	0.04966	0.014753	0.073721	ENSG00000186795	ENST00000334549	T	0.15139	2.45	4.17	-5.42	0.02640	.	0.578272	0.17448	N	0.173873	T	0.00073	0.0002	L	0.27053	0.805	0.80722	P	0.0	B	0.18461	0.028	B	0.11329	0.006	T	0.27806	-1.0063	9	0.32370	T	0.25	.	1.5064	0.02487	0.2499:0.2895:0.3192:0.1414	.	10	Q7Z418	KCNKI_HUMAN	G	10	ENSP00000334650:R10G	ENSP00000334650:R10G	R	+	1	2	KCNK18	118947017	0.000000	0.05858	0.000000	0.03702	0.202000	0.24057	-1.206000	0.03011	-1.060000	0.03189	-1.320000	0.01293	AGG	A|0.941;G|0.059	0.059	strong		0.632	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840	
RBM19	9904	hgsc.bcm.edu	37	12	114395651	114395651	+	Missense_Mutation	SNP	T	T	C	rs10850256	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:114395651T>C	ENST00000545145.2	-	6	854	c.776A>G	c.(775-777)aAg>aGg	p.K259R	RBM19_ENST00000261741.5_Missense_Mutation_p.K259R|RBM19_ENST00000392561.3_Missense_Mutation_p.K259R	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	259				K -> R (in Ref. 1; BAA31657 and 6; AAH06137/AAH04289). {ECO:0000305}.	multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GCCTGCACCCTTGCTGTCTCT	0.592													T|||	1069	0.213458	0.407	0.0821	5008	,	,		17914	0.1806		0.1143	False		,,,				2504	0.181				p.K259R		Atlas-SNP	.											.	RBM19	117	.	0			c.A776G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	1678,2728	509.1+/-367.1	339,1000,864	156.0	138.0	144.0		776,776,776	-6.1	0.0	12	dbSNP_120	144	886,7714	198.7+/-243.0	38,810,3452	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	26,26,26	377,1810,4316	CC,CT,TT		10.3023,38.0844,19.714	benign,benign,benign	259/961,259/961,259/961	114395651	2564,10442	2203	4300	6503	SO:0001583	missense	9904	exon6			GCACCCTTGCTGT	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.776A>G	12.37:g.114395651T>C	ENSP00000442053:p.Lys259Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	156	65	0.416667	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	378	0.17307692307692307	165	0.3353658536585366	29	0.08011049723756906	98	0.17132867132867133	86	0.11345646437994723	T	7.544	0.661283	0.14645	0.380844	0.103023	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05649	3.41;3.41;3.41	4.51	-6.07	0.02158	Nucleotide-binding, alpha-beta plait (1);	4.525770	0.00710	N	0.000820	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47249	-0.9132	9	0.20519	T	0.43	0.3269	7.0053	0.24833	0.0:0.3222:0.3793:0.2985	rs10850256;rs17850047;rs17857776;rs10850256	259	Q9Y4C8	RBM19_HUMAN	R	259	ENSP00000442053:K259R;ENSP00000376344:K259R;ENSP00000261741:K259R	ENSP00000261741:K259R	K	-	2	0	RBM19	112880034	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.091000	0.11146	-1.269000	0.02436	-1.074000	0.02243	AAG	T|0.808;C|0.192	0.192	strong		0.592	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
RBMXL3	139804	hgsc.bcm.edu	37	X	114424941	114424941	+	Missense_Mutation	SNP	G	G	A	rs62601530		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:114424941G>A	ENST00000424776.3	+	1	979	c.937G>A	c.(937-939)Gct>Act	p.A313T	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	313							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						CCCATGCGGCGCTGCCCCTGT	0.622													G|||	225	0.0596026	0.0053	0.0533	3775	,	,		11134	0.002		0.1133	False		,,,				2504	0.0665				p.A313T		Atlas-SNP	.											.	RBMXL3	83	.	0			c.G937A						PASS	.	G	THR/ALA,	34,1175		1,25,7,491,168	30.0	34.0	33.0		937,	-0.3	0.0	X	dbSNP_129	33	392,1999		18,215,141,567,650	yes	missense,intron	LRCH2,RBMXL3	NM_001145346.1,NM_020871.3	58,	19,240,148,1058,818	AA,AG,A,GG,G		16.3948,2.8122,11.8333	benign,	313/1068,	114424941	426,3174	692	1591	2283	SO:0001583	missense	139804	exon1			TGCGGCGCTGCCC	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.937G>A	X.37:g.114424941G>A	ENSP00000417451:p.Ala313Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	203	191	0.940887	NM_001145346	B4DXC0	Missense_Mutation	SNP	ENST00000424776.3	37	CCDS55478.1	117	0.0705244122965642	3	0.006122448979591836	20	0.056179775280898875	2	0.0034965034965034965	53	0.07703488372093023	G	11.07	1.531256	0.27387	0.028122	0.163948	ENSG00000175718	ENST00000424776	T	0.05513	3.43	0.682	-0.276	0.12902	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.36837	0.571	B	0.17098	0.017	T	0.48352	-0.9043	7	0.87932	D	0	.	.	.	.	rs62601530	313	Q8N7X1	RMXL3_HUMAN	T	313	ENSP00000417451:A313T	ENSP00000417451:A313T	A	+	1	0	RBMXL3	114331197	0.026000	0.19158	0.000000	0.03702	0.000000	0.00434	1.366000	0.34193	-0.218000	0.10018	-0.494000	0.04653	GCT	G|0.929;A|0.071	0.071	strong		0.622	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
DLEC1	9940	hgsc.bcm.edu	37	3	38080952	38080952	+	Missense_Mutation	SNP	T	T	G	rs7625806	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:38080952T>G	ENST00000308059.6	+	1	257	c.236T>G	c.(235-237)cTg>cGg	p.L79R	DLEC1_ENST00000346219.3_Missense_Mutation_p.L79R|DLEC1_ENST00000452631.2_Missense_Mutation_p.L79R					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		GAGCCTCAGCTGCTTCGTCTG	0.652													G|||	2258	0.450879	0.5658	0.4092	5008	,	,		18071	0.6062		0.3429	False		,,,				2504	0.2761				p.L79R		Atlas-SNP	.											DLEC1_ENST00000346219,NS,carcinoma,0,2	DLEC1	278	2	0			c.T236G						PASS	.	G	ARG/LEU,ARG/LEU	2107,1909		567,973,468	35.0	40.0	39.0		236,236	0.3	0.0	3	dbSNP_116	39	2839,5501		509,1821,1840	yes	missense,missense	DLEC1	NM_007335.2,NM_007337.2	102,102	1076,2794,2308	GG,GT,TT		34.0408,47.5349,40.0291	probably-damaging,probably-damaging	79/1756,79/1779	38080952	4946,7410	2008	4170	6178	SO:0001583	missense	9940	exon1			CTCAGCTGCTTCG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.236T>G	3.37:g.38080952T>G	ENSP00000308597:p.Leu79Arg	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	38	12	0.315789	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	988	0.4523809523809524	267	0.5426829268292683	142	0.39226519337016574	328	0.5734265734265734	251	0.3311345646437995	G	10.55	1.381461	0.24944	0.524651	0.340408	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.06528	3.32;3.29;3.54	5.47	0.309	0.15820	.	0.942952	0.08797	N	0.892317	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B;B	0.12630	0.006;0.006;0.006	B;B;B	0.17098	0.017;0.017;0.017	T	0.34725	-0.9817	9	0.30078	T	0.28	0.0241	2.3534	0.04290	0.1262:0.1483:0.132:0.5935	rs7625806;rs60689091;rs7625806	79;79;79	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	R	79	ENSP00000308597:L79R;ENSP00000315914:L79R;ENSP00000410427:L79R	ENSP00000308597:L79R	L	+	2	0	DLEC1	38055956	0.383000	0.25156	0.028000	0.17463	0.050000	0.14768	0.147000	0.16202	-0.457000	0.07033	-1.717000	0.00709	CTG	T|0.555;G|0.445	0.445	strong		0.652	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807781	18807781	+	Silent	SNP	C	C	T	rs35013594	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18807781C>T	ENST00000400664.1	+	1	358	c.306C>T	c.(304-306)ggC>ggT	p.G102G		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	102						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ATCCAAGAGGCCCCTATGTCC	0.652													C|||	445	0.0888578	0.1021	0.1239	5008	,	,		17088	0.0377		0.1233	False		,,,				2504	0.0634				p.G102G		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C306T						PASS	.	C		309,3613		11,287,1663	18.0	21.0	20.0		306	-5.4	0.0	1	dbSNP_126	20	1028,7288		66,896,3196	no	coding-synonymous	KLHDC7A	NM_152375.2		77,1183,4859	TT,TC,CC		12.3617,7.8786,10.925		102/778	18807781	1337,10901	1961	4158	6119	SO:0001819	synonymous_variant	127707	exon1			AAGAGGCCCCTAT	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.306C>T	1.37:g.18807781C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																			C|0.899;T|0.101	0.101	strong		0.652	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
CYP51A1	1595	hgsc.bcm.edu	37	7	91743150	91743150	+	Silent	SNP	A	A	G	rs7797834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:91743150A>G	ENST00000003100.8	-	10	1524	c.1359T>C	c.(1357-1359)caT>caC	p.H453H	CYP51A1_ENST00000450723.1_Silent_p.H348H|LRRD1_ENST00000422722.1_5'UTR	NM_000786.3	NP_000777.1	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A, polypeptide 1	447					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via 24,25-dihydrolanosterol (GO:0033488)|demethylation (GO:0070988)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|sterol 14-demethylase activity (GO:0008398)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	10	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Itraconazole(DB01167)|Ketoconazole(DB01026)|Sertaconazole(DB01153)|Tioconazole(DB01007)	CAATACAACGATGACGCCCTA	0.323													A|||	1801	0.359625	0.4539	0.3588	5008	,	,		16445	0.1607		0.3867	False		,,,				2504	0.41				p.H453H	GBM(70;1100 1190 11592 25836 51397)	Atlas-SNP	.											.	CYP51A1	30	.	0			c.T1359C						PASS	.	A	,	2077,2329	553.2+/-378.7	487,1103,613	59.0	61.0	61.0		1359,1044	3.7	1.0	7	dbSNP_116	61	3453,5147	503.1+/-375.8	672,2109,1519	no	coding-synonymous,coding-synonymous	CYP51A1	NM_000786.3,NM_001146152.1	,	1159,3212,2132	GG,GA,AA		40.1512,47.1403,42.5188	,	453/510,348/405	91743150	5530,7476	2203	4300	6503	SO:0001819	synonymous_variant	1595	exon10			ACAACGATGACGC	U51685	CCDS5623.1, CCDS55123.1	7q21.2	2012-10-10	2003-02-14	2003-02-28	ENSG00000001630	ENSG00000001630		"""Cytochrome P450s"""	2649	protein-coding gene	gene with protein product		601637	"""cytochrome P450, 51 (lanosterol 14-alpha-demethylase)"""	CYP51		8975714	Standard	NM_000786		Approved	CP51, CYPL1, P450L1, LDM, P450-14DM	uc003ulm.4	Q16850	OTTHUMG00000131131	ENST00000003100.8:c.1359T>C	7.37:g.91743150A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_000786	A4D1F8|B2RAI4|B4DJ55|O00770|O00772|Q16784|Q8N1A8|Q99868	Silent	SNP	ENST00000003100.8	37	CCDS5623.1	775	0.35485347985347987	241	0.4898373983739837	137	0.3784530386740331	100	0.17482517482517482	297	0.391820580474934	A	13.19	2.164343	0.38217	0.471403	0.401512	ENSG00000001630	ENST00000422867	.	.	.	4.88	3.73	0.42828	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.49735	-0.8908	3	.	.	.	.	10.4441	0.44483	0.9233:0.0:0.0767:0.0	rs7797834;rs10360207;rs57944744;rs7797834	.	.	.	P	166	.	.	S	-	1	0	CYP51A1	91581086	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.131000	0.50515	0.894000	0.36317	-0.353000	0.07706	TCG	A|0.620;G|0.380	0.380	strong		0.323	CYP51A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253812.4		
BAG6	7917	hgsc.bcm.edu	37	6	31611746	31611746	+	Silent	SNP	G	G	A	rs7770976	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31611746G>A	ENST00000375964.6	-	13	1900	c.1587C>T	c.(1585-1587)gcC>gcT	p.A529A	BAG6_ENST00000211379.5_Silent_p.A523A|BAG6_ENST00000439687.2_Silent_p.A522A|BAG6_ENST00000470875.1_5'UTR|BAG6_ENST00000375976.4_Silent_p.A523A|BAG6_ENST00000362049.6_Silent_p.A523A|BAG6_ENST00000404765.2_Silent_p.A559A	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	529	4 X 29 AA approximate repeats.|Pro-rich.				brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						TACCCAGACCGGCGCCCTGCT	0.572													g|||	249	0.0497204	0.1089	0.0706	5008	,	,		16839	0.0179		0.0229	False		,,,				2504	0.0153				p.A529A		Atlas-SNP	.											.	BAG6	73	.	0			c.C1587T						PASS	.		,,,,,	270,2752		11,248,1252	56.0	49.0	52.0		1569,1566,1569,1587,1569,1569	-9.5	0.0	6	dbSNP_116	52	150,5268		1,148,2560	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAG6	NM_001098534.1,NM_001199697.1,NM_001199698.1,NM_004639.3,NM_080702.2,NM_080703.2	,,,,,	12,396,3812	AA,AG,GG		2.7685,8.9345,4.9763	,,,,,	523/1127,522/904,523/1078,529/1133,523/1127,523/1127	31611746	420,8020	1511	2709	4220	SO:0001819	synonymous_variant	7917	exon13			CAGACCGGCGCCC	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"""HLA-B associated transcript 3"""	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.1587C>T	6.37:g.31611746G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Silent	SNP	ENST00000375964.6	37	CCDS47403.1	120	0.054945054945054944	62	0.12601626016260162	26	0.0718232044198895	16	0.027972027972027972	16	0.021108179419525065	g	10.06	1.247589	0.22880	0.089345	0.027685	ENSG00000204463	ENST00000453833	.	.	.	5.71	-9.46	0.00597	.	.	.	.	.	T	0.10121	0.0248	.	.	.	0.58432	P	5.000000000032756E-6	.	.	.	.	.	.	T	0.25606	-1.0127	3	.	.	.	.	7.8245	0.29307	0.1575:0.0958:0.5816:0.1651	rs7770976;rs11548859;rs7770976	.	.	.	W	158	.	.	R	-	1	2	BAG6	31719725	0.005000	0.15991	0.011000	0.14972	0.374000	0.29953	-0.801000	0.04550	-1.067000	0.03160	-0.311000	0.09066	CGG	G|0.940;A|0.060	0.060	strong		0.572	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703	
PIK3R5	23533	hgsc.bcm.edu	37	17	8809025	8809025	+	Silent	SNP	G	G	A	rs61753147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:8809025G>A	ENST00000447110.1	-	4	358	c.234C>T	c.(232-234)ctC>ctT	p.L78L	PIK3R5_ENST00000581552.1_Silent_p.L78L|PIK3R5_ENST00000584803.1_Silent_p.L78L	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	78	Heterodimerization. {ECO:0000250}.				blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						CCAGCGGGGTGAGCAGGTCGT	0.602													G|||	115	0.0229633	0.0038	0.0043	5008	,	,		16488	0.001		0.0507	False		,,,				2504	0.0562				p.L78L	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.C234T						PASS	.	G	,	37,4367	40.8+/-73.8	0,37,2165	65.0	50.0	55.0		234,234	-10.9	0.0	17	dbSNP_129	55	483,8109	129.0+/-187.1	17,449,3830	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	17,486,5995	AA,AG,GG		5.6215,0.8401,4.0012	,	78/881,78/881	8809025	520,12476	2202	4296	6498	SO:0001819	synonymous_variant	23533	exon4			CGGGGTGAGCAGG	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.234C>T	17.37:g.8809025G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			G|0.972;A|0.028	0.028	strong		0.602	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
CFAP61	26074	hgsc.bcm.edu	37	20	20232356	20232356	+	Silent	SNP	C	C	T	rs56102210	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:20232356C>T	ENST00000245957.5	+	20	2353	c.2277C>T	c.(2275-2277)gaC>gaT	p.D759D	C20orf26_ENST00000377293.1_Silent_p.D115D|C20orf26_ENST00000389656.3_Silent_p.D115D|C20orf26_ENST00000377309.2_Silent_p.D115D	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		759										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		TTTCCACGGACGAGATCGTGC	0.587													C|||	335	0.066893	0.028	0.0663	5008	,	,		16129	0.0208		0.1372	False		,,,				2504	0.0951				p.D759D		Atlas-SNP	.											.	C20orf26	188	.	0			c.C2277T						PASS	.	C		184,4222	118.4+/-156.1	5,174,2024	158.0	128.0	138.0		2277	-9.2	0.0	20	dbSNP_129	138	1040,7560	221.3+/-258.8	66,908,3326	no	coding-synonymous	C20orf26	NM_015585.3		71,1082,5350	TT,TC,CC		12.093,4.1761,9.411		759/1238	20232356	1224,11782	2203	4300	6503	SO:0001819	synonymous_variant	26074	exon20			CACGGACGAGATC																												ENST00000245957.5:c.2277C>T	20.37:g.20232356C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	73	26	0.356164	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Silent	SNP	ENST00000245957.5	37	CCDS33447.1																																																																																			C|0.914;T|0.086	0.086	strong		0.587	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
ZNF521	25925	hgsc.bcm.edu	37	18	22805218	22805218	+	Silent	SNP	G	G	A	rs35535552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:22805218G>A	ENST00000361524.3	-	4	2812	c.2664C>T	c.(2662-2664)tgC>tgT	p.C888C	ZNF521_ENST00000584787.1_Silent_p.C668C|ZNF521_ENST00000538137.2_Silent_p.C888C|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	888					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CACAAATGTCGCAGCCGTACA	0.522			T	PAX5	ALL								g|||	10	0.00199681	0.0	0.0072	5008	,	,		19940	0.0		0.004	False		,,,				2504	0.001				p.C888C		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,caecum,carcinoma,0,1	ZNF521	269	1	0			c.C2664T						scavenged	.	A		4,4402	8.1+/-20.4	0,4,2199	121.0	113.0	115.0		2664	-11.7	0.0	18	dbSNP_126	115	42,8558	27.9+/-77.7	0,42,4258	no	coding-synonymous	ZNF521	NM_015461.2		0,46,6457	AA,AG,GG		0.4884,0.0908,0.3537		888/1312	22805218	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			AATGTCGCAGCCG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2664C>T	18.37:g.22805218G>A		Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	285	128	0.449123	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																			G|0.995;A|0.005	0.005	strong		0.522	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
ANKRD55	79722	hgsc.bcm.edu	37	5	55406952	55406952	+	Silent	SNP	T	T	C	rs321775	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:55406952T>C	ENST00000341048.4	-	10	1774	c.1623A>G	c.(1621-1623)ccA>ccG	p.P541P	ANKRD55_ENST00000505970.2_5'Flank|ANKRD55_ENST00000504958.2_Silent_p.P498P|ANKRD55_ENST00000434982.2_Silent_p.P253P	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	541								p.P541P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				TACCTGATGATGGATTATGTA	0.478													t|||	1090	0.217652	0.0862	0.1311	5008	,	,		20374	0.3065		0.2813	False		,,,				2504	0.2996				p.P541P		Atlas-SNP	.											ANKRD55,NS,carcinoma,0,1	ANKRD55	70	1	1	Substitution - coding silent(1)	stomach(1)	c.A1623G						PASS	.	C		509,3897		34,441,1728	125.0	121.0	122.0		1623	-8.5	0.0	5	dbSNP_79	122	2317,6283		323,1671,2306	no	coding-synonymous	ANKRD55	NM_024669.2		357,2112,4034	CC,CT,TT		26.9419,11.5524,21.7284		541/615	55406952	2826,10180	2203	4300	6503	SO:0001819	synonymous_variant	79722	exon10			TGATGATGGATTA	AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"""Ankyrin repeat domain containing"""	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.1623A>G	5.37:g.55406952T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_024669	B3KVT8|Q3KP45|Q9HAD3	Silent	SNP	ENST00000341048.4	37	CCDS34161.1																																																																																			T|0.779;C|0.221	0.221	strong		0.478	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368510.4	NM_024669	
SLC45A1	50651	hgsc.bcm.edu	37	1	8395560	8395560	+	Missense_Mutation	SNP	G	G	T	rs7535752	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:8395560G>T	ENST00000471889.1	+	6	1892	c.1507G>T	c.(1507-1509)Gcg>Tcg	p.A503S	SLC45A1_ENST00000377479.2_Missense_Mutation_p.A537S|SLC45A1_ENST00000481265.1_3'UTR|SLC45A1_ENST00000289877.8_Missense_Mutation_p.A503S			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	503					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(2)	33	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCGAGCGCGCGGAGCAGCC	0.647													G|||	773	0.154353	0.0961	0.1859	5008	,	,		16601	0.0228		0.1839	False		,,,				2504	0.316				p.A503S		Atlas-SNP	.											.	SLC45A1	85	.	0			c.G1507T						PASS	.	G	SER/ALA	462,3944	219.1+/-236.9	21,420,1762	55.0	63.0	60.0		1507	-10.2	0.0	1	dbSNP_116	60	1644,6956	302.1+/-305.8	157,1330,2813	yes	missense	SLC45A1	NM_001080397.1	99	178,1750,4575	TT,TG,GG		19.1163,10.4857,16.1925	benign	503/749	8395560	2106,10900	2203	4300	6503	SO:0001583	missense	50651	exon5			GAGCGCGCGGAGC	AF118274	CCDS30577.1	1p36.23	2014-01-28	2005-10-04	2005-10-04	ENSG00000162426	ENSG00000162426		"""Solute carriers"""	17939	protein-coding gene	gene with protein product	"""H+/sugar symporter"""	605763	"""deleted in neuroblastoma 5"""	DNB5		10729226	Standard	XM_005263467		Approved		uc001apb.3	Q9Y2W3	OTTHUMG00000000503	ENST00000471889.1:c.1507G>T	1.37:g.8395560G>T	ENSP00000418096:p.Ala503Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001080397	Q5VY46|Q5VY49	Missense_Mutation	SNP	ENST00000471889.1	37	CCDS30577.1	240	0.10989010989010989	40	0.08130081300813008	72	0.19889502762430938	3	0.005244755244755245	125	0.16490765171503957	G	0.061	-1.223735	0.01530	0.104857	0.191163	ENSG00000162426	ENST00000471889;ENST00000377479;ENST00000289877	T;T;T	0.78246	-1.16;-1.16;-1.16	5.09	-10.2	0.00374	.	0.826256	0.11218	N	0.587016	T	0.00039	0.0001	N	0.00996	-1.065	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.16689	-1.0394	9	0.08599	T	0.76	-2.1771	13.6969	0.62585	0.0:0.1439:0.1103:0.7457	rs7535752;rs57840924;rs7535752	503	Q9Y2W3	S45A1_HUMAN	S	503;537;503	ENSP00000418096:A503S;ENSP00000366699:A537S;ENSP00000289877:A503S	ENSP00000289877:A503S	A	+	1	0	SLC45A1	8318147	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.306000	0.08178	-1.967000	0.01008	0.561000	0.74099	GCG	G|0.849;T|0.151	0.151	strong		0.647	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5		
MYO7B	4648	hgsc.bcm.edu	37	2	128381808	128381808	+	Silent	SNP	C	C	T	rs13422424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:128381808C>T	ENST00000409816.2	+	28	3914	c.3882C>T	c.(3880-3882)caC>caT	p.H1294H	RP11-286H15.1_ENST00000609697.1_RNA|MYO7B_ENST00000409090.1_Silent_p.H147H|MYO7B_ENST00000389524.4_Silent_p.H1294H|MYO7B_ENST00000428314.1_Silent_p.H1294H			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1294	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.H1294H(2)		breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CCCCCTGGCACGACTCCCGGG	0.632													C|||	816	0.162939	0.0938	0.1196	5008	,	,		18399	0.1448		0.2038	False		,,,				2504	0.2638				p.H1294H		Atlas-SNP	.											MYO7B_ENST00000428314,NS,carcinoma,0,2	MYO7B	359	2	2	Substitution - coding silent(2)	prostate(2)	c.C3882T						PASS	.	C		413,3487		23,367,1560	23.0	26.0	25.0		3882	-7.1	0.7	2	dbSNP_121	25	1423,6829		118,1187,2821	no	coding-synonymous	MYO7B	NM_001080527.1		141,1554,4381	TT,TC,CC		17.2443,10.5897,15.1086		1294/2117	128381808	1836,10316	1950	4126	6076	SO:0001819	synonymous_variant	4648	exon29			CTGGCACGACTCC		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3882C>T	2.37:g.128381808C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	37	CCDS46405.1																																																																																			C|0.847;T|0.153	0.153	strong		0.632	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
PANK4	55229	hgsc.bcm.edu	37	1	2444414	2444414	+	Missense_Mutation	SNP	G	G	A	rs7535528	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:2444414G>A	ENST00000378466.3	-	13	1652	c.1640C>T	c.(1639-1641)gCg>gTg	p.A547V	PANK4_ENST00000435556.3_Missense_Mutation_p.A508V	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	547			A -> V (in dbSNP:rs7535528). {ECO:0000269|PubMed:17974005}.		coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CCAGCCCAGCGCGTCCAGGGA	0.667													G|||	1130	0.225639	0.0136	0.2983	5008	,	,		17320	0.3046		0.3867	False		,,,				2504	0.2137				p.A547V		Atlas-SNP	.											.	PANK4	64	.	0			c.C1640T						PASS	.	G	VAL/ALA	316,4090	166.2+/-197.5	13,290,1900	79.0	87.0	84.0		1640	5.6	0.0	1	dbSNP_116	84	3222,5374	484.2+/-371.3	588,2046,1664	no	missense	PANK4	NM_018216.1	64	601,2336,3564	AA,AG,GG		37.4826,7.172,27.2112	benign	547/774	2444414	3538,9464	2203	4298	6501	SO:0001583	missense	55229	exon13			CCCAGCGCGTCCA	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.1640C>T	1.37:g.2444414G>A	ENSP00000367727:p.Ala547Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	213	107	0.502347	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	612	0.2802197802197802	10	0.02032520325203252	116	0.32044198895027626	200	0.34965034965034963	286	0.37730870712401055	G	12.05	1.822331	0.32237	0.07172	0.374826	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.07444	3.19;3.19	5.59	5.59	0.84812	Domain of unknown function DUF89 (2);	0.731136	0.13776	N	0.363562	T	0.00012	0.0000	L	0.49778	1.585	0.80722	P	0.0	P;B	0.42039	0.769;0.315	B;B	0.30716	0.119;0.098	T	0.51687	-0.8674	9	0.66056	D	0.02	-3.4175	18.5677	0.91122	0.0:0.0:1.0:0.0	rs7535528;rs57417772;rs7535528	508;547	E9PHT6;Q9NVE7	.;PANK4_HUMAN	V	547;508	ENSP00000367727:A547V;ENSP00000421433:A508V	ENSP00000367727:A547V	A	-	2	0	PANK4	2434274	0.569000	0.26643	0.008000	0.14137	0.017000	0.09413	3.927000	0.56499	2.635000	0.89317	0.561000	0.74099	GCG	G|0.727;A|0.273	0.273	strong		0.667	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1		
MYO7B	4648	hgsc.bcm.edu	37	2	128367092	128367092	+	Silent	SNP	G	G	A	rs777432	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:128367092G>A	ENST00000409816.2	+	22	2858	c.2826G>A	c.(2824-2826)tcG>tcA	p.S942S	MYO7B_ENST00000389524.4_Silent_p.S942S|MYO7B_ENST00000428314.1_Silent_p.S942S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	942						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		ATCTGGAATCGAAGACCCAGA	0.597													A|||	1608	0.321086	0.3661	0.2478	5008	,	,		19290	0.1319		0.3857	False		,,,				2504	0.4407				p.S942S		Atlas-SNP	.											MYO7B_ENST00000428314,colon,carcinoma,0,2	MYO7B	359	2	0			c.G2826A						scavenged	.	A		1392,2710		242,908,901	36.0	42.0	40.0		2826	-6.9	0.0	2	dbSNP_86	40	2971,5405		527,1917,1744	no	coding-synonymous	MYO7B	NM_001080527.1		769,2825,2645	AA,AG,GG		35.4704,33.9347,34.9655		942/2117	128367092	4363,8115	2051	4188	6239	SO:0001819	synonymous_variant	4648	exon23			GGAATCGAAGACC		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.2826G>A	2.37:g.128367092G>A		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	126	51	0.404762	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	37	CCDS46405.1																																																																																			G|0.692;A|0.308	0.308	strong		0.597	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
ISX	91464	hgsc.bcm.edu	37	22	35478529	35478529	+	Missense_Mutation	SNP	G	G	A	rs8140287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:35478529G>A	ENST00000308700.6	+	2	1200	c.248G>A	c.(247-249)cGg>cAg	p.R83Q	ISX_ENST00000404699.2_Missense_Mutation_p.R83Q	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	83			R -> Q (in dbSNP:rs8140287).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						AAGAGCAAGCGGAGGGTTCGT	0.557													G|||	154	0.0307508	0.0023	0.0317	5008	,	,		20015	0.003		0.0557	False		,,,				2504	0.0716				p.R83Q		Atlas-SNP	.											.	ISX	62	.	0			c.G248A						PASS	.	G	GLN/ARG	51,4355	52.9+/-88.7	0,51,2152	142.0	115.0	124.0		248	4.9	0.7	22	dbSNP_116	124	462,8138	137.6+/-194.5	13,436,3851	yes	missense	ISX	NM_001008494.1	43	13,487,6003	AA,AG,GG		5.3721,1.1575,3.9443	probably-damaging	83/246	35478529	513,12493	2203	4300	6503	SO:0001583	missense	91464	exon2			GCAAGCGGAGGGT	AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"""Homeoboxes / PRD class"""	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.248G>A	22.37:g.35478529G>A	ENSP00000311492:p.Arg83Gln	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_001008494	Q68DJ5	Missense_Mutation	SNP	ENST00000308700.6	37	CCDS33640.1	56	0.02564102564102564	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	47	0.06200527704485488	G	28.4	4.916181	0.92249	0.011575	0.053721	ENSG00000175329	ENST00000308700;ENST00000404699	D;D	0.97209	-4.29;-4.29	4.94	4.94	0.65067	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.47852	D	0.000205	D	0.91878	0.7429	M	0.93898	3.47	0.54753	D	0.99998	D	0.89917	1.0	D	0.91635	0.999	D	0.85305	0.1075	10	0.40728	T	0.16	.	15.6832	0.77388	0.0:0.0:1.0:0.0	rs8140287;rs52820185;rs8140287	83	Q2M1V0	ISX_HUMAN	Q	83	ENSP00000311492:R83Q;ENSP00000386037:R83Q	ENSP00000311492:R83Q	R	+	2	0	ISX	33808529	1.000000	0.71417	0.702000	0.30337	0.788000	0.44548	8.758000	0.91663	2.545000	0.85829	0.650000	0.86243	CGG	G|0.965;A|0.035	0.035	strong		0.557	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494	
OR2B6	26212	hgsc.bcm.edu	37	6	27925367	27925367	+	Missense_Mutation	SNP	G	G	A	rs7767176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:27925367G>A	ENST00000244623.1	+	1	349	c.349G>A	c.(349-351)Gtc>Atc	p.V117I		NM_012367.1	NP_036499.1	P58173	OR2B6_HUMAN	olfactory receptor, family 2, subfamily B, member 6	117			V -> I (in dbSNP:rs7767176).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TCTCCTGGCCGTCATGTCCTT	0.473													G|||	541	0.108027	0.1914	0.098	5008	,	,		19411	0.0288		0.0755	False		,,,				2504	0.1176				p.V117I		Atlas-SNP	.											.	OR2B6	48	.	0			c.G349A						PASS	.	G	ILE/VAL	700,3706	288.1+/-279.7	47,606,1550	74.0	73.0	73.0		349	2.8	0.4	6	dbSNP_116	73	686,7912	169.7+/-221.0	27,632,3640	yes	missense	OR2B6	NM_012367.1	29	74,1238,5190	AA,AG,GG		7.9786,15.8874,10.6583	benign	117/314	27925367	1386,11618	2203	4299	6502	SO:0001583	missense	26212	exon1			CTGGCCGTCATGT	U86275	CCDS4642.1	6p22.1	2012-08-09			ENSG00000124657	ENSG00000124657		"""GPCR / Class A : Olfactory receptors"""	8241	protein-coding gene	gene with protein product				OR2B6P, OR2B1, OR2B1P, OR2B5		9500546	Standard	NM_012367		Approved	OR6-31, dJ408B20.2, OR5-40, OR5-41	uc011dkx.2	P58173	OTTHUMG00000014497	ENST00000244623.1:c.349G>A	6.37:g.27925367G>A	ENSP00000244623:p.Val117Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	177	85	0.480226	NM_012367	O43883|Q6IF89|Q9H5B0	Missense_Mutation	SNP	ENST00000244623.1	37	CCDS4642.1	191	0.08745421245421245	98	0.1991869918699187	35	0.09668508287292818	8	0.013986013986013986	50	0.06596306068601583	g	5.091	0.202345	0.09652	0.158874	0.079786	ENSG00000124657	ENST00000244623	T	0.04862	3.54	3.68	2.8	0.32819	GPCR, rhodopsin-like superfamily (1);	0.346611	0.16009	U	0.233899	T	0.02807	0.0084	L	0.54965	1.715	0.42602	P	0.006712000000000051	B	0.10296	0.003	B	0.12837	0.008	T	0.20538	-1.0272	9	0.52906	T	0.07	.	9.1882	0.37182	0.1146:0.0:0.8854:0.0	rs7767176;rs52838310;rs58027283;rs7767176	117	P58173	OR2B6_HUMAN	I	117	ENSP00000244623:V117I	ENSP00000244623:V117I	V	+	1	0	OR2B6	28033346	0.017000	0.18338	0.394000	0.26270	0.022000	0.10575	0.977000	0.29475	0.814000	0.34374	0.563000	0.77884	GTC	G|0.897;A|0.103	0.103	strong		0.473	OR2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040165.1		
CDH23	64072	hgsc.bcm.edu	37	10	73455201	73455201	+	Silent	SNP	T	T	C	rs3752752	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:73455201T>C	ENST00000224721.6	+	21	2336	c.2331T>C	c.(2329-2331)aaT>aaC	p.N777N	CDH23_ENST00000299366.7_Silent_p.N817N	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	772	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						TGGACATCAATGACAACCACC	0.592													C|||	2777	0.554513	0.5038	0.5187	5008	,	,		18623	0.4385		0.7068	False		,,,				2504	0.6115				p.N772N		Atlas-SNP	.											.	CDH23	365	.	0			c.T2316C						PASS	.	C	,,	2297,1867		652,993,437	108.0	115.0	113.0		2316,2316,2316	-9.3	0.3	10	dbSNP_107	113	6123,2303		2220,1683,310	no	coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_022124.5	,,	2872,2676,747	CC,CT,TT		27.3321,44.8367,33.1215	,,	772/1382,772/1062,772/3355	73455201	8420,4170	2082	4213	6295	SO:0001819	synonymous_variant	64072	exon21			CATCAATGACAAC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.2331T>C	10.37:g.73455201T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	142	139	0.978873	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				T|0.407;C|0.593	0.593	strong		0.592	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
OR8I2	120586	hgsc.bcm.edu	37	11	55861650	55861650	+	Nonsense_Mutation	SNP	C	C	G	rs61887097	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55861650C>G	ENST00000302124.2	+	1	898	c.867C>G	c.(865-867)taC>taG	p.Y289*		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	289						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					CACTCATCTACAGTCTGAGGA	0.388													C|||	195	0.0389377	0.0121	0.0447	5008	,	,		20568	0.001		0.0944	False		,,,				2504	0.0532				p.Y289X		Atlas-SNP	.											.	OR8I2	119	.	0			c.C867G						PASS	.	C	stop/TYR	96,4306	76.8+/-115.0	0,96,2105	39.0	39.0	39.0		867	-6.0	0.8	11	dbSNP_129	39	690,7896	167.1+/-218.9	34,622,3637	no	stop-gained	OR8I2	NM_001003750.1		34,718,5742	GG,GC,CC		8.0363,2.1808,6.0517		289/311	55861650	786,12202	2201	4293	6494	SO:0001587	stop_gained	120586	exon1			CATCTACAGTCTG	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.867C>G	11.37:g.55861650C>G	ENSP00000303864:p.Tyr289*	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Nonsense_Mutation	SNP	ENST00000302124.2	37	CCDS31517.1	86	0.039377289377289376	4	0.008130081300813009	14	0.03867403314917127	0	0.0	68	0.08970976253298153	C	3.054	-0.194841	0.06259	0.021808	0.080363	ENSG00000172154	ENST00000302124	.	.	.	4.33	-6.01	0.02199	.	0.000000	0.36740	U	0.002431	.	.	.	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.7611	15.6893	0.77436	0.0:0.8302:0.0:0.1698	rs61887097	.	.	.	X	289	.	ENSP00000303864:Y289X	Y	+	3	2	OR8I2	55618226	0.000000	0.05858	0.787000	0.31911	0.016000	0.09150	-1.608000	0.02068	-0.644000	0.05465	-0.760000	0.03462	TAC	.	.	weak		0.388	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
SLC4A7	9497	hgsc.bcm.edu	37	3	27436597	27436597	+	Missense_Mutation	SNP	G	G	A	rs114662202	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:27436597G>A	ENST00000295736.5	-	19	2756	c.2686C>T	c.(2686-2688)Cca>Tca	p.P896S	SLC4A7_ENST00000440156.1_Missense_Mutation_p.P892S|SLC4A7_ENST00000428386.1_Missense_Mutation_p.P772S|SLC4A7_ENST00000445684.1_Missense_Mutation_p.P892S|SLC4A7_ENST00000388777.4_Missense_Mutation_p.P446S|SLC4A7_ENST00000454389.1_Missense_Mutation_p.P905S|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000446700.1_Missense_Mutation_p.P888S|SLC4A7_ENST00000435667.2_Missense_Mutation_p.P781S|SLC4A7_ENST00000455077.1_Missense_Mutation_p.P777S|SLC4A7_ENST00000437179.1_Missense_Mutation_p.P777S	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	896					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CCTCTCTCTGGATGAGTAGGC	0.358													G|||	35	0.00698882	0.0106	0.0086	5008	,	,		17732	0.0		0.0129	False		,,,				2504	0.002				p.P896S		Atlas-SNP	.											SLC4A7,rectum,carcinoma,+2,4	SLC4A7	119	4	0			c.C2686T						scavenged	.	G	SER/PRO	50,4356	51.6+/-87.1	0,50,2153	60.0	59.0	59.0		2686	3.0	1.0	3	dbSNP_132	59	144,8456	66.7+/-129.0	2,140,4158	yes	missense	SLC4A7	NM_003615.3	74	2,190,6311	AA,AG,GG		1.6744,1.1348,1.4916	benign	896/1215	27436597	194,12812	2203	4300	6503	SO:0001583	missense	9497	exon19			TCTCTGGATGAGT	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2686C>T	3.37:g.27436597G>A	ENSP00000295736:p.Pro896Ser	Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	154	64	0.415584	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	13	0.005952380952380952	4	0.008130081300813009	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	10.88	1.475427	0.26511	0.011348	0.016744	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000428179	T;T;T;T;T;T;T;T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	6.06	2.95	0.34219	Bicarbonate transporter, C-terminal (1);	0.308279	0.38217	N	0.001764	T	0.49406	0.1555	N	0.25890	0.77	0.80722	D	1	B;B;B;B;B;B;B;B;B	0.19445	0.033;0.033;0.014;0.036;0.033;0.005;0.026;0.033;0.033	B;B;B;B;B;B;B;B;B	0.29176	0.099;0.04;0.04;0.099;0.099;0.015;0.06;0.099;0.04	T	0.53556	-0.8422	10	0.36615	T	0.2	.	9.3212	0.37966	0.0:0.1003:0.3472:0.5525	.	892;777;888;892;905;446;772;896;777	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	S	447;896;772;905;892;777;888;777;892;781;446;792	ENSP00000411031:P447S;ENSP00000295736:P896S;ENSP00000416368:P772S;ENSP00000390394:P905S;ENSP00000414797:P892S;ENSP00000394252:P777S;ENSP00000406605:P888S;ENSP00000407382:P777S;ENSP00000406804:P892S;ENSP00000395336:P781S;ENSP00000373429:P446S;ENSP00000388703:P792S	ENSP00000295736:P896S	P	-	1	0	SLC4A7	27411601	1.000000	0.71417	0.992000	0.48379	0.649000	0.38597	1.998000	0.40796	0.842000	0.35045	0.655000	0.94253	CCA	G|0.988;A|0.012	0.012	strong		0.358	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
ZFAT	57623	hgsc.bcm.edu	37	8	135612745	135612745	+	Silent	SNP	A	A	G	rs894344	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:135612745A>G	ENST00000377838.3	-	7	2583	c.2409T>C	c.(2407-2409)gaT>gaC	p.D803D	ZFAT_ENST00000520214.1_Silent_p.D791D|ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000520356.1_Silent_p.D791D|ZFAT_ENST00000523399.1_Silent_p.D741D|ZFAT_ENST00000520727.1_Silent_p.D791D|ZFAT_ENST00000429442.2_Silent_p.D791D	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	803					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			AGTCACAGCCATCGGTGGGAC	0.453													G|||	2459	0.491014	0.4168	0.6225	5008	,	,		16931	0.5486		0.4274	False		,,,				2504	0.5041				p.D803D		Atlas-SNP	.											.	ZFAT	265	.	0			c.T2409C						PASS	.	G	,,,,	1543,2401		313,917,742	180.0	178.0	178.0		2373,2373,2223,2373,2409	1.6	1.0	8	dbSNP_86	178	3340,4974		671,1998,1488	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	,,,,	984,2915,2230	GG,GA,AA		40.1732,39.1227,39.8352	,,,,	791/1232,791/1232,741/1182,791/1146,803/1244	135612745	4883,7375	1972	4157	6129	SO:0001819	synonymous_variant	57623	exon7			ACAGCCATCGGTG	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.2409T>C	8.37:g.135612745A>G		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	216	96	0.444444	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Silent	SNP	ENST00000377838.3	37	CCDS47924.1																																																																																			A|0.542;G|0.458	0.458	strong		0.453	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
MUC16	94025	hgsc.bcm.edu	37	19	9048170	9048170	+	Missense_Mutation	SNP	G	G	A	rs10417600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9048170G>A	ENST00000397910.4	-	5	33664	c.33461C>T	c.(33460-33462)tCt>tTt	p.S11154F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11156	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGTGACCAGAGAGGTCACCAT	0.478													G|||	948	0.189297	0.1982	0.1988	5008	,	,		23687	0.0258		0.2813	False		,,,				2504	0.2444				p.S11154F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C33461T						PASS	.		PHE/SER	749,3069		69,611,1229	86.0	79.0	81.0		33461	2.4	0.0	19	dbSNP_119	81	2497,5763		399,1699,2032	yes	missense	MUC16	NM_024690.2	155	468,2310,3261	AA,AG,GG		30.23,19.6176,26.8753	probably-damaging	11154/14508	9048170	3246,8832	1909	4130	6039	SO:0001583	missense	94025	exon5			ACCAGAGAGGTCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33461C>T	19.37:g.9048170G>A	ENSP00000381008:p.Ser11154Phe	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	406	0.1858974358974359	103	0.20934959349593496	76	0.20994475138121546	11	0.019230769230769232	216	0.2849604221635884	g	6.853	0.526597	0.13066	0.196176	0.3023	ENSG00000181143	ENST00000397910	T	0.02737	4.18	3.43	2.39	0.29439	.	.	.	.	.	T	0.00012	0.0000	L	0.55481	1.735	.	.	.	D	0.76494	0.999	D	0.78314	0.991	T	0.48843	-0.8999	8	0.87932	D	0	.	6.5891	0.22636	0.1311:0.0:0.8689:0.0	rs10417600;rs52818682;rs10417600	11154	B5ME49	.	F	11154	ENSP00000381008:S11154F	ENSP00000381008:S11154F	S	-	2	0	MUC16	8909170	0.001000	0.12720	0.002000	0.10522	0.011000	0.07611	0.463000	0.21972	0.994000	0.38892	0.550000	0.68814	TCT	G|0.796;A|0.204	0.204	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CC2D1A	54862	hgsc.bcm.edu	37	19	14040420	14040420	+	Missense_Mutation	SNP	G	G	A	rs201921029		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14040420G>A	ENST00000318003.7	+	26	2898	c.2657G>A	c.(2656-2658)cGc>cAc	p.R886H	CC2D1A_ENST00000589606.1_Missense_Mutation_p.R885H	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	886					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			ATCATGCAACGCAGCCAGTGG	0.657																																					p.R886H		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G2657A						PASS	.	G	HIS/ARG	1,4027		0,1,2013	10.0	14.0	12.0		2657	2.3	1.0	19		12	11,8333		0,11,4161	yes	missense	CC2D1A	NM_017721.4	29	0,12,6174	AA,AG,GG		0.1318,0.0248,0.097	benign	886/952	14040420	12,12360	2014	4172	6186	SO:0001583	missense	54862	exon26			TGCAACGCAGCCA	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.2657G>A	19.37:g.14040420G>A	ENSP00000313601:p.Arg886His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.008455	0.35415	2.48E-4	0.001318	ENSG00000132024	ENST00000318003;ENST00000254346	T	0.20738	2.05	4.89	2.33	0.28932	.	0.066900	0.56097	D	0.000037	T	0.11879	0.0289	L	0.29908	0.895	0.41298	D	0.987024	B;B;B	0.29232	0.088;0.017;0.238	B;B;B	0.18561	0.015;0.005;0.022	T	0.10636	-1.0621	10	0.49607	T	0.09	-17.143	5.6295	0.17501	0.0919:0.1409:0.6232:0.144	.	507;885;886	Q9NX28;Q6P1N0-2;Q6P1N0	.;.;C2D1A_HUMAN	H	886;508	ENSP00000313601:R886H	ENSP00000254346:R508H	R	+	2	0	CC2D1A	13901420	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	3.033000	0.49743	1.044000	0.40200	-0.440000	0.05779	CGC	.	.	weak		0.657	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
KHDRBS2	202559	hgsc.bcm.edu	37	6	62442604	62442604	+	Silent	SNP	A	A	G	rs10484690	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:62442604A>G	ENST00000281156.4	-	7	1154	c.876T>C	c.(874-876)taT>taC	p.Y292Y		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	292					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		TTTGGGTCGCATAGCTGTTAT	0.383													A|||	1957	0.390775	0.6218	0.3242	5008	,	,		17006	0.3046		0.2813	False		,,,				2504	0.3272				p.Y292Y		Atlas-SNP	.											.	KHDRBS2	103	.	0			c.T876C						PASS	.	A		2511,1895	629.1+/-395.2	731,1049,423	191.0	184.0	187.0		876	3.2	1.0	6	dbSNP_119	187	2637,5963	426.4+/-355.3	402,1833,2065	no	coding-synonymous	KHDRBS2	NM_152688.2		1133,2882,2488	GG,GA,AA		30.6628,43.0095,39.5817		292/350	62442604	5148,7858	2203	4300	6503	SO:0001819	synonymous_variant	202559	exon7			GGTCGCATAGCTG	BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"""Sam68-like mammalian protein 1"""	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.876T>C	6.37:g.62442604A>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	201	103	0.512438	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Silent	SNP	ENST00000281156.4	37	CCDS4963.1																																																																																			A|0.601;G|0.399	0.399	strong		0.383	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688	
FXYD5	53827	hgsc.bcm.edu	37	19	35649281	35649281	+	Silent	SNP	A	A	G	rs1128882	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:35649281A>G	ENST00000342879.3	+	3	955	c.177A>G	c.(175-177)ccA>ccG	p.P59P	FXYD5_ENST00000541435.2_Silent_p.P59P|FXYD5_ENST00000543307.1_Silent_p.P59P|FXYD5_ENST00000392218.2_Silent_p.P59P|FXYD5_ENST00000392219.2_Silent_p.P59P|FXYD5_ENST00000423817.3_Silent_p.P59P|FXYD5_ENST00000588699.1_Silent_p.P59P|FXYD5_ENST00000590686.1_Silent_p.P59P			Q96DB9	FXYD5_HUMAN	FXYD domain containing ion transport regulator 5	59					microvillus assembly (GO:0030033)|negative regulation of calcium-dependent cell-cell adhesion (GO:0046588)	integral component of membrane (GO:0016021)	actin binding (GO:0003779)|cadherin binding (GO:0045296)|ion channel activity (GO:0005216)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9	all_lung(56;9.4e-09)|Lung NSC(56;1.4e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.75e-22)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;7.07e-19)|LUSC - Lung squamous cell carcinoma(66;0.0221)			CCACCTCTCCAACCCCAACCT	0.537													a|||	1018	0.203275	0.1914	0.245	5008	,	,		16035	0.1171		0.1779	False		,,,				2504	0.3047				p.P59P		Atlas-SNP	.											.	FXYD5	41	.	0			c.A177G						PASS	.	G	,,	964,3442	364.1+/-316.8	100,764,1339	78.0	72.0	74.0		177,177,177	1.8	0.0	19	dbSNP_86	74	1469,7131	278.6+/-293.5	134,1201,2965	no	coding-synonymous,coding-synonymous,coding-synonymous	FXYD5	NM_001164605.1,NM_014164.5,NM_144779.2	,,	234,1965,4304	GG,GA,AA		17.0814,21.8793,18.7068	,,	59/179,59/179,59/179	35649281	2433,10573	2203	4300	6503	SO:0001819	synonymous_variant	53827	exon4			CTCTCCAACCCCA	AF161462	CCDS12447.1	19q13.12	2008-02-05	2002-01-14		ENSG00000089327	ENSG00000089327			4029	protein-coding gene	gene with protein product	"""dysadherin"""	606669	"""FXYD domain-containing ion transport regulator 5"""				Standard	NM_144779		Approved	OIT2	uc002nyg.2	Q96DB9	OTTHUMG00000048092	ENST00000342879.3:c.177A>G	19.37:g.35649281A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_014164	B7WNZ8|Q6UW44|Q9HC34|Q9P039	Silent	SNP	ENST00000342879.3	37	CCDS12447.1																																																																																			A|0.828;G|0.172	0.172	strong		0.537	FXYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109443.1	NM_014164	
GPX7	2882	hgsc.bcm.edu	37	1	53068093	53068093	+	Silent	SNP	G	G	T	rs11205977	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:53068093G>T	ENST00000361314.4	+	1	50	c.12G>T	c.(10-12)gcG>gcT	p.A4A	GPX7_ENST00000459779.1_3'UTR	NM_015696.4	NP_056511.2	Q96SL4	GPX7_HUMAN	glutathione peroxidase 7	4					response to oxidative stress (GO:0006979)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	glutathione peroxidase activity (GO:0004602)|peroxidase activity (GO:0004601)			breast(1)|kidney(1)|lung(4)|upper_aerodigestive_tract(1)	7					Glutathione(DB00143)	TGGTGGCGGCGACGGTGGCAG	0.721													G|||	240	0.0479233	0.0272	0.0706	5008	,	,		8720	0.001		0.0944	False		,,,				2504	0.0603				p.A4A		Atlas-SNP	.											.	GPX7	16	.	0			c.G12T						PASS	.	G		118,4028		2,114,1957	9.0	8.0	8.0		12	-6.0	0.0	1	dbSNP_120	8	647,7525		22,603,3461	no	coding-synonymous	GPX7	NM_015696.4		24,717,5418	TT,TG,GG		7.9173,2.8461,6.2104		4/188	53068093	765,11553	2073	4086	6159	SO:0001819	synonymous_variant	2882	exon1			GGCGGCGACGGTG	AF091092	CCDS569.1	1p32	2008-02-05			ENSG00000116157	ENSG00000116157			4559	protein-coding gene	gene with protein product		615784				15294905	Standard	NM_015696		Approved	FLJ14777, GPX6, NPGPx	uc001cue.3	Q96SL4	OTTHUMG00000008322	ENST00000361314.4:c.12G>T	1.37:g.53068093G>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	31	23	0.741935	NM_015696	O95337|Q5T501	Silent	SNP	ENST00000361314.4	37	CCDS569.1																																																																																			G|0.951;T|0.049	0.049	strong		0.721	GPX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022913.1	NM_015696	
FAM26F	441168	hgsc.bcm.edu	37	6	116783330	116783330	+	Missense_Mutation	SNP	G	G	A	rs1057192	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:116783330G>A	ENST00000368605.1	+	2	333	c.238G>A	c.(238-240)Gga>Aga	p.G80R	FAM26F_ENST00000368606.3_Intron|RP1-93H18.6_ENST00000476099.1_RNA	NM_001010919.1	NP_001010919.1	Q5R3K3	FA26F_HUMAN	family with sequence similarity 26, member F	80			G -> R (in dbSNP:rs1057192).		ion transport (GO:0006811)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(1)	3				GBM - Glioblastoma multiforme(226;0.0402)|all cancers(137;0.0627)|OV - Ovarian serous cystadenocarcinoma(136;0.0655)|Epithelial(106;0.231)		CCTGCTCACCGGATGCTGCTC	0.721													G|||	1200	0.239617	0.0628	0.17	5008	,	,		13100	0.3651		0.2485	False		,,,				2504	0.3896				p.E80K		Atlas-SNP	.											.	FAM26F	12	.	0			c.G238A						PASS	.	G	ARG/GLY	285,3437		11,263,1587	4.0	4.0	4.0		238	4.2	1.0	6	dbSNP_86	4	1331,5787		122,1087,2350	yes	missense	FAM26F	NM_001010919.1	125	133,1350,3937	AA,AG,GG		18.6991,7.6572,14.9077	probably-damaging	80/316	116783330	1616,9224	1861	3559	5420	SO:0001583	missense	441168	exon2			CTCACCGGATGCT	AF086130	CCDS34519.1, CCDS64506.1	6q22.1	2007-06-20			ENSG00000188820	ENSG00000188820			33391	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 187"""	C6orf187			Standard	NM_001010919		Approved	RP1-93H18.5, OTTHUMP00000017061, OTTHUMP00000017062, dJ93H18.5	uc003pwv.4	Q5R3K3	OTTHUMG00000015438	ENST00000368605.1:c.238G>A	6.37:g.116783330G>A	ENSP00000357594:p.Gly80Arg	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_001010919	B9EJB0|Q5R3K4	Missense_Mutation	SNP	ENST00000368605.1	37	CCDS34519.1	492	0.22527472527472528	23	0.046747967479674794	64	0.17679558011049723	209	0.36538461538461536	196	0.25857519788918204	G	19.26	3.793370	0.70452	0.076572	0.186991	ENSG00000188820	ENST00000368605	T	0.24908	1.83	5.1	4.22	0.49857	.	0.060943	0.64402	D	0.000004	T	0.45498	0.1345	M	0.83223	2.63	0.09310	P	0.999999384292	D	0.89917	1.0	D	0.79784	0.993	T	0.59150	-0.7508	9	0.87932	D	0	-20.7189	15.7243	0.77743	0.0:0.137:0.863:0.0	rs1057192;rs3173147	80	Q5R3K3	FA26F_HUMAN	R	80	ENSP00000357594:G80R	ENSP00000357594:G80R	G	+	1	0	FAM26F	116890023	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	4.925000	0.63425	1.372000	0.46190	0.491000	0.48974	GGA	.	.	weak		0.721	FAM26F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041946.1	NM_001010919	
CHIA	27159	hgsc.bcm.edu	37	1	111861822	111861822	+	Silent	SNP	G	G	A	rs17027410	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111861822G>A	ENST00000369740.1	+	10	1099	c.996G>A	c.(994-996)gtG>gtA	p.V332V	CHIA_ENST00000430615.1_Silent_p.V224V|CHIA_ENST00000343320.6_Silent_p.V332V|CHIA_ENST00000483391.1_Silent_p.V171V|CHIA_ENST00000451398.2_Silent_p.V171V|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000353665.6_Silent_p.V171V	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	332					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		AGGGCAATGTGTGGGTTGGCT	0.473													G|||	374	0.0746805	0.0893	0.0735	5008	,	,		19405	0.0		0.1093	False		,,,				2504	0.0971				p.V332V		Atlas-SNP	.											.	CHIA	115	.	0			c.G996A						PASS	.	G	,	432,3974	207.8+/-229.1	14,404,1785	139.0	129.0	132.0		672,996	2.1	0.4	1	dbSNP_123	132	1013,7587	215.9+/-255.1	51,911,3338	no	coding-synonymous,coding-synonymous	CHIA	NM_021797.2,NM_201653.2	,	65,1315,5123	AA,AG,GG		11.7791,9.8048,11.1103	,	224/369,332/477	111861822	1445,11561	2203	4300	6503	SO:0001819	synonymous_variant	27159	exon10			CAATGTGTGGGTT	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.996G>A	1.37:g.111861822G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	195	82	0.420513	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	37	CCDS41368.1																																																																																			G|0.898;A|0.102	0.102	strong		0.473	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
ELF1	1997	hgsc.bcm.edu	37	13	41515371	41515371	+	Silent	SNP	C	C	T	rs7987185	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:41515371C>T	ENST00000239882.3	-	8	1256	c.942G>A	c.(940-942)tcG>tcA	p.S314S	ELF1_ENST00000442101.1_Silent_p.S290S|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	314					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		ATGAAGATAGCGATGGATCTG	0.418													C|||	663	0.132388	0.2209	0.1282	5008	,	,		15035	0.0843		0.1362	False		,,,				2504	0.0613				p.S314S		Atlas-SNP	.											.	ELF1	65	.	0			c.G942A						PASS	.	C	,	973,3433	368.3+/-318.6	101,771,1331	112.0	123.0	119.0		870,942	-1.3	0.1	13	dbSNP_116	119	1486,7114	282.8+/-295.8	124,1238,2938	no	coding-synonymous,coding-synonymous	ELF1	NM_001145353.1,NM_172373.3	,	225,2009,4269	TT,TC,CC		17.2791,22.0835,18.9067	,	290/596,314/620	41515371	2459,10547	2203	4300	6503	SO:0001819	synonymous_variant	1997	exon8			AGATAGCGATGGA	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.942G>A	13.37:g.41515371C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	62	55	0.887097	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Silent	SNP	ENST00000239882.3	37	CCDS9374.1																																																																																			C|0.830;T|0.170	0.170	strong		0.418	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
LPCAT3	10162	hgsc.bcm.edu	37	12	7090193	7090193	+	Missense_Mutation	SNP	A	A	G	rs1984564	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7090193A>G	ENST00000261407.4	-	6	735	c.650T>C	c.(649-651)aTt>aCt	p.I217T	U47924.30_ENST00000606112.1_lincRNA|LPCAT3_ENST00000535021.1_5'UTR	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	217			I -> T (in dbSNP:rs1984564).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						TGGTATGTCAATCAGCTCTCC	0.478													G|||	1238	0.247204	0.6437	0.1455	5008	,	,		-128	0.0615		0.0885	False		,,,				2504	0.138				p.I217T		Atlas-SNP	.											.	LPCAT3	33	.	0			c.T650C						PASS	.	G	THR/ILE	2409,1997	560.2+/-380.4	668,1073,462	158.0	154.0	156.0		650	5.9	1.0	12	dbSNP_92	156	726,7874	786.7+/-407.6	32,662,3606	yes	missense	LPCAT3	NM_005768.5	89	700,1735,4068	GG,GA,AA		8.4419,45.3246,24.1043	benign	217/488	7090193	3135,9871	2203	4300	6503	SO:0001583	missense	10162	exon6			ATGTCAATCAGCT	U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"""O-acyltransferase (membrane bound) domain containing 5"", ""membrane bound O-acyltransferase domain containing 5"""	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970	ENST00000261407.4:c.650T>C	12.37:g.7090193A>G	ENSP00000261407:p.Ile217Thr	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	200	96	0.48	NM_005768	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Missense_Mutation	SNP	ENST00000261407.4	37	CCDS8572.1	459	0.21016483516483517	309	0.6280487804878049	57	0.1574585635359116	27	0.0472027972027972	66	0.0870712401055409	G	6.439	0.449195	0.12223	0.546754	0.084419	ENSG00000111684	ENST00000261407	T	0.72615	-0.67	5.88	5.88	0.94601	.	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.02315	-0.6	0.45899	P	0.0012550000000000061	B	0.02656	0.0	B	0.01281	0.0	T	0.39396	-0.9616	9	0.13470	T	0.59	-16.3892	15.2962	0.73910	0.0668:0.0:0.9332:0.0	rs1984564;rs52822576;rs57995561;rs1984564	217	Q6P1A2	MBOA5_HUMAN	T	217	ENSP00000261407:I217T	ENSP00000261407:I217T	I	-	2	0	LPCAT3	6960454	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	4.949000	0.63596	1.508000	0.48769	-0.119000	0.15052	ATT	A|0.759;G|0.241	0.241	strong		0.478	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768	
NRK	203447	hgsc.bcm.edu	37	X	105152282	105152282	+	Missense_Mutation	SNP	G	G	A	rs209373	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:105152282G>A	ENST00000243300.9	+	12	1375	c.1072G>A	c.(1072-1074)Gtg>Atg	p.V358M	NRK_ENST00000428173.2_Missense_Mutation_p.V359M	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	358			V -> M (in dbSNP:rs209373). {ECO:0000269|PubMed:17344846}.		activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						ACAGTACACCGTGAGAAGATT	0.353										HNSCC(51;0.14)			A|||	1404	0.371921	0.5567	0.1441	3775	,	,		14623	0.1796		0.168	False		,,,				2504	0.2229				p.V358M		Atlas-SNP	.											.	NRK	321	.	0			c.G1072A						PASS	.	A	MET/VAL	1890,1045		518,533,321,171,170	45.0	39.0	41.0		1072	1.8	0.0	X	dbSNP_79	41	1294,4681		129,677,359,1402,1200	yes	missense	NRK	NM_198465.2	21	647,1210,680,1573,1370	AA,AG,A,GG,G		21.6569,35.6048,35.7351	benign	358/1583	105152282	3184,5726	1713	3767	5480	SO:0001583	missense	203447	exon12			TACACCGTGAGAA	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.1072G>A	X.37:g.105152282G>A	ENSP00000434830:p.Val358Met	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	344	16	0.0465116	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		522	0.31464737793851716	192	0.6	38	0.11377245508982035	54	0.10344827586206896	82	0.11781609195402298	A	0.017	-1.498128	0.01001	0.643952	0.216569	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.76839	1.81;-1.05	4.2	1.83	0.25207	Protein kinase-like domain (1);	1.004370	0.08017	N	0.991435	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45673	-0.9245	9	0.30854	T	0.27	.	5.7859	0.18333	0.6408:0.0:0.3592:0.0	rs209373;rs615456;rs52833891;rs60442877;rs209373	26;358	Q7Z2Y5-2;Q7Z2Y5	.;NRK_HUMAN	M	358;359	ENSP00000434830:V358M;ENSP00000438378:V359M	ENSP00000434830:V358M	V	+	1	0	NRK	105038938	0.025000	0.19082	0.042000	0.18584	0.980000	0.70556	1.472000	0.35376	-0.013000	0.14199	-0.314000	0.08810	GTG	0|0.030;A|0.341	0.341	strong		0.353	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465	
MUC16	94025	hgsc.bcm.edu	37	19	9074697	9074697	+	Missense_Mutation	SNP	G	G	A	rs202216364		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9074697G>A	ENST00000397910.4	-	3	12952	c.12749C>T	c.(12748-12750)aCg>aTg	p.T4250M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4252	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTCCATATTCGTCACTGCTGT	0.478													G|||	1	0.000199681	0.0008	0.0	5008	,	,		24112	0.0		0.0	False		,,,				2504	0.0				p.T4250M		Atlas-SNP	.											.	MUC16	4315	.	0			c.C12749T						PASS	.	G	MET/THR	2,4014		0,2,2006	116.0	113.0	114.0		12749	1.6	0.0	19		114	11,8319		0,11,4154	yes	missense	MUC16	NM_024690.2	81	0,13,6160	AA,AG,GG		0.1321,0.0498,0.1053	probably-damaging	4250/14508	9074697	13,12333	2008	4165	6173	SO:0001583	missense	94025	exon3			ATATTCGTCACTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.12749C>T	19.37:g.9074697G>A	ENSP00000381008:p.Thr4250Met	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	157	70	0.44586	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.052	-0.195075	0.06259	4.98E-4	0.001321	ENSG00000181143	ENST00000397910	T	0.33654	1.4	1.63	1.63	0.23807	.	.	.	.	.	T	0.43809	0.1264	L	0.48642	1.525	.	.	.	D	0.89917	1.0	P	0.61070	0.883	T	0.54430	-0.8295	8	0.87932	D	0	.	6.6867	0.23148	0.0:0.0:1.0:0.0	.	4250	B5ME49	.	M	4250	ENSP00000381008:T4250M	ENSP00000381008:T4250M	T	-	2	0	MUC16	8935697	0.000000	0.05858	0.002000	0.10522	0.043000	0.13939	0.138000	0.16016	1.205000	0.43262	0.205000	0.17691	ACG	.	.	weak		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DAGLB	221955	hgsc.bcm.edu	37	7	6449967	6449967	+	Silent	SNP	T	T	G	rs77154720	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:6449967T>G	ENST00000297056.6	-	14	1783	c.1614A>C	c.(1612-1614)ggA>ggC	p.G538G	DAGLB_ENST00000425398.2_Silent_p.G409G|DAGLB_ENST00000436575.1_Silent_p.G497G|DAGLB_ENST00000428902.2_3'UTR	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	538					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		TGTTGGGGTTTCCTCCAAACA	0.592													T|||	81	0.0161741	0.0	0.0331	5008	,	,		17622	0.0		0.0417	False		,,,				2504	0.0164				p.G538G		Atlas-SNP	.											DAGLB,bladder,carcinoma,-1,1	DAGLB	74	1	0			c.A1614C						PASS	.	T	,	28,4378		1,26,2176	69.0	61.0	64.0		1227,1614	-5.2	0.0	7	dbSNP_132	64	315,8285		4,307,3989	no	coding-synonymous,coding-synonymous	DAGLB	NM_001142936.1,NM_139179.3	,	5,333,6165	GG,GT,TT		3.6628,0.6355,2.6372	,	409/544,538/673	6449967	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	221955	exon14			GGGGTTTCCTCCA	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.1614A>C	7.37:g.6449967T>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	240	117	0.4875	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Silent	SNP	ENST00000297056.6	37	CCDS5350.1																																																																																			T|0.974;G|0.026	0.026	strong		0.592	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
FREM2	341640	hgsc.bcm.edu	37	13	39263218	39263218	+	Silent	SNP	C	C	T	rs144811771		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:39263218C>T	ENST00000280481.7	+	1	1953	c.1737C>T	c.(1735-1737)atC>atT	p.I579I		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	579					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CAGTGCCCATCCTGCCCCTTT	0.532																																					p.I579I		Atlas-SNP	.											.	FREM2	385	.	0			c.C1737T						PASS	.	C		0,4406		0,0,2203	126.0	122.0	123.0		1737	3.5	1.0	13	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FREM2	NM_207361.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		579/3170	39263218	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			GCCCATCCTGCCC	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.1737C>T	13.37:g.39263218C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	18	17	0.944444	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|1.000;T|0.000	0.000	weak		0.532	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
OR52A5	390054	hgsc.bcm.edu	37	11	5153261	5153261	+	Silent	SNP	A	A	G	rs2472530	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5153261A>G	ENST00000307388.1	-	1	611	c.612T>C	c.(610-612)ttT>ttC	p.F204F		NM_001005160.2	NP_001005160.1	Q9H2C5	O52A5_HUMAN	olfactory receptor, family 52, subfamily A, member 5	204					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(18)|skin(3)	35		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		CAAAGGCAACAAATAGGCCAT	0.423													A|||	995	0.198682	0.0144	0.232	5008	,	,		23011	0.3929		0.2028	False		,,,				2504	0.2198				p.F204F		Atlas-SNP	.											.	OR52A5	80	.	0			c.T612C						PASS	.	A		220,4182	131.0+/-167.6	7,206,1988	108.0	104.0	105.0		612	5.1	1.0	11	dbSNP_100	105	1823,6773	326.6+/-317.4	213,1397,2688	no	coding-synonymous	OR52A5	NM_001005160.2		220,1603,4676	GG,GA,AA		21.2075,4.9977,15.7178		204/317	5153261	2043,10955	2201	4298	6499	SO:0001819	synonymous_variant	390054	exon1			GGCAACAAATAGG	BK004433	CCDS31373.1	11p15.4	2012-08-09			ENSG00000171944	ENSG00000171944		"""GPCR / Class A : Olfactory receptors"""	19580	protein-coding gene	gene with protein product							Standard	NM_001005160		Approved		uc010qyx.2	Q9H2C5	OTTHUMG00000066616	ENST00000307388.1:c.612T>C	11.37:g.5153261A>G		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_001005160		Silent	SNP	ENST00000307388.1	37	CCDS31373.1																																																																																			A|0.815;G|0.185	0.185	strong		0.423	OR52A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142823.1	NM_001005160	
DCAF13	25879	hgsc.bcm.edu	37	8	104432631	104432631	+	Silent	SNP	T	T	C	rs3098238	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:104432631T>C	ENST00000297579.5	+	2	943	c.666T>C	c.(664-666)aaT>aaC	p.N222N	DCAF13_ENST00000519682.1_Silent_p.N66N|DCAF13_ENST00000521971.1_Silent_p.N66N|DCAF13_ENST00000521999.1_Intron|DCAF13_ENST00000521716.1_Silent_p.N66N	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	70					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						ATGGAGTCAATTGCTTGGCAA	0.438													T|||	126	0.0251597	0.0151	0.0418	5008	,	,		19085	0.001		0.0626	False		,,,				2504	0.0133				p.N222N		Atlas-SNP	.											.	DCAF13	66	.	0			c.T666C						PASS	.	T		114,4292	86.3+/-125.0	4,106,2093	84.0	81.0	82.0		666	5.3	1.0	8	dbSNP_103	82	677,7923	169.6+/-220.9	31,615,3654	no	coding-synonymous	DCAF13	NM_015420.6		35,721,5747	CC,CT,TT		7.8721,2.5874,6.0818		222/598	104432631	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	25879	exon2			AGTCAATTGCTTG	AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	24535	protein-coding gene	gene with protein product			"""WD repeats and SOF1 domain containing"""	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.666T>C	8.37:g.104432631T>C		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	178	92	0.516854	NM_015420	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Silent	SNP	ENST00000297579.5	37	CCDS34934.1																																																																																			T|0.945;C|0.055	0.055	strong		0.438	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420	
ZBTB46	140685	hgsc.bcm.edu	37	20	62378349	62378349	+	Silent	SNP	C	C	T	rs5019252	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62378349C>T	ENST00000245663.4	-	5	1854	c.1704G>A	c.(1702-1704)gaG>gaA	p.E568E	ZBTB46_ENST00000302995.2_Silent_p.E568E|RP4-583P15.10_ENST00000447343.2_RNA|RP4-583P15.10_ENST00000433905.2_RNA|ZBTB46_ENST00000395104.1_Silent_p.E568E	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	568					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GCGAGTCTTCCTCATCCTTGT	0.726													c|||	1350	0.269569	0.1498	0.379	5008	,	,		10337	0.3472		0.336	False		,,,				2504	0.2055				p.E568E		Atlas-SNP	.											ZBTB46,rectum,carcinoma,0,1	ZBTB46	72	1	0			c.G1704A						PASS	.	T		770,3626		79,612,1507	25.0	24.0	25.0		1704	-7.5	0.0	20	dbSNP_113	25	2820,5768		445,1930,1919	no	coding-synonymous	ZBTB46	NM_025224.3		524,2542,3426	TT,TC,CC		32.8365,17.5159,27.6494		568/590	62378349	3590,9394	2198	4294	6492	SO:0001819	synonymous_variant	140685	exon5			GTCTTCCTCATCC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1704G>A	20.37:g.62378349C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			C|0.724;T|0.276	0.276	strong		0.726	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
IFIT1	3434	hgsc.bcm.edu	37	10	91162677	91162677	+	Silent	SNP	C	C	T	rs303210	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:91162677C>T	ENST00000371804.3	+	2	812	c.645C>T	c.(643-645)gaC>gaT	p.D215D	IFIT1_ENST00000546318.1_Silent_p.D184D|LIPA_ENST00000371837.1_Intron	NM_001270927.1|NM_001548.4	NP_001257856.1|NP_001539.3	P09914	IFIT1_HUMAN	interferon-induced protein with tetratricopeptide repeats 1	215					cellular response to exogenous dsRNA (GO:0071360)|cellular response to type I interferon (GO:0071357)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|intracellular transport of viral protein in host cell (GO:0019060)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of helicase activity (GO:0051097)|negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	15						TAAATCCAGACAATGGATATA	0.448													C|||	1217	0.243011	0.0318	0.2522	5008	,	,		20642	0.4395		0.2068	False		,,,				2504	0.3569				p.D215D		Atlas-SNP	.											.	IFIT1	30	.	0			c.C645T						PASS	.	C		254,4152	145.4+/-180.2	10,234,1959	223.0	226.0	225.0		645	-1.7	0.0	10	dbSNP_79	225	1657,6943	302.6+/-306.0	155,1347,2798	no	coding-synonymous	IFIT1	NM_001548.3		165,1581,4757	TT,TC,CC		19.2674,5.7649,14.6932		215/479	91162677	1911,11095	2203	4300	6503	SO:0001819	synonymous_variant	3434	exon3			TCCAGACAATGGA	M24594	CCDS31243.1, CCDS59220.1	10q23.31	2014-05-22			ENSG00000185745	ENSG00000185745		"""Tetratricopeptide (TTC) repeat domain containing"""	5407	protein-coding gene	gene with protein product		147690		G10P1, IFI56, IFNAI1		1377167, 3360121	Standard	NM_001548		Approved	GARG-16	uc001kgi.4	P09914	OTTHUMG00000018712	ENST00000371804.3:c.645C>T	10.37:g.91162677C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	36	33	0.916667	NM_001270927	B3KS50|D3DR31|Q5T7J1|Q96QM5	Silent	SNP	ENST00000371804.3	37	CCDS31243.1																																																																																			C|0.815;T|0.185	0.185	strong		0.448	IFIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049302.1	NM_001548	
CFAP46	54777	hgsc.bcm.edu	37	10	134726621	134726621	+	Silent	SNP	G	G	C	rs4880467	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:134726621G>C	ENST00000368586.5	-	18	2362	c.2262C>G	c.(2260-2262)gcC>gcG	p.A754A	TTC40_ENST00000368582.2_Silent_p.A754A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TCTGCCGCCCGGCCAGGATCA	0.637													G|||	1435	0.286542	0.264	0.3429	5008	,	,		18941	0.1498		0.34	False		,,,				2504	0.363				p.A754A		Atlas-SNP	.											.	TTC40	100	.	0			c.C2262G						PASS	.																																			SO:0001819	synonymous_variant	54777	exon18			CCGCCCGGCCAGG																												ENST00000368586.5:c.2262C>G	10.37:g.134726621G>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	194	87	0.448454	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			G|0.740;C|0.260	0.260	strong		0.637	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
ARSG	22901	hgsc.bcm.edu	37	17	66366659	66366659	+	Missense_Mutation	SNP	C	C	G	rs144503106	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:66366659C>G	ENST00000448504.2	+	8	1772	c.976C>G	c.(976-978)Cgt>Ggt	p.R326G	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Missense_Mutation_p.R162G	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	326					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.R326C(1)		NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTGGCAAACTCGTCAAGGTAA	0.552													C|||	19	0.00379393	0.0008	0.0058	5008	,	,		18113	0.001		0.0129	False		,,,				2504	0.0				p.R326G		Atlas-SNP	.											ARSG,rectum,carcinoma,0,1	ARSG	55	1	1	Substitution - Missense(1)	large_intestine(1)	c.C976G						scavenged	.	C	GLY/ARG	12,4394	20.2+/-43.8	0,12,2191	99.0	82.0	87.0		976	4.0	0.0	17	dbSNP_134	87	186,8414	82.6+/-145.2	1,184,4115	yes	missense	ARSG	NM_014960.3	125	1,196,6306	GG,GC,CC		2.1628,0.2724,1.5224	benign	326/526	66366659	198,12808	2203	4300	6503	SO:0001583	missense	22901	exon8			CAAACTCGTCAAG	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"""Arylsulfatase family"""	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.976C>G	17.37:g.66366659C>G	ENSP00000407193:p.Arg326Gly	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	247	107	0.433198	NM_001267727	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	37	CCDS11676.1	15	0.006868131868131868	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	11	0.014511873350923483	C	4.144	0.025005	0.08054	0.002724	0.021628	ENSG00000141337	ENST00000452479;ENST00000448504	.	.	.	5.0	3.97	0.46021	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.826360	0.11156	N	0.593620	T	0.11623	0.0283	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13098	-1.0522	9	0.11794	T	0.64	.	7.5126	0.27583	0.1953:0.6383:0.1664:0.0	.	326	Q96EG1	ARSG_HUMAN	G	326;225	.	ENSP00000407193:R225G	R	+	1	0	ARSG	63878254	0.000000	0.05858	0.018000	0.16275	0.037000	0.13140	0.480000	0.22244	2.596000	0.87737	0.561000	0.74099	CGT	C|0.988;G|0.012	0.012	strong		0.552	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
PRR3	80742	hgsc.bcm.edu	37	6	30530245	30530245	+	Silent	SNP	T	T	C	rs2074504	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30530245T>C	ENST00000376560.3	+	4	999	c.540T>C	c.(538-540)caT>caC	p.H180H	PRR3_ENST00000498336.1_3'UTR|PRR3_ENST00000376557.3_Silent_p.H159H	NM_025263.3	NP_079539.2	P79522	PRR3_HUMAN	proline rich 3	180							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						CCTTCTACCATCCAGGCGTCA	0.522													.|||	3769	0.752596	0.8419	0.6153	5008	,	,		20539	0.6994		0.6988	False		,,,				2504	0.8395				p.H180H		Atlas-SNP	.											PRR3,NS,carcinoma,+2,1	PRR3	5	1	0			c.T540C						PASS	.	C	,	3413,657		1434,545,56	167.0	167.0	167.0		477,540	0.9	1.0	6	dbSNP_96	167	5915,2519		2099,1717,401	yes	coding-synonymous,coding-synonymous	PRR3	NM_001077497.2,NM_025263.3	,	3533,2262,457	CC,CT,TT		29.8672,16.1425,25.3999	,	159/168,180/189	30530245	9328,3176	2035	4217	6252	SO:0001819	synonymous_variant	80742	exon4			CTACCATCCAGGC	AK074531	CCDS43440.1, CCDS43441.1	6p21.32	2013-01-18	2004-05-27		ENSG00000204576	ENSG00000204576		"""Zinc fingers, CCCH-type domain containing"""	21149	protein-coding gene	gene with protein product			"""proline-rich polpeptide 3"""				Standard	NM_025263		Approved	CAT56, Em:AB014077.1, Em:AB023052.2	uc003nqi.2	P79522	OTTHUMG00000031037	ENST00000376560.3:c.540T>C	6.37:g.30530245T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_025263	A1A4H4|Q5RJB5|Q5STN6	Silent	SNP	ENST00000376560.3	37	CCDS43440.1																																																																																			T|0.274;C|0.726	0.726	strong		0.522	PRR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076033.2	NM_025263	
ZNF486	90649	hgsc.bcm.edu	37	19	20308488	20308488	+	Silent	SNP	G	G	T	rs181719180	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:20308488G>T	ENST00000335117.8	+	4	1026	c.969G>T	c.(967-969)acG>acT	p.T323T	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	323					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						AACCGTACACGTGTGATAAAT	0.388													G|||	17	0.00339457	0.0	0.0058	5008	,	,		21939	0.0		0.0109	False		,,,				2504	0.002				p.T323T		Atlas-SNP	.											ZNF486_ENST00000335117,NS,carcinoma,+1,4	ZNF486	74	4	0			c.G969T						PASS	.	G		6,4348		0,6,2171	47.0	52.0	50.0		969	-1.7	0.1	19		50	53,8525		0,53,4236	no	coding-synonymous	ZNF486	NM_052852.2		0,59,6407	TT,TG,GG		0.6179,0.1378,0.4562		323/464	20308488	59,12873	2177	4289	6466	SO:0001819	synonymous_variant	90649	exon4			GTACACGTGTGAT	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"""Zinc fingers, C2H2-type"", ""-"""	20807	protein-coding gene	gene with protein product			"""KRAB domain only 2"""	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.969G>T	19.37:g.20308488G>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	24	9	0.375	NM_052852	Q0VG00	Silent	SNP	ENST00000335117.8	37	CCDS46029.1																																																																																			G|0.995;T|0.005	0.005	strong		0.388	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
NALCN	259232	hgsc.bcm.edu	37	13	101759897	101759897	+	Silent	SNP	G	G	A	rs34513106	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:101759897G>A	ENST00000251127.6	-	22	2601	c.2520C>T	c.(2518-2520)gtC>gtT	p.V840V		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	840					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTTCTCGCCCGACAATGAACA	0.502													G|||	56	0.0111821	0.0318	0.0043	5008	,	,		16303	0.0		0.002	False		,,,				2504	0.0092				p.V840V		Atlas-SNP	.											.	NALCN	431	.	0			c.C2520T						PASS	.	G		113,4293	86.8+/-125.4	4,105,2094	149.0	130.0	137.0		2520	-6.8	0.0	13	dbSNP_126	137	68,8532	40.3+/-97.0	0,68,4232	no	coding-synonymous	NALCN	NM_052867.2		4,173,6326	AA,AG,GG		0.7907,2.5647,1.3917		840/1739	101759897	181,12825	2203	4300	6503	SO:0001819	synonymous_variant	259232	exon22			TCGCCCGACAATG	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.2520C>T	13.37:g.101759897G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	179	88	0.49162	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																			G|0.990;A|0.010	0.010	strong		0.502	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
COL25A1	84570	hgsc.bcm.edu	37	4	109745336	109745336	+	Silent	SNP	T	T	G	rs7689008	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:109745336T>G	ENST00000399132.1	-	35	2369	c.1839A>C	c.(1837-1839)ggA>ggC	p.G613G	COL25A1_ENST00000399127.1_Silent_p.G616G|COL25A1_ENST00000399126.1_Silent_p.G613G	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1											NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		TCACCTTTTCTCCCTTTTCTC	0.438													T|||	1553	0.310104	0.3404	0.2565	5008	,	,		16817	0.3502		0.34	False		,,,				2504	0.2352				p.G616G		Atlas-SNP	.											.	COL25A1	178	.	0			c.A1848C						PASS	.	T	,	1350,2590		242,866,862	173.0	181.0	178.0		1839,1839	3.4	1.0	4	dbSNP_116	178	2963,5357		521,1921,1718	no	coding-synonymous,coding-synonymous	COL25A1	NM_032518.2,NM_198721.1	,	763,2787,2580	GG,GT,TT		35.613,34.264,35.1794	,	613/643,613/655	109745336	4313,7947	1970	4160	6130	SO:0001819	synonymous_variant	84570	exon32			CTTTTCTCCCTTT	AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"""Collagens"""	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.1839A>C	4.37:g.109745336T>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	185	99	0.535135	NM_001256074		Silent	SNP	ENST00000399132.1	37	CCDS43258.1																																																																																			T|0.648;G|0.352	0.352	strong		0.438	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518	
ATG4C	84938	hgsc.bcm.edu	37	1	63299751	63299751	+	Missense_Mutation	SNP	A	A	C	rs146422144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:63299751A>C	ENST00000317868.4	+	8	1183	c.976A>C	c.(976-978)Aaa>Caa	p.K326Q	ATG4C_ENST00000371120.3_Missense_Mutation_p.K326Q	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	326					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						TATTGGTGGCAAACCTAAACA	0.299													A|||	5	0.000998403	0.0	0.0014	5008	,	,		17562	0.0		0.004	False		,,,				2504	0.0				p.K326Q		Atlas-SNP	.											.	ATG4C	96	.	0			c.A976C						PASS	.	A	GLN/LYS,GLN/LYS	4,4402	8.1+/-20.4	0,4,2199	186.0	196.0	193.0		976,976	6.0	1.0	1	dbSNP_134	193	21,8579	14.6+/-50.1	0,21,4279	yes	missense,missense	ATG4C	NM_032852.3,NM_178221.2	53,53	0,25,6478	CC,CA,AA		0.2442,0.0908,0.1922	probably-damaging,probably-damaging	326/459,326/459	63299751	25,12981	2203	4300	6503	SO:0001583	missense	84938	exon8			GGTGGCAAACCTA	AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"""AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog C (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog C (S. cerevisiae)"""	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.976A>C	1.37:g.63299751A>C	ENSP00000322159:p.Lys326Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	21.5	4.159289	0.78226	9.08E-4	0.002442	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000414558	T;T	0.48836	0.8;0.8	5.97	5.97	0.96955	.	0.042802	0.85682	D	0.000000	T	0.67683	0.2919	M	0.87547	2.89	0.80722	D	1	D	0.67145	0.996	D	0.70716	0.97	T	0.74562	-0.3624	10	0.72032	D	0.01	-20.3301	16.4534	0.84003	1.0:0.0:0.0:0.0	.	326	Q96DT6	ATG4C_HUMAN	Q	326;326;326;70	ENSP00000322159:K326Q;ENSP00000360161:K326Q	ENSP00000322159:K326Q	K	+	1	0	ATG4C	63072339	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.285000	0.76669	0.477000	0.44152	AAA	A|0.998;C|0.002	0.002	strong		0.299	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852	
HOXD12	3238	hgsc.bcm.edu	37	2	176964904	176964904	+	Silent	SNP	G	G	A	rs847151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:176964904G>A	ENST00000406506.2	+	1	447	c.375G>A	c.(373-375)ctG>ctA	p.L125L	HOXD12_ENST00000404162.2_Silent_p.L125L			P35452	HXD12_HUMAN	homeobox D12	125					embryonic digit morphogenesis (GO:0042733)|pattern specification process (GO:0007389)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		AGTCTAGCCTGGCTCCTGCAG	0.687													G|||	1516	0.302716	0.5076	0.4121	5008	,	,		14543	0.0585		0.3052	False		,,,				2504	0.1973				p.L125L		Atlas-SNP	.											.	HOXD12	25	.	0			c.G375A						PASS	.	G		1767,2087		421,925,581	17.0	20.0	19.0		375	5.4	0.9	2	dbSNP_86	19	2688,5598		454,1780,1909	no	coding-synonymous	HOXD12	NM_021193.3		875,2705,2490	AA,AG,GG		32.4403,45.8485,36.6969		125/271	176964904	4455,7685	1927	4143	6070	SO:0001819	synonymous_variant	3238	exon1			TAGCCTGGCTCCT		CCDS46456.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170178	ENSG00000170178		"""Homeoboxes / ANTP class : HOXL subclass"""	5135	protein-coding gene	gene with protein product		142988	"""homeo box D12"""	HOX4H		1675198, 1973146	Standard	NM_021193		Approved		uc010zev.1	P35452	OTTHUMG00000150358	ENST00000406506.2:c.375G>A	2.37:g.176964904G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_021193	B5MCP0|Q0VAD7|Q0VAD8|Q9NS03	Silent	SNP	ENST00000406506.2	37	CCDS46456.1																																																																																			G|0.702;A|0.298	0.298	strong		0.687	HOXD12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359253.2	NM_021193	
SCARA5	286133	hgsc.bcm.edu	37	8	27729532	27729532	+	Silent	SNP	G	G	A	rs61737291	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27729532G>A	ENST00000354914.3	-	9	1892	c.1407C>T	c.(1405-1407)atC>atT	p.I469I	SCARA5_ENST00000380385.2_Silent_p.I244I	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	469	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)			central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		TGCAGCGGAAGATGGTTTCCT	0.552													G|||	762	0.152157	0.1074	0.0908	5008	,	,		22281	0.245		0.1243	False		,,,				2504	0.1892				p.I469I		Atlas-SNP	.											.	SCARA5	53	.	0			c.C1407T						PASS	.	G		498,3908	230.4+/-244.6	25,448,1730	149.0	102.0	118.0		1407	4.3	1.0	8	dbSNP_129	118	1053,7547	222.3+/-259.4	71,911,3318	no	coding-synonymous	SCARA5	NM_173833.5		96,1359,5048	AA,AG,GG		12.2442,11.3028,11.9253		469/496	27729532	1551,11455	2203	4300	6503	SO:0001819	synonymous_variant	286133	exon9			GCGGAAGATGGTT	AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"""scavenger receptor class A, member 5 (putative)"""			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.1407C>T	8.37:g.27729532G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Silent	SNP	ENST00000354914.3	37	CCDS6064.1																																																																																			G|0.870;A|0.130	0.130	strong		0.552	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833	
PLSCR4	57088	hgsc.bcm.edu	37	3	145917761	145917761	+	Missense_Mutation	SNP	T	T	C	rs1061409	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:145917761T>C	ENST00000354952.2	-	6	703	c.463A>G	c.(463-465)Att>Gtt	p.I155V	PLSCR4_ENST00000446574.2_Missense_Mutation_p.I155V|PLSCR4_ENST00000433593.2_Intron|PLSCR4_ENST00000493382.1_Missense_Mutation_p.I155V|PLSCR4_ENST00000383083.2_Intron	NM_020353.2	NP_065086.2	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4	155			I -> V (in dbSNP:rs1061409). {ECO:0000269|PubMed:10930526, ECO:0000269|Ref.2}.		cellular response to lipopolysaccharide (GO:0071222)|phospholipid scrambling (GO:0017121)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|enzyme binding (GO:0019899)|phospholipid scramblase activity (GO:0017128)			kidney(1)|large_intestine(6)|lung(9)|urinary_tract(1)	17						TCGGTTACAATGTAAACCATC	0.373													T|||	1203	0.240216	0.0991	0.3847	5008	,	,		18175	0.1925		0.3429	False		,,,				2504	0.272				p.I155V		Atlas-SNP	.											.	PLSCR4	44	.	0			c.A463G						PASS	.	T	,,VAL/ILE	676,3730	284.6+/-277.7	51,574,1578	89.0	87.0	88.0		,,463	-4.7	0.1	3	dbSNP_86	88	2997,5603	463.8+/-366.1	535,1927,1838	yes	intron,intron,missense	PLSCR4	NM_001128306.1,NM_001177304.1,NM_020353.2	,,29	586,2501,3416	CC,CT,TT		34.8488,15.3427,28.2408	,,benign	,,155/330	145917761	3673,9333	2203	4300	6503	SO:0001583	missense	57088	exon6			TTACAATGTAAAC	AF199023	CCDS3133.1, CCDS54651.1	3q24	2008-07-18			ENSG00000114698	ENSG00000114698			16497	protein-coding gene	gene with protein product		607612				10930526	Standard	NM_020353		Approved		uc003evt.4	Q9NRQ2	OTTHUMG00000159415	ENST00000354952.2:c.463A>G	3.37:g.145917761T>C	ENSP00000347038:p.Ile155Val	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	159	159	1	NM_020353	A8K2E9|Q2TTR3|Q658L3|Q6ZR73|Q7Z505	Missense_Mutation	SNP	ENST00000354952.2	37	CCDS3133.1	562	0.2573260073260073	55	0.11178861788617886	122	0.3370165745856354	117	0.20454545454545456	268	0.35356200527704484	T	9.200	1.028131	0.19512	0.153427	0.348488	ENSG00000114698	ENST00000354952;ENST00000446574;ENST00000493382;ENST00000460350;ENST00000476202	T;T;T;T;T	0.29397	1.57;1.57;1.57;2.04;2.04	4.87	-4.72	0.03269	.	0.919954	0.09282	N	0.823544	T	0.00012	0.0000	N	0.11927	0.2	0.25293	P	0.9893425	B	0.02656	0.0	B	0.04013	0.001	T	0.45454	-0.9260	9	0.42905	T	0.14	.	2.8737	0.05625	0.5697:0.1473:0.1:0.183	rs1061409;rs3202511;rs3762689;rs17348947;rs58938364;rs1061409	155	Q9NRQ2	PLS4_HUMAN	V	155	ENSP00000347038:I155V;ENSP00000399315:I155V;ENSP00000419040:I155V;ENSP00000417896:I155V;ENSP00000418173:I155V	ENSP00000347038:I155V	I	-	1	0	PLSCR4	147400451	0.004000	0.15560	0.095000	0.20976	0.564000	0.35744	-1.353000	0.02617	-0.906000	0.03866	0.533000	0.62120	ATT	T|0.734;C|0.266	0.266	strong		0.373	PLSCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355172.1	NM_020353	
RNF213	57674	hgsc.bcm.edu	37	17	78272294	78272294	+	Missense_Mutation	SNP	C	C	T	rs72849841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78272294C>T	ENST00000582970.1	+	11	2329	c.2186C>T	c.(2185-2187)cCg>cTg	p.P729L	RNF213_ENST00000508628.2_Missense_Mutation_p.P778L|RNF213_ENST00000456466.1_Missense_Mutation_p.P729L|RNF213_ENST00000319921.4_Missense_Mutation_p.P729L	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	729					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TCCTTCTCACCGTTCCGGGAA	0.572													c|||	570	0.113818	0.1997	0.0692	5008	,	,		17967	0.0149		0.1402	False		,,,				2504	0.1043				p.P729L		Atlas-SNP	.											RNF213_ENST00000456466,colon,carcinoma,-1,3	RNF213	766	3	0			c.C2186T						PASS	.	C	LEU/PRO,LEU/PRO	707,3699	295.6+/-283.7	56,595,1552	82.0	70.0	74.0		2333,2186	2.1	0.0	17	dbSNP_130	74	1182,7418	239.4+/-270.5	82,1018,3200	yes	missense,missense	RNF213	NM_020914.4,NM_020954.2	98,98	138,1613,4752	TT,TC,CC		13.7442,16.0463,14.5241	benign,benign	778/5257,729/1064	78272294	1889,11117	2203	4300	6503	SO:0001583	missense	57674	exon11			TCTCACCGTTCCG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.2186C>T	17.37:g.78272294C>T	ENSP00000464087:p.Pro729Leu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	159	74	0.465409	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	245	0.11217948717948718	112	0.22764227642276422	27	0.07458563535911603	9	0.015734265734265736	97	0.1279683377308707	c	1.845	-0.466542	0.04476	0.160463	0.137442	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.14144	2.53;2.53	4.45	2.14	0.27477	.	0.990181	0.08196	N	0.982985	T	0.00012	0.0000	N	0.08118	0	0.51767	P	6.399999999995298E-5	B;B	0.23806	0.045;0.091	B;B	0.17098	0.017;0.017	T	0.42582	-0.9443	9	0.48119	T	0.1	-14.6717	10.3194	0.43756	0.4867:0.5133:0.0:0.0	.	729;729	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	L	729;778;729;729	ENSP00000392123:P729L;ENSP00000324392:P729L	ENSP00000324392:P729L	P	+	2	0	RNF213	75886889	0.001000	0.12720	0.040000	0.18447	0.004000	0.04260	0.629000	0.24538	0.300000	0.22699	-0.280000	0.10049	CCG	C|0.869;T|0.131	0.131	strong		0.572	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
ATP2B3	492	hgsc.bcm.edu	37	X	152823728	152823728	+	Silent	SNP	G	G	C	rs2269415	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:152823728G>C	ENST00000349466.2	+	16	2918	c.2592G>C	c.(2590-2592)gtG>gtC	p.V864V	ATP2B3_ENST00000263519.4_Silent_p.V864V|ATP2B3_ENST00000460549.1_3'UTR|ATP2B3_ENST00000393842.1_Silent_p.V850V|ATP2B3_ENST00000370186.1_Silent_p.V850V|ATP2B3_ENST00000359149.3_Silent_p.V864V|ATP2B3_ENST00000370181.2_Silent_p.V850V			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	864					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGTGGCTGTGATCGTGGCCT	0.572													G|||	1789	0.473907	0.0719	0.4914	3775	,	,		12276	0.4841		0.3867	False		,,,				2504	0.4867				p.V864V		Atlas-SNP	.											.	ATP2B3	552	.	0			c.G2592C						PASS	.	G	,	555,3280		39,406,71,1187,500	209.0	144.0	166.0		2592,2592	4.8	1.0	X	dbSNP_100	166	3558,3170		708,1174,968,546,904	no	coding-synonymous,coding-synonymous	ATP2B3	NM_001001344.2,NM_021949.3	,	747,1580,1039,1733,1404	CC,CG,C,GG,G		47.1165,14.472,38.9378	,	864/1221,864/1174	152823728	4113,6450	2203	4300	6503	SO:0001819	synonymous_variant	492	exon15			GGCTGTGATCGTG	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"""ATPases / P-type"""	816	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 3"", ""cilia and flagella associated protein 39"""	300014	"""spinocerebellar ataxia, X-linked 1"", ""cerebellar ataxia 2 (X-linked)"""	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.2592G>C	X.37:g.152823728G>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	339	217	0.640118	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	37	CCDS35440.1																																																																																			0|0.002;C|0.416	0.416	strong		0.572	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14848820	14848820	+	Missense_Mutation	SNP	C	C	T	rs4090319	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:14848820C>T	ENST00000358984.4	+	34	3110	c.2930C>T	c.(2929-2931)aCg>aTg	p.T977M		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	977				T -> M (in Ref. 3; AAK27326 and 4; BAG57852). {ECO:0000305}.				p.T977M(1)		breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						ATGGAACAAACGAAAAATAAG	0.348													C|||	2007	0.400759	0.0257	0.5173	5008	,	,		15920	0.5685		0.4801	False		,,,				2504	0.5706				p.T977M		Atlas-SNP	.											ANKRD30B_ENST00000358984,NS,carcinoma,0,1	ANKRD30B	237	1	1	Substitution - Missense(1)	kidney(1)	c.C2930T						PASS	.						76.0	56.0	62.0					18																	14848820		692	1587	2279	SO:0001583	missense	374860	exon34			AACAAACGAAAAA	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.2930C>T	18.37:g.14848820C>T	ENSP00000351875:p.Thr977Met	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	250	123	0.492	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	37	CCDS54182.1	777	0.3557692307692308	21	0.042682926829268296	165	0.4558011049723757	281	0.49125874125874125	310	0.40897097625329815	C	0.001	-3.829587	0.00004	.	.	ENSG00000180777	ENST00000358984;ENST00000320584;ENST00000277669	T	0.15952	2.38	1.48	0.0525	0.14302	.	.	.	.	.	T	0.00012	0.0000	N	0.01048	-1.04	0.09310	P	0.999999854054	B;B	0.12630	0.0;0.006	B;B	0.04013	0.0;0.001	T	0.45469	-0.9259	8	0.02654	T	1	.	4.8651	0.13604	0.0:0.1894:0.0:0.8106	rs4090319	1062;977	Q9BXX2;F8WAG3	AN30B_HUMAN;.	M	977;371;397	ENSP00000351875:T977M	ENSP00000277669:T397M	T	+	2	0	ANKRD30B	14838820	0.992000	0.36948	0.027000	0.17364	0.012000	0.07955	2.178000	0.42519	0.068000	0.16574	-1.169000	0.01745	ACG	.	.	weak		0.348	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
OVCH1	341350	hgsc.bcm.edu	37	12	29596365	29596365	+	Missense_Mutation	SNP	T	T	C	rs78265994	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:29596365T>C	ENST00000318184.5	-	25	3085	c.3086A>G	c.(3085-3087)aAg>aGg	p.K1029R	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	1029						extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AGTTGTTGGCTTCATCGGGAA	0.363													T|||	207	0.0413339	0.0151	0.0591	5008	,	,		16493	0.001		0.0915	False		,,,				2504	0.0542				p.K1029R		Atlas-SNP	.											.	OVCH1	195	.	0			c.A3086G						PASS	.	T	ARG/LYS	90,3574		1,88,1743	131.0	131.0	131.0		3086	1.2	0.1	12	dbSNP_131	131	660,7528		30,600,3464	yes	missense	OVCH1	NM_183378.2	26	31,688,5207	CC,CT,TT		8.0606,2.4563,6.328	possibly-damaging	1029/1135	29596365	750,11102	1832	4094	5926	SO:0001583	missense	341350	exon25			GTTGGCTTCATCG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.3086A>G	12.37:g.29596365T>C	ENSP00000326708:p.Lys1029Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		95	0.043498168498168496	8	0.016260162601626018	15	0.04143646408839779	0	0.0	72	0.09498680738786279	T	2.410	-0.335546	0.05278	0.024563	0.080606	ENSG00000187950	ENST00000318184;ENST00000537054	T;T	0.34072	1.38;2.12	2.43	1.22	0.21188	CUB (2);	.	.	.	.	T	0.00440	0.0014	N	0.08118	0	0.80722	P	0.0	P	0.39480	0.675	B	0.22386	0.039	T	0.12811	-1.0533	8	0.34782	T	0.22	.	5.3715	0.16142	0.0:0.0:0.2973:0.7027	.	1029	Q7RTY7	OVCH1_HUMAN	R	1029;54	ENSP00000326708:K1029R;ENSP00000445480:K54R	ENSP00000326708:K1029R	K	-	2	0	OVCH1	29487632	0.202000	0.23423	0.070000	0.20053	0.083000	0.17756	1.476000	0.35420	0.348000	0.23949	0.533000	0.62120	AAG	T|0.952;C|0.048	0.048	strong		0.363	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
CCND3	896	hgsc.bcm.edu	37	6	41903783	41903783	+	Silent	SNP	G	G	A	rs386700585|rs3218102	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41903783G>A	ENST00000372991.4	-	5	972	c.774C>T	c.(772-774)gcC>gcT	p.A258A	CCND3_ENST00000510503.1_Missense_Mutation_p.L132F|CCND3_ENST00000372987.4_Silent_p.A208A|CCND3_ENST00000511642.1_Silent_p.A177A|CCND3_ENST00000511686.1_5'UTR|CCND3_ENST00000372988.4_Silent_p.A177A|CCND3_ENST00000414200.2_Silent_p.A186A|CCND3_ENST00000415497.2_Silent_p.A62A	NM_001760.3	NP_001751.1	P30281	CCND3_HUMAN	cyclin D3	258					cell cycle (GO:0007049)|cell division (GO:0051301)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase binding (GO:0019901)			endometrium(2)|haematopoietic_and_lymphoid_tissue(13)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	20	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGGTCTGAGAGGCTTCCCTGA	0.637			T	IGH@	MM								G|||	322	0.0642971	0.1195	0.1513	5008	,	,		14932	0.002		0.0209	False		,,,				2504	0.0368				p.A258A		Atlas-SNP	.		Dom	yes		6	6p21	896	cyclin D3		L	.	CCND3	40	.	0			c.C774T						PASS	.						44.0	49.0	47.0					6																	41903783		2203	4300	6503	SO:0001819	synonymous_variant	896	exon5			CTGAGAGGCTTCC		CCDS4863.1, CCDS47425.1, CCDS47426.1, CCDS47427.1, CCDS75452.1	6p21	2008-08-26			ENSG00000112576	ENSG00000112576			1585	protein-coding gene	gene with protein product		123834				1386335	Standard	NM_001136125		Approved		uc003orn.3	P30281	OTTHUMG00000014690	ENST00000372991.4:c.774C>T	6.37:g.41903783G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	130	67	0.515385	NM_001760	B2RD63|B3KQ22|E9PAS4|E9PB36|Q5T8J0|Q6FG62|Q96F49	Silent	SNP	ENST00000372991.4	37	CCDS4863.1	78	0.03571428571428571	36	0.07317073170731707	30	0.08287292817679558	0	0.0	12	0.0158311345646438	g	9.151	1.016271	0.19355	.	.	ENSG00000112576	ENST00000510503	T	0.36878	1.23	5.29	-10.4	0.00318	.	.	.	.	.	T	0.11324	0.0276	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.35549	-0.9784	6	0.52906	T	0.07	.	6.9935	0.24767	0.612:0.0829:0.2216:0.0836	rs3218102	.	.	.	F	132	ENSP00000425986:L132F	ENSP00000425986:L132F	L	-	1	0	CCND3	42011761	0.000000	0.05858	0.003000	0.11579	0.256000	0.26092	-1.673000	0.01951	-2.526000	0.00494	-1.446000	0.01064	CTC	G|0.956;A|0.044	0.044	strong		0.637	CCND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040540.2	NM_001760	
URB2	9816	hgsc.bcm.edu	37	1	229773441	229773441	+	Silent	SNP	C	C	T	rs3811475	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:229773441C>T	ENST00000258243.2	+	4	3217	c.3081C>T	c.(3079-3081)acC>acT	p.T1027T		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1027						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						GAAAAATCACCGCATTCCTCT	0.463													C|||	1027	0.205072	0.2156	0.2464	5008	,	,		20811	0.4315		0.0626	False		,,,				2504	0.0746				p.T1027T		Atlas-SNP	.											.	URB2	152	.	0			c.C3081T						PASS	.	C		932,3474	354.1+/-312.5	101,730,1372	67.0	69.0	68.0		3081	-6.6	0.0	1	dbSNP_107	68	555,8045	150.6+/-205.5	14,527,3759	no	coding-synonymous	URB2	NM_014777.2		115,1257,5131	TT,TC,CC		6.4535,21.153,11.4332		1027/1525	229773441	1487,11519	2203	4300	6503	SO:0001819	synonymous_variant	9816	exon4			AATCACCGCATTC	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.3081C>T	1.37:g.229773441C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	199	92	0.462312	NM_014777	Q5VYC9	Silent	SNP	ENST00000258243.2	37	CCDS31052.1																																																																																			C|0.857;T|0.143	0.143	strong		0.463	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
WDR90	197335	hgsc.bcm.edu	37	16	706534	706534	+	Silent	SNP	G	G	A	rs28485323	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:706534G>A	ENST00000293879.4	+	18	2199	c.2199G>A	c.(2197-2199)caG>caA	p.Q733Q	LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Silent_p.Q733Q			Q96KV7	WDR90_HUMAN	WD repeat domain 90	733										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCACCCTGCAGCAGGTGGGGT	0.701													G|||	1949	0.389177	0.2708	0.3948	5008	,	,		14412	0.6756		0.2584	False		,,,				2504	0.3845				p.Q733Q		Atlas-SNP	.											.	WDR90	107	.	0			c.G2199A						PASS	.	G		857,2909		112,633,1138	6.0	8.0	8.0		2199	2.7	1.0	16	dbSNP_125	8	1762,6382		204,1354,2514	no	coding-synonymous	WDR90	NM_145294.4		316,1987,3652	AA,AG,GG		21.6356,22.7562,21.9899		733/1749	706534	2619,9291	1883	4072	5955	SO:0001819	synonymous_variant	197335	exon18			CCTGCAGCAGGTG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.2199G>A	16.37:g.706534G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			G|0.606;A|0.394	0.394	strong		0.701	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
ZC3H11A	9877	hgsc.bcm.edu	37	1	203818973	203818973	+	Silent	SNP	C	C	A	rs41299639	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:203818973C>A	ENST00000545588.1	+	14	5585	c.1758C>A	c.(1756-1758)gcC>gcA	p.A586A	ZC3H11A_ENST00000367212.3_Silent_p.A586A|ZC3H11A_ENST00000367210.1_Silent_p.A586A|ZC3H11A_ENST00000367214.1_Silent_p.A586A|ZC3H11A_ENST00000332127.4_Silent_p.A586A	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	586					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GAGATGTAGCCTCTTGCAATA	0.507													C|||	877	0.17512	0.1112	0.183	5008	,	,		18937	0.1558		0.2197	False		,,,				2504	0.2301				p.A586A		Atlas-SNP	.											.	ZC3H11A	71	.	0			c.C1758A						PASS	.	C		569,3837	253.0+/-259.1	23,523,1657	94.0	88.0	90.0		1758	0.5	0.0	1	dbSNP_127	90	1796,6804	323.2+/-315.9	196,1404,2700	no	coding-synonymous	ZC3H11A	NM_014827.4		219,1927,4357	AA,AC,CC		20.8837,12.9142,18.1839		586/811	203818973	2365,10641	2203	4300	6503	SO:0001819	synonymous_variant	9877	exon17			TGTAGCCTCTTGC		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"""Zinc fingers, CCCH-type domain containing"""	29093	protein-coding gene	gene with protein product		613513	"""zinc finger CCCH-type domain containing 11A"""	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.1758C>A	1.37:g.203818973C>A		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	364	169	0.464286	NM_014827	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Silent	SNP	ENST00000545588.1	37	CCDS30978.1																																																																																			C|0.815;A|0.185	0.185	strong		0.507	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827	
FIGN	55137	hgsc.bcm.edu	37	2	164467208	164467208	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:164467208T>C	ENST00000333129.3	-	3	1448	c.1134A>G	c.(1132-1134)ccA>ccG	p.P378P	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	378					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						GCTGCTTCGTTGGCTTAAATG	0.458																																					p.P378P		Atlas-SNP	.											FIGN,NS,lymphoid_neoplasm,-1,1	FIGN	106	1	0			c.A1134G						scavenged	.						111.0	108.0	109.0					2																	164467208		1986	4177	6163	SO:0001819	synonymous_variant	55137	exon3			CTTCGTTGGCTTA	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"""ATPases / AAA-type"""	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.1134A>G	2.37:g.164467208T>C		Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	137	3	0.0218978	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Silent	SNP	ENST00000333129.3	37	CCDS2221.2																																																																																			.	.	none		0.458	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086	
TBL3	10607	hgsc.bcm.edu	37	16	2025206	2025206	+	Silent	SNP	A	A	C	rs8053843	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2025206A>C	ENST00000568546.1	+	8	782	c.654A>C	c.(652-654)atA>atC	p.I218I		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	218					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						GTGACAAGATATGTATCATCT	0.612													C|||	1143	0.228235	0.2905	0.2637	5008	,	,		19224	0.0427		0.2356	False		,,,				2504	0.3027				p.I218I	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.A654C						PASS	.	C		1117,3279	716.0+/-408.5	144,829,1225	95.0	101.0	99.0		654	5.4	1.0	16	dbSNP_116	99	1945,6655	724.7+/-406.5	213,1519,2568	no	coding-synonymous	TBL3	NM_006453.2		357,2348,3793	CC,CA,AA		22.6163,25.4095,23.5611		218/809	2025206	3062,9934	2198	4300	6498	SO:0001819	synonymous_variant	10607	exon8			CAAGATATGTATC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.654A>C	16.37:g.2025206A>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			A|0.782;C|0.218	0.218	strong		0.612	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
KCNG2	26251	hgsc.bcm.edu	37	18	77659553	77659553	+	Silent	SNP	C	C	T	rs75339189	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:77659553C>T	ENST00000316249.3	+	2	1138	c.1138C>T	c.(1138-1140)Ctg>Ttg	p.L380L	KCNG2_ENST00000590307.1_3'UTR	NM_012283.1	NP_036415.1	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G, member 2	380					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(2)|endometrium(4)|lung(7)|skin(1)|upper_aerodigestive_tract(4)	18		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)		CCCGCGCAGCCTGCCCGGGCA	0.677													C|||	212	0.0423323	0.0083	0.0706	5008	,	,		10473	0.0169		0.1093	False		,,,				2504	0.0256				p.L380L		Atlas-SNP	.											.	KCNG2	48	.	0			c.C1138T						PASS	.	C		104,4300	78.8+/-117.2	2,100,2100	50.0	46.0	47.0		1138	1.0	1.0	18	dbSNP_131	47	926,7670	203.0+/-246.1	47,832,3419	no	coding-synonymous	KCNG2	NM_012283.1		49,932,5519	TT,TC,CC		10.7725,2.3615,7.9231		380/467	77659553	1030,11970	2202	4298	6500	SO:0001819	synonymous_variant	26251	exon2			CGCAGCCTGCCCG	AJ011021	CCDS12019.1	18q23	2011-07-05			ENSG00000178342	ENSG00000178342		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6249	protein-coding gene	gene with protein product		605696				10551266, 16382104	Standard	NM_012283		Approved	Kv6.2, KCNF2	uc010xfl.2	Q9UJ96	OTTHUMG00000044541	ENST00000316249.3:c.1138C>T	18.37:g.77659553C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	212	118	0.556604	NM_012283		Silent	SNP	ENST00000316249.3	37	CCDS12019.1																																																																																			C|0.926;T|0.074	0.074	strong		0.677	KCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103906.1	NM_012283	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461062	141461062	+	Silent	SNP	G	G	A	rs3735803	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:141461062G>A	ENST00000438773.2	-	2	544	c.411C>T	c.(409-411)aaC>aaT	p.N137N	TRAPPC9_ENST00000389328.4_Silent_p.N235N|TRAPPC9_ENST00000389327.3_Silent_p.N137N	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	137					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						AGTCCTCGTAGTTGGGGTAGA	0.577													G|||	2337	0.466653	0.4418	0.3372	5008	,	,		19654	0.5179		0.4791	False		,,,				2504	0.5266				p.N235N		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C705T						PASS	.	G	,	1845,2561	535.9+/-374.3	389,1067,747	68.0	59.0	62.0		411,705	3.2	1.0	8	dbSNP_107	62	4180,4420	568.1+/-389.0	1022,2136,1142	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	1411,3203,1889	AA,AG,GG		48.6047,41.8747,46.3248	,	137/1149,235/1247	141461062	6025,6981	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon2			CTCGTAGTTGGGG	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.411C>T	8.37:g.141461062G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1																																																																																			G|0.538;A|0.462	0.462	strong		0.577	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
PARP4	143	hgsc.bcm.edu	37	13	25068808	25068808	+	Missense_Mutation	SNP	A	A	T	rs9318600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25068808A>T	ENST00000381989.3	-	7	749	c.644T>A	c.(643-645)tTt>tAt	p.F215Y		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	215			F -> Y (in dbSNP:rs9318600).		cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GTAATTTTCAAAGTATTCACT	0.338													.|||	379	0.0756789	0.118	0.0634	5008	,	,		15488	0.0317		0.0944	False		,,,				2504	0.0532				p.F215Y		Atlas-SNP	.											.	PARP4	142	.	0			c.T644A						PASS	.	T	TYR/PHE	553,3851	774.1+/-414.0	40,473,1689	144.0	141.0	142.0		644	3.3	0.7	13	dbSNP_119	142	989,7611	772.9+/-407.7	67,855,3378	yes	missense	PARP4	NM_006437.3	22	107,1328,5067	TT,TA,AA		11.5,12.5568,11.8579	benign	215/1725	25068808	1542,11462	2202	4300	6502	SO:0001583	missense	143	exon7			TTTTCAAAGTATT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.644T>A	13.37:g.25068808A>T	ENSP00000371419:p.Phe215Tyr	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	190	181	0.952632	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	178	0.0815018315018315	66	0.13414634146341464	24	0.06629834254143646	8	0.013986013986013986	80	0.10554089709762533	T	0.016	-1.523172	0.00967	0.125568	0.115	ENSG00000102699	ENST00000381989	T	0.39787	1.06	4.52	3.26	0.37387	.	0.080006	0.52532	N	0.000078	T	0.00073	0.0002	N	0.00170	-1.935	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.25606	-1.0127	9	0.02654	T	1	-10.8909	8.2978	0.31995	0.3131:0.0:0.0:0.6869	rs9318600;rs17470108;rs52836352;rs9318600	215	Q9UKK3	PARP4_HUMAN	Y	215	ENSP00000371419:F215Y	ENSP00000371419:F215Y	F	-	2	0	PARP4	23966808	1.000000	0.71417	0.658000	0.29665	0.057000	0.15508	1.886000	0.39688	0.782000	0.33613	-0.383000	0.06682	TTT	A|0.889;T|0.111	0.111	strong		0.338	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
ADAM7	8756	hgsc.bcm.edu	37	8	24356818	24356818	+	Missense_Mutation	SNP	A	A	C	rs13259668	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:24356818A>C	ENST00000175238.6	+	17	1995	c.1912A>C	c.(1912-1914)Aat>Cat	p.N638H	RP11-624C23.1_ENST00000523578.1_RNA|RP11-561E1.1_ENST00000519364.1_RNA|ADAM7_ENST00000520720.1_Missense_Mutation_p.N410H|ADAM7_ENST00000380789.1_Missense_Mutation_p.N638H|RP11-624C23.1_ENST00000519689.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	638	Cys-rich.		N -> H (in dbSNP:rs13259668).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		CTCTCAGTGCAATGAAAATCC	0.343													C|||	1634	0.326278	0.3185	0.4452	5008	,	,		16940	0.1935		0.3062	False		,,,				2504	0.41				p.N638H		Atlas-SNP	.											.	ADAM7	165	.	0			c.A1912C						PASS	.	C	HIS/ASN	1430,2976	683.4+/-404.3	232,966,1005	130.0	120.0	123.0		1912	-4.4	0.0	8	dbSNP_121	123	2868,5732	671.8+/-402.9	486,1896,1918	yes	missense	ADAM7	NM_003817.2	68	718,2862,2923	CC,CA,AA		33.3488,32.4557,33.0463	benign	638/755	24356818	4298,8708	2203	4300	6503	SO:0001583	missense	8756	exon17			CAGTGCAATGAAA	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.1912A>C	8.37:g.24356818A>C	ENSP00000175238:p.Asn638His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	653	0.298992673992674	148	0.3008130081300813	156	0.430939226519337	115	0.20104895104895104	234	0.3087071240105541	C	0.278	-0.988090	0.02162	0.324557	0.333488	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.53857	1.48;1.49;0.6	4.92	-4.36	0.03645	.	1.962480	0.02172	N	0.059785	T	0.00012	0.0000	L	0.27944	0.81	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.33163	-0.9879	9	0.11182	T	0.66	.	3.2326	0.06754	0.5961:0.1976:0.113:0.0933	rs13259668;rs52834855;rs59851115;rs13259668	410;638	E5RK87;Q9H2U9	.;ADAM7_HUMAN	H	638;638;410;453	ENSP00000175238:N638H;ENSP00000370166:N638H;ENSP00000430400:N410H	ENSP00000175238:N638H	N	+	1	0	ADAM7	24412708	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.275000	0.02817	-0.866000	0.04068	-1.782000	0.00648	AAT	A|0.694;C|0.306	0.306	strong		0.343	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
TADA2A	6871	hgsc.bcm.edu	37	17	35771468	35771468	+	Missense_Mutation	SNP	C	C	T	rs7211875|rs112855394	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:35771468C>T	ENST00000394395.2	+	2	189	c.16C>T	c.(16-18)Ccc>Tcc	p.P6S	TADA2A_ENST00000225396.6_Missense_Mutation_p.P6S|TADA2A_ENST00000417170.1_Missense_Mutation_p.P6S|TADA2A_ENST00000586023.1_Missense_Mutation_p.P6S|RP11-378E13.4_ENST00000590364.1_RNA	NM_001166105.1	NP_001159577.1	O75478	TAD2A_HUMAN	transcriptional adaptor 2A	6			P -> S (in dbSNP:rs7211875). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8552087, ECO:0000269|Ref.2}.		chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)|skin(1)	13						CCGTTTGGGTCCCTTTAGCAG	0.473													T|||	4281	0.854832	0.9539	0.8761	5008	,	,		18736	0.7391		0.83	False		,,,				2504	0.8507				p.P6S		Atlas-SNP	.											.	TADA2A	91	.	0			c.C16T						PASS	.	T	SER/PRO,SER/PRO,SER/PRO	4105,301	166.2+/-197.5	1910,285,8	141.0	131.0	135.0		16,16,16	4.8	1.0	17	dbSNP_116	135	7381,1219	247.2+/-275.4	3173,1035,92	yes	missense,missense,missense	TADA2A	NM_001166105.1,NM_001488.3,NM_133439.2	74,74,74	5083,1320,100	TT,TC,CC		14.1744,6.8316,11.6869	benign,benign,benign	6/444,6/444,6/306	35771468	11486,1520	2203	4300	6503	SO:0001583	missense	6871	exon2			TTGGGTCCCTTTA	AK022767	CCDS11319.1, CCDS45656.1	17q12-q21	2014-04-10	2009-10-02	2009-10-02	ENSG00000108264	ENSG00000276234			11531	protein-coding gene	gene with protein product		602276	"""transcriptional adaptor 2 (ADA2 homolog, yeast)-like"""	TADA2L		8552087	Standard	XM_006722043		Approved	ADA2, hADA2, ADA2A	uc002hnt.3	O75478	OTTHUMG00000188469	ENST00000394395.2:c.16C>T	17.37:g.35771468C>T	ENSP00000377918:p.Pro6Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_001488	A8MVD0|B3KMU9|Q9BVJ0|Q9UCW2|Q9UP49	Missense_Mutation	SNP	ENST00000394395.2	37	CCDS11319.1	1844	0.8443223443223443	472	0.959349593495935	317	0.8756906077348067	428	0.7482517482517482	627	0.8271767810026385	T	3.765	-0.048816	0.07407	0.931684	0.858256	ENSG00000108264	ENST00000394395;ENST00000225396;ENST00000417170	T;T;T	0.26957	2.15;2.15;1.7	4.79	4.79	0.61399	.	0.113042	0.64402	N	0.000006	T	0.00012	0.0000	N	0.03115	-0.41	0.51012	P	9.499999999995623E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41378	-0.9512	9	0.02654	T	1	15.1675	7.4762	0.27378	0.0:0.0969:0.0:0.9031	rs7211875;rs17138764;rs17856035;rs17856372;rs52814727;rs56878335;rs7211875	6;6	O75478-2;O75478	.;TAD2A_HUMAN	S	6	ENSP00000377918:P6S;ENSP00000225396:P6S;ENSP00000406699:P6S	ENSP00000225396:P6S	P	+	1	0	TADA2A	32845581	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.970000	0.40520	0.986000	0.38683	-0.368000	0.07277	CCC	C|0.135;N|0.000	.	strong		0.473	TADA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256677.3	NM_001488	
SLC4A7	9497	hgsc.bcm.edu	37	3	27442336	27442336	+	Silent	SNP	G	G	A	rs3736312	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:27442336G>A	ENST00000295736.5	-	16	2389	c.2319C>T	c.(2317-2319)aaC>aaT	p.N773N	SLC4A7_ENST00000440156.1_Silent_p.N769N|SLC4A7_ENST00000428386.1_Silent_p.N649N|SLC4A7_ENST00000445684.1_Silent_p.N769N|SLC4A7_ENST00000388777.4_Silent_p.N323N|SLC4A7_ENST00000454389.1_Silent_p.N782N|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000446700.1_Silent_p.N765N|SLC4A7_ENST00000435667.2_Silent_p.N658N|SLC4A7_ENST00000455077.1_Silent_p.N654N|SLC4A7_ENST00000437179.1_Silent_p.N654N	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	773					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CATTGCTGGGGTTTGGAGGTT	0.313													G|||	642	0.128195	0.0446	0.1614	5008	,	,		17831	0.0565		0.2247	False		,,,				2504	0.1922				p.N773N		Atlas-SNP	.											.	SLC4A7	119	.	0			c.C2319T						PASS	.	G		354,4052	182.6+/-210.3	9,336,1858	152.0	149.0	150.0		2319	1.3	1.0	3	dbSNP_107	150	2129,6465	365.1+/-333.8	264,1601,2432	no	coding-synonymous	SLC4A7	NM_003615.3		273,1937,4290	AA,AG,GG		24.7731,8.0345,19.1		773/1215	27442336	2483,10517	2203	4297	6500	SO:0001819	synonymous_variant	9497	exon16			GCTGGGGTTTGGA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2319C>T	3.37:g.27442336G>A		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	173	172	0.99422	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			G|0.828;A|0.172	0.172	strong		0.313	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
WDR87	83889	hgsc.bcm.edu	37	19	38377773	38377773	+	Missense_Mutation	SNP	G	G	A	rs34785154	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:38377773G>A	ENST00000303868.5	-	6	6645	c.6421C>T	c.(6421-6423)Cgg>Tgg	p.R2141W	WDR87_ENST00000447313.2_Missense_Mutation_p.R2180W	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2141	Glu-rich.									NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						CTCTGCTTCCGAGCCAGTTTC	0.398																																					p.R2141W		Atlas-SNP	.											.	WDR87	191	.	0			c.C6421T						PASS	.	G	TRP/ARG	584,800		119,346,227	132.0	93.0	105.0		6421	-5.8	0.0	19	dbSNP_126	105	572,2610		49,474,1068	yes	missense	WDR87	NM_031951.3	101	168,820,1295	AA,AG,GG		17.9761,42.1965,25.3176	probably-damaging	2141/2874	38377773	1156,3410	692	1591	2283	SO:0001583	missense	83889	exon6			GCTTCCGAGCCAG	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.6421C>T	19.37:g.38377773G>A	ENSP00000368025:p.Arg2141Trp	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	140	61	0.435714	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	814	0.3727106227106227	251	0.5101626016260162	100	0.27624309392265195	334	0.583916083916084	129	0.17018469656992086	G	11.66	1.705740	0.30232	0.421965	0.179761	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.65732	-0.17;-0.17	4.6	-5.85	0.02311	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.45483	-0.9258	8	0.72032	D	0.01	.	2.8254	0.05484	0.1754:0.0811:0.4187:0.3248	rs34785154;rs60341863	2141;2180	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	W	2180;2141	ENSP00000405012:R2180W;ENSP00000368025:R2141W	ENSP00000368025:R2141W	R	-	1	2	WDR87	43069613	0.000000	0.05858	0.015000	0.15790	0.694000	0.40290	-0.512000	0.06313	-0.872000	0.04037	-0.321000	0.08615	CGG	G|0.663;A|0.337	0.337	strong		0.398	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
KDSR	2531	hgsc.bcm.edu	37	18	61022791	61022791	+	Silent	SNP	C	C	T	rs2003149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:61022791C>T	ENST00000406396.3	-	4	652	c.261G>A	c.(259-261)gtG>gtA	p.V87V	KDSR_ENST00000326575.5_Silent_p.V87V	NM_002035.2	NP_002026.1	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase	87					3-keto-sphinganine metabolic process (GO:0006666)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-dehydrosphinganine reductase activity (GO:0047560)	p.V87V(1)		endometrium(2)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	9						ATATGCAAAGCACCACCTGTT	0.318													C|||	2789	0.556909	0.438	0.6628	5008	,	,		18665	0.4335		0.6481	False		,,,				2504	0.6759				p.V87V		Atlas-SNP	.											KDSR,NS,carcinoma,0,1	KDSR	17	1	1	Substitution - coding silent(1)	stomach(1)	c.G261A						PASS	.	C		2176,2230	582.9+/-385.7	535,1106,562	108.0	101.0	104.0		261	2.7	1.0	18	dbSNP_92	104	5652,2948	667.0+/-402.4	1840,1972,488	no	coding-synonymous	KDSR	NM_002035.2		2375,3078,1050	TT,TC,CC		34.2791,49.3872,39.8124		87/333	61022791	7828,5178	2203	4300	6503	SO:0001819	synonymous_variant	2531	exon4			GCAAAGCACCACC		CCDS11982.1	18q21	2011-09-20	2008-02-20	2008-02-20	ENSG00000119537	ENSG00000119537	1.1.1.102	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	4021	protein-coding gene	gene with protein product	"""3-dehydrosphinganine reductase"", ""short chain dehydrogenase/reductase family 35C, member 1"""	136440	"""follicular lymphoma variant translocation 1"""	FVT1		8417785, 15328338, 17420465, 19027726	Standard	NM_002035		Approved	DHSR, SDR35C1	uc010dpw.3	Q06136	OTTHUMG00000132792	ENST00000406396.3:c.261G>A	18.37:g.61022791C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_002035	B2R5Y1|B4DMX0	Silent	SNP	ENST00000406396.3	37	CCDS11982.1																																																																																			C|0.423;T|0.577	0.577	strong		0.318	KDSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256200.2		
GABRG1	2565	hgsc.bcm.edu	37	4	46086060	46086060	+	Silent	SNP	T	T	C	rs976156	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:46086060T>C	ENST00000295452.4	-	3	431	c.264A>G	c.(262-264)acA>acG	p.T88T		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	88					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.T88T(1)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTTCAATTACTGTGGGCCTCA	0.284													T|||	2549	0.508986	0.7209	0.562	5008	,	,		15395	0.3304		0.5517	False		,,,				2504	0.3252				p.T88T		Atlas-SNP	.											GABRG1,NS,carcinoma,0,1	GABRG1	172	1	1	Substitution - coding silent(1)	stomach(1)	c.A264G						PASS	.	T		3079,1319		1085,909,205	40.0	40.0	40.0		264	-3.8	1.0	4	dbSNP_86	40	4741,3843		1345,2051,896	no	coding-synonymous	GABRG1	NM_173536.3		2430,2960,1101	CC,CT,TT		44.7693,29.9909,39.7627		88/466	46086060	7820,5162	2199	4292	6491	SO:0001819	synonymous_variant	2565	exon3			AATTACTGTGGGC	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4086	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma"""	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.264A>G	4.37:g.46086060T>C		Somatic	386	0	0		WXS	Illumina HiSeq	Phase_I	417	184	0.441247	NM_173536	Q5H9T8	Silent	SNP	ENST00000295452.4	37	CCDS3470.1																																																																																			T|0.435;C|0.565	0.565	strong		0.284	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536	
LPCAT1	79888	hgsc.bcm.edu	37	5	1467004	1467004	+	Splice_Site	SNP	A	A	G	rs35452723	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1467004A>G	ENST00000283415.3	-	13	1412	c.1280T>C	c.(1279-1281)aTg>aCg	p.M427T	LPCAT1_ENST00000503252.1_5'UTR	NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	427					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		CGCTCCGTACATCTGCAAGGC	0.662													A|||	829	0.165535	0.0393	0.2233	5008	,	,		17857	0.1319		0.2326	False		,,,				2504	0.2607				p.M427T		Atlas-SNP	.											.	LPCAT1	70	.	0			c.T1280C						PASS	.	A	THR/MET	362,4044	186.7+/-213.5	14,334,1855	107.0	88.0	94.0		1280	4.5	1.0	5	dbSNP_126	94	2224,6376	378.0+/-338.7	266,1692,2342	yes	missense-near-splice	LPCAT1	NM_024830.3	81	280,2026,4197	GG,GA,AA		25.8605,8.2161,19.8831	benign	427/535	1467004	2586,10420	2203	4300	6503	SO:0001630	splice_region_variant	79888	exon13			CCGTACATCTGCA	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"""EF-hand domain containing"""	25718	protein-coding gene	gene with protein product		610472	"""acyltransferase like 2"""	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.1279-1T>C	5.37:g.1467004A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	82	48	0.585366	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Missense_Mutation	SNP	ENST00000283415.3	37	CCDS3864.1	362	0.16575091575091574	26	0.052845528455284556	77	0.212707182320442	77	0.1346153846153846	182	0.24010554089709762	A	13.64	2.298881	0.40694	0.082161	0.258605	ENSG00000153395	ENST00000283415	T	0.67523	-0.27	4.47	4.47	0.54385	EF-hand-like domain (1);	0.039739	0.85682	D	0.000000	T	0.00039	0.0001	M	0.80028	2.48	0.09310	P	0.99999418856	B	0.22003	0.063	B	0.20184	0.028	T	0.09250	-1.0683	9	0.46703	T	0.11	-55.0433	12.0333	0.53410	1.0:0.0:0.0:0.0	rs35452723;rs62331140	427	Q8NF37	PCAT1_HUMAN	T	427	ENSP00000283415:M427T	ENSP00000283415:M427T	M	-	2	0	LPCAT1	1520004	1.000000	0.71417	0.998000	0.56505	0.099000	0.18886	5.569000	0.67391	1.793000	0.52555	0.459000	0.35465	ATG	A|0.815;G|0.185;T|0.000	0.185	strong		0.662	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830	Missense_Mutation
RPTOR	57521	hgsc.bcm.edu	37	17	78921117	78921117	+	Silent	SNP	C	C	T	rs4969231	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78921117C>T	ENST00000306801.3	+	27	3593	c.3231C>T	c.(3229-3231)aaC>aaT	p.N1077N	RPTOR_ENST00000544334.2_Silent_p.N919N|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1077					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						AGTATCTGAACGGCCAGGACT	0.582													C|||	990	0.197684	0.0219	0.2795	5008	,	,		17535	0.2044		0.3052	False		,,,				2504	0.2597				p.N1077N		Atlas-SNP	.											RPTOR,colon,carcinoma,0,1	RPTOR	122	1	0			c.C3231T						PASS	.	C	,	324,4082	173.0+/-202.9	5,314,1884	71.0	59.0	63.0		2757,3231	-10.5	0.3	17	dbSNP_111	63	2755,5845	438.5+/-358.9	426,1903,1971	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	431,2217,3855	TT,TC,CC		32.0349,7.3536,23.6737	,	919/1178,1077/1336	78921117	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon27			TCTGAACGGCCAG		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.3231C>T	17.37:g.78921117C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			C|0.763;T|0.237	0.237	strong		0.582	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
ABLIM2	84448	hgsc.bcm.edu	37	4	8031471	8031471	+	Silent	SNP	A	A	G	rs2385904	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:8031471A>G	ENST00000341937.5	-	11	1144	c.1080T>C	c.(1078-1080)tgT>tgC	p.C360C	ABLIM2_ENST00000407564.3_Silent_p.C360C|ABLIM2_ENST00000428004.2_Silent_p.C371C|ABLIM2_ENST00000545242.1_Silent_p.C360C|ABLIM2_ENST00000447017.2_Silent_p.C360C|ABLIM2_ENST00000361737.5_Silent_p.C371C|ABLIM2_ENST00000361581.5_Silent_p.C360C|ABLIM2_ENST00000505872.1_Silent_p.C360C|ABLIM2_ENST00000318888.4_Silent_p.C128C|ABLIM2_ENST00000515079.1_5'UTR|ABLIM2_ENST00000514025.1_Silent_p.C128C|ABLIM2_ENST00000296372.8_Silent_p.C360C|ABLIM2_ENST00000546334.1_Silent_p.C371C	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	360					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|myofibril (GO:0030016)	zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|pancreas(3)|prostate(2)|urinary_tract(1)	25						TGGAGGTCCGACACTGCTTGT	0.632													G|||	3674	0.733626	0.7731	0.732	5008	,	,		14076	0.7808		0.7425	False		,,,				2504	0.6237				p.C371C		Atlas-SNP	.											.	ABLIM2	59	.	0			c.T1113C						PASS	.	G	,,,,,,	3227,797		1298,631,83	37.0	48.0	45.0		1080,1080,1080,1080,1113,1113,1080	3.8	1.0	4	dbSNP_100	45	6036,2282		2196,1644,319	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABLIM2	NM_001130083.1,NM_001130084.1,NM_001130085.1,NM_001130086.1,NM_001130087.1,NM_001130088.1,NM_032432.4	,,,,,,	3494,2275,402	GG,GA,AA		27.4345,19.8062,24.9473	,,,,,,	360/646,360/612,360/573,360/560,371/532,371/471,360/522	8031471	9263,3079	2012	4159	6171	SO:0001819	synonymous_variant	84448	exon12			GGTCCGACACTGC	AB058711	CCDS47011.1, CCDS47012.1, CCDS47013.1, CCDS47014.1, CCDS47015.1, CCDS47016.1, CCDS54719.1, CCDS68669.1	4p16.1	2012-05-16			ENSG00000163995	ENSG00000163995			19195	protein-coding gene	gene with protein product		612544	"""actin binding LIM protein 2"""				Standard	NM_001130083		Approved	KIAA1808	uc003gkj.4	Q6H8Q1	OTTHUMG00000057427	ENST00000341937.5:c.1080T>C	4.37:g.8031471A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_001130087	E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Silent	SNP	ENST00000341937.5	37	CCDS47013.1																																																																																			A|0.269;G|0.731	0.731	strong		0.632	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083	
TMTC1	83857	hgsc.bcm.edu	37	12	29671406	29671406	+	Splice_Site	SNP	G	G	A	rs192684476		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:29671406G>A	ENST00000539277.1	-	13	2081	c.2023C>T	c.(2023-2025)Cgc>Tgc	p.R675C	RP11-310I24.1_ENST00000549070.1_RNA|TMTC1_ENST00000552618.1_Splice_Site_p.R699C|TMTC1_ENST00000256062.5_Splice_Site_p.R567C|TMTC1_ENST00000551659.1_Splice_Site_p.R737C|TMTC1_ENST00000319685.8_5'UTR	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	675						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					GAACTTTACCGCTTGTACCAT	0.458													G|||	1	0.000199681	0.0	0.0	5008	,	,		18068	0.001		0.0	False		,,,				2504	0.0				p.R675C		Atlas-SNP	.											.	TMTC1	147	.	0			c.C2023T						PASS	.						170.0	155.0	160.0					12																	29671406		2203	4300	6503	SO:0001630	splice_region_variant	83857	exon13			TTTACCGCTTGTA		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.2024+1C>T	12.37:g.29671406G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	204	88	0.431373	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	37	CCDS53772.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.48	3.135053	0.56828	.	.	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277	T;T;T;T	0.59638	0.25;0.25;0.46;0.25	4.79	3.89	0.44902	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.059624	0.64402	D	0.000007	T	0.80287	0.4595	H	0.94620	3.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.993	D	0.84100	0.0395	9	.	.	.	-18.2441	10.3987	0.44216	0.0:0.0:0.6447:0.3553	.	675;737	Q8IUR5;F8VTQ9	TMTC1_HUMAN;.	C	438;567;737;699;675	ENSP00000256062:R567C;ENSP00000448112:R737C;ENSP00000449043:R699C;ENSP00000442046:R675C	.	R	-	1	0	TMTC1	29562673	1.000000	0.71417	1.000000	0.80357	0.602000	0.36980	1.784000	0.38674	1.370000	0.46153	0.655000	0.94253	CGC	G|1.000;A|0.000	0.000	strong		0.458	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	Missense_Mutation
PSMC5	5705	hgsc.bcm.edu	37	17	61908556	61908556	+	Silent	SNP	C	C	T	rs13030	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:61908556C>T	ENST00000310144.6	+	8	1148	c.840C>T	c.(838-840)ctC>ctT	p.L280L	PSMC5_ENST00000580864.1_Silent_p.L272L|PSMC5_ENST00000375812.4_Silent_p.L272L|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000581882.1_Silent_p.L272L	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	280	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						TCAACCAGCTCGACGGCTTTG	0.602													C|||	1986	0.396565	0.1884	0.4467	5008	,	,		18688	0.505		0.327	False		,,,				2504	0.6022				p.L280L		Atlas-SNP	.											.	PSMC5	41	.	0			c.C840T						PASS	.	C	,	916,3490	346.2+/-308.9	104,708,1391	98.0	102.0	100.0		816,840	2.6	1.0	17	dbSNP_52	100	2770,5830	434.2+/-357.7	457,1856,1987	yes	coding-synonymous,coding-synonymous	PSMC5	NM_001199163.1,NM_002805.5	,	561,2564,3378	TT,TC,CC		32.2093,20.7898,28.3408	,	272/399,280/407	61908556	3686,9320	2203	4300	6503	SO:0001819	synonymous_variant	5705	exon8			CCAGCTCGACGGC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.840C>T	17.37:g.61908556C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_002805	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Silent	SNP	ENST00000310144.6	37	CCDS11645.1																																																																																			C|0.689;T|0.311	0.311	strong		0.602	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
WDR90	197335	hgsc.bcm.edu	37	16	717523	717523	+	Silent	SNP	G	G	T	rs3752493	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:717523G>T	ENST00000293879.4	+	41	5181	c.5181G>T	c.(5179-5181)ccG>ccT	p.P1727P	RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000547944.1_Silent_p.P326P|WDR90_ENST00000549091.1_Silent_p.P1729P|WDR90_ENST00000315764.4_Silent_p.P278P			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1727										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GGTTTACACCGTCCGCCAGGC	0.632													G|||	3507	0.70028	0.8865	0.5951	5008	,	,		19418	0.9841		0.3718	False		,,,				2504	0.5685				p.P1727P		Atlas-SNP	.											WDR90,colon,carcinoma,0,2	WDR90	107	2	0			c.G5181T						scavenged	.	G		3323,951		1279,765,93	52.0	59.0	57.0		5181	-9.8	0.0	16	dbSNP_107	57	3040,5418		539,1962,1728	no	coding-synonymous	WDR90	NM_145294.4		1818,2727,1821	TT,TG,GG		35.9423,22.2508,49.9764		1727/1749	717523	6363,6369	2137	4229	6366	SO:0001819	synonymous_variant	197335	exon41			TACACCGTCCGCC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.5181G>T	16.37:g.717523G>T		Somatic	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1	1460	0.6684981684981685	417	0.8475609756097561	198	0.5469613259668509	562	0.9825174825174825	283	0.3733509234828496	G	3.719	-0.057914	0.07317	0.777492	0.359423	ENSG00000161996	ENST00000546896	.	.	.	4.9	-9.79	0.00494	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22610	P	0.99893303	.	.	.	.	.	.	T	0.30149	-0.9988	4	0.87932	D	0	.	4.9016	0.13777	0.4854:0.2194:0.2216:0.0735	rs3752493;rs61206807;rs3752493	.	.	.	L	30	.	ENSP00000447915:R30L	R	+	2	0	WDR90	657524	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	-4.993000	0.00162	-3.261000	0.00202	-1.065000	0.02276	CGT	G|0.369;T|0.631	0.631	strong		0.632	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
EPHA2	1969	hgsc.bcm.edu	37	1	16456763	16456763	+	Missense_Mutation	SNP	C	C	T	rs35903225	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:16456763C>T	ENST00000358432.5	-	15	2781	c.2627G>A	c.(2626-2628)cGt>cAt	p.R876H		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	876	Mediates interaction with ARHGEF16 and ELMO2.		R -> H (in dbSNP:rs35903225). {ECO:0000269|PubMed:17344846}.		activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	GTCAGGGGCACGAATGAGCTT	0.582													C|||	39	0.00778754	0.0015	0.0144	5008	,	,		17836	0.002		0.0239	False		,,,				2504	0.001				p.R876H		Atlas-SNP	.											.	EPHA2	102	.	0			c.G2627A						PASS	.	C	HIS/ARG	34,4372	39.2+/-71.8	0,34,2169	99.0	93.0	95.0		2627	5.6	1.0	1	dbSNP_126	95	220,8380	92.8+/-154.8	0,220,4080	yes	missense	EPHA2	NM_004431.3	29	0,254,6249	TT,TC,CC		2.5581,0.7717,1.9529	probably-damaging	876/977	16456763	254,12752	2203	4300	6503	SO:0001583	missense	1969	exon15			GGGGCACGAATGA	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.2627G>A	1.37:g.16456763C>T	ENSP00000351209:p.Arg876His	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	309	148	0.478964	NM_004431	B5A968|Q8N3Z2	Missense_Mutation	SNP	ENST00000358432.5	37	CCDS169.1	23	0.010531135531135532	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	16	0.021108179419525065	C	29.2	4.986612	0.93106	0.007717	0.025581	ENSG00000142627	ENST00000358432	T	0.62364	0.03	5.63	5.63	0.86233	Protein kinase-like domain (1);	0.000000	0.49305	D	0.000155	T	0.56775	0.2008	M	0.84326	2.69	0.80722	D	1	D	0.76494	0.999	P	0.55112	0.769	T	0.74671	-0.3587	10	0.87932	D	0	.	18.2443	0.89979	0.0:1.0:0.0:0.0	rs35903225;rs61731099	876	P29317	EPHA2_HUMAN	H	876	ENSP00000351209:R876H	ENSP00000351209:R876H	R	-	2	0	EPHA2	16329350	1.000000	0.71417	0.962000	0.40283	0.926000	0.56050	4.709000	0.61867	2.670000	0.90874	0.655000	0.94253	CGT	C|0.983;T|0.017	0.017	strong		0.582	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
TET2	54790	hgsc.bcm.edu	37	4	106196951	106196951	+	Missense_Mutation	SNP	A	A	G	rs2454206	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:106196951A>G	ENST00000540549.1	+	11	6144	c.5284A>G	c.(5284-5286)Ata>Gta	p.I1762V	TET2_ENST00000380013.4_Missense_Mutation_p.I1762V|TET2_ENST00000513237.1_Missense_Mutation_p.I1783V|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1762			I -> V (in dbSNP:rs2454206). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19483684}.		5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.I1762fs*3(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ACCTTCTCACATAATCCATAA	0.458			"""Mis N, F"""		MDS								A|||	1154	0.230431	0.0658	0.2795	5008	,	,		23352	0.1895		0.3718	False		,,,				2504	0.3149				p.I1762V		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.A5284G						PASS	.	A	VAL/ILE	124,1260		11,102,579	19.0	16.0	17.0		5284	-10.3	0.0	4	dbSNP_100	17	1188,1994		223,742,626	yes	missense	TET2	NM_001127208.2	29	234,844,1205	GG,GA,AA		37.335,8.9595,28.7341	benign	1762/2003	106196951	1312,3254	692	1591	2283	SO:0001583	missense	54790	exon11			TCTCACATAATCC	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.5284A>G	4.37:g.106196951A>G	ENSP00000442788:p.Ile1762Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	526	0.24084249084249085	33	0.06707317073170732	92	0.2541436464088398	107	0.18706293706293706	294	0.38786279683377306	A	8.920	0.960733	0.18583	0.089595	0.37335	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.01963	4.53;4.53;4.53	5.16	-10.3	0.00346	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.58432	P	1.0000000000287557E-6	B;B	0.15141	0.001;0.012	B;B	0.19666	0.001;0.026	T	0.48340	-0.9044	8	0.13853	T	0.58	0.7576	3.9686	0.09443	0.1159:0.4443:0.2131:0.2267	rs2454206;rs52829850;rs58031039;rs2454206	1783;1762	E7EQS8;Q6N021	.;TET2_HUMAN	V	1762;1783;1762	ENSP00000442788:I1762V;ENSP00000425443:I1783V;ENSP00000369351:I1762V	ENSP00000369351:I1762V	I	+	1	0	TET2	106416400	0.000000	0.05858	0.000000	0.03702	0.738000	0.42128	-0.301000	0.08232	-1.622000	0.01560	-0.456000	0.05471	ATA	A|0.768;G|0.232	0.232	strong		0.458	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
TAF10	6881	hgsc.bcm.edu	37	11	6636106	6636106	+	5'Flank	SNP	T	T	A	rs1128396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6636106T>A	ENST00000299424.4	-	0	0				TPP1_ENST00000534644.1_5'Flank|TPP1_ENST00000533371.1_Silent_p.G271G|TPP1_ENST00000299427.6_Silent_p.G514G|TAF10_ENST00000531760.1_5'Flank	NM_006284.3	NP_006275.1	Q12962	TAF10_HUMAN	TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa						chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|perinuclear region of cytoplasm (GO:0048471)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|RNA polymerase binding (GO:0070063)|transcription coactivator activity (GO:0003713)						Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.0481)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATCAAAGAGTCCTGCCCCAT	0.537													T|||	1158	0.23123	0.23	0.2075	5008	,	,		18533	0.3512		0.161	False		,,,				2504	0.1984				p.G514G		Atlas-SNP	.											.	TPP1	71	.	0			c.A1542T						PASS	.	T		978,3424	367.1+/-318.1	111,756,1334	244.0	266.0	259.0		1542	3.8	1.0	11	dbSNP_86	259	1431,7161	275.0+/-291.5	129,1173,2994	no	coding-synonymous	TPP1	NM_000391.3		240,1929,4328	AA,AT,TT		16.655,22.2172,18.5393		514/564	6636106	2409,10585	2201	4296	6497	SO:0001631	upstream_gene_variant	1200	exon12			AAAGAGTCCTGCC	U13991, U25816	CCDS7769.1	11p15.5-p15.2	2006-11-14	2002-08-29	2001-12-07	ENSG00000166337	ENSG00000166337			11543	protein-coding gene	gene with protein product		600475	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, H, 30kD"""	TAF2H, TAF2A		7923369	Standard	NM_006284		Approved	TAFII30	uc001mej.2	Q12962	OTTHUMG00000133402		11.37:g.6636106T>A	Exception_encountered	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_000391	O00703|Q13175|Q6FH13	Silent	SNP	ENST00000299424.4	37	CCDS7769.1																																																																																			T|0.785;A|0.215	0.215	strong		0.537	TAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257259.2	NM_006284	
CDKAL1	54901	hgsc.bcm.edu	37	6	21201493	21201493	+	Silent	SNP	G	G	A	rs9465994	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:21201493G>A	ENST00000378610.1	+	13	1546	c.1536G>A	c.(1534-1536)tcG>tcA	p.S512S	CDKAL1_ENST00000274695.4_Silent_p.S512S|CDKAL1_ENST00000476517.1_3'UTR|CDKAL1_ENST00000378624.4_Silent_p.S421S			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	512					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			GAGAAGTCTCGGGTTTGACAA	0.458													A|||	2662	0.53155	0.8139	0.5937	5008	,	,		18594	0.4018		0.4503	False		,,,				2504	0.3231				p.S512S		Atlas-SNP	.											CDKAL1,NS,carcinoma,+1,1	CDKAL1	55	1	0			c.G1536A						PASS	.	A		3311,1095	395.8+/-329.8	1254,803,146	107.0	88.0	94.0		1536	-12.3	0.0	6	dbSNP_119	94	3915,4685	605.4+/-395.0	895,2125,1280	no	coding-synonymous	CDKAL1	NM_017774.3		2149,2928,1426	AA,AG,GG		45.5233,24.8525,44.441		512/580	21201493	7226,5780	2203	4300	6503	SO:0001819	synonymous_variant	54901	exon15			AGTCTCGGGTTTG	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.1536G>A	6.37:g.21201493G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Silent	SNP	ENST00000378610.1	37	CCDS4546.1																																																																																			G|0.451;A|0.549	0.549	strong		0.458	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774	
ATP7A	538	hgsc.bcm.edu	37	X	77268502	77268502	+	Missense_Mutation	SNP	G	G	C	rs2227291	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:77268502G>C	ENST00000341514.6	+	10	2454	c.2299G>C	c.(2299-2301)Gtt>Ctt	p.V767L	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	767			V -> L (in dbSNP:rs2227291). {ECO:0000269|PubMed:7977350}.		blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TATTCTTCTAGTTGCAATGTA	0.418													G|||	1130	0.299338	0.2557	0.1844	3775	,	,		13952	0.2421		0.165	False		,,,				2504	0.2597				p.V767L		Atlas-SNP	.											.	ATP7A	248	.	0			c.G2299C						PASS	.	G	LEU/VAL	1260,2575		182,717,179,733,392	244.0	199.0	214.0		2299	5.6	1.0	X	dbSNP_98	214	1438,5285		110,802,416,1515,1453	yes	missense	ATP7A	NM_000052.4	32	292,1519,595,2248,1845	CC,CG,C,GG,G		21.3893,32.8553,25.5541	probably-damaging	767/1501	77268502	2698,7860	2203	4296	6499	SO:0001583	missense	538	exon10			CTTCTAGTTGCAA	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"""ATPases / P-type"""	869	protein-coding gene	gene with protein product	"""copper pump 1"", ""copper-transporting ATPase 1"""	300011	"""Menkes syndrome"""	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.2299G>C	X.37:g.77268502G>C	ENSP00000345728:p.Val767Leu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	141	123	0.87234	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	37	CCDS35339.1	458	0.2760699216395419	106	0.2535885167464115	35	0.10869565217391304	81	0.16666666666666666	95	0.14053254437869822	G	25.3	4.628948	0.87560	0.328553	0.213893	ENSG00000165240	ENST00000341514	D	0.96300	-3.97	5.64	5.64	0.86602	ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	L	0.52905	1.665	0.09310	P	1.0	D	0.76494	0.999	D	0.68943	0.961	T	0.00000	-1.5766	9	0.49607	T	0.09	-0.6628	18.7615	0.91853	0.0:0.0:1.0:0.0	rs2227291;rs16978770;rs60987629;rs2227291	767	Q04656	ATP7A_HUMAN	L	767	ENSP00000345728:V767L	ENSP00000345728:V767L	V	+	1	0	ATP7A	77155158	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	7.976000	0.88070	2.377000	0.81083	0.468000	0.43344	GTT	0|0.066;C|0.253	0.253	strong		0.418	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052	
PRR5L	79899	hgsc.bcm.edu	37	11	36458997	36458997	+	Missense_Mutation	SNP	A	A	G	rs62621409	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:36458997A>G	ENST00000378867.3	+	7	770	c.415A>G	c.(415-417)Acc>Gcc	p.T139A	PRR5L_ENST00000389693.3_3'UTR|PRR5L_ENST00000311599.5_Missense_Mutation_p.T113A|PRR5L_ENST00000530639.1_Missense_Mutation_p.T139A|PRR5L_ENST00000527487.1_Missense_Mutation_p.T139A	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	139					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|regulation of fibroblast migration (GO:0010762)|TORC2 signaling (GO:0038203)	mitochondrion (GO:0005739)|TORC2 complex (GO:0031932)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						GACTCTCCCTACCCTGCAGGC	0.517													A|||	94	0.01877	0.0015	0.0202	5008	,	,		20169	0.0		0.0586	False		,,,				2504	0.0194				p.T139A		Atlas-SNP	.											.	PRR5L	35	.	0			c.A415G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR	25,4379	31.7+/-61.6	0,25,2177	225.0	196.0	206.0		415,172,415,415	5.3	1.0	11	dbSNP_129	206	350,8246	118.6+/-178.1	6,338,3954	yes	missense,missense,missense,missense	PRR5L	NM_001160167.1,NM_001160168.1,NM_001160169.1,NM_024841.4	58,58,58,58	6,363,6131	GG,GA,AA		4.0717,0.5677,2.8846	probably-damaging,probably-damaging,probably-damaging,probably-damaging	139/369,58/241,139/206,139/369	36458997	375,12625	2202	4298	6500	SO:0001583	missense	79899	exon7			CTCCCTACCCTGC		CCDS31463.1, CCDS53617.1	11p13-p12	2009-07-09				ENSG00000135362			25878	protein-coding gene	gene with protein product	"""protein observed with Rictor-2"""	611728				17461779	Standard	NM_024841		Approved	FLJ14213, PROTOR-2	uc001mwp.3	Q6MZQ0		ENST00000378867.3:c.415A>G	11.37:g.36458997A>G	ENSP00000368144:p.Thr139Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	99	36	0.363636	NM_024841	A4QN22|E9PKY1|Q96H46|Q9H7V4	Missense_Mutation	SNP	ENST00000378867.3	37	CCDS31463.1	52	0.023809523809523808	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	42	0.055408970976253295	A	21.3	4.134067	0.77662	0.005677	0.040717	ENSG00000135362	ENST00000530639;ENST00000311599;ENST00000378867;ENST00000527487	T;T;T;T	0.76186	1.79;1.94;1.79;-1.0	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.39682	0.1087	L	0.46157	1.445	0.58432	D	0.999997	P;D;P	0.67145	0.857;0.996;0.726	P;D;P	0.77557	0.588;0.99;0.506	T	0.67292	-0.5707	10	0.44086	T	0.13	-32.3272	15.1352	0.72558	1.0:0.0:0.0:0.0	rs62621409	139;58;139	E9PKY1;Q6MZQ0-3;Q6MZQ0	.;.;PRR5L_HUMAN	A	139;113;139;139	ENSP00000435050:T139A;ENSP00000310103:T113A;ENSP00000368144:T139A;ENSP00000435241:T139A	ENSP00000310103:T113A	T	+	1	0	PRR5L	36415573	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.737000	0.68606	2.103000	0.63969	0.533000	0.62120	ACC	A|0.972;G|0.028	0.028	strong		0.517	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841	
EXTL1	2134	hgsc.bcm.edu	37	1	26357667	26357667	+	Silent	SNP	G	G	A	rs11247848	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26357667G>A	ENST00000374280.3	+	5	2013	c.1146G>A	c.(1144-1146)ctG>ctA	p.L382L	EXTL1_ENST00000484339.1_3'UTR	NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	382					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)	p.L382L(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		ACCCCTCACTGCTGTGGAACA	0.567													G|||	748	0.149361	0.1513	0.1484	5008	,	,		18563	0.1845		0.1859	False		,,,				2504	0.0736				p.L382L		Atlas-SNP	.											EXTL1,NS,carcinoma,0,1	EXTL1	61	1	1	Substitution - coding silent(1)	stomach(1)	c.G1146A						PASS	.	G		702,3704	291.5+/-281.6	54,594,1555	108.0	105.0	106.0		1146	-0.4	0.0	1	dbSNP_120	106	1751,6849	317.9+/-313.4	173,1405,2722	no	coding-synonymous	EXTL1	NM_004455.2		227,1999,4277	AA,AG,GG		20.3605,15.9328,18.8605		382/677	26357667	2453,10553	2203	4300	6503	SO:0001819	synonymous_variant	2134	exon5			CTCACTGCTGTGG	U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"""Exostosin glycosyltransferase family"""	3515	protein-coding gene	gene with protein product	"""glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""alpha-N-acetylglucosaminyltransferase II"", ""glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase"", ""exostosin-L"""	601738	"""exostoses (multiple)-like 1"""			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.1146G>A	1.37:g.26357667G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	166	83	0.5	NM_004455	Q6GSC1	Silent	SNP	ENST00000374280.3	37	CCDS271.1																																																																																			G|0.819;A|0.181	0.181	strong		0.567	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455	
HECW2	57520	hgsc.bcm.edu	37	2	197183856	197183856	+	Silent	SNP	A	A	G	rs61744819	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:197183856A>G	ENST00000260983.3	-	9	1940	c.1758T>C	c.(1756-1758)gaT>gaC	p.D586D	HECW2_ENST00000409111.1_Silent_p.D230D	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	586					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						CTCCTGATGCATCGGAAGTCC	0.587													A|||	39	0.00778754	0.0038	0.013	5008	,	,		20126	0.0		0.0209	False		,,,				2504	0.0041				p.D586D		Atlas-SNP	.											.	HECW2	239	.	0			c.T1758C						PASS	.	A		23,4383	29.0+/-57.7	0,23,2180	48.0	44.0	45.0		1758	0.9	0.6	2	dbSNP_129	45	191,8409	83.4+/-145.9	2,187,4111	no	coding-synonymous	HECW2	NM_020760.1		2,210,6291	GG,GA,AA		2.2209,0.522,1.6454		586/1573	197183856	214,12792	2203	4300	6503	SO:0001819	synonymous_variant	57520	exon9			TGATGCATCGGAA	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.1758T>C	2.37:g.197183856A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Silent	SNP	ENST00000260983.3	37	CCDS33354.1																																																																																			A|0.982;G|0.018	0.018	strong		0.587	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760	
MUC21	394263	hgsc.bcm.edu	37	6	30954552	30954552	+	Silent	SNP	C	C	T	rs144720609		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954552C>T	ENST00000376296.3	+	2	841	c.600C>T	c.(598-600)tcC>tcT	p.S200S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	200	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACTCTGAGTCCAGCACAACCT	0.607																																					p.S200S		Atlas-SNP	.											.	MUC21	98	.	0			c.C600T						PASS	.						163.0	157.0	159.0					6																	30954552		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			TGAGTCCAGCACA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.600C>T	6.37:g.30954552C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	135	12	0.0888889	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			C|0.999;T|0.001	0.001	weak		0.607	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
FGFR4	2264	hgsc.bcm.edu	37	5	176516631	176516631	+	Missense_Mutation	SNP	G	G	A	rs1966265	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:176516631G>A	ENST00000292408.4	+	2	273	c.28G>A	c.(28-30)Gtc>Atc	p.V10I	FGFR4_ENST00000502906.1_Missense_Mutation_p.V10I|FGFR4_ENST00000507708.1_3'UTR|FGFR4_ENST00000393648.2_Missense_Mutation_p.V10I|FGFR4_ENST00000292410.3_Missense_Mutation_p.V10I|FGFR4_ENST00000393637.1_Missense_Mutation_p.V10I	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	10			V -> I (in dbSNP:rs1966265). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:21882254, ECO:0000269|Ref.8}.		alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	CCTGTTGGGGGTCCTGCTGAG	0.607										TSP Lung(9;0.080)			g|||	1146	0.228834	0.0182	0.3184	5008	,	,		17888	0.5069		0.1799	False		,,,				2504	0.2137				p.V10I		Atlas-SNP	.											.	FGFR4	174	.	0			c.G28A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	269,4137	148.8+/-183.1	6,257,1940	59.0	54.0	55.0		28,28,28	-2.2	0.6	5	dbSNP_92	55	1952,6648	332.9+/-320.3	235,1482,2583	yes	missense,missense,missense	FGFR4	NM_002011.3,NM_022963.2,NM_213647.1	29,29,29	241,1739,4523	AA,AG,GG		22.6977,6.1053,17.0767	benign,benign,benign	10/803,10/763,10/803	176516631	2221,10785	2203	4300	6503	SO:0001583	missense	2264	exon1			TTGGGGGTCCTGC	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.28G>A	5.37:g.176516631G>A	ENSP00000292408:p.Val10Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	199	82	0.41206	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	37	CCDS4410.1	545	0.24954212454212454	13	0.026422764227642278	95	0.26243093922651933	304	0.5314685314685315	133	0.17546174142480211	g	0.003	-2.512008	0.00153	0.061053	0.226977	ENSG00000160867	ENST00000292408;ENST00000503708;ENST00000393648;ENST00000514472;ENST00000502906;ENST00000292410;ENST00000510911;ENST00000513166;ENST00000393637	T;T;T;D;T;T;T;D;T	0.88509	-1.17;-0.84;-1.13;-2.39;-1.17;-1.17;0.9;-2.32;-1.17	4.63	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	6.999999999979245E-6	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0	T	0.36648	-0.9739	8	0.31617	T	0.26	.	1.5311	0.02536	0.3612:0.135:0.3665:0.1373	rs1966265;rs2230268;rs17839798;rs59346453;rs1966265	10;10;10;10;10	B5A965;B4DVP5;P22455-2;E7EWF4;P22455	.;.;.;.;FGFR4_HUMAN	I	10	ENSP00000292408:V10I;ENSP00000424905:V10I;ENSP00000377259:V10I;ENSP00000426492:V10I;ENSP00000424960:V10I;ENSP00000292410:V10I;ENSP00000427222:V10I;ENSP00000422889:V10I;ENSP00000377254:V10I	ENSP00000292408:V10I	V	+	1	0	FGFR4	176449237	0.864000	0.29904	0.612000	0.29024	0.022000	0.10575	-0.136000	0.10405	-0.406000	0.07588	-1.652000	0.00757	GTC	G|0.804;A|0.196	0.196	strong		0.607	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
LMNA	4000	hgsc.bcm.edu	37	1	156105028	156105028	+	Silent	SNP	T	T	C	rs538089	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156105028T>C	ENST00000368300.4	+	5	1073	c.861T>C	c.(859-861)gcT>gcC	p.A287A	LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000347559.2_Silent_p.A287A|LMNA_ENST00000368297.1_Silent_p.A206A|LMNA_ENST00000361308.4_Silent_p.A287A|LMNA_ENST00000368301.2_Silent_p.A287A|LMNA_ENST00000392353.3_Silent_p.A206A|LMNA_ENST00000473598.2_Silent_p.A188A|LMNA_ENST00000368299.3_Silent_p.A287A|LMNA_ENST00000448611.2_Silent_p.A175A	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	287	Coil 2.|Rod.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					TGGTGGGGGCTGCCCACGAGG	0.632									Werner syndrome;Hutchinson-Gilford Progeria Syndrome				C|||	967	0.193091	0.5242	0.085	5008	,	,		16210	0.0228		0.0865	False		,,,				2504	0.1074				p.A287A		Atlas-SNP	.											.	LMNA	31	.	0			c.T861C						PASS	.	C	,,	1927,2479	623.6+/-394.2	411,1105,687	42.0	44.0	43.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	861,861,861	-11.0	0.4	1	dbSNP_83	43	646,7954	788.8+/-407.6	20,606,3674	no	coding-synonymous,coding-synonymous,coding-synonymous	LMNA	NM_005572.3,NM_170707.2,NM_170708.2	,,	431,1711,4361	CC,CT,TT		7.5116,43.7358,19.7832	,,	287/573,287/665,287/635	156105028	2573,10433	2203	4300	6503	SO:0001819	synonymous_variant	4000	exon5	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	GGGGGCTGCCCAC	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"""Intermediate filaments type V, lamins"""	6636	protein-coding gene	gene with protein product		150330	"""cardiomyopathy, dilated 1A (autosomal dominant)"", ""limb girdle muscular dystrophy 1B (autosomal dominant)"", ""progeria 1 (Hutchinson-Gilford type)"", ""lamin A/C-like 1"""	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.861T>C	1.37:g.156105028T>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	216	96	0.444444	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	37	CCDS1129.1																																																																																			T|0.808;C|0.192	0.192	strong		0.632	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	
C17orf82	388407	hgsc.bcm.edu	37	17	59489893	59489893	+	Missense_Mutation	SNP	T	T	C	rs200497494|rs9907379	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:59489893T>C	ENST00000335108.2	+	1	782	c.557T>C	c.(556-558)cTc>cCc	p.L186P	RP11-332H18.4_ENST00000592009.1_RNA	NM_203425.1	NP_982249	Q86X59	CQ082_HUMAN	chromosome 17 open reading frame 82	186			L -> P (in dbSNP:rs9907379). {ECO:0000269|PubMed:15489334}.							cervix(1)|lung(1)	2						CGGCAACTCCTCACAGGTCCA	0.731													C|||	3623	0.723442	0.7769	0.6571	5008	,	,		12512	0.7004		0.8002	False		,,,				2504	0.6431				p.L186P		Atlas-SNP	.											C17orf82_ENST00000335108,NS,carcinoma,0,2	C17orf82	16	2	0			c.T557C						scavenged	.	C	PRO/LEU	3143,775		1281,581,97	4.0	6.0	5.0		557	0.9	0.1	17	dbSNP_119	5	6355,1647		2560,1235,206	no	missense	C17orf82	NM_203425.1	98	3841,1816,303	CC,CT,TT		20.5824,19.7805,20.3188	benign	186/252	59489893	9498,2422	1959	4001	5960	SO:0001583	missense	388407	exon1			AACTCCTCACAGG	BC046200	CCDS11628.1	17q23.2	2012-10-23			ENSG00000187013	ENSG00000187013			32699	protein-coding gene	gene with protein product							Standard	NM_203425		Approved		uc002izh.1	Q86X59	OTTHUMG00000180077	ENST00000335108.2:c.557T>C	17.37:g.59489893T>C	ENSP00000335229:p.Leu186Pro	Somatic	1	1	1		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_203425		Missense_Mutation	SNP	ENST00000335108.2	37	CCDS11628.1	1628	0.7454212454212454	382	0.7764227642276422	236	0.6519337016574586	399	0.6975524475524476	611	0.8060686015831134	C	8.991	0.977736	0.18812	0.802195	0.794176	ENSG00000187013	ENST00000335108	T	0.58210	0.35	4.29	0.931	0.19460	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.40031	P	0.024463000000000013	B	0.02656	0.0	B	0.01281	0.0	T	0.21109	-1.0255	8	0.39692	T	0.17	.	1.8756	0.03217	0.1483:0.381:0.2903:0.1804	rs9907379;rs17846388;rs17859430;rs57634035;rs9907379	186	Q86X59	CQ082_HUMAN	P	186	ENSP00000335229:L186P	ENSP00000335229:L186P	L	+	2	0	C17orf82	56844675	0.009000	0.17119	0.119000	0.21687	0.106000	0.19336	0.032000	0.13732	-0.103000	0.12175	-0.380000	0.06706	CTC	T|0.261;C|0.739	0.739	strong		0.731	C17orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449646.1	NM_203425	
DCAF10	79269	hgsc.bcm.edu	37	9	37861380	37861380	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:37861380C>T	ENST00000377724.3	+	7	1920	c.1555C>T	c.(1555-1557)Cgg>Tgg	p.R519W	DCAF10_ENST00000242323.7_Missense_Mutation_p.R482W|DCAF10_ENST00000483167.1_3'UTR|RP11-613M10.9_ENST00000540557.1_Intron	NM_024345.3	NP_077321.3	Q5QP82	DCA10_HUMAN	DDB1 and CUL4 associated factor 10	519					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	12						CAGTCCCCTGCGGGTGATCCG	0.483																																					p.R519W		Atlas-SNP	.											DCAF10,NS,carcinoma,0,1	DCAF10	31	1	0			c.C1555T						PASS	.						103.0	97.0	99.0					9																	37861380		2203	4300	6503	SO:0001583	missense	79269	exon7			CCCCTGCGGGTGA	BC003520	CCDS6613.2, CCDS75835.1	9p13.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000122741	ENSG00000122741		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	23686	protein-coding gene	gene with protein product			"""WD repeat domain 32"""	WDR32			Standard	NM_001286810		Approved	MGC10765, FLJ23201	uc004aao.3	Q5QP82	OTTHUMG00000019934	ENST00000377724.3:c.1555C>T	9.37:g.37861380C>T	ENSP00000366953:p.Arg519Trp	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	236	107	0.45339	NM_024345	A4VCJ5|Q32NE2|Q8N2Q5|Q96ET5|Q9BTQ5|Q9H5P6	Missense_Mutation	SNP	ENST00000377724.3	37	CCDS6613.2	.	.	.	.	.	.	.	.	.	.	C	18.69	3.677247	0.68042	.	.	ENSG00000122741	ENST00000377724;ENST00000242323	T;T	0.01388	4.95;4.95	6.06	6.06	0.98353	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.161766	0.56097	D	0.000033	T	0.03783	0.0107	N	0.22421	0.69	0.47698	D	0.99949	P;D	0.65815	0.894;0.995	B;P	0.59703	0.312;0.862	T	0.59862	-0.7374	10	0.56958	D	0.05	.	18.1147	0.89549	0.0:1.0:0.0:0.0	.	482;519	Q5QP82-2;Q5QP82	.;DCA10_HUMAN	W	519;482	ENSP00000366953:R519W;ENSP00000242323:R482W	ENSP00000242323:R482W	R	+	1	2	DCAF10	37851380	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.548000	0.36201	2.882000	0.98803	0.655000	0.94253	CGG	.	.	none		0.483	DCAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052485.2	NM_024345	
OR8B2	26595	hgsc.bcm.edu	37	11	124252422	124252422	+	Missense_Mutation	SNP	G	G	A	rs503220	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124252422G>A	ENST00000375013.2	-	1	836	c.818C>T	c.(817-819)tCt>tTt	p.S273F		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	273			S -> F (in dbSNP:rs503220).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		GAAAACAGAAGAAACTTTTCC	0.408													g|||	1786	0.356629	0.4402	0.3026	5008	,	,		18343	0.2788		0.3072	False		,,,				2504	0.4131				p.S273F		Atlas-SNP	.											.	OR8B2	42	.	0			c.C818T						PASS	.						59.0	63.0	62.0					11																	124252422		2201	4299	6500	SO:0001583	missense	26595	exon1			ACAGAAGAAACTT	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"""GPCR / Class A : Olfactory receptors"""	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.818C>T	11.37:g.124252422G>A	ENSP00000364152:p.Ser273Phe	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	243	130	0.534979	NM_001005468	Q8NGH2	Missense_Mutation	SNP	ENST00000375013.2	37	CCDS31708.1	719	0.3292124542124542	226	0.45934959349593496	112	0.30939226519337015	144	0.2517482517482518	237	0.31266490765171506	g	15.87	2.961371	0.53400	.	.	ENSG00000204293	ENST00000375013	T	0.34859	1.34	3.7	-2.01	0.07410	GPCR, rhodopsin-like superfamily (1);	0.215393	0.33346	N	0.005020	T	0.00012	0.0000	N	0.17922	0.545	0.80722	P	0.0	D	0.76494	0.999	D	0.87578	0.998	T	0.47058	-0.9146	9	0.66056	D	0.02	.	0.3658	0.00371	0.3459:0.1326:0.2523:0.2692	rs503220	273	Q96RD0	OR8B2_HUMAN	F	273	ENSP00000364152:S273F	ENSP00000364152:S273F	S	-	2	0	OR8B2	123757632	0.000000	0.05858	0.000000	0.03702	0.646000	0.38490	-0.902000	0.04088	-0.545000	0.06224	0.505000	0.49811	TCT	.	.	weak		0.408	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468	
MUC21	394263	hgsc.bcm.edu	37	6	30955218	30955218	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30955218T>C	ENST00000376296.3	+	2	1507	c.1266T>C	c.(1264-1266)aaT>aaC	p.N422N	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	422	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N422N(1)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CTGCCACCAATTCTGAGTCCA	0.612																																					p.N422N		Atlas-SNP	.											MUC21,NS,carcinoma,0,1	MUC21	98	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T1266C						PASS	.						138.0	133.0	135.0					6																	30955218		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			CACCAATTCTGAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1266T>C	6.37:g.30955218T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	169	26	0.153846	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			T|0.858;C|0.142	0.142	strong		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
EMILIN3	90187	hgsc.bcm.edu	37	20	39990700	39990700	+	Silent	SNP	T	T	C	rs41278104	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:39990700T>C	ENST00000332312.3	-	4	1701	c.1509A>G	c.(1507-1509)gtA>gtG	p.V503V		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	503						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				GCTCTGTCTGTACAAGGGGCC	0.632													C|||	764	0.152556	0.3132	0.147	5008	,	,		17537	0.003		0.1799	False		,,,				2504	0.0654				p.V503V		Atlas-SNP	.											.	EMILIN3	63	.	0			c.A1509G						PASS	.	C		1392,3014	683.9+/-404.3	220,952,1031	70.0	65.0	66.0		1509	4.2	0.9	20	dbSNP_127	66	1492,7108	746.0+/-407.3	141,1210,2949	no	coding-synonymous	EMILIN3	NM_052846.1		361,2162,3980	CC,CT,TT		17.3488,31.5933,22.1744		503/767	39990700	2884,10122	2203	4300	6503	SO:0001819	synonymous_variant	90187	exon4			TGTCTGTACAAGG	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1509A>G	20.37:g.39990700T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																			T|0.802;C|0.198	0.198	strong		0.632	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
ICAM5	7087	hgsc.bcm.edu	37	19	10402938	10402938	+	Missense_Mutation	SNP	G	G	A	rs1056538	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10402938G>A	ENST00000221980.4	+	4	964	c.901G>A	c.(901-903)Gtc>Atc	p.V301I		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	301	Ig-like C2-type 3.		V -> I (in dbSNP:rs1056538). {ECO:0000269|PubMed:8995416}.		phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CAGGCAGCTGGTCTGCAACGT	0.642													G|||	1450	0.289537	0.0439	0.5202	5008	,	,		16487	0.2371		0.4056	False		,,,				2504	0.3926				p.V301I		Atlas-SNP	.											.	ICAM5	53	.	0			c.G901A						PASS	.	G	ILE/VAL	436,3970	202.8+/-225.5	19,398,1786	36.0	29.0	31.0		901	3.3	1.0	19	dbSNP_86	31	3345,5253	473.0+/-368.5	669,2007,1623	no	missense	ICAM5	NM_003259.3	29	688,2405,3409	AA,AG,GG		38.9044,9.8956,29.0757	benign	301/925	10402938	3781,9223	2203	4299	6502	SO:0001583	missense	7087	exon4			CAGCTGGTCTGCA	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.901G>A	19.37:g.10402938G>A	ENSP00000221980:p.Val301Ile	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_003259	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	641	0.2934981684981685	11	0.022357723577235773	175	0.48342541436464087	145	0.2534965034965035	310	0.40897097625329815	G	16.96	3.265958	0.59540	0.098956	0.389044	ENSG00000105376	ENST00000221980	T	0.05447	3.44	5.54	3.27	0.37495	Immunoglobulin-like fold (1);	0.652062	0.14359	N	0.324603	T	0.00012	0.0000	L	0.60455	1.87	0.45867	P	0.0012799999999999478	B	0.12630	0.006	B	0.11329	0.006	T	0.41395	-0.9511	9	0.30078	T	0.28	-22.8733	5.0439	0.14473	0.3049:0.0:0.6951:0.0	rs1056538;rs2228616;rs11549918;rs17845811;rs17858776;rs61530381	301	Q9UMF0	ICAM5_HUMAN	I	301	ENSP00000221980:V301I	ENSP00000221980:V301I	V	+	1	0	ICAM5	10263938	0.401000	0.25303	1.000000	0.80357	0.884000	0.51177	0.359000	0.20233	1.336000	0.45506	0.485000	0.47835	GTC	G|0.719;A|0.281	0.281	strong		0.642	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
COG6	57511	hgsc.bcm.edu	37	13	40229957	40229957	+	Missense_Mutation	SNP	T	T	A	rs3812883	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:40229957T>A	ENST00000455146.3	+	1	144	c.94T>A	c.(94-96)Tgc>Agc	p.C32S	COG6_ENST00000416691.1_Missense_Mutation_p.C32S	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	32			C -> S (in dbSNP:rs3812883). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.6}.		glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		GGCGACGACCTGCAACCCGCT	0.677													A|||	2425	0.484225	0.5015	0.5879	5008	,	,		14507	0.4573		0.3767	False		,,,				2504	0.5256				p.C32S		Atlas-SNP	.											.	COG6	49	.	0			c.T94A						PASS	.	A	SER/CYS,SER/CYS	2079,2315		492,1095,610	19.0	19.0	19.0		94,94	3.0	0.0	13	dbSNP_107	19	3324,5268		694,1936,1666	yes	missense,missense	COG6	NM_001145079.1,NM_020751.2	112,112	1186,3031,2276	AA,AT,TT		38.6872,47.3145,41.6063	benign,benign	32/616,32/658	40229957	5403,7583	2197	4296	6493	SO:0001583	missense	57511	exon1			ACGACCTGCAACC	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"""Components of oligomeric golgi complex"""	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.94T>A	13.37:g.40229957T>A	ENSP00000397441:p.Cys32Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	37	CCDS9370.1	1013	0.46382783882783885	249	0.5060975609756098	210	0.580110497237569	261	0.4562937062937063	293	0.3865435356200528	A	5.269	0.235062	0.09969	0.473145	0.386872	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000422759;ENST00000455146	T;T;T	0.32515	1.45;1.71;1.46	5.41	3.0	0.34707	.	0.624277	0.17468	N	0.173170	T	0.00012	0.0000	N	0.01048	-1.04	0.54753	P	1.2000000000012001E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45906	-0.9229	9	0.02654	T	1	-27.9087	2.2529	0.04048	0.5888:0.1751:0.0858:0.1503	rs3812883;rs3812883	53;32	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	S	32;63;32;32	ENSP00000403733:C32S;ENSP00000412877:C32S;ENSP00000397441:C32S	ENSP00000255468:C63S	C	+	1	0	COG6	39127957	0.980000	0.34600	0.016000	0.15963	0.004000	0.04260	2.549000	0.45803	0.056000	0.16144	-0.364000	0.07487	TGC	T|0.567;A|0.433	0.433	strong		0.677	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3		
SERPINB5	5268	hgsc.bcm.edu	37	18	61156606	61156606	+	Silent	SNP	G	G	C	rs12454742	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:61156606G>C	ENST00000382771.4	+	4	625	c.333G>C	c.(331-333)ccG>ccC	p.P111P	SERPINB5_ENST00000489441.1_Silent_p.P111P	NM_002639.4	NP_002630.2	P36952	SPB5_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 5	111					cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelium (GO:0002009)|negative regulation of endopeptidase activity (GO:0010951)|prostate gland morphogenesis (GO:0060512)|regulation of epithelial cell proliferation (GO:0050678)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(3)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	12						CGAAGAGACCGTATGCAAAGG	0.378													C|||	3578	0.714457	0.8722	0.6167	5008	,	,		18982	0.621		0.6889	False		,,,				2504	0.6933				p.P111P		Atlas-SNP	.											.	SERPINB5	35	.	0			c.G333C						PASS	.	C		3707,699	291.3+/-281.4	1553,601,49	105.0	102.0	103.0		333	-0.9	0.9	18	dbSNP_120	103	5913,2687	430.1+/-356.4	2036,1841,423	no	coding-synonymous	SERPINB5	NM_002639.4		3589,2442,472	CC,CG,GG		31.2442,15.8647,26.0341		111/376	61156606	9620,3386	2203	4300	6503	SO:0001819	synonymous_variant	5268	exon4			GAGACCGTATGCA	U04313	CCDS32839.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206075	ENSG00000206075		"""Serine (or cysteine) peptidase inhibitors"""	8949	protein-coding gene	gene with protein product	"""protease inhibitor 5 (maspin)"""	154790	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5"""	PI5		8290962, 7724531, 16720730, 24172014	Standard	NM_002639		Approved	maspin	uc002liz.4	P36952	OTTHUMG00000141307	ENST00000382771.4:c.333G>C	18.37:g.61156606G>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	102	99	0.970588	NM_002639	B2R6Y4|Q6N0B4|Q8WW89	Silent	SNP	ENST00000382771.4	37	CCDS32839.1																																																																																			G|0.285;C|0.715	0.715	strong		0.378	SERPINB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280629.1	NM_002639	
MIOS	54468	hgsc.bcm.edu	37	7	7613039	7613039	+	Silent	SNP	C	C	T	rs61744397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:7613039C>T	ENST00000340080.4	+	4	1354	c.933C>T	c.(931-933)ccC>ccT	p.P311P	MIOS_ENST00000405785.1_Silent_p.P311P	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	311						lysosomal membrane (GO:0005765)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AAACTGAACCCACAATAATTG	0.403													C|||	498	0.0994409	0.0968	0.0893	5008	,	,		22630	0.0506		0.1143	False		,,,				2504	0.1452				p.P311P		Atlas-SNP	.											.	MIOS	68	.	0			c.C933T						PASS	.	C		281,3595		13,255,1670	116.0	111.0	113.0		933	1.6	1.0	7	dbSNP_129	113	883,7391		49,785,3303	no	coding-synonymous	MIOS	NM_019005.3		62,1040,4973	TT,TC,CC		10.672,7.2497,9.5802		311/876	7613039	1164,10986	1938	4137	6075	SO:0001819	synonymous_variant	54468	exon4			TGAACCCACAATA		CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"""WD repeat-containing protein mio"""	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.933C>T	7.37:g.7613039C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	172	69	0.401163	NM_019005	B2RTV6|O75216|Q7L551|Q9H092	Silent	SNP	ENST00000340080.4	37	CCDS43554.1																																																																																			C|0.902;T|0.098	0.098	strong		0.403	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005	
GRIK1	2897	hgsc.bcm.edu	37	21	30926024	30926024	+	Splice_Site	SNP	G	G	A	rs363503	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:30926024G>A	ENST00000399907.1	-	17	3020	c.2609C>T	c.(2608-2610)gCt>gTt	p.A870V	GRIK1_ENST00000399914.1_Intron|GRIK1_ENST00000399913.1_Intron|GRIK1_ENST00000389124.2_Intron|GRIK1_ENST00000399909.1_Splice_Site_p.A855V|GRIK1_ENST00000309434.7_Splice_Site_p.A872V|GRIK1_ENST00000389125.3_Intron|GRIK1_ENST00000327783.4_Intron|GRIK1_ENST00000535441.1_Intron	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	870			A -> V (in dbSNP:rs363503).		adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	GAAACAAAAAGCCTTGCATGC	0.313													G|||	31	0.0061901	0.0015	0.0072	5008	,	,		16981	0.001		0.005	False		,,,				2504	0.0184				p.A870V		Atlas-SNP	.											.	GRIK1	293	.	0			c.C2609T						PASS	.	G	VAL/ALA,	9,3601		0,9,1796	96.0	98.0	97.0		2609,	4.5	1.0	21	dbSNP_79	97	58,8104		0,58,4023	yes	missense-near-splice,intron	GRIK1	NM_000830.3,NM_175611.2	64,	0,67,5819	AA,AG,GG		0.7106,0.2493,0.5691	benign,	870/919,	30926024	67,11705	1805	4081	5886	SO:0001630	splice_region_variant	2897	exon17			CAAAAAGCCTTGC		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.2608-1C>T	21.37:g.30926024G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_000830	Q13001|Q86SU9	Missense_Mutation	SNP	ENST00000399907.1	37	CCDS42913.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	G	17.20	3.327836	0.60743	0.002493	0.007106	ENSG00000171189	ENST00000399907;ENST00000399909;ENST00000309434	T;T;T	0.11277	2.8;2.79;2.8	5.4	4.52	0.55395	.	.	.	.	.	T	0.04182	0.0116	N	0.08118	0	0.31142	N	0.706501	B	0.20261	0.043	B	0.17433	0.018	T	0.16041	-1.0416	9	0.19147	T	0.46	.	13.6508	0.62310	0.0746:0.0:0.9254:0.0	rs363503	870	P39086	GRIK1_HUMAN	V	870;855;872	ENSP00000382791:A870V;ENSP00000382793:A855V;ENSP00000311646:A872V	ENSP00000311646:A872V	A	-	2	0	GRIK1	29847895	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.782000	0.68973	1.503000	0.48686	0.655000	0.94253	GCT	G|0.997;A|0.003	0.003	strong		0.313	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1		Missense_Mutation
AKNAD1	254268	hgsc.bcm.edu	37	1	109366286	109366286	+	Missense_Mutation	SNP	C	C	T	rs7522157	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:109366286C>T	ENST00000370001.3	-	12	2229	c.1961G>A	c.(1960-1962)tGt>tAt	p.C654Y	AKNAD1_ENST00000357393.4_Missense_Mutation_p.C361Y|AKNAD1_ENST00000369995.3_Missense_Mutation_p.C654Y|AKNAD1_ENST00000369994.1_Missense_Mutation_p.C624Y	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	654			C -> Y (in dbSNP:rs7522157). {ECO:0000269|Ref.6}.			cytoplasm (GO:0005737)		p.C654Y(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						AGAATCAGAACAGAAGCTGTG	0.438													C|||	830	0.165735	0.0598	0.1787	5008	,	,		19769	0.1121		0.2873	False		,,,				2504	0.2301				p.C654Y		Atlas-SNP	.											AKNAD1,NS,adenoma,0,2	AKNAD1	83	2	1	Substitution - Missense(1)	stomach(1)	c.G1961A						PASS	.	C	TYR/CYS	474,3932	222.6+/-239.4	24,426,1753	122.0	110.0	114.0		1961	-3.2	0.0	1	dbSNP_116	114	2706,5894	434.1+/-357.6	434,1838,2028	yes	missense	AKNAD1	NM_152763.3	194	458,2264,3781	TT,TC,CC		31.4651,10.7581,24.4503	possibly-damaging	654/837	109366286	3180,9826	2203	4300	6503	SO:0001583	missense	254268	exon12			TCAGAACAGAAGC	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 62"""	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.1961G>A	1.37:g.109366286C>T	ENSP00000359018:p.Cys654Tyr	Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	233	121	0.519313	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	37	CCDS791.2	376	0.17216117216117216	29	0.05894308943089431	63	0.17403314917127072	72	0.1258741258741259	212	0.2796833773087071	C	3.789	-0.044103	0.07452	0.107581	0.314651	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	4.83	-3.24	0.05094	.	0.899723	0.09329	N	0.817134	T	0.02012	0.0063	N	0.12746	0.255	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.002	T	0.48127	-0.9062	9	0.16420	T	0.52	0.472	6.5162	0.22248	0.1528:0.5632:0.0:0.2839	rs7522157;rs9440617;rs17562500;rs52807178;rs59423546;rs7522157	361;654	B4DET8;Q5T1N1	.;AKND1_HUMAN	Y	654;361;624;654	ENSP00000359018:C654Y;ENSP00000349968:C361Y;ENSP00000359011:C624Y;ENSP00000359012:C654Y	ENSP00000349968:C361Y	C	-	2	0	AKNAD1	109167809	0.000000	0.05858	0.000000	0.03702	0.868000	0.49771	-2.023000	0.01438	-0.360000	0.08138	0.561000	0.74099	TGT	C|0.793;G|0.000;N|0.000;T|0.206	0.206	strong		0.438	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
TAF1A	9015	hgsc.bcm.edu	37	1	222732027	222732027	+	Missense_Mutation	SNP	T	T	C	rs76003336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:222732027T>C	ENST00000352967.4	-	11	1516	c.1328A>G	c.(1327-1329)tAc>tGc	p.Y443C	TAF1A_ENST00000366890.1_Missense_Mutation_p.Y329C|TAF1A_ENST00000391882.1_Missense_Mutation_p.Y329C|TAF1A_ENST00000350027.4_Missense_Mutation_p.Y443C	NM_005681.3	NP_005672.1	Q15573	TAF1A_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa	443					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA binding (GO:0003677)			kidney(3)|large_intestine(3)|lung(11)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(131;0.0186)		TACAATACTGTATTTTTTCAC	0.308													T|||	64	0.0127796	0.0	0.0173	5008	,	,		12230	0.0		0.0358	False		,,,				2504	0.0164				p.Y443C		Atlas-SNP	.											.	TAF1A	35	.	0			c.A1328G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR	22,4380	28.1+/-56.4	0,22,2179	75.0	77.0	76.0		1328,1328,986	-0.2	0.6	1	dbSNP_131	76	207,8351	89.2+/-151.4	2,203,4074	yes	missense,missense,missense	TAF1A	NM_001201536.1,NM_005681.3,NM_139352.2	194,194,194	2,225,6253	CC,CT,TT		2.4188,0.4998,1.767	probably-damaging,probably-damaging,probably-damaging	443/451,443/451,329/337	222732027	229,12731	2201	4279	6480	SO:0001583	missense	9015	exon11			ATACTGTATTTTT	L39060	CCDS1531.1, CCDS1532.1	1q42	2008-02-05	2002-08-29		ENSG00000143498	ENSG00000143498			11532	protein-coding gene	gene with protein product		604903	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kD"""			7801123	Standard	NM_005681		Approved	TAFI48, SL1	uc009xdz.2	Q15573	OTTHUMG00000037544	ENST00000352967.4:c.1328A>G	1.37:g.222732027T>C	ENSP00000327072:p.Tyr443Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_001201536	B2RDZ8|D3DTB7|Q9NWA1	Missense_Mutation	SNP	ENST00000352967.4	37	CCDS1531.1	34	0.015567765567765568	0	0.0	8	0.022099447513812154	0	0.0	26	0.03430079155672823	T	11.72	1.722636	0.30503	0.004998	0.024188	ENSG00000143498	ENST00000366890;ENST00000350027;ENST00000352967;ENST00000391882	T;T	0.47177	0.85;0.85	5.34	-0.19	0.13256	.	0.305531	0.35466	N	0.003185	T	0.16428	0.0395	M	0.67953	2.075	0.48452	D	0.999659	B	0.02656	0.0	B	0.08055	0.003	T	0.09862	-1.0655	10	0.87932	D	0	-5.6164	3.2403	0.06778	0.3517:0.1695:0.0:0.4787	.	443	Q15573	TAF1A_HUMAN	C	329;443;443;329	ENSP00000339976:Y443C;ENSP00000327072:Y443C	ENSP00000339976:Y443C	Y	-	2	0	TAF1A	220798650	0.890000	0.30428	0.625000	0.29200	0.052000	0.14988	1.054000	0.30455	-0.236000	0.09753	-0.290000	0.09829	TAC	T|0.979;C|0.021	0.021	strong		0.308	TAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091493.2	NM_005681	
CLIP4	79745	hgsc.bcm.edu	37	2	29383256	29383256	+	Missense_Mutation	SNP	G	G	T	rs3100246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29383256G>T	ENST00000320081.5	+	12	1712	c.1457G>T	c.(1456-1458)cGc>cTc	p.R486L	CLIP4_ENST00000401617.2_Missense_Mutation_p.R379L|CLIP4_ENST00000401605.1_Missense_Mutation_p.R486L|CLIP4_ENST00000404424.1_Missense_Mutation_p.R486L	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	486			R -> L (in dbSNP:rs3100246).							endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					GGGGAACTCCGCCTCGGAGAG	0.488													G|||	255	0.0509185	0.0091	0.1023	5008	,	,		16976	0.001		0.1441	False		,,,				2504	0.0266				p.R486L		Atlas-SNP	.											.	CLIP4	69	.	0			c.G1457T						PASS	.	G	LEU/ARG	148,4258	101.2+/-139.8	2,144,2057	104.0	98.0	100.0		1457	-8.6	0.0	2	dbSNP_103	100	1277,7323	255.1+/-280.1	80,1117,3103	yes	missense	CLIP4	NM_024692.4	102	82,1261,5160	TT,TG,GG		14.8488,3.3591,10.9565	benign	486/706	29383256	1425,11581	2203	4300	6503	SO:0001583	missense	79745	exon12			AACTCCGCCTCGG	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"""Ankyrin repeat domain containing"""	26108	protein-coding gene	gene with protein product			"""restin-like 2"""	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.1457G>T	2.37:g.29383256G>T	ENSP00000327009:p.Arg486Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	126	69	0.547619	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Missense_Mutation	SNP	ENST00000320081.5	37	CCDS1770.1	145	0.06639194139194139	6	0.012195121951219513	41	0.1132596685082873	1	0.0017482517482517483	97	0.1279683377308707	G	14.12	2.440097	0.43326	0.033591	0.148488	ENSG00000115295	ENST00000401605;ENST00000401617;ENST00000404424;ENST00000402240;ENST00000320081;ENST00000379543;ENST00000530644	T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82	6.16	-8.63	0.00878	Cytoskeleton-associated protein, Gly-rich domain (2);	0.978007	0.08466	N	0.941749	T	0.00496	0.0016	L	0.29908	0.895	0.09310	N	1	B	0.25007	0.116	B	0.22601	0.04	T	0.04140	-1.0974	10	0.33940	T	0.23	.	15.3941	0.74778	0.4545:0.0:0.5455:0.0	rs3100246;rs52833373;rs57545939;rs3100246	486	Q8N3C7	CLIP4_HUMAN	L	486;379;486;486;486;504;446	ENSP00000384242:R486L;ENSP00000385148:R379L;ENSP00000385594:R486L;ENSP00000327009:R486L	ENSP00000327009:R486L	R	+	2	0	CLIP4	29236760	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.044000	0.12023	-1.766000	0.01302	-0.355000	0.07637	CGC	G|0.905;T|0.095	0.095	strong		0.488	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692	
ZNF19	7567	hgsc.bcm.edu	37	16	71509634	71509634	+	Silent	SNP	G	G	C	rs2288488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:71509634G>C	ENST00000288177.5	-	6	1071	c.816C>G	c.(814-816)ccC>ccG	p.P272P	ZNF19_ENST00000567225.1_Intron|AC010547.9_ENST00000561908.1_Intron|ZNF19_ENST00000565637.1_Silent_p.P230P|ZNF19_ENST00000565100.2_Silent_p.P202P|ZNF19_ENST00000564230.1_Silent_p.P272P	NM_006961.3	NP_008892.2	P17023	ZNF19_HUMAN	zinc finger protein 19	272					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(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|prostate(1)|stomach(1)	22		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		TACACTCATAGGGTTTCTCCC	0.443													G|||	1287	0.256989	0.0212	0.1787	5008	,	,		19045	0.2817		0.2962	False		,,,				2504	0.5654				p.P272P		Atlas-SNP	.											.	ZNF19	46	.	0			c.C816G						PASS	.	G		294,4102	162.2+/-194.2	14,266,1918	105.0	106.0	106.0		816	-4.8	0.2	16	dbSNP_100	106	2636,5964	425.3+/-354.9	415,1806,2079	no	coding-synonymous	ZNF19	NM_006961.3		429,2072,3997	CC,CG,GG		30.6512,6.6879,22.5454		272/459	71509634	2930,10066	2198	4300	6498	SO:0001819	synonymous_variant	7567	exon6			CTCATAGGGTTTC	X52343	CCDS10901.1	16q22	2013-01-08	2006-05-10		ENSG00000157429	ENSG00000157429		"""Zinc fingers, C2H2-type"", ""-"""	12981	protein-coding gene	gene with protein product		194525	"""zinc finger protein 19 (KOX 12)"""			1505991, 1946370	Standard	NM_006961		Approved	KOX12, MGC51021	uc002fam.1	P17023	OTTHUMG00000137593	ENST00000288177.5:c.816C>G	16.37:g.71509634G>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_006961	A8K895|Q86Y66|Q8NDE2|Q96M79|Q96NE5	Silent	SNP	ENST00000288177.5	37	CCDS10901.1																																																																																			G|0.765;C|0.235	0.235	strong		0.443	ZNF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268993.2	NM_006961	
PCDHGA11	56105	hgsc.bcm.edu	37	5	140802723	140802723	+	Silent	SNP	C	C	T	rs62378456	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140802723C>T	ENST00000398587.2	+	1	1962	c.1929C>T	c.(1927-1929)ctC>ctT	p.L643L	PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA9_ENST00000573521.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	643	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCAGAGCCTCGTGGTGGCCG	0.701													c|||	190	0.0379393	0.0756	0.036	5008	,	,		16447	0.001		0.0328	False		,,,				2504	0.0317				p.L643L		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.C1929T						PASS	.	C	,,,,,,,,,,,,,,,,,,,	254,4152	127.8+/-164.7	7,240,1956	41.0	49.0	46.0		,,,1929,,,,,,,,,,,,,,,1929,	-4.8	1.0	5	dbSNP_129	46	315,8281	107.6+/-168.3	6,303,3989	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032091.1,NM_032092.1	,,,,,,,,,,,,,,,,,,,	13,543,5945	TT,TC,CC		3.6645,5.7649,4.3762	,,,,,,,,,,,,,,,,,,,	,,,643/936,,,,,,,,,,,,,,,643/838,	140802723	569,12433	2203	4298	6501	SO:0001819	synonymous_variant	56105	exon1			GAGCCTCGTGGTG	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"""Cadherins / Protocadherins : Clustered"""	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.1929C>T	5.37:g.140802723C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_032091	B7ZVY8|Q9Y5D8|Q9Y5D9	Silent	SNP	ENST00000398587.2	37	CCDS47294.1																																																																																			C|0.963;T|0.037	0.037	strong		0.701	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914	
PDE9A	5152	hgsc.bcm.edu	37	21	44106372	44106372	+	Splice_Site	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:44106372G>A	ENST00000291539.6	+	2	200	c.140G>A	c.(139-141)cGg>cAg	p.R47Q	PDE9A_ENST00000380328.2_Splice_Site_p.R47Q|PDE9A_ENST00000335512.4_Splice_Site_p.R47Q|PDE9A_ENST00000335440.6_Intron|PDE9A_ENST00000398232.3_Intron|PDE9A_ENST00000398229.3_Intron|PDE9A_ENST00000349112.3_Intron|PDE9A_ENST00000539837.1_Splice_Site_p.R12Q|PDE9A_ENST00000398224.3_Intron|PDE9A_ENST00000398227.3_Intron|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000328862.6_Splice_Site_p.R47H|PDE9A_ENST00000398234.3_Intron|PDE9A_ENST00000398236.3_Splice_Site_p.R47H|PDE9A_ENST00000398225.3_Intron	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	47					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	GGCCTGCCTCGGTGAGTGCGC	0.662																																					p.R47Q		Atlas-SNP	.											PDE9A,NS,carcinoma,0,1	PDE9A	69	1	0			c.G140A						scavenged	.						69.0	60.0	63.0					21																	44106372		2203	4300	6503	SO:0001630	splice_region_variant	5152	exon2			TGCCTCGGTGAGT	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.140+1G>A	21.37:g.44106372G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	2	0.0235294	NM_001001570	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	17.69|17.69	3.451487|3.451487	0.63290|0.63290	.|.	.|.	ENSG00000160191|ENSG00000160191	ENST00000398236;ENST00000328862|ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328	T;T|T;T;T;T	0.74421|0.75938	-0.8;-0.84|-0.45;-0.98;-0.68;-0.62	4.92|4.92	4.92|4.92	0.64577|0.64577	.|.	0.110203|0.110203	0.64402|0.64402	D|D	0.000013|0.000013	T|T	0.80121|0.80121	0.4565|0.4565	L|L	0.52573|0.52573	1.65|1.65	0.35333|0.35333	D|D	0.785799|0.785799	B;D|D;D;D	0.62365|0.89917	0.044;0.991|0.992;0.994;1.0	B;P|P;P;D	0.59643|0.64776	0.018;0.861|0.789;0.789;0.929	T|T	0.81684|0.81684	-0.0821|-0.0821	10|10	0.72032|0.27082	D|T	0.01|0.32	.|.	13.9807|13.9807	0.64304|0.64304	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	47;47|47;47;47	O76083-8;O76083-15|O76083-2;O76083-5;O76083	.;.|.;.;PDE9A_HUMAN	H|Q	47|47;12;47;47	ENSP00000381291:R47H;ENSP00000328699:R47H|ENSP00000335242:R47Q;ENSP00000441899:R12Q;ENSP00000291539:R47Q;ENSP00000369685:R47Q	ENSP00000328699:R47H|ENSP00000291539:R47Q	R|R	+|+	2|2	0|0	PDE9A|PDE9A	42979441|42979441	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.251000|0.251000	0.25915|0.25915	4.967000|4.967000	0.63722|0.63722	2.419000|2.419000	0.82065|0.82065	0.655000|0.655000	0.94253|0.94253	CGC|CGG	.	.	none		0.662	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		Missense_Mutation
PKHD1	5314	hgsc.bcm.edu	37	6	51613177	51613177	+	Silent	SNP	C	C	T	rs765525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:51613177C>T	ENST00000371117.3	-	58	9512	c.9237G>A	c.(9235-9237)gcG>gcA	p.A3079A	PKHD1_ENST00000340994.4_Silent_p.A3079A	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3079					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CTTTGATTCCCGCCACCCAAA	0.517													T|||	1933	0.385982	0.0318	0.4769	5008	,	,		21619	0.6548		0.3926	False		,,,				2504	0.5164				p.A3079A		Atlas-SNP	.											.	PKHD1	927	.	0			c.G9237A						PASS	.	T	,	452,3954	784.9+/-414.7	16,420,1767	190.0	166.0	174.0		9237,9237	3.3	1.0	6	dbSNP_86	174	3112,5488	658.0+/-401.5	567,1978,1755	yes	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	583,2398,3522	TT,TC,CC		36.186,10.2587,27.4027	,	3079/4075,3079/3397	51613177	3564,9442	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon58			GATTCCCGCCACC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.9237G>A	6.37:g.51613177C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			T|0.317;G|0.011	0.317	strong		0.517	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
CYP4F22	126410	hgsc.bcm.edu	37	19	15648715	15648715	+	Silent	SNP	G	G	A	rs11666601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:15648715G>A	ENST00000269703.3	+	7	781	c.582G>A	c.(580-582)gcG>gcA	p.A194A	CYP4F22_ENST00000601005.2_Silent_p.A194A	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	194						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.A194A(1)		endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						AGGGCTCAGCGGTCTCCCTTG	0.517													G|||	413	0.0824681	0.056	0.0735	5008	,	,		19961	0.0764		0.1083	False		,,,				2504	0.1043				p.A194A		Atlas-SNP	.											CYP4F22,NS,carcinoma,0,1	CYP4F22	74	1	1	Substitution - coding silent(1)	prostate(1)	c.G582A						PASS	.	G		241,4165	141.5+/-176.9	7,227,1969	126.0	107.0	113.0		582	-5.2	0.0	19	dbSNP_120	113	969,7631	211.0+/-251.7	42,885,3373	no	coding-synonymous	CYP4F22	NM_173483.3		49,1112,5342	AA,AG,GG		11.2674,5.4698,9.3034		194/532	15648715	1210,11796	2203	4300	6503	SO:0001819	synonymous_variant	126410	exon7			CTCAGCGGTCTCC		CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"""Cytochrome P450s"""	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.582G>A	19.37:g.15648715G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_173483	Q8N8H4	Silent	SNP	ENST00000269703.3	37	CCDS12331.1																																																																																			G|0.907;A|0.093	0.093	strong		0.517	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483	
SLCO2A1	6578	hgsc.bcm.edu	37	3	133666209	133666209	+	Missense_Mutation	SNP	C	C	T	rs34550074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:133666209C>T	ENST00000310926.4	-	9	1459	c.1186G>A	c.(1186-1188)Gcc>Acc	p.A396T	SLCO2A1_ENST00000493729.1_Missense_Mutation_p.A320T	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	396			A -> T (in dbSNP:rs34550074). {ECO:0000269|PubMed:8787677, ECO:0000269|PubMed:9618293}.		lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)	p.A396T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	CGGGGAATGGCTTGTAGAGAG	0.502													T|||	1421	0.283746	0.4297	0.2536	5008	,	,		19189	0.2817		0.1899	False		,,,				2504	0.2065				p.A396T		Atlas-SNP	.											SLCO2A1,NS,carcinoma,0,1	SLCO2A1	72	1	1	Substitution - Missense(1)	stomach(1)	c.G1186A						scavenged	.	T	THR/ALA	1807,2599	640.3+/-397.3	388,1031,784	126.0	112.0	117.0		1186	4.6	1.0	3	dbSNP_126	117	1608,6992	743.2+/-407.2	152,1304,2844	yes	missense	SLCO2A1	NM_005630.2	58	540,2335,3628	TT,TC,CC		18.6977,41.0123,26.2571	benign	396/644	133666209	3415,9591	2203	4300	6503	SO:0001583	missense	6578	exon9			GAATGGCTTGTAG		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"""Solute carriers"""	10955	protein-coding gene	gene with protein product		601460	"""solute carrier family 21 (prostaglandin transporter), member 2"", ""matrin F/G 1"""	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.1186G>A	3.37:g.133666209C>T	ENSP00000311291:p.Ala396Thr	Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	140	69	0.492857	NM_005630	Q86V98|Q8IUN2	Missense_Mutation	SNP	ENST00000310926.4	37	CCDS3084.1	605	0.27701465201465203	202	0.4105691056910569	95	0.26243093922651933	152	0.26573426573426573	156	0.20580474934036938	T	1.317	-0.600463	0.03744	0.410123	0.186977	ENSG00000174640	ENST00000310926;ENST00000493729	T;T	0.39229	1.09;1.09	5.72	4.55	0.56014	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.342974	0.34291	N	0.004099	T	0.00012	0.0000	N	0.03224	-0.385	0.47123	P	6.749999999999812E-4	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.47560	-0.9108	9	0.20519	T	0.43	.	8.1198	0.30965	0.0:0.2794:0.0:0.7206	rs34550074	320;396	E7EU40;Q92959	.;SO2A1_HUMAN	T	396;320	ENSP00000311291:A396T;ENSP00000418893:A320T	ENSP00000311291:A396T	A	-	1	0	SLCO2A1	135148899	0.959000	0.32827	1.000000	0.80357	0.096000	0.18686	0.518000	0.22847	0.437000	0.26423	-0.254000	0.11334	GCC	C|0.732;T|0.268	0.268	strong		0.502	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630	
NUBP1	4682	hgsc.bcm.edu	37	16	10837913	10837913	+	Missense_Mutation	SNP	C	C	G	rs2233531	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:10837913C>G	ENST00000283027.5	+	2	134	c.115C>G	c.(115-117)Ccg>Gcg	p.P39A	NUBP1_ENST00000433392.2_Missense_Mutation_p.P39A|NUBP1_ENST00000571790.1_3'UTR	NM_002484.2	NP_002475.2			nucleotide binding protein 1											large_intestine(2)|lung(3)|ovary(1)|skin(4)	10						GGGGGCCACTCCGGACACGGG	0.682													C|||	558	0.111422	0.1407	0.0663	5008	,	,		13120	0.0317		0.0984	False		,,,				2504	0.1994				p.P39A		Atlas-SNP	.											.	NUBP1	31	.	0			c.C115G						PASS	.	C	ALA/PRO	477,3909		29,419,1745	11.0	12.0	12.0		115	3.8	0.5	16	dbSNP_98	12	857,7721		38,781,3470	yes	missense	NUBP1	NM_002484.2	27	67,1200,5215	GG,GC,CC		9.9907,10.8755,10.29	benign	39/321	10837913	1334,11630	2193	4289	6482	SO:0001583	missense	4682	exon2			GCCACTCCGGACA	U01833	CCDS10543.1, CCDS61839.1	16p13.13	2014-01-13	2011-05-19		ENSG00000103274	ENSG00000103274			8041	protein-coding gene	gene with protein product		600280	"""nucleotide binding protein 1 (E.coli MinD like)"", ""nucleotide binding protein 1 (MinD homolog, E. coli)"""	NBP1		7926816	Standard	NM_002484		Approved	NBP35	uc002daa.1	P53384	OTTHUMG00000129751	ENST00000283027.5:c.115C>G	16.37:g.10837913C>G	ENSP00000283027:p.Pro39Ala	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_002484		Missense_Mutation	SNP	ENST00000283027.5	37	CCDS10543.1	199	0.09111721611721611	74	0.15040650406504066	29	0.08011049723756906	20	0.03496503496503497	76	0.10026385224274406	C	13.80	2.345168	0.41498	0.108755	0.099907	ENSG00000103274	ENST00000283027;ENST00000433392	T;T	0.18016	2.24;2.27	3.83	3.83	0.44106	.	0.144840	0.45606	D	0.000360	T	0.00109	0.0003	L	0.58810	1.83	0.09310	P	0.99999802043	B;B	0.09022	0.002;0.001	B;B	0.19946	0.027;0.012	T	0.05886	-1.0858	9	0.66056	D	0.02	-23.104	10.9413	0.47275	0.1878:0.8122:0.0:0.0	rs2233531;rs11557238;rs2233531	39;39	P53384-2;P53384	.;NUBP1_HUMAN	A	39	ENSP00000283027:P39A;ENSP00000409654:P39A	ENSP00000283027:P39A	P	+	1	0	NUBP1	10745414	0.953000	0.32496	0.509000	0.27700	0.591000	0.36615	2.659000	0.46741	1.835000	0.53391	0.563000	0.77884	CCG	C|0.909;G|0.091	0.091	strong		0.682	NUBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251964.2	NM_002484	
ZNF768	79724	hgsc.bcm.edu	37	16	30536798	30536798	+	Silent	SNP	C	C	T	rs138236969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30536798C>T	ENST00000380412.5	-	2	838	c.663G>A	c.(661-663)ggG>ggA	p.G221G	ZNF768_ENST00000562803.1_Silent_p.G190G	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	221					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	DNA-directed RNA polymerase II, core complex (GO:0005665)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						ACAGCAGGGCCCCTGTGGGCA	0.642													C|||	11	0.00219649	0.0	0.0014	5008	,	,		14345	0.0		0.0099	False		,,,				2504	0.0				p.G221G		Atlas-SNP	.											.	ZNF768	28	.	0			c.G663A						PASS	.	C		7,4387	11.4+/-27.6	0,7,2190	65.0	70.0	68.0		663	2.2	1.0	16	dbSNP_134	68	77,8523	41.2+/-98.3	0,77,4223	no	coding-synonymous	ZNF768	NM_024671.3		0,84,6413	TT,TC,CC		0.8953,0.1593,0.6465		221/541	30536798	84,12910	2197	4300	6497	SO:0001819	synonymous_variant	79724	exon2			CAGGGCCCCTGTG	BC013760	CCDS10681.2	16p11.2	2013-01-08			ENSG00000169957	ENSG00000169957		"""Zinc fingers, C2H2-type"""	26273	protein-coding gene	gene with protein product						12477932	Standard	NM_024671		Approved	FLJ23436	uc002dyk.4	Q9H5H4	OTTHUMG00000132392	ENST00000380412.5:c.663G>A	16.37:g.30536798C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_024671	Q569L7|Q96CX4	Silent	SNP	ENST00000380412.5	37	CCDS10681.2																																																																																			C|0.995;T|0.005	0.005	strong		0.642	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671	
ZSCAN31	64288	hgsc.bcm.edu	37	6	28294550	28294550	+	Missense_Mutation	SNP	T	T	C	rs853684	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28294550T>C	ENST00000414429.1	-	8	1517	c.614A>G	c.(613-615)aAa>aGa	p.K205R	ZSCAN31_ENST00000396838.2_Missense_Mutation_p.K205R|ZSCAN31_ENST00000481934.1_5'Flank|ZSCAN31_ENST00000344279.6_Missense_Mutation_p.K205R|ZSCAN31_ENST00000446474.1_Missense_Mutation_p.K46R|ZSCAN31_ENST00000439158.1_Missense_Mutation_p.K205R			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	205			K -> R (in dbSNP:rs853684).		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)										TCTTTGGAGTTTGCTATCCCC	0.418													C|||	3083	0.615615	0.9531	0.4899	5008	,	,		21109	0.6042		0.3807	False		,,,				2504	0.502				p.K205R		Atlas-SNP	.											.	.	.	.	0			c.A614G						PASS	.	C	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	3733,673	283.7+/-277.2	1594,545,64	85.0	87.0	86.0		614,614,614,614	-0.8	0.0	6	dbSNP_86	86	3302,5298	645.1+/-400.1	639,2024,1637	yes	missense,missense,missense,missense	ZNF323	NM_001135215.1,NM_001135216.1,NM_030899.4,NM_145909.2	26,26,26,26	2233,2569,1701	CC,CT,TT		38.3953,15.2746,45.9096	benign,benign,benign,benign	205/407,205/407,205/407,205/407	28294550	7035,5971	2203	4300	6503	SO:0001583	missense	64288	exon4			TGGAGTTTGCTAT		CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"""-"", ""Zinc fingers, C2H2-type"""	14097	protein-coding gene	gene with protein product		610794	"""zinc finger protein 310 pseudogene"", ""zinc finger protein 323"""	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.614A>G	6.37:g.28294550T>C	ENSP00000390076:p.Lys205Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	160	65	0.40625	NM_030899	Q6P178|Q8WWS5	Missense_Mutation	SNP	ENST00000414429.1	37	CCDS4649.1	1265	0.5792124542124543	464	0.943089430894309	176	0.4861878453038674	348	0.6083916083916084	277	0.3654353562005277	C	4.994	0.184589	0.09495	0.847254	0.383953	ENSG00000235109	ENST00000396838;ENST00000439158;ENST00000414429;ENST00000446474;ENST00000344279;ENST00000435857;ENST00000414431;ENST00000453745	T;T;T;T;T;T;T;T	0.05855	3.43;3.43;3.43;3.38;3.43;3.45;5.95;4.41	4.32	-0.837	0.10766	.	.	.	.	.	T	0.00440	0.0014	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44143	-0.9347	8	0.10377	T	0.69	.	0.317	0.00297	0.3355:0.2437:0.1293:0.2916	rs853684;rs52811904;rs61223141;rs853684	205	Q96LW9	ZN323_HUMAN	R	205;205;205;46;205;46;46;205	ENSP00000380050:K205R;ENSP00000413705:K205R;ENSP00000390076:K205R;ENSP00000402937:K46R;ENSP00000345339:K205R;ENSP00000391235:K46R;ENSP00000407529:K46R;ENSP00000389479:K205R	ENSP00000345339:K205R	K	-	2	0	ZNF323	28402529	0.004000	0.15560	0.015000	0.15790	0.021000	0.10359	-0.260000	0.08708	-0.197000	0.10350	-1.201000	0.01664	AAA	T|0.428;C|0.572	0.572	strong		0.418	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899	
CCDC88B	283234	hgsc.bcm.edu	37	11	64109118	64109118	+	Missense_Mutation	SNP	T	T	G	rs647152	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64109118T>G	ENST00000356786.5	+	7	623	c.579T>G	c.(577-579)gaT>gaG	p.D193E	CCDC88B_ENST00000301897.4_5'Flank|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	193			D -> E (in dbSNP:rs647152).			membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTGGGCCAGATCCTGGGGAGC	0.697													G|||	1768	0.353035	0.3502	0.3991	5008	,	,		12964	0.2401		0.3708	False		,,,				2504	0.4223				p.D193E		Atlas-SNP	.											CCDC88B,NS,carcinoma,0,1	CCDC88B	89	1	0			c.T579G						scavenged	.	G	GLU/ASP	1526,2870		283,960,955	18.0	21.0	20.0		579	2.1	0.9	11	dbSNP_83	20	3090,5492		563,1964,1764	yes	missense	CCDC88B	NM_032251.5	45	846,2924,2719	GG,GT,TT		36.0056,34.7134,35.5679	benign	193/1477	64109118	4616,8362	2198	4291	6489	SO:0001583	missense	283234	exon7			GCCAGATCCTGGG	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.579T>G	11.37:g.64109118T>G	ENSP00000349238:p.Asp193Glu	Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	144	69	0.479167	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Missense_Mutation	SNP	ENST00000356786.5	37	CCDS8072.2	760	0.34798534798534797	185	0.37601626016260165	134	0.3701657458563536	147	0.256993006993007	294	0.38786279683377306	.	1.011	-0.687781	0.03328	0.347134	0.360056	ENSG00000168071	ENST00000377638;ENST00000356786	T	0.26223	1.75	4.09	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	N	0.00652	-1.29	0.09310	P	0.99999999176656	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45056	-0.9287	8	0.02654	T	1	.	2.3045	0.04171	0.112:0.1937:0.4945:0.1997	rs647152;rs1201767;rs647152	193;193	B2RTU8;A6NC98	.;CC88B_HUMAN	E	193	ENSP00000349238:D193E	ENSP00000349238:D193E	D	+	3	2	CCDC88B	63865694	0.285000	0.24296	0.937000	0.37676	0.408000	0.30992	0.044000	0.13992	0.129000	0.18514	-0.383000	0.06682	GAT	T|0.649;G|0.351	0.351	strong		0.697	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
FAM135B	51059	hgsc.bcm.edu	37	8	139164570	139164570	+	Silent	SNP	C	C	T	rs3750307	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:139164570C>T	ENST00000395297.1	-	13	2318	c.2148G>A	c.(2146-2148)ccG>ccA	p.P716P		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	716										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TTCGAACAAACGGGTGCAAGA	0.562										HNSCC(54;0.14)			C|||	1070	0.213658	0.2057	0.1931	5008	,	,		18235	0.2321		0.173	False		,,,				2504	0.2618				p.P716P		Atlas-SNP	.											LOC51059,caecum,carcinoma,0,2	FAM135B	423	2	0			c.G2148A						PASS	.	C		758,3178		87,584,1297	45.0	46.0	46.0		2148	-4.7	0.0	8	dbSNP_107	46	1511,6779		131,1249,2765	no	coding-synonymous	FAM135B	NM_015912.3		218,1833,4062	TT,TC,CC		18.2268,19.2581,18.5588		716/1407	139164570	2269,9957	1968	4145	6113	SO:0001819	synonymous_variant	51059	exon13			AACAAACGGGTGC	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.2148G>A	8.37:g.139164570C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			C|0.791;N|0.000	.	strong		0.562	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
SYNPO2L	79933	hgsc.bcm.edu	37	10	75406952	75406952	+	Missense_Mutation	SNP	A	A	G	rs200429699		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:75406952A>G	ENST00000394810.2	-	4	2607	c.2458T>C	c.(2458-2460)Ttt>Ctt	p.F820L	SYNPO2L_ENST00000372873.4_Missense_Mutation_p.F596L	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	820	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					TGGGGGAAAAAGGGAGAGAGC	0.577													A|||	1	0.000199681	0.0	0.0	5008	,	,		15267	0.0		0.001	False		,,,				2504	0.0				p.F820L		Atlas-SNP	.											SYNPO2L_ENST00000394810,NS,carcinoma,+1,4	SYNPO2L	118	4	0			c.T2458C						scavenged	.						62.0	74.0	70.0					10																	75406952		2202	4300	6502	SO:0001583	missense	79933	exon4			GGAAAAAGGGAGA	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.2458T>C	10.37:g.75406952A>G	ENSP00000378289:p.Phe820Leu	Somatic	62	1	0.016129		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_001114133	A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	37	CCDS44438.1	.	.	.	.	.	.	.	.	.	.	A	19.36	3.813125	0.70912	.	.	ENSG00000166317	ENST00000372873;ENST00000394810	T;T	0.22539	1.95;2.26	4.98	4.98	0.66077	.	0.119748	0.64402	D	0.000019	T	0.23766	0.0575	L	0.54323	1.7	0.44500	D	0.997447	P;P	0.45531	0.666;0.86	B;P	0.44561	0.162;0.453	T	0.03597	-1.1021	10	0.12103	T	0.63	-5.368	14.8374	0.70194	1.0:0.0:0.0:0.0	.	820;596	Q9H987;Q9H987-2	SYP2L_HUMAN;.	L	596;820	ENSP00000361964:F596L;ENSP00000378289:F820L	ENSP00000361964:F596L	F	-	1	0	SYNPO2L	75076958	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.139000	0.94554	2.090000	0.63153	0.402000	0.26972	TTT	.	.	weak		0.577	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
EFHD1	80303	hgsc.bcm.edu	37	2	233498669	233498669	+	Silent	SNP	G	G	T	rs2276557	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233498669G>T	ENST00000264059.3	+	1	732	c.255G>T	c.(253-255)ccG>ccT	p.P85P	EFHD1_ENST00000409613.1_Intron	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	85					neuron projection development (GO:0031175)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|large_intestine(2)|lung(3)	7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		CGGAGTTCCCGGAGTTCAGCC	0.701													G|||	1213	0.242212	0.1286	0.1571	5008	,	,		9824	0.6329		0.1899	False		,,,				2504	0.1074				p.P85P		Atlas-SNP	.											.	EFHD1	28	.	0			c.G255T						PASS	.	G		572,3778		37,498,1640	16.0	19.0	18.0		255	-3.3	0.9	2	dbSNP_100	18	1649,6885		159,1331,2777	no	coding-synonymous	EFHD1	NM_025202.3		196,1829,4417	TT,TG,GG		19.3227,13.1494,17.2384		85/240	233498669	2221,10663	2175	4267	6442	SO:0001819	synonymous_variant	80303	exon1			GTTCCCGGAGTTC		CCDS2497.1, CCDS58755.1	2q37.1	2014-07-01	2005-01-25		ENSG00000115468	ENSG00000115468		"""EF-hand domain containing"""	29556	protein-coding gene	gene with protein product	"""swiprosin-2"""	611617	"""EF hand domain containing 1"""			21244694	Standard	NM_025202		Approved	FLJ13612	uc002vtc.3	Q9BUP0	OTTHUMG00000133263	ENST00000264059.3:c.255G>T	2.37:g.233498669G>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	6	0.75	NM_025202	B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	Silent	SNP	ENST00000264059.3	37	CCDS2497.1																																																																																			G|0.726;T|0.274	0.274	strong		0.701	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202	
RMDN1	51115	hgsc.bcm.edu	37	8	87497176	87497176	+	Silent	SNP	G	G	A	rs11539113	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:87497176G>A	ENST00000406452.3	-	5	669	c.510C>T	c.(508-510)tgC>tgT	p.C170C	RMDN1_ENST00000523911.1_Silent_p.C126C|RMDN1_ENST00000519966.1_Intron|RMDN1_ENST00000430676.2_Intron|CPNE3_ENST00000198765.4_Intron	NM_016033.2	NP_057117.2	Q96DB5	RMD1_HUMAN	regulator of microtubule dynamics 1	170						microtubule (GO:0005874)|mitochondrion (GO:0005739)											CATCACTAAGGCAGATTGCAT	0.289													G|||	1782	0.355831	0.1641	0.5072	5008	,	,		16591	0.5327		0.2694	False		,,,				2504	0.4141				p.C170C		Atlas-SNP	.											.	.	.	.	0			c.C510T						PASS	.	G		746,3660	298.7+/-285.4	69,608,1526	67.0	62.0	64.0		510	1.4	1.0	8	dbSNP_120	64	2115,6477	360.0+/-331.8	268,1579,2449	no	coding-synonymous	FAM82B	NM_016033.2		337,2187,3975	AA,AG,GG		24.6159,16.9315,22.0111		170/315	87497176	2861,10137	2203	4296	6499	SO:0001819	synonymous_variant	51115	exon5			ACTAAGGCAGATT	AK000672	CCDS34918.1, CCDS69509.1, CCDS69510.1	8q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000176623	ENSG00000176623			24285	protein-coding gene	gene with protein product		611871	"""family with sequence similarity 82, member B"""	FAM82B		10810093	Standard	NM_016033		Approved	CGI-90, FLJ20665, RMD1	uc003ydu.3	Q96DB5	OTTHUMG00000163692	ENST00000406452.3:c.510C>T	8.37:g.87497176G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	175	173	0.988571	NM_016033	A9UMZ8|B4DNF5|B4DZW6|B5MC61|C9JSC6|E7EVI2|Q9Y398	Silent	SNP	ENST00000406452.3	37	CCDS34918.1	755|755	0.3456959706959707|0.3456959706959707	81|81	0.16463414634146342|0.16463414634146342	163|163	0.45027624309392267|0.45027624309392267	308|308	0.5384615384615384|0.5384615384615384	203|203	0.2678100263852243|0.2678100263852243	G|G	9.069|9.069	0.996302|0.996302	0.19043|0.19043	0.169315|0.169315	0.246159|0.246159	ENSG00000176623|ENSG00000176623	ENST00000519639|ENST00000519789	.|.	.|.	.|.	5.63|5.63	1.36|1.36	0.22044|0.22044	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49513|0.49513	-0.8932|-0.8932	3|3	.|.	.|.	.|.	-14.3246|-14.3246	13.866|13.866	0.63590|0.63590	0.217:0.0:0.783:0.0|0.217:0.0:0.783:0.0	rs11539113;rs13259590;rs13259590|rs11539113;rs13259590;rs13259590	.|.	.|.	.|.	V|S	16|116	.|.	.|.	A|P	-|-	2|1	0|0	FAM82B|FAM82B	87566292|87566292	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	0.670000|0.670000	0.25157|0.25157	0.239000|0.239000	0.21243|0.21243	0.655000|0.655000	0.94253|0.94253	GCC|CCT	G|0.596;T|0.065	.	strong		0.289	RMDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374770.2	NM_016033	
CDC25B	994	hgsc.bcm.edu	37	20	3783764	3783764	+	Silent	SNP	C	C	T	rs2228464	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3783764C>T	ENST00000245960.5	+	13	1964	c.1267C>T	c.(1267-1269)Cta>Tta	p.L423L	CDC25B_ENST00000439880.2_Silent_p.L409L|CDC25B_ENST00000340833.4_Silent_p.L382L|CDC25B_ENST00000379598.5_Silent_p.L332L|CDC25B_ENST00000344256.6_Silent_p.L359L|CDC25B_ENST00000467519.1_3'UTR	NM_004358.3|NM_021872.2|NM_021873.2	NP_004349.1|NP_068658.1|NP_068659.1	P30305	MPIP2_HUMAN	cell division cycle 25B	423					female meiosis I (GO:0007144)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|oocyte maturation (GO:0001556)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein kinase activity (GO:0045860)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(1)	18						GATGGTGGCCCTATTGACGGG	0.552													C|||	145	0.0289537	0.0061	0.0331	5008	,	,		21658	0.005		0.0795	False		,,,				2504	0.0297				p.L423L		Atlas-SNP	.											.	CDC25B	76	.	0			c.C1267T						PASS	.	C	,,	77,4329	68.1+/-105.8	2,73,2128	81.0	70.0	73.0		1225,1144,1267	1.5	1.0	20	dbSNP_98	73	598,8002	157.5+/-211.1	19,560,3721	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC25B	NM_004358.3,NM_021872.2,NM_021873.2	,,	21,633,5849	TT,TC,CC		6.9535,1.7476,5.1899	,,	409/567,382/540,423/581	3783764	675,12331	2203	4300	6503	SO:0001819	synonymous_variant	994	exon13			GTGGCCCTATTGA		CCDS13065.1, CCDS13066.1, CCDS13067.1, CCDS74700.1, CCDS74701.1	20p13	2013-01-17	2013-01-17		ENSG00000101224	ENSG00000101224		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"""	1726	protein-coding gene	gene with protein product		116949	"""cell division cycle 25B"", ""cell division cycle 25 homolog B (S. cerevisiae)"", ""cell division cycle 25 homolog B (S. pombe)"""			1836978	Standard	NM_021873		Approved		uc002wjn.3	P30305	OTTHUMG00000031764	ENST00000245960.5:c.1267C>T	20.37:g.3783764C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	174	75	0.431034	NM_021873	D3DVY1|D3DVY2|D3DVY3|D3DVY4|O43551|Q13971|Q5JX77|Q6RSS1|Q9BRA6	Silent	SNP	ENST00000245960.5	37	CCDS13067.1																																																																																			C|0.955;T|0.045	0.045	strong		0.552	CDC25B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077779.2	NM_021874	
DGKH	160851	hgsc.bcm.edu	37	13	42764564	42764564	+	Silent	SNP	C	C	G	rs7324235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:42764564C>G	ENST00000337343.4	+	16	1959	c.1938C>G	c.(1936-1938)ccC>ccG	p.P646P	DGKH_ENST00000379274.2_Silent_p.P510P|DGKH_ENST00000536612.1_Silent_p.P510P|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_Silent_p.P401P|DGKH_ENST00000540693.1_Silent_p.P646P|DGKH_ENST00000261491.5_Silent_p.P646P	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	646					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		CAGTTCACCCCTGTGAACCAG	0.388													C|||	871	0.173922	0.0643	0.2666	5008	,	,		15383	0.0942		0.2624	False		,,,				2504	0.2474				p.P646P		Atlas-SNP	.											DGKH,caecum,carcinoma,0,1	DGKH	106	1	0			c.C1938G						PASS	.	C	,,,,	445,3961	216.1+/-234.9	22,401,1780	121.0	117.0	119.0		1938,1530,1530,1938,1938	-2.6	0.1	13	dbSNP_116	119	2332,6268	390.9+/-343.5	335,1662,2303	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DGKH	NM_001204504.1,NM_001204505.1,NM_001204506.1,NM_152910.4,NM_178009.3	,,,,	357,2063,4083	GG,GC,CC		27.1163,10.0999,21.3517	,,,,	646/1165,510/1101,510/1085,646/1165,646/1221	42764564	2777,10229	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon17			TCACCCCTGTGAA	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.1938C>G	13.37:g.42764564C>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	39	33	0.846154	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			C|0.796;G|0.204	0.204	strong		0.388	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
GPR162	27239	hgsc.bcm.edu	37	12	6934804	6934804	+	Silent	SNP	C	C	T	rs148277722	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6934804C>T	ENST00000311268.3	+	3	1810	c.1023C>T	c.(1021-1023)tgC>tgT	p.C341C	LEPREL2_ENST00000396725.2_RNA|GPR162_ENST00000428545.2_Silent_p.C57C|LEPREL2_ENST00000606935.1_RNA|LEPREL2_ENST00000251761.8_RNA|GPR162_ENST00000382315.3_Silent_p.C37C	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	341						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						GGGAGCAATGCGTGGCCATCA	0.607											OREG0021636	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	4	0.000798722	0.0015	0.0	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.002				p.C341C		Atlas-SNP	.											.	GPR162	55	.	0			c.C1023T						PASS	.	C	,	2,4400		0,2,2199	92.0	56.0	68.0		171,1023	0.7	1.0	12	dbSNP_134	68	17,8577		0,17,4280	no	coding-synonymous,coding-synonymous	GPR162	NM_014449.1,NM_019858.1	,	0,19,6479	TT,TC,CC		0.1978,0.0454,0.1462	,	57/305,341/589	6934804	19,12977	2201	4297	6498	SO:0001819	synonymous_variant	27239	exon3			GCAATGCGTGGCC	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"""GPCR / Class A : Orphans"""	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.1023C>T	12.37:g.6934804C>T		Somatic	97	0	0	637	WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_019858	Q16664|Q59EH5|Q66K56	Silent	SNP	ENST00000311268.3	37	CCDS8563.1																																																																																			C|0.999;T|0.001	0.001	strong		0.607	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
GPRC6A	222545	hgsc.bcm.edu	37	6	117114290	117114290	+	Missense_Mutation	SNP	A	A	G	rs35937022	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:117114290A>G	ENST00000310357.3	-	6	1817	c.1796T>C	c.(1795-1797)aTt>aCt	p.I599T	GPRC6A_ENST00000530250.1_Missense_Mutation_p.I424T|GPRC6A_ENST00000368549.3_Missense_Mutation_p.I528T	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	599			I -> T (in dbSNP:rs35937022).		calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TAGGGAGAGAATCAGGAGTAG	0.433													A|||	661	0.131989	0.0136	0.1556	5008	,	,		19254	0.0218		0.3042	False		,,,				2504	0.2117				p.I599T		Atlas-SNP	.											.	GPRC6A	152	.	0			c.T1796C						PASS	.	A	THR/ILE	270,4136	151.4+/-185.3	22,226,1955	107.0	103.0	104.0		1796	2.4	1.0	6	dbSNP_126	104	2652,5948	427.6+/-355.6	408,1836,2056	yes	missense	GPRC6A	NM_148963.2	89	430,2062,4011	GG,GA,AA		30.8372,6.128,22.4666	benign	599/927	117114290	2922,10084	2203	4300	6503	SO:0001583	missense	222545	exon6			GAGAGAATCAGGA	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1796T>C	6.37:g.117114290A>G	ENSP00000309493:p.Ile599Thr	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	174	90	0.517241	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	CCDS5112.1	304	0.1391941391941392	7	0.014227642276422764	59	0.16298342541436464	13	0.022727272727272728	225	0.29683377308707126	A	0.267	-0.995430	0.02145	0.06128	0.308372	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.90844	-2.51;-2.74;-2.73	5.17	2.37	0.29283	GPCR, family 3, C-terminal (1);	1.162580	0.06303	N	0.701252	T	0.59609	0.2206	N	0.08118	0	0.80722	P	0.0	B;B;B	0.11235	0.001;0.004;0.002	B;B;B	0.10450	0.002;0.005;0.001	T	0.44034	-0.9354	9	0.12430	T	0.62	.	4.4929	0.11822	0.2894:0.4026:0.308:0.0	rs35937022	528;424;599	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	T	599;528;424	ENSP00000309493:I599T;ENSP00000357537:I528T;ENSP00000433465:I424T	ENSP00000309493:I599T	I	-	2	0	GPRC6A	117220983	0.005000	0.15991	0.955000	0.39395	0.008000	0.06430	1.768000	0.38511	0.315000	0.23110	-1.182000	0.01712	ATT	A|0.803;G|0.197	0.197	strong		0.433	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
EML2	24139	hgsc.bcm.edu	37	19	46133251	46133251	+	Silent	SNP	C	C	T	rs7251952	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:46133251C>T	ENST00000245925.3	-	7	614	c.564G>A	c.(562-564)tcG>tcA	p.S188S	EML2_ENST00000589876.1_Silent_p.S188S|EML2_ENST00000586902.1_5'UTR|EML2_ENST00000587152.1_Silent_p.S389S|EML2_ENST00000536630.1_Silent_p.S335S	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	188	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		AGTCCCACACCGAGAGCATGT	0.562													C|||	643	0.128395	0.1611	0.1282	5008	,	,		17260	0.1032		0.1074	False		,,,				2504	0.1319				p.S389S		Atlas-SNP	.											.	EML2	64	.	0			c.G1167A						PASS	.		,,	658,3748	279.6+/-274.9	61,536,1606	195.0	124.0	148.0		1167,1005,564	-8.1	0.7	19	dbSNP_116	148	1129,7471	232.5+/-266.1	78,973,3249	no	coding-synonymous,coding-synonymous,coding-synonymous	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	,,	139,1509,4855	TT,TC,CC		13.1279,14.9342,13.7398	,,	389/851,335/797,188/650	46133251	1787,11219	2203	4300	6503	SO:0001819	synonymous_variant	24139	exon10			CCACACCGAGAGC	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.564G>A	19.37:g.46133251C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Silent	SNP	ENST00000245925.3	37	CCDS12670.1																																																																																			C|0.871;T|0.129	0.129	strong		0.562	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
ZSCAN12	9753	hgsc.bcm.edu	37	6	28359170	28359170	+	Silent	SNP	A	A	G	rs2859348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28359170A>G	ENST00000361028.1	-	4	1042	c.897T>C	c.(895-897)gaT>gaC	p.D299D	ZSCAN12_ENST00000396827.3_Silent_p.D299D			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12	299					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|urinary_tract(1)	6						TGTAGGGTCTATCTCCAGTAT	0.423													a|||	3208	0.640575	0.9697	0.4942	5008	,	,		20015	0.5952		0.4583	False		,,,				2504	0.5337				p.D299D		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.T897C						PASS	.	A		1203,181		526,151,15	131.0	118.0	122.0		897	-0.2	1.0	6	dbSNP_100	122	1421,1761		315,791,485	no	coding-synonymous	ZSCAN12	NM_001163391.1		841,942,500	GG,GA,AA		44.6574,13.078,42.5318		299/612	28359170	2624,1942	692	1591	2283	SO:0001819	synonymous_variant	9753	exon4			GGGTCTATCTCCA	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"""-"", ""Zinc fingers, C2H2-type"""	13172	protein-coding gene	gene with protein product		603978	"""zinc finger protein 305"", ""zinc finger protein 96"""	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.897T>C	6.37:g.28359170A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	179	93	0.519553	NM_001163391	O43724	Silent	SNP	ENST00000361028.1	37																																																																																				A|0.407;G|0.593	0.593	strong		0.423	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724	
MAFA	389692	hgsc.bcm.edu	37	8	144512157	144512157	+	Silent	SNP	C	C	T	rs373992315		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144512157C>T	ENST00000333480.2	-	1	419	c.420G>A	c.(418-420)gaG>gaA	p.E140E	MAFA_ENST00000528185.1_5'Flank	NM_201589.3	NP_963883.2	Q8NHW3	MAFA_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog A	140					insulin secretion (GO:0030073)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|lung(1)|upper_aerodigestive_tract(2)	4	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.237)			CGATGAGCGCCTCCACCGCGT	0.741										HNSCC(29;0.082)			.|||	1	0.000199681	0.0	0.0	5008	,	,		4841	0.0		0.001	False		,,,				2504	0.0				p.E140E		Atlas-SNP	.											.	MAFA	9	.	0			c.G420A						PASS	.	C		0,4076		0,0,2038	7.0	5.0	6.0		420	2.9	1.0	8		6	10,7996		0,10,3993	no	coding-synonymous	MAFA	NM_201589.3		0,10,6031	TT,TC,CC		0.1249,0.0,0.0828		140/354	144512157	10,12072	2038	4003	6041	SO:0001819	synonymous_variant	389692	exon1			GAGCGCCTCCACC	AY083269	CCDS34955.1	8q24.3	2013-07-09	2013-07-09			ENSG00000182759			23145	protein-coding gene	gene with protein product		610303					Standard	NM_201589		Approved	RIPE3b1, hMafA	uc003yyc.2	Q8NHW3		ENST00000333480.2:c.420G>A	8.37:g.144512157C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	7	5	0.714286	NM_201589		Silent	SNP	ENST00000333480.2	37	CCDS34955.1																																																																																			.	.	weak		0.741	MAFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381511.2	NM_201589	
NLRP11	204801	hgsc.bcm.edu	37	19	56321517	56321517	+	Silent	SNP	T	T	C	rs7249635	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56321517T>C	ENST00000589093.1	-	3	552	c.459A>G	c.(457-459)ggA>ggG	p.G153G	NLRP11_ENST00000589824.2_Silent_p.G153G|NLRP11_ENST00000443188.1_Silent_p.G153G|NLRP11_ENST00000592953.1_Silent_p.G54G|NLRP11_ENST00000360133.3_Silent_p.G153G			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	153	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		ATGCTCTCTCTCCCATCAGGA	0.413													T|||	878	0.175319	0.3366	0.0519	5008	,	,		20720	0.2351		0.0517	False		,,,				2504	0.1104				p.G153G		Atlas-SNP	.											.	NLRP11	139	.	0			c.A459G						PASS	.	T		1215,3191	406.6+/-333.9	172,871,1160	81.0	75.0	77.0		459	2.2	0.0	19	dbSNP_116	77	424,8176	125.1+/-183.8	9,406,3885	no	coding-synonymous	NLRP11	NM_145007.3		181,1277,5045	CC,CT,TT		4.9302,27.576,12.6019		153/1034	56321517	1639,11367	2203	4300	6503	SO:0001819	synonymous_variant	204801	exon5			TCTCTCTCCCATC	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.459A>G	19.37:g.56321517T>C		Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	207	109	0.52657	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Silent	SNP	ENST00000589093.1	37	CCDS12935.1																																																																																			T|0.849;C|0.151	0.151	strong		0.413	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
RNF17	56163	hgsc.bcm.edu	37	13	25428002	25428002	+	Missense_Mutation	SNP	C	C	A	rs3783082	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25428002C>A	ENST00000255324.5	+	25	3382	c.3330C>A	c.(3328-3330)aaC>aaA	p.N1110K	RNF17_ENST00000381921.1_Missense_Mutation_p.N1110K|RNF17_ENST00000339524.3_Missense_Mutation_p.N162K	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1110			N -> K (in dbSNP:rs3783082).		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		GAATTAATAACTTAGATAACA	0.318													A|||	605	0.120807	0.0802	0.1744	5008	,	,		6377	0.1835		0.1342	False		,,,				2504	0.0593				p.N1110K		Atlas-SNP	.											.	RNF17	259	.	0			c.C3330A						PASS	.	A	LYS/ASN,LYS/ASN	405,3995	767.3+/-413.5	23,359,1818	42.0	44.0	43.0		3318,3330	3.8	0.8	13	dbSNP_107	43	1153,7445	755.7+/-407.5	83,987,3229	yes	missense,missense	RNF17	NM_001184993.1,NM_031277.2	94,94	106,1346,5047	AA,AC,CC		13.4101,9.2045,11.9865	benign,benign	1106/1620,1110/1624	25428002	1558,11440	2200	4299	6499	SO:0001583	missense	56163	exon25			TAATAACTTAGAT	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"""RING-type (C3HC4) zinc fingers"", ""Tudor domain containing"""	10060	protein-coding gene	gene with protein product	"""spermatogenesis associated 23"""	605793	"""tudor domain containing 4"""	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.3330C>A	13.37:g.25428002C>A	ENSP00000255324:p.Asn1110Lys	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_031277	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	321	0.14697802197802198	42	0.08536585365853659	52	0.143646408839779	121	0.21153846153846154	106	0.13984168865435356	A	0.011	-1.714727	0.00706	0.092045	0.134101	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000418120;ENST00000339524	T;T;T;T	0.20598	3.63;3.63;2.87;2.06	4.96	3.78	0.43462	.	0.229124	0.39274	N	0.001413	T	0.00012	0.0000	N	0.00170	-1.935	0.18873	P	0.9999861813	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.36601	-0.9741	9	0.02654	T	1	-13.1537	5.1228	0.14869	0.7231:0.1838:0.0931:0.0	rs3783082;rs52827814;rs60804193;rs3783082	1106;162;1110;1110	B7Z7S1;Q5T6R1;Q9BXT8-5;Q9BXT8	.;.;.;RNF17_HUMAN	K	1110;1110;969;434;162	ENSP00000255324:N1110K;ENSP00000371346:N1110K;ENSP00000388892:N434K;ENSP00000344776:N162K	ENSP00000255324:N1110K	N	+	3	2	RNF17	24326002	0.996000	0.38824	0.787000	0.31911	0.385000	0.30292	2.231000	0.43009	0.466000	0.27193	-0.335000	0.08231	AAC	C|0.876;A|0.124	0.124	strong		0.318	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505141	37505141	+	Missense_Mutation	SNP	G	G	A	rs1200876	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:37505141G>A	ENST00000602533.1	+	32	2833	c.2734G>A	c.(2734-2736)Gtt>Att	p.V912I	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.V1031I|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.V912I			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	968					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CTTGGATACAGTTCATTCTTG	0.323													G|||	640	0.127796	0.0129	0.2666	5008	,	,		16068	0.0853		0.2634	False		,,,				2504	0.089				p.V912I		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.G2734A						PASS	.	G	ILE/VAL	162,3448		8,146,1651	60.0	56.0	57.0		2734	-4.6	0.0	10	dbSNP_87	57	1887,6247		212,1463,2392	yes	missense	ANKRD30A	NM_052997.2	29	220,1609,4043	AA,AG,GG		23.1989,4.4875,17.4472	benign	912/1342	37505141	2049,9695	1805	4067	5872	SO:0001583	missense	91074	exon32			GATACAGTTCATT	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.2734G>A	10.37:g.37505141G>A	ENSP00000473551:p.Val912Ile	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		352	0.16117216117216118	9	0.018292682926829267	95	0.26243093922651933	52	0.09090909090909091	196	0.25857519788918204	g	0.006	-2.086553	0.00367	0.044875	0.231989	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.16897	2.31;2.31	2.63	-4.61	0.03380	.	.	.	.	.	T	0.00012	0.0000	N	0.10916	0.065	0.80722	P	0.0	B	0.22080	0.064	B	0.15052	0.012	T	0.47235	-0.9133	8	0.11485	T	0.65	.	9.9166	0.41439	0.7535:0.0:0.2465:0.0	rs1200876;rs1782080;rs16937431;rs17606834	968	Q9BXX3	AN30A_HUMAN	I	912;1031	ENSP00000354432:V912I;ENSP00000363792:V1031I	ENSP00000354432:V912I	V	+	1	0	ANKRD30A	37545147	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.533000	0.02215	-1.702000	0.01411	-0.698000	0.03680	GTT	G|0.826;A|0.174	0.174	strong		0.323	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
TTN	7273	hgsc.bcm.edu	37	2	179395958	179395958	+	Silent	SNP	T	T	C	rs3813250	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179395958T>C	ENST00000591111.1	-	308	100685	c.100461A>G	c.(100459-100461)gcA>gcG	p.A33487A	TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Silent_p.A26063A|TTN_ENST00000342992.6_Silent_p.A32560A|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000589042.1_Silent_p.A35128A|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Silent_p.A26188A|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.A26255A|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000588804.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33487					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAATTCTTGCTGCCAAAGTCG	0.463													C|||	2545	0.508187	0.5681	0.4049	5008	,	,		20546	0.7123		0.2535	False		,,,				2504	0.5521				p.A35128A		Atlas-SNP	.											.	TTN	18412	.	0			c.A105384G						PASS	.	C	,,,	2024,1820		550,924,448	158.0	169.0	166.0		78189,97680,78564,78765	-0.2	0.5	2	dbSNP_107	166	1845,6423		194,1457,2483	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	744,2381,2931	CC,CT,TT		22.3149,47.3465,31.9435	,,,	26063/26927,32560/33424,26188/27052,26255/27119	179395958	3869,8243	1922	4134	6056	SO:0001819	synonymous_variant	7273	exon358			TCTTGCTGCCAAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.100461A>G	2.37:g.179395958T>C		Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	403	197	0.488834	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.562;C|0.438	0.438	strong		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MRTO4	51154	hgsc.bcm.edu	37	1	19583636	19583636	+	Silent	SNP	C	C	T	rs1126682	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:19583636C>T	ENST00000330263.4	+	4	567	c.270C>T	c.(268-270)caC>caT	p.H90H		NM_016183.3	NP_057267.2	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog (S. cerevisiae)	90					ribosome biogenesis (GO:0042254)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|liver(2)|ovary(1)|pancreas(1)|stomach(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ACAACCTGCACCAGGTAAGTC	0.557													C|||	681	0.135982	0.1293	0.1311	5008	,	,		20981	0.0238		0.2008	False		,,,				2504	0.1973				p.H90H	GBM(192;2418 3032 7540 48714)	Atlas-SNP	.											MRTO4,NS,carcinoma,0,1	MRTO4	17	1	0			c.C270T						PASS	.	C		595,3811	261.0+/-264.0	43,509,1651	184.0	174.0	178.0		270	0.2	1.0	1	dbSNP_86	178	1553,7047	292.8+/-301.0	141,1271,2888	no	coding-synonymous	MRTO4	NM_016183.3		184,1780,4539	TT,TC,CC		18.0581,13.5043,16.5155		90/240	19583636	2148,10858	2203	4300	6503	SO:0001819	synonymous_variant	51154	exon4			CCTGCACCAGGTA	AK027569	CCDS191.1	1p36.13	2008-02-05	2006-12-21	2007-01-05	ENSG00000053372	ENSG00000053372			18477	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 33"", ""MRT4, mRNA turnover 4, homolog (S. cerevisiae)"""	C1orf33			Standard	NM_016183		Approved	dJ657E11.4, MRT4	uc001bbs.3	Q9UKD2	OTTHUMG00000002496	ENST00000330263.4:c.270C>T	1.37:g.19583636C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	149	81	0.543624	NM_016183	B3KNB3|Q5TG55|Q96SS6|Q9BPV9	Silent	SNP	ENST00000330263.4	37	CCDS191.1																																																																																			C|0.842;T|0.158	0.158	strong		0.557	MRTO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007075.2	NM_016183	
AIM1L	55057	hgsc.bcm.edu	37	1	26673076	26673076	+	5'Flank	SNP	G	G	A	rs11247924	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26673076G>A	ENST00000308182.5	-	0	0				AIM1L_ENST00000527815.1_5'Flank|RN7SL490P_ENST00000579210.1_RNA			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like								carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		GTGGGGGGCCGCTGCCGCCAT	0.622													G|||	899	0.179513	0.1505	0.1931	5008	,	,		15200	0.1458		0.1918	False		,,,				2504	0.2311				p.R25W		Atlas-SNP	.											.	AIM1L	98	.	0			c.C73T						PASS	.	G	TRP/ARG	524,3272		33,458,1407	13.0	15.0	14.0		73	3.0	1.0	1	dbSNP_120	14	1591,6607		162,1267,2670	yes	missense	AIM1L	NM_001039775.3	101	195,1725,4077	AA,AG,GG		19.4072,13.804,17.6338	benign	25/1662	26673076	2115,9879	1898	4099	5997	SO:0001631	upstream_gene_variant	55057	exon2			GGGGCCGCTGCCG			1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490		1.37:g.26673076G>A	Exception_encountered	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_001039775	B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	37		377	0.17261904761904762	71	0.1443089430894309	73	0.20165745856353592	101	0.17657342657342656	132	0.1741424802110818	G	18.91	3.724308	0.68959	0.13804	0.194072	ENSG00000176092	ENST00000538018;ENST00000475866	T	0.22134	1.97	5.04	3.01	0.34805	.	.	.	.	.	T	0.00039	0.0001	L	0.29908	0.895	0.41275	P	0.013122999999999996	D	0.89917	1.0	D	0.80764	0.994	T	0.10823	-1.0613	8	0.59425	D	0.04	.	9.8058	0.40792	0.0:0.0:0.6286:0.3714	rs11247924;rs60455159	25	E7ET48	.	W	25	ENSP00000428746:R25W	ENSP00000428746:R25W	R	-	1	2	AIM1L	26545663	0.127000	0.22367	1.000000	0.80357	0.970000	0.65996	0.700000	0.25601	1.096000	0.41439	0.655000	0.94253	CGG	G|0.828;A|0.172	0.172	strong		0.622	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2	
PRPF8	10594	hgsc.bcm.edu	37	17	1584324	1584324	+	Silent	SNP	A	A	G	rs7503397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1584324A>G	ENST00000572621.1	-	6	1156	c.891T>C	c.(889-891)aaT>aaC	p.N297N	PRPF8_ENST00000304992.6_Silent_p.N297N			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	297					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		TGTTAATATCATTGAATTCAT	0.408													a|||	1363	0.272165	0.6324	0.147	5008	,	,		22532	0.0903		0.1948	False		,,,				2504	0.1411				p.N297N		Atlas-SNP	.											.	PRPF8	169	.	0			c.T891C						PASS	.	G		2452,1954	551.8+/-378.4	684,1084,435	125.0	115.0	119.0		891	-2.8	1.0	17	dbSNP_116	119	1833,6767	728.9+/-406.7	190,1453,2657	no	coding-synonymous	PRPF8	NM_006445.3		874,2537,3092	GG,GA,AA		21.314,44.3486,32.9463		297/2336	1584324	4285,8721	2203	4300	6503	SO:0001819	synonymous_variant	10594	exon7			AATATCATTGAAT	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.891T>C	17.37:g.1584324A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	164	81	0.493902	NM_006445	O14547|O75965	Silent	SNP	ENST00000572621.1	37	CCDS11010.1																																																																																			A|0.695;G|0.305	0.305	strong		0.408	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
CYP4A22	284541	hgsc.bcm.edu	37	1	47607281	47607281	+	Missense_Mutation	SNP	C	C	T	rs12564525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:47607281C>T	ENST00000371891.3	+	3	407	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000294337.3_Missense_Mutation_p.R126W|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000371890.3_Missense_Mutation_p.R126W	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	126			R -> W (in allele CYP4A22*8, allele CYP4A22*9, allele CYP4A22*11, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs12564525). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCTGGCTCCACGGATTGGTAT	0.453													c|||	1859	0.371206	0.2254	0.2867	5008	,	,		23221	0.6141		0.2058	False		,,,				2504	0.5481				p.R126W	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.C376T						PASS	.	T	TRP/ARG	1099,3307	720.2+/-409.0	129,841,1233	132.0	122.0	125.0		376	1.7	0.7	1	dbSNP_120	125	1802,6798	732.5+/-406.8	197,1408,2695	yes	missense	CYP4A22	NM_001010969.2	101	326,2249,3928	TT,TC,CC		20.9535,24.9433,22.3051	benign	126/520	47607281	2901,10105	2203	4300	6503	SO:0001583	missense	284541	exon3			GCTCCACGGATTG		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.376C>T	1.37:g.47607281C>T	ENSP00000360958:p.Arg126Trp	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	202	98	0.485149	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	682	0.31227106227106227	103	0.20934959349593496	90	0.24861878453038674	342	0.5979020979020979	147	0.19393139841688653	t	0.721	-0.783423	0.02907	0.249433	0.209535	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.67865	-0.27;-0.29;-0.29	1.66	1.66	0.24008	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00003	-3.465	0.51482	P	7.900000000005125E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48514	-0.9029	9	0.02654	T	1	.	6.8608	0.24066	0.0:0.126:0.0:0.874	rs12564525;rs57365220	126;126	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	W	126	ENSP00000360957:R126W;ENSP00000360958:R126W;ENSP00000294337:R126W	ENSP00000294337:R126W	R	+	1	2	CYP4A22	47379868	1.000000	0.71417	0.697000	0.30258	0.155000	0.21991	2.836000	0.48183	0.117000	0.18138	-0.665000	0.03846	CGG	C|0.715;T|0.285	0.285	strong		0.453	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
HS1BP3	64342	hgsc.bcm.edu	37	2	20840851	20840851	+	Silent	SNP	C	C	T	rs148915944		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:20840851C>T	ENST00000304031.3	-	3	313	c.288G>A	c.(286-288)aaG>aaA	p.K96K	HS1BP3_ENST00000406618.3_Silent_p.K96K|HS1BP3_ENST00000402541.1_Silent_p.K96K	NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	96	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.						phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAACAGGACCTTCCTGGGTA	0.552													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20113	0.0		0.0	False		,,,				2504	0.0				p.K96K		Atlas-SNP	.											.	HS1BP3	33	.	0			c.G288A						PASS	.	C		0,4406		0,0,2203	166.0	168.0	167.0		288	3.7	1.0	2	dbSNP_134	167	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	HS1BP3	NM_022460.3		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		96/393	20840851	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	64342	exon3			CAGGACCTTCCTG		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.288G>A	2.37:g.20840851C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	37	CCDS1700.1																																																																																			C|0.999;T|0.001	0.001	strong		0.552	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
SULT1A1	6817	hgsc.bcm.edu	37	16	28619920	28619920	+	Silent	SNP	A	A	G	rs1126446	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28619920A>G	ENST00000395607.1	-	3	426	c.153T>C	c.(151-153)acT>acC	p.T51T	SULT1A1_ENST00000314752.7_Silent_p.T51T|SULT1A1_ENST00000395609.1_Silent_p.T51T|SULT1A1_ENST00000569554.1_Silent_p.T51T|SULT1A1_ENST00000350842.4_Intron	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	51					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)	p.T51T(1)		endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	TTACCCAGGTAGTGCCTGGAG	0.622													.|||	1456	0.290735	0.2292	0.4769	5008	,	,		24362	0.2669		0.335	False		,,,				2504	0.2209				p.T51T		Atlas-SNP	.											SULT1A1,caecum,carcinoma,-2,2	SULT1A1	53	2	1	Substitution - coding silent(1)	stomach(1)	c.T153C						PASS	.	G	,,,,	856,3538		132,592,1473	101.0	71.0	81.0		153,153,153,153,	1.3	1.0	16	dbSNP_86	81	2798,5802		611,1576,2113	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	SULT1A1	NM_001055.3,NM_177529.2,NM_177530.2,NM_177534.2,NM_177536.3	,,,,	743,2168,3586	GG,GA,AA		32.5349,19.4811,28.1207	,,,,	51/296,51/296,51/296,51/296,	28619920	3654,9340	2197	4300	6497	SO:0001819	synonymous_variant	6817	exon2			CCAGGTAGTGCCT	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.153T>C	16.37:g.28619920A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	207	65	0.31401	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Silent	SNP	ENST00000395607.1	37	CCDS32420.1																																																																																			A|0.735;G|0.265	0.265	strong		0.622	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
PHACTR4	65979	hgsc.bcm.edu	37	1	28800482	28800482	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:28800482C>T	ENST00000373839.3	+	7	1501	c.1240C>T	c.(1240-1242)Cca>Tca	p.P414S	PHACTR4_ENST00000373836.3_Missense_Mutation_p.P424S|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	414	Pro-rich.				actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		TAGGCTGCCTCCACTCCCACT	0.527																																					p.P424S		Atlas-SNP	.											PHACTR4,NS,carcinoma,0,1	PHACTR4	64	1	0			c.C1270T						scavenged	.						74.0	76.0	75.0					1																	28800482		1958	4153	6111	SO:0001583	missense	65979	exon6			CTGCCTCCACTCC	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"""Phosphatase and actin regulators"""	25793	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 124"""	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1240C>T	1.37:g.28800482C>T	ENSP00000362945:p.Pro414Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	104	2	0.0192308	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	37	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.392662	0.62066	.	.	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.22539	1.95;1.95	5.75	5.75	0.90469	.	0.645763	0.16333	N	0.219046	T	0.21921	0.0528	L	0.52573	1.65	0.53005	D	0.999969	P;P	0.47762	0.9;0.651	B;B	0.39258	0.295;0.165	T	0.08027	-1.0742	10	0.14656	T	0.56	-1.1787	18.9126	0.92491	0.0:1.0:0.0:0.0	.	424;414	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	S	414;424;413	ENSP00000362945:P414S;ENSP00000362942:P424S	ENSP00000362942:P424S	P	+	1	0	PHACTR4	28673069	0.999000	0.42202	0.977000	0.42913	0.749000	0.42624	4.498000	0.60373	2.712000	0.92718	0.655000	0.94253	CCA	.	.	none		0.527	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923	
BTNL2	56244	hgsc.bcm.edu	37	6	32370816	32370816	+	Missense_Mutation	SNP	G	G	A	rs28362680	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32370816G>A	ENST00000374993.1	-	3	604	c.605C>T	c.(604-606)gCg>gTg	p.A202V	BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000454136.3_Missense_Mutation_p.A202V|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000374995.3_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	202	Ig-like V-type 2.		A -> V (in dbSNP:rs28362680).			integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						GGTGGCTTCCGCATAGAACAG	0.587													A|||	945	0.188698	0.1551	0.1556	5008	,	,		19105	0.3155		0.1004	False		,,,				2504	0.2178				p.A202V		Atlas-SNP	.											.	BTNL2	50	.	0			c.C605T						PASS	.	A	VAL/ALA	398,2624		23,352,1136	98.0	85.0	90.0		605	4.4	1.0	6	dbSNP_125	90	476,4942		21,434,2254	yes	missense	BTNL2	NM_019602.1	64	44,786,3390	AA,AG,GG		8.7855,13.1701,10.3555	benign	202/456	32370816	874,7566	1511	2709	4220	SO:0001583	missense	56244	exon3			GCTTCCGCATAGA	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.605C>T	6.37:g.32370816G>A	ENSP00000364132:p.Ala202Val	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	201	102	0.507463	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		372	0.17032967032967034	67	0.13617886178861788	57	0.1574585635359116	169	0.29545454545454547	79	0.10422163588390501	A	0.565	-0.843437	0.02671	0.131701	0.087855	ENSG00000204290	ENST00000468270;ENST00000374993	T	0.72167	-0.63	4.44	4.44	0.53790	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.45126	N	0.000389	T	0.06781	0.0173	N	0.00034	-2.555	0.09310	P	0.99999999935878	B	0.02656	0.0	B	0.01281	0.0	T	0.26360	-1.0105	9	0.02654	T	1	.	7.2911	0.26366	0.899:0.0:0.101:0.0	rs28362680;rs59710155;rs28362680	202	Q9UIR0	BTNL2_HUMAN	V	202	ENSP00000364132:A202V	ENSP00000364132:A202V	A	-	2	0	BTNL2	32478794	0.251000	0.23961	0.993000	0.49108	0.090000	0.18270	1.474000	0.35398	0.846000	0.35142	-0.377000	0.06932	GCG	G|0.869;A|0.131	0.131	strong		0.587	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
ATP13A2	23400	hgsc.bcm.edu	37	1	17312743	17312743	+	Silent	SNP	C	C	T	rs3170740	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17312743C>T	ENST00000326735.8	-	29	3549	c.3516G>A	c.(3514-3516)ccG>ccA	p.P1172P	ATP13A2_ENST00000452699.1_Silent_p.P1167P|ATP13A2_ENST00000341676.5_Missense_Mutation_p.A1072T|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2	1172					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CGGGCAGCGGCGGCCAGGGCT	0.711													C|||	1659	0.33127	0.1445	0.4553	5008	,	,		12200	0.246		0.5099	False		,,,				2504	0.3998				p.A1072T		Atlas-SNP	.											.	ATP13A2	85	.	0			c.G3214A						PASS	.	C	,THR/ALA,	944,3410		135,674,1368	16.0	24.0	22.0		3501,3214,3516	-7.1	0.0	1	dbSNP_105	22	4491,4055		1201,2089,983	yes	coding-synonymous,missense,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,58,	1336,2763,2351	TT,TC,CC		47.4491,21.6812,42.1318	,,	1167/1176,1072/1159,1172/1181	17312743	5435,7465	2177	4273	6450	SO:0001819	synonymous_variant	23400	exon27			CAGCGGCGGCCAG	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.3516G>A	1.37:g.17312743C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001141974	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	37	CCDS175.1	773	0.35393772893772896	65	0.13211382113821138	158	0.43646408839779005	161	0.28146853146853146	389	0.5131926121372031	C	0.008	-1.900646	0.00517	0.216812	0.525509	ENSG00000159363	ENST00000341676;ENST00000502418	D;D	0.96967	-3.3;-4.19	3.56	-7.11	0.01542	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.26789	P	0.9694444	B	0.06786	0.001	B	0.04013	0.001	T	0.18681	-1.0329	7	0.02654	T	1	-23.2806	7.7309	0.28786	0.0:0.2877:0.2133:0.499	rs3170740	1072	Q5JXY1	.	T	1072;312	ENSP00000341115:A1072T;ENSP00000423065:A312T	ENSP00000341115:A1072T	A	-	1	0	ATP13A2	17185330	0.001000	0.12720	0.015000	0.15790	0.046000	0.14306	-2.548000	0.00930	-1.707000	0.01402	-0.914000	0.02751	GCC	C|0.645;T|0.355	0.355	strong		0.711	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
KCNA7	3743	hgsc.bcm.edu	37	19	49573438	49573438	+	Missense_Mutation	SNP	A	A	G	rs1017219	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49573438A>G	ENST00000221444.1	-	2	1608	c.1253T>C	c.(1252-1254)aTg>aCg	p.M418T		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	418			M -> T (in dbSNP:rs1017219). {ECO:0000269|PubMed:11368907, ECO:0000269|PubMed:11896454}.		protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	ACAAGGCTGCATGTCCACATG	0.592													a|||	1833	0.366014	0.4766	0.3213	5008	,	,		16717	0.3353		0.328	False		,,,				2504	0.319				p.M418T	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											.	KCNA7	30	.	0			c.T1253C						PASS	.	A	THR/MET	2022,2384	563.5+/-381.2	459,1104,640	77.0	72.0	73.0		1253	3.2	1.0	19	dbSNP_86	73	2989,5611	463.8+/-366.1	533,1923,1844	yes	missense	KCNA7	NM_031886.2	81	992,3027,2484	GG,GA,AA		34.7558,45.892,38.5284	benign	418/457	49573438	5011,7995	2203	4300	6503	SO:0001583	missense	3743	exon2			GGCTGCATGTCCA	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.1253T>C	19.37:g.49573438A>G	ENSP00000221444:p.Met418Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	83	81	0.975904	NM_031886	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	37	CCDS12755.1	801	0.36675824175824173	240	0.4878048780487805	141	0.38950276243093923	179	0.3129370629370629	241	0.3179419525065963	a	1.053	-0.675176	0.03378	0.45892	0.347558	ENSG00000104848	ENST00000221444	D	0.97455	-4.39	4.27	3.23	0.37069	.	0.869427	0.09899	N	0.741250	T	0.00012	0.0000	N	0.00321	-1.65	0.48632	P	3.170000000000117E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.30446	-0.9978	9	0.23891	T	0.37	.	11.6813	0.51458	0.0899:0.0:0.9101:0.0	rs1017219;rs3810187;rs57874828;rs1017219	418	Q96RP8	KCNA7_HUMAN	T	418	ENSP00000221444:M418T	ENSP00000221444:M418T	M	-	2	0	KCNA7	54265250	0.797000	0.28877	0.994000	0.49952	0.913000	0.54294	0.606000	0.24194	1.179000	0.42884	-0.362000	0.07510	ATG	A|0.619;G|0.381	0.381	strong		0.592	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886	
COX6C	1345	hgsc.bcm.edu	37	8	100899793	100899793	+	Silent	SNP	G	G	A	rs1130569	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:100899793G>A	ENST00000520468.2	-	3	622	c.168C>T	c.(166-168)taC>taT	p.Y56Y	COX6C_ENST00000518171.1_Silent_p.Y56Y|COX6C_ENST00000523016.1_Silent_p.Y56Y|COX6C_ENST00000520271.1_Silent_p.Y56Y|COX6C_ENST00000522940.1_Silent_p.Y56Y|COX6C_ENST00000517682.2_Silent_p.Y56Y|COX6C_ENST00000524245.1_Silent_p.Y56Y|COX6C_ENST00000297564.2_Silent_p.Y56Y	NM_004374.3	NP_004365.1	P09669	COX6C_HUMAN	cytochrome c oxidase subunit VIc	56					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)	p.Y56Y(1)	HMGA2/COX6C(2)	liver(1)|lung(2)	3			all cancers(13;8.32e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			TCATGACATCGTAGTTTCTGT	0.343			T	HMGA2	uterine leiomyoma								A|||	1249	0.249401	0.5265	0.1758	5008	,	,		17900	0.13		0.1819	False		,,,				2504	0.1196				p.Y56Y	NSCLC(46;1123 1136 1705 23767 45086)	Atlas-SNP	.		Dom	yes		8	8q22-q23	1345	cytochrome c oxidase subunit VIc		M	COX6C_ENST00000520468,NS,carcinoma,0,1	COX6C	25	1	1	Substitution - coding silent(1)	stomach(1)	c.C168T						PASS	.	A		2157,2249	592.6+/-387.8	520,1117,566	59.0	60.0	60.0		168	4.4	1.0	8	dbSNP_86	60	1546,7050	744.5+/-407.2	123,1300,2875	no	coding-synonymous	COX6C	NM_004374.3		643,2417,3441	AA,AG,GG		17.9851,48.956,28.4802		56/76	100899793	3703,9299	2203	4298	6501	SO:0001819	synonymous_variant	1345	exon3			GACATCGTAGTTT	X13238	CCDS6284.1	8q22.2	2011-07-04			ENSG00000164919	ENSG00000164919	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2285	protein-coding gene	gene with protein product		124090				10072584	Standard	NM_004374		Approved		uc003yiy.2	P09669	OTTHUMG00000164703	ENST00000520468.2:c.168C>T	8.37:g.100899793G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_004374	B2R4D7	Silent	SNP	ENST00000520468.2	37	CCDS6284.1																																																																																			G|0.733;A|0.267	0.267	strong		0.343	COX6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379834.3	NM_004374	
SPTB	6710	hgsc.bcm.edu	37	14	65245962	65245962	+	Silent	SNP	A	A	G	rs1741487	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:65245962A>G	ENST00000389721.5	-	21	4508	c.4476T>C	c.(4474-4476)ctT>ctC	p.L1492L	SPTB_ENST00000542895.1_Silent_p.L1492L|SPTB_ENST00000389722.3_Silent_p.L1492L|SPTB_ENST00000389720.3_Silent_p.L1492L|SPTB_ENST00000556626.1_Silent_p.L1492L	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1492					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CCTCCACCCAAAGCTGCAGAG	0.567													G|||	2063	0.411941	0.7012	0.1657	5008	,	,		14583	0.3532		0.2445	False		,,,				2504	0.4284				p.L1492L		Atlas-SNP	.											.	SPTB	378	.	0			c.T4476C						PASS	.	G	,	2662,1744	502.4+/-365.2	813,1036,354	55.0	59.0	58.0		4476,4476	3.4	1.0	14	dbSNP_89	58	2045,6555	710.4+/-405.8	250,1545,2505	yes	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	1063,2581,2859	GG,GA,AA		23.7791,39.5824,36.191	,	1492/2138,1492/2329	65245962	4707,8299	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon21			CACCCAAAGCTGC		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4476T>C	14.37:g.65245962A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	155	72	0.464516	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			A|0.635;G|0.365	0.365	strong		0.567	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
SPTB	6710	hgsc.bcm.edu	37	14	65246623	65246623	+	Silent	SNP	T	T	C	rs1626923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:65246623T>C	ENST00000389721.5	-	20	4325	c.4293A>G	c.(4291-4293)cgA>cgG	p.R1431R	SPTB_ENST00000542895.1_Silent_p.R1431R|SPTB_ENST00000389722.3_Silent_p.R1431R|SPTB_ENST00000389720.3_Silent_p.R1431R|SPTB_ENST00000556626.1_Silent_p.R1431R	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1431					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GCTCCTCTTTTCGCACATTCA	0.582													C|||	2229	0.445088	0.7057	0.2176	5008	,	,		21086	0.377		0.326	False		,,,				2504	0.4468				p.R1431R		Atlas-SNP	.											SPTB_ENST00000542895,NS,malignant_melanoma,-1,6	SPTB	378	6	0			c.A4293G						PASS	.	C	,	2747,1659	505.9+/-366.3	858,1031,314	112.0	109.0	110.0		4293,4293	1.2	1.0	14	dbSNP_89	110	2762,5838	677.8+/-403.4	453,1856,1991	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	1311,2887,2305	CC,CT,TT		32.1163,37.6532,42.3574	,	1431/2138,1431/2329	65246623	5509,7497	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon20			CTCTTTTCGCACA		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4293A>G	14.37:g.65246623T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			T|0.575;C|0.425	0.425	strong		0.582	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
STPG2	285555	hgsc.bcm.edu	37	4	99049593	99049593	+	Missense_Mutation	SNP	A	A	G	rs17558193	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:99049593A>G	ENST00000295268.3	-	3	462	c.373T>C	c.(373-375)Tac>Cac	p.Y125H		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	125			Y -> H (in dbSNP:rs17558193).														TGAGGTTTGTAGTATGCTGGA	0.318													A|||	1879	0.3752	0.4425	0.2882	5008	,	,		16898	0.2748		0.4026	False		,,,				2504	0.4213				p.Y125H		Atlas-SNP	.											.	.	.	.	0			c.T373C						PASS	.	A	HIS/TYR	1973,2433	553.7+/-378.8	454,1065,684	65.0	62.0	63.0		373	5.2	0.7	4	dbSNP_123	63	3409,5189	501.0+/-375.3	694,2021,1584	yes	missense	C4orf37	NM_174952.2	83	1148,3086,2268	GG,GA,AA		39.6488,44.7798,41.3873	probably-damaging	125/460	99049593	5382,7622	2203	4299	6502	SO:0001583	missense	285555	exon3			GTTTGTAGTATGC	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.373T>C	4.37:g.99049593A>G	ENSP00000295268:p.Tyr125His	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	227	226	0.995595	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	759	0.3475274725274725	192	0.3902439024390244	106	0.292817679558011	161	0.28146853146853146	300	0.39577836411609496	A	17.14	3.312649	0.60414	0.447798	0.396488	ENSG00000163116	ENST00000295268	T	0.28666	1.6	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66939	2.045	0.28965	P	0.8896	D	0.89917	1.0	D	0.91635	0.999	T	0.47824	-0.9087	9	0.87932	D	0	-19.6536	12.8257	0.57718	1.0:0.0:0.0:0.0	rs17558193;rs52818476;rs17558193	125	Q8N412	CD037_HUMAN	H	125	ENSP00000295268:Y125H	ENSP00000295268:Y125H	Y	-	1	0	C4orf37	99268616	1.000000	0.71417	0.696000	0.30242	0.819000	0.46315	4.980000	0.63812	2.064000	0.61679	0.533000	0.62120	TAC	A|0.611;G|0.389	0.389	strong		0.318	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
KIAA1551	55196	hgsc.bcm.edu	37	12	32137512	32137512	+	Missense_Mutation	SNP	C	C	G	rs3759299	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:32137512C>G	ENST00000312561.4	+	4	4037	c.3623C>G	c.(3622-3624)tCt>tGt	p.S1208C	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1208			S -> C (in dbSNP:rs3759299). {ECO:0000269|PubMed:14702039}.														GAGCAGTGTTCTCCTTTGGAT	0.413													C|||	879	0.175519	0.0477	0.1758	5008	,	,		20662	0.247		0.2366	False		,,,				2504	0.2117				p.S1208C		Atlas-SNP	.											.	.	.	.	0			c.C3623G						PASS	.	C	CYS/SER	357,4049	184.3+/-211.7	11,335,1857	102.0	99.0	100.0		3623	0.9	0.0	12	dbSNP_107	100	2229,6371	378.6+/-339.0	279,1671,2350	yes	missense	C12orf35	NM_018169.3	112	290,2006,4207	GG,GC,CC		25.9186,8.1026,19.8831	probably-damaging	1208/1748	32137512	2586,10420	2203	4300	6503	SO:0001583	missense	55196	exon4			AGTGTTCTCCTTT	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3623C>G	12.37:g.32137512C>G	ENSP00000310338:p.Ser1208Cys	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	124	65	0.524194	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	410	0.18772893772893773	26	0.052845528455284556	62	0.1712707182320442	137	0.2395104895104895	185	0.24406332453825857	C	13.40	2.226572	0.39300	0.081026	0.259186	ENSG00000174718	ENST00000312561	T	0.14640	2.49	4.05	0.933	0.19471	.	0.922951	0.08974	N	0.866898	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B	0.20261	0.043	B	0.18871	0.023	T	0.43653	-0.9378	8	.	.	.	.	2.6973	0.05138	0.1883:0.5217:0.183:0.107	rs3759299;rs17511269;rs61122766;rs3759299	1208	Q9HCM1	CL035_HUMAN	C	1208	ENSP00000310338:S1208C	.	S	+	2	0	C12orf35	32028779	0.005000	0.15991	0.000000	0.03702	0.035000	0.12851	0.687000	0.25407	-0.022000	0.13986	-0.274000	0.10170	TCT	C|0.797;G|0.203	0.203	strong		0.413	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
DPCR1	135656	hgsc.bcm.edu	37	6	30918441	30918441	+	Missense_Mutation	SNP	A	A	G	rs111658797	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30918441A>G	ENST00000462446.1	+	2	2228	c.2200A>G	c.(2200-2202)Aca>Gca	p.T734A	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	298						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						TGAGAAGACCACACCATTCCC	0.502													-|||	243	0.0485224	0.0582	0.072	5008	,	,		23856	0.0476		0.0348	False		,,,				2504	0.0337				p.T734A		Atlas-SNP	.											.	DPCR1	99	.	0			c.A2200G						PASS	.	A	ALA/THR	82,1302		1,80,611	61.0	66.0	64.0		2200	-1.2	0.0	6	dbSNP_132	64	105,3077		2,101,1488	no	missense	DPCR1	NM_080870.3	58	3,181,2099	GG,GA,AA		3.2998,5.9249,4.0955	possibly-damaging	734/1394	30918441	187,4379	692	1591	2283	SO:0001583	missense	135656	exon2			AAGACCACACCAT	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2200A>G	6.37:g.30918441A>G	ENSP00000417182:p.Thr734Ala	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	124	0.056776556776556776	31	0.06300813008130081	33	0.09116022099447514	33	0.057692307692307696	27	0.03562005277044855	-	9.564	1.119132	0.20877	0.059249	0.032998	ENSG00000168631	ENST00000462446	T	0.42900	0.96	1.73	-1.24	0.09435	.	.	.	.	.	T	0.13415	0.0325	M	0.68593	2.085	0.09310	N	0.999998	P	0.39424	0.673	B	0.34991	0.193	T	0.15867	-1.0422	9	0.22706	T	0.39	.	2.8591	0.05580	0.3892:0.2634:0.3473:0.0	.	734	E9PEI6	.	A	734	ENSP00000417182:T734A	ENSP00000417182:T734A	T	+	1	0	DPCR1	31026420	0.000000	0.05858	0.001000	0.08648	0.129000	0.20672	0.098000	0.15189	-0.252000	0.09528	0.234000	0.17832	ACA	A|0.944;G|0.056	0.056	strong		0.502	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
TTC27	55622	hgsc.bcm.edu	37	2	32983480	32983480	+	Missense_Mutation	SNP	G	G	A	rs2273664	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:32983480G>A	ENST00000317907.4	+	13	1805	c.1574G>A	c.(1573-1575)cGc>cAc	p.R525H		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	525			R -> H (in dbSNP:rs2273664). {ECO:0000269|PubMed:14702039}.							breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						TCCCGGTACCGCAGTGCTCGT	0.507													G|||	329	0.0656949	0.003	0.036	5008	,	,		17696	0.1954		0.0646	False		,,,				2504	0.0389				p.R525H		Atlas-SNP	.											.	TTC27	71	.	0			c.G1574A						PASS	.	G	HIS/ARG,HIS/ARG	67,4339	60.5+/-97.4	0,67,2136	118.0	110.0	113.0		1424,1574	5.8	1.0	2	dbSNP_100	113	617,7983	161.4+/-214.4	33,551,3716	yes	missense,missense	TTC27	NM_001193509.1,NM_017735.4	29,29	33,618,5852	AA,AG,GG		7.1744,1.5207,5.2591	probably-damaging,probably-damaging	475/794,525/844	32983480	684,12322	2203	4300	6503	SO:0001583	missense	55622	exon13			GGTACCGCAGTGC	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"""Tetratricopeptide (TTC) repeat domain containing"""	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1574G>A	2.37:g.32983480G>A	ENSP00000313953:p.Arg525His	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	149	84	0.563758	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	177	0.08104395604395605	4	0.008130081300813009	13	0.03591160220994475	116	0.20279720279720279	44	0.05804749340369393	G	34	5.349794	0.95830	0.015207	0.071744	ENSG00000018699	ENST00000317907	T	0.73897	-0.79	5.79	5.79	0.91817	Tetratricopeptide-like helical (1);	0.049787	0.85682	D	0.000000	T	0.00384	0.0012	L	0.56199	1.76	0.09310	P	0.99999999316719	D	0.89917	1.0	D	0.69654	0.965	T	0.03103	-1.1072	9	0.59425	D	0.04	-8.408	20.032	0.97543	0.0:0.0:1.0:0.0	rs2273664;rs52832043;rs58926037;rs2273664	525	Q6P3X3	TTC27_HUMAN	H	525	ENSP00000313953:R525H	ENSP00000313953:R525H	R	+	2	0	TTC27	32836984	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	9.869000	0.99810	2.743000	0.94032	0.655000	0.94253	CGC	G|0.933;A|0.067	0.067	strong		0.507	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735	
MTMR12	54545	hgsc.bcm.edu	37	5	32263316	32263316	+	Missense_Mutation	SNP	C	C	T	rs61748194	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:32263316C>T	ENST00000382142.3	-	7	786	c.616G>A	c.(616-618)Gac>Aac	p.D206N	MTMR12_ENST00000264934.5_Missense_Mutation_p.D206N|MTMR12_ENST00000280285.5_Missense_Mutation_p.D206N	NM_001040446.1	NP_001035536.1	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	206	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	phosphatase activity (GO:0016791)			breast(3)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TTAAGTGTGTCAAACATTACG	0.398													C|||	37	0.00738818	0.0008	0.0173	5008	,	,		21370	0.0		0.0219	False		,,,				2504	0.002				p.D206N		Atlas-SNP	.											.	MTMR12	76	.	0			c.G616A						PASS	.	C	ASN/ASP	21,4385	29.0+/-57.7	0,21,2182	274.0	225.0	241.0		616	5.5	1.0	5	dbSNP_129	241	196,8404	86.1+/-148.5	3,190,4107	yes	missense	MTMR12	NM_001040446.1	23	3,211,6289	TT,TC,CC		2.2791,0.4766,1.6685	possibly-damaging	206/748	32263316	217,12789	2203	4300	6503	SO:0001583	missense	54545	exon7			GTGTGTCAAACAT	AB051469	CCDS34138.1, CCDS75230.1	5p15.33	2011-06-09	2005-04-07	2005-04-07	ENSG00000150712	ENSG00000150712		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	18191	protein-coding gene	gene with protein product		606501	"""phosphatidylinositol-3-phosphate associated protein"""	PIP3AP		11504939, 12495846	Standard	XM_005248313		Approved	3-PAP, FLJ20476, KIAA1682, 3PAP	uc003jhq.3	Q9C0I1	OTTHUMG00000161978	ENST00000382142.3:c.616G>A	5.37:g.32263316C>T	ENSP00000371577:p.Asp206Asn	Somatic	370	1	0.0027027		WXS	Illumina HiSeq	Phase_I	348	151	0.433908	NM_001040446	Q69YJ4|Q6PFW3|Q96QU2|Q9NX27	Missense_Mutation	SNP	ENST00000382142.3	37	CCDS34138.1	25	0.011446886446886446	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	20	0.026385224274406333	C	19.09	3.760426	0.69763	0.004766	0.022791	ENSG00000150712	ENST00000280285;ENST00000382142;ENST00000264934	D;D;D	0.89681	-2.55;-2.55;-2.55	5.47	5.47	0.80525	Myotubularin phosphatase domain (1);	0.343414	0.29087	N	0.013200	T	0.78233	0.4251	M	0.62723	1.935	0.51767	D	0.999935	P;P;P	0.37370	0.592;0.592;0.457	B;B;B	0.42959	0.403;0.403;0.227	T	0.81867	-0.0735	10	0.19147	T	0.46	.	19.3518	0.94392	0.0:1.0:0.0:0.0	rs61748194	206;206;206	Q9C0I1-3;Q9C0I1-2;Q9C0I1	.;.;MTMRC_HUMAN	N	206	ENSP00000280285:D206N;ENSP00000371577:D206N;ENSP00000264934:D206N	ENSP00000264934:D206N	D	-	1	0	MTMR12	32299073	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	2.746000	0.47467	2.571000	0.86741	0.650000	0.86243	GAC	C|0.985;T|0.015	0.015	strong		0.398	MTMR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366579.1	NM_019061	
MOV10L1	54456	hgsc.bcm.edu	37	22	50588131	50588131	+	Silent	SNP	C	C	T	rs138271	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50588131C>T	ENST00000262794.5	+	20	2798	c.2715C>T	c.(2713-2715)gaC>gaT	p.D905D	MOV10L1_ENST00000395843.1_Silent_p.D3D|MOV10L1_ENST00000354853.2_Silent_p.D3D|MOV10L1_ENST00000395858.3_Silent_p.D905D|MOV10L1_ENST00000540615.1_Silent_p.D885D|MOV10L1_ENST00000395852.1_Silent_p.D32D|MOV10L1_ENST00000545383.1_Silent_p.D905D	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	905					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGATGTCGGACATCAGTGGCC	0.582											OREG0026674	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	641	0.127995	0.0431	0.1974	5008	,	,		18773	0.0109		0.2823	False		,,,				2504	0.1554				p.D905D		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C2715T						PASS	.	C	,,,	408,3996	201.1+/-224.2	15,378,1809	134.0	99.0	111.0		2715,2655,96,2715	-4.9	0.0	22	dbSNP_78	111	2783,5817	437.4+/-358.6	429,1925,1946	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_001164106.1,NM_018995.2	,,,	444,2303,3755	TT,TC,CC		32.3605,9.2643,24.5386	,,,	905/1166,885/1166,32/339,905/1212	50588131	3191,9813	2202	4300	6502	SO:0001819	synonymous_variant	54456	exon20			GTCGGACATCAGT	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2715C>T	22.37:g.50588131C>T		Somatic	139	0	0	970	WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			C|0.799;T|0.201	0.201	strong		0.582	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
KIAA1462	57608	hgsc.bcm.edu	37	10	30316208	30316208	+	Missense_Mutation	SNP	T	T	C	rs2185724	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:30316208T>C	ENST00000375377.1	-	3	2970	c.2869A>G	c.(2869-2871)Aga>Gga	p.R957G		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	957			R -> G (in dbSNP:rs2185724). {ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						TCCAGGTGTCTCTTCTCTGCA	0.587													T|||	1688	0.337061	0.3691	0.2968	5008	,	,		19294	0.3036		0.4334	False		,,,				2504	0.2577				p.R957G		Atlas-SNP	.											KIAA1462,NS,carcinoma,0,1	KIAA1462	162	1	0			c.A2869G						PASS	.	T	GLY/ARG	1561,2541		288,985,778	66.0	68.0	67.0		2869	-11.2	0.0	10	dbSNP_96	67	3514,4900		731,2052,1424	yes	missense	KIAA1462	NM_020848.2	125	1019,3037,2202	CC,CT,TT		41.7637,38.0546,40.5481	benign	957/1360	30316208	5075,7441	2051	4207	6258	SO:0001583	missense	57608	exon3			GGTGTCTCTTCTC	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.2869A>G	10.37:g.30316208T>C	ENSP00000364526:p.Arg957Gly	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	37	CCDS41500.1	807	0.3695054945054945	185	0.37601626016260165	128	0.35359116022099446	178	0.3111888111888112	316	0.41688654353562005	T	11.66	1.705407	0.30232	0.380546	0.417637	ENSG00000165757	ENST00000375377	T	0.13307	2.6	5.62	-11.2	0.00127	.	0.879175	0.09941	N	0.735961	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.14438	0.01	B	0.13407	0.009	T	0.40850	-0.9541	9	0.33141	T	0.24	-0.1293	5.8512	0.18694	0.0758:0.3657:0.363:0.1955	rs2185724;rs3739997;rs17229216;rs52799531;rs58136451;rs2185724	957	Q9P266	K1462_HUMAN	G	957	ENSP00000364526:R957G	ENSP00000364526:R957G	R	-	1	2	KIAA1462	30356214	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.378000	0.07446	-3.245000	0.00206	0.460000	0.39030	AGA	C|0.373;N|0.000	0.373	strong		0.587	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
KIAA0753	9851	hgsc.bcm.edu	37	17	6515454	6515454	+	Missense_Mutation	SNP	C	C	T	rs386794940|rs2289643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:6515454C>T	ENST00000361413.3	-	8	1688	c.1330G>A	c.(1330-1332)Gat>Aat	p.D444N	KIAA0753_ENST00000572370.1_Missense_Mutation_p.D145N|KIAA0753_ENST00000542606.1_Missense_Mutation_p.D145N|KIAA0753_ENST00000589033.1_Intron	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	444			D -> N (in dbSNP:rs2289643). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.D444N(1)		endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		AGCTCCGTATCGGGCTGATAC	0.398													C|||	2686	0.536342	0.3275	0.621	5008	,	,		20370	0.7103		0.5149	False		,,,				2504	0.6012				p.D444N		Atlas-SNP	.											KIAA0753,NS,carcinoma,0,1	KIAA0753	63	1	1	Substitution - Missense(1)	prostate(1)	c.G1330A						PASS	.	C	ASN/ASP	1366,2330		252,862,734	94.0	93.0	93.0		1330	3.4	0.0	17	dbSNP_100	93	4397,3793		1174,2049,872	yes	missense	KIAA0753	NM_014804.2	23	1426,2911,1606	TT,TC,CC		46.3126,36.9589,48.4856	benign	444/968	6515454	5763,6123	1848	4095	5943	SO:0001583	missense	9851	exon8			CCGTATCGGGCTG		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.1330G>A	17.37:g.6515454C>T	ENSP00000355250:p.Asp444Asn	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	161	69	0.428571	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	1171	0.5361721611721612	184	0.37398373983739835	225	0.6215469613259669	391	0.6835664335664335	371	0.4894459102902375	C	8.089	0.774006	0.16051	0.369589	0.536874	ENSG00000198920	ENST00000361413;ENST00000542606	T;T	0.08896	3.04;3.04	4.33	3.36	0.38483	.	1.505420	0.03377	N	0.199827	T	0.00012	0.0000	L	0.51422	1.61	0.50813	P	1.0699999999996823E-4	B	0.18013	0.025	B	0.10450	0.005	T	0.41980	-0.9478	9	0.21540	T	0.41	0.075	8.2745	0.31864	0.0:0.8936:0.0:0.1064	rs2289643;rs17731526;rs52837019;rs59901755;rs2289643	444	Q2KHM9	K0753_HUMAN	N	444;145	ENSP00000355250:D444N;ENSP00000444634:D145N	ENSP00000355250:D444N	D	-	1	0	KIAA0753	6456178	0.245000	0.23899	0.040000	0.18447	0.004000	0.04260	1.423000	0.34837	1.434000	0.47414	0.591000	0.81541	GAT	C|0.456;T|0.544	0.544	strong		0.398	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
TOR1A	1861	hgsc.bcm.edu	37	9	132585058	132585058	+	Silent	SNP	G	G	A	rs2296793	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:132585058G>A	ENST00000351698.4	-	2	294	c.246C>T	c.(244-246)gcC>gcT	p.A82A	TOR1A_ENST00000473084.1_5'UTR	NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	82					ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)	p.A82A(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				AACCAAACACGGCATTTAAGA	0.488													A|||	1133	0.226238	0.2179	0.2118	5008	,	,		21361	0.2133		0.2753	False		,,,				2504	0.2106				p.A82A		Atlas-SNP	.											TOR1A,NS,carcinoma,0,1	TOR1A	36	1	1	Substitution - coding silent(1)	stomach(1)	c.C246T						PASS	.	A		981,3425	733.0+/-410.4	107,767,1329	167.0	152.0	157.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	246	-10.4	0.0	9	dbSNP_100	157	2066,6534	718.9+/-406.2	263,1540,2497	no	coding-synonymous	TOR1A	NM_000113.2		370,2307,3826	AA,AG,GG		24.0233,22.2651,23.4276		82/333	132585058	3047,9959	2203	4300	6503	SO:0001819	synonymous_variant	1861	exon2			AAACACGGCATTT	AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"""dystonia 1, torsion (autosomal dominant; torsin A)"""	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.246C>T	9.37:g.132585058G>A		Somatic	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	218	108	0.495413	NM_000113	B2RB58|Q53Y64|Q96CA0	Silent	SNP	ENST00000351698.4	37	CCDS6930.1																																																																																			G|0.763;A|0.237	0.237	strong		0.488	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113	
SPTA1	6708	hgsc.bcm.edu	37	1	158626378	158626378	+	Silent	SNP	C	C	T	rs857691	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:158626378C>T	ENST00000368147.4	-	20	3054	c.2874G>A	c.(2872-2874)ctG>ctA	p.L958L		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	958					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CCTGATTCCGCAGAGCTTTCA	0.398													T|||	2121	0.423522	0.7935	0.3588	5008	,	,		16600	0.4087		0.2495	False		,,,				2504	0.1636				p.L958L		Atlas-SNP	.											.	SPTA1	720	.	0			c.G2874A						PASS	.	T		2587,1125		905,777,174	167.0	171.0	170.0		2874	-9.1	0.0	1	dbSNP_86	170	2017,6169		273,1471,2349	no	coding-synonymous	SPTA1	NM_003126.2		1178,2248,2523	TT,TC,CC		24.6396,30.3071,38.6956		958/2420	158626378	4604,7294	1856	4093	5949	SO:0001819	synonymous_variant	6708	exon20			ATTCCGCAGAGCT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2874G>A	1.37:g.158626378C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			C|0.581;T|0.419	0.419	strong		0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
CHAF1B	8208	hgsc.bcm.edu	37	21	37759957	37759957	+	Missense_Mutation	SNP	C	C	T	rs62229404	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:37759957C>T	ENST00000314103.5	+	3	339	c.188C>T	c.(187-189)gCt>gTt	p.A63V	CHAF1B_ENST00000480486.1_3'UTR	NM_005441.2	NP_005432.1	Q13112	CAF1B_HUMAN	chromatin assembly factor 1, subunit B (p60)	63					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(2)	20						TCCAATCTTGCTCGTCATACC	0.418													C|||	201	0.0401358	0.0053	0.0418	5008	,	,		19010	0.0298		0.1034	False		,,,				2504	0.0317				p.A63V		Atlas-SNP	.											.	CHAF1B	47	.	0			c.C188T						PASS	.	C	VAL/ALA	68,4338	62.3+/-99.4	0,68,2135	229.0	232.0	231.0		188	1.9	1.0	21	dbSNP_129	231	761,7839	183.0+/-231.3	37,687,3576	yes	missense	CHAF1B	NM_005441.2	64	37,755,5711	TT,TC,CC		8.8488,1.5433,6.374	benign	63/560	37759957	829,12177	2203	4300	6503	SO:0001583	missense	8208	exon3			ATCTTGCTCGTCA	U20980	CCDS13644.1	21q22.2	2013-01-10			ENSG00000159259	ENSG00000159259		"""WD repeat domain containing"""	1911	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 7"", ""Chromatin assembly factor I, p60 subunit"", ""human chromatin assembly factor-I p60 subunit"""	601245				7600578, 8792829	Standard	NM_005441		Approved	CAF1P60, CAF-1, CAF1, CAF1A, MPP7, MPHOSPH7	uc002yvj.3	Q13112	OTTHUMG00000086606	ENST00000314103.5:c.188C>T	21.37:g.37759957C>T	ENSP00000315700:p.Ala63Val	Somatic	316	1	0.00316456		WXS	Illumina HiSeq	Phase_I	342	157	0.459064	NM_005441	Q99548	Missense_Mutation	SNP	ENST00000314103.5	37	CCDS13644.1	114	0.0521978021978022	3	0.006097560975609756	16	0.04419889502762431	5	0.008741258741258742	90	0.11873350923482849	C	16.31	3.087260	0.55968	0.015433	0.088488	ENSG00000159259	ENST00000314103	T	0.65549	-0.16	4.69	1.88	0.25563	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.355399	0.32093	N	0.006591	T	0.00845	0.0028	N	0.16478	0.41	0.22531	P	0.999011324	B	0.31859	0.343	B	0.39339	0.297	T	0.18493	-1.0335	9	0.41790	T	0.15	-0.0166	10.0486	0.42201	0.0:0.7743:0.0:0.2257	rs62229404	63	Q13112	CAF1B_HUMAN	V	63	ENSP00000315700:A63V	ENSP00000315700:A63V	A	+	2	0	CHAF1B	36681827	0.996000	0.38824	0.964000	0.40570	0.959000	0.62525	3.510000	0.53393	0.192000	0.20272	-0.418000	0.06021	GCT	C|0.940;T|0.060	0.060	strong		0.418	CHAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194616.2	NM_005441	
TMEM171	134285	hgsc.bcm.edu	37	5	72419267	72419267	+	Missense_Mutation	SNP	T	T	C	rs638333	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:72419267T>C	ENST00000454765.2	+	2	540	c.67T>C	c.(67-69)Ttc>Ctc	p.F23L	TMEM171_ENST00000287773.5_Missense_Mutation_p.F23L			Q8WVE6	TM171_HUMAN	transmembrane protein 171	23			F -> L (in dbSNP:rs638333). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|stomach(1)	15		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.87e-54)|Lung(70;0.115)		CAAACTCATCTTCTGCTTCTT	0.592													T|||	846	0.16893	0.0855	0.3458	5008	,	,		18441	0.0962		0.2883	False		,,,				2504	0.1084				p.F23L	NSCLC(112;638 2280 27369 30736)	Atlas-SNP	.											.	TMEM171	41	.	0			c.T67C						PASS	.	T	LEU/PHE,LEU/PHE	512,3894	235.2+/-247.8	35,442,1726	124.0	117.0	120.0		67,67	5.1	1.0	5	dbSNP_83	120	2437,6163	404.7+/-348.2	336,1765,2199	yes	missense,missense	TMEM171	NM_001161342.1,NM_173490.6	22,22	371,2207,3925	CC,CT,TT		28.3372,11.6205,22.6742	probably-damaging,probably-damaging	23/324,23/325	72419267	2949,10057	2203	4300	6503	SO:0001583	missense	134285	exon2			CTCATCTTCTGCT	BC018083	CCDS4017.1, CCDS54869.1	5q13.2	2008-02-05			ENSG00000157111	ENSG00000157111			27031	protein-coding gene	gene with protein product						12477932	Standard	NM_173490		Approved	PRP2	uc003kcm.2	Q8WVE6	OTTHUMG00000131269	ENST00000454765.2:c.67T>C	5.37:g.72419267T>C	ENSP00000415030:p.Phe23Leu	Somatic	336	1	0.00297619		WXS	Illumina HiSeq	Phase_I	349	173	0.495702	NM_173490	Q8N0S1|Q8TDT7	Missense_Mutation	SNP	ENST00000454765.2	37	CCDS4017.1	456	0.2087912087912088	47	0.09552845528455285	122	0.3370165745856354	67	0.11713286713286714	220	0.29023746701846964	T	22.2	4.257271	0.80246	0.116205	0.283372	ENSG00000157111	ENST00000454765;ENST00000287773	T;T	0.34072	1.38;1.38	5.09	5.09	0.68999	.	0.074689	0.56097	N	0.000028	T	0.00012	0.0000	M	0.76002	2.32	0.23933	P	0.99642717	B;B	0.23540	0.087;0.087	B;B	0.19946	0.027;0.027	T	0.19943	-1.0290	9	0.66056	D	0.02	-23.8583	14.8705	0.70453	0.0:0.0:0.0:1.0	rs638333;rs17851615;rs59015469;rs638333	23;23	Q8WVE6-2;Q8WVE6	.;TM171_HUMAN	L	23	ENSP00000415030:F23L;ENSP00000287773:F23L	ENSP00000287773:F23L	F	+	1	0	TMEM171	72455023	1.000000	0.71417	0.990000	0.47175	0.720000	0.41350	5.398000	0.66308	1.922000	0.55676	0.379000	0.24179	TTC	T|0.791;C|0.209	0.209	strong		0.592	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490	
STAG2	10735	hgsc.bcm.edu	37	X	123184082	123184082	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:123184082A>G	ENST00000371160.1	+	11	1230	c.940A>G	c.(940-942)Att>Gtt	p.I314V	STAG2_ENST00000371145.3_Missense_Mutation_p.I314V|STAG2_ENST00000371157.3_Missense_Mutation_p.I314V|STAG2_ENST00000371144.3_Missense_Mutation_p.I314V|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.I314V|STAG2_ENST00000354548.5_Missense_Mutation_p.I245V	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	314	SCD. {ECO:0000255|PROSITE- ProRule:PRU00750}.				meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AGAGATTGGCATTTGGATGAA	0.378																																					p.I314V		Atlas-SNP	.											.	STAG2	309	.	0			c.A940G						PASS	.						283.0	235.0	252.0					X																	123184082		2203	4300	6503	SO:0001583	missense	10735	exon11			ATTGGCATTTGGA	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.940A>G	X.37:g.123184082A>G	ENSP00000360202:p.Ile314Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	231	78	0.337662	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	5.398	0.258667	0.10239	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48	5.54	5.54	0.83059	Stromalin conservative domain (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.149337	0.64402	D	0.000013	T	0.10078	0.0247	N	0.01771	-0.73	0.42561	D	0.993144	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.18304	-1.0341	10	0.02654	T	1	-9.3005	9.4174	0.38530	0.9193:0.0:0.0807:0.0	.	314;314	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	V	314;314;245;314;314;314;314	ENSP00000218089:I314V;ENSP00000397265:I314V;ENSP00000346555:I245V;ENSP00000360202:I314V;ENSP00000360199:I314V;ENSP00000360187:I314V;ENSP00000360186:I314V	ENSP00000218089:I314V	I	+	1	0	STAG2	123011763	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.344000	0.65981	1.952000	0.56665	0.486000	0.48141	ATT	.	.	none		0.378	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
TTLL6	284076	hgsc.bcm.edu	37	17	46877063	46877063	+	Missense_Mutation	SNP	G	G	A	rs61739953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:46877063G>A	ENST00000393382.3	-	6	812	c.671C>T	c.(670-672)cCg>cTg	p.P224L		NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						GCCCGAATCCGGCTTACAAAT	0.453													G|||	391	0.0780751	0.0439	0.0375	5008	,	,		19751	0.0952		0.0447	False		,,,				2504	0.1697				p.P224L		Atlas-SNP	.											.	TTLL6	113	.	0			c.C671T						PASS	.	G	LEU/PRO	62,1322		1,60,631	121.0	97.0	104.0		671	5.4	1.0	17	dbSNP_129	104	100,3082		2,96,1493	yes	missense	TTLL6	NM_001130918.1	98	3,156,2124	AA,AG,GG		3.1427,4.4798,3.548		224/892	46877063	162,4404	692	1591	2283	SO:0001583	missense	284076	exon6			GAATCCGGCTTAC	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"""Tubulin tyrosine ligase-like family"""	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.671C>T	17.37:g.46877063G>A	ENSP00000377043:p.Pro224Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_001130918		Missense_Mutation	SNP	ENST00000393382.3	37	CCDS45724.1	111	0.050824175824175824	26	0.052845528455284556	14	0.03867403314917127	40	0.06993006993006994	31	0.040897097625329816	G	29.7	5.029883	0.93575	0.044798	0.031427	ENSG00000170703	ENST00000440941;ENST00000393382	.	.	.	5.45	5.45	0.79879	.	0.000000	0.64402	U	0.000007	T	0.51787	0.1695	H	0.97415	4	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81769	-0.0781	9	0.72032	D	0.01	.	18.0737	0.89421	0.0:0.0:1.0:0.0	rs61739953	176	Q8N841	TTLL6_HUMAN	L	224;176	.	ENSP00000377043:P176L	P	-	2	0	TTLL6	44232062	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.615000	0.83006	2.555000	0.86185	0.655000	0.94253	CCG	G|0.953;A|0.047	0.047	strong		0.453	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623	
CXADR	1525	hgsc.bcm.edu	37	21	18937758	18937758	+	Silent	SNP	A	A	G	rs437470	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:18937758A>G	ENST00000284878.7	+	7	1594	c.846A>G	c.(844-846)ccA>ccG	p.P282P	CXADR_ENST00000400166.1_Missense_Mutation_p.H195R|CXADR_ENST00000356275.6_Missense_Mutation_p.T75A|CXADR_ENST00000306618.10_Silent_p.P241P|CXADR_ENST00000400169.1_Silent_p.P282P|CXADR_ENST00000400165.1_Missense_Mutation_p.H143R	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	282					actin cytoskeleton reorganization (GO:0031532)|AV node cell to bundle of His cell communication (GO:0086067)|blood coagulation (GO:0007596)|cardiac muscle fiber development (GO:0048739)|cell-cell junction organization (GO:0045216)|defense response to virus (GO:0051607)|epithelial structure maintenance (GO:0010669)|gamma-delta T cell activation (GO:0046629)|germ cell migration (GO:0008354)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|homotypic cell-cell adhesion (GO:0034109)|leukocyte migration (GO:0050900)|mitochondrion organization (GO:0007005)|neutrophil chemotaxis (GO:0030593)|regulation of immune response (GO:0050776)|transepithelial transport (GO:0070633)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|adherens junction (GO:0005912)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|filopodium (GO:0030175)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|cell adhesion molecule binding (GO:0050839)|connexin binding (GO:0071253)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|virus receptor activity (GO:0001618)			endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		AAGATGTGCCACCTCCAAAGA	0.443													G|||	937	0.187101	0.3737	0.1196	5008	,	,		20493	0.1468		0.1233	False		,,,				2504	0.09				p.H195R		Atlas-SNP	.											.	CXADR	44	.	0			c.A584G						PASS	.	G	ARG/HIS,ARG/HIS,ALA/THR,,	1405,3001	684.2+/-404.4	232,941,1030	75.0	79.0	78.0		584,428,223,846,846	-10.6	0.0	21	dbSNP_80	78	1079,7521	768.6+/-407.6	63,953,3284	yes	missense,missense,missense,coding-synonymous,coding-synonymous	CXADR	NM_001207063.1,NM_001207064.1,NM_001207065.1,NM_001207066.1,NM_001338.4	29,29,58,,	295,1894,4314	GG,GA,AA		12.5465,31.8883,19.0989	,,,,	195/253,143/201,75/90,282/353,282/366	18937758	2484,10522	2203	4300	6503	SO:0001819	synonymous_variant	1525	exon5			TGTGCCACCTCCA	Y07593	CCDS33519.1, CCDS56204.1, CCDS56205.1, CCDS56206.1, CCDS56207.1	21q21.1	2013-01-29			ENSG00000154639	ENSG00000154639		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2559	protein-coding gene	gene with protein product		602621				9036860, 9096397	Standard	NM_001338		Approved	CAR	uc002yki.3	P78310	OTTHUMG00000074508	ENST00000284878.7:c.846A>G	21.37:g.18937758A>G		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	218	112	0.513761	NM_001207063	B2R8V8|B7WPI3|D3YHP0|O00694|Q8WWT6|Q8WWT7|Q8WWT8|Q9UKV4	Missense_Mutation	SNP	ENST00000284878.7	37	CCDS33519.1	394|394	0.1804029304029304|0.1804029304029304	185|185	0.37601626016260165|0.37601626016260165	46|46	0.1270718232044199|0.1270718232044199	86|86	0.15034965034965034|0.15034965034965034	77|77	0.10158311345646438|0.10158311345646438	G|G	0.381|0.381	-0.928851|-0.928851	0.02359|0.02359	0.318883|0.318883	0.125465|0.125465	ENSG00000154639|ENSG00000154639	ENST00000400166;ENST00000400165|ENST00000356275	D;D|.	0.90563|.	-2.52;-2.69|.	5.3|5.3	-10.6|-10.6	0.00265|0.00265	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999797698|0.9999999999797698	B;B|B	0.02656|0.02656	0.0;0.0|0.0	B;B|B	0.04013|0.01281	0.001;0.001|0.0	T|T	0.10989|0.10989	-1.0606|-1.0606	7|6	0.23891|0.30854	T|T	0.37|0.27	.|.	3.0005|3.0005	0.06012|0.06012	0.3924:0.1382:0.339:0.1304|0.3924:0.1382:0.339:0.1304	rs437470;rs1050672;rs57119523;rs437470|rs437470;rs1050672;rs57119523;rs437470	143;195|75	P78310-4;P78310-5|P78310-3	.;.|.	R|A	195;143|75	ENSP00000383030:H195R;ENSP00000383029:H143R|.	ENSP00000383029:H143R|ENSP00000348620:T75A	H|T	+|+	2|1	0|0	CXADR|CXADR	17859629|17859629	0.000000|0.000000	0.05858|0.05858	0.016000|0.016000	0.15963|0.15963	0.492000|0.492000	0.33523|0.33523	-2.428000|-2.428000	0.01025|0.01025	-4.439000|-4.439000	0.00049|0.00049	-4.053000|-4.053000	0.00012|0.00012	CAC|ACC	A|0.808;G|0.192	0.192	strong		0.443	CXADR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000158209.1		
HLX	3142	hgsc.bcm.edu	37	1	221057662	221057662	+	Silent	SNP	G	G	A	rs3738182	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:221057662G>A	ENST00000366903.6	+	4	2584	c.1083G>A	c.(1081-1083)gaG>gaA	p.E361E	HLX_ENST00000549319.1_Silent_p.E147E	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	361					cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		CGGATGGCGAGCAGGACGAGA	0.667													G|||	936	0.186901	0.2572	0.1801	5008	,	,		11857	0.0942		0.1779	False		,,,				2504	0.2014				p.E361E		Atlas-SNP	.											.	HLX	67	.	0			c.G1083A						PASS	.	G		1007,3399	342.5+/-307.2	124,759,1320	34.0	35.0	35.0		1083	-2.2	0.0	1	dbSNP_107	35	1707,6893	294.6+/-302.0	151,1405,2744	no	coding-synonymous	HLX	NM_021958.3		275,2164,4064	AA,AG,GG		19.8488,22.8552,20.8673		361/489	221057662	2714,10292	2203	4300	6503	SO:0001819	synonymous_variant	3142	exon4			TGGCGAGCAGGAC	BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"""Homeoboxes / ANTP class : NKL subclass"""	4978	protein-coding gene	gene with protein product		142995	"""H2.0 (Drosophila)-like homeo box 1"", ""H2.0-like homeobox 1 (Drosophila)"", ""H2.0-like homeobox 1"""	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.1083G>A	1.37:g.221057662G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	187	101	0.540107	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Silent	SNP	ENST00000366903.6	37	CCDS1527.1																																																																																			G|0.810;A|0.190	0.190	strong		0.667	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
KLHL33	123103	hgsc.bcm.edu	37	14	20898308	20898308	+	Missense_Mutation	SNP	C	C	T	rs17242648	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20898308C>T	ENST00000344581.4	-	2	749	c.527G>A	c.(526-528)cGg>cAg	p.R176Q		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	176			R -> Q (in dbSNP:rs17242648).									all_cancers(95;0.00123)		Epithelial(56;7.57e-08)|all cancers(55;8.63e-07)	GBM - Glioblastoma multiforme(265;0.0223)|READ - Rectum adenocarcinoma(17;0.193)		CCCGGCTGCCCGCACCCTCCG	0.652													C|||	625	0.1248	0.1089	0.0576	5008	,	,		19012	0.2143		0.0915	False		,,,				2504	0.136				p.R176Q		Atlas-SNP	.											.	KLHL33	37	.	0			c.G527A						PASS	.	C	GLN/ARG	130,1254		11,108,573	32.0	37.0	36.0		527	3.9	1.0	14	dbSNP_123	36	256,2926		10,236,1345	yes	missense	KLHL33	NM_001109997.2	43	21,344,1918	TT,TC,CC		8.0453,9.3931,8.4538	possibly-damaging	176/534	20898308	386,4180	692	1591	2283	SO:0001583	missense	123103	exon2			GCTGCCCGCACCC		CCDS53882.1	14q11.2	2013-10-15	2013-02-22		ENSG00000185271	ENSG00000185271		"""Kelch-like"""	31952	protein-coding gene	gene with protein product			"""kelch-like 33 (Drosophila)"""				Standard	NM_001109997		Approved		uc010tli.2	A6NCF5	OTTHUMG00000170982	ENST00000344581.4:c.527G>A	14.37:g.20898308C>T	ENSP00000341549:p.Arg176Gln	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_001109997		Missense_Mutation	SNP	ENST00000344581.4	37	CCDS53882.1	270	0.12362637362637363	59	0.11991869918699187	25	0.06906077348066299	113	0.19755244755244755	73	0.09630606860158311	C	13.25	2.179740	0.38511	0.093931	0.080453	ENSG00000185271	ENST00000344581	T	0.72167	-0.63	4.75	3.86	0.44501	BTB/Kelch-associated (1);	0.070861	0.53938	D	0.000042	T	0.00073	0.0002	L	0.27053	0.805	0.40890	P	0.015932999999999975	P	0.44478	0.836	B	0.40782	0.34	T	0.04811	-1.0925	9	0.19590	T	0.45	.	9.8808	0.41231	0.0:0.9041:0.0:0.0959	rs17242648;rs52804888;rs57177627;rs17242648	176	A6NCF5	KLH33_HUMAN	Q	176	ENSP00000341549:R176Q	ENSP00000341549:R176Q	R	-	2	0	KLHL33	19968148	0.302000	0.24454	0.972000	0.41901	0.925000	0.55904	1.494000	0.35616	1.207000	0.43291	0.655000	0.94253	CGG	C|0.873;T|0.127	0.127	strong		0.652	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
KCNJ1	3758	hgsc.bcm.edu	37	11	128709126	128709126	+	Missense_Mutation	SNP	A	A	G	rs59172778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:128709126A>G	ENST00000392664.2	-	2	1186	c.1070T>C	c.(1069-1071)aTg>aCg	p.M357T	KCNJ1_ENST00000392666.1_Missense_Mutation_p.M338T|KCNJ1_ENST00000324036.3_Missense_Mutation_p.M338T|KCNJ1_ENST00000392665.2_Missense_Mutation_p.M338T|KCNJ1_ENST00000440599.2_Missense_Mutation_p.M338T	NM_000220.4	NP_000211.1	P48048	KCNJ1_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 1	357			M -> T (in BS2; dbSNP:rs59172778). {ECO:0000269|PubMed:8841184}.		cardiovascular system development (GO:0072358)|excretion (GO:0007588)|kidney development (GO:0001822)|post-embryonic development (GO:0009791)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of G-protein activated inward rectifier potassium channel activity (GO:1900128)|renal sodium ion absorption (GO:0070294)|synaptic transmission (GO:0007268)|tissue homeostasis (GO:0001894)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)	23	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Bethanidine(DB00217)|Glimepiride(DB00222)|Glyburide(DB01016)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Tolazamide(DB00839)|Tolbutamide(DB01124)|Yohimbine(DB01392)	ATAAAGGCACATGGCACAGTG	0.438													A|||	14	0.00279553	0.0	0.0029	5008	,	,		21343	0.0		0.0119	False		,,,				2504	0.0				p.M357T		Atlas-SNP	.											.	KCNJ1	68	.	0			c.T1070C	GRCh37	CM960893	KCNJ1	M	rs59172778	PASS	.	A	THR/MET,THR/MET,THR/MET,THR/MET,THR/MET	8,4394	14.3+/-33.2	0,8,2193	119.0	114.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1070,1013,1013,1013,1013	5.9	1.0	11	dbSNP_129	115	81,8513	46.7+/-105.8	1,79,4217	yes	missense,missense,missense,missense,missense	KCNJ1	NM_000220.2,NM_153764.1,NM_153765.1,NM_153766.1,NM_153767.2	81,81,81,81,81	1,87,6410	GG,GA,AA		0.9425,0.1817,0.6848	benign,benign,benign,benign,benign	357/392,338/373,338/373,338/373,338/373	128709126	89,12907	2201	4297	6498	SO:0001583	missense	3758	exon2			AGGCACATGGCAC	BC063109	CCDS8476.1, CCDS8477.1	11q24	2011-07-05			ENSG00000151704	ENSG00000151704		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6255	protein-coding gene	gene with protein product		600359				7680431, 8190102, 16382105	Standard	NM_153765		Approved	Kir1.1, ROMK1	uc001qeo.2	P48048	OTTHUMG00000048247	ENST00000392664.2:c.1070T>C	11.37:g.128709126A>G	ENSP00000376432:p.Met357Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_000220	B2RMR4|Q6LD67	Missense_Mutation	SNP	ENST00000392664.2	37	CCDS8476.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	A	8.138	0.784569	0.16189	0.001817	0.009425	ENSG00000151704	ENST00000392665;ENST00000392666;ENST00000440599;ENST00000324036;ENST00000392664	D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23	5.9	5.9	0.94986	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.432611	0.29212	N	0.012803	D	0.86280	0.5895	N	0.24115	0.695	0.25998	N	0.982157	B	0.11235	0.004	B	0.22753	0.041	T	0.80714	-0.1259	10	0.72032	D	0.01	.	16.3245	0.82970	1.0:0.0:0.0:0.0	rs59172778;rs62625013	357	P48048	IRK1_HUMAN	T	338;338;338;338;357	ENSP00000376433:M338T;ENSP00000376434:M338T;ENSP00000406320:M338T;ENSP00000316233:M338T;ENSP00000376432:M357T	ENSP00000316233:M338T	M	-	2	0	KCNJ1	128214336	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.870000	0.63035	2.254000	0.74563	0.460000	0.39030	ATG	A|0.993;G|0.007	0.007	strong		0.438	KCNJ1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386233.1	NM_000220	
PNP	4860	hgsc.bcm.edu	37	14	20940515	20940515	+	Silent	SNP	C	C	T	rs1049562	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20940515C>T	ENST00000361505.5	+	2	206	c.60C>T	c.(58-60)caC>caT	p.H20H	RP11-203M5.8_ENST00000554678.1_lincRNA	NM_000270.3	NP_000261.2	P01298	PAHO_HUMAN	purine nucleoside phosphorylase	0					digestion (GO:0007586)|protein secretion (GO:0009306)	extracellular region (GO:0005576)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|stomach(2)	10						TTCTGTCTCACACTAAGCACC	0.433													C|||	862	0.172125	0.2201	0.1383	5008	,	,		21318	0.123		0.1918	False		,,,				2504	0.1616				p.H20H		Atlas-SNP	.											.	PNP	21	.	0			c.C60T						PASS	.	C		912,3494	352.8+/-311.9	92,728,1383	153.0	138.0	143.0		60	-0.6	0.8	14	dbSNP_86	143	1445,7155	277.1+/-292.7	131,1183,2986	no	coding-synonymous	PNP	NM_000270.3		223,1911,4369	TT,TC,CC		16.8023,20.699,18.1224		20/290	20940515	2357,10649	2203	4300	6503	SO:0001819	synonymous_variant	4860	exon2			GTCTCACACTAAG		CCDS9552.1	14q11.2	2014-09-17	2009-12-02	2009-12-02	ENSG00000198805	ENSG00000198805	2.4.2.1		7892	protein-coding gene	gene with protein product		164050	"""nucleoside phosphorylase"""	NP		6087295	Standard	NM_000270		Approved	PUNP	uc001vxo.4	P00491	OTTHUMG00000029546	ENST00000361505.5:c.60C>T	14.37:g.20940515C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	180	87	0.483333	NM_000270		Silent	SNP	ENST00000361505.5	37	CCDS9552.1																																																																																			C|0.817;T|0.183	0.183	strong		0.433	PNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073646.2	NM_000270.2	
PARD3B	117583	hgsc.bcm.edu	37	2	205986321	205986321	+	Silent	SNP	A	A	G	rs2289023	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:205986321A>G	ENST00000406610.2	+	8	1020	c.813A>G	c.(811-813)caA>caG	p.Q271Q	PARD3B_ENST00000462231.1_Silent_p.Q271Q|PARD3B_ENST00000349953.3_Silent_p.Q271Q|PARD3B_ENST00000358768.2_Silent_p.Q271Q|PARD3B_ENST00000351153.1_Silent_p.Q271Q	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	271	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		CCAGGGCTCAAGATGTCTTCC	0.478													A|||	1354	0.270367	0.1384	0.1585	5008	,	,		20015	0.4058		0.2256	False		,,,				2504	0.4346				p.Q271Q		Atlas-SNP	.											PARD3B_ENST00000358768,right_upper_lobe,carcinoma,+2,3	PARD3B	314	3	0			c.A813G						PASS	.	A	,,	606,3376		39,528,1424	111.0	113.0	113.0		813,813,813	-1.2	1.0	2	dbSNP_100	113	1880,6438		222,1436,2501	yes	coding-synonymous,coding-synonymous,coding-synonymous	PARD3B	NM_057177.6,NM_152526.5,NM_205863.3	,,	261,1964,3925	GG,GA,AA		22.6016,15.2185,20.2114	,,	271/1137,271/1144,271/1105	205986321	2486,9814	1991	4159	6150	SO:0001819	synonymous_variant	117583	exon8			GGCTCAAGATGTC	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19"", ""par-3 partitioning defective 3 homolog B (C. elegans)"""	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.813A>G	2.37:g.205986321A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	133	58	0.43609	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	37																																																																																				A|0.743;G|0.257	0.257	strong		0.478	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
CD109	135228	hgsc.bcm.edu	37	6	74493432	74493432	+	Missense_Mutation	SNP	A	A	C	rs10455097	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:74493432A>C	ENST00000287097.5	+	19	2220	c.2108A>C	c.(2107-2109)tAc>tCc	p.Y703S	CD109_ENST00000437994.2_Missense_Mutation_p.Y703S|CD109_ENST00000422508.2_Missense_Mutation_p.Y626S			Q6YHK3	CD109_HUMAN	CD109 molecule	703			Y -> S (in allele Gov(b); dbSNP:rs10455097). {ECO:0000269|PubMed:11861285, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14980714, ECO:0000269|PubMed:16754747, ECO:0000269|PubMed:17974005}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GACTTCAGTTACAGGATTTAC	0.333													C|||	2582	0.515575	0.6551	0.5072	5008	,	,		16327	0.5268		0.495	False		,,,				2504	0.3425				p.Y703S		Atlas-SNP	.											.	CD109	170	.	0			c.A2108C	GRCh37	CM020385	CD109	M	rs10455097	PASS	.	C	SER/TYR,SER/TYR,SER/TYR	2841,1565	490.3+/-361.7	914,1013,276	95.0	86.0	89.0		2108,1877,2108	5.2	0.7	6	dbSNP_119	89	4395,4205	568.4+/-389.0	1142,2111,1047	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	144,144,144	2056,3124,1323	CC,CA,AA		48.8953,35.5197,44.3641	benign,benign,benign	703/1429,626/1369,703/1446	74493432	7236,5770	2203	4300	6503	SO:0001583	missense	135228	exon19			TCAGTTACAGGAT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2108A>C	6.37:g.74493432A>C	ENSP00000287097:p.Tyr703Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	1183	0.5416666666666666	332	0.6747967479674797	187	0.5165745856353591	298	0.5209790209790209	366	0.48284960422163586	C	0.007	-1.977407	0.00452	0.644803	0.511047	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.23348	1.91;1.91;1.91	5.16	5.16	0.70880	Alpha-2-macroglobulin (1);	1.522320	0.04338	N	0.353567	T	0.02342	0.0072	N	0.00459	-1.475	0.52501	P	4.499999999996174E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.36187	-0.9758	9	0.12430	T	0.62	.	10.6226	0.45489	0.1331:0.7968:0.0:0.0701	rs10455097;rs52799109;rs56864921;rs10455097	626;703;703	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	S	703;626;703	ENSP00000388062:Y703S;ENSP00000404475:Y626S;ENSP00000287097:Y703S	ENSP00000287097:Y703S	Y	+	2	0	CD109	74550153	0.936000	0.31750	0.680000	0.29994	0.003000	0.03518	0.728000	0.26013	1.413000	0.46997	-0.127000	0.14921	TAC	A|0.454;C|0.546	0.546	strong		0.333	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
NACA	4666	hgsc.bcm.edu	37	12	57109792	57109792	+	Missense_Mutation	SNP	A	A	G	rs2958149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57109792A>G	ENST00000454682.1	-	3	5803	c.5522T>C	c.(5521-5523)cTg>cCg	p.L1841P	NACA_ENST00000546392.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.L688P|NACA_ENST00000548563.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000551793.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1841	Pro-rich.		L -> P (in dbSNP:rs2958149). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						AATCAGAGGCAGCAGCTCATC	0.577			T	BCL6	NHL								G|||	4052	0.809105	0.9092	0.7594	5008	,	,		17714	0.748		0.7316	False		,,,				2504	0.8517				p.L688P		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.T2063C						PASS	.	G	,,PRO/LEU,	2813,323		1265,283,20	60.0	60.0	60.0		,,2063,	4.1	1.0	12	dbSNP_101	60	5166,1998		1868,1430,284	yes	intron,intron,missense,intron	NACA	NM_001113201.1,NM_001113202.1,NM_001113203.2,NM_005594.4	,,98,	3133,1713,304	GG,GA,AA		27.8894,10.2997,22.534	,,benign,	,,688/926,	57109792	7979,2321	1568	3582	5150	SO:0001583	missense	4666	exon5			AGAGGCAGCAGCT	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.5522T>C	12.37:g.57109792A>G	ENSP00000403817:p.Leu1841Pro	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	117	59	0.504274	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	37		1714	0.7847985347985348	443	0.9004065040650406	284	0.7845303867403315	434	0.7587412587412588	553	0.7295514511873351	G	1.161	-0.643742	0.03531	0.897003	0.721106	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.39787	1.11;1.06	4.08	4.08	0.47627	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.26105	P	0.98077	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29366	-1.0014	8	0.09843	T	0.71	.	10.999	0.47593	0.0953:0.0:0.9047:0.0	rs2958149;rs3782230;rs58362731;rs2958149	1841;688	E9PAV3;F8VU71	.;.	P	1841;688	ENSP00000403817:L1841P;ENSP00000448035:L688P	ENSP00000403817:L1841P	L	-	2	0	NACA	55396059	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.591000	0.53986	0.932000	0.37266	-0.338000	0.08134	CTG	A|0.211;G|0.789	0.789	strong		0.577	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
MICA	100507436	hgsc.bcm.edu	37	6	31379752	31379752	+	Silent	SNP	C	C	T	rs17206680	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31379752C>T	ENST00000449934.2	+	4	696	c.642C>T	c.(640-642)agC>agT	p.S214S	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				TCACCCGCAGCGAGGCCTCAG	0.582													c|||	149	0.0297524	0.0106	0.013	5008	,	,		20941	0.0536		0.0477	False		,,,				2504	0.0245				p.S214S		Atlas-SNP	.											.	MICA	21	.	0			c.C642T						PASS	.	T		9,1375		0,9,683	32.0	36.0	35.0		642	-2.0	0.0	6	dbSNP_123	35	128,3054		3,122,1466	no	coding-synonymous	MICA	NM_001177519.1		3,131,2149	TT,TC,CC		4.0226,0.6503,3.0004		214/333	31379752	137,4429	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon4			CCGCAGCGAGGCC	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.642C>T	6.37:g.31379752C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	68	24	0.352941	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.967;T|0.033	0.033	strong		0.582	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
ZNF19	7567	hgsc.bcm.edu	37	16	71509588	71509588	+	Silent	SNP	G	G	A	rs2288487	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:71509588G>A	ENST00000288177.5	-	6	1117	c.862C>T	c.(862-864)Cta>Tta	p.L288L	ZNF19_ENST00000567225.1_Intron|AC010547.9_ENST00000561908.1_Intron|ZNF19_ENST00000565637.1_Silent_p.L246L|ZNF19_ENST00000565100.2_Silent_p.L218L|ZNF19_ENST00000564230.1_Silent_p.L288L	NM_006961.3	NP_008892.2	P17023	ZNF19_HUMAN	zinc finger protein 19	288					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)	p.L288L(1)		NS(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|prostate(1)|stomach(1)	22		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		TGCCGAAGTAGGGGTGAATTA	0.453													G|||	1408	0.28115	0.1074	0.183	5008	,	,		19107	0.2877		0.2942	False		,,,				2504	0.5654				p.L288L		Atlas-SNP	.											ZNF19,NS,carcinoma,0,1	ZNF19	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C862T						PASS	.	G		556,3840	250.0+/-257.2	32,492,1674	88.0	86.0	86.0		862	1.5	0.0	16	dbSNP_100	86	2632,5968	424.1+/-354.6	415,1802,2083	no	coding-synonymous	ZNF19	NM_006961.3		447,2294,3757	AA,AG,GG		30.6047,12.6479,24.5306		288/459	71509588	3188,9808	2198	4300	6498	SO:0001819	synonymous_variant	7567	exon6			GAAGTAGGGGTGA	X52343	CCDS10901.1	16q22	2013-01-08	2006-05-10		ENSG00000157429	ENSG00000157429		"""Zinc fingers, C2H2-type"", ""-"""	12981	protein-coding gene	gene with protein product		194525	"""zinc finger protein 19 (KOX 12)"""			1505991, 1946370	Standard	NM_006961		Approved	KOX12, MGC51021	uc002fam.1	P17023	OTTHUMG00000137593	ENST00000288177.5:c.862C>T	16.37:g.71509588G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	62	36	0.580645	NM_006961	A8K895|Q86Y66|Q8NDE2|Q96M79|Q96NE5	Silent	SNP	ENST00000288177.5	37	CCDS10901.1																																																																																			G|0.747;A|0.253	0.253	strong		0.453	ZNF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268993.2	NM_006961	
TEP1	7011	hgsc.bcm.edu	37	14	20876282	20876282	+	Missense_Mutation	SNP	G	G	A	rs41310936	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20876282G>A	ENST00000262715.5	-	2	357	c.317C>T	c.(316-318)tCc>tTc	p.S106F	TEP1_ENST00000556935.1_Missense_Mutation_p.S106F	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	106					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)		GTTCTCCAAGGAGAGGATGTC	0.537													G|||	22	0.00439297	0.0	0.0029	5008	,	,		22949	0.0		0.0149	False		,,,				2504	0.0051				p.S106F		Atlas-SNP	.											.	TEP1	224	.	0			c.C317T						PASS	.	G	PHE/SER	23,4383	29.9+/-59.1	0,23,2180	109.0	110.0	109.0		317	5.1	1.0	14	dbSNP_127	109	183,8417	82.3+/-144.9	2,179,4119	yes	missense	TEP1	NM_007110.4	155	2,202,6299	AA,AG,GG		2.1279,0.522,1.5839	probably-damaging	106/2628	20876282	206,12800	2203	4300	6503	SO:0001583	missense	7011	exon2			TCCAAGGAGAGGA		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.317C>T	14.37:g.20876282G>A	ENSP00000262715:p.Ser106Phe	Somatic	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	195	115	0.589744	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	G	15.76	2.927823	0.52759	0.00522	0.021279	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000556549	T;T;T	0.78246	-1.16;-1.16;-1.16	5.08	5.08	0.68730	.	0.111661	0.41294	D	0.000915	T	0.71099	0.3300	L	0.32530	0.975	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.998;0.999	T	0.79495	-0.1780	10	0.87932	D	0	-12.2698	14.1599	0.65441	0.0:0.0:1.0:0.0	rs41310936	106;106	G3V5X7;Q99973	.;TEP1_HUMAN	F	106	ENSP00000262715:S106F;ENSP00000452574:S106F;ENSP00000452240:S106F	ENSP00000262715:S106F	S	-	2	0	TEP1	19946122	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	4.230000	0.58632	2.791000	0.96007	0.650000	0.86243	TCC	G|0.988;A|0.012	0.012	strong		0.537	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39913634	39913634	+	Missense_Mutation	SNP	G	G	A	rs10407035	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:39913634G>A	ENST00000409794.3	+	18	2790	c.1940G>A	c.(1939-1941)cGc>cAc	p.R647H	PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.R588H|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.R618H|CTB-60E11.4_ENST00000601124.1_lincRNA	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	647			R -> H (in dbSNP:rs10407035). {ECO:0000269|PubMed:15489334}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			ATTCCCAGCCGCTGTGAAATT	0.522													G|||	1227	0.245008	0.202	0.1974	5008	,	,		19345	0.3909		0.1571	False		,,,				2504	0.2771				p.R647H		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G1940A						PASS	.	G	HIS/ARG	921,3485	353.6+/-312.2	86,749,1368	89.0	93.0	91.0		1940	-2.8	0.0	19	dbSNP_119	91	970,7630	210.5+/-251.4	54,862,3384	yes	missense	PLEKHG2	NM_022835.2	29	140,1611,4752	AA,AG,GG		11.2791,20.9033,14.5394	benign	647/1387	39913634	1891,11115	2203	4300	6503	SO:0001583	missense	64857	exon18			CCAGCCGCTGTGA	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.1940G>A	19.37:g.39913634G>A	ENSP00000386733:p.Arg647His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	493|493	0.22573260073260074|0.22573260073260074	111|111	0.22560975609756098|0.22560975609756098	63|63	0.17403314917127072|0.17403314917127072	208|208	0.36363636363636365|0.36363636363636365	111|111	0.14643799472295516|0.14643799472295516	G|G	7.223|7.223	0.597725|0.597725	0.13875|0.13875	0.209033|0.209033	0.112791|0.112791	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000458508	.|T;T;T	.|0.68479	.|-0.21;-0.21;-0.33	3.19|3.19	-2.84|-2.84	0.05751|0.05751	.|.	.|0.776000	.|0.10572	.|N	.|0.659076	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|P;P;D	.|0.53151	.|0.955;0.925;0.958	.|B;B;B	.|0.41723	.|0.365;0.2;0.27	T|T	0.18524|0.18524	-1.0334|-1.0334	4|9	.|0.41790	.|T	.|0.15	.|.	4.667|4.667	0.12671|0.12671	0.2592:0.0:0.3855:0.3552|0.2592:0.0:0.3855:0.3552	rs10407035;rs17845383;rs17858238;rs57929826;rs10407035|rs10407035;rs17845383;rs17858238;rs57929826;rs10407035	.|618;647;588	.|Q9H7P9-3;Q9H7P9;E7ESZ3	.|.;PKHG2_HUMAN;.	T|H	515|647;618;588	.|ENSP00000386733:R647H;ENSP00000392906:R618H;ENSP00000408857:R588H	.|ENSP00000386733:R647H	A|R	+|+	1|2	0|0	PLEKHG2|PLEKHG2	44605474|44605474	0.000000|0.000000	0.05858|0.05858	0.038000|0.038000	0.18304|0.18304	0.082000|0.082000	0.17680|0.17680	-0.547000|-0.547000	0.06055|0.06055	-0.311000|-0.311000	0.08754|0.08754	-1.250000|-1.250000	0.01514|0.01514	GCT|CGC	G|0.823;A|0.177	0.177	strong		0.522	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
TBX2	6909	hgsc.bcm.edu	37	17	59477903	59477903	+	Silent	SNP	C	C	A	rs75743672	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:59477903C>A	ENST00000240328.3	+	1	647	c.366C>A	c.(364-366)ggC>ggA	p.G122G	RP11-332H18.4_ENST00000590421.1_RNA|RP11-332H18.4_ENST00000589814.1_RNA|RP11-332H18.5_ENST00000585765.1_RNA|RP11-332H18.4_ENST00000592009.1_RNA|RP11-332H18.4_ENST00000591313.1_RNA	NM_005994.3	NP_005985.3	Q13207	TBX2_HUMAN	T-box 2	122					aorta morphogenesis (GO:0035909)|atrioventricular canal development (GO:0036302)|cardiac muscle tissue development (GO:0048738)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|developmental growth involved in morphogenesis (GO:0060560)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|endocardial cushion morphogenesis (GO:0003203)|mammary placode formation (GO:0060596)|muscle cell fate determination (GO:0007521)|negative regulation of cardiac chamber formation (GO:1901211)|negative regulation of heart looping (GO:1901208)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|palate development (GO:0060021)|pharynx development (GO:0060465)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(7)|ovary(1)	9						ACAAGCTAGGCACGGAGATGG	0.697													C|||	750	0.14976	0.0953	0.1729	5008	,	,		4864	0.2847		0.0716	False		,,,				2504	0.1483				p.G122G	GBM(3;187 253 11467 14965 23079)	Atlas-SNP	.											.	TBX2	30	.	0			c.C366A						PASS	.	C		438,3914		18,402,1756	15.0	13.0	14.0		366	3.6	1.0	17	dbSNP_131	14	456,8076		13,430,3823	no	coding-synonymous	TBX2	NM_005994.3		31,832,5579	AA,AC,CC		5.3446,10.0643,6.9388		122/713	59477903	894,11990	2176	4266	6442	SO:0001819	synonymous_variant	6909	exon1			GCTAGGCACGGAG	AB209378	CCDS11627.2	17q23.2	2012-01-23			ENSG00000121068	ENSG00000121068		"""T-boxes"""	11597	protein-coding gene	gene with protein product		600747				8530034	Standard	NM_005994		Approved		uc010wox.2	Q13207	OTTHUMG00000156986	ENST00000240328.3:c.366C>A	17.37:g.59477903C>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	30	10	0.333333	NM_005994	Q16424|Q7Z647	Silent	SNP	ENST00000240328.3	37	CCDS11627.2																																																																																			C|0.894;A|0.106	0.106	strong		0.697	TBX2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346977.2	NM_005994	
SEC14L2	23541	hgsc.bcm.edu	37	22	30793137	30793137	+	Missense_Mutation	SNP	G	G	A	rs757660	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:30793137G>A	ENST00000312932.9	+	1	292	c.32G>A	c.(31-33)aGg>aAg	p.R11K	SEC14L2_ENST00000405717.3_Missense_Mutation_p.R11K|SEC14L2_ENST00000459728.1_3'UTR|SEC14L2_ENST00000403484.1_5'UTR|SEC14L2_ENST00000402592.3_Missense_Mutation_p.R11K	NM_012429.3	NP_036561.1	O76054	S14L2_HUMAN	SEC14-like 2 (S. cerevisiae)	11			R -> K (in dbSNP:rs757660). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.8}.		positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cholesterol biosynthetic process (GO:0045540)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	10					Vitamin E(DB00163)	CTGAGCCCCAGGCAGAAGGAG	0.716													A|||	1857	0.370807	0.4085	0.3617	5008	,	,		10837	0.3849		0.3121	False		,,,				2504	0.3722				p.R11K		Atlas-SNP	.											.	SEC14L2	24	.	0			c.G32A						PASS	.	A	LYS/ARG,LYS/ARG,LYS/ARG	1467,2675		287,893,891	17.0	13.0	14.0		32,32,32	0.6	1.0	22	dbSNP_86	14	2010,6066		255,1500,2283	yes	missense,missense,missense	SEC14L2	NM_001204204.1,NM_012429.3,NM_033382.2	26,26,26	542,2393,3174	AA,AG,GG		24.8886,35.4177,28.458	benign,benign,benign	11/321,11/404,11/393	30793137	3477,8741	2071	4038	6109	SO:0001583	missense	23541	exon1			GCCCCAGGCAGAA	AL096881	CCDS13876.1, CCDS46685.1, CCDS56228.1	22q12.2	2010-08-19	2001-11-28		ENSG00000100003	ENSG00000100003			10699	protein-coding gene	gene with protein product	"""supernatant protein factor"""	607558	"""SEC14 (S. cerevisiae)-like 2"""	C22orf6		10591208	Standard	NM_033382		Approved	TAP, SPF, KIAA1186, KIAA1658	uc003ahr.3	O76054	OTTHUMG00000151024	ENST00000312932.9:c.32G>A	22.37:g.30793137G>A	ENSP00000316203:p.Arg11Lys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_001204204	B7Z8Q1|F5H3U4|Q53EQ2|Q6PD61|Q9ULN4	Missense_Mutation	SNP	ENST00000312932.9	37	CCDS13876.1	795	0.364010989010989	216	0.43902439024390244	118	0.3259668508287293	221	0.38636363636363635	240	0.316622691292876	A	6.498	0.460151	0.12342	0.354177	0.248886	ENSG00000100003	ENST00000312932;ENST00000416523;ENST00000405717;ENST00000402592	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	4.15	0.645	0.17782	Phosphatidylinositol transfer protein-like, N-terminal (1);	0.138996	0.47852	N	0.000208	T	0.00012	0.0000	N	0.00521	-1.4	0.09310	P	0.99999999615629	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45804	-0.9236	9	0.05436	T	0.98	-2.7632	7.7743	0.29029	0.5955:0.0:0.4045:0.0	rs757660;rs11556717;rs52809732;rs60495705;rs757660	11;11;11	F5H3U4;O76054;O76054-4	.;S14L2_HUMAN;.	K	11	ENSP00000316203:R11K;ENSP00000400567:R11K;ENSP00000385186:R11K;ENSP00000383882:R11K	ENSP00000316203:R11K	R	+	2	0	SEC14L2	29123137	0.197000	0.23362	0.956000	0.39512	0.881000	0.50899	0.584000	0.23864	-0.099000	0.12263	-0.361000	0.07541	AGG	G|0.644;A|0.356	0.356	strong		0.716	SEC14L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321018.4	NM_012429	
GAS8	2622	hgsc.bcm.edu	37	16	90097748	90097748	+	Silent	SNP	C	C	T	rs2302513	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90097748C>T	ENST00000268699.4	+	3	254	c.132C>T	c.(130-132)cgC>cgT	p.R44R	GAS8_ENST00000536122.1_Silent_p.R19R|GAS8_ENST00000540721.1_3'UTR|C16orf3_ENST00000408886.2_5'Flank	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	44	Regulates microtubule-binding. {ECO:0000250}.				cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		AGCTGGACCGCGAGCGGGAGG	0.642													c|||	1244	0.248403	0.1233	0.2954	5008	,	,		16413	0.627		0.1213	False		,,,				2504	0.1247				p.R44R		Atlas-SNP	.											GAS8,NS,carcinoma,+1,1	GAS8	29	1	0			c.C132T						PASS	.	T		549,3847	242.8+/-252.7	39,471,1688	80.0	73.0	75.0		132	-11.8	0.1	16	dbSNP_100	75	802,7798	187.9+/-235.0	46,710,3544	no	coding-synonymous	GAS8	NM_001481.2		85,1181,5232	TT,TC,CC		9.3256,12.4886,10.3955		44/479	90097748	1351,11645	2198	4300	6498	SO:0001819	synonymous_variant	2622	exon3			GGACCGCGAGCGG	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.132C>T	16.37:g.90097748C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	29	18	0.62069	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Silent	SNP	ENST00000268699.4	37	CCDS10992.1																																																																																			T|0.179;G|0.000;C|0.821	0.179	strong		0.642	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
ZNF512B	57473	hgsc.bcm.edu	37	20	62598815	62598815	+	Silent	SNP	C	C	T	rs817330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62598815C>T	ENST00000450537.1	-	3	243	c.183G>A	c.(181-183)ccG>ccA	p.P61P	ZNF512B_ENST00000369888.1_Silent_p.P61P|ZNF512B_ENST00000217130.3_Silent_p.P61P			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	61					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTGGACTTCCCGGGTCAAAGC	0.617													T|||	1598	0.319089	0.4402	0.2507	5008	,	,		16334	0.0516		0.3767	False		,,,				2504	0.4202				p.P61P		Atlas-SNP	.											ZNF512B,colon,carcinoma,0,1	ZNF512B	72	1	0			c.G183A						PASS	.	T		1970,2436	616.2+/-392.7	444,1082,677	99.0	105.0	103.0		183	-4.0	0.3	20	dbSNP_86	103	3200,5400	652.4+/-400.9	603,1994,1703	no	coding-synonymous	ZNF512B	NM_020713.1		1047,3076,2380	TT,TC,CC		37.2093,44.7118,39.7509		61/893	62598815	5170,7836	2203	4300	6503	SO:0001819	synonymous_variant	57473	exon3			ACTTCCCGGGTCA	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.183G>A	20.37:g.62598815C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	139	64	0.460432	NM_020713	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	37	CCDS13548.1																																																																																			C|0.646;T|0.354	0.354	strong		0.617	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
RBBP7	5931	hgsc.bcm.edu	37	X	16887655	16887655	+	Intron	SNP	C	C	T	rs67984110		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:16887655C>T	ENST00000380087.2	-	2	377				RBBP7_ENST00000380084.4_Missense_Mutation_p.R37H|RBBP7_ENST00000404022.1_Intron			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7						cell proliferation (GO:0008283)|cellular heat acclimation (GO:0070370)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	RNA binding (GO:0003723)			biliary_tract(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	25	Hepatocellular(33;0.0997)					AGGGGCTGCGCGACCCAGTCG	0.572													C|||	989	0.261987	0.1157	0.1556	3775	,	,		10610	0.0437		0.3201	False		,,,				2504	0.3701				p.R37H		Atlas-SNP	.											.	RBBP7	58	.	0			c.G110A						PASS	.																																			SO:0001627	intron_variant	5931	exon1			GCTGCGCGACCCA	U35143	CCDS14179.1, CCDS56598.1	Xp22.22	2013-01-10	2001-11-28		ENSG00000102054	ENSG00000102054		"""WD repeat domain containing"""	9890	protein-coding gene	gene with protein product	"""G1/S transition control protein-binding protein RbAp46"", ""retinoblastoma-binding protein 7"", ""retinoblastoma-binding protein RbAp46"", ""histone acetyltransferase type B subunit 2"", ""retinoblastoma-binding protein p46"""	300825	"""retinoblastoma-binding protein 7"""			7503932	Standard	NM_002893		Approved	RbAp46	uc004cxs.2	Q16576	OTTHUMG00000021198	ENST00000380087.2:c.17-312G>A	X.37:g.16887655C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	146	138	0.945205	NM_001198719	Q5JP00	Missense_Mutation	SNP	ENST00000380087.2	37	CCDS14179.1	383	0.23086196503918022	43	0.09347826086956522	41	0.12654320987654322	10	0.017793594306049824	165	0.2796610169491525	C	15.32	2.798641	0.50208	.	.	ENSG00000102054	ENST00000380084	T	0.74106	-0.81	3.88	3.88	0.44766	.	0.540328	0.16034	N	0.232734	T	0.00012	0.0000	.	.	.	0.23978	P	0.996286	P	0.47841	0.901	B	0.26864	0.074	T	0.10200	-1.0640	8	0.59425	D	0.04	-11.0168	10.2474	0.43350	0.0:1.0:0.0:0.0	.	37	Q5JP00	.	H	37	ENSP00000369424:R37H	ENSP00000369424:R37H	R	-	2	0	RBBP7	16797576	0.004000	0.15560	0.250000	0.24296	0.009000	0.06853	1.149000	0.31626	2.173000	0.68751	0.594000	0.82650	CGC	C|0.769;T|0.231	0.231	strong		0.572	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893	
RNF213	57674	hgsc.bcm.edu	37	17	78338305	78338305	+	Silent	SNP	C	C	T	rs148958011	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78338305C>T	ENST00000582970.1	+	42	11966	c.11823C>T	c.(11821-11823)gtC>gtT	p.V3941V	RNF213_ENST00000336301.6_Silent_p.V2014V|RNF213_ENST00000508628.2_Silent_p.V3990V|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3941					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AGAGCCGCGTCCCCGAGTTAC	0.582													C|||	4	0.000798722	0.0	0.0014	5008	,	,		17383	0.0		0.001	False		,,,				2504	0.002				p.V3941V		Atlas-SNP	.											.	RNF213	766	.	0			c.C11823T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	74.0	70.0	71.0		11970	-3.7	0.0	17	dbSNP_134	71	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	RNF213	NM_020914.4		0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384		3990/5257	78338305	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon42			CCGCGTCCCCGAG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11823C>T	17.37:g.78338305C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	137	79	0.576642	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
OR6Y1	391112	hgsc.bcm.edu	37	1	158517142	158517142	+	Missense_Mutation	SNP	C	C	T	rs41273491	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:158517142C>T	ENST00000302617.3	-	1	753	c.754G>A	c.(754-756)Gtc>Atc	p.V252I		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	252						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V252I(1)		NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					AGAATTACGACGGTCAGGTGG	0.507													C|||	1009	0.201478	0.0537	0.219	5008	,	,		23681	0.377		0.2416	False		,,,				2504	0.1667				p.V252I		Atlas-SNP	.											OR6Y1,rectum,carcinoma,0,2	OR6Y1	73	2	1	Substitution - Missense(1)	large_intestine(1)	c.G754A						PASS	.	C	ILE/VAL	396,4010	197.1+/-221.3	24,348,1831	179.0	172.0	175.0		754	3.5	0.9	1	dbSNP_127	175	1985,6615	347.0+/-326.4	252,1481,2567	yes	missense	OR6Y1	NM_001005189.1	29	276,1829,4398	TT,TC,CC		23.0814,8.9877,18.3069	possibly-damaging	252/326	158517142	2381,10625	2203	4300	6503	SO:0001583	missense	391112	exon1			TTACGACGGTCAG	BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"""GPCR / Class A : Olfactory receptors"""	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.754G>A	1.37:g.158517142C>T	ENSP00000304807:p.Val252Ile	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	37	CCDS30899.1	510	0.23351648351648352	29	0.05894308943089431	74	0.20441988950276244	221	0.38636363636363635	186	0.24538258575197888	C	15.12	2.737955	0.49045	0.089877	0.230814	ENSG00000197532	ENST00000302617	T	0.00253	8.43	5.34	3.5	0.40072	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38005	N	0.001848	T	0.00144	0.0004	M	0.89030	3	0.80722	P	0.0	D	0.58620	0.983	P	0.46659	0.523	T	0.38286	-0.9668	9	0.39692	T	0.17	.	6.2283	0.20720	0.1489:0.6944:0.0:0.1567	rs41273491	252	Q8NGX8	OR6Y1_HUMAN	I	252	ENSP00000304807:V252I	ENSP00000304807:V252I	V	-	1	0	OR6Y1	156783766	0.000000	0.05858	0.894000	0.35097	0.910000	0.53928	0.454000	0.21827	0.827000	0.34685	-0.137000	0.14449	GTC	C|0.799;T|0.201	0.201	strong		0.507	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189	
TMEM132D	121256	hgsc.bcm.edu	37	12	129566469	129566469	+	Silent	SNP	C	C	T	rs77363876	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:129566469C>T	ENST00000422113.2	-	7	2084	c.1758G>A	c.(1756-1758)gaG>gaA	p.E586E	TMEM132D_ENST00000389441.4_Silent_p.E124E	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	586					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GGCCGGCCGCCTCAGCCACAA	0.647													C|||	372	0.0742812	0.0038	0.2046	5008	,	,		14998	0.1548		0.0209	False		,,,				2504	0.0491				p.E586E		Atlas-SNP	.											TMEM132D,NS,carcinoma,-2,1	TMEM132D	299	1	0			c.G1758A						PASS	.	C		23,4383	27.2+/-55.0	0,23,2180	39.0	42.0	41.0		1758	0.8	0.3	12	dbSNP_131	41	131,8467	64.2+/-126.4	1,129,4169	no	coding-synonymous	TMEM132D	NM_133448.2		1,152,6349	TT,TC,CC		1.5236,0.522,1.1843		586/1100	129566469	154,12850	2203	4299	6502	SO:0001819	synonymous_variant	121256	exon7			GGCCGCCTCAGCC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1758G>A	12.37:g.129566469C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	186	100	0.537634	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																			C|0.970;T|0.030	0.030	strong		0.647	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
RIPK4	54101	hgsc.bcm.edu	37	21	43164232	43164232	+	Silent	SNP	C	C	A	rs2277789	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:43164232C>A	ENST00000352483.2	-	8	1213	c.1149G>T	c.(1147-1149)ctG>ctT	p.L383L	AP001615.9_ENST00000423276.1_RNA|RIPK4_ENST00000332512.3_Silent_p.L335L|RIPK4_ENST00000542057.1_Silent_p.L272L|RIPK4_ENST00000544709.1_Silent_p.L272L			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	383					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GCTGTGAGAGCAGCTCGGAGA	0.642													C|||	1924	0.384185	0.233	0.4193	5008	,	,		17674	0.4772		0.4573	False		,,,				2504	0.3926				p.L335L		Atlas-SNP	.											.	RIPK4	151	.	0			c.G1005T						PASS	.	C		1194,3212		159,876,1168	19.0	23.0	22.0		1005	1.0	1.0	21	dbSNP_100	22	3526,5074		751,2024,1525	no	coding-synonymous	RIPK4	NM_020639.2		910,2900,2693	AA,AC,CC		41.0,27.0994,36.2909		335/785	43164232	4720,8286	2203	4300	6503	SO:0001819	synonymous_variant	54101	exon7			TGAGAGCAGCTCG	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.1149G>T	21.37:g.43164232C>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_020639	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				C|0.623;A|0.377	0.377	strong		0.642	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
EXO1	9156	hgsc.bcm.edu	37	1	242030151	242030151	+	Missense_Mutation	SNP	A	A	G	rs735943	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:242030151A>G	ENST00000366548.3	+	11	1654	c.1061A>G	c.(1060-1062)cAt>cGt	p.H354R	EXO1_ENST00000348581.5_Missense_Mutation_p.H354R|EXO1_ENST00000518483.1_Missense_Mutation_p.H354R	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	354	Interaction with MSH3.		H -> R (in dbSNP:rs735943). {ECO:0000269|PubMed:10364235, ECO:0000269|PubMed:9685493, ECO:0000269|PubMed:9788596, ECO:0000269|PubMed:9823303, ECO:0000269|Ref.5}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			TCAAGAAGTCATAGTTGGGAT	0.358								Editing and processing nucleases					G|||	3190	0.636981	0.615	0.6902	5008	,	,		18299	0.7956		0.5716	False		,,,				2504	0.5327				p.H354R		Atlas-SNP	.											.	EXO1	103	.	0			c.A1061G						PASS	.	G	ARG/HIS,ARG/HIS,ARG/HIS	2739,1667	506.6+/-366.4	838,1063,302	107.0	101.0	103.0		1061,1061,1061	-0.8	0.8	1	dbSNP_86	103	4641,3959	550.5+/-385.8	1275,2091,934	yes	missense,missense,missense	EXO1	NM_003686.4,NM_006027.4,NM_130398.3	29,29,29	2113,3154,1236	GG,GA,AA		46.0349,37.8348,43.257	benign,benign,benign	354/804,354/847,354/847	242030151	7380,5626	2203	4300	6503	SO:0001583	missense	9156	exon9			GAAGTCATAGTTG	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"""rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"""	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1061A>G	1.37:g.242030151A>G	ENSP00000355506:p.His354Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_006027	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	37	CCDS1620.1	1423	0.6515567765567766	294	0.5975609756097561	244	0.6740331491712708	448	0.7832167832167832	437	0.5765171503957783	G	0.007	-1.936856	0.00484	0.621652	0.539651	ENSG00000174371	ENST00000366548;ENST00000348581;ENST00000518483	T;T;T	0.34667	1.41;1.41;1.35	5.75	-0.821	0.10822	-3&apos (1); exonuclease, C-terminal domain (1);5&apos (1);	0.693627	0.15870	N	0.240566	T	0.00012	0.0000	L	0.32530	0.975	0.49798	P	1.7699999999998273E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.32666	-0.9898	9	0.12430	T	0.62	-1.583	11.7251	0.51704	0.5927:0.0:0.4073:0.0	rs735943;rs17391620;rs52795383;rs59790129;rs735943	354;354	Q9UQ84-4;Q9UQ84	.;EXO1_HUMAN	R	354	ENSP00000355506:H354R;ENSP00000311873:H354R;ENSP00000430251:H354R	ENSP00000311873:H354R	H	+	2	0	EXO1	240096774	0.989000	0.36119	0.815000	0.32552	0.291000	0.27294	0.382000	0.20635	-0.369000	0.08028	-1.088000	0.02184	CAT	T|0.001;G|0.609	0.609	strong		0.358	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027	
LMF2	91289	hgsc.bcm.edu	37	22	50943004	50943004	+	Silent	SNP	C	C	A	rs762671	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50943004C>A	ENST00000474879.2	-	11	1605	c.1590G>T	c.(1588-1590)ctG>ctT	p.L530L	LMF2_ENST00000216080.5_Silent_p.L505L|LMF2_ENST00000505981.1_5'Flank|LMF2_ENST00000380796.3_Silent_p.L417L	NM_033200.2	NP_149977.2	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	530						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|cervix(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCTTGCCCTGCAGCAGGCGCA	0.711													c|||	714	0.142572	0.1641	0.1398	5008	,	,		8644	0.0397		0.2326	False		,,,				2504	0.1288				p.L530L		Atlas-SNP	.											.	LMF2	40	.	0			c.G1590T						PASS	.	C		709,3663		64,581,1541	17.0	18.0	17.0		1590	3.3	1.0	22	dbSNP_86	17	1967,6597		231,1505,2546	no	coding-synonymous	LMF2	NM_033200.2		295,2086,4087	AA,AC,CC		22.9682,16.2168,20.6865		530/708	50943004	2676,10260	2186	4282	6468	SO:0001819	synonymous_variant	91289	exon11			GCCCTGCAGCAGG	BC002942	CCDS14093.1, CCDS14093.2	22q13.33	2008-02-04	2007-11-29	2007-11-29	ENSG00000100258	ENSG00000100258			25096	protein-coding gene	gene with protein product			"""transmembrane protein 153"", ""transmembrane protein 112B"""	TMEM153, TMEM112B		12477932	Standard	NM_033200		Approved		uc003blp.2	Q9BU23	OTTHUMG00000150206	ENST00000474879.2:c.1590G>T	22.37:g.50943004C>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_033200	A6NEZ0|Q13392|Q6ZNR2|Q8WU74|Q96C62	Silent	SNP	ENST00000474879.2	37	CCDS14093.2	344	0.1575091575091575	88	0.17886178861788618	58	0.16022099447513813	18	0.03146853146853147	180	0.23746701846965698	C	10.02	1.235038	0.22626	0.162168	0.229682	ENSG00000100258	ENST00000487499	.	.	.	5.63	3.31	0.37934	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.10177	-1.0641	3	.	.	.	-15.049	10.3398	0.43870	0.1435:0.7748:0.0:0.0817	rs762671;rs57346067	.	.	.	S	537	.	.	A	-	1	0	LMF2	49289870	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.217000	0.42880	1.351000	0.45789	0.643000	0.83706	GCA	C|0.815;A|0.185	0.185	strong		0.711	LMF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316833.2	NM_033200	
DOCK2	1794	hgsc.bcm.edu	37	5	169504743	169504743	+	Silent	SNP	T	T	C	rs1045168	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:169504743T>C	ENST00000256935.8	+	48	4976	c.4896T>C	c.(4894-4896)cgT>cgC	p.R1632R	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Silent_p.R693R|DOCK2_ENST00000520908.1_Silent_p.R1124R	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1632					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.R1632R(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAGTGGGCCGTCCCAGGTCTA	0.577													C|||	1458	0.291134	0.3782	0.2579	5008	,	,		15757	0.1071		0.334	False		,,,				2504	0.3425				p.R1632R		Atlas-SNP	.											DOCK2,NS,carcinoma,0,3	DOCK2	389	3	1	Substitution - coding silent(1)	stomach(1)	c.T4896C						scavenged	.	C		1660,2746	658.5+/-400.4	303,1054,846	132.0	119.0	124.0		4896	-5.4	0.9	5	dbSNP_86	124	2650,5950	685.7+/-404.1	414,1822,2064	no	coding-synonymous	DOCK2	NM_004946.2		717,2876,2910	CC,CT,TT		30.814,37.6759,33.1386		1632/1831	169504743	4310,8696	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon48			GGGCCGTCCCAGG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4896T>C	5.37:g.169504743T>C		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			A|0.000;C|0.311;T|0.689	0.311	strong		0.577	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
RBMXL3	139804	hgsc.bcm.edu	37	X	114425923	114425923	+	Missense_Mutation	SNP	C	C	A	rs142223554		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:114425923C>A	ENST00000424776.3	+	1	1961	c.1919C>A	c.(1918-1920)gCc>gAc	p.A640D	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	640	Gly-rich.			A -> D (in Ref. 1; AK097568). {ECO:0000305}.			nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						TCCCTTGATGCCAACAGTGGA	0.657													C|||	220	0.0582781	0.0038	0.0533	3775	,	,		14344	0.002		0.1123	False		,,,				2504	0.0644				p.A640D		Atlas-SNP	.											.	RBMXL3	83	.	0			c.C1919A						PASS	.	C	ASP/ALA,	34,1175		1,25,7,491,168	52.0	53.0	53.0		1919,		0.0	X	dbSNP_134	53	391,2000		18,215,140,567,651	no	missense,intron	LRCH2,RBMXL3	NM_001145346.1,NM_020871.3	126,	19,240,147,1058,819	AA,AC,A,CC,C		16.353,2.8122,11.8056	possibly-damaging,	640/1068,	114425923	425,3175	692	1591	2283	SO:0001583	missense	139804	exon1			TTGATGCCAACAG	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.1919C>A	X.37:g.114425923C>A	ENSP00000417451:p.Ala640Asp	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	187	167	0.893048	NM_001145346	B4DXC0	Missense_Mutation	SNP	ENST00000424776.3	37	CCDS55478.1	117	0.0705244122965642	3	0.006122448979591836	20	0.056179775280898875	2	0.0034965034965034965	53	0.07703488372093023	C	9.422	1.083366	0.20309	0.028122	0.16353	ENSG00000175718	ENST00000424776	T	0.05717	3.4	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.52842	0.956	B	0.39465	0.3	T	0.50118	-0.8865	6	0.87932	D	0	.	.	.	.	.	640	Q8N7X1	RMXL3_HUMAN	D	640	ENSP00000417451:A640D	ENSP00000417451:A640D	A	+	2	0	RBMXL3	114332179	0.002000	0.14202	0.004000	0.12327	0.004000	0.04260	0.148000	0.16224	0.108000	0.17862	0.110000	0.15639	GCC	C|0.930;A|0.070	0.070	strong		0.657	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
OTOGL	283310	hgsc.bcm.edu	37	12	80750659	80750659	+	Missense_Mutation	SNP	G	G	A	rs11836060	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:80750659G>A	ENST00000547103.1	+	48	5927	c.5921G>A	c.(5920-5922)cGa>cAa	p.R1974Q	OTOGL_ENST00000546620.1_Missense_Mutation_p.R5Q|OTOGL_ENST00000458043.2_Missense_Mutation_p.R1986Q			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1974	Cys-rich.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						ATTCAAGTTCGACAGGAAGAA	0.348													A|||	859	0.171526	0.1838	0.2075	5008	,	,		13699	0.0506		0.1819	False		,,,				2504	0.2434				p.R1986Q		Atlas-SNP	.											.	OTOGL	235	.	0			c.G5957A						PASS	.	A	GLN/ARG	823,3583	747.6+/-411.9	74,675,1454	110.0	98.0	102.0		5957	4.1	1.0	12	dbSNP_120	102	1690,6910	738.1+/-407.0	170,1350,2780	yes	missense	OTOGL	NM_173591.3	43	244,2025,4234	AA,AG,GG		19.6512,18.6791,19.3219	benign	1986/2345	80750659	2513,10493	2203	4300	6503	SO:0001583	missense	283310	exon48			AAGTTCGACAGGA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5921G>A	12.37:g.80750659G>A	ENSP00000447211:p.Arg1974Gln	Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	185	92	0.497297	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		324|324	0.14835164835164835|0.14835164835164835	86|86	0.17479674796747968|0.17479674796747968	75|75	0.20718232044198895|0.20718232044198895	27|27	0.0472027972027972|0.0472027972027972	136|136	0.17941952506596306|0.17941952506596306	A|A	13.96|13.96	2.393127|2.393127	0.42410|0.42410	0.186791|0.186791	0.196512|0.196512	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182	.|T;T;T;T	.|0.28454	.|1.61;1.61;1.61;1.61	5.36|5.36	4.06|4.06	0.47325|0.47325	.|.	.|0.264710	.|0.30244	.|N	.|0.010074	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.13168|0.13168	0.305|0.305	0.48830|0.48830	P|P	2.9000000000001247E-4|2.9000000000001247E-4	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.37641|0.37641	-0.9697|-0.9697	4|9	.|0.15952	.|T	.|0.53	.|.	7.6258|7.6258	0.28212|0.28212	0.7196:0.0:0.2804:0.0|0.7196:0.0:0.2804:0.0	rs11836060;rs17309026;rs52804264;rs60470781;rs11836060|rs11836060;rs17309026;rs52804264;rs60470781;rs11836060	.|351	.|Q3ZCN5	.|OTOGL_HUMAN	N|Q	429|1974;1986;5;3	.|ENSP00000447211:R1974Q;ENSP00000400895:R1986Q;ENSP00000449094:R5Q;ENSP00000449641:R3Q	.|ENSP00000400895:R1986Q	D|R	+|+	1|2	0|0	OTOGL|OTOGL	79274790|79274790	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.988000|0.988000	0.76386|0.76386	3.251000|3.251000	0.51453|0.51453	0.253000|0.253000	0.21552|0.21552	-0.381000|-0.381000	0.06696|0.06696	GAC|CGA	G|0.823;A|0.177	0.177	strong		0.348	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
MOV10L1	54456	hgsc.bcm.edu	37	22	50558946	50558946	+	Silent	SNP	A	A	G	rs71316583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50558946A>G	ENST00000262794.5	+	10	1553	c.1470A>G	c.(1468-1470)caA>caG	p.Q490Q	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Silent_p.Q490Q|MOV10L1_ENST00000540615.1_Silent_p.Q470Q|MOV10L1_ENST00000545383.1_Silent_p.Q490Q	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	490					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		CAAGACGACAACTTCCAAGTT	0.353													A|||	123	0.0245607	0.003	0.0389	5008	,	,		21643	0.0		0.0696	False		,,,				2504	0.0225				p.Q490Q		Atlas-SNP	.											.	MOV10L1	238	.	0			c.A1470G						PASS	.	A	,,	55,4351	54.2+/-90.2	2,51,2150	101.0	102.0	102.0		1470,1410,1470	-6.0	0.9	22	dbSNP_130	102	592,8008	158.3+/-211.8	17,558,3725	no	coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	19,609,5875	GG,GA,AA		6.8837,1.2483,4.9746	,,	490/1166,470/1166,490/1212	50558946	647,12359	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon10			ACGACAACTTCCA	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1470A>G	22.37:g.50558946A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	74	47	0.635135	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			A|0.954;G|0.046	0.046	strong		0.353	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
SLK	9748	hgsc.bcm.edu	37	10	105758670	105758670	+	Silent	SNP	A	A	G	rs10883960	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:105758670A>G	ENST00000369755.3	+	5	1073	c.528A>G	c.(526-528)gtA>gtG	p.V176V	SLK_ENST00000335753.4_Silent_p.V176V	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		ATTTTGGAGTATCAGCTAAAA	0.308													A|||	837	0.167133	0.0802	0.2147	5008	,	,		18987	0.1389		0.2256	False		,,,				2504	0.2198				p.V176V	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.A528G						PASS	.	A		510,3894	232.3+/-245.9	36,438,1728	92.0	94.0	93.0		528	-2.2	1.0	10	dbSNP_120	93	2067,6531	357.0+/-330.6	232,1603,2464	no	coding-synonymous	SLK	NM_014720.2		268,2041,4192	GG,GA,AA		24.0405,11.5804,19.82		176/1236	105758670	2577,10425	2202	4299	6501	SO:0001819	synonymous_variant	9748	exon5			TGGAGTATCAGCT		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"""SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)"", ""STE20-like kinase (yeast)"""			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.528A>G	10.37:g.105758670A>G		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	104	102	0.980769	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Silent	SNP	ENST00000369755.3	37	CCDS7553.1																																																																																			A|0.817;G|0.183	0.183	strong		0.308	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
NDUFAF1	51103	hgsc.bcm.edu	37	15	41679685	41679685	+	Missense_Mutation	SNP	G	G	C	rs12900702	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:41679685G>C	ENST00000260361.4	-	5	1322	c.941C>G	c.(940-942)gCc>gGc	p.A314G		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	314			A -> G (in dbSNP:rs12900702). {ECO:0000269|PubMed:11935339}.		mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		ATTTTCATAGGCAAATTCTTC	0.358													G|||	361	0.0720847	0.0121	0.111	5008	,	,		15415	0.0		0.1849	False		,,,				2504	0.0838				p.A314G		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.C941G						PASS	.	G	GLY/ALA	163,4243	108.2+/-146.6	5,153,2045	78.0	87.0	84.0		941	5.6	1.0	15	dbSNP_121	84	1634,6966	299.4+/-304.4	153,1328,2819	yes	missense	NDUFAF1	NM_016013.2	60	158,1481,4864	CC,CG,GG		19.0,3.6995,13.8167	probably-damaging	314/328	41679685	1797,11209	2203	4300	6503	SO:0001583	missense	51103	exon5			TCATAGGCAAATT	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"""Mitochondrial respiratory chain complex assembly factors"""	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.941C>G	15.37:g.41679685G>C	ENSP00000260361:p.Ala314Gly	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	63	57	0.904762	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	37	CCDS10075.1	193	0.08836996336996338	5	0.01016260162601626	47	0.1298342541436464	0	0.0	141	0.18601583113456466	G	32	5.189559	0.94923	0.036995	0.19	ENSG00000137806	ENST00000260361	T	0.65178	-0.14	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.00271	0.0008	M	0.71871	2.18	0.09310	P	0.99999999756846	P	0.52316	0.952	P	0.51895	0.683	T	0.00403	-1.1761	9	0.72032	D	0.01	-22.3975	19.5923	0.95520	0.0:0.0:1.0:0.0	rs12900702;rs52792714;rs12900702	314	Q9Y375	CIA30_HUMAN	G	314	ENSP00000260361:A314G	ENSP00000260361:A314G	A	-	2	0	NDUFAF1	39466977	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.859000	0.92264	2.644000	0.89710	0.557000	0.71058	GCC	G|0.873;C|0.127	0.127	strong		0.358	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
NDUFV3	4731	hgsc.bcm.edu	37	21	44323461	44323461	+	Intron	SNP	G	G	A	rs4148972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:44323461G>A	ENST00000340344.4	+	3	235				NDUFV3_ENST00000354250.2_Silent_p.P113P|NDUFV3_ENST00000460259.1_3'UTR	NM_001001503.1	NP_001001503.1	P56181	NDUV3_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	10				STAD - Stomach adenocarcinoma(101;0.0606)		AAGGGGTTCCGAAATTTTTGT	0.488													G|||	495	0.0988419	0.0484	0.0648	5008	,	,		18172	0.1746		0.0616	False		,,,				2504	0.1513				p.P113P		Atlas-SNP	.											.	NDUFV3	23	.	0			c.G339A						PASS	.	G	,	202,4204	125.7+/-162.9	4,194,2005	123.0	135.0	131.0		,339	-1.0	0.0	21	dbSNP_110	131	547,8053	150.1+/-205.1	17,513,3770	no	intron,coding-synonymous	NDUFV3	NM_001001503.1,NM_021075.3	,	21,707,5775	AA,AG,GG		6.3605,4.5847,5.7589	,	,113/474	44323461	749,12257	2203	4300	6503	SO:0001627	intron_variant	4731	exon3			GGTTCCGAAATTT		CCDS33572.1, CCDS33573.1	21q22.3	2011-07-04	2002-08-29		ENSG00000160194	ENSG00000160194	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7719	protein-coding gene	gene with protein product	"""complex I 10kDa subunit"""	602184	"""NADH dehydrogenase (ubiquinone) flavoprotein 3 (10kD)"""			9344673	Standard	NM_021075		Approved	CI-10k	uc002zcm.3	P56181	OTTHUMG00000086823	ENST00000340344.4:c.170-5513G>A	21.37:g.44323461G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_021075	A8K0M1|J3KNX7|Q6FGD3|Q8WU60|Q9HCR5	Silent	SNP	ENST00000340344.4	37	CCDS33573.1																																																																																			G|0.930;A|0.070	0.070	strong		0.488	NDUFV3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195448.2		
FCGR3A	2214	hgsc.bcm.edu	37	1	161512873	161512873	+	Missense_Mutation	SNP	T	T	A	rs115866423	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:161512873T>A	ENST00000436743.1	-	6	848	c.694A>T	c.(694-696)Aac>Tac	p.N232Y	RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000476031.1_5'Flank|FCGR3A_ENST00000443193.1_Missense_Mutation_p.N267Y|FCGR3A_ENST00000367969.3_Missense_Mutation_p.N268Y|FCGR3A_ENST00000540048.1_Missense_Mutation_p.N232Y	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	232					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTTCGAATGTTTGTCTTCACA	0.443													T|||	29	0.00579073	0.0	0.0086	5008	,	,		22717	0.0		0.0099	False		,,,				2504	0.0133				p.N268Y		Atlas-SNP	.											.	FCGR3A	38	.	0			c.A802T						PASS	.	T	TYR/ASN,TYR/ASN,TYR/ASN,TYR/ASN,TYR/ASN	11,4395	19.1+/-41.9	0,11,2192	151.0	149.0	150.0		691,694,694,799,802	-2.9	0.0	1	dbSNP_132	150	100,8500	56.4+/-117.6	2,96,4202	no	missense,missense,missense,missense,missense	FCGR3A	NM_001127596.1,NM_001127595.1,NM_001127593.1,NM_001127592.1,NM_000569.6	143,143,143,143,143	2,107,6394	AA,AT,TT		1.1628,0.2497,0.8535	benign,benign,benign,benign,benign	231/254,232/255,232/255,267/290,268/291	161512873	111,12895	2203	4300	6503	SO:0001583	missense	2214	exon5			GAATGTTTGTCTT	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000436743.1:c.694A>T	1.37:g.161512873T>A	ENSP00000416607:p.Asn232Tyr	Somatic	417	0	0		WXS	Illumina HiSeq	Phase_I	407	196	0.481572	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	7|7	0.009234828496042216|0.009234828496042216	T|T	9.319|9.319	1.057646|1.057646	0.19907|0.19907	0.002497|0.002497	0.011628|0.011628	ENSG00000203747|ENSG00000203747	ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048|ENST00000426740	T;T;T;T;T|.	0.01484|.	4.84;4.84;4.89;4.89;4.89|.	3.88|3.88	-2.9|-2.9	0.05648|0.05648	.|.	14.258800|.	0.00166|.	U|.	0.000000|.	T|T	0.12860|0.12860	0.0312|0.0312	L|L	0.38175|0.38175	1.15|1.15	0.09310|0.09310	N|N	1|1	B;P;P|.	0.37864|.	0.087;0.61;0.49|.	B;B;B|.	0.31812|.	0.029;0.101;0.136|.	T|T	0.33979|0.33979	-0.9847|-0.9847	10|5	0.66056|.	D|.	0.02|.	.|.	4.9176|4.9176	0.13853|0.13853	0.0:0.3545:0.157:0.4885|0.0:0.3545:0.157:0.4885	.|.	232;267;232|.	P08637;E9PG94;Q9UPY7|.	FCG3A_HUMAN;.;.|.	Y|H	268;267;232;232;232|248	ENSP00000356946:N268Y;ENSP00000392047:N267Y;ENSP00000416607:N232Y;ENSP00000356944:N232Y;ENSP00000444971:N232Y|.	ENSP00000356944:N232Y|.	N|Q	-|-	1|3	0|2	FCGR3A|FCGR3A	159779497|159779497	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-1.623000|-1.623000	0.02040|0.02040	-0.510000|-0.510000	0.06523|0.06523	0.482000|0.482000	0.46254|0.46254	AAC|CAA	T|0.993;A|0.007	0.007	strong		0.443	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
CD163L1	283316	hgsc.bcm.edu	37	12	7585247	7585247	+	Silent	SNP	T	T	C	rs58195891	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7585247T>C	ENST00000313599.3	-	4	588	c.531A>G	c.(529-531)ggA>ggG	p.G177G	CD163L1_ENST00000416109.2_Silent_p.G187G|CD163L1_ENST00000396630.1_Silent_p.G177G			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	177	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CACATATAGTTCCCCACCTTT	0.458													C|||	3034	0.605831	0.8843	0.5706	5008	,	,		-128	0.6409		0.3221	False		,,,				2504	0.5102				p.G177G		Atlas-SNP	.											.	CD163L1	238	.	0			c.A531G						PASS	.	C		3455,951	360.6+/-315.3	1371,713,119	121.0	110.0	113.0		531	1.3	0.0	12	dbSNP_129	113	2589,6011	689.8+/-404.4	397,1795,2108	no	coding-synonymous	CD163L1	NM_174941.4		1768,2508,2227	CC,CT,TT		30.1047,21.5842,46.4709		177/1454	7585247	6044,6962	2203	4300	6503	SO:0001819	synonymous_variant	283316	exon4			TATAGTTCCCCAC	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.531A>G	12.37:g.7585247T>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	222	106	0.477477	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																			T|0.523;C|0.477	0.477	strong		0.458	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
FSIP2	401024	hgsc.bcm.edu	37	2	186671256	186671256	+	Silent	SNP	T	T	C	rs17826498	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:186671256T>C	ENST00000424728.1	+	17	17223	c.17223T>C	c.(17221-17223)aaT>aaC	p.N5741N	FSIP2_ENST00000343098.5_Silent_p.N5830N			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5741										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						CTAACAAAAATATCTCTGCCA	0.378													T|||	39	0.00778754	0.0023	0.0101	5008	,	,		17132	0.001		0.0229	False		,,,				2504	0.0051				p.N5830N		Atlas-SNP	.											.	FSIP2	251	.	0			c.T17490C						PASS	.	T		16,3594		0,16,1789	53.0	49.0	50.0		17490	0.7	0.0	2	dbSNP_123	50	242,7898		4,234,3832	no	coding-synonymous	FSIP2	NM_173651.2		4,250,5621	CC,CT,TT		2.973,0.4432,2.1957		5830/6997	186671256	258,11492	1805	4070	5875	SO:0001819	synonymous_variant	401024	exon17			CAAAAATATCTCT	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.17223T>C	2.37:g.186671256T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	120	67	0.558333	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Silent	SNP	ENST00000424728.1	37																																																																																				T|0.985;C|0.015	0.015	strong		0.378	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
OR4N2	390429	hgsc.bcm.edu	37	14	20295778	20295778	+	Silent	SNP	C	C	A	rs11621883	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20295778C>A	ENST00000315947.1	+	1	171	c.171C>A	c.(169-171)gcC>gcA	p.A57A	OR4N2_ENST00000568211.1_Silent_p.A57A	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	57						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GGCTCACAGCCCCCCTCTATT	0.473													.|||	1054	0.210463	0.2769	0.1657	5008	,	,		26389	0.1161		0.2107	False		,,,				2504	0.2495				p.A57A		Atlas-SNP	.											.	OR4N2	125	.	0			c.C171A						PASS	.	C		106,4300		30,46,2127	178.0	214.0	202.0		171	-5.2	0.1	14	dbSNP_120	202	130,8466		39,52,4207	no	coding-synonymous	OR4N2	NM_001004723.1		69,98,6334	AA,AC,CC		1.5123,2.4058,1.8151		57/308	20295778	236,12766	2203	4298	6501	SO:0001819	synonymous_variant	390429	exon1			CACAGCCCCCCTC		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.171C>A	14.37:g.20295778C>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	203	197	0.970443	NM_001004723	Q6IEY9|Q6IFA2	Silent	SNP	ENST00000315947.1	37	CCDS32022.1																																																																																			A|0.114;C|0.886;T|0.000	0.114	strong		0.473	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557510	32557510	+	Silent	SNP	G	G	A	rs201125976	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32557510G>A	ENST00000360004.5	-	1	115	c.10C>T	c.(10-12)Ctg>Ttg	p.L4L		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	4					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GGGAGCTTCAGACACACCATG	0.572										Multiple Myeloma(14;0.17)			G|||	113	0.0225639	0.0386	0.0245	5008	,	,		24903	0.0099		0.0288	False		,,,				2504	0.0061				p.L4L		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C10T						PASS	.						75.0	89.0	84.0					6																	32557510		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon1			GCTTCAGACACAC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.10C>T	6.37:g.32557510G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	233	25	0.107296	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.981;A|0.019	0.019	strong		0.572	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
GOT1L1	137362	hgsc.bcm.edu	37	8	37797467	37797467	+	Silent	SNP	A	A	G	rs151011886	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:37797467A>G	ENST00000307599.4	-	1	180	c.81T>C	c.(79-81)gaT>gaC	p.D27D		NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	glutamic-oxaloacetic transaminase 1-like 1	27					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)	cytoplasm (GO:0005737)	pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)			TCGGGTAATCATCTTGTTTGT	0.458													A|||	4	0.000798722	0.0	0.0	5008	,	,		21029	0.0		0.003	False		,,,				2504	0.001				p.D27D		Atlas-SNP	.											.	GOT1L1	87	.	0			c.T81C						PASS	.	A		2,3874		0,2,1936	141.0	127.0	132.0		81	-10.2	0.0	8	dbSNP_134	132	35,8205		0,35,4085	no	coding-synonymous	GOT1L1	NM_152413.2		0,37,6021	GG,GA,AA		0.4248,0.0516,0.3054		27/422	37797467	37,12079	1938	4120	6058	SO:0001819	synonymous_variant	137362	exon1			GTAATCATCTTGT	BC029504	CCDS47839.1	8p12	2005-09-22			ENSG00000169154	ENSG00000169154			28487	protein-coding gene	gene with protein product						12477932	Standard	NM_152413		Approved	MGC33309	uc011lbj.1	Q8NHS2	OTTHUMG00000164027	ENST00000307599.4:c.81T>C	8.37:g.37797467A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	196	96	0.489796	NM_152413	A8MWL4	Silent	SNP	ENST00000307599.4	37	CCDS47839.1																																																																																			A|0.999;G|0.001	0.001	strong		0.458	GOT1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376823.1	NM_152413	
IARS	3376	hgsc.bcm.edu	37	9	94985637	94985637	+	Missense_Mutation	SNP	T	T	C	rs556155	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:94985637T>C	ENST00000375643.3	-	32	3810	c.3544A>G	c.(3544-3546)Aag>Gag	p.K1182E	IARS_ENST00000443024.2_Missense_Mutation_p.K1182E|IARS_ENST00000447699.2_Missense_Mutation_p.K1072E|IARS_ENST00000375629.3_3'UTR	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	1182			K -> E (in dbSNP:rs556155). {ECO:0000269|PubMed:17974005}.		gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)	p.K1182Q(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	CCTTGTGGCTTTGCATTCAGG	0.453													C|||	804	0.160543	0.0537	0.1988	5008	,	,		18188	0.121		0.1461	False		,,,				2504	0.3333				p.K1182E		Atlas-SNP	.											IARS,rectum,carcinoma,0,1	IARS	74	1	1	Substitution - Missense(1)	large_intestine(1)	c.A3544G						PASS	.	C	GLU/LYS,GLU/LYS	321,4085	797.7+/-415.4	12,297,1894	112.0	104.0	107.0		3544,3544	2.6	0.2	9	dbSNP_83	107	1391,7209	754.2+/-407.5	105,1181,3014	yes	missense,missense	IARS	NM_002161.4,NM_013417.2	56,56	117,1478,4908	CC,CT,TT		16.1744,7.2855,13.1632	benign,benign	1182/1263,1182/1263	94985637	1712,11294	2203	4300	6503	SO:0001583	missense	3376	exon32			GTGGCTTTGCATT	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"""Aminoacyl tRNA synthetases / Class I"""	5330	protein-coding gene	gene with protein product	"""isoleucine tRNA ligase 1, cytoplasmic"""	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.3544A>G	9.37:g.94985637T>C	ENSP00000364794:p.Lys1182Glu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	37	CCDS6694.1	269	0.12316849816849818	23	0.046747967479674794	63	0.17403314917127072	69	0.12062937062937062	114	0.1503957783641161	C	2.687	-0.274075	0.05679	0.072855	0.161744	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000543028;ENST00000447699;ENST00000375660;ENST00000421189	T;T;T	0.43688	0.94;0.94;0.94	5.86	2.58	0.30949	.	0.608943	0.19546	N	0.111689	T	0.00039	0.0001	N	0.02802	-0.49	0.53688	P	2.2999999999995246E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.0	T	0.23511	-1.0186	9	0.06625	T	0.88	-1.4842	6.5975	0.22683	0.0:0.5393:0.0:0.4607	rs556155;rs2070054;rs2230406;rs59750466;rs556155	692;1182;975	F5H1M4;P41252;Q6P0M4	.;SYIC_HUMAN;.	E	1182;1182;191;1072;1182;191	ENSP00000364794:K1182E;ENSP00000406448:K1182E;ENSP00000415020:K1072E	ENSP00000364794:K1182E	K	-	1	0	IARS	94025458	0.997000	0.39634	0.173000	0.22940	0.714000	0.41099	0.383000	0.20651	0.499000	0.27970	-0.128000	0.14901	AAG	A|0.007;C|0.130	0.130	strong		0.453	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161	
MUC1	4582	hgsc.bcm.edu	37	1	155161794	155161794	+	Silent	SNP	C	C	T	rs147048677	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:155161794C>T	ENST00000368395.1	-	2	410	c.339G>A	c.(337-339)ccG>ccA	p.P113P	MUC1_ENST00000438413.1_Intron|MUC1_ENST00000368396.4_Intron|MUC1_ENST00000457295.2_Intron|MUC1_ENST00000368392.3_Intron|MUC1_ENST00000342482.4_Intron|RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000462215.1_Intron|MUC1_ENST00000368389.2_Intron|MUC1_ENST00000343256.5_Intron|MUC1_ENST00000368398.3_Intron|MUC1_ENST00000368390.3_Intron|MUC1_ENST00000368393.3_Intron|MUC1_ENST00000338684.5_Intron|MUC1_ENST00000337604.5_Intron	NM_001204285.1|NM_001204286.1	NP_001191214.1|NP_001191215.1	P15941	MUC1_HUMAN	mucin 1, cell surface associated	893					cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription by competitive promoter binding (GO:0010944)|O-glycan processing (GO:0016266)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|post-translational protein modification (GO:0043687)|regulation of transcription from RNA polymerase II promoter in response to stress (GO:0043618)|response to hypoxia (GO:0001666)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|nuclear chromatin (GO:0000790)|vesicle (GO:0031982)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|skin(2)	10	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CGTGGGCTGGCGGGGTGGTGG	0.721			T	IGH@	B-NHL								C|||	129	0.0257588	0.0038	0.0389	5008	,	,		9243	0.0109		0.0457	False		,,,				2504	0.0409				p.P122P		Atlas-SNP	.		Dom	yes		1	1q21	4582	"""mucin 1, transmembrane"""		L	.	MUC1	94	.	0			c.G366A						PASS	.																																			SO:0001819	synonymous_variant	4582	exon2			GGCTGGCGGGGTG	J05581	CCDS1098.1, CCDS30882.1, CCDS30883.1, CCDS41408.1, CCDS41409.1, CCDS55640.1, CCDS55641.1, CCDS55642.1, CCDS55640.2, CCDS72933.1, CCDS72934.1, CCDS72935.1, CCDS72936.1	1q22	2014-01-31	2006-03-14		ENSG00000185499	ENSG00000185499		"""CD molecules"", ""Mucins"""	7508	protein-coding gene	gene with protein product		158340	"""mucin 1, transmembrane"", ""medullary cystic kidney disease 1 (autosomal dominant)"""	PUM, MCKD1		1697589, 23396133	Standard	NM_002456		Approved	CD227, PEM, ADMCKD, ADMCKD1, MCKD, MCD	uc031ppv.1	P15941	OTTHUMG00000035681	ENST00000368395.1:c.339G>A	1.37:g.155161794C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	28	12	0.428571	NM_001204286	A5YRV1|A6ZID9|A6ZIE0|B1AVQ8|B1AVR0|B6ECA1|E7ESE5|E7EUG9|P13931|P15942|P17626|Q0VAP5|Q0VAP6|Q14128|Q14876|Q16437|Q16442|Q16615|Q6S4Y3|Q7Z547|Q7Z548|Q7Z550|Q7Z552|Q9BXA4|Q9UE75|Q9UE76|Q9UQL1|Q9Y4J2	Silent	SNP	ENST00000368395.1	37	CCDS55640.1																																																																																			C|0.971;T|0.029	0.029	strong		0.721	MUC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086735.1	NM_002456	
PKD1L1	168507	hgsc.bcm.edu	37	7	47854956	47854956	+	Silent	SNP	C	C	T	rs17545564	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:47854956C>T	ENST00000289672.2	-	47	7115	c.7065G>A	c.(7063-7065)ccG>ccA	p.P2355P	C7orf69_ENST00000258776.4_Intron|C7orf69_ENST00000418326.2_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2355					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CACGGGCTGACGGGGTGCCTC	0.557													c|||	739	0.147564	0.0174	0.2017	5008	,	,		18335	0.2153		0.173	False		,,,				2504	0.1892				p.P2355P		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G7065A						PASS	.	C	,	222,4184	132.5+/-169.0	4,214,1985	59.0	56.0	57.0		,7065	-7.9	0.0	7	dbSNP_123	57	1338,7262	262.5+/-284.5	96,1146,3058	no	intron,coding-synonymous	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,	100,1360,5043	TT,TC,CC		15.5581,5.0386,11.9945	,	,2355/2850	47854956	1560,11446	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon47			GGCTGACGGGGTG	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.7065G>A	7.37:g.47854956C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			C|0.867;T|0.133	0.133	strong		0.557	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
RNF20	56254	hgsc.bcm.edu	37	9	104309445	104309445	+	Silent	SNP	T	T	C	rs2273976	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:104309445T>C	ENST00000389120.3	+	8	1011	c.921T>C	c.(919-921)taT>taC	p.Y307Y	AL591377.1_ENST00000584534.1_RNA	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	307					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		ATAAGGTGTATGGAGCGGGGA	0.413													T|||	551	0.110024	0.0847	0.1513	5008	,	,		20243	0.1111		0.1461	False		,,,				2504	0.0767				p.Y307Y		Atlas-SNP	.											.	RNF20	110	.	0			c.T921C						PASS	.	T		437,3969	209.8+/-230.5	17,403,1783	128.0	122.0	124.0		921	0.6	1.0	9	dbSNP_100	124	1389,7211	269.8+/-288.6	118,1153,3029	no	coding-synonymous	RNF20	NM_019592.5		135,1556,4812	CC,CT,TT		16.1512,9.9183,14.0397		307/976	104309445	1826,11180	2203	4300	6503	SO:0001819	synonymous_variant	56254	exon8			GGTGTATGGAGCG	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"""RING-type (C3HC4) zinc fingers"""	10062	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"""	607699	"""ring finger protein 20"""			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.921T>C	9.37:g.104309445T>C		Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	215	106	0.493023	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Silent	SNP	ENST00000389120.3	37	CCDS35084.1																																																																																			T|0.867;C|0.133	0.133	strong		0.413	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592	
PPP3CC	5533	hgsc.bcm.edu	37	8	22390522	22390522	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22390522A>G	ENST00000240139.5	+	12	1639	c.1312A>G	c.(1312-1314)Atc>Gtc	p.I438V	PPP3CC_ENST00000397775.3_Missense_Mutation_p.I447V|PPP3CC_ENST00000289963.8_Missense_Mutation_p.I438V	NM_005605.4	NP_005596.2	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma isozyme	438					apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		CAAGCAGACTATCGAGACAGG	0.542																																					p.I447V		Atlas-SNP	.											.	PPP3CC	39	.	0			c.A1339G						PASS	.						84.0	66.0	72.0					8																	22390522		2203	4300	6503	SO:0001583	missense	5533	exon13			CAGACTATCGAGA		CCDS34859.1, CCDS59094.1, CCDS59093.1	8p21.3	2010-03-17	2010-03-05		ENSG00000120910	ENSG00000120910	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9316	protein-coding gene	gene with protein product	"""calcineurin A gamma"", ""protein phosphatase 2B, catalytic subunit, gamma isoform"""	114107	"""protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform (calcineurin A gamma)"", ""protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform"""			1339277	Standard	NM_005605		Approved	CALNA3, PP2Bgamma	uc011kzi.2	P48454	OTTHUMG00000163802	ENST00000240139.5:c.1312A>G	8.37:g.22390522A>G	ENSP00000240139:p.Ile438Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	103	48	0.466019	NM_001243974	B4DRT5|Q9BSS6|Q9H4M5	Missense_Mutation	SNP	ENST00000240139.5	37	CCDS34859.1	.	.	.	.	.	.	.	.	.	.	A	8.509	0.866175	0.17250	.	.	ENSG00000120910	ENST00000240139;ENST00000289963;ENST00000397775	T;T;T	0.05382	3.45;3.45;3.45	5.74	1.72	0.24424	.	0.185247	0.47455	D	0.000236	T	0.04588	0.0125	N	0.15975	0.35	0.34146	D	0.667017	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.12837	0.004;0.008;0.005	T	0.18745	-1.0327	10	0.45353	T	0.12	-16.5588	13.6583	0.62352	0.386:0.614:0.0:0.0	.	447;438;438	B4DRT5;P48454-2;P48454	.;.;PP2BC_HUMAN	V	438;438;447	ENSP00000240139:I438V;ENSP00000289963:I438V;ENSP00000380878:I447V	ENSP00000240139:I438V	I	+	1	0	PPP3CC	22446467	0.826000	0.29277	0.849000	0.33467	0.006000	0.05464	1.656000	0.37355	0.401000	0.25424	-0.313000	0.08912	ATC	.	.	none		0.542	PPP3CC-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375652.1	NM_005605	
Unknown	0	hgsc.bcm.edu	37	11	5989180	5989180	+	IGR	SNP	C	C	T	rs147979628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5989180C>T								OR56A3 (19589 upstream) : OR52L1 (17941 downstream)																							CACGTTAGTACAGATGCAGTT	0.458													.|||	6	0.00119808	0.0	0.0	5008	,	,		23124	0.0		0.006	False		,,,				2504	0.0				p.C182Y		Atlas-SNP	.											.	.	.	.	0			c.G545A						PASS	.	C	TYR/CYS	0,1384		0,0,692	105.0	86.0	92.0		545	2.9	0.9	11	dbSNP_134	92	7,3175		0,7,1584	yes	missense	OR56A5	NM_001146033.1	194	0,7,2276	TT,TC,CC		0.22,0.0,0.1533	possibly-damaging	182/314	5989180	7,4559	692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			TTAGTACAGATGC																													11.37:g.5989180C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_001146033		Missense_Mutation	SNP		37																																																																																				C|0.998;T|0.002	0.002	strong	0	0.458								
TCEAL4	79921	hgsc.bcm.edu	37	X	102842041	102842041	+	Silent	SNP	T	T	C	rs11010	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:102842041T>C	ENST00000472745.1	+	3	990	c.438T>C	c.(436-438)caT>caC	p.H146H	TCEAL4_ENST00000372629.4_Silent_p.H289H|TCEAL4_ENST00000415568.2_Silent_p.H146H|TCEAL4_ENST00000468024.1_Silent_p.H146H|TCEAL4_ENST00000472484.1_Silent_p.H146H|TCEAL4_ENST00000494801.1_Silent_p.H146H			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|skin(2)	6						AGGCCATACATGATATGAATT	0.423													C|||	977	0.258808	0.357	0.1686	3775	,	,		16721	0.0308		0.2515	False		,,,				2504	0.1063				p.H146H		Atlas-SNP	.											.	TCEAL4	18	.	0			c.T438C						PASS	.	C	,,	1737,2098		333,820,251,479,320	122.0	125.0	124.0		438,438,438	-8.0	0.0	X	dbSNP_52	124	2459,4269		343,1084,689,1001,1183	no	coding-synonymous,coding-synonymous,coding-synonymous	TCEAL4	NM_001006935.1,NM_001006937.1,NM_024863.4	,,	676,1904,940,1480,1503	CC,CT,C,TT,T		36.5488,45.2934,39.7236	,,	146/216,146/216,146/216	102842041	4196,6367	2203	4300	6503	SO:0001819	synonymous_variant	79921	exon3			CATACATGATATG	AF314542	CCDS14510.2, CCDS76004.1	Xq22.2	2014-03-21			ENSG00000133142	ENSG00000133142			26121	protein-coding gene	gene with protein product						14702039, 16221301	Standard	XM_005262192		Approved	FLJ21174, WEX7	uc004ekn.3	Q96EI5	OTTHUMG00000022103	ENST00000472745.1:c.438T>C	X.37:g.102842041T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	91	8	0.0879121	NM_001006935	Q8WY12|Q9H2H1|Q9H775	Silent	SNP	ENST00000472745.1	37	CCDS14510.2																																																																																			0|0.006;C|0.292	0.292	strong		0.423	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863	
YIPF3	25844	hgsc.bcm.edu	37	6	43484532	43484532	+	Missense_Mutation	SNP	G	G	A	rs2231763	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:43484532G>A	ENST00000372422.2	-	1	196	c.14C>T	c.(13-15)gCg>gTg	p.A5V	YIPF3_ENST00000506469.1_Missense_Mutation_p.A5V|POLR1C_ENST00000372389.3_5'Flank|RP3-337H4.9_ENST00000607571.1_RNA|POLR1C_ENST00000304004.3_5'Flank|POLR1C_ENST00000372344.2_5'Flank	NM_015388.3	NP_056203.2	Q9GZM5	YIPF3_HUMAN	Yip1 domain family, member 3	5			A -> V (in dbSNP:rs2231763).		cell differentiation (GO:0030154)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			cgccggcgccgcTGTAGTTGC	0.672													G|||	70	0.0139776	0.0038	0.0231	5008	,	,		12922	0.0		0.0348	False		,,,				2504	0.0143				p.A5V		Atlas-SNP	.											YIPF3,lymph_node,lymphoid_neoplasm,0,1	YIPF3	20	1	0			c.C14T						PASS	.	G	VAL/ALA	31,4309		0,31,2139	8.0	10.0	9.0		14	2.5	0.3	6	dbSNP_98	9	300,8184		3,294,3945	yes	missense	YIPF3	NM_015388.3	64	3,325,6084	AA,AG,GG		3.5361,0.7143,2.5811	benign	5/351	43484532	331,12493	2170	4242	6412	SO:0001583	missense	25844	exon1			GGCGCCGCTGTAG	AK000946	CCDS4899.1	6p21.1	2009-10-06	2005-07-04	2005-07-04	ENSG00000137207	ENSG00000137207		"""Yip1 domain family"""	21023	protein-coding gene	gene with protein product		609775	"""chromosome 6 open reading frame 109"""	C6orf109			Standard	NM_015388		Approved	DKFZp566C243, KLIP1, dJ337H4.3, FinGER3	uc003ovl.2	Q9GZM5	OTTHUMG00000014738	ENST00000372422.2:c.14C>T	6.37:g.43484532G>A	ENSP00000361499:p.Ala5Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_015388	Q5JTD2|Q6FI85|Q8NI57|Q9NWE3|Q9Y3U9	Missense_Mutation	SNP	ENST00000372422.2	37	CCDS4899.1	42	0.019230769230769232	4	0.008130081300813009	9	0.024861878453038673	0	0.0	29	0.03825857519788918	G	15.42	2.829622	0.50845	0.007143	0.035361	ENSG00000137207	ENST00000372422;ENST00000504851;ENST00000506469;ENST00000503972	T;T;T	0.46063	0.88;0.88;0.88	5.06	2.54	0.30619	.	0.763971	0.12361	N	0.475610	T	0.15739	0.0379	L	0.44542	1.39	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.0	T	0.25257	-1.0137	10	0.54805	T	0.06	-6.0049	6.9902	0.24751	0.3046:0.0:0.6954:0.0	rs2231763;rs2231763	5;5;5	D6RED8;E7EQR8;Q9GZM5	.;.;YIPF3_HUMAN	V	5	ENSP00000361499:A5V;ENSP00000425494:A5V;ENSP00000421461:A5V	ENSP00000259737:A5V	A	-	2	0	YIPF3	43592510	0.704000	0.27836	0.324000	0.25361	0.763000	0.43281	1.582000	0.36568	0.883000	0.36040	0.407000	0.27541	GCG	G|0.978;A|0.022	0.022	strong		0.672	YIPF3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040639.2	NM_015388	
C11orf52	91894	hgsc.bcm.edu	37	11	111795085	111795085	+	Missense_Mutation	SNP	C	C	G	rs7124407	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:111795085C>G	ENST00000278601.5	+	2	164	c.68C>G	c.(67-69)aCa>aGa	p.T23R	DIXDC1_ENST00000529225.1_5'Flank|HSPB2-C11orf52_ENST00000534100.1_3'UTR|C11orf52_ENST00000527286.1_3'UTR|CRYAB_ENST00000527950.1_5'Flank	NM_080659.2	NP_542390.2	Q96A22	CK052_HUMAN	chromosome 11 open reading frame 52	23			T -> R (in dbSNP:rs7124407). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)				lung(2)|ovary(1)	3		all_cancers(61;8.8e-15)|all_epithelial(67;6.27e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.63e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.7e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)		AAAAAGAAAACAGGTAACTTT	0.478													C|||	1685	0.336462	0.146	0.3458	5008	,	,		18365	0.5883		0.3052	False		,,,				2504	0.3599				p.T23R		Atlas-SNP	.											.	C11orf52	5	.	0			c.C68G						PASS	.	C	ARG/THR	660,3742	284.3+/-277.5	50,560,1591	89.0	99.0	96.0		68	-3.2	0.3	11	dbSNP_116	96	2847,5747	447.4+/-361.5	477,1893,1927	yes	missense	C11orf52	NM_080659.2	71	527,2453,3518	GG,GC,CC		33.1278,14.9932,26.9852	probably-damaging	23/124	111795085	3507,9489	2201	4297	6498	SO:0001583	missense	91894	exon2			AGAAAACAGGTAA	AK057948	CCDS8353.1	11q23.1	2006-02-06	2006-02-06		ENSG00000149300	ENSG00000149300			30531	protein-coding gene	gene with protein product							Standard	NM_080659		Approved	MGC14839, FLJ25219		Q96A22	OTTHUMG00000166888	ENST00000278601.5:c.68C>G	11.37:g.111795085C>G	ENSP00000278601:p.Thr23Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_080659		Missense_Mutation	SNP	ENST00000278601.5	37	CCDS8353.1	749	0.34294871794871795	76	0.15447154471544716	106	0.292817679558011	340	0.5944055944055944	227	0.2994722955145119	C	1.784	-0.481184	0.04383	0.149932	0.331278	ENSG00000149300	ENST00000529342;ENST00000278601	T;T	0.46819	0.86;0.86	5.2	-3.15	0.05233	.	0.817528	0.10682	N	0.646266	T	0.00012	0.0000	N	0.04508	-0.205	0.49687	P	1.8899999999999473E-4	B	0.06786	0.001	B	0.08055	0.003	T	0.46275	-0.9203	9	0.08837	T	0.75	0.9446	1.0563	0.01591	0.1346:0.2622:0.264:0.3392	rs7124407;rs52822055;rs57098449;rs7124407	23	Q96A22	CK052_HUMAN	R	23	ENSP00000436268:T23R;ENSP00000278601:T23R	ENSP00000278601:T23R	T	+	2	0	C11orf52	111300295	0.295000	0.24389	0.300000	0.25030	0.004000	0.04260	-0.485000	0.06520	-0.324000	0.08589	-0.819000	0.03115	ACA	C|0.705;G|0.295	0.295	strong		0.478	C11orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391673.1	NM_080659	
EFCAB7	84455	hgsc.bcm.edu	37	1	64021096	64021096	+	Missense_Mutation	SNP	G	G	A	rs2273367	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:64021096G>A	ENST00000371088.4	+	9	1370	c.1124G>A	c.(1123-1125)aGg>aAg	p.R375K	EFCAB7_ENST00000461039.1_3'UTR	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	375			R -> K (in dbSNP:rs2273367). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.				calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						ACTGGCTGTAGGCTGAGGAAA	0.358													G|||	701	0.139976	0.0673	0.1585	5008	,	,		15942	0.1855		0.1441	False		,,,				2504	0.1738				p.R375K		Atlas-SNP	.											EFCAB7,right_upper_lobe,carcinoma,-1,1	EFCAB7	45	1	0			c.G1124A						PASS	.	G	LYS/ARG	348,4058	179.7+/-208.2	8,332,1863	140.0	138.0	139.0		1124	4.0	1.0	1	dbSNP_100	139	1326,7274	260.9+/-283.5	93,1140,3067	yes	missense	EFCAB7	NM_032437.2	26	101,1472,4930	AA,AG,GG		15.4186,7.8983,12.871	benign	375/630	64021096	1674,11332	2203	4300	6503	SO:0001583	missense	84455	exon9			GCTGTAGGCTGAG	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.1124G>A	1.37:g.64021096G>A	ENSP00000360129:p.Arg375Lys	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	171	89	0.520468	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	315	0.14423076923076922	41	0.08333333333333333	61	0.1685082872928177	105	0.18356643356643357	108	0.1424802110817942	G	13.30	2.196337	0.38806	0.078983	0.154186	ENSG00000203965	ENST00000371088	T	0.44881	0.91	5.96	4.04	0.47022	.	0.214437	0.53938	N	0.000044	T	0.20618	0.0496	L	0.57536	1.79	0.09310	P	0.9999999999995571	B	0.06786	0.001	B	0.06405	0.002	T	0.05435	-1.0885	9	0.32370	T	0.25	-6.8388	10.965	0.47408	0.1579:0.0:0.8421:0.0	rs2273367;rs17851338;rs52834573;rs61180196;rs2273367	375	A8K855	EFCB7_HUMAN	K	375	ENSP00000360129:R375K	ENSP00000360129:R375K	R	+	2	0	EFCAB7	63793684	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.663000	0.61532	0.773000	0.33404	0.655000	0.94253	AGG	G|0.849;A|0.151	0.151	strong		0.358	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
OR51A7	119687	hgsc.bcm.edu	37	11	4928866	4928866	+	Silent	SNP	C	C	T	rs7941509	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:4928866C>T	ENST00000359350.4	+	1	267	c.267C>T	c.(265-267)gcC>gcT	p.A89A	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGTTCAATGCCATGGGAATTT	0.453													C|||	1995	0.398363	0.2625	0.3919	5008	,	,		21957	0.0804		0.6143	False		,,,				2504	0.6922				p.A89A		Atlas-SNP	.											OR51A7,rectum,carcinoma,0,1	OR51A7	86	1	0			c.C267T						PASS	.	C		1333,3069	445.7+/-347.8	197,939,1065	153.0	131.0	138.0		267	-2.3	0.2	11	dbSNP_116	138	5302,3294	646.7+/-400.3	1637,2028,633	no	coding-synonymous	OR51A7	NM_001004749.1		1834,2967,1698	TT,TC,CC		38.3201,30.2817,48.9537		89/313	4928866	6635,6363	2201	4298	6499	SO:0001819	synonymous_variant	119687	exon1			CAATGCCATGGGA	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"""GPCR / Class A : Olfactory receptors"""	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.267C>T	11.37:g.4928866C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	175	175	1	NM_001004749	Q6IFH8	Silent	SNP	ENST00000359350.4	37	CCDS31364.1																																																																																			C|0.549;T|0.451	0.451	strong		0.453	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749	
ZBED9	114821	hgsc.bcm.edu	37	6	28543264	28543264	+	Silent	SNP	C	C	T	rs17336532	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28543264C>T	ENST00000452236.2	-	3	1835	c.1218G>A	c.(1216-1218)ttG>ttA	p.L406L	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						TTAATGACCGCAAAAAAGTTA	0.373													C|||	892	0.178115	0.1899	0.1729	5008	,	,		19492	0.1419		0.173	False		,,,				2504	0.2086				p.L406L		Atlas-SNP	.											.	SCAND3	156	.	0			c.G1218A						PASS	.	C		786,3614	288.1+/-279.7	64,658,1478	47.0	50.0	49.0		1218	3.5	1.0	6	dbSNP_123	49	1767,6833	311.6+/-310.4	184,1399,2717	no	coding-synonymous	SCAND3	NM_052923.1		248,2057,4195	TT,TC,CC		20.5465,17.8636,19.6385		406/1326	28543264	2553,10447	2200	4300	6500	SO:0001819	synonymous_variant	114821	exon3			TGACCGCAAAAAA																												ENST00000452236.2:c.1218G>A	6.37:g.28543264C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_052923		Silent	SNP	ENST00000452236.2	37	CCDS34355.1																																																																																			C|0.820;T|0.180	0.180	strong		0.373	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3		
EZH2	2146	hgsc.bcm.edu	37	7	148525904	148525904	+	Missense_Mutation	SNP	C	C	G	rs2302427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:148525904C>G	ENST00000460911.1	-	6	641	c.553G>C	c.(553-555)Gac>Cac	p.D185H	EZH2_ENST00000541220.1_Missense_Mutation_p.D176H|EZH2_ENST00000478654.1_Missense_Mutation_p.D176H|EZH2_ENST00000536783.1_Missense_Mutation_p.D76H|EZH2_ENST00000483967.1_Missense_Mutation_p.D176H|EZH2_ENST00000320356.2_Missense_Mutation_p.D185H|EZH2_ENST00000350995.2_Missense_Mutation_p.D146H|EZH2_ENST00000476773.1_Missense_Mutation_p.D176H			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	185	Interaction with DNMT1, DNMT3A and DNMT3B.		D -> H (in dbSNP:rs2302427).		cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			tcatcatcgtcatcatcatta	0.393			Mis		DLBCL								C|||	400	0.0798722	0.0038	0.0461	5008	,	,		19098	0.2063		0.0696	False		,,,				2504	0.0869				p.D185H		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,NS,carcinoma,+2,2	EZH2	823	2	0			c.G553C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	66,4340	60.5+/-97.4	0,66,2137	178.0	146.0	157.0		553,526,526,553,436	5.7	0.9	7	dbSNP_100	157	719,7881	175.3+/-225.4	30,659,3611	yes	missense,missense,missense,missense,missense	EZH2	NM_001203247.1,NM_001203248.1,NM_001203249.1,NM_004456.4,NM_152998.2	81,81,81,81,81	30,725,5748	GG,GC,CC		8.3605,1.498,6.0357	benign,benign,benign,benign,benign	185/747,176/738,176/696,185/752,146/708	148525904	785,12221	2203	4300	6503	SO:0001583	missense	2146	exon6			CATCGTCATCATC		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.553G>C	7.37:g.148525904C>G	ENSP00000419711:p.Asp185His	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	203	103	0.507389	NM_001203247	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	161	0.07371794871794872	3	0.006097560975609756	21	0.058011049723756904	83	0.1451048951048951	54	0.0712401055408971	C	19.43	3.826662	0.71143	0.01498	0.083605	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967;ENST00000536783	D;D;D;D;D;D;D;T	0.94828	-3.46;-3.5;-3.46;-3.5;-3.46;-3.46;-3.53;0.81	5.69	5.69	0.88448	SANT domain, DNA binding (1);	0.168733	0.49916	D	0.000127	T	0.08980	0.0222	L	0.34521	1.04	0.09310	P	0.99999641944	P;B;B;B;P;P	0.47604	0.898;0.348;0.348;0.41;0.659;0.676	P;B;B;B;B;P	0.49226	0.553;0.393;0.393;0.299;0.393;0.603	T	0.59161	-0.7506	9	0.72032	D	0.01	.	19.4235	0.94732	0.0:1.0:0.0:0.0	rs2302427;rs52833659	185;176;176;185;146;185	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	H	176;185;185;146;176;176;176;76	ENSP00000417062:D176H;ENSP00000320147:D185H;ENSP00000419711:D185H;ENSP00000223193:D146H;ENSP00000443219:D176H;ENSP00000419050:D176H;ENSP00000419856:D176H;ENSP00000439305:D76H	ENSP00000320147:D185H	D	-	1	0	EZH2	148156837	1.000000	0.71417	0.919000	0.36401	0.821000	0.46438	7.538000	0.82048	2.682000	0.91365	0.585000	0.79938	GAC	C|0.926;G|0.074	0.074	strong		0.393	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
CENPJ	55835	hgsc.bcm.edu	37	13	25487103	25487103	+	Missense_Mutation	SNP	T	T	C	rs35498994	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25487103T>C	ENST00000381884.4	-	2	246	c.61A>G	c.(61-63)Atg>Gtg	p.M21V	CENPJ_ENST00000545981.1_Missense_Mutation_p.M21V	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	21			M -> V (in dbSNP:rs35498994).		cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		GGATTGGTCATCCACTGGGTT	0.433													T|||	777	0.155152	0.0794	0.1628	5008	,	,		18447	0.3462		0.1382	False		,,,				2504	0.0726				p.M21V		Atlas-SNP	.											.	CENPJ	116	.	0			c.A61G						PASS	.	T	VAL/MET	422,3984	207.8+/-229.1	25,372,1806	65.0	57.0	60.0		61	5.3	1.0	13	dbSNP_126	60	1162,7438	232.8+/-266.3	83,996,3221	yes	missense	CENPJ	NM_018451.3	21	108,1368,5027	CC,CT,TT		13.5116,9.5778,12.179	possibly-damaging	21/1339	25487103	1584,11422	2203	4300	6503	SO:0001583	missense	55835	exon2			TGGTCATCCACTG	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"""centrosomal P4.1-associated protein"""	609279	"""microcephaly, primary autosomal recessive 6"""	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.61A>G	13.37:g.25487103T>C	ENSP00000371308:p.Met21Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	121	48	0.396694	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Missense_Mutation	SNP	ENST00000381884.4	37	CCDS9310.1	390	0.17857142857142858	40	0.08130081300813008	50	0.13812154696132597	190	0.3321678321678322	110	0.14511873350923482	T	19.04	3.750856	0.69533	0.095778	0.135116	ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729	T;T	0.16743	2.32;2.32	5.28	5.28	0.74379	.	0.064543	0.64402	D	0.000004	T	0.00012	0.0000	M	0.78637	2.42	0.37049	P	0.10248000000000002	P	0.43431	0.807	B	0.35182	0.197	T	0.40850	-0.9541	9	0.87932	D	0	.	12.7331	0.57208	0.0:0.0:0.0:1.0	rs35498994;rs59706954	21	Q9HC77	CENPJ_HUMAN	V	21	ENSP00000371308:M21V;ENSP00000441090:M21V	ENSP00000371308:M21V	M	-	1	0	CENPJ	24385103	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.631000	0.46502	2.006000	0.58801	0.533000	0.62120	ATG	A|0.000;C|0.138;T|0.862	0.138	strong		0.433	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451	
GRPR	2925	hgsc.bcm.edu	37	X	16168677	16168677	+	Silent	SNP	T	T	C	rs4986946	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:16168677T>C	ENST00000380289.2	+	2	1061	c.663T>C	c.(661-663)atT>atC	p.I221I	RP11-431J24.2_ENST00000422438.1_RNA|RP11-431J24.2_ENST00000454712.2_RNA|RP11-431J24.2_ENST00000435789.1_RNA	NM_005314.2	NP_005305.1	P30550	GRPR_HUMAN	gastrin-releasing peptide receptor	221					cell proliferation (GO:0008283)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cell proliferation (GO:0042127)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)|G-protein coupled peptide receptor activity (GO:0008528)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(3)|stomach(1)|upper_aerodigestive_tract(3)	25	Hepatocellular(33;0.183)					TCTACGTCATTCCACTGTCGA	0.443													C|||	1471	0.389669	0.5257	0.2378	3775	,	,		15144	0.126		0.2555	False		,,,				2504	0.2321				p.I221I		Atlas-SNP	.											.	GRPR	51	.	0			c.T663C						PASS	.	C		2538,1297		717,729,375,186,196	190.0	144.0	160.0		663	3.6	1.0	X	dbSNP_111	160	2343,4385		303,1090,647,1035,1225	no	coding-synonymous	GRPR	NM_005314.2		1020,1819,1022,1221,1421	CC,CT,C,TT,T		34.8246,33.8201,46.2085		221/385	16168677	4881,5682	2203	4300	6503	SO:0001819	synonymous_variant	2925	exon2			CGTCATTCCACTG		CCDS14174.1	Xp22.2	2014-02-21			ENSG00000126010	ENSG00000126010		"""GPCR / Class A : Bombesin receptors"""	4609	protein-coding gene	gene with protein product	"""bombesin receptor 2"""	305670					Standard	NM_005314		Approved	BB2	uc004cxj.3	P30550	OTTHUMG00000021189	ENST00000380289.2:c.663T>C	X.37:g.16168677T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	129	122	0.945736	NM_005314	B2R910	Silent	SNP	ENST00000380289.2	37	CCDS14174.1																																																																																			0|0.003;C|0.426	0.426	strong		0.443	GRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055901.1	NM_005314	
OR1N2	138882	hgsc.bcm.edu	37	9	125315557	125315557	+	Missense_Mutation	SNP	T	T	C	rs1831370	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:125315557T>C	ENST00000373688.2	+	1	167	c.109T>C	c.(109-111)Tgg>Cgg	p.W37R		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	37			W -> R (in dbSNP:rs1831370). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.W37R(1)		breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						ACTCTCTGAGTGGCCAGAGGA	0.517													C|||	2797	0.558506	0.5946	0.5908	5008	,	,		18962	0.6637		0.4791	False		,,,				2504	0.4601				p.W37R		Atlas-SNP	.											OR1N2,colon,carcinoma,-1,2	OR1N2	51	2	1	Substitution - Missense(1)	stomach(1)	c.T109C						PASS	.	C	ARG/TRP	2528,1878	541.4+/-375.8	714,1100,389	107.0	98.0	101.0		109	-2.6	0.0	9	dbSNP_92	101	4212,4388	583.3+/-391.5	1011,2190,1099	yes	missense	OR1N2	NM_001004457.1	101	1725,3290,1488	CC,CT,TT		48.9767,42.6237,48.1778	benign	37/331	125315557	6740,6266	2203	4300	6503	SO:0001583	missense	138882	exon1			TCTGAGTGGCCAG		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.109T>C	9.37:g.125315557T>C	ENSP00000362792:p.Trp37Arg	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	210	97	0.461905	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Missense_Mutation	SNP	ENST00000373688.2	37	CCDS35123.1	1197	0.5480769230769231	280	0.5691056910569106	211	0.5828729281767956	353	0.6171328671328671	353	0.4656992084432718	C	1.129	-0.653039	0.03480	0.573763	0.489767	ENSG00000171501	ENST00000373688	T	0.01059	5.39	4.31	-2.62	0.06152	.	1.300740	0.05678	N	0.589889	T	0.00012	0.0000	N	0.02842	-0.48	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07927	-1.0747	9	0.28530	T	0.3	.	0.6697	0.00856	0.2434:0.3281:0.1193:0.3093	rs1831370;rs17530879;rs60632643;rs1831370	37	Q8NGR9	OR1N2_HUMAN	R	37	ENSP00000362792:W37R	ENSP00000362792:W37R	W	+	1	0	OR1N2	124355378	0.000000	0.05858	0.002000	0.10522	0.463000	0.32649	-5.227000	0.00139	-0.761000	0.04670	-0.860000	0.03012	TGG	T|0.471;C|0.529	0.529	strong		0.517	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
MADCAM1	8174	hgsc.bcm.edu	37	19	496532	496532	+	Silent	SNP	G	G	A	rs78668504	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:496532G>A	ENST00000215637.3	+	1	79	c.33G>A	c.(31-33)ggG>ggA	p.G11G	MADCAM1_ENST00000382683.4_Silent_p.G11G|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Silent_p.G11G|MADCAM1_ENST00000587541.1_Intron	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	11					aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCTGGCGGGGCTTCTGGGGC	0.682													G|||	774	0.154553	0.2307	0.1412	5008	,	,		7493	0.1002		0.0805	False		,,,				2504	0.1933				p.G11G		Atlas-SNP	.											.	MADCAM1	29	.	0			c.G33A						PASS	.	G	,	852,3516		100,652,1432	14.0	15.0	15.0		33,33	0.5	0.0	19	dbSNP_132	15	753,7811		36,681,3565	no	coding-synonymous,coding-synonymous	MADCAM1	NM_130760.2,NM_130762.2	,	136,1333,4997	AA,AG,GG		8.7926,19.5055,12.4111	,	11/383,11/296	496532	1605,11327	2184	4282	6466	SO:0001819	synonymous_variant	8174	exon1			GGCGGGGCTTCTG	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.33G>A	19.37:g.496532G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	252	138	0.547619	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Silent	SNP	ENST00000215637.3	37	CCDS12028.1																																																																																			G|0.875;A|0.125	0.125	strong		0.682	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
MYH13	8735	hgsc.bcm.edu	37	17	10247199	10247199	+	Silent	SNP	G	G	A	rs12938754	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:10247199G>A	ENST00000418404.3	-	15	1975	c.1812C>T	c.(1810-1812)aaC>aaT	p.N604N	RP11-401O9.3_ENST00000577743.1_RNA|MYH13_ENST00000252172.4_Silent_p.N604N			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	604	Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CCACAGTCTCGTTCAGGGGGT	0.527													G|||	486	0.0970447	0.0189	0.1527	5008	,	,		19644	0.0		0.3062	False		,,,				2504	0.0481				p.N604N		Atlas-SNP	.											.	MYH13	533	.	0			c.C1812T						PASS	.	G		253,4153	146.5+/-181.1	3,247,1953	81.0	78.0	79.0		1812	-8.7	0.2	17	dbSNP_121	79	2512,6088	411.0+/-350.3	372,1768,2160	no	coding-synonymous	MYH13	NM_003802.2		375,2015,4113	AA,AG,GG		29.2093,5.7422,21.2594		604/1939	10247199	2765,10241	2203	4300	6503	SO:0001819	synonymous_variant	8735	exon16			AGTCTCGTTCAGG	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.1812C>T	17.37:g.10247199G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	155	88	0.567742	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																			G|0.817;A|0.183	0.183	strong		0.527	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
ZFHX3	463	hgsc.bcm.edu	37	16	72993925	72993925	+	Silent	SNP	C	C	T	rs62053192	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72993925C>T	ENST00000268489.5	-	2	792	c.120G>A	c.(118-120)gaG>gaA	p.E40E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	40					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CTGTGGACTGCTCCATGCTAC	0.662													C|||	139	0.0277556	0.0045	0.0331	5008	,	,		14497	0.003		0.0596	False		,,,				2504	0.0481				p.E40E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G120A						PASS	.	C	,	73,4323	64.1+/-101.4	1,71,2126	118.0	115.0	116.0		,120	5.1	1.0	16	dbSNP_129	116	596,8004	157.9+/-211.5	24,548,3728	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	25,619,5854	TT,TC,CC		6.9302,1.6606,5.1477	,	,40/3704	72993925	669,12327	2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			GGACTGCTCCATG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.120G>A	16.37:g.72993925C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			C|0.955;T|0.045	0.045	strong		0.662	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
KRT40	125115	hgsc.bcm.edu	37	17	39135089	39135089	+	Missense_Mutation	SNP	G	G	A	rs11649834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39135089G>A	ENST00000398486.2	-	8	1323	c.1163C>T	c.(1162-1164)aCg>aTg	p.T388M	AC004231.2_ENST00000418393.1_RNA|KRT40_ENST00000377755.4_Missense_Mutation_p.T388M	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	388	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				GCCCCAGTACGTGTTGATCTC	0.572													G|||	338	0.067492	0.0098	0.0965	5008	,	,		15927	0.0556		0.1272	False		,,,				2504	0.0757				p.T388M		Atlas-SNP	.											.	KRT40	27	.	0			c.C1163T						PASS	.	G	MET/THR	131,4275	93.4+/-132.2	2,127,2074	70.0	78.0	75.0		1163	5.6	0.6	17	dbSNP_120	75	1174,7418	235.0+/-267.7	77,1020,3199	yes	missense	KRT40	NM_182497.3	81	79,1147,5273	AA,AG,GG		13.6639,2.9732,10.04	probably-damaging	388/432	39135089	1305,11693	2203	4296	6499	SO:0001583	missense	125115	exon8			CAGTACGTGTTGA	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.1163C>T	17.37:g.39135089G>A	ENSP00000381500:p.Thr388Met	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	167	0.07646520146520147	5	0.01016260162601626	36	0.09944751381215469	27	0.0472027972027972	99	0.13060686015831136	G	12.67	2.006968	0.35415	0.029732	0.136639	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.91996	-2.95;-2.95	5.56	5.56	0.83823	Filament (1);	0.000000	0.34676	N	0.003774	T	0.27241	0.0668	M	0.92507	3.315	0.32698	P	0.5133220000000001	D	0.89917	1.0	D	0.79108	0.992	T	0.57831	-0.7743	9	0.72032	D	0.01	.	15.3367	0.74263	0.0:0.0:0.86:0.14	rs11649834	388	Q6A162	K1C40_HUMAN	M	388	ENSP00000366984:T388M;ENSP00000381500:T388M	ENSP00000366984:T388M	T	-	2	0	KRT40	36388615	0.030000	0.19436	0.625000	0.29200	0.067000	0.16453	1.408000	0.34668	2.784000	0.95788	0.655000	0.94253	ACG	G|0.922;A|0.078	0.078	strong		0.572	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
KANSL1	284058	hgsc.bcm.edu	37	17	44117119	44117119	+	Missense_Mutation	SNP	A	A	G	rs34043286	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44117119A>G	ENST00000262419.6	-	8	2622	c.2152T>C	c.(2152-2154)Tca>Cca	p.S718P	KANSL1_ENST00000574590.1_Missense_Mutation_p.S718P|KANSL1_ENST00000575318.1_Missense_Mutation_p.S718P|KANSL1_ENST00000572904.1_Missense_Mutation_p.S718P|KANSL1_ENST00000432791.1_Missense_Mutation_p.S718P|KANSL1_ENST00000393476.3_Missense_Mutation_p.S75P	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	718			S -> P (in dbSNP:rs34043286).		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TTACGAGCTGAATCTGGCAGA	0.498													G|||	432	0.086262	0.0151	0.1571	5008	,	,		19661	0.001		0.2406	False		,,,				2504	0.0613				p.S718P		Atlas-SNP	.											.	.	.	.	0			c.T2152C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER	202,4204	807.9+/-415.9	5,192,2006	114.0	106.0	109.0		2152,2152,2152	6.1	1.0	17	dbSNP_126	109	1927,6673	726.3+/-406.6	220,1487,2593	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	74,74,74	225,1679,4599	GG,GA,AA		22.407,4.5847,16.3694	benign,benign,benign	718/1105,718/1106,718/1106	44117119	2129,10877	2203	4300	6503	SO:0001583	missense	284058	exon8			GAGCTGAATCTGG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2152T>C	17.37:g.44117119A>G	ENSP00000262419:p.Ser718Pro	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	130	68	0.523077	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	8.847	0.943571	0.18281	0.045847	0.22407	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.22336	2.74;2.74;1.96	6.05	6.05	0.98169	.	0.072151	0.64402	N	0.000014	T	0.00012	0.0000	N	0.00308	-1.67	0.46678	P	8.470000000000422E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38045	-0.9679	9	0.17369	T	0.5	-5.2424	12.6915	0.56976	0.0762:0.0:0.9238:0.0	rs34043286	49;718	Q7Z3B3-2;Q7Z3B3	.;K1267_HUMAN	P	718;718;75	ENSP00000262419:S718P;ENSP00000387393:S718P;ENSP00000377117:S75P	ENSP00000262419:S718P	S	-	1	0	KIAA1267	41472966	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	4.936000	0.63506	1.587000	0.49959	-0.128000	0.14901	TCA	A|0.853;G|0.147	0.147	strong		0.498	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
FXYD3	5349	hgsc.bcm.edu	37	19	35612159	35612159	+	Intron	SNP	C	C	G	rs2290649	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:35612159C>G	ENST00000344013.6	+	5	293				FXYD3_ENST00000454903.2_Missense_Mutation_p.P36R|FXYD3_ENST00000346446.5_Intron|FXYD3_ENST00000535103.1_Intron|FXYD3_ENST00000603449.1_Missense_Mutation_p.P36R|FXYD3_ENST00000604804.1_Intron|FXYD3_ENST00000406988.1_Intron|FXYD3_ENST00000604621.1_Intron|FXYD3_ENST00000603524.1_Intron|FXYD3_ENST00000406242.3_Intron|FXYD3_ENST00000605550.1_Intron|FXYD3_ENST00000605552.1_Missense_Mutation_p.P36R|FXYD3_ENST00000604404.1_Intron|FXYD3_ENST00000603181.1_Intron|FXYD3_ENST00000605677.1_Intron|FXYD3_ENST00000435734.2_Intron|FXYD3_ENST00000604255.1_Intron			Q14802	FXYD3_HUMAN	FXYD domain containing ion transport regulator 3						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of catalytic activity (GO:0050790)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			endometrium(1)|lung(2)|prostate(1)	4	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			GGTGAGAGCCCGTGCCCCCTT	0.532													C|||	1186	0.236821	0.1815	0.415	5008	,	,		16551	0.2798		0.2455	False		,,,				2504	0.1319				p.P36R		Atlas-SNP	.											.	FXYD3	15	.	0			c.C107G						PASS	.	C	,,ARG/PRO,ARG/PRO,,,,	875,3531	336.5+/-304.4	90,695,1418	78.0	81.0	80.0		,,107,107,,,,	-8.3	0.0	19	dbSNP_100	80	2177,6423	370.0+/-335.7	295,1587,2418	yes	intron,intron,missense,missense,intron,intron,intron,intron	FXYD3	NM_001136007.1,NM_001136008.1,NM_001136009.1,NM_001136010.1,NM_001136011.1,NM_001136012.1,NM_005971.3,NM_021910.2	,,103,103,,,,	385,2282,3836	GG,GC,CC		25.314,19.8593,23.4661	,,,,,,,	,,36/62,36/62,,,,	35612159	3052,9954	2203	4300	6503	SO:0001627	intron_variant	5349	exon5			AGAGCCCGTGCCC	X93036	CCDS12442.1, CCDS12443.1, CCDS46048.1, CCDS46049.1, CCDS46050.1	19q13.11-q13.12	2008-05-14	2002-01-14			ENSG00000089356			4027	protein-coding gene	gene with protein product		604996	"""FXYD domain-containing ion transport regulator 3"""	PLML		7836447, 10950925	Standard	NM_005971		Approved	MAT-8	uc010xsm.2	Q14802		ENST00000344013.6:c.97+10C>G	19.37:g.35612159C>G		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	233	91	0.390558	NM_001136010	A6NDE0|C9JDU2|F5H174|F8WB34|Q13211|Q6IB59	Missense_Mutation	SNP	ENST00000344013.6	37	CCDS12442.1	615	0.2815934065934066	103	0.20934959349593496	138	0.3812154696132597	187	0.3269230769230769	187	0.24670184696569922	C	1.879	-0.458439	0.04508	0.198593	0.25314	ENSG00000089356	ENST00000454903	.	.	.	4.16	-8.32	0.00996	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35226	-0.9797	5	.	.	.	.	4.2527	0.10702	0.0743:0.1728:0.2715:0.4814	rs2290649	36	C9JDU2	.	R	36	.	.	P	+	2	0	FXYD3	40303999	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.795000	0.01752	-2.597000	0.00453	-1.729000	0.00701	CCG	C|0.741;G|0.259	0.259	strong		0.532	FXYD3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000468985.1	NM_021910	
TRPM3	80036	hgsc.bcm.edu	37	9	73150873	73150873	+	Missense_Mutation	SNP	T	T	G	rs17535963	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:73150873T>G	ENST00000377110.3	-	25	5363	c.5120A>C	c.(5119-5121)aAc>aCc	p.N1707T	TRPM3_ENST00000377105.1_Missense_Mutation_p.N1566T|TRPM3_ENST00000396280.5_Missense_Mutation_p.N1556T|TRPM3_ENST00000358082.3_Missense_Mutation_p.N1569T|TRPM3_ENST00000396292.4_Missense_Mutation_p.N1579T|TRPM3_ENST00000408909.2_Missense_Mutation_p.N1566T|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000357533.2_Missense_Mutation_p.N1711T|TRPM3_ENST00000396285.1_Missense_Mutation_p.N1566T|TRPM3_ENST00000423814.3_Missense_Mutation_p.N1734T|TRPM3_ENST00000360823.2_Missense_Mutation_p.N1569T|TRPM3_ENST00000377106.1_Missense_Mutation_p.N1579T			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1732					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						GAAGGTTTAGTTGTGCTTGCT	0.488													T|||	1047	0.209065	0.0681	0.3285	5008	,	,		21131	0.1766		0.2823	False		,,,				2504	0.273				p.N1707T		Atlas-SNP	.											.	TRPM3	700	.	0			c.A5120C						PASS	.	T	THR/ASN,THR/ASN,THR/ASN,THR/ASN,THR/ASN,THR/ASN,THR/ASN	442,3964	210.2+/-230.7	32,378,1793	118.0	118.0	118.0		5120,4661,4697,4631,4667,4736,4706	1.4	1.0	9	dbSNP_123	118	2623,5977	424.7+/-354.7	420,1783,2097	yes	missense,missense,missense,missense,missense,missense,missense	TRPM3	NM_001007471.2,NM_020952.4,NM_024971.5,NM_206944.3,NM_206945.3,NM_206946.3,NM_206947.3	65,65,65,65,65,65,65	452,2161,3890	GG,GT,TT		30.5,10.0318,23.566	benign,benign,benign,benign,benign,benign,benign	1707/1708,1554/1555,1566/1567,1544/1545,1556/1557,1579/1580,1569/1570	73150873	3065,9941	2203	4300	6503	SO:0001583	missense	80036	exon25			GTTTAGTTGTGCT	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.5120A>C	9.37:g.73150873T>G	ENSP00000366314:p.Asn1707Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377110.3	37	CCDS43835.1	464|464	0.21245421245421245|0.21245421245421245	30|30	0.06097560975609756|0.06097560975609756	129|129	0.356353591160221|0.356353591160221	98|98	0.17132867132867133|0.17132867132867133	207|207	0.27308707124010556|0.27308707124010556	T|T	6.388|6.388	0.439718|0.439718	0.12104|0.12104	0.100318|0.100318	0.305|0.305	ENSG00000083067|ENSG00000083067	ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814|ENST00000396280	T;T;T;T;T;T;T;T;T;T|.	0.58060|.	0.43;0.38;0.38;0.36;0.42;0.36;0.39;0.38;0.38;0.42|.	5.59|5.59	1.42|1.42	0.22433|0.22433	.|.	0.301156|.	0.36854|.	N|.	0.002362|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.19112|0.19112	0.55|0.55	0.32767|0.32767	P|P	0.504351|0.504351	B;B;B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B;B;B|.	0.08055|.	0.002;0.003;0.001;0.0;0.001;0.001;0.0|.	T|T	0.45483|0.45483	-0.9258|-0.9258	9|4	0.41790|.	T|.	0.15|.	.|.	4.4477|4.4477	0.11606|0.11606	0.0:0.2809:0.3148:0.4044|0.0:0.2809:0.3148:0.4044	rs17535963;rs52797952;rs17535963|rs17535963;rs52797952;rs17535963	1707;1697;1711;1569;1566;1679;1566|.	Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3|.	.;.;.;.;.;.;.|.	T|H	1707;1579;1569;1566;1711;1566;1566;1579;1569;1734|1555	ENSP00000366314:N1707T;ENSP00000366310:N1579T;ENSP00000354066:N1569T;ENSP00000366309:N1566T;ENSP00000350140:N1711T;ENSP00000386127:N1566T;ENSP00000379581:N1566T;ENSP00000379587:N1579T;ENSP00000350791:N1569T;ENSP00000389542:N1734T|.	ENSP00000350140:N1711T|.	N|Q	-|-	2|3	0|2	TRPM3|TRPM3	72340693|72340693	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.369000|0.369000	0.29798|0.29798	1.940000|1.940000	0.40223|0.40223	0.378000|0.378000	0.24764|0.24764	0.460000|0.460000	0.39030|0.39030	AAC|CAA	T|0.781;G|0.219	0.219	strong		0.488	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945	
ERCC6	2074	hgsc.bcm.edu	37	10	50681033	50681033	+	Silent	SNP	G	G	A	rs2229760	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50681033G>A	ENST00000355832.5	-	15	2829	c.2751C>T	c.(2749-2751)ggC>ggT	p.G917G	RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000542458.1_Silent_p.G287G|ERCC6_ENST00000465653.1_5'Flank	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	917	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)	p.G917G(1)		breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CACCTAAGCCGCCCACCCGCG	0.473								Direct reversal of damage;Nucleotide excision repair (NER)					G|||	1273	0.254193	0.0893	0.2968	5008	,	,		14918	0.3155		0.3926	False		,,,				2504	0.2413				p.R917R		Atlas-SNP	.											ERCC6,NS,carcinoma,0,1	ERCC6	162	1	1	Substitution - coding silent(1)	stomach(1)	c.G2751T						PASS	.	G		659,3747	281.4+/-275.9	47,565,1591	67.0	62.0	64.0		2751	-8.2	0.5	10	dbSNP_98	64	3552,5048	516.8+/-378.9	720,2112,1468	no	coding-synonymous	ERCC6	NM_000124.2		767,2677,3059	AA,AG,GG		41.3023,14.9569,32.3774		917/1494	50681033	4211,8795	2203	4300	6503	SO:0001819	synonymous_variant	2074	exon15			TAAGCCGCCCACC	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.2751C>T	10.37:g.50681033G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_000124	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																			G|0.702;A|0.298	0.298	strong		0.473	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
OR4C16	219428	hgsc.bcm.edu	37	11	55339676	55339676	+	Missense_Mutation	SNP	G	G	T	rs12800642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55339676G>T	ENST00000314634.3	+	1	73	c.73G>T	c.(73-75)Gtg>Ttg	p.V25L		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	25			V -> L (in dbSNP:rs12800642).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				GAAGAAAATAGTGTTTGTTAT	0.393													g|||	869	0.173522	0.1188	0.2378	5008	,	,		18312	0.1528		0.2117	False		,,,				2504	0.184				p.V25L		Atlas-SNP	.											.	OR4C16	104	.	0			c.G73T						PASS	.	G	LEU/VAL	593,3809	260.7+/-263.8	40,513,1648	163.0	152.0	155.0		73	-2.1	0.0	11	dbSNP_121	155	1890,6702	337.3+/-322.2	226,1438,2632	yes	missense	OR4C16	NM_001004701.2	32	266,1951,4280	TT,TG,GG		21.9972,13.4711,19.1088	benign	25/311	55339676	2483,10511	2201	4296	6497	SO:0001583	missense	219428	exon1			AAAATAGTGTTTG	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.73G>T	11.37:g.55339676G>T	ENSP00000324913:p.Val25Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_001004701	Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	380	0.17399267399267399	36	0.07317073170731707	84	0.23204419889502761	94	0.16433566433566432	166	0.21899736147757257	G	9.773	1.173101	0.21704	0.134711	0.219972	ENSG00000181935	ENST00000314634	T	0.00682	5.86	4.98	-2.08	0.07254	.	0.595988	0.15457	N	0.261315	T	0.00012	0.0000	N	0.02192	-0.645	0.80722	P	0.0	B	0.14012	0.009	B	0.16722	0.016	T	0.34229	-0.9837	9	0.02654	T	1	.	1.1987	0.01880	0.2607:0.2863:0.3151:0.1378	rs12800642;rs52798686;rs58232726;rs12800642	25	Q8NGL9	OR4CG_HUMAN	L	25	ENSP00000324913:V25L	ENSP00000324913:V25L	V	+	1	0	OR4C16	55096252	0.000000	0.05858	0.000000	0.03702	0.680000	0.39746	-1.171000	0.03115	-0.203000	0.10251	0.549000	0.68633	GTG	G|0.817;T|0.183	0.183	strong		0.393	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
DNAH9	1770	hgsc.bcm.edu	37	17	11687721	11687721	+	Silent	SNP	G	G	A	rs16945337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:11687721G>A	ENST00000262442.4	+	41	7994	c.7926G>A	c.(7924-7926)gcG>gcA	p.A2642A	DNAH9_ENST00000454412.2_Silent_p.A2642A	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2642	AAA 3. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		ACTTCCCGGCGTCCCTGCAGA	0.542													G|||	239	0.0477236	0.0877	0.0058	5008	,	,		17425	0.002		0.0348	False		,,,				2504	0.0838				p.A2642A		Atlas-SNP	.											DNAH9,NS,carcinoma,+1,1	DNAH9	695	1	0			c.G7926A						PASS	.	G		358,4048	185.0+/-212.2	14,330,1859	177.0	169.0	172.0		7926	-2.6	0.0	17	dbSNP_123	172	195,8405	86.1+/-148.5	0,195,4105	no	coding-synonymous	DNAH9	NM_001372.3		14,525,5964	AA,AG,GG		2.2674,8.1253,4.2519		2642/4487	11687721	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon41			CCCGGCGTCCCTG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.7926G>A	17.37:g.11687721G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	219	107	0.488584	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.956;A|0.044	0.044	strong		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
SLC25A29	123096	hgsc.bcm.edu	37	14	100759690	100759690	+	Missense_Mutation	SNP	C	C	T	rs200054689		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100759690C>T	ENST00000359232.3	-	3	403	c.103G>A	c.(103-105)Gag>Aag	p.E35K	AL157871.2_ENST00000553954.1_RNA|SLC25A29_ENST00000555927.1_5'UTR|SLC25A29_ENST00000554912.1_5'UTR|SLC25A29_ENST00000392908.3_Missense_Mutation_p.G20E|SLC25A29_ENST00000556505.1_5'UTR|RP11-638I2.6_ENST00000556458.1_lincRNA|SLC25A29_ENST00000539621.1_5'UTR	NM_001039355.1	NP_001034444.1	Q8N8R3	MCATL_HUMAN	solute carrier family 25 (mitochondrial carnitine/acylcarnitine carrier), member 29	35						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	acyl carnitine transmembrane transporter activity (GO:0015227)			NS(1)|endometrium(1)|ovary(1)	3		Melanoma(154;0.152)			L-Carnitine(DB00583)	TGAGGCTTCTCCACGCTCTGG	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		17380	0.0		0.001	False		,,,				2504	0.0				p.E35K		Atlas-SNP	.											.	SLC25A29	14	.	0			c.G103A						PASS	.						73.0	49.0	57.0					14																	100759690		2202	4300	6502	SO:0001583	missense	123096	exon3			GCTTCTCCACGCT	AK095532	CCDS32156.1	14q32.2	2013-05-22	2012-03-29	2004-01-21	ENSG00000197119	ENSG00000197119		"""Solute carriers"""	20116	protein-coding gene	gene with protein product		615064	"""chromosome 14 open reading frame 69"", ""solute carrier family 25, member 29"""	C14orf69			Standard	XM_005267343		Approved	FLJ38975	uc010twx.2	Q8N8R3	OTTHUMG00000171569	ENST00000359232.3:c.103G>A	14.37:g.100759690C>T	ENSP00000352167:p.Glu35Lys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	96	57	0.59375	NM_001039355	A3KMR5|Q541V0	Missense_Mutation	SNP	ENST00000359232.3	37	CCDS32156.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	7.062|7.062	0.566669|0.566669	0.13560|0.13560	.|.	.|.	ENSG00000197119|ENSG00000197119	ENST00000359232|ENST00000392908;ENST00000554060	T|.	0.78595|.	-1.19|.	4.41|4.41	4.41|4.41	0.53225|0.53225	Mitochondrial carrier domain (2);|.	0.175049|.	0.49305|.	D|.	0.000143|.	T|T	0.34135|0.34135	0.0887|0.0887	N|N	0.02334|0.02334	-0.595|-0.595	0.80722|0.80722	D|D	1|1	B|.	0.11235|.	0.004|.	B|.	0.15052|.	0.012|.	T|T	0.48536|0.48536	-0.9027|-0.9027	10|6	0.09590|0.87932	T|D	0.72|0	-26.801|-26.801	12.1754|12.1754	0.54182|0.54182	0.1709:0.8291:0.0:0.0|0.1709:0.8291:0.0:0.0	.|.	35|.	Q8N8R3|.	MCATL_HUMAN|.	K|E	35|20	ENSP00000352167:E35K|.	ENSP00000352167:E35K|ENSP00000376640:G20E	E|G	-|-	1|2	0|0	SLC25A29|SLC25A29	99829443|99829443	1.000000|1.000000	0.71417|0.71417	0.669000|0.669000	0.29828|0.29828	0.005000|0.005000	0.04900|0.04900	3.411000|3.411000	0.52672|0.52672	2.020000|2.020000	0.59435|0.59435	0.591000|0.591000	0.81541|0.81541	GAG|GGA	C|1.000;T|0.000	0.000	strong		0.632	SLC25A29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072449.3		
AHNAK	79026	hgsc.bcm.edu	37	11	62297162	62297162	+	Missense_Mutation	SNP	G	G	A	rs75855515	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62297162G>A	ENST00000378024.4	-	5	5001	c.4727C>T	c.(4726-4728)aCg>aTg	p.T1576M	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1576					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GATTTTGTGCGTCTGTATATT	0.433													g|||	133	0.0265575	0.0393	0.0274	5008	,	,		21052	0.0119		0.0258	False		,,,				2504	0.0245				p.T1576M		Atlas-SNP	.											.	AHNAK	532	.	0			c.C4727T						PASS	.	G	MET/THR,	201,4203	121.3+/-158.8	4,193,2005	94.0	102.0	99.0		4727,	4.4	0.1	11	dbSNP_131	99	220,8378	91.6+/-153.7	4,212,4083	yes	missense,intron	AHNAK	NM_001620.1,NM_024060.2	81,	8,405,6088	AA,AG,GG		2.5587,4.564,3.238	probably-damaging,	1576/5891,	62297162	421,12581	2202	4299	6501	SO:0001583	missense	79026	exon5			TTGTGCGTCTGTA	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.4727C>T	11.37:g.62297162G>A	ENSP00000367263:p.Thr1576Met	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	57	0.0260989010989011	20	0.04065040650406504	13	0.03591160220994475	7	0.012237762237762238	17	0.022427440633245383	g	6.854	0.526769	0.13066	0.04564	0.025587	ENSG00000124942	ENST00000378024	T	0.00922	5.54	4.4	4.4	0.53042	.	.	.	.	.	T	0.00271	0.0008	N	0.25890	0.77	0.09310	N	1	P	0.49358	0.923	P	0.45610	0.487	T	0.61446	-0.7061	9	0.44086	T	0.13	.	14.7608	0.69604	0.0:0.0:1.0:0.0	.	1576	Q09666	AHNK_HUMAN	M	1576	ENSP00000367263:T1576M	ENSP00000367263:T1576M	T	-	2	0	AHNAK	62053738	0.284000	0.24287	0.055000	0.19348	0.001000	0.01503	-0.290000	0.08354	1.982000	0.57802	0.305000	0.20034	ACG	G|0.968;A|0.032	0.032	strong		0.433	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
TNXB	7148	hgsc.bcm.edu	37	6	32049423	32049423	+	Missense_Mutation	SNP	C	C	T	rs12211410	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32049423C>T	ENST00000375244.3	-	10	3965	c.3764G>A	c.(3763-3765)cGc>cAc	p.R1255H	TNXB_ENST00000375247.2_Missense_Mutation_p.R1255H			P22105	TENX_HUMAN	tenascin XB	1342	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GAACTCAGGGCGGGGGGGCTC	0.637													C|||	495	0.0988419	0.1127	0.0389	5008	,	,		14173	0.0347		0.0994	False		,,,				2504	0.1881				p.R1255H		Atlas-SNP	.											.	TNXB	553	.	0			c.G3764A						PASS	.	C	HIS/ARG	352,3382		18,316,1533	11.0	12.0	12.0		3764	-2.7	0.0	6	dbSNP_120	12	722,7478		43,636,3421	yes	missense	TNXB	NM_019105.6	29	61,952,4954	TT,TC,CC		8.8049,9.4269,8.9995	benign	1255/4243	32049423	1074,10860	1867	4100	5967	SO:0001583	missense	7148	exon10			TCAGGGCGGGGGG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.3764G>A	6.37:g.32049423C>T	ENSP00000364393:p.Arg1255His	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	141	55	0.390071	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		189	0.08653846153846154	75	0.1524390243902439	11	0.03038674033149171	22	0.038461538461538464	81	0.10686015831134564	C	6.644	0.487243	0.12641	0.094269	0.088049	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.55930	0.66;0.49	3.95	-2.69	0.06022	.	1.641460	0.04049	N	0.304352	T	0.11239	0.0274	N	0.03948	-0.315	0.80722	P	0.0	B	0.12013	0.005	B	0.04013	0.001	T	0.14783	-1.0460	9	0.41790	T	0.15	.	9.1549	0.36988	0.0:0.2512:0.0:0.7488	rs12211410;rs52822791;rs12211410	1255	P22105-3	.	H	1255	ENSP00000364393:R1255H;ENSP00000364396:R1255H	ENSP00000364393:R1255H	R	-	2	0	TNXB	32157401	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-3.560000	0.00431	-0.548000	0.06199	-0.501000	0.04562	CGC	C|0.904;T|0.096	0.096	strong		0.637	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
OR5M9	390162	hgsc.bcm.edu	37	11	56230611	56230611	+	Silent	SNP	G	G	T	rs79837116	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56230611G>T	ENST00000279791.1	-	1	266	c.267C>A	c.(265-267)acC>acA	p.T89T		NM_001004743.1	NP_001004743.1	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M, member 9	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	36	Esophageal squamous(21;0.00448)					CATAGGAAATGGTTTTTGTCT	0.463													g|||	182	0.0363419	0.003	0.0432	5008	,	,		21183	0.001		0.0934	False		,,,				2504	0.0542				p.T89T		Atlas-SNP	.											OR5M9,NS,carcinoma,-1,1	OR5M9	75	1	0			c.C267A						scavenged	.	G		55,4347	53.6+/-89.4	0,55,2146	104.0	102.0	103.0		267	-3.0	0.5	11	dbSNP_131	103	692,7900	171.3+/-222.3	35,622,3639	no	coding-synonymous	OR5M9	NM_001004743.1		35,677,5785	TT,TG,GG		8.054,1.2494,5.7488		89/311	56230611	747,12247	2201	4296	6497	SO:0001819	synonymous_variant	390162	exon1			GGAAATGGTTTTT	AB065747	CCDS31531.1	11q11	2012-08-09			ENSG00000150269	ENSG00000150269		"""GPCR / Class A : Olfactory receptors"""	15294	protein-coding gene	gene with protein product							Standard	NM_001004743		Approved		uc010rjj.2	Q8NGP3	OTTHUMG00000166874	ENST00000279791.1:c.267C>A	11.37:g.56230611G>T		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_001004743	Q6IEW5|Q96RB9	Silent	SNP	ENST00000279791.1	37	CCDS31531.1																																																																																			G|0.950;T|0.050	0.050	strong		0.463	OR5M9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391638.1	NM_001004743	
DMKN	93099	hgsc.bcm.edu	37	19	36004171	36004171	+	Missense_Mutation	SNP	C	C	A	rs12460932	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:36004171C>A	ENST00000339686.3	-	1	383	c.207G>T	c.(205-207)gaG>gaT	p.E69D	DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Missense_Mutation_p.E69D|DMKN_ENST00000418261.1_Missense_Mutation_p.E69D|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.E69D|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000429837.1_Missense_Mutation_p.E69D|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.E69D|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.E69D|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.E69D|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000436012.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	69	Gly-rich.		E -> D (in dbSNP:rs12460932).			extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GGCCAAGGGCCTCACTGACTT	0.627													C|||	1585	0.316494	0.3994	0.3357	5008	,	,		17452	0.3542		0.1431	False		,,,				2504	0.3303				p.E69D		Atlas-SNP	.											.	DMKN	116	.	0			c.G207T						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	1706,2700	516.7+/-369.2	344,1018,841	131.0	109.0	117.0		207,207,207,207,207,207,207	-5.7	0.0	19	dbSNP_120	117	1252,7348	250.3+/-277.2	106,1040,3154	yes	missense,missense,missense,missense,missense,missense,missense	DMKN	NM_001126056.2,NM_001126057.2,NM_001126058.2,NM_001190347.1,NM_001190348.1,NM_001190349.1,NM_033317.4	45,45,45,45,45,45,45	450,2058,3995	AA,AC,CC		14.5581,38.7199,22.7433	benign,benign,benign,benign,benign,benign,benign	69/466,69/399,69/387,69/450,69/437,69/370,69/477	36004171	2958,10048	2203	4300	6503	SO:0001583	missense	93099	exon1			AAGGGCCTCACTG	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.207G>T	19.37:g.36004171C>A	ENSP00000342012:p.Glu69Asp	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	110	48	0.436364	NM_001190347	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	592	0.27106227106227104	181	0.3678861788617886	98	0.27071823204419887	204	0.35664335664335667	109	0.1437994722955145	C	13.20	2.165566	0.38217	0.387199	0.145581	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000429837;ENST00000419602;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T;T;T	0.18016	2.75;2.51;2.51;2.27;2.27;2.26;2.26;2.24	2.87	-5.74	0.02391	.	1.443180	0.04827	N	0.438056	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B;D;D;B;B;B;B	0.56035	0.002;0.974;0.974;0.002;0.0;0.0;0.0	B;D;D;B;B;B;B	0.70487	0.0;0.969;0.969;0.0;0.0;0.0;0.0	T	0.17776	-1.0358	9	0.40728	T	0.16	0.0114	8.0196	0.30402	0.216:0.6689:0.1151:0.0	rs12460932;rs61157480;rs12460932	69;69;69;69;69;69;69	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;C9J4P6;Q6E0U4-4;Q6E0U4	.;.;.;.;.;.;DMKN_HUMAN	D	69	ENSP00000342012:E69D;ENSP00000405503:E69D;ENSP00000391036:E69D;ENSP00000394908:E69D;ENSP00000415277:E69D;ENSP00000414743:E69D;ENSP00000388404:E69D;ENSP00000409513:E69D	ENSP00000342012:E69D	E	-	3	2	DMKN	40696011	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.678000	0.05209	-0.832000	0.04251	-0.555000	0.04198	GAG	C|0.751;A|0.249	0.249	strong		0.627	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
MLXIPL	51085	hgsc.bcm.edu	37	7	73011060	73011060	+	Silent	SNP	C	C	T	rs41271232	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:73011060C>T	ENST00000313375.3	-	11	1778	c.1731G>A	c.(1729-1731)ccG>ccA	p.P577P	MLXIPL_ENST00000434326.1_Silent_p.P483P|MLXIPL_ENST00000395189.1_Silent_p.P484P|MLXIPL_ENST00000354613.1_Silent_p.P577P|MLXIPL_ENST00000429400.2_Silent_p.P577P|MLXIPL_ENST00000414749.2_Silent_p.P577P	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	577					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				GTGGCCGGGGCGGTGTAGGGG	0.687													c|||	187	0.0373403	0.0159	0.0476	5008	,	,		9963	0.0		0.0686	False		,,,				2504	0.0654				p.P577P		Atlas-SNP	.											.	MLXIPL	54	.	0			c.G1731A						PASS	.	C	,,,	128,3824		1,126,1849	8.0	11.0	10.0		1731,1731,1731,1731	-8.4	0.1	7	dbSNP_127	10	670,7562		23,624,3469	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MLXIPL	NM_032951.2,NM_032952.2,NM_032953.2,NM_032954.2	,,,	24,750,5318	TT,TC,CC		8.139,3.2389,6.5496	,,,	577/853,577/834,577/851,577/832	73011060	798,11386	1976	4116	6092	SO:0001819	synonymous_variant	51085	exon11			CCGGGGCGGTGTA	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"""carbohydrate response element binding protein"""	605678	"""Williams Beuren syndrome chromosome region 14"""	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.1731G>A	7.37:g.73011060C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Silent	SNP	ENST00000313375.3	37	CCDS5553.1																																																																																			C|0.958;T|0.042	0.042	strong		0.687	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951	
CSF3	1440	hgsc.bcm.edu	37	17	38173143	38173143	+	Silent	SNP	G	G	A	rs25645	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:38173143G>A	ENST00000225474.2	+	5	586	c.555G>A	c.(553-555)ctG>ctA	p.L185L	CSF3_ENST00000394149.3_Silent_p.L182L|CSF3_ENST00000577675.1_Silent_p.L142L|RP11-387H17.6_ENST00000583462.1_lincRNA|CSF3_ENST00000331769.2_Silent_p.L178L|CSF3_ENST00000394148.3_Silent_p.L149L			P09919	CSF3_HUMAN	colony stimulating factor 3 (granulocyte)	185					cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|granulocyte differentiation (GO:0030851)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of neuron death (GO:1901215)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|enzyme binding (GO:0019899)|granulocyte colony-stimulating factor receptor binding (GO:0005130)			endometrium(1)|ovary(1)|prostate(1)	3	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)				GAGGGGTCCTGGTTGCCTCCC	0.637													G|||	1571	0.313698	0.0514	0.4135	5008	,	,		16552	0.4276		0.3668	False		,,,				2504	0.4254				p.L185L		Atlas-SNP	.											.	CSF3	9	.	0			c.G555A						PASS	.	G	,,,	432,3974	209.8+/-230.5	18,396,1789	45.0	40.0	42.0		555,438,546,447	4.2	1.0	17	dbSNP_72	42	3203,5397	481.4+/-370.6	583,2037,1680	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CSF3	NM_000759.3,NM_001178147.1,NM_172219.2,NM_172220.2	,,,	601,2433,3469	AA,AG,GG		37.2442,9.8048,27.9486	,,,	185/208,146/169,182/205,149/172	38173143	3635,9371	2203	4300	6503	SO:0001819	synonymous_variant	1440	exon5			GGTCCTGGTTGCC		CCDS11357.1, CCDS11358.1, CCDS42314.1, CCDS11358.2	17q11.2-q12	2014-01-30			ENSG00000108342	ENSG00000108342		"""Endogenous ligands"""	2438	protein-coding gene	gene with protein product	"""granulocyte colony stimulating factor"", ""pluripoietin"", ""filgrastim"", ""lenograstim"""	138970	"""chromosome 17 open reading frame 33"""	GCSF, G-CSF, C17orf33		3499671, 3501046	Standard	NM_000759		Approved	MGC45931	uc002htp.3	P09919	OTTHUMG00000133247	ENST00000225474.2:c.555G>A	17.37:g.38173143G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	50	30	0.6	NM_000759	A8MXR7	Silent	SNP	ENST00000225474.2	37	CCDS11357.1																																																																																			G|0.705;A|0.295	0.295	strong		0.637	CSF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256988.2	NM_172220	
ILK	3611	hgsc.bcm.edu	37	11	6629665	6629665	+	Silent	SNP	C	C	T	rs1043388	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6629665C>T	ENST00000396751.2	+	3	753	c.297C>T	c.(295-297)caC>caT	p.H99H	ILK_ENST00000299421.4_Silent_p.H99H|RP11-732A19.2_ENST00000527398.1_RNA|TAF10_ENST00000531760.1_5'Flank|ILK_ENST00000420936.2_Silent_p.H99H|ILK_ENST00000537806.1_5'UTR|ILK_ENST00000528995.1_Silent_p.H99H	NM_001014795.1	NP_001014795.1	Q13418	ILK_HUMAN	integrin-linked kinase	99	Interaction with LIMS1.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell junction assembly (GO:0034329)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|extracellular fibril organization (GO:0043206)|fibroblast migration (GO:0010761)|integrin-mediated signaling pathway (GO:0007229)|myelin assembly (GO:0032288)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|peptidyl-serine phosphorylation (GO:0018105)|platelet aggregation (GO:0070527)|positive regulation of axon extension (GO:0045773)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)		TGAATGAACACGGGAATGTGC	0.483													T|||	1576	0.314696	0.4153	0.2608	5008	,	,		24191	0.3512		0.2535	False		,,,				2504	0.2423				p.H99H		Atlas-SNP	.											.	ILK	41	.	0			c.C297T						PASS	.	T	,,	1685,2717	654.2+/-399.7	315,1055,831	138.0	118.0	124.0		297,297,297	2.4	1.0	11	dbSNP_86	124	2148,6444	713.9+/-406.0	260,1628,2408	no	coding-synonymous,coding-synonymous,coding-synonymous	ILK	NM_001014794.1,NM_001014795.1,NM_004517.2	,,	575,2683,3239	TT,TC,CC		25.0,38.2781,29.4982	,,	99/453,99/453,99/453	6629665	3833,9161	2201	4296	6497	SO:0001819	synonymous_variant	3611	exon4			TGAACACGGGAAT	U40282	CCDS7768.1, CCDS60712.1, CCDS60713.1	11p15.4	2014-09-17			ENSG00000166333	ENSG00000166333		"""Ankyrin repeat domain containing"""	6040	protein-coding gene	gene with protein product		602366				8538749	Standard	NM_004517		Approved		uc001mef.3	Q13418	OTTHUMG00000133407	ENST00000396751.2:c.297C>T	11.37:g.6629665C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	175	86	0.491429	NM_001014794	B7Z1I0|B7Z418|D3DQU0|P57043|Q68DZ3	Silent	SNP	ENST00000396751.2	37	CCDS7768.1																																																																																			C|0.690;T|0.310	0.310	strong		0.483	ILK-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384519.1	NM_004517	
LDHAL6A	160287	hgsc.bcm.edu	37	11	18487305	18487305	+	Silent	SNP	C	C	G	rs17851143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18487305C>G	ENST00000280706.2	+	3	1163	c.366C>G	c.(364-366)ccC>ccG	p.P122P	LDHAL6A_ENST00000396213.3_Silent_p.P122P	NM_144972.4	NP_659409.2	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	122					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	L-lactate dehydrogenase activity (GO:0004459)			large_intestine(3)|lung(9)|urinary_tract(1)	13						TAATGATTCCCAATATTACCC	0.388													C|||	438	0.0874601	0.0545	0.1268	5008	,	,		20083	0.0615		0.1233	False		,,,				2504	0.0941				p.P122P		Atlas-SNP	.											LDHAL6A,NS,adenoma,0,1	LDHAL6A	35	1	0			c.C366G						PASS	.	C	,	317,4081	169.8+/-200.3	16,285,1898	131.0	133.0	133.0		366,366	-0.8	0.0	11	dbSNP_123	133	1153,7433	236.8+/-268.9	74,1005,3214	no	coding-synonymous,coding-synonymous	LDHAL6A	NM_001144071.1,NM_144972.4	,	90,1290,5112	GG,GC,CC		13.4288,7.2078,11.3216	,	122/333,122/333	18487305	1470,11514	2199	4293	6492	SO:0001819	synonymous_variant	160287	exon3			GATTCCCAATATT	AK131523	CCDS7841.1	11p15.1	2011-01-27			ENSG00000166800	ENSG00000166800			28335	protein-coding gene	gene with protein product						12477932	Standard	NM_001144071		Approved	MGC23940, LDH6A	uc001mop.1	Q6ZMR3	OTTHUMG00000167724	ENST00000280706.2:c.366C>G	11.37:g.18487305C>G		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	235	108	0.459574	NM_144972	D3DQY5	Silent	SNP	ENST00000280706.2	37	CCDS7841.1																																																																																			C|0.890;G|0.110	0.110	strong		0.388	LDHAL6A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395904.1	NM_144972	
PJA1	64219	hgsc.bcm.edu	37	X	68382836	68382836	+	Silent	SNP	G	G	A	rs7067170	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:68382836G>A	ENST00000361478.1	-	2	623	c.246C>T	c.(244-246)agC>agT	p.S82S	PJA1_ENST00000477231.1_5'UTR|PJA1_ENST00000374584.3_Silent_p.S82S|PJA1_ENST00000374571.4_Silent_p.S27S|PJA1_ENST00000374583.1_Silent_p.S82S	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	82					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						CCGAACTCTCGCTGTCGTCCC	0.517													G|||	330	0.0874172	0.0507	0.0865	3775	,	,		14395	0.0		0.1829	False		,,,				2504	0.0194				p.S82S		Atlas-SNP	.											.	PJA1	106	.	0			c.C246T						PASS	.	G	,,	327,3508		15,255,42,1362,529	147.0	126.0	133.0		81,246,246	-2.1	0.0	X	dbSNP_116	133	1593,5135		144,860,445,1424,1427	no	coding-synonymous,coding-synonymous,coding-synonymous	PJA1	NM_001032396.2,NM_022368.4,NM_145119.3	,,	159,1115,487,2786,1956	AA,AG,A,GG,G		23.6772,8.5267,18.1767	,,	27/589,82/456,82/644	68382836	1920,8643	2203	4300	6503	SO:0001819	synonymous_variant	64219	exon2			ACTCTCGCTGTCG	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"""RING-type (C3HC4) zinc fingers"""	16648	protein-coding gene	gene with protein product		300420	"""praja 1"", ""praja ring finger 1"""			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.246C>T	X.37:g.68382836G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	76	68	0.894737	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Silent	SNP	ENST00000361478.1	37	CCDS14393.1																																																																																			0|0.013;A|0.149	0.149	strong		0.517	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119	
SARDH	1757	hgsc.bcm.edu	37	9	136573412	136573412	+	Silent	SNP	G	G	A	rs2073815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:136573412G>A	ENST00000371872.4	-	11	1724	c.1467C>T	c.(1465-1467)caC>caT	p.H489H	SARDH_ENST00000439388.1_Silent_p.H489H|SARDH_ENST00000422262.2_Silent_p.H321H	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	489					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		GCGTTACCTCGTGCAGCGGGT	0.637													G|||	2123	0.423922	0.2254	0.464	5008	,	,		17063	0.4891		0.5577	False		,,,				2504	0.4591				p.H489H		Atlas-SNP	.											SARDH,NS,carcinoma,0,2	SARDH	112	2	0			c.C1467T						PASS	.	G	,	1190,3216	415.0+/-337.0	157,876,1170	73.0	66.0	68.0		1467,1467	0.6	1.0	9	dbSNP_96	68	4982,3618	625.8+/-397.8	1437,2108,755	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	1594,2984,1925	AA,AG,GG		42.0698,27.0086,47.455	,	489/919,489/919	136573412	6172,6834	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon11			TACCTCGTGCAGC		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1467C>T	9.37:g.136573412G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			G|0.539;A|0.461	0.461	strong		0.637	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
KIF15	56992	hgsc.bcm.edu	37	3	44871505	44871505	+	Missense_Mutation	SNP	A	A	T	rs11710339	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:44871505A>T	ENST00000326047.4	+	25	3135	c.2986A>T	c.(2986-2988)Aca>Tca	p.T996S	KIF15_ENST00000425755.1_Missense_Mutation_p.T631S	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	996			T -> S (in dbSNP:rs11710339). {ECO:0000269|PubMed:12747765, ECO:0000269|PubMed:17974005}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		GGAGCTAAGAACATCGGTCTG	0.373													A|||	316	0.063099	0.0159	0.0836	5008	,	,		13014	0.0		0.2197	False		,,,				2504	0.0164				p.T996S		Atlas-SNP	.											.	KIF15	103	.	0			c.A2986T						PASS	.	A	SER/THR	198,4208	123.3+/-160.7	4,190,2009	117.0	106.0	110.0		2986	-4.0	0.0	3	dbSNP_120	110	1794,6806	324.6+/-316.5	174,1446,2680	yes	missense	KIF15	NM_020242.2	58	178,1636,4689	TT,TA,AA		20.8605,4.4939,15.316	benign	996/1389	44871505	1992,11014	2203	4300	6503	SO:0001583	missense	56992	exon25			CTAAGAACATCGG	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"""Kinesins"""	17273	protein-coding gene	gene with protein product			"""kinesin-like 7"""	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.2986A>T	3.37:g.44871505A>T	ENSP00000324020:p.Thr996Ser	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	189	88	0.465608	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	37	CCDS33744.1	200	0.09157509157509157	7	0.014227642276422764	28	0.07734806629834254	0	0.0	165	0.21767810026385223	A	9.425	1.084041	0.20309	0.044939	0.208605	ENSG00000163808	ENST00000326047;ENST00000396031;ENST00000425755	T;T	0.40756	1.02;1.02	5.61	-4.04	0.04010	.	0.730438	0.12092	N	0.500355	T	0.00012	0.0000	N	0.20685	0.6	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.13407	0.009	T	0.31668	-0.9935	9	0.08381	T	0.77	.	6.5448	0.22400	0.443:0.0:0.3782:0.1788	rs11710339;rs17631234;rs11710339	996	Q9NS87	KIF15_HUMAN	S	996;995;631	ENSP00000324020:T996S;ENSP00000389982:T631S	ENSP00000324020:T996S	T	+	1	0	KIF15	44846509	0.500000	0.26091	0.031000	0.17742	0.989000	0.77384	0.083000	0.14871	-0.345000	0.08325	0.482000	0.46254	ACA	A|0.868;T|0.132	0.132	strong		0.373	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2		
MYO18B	84700	hgsc.bcm.edu	37	22	26304363	26304363	+	Silent	SNP	G	G	A	rs58609797	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:26304363G>A	ENST00000407587.2	+	32	5395	c.5226G>A	c.(5224-5226)gaG>gaA	p.E1742E	MYO18B_ENST00000536101.1_Silent_p.E1741E|MYO18B_ENST00000335473.7_Silent_p.E1741E			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1741	Gln-rich.|Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						ACCAGGAGGAGGAACTGGAGG	0.607													G|||	259	0.0517173	0.1589	0.0159	5008	,	,		19484	0.0		0.0219	False		,,,				2504	0.0164				p.E1741E		Atlas-SNP	.											.	MYO18B	322	.	0			c.G5223A						PASS	.	G		439,3823		21,397,1713	54.0	66.0	62.0		5223	-0.9	1.0	22	dbSNP_129	62	122,8348		2,118,4115	no	coding-synonymous	MYO18B	NM_032608.5		23,515,5828	AA,AG,GG		1.4404,10.3003,4.4062		1741/2568	26304363	561,12171	2131	4235	6366	SO:0001819	synonymous_variant	84700	exon32			GGAGGAGGAACTG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.5226G>A	22.37:g.26304363G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				G|0.952;A|0.048	0.048	strong		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
LRRC16A	55604	hgsc.bcm.edu	37	6	25420350	25420350	+	Silent	SNP	A	A	C	rs41271807	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:25420350A>C	ENST00000329474.6	+	3	515	c.147A>C	c.(145-147)acA>acC	p.T49T	LRRC16A_ENST00000377969.3_5'UTR	NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	49					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						AGGTCCTTACATCATGCCGAG	0.488													A|||	578	0.115415	0.0242	0.0922	5008	,	,		19555	0.128		0.1839	False		,,,				2504	0.1718				p.T49T		Atlas-SNP	.											.	LRRC16A	168	.	0			c.A147C						PASS	.	A	,	189,3843		1,187,1828	189.0	174.0	179.0		147,147	-3.9	0.9	6	dbSNP_127	179	1378,6988		122,1134,2927	no	coding-synonymous,coding-synonymous	LRRC16A	NM_001173977.1,NM_017640.5	,	123,1321,4755	CC,CA,AA		16.4714,4.6875,12.6391	,	49/1366,49/1372	25420350	1567,10831	2016	4183	6199	SO:0001819	synonymous_variant	55604	exon3			CCTTACATCATGC	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"""capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"""	609593	"""leucine rich repeat containing 16"""	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.147A>C	6.37:g.25420350A>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	160	67	0.41875	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Silent	SNP	ENST00000329474.6	37	CCDS54973.1																																																																																			A|0.861;C|0.139	0.139	strong		0.488	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
RHBDD3	25807	hgsc.bcm.edu	37	22	29656431	29656431	+	Nonsense_Mutation	SNP	C	C	T	rs138870856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29656431C>T	ENST00000216085.7	-	6	1291	c.867G>A	c.(865-867)tgG>tgA	p.W289*	CTA-984G1.5_ENST00000433125.1_RNA	NM_012265.1	NP_036397.1	Q9Y3P4	RHBD3_HUMAN	rhomboid domain containing 3	289					liver development (GO:0001889)|MAPK cascade (GO:0000165)|negative regulation of natural killer cell activation (GO:0032815)|positive regulation of protein catabolic process (GO:0045732)|regulation of acute inflammatory response (GO:0002673)|regulation of protein secretion (GO:0050708)|response to xenobiotic stimulus (GO:0009410)	integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			lung(1)|ovary(1)	2						CCAAGGCCGCCCACATCGGAG	0.677													C|||	15	0.00299521	0.0	0.0029	5008	,	,		16272	0.0		0.0129	False		,,,				2504	0.0				p.W289X		Atlas-SNP	.											.	RHBDD3	17	.	0			c.G867A						PASS	.	C	stop/TRP	8,4398		0,8,2195	17.0	19.0	18.0		867	5.4	1.0	22	dbSNP_134	18	104,8496		2,100,4198	yes	stop-gained	RHBDD3	NM_012265.1		2,108,6393	TT,TC,CC		1.2093,0.1816,0.8611		289/387	29656431	112,12894	2203	4300	6503	SO:0001587	stop_gained	25807	exon6			GGCCGCCCACATC	AL050346	CCDS13850.1	22q12.2	2006-02-22	2006-02-22	2006-02-22	ENSG00000100263	ENSG00000100263			1308	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 3"""	C22orf3		10591208, 15105437	Standard	NM_012265		Approved	PTAG	uc003aeq.1	Q9Y3P4	OTTHUMG00000151032	ENST00000216085.7:c.867G>A	22.37:g.29656431C>T	ENSP00000216085:p.Trp289*	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	91	35	0.384615	NM_012265	Q6I9X3|Q9UGQ7	Nonsense_Mutation	SNP	ENST00000216085.7	37	CCDS13850.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	C	37	6.024734	0.97211	0.001816	0.012093	ENSG00000100263	ENST00000216085	.	.	.	5.38	5.38	0.77491	.	0.116120	0.38720	N	0.001598	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-8.6866	16.0353	0.80625	0.0:1.0:0.0:0.0	.	.	.	.	X	289	.	ENSP00000216085:W289X	W	-	3	0	RHBDD3	27986431	0.997000	0.39634	0.986000	0.45419	0.363000	0.29612	2.318000	0.43779	2.533000	0.85409	0.643000	0.83706	TGG	C|0.993;T|0.007	0.007	strong		0.677	RHBDD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321085.1	NM_012265	
MUC21	394263	hgsc.bcm.edu	37	6	30954438	30954438	+	Silent	SNP	C	C	T	rs41288646	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954438C>T	ENST00000376296.3	+	2	727	c.486C>T	c.(484-486)gcC>gcT	p.A162A	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	162	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAGTGAGGCCAGCACAGCCA	0.617													C|||	26	0.00519169	0.0038	0.0086	5008	,	,		24561	0.002		0.007	False		,,,				2504	0.0061				p.A162A		Atlas-SNP	.											.	MUC21	98	.	0			c.C486T						PASS	.						145.0	136.0	139.0					6																	30954438		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			TGAGGCCAGCACA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.486C>T	6.37:g.30954438C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	105	14	0.133333	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			C|0.997;T|0.003	0.003	strong		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
DST	667	hgsc.bcm.edu	37	6	56485365	56485365	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:56485365C>T	ENST00000370765.6	-	23	3574	c.3467G>A	c.(3466-3468)cGa>cAa	p.R1156Q	DST_ENST00000370769.4_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000370754.5_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	0					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.R1156P(2)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTCCTCTACTCGGGACTTTTG	0.428																																					p.R1156Q		Atlas-SNP	.											DST_ENST00000370765,NS,carcinoma,-1,4	DST	1427	4	2	Substitution - Missense(2)	upper_aerodigestive_tract(2)	c.G3467A						scavenged	.						178.0	173.0	175.0					6																	56485365		2203	4300	6503	SO:0001583	missense	667	exon23			TCTACTCGGGACT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.3467G>A	6.37:g.56485365C>T	ENSP00000359801:p.Arg1156Gln	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	168	6	0.0357143	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	0.673	-0.801010	0.02841	.	.	ENSG00000151914	ENST00000370765	T	0.23754	1.89	4.48	1.47	0.22746	.	.	.	.	.	T	0.02929	0.0087	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.44143	-0.9347	7	0.12103	T	0.63	.	2.5944	0.04850	0.2163:0.3499:0.0:0.4337	.	1156	Q03001-3	.	Q	1156	ENSP00000359801:R1156Q	ENSP00000359801:R1156Q	R	-	2	0	DST	56593324	0.014000	0.17966	0.321000	0.25320	0.688000	0.40055	-0.040000	0.12104	0.525000	0.28522	0.460000	0.39030	CGA	.	.	none		0.428	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723	
TCP10	6953	hgsc.bcm.edu	37	6	167789473	167789473	+	Silent	SNP	C	C	T	rs76263155	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:167789473C>T	ENST00000397829.4	-	6	836	c.669G>A	c.(667-669)acG>acA	p.T223T	TCP10_ENST00000366827.2_Silent_p.T223T	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	250						cytosol (GO:0005829)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(6)	18		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		TGGCTGCTGCCGTCTGCTCCT	0.577													c|||	83	0.0165735	0.0008	0.0288	5008	,	,		15015	0.001		0.0417	False		,,,				2504	0.0194				p.T223T		Atlas-SNP	.											.	TCP10	35	.	0			c.G669A						PASS	.	C		28,3932		1,26,1953	20.0	24.0	23.0		669	-3.3	0.0	6	dbSNP_131	23	227,8107		9,209,3949	no	coding-synonymous	TCP10	NM_004610.3		10,235,5902	TT,TC,CC		2.7238,0.7071,2.0742		223/327	167789473	255,12039	1980	4167	6147	SO:0001819	synonymous_variant	6953	exon6			TGCTGCCGTCTGC	U03399	CCDS43527.1	6q27	2012-09-20	2012-09-20		ENSG00000203690	ENSG00000203690			11656	protein-coding gene	gene with protein product		187020	"""t-complex 10 (a murine tcp homolog)"", ""t-complex 10 (mouse)"", ""t-complex 10 homolog (mouse)"""			8111376	Standard	NM_004610		Approved		uc003qvv.1	Q12799	OTTHUMG00000016026	ENST00000397829.4:c.669G>A	6.37:g.167789473C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_004610	Q5JR60|Q6P4F4	Silent	SNP	ENST00000397829.4	37	CCDS43527.1																																																																																			C|0.980;T|0.020	0.020	strong		0.577	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1	NM_004610	
ING2	3622	hgsc.bcm.edu	37	4	184426387	184426387	+	Silent	SNP	C	C	T	rs8872	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:184426387C>T	ENST00000302327.3	+	1	241	c.39C>T	c.(37-39)gcC>gcT	p.A13A	RP11-367N14.2_ENST00000457303.3_RNA|ING2_ENST00000434682.2_5'Flank	NM_001564.2	NP_001555.1	Q9H160	ING2_HUMAN	inhibitor of growth family, member 2	13					chromatin modification (GO:0016568)|male germ-line stem cell asymmetric division (GO:0048133)|male meiosis I (GO:0007141)|negative regulation of cell proliferation (GO:0008285)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cellular senescence (GO:2000772)|regulation of growth (GO:0040008)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|seminiferous tubule development (GO:0072520)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleus (GO:0005634)|Sin3 complex (GO:0016580)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)	7		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|all_hematologic(60;0.0207)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		ACTCGTCGGCCGCGCTCCTGA	0.687													C|||	3572	0.713259	0.7209	0.6527	5008	,	,		11142	0.6349		0.8022	False		,,,				2504	0.7352				p.A13A		Atlas-SNP	.											ING2,NS,carcinoma,0,1	ING2	20	1	0			c.C39T						PASS	.	C		3078,1286		1122,834,226	16.0	15.0	15.0		39	3.2	1.0	4	dbSNP_52	15	6756,1796		2710,1336,230	no	coding-synonymous	ING2	NM_001564.2		3832,2170,456	TT,TC,CC		21.0009,29.4684,23.8619		13/281	184426387	9834,3082	2182	4276	6458	SO:0001819	synonymous_variant	3622	exon1			GTCGGCCGCGCTC	AB012853	CCDS3833.1	4q35.1	2013-01-28	2005-02-10	2005-02-11	ENSG00000168556	ENSG00000168556		"""Zinc fingers, PHD-type"""	6063	protein-coding gene	gene with protein product		604215	"""inhibitor of growth family, member 1-like"""	ING1L		10072587	Standard	XM_005262982		Approved	p33ING2	uc003ivs.1	Q9H160	OTTHUMG00000150502	ENST00000302327.3:c.39C>T	4.37:g.184426387C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	116	113	0.974138	NM_001564	B6ZDS1|O95698	Silent	SNP	ENST00000302327.3	37	CCDS3833.1																																																																																			C|0.275;T|0.725	0.725	strong		0.687	ING2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318652.1	NM_001564	
LEPR	3953	hgsc.bcm.edu	37	1	66036441	66036441	+	Missense_Mutation	SNP	A	A	G	rs1137100	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:66036441A>G	ENST00000349533.6	+	4	511	c.326A>G	c.(325-327)aAg>aGg	p.K109R	snoU13_ENST00000459362.1_RNA|LEPR_ENST00000406510.3_5'UTR|LEPR_ENST00000371059.3_Missense_Mutation_p.K109R|LEPR_ENST00000371058.1_Missense_Mutation_p.K109R|LEPR_ENST00000371060.3_Missense_Mutation_p.K109R|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000344610.8_Missense_Mutation_p.K109R	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		ATTGAAGGAAAGACATTTGTT	0.318													A|||	1604	0.320288	0.1528	0.2378	5008	,	,		18463	0.8046		0.2704	False		,,,				2504	0.1575				p.K109R		Atlas-SNP	.											.	LEPR	284	.	0			c.A326G	GRCh37	CM032948	LEPR	M	rs1137100	PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	762,3644	301.0+/-286.6	58,646,1499	65.0	66.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	326,326,326,326,326,326	4.6	0.9	1	dbSNP_86	65	2273,6327	377.6+/-338.6	304,1665,2331	yes	missense,missense,missense,missense,missense,missense	LEPR	NM_001003679.3,NM_001003680.3,NM_001198687.1,NM_001198688.1,NM_001198689.1,NM_002303.5	26,26,26,26,26,26	362,2311,3830	GG,GA,AA		26.4302,17.2946,23.3354	benign,benign,benign,benign,benign,benign	109/897,109/959,109/959,109/907,109/897,109/1166	66036441	3035,9971	2203	4300	6503	SO:0001583	missense	3953	exon4			AAGGAAAGACATT	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.326A>G	1.37:g.66036441A>G	ENSP00000330393:p.Lys109Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	111	47	0.423423	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	841	0.3850732600732601	63	0.12804878048780488	96	0.26519337016574585	464	0.8111888111888111	218	0.287598944591029	A	11.95	1.792657	0.31685	0.172946	0.264302	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.59906	0.27;0.26;0.29;0.23;0.27	5.69	4.55	0.56014	.	0.204186	0.43260	D	0.000583	T	0.50188	0.1601	L	0.53249	1.67	0.09310	P	0.999999999901199	D;B;B;D	0.61697	0.971;0.077;0.204;0.99	P;B;B;P	0.59056	0.725;0.021;0.084;0.851	T	0.50206	-0.8855	9	0.20519	T	0.43	-5.8543	8.8143	0.34987	0.9121:0.0:0.0879:0.0	rs1137100;rs1805092;rs3200841;rs3790430;rs17127718;rs17356583;rs17434225;rs59932898;rs1137100	109;109;109;109	P48357-4;P48357;P48357-2;P48357-3	.;LEPR_HUMAN;.;.	R	109	ENSP00000340884:K109R;ENSP00000330393:K109R;ENSP00000360099:K109R;ENSP00000360098:K109R;ENSP00000360097:K109R	ENSP00000340884:K109R	K	+	2	0	LEPR	65809029	0.986000	0.35501	0.871000	0.34182	0.808000	0.45660	2.343000	0.44001	2.167000	0.68274	0.455000	0.32223	AAG	A|0.705;G|0.295	0.295	strong		0.318	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
A1CF	29974	hgsc.bcm.edu	37	10	52573698	52573698	+	Silent	SNP	G	G	A	rs41274048	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:52573698G>A	ENST00000373993.1	-	8	1310	c.1266C>T	c.(1264-1266)ctC>ctT	p.L422L	A1CF_ENST00000373995.3_Silent_p.L422L|A1CF_ENST00000374001.2_Silent_p.L414L|A1CF_ENST00000373997.3_Silent_p.L414L|ASAH2B_ENST00000483649.1_Intron|A1CF_ENST00000282641.2_Silent_p.L422L|A1CF_ENST00000395489.2_Silent_p.L415L|A1CF_ENST00000493415.1_5'UTR|A1CF_ENST00000395495.1_Silent_p.L367L			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	422					cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						AAATGTCATAGAGTTTGTCTT	0.507													G|||	531	0.10603	0.1498	0.0432	5008	,	,		16897	0.0883		0.0865	False		,,,				2504	0.1299				p.L430L		Atlas-SNP	.											.	A1CF	190	.	0			c.C1290T						PASS	.	G	,,,,,	561,3845	252.1+/-258.6	33,495,1675	156.0	154.0	155.0		1242,1290,1266,1242,1266,1266	5.0	1.0	10	dbSNP_127	155	646,7954	165.2+/-217.4	22,602,3676	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	A1CF	NM_001198818.1,NM_001198819.1,NM_001198820.1,NM_014576.3,NM_138932.2,NM_138933.2	,,,,,	55,1097,5351	AA,AG,GG		7.5116,12.7326,9.2803	,,,,,	414/587,430/603,422/595,414/587,422/595,422/595	52573698	1207,11799	2203	4300	6503	SO:0001819	synonymous_variant	29974	exon12			GTCATAGAGTTTG	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.1266C>T	10.37:g.52573698G>A		Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	271	143	0.527675	NM_001198819	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Silent	SNP	ENST00000373993.1	37	CCDS7242.1																																																																																			G|0.908;A|0.092	0.092	strong		0.507	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576	
PCSK5	5125	hgsc.bcm.edu	37	9	78969059	78969059	+	Missense_Mutation	SNP	C	C	A	rs7036921	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:78969059C>A	ENST00000545128.1	+	36	5635	c.5097C>A	c.(5095-5097)gaC>gaA	p.D1699E		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1699	CRM (Cys-rich motif).				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						ACATGGACGACAGCCACTGCC	0.592													C|||	1162	0.232029	0.2579	0.1873	5008	,	,		18912	0.0863		0.2932	False		,,,				2504	0.316				p.D1699E		Atlas-SNP	.											PCSK5_ENST00000545128,NS,carcinoma,+1,1	PCSK5	329	1	0			c.C5097A						scavenged	.						17.0	15.0	16.0					9																	78969059		876	1991	2867	SO:0001583	missense	5125	exon36			GGACGACAGCCAC		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.5097C>A	9.37:g.78969059C>A	ENSP00000446280:p.Asp1699Glu	Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	185	98	0.52973	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	477	0.2184065934065934	135	0.27439024390243905	79	0.21823204419889503	50	0.08741258741258741	213	0.28100263852242746	C	3.362	-0.130284	0.06753	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.64438	-0.1;-0.1	5.82	0.0282	0.14158	.	0.322809	0.33457	N	0.004898	T	0.00012	0.0000	N	0.21240	0.645	0.46028	P	0.0011710000000000331	.	.	.	.	.	.	T	0.11203	-1.0597	7	0.05959	T	0.93	-21.1474	2.861	0.05586	0.2044:0.2208:0.4208:0.154	rs7036921;rs56654594;rs7036921	.	.	.	E	1699;1429;1399	ENSP00000446280:D1699E;ENSP00000411654:D1399E	ENSP00000365945:D1429E	D	+	3	2	PCSK5	78158879	0.000000	0.05858	0.148000	0.22405	0.115000	0.19883	-0.235000	0.09016	0.341000	0.23771	-0.304000	0.09214	GAC	C|0.769;A|0.231	0.231	strong		0.592	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
REST	5978	hgsc.bcm.edu	37	4	57797414	57797414	+	Missense_Mutation	SNP	C	C	T	rs3796529	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:57797414C>T	ENST00000309042.7	+	4	2704	c.2390C>T	c.(2389-2391)cCa>cTa	p.P797L		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	797	Pro-rich.		P -> L (in dbSNP:rs3796529). {ECO:0000269|PubMed:8568247}.		cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P797L(2)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CAGAGGGAGCCACCTCCTCCC	0.532													C|||	1306	0.260783	0.2738	0.2248	5008	,	,		18741	0.377		0.1849	False		,,,				2504	0.227				p.P797L		Atlas-SNP	.											REST,NS,carcinoma,0,1	REST	104	1	2	Substitution - Missense(2)	prostate(2)	c.C2390T						PASS	.	C	LEU/PRO,LEU/PRO	1121,3285	398.3+/-330.8	125,871,1207	108.0	120.0	116.0		2390,2390	0.4	0.0	4	dbSNP_107	116	1636,6964	302.2+/-305.8	141,1354,2805	yes	missense,missense	REST	NM_001193508.1,NM_005612.4	98,98	266,2225,4012	TT,TC,CC		19.0233,25.4426,21.1979	probably-damaging,probably-damaging	797/1098,797/1098	57797414	2757,10249	2203	4300	6503	SO:0001583	missense	5978	exon4			GGGAGCCACCTCC	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.2390C>T	4.37:g.57797414C>T	ENSP00000311816:p.Pro797Leu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	CCDS3509.1	544	0.2490842490842491	123	0.25	71	0.19613259668508287	208	0.36363636363636365	142	0.18733509234828497	C	12.13	1.845760	0.32606	0.254426	0.190233	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.06218	3.33	3.08	0.384	0.16244	.	1.097820	0.07026	N	0.827581	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.11235	0.004;0.001	B;B	0.09377	0.004;0.001	T	0.48007	-0.9072	9	0.42905	T	0.14	-0.8172	5.4341	0.16472	0.0:0.6053:0.0:0.3947	rs3796529;rs57306785;rs3796529	774;797	F8WAN5;Q13127	.;REST_HUMAN	L	797;774	ENSP00000311816:P797L	ENSP00000311816:P797L	P	+	2	0	REST	57492171	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-1.057000	0.03486	0.027000	0.15297	-0.192000	0.12808	CCA	C|0.784;T|0.216	0.216	strong		0.532	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
NACA	4666	hgsc.bcm.edu	37	12	57109931	57109931	+	Missense_Mutation	SNP	A	A	T	rs2926747	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57109931A>T	ENST00000454682.1	-	3	5664	c.5383T>A	c.(5383-5385)Tcc>Acc	p.S1795T	NACA_ENST00000546392.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.S642T|NACA_ENST00000548563.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000551793.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1795	Pro-rich.		S -> T (in dbSNP:rs2926747). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						ACTGGTGGGGAGGGTGCTGCA	0.567			T	BCL6	NHL								T|||	3248	0.648562	0.4826	0.6744	5008	,	,		18231	0.7421		0.6262	False		,,,				2504	0.7812				p.S642T		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.T1924A						PASS	.	T	,,THR/SER,	1633,1503		429,775,364	43.0	41.0	41.0		,,1924,	2.5	0.0	12	dbSNP_101	41	4453,2711		1392,1669,521	yes	intron,intron,missense,intron	NACA	NM_001113201.1,NM_001113202.1,NM_001113203.2,NM_005594.4	,,58,	1821,2444,885	TT,TA,AA		37.842,47.9273,40.9126	,,benign,	,,642/926,	57109931	6086,4214	1568	3582	5150	SO:0001583	missense	4666	exon5			GTGGGGAGGGTGC	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.5383T>A	12.37:g.57109931A>T	ENSP00000403817:p.Ser1795Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	37		1392	0.6373626373626373	248	0.5040650406504065	252	0.6961325966850829	426	0.7447552447552448	466	0.6147757255936676	T	0.563	-0.844356	0.02671	0.520727	0.62158	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.41400	1.0;1.02	3.77	2.55	0.30701	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27806	-1.0063	8	0.26408	T	0.33	.	4.1621	0.10289	0.1778:0.1045:0.0:0.7177	rs2926747;rs3782231;rs59687646	1795;642	E9PAV3;F8VU71	.;.	T	1795;642	ENSP00000403817:S1795T;ENSP00000448035:S642T	ENSP00000403817:S1795T	S	-	1	0	NACA	55396198	0.000000	0.05858	0.043000	0.18650	0.174000	0.22865	-0.595000	0.05727	0.051000	0.15978	-0.514000	0.04452	TCC	A|0.363;T|0.637	0.637	strong		0.567	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
SLC25A37	51312	hgsc.bcm.edu	37	8	23423669	23423669	+	Missense_Mutation	SNP	A	A	G	rs2942194	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:23423669A>G	ENST00000519973.1	+	2	457	c.259A>G	c.(259-261)Atc>Gtc	p.I87V	SLC25A37_ENST00000517923.1_3'UTR	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	87			I -> V (in dbSNP:rs2942194).		iron ion homeostasis (GO:0055072)|mitochondrial iron ion transport (GO:0048250)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	iron ion transmembrane transporter activity (GO:0005381)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)		GTACACAAGTATCTACGGAGC	0.522													A|||	867	0.173123	0.0197	0.2421	5008	,	,		17834	0.2163		0.2922	False		,,,				2504	0.1646				p.I87V		Atlas-SNP	.											.	SLC25A37	27	.	0			c.A259G						PASS	.	A	VAL/ILE	224,3528		8,208,1660	50.0	46.0	48.0		259	3.5	0.6	8	dbSNP_101	48	2270,5940		334,1602,2169	yes	missense	SLC25A37	NM_016612.2	29	342,1810,3829	GG,GA,AA		27.6492,5.9701,20.8494	benign	87/339	23423669	2494,9468	1876	4105	5981	SO:0001583	missense	51312	exon2			ACAAGTATCTACG	AF495725	CCDS47828.1	8p21.2	2013-05-22	2012-03-29		ENSG00000147454	ENSG00000147454		"""Solute carriers"""	29786	protein-coding gene	gene with protein product	"""mitoferrin"""	610387	"""solute carrier family 25, member 37"""			16511496	Standard	XM_006716352		Approved	MSCP, MFRN, MFRN1	uc003xdo.3	Q9NYZ2	OTTHUMG00000163865	ENST00000519973.1:c.259A>G	8.37:g.23423669A>G	ENSP00000429200:p.Ile87Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Missense_Mutation	SNP	ENST00000519973.1	37	CCDS47828.1	436	0.19963369963369965	9	0.018292682926829267	101	0.27900552486187846	114	0.1993006993006993	212	0.2796833773087071	A	4.840	0.156136	0.09236	0.059701	0.276492	ENSG00000147454	ENST00000519973;ENST00000523930	T;T	0.79352	-1.26;-1.26	5.63	3.49	0.39957	Mitochondrial carrier domain (2);	0.108721	0.64402	N	0.000008	T	0.00012	0.0000	N	0.02865	-0.47	0.30069	P	0.8102119999999999	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.09818	-1.0657	9	0.02654	T	1	-0.971	5.0266	0.14389	0.4417:0.0:0.5583:0.0	rs2942194;rs3736031;rs17778429;rs61300777;rs2942194	87;87	Q9NYZ2;Q9NYZ2-2	MFRN1_HUMAN;.	V	87;68	ENSP00000429200:I87V;ENSP00000428066:I68V	ENSP00000290075:I87V	I	+	1	0	SLC25A37	23479614	1.000000	0.71417	0.591000	0.28745	0.960000	0.62799	4.460000	0.60108	0.457000	0.26962	0.533000	0.62120	ATC	A|0.818;G|0.182	0.182	strong		0.522	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612	
DNM1L	10059	hgsc.bcm.edu	37	12	32860302	32860302	+	Splice_Site	SNP	G	G	A	rs2272238	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:32860302G>A	ENST00000549701.1	+	3	326	c.252G>A	c.(250-252)ggG>ggA	p.G84G	Y_RNA_ENST00000364693.1_RNA|DNM1L_ENST00000548671.1_3'UTR|DNM1L_ENST00000452533.2_Splice_Site_p.G84G|DNM1L_ENST00000547312.1_Splice_Site_p.G84G|DNM1L_ENST00000414834.2_Splice_Site_p.G29E|DNM1L_ENST00000553257.1_Splice_Site_p.G97G|DNM1L_ENST00000381000.4_Splice_Site_p.G97G|DNM1L_ENST00000266481.6_Splice_Site_p.G84G|DNM1L_ENST00000358214.5_Splice_Site_p.G97G			O00429	DNM1L_HUMAN	dynamin 1-like	84	Dynamin-type G.|GTPase domain.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					TTTTTCCAGGGGTGGAAGCAG	0.284													G|||	721	0.14397	0.2103	0.1037	5008	,	,		14724	0.0833		0.164	False		,,,				2504	0.1247				p.G84G		Atlas-SNP	.											.	DNM1L	52	.	0			c.G252A						PASS	.	G	,,	861,3543	329.6+/-301.1	79,703,1420	89.0	92.0	91.0		252,252,252	-3.5	1.0	12	dbSNP_100	91	1251,7323	248.6+/-276.2	102,1047,3138	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	DNM1L	NM_005690.3,NM_012062.3,NM_012063.2	,,	181,1750,4558	AA,AG,GG		14.5906,19.5504,16.2737	,,	84/700,84/737,84/711	32860302	2112,10866	2202	4287	6489	SO:0001630	splice_region_variant	10059	exon3			TCCAGGGGTGGAA	AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.251-1G>A	12.37:g.32860302G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	224	105	0.46875	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Silent	SNP	ENST00000549701.1	37	CCDS8729.1	306	0.1401098901098901	108	0.21951219512195122	37	0.10220994475138122	41	0.07167832167832168	120	0.158311345646438	G	15.65	2.895173	0.52121	0.195504	0.145906	ENSG00000087470	ENST00000414834	D	0.95447	-3.71	4.81	-3.54	0.04653	.	0.295993	0.19558	U	0.111387	T	0.00328	0.0010	.	.	.	0.44432	P	0.0026439999999999797	B	0.02656	0.0	B	0.01281	0.0	T	0.50617	-0.8807	8	0.87932	D	0	.	2.0606	0.03591	0.2703:0.219:0.3991:0.1115	rs2272238;rs2272238	29	B4DGC9	.	E	29	ENSP00000404160:G29E	ENSP00000404160:G29E	G	+	2	0	DNM1L	32751569	0.125000	0.22332	0.993000	0.49108	0.998000	0.95712	-0.519000	0.06260	-0.090000	0.12462	0.650000	0.86243	GGG	G|0.839;A|0.161	0.161	strong		0.284	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062	Silent
PTPN13	5783	hgsc.bcm.edu	37	4	87706506	87706506	+	Missense_Mutation	SNP	T	T	G	rs989902	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:87706506T>G	ENST00000411767.2	+	39	6304	c.6241T>G	c.(6241-6243)Tac>Gac	p.Y2081D	PTPN13_ENST00000316707.6_Missense_Mutation_p.Y1890D|PTPN13_ENST00000427191.2_Missense_Mutation_p.Y2062D|PTPN13_ENST00000436978.1_Missense_Mutation_p.Y2086D|PTPN13_ENST00000511467.1_Missense_Mutation_p.Y2086D			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2081			Y -> D (in dbSNP:rs989902).		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TGCAGCAGGATACTCCTGTGG	0.393													A|||	2537	0.506589	0.8268	0.464	5008	,	,		16008	0.4454		0.4026	False		,,,				2504	0.274				p.Y2086D		Atlas-SNP	.											.	PTPN13	203	.	0			c.T6256G						PASS	.	A	ASP/TYR,ASP/TYR,ASP/TYR,ASP/TYR	2899,797		1142,615,91	54.0	55.0	55.0		6184,6241,5668,6256	2.8	0.0	4	dbSNP_86	55	3432,4748		720,1992,1378	yes	missense,missense,missense,missense	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	160,160,160,160	1862,2607,1469	GG,GT,TT		41.956,21.5639,46.6908	benign,benign,benign,benign	2062/2467,2081/2486,1890/2295,2086/2491	87706506	6331,5545	1848	4090	5938	SO:0001583	missense	5783	exon39			GCAGGATACTCCT		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.6241T>G	4.37:g.87706506T>G	ENSP00000407249:p.Tyr2081Asp	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	160	159	0.99375	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	1106	0.5064102564102564	391	0.7947154471544715	180	0.4972375690607735	242	0.4230769230769231	293	0.3865435356200528	A	0.017	-1.489954	0.01018	0.784361	0.41956	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.49432	0.78;0.81;0.88;0.78;0.81	4.65	2.83	0.33086	.	0.774897	0.11052	N	0.604978	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.34004	-0.9846	9	0.22706	T	0.39	.	0.989	0.01452	0.1803:0.1535:0.3509:0.3153	rs989902;rs2230599;rs52802484;rs58380568;rs989902	1890;2062;2081;2086	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	D	2062;2086;1890;2081;2086;2030	ENSP00000408368:Y2062D;ENSP00000394794:Y2086D;ENSP00000322675:Y1890D;ENSP00000407249:Y2081D;ENSP00000426626:Y2086D	ENSP00000322675:Y1890D	Y	+	1	0	PTPN13	87925530	0.017000	0.18338	0.024000	0.17045	0.075000	0.17131	0.517000	0.22832	0.160000	0.19432	-1.386000	0.01163	TAC	T|0.475;G|0.513	0.513	strong		0.393	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
C16orf46	123775	hgsc.bcm.edu	37	16	81095091	81095091	+	Missense_Mutation	SNP	A	A	G	rs7198494	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81095091A>G	ENST00000299578.5	-	4	1098	c.863T>C	c.(862-864)aTa>aCa	p.I288T	C16orf46_ENST00000444657.3_5'Flank|C16orf46_ENST00000378611.4_Missense_Mutation_p.I288T|RP11-303E16.8_ENST00000564536.1_RNA	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	288			I -> T (in dbSNP:rs7198494).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						CAGCAGGGATATCTGGGCCGC	0.577													G|||	790	0.157748	0.2791	0.1643	5008	,	,		17378	0.0198		0.2048	False		,,,				2504	0.0828				p.I288T		Atlas-SNP	.											.	C16orf46	57	.	0			c.T863C						PASS	.	G	THR/ILE,THR/ILE	1168,3236	707.8+/-407.5	143,882,1177	112.0	107.0	108.0		863,863	2.4	0.0	16	dbSNP_116	108	1943,6657	716.5+/-406.1	224,1495,2581	yes	missense,missense	C16orf46	NM_001100873.1,NM_152337.2	89,89	367,2377,3758	GG,GA,AA		22.593,26.5213,23.9234	benign,benign	288/389,288/396	81095091	3111,9893	2202	4300	6502	SO:0001583	missense	123775	exon3			AGGGATATCTGGG	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.863T>C	16.37:g.81095091A>G	ENSP00000299578:p.Ile288Thr	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	273	122	0.446886	NM_001100873	Q96MA7	Missense_Mutation	SNP	ENST00000299578.5	37	CCDS10932.1	372	0.17032967032967034	140	0.2845528455284553	69	0.19060773480662985	13	0.022727272727272728	150	0.19788918205804748	G	0.004	-2.315748	0.00235	0.265213	0.22593	ENSG00000166455	ENST00000378611;ENST00000444657;ENST00000299578	T;T	0.12774	2.65;2.65	5.53	2.4	0.29515	.	0.813420	0.11056	N	0.604525	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46624	-0.9178	9	0.02654	T	1	.	3.4169	0.07378	0.1687:0.1419:0.5584:0.131	rs7198494;rs61064956;rs7198494	288;288	Q6P387-2;Q6P387	.;CP046_HUMAN	T	288;15;288	ENSP00000367874:I288T;ENSP00000299578:I288T	ENSP00000299578:I288T	I	-	2	0	C16orf46	79652592	0.008000	0.16893	0.003000	0.11579	0.036000	0.12997	1.169000	0.31871	0.717000	0.32145	-0.213000	0.12676	ATA	A|0.792;G|0.208	0.208	strong		0.577	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337	
NPTX1	4884	hgsc.bcm.edu	37	17	78444679	78444679	+	Silent	SNP	T	T	C	rs28364735	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78444679T>C	ENST00000306773.4	-	5	1390	c.1233A>G	c.(1231-1233)gaA>gaG	p.E411E	NPTX1_ENST00000575212.1_5'Flank	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	411	Pentaxin.				axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			CGATGTGGGATTCAGCCCAGG	0.642													T|||	965	0.192692	0.0295	0.1657	5008	,	,		14102	0.3175		0.2684	False		,,,				2504	0.226				p.E411E		Atlas-SNP	.											.	NPTX1	28	.	0			c.A1233G						PASS	.	T		337,4069	177.3+/-206.3	11,315,1877	95.0	83.0	87.0		1233	3.6	0.8	17	dbSNP_125	87	2488,6112	408.9+/-349.7	342,1804,2154	no	coding-synonymous	NPTX1	NM_002522.3		353,2119,4031	CC,CT,TT		28.9302,7.6487,21.7207		411/433	78444679	2825,10181	2203	4300	6503	SO:0001819	synonymous_variant	4884	exon5			GTGGGATTCAGCC	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.1233A>G	17.37:g.78444679T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_002522	B3KXH3|Q5FWE6	Silent	SNP	ENST00000306773.4	37	CCDS32762.1																																																																																			T|0.780;C|0.220	0.220	strong		0.642	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1		
TRAF3IP3	80342	hgsc.bcm.edu	37	1	209948711	209948711	+	Silent	SNP	A	A	C	rs17015183	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:209948711A>C	ENST00000367024.1	+	10	1308	c.792A>C	c.(790-792)ggA>ggC	p.G264G	TRAF3IP3_ENST00000010338.4_Silent_p.G244G|TRAF3IP3_ENST00000477431.1_5'UTR|TRAF3IP3_ENST00000400959.3_Silent_p.G244G|TRAF3IP3_ENST00000367023.1_5'UTR|TRAF3IP3_ENST00000367025.3_Silent_p.G264G|TRAF3IP3_ENST00000367026.3_Silent_p.G244G			Q9Y228	T3JAM_HUMAN	TRAF3 interacting protein 3	264						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32				OV - Ovarian serous cystadenocarcinoma(81;0.045)		CCCCTTGGGGAATGAAAAAAG	0.418													A|||	1049	0.209465	0.2784	0.1052	5008	,	,		20593	0.247		0.1441	False		,,,				2504	0.2188				p.G264G		Atlas-SNP	.											.	TRAF3IP3	68	.	0			c.A792C						PASS	.	A		1184,3222	399.0+/-331.0	166,852,1185	48.0	50.0	49.0		792	-4.8	1.0	1	dbSNP_123	49	1378,7222	262.7+/-284.6	130,1118,3052	no	coding-synonymous	TRAF3IP3	NM_025228.2		296,1970,4237	CC,CA,AA		16.0233,26.8724,19.6986		264/552	209948711	2562,10444	2203	4300	6503	SO:0001819	synonymous_variant	80342	exon10			TTGGGGAATGAAA		CCDS1490.1, CCDS1490.2, CCDS73023.1	1q32.3-q41	2008-02-05			ENSG00000009790	ENSG00000009790			30766	protein-coding gene	gene with protein product	"""TRAF3 interacting Jun N terminal kinase (JNK) activating modulator"""	608255				14572659	Standard	XR_247044		Approved	T3JAM	uc001hho.3	Q9Y228	OTTHUMG00000036480	ENST00000367024.1:c.792A>C	1.37:g.209948711A>C		Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	201	200	0.995025	NM_025228	A1L464|A6NIU9|Q2YDB5|Q4VY06|Q7Z706	Silent	SNP	ENST00000367024.1	37	CCDS1490.2																																																																																			A|0.807;C|0.193	0.193	strong		0.418	TRAF3IP3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088734.2		
AKT1	207	hgsc.bcm.edu	37	14	105239894	105239894	+	Silent	SNP	C	C	T	rs1130233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105239894C>T	ENST00000554581.1	-	8	2206	c.726G>A	c.(724-726)gaG>gaA	p.E242E	AKT1_ENST00000555528.1_Silent_p.E242E|AKT1_ENST00000554848.1_Silent_p.E242E|AKT1_ENST00000402615.2_Silent_p.E242E|AKT1_ENST00000555458.1_5'Flank|AKT1_ENST00000407796.2_Silent_p.E242E|AKT1_ENST00000349310.3_Silent_p.E242E|AKT1_ENST00000544168.1_Silent_p.E180E|AKT1_ENST00000554585.1_5'Flank|AKT1_ENST00000554192.1_5'Flank			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	AGAACACACGCTCCCGGGACA	0.652		1	Mis		"""breast, colorectal, ovarian, NSCLC"""								C|||	1615	0.322484	0.0787	0.4222	5008	,	,		14497	0.6002		0.2425	False		,,,				2504	0.3773				p.E242E		Atlas-SNP	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.G726A	GRCh37	CM081515	AKT1	M	rs1130233	PASS	.	C	,,	507,3897	216.1+/-234.9	33,441,1728	31.0	26.0	28.0		726,726,726	4.8	0.9	14	dbSNP_86	28	2115,6485	334.9+/-321.2	269,1577,2454	no	coding-synonymous,coding-synonymous,coding-synonymous	AKT1	NM_001014431.1,NM_001014432.1,NM_005163.2	,,	302,2018,4182	TT,TC,CC		24.593,11.5123,20.163	,,	242/481,242/481,242/481	105239894	2622,10382	2202	4300	6502	SO:0001819	synonymous_variant	207	exon9			CACACGCTCCCGG	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.726G>A	14.37:g.105239894C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	138	56	0.405797	NM_005163	B2RAM5|B7Z5R1|Q9BWB6	Silent	SNP	ENST00000554581.1	37	CCDS9994.1																																																																																			C|0.769;T|0.231	0.231	strong		0.652	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163	
CXorf56	63932	hgsc.bcm.edu	37	X	118678364	118678364	+	Silent	SNP	G	G	A	rs5910611	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:118678364G>A	ENST00000371594.4	-	4	453	c.375C>T	c.(373-375)ggC>ggT	p.G125G	CXorf56_ENST00000320339.4_Silent_p.G76G|CXorf56_ENST00000536133.1_Silent_p.G111G|CXorf56_ENST00000469448.1_5'Flank	NM_022101.3	NP_071384.1	Q9H5V9	CX056_HUMAN	chromosome X open reading frame 56	125										cervix(1)|endometrium(2)|lung(7)	10						TTTTCCCAAAGCCCTGGCCAA	0.443													G|||	2287	0.605828	0.3101	0.4741	3775	,	,		11258	0.5813		0.4831	False		,,,				2504	0.4867				p.G125G		Atlas-SNP	.											.	CXorf56	26	.	0			c.C375T						PASS	.	G	,,	1822,2013		370,801,281,461,290	125.0	106.0	112.0		228,333,375	-3.1	1.0	X	dbSNP_114	112	4235,2493		953,1143,1186,332,686	no	coding-synonymous,coding-synonymous,coding-synonymous	CXorf56	NM_001170569.1,NM_001170570.1,NM_022101.3	,,	1323,1944,1467,793,976	AA,AG,A,GG,G		37.0541,47.5098,42.6583	,,	76/174,111/209,125/223	118678364	6057,4506	2203	4300	6503	SO:0001819	synonymous_variant	63932	exon4			CCCAAAGCCCTGG	AK026618	CCDS55484.1, CCDS55485.1	Xq24	2008-02-05			ENSG00000018610	ENSG00000018610			26239	protein-coding gene	gene with protein product						12477932	Standard	NM_022101		Approved	FLJ22965	uc004erk.2	Q9H5V9	OTTHUMG00000022276	ENST00000371594.4:c.375C>T	X.37:g.118678364G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	129	26	0.20155	NM_022101	A8MPX7|B4DQN2|D3DWH9|F5GWL7|O43351	Silent	SNP	ENST00000371594.4	37	CCDS14579.1																																																																																			G|0.425;A|0.575	0.575	strong		0.443	CXorf56-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022101	
ASTL	431705	hgsc.bcm.edu	37	2	96795608	96795608	+	Missense_Mutation	SNP	T	T	G	rs1657502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:96795608T>G	ENST00000342380.2	-	8	828	c.829A>C	c.(829-831)Aaa>Caa	p.K277Q		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						CCGTAGAGTTTGAGGACCCGG	0.642													T|||	1924	0.384185	0.2784	0.4712	5008	,	,		17072	0.621		0.3559	False		,,,				2504	0.2505				p.K277Q		Atlas-SNP	.											.	ASTL	59	.	0			c.A829C						PASS	.	T	GLN/LYS	1297,3109	427.8+/-341.7	187,923,1093	42.0	49.0	47.0		829	-2.3	0.2	2	dbSNP_89	47	3115,5485	466.1+/-366.7	555,2005,1740	yes	missense	ASTL	NM_001002036.3	53	742,2928,2833	GG,GT,TT		36.2209,29.4371,33.9228	benign	277/432	96795608	4412,8594	2203	4300	6503	SO:0001583	missense	431705	exon8			AGAGTTTGAGGAC	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"""sperm acrosomal SLLP1 binding"""	608860	"""astacin-like metalloendopeptidase (M12 family)"""			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.829A>C	2.37:g.96795608T>G	ENSP00000343674:p.Lys277Gln	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	187	186	0.994652	NM_001002036		Missense_Mutation	SNP	ENST00000342380.2	37	CCDS33249.1	914	0.4184981684981685	130	0.26422764227642276	152	0.4198895027624309	350	0.6118881118881119	282	0.3720316622691293	T	12.41	1.930962	0.34096	0.294371	0.362209	ENSG00000188886	ENST00000342380	T	0.64438	-0.1	4.14	-2.33	0.06724	Peptidase M12A, astacin (2);Metallopeptidase, catalytic domain (1);	0.580059	0.15533	N	0.257382	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	B	0.18166	0.026	B	0.19391	0.025	T	0.48043	-0.9069	9	0.31617	T	0.26	-6.2836	12.28	0.54759	0.0:0.0:0.6883:0.3117	rs1657502;rs56587001;rs1657502	277	Q6HA08	ASTL_HUMAN	Q	277	ENSP00000343674:K277Q	ENSP00000343674:K277Q	K	-	1	0	ASTL	96159335	0.552000	0.26505	0.206000	0.23566	0.953000	0.61014	0.677000	0.25262	-0.187000	0.10516	0.454000	0.30748	AAA	T|0.636;G|0.364	0.364	strong		0.642	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1		
CA9	768	hgsc.bcm.edu	37	9	35674101	35674101	+	Silent	SNP	T	T	C	rs113003874|rs12553173	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35674101T>C	ENST00000378357.4	+	1	249	c.145T>C	c.(145-147)Ttg>Ctg	p.L49L	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	49	Proteoglycan-like (PG).				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	GGATTCCCCCTTGGGAGGAGG	0.627													C|||	1032	0.20607	0.4251	0.1037	5008	,	,		18753	0.1726		0.1362	False		,,,				2504	0.089				p.L49L		Atlas-SNP	.											.	CA9	48	.	0			c.T145C						PASS	.	C		1627,2779	650.2+/-399.0	314,999,890	53.0	51.0	51.0		145	-7.4	0.0	9	dbSNP_120	51	1138,7462	759.5+/-407.6	81,976,3243	no	coding-synonymous	CA9	NM_001216.2		395,1975,4133	CC,CT,TT		13.2326,36.9269,21.2594		49/460	35674101	2765,10241	2203	4300	6503	SO:0001819	synonymous_variant	768	exon1			TCCCCCTTGGGAG	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.145T>C	9.37:g.35674101T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	NM_001216	Q5T4R1	Silent	SNP	ENST00000378357.4	37	CCDS6585.1																																																																																			T|0.791;C|0.209	0.209	strong		0.627	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
MUC16	94025	hgsc.bcm.edu	37	19	9068990	9068990	+	Missense_Mutation	SNP	G	G	T	rs35092547	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9068990G>T	ENST00000397910.4	-	3	18659	c.18456C>A	c.(18454-18456)caC>caA	p.H6152Q		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6154	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CGATGGTCTTGTGTGTAGATA	0.507													g|||	49	0.00978435	0.0008	0.0216	5008	,	,		17653	0.001		0.0268	False		,,,				2504	0.0051				p.H6152Q		Atlas-SNP	.											.	MUC16	4315	.	0			c.C18456A						PASS	.	G	GLN/HIS	17,4221		0,17,2102	66.0	70.0	69.0		18456	-2.7	0.0	19	dbSNP_126	69	249,8207		5,239,3984	yes	missense	MUC16	NM_024690.2	24	5,256,6086	TT,TG,GG		2.9447,0.4011,2.0955	benign	6152/14508	9068990	266,12428	2119	4228	6347	SO:0001583	missense	94025	exon3			GGTCTTGTGTGTA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.18456C>A	19.37:g.9068990G>T	ENSP00000381008:p.His6152Gln	Somatic	459	0	0		WXS	Illumina HiSeq	Phase_I	527	266	0.504744	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	28	0.01282051282051282	0	0.0	6	0.016574585635359115	1	0.0017482517482517483	21	0.027704485488126648	g	2.171	-0.389912	0.04932	0.004011	0.029447	ENSG00000181143	ENST00000397910	T	0.02525	4.26	1.35	-2.71	0.05986	.	.	.	.	.	T	0.00468	0.0015	N	0.08118	0	.	.	.	B	0.31174	0.311	B	0.20577	0.03	T	0.44452	-0.9327	8	0.87932	D	0	.	2.4961	0.04621	0.3275:0.0:0.4389:0.2335	rs35092547;rs61737587	6152	B5ME49	.	Q	6152	ENSP00000381008:H6152Q	ENSP00000381008:H6152Q	H	-	3	2	MUC16	8929990	0.000000	0.05858	0.000000	0.03702	0.173000	0.22820	-2.276000	0.01161	-1.154000	0.02825	0.163000	0.16589	CAC	G|0.981;T|0.019	0.019	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
HGFAC	3083	hgsc.bcm.edu	37	4	3449886	3449886	+	Silent	SNP	G	G	A	rs28468427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:3449886G>A	ENST00000382774.3	+	13	1783	c.1668G>A	c.(1666-1668)gaG>gaA	p.E556E	HGFAC_ENST00000511533.1_Silent_p.E563E	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	556	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CCCTGCGGGAGGCCCTGGTCC	0.672													G|||	1393	0.278155	0.2943	0.3285	5008	,	,		15192	0.3581		0.2336	False		,,,				2504	0.184				p.E556E		Atlas-SNP	.											.	HGFAC	69	.	0			c.G1668A						PASS	.	G		1189,3185		196,797,1194	23.0	21.0	22.0		1668	2.1	1.0	4	dbSNP_125	22	1931,6629		246,1439,2595	no	coding-synonymous	HGFAC	NM_001528.2		442,2236,3789	AA,AG,GG		22.5584,27.1834,24.1225		556/656	3449886	3120,9814	2187	4280	6467	SO:0001819	synonymous_variant	3083	exon13			GCGGGAGGCCCTG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.1668G>A	4.37:g.3449886G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	148	86	0.581081	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	37	CCDS3369.1																																																																																			G|0.745;A|0.255	0.255	strong		0.672	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
ART4	420	hgsc.bcm.edu	37	12	14982352	14982352	+	Missense_Mutation	SNP	G	G	C	rs3088190	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:14982352G>C	ENST00000228936.4	-	3	1279	c.898C>G	c.(898-900)Ctc>Gtc	p.L300V	C12orf60_ENST00000527783.1_Intron	NM_021071.2	NP_066549.2	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 (Dombrock blood group)	300			L -> V (in Hy1; dbSNP:rs3088190). {ECO:0000269|Ref.3}.		arginine metabolic process (GO:0006525)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)			large_intestine(5)|liver(1)|lung(3)|prostate(1)|skin(2)|stomach(3)	15						AAAAAGGAGAGAGATGCAATA	0.294													G|||	608	0.121406	0.1165	0.2839	5008	,	,		15742	0.0744		0.1034	False		,,,				2504	0.0798				p.L300V		Atlas-SNP	.											ART4,NS,carcinoma,0,1	ART4	27	1	0			c.C898G	GRCh37	CM024387	ART4	M	rs3088190	PASS	.	G	VAL/LEU	508,3898	229.1+/-243.8	26,456,1721	61.0	64.0	63.0		898	-5.7	0.0	12	dbSNP_102	63	841,7759	191.7+/-237.8	39,763,3498	yes	missense	ART4	NM_021071.2	32	65,1219,5219	CC,CG,GG		9.7791,11.5297,10.3721	benign	300/315	14982352	1349,11657	2203	4300	6503	SO:0001583	missense	420	exon3			AGGAGAGAGATGC	X95826	CCDS8668.1	12q13.2-q13.3	2014-07-18	2014-01-02	2006-01-12	ENSG00000111339	ENSG00000111339		"""CD molecules"", ""Blood group antigens"""	726	protein-coding gene	gene with protein product		110600	"""Dombrock blood group"", ""ADP-ribosyltransferase 4 (DO blood group)"", ""ADP-ribosyltransferase 4"""	DO		9119374	Standard	NM_021071		Approved	DOK1, CD297	uc001rcl.1	Q93070	OTTHUMG00000168738	ENST00000228936.4:c.898C>G	12.37:g.14982352G>C	ENSP00000228936:p.Leu300Val	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	140	69	0.492857	NM_021071	Q9BZ50|Q9BZ51|Q9HB06	Missense_Mutation	SNP	ENST00000228936.4	37	CCDS8668.1	270	0.12362637362637363	56	0.11382113821138211	82	0.2265193370165746	50	0.08741258741258741	82	0.10817941952506596	G	6.989	0.552617	0.13374	0.115297	0.097791	ENSG00000111339	ENST00000228936	T	0.08546	3.08	4.04	-5.73	0.02398	.	0.345102	0.21359	N	0.075833	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.43130	-0.9410	9	0.15952	T	0.53	-12.6381	3.4726	0.07573	0.2308:0.4742:0.1749:0.12	rs3088190;rs52803008;rs3088190	300	Q93070	NAR4_HUMAN	V	300	ENSP00000228936:L300V	ENSP00000228936:L300V	L	-	1	0	ART4	14873619	0.001000	0.12720	0.000000	0.03702	0.012000	0.07955	-0.564000	0.05936	-1.330000	0.02255	-2.106000	0.00359	CTC	G|0.894;C|0.106	0.106	strong		0.294	ART4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400859.1	NM_021071	
PRDM5	11107	hgsc.bcm.edu	37	4	121738049	121738049	+	Silent	SNP	T	T	C	rs343192	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:121738049T>C	ENST00000264808.3	-	6	921	c.681A>G	c.(679-681)ctA>ctG	p.L227L	PRDM5_ENST00000428209.2_Intron|PRDM5_ENST00000515109.1_Intron	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	227					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						AAGACTCCTTTAGACTGCTTT	0.363													C|||	1377	0.27496	0.2057	0.3948	5008	,	,		17855	0.3562		0.3191	False		,,,				2504	0.1544				p.L227L		Atlas-SNP	.											PRDM5,NS,carcinoma,-2,1	PRDM5	76	1	0			c.A681G						PASS	.	C		947,3459	735.3+/-410.7	106,735,1362	154.0	159.0	157.0		681	2.4	1.0	4	dbSNP_79	157	2711,5889	682.3+/-403.8	446,1819,2035	no	coding-synonymous	PRDM5	NM_018699.2		552,2554,3397	CC,CT,TT		31.5233,21.4934,28.1255		227/631	121738049	3658,9348	2203	4300	6503	SO:0001819	synonymous_variant	11107	exon6			CTCCTTTAGACTG	AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"""Zinc fingers, C2H2-type"""	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.681A>G	4.37:g.121738049T>C		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	226	226	1	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Silent	SNP	ENST00000264808.3	37	CCDS3716.1																																																																																			T|0.707;C|0.293	0.293	strong		0.363	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2		
EHD2	30846	hgsc.bcm.edu	37	19	48244401	48244401	+	Silent	SNP	G	G	A	rs35910701	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48244401G>A	ENST00000263277.3	+	6	1595	c.1344G>A	c.(1342-1344)aaG>aaA	p.K448K	EHD2_ENST00000540884.1_3'UTR|EHD2_ENST00000538399.1_Silent_p.K312K	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	448					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		TGGTGACCAAGGACAAGTCCA	0.647													G|||	458	0.0914537	0.0416	0.1052	5008	,	,		16302	0.006		0.2187	False		,,,				2504	0.1063				p.K448K		Atlas-SNP	.											.	EHD2	59	.	0			c.G1344A						PASS	.	G		312,4094	164.4+/-196.0	10,292,1901	91.0	72.0	78.0		1344	4.1	1.0	19	dbSNP_126	78	1683,6917	307.4+/-308.4	146,1391,2763	no	coding-synonymous	EHD2	NM_014601.3		156,1683,4664	AA,AG,GG		19.5698,7.0813,15.3391		448/544	48244401	1995,11011	2203	4300	6503	SO:0001819	synonymous_variant	30846	exon6			GACCAAGGACAAG	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.1344G>A	19.37:g.48244401G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	37	CCDS12704.1	229	0.10485347985347986	18	0.036585365853658534	45	0.12430939226519337	4	0.006993006993006993	162	0.21372031662269128	G	9.962	1.223109	0.22457	0.070813	0.195698	ENSG00000024422	ENST00000454483	.	.	.	4.13	4.13	0.48395	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.03202	-1.1061	4	0.29301	T	0.29	-34.6291	14.267	0.66126	0.0:0.0:1.0:0.0	rs35910701	.	.	.	R	118	.	ENSP00000391634:G118R	G	+	1	0	EHD2	52936213	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.995000	0.49441	2.024000	0.59613	0.561000	0.74099	GGA	A|0.141;C|0.000;G|0.858	0.141	strong		0.647	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
FBLN7	129804	hgsc.bcm.edu	37	2	112922697	112922697	+	Missense_Mutation	SNP	G	G	A	rs35586251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:112922697G>A	ENST00000331203.2	+	3	626	c.355G>A	c.(355-357)Gtg>Atg	p.V119M	FBLN7_ENST00000409903.1_Missense_Mutation_p.V119M|FBLN7_ENST00000409450.3_Missense_Mutation_p.V119M|FBLN7_ENST00000409667.3_Missense_Mutation_p.V119M|FBLN7_ENST00000472377.1_3'UTR	NM_001128165.1|NM_153214.2	NP_001121637.1|NP_694946.2	Q53RD9	FBLN7_HUMAN	fibulin 7	119	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.		V -> M (in dbSNP:rs35586251). {ECO:0000269|PubMed:14702039}.		cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GCCCAGCAGCGTGGTGTGTCT	0.582													G|||	155	0.0309505	0.0567	0.0231	5008	,	,		18022	0.002		0.0209	False		,,,				2504	0.0419				p.V119M		Atlas-SNP	.											.	FBLN7	49	.	0			c.G355A						PASS	.	G	MET/VAL,MET/VAL	185,4221	119.6+/-157.3	3,179,2021	88.0	82.0	84.0		355,355	4.5	1.0	2	dbSNP_126	84	204,8396	88.1+/-150.5	3,198,4099	yes	missense,missense	FBLN7	NM_001128165.1,NM_153214.2	21,21	6,377,6120	AA,AG,GG		2.3721,4.1988,2.9909	possibly-damaging,possibly-damaging	119/394,119/440	112922697	389,12617	2203	4300	6503	SO:0001583	missense	129804	exon3			AGCAGCGTGGTGT		CCDS2095.1, CCDS46391.1	2q13	2010-06-15			ENSG00000144152	ENSG00000144152		"""Fibulins"""	26740	protein-coding gene	gene with protein product		611551				17699513	Standard	NM_153214		Approved	FLJ37440, TM14	uc002tho.1	Q53RD9	OTTHUMG00000153267	ENST00000331203.2:c.355G>A	2.37:g.112922697G>A	ENSP00000331411:p.Val119Met	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	182	82	0.450549	NM_153214	A0JNV1|A0JNV2|Q5H9P5|Q8N9G0	Missense_Mutation	SNP	ENST00000331203.2	37	CCDS2095.1	51	0.023351648351648352	30	0.06097560975609756	5	0.013812154696132596	1	0.0017482517482517483	15	0.01978891820580475	G	15.35	2.808420	0.50421	0.041988	0.023721	ENSG00000144152	ENST00000331203;ENST00000409903;ENST00000409667;ENST00000409450	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	5.36	4.47	0.54385	Complement control module (2);Sushi/SCR/CCP (3);	0.132552	0.48767	D	0.000180	T	0.12860	0.0312	L	0.49350	1.555	0.33168	D	0.547928	D;P;P;D	0.61697	0.985;0.682;0.854;0.99	P;B;B;P	0.47827	0.522;0.163;0.342;0.558	T	0.54450	-0.8292	10	0.37606	T	0.19	-19.8017	7.0264	0.24942	0.1013:0.2745:0.6243:0.0	rs35586251	119;119;119;119	Q53RD9-4;Q53RD9-2;Q53RD9;B8ZZC1	.;.;FBLN7_HUMAN;.	M	119	ENSP00000331411:V119M;ENSP00000386295:V119M;ENSP00000386822:V119M;ENSP00000387000:V119M	ENSP00000331411:V119M	V	+	1	0	FBLN7	112639168	0.589000	0.26807	0.986000	0.45419	0.987000	0.75469	0.954000	0.29175	2.533000	0.85409	0.655000	0.94253	GTG	G|0.972;A|0.028	0.028	strong		0.582	FBLN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330505.1	NM_153214	
HLA-B	3106	hgsc.bcm.edu	37	6	31324025	31324025	+	Missense_Mutation	SNP	G	G	A	rs200488894|rs376871308|rs9266144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324025G>A	ENST00000412585.2	-	3	566	c.538C>T	c.(538-540)Cgg>Tgg	p.R180W		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	180	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TAGGCTCTCCGCTGCTCCGCC	0.682									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				G|||	836	0.166933	0.1172	0.1527	5008	,	,		10426	0.2401		0.1551	False		,,,				2504	0.181				p.R180W		Atlas-SNP	.											.	HLA-B	54	.	0			c.C538T						PASS	.						26.0	19.0	21.0					6																	31324025		2153	4211	6364	SO:0001583	missense	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	CTCTCCGCTGCTC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.538C>T	6.37:g.31324025G>A	ENSP00000399168:p.Arg180Trp	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	232	78	0.336207	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	451	0.2065018315018315	92	0.18699186991869918	56	0.15469613259668508	141	0.2465034965034965	162	0.21372031662269128	N	0.320	-0.962555	0.02249	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T;T	0.00958	9.46;5.5;9.46	3.18	-6.36	0.01969	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	4.810940	0.02631	N	0.104292	T	0.00144	0.0004	N	0.11255	0.115	0.80722	P	0.0	B	0.22346	0.068	B	0.13407	0.009	T	0.43343	-0.9397	9	0.21540	T	0.41	.	2.0485	0.03566	0.1822:0.3881:0.2095:0.2201	rs9266144;rs12721865;rs17840082	180	P01889	1B07_HUMAN	W	180;59;59;191	ENSP00000399168:R180W;ENSP00000396980:R59W;ENSP00000405931:R191W	ENSP00000399168:R180W	R	-	1	2	HLA-B	31432004	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-10.352000	0.00006	-4.708000	0.00035	-2.014000	0.00435	CGG	A|0.189;C|0.007;G|0.804	0.189	strong		0.682	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
PRKD3	23683	hgsc.bcm.edu	37	2	37505108	37505108	+	Silent	SNP	C	C	T	rs116096831	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:37505108C>T	ENST00000379066.1	-	9	1959	c.1197G>A	c.(1195-1197)ccG>ccA	p.P399P	PRKD3_ENST00000234179.2_Silent_p.P399P			O94806	KPCD3_HUMAN	protein kinase D3	399					intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				CCCTCATTAGCGGAATATTAT	0.368													C|||	10	0.00199681	0.0	0.0029	5008	,	,		16204	0.0		0.005	False		,,,				2504	0.0031				p.P399P	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.G1197A						PASS	.	C		3,4403	8.1+/-20.4	0,3,2200	191.0	157.0	168.0		1197	-6.0	0.9	2	dbSNP_132	168	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous	PRKD3	NM_005813.3		0,49,6454	TT,TC,CC		0.5349,0.0681,0.3767		399/891	37505108	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	23683	exon8			CATTAGCGGAATA	AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"""Pleckstrin homology (PH) domain containing"""	9408	protein-coding gene	gene with protein product		607077	"""protein kinase C, nu"""	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.1197G>A	2.37:g.37505108C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	140	82	0.585714	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1																																																																																			C|0.996;T|0.004	0.004	strong		0.368	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	
TNS1	7145	hgsc.bcm.edu	37	2	218745685	218745685	+	Silent	SNP	G	G	A	rs10199795	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:218745685G>A	ENST00000171887.4	-	16	1442	c.990C>T	c.(988-990)tcC>tcT	p.S330S	TNS1_ENST00000430930.1_Silent_p.S330S|TNS1_ENST00000419504.1_Silent_p.S330S|TNS1_ENST00000310858.6_Silent_p.S361S	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	330					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.S330S(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TGAGGGGGTCGGAGGTGTTAT	0.607													G|||	2658	0.530751	0.584	0.536	5008	,	,		16626	0.5347		0.6074	False		,,,				2504	0.3722				p.S330S		Atlas-SNP	.											TNS1,NS,carcinoma,0,1	TNS1	251	1	1	Substitution - coding silent(1)	stomach(1)	c.C990T						PASS	.	G		2578,1828	637.0+/-396.7	755,1068,380	128.0	105.0	113.0		990	-5.4	0.9	2	dbSNP_119	113	5197,3403	640.2+/-399.6	1562,2073,665	no	coding-synonymous	TNS1	NM_022648.4		2317,3141,1045	AA,AG,GG		39.5698,41.4889,40.2199		330/1736	218745685	7775,5231	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon16			GGGGTCGGAGGTG	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.990C>T	2.37:g.218745685G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1	1257	0.5755494505494505	276	0.5609756097560976	209	0.5773480662983426	308	0.5384615384615384	464	0.6121372031662269	G	10.01	1.233765	0.22626	0.585111	0.604302	ENSG00000079308	ENST00000453356	.	.	.	4.97	-5.36	0.02689	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999849	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.5954	0.17323	0.5138:0.0:0.1622:0.3239	rs10199795;rs58104927;rs10199795	.	.	.	X	106	.	.	R	-	1	2	TNS1	218453930	0.000000	0.05858	0.919000	0.36401	0.980000	0.70556	-4.843000	0.00179	-0.981000	0.03520	-0.378000	0.06908	CGA	A|0.589;G|0.411;T|0.000	0.589	strong		0.607	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
NGEF	25791	hgsc.bcm.edu	37	2	233757679	233757679	+	Silent	SNP	G	G	A	rs748002	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233757679G>A	ENST00000264051.3	-	7	1349	c.1071C>T	c.(1069-1071)gcC>gcT	p.A357A	NGEF_ENST00000373552.4_Silent_p.A265A|NGEF_ENST00000539537.1_Silent_p.A80A	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	357	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		AGAAGTGGTCGGCCGCATAAC	0.567													G|||	1504	0.300319	0.2791	0.3963	5008	,	,		20098	0.3492		0.326	False		,,,				2504	0.184				p.A357A		Atlas-SNP	.											NGEF_ENST00000264051,caecum,carcinoma,-1,4	NGEF	198	4	0			c.C1071T						PASS	.	G	,	1260,3146	430.6+/-342.6	172,916,1115	192.0	157.0	169.0		795,1071	3.5	1.0	2	dbSNP_86	169	2603,5997	420.7+/-353.5	398,1807,2095	no	coding-synonymous,coding-synonymous	NGEF	NM_001114090.1,NM_019850.2	,	570,2723,3210	AA,AG,GG		30.2674,28.5974,29.7017	,	265/619,357/711	233757679	3863,9143	2203	4300	6503	SO:0001819	synonymous_variant	25791	exon7			GTGGTCGGCCGCA	AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"""Rho guanine nucleotide exchange factors"""	7807	protein-coding gene	gene with protein product	"""ephexin"""	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.1071C>T	2.37:g.233757679G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	195	193	0.989744	NM_019850	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Silent	SNP	ENST00000264051.3	37	CCDS2500.1	740	0.33882783882783885	134	0.27235772357723576	134	0.3701657458563536	221	0.38636363636363635	251	0.3311345646437995	G	2.595	-0.294311	0.05568	0.285974	0.302674	ENSG00000066248	ENST00000420650	.	.	.	5.28	3.46	0.39613	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	4.000000000004E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	-33.2265	5.3969	0.16275	0.2597:0.1473:0.593:0.0	rs748002;rs16829683;rs17852957;rs748002	.	.	.	X	150	.	.	R	-	1	2	NGEF	233465923	0.000000	0.05858	0.987000	0.45799	0.327000	0.28475	-0.253000	0.08794	0.597000	0.29811	0.561000	0.74099	CGA	G|0.695;A|0.305	0.305	strong		0.567	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799	
CDH15	1013	hgsc.bcm.edu	37	16	89245884	89245884	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89245884C>T	ENST00000289746.2	+	2	168	c.103C>T	c.(103-105)Cgc>Tgc	p.R35C	CDH15_ENST00000521087.1_3'UTR	NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	35					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		GTACCCCTGGCGCCGGGCGCC	0.657																																					p.R35C		Atlas-SNP	.											CDH15,NS,carcinoma,-1,2	CDH15	54	2	0			c.C103T						PASS	.						83.0	82.0	82.0					16																	89245884		2198	4300	6498	SO:0001583	missense	1013	exon2			CCCTGGCGCCGGG	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"""Cadherins / Major cadherins"""	1754	protein-coding gene	gene with protein product		114019	"""cadherin 15, M-cadherin (myotubule)"""	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.103C>T	16.37:g.89245884C>T	ENSP00000289746:p.Arg35Cys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	147	82	0.557823	NM_004933		Missense_Mutation	SNP	ENST00000289746.2	37	CCDS10976.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.713980	0.48622	.	.	ENSG00000129910	ENST00000289746	T	0.58940	0.3	4.58	3.57	0.40892	.	0.454073	0.15889	N	0.239671	T	0.49643	0.1569	N	0.14661	0.345	0.58432	D	0.999997	D	0.69078	0.997	P	0.52343	0.696	T	0.54655	-0.8261	10	0.66056	D	0.02	.	11.1776	0.48610	0.1834:0.8166:0.0:0.0	.	35	P55291	CAD15_HUMAN	C	35	ENSP00000289746:R35C	ENSP00000289746:R35C	R	+	1	0	CDH15	87773385	0.038000	0.19896	0.916000	0.36221	0.077000	0.17291	0.119000	0.15626	2.104000	0.64026	0.407000	0.27541	CGC	.	.	none		0.657	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933	
UTRN	7402	hgsc.bcm.edu	37	6	144898276	144898276	+	Missense_Mutation	SNP	C	C	T	rs367807203		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:144898276C>T	ENST00000367545.3	+	50	7331	c.7331C>T	c.(7330-7332)aCg>aTg	p.T2444M		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2444					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GAGTGGAGGACGGTGCAGGCC	0.493																																					p.T2444M		Atlas-SNP	.											.	UTRN	327	.	0			c.C7331T						PASS	.	C	MET/THR	0,4406		0,0,2203	105.0	86.0	93.0		7331	1.1	0.0	6		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	UTRN	NM_007124.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	2444/3434	144898276	1,13005	2203	4300	6503	SO:0001583	missense	7402	exon50			GGAGGACGGTGCA	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.7331C>T	6.37:g.144898276C>T	ENSP00000356515:p.Thr2444Met	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	179	89	0.497207	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.333825	0.41297	0.0	1.16E-4	ENSG00000152818	ENST00000367545	T	0.60299	0.2	6.03	1.14	0.20703	.	0.371682	0.22724	N	0.056418	T	0.20088	0.0483	L	0.33485	1.01	0.09310	N	1	B	0.20261	0.043	B	0.25291	0.059	T	0.19910	-1.0291	10	0.48119	T	0.1	.	2.8168	0.05458	0.1134:0.528:0.11:0.2486	.	2444	P46939	UTRO_HUMAN	M	2444	ENSP00000356515:T2444M	ENSP00000356515:T2444M	T	+	2	0	UTRN	144939969	0.006000	0.16342	0.001000	0.08648	0.663000	0.39108	0.115000	0.15540	0.134000	0.18681	-0.137000	0.14449	ACG	.	.	weak		0.493	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
TMEM106B	54664	hgsc.bcm.edu	37	7	12263971	12263971	+	Missense_Mutation	SNP	G	G	A	rs147889591	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:12263971G>A	ENST00000396667.3	+	5	723	c.401G>A	c.(400-402)aGt>aAt	p.S134N	TMEM106B_ENST00000396668.3_Missense_Mutation_p.S134N	NM_018374.3	NP_060844.2	Q9NUM4	T106B_HUMAN	transmembrane protein 106B	134					cell death (GO:0008219)|dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(8)|large_intestine(2)|lung(7)	18				UCEC - Uterine corpus endometrioid carcinoma (126;0.185)		GCCTATGTCAGTTATGATGTT	0.338													G|||	32	0.00638978	0.0	0.0144	5008	,	,		18403	0.0		0.0179	False		,,,				2504	0.0041				p.S134N		Atlas-SNP	.											.	TMEM106B	34	.	0			c.G401A						PASS	.	G	ASN/SER,ASN/SER	20,4386	28.1+/-56.4	0,20,2183	214.0	183.0	194.0		401,401	5.1	1.0	7	dbSNP_134	194	165,8435	77.2+/-139.8	0,165,4135	yes	missense,missense	TMEM106B	NM_001134232.1,NM_018374.3	46,46	0,185,6318	AA,AG,GG		1.9186,0.4539,1.4224	benign,benign	134/275,134/275	12263971	185,12821	2203	4300	6503	SO:0001583	missense	54664	exon4			ATGTCAGTTATGA	BC033901	CCDS5358.1	7p21.3	2012-06-06			ENSG00000106460	ENSG00000106460			22407	protein-coding gene	gene with protein product		613413				20154673, 22511793	Standard	NM_018374		Approved	MGC33727, FLJ11273	uc003ssh.3	Q9NUM4	OTTHUMG00000125537	ENST00000396667.3:c.401G>A	7.37:g.12263971G>A	ENSP00000379901:p.Ser134Asn	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	280	123	0.439286	NM_001134232	A4D108|Q53FL9|Q8N4L0	Missense_Mutation	SNP	ENST00000396667.3	37	CCDS5358.1	16	0.007326007326007326	0	0.0	6	0.016574585635359115	0	0.0	10	0.013192612137203167	G	12.65	2.002135	0.35320	0.004539	0.019186	ENSG00000106460	ENST00000396668;ENST00000396667	T;T	0.26810	1.71;1.71	5.12	5.12	0.69794	.	0.265686	0.47093	D	0.000255	T	0.07143	0.0181	N	0.11927	0.2	0.36704	D	0.880253	B	0.02656	0.0	B	0.04013	0.001	T	0.08249	-1.0731	10	0.38643	T	0.18	.	11.0422	0.47838	0.0733:0.1318:0.7949:0.0	.	134	Q9NUM4	T106B_HUMAN	N	134	ENSP00000379902:S134N;ENSP00000379901:S134N	ENSP00000379901:S134N	S	+	2	0	TMEM106B	12230496	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.494000	0.35616	2.764000	0.94973	0.650000	0.86243	AGT	G|0.988;A|0.012	0.012	strong		0.338	TMEM106B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246870.3	NM_018374	
TC2N	123036	hgsc.bcm.edu	37	14	92251587	92251587	+	Silent	SNP	A	A	G	rs61990064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:92251587A>G	ENST00000435962.2	-	11	1604	c.1281T>C	c.(1279-1281)ctT>ctC	p.L427L	TC2N_ENST00000340892.5_Silent_p.L427L|TC2N_ENST00000360594.5_Silent_p.L427L|TC2N_ENST00000556018.1_Silent_p.L363L	NM_001128596.1	NP_001122068	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear	427	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(5)|skin(1)|upper_aerodigestive_tract(2)	18				COAD - Colon adenocarcinoma(157;0.218)		CACTCTGTATAAGTGGAAAAA	0.383													A|||	557	0.111222	0.0582	0.121	5008	,	,		14404	0.1151		0.173	False		,,,				2504	0.1084				p.L427L		Atlas-SNP	.											TC2N,NS,adenoma,0,2	TC2N	49	2	0			c.T1281C						PASS	.	A	,,	307,4099	165.4+/-196.9	9,289,1905	167.0	182.0	177.0		1281,1281,1281	-3.5	0.4	14	dbSNP_129	177	1436,7164	274.9+/-291.5	119,1198,2983	no	coding-synonymous,coding-synonymous,coding-synonymous	TC2N	NM_001128595.1,NM_001128596.1,NM_152332.4	,,	128,1487,4888	GG,GA,AA		16.6977,6.9678,13.4015	,,	427/491,427/491,427/491	92251587	1743,11263	2203	4300	6503	SO:0001819	synonymous_variant	123036	exon11			CTGTATAAGTGGA	AA243837	CCDS9897.1, CCDS73679.1	14q32.12	2007-10-17	2007-08-17	2007-08-17		ENSG00000165929			19859	protein-coding gene	gene with protein product	"""C2 calcium-dependent domain containing 1"""		"""chromosome 14 open reading frame 47"", ""membrane targeting (tandem) C2 domain containing 1"""	C14orf47, MTAC2D1		11526914	Standard	NM_001128596		Approved	FLJ36557, Tac2-N, C2CD1	uc001xzt.4	Q8N9U0		ENST00000435962.2:c.1281T>C	14.37:g.92251587A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_001128596		Silent	SNP	ENST00000435962.2	37	CCDS9897.1																																																																																			A|0.864;G|0.136	0.136	strong		0.383	TC2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411778.1	NM_152332	
KIAA1683	80726	hgsc.bcm.edu	37	19	18375815	18375815	+	Silent	SNP	G	G	A	rs8103177	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18375815G>A	ENST00000600328.3	-	3	2728	c.2535C>T	c.(2533-2535)aaC>aaT	p.N845N	KIAA1683_ENST00000392413.4_Silent_p.N845N|KIAA1683_ENST00000600359.3_Silent_p.N799N			Q9H0B3	K1683_HUMAN	KIAA1683	845						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						AGGACTCAACGTTGCATGTGG	0.677													A|||	1503	0.30012	0.4554	0.2478	5008	,	,		19187	0.3165		0.1581	False		,,,				2504	0.2566				p.N845N		Atlas-SNP	.											.	KIAA1683	190	.	0			c.C2535T						PASS	.	A	,,	1853,2553	630.4+/-395.5	396,1061,746	63.0	61.0	62.0		2535,2397,2535	-4.6	0.0	19	dbSNP_116	62	1405,7193	749.9+/-407.4	110,1185,3004	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	506,2246,3750	AA,AG,GG		16.341,42.0563,25.0538	,,	845/1368,799/1135,845/1181	18375815	3258,9746	2203	4299	6502	SO:0001819	synonymous_variant	80726	exon3			CTCAACGTTGCAT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2535C>T	19.37:g.18375815G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			G|0.737;A|0.263	0.263	strong		0.677	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
CEACAM18	729767	hgsc.bcm.edu	37	19	51984725	51984725	+	Missense_Mutation	SNP	T	T	A	rs8106673	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51984725T>A	ENST00000396477.4	+	3	500	c.479T>A	c.(478-480)cTc>cAc	p.L160H	CEACAM18_ENST00000451626.1_Missense_Mutation_p.L221H	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	160			L -> H (in dbSNP:rs8106673).							breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GCTGACTGCCTCACAAATGTC	0.522													a|||	4443	0.887181	0.9637	0.853	5008	,	,		20040	0.9246		0.7684	False		,,,				2504	0.8916				p.L221H		Atlas-SNP	.											.	CEACAM18	96	.	0			c.T662A						PASS	.	A	HIS/LEU	3863,281		1800,263,9	65.0	65.0	65.0		662	1.7	0.2	19	dbSNP_116	65	6513,1901		2533,1447,227	yes	missense	CEACAM18	NM_001080405.1	99	4333,1710,236	AA,AT,TT		22.5933,6.7809,17.3754	benign	221/399	51984725	10376,2182	2072	4207	6279	SO:0001583	missense	729767	exon4			ACTGCCTCACAAA			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.479T>A	19.37:g.51984725T>A	ENSP00000379738:p.Leu160His	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	160	157	0.98125	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		1873	0.8576007326007326	463	0.9410569105691057	303	0.8370165745856354	529	0.9248251748251748	578	0.762532981530343	.	0.232	-1.019999	0.02078	0.932191	0.774067	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.05139	3.49	2.82	1.71	0.24356	.	.	.	.	.	T	0.00012	0.0000	L	0.28608	0.87	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.19095	-1.0316	8	0.14252	T	0.57	-1.1069	5.3935	0.16257	0.5326:0.0:0.0:0.4674	rs8106673;rs17206910;rs8106673	221	A8MTB9	CEA18_HUMAN	H	221;160;160	ENSP00000402203:L221H	ENSP00000379738:L160H	L	+	2	0	CEACAM18	56676537	0.000000	0.05858	0.231000	0.23993	0.045000	0.14185	0.025000	0.13577	0.043000	0.15746	-0.372000	0.07161	CTC	T|0.151;A|0.849	0.849	strong		0.522	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
MYCT1	80177	hgsc.bcm.edu	37	6	153043035	153043035	+	Missense_Mutation	SNP	G	G	A	rs17710008	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:153043035G>A	ENST00000367245.5	+	2	363	c.355G>A	c.(355-357)Ggc>Agc	p.G119S	MYCT1_ENST00000529453.1_Intron	NM_025107.2	NP_079383.2	Q8N699	MYCT1_HUMAN	myc target 1	119			G -> S (in dbSNP:rs17710008).			nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	20		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		TTACACCCACGGCCTCAACAG	0.522													G|||	550	0.109824	0.0098	0.2392	5008	,	,		16013	0.0893		0.159	False		,,,				2504	0.1237				p.G119S		Atlas-SNP	.											.	MYCT1	48	.	0			c.G355A						PASS	.	G	SER/GLY	183,4223	119.2+/-156.9	3,177,2023	126.0	120.0	122.0		355	3.8	1.0	6	dbSNP_123	122	1435,7165	275.8+/-292.0	112,1211,2977	yes	missense	MYCT1	NM_025107.2	56	115,1388,5000	AA,AG,GG		16.686,4.1534,12.4404	benign	119/236	153043035	1618,11388	2203	4300	6503	SO:0001583	missense	80177	exon2			ACCCACGGCCTCA	AF527367	CCDS5239.1	6q25.1	2008-02-05			ENSG00000120279	ENSG00000120279			23172	protein-coding gene	gene with protein product						12477932	Standard	NM_025107		Approved	MTLC, FLJ21269	uc003qpc.4	Q8N699	OTTHUMG00000015850	ENST00000367245.5:c.355G>A	6.37:g.153043035G>A	ENSP00000356214:p.Gly119Ser	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	270	118	0.437037	NM_025107	Q8N396|Q8TBE8|Q9H763	Missense_Mutation	SNP	ENST00000367245.5	37	CCDS5239.1	282	0.12912087912087913	12	0.024390243902439025	86	0.23756906077348067	62	0.10839160839160839	122	0.16094986807387862	G	11.15	1.552847	0.27739	0.041534	0.16686	ENSG00000120279	ENST00000367245	T	0.28895	1.59	5.78	3.77	0.43336	.	0.440979	0.24652	N	0.036711	T	0.04588	0.0125	N	0.13043	0.29	0.09310	P	0.99999877397	B	0.31817	0.341	B	0.20384	0.029	T	0.27971	-1.0058	9	0.10377	T	0.69	-16.9903	8.1426	0.31093	0.1779:0.0:0.6906:0.1315	rs17710008;rs52810941;rs17710008	119	Q8N699	MYCT1_HUMAN	S	119	ENSP00000356214:G119S	ENSP00000356214:G119S	G	+	1	0	MYCT1	153084728	0.329000	0.24696	0.967000	0.41034	0.954000	0.61252	0.603000	0.24149	1.451000	0.47736	0.579000	0.79373	GGC	G|0.882;A|0.118	0.118	strong		0.522	MYCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042750.2	NM_025107	
MDH1B	130752	hgsc.bcm.edu	37	2	207603234	207603234	+	Splice_Site	SNP	T	T	G	rs2287631	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:207603234T>G	ENST00000374412.3	-	12	1805	c.1530A>C	c.(1528-1530)gaA>gaC	p.E510D	MDH1B_ENST00000449792.1_Splice_Site_p.E412D|MDH1B_ENST00000454776.2_Splice_Site_p.E509D	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	510			E -> D (in dbSNP:rs2287631).		carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		TGCCTTCAAATTCTGTAAAAG	0.274													G|||	2092	0.417732	0.5961	0.3617	5008	,	,		19969	0.5347		0.1412	False		,,,				2504	0.3804				p.E510D	Pancreas(76;29 1355 28675 37177 51207)	Atlas-SNP	.											.	MDH1B	89	.	0			c.A1530C						PASS	.	G	ASP/GLU	2223,2181	573.3+/-383.5	552,1119,531	78.0	80.0	80.0		1530	-3.1	0.0	2	dbSNP_100	80	1278,7314	752.3+/-407.4	97,1084,3115	yes	missense-near-splice	MDH1B	NM_001039845.1	45	649,2203,3646	GG,GT,TT		14.8743,49.5232,26.9391	benign	510/519	207603234	3501,9495	2202	4296	6498	SO:0001630	splice_region_variant	130752	exon12			TTCAAATTCTGTA		CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.1529-1A>C	2.37:g.207603234T>G		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	172	172	1	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	37	CCDS33365.1	832	0.38095238095238093	296	0.6016260162601627	120	0.3314917127071823	322	0.5629370629370629	94	0.12401055408970976	G	0.026	-1.375286	0.01214	0.504768	0.148743	ENSG00000138400	ENST00000374412;ENST00000449792;ENST00000454776	T;T;T	0.34072	1.41;1.38;1.4	4.44	-3.1	0.05315	.	0.872837	0.09496	N	0.794337	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45026	-0.9289	9	0.02654	T	1	.	0.4693	0.00529	0.2913:0.1262:0.1992:0.3834	rs2287631;rs52818171;rs60689609;rs2287631	509;510	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	D	510;412;509	ENSP00000363533:E510D;ENSP00000416577:E412D;ENSP00000389916:E509D	ENSP00000363533:E510D	E	-	3	2	MDH1B	207311479	0.000000	0.05858	0.015000	0.15790	0.001000	0.01503	-1.583000	0.02115	-0.964000	0.03595	-2.042000	0.00416	GAA	T|0.683;G|0.317	0.317	strong		0.274	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845	Missense_Mutation
SLCO1B1	10599	hgsc.bcm.edu	37	12	21331625	21331625	+	Silent	SNP	C	C	T	rs2291075	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:21331625C>T	ENST00000256958.2	+	6	693	c.597C>T	c.(595-597)ttC>ttT	p.F199F		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	199					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	TTGATGATTTCGCTAAAGAAG	0.358													T|||	2081	0.415535	0.5598	0.3314	5008	,	,		15258	0.5109		0.3966	False		,,,				2504	0.2014				p.F199F		Atlas-SNP	.											SLCO1B1,NS,carcinoma,+2,1	SLCO1B1	151	1	0			c.C597T						scavenged	.	T		2401,2005	559.9+/-380.3	649,1103,451	122.0	113.0	116.0		597	2.5	1.0	12	dbSNP_100	116	3438,5162	636.0+/-399.1	695,2048,1557	yes	coding-synonymous	SLCO1B1	NM_006446.4		1344,3151,2008	TT,TC,CC		39.9767,45.5061,44.8947		199/692	21331625	5839,7167	2203	4300	6503	SO:0001819	synonymous_variant	10599	exon6			TGATTTCGCTAAA		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.597C>T	12.37:g.21331625C>T		Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	164	71	0.432927	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Silent	SNP	ENST00000256958.2	37	CCDS8685.1																																																																																			C|0.548;T|0.452	0.452	strong		0.358	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
ZFHX3	463	hgsc.bcm.edu	37	16	72993622	72993622	+	Silent	SNP	C	C	T	rs62053190	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72993622C>T	ENST00000268489.5	-	2	1095	c.423G>A	c.(421-423)gcG>gcA	p.A141A	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	141					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CCACAATGTACGCGGAGCCGT	0.667													C|||	219	0.04373	0.0507	0.0317	5008	,	,		13453	0.003		0.0616	False		,,,				2504	0.0665				p.A141A		Atlas-SNP	.											ZFHX3,NS,carcinoma,0,2	ZFHX3	404	2	0			c.G423A						PASS	.	C	,	276,4120	146.9+/-181.5	9,258,1931	35.0	39.0	38.0		,423	-10.2	0.4	16	dbSNP_129	38	604,7996	152.8+/-207.3	25,554,3721	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	34,812,5652	TT,TC,CC		7.0233,6.2784,6.7713	,	,141/3704	72993622	880,12116	2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			AATGTACGCGGAG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.423G>A	16.37:g.72993622C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			C|0.941;T|0.059	0.059	strong		0.667	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
EI24	9538	hgsc.bcm.edu	37	11	125452313	125452313	+	Missense_Mutation	SNP	A	A	G	rs4627097	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:125452313A>G	ENST00000343678.4	+	10	985	c.743A>G	c.(742-744)cAt>cGt	p.H248R	STT3A-AS1_ENST00000532714.1_RNA|EI24_ENST00000278903.6_Silent_p.A285A|STT3A-AS1_ENST00000530526.1_RNA|EI24_ENST00000530985.1_3'UTR	NM_001007277.1	NP_001007278.1	O14681	EI24_HUMAN	etoposide induced 2.4	0					apoptotic process (GO:0006915)|autophagy (GO:0006914)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of cell growth (GO:0030308)|neuromuscular process controlling balance (GO:0050885)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|response to drug (GO:0042493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(1)|lung(9)|ovary(1)	11	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)		CTGGCAAAGCATAGTAAGTAT	0.343													G|||	1705	0.340455	0.3835	0.2594	5008	,	,		13966	0.2976		0.3658	False		,,,				2504	0.3579				p.I249V		Atlas-SNP	.											.	EI24	33	.	0			c.A745G						PASS	.	G	,ARG/HIS	1334,2298		248,838,730	35.0	34.0	34.0		857,745	-7.7	0.8	11	dbSNP_111	34	2872,5278		483,1906,1686	yes	coding-synonymous,missense	EI24	NM_004879.3,NM_001007277.1	,29	731,2744,2416	GG,GA,AA		35.2393,36.7291,35.6985	,benign	286/341,249/263	125452313	4206,7576	1816	4075	5891	SO:0001583	missense	9538	exon9			CAAAGCATAGTAA	AF010313	CCDS73410.1	11q24.2	2012-11-19	2012-11-16		ENSG00000149547	ENSG00000149547			13276	protein-coding gene	gene with protein product	"""ectopic P-granules autophagy protein 4 homolog (C. elegans)"""	605170	"""etoposide induced 2.4 mRNA"""			10594026, 9305847	Standard	NM_001290135		Approved	PIG8, TP53I8, EPG4	uc001qcb.3	O14681	OTTHUMG00000165851	ENST00000343678.4:c.743A>G	11.37:g.125452313A>G	ENSP00000364081:p.His248Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_001007277	A8K7D6|B4DKL6|Q9BUQ1	Missense_Mutation	SNP	ENST00000343678.4	37		742	0.33974358974358976	199	0.40447154471544716	101	0.27900552486187846	165	0.28846153846153844	277	0.3654353562005277	G	9.401	1.078074	0.20227	0.367291	0.352393	ENSG00000149547	ENST00000343678	.	.	.	4.73	-7.71	0.01254	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41840	-0.9486	6	0.46703	T	0.11	.	6.6214	0.22806	0.3693:0.0:0.381:0.2496	rs4627097;rs17174519;rs59674749;rs4627097	248	A6NES3	.	R	248	.	ENSP00000364081:H248R	H	+	2	0	EI24	124957523	0.001000	0.12720	0.795000	0.32087	0.882000	0.50991	-1.460000	0.02368	-1.390000	0.02087	-1.951000	0.00486	CAT	A|0.658;G|0.342	0.342	strong		0.343	EI24-202	KNOWN	basic	protein_coding	protein_coding		NM_004879	
MUC21	394263	hgsc.bcm.edu	37	6	30954572	30954572	+	Missense_Mutation	SNP	C	C	T	rs146037191		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954572C>T	ENST00000376296.3	+	2	861	c.620C>T	c.(619-621)gCc>gTc	p.A207V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	207	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A207V(2)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGTGGGGCCAGCACAGCC	0.627																																					p.A207V		Atlas-SNP	.											MUC21,NS,malignant_melanoma,0,2	MUC21	98	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.C620T						PASS	.						152.0	149.0	150.0					6																	30954572		2203	4300	6503	SO:0001583	missense	394263	exon2			GTGGGGCCAGCAC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.620C>T	6.37:g.30954572C>T	ENSP00000365473:p.Ala207Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	138	10	0.0724638	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	C	8.950	0.968056	0.18659	.	.	ENSG00000204544	ENST00000376296	T	0.02737	4.18	3.86	-1.98	0.07480	.	.	.	.	.	T	0.00356	0.0011	N	0.04508	-0.205	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.45190	-0.9278	8	.	.	.	-2.1025	0.8413	0.01150	0.1528:0.2516:0.2999:0.2958	.	207	Q5SSG8	MUC21_HUMAN	V	207	ENSP00000365473:A207V	.	A	+	2	0	MUC21	31062551	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.003000	0.12901	-0.201000	0.10284	-0.424000	0.05967	GCC	C|0.998;T|0.002	0.002	weak		0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
CIC	23152	hgsc.bcm.edu	37	19	42799049	42799049	+	Silent	SNP	C	C	T	rs1052023	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:42799049C>T	ENST00000575354.2	+	20	4573	c.4533C>T	c.(4531-4533)atC>atT	p.I1511I	CIC_ENST00000572681.2_Silent_p.I2417I|CIC_ENST00000160740.3_Silent_p.I1509I	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1511					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				AGTTGAAGATCCGTGAGGTGC	0.627			"""Mis, F, S"""		oligodendroglioma								C|||	600	0.119808	0.0106	0.1945	5008	,	,		14163	0.0		0.3907	False		,,,				2504	0.0593				p.I1511I		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.C4533T						PASS	.	C		339,4067	173.0+/-202.9	15,309,1879	53.0	53.0	53.0		4533	3.4	1.0	19	dbSNP_86	53	3246,5354	475.6+/-369.2	620,2006,1674	no	coding-synonymous	CIC	NM_015125.3		635,2315,3553	TT,TC,CC		37.7442,7.6941,27.5642		1511/1609	42799049	3585,9421	2203	4300	6503	SO:0001819	synonymous_variant	23152	exon20			GAAGATCCGTGAG	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4533C>T	19.37:g.42799049C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Silent	SNP	ENST00000575354.2	37	CCDS12601.1																																																																																			C|0.756;T|0.244	0.244	strong		0.627	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2		
ARHGEF12	23365	hgsc.bcm.edu	37	11	120317731	120317731	+	Missense_Mutation	SNP	G	G	A	rs138160103	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:120317731G>A	ENST00000397843.2	+	18	1692	c.1526G>A	c.(1525-1527)cGa>cAa	p.R509Q	ARHGEF12_ENST00000356641.3_Missense_Mutation_p.R490Q|ARHGEF12_ENST00000532993.1_Missense_Mutation_p.R406Q	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	509	RGSL.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		GACAAGGACCGATTGACTTTG	0.443			T	MLL	AML								G|||	4	0.000798722	0.0	0.0	5008	,	,		22212	0.0		0.003	False		,,,				2504	0.001				p.R509Q		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.G1526A						PASS	.	G	GLN/ARG,GLN/ARG	2,3952		0,2,1975	137.0	128.0	131.0		1469,1526	5.4	1.0	11	dbSNP_134	131	18,8334		0,18,4158	yes	missense,missense	ARHGEF12	NM_001198665.1,NM_015313.2	43,43	0,20,6133	AA,AG,GG		0.2155,0.0506,0.1625	probably-damaging,probably-damaging	490/1526,509/1545	120317731	20,12286	1977	4176	6153	SO:0001583	missense	23365	exon18			AGGACCGATTGAC	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"""Rho guanine nucleotide exchange factors"""	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.1526G>A	11.37:g.120317731G>A	ENSP00000380942:p.Arg509Gln	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	180	96	0.533333	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	37	CCDS41727.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	37	6.004474	0.97195	5.06E-4	0.002155	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	D;D;D	0.83837	-1.77;-1.77;-1.77	5.44	5.44	0.79542	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.000000	0.41712	D	0.000824	D	0.90086	0.6903	M	0.76328	2.33	0.58432	D	0.999997	D;D;D	0.71674	0.998;0.987;0.989	P;P;P	0.60173	0.87;0.742;0.832	D	0.90454	0.4441	10	0.62326	D	0.03	-16.9171	19.6363	0.95735	0.0:0.0:1.0:0.0	.	406;490;509	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	Q	509;490;406	ENSP00000380942:R509Q;ENSP00000349056:R490Q;ENSP00000432984:R406Q	ENSP00000349056:R490Q	R	+	2	0	ARHGEF12	119822941	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.416000	0.80143	2.714000	0.92807	0.650000	0.86243	CGA	G|0.998;A|0.002	0.002	strong		0.443	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313	
DNAH3	55567	hgsc.bcm.edu	37	16	21045369	21045369	+	Silent	SNP	A	A	G	rs2112494	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:21045369A>G	ENST00000261383.3	-	36	5123	c.5124T>C	c.(5122-5124)atT>atC	p.I1708I	DNAH3_ENST00000415178.1_Silent_p.I1708I	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1708	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GGTCTCCTACAATCATATAGC	0.488													A|||	525	0.104832	0.0212	0.0908	5008	,	,		19360	0.1597		0.1044	False		,,,				2504	0.1718				p.I1708I		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T5124C						PASS	.	A		140,4262	96.7+/-135.4	4,132,2065	93.0	82.0	86.0		5124	0.1	1.0	16	dbSNP_96	86	856,7744	195.6+/-240.8	46,764,3490	no	coding-synonymous	DNAH3	NM_017539.1		50,896,5555	GG,GA,AA		9.9535,3.1804,7.6604		1708/4117	21045369	996,12006	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon36			TCCTACAATCATA	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.5124T>C	16.37:g.21045369A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			A|0.912;G|0.088	0.088	strong		0.488	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
CHIA	27159	hgsc.bcm.edu	37	1	111854889	111854889	+	Missense_Mutation	SNP	A	A	G	rs41282492	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111854889A>G	ENST00000369740.1	+	4	236	c.133A>G	c.(133-135)Aac>Gac	p.N45D	CHIA_ENST00000430615.1_Intron|CHIA_ENST00000343320.6_Missense_Mutation_p.N45D|CHIA_ENST00000483391.1_Intron|CHIA_ENST00000451398.2_Intron|CHIA_ENST00000353665.6_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	45			N -> D (increased chitinase activity; when associated with N-47 and M-61; dbSNP:rs41282492). {ECO:0000269|PubMed:19435888}.		apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		CATGCCTGACAACATCGACCC	0.572													G|||	544	0.108626	0.2126	0.0836	5008	,	,		17991	0.0		0.1093	False		,,,				2504	0.0971				p.N45D		Atlas-SNP	.											CHIA_ENST00000369740,NS,carcinoma,-1,1	CHIA	115	1	0			c.A133G						scavenged	.	G	,ASP/ASN	775,3397		67,641,1378	96.0	97.0	97.0		,133	-2.9	0.0	1	dbSNP_127	97	976,7454		49,878,3288	yes	intron,missense	CHIA	NM_021797.2,NM_201653.2	,23	116,1519,4666	GG,GA,AA		11.5777,18.5762,13.8946	,benign	,45/477	111854889	1751,10851	2086	4215	6301	SO:0001583	missense	27159	exon4			CCTGACAACATCG	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.133A>G	1.37:g.111854889A>G	ENSP00000358755:p.Asn45Asp	Somatic	142	2	0.0140845		WXS	Illumina HiSeq	Phase_I	147	61	0.414966	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	229	0.10485347985347986	105	0.21341463414634146	36	0.09944751381215469	0	0.0	88	0.11609498680738786	G	0.032	-1.328299	0.01309	0.185762	0.115777	ENSG00000134216	ENST00000369740;ENST00000343320	T;T	0.04654	3.58;3.58	5.08	-2.92	0.05615	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.460557	0.17861	N	0.159511	T	0.00637	0.0021	N	0.10760	0.04	0.24700	P	0.99326224	B	0.02656	0.0	B	0.14023	0.01	T	0.44345	-0.9334	9	0.02654	T	1	-5.6473	13.4826	0.61345	0.6795:0.0:0.3205:0.0	rs41282492;rs61752465	45	Q9BZP6	CHIA_HUMAN	D	45	ENSP00000358755:N45D;ENSP00000341828:N45D	ENSP00000341828:N45D	N	+	1	0	CHIA	111656412	0.001000	0.12720	0.006000	0.13384	0.382000	0.30200	0.070000	0.14573	-0.854000	0.04131	-0.766000	0.03442	AAC	A|0.881;G|0.119	0.119	strong		0.572	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
RIPK2	8767	hgsc.bcm.edu	37	8	90770393	90770393	+	Silent	SNP	C	C	T	rs200258974		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:90770393C>T	ENST00000220751.4	+	1	419	c.105C>T	c.(103-105)gcC>gcT	p.A35A	RIPK2_ENST00000540020.1_5'UTR|RP11-37B2.1_ENST00000504145.1_lincRNA	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	35	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immature T cell proliferation (GO:0033091)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|response to exogenous dsRNA (GO:0043330)|response to interleukin-1 (GO:0070555)|response to interleukin-12 (GO:0070671)|response to interleukin-18 (GO:0070673)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|LIM domain binding (GO:0030274)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			TGTCGTCCGCCCGCCACGCAG	0.677																																					p.A35A		Atlas-SNP	.											RIPK2,NS,malignant_melanoma,+2,1	RIPK2	37	1	0			c.C105T						PASS	.																																			SO:0001819	synonymous_variant	8767	exon1			GTCCGCCCGCCAC	AC004003	CCDS6247.1	8q21	2008-05-02			ENSG00000104312	ENSG00000104312			10020	protein-coding gene	gene with protein product		603455				9575181, 9705938	Standard	XM_005251092		Approved	RICK, RIP2, CARDIAK, CARD3	uc003yee.3	O43353	OTTHUMG00000163809	ENST00000220751.4:c.105C>T	8.37:g.90770393C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	86	55	0.639535	NM_003821	B7Z748|Q6UWF0	Silent	SNP	ENST00000220751.4	37	CCDS6247.1																																																																																			.	.	weak		0.677	RIPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375686.1		
IL6ST	3572	hgsc.bcm.edu	37	5	55248135	55248135	+	Missense_Mutation	SNP	C	C	T	rs34417936	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:55248135C>T	ENST00000381298.2	-	12	1807	c.1495G>A	c.(1495-1497)Gta>Ata	p.V499I	IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000502326.3_Missense_Mutation_p.V499I|IL6ST_ENST00000381294.3_Missense_Mutation_p.V438I|IL6ST_ENST00000522633.2_3'UTR|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.V499I	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	499	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs34417936).		ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				TCAGCATATACTGGAGTAACT	0.363			O		hepatocellular ca								C|||	54	0.0107827	0.003	0.0259	5008	,	,		18030	0.0		0.0258	False		,,,				2504	0.0061				p.V499I		Atlas-SNP	.		Dom	yes		5	5q11	3572	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""		E	.	IL6ST	75	.	0			c.G1495A						PASS	.	C	ILE/VAL,ILE/VAL,	25,4381	29.9+/-59.1	0,25,2178	97.0	94.0	95.0		1312,1495,	5.9	0.8	5	dbSNP_126	95	259,8341	101.0+/-162.3	4,251,4045	yes	missense,missense,utr-3	IL6ST	NM_001190981.1,NM_002184.3,NM_175767.2	29,29,	4,276,6223	TT,TC,CC		3.0116,0.5674,2.1836	benign,benign,	438/858,499/919,	55248135	284,12722	2203	4300	6503	SO:0001583	missense	3572	exon12			CATATACTGGAGT	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6021	protein-coding gene	gene with protein product	"""gp130, oncostatin M receptor"""	600694	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.1495G>A	5.37:g.55248135C>T	ENSP00000370698:p.Val499Ile	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	30	0.013736263736263736	2	0.0040650406504065045	14	0.03867403314917127	0	0.0	14	0.018469656992084433	C	11.85	1.761705	0.31228	0.005674	0.030116	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.55234	0.53;0.53;1.12	5.93	5.93	0.95920	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.131931	0.53938	D	0.000041	T	0.11623	0.0283	L	0.31926	0.97	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.07578	-1.0765	10	0.12766	T	0.61	.	10.6199	0.45474	0.1248:0.6405:0.2347:0.0	rs34417936	499;438;499	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	I	499;499;438	ENSP00000370698:V499I;ENSP00000338799:V499I;ENSP00000370694:V438I	ENSP00000338799:V499I	V	-	1	0	IL6ST	55283892	0.919000	0.31177	0.836000	0.33094	0.996000	0.88848	0.610000	0.24253	2.826000	0.97356	0.655000	0.94253	GTA	C|0.980;T|0.020	0.020	strong		0.363	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184	
ACTRT2	140625	hgsc.bcm.edu	37	1	2938989	2938989	+	Missense_Mutation	SNP	G	G	A	rs3795263	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:2938989G>A	ENST00000378404.2	+	1	944	c.739G>A	c.(739-741)Ggg>Agg	p.G247R		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	247			G -> R (in dbSNP:rs3795263).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		GCTGCCCGACGGGAACATCAT	0.652													G|||	611	0.122005	0.0106	0.121	5008	,	,		16197	0.1607		0.2584	False		,,,				2504	0.093				p.G247R		Atlas-SNP	.											.	ACTRT2	69	.	0			c.G739A						PASS	.	G	ARG/GLY	218,4188		11,196,1996	36.0	41.0	40.0		739	4.8	0.9	1	dbSNP_107	40	2009,6589		245,1519,2535	yes	missense	ACTRT2	NM_080431.4	125	256,1715,4531	AA,AG,GG		23.3659,4.9478,17.1255	probably-damaging	247/378	2938989	2227,10777	2203	4299	6502	SO:0001583	missense	140625	exon1			CCCGACGGGAACA	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.739G>A	1.37:g.2938989G>A	ENSP00000367658:p.Gly247Arg	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_080431	B1AN52|Q8NHS6|Q8TDG1	Missense_Mutation	SNP	ENST00000378404.2	37	CCDS45.1	348	0.15934065934065933	4	0.008130081300813009	57	0.1574585635359116	96	0.16783216783216784	191	0.2519788918205805	G	16.11	3.029664	0.54790	0.049478	0.233659	ENSG00000169717	ENST00000378404;ENST00000543312	D	0.97089	-4.24	4.85	4.85	0.62838	.	0.000000	0.56097	D	0.000026	T	0.01254	0.0041	M	0.94142	3.5	0.09310	P	0.99999892596	D	0.89917	1.0	D	0.83275	0.996	T	0.00000	-1.6286	9	0.87932	D	0	.	11.1701	0.48567	0.0907:0.0:0.9093:0.0	rs3795263;rs17390011;rs60765657;rs3795263	247	Q8TDY3	ACTT2_HUMAN	R	247	ENSP00000367658:G247R	ENSP00000367658:G247R	G	+	1	0	ACTRT2	2928849	1.000000	0.71417	0.915000	0.36163	0.341000	0.28922	6.582000	0.74049	2.228000	0.72767	0.561000	0.74099	GGG	G|0.842;A|0.158	0.158	strong		0.652	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431	
DPP4	1803	hgsc.bcm.edu	37	2	162865133	162865133	+	Silent	SNP	C	C	T	rs41268649	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:162865133C>T	ENST00000360534.3	-	22	2486	c.1926G>A	c.(1924-1926)tcG>tcA	p.S642S	DPP4_ENST00000491591.1_5'UTR	NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	642					cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.S642S(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	CGCCACTTCCCGATCCCAGGA	0.463													C|||	67	0.0133786	0.0023	0.0187	5008	,	,		18673	0.0		0.0477	False		,,,				2504	0.0031				p.S642S		Atlas-SNP	.											DPP4,colon,carcinoma,0,1	DPP4	90	1	1	Substitution - coding silent(1)	lung(1)	c.G1926A						PASS	.	C		39,4367	43.8+/-77.6	0,39,2164	101.0	88.0	92.0		1926	-7.0	1.0	2	dbSNP_127	92	394,8206	126.5+/-185.0	12,370,3918	no	coding-synonymous	DPP4	NM_001935.3		12,409,6082	TT,TC,CC		4.5814,0.8852,3.3292		642/767	162865133	433,12573	2203	4300	6503	SO:0001819	synonymous_variant	1803	exon22			ACTTCCCGATCCC	M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"""CD molecules"""	3009	protein-coding gene	gene with protein product		102720	"""dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)"", ""adenosine deaminase complexing protein 2"""	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.1926G>A	2.37:g.162865133C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	105	45	0.428571	NM_001935	Q53TN1	Silent	SNP	ENST00000360534.3	37	CCDS2216.1																																																																																			C|0.969;T|0.031	0.031	strong		0.463	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2		
HSPBAP1	79663	hgsc.bcm.edu	37	3	122474121	122474121	+	Missense_Mutation	SNP	G	G	C	rs61756481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:122474121G>C	ENST00000306103.2	-	5	870	c.727C>G	c.(727-729)Ctg>Gtg	p.L243V	HSPBAP1_ENST00000465044.1_5'UTR|HSPBAP1_ENST00000383659.1_3'UTR	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	243	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.					cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(114;0.0531)		CCTGGGCTCAGTGTAACCGCA	0.448													G|||	134	0.0267572	0.0106	0.0533	5008	,	,		18520	0.0		0.0706	False		,,,				2504	0.0123				p.L243V		Atlas-SNP	.											.	HSPBAP1	32	.	0			c.C727G						PASS	.	G	VAL/LEU	96,4310	79.3+/-117.8	1,94,2108	104.0	91.0	95.0		727	3.4	0.3	3	dbSNP_129	95	658,7942	167.0+/-218.8	33,592,3675	yes	missense	HSPBAP1	NM_024610.5	32	34,686,5783	CC,CG,GG		7.6512,2.1788,5.7973	probably-damaging	243/489	122474121	754,12252	2203	4300	6503	SO:0001583	missense	79663	exon5			GGCTCAGTGTAAC	AF400663	CCDS3017.1	3q21.1	2008-07-18	2002-08-29		ENSG00000169087	ENSG00000169087			16389	protein-coding gene	gene with protein product		608263	"""HSPB (heat shock 27kD) associated protein 1"""			11978969	Standard	NM_024610		Approved	FLJ22623, PASS1	uc003efu.2	Q96EW2	OTTHUMG00000159550	ENST00000306103.2:c.727C>G	3.37:g.122474121G>C	ENSP00000302562:p.Leu243Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	150	71	0.473333	NM_024610	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	Missense_Mutation	SNP	ENST00000306103.2	37	CCDS3017.1	71	0.03250915750915751	6	0.012195121951219513	20	0.055248618784530384	0	0.0	45	0.059366754617414245	G	16.87	3.242889	0.58995	0.021788	0.076512	ENSG00000169087	ENST00000306103	T	0.35605	1.3	5.24	3.42	0.39159	Cupin, JmjC-type (1);Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.341374	0.30820	N	0.008816	T	0.04907	0.0132	M	0.64260	1.97	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00577	-1.1662	10	0.45353	T	0.12	.	8.884	0.35392	0.2331:0.0:0.7669:0.0	rs61756481	243	Q96EW2	HBAP1_HUMAN	V	243	ENSP00000302562:L243V	ENSP00000302562:L243V	L	-	1	2	HSPBAP1	123956811	1.000000	0.71417	0.347000	0.25668	0.865000	0.49528	3.707000	0.54838	0.586000	0.29626	0.580000	0.79431	CTG	G|0.952;C|0.048	0.048	strong		0.448	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610	
ACP1	52	hgsc.bcm.edu	37	2	277003	277003	+	Missense_Mutation	SNP	A	A	G	rs79716074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:277003A>G	ENST00000272065.5	+	5	410	c.317A>G	c.(316-318)cAa>cGa	p.Q106R	ACP1_ENST00000484464.1_3'UTR|ACP1_ENST00000272067.6_Missense_Mutation_p.Q106R	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble	106			Q -> R (in allele ACP1*A; dbSNP:rs7576247). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	AAAAGTAATCAAGTTAAAACC	0.323													A|||	1323	0.264177	0.2065	0.2363	5008	,	,		18004	0.246		0.335	False		,,,				2504	0.3078				p.Q106R		Atlas-SNP	.											ACP1_ENST00000272067,NS,carcinoma,+1,4	ACP1	42	4	0			c.A317G						PASS	.	A	ARG/GLN,ARG/GLN	983,3417	336.0+/-304.2	107,769,1324	52.0	55.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	317,317	3.1	1.0	2	dbSNP_131	54	2959,5631	442.4+/-360.1	483,1993,1819	yes	missense,missense	ACP1	NM_004300.3,NM_007099.3	43,43	590,2762,3143	GG,GA,AA		34.447,22.3409,30.3464	benign,benign	106/159,106/159	277003	3942,9048	2200	4295	6495	SO:0001583	missense	52	exon5			GTAATCAAGTTAA	M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"""Protein tyrosine phosphatases / Class II Cys-based PTPs"""	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.317A>G	2.37:g.277003A>G	ENSP00000272065:p.Gln106Arg	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	201	80	0.39801	NM_007099	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Missense_Mutation	SNP	ENST00000272065.5	37	CCDS1639.1	551	0.2522893772893773	87	0.17682926829268292	87	0.24033149171270718	126	0.2202797202797203	251	0.3311345646437995	A	11.29	1.595656	0.28445	0.223409	0.34447	ENSG00000143727	ENST00000272067;ENST00000272065	T;T	0.16457	2.34;2.34	5.48	3.09	0.35607	Phosphotyrosine protein phosphatase I superfamily (3);	0.404011	0.29624	N	0.011622	T	0.00012	0.0000	N	0.05414	-0.055	0.09310	P	0.9999999842883	B;B	0.10296	0.0;0.003	B;B	0.14578	0.003;0.011	T	0.49679	-0.8914	9	0.23302	T	0.38	-2.9532	6.7926	0.23707	0.7665:0.1527:0.0807:0.0	rs7576247;rs17357270;rs59972259	106;106	P24666-2;P24666	.;PPAC_HUMAN	R	106	ENSP00000272067:Q106R;ENSP00000272065:Q106R	ENSP00000272065:Q106R	Q	+	2	0	ACP1	267003	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.840000	0.48215	0.370000	0.24538	0.533000	0.62120	CAA	A|0.725;G|0.275	0.275	strong		0.323	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3		
PZP	5858	hgsc.bcm.edu	37	12	9315209	9315209	+	Silent	SNP	A	A	G	rs10771381	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:9315209A>G	ENST00000261336.2	-	22	2800	c.2772T>C	c.(2770-2772)tcT>tcC	p.S924S	PZP_ENST00000539983.1_5'UTR|PZP_ENST00000381997.2_Silent_p.S710S	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	924					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CACAGGTCATAGAACTGAAAG	0.388													G|||	2036	0.40655	0.3933	0.366	5008	,	,		-128	0.4226		0.3966	False		,,,				2504	0.4468				p.S924S	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.T2772C						PASS	.	G		1870,2536	630.9+/-395.5	405,1060,738	151.0	134.0	140.0		2772	-4.4	0.0	12	dbSNP_120	140	3698,4902	620.1+/-397.0	802,2094,1404	no	coding-synonymous	PZP	NM_002864.2		1207,3154,2142	GG,GA,AA		43.0,42.4421,42.811		924/1483	9315209	5568,7438	2203	4300	6503	SO:0001819	synonymous_variant	5858	exon22			GGTCATAGAACTG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2772T>C	12.37:g.9315209A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Silent	SNP	ENST00000261336.2	37	CCDS8600.1																																																																																			A|0.580;G|0.420	0.420	strong		0.388	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
TUBA1B	10376	hgsc.bcm.edu	37	12	49522578	49522578	+	Silent	SNP	T	T	C	rs1057725|rs11267025	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:49522578T>C	ENST00000336023.5	-	4	613	c.519A>G	c.(517-519)ccA>ccG	p.P173P	RP11-386G11.10_ENST00000547712.1_RNA|RP11-386G11.10_ENST00000548149.1_RNA|RP11-386G11.10_ENST00000547387.1_RNA|RP11-386G11.10_ENST00000551496.1_RNA|RP11-386G11.10_ENST00000552893.1_RNA	NM_006082.2	NP_006073.2	P68363	TBA1B_HUMAN	tubulin, alpha 1b	173					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(4)	12						CCTGGGGTGCTGGGTAAATGG	0.532													C|||	2729	0.544928	0.6664	0.3617	5008	,	,		16490	0.6835		0.333	False		,,,				2504	0.5859				p.P173P		Atlas-SNP	.											.	TUBA1B	24	.	0			c.A519G						PASS	.						42.0	63.0	56.0					12																	49522578		2200	4295	6495	SO:0001819	synonymous_variant	10376	exon4			GGGTGCTGGGTAA	AF081484	CCDS31792.1	12q13.12	2007-02-12				ENSG00000123416		"""Tubulins"""	18809	protein-coding gene	gene with protein product	"""tubulin, alpha, ubiquitous"""	602530				12054644, 6646120	Standard	NM_006082		Approved	K-ALPHA-1	uc001rtm.3	P68363	OTTHUMG00000170410	ENST00000336023.5:c.519A>G	12.37:g.49522578T>C		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	215	73	0.339535	NM_006082	P04687|P05209|Q27I68|Q8WU19	Silent	SNP	ENST00000336023.5	37	CCDS31792.1																																																																																			T|0.527;C|0.473	0.473	strong		0.532	TUBA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409005.1	NM_006082	
CPA5	93979	hgsc.bcm.edu	37	7	130007381	130007381	+	Missense_Mutation	SNP	T	T	C	rs11761888	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:130007381T>C	ENST00000485477.1	+	10	2136	c.1007T>C	c.(1006-1008)tTg>tCg	p.L336S	CPA5_ENST00000466363.2_Missense_Mutation_p.L336S|CPA5_ENST00000393213.3_Missense_Mutation_p.L336S|CPA5_ENST00000355388.3_Missense_Mutation_p.L336S|CPA5_ENST00000431780.2_Missense_Mutation_p.L336S|CPA5_ENST00000474905.1_Missense_Mutation_p.L336S|CPA5_ENST00000461828.1_Missense_Mutation_p.L336S			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	336			L -> S (in dbSNP:rs11761888). {ECO:0000269|PubMed:11920156, ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					TACGGCCGATTGCTGGAGCCC	0.517													C|||	1014	0.202476	0.4259	0.1225	5008	,	,		18328	0.0258		0.2048	False		,,,				2504	0.137				p.L336S		Atlas-SNP	.											.	CPA5	61	.	0			c.T1007C						PASS	.	C	SER/LEU,SER/LEU,SER/LEU	1672,2734	655.8+/-400.0	307,1058,838	124.0	118.0	120.0		1007,1007,1007	3.7	0.3	7	dbSNP_120	120	1854,6746	730.2+/-406.8	202,1450,2648	yes	missense,missense,missense	CPA5	NM_001127441.1,NM_001127442.1,NM_080385.4	145,145,145	509,2508,3486	CC,CT,TT		21.5581,37.9483,27.1106	benign,benign,benign	336/437,336/404,336/437	130007381	3526,9480	2203	4300	6503	SO:0001583	missense	93979	exon11			GCCGATTGCTGGA	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.1007T>C	7.37:g.130007381T>C	ENSP00000420237:p.Leu336Ser	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	379	187	0.493404	NM_080385	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	37	CCDS5819.1	417	0.19093406593406592	198	0.4024390243902439	46	0.1270718232044199	12	0.02097902097902098	161	0.21240105540897097	C	2.814	-0.246343	0.05867	0.379483	0.215581	ENSG00000158525	ENST00000355388;ENST00000461828;ENST00000466363;ENST00000485477;ENST00000431780;ENST00000474905;ENST00000393213	T;T;T;T;T;T;T	0.02656	4.21;4.21;4.21;4.21;4.21;4.21;4.21	5.61	3.73	0.42828	Peptidase M14, carboxypeptidase A (2);	0.780103	0.11283	N	0.580123	T	0.00012	0.0000	N	0.00053	-2.385	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40059	-0.9583	8	.	.	.	.	4.6819	0.12739	0.2065:0.5242:0.1911:0.0783	rs11761888;rs17857277;rs61540978;rs11761888	336;336	G3V0G8;Q8WXQ8	.;CBPA5_HUMAN	S	336	ENSP00000347549:L336S;ENSP00000418183:L336S;ENSP00000419025:L336S;ENSP00000420237:L336S;ENSP00000393045:L336S;ENSP00000417314:L336S;ENSP00000376907:L336S	.	L	+	2	0	CPA5	129794617	0.736000	0.28164	0.289000	0.24876	0.002000	0.02628	0.926000	0.28804	1.389000	0.46526	-0.355000	0.07637	TTG	C|0.239;T|0.761	0.239	strong		0.517	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441	
CELA3A	10136	hgsc.bcm.edu	37	1	22336305	22336305	+	Silent	SNP	C	C	T	rs9187	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22336305C>T	ENST00000290122.3	+	7	769	c.750C>T	c.(748-750)ccC>ccT	p.P250P	RN7SL186P_ENST00000466485.2_RNA|RNU6-776P_ENST00000364403.1_RNA	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	250	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCTGGAAGCCCACGGTGTTCA	0.607													c|||	1435	0.286542	0.2315	0.4107	5008	,	,		16390	0.4018		0.2207	False		,,,				2504	0.2219				p.P250P		Atlas-SNP	.											CELA3A,NS,carcinoma,+2,1	CELA3A	35	1	0			c.C750T						PASS	.	T		1148,3258		191,766,1246	77.0	69.0	72.0		750	0.6	1.0	1	dbSNP_52	72	1960,6640		250,1460,2590	no	coding-synonymous	CELA3A	NM_005747.4		441,2226,3836	TT,TC,CC		22.7907,26.0554,23.8967		250/271	22336305	3108,9898	2203	4300	6503	SO:0001819	synonymous_variant	10136	exon7			GAAGCCCACGGTG	D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"""protease E"""		"""elastase 3A, pancreatic (protease E)"", ""elastase 3A, pancreatic"""	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.750C>T	1.37:g.22336305C>T		Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	247	111	0.449393	NM_005747	B1AQ53|Q9BRW4	Silent	SNP	ENST00000290122.3	37	CCDS220.1																																																																																			C|0.737;T|0.263	0.263	strong		0.607	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747	
MICA	100507436	hgsc.bcm.edu	37	6	31379990	31379990	+	Missense_Mutation	SNP	C	C	G	rs41553616	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31379990C>G	ENST00000449934.2	+	4	934	c.880C>G	c.(880-882)Cct>Gct	p.P294A	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CAGCACTCACCCTGTGCCCTC	0.597													c|||	77	0.0153754	0.0182	0.0533	5008	,	,		18963	0.001		0.0149	False		,,,				2504	0.0				p.P294A		Atlas-SNP	.											.	MICA	21	.	0			c.C880G						PASS	.	C	ALA/PRO	28,1356		1,26,665	81.0	66.0	71.0		880	-0.3	0.0	6	dbSNP_127	71	99,3083		4,91,1496	no	missense	MICA	NM_001177519.1	27	5,117,2161	GG,GC,CC		3.1113,2.0231,2.7814	possibly-damaging	294/333	31379990	127,4439	692	1591	2283	SO:0001583	missense	100507436	exon4			ACTCACCCTGTGC	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.880C>G	6.37:g.31379990C>G	ENSP00000413079:p.Pro294Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	44	0.020146520146520148	7	0.014227642276422764	24	0.06629834254143646	1	0.0017482517482517483	12	0.0158311345646438	c	7.781	0.709428	0.15239	0.020231	0.031113	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.01234	5.59;5.13	2.72	-0.265	0.12946	.	.	.	.	.	T	0.00875	0.0029	L	0.56769	1.78	0.09310	N	0.999999	B;D	0.54601	0.013;0.967	B;P	0.47744	0.012;0.556	T	0.48736	-0.9009	9	0.72032	D	0.01	.	3.8434	0.08925	0.0:0.3345:0.4033:0.2622	rs41553616;rs61733194	156;294	Q5SS58;Q96QC4	.;.	A	156;294;251;294;185	ENSP00000413079:P294A;ENSP00000402410:P185A	ENSP00000365394:P294A	P	+	1	0	MICA	31487969	0.000000	0.05858	0.010000	0.14722	0.115000	0.19883	-0.340000	0.07821	0.067000	0.16545	-0.551000	0.04211	CCT	C|0.977;G|0.023	0.023	strong		0.597	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
CCDC77	84318	hgsc.bcm.edu	37	12	520947	520947	+	Missense_Mutation	SNP	A	A	C	rs4980895	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:520947A>C	ENST00000239830.4	+	4	252	c.73A>C	c.(73-75)Agt>Cgt	p.S25R	CCDC77_ENST00000412006.2_5'UTR|CCDC77_ENST00000422000.1_5'UTR|CCDC77_ENST00000540180.1_5'UTR|CCDC77_ENST00000540344.1_3'UTR	NM_032358.3	NP_115734.1	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77	25			S -> R (in dbSNP:rs4980895).			centrosome (GO:0005813)|membrane (GO:0016020)				cervix(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			TGTTGCCGTCAGTGGTCCCAC	0.478													A|||	1117	0.223043	0.3563	0.1455	5008	,	,		18584	0.2996		0.0825	False		,,,				2504	0.1636				p.S25R		Atlas-SNP	.											.	CCDC77	35	.	0			c.A73C						PASS	.	A	,,,ARG/SER	1459,2947	472.2+/-356.3	235,989,979	94.0	82.0	86.0		,,,73	1.0	0.0	12	dbSNP_111	86	777,7823	183.3+/-231.6	46,685,3569	yes	utr-5,utr-5,utr-5,missense	CCDC77	NM_001130146.1,NM_001130147.1,NM_001130148.1,NM_032358.3	,,,110	281,1674,4548	CC,CA,AA		9.0349,33.1139,17.1921	,,,possibly-damaging	,,,25/489	520947	2236,10770	2203	4300	6503	SO:0001583	missense	84318	exon4			GCCGTCAGTGGTC	AK027638	CCDS8503.1, CCDS44781.1	12p13.33	2006-02-16			ENSG00000120647	ENSG00000120647			28203	protein-coding gene	gene with protein product						12477932	Standard	NM_001130148		Approved	MGC13183	uc001qig.3	Q9BR77	OTTHUMG00000129214	ENST00000239830.4:c.73A>C	12.37:g.520947A>C	ENSP00000239830:p.Ser25Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_032358	B4DDE8	Missense_Mutation	SNP	ENST00000239830.4	37	CCDS8503.1	459	0.21016483516483517	166	0.33739837398373984	48	0.13259668508287292	179	0.3129370629370629	66	0.0870712401055409	A	14.27	2.484731	0.44147	0.331139	0.090349	ENSG00000120647	ENST00000535052;ENST00000239830	T;T	0.34072	1.38;1.38	5.04	0.99	0.19807	.	0.834183	0.11059	N	0.604143	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	2.9999999999752447E-6	B	0.06786	0.001	B	0.08055	0.003	T	0.40831	-0.9542	9	0.52906	T	0.07	0.312	3.8572	0.08981	0.5036:0.0:0.3373:0.1592	rs4980895;rs57046946;rs4980895	25	Q9BR77	CCD77_HUMAN	R	25	ENSP00000443209:S25R;ENSP00000239830:S25R	ENSP00000239830:S25R	S	+	1	0	CCDC77	391208	0.002000	0.14202	0.000000	0.03702	0.025000	0.11179	0.522000	0.22909	0.054000	0.16065	0.454000	0.30748	AGT	A|0.803;C|0.197	0.197	strong		0.478	CCDC77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251296.1	NM_032358	
AMPH	273	hgsc.bcm.edu	37	7	38431436	38431436	+	Silent	SNP	C	C	T	rs1058656	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:38431436C>T	ENST00000356264.2	-	19	2006	c.1791G>A	c.(1789-1791)acG>acA	p.T597T	AMPH_ENST00000428293.2_Silent_p.T555T|AMPH_ENST00000325590.5_Silent_p.T555T|AMPH_ENST00000471913.1_5'Flank	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	597					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						GTGCAGAAGGCGTGGGCTGAG	0.612													C|||	896	0.178914	0.2322	0.2248	5008	,	,		13855	0.127		0.1759	False		,,,				2504	0.1309				p.T597T		Atlas-SNP	.											.	AMPH	157	.	0			c.G1791A						PASS	.	C	,	948,3458	360.1+/-315.1	99,750,1354	52.0	49.0	50.0		1791,1665	-1.8	0.0	7	dbSNP_86	50	1860,6740	330.3+/-319.2	197,1466,2637	no	coding-synonymous,coding-synonymous	AMPH	NM_001635.3,NM_139316.2	,	296,2216,3991	TT,TC,CC		21.6279,21.5161,21.59	,	597/696,555/654	38431436	2808,10198	2203	4300	6503	SO:0001819	synonymous_variant	273	exon19			AGAAGGCGTGGGC		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1791G>A	7.37:g.38431436C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	134	75	0.559702	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Silent	SNP	ENST00000356264.2	37	CCDS5456.1	395	0.18086080586080586	105	0.21341463414634146	74	0.20441988950276244	73	0.12762237762237763	143	0.18865435356200527	C	5.413	0.261367	0.10239	0.215161	0.216279	ENSG00000078053	ENST00000441628	.	.	.	5.34	-1.8	0.07907	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.29761	-1.0001	3	.	.	.	0.6258	3.0635	0.06207	0.106:0.3229:0.3573:0.2139	rs1058656;rs3199302;rs11553335;rs56947214	.	.	.	T	480	.	.	A	-	1	0	AMPH	38397961	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.475000	0.06599	-0.035000	0.13691	0.591000	0.81541	GCC	C|0.804;T|0.196	0.196	strong		0.612	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
PLCB3	5331	hgsc.bcm.edu	37	11	64031241	64031241	+	Missense_Mutation	SNP	C	C	T	rs35169799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64031241C>T	ENST00000540288.1	+	21	2637	c.2534C>T	c.(2533-2535)tCg>tTg	p.S845L	PLCB3_ENST00000279230.6_Missense_Mutation_p.S845L|PLCB3_ENST00000325234.5_Missense_Mutation_p.S778L	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	845				S -> L (in Ref. 6; CAA78903). {ECO:0000305}.	inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						ACCGAAGCCTCGGACTACATT	0.667													C|||	114	0.0227636	0.0023	0.0303	5008	,	,		16910	0.0		0.0666	False		,,,				2504	0.0235				p.S845L		Atlas-SNP	.											PLCB3,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,1	PLCB3	103	1	0			c.C2534T						scavenged	.	C	LEU/SER,LEU/SER	67,4335	59.9+/-96.7	3,61,2137	89.0	87.0	88.0		2534,2333	5.2	1.0	11	dbSNP_126	88	578,8016	155.5+/-209.5	22,534,3741	yes	missense,missense	PLCB3	NM_000932.2,NM_001184883.1	145,145	25,595,5878	TT,TC,CC		6.7256,1.522,4.9631	benign,benign	845/1235,778/1168	64031241	645,12351	2201	4297	6498	SO:0001583	missense	5331	exon21			AAGCCTCGGACTA	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.2534C>T	11.37:g.64031241C>T	ENSP00000443631:p.Ser845Leu	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	96	42	0.4375	NM_000932	A5PKZ6|G5E960|Q8N1A4	Missense_Mutation	SNP	ENST00000540288.1	37	CCDS8064.1	67	0.030677655677655676	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	50	0.06596306068601583	C	15.73	2.918361	0.52546	0.01522	0.067256	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	T;T;T	0.21932	2.11;2.11;1.98	5.25	5.25	0.73442	C2 calcium/lipid-binding domain, CaLB (1);	0.184175	0.48767	D	0.000167	T	0.01156	0.0038	N	0.25647	0.755	0.36001	D	0.837379	D;P	0.58268	0.982;0.838	B;B	0.42138	0.377;0.177	T	0.05084	-1.0907	10	0.72032	D	0.01	.	13.2818	0.60219	0.1592:0.8407:0.0:0.0	rs35169799;rs61755083;rs35169799	778;845	G5E960;Q01970	.;PLCB3_HUMAN	L	845;845;778	ENSP00000279230:S845L;ENSP00000443631:S845L;ENSP00000324660:S778L	ENSP00000279230:S845L	S	+	2	0	PLCB3	63787817	0.637000	0.27216	0.952000	0.39060	0.334000	0.28698	2.527000	0.45615	2.462000	0.83206	0.561000	0.74099	TCG	C|0.957;T|0.043	0.043	strong		0.667	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
OR7C1	26664	hgsc.bcm.edu	37	19	14910321	14910321	+	Missense_Mutation	SNP	A	A	G	rs16979912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14910321A>G	ENST00000248073.2	-	1	702	c.628T>C	c.(628-630)Tcc>Ccc	p.S210P	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	210			S -> P (in dbSNP:rs16979912). {ECO:0000269|PubMed:9119360}.		spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(2)|ovary(2)|prostate(1)	18						CCAGTGAAGGAAATCACACCC	0.408													G|||	1217	0.243011	0.4569	0.2233	5008	,	,		21485	0.0546		0.2177	False		,,,				2504	0.1881				p.S210P		Atlas-SNP	.											.	OR7C1	58	.	0			c.T628C						PASS	.	G	PRO/SER	1770,2636	621.5+/-393.8	348,1074,781	60.0	61.0	61.0		628	2.6	0.0	19	dbSNP_123	61	1739,6861	723.1+/-406.4	176,1387,2737	yes	missense	OR7C1	NM_198944.1	74	524,2461,3518	GG,GA,AA		20.2209,40.1725,26.9799	benign	210/321	14910321	3509,9497	2203	4300	6503	SO:0001583	missense	26664	exon1			TGAAGGAAATCAC	X89676	CCDS12317.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8373	protein-coding gene	gene with protein product				OR7C4			Standard	NM_198944		Approved	OR19-5	uc010xnz.2	O76099		ENST00000248073.2:c.628T>C	19.37:g.14910321A>G	ENSP00000248073:p.Ser210Pro	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_198944	Q15621|Q6IFP2|Q96R94	Missense_Mutation	SNP	ENST00000248073.2	37	CCDS12317.1	485	0.22206959706959706	213	0.4329268292682927	82	0.2265193370165746	18	0.03146853146853147	172	0.22691292875989447	g	0.013	-1.623366	0.00820	0.401725	0.202209	ENSG00000127530	ENST00000248073	T	0.22134	1.97	3.64	2.59	0.31030	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36778	N	0.002417	T	0.00012	0.0000	N	0.00321	-1.65	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.46816	-0.9164	9	0.02654	T	1	.	5.8324	0.18588	0.3451:0.0:0.6549:0.0	rs16979912;rs52837227;rs16979912	210	O76099	OR7C1_HUMAN	P	210	ENSP00000248073:S210P	ENSP00000248073:S210P	S	-	1	0	OR7C1	14771321	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.747000	0.04823	0.349000	0.23975	-1.085000	0.02201	TCC	A|0.757;G|0.243	0.243	strong		0.408	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1		
CCDC181	57821	hgsc.bcm.edu	37	1	169390957	169390957	+	Missense_Mutation	SNP	A	A	T	rs35107735	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:169390957A>T	ENST00000367806.3	-	3	864	c.712T>A	c.(712-714)Ttt>Att	p.F238I	CCDC181_ENST00000491570.1_5'UTR|CCDC181_ENST00000367805.3_Missense_Mutation_p.F238I|CCDC181_ENST00000545005.1_Missense_Mutation_p.F238I	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	238			F -> I (in dbSNP:rs35107735). {ECO:0000269|Ref.2}.			nucleus (GO:0005634)											GGAGGCAAAAACCCCTGACTG	0.403													A|||	720	0.14377	0.0696	0.1873	5008	,	,		19575	0.001		0.3678	False		,,,				2504	0.1299				p.F238I		Atlas-SNP	.											.	C1orf114	67	.	0			c.T712A						PASS	.	A	ILE/PHE	516,3890	237.7+/-249.4	30,456,1717	114.0	115.0	115.0		712	1.5	0.2	1	dbSNP_126	115	3158,5442	479.7+/-370.2	580,1998,1722	no	missense	C1orf114	NM_021179.1	21	610,2454,3439	TT,TA,AA		36.7209,11.7113,28.2485	benign	238/509	169390957	3674,9332	2203	4300	6503	SO:0001583	missense	57821	exon3			GCAAAAACCCCTG	AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 114"""	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.712T>A	1.37:g.169390957A>T	ENSP00000356780:p.Phe238Ile	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	209	103	0.492823	NM_021179	O60780|Q53FD5|Q5TID9|Q8TC48	Missense_Mutation	SNP	ENST00000367806.3	37		404	0.184981684981685	41	0.08333333333333333	80	0.22099447513812154	0	0.0	283	0.3733509234828496	A	13.39	2.224273	0.39300	0.117113	0.367209	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005;ENST00000456107	T;T;T;T	0.22539	1.96;1.96;1.96;1.95	5.31	1.53	0.23141	.	0.170180	0.53938	D	0.000060	T	0.10423	0.0255	M	0.67953	2.075	0.37524	D	0.917639	B;P;P	0.47841	0.103;0.901;0.901	B;B;B	0.41135	0.082;0.348;0.348	T	0.06552	-1.0820	9	0.52906	T	0.07	-0.8188	9.1053	0.36694	0.5219:0.3623:0.0:0.1158	rs35107735;rs61808029	238;238;238	Q5TID7-2;Q5TID7;Q5TID7-3	.;CA114_HUMAN;.	I	238	ENSP00000356779:F238I;ENSP00000356780:F238I;ENSP00000442297:F238I;ENSP00000411000:F238I	ENSP00000356779:F238I	F	-	1	0	C1orf114	167657581	0.981000	0.34729	0.172000	0.22920	0.884000	0.51177	2.390000	0.44416	-0.002000	0.14469	0.455000	0.32223	TTT	A|0.752;T|0.248	0.248	strong		0.403	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179	
ZNF460	10794	hgsc.bcm.edu	37	19	57802824	57802824	+	Silent	SNP	G	G	A	rs2041110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57802824G>A	ENST00000360338.3	+	3	1237	c.915G>A	c.(913-915)aaG>aaA	p.K305K	ZNF460_ENST00000537645.1_Silent_p.K264K	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	305					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ACAATGAGAAGAAACCCTTCG	0.463													a|||	933	0.186302	0.0983	0.3084	5008	,	,		23078	0.1657		0.2515	False		,,,				2504	0.1728				p.K305K		Atlas-SNP	.											.	ZNF460	59	.	0			c.G915A						PASS	.	A		534,3872	776.9+/-414.2	29,476,1698	100.0	89.0	93.0		915	-3.0	0.0	19	dbSNP_94	93	2197,6403	711.0+/-405.8	294,1609,2397	no	coding-synonymous	ZNF460	NM_006635.3		323,2085,4095	AA,AG,GG		25.5465,12.1198,20.998		305/563	57802824	2731,10275	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			TGAGAAGAAACCC	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.915G>A	19.37:g.57802824G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			G|0.806;A|0.194	0.194	strong		0.463	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
CTSH	1512	hgsc.bcm.edu	37	15	79224727	79224727	+	Missense_Mutation	SNP	T	T	C	rs78155742	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:79224727T>C	ENST00000220166.5	-	6	588	c.479A>G	c.(478-480)aAg>aGg	p.K160R	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	160					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						GGACAGCATCTTTCCGGTTGC	0.622													T|||	41	0.0081869	0.0023	0.0144	5008	,	,		17994	0.0		0.0278	False		,,,				2504	0.0				p.K160R		Atlas-SNP	.											.	CTSH	23	.	0			c.A479G						PASS	.	T	ARG/LYS	25,4367	31.7+/-61.6	0,25,2171	73.0	72.0	72.0		479	3.6	0.3	15	dbSNP_131	72	224,8362	92.1+/-154.2	3,218,4072	yes	missense	CTSH	NM_004390.3	26	3,243,6243	CC,CT,TT		2.6089,0.5692,1.9186	benign	160/336	79224727	249,12729	2196	4293	6489	SO:0001583	missense	1512	exon6			AGCATCTTTCCGG	X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.479A>G	15.37:g.79224727T>C	ENSP00000220166:p.Lys160Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Missense_Mutation	SNP	ENST00000220166.5	37	CCDS10308.1	28	0.01282051282051282	0	0.0	6	0.016574585635359115	0	0.0	22	0.029023746701846966	T	13.08	2.130253	0.37630	0.005692	0.026089	ENSG00000103811	ENST00000220166;ENST00000394758;ENST00000528741	D;D	0.88046	-2.33;-2.33	4.72	3.57	0.40892	.	0.111184	0.64402	D	0.000013	T	0.59905	0.2228	L	0.31845	0.965	0.43734	D	0.996224	B	0.29188	0.236	B	0.30495	0.116	T	0.68277	-0.5451	10	0.72032	D	0.01	.	7.3626	0.26756	0.0:0.1022:0.0:0.8978	.	148	E9PBP2	.	R	160;148;84	ENSP00000220166:K160R;ENSP00000435329:K84R	ENSP00000220166:K160R	K	-	2	0	CTSH	77011782	1.000000	0.71417	0.330000	0.25442	0.545000	0.35147	4.647000	0.61418	0.632000	0.30432	0.533000	0.62120	AAG	T|0.984;C|0.016	0.016	strong		0.622	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
ABCA4	24	hgsc.bcm.edu	37	1	94544234	94544234	+	Missense_Mutation	SNP	T	T	C	rs3112831	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:94544234T>C	ENST00000370225.3	-	10	1354	c.1268A>G	c.(1267-1269)cAc>cGc	p.H423R	ABCA4_ENST00000535735.1_Missense_Mutation_p.H423R	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	423			H -> R (in dbSNP:rs3112831). {ECO:0000269|PubMed:10958763, ECO:0000269|PubMed:11379881, ECO:0000269|PubMed:11384574, ECO:0000269|PubMed:11527935, ECO:0000269|PubMed:12111378}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CTTCCTAACGTGTTCCAGTTC	0.453													C|||	1106	0.220847	0.1316	0.3026	5008	,	,		14062	0.254		0.2913	False		,,,				2504	0.1769				p.H423R		Atlas-SNP	.											ABCA4,NS,carcinoma,-1,2	ABCA4	275	2	0			c.A1268G	GRCh37	CM015072|CM032802	ABCA4	M	rs3112831	PASS	.	C	ARG/HIS	729,3677	757.8+/-412.8	63,603,1537	196.0	184.0	188.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1268	5.5	0.2	1	dbSNP_103	188	2661,5939	685.7+/-404.1	395,1871,2034	yes	missense	ABCA4	NM_000350.2	29	458,2474,3571	CC,CT,TT		30.9419,16.5456,26.0649	benign	423/2274	94544234	3390,9616	2203	4300	6503	SO:0001583	missense	24	exon10			CTAACGTGTTCCA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.1268A>G	1.37:g.94544234T>C	ENSP00000359245:p.His423Arg	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	200	114	0.57	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	538	0.24633699633699635	77	0.1565040650406504	106	0.292817679558011	133	0.23251748251748253	222	0.2928759894459103	C	11.96	1.795287	0.31777	0.165456	0.309419	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.83591	-1.74;-1.74	5.49	5.49	0.81192	.	0.000000	0.85682	N	0.000000	T	0.30135	0.0755	N	0.00074	-2.255	0.47245	P	6.399999999999739E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08994	-1.0695	9	0.22706	T	0.39	.	14.5395	0.67982	0.0:0.9297:0.0:0.0703	rs3112831;rs17461660;rs60698303;rs3112831	423;423	F5H6E5;P78363	.;ABCA4_HUMAN	R	423	ENSP00000359245:H423R;ENSP00000437682:H423R	ENSP00000359245:H423R	H	-	2	0	ABCA4	94316822	0.950000	0.32346	0.222000	0.23844	0.141000	0.21300	2.204000	0.42761	1.341000	0.45600	-0.215000	0.12644	CAC	T|0.748;C|0.251;N|0.001	0.251	strong		0.453	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
PI4KA	5297	hgsc.bcm.edu	37	22	21066897	21066897	+	Silent	SNP	G	G	A	rs1135929	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:21066897G>A	ENST00000572273.1	-	50	5735	c.5505C>T	c.(5503-5505)tgC>tgT	p.C1835C	PI4KA_ENST00000255882.6_Silent_p.C1893C|PI4KA_ENST00000414196.3_Silent_p.C645C			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1835	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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)	p.C1835C(2)		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)			CGATCACCCCGCACTAGGAGG	0.652													g|||	2170	0.433307	0.5083	0.4683	5008	,	,		12263	0.4752		0.3976	False		,,,				2504	0.3006				p.C1893C	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,0,2	PI4KA	313	2	2	Substitution - coding silent(2)	stomach(2)	c.C5679T						scavenged	.						20.0	24.0	23.0					22																	21066897		2111	4203	6314	SO:0001819	synonymous_variant	5297	exon50			CACCCCGCACTAG	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.5505C>T	22.37:g.21066897G>A		Somatic	378	1	0.0026455		WXS	Illumina HiSeq	Phase_I	208	161	0.774038	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				A|1.000;|0.000	1.000	weak		0.652	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
KIF25	3834	hgsc.bcm.edu	37	6	168440826	168440826	+	Silent	SNP	C	C	T	rs6928620	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168440826C>T	ENST00000443060.2	+	7	967	c.576C>T	c.(574-576)caC>caT	p.H192H	KIF25_ENST00000351261.3_Silent_p.H192H|KIF25_ENST00000354419.2_Silent_p.H192H			Q9UIL4	KIF25_HUMAN	kinesin family member 25	192	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.H192H(1)		NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		CCCTGGTGCACGCGGATTCCT	0.577													C|||	351	0.0700879	0.1316	0.0447	5008	,	,		19205	0.0982		0.0179	False		,,,				2504	0.0297				p.H192H		Atlas-SNP	.											KIF25,NS,carcinoma,0,1	KIF25	75	1	1	Substitution - coding silent(1)	stomach(1)	c.C576T						PASS	.	C	,	531,3875	240.9+/-251.5	33,465,1705	86.0	74.0	78.0		576,576	-5.8	0.0	6	dbSNP_116	78	124,8476	63.5+/-125.6	0,124,4176	no	coding-synonymous,coding-synonymous	KIF25	NM_005355.3,NM_030615.2	,	33,589,5881	TT,TC,CC		1.4419,12.0517,5.0361	,	192/333,192/385	168440826	655,12351	2203	4300	6503	SO:0001819	synonymous_variant	3834	exon6			GGTGCACGCGGAT	AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"""Kinesins"""	6390	protein-coding gene	gene with protein product		603815	"""kinesin-like 3"""	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.576C>T	6.37:g.168440826C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_030615	O94775|Q5SZU9	Silent	SNP	ENST00000443060.2	37	CCDS5305.1																																																																																			C|0.944;T|0.056	0.056	strong		0.577	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1		
APEH	327	hgsc.bcm.edu	37	3	49714225	49714225	+	Silent	SNP	T	T	C	rs1131095	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49714225T>C	ENST00000296456.5	+	9	1252	c.852T>C	c.(850-852)taT>taC	p.Y284Y	APEH_ENST00000438011.1_Silent_p.Y284Y	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	284					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.Y284Y(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCCTGTATTATGTGGACCTCA	0.587													T|||	1015	0.202676	0.2413	0.17	5008	,	,		22856	0.0565		0.3241	False		,,,				2504	0.1994				p.Y284Y		Atlas-SNP	.											APEH,NS,carcinoma,0,1	APEH	45	1	1	Substitution - coding silent(1)	stomach(1)	c.T852C						PASS	.	T		1101,3305	397.0+/-330.2	135,831,1237	171.0	152.0	158.0		852	-8.4	0.7	3	dbSNP_86	158	2578,6022	419.6+/-353.1	402,1774,2124	no	coding-synonymous	APEH	NM_001640.3		537,2605,3361	CC,CT,TT		29.9767,24.9887,28.2869		284/733	49714225	3679,9327	2203	4300	6503	SO:0001819	synonymous_variant	327	exon9			GTATTATGTGGAC	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.852T>C	3.37:g.49714225T>C		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	349	184	0.527221	NM_001640	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	37	CCDS2801.1																																																																																			T|0.737;C|0.263	0.263	strong		0.587	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
FCGBP	8857	hgsc.bcm.edu	37	19	40399385	40399385	+	Missense_Mutation	SNP	C	C	T	rs201168964		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40399385C>T	ENST00000221347.6	-	13	6317	c.6310G>A	c.(6310-6312)Gga>Aga	p.G2104R		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2104	VWFD 5. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AAGGGTGGTCCGTGGCAGGGT	0.597																																					p.G2104R		Atlas-SNP	.											FCGBP,NS,carcinoma,0,2	FCGBP	416	2	0			c.G6310A						scavenged	.						9.0	12.0	11.0					19																	40399385		1085	2084	3169	SO:0001583	missense	8857	exon13			GTGGTCCGTGGCA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.6310G>A	19.37:g.40399385C>T	ENSP00000221347:p.Gly2104Arg	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	242	50	0.206612	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	0.241	-1.013596	0.02095	.	.	ENSG00000090920	ENST00000221347	T	0.59083	0.29	3.01	0.723	0.18231	von Willebrand factor, type D domain (3);	.	.	.	.	T	0.43389	0.1245	L	0.43923	1.385	0.09310	N	1	B	0.19445	0.036	B	0.10450	0.005	T	0.26780	-1.0093	9	0.28530	T	0.3	.	5.6999	0.17877	0.0:0.5011:0.0:0.4989	.	2104	Q9Y6R7	FCGBP_HUMAN	R	2104	ENSP00000221347:G2104R	ENSP00000221347:G2104R	G	-	1	0	FCGBP	45091225	0.000000	0.05858	0.002000	0.10522	0.254000	0.26022	-2.133000	0.01308	0.480000	0.27534	0.298000	0.19748	GGA	C|0.500;T|0.500	0.500	strong		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF418	147686	hgsc.bcm.edu	37	19	58437791	58437791	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58437791A>G	ENST00000396147.1	-	4	2049	c.1758T>C	c.(1756-1758)acT>acC	p.T586T	ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000595830.1_Silent_p.T586T|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599852.1_Silent_p.T501T|ZNF418_ENST00000425570.3_Silent_p.T607T	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	586					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		GCCTTTCTCCAGTGTGAACTC	0.438																																					p.T586T		Atlas-SNP	.											.	ZNF418	76	.	0			c.T1758C						PASS	.						78.0	81.0	80.0					19																	58437791		2202	4300	6502	SO:0001819	synonymous_variant	147686	exon4			TTCTCCAGTGTGA	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1758T>C	19.37:g.58437791A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	85	20	0.235294	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			.	.	none		0.438	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
CCDC38	120935	hgsc.bcm.edu	37	12	96312686	96312686	+	Missense_Mutation	SNP	C	C	A	rs12368787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:96312686C>A	ENST00000344280.3	-	3	663	c.106G>T	c.(106-108)Gtc>Ttc	p.V36F	CCDC38_ENST00000549752.1_5'Flank	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	36			V -> F (in dbSNP:rs12368787).							breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTTTCTTTGACAAGAAAGAGA	0.318													A|||	335	0.066893	0.0401	0.0749	5008	,	,		21521	0.0278		0.1372	False		,,,				2504	0.0654				p.V36F		Atlas-SNP	.											.	CCDC38	45	.	0			c.G106T						PASS	.	A	PHE/VAL	213,4191	806.9+/-415.9	4,205,1993	156.0	148.0	150.0		106	4.8	1.0	12	dbSNP_120	150	1070,7530	769.8+/-407.6	67,936,3297	yes	missense	CCDC38	NM_182496.2	50	71,1141,5290	AA,AC,CC		12.4419,4.8365,9.8662	benign	36/564	96312686	1283,11721	2202	4300	6502	SO:0001583	missense	120935	exon3			CTTTGACAAGAAA	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.106G>T	12.37:g.96312686C>A	ENSP00000345470:p.Val36Phe	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	176	68	0.386364	NM_182496	Q8N835	Missense_Mutation	SNP	ENST00000344280.3	37	CCDS9056.1	159	0.07280219780219781	24	0.04878048780487805	25	0.06906077348066299	10	0.017482517482517484	100	0.13192612137203166	A	3.234	-0.156872	0.06544	0.048365	0.124419	ENSG00000165972	ENST00000344280	T	0.26957	1.7	4.85	4.85	0.62838	.	0.267312	0.34777	N	0.003681	T	0.00073	0.0002	N	0.01168	-0.975	0.09310	P	0.9999999999622513	B	0.02656	0.0	B	0.01281	0.0	T	0.24476	-1.0159	9	0.12430	T	0.62	-4.2424	8.8974	0.35472	0.811:0.189:0.0:0.0	rs12368787;rs52827128;rs61694415;rs12368787	36	Q502W7	CCD38_HUMAN	F	36	ENSP00000345470:V36F	ENSP00000345470:V36F	V	-	1	0	CCDC38	94836817	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	2.491000	0.45303	0.983000	0.38602	-0.363000	0.07495	GTC	C|0.915;A|0.085	0.085	strong		0.318	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
SLC25A32	81034	hgsc.bcm.edu	37	8	104417045	104417045	+	Missense_Mutation	SNP	C	C	T	rs17803441	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:104417045C>T	ENST00000297578.4	-	3	516	c.350G>A	c.(349-351)cGt>cAt	p.R117H	SLC25A32_ENST00000543107.1_Intron|SLC25A32_ENST00000523701.1_5'Flank	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32	117			R -> H (in dbSNP:rs17803441). {ECO:0000269|PubMed:10978331}.		folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	TGCCTCTAAACGTTCAGCTCT	0.343													C|||	124	0.0247604	0.0098	0.0447	5008	,	,		20061	0.005		0.0616	False		,,,				2504	0.0133				p.R117H		Atlas-SNP	.											.	SLC25A32	36	.	0			c.G350A						PASS	.	C	HIS/ARG	106,4300	82.4+/-120.9	4,98,2101	150.0	121.0	131.0		350	-2.2	0.1	8	dbSNP_123	131	676,7924	169.3+/-220.7	30,616,3654	yes	missense	SLC25A32	NM_030780.3	29	34,714,5755	TT,TC,CC		7.8605,2.4058,6.0126	possibly-damaging	117/316	104417045	782,12224	2203	4300	6503	SO:0001583	missense	81034	exon3			TCTAAACGTTCAG	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790	ENST00000297578.4:c.350G>A	8.37:g.104417045C>T	ENSP00000297578:p.Arg117His	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	146	87	0.59589	NM_030780	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	37	CCDS6300.1	70	0.03205128205128205	4	0.008130081300813009	17	0.04696132596685083	0	0.0	49	0.06464379947229551	C	15.49	2.849539	0.51270	0.024058	0.078605	ENSG00000164933	ENST00000297578;ENST00000424899	T	0.78246	-1.16	6.06	-2.19	0.07015	Mitochondrial carrier domain (2);	0.592881	0.18862	N	0.129107	T	0.05731	0.0150	N	0.12569	0.235	0.09310	N	1	B	0.22746	0.074	B	0.26202	0.067	T	0.14980	-1.0453	10	0.45353	T	0.12	-19.4225	7.3207	0.26526	0.0:0.3715:0.116:0.5126	rs17803441;rs52813171;rs17803441	117	Q9H2D1	MFTC_HUMAN	H	117;101	ENSP00000297578:R117H	ENSP00000297578:R117H	R	-	2	0	SLC25A32	104486221	0.015000	0.18098	0.069000	0.20011	0.979000	0.70002	0.059000	0.14322	-0.161000	0.10983	0.655000	0.94253	CGT	C|0.952;T|0.048	0.048	strong		0.343	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780	
DND1	373863	hgsc.bcm.edu	37	5	140050926	140050926	+	Silent	SNP	G	G	A	rs62384220	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140050926G>A	ENST00000542735.1	-	4	1057	c.1014C>T	c.(1012-1014)aaC>aaT	p.N338N	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	338					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)	p.N338N(1)		central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCACAGGAGGTTGGCCCCAG	0.587													G|||	20	0.00399361	0.0008	0.0072	5008	,	,		20122	0.0		0.0109	False		,,,				2504	0.0031				p.N338N		Atlas-SNP	.											DND1,NS,carcinoma,0,1	DND1	15	1	1	Substitution - coding silent(1)	prostate(1)	c.C1014T						scavenged	.						73.0	65.0	67.0					5																	140050926		1984	4006	5990	SO:0001819	synonymous_variant	373863	exon4			CAGGAGGTTGGCC	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1014C>T	5.37:g.140050926G>A		Somatic	441	2	0.00453515		WXS	Illumina HiSeq	Phase_I	752	100	0.132979	NM_194249		Silent	SNP	ENST00000542735.1	37	CCDS4236.1																																																																																			G|0.970;A|0.030	0.030	strong		0.587	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
GIGYF2	26058	hgsc.bcm.edu	37	2	233712223	233712223	+	Missense_Mutation	SNP	T	T	A	rs114013774|rs527464858	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233712223T>A	ENST00000409547.1	+	29	3937	c.3626T>A	c.(3625-3627)cTg>cAg	p.L1209Q	GIGYF2_ENST00000409451.3_Missense_Mutation_p.L1230Q|GIGYF2_ENST00000373566.3_Missense_Mutation_p.L1231Q|GIGYF2_ENST00000409480.1_Missense_Mutation_p.L1231Q|GIGYF2_ENST00000373563.4_Missense_Mutation_p.L1209Q|GIGYF2_ENST00000409196.3_Missense_Mutation_p.L1203Q	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1209	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		cagcagcagctgccacagcag	0.557																																					p.L1230Q		Atlas-SNP	.											.	GIGYF2	288	.	0			c.T3689A						PASS	.						14.0	16.0	15.0					2																	233712223		2161	4224	6385	SO:0001583	missense	26058	exon29			AGCAGCTGCCACA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3626T>A	2.37:g.233712223T>A	ENSP00000386537:p.Leu1209Gln	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	38	9	0.236842	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	T	0.021	-1.427088	0.01117	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451	T;T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07;0.07	1.39	-2.77	0.05877	.	.	.	.	.	T	0.25344	0.0616	N	0.04959	-0.14	0.39400	D	0.966566	B;B;B	0.12630	0.0;0.006;0.0	B;B;B	0.08055	0.0;0.003;0.0	T	0.32322	-0.9911	9	0.13108	T	0.6	-0.0091	3.5635	0.07890	0.3937:0.4039:0.0:0.2024	.	1230;1209;1203	A6H8W4;Q6Y7W6;E9PBB0	.;PERQ2_HUMAN;.	Q	1231;1209;1231;1209;1203;1230	ENSP00000362667:L1231Q;ENSP00000362664:L1209Q;ENSP00000386765:L1231Q;ENSP00000386537:L1209Q;ENSP00000387070:L1203Q;ENSP00000387170:L1230Q	ENSP00000362664:L1209Q	L	+	2	0	GIGYF2	233420467	0.003000	0.15002	0.361000	0.25849	0.026000	0.11368	0.028000	0.13644	-2.729000	0.00385	-2.797000	0.00114	CTG	T|0.966;A|0.034	0.034	strong		0.557	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
KDM4B	23030	hgsc.bcm.edu	37	19	5110794	5110794	+	Silent	SNP	A	A	G	rs2613739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:5110794A>G	ENST00000159111.4	+	10	1298	c.1080A>G	c.(1078-1080)gcA>gcG	p.A360A	KDM4B_ENST00000536461.1_Silent_p.A360A|KDM4B_ENST00000381759.4_Silent_p.A360A	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	360					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						CCTGGAGTGCATCCCGGGCCT	0.701													G|||	3178	0.634585	0.6838	0.5706	5008	,	,		14508	0.6677		0.5656	False		,,,				2504	0.6503				p.A360A		Atlas-SNP	.											.	KDM4B	120	.	0			c.A1080G						PASS	.	G		2819,1581		904,1011,285	23.0	22.0	22.0		1080	-2.6	0.9	19	dbSNP_100	22	4747,3847		1318,2111,868	no	coding-synonymous	KDM4B	NM_015015.2		2222,3122,1153	GG,GA,AA		44.7638,35.9318,41.7731		360/1097	5110794	7566,5428	2200	4297	6497	SO:0001819	synonymous_variant	23030	exon10			GAGTGCATCCCGG	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1080A>G	19.37:g.5110794A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Silent	SNP	ENST00000159111.4	37	CCDS12138.1																																																																																			A|0.406;G|0.594	0.594	strong		0.701	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015	
DCAKD	79877	hgsc.bcm.edu	37	17	43111688	43111688	+	Silent	SNP	G	G	A	rs9900173	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43111688G>A	ENST00000452796.2	-	2	438	c.183C>T	c.(181-183)aaC>aaT	p.N61N	DCAKD_ENST00000310604.4_Silent_p.N61N|DCAKD_ENST00000588295.1_5'UTR|DCAKD_ENST00000588499.1_Silent_p.N61N|DCAKD_ENST00000342350.5_Silent_p.N61N			Q8WVC6	DCAKD_HUMAN	dephospho-CoA kinase domain containing	61	DPCK.				coenzyme A biosynthetic process (GO:0015937)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)			cervix(1)|endometrium(1)|large_intestine(1)|lung(2)|skin(1)	6		Prostate(33;0.155)				TTATGTCGCCGTTCTCCAGCA	0.607													G|||	1281	0.255791	0.1634	0.2161	5008	,	,		17004	0.2738		0.3499	False		,,,				2504	0.2935				p.N61N		Atlas-SNP	.											.	DCAKD	25	.	0			c.C183T						PASS	.	G	,	876,3530	339.9+/-306.0	87,702,1414	89.0	78.0	82.0		183,183	-0.1	0.9	17	dbSNP_119	82	2976,5624	461.5+/-365.4	505,1966,1829	no	coding-synonymous,coding-synonymous	DCAKD	NM_001128631.1,NM_024819.4	,	592,2668,3243	AA,AG,GG		34.6047,19.882,29.6171	,	61/232,61/232	43111688	3852,9154	2203	4300	6503	SO:0001819	synonymous_variant	79877	exon3			GTCGCCGTTCTCC	BC006546	CCDS11493.1	17q21.31	2005-12-20				ENSG00000172992			26238	protein-coding gene	gene with protein product							Standard	XM_005257688		Approved	FLJ22955	uc010daa.1	Q8WVC6		ENST00000452796.2:c.183C>T	17.37:g.43111688G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_001128631	A8K3Z0|D3DX60|D3DX62|Q9BR71|Q9H5W1	Silent	SNP	ENST00000452796.2	37	CCDS11493.1																																																																																			G|0.719;A|0.281	0.281	strong		0.607	DCAKD-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449066.1	NM_024819	
C19orf45	374877	hgsc.bcm.edu	37	19	7573098	7573098	+	Missense_Mutation	SNP	T	T	A	rs475923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7573098T>A	ENST00000361664.2	+	9	1441	c.1300T>A	c.(1300-1302)Tac>Aac	p.Y434N	CTD-2207O23.12_ENST00000599312.1_Intron	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	434			Y -> N (in dbSNP:rs475923). {ECO:0000269|PubMed:14702039}.							endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						ACAGTGCAAGTACAGCCACAT	0.607													T|||	1444	0.288339	0.295	0.3833	5008	,	,		14829	0.1746		0.3628	False		,,,				2504	0.2526				p.Y434N		Atlas-SNP	.											C19orf45,NS,carcinoma,0,1	C19orf45	36	1	0			c.T1300A						PASS	.	T	ASN/TYR	1315,3091	436.8+/-344.8	202,911,1090	40.0	40.0	40.0		1300	4.1	1.0	19	dbSNP_83	40	3129,5469	470.3+/-367.8	572,1985,1742	yes	missense	C19orf45	NM_198534.2	143	774,2896,2832	AA,AT,TT		36.3922,29.8457,34.1741	probably-damaging	434/506	7573098	4444,8560	2203	4299	6502	SO:0001583	missense	374877	exon9			TGCAAGTACAGCC	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.1300T>A	19.37:g.7573098T>A	ENSP00000355241:p.Tyr434Asn	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	150	64	0.426667	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	695	0.3182234432234432	150	0.3048780487804878	152	0.4198895027624309	112	0.1958041958041958	281	0.370712401055409	T	14.11	2.436592	0.43224	0.298457	0.363922	ENSG00000198723	ENST00000361664	T	0.36699	1.24	4.05	4.05	0.47172	.	0.306075	0.27349	N	0.019762	T	0.00012	0.0000	M	0.61703	1.905	0.33234	P	0.44373799999999997	D	0.89917	1.0	D	0.91635	0.999	T	0.37174	-0.9717	9	0.07813	T	0.8	-30.0092	9.5768	0.39463	0.0:0.0:0.0:1.0	rs475923;rs793874;rs3745355;rs17256987;rs475923	434	Q8NA69	CS045_HUMAN	N	434	ENSP00000355241:Y434N	ENSP00000355241:Y434N	Y	+	1	0	C19orf45	7479098	0.673000	0.27539	0.993000	0.49108	0.562000	0.35680	0.047000	0.14056	1.839000	0.53478	0.379000	0.24179	TAC	T|0.677;A|0.323	0.323	strong		0.607	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
SMPDL3B	27293	hgsc.bcm.edu	37	1	28282292	28282292	+	Missense_Mutation	SNP	T	T	C	rs3813803	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:28282292T>C	ENST00000373894.3	+	6	979	c.788T>C	c.(787-789)gTc>gCc	p.V263A	RP11-460I13.2_ENST00000448015.1_RNA|SMPDL3B_ENST00000373888.4_Missense_Mutation_p.V263A|SMPDL3B_ENST00000549094.1_Missense_Mutation_p.V215A	NM_014474.2	NP_055289.2	Q92485	ASM3B_HUMAN	sphingomyelin phosphodiesterase, acid-like 3B	263					sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	16		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)		CTGAAGGTGGTCCGGAAGCAT	0.542													T|||	933	0.186302	0.0703	0.255	5008	,	,		19887	0.2123		0.2684	False		,,,				2504	0.183				p.V263A		Atlas-SNP	.											.	SMPDL3B	54	.	0			c.T788C						PASS	.	T	ALA/VAL,ALA/VAL	464,3942	219.1+/-236.9	31,402,1770	105.0	92.0	97.0		788,788	5.3	0.8	1	dbSNP_107	97	2549,6051	416.1+/-352.0	389,1771,2140	yes	missense,missense	SMPDL3B	NM_001009568.1,NM_014474.2	64,64	420,2173,3910	CC,CT,TT		29.6395,10.5311,23.1662	possibly-damaging,possibly-damaging	263/374,263/456	28282292	3013,9993	2203	4300	6503	SO:0001583	missense	27293	exon6			AGGTGGTCCGGAA	Y08134	CCDS30655.1, CCDS30656.1	1p35.3	2008-02-05			ENSG00000130768	ENSG00000130768			21416	protein-coding gene	gene with protein product							Standard	NM_014474		Approved	ASML3B	uc001bpg.3	Q92485	OTTHUMG00000003910	ENST00000373894.3:c.788T>C	1.37:g.28282292T>C	ENSP00000363001:p.Val263Ala	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	135	73	0.540741	NM_001009568	B7ZB35|Q5T0Z0|Q96CB7	Missense_Mutation	SNP	ENST00000373894.3	37	CCDS30655.1	475	0.2174908424908425	37	0.07520325203252033	91	0.2513812154696133	138	0.24125874125874125	209	0.2757255936675462	T	17.52	3.409377	0.62399	0.105311	0.296395	ENSG00000130768	ENST00000373894;ENST00000373888;ENST00000549094;ENST00000412515	D;D;D	0.92752	-3.1;-3.1;-3.1	5.34	5.34	0.76211	Metallophosphoesterase domain (1);	0.184020	0.47455	D	0.000238	T	0.00039	0.0001	M	0.68952	2.095	0.32187	P	0.5795939999999999	D;D;D	0.63046	0.99;0.992;0.971	P;P;P	0.57152	0.716;0.814;0.716	T	0.00000	-1.5165	9	0.54805	T	0.06	-26.7775	15.2914	0.73868	0.0:0.0:0.0:1.0	rs3813803;rs52818124;rs56731368;rs3813803	215;263;263	F8VWW8;Q92485;Q92485-2	.;ASM3B_HUMAN;.	A	263;263;215;215	ENSP00000363001:V263A;ENSP00000362995:V263A;ENSP00000449450:V215A	ENSP00000362995:V263A	V	+	2	0	SMPDL3B	28154879	1.000000	0.71417	0.796000	0.32109	0.013000	0.08279	7.608000	0.82898	2.009000	0.58944	0.379000	0.24179	GTC	T|0.782;C|0.218	0.218	strong		0.542	SMPDL3B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011170.1	NM_014474	
CSF2RB	1439	hgsc.bcm.edu	37	22	37326443	37326443	+	Missense_Mutation	SNP	G	G	C	rs16845	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:37326443G>C	ENST00000403662.3	+	7	967	c.745G>C	c.(745-747)Gag>Cag	p.E249Q	CSF2RB_ENST00000262825.5_Missense_Mutation_p.E249Q|CSF2RB_ENST00000406230.1_Missense_Mutation_p.E249Q|CSF2RB_ENST00000536485.1_Missense_Mutation_p.E190Q			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	249			E -> Q (in dbSNP:rs16845).		cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	CCAGAACCTGGAGTGCTTCTT	0.622													C|||	521	0.104034	0.2148	0.0476	5008	,	,		18469	0.004		0.0477	False		,,,				2504	0.1554				p.E249Q		Atlas-SNP	.											.	CSF2RB	104	.	0			c.G745C						PASS	.	C	GLN/GLU	934,3472	735.2+/-410.7	93,748,1362	106.0	106.0	106.0		745	5.0	1.0	22	dbSNP_60	106	468,8132	797.6+/-407.4	7,454,3839	yes	missense	CSF2RB	NM_000395.2	29	100,1202,5201	CC,CG,GG		5.4419,21.1984,10.7796	benign	249/898	37326443	1402,11604	2203	4300	6503	SO:0001583	missense	1439	exon7			AACCTGGAGTGCT	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.745G>C	22.37:g.37326443G>C	ENSP00000384053:p.Glu249Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	37	CCDS13936.1	177	0.08104395604395605	120	0.24390243902439024	18	0.049723756906077346	4	0.006993006993006993	35	0.04617414248021108	C	6.917	0.538836	0.13250	0.211984	0.054419	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000421539;ENST00000536485	T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07	5.04	5.04	0.67666	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.174780	0.28360	N	0.015633	T	0.00012	0.0000	N	0.00063	-2.32	0.52501	P	4.999999999999449E-5	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.22695	-1.0209	9	0.02654	T	1	-18.811	13.2198	0.59881	0.0:0.8396:0.1604:0.0	rs16845;rs2228091;rs17402640;rs16845	249;249	P32927-2;P32927	.;IL3RB_HUMAN	Q	249;249;249;249;169;190	ENSP00000384053:E249Q;ENSP00000262825:E249Q;ENSP00000385271:E249Q;ENSP00000393585:E169Q;ENSP00000440003:E190Q	ENSP00000262825:E249Q	E	+	1	0	CSF2RB	35656389	0.905000	0.30787	0.986000	0.45419	0.953000	0.61014	1.340000	0.33896	1.255000	0.44051	-0.322000	0.08575	GAG	G|0.901;C|0.099	0.099	strong		0.622	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
TTYH2	94015	hgsc.bcm.edu	37	17	72240177	72240177	+	Missense_Mutation	SNP	T	T	G	rs35999669	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72240177T>G	ENST00000269346.4	+	6	867	c.793T>G	c.(793-795)Tct>Gct	p.S265A	TTYH2_ENST00000529107.1_Missense_Mutation_p.S244A|TTYH2_ENST00000534346.1_3'UTR	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	265			S -> A (in dbSNP:rs35999669). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						CGCTGATGGCTCTGCGGCAGT	0.657													G|||	1913	0.381989	0.6225	0.3055	5008	,	,		13747	0.0972		0.3579	False		,,,				2504	0.4294				p.S265A		Atlas-SNP	.											TTYH2,NS,carcinoma,0,1	TTYH2	63	1	0			c.T793G						PASS	.	G	ALA/SER	2637,1769	523.1+/-371.0	789,1059,355	64.0	61.0	62.0		793	4.0	0.0	17	dbSNP_126	62	3331,5269	642.8+/-399.9	667,1997,1636	yes	missense	TTYH2	NM_032646.5	99	1456,3056,1991	GG,GT,TT		38.7326,40.1498,45.8865	benign	265/535	72240177	5968,7038	2203	4300	6503	SO:0001583	missense	94015	exon6			GATGGCTCTGCGG		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.793T>G	17.37:g.72240177T>G	ENSP00000269346:p.Ser265Ala	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	759	0.3475274725274725	308	0.6260162601626016	100	0.27624309392265195	61	0.10664335664335664	290	0.38258575197889183	G	4.610	0.113410	0.08831	0.598502	0.387326	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.07800	3.16;3.16	5.01	4.04	0.47022	.	0.053637	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00313	-1.665	0.09310	P	0.9999999999999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38802	-0.9644	9	0.02654	T	1	-1.8901	6.8875	0.24209	0.082:0.0:0.609:0.3089	rs35999669;rs62065675	244;265	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	A	265;244	ENSP00000269346:S265A;ENSP00000433089:S244A	ENSP00000269346:S265A	S	+	1	0	TTYH2	69751772	0.985000	0.35326	0.006000	0.13384	0.307000	0.27823	2.541000	0.45735	0.539000	0.28788	-0.401000	0.06369	TCT	T|0.580;G|0.420	0.420	strong		0.657	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
CERS4	79603	hgsc.bcm.edu	37	19	8326944	8326944	+	Missense_Mutation	SNP	G	G	A	rs17160349	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8326944G>A	ENST00000251363.5	+	12	1436	c.1136G>A	c.(1135-1137)cGg>cAg	p.R379Q	CERS4_ENST00000558331.1_Missense_Mutation_p.R328Q|CERS4_ENST00000559336.1_Missense_Mutation_p.R291Q|CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000559450.1_Missense_Mutation_p.R379Q	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	379			R -> Q (in dbSNP:rs17160349). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GATGGCCCTCGGAGCCGGGTG	0.682													G|||	627	0.1252	0.1241	0.1744	5008	,	,		11860	0.0863		0.162	False		,,,				2504	0.0941				p.R379Q		Atlas-SNP	.											LASS4,NS,carcinoma,0,1	.	.	1	0			c.G1136A						PASS	.	G	GLN/ARG	551,3801		44,463,1669	8.0	11.0	10.0		1136	3.6	0.6	19	dbSNP_123	10	1323,7159		127,1069,3045	yes	missense	CERS4	NM_024552.2	43	171,1532,4714	AA,AG,GG		15.5977,12.6608,14.6018	probably-damaging	379/395	8326944	1874,10960	2176	4241	6417	SO:0001583	missense	79603	exon12			GCCCTCGGAGCCG		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.1136G>A	19.37:g.8326944G>A	ENSP00000251363:p.Arg379Gln	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_024552	D6W665	Missense_Mutation	SNP	ENST00000251363.5	37	CCDS12197.1	317	0.14514652014652016	77	0.1565040650406504	69	0.19060773480662985	41	0.07167832167832168	130	0.17150395778364116	G	21.6	4.172695	0.78452	0.126608	0.155977	ENSG00000090661	ENST00000251363	T	0.05855	3.38	4.61	3.57	0.40892	.	46.516500	0.00166	N	0.000000	T	0.00039	0.0001	M	0.66506	2.035	0.80722	P	0.0	D;D	0.71674	0.998;0.998	P;P	0.54346	0.665;0.749	T	0.15065	-1.0450	9	0.18710	T	0.47	-47.2197	8.9184	0.35596	0.1066:0.0:0.8934:0.0	rs17160349;rs17855413;rs17160349	379;379	Q53HF9;Q9HA82	.;CERS4_HUMAN	Q	379	ENSP00000251363:R379Q	ENSP00000251363:R379Q	R	+	2	0	CERS4	8232944	0.988000	0.35896	0.556000	0.28293	0.023000	0.10783	2.081000	0.41596	1.067000	0.40740	0.491000	0.48974	CGG	A|0.139;C|0.000;G|0.860	0.139	strong		0.682	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
ARSD	414	hgsc.bcm.edu	37	X	2836037	2836037	+	Missense_Mutation	SNP	G	G	C	rs211653	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:2836037G>C	ENST00000381154.1	-	5	746	c.671C>G	c.(670-672)tCt>tGt	p.S224C	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	224			S -> C (in dbSNP:rs211653). {ECO:0000269|PubMed:11177574}.		cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CGCGGAGACAGAGAAGAAACC	0.627													g|||	1534	0.406358	0.3396	0.4006	3775	,	,		13839	0.255		0.3489	False		,,,				2504	0.2035				p.S224C		Atlas-SNP	.											.	ARSD	47	.	0			c.C671G						PASS	.	G	CYS/SER	1666,2169		339,779,209,514,362	19.0	23.0	22.0		671	2.5	0.0	X	dbSNP_79	22	3030,3696		560,1221,689,647,1181	no	missense	ARSD	NM_001669.3	112	899,2000,898,1161,1543	CC,CG,C,GG,G		45.0491,43.442,44.4655	benign	224/594	2836037	4696,5865	2203	4298	6501	SO:0001583	missense	414	exon5			GAGACAGAGAAGA	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.671C>G	X.37:g.2836037G>C	ENSP00000370546:p.Ser224Cys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	72	4	0.0555556	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	680	0.4098854731766124	138	0.3	139	0.4371069182389937	158	0.286231884057971	282	0.4051724137931034	g	9.900	1.206692	0.22205	0.43442	0.450491	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.94000	-3.33	3.47	2.55	0.30701	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.450854	0.20036	U	0.100602	T	0.00012	0.0000	M	0.82923	2.615	0.80722	P	0.0	B;B	0.25206	0.12;0.045	B;B	0.34301	0.179;0.076	T	0.01791	-1.1273	9	0.33940	T	0.23	.	11.8883	0.52615	0.0:0.1742:0.8258:0.0	rs211653;rs17325736;rs56637515;rs211653	224;224	E9PAW5;P51689	.;ARSD_HUMAN	C	224	ENSP00000370546:S224C	ENSP00000217890:S224C	S	-	2	0	ARSD	2846037	0.137000	0.22531	0.012000	0.15200	0.071000	0.16799	3.128000	0.50492	0.342000	0.23796	0.420000	0.28162	TCT	0|0.004;C|0.405	0.405	strong		0.627	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
ZBTB37	84614	hgsc.bcm.edu	37	1	173855208	173855208	+	Silent	SNP	A	A	G	rs16846520	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:173855208A>G	ENST00000367701.5	+	4	1649	c.1458A>G	c.(1456-1458)acA>acG	p.T486T	ZBTB37_ENST00000367704.1_3'UTR|ZBTB37_ENST00000427304.1_Silent_p.T486T			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	486					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						AGGAAGAGACAGTTGCTCCTG	0.577													A|||	475	0.0948482	0.0083	0.121	5008	,	,		19240	0.0605		0.1511	False		,,,				2504	0.1708				p.T486T		Atlas-SNP	.											.	ZBTB37	38	.	0			c.A1458G						PASS	.	A		38,1346		0,38,654	17.0	16.0	16.0		1458	-0.5	0.3	1	dbSNP_123	16	426,2756		29,368,1194	no	coding-synonymous	ZBTB37	NM_001122770.1		29,406,1848	GG,GA,AA		13.3878,2.7457,10.1621		486/504	173855208	464,4102	692	1591	2283	SO:0001819	synonymous_variant	84614	exon5			AGAGACAGTTGCT	AK057310	CCDS1312.1, CCDS44278.1	1q24.2	2013-01-08			ENSG00000185278	ENSG00000185278		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	28365	protein-coding gene	gene with protein product						12477932	Standard	NM_032522		Approved	MGC2629, ZNF908	uc009wwp.1	Q5TC79	OTTHUMG00000037274	ENST00000367701.5:c.1458A>G	1.37:g.173855208A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_001122770	Q5TC80|Q96M87|Q9BQ88	Silent	SNP	ENST00000367701.5	37	CCDS44278.1																																																																																			A|0.907;G|0.093	0.093	strong		0.577	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522	
GAS2L2	246176	hgsc.bcm.edu	37	17	34077232	34077232	+	Missense_Mutation	SNP	G	G	A	rs11654604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:34077232G>A	ENST00000254466.6	-	2	518	c.491C>T	c.(490-492)gCg>gTg	p.A164V	GAS2L2_ENST00000587565.1_Missense_Mutation_p.A164V	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	164			A -> V (in dbSNP:rs11654604).		cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TGTGGGCGCCGCAACACCAAA	0.697													G|||	718	0.143371	0.1014	0.2046	5008	,	,		13807	0.1567		0.162	False		,,,				2504	0.1237				p.A164V		Atlas-SNP	.											.	GAS2L2	94	.	0			c.C491T						PASS	.	G	VAL/ALA	479,3927	225.2+/-241.2	24,431,1748	110.0	124.0	119.0		491	5.1	1.0	17	dbSNP_120	119	1267,7331	252.2+/-278.4	99,1069,3131	yes	missense	GAS2L2	NM_139285.3	64	123,1500,4879	AA,AG,GG		14.736,10.8715,13.4266	possibly-damaging	164/881	34077232	1746,11258	2203	4299	6502	SO:0001583	missense	246176	exon2			GGCGCCGCAACAC	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.491C>T	17.37:g.34077232G>A	ENSP00000254466:p.Ala164Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	67	40	0.597015	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	345	0.15796703296703296	57	0.11585365853658537	74	0.20441988950276244	81	0.14160839160839161	133	0.17546174142480211	G	14.60	2.583429	0.46006	0.108715	0.14736	ENSG00000132139	ENST00000254466;ENST00000359507	T	0.42131	0.98	5.11	5.11	0.69529	Calponin homology domain (2);	0.649555	0.14468	N	0.317778	T	0.00073	0.0002	M	0.63428	1.95	0.33455	P	0.41575300000000004	D	0.71674	0.998	P	0.55303	0.773	T	0.05599	-1.0875	9	0.22109	T	0.4	-4.1232	12.7326	0.57206	0.0:0.2814:0.7186:0.0	rs11654604	164	Q8NHY3	GA2L2_HUMAN	V	164	ENSP00000254466:A164V	ENSP00000254466:A164V	A	-	2	0	GAS2L2	31101345	0.745000	0.28261	0.991000	0.47740	0.462000	0.32619	1.608000	0.36847	2.370000	0.80446	0.561000	0.74099	GCG	G|0.857;A|0.143	0.143	strong		0.697	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285	
MROH7	374977	hgsc.bcm.edu	37	1	55119515	55119515	+	Missense_Mutation	SNP	T	T	G	rs1655519	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:55119515T>G	ENST00000421030.2	+	3	1201	c.916T>G	c.(916-918)Tat>Gat	p.Y306D	MROH7_ENST00000545244.1_Intron|MROH7_ENST00000454855.2_Intron|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.Y306D|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000409996.1_Intron|MROH7_ENST00000395690.2_Missense_Mutation_p.Y306D|MROH7_ENST00000339553.5_Missense_Mutation_p.Y306D	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	306	Ser-rich.		Y -> D (in dbSNP:rs1655519). {ECO:0000269|PubMed:17974005}.			extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											TGGCTCCAGCTATGGTATCAG	0.532													G|||	2131	0.425519	0.4251	0.3833	5008	,	,		21265	0.4157		0.328	False		,,,				2504	0.5665				p.Y306D		Atlas-SNP	.											.	.	.	.	0			c.T916G						PASS	.	G	ASP/TYR	1728,2572		344,1040,766	120.0	116.0	117.0		916	3.0	0.0	1	dbSNP_89	117	2803,5677		475,1853,1912	yes	missense	HEATR8	NM_001039464.2	160	819,2893,2678	GG,GT,TT		33.0542,40.186,35.4538	benign	306/1324	55119515	4531,8249	2150	4240	6390	SO:0001583	missense	374977	exon3			TCCAGCTATGGTA	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"""maestro heat-like repeat containing"""	24802	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 175"", ""HEAT repeat containing 8"""	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.916T>G	1.37:g.55119515T>G	ENSP00000396622:p.Tyr306Asp	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	845	0.3869047619047619	231	0.4695121951219512	136	0.3756906077348066	224	0.3916083916083916	254	0.33509234828496043	G	0.015	-1.558021	0.00910	0.40186	0.330542	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000339553;ENST00000395690	T;T;T	0.03772	3.81;3.81;3.81	3.89	2.98	0.34508	.	1.059900	0.07470	N	0.902154	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43829	-0.9367	9	0.02654	T	1	.	5.0515	0.14511	0.1073:0.0:0.6876:0.2051	rs1655519;rs17110897;rs57779323;rs1655519	306;306;306	F8W8P2;Q68CQ1;Q68CQ1-4	.;HEAT8_HUMAN;.	D	306	ENSP00000396622:Y306D;ENSP00000343211:Y306D;ENSP00000379044:Y306D	ENSP00000343211:Y306D	Y	+	1	0	HEATR8	54892103	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.353000	0.20130	0.629000	0.30376	-0.121000	0.15023	TAT	T|0.604;G|0.396	0.396	strong		0.532	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
ZBED1	9189	hgsc.bcm.edu	37	X	2408434	2408434	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:2408434C>T	ENST00000381223.4	-	2	530	c.327G>A	c.(325-327)gcG>gcA	p.A109A	DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381222.2_Silent_p.A109A|ZBED1_ENST00000515319.1_5'Flank|ZBED1_ENST00000381218.3_Silent_p.A109A	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	109					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)			endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGACGGCCAGCGCGTCCTGCC	0.672																																					p.A109A		Atlas-SNP	.											.	ZBED1	64	.	0			c.G327A						PASS	.						59.0	59.0	59.0					X																	2408434		2203	4296	6499	SO:0001819	synonymous_variant	9189	exon2			GGCCAGCGCGTCC	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"""Pseudoautosomal regions / PAR1"", ""Zinc fingers, BED-type"""	447	protein-coding gene	gene with protein product		300178	"""Ac-like transposable element"""	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.327G>A	X.37:g.2408434C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	87	79	0.908046	NM_001171135	Q96BY4	Silent	SNP	ENST00000381223.4	37	CCDS14118.1																																																																																			C|0.999;G|0.001	.	alt		0.672	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729	
TANC2	26115	hgsc.bcm.edu	37	17	61498500	61498500	+	Silent	SNP	C	C	T	rs117474655	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:61498500C>T	ENST00000424789.2	+	25	5161	c.5157C>T	c.(5155-5157)cgC>cgT	p.R1719R	RP11-269G24.3_ENST00000583552.1_RNA|TANC2_ENST00000389520.4_Silent_p.R1729R	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	1719					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						AGATCGGACGCAGCCAGTCAG	0.522													C|||	45	0.00898562	0.0	0.0014	5008	,	,		20011	0.0		0.0149	False		,,,				2504	0.0297				p.R1719R		Atlas-SNP	.											.	TANC2	266	.	0			c.C5157T						PASS	.	C		21,4255		0,21,2117	186.0	189.0	188.0		5157	-5.8	0.8	17	dbSNP_132	188	148,8346		3,142,4102	no	coding-synonymous	TANC2	NM_025185.3		3,163,6219	TT,TC,CC		1.7424,0.4911,1.3234		1719/1991	61498500	169,12601	2138	4247	6385	SO:0001819	synonymous_variant	26115	exon25			CGGACGCAGCCAG	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30212	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.5157C>T	17.37:g.61498500C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	163	83	0.509202	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Silent	SNP	ENST00000424789.2	37	CCDS45754.1																																																																																			C|0.988;T|0.012	0.012	strong		0.522	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1		
CFTR	1080	hgsc.bcm.edu	37	7	117235055	117235055	+	Silent	SNP	T	T	G	rs397508396|rs1042077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:117235055T>G	ENST00000003084.6	+	15	2694	c.2562T>G	c.(2560-2562)acT>acG	p.T854T	CFTR_ENST00000454343.1_Silent_p.T793T	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	854					cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	GATATATTACTGTCCACAAGA	0.328									Cystic Fibrosis				T|||	2400	0.479233	0.7065	0.428	5008	,	,		12659	0.3919		0.335	False		,,,				2504	0.4468				p.T854T		Atlas-SNP	.											.	CFTR	171	.	0			c.T2562G	GRCh37	CD003291|CS042144	CFTR	D|S	rs1042077	PASS	.	T		2726,1680	653.8+/-399.6	838,1050,315	158.0	148.0	151.0		2562	0.2	0.0	7	dbSNP_86	151	2513,6087	411.7+/-350.6	373,1767,2160	no	coding-synonymous	CFTR	NM_000492.3		1211,2817,2475	GG,GT,TT		29.2209,38.1298,40.2814		854/1481	117235055	5239,7767	2203	4300	6503	SO:0001819	synonymous_variant	1080	exon15	Familial Cancer Database	CF	TATTACTGTCCAC	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.2562T>G	7.37:g.117235055T>G		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	216	105	0.486111	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	37	CCDS5773.1																																																																																			G|0.425;N|0.000	0.425	strong		0.328	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
MYH11	4629	hgsc.bcm.edu	37	16	15814100	15814100	+	Missense_Mutation	SNP	T	T	G	rs34321232		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15814100T>G	ENST00000300036.5	-	34	4970	c.4861A>C	c.(4861-4863)Aag>Cag	p.K1621Q	NDE1_ENST00000396354.1_Intron|NDE1_ENST00000396355.1_Intron|NDE1_ENST00000342673.5_Intron|MYH11_ENST00000452625.2_Missense_Mutation_p.K1628Q|MYH11_ENST00000396324.3_Missense_Mutation_p.K1628Q|MYH11_ENST00000576790.2_Missense_Mutation_p.K1621Q	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1621					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CCTTCCAGCTTCTTCTTTGCT	0.577			T	CBFB	AML								T|||	1	0.000199681	0.0	0.0	5008	,	,		20791	0.0		0.0	False		,,,				2504	0.001				p.K1628Q		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.A4882C						PASS	.	T	GLN/LYS,GLN/LYS,,GLN/LYS,,GLN/LYS	0,4394		0,0,2197	121.0	104.0	110.0		4882,4882,,4861,,4861	4.9	1.0	16	dbSNP_126	110	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,intron,missense,intron,missense	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	53,53,,53,,53	0,3,6494	GG,GT,TT		0.0349,0.0,0.0231	probably-damaging,probably-damaging,,probably-damaging,,probably-damaging	1628/1946,1628/1980,,1621/1973,,1621/1939	15814100	3,12991	2197	4300	6497	SO:0001583	missense	4629	exon35			CCAGCTTCTTCTT	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.4861A>C	16.37:g.15814100T>G	ENSP00000300036:p.Lys1621Gln	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	190	98	0.515789	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.056096	0.76074	0.0	3.49E-4	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05	4.95	4.95	0.65309	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.92176	0.7519	M	0.87827	2.91	0.80722	D	1	D;P;P;P;P	0.61697	0.99;0.893;0.893;0.742;0.893	D;P;P;P;P	0.63283	0.913;0.732;0.732;0.732;0.732	D	0.93505	0.6848	10	0.87932	D	0	.	13.7947	0.63164	0.0:0.0:0.0:1.0	rs34321232	1628;1621;1628;1621;1628	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	Q	1621;1621;1628;1628;1628	ENSP00000300036:K1621Q;ENSP00000345136:K1621Q;ENSP00000379616:K1628Q;ENSP00000407821:K1628Q	ENSP00000300036:K1621Q	K	-	1	0	MYH11	15721601	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	7.950000	0.87804	1.864000	0.54056	0.528000	0.53228	AAG	T|0.987;G|0.013	0.013	weak		0.577	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
HOPX	84525	hgsc.bcm.edu	37	4	57516896	57516896	+	Intron	SNP	G	G	A	rs4371677	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:57516896G>A	ENST00000337881.7	-	3	801				HOPX_ENST00000554144.1_Missense_Mutation_p.P94L|HOPX_ENST00000555760.2_Intron|HOPX_ENST00000317745.7_Intron|HOPX_ENST00000553379.2_Intron|HOPX_ENST00000508121.1_Intron|HOPX_ENST00000381260.3_Missense_Mutation_p.P76L|HOPX_ENST00000556614.2_Intron|HOPX_ENST00000556376.2_Intron|HOPX_ENST00000420433.1_Intron|HOPX_ENST00000503639.3_Intron|HOPX_ENST00000381255.3_Intron	NM_139212.3	NP_631958.1	Q9BPY8	HOP_HUMAN	HOP homeobox						heart development (GO:0007507)|histone deacetylation (GO:0016575)|lung alveolus development (GO:0048286)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of heart contraction (GO:0008016)|regulation of protein binding (GO:0043393)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P94L(1)		large_intestine(2)|lung(5)|skin(1)	8	Glioma(25;0.08)|all_neural(26;0.101)					AGCCAAGCACGGCAGACTATC	0.458													A|||	2435	0.486222	0.6725	0.3617	5008	,	,		19278	0.4712		0.4791	False		,,,				2504	0.3456				p.P94L		Atlas-SNP	.											HOPX_ENST00000554144,NS,carcinoma,0,1	HOPX	28	1	1	Substitution - Missense(1)	stomach(1)	c.C281T						PASS	.	A	,LEU/PRO,,,	894,490		280,334,78	75.0	69.0	71.0		,281,,,	0.5	0.0	4	dbSNP_111	71	1438,1744		323,792,476	yes	intron,missense,intron,intron,intron	HOPX	NM_001145459.1,NM_001145460.1,NM_032495.5,NM_139211.4,NM_139212.3	,98,,,	603,1126,554	AA,AG,GG		45.1917,35.4046,48.9269	,,,,	,94/113,,,	57516896	2332,2234	692	1591	2283	SO:0001627	intron_variant	84525	exon4			AAGCACGGCAGAC		CCDS3507.1, CCDS47062.1, CCDS54767.1	4q12	2011-06-20			ENSG00000171476	ENSG00000171476		"""Homeoboxes / PRD class"""	24961	protein-coding gene	gene with protein product	"""homeobox only domain"""	607275				12297045	Standard	NM_032495		Approved	LAGY, HOP, OB1, NECC1, SMAP31	uc003hbz.2	Q9BPY8	OTTHUMG00000128768	ENST00000337881.7:c.145-1933C>T	4.37:g.57516896G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_001145460	A8K0Z2|E9PB55|G3V294|Q8N0V6|Q96CI1	Missense_Mutation	SNP	ENST00000337881.7	37	CCDS3507.1	1076	0.4926739926739927	340	0.6910569105691057	138	0.3812154696132597	246	0.43006993006993005	352	0.46437994722955145	A	0.011	-1.702512	0.00719	0.645954	0.451917	ENSG00000171476	ENST00000554144;ENST00000381260;ENST00000503864;ENST00000509435	.	.	.	3.22	0.473	0.16763	.	.	.	.	.	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39901	-0.9591	7	0.02654	T	1	.	3.3623	0.07192	0.5528:0.2065:0.2407:0.0	rs4371677;rs52837923;rs59676692;rs4371677	94	G3V294	.	L	94;76;76;76	.	ENSP00000370659:P94L	P	-	2	0	HOPX	57211653	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.278000	0.08490	-0.146000	0.11274	-0.269000	0.10298	CCG	G|0.501;A|0.499	0.499	strong		0.458	HOPX-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250689.4		
MRPL51	51258	hgsc.bcm.edu	37	12	6601475	6601475	+	Missense_Mutation	SNP	G	G	A	rs11380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6601475G>A	ENST00000229238.3	-	3	810	c.349C>T	c.(349-351)Ctc>Ttc	p.L117F	NCAPD2_ENST00000545962.1_5'Flank|MRPL51_ENST00000543164.1_5'UTR|NCAPD2_ENST00000315579.5_5'Flank|MRPL51_ENST00000543703.1_Missense_Mutation_p.L21F	NM_016497.3	NP_057581.2	Q4U2R6	RM51_HUMAN	mitochondrial ribosomal protein L51	117					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			kidney(2)|large_intestine(1)|lung(3)	6						TGTTTGTAGAGATAGCGGATG	0.433													G|||	2	0.000399361	0.0	0.0	5008	,	,		21574	0.0		0.002	False		,,,				2504	0.0				p.L117F		Atlas-SNP	.											MRPL51,NS,carcinoma,0,1	MRPL51	17	1	0			c.C349T						PASS	.	G	PHE/LEU	2,4404	4.2+/-10.8	0,2,2201	232.0	220.0	224.0		349	5.3	1.0	12	dbSNP_52	224	9,8591	7.1+/-27.0	0,9,4291	yes	missense	MRPL51	NM_016497.3	22	0,11,6492	AA,AG,GG		0.1047,0.0454,0.0846	probably-damaging	117/129	6601475	11,12995	2203	4300	6503	SO:0001583	missense	51258	exon3			TGTAGAGATAGCG	AB051355	CCDS8547.1	12p13.3-p13.1	2014-02-19	2002-01-07	2002-01-11		ENSG00000111639		"""Mitochondrial ribosomal proteins / large subunits"""	14044	protein-coding gene	gene with protein product		611855	"""mitochondrial ribosomal protein 64"""	MRP64		11551941, 11543634	Standard	NM_016497		Approved	CDA09, HSPC241, bMRP64	uc001qom.2	Q4U2R6		ENST00000229238.3:c.349C>T	12.37:g.6601475G>A	ENSP00000229238:p.Leu117Phe	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	331	166	0.501511	NM_016497	Q96Q57|Q9BQ36|Q9P0N7	Missense_Mutation	SNP	ENST00000229238.3	37	CCDS8547.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	26.9	4.780307	0.90195	4.54E-4	0.001047	ENSG00000111639	ENST00000229238	T	0.63255	-0.03	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.81128	0.4758	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84217	0.0459	10	0.87932	D	0	-15.4554	10.5659	0.45173	0.1242:0.0:0.8758:0.0	rs11380;rs52796309	117	Q4U2R6	RM51_HUMAN	F	117	ENSP00000229238:L117F	ENSP00000229238:L117F	L	-	1	0	MRPL51	6471736	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.291000	0.65667	2.478000	0.83669	0.462000	0.41574	CTC	G|0.999;A|0.001	0.001	strong		0.433	MRPL51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399956.1	NM_016497	
PRUNE	58497	hgsc.bcm.edu	37	1	150999737	150999737	+	Silent	SNP	A	A	G	rs11204762	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:150999737A>G	ENST00000271620.3	+	6	864	c.708A>G	c.(706-708)aaA>aaG	p.K236K	PRUNE_ENST00000368935.1_Silent_p.K4K|PRUNE_ENST00000368937.1_Silent_p.K54K|PRUNE_ENST00000368934.1_Silent_p.K54K|PRUNE_ENST00000467771.1_3'UTR|PRUNE_ENST00000271619.8_Silent_p.K77K|PRUNE_ENST00000368936.1_Silent_p.K54K	NM_021222.1	NP_067045.1	Q86TP1	PRUNE_HUMAN	prune exopolyphosphatase	236						cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TGCTGAGAAAAGACCAGAAGA	0.498													N|||	1381	0.275759	0.2474	0.1974	5008	,	,		19430	0.4613		0.2107	False		,,,				2504	0.2454				p.K236K		Atlas-SNP	.											.	PRUNE	40	.	0			c.A708G						PASS	.	G		1140,3266		167,806,1230	152.0	129.0	137.0		708	3.6	1.0	1	dbSNP_120	137	1939,6661		251,1437,2612	no	coding-synonymous	PRUNE	NM_021222.1		418,2243,3842	GG,GA,AA		22.5465,25.8738,23.6737		236/454	150999737	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	58497	exon6			GAGAAAAGACCAG	U67085	CCDS977.1	1q21.2	2013-04-29	2013-04-29		ENSG00000143363	ENSG00000143363	3.6.1.11		13420	protein-coding gene	gene with protein product			"""prune homolog (Drosophila)"""			10602478, 11687967, 18700747	Standard	NM_021222		Approved	DRES-17, HTCD37	uc001ewh.1	Q86TP1	OTTHUMG00000035062	ENST00000271620.3:c.708A>G	1.37:g.150999737A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	153	66	0.431373	NM_021222	B2RCH8|B4DFL7|Q5SZF9|Q659E5|Q6P4E0|Q8N654|Q96JU5|Q9C071|Q9C072|Q9UIV0	Silent	SNP	ENST00000271620.3	37	CCDS977.1																																																																																			A|0.743;G|0.257	0.257	strong		0.498	PRUNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084885.1	NM_021222	
DKKL1	27120	hgsc.bcm.edu	37	19	49878196	49878196	+	Missense_Mutation	SNP	G	G	A	rs2288481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49878196G>A	ENST00000221498.2	+	5	1045	c.640G>A	c.(640-642)Gaa>Aaa	p.E214K	AC010524.2_ENST00000599433.1_RNA|DKKL1_ENST00000594268.1_Missense_Mutation_p.E72K	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	214			E -> K (in dbSNP:rs2288481).		anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		GGACGTCCTAGAAGAGGGGAC	0.662													G|||	1294	0.258387	0.1952	0.2003	5008	,	,		17220	0.3264		0.2068	False		,,,				2504	0.3681				p.E214K		Atlas-SNP	.											.	DKKL1	23	.	0			c.G640A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	887,3519	314.7+/-293.7	95,697,1411	33.0	35.0	34.0		547,415,640	3.1	0.0	19	dbSNP_100	34	1979,6621	320.3+/-314.5	240,1499,2561	yes	missense,missense,missense	DKKL1	NM_001197301.1,NM_001197302.1,NM_014419.3	56,56,56	335,2196,3972	AA,AG,GG		23.0116,20.1316,22.036	possibly-damaging,possibly-damaging,possibly-damaging	183/212,139/168,214/243	49878196	2866,10140	2203	4300	6503	SO:0001583	missense	27120	exon5			GTCCTAGAAGAGG	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"""cancer/testis antigen 34"", ""soggy"""	605418	"""dickkopf-like 1 (soggy)"""			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.640G>A	19.37:g.49878196G>A	ENSP00000221498:p.Glu214Lys	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	37	CCDS12762.1	490	0.22435897435897437	83	0.16869918699186992	73	0.20165745856353592	179	0.3129370629370629	155	0.20448548812664907	G	14.07	2.424616	0.43020	0.201316	0.230116	ENSG00000104901	ENST00000221498	T	0.14266	2.52	4.15	3.09	0.35607	.	0.449220	0.18957	N	0.126514	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	P	0.36909	0.573	B	0.36666	0.23	T	0.47235	-0.9133	9	0.87932	D	0	-7.7924	10.0305	0.42099	0.0:0.2047:0.7953:0.0	rs2288481;rs3195289;rs61144855;rs2288481	214	Q9UK85	DKKL1_HUMAN	K	214	ENSP00000221498:E214K	ENSP00000221498:E214K	E	+	1	0	DKKL1	54570008	0.014000	0.17966	0.007000	0.13788	0.009000	0.06853	0.384000	0.20668	1.320000	0.45209	0.655000	0.94253	GAA	G|0.767;A|0.233	0.233	strong		0.662	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419	
MAB21L3	126868	hgsc.bcm.edu	37	1	116670774	116670774	+	Silent	SNP	A	A	G	rs10754431	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:116670774A>G	ENST00000369500.3	+	6	934	c.669A>G	c.(667-669)ggA>ggG	p.G223G	MAB21L3_ENST00000464946.1_3'UTR	NM_152367.2	NP_689580.2	Q8N8X9	MB213_HUMAN	mab-21-like 3 (C. elegans)	223										breast(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|urinary_tract(1)	19						AGTCGTTTGGATTTAACTTGT	0.468													G|||	2091	0.417532	0.9009	0.2983	5008	,	,		21590	0.2748		0.2227	False		,,,				2504	0.1963				p.G223G		Atlas-SNP	.											.	MAB21L3	33	.	0			c.A669G						PASS	.	G		3409,997	370.8+/-319.7	1330,749,124	108.0	116.0	113.0		669	0.2	0.4	1	dbSNP_120	113	1850,6750	730.1+/-406.7	190,1470,2640	no	coding-synonymous	MAB21L3	NM_152367.2		1520,2219,2764	GG,GA,AA		21.5116,22.6282,40.4352		223/363	116670774	5259,7747	2203	4300	6503	SO:0001819	synonymous_variant	126868	exon6			GTTTGGATTTAAC	AK096035	CCDS886.1	1p13.1	2011-02-23	2011-02-23	2011-02-23	ENSG00000173212	ENSG00000173212			26787	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 161"""	C1orf161		14702039	Standard	NM_152367		Approved	FLJ38716	uc001egc.1	Q8N8X9	OTTHUMG00000012110	ENST00000369500.3:c.669A>G	1.37:g.116670774A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	151	73	0.483444	NM_152367	Q5TDL7	Silent	SNP	ENST00000369500.3	37	CCDS886.1																																																																																			A|0.608;G|0.392	0.392	strong		0.468	MAB21L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033486.1	NM_152367	
PCDH15	65217	hgsc.bcm.edu	37	10	56106173	56106173	+	Silent	SNP	T	T	C	rs34164469	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:56106173T>C	ENST00000320301.6	-	6	940	c.546A>G	c.(544-546)ggA>ggG	p.G182G	PCDH15_ENST00000437009.1_Silent_p.G182G|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000373965.2_Silent_p.G182G|AC013737.1_ENST00000583830.1_RNA|PCDH15_ENST00000395430.1_Silent_p.G182G|PCDH15_ENST00000395432.2_Silent_p.G182G|PCDH15_ENST00000414778.1_Silent_p.G187G|PCDH15_ENST00000395438.1_Silent_p.G182G|PCDH15_ENST00000395442.1_Silent_p.G182G|PCDH15_ENST00000395440.1_Silent_p.G182G|PCDH15_ENST00000373955.1_Silent_p.G182G|PCDH15_ENST00000395433.1_Silent_p.G160G|PCDH15_ENST00000373957.3_Silent_p.G160G|PCDH15_ENST00000395445.1_Silent_p.G182G|PCDH15_ENST00000395446.1_Silent_p.G182G|PCDH15_ENST00000361849.3_Silent_p.G182G	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	182	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GTCCATTTGGTCCATCATCTA	0.318										HNSCC(58;0.16)			T|||	36	0.0071885	0.0	0.0043	5008	,	,		16771	0.0		0.0258	False		,,,				2504	0.0072				p.G187G		Atlas-SNP	.											.	PCDH15	1715	.	0			c.A561G						PASS	.	T	,,,,,,,,,,,	19,4387	24.3+/-50.5	0,19,2184	144.0	143.0	144.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	561,546,546,546,546,480,561,546,561,546,480,546	1.4	1.0	10	dbSNP_126	144	199,8401	87.1+/-149.5	3,193,4104	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	,,,,,,,,,,,	3,212,6288	CC,CT,TT		2.314,0.4312,1.6761	,,,,,,,,,,,	187/1963,182/1958,182/1887,182/1953,182/1916,160/1936,187/1791,182/1540,187/1683,182/1678,160/1933,182/1956	56106173	218,12788	2203	4300	6503	SO:0001819	synonymous_variant	65217	exon7			ATTTGGTCCATCA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.546A>G	10.37:g.56106173T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	177	85	0.480226	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			T|0.986;C|0.014	0.014	strong		0.318	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
MYH1	4619	hgsc.bcm.edu	37	17	10404046	10404046	+	Silent	SNP	G	G	A	rs17811250	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:10404046G>A	ENST00000226207.5	-	28	3856	c.3762C>T	c.(3760-3762)cgC>cgT	p.R1254R	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1254					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CTTCTAGAGCGCGGCACATCT	0.448													G|||	348	0.0694888	0.0182	0.1009	5008	,	,		16463	0.001		0.2266	False		,,,				2504	0.0256				p.R1254R		Atlas-SNP	.											.	MYH1	403	.	0			c.C3762T						PASS	.	A		169,4237	112.9+/-151.0	4,161,2038	141.0	125.0	131.0		3762	-0.1	0.2	17	dbSNP_123	131	1600,7000	297.7+/-303.5	144,1312,2844	no	coding-synonymous	MYH1	NM_005963.3		148,1473,4882	AA,AG,GG		18.6047,3.8357,13.6014		1254/1940	10404046	1769,11237	2203	4300	6503	SO:0001819	synonymous_variant	4619	exon28			TAGAGCGCGGCAC		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3762C>T	17.37:g.10404046G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	136	63	0.463235	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	37	CCDS11155.1																																																																																			G|0.880;A|0.120	0.120	strong		0.448	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
ARMCX2	9823	hgsc.bcm.edu	37	X	100911066	100911066	+	Silent	SNP	C	C	T	rs3850315	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:100911066C>T	ENST00000328766.5	-	5	1962	c.1509G>A	c.(1507-1509)caG>caA	p.Q503Q	ARMCX2_ENST00000330154.2_Silent_p.Q503Q|ARMCX2_ENST00000467416.1_5'Flank|ARMCX2_ENST00000356824.4_Silent_p.Q503Q	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	503						integral component of membrane (GO:0016021)				NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(6)|prostate(1)|skin(1)	29						CAAGCAGGTGCTGGTAGTCAT	0.373													c|||	3650	0.966887	0.7496	0.7205	3775	,	,		14782	0.7579		0.6889	False		,,,				2504	0.7178				p.Q503Q		Atlas-SNP	.											.	ARMCX2	75	.	0			c.G1509A						PASS	.	T	,	3773,62		1579,52,563,1,8	122.0	121.0	122.0		1509,1509	1.2	1.0	X	dbSNP_108	122	6184,544		2048,360,1728,20,144	no	coding-synonymous,coding-synonymous	ARMCX2	NM_014782.5,NM_177949.2	,	3627,412,2291,21,152	TT,TC,T,CC,C		8.0856,1.6167,5.737	,	503/633,503/633	100911066	9957,606	2203	4300	6503	SO:0001819	synonymous_variant	9823	exon5			CAGGTGCTGGTAG	AB011084	CCDS14490.1	Xq21.33-q22.2	2014-03-21			ENSG00000184867	ENSG00000184867		"""Armadillo repeat containing"""	16869	protein-coding gene	gene with protein product		300363				9628581, 11162520, 16221301, 22569362	Standard	XM_005278109		Approved	ALEX2, KIAA0512, GASP9	uc004eif.3	Q7L311	OTTHUMG00000022038	ENST00000328766.5:c.1509G>A	X.37:g.100911066C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_014782	O60267|Q5H9D9	Silent	SNP	ENST00000328766.5	37	CCDS14490.1																																																																																			C|0.042;T|0.958	0.958	strong		0.373	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057586.1	NM_014782	
MZF1	7593	hgsc.bcm.edu	37	19	59082605	59082605	+	Missense_Mutation	SNP	C	C	T	rs3752109	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:59082605C>T	ENST00000215057.2	-	2	712	c.152G>A	c.(151-153)cGc>cAc	p.R51H	MZF1_ENST00000599369.1_Missense_Mutation_p.R51H|MZF1_ENST00000594108.1_Missense_Mutation_p.R51H|AC016629.8_ENST00000600534.1_RNA|MZF1_ENST00000594234.1_Missense_Mutation_p.R51H|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	51	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.		R -> H (in dbSNP:rs3752109). {ECO:0000269|PubMed:10974541, ECO:0000269|PubMed:15489334}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		CTCCTCATAGCGGAAGCACCG	0.647													.|||	1037	0.207069	0.0688	0.2378	5008	,	,		18124	0.2996		0.2744	False		,,,				2504	0.2076				p.R51H		Atlas-SNP	.											.	MZF1	37	.	0			c.G152A						PASS	.	C	HIS/ARG,HIS/ARG	411,3995		22,367,1814	21.0	22.0	22.0		152,152	-1.9	0.0	19	dbSNP_107	22	2432,6166		334,1764,2201	yes	missense,missense	MZF1	NM_003422.2,NM_198055.1	29,29	356,2131,4015	TT,TC,CC		28.2856,9.3282,21.8625	benign,benign	51/735,51/735	59082605	2843,10161	2203	4299	6502	SO:0001583	missense	7593	exon2			TCATAGCGGAAGC	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"""-"", ""Zinc fingers, C2H2-type"""	13108	protein-coding gene	gene with protein product		194550	"""zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"""	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.152G>A	19.37:g.59082605C>T	ENSP00000215057:p.Arg51His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_198055	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	37	CCDS12988.1	511	0.23397435897435898	38	0.07723577235772358	86	0.23756906077348067	169	0.29545454545454547	218	0.287598944591029	.	9.266	1.044385	0.19748	0.093282	0.282856	ENSG00000099326	ENST00000215057	T	0.04317	3.65	4.35	-1.86	0.07760	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.997429	0.08115	N	0.995595	T	0.00012	0.0000	L	0.43646	1.37	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.46190	-0.9209	8	.	.	.	-6.6894	7.7165	0.28708	0.0:0.4866:0.0:0.5134	rs3752109;rs17846501;rs17859570;rs58492417;rs3752109	51	P28698	MZF1_HUMAN	H	51	ENSP00000215057:R51H	.	R	-	2	0	MZF1	63774417	0.000000	0.05858	0.008000	0.14137	0.493000	0.33554	-2.046000	0.01409	-0.298000	0.08921	-0.253000	0.11424	CGC	C|0.795;T|0.205	0.205	strong		0.647	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055	
NACA	4666	hgsc.bcm.edu	37	12	57114307	57114307	+	Missense_Mutation	SNP	A	A	T	rs2958127	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57114307A>T	ENST00000454682.1	-	3	1288	c.1007T>A	c.(1006-1008)gTg>gAg	p.V336E	NACA_ENST00000546392.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.V336E|NACA_ENST00000548563.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000551793.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	336	Pro-rich.		V -> E (in dbSNP:rs2958127). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						AATGGTCTTCACTGTAGGGTC	0.448			T	BCL6	NHL								A|||	3044	0.607827	0.3343	0.6657	5008	,	,		20399	0.7401		0.6252	False		,,,				2504	0.7822				p.V336E		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	NACA_ENST00000550952,caecum,carcinoma,+1,1	NACA	131	1	0			c.T1007A						PASS	.	A	,,,GLU/VAL	1292,1844		271,750,547	69.0	62.0	64.0		,,,1007	-4.8	0.0	12	dbSNP_101	64	4451,2713		1388,1675,519	yes	intron,intron,intron,missense	NACA	NM_001113201.1,NM_001113202.1,NM_005594.4,NM_001113203.2	,,,121	1659,2425,1066	TT,TA,AA		37.8699,41.199,44.2427	,,,benign	,,,336/926	57114307	5743,4557	1568	3582	5150	SO:0001583	missense	4666	exon3			GTCTTCACTGTAG	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.1007T>A	12.37:g.57114307A>T	ENSP00000403817:p.Val336Glu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	37		1313	0.6011904761904762	173	0.3516260162601626	248	0.6850828729281768	427	0.7465034965034965	465	0.6134564643799473	A	13.81	2.347203	0.41599	0.41199	0.621301	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.51325	0.71;0.95	4.09	-4.83	0.03161	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.21225	0.053;0.002	B;B	0.14578	0.011;0.005	T	0.40627	-0.9553	8	0.87932	D	0	.	1.7965	0.03062	0.3004:0.149:0.3915:0.1591	rs2958127;rs58365009;rs2958127	336;336	E9PAV3;F8VU71	.;.	E	336	ENSP00000403817:V336E;ENSP00000448035:V336E	ENSP00000403817:V336E	V	-	2	0	NACA	55400574	0.000000	0.05858	0.000000	0.03702	0.282000	0.26991	-0.114000	0.10757	-0.683000	0.05190	0.254000	0.18369	GTG	A|0.412;T|0.588	0.588	strong		0.448	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
LENG8	114823	hgsc.bcm.edu	37	19	54966557	54966557	+	Missense_Mutation	SNP	G	G	C	rs35061854	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54966557G>C	ENST00000326764.5	+	8	1315	c.836G>C	c.(835-837)cGg>cCg	p.R279P	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	242										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		TCCTCTGCCCGGGGGAACCTG	0.627													G|||	85	0.0169728	0.003	0.0115	5008	,	,		15324	0.0347		0.0268	False		,,,				2504	0.0112				p.R279P		Atlas-SNP	.											.	LENG8	73	.	0			c.G836C						PASS	.	G	PRO/ARG	17,4389	17.9+/-39.9	0,17,2186	45.0	52.0	50.0		836	5.4	0.9	19	dbSNP_126	50	176,8424	63.1+/-125.2	6,164,4130	yes	missense	LENG8	NM_052925.2	103	6,181,6316	CC,CG,GG		2.0465,0.3858,1.4839	probably-damaging	279/801	54966557	193,12813	2203	4300	6503	SO:0001583	missense	114823	exon8			CTGCCCGGGGGAA	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.836G>C	19.37:g.54966557G>C	ENSP00000318374:p.Arg279Pro	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	37	CCDS12894.1	50	0.022893772893772892	4	0.008130081300813009	5	0.013812154696132596	13	0.022727272727272728	28	0.036939313984168866	G	24.7	4.555127	0.86231	0.003858	0.020465	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000439657;ENST00000376526;ENST00000431846	T;T;T;T	0.44482	1.53;0.92;1.5;1.5	5.38	5.38	0.77491	.	0.460029	0.19130	N	0.121950	T	0.18551	0.0445	L	0.51422	1.61	0.80722	D	1	P;D	0.54772	0.943;0.968	P;P	0.49683	0.619;0.614	T	0.15809	-1.0424	10	0.59425	D	0.04	-13.2903	17.0041	0.86388	0.0:0.0:1.0:0.0	rs35061854;rs61146349	279;242	Q96PV6-2;F8W9Q9	.;.	P	279;242;279;242;279	ENSP00000318374:R279P;ENSP00000399507:R279P;ENSP00000365709:R242P;ENSP00000388053:R279P	ENSP00000301196:R242P	R	+	2	0	LENG8	59658369	1.000000	0.71417	0.932000	0.37286	0.926000	0.56050	4.389000	0.59639	2.688000	0.91661	0.655000	0.94253	CGG	G|0.983;C|0.017	0.017	strong		0.627	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	
KIAA0753	9851	hgsc.bcm.edu	37	17	6513329	6513329	+	Missense_Mutation	SNP	G	G	A	rs2304977	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:6513329G>A	ENST00000361413.3	-	9	2055	c.1697C>T	c.(1696-1698)cCa>cTa	p.P566L	KIAA0753_ENST00000572370.1_Missense_Mutation_p.P267L|KIAA0753_ENST00000542606.1_Missense_Mutation_p.P267L|KIAA0753_ENST00000589033.1_Missense_Mutation_p.P22L	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	566			P -> L (in dbSNP:rs2304977).			centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		AGGAGACGCTGGTGGGGATGT	0.473													G|||	1361	0.271765	0.0303	0.3876	5008	,	,		16778	0.3562		0.3459	False		,,,				2504	0.3528				p.P566L		Atlas-SNP	.											.	KIAA0753	63	.	0			c.C1697T						PASS	.	G	LEU/PRO	325,3485		15,295,1595	155.0	154.0	154.0		1697	4.2	1.0	17	dbSNP_100	154	3087,5129		548,1991,1569	yes	missense	KIAA0753	NM_014804.2	98	563,2286,3164	AA,AG,GG		37.573,8.5302,28.3719	probably-damaging	566/968	6513329	3412,8614	1905	4108	6013	SO:0001583	missense	9851	exon9			GACGCTGGTGGGG		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.1697C>T	17.37:g.6513329G>A	ENSP00000355250:p.Pro566Leu	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	281	150	0.533808	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	601	0.2751831501831502	20	0.04065040650406504	148	0.4088397790055249	178	0.3111888111888112	255	0.33641160949868076	G	18.74	3.688818	0.68271	0.085302	0.37573	ENSG00000198920	ENST00000361413;ENST00000542606;ENST00000542826	D;D	0.85702	-2.02;-2.02	5.14	4.15	0.48705	.	0.112488	0.64402	D	0.000007	T	0.00012	0.0000	M	0.78916	2.43	0.20563	P	0.99988895	D	0.57257	0.979	P	0.54270	0.747	T	0.01409	-1.1362	9	0.27785	T	0.31	-9.5145	11.2919	0.49256	0.0:0.0:0.8174:0.1826	rs2304977;rs17731495;rs52796942;rs60289833;rs2304977	566	Q2KHM9	K0753_HUMAN	L	566;267;22	ENSP00000355250:P566L;ENSP00000444634:P267L	ENSP00000355250:P566L	P	-	2	0	KIAA0753	6454053	0.999000	0.42202	0.998000	0.56505	0.886000	0.51366	2.037000	0.41174	1.275000	0.44379	0.650000	0.86243	CCA	G|0.714;A|0.286	0.286	strong		0.473	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
UBAP2L	9898	hgsc.bcm.edu	37	1	154209591	154209591	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:154209591T>C	ENST00000361546.2	+	7	724	c.682T>C	c.(682-684)Ttt>Ctt	p.F228L	UBAP2L_ENST00000428931.1_Missense_Mutation_p.F228L|UBAP2L_ENST00000343815.6_Missense_Mutation_p.F228L|UBAP2L_ENST00000271877.7_Missense_Mutation_p.F239L			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	228					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CACTGGCCACTTTGAACCAGA	0.393																																					p.F228L		Atlas-SNP	.											UBAP2L_ENST00000343815,right_lower_lobe,carcinoma,-2,2	UBAP2L	197	2	0			c.T682C						scavenged	.						131.0	108.0	116.0					1																	154209591		2203	4300	6503	SO:0001583	missense	9898	exon8			GGCCACTTTGAAC	BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.682T>C	1.37:g.154209591T>C	ENSP00000355343:p.Phe228Leu	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	344	6	0.0174419	NM_001127320	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	37	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.256913	0.39896	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000271877;ENST00000412596;ENST00000368504;ENST00000437652;ENST00000456325;ENST00000361546	T;T;T;T;T;T;T;T	0.40756	2.88;2.88;2.85;1.05;1.03;1.02;1.02;2.88	5.68	5.68	0.88126	.	0.328747	0.34245	N	0.004134	T	0.08758	0.0217	N	0.02011	-0.69	0.29370	N	0.864099	B;B;B;B;B	0.15719	0.0;0.014;0.001;0.001;0.0	B;B;B;B;B	0.20955	0.001;0.032;0.001;0.001;0.001	T	0.15093	-1.0449	10	0.27082	T	0.32	-8.3731	15.1058	0.72322	0.0:0.0:0.0:1.0	.	142;239;221;228;228	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	L	228;228;239;228;239;221;228;228	ENSP00000345308:F228L;ENSP00000389445:F228L;ENSP00000271877:F239L;ENSP00000389052:F228L;ENSP00000357490:F239L;ENSP00000389717:F221L;ENSP00000415310:F228L;ENSP00000355343:F228L	ENSP00000271877:F239L	F	+	1	0	UBAP2L	152476215	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.845000	0.55880	2.161000	0.67846	0.482000	0.46254	TTT	.	.	none		0.393	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847	
USP3	9960	hgsc.bcm.edu	37	15	63855190	63855190	+	Silent	SNP	G	G	A	rs61751106	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:63855190G>A	ENST00000380324.3	+	8	873	c.744G>A	c.(742-744)aaG>aaA	p.K248K	USP3_ENST00000559711.1_Silent_p.K159K|USP3_ENST00000539772.1_5'UTR|USP3_ENST00000540797.1_Silent_p.K204K|USP3-AS1_ENST00000559357.1_RNA|USP3-AS1_ENST00000560350.1_RNA|USP3_ENST00000536001.1_3'UTR|USP3_ENST00000558285.1_Silent_p.K231K|USP3_ENST00000268049.7_Silent_p.K226K|USP3-AS1_ENST00000559861.1_RNA	NM_006537.3	NP_006528.2	Q9Y6I4	UBP3_HUMAN	ubiquitin specific peptidase 3	248	USP.				DNA repair (GO:0006281)|histone deubiquitination (GO:0016578)|mitotic cell cycle (GO:0000278)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear chromatin (GO:0000790)	histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(7)|lung(4)	14				GBM - Glioblastoma multiforme(80;0.0187)		TTGTTTGGAAGATTATGCCAA	0.338													G|||	26	0.00519169	0.0008	0.0086	5008	,	,		18673	0.0		0.0119	False		,,,				2504	0.0072				p.K248K		Atlas-SNP	.											.	USP3	37	.	0			c.G744A						PASS	.	G		11,4395	16.8+/-37.8	0,11,2192	111.0	112.0	111.0		744	4.0	1.0	15	dbSNP_129	111	133,8467	62.1+/-124.0	2,129,4169	no	coding-synonymous	USP3	NM_006537.2		2,140,6361	AA,AG,GG		1.5465,0.2497,1.1072		248/521	63855190	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	9960	exon8			TTGGAAGATTATG	AF073344	CCDS32265.1, CCDS58370.1	15q22.3	2008-04-11	2005-08-08			ENSG00000140455		"""Ubiquitin-specific peptidases"""	12626	protein-coding gene	gene with protein product		604728	"""ubiquitin specific protease 3"""			12838346	Standard	NM_006537		Approved		uc002amf.4	Q9Y6I4		ENST00000380324.3:c.744G>A	15.37:g.63855190G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_006537	B4DVU5|F5H1A6|Q8WVD0	Silent	SNP	ENST00000380324.3	37	CCDS32265.1																																																																																			G|0.990;A|0.010	0.010	strong		0.338	USP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417773.1		
PCDHB15	56121	hgsc.bcm.edu	37	5	140626767	140626767	+	Silent	SNP	C	C	T	rs3096081	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140626767C>T	ENST00000231173.3	+	1	1621	c.1621C>T	c.(1621-1623)Ctg>Ttg	p.L541L		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	541	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTCCCGGCGCTGAGCAGCGA	0.687													C|||	1081	0.215855	0.4213	0.1499	5008	,	,		15746	0.0992		0.1571	False		,,,				2504	0.1656				p.L541L		Atlas-SNP	.											PCDHB15,NS,carcinoma,-2,1	PCDHB15	138	1	0			c.C1621T						PASS	.	C		1704,2702	483.2+/-359.6	349,1006,848	42.0	53.0	49.0		1621	4.4	1.0	5	dbSNP_103	49	1523,7075	273.5+/-290.7	158,1207,2934	no	coding-synonymous	PCDHB15	NM_018935.2		507,2213,3782	TT,TC,CC		17.7134,38.6745,24.8154		541/788	140626767	3227,9777	2203	4299	6502	SO:0001819	synonymous_variant	56121	exon1			CCGGCGCTGAGCA	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1621C>T	5.37:g.140626767C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			C|0.770;T|0.230	0.230	strong		0.687	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
XRRA1	143570	hgsc.bcm.edu	37	11	74559446	74559446	+	Missense_Mutation	SNP	G	G	C	rs4944960	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:74559446G>C	ENST00000340360.6	-	15	1749	c.1418C>G	c.(1417-1419)aCg>aGg	p.T473R	RN7SL239P_ENST00000490061.2_RNA|XRRA1_ENST00000321448.8_Missense_Mutation_p.T198R|XRRA1_ENST00000527087.1_Missense_Mutation_p.T386R	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						CTTGGTTGTCGTCATGCGCGG	0.527													G|||	1417	0.282947	0.1452	0.4885	5008	,	,		20319	0.5089		0.2843	False		,,,				2504	0.089				p.T473R		Atlas-SNP	.											.	XRRA1	46	.	0			c.C1418G						PASS	.	G	ARG/THR	663,3461		68,527,1467	53.0	58.0	57.0		1418	-4.1	0.0	11	dbSNP_111	57	2197,6165		288,1621,2272	yes	missense	XRRA1	NM_182969.1	71	356,2148,3739	CC,CG,GG		26.2736,16.0766,22.9057	benign	473/793	74559446	2860,9626	2062	4181	6243	SO:0001583	missense	143570	exon15			GTTGTCGTCATGC	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1418C>G	11.37:g.74559446G>C	ENSP00000339918:p.Thr473Arg	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	137	50	0.364964	NM_182969		Missense_Mutation	SNP	ENST00000340360.6	37	CCDS44680.1	748	0.3424908424908425	67	0.13617886178861788	161	0.4447513812154696	301	0.5262237762237763	219	0.28891820580474936	G	13.66	2.302324	0.40694	0.160766	0.262736	ENSG00000166435	ENST00000340360;ENST00000321448;ENST00000344880;ENST00000398418;ENST00000527087	T;T;T	0.50813	0.76;1.48;0.73	3.91	-4.08	0.03963	.	1.344830	0.04736	N	0.421977	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	P;D;P;P;P	0.59357	0.691;0.985;0.897;0.772;0.772	B;P;B;B;B	0.55999	0.171;0.789;0.417;0.424;0.424	T	0.44544	-0.9321	9	0.12103	T	0.63	-0.0273	0.2488	0.00202	0.3433:0.1407:0.2311:0.2849	rs4944960;rs52834190;rs57640924;rs4944960	473;29;386;417;459	Q6P2D8;E9PP69;Q6P2D8-2;Q6P2D8-4;Q6P2D8-3	XRRA1_HUMAN;.;.;.;.	R	473;198;459;417;386	ENSP00000339918:T473R;ENSP00000319303:T198R;ENSP00000435838:T386R	ENSP00000319303:T198R	T	-	2	0	XRRA1	74237094	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.008000	0.12788	-0.876000	0.04017	0.591000	0.81541	ACG	G|0.659;C|0.341	0.341	strong		0.527	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969	
ZSCAN20	7579	hgsc.bcm.edu	37	1	33957130	33957130	+	Silent	SNP	C	C	A	rs3795419	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:33957130C>A	ENST00000361328.3	+	6	1425	c.1272C>A	c.(1270-1272)gcC>gcA	p.A424A	ZSCAN20_ENST00000373413.2_Silent_p.A370A	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	424					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A424A(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CAGGAGAGGCCGTGGCACTTC	0.612													C|||	974	0.194489	0.0204	0.2104	5008	,	,		17850	0.3651		0.162	False		,,,				2504	0.2761				p.A424A		Atlas-SNP	.											ZSCAN20,NS,carcinoma,0,1	ZSCAN20	107	1	1	Substitution - coding silent(1)	stomach(1)	c.C1272A						scavenged	.	C		175,3689		2,171,1759	59.0	66.0	64.0		1272	-8.6	0.0	1	dbSNP_107	64	1422,6836		136,1150,2843	no	coding-synonymous	ZSCAN20	NM_145238.3		138,1321,4602	AA,AC,CC		17.2197,4.529,13.1744		424/1044	33957130	1597,10525	1932	4129	6061	SO:0001819	synonymous_variant	7579	exon6			AGAGGCCGTGGCA	X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"""-"", ""Zinc fingers, C2H2-type"""	13093	protein-coding gene	gene with protein product		611315	"""zinc finger protein 31 (KOX 29)"", ""zinc finger protein 31"""	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.1272C>A	1.37:g.33957130C>A		Somatic	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Silent	SNP	ENST00000361328.3	37	CCDS41300.1																																																																																			C|0.824;A|0.176	0.176	strong		0.612	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238	
BACE2	25825	hgsc.bcm.edu	37	21	42622786	42622786	+	Silent	SNP	C	C	T	rs1046210	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:42622786C>T	ENST00000330333.6	+	7	1555	c.1092C>T	c.(1090-1092)gaC>gaT	p.D364D	BACE2_ENST00000466122.1_3'UTR|BACE2_ENST00000328735.6_Silent_p.D364D|BACE2_ENST00000347667.5_Intron	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2	364					membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				ACCTGAGAGACGAGAACTCCA	0.463													C|||	2098	0.41893	0.0764	0.5403	5008	,	,		22321	0.6865		0.3797	False		,,,				2504	0.5603				p.D364D		Atlas-SNP	.											.	BACE2	45	.	0			c.C1092T						PASS	.	C	,,	568,3838	253.0+/-259.1	53,462,1688	109.0	90.0	97.0		1092,,1092	-10.5	0.1	21	dbSNP_86	97	3351,5249	498.8+/-374.8	641,2069,1590	no	coding-synonymous,intron,coding-synonymous	BACE2	NM_012105.3,NM_138991.1,NM_138992.1	,,	694,2531,3278	TT,TC,CC		38.9651,12.8915,30.1322	,,	364/519,,364/397	42622786	3919,9087	2203	4300	6503	SO:0001819	synonymous_variant	25825	exon7			GAGAGACGAGAAC	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.1092C>T	21.37:g.42622786C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	150	67	0.446667	NM_138992	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Silent	SNP	ENST00000330333.6	37	CCDS13668.1																																																																																			C|0.656;G|0.000	.	strong		0.463	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1		
HAND1	9421	hgsc.bcm.edu	37	5	153857101	153857101	+	Silent	SNP	A	A	C	rs34402828	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:153857101A>C	ENST00000231121.2	-	1	723	c.468T>G	c.(466-468)tcT>tcG	p.S156S		NM_004821.2	NP_004812.1	O96004	HAND1_HUMAN	heart and neural crest derivatives expressed 1	156					angiogenesis (GO:0001525)|blastocyst development (GO:0001824)|cardiac left ventricle formation (GO:0003218)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cartilage morphogenesis (GO:0060536)|embryonic heart tube development (GO:0035050)|embryonic heart tube formation (GO:0003144)|heart development (GO:0007507)|heart looping (GO:0001947)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)|trophoblast giant cell differentiation (GO:0060707)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			CGGGATCGCCAGACTGTGCAT	0.612													A|||	118	0.0235623	0.003	0.0519	5008	,	,		18274	0.0		0.0626	False		,,,				2504	0.0153				p.S156S		Atlas-SNP	.											.	HAND1	21	.	0			c.T468G						PASS	.	A		48,4358	50.2+/-85.5	0,48,2155	157.0	135.0	142.0		468	-2.4	1.0	5	dbSNP_126	142	552,8048	151.3+/-206.1	19,514,3767	no	coding-synonymous	HAND1	NM_004821.2		19,562,5922	CC,CA,AA		6.4186,1.0894,4.6133		156/216	153857101	600,12406	2203	4300	6503	SO:0001819	synonymous_variant	9421	exon1			ATCGCCAGACTGT	AF061756	CCDS4327.1	5q33	2013-05-21			ENSG00000113196	ENSG00000113196		"""Basic helix-loop-helix proteins"""	4807	protein-coding gene	gene with protein product		602406				9337404, 9931445	Standard	NM_004821		Approved	eHand, Thing1, Hxt, bHLHa27	uc003lvn.3	O96004	OTTHUMG00000130193	ENST00000231121.2:c.468T>G	5.37:g.153857101A>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	237	100	0.421941	NM_004821		Silent	SNP	ENST00000231121.2	37	CCDS4327.1																																																																																			A|0.958;C|0.042	0.042	strong		0.612	HAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252511.1	NM_004821	
GBP4	115361	hgsc.bcm.edu	37	1	89652072	89652072	+	Missense_Mutation	SNP	C	C	T	rs561037|rs386633303	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89652072C>T	ENST00000355754.6	-	10	1748	c.1651G>A	c.(1651-1653)Gag>Aag	p.E551K	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	551			E -> G (in dbSNP:rs561042).|E -> K (in dbSNP:rs561037).	LEE -> MER (in Ref. 1; AAL02054 and 3; BAC85144). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		TCCCTTTCCTCCTCCAACTTC	0.493													C|||	1797	0.358826	0.1445	0.3141	5008	,	,		19123	0.3978		0.4891	False		,,,				2504	0.5061				p.E551K		Atlas-SNP	.											GBP4,NS,carcinoma,+2,1	GBP4	89	1	0			c.G1651A						PASS	.	C	LYS/GLU	21,4385		1,19,2183	193.0	135.0	155.0		1651	-4.4	0.0	1	dbSNP_83	155	118,8482		8,102,4190	yes	missense	GBP4	NM_052941.4	56	9,121,6373	TT,TC,CC		1.3721,0.4766,1.0687	benign	551/641	89652072	139,12867	2203	4300	6503	SO:0001583	missense	115361	exon10			TTTCCTCCTCCAA	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1651G>A	1.37:g.89652072C>T	ENSP00000359490:p.Glu551Lys	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	143	139	0.972028	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	.	.	.	.	.	.	.	.	.	.	C	5.059	0.196600	0.09599	0.004766	0.013721	ENSG00000162654	ENST00000355754	T	0.01981	4.52	4.29	-4.45	0.03546	Guanylate-binding protein, C-terminal (3);	1.061500	0.07205	N	0.858069	T	0.00384	0.0012	N	0.13098	0.295	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.47355	-0.9124	10	0.23891	T	0.37	.	1.5862	0.02644	0.141:0.322:0.2889:0.2481	rs561037;rs34980170;rs52804413;rs561037	551	Q96PP9	GBP4_HUMAN	K	551	ENSP00000359490:E551K	ENSP00000359490:E551K	E	-	1	0	GBP4	89424660	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.422000	0.07043	-0.652000	0.05408	-3.050000	0.00069	GAG	C|0.633;T|0.367	0.367	strong		0.493	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
OR4A15	81328	hgsc.bcm.edu	37	11	55136157	55136157	+	Silent	SNP	C	C	T	rs147678504	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55136157C>T	ENST00000314706.3	+	1	798	c.798C>T	c.(796-798)taC>taT	p.Y266Y		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						AAGCTTTCTACACCTGTGCAT	0.423													.|||	7	0.00139776	0.0008	0.0	5008	,	,		20139	0.0		0.005	False		,,,				2504	0.001				p.Y266Y		Atlas-SNP	.											.	OR4A15	161	.	0			c.C798T						PASS	.	C		2,4400		0,2,2199	211.0	189.0	197.0		798	-0.7	0.0	11	dbSNP_134	197	29,8563		0,29,4267	no	coding-synonymous	OR4A15	NM_001005275.1		0,31,6466	TT,TC,CC		0.3375,0.0454,0.2386		266/345	55136157	31,12963	2201	4296	6497	SO:0001819	synonymous_variant	81328	exon1			TTTCTACACCTGT	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"""GPCR / Class A : Olfactory receptors"""	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.798C>T	11.37:g.55136157C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	236	107	0.45339	NM_001005275	Q6IFL4|Q96R65	Silent	SNP	ENST00000314706.3	37	CCDS31500.1																																																																																			C|0.997;T|0.003	0.003	strong		0.423	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275	
ITGB4	3691	hgsc.bcm.edu	37	17	73750859	73750859	+	Silent	SNP	C	C	G	rs8669	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73750859C>G	ENST00000200181.3	+	34	4708	c.4521C>G	c.(4519-4521)ccC>ccG	p.P1507P	ITGB4_ENST00000339591.3_Silent_p.P1437P|ITGB4_ENST00000449880.2_Silent_p.P1437P|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000450894.3_Silent_p.P1437P|ITGB4_ENST00000579662.1_Silent_p.P1437P	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1507					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCACACTGCCCAGGGACTACT	0.622													C|||	1889	0.377196	0.0756	0.4539	5008	,	,		19393	0.5149		0.4732	False		,,,				2504	0.4898				p.P1507P		Atlas-SNP	.											.	ITGB4	165	.	0			c.C4521G						PASS	.	C	,,	653,3753	279.9+/-275.1	55,543,1605	316.0	189.0	232.0		4521,4311,4311	4.4	1.0	17	dbSNP_52	232	4101,4499	561.4+/-387.8	957,2187,1156	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	,,	1012,2730,2761	GG,GC,CC		47.686,14.8207,36.5524	,,	1507/1823,1437/1806,1437/1753	73750859	4754,8252	2203	4300	6503	SO:0001819	synonymous_variant	3691	exon34			ACTGCCCAGGGAC		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.4521C>G	17.37:g.73750859C>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	166	84	0.506024	NM_000213	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	37	CCDS11727.1																																																																																			C|0.640;G|0.360	0.360	strong		0.622	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
KDM3B	51780	hgsc.bcm.edu	37	5	137754808	137754808	+	Missense_Mutation	SNP	G	G	A	rs7706614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:137754808G>A	ENST00000314358.5	+	14	3802	c.3602G>A	c.(3601-3603)aGc>aAc	p.S1201N	KDM3B_ENST00000508386.1_3'UTR|KDM3B_ENST00000394866.1_Missense_Mutation_p.S857N|KDM3B_ENST00000542866.1_Missense_Mutation_p.S233N	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1201			S -> N (in dbSNP:rs7706614).		chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						GCATCAAATAGCAATAGTGAA	0.532													G|||	299	0.0597045	0.0764	0.0187	5008	,	,		17731	0.0208		0.0318	False		,,,				2504	0.135				p.S1201N		Atlas-SNP	.											.	KDM3B	177	.	0			c.G3602A						PASS	.	G	ASN/SER	242,4164	143.1+/-178.2	8,226,1969	83.0	78.0	79.0		3602	5.6	1.0	5	dbSNP_116	79	279,8321	104.8+/-165.8	4,271,4025	yes	missense	KDM3B	NM_016604.3	46	12,497,5994	AA,AG,GG		3.2442,5.4925,4.0058	benign	1201/1762	137754808	521,12485	2203	4300	6503	SO:0001583	missense	51780	exon14			CAAATAGCAATAG	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"""Chromatin-modifying enzymes / K-demethylases"""	1337	protein-coding gene	gene with protein product		609373	"""chromosome 5 open reading frame 7"", ""jumonji domain containing 1B"""	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.3602G>A	5.37:g.137754808G>A	ENSP00000326563:p.Ser1201Asn	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	289	142	0.491349	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	37	CCDS34242.1	84	0.038461538461538464	39	0.07926829268292683	6	0.016574585635359115	10	0.017482517482517484	29	0.03825857519788918	G	13.74	2.328710	0.41197	0.054925	0.032442	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	T;T;T	0.71341	0.03;-0.56;-0.54	5.63	5.63	0.86233	.	0.216515	0.56097	D	0.000039	T	0.06050	0.0157	L	0.27053	0.805	0.39818	D	0.972792	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.13791	-1.0496	10	0.19147	T	0.46	-5.3037	13.3783	0.60752	0.0814:0.0:0.9186:0.0	rs7706614;rs17460129;rs56548578;rs57723304;rs7706614	857;1201	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	N	1201;991;857;233	ENSP00000326563:S1201N;ENSP00000378335:S857N;ENSP00000439462:S233N	ENSP00000326563:S1201N	S	+	2	0	KDM3B	137782707	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.336000	0.52113	2.665000	0.90641	0.650000	0.86243	AGC	G|0.953;A|0.047	0.047	strong		0.532	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
AGL	178	hgsc.bcm.edu	37	1	100316589	100316589	+	Splice_Site	SNP	A	A	G	rs2307130	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:100316589A>G	ENST00000370165.3	+	2	130		c.e2-1		AGL_ENST00000294724.4_5'UTR|AGL_ENST00000361302.3_5'UTR|AGL_ENST00000361915.3_5'UTR|AGL_ENST00000370163.3_5'UTR|AGL_ENST00000370161.2_5'Flank	NM_000644.2	NP_000635.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase						carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		CAAATCCTCTAGAAGCCAAAA	0.353													A|||	2139	0.427117	0.2231	0.4726	5008	,	,		16810	0.5198		0.4573	False		,,,				2504	0.544				.		Atlas-SNP	.											.	AGL	137	.	0			.						PASS	.	A	,,,,	1222,3184	418.5+/-338.3	165,892,1146	110.0	120.0	117.0		,,,,	2.6	0.3	1	dbSNP_100	117	4185,4415	567.4+/-388.8	1020,2145,1135	yes	utr-5,utr-5,utr-5,splice-3,utr-5	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000646.2	,,,,	1185,3037,2281	GG,GA,AA		48.6628,27.7349,41.5731	,,,,	,,,,	100316589	5407,7599	2203	4300	6503	SO:0001630	splice_region_variant	178	.			TCCTCTAGAAGCC	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000370165.3:c.-8-1A>G	1.37:g.100316589A>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	147	66	0.44898	.	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Splice_Site	SNP	ENST00000370165.3	37	CCDS759.1																																																																																			A|0.571;G|0.429	0.429	strong		0.353	AGL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029776.1	NM_000028	Intron
KANSL1	284058	hgsc.bcm.edu	37	17	44111613	44111613	+	Silent	SNP	A	A	G	rs17574604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44111613A>G	ENST00000262419.6	-	11	3050	c.2580T>C	c.(2578-2580)ttT>ttC	p.F860F	KANSL1_ENST00000574590.1_Silent_p.F860F|KANSL1_ENST00000575318.1_Silent_p.F796F|KANSL1_ENST00000572904.1_Silent_p.F860F|KANSL1_ENST00000432791.1_Silent_p.F860F|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000393476.3_Silent_p.F154F	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	860	Required for activation of KAT8 histone acetyltransferase activity.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.F860F(2)									TGTTAATATCAAATGAGCTCT	0.398													G|||	432	0.086262	0.0151	0.1571	5008	,	,		21592	0.001		0.2406	False		,,,				2504	0.0613				p.F860F		Atlas-SNP	.											KIAA1267,NS,carcinoma,0,1	.	.	1	2	Substitution - coding silent(2)	prostate(2)	c.T2580C						PASS	.	G	,,	202,4204	807.7+/-415.9	5,192,2006	187.0	157.0	167.0		2577,2580,2580	-6.8	0.2	17	dbSNP_123	167	1928,6672	726.2+/-406.6	220,1488,2592	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	225,1680,4598	GG,GA,AA		22.4186,4.5847,16.3771	,,	859/1105,860/1106,860/1106	44111613	2130,10876	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon11			AATATCAAATGAG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2580T>C	17.37:g.44111613A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	199	90	0.452261	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.853;G|0.147	0.147	strong		0.398	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
GPR55	9290	hgsc.bcm.edu	37	2	231775297	231775297	+	Silent	SNP	T	T	G	rs1992186	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:231775297T>G	ENST00000392040.1	-	2	573	c.381A>C	c.(379-381)ctA>ctC	p.L127L	AC012507.4_ENST00000454890.1_RNA|GPR55_ENST00000392039.2_Silent_p.L127L	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	127					activation of phospholipase C activity (GO:0007202)|bone resorption (GO:0045453)|cannabinoid signaling pathway (GO:0038171)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho protein signal transduction (GO:0035025)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|G-protein coupled receptor activity (GO:0004930)			endometrium(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)		GGCTCACCAGTAGCGGGTAAC	0.567													G|||	2485	0.496206	0.9153	0.3199	5008	,	,		21085	0.2679		0.3489	False		,,,				2504	0.4417				p.L127L		Atlas-SNP	.											.	GPR55	46	.	0			c.A381C						PASS	.	G		3603,803	312.5+/-292.6	1482,639,82	53.0	46.0	48.0		381	-1.1	0.3	2	dbSNP_92	48	3286,5314	630.7+/-398.4	631,2024,1645	no	coding-synonymous	GPR55	NM_005683.3		2113,2663,1727	GG,GT,TT		38.2093,18.2251,47.0321		127/320	231775297	6889,6117	2203	4300	6503	SO:0001819	synonymous_variant	9290	exon2			CACCAGTAGCGGG	AF096786	CCDS2480.1	2q37	2012-08-21			ENSG00000135898	ENSG00000135898		"""GPCR / Class A : Orphans"""	4511	protein-coding gene	gene with protein product		604107				9931487	Standard	NM_005683		Approved		uc002vrg.3	Q9Y2T6	OTTHUMG00000133224	ENST00000392040.1:c.381A>C	2.37:g.231775297T>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_005683	Q8N580	Silent	SNP	ENST00000392040.1	37	CCDS2480.1																																																																																			T|0.502;G|0.498	0.498	strong		0.567	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683	
POLD3	10714	hgsc.bcm.edu	37	11	74347244	74347244	+	Silent	SNP	C	C	T	rs35745457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:74347244C>T	ENST00000263681.2	+	11	1251	c.1122C>T	c.(1120-1122)agC>agT	p.S374S	POLD3_ENST00000527458.1_Silent_p.S335S|POLD3_ENST00000532497.1_Silent_p.S268S	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	374					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					CCTTTTAGAGCTCAAGTGGAG	0.343													C|||	20	0.00399361	0.0015	0.0014	5008	,	,		20618	0.0		0.0159	False		,,,				2504	0.001				p.S374S		Atlas-SNP	.											.	POLD3	87	.	0			c.C1122T						PASS	.	C		9,4391	15.5+/-35.6	0,9,2191	70.0	67.0	68.0		1122	2.0	1.0	11	dbSNP_126	68	110,8476	57.9+/-119.4	1,108,4184	no	coding-synonymous	POLD3	NM_006591.1		1,117,6375	TT,TC,CC		1.2812,0.2045,0.9164		374/467	74347244	119,12867	2200	4293	6493	SO:0001819	synonymous_variant	10714	exon11			TTAGAGCTCAAGT	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.1122C>T	11.37:g.74347244C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	159	73	0.459119	NM_006591	B7ZAI6|Q32MZ9|Q32N00	Silent	SNP	ENST00000263681.2	37	CCDS8233.1	13	0.005952380952380952	1	0.0020325203252032522	0	0.0	0	0.0	12	0.0158311345646438	C	12.52	1.961262	0.34565	0.002045	0.012812	ENSG00000077514	ENST00000524752	.	.	.	5.92	1.96	0.26148	.	.	.	.	.	T	0.41465	0.1160	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37033	-0.9723	4	.	.	.	-38.8421	8.8571	0.35234	0.0:0.7328:0.0:0.2672	rs35745457;rs61749198	.	.	.	V	98	.	.	A	+	2	0	POLD3	74024892	0.626000	0.27120	0.979000	0.43373	0.990000	0.78478	0.375000	0.20518	0.113000	0.18004	0.561000	0.74099	GCT	C|0.990;T|0.010	0.010	strong		0.343	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591	
HEXDC	284004	hgsc.bcm.edu	37	17	80391684	80391684	+	Missense_Mutation	SNP	A	A	G	rs4789773	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:80391684A>G	ENST00000327949.9	+	4	444	c.433A>G	c.(433-435)Atc>Gtc	p.I145V	HEXDC_ENST00000337014.6_Missense_Mutation_p.I145V|HEXDC_ENST00000577944.1_Missense_Mutation_p.I145V			Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	145			I -> V (in dbSNP:rs4789773).		carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	beta-N-acetylhexosaminidase activity (GO:0004563)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GCGGCTGCACATCGGGTGTGA	0.602													G|||	2821	0.563299	0.5008	0.6239	5008	,	,		16497	0.9018		0.3678	False		,,,				2504	0.4571				p.I145V		Atlas-SNP	.											.	HEXDC	43	.	0			c.A433G						PASS	.	G	VAL/ILE	1839,2043		454,931,556	24.0	28.0	26.0		433	0.0	0.7	17	dbSNP_111	26	2796,5466		485,1826,1820	yes	missense	HEXDC	NM_173620.2	29	939,2757,2376	GG,GA,AA		33.8417,47.3725,38.167	benign	145/586	80391684	4635,7509	1941	4131	6072	SO:0001583	missense	284004	exon5			CTGCACATCGGGT	AK074405	CCDS42402.1	17q25.3	2011-12-19			ENSG00000169660	ENSG00000169660			26307	protein-coding gene	gene with protein product						12477932	Standard	NM_173620		Approved	FLJ23825	uc002kev.4	Q8WVB3		ENST00000327949.9:c.433A>G	17.37:g.80391684A>G	ENSP00000332634:p.Ile145Val	Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	297	137	0.461279	NM_173620	B7UUP6|Q8IYN4|Q8TE81	Missense_Mutation	SNP	ENST00000327949.9	37		1231	0.5636446886446886	237	0.4817073170731707	215	0.5939226519337016	517	0.9038461538461539	262	0.34564643799472294	G	4.098	0.016250	0.07959	0.473725	0.338417	ENSG00000169660	ENST00000337014;ENST00000327949	D;D	0.91521	-2.86;-2.86	5.3	0.0361	0.14190	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);	0.267428	0.41712	N	0.000837	T	0.00012	0.0000	M	0.62016	1.91	0.42985	P	0.005522000000000027	B;B	0.24576	0.001;0.106	B;B	0.31869	0.012;0.137	T	0.39272	-0.9622	9	0.37606	T	0.19	-14.6934	10.9334	0.47230	0.5838:0.0:0.4162:0.0	rs4789773;rs11538532;rs57504807;rs4789773	145;145	Q8WVB3;Q8WVB3-2	HEXDC_HUMAN;.	V	145	ENSP00000337854:I145V;ENSP00000332634:I145V	ENSP00000332634:I145V	I	+	1	0	HEXDC	77984973	0.949000	0.32298	0.740000	0.30986	0.008000	0.06430	0.196000	0.17176	-0.641000	0.05487	-0.971000	0.02607	ATC	A|0.477;G|0.523	0.523	strong		0.602	HEXDC-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000443513.1	NM_173620	
SERPINB10	5273	hgsc.bcm.edu	37	18	61602360	61602360	+	Missense_Mutation	SNP	G	G	A	rs35453062	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:61602360G>A	ENST00000238508.3	+	8	1137	c.1078G>A	c.(1078-1080)Gat>Aat	p.D360N	AC009802.1_ENST00000599868.1_Intron	NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	360			D -> N (in dbSNP:rs35453062). {ECO:0000269|PubMed:15489334}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				GAGTGAGATAGATATACGAAT	0.383													G|||	142	0.0283546	0.0023	0.0605	5008	,	,		22299	0.0		0.0835	False		,,,				2504	0.0133				p.D360N		Atlas-SNP	.											.	SERPINB10	53	.	0			c.G1078A						PASS	.	G	ASN/ASP	71,4335	64.7+/-102.0	0,71,2132	128.0	122.0	124.0		1078	-10.1	0.0	18	dbSNP_126	124	872,7728	196.8+/-241.6	38,796,3466	yes	missense	SERPINB10	NM_005024.1	23	38,867,5598	AA,AG,GG		10.1395,1.6114,7.2505		360/398	61602360	943,12063	2203	4300	6503	SO:0001583	missense	5273	exon7			GAGATAGATATAC	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.1078G>A	18.37:g.61602360G>A	ENSP00000238508:p.Asp360Asn	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	138	57	0.413043	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	94	0.04304029304029304	3	0.006097560975609756	30	0.08287292817679558	0	0.0	61	0.08047493403693931	G	0.105	-1.147125	0.01714	0.016114	0.101395	ENSG00000242550	ENST00000238508	D	0.82255	-1.59	5.65	-10.1	0.00402	Serpin domain (3);	1.938390	0.01917	N	0.040208	T	0.02533	0.0077	N	0.04320	-0.23	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28427	-1.0044	10	0.12430	T	0.62	.	4.2523	0.10700	0.4435:0.079:0.3531:0.1244	rs35453062;rs61751999	360	P48595	SPB10_HUMAN	N	360	ENSP00000238508:D360N	ENSP00000238508:D360N	D	+	1	0	SERPINB10	59753340	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.530000	0.02221	-1.532000	0.01747	-0.794000	0.03295	GAT	G|0.938;A|0.062	0.062	strong		0.383	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
CDC42BPG	55561	hgsc.bcm.edu	37	11	64606177	64606177	+	Silent	SNP	C	C	T	rs653343	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64606177C>T	ENST00000342711.5	-	8	1073	c.1074G>A	c.(1072-1074)ggG>ggA	p.G358G		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						TGTCCATGGGCCCCCGCAGCT	0.612													C|||	1343	0.268171	0.2829	0.366	5008	,	,		16489	0.4544		0.1233	False		,,,				2504	0.136				p.G358G		Atlas-SNP	.											CDC42BPG_ENST00000342711,NS,carcinoma,-1,1	CDC42BPG	101	1	0			c.G1074A						PASS	.	C		1122,3280	398.5+/-330.9	132,858,1211	69.0	69.0	69.0		1074	-3.0	0.0	11	dbSNP_83	69	821,7773	190.7+/-237.1	44,733,3520	no	coding-synonymous	CDC42BPG	NM_017525.2		176,1591,4731	TT,TC,CC		9.5532,25.4884,14.9508		358/1552	64606177	1943,11053	2201	4297	6498	SO:0001819	synonymous_variant	55561	exon8			CATGGGCCCCCGC	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.1074G>A	11.37:g.64606177C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	87	54	0.62069	NM_017525		Silent	SNP	ENST00000342711.5	37	CCDS31601.1																																																																																			C|0.813;T|0.187	0.187	strong		0.612	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	
SLC9A7	84679	hgsc.bcm.edu	37	X	46472826	46472826	+	Silent	SNP	G	G	A	rs3208940	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:46472826G>A	ENST00000328306.4	-	16	1849	c.1824C>T	c.(1822-1824)taC>taT	p.Y608Y	SLC9A7_ENST00000464933.1_5'UTR	NM_001257291.1|NM_032591.2	NP_001244220.1|NP_115980.1	Q96T83	SL9A7_HUMAN	solute carrier family 9, subfamily A (NHE7, cation proton antiporter 7), member 7	608					ion transport (GO:0006811)|potassium ion transmembrane transport (GO:0071805)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)	potassium:proton antiporter activity (GO:0015386)|protein homodimerization activity (GO:0042803)|sodium:proton antiporter activity (GO:0015385)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|skin(1)	21						TGGGCTTCAGGTAACTTTAAA	0.468													G|||	2712	0.718411	0.7027	0.4914	3775	,	,		14356	0.5456		0.3936	False		,,,				2504	0.5072				p.Y609Y	Pancreas(118;454 1696 1930 13865 39976)	Atlas-SNP	.											.	SLC9A7	73	.	0			c.C1827T						PASS	.	G		3302,533		1227,373,475,32,96	88.0	76.0	80.0		1824	3.5	1.0	X	dbSNP_105	80	3336,3392		594,1194,954,640,918	no	coding-synonymous	SLC9A7	NM_032591.1		1821,1567,1429,672,1014	AA,AG,A,GG,G		49.5838,13.8983,37.158		608/726	46472826	6638,3925	2203	4300	6503	SO:0001819	synonymous_variant	84679	exon16			CTTCAGGTAACTT	AF298591	CCDS14269.1, CCDS75967.1	Xp11.3	2013-05-22	2012-03-22		ENSG00000065923	ENSG00000065923		"""Solute carriers"""	17123	protein-coding gene	gene with protein product		300368	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 7"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 7"""			11279194	Standard	NM_001257291		Approved	NHE7	uc004dgv.2	Q96T83	OTTHUMG00000021428	ENST00000328306.4:c.1824C>T	X.37:g.46472826G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_001257291	O75827|Q5JXP9	Silent	SNP	ENST00000328306.4	37	CCDS14269.1																																																																																			G|0.321;A|0.679	0.679	strong		0.468	SLC9A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056370.1	NM_032591	
FUCA2	2519	hgsc.bcm.edu	37	6	143825104	143825104	+	Missense_Mutation	SNP	G	G	T	rs11155297	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:143825104G>T	ENST00000002165.6	-	3	753	c.698C>A	c.(697-699)gCa>gAa	p.A233E	RP1-20N2.6_ENST00000591189.1_RNA|FUCA2_ENST00000367585.1_Intron|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA|RP1-20N2.6_ENST00000593175.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000589489.1_RNA|RP1-20N2.6_ENST00000415586.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|RP1-20N2.6_ENST00000593045.1_RNA|FUCA2_ENST00000438118.2_Intron	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	233			A -> E (in dbSNP:rs11155297).		fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		TTGATCCGGTGCTCCTCCGTC	0.458													G|||	446	0.0890575	0.0144	0.1268	5008	,	,		18466	0.002		0.2724	False		,,,				2504	0.0644				p.A233E		Atlas-SNP	.											FUCA2,colon,carcinoma,0,1	FUCA2	28	1	0			c.C698A						PASS	.	G	GLU/ALA	209,4197	126.6+/-163.6	8,193,2002	82.0	75.0	77.0		698	3.8	0.0	6	dbSNP_120	77	2282,6318	384.5+/-341.1	278,1726,2296	yes	missense	FUCA2	NM_032020.4	107	286,1919,4298	TT,TG,GG		26.5349,4.7435,19.1527	benign	233/468	143825104	2491,10515	2203	4300	6503	SO:0001583	missense	2519	exon3			TCCGGTGCTCCTC	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.698C>A	6.37:g.143825104G>T	ENSP00000002165:p.Ala233Glu	Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	183	105	0.57377	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	280	0.1282051282051282	10	0.02032520325203252	58	0.16022099447513813	2	0.0034965034965034965	210	0.2770448548812665	G	14.98	2.698181	0.48307	0.047435	0.265349	ENSG00000001036	ENST00000002165	T	0.56275	0.47	5.62	3.81	0.43845	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.58935	0.2157	M	0.81112	2.525	0.09310	P	1.0	D	0.76494	0.999	D	0.81914	0.995	T	0.61739	-0.7001	9	0.17369	T	0.5	-20.7489	11.8248	0.52261	0.0674:0.1219:0.8107:0.0	rs11155297;rs17286188;rs61663154;rs11155297	233	Q9BTY2	FUCO2_HUMAN	E	233	ENSP00000002165:A233E	ENSP00000002165:A233E	A	-	2	0	FUCA2	143866797	1.000000	0.71417	0.012000	0.15200	0.002000	0.02628	7.638000	0.83328	1.346000	0.45694	0.650000	0.86243	GCA	G|0.844;T|0.156	0.156	strong		0.458	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
TARSL2	123283	hgsc.bcm.edu	37	15	102224341	102224341	+	Silent	SNP	G	G	A	rs12901450	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:102224341G>A	ENST00000335968.3	-	12	1803	c.1587C>T	c.(1585-1587)agC>agT	p.S529S	snoU13_ENST00000458877.1_RNA	NM_152334.2	NP_689547.2	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	529					threonyl-tRNA aminoacylation (GO:0006435)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|skin(1)|urinary_tract(1)	29	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGGTCAAGCCGCTGAGAGTCC	0.478													G|||	1997	0.398762	0.2489	0.438	5008	,	,		17028	0.7014		0.2833	False		,,,				2504	0.3804				p.S529S		Atlas-SNP	.											TARSL2,NS,carcinoma,-1,1	TARSL2	63	1	0			c.C1587T						PASS	.	G		1092,3314	396.3+/-330.0	128,836,1239	78.0	70.0	73.0		1587	-4.3	0.0	15	dbSNP_121	73	2211,6389	375.8+/-337.9	290,1631,2379	no	coding-synonymous	TARSL2	NM_152334.2		418,2467,3618	AA,AG,GG		25.7093,24.7844,25.396		529/803	102224341	3303,9703	2203	4300	6503	SO:0001819	synonymous_variant	123283	exon12			CAAGCCGCTGAGA	AL833188	CCDS10394.1	15q26.3	2008-02-05			ENSG00000185418	ENSG00000185418			24728	protein-coding gene	gene with protein product							Standard	NM_152334		Approved	FLJ25005	uc002bxm.3	A2RTX5	OTTHUMG00000149869	ENST00000335968.3:c.1587C>T	15.37:g.102224341G>A		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	163	90	0.552147	NM_152334	B2RMP7|Q6B0A1|Q6IS76|Q96LW3|Q96MP4	Silent	SNP	ENST00000335968.3	37	CCDS10394.1																																																																																			G|0.676;A|0.324	0.324	strong		0.478	TARSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313619.3	NM_152334	
SFSWAP	6433	hgsc.bcm.edu	37	12	132240010	132240010	+	Missense_Mutation	SNP	G	G	A	rs34541796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:132240010G>A	ENST00000261674.4	+	10	1675	c.1534G>A	c.(1534-1536)Ggc>Agc	p.G512S	RP11-495K9.5_ENST00000537032.1_lincRNA|SFSWAP_ENST00000541286.1_Missense_Mutation_p.G512S	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	512			G -> S (in dbSNP:rs34541796).		mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						GAAAGAAGGGGGCGATAGCAT	0.473											OREG0022261	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	14	0.00279553	0.0	0.0029	5008	,	,		20123	0.0		0.0119	False		,,,				2504	0.0				p.G512S		Atlas-SNP	.											SFSWAP,colon,carcinoma,-2,1	SFSWAP	69	1	0			c.G1534A						PASS	.	G	SER/GLY	23,4383	29.9+/-59.1	0,23,2180	84.0	82.0	83.0		1534	2.7	0.0	12	dbSNP_126	83	222,8378	92.1+/-154.2	3,216,4081	yes	missense	SFSWAP	NM_004592.2	56	3,239,6261	AA,AG,GG		2.5814,0.522,1.8837	benign	512/952	132240010	245,12761	2203	4300	6503	SO:0001583	missense	6433	exon10			GAAGGGGGCGATA	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.1534G>A	12.37:g.132240010G>A	ENSP00000261674:p.Gly512Ser	Somatic	35	0	0	1593	WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	37	CCDS9273.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	5.528	0.282302	0.10458	0.00522	0.025814	ENSG00000061936	ENST00000261674;ENST00000544623;ENST00000535236;ENST00000541286	T;T;T	0.24538	2.84;1.85;2.87	5.49	2.69	0.31865	.	0.412335	0.27946	N	0.017203	T	0.03220	0.0094	N	0.12746	0.255	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.34153	-0.9840	10	0.09084	T	0.74	-12.0835	5.7966	0.18389	0.3482:0.1294:0.5224:0.0	rs34541796	512;512	F5H6B8;Q12872	.;SFSWA_HUMAN	S	512;449;305;512	ENSP00000261674:G512S;ENSP00000443045:G305S;ENSP00000437738:G512S	ENSP00000261674:G512S	G	+	1	0	SFSWAP	130805963	0.000000	0.05858	0.007000	0.13788	0.312000	0.27988	0.482000	0.22276	0.294000	0.22547	0.561000	0.74099	GGC	G|0.987;A|0.013	0.013	strong		0.473	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
HUWE1	10075	hgsc.bcm.edu	37	X	53641647	53641647	+	Silent	SNP	T	T	C	rs6638360	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:53641647T>C	ENST00000342160.3	-	22	2566	c.2109A>G	c.(2107-2109)tcA>tcG	p.S703S	HUWE1_ENST00000262854.6_Silent_p.S703S|HUWE1_ENST00000218328.8_Silent_p.S703S			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	703					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CCTTCTGGATTGATGGCTTCT	0.458													T|||	1471	0.389669	0.0265	0.3689	3775	,	,		13513	0.3958		0.4294	False		,,,				2504	0.3569				p.S703S		Atlas-SNP	.											.	HUWE1	724	.	0			c.A2109G						PASS	.	T		374,3461		15,283,61,1334,510	113.0	95.0	101.0		2109	-1.2	1.0	X	dbSNP_116	101	3618,3110		713,1197,995,518,877	no	coding-synonymous	HUWE1	NM_031407.4		728,1480,1056,1852,1387	CC,CT,C,TT,T		46.2247,9.7523,37.7923		703/4375	53641647	3992,6571	2203	4300	6503	SO:0001819	synonymous_variant	10075	exon23			CTGGATTGATGGC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.2109A>G	X.37:g.53641647T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	106	101	0.95283	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	37	CCDS35301.1																																																																																			T|0.629;C|0.371	0.371	strong		0.458	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
BTNL3	10917	hgsc.bcm.edu	37	5	180432416	180432416	+	Silent	SNP	C	C	T	rs7726150	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:180432416C>T	ENST00000342868.6	+	8	1129	c.945C>T	c.(943-945)ccC>ccT	p.P315P	RNU6-1036P_ENST00000383959.1_RNA	NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3	315	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			GAAAAGCTCCCCAGGAGGTGC	0.547													C|||	2313	0.461861	0.6135	0.4856	5008	,	,		19347	0.3621		0.4414	False		,,,				2504	0.364				p.P315P		Atlas-SNP	.											BTNL3,NS,carcinoma,+1,1	BTNL3	55	1	0			c.C945T						PASS	.						57.0	63.0	61.0					5																	180432416		2193	4295	6488	SO:0001819	synonymous_variant	10917	exon8			AGCTCCCCAGGAG	AB020625	CCDS47358.1	5q35	2014-01-14			ENSG00000168903	ENSG00000168903		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1143	protein-coding gene	gene with protein product	"""butyrophilin-like receptor"""	606192				10429365	Standard	NM_197975		Approved	BTNLR, BTN9.1	uc003mmr.3	Q6UXE8	OTTHUMG00000162091	ENST00000342868.6:c.945C>T	5.37:g.180432416C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	213	209	0.981221	NM_197975	Q496L7|Q9Y2C7	Silent	SNP	ENST00000342868.6	37	CCDS47358.1																																																																																			T|1.000;|0.000	1.000	weak		0.547	BTNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367176.2	NM_197975	
PAAF1	80227	hgsc.bcm.edu	37	11	73620537	73620537	+	Missense_Mutation	SNP	C	C	G	rs3741138	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:73620537C>G	ENST00000310571.3	+	7	679	c.626C>G	c.(625-627)gCc>gGc	p.A209G	PAAF1_ENST00000376384.5_Missense_Mutation_p.A192G|PAAF1_ENST00000544909.1_Missense_Mutation_p.A210G|PAAF1_ENST00000535604.1_Missense_Mutation_p.A94G|PAAF1_ENST00000536003.1_Missense_Mutation_p.A192G|PAAF1_ENST00000544552.1_Missense_Mutation_p.A192G|PAAF1_ENST00000541951.1_Missense_Mutation_p.A94G	NM_025155.2	NP_079431.1	Q9BRP4	PAAF1_HUMAN	proteasomal ATPase-associated factor 1	209			A -> G (in dbSNP:rs3741138). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		viral process (GO:0016032)	proteasome complex (GO:0000502)				breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(11;7.42e-05)					GGGCGCTCAGCCTGCTTGGGA	0.552													C|||	610	0.121805	0.1188	0.0778	5008	,	,		19099	0.1716		0.0984	False		,,,				2504	0.1299				p.A209G		Atlas-SNP	.											.	PAAF1	39	.	0			c.C626G						PASS	.	C	GLY/ALA	448,3952	216.8+/-235.3	18,412,1770	200.0	169.0	179.0		626	4.2	1.0	11	dbSNP_107	179	841,7745	194.2+/-239.7	43,755,3495	yes	missense	PAAF1	NM_025155.1	60	61,1167,5265	GG,GC,CC		9.795,10.1818,9.9261	benign	209/393	73620537	1289,11697	2200	4293	6493	SO:0001583	missense	80227	exon7			GCTCAGCCTGCTT	BC006142	CCDS8226.1, CCDS58157.1, CCDS58158.1	11q13.4	2013-05-21	2007-08-16	2007-08-16	ENSG00000175575	ENSG00000175575		"""WD repeat domain containing"""	25687	protein-coding gene	gene with protein product			"""WD repeat domain 71"""	WDR71		15831487, 17317272, 17289585	Standard	NM_001267803		Approved	FLJ11848, Rpn14	uc001ouk.2	Q9BRP4	OTTHUMG00000168062	ENST00000310571.3:c.626C>G	11.37:g.73620537C>G	ENSP00000311665:p.Ala209Gly	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	206	111	0.538835	NM_025155	A6NDR5|B4DPB0|B7ZAS9|Q4G165|Q53HS9|Q7Z500|Q8TBU6|Q9HAB6	Missense_Mutation	SNP	ENST00000310571.3	37	CCDS8226.1	265|265	0.12133699633699634|0.12133699633699634	52|52	0.10569105691056911|0.10569105691056911	39|39	0.10773480662983426|0.10773480662983426	103|103	0.18006993006993008|0.18006993006993008	71|71	0.09366754617414248|0.09366754617414248	C|C	11.82|11.82	1.753587|1.753587	0.31046|0.31046	0.101818|0.101818	0.09795|0.09795	ENSG00000175575|ENSG00000175575	ENST00000541951;ENST00000310571;ENST00000504441;ENST00000543814;ENST00000535604;ENST00000542293;ENST00000536003;ENST00000544552;ENST00000546039;ENST00000376384;ENST00000544909|ENST00000540659	T;T;T;T;T;T;T;T;T;T;T|T	0.81415|0.80909	2.21;2.21;-1.49;-1.49;2.21;-1.49;2.21;2.21;2.21;2.21;2.21|-1.43	5.06|5.06	4.15|4.15	0.48705|0.48705	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.166885|.	0.40728|.	N|.	0.001026|.	T|T	0.00695|0.00695	0.0023|0.0023	L|L	0.54323|0.54323	1.7|1.7	0.27539|0.27539	P|P	0.9508404|0.9508404	B;B|.	0.22800|.	0.002;0.075|.	B;B|.	0.19946|.	0.005;0.027|.	T|T	0.22382|0.22382	-1.0218|-1.0218	9|6	0.35671|0.66056	T|D	0.21|0.02	-6.468|-6.468	14.292|14.292	0.66284|0.66284	0.0:0.8501:0.1499:0.0|0.0:0.8501:0.1499:0.0	rs3741138;rs17845650;rs17858583;rs52834465;rs3741138|rs3741138;rs17845650;rs17858583;rs52834465;rs3741138	192;209|.	Q9BRP4-2;Q9BRP4|.	.;PAAF1_HUMAN|.	G|R	94;209;192;192;94;94;192;192;73;192;210|49	ENSP00000441333:A94G;ENSP00000311665:A209G;ENSP00000439747:A192G;ENSP00000438894:A192G;ENSP00000438789:A94G;ENSP00000439143:A94G;ENSP00000438124:A192G;ENSP00000441494:A192G;ENSP00000439877:A73G;ENSP00000365564:A192G;ENSP00000438071:A210G|ENSP00000442434:S49R	ENSP00000311665:A209G|ENSP00000442434:S49R	A|S	+|+	2|3	0|2	PAAF1|PAAF1	73298185|73298185	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.746000|0.746000	0.42486|0.42486	2.779000|2.779000	0.47734|0.47734	1.135000|1.135000	0.42183|0.42183	-0.304000|-0.304000	0.09214|0.09214	GCC|AGC	C|0.891;G|0.109	0.109	strong		0.552	PAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397885.1	NM_025155	
ARHGEF12	23365	hgsc.bcm.edu	37	11	120328858	120328858	+	Silent	SNP	T	T	C	rs766894	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:120328858T>C	ENST00000397843.2	+	25	2461	c.2295T>C	c.(2293-2295)gaT>gaC	p.D765D	ARHGEF12_ENST00000356641.3_Silent_p.D746D|ARHGEF12_ENST00000532993.1_Silent_p.D662D	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	765					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		TAGAGACAGATCCACCCAACT	0.373			T	MLL	AML								T|||	625	0.1248	0.1823	0.1412	5008	,	,		18458	0.001		0.2237	False		,,,				2504	0.0613				p.D765D		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	ARHGEF12,NS,carcinoma,+2,1	ARHGEF12	133	1	0			c.T2295C						scavenged	.	T	,	726,3020		76,574,1223	120.0	120.0	120.0		2238,2295	-2.3	1.0	11	dbSNP_86	120	1889,6341		221,1447,2447	no	coding-synonymous,coding-synonymous	ARHGEF12	NM_001198665.1,NM_015313.2	,	297,2021,3670	CC,CT,TT		22.9526,19.3807,21.8353	,	746/1526,765/1545	120328858	2615,9361	1873	4115	5988	SO:0001819	synonymous_variant	23365	exon25			GACAGATCCACCC	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"""Rho guanine nucleotide exchange factors"""	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.2295T>C	11.37:g.120328858T>C		Somatic	205	3	0.0146341		WXS	Illumina HiSeq	Phase_I	188	96	0.510638	NM_015313	O15086|Q6P526	Silent	SNP	ENST00000397843.2	37	CCDS41727.1																																																																																			T|0.833;C|0.167	0.167	strong		0.373	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313	
DNAH3	55567	hgsc.bcm.edu	37	16	20975069	20975069	+	Silent	SNP	G	G	A	rs3743696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20975069G>A	ENST00000261383.3	-	53	10136	c.10137C>T	c.(10135-10137)atC>atT	p.I3379I	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3379					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TCATGATGCCGATGGTCAGGA	0.498													G|||	426	0.0850639	0.0204	0.0663	5008	,	,		24056	0.1716		0.0726	False		,,,				2504	0.1094				p.I3379I		Atlas-SNP	.											.	DNAH3	1142	.	0			c.C10137T						PASS	.	G		113,4289	86.3+/-125.0	3,107,2091	104.0	85.0	92.0		10137	-8.5	0.1	16	dbSNP_107	92	667,7933	169.0+/-220.4	23,621,3656	no	coding-synonymous	DNAH3	NM_017539.1		26,728,5747	AA,AG,GG		7.7558,2.567,5.9991		3379/4117	20975069	780,12222	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon53			GATGCCGATGGTC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.10137C>T	16.37:g.20975069G>A		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	200	197	0.985	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			G|0.930;A|0.070	0.070	strong		0.498	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
PIP4K2A	5305	hgsc.bcm.edu	37	10	22839628	22839628	+	Missense_Mutation	SNP	T	T	C	rs2230469	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:22839628T>C	ENST00000376573.4	-	7	980	c.752A>G	c.(751-753)aAc>aGc	p.N251S	PIP4K2A_ENST00000545335.1_Missense_Mutation_p.N192S|PIP4K2A_ENST00000323883.7_Missense_Mutation_p.N111S	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	251	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.		N -> S (in dbSNP:rs10828317). {ECO:0000269|PubMed:7639683}.		megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						GACCTTCTTGTTGTTGTCATC	0.363											OREG0020068	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1063	0.21226	0.0696	0.134	5008	,	,		18073	0.3839		0.3131	False		,,,				2504	0.18				p.N251S		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.A752G	GRCh37	CM068312	PIP4K2A	M	rs10828317	PASS	.	T	SER/ASN	456,3948	217.4+/-235.8	29,398,1775	180.0	175.0	177.0		752	6.1	1.0	10	dbSNP_120	177	2740,5860	437.2+/-358.5	451,1838,2011	yes	missense	PIP4K2A	NM_005028.4	46	480,2236,3786	CC,CT,TT		31.8605,10.3542,24.5771	benign	251/407	22839628	3196,9808	2202	4300	6502	SO:0001583	missense	5305	exon7			TTCTTGTTGTTGT	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"""phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"""	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.752A>G	10.37:g.22839628T>C	ENSP00000365757:p.Asn251Ser	Somatic	176	0	0	759	WXS	Illumina HiSeq	Phase_I	186	87	0.467742	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Missense_Mutation	SNP	ENST00000376573.4	37	CCDS7141.1	564	0.25824175824175827	38	0.07723577235772358	44	0.12154696132596685	232	0.40559440559440557	250	0.32981530343007914	T	9.613	1.131741	0.21041	0.103542	0.318605	ENSG00000150867	ENST00000376573;ENST00000323883;ENST00000545335	T;T;T	0.34275	1.37;1.37;1.37	6.07	6.07	0.98685	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.042713	0.85682	D	0.000000	T	0.00012	0.0000	N	0.11673	0.155	0.09310	P	0.999999748043	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.004	T	0.45760	-0.9239	9	0.15066	T	0.55	-58.1863	16.6277	0.84984	0.0:0.0:0.0:1.0	rs10828317;rs52795826;rs59726485;rs10828317	111;251	B4DH09;P48426	.;PI42A_HUMAN	S	251;111;192	ENSP00000365757:N251S;ENSP00000326294:N111S;ENSP00000442098:N192S	ENSP00000326294:N111S	N	-	2	0	PIP4K2A	22879634	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.912000	0.69948	2.330000	0.79161	0.528000	0.53228	AAC	T|0.753;C|0.247	0.247	strong		0.363	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028	
MAP6	4135	hgsc.bcm.edu	37	11	75298797	75298797	+	Silent	SNP	A	A	G	rs1231128	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:75298797A>G	ENST00000304771.3	-	4	2499	c.1749T>C	c.(1747-1749)gaT>gaC	p.D583D	CTD-2530H12.4_ENST00000527803.1_RNA|MAP6_ENST00000526740.1_Silent_p.D254D|MAP6_ENST00000526689.1_5'Flank	NM_033063.1	NP_149052.1	Q96JE9	MAP6_HUMAN	microtubule-associated protein 6	583	Pro-rich.				dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|microtubule cytoskeleton organization (GO:0000226)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	19	Ovarian(111;0.11)					TGGGACCTTCATCCTTGACAG	0.522													A|||	1884	0.376198	0.3041	0.5648	5008	,	,		21623	0.2579		0.3161	False		,,,				2504	0.5235				p.D583D	Esophageal Squamous(181;1115 2007 8647 17065 22697)	Atlas-SNP	.											.	MAP6	45	.	0			c.T1749C						PASS	.	A		1262,3138	432.2+/-343.2	192,878,1130	145.0	135.0	139.0		1749	-5.5	0.0	11	dbSNP_87	139	2625,5961	425.0+/-354.8	391,1843,2059	no	coding-synonymous	MAP6	NM_033063.1		583,2721,3189	GG,GA,AA		30.573,28.6818,29.9322		583/814	75298797	3887,9099	2200	4293	6493	SO:0001819	synonymous_variant	4135	exon4			ACCTTCATCCTTG	AK123340	CCDS31641.1, CCDS44686.1	11q13.5	2005-10-11			ENSG00000171533	ENSG00000171533			6868	protein-coding gene	gene with protein product		601783				10516426, 12231625	Standard	NM_207577		Approved	KIAA1878, STOP, FLJ41346	uc001owu.3	Q96JE9	OTTHUMG00000165343	ENST00000304771.3:c.1749T>C	11.37:g.75298797A>G		Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	328	175	0.533537	NM_033063	A7E2A1|Q6P3T0|Q6ZWB8	Silent	SNP	ENST00000304771.3	37	CCDS31641.1																																																																																			A|0.685;G|0.315	0.315	strong		0.522	MAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383527.1	NM_033063	
PI4KA	5297	hgsc.bcm.edu	37	22	21064203	21064203	+	Missense_Mutation	SNP	G	G	A	rs535848772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:21064203G>A	ENST00000572273.1	-	53	6222	c.5992C>T	c.(5992-5994)Ctc>Ttc	p.L1998F	PI4KA_ENST00000255882.6_Missense_Mutation_p.L2056F|PI4KA_ENST00000414196.3_Missense_Mutation_p.L808F			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1998	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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)	p.L1998F(2)		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)			TACTTCAAGAGCTTGATTGTC	0.552													N|||	2	0.000399361	0.0	0.0	5008	,	,		20722	0.0		0.001	False		,,,				2504	0.001				p.L2056F	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,trunk,malignant_melanoma,0,4	PI4KA	313	4	2	Substitution - Missense(2)	skin(2)	c.C6166T						scavenged	.						77.0	64.0	68.0					22																	21064203		2203	4298	6501	SO:0001583	missense	5297	exon53			TCAAGAGCTTGAT	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.5992C>T	22.37:g.21064203G>A	ENSP00000458238:p.Leu1998Phe	Somatic	731	9	0.0123119		WXS	Illumina HiSeq	Phase_I	705	21	0.0297872	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	G	15.61	2.884950	0.51908	.	.	ENSG00000241973	ENST00000255882;ENST00000414196;ENST00000399213	T;T	0.13538	2.58;2.58	5.02	4.01	0.46588	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.067129	0.64402	D	0.000009	T	0.17450	0.0419	M	0.76002	2.32	0.80722	D	1	B;B	0.32731	0.008;0.382	B;B	0.32677	0.031;0.15	T	0.02053	-1.1222	10	0.37606	T	0.19	-16.0004	10.5242	0.44938	0.1567:0.0:0.8433:0.0	.	389;1998	A8MTF1;P42356	.;PI4KA_HUMAN	F	1998;808;389	ENSP00000402981:L808F;ENSP00000382162:L389F	ENSP00000255882:L1998F	L	-	1	0	PI4KA	19394203	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.055000	0.57441	1.116000	0.41820	0.544000	0.68410	CTC	.	.	weak		0.552	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
SPAG1	6674	hgsc.bcm.edu	37	8	101206484	101206484	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:101206484G>T	ENST00000388798.2	+	10	1275	c.1084G>T	c.(1084-1086)Ggt>Tgt	p.G362C	SPAG1_ENST00000520508.1_Missense_Mutation_p.G362C|SPAG1_ENST00000251809.3_Missense_Mutation_p.G362C|SPAG1_ENST00000520643.1_Missense_Mutation_p.G362C	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	362					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		TGAAGATGGCGGTGGAGATAA	0.353																																					p.G362C		Atlas-SNP	.											SPAG1,NS,carcinoma,0,1	SPAG1	80	1	0			c.G1084T						scavenged	.						53.0	55.0	55.0					8																	101206484		2203	4300	6503	SO:0001583	missense	6674	exon10			GATGGCGGTGGAG	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"""Tetratricopeptide (TTC) repeat domain containing"""	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.1084G>T	8.37:g.101206484G>T	ENSP00000373450:p.Gly362Cys	Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	232	3	0.012931	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	37	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.425552	0.43020	.	.	ENSG00000104450	ENST00000520643;ENST00000251809;ENST00000520508;ENST00000388798	T;T;T;T	0.63744	2.77;-0.06;2.77;-0.06	5.39	3.03	0.35002	.	0.847359	0.10685	N	0.645929	T	0.58047	0.2095	L	0.38175	1.15	0.36469	D	0.867138	P;P	0.44877	0.64;0.845	B;P	0.48334	0.176;0.574	T	0.56786	-0.7921	10	0.52906	T	0.07	-0.408	7.2234	0.26002	0.8168:0.0:0.1832:0.0	.	362;362	Q07617;G3XAM3	SPAG1_HUMAN;.	C	362	ENSP00000427716:G362C;ENSP00000251809:G362C;ENSP00000428070:G362C;ENSP00000373450:G362C	ENSP00000251809:G362C	G	+	1	0	SPAG1	101275660	0.058000	0.20735	0.287000	0.24848	0.621000	0.37620	0.650000	0.24858	0.390000	0.25115	-0.475000	0.04921	GGT	.	.	none		0.353	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218	
C17orf97	400566	hgsc.bcm.edu	37	17	263516	263516	+	Silent	SNP	C	C	T	rs75627881|rs71369085|rs71369084		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:263516C>T	ENST00000360127.6	+	2	898	c.882C>T	c.(880-882)ggC>ggT	p.G294G	C17orf97_ENST00000571106.1_Intron|AC108004.3_ENST00000466740.2_RNA	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	324	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.									breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						CCCTCAAGGGCTTCCACCCCG	0.667																																					p.G294G		Atlas-SNP	.											.	C17orf97	76	.	0			c.C882T						PASS	.						20.0	22.0	21.0					17																	263516		2174	4278	6452	SO:0001819	synonymous_variant	400566	exon2			CAAGGGCTTCCAC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.882C>T	17.37:g.263516C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	347	113	0.325648	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Silent	SNP	ENST00000360127.6	37	CCDS32519.2																																																																																			C|0.913;T|0.087	0.087	strong		0.667	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
URGCP	55665	hgsc.bcm.edu	37	7	43917604	43917604	+	Silent	SNP	C	C	T	rs2232098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:43917604C>T	ENST00000453200.1	-	6	1951	c.1458G>A	c.(1456-1458)tcG>tcA	p.S486S	URGCP_ENST00000223341.7_Silent_p.S443S|URGCP_ENST00000443736.1_Silent_p.S443S|URGCP_ENST00000336086.6_Silent_p.S443S|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000447717.3_Silent_p.S443S|URGCP_ENST00000402306.3_Silent_p.S477S|URGCP_ENST00000497914.1_5'UTR			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	486					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGTAGGCATCCGAGTCTTTGA	0.587													C|||	92	0.0183706	0.0673	0.0043	5008	,	,		19017	0.0		0.0	False		,,,				2504	0.0				p.S486S		Atlas-SNP	.											.	URGCP	170	.	0			c.G1458A						PASS	.	C	,,,	214,3798		7,200,1799	136.0	141.0	140.0		1458,1329,,1431	-7.3	0.0	7	dbSNP_98	140	5,8311		0,5,4153	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	URGCP,URGCP-MRPS24	NM_001077663.1,NM_001077664.1,NM_001204871.1,NM_017920.3	,,,	7,205,5952	TT,TC,CC		0.0601,5.334,1.7764	,,,	486/932,443/889,,477/923	43917604	219,12109	2006	4158	6164	SO:0001819	synonymous_variant	55665	exon6			GGCATCCGAGTCT		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"""up-regulated gene 4"""	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.1458G>A	7.37:g.43917604C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	164	82	0.5	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Silent	SNP	ENST00000453200.1	37	CCDS47578.1																																																																																			C|0.972;T|0.028	0.028	strong		0.587	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
PMEPA1	56937	hgsc.bcm.edu	37	20	56227514	56227514	+	Silent	SNP	T	T	C	rs6025698	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:56227514T>C	ENST00000341744.3	-	4	778	c.459A>G	c.(457-459)tcA>tcG	p.S153S	PMEPA1_ENST00000395814.1_Silent_p.S103S|PMEPA1_ENST00000265626.4_Silent_p.S103S|PMEPA1_ENST00000347215.4_Silent_p.S118S|PMEPA1_ENST00000395816.3_Silent_p.S103S	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	153					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)	p.S153S(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						CCTCCCCGTCTGACAGCGAGA	0.701													C|||	1558	0.311102	0.5484	0.1801	5008	,	,		14970	0.3661		0.1451	False		,,,				2504	0.1973				p.S153S		Atlas-SNP	.											PMEPA1,NS,lymphoid_neoplasm,0,1	PMEPA1	29	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.A459G						PASS	.	C	,,,	2058,2348	599.9+/-389.4	507,1044,652	34.0	37.0	36.0		459,354,309,309	-6.5	0.5	20	dbSNP_114	36	1471,7129	742.0+/-407.2	137,1197,2966	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PMEPA1	NM_020182.3,NM_199169.1,NM_199170.1,NM_199171.1	,,,	644,2241,3618	CC,CT,TT		17.1047,46.709,27.1336	,,,	153/288,118/253,103/238,103/238	56227514	3529,9477	2203	4300	6503	SO:0001819	synonymous_variant	56937	exon4			CCCGTCTGACAGC	AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"""solid tumor-associated 1"""	606564	"""transmembrane, prostate androgen induced RNA"""	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.459A>G	20.37:g.56227514T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	120	46	0.383333	NM_020182	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Silent	SNP	ENST00000341744.3	37	CCDS13463.1																																																																																			T|0.715;C|0.285	0.285	strong		0.701	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182	
ESX1	80712	hgsc.bcm.edu	37	X	103495552	103495552	+	Missense_Mutation	SNP	T	T	C	rs41305431	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:103495552T>C	ENST00000372588.4	-	4	661	c.578A>G	c.(577-579)aAg>aGg	p.K193R		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	193					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	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 (GO:0043565)			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						TCGTTTCCACTTGGCTCTTCT	0.418													T|||	69	0.0182781	0.0015	0.0173	3775	,	,		13325	0.0		0.0507	False		,,,				2504	0.0041				p.K193R	Pancreas(200;1705 2227 25194 28471 45274)	Atlas-SNP	.											.	ESX1	57	.	0			c.A578G						PASS	.	T	ARG/LYS	47,3788		0,42,5,1590,566	134.0	115.0	121.0		578	5.0	1.0	X	dbSNP_127	121	588,6140		24,384,156,2020,1716	yes	missense	ESX1	NM_153448.3	26	24,426,161,3610,2282	CC,CT,C,TT,T		8.7396,1.2256,6.0115	benign	193/407	103495552	635,9928	2203	4300	6503	SO:0001583	missense	80712	exon4			TTCCACTTGGCTC	AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"""Homeoboxes / PRD class"""	14865	protein-coding gene	gene with protein product		300154	"""extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"""	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.578A>G	X.37:g.103495552T>C	ENSP00000361669:p.Lys193Arg	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	CCDS14516.1	44	0.02652200120554551	3	0.006097560975609756	4	0.011111111111111112	0	0.0	28	0.03783783783783784	T	16.03	3.007318	0.54361	0.012256	0.087396	ENSG00000123576	ENST00000372588	D	0.97256	-4.31	4.96	4.96	0.65561	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	.	.	.	.	T	0.59905	0.2228	N	0.16066	0.365	0.29263	P	0.871183	D	0.89917	1.0	D	0.79784	0.993	T	0.81564	-0.0875	8	0.62326	D	0.03	-40.3685	8.6024	0.33754	0.1738:0.0:0.0:0.8262	rs41305431	193	Q8N693	ESX1_HUMAN	R	193	ENSP00000361669:K193R	ENSP00000361669:K193R	K	-	2	0	ESX1	103382208	1.000000	0.71417	0.999000	0.59377	0.200000	0.23975	2.488000	0.45276	1.902000	0.55061	0.486000	0.48141	AAG	T|0.951;C|0.049	0.049	strong		0.418	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448	
EMC1	23065	hgsc.bcm.edu	37	1	19566881	19566881	+	Silent	SNP	C	C	T	rs12084825	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:19566881C>T	ENST00000477853.1	-	7	738	c.696G>A	c.(694-696)gaG>gaA	p.E232E	RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375199.3_Silent_p.E232E|EMC1_ENST00000375208.3_Silent_p.E210E	NM_001271427.1|NM_001271428.1|NM_015047.2	NP_001258356.1|NP_001258357.1|NP_055862.1	Q8N766	EMC1_HUMAN	ER membrane protein complex subunit 1	232						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											CCAGGACAGCCTCATCCACCA	0.542													C|||	430	0.0858626	0.1051	0.1455	5008	,	,		17569	0.001		0.166	False		,,,				2504	0.0225				p.E232E		Atlas-SNP	.											.	.	.	.	0			c.G696A						PASS	.	C		477,3929	223.9+/-240.3	18,441,1744	109.0	98.0	102.0		696	-1.4	1.0	1	dbSNP_120	102	1399,7201	271.1+/-289.3	115,1169,3016	no	coding-synonymous	KIAA0090	NM_015047.1		133,1610,4760	TT,TC,CC		16.2674,10.8261,14.4241		232/994	19566881	1876,11130	2203	4300	6503	SO:0001819	synonymous_variant	23065	exon7			GACAGCCTCATCC		CCDS190.1, CCDS59190.1, CCDS59191.1	1p36.13	2012-05-23	2012-05-23	2012-05-23	ENSG00000127463	ENSG00000127463			28957	protein-coding gene	gene with protein product			"""KIAA0090"""	KIAA0090		22119785	Standard	NM_015047		Approved		uc001bbo.4	Q8N766	OTTHUMG00000002497	ENST00000477853.1:c.696G>A	1.37:g.19566881C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_001271427	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Silent	SNP	ENST00000477853.1	37	CCDS190.1																																																																																			C|0.864;T|0.136	0.136	strong		0.542	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047	
PCDHA1	56147	hgsc.bcm.edu	37	5	140167463	140167463	+	Silent	SNP	C	C	T	rs3733710	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140167463C>T	ENST00000504120.2	+	1	1588	c.1588C>T	c.(1588-1590)Ctg>Ttg	p.L530L	PCDHA1_ENST00000378133.3_Silent_p.L530L|PCDHA1_ENST00000394633.3_Silent_p.L530L	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	530	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGCTGGAGCTGCTGCAGTT	0.687													.|||	2612	0.521565	0.4796	0.5865	5008	,	,		16751	0.5149		0.5368	False		,,,				2504	0.5235				p.L530L		Atlas-SNP	.											PCDHA1_ENST00000504120,NS,carcinoma,0,2	PCDHA1	387	2	0			c.C1588T						PASS	.	C	,,	2186,2220	568.1+/-382.3	529,1128,546	70.0	74.0	73.0		1588,1588,1588	1.7	1.0	5	dbSNP_107	73	4543,4057	573.5+/-389.9	1196,2151,953	no	coding-synonymous,coding-synonymous,coding-synonymous	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	,,	1725,3279,1499	TT,TC,CC		47.1744,49.6142,48.2623	,,	530/951,530/808,530/687	140167463	6729,6277	2203	4300	6503	SO:0001819	synonymous_variant	56147	exon1			CTGGAGCTGCTGC	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1588C>T	5.37:g.140167463C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_031411	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	37	CCDS54913.1																																																																																			C|0.485;T|0.515	0.515	strong		0.687	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
VWA5B2	90113	hgsc.bcm.edu	37	3	183953972	183953972	+	Silent	SNP	G	G	A	rs1709657	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:183953972G>A	ENST00000426955.2	+	8	1234	c.1134G>A	c.(1132-1134)ccG>ccA	p.P378P	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Silent_p.P159P	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	389	VWFA.									breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						AGTCCCTCCCGCCCCAGACGC	0.627													G|||	998	0.199281	0.1369	0.1888	5008	,	,		17637	0.2351		0.2256	False		,,,				2504	0.227				p.P378P		Atlas-SNP	.											.	VWA5B2	47	.	0			c.G1134A						PASS	.	G		207,1177		17,173,502	78.0	72.0	74.0		1134	-7.7	0.0	3	dbSNP_89	74	660,2522		69,522,1000	yes	coding-synonymous	VWA5B2	NM_138345.1		86,695,1502	AA,AG,GG		20.7417,14.9566,18.9882		378/1243	183953972	867,3699	692	1591	2283	SO:0001819	synonymous_variant	90113	exon8			CCTCCCGCCCCAG		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.1134G>A	3.37:g.183953972G>A		Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	243	218	0.897119	NM_138345	B9EGN7	Silent	SNP	ENST00000426955.2	37	CCDS54686.1																																																																																			G|0.823;A|0.177	0.177	strong		0.627	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
NEFH	4744	hgsc.bcm.edu	37	22	29885562	29885562	+	Missense_Mutation	SNP	G	G	A	rs370929798		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29885562G>A	ENST00000310624.6	+	4	1966	c.1933G>A	c.(1933-1935)Gaa>Aaa	p.E645K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AACGAAGGAGGAAGCAAAGTC	0.562																																					p.E645K		Atlas-SNP	.											NEFH,rectum,carcinoma,-2,1	NEFH	178	1	0			c.G1933A						PASS	.						82.0	88.0	86.0					22																	29885562		2203	4300	6503	SO:0001583	missense	4744	exon4			AAGGAGGAAGCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1933G>A	22.37:g.29885562G>A	ENSP00000311997:p.Glu645Lys	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	40	12	0.3	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031217	0.19590	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.83914	-1.78	4.97	4.97	0.65823	.	0.115504	0.38778	N	0.001569	D	0.87783	0.6264	L	0.61218	1.895	0.29104	N	0.881289	P	0.36712	0.566	P	0.52267	0.694	D	0.83526	0.0088	10	0.44086	T	0.13	.	16.1111	0.81263	0.0:0.0:1.0:0.0	.	645	P12036	NFH_HUMAN	K	645	ENSP00000311997:E645K	ENSP00000311997:E645K	E	+	1	0	NEFH	28215562	0.001000	0.12720	0.367000	0.25926	0.091000	0.18340	0.923000	0.28757	2.745000	0.94114	0.491000	0.48974	GAA	.	.	weak		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
MMP14	4323	hgsc.bcm.edu	37	14	23313633	23313633	+	Missense_Mutation	SNP	G	G	A	rs17880989	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23313633G>A	ENST00000311852.6	+	7	1326	c.1065G>A	c.(1063-1065)atG>atA	p.M355I	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	355			M -> I (in dbSNP:rs17880989). {ECO:0000269|Ref.8}.		angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	GATACCCAATGCCCATTGGCC	0.547													G|||	28	0.00559105	0.0023	0.0072	5008	,	,		16272	0.0		0.0199	False		,,,				2504	0.0				p.M355I		Atlas-SNP	.											.	MMP14	40	.	0			c.G1065A						PASS	.	G	ILE/MET	26,4380	34.3+/-65.2	0,26,2177	167.0	165.0	166.0		1065	5.0	1.0	14	dbSNP_124	166	176,8424	80.9+/-143.5	0,176,4124	yes	missense	MMP14	NM_004995.2	10	0,202,6301	AA,AG,GG		2.0465,0.5901,1.5531	probably-damaging	355/583	23313633	202,12804	2203	4300	6503	SO:0001583	missense	4323	exon7			CCCAATGCCCATT		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"""membrane type 1 metalloprotease"""	600754	"""matrix metalloproteinase 14 (membrane-inserted)"""			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.1065G>A	14.37:g.23313633G>A	ENSP00000308208:p.Met355Ile	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	167	93	0.556886	NM_004995	A8K5L0|Q6GSF3|Q92678	Missense_Mutation	SNP	ENST00000311852.6	37	CCDS9577.1	20	0.009157509157509158	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	16	0.021108179419525065	G	18.54	3.646266	0.67358	0.005901	0.020465	ENSG00000157227	ENST00000311852	T	0.02323	4.34	5.91	4.97	0.65823	Hemopexin/matrixin (2);	0.037325	0.85682	D	0.000000	T	0.02970	0.0088	M	0.78637	2.42	0.58432	D	0.999999	B	0.29988	0.264	B	0.37198	0.243	T	0.15178	-1.0446	10	0.32370	T	0.25	.	11.143	0.48413	0.0:0.1369:0.7218:0.1413	rs17880989;rs17880989	355	P50281	MMP14_HUMAN	I	355	ENSP00000308208:M355I	ENSP00000308208:M355I	M	+	3	0	MMP14	22383473	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.564000	0.67359	2.799000	0.96334	0.650000	0.86243	ATG	G|0.985;A|0.015	0.015	strong		0.547	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	
MEGF6	1953	hgsc.bcm.edu	37	1	3418428	3418428	+	Missense_Mutation	SNP	G	G	A	rs200472001	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:3418428G>A	ENST00000356575.4	-	18	2472	c.2246C>T	c.(2245-2247)gCc>gTc	p.A749V	MEGF6_ENST00000294599.4_Missense_Mutation_p.A644V	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	749	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GTGGCAGGGGGCCCCCCCACA	0.697													G|||	9	0.00179712	0.0	0.0	5008	,	,		14048	0.0		0.001	False		,,,				2504	0.0082				p.A749V	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C2246T						PASS	.	G	VAL/ALA	0,3974		0,0,1987	21.0	30.0	27.0		2246	2.6	0.1	1		27	8,8250		0,8,4121	yes	missense	MEGF6	NM_001409.3	64	0,8,6108	AA,AG,GG		0.0969,0.0,0.0654	probably-damaging	749/1542	3418428	8,12224	1987	4129	6116	SO:0001583	missense	1953	exon18			CAGGGGGCCCCCC	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.2246C>T	1.37:g.3418428G>A	ENSP00000348982:p.Ala749Val	Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	250	137	0.548	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.947341	0.34377	0.0	9.69E-4	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.33438	1.41;1.41	3.58	2.61	0.31194	EGF-like, laminin (1);Epidermal growth factor-like, type 3 (1);	0.071934	0.53938	U	0.000043	T	0.59702	0.2213	M	0.91038	3.17	0.32858	D	0.507526	D;D	0.76494	0.999;0.999	D;D	0.72982	0.979;0.979	T	0.73177	-0.4065	10	0.66056	D	0.02	-11.9588	11.1649	0.48537	0.0:0.1871:0.8129:0.0	.	749;644	O75095;O75095-2	MEGF6_HUMAN;.	V	644;749	ENSP00000294599:A644V;ENSP00000348982:A749V	ENSP00000294599:A644V	A	-	2	0	MEGF6	3408288	0.993000	0.37304	0.112000	0.21494	0.318000	0.28184	4.377000	0.59562	0.548000	0.28955	0.455000	0.32223	GCC	G|0.996;A|0.004	0.004	strong		0.697	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
SP9	100131390	hgsc.bcm.edu	37	2	175200903	175200903	+	Silent	SNP	G	G	C	rs35548534	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:175200903G>C	ENST00000394967.2	+	2	237	c.90G>C	c.(88-90)acG>acC	p.T30T	AC018470.1_ENST00000595354.1_Missense_Mutation_p.R417G	NM_001145250.1	NP_001138722.1	P0CG40	SP9_HUMAN	Sp9 transcription factor	30					embryonic limb morphogenesis (GO:0030326)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(1)	1						TCGGCAACACGAGCCCGCTGA	0.657													G|||	845	0.16873	0.1233	0.2061	5008	,	,		12237	0.0248		0.2763	False		,,,				2504	0.2413				p.T30T		Atlas-SNP	.											.	SP9	15	.	0			c.G90C						PASS	.	G		192,1192		13,166,513	52.0	50.0	51.0		90	-1.9	1.0	2	dbSNP_126	51	921,2261		121,679,791	no	coding-synonymous	SP9	NM_001145250.1		134,845,1304	CC,CG,GG		28.9441,13.8728,24.3758		30/485	175200903	1113,3453	692	1591	2283	SO:0001819	synonymous_variant	100131390	exon2			CAACACGAGCCCG		CCDS46453.1	2q31.1	2013-01-08	2012-12-07		ENSG00000217236	ENSG00000217236		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	30690	protein-coding gene	gene with protein product	"""zinc finger protein 990"""		"""Sp9 transcription factor homolog (mouse)"""				Standard	NM_001145250		Approved	ZNF990	uc010zem.1	P0CG40	OTTHUMG00000150371	ENST00000394967.2:c.90G>C	2.37:g.175200903G>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	139	63	0.453237	NM_001145250		Silent	SNP	ENST00000394967.2	37	CCDS46453.1																																																																																			G|0.839;C|0.161	0.161	strong		0.657	SP9-001	NOVEL	not_organism_supported|not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317878.1	NM_001145250	
ALPK2	115701	hgsc.bcm.edu	37	18	56204671	56204671	+	Missense_Mutation	SNP	A	A	T	rs4940404	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56204671A>T	ENST00000361673.3	-	5	2961	c.2748T>A	c.(2746-2748)aaT>aaA	p.N916K	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	916			N -> K (in dbSNP:rs4940404). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GGTAGGTGGAATTCTCCACCT	0.507													A|||	2024	0.404153	0.4312	0.4294	5008	,	,		19055	0.2361		0.5726	False		,,,				2504	0.3497				p.N916K		Atlas-SNP	.											ALPK2_ENST00000361673,NS,carcinoma,-1,2	ALPK2	487	2	0			c.T2748A						PASS	.	A	LYS/ASN	1984,2422	556.3+/-379.5	446,1092,665	75.0	75.0	75.0		2748	2.8	0.1	18	dbSNP_111	75	4592,4008	597.8+/-393.8	1238,2116,946	yes	missense	ALPK2	NM_052947.3	94	1684,3208,1611	TT,TA,AA		46.6047,45.0295,49.4387	probably-damaging	916/2171	56204671	6576,6430	2203	4300	6503	SO:0001583	missense	115701	exon5			GGTGGAATTCTCC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2748T>A	18.37:g.56204671A>T	ENSP00000354991:p.Asn916Lys	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	935	0.4281135531135531	186	0.3780487804878049	184	0.5082872928176796	136	0.23776223776223776	429	0.5659630606860159	A	17.15	3.314820	0.60524	0.450295	0.533953	ENSG00000198796	ENST00000361673	T	0.54279	0.58	5.57	2.8	0.32819	.	0.657975	0.14928	N	0.290234	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P;P	0.46912	0.886;0.59	B;B	0.42245	0.381;0.197	T	0.48186	-0.9057	9	0.54805	T	0.06	-3.5085	5.5695	0.17188	0.724:0.1763:0.0996:0.0	rs4940404;rs52809276;rs56910431;rs4940404	916;916	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	K	916	ENSP00000354991:N916K	ENSP00000354991:N916K	N	-	3	2	ALPK2	54355651	0.000000	0.05858	0.051000	0.19133	0.023000	0.10783	-0.367000	0.07553	0.915000	0.36847	0.482000	0.46254	AAT	A|0.514;T|0.486	0.486	strong		0.507	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
GRIK2	2898	hgsc.bcm.edu	37	6	102503317	102503317	+	Silent	SNP	G	G	A	rs2227283	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:102503317G>A	ENST00000421544.1	+	15	2914	c.2424G>A	c.(2422-2424)gaG>gaA	p.E808E	GRIK2_ENST00000369137.3_Silent_p.E732E|GRIK2_ENST00000369134.4_Silent_p.E759E|GRIK2_ENST00000318991.6_Silent_p.E808E|GRIK2_ENST00000413795.1_Silent_p.E808E|GRIK2_ENST00000369138.1_Silent_p.E808E	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	808					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	CAGAAGAGGAGAGCAAAGAGG	0.493													G|||	1640	0.327476	0.2375	0.4107	5008	,	,		14836	0.3601		0.4414	False		,,,				2504	0.2393				p.E808E		Atlas-SNP	.											.	GRIK2	487	.	0			c.G2424A						PASS	.	G	,,	1237,3169	424.9+/-340.6	172,893,1138	110.0	114.0	113.0		2424,2424,2424	0.9	1.0	6	dbSNP_98	113	3789,4811	536.8+/-383.1	847,2095,1358	no	coding-synonymous,coding-synonymous,coding-synonymous	GRIK2	NM_001166247.1,NM_021956.4,NM_175768.3	,,	1019,2988,2496	AA,AG,GG		44.0581,28.0754,38.6437	,,	808/893,808/909,808/870	102503317	5026,7980	2203	4300	6503	SO:0001819	synonymous_variant	2898	exon15			AGAGGAGAGCAAA		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2424G>A	6.37:g.102503317G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Silent	SNP	ENST00000421544.1	37	CCDS5048.1																																																																																			A|0.381;C|0.006	0.381	strong		0.493	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1		
ZNF578	147660	hgsc.bcm.edu	37	19	53015366	53015366	+	Missense_Mutation	SNP	C	C	T	rs376297084		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53015366C>T	ENST00000421239.2	+	6	1976	c.1732C>T	c.(1732-1734)Cac>Tac	p.H578Y	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	578					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GGCTCACAATCACTTGATTGA	0.393																																					p.H578Y		Atlas-SNP	.											.	.	.	.	0			c.C1732T						PASS	.	C	TYR/HIS	1,4397		0,1,2198	55.0	57.0	56.0		1732	0.1	0.0	19		56	5,8591		0,5,4293	no	missense	ZNF578	NM_001099694.1	83	0,6,6491	TT,TC,CC		0.0582,0.0227,0.0462	possibly-damaging	578/591	53015366	6,12988	2199	4298	6497	SO:0001583	missense	147660	exon6			CACAATCACTTGA	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1732C>T	19.37:g.53015366C>T	ENSP00000459216:p.His578Tyr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	0.389	-0.924629	0.02377	2.27E-4	5.82E-4	ENSG00000258405	ENST00000553364	.	.	.	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.15825	0.0381	N	0.13098	0.295	0.09310	N	1	B	0.31485	0.325	B	0.20767	0.031	T	0.18777	-1.0326	6	.	.	.	.	.	.	.	.	578	G3V4F6	.	Y	578	.	.	H	+	1	0	ZNF578	57707178	0.033000	0.19621	0.009000	0.14445	0.011000	0.07611	0.000000	0.12993	0.132000	0.18615	0.134000	0.15878	CAC	.	.	weak		0.393	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
A4GALT	53947	hgsc.bcm.edu	37	22	43089849	43089849	+	Missense_Mutation	SNP	T	T	C	rs11541159	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:43089849T>C	ENST00000401850.1	-	2	598	c.109A>G	c.(109-111)Atg>Gtg	p.M37V	A4GALT_ENST00000465765.2_5'Flank|A4GALT_ENST00000381278.3_Missense_Mutation_p.M37V|A4GALT_ENST00000249005.2_Missense_Mutation_p.M37V			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	37			M -> V (in dbSNP:rs11541159). {ECO:0000269|PubMed:10747952, ECO:0000269|PubMed:10993874, ECO:0000269|Ref.4}.		globoside biosynthetic process (GO:0001576)|glycosphingolipid biosynthetic process (GO:0006688)|plasma membrane organization (GO:0007009)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	galactosyltransferase activity (GO:0008378)|lactosylceramide 4-alpha-galactosyltransferase activity (GO:0050512)|toxic substance binding (GO:0015643)			NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						CAGTAGATCATGATGGAGACG	0.627													T|||	1756	0.350639	0.5083	0.3415	5008	,	,		12771	0.1319		0.3827	False		,,,				2504	0.3364				p.M37V		Atlas-SNP	.											.	A4GALT	35	.	0			c.A109G						PASS	.	T	VAL/MET	2075,2329		499,1077,626	29.0	20.0	23.0		109	-4.6	0.0	22	dbSNP_120	23	3183,5415		599,1985,1715	yes	missense	A4GALT	NM_017436.4	21	1098,3062,2341	CC,CT,TT		37.0202,47.1163,40.4399	benign	37/354	43089849	5258,7744	2202	4299	6501	SO:0001583	missense	53947	exon3			AGATCATGATGGA		CCDS14041.1	22q13.2	2014-07-18	2008-07-31		ENSG00000128274	ENSG00000128274	2.4.1.228		18149	protein-coding gene	gene with protein product	"""Gb3 synthase"", ""CD77 synthase"", ""globotriaosylceramide synthase"", ""lactosylceramide 4-alpha-galactosyltransferase"""	607922	"""alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"""			10854428	Standard	XM_005261643		Approved	A14GALT, Gb3S, P(k)	uc003bdb.3	Q9NPC4	OTTHUMG00000150744	ENST00000401850.1:c.109A>G	22.37:g.43089849T>C	ENSP00000384794:p.Met37Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	137	62	0.452555	NM_017436	B2R7C4|Q9P1X5	Missense_Mutation	SNP	ENST00000401850.1	37	CCDS14041.1	736	0.336996336996337	236	0.4796747967479675	146	0.40331491712707185	75	0.13111888111888112	279	0.36807387862796836	T	9.896	1.205490	0.22205	0.471163	0.370202	ENSG00000128274	ENST00000401850;ENST00000249005;ENST00000381278;ENST00000535654	T;T;T	0.80033	-1.33;-1.33;-1.33	5.34	-4.6	0.03390	.	0.593745	0.14525	U	0.314222	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14200	-1.0481	9	0.05833	T	0.94	-19.2207	3.7109	0.08420	0.1021:0.3574:0.3264:0.2141	rs11541159;rs17846531;rs17859605;rs59149669;rs11541159	37	Q9NPC4	A4GAT_HUMAN	V	37	ENSP00000384794:M37V;ENSP00000249005:M37V;ENSP00000370678:M37V	ENSP00000249005:M37V	M	-	1	0	A4GALT	41419793	0.000000	0.05858	0.016000	0.15963	0.941000	0.58515	-1.483000	0.02318	-1.433000	0.01977	0.459000	0.35465	ATG	T|0.620;C|0.380	0.380	strong		0.627	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436	
ZNF443	10224	hgsc.bcm.edu	37	19	12541250	12541250	+	Missense_Mutation	SNP	T	T	C	rs45531232	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12541250T>C	ENST00000301547.5	-	4	1933	c.1736A>G	c.(1735-1737)gAa>gGa	p.E579G	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	579					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						GTGAATTCTTTCATGTCGTAG	0.393													.|||	229	0.0457268	0.0431	0.0346	5008	,	,		21395	0.0		0.0497	False		,,,				2504	0.1002				p.E579G		Atlas-SNP	.											.	ZNF443	63	.	0			c.A1736G						PASS	.	T	GLY/GLU	190,4216	112.9+/-151.0	2,186,2015	102.0	102.0	102.0		1736	-1.4	0.0	19	dbSNP_127	102	454,8144	134.4+/-191.8	11,432,3856	no	missense	ZNF443	NM_005815.4	98	13,618,5871	CC,CT,TT		5.2803,4.3123,4.9523	probably-damaging	579/672	12541250	644,12360	2203	4299	6502	SO:0001583	missense	10224	exon4			ATTCTTTCATGTC	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1736A>G	19.37:g.12541250T>C	ENSP00000301547:p.Glu579Gly	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	68	0.031135531135531136	22	0.044715447154471545	12	0.03314917127071823	0	0.0	34	0.044854881266490766	T	5.721	0.317544	0.10845	0.043123	0.052803	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.18657	2.2	1.37	-1.44	0.08856	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	L	0.49350	1.555	0.09310	N	1	B	0.17038	0.02	B	0.20384	0.029	T	0.27938	-1.0059	9	0.54805	T	0.06	.	3.6171	0.08082	0.2421:0.1583:0.0:0.5996	rs45531232;rs62114862	579	Q9Y2A4	ZN443_HUMAN	G	579;551	ENSP00000301547:E579G	ENSP00000301547:E579G	E	-	2	0	ZNF443	12402250	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.092000	0.11129	-0.523000	0.06409	-0.530000	0.04314	GAA	T|0.955;C|0.045	0.045	strong		0.393	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
KRT4	3851	hgsc.bcm.edu	37	12	53207583	53207583	+	Missense_Mutation	SNP	C	C	G	rs76773498|rs11267392	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53207583C>G	ENST00000551956.1	-	1	752	c.260G>C	c.(259-261)gGt>gCt	p.G87A	KRT4_ENST00000293774.4_Missense_Mutation_p.G161A|KRT4_ENST00000458244.2_Missense_Mutation_p.G67A			P19013	K2C4_HUMAN	keratin 4	87	Gly-rich.|Head.		Missing (in allele K4B). {ECO:0000269|PubMed:16541075, ECO:0000269|PubMed:7684424}.		cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CCCAAATCCACCACCAAAGCC	0.602																																					p.G87A	Pancreas(190;284 2995 41444 45903)	Atlas-SNP	.											KRT4,rectum,carcinoma,+1,2	KRT4	110	2	0			c.G260C						scavenged	.						43.0	59.0	54.0					12																	53207583		2120	4256	6376	SO:0001583	missense	3851	exon1			AATCCACCACCAA		CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.260G>C	12.37:g.53207583C>G	ENSP00000448220:p.Gly87Ala	Somatic	48	2	0.0416667		WXS	Illumina HiSeq	Phase_I	71	6	0.084507	NM_002272	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Missense_Mutation	SNP	ENST00000551956.1	37	CCDS41787.2	.	.	.	.	.	.	.	.	.	.	C	11.36	1.614915	0.28712	.	.	ENSG00000170477	ENST00000551956;ENST00000293774;ENST00000458244	D;T;D	0.98717	-3.14;0.68;-5.09	5.14	4.25	0.50352	.	0.974741	0.08394	N	0.952444	D	0.97123	0.9060	L	0.45581	1.43	0.29836	N	0.829633	B	0.21071	0.051	B	0.17979	0.02	D	0.93594	0.6924	10	0.31617	T	0.26	.	14.3364	0.66592	0.1484:0.8516:0.0:0.0	.	101	P19013	K2C4_HUMAN	A	87;161;67	ENSP00000448220:G87A;ENSP00000293774:G161A;ENSP00000387904:G67A	ENSP00000293774:G161A	G	-	2	0	KRT4	51493850	0.011000	0.17503	0.856000	0.33681	0.125000	0.20455	0.972000	0.29409	1.483000	0.48342	0.585000	0.79938	GGT	.	.	weak		0.602	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
OR2AG1	144125	hgsc.bcm.edu	37	11	6807163	6807163	+	Missense_Mutation	SNP	C	C	G	rs2659879	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6807163C>G	ENST00000307401.4	+	1	916	c.895C>G	c.(895-897)Cgg>Ggg	p.R299G		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	299			R -> G (in dbSNP:rs2659879). {ECO:0000269|PubMed:11416212}.|R -> W (in dbSNP:rs2659879).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GGAGGTCATGCGGGCCTTGAG	0.512													G|||	989	0.197484	0.1089	0.2075	5008	,	,		19881	0.1815		0.339	False		,,,				2504	0.181				p.R299G		Atlas-SNP	.											OR2AG1,colon,carcinoma,0,5	OR2AG1	57	5	0			c.C895G						scavenged	.	G	GLY/ARG	558,3844	739.8+/-411.1	41,476,1684	93.0	84.0	87.0		895	3.5	1.0	11	dbSNP_100	87	2900,5692	664.8+/-402.2	515,1870,1911	yes	missense	OR2AG1	NM_001004489.2	125	556,2346,3595	GG,GC,CC		33.7523,12.6761,26.6123	benign	299/317	6807163	3458,9536	2201	4296	6497	SO:0001583	missense	144125	exon1			GTCATGCGGGCCT	AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"""GPCR / Class A : Olfactory receptors"""	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.895C>G	11.37:g.6807163C>G	ENSP00000307447:p.Arg299Gly	Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	259	127	0.490348	NM_001004489	B9EKV7|Q6IFG7|Q96R26	Missense_Mutation	SNP	ENST00000307401.4	37	CCDS31414.1	557	0.25503663003663	54	0.10975609756097561	95	0.26243093922651933	150	0.26223776223776224	258	0.3403693931398417	G	0.016	-1.530312	0.00951	0.126761	0.337523	ENSG00000170803	ENST00000307401	T	0.39056	1.1	4.39	3.47	0.39725	.	0.130893	0.35067	N	0.003466	T	0.00012	0.0000	N	0.10707	0.03	0.58432	P	9.99999999995449E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39583	-0.9607	9	0.02654	T	1	.	6.8024	0.23758	0.0943:0.344:0.5617:0.0	rs2659879	299	Q9H205	O2AG1_HUMAN	G	299	ENSP00000307447:R299G	ENSP00000307447:R299G	R	+	1	2	OR2AG1	6763739	0.000000	0.05858	1.000000	0.80357	0.738000	0.42128	0.294000	0.19047	0.626000	0.30322	-0.729000	0.03580	CGG	G|0.250;C|0.750	0.250	strong		0.512	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385980.1	NM_001004489	
RHAG	6005	hgsc.bcm.edu	37	6	49580247	49580247	+	Splice_Site	SNP	C	C	T	rs16879498	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:49580247C>T	ENST00000371175.4	-	6	834	c.808G>A	c.(808-810)Gtt>Att	p.V270I	RHAG_ENST00000229810.7_Splice_Site_p.V270I	NM_000324.2	NP_000315.2	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	270			V -> I (in RHN; dbSNP:rs16879498). {ECO:0000269|PubMed:10467273, ECO:0000269|PubMed:14702039}.		ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|carbon dioxide transport (GO:0015670)|cellular ion homeostasis (GO:0006873)|erythrocyte development (GO:0048821)|multicellular organismal iron ion homeostasis (GO:0060586)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	39	Lung NSC(77;0.0255)					TGAATGTGAACCTGTGTGAGC	0.468													C|||	349	0.0696885	0.0809	0.036	5008	,	,		18183	0.0655		0.0189	False		,,,				2504	0.135				p.V270I	Ovarian(176;476 2003 7720 43408 44749)	Atlas-SNP	.											RHAG,NS,carcinoma,+1,1	RHAG	85	1	0			c.G808A	GRCh37	CM991100	RHAG	M	rs16879498	PASS	.	C	ILE/VAL	295,4111	162.2+/-194.2	8,279,1916	72.0	62.0	66.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	808	5.5	1.0	6	dbSNP_123	66	233,8367	94.0+/-155.9	1,231,4068	yes	missense-near-splice	RHAG	NM_000324.2	29	9,510,5984	TT,TC,CC		2.7093,6.6954,4.0597	probably-damaging	270/410	49580247	528,12478	2203	4300	6503	SO:0001630	splice_region_variant	6005	exon6			TGTGAACCTGTGT		CCDS4927.1	6p12.3	2014-07-19	2006-02-23		ENSG00000112077	ENSG00000112077		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	10006	protein-coding gene	gene with protein product		180297	"""Rhesus blood group-associated glycoprotein"""			9479501	Standard	NM_000324		Approved	RH50A, CD241, SLC42A1	uc003ozk.4	Q02094	OTTHUMG00000016377	ENST00000371175.4:c.808-1G>A	6.37:g.49580247C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_000324	B2R8T8|O43514|O43515|Q7L8L3|Q9H454	Missense_Mutation	SNP	ENST00000371175.4	37	CCDS4927.1	112	0.05128205128205128	47	0.09552845528455285	12	0.03314917127071823	36	0.06293706293706294	17	0.022427440633245383	C	28.2	4.896963	0.91962	0.066954	0.027093	ENSG00000112077	ENST00000371175;ENST00000229810;ENST00000418071;ENST00000539403	T;T	0.24723	1.84;1.84	5.54	5.54	0.83059	Ammonium transporter AmtB-like (3);	0.000000	0.85682	D	0.000000	T	0.38957	0.1060	M	0.87381	2.88	0.80722	A	1	P;P;P	0.48350	0.909;0.909;0.909	P;P;P	0.48952	0.596;0.596;0.596	T	0.50389	-0.8834	9	0.72032	D	0.01	-30.9614	18.4694	0.90767	0.0:1.0:0.0:0.0	rs16879498;rs52801665;rs16879498	270;270;270	O43515;Q9UHG9;Q02094	.;.;RHAG_HUMAN	I	270	ENSP00000360217:V270I;ENSP00000229810:V270I	ENSP00000229810:V270I	V	-	1	0	RHAG	49688206	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	4.953000	0.63624	2.600000	0.87896	0.655000	0.94253	GTT	C|0.956;T|0.044	0.044	strong		0.468	RHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043806.1		Missense_Mutation
PPP1R26	9858	hgsc.bcm.edu	37	9	138377498	138377498	+	Missense_Mutation	SNP	G	G	T	rs34151777	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:138377498G>T	ENST00000356818.2	+	4	1691	c.1142G>T	c.(1141-1143)cGc>cTc	p.R381L	PPP1R26_ENST00000401470.3_Missense_Mutation_p.R381L|PPP1R26_ENST00000605286.1_Missense_Mutation_p.R381L|PPP1R26_ENST00000604351.1_Missense_Mutation_p.R381L|PPP1R26_ENST00000605660.1_Missense_Mutation_p.R381L|PPP1R26_ENST00000602993.1_Intron	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	381					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CAGAAAACACGCAAGGAGGCC	0.632													G|||	114	0.0227636	0.003	0.0476	5008	,	,		18578	0.0		0.0746	False		,,,				2504	0.002				p.R381L		Atlas-SNP	.											.	.	.	.	0			c.G1142T						PASS	.	G	LEU/ARG	50,4356	47.5+/-82.1	1,48,2154	40.0	45.0	44.0		1142	4.9	0.9	9	dbSNP_126	44	580,8020	146.6+/-202.2	21,538,3741	no	missense	KIAA0649	NM_014811.3	102	22,586,5895	TT,TG,GG		6.7442,1.1348,4.8439	probably-damaging	381/1210	138377498	630,12376	2203	4300	6503	SO:0001583	missense	9858	exon4			AAACACGCAAGGA	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.1142G>T	9.37:g.138377498G>T	ENSP00000349274:p.Arg381Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	77	0.035256410256410256	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	58	0.07651715039577836	G	17.96	3.515599	0.64634	0.011348	0.067442	ENSG00000196422	ENST00000356818	T	0.17054	2.3	4.92	4.92	0.64577	.	0.215951	0.37715	N	0.001969	T	0.02848	0.0085	M	0.68593	2.085	0.23430	P	0.99769767	D	0.89917	1.0	D	0.91635	0.999	T	0.01570	-1.1322	9	0.87932	D	0	-6.0072	17.1139	0.86683	0.0:0.0:1.0:0.0	rs34151777	381	Q5T8A7	PPR26_HUMAN	L	381	ENSP00000349274:R381L	ENSP00000349274:R381L	R	+	2	0	KIAA0649	137517319	0.960000	0.32886	0.921000	0.36526	0.014000	0.08584	2.336000	0.43938	2.262000	0.75019	0.655000	0.94253	CGC	G|0.956;T|0.044	0.044	strong		0.632	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
CGB2	114336	hgsc.bcm.edu	37	19	49536390	49536390	+	Missense_Mutation	SNP	C	C	A	rs62126039	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49536390C>A	ENST00000359342.6	+	3	522	c.404C>A	c.(403-405)gCc>gAc	p.A135D	CTB-60B18.6_ENST00000591656.1_Intron	NM_033378.1	NP_203696.2	Q6NT52	CGB2_HUMAN	chorionic gonadotropin, beta polypeptide 2	167						extracellular region (GO:0005576)		p.A135D(1)		large_intestine(1)|lung(1)|stomach(1)	3		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		CGCTTCCAGGCCTCCTCTTCC	0.637													c|||	1481	0.295727	0.3381	0.3718	5008	,	,		12440	0.1567		0.336	False		,,,				2504	0.2863				p.A135D		Atlas-SNP	.											CGB2,NS,carcinoma,0,1	CGB2	6	1	1	Substitution - Missense(1)	stomach(1)	c.C404A						scavenged	.						19.0	27.0	24.0					19																	49536390		2161	4265	6426	SO:0001583	missense	114336	exon3			TCCAGGCCTCCTC	K03184	CCDS12750.2	19q13.32	2008-02-05			ENSG00000104818	ENSG00000104818			16722	protein-coding gene	gene with protein product		608824				6194155	Standard	NM_033378		Approved		uc002plw.3	Q6NT52	OTTHUMG00000150185	ENST00000359342.6:c.404C>A	19.37:g.49536390C>A	ENSP00000352295:p.Ala135Asp	Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	114	103	0.903509	NM_033378	B9ZVM5	Missense_Mutation	SNP	ENST00000359342.6	37	CCDS12750.2	.	.	.	.	.	.	.	.	.	.	c	0.395	-0.921146	0.02396	.	.	ENSG00000104818	ENST00000359342	T	0.36520	1.25	1.79	0.719	0.18208	.	.	.	.	.	T	0.11707	0.0285	N	0.02916	-0.46	0.47905	P	4.6000000000001595E-4	.	.	.	.	.	.	T	0.34254	-0.9836	6	0.11182	T	0.66	.	5.5188	0.16921	0.3275:0.6725:0.0:0.0	.	.	.	.	D	135	ENSP00000352295:A135D	ENSP00000352295:A135D	A	+	2	0	CGB2	54228202	0.010000	0.17322	0.167000	0.22817	0.014000	0.08584	0.011000	0.13264	0.323000	0.23307	-1.276000	0.01395	GCC	A|1.000;|0.000	1.000	weak		0.637	CGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316745.1	NM_033378	
OVCH1	341350	hgsc.bcm.edu	37	12	29604392	29604392	+	Missense_Mutation	SNP	C	C	G	rs1347570	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:29604392C>G	ENST00000318184.5	-	22	2640	c.2641G>C	c.(2641-2643)Gca>Cca	p.A881P	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	881	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.		P -> A (in dbSNP:rs1347570).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					ATACTGCTTGCTGAAACTCTG	0.423													G|||	2557	0.510583	0.621	0.3934	5008	,	,		15119	0.4008		0.5726	False		,,,				2504	0.4939				p.A881P		Atlas-SNP	.											.	OVCH1	195	.	0			c.G2641C						PASS	.	G	PRO/ALA	2456,1304		801,854,225	88.0	84.0	85.0		2641	2.4	0.1	12	dbSNP_88	85	4638,3586		1299,2040,773	yes	missense	OVCH1	NM_183378.2	27	2100,2894,998	GG,GC,CC		43.6041,34.6809,40.8044	probably-damaging	881/1135	29604392	7094,4890	1880	4112	5992	SO:0001583	missense	341350	exon22			TGCTTGCTGAAAC	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.2641G>C	12.37:g.29604392C>G	ENSP00000326708:p.Ala881Pro	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	168	76	0.452381	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		1147	0.5251831501831502	313	0.6361788617886179	141	0.38950276243093923	260	0.45454545454545453	433	0.5712401055408971	G	1.388	-0.581633	0.03854	0.653191	0.563959	ENSG00000187950	ENST00000318184	T	0.16897	2.31	2.36	2.36	0.29203	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.40232	-0.9574	5	0.02654	T	1	.	7.1197	0.25437	0.0:0.2815:0.7185:0.0	rs1347570;rs52827123;rs1347570	.	.	.	P	881	ENSP00000326708:A881P	ENSP00000326708:A881P	A	-	1	0	OVCH1	29495659	0.014000	0.17966	0.096000	0.21009	0.611000	0.37282	1.469000	0.35343	0.572000	0.29383	-0.225000	0.12378	GCA	C|0.461;G|0.539	0.539	strong		0.423	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
OR2A5	393046	hgsc.bcm.edu	37	7	143748364	143748364	+	Silent	SNP	T	T	C	rs4407791	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143748364T>C	ENST00000408906.2	+	1	904	c.870T>C	c.(868-870)taT>taC	p.Y290Y		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					CCTTGATCTATAGCCTGAGGA	0.517													.|||	3414	0.681709	0.8911	0.7522	5008	,	,		20215	0.6637		0.502	False		,,,				2504	0.5521				p.Y290Y		Atlas-SNP	.											.	OR2A5	78	.	0			c.T870C						PASS	.	C		3276,640		1372,532,54	108.0	105.0	106.0		870	3.4	1.0	7	dbSNP_111	106	4503,3841		1230,2043,899	no	coding-synonymous	OR2A5	NM_012365.1		2602,2575,953	CC,CT,TT		46.0331,16.3432,36.5498		290/312	143748364	7779,4481	1958	4172	6130	SO:0001819	synonymous_variant	393046	exon1			GATCTATAGCCTG	U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"""GPCR / Class A : Olfactory receptors"""	8232	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 5"""	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.870T>C	7.37:g.143748364T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_012365	B9EGX2|O43885|O43888	Silent	SNP	ENST00000408906.2	37	CCDS43668.1																																																																																			T|0.357;C|0.643	0.643	strong		0.517	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1		
PSG9	5678	hgsc.bcm.edu	37	19	43763059	43763059	+	Missense_Mutation	SNP	C	C	T	rs12977717	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:43763059C>T	ENST00000270077.3	-	4	1034	c.938G>A	c.(937-939)cGg>cAg	p.R313Q	PSG9_ENST00000244293.7_Intron|PSG9_ENST00000291752.5_Intron|PSG9_ENST00000443718.3_Missense_Mutation_p.R220Q|PSG9_ENST00000418820.2_Missense_Mutation_p.R220Q|PSG9_ENST00000596730.1_Intron|PSG9_ENST00000593948.1_Intron	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	313	Ig-like C2-type 2.			R -> Q (in Ref. 9; AAH20759). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				ATATCGGTCCCGTATTTCACA	0.498													C|||	402	0.0802716	0.0113	0.1124	5008	,	,		16751	0.0		0.2177	False		,,,				2504	0.092				p.R313Q		Atlas-SNP	.											PSG9,trunk,malignant_melanoma,+1,1	PSG9	77	1	0			c.G938A						PASS	.	C	GLN/ARG	248,4030		51,146,1942	118.0	121.0	120.0		938	-2.5	0.0	19	dbSNP_121	120	1876,6692		307,1262,2715	no	missense	PSG9	NM_002784.3	43	358,1408,4657	TT,TC,CC		21.8954,5.7971,16.5343	benign	313/427	43763059	2124,10722	2139	4284	6423	SO:0001583	missense	5678	exon4			CGGTCCCGTATTT	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.938G>A	19.37:g.43763059C>T	ENSP00000270077:p.Arg313Gln	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	37	CCDS12618.1	217	0.09935897435897435	5	0.01016260162601626	40	0.11049723756906077	2	0.0034965034965034965	170	0.22427440633245382	N	0.658	-0.806935	0.02819	0.057971	0.218954	ENSG00000183668	ENST00000270077;ENST00000443718;ENST00000435220	T;T	0.12672	2.66;2.66	1.39	-2.48	0.06423	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	P;B	0.37176	0.586;0.128	B;B	0.28784	0.094;0.055	T	0.43507	-0.9387	8	0.32370	T	0.25	.	4.6661	0.12666	0.0:0.416:0.0:0.584	rs12977717;rs17855485	220;313	E7EW65;Q00887	.;PSG9_HUMAN	Q	313;220;274	ENSP00000270077:R313Q;ENSP00000396753:R220Q	ENSP00000270077:R313Q	R	-	2	0	PSG9	48454899	0.001000	0.12720	0.000000	0.03702	0.016000	0.09150	-0.492000	0.06467	-0.676000	0.05238	0.194000	0.17425	CGG	C|0.865;T|0.135	0.135	strong		0.498	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
SERPINB7	8710	hgsc.bcm.edu	37	18	61471529	61471529	+	Missense_Mutation	SNP	C	C	T	rs61735186	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:61471529C>T	ENST00000398019.2	+	8	1128	c.803C>T	c.(802-804)aCc>aTc	p.T268I	SERPINB7_ENST00000540675.1_Missense_Mutation_p.T251I|SERPINB7_ENST00000336429.2_Missense_Mutation_p.T268I|SERPINB7_ENST00000546027.1_Missense_Mutation_p.T268I	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	268					negative regulation of endopeptidase activity (GO:0010951)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of transforming growth factor beta1 production (GO:0032914)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	27		Esophageal squamous(42;0.129)				AGGCGAATGACCTCTAAGTAT	0.328													C|||	135	0.0269569	0.003	0.0562	5008	,	,		20204	0.0		0.0785	False		,,,				2504	0.0133				p.T268I		Atlas-SNP	.											.	SERPINB7	66	.	0			c.C803T						PASS	.	C	ILE/THR,ILE/THR	69,4337	63.5+/-100.7	0,69,2134	47.0	46.0	46.0		803,803	-6.0	0.0	18	dbSNP_129	46	875,7725	193.9+/-239.5	37,801,3462	yes	missense,missense	SERPINB7	NM_001040147.1,NM_003784.2	89,89	37,870,5596	TT,TC,CC		10.1744,1.566,7.2582	benign,benign	268/381,268/381	61471529	944,12062	2203	4300	6503	SO:0001583	missense	8710	exon8			GAATGACCTCTAA	AF027866	CCDS11988.1, CCDS58633.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166396	ENSG00000166396		"""Serine (or cysteine) peptidase inhibitors"""	13902	protein-coding gene	gene with protein product		603357	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 7"""			24172014	Standard	NM_003784		Approved	MEGSIN	uc002ljl.4	O75635	OTTHUMG00000060591	ENST00000398019.2:c.803C>T	18.37:g.61471529C>T	ENSP00000381101:p.Thr268Ile	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_001261830	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Missense_Mutation	SNP	ENST00000398019.2	37	CCDS11988.1	92	0.04212454212454213	3	0.006097560975609756	28	0.07734806629834254	0	0.0	61	0.08047493403693931	C	11.72	1.721408	0.30503	0.01566	0.101744	ENSG00000166396	ENST00000336429;ENST00000398019;ENST00000540675;ENST00000546027	D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9	5.92	-5.99	0.02213	Serpin domain (3);	1.287280	0.05038	N	0.475719	T	0.07324	0.0185	N	0.21324	0.655	0.09310	N	1	B;P	0.36048	0.34;0.534	B;B	0.33392	0.101;0.163	T	0.48502	-0.9030	10	0.40728	T	0.16	.	13.6911	0.62547	0.7932:0.1174:0.0895:0.0	rs61735186	251;268	F5GZC0;O75635	.;SPB7_HUMAN	I	268;268;251;268	ENSP00000337212:T268I;ENSP00000381101:T268I;ENSP00000444572:T251I;ENSP00000444861:T268I	ENSP00000337212:T268I	T	+	2	0	SERPINB7	59622509	0.005000	0.15991	0.002000	0.10522	0.953000	0.61014	0.096000	0.15147	-1.003000	0.03425	0.655000	0.94253	ACC	C|0.939;T|0.061	0.061	strong		0.328	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134007.1	NM_003784	
PPP1R9A	55607	hgsc.bcm.edu	37	7	94540527	94540527	+	Missense_Mutation	SNP	G	G	A	rs61737465	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:94540527G>A	ENST00000433881.1	+	2	1634	c.1102G>A	c.(1102-1104)Gat>Aat	p.D368N	PPP1R9A_ENST00000289495.5_Missense_Mutation_p.D368N|PPP1R9A_ENST00000456331.2_Missense_Mutation_p.D368N|PPP1R9A_ENST00000424654.1_Missense_Mutation_p.D368N|PPP1R9A_ENST00000340694.4_Missense_Mutation_p.D368N|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.D368N			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	368					actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			TGCAGGTGGTGATTTCACCTC	0.438										HNSCC(28;0.073)			G|||	80	0.0159744	0.0	0.0274	5008	,	,		21939	0.0		0.0497	False		,,,				2504	0.0112				p.D368N		Atlas-SNP	.											.	PPP1R9A	264	.	0			c.G1102A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	66,4340	61.7+/-98.7	0,66,2137	90.0	93.0	92.0		1102,1102,1102,1102,1102	4.5	1.0	7	dbSNP_129	92	582,8018	156.3+/-210.2	19,544,3737	yes	missense,missense,missense,missense,missense	PPP1R9A	NM_001166160.1,NM_001166161.1,NM_001166162.1,NM_001166163.1,NM_017650.2	23,23,23,23,23	19,610,5874	AA,AG,GG		6.7674,1.498,4.9823	benign,benign,benign,benign,benign	368/1375,368/1297,368/1254,368/1091,368/1099	94540527	648,12358	2203	4300	6503	SO:0001583	missense	55607	exon2			GGTGGTGATTTCA	AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Sterile alpha motif (SAM) domain containing"""	14946	protein-coding gene	gene with protein product		602468	"""protein phosphatase 1, regulatory (inhibitor) subunit 9A"""			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.1102G>A	7.37:g.94540527G>A	ENSP00000398870:p.Asp368Asn	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	177	88	0.497175	NM_017650	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Missense_Mutation	SNP	ENST00000433881.1	37	CCDS34683.1	46	0.021062271062271064	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	38	0.05013192612137203	G	12.87	2.068739	0.36470	0.01498	0.067674	ENSG00000158528	ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331	D;D;D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28;-3.28;-3.28	5.41	4.52	0.55395	.	0.256457	0.39687	N	0.001298	T	0.45538	0.1347	L	0.41027	1.25	0.33724	D	0.617362	B;B;B;B;B	0.06786	0.001;0.0;0.001;0.0;0.001	B;B;B;B;B	0.06405	0.001;0.002;0.002;0.001;0.001	T	0.74200	-0.3742	9	.	.	.	.	8.7904	0.34848	0.2262:0.0:0.7738:0.0	rs61737465	368;368;368;368;368	B7ZLX4;F8W7J9;E9PDX1;E9PCK6;Q9ULJ8	.;.;.;.;NEB1_HUMAN	N	368	ENSP00000405514:D368N;ENSP00000344524:D368N;ENSP00000411342:D368N;ENSP00000398870:D368N;ENSP00000289495:D368N;ENSP00000402893:D368N	.	D	+	1	0	PPP1R9A	94378463	1.000000	0.71417	1.000000	0.80357	0.266000	0.26442	2.826000	0.48104	1.426000	0.47256	0.555000	0.69702	GAT	G|0.960;A|0.040	0.040	strong		0.438	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037522	33037522	+	Missense_Mutation	SNP	T	T	C	rs1042178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33037522T>C	ENST00000419277.1	-	3	371	c.242A>G	c.(241-243)cAa>cGa	p.Q81R	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.Q81R	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	81	Alpha-1.		Q -> R (in allele DPA1*01:08, allele DPA1*02:01, allele DPA1*02:02, allele DPA1*02:03, allele DPA1*02:04 and allele DPA1*04:01; dbSNP:rs1042178).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						GGAAAAGGCTTGGCCAAACTC	0.478													.|||	2196	0.438498	0.5809	0.281	5008	,	,		19699	0.6796		0.1869	False		,,,				2504	0.3681				p.Q81R		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.A242G						PASS	.	C	ARG/GLN,ARG/GLN,ARG/GLN	1412,1610		328,756,427	85.0	96.0	92.0		242,242,242	-4.5	0.0	6	dbSNP_86	92	953,4465		72,809,1828	no	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	43,43,43	400,1565,2255	CC,CT,TT		17.5895,46.724,28.0213	benign,benign,benign	81/261,81/261,81/261	33037522	2365,6075	1511	2709	4220	SO:0001583	missense	3113	exon2			AAGGCTTGGCCAA	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.242A>G	6.37:g.33037522T>C	ENSP00000393566:p.Gln81Arg	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	159	52	0.327044	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	862	0.3946886446886447	276	0.5609756097560976	87	0.24033149171270718	371	0.6486013986013986	128	0.16886543535620052	C	0.008	-1.876631	0.00537	0.46724	0.175895	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.00717	5.79;5.79;5.79	3.0	-4.48	0.03515	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	0.767258	0.11484	N	0.559428	T	0.00144	0.0004	N	0.04705	-0.18	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24190	-1.0167	9	0.05525	T	0.97	.	13.2798	0.60208	0.0:0.1377:0.0:0.8623	rs1042178;rs2308915;rs3173302;rs16868557;rs16868559;rs45614833;rs52792876;rs60098014;rs1042178	81	P20036	DPA1_HUMAN	R	81	ENSP00000393566:Q81R;ENSP00000402872:Q81R;ENSP00000390929:Q81R	ENSP00000393566:Q81R	Q	-	2	0	HLA-DPA1	33145500	0.000000	0.05858	0.000000	0.03702	0.683000	0.39861	-3.957000	0.00325	-1.675000	0.01459	-1.124000	0.02001	CAA	T|0.688;C|0.310	0.310	strong		0.478	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
MUC16	94025	hgsc.bcm.edu	37	19	9086123	9086123	+	Missense_Mutation	SNP	A	A	C	rs10402812	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9086123A>C	ENST00000397910.4	-	1	5895	c.5692T>G	c.(5692-5694)Tac>Gac	p.Y1898D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1898	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCTCTGTGTAAGTCATGGAA	0.493													A|||	1134	0.226438	0.27	0.2983	5008	,	,		21776	0.0228		0.3111	False		,,,				2504	0.2393				p.Y1898D		Atlas-SNP	.											.	MUC16	4315	.	0			c.T5692G						PASS	.	A	ASP/TYR	1034,2846		147,740,1053	90.0	84.0	86.0		5692	0.2	0.0	19	dbSNP_119	86	2740,5574		461,1818,1878	yes	missense	MUC16	NM_024690.2	160	608,2558,2931	CC,CA,AA		32.9565,26.6495,30.9496	probably-damaging	1898/14508	9086123	3774,8420	1940	4157	6097	SO:0001583	missense	94025	exon1			CTGTGTAAGTCAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5692T>G	19.37:g.9086123A>C	ENSP00000381008:p.Tyr1898Asp	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	490	0.22435897435897437	127	0.258130081300813	111	0.30662983425414364	14	0.024475524475524476	238	0.31398416886543534	a	0.462	-0.888737	0.02511	0.266495	0.329565	ENSG00000181143	ENST00000397910	T	0.01560	4.77	0.225	0.225	0.15325	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	D	0.62365	0.991	D	0.68039	0.955	T	0.50171	-0.8859	6	0.87932	D	0	.	.	.	.	rs10402812;rs58531423;rs10402812	1898	B5ME49	.	D	1898	ENSP00000381008:Y1898D	ENSP00000381008:Y1898D	Y	-	1	0	MUC16	8947123	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-1.057000	0.03486	0.257000	0.21650	0.254000	0.18369	TAC	A|0.765;C|0.235	0.235	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PRL	5617	hgsc.bcm.edu	37	6	22287745	22287745	+	Silent	SNP	C	C	T	rs6239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:22287745C>T	ENST00000306482.1	-	5	1088	c.570G>A	c.(568-570)gaG>gaA	p.E190E	RP3-404K8.2_ENST00000561912.1_RNA	NM_000948.5|NM_001163558.2	NP_000939.1|NP_001157030.1	P01236	PRL_HUMAN	prolactin	190				ES -> SE (in Ref. 7; AA sequence). {ECO:0000305}.	cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|circadian rhythm (GO:0007623)|female pregnancy (GO:0007565)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|multicellular organismal response to stress (GO:0033555)|ovulation cycle (GO:0042698)|parturition (GO:0007567)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of JAK-STAT cascade (GO:0046427)|regulation of multicellular organism growth (GO:0040014)|regulation of ossification (GO:0030278)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	prolactin receptor binding (GO:0005148)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)|prostate(1)	16	Ovarian(93;0.163)					AAAGGCGAGACTCTTCATCAG	0.448													C|||	518	0.103435	0.0257	0.17	5008	,	,		18599	0.2421		0.0189	False		,,,				2504	0.1053				p.E190E		Atlas-SNP	.											.	PRL	41	.	0			c.G570A						PASS	.	C	,	120,4286	89.7+/-128.4	0,120,2083	177.0	155.0	163.0		570,570	-10.3	0.0	6	dbSNP_52	163	154,8446	74.8+/-137.4	4,146,4150	no	coding-synonymous,coding-synonymous	PRL	NM_000948.5,NM_001163558.2	,	4,266,6233	TT,TC,CC		1.7907,2.7236,2.1067	,	190/228,190/228	22287745	274,12732	2203	4300	6503	SO:0001819	synonymous_variant	5617	exon5			GCGAGACTCTTCA	D00411	CCDS4548.1	6p22.3	2013-09-16			ENSG00000172179	ENSG00000172179			9445	protein-coding gene	gene with protein product		176760					Standard	NM_000948		Approved		uc003ndq.3	P01236	OTTHUMG00000016111	ENST00000306482.1:c.570G>A	6.37:g.22287745C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_000948	Q15199|Q92996	Silent	SNP	ENST00000306482.1	37	CCDS4548.1																																																																																			C|0.946;T|0.054	0.054	strong		0.448	PRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043327.1	NM_000948	
ZBTB7B	51043	hgsc.bcm.edu	37	1	154988957	154988957	+	Silent	SNP	A	A	G	rs2242195	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:154988957A>G	ENST00000368426.3	+	4	1553	c.1416A>G	c.(1414-1416)ccA>ccG	p.P472P	ZBTB7B_ENST00000292176.2_Silent_p.P472P|ZBTB7B_ENST00000535420.1_Silent_p.P472P|ZBTB7B_ENST00000417934.2_Silent_p.P506P	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	472					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CCCACTACCCACCACCCTCTA	0.657													G|||	3373	0.673522	0.4811	0.7478	5008	,	,		17839	0.9127		0.5785	False		,,,				2504	0.7321				p.P506P		Atlas-SNP	.											ZBTB7B,NS,carcinoma,+1,1	ZBTB7B	69	1	0			c.A1518G						PASS	.	G		2259,2147	576.8+/-384.3	574,1111,518	103.0	79.0	87.0		1416	-7.6	0.8	1	dbSNP_98	87	4787,3813	538.4+/-383.4	1330,2127,843	no	coding-synonymous	ZBTB7B	NM_015872.2		1904,3238,1361	GG,GA,AA		44.3372,48.729,45.825		472/540	154988957	7046,5960	2203	4300	6503	SO:0001819	synonymous_variant	51043	exon5			CTACCCACCACCC	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	18668	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 15"""	607646	"""zinc finger protein 67 homolog (mouse)"""	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.1416A>G	1.37:g.154988957A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	129	125	0.968992	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Silent	SNP	ENST00000368426.3	37	CCDS1081.1																																																																																			A|0.422;G|0.578	0.578	strong		0.657	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872	
CACNA1H	8912	hgsc.bcm.edu	37	16	1272684	1272684	+	IGR	SNP	C	C	G	rs4984638	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1272684C>G	ENST00000348261.5	+	0	8084				TPSG1_ENST00000234798.4_Missense_Mutation_p.W160S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit						aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GCCGGTCACCCAGCACCGGAT	0.682													c|||	612	0.122204	0.0401	0.1412	5008	,	,		16523	0.1637		0.1918	False		,,,				2504	0.1053				p.W160S		Atlas-SNP	.											.	TPSG1	19	.	0			c.G479C						PASS	.		SER/TRP	243,4153	135.7+/-171.8	8,227,1963	66.0	82.0	77.0		479	2.5	0.8	16	dbSNP_111	77	1656,6942	292.7+/-301.0	154,1348,2797	yes	missense	TPSG1	NM_012467.3	177	162,1575,4760	GG,GC,CC		19.2603,5.5278,14.6144	probably-damaging	160/322	1272684	1899,11095	2198	4299	6497	SO:0001628	intergenic_variant	25823	exon4			GTCACCCAGCACC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180			16.37:g.1272684C>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	172	89	0.517442	NM_012467	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	304	0.1391941391941392	16	0.032520325203252036	50	0.13812154696132597	91	0.1590909090909091	147	0.19393139841688653	c	10.85	1.466579	0.26335	0.055278	0.192603	ENSG00000116176	ENST00000234798	D	0.92805	-3.11	3.47	2.48	0.30137	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.01387	0.0045	L	0.35487	1.065	0.24027	P	0.99612212	D	0.89917	1.0	D	0.80764	0.994	T	0.45527	-0.9255	8	0.52906	T	0.07	.	9.8621	0.41120	0.2067:0.7933:0.0:0.0	rs4984638	160	Q9NRR2	TRYG1_HUMAN	S	160	ENSP00000234798:W160S	ENSP00000234798:W160S	W	-	2	0	TPSG1	1212685	0.000000	0.05858	0.753000	0.31225	0.255000	0.26057	0.279000	0.18771	0.517000	0.28361	0.556000	0.70494	TGG	C|0.853;G|0.147	0.147	strong		0.682	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
YBEY	54059	hgsc.bcm.edu	37	21	47717493	47717493	+	Missense_Mutation	SNP	G	G	T	rs61736728	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47717493G>T	ENST00000329319.3	+	5	847	c.449G>T	c.(448-450)cGa>cTa	p.R150L	YBEY_ENST00000397692.1_Missense_Mutation_p.R62L|YBEY_ENST00000397701.4_Missense_Mutation_p.R150L|YBEY_ENST00000397691.1_Missense_Mutation_p.R150L|YBEY_ENST00000397694.1_Missense_Mutation_p.R105L|YBEY_ENST00000339195.6_Missense_Mutation_p.R107L	NM_058181.1	NP_478061.1	P58557	YBEY_HUMAN	ybeY metallopeptidase (putative)	150					rRNA processing (GO:0006364)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)	9						GAGCTGGGCCGACGCACGGGG	0.701													G|||	87	0.0173722	0.0015	0.0245	5008	,	,		10890	0.001		0.0626	False		,,,				2504	0.0041				p.R150L		Atlas-SNP	.											YBEY,NS,carcinoma,0,1	YBEY	23	1	0			c.G449T						PASS	.	G	LEU/ARG	49,4099		1,47,2026	6.0	7.0	7.0		449	0.1	0.0	21	dbSNP_129	7	459,7799		8,443,3678	yes	missense	YBEY	NM_058181.1	102	9,490,5704	TT,TG,GG		5.5582,1.1813,4.0948	probably-damaging	150/168	47717493	508,11898	2074	4129	6203	SO:0001583	missense	54059	exon5			TGGGCCGACGCAC	AK294975	CCDS33591.1	21q22.3	2010-12-08	2010-12-08	2010-12-08	ENSG00000182362	ENSG00000182362			1299	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 57"""	C21orf57			Standard	XM_005261155		Approved		uc002ziv.3	P58557	OTTHUMG00000090632	ENST00000329319.3:c.449G>T	21.37:g.47717493G>T	ENSP00000329614:p.Arg150Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	82	51	0.621951	NM_058181	B7WPA9|B7WPF7|D3DSN2	Missense_Mutation	SNP	ENST00000329319.3	37	CCDS33591.1	70	0.03205128205128205	3	0.006097560975609756	13	0.03591160220994475	1	0.0017482517482517483	53	0.06992084432717678	G	9.562	1.118668	0.20877	0.011813	0.055582	ENSG00000182362	ENST00000397701;ENST00000397694;ENST00000329319;ENST00000339195;ENST00000397692;ENST00000397691	.	.	.	4.96	0.0754	0.14399	.	0.158082	0.35838	N	0.002954	T	0.01029	0.0034	N	0.17594	0.5	0.09310	N	1	P;P;P;P	0.44044	0.462;0.825;0.804;0.704	B;B;B;B	0.43950	0.151;0.437;0.28;0.197	T	0.16364	-1.0405	9	0.02654	T	1	-8.7638	7.6929	0.28577	0.4468:0.0:0.5532:0.0	rs61736728	62;107;105;150	P58557-4;P58557-2;P58557-3;P58557	.;.;.;YBEY_HUMAN	L	150;105;150;107;62;150	.	ENSP00000329614:R150L	R	+	2	0	YBEY	46541921	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.015000	0.13355	-0.096000	0.12329	-1.036000	0.02392	CGA	G|0.968;T|0.032	0.032	strong		0.701	YBEY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207265.1	NM_058181	
PTPRF	5792	hgsc.bcm.edu	37	1	44072018	44072018	+	Silent	SNP	C	C	T	rs1065772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:44072018C>T	ENST00000359947.4	+	20	3931	c.3591C>T	c.(3589-3591)acC>acT	p.T1197T	PTPRF_ENST00000372414.3_Silent_p.T1197T|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000438120.1_Silent_p.T1188T|PTPRF_ENST00000422171.2_Silent_p.T545T|PTPRF_ENST00000372413.3_Silent_p.T1188T	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1197					cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TCCCGGAGACCTTTACCTTGG	0.602													C|||	1393	0.278155	0.0371	0.268	5008	,	,		15577	0.4702		0.3569	False		,,,				2504	0.3323				p.T1197T		Atlas-SNP	.											.	PTPRF	172	.	0			c.C3591T						PASS	.	C	,	418,3988	203.8+/-226.2	21,376,1806	118.0	129.0	125.0		3591,3564	1.1	1.0	1	dbSNP_86	125	3000,5600	462.2+/-365.6	525,1950,1825	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	546,2326,3631	TT,TC,CC		34.8837,9.4871,26.2802	,	1197/1908,1188/1899	44072018	3418,9588	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon20			GGAGACCTTTACC	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.3591C>T	1.37:g.44072018C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	121	70	0.578512	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	629|629	0.288003663003663|0.288003663003663	24|24	0.04878048780487805|0.04878048780487805	109|109	0.3011049723756906|0.3011049723756906	228|228	0.3986013986013986|0.3986013986013986	268|268	0.35356200527704484|0.35356200527704484	C|C	0.778|0.778	-0.763508|-0.763508	0.02996|0.02996	0.094871|0.094871	0.348837|0.348837	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	5.2|5.2	1.07|1.07	0.20283|0.20283	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.44937|0.44937	-0.9295|-0.9295	3|3	.|.	.|.	.|.	.|.	5.306|5.306	0.15803|0.15803	0.2361:0.4699:0.2289:0.0652|0.2361:0.4699:0.2289:0.0652	rs1065772;rs17849110;rs1065772|rs1065772;rs17849110;rs1065772	.|.	.|.	.|.	F|L	570;611|843	.|.	.|.	L|P	+|+	1|2	0|0	PTPRF|PTPRF	43844605|43844605	0.268000|0.268000	0.24133|0.24133	0.996000|0.996000	0.52242|0.52242	0.030000|0.030000	0.12068|0.12068	0.196000|0.196000	0.17176|0.17176	0.023000|0.023000	0.15187|0.15187	-1.083000|-1.083000	0.02208|0.02208	CTT|CCT	C|0.732;T|0.268	0.268	strong		0.602	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
NCKAP1L	3071	hgsc.bcm.edu	37	12	54911426	54911426	+	Splice_Site	SNP	C	C	T	rs2270581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:54911426C>T	ENST00000293373.6	+	12	1284	c.1205C>T	c.(1204-1206)tCg>tTg	p.S402L	NCKAP1L_ENST00000545638.2_Splice_Site_p.S352L	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	402			S -> L (in dbSNP:rs2270581).		actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)	p.S402L(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						TATGCTGACTCGTTAGTACTT	0.502													C|||	382	0.076278	0.0877	0.1225	5008	,	,		20361	0.0675		0.0626	False		,,,				2504	0.0511				p.S402L		Atlas-SNP	.											NCKAP1L,NS,carcinoma,0,1	NCKAP1L	180	1	1	Substitution - Missense(1)	stomach(1)	c.C1205T						PASS	.	C	LEU/SER,LEU/SER	465,3941	221.0+/-238.3	21,423,1759	126.0	107.0	113.0		1055,1205	3.8	1.0	12	dbSNP_100	113	537,8063	150.0+/-205.0	16,505,3779	yes	missense-near-splice,missense-near-splice	NCKAP1L	NM_001184976.1,NM_005337.4	145,145	37,928,5538	TT,TC,CC		6.2442,10.5538,7.7041	benign,benign	352/1078,402/1128	54911426	1002,12004	2203	4300	6503	SO:0001630	splice_region_variant	3071	exon12			CTGACTCGTTAGT	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"""hematopoietic protein 1"""	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.1205+1C>T	12.37:g.54911426C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_005337	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	37	CCDS31813.1	159	0.07280219780219781	42	0.08536585365853659	45	0.12430939226519337	25	0.043706293706293704	47	0.06200527704485488	C	14.24	2.477116	0.44044	0.105538	0.062442	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.31769	1.48;1.48	5.8	3.82	0.43975	.	0.985370	0.08333	N	0.962057	T	0.00271	0.0008	N	0.14661	0.345	0.27257	P	0.958738	B	0.10296	0.003	B	0.06405	0.002	T	0.18493	-1.0335	9	0.31617	T	0.26	3.1084	7.9946	0.30261	0.0:0.7319:0.0:0.2681	rs2270581;rs17726286;rs52829527;rs59596035;rs2270581	402	P55160	NCKPL_HUMAN	L	402;352	ENSP00000293373:S402L;ENSP00000445596:S352L	ENSP00000293373:S402L	S	+	2	0	NCKAP1L	53197693	0.987000	0.35691	0.961000	0.40146	0.902000	0.53008	1.326000	0.33735	0.684000	0.31448	0.462000	0.41574	TCG	C|0.929;T|0.071	0.071	strong		0.502	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337	Missense_Mutation
SLC22A14	9389	hgsc.bcm.edu	37	3	38357961	38357961	+	Missense_Mutation	SNP	C	C	G	rs240033	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:38357961C>G	ENST00000273173.4	+	9	1770	c.1679C>G	c.(1678-1680)cCg>cGg	p.P560R	SLC22A14_ENST00000448498.1_Missense_Mutation_p.P560R	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	560			P -> R (in dbSNP:rs240033). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		TCCCTGCTGCCGGAAACGCGA	0.612													C|||	1282	0.25599	0.2504	0.2767	5008	,	,		19883	0.2599		0.2535	False		,,,				2504	0.2474				p.P560R		Atlas-SNP	.											.	SLC22A14	64	.	0			c.C1679G						PASS	.	C	ARG/PRO	1180,3226	415.0+/-337.0	147,886,1170	99.0	78.0	85.0		1679	2.4	0.0	3	dbSNP_79	85	2436,6164	401.1+/-347.0	351,1734,2215	yes	missense	SLC22A14	NM_004803.3	103	498,2620,3385	GG,GC,CC		28.3256,26.7817,27.8026	probably-damaging	560/595	38357961	3616,9390	2203	4300	6503	SO:0001583	missense	9389	exon9			TGCTGCCGGAAAC	AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"""Solute carriers"""	8495	protein-coding gene	gene with protein product		604048	"""organic cationic transporter-like 4"", ""solute carrier family 22 (organic cation transporter), member 14"""	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.1679C>G	3.37:g.38357961C>G	ENSP00000273173:p.Pro560Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	574	0.26282051282051283	115	0.23373983739837398	112	0.30939226519337015	158	0.2762237762237762	189	0.24934036939313983	C	12.47	1.948947	0.34377	0.267817	0.283256	ENSG00000144671	ENST00000448498;ENST00000423219;ENST00000273173	T;T	0.79940	-1.32;-1.32	4.2	2.39	0.29439	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.88241	2.94	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.01159	-1.1433	9	0.62326	D	0.03	.	6.0188	0.19618	0.0:0.7052:0.1913:0.1035	rs240033;rs1618758;rs17732434;rs59679116;rs240033	560	Q9Y267	S22AE_HUMAN	R	560;545;560	ENSP00000396283:P560R;ENSP00000273173:P560R	ENSP00000273173:P560R	P	+	2	0	SLC22A14	38332965	0.995000	0.38212	0.006000	0.13384	0.000000	0.00434	2.693000	0.47027	0.699000	0.31761	-0.892000	0.02923	CCG	C|0.724;G|0.276	0.276	strong		0.612	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803	
F13B	2165	hgsc.bcm.edu	37	1	197030087	197030087	+	Silent	SNP	C	C	T	rs17514253	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:197030087C>T	ENST00000367412.1	-	4	613	c.570G>A	c.(568-570)aaG>aaA	p.K190K		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	190	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						CCTCTGTCTTCTTTCCTCCAG	0.383													C|||	17	0.00339457	0.0008	0.0	5008	,	,		13063	0.0		0.0159	False		,,,				2504	0.0				p.K190K		Atlas-SNP	.											F13B,NS,carcinoma,0,2	F13B	137	2	0			c.G570A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	236.0	215.0	222.0		570	0.9	0.0	1	dbSNP_123	222	71,8529	42.2+/-99.7	0,71,4229	no	coding-synonymous	F13B	NM_001994.2		0,76,6427	TT,TC,CC		0.8256,0.1135,0.5843		190/662	197030087	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	2165	exon4			TGTCTTCTTTCCT	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.570G>A	1.37:g.197030087C>T		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	224	102	0.455357	NM_001994	A8K3E5|Q5VYL5	Silent	SNP	ENST00000367412.1	37	CCDS1388.1																																																																																			C|0.995;T|0.005	0.005	strong		0.383	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994	
HLTF	6596	hgsc.bcm.edu	37	3	148766666	148766666	+	Silent	SNP	T	T	C	rs34474865	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:148766666T>C	ENST00000310053.5	-	16	1933	c.1740A>G	c.(1738-1740)agA>agG	p.R580R	HLTF_ENST00000494055.1_Silent_p.R580R|HLTF_ENST00000392912.2_Silent_p.R580R|HLTF_ENST00000465259.1_Silent_p.R579R	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	580	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AAACCCATCTTCTTTCTGATT	0.333													T|||	136	0.0271565	0.0015	0.0605	5008	,	,		15402	0.0		0.0795	False		,,,				2504	0.0123				p.R580R		Atlas-SNP	.											.	HLTF	87	.	0			c.A1740G						PASS	.	T	,	59,4347	57.4+/-93.9	0,59,2144	167.0	154.0	159.0		1740,1740	0.7	1.0	3	dbSNP_126	159	615,7983	160.3+/-213.4	18,579,3702	no	coding-synonymous,coding-synonymous	HLTF	NM_003071.3,NM_139048.2	,	18,638,5846	CC,CT,TT		7.1528,1.3391,5.183	,	580/1010,580/1010	148766666	674,12330	2203	4299	6502	SO:0001819	synonymous_variant	6596	exon16			CCATCTTCTTTCT	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"""RING-type (C3HC4) zinc fingers"""	11099	protein-coding gene	gene with protein product		603257	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"""	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.1740A>G	3.37:g.148766666T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	154	80	0.519481	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Silent	SNP	ENST00000310053.5	37	CCDS33875.1																																																																																			T|0.950;C|0.050	0.050	strong		0.333	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
OR51B2	79345	hgsc.bcm.edu	37	11	5344681	5344681	+	Missense_Mutation	SNP	G	G	A	rs11036815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5344681G>A	ENST00000328813.2	-	1	901	c.847C>T	c.(847-849)Cct>Tct	p.P283S	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron	NM_033180.4	NP_149420.4	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B, member 2	283			P -> S (in dbSNP:rs11036815).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|biliary_tract(1)|central_nervous_system(1)|large_intestine(6)|lung(21)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTCATTAAAGGAGGAAAGAGG	0.373													G|||	1326	0.264776	0.2897	0.2954	5008	,	,		21267	0.2173		0.2853	False		,,,				2504	0.2372				p.P283S		Atlas-SNP	.											.	OR51B2	69	.	0			c.C847T						PASS	.	G	SER/PRO	1323,3079	443.3+/-347.0	190,943,1068	113.0	106.0	108.0		847	4.4	0.8	11	dbSNP_120	108	2469,6125	405.5+/-348.5	336,1797,2164	yes	missense	OR51B2	NM_033180.4	74	526,2740,3232	AA,AG,GG		28.7293,30.0545,29.1782	probably-damaging	283/313	5344681	3792,9204	2201	4297	6498	SO:0001583	missense	79345	exon1			TTAAAGGAGGAAA	AF399503	CCDS31377.1	11p15.4	2012-08-09			ENSG00000184881	ENSG00000184881		"""GPCR / Class A : Olfactory receptors"""	14703	protein-coding gene	gene with protein product				OR51B1P			Standard	NM_033180		Approved		uc001mao.1	Q9Y5P1	OTTHUMG00000066682	ENST00000328813.2:c.847C>T	11.37:g.5344681G>A	ENSP00000327540:p.Pro283Ser	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	186	90	0.483871	NM_033180	Q96RD4	Missense_Mutation	SNP	ENST00000328813.2	37	CCDS31377.1	578	0.26465201465201466	159	0.3231707317073171	102	0.281767955801105	116	0.20279720279720279	201	0.26517150395778366	G	21.5	4.162103	0.78226	0.300545	0.287293	ENSG00000184881	ENST00000328813	T	0.00330	8.08	4.38	4.38	0.52667	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38272	U	0.001747	T	0.00012	0.0000	M	0.89214	3.015	0.26462	P	0.9754303	D	0.89917	1.0	D	0.97110	1.0	T	0.60712	-0.7209	9	0.72032	D	0.01	.	15.8595	0.79012	0.0:0.0:1.0:0.0	rs11036815;rs52816306;rs60406440;rs11036815	283	Q9Y5P1	O51B2_HUMAN	S	283	ENSP00000327540:P283S	ENSP00000327540:P283S	P	-	1	0	OR51B2	5301257	0.997000	0.39634	0.805000	0.32314	0.987000	0.75469	2.460000	0.45031	2.306000	0.77630	0.638000	0.83543	CCT	G|0.720;A|0.280	0.280	strong		0.373	OR51B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142983.1	NM_033180	
KIAA0825	285600	hgsc.bcm.edu	37	5	93722036	93722036	+	Missense_Mutation	SNP	G	G	A	rs72771666	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:93722036G>A	ENST00000513200.3	-	18	3602	c.3530C>T	c.(3529-3531)aCg>aTg	p.T1177M	KIAA0825_ENST00000427991.2_Missense_Mutation_p.T1177M	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	1177										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						CCTCAAGGTCGTCTTTAAAGG	0.363													G|||	158	0.0315495	0.0023	0.0173	5008	,	,		17528	0.0685		0.0249	False		,,,				2504	0.0501				p.T1177M		Atlas-SNP	.											KIAA0825_ENST00000513200,NS,carcinoma,+1,1	KIAA0825	172	1	0			c.C3530T						PASS	.						165.0	145.0	151.0					5																	93722036		692	1591	2283	SO:0001583	missense	285600	exon19			AAGGTCGTCTTTA	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 36"""	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.3530C>T	5.37:g.93722036G>A	ENSP00000424618:p.Thr1177Met	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	164	63	0.384146	NM_001145678	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000513200.3	37		68	0.031135531135531136	2	0.0040650406504065045	9	0.024861878453038673	37	0.06468531468531469	20	0.026385224274406333	G	7.600	0.672637	0.14776	.	.	ENSG00000185261	ENST00000513200;ENST00000427991	T;T	0.44083	0.93;0.93	5.97	-3.57	0.04612	.	.	.	.	.	T	0.01870	0.0059	N	0.02539	-0.55	0.09310	N	1	B;B	0.15719	0.014;0.014	B;B	0.08055	0.003;0.002	T	0.10683	-1.0619	9	0.46703	T	0.11	7.7312	13.5506	0.61730	0.9083:0.0:0.0917:0.0	.	1177;1177	Q8IV33;C9J0Q2	K0825_HUMAN;.	M	1177	ENSP00000424618:T1177M;ENSP00000400288:T1177M	ENSP00000400288:T1177M	T	-	2	0	KIAA0825	93747792	0.007000	0.16637	0.000000	0.03702	0.495000	0.33615	-0.032000	0.12266	-0.908000	0.03857	-0.312000	0.09012	ACG	G|0.969;A|0.031	0.031	strong		0.363	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665	
B4GALNT3	283358	hgsc.bcm.edu	37	12	644351	644351	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:644351A>G	ENST00000266383.5	+	2	202	c.189A>G	c.(187-189)gaA>gaG	p.E63E		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	63					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			GCTGGAGAGAACTGGCCAAGG	0.567																																					p.E63E		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.A189G						PASS	.						50.0	46.0	47.0					12																	644351		2203	4300	6503	SO:0001819	synonymous_variant	283358	exon2			GAGAGAACTGGCC	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.189A>G	12.37:g.644351A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	46	4	0.0869565	NM_173593	Q6ZNC1|Q8N7T6	Silent	SNP	ENST00000266383.5	37	CCDS8504.1																																																																																			.	.	none		0.567	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
ZNF471	57573	hgsc.bcm.edu	37	19	57037103	57037103	+	Missense_Mutation	SNP	C	C	G	rs16987303	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57037103C>G	ENST00000308031.5	+	5	1800	c.1667C>G	c.(1666-1668)tCc>tGc	p.S556C	ZNF471_ENST00000591537.1_3'UTR|ZNF471_ENST00000593197.1_3'UTR	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	556			S -> C (in dbSNP:rs16987303). {ECO:0000269|PubMed:10718198}.		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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		AGCCAAACTTCCAATCTTACT	0.408													C|||	414	0.0826677	0.0068	0.0994	5008	,	,		20133	0.004		0.2008	False		,,,				2504	0.1329				p.S556C	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.C1667G						PASS	.	C	CYS/SER	138,4268	99.4+/-138.0	5,128,2070	90.0	93.0	92.0		1667	3.9	0.0	19	dbSNP_123	92	1609,6991	299.5+/-304.5	158,1293,2849	no	missense	ZNF471	NM_020813.2	112	163,1421,4919	GG,GC,CC		18.7093,3.1321,13.4323	probably-damaging	556/627	57037103	1747,11259	2203	4300	6503	SO:0001583	missense	57573	exon5			AAACTTCCAATCT	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"""Zinc fingers, C2H2-type"", ""-"""	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1667C>G	19.37:g.57037103C>G	ENSP00000309161:p.Ser556Cys	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	198	0.09065934065934066	7	0.014227642276422764	43	0.11878453038674033	1	0.0017482517482517483	147	0.19393139841688653	C	13.46	2.244568	0.39697	0.031321	0.187093	ENSG00000196263	ENST00000308031	T	0.01725	4.67	3.9	3.9	0.45041	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.83312	2.635	0.37354	P	0.08905799999999997	P	0.47350	0.894	B	0.43916	0.436	T	0.33574	-0.9863	8	0.66056	D	0.02	.	10.2455	0.43339	0.1985:0.8015:0.0:0.0	rs16987303;rs52813441;rs16987303	556	Q9BX82	ZN471_HUMAN	C	556	ENSP00000309161:S556C	ENSP00000309161:S556C	S	+	2	0	ZNF471	61728915	0.000000	0.05858	0.009000	0.14445	0.932000	0.56968	-0.046000	0.11983	2.005000	0.58758	0.462000	0.41574	TCC	C|0.882;G|0.118	0.118	strong		0.408	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813	
PRRC2A	7916	hgsc.bcm.edu	37	6	31603189	31603189	+	Missense_Mutation	SNP	G	G	A	rs11538264	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31603189G>A	ENST00000376033.2	+	23	5554	c.5320G>A	c.(5320-5322)Gtg>Atg	p.V1774M	PRRC2A_ENST00000376007.4_Missense_Mutation_p.V1774M	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1774	4 X 57 AA type A repeats.		V -> M (in dbSNP:rs11538264).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CTTACGCCTAGTGGTAGGAGA	0.498													G|||	232	0.0463259	0.1006	0.0634	5008	,	,		24475	0.0179		0.0219	False		,,,				2504	0.0153				p.V1774M		Atlas-SNP	.											.	PRRC2A	152	.	0			c.G5320A						PASS	.	G	MET/VAL,MET/VAL	257,2765		10,237,1264	121.0	109.0	113.0		5320,5320	3.7	1.0	6	dbSNP_120	113	147,5271		1,145,2563	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	21,21	11,382,3827	AA,AG,GG		2.7132,8.5043,4.7867	probably-damaging,probably-damaging	1774/2158,1774/2158	31603189	404,8036	1511	2709	4220	SO:0001583	missense	7916	exon23			CGCCTAGTGGTAG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5320G>A	6.37:g.31603189G>A	ENSP00000365201:p.Val1774Met	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	302	137	0.453642	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	111	0.050824175824175824	55	0.11178861788617886	24	0.06629834254143646	16	0.027972027972027972	16	0.021108179419525065	G	5.652	0.304984	0.10678	0.085043	0.027132	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01647	4.71;4.71	5.51	3.71	0.42584	.	0.246078	0.28971	N	0.013543	T	0.00552	0.0018	N	0.22421	0.69	0.37881	P	0.06961200000000001	B	0.10296	0.003	B	0.09377	0.004	T	0.47983	-0.9074	9	0.87932	D	0	-3.1123	4.9425	0.13973	0.1686:0.0:0.6615:0.1699	rs11538264;rs17207253;rs11538264	1774	P48634	PRC2A_HUMAN	M	1768;1757;1774;1774;999	ENSP00000365175:V1774M;ENSP00000365201:V1774M	ENSP00000365175:V1774M	V	+	1	0	PRRC2A	31711168	0.924000	0.31332	0.977000	0.42913	0.401000	0.30781	2.140000	0.42159	0.863000	0.35553	-0.258000	0.10820	GTG	G|0.943;A|0.057	0.057	strong		0.498	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
SLC26A8	116369	hgsc.bcm.edu	37	6	35980121	35980121	+	Missense_Mutation	SNP	C	C	T	rs743923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:35980121C>T	ENST00000490799.1	-	3	570	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	SLC26A8_ENST00000355574.2_Missense_Mutation_p.V73M|SLC26A8_ENST00000394602.2_Missense_Mutation_p.V73M	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						ATTGTAAGCACGCATCGTAGG	0.458													T|||	1307	0.260982	0.4652	0.2277	5008	,	,		21601	0.1151		0.2366	False		,,,				2504	0.184				p.V73M		Atlas-SNP	.											.	SLC26A8	95	.	0			c.G217A						PASS	.	T	MET/VAL,MET/VAL,MET/VAL	1815,2591	638.7+/-397.0	369,1077,757	163.0	148.0	153.0		217,217,217	-2.6	0.1	6	dbSNP_86	153	2119,6481	716.1+/-406.1	273,1573,2454	yes	missense,missense,missense	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	21,21,21	642,2650,3211	TT,TC,CC		24.6395,41.1938,30.2476	benign,benign,benign	73/971,73/971,73/866	35980121	3934,9072	2203	4300	6503	SO:0001583	missense	116369	exon3			TAAGCACGCATCG	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"""Solute carriers"""	14468	protein-coding gene	gene with protein product		608480	"""solute carrier family 26, member 8"""			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.217G>A	6.37:g.35980121C>T	ENSP00000417638:p.Val73Met	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_052961		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	555	0.2541208791208791	208	0.42276422764227645	93	0.2569060773480663	73	0.12762237762237763	181	0.23878627968337732	T	4.919	0.170748	0.09391	0.411938	0.246395	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574;ENST00000480663	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.81	-2.58	0.06228	.	0.746757	0.13261	N	0.401271	T	0.03178	0.0093	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.001	T	0.36915	-0.9728	9	0.23891	T	0.37	.	1.9852	0.03435	0.1208:0.1984:0.3719:0.3089	rs743923;rs16883644;rs17845762;rs17858719;rs52822911;rs61568225;rs743923	73;73	Q96RN1;Q96RN1-2	S26A8_HUMAN;.	M	73;73;73;159	ENSP00000417638:V73M;ENSP00000378100:V73M;ENSP00000347778:V73M;ENSP00000420488:V159M	ENSP00000347778:V73M	V	-	1	0	SLC26A8	36088099	0.614000	0.27017	0.066000	0.19879	0.692000	0.40212	0.027000	0.13621	-0.450000	0.07107	-0.269000	0.10298	GTG	C|0.714;T|0.286	0.286	strong		0.458	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
RPA4	29935	hgsc.bcm.edu	37	X	96139459	96139459	+	Silent	SNP	T	T	C	rs2642218	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:96139459T>C	ENST00000373040.3	+	1	553	c.150T>C	c.(148-150)aaT>aaC	p.N50N	DIAPH2_ENST00000373054.4_Intron|DIAPH2_ENST00000355827.4_Intron|DIAPH2_ENST00000373061.3_Intron|DIAPH2_ENST00000373049.4_Intron|DIAPH2_ENST00000324765.8_Intron	NM_013347.4	NP_037479.1	Q13156	RFA4_HUMAN	replication protein A4, 30kDa	50					DNA damage checkpoint (GO:0000077)|DNA recombination (GO:0006310)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)	DNA replication factor A complex (GO:0005662)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	13						TACCGTGTAATGTGAACCAGC	0.502								Other identified genes with known or suspected DNA repair function					T|||	1533	0.406093	0.5166	0.2954	3775	,	,		15500	0.2837		0.2087	False		,,,				2504	0.1524				p.N50N		Atlas-SNP	.											.	RPA4	29	.	0			c.T150C						PASS	.	T	,,	2465,1370		671,765,358,196,213	158.0	130.0	139.0		,,150	2.1	0.0	X	dbSNP_100	139	2005,4723		212,1021,560,1195,1312	no	intron,intron,coding-synonymous	DIAPH2,RPA4	NM_006729.4,NM_007309.3,NM_013347.4	,,	883,1786,918,1391,1525	CC,CT,C,TT,T		29.8008,35.7236,42.3175	,,	,,50/262	96139459	4470,6093	2203	4300	6503	SO:0001819	synonymous_variant	29935	exon1			GTGTAATGTGAAC	U24186	CCDS35345.1	Xq21	2010-04-09	2010-04-09		ENSG00000204086	ENSG00000204086			30305	protein-coding gene	gene with protein product		300767	"""replication protein A4, 34kDa"""			7760808	Standard	NM_013347		Approved	HSU24186	uc004efv.4	Q13156	OTTHUMG00000021987	ENST00000373040.3:c.150T>C	X.37:g.96139459T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	138	10	0.0724638	NM_013347	Q3SY03	Silent	SNP	ENST00000373040.3	37	CCDS35345.1																																																																																			T|0.558;0|0.003	.	strong		0.502	RPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057464.1	NM_013347	
NPAT	4863	hgsc.bcm.edu	37	11	108043988	108043988	+	Missense_Mutation	SNP	C	C	T	rs2070661	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:108043988C>T	ENST00000278612.8	-	13	1828	c.1723G>A	c.(1723-1725)Gtt>Att	p.V575I	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	575			V -> I (in dbSNP:rs2070661). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8743993, ECO:0000269|PubMed:8923007, ECO:0000269|PubMed:9205109}.		positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		CTCTTGTGAACTTCACTAGAA	0.294													T|||	3083	0.615615	0.652	0.6729	5008	,	,		19423	0.4554		0.6302	False		,,,				2504	0.6759				p.V575I		Atlas-SNP	.											.	NPAT	124	.	0			c.G1723A						PASS	.	T	ILE/VAL	2292,1324		716,860,232	79.0	76.0	77.0		1723	4.9	0.9	11	dbSNP_96	77	4676,3454		1378,1920,767	yes	missense	NPAT	NM_002519.2	29	2094,2780,999	TT,TC,CC		42.4846,36.615,40.6777	benign	575/1428	108043988	6968,4778	1808	4065	5873	SO:0001583	missense	4863	exon13			TGTGAACTTCACT	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.1723G>A	11.37:g.108043988C>T	ENSP00000278612:p.Val575Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	1287	0.5892857142857143	308	0.6260162601626016	240	0.6629834254143646	267	0.46678321678321677	472	0.6226912928759895	T	0.016	-1.529948	0.00951	0.63385	0.575154	ENSG00000149308	ENST00000278612	T	0.19806	2.12	6.08	4.93	0.64822	.	0.350905	0.30201	N	0.010179	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42565	-0.9444	9	0.05959	T	0.93	-5.3002	4.4367	0.11554	0.0:0.1957:0.1665:0.6378	rs2070661;rs52799779;rs2070661	575	Q14207	NPAT_HUMAN	I	575	ENSP00000278612:V575I	ENSP00000278612:V575I	V	-	1	0	NPAT	107549198	0.979000	0.34478	0.934000	0.37439	0.395000	0.30598	1.311000	0.33562	0.518000	0.28383	-0.254000	0.11334	GTT	T|0.575;G|0.005	0.575	strong		0.294	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519	
ABCA2	20	hgsc.bcm.edu	37	9	139916833	139916833	+	Silent	SNP	T	T	G	rs35590326	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139916833T>G	ENST00000371605.3	-	5	681	c.534A>C	c.(532-534)gcA>gcC	p.A178A	ABCA2_ENST00000341511.6_Silent_p.A179A|ABCA2_ENST00000492260.1_5'UTR|ABCA2_ENST00000265662.5_Silent_p.A179A			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	178					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CGGCCAAGAGTGCTTGGGCCG	0.652													g|||	460	0.091853	0.1732	0.0937	5008	,	,		13783	0.0317		0.0994	False		,,,				2504	0.0348				p.A209A		Atlas-SNP	.											ABCA2,NS,carcinoma,0,1	ABCA2	113	1	0			c.A627C						scavenged	.	G	,	757,3287		82,593,1347	27.0	34.0	31.0		537,627	-0.6	0.8	9	dbSNP_126	31	714,7574		31,652,3461	yes	coding-synonymous,coding-synonymous	ABCA2	NM_001606.4,NM_212533.2	,	113,1245,4808	GG,GT,TT		8.6149,18.7191,11.9283	,	179/2437,209/2467	139916833	1471,10861	2022	4144	6166	SO:0001819	synonymous_variant	20	exon6			CAAGAGTGCTTGG	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.534A>C	9.37:g.139916833T>G		Somatic	175	11	0.0628571		WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	37																																																																																				T|0.914;G|0.086	0.086	strong		0.652	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	
C16orf96	342346	hgsc.bcm.edu	37	16	4625274	4625274	+	Missense_Mutation	SNP	A	A	G	rs1256768	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:4625274A>G	ENST00000444310.4	+	5	793	c.793A>G	c.(793-795)Atc>Gtc	p.I265V		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96											NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						TACTCGTGCCATCCAGGTCTC	0.592													A|||	726	0.144968	0.087	0.0951	5008	,	,		17680	0.131		0.163	False		,,,				2504	0.2546				p.I265V		Atlas-SNP	.											.	C16orf96	28	.	0			c.A793G						PASS	.	A	VAL/ILE	149,1235		6,137,549	47.0	46.0	46.0		793	-6.7	0.0	16	dbSNP_87	46	519,2663		44,431,1116	yes	missense	C16orf96	NM_001145011.1	29	50,568,1665	GG,GA,AA		16.3105,10.7659,14.6299	benign	265/1142	4625274	668,3898	692	1591	2283	SO:0001583	missense	342346	exon5			CGTGCCATCCAGG		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.793A>G	16.37:g.4625274A>G	ENSP00000415027:p.Ile265Val	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_001145011		Missense_Mutation	SNP	ENST00000444310.4	37	CCDS53986.1	286	0.13095238095238096	56	0.11382113821138211	43	0.11878453038674033	62	0.10839160839160839	125	0.16490765171503957	A	3.473	-0.107540	0.06924	0.107659	0.163105	ENSG00000205832	ENST00000444310	.	.	.	3.33	-6.66	0.01789	.	.	.	.	.	T	0.00073	0.0002	N	0.19112	0.55	0.80722	P	0.0	B	0.12013	0.005	B	0.08055	0.003	T	0.19321	-1.0309	7	0.15952	T	0.53	.	7.8742	0.29584	0.1785:0.5159:0.3056:0.0	rs1256768;rs1256768	265	A6NNT2	CP096_HUMAN	V	265	.	ENSP00000415027:I265V	I	+	1	0	C16orf96	4565275	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-3.668000	0.00398	-2.190000	0.00757	0.379000	0.24179	ATC	A|0.856;G|0.144	0.144	strong		0.592	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432384.1	NM_001145011	
NAALADL2	254827	hgsc.bcm.edu	37	3	174814738	174814738	+	Missense_Mutation	SNP	G	G	A	rs9823911	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:174814738G>A	ENST00000454872.1	+	2	330	c.202G>A	c.(202-204)Ggt>Agt	p.G68S	NAALADL2-AS3_ENST00000453180.1_RNA|NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	68			G -> S (in dbSNP:rs9823911). {ECO:0000269|PubMed:15168106, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		CCAGCTAGACGGTGCTGAGAA	0.463													A|||	1893	0.377995	0.2852	0.4179	5008	,	,		14330	0.4375		0.3926	False		,,,				2504	0.3988				p.G68S		Atlas-SNP	.											.	NAALADL2	86	.	0			c.G202A						PASS	.	A	SER/GLY	1024,2766		148,728,1019	77.0	73.0	74.0		202	1.0	0.0	3	dbSNP_119	74	3188,5052		627,1934,1559	yes	missense	NAALADL2	NM_207015.2	56	775,2662,2578	AA,AG,GG		38.6893,27.0185,35.0125	benign	68/796	174814738	4212,7818	1895	4120	6015	SO:0001583	missense	254827	exon2			CTAGACGGTGCTG		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.202G>A	3.37:g.174814738G>A	ENSP00000404705:p.Gly68Ser	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	223	119	0.533632	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	37	CCDS46960.1	828	0.3791208791208791	145	0.29471544715447157	161	0.4447513812154696	236	0.4125874125874126	286	0.37730870712401055	A	7.764	0.706087	0.15172	0.270185	0.386893	ENSG00000177694	ENST00000434257;ENST00000454872	T;T	0.30182	1.62;1.54	5.72	0.957	0.19613	.	0.757199	0.12476	N	0.465639	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46541	-0.9184	9	0.02654	T	1	-0.2147	5.8982	0.18951	0.4966:0.2423:0.2611:0.0	rs9823911;rs52835565;rs58142944;rs9823911	51;68	Q58DX5-2;Q58DX5	.;NADL2_HUMAN	S	51;68	ENSP00000409858:G51S;ENSP00000404705:G68S	ENSP00000409858:G51S	G	+	1	0	NAALADL2	176297432	0.007000	0.16637	0.018000	0.16275	0.704000	0.40688	0.523000	0.22925	-0.042000	0.13535	-0.269000	0.10298	GGT	G|0.642;A|0.358	0.358	strong		0.463	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015	
STPG1	90529	hgsc.bcm.edu	37	1	24706292	24706292	+	Missense_Mutation	SNP	T	T	C	rs1142057	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24706292T>C	ENST00000374409.1	-	5	567	c.313A>G	c.(313-315)Att>Gtt	p.I105V	STPG1_ENST00000003583.8_Missense_Mutation_p.I58V|STPG1_ENST00000468303.1_5'UTR|STPG1_ENST00000337248.4_Missense_Mutation_p.I105V|STPG1_ENST00000440416.1_Missense_Mutation_p.I58V	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	105				I -> V (in Ref. 2; AAH35061). {ECO:0000305}.	apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											TATTTAGAAATGATGGTGTCC	0.423													T|||	1831	0.365615	0.3086	0.4841	5008	,	,		20191	0.4444		0.3549	False		,,,				2504	0.2883				p.I105V		Atlas-SNP	.											.	.	.	.	0			c.A313G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1472,2934	474.6+/-357.0	234,1004,965	85.0	83.0	84.0		313,313,37,172	-0.6	0.0	1	dbSNP_86	84	2862,5738	450.5+/-362.4	452,1958,1890	yes	missense,missense,missense,missense	C1orf201	NM_001199012.1,NM_001199013.1,NM_001199014.1,NM_178122.4	29,29,29,29	686,2962,2855	CC,CT,TT		33.2791,33.409,33.3231	benign,benign,benign,benign	105/335,105/335,13/243,58/288	24706292	4334,8672	2203	4300	6503	SO:0001583	missense	90529	exon5			TAGAAATGATGGT	BC047705	CCDS253.1, CCDS55581.1	1p36.11	2012-10-31	2012-07-30	2012-07-30	ENSG00000001460	ENSG00000001460			28070	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 2"""	615826	"""chromosome 1 open reading frame 201"""	C1orf201		23028632	Standard	NM_001199012		Approved	FLJ33340, MAPO2	uc001bjc.3	Q5TH74	OTTHUMG00000003297	ENST00000374409.1:c.313A>G	1.37:g.24706292T>C	ENSP00000363530:p.Ile105Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	126	48	0.380952	NM_001199012	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Missense_Mutation	SNP	ENST00000374409.1	37	CCDS55581.1	864	0.3956043956043956	173	0.3516260162601626	162	0.44751381215469616	249	0.4353146853146853	280	0.36939313984168864	T	0.032	-1.326420	0.01309	0.33409	0.332791	ENSG00000001460	ENST00000374409;ENST00000440416;ENST00000003583;ENST00000337248;ENST00000437986;ENST00000438866;ENST00000374404	.	.	.	5.79	-0.614	0.11590	.	1.153860	0.06103	N	0.665856	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.14023	0.01;0.006	T	0.45644	-0.9247	8	0.15066	T	0.55	-18.3867	9.3433	0.38093	0.0:0.387:0.0:0.613	rs1142057;rs3180006;rs3205834;rs3765430;rs11538187;rs17401513;rs52835238;rs56600081;rs59766180;rs1142057	105;58	Q5TH74;Q5TH74-3	CA201_HUMAN;.	V	105;58;58;105;105;8;9	.	ENSP00000003583:I58V	I	-	1	0	C1orf201	24578879	0.031000	0.19500	0.002000	0.10522	0.002000	0.02628	-0.059000	0.11731	-0.090000	0.12462	-0.376000	0.06991	ATT	T|0.638;C|0.362	0.362	strong		0.423	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122	
CCDC155	147872	hgsc.bcm.edu	37	19	49901318	49901318	+	Silent	SNP	T	T	C	rs10421748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49901318T>C	ENST00000447857.3	+	7	752	c.547T>C	c.(547-549)Ttg>Ctg	p.L183L		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	183						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						GAATGCCAAATTGCAGCGGAG	0.607													C|||	2864	0.571885	0.6324	0.4625	5008	,	,		15853	0.5129		0.5239	False		,,,				2504	0.6779				p.L183L		Atlas-SNP	.											.	CCDC155	46	.	0			c.T547C						PASS	.	C		2566,1612		810,946,333	53.0	57.0	56.0		547	4.2	1.0	19	dbSNP_119	56	4617,3803		1262,2093,855	no	coding-synonymous	CCDC155	NM_144688.4		2072,3039,1188	CC,CT,TT		45.1663,38.5831,42.983		183/563	49901318	7183,5415	2089	4210	6299	SO:0001819	synonymous_variant	147872	exon7			GCCAAATTGCAGC		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.547T>C	19.37:g.49901318T>C		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	162	162	1	NM_144688	Q96MC3	Silent	SNP	ENST00000447857.3	37	CCDS46140.1																																																																																			T|0.445;C|0.555	0.555	strong		0.607	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688	
MUC21	394263	hgsc.bcm.edu	37	6	30955211	30955211	+	Missense_Mutation	SNP	C	C	T	rs2429292|rs56572740	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30955211C>T	ENST00000376296.3	+	2	1500	c.1259C>T	c.(1258-1260)gCc>gTc	p.A420V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	420	28 X 15 AA approximate tandem repeats.|Ser-rich.			A -> V (in Ref. 3; AAQ88781 and 4; CAQ08321). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GCCAGCACTGCCACCAATTCT	0.617													c|||	500	0.0998403	0.084	0.1801	5008	,	,		20254	0.0784		0.1093	False		,,,				2504	0.0767				p.A420V		Atlas-SNP	.											.	MUC21	98	.	0			c.C1259T						PASS	.						141.0	135.0	137.0					6																	30955211		2203	4300	6503	SO:0001583	missense	394263	exon2			GCACTGCCACCAA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1259C>T	6.37:g.30955211C>T	ENSP00000365473:p.Ala420Val	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	156	46	0.294872	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	249	0.11401098901098901	48	0.0975609756097561	63	0.17403314917127072	68	0.11888111888111888	70	0.09234828496042216	c	0.026	-1.366790	0.01225	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.01414	4.92	3.43	-2.37	0.06643	.	.	.	.	.	T	0.00210	0.0006	N	0.11560	0.145	0.09310	N	1	B	0.27656	0.184	B	0.23574	0.047	T	0.37291	-0.9712	9	0.15066	T	0.55	-0.274	1.1262	0.01736	0.1369:0.3192:0.2693:0.2746	rs2429292;rs2429292	420	Q5SSG8	MUC21_HUMAN	V	270;420	ENSP00000365473:A420V	ENSP00000365473:A420V	A	+	2	0	MUC21	31063190	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.147000	0.16202	-0.808000	0.04387	-1.713000	0.00713	GCC	C|0.886;T|0.114	0.114	strong		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
FNDC1	84624	hgsc.bcm.edu	37	6	159672419	159672419	+	Silent	SNP	G	G	C	rs551392	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:159672419G>C	ENST00000297267.9	+	17	5120	c.4920G>C	c.(4918-4920)ctG>ctC	p.L1640L	FNDC1_ENST00000340366.6_Silent_p.L1577L	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1640					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TGGACAGCCTGGATGAAATCA	0.532													G|||	1099	0.219449	0.1899	0.1772	5008	,	,		22374	0.3343		0.1382	False		,,,				2504	0.2546				p.L1640L		Atlas-SNP	.											.	FNDC1	250	.	0			c.G4920C						PASS	.	G		716,3384		53,610,1387	75.0	72.0	73.0		4920	3.7	1.0	6	dbSNP_83	73	1094,7302		78,938,3182	no	coding-synonymous	FNDC1	NM_032532.2		131,1548,4569	CC,CG,GG		13.03,17.4634,14.4846		1640/1895	159672419	1810,10686	2050	4198	6248	SO:0001819	synonymous_variant	84624	exon17			CAGCCTGGATGAA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.4920G>C	6.37:g.159672419G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	135	58	0.42963	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	475	0.2174908424908425	115	0.23373983739837398	59	0.16298342541436464	201	0.3513986013986014	100	0.13192612137203166	G	8.942	0.966161	0.18659	0.174634	0.1303	ENSG00000164694	ENST00000329629	.	.	.	5.51	3.7	0.42460	.	.	.	.	.	T	0.33876	0.0878	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.15206	-1.0445	3	.	.	.	-18.2795	8.6871	0.34245	0.0739:0.0:0.603:0.3231	rs551392;rs3814445;rs61299761;rs551392	.	.	.	R	1536	.	.	G	+	1	0	FNDC1	159592409	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.993000	0.49425	0.683000	0.31428	0.585000	0.79938	GGA	G|0.777;C|0.222	0.222	strong		0.532	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
FLVCR2	55640	hgsc.bcm.edu	37	14	76045362	76045362	+	Missense_Mutation	SNP	T	T	C	rs2287015	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:76045362T>C	ENST00000238667.4	+	1	403	c.47T>C	c.(46-48)gTg>gCg	p.V16A	AC007182.6_ENST00000455232.1_RNA	NM_017791.2	NP_060261.2	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular receptor family, member 2	16			V -> A (in dbSNP:rs2287015). {ECO:0000269|PubMed:14702039}.		heme transport (GO:0015886)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	heme binding (GO:0020037)|heme transporter activity (GO:0015232)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15				BRCA - Breast invasive adenocarcinoma(234;0.029)		GACACCCCTGTGCCGGAGTCC	0.617											OREG0022816	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2373	0.473842	0.7194	0.3501	5008	,	,		16727	0.5694		0.2137	False		,,,				2504	0.3988				p.V16A		Atlas-SNP	.											.	FLVCR2	39	.	0			c.T47C						PASS	.	C	ALA/VAL	2920,1486	475.5+/-357.3	974,972,257	70.0	78.0	75.0		47	-2.6	0.0	14	dbSNP_100	75	1931,6669	726.2+/-406.6	217,1497,2586	yes	missense	FLVCR2	NM_017791.2	64	1191,2469,2843	CC,CT,TT		22.4535,33.7267,37.2982	benign	16/527	76045362	4851,8155	2203	4300	6503	SO:0001583	missense	55640	exon1			CCCCTGTGCCGGA	AK000378	CCDS9844.1, CCDS55933.1	14q24.3	2013-05-22	2007-05-01	2007-05-01	ENSG00000119686	ENSG00000119686		"""Solute carriers"""	20105	protein-coding gene	gene with protein product		610865	"""chromosome 14 open reading frame 58"", ""feline leukemia virus subgroup C cellular receptor 2"""	C14orf58		16439531, 20206334	Standard	NM_017791		Approved	FLJ20371, MFSD7C	uc001xrs.2	Q9UPI3	OTTHUMG00000171487	ENST00000238667.4:c.47T>C	14.37:g.76045362T>C	ENSP00000238667:p.Val16Ala	Somatic	89	0	0	1165	WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_017791	B7Z485|Q53ZT9|Q96JY3|Q9NX90	Missense_Mutation	SNP	ENST00000238667.4	37	CCDS9844.1	953	0.43635531135531136	339	0.6890243902439024	121	0.3342541436464088	327	0.5716783216783217	166	0.21899736147757257	C	7.684	0.689647	0.14973	0.662733	0.224535	ENSG00000119686	ENST00000238667	T	0.30448	1.53	4.17	-2.59	0.06209	.	1.965160	0.02414	N	0.081943	T	0.00012	0.0000	N	0.04508	-0.205	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.38714	-0.9648	9	0.06891	T	0.86	-18.7698	3.8932	0.09128	0.2941:0.2763:0.0:0.4296	rs2287015;rs59533558;rs2287015	16	Q9UPI3	FLVC2_HUMAN	A	16	ENSP00000238667:V16A	ENSP00000238667:V16A	V	+	2	0	AC007182.1	75115115	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.546000	0.06062	-0.886000	0.03966	-0.847000	0.03039	GTG	T|0.591;C|0.409	0.409	strong		0.617	FLVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413672.1	NM_017791	
TET2	54790	hgsc.bcm.edu	37	4	106196829	106196829	+	Missense_Mutation	SNP	T	T	G	rs34402524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:106196829T>G	ENST00000540549.1	+	11	6022	c.5162T>G	c.(5161-5163)tTg>tGg	p.L1721W	TET2_ENST00000380013.4_Missense_Mutation_p.L1721W|TET2_ENST00000513237.1_Missense_Mutation_p.L1742W|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1721			L -> W (in dbSNP:rs34402524). {ECO:0000269|PubMed:19483684}.		5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.L1721*(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		GTAGGGAAATTGCCTCCTTAT	0.408			"""Mis N, F"""		MDS								T|||	459	0.0916534	0.0915	0.0893	5008	,	,		23039	0.0466		0.1402	False		,,,				2504	0.09				p.L1721W		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2,NS,haematopoietic_neoplasm,0,1	TET2	1762	1	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T5162G						PASS	.	T	TRP/LEU	134,1250		4,126,562	102.0	85.0	91.0		5162	5.2	0.1	4	dbSNP_126	91	429,2753		23,383,1185	yes	missense	TET2	NM_001127208.2	61	27,509,1747	GG,GT,TT		13.4821,9.6821,12.3303	possibly-damaging	1721/2003	106196829	563,4003	692	1591	2283	SO:0001583	missense	54790	exon11			GGAAATTGCCTCC	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.5162T>G	4.37:g.106196829T>G	ENSP00000442788:p.Leu1721Trp	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	221	107	0.484163	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	201	0.09203296703296704	33	0.06707317073170732	43	0.11878453038674033	22	0.038461538461538464	103	0.1358839050131926	T	10.42	1.344270	0.24339	0.096821	0.134821	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.02301	4.35;4.35;4.35	5.16	5.16	0.70880	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.37752	P	0.07400899999999999	P;P	0.42941	0.794;0.794	P;P	0.54499	0.754;0.478	T	0.65076	-0.6256	8	0.49607	T	0.09	-5.4358	13.5897	0.61953	0.0:0.0:0.0:1.0	rs34402524;rs56501389;rs34402524	1742;1721	E7EQS8;Q6N021	.;TET2_HUMAN	W	1721;1742;1721	ENSP00000442788:L1721W;ENSP00000425443:L1742W;ENSP00000369351:L1721W	ENSP00000369351:L1721W	L	+	2	0	TET2	106416278	0.980000	0.34600	0.053000	0.19242	0.139000	0.21198	3.357000	0.52277	1.937000	0.56155	0.383000	0.25322	TTG	T|0.903;G|0.097	0.097	strong		0.408	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
AHNAK	79026	hgsc.bcm.edu	37	11	62285441	62285441	+	Missense_Mutation	SNP	A	A	G	rs61312994	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62285441A>G	ENST00000378024.4	-	5	16722	c.16448T>C	c.(16447-16449)aTt>aCt	p.I5483T	AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5483	Gly-rich.				protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TTGAACACCAATGCCTGGAAG	0.527													A|||	163	0.0325479	0.062	0.0274	5008	,	,		18564	0.0119		0.0258	False		,,,				2504	0.0245				p.I5483T		Atlas-SNP	.											.	AHNAK	532	.	0			c.T16448C						PASS	.	A	THR/ILE,	307,4097	164.7+/-196.3	11,285,1906	67.0	71.0	70.0		16448,	4.5	0.1	11	dbSNP_129	70	218,8380	91.1+/-153.3	4,210,4085	yes	missense,intron	AHNAK	NM_001620.1,NM_024060.2	89,	15,495,5991	GG,GA,AA		2.5355,6.9709,4.0378	possibly-damaging,	5483/5891,	62285441	525,12477	2202	4299	6501	SO:0001583	missense	79026	exon5			ACACCAATGCCTG	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.16448T>C	11.37:g.62285441A>G	ENSP00000367263:p.Ile5483Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	73	0.033424908424908424	36	0.07317073170731707	13	0.03591160220994475	7	0.012237762237762238	17	0.022427440633245383	A	8.976	0.974253	0.18736	0.069709	0.025355	ENSG00000124942	ENST00000378024	T	0.00760	5.73	4.52	4.52	0.55395	.	0.158715	0.29239	U	0.012722	T	0.00144	0.0004	L	0.49126	1.545	0.29882	N	0.825931	P	0.47762	0.9	P	0.45794	0.493	T	0.48843	-0.8999	10	0.10636	T	0.68	-4.5768	13.5264	0.61597	1.0:0.0:0.0:0.0	rs61312994	5483	Q09666	AHNK_HUMAN	T	5483	ENSP00000367263:I5483T	ENSP00000367263:I5483T	I	-	2	0	AHNAK	62042017	0.717000	0.27966	0.053000	0.19242	0.008000	0.06430	5.724000	0.68500	1.664000	0.50801	0.410000	0.27636	ATT	A|0.958;G|0.042	0.042	strong		0.527	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
CEP290	80184	hgsc.bcm.edu	37	12	88508258	88508258	+	Missense_Mutation	SNP	T	T	C	rs79705698	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:88508258T>C	ENST00000552810.1	-	20	2334	c.1991A>G	c.(1990-1992)gAt>gGt	p.D664G	CEP290_ENST00000309041.7_Missense_Mutation_p.D666G|CEP290_ENST00000397838.3_5'UTR	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	664			D -> G (found in a patient with Joubert syndrome; unknown pathological significance; dbSNP:rs79705698). {ECO:0000269|PubMed:17564967, ECO:0000269|PubMed:17617513}.		cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						AACATCAGGATCTTTCTGCAT	0.303													T|||	223	0.0445288	0.0015	0.0922	5008	,	,		19226	0.1319		0.0129	False		,,,				2504	0.0112				p.D664G		Atlas-SNP	.											.	CEP290	195	.	0			c.A1991G						PASS	.	T	GLY/ASP	11,3475		0,11,1732	167.0	149.0	155.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1991	5.9	1.0	12	dbSNP_131	155	94,7640		0,94,3773	yes	missense	CEP290	NM_025114.3	94	0,105,5505	CC,CT,TT		1.2154,0.3155,0.9358	possibly-damaging	664/2480	88508258	105,11115	1743	3867	5610	SO:0001583	missense	80184	exon20			TCAGGATCTTTCT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.1991A>G	12.37:g.88508258T>C	ENSP00000448012:p.Asp664Gly	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	206	92	0.446602	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	128	0.05860805860805861	0	0.0	28	0.07734806629834254	90	0.15734265734265734	10	0.013192612137203167	T	16.64	3.179619	0.57800	0.003155	0.012154	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998	T;T	0.81078	-1.45;-1.45	5.87	5.87	0.94306	.	0.480248	0.24074	N	0.041800	T	0.01254	0.0041	L	0.44542	1.39	0.09310	P	1.0	D;B	0.55385	0.971;0.201	P;B	0.52823	0.71;0.045	T	0.19128	-1.0315	9	0.41790	T	0.15	.	16.2631	0.82557	0.0:0.0:0.0:1.0	.	664;664	Q05BJ6;O15078	.;CE290_HUMAN	G	664;666;664	ENSP00000448012:D664G;ENSP00000308021:D666G	ENSP00000308021:D666G	D	-	2	0	CEP290	87032389	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	6.674000	0.74487	2.239000	0.73571	0.528000	0.53228	GAT	T|0.950;C|0.050	0.050	strong		0.303	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
KIAA1683	80726	hgsc.bcm.edu	37	19	18375608	18375608	+	Intron	SNP	G	G	A	rs8102923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18375608G>A	ENST00000600328.3	-	3	2810				KIAA1683_ENST00000392413.4_Silent_p.A914A|KIAA1683_ENST00000600359.3_Intron			Q9H0B3	K1683_HUMAN	KIAA1683							mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						CCTTGGACAGGGCCTGGTTCA	0.632													G|||	1504	0.300319	0.4561	0.2478	5008	,	,		18615	0.3165		0.1581	False		,,,				2504	0.2566				p.A914A		Atlas-SNP	.											.	KIAA1683	190	.	0			c.C2742T						PASS	.	G	,,	593,791		121,351,220	29.0	32.0	31.0		2742,,	1.0	1.0	19	dbSNP_116	31	517,2665		42,433,1116	no	coding-synonymous,intron,intron	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	163,784,1336	AA,AG,GG		16.2476,42.8468,24.3101	,,	914/1368,,	18375608	1110,3456	692	1591	2283	SO:0001627	intron_variant	80726	exon3			GGACAGGGCCTGG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2616+125C>T	19.37:g.18375608G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			G|0.726;A|0.274	0.274	strong		0.632	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
ZNF202	7753	hgsc.bcm.edu	37	11	123598941	123598941	+	Silent	SNP	T	T	C	rs2282644	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:123598941T>C	ENST00000529691.1	-	5	951	c.732A>G	c.(730-732)gtA>gtG	p.V244V	ZNF202_ENST00000336139.4_Silent_p.V244V|ZNF202_ENST00000530393.1_Silent_p.V244V			O95125	ZN202_HUMAN	zinc finger protein 202	244	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		GGGAAAAGCATACGGCCACAT	0.458													T|||	1148	0.229233	0.0159	0.2968	5008	,	,		20310	0.3552		0.2694	False		,,,				2504	0.2986				p.V244V		Atlas-SNP	.											.	ZNF202	72	.	0			c.A732G						PASS	.	T		264,4140	149.2+/-183.4	13,238,1951	124.0	115.0	118.0		732	-8.9	0.1	11	dbSNP_100	118	2411,6187	402.3+/-347.4	342,1727,2230	no	coding-synonymous	ZNF202	NM_003455.2		355,1965,4181	CC,CT,TT		28.0414,5.9946,20.5738		244/649	123598941	2675,10327	2202	4299	6501	SO:0001819	synonymous_variant	7753	exon7			AAAGCATACGGCC	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.732A>G	11.37:g.123598941T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	182	89	0.489011	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Silent	SNP	ENST00000529691.1	37	CCDS8443.1																																																																																			T|0.784;C|0.216	0.216	strong		0.458	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
ZBBX	79740	hgsc.bcm.edu	37	3	167051769	167051769	+	Missense_Mutation	SNP	T	T	C	rs11923054	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:167051769T>C	ENST00000392766.2	-	10	873	c.533A>G	c.(532-534)aAa>aGa	p.K178R	ZBBX_ENST00000392767.2_Missense_Mutation_p.K178R|ZBBX_ENST00000307529.5_Missense_Mutation_p.K178R|ZBBX_ENST00000455345.2_Missense_Mutation_p.K178R|ZBBX_ENST00000392764.1_Missense_Mutation_p.K149R|ZBBX_ENST00000469220.1_Intron	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	178			K -> R (in dbSNP:rs11923054).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						TATTTGAGATTTTGCCTATTA	0.289													T|||	1283	0.25619	0.0711	0.3343	5008	,	,		14277	0.1786		0.4115	False		,,,				2504	0.3712				p.K178R		Atlas-SNP	.											.	ZBBX	299	.	0			c.A533G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	457,3111		29,399,1356	62.0	55.0	57.0		533,446,533	1.1	1.0	3	dbSNP_120	57	3454,4662		724,2006,1328	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	26,26,26	753,2405,2684	CC,CT,TT		42.5579,12.8083,33.4731	probably-damaging,probably-damaging,probably-damaging	178/840,149/772,178/801	167051769	3911,7773	1784	4058	5842	SO:0001583	missense	79740	exon10			TGAGATTTTGCCT	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.533A>G	3.37:g.167051769T>C	ENSP00000376519:p.Lys178Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	586	0.2683150183150183	50	0.1016260162601626	128	0.35359116022099446	101	0.17657342657342656	307	0.4050131926121372	T	7.602	0.673020	0.14776	0.128083	0.425579	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	4.79	1.08	0.20341	.	0.000000	0.34025	U	0.004322	T	0.00012	0.0000	L	0.59436	1.845	0.40911	P	0.015764	B;B	0.28552	0.215;0.064	B;B	0.28991	0.097;0.02	T	0.45716	-0.9242	9	0.34782	T	0.22	-17.7062	6.8506	0.24012	0.0:0.3027:0.0:0.6973	rs11923054;rs17853282;rs52807714;rs58791197;rs11923054	178;178	A8MT70-2;A8MT70	.;ZBBX_HUMAN	R	178;178;178;178;149	ENSP00000376519:K178R;ENSP00000376520:K178R;ENSP00000390232:K178R;ENSP00000305065:K178R;ENSP00000376517:K149R	ENSP00000305065:K178R	K	-	2	0	ZBBX	168534463	1.000000	0.71417	0.999000	0.59377	0.382000	0.30200	1.631000	0.37092	0.287000	0.22375	-0.256000	0.11100	AAA	T|0.719;C|0.281	0.281	strong		0.289	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
TNK1	8711	hgsc.bcm.edu	37	17	7286266	7286266	+	Silent	SNP	C	C	T	rs1554947	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7286266C>T	ENST00000576812.1	+	2	390	c.21C>T	c.(19-21)tcC>tcT	p.S7S	TNK1_ENST00000311668.2_Silent_p.S7S|TNK1_ENST00000570896.1_Silent_p.S7S	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				AGGCTGGCTCCCTGTGGCTAC	0.557													.|||	1372	0.273962	0.0356	0.3934	5008	,	,		20569	0.4593		0.4056	False		,,,				2504	0.1851				p.S7S		Atlas-SNP	.											.	TNK1	31	.	0			c.C21T						PASS	.	C		409,3943		19,371,1786	53.0	57.0	56.0		21	2.6	0.9	17	dbSNP_88	56	3381,5181		662,2057,1562	no	coding-synonymous	TNK1	NM_003985.3		681,2428,3348	TT,TC,CC		39.4884,9.398,29.348		7/662	7286266	3790,9124	2176	4281	6457	SO:0001819	synonymous_variant	8711	exon2			TGGCTCCCTGTGG	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.21C>T	17.37:g.7286266C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_003985		Silent	SNP	ENST00000576812.1	37	CCDS58510.1																																																																																			C|0.631;T|0.369	0.369	strong		0.557	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985	
LYZL2	119180	hgsc.bcm.edu	37	10	30918597	30918597	+	Missense_Mutation	SNP	T	T	C	rs74551644		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:30918597T>C	ENST00000375318.2	-	1	94	c.38A>G	c.(37-39)aAg>aGg	p.K13R		NM_183058.2	NP_898881.2	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	0					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)	p.K13R(1)		NS(2)|central_nervous_system(1)|large_intestine(1)|lung(14)|prostate(1)	19		Prostate(175;0.151)				ACTGCTCCACTTAGTCGGTGA	0.498																																					p.K13R		Atlas-SNP	.											LYZL2,NS,carcinoma,0,1	LYZL2	33	1	1	Substitution - Missense(1)	prostate(1)	c.A38G						scavenged	.						75.0	68.0	71.0					10																	30918597		2203	4298	6501	SO:0001583	missense	119180	exon1			CTCCACTTAGTCG	AF139543	CCDS7167.2	10p11.23	2009-12-04			ENSG00000151033	ENSG00000151033			29613	protein-coding gene	gene with protein product		612748					Standard	NM_183058		Approved		uc001ivk.3	Q7Z4W2	OTTHUMG00000017898	ENST00000375318.2:c.38A>G	10.37:g.30918597T>C	ENSP00000364467:p.Lys13Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	136	13	0.0955882	NM_183058	Q6NZ69	Missense_Mutation	SNP	ENST00000375318.2	37	CCDS7167.2	.	.	.	.	.	.	.	.	.	.	T	7.959	0.746565	0.15710	.	.	ENSG00000151033	ENST00000375318	T	0.67865	-0.29	2.18	2.18	0.27775	.	6.432820	0.00541	N	0.000231	T	0.73999	0.3659	.	.	.	0.21719	N	0.999579	D	0.60575	0.988	D	0.73708	0.981	T	0.59306	-0.7479	9	0.19147	T	0.46	-9.5578	6.3337	0.21285	0.0:0.0:0.0:1.0	rs2532753;rs3736977;rs10826590;rs2532753	13	Q7Z4W2-2	.	R	13	ENSP00000364467:K13R	ENSP00000364467:K13R	K	-	2	0	LYZL2	30958603	0.998000	0.40836	0.964000	0.40570	0.029000	0.11900	1.416000	0.34759	1.241000	0.43820	0.377000	0.23210	AAG	.	.	weak		0.498	LYZL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047434.1	NM_183058	
MUC16	94025	hgsc.bcm.edu	37	19	9057750	9057750	+	Missense_Mutation	SNP	T	T	A	rs12982113	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9057750T>A	ENST00000397910.4	-	3	29899	c.29696A>T	c.(29695-29697)tAt>tTt	p.Y9899F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9901	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGCACTCCATAAAGGACTGC	0.468													A|||	1095	0.21865	0.2352	0.2896	5008	,	,		21423	0.0258		0.3121	False		,,,				2504	0.2485				p.Y9899F		Atlas-SNP	.											.	MUC16	4315	.	0			c.A29696T						PASS	.	A	PHE/TYR	916,2978		99,718,1130	132.0	124.0	127.0		29696	-1.0	0.0	19	dbSNP_121	127	2816,5470		497,1822,1824	yes	missense	MUC16	NM_024690.2	22	596,2540,2954	AA,AT,TT		33.985,23.5234,30.6404	benign	9899/14508	9057750	3732,8448	1947	4143	6090	SO:0001583	missense	94025	exon3			ACTCCATAAAGGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29696A>T	19.37:g.9057750T>A	ENSP00000381008:p.Tyr9899Phe	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	281	281	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	474	0.21703296703296704	123	0.25	101	0.27900552486187846	11	0.019230769230769232	239	0.3153034300791557	a	5.303	0.241363	0.10077	0.235234	0.33985	ENSG00000181143	ENST00000397910	T	0.02631	4.22	2.62	-1.0	0.10196	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.47736	-0.9094	8	0.87932	D	0	.	2.3546	0.04293	0.2955:0.0:0.2972:0.4073	rs12982113;rs52835804;rs12982113	9899	B5ME49	.	F	9899	ENSP00000381008:Y9899F	ENSP00000381008:Y9899F	Y	-	2	0	MUC16	8918750	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.375000	0.07475	-0.471000	0.06891	-2.479000	0.00199	TAT	T|0.754;A|0.246	0.246	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZBTB45	84878	hgsc.bcm.edu	37	19	59028162	59028162	+	Missense_Mutation	SNP	G	G	C	rs35430780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:59028162G>C	ENST00000594051.1	-	2	1359	c.879C>G	c.(877-879)gaC>gaG	p.D293E	ZBTB45_ENST00000354590.3_Missense_Mutation_p.D293E|ZBTB45_ENST00000600990.1_Missense_Mutation_p.D293E			Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	293			D -> E (in dbSNP:rs35430780).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|lung(5)|urinary_tract(1)	11		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0165)|Lung(386;0.18)		CGCCATCCTCGTCGTGCCAAG	0.617													G|||	83	0.0165735	0.003	0.0159	5008	,	,		14162	0.0		0.0567	False		,,,				2504	0.0112				p.D293E	NSCLC(164;1383 2017 5233 27540 46677)	Atlas-SNP	.											.	ZBTB45	37	.	0			c.C879G						PASS	.	G	GLU/ASP	57,4349	52.9+/-88.7	0,57,2146	41.0	43.0	43.0		879	-6.9	0.0	19	dbSNP_126	43	434,8162	126.7+/-185.1	11,412,3875	no	missense	ZBTB45	NM_032792.2	45	11,469,6021	CC,CG,GG		5.0489,1.2937,3.7763	benign	293/512	59028162	491,12511	2203	4298	6501	SO:0001583	missense	84878	exon2			ATCCTCGTCGTGC	AK027392	CCDS12984.1	19q13.43	2013-10-10	2006-09-19	2006-09-19	ENSG00000119574	ENSG00000119574		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	23715	protein-coding gene	gene with protein product			"""zinc finger protein 499"""	ZNF499			Standard	NM_032792		Approved	FLJ14486	uc002qtd.3	Q96K62	OTTHUMG00000183545	ENST00000594051.1:c.879C>G	19.37:g.59028162G>C	ENSP00000469089:p.Asp293Glu	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	325	145	0.446154	NM_032792		Missense_Mutation	SNP	ENST00000594051.1	37	CCDS12984.1	54	0.024725274725274724	3	0.006097560975609756	8	0.022099447513812154	0	0.0	43	0.05672823218997362	g	0.007	-1.944193	0.00479	0.012937	0.050489	ENSG00000119574	ENST00000354590	T	0.08193	3.12	3.46	-6.92	0.01644	.	1.304990	0.05331	N	0.528343	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38023	-0.9680	10	0.06365	T	0.9	.	5.086	0.14682	0.484:0.3286:0.1066:0.0807	rs35430780	293	Q96K62	ZBT45_HUMAN	E	293	ENSP00000346603:D293E	ENSP00000346603:D293E	D	-	3	2	ZBTB45	63719974	0.000000	0.05858	0.000000	0.03702	0.119000	0.20118	-1.662000	0.01970	-2.499000	0.00511	-2.589000	0.00165	GAC	G|0.965;C|0.035	0.035	strong		0.617	ZBTB45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467067.1	NM_032792	
RAMP3	10268	hgsc.bcm.edu	37	7	45217015	45217015	+	Missense_Mutation	SNP	T	T	C	rs2074654	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:45217015T>C	ENST00000242249.4	+	2	204	c.166T>C	c.(166-168)Tgg>Cgg	p.W56R	RAMP3_ENST00000481345.1_Missense_Mutation_p.W56R|RAMP3_ENST00000496212.1_Missense_Mutation_p.W56R	NM_005856.2	NP_005847.1	O60896	RAMP3_HUMAN	receptor (G protein-coupled) activity modifying protein 3	56			W -> R (in dbSNP:rs2074654).		calcium ion transport (GO:0006816)|cellular response to estradiol stimulus (GO:0071392)|G-protein coupled receptor signaling pathway involved in heart process (GO:0086103)|intracellular protein transport (GO:0006886)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of receptor recycling (GO:0001921)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.W56R(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	11					Pramlintide(DB01278)	CGTCTGGAAGTGGTGCAACCT	0.612													t|||	321	0.0640974	0.0234	0.0807	5008	,	,		19280	0.1071		0.0547	False		,,,				2504	0.0726				p.W56R		Atlas-SNP	.											RAMP3,NS,carcinoma,-2,2	RAMP3	32	2	1	Substitution - Missense(1)	stomach(1)	c.T166C						PASS	.	C	ARG/TRP	116,4290	89.2+/-127.9	3,110,2090	281.0	191.0	221.0		166	1.8	1.0	7	dbSNP_96	221	514,8086	145.9+/-201.5	10,494,3796	yes	missense	RAMP3	NM_005856.2	101	13,604,5886	CC,CT,TT		5.9767,2.6328,4.8439	probably-damaging	56/149	45217015	630,12376	2203	4300	6503	SO:0001583	missense	10268	exon2			TGGAAGTGGTGCA	AJ001016	CCDS5503.1	7p13-p12	2006-11-21	2006-11-21		ENSG00000122679	ENSG00000122679		"""Receptor (G protein-coupled) activity modifying proteins"""	9845	protein-coding gene	gene with protein product		605155	"""receptor activity modifying protein 3"", ""receptor (calcitonin) activity modifying protein 3"""				Standard	NM_005856		Approved		uc003tnb.3	O60896	OTTHUMG00000023729	ENST00000242249.4:c.166T>C	7.37:g.45217015T>C	ENSP00000242249:p.Trp56Arg	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	203	92	0.453202	NM_005856	Q7Z2Y1	Missense_Mutation	SNP	ENST00000242249.4	37	CCDS5503.1	141	0.06456043956043957	12	0.024390243902439025	32	0.08839779005524862	57	0.09965034965034965	40	0.052770448548812667	t	15.45	2.838217	0.51057	0.026328	0.059767	ENSG00000122679	ENST00000242249;ENST00000481345;ENST00000496212	T;T;T	0.57595	0.39;0.39;0.39	4.24	1.79	0.24919	.	0.139018	0.52532	N	0.000075	T	0.05960	0.0155	M	0.89414	3.03	0.26348	P	0.9772524	D	0.89917	1.0	D	0.97110	1.0	T	0.54938	-0.8218	9	0.66056	D	0.02	-22.4246	6.1028	0.20057	0.0:0.218:0.0:0.782	rs2074654;rs59329729;rs2074654	56	O60896	RAMP3_HUMAN	R	56	ENSP00000242249:W56R;ENSP00000419012:W56R;ENSP00000418460:W56R	ENSP00000242249:W56R	W	+	1	0	RAMP3	45183540	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	0.834000	0.27518	0.075000	0.16796	-1.320000	0.01293	TGG	T|0.943;C|0.057	0.057	strong		0.612	RAMP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251343.1	NM_005856	
CRYBB3	1417	hgsc.bcm.edu	37	22	25599849	25599849	+	Missense_Mutation	SNP	G	G	A	rs17670506	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25599849G>A	ENST00000215855.2	+	4	394	c.314G>A	c.(313-315)cGg>cAg	p.R105Q	CRYBB3_ENST00000404334.1_Missense_Mutation_p.R105Q	NM_004076.3	NP_004067.1	P26998	CRBB3_HUMAN	crystallin, beta B3	105	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.		R -> Q (in dbSNP:rs17670506). {ECO:0000269|PubMed:15489334}.		visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(2)|lung(2)|prostate(1)	5						CTGTCCCTCCGGCCTCTGAAT	0.582													G|||	126	0.0251597	0.0318	0.0259	5008	,	,		19972	0.0		0.0477	False		,,,				2504	0.0184				p.E105E		Atlas-SNP	.											.	CRYBB3	13	.	0			c.A314A						PASS	.	G	GLN/ARG	139,4267	98.5+/-137.1	2,135,2066	133.0	133.0	133.0		314	3.5	1.0	22	dbSNP_123	133	465,8135	138.1+/-194.9	15,435,3850	yes	missense	CRYBB3	NM_004076.3	43	17,570,5916	AA,AG,GG		5.407,3.1548,4.644	probably-damaging	105/212	25599849	604,12402	2203	4300	6503	SO:0001583	missense	1417	exon4			CCCTCCGGCCTCT		CCDS13830.1	22q11.23	2008-06-10			ENSG00000100053	ENSG00000100053			2400	protein-coding gene	gene with protein product		123630		CRYB3		8999933	Standard	NM_004076		Approved		uc003abo.2	P26998	OTTHUMG00000150869	ENST00000215855.2:c.314G>A	22.37:g.25599849G>A	ENSP00000215855:p.Arg105Gln	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	169	93	0.550296	NM_004076	Q3B7S9|Q3T1B7|Q6ISK6|Q92965|Q9UH09	Silent	SNP	ENST00000215855.2	37	CCDS13830.1	62	0.028388278388278388	14	0.028455284552845527	11	0.03038674033149171	0	0.0	37	0.048812664907651716	G	17.15	3.316864	0.60524	0.031548	0.05407	ENSG00000100053	ENST00000215855;ENST00000404334	D;D	0.82344	-1.6;-1.51	4.52	3.48	0.39840	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	T	0.71256	0.3318	M	0.89478	3.035	0.47698	D	0.999492	D	0.89917	1.0	D	0.87578	0.998	T	0.82816	-0.0270	10	0.62326	D	0.03	.	13.1361	0.59409	0.0:0.1625:0.8375:0.0	rs17670506;rs52790923;rs17670506	105	P26998	CRBB3_HUMAN	Q	105	ENSP00000215855:R105Q;ENSP00000386123:R105Q	ENSP00000215855:R105Q	R	+	2	0	CRYBB3	23929849	0.998000	0.40836	0.979000	0.43373	0.690000	0.40134	7.427000	0.80284	0.849000	0.35215	0.471000	0.43371	CGG	G|0.956;A|0.044	0.044	strong		0.582	CRYBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320352.1	NM_004076	
C7orf72	100130988	hgsc.bcm.edu	37	7	50180972	50180972	+	Missense_Mutation	SNP	C	C	T	rs1456908	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:50180972C>T	ENST00000297001.6	+	7	1123	c.1073C>T	c.(1072-1074)aCa>aTa	p.T358I	AC020743.2_ENST00000454877.1_RNA	NM_001161834.2	NP_001155306	A4D263	CG072_HUMAN	chromosome 7 open reading frame 72	358				T -> I (in Ref. 2; EAL23902). {ECO:0000305}.						NS(1)|breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|prostate(2)	9						CCTCTTTATACAAACACAAGT	0.398													C|||	1658	0.33107	0.3147	0.2651	5008	,	,		17515	0.1974		0.3986	False		,,,				2504	0.4683				p.T358I		Atlas-SNP	.											.	C7orf72	26	.	0			c.C1073T						PASS	.	C	ILE/THR	477,907		75,327,290	125.0	105.0	111.0		1073	5.8	0.1	7	dbSNP_88	111	1344,1838		292,760,539	yes	missense	C7orf72	NM_001161834.2	89	367,1087,829	TT,TC,CC		42.2376,34.4653,39.8817	probably-damaging	358/439	50180972	1821,2745	692	1591	2283	SO:0001583	missense	100130988	exon7			TTTATACAAACAC		CCDS47585.1	7p12.2	2009-10-15			ENSG00000164500	ENSG00000164500			22564	protein-coding gene	gene with protein product							Standard	NM_001161834		Approved		uc011kcj.2	A4D263	OTTHUMG00000155883	ENST00000297001.6:c.1073C>T	7.37:g.50180972C>T	ENSP00000297001:p.Thr358Ile	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	155	153	0.987097	NM_001161834	A6NDX9	Missense_Mutation	SNP	ENST00000297001.6	37	CCDS47585.1	666	0.30494505494505497	167	0.3394308943089431	102	0.281767955801105	94	0.16433566433566432	303	0.3997361477572559	C	13.81	2.348928	0.41599	0.344653	0.422376	ENSG00000164500	ENST00000297001	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	T	0.00012	0.0000	L	0.48642	1.525	0.40751	P	0.01708900000000002	D	0.89917	1.0	D	0.87578	0.998	T	0.35051	-0.9804	7	0.52906	T	0.07	.	15.5045	0.75728	0.0:1.0:0.0:0.0	rs1456908;rs60427088;rs1456908	358	A4D263	CG072_HUMAN	I	358	.	ENSP00000297001:T358I	T	+	2	0	C7orf72	50151518	0.180000	0.23148	0.104000	0.21259	0.597000	0.36814	3.850000	0.55918	2.714000	0.92807	0.650000	0.86243	ACA	C|0.671;T|0.329	0.329	strong		0.398	C7orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342124.1	NM_001161834	
HS3ST3B1	9953	hgsc.bcm.edu	37	17	14248423	14248423	+	Silent	SNP	T	T	C	rs9906855	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:14248423T>C	ENST00000360954.2	+	2	1069	c.633T>C	c.(631-633)ccT>ccC	p.P211P		NM_006041.1	NP_006032.1	Q9Y662	HS3SB_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	211					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)			large_intestine(3)|lung(3)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)		GGGAGGCCCCTGCGCGCATCT	0.617																																					p.P211P		Atlas-SNP	.											.	HS3ST3B1	19	.	0			c.T633C						PASS	.						72.0	43.0	53.0					17																	14248423		2203	4287	6490	SO:0001819	synonymous_variant	9953	exon2			GGCCCCTGCGCGC	AF105377	CCDS11167.1	17p12	2007-04-02			ENSG00000125430	ENSG00000125430	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5198	protein-coding gene	gene with protein product		604058				9988767	Standard	NM_006041		Approved	3OST3B1, 30ST3B1	uc002goh.1	Q9Y662	OTTHUMG00000058810	ENST00000360954.2:c.633T>C	17.37:g.14248423T>C		Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	76	73	0.960526	NM_006041	B3KN58|D3DTS6	Silent	SNP	ENST00000360954.2	37	CCDS11167.1																																																																																			T|0.518;C|0.482	0.482	strong		0.617	HS3ST3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129998.1	NM_006041	
CMYA5	202333	hgsc.bcm.edu	37	5	79095299	79095299	+	Missense_Mutation	SNP	A	A	G	rs115059007	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:79095299A>G	ENST00000446378.2	+	13	12101	c.12070A>G	c.(12070-12072)Aac>Gac	p.N4024D	CTC-431G16.2_ENST00000421252.2_RNA	NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	4024	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TATCTTCATCAACGCAGAGAG	0.483													A|||	40	0.00798722	0.0015	0.0144	5008	,	,		18985	0.0		0.0219	False		,,,				2504	0.0061				p.N4024D		Atlas-SNP	.											.	CMYA5	643	.	0			c.A12070G						PASS	.	A	ASP/ASN	13,4055		0,13,2021	141.0	137.0	138.0		12070	6.2	0.3	5	dbSNP_132	138	143,8235		3,137,4049	yes	missense	CMYA5	NM_153610.3	23	3,150,6070	GG,GA,AA		1.7069,0.3196,1.2534	benign	4024/4070	79095299	156,12290	2034	4189	6223	SO:0001583	missense	202333	exon13			TTCATCAACGCAG	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.12070A>G	5.37:g.79095299A>G	ENSP00000394770:p.Asn4024Asp	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	197	93	0.472081	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	21	0.009615384615384616	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	17	0.022427440633245383	A	16.47	3.131843	0.56828	0.003196	0.017069	ENSG00000164309	ENST00000446378	T	0.13538	2.58	6.17	6.17	0.99709	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.15998	0.0385	L	0.35644	1.08	0.53688	D	0.999974	D	0.89917	1.0	D	0.97110	1.0	T	0.00299	-1.1836	9	0.46703	T	0.11	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	4024	Q8N3K9	CMYA5_HUMAN	D	4024	ENSP00000394770:N4024D	ENSP00000394770:N4024D	N	+	1	0	CMYA5	79131055	1.000000	0.71417	0.285000	0.24819	0.013000	0.08279	7.964000	0.87933	2.371000	0.80710	0.533000	0.62120	AAC	A|0.987;G|0.013	0.013	strong		0.483	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
SETBP1	26040	hgsc.bcm.edu	37	18	42532693	42532693	+	Missense_Mutation	SNP	C	C	A	rs1064204	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:42532693C>A	ENST00000282030.5	+	4	3684	c.3388C>A	c.(3388-3390)Cct>Act	p.P1130T		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1130			P -> T (in dbSNP:rs1064204).			nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		TGACATGCAGCCTTCTCTGAA	0.527									Schinzel-Giedion syndrome				C|||	594	0.11861	0.0182	0.2435	5008	,	,		20858	0.1895		0.1103	False		,,,				2504	0.1012				p.P1130T		Atlas-SNP	.											.	SETBP1	577	.	0			c.C3388A						PASS	.	C	THR/PRO	212,4194	130.2+/-166.9	5,202,1996	109.0	87.0	94.0		3388	4.1	1.0	18	dbSNP_86	94	1030,7570	219.0+/-257.2	57,916,3327	yes	missense	SETBP1	NM_015559.2	38	62,1118,5323	AA,AC,CC		11.9767,4.8116,9.5494	benign	1130/1597	42532693	1242,11764	2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	ATGCAGCCTTCTC	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.3388C>A	18.37:g.42532693C>A	ENSP00000282030:p.Pro1130Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	289	0.13232600732600733	11	0.022357723577235773	74	0.20441988950276244	120	0.2097902097902098	84	0.11081794195250659	C	5.865	0.343735	0.11126	0.048116	0.119767	ENSG00000152217	ENST00000282030	T	0.69175	-0.38	5.88	4.09	0.47781	.	0.283324	0.36482	N	0.002561	T	0.00039	0.0001	N	0.24115	0.695	0.33516	P	0.40827899999999995	B	0.02656	0.0	B	0.08055	0.003	T	0.05716	-1.0868	9	0.39692	T	0.17	.	2.183	0.03879	0.1765:0.4964:0.1718:0.1553	rs1064204;rs3205204;rs3744826;rs52806906;rs61239753;rs1064204	1130	Q9Y6X0	SETBP_HUMAN	T	1130	ENSP00000282030:P1130T	ENSP00000282030:P1130T	P	+	1	0	SETBP1	40786691	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	1.873000	0.39558	0.823000	0.34589	0.561000	0.74099	CCT	C|0.892;A|0.108	0.108	strong		0.527	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
WDR17	116966	hgsc.bcm.edu	37	4	177100644	177100644	+	Missense_Mutation	SNP	G	G	A	rs11736872	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:177100644G>A	ENST00000280190.4	+	31	4039	c.3883G>A	c.(3883-3885)Gct>Act	p.A1295T	WDR17_ENST00000393643.2_Missense_Mutation_p.A1271T|WDR17_ENST00000507824.2_Missense_Mutation_p.A1270T|WDR17_ENST00000508596.1_Missense_Mutation_p.A1256T			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1295			A -> T (in dbSNP:rs11736872). {ECO:0000269|PubMed:12401215}.							breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CGGGAAATCTGCTATCTCCTT	0.388													G|||	1037	0.207069	0.1369	0.2104	5008	,	,		12251	0.13		0.2783	False		,,,				2504	0.3057				p.A1295T		Atlas-SNP	.											.	WDR17	198	.	0			c.G3883A						PASS	.	G	THR/ALA,THR/ALA	678,3728	285.7+/-278.4	58,562,1583	152.0	138.0	143.0		3883,3766	-0.9	0.3	4	dbSNP_120	143	2558,6042	417.4+/-352.4	365,1828,2107	yes	missense,missense	WDR17	NM_170710.4,NM_181265.3	58,58	423,2390,3690	AA,AG,GG		29.7442,15.3881,24.8808	benign,benign	1295/1323,1256/1284	177100644	3236,9770	2203	4300	6503	SO:0001583	missense	116966	exon31			AAATCTGCTATCT	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"""WD repeat domain containing"""	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3883G>A	4.37:g.177100644G>A	ENSP00000280190:p.Ala1295Thr	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	294	117	0.397959	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	428|428	0.19597069597069597|0.19597069597069597	68|68	0.13821138211382114|0.13821138211382114	85|85	0.23480662983425415|0.23480662983425415	63|63	0.11013986013986014|0.11013986013986014	212|212	0.2796833773087071|0.2796833773087071	G|G	12.85|12.85	2.060188|2.060188	0.36373|0.36373	0.153881|0.153881	0.297442|0.297442	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.58210|.	0.37;0.4;0.35|.	5.51|5.51	-0.869|-0.869	0.10649|0.10649	.|.	0.254658|.	0.38058|.	N|.	0.001838|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.11927|0.11927	0.2|0.2	0.23381|0.23381	P|P	0.99779477|0.99779477	B;B;B|.	0.17038|.	0.02;0.001;0.003|.	B;B;B|.	0.13407|.	0.009;0.006;0.006|.	T|T	0.39354|0.39354	-0.9618|-0.9618	9|4	0.16896|.	T|.	0.51|.	-5.5383|-5.5383	10.6133|10.6133	0.45434|0.45434	0.3901:0.0:0.6099:0.0|0.3901:0.0:0.6099:0.0	rs11736872;rs17671753;rs52832800;rs60810877;rs11736872|rs11736872;rs17671753;rs52832800;rs60810877;rs11736872	1271;1256;1295|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	T|Y	1256;1271;1295;1271|529	ENSP00000422763:A1256T;ENSP00000377258:A1271T;ENSP00000280190:A1295T|.	ENSP00000280190:A1295T|.	A|C	+|+	1|2	0|0	WDR17|WDR17	177337638|177337638	0.202000|0.202000	0.23423|0.23423	0.315000|0.315000	0.25238|0.25238	0.997000|0.997000	0.91878|0.91878	0.596000|0.596000	0.24044|0.24044	-0.180000|-0.180000	0.10637|0.10637	0.655000|0.655000	0.94253|0.94253	GCT|TGC	G|0.774;A|0.226	0.226	strong		0.388	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048539	33048539	+	Missense_Mutation	SNP	T	T	A	rs1042117	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33048539T>A	ENST00000418931.2	+	2	307	c.191T>A	c.(190-192)tTc>tAc	p.F64Y	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.F64Y	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	64	Beta-1.		F -> L (in allele DPB1*02:02, allele DPB1*02:03, allele DPB1*05:01, allele DPB1*15:02, allele DPB1*17:02, allele DPB1*19:02, allele DPB1*21:01, allele DPB1*21:01, allele DPB1*22:01, allele DPB1*34:01, allele DPB1*36:01, allele DPB1*38:01, allele DPB1*44:01, allele DPB1*48:01, allele DPB1*58:01, allele DPB1*62:01, allele DPB1*63:01, allele DPB1*95:01 and allele DPB1*97:01; dbSNP:rs9277348).|F -> Y (in allele DPB1*01:01, allele DPB1*01:02, allele DPB1*09:02, allele DPB1*11:01, allele DPB1*13:01, allele DPB1*15:01, allele DPB1*20:02, allele DPB1*21:02, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*27:01, allele DPB1*39:01, allele DPB1*40:01, allele DPB1*49:01, allele DPB1*53:01, allele DPB1*65:01, allele DPB1*74:01, allele DPB1*85:01, allele DPB1*89:01 and allele DPB1*96:01; dbSNP:rs1042117).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CGGGAGGAGTTCGCGCGCTTC	0.612													.|||	1045	0.208666	0.4781	0.1124	5008	,	,		14806	0.0863		0.0944	False		,,,				2504	0.1564				p.F64Y		Atlas-SNP	.											HLA-DPB1,rectum,carcinoma,-1,1	HLA-DPB1	28	1	0			c.T191A						PASS	.	A	,,TYR/PHE	1181,1841		220,741,550	69.0	70.0	69.0		,,191	-7.9	0.0	6	dbSNP_86	69	519,4899		24,471,2214	no	utr-5,utr-5,missense	HLA-DPA1,HLA-DPB1	NM_001242524.1,NM_001242525.1,NM_002121.5	,,22	244,1212,2764	AA,AT,TT		9.5792,39.0801,20.1422	,,benign	,,64/259	33048539	1700,6740	1511	2709	4220	SO:0001583	missense	3115	exon2			AGGAGTTCGCGCG		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.191T>A	6.37:g.33048539T>A	ENSP00000408146:p.Phe64Tyr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	94	38	0.404255	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	386|386	0.17673992673992675|0.17673992673992675	233|233	0.4735772357723577|0.4735772357723577	41|41	0.1132596685082873|0.1132596685082873	39|39	0.06818181818181818|0.06818181818181818	73|73	0.09630606860158311|0.09630606860158311	A|A	0.008|0.008	-1.922143|-1.922143	0.00498|0.00498	0.390801|0.390801	0.095792|0.095792	ENSG00000223865|ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835|ENST00000416804	T;T;T|.	0.00262|.	8.4;8.4;8.4|.	3.94|3.94	-7.87|-7.87	0.01183|0.01183	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);|.	1.117700|.	0.06944|.	N|.	0.813382|.	T|T	0.02888|0.02888	0.0086|0.0086	N|N	0.04508|0.04508	-0.205|-0.205	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.10450|.	0.005;0.003|.	T|T	0.13388|0.13388	-1.0511|-1.0511	9|4	0.02654|.	T|.	1|.	.|.	6.7891|6.7891	0.23689|0.23689	0.5161:0.0:0.1925:0.2914|0.5161:0.0:0.1925:0.2914	rs1042117;rs3173298;rs16868592;rs17221108;rs58131392|rs1042117;rs3173298;rs16868592;rs17221108;rs58131392	74;64|.	Q59GY1;P04440|.	.;DPB1_HUMAN|.	Y|T	64;64;64;41|31	ENSP00000408146:F64Y;ENSP00000439674:F64Y;ENSP00000412654:F41Y|.	ENSP00000389210:F64Y|.	F|S	+|+	2|1	0|0	HLA-DPB1|HLA-DPB1	33156517|33156517	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-4.771000|-4.771000	0.00188|0.00188	-3.676000|-3.676000	0.00122|0.00122	-5.201000|-5.201000	0.00001|0.00001	TTC|TCG	T|0.803;A|0.197	0.197	strong		0.612	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
CNTROB	116840	hgsc.bcm.edu	37	17	7843053	7843053	+	Silent	SNP	C	C	T	rs11078719	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7843053C>T	ENST00000563694.1	+	8	2075	c.1150C>T	c.(1150-1152)Ctg>Ttg	p.L384L	CNTROB_ENST00000565740.1_Silent_p.L384L|CNTROB_ENST00000380255.3_Silent_p.L384L|CNTROB_ENST00000380262.3_Silent_p.L384L	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	384	Required for centrosome localization.				centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				CCAGGCTCAGCTGGAAAGGGA	0.522													T|||	2979	0.594848	0.4433	0.6398	5008	,	,		20015	0.8016		0.4274	False		,,,				2504	0.727				p.L384L		Atlas-SNP	.											.	CNTROB	61	.	0			c.C1150T						PASS	.	T	,	2044,2362	578.7+/-384.7	482,1080,641	45.0	48.0	47.0		1150,1150	-6.8	0.2	17	dbSNP_120	47	3745,4853	586.7+/-392.1	829,2087,1383	no	coding-synonymous,coding-synonymous	CNTROB	NM_001037144.5,NM_053051.3	,	1311,3167,2024	TT,TC,CC		43.5566,46.3913,44.5171	,	384/926,384/904	7843053	5789,7215	2203	4299	6502	SO:0001819	synonymous_variant	116840	exon8			GCTCAGCTGGAAA	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.1150C>T	17.37:g.7843053C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Silent	SNP	ENST00000563694.1	37	CCDS11126.1																																																																																			C|0.506;T|0.494	0.494	strong		0.522	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	
LPIN3	64900	hgsc.bcm.edu	37	20	39986085	39986085	+	Missense_Mutation	SNP	A	A	C	rs12625565	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:39986085A>C	ENST00000373257.3	+	16	2128	c.2037A>C	c.(2035-2037)caA>caC	p.Q679H		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	679	C-LIP.		Q -> H (in dbSNP:rs12625565).		fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				ACAAAATCCAACTGTGAGTGC	0.602													C|||	1816	0.36262	0.4561	0.3501	5008	,	,		20475	0.5754		0.2346	False		,,,				2504	0.1575				p.Q679H		Atlas-SNP	.											.	LPIN3	69	.	0			c.A2037C						PASS	.	C	HIS/GLN	1934,2472	621.7+/-393.8	428,1078,697	60.0	53.0	55.0		2037	4.2	1.0	20	dbSNP_120	55	1882,6718	727.0+/-406.6	225,1432,2643	yes	missense	LPIN3	NM_022896.1	24	653,2510,3340	CC,CA,AA		21.8837,43.8947,29.3403	benign	679/852	39986085	3816,9190	2203	4300	6503	SO:0001583	missense	64900	exon16			AATCCAACTGTGA	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"""lipin 3-like"""	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.2037A>C	20.37:g.39986085A>C	ENSP00000362354:p.Gln679His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Missense_Mutation	SNP	ENST00000373257.3	37	CCDS33469.1	837|837	0.38324175824175827|0.38324175824175827	216|216	0.43902439024390244|0.43902439024390244	112|112	0.30939226519337015|0.30939226519337015	321|321	0.5611888111888111|0.5611888111888111	188|188	0.24802110817941952|0.24802110817941952	C|C	5.601|5.601	0.295673|0.295673	0.10622|0.10622	0.438947|0.438947	0.218837|0.218837	ENSG00000132793|ENSG00000132793	ENST00000445975|ENST00000373257;ENST00000373259	.|T	.|0.76709	.|-1.04	5.2|5.2	4.24|4.24	0.50183|0.50183	.|HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	.|0.000000	.|0.85682	.|N	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00471|0.00471	-1.455|-1.455	0.47308|0.47308	P|P	6.110000000000282E-4|6.110000000000282E-4	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.45731|0.45731	-0.9241|-0.9241	4|8	.|.	.|.	.|.	-15.3171|-15.3171	6.8264|6.8264	0.23885|0.23885	0.1436:0.7034:0.0:0.153|0.1436:0.7034:0.0:0.153	rs12625565;rs52822966;rs57276596;rs12625565|rs12625565;rs52822966;rs57276596;rs12625565	.|680;679	.|Q9BQK8-2;Q9BQK8	.|.;LPIN3_HUMAN	T|H	169|679;312	.|ENSP00000362354:Q679H	.|.	N|Q	+|+	2|3	0|2	LPIN3|LPIN3	39419499|39419499	0.854000|0.854000	0.29725|0.29725	1.000000|1.000000	0.80357|0.80357	0.941000|0.941000	0.58515|0.58515	0.392000|0.392000	0.20801|0.20801	0.572000|0.572000	0.29383|0.29383	-0.215000|-0.215000	0.12644|0.12644	AAC|CAA	A|0.667;C|0.333	0.333	strong		0.602	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896	
SIGLEC15	284266	hgsc.bcm.edu	37	18	43420177	43420177	+	Splice_Site	SNP	G	G	A	rs61104666	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:43420177G>A	ENST00000389474.3	+	5	1093	c.876G>A	c.(874-876)gaG>gaA	p.E292E	SIGLEC15_ENST00000587418.1_Splice_Site_p.S62N|SIGLEC15_ENST00000602118.2_3'UTR|SIGLEC15_ENST00000546268.1_Splice_Site_p.E138E	NM_213602.2	NP_998767.1	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	292					cellular response to lipoprotein particle stimulus (GO:0071402)|innate immune response (GO:0045087)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of bone resorption (GO:0045124)|regulation of osteoclast development (GO:2001204)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						CTCCCACAGAGCATCTGGACA	0.652													G|||	1267	0.252995	0.1536	0.3689	5008	,	,		14636	0.371		0.1322	False		,,,				2504	0.3078				p.E292E		Atlas-SNP	.											.	SIGLEC15	10	.	0			c.G876A						PASS	.	G		674,3732	284.3+/-277.5	54,566,1583	129.0	101.0	110.0		876	1.0	0.9	18	dbSNP_129	110	974,7626	210.7+/-251.5	54,866,3380	yes	coding-synonymous-near-splice	SIGLEC15	NM_213602.2		108,1432,4963	AA,AG,GG		11.3256,15.2973,12.6711		292/329	43420177	1648,11358	2203	4300	6503	SO:0001630	splice_region_variant	284266	exon5			CACAGAGCATCTG	AK095432	CCDS32819.1	18q21.1	2014-01-28	2007-05-31	2007-05-31	ENSG00000197046	ENSG00000197046		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27596	protein-coding gene	gene with protein product			"""CD33 antigen-like 3"", ""CD33 molecule-like 3"""	CD33L3		17483134	Standard	NM_213602		Approved	HsT1361	uc002lbl.1	Q6ZMC9		ENST00000389474.3:c.875-1G>A	18.37:g.43420177G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_213602	A8K2Y5|B4DVQ9	Silent	SNP	ENST00000389474.3	37	CCDS32819.1																																																																																			G|0.844;A|0.156	0.156	strong		0.652	SIGLEC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410768.2	NM_213602	Silent
CCDC68	80323	hgsc.bcm.edu	37	18	52605279	52605279	+	Missense_Mutation	SNP	C	C	T	rs72928889	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:52605279C>T	ENST00000591504.1	-	5	528	c.254G>A	c.(253-255)tGt>tAt	p.C85Y	CCDC68_ENST00000337363.4_Missense_Mutation_p.C85Y|CCDC68_ENST00000432185.1_Missense_Mutation_p.C85Y	NM_025214.2	NP_079490.1	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68	85										breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|stomach(1)	14				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)		CAAACTGCAACAAGAAGGATC	0.358													C|||	65	0.0129792	0.003	0.0173	5008	,	,		18079	0.0		0.0417	False		,,,				2504	0.0072				p.C85Y		Atlas-SNP	.											.	CCDC68	38	.	0			c.G254A						PASS	.	C	TYR/CYS,TYR/CYS	31,4375	37.6+/-69.7	1,29,2173	98.0	90.0	93.0		254,254	1.1	0.0	18	dbSNP_130	93	309,8291	111.8+/-172.0	5,299,3996	yes	missense,missense	CCDC68	NM_001143829.1,NM_025214.2	194,194	6,328,6169	TT,TC,CC		3.593,0.7036,2.6142	benign,benign	85/336,85/336	52605279	340,12666	2203	4300	6503	SO:0001583	missense	80323	exon5			CTGCAACAAGAAG		CCDS11959.1	18q21	2006-02-07			ENSG00000166510	ENSG00000166510			24350	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma associated antigen"""					11149944, 15142679	Standard	NM_025214		Approved	SE57-1	uc002lft.3	Q9H2F9	OTTHUMG00000132708	ENST00000591504.1:c.254G>A	18.37:g.52605279C>T	ENSP00000466690:p.Cys85Tyr	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	188	89	0.473404	NM_025214	B2R9I3	Missense_Mutation	SNP	ENST00000591504.1	37	CCDS11959.1	37	0.01694139194139194	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	25	0.032981530343007916	C	14.87	2.663408	0.47572	0.007036	0.03593	ENSG00000166510	ENST00000337363;ENST00000432185	T;T	0.21361	2.01;2.01	5.18	1.09	0.20402	.	0.935721	0.09027	N	0.859369	T	0.03263	0.0095	L	0.46157	1.445	0.09310	N	1	P	0.51351	0.944	B	0.41036	0.346	T	0.14227	-1.0480	10	0.22109	T	0.4	2.9925	2.645	0.04981	0.1348:0.4379:0.2634:0.1639	.	85	Q9H2F9	CCD68_HUMAN	Y	85	ENSP00000337209:C85Y;ENSP00000413406:C85Y	ENSP00000337209:C85Y	C	-	2	0	CCDC68	50756277	0.000000	0.05858	0.009000	0.14445	0.868000	0.49771	-0.460000	0.06720	0.563000	0.29222	-0.181000	0.13052	TGT	C|0.975;T|0.025	0.025	strong		0.358	CCDC68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256006.1	NM_025214	
ERBB2IP	55914	hgsc.bcm.edu	37	5	65321311	65321311	+	Missense_Mutation	SNP	C	C	T	rs3213837	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:65321311C>T	ENST00000284037.5	+	11	1210	c.821C>T	c.(820-822)tCg>tTg	p.S274L	ERBB2IP_ENST00000380939.2_Missense_Mutation_p.S274L|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.S274L|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.S274L|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.S274L|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.S274L|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.S274L|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.S274L|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.S274L|ERBB2IP_ENST00000416865.2_Missense_Mutation_p.S274L	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	274			S -> L (in dbSNP:rs3213837). {ECO:0000269|PubMed:15489334}.		basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		TCATTAGGTTCGTTGAAGAAT	0.358													C|||	606	0.121006	0.0091	0.1744	5008	,	,		18791	0.0942		0.1541	False		,,,				2504	0.228				p.S274L		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.C821T						PASS	.	C	LEU/SER,LEU/SER	154,4252	103.8+/-142.4	4,146,2053	169.0	161.0	164.0		821,821	2.3	1.0	5	dbSNP_106	164	1344,7254	262.4+/-284.4	105,1134,3060	yes	missense,missense	ERBB2IP	NM_001006600.1,NM_018695.2	145,145	109,1280,5113	TT,TC,CC		15.6315,3.4952,11.5195	benign,benign	274/1303,274/1372	65321311	1498,11506	2203	4299	6502	SO:0001583	missense	55914	exon11			TAGGTTCGTTGAA		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.821C>T	5.37:g.65321311C>T	ENSP00000284037:p.Ser274Leu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_001253701	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	228	0.1043956043956044	7	0.014227642276422764	55	0.15193370165745856	51	0.08916083916083917	115	0.1517150395778364	C	9.444	1.088912	0.20390	0.034952	0.156315	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000416865;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83	5.11	2.3	0.28687	.	0.124185	0.56097	D	0.000024	T	0.00073	0.0002	L	0.28694	0.88	0.22034	P	0.999405699	B;B;B;B;B;B;B;B	0.17852	0.024;0.002;0.002;0.006;0.001;0.001;0.0;0.001	B;B;B;B;B;B;B;B	0.17433	0.018;0.003;0.001;0.004;0.001;0.001;0.001;0.002	T	0.22277	-1.0221	9	0.25751	T	0.34	.	4.4646	0.11682	0.1148:0.5829:0.1122:0.1902	rs3213837;rs17248606;rs52791318;rs60398656;rs3213837	274;274;274;274;274;274;274;274	B4DIP2;Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;.;LAP2_HUMAN;.;.	L	274	ENSP00000284037:S274L;ENSP00000370330:S274L;ENSP00000397833:S274L;ENSP00000370326:S274L;ENSP00000370323:S274L;ENSP00000370322:S274L;ENSP00000370325:S274L;ENSP00000422766:S274L;ENSP00000426632:S274L;ENSP00000422015:S274L	ENSP00000284037:S274L	S	+	2	0	ERBB2IP	65357067	0.127000	0.22367	0.975000	0.42487	0.852000	0.48524	0.636000	0.24644	0.654000	0.30846	-0.143000	0.13931	TCG	C|0.896;T|0.104	0.104	strong		0.358	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
SH3BP4	23677	hgsc.bcm.edu	37	2	235951819	235951819	+	Silent	SNP	A	A	G	rs3795962	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:235951819A>G	ENST00000409212.1	+	4	2913	c.2406A>G	c.(2404-2406)ctA>ctG	p.L802L	SH3BP4_ENST00000392011.2_Silent_p.L802L|SH3BP4_ENST00000344528.4_Silent_p.L802L			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	802					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)	p.L802L(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		CGTCCGTCCTAGAAAAGCTGA	0.587													G|||	3767	0.752196	0.9576	0.6499	5008	,	,		22177	0.9157		0.4612	False		,,,				2504	0.6779				p.L802L		Atlas-SNP	.											SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	1	Substitution - coding silent(1)	prostate(1)	c.A2406G						scavenged	.	G		3881,525	224.3+/-240.5	1716,449,38	46.0	46.0	46.0		2406	2.0	1.0	2	dbSNP_107	46	3994,4606	566.4+/-388.7	926,2142,1232	no	coding-synonymous	SH3BP4	NM_014521.2		2642,2591,1270	GG,GA,AA		46.4419,11.9156,39.451		802/964	235951819	7875,5131	2203	4300	6503	SO:0001819	synonymous_variant	23677	exon4			CGTCCTAGAAAAG	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.2406A>G	2.37:g.235951819A>G		Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	191	87	0.455497	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	CCDS2513.1																																																																																			G|0.647;N|0.001	0.647	strong		0.587	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
MAST2	23139	hgsc.bcm.edu	37	1	46493460	46493460	+	Missense_Mutation	SNP	T	T	G	rs1707336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:46493460T>G	ENST00000361297.2	+	17	2260	c.1977T>G	c.(1975-1977)atT>atG	p.I659M	MAST2_ENST00000372009.2_Missense_Mutation_p.I589M	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					TGTCCAAAATTGGCCTCATGA	0.438													T|||	2430	0.485224	0.4259	0.4827	5008	,	,		21616	0.6607		0.4463	False		,,,				2504	0.4264				p.I659M		Atlas-SNP	.											.	MAST2	136	.	0			c.T1977G						PASS	.	T	MET/ILE	1588,2230		341,906,662	116.0	112.0	113.0		1977	-0.6	1.0	1	dbSNP_89	113	3613,4673		806,2001,1336	yes	missense	MAST2	NM_015112.2	10	1147,2907,1998	GG,GT,TT		43.6037,41.5925,42.9693	benign	659/1799	46493460	5201,6903	1909	4143	6052	SO:0001583	missense	23139	exon17			CAAAATTGGCCTC	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.1977T>G	1.37:g.46493460T>G	ENSP00000354671:p.Ile659Met	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	169	88	0.52071	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	37	CCDS41326.1	1011	0.46291208791208793	196	0.3983739837398374	170	0.4696132596685083	343	0.5996503496503497	302	0.39841688654353563	T	12.25	1.881032	0.33255	0.415925	0.436037	ENSG00000086015	ENST00000361297;ENST00000372009;ENST00000432341;ENST00000372008	T;T;T	0.65364	-0.15;-0.15;-0.15	5.41	-0.618	0.11576	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.21545	0.675	0.20307	P	0.9999129408	D;B;D;B	0.89917	0.988;0.12;1.0;0.379	D;B;D;P	0.91635	0.977;0.068;0.999;0.45	T	0.39440	-0.9614	9	0.02654	T	1	-11.8172	5.7492	0.18138	0.1423:0.203:0.0:0.6546	rs1707336;rs17402588;rs17845481;rs17858361;rs61064119;rs1707336	589;333;589;659	Q6P0Q8-2;E7EWL1;E7ERL6;Q6P0Q8	.;.;.;MAST2_HUMAN	M	659;589;333;544	ENSP00000354671:I659M;ENSP00000361079:I589M;ENSP00000361078:I544M	ENSP00000354671:I659M	I	+	3	3	MAST2	46266047	0.264000	0.24093	1.000000	0.80357	0.937000	0.57800	-0.392000	0.07314	0.093000	0.17368	0.459000	0.35465	ATT	G|0.474;N|0.000	0.474	strong		0.438	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
ARVCF	421	hgsc.bcm.edu	37	22	19969495	19969495	+	Silent	SNP	G	G	T	rs33992092	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:19969495G>T	ENST00000263207.3	-	4	621	c.330C>A	c.(328-330)gtC>gtA	p.V110V	ARVCF_ENST00000344269.3_Silent_p.V47V|ARVCF_ENST00000401994.1_Silent_p.V47V|ARVCF_ENST00000487793.1_5'UTR|ARVCF_ENST00000406259.1_Silent_p.V110V|ARVCF_ENST00000406522.1_Silent_p.V47V	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	110					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CTTCGGATGTGACAATAGACA	0.652													G|||	108	0.0215655	0.0711	0.0086	5008	,	,		17773	0.0		0.008	False		,,,				2504	0.0				p.V110V		Atlas-SNP	.											.	ARVCF	54	.	0			c.C330A						PASS	.	G		239,4167	138.8+/-174.5	7,225,1971	123.0	94.0	104.0		330	1.3	1.0	22	dbSNP_126	104	38,8562	26.3+/-74.7	0,38,4262	no	coding-synonymous	ARVCF	NM_001670.2		7,263,6233	TT,TG,GG		0.4419,5.4244,2.1298		110/963	19969495	277,12729	2203	4300	6503	SO:0001819	synonymous_variant	421	exon4			GGATGTGACAATA		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"""Armadillo repeat containing"""	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.330C>A	22.37:g.19969495G>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	229	108	0.471616	NM_001670	B7WNV2	Silent	SNP	ENST00000263207.3	37	CCDS13771.1																																																																																			G|0.979;T|0.021	0.021	strong		0.652	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
TREML2	79865	hgsc.bcm.edu	37	6	41166022	41166022	+	Silent	SNP	A	A	G	rs386700523|rs139267947		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41166022A>G	ENST00000483722.1	-	2	386	c.201T>C	c.(199-201)ttT>ttC	p.F67F		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	67	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					AGACTCGGGCAAAGCCAGGCT	0.572																																					p.F67F		Atlas-SNP	.											TREML2,caecum,carcinoma,0,1	TREML2	41	1	0			c.T201C						scavenged	.						135.0	134.0	134.0					6																	41166022		2203	4300	6503	SO:0001819	synonymous_variant	79865	exon2			TCGGGCAAAGCCA	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.201T>C	6.37:g.41166022A>G		Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	104	7	0.0673077	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Silent	SNP	ENST00000483722.1	37	CCDS4853.2																																																																																			A|0.997;G|0.003	0.003	weak		0.572	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
C11orf44	283171	hgsc.bcm.edu	37	11	130542882	130542882	+	Silent	SNP	C	C	T	rs7933829	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130542882C>T	ENST00000317019.2	+	1	32	c.9C>T	c.(7-9)ctC>ctT	p.L3L		NM_001271983.1	NP_001258912.1	Q8N8P7	CK044_HUMAN	chromosome 11 open reading frame 44	3						extracellular region (GO:0005576)				central_nervous_system(1)	1						ACATGGTCCTCCTCTGTCTCT	0.587													C|||	1310	0.261581	0.3638	0.1988	5008	,	,		15454	0.3274		0.1928	False		,,,				2504	0.1708				p.L3L		Atlas-SNP	.											.	C11orf44	6	.	0			c.C9T						PASS	.	C		478,906		83,312,297	62.0	55.0	57.0			1.0	0.0	11	dbSNP_116	57	708,2474		89,530,972	no	intergenic				172,842,1269	TT,TC,CC		22.2502,34.5376,25.9746			130542882	1186,3380	692	1591	2283	SO:0001819	synonymous_variant	283171	exon1			GGTCCTCCTCTGT	AK096377	CCDS8489.1	11q24.3	2005-10-27			ENSG00000175728	ENSG00000175728			26805	protein-coding gene	gene with protein product							Standard	NM_001271983		Approved	FLJ39058	uc031qfg.1	Q8N8P7	OTTHUMG00000150705	ENST00000317019.2:c.9C>T	11.37:g.130542882C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	135	74	0.548148	NM_001271983		Silent	SNP	ENST00000317019.2	37																																																																																				C|0.739;T|0.261	0.261	strong		0.587	C11orf44-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000319680.1	NM_173580	
LGALS14	56891	hgsc.bcm.edu	37	19	40197924	40197924	+	Missense_Mutation	SNP	T	T	C	rs4830	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40197924T>C	ENST00000392052.3	+	3	422	c.199T>C	c.(199-201)Tgt>Cgt	p.C67R	LGALS14_ENST00000360675.3_Missense_Mutation_p.C96R	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14	67	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.		C -> R (in dbSNP:rs4830). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19497882, ECO:0000269|Ref.1, ECO:0000269|Ref.6}.		apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)	p.C96R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			CATGAACAGTTGTGTGTTTGG	0.438													C|||	3191	0.637181	0.8048	0.5245	5008	,	,		24240	0.376		0.7038	False		,,,				2504	0.6912				p.C96R		Atlas-SNP	.											LGALS14,NS,carcinoma,0,1	LGALS14	38	1	1	Substitution - Missense(1)	stomach(1)	c.T286C						PASS	.	C	ARG/CYS,ARG/CYS	3465,941		1358,749,96	279.0	237.0	251.0		199,286	1.0	0.0	19	dbSNP_52	251	5793,2807		1928,1937,435	yes	missense,missense	LGALS14	NM_020129.2,NM_203471.1	180,180	3286,2686,531	CC,CT,TT		32.6395,21.3572,28.8175	benign,benign	67/140,96/169	40197924	9258,3748	2203	4300	6503	SO:0001583	missense	56891	exon4			AACAGTTGTGTGT	AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"""Lectins, galactoside-binding"""	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.199T>C	19.37:g.40197924T>C	ENSP00000375905:p.Cys67Arg	Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	367	181	0.493188	NM_203471	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Missense_Mutation	SNP	ENST00000392052.3	37	CCDS46073.1	1342	0.6144688644688645	406	0.8252032520325203	194	0.5359116022099447	219	0.38286713286713286	523	0.6899736147757256	.	0	-2.625072	0.00117	0.786428	0.673605	ENSG00000006659	ENST00000392052;ENST00000360675	T;T	0.05513	3.43;3.43	1.05	1.05	0.20165	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.00012	0.0000	N	0.00637	-1.305	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20806	-1.0264	8	0.02654	T	1	.	3.5017	0.07676	0.0:0.7217:0.0:0.2783	rs4830;rs3170360;rs17709333;rs17855495;rs56595801;rs57731511;rs4830	67;96	Q8TCE9;A8MPV8	PPL13_HUMAN;.	R	67;96	ENSP00000375905:C67R;ENSP00000353893:C96R	ENSP00000353893:C96R	C	+	1	0	LGALS14	44889764	0.050000	0.20438	0.005000	0.12908	0.008000	0.06430	0.232000	0.17891	0.034000	0.15491	-0.642000	0.03964	TGT	T|0.330;C|0.670	0.670	strong		0.438	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129	
OR5W2	390148	hgsc.bcm.edu	37	11	55681149	55681149	+	Missense_Mutation	SNP	G	G	C	rs62639688	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55681149G>C	ENST00000344514.1	-	1	909	c.910C>G	c.(910-912)Ctg>Gtg	p.L304V		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	304						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						ttatttttCAGTTTTTTCAGG	0.303													G|||	161	0.0321486	0.0038	0.0331	5008	,	,		14664	0.001		0.0905	False		,,,				2504	0.0419				p.L304V	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.C910G						PASS	.	G	VAL/LEU	64,4262		0,64,2099	17.0	19.0	18.0		910	-2.8	0.0	11	dbSNP_129	18	669,7893		31,607,3643	yes	missense	OR5W2	NM_001001960.1	32	31,671,5742	CC,CG,GG		7.8136,1.4794,5.6875	benign	304/311	55681149	733,12155	2163	4281	6444	SO:0001583	missense	390148	exon1			TTTTCAGTTTTTT	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.910C>G	11.37:g.55681149G>C	ENSP00000342448:p.Leu304Val	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	77	0.035256410256410256	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	67	0.08839050131926121	G	0.017	-1.493482	0.01009	0.014794	0.078136	ENSG00000187612	ENST00000344514	T	0.41400	1.0	5.01	-2.85	0.05734	.	1.150270	0.07009	N	0.824721	T	0.00580	0.0019	N	0.12746	0.255	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.11717	-1.0576	10	0.05833	T	0.94	.	2.2493	0.04039	0.3929:0.1178:0.3696:0.1197	rs62639688	304	Q8NH69	OR5W2_HUMAN	V	304	ENSP00000342448:L304V	ENSP00000342448:L304V	L	-	1	2	OR5W2	55437725	0.000000	0.05858	0.001000	0.08648	0.522000	0.34438	-2.704000	0.00822	-0.601000	0.05783	-1.146000	0.01853	CTG	G|0.941;C|0.059	0.059	strong		0.303	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
ZNF440	126070	hgsc.bcm.edu	37	19	11942362	11942362	+	Missense_Mutation	SNP	A	A	G	rs427880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11942362A>G	ENST00000304060.5	+	4	535	c.371A>G	c.(370-372)aAc>aGc	p.N124S		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	124			N -> S (in dbSNP:rs427880).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TTTAATATGAACATCAGAGGT	0.418													N|||	2684	0.535942	0.8714	0.4683	5008	,	,		19794	0.4236		0.4036	False		,,,				2504	0.3824				p.N124S		Atlas-SNP	.											.	ZNF440	56	.	0			c.A371G						PASS	.	G	SER/ASN	3524,882	742.3+/-411.4	1416,692,95	176.0	179.0	178.0		371	-0.2	0.0	19	dbSNP_80	178	3678,4920	527.4+/-381.2	773,2132,1394	no	missense	ZNF440	NM_152357.2	46	2189,2824,1489	GG,GA,AA		42.7774,20.0182,44.617	benign	124/596	11942362	7202,5802	2203	4299	6502	SO:0001583	missense	126070	exon4			ATATGAACATCAG	AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"""Zinc fingers, C2H2-type"", ""-"""	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.371A>G	19.37:g.11942362A>G	ENSP00000305373:p.Asn124Ser	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	223	120	0.538117	NM_152357	Q8N1R9	Missense_Mutation	SNP	ENST00000304060.5	37	CCDS42503.1	1064	0.48717948717948717	387	0.7865853658536586	146	0.40331491712707185	239	0.4178321678321678	292	0.38522427440633245	a	3.527	-0.096629	0.07010	0.799818	0.427774	ENSG00000171295	ENST00000304060;ENST00000457526;ENST00000427505;ENST00000414255	T;T;T;T	0.06768	3.26;6.78;3.37;5.66	0.87	-0.224	0.13115	.	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.19706	0.038	B	0.19148	0.024	T	0.06285	-1.0835	8	0.62326	D	0.03	.	4.3544	0.11170	0.7724:0.0:0.2276:0.0	rs427880	124	Q8IYI8	ZN440_HUMAN	S	124;2;127;126	ENSP00000305373:N124S;ENSP00000404425:N2S;ENSP00000393489:N127S;ENSP00000411974:N126S	ENSP00000305373:N124S	N	+	2	0	ZNF440	11803362	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	-0.037000	0.12164	-0.119000	0.11830	-1.211000	0.01629	AAC	A|0.546;G|0.454	0.454	strong		0.418	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2930339	2930339	+	Silent	SNP	G	G	A	rs4790115	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:2930339G>A	ENST00000254695.8	+	22	2172	c.2082G>A	c.(2080-2082)ccG>ccA	p.P694P	RAP1GAP2_ENST00000540393.2_Silent_p.P675P|RAP1GAP2_ENST00000542807.1_Silent_p.P694P|RAP1GAP2_ENST00000366401.4_Silent_p.P679P	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	694	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CTGCCACCCCGATCATCATGA	0.657													G|||	2140	0.427316	0.2428	0.4942	5008	,	,		17712	0.5486		0.4066	False		,,,				2504	0.5256				p.P694P		Atlas-SNP	.											RAP1GAP2_ENST00000254695,colon,carcinoma,0,2	RAP1GAP2	90	2	0			c.G2082A						PASS	.	G	,	1208,3184		180,848,1168	22.0	27.0	25.0		2037,2082	-1.5	1.0	17	dbSNP_111	25	3488,5074		722,2044,1515	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	902,2892,2683	AA,AG,GG		40.7381,27.5046,36.2514	,	679/716,694/731	2930339	4696,8258	2196	4281	6477	SO:0001819	synonymous_variant	23108	exon22			CACCCCGATCATC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.2082G>A	17.37:g.2930339G>A		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	257	131	0.509728	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			G|0.567;A|0.433	0.433	strong		0.657	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
CHD2	1106	hgsc.bcm.edu	37	15	93552488	93552488	+	Silent	SNP	C	C	T	rs34315566	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:93552488C>T	ENST00000394196.4	+	35	5595	c.4527C>T	c.(4525-4527)atC>atT	p.I1509I	CHD2_ENST00000557381.1_Silent_p.I1509I	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1509					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TGCTGAAAATCGGAGACCGGA	0.527													C|||	74	0.0147764	0.0038	0.0086	5008	,	,		18724	0.0		0.0557	False		,,,				2504	0.0072				p.I1509I		Atlas-SNP	.											.	CHD2	280	.	0			c.C4527T						PASS	.	C		42,4352	43.1+/-76.7	2,38,2157	106.0	86.0	93.0		4527	-5.5	1.0	15	dbSNP_126	93	466,8130	137.5+/-194.4	12,442,3844	no	coding-synonymous	CHD2	NM_001271.3		14,480,6001	TT,TC,CC		5.4211,0.9558,3.9107		1509/1829	93552488	508,12482	2197	4298	6495	SO:0001819	synonymous_variant	1106	exon35			GAAAATCGGAGAC	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4527C>T	15.37:g.93552488C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	79	48	0.607595	NM_001271	C6G482|Q96IP5	Silent	SNP	ENST00000394196.4	37	CCDS10374.2																																																																																			C|0.967;T|0.033	0.033	strong		0.527	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
CT45A5	441521	hgsc.bcm.edu	37	X	134948034	134948034	+	Silent	SNP	A	A	G	rs2034920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:134948034A>G	ENST00000463085.2	-	3	380	c.291T>C	c.(289-291)aaT>aaC	p.N97N	CT45A4_ENST00000420087.2_Intron|CT45A5_ENST00000491480.1_Silent_p.N97N|CT45A5_ENST00000370724.3_Silent_p.N97N			Q6NSH3	CT455_HUMAN	cancer/testis antigen family 45, member A5	97										endometrium(1)|large_intestine(2)|lung(6)	9						TGCTGGTAACATTTCCTCCCA	0.433													.|||	3151	0.834702	0.6876	0.5937	3775	,	,		15275	0.6577		0.5487	False		,,,				2504	0.6288				p.N97N		Atlas-SNP	.											.	CT45A5	26	.	0			c.T291C						PASS	.	G	,	3268,552		1196,387,489,49,67	207.0	192.0	197.0		291,291	0.5	0.0	X	dbSNP_94	197	4926,1768		1325,883,1393,217,451	no	coding-synonymous,coding-synonymous	CT45A5	NM_001007551.3,NM_001172288.1	,	2521,1270,1882,266,518	GG,GA,G,AA,A		26.4117,14.4503,22.0658	,	97/190,97/190	134948034	8194,2320	2188	4269	6457	SO:0001819	synonymous_variant	441521	exon3			GGTAACATTTCCT	AY743713	CCDS35406.1	Xq26.3	2009-03-12				ENSG00000269586			33270	protein-coding gene	gene with protein product	"""cancer/testis antigen CT45-5"""	300796				15905330	Standard	XM_006724759		Approved	CT45-5, CT45.5	uc022ces.1	Q6NSH3		ENST00000463085.2:c.291T>C	X.37:g.134948034A>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	137	122	0.890511	NM_001007551	A8K842|B7ZMC5	Silent	SNP	ENST00000463085.2	37	CCDS35406.1																																																																																			0|0.004;G|0.789	0.789	strong		0.433	CT45A5-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472589.1	NM_001007551	
LZTFL1	54585	hgsc.bcm.edu	37	3	45869972	45869972	+	Missense_Mutation	SNP	C	C	T	rs1129183	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:45869972C>T	ENST00000296135.6	-	8	910	c.736G>A	c.(736-738)Gat>Aat	p.D246N	LZTFL1_ENST00000536047.1_Missense_Mutation_p.D229N|LZTFL1_ENST00000490463.1_5'Flank|LZTFL1_ENST00000539217.1_Missense_Mutation_p.D242N	NM_001276378.1|NM_020347.2	NP_001263307.1|NP_065080.1	Q9NQ48	LZTL1_HUMAN	leucine zipper transcription factor-like 1	246	Interaction with BSS9.		D -> N (in dbSNP:rs1129183). {ECO:0000269|PubMed:11352561}.		establishment of protein localization to organelle (GO:0072594)	BBSome (GO:0034464)|cytoplasm (GO:0005737)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	8				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		CTGAGTAGATCGTGCTTGGCT	0.443													C|||	271	0.0541134	0.0431	0.0375	5008	,	,		19402	0.0387		0.0736	False		,,,				2504	0.0767				p.D246N		Atlas-SNP	.											LZTFL1_ENST00000539217,lymph_node,lymphoid_neoplasm,0,2	LZTFL1	37	2	0			c.G736A						PASS	.	C	ASN/ASP	190,4216	120.8+/-158.4	6,178,2019	130.0	126.0	128.0		736	4.9	0.6	3	dbSNP_86	128	686,7914	171.6+/-222.5	28,630,3642	yes	missense	LZTFL1	NM_020347.2	23	34,808,5661	TT,TC,CC		7.9767,4.3123,6.7354	possibly-damaging	246/300	45869972	876,12130	2203	4300	6503	SO:0001583	missense	54585	exon8			GTAGATCGTGCTT	AJ297351	CCDS2731.1, CCDS63608.1, CCDS63609.1	3p21.3	2014-01-28			ENSG00000163818	ENSG00000163818			6741	protein-coding gene	gene with protein product		606568				11352561, 22510444	Standard	NM_020347		Approved	BBS17	uc003cox.2	Q9NQ48	OTTHUMG00000133452	ENST00000296135.6:c.736G>A	3.37:g.45869972C>T	ENSP00000296135:p.Asp246Asn	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	269	143	0.531599	NM_020347	B3KSI9|B4E0K7|Q8TC61|Q9NQ56	Missense_Mutation	SNP	ENST00000296135.6	37	CCDS2731.1	126|126	0.057692307692307696|0.057692307692307696	30|30	0.06097560975609756|0.06097560975609756	19|19	0.052486187845303865|0.052486187845303865	27|27	0.0472027972027972|0.0472027972027972	50|50	0.06596306068601583|0.06596306068601583	C|C	15.52|15.52	2.858671|2.858671	0.51376|0.51376	0.043123|0.043123	0.079767|0.079767	ENSG00000163818|ENSG00000163818	ENST00000296135;ENST00000536047;ENST00000539217|ENST00000440576	T;T;T|.	0.22743|.	1.94;1.94;1.94|.	5.78|5.78	4.89|4.89	0.63831|0.63831	.|.	0.230493|.	0.50627|.	D|.	0.000101|.	T|T	0.13884|0.13884	0.0336|0.0336	M|M	0.67953|0.67953	2.075|2.075	0.20764|0.20764	P|P	0.999850701|0.999850701	P|.	0.50819|.	0.939|.	B|.	0.39971|.	0.315|.	T|T	0.52298|0.52298	-0.8594|-0.8594	9|4	0.62326|.	D|.	0.03|.	-18.6324|-18.6324	16.7351|16.7351	0.85445|0.85445	0.0:0.8707:0.1293:0.0|0.0:0.8707:0.1293:0.0	rs1129183;rs2633735;rs58495879;rs1129183|rs1129183;rs2633735;rs58495879;rs1129183	246|.	Q9NQ48|.	LZTL1_HUMAN|.	N|Q	246;229;242|181	ENSP00000296135:D246N;ENSP00000439522:D229N;ENSP00000441784:D242N|.	ENSP00000296135:D246N|.	D|R	-|-	1|2	0|0	LZTFL1|LZTFL1	45844976|45844976	1.000000|1.000000	0.71417|0.71417	0.627000|0.627000	0.29227|0.29227	0.147000|0.147000	0.21601|0.21601	4.448000|4.448000	0.60027|0.60027	1.398000|1.398000	0.46701|0.46701	0.655000|0.655000	0.94253|0.94253	GAT|CGA	C|0.937;T|0.063	0.063	strong		0.443	LZTFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257326.3	NM_020347	
MMEL1	79258	hgsc.bcm.edu	37	1	2560903	2560903	+	Silent	SNP	T	T	G	rs4648659	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:2560903T>G	ENST00000378412.3	-	2	182	c.21A>C	c.(19-21)ccA>ccC	p.P7P	MMEL1_ENST00000511099.1_5'Flank|MMEL1_ENST00000288709.6_5'UTR|MMEL1_ENST00000502556.1_Silent_p.P7P			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	7						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		CCATCCCCACTGGGCCTTCGG	0.721													-|||	2583	0.515775	0.4334	0.5519	5008	,	,		11780	0.4683		0.6909	False		,,,				2504	0.4703				p.P7P		Atlas-SNP	.											.	MMEL1	64	.	0			c.A21C						PASS	.	G		1843,1861		506,831,515	9.0	10.0	10.0		21	-6.5	0.0	1	dbSNP_111	10	5044,2006		1842,1360,323	no	coding-synonymous	MMEL1	NM_033467.3		2348,2191,838	GG,GT,TT		28.4539,49.757,35.9587		7/780	2560903	6887,3867	1852	3525	5377	SO:0001819	synonymous_variant	79258	exon2			CCCCACTGGGCCT	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"""membrane metallo-endopeptidase-like 2"""	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.21A>C	1.37:g.2560903T>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	78	76	0.974359	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Silent	SNP	ENST00000378412.3	37	CCDS30569.2																																																																																			T|0.424;G|0.576	0.576	strong		0.721	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
TMEM184A	202915	hgsc.bcm.edu	37	7	1587440	1587440	+	Missense_Mutation	SNP	G	G	A	rs61747419	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1587440G>A	ENST00000297477.5	-	8	1266	c.950C>T	c.(949-951)tCc>tTc	p.S317F	TMEM184A_ENST00000449955.1_5'Flank	NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	317					germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		CAGGGCCACGGAGGCGAACAG	0.642													G|||	17	0.00339457	0.0	0.0086	5008	,	,		17254	0.0		0.0109	False		,,,				2504	0.0				p.S317F		Atlas-SNP	.											.	TMEM184A	35	.	0			c.C950T						PASS	.		PHE/SER	6,4332		0,6,2163	45.0	54.0	51.0		950	5.8	0.0	7	dbSNP_129	51	87,8491		1,85,4203	yes	missense	TMEM184A	NM_001097620.1	155	1,91,6366	AA,AG,GG		1.0142,0.1383,0.72	probably-damaging	317/414	1587440	93,12823	2169	4289	6458	SO:0001583	missense	202915	exon8			GCCACGGAGGCGA		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.950C>T	7.37:g.1587440G>A	ENSP00000297477:p.Ser317Phe	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	156	76	0.487179	NM_001097620	Q8TBQ6	Missense_Mutation	SNP	ENST00000297477.5	37	CCDS43537.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	17.25	3.340697	0.60963	0.001383	0.010142	ENSG00000164855	ENST00000297477	T	0.50277	0.75	5.82	5.82	0.92795	.	0.205916	0.41823	U	0.000801	T	0.67748	0.2926	M	0.85041	2.73	0.43745	D	0.996242	D	0.71674	0.998	D	0.76071	0.987	T	0.75184	-0.3407	10	0.87932	D	0	-6.871	20.0773	0.97749	0.0:0.0:1.0:0.0	rs61747419	317	Q6ZMB5	T184A_HUMAN	F	317	ENSP00000297477:S317F	ENSP00000297477:S317F	S	-	2	0	TMEM184A	1553966	1.000000	0.71417	0.026000	0.17262	0.093000	0.18481	9.557000	0.98129	2.750000	0.94351	0.561000	0.74099	TCC	G|0.992;A|0.008	0.008	strong		0.642	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689	
RNF152	220441	hgsc.bcm.edu	37	18	59483514	59483514	+	Silent	SNP	A	A	G	rs9319985	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:59483514A>G	ENST00000312828.3	-	2	1282	c.183T>C	c.(181-183)ccT>ccC	p.P61P		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	61					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				AGAAGCCGGGAGGCAGCTTGG	0.622													G|||	1087	0.217053	0.3343	0.1931	5008	,	,		18490	0.0992		0.2515	False		,,,				2504	0.1616				p.P61P		Atlas-SNP	.											RNF152,caecum,carcinoma,0,1	RNF152	37	1	0			c.T183C						scavenged	.	G		1328,3078	683.5+/-404.3	196,936,1071	55.0	59.0	57.0		183	3.2	1.0	18	dbSNP_119	57	2059,6541	709.6+/-405.7	252,1555,2493	no	coding-synonymous	RNF152	NM_173557.2		448,2491,3564	GG,GA,AA		23.9419,30.1407,26.0418		61/204	59483514	3387,9619	2203	4300	6503	SO:0001819	synonymous_variant	220441	exon2			GCCGGGAGGCAGC	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"""RING-type (C3HC4) zinc fingers"""	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.183T>C	18.37:g.59483514A>G		Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_173557	B3KV99|Q52LA4	Silent	SNP	ENST00000312828.3	37	CCDS11978.1																																																																																			A|0.767;G|0.233	0.233	strong		0.622	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557	
BRCA2	675	hgsc.bcm.edu	37	13	32911463	32911463	+	Missense_Mutation	SNP	A	A	G	rs1799944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:32911463A>G	ENST00000380152.3	+	11	3204	c.2971A>G	c.(2971-2973)Aac>Gac	p.N991D	BRCA2_ENST00000544455.1_Missense_Mutation_p.N991D			P51587	BRCA2_HUMAN	breast cancer 2, early onset	991	Interaction with NPM1.		N -> D (common polymorphism; dbSNP:rs1799944). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:10978364, ECO:0000269|PubMed:12552570, ECO:0000269|PubMed:15026808, ECO:0000269|PubMed:15172753, ECO:0000269|PubMed:15365993, ECO:0000269|PubMed:8673091, ECO:0000269|Ref.3}.		brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TGATTACATGAACAAATGGGC	0.333			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			G|||	401	0.0800719	0.0552	0.0937	5008	,	,		19344	0.0972		0.0348	False		,,,				2504	0.1329				p.N991D	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.A2971G						PASS	.	G	ASP/ASN	170,4236	778.4+/-414.3	0,170,2033	51.0	58.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2971	3.1	0.0	13	dbSNP_89	56	314,8272	785.4+/-407.6	8,298,3987	yes	missense	BRCA2	NM_000059.3	23	8,468,6020	GG,GA,AA		3.6571,3.8584,3.7254	benign	991/3419	32911463	484,12508	2203	4293	6496	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TACATGAACAAAT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.2971A>G	13.37:g.32911463A>G	ENSP00000369497:p.Asn991Asp	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	57	53	0.929825	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	136	0.06227106227106227	15	0.03048780487804878	33	0.09116022099447514	60	0.1048951048951049	28	0.036939313984168866	G	0	-2.589843	0.00126	0.038584	0.036571	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00635	6.06;6.06	5.89	3.08	0.35506	.	0.490245	0.20992	N	0.082013	T	0.00012	0.0000	N	0.00841	-1.15	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28586	-1.0039	9	0.02654	T	1	.	5.1551	0.15031	0.2929:0.2595:0.4476:0.0	rs1799944;rs4986857;rs17635860;rs1799944	991	P51587	BRCA2_HUMAN	D	991	ENSP00000369497:N991D;ENSP00000439902:N991D	ENSP00000369497:N991D	N	+	1	0	BRCA2	31809463	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.058000	0.11750	0.357000	0.24183	-0.124000	0.14976	AAC	A|0.948;G|0.052	0.052	strong		0.333	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
PCDH15	65217	hgsc.bcm.edu	37	10	56423968	56423968	+	Missense_Mutation	SNP	A	A	C	rs11004439	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:56423968A>C	ENST00000320301.6	-	2	449	c.55T>G	c.(55-57)Tct>Gct	p.S19A	PCDH15_ENST00000437009.1_Missense_Mutation_p.S19A|PCDH15_ENST00000409834.1_5'UTR|PCDH15_ENST00000373965.2_Missense_Mutation_p.S19A|PCDH15_ENST00000395430.1_Missense_Mutation_p.S19A|PCDH15_ENST00000395432.2_Missense_Mutation_p.S19A|PCDH15_ENST00000414778.1_Missense_Mutation_p.S19A|PCDH15_ENST00000395438.1_Missense_Mutation_p.S19A|PCDH15_ENST00000395442.1_Missense_Mutation_p.S19A|PCDH15_ENST00000395440.1_Missense_Mutation_p.S19A|PCDH15_ENST00000373955.1_Missense_Mutation_p.S19A|PCDH15_ENST00000395433.1_Missense_Mutation_p.S19A|PCDH15_ENST00000373957.3_Missense_Mutation_p.S19A|PCDH15_ENST00000395445.1_Missense_Mutation_p.S19A|PCDH15_ENST00000395446.1_Missense_Mutation_p.S19A|PCDH15_ENST00000361849.3_Missense_Mutation_p.S19A	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	19			S -> A (in dbSNP:rs11004439). {ECO:0000269|PubMed:16369489, ECO:0000269|PubMed:22815625}.		equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TCAAAGAGAGAGCCCAGGATG	0.383										HNSCC(58;0.16)			A|||	866	0.172923	0.1248	0.268	5008	,	,		17077	0.1409		0.2485	False		,,,				2504	0.1258				p.S19A		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T55G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER	662,3744	279.6+/-274.9	38,586,1579	82.0	74.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	55,55,55,55,55,55,55,55,55,55,55,55	0.6	0.0	10	dbSNP_120	77	2148,6452	363.6+/-333.2	290,1568,2442	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	99,99,99,99,99,99,99,99,99,99,99,99	328,2154,4021	CC,CA,AA		24.9767,15.025,21.6054	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	19/1963,19/1958,19/1887,19/1953,19/1916,19/1936,19/1791,19/1540,19/1683,19/1678,19/1933,19/1956	56423968	2810,10196	2203	4300	6503	SO:0001583	missense	65217	exon2			AGAGAGAGCCCAG	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.55T>G	10.37:g.56423968A>C	ENSP00000322604:p.Ser19Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	455	0.20833333333333334	70	0.14227642276422764	105	0.2900552486187845	86	0.15034965034965034	194	0.2559366754617414	A	6.536	0.467173	0.12402	0.15025	0.249767	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955;ENST00000458638	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.63096	0.54;0.58;0.5;0.49;0.49;0.73;0.63;0.48;0.47;-0.02;0.11;0.48;0.48;0.51;0.61;0.93	5.8	0.635	0.17723	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.27229	0.033;0.033;0.033;0.033;0.112;0.033;0.033;0.059;0.105;0.048;0.172;0.0;0.023;0.0;0.033	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.26416	0.035;0.066;0.066;0.066;0.014;0.066;0.035;0.023;0.034;0.034;0.034;0.002;0.069;0.001;0.066	T	0.14671	-1.0464	8	0.49607	T	0.09	.	5.8385	0.18621	0.337:0.3921:0.0:0.271	rs11004439;rs17500214;rs52833921;rs61191357;rs11004439	19;19;19;19;19;19;19;19;19;19;19;19;19;19;19	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	A	19	ENSP00000363076:S19A;ENSP00000410304:S19A;ENSP00000378826:S19A;ENSP00000378832:S19A;ENSP00000378833:S19A;ENSP00000378829:S19A;ENSP00000378827:S19A;ENSP00000378820:S19A;ENSP00000354950:S19A;ENSP00000378821:S19A;ENSP00000363068:S19A;ENSP00000322604:S19A;ENSP00000378818:S19A;ENSP00000412628:S19A;ENSP00000363066:S19A;ENSP00000394465:S19A	ENSP00000322604:S19A	S	-	1	0	PCDH15	56093974	0.000000	0.05858	0.004000	0.12327	0.036000	0.12997	-0.338000	0.07842	0.451000	0.26802	-0.723000	0.03601	TCT	A|0.797;C|0.203	0.203	strong		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
DND1	373863	hgsc.bcm.edu	37	5	140052320	140052320	+	Missense_Mutation	SNP	T	T	C	rs201446376	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140052320T>C	ENST00000542735.1	-	3	357	c.314A>G	c.(313-315)tAc>tGc	p.Y105C		NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	105	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTCGAGCTGTAGCGGGCATA	0.687																																					p.Y105C		Atlas-SNP	.											DND1,NS,carcinoma,0,1	DND1	15	1	0			c.A314G						scavenged	.						9.0	11.0	10.0					5																	140052320		2177	4273	6450	SO:0001583	missense	373863	exon3			GAGCTGTAGCGGG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.314A>G	5.37:g.140052320T>C	ENSP00000445366:p.Tyr105Cys	Somatic	6	1	0.166667		WXS	Illumina HiSeq	Phase_I	9	3	0.333333	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.009699	0.54361	.	.	ENSG00000256453	ENST00000542735	T	0.21191	2.02	5.71	5.71	0.89125	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.64402	D	0.000005	T	0.60573	0.2279	H	0.97365	3.99	0.58432	D	0.999997	D	0.57899	0.981	D	0.63033	0.91	T	0.76116	-0.3077	10	0.87932	D	0	-15.4633	15.6328	0.76926	0.0:0.0:0.0:1.0	.	105	Q8IYX4	DND1_HUMAN	C	105	ENSP00000445366:Y105C	ENSP00000445366:Y105C	Y	-	2	0	DND1	140032504	1.000000	0.71417	1.000000	0.80357	0.203000	0.24098	7.940000	0.87693	2.180000	0.69256	0.377000	0.23210	TAC	T|0.983;C|0.016	0.016	strong		0.687	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
FAM186A	121006	hgsc.bcm.edu	37	12	50749294	50749294	+	Silent	SNP	A	A	G	rs4421818	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:50749294A>G	ENST00000327337.5	-	4	1320	c.1321T>C	c.(1321-1323)Ttg>Ctg	p.L441L	FAM186A_ENST00000543111.1_Silent_p.L441L	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	441																	CCTTTCTTCAATGATACGTTA	0.398													A|||	1739	0.347244	0.3427	0.2565	5008	,	,		20851	0.2569		0.34	False		,,,				2504	0.5184				p.L441L	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.T1321C						PASS	.	A		464,920		77,310,305	143.0	97.0	111.0		1321	-1.1	0.0	12	dbSNP_111	111	1115,2067		228,659,704	no	coding-synonymous	FAM186A	NM_001145475.1		305,969,1009	GG,GA,AA		35.0409,33.526,34.5817		441/2352	50749294	1579,2987	692	1591	2283	SO:0001819	synonymous_variant	121006	exon4			TCTTCAATGATAC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.1321T>C	12.37:g.50749294A>G		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	196	98	0.5	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			A|0.677;G|0.323	0.323	strong		0.398	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
OS9	10956	hgsc.bcm.edu	37	12	58114677	58114677	+	Silent	SNP	C	C	T	rs564358823		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:58114677C>T	ENST00000315970.7	+	15	2030	c.1989C>T	c.(1987-1989)gaC>gaT	p.D663D	OS9_ENST00000435406.2_Silent_p.D556D|OS9_ENST00000552285.1_Silent_p.D608D|OS9_ENST00000439210.2_Silent_p.D534D|RP11-571M6.7_ENST00000549477.1_RNA|OS9_ENST00000413095.2_Silent_p.D402D|OS9_ENST00000389146.6_Silent_p.D648D|OS9_ENST00000551035.1_Silent_p.D576D|OS9_ENST00000389142.5_Silent_p.D593D|RP11-571M6.8_ENST00000548410.2_RNA|OS9_ENST00000257966.8_Silent_p.D609D	NM_001017958.2|NM_006812.3	NP_001017958.1|NP_006803.1	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum lectin	663					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein retention in ER lumen (GO:0006621)|protein targeting (GO:0006605)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum lumen (GO:0005788)|Hrd1p ubiquitin ligase complex (GO:0000836)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	21	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			GGGACCTGGACGAATTTGACT	0.607																																					p.D663D		Atlas-SNP	.											.	OS9	55	.	0			c.C1989T						PASS	.						74.0	78.0	77.0					12																	58114677		2203	4300	6503	SO:0001819	synonymous_variant	10956	exon15			CCTGGACGAATTT	AB002806	CCDS31843.1, CCDS31844.1, CCDS31845.1, CCDS31846.1, CCDS58246.1, CCDS58247.1, CCDS58248.1, CCDS58249.1	12q13	2009-08-26	2009-08-26						16994	protein-coding gene	gene with protein product	"""endoplasmic reticulum lectin 2"", ""erlectin 2"""	609677				8634085, 9498564, 19346256, 18264092	Standard	NM_006812		Approved	OS-9, ERLEC2	uc001spj.3	Q13438	OTTHUMG00000170284	ENST00000315970.7:c.1989C>T	12.37:g.58114677C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_006812	A6NDD1|A6NFR7|A6NLB2|A8K5Q9|B4DE28|B4DPX1|B4E1I6|E7ENT8|E7EW91|F8VUH2|G3XA88|O00579|Q6IBL2|Q8IZ58|Q9BW99	Silent	SNP	ENST00000315970.7	37	CCDS31843.1																																																																																			.	.	none		0.607	OS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408344.1	NM_006812	
OR5I1	10798	hgsc.bcm.edu	37	11	55702961	55702961	+	Missense_Mutation	SNP	C	C	T	rs9665861	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55702961C>T	ENST00000301532.3	-	1	915	c.916G>A	c.(916-918)Gtt>Att	p.V306I		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	306			V -> I (in dbSNP:rs9665861).		signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GATCTTAGAACTTTCTCAGCT	0.333													C|||	171	0.0341454	0.0106	0.0346	5008	,	,		19174	0.001		0.0905	False		,,,				2504	0.0419				p.V306I		Atlas-SNP	.											.	OR5I1	110	.	0			c.G916A						PASS	.	C	ILE/VAL	95,4305	71.4+/-109.4	3,89,2108	65.0	62.0	63.0		916	3.1	0.0	11	dbSNP_119	63	667,7921	163.0+/-215.7	32,603,3659	yes	missense	OR5I1	NM_006637.1	29	35,692,5767	TT,TC,CC		7.7667,2.1591,5.867	benign	306/315	55702961	762,12226	2200	4294	6494	SO:0001583	missense	10798	exon1			TTAGAACTTTCTC	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.916G>A	11.37:g.55702961C>T	ENSP00000301532:p.Val306Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	84	33	0.392857	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	37	CCDS7949.1	80	0.03663003663003663	3	0.006097560975609756	10	0.027624309392265192	0	0.0	67	0.08839050131926121	C	0.026	-1.372901	0.01214	0.021591	0.077667	ENSG00000167825	ENST00000301532	T	0.36520	1.25	4.96	3.09	0.35607	.	1.017700	0.07872	N	0.968070	T	0.00666	0.0022	N	0.15975	0.35	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24657	-1.0154	10	0.12430	T	0.62	.	5.0026	0.14271	0.1658:0.6557:0.0:0.1785	rs9665861;rs52798311;rs57127522;rs9665861	306	Q13606	OR5I1_HUMAN	I	306	ENSP00000301532:V306I	ENSP00000301532:V306I	V	-	1	0	OR5I1	55459537	.	.	0.001000	0.08648	0.031000	0.12232	.	.	0.602000	0.29896	0.643000	0.83706	GTT	C|0.955;T|0.045	0.045	strong		0.333	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
ATP8A1	10396	hgsc.bcm.edu	37	4	42457332	42457332	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:42457332G>A	ENST00000381668.5	-	29	3030	c.2799C>T	c.(2797-2799)gcC>gcT	p.A933A	ATP8A1_ENST00000264449.10_Silent_p.A918A	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	933					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	TGAAGTCCAGGGCATTCTGAG	0.428																																					p.A933A		Atlas-SNP	.											ATP8A1_ENST00000264449,NS,carcinoma,-1,2	ATP8A1	206	2	0			c.C2799T						scavenged	.						172.0	145.0	154.0					4																	42457332		2203	4300	6503	SO:0001819	synonymous_variant	10396	exon29			GTCCAGGGCATTC	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"""ATPases / P-type"""	13531	protein-coding gene	gene with protein product		609542	"""ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"""			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.2799C>T	4.37:g.42457332G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	260	4	0.0153846	NM_006095	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Silent	SNP	ENST00000381668.5	37	CCDS3466.1																																																																																			.	.	none		0.428	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095	
UGT2B7	7364	hgsc.bcm.edu	37	4	69973921	69973921	+	Silent	SNP	C	C	T	rs57913007	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:69973921C>T	ENST00000305231.7	+	5	1237	c.1191C>T	c.(1189-1191)gcC>gcT	p.A397A	UGT2B7_ENST00000509763.1_Intron|UGT2B7_ENST00000508661.1_Intron	NM_001074.2	NP_001065.2	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	397					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CATTGTTTGCCGATCAACCTG	0.473													c|||	136	0.0271565	0.0484	0.0331	5008	,	,		16236	0.0		0.0388	False		,,,				2504	0.0102				p.A397A		Atlas-SNP	.											UGT2B7,colon,carcinoma,0,2	UGT2B7	79	2	0			c.C1191T						scavenged	.	C		173,4233	114.2+/-152.2	3,167,2033	176.0	165.0	168.0		1191	-5.4	0.1	4	dbSNP_129	168	293,8307	108.0+/-168.7	5,283,4012	no	coding-synonymous	UGT2B7	NM_001074.2		8,450,6045	TT,TC,CC		3.407,3.9265,3.583		397/530	69973921	466,12540	2203	4300	6503	SO:0001819	synonymous_variant	7364	exon5			GTTTGCCGATCAA	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000305231.7:c.1191C>T	4.37:g.69973921C>T		Somatic	390	2	0.00512821		WXS	Illumina HiSeq	Phase_I	400	191	0.4775	NM_001074	B2R810|Q6GTW0	Silent	SNP	ENST00000305231.7	37	CCDS3526.1																																																																																			C|0.963;T|0.037	0.037	strong		0.473	UGT2B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251560.1	NM_001074	
SLC36A2	153201	hgsc.bcm.edu	37	5	150696498	150696498	+	Silent	SNP	G	G	A	rs428064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150696498G>A	ENST00000335244.4	-	10	1461	c.1332C>T	c.(1330-1332)gaC>gaT	p.D444D	SLC36A2_ENST00000450886.1_Silent_p.D168D	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	444					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	TGATCAGGGCGTCCTTGAAGA	0.612													G|||	1586	0.316693	0.0136	0.5173	5008	,	,		15015	0.4335		0.3678	False		,,,				2504	0.411				p.D444D		Atlas-SNP	.											.	SLC36A2	71	.	0			c.C1332T						PASS	.	G		360,4046	184.7+/-212.0	19,322,1862	79.0	70.0	73.0		1332	1.1	0.9	5	dbSNP_80	73	3155,5445	478.7+/-369.9	605,1945,1750	no	coding-synonymous	SLC36A2	NM_181776.2		624,2267,3612	AA,AG,GG		36.686,8.1707,27.026		444/484	150696498	3515,9491	2203	4300	6503	SO:0001819	synonymous_variant	153201	exon10			CAGGGCGTCCTTG	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"""Solute carriers"""	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.1332C>T	5.37:g.150696498G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Silent	SNP	ENST00000335244.4	37	CCDS4315.1																																																																																			G|0.708;A|0.292	0.292	strong		0.612	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1		
MICA	100507436	hgsc.bcm.edu	37	6	31382910	31382910	+	3'UTR	SNP	C	C	T	rs41545213	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31382910C>T	ENST00000449934.2	+	0	1204				HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CCACtgagggcacctagactc	0.547													c|||	78	0.0155751	0.0182	0.0533	5008	,	,		14131	0.002		0.0149	False		,,,				2504	0.0				p.G382G		Atlas-SNP	.											.	MICA	21	.	0			c.C1146T						PASS	.	C		13,1371		1,11,680	114.0	108.0	110.0			-2.6	0.0	6	dbSNP_127	110	37,3145		4,29,1558	no	utr-3	MICA	NM_001177519.1		5,40,2238	TT,TC,CC		1.1628,0.9393,1.0951			31382910	50,4516	692	1591	2283	SO:0001624	3_prime_UTR_variant	100507436	exon7			TGAGGGCACCTAG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.*151C>T	6.37:g.31382910C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_000247		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.984;T|0.016	0.016	strong		0.547	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
RAC3	5881	hgsc.bcm.edu	37	17	79990881	79990881	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79990881C>T	ENST00000306897.4	+	4	422	c.284C>T	c.(283-285)gCc>gTc	p.A95V		NM_005052.2	NP_005043.1	P60763	RAC3_HUMAN	ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3)	95					actin cytoskeleton organization (GO:0030036)|cell projection assembly (GO:0030031)|GTP catabolic process (GO:0006184)|intracellular signal transduction (GO:0035556)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.A95V(1)		NS(1)|kidney(1)|skin(1)	3	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			AATGTTCGTGCCAAGGTAGGG	0.602																																					p.A95V		Atlas-SNP	.											RAC3,NS,carcinoma,0,1	RAC3	8	1	1	Substitution - Missense(1)	kidney(1)	c.C284T						scavenged	.						64.0	71.0	69.0					17																	79990881		2203	4300	6503	SO:0001583	missense	5881	exon4			TTCGTGCCAAGGT	AF008591	CCDS11798.1	17q25.3	2014-01-30				ENSG00000169750		"""Endogenous ligands"""	9803	protein-coding gene	gene with protein product		602050					Standard	NM_005052		Approved		uc002kdf.3	P60763		ENST00000306897.4:c.284C>T	17.37:g.79990881C>T	ENSP00000304283:p.Ala95Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	163	3	0.0184049	NM_005052	O14658|Q5U0M8	Missense_Mutation	SNP	ENST00000306897.4	37	CCDS11798.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.205156	0.79127	.	.	ENSG00000169750	ENST00000306897	T	0.69806	-0.43	3.72	3.72	0.42706	Small GTP-binding protein domain (1);	0.129140	0.52532	D	0.000079	T	0.56337	0.1978	N	0.19112	0.55	0.80722	D	1	B	0.25105	0.118	B	0.36922	0.236	T	0.52109	-0.8619	9	.	.	.	.	15.6871	0.77421	0.0:1.0:0.0:0.0	.	95	P60763	RAC3_HUMAN	V	95	ENSP00000304283:A95V	.	A	+	2	0	RAC3	77584170	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	7.442000	0.80503	1.909000	0.55274	0.561000	0.74099	GCC	.	.	none		0.602	RAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442064.1		
MT-ND2	4536	hgsc.bcm.edu	37	M	5231	5231	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:5231G>A	ENST00000361453.3	+	1	762	c.762G>A	c.(760-762)ctG>ctA	p.L254L	MT-TC_ENST00000387405.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-TL1_ENST00000386347.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-RNR2_ENST00000387347.2_RNA|MT-TN_ENST00000387400.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TS1_ENST00000387416.2_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2	254					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|lung(1)	3						CTAGGAGGCCTGCCCCCGCTA	0.498																																					p.L254L		Atlas-SNP	.											.	.	.	.	0			c.G762A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			AGGCCTGCCCCCG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891		ENST00000361453.3:c.762G>A	M.37:g.5231G>A		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	ENST00000361453	Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	Silent	SNP	ENST00000361453.3	37																																																																																				.	.	none		0.498	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024027	
SPIRE2	84501	hgsc.bcm.edu	37	16	89920957	89920957	+	Silent	SNP	A	A	G	rs12598737	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89920957A>G	ENST00000378247.3	+	5	832	c.789A>G	c.(787-789)caA>caG	p.Q263Q	SPIRE2_ENST00000393062.2_Silent_p.Q263Q	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	263					actin cytoskeleton organization (GO:0030036)|cleavage furrow formation (GO:0036089)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|intracellular transport (GO:0046907)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		AGAAGGTGCAAGAGCAGGAGT	0.637													G|||	378	0.0754792	0.0061	0.0259	5008	,	,		18474	0.2708		0.0606	False		,,,				2504	0.0184				p.Q263Q		Atlas-SNP	.											.	SPIRE2	63	.	0			c.A789G						PASS	.	G		86,4308	812.2+/-416.1	1,84,2112	77.0	75.0	76.0		789	2.4	1.0	16	dbSNP_120	76	699,7893	785.0+/-407.6	28,643,3625	no	coding-synonymous	SPIRE2	NM_032451.1		29,727,5737	GG,GA,AA		8.1355,1.9572,6.045		263/715	89920957	785,12201	2197	4296	6493	SO:0001819	synonymous_variant	84501	exon5			GGTGCAAGAGCAG	AL834408	CCDS32516.1	16q24	2013-08-27	2013-08-27			ENSG00000204991			30623	protein-coding gene	gene with protein product		609217	"""spire homolog 2 (Drosophila)"", ""spire family actin nucleation factor 2"""			11347906	Standard	NM_032451		Approved	spir-2, KIAA1832	uc002foz.1	Q8WWL2		ENST00000378247.3:c.789A>G	16.37:g.89920957A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	119	66	0.554622	NM_032451	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Silent	SNP	ENST00000378247.3	37	CCDS32516.1																																																																																			A|0.933;G|0.067	0.067	strong		0.637	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462	
KCTD9	54793	hgsc.bcm.edu	37	8	25287397	25287397	+	Silent	SNP	T	T	C	rs1812594	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:25287397T>C	ENST00000221200.4	-	12	1366	c.1146A>G	c.(1144-1146)ctA>ctG	p.L382L		NM_017634.3	NP_060104.2	Q7L273	KCTD9_HUMAN	potassium channel tetramerization domain containing 9	382					protein homooligomerization (GO:0051260)					breast(1)|endometrium(2)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	12		all_cancers(63;0.0164)|Ovarian(32;0.000878)|all_epithelial(46;0.00542)|Breast(100;0.0164)|Hepatocellular(4;0.114)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Epithelial(17;2.39e-12)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0438)		GTGACATGTGTAGTGGTGTCA	0.428													T|||	809	0.161542	0.062	0.1988	5008	,	,		17653	0.2421		0.2167	False		,,,				2504	0.1299				p.L382L		Atlas-SNP	.											.	KCTD9	33	.	0			c.A1146G						PASS	.	T		396,4010	196.4+/-220.7	24,348,1831	136.0	122.0	127.0		1146	-4.8	1.0	8	dbSNP_92	127	1794,6806	322.6+/-315.6	192,1410,2698	no	coding-synonymous	KCTD9	NM_017634.3		216,1758,4529	CC,CT,TT		20.8605,8.9877,16.8384		382/390	25287397	2190,10816	2203	4300	6503	SO:0001819	synonymous_variant	54793	exon12			CATGTGTAGTGGT	BC021216	CCDS6048.1	8p21.1	2013-06-20	2013-06-20		ENSG00000104756	ENSG00000104756		"""BTB/POZ domain containing"""	22401	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 9"""			11483580	Standard	NM_017634		Approved	FLJ20038, BTBD27	uc003xeo.3	Q7L273	OTTHUMG00000099428	ENST00000221200.4:c.1146A>G	8.37:g.25287397T>C		Somatic	407	0	0		WXS	Illumina HiSeq	Phase_I	463	203	0.438445	NM_017634	Q6NUM8|Q9NXV4	Silent	SNP	ENST00000221200.4	37	CCDS6048.1																																																																																			T|0.828;C|0.172	0.172	strong		0.428	KCTD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216890.1	NM_017634	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18777196	18777196	+	Missense_Mutation	SNP	A	A	C	rs41268983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:18777196A>C	ENST00000380548.4	+	19	3308	c.2969A>C	c.(2968-2970)gAg>gCg	p.E990A		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	990						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		GGCCCGAAGGAGGCCCTGCAG	0.662													A|||	457	0.091254	0.0113	0.0749	5008	,	,		15776	0.122		0.1431	False		,,,				2504	0.1258				p.E990A		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.A2969C						PASS	.	A	ALA/GLU	143,3647		5,133,1757	24.0	28.0	27.0		2969	5.8	1.0	9	dbSNP_127	27	1265,6929		95,1075,2927	yes	missense	ADAMTSL1	NM_001040272.5	107	100,1208,4684	CC,CA,AA		15.4381,3.7731,11.749	benign	990/1763	18777196	1408,10576	1895	4097	5992	SO:0001583	missense	92949	exon19			CGAAGGAGGCCCT	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.2969A>C	9.37:g.18777196A>C	ENSP00000369921:p.Glu990Ala	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	208	0.09523809523809523	7	0.014227642276422764	30	0.08287292817679558	60	0.1048951048951049	111	0.14643799472295516	A	12.05	1.821260	0.32237	0.037731	0.154381	ENSG00000178031	ENST00000380548	T	0.63417	-0.04	5.75	5.75	0.90469	.	2.098050	0.05591	N	0.574590	T	0.00440	0.0014	N	0.14661	0.345	0.09310	P	1.0	P	0.52316	0.952	P	0.46885	0.53	T	0.11817	-1.0572	9	0.18276	T	0.48	.	16.0488	0.80740	1.0:0.0:0.0:0.0	rs41268983	990	Q8N6G6	ATL1_HUMAN	A	990	ENSP00000369921:E990A	ENSP00000369921:E990A	E	+	2	0	ADAMTSL1	18767196	1.000000	0.71417	0.999000	0.59377	0.909000	0.53808	4.474000	0.60203	2.199000	0.70637	0.374000	0.22700	GAG	A|0.895;C|0.105	0.105	strong		0.662	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
WDTC1	23038	hgsc.bcm.edu	37	1	27622847	27622847	+	Missense_Mutation	SNP	C	C	T	rs140726657		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:27622847C>T	ENST00000319394.3	+	10	1439	c.904C>T	c.(904-906)Cgg>Tgg	p.R302W	WDTC1_ENST00000361771.3_Missense_Mutation_p.R302W	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	302					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		TTACAAGCAGCGGCCGTACAC	0.507																																					p.R302W		Atlas-SNP	.											WDTC1,NS,carcinoma,-1,1	WDTC1	69	1	0			c.C904T						scavenged	.						221.0	214.0	217.0					1																	27622847		2203	4300	6503	SO:0001583	missense	23038	exon10			AAGCAGCGGCCGT	AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29175	protein-coding gene	gene with protein product	"""adipose homolog (Drosophila)"", ""DDB1 and CUL4 associated factor 9"""					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.904C>T	1.37:g.27622847C>T	ENSP00000317971:p.Arg302Trp	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	240	3	0.0125	NM_015023	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Missense_Mutation	SNP	ENST00000319394.3	37		.	.	.	.	.	.	.	.	.	.	C	26.6	4.750014	0.89753	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	T;T	0.81415	-1.49;-1.49	5.91	4.98	0.66077	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.210707	0.47852	D	0.000213	T	0.81763	0.4891	L	0.46157	1.445	0.80722	D	1	D;D	0.63880	0.993;0.993	P;P	0.52957	0.522;0.714	T	0.83318	-0.0019	10	0.66056	D	0.02	.	13.1451	0.59456	0.2909:0.7091:0.0:0.0	.	302;302	Q8N5D0;Q8N5D0-4	WDTC1_HUMAN;.	W	302	ENSP00000317971:R302W;ENSP00000355317:R302W	ENSP00000317971:R302W	R	+	1	2	WDTC1	27495434	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.392000	0.44433	1.464000	0.47987	0.655000	0.94253	CGG	C|0.999;A|0.001	.	alt		0.507	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023	
ZNF100	163227	hgsc.bcm.edu	37	19	21948570	21948570	+	Missense_Mutation	SNP	T	T	C	rs12974842	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:21948570T>C	ENST00000358296.6	-	2	220	c.22A>G	c.(22-24)Atg>Gtg	p.M8V	ZNF100_ENST00000596452.1_5'UTR	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	8			M -> V (in dbSNP:rs12974842).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						AGAGGACACATTCCATACCTC	0.468													T|||	362	0.0722843	0.0045	0.0432	5008	,	,		16637	0.0546		0.0586	False		,,,				2504	0.2168				p.M8V		Atlas-SNP	.											.	ZNF100	62	.	0			c.A22G						PASS	.	T	VAL/MET	73,4297	63.5+/-100.7	2,69,2114	78.0	84.0	82.0		22	-0.9	0.0	19	dbSNP_121	82	649,7949	164.3+/-216.7	26,597,3676	yes	missense	ZNF100	NM_173531.3	21	28,666,5790	CC,CT,TT		7.5483,1.6705,5.5676	benign	8/543	21948570	722,12246	2185	4299	6484	SO:0001583	missense	163227	exon2			GACACATTCCATA	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"""Zinc fingers, C2H2-type"", ""-"""	12880	protein-coding gene	gene with protein product		603982	"""zinc finger protein 100 (Y1)"""			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.22A>G	19.37:g.21948570T>C	ENSP00000351042:p.Met8Val	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_173531	Q7M4M0	Missense_Mutation	SNP	ENST00000358296.6	37	CCDS42538.1	89	0.04075091575091575	2	0.0040650406504065045	21	0.058011049723756904	23	0.04020979020979021	43	0.05672823218997362	T	0.001	-3.439773	0.00012	0.016705	0.075483	ENSG00000197020	ENST00000358296	T	0.04275	3.66	0.461	-0.922	0.10468	.	.	.	.	.	T	0.00144	0.0004	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46707	-0.9172	8	0.11182	T	0.66	.	.	.	.	rs12974842;rs17686398;rs12974842	8	Q8IYN0	ZN100_HUMAN	V	8	ENSP00000351042:M8V	ENSP00000351042:M8V	M	-	1	0	ZNF100	21740410	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	-1.890000	0.01613	-0.591000	0.05859	-0.782000	0.03352	ATG	T|0.950;C|0.050	0.050	strong		0.468	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
KLHL36	79786	hgsc.bcm.edu	37	16	84695280	84695280	+	Silent	SNP	A	A	G	rs17755815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84695280A>G	ENST00000564996.1	+	5	1533	c.1392A>G	c.(1390-1392)ctA>ctG	p.L464L	KLHL36_ENST00000258157.5_Silent_p.L401L	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	464					protein ubiquitination (GO:0016567)					endometrium(3)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						AGAACCTGCTATGCTACGACC	0.627													A|||	887	0.177117	0.3714	0.1081	5008	,	,		15033	0.0347		0.2068	False		,,,				2504	0.0798				p.L464L		Atlas-SNP	.											KLHL36,NS,carcinoma,0,1	KLHL36	51	1	0			c.A1392G						scavenged	.	A		1570,2828	491.5+/-362.1	277,1016,906	83.0	78.0	80.0		1392	1.4	1.0	16	dbSNP_123	80	1956,6644	344.6+/-325.4	231,1494,2575	no	coding-synonymous	KLHL36	NM_024731.2		508,2510,3481	GG,GA,AA		22.7442,35.698,27.1273		464/617	84695280	3526,9472	2199	4300	6499	SO:0001819	synonymous_variant	79786	exon5			CCTGCTATGCTAC	AK022605	CCDS10948.1	16q24.1	2013-02-22	2013-02-22	2008-07-07	ENSG00000135686	ENSG00000135686		"""Kelch-like"", ""BTB/POZ domain containing"""	17844	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 44"", ""kelch-like 36 (Drosophila)"""	C16orf44			Standard	NM_024731		Approved	FLJ12543	uc002fig.3	Q8N4N3	OTTHUMG00000137642	ENST00000564996.1:c.1392A>G	16.37:g.84695280A>G		Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_024731	Q8N5G6|Q9H9U6	Silent	SNP	ENST00000564996.1	37	CCDS10948.1																																																																																			A|0.757;G|0.243	0.243	strong		0.627	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2		
FAM65C	140876	hgsc.bcm.edu	37	20	49214188	49214188	+	Silent	SNP	C	C	T	rs35976890	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:49214188C>T	ENST00000327979.2	-	14	2118	c.1707G>A	c.(1705-1707)gaG>gaA	p.E569E	FAM65C_ENST00000535356.1_Silent_p.E573E|FAM65C_ENST00000045083.2_Silent_p.E569E			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	569										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGGCGAAGCTCTCCAGGATGC	0.652													C|||	122	0.024361	0.0023	0.036	5008	,	,		15258	0.001		0.0765	False		,,,				2504	0.0164				p.E569E		Atlas-SNP	.											.	FAM65C	87	.	0			c.G1707A						PASS	.	C		76,4328	65.8+/-103.3	1,74,2127	73.0	56.0	62.0		1707	-0.2	1.0	20	dbSNP_126	62	648,7952	156.4+/-210.3	20,608,3672	no	coding-synonymous	FAM65C	NM_080829.2		21,682,5799	TT,TC,CC		7.5349,1.7257,5.5675		569/947	49214188	724,12280	2202	4300	6502	SO:0001819	synonymous_variant	140876	exon14			GAAGCTCTCCAGG	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 175"", ""chromosome 20 open reading frame 176"""	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.1707G>A	20.37:g.49214188C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_080829	Q5QPB6|Q9NQQ2	Silent	SNP	ENST00000327979.2	37	CCDS13431.2																																																																																			C|0.957;T|0.043	0.043	strong		0.652	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1		
KIF20B	9585	hgsc.bcm.edu	37	10	91497631	91497631	+	Missense_Mutation	SNP	T	T	A	rs1062465	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:91497631T>A	ENST00000371728.3	+	20	3098	c.3033T>A	c.(3031-3033)gaT>gaA	p.D1011E	KIF20B_ENST00000416354.1_Missense_Mutation_p.D1041E|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.D971E|KIF20B_ENST00000394289.2_Missense_Mutation_p.D1011E	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1011			D -> E (in dbSNP:rs1062465).		ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						ATCTCAGGGATCTGTCAAATG	0.328													T|||	1772	0.353834	0.4697	0.2147	5008	,	,		19562	0.3085		0.2326	False		,,,				2504	0.4673				p.D971E		Atlas-SNP	.											.	KIF20B	191	.	0			c.T2913A						PASS	.	T	GLU/ASP	2027,2379	541.1+/-375.7	469,1089,645	62.0	66.0	65.0		2913	2.2	0.0	10	dbSNP_86	65	2005,6593	341.8+/-324.2	224,1557,2518	yes	missense	KIF20B	NM_016195.2	45	693,2646,3163	AA,AT,TT		23.3194,46.0054,31.0058	benign	971/1781	91497631	4032,8972	2203	4299	6502	SO:0001583	missense	9585	exon20			CAGGGATCTGTCA	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"""cancer/testis antigen 90"""	605498	"""M-phase phosphoprotein 1"""	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.3033T>A	10.37:g.91497631T>A	ENSP00000360793:p.Asp1011Glu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	54	6	0.111111	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		638	0.29212454212454214	210	0.4268292682926829	82	0.2265193370165746	170	0.2972027972027972	176	0.23218997361477572	T	8.780	0.928087	0.18131	0.460054	0.233194	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.69926	-0.34;-0.39;-0.44;-0.37	5.69	2.17	0.27698	.	0.487974	0.18928	N	0.127288	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	P;P	0.41848	0.651;0.763	B;B	0.34242	0.086;0.178	T	0.42050	-0.9474	9	0.72032	D	0.01	-3.3623	5.5908	0.17299	0.1231:0.2418:0.0:0.6351	rs1062465;rs3203530;rs60388762;rs1062465	1011;971	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	E	971;1041;1011;1011	ENSP00000260753:D971E;ENSP00000411545:D1041E;ENSP00000377830:D1011E;ENSP00000360793:D1011E	ENSP00000260753:D971E	D	+	3	2	KIF20B	91487611	0.000000	0.05858	0.031000	0.17742	0.224000	0.24922	0.037000	0.13840	0.968000	0.38212	0.482000	0.46254	GAT	T|0.696;A|0.304	0.304	strong		0.328	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
OR8H2	390151	hgsc.bcm.edu	37	11	55872990	55872990	+	Missense_Mutation	SNP	G	G	C	rs61734403	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55872990G>C	ENST00000313503.1	+	1	472	c.472G>C	c.(472-474)Gtc>Ctc	p.V158L		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	158						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					AGACTCCTTTGTCAACGTGGT	0.443										HNSCC(53;0.14)			g|||	195	0.0389377	0.0121	0.0447	5008	,	,		20577	0.001		0.0944	False		,,,				2504	0.0532				p.V158L		Atlas-SNP	.											.	OR8H2	117	.	0			c.G472C						PASS	.	G	LEU/VAL	98,4304	78.3+/-116.7	0,98,2103	228.0	203.0	212.0		472	-3.6	0.0	11	dbSNP_129	212	693,7899	171.2+/-222.1	34,625,3637	yes	missense	OR8H2	NM_001005200.1	32	34,723,5740	CC,CG,GG		8.0656,2.2263,6.0874	benign	158/313	55872990	791,12203	2201	4296	6497	SO:0001583	missense	390151	exon1			TCCTTTGTCAACG	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.472G>C	11.37:g.55872990G>C	ENSP00000323982:p.Val158Leu	Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	288	141	0.489583	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	84	0.038461538461538464	4	0.008130081300813009	14	0.03867403314917127	0	0.0	66	0.0870712401055409	g	12.18	1.860895	0.32884	0.022263	0.080656	ENSG00000181767	ENST00000313503	T	0.35421	1.31	3.35	-3.56	0.04626	GPCR, rhodopsin-like superfamily (1);	1.117260	0.06780	N	0.785094	T	0.00936	0.0031	N	0.21448	0.665	0.09310	N	1	P	0.35307	0.494	B	0.41666	0.363	T	0.20505	-1.0273	10	0.54805	T	0.06	.	4.9242	0.13885	0.3512:0.0:0.5149:0.1339	rs61734403	158	Q8N162	OR8H2_HUMAN	L	158	ENSP00000323982:V158L	ENSP00000323982:V158L	V	+	1	0	OR8H2	55629566	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.852000	0.04308	-0.947000	0.03673	-0.423000	0.05987	GTC	G|0.948;C|0.052	0.052	strong		0.443	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
PECR	55825	hgsc.bcm.edu	37	2	216923679	216923679	+	Missense_Mutation	SNP	C	C	T	rs1429148	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:216923679C>T	ENST00000265322.7	-	4	519	c.445G>A	c.(445-447)Gag>Aag	p.E149K	PECR_ENST00000497889.1_5'UTR	NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	149			E -> K (in dbSNP:rs1429148).		fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	CCTCCATGCTCTTTCATCCAG	0.393													C|||	877	0.17512	0.2451	0.1167	5008	,	,		19157	0.1935		0.0497	False		,,,				2504	0.2321				p.E149K		Atlas-SNP	.											.	PECR	22	.	0			c.G445A						PASS	.	C	LYS/GLU	941,3465	358.6+/-314.5	97,747,1359	111.0	107.0	108.0		445	-1.0	0.2	2	dbSNP_88	108	508,8092	145.1+/-200.9	12,484,3804	yes	missense	PECR	NM_018441.5	56	109,1231,5163	TT,TC,CC		5.907,21.3572,11.141	benign	149/304	216923679	1449,11557	2203	4300	6503	SO:0001583	missense	55825	exon4			CATGCTCTTTCAT	AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18281	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 29C, member 1"""	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.445G>A	2.37:g.216923679C>T	ENSP00000265322:p.Glu149Lys	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	185	87	0.47027	NM_018441	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	Missense_Mutation	SNP	ENST00000265322.7	37	CCDS33375.1	334	0.15293040293040294	118	0.23983739837398374	37	0.10220994475138122	141	0.2465034965034965	38	0.05013192612137203	C	8.624	0.892018	0.17613	0.213572	0.05907	ENSG00000115425	ENST00000265322	T	0.42513	0.97	5.77	-1.01	0.10169	Apoptosis regulator, Bcl-2, BH (1);NAD(P)-binding domain (1);	0.630718	0.17997	N	0.155025	T	0.00012	0.0000	N	0.02775	-0.495	0.28925	P	0.891905	B;B	0.15930	0.005;0.015	B;B	0.25614	0.027;0.062	T	0.34650	-0.9820	9	0.10377	T	0.69	.	6.3072	0.21145	0.0:0.4753:0.1195:0.4052	rs1429148;rs3732029;rs59553324;rs1429148	149;3	Q9BY49;Q9BY49-2	PECR_HUMAN;.	K	149	ENSP00000265322:E149K	ENSP00000265322:E149K	E	-	1	0	PECR	216631924	0.024000	0.19004	0.180000	0.23079	0.930000	0.56654	-0.209000	0.09358	-0.531000	0.06340	-1.106000	0.02097	GAG	C|0.862;T|0.138	0.138	strong		0.393	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441	
SLC41A2	84102	hgsc.bcm.edu	37	12	105282893	105282893	+	Silent	SNP	T	T	C	rs17036463	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:105282893T>C	ENST00000258538.3	-	4	925	c.798A>G	c.(796-798)ccA>ccG	p.P266P		NM_032148.3	NP_115524.3	Q96JW4	S41A2_HUMAN	solute carrier family 41 (magnesium transporter), member 2	266					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	22						ATTTTCCTTCTGGAATCCAGC	0.383													T|||	326	0.0650958	0.0393	0.0663	5008	,	,		15534	0.1091		0.0368	False		,,,				2504	0.0828				p.P266P	Esophageal Squamous(195;176 2919 4272 35572)	Atlas-SNP	.											.	SLC41A2	66	.	0			c.A798G						PASS	.	T		127,4279	93.0+/-131.7	2,123,2078	90.0	87.0	88.0		798	-3.9	0.9	12	dbSNP_123	88	260,8340	101.2+/-162.5	3,254,4043	no	coding-synonymous	SLC41A2	NM_032148.3		5,377,6121	CC,CT,TT		3.0233,2.8824,2.9755		266/574	105282893	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	84102	exon4			TCCTTCTGGAATC	BC036734	CCDS9100.2	12q24.11	2013-07-17	2013-07-17		ENSG00000136052	ENSG00000136052		"""Solute carriers"""	31045	protein-coding gene	gene with protein product		610802	"""solute carrier family 41, member 2"""				Standard	NM_032148		Approved	DKFZP434K0427	uc001tla.3	Q96JW4	OTTHUMG00000156965	ENST00000258538.3:c.798A>G	12.37:g.105282893T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	184	77	0.418478	NM_032148	Q3KP68|Q9H0E5	Silent	SNP	ENST00000258538.3	37	CCDS9100.2	147	0.0673076923076923	25	0.0508130081300813	19	0.052486187845303865	71	0.12412587412587413	32	0.04221635883905013	T	8.729	0.916095	0.17907	0.028824	0.030233	ENSG00000136052	ENST00000437220	.	.	.	5.55	-3.88	0.04205	.	.	.	.	.	T	0.00271	0.0008	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.18493	-1.0335	3	.	.	.	-12.4526	2.9982	0.06005	0.0896:0.1727:0.276:0.4617	rs17036463;rs17036463	.	.	.	R	122	.	.	Q	-	2	0	SLC41A2	103807023	0.996000	0.38824	0.863000	0.33907	0.937000	0.57800	0.229000	0.17833	-1.478000	0.01869	-1.431000	0.01090	CAG	T|0.956;C|0.044	0.044	strong		0.383	SLC41A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346850.3	NM_032148	
LRRC74A	145497	hgsc.bcm.edu	37	14	77332408	77332408	+	Missense_Mutation	SNP	T	T	C	rs7160583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77332408T>C	ENST00000393774.3	+	12	1473	c.1349T>C	c.(1348-1350)gTg>gCg	p.V450A		NM_194287.2	NP_919263.2														breast(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(1)	18			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		TTCCAGAAAGTGATGATAGAG	0.498													T|||	1145	0.228634	0.2216	0.3343	5008	,	,		22400	0.0853		0.329	False		,,,				2504	0.2076				p.V450A	Ovarian(165;1056 1958 32571 36789 48728)	Atlas-SNP	.											C14orf166B,trunk,malignant_melanoma,+1,1	C14orf166B	52	1	0			c.T1349C						scavenged	.	T	ALA/VAL	905,3255		96,713,1271	154.0	161.0	159.0		1349	0.5	0.0	14	dbSNP_116	159	2856,5562		481,1894,1834	yes	missense	C14orf166B	NM_194287.2	64	577,2607,3105	CC,CT,TT		33.9273,21.7548,29.9014	benign	450/489	77332408	3761,8817	2080	4209	6289	SO:0001583	missense	145497	exon12			AGAAAGTGATGAT																												ENST00000393774.3:c.1349T>C	14.37:g.77332408T>C	ENSP00000377369:p.Val450Ala	Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	145	58	0.4	NM_194287		Missense_Mutation	SNP	ENST00000393774.3	37	CCDS9853.2	534	0.2445054945054945	106	0.21544715447154472	123	0.3397790055248619	48	0.08391608391608392	257	0.3390501319261214	T	0.062	-1.221788	0.01530	0.217548	0.339273	ENSG00000100565	ENST00000393774	T	0.06849	3.25	5.5	0.535	0.17133	.	0.620361	0.14695	N	0.303900	T	0.00012	0.0000	N	0.00563	-1.375	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46317	-0.9200	9	0.02654	T	1	.	7.8273	0.29322	0.0:0.5517:0.0:0.4483	rs7160583;rs60227462;rs7160583	450	Q0VAA2	CN16B_HUMAN	A	450	ENSP00000377369:V450A	ENSP00000377369:V450A	V	+	2	0	C14orf166B	76402161	0.136000	0.22515	0.003000	0.11579	0.035000	0.12851	0.261000	0.18442	-0.099000	0.12263	-0.464000	0.05259	GTG	T|0.768;C|0.232	0.232	strong		0.498	C14orf166B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316592.1		
TPTE	7179	hgsc.bcm.edu	37	21	10959771	10959771	+	Missense_Mutation	SNP	A	A	T	rs111657679	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:10959771A>T	ENST00000361285.4	-	8	532	c.203T>A	c.(202-204)gTt>gAt	p.V68D	TPTE_ENST00000342420.5_Intron|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Missense_Mutation_p.V50D	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	68					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGCATCTTCAACTTCAAACTT	0.333																																					p.V68D		Atlas-SNP	.											.	TPTE	513	.	0			c.T203A						PASS	.	A	ASP/VAL,,ASP/VAL	54,4352		0,54,2149	95.0	92.0	93.0		149,,203	-3.0	0.0	21	dbSNP_132	93	562,8038		1,560,3739	no	missense,intron,missense	TPTE	NM_199259.2,NM_199260.2,NM_199261.2	152,,152	1,614,5888	TT,TA,AA		6.5349,1.2256,4.7363	benign,,benign	50/534,,68/552	10959771	616,12390	2203	4300	6503	SO:0001583	missense	7179	exon8			TCTTCAACTTCAA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.203T>A	21.37:g.10959771A>T	ENSP00000355208:p.Val68Asp	Somatic	550	0	0		WXS	Illumina HiSeq	Phase_I	555	113	0.203604	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	64	0.029304029304029304	3	0.006097560975609756	17	0.04696132596685083	0	0.0	44	0.05804749340369393	A	4.598	0.111032	0.08831	0.012256	0.065349	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000328758	D;D	0.94931	-3.39;-3.56	1.49	-2.99	0.05497	.	0.427833	0.20668	N	0.087887	T	0.31765	0.0807	N	0.11064	0.09	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.61267	-0.7097	10	0.51188	T	0.08	-0.0112	0.0434	0.00009	0.2665:0.1846:0.2078:0.341	.	50;68	P56180-2;P56180	.;TPTE_HUMAN	D	50;68;50	ENSP00000298232:V50D;ENSP00000355208:V68D	ENSP00000298232:V50D	V	-	2	0	TPTE	9981642	0.002000	0.14202	0.000000	0.03702	0.090000	0.18270	0.045000	0.14013	-1.680000	0.01450	0.333000	0.21579	GTT	A|0.964;T|0.036	0.036	strong		0.333	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
ARHGAP35	2909	hgsc.bcm.edu	37	19	47422388	47422388	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:47422388C>T	ENST00000404338.3	+	1	456	c.456C>T	c.(454-456)gaC>gaT	p.D152D		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	152					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										AAATGCCAGACGGAAAGCTGC	0.473																																					p.D152D		Atlas-SNP	.											GRLF1_ENST00000317082,NS,carcinoma,+1,2	.	.	2	0			c.C456T						PASS	.						81.0	76.0	78.0					19																	47422388		1933	4138	6071	SO:0001819	synonymous_variant	2909	exon1			GCCAGACGGAAAG	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.456C>T	19.37:g.47422388C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_004491	A7E2A4|Q14452|Q9C0E1	Silent	SNP	ENST00000404338.3	37	CCDS46127.1																																																																																			.	.	none		0.473	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491	
TTN	7273	hgsc.bcm.edu	37	2	179400895	179400895	+	Missense_Mutation	SNP	C	C	T	rs2278196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179400895C>T	ENST00000591111.1	-	307	95880	c.95656G>A	c.(95656-95658)Gtc>Atc	p.V31886I	TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V24462I|TTN_ENST00000342992.6_Missense_Mutation_p.V30959I|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V33527I|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V24587I|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V24654I|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588804.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31886	Ig-like 141.		V -> I. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACCATTTGACGATAGGTTTT	0.403													C|||	328	0.0654952	0.0847	0.036	5008	,	,		21422	0.1488		0.0298	False		,,,				2504	0.0112				p.V33527I		Atlas-SNP	.											.	TTN	18412	.	0			c.G100579A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	247,3549		8,231,1659	122.0	107.0	112.0		73384,92875,73759,73960	5.8	1.0	2	dbSNP_100	112	143,8087		3,137,3975	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	11,368,5634	TT,TC,CC		1.7375,6.5068,3.243	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	24462/26927,30959/33424,24587/27052,24654/27119	179400895	390,11636	1898	4115	6013	SO:0001583	missense	7273	exon357			ATTTGACGATAGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.95656G>A	2.37:g.179400895C>T	ENSP00000465570:p.Val31886Ile	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	264	119	0.450758	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		155	0.07097069597069597	37	0.07520325203252033	13	0.03591160220994475	84	0.14685314685314685	21	0.027704485488126648	C	14.71	2.617959	0.46736	0.065068	0.017375	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	5.76	5.76	0.90799	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00384	0.0012	N	0.11789	0.175	0.22771	P	0.99875326	P;P;P;P	0.42248	0.774;0.774;0.774;0.774	B;B;B;B	0.27380	0.079;0.079;0.079;0.079	T	0.34700	-0.9818	8	0.87932	D	0	.	19.9595	0.97236	0.0:1.0:0.0:0.0	rs2278196;rs52810709;rs2278196	24462;24587;24654;31886	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	30959;24462;24654;24587;24459	ENSP00000343764:V30959I;ENSP00000434586:V24462I;ENSP00000340554:V24654I;ENSP00000352154:V24587I	ENSP00000340554:V24654I	V	-	1	0	TTN	179109141	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	4.881000	0.63114	2.706000	0.92434	0.563000	0.77884	GTC	C|0.930;T|0.070	0.070	strong		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PSMG1	8624	hgsc.bcm.edu	37	21	40552307	40552307	+	Silent	SNP	A	A	G	rs3171465	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:40552307A>G	ENST00000331573.3	-	3	762	c.297T>C	c.(295-297)gcT>gcC	p.A99A	PSMG1_ENST00000380900.2_Silent_p.A99A	NM_001261824.1|NM_003720.3	NP_001248753.1|NP_003711.1	O95456	PSMG1_HUMAN	proteasome (prosome, macropain) assembly chaperone 1	99					cerebellar granule cell precursor proliferation (GO:0021930)|proteasome assembly (GO:0043248)|proteasome core complex assembly (GO:0080129)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	8		Prostate(19;8.44e-08)				TCCAGAGTTTAGCACAACCAA	0.398													A|||	2373	0.473842	0.4402	0.5648	5008	,	,		18664	0.4117		0.4801	False		,,,				2504	0.5123				p.A99A		Atlas-SNP	.											PSMG1,colon,carcinoma,0,1	PSMG1	11	1	0			c.T297C						PASS	.	A	,	2026,2380	563.4+/-381.2	463,1100,640	110.0	100.0	104.0		297,297	-2.7	1.0	21	dbSNP_105	104	3905,4695	547.2+/-385.1	887,2131,1282	no	coding-synonymous,coding-synonymous	PSMG1	NM_003720.2,NM_203433.1	,	1350,3231,1922	GG,GA,AA		45.407,45.9828,45.602	,	99/289,99/268	40552307	5931,7075	2203	4300	6503	SO:0001819	synonymous_variant	8624	exon3			GAGTTTAGCACAA	AJ006291	CCDS13660.1, CCDS13661.1	21q22.3	2007-10-23	2007-10-23	2007-10-23	ENSG00000183527	ENSG00000183527			3043	protein-coding gene	gene with protein product		605296	"""Down syndrome critical region gene 2"""	DSCR2		10872820, 17189198	Standard	NM_003720		Approved	c21-LRP, LRPC21, PAC1	uc002yxi.4	O95456	OTTHUMG00000066034	ENST00000331573.3:c.297T>C	21.37:g.40552307A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	NM_203433	B5BUN2|Q6FHA3|Q6FHD3|Q6S713	Silent	SNP	ENST00000331573.3	37	CCDS13660.1	1011	0.46291208791208793	213	0.4329268292682927	204	0.56353591160221	226	0.3951048951048951	368	0.48548812664907653	A	8.856	0.945765	0.18356	0.459828	0.45407	ENSG00000183527	ENST00000440607	.	.	.	5.7	-2.7	0.06004	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999723289	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.4312	6.3859	0.21559	0.3858:0.2475:0.3667:0.0	rs3171465;rs61023266;rs3171465	.	.	.	Q	20	.	.	X	-	1	0	PSMG1	39474177	0.940000	0.31905	0.988000	0.46212	0.996000	0.88848	0.005000	0.13129	-0.408000	0.07565	0.455000	0.32223	TAA	A|0.545;G|0.455	0.455	strong		0.398	PSMG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141404.2	NM_003720	
COLEC11	78989	hgsc.bcm.edu	37	2	3691548	3691548	+	Missense_Mutation	SNP	A	A	G	rs7567833	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:3691548A>G	ENST00000349077.4	+	7	759	c.656A>G	c.(655-657)cAc>cGc	p.H219R	COLEC11_ENST00000403096.3_Missense_Mutation_p.H193R|COLEC11_ENST00000404205.1_Missense_Mutation_p.H145R|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000418971.2_Missense_Mutation_p.H233R|COLEC11_ENST00000236693.7_Missense_Mutation_p.H216R|COLEC11_ENST00000382062.2_Missense_Mutation_p.H195R|COLEC11_ENST00000402922.1_Missense_Mutation_p.H169R|COLEC11_ENST00000402794.1_Missense_Mutation_p.H169R	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	219	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		H -> R (in dbSNP:rs7567833). {ECO:0000269|PubMed:14702039}.		developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		TACTCTGACCACTCCCCCATG	0.637													G|||	1223	0.244209	0.7436	0.0908	5008	,	,		18858	0.0218		0.0348	False		,,,				2504	0.1227				p.H233R		Atlas-SNP	.											.	COLEC11	93	.	0			c.A698G						PASS	.	G	ARG/HIS,ARG/HIS	2910,1496	476.1+/-357.5	979,952,272	63.0	75.0	71.0		656,647	5.3	1.0	2	dbSNP_116	71	279,8321	807.0+/-407.2	5,269,4026	yes	missense,missense	COLEC11	NM_024027.3,NM_199235.1	29,29	984,1221,4298	GG,GA,AA		3.2442,33.9537,24.5195	benign,benign	219/272,216/269	3691548	3189,9817	2203	4300	6503	SO:0001583	missense	78989	exon8			CTGACCACTCCCC	BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"""Collectins"""	17213	protein-coding gene	gene with protein product	"""Collectin K1"""	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.656A>G	2.37:g.3691548A>G	ENSP00000339168:p.His219Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_001255985	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Missense_Mutation	SNP	ENST00000349077.4	37	CCDS1649.1	419	0.19184981684981686	364	0.7398373983739838	31	0.0856353591160221	6	0.01048951048951049	18	0.023746701846965697	G	5.512	0.279351	0.10458	0.660463	0.032442	ENSG00000118004	ENST00000382062;ENST00000236693;ENST00000349077;ENST00000418971;ENST00000403096;ENST00000402794;ENST00000404205;ENST00000402922	T;T;T;T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34;2.34;2.34;2.34	5.3	5.3	0.74995	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.273464	0.41396	N	0.000893	T	0.00012	0.0000	N	0.00621	-1.32	0.58432	P	5.000000000032756E-6	B;B;B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B;B;B;B	0.06405	0.0;0.001;0.001;0.0;0.001;0.0;0.001;0.001;0.002	T	0.13872	-1.0493	9	0.41790	T	0.15	-15.7946	13.2666	0.60137	0.0767:0.0:0.9233:0.0	rs7567833;rs60526563;rs7567833	145;169;169;193;171;195;195;219;216	Q9BWP8-8;Q9BWP8-7;Q9BWP8-6;Q9BWP8-4;Q9BWP8-5;Q9BWP8-3;Q9BWP8-2;Q9BWP8;Q9BWP8-9	.;.;.;.;.;.;.;COL11_HUMAN;.	R	195;216;219;233;193;169;145;169	ENSP00000371494:H195R;ENSP00000236693:H216R;ENSP00000339168:H219R;ENSP00000411770:H233R;ENSP00000385130:H193R;ENSP00000384882:H169R;ENSP00000385827:H145R;ENSP00000385653:H169R	ENSP00000236693:H216R	H	+	2	0	COLEC11	3669423	1.000000	0.71417	0.992000	0.48379	0.002000	0.02628	4.613000	0.61176	1.240000	0.43803	-0.349000	0.07799	CAC	A|0.765;G|0.235	0.235	strong		0.637	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178770981	178770981	+	Silent	SNP	A	A	G	rs2271212	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:178770981A>G	ENST00000251582.7	-	2	422	c.321T>C	c.(319-321)agT>agC	p.S107S	ADAMTS2_ENST00000274609.5_Silent_p.S107S	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	107					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		AGAAGAGGTGACTGCCAGGCT	0.701																																					p.S107S		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.T321C						PASS	.	G	,	986,3412		117,752,1330	21.0	25.0	24.0		321,321	-0.6	0.0	5	dbSNP_100	24	3026,5562		541,1944,1809	no	coding-synonymous,coding-synonymous	ADAMTS2	NM_014244.4,NM_021599.2	,	658,2696,3139	GG,GA,AA		35.2352,22.4193,30.8948	,	107/1212,107/567	178770981	4012,8974	2199	4294	6493	SO:0001819	synonymous_variant	9509	exon2			GAGGTGACTGCCA	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.321T>C	5.37:g.178770981A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_021599		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			A|0.677;G|0.323	0.323	strong		0.701	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
BAI2	576	hgsc.bcm.edu	37	1	32193647	32193647	+	Silent	SNP	T	T	C	rs1127100	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32193647T>C	ENST00000373658.3	-	32	4892	c.4551A>G	c.(4549-4551)gcA>gcG	p.A1517A	BAI2_ENST00000527361.1_Silent_p.A1483A|BAI2_ENST00000398547.1_Intron|BAI2_ENST00000398538.1_Intron|BAI2_ENST00000257070.4_Silent_p.A1483A|BAI2_ENST00000398556.3_Silent_p.A1432A|BAI2_ENST00000398542.1_Intron|BAI2_ENST00000373655.2_Silent_p.A1516A|BAI2_ENST00000440175.2_Intron|BAI2_ENST00000465256.1_5'UTR	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1517					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		TCCGCTCGGCTGCCCCACCCG	0.731													C|||	3025	0.604034	0.8321	0.5159	5008	,	,		13392	0.3492		0.6531	False		,,,				2504	0.5706				p.A1517A		Atlas-SNP	.											.	BAI2	128	.	0			c.A4551G						PASS	.	C		3482,898		1394,694,102	19.0	19.0	19.0		4551	-6.0	0.0	1	dbSNP_86	19	5523,3035		1820,1883,576	no	coding-synonymous	BAI2	NM_001703.2		3214,2577,678	CC,CT,TT		35.4639,20.5023,30.3988		1517/1586	32193647	9005,3933	2190	4279	6469	SO:0001819	synonymous_variant	576	exon32			CTCGGCTGCCCCA	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.4551A>G	1.37:g.32193647T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	37	CCDS346.2																																																																																			T|0.343;C|0.657	0.657	strong		0.731	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
CYP4A22	284541	hgsc.bcm.edu	37	1	47607851	47607851	+	Missense_Mutation	SNP	A	A	T	rs2056899	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:47607851A>T	ENST00000371891.3	+	4	485	c.454A>T	c.(454-456)Aat>Tat	p.N152Y	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000294337.3_Missense_Mutation_p.N152Y|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000371890.3_Missense_Mutation_p.N152Y	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	152			N -> Y (in allele CYP4A22*2, allele CYP4A22*3, allele CYP4A22*4, allele CYP4A22*5, allele CYP4A22*6, allele CYP4A22*7, allele CYP4A22*8, allele CYP4A22*9, allele CYP4A22*10, allele CYP4A22*11, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs2056899). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGCCTTCCACAATGACATCCT	0.542													T|||	3660	0.730831	0.944	0.5072	5008	,	,		20966	0.9802		0.4036	False		,,,				2504	0.681				p.N152Y	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.A454T						PASS	.	T	TYR/ASN	3737,669	282.8+/-276.7	1591,555,57	115.0	99.0	104.0		454	0.2	1.0	1	dbSNP_94	104	3324,5276	644.4+/-400.0	634,2056,1610	no	missense	CYP4A22	NM_001010969.2	143	2225,2611,1667	TT,TA,AA		38.6512,15.1838,45.7097	benign	152/520	47607851	7061,5945	2203	4300	6503	SO:0001583	missense	284541	exon4			TTCCACAATGACA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.454A>T	1.37:g.47607851A>T	ENSP00000360958:p.Asn152Tyr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	184	84	0.456522	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	1483	0.6790293040293041	447	0.9085365853658537	168	0.46408839779005523	568	0.993006993006993	300	0.39577836411609496	t	0.006	-2.066875	0.00382	0.848162	0.386512	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.68903	-0.36;-0.36;-0.36	1.7	0.248	0.15526	.	0.070255	0.64402	N	0.000015	T	0.00012	0.0000	N	0.00016	-2.85	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38714	-0.9648	9	0.02654	T	1	.	6.7756	0.23619	0.365:0.0:0.0:0.635	rs2056899;rs52810631;rs56721463;rs2056899	152;152	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	Y	152	ENSP00000360957:N152Y;ENSP00000360958:N152Y;ENSP00000294337:N152Y	ENSP00000294337:N152Y	N	+	1	0	CYP4A22	47380438	0.997000	0.39634	0.957000	0.39632	0.243000	0.25628	2.912000	0.48782	-0.032000	0.13758	-1.247000	0.01520	AAT	.	.	weak		0.542	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240627	39240627	+	Missense_Mutation	SNP	T	T	C	rs189343211		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240627T>C	ENST00000391417.4	+	1	169	c.169T>C	c.(169-171)Tct>Cct	p.S57P		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	57	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.S57P(4)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						GTGCTGCCAGTCTGTGTGCTG	0.667																																					p.S57P		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,22	KRTAP4-7	49	22	4	Substitution - Missense(4)	urinary_tract(2)|kidney(2)	c.T169C						scavenged	.						18.0	28.0	25.0					17																	39240627		691	1590	2281	SO:0001583	missense	100132476	exon1			TGCCAGTCTGTGT	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.169T>C	17.37:g.39240627T>C	ENSP00000375236:p.Ser57Pro	Somatic	49	4	0.0816327		WXS	Illumina HiSeq	Phase_I	81	16	0.197531	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.387	-0.925721	0.02377	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.01272	5.07	3.6	-0.386	0.12466	.	1.254490	0.05892	N	0.628448	T	0.00695	0.0023	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.43572	-0.9383	9	0.02654	T	1	.	4.4551	0.11639	0.0:0.4346:0.1731:0.3923	.	57	Q9BYR0	KRA47_HUMAN	P	57	ENSP00000375236:S57P	ENSP00000375236:S57P	S	+	1	0	KRTAP4-9;KRTAP4-7	36494153	0.000000	0.05858	0.033000	0.17914	0.157000	0.22087	-0.806000	0.04525	0.004000	0.14682	0.374000	0.22700	TCT	.	.	weak		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
RAI14	26064	hgsc.bcm.edu	37	5	34807928	34807928	+	Silent	SNP	C	C	T	rs6895634	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:34807928C>T	ENST00000265109.3	+	6	632	c.345C>T	c.(343-345)gtC>gtT	p.V115V	RAI14_ENST00000397449.1_Silent_p.V108V|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000428746.2_Silent_p.V115V|RAI14_ENST00000512629.1_Silent_p.V115V|RAI14_ENST00000515799.1_Silent_p.V118V|RAI14_ENST00000506376.1_Silent_p.V107V|RAI14_ENST00000503673.1_Silent_p.V115V	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	115						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					CCGAAAGTGTCGACAGCTCTG	0.358													T|||	1952	0.389776	0.239	0.549	5008	,	,		18310	0.3591		0.4264	False		,,,				2504	0.4744				p.V118V		Atlas-SNP	.											.	RAI14	100	.	0			c.C354T						PASS	.	T	,,,,,	1215,3191	707.8+/-407.5	169,877,1157	181.0	183.0	182.0		345,345,345,321,354,345	-0.7	0.0	5	dbSNP_116	182	3623,4977	624.4+/-397.6	764,2095,1441	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAI14	NM_001145520.1,NM_001145521.1,NM_001145522.1,NM_001145523.1,NM_001145525.1,NM_015577.2	,,,,,	933,2972,2598	TT,TC,CC		42.1279,27.576,37.1982	,,,,,	115/981,115/981,115/952,107/973,118/984,115/981	34807928	4838,8168	2203	4300	6503	SO:0001819	synonymous_variant	26064	exon8			AAGTGTCGACAGC	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.345C>T	5.37:g.34807928C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	206	96	0.466019	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Silent	SNP	ENST00000265109.3	37	CCDS34142.1																																																																																			C|0.628;T|0.372	0.372	strong		0.358	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
APOBEC4	403314	hgsc.bcm.edu	37	1	183617105	183617105	+	Missense_Mutation	SNP	A	A	G	rs1174658	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:183617105A>G	ENST00000308641.4	-	2	1083	c.812T>C	c.(811-813)tTt>tCt	p.F271S	APOBEC4_ENST00000481562.1_Intron|RGL1_ENST00000304685.4_Intron|RGL1_ENST00000536277.1_Intron	NM_203454.2	NP_982279.1	Q8WW27	ABEC4_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	271			F -> S (in dbSNP:rs1174658). {ECO:0000269|PubMed:14702039}.		mRNA processing (GO:0006397)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(6)|skin(1)	21						CATTTGAAAAAACTGTCCAGG	0.468													G|||	1854	0.370208	0.4932	0.3473	5008	,	,		20550	0.244		0.4006	False		,,,				2504	0.319				p.F271S		Atlas-SNP	.											APOBEC4,NS,carcinoma,0,1	APOBEC4	45	1	0			c.T812C						PASS	.	G	,SER/PHE	2068,2338	606.4+/-390.7	487,1094,622	89.0	92.0	91.0		,812	4.6	0.0	1	dbSNP_87	91	3401,5199	639.9+/-399.5	679,2043,1578	yes	intron,missense	RGL1,APOBEC4	NM_015149.3,NM_203454.2	,155	1166,3137,2200	GG,GA,AA		39.5465,46.936,42.0498	,benign	,271/368	183617105	5469,7537	2203	4300	6503	SO:0001583	missense	403314	exon2			TGAAAAAACTGTC	BC021711	CCDS1358.1	1q25.3	2008-02-05	2005-10-27	2005-10-27	ENSG00000173627	ENSG00000173627		"""Apolipoprotein B mRNA editing enzymes"""	32152	protein-coding gene	gene with protein product		609908	"""chromosome 1 open reading frame 169"""	C1orf169		16082223	Standard	NM_203454		Approved	MGC26594, FLJ25691, RP1-127C7.4	uc001gqn.3	Q8WW27	OTTHUMG00000035459	ENST00000308641.4:c.812T>C	1.37:g.183617105A>G	ENSP00000310622:p.Phe271Ser	Somatic	428	1	0.00233645		WXS	Illumina HiSeq	Phase_I	488	257	0.526639	NM_203454	Q8N7F6	Missense_Mutation	SNP	ENST00000308641.4	37	CCDS1358.1	783	0.3585164835164835	237	0.4817073170731707	140	0.3867403314917127	106	0.1853146853146853	300	0.39577836411609496	G	0.026	-1.372911	0.01214	0.46936	0.395465	ENSG00000173627	ENST00000308641	T	0.10099	2.91	4.55	4.55	0.56014	.	0.194476	0.24917	N	0.034575	T	0.00012	0.0000	N	0.00197	-1.87	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37709	-0.9694	9	0.23302	T	0.38	.	8.1901	0.31363	0.1861:0.0:0.8139:0.0	rs1174658;rs17489801;rs52801116;rs60238997;rs1174658	271	Q8WW27	ABEC4_HUMAN	S	271	ENSP00000310622:F271S	ENSP00000310622:F271S	F	-	2	0	APOBEC4	181883728	0.034000	0.19679	0.005000	0.12908	0.011000	0.07611	1.385000	0.34408	0.918000	0.36919	-0.119000	0.15052	TTT	A|0.606;G|0.394	0.394	strong		0.468	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454	
ZNF292	23036	hgsc.bcm.edu	37	6	87969480	87969480	+	Missense_Mutation	SNP	G	G	A	rs6910541	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:87969480G>A	ENST00000369577.3	+	8	6176	c.6133G>A	c.(6133-6135)Gta>Ata	p.V2045I	ZNF292_ENST00000339907.4_Missense_Mutation_p.V2040I	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2045			V -> I (in dbSNP:rs6910541). {ECO:0000269|PubMed:9628581}.			nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AAAACAACTTGTAGAAAAAAA	0.358													G|||	563	0.11242	0.1112	0.1527	5008	,	,		18764	0.0972		0.1064	False		,,,				2504	0.1074				p.V2045I		Atlas-SNP	.											.	ZNF292	479	.	0			c.G6133A						PASS	.	G	ILE/VAL	437,3161		24,389,1386	28.0	25.0	26.0		6133	-9.9	0.0	6	dbSNP_116	26	846,7270		37,772,3249	yes	missense	ZNF292	NM_015021.1	29	61,1161,4635	AA,AG,GG		10.4239,12.1456,10.9527	benign	2045/2724	87969480	1283,10431	1799	4058	5857	SO:0001583	missense	23036	exon8			CAACTTGTAGAAA	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.6133G>A	6.37:g.87969480G>A	ENSP00000358590:p.Val2045Ile	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	231	88	0.380952	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	275	0.1259157509157509	71	0.1443089430894309	61	0.1685082872928177	63	0.11013986013986014	80	0.10554089709762533	G	4.208	0.037399	0.08148	0.121456	0.104239	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.07114	3.22;3.23	5.87	-9.85	0.00476	.	1.934300	0.01884	N	0.038072	T	0.00608	0.0020	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40627	-0.9553	9	0.19147	T	0.46	.	6.9653	0.24619	0.1398:0.3551:0.4245:0.0806	rs6910541;rs52830459;rs61648684;rs6910541	2045	O60281	ZN292_HUMAN	I	2045;2040	ENSP00000358590:V2045I;ENSP00000342847:V2040I	ENSP00000342847:V2040I	V	+	1	0	ZNF292	88026199	0.000000	0.05858	0.000000	0.03702	0.445000	0.32107	-0.649000	0.05384	-1.686000	0.01439	-0.345000	0.07892	GTA	G|0.875;A|0.125	0.125	strong		0.358	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
DNALI1	7802	hgsc.bcm.edu	37	1	38023316	38023316	+	Missense_Mutation	SNP	C	C	T	rs11749	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:38023316C>T	ENST00000296218.7	+	2	270	c.260C>T	c.(259-261)gCa>gTa	p.A87V	DNALI1_ENST00000541606.1_5'UTR	NM_003462.3	NP_003453.2	O14645	IDLC_HUMAN	dynein, axonemal, light intermediate chain 1	65					cellular component movement (GO:0006928)|metabolic process (GO:0008152)|single fertilization (GO:0007338)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|filopodium (GO:0030175)	microtubule motor activity (GO:0003777)			breast(1)|kidney(1)|large_intestine(2)|ovary(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ACAAAGCAGGCAGAAGAAATC	0.537													C|||	1023	0.204273	0.0681	0.2046	5008	,	,		20615	0.3502		0.2535	False		,,,				2504	0.1871				p.A87V		Atlas-SNP	.											.	DNALI1	25	.	0			c.C260T						PASS	.	C	VAL/ALA	427,3979	208.8+/-229.8	19,389,1795	176.0	170.0	172.0		260	5.8	1.0	1	dbSNP_52	172	2211,6389	376.5+/-338.2	297,1617,2386	yes	missense	DNALI1	NM_003462.3	64	316,2006,4181	TT,TC,CC		25.7093,9.6913,20.2829	possibly-damaging	87/281	38023316	2638,10368	2203	4300	6503	SO:0001583	missense	7802	exon2			AGCAGGCAGAAGA	AF006386	CCDS420.1	1p35.1	2008-07-18	2006-09-04		ENSG00000163879	ENSG00000163879		"""Axonemal dyneins"""	14353	protein-coding gene	gene with protein product	"""inner dynein arm, homolog of clamydomonas"", ""dJ423B22.5 (axonemal dynein light chain (hp28))"""	602135	"""dynein, axonemal, light intermediate polypeptide 1"""			9284741	Standard	NM_003462		Approved	P28, hp28, dJ423B22.5	uc001cbj.3	O14645	OTTHUMG00000004222	ENST00000296218.7:c.260C>T	1.37:g.38023316C>T	ENSP00000296218:p.Ala87Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_003462	A8K387|B4DHN6|Q05BL9|Q5HYE2|Q5TGH0|Q7L0I5	Missense_Mutation	SNP	ENST00000296218.7	37	CCDS420.1	522	0.23901098901098902	34	0.06910569105691057	83	0.2292817679558011	216	0.3776223776223776	189	0.24934036939313983	C	22.9	4.346647	0.82022	0.096913	0.257093	ENSG00000163879	ENST00000296218	T	0.42513	0.97	5.76	5.76	0.90799	.	0.313134	0.38663	N	0.001610	T	0.00012	0.0000	N	0.12182	0.205	0.09310	P	1.0	P	0.41420	0.749	P	0.45753	0.492	T	0.47812	-0.9088	9	0.27082	T	0.32	-6.8937	17.4499	0.87589	0.0:1.0:0.0:0.0	rs11749;rs1047072;rs3170935;rs11540746;rs17350512;rs52811198;rs60888941;rs11540746	65	O14645	IDLC_HUMAN	V	87	ENSP00000296218:A87V	ENSP00000296218:A87V	A	+	2	0	DNALI1	37795903	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.974000	0.56852	2.725000	0.93324	0.591000	0.81541	GCA	C|0.786;G|0.000;N|0.000;T|0.213	0.213	strong		0.537	DNALI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012159.1	NM_003462	
EARS2	124454	hgsc.bcm.edu	37	16	23544061	23544061	+	Silent	SNP	C	C	T	rs77939239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:23544061C>T	ENST00000563459.1	-	5	990	c.984G>A	c.(982-984)ccG>ccA	p.P328P	EARS2_ENST00000564987.1_5'UTR|EARS2_ENST00000449606.1_Silent_p.P328P|EARS2_ENST00000563232.1_Silent_p.P328P|EARS2_ENST00000564501.1_Silent_p.P328P			Q5JPH6	SYEM_HUMAN	glutamyl-tRNA synthetase 2, mitochondrial	328					gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|tRNA aminoacylation for mitochondrial protein translation (GO:0070127)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|glutamate-tRNA(Gln) ligase activity (GO:0050561)|tRNA binding (GO:0000049)			central_nervous_system(1)|endometrium(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	8				GBM - Glioblastoma multiforme(48;0.0353)		TGATCAGCTCCGGCAGGGTCC	0.532													C|||	69	0.013778	0.0212	0.0159	5008	,	,		17676	0.0		0.0268	False		,,,				2504	0.0031				p.P328P		Atlas-SNP	.											.	EARS2	26	.	0			c.G984A						PASS	.	C		103,3781		2,99,1841	59.0	61.0	60.0		984	-8.5	0.4	16	dbSNP_132	60	217,8067		2,213,3927	no	coding-synonymous	EARS2	NM_001083614.1		4,312,5768	TT,TC,CC		2.6195,2.6519,2.6298		328/524	23544061	320,11848	1942	4142	6084	SO:0001819	synonymous_variant	124454	exon5			CAGCTCCGGCAGG	AB075850	CCDS42132.1	16p12.2	2014-05-06	2012-10-26		ENSG00000103356	ENSG00000103356	6.1.1.17	"""Aminoacyl tRNA synthetases / Class I"""	29419	protein-coding gene	gene with protein product	"""glutamate tRNA ligase 2, mitochondrial"""	612799	"""glutamyl-tRNA synthetase 2, mitochondrial (putative)"""			15779907, 19805282, 22492562	Standard	NM_001083614		Approved	KIAA1970, MSE1	uc002dlt.4	Q5JPH6	OTTHUMG00000177018	ENST00000563459.1:c.984G>A	16.37:g.23544061C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_001083614	B3KTT2|D3DWF1|Q86YH3|Q8TF31	Silent	SNP	ENST00000563459.1	37	CCDS42132.1																																																																																			C|0.976;T|0.024	0.024	strong		0.532	EARS2-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434844.1	NM_133451	
ZBED9	114821	hgsc.bcm.edu	37	6	28542424	28542424	+	Silent	SNP	G	G	A	rs450630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28542424G>A	ENST00000452236.2	-	3	2675	c.2058C>T	c.(2056-2058)gaC>gaT	p.D686D	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						ATCTTACCCAGTCTCCTACTT	0.398													A|||	3263	0.651558	0.9274	0.5461	5008	,	,		19567	0.6716		0.4354	False		,,,				2504	0.5552				p.D686D		Atlas-SNP	.											.	SCAND3	156	.	0			c.C2058T						PASS	.	A		3729,677	283.7+/-277.2	1589,551,63	137.0	142.0	140.0		2058	-1.0	1.0	6	dbSNP_80	140	3876,4724	607.9+/-395.3	889,2098,1313	no	coding-synonymous	SCAND3	NM_052923.1		2478,2649,1376	AA,AG,GG		45.0698,15.3654,41.527		686/1326	28542424	7605,5401	2203	4300	6503	SO:0001819	synonymous_variant	114821	exon3			TACCCAGTCTCCT																												ENST00000452236.2:c.2058C>T	6.37:g.28542424G>A		Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	256	119	0.464844	NM_052923		Silent	SNP	ENST00000452236.2	37	CCDS34355.1																																																																																			G|0.391;A|0.609	0.609	strong		0.398	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3		
IGF1R	3480	hgsc.bcm.edu	37	15	99500605	99500605	+	Silent	SNP	C	C	T	rs17847203	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:99500605C>T	ENST00000268035.6	+	21	4649	c.4038C>T	c.(4036-4038)taC>taT	p.Y1346Y	IGF1R_ENST00000558762.1_Silent_p.Y1345Y|RP11-654A16.3_ENST00000559468.1_RNA	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1346					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	GACAGCCTTACGCCCACATGA	0.642													C|||	389	0.0776757	0.1475	0.0807	5008	,	,		15753	0.0407		0.0408	False		,,,				2504	0.0573				p.Y1346Y		Atlas-SNP	.											IGF1R,NS,carcinoma,0,1	IGF1R	147	1	0			c.C4038T						scavenged	.	C		525,3869		34,457,1706	35.0	39.0	38.0		4038	2.8	1.0	15	dbSNP_123	38	346,8248		12,322,3963	no	coding-synonymous	IGF1R	NM_000875.3		46,779,5669	TT,TC,CC		4.0261,11.9481,6.7062		1346/1368	99500605	871,12117	2197	4297	6494	SO:0001819	synonymous_variant	3480	exon21			GCCTTACGCCCAC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.4038C>T	15.37:g.99500605C>T		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	37	CCDS10378.1																																																																																			C|0.936;T|0.064	0.064	strong		0.642	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
PARP4	143	hgsc.bcm.edu	37	13	25029295	25029295	+	Missense_Mutation	SNP	C	C	T	rs7140044	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25029295C>T	ENST00000381989.3	-	22	2723	c.2618G>A	c.(2617-2619)aGt>aAt	p.S873N	PARP4_ENST00000480576.1_5'Flank	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	873			S -> N (in dbSNP:rs7140044). {ECO:0000269|PubMed:10644454, ECO:0000269|PubMed:8724849}.		cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TTCGCTCTCACTGGCTAGGTC	0.512													t|||	1125	0.224641	0.2118	0.147	5008	,	,		16575	0.3194		0.1769	False		,,,				2504	0.2485				p.S873N		Atlas-SNP	.											.	PARP4	142	.	0			c.G2618A						PASS	.	T	ASN/SER	910,3496	740.1+/-411.1	104,702,1397	167.0	145.0	153.0		2618	-6.7	0.0	13	dbSNP_116	153	1622,6978	742.3+/-407.2	176,1270,2854	yes	missense	PARP4	NM_006437.3	46	280,1972,4251	TT,TC,CC		18.8605,20.6537,19.4679	benign	873/1725	25029295	2532,10474	2203	4300	6503	SO:0001583	missense	143	exon22			CTCTCACTGGCTA	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2618G>A	13.37:g.25029295C>T	ENSP00000371419:p.Ser873Asn	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	506	0.2316849816849817	109	0.22154471544715448	62	0.1712707182320442	195	0.3409090909090909	140	0.18469656992084432	T	6.364	0.435339	0.12045	0.206537	0.188605	ENSG00000102699	ENST00000381989	T	0.01918	4.56	4.82	-6.65	0.01795	.	1.901400	0.02434	N	0.083932	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48559	-0.9025	9	0.17369	T	0.5	3.8672	4.2869	0.10858	0.1071:0.4176:0.1098:0.3655	rs7140044;rs59261450;rs7140044	873	Q9UKK3	PARP4_HUMAN	N	873	ENSP00000371419:S873N	ENSP00000371419:S873N	S	-	2	0	PARP4	23927295	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.436000	0.06922	-1.983000	0.00987	-1.021000	0.02439	AGT	C|0.795;T|0.205	0.205	strong		0.512	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
SLC1A4	6509	hgsc.bcm.edu	37	2	65245365	65245365	+	Missense_Mutation	SNP	G	G	A	rs759458	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:65245365G>A	ENST00000234256.3	+	6	1438	c.1195G>A	c.(1195-1197)Gta>Ata	p.V399I	SLC1A4_ENST00000531327.1_Missense_Mutation_p.V101I	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	399			V -> I (in dbSNP:rs759458).		amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	ACTCAACAACGTAGAGCTCAA	0.493													G|||	961	0.191893	0.1354	0.1945	5008	,	,		21801	0.1091		0.2435	False		,,,				2504	0.2986				p.V399I		Atlas-SNP	.											SLC1A4,NS,carcinoma,-2,1	SLC1A4	33	1	0			c.G1195A						PASS	.	G	ILE/VAL,ILE/VAL	772,3634	313.0+/-292.9	68,636,1499	142.0	131.0	135.0		301,1195	0.2	0.0	2	dbSNP_86	135	2257,6343	382.3+/-340.3	297,1663,2340	yes	missense,missense	SLC1A4	NM_001193493.1,NM_003038.4	29,29	365,2299,3839	AA,AG,GG		26.2442,17.5216,23.2893	benign,benign	101/235,399/533	65245365	3029,9977	2203	4300	6503	SO:0001583	missense	6509	exon6			AACAACGTAGAGC		CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"""Solute carriers"""	10942	protein-coding gene	gene with protein product	"""alanine/serine/cysteine/threonine transporter"""	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.1195G>A	2.37:g.65245365G>A	ENSP00000234256:p.Val399Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	172	55	0.319767	NM_003038	B7Z3C0|D6W5F0	Missense_Mutation	SNP	ENST00000234256.3	37	CCDS1879.1	393	0.17994505494505494	59	0.11991869918699187	88	0.2430939226519337	62	0.10839160839160839	184	0.24274406332453827	G	5.480	0.273673	0.10403	0.175216	0.262442	ENSG00000115902	ENST00000531327;ENST00000448784;ENST00000234256	T;T	0.58940	0.3;0.3	6.17	0.22	0.15279	.	0.444350	0.25711	N	0.028808	T	0.00012	0.0000	N	0.10809	0.05	0.80722	P	0.0	B;B;B	0.18166	0.002;0.026;0.002	B;B;B	0.13407	0.002;0.009;0.004	T	0.24799	-1.0150	8	.	.	.	-27.4704	5.6816	0.17780	0.2405:0.0:0.565:0.1945	rs759458;rs1064513;rs59381701;rs759458	399;101;399	P43007;B7Z3C0;B2R7N6	SATT_HUMAN;.;.	I	101;319;399	ENSP00000431942:V101I;ENSP00000234256:V399I	.	V	+	1	0	SLC1A4	65098869	0.004000	0.15560	0.003000	0.11579	0.253000	0.25986	0.495000	0.22483	-0.237000	0.09739	0.655000	0.94253	GTA	G|0.791;N|0.001	.	strong		0.493	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48603503	48603503	+	Missense_Mutation	SNP	C	C	T	rs9890721	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48603503C>T	ENST00000323776.5	+	14	2335	c.2173C>T	c.(2173-2175)Cgg>Tgg	p.R725W	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.R688W	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			GAGTCCTCAGCGGAAGAGCAT	0.622													C|||	2693	0.53774	0.2163	0.5548	5008	,	,		14998	0.8363		0.5507	False		,,,				2504	0.6391				p.R725W		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.C2173T						PASS	.	C	TRP/ARG	1145,3261	398.5+/-330.9	158,829,1216	69.0	68.0	68.0		2173	-4.6	0.0	17	dbSNP_119	68	4678,3922	593.9+/-393.2	1282,2114,904	yes	missense	MYCBPAP	NM_032133.4	101	1440,2943,2120	TT,TC,CC		45.6047,25.9873,44.7716	benign	725/985	48603503	5823,7183	2203	4300	6503	SO:0001583	missense	84073	exon14			CCTCAGCGGAAGA	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.2173C>T	17.37:g.48603503C>T	ENSP00000323184:p.Arg725Trp	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	1222	0.5595238095238095	117	0.23780487804878048	200	0.5524861878453039	487	0.8513986013986014	418	0.5514511873350924	C	10.55	1.380972	0.24944	0.259873	0.543953	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.26810	1.71;1.71	5.35	-4.59	0.03400	.	1.293160	0.05121	N	0.490681	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.40175	-0.9577	9	0.51188	T	0.08	-1.8414	3.847	0.08939	0.3639:0.273:0.0:0.363	rs9890721;rs17642285;rs17856809;rs59499446;rs9890721	688	Q8TBZ2	MYBPP_HUMAN	W	725;688	ENSP00000323184:R725W;ENSP00000397209:R688W	ENSP00000323184:R725W	R	+	1	2	MYCBPAP	45958502	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.121000	0.01322	-1.075000	0.03129	-2.299000	0.00261	CGG	C|0.507;N|0.000	.	strong		0.622	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
DNAH17	8632	hgsc.bcm.edu	37	17	76503624	76503624	+	Silent	SNP	C	C	T	rs626439	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:76503624C>T	ENST00000585328.1	-	28	4615	c.4491G>A	c.(4489-4491)gaG>gaA	p.E1497E	DNAH17_ENST00000389840.5_Silent_p.E1496E	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1496	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TGAAGATGCTCTCCAGGTGGC	0.597													C|||	1621	0.323682	0.1906	0.4164	5008	,	,		19385	0.4583		0.2406	False		,,,				2504	0.3845				p.E1500E		Atlas-SNP	.											.	DNAH17	347	.	0			c.G4500A						PASS	.	C		776,3486		77,622,1432	46.0	53.0	51.0		4500	4.0	1.0	17	dbSNP_83	51	1990,6540		240,1510,2515	no	coding-synonymous	DNAH17	NM_173628.3		317,2132,3947	TT,TC,CC		23.3294,18.2074,21.6229		1500/4463	76503624	2766,10026	2131	4265	6396	SO:0001819	synonymous_variant	8632	exon28			GATGCTCTCCAGG	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.4491G>A	17.37:g.76503624C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				C|0.716;T|0.284	0.284	strong		0.597	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
JAKMIP2	9832	hgsc.bcm.edu	37	5	147024509	147024509	+	Silent	SNP	C	C	T	rs2116765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:147024509C>T	ENST00000265272.5	-	6	1454	c.987G>A	c.(985-987)agG>agA	p.R329R	JAKMIP2_ENST00000507386.1_Silent_p.R329R|JAKMIP2_ENST00000333010.6_Silent_p.R287R	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	329						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCACTTGTTCCTTTCCAGGA	0.458													C|||	1842	0.367812	0.5136	0.3631	5008	,	,		18363	0.4712		0.162	False		,,,				2504	0.2791				p.R329R		Atlas-SNP	.											.	JAKMIP2	154	.	0			c.G987A						PASS	.	C		1914,2492	547.2+/-377.2	426,1062,715	195.0	191.0	193.0		987	5.5	1.0	5	dbSNP_96	193	1185,7415	241.3+/-271.7	80,1025,3195	no	coding-synonymous	JAKMIP2	NM_014790.3		506,2087,3910	TT,TC,CC		13.7791,43.4408,23.8275		329/811	147024509	3099,9907	2203	4300	6503	SO:0001819	synonymous_variant	9832	exon6			CTTGTTCCTTTCC	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.987G>A	5.37:g.147024509C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	244	127	0.520492	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Silent	SNP	ENST00000265272.5	37	CCDS4285.1																																																																																			C|0.698;T|0.302	0.302	strong		0.458	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
CST5	1473	hgsc.bcm.edu	37	20	23860178	23860178	+	Missense_Mutation	SNP	A	A	G	rs1799841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:23860178A>G	ENST00000304710.4	-	1	209	c.136T>C	c.(136-138)Tgt>Cgt	p.C46R		NM_001900.4	NP_001891.2	P28325	CYTD_HUMAN	cystatin D	46			C -> R (in 45% of the population; dbSNP:rs1799841). {ECO:0000269|PubMed:8444475}.		negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.C46R(1)		breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11						TCCAGGGCACACTGCACACTC	0.577													g|||	2830	0.565096	0.8139	0.5476	5008	,	,		17019	0.494		0.4453	False		,,,				2504	0.4376				p.C46R		Atlas-SNP	.											CST5,NS,carcinoma,0,1	CST5	24	1	1	Substitution - Missense(1)	stomach(1)	c.T136C						PASS	.	G	ARG/CYS	3301,1105		1250,801,152	182.0	166.0	171.0		136	-0.4	0.0	20	dbSNP_89	171	3740,4860		816,2108,1376	yes	missense	CST5	NM_001900.4	180	2066,2909,1528	GG,GA,AA		43.4884,25.0794,45.8634	benign	46/143	23860178	7041,5965	2203	4300	6503	SO:0001583	missense	1473	exon1			GGGCACACTGCAC		CCDS13162.1	20p11.21	2008-04-15			ENSG00000170367	ENSG00000170367			2477	protein-coding gene	gene with protein product		123858				1939105	Standard	NM_001900		Approved		uc002wtr.1	P28325	OTTHUMG00000032089	ENST00000304710.4:c.136T>C	20.37:g.23860178A>G	ENSP00000307132:p.Cys46Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_001900	Q5JRF5|Q9UCA0	Missense_Mutation	SNP	ENST00000304710.4	37	CCDS13162.1	1186	0.543040293040293	389	0.790650406504065	192	0.5303867403314917	270	0.47202797202797203	335	0.4419525065963061	N	0.003	-2.500876	0.00157	0.749206	0.434884	ENSG00000170367	ENST00000304710	T	0.24723	1.84	1.99	-0.399	0.12415	Proteinase inhibitor I25, cystatin (2);	0.860793	0.10208	N	0.702474	T	0.00012	0.0000	N	0.00054	-2.38	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37526	-0.9702	9	0.06757	T	0.87	.	0.8314	0.01131	0.162:0.2324:0.3697:0.236	rs1799841;rs52827118;rs61231587;rs1799841	46	P28325	CYTD_HUMAN	R	46	ENSP00000307132:C46R	ENSP00000307132:C46R	C	-	1	0	CST5	23808178	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.217000	0.02979	-0.410000	0.07542	-0.380000	0.06706	TGT	A|0.455;G|0.545	0.545	strong		0.577	CST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078355.2	NM_001900	
WDR81	124997	hgsc.bcm.edu	37	17	1636950	1636950	+	Missense_Mutation	SNP	C	C	A	rs11657394	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1636950C>A	ENST00000409644.1	+	7	4619	c.4619C>A	c.(4618-4620)cCc>cAc	p.P1540H	WDR81_ENST00000545662.1_Missense_Mutation_p.P171H|WDR81_ENST00000419248.1_Missense_Mutation_p.P313H|WDR81_ENST00000446363.1_Missense_Mutation_p.P179H|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Missense_Mutation_p.P489H|WDR81_ENST00000437219.2_Missense_Mutation_p.P337H	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1540				P -> H (in Ref. 1; BAB84937). {ECO:0000305}.	negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GGCACCGGGCCCGAGTGGGAC	0.677													C|||	165	0.0329473	0.0295	0.0331	5008	,	,		15625	0.0		0.0716	False		,,,				2504	0.0317				p.P1540H		Atlas-SNP	.											.	WDR81	180	.	0			c.C4619A						PASS	.	C	HIS/PRO,HIS/PRO,HIS/PRO,HIS/PRO	170,4230		6,158,2036	27.0	31.0	30.0		1010,4619,938,1466	3.0	0.4	17	dbSNP_120	30	646,7940		23,600,3670	yes	missense,missense,missense,missense	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	77,77,77,77	29,758,5706	AA,AC,CC		7.5239,3.8636,6.2837	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	337/739,1540/1942,313/715,489/891	1636950	816,12170	2200	4293	6493	SO:0001583	missense	124997	exon7			CCGGGCCCGAGTG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.4619C>A	17.37:g.1636950C>A	ENSP00000386609:p.Pro1540His	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	80	0.03663003663003663	18	0.036585365853658534	10	0.027624309392265192	0	0.0	52	0.06860158311345646	C	9.979	1.227684	0.22542	0.038636	0.075239	ENSG00000167716	ENST00000437219;ENST00000309182;ENST00000446363;ENST00000419248;ENST00000418841;ENST00000409644;ENST00000354680;ENST00000545662	T;T;T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32	4.99	2.99	0.34606	.	0.416547	0.23768	N	0.044749	T	0.12050	0.0293	L	0.38531	1.155	0.09310	N	0.999998	P;P;P	0.39624	0.681;0.681;0.681	B;B;B	0.39971	0.315;0.315;0.215	T	0.10800	-1.0614	9	.	.	.	.	8.0582	0.30617	0.0:0.7513:0.0:0.2487	rs11657394	171;337;489	B7Z6V3;B7Z579;Q562E7	.;.;WDR81_HUMAN	H	337;489;179;313;125;1540;291;171	ENSP00000391074:P337H;ENSP00000312074:P489H;ENSP00000401560:P179H;ENSP00000407845:P313H;ENSP00000395198:P125H;ENSP00000386609:P1540H;ENSP00000442726:P171H	.	P	+	2	0	WDR81	1583700	0.000000	0.05858	0.424000	0.26647	0.467000	0.32768	0.449000	0.21744	0.519000	0.28406	0.563000	0.77884	CCC	C|0.946;A|0.054	0.054	strong		0.677	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
CGB8	94115	hgsc.bcm.edu	37	19	49551573	49551573	+	Silent	SNP	C	C	T	rs151241744	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49551573C>T	ENST00000448456.3	-	2	438	c.72G>A	c.(70-72)ccG>ccA	p.P24P	CGB8_ENST00000355414.2_Silent_p.P22P|CGB1_ENST00000391869.3_Intron	NM_033183.2	NP_149439.1	P01233	CGHB_HUMAN	chorionic gonadotropin, beta polypeptide 8	24			P -> M (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:11861891, ECO:0000269|PubMed:6194155}.		apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|peptide hormone processing (GO:0016486)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			pancreas(1)	1		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		GTGGCCGAAGCGGCTCCTTGG	0.657																																					p.P24P		Atlas-SNP	.											CGB8,NS,carcinoma,0,1	CGB8	2	1	0			c.G72A						scavenged	.						1.0	1.0	1.0					19																	49551573		258	679	937	SO:0001819	synonymous_variant	94115	exon2			CCGAAGCGGCTCC	BG435249	CCDS12753.1	19q13.32	2011-05-26							16453	protein-coding gene	gene with protein product		608827				6194155	Standard	NM_033183		Approved		uc002pmb.4	P01233		ENST00000448456.3:c.72G>A	19.37:g.49551573C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	135	25	0.185185	NM_033183	A1A5E0|B9ZVP5|Q13991|Q14000|Q3KPI3|Q3SY41|Q8WTT5|Q8WXL1|Q8WXL2|Q8WXL3|Q8WXL4	Silent	SNP	ENST00000448456.3	37	CCDS12753.1																																																																																			T|1.000;|0.000	1.000	weak		0.657	CGB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452168.1	NM_033183	
SP8	221833	hgsc.bcm.edu	37	7	20825271	20825271	+	Silent	SNP	C	C	T	rs145875827		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:20825271C>T	ENST00000361443.4	-	3	348	c.111G>A	c.(109-111)tcG>tcA	p.S37S	SP8_ENST00000418710.2_Silent_p.S55S	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	37	Ser-rich.				dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						AAGAAGAGGACGAGGAGCGTT	0.632																																					p.S55S		Atlas-SNP	.											.	SP8	43	.	0			c.G165A						PASS	.	C	,	1,4405		0,1,2202	46.0	47.0	47.0		165,111	-4.4	1.0	7	dbSNP_134	47	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	SP8	NM_182700.4,NM_198956.2	,	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	,	55/509,37/491	20825271	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	221833	exon2			AGAGGACGAGGAG		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.111G>A	7.37:g.20825271C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	62	34	0.548387	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			C|1.000;T|0.000	0.000	weak		0.632	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2		
CATSPER2	117155	hgsc.bcm.edu	37	15	43927973	43927973	+	Missense_Mutation	SNP	C	C	T	rs148320269	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:43927973C>T	ENST00000321596.5	-	9	1272	c.1073G>A	c.(1072-1074)cGg>cAg	p.R358Q	CATSPER2_ENST00000354127.4_Missense_Mutation_p.R358Q|STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000381761.1_Missense_Mutation_p.R364Q|CATSPER2_ENST00000396879.1_Missense_Mutation_p.R358Q|RNU6-610P_ENST00000384264.1_RNA|CATSPER2_ENST00000355438.2_Missense_Mutation_p.R358Q			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	358					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CTGAACCTCCCGACGCGCCAT	0.498													.|||	22	0.00439297	0.0	0.0058	5008	,	,		19451	0.0		0.006	False		,,,				2504	0.0123				p.R358Q		Atlas-SNP	.											CATSPER2,colon,carcinoma,-1,1	CATSPER2	49	1	0			c.G1073A						PASS	.	C	GLN/ARG,GLN/ARG	9,4389	15.5+/-35.6	0,9,2190	77.0	70.0	72.0		1073,1073	0.8	0.5	15	dbSNP_134	72	76,8518	42.2+/-99.7	1,74,4222	yes	missense,missense	CATSPER2	NM_054020.2,NM_172095.1	43,43	1,83,6412	TT,TC,CC		0.8843,0.2046,0.6542	benign,benign	358/529,358/531	43927973	85,12907	2199	4297	6496	SO:0001583	missense	117155	exon9			ACCTCCCGACGCG	AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"""Voltage-gated ion channels / Cation channels, sperm associated"""	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.1073G>A	15.37:g.43927973C>T	ENSP00000321463:p.Arg358Gln	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	91	86	0.945055	NM_054020	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	37	CCDS10099.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	C	1.962	-0.438657	0.04636	0.002046	0.008843	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127;ENST00000355438	D;D;D;D;D	0.96427	-3.98;-3.99;-3.98;-3.98;-4.01	4.62	0.808	0.18719	.	18.738300	0.01181	N	0.007082	D	0.87561	0.6208	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.80513	-0.1349	10	0.25106	T	0.35	.	2.454	0.04524	0.3882:0.3811:0.0885:0.1423	.	364;358	F8W9H2;Q96P56	.;CTSR2_HUMAN	Q	358;358;364;358;358;358	ENSP00000380088:R358Q;ENSP00000371180:R364Q;ENSP00000321463:R358Q;ENSP00000339137:R358Q;ENSP00000347613:R358Q	ENSP00000299989:R358Q	R	-	2	0	CATSPER2	41715265	0.998000	0.40836	0.469000	0.27204	0.001000	0.01503	1.097000	0.30988	-0.060000	0.13132	-2.636000	0.00152	CGG	C|0.995;T|0.005	0.005	strong		0.498	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020	
TAPBPL	55080	hgsc.bcm.edu	37	12	6562285	6562285	+	Silent	SNP	C	C	T	rs2041384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6562285C>T	ENST00000266556.7	+	2	282	c.117C>T	c.(115-117)tgC>tgT	p.C39C	CD27-AS1_ENST00000545339.1_RNA|TAPBPL_ENST00000544021.1_Intron|CD27-AS1_ENST00000399492.2_RNA|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	39					negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						TCCTAGACTGCTTCCTGGCGA	0.652													C|||	1142	0.228035	0.1074	0.1628	5008	,	,		17387	0.3224		0.2932	False		,,,				2504	0.273				p.C39C		Atlas-SNP	.											.	TAPBPL	21	.	0			c.C117T						PASS	.	C		534,3868		40,454,1707	40.0	35.0	37.0		117	3.2	1.0	12	dbSNP_94	37	2464,6132		361,1742,2195	no	coding-synonymous	TAPBPL	NM_018009.4		401,2196,3902	TT,TC,CC		28.6645,12.1308,23.0651		39/469	6562285	2998,10000	2201	4298	6499	SO:0001819	synonymous_variant	55080	exon2			AGACTGCTTCCTG	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.117C>T	12.37:g.6562285C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_018009	Q9NWB8	Silent	SNP	ENST00000266556.7	37	CCDS8546.1																																																																																			C|0.782;G|0.000;T|0.218	0.218	strong		0.652	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
KIF18B	146909	hgsc.bcm.edu	37	17	43003484	43003484	+	Silent	SNP	T	T	C	rs3169733	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43003484T>C	ENST00000593135.1	-	16	2620	c.2523A>G	c.(2521-2523)gcA>gcG	p.A841A	KIF18B_ENST00000438933.2_3'UTR|KIF18B_ENST00000339151.4_Silent_p.A844A|KIF18B_ENST00000587309.1_3'UTR	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	853					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				CTGCTGAGAGTGCTCTCCCCA	0.622													C|||	1798	0.359026	0.5779	0.3098	5008	,	,		19672	0.1488		0.2445	False		,,,				2504	0.4325				p.A841A		Atlas-SNP	.											.	KIF18B	63	.	0			c.A2523G						PASS	.	C		2165,2051		573,1019,516	111.0	124.0	120.0		2532	-8.1	0.0	17	dbSNP_105	120	2317,6119		333,1651,2234	no	coding-synonymous	KIF18B	NM_001080443.1		906,2670,2750	CC,CT,TT		27.4656,48.648,35.4252		844/856	43003484	4482,8170	2108	4218	6326	SO:0001819	synonymous_variant	146909	exon16			TGAGAGTGCTCTC		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"""Kinesins"""	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.2523A>G	17.37:g.43003484T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	38	0.395833	NM_001265577	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Silent	SNP	ENST00000593135.1	37	CCDS45709.2																																																																																			T|0.699;C|0.301	0.301	strong		0.622	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443	
PCDHA13	56136	hgsc.bcm.edu	37	5	140262492	140262492	+	Silent	SNP	A	A	T	rs11744560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140262492A>T	ENST00000289272.2	+	1	639	c.639A>T	c.(637-639)acA>acT	p.T213T	PCDHA13_ENST00000409494.1_Silent_p.T213T|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	213	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TATTACTGACAGCCAGTGATG	0.453													.|||	405	0.0808706	0.0809	0.1239	5008	,	,		21202	0.0179		0.1421	False		,,,				2504	0.0521				p.T213T	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.A639T						PASS	.	A	,,,,,,,,,,,,,,,,	394,4012	197.1+/-221.3	12,370,1821	59.0	61.0	60.0		,,,,639,,,,,,,,,,,,639	0.2	0.8	5	dbSNP_120	60	1320,7280	260.1+/-283.0	91,1138,3071	no	intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031865.1	,,,,,,,,,,,,,,,,	103,1508,4892	TT,TA,AA		15.3488,8.9424,13.1785	,,,,,,,,,,,,,,,,	,,,,213/951,,,,,,,,,,,,213/808	140262492	1714,11292	2203	4300	6503	SO:0001819	synonymous_variant	56136	exon1			ACTGACAGCCAGT	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"""Cadherins / Protocadherins : Clustered"""	8667	other	complex locus constituent	"""KIAA0345-like 1"", ""ortholog of mouse CNR5"""	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.639A>T	5.37:g.140262492A>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_031865	O75277	Silent	SNP	ENST00000289272.2	37	CCDS4240.1																																																																																			A|0.877;T|0.123	0.123	strong		0.453	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904	
ZNF880	400713	hgsc.bcm.edu	37	19	52887282	52887282	+	Missense_Mutation	SNP	A	A	G	rs324125	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52887282A>G	ENST00000422689.2	+	4	464	c.449A>G	c.(448-450)tAt>tGt	p.Y150C		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	150					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						CAAAAAATTTATTCTAGTGTC	0.323													A|||	776	0.154952	0.2534	0.1124	5008	,	,		19781	0.1468		0.1451	False		,,,				2504	0.0706				p.Y150C		Atlas-SNP	.											.	ZNF880	45	.	0			c.A449G						PASS	.	A	CYS/TYR	327,1057		37,253,402	53.0	44.0	47.0		449	-2.9	0.0	19	dbSNP_79	47	454,2728		31,392,1168	yes	missense	ZNF880	NM_001145434.1	194	68,645,1570	GG,GA,AA		14.2678,23.6272,17.1047	benign	150/578	52887282	781,3785	692	1591	2283	SO:0001583	missense	400713	exon4			AAATTTATTCTAG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.449A>G	19.37:g.52887282A>G	ENSP00000406318:p.Tyr150Cys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	178	74	0.41573	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	352	0.16117216117216118	122	0.24796747967479674	38	0.10497237569060773	82	0.14335664335664336	110	0.14511873350923482	A	6.084	0.383720	0.11524	0.236272	0.142678	ENSG00000221923	ENST00000422689	T	0.06142	3.34	1.46	-2.92	0.05615	.	.	.	.	.	T	0.00012	0.0000	N	0.16368	0.405	0.80722	P	0.0	B	0.16396	0.017	B	0.17098	0.017	T	0.48222	-0.9054	7	.	.	.	.	3.6589	0.08232	0.4436:0.3632:0.0:0.1931	rs324125;rs327534;rs61690649;rs324125	150	Q6PDB4	ZN880_HUMAN	C	150	ENSP00000406318:Y150C	.	Y	+	2	0	ZNF880	57579094	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.103000	0.15292	-1.392000	0.02082	-0.486000	0.04755	TAT	A|0.833;G|0.167	0.167	strong		0.323	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
MOV10L1	54456	hgsc.bcm.edu	37	22	50555635	50555635	+	Silent	SNP	C	C	T	rs882753	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50555635C>T	ENST00000262794.5	+	9	1392	c.1309C>T	c.(1309-1311)Cta>Tta	p.L437L	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Silent_p.L437L|MOV10L1_ENST00000540615.1_Silent_p.L417L|MOV10L1_ENST00000545383.1_Silent_p.L437L	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	437					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TTCCGATTTCCTAATTGGGCG	0.393													C|||	696	0.138978	0.0893	0.2003	5008	,	,		17323	0.1518		0.1352	False		,,,				2504	0.1534				p.L437L		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C1309T						PASS	.	C	,,	458,3948	219.1+/-236.9	27,404,1772	98.0	98.0	98.0		1309,1249,1309	1.1	0.3	22	dbSNP_86	98	1242,7358	249.9+/-277.0	90,1062,3148	no	coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	117,1466,4920	TT,TC,CC		14.4419,10.3949,13.0709	,,	437/1166,417/1166,437/1212	50555635	1700,11306	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon9			GATTTCCTAATTG	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1309C>T	22.37:g.50555635C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			C|0.869;T|0.131	0.131	strong		0.393	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
PCMTD1	115294	hgsc.bcm.edu	37	8	52733209	52733209	+	Missense_Mutation	SNP	A	A	G	rs202074278		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:52733209A>G	ENST00000360540.5	-	7	1182	c.776T>C	c.(775-777)aTa>aCa	p.I259T	PCMTD1_ENST00000544451.1_Missense_Mutation_p.I183T|PCMTD1_ENST00000522514.1_Missense_Mutation_p.I259T|PCMTD1_ENST00000519559.1_5'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	259						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)	p.I259T(1)		NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				CTCATCATTTATGAAATTTCT	0.403																																					p.I259T		Atlas-SNP	.											PCMTD1,NS,carcinoma,0,2	PCMTD1	73	2	1	Substitution - Missense(1)	prostate(1)	c.T776C						scavenged	.																																			SO:0001583	missense	115294	exon6			TCATTTATGAAAT		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.776T>C	8.37:g.52733209A>G	ENSP00000353739:p.Ile259Thr	Somatic	170	4	0.0235294		WXS	Illumina HiSeq	Phase_I	193	7	0.0362694	NM_052937	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.469272	0.43839	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.44881	0.91;0.91;0.91	5.77	5.77	0.91146	.	0.154593	0.64402	D	0.000017	T	0.43055	0.1230	L	0.34521	1.04	0.51482	D	0.999929	B;D;B	0.56287	0.01;0.975;0.009	B;P;B	0.48815	0.005;0.591;0.015	T	0.38628	-0.9652	10	0.59425	D	0.04	-40.7211	16.0858	0.81049	1.0:0.0:0.0:0.0	.	129;183;259	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	T	259;183;259	ENSP00000353739:I259T;ENSP00000444026:I183T;ENSP00000428099:I259T	ENSP00000353739:I259T	I	-	2	0	PCMTD1	52895762	1.000000	0.71417	0.991000	0.47740	0.990000	0.78478	6.577000	0.74027	2.198000	0.70561	0.533000	0.62120	ATA	.	.	weak		0.403	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
PDXDC1	23042	hgsc.bcm.edu	37	16	15111265	15111265	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15111265G>A	ENST00000396410.4	+	11	1046	c.949G>A	c.(949-951)Gat>Aat	p.D317N	PDXDC1_ENST00000325823.7_Missense_Mutation_p.D302N|PDXDC1_ENST00000447912.2_Missense_Mutation_p.D226N|RP11-680G24.5_ENST00000565178.1_RNA|PDXDC1_ENST00000535621.2_Missense_Mutation_p.D317N|PDXDC1_ENST00000450288.2_Missense_Mutation_p.D289N|PDXDC1_ENST00000455313.2_Missense_Mutation_p.D294N|PDXDC1_ENST00000563679.1_Missense_Mutation_p.D335N|PDXDC1_ENST00000569715.1_Missense_Mutation_p.D290N	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	317					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GTATAAACACGATGACCCTGC	0.502																																					p.D317N		Atlas-SNP	.											.	PDXDC1	59	.	0			c.G949A						PASS	.						112.0	114.0	113.0					16																	15111265		2197	4300	6497	SO:0001583	missense	23042	exon11			AAACACGATGACC	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.949G>A	16.37:g.15111265G>A	ENSP00000379691:p.Asp317Asn	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	147	34	0.231293	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.526001	0.85600	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000537781;ENST00000455313	T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0	5.45	5.45	0.79879	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.044008	0.85682	D	0.000000	T	0.26629	0.0651	L	0.36672	1.1	0.47374	D	0.999404	P;P;P;P;P;P	0.51240	0.88;0.943;0.94;0.88;0.88;0.625	B;P;P;B;B;B	0.49597	0.288;0.463;0.616;0.288;0.288;0.2	T	0.00827	-1.1550	10	0.23891	T	0.37	-11.8011	18.2726	0.90073	0.0:0.0:1.0:0.0	.	289;226;317;289;317;294	E7EPL4;E7EMH5;Q86XE2;B4DR55;Q6P996;Q6P996-2	.;.;.;.;PDXD1_HUMAN;.	N	302;226;317;317;289;23;294	ENSP00000322807:D302N;ENSP00000400310:D226N;ENSP00000437835:D317N;ENSP00000379691:D317N;ENSP00000391147:D289N;ENSP00000406703:D294N	ENSP00000322807:D302N	D	+	1	0	PDXDC1	15018766	1.000000	0.71417	0.619000	0.29118	0.845000	0.48019	8.666000	0.91149	2.546000	0.85860	0.542000	0.68232	GAT	.	.	none		0.502	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
LRRK1	79705	hgsc.bcm.edu	37	15	101567547	101567547	+	Silent	SNP	G	G	C	rs41319544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:101567547G>C	ENST00000388948.3	+	18	2846	c.2487G>C	c.(2485-2487)gtG>gtC	p.V829V	LRRK1_ENST00000284395.5_Silent_p.V826V	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGAAGGACGTGGGCAGCACCA	0.587													G|||	440	0.0878594	0.0938	0.0749	5008	,	,		20181	0.0278		0.1322	False		,,,				2504	0.1053				p.V829V		Atlas-SNP	.											.	LRRK1	310	.	0			c.G2487C						PASS	.	G		368,3670		14,340,1665	42.0	48.0	46.0		2487	-0.8	1.0	15	dbSNP_127	46	1236,7124		93,1050,3037	no	coding-synonymous	LRRK1	NM_024652.3		107,1390,4702	CC,CG,GG		14.7847,9.1134,12.9376		829/2016	101567547	1604,10794	2019	4180	6199	SO:0001819	synonymous_variant	79705	exon18			GGACGTGGGCAGC	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.2487G>C	15.37:g.101567547G>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			G|0.892;C|0.108	0.108	strong		0.587	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
ERAP1	51752	hgsc.bcm.edu	37	5	96129535	96129535	+	Missense_Mutation	SNP	T	T	C	rs2287987	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96129535T>C	ENST00000443439.2	-	6	1111	c.1045A>G	c.(1045-1047)Atg>Gtg	p.M349V	ERAP1_ENST00000296754.3_Missense_Mutation_p.M349V	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	349			M -> V (in dbSNP:rs2287987). {ECO:0000269|PubMed:11481040, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:9628581}.		angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		GCCACAGTCATTGTGATGCCA	0.398													T|||	526	0.105032	0.0658	0.1268	5008	,	,		18025	0.0575		0.2247	False		,,,				2504	0.0685				p.M349V		Atlas-SNP	.											.	ERAP1	59	.	0			c.A1045G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	462,3944	217.8+/-236.0	21,420,1762	62.0	56.0	58.0		1045,1045,1045	4.6	1.0	5	dbSNP_100	58	1822,6778	326.6+/-317.4	202,1418,2680	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	21,21,21	223,1838,4442	CC,CT,TT		21.186,10.4857,17.5611	benign,benign,benign	349/942,349/942,349/949	96129535	2284,10722	2203	4300	6503	SO:0001583	missense	51752	exon6			CAGTCATTGTGAT	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.1045A>G	5.37:g.96129535T>C	ENSP00000406304:p.Met349Val	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	248	105	0.423387	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	285	0.1304945054945055	27	0.054878048780487805	48	0.13259668508287292	40	0.06993006993006994	170	0.22427440633245382	T	10.79	1.450308	0.26074	0.104857	0.21186	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.02498	4.27;4.27	5.82	4.64	0.57946	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.125717	0.64402	D	0.000001	T	0.00012	0.0000	N	0.17872	0.535	0.28558	P	0.9112808	B;B;B	0.28208	0.002;0.157;0.203	B;B;B	0.33121	0.001;0.158;0.098	T	0.54990	-0.8210	9	0.23302	T	0.38	.	10.4738	0.44652	0.272:0.0:0.0:0.728	rs2287987;rs17404429;rs2287987	349;349;349	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	V	349	ENSP00000296754:M349V;ENSP00000406304:M349V	ENSP00000296754:M349V	M	-	1	0	ERAP1	96155291	0.989000	0.36119	0.998000	0.56505	0.827000	0.46813	2.125000	0.42016	1.010000	0.39314	0.533000	0.62120	ATG	T|0.857;C|0.143	0.143	strong		0.398	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
AEBP1	165	hgsc.bcm.edu	37	7	44153780	44153780	+	Missense_Mutation	SNP	A	A	G	rs13928	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:44153780A>G	ENST00000223357.3	+	21	3702	c.3397A>G	c.(3397-3399)Aaa>Gaa	p.K1133E	AEBP1_ENST00000450684.2_Missense_Mutation_p.K708E	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	1133	Glu-rich.|Interaction with MAPK1 and MAPK3. {ECO:0000250}.|Required for transcriptional repression. {ECO:0000250}.		K -> E (in dbSNP:rs13928). {ECO:0000269|Ref.3}.		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						ggaggaggagaaagaggagga	0.547													a|||	1846	0.36861	0.4062	0.4006	5008	,	,		15723	0.2629		0.4583	False		,,,				2504	0.3119				p.K1133E		Atlas-SNP	.											.	AEBP1	102	.	0			c.A3397G						PASS	.	G	GLU/LYS	1834,2572	635.8+/-396.5	389,1056,758	106.0	100.0	102.0		3397	3.7	0.0	7	dbSNP_52	102	4098,4502	590.8+/-392.7	948,2202,1150	yes	missense	AEBP1	NM_001129.3	56	1337,3258,1908	GG,GA,AA		47.6512,41.6251,45.6097	benign	1133/1159	44153780	5932,7074	2203	4300	6503	SO:0001583	missense	165	exon21			GAGGAGAAAGAGG	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.3397A>G	7.37:g.44153780A>G	ENSP00000223357:p.Lys1133Glu	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	CCDS5476.1	845	0.3869047619047619	191	0.3882113821138211	152	0.4198895027624309	155	0.270979020979021	347	0.4577836411609499	G	1.679	-0.506908	0.04231	0.416251	0.476512	ENSG00000106624	ENST00000223357;ENST00000450684	D;D	0.94138	-3.36;-2.79	3.7	3.7	0.42460	.	1818.460000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48581	-0.9023	9	0.02654	T	1	-0.0093	7.4085	0.27004	0.1234:0.0:0.8766:0.0	rs13928;rs3173775;rs11558047;rs56834340;rs13928	708;1133	Q8IUX7-2;Q8IUX7	.;AEBP1_HUMAN	E	1133;708	ENSP00000223357:K1133E;ENSP00000398878:K708E	ENSP00000223357:K1133E	K	+	1	0	AEBP1	44120305	0.689000	0.27690	0.003000	0.11579	0.002000	0.02628	1.342000	0.33919	0.921000	0.36994	-0.355000	0.07637	AAA	A|0.582;G|0.418	0.418	strong		0.547	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129	
DEFB104A	140596	hgsc.bcm.edu	37	8	7694034	7694034	+	Missense_Mutation	SNP	A	A	G	rs202183310		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:7694034A>G	ENST00000314265.2	+	1	42	c.28A>G	c.(28-30)Att>Gtt	p.I10V		NM_080389.2	NP_525128.2	Q8WTQ1	D104A_HUMAN	defensin, beta 104A	10			I -> V (in dbSNP:rs2680507). {ECO:0000269|PubMed:11481241, ECO:0000269|PubMed:15489334}.		defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.I10V(1)		liver(2)|pancreas(1)|skin(1)	4				COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)		GCTATTAGCCATTTCTCTTCT	0.502																																					p.I10V		Atlas-SNP	.											DEFB104A,NS,other,0,1	.	.	1	1	Substitution - Missense(1)	pancreas(1)	c.A28G						scavenged	.						10.0	11.0	11.0					8																	7694034		2052	4155	6207	SO:0001583	missense	503618	exon1			TTAGCCATTTCTC	AJ314835	CCDS34834.1	8p23.1	2011-03-29	2005-02-25	2005-02-25	ENSG00000176782	ENSG00000176782		"""Defensins, beta"""	18115	protein-coding gene	gene with protein product			"""defensin, beta 104"""	DEFB104			Standard	NM_080389		Approved	DEFB4, DEFB-4		Q8WTQ1	OTTHUMG00000150014	ENST00000314265.2:c.28A>G	8.37:g.7694034A>G	ENSP00000320813:p.Ile10Val	Somatic	1434	2	0.0013947		WXS	Illumina HiSeq	Phase_I	1679	421	0.250744	NM_001040702	Q496I2|Q496I3|Q496I4	Missense_Mutation	SNP	ENST00000314265.2	37	CCDS34834.1	621	0.28434065934065933	42	0.08536585365853659	128	0.35359116022099446	206	0.36013986013986016	245	0.3232189973614776	A	0.670	-0.802337	0.02841	.	.	ENSG00000176782	ENST00000314265	T	0.14144	2.53	1.69	-1.4	0.08968	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47761	-0.9092	5	0.32370	T	0.25	.	1.7865	0.03043	0.5325:0.0:0.1902:0.2773	.	.	.	.	V	10	ENSP00000320813:I10V	ENSP00000320813:I10V	I	+	1	0	DEFB104A	7731444	0.000000	0.05858	0.011000	0.14972	0.076000	0.17211	-0.448000	0.06820	-0.348000	0.08286	-0.641000	0.03968	ATT	A|0.250;G|0.750	0.750	weak		0.502	DEFB104A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315761.1	NM_080389	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798533	55798533	+	Silent	SNP	A	A	C	rs17528803	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55798533A>C	ENST00000313555.1	+	1	639	c.639A>C	c.(637-639)gtA>gtC	p.V213V		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					CTTTTGTGGTAATATTTATTT	0.443													C|||	192	0.0383387	0.0129	0.0403	5008	,	,		21012	0.001		0.0934	False		,,,				2504	0.0532				p.V213V		Atlas-SNP	.											OR5AS1,NS,carcinoma,0,1	OR5AS1	121	1	0			c.A639C						PASS	.	C		110,4292	816.2+/-416.2	3,104,2094	239.0	235.0	236.0		639	2.0	0.1	11	dbSNP_123	236	692,7900	787.9+/-407.6	34,624,3638	no	coding-synonymous	OR5AS1	NM_001001921.1		37,728,5732	CC,CA,AA		8.054,2.4989,6.1721		213/325	55798533	802,12192	2201	4296	6497	SO:0001819	synonymous_variant	219447	exon1			TGTGGTAATATTT	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.639A>C	11.37:g.55798533A>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	288	136	0.472222	NM_001001921	Q6IFB8	Silent	SNP	ENST00000313555.1	37	CCDS31516.1																																																																																			A|0.948;C|0.052	0.052	strong		0.443	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
CTSF	8722	hgsc.bcm.edu	37	11	66335548	66335548	+	Silent	SNP	A	A	G	rs1127894	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:66335548A>G	ENST00000310325.5	-	2	328	c.219T>C	c.(217-219)ggT>ggC	p.G73G	CTSF_ENST00000533168.1_5'Flank	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F	73					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)			endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GCGACCCCTGACCCGCCTGGA	0.682													G|||	2918	0.582668	0.8767	0.415	5008	,	,		10960	0.5407		0.5378	False		,,,				2504	0.3937				p.G73G		Atlas-SNP	.											CTSF,rectum,carcinoma,0,5	CTSF	42	5	0			c.T219C						scavenged	.						14.0	23.0	20.0					11																	66335548		2196	4292	6488	SO:0001819	synonymous_variant	8722	exon2			CCCCTGACCCGCC	AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"""Cathepsins"""	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090	ENST00000310325.5:c.219T>C	11.37:g.66335548A>G		Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_003793	B2R964|O95240|Q9NSU4|Q9UKQ5	Silent	SNP	ENST00000310325.5	37	CCDS8144.1																																																																																			A|0.416;G|0.584	0.584	strong		0.682	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793	
FUT5	2527	hgsc.bcm.edu	37	19	5867177	5867177	+	Missense_Mutation	SNP	G	G	A	rs778970	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:5867177G>A	ENST00000588525.1	-	2	647	c.560C>T	c.(559-561)cCg>cTg	p.P187L	FUT5_ENST00000252675.5_Missense_Mutation_p.P187L	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	187			P -> L (in dbSNP:rs778970).		carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						GCCGGACCACGGCTCCAGCCA	0.662													G|||	2238	0.446885	0.2905	0.5706	5008	,	,		12307	0.5863		0.4563	False		,,,				2504	0.4172				p.P187L		Atlas-SNP	.											.	FUT5	29	.	0			c.C560T						PASS	.						17.0	16.0	17.0					19																	5867177		2162	4222	6384	SO:0001583	missense	2527	exon2			GACCACGGCTCCA		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"""Fucosyltransferases"""	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.560C>T	19.37:g.5867177G>A	ENSP00000466880:p.Pro187Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	148	65	0.439189	NM_002034	A8K4X2	Missense_Mutation	SNP	ENST00000588525.1	37	CCDS12154.1	1034	0.4734432234432234	139	0.28252032520325204	202	0.5580110497237569	357	0.6241258741258742	336	0.44327176781002636	G	9.702	1.154871	0.21371	.	.	ENSG00000130383	ENST00000252675	T	0.24908	1.83	2.34	1.25	0.21368	.	0.240689	0.29335	U	0.012460	T	0.00012	0.0000	M	0.77486	2.375	0.48762	P	2.950000000000452E-4	P	0.46621	0.881	P	0.45794	0.493	T	0.43081	-0.9413	9	0.22706	T	0.39	.	2.534	0.04710	0.1847:0.0:0.5298:0.2854	rs778970;rs3745634;rs3854697;rs57372090	187	Q11128	FUT5_HUMAN	L	187	ENSP00000252675:P187L	ENSP00000252675:P187L	P	-	2	0	FUT5	5818177	0.056000	0.20664	0.579000	0.28588	0.136000	0.21042	0.493000	0.22451	0.275000	0.22094	0.407000	0.27541	CCG	A|1.000;|0.000	1.000	weak		0.662	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034	
EIF5B	9669	hgsc.bcm.edu	37	2	99995804	99995804	+	Silent	SNP	T	T	C	rs1376443	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:99995804T>C	ENST00000289371.6	+	12	2176	c.1974T>C	c.(1972-1974)gaT>gaC	p.D658D		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	658	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATGTACAAGATGGTGAAGCAG	0.363													C|||	3024	0.603834	0.7602	0.7104	5008	,	,		17893	0.3681		0.5865	False		,,,				2504	0.5777				p.D658D	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											.	EIF5B	95	.	0			c.T1974C						PASS	.	C		2839,941		1071,697,122	90.0	83.0	85.0		1974	2.0	1.0	2	dbSNP_88	85	4694,3514		1343,2008,753	no	coding-synonymous	EIF5B	NM_015904.3		2414,2705,875	CC,CT,TT		42.8119,24.8942,37.1622		658/1221	99995804	7533,4455	1890	4104	5994	SO:0001819	synonymous_variant	9669	exon12			ACAAGATGGTGAA	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"""translation initiation factor IF2"""	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.1974T>C	2.37:g.99995804T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	193	193	1	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	37	CCDS42721.1																																																																																			T|0.415;C|0.585	0.585	strong		0.363	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904	
MLLT10	8028	hgsc.bcm.edu	37	10	21827796	21827796	+	Silent	SNP	G	G	A	rs1802669	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:21827796G>A	ENST00000307729.7	+	3	373	c.195G>A	c.(193-195)ccG>ccA	p.P65P	MLLT10_ENST00000377100.3_Silent_p.P65P|MLLT10_ENST00000377059.3_Silent_p.P65P|MLLT10_ENST00000495130.1_3'UTR|MLLT10_ENST00000446906.2_Silent_p.P65P|MLLT10_ENST00000377091.2_Silent_p.P65P|MLLT10_ENST00000377072.3_Silent_p.P65P			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	65					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						CCACTGGACCGTGGTTTTGCA	0.368			T	"""MLL, PICALM, CDK6"""	AL								A|||	1389	0.277356	0.4327	0.2277	5008	,	,		19521	0.0546		0.3579	False		,,,				2504	0.2495				p.P65P		Atlas-SNP	.		Dom	yes		10	10p12	8028	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"""		L	.	MLLT10	183	.	0			c.G195A						PASS	.	A	,,,,	1741,2665	648.1+/-398.7	366,1009,828	108.0	104.0	105.0		195,195,195,195,195	0.2	1.0	10	dbSNP_89	105	3025,5575	663.6+/-402.1	527,1971,1802	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MLLT10	NM_001195626.1,NM_001195627.1,NM_001195628.1,NM_001195630.1,NM_004641.3	,,,,	893,2980,2630	AA,AG,GG		35.1744,39.5143,36.6446	,,,,	65/1069,65/127,65/180,65/180,65/1028	21827796	4766,8240	2203	4300	6503	SO:0001819	synonymous_variant	8028	exon2			TGGACCGTGGTTT	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"""Zinc fingers, PHD-type"""	16063	protein-coding gene	gene with protein product		602409	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"""			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.195G>A	10.37:g.21827796G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	89	53	0.595506	NM_001195626	B1ANA8|Q5JT37|Q5VX90|Q66K63	Silent	SNP	ENST00000307729.7	37	CCDS55708.1	604	0.2765567765567766	227	0.4613821138211382	92	0.2541436464088398	16	0.027972027972027972	269	0.3548812664907652	A	9.769	1.172082	0.21704	0.395143	0.351744	ENSG00000078403	ENST00000430455	.	.	.	5.64	0.171	0.15026	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46091	-0.9216	3	.	.	.	.	0.7844	0.01046	0.2486:0.194:0.3192:0.2382	rs1802669;rs57900300	.	.	.	M	31	.	.	V	+	1	0	MLLT10	21867802	0.224000	0.23674	0.997000	0.53966	0.986000	0.74619	-0.310000	0.08135	-0.145000	0.11294	-1.087000	0.02190	GTG	A|0.343;G|0.657;T|0.000	0.343	strong		0.368	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1		
IL4R	3566	hgsc.bcm.edu	37	16	27373915	27373915	+	Silent	SNP	G	G	T	rs2234898	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:27373915G>T	ENST00000395762.2	+	11	1501	c.1242G>T	c.(1240-1242)ctG>ctT	p.L414L	IL4R_ENST00000380922.3_Silent_p.L399L|IL4R_ENST00000543915.2_Silent_p.L414L|IL4R_ENST00000170630.2_Silent_p.L414L	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	414					defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)	p.L414L(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						TCCTGGACCTGCTCGGAGAGG	0.592													G|||	1180	0.235623	0.6225	0.1599	5008	,	,		20234	0.0774		0.1064	False		,,,				2504	0.0624				p.L414L		Atlas-SNP	.											IL4R,NS,carcinoma,0,1	IL4R	70	1	1	Substitution - coding silent(1)	stomach(1)	c.G1242T						scavenged	.	G		2304,2090	601.6+/-389.7	600,1104,493	67.0	69.0	69.0		1242	-0.4	0.4	16	dbSNP_98	69	956,7644	208.2+/-249.7	59,838,3403	no	coding-synonymous	IL4R	NM_000418.2		659,1942,3896	TT,TG,GG		11.1163,47.5649,25.0885		414/826	27373915	3260,9734	2197	4300	6497	SO:0001819	synonymous_variant	3566	exon11			GGACCTGCTCGGA	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1242G>T	16.37:g.27373915G>T		Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Silent	SNP	ENST00000395762.2	37	CCDS10629.1																																																																																			G|0.756;T|0.244	0.244	strong		0.592	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
HLA-C	3107	hgsc.bcm.edu	37	6	31238010	31238010	+	Missense_Mutation	SNP	T	T	G	rs1131015	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238010T>G	ENST00000376228.5	-	4	886	c.872A>C	c.(871-873)cAa>cCa	p.Q291P	HLA-C_ENST00000383329.3_Missense_Mutation_p.Q291P	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	291	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GAGGGGCTCTTGCAGCCCCTC	0.587													g|||	3612	0.721246	0.6891	0.7723	5008	,	,		13143	0.7758		0.6909	False		,,,				2504	0.7035				p.Q291P		Atlas-SNP	.											HLA-C_ENST00000383329,colon,carcinoma,+1,2	HLA-C	92	2	0			c.A872C						PASS	.						23.0	30.0	28.0					6																	31238010		2131	4204	6335	SO:0001583	missense	3107	exon4			GGCTCTTGCAGCC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.872A>C	6.37:g.31238010T>G	ENSP00000365402:p.Gln291Pro	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1245|1245	0.570054945054945|0.570054945054945	247|247	0.5020325203252033|0.5020325203252033	233|233	0.643646408839779|0.643646408839779	365|365	0.6381118881118881|0.6381118881118881	400|400	0.5277044854881267|0.5277044854881267	.|.	0.011|0.011	-1.716298|-1.716298	0.00706|0.00706	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.02787	.|4.16;4.16	2.67|2.67	-1.54|-1.54	0.08584|0.08584	.|Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	.|0.909660	.|0.08985	.|N	.|0.865274	T|T	0.00300|0.00300	0.0009|0.0009	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.01281	.|0.0;0.0;0.0;0.0	T|T	0.44205|0.44205	-0.9343|-0.9343	3|8	.|0.02654	.|T	.|1	.|.	3.57|3.57	0.07913|0.07913	0.2392:0.0:0.4421:0.3187|0.2392:0.0:0.4421:0.3187	rs2308624;rs2308625;rs9264631|rs2308624;rs2308625;rs9264631	.|291;291;291;291	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	Q|P	255|291;291;291;328	.|ENSP00000365402:Q291P;ENSP00000372819:Q291P	.|ENSP00000365402:Q291P	K|Q	-|-	1|2	0|0	HLA-C|HLA-C	31345989|31345989	0.015000|0.015000	0.18098|0.18098	0.113000|0.113000	0.21522|0.21522	0.012000|0.012000	0.07955|0.07955	0.038000|0.038000	0.13862|0.13862	-0.793000|-0.793000	0.04475|0.04475	-2.419000|-2.419000	0.00218|0.00218	AAG|CAA	T|0.429;G|0.571	0.571	strong		0.587	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
UGT1A1	54658	hgsc.bcm.edu	37	2	234526871	234526871	+	Missense_Mutation	SNP	C	C	G	rs1042597	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:234526871C>G	ENST00000373450.4	+	1	581	c.518C>G	c.(517-519)gCt>gGt	p.A173G		NM_019076.4	NP_061949.3	P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	176					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	AGGGGAATAGCTTGCCACTAT	0.473													-|||	1282	0.25599	0.0325	0.2954	5008	,	,		17737	0.506		0.2495	False		,,,				2504	0.2791				p.A173G		Atlas-SNP	.											.	UGT1A8	69	.	0			c.C518G						PASS	.	C	GLY/ALA	345,4061	178.0+/-206.8	12,321,1870	182.0	183.0	183.0		518	-0.2	0.0	2	dbSNP_86	183	2127,6473	367.0+/-334.5	269,1589,2442	no	missense	UGT1A8	NM_019076.4	60	281,1910,4312	GG,GC,CC		24.7326,7.8302,19.0066		173/531	234526871	2472,10534	2203	4300	6503	SO:0001583	missense	54576	exon1			GAATAGCTTGCCA	M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"""UDP glucuronosyltransferases"""	12530	other	complex locus constituent		191740	"""UDP glycosyltransferase 1 family, polypeptide A1"""	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	ENST00000373450.4:c.518C>G	2.37:g.234526871C>G	ENSP00000362549:p.Ala173Gly	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	192	85	0.442708	NM_019076	A6NJC3|B8K286	Missense_Mutation	SNP	ENST00000373450.4	37	CCDS33402.1	625	0.28617216117216115	23	0.046747967479674794	110	0.30386740331491713	292	0.5104895104895105	200	0.2638522427440633	C	2.320	-0.355915	0.05138	0.078302	0.247326	ENSG00000242366	ENST00000373450	T	0.66460	-0.21	3.96	-0.18	0.13295	.	.	.	.	.	T	0.00012	0.0000	N	0.04373	-0.215	0.80722	P	0.0	B;B	0.20368	0.044;0.044	B;B	0.30495	0.116;0.116	T	0.45234	-0.9275	8	0.51188	T	0.08	.	6.5183	0.22260	0.0:0.4965:0.1616:0.3419	rs1042597;rs2071043;rs13387262;rs17862843;rs56696602	173;173	Q5DSZ6;Q9HAW9	.;UD18_HUMAN	G	173	ENSP00000362549:A173G	ENSP00000362549:A173G	A	+	2	0	UGT1A8	234191610	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.056000	0.14256	-0.052000	0.13311	-1.422000	0.01108	GCT	C|0.755;G|0.245	0.245	strong		0.473	UGT1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130994.1		
SYTL2	54843	hgsc.bcm.edu	37	11	85447611	85447611	+	Silent	SNP	T	T	C	rs680498	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:85447611T>C	ENST00000528231.1	-	5	793	c.516A>G	c.(514-516)tcA>tcG	p.S172S	SYTL2_ENST00000316356.4_Silent_p.S173S|SYTL2_ENST00000527523.1_Silent_p.S124S|SYTL2_ENST00000524452.1_Silent_p.S172S|SYTL2_ENST00000389960.4_Silent_p.S172S	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	172					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TTTGTTGTGATGAGTGACCTT	0.313													C|||	3275	0.653954	0.823	0.5677	5008	,	,		16958	0.6171		0.6551	False		,,,				2504	0.5235				p.S173S		Atlas-SNP	.											SYTL2_ENST00000316356,bladder,carcinoma,-1,1	SYTL2	231	1	0			c.A519G						PASS	.	C	,,	3463,943	356.9+/-313.7	1363,737,103	128.0	126.0	127.0		516,519,516	2.2	0.3	11	dbSNP_83	127	5655,2941	456.2+/-364.0	1884,1887,527	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3	,,	3247,2624,630	CC,CT,TT		34.2136,21.4026,29.8723	,,	172/935,173/936,172/911	85447611	9118,3884	2203	4298	6501	SO:0001819	synonymous_variant	54843	exon5			TTGTGATGAGTGA	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.516A>G	11.37:g.85447611T>C		Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001162953	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			C|0.687;T|0.313	0.687	strong		0.313	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
HELZ2	85441	hgsc.bcm.edu	37	20	62191558	62191558	+	Silent	SNP	G	G	A	rs3810479	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62191558G>A	ENST00000467148.1	-	17	7692	c.7623C>T	c.(7621-7623)gcC>gcT	p.A2541A	HELZ2_ENST00000427522.2_Silent_p.A1972A	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2541	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CGGCCACCCCGGCGATGCCCT	0.716													g|||	786	0.156949	0.0083	0.0821	5008	,	,		12764	0.3433		0.16	False		,,,				2504	0.2157				p.A2541A		Atlas-SNP	.											.	.	.	.	0			c.C7623T						PASS	.	A	,	161,4179		4,153,2013	24.0	19.0	21.0		7623,5916	-7.9	0.0	20	dbSNP_107	21	1308,7220		111,1086,3067	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	115,1239,5080	AA,AG,GG		15.3377,3.7097,11.4159	,	2541/2650,1972/2081	62191558	1469,11399	2170	4264	6434	SO:0001819	synonymous_variant	85441	exon18			CACCCCGGCGATG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.7623C>T	20.37:g.62191558G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	16	0.390244	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			G|0.863;A|0.137	0.137	strong		0.716	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
CCDC9	26093	hgsc.bcm.edu	37	19	47774772	47774772	+	Missense_Mutation	SNP	T	T	C	rs888836	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:47774772T>C	ENST00000221922.6	+	12	1655	c.1433T>C	c.(1432-1434)cTg>cCg	p.L478P		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	478			L -> P (in dbSNP:rs888836).				poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		GAGCCCCTGCTGGAGCCCCAG	0.677													C|||	2564	0.511981	0.3396	0.5836	5008	,	,		12240	0.6825		0.4304	False		,,,				2504	0.6022				p.L478P		Atlas-SNP	.											.	CCDC9	37	.	0			c.T1433C						PASS	.	C	PRO/LEU	1400,3006		234,932,1037	49.0	59.0	56.0		1433	0.7	0.0	19	dbSNP_86	56	3759,4841		834,2091,1375	no	missense	CCDC9	NM_015603.2	98	1068,3023,2412	CC,CT,TT		43.7093,31.7749,39.6663	benign	478/532	47774772	5159,7847	2203	4300	6503	SO:0001583	missense	26093	exon12			CCCTGCTGGAGCC	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1433T>C	19.37:g.47774772T>C	ENSP00000221922:p.Leu478Pro	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	NM_015603		Missense_Mutation	SNP	ENST00000221922.6	37	CCDS12698.1	1106	0.5064102564102564	190	0.3861788617886179	200	0.5524861878453039	374	0.6538461538461539	342	0.45118733509234826	.	2.454	-0.325757	0.05350	0.317749	0.437093	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.22134	1.97	3.14	0.712	0.18167	.	0.524747	0.16680	N	0.203984	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30238	-0.9985	9	0.10902	T	0.67	-0.2533	2.6765	0.05082	0.3097:0.4044:0.0:0.2859	rs888836;rs58257475;rs888836	478	Q9Y3X0	CCDC9_HUMAN	P	478;460	ENSP00000221922:L478P	ENSP00000221922:L478P	L	+	2	0	CCDC9	52466612	0.000000	0.05858	0.004000	0.12327	0.118000	0.20060	-0.293000	0.08320	0.087000	0.17167	-0.817000	0.03123	CTG	T|0.563;C|0.437	0.437	strong		0.677	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
BRCA1	672	hgsc.bcm.edu	37	17	41245237	41245237	+	Silent	SNP	A	A	G	rs397508955|rs16940	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:41245237A>G	ENST00000357654.3	-	10	2429	c.2311T>C	c.(2311-2313)Ttg>Ctg	p.L771L	BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Silent_p.L771L|BRCA1_ENST00000471181.2_Silent_p.L771L|BRCA1_ENST00000309486.4_Silent_p.L475L|BRCA1_ENST00000354071.3_Silent_p.L771L|BRCA1_ENST00000493795.1_Silent_p.L724L|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	771					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CCAGGTACCAATGAAATACTG	0.393			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			A|||	1679	0.335264	0.1573	0.3674	5008	,	,		21318	0.371		0.3529	False		,,,				2504	0.498				p.L771L		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.T2311C	GRCh37	CI004175|CI063645	BRCA1	I	rs16940	PASS	.	A	,,,,	827,3579	327.5+/-300.1	75,677,1451	203.0	188.0	193.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2311,2170,,,2311	-2.8	0.0	17	dbSNP_60	193	2784,5816	442.1+/-360.0	442,1900,1958	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	,,,,	517,2577,3409	GG,GA,AA		32.3721,18.7699,27.7641	,,,,	771/1864,724/1817,,,771/1885	41245237	3611,9395	2203	4300	6503	SO:0001819	synonymous_variant	672	exon10	Familial Cancer Database		GTACCAATGAAAT	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.2311T>C	17.37:g.41245237A>G		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	232	113	0.487069	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	37	CCDS11453.1																																																																																			A|0.716;G|0.284	0.284	strong		0.393	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
TPSD1	23430	hgsc.bcm.edu	37	16	1306986	1306986	+	Missense_Mutation	SNP	C	C	T	rs72775467		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306986C>T	ENST00000211076.3	+	3	591	c.443C>T	c.(442-444)aCg>aTg	p.T148M	TPSD1_ENST00000397534.2_Missense_Mutation_p.T141M|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	148	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CACACGGTCACGCTGCCCCCT	0.652																																					p.T148M		Atlas-SNP	.											TPSD1,NS,NS,0,1	TPSD1	47	1	0			c.C443T						PASS	.						46.0	44.0	45.0					16																	1306986		2198	4299	6497	SO:0001583	missense	23430	exon3			CGGTCACGCTGCC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.443C>T	16.37:g.1306986C>T	ENSP00000211076:p.Thr148Met	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	427	80	0.187354	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	772	0.3534798534798535	141	0.2865853658536585	112	0.30939226519337015	251	0.4388111888111888	268	0.35356200527704484	c	4.148	0.025917	0.08054	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.81659	-1.52;-1.52	2.55	1.57	0.23409	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.879151	0.09575	N	0.783735	T	0.00012	0.0000	L	0.49126	1.545	0.52501	P	4.099999999995774E-5	P;P	0.39250	0.468;0.665	B;B	0.32342	0.144;0.144	T	0.17899	-1.0354	9	0.52906	T	0.07	.	3.811	0.08796	0.0:0.5891:0.2553:0.1556	.	132;148	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	M	141;148	ENSP00000380668:T141M;ENSP00000211076:T148M	ENSP00000211076:T148M	T	+	2	0	TPSD1	1246987	0.000000	0.05858	0.004000	0.12327	0.060000	0.15804	0.429000	0.21412	0.384000	0.24942	0.185000	0.17295	ACG	C|0.646;T|0.354	0.354	strong		0.652	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
ERAP2	64167	hgsc.bcm.edu	37	5	96231000	96231000	+	Missense_Mutation	SNP	G	G	T	rs2549782	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96231000G>T	ENST00000437043.3	+	7	1887	c.1176G>T	c.(1174-1176)aaG>aaT	p.K392N	CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000515095.1_3'UTR|ERAP2_ENST00000379904.4_Missense_Mutation_p.K347N	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	392			K -> N (in dbSNP:rs2549782). {ECO:0000269|PubMed:12799365, ECO:0000269|PubMed:15691326}.		antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		TTTGGCTTAAGGAGGGTTTTG	0.338													T|||	2768	0.552716	0.6014	0.5793	5008	,	,		17747	0.5278		0.5199	False		,,,				2504	0.5276				p.K392N		Atlas-SNP	.											.	ERAP2	77	.	0			c.G1176T						PASS	.	T	ASN/LYS,ASN/LYS	2555,1851	538.1+/-374.9	724,1107,372	160.0	157.0	158.0		1176,1176	0.7	0.9	5	dbSNP_100	158	4481,4119	563.9+/-388.2	1151,2179,970	yes	missense,missense	ERAP2	NM_001130140.1,NM_022350.3	94,94	1875,3286,1342	TT,TG,GG		47.8953,42.0109,45.9019	benign,benign	392/961,392/961	96231000	7036,5970	2203	4300	6503	SO:0001583	missense	64167	exon7			GCTTAAGGAGGGT	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1176G>T	5.37:g.96231000G>T	ENSP00000400376:p.Lys392Asn	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	37	CCDS4086.1	1211|1211	0.5544871794871795|0.5544871794871795	272|272	0.5528455284552846|0.5528455284552846	212|212	0.585635359116022|0.585635359116022	331|331	0.5786713286713286|0.5786713286713286	396|396	0.5224274406332454|0.5224274406332454	T|T	0.707|0.707	-0.788574|-0.788574	0.02884|0.02884	0.579891|0.579891	0.521047|0.521047	ENSG00000164308|ENSG00000164308	ENST00000508077|ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904	.|T;T;T;T	.|0.01430	.|4.9;4.9;4.9;4.9	4.74|4.74	0.68|0.68	0.17980|0.17980	.|Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	.|0.137856	.|0.46145	.|N	.|0.000315	.|T	.|0.00012	.|0.0000	N|N	0.00057|0.00057	-2.355|-2.355	0.09310|0.09310	P|P	1.0|1.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	.|T	.|0.15694	.|-1.0428	.|9	.|0.02654	.|T	.|1	.|.	3.4516|3.4516	0.07501|0.07501	0.1238:0.072:0.2577:0.5466|0.1238:0.072:0.2577:0.5466	rs2549782;rs3734014;rs17407451;rs52790432;rs57875026;rs2549782|rs2549782;rs3734014;rs17407451;rs52790432;rs57875026;rs2549782	.|347;392	.|Q6P179-3;Q6P179	.|.;ERAP2_HUMAN	X|N	99|392;392;392;347	.|ENSP00000400376:K392N;ENSP00000421175:K392N;ENSP00000421849:K392N;ENSP00000369235:K347N	.|ENSP00000369235:K347N	G|K	+|+	1|3	0|2	ERAP2|ERAP2	96256756|96256756	0.999000|0.999000	0.42202|0.42202	0.938000|0.938000	0.37757|0.37757	0.675000|0.675000	0.39556|0.39556	0.405000|0.405000	0.21015|0.21015	-0.325000|-0.325000	0.08577|0.08577	-1.735000|-1.735000	0.00691|0.00691	GGA|AAG	G|0.452;N|0.000	.	strong		0.338	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
OR1S1	219959	hgsc.bcm.edu	37	11	57982832	57982832	+	Missense_Mutation	SNP	T	T	A	rs2867400	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57982832T>A	ENST00000309433.6	+	1	616	c.616T>A	c.(616-618)Ttg>Atg	p.L206M		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	206			L -> M (in dbSNP:rs2867400).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L206M(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTCAGATACATTGATCAATGA	0.438													t|||	2629	0.52496	0.2829	0.5403	5008	,	,		19594	0.8046		0.4225	False		,,,				2504	0.6585				p.L206M		Atlas-SNP	.											OR1S1,NS,carcinoma,0,1	OR1S1	139	1	1	Substitution - Missense(1)	stomach(1)	c.T616A						scavenged	.						179.0	140.0	153.0					11																	57982832		2201	4294	6495	SO:0001583	missense	219959	exon1			GATACATTGATCA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.616T>A	11.37:g.57982832T>A	ENSP00000311688:p.Leu206Met	Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	172	56	0.325581	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	980	0.44871794871794873	120	0.24390243902439024	175	0.48342541436464087	413	0.722027972027972	272	0.35883905013192613	T	0.120	-1.126825	0.01770	.	.	ENSG00000172774	ENST00000309433	T	0.00115	8.71	3.23	0.689	0.18033	GPCR, rhodopsin-like superfamily (1);	1.756970	0.02885	N	0.133431	T	0.00012	0.0000	L	0.56280	1.765	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23583	-1.0184	9	0.49607	T	0.09	.	1.1022	0.01686	0.3279:0.1471:0.1014:0.4237	rs2867400;rs2867400	206	Q8NH92	OR1S1_HUMAN	M	206	ENSP00000311688:L206M	ENSP00000311688:L206M	L	+	1	2	OR1S1	57739408	0.000000	0.05858	0.005000	0.12908	0.171000	0.22731	-1.315000	0.02713	0.339000	0.23719	-0.562000	0.04174	TTG	T|0.703;A|0.297	0.297	strong		0.438	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
WSCD1	23302	hgsc.bcm.edu	37	17	5984001	5984001	+	Missense_Mutation	SNP	T	T	C	rs199969111	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:5984001T>C	ENST00000574946.1	+	2	413	c.23T>C	c.(22-24)cTc>cCc	p.L8P	WSCD1_ENST00000574232.1_Missense_Mutation_p.L8P|WSCD1_ENST00000317744.5_Missense_Mutation_p.L8P|WSCD1_ENST00000573634.1_Intron|WSCD1_ENST00000539421.1_Missense_Mutation_p.L8P			Q658N2	WSCD1_HUMAN	WSC domain containing 1	8						integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						TTCTTCCGACTCCAGAAGTTT	0.662													T|||	10	0.00199681	0.0	0.0	5008	,	,		16288	0.0		0.002	False		,,,				2504	0.0082				p.L8P		Atlas-SNP	.											.	WSCD1	84	.	0			c.T23C						PASS	.	T	PRO/LEU	0,4242		0,0,2121	42.0	41.0	41.0		23	5.1	1.0	17		41	6,8158		0,6,4076	yes	missense	WSCD1	NM_015253.1	98	0,6,6197	CC,CT,TT		0.0735,0.0,0.0484	probably-damaging	8/576	5984001	6,12400	2121	4082	6203	SO:0001583	missense	23302	exon2			TCCGACTCCAGAA		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.23T>C	17.37:g.5984001T>C	ENSP00000460825:p.Leu8Pro	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	186	93	0.5	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Missense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.064321	0.55432	0.0	7.35E-4	ENSG00000179314	ENST00000317744;ENST00000539421	D;D	0.83163	-1.69;-1.69	5.07	5.07	0.68467	.	0.088957	0.46145	D	0.000303	D	0.86665	0.5987	L	0.39898	1.24	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.87073	0.2161	10	0.52906	T	0.07	-33.0853	12.7983	0.57571	0.0:0.0:0.0:1.0	.	8	Q658N2	WSCD1_HUMAN	P	8	ENSP00000323087:L8P;ENSP00000446032:L8P	ENSP00000323087:L8P	L	+	2	0	WSCD1	5924725	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.853000	0.62911	1.904000	0.55121	0.455000	0.32223	CTC	T|0.999;C|0.001	0.001	weak		0.662	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253	
PGM2	55276	hgsc.bcm.edu	37	4	37857342	37857342	+	Silent	SNP	G	G	C	rs11554509	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:37857342G>C	ENST00000381967.4	+	13	1816	c.1716G>C	c.(1714-1716)ctG>ctC	p.L572L	PGM2_ENST00000537241.1_Silent_p.L412L	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	572					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						ATGCAGAGCTGTGTGCCCCAC	0.493													G|||	862	0.172125	0.323	0.1167	5008	,	,		16436	0.1091		0.1471	False		,,,				2504	0.0982				p.L572L		Atlas-SNP	.											.	PGM2	45	.	0			c.G1716C						PASS	.	G		1271,3135	434.9+/-344.1	192,887,1124	98.0	90.0	93.0		1716	3.0	1.0	4	dbSNP_120	93	1189,7411	241.8+/-272.0	92,1005,3203	no	coding-synonymous	PGM2	NM_018290.3		284,1892,4327	CC,CG,GG		13.8256,28.847,18.9143		572/613	37857342	2460,10546	2203	4300	6503	SO:0001819	synonymous_variant	55276	exon13			AGAGCTGTGTGCC	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"""phosphopentomutase"""	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.1716G>C	4.37:g.37857342G>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	148	72	0.486486	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Silent	SNP	ENST00000381967.4	37	CCDS3443.1																																																																																			G|0.826;C|0.174	0.174	strong		0.493	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290	
MICAL3	57553	hgsc.bcm.edu	37	22	18300594	18300594	+	Silent	SNP	G	G	A	rs11704160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:18300594G>A	ENST00000441493.2	-	26	5185	c.4833C>T	c.(4831-4833)gaC>gaT	p.D1611D	MICAL3_ENST00000580469.1_5'Flank	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1611					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		TGGCCATGGCGTCCCGCAGCG	0.692													G|||	757	0.151158	0.028	0.1859	5008	,	,		13343	0.0863		0.3171	False		,,,				2504	0.1892				p.D1611D		Atlas-SNP	.											.	MICAL3	53	.	0			c.C4833T						PASS	.	G		293,3825		10,273,1776	12.0	16.0	15.0		4833	-9.8	0.1	22	dbSNP_120	15	2774,5666		461,1852,1907	no	coding-synonymous	MICAL3	NM_015241.2		471,2125,3683	AA,AG,GG		32.8673,7.1151,24.4227		1611/2003	18300594	3067,9491	2059	4220	6279	SO:0001819	synonymous_variant	57553	exon26			CATGGCGTCCCGC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.4833C>T	22.37:g.18300594G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1	366	0.16758241758241757	18	0.036585365853658534	74	0.20441988950276244	46	0.08041958041958042	228	0.3007915567282322	G	7.269	0.606705	0.14002	0.071151	0.328673	ENSG00000093100	ENST00000252134	.	.	.	4.9	-9.8	0.00490	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999825	.	.	.	.	.	.	T	0.45527	-0.9255	3	.	.	.	.	21.8178	0.99961	0.2591:0.0:0.7409:0.0	rs11704160;rs17339575	.	.	.	M	593	.	.	T	-	2	0	XXbac-B461K10.4	16680594	0.005000	0.15991	0.080000	0.20451	0.955000	0.61496	-1.313000	0.02718	-2.868000	0.00324	-1.069000	0.02264	ACG	G|0.811;A|0.189	0.189	strong		0.692	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
TRPC3	7222	hgsc.bcm.edu	37	4	122854116	122854116	+	Silent	SNP	G	G	C	rs13121031	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:122854116G>C	ENST00000379645.3	-	2	370	c.297C>G	c.(295-297)gcC>gcG	p.A99A	TRPC3_ENST00000513531.1_Silent_p.A26A|TRPC3_ENST00000264811.5_Silent_p.A26A	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	14					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						TGAACATGAAGGCCGGGCCCC	0.637													G|||	209	0.0417332	0.0045	0.0562	5008	,	,		16913	0.0		0.1133	False		,,,				2504	0.0511				p.A99A		Atlas-SNP	.											.	TRPC3	201	.	0			c.C297G						PASS	.	G	,	89,4317		0,89,2114	29.0	31.0	31.0		297,78	-1.0	1.0	4	dbSNP_121	31	852,7746		49,754,3496	no	coding-synonymous,coding-synonymous	TRPC3	NM_001130698.1,NM_003305.2	,	49,843,5610	CC,CG,GG		9.9093,2.02,7.2362	,	99/922,26/849	122854116	941,12063	2203	4299	6502	SO:0001819	synonymous_variant	7222	exon2			CATGAAGGCCGGG	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.297C>G	4.37:g.122854116G>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	ENST00000379645.3	37	CCDS47130.1																																																																																			G|0.932;C|0.068	0.068	strong		0.637	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305	
HCN4	10021	hgsc.bcm.edu	37	15	73660505	73660505	+	Missense_Mutation	SNP	C	C	T	rs143090627	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:73660505C>T	ENST00000261917.3	-	1	1100	c.107G>A	c.(106-108)gGg>gAg	p.G36E		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	36					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GCCCCCGGCCCCCTCCTCCTC	0.746													C|||	125	0.0249601	0.0068	0.0447	5008	,	,		7263	0.0		0.0696	False		,,,				2504	0.0153				p.G36E		Atlas-SNP	.											.	HCN4	150	.	0			c.G107A						PASS	.	C	GLU/GLY	27,3487		0,27,1730	3.0	4.0	3.0		107	2.0	0.5	15	dbSNP_134	3	378,7070		3,372,3349	yes	missense	HCN4	NM_005477.2	98	3,399,5079	TT,TC,CC		5.0752,0.7684,3.6946	probably-damaging	36/1204	73660505	405,10557	1757	3724	5481	SO:0001583	missense	10021	exon1			CCGGCCCCCTCCT	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.107G>A	15.37:g.73660505C>T	ENSP00000261917:p.Gly36Glu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	22	15	0.681818	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	95	0.043498168498168496	4	0.008130081300813009	20	0.055248618784530384	19	0.033216783216783216	52	0.06860158311345646	C	11.44	1.638041	0.29157	0.007684	0.050752	ENSG00000138622	ENST00000261917	D	0.98044	-4.68	2.89	1.96	0.26148	.	.	.	.	.	T	0.60051	0.2239	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.75875	-0.3163	9	0.41790	T	0.15	.	6.7141	0.23294	0.0:0.8562:0.0:0.1438	.	36	Q9Y3Q4	HCN4_HUMAN	E	36	ENSP00000261917:G36E	ENSP00000261917:G36E	G	-	2	0	HCN4	71447558	0.002000	0.14202	0.512000	0.27736	0.852000	0.48524	0.620000	0.24403	0.419000	0.25927	0.298000	0.19748	GGG	C|0.957;T|0.043	0.043	strong		0.746	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
LINS	55180	hgsc.bcm.edu	37	15	101109677	101109677	+	Missense_Mutation	SNP	C	C	A	rs8451	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:101109677C>A	ENST00000314742.8	-	7	2262	c.2040G>T	c.(2038-2040)agG>agT	p.R680S	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	680			R -> S (in dbSNP:rs8451).					p.R680S(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						GAACCAGAGGCCTTGATGGAG	0.418													C|||	1560	0.311502	0.2375	0.2493	5008	,	,		18240	0.246		0.4513	False		,,,				2504	0.3793				p.R680S		Atlas-SNP	.											LINS,NS,carcinoma,0,1	LINS	62	1	1	Substitution - Missense(1)	stomach(1)	c.G2040T						PASS	.	C	SER/ARG	1245,3161	426.8+/-341.3	157,931,1115	85.0	86.0	86.0		2040	0.4	0.0	15	dbSNP_52	86	4037,4563	556.8+/-386.9	959,2119,1222	yes	missense	LINS	NM_001040616.2	110	1116,3050,2337	AA,AC,CC		46.9419,28.2569,40.612	benign	680/758	101109677	5282,7724	2203	4300	6503	SO:0001583	missense	55180	exon7			CAGAGGCCTTGAT	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"""lines homolog 1 (Drosophila)"""	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.2040G>T	15.37:g.101109677C>A	ENSP00000318423:p.Arg680Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	164	80	0.487805	NM_001040616	Q96FW2|Q9NVQ3	Missense_Mutation	SNP	ENST00000314742.8	37	CCDS10385.1	720	0.32967032967032966	124	0.25203252032520324	104	0.287292817679558	142	0.24825174825174826	350	0.46174142480211083	C	13.46	2.243482	0.39697	0.282569	0.469419	ENSG00000140471	ENST00000314742	T	0.09911	2.93	5.62	0.38	0.16222	.	0.615435	0.16680	N	0.203988	T	0.00012	0.0000	L	0.32530	0.975	0.58432	P	1.0000000000287557E-6	B	0.17667	0.023	B	0.15484	0.013	T	0.45131	-0.9282	9	0.24483	T	0.36	-0.334	5.9971	0.19499	0.0:0.4753:0.1285:0.3962	rs8451;rs3169081;rs17715633;rs52797285;rs8451	680	Q8NG48	LINES_HUMAN	S	680	ENSP00000318423:R680S	ENSP00000318423:R680S	R	-	3	2	LINS	98927200	0.000000	0.05858	0.011000	0.14972	0.367000	0.29736	-0.310000	0.08135	0.292000	0.22492	0.591000	0.81541	AGG	C|0.633;A|0.367	0.367	strong		0.418	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141381103	141381103	+	Silent	SNP	G	G	A	rs3735804	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:141381103G>A	ENST00000438773.2	-	8	1444	c.1311C>T	c.(1309-1311)ccC>ccT	p.P437P	TRAPPC9_ENST00000389328.4_Silent_p.P535P|TRAPPC9_ENST00000389327.3_Silent_p.P428P	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	437					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						GACTGTAGCCGGGCAGCGTTT	0.597													G|||	5	0.000998403	0.0	0.0	5008	,	,		17975	0.005		0.0	False		,,,				2504	0.0				p.P535P		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C1605T						PASS	.						83.0	83.0	83.0					8																	141381103		2203	4300	6503	SO:0001819	synonymous_variant	83696	exon8			GTAGCCGGGCAGC	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.1311C>T	8.37:g.141381103G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	G	7.589	0.670340	0.14776	.	.	ENSG00000167632	ENST00000520857	.	.	.	5.5	-6.88	0.01665	.	.	.	.	.	T	0.43478	0.1249	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55471	-0.8136	4	.	.	.	.	10.8351	0.46683	0.6972:0.0949:0.2079:0.0	rs3735804;rs3735804	.	.	.	W	281	.	.	R	-	1	2	TRAPPC9	141450285	0.044000	0.20184	0.707000	0.30419	0.576000	0.36127	-0.575000	0.05861	-1.330000	0.02255	-0.391000	0.06502	CGG	G|0.996;A|0.004	0.004	strong		0.597	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
GBP7	388646	hgsc.bcm.edu	37	1	89599037	89599037	+	Silent	SNP	A	A	G	rs72728707	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89599037A>G	ENST00000294671.2	-	10	1704	c.1566T>C	c.(1564-1566)agT>agC	p.S522S		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	522						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		TTTCCTGGAAACTTCTCTCTT	0.438																																					p.S522S		Atlas-SNP	.											.	GBP7	57	.	0			c.T1566C						PASS	.						270.0	250.0	257.0					1																	89599037		2202	4300	6502	SO:0001819	synonymous_variant	388646	exon10			CTGGAAACTTCTC	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1566T>C	1.37:g.89599037A>G		Somatic	444	0	0		WXS	Illumina HiSeq	Phase_I	550	84	0.152727	NM_207398		Silent	SNP	ENST00000294671.2	37	CCDS720.1																																																																																			A|0.989;G|0.011	0.011	strong		0.438	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
DNAJC11	55735	hgsc.bcm.edu	37	1	6705874	6705874	+	Missense_Mutation	SNP	G	G	C	rs200454	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:6705874G>C	ENST00000377577.5	-	8	992	c.869C>G	c.(868-870)aCc>aGc	p.T290S	DNAJC11_ENST00000465508.1_5'Flank|DNAJC11_ENST00000542246.1_Missense_Mutation_p.T252S|DNAJC11_ENST00000349363.6_Intron|DNAJC11_ENST00000377573.5_Missense_Mutation_p.T200S|DNAJC11_ENST00000294401.7_Missense_Mutation_p.T290S	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	290			T -> A (in dbSNP:rs200454).|T -> S (in dbSNP:rs200454). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		GAAGTGGCTGGTTTTAGTGTC	0.592													G|||	807	0.161142	0.1982	0.3559	5008	,	,		17937	0.002		0.2266	False		,,,				2504	0.0695				p.T290S		Atlas-SNP	.											.	DNAJC11	93	.	0			c.C869G						PASS	.	G	SER/THR	986,3420	353.3+/-312.1	113,760,1330	138.0	131.0	133.0		869	4.3	1.0	1	dbSNP_79	133	1771,6829	306.6+/-308.0	170,1431,2699	yes	missense	DNAJC11	NM_018198.3	58	283,2191,4029	CC,CG,GG		20.593,22.3786,21.1979	benign	290/560	6705874	2757,10249	2203	4300	6503	SO:0001583	missense	55735	exon8			TGGCTGGTTTTAG	AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"""Heat shock proteins / DNAJ (HSP40)"""	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.869C>G	1.37:g.6705874G>C	ENSP00000366800:p.Thr290Ser	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	144	65	0.451389	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Missense_Mutation	SNP	ENST00000377577.5	37	CCDS87.1	406	0.1858974358974359	113	0.22967479674796748	118	0.3259668508287293	2	0.0034965034965034965	173	0.22823218997361477	G	9.833	1.188875	0.21954	0.223786	0.20593	ENSG00000007923	ENST00000377577;ENST00000294401;ENST00000542246;ENST00000377573;ENST00000426784	T;T;T;T;T	0.22336	2.56;2.55;2.29;1.96;2.51	5.27	4.33	0.51752	.	0.136479	0.64402	D	0.000003	T	0.00012	0.0000	N	0.11427	0.14	0.24466	P	0.99441492	B;B;B	0.12013	0.0;0.003;0.005	B;B;B	0.10450	0.0;0.005;0.002	T	0.42582	-0.9443	9	0.09084	T	0.74	-16.7799	12.0357	0.53423	0.0:0.0:0.6861:0.3139	rs200454;rs201177;rs3949837;rs200454	200;290;290	B4DGD5;Q9NVH1-3;Q9NVH1	.;.;DJC11_HUMAN	S	290;290;252;200;320	ENSP00000366800:T290S;ENSP00000294401:T290S;ENSP00000444020:T252S;ENSP00000366796:T200S;ENSP00000410194:T320S	ENSP00000294401:T290S	T	-	2	0	DNAJC11	6628461	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.913000	0.39956	1.172000	0.42781	0.650000	0.86243	ACC	G|0.786;C|0.214	0.214	strong		0.592	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198	
FMN2	56776	hgsc.bcm.edu	37	1	240370952	240370952	+	Missense_Mutation	SNP	C	C	T	rs201741828	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:240370952C>T	ENST00000319653.9	+	5	3070	c.2840C>T	c.(2839-2841)cCt>cTt	p.P947L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	947	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCTCCGCCCCCTCTACCCGGA	0.692																																					p.P947L		Atlas-SNP	.											FMN2,NS,carcinoma,+1,2	FMN2	451	2	0			c.C2840T						PASS	.						25.0	30.0	29.0					1																	240370952		2201	4295	6496	SO:0001583	missense	56776	exon5			CGCCCCCTCTACC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2840C>T	1.37:g.240370952C>T	ENSP00000318884:p.Pro947Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	9	0.09375	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	C	10.92	1.486864	0.26686	.	.	ENSG00000155816	ENST00000319653	T	0.57436	0.4	4.22	3.31	0.37934	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.64843	0.2635	M	0.78456	2.415	0.80722	D	1	D	0.60575	0.988	P	0.59761	0.863	T	0.65421	-0.6172	8	.	.	.	.	7.9072	0.29769	0.0:0.7888:0.0:0.2112	.	947	Q9NZ56	FMN2_HUMAN	L	947	ENSP00000318884:P947L	.	P	+	2	0	FMN2	238437575	0.192000	0.23301	0.105000	0.21289	0.009000	0.06853	1.683000	0.37638	1.135000	0.42183	-0.361000	0.07541	CCT	C|0.986;G|0.000;T|0.014	0.014	strong		0.692	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
ACIN1	22985	hgsc.bcm.edu	37	14	23530622	23530622	+	Silent	SNP	T	T	C	rs60168438	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23530622T>C	ENST00000262710.1	-	17	3810	c.3483A>G	c.(3481-3483)tcA>tcG	p.S1161S	ACIN1_ENST00000555053.1_Silent_p.S1148S|ACIN1_ENST00000357481.2_Silent_p.S403S|ACIN1_ENST00000557515.1_Silent_p.S402S|ACIN1_ENST00000338631.6_Silent_p.S434S|ACIN1_ENST00000457657.1_Silent_p.S1121S|ACIN1_ENST00000397341.3_Silent_p.S403S|ACIN1_ENST00000605057.1_Silent_p.S1103S	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	1161	Arg/Asp/Glu/Lys-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		ATTCACGCTCTGATCGAGTCC	0.632													C|||	1227	0.245008	0.2655	0.1873	5008	,	,		9118	0.2708		0.2276	False		,,,				2504	0.2495				p.S1161S		Atlas-SNP	.											.	ACIN1	147	.	0			c.A3483G						PASS	.	C	,,,,	1224,3182	706.8+/-407.4	169,886,1148	86.0	88.0	87.0		3444,3363,1302,1209,3483	-8.9	0.6	14	dbSNP_129	87	2043,6557	719.0+/-406.2	247,1549,2504	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACIN1	NM_001164814.1,NM_001164815.1,NM_001164816.1,NM_001164817.1,NM_014977.3	,,,,	416,2435,3652	CC,CT,TT		23.7558,27.7803,25.1192	,,,,	1148/1329,1121/1302,434/615,403/584,1161/1342	23530622	3267,9739	2203	4300	6503	SO:0001819	synonymous_variant	22985	exon17			ACGCTCTGATCGA	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.3483A>G	14.37:g.23530622T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	37	CCDS9587.1																																																																																			T|0.751;C|0.249	0.249	strong		0.632	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
LAMB3	3914	hgsc.bcm.edu	37	1	209807972	209807972	+	Silent	SNP	G	G	A	rs1130667	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:209807972G>A	ENST00000356082.4	-	6	518	c.384C>T	c.(382-384)ccC>ccT	p.P128P	LAMB3_ENST00000391911.1_Silent_p.P128P|LAMB3_ENST00000367030.3_Silent_p.P128P	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	128	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GCATGCCGGCGGGCATGGGCC	0.652													G|||	1229	0.245407	0.0908	0.2421	5008	,	,		16590	0.2381		0.3887	False		,,,				2504	0.317				p.P128P		Atlas-SNP	.											.	LAMB3	136	.	0			c.C384T						PASS	.	G	,,	678,3728	275.4+/-272.5	54,570,1579	32.0	28.0	30.0		384,384,384	-8.5	0.4	1	dbSNP_86	30	3402,5198	476.1+/-369.3	669,2064,1567	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	723,2634,3146	AA,AG,GG		39.5581,15.3881,31.3701	,,	128/1173,128/1173,128/1173	209807972	4080,8926	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon6			GCCGGCGGGCATG	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.384C>T	1.37:g.209807972G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	91	35	0.384615	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			G|0.713;A|0.287	0.287	strong		0.652	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
SLCO1B3	28234	hgsc.bcm.edu	37	12	21069049	21069049	+	Silent	SNP	G	G	A	rs60571683	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:21069049G>A	ENST00000381545.3	+	16	2196	c.1977G>A	c.(1975-1977)tcG>tcA	p.S659S	LST3_ENST00000540229.1_Intron|SLCO1B3_ENST00000553473.1_Intron|SLCO1B3_ENST00000261196.2_Silent_p.S659S|LST3_ENST00000381541.3_Intron|SLCO1B7_ENST00000554957.1_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	659					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	CCAAGGCATCGGACAATGAAA	0.308													G|||	104	0.0207668	0.0023	0.0591	5008	,	,		15946	0.0		0.0527	False		,,,				2504	0.0072				p.S659S		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.G1977A						PASS	.	G		39,4367		0,39,2164	88.0	85.0	86.0		1977	-7.2	0.0	12	dbSNP_129	86	526,8074		15,496,3789	no	coding-synonymous	SLCO1B3	NM_019844.2		15,535,5953	AA,AG,GG		6.1163,0.8852,4.3441		659/703	21069049	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	28234	exon16			GGCATCGGACAAT		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1977G>A	12.37:g.21069049G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	138	71	0.514493	NM_019844	E7EMT8|Q5JAR4	Silent	SNP	ENST00000381545.3	37	CCDS8684.1																																																																																			G|0.964;A|0.036	0.036	strong		0.308	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
ZNF630	57232	hgsc.bcm.edu	37	X	47918205	47918205	+	Silent	SNP	G	G	A	rs501128	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:47918205G>A	ENST00000409324.3	-	5	1852	c.1626C>T	c.(1624-1626)ccC>ccT	p.P542P	ZNF630-AS1_ENST00000436124.1_RNA|ZNF630_ENST00000442455.3_Silent_p.P528P|ZNF630_ENST00000276054.4_Silent_p.P418P	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	542					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)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						TACACTCATAGGGTTTCTCCC	0.448													G|||	2415	0.639735	0.4486	0.5231	3775	,	,		15237	0.6567		0.4115	False		,,,				2504	0.3916				p.P542P		Atlas-SNP	.											.	ZNF630	71	.	0			c.C1626T						PASS	.	G	,	2169,1655		539,767,324,325,238	52.0	48.0	49.0		1626,1584	-2.4	0.0	X	dbSNP_83	49	3605,3110		717,1173,998,538,861	no	coding-synonymous,coding-synonymous	ZNF630	NM_001037735.2,NM_001190255.1	,	1256,1940,1322,863,1099	AA,AG,A,GG,G		46.3142,43.2793,45.213	,	542/658,528/644	47918205	5774,4765	2193	4287	6480	SO:0001819	synonymous_variant	57232	exon5			CTCATAGGGTTTC	AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"""Zinc fingers, C2H2-type"", ""-"""	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.1626C>T	X.37:g.47918205G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	51	50	0.980392	NM_001037735	F8WAG4|Q5H8Z5	Silent	SNP	ENST00000409324.3	37	CCDS35237.2																																																																																			0|0.004;A|0.588	0.588	strong		0.448	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735	
ZNF426	79088	hgsc.bcm.edu	37	19	9639710	9639710	+	Silent	SNP	T	T	C	rs45489098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9639710T>C	ENST00000535489.1	-	6	1347	c.1011A>G	c.(1009-1011)gtA>gtG	p.V337V	ZNF426_ENST00000593003.1_Silent_p.V299V|ZNF426_ENST00000253115.2_Silent_p.V337V			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	337					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						ATTCCTTACATACATAGGGTT	0.433													T|||	10	0.00199681	0.0015	0.0043	5008	,	,		22000	0.0		0.005	False		,,,				2504	0.0				p.V337V		Atlas-SNP	.											.	ZNF426	56	.	0			c.A1011G						PASS	.	T		6,4400	12.9+/-30.5	0,6,2197	96.0	96.0	96.0		1011	-0.1	0.0	19	dbSNP_127	96	55,8545	35.3+/-89.8	0,55,4245	no	coding-synonymous	ZNF426	NM_024106.1		0,61,6442	CC,CT,TT		0.6395,0.1362,0.469		337/555	9639710	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	79088	exon8			CTTACATACATAG	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"""Zinc fingers, C2H2-type"", ""-"""	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.1011A>G	19.37:g.9639710T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	110	54	0.490909	NM_024106	B3KTL2	Silent	SNP	ENST00000535489.1	37	CCDS12215.1																																																																																			T|0.995;C|0.005	0.005	strong		0.433	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106	
POLR3A	11128	hgsc.bcm.edu	37	10	79769647	79769647	+	Missense_Mutation	SNP	C	C	A	rs34588967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:79769647C>A	ENST00000372371.3	-	13	1882	c.1745G>T	c.(1744-1746)cGc>cTc	p.R582L		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	582			R -> L (in dbSNP:rs34588967).		defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			CGGTGGGAGGCGAACTTTAAT	0.483													C|||	17	0.00339457	0.0008	0.0101	5008	,	,		20588	0.0		0.0089	False		,,,				2504	0.0				p.R582L		Atlas-SNP	.											POLR3A,NS,carcinoma,-1,2	POLR3A	104	2	0			c.G1745T						scavenged	.	C	LEU/ARG	11,4395	19.1+/-41.9	0,11,2192	123.0	112.0	116.0		1745	3.9	1.0	10	dbSNP_126	116	142,8458	70.3+/-132.9	0,142,4158	yes	missense	POLR3A	NM_007055.3	102	0,153,6350	AA,AC,CC		1.6512,0.2497,1.1764	benign	582/1391	79769647	153,12853	2203	4300	6503	SO:0001583	missense	11128	exon13			GGGAGGCGAACTT	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"""RNA polymerase subunits"""	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.1745G>T	10.37:g.79769647C>A	ENSP00000361446:p.Arg582Leu	Somatic	154	2	0.012987		WXS	Illumina HiSeq	Phase_I	177	96	0.542373	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	16.88	3.244567	0.59103	0.002497	0.016512	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.74947	-0.89	5.72	3.88	0.44766	RNA polymerase Rpb1, domain 3 (1);	0.163679	0.56097	D	0.000023	T	0.42675	0.1213	N	0.20881	0.62	0.48830	D	0.999718	B	0.26602	0.154	B	0.28139	0.086	T	0.40289	-0.9571	9	.	.	.	-12.3618	10.576	0.45227	0.0:0.7932:0.0:0.2068	rs34588967	582	O14802	RPC1_HUMAN	L	582	ENSP00000361446:R582L	.	R	-	2	0	POLR3A	79439653	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	2.431000	0.44775	0.782000	0.33613	0.655000	0.94253	CGC	A|0.005;C|0.990;T|0.006	0.005	strong		0.483	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055	
CACNA1A	773	hgsc.bcm.edu	37	19	13470522	13470522	+	Silent	SNP	T	T	C	rs16006	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:13470522T>C	ENST00000360228.5	-	6	875	c.876A>G	c.(874-876)gaA>gaG	p.E292E	CACNA1A_ENST00000573710.2_Silent_p.E292E	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	292					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TGTTGGGCCCTTCCCAGTAGG	0.542													T|||	561	0.112021	0.1974	0.0288	5008	,	,		19652	0.1429		0.0308	False		,,,				2504	0.1074				p.E292E		Atlas-SNP	.											.	CACNA1A	715	.	0			c.A876G						PASS	.	T	,,,,	618,3392		34,550,1421	88.0	82.0	84.0		876,876,876,876,876	2.2	1.0	19	dbSNP_54	84	249,8089		4,241,3924	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	38,791,5345	CC,CT,TT		2.9863,15.4115,7.0214	,,,,	292/2267,292/2262,292/2507,292/2264,292/2513	13470522	867,11481	2005	4169	6174	SO:0001819	synonymous_variant	773	exon6			GGGCCCTTCCCAG	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.876A>G	19.37:g.13470522T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	224	101	0.450893	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			T|0.909;C|0.089	0.089	strong		0.542	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
OGDHL	55753	hgsc.bcm.edu	37	10	50953406	50953406	+	Missense_Mutation	SNP	G	G	T	rs145957744		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50953406G>T	ENST00000374103.4	-	12	1698	c.1613C>A	c.(1612-1614)aCc>aAc	p.T538N	OGDHL_ENST00000432695.1_Missense_Mutation_p.T329N|OGDHL_ENST00000419399.1_Missense_Mutation_p.T481N	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	538					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CTCCTGCAGGGTGACTGTGCC	0.592																																					p.T538N		Atlas-SNP	.											.	OGDHL	149	.	0			c.C1613A						PASS	.						72.0	64.0	67.0					10																	50953406		2203	4300	6503	SO:0001583	missense	55753	exon12			TGCAGGGTGACTG	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.1613C>A	10.37:g.50953406G>T	ENSP00000363216:p.Thr538Asn	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.682876	0.47991	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	T;T;D	0.95690	2.45;2.45;-3.78	5.4	5.4	0.78164	Dehydrogenase, E1 component (1);	0.051680	0.85682	D	0.000000	D	0.93903	0.8049	L	0.52011	1.625	0.58432	D	0.999999	B;B;B	0.12013	0.004;0.001;0.005	B;B;B	0.20577	0.012;0.007;0.03	D	0.90070	0.4162	10	0.37606	T	0.19	.	19.5511	0.95322	0.0:0.0:1.0:0.0	.	481;329;538	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	N	538;481;329	ENSP00000363216:T538N;ENSP00000401356:T481N;ENSP00000390240:T329N	ENSP00000363216:T538N	T	-	2	0	OGDHL	50623412	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	4.517000	0.60503	2.704000	0.92352	0.650000	0.86243	ACC	G|1.000;T|0.000	0.000	weak		0.592	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
DMBX1	127343	hgsc.bcm.edu	37	1	46976717	46976717	+	Silent	SNP	C	C	T	rs12045245	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:46976717C>T	ENST00000360032.3	+	3	458	c.444C>T	c.(442-444)gcC>gcT	p.A148A	DMBX1_ENST00000371956.4_Silent_p.A153A	NM_172225.1	NP_757379.1			diencephalon/mesencephalon homeobox 1											endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)					AAGGCAAGGCCGAGGCCCCCA	0.637													C|||	1516	0.302716	0.4924	0.1916	5008	,	,		17349	0.2718		0.175	False		,,,				2504	0.2883				p.A153A		Atlas-SNP	.											.	DMBX1	50	.	0			c.C459T						PASS	.	C	,	1891,2515	537.0+/-374.6	392,1107,704	51.0	61.0	58.0		459,444	-9.7	0.0	1	dbSNP_120	58	1401,7199	269.1+/-288.2	146,1109,3045	no	coding-synonymous,coding-synonymous	DMBX1	NM_147192.2,NM_172225.1	,	538,2216,3749	TT,TC,CC		16.2907,42.9187,25.3114	,	153/383,148/378	46976717	3292,9714	2203	4300	6503	SO:0001819	synonymous_variant	127343	exon3			CAAGGCCGAGGCC	AB037699	CCDS536.1	1p34.1	2011-06-20	2004-03-29	2004-03-30	ENSG00000197587	ENSG00000197587		"""Homeoboxes / PRD class"""	19026	protein-coding gene	gene with protein product		607410	"""orthodenticle homolog 3 (Drosophila)"""	OTX3			Standard	NM_147192		Approved	PAXB	uc001cpx.3	Q8NFW5	OTTHUMG00000007982	ENST00000360032.3:c.444C>T	1.37:g.46976717C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	150	81	0.54	NM_147192		Silent	SNP	ENST00000360032.3	37	CCDS536.1																																																																																			C|0.749;T|0.251	0.251	strong		0.637	DMBX1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021895.1		
AHNAK	79026	hgsc.bcm.edu	37	11	62284468	62284468	+	Silent	SNP	A	A	C	rs11555629|rs386754220	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62284468A>C	ENST00000378024.4	-	5	17695	c.17421T>G	c.(17419-17421)tcT>tcG	p.S5807S	AHNAK_ENST00000525875.1_Intron|AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5807					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CACCTTCCAGAGACACTTCCC	0.512													C|||	224	0.0447284	0.1067	0.0303	5008	,	,		17704	0.0119		0.0258	False		,,,				2504	0.0245				p.S5807S		Atlas-SNP	.											.	AHNAK	532	.	0			c.T17421G						PASS	.	C	,	366,4038	792.3+/-415.1	17,332,1853	118.0	114.0	115.0		17421,	-9.2	0.0	11	dbSNP_120	115	222,8376	809.3+/-407.2	4,214,4081	no	coding-synonymous,intron	AHNAK	NM_001620.1,NM_024060.2	,	21,546,5934	CC,CA,AA		2.582,8.3106,4.5224	,	5807/5891,	62284468	588,12414	2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			TTCCAGAGACACT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.17421T>G	11.37:g.62284468A>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	180	87	0.483333	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																			T|0.000;C|0.050;A|0.950	0.050	strong		0.512	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
USP30	84749	hgsc.bcm.edu	37	12	109511256	109511256	+	Silent	SNP	T	T	C	rs7967322	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:109511256T>C	ENST00000257548.5	+	7	732	c.639T>C	c.(637-639)ccT>ccC	p.P213P	USP30_ENST00000392784.2_Silent_p.P182P	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	213	USP.				mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(7)|kidney(1)|large_intestine(1)|liver(2)|lung(11)|prostate(1)|skin(3)|stomach(2)	28						CACCTCACCCTACATCCAATC	0.413													C|||	4292	0.857029	0.7587	0.853	5008	,	,		20757	0.9762		0.829	False		,,,				2504	0.8988				p.P213P		Atlas-SNP	.											.	USP30	48	.	0			c.T639C						PASS	.	C		3389,1017	377.5+/-322.5	1304,781,118	114.0	94.0	101.0		639	4.3	0.0	12	dbSNP_116	101	6889,1711	313.0+/-311.1	2761,1367,172	no	coding-synonymous	USP30	NM_032663.3		4065,2148,290	CC,CT,TT		19.8953,23.0822,20.9749		213/518	109511256	10278,2728	2203	4300	6503	SO:0001819	synonymous_variant	84749	exon7			TCACCCTACATCC	BC022094	CCDS9123.2	12q23.3	2006-01-20	2005-08-08		ENSG00000135093	ENSG00000135093		"""Ubiquitin-specific peptidases"""	20065	protein-coding gene	gene with protein product		612492	"""ubiquitin specific protease 30"""			12838346	Standard	XM_005253962		Approved	MGC10702, FLJ40511	uc010sxi.2	Q70CQ3	OTTHUMG00000133613	ENST00000257548.5:c.639T>C	12.37:g.109511256T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_032663	Q8WTU7|Q96JX4|Q9BSS3	Silent	SNP	ENST00000257548.5	37	CCDS9123.2																																																																																			C|0.814;T|0.186	0.814	strong		0.413	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663	
RADIL	55698	hgsc.bcm.edu	37	7	4874334	4874334	+	Silent	SNP	C	C	G	rs75074289	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:4874334C>G	ENST00000399583.3	-	4	1507	c.1320G>C	c.(1318-1320)ctG>ctC	p.L440L	RADIL_ENST00000536091.1_Silent_p.L440L|RADIL_ENST00000538469.1_Silent_p.L200L	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	440					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		TGCAGAGGCACAGGAGGAAGG	0.637													C|||	390	0.0778754	0.0946	0.036	5008	,	,		11085	0.1349		0.0567	False		,,,				2504	0.0481				p.L440L		Atlas-SNP	.											.	RADIL	110	.	0			c.G1320C						PASS	.	C		354,3892		9,336,1778	20.0	26.0	24.0		1320	-1.1	0.9	7	dbSNP_131	24	630,7838		30,570,3634	no	coding-synonymous	RADIL	NM_018059.4		39,906,5412	GG,GC,CC		7.4398,8.3373,7.7395		440/1076	4874334	984,11730	2123	4234	6357	SO:0001819	synonymous_variant	55698	exon4			GAGGCACAGGAGG	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.1320G>C	7.37:g.4874334C>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			C|0.925;G|0.075	0.075	strong		0.637	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
OSR1	130497	hgsc.bcm.edu	37	2	19552913	19552913	+	Silent	SNP	C	C	T	rs12329305	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:19552913C>T	ENST00000272223.2	-	2	998	c.654G>A	c.(652-654)ctG>ctA	p.L218L	OSR1_ENST00000536433.1_Silent_p.L218L	NM_145260.2	NP_660303.1	Q8TAX0	OSR1_HUMAN	odd-skipped related transciption factor 1	218					cell differentiation (GO:0030154)|cell proliferation involved in kidney development (GO:0072111)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|gonad development (GO:0008406)|heart development (GO:0007507)|intermediate mesoderm development (GO:0048389)|mesangial cell development (GO:0072143)|mesonephric duct morphogenesis (GO:0072180)|mesonephros development (GO:0001823)|metanephric cap mesenchymal cell proliferation involved in metanephros development (GO:0090094)|metanephric epithelium development (GO:0072207)|metanephric glomerulus vasculature development (GO:0072239)|metanephric interstitial fibroblast development (GO:0072259)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephric nephron tubule development (GO:0072234)|metanephric smooth muscle tissue development (GO:0072208)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of nephron tubule epithelial cell differentiation (GO:0072183)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|palate development (GO:0060021)|pattern specification involved in metanephros development (GO:0072268)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posterior mesonephric tubule development (GO:0072166)|pronephros development (GO:0048793)|renal vesicle progenitor cell differentiation (GO:0072184)|specification of anterior mesonephric tubule identity (GO:0072168)|specification of posterior mesonephric tubule identity (GO:0072169)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)|ureter urothelium development (GO:0072190)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|large_intestine(2)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)				TGTGGTCTCGCAGGTGGTCTT	0.597													T|||	475	0.0948482	0.2867	0.0432	5008	,	,		17432	0.0		0.0388	False		,,,				2504	0.0276				p.L218L		Atlas-SNP	.											.	OSR1	29	.	0			c.G654A						PASS	.	T		1184,3222	710.3+/-407.9	167,850,1186	71.0	73.0	72.0		654	-3.0	1.0	2	dbSNP_120	72	390,8210	801.5+/-407.4	8,374,3918	no	coding-synonymous	OSR1	NM_145260.2		175,1224,5104	TT,TC,CC		4.5349,26.8724,12.1021		218/267	19552913	1574,11432	2203	4300	6503	SO:0001819	synonymous_variant	130497	exon2			GTCTCGCAGGTGG	BC025712	CCDS1694.1	2p24.1	2013-10-17	2013-10-17	2004-11-26	ENSG00000143867	ENSG00000143867		"""Zinc fingers, C2H2-type"""	8111	protein-coding gene	gene with protein product		608891	"""odd-skipped (Drosophila) homolog"", ""odd-skipped related 1 (Drosophila)"""	ODD		2120051, 12119563	Standard	XM_006711942		Approved		uc002rdc.3	Q8TAX0	OTTHUMG00000088793	ENST00000272223.2:c.654G>A	2.37:g.19552913C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_145260	B3KV97|D6W521	Silent	SNP	ENST00000272223.2	37	CCDS1694.1																																																																																			C|0.894;T|0.106	0.106	strong		0.597	OSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000201432.2	NM_145260	
WDR81	124997	hgsc.bcm.edu	37	17	1634183	1634183	+	Missense_Mutation	SNP	C	C	T	rs375054918		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1634183C>T	ENST00000409644.1	+	3	3910	c.3910C>T	c.(3910-3912)Cgc>Tgc	p.R1304C	WDR81_ENST00000545662.1_5'UTR|WDR81_ENST00000419248.1_Missense_Mutation_p.R77C|WDR81_ENST00000446363.1_5'UTR|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Missense_Mutation_p.R253C|WDR81_ENST00000437219.2_Missense_Mutation_p.R101C	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1304					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCACATCGCCCGCCTGTATGG	0.652																																					p.R1304C		Atlas-SNP	.											.	WDR81	180	.	0			c.C3910T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	68.0	68.0	68.0		757,229,3910,301	-0.5	1.0	17		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	WDR81	NM_152348.3,NM_001163811.1,NM_001163809.1,NM_001163673.1	180,180,180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign	253/891,77/715,1304/1942,101/739	1634183	1,13005	2203	4300	6503	SO:0001583	missense	124997	exon3			ATCGCCCGCCTGT	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.3910C>T	17.37:g.1634183C>T	ENSP00000386609:p.Arg1304Cys	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.146331	0.37923	0.0	1.16E-4	ENSG00000167716	ENST00000455636;ENST00000437219;ENST00000309182;ENST00000419248;ENST00000409644	T;T;T;T	0.50813	2.45;2.45;2.45;0.73	5.69	-0.476	0.12100	.	0.474665	0.24649	N	0.036728	T	0.19967	0.0480	N	0.02011	-0.69	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.04840	-1.0923	10	0.38643	T	0.18	.	12.3797	0.55299	0.0:0.5955:0.0:0.4045	.	101;431;253	B7Z579;Q8TEL1;Q562E7	.;.;WDR81_HUMAN	C	101;101;253;77;1304	ENSP00000391074:R101C;ENSP00000312074:R253C;ENSP00000407845:R77C;ENSP00000386609:R1304C	ENSP00000312074:R253C	R	+	1	0	WDR81	1580933	0.804000	0.28969	0.983000	0.44433	0.645000	0.38454	1.280000	0.33202	0.064000	0.16427	0.655000	0.94253	CGC	.	.	weak		0.652	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
DAPK1	1612	hgsc.bcm.edu	37	9	90219920	90219920	+	Silent	SNP	G	G	A	rs36207428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:90219920G>A	ENST00000408954.3	+	3	449	c.114G>A	c.(112-114)caG>caA	p.Q38Q	DAPK1_ENST00000469640.2_Silent_p.Q38Q|DAPK1_ENST00000491893.1_Silent_p.Q38Q|DAPK1_ENST00000358077.5_Silent_p.Q38Q|DAPK1_ENST00000472284.1_Silent_p.Q38Q	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	38	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						CCGGCCTCCAGTATGCCGCCA	0.507									Chronic Lymphocytic Leukemia, Familial Clustering of				G|||	433	0.0864617	0.2269	0.0461	5008	,	,		17937	0.0		0.0656	False		,,,				2504	0.0358				p.Q38Q		Atlas-SNP	.											.	DAPK1	329	.	0			c.G114A						PASS	.	G		709,3473		60,589,1442	37.0	40.0	39.0		114	3.1	1.0	9	dbSNP_126	39	425,8057		8,409,3824	no	coding-synonymous	DAPK1	NM_004938.2		68,998,5266	AA,AG,GG		5.0106,16.9536,8.9545		38/1431	90219920	1134,11530	2091	4241	6332	SO:0001819	synonymous_variant	1612	exon3	Familial Cancer Database	Familial CLL	CCTCCAGTATGCC	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.114G>A	9.37:g.90219920G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	143	73	0.51049	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																			G|0.931;A|0.069	0.069	strong		0.507	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
PKD1	5310	hgsc.bcm.edu	37	16	2140321	2140321	+	Silent	SNP	G	G	A	rs79899502	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2140321G>A	ENST00000262304.4	-	45	12617	c.12409C>T	c.(12409-12411)Ctg>Ttg	p.L4137L	PKD1_ENST00000423118.1_Silent_p.L4136L|MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	4137					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CAGAGGCGCAGCCTGCGCAGG	0.672													G|||	181	0.0361422	0.0008	0.0389	5008	,	,		16205	0.0		0.0895	False		,,,				2504	0.0644				p.L4137L		Atlas-SNP	.											PKD1,NS,haematopoietic_neoplasm,0,2	PKD1	184	2	0			c.C12409T	GRCh37	CD010654	PKD1	D	rs79899502	PASS	.	G	,	65,4331	57.4+/-93.9	0,65,2133	42.0	50.0	47.0		12406,12409	3.1	1.0	16	dbSNP_131	47	694,7900	159.5+/-212.8	25,644,3628	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	25,709,5761	AA,AG,GG		8.0754,1.4786,5.843	,	4136/4303,4137/4304	2140321	759,12231	2198	4297	6495	SO:0001819	synonymous_variant	5310	exon45			GGCGCAGCCTGCG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.12409C>T	16.37:g.2140321G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	165	91	0.551515	NM_001009944	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			G|0.946;A|0.054	0.054	strong		0.672	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
PPP1R12C	54776	hgsc.bcm.edu	37	19	55614923	55614923	+	Silent	SNP	T	T	C	rs2532060	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55614923T>C	ENST00000263433.3	-	4	600	c.585A>G	c.(583-585)gaA>gaG	p.E195E	PPP1R12C_ENST00000435544.2_Silent_p.E121E|PPP1R12C_ENST00000376393.2_Silent_p.E195E	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		GCTTGGCTGCTTCCACATCCA	0.617													C|||	3413	0.68151	0.9145	0.5072	5008	,	,		16289	0.754		0.4056	False		,,,				2504	0.6994				p.E195E		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.A585G						PASS	.	C		3774,632		1637,500,66	45.0	37.0	39.0		585	3.1	1.0	19	dbSNP_100	39	3643,4951		816,2011,1470	no	coding-synonymous	PPP1R12C	NM_017607.2		2453,2511,1536	CC,CT,TT		42.39,14.3441,42.9462		195/783	55614923	7417,5583	2203	4297	6500	SO:0001819	synonymous_variant	54776	exon4			GGCTGCTTCCACA	AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14947	protein-coding gene	gene with protein product	"""myosin-binding subunit 85"""	613245	"""leukocyte receptor cluster (LRC) member 3"", ""protein phosphatase 1, regulatory (inhibitor) subunit 12C"""	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.585A>G	19.37:g.55614923T>C		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	169	69	0.408284	NM_017607		Silent	SNP	ENST00000263433.3	37	CCDS12916.1																																																																																			T|0.385;C|0.615	0.615	strong		0.617	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
WDR90	197335	hgsc.bcm.edu	37	16	705795	705795	+	Silent	SNP	C	C	T	rs12599798	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:705795C>T	ENST00000293879.4	+	17	1872	c.1872C>T	c.(1870-1872)agC>agT	p.S624S	LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Silent_p.S624S			Q96KV7	WDR90_HUMAN	WD repeat domain 90	624										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCATCAGCAGCCTCAGCGTCT	0.682													C|||	1233	0.246206	0.4123	0.1758	5008	,	,		17229	0.3026		0.1163	False		,,,				2504	0.1472				p.S624S		Atlas-SNP	.											.	WDR90	107	.	0			c.C1872T						PASS	.	C		1492,2804		264,964,920	22.0	25.0	24.0		1872	4.6	1.0	16	dbSNP_120	24	1094,7372		62,970,3201	no	coding-synonymous	WDR90	NM_145294.4		326,1934,4121	TT,TC,CC		12.9223,34.73,20.2633		624/1749	705795	2586,10176	2148	4233	6381	SO:0001819	synonymous_variant	197335	exon17			CAGCAGCCTCAGC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.1872C>T	16.37:g.705795C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			C|0.785;T|0.215	0.215	strong		0.682	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
CACNA1H	8912	hgsc.bcm.edu	37	16	1270162	1270162	+	Missense_Mutation	SNP	G	G	A	rs1054645	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1270162G>A	ENST00000348261.5	+	35	6478	c.6230G>A	c.(6229-6231)cGc>cAc	p.R2077H	CACNA1H_ENST00000358590.4_Missense_Mutation_p.R2071H|CACNA1H_ENST00000565831.1_Missense_Mutation_p.R2071H	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	2077			R -> H (in dbSNP:rs1054645). {ECO:0000269|PubMed:12891677, ECO:0000269|PubMed:9930755, ECO:0000269|Ref.7}.		aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TTCGGACAGCGCTGCGTCTCC	0.741													G|||	3509	0.700679	0.7262	0.7075	5008	,	,		12781	0.8681		0.6441	False		,,,				2504	0.547				p.R2077H		Atlas-SNP	.											CACNA1H_ENST00000358590,NS,carcinoma,0,2	CACNA1H	317	2	0			c.G6230A						PASS	.	G	HIS/ARG,HIS/ARG	2894,1084		1068,758,163	10.0	13.0	12.0		6212,6230	0.8	1.0	16	dbSNP_86	12	5031,3243		1584,1863,690	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	29,29	2652,2621,853	AA,AG,GG		39.1951,27.2499,35.3167	benign,benign	2071/2348,2077/2354	1270162	7925,4327	1989	4137	6126	SO:0001583	missense	8912	exon35			GACAGCGCTGCGT	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.6230G>A	16.37:g.1270162G>A	ENSP00000334198:p.Arg2077His	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	28	27	0.964286	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	1589	0.7275641025641025	346	0.7032520325203252	245	0.6767955801104972	519	0.9073426573426573	479	0.6319261213720316	G	7.681	0.689039	0.14973	0.727501	0.608049	ENSG00000196557	ENST00000348261;ENST00000358590	T;T	0.32988	1.43;1.43	4.02	0.758	0.18432	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.54753	P	1.799999999996249E-5	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.14172	-1.0482	8	0.28530	T	0.3	.	8.2472	0.31695	0.4591:0.0:0.5409:0.0	rs1054645;rs3195163;rs3751890;rs17745303;rs60109536;rs1054645	2071;2077	O95180-2;O95180	.;CAC1H_HUMAN	H	2077;2071	ENSP00000334198:R2077H;ENSP00000351401:R2071H	ENSP00000334198:R2077H	R	+	2	0	CACNA1H	1210163	0.000000	0.05858	0.956000	0.39512	0.169000	0.22640	-0.663000	0.05299	0.095000	0.17434	0.306000	0.20318	CGC	G|0.269;A|0.731	0.731	strong		0.741	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
IL17C	27189	hgsc.bcm.edu	37	16	88706330	88706330	+	Silent	SNP	C	C	T	rs11076688	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:88706330C>T	ENST00000244241.4	+	3	493	c.444C>T	c.(442-444)tcC>tcT	p.S148S		NM_013278.3	NP_037410.1	Q9P0M4	IL17C_HUMAN	interleukin 17C	148					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|neutrophil differentiation (GO:0030223)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)			large_intestine(1)|lung(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0477)		CGCTCAACTCCGTGCGGCTGC	0.692													C|||	307	0.0613019	0.0484	0.1066	5008	,	,		15275	0.004		0.0865	False		,,,				2504	0.0798				p.S148S		Atlas-SNP	.											.	IL17C	6	.	0			c.C444T						PASS	.	C		209,3935		8,193,1871	24.0	30.0	28.0		444	-8.9	0.2	16	dbSNP_120	28	768,7612		44,680,3466	no	coding-synonymous	IL17C	NM_013278.3		52,873,5337	TT,TC,CC		9.1647,5.0434,7.801		148/198	88706330	977,11547	2072	4190	6262	SO:0001819	synonymous_variant	27189	exon3			CAACTCCGTGCGG	AF152099	CCDS42217.1	16q24	2011-07-14			ENSG00000124391	ENSG00000124391		"""Interleukins and interleukin receptors"""	5983	protein-coding gene	gene with protein product		604628				10639155	Standard	NM_013278		Approved	IL-17C, CX2, IL-21, MGC126884, MGC138401	uc002fla.3	Q9P0M4		ENST00000244241.4:c.444C>T	16.37:g.88706330C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_013278	Q3MIG8|Q9HC75	Silent	SNP	ENST00000244241.4	37	CCDS42217.1																																																																																			C|0.932;T|0.068	0.068	strong		0.692	IL17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422575.1	NM_013278	
ZNF519	162655	hgsc.bcm.edu	37	18	14104957	14104957	+	Missense_Mutation	SNP	G	G	A	rs149267105	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:14104957G>A	ENST00000590202.1	-	3	1734	c.1582C>T	c.(1582-1584)Cgc>Tgc	p.R528C	ZNF519_ENST00000589203.1_Intron|ZNF519_ENST00000589498.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	528					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						AGGGTTGAGCGTCTGTTAAAA	0.398													G|||	3	0.000599042	0.0008	0.0	5008	,	,		19567	0.0		0.002	False		,,,				2504	0.0				p.R528C		Atlas-SNP	.											.	ZNF519	53	.	0			c.C1582T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	134.0	137.0	136.0		1582	-2.4	0.0	18	dbSNP_134	136	29,8571	21.6+/-65.8	0,29,4271	yes	missense	ZNF519	NM_145287.3	180	0,35,6468	AA,AG,GG		0.3372,0.1362,0.2691	probably-damaging	528/541	14104957	35,12971	2203	4300	6503	SO:0001583	missense	162655	exon3			TTGAGCGTCTGTT	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.1582C>T	18.37:g.14104957G>A	ENSP00000464872:p.Arg528Cys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	G	5.238	0.229427	0.09916	0.001362	0.003372	ENSG00000175322	ENST00000309305	.	.	.	1.2	-2.4	0.06583	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30510	0.0767	M	0.64404	1.975	0.09310	N	1	B	0.32829	0.386	B	0.26416	0.069	T	0.11717	-1.0576	8	0.45353	T	0.12	.	2.7452	0.05264	0.232:0.0:0.2362:0.5318	.	528	Q8TB69	ZN519_HUMAN	C	528	.	ENSP00000307908:R528C	R	-	1	0	ZNF519	14094957	0.000000	0.05858	0.000000	0.03702	0.509000	0.34042	-1.143000	0.03200	-1.216000	0.02607	0.089000	0.15464	CGC	G|0.998;A|0.002	0.002	strong		0.398	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
GAS8	2622	hgsc.bcm.edu	37	16	90095484	90095484	+	Intron	SNP	C	C	T	rs3785184	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90095484C>T	ENST00000268699.4	+	2	212				GAS8_ENST00000536122.1_Intron|GAS8_ENST00000540721.1_Intron|C16orf3_ENST00000408886.2_Silent_p.T89T	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		AGCTGCTGCCCGTCTCCCTGT	0.597													C|||	1176	0.234824	0.0946	0.2968	5008	,	,		16761	0.62		0.1213	False		,,,				2504	0.1002				p.T89T		Atlas-SNP	.											C16orf3,rectum,carcinoma,-2,2	C16orf3	14	2	0			c.G267A						PASS	.	C	,	352,3822		14,324,1749	85.0	47.0	60.0		267,	-0.4	0.0	16	dbSNP_107	60	648,7580		23,602,3489	no	coding-synonymous,intron	C16orf3,GAS8	NM_001214.3,NM_001481.2	,	37,926,5238	TT,TC,CC		7.8755,8.4332,8.0632	,	89/118,	90095484	1000,11402	2087	4114	6201	SO:0001627	intron_variant	750	exon1			GCTGCCCGTCTCC	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1354C>T	16.37:g.90095484C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	104	34	0.326923	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Silent	SNP	ENST00000268699.4	37	CCDS10992.1																																																																																			C|0.821;T|0.179	0.179	strong		0.597	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
PCDHA5	56143	hgsc.bcm.edu	37	5	140201420	140201420	+	Silent	SNP	T	T	C	rs386692889|rs11958868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140201420T>C	ENST00000529859.1	+	1	60	c.60T>C	c.(58-60)ctT>ctC	p.L20L	PCDHA5_ENST00000529619.1_Silent_p.L20L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Silent_p.L20L|PCDHA4_ENST00000512229.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	20					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCTTCTCCTTGCCTACTGGA	0.572													.|||	3010	0.601038	0.7557	0.6037	5008	,	,		14682	0.5337		0.5388	False		,,,				2504	0.5235				p.L20L		Atlas-SNP	.											.	PCDHA5	361	.	0			c.T60C						PASS	.	C	,,,,,,	3043,1363		1181,681,341	59.0	67.0	64.0		,,,,60,,60	2.0	0.0	5	dbSNP_120	64	4543,4057		1193,2157,950	no	intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,,,	2374,2838,1291	CC,CT,TT		47.1744,30.9351,41.6731	,,,,,,	,,,,20/937,,20/817	140201420	7586,5420	2203	4300	6503	SO:0001819	synonymous_variant	56143	exon1			TCTCCTTGCCTAC	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.60T>C	5.37:g.140201420T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_018908	O75284|Q8N4R3	Silent	SNP	ENST00000529859.1	37	CCDS54917.1																																																																																			T|0.406;C|0.594	0.594	strong		0.572	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
FCGR3A	2214	hgsc.bcm.edu	37	1	161599571	161599571	+	Intron	SNP	T	T	C	rs2290834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:161599571T>C	ENST00000540048.1	-	2	94				FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR2B_ENST00000403078.3_Intron|FCGR3B_ENST00000531221.1_Missense_Mutation_p.I142V|FCGR3B_ENST00000367964.2_Missense_Mutation_p.I106V|FCGR2B_ENST00000367962.4_Intron|FCGR3B_ENST00000294800.3_Missense_Mutation_p.I106V			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AACTCACCGATATGGACTTCT	0.478																																					p.I142V		Atlas-SNP	.											FCGR3B,NS,carcinoma,+2,1	FCGR3B	35	1	0			c.A424G						scavenged	.						24.0	26.0	25.0					1																	161599571		2124	4279	6403	SO:0001627	intron_variant	2215	exon3			CACCGATATGGAC	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+586A>G	1.37:g.161599571T>C		Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	120	73	0.608333	NM_001244753	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	1.794|1.794	-0.478839|-0.478839	0.04414|0.04414	.|.	.|.	ENSG00000162747|ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221;ENST00000534776|ENST00000421702	T;T;T;T|.	0.02787|.	4.91;4.91;5.01;4.16|.	2.79|2.79	-5.57|-5.57	0.02521|0.02521	.|.	4.037030|.	0.00559|.	N|.	0.000262|.	T|T	0.02727|0.02727	0.0082|0.0082	N|N	0.04508|0.04508	-0.205|-0.205	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.16660|0.16660	-1.0395|-1.0395	9|4	0.20046|.	T|.	0.44|.	.|.	3.2984|3.2984	0.06974|0.06974	0.1208:0.478:0.2427:0.1584|0.1208:0.478:0.2427:0.1584	.|.	106|.	O75015|.	FCG3B_HUMAN|.	V|C	106;106;142;89|126	ENSP00000356941:I106V;ENSP00000294800:I106V;ENSP00000433642:I142V;ENSP00000437084:I89V|.	ENSP00000294800:I106V|.	I|Y	-|-	1|2	0|0	FCGR3B|FCGR3B	159866195|159866195	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	-7.325000|-7.325000	0.00039|0.00039	-3.260000|-3.260000	0.00202|0.00202	0.319000|0.319000	0.21371|0.21371	ATC|TAT	.	.	weak		0.478	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569	
KRT40	125115	hgsc.bcm.edu	37	17	39137104	39137104	+	Missense_Mutation	SNP	A	A	G	rs9908389	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39137104A>G	ENST00000398486.2	-	7	1068	c.908T>C	c.(907-909)aTg>aCg	p.M303T	KRT40_ENST00000377755.4_Missense_Mutation_p.M303T	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	303	Coil 2.|Rod.		M -> T (in dbSNP:rs9908389).			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				CAAGATCTCCATCTGGCAGCC	0.522													G|||	1807	0.360823	0.6853	0.2378	5008	,	,		20802	0.1716		0.2684	False		,,,				2504	0.2996				p.M303T		Atlas-SNP	.											.	KRT40	27	.	0			c.T908C						PASS	.	G	THR/MET	2397,1667		726,945,361	107.0	109.0	108.0		908	-0.1	0.0	17	dbSNP_119	108	2319,6101		316,1687,2207	yes	missense	KRT40	NM_182497.3	81	1042,2632,2568	GG,GA,AA		27.5416,41.0187,37.7764	benign	303/432	39137104	4716,7768	2032	4210	6242	SO:0001583	missense	125115	exon7			ATCTCCATCTGGC	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.908T>C	17.37:g.39137104A>G	ENSP00000381500:p.Met303Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	42	0.43299	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	733	0.3356227106227106	338	0.6869918699186992	92	0.2541436464088398	96	0.16783216783216784	207	0.27308707124010556	G	1.798	-0.477697	0.04414	0.589813	0.275416	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.87650	-2.28;-2.28	5.4	-0.0938	0.13647	Filament (1);	0.281117	0.19844	N	0.104796	T	0.00012	0.0000	N	0.02334	-0.595	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40942	-0.9536	9	0.11182	T	0.66	.	2.8327	0.05505	0.3153:0.1046:0.4726:0.1075	rs9908389;rs17646642	303	Q6A162	K1C40_HUMAN	T	303	ENSP00000366984:M303T;ENSP00000381500:M303T	ENSP00000366984:M303T	M	-	2	0	KRT40	36390630	0.001000	0.12720	0.017000	0.16124	0.751000	0.42716	1.034000	0.30204	-0.355000	0.08199	-0.766000	0.03442	ATG	A|0.657;G|0.343	0.343	strong		0.522	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
DDX11	1663	hgsc.bcm.edu	37	12	31256546	31256546	+	Missense_Mutation	SNP	G	G	A	rs1046457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:31256546G>A	ENST00000407793.2	+	26	2818	c.2567G>A	c.(2566-2568)cGt>cAt	p.R856H	DDX11_ENST00000545668.1_Missense_Mutation_p.R856H|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000228264.6_Missense_Mutation_p.V832I|DDX11_ENST00000542838.1_Missense_Mutation_p.V858I|DDX11_ENST00000350437.4_Missense_Mutation_p.V808I	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	856			R -> H (in dbSNP:rs1046457).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					TTTTGCCAGCGTAGTGCTCCT	0.647										Multiple Myeloma(12;0.14)			A|||	3176	0.634185	0.708	0.611	5008	,	,		14475	0.8075		0.4384	False		,,,				2504	0.5736				p.V858I		Atlas-SNP	.											.	DDX11	188	.	0			c.G2572A						PASS	.	A	HIS/ARG,ILE/VAL,ILE/VAL	2845,1557		1010,825,366	26.0	39.0	34.0		2567,2572,2422	3.1	1.0	12	dbSNP_86	34	3631,4965		886,1859,1553	no	missense,missense,missense	DDX11	NM_152438.1,NM_030653.3,NM_004399.2	29,29,29	1896,2684,1919	AA,AG,GG		42.2406,35.3703,49.823	benign,benign,benign	856/971,858/907,808/857	31256546	6476,6522	2201	4298	6499	SO:0001583	missense	1663	exon26			GCCAGCGTAGTGC	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.2567G>A	12.37:g.31256546G>A	ENSP00000384703:p.Arg856His	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	156	70	0.448718	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	1165|1165	0.5334249084249084|0.5334249084249084	293|293	0.5955284552845529|0.5955284552845529	193|193	0.5331491712707183|0.5331491712707183	423|423	0.7395104895104895|0.7395104895104895	256|256	0.33773087071240104|0.33773087071240104	A|A	0.021|0.021	-1.427665|-1.427665	0.01117|0.01117	0.646297|0.646297	0.422406|0.422406	ENSG00000013573|ENSG00000013573	ENST00000407793;ENST00000545668|ENST00000542838;ENST00000228264;ENST00000350437	T;T|D;D;D	0.74106|0.90955	-0.81;-0.81|-2.76;-2.76;-2.76	3.14|3.14	3.14|3.14	0.36123|0.36123	Helicase, ATP-dependent, c2 type (1);|.	.|0.646978	.|0.15103	.|N	.|0.280427	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999996408|0.9999999999996408	B|B;B;B	0.02656|0.06786	0.0|0.0;0.001;0.0	B|B;B;B	0.01281|0.01281	0.0|0.0;0.0;0.0	T|T	0.43032|0.43032	-0.9416|-0.9416	7|8	0.46703|0.02654	T|T	0.11|1	.|.	6.4922|6.4922	0.22121|0.22121	0.8746:0.0:0.1254:0.0|0.8746:0.0:0.1254:0.0	rs1046457;rs3177434;rs3186439;rs17415422;rs58379983|rs1046457;rs3177434;rs3186439;rs17415422;rs58379983	856|832;808;858	Q96FC9|Q96FC9-3;Q96FC9-4;Q96FC9-2	DDX11_HUMAN|.;.;.	H|I	856|858;832;808	ENSP00000384703:R856H;ENSP00000440402:R856H|ENSP00000443426:V858I;ENSP00000228264:V832I;ENSP00000309965:V808I	ENSP00000384703:R856H|ENSP00000228264:V832I	R|V	+|+	2|1	0|0	DDX11|DDX11	31147813|31147813	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.179000|0.179000	0.23085|0.23085	2.796000|2.796000	0.47869|0.47869	0.313000|0.313000	0.23062|0.23062	-0.707000|-0.707000	0.03653|0.03653	CGT|GTA	G|0.494;A|0.506	0.506	strong		0.647	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
ZNF99	7652	hgsc.bcm.edu	37	19	22940899	22940899	+	Silent	SNP	G	G	A	rs59017672	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:22940899G>A	ENST00000596209.1	-	4	1902	c.1812C>T	c.(1810-1812)caC>caT	p.H604H	ZNF99_ENST00000397104.3_Silent_p.H513H	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	604					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GGGCTGAGAAGTGGTTAAAAG	0.383													g|||	1838	0.367013	0.5378	0.3256	5008	,	,		19631	0.3452		0.2783	False		,,,				2504	0.2791				p.H604H		Atlas-SNP	.											.	ZNF99	273	.	0			c.C1812T						PASS	.	A		1886,2154		462,962,596	41.0	47.0	45.0		1539	-2.3	0.0	19	dbSNP_129	45	2325,6129		325,1675,2227	no	coding-synonymous	ZNF99	NM_001080409.2		787,2637,2823	AA,AG,GG		27.5018,46.6832,33.7042		513/912	22940899	4211,8283	2020	4227	6247	SO:0001819	synonymous_variant	7652	exon4			TGAGAAGTGGTTA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1812C>T	19.37:g.22940899G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_001080409	M0R335	Silent	SNP	ENST00000596209.1	37	CCDS59369.1																																																																																			A|0.316;G|0.683;T|0.001	0.316	strong		0.383	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
PEX6	5190	hgsc.bcm.edu	37	6	42933464	42933464	+	Missense_Mutation	SNP	G	G	A	rs35830695	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:42933464G>A	ENST00000304611.8	-	13	2495	c.2426C>T	c.(2425-2427)gCc>gTc	p.A809V	PEX6_ENST00000244546.4_Missense_Mutation_p.P727S	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	809			A -> V (in dbSNP:rs35830695). {ECO:0000269|PubMed:19105186}.		ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			CCGGCTTGGGGCCAAAGAGTC	0.572													G|||	376	0.0750799	0.1362	0.0476	5008	,	,		16293	0.0407		0.0586	False		,,,				2504	0.0644				p.A809V		Atlas-SNP	.											.	PEX6	44	.	0			c.C2426T						PASS	.	G	VAL/ALA	585,3821	258.0+/-262.2	32,521,1650	143.0	158.0	153.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2426	5.8	1.0	6	dbSNP_126	153	460,8140	136.8+/-193.9	7,446,3847	yes	missense	PEX6	NM_000287.3	64	39,967,5497	AA,AG,GG		5.3488,13.2773,8.0348	probably-damaging	809/981	42933464	1045,11961	2203	4300	6503	SO:0001583	missense	5190	exon13			CTTGGGGCCAAAG	U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"""ATPases / AAA-type"""	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.2426C>T	6.37:g.42933464G>A	ENSP00000303511:p.Ala809Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	37	CCDS4877.1	174|174	0.07967032967032966|0.07967032967032966	78|78	0.15853658536585366|0.15853658536585366	19|19	0.052486187845303865|0.052486187845303865	27|27	0.0472027972027972|0.0472027972027972	50|50	0.06596306068601583|0.06596306068601583	G|G	36|36	5.702353|5.702353	0.96812|0.96812	0.132773|0.132773	0.053488|0.053488	ENSG00000124587|ENSG00000124587	ENST00000304611|ENST00000244546	D|D	0.93247|0.95238	-3.19|-3.65	5.76|5.76	5.76|5.76	0.90799|0.90799	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.93363|0.93363	0.7884|0.7884	L|L	0.31804|0.31804	0.96|0.96	0.24042|0.24042	P|P	0.99607886|0.99607886	D|.	0.64830|.	0.994|.	D|.	0.79784|.	0.993|.	D|D	0.94196|0.94196	0.7445|0.7445	9|6	0.72032|0.72032	D|D	0.01|0.01	-23.1887|-23.1887	19.5876|19.5876	0.95496|0.95496	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs35830695;rs56929785;rs61753227|rs35830695;rs56929785;rs61753227	809|.	Q13608|.	PEX6_HUMAN|.	V|S	809|727	ENSP00000303511:A809V|ENSP00000244546:P727S	ENSP00000303511:A809V|ENSP00000244546:P727S	A|P	-|-	2|1	0|0	PEX6|PEX6	43041442|43041442	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.842000|9.842000	0.99487|0.99487	2.724000|2.724000	0.93272|0.93272	0.563000|0.563000	0.77884|0.77884	GCC|CCC	G|0.921;A|0.079	0.079	strong		0.572	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287	
AFAP1L2	84632	hgsc.bcm.edu	37	10	116073801	116073801	+	Silent	SNP	T	T	C	rs621375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:116073801T>C	ENST00000304129.4	-	7	650	c.621A>G	c.(619-621)aaA>aaG	p.K207K	AFAP1L2_ENST00000545353.1_Silent_p.K260K|AFAP1L2_ENST00000369271.3_Silent_p.K207K			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	207	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		CCTTGGAGGATTTGTAGCACT	0.567													T|||	1775	0.354433	0.7322	0.1671	5008	,	,		20693	0.1071		0.2097	False		,,,				2504	0.3804				p.K207K		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.A621G						PASS	.	T	,	2790,1616	662.7+/-401.1	899,992,312	116.0	88.0	98.0		621,621	1.2	1.0	10	dbSNP_83	98	1672,6928	306.4+/-307.9	163,1346,2791	no	coding-synonymous,coding-synonymous	AFAP1L2	NM_001001936.1,NM_032550.2	,	1062,2338,3103	CC,CT,TT		19.4419,36.6773,34.3072	,	207/819,207/815	116073801	4462,8544	2203	4300	6503	SO:0001819	synonymous_variant	84632	exon7			GGAGGATTTGTAG	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"""Pleckstrin homology (PH) domain containing"""	25901	protein-coding gene	gene with protein product		612420	"""KIAA1914"""	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.621A>G	10.37:g.116073801T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	147	64	0.435374	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																			C|0.337;N|0.000	0.337	strong		0.567	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
PSPN	5623	hgsc.bcm.edu	37	19	6375831	6375831	+	Silent	SNP	G	G	A	rs2304198	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:6375831G>A	ENST00000245810.1	-	1	29	c.30C>T	c.(28-30)tcC>tcT	p.S10S	PSPN_ENST00000597721.1_Silent_p.S10S	NM_004158.2	NP_004149.1	O60542	PSPN_HUMAN	persephin	10					axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|central nervous system development (GO:0007417)|nervous system development (GO:0007399)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			lung(1)|ovary(1)|skin(1)	3						GGAGCAGCAGGGAGCCCAGCA	0.642													A|||	2204	0.440096	0.8744	0.2032	5008	,	,		14171	0.3889		0.1789	False		,,,				2504	0.3425				p.S10S		Atlas-SNP	.											PSPN,colon,carcinoma,0,1	PSPN	5	1	0			c.C30T						PASS	.	A		3333,1073	382.3+/-324.4	1267,799,137	41.0	44.0	43.0		30	-0.4	0.0	19	dbSNP_100	43	1395,7205	749.3+/-407.4	109,1177,3014	no	coding-synonymous	PSPN	NM_004158.2		1376,1976,3151	AA,AG,GG		16.2209,24.3532,36.3525		10/157	6375831	4728,8278	2203	4300	6503	SO:0001819	synonymous_variant	5623	exon1			CAGCAGGGAGCCC	AF040962	CCDS12164.1	19p13.3	2014-01-30				ENSG00000125650		"""Endogenous ligands"""	9579	protein-coding gene	gene with protein product		602921				10072588	Standard	NM_004158		Approved	PSP	uc010xja.2	O60542		ENST00000245810.1:c.30C>T	19.37:g.6375831G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	146	73	0.5	NM_004158		Silent	SNP	ENST00000245810.1	37	CCDS12164.1																																																																																			G|0.609;A|0.391	0.391	strong		0.642	PSPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398032.1	NM_004158	
PKD1	5310	hgsc.bcm.edu	37	16	2144176	2144176	+	Missense_Mutation	SNP	G	G	A	rs34197769	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2144176G>A	ENST00000262304.4	-	35	10743	c.10535C>T	c.(10534-10536)gCg>gTg	p.A3512V	PKD1_ENST00000423118.1_Missense_Mutation_p.A3511V|RP11-304L19.3_ENST00000565937.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3512			A -> V (in dbSNP:rs34197769). {ECO:0000269|PubMed:11967008, ECO:0000269|PubMed:15772804, ECO:0000269|PubMed:18837007}.		anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CCTCTGCAGCGCCAGCGTCTC	0.657													g|||	332	0.0662939	0.1203	0.0562	5008	,	,		16658	0.0		0.0934	False		,,,				2504	0.0409				p.A3512V		Atlas-SNP	.											.	PKD1	184	.	0			c.C10535T						PASS	.	G	VAL/ALA,VAL/ALA	547,3845		39,469,1688	19.0	17.0	18.0		10532,10535	-9.0	0.0	16	dbSNP_126	18	701,7889		27,647,3621	yes	missense,missense	PKD1	NM_000296.3,NM_001009944.2	64,64	66,1116,5309	AA,AG,GG		8.1607,12.4545,9.6133	benign,benign	3511/4303,3512/4304	2144176	1248,11734	2196	4295	6491	SO:0001583	missense	5310	exon35			TGCAGCGCCAGCG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.10535C>T	16.37:g.2144176G>A	ENSP00000262304:p.Ala3512Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	219	105	0.479452	NM_001009944	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	150	0.06868131868131869	57	0.11585365853658537	23	0.06353591160220995	0	0.0	70	0.09234828496042216	G	4.521	0.096772	0.08681	0.124545	0.081607	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.33216	1.42;1.42	4.66	-9.01	0.00744	.	1.060420	0.07438	N	0.896761	T	0.00144	0.0004	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.28971	0.005;0.229	B;B	0.12837	0.001;0.008	T	0.21965	-1.0230	9	0.11182	T	0.66	.	9.7513	0.40477	0.24:0.0:0.5482:0.2118	rs34197769	3511;3512	P98161-3;P98161	.;PKD1_HUMAN	V	3512;3511;2846	ENSP00000262304:A3512V;ENSP00000399501:A3511V	ENSP00000262304:A3512V	A	-	2	0	PKD1	2084177	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.663000	0.25053	-2.116000	0.00830	-2.430000	0.00215	GCG	G|0.911;A|0.089	0.089	strong		0.657	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
ZNF653	115950	hgsc.bcm.edu	37	19	11598483	11598483	+	Silent	SNP	T	T	C	rs311805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11598483T>C	ENST00000293771.5	-	4	931	c.795A>G	c.(793-795)ccA>ccG	p.P265P	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						CATTGCCTGCTGGGTTGGAGC	0.662													C|||	1540	0.307508	0.7632	0.2089	5008	,	,		14453	0.1181		0.1153	False		,,,				2504	0.1544				p.P265P	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											ZNF653,NS,carcinoma,0,2	ZNF653	48	2	0			c.A795G						PASS	.	C		2938,1468	448.3+/-348.6	988,962,253	43.0	46.0	45.0		795	-9.0	0.0	19	dbSNP_79	45	847,7751	757.7+/-407.5	45,757,3497	no	coding-synonymous	ZNF653	NM_138783.3		1033,1719,3750	CC,CT,TT		9.8511,33.3182,29.1064		265/616	11598483	3785,9219	2203	4299	6502	SO:0001819	synonymous_variant	115950	exon4			GCCTGCTGGGTTG	AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.795A>G	19.37:g.11598483T>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	192	78	0.40625	NM_138783	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			T|0.731;C|0.269	0.269	strong		0.662	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
OR5M3	219482	hgsc.bcm.edu	37	11	56237410	56237410	+	Silent	SNP	A	A	G	rs617315	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56237410A>G	ENST00000312240.2	-	1	604	c.564T>C	c.(562-564)gcT>gcC	p.A188A		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	188						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					CAAAGGTCCCAGCACAGGCCA	0.393													a|||	750	0.14976	0.1112	0.1268	5008	,	,		19469	0.129		0.2237	False		,,,				2504	0.1636				p.A188A		Atlas-SNP	.											OR5M3,NS,carcinoma,-1,1	OR5M3	103	1	0			c.T564C						PASS	.	A		516,3886	221.7+/-238.7	24,468,1709	131.0	121.0	124.0		564	-10.2	0.2	11	dbSNP_83	124	1911,6681	321.1+/-314.9	261,1389,2646	no	coding-synonymous	OR5M3	NM_001004742.2		285,1857,4355	GG,GA,AA		22.2416,11.7219,18.6779		188/308	56237410	2427,10567	2201	4296	6497	SO:0001819	synonymous_variant	219482	exon1			GGTCCCAGCACAG	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"""GPCR / Class A : Olfactory receptors"""	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.564T>C	11.37:g.56237410A>G		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	226	116	0.513274	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Silent	SNP	ENST00000312240.2	37	CCDS31532.1																																																																																			A|0.822;G|0.178	0.178	strong		0.393	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742	
LEPR	3953	hgsc.bcm.edu	37	1	66058513	66058513	+	Missense_Mutation	SNP	A	A	G	rs1137101	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:66058513A>G	ENST00000349533.6	+	6	853	c.668A>G	c.(667-669)cAg>cGg	p.Q223R	LEPR_ENST00000406510.3_Intron|LEPR_ENST00000371059.3_Missense_Mutation_p.Q223R|LEPR_ENST00000371058.1_Missense_Mutation_p.Q223R|LEPR_ENST00000371060.3_Missense_Mutation_p.Q223R|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000344610.8_Missense_Mutation_p.Q223R	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		GTAATTTTCCAGTCACCTCTA	0.363													A|||	2926	0.584265	0.5923	0.4366	5008	,	,		18691	0.869		0.4692	False		,,,				2504	0.5031				p.Q223R		Atlas-SNP	.											.	LEPR	284	.	0			c.A668G	GRCh37	CM010905	LEPR	M	rs1137101	PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	2471,1935	623.5+/-394.1	694,1083,426	97.0	95.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	668,668,668,668,668,668	3.7	1.0	1	dbSNP_86	95	3906,4694	544.9+/-384.7	901,2104,1295	yes	missense,missense,missense,missense,missense,missense	LEPR	NM_001003679.3,NM_001003680.3,NM_001198687.1,NM_001198688.1,NM_001198689.1,NM_002303.5	43,43,43,43,43,43	1595,3187,1721	GG,GA,AA		45.4186,43.9174,49.0312	benign,benign,benign,benign,benign,benign	223/897,223/959,223/959,223/907,223/897,223/1166	66058513	6377,6629	2203	4300	6503	SO:0001583	missense	3953	exon6			TTTTCCAGTCACC	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.668A>G	1.37:g.66058513A>G	ENSP00000330393:p.Gln223Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	158	158	1	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	1287	0.5892857142857143	265	0.5386178861788617	153	0.42265193370165743	496	0.8671328671328671	373	0.4920844327176781	A	13.55	2.271131	0.40194	0.560826	0.454186	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.54675	0.57;0.56;0.58;0.56;0.57	5.96	3.66	0.41972	.	0.550372	0.19543	N	0.111741	T	0.20740	0.0499	L	0.42245	1.32	0.09310	P	0.999999999633346	B;B;P	0.44195	0.282;0.404;0.828	B;B;B	0.36845	0.081;0.109;0.234	T	0.03566	-1.1024	9	0.21540	T	0.41	-0.1619	9.2279	0.37418	0.7896:0.0:0.2104:0.0	rs1137101;rs1805093;rs2229418;rs3200842;rs9282885;rs12131454;rs17356624;rs52820808;rs59347832;rs1137101	223;223;223	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	R	223	ENSP00000340884:Q223R;ENSP00000330393:Q223R;ENSP00000360099:Q223R;ENSP00000360098:Q223R;ENSP00000360097:Q223R	ENSP00000340884:Q223R	Q	+	2	0	LEPR	65831101	1.000000	0.71417	0.999000	0.59377	0.899000	0.52679	2.850000	0.48294	0.513000	0.28278	0.528000	0.53228	CAG	A|0.463;G|0.537	0.537	strong		0.363	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
KIAA1683	80726	hgsc.bcm.edu	37	19	18376522	18376522	+	Missense_Mutation	SNP	T	T	G	rs2277922	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18376522T>G	ENST00000600328.3	-	3	2021	c.1828A>C	c.(1828-1830)Acc>Ccc	p.T610P	KIAA1683_ENST00000392413.4_Missense_Mutation_p.T610P|KIAA1683_ENST00000600359.3_Missense_Mutation_p.T564P			Q9H0B3	K1683_HUMAN	KIAA1683	610			T -> P (in dbSNP:rs2277922). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TGTTTCTGGGTGCCAGTCTTG	0.552													G|||	2810	0.561102	0.7307	0.6052	5008	,	,		19984	0.5516		0.4533	False		,,,				2504	0.4213				p.T610P		Atlas-SNP	.											KIAA1683_ENST00000392413,brain,glioma,0,2	KIAA1683	190	2	0			c.A1828C						scavenged	.	G	PRO/THR,PRO/THR,PRO/THR	3109,1297	429.5+/-342.2	1115,879,209	51.0	58.0	56.0		1828,1690,1828	-4.4	0.0	19	dbSNP_100	56	3817,4783	607.3+/-395.2	866,2085,1349	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	38,38,38	1981,2964,1558	GG,GT,TT		44.3837,29.4371,46.7477	benign,benign,benign	610/1368,564/1135,610/1181	18376522	6926,6080	2203	4300	6503	SO:0001583	missense	80726	exon3			TCTGGGTGCCAGT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1828A>C	19.37:g.18376522T>G	ENSP00000470780:p.Thr610Pro	Somatic	212	5	0.0235849		WXS	Illumina HiSeq	Phase_I	200	98	0.49	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	1193	0.5462454212454212	356	0.7235772357723578	197	0.5441988950276243	298	0.5209790209790209	342	0.45118733509234826	G	0.109	-1.141439	0.01728	0.705629	0.443837	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634	T;T;T	0.03124	4.09;4.12;4.04	4.34	-4.38	0.03622	.	0.809793	0.10113	N	0.714497	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38243	-0.9670	9	0.02654	T	1	-2.4665	0.6945	0.00897	0.2027:0.2496:0.2971:0.2506	rs2277922;rs17724861;rs57437809;rs2277922	610;610	E9PDE0;Q9H0B3	.;K1683_HUMAN	P	610;610;564	ENSP00000376213:T610P;ENSP00000352774:T610P;ENSP00000404501:T564P	ENSP00000352774:T610P	T	-	1	0	KIAA1683	18237522	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.257000	0.02866	-1.210000	0.02627	-0.121000	0.15023	ACC	T|0.469;G|0.531	0.531	strong		0.552	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
HLA-B	3106	hgsc.bcm.edu	37	6	31323115	31323115	+	Missense_Mutation	SNP	T	T	C	rs281864645|rs41541515		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323115T>C	ENST00000412585.2	-	4	902	c.874A>G	c.(874-876)Aag>Gag	p.K292E		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	292	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GTGAGGGGCTTCGGCAGCCCC	0.577									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.K292E		Atlas-SNP	.											.	HLA-B	54	.	0			c.A874G						PASS	.						60.0	57.0	58.0					6																	31323115		2203	4300	6503	SO:0001583	missense	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	GGGGCTTCGGCAG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.874A>G	6.37:g.31323115T>C	ENSP00000399168:p.Lys292Glu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	171	47	0.274854	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	1.213	-0.629122	0.03610	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596	T	0.12361	2.69	3.16	-1.11	0.09840	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.181463	0.26062	N	0.026571	T	0.00754	0.0025	N	0.00729	-1.24	0.09310	N	0.999999	B	0.02656	0.0	B	0.06405	0.002	T	0.41822	-0.9487	10	0.16420	T	0.52	.	4.7803	0.13199	0.0:0.5345:0.1577:0.3077	rs41541515	292	P01889	1B07_HUMAN	E	292;171;171	ENSP00000399168:K292E	ENSP00000399168:K292E	K	-	1	0	HLA-B	31431094	0.000000	0.05858	0.047000	0.18901	0.189000	0.23516	-2.426000	0.01027	-0.413000	0.07507	-0.417000	0.06048	AAG	.	.	weak		0.577	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
AK9	221264	hgsc.bcm.edu	37	6	109827716	109827716	+	Missense_Mutation	SNP	C	C	T	rs2277114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:109827716C>T	ENST00000424296.2	-	35	4739	c.4663G>A	c.(4663-4665)Gta>Ata	p.V1555I	AL109947.2_ENST00000517228.1_RNA|RP5-919F19.5_ENST00000423747.2_RNA	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1555	Adenylate kinase 3.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TTGACAGCTACAATTTGTGCA	0.348													T|||	1905	0.380391	0.2814	0.4092	5008	,	,		20615	0.378		0.4105	False		,,,				2504	0.4652				p.V1555I		Atlas-SNP	.											.	AKD1	223	.	0			c.G4663A						PASS	.	T	ILE/VAL	399,985		60,279,353	186.0	133.0	149.0		4663	0.9	1.0	6	dbSNP_100	149	1222,1960		247,728,616	yes	missense	AKD1	NM_001145128.2	29	307,1007,969	TT,TC,CC		38.4035,28.8295,35.5015	benign	1555/1912	109827716	1621,2945	692	1591	2283	SO:0001583	missense	221264	exon35			CAGCTACAATTTG	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.4663G>A	6.37:g.109827716C>T	ENSP00000410186:p.Val1555Ile	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	227	92	0.405286	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	37	CCDS55048.1	865	0.39606227106227104	148	0.3008130081300813	146	0.40331491712707185	260	0.45454545454545453	311	0.4102902374670185	T	3.803	-0.041245	0.07452	0.288295	0.384035	ENSG00000155085	ENST00000424296	T	0.78003	-1.14	4.76	0.879	0.19155	ATPase, AAA+ type, core (1);	.	.	.	.	T	0.18341	0.0440	N	0.01048	-1.04	0.09310	P	0.999999999184006	B	0.02656	0.0	B	0.01281	0.0	T	0.07177	-1.0786	7	.	.	.	.	1.7741	0.03018	0.1123:0.184:0.3305:0.3733	rs2277114;rs61486674;rs2277114	1555	Q5TCS8	AKD1_HUMAN	I	1555	ENSP00000410186:V1555I	.	V	-	1	0	AKD1	109934409	1.000000	0.71417	0.978000	0.43139	0.024000	0.10985	1.754000	0.38369	0.269000	0.21961	-1.087000	0.02190	GTA	C|0.610;T|0.390	0.390	strong		0.348	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
ADCY3	109	hgsc.bcm.edu	37	2	25062875	25062875	+	Missense_Mutation	SNP	C	C	T	rs201606553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:25062875C>T	ENST00000260600.5	-	6	2073	c.1222G>A	c.(1222-1224)Ggg>Agg	p.G408R	ADCY3_ENST00000405392.1_Missense_Mutation_p.G19R	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	408					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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					ATGTCCACCCCAGTCTTGGTC	0.642													C|||	4	0.000798722	0.0	0.0058	5008	,	,		18860	0.0		0.0	False		,,,				2504	0.0				p.G408R		Atlas-SNP	.											.	ADCY3	114	.	0			c.G1222A						PASS	.	C	ARG/GLY	0,4406		0,0,2203	94.0	100.0	98.0		1222	5.1	0.5	2		98	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ADCY3	NM_004036.3	125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	408/1145	25062875	1,13005	2203	4300	6503	SO:0001583	missense	109	exon6			CCACCCCAGTCTT	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.1222G>A	2.37:g.25062875C>T	ENSP00000260600:p.Gly408Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_004036	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	37	CCDS1715.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417937	0.62622	0.0	1.16E-4	ENSG00000138031	ENST00000260600;ENST00000405392;ENST00000415879;ENST00000454027;ENST00000427849;ENST00000435135	D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87	5.05	5.05	0.67936	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.248631	0.39759	N	0.001263	D	0.83188	0.5200	N	0.20986	0.625	0.22827	N	0.998681	P;P;D	0.52996	0.843;0.843;0.957	P;P;P	0.55455	0.673;0.673;0.776	T	0.76016	-0.3113	10	0.44086	T	0.13	.	12.4747	0.55807	0.0:0.9179:0.0:0.0821	.	408;408;19	B7ZLX9;O60266;B3KT86	.;ADCY3_HUMAN;.	R	408;19;383;34;164;358	ENSP00000260600:G408R;ENSP00000384484:G19R;ENSP00000410120:G34R;ENSP00000399275:G164R;ENSP00000389799:G358R	ENSP00000260600:G408R	G	-	1	0	ADCY3	24916379	0.021000	0.18746	0.474000	0.27266	0.995000	0.86356	1.371000	0.34250	2.325000	0.78763	0.549000	0.68633	GGG	.	.	weak		0.642	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
OR5B12	390191	hgsc.bcm.edu	37	11	58207036	58207036	+	Missense_Mutation	SNP	T	T	A	rs201567144|rs148519730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:58207036T>A	ENST00000302572.2	-	1	610	c.589A>T	c.(589-591)Att>Ttt	p.I197F		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ACAAAAAAAATAACCATCTCA	0.393																																					p.I197F		Atlas-SNP	.											.	OR5B12	80	.	0			c.A589T						PASS	.						69.0	65.0	66.0					11																	58207036		2201	4295	6496	SO:0001583	missense	390191	exon1			AAAAAATAACCAT	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"""GPCR / Class A : Olfactory receptors"""	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.589A>T	11.37:g.58207036T>A	ENSP00000306657:p.Ile197Phe	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	136	59	0.433824	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	.	.	.	.	.	.	.	.	.	.	T	8.659	0.900137	0.17686	.	.	ENSG00000172362	ENST00000302572	T	0.00137	8.68	4.3	3.15	0.36227	GPCR, rhodopsin-like superfamily (1);	0.422268	0.20017	N	0.100981	T	0.00178	0.0005	L	0.52573	1.65	0.09310	N	1	B	0.14012	0.009	B	0.17979	0.02	T	0.28038	-1.0056	10	0.54805	T	0.06	-24.7022	9.4514	0.38727	0.1587:0.0:0.0:0.8413	.	197	Q96R08	OR5BC_HUMAN	F	197	ENSP00000306657:I197F	ENSP00000306657:I197F	I	-	1	0	OR5B12	57963612	0.000000	0.05858	0.617000	0.29091	0.689000	0.40095	-5.918000	0.00090	0.772000	0.33382	0.379000	0.24179	ATT	T|0.996;A|0.004	0.004	strong		0.393	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733	
FKBP15	23307	hgsc.bcm.edu	37	9	115931692	115931692	+	Silent	SNP	A	A	G	rs3810909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:115931692A>G	ENST00000238256.3	-	26	3414	c.3297T>C	c.(3295-3297)acT>acC	p.T1099T		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1099					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)		p.T1099T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						CGGGGTCTGAAGTCAGGGACA	0.572													A|||	964	0.192492	0.2133	0.2767	5008	,	,		18055	0.1925		0.167	False		,,,				2504	0.1309				p.T1099T		Atlas-SNP	.											FKBP15_ENST00000238256,NS,carcinoma,0,1	FKBP15	128	1	1	Substitution - coding silent(1)	stomach(1)	c.T3297C						PASS	.	A		832,3038		97,638,1200	82.0	85.0	84.0		3297	-0.2	0.9	9	dbSNP_107	84	1506,6760		139,1228,2766	no	coding-synonymous	FKBP15	NM_015258.1		236,1866,3966	GG,GA,AA		18.2192,21.4987,19.265		1099/1220	115931692	2338,9798	1935	4133	6068	SO:0001819	synonymous_variant	23307	exon26			GTCTGAAGTCAGG	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.3297T>C	9.37:g.115931692A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	235	118	0.502128	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			A|0.798;G|0.202	0.202	strong		0.572	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
OR2A14	135941	hgsc.bcm.edu	37	7	143826697	143826697	+	Missense_Mutation	SNP	C	C	G	rs2961161	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143826697C>G	ENST00000408899.2	+	1	547	c.492C>G	c.(490-492)agC>agG	p.S164R		NM_001001659.1	NP_001001659.1	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A, member 14	164			S -> R (in dbSNP:rs2961161). {ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:14983052}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(17)|skin(1)	22	Melanoma(164;0.0783)					TCATCCTGAGCCTGCCCTTCT	0.547													G|||	3383	0.675519	0.8154	0.745	5008	,	,		19163	0.7371		0.4851	False		,,,				2504	0.5695				p.S164R		Atlas-SNP	.											.	OR2A14	66	.	0			c.C492G						PASS	.	G	ARG/SER	3287,897		1294,699,99	211.0	231.0	224.0		492	2.4	1.0	7	dbSNP_101	224	4532,3928		1234,2064,932	no	missense	OR2A14	NM_001001659.1	110	2528,2763,1031	GG,GC,CC		46.4303,21.4388,38.1604	benign	164/311	143826697	7819,4825	2092	4230	6322	SO:0001583	missense	135941	exon1			CCTGAGCCTGCCC		CCDS43672.1	7q35	2013-09-20		2004-03-08	ENSG00000221938	ENSG00000221938		"""GPCR / Class A : Olfactory receptors"""	15084	protein-coding gene	gene with protein product				OR2A14P, OR2A6			Standard	NM_001001659		Approved	OST182	uc011kua.2	Q96R47	OTTHUMG00000158003	ENST00000408899.2:c.492C>G	7.37:g.143826697C>G	ENSP00000386137:p.Ser164Arg	Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	267	112	0.419476	NM_001001659	Q6IF41|Q8NGT8	Missense_Mutation	SNP	ENST00000408899.2	37	CCDS43672.1	1418	0.6492673992673993	394	0.8008130081300813	257	0.7099447513812155	426	0.7447552447552448	341	0.449868073878628	G	0.001	-2.896744	0.00059	0.785612	0.535697	ENSG00000221938	ENST00000408899	T	0.00169	8.63	4.18	2.36	0.29203	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33938	N	0.004406	T	0.00012	0.0000	N	0.01640	-0.785	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40059	-0.9583	9	0.02654	T	1	-5.8627	4.0211	0.09665	0.2932:0.1765:0.5303:0.0	rs2961161;rs12703585;rs17469121;rs33967479;rs52826416;rs61657644;rs2961161	164	Q96R47	O2A14_HUMAN	R	164	ENSP00000386137:S164R	ENSP00000386137:S164R	S	+	3	2	OR2A14	143457630	0.000000	0.05858	0.991000	0.47740	0.062000	0.15995	-3.450000	0.00466	0.167000	0.19631	-0.216000	0.12614	AGC	C|0.374;G|0.626	0.626	strong		0.547	OR2A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349980.1		
SF3B3	23450	hgsc.bcm.edu	37	16	70602221	70602221	+	Silent	SNP	C	C	T	rs12909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:70602221C>T	ENST00000302516.5	+	22	3199	c.2988C>T	c.(2986-2988)atC>atT	p.I996I		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	996					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)	p.I996I(1)		breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				TCCAGACTATCGGACATAGGG	0.418													T|||	2538	0.506789	0.4175	0.4193	5008	,	,		21558	0.5804		0.4155	False		,,,				2504	0.7076				p.I996I		Atlas-SNP	.											SF3B3,NS,carcinoma,0,1	SF3B3	99	1	1	Substitution - coding silent(1)	stomach(1)	c.C2988T						PASS	.	T		1727,2669	649.6+/-398.9	328,1071,799	126.0	121.0	123.0		2988	3.6	1.0	16	dbSNP_52	123	3642,4958	624.6+/-397.6	785,2072,1443	no	coding-synonymous	SF3B3	NM_012426.4		1113,3143,2242	TT,TC,CC		42.3488,39.2857,41.3127		996/1218	70602221	5369,7627	2198	4300	6498	SO:0001819	synonymous_variant	23450	exon22			GACTATCGGACAT	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"""splicing factor 3b, subunit 3, 130kD"""			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.2988C>T	16.37:g.70602221C>T		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	283	142	0.501767	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Silent	SNP	ENST00000302516.5	37	CCDS10894.1																																																																																			C|0.569;T|0.431	0.431	strong		0.418	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426	
DNAH7	56171	hgsc.bcm.edu	37	2	196791276	196791276	+	Silent	SNP	T	T	G	rs1489802	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:196791276T>G	ENST00000312428.6	-	22	3586	c.3486A>C	c.(3484-3486)gcA>gcC	p.A1162A		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1162	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AGGCAAAAGTTGCATCTCCAG	0.333													T|||	2404	0.480032	0.093	0.5764	5008	,	,		16510	0.5635		0.6471	False		,,,				2504	0.6769				p.A1162A		Atlas-SNP	.											.	DNAH7	512	.	0			c.A3486C						PASS	.	T		663,2965		71,521,1222	112.0	100.0	104.0		3486	-10.2	0.0	2	dbSNP_88	104	5083,3075		1569,1945,565	no	coding-synonymous	DNAH7	NM_018897.2		1640,2466,1787	GG,GT,TT		37.6931,18.2745,48.7528		1162/4025	196791276	5746,6040	1814	4079	5893	SO:0001819	synonymous_variant	56171	exon22			AAAAGTTGCATCT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.3486A>C	2.37:g.196791276T>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																			T|0.505;G|0.495	0.495	strong		0.333	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
EGF	1950	hgsc.bcm.edu	37	4	110897315	110897315	+	Silent	SNP	C	C	T	rs11568993	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:110897315C>T	ENST00000265171.5	+	13	2422	c.1977C>T	c.(1975-1977)tgC>tgT	p.C659C	EGF_ENST00000509793.1_Silent_p.C617C|EGF_ENST00000503392.1_Silent_p.C659C	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	659					activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	TGTACTGGTGCGATGCCAAGC	0.488													C|||	160	0.0319489	0.0053	0.0476	5008	,	,		19196	0.0		0.1034	False		,,,				2504	0.0164				p.C659C		Atlas-SNP	.											.	EGF	113	.	0			c.C1977T						PASS	.	C	,,	56,4350	54.2+/-90.2	0,56,2147	143.0	126.0	132.0		1977,1851,1977	-5.7	1.0	4	dbSNP_120	132	708,7892	174.9+/-225.1	33,642,3625	no	coding-synonymous,coding-synonymous,coding-synonymous	EGF	NM_001178130.1,NM_001178131.1,NM_001963.4	,,	33,698,5772	TT,TC,CC		8.2326,1.271,5.8742	,,	659/1167,617/1166,659/1208	110897315	764,12242	2203	4300	6503	SO:0001819	synonymous_variant	1950	exon13			CTGGTGCGATGCC	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"""epidermal growth factor (beta-urogastrone)"""				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.1977C>T	4.37:g.110897315C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	212	100	0.471698	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Silent	SNP	ENST00000265171.5	37	CCDS3689.1																																																																																			C|0.950;T|0.050	0.050	strong		0.488	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1		
TJP1	7082	hgsc.bcm.edu	37	15	30020172	30020172	+	Missense_Mutation	SNP	C	C	T	rs201475376		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:30020172C>T	ENST00000346128.6	-	16	2543	c.2069G>A	c.(2068-2070)cGc>cAc	p.R690H	RP11-680F8.4_ENST00000560740.1_RNA|TJP1_ENST00000400011.2_Missense_Mutation_p.R694H|TJP1_ENST00000356107.6_Missense_Mutation_p.R690H|TJP1_ENST00000545208.2_Missense_Mutation_p.R690H	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	690	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TGTATGCAGGCGAATAATGCC	0.363																																					p.R690H	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											TJP1,NS,carcinoma,0,1	TJP1	140	1	0			c.G2069A						scavenged	.						135.0	127.0	129.0					15																	30020172		1888	4131	6019	SO:0001583	missense	7082	exon16			TGCAGGCGAATAA		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"""zona occludens 1"", ""tight junction protein ZO-1"""	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.2069G>A	15.37:g.30020172C>T	ENSP00000281537:p.Arg690His	Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	139	3	0.0215827	NM_175610	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	C	35	5.502455	0.96371	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.08634	3.07;3.25;3.17;3.07	5.42	5.42	0.78866	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	0.000000	0.85682	D	0.000000	T	0.36826	0.0981	M	0.86953	2.85	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;0.998	T	0.20107	-1.0285	9	.	.	.	.	19.5771	0.95449	0.0:1.0:0.0:0.0	.	683;690;690;694	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	H	690;694;690;690;690	ENSP00000281537:R690H;ENSP00000382890:R694H;ENSP00000441202:R690H;ENSP00000348416:R690H	.	R	-	2	0	TJP1	27807464	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.664000	0.83830	2.687000	0.91594	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	weak		0.363	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257	
MFSD5	84975	hgsc.bcm.edu	37	12	53647373	53647373	+	Silent	SNP	T	T	C	rs10876422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53647373T>C	ENST00000329548.4	+	2	945	c.754T>C	c.(754-756)Ttg>Ctg	p.L252L	MFSD5_ENST00000534842.1_Silent_p.L359L	NM_032889.4	NP_116278.3	Q6N075	MFSD5_HUMAN	major facilitator superfamily domain containing 5	252					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(3)|urinary_tract(1)	16						CGTGCTGCTGTTGGGCACCAT	0.587													T|||	2320	0.463259	0.2625	0.4135	5008	,	,		21472	0.5972		0.4632	False		,,,				2504	0.6319				p.L359L		Atlas-SNP	.											.	MFSD5	40	.	0			c.T1075C						PASS	.	T	,	1332,3074	444.9+/-347.5	198,936,1069	103.0	101.0	101.0		1075,754	2.0	1.0	12	dbSNP_120	101	4039,4561	556.5+/-386.9	956,2127,1217	no	coding-synonymous,coding-synonymous	MFSD5	NM_001170790.1,NM_032889.4	,	1154,3063,2286	CC,CT,TT		46.9651,30.2315,41.2963	,	359/558,252/451	53647373	5371,7635	2203	4300	6503	SO:0001819	synonymous_variant	84975	exon2			CTGCTGTTGGGCA	AK097576	CCDS8851.1, CCDS53796.1	12q13.13	2012-03-09			ENSG00000182544	ENSG00000182544			28156	protein-coding gene	gene with protein product							Standard	NM_032889		Approved	MGC11308	uc001sch.2	Q6N075	OTTHUMG00000170028	ENST00000329548.4:c.754T>C	12.37:g.53647373T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_001170790	G3V1N7|Q6NW04|Q8N7W8|Q8NCK0|Q96IA5	Silent	SNP	ENST00000329548.4	37	CCDS8851.1																																																																																			T|0.569;C|0.431	0.431	strong		0.587	MFSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406896.1	NM_032889	
CCDC155	147872	hgsc.bcm.edu	37	19	49899076	49899076	+	Missense_Mutation	SNP	G	G	A	rs10405154	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49899076G>A	ENST00000447857.3	+	5	591	c.386G>A	c.(385-387)cGg>cAg	p.R129Q		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	129			R -> Q (in dbSNP:rs10405154). {ECO:0000269|PubMed:15489334}.			chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						CTGACCTCCCGGCAACTGCCA	0.577													G|||	2650	0.529153	0.4773	0.451	5008	,	,		19601	0.5119		0.5239	False		,,,				2504	0.6779				p.R129Q		Atlas-SNP	.											.	CCDC155	46	.	0			c.G386A						PASS	.	G	GLN/ARG	1929,1923		504,921,501	17.0	20.0	19.0		386	-8.4	0.5	19	dbSNP_119	19	4505,3711		1272,1961,875	yes	missense	CCDC155	NM_144688.4	43	1776,2882,1376	AA,AG,GG		45.168,49.9221,46.6854	benign	129/563	49899076	6434,5634	1926	4108	6034	SO:0001583	missense	147872	exon5			CCTCCCGGCAACT		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.386G>A	19.37:g.49899076G>A	ENSP00000404220:p.Arg129Gln	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_144688	Q96MC3	Missense_Mutation	SNP	ENST00000447857.3	37	CCDS46140.1	1093	0.5004578754578755	239	0.48577235772357724	177	0.4889502762430939	292	0.5104895104895105	385	0.5079155672823219	G	4.338	0.062162	0.08388	0.500779	0.54832	ENSG00000161609	ENST00000447857	T	0.28666	1.6	4.4	-8.35	0.00984	.	1.253840	0.05463	N	0.551692	T	0.00012	0.0000	N	0.00690	-1.25	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.40739	-0.9547	9	0.07030	T	0.85	-8.7147	7.1989	0.25868	0.399:0.2708:0.3303:0.0	rs10405154;rs17852702;rs61236743;rs10405154	129;129	C9JGW3;Q8N6L0	.;CC155_HUMAN	Q	129	ENSP00000404220:R129Q	ENSP00000404220:R129Q	R	+	2	0	CCDC155	54590888	0.983000	0.35010	0.470000	0.27216	0.905000	0.53344	-0.126000	0.10563	-1.579000	0.01646	-2.837000	0.00105	CGG	G|0.485;A|0.515	0.515	strong		0.577	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688	
LCP2	3937	hgsc.bcm.edu	37	5	169685163	169685163	+	Silent	SNP	C	C	T	rs315717	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:169685163C>T	ENST00000046794.5	-	16	1593	c.978G>A	c.(976-978)caG>caA	p.Q326Q	LCP2_ENST00000521416.1_Silent_p.Q121Q	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	326					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		GCAAAGGTCTCTGATGCACTG	0.493													T|||	2781	0.555312	0.6762	0.5865	5008	,	,		19183	0.5675		0.4712	False		,,,				2504	0.4438				p.Q326Q		Atlas-SNP	.											.	LCP2	133	.	0			c.G978A						PASS	.	T		2494,1374		820,854,260	166.0	164.0	165.0		978	-11.4	0.0	5	dbSNP_79	165	4023,4259		962,2099,1080	yes	coding-synonymous	LCP2	NM_005565.3		1782,2953,1340	TT,TC,CC		48.5752,35.5222,46.3621		326/534	169685163	6517,5633	1934	4141	6075	SO:0001819	synonymous_variant	3937	exon16			AGGTCTCTGATGC		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.978G>A	5.37:g.169685163C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	154	153	0.993506	NM_005565	A8KA25|Q53XV4	Silent	SNP	ENST00000046794.5	37	CCDS47339.1																																																																																			C|0.429;T|0.571	0.571	strong		0.493	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
TMEM259	91304	hgsc.bcm.edu	37	19	1012120	1012120	+	Silent	SNP	G	G	A	rs7145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1012120G>A	ENST00000356663.3	-	5	907	c.786C>T	c.(784-786)taC>taT	p.Y262Y	TMEM259_ENST00000333175.5_Silent_p.Y262Y	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	262						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GGATGTCATCGTAGCCCAGGA	0.692													g|||	698	0.139377	0.143	0.1124	5008	,	,		14783	0.0972		0.1561	False		,,,				2504	0.18				p.Y262Y		Atlas-SNP	.											C19orf6,NS,carcinoma,0,1	.	.	1	0			c.C786T						PASS	.	G	,	499,3899	217.4+/-235.8	29,441,1729	34.0	28.0	30.0		786,786	-6.6	0.8	19	dbSNP_52	30	1238,7358	228.9+/-263.8	91,1056,3151	no	coding-synonymous,coding-synonymous	C19orf6	NM_001033026.1,NM_033420.3	,	120,1497,4880	AA,AG,GG		14.402,11.3461,13.3677	,	262/621,262/409	1012120	1737,11257	2199	4298	6497	SO:0001819	synonymous_variant	91304	exon5			GTCATCGTAGCCC	BC008957	CCDS12052.1, CCDS32862.1	19p13.3	2013-02-06	2013-02-06	2013-02-06	ENSG00000182087	ENSG00000182087			17039	protein-coding gene	gene with protein product	"""membralin"", ""aspecific BCL2 ARE-binding protein 1"""	611011	"""chromosome 19 open reading frame 6"""	C19orf6		12638133, 16084606	Standard	XM_005259675		Approved	MGC4022, ASBABP1, MBRL	uc002lqr.1	Q4ZIN3		ENST00000356663.3:c.786C>T	19.37:g.1012120G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_033420	O60392|Q8NF79|Q96H30	Silent	SNP	ENST00000356663.3	37	CCDS32862.1																																																																																			G|0.868;A|0.132	0.132	strong		0.692	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420	
UTRN	7402	hgsc.bcm.edu	37	6	145103215	145103215	+	Silent	SNP	C	C	T	rs10499236	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:145103215C>T	ENST00000367545.3	+	60	8790	c.8790C>T	c.(8788-8790)ctC>ctT	p.L2930L	UTRN_ENST00000367526.4_Silent_p.L485L	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2930	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ACGTTCCACTCTGTGTTGATA	0.368													C|||	207	0.0413339	0.0023	0.0274	5008	,	,		20324	0.0476		0.0497	False		,,,				2504	0.089				p.L2930L		Atlas-SNP	.											.	UTRN	327	.	0			c.C8790T						PASS	.	C		32,4374	37.6+/-69.7	0,32,2171	114.0	103.0	107.0		8790	5.6	1.0	6	dbSNP_119	107	382,8218	124.4+/-183.2	11,360,3929	no	coding-synonymous	UTRN	NM_007124.2		11,392,6100	TT,TC,CC		4.4419,0.7263,3.1831		2930/3434	145103215	414,12592	2203	4300	6503	SO:0001819	synonymous_variant	7402	exon60			TCCACTCTGTGTT	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.8790C>T	6.37:g.145103215C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	261	118	0.452107	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	37	CCDS34547.1																																																																																			C|0.961;T|0.039	0.039	strong		0.368	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
TCEANC	170082	hgsc.bcm.edu	37	X	13681115	13681115	+	Missense_Mutation	SNP	C	C	T	rs2361159	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:13681115C>T	ENST00000380600.1	+	2	575	c.488C>T	c.(487-489)tCg>tTg	p.S163L	TCEANC_ENST00000544987.1_Missense_Mutation_p.S163L|TCEANC_ENST00000545566.1_Missense_Mutation_p.S163L|TCEANC_ENST00000314720.4_Missense_Mutation_p.S193L|TCEANC_ENST00000490617.1_3'UTR			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	163			S -> L (in dbSNP:rs2361159). {ECO:0000269|PubMed:14702039}.		regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						GGCAAGAGATCGAGTGAGTTG	0.433													C|||	2099	0.556026	0.3177	0.4035	3775	,	,		14768	0.4931		0.3847	False		,,,				2504	0.5266				p.S193L		Atlas-SNP	.											.	TCEANC	29	.	0			c.C578T						PASS	.	C	LEU/SER	1316,1977		225,633,233,503,338	118.0	109.0	112.0		578	1.1	0.0	X	dbSNP_100	112	3465,2990		663,1194,945,475,846	yes	missense	TCEANC	NM_152634.2	145	888,1827,1178,978,1184	TT,TC,T,CC,C		46.3207,39.9636,49.046	possibly-damaging	193/382	13681115	4781,4967	1932	4123	6055	SO:0001583	missense	170082	exon4			AGAGATCGAGTGA		CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.488C>T	X.37:g.13681115C>T	ENSP00000369974:p.Ser163Leu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	81	6	0.0740741	NM_152634	A6NI06|B2RDM3	Missense_Mutation	SNP	ENST00000380600.1	37		883	0.5322483423749247	113	0.2810945273631841	112	0.417910447761194	175	0.4654255319148936	193	0.34587813620071683	C	1.646	-0.515339	0.04200	0.399636	0.536793	ENSG00000176896	ENST00000545566;ENST00000544987;ENST00000314720;ENST00000380600	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.05	1.06	0.20224	Transcription elongation factor S-II, central domain (2);	1.011290	0.07944	N	0.979847	T	0.00012	0.0000	N	0.20986	0.625	0.80722	P	0.0	P;P	0.43352	0.78;0.804	B;B	0.31495	0.131;0.062	T	0.46735	-0.9170	9	0.21014	T	0.42	.	4.1344	0.10164	0.221:0.5369:0.1063:0.1358	rs2361159;rs12854188;rs59224066;rs2361159	193;163	Q8N8B7-2;Q8N8B7	.;TEANC_HUMAN	L	163;163;193;163	ENSP00000438952:S163L;ENSP00000440038:S163L;ENSP00000313886:S193L;ENSP00000369974:S163L	ENSP00000313886:S193L	S	+	2	0	TCEANC	13591036	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.826000	0.27407	-0.415000	0.07484	-0.905000	0.02835	TCG	C|0.472;T|0.528	0.528	strong		0.433	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055796.1	NM_152634	
MT-ND4L	4539	hgsc.bcm.edu	37	M	10550	10550	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:10550A>G	ENST00000361335.1	+	1	81	c.81A>G	c.(79-81)atA>atG	p.I27M	MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-ND4_ENST00000361381.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P03901	NU4LM_HUMAN	mitochondrially encoded NADH dehydrogenase 4L	27					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(2)|kidney(2)	5						TCACACCTCATATCCTCCCTA	0.373																																					p.M27M		Atlas-SNP	.											.	.	.	.	0			c.A81G						PASS	.																																			SO:0001583	missense	0	exon1			CCTCATATCCTCC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000212907	ENSG00000212907	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7460	protein-coding gene	gene with protein product	"""complex I ND4L subunit"", ""NADH-ubiquinone oxidoreductase chain 4L"""	516004	"""NADH dehydrogenase 4L"""	MTND4L			Standard			Approved	ND4L, NAD4L		P03901		ENST00000361335.1:c.81A>G	M.37:g.10550A>G	ENSP00000354728:p.Ile27Met	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	ENST00000361335		Silent	SNP	ENST00000361335.1	37																																																																																				.	.	none		0.373	MT-ND4L-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024034	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84609913	84609913	+	Silent	SNP	C	C	T	rs12341627	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:84609913C>T	ENST00000344803.2	+	4	4575	c.4528C>T	c.(4528-4530)Ctg>Ttg	p.L1510L		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1510					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGGGAAGATACTGTGTCAAAG	0.522													T|||	679	0.135583	0.3396	0.0807	5008	,	,		18160	0.0179		0.1292	False		,,,				2504	0.0266				p.L1510L		Atlas-SNP	.											.	.	.	.	0			c.C4528T						PASS	.	T		1246,2972		172,902,1035	49.0	50.0	50.0		4528	-1.7	0.0	9	dbSNP_120	50	880,7580		54,772,3404	no	coding-synonymous	FAM75D1	NM_001001670.2		226,1674,4439	TT,TC,CC		10.4019,29.5401,16.7692		1510/1577	84609913	2126,10552	2109	4230	6339	SO:0001819	synonymous_variant	389763	exon4			AAGATACTGTGTC		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.4528C>T	9.37:g.84609913C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	NM_001001670		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																			C|0.882;T|0.118	0.118	strong		0.522	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
STK10	6793	hgsc.bcm.edu	37	5	171523513	171523513	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:171523513C>A	ENST00000176763.5	-	8	1265	c.922G>T	c.(922-924)Gct>Tct	p.A308S	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	308					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTGGCCTCAGCCACCAGCTCC	0.622																																					p.A308S		Atlas-SNP	.											.	STK10	100	.	0			c.G922T						PASS	.						109.0	105.0	106.0					5																	171523513		2203	4300	6503	SO:0001583	missense	6793	exon8			CCTCAGCCACCAG	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.922G>T	5.37:g.171523513C>A	ENSP00000176763:p.Ala308Ser	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	62	7	0.112903	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.920058	0.73098	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.68479	-0.33	4.96	4.96	0.65561	Protein kinase-like domain (1);	0.061568	0.64402	N	0.000005	T	0.72495	0.3467	M	0.74647	2.275	0.80722	D	1	B	0.27140	0.169	B	0.41510	0.359	T	0.67492	-0.5657	10	0.14656	T	0.56	.	15.7705	0.78164	0.0:1.0:0.0:0.0	.	308	O94804	STK10_HUMAN	S	308	ENSP00000176763:A308S	ENSP00000176763:A308S	A	-	1	0	STK10	171456118	1.000000	0.71417	0.997000	0.53966	0.953000	0.61014	7.791000	0.85805	2.320000	0.78422	0.485000	0.47835	GCT	.	.	none		0.622	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
MUC2	4583	hgsc.bcm.edu	37	11	1103296	1103296	+	Silent	SNP	T	T	C	rs7126405	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1103296T>C	ENST00000441003.2	+	46	8073	c.8046T>C	c.(8044-8046)ttT>ttC	p.F2682F		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5044					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCCCCAACTTTGATGCCAGCA	0.597													C|||	833	0.166334	0.4259	0.0778	5008	,	,		18842	0.0357		0.1123	False		,,,				2504	0.0685				p.F2678F		Atlas-SNP	.											.	MUC2	614	.	0			c.T8034C						PASS	.	C		1439,2763		236,967,898	124.0	132.0	129.0		8031	-1.3	0.0	11	dbSNP_116	129	864,7562		36,792,3385	no	coding-synonymous	MUC2	NM_002457.2		272,1759,4283	CC,CT,TT		10.254,34.2456,18.2373		2677/2813	1103296	2303,10325	2101	4213	6314	SO:0001819	synonymous_variant	4583	exon47			CAACTTTGATGCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.8046T>C	11.37:g.1103296T>C		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	282	137	0.485816	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.845;C|0.155	0.155	strong		0.597	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
HLA-C	3107	hgsc.bcm.edu	37	6	31238868	31238868	+	Missense_Mutation	SNP	C	C	T	rs1131103	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238868C>T	ENST00000376228.5	-	3	615	c.601G>A	c.(601-603)Gag>Aag	p.E201K	HLA-C_ENST00000383329.3_Missense_Mutation_p.E201K	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	201	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TGCAGCGTCTCCTTCCCGTTC	0.662																																					p.E201K		Atlas-SNP	.											.	HLA-C	92	.	0			c.G601A						PASS	.						54.0	45.0	48.0					6																	31238868		2203	4299	6502	SO:0001583	missense	3107	exon3			GCGTCTCCTTCCC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.601G>A	6.37:g.31238868C>T	ENSP00000365402:p.Glu201Lys	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	187	65	0.347594	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	258|258	0.11813186813186813|0.11813186813186813	48|48	0.0975609756097561|0.0975609756097561	59|59	0.16298342541436464|0.16298342541436464	56|56	0.0979020979020979|0.0979020979020979	95|95	0.12532981530343007|0.12532981530343007	.|.	11.76|11.76	1.734775|1.734775	0.30774|0.30774	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00808|.	5.67;5.67|.	2.55|2.55	2.55|2.55	0.30701|0.30701	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	1.613380|.	0.04968|.	U|.	0.463348|.	T|T	0.39091|0.39091	0.1065|0.1065	.|.	.|.	.|.	0.39265|0.39265	P|P	0.035726000000000036|0.035726000000000036	B;B;B;B|.	0.06786|.	0.0;0.0;0.0;0.001|.	B;B;B;B|.	0.12156|.	0.004;0.004;0.007;0.006|.	T|T	0.26430|0.26430	-1.0103|-1.0103	8|3	0.54805|.	T|.	0.06|.	.|.	11.1964|11.1964	0.48715|0.48715	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs1131103;rs3177875;rs3190647;rs17362022;rs17416835|rs1131103;rs3177875;rs3190647;rs17362022;rs17416835	201;201;201;201|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	K|E	201;201;201;238|200	ENSP00000365402:E201K;ENSP00000372819:E201K|.	ENSP00000365402:E201K|.	E|G	-|-	1|2	0|0	HLA-C|HLA-C	31346847|31346847	0.045000|0.045000	0.20229|0.20229	0.992000|0.992000	0.48379|0.48379	0.083000|0.083000	0.17756|0.17756	0.926000|0.926000	0.28804|0.28804	1.745000|1.745000	0.51790|0.51790	0.305000|0.305000	0.20034|0.20034	GAG|GGA	T|0.114;C|0.886	0.114	strong		0.662	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994488	45994488	+	Missense_Mutation	SNP	G	G	T	rs396912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:45994488G>T	ENST00000400374.3	+	1	883	c.853G>T	c.(853-855)Ggc>Tgc	p.G285C	TSPEAR_ENST00000397916.1_5'Flank|TSPEAR_ENST00000323084.4_Intron	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	285	36 X 5 AA repeats of C-C-X(3).		G -> C (in dbSNP:rs396912).			keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CAAGCCTGTCGGCTCTGTGCC	0.642													.|||	931	0.185903	0.3812	0.0937	5008	,	,		22814	0.2054		0.0368	False		,,,				2504	0.1207				p.G285C		Atlas-SNP	.											KRTAP10-4,colon,carcinoma,-1,1	KRTAP10-4	44	1	0			c.G853T						PASS	.	T	,CYS/GLY	1527,2879	669.8+/-402.2	259,1009,935	115.0	120.0	118.0		,853	1.9	0.0	21	dbSNP_80	118	266,8334	803.6+/-407.3	4,258,4038	no	intron,missense	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,159	263,1267,4973	TT,TG,GG		3.093,34.6573,13.7859	,benign	,285/402	45994488	1793,11213	2203	4300	6503	SO:0001583	missense	386672	exon1			CCTGTCGGCTCTG	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.853G>T	21.37:g.45994488G>T	ENSP00000383225:p.Gly285Cys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	181	87	0.480663	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	365|365	0.1671245421245421|0.1671245421245421	181|181	0.3678861788617886|0.3678861788617886	33|33	0.09116022099447514|0.09116022099447514	130|130	0.22727272727272727|0.22727272727272727	21|21	0.027704485488126648|0.027704485488126648	T|t	0.403|0.403	-0.917088|-0.917088	0.02415|0.02415	0.346573|0.346573	0.03093|0.03093	ENSG00000215454|ENSG00000215454	ENST00000334871|ENST00000400374	.|T	.|0.00686	.|5.85	4.38|4.38	1.89|1.89	0.25635|0.25635	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	N|N	0.00019|0.00019	-2.79|-2.79	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	.|T	.|0.41698	.|-0.9494	.|8	.|0.02654	.|T	.|1	.|.	1.2795|1.2795	0.02037|0.02037	0.299:0.0913:0.154:0.4556|0.299:0.0913:0.154:0.4556	rs396912;rs396912|rs396912;rs396912	.|285	.|P60372	.|KR104_HUMAN	.|C	-1|285	.|ENSP00000383225:G285C	.|ENSP00000383225:G285C	.|G	+|+	.|1	.|0	KRTAP10-4|KRTAP10-4	44818916|44818916	0.040000|0.040000	0.19996|0.19996	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-0.499000|-0.499000	0.06413|0.06413	0.160000|0.160000	0.19432|0.19432	-0.320000|-0.320000	0.08662|0.08662	.|GGC	G|0.785;T|0.215	0.215	strong		0.642	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
AKAP13	11214	hgsc.bcm.edu	37	15	86122916	86122916	+	Silent	SNP	T	T	C	rs2061823	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86122916T>C	ENST00000394518.2	+	7	1712	c.1617T>C	c.(1615-1617)gcT>gcC	p.A539A	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Silent_p.A539A	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	539					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						GTGCCCCTGCTGCCAGTTCCC	0.448													C|||	2921	0.583267	0.5507	0.6182	5008	,	,		21386	0.5794		0.6153	False		,,,				2504	0.5736				p.A539A	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											AKAP13_ENST00000394518,NS,carcinoma,+2,2	AKAP13	394	2	0			c.T1617C						scavenged	.	C	,	2609,1795	524.3+/-371.3	784,1041,377	82.0	89.0	87.0		1617,1617	1.2	0.0	15	dbSNP_94	87	5536,3062	465.0+/-366.4	1796,1944,559	no	coding-synonymous,coding-synonymous	AKAP13	NM_006738.4,NM_007200.3	,	2580,2985,936	CC,CT,TT		35.6129,40.7584,37.3558	,	539/2818,539/2814	86122916	8145,4857	2202	4299	6501	SO:0001819	synonymous_variant	11214	exon7			CCCTGCTGCCAGT	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.1617T>C	15.37:g.86122916T>C		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	37	CCDS32319.1																																																																																			T|0.379;C|0.621	0.621	strong		0.448	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
ERI2	112479	hgsc.bcm.edu	37	16	20809283	20809283	+	Silent	SNP	C	C	A	rs11648835	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20809283C>A	ENST00000357967.4	-	9	1881	c.1839G>T	c.(1837-1839)ccG>ccT	p.P613P	ERI2_ENST00000569729.1_3'UTR|ERI2_ENST00000563117.1_Silent_p.P520P|ERI2_ENST00000564349.1_Silent_p.P520P|ERI2_ENST00000300005.3_Intron|ERI2_ENST00000389345.5_Silent_p.P348P	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	613							exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(2)	11						TTCCATGGTTCGGTCCATTAT	0.393													C|||	1025	0.204673	0.3064	0.1023	5008	,	,		18283	0.2212		0.1262	False		,,,				2504	0.2035				p.P613P		Atlas-SNP	.											.	ERI2	50	.	0			c.G1839T						PASS	.	C	,	377,1007		53,271,368	110.0	88.0	95.0		1839,	-2.5	1.0	16	dbSNP_120	95	450,2732		33,384,1174	no	coding-synonymous,intron	ERI2	NM_001142725.1,NM_080663.2	,	86,655,1542	AA,AC,CC		14.142,27.2399,18.1121	,	613/692,	20809283	827,3739	692	1591	2283	SO:0001819	synonymous_variant	112479	exon9			ATGGTTCGGTCCA	BC010503	CCDS10590.1, CCDS45436.1	16p12.3	2014-02-18	2009-10-07	2008-12-16	ENSG00000196678	ENSG00000196678		"""Enhanced RNAi three prime mRNA exonucleases"""	30541	protein-coding gene	gene with protein product	"""enhanced RNAi three prime mRNA exonuclease homolog 2 (C.elegans)"", ""exoribonuclease 2"", ""zinc finger, GRF-type containing 5"""		"""exonuclease domain containing 1"""	EXOD1		10819331	Standard	NM_080663		Approved	KIAA1504, MGC16943, ZGRF5	uc010vbb.1	A8K979	OTTHUMG00000131557	ENST00000357967.4:c.1839G>T	16.37:g.20809283C>A		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	277	142	0.512635	NM_001142725	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Silent	SNP	ENST00000357967.4	37	CCDS45436.1																																																																																			C|0.817;A|0.183	0.183	strong		0.393	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663	
OR2F2	135948	hgsc.bcm.edu	37	7	143633157	143633157	+	Missense_Mutation	SNP	T	T	C	rs13235235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143633157T>C	ENST00000408955.2	+	1	899	c.832T>C	c.(832-834)Tat>Cat	p.Y278H		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, member 2	278			Y -> H (in dbSNP:rs13235235).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(19)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	32	Melanoma(164;0.0903)					CTCTGTCTTCTATGCCATTGT	0.478													T|||	829	0.165535	0.3464	0.1657	5008	,	,		21510	0.002		0.2028	False		,,,				2504	0.0511				p.Y278H		Atlas-SNP	.											.	OR2F2	63	.	0			c.T832C						PASS	.	T	HIS/TYR	1462,2926	434.7+/-344.0	237,988,969	96.0	98.0	98.0		832	3.6	0.6	7	dbSNP_121	98	1923,6675	330.9+/-319.4	205,1513,2581	yes	missense	OR2F2	NM_001004685.1	83	442,2501,3550	CC,CT,TT		22.3657,33.3181,26.0665	probably-damaging	278/318	143633157	3385,9601	2194	4299	6493	SO:0001583	missense	135948	exon1			GTCTTCTATGCCA		CCDS43666.1	7q33-q35	2012-08-09			ENSG00000221910	ENSG00000221910		"""GPCR / Class A : Olfactory receptors"""	8247	protein-coding gene	gene with protein product							Standard	NM_001004685		Approved	OR7-1	uc011ktv.2	O95006	OTTHUMG00000157768	ENST00000408955.2:c.832T>C	7.37:g.143633157T>C	ENSP00000386222:p.Tyr278His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_001004685	A4D2G0|Q6IFP8	Missense_Mutation	SNP	ENST00000408955.2	37	CCDS43666.1	371	0.16987179487179488	159	0.3231707317073171	68	0.1878453038674033	0	0.0	144	0.18997361477572558	T	9.646	1.140355	0.21205	0.333181	0.223657	ENSG00000221910	ENST00000408955	T	0.00321	8.11	3.57	3.57	0.40892	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43919	D	0.000515	T	0.00012	0.0000	M	0.91196	3.185	0.39213	P	0.03664500000000004	D	0.89917	1.0	D	0.91635	0.999	T	0.41980	-0.9478	9	0.87932	D	0	-21.8475	10.4204	0.44346	0.0:0.0:0.0:1.0	rs13235235;rs17164452;rs52806957;rs13235235	278	O95006	OR2F2_HUMAN	H	278	ENSP00000386222:Y278H	ENSP00000386222:Y278H	Y	+	1	0	OR2F2	143264090	0.970000	0.33590	0.616000	0.29078	0.088000	0.18126	4.377000	0.59562	1.626000	0.50381	0.402000	0.26972	TAT	T|0.805;C|0.195	0.195	strong		0.478	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1		
POLE	5426	hgsc.bcm.edu	37	12	133233812	133233812	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133233812G>A	ENST00000320574.5	-	29	3535	c.3492C>T	c.(3490-3492)ccC>ccT	p.P1164P	POLE_ENST00000535270.1_Silent_p.P1137P	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1164					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GCAGCCAGTCGGGGTGTTTGA	0.532								DNA polymerases (catalytic subunits)																													p.P1164P		Atlas-SNP	.											.	POLE	416	.	0			c.C3492T						PASS	.						100.0	98.0	99.0					12																	133233812		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon29			CCAGTCGGGGTGT		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.3492C>T	12.37:g.133233812G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	201	101	0.502488	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			.	.	none		0.532	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
ITGB1	3688	hgsc.bcm.edu	37	10	33211227	33211227	+	Silent	SNP	T	T	G	rs2230395	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:33211227T>G	ENST00000396033.2	-	9	1221	c.1086A>C	c.(1084-1086)gcA>gcC	p.A362A	ITGB1_ENST00000423113.1_Silent_p.A362A|ITGB1_ENST00000302278.3_Silent_p.A362A|ITGB1_ENST00000374956.4_Silent_p.A362A	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	362	VWFA.				axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	TGCTAGAATTTGCAGATAATG	0.328													T|||	956	0.190895	0.2511	0.0937	5008	,	,		18921	0.3115		0.1233	False		,,,				2504	0.1237				p.A362A		Atlas-SNP	.											ITGB1_ENST00000396033,colon,carcinoma,0,2	ITGB1	156	2	0			c.A1086C						PASS	.	T	,,	1047,3359	382.8+/-324.6	131,785,1287	172.0	158.0	163.0		1086,1086,1086	-1.6	1.0	10	dbSNP_98	163	865,7735	197.2+/-241.9	39,787,3474	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB1	NM_002211.3,NM_033668.2,NM_133376.2	,,	170,1572,4761	GG,GT,TT		10.0581,23.7631,14.7009	,,	362/799,362/802,362/799	33211227	1912,11094	2203	4300	6503	SO:0001819	synonymous_variant	3688	exon9			AGAATTTGCAGAT	BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"""CD molecules"", ""Integrins"""	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.1086A>C	10.37:g.33211227T>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_002211	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Silent	SNP	ENST00000396033.2	37	CCDS7174.1																																																																																			T|0.709;G|0.135;C|0.036;A|0.120	0.135	strong		0.328	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211	
OR2T34	127068	hgsc.bcm.edu	37	1	248737511	248737511	+	Missense_Mutation	SNP	A	A	G	rs150608839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248737511A>G	ENST00000328782.2	-	1	569	c.548T>C	c.(547-549)tTc>tCc	p.F183S		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F183S(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGTCTCACAGAAAAAACTCAG	0.517													a|||	776	0.154952	0.2935	0.111	5008	,	,		20908	0.0942		0.1034	False		,,,				2504	0.1145				p.F183S		Atlas-SNP	.											OR2T34,NS,haematopoietic_neoplasm,0,2	OR2T34	72	2	1	Substitution - Missense(1)	stomach(1)	c.T548C						PASS	.	A	SER/PHE	894,3422		141,612,1405	67.0	84.0	78.0		548	-0.6	0.2	1	dbSNP_134	78	279,8315		1,277,4019	no	missense	OR2T34	NM_001001821.1	155	142,889,5424	GG,GA,AA		3.2465,20.7136,9.086	probably-damaging	183/319	248737511	1173,11737	2158	4297	6455	SO:0001583	missense	127068	exon1			TCACAGAAAAAAC	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.548T>C	1.37:g.248737511A>G	ENSP00000330904:p.Phe183Ser	Somatic	469	0	0		WXS	Illumina HiSeq	Phase_I	632	140	0.221519	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	316	0.1446886446886447	135	0.27439024390243905	47	0.1298342541436464	51	0.08916083916083917	83	0.10949868073878628	.	12.99	2.104183	0.37145	0.207136	0.032465	ENSG00000183310	ENST00000328782	T	0.00258	8.41	2.37	-0.608	0.11611	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.88570	2.965	0.48288	P	3.769999999999607E-4	D	0.76494	0.999	D	0.79784	0.993	T	0.50110	-0.8866	8	0.87932	D	0	.	3.4931	0.07645	0.6779:0.0:0.1275:0.1946	.	183	Q8NGX1	O2T34_HUMAN	S	183	ENSP00000330904:F183S	ENSP00000330904:F183S	F	-	2	0	OR2T34	246804134	1.000000	0.71417	0.152000	0.22495	0.007000	0.05969	1.350000	0.34010	0.088000	0.17205	0.104000	0.15600	TTC	.	.	weak		0.517	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
OR5R1	219479	hgsc.bcm.edu	37	11	56185224	56185224	+	Missense_Mutation	SNP	A	A	G	rs12785840	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56185224A>G	ENST00000312253.1	-	1	484	c.485T>C	c.(484-486)aTc>aCc	p.I162T		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	162			I -> T (in dbSNP:rs12785840).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I162T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					ACGGAAAGTGATAACGGTGTG	0.453													A|||	621	0.124002	0.1944	0.0663	5008	,	,		21271	0.0933		0.1402	False		,,,				2504	0.0849				p.I162T		Atlas-SNP	.											OR5R1,NS,carcinoma,0,1	OR5R1	83	1	1	Substitution - Missense(1)	stomach(1)	c.T485C						PASS	.	A	THR/ILE	762,3640	313.0+/-292.9	67,628,1506	113.0	112.0	112.0		485	3.5	0.7	11	dbSNP_121	112	1191,7401	243.3+/-273.0	75,1041,3180	yes	missense	OR5R1	NM_001004744.1	89	142,1669,4686	GG,GA,AA		13.8617,17.3103,15.03	possibly-damaging	162/325	56185224	1953,11041	2201	4296	6497	SO:0001583	missense	219479	exon1			AAAGTGATAACGG	AB065504	CCDS31530.1	11q11	2012-08-09		2004-03-10	ENSG00000174942	ENSG00000174942		"""GPCR / Class A : Olfactory receptors"""	14841	protein-coding gene	gene with protein product				OR5R1P			Standard	NM_001004744		Approved		uc010rji.2	Q8NH85	OTTHUMG00000154219	ENST00000312253.1:c.485T>C	11.37:g.56185224A>G	ENSP00000308595:p.Ile162Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	37	CCDS31530.1	294	0.1346153846153846	112	0.22764227642276422	38	0.10497237569060773	42	0.07342657342657342	102	0.1345646437994723	A	1.240	-0.621485	0.03636	0.173103	0.138617	ENSG00000174942	ENST00000312253	T	0.00123	8.7	5.91	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.249670	0.20616	U	0.088874	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.29955	0.263	B	0.33121	0.158	T	0.00030	-1.2284	9	0.22109	T	0.4	-14.6421	4.351	0.11155	0.613:0.0:0.1359:0.2511	rs12785840;rs17627213;rs61597384;rs12785840	162	Q8NH85	OR5R1_HUMAN	T	162	ENSP00000308595:I162T	ENSP00000308595:I162T	I	-	2	0	OR5R1	55941800	0.000000	0.05858	0.663000	0.29738	0.021000	0.10359	1.455000	0.35190	1.028000	0.39785	0.472000	0.43445	ATC	A|0.853;G|0.147	0.147	strong		0.453	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744	
MUC16	94025	hgsc.bcm.edu	37	19	9083174	9083174	+	Missense_Mutation	SNP	G	G	A	rs7245960	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9083174G>A	ENST00000397910.4	-	1	8844	c.8641C>T	c.(8641-8643)Cca>Tca	p.P2881S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2881	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCCCAAGTTGGGGGAGCTGTA	0.527													G|||	1135	0.226637	0.2708	0.2983	5008	,	,		21319	0.0228		0.3111	False		,,,				2504	0.2393				p.P2881S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C8641T						PASS	.	G	SER/PRO	1025,2837		145,735,1051	65.0	61.0	62.0		8641	-1.5	0.0	19	dbSNP_116	62	2725,5561		461,1803,1879	yes	missense	MUC16	NM_024690.2	74	606,2538,2930	AA,AG,GG		32.8868,26.5407,30.8693	benign	2881/14508	9083174	3750,8398	1931	4143	6074	SO:0001583	missense	94025	exon1			AAGTTGGGGGAGC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8641C>T	19.37:g.9083174G>A	ENSP00000381008:p.Pro2881Ser	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	202	201	0.995049	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	490	0.22435897435897437	127	0.258130081300813	111	0.30662983425414364	14	0.024475524475524476	238	0.31398416886543534	g	0.010	-1.770807	0.00645	0.265407	0.328868	ENSG00000181143	ENST00000397910	T	0.03124	4.04	0.773	-1.55	0.08558	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.06786	0.001	B	0.04013	0.001	T	0.48281	-0.9049	8	0.87932	D	0	.	3.4546	0.07511	0.2113:0.0:0.551:0.2378	rs7245960;rs7245960	2881	B5ME49	.	S	2881	ENSP00000381008:P2881S	ENSP00000381008:P2881S	P	-	1	0	MUC16	8944174	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-1.153000	0.03169	-2.439000	0.00551	-2.281000	0.00270	CCA	G|0.757;A|0.243	0.243	strong		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LILRA6	79168	hgsc.bcm.edu	37	19	54745907	54745907	+	Missense_Mutation	SNP	A	A	G	rs62133127	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54745907A>G	ENST00000396365.2	-	3	389	c.350T>C	c.(349-351)aTg>aCg	p.M117T	LILRA6_ENST00000245621.5_Missense_Mutation_p.M117T|LILRA6_ENST00000419410.2_Missense_Mutation_p.M117T|LILRB3_ENST00000407860.2_Missense_Mutation_p.M117T|LILRA6_ENST00000440558.2_Missense_Mutation_p.M117T|LILRA6_ENST00000270464.5_Missense_Mutation_p.M117T|LILRA6_ENST00000391735.3_Missense_Mutation_p.M117T	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	117					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CTCACCTGTCATCACCAGCTC	0.647																																					p.M117T		Atlas-SNP	.											LILRA6,NS,neuroblastoma,0,2	LILRA6	75	2	0			c.T350C						PASS	.						184.0	183.0	183.0					19																	54745907		2203	4300	6503	SO:0001583	missense	79168	exon3			CCTGTCATCACCA	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.350T>C	19.37:g.54745907A>G	ENSP00000379651:p.Met117Thr	Somatic	385	0	0		WXS	Illumina HiSeq	Phase_I	422	118	0.279621	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	209	0.09569597069597069	6	0.012195121951219513	50	0.13812154696132597	30	0.05244755244755245	123	0.16226912928759896	A	5.562	0.288572	0.10513	.	.	ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T;T	0.09163	3.01;3.01;3.01;3.01;3.01;3.01;3.01	3.4	3.4	0.38934	Immunoglobulin-like fold (1);	0.267597	0.26355	N	0.024855	T	0.00073	0.0002	M	0.69358	2.11	0.09310	N	0.999999	B;B;B;B;D;B;B;B;B;B	0.53151	0.015;0.128;0.019;0.001;0.958;0.02;0.029;0.051;0.041;0.041	B;B;B;B;P;B;B;B;B;B	0.53062	0.112;0.136;0.06;0.015;0.717;0.043;0.01;0.033;0.164;0.019	T	0.03077	-1.1075	10	0.87932	D	0	.	8.4256	0.32727	1.0:0.0:0.0:0.0	rs62133127	117;117;117;117;117;117;117;117;117;117	C9JFH3;Q6PI73-2;B5MCX0;B5ME96;Q6PI73;F8WCY4;F8WD89;D3YTC4;F8W6G6;O75022-2	.;.;.;.;LIRA6_HUMAN;.;.;.;.;.	T	117	ENSP00000384274:M117T;ENSP00000390120:M117T;ENSP00000270464:M117T;ENSP00000411227:M117T;ENSP00000375615:M117T;ENSP00000379651:M117T;ENSP00000245621:M117T	ENSP00000245621:M117T	M	-	2	0	LILRB3;LILRA6	59437719	0.209000	0.23505	0.996000	0.52242	0.049000	0.14656	1.457000	0.35212	1.574000	0.49760	0.155000	0.16302	ATG	A|0.250;G|0.750	0.750	weak		0.647	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
SCN7A	6332	hgsc.bcm.edu	37	2	167262939	167262939	+	Silent	SNP	A	A	G	rs33953730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:167262939A>G	ENST00000409855.1	-	25	4326	c.4200T>C	c.(4198-4200)taT>taC	p.Y1400Y		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1400					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	AGGCAAAATTATACATTCCAA	0.353													G|||	266	0.053115	0.031	0.0288	5008	,	,		20106	0.0129		0.0775	False		,,,				2504	0.1166				p.Y1400Y		Atlas-SNP	.											SCN7A_ENST00000409855,NS,carcinoma,-1,2	SCN7A	410	2	0			c.T4200C						PASS	.	G		181,3697		3,175,1761	111.0	110.0	110.0		4200	2.2	1.0	2	dbSNP_126	110	821,7515		38,745,3385	no	coding-synonymous	SCN7A	NM_002976.3		41,920,5146	GG,GA,AA		9.8488,4.6674,8.2037		1400/1683	167262939	1002,11212	1939	4168	6107	SO:0001819	synonymous_variant	6332	exon25			AAAATTATACATT	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.4200T>C	2.37:g.167262939A>G		Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	418	209	0.5	NM_002976		Silent	SNP	ENST00000409855.1	37	CCDS46442.1																																																																																			A|0.948;G|0.052	0.052	strong		0.353	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
SDK2	54549	hgsc.bcm.edu	37	17	71384010	71384010	+	Silent	SNP	G	G	A	rs35928335	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:71384010G>A	ENST00000392650.3	-	30	4359	c.4359C>T	c.(4357-4359)tcC>tcT	p.S1453S	SDK2_ENST00000388726.3_Silent_p.S1453S	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1453	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						TGTGGCTCACGGAGGCCGAGT	0.677													G|||	279	0.0557109	0.1006	0.049	5008	,	,		13940	0.0		0.0676	False		,,,				2504	0.045				p.S1453S		Atlas-SNP	.											.	SDK2	219	.	0			c.C4359T						PASS	.	G		350,4046		18,314,1866	27.0	18.0	21.0		4359	-3.2	0.9	17	dbSNP_126	21	467,8093		17,433,3830	no	coding-synonymous	SDK2	NM_001144952.1		35,747,5696	AA,AG,GG		5.4556,7.9618,6.306		1453/2173	71384010	817,12139	2198	4280	6478	SO:0001819	synonymous_variant	54549	exon30			GCTCACGGAGGCC	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.4359C>T	17.37:g.71384010G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	158	88	0.556962	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1																																																																																			G|0.944;A|0.056	0.056	strong		0.677	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
PDZD2	23037	hgsc.bcm.edu	37	5	32087802	32087802	+	Silent	SNP	A	A	G	rs157497|rs113511990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:32087802A>G	ENST00000438447.1	+	20	4636	c.4248A>G	c.(4246-4248)ccA>ccG	p.P1416P	PDZD2_ENST00000282493.3_Silent_p.P1416P			O15018	PDZD2_HUMAN	PDZ domain containing 2	1416					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						ACTGCTGCCCAGGGGGGAGTA	0.592													G|||	2457	0.490615	0.4115	0.3905	5008	,	,		19362	0.6508		0.3728	False		,,,				2504	0.6247				p.P1416P		Atlas-SNP	.											.	PDZD2	306	.	0			c.A4248G						PASS	.	G		1639,2767		364,911,928	41.0	41.0	41.0		4248	-9.4	0.0	5	dbSNP_79	41	2235,6365		441,1353,2506	no	coding-synonymous	PDZD2	NM_178140.2		805,2264,3434	GG,GA,AA		25.9884,37.1993,29.7863		1416/2840	32087802	3874,9132	2203	4300	6503	SO:0001819	synonymous_variant	23037	exon19			CTGCCCAGGGGGG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.4248A>G	5.37:g.32087802A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	154	73	0.474026	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			A|0.596;G|0.404	0.404	strong		0.592	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
ZNF280C	55609	hgsc.bcm.edu	37	X	129349295	129349295	+	Silent	SNP	T	T	G	rs209238	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:129349295T>G	ENST00000370978.4	-	15	2004	c.1851A>C	c.(1849-1851)ggA>ggC	p.G617G		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	617					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						ACTTGTGAATTCCCCGACGAC	0.318													T|||	1969	0.521589	0.5681	0.353	3775	,	,		12569	0.2738		0.3151	False		,,,				2504	0.3885				p.G617G		Atlas-SNP	.											.	ZNF280C	63	.	0			c.A1851C						PASS	.	T		2618,1217		769,679,401,184,170	77.0	81.0	80.0		1851	3.2	0.8	X	dbSNP_79	80	2698,4030		394,1164,746,870,1126	no	coding-synonymous	ZNF280C	NM_017666.4		1163,1843,1147,1054,1296	GG,GT,G,TT,T		40.1011,31.734,49.6734		617/738	129349295	5316,5247	2203	4300	6503	SO:0001819	synonymous_variant	55609	exon15			GTGAATTCCCCGA	AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 3 (Drosophila)"""	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.1851A>C	X.37:g.129349295T>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	108	99	0.916667	NM_017666	A8K2V8|Q9NXR3	Silent	SNP	ENST00000370978.4	37	CCDS14622.1																																																																																			0|0.003;G|0.509	0.509	strong		0.318	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666	
FANCA	2175	hgsc.bcm.edu	37	16	89805914	89805914	+	Missense_Mutation	SNP	T	T	C	rs9282681	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89805914T>C	ENST00000389301.3	-	40	4012	c.3982A>G	c.(3982-3984)Acc>Gcc	p.T1328A	FANCA_ENST00000568369.1_Missense_Mutation_p.T1328A|ZNF276_ENST00000289816.5_3'UTR	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1328			T -> A (in dbSNP:rs9282681). {ECO:0000269|PubMed:9371798}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		AGCAGCCTGGTGTGCTGATCC	0.607			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				T|||	362	0.0722843	0.0038	0.0202	5008	,	,		18297	0.2599		0.0646	False		,,,				2504	0.0164				p.T1328A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.A3982G						PASS	.	T	ALA/THR,,	57,4137		0,57,2040	21.0	18.0	19.0		3982,,	-1.7	0.0	16	dbSNP_118	19	579,7621		12,555,3533	yes	missense,utr-3,utr-3	FANCA,ZNF276	NM_000135.2,NM_001113525.1,NM_152287.3	58,,	12,612,5573	CC,CT,TT		7.061,1.3591,5.1315	benign,,	1328/1456,,	89805914	636,11758	2097	4100	6197	SO:0001583	missense	2175	exon40	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GCCTGGTGTGCTG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3982A>G	16.37:g.89805914T>C	ENSP00000373952:p.Thr1328Ala	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	169	73	0.431953	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	182	0.08333333333333333	3	0.006097560975609756	10	0.027624309392265192	119	0.20804195804195805	50	0.06596306068601583	T	1.996	-0.430624	0.04669	0.013591	0.07061	ENSG00000187741	ENST00000389301	D	0.84442	-1.85	5.25	-1.66	0.08265	.	0.642380	0.14965	N	0.288135	T	0.00144	0.0004	L	0.44542	1.39	0.58432	P	6.999999999979245E-6	B;B	0.12013	0.005;0.005	B;B	0.08055	0.003;0.003	T	0.03619	-1.1019	9	0.28530	T	0.3	-7.1655	6.8317	0.23913	0.0:0.3146:0.1159:0.5695	rs9282681;rs11643682;rs17233776;rs9282681	1328;1328	B4DRI7;O15360	.;FANCA_HUMAN	A	1328	ENSP00000373952:T1328A	ENSP00000373952:T1328A	T	-	1	0	FANCA	88333415	0.000000	0.05858	0.006000	0.13384	0.001000	0.01503	-1.022000	0.03611	-0.515000	0.06479	-0.408000	0.06270	ACC	T|0.933;C|0.067	0.067	strong		0.607	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39190943	39190943	+	Missense_Mutation	SNP	A	A	C	rs547336438	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39190943A>C	ENST00000344363.5	-	1	164	c.131T>G	c.(130-132)tTc>tGc	p.F44C		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	54			Missing (in allele KAP1.1). {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:12228244, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AAATCCGCAGAAGCTGGTCTG	0.617													a|||	143	0.0285543	0.0393	0.0231	5008	,	,		19224	0.0238		0.0169	False		,,,				2504	0.0348				p.F44C		Atlas-SNP	.											.	KRTAP1-3	18	.	0			c.T131G						PASS	.						51.0	57.0	55.0					17																	39190943		1964	4165	6129	SO:0001583	missense	81850	exon1			CCGCAGAAGCTGG	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"""Keratin associated proteins"""	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.131T>G	17.37:g.39190943A>C	ENSP00000344420:p.Phe44Cys	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	181	16	0.0883978	NM_030966	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	.	.	.	.	.	.	.	.	.	.	A	3.165	-0.171169	0.06421	.	.	ENSG00000221880	ENST00000344363	T	0.26518	1.73	3.06	0.556	0.17253	.	.	.	.	.	T	0.09113	0.0225	.	.	.	0.25699	N	0.985603	B	0.02656	0.0	B	0.04013	0.001	T	0.37502	-0.9703	8	0.02654	T	1	.	6.9707	0.24646	0.5657:0.4343:0.0:0.0	.	54	Q8IUG1	KRA13_HUMAN	C	44	ENSP00000344420:F44C	ENSP00000344420:F44C	F	-	2	0	KRTAP1-3	36444469	0.489000	0.26004	0.840000	0.33206	0.502000	0.33828	0.021000	0.13489	0.499000	0.27970	0.383000	0.25322	TTC	.	.	none		0.617	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1		
VWA3B	200403	hgsc.bcm.edu	37	2	98844674	98844674	+	Missense_Mutation	SNP	C	C	G	rs7601049	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:98844674C>G	ENST00000477737.1	+	15	2233	c.2029C>G	c.(2029-2031)Ctg>Gtg	p.L677V		NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	677	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		L -> V (in dbSNP:rs7601049). {ECO:0000269|PubMed:17974005}.							NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						GAATGAAGATCTGACTCTTTT	0.373													C|||	3451	0.689097	0.6346	0.5331	5008	,	,		20042	0.7986		0.6034	False		,,,				2504	0.8487				p.L677V		Atlas-SNP	.											.	VWA3B	138	.	0			c.C2029G						PASS	.	C	VAL/LEU	2444,1386		774,896,245	100.0	98.0	99.0		2029	-5.1	0.0	2	dbSNP_116	99	5055,3197		1546,1963,617	yes	missense	VWA3B	NM_144992.4	32	2320,2859,862	GG,GC,CC		38.7421,36.188,37.9325	benign	677/1295	98844674	7499,4583	1915	4126	6041	SO:0001583	missense	200403	exon15			GAAGATCTGACTC	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.2029C>G	2.37:g.98844674C>G	ENSP00000417955:p.Leu677Val	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	1395|1395	0.6387362637362637|0.6387362637362637	314|314	0.6382113821138211|0.6382113821138211	198|198	0.5469613259668509|0.5469613259668509	439|439	0.7674825174825175|0.7674825174825175	444|444	0.5857519788918206|0.5857519788918206	C|C	9.203|9.203	1.029089|1.029089	0.19512|0.19512	0.63812|0.63812	0.612579|0.612579	ENSG00000168658|ENSG00000168658	ENST00000477737|ENST00000473149	T|.	0.05717|.	3.4|.	5.8|5.8	-5.07|-5.07	0.02938|0.02938	von Willebrand factor, type A (1);|.	0.945622|.	0.08741|.	N|.	0.900507|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25890|0.25890	0.77|0.77	0.44816|0.44816	P|P	0.0021769999999999845|0.0021769999999999845	B;B;B;B|.	0.31318|.	0.319;0.064;0.023;0.141|.	B;B;B;B|.	0.22753|.	0.041;0.015;0.015;0.041|.	T|T	0.36432|0.36432	-0.9748|-0.9748	9|4	0.07030|.	T|.	0.85|.	.|.	3.0445|3.0445	0.06149|0.06149	0.1981:0.2596:0.3913:0.151|0.1981:0.2596:0.3913:0.151	rs7601049;rs52808975;rs58638435;rs7601049|rs7601049;rs52808975;rs58638435;rs7601049	69;677;677;677|.	Q502W6-5;Q502W6;Q502W6-8;Q502W6-6|.	.;VWA3B_HUMAN;.;.|.	V|C	677|87	ENSP00000417955:L677V|.	ENSP00000417955:L677V|.	L|S	+|+	1|2	2|0	VWA3B|VWA3B	98211106|98211106	0.001000|0.001000	0.12720|0.12720	0.033000|0.033000	0.17914|0.17914	0.874000|0.874000	0.50279|0.50279	-1.794000|-1.794000	0.01753|0.01753	-0.468000|-0.468000	0.06922|0.06922	0.467000|0.467000	0.42956|0.42956	CTG|TCT	C|0.354;G|0.646	0.646	strong		0.373	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
FAM171B	165215	hgsc.bcm.edu	37	2	187626338	187626338	+	Silent	SNP	C	C	T	rs13026081	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:187626338C>T	ENST00000304698.5	+	8	1472	c.1269C>T	c.(1267-1269)gaC>gaT	p.D423D		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	423						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						AAGCTGAGGACAAGTCGCAGT	0.373													C|||	828	0.165335	0.0113	0.232	5008	,	,		16751	0.0456		0.3171	False		,,,				2504	0.2935				p.D423D		Atlas-SNP	.											.	FAM171B	146	.	0			c.C1269T						PASS	.	C		252,4154	139.2+/-174.8	17,218,1968	98.0	102.0	101.0		1269	2.0	1.0	2	dbSNP_121	101	2618,5978	419.7+/-353.2	399,1820,2079	no	coding-synonymous	FAM171B	NM_177454.3		416,2038,4047	TT,TC,CC		30.456,5.7195,22.0735		423/827	187626338	2870,10132	2203	4298	6501	SO:0001819	synonymous_variant	165215	exon8			TGAGGACAAGTCG	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"""KIAA1946"""	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.1269C>T	2.37:g.187626338C>T		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	253	133	0.525692	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Silent	SNP	ENST00000304698.5	37	CCDS33347.1																																																																																			C|0.809;N|0.000	.	strong		0.373	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
SH3BP1	23616	hgsc.bcm.edu	37	22	38044341	38044341	+	Silent	SNP	C	C	T	rs118183308	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38044341C>T	ENST00000357436.4	+	14	1528	c.1215C>T	c.(1213-1215)ttC>ttT	p.F405F	SH3BP1_ENST00000599616.1_Silent_p.F341F|SH3BP1_ENST00000442465.2_Silent_p.F405F|SH3BP1_ENST00000336738.5_Silent_p.F405F|Z83844.1_ENST00000456099.1_RNA	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	405	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					TGATGAAGTTCCTGGCACGGC	0.582													C|||	45	0.00898562	0.0008	0.0274	5008	,	,		17464	0.0		0.0239	False		,,,				2504	0.001				p.F405F		Atlas-SNP	.											SH3BP1,NS,haematopoietic_neoplasm,0,1	SH3BP1	41	1	0			c.C1215T						PASS	.	C		14,4384		0,14,2185	42.0	34.0	37.0		1215	4.2	1.0	22	dbSNP_132	37	161,8435		0,161,4137	no	coding-synonymous	SH3BP1	NM_018957.3		0,175,6322	TT,TC,CC		1.873,0.3183,1.3468		405/702	38044341	175,12819	2199	4298	6497	SO:0001819	synonymous_variant	23616	exon14			GAAGTTCCTGGCA		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.1215C>T	22.37:g.38044341C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	23	13	0.565217	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			C|0.986;T|0.014	0.014	strong		0.582	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
PSAT1	29968	hgsc.bcm.edu	37	9	80919756	80919756	+	Silent	SNP	T	T	G	rs3739474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:80919756T>G	ENST00000376588.3	+	4	365	c.297T>G	c.(295-297)gcT>gcG	p.A99A	PSAT1_ENST00000347159.2_Silent_p.A99A	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1	99					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-serine biosynthetic process (GO:0006564)|pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	O-phospho-L-serine:2-oxoglutarate aminotransferase activity (GO:0004648)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						GAAGGTGTGCTGACTATGTGG	0.473													G|||	2501	0.499401	0.5023	0.5461	5008	,	,		17429	0.2649		0.6352	False		,,,				2504	0.5644				p.A99A	Colon(34;187 791 10662 18313 37609)	Atlas-SNP	.											.	PSAT1	33	.	0			c.T297G						PASS	.	G	,	2364,2042	566.8+/-382.0	654,1056,493	115.0	106.0	109.0		297,297	-11.3	0.0	9	dbSNP_107	109	5903,2697	432.7+/-357.2	2001,1901,398	no	coding-synonymous,coding-synonymous	PSAT1	NM_021154.3,NM_058179.2	,	2655,2957,891	GG,GT,TT		31.3605,46.3459,36.437	,	99/325,99/371	80919756	8267,4739	2203	4300	6503	SO:0001819	synonymous_variant	29968	exon4			GTGTGCTGACTAT	BC004863	CCDS6659.1, CCDS6660.1	9q21.2	2008-08-11			ENSG00000135069	ENSG00000135069			19129	protein-coding gene	gene with protein product		610936				12633500, 3651428	Standard	NM_058179		Approved	PSA	uc004ala.3	Q9Y617	OTTHUMG00000020066	ENST00000376588.3:c.297T>G	9.37:g.80919756T>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_021154	Q5T7G5|Q5T7G6|Q96AW2|Q9BQ12	Silent	SNP	ENST00000376588.3	37	CCDS6660.1																																																																																			T|0.414;G|0.586	0.586	strong		0.473	PSAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052777.1	NM_021154	
IGLL1	3543	hgsc.bcm.edu	37	22	23922281	23922281	+	Missense_Mutation	SNP	C	C	T	rs116760479	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:23922281C>T	ENST00000330377.2	-	1	214	c.97G>A	c.(97-99)Gtg>Atg	p.V33M	IGLL1_ENST00000249053.3_Missense_Mutation_p.V33M|KB-208E9.1_ENST00000608615.1_lincRNA	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	33					immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						TGGGTTACCACGGCCAGACCC	0.721													C|||	190	0.0379393	0.0953	0.013	5008	,	,		14290	0.0		0.0119	False		,,,				2504	0.044				p.V33M		Atlas-SNP	.											.	IGLL1	27	.	0			c.G97A						PASS	.	C	MET/VAL,MET/VAL	323,4029		7,309,1860	7.0	8.0	8.0		97,97	-2.2	0.0	22	dbSNP_132	8	121,8377		0,121,4128	yes	missense,missense	IGLL1	NM_020070.2,NM_152855.1	21,21	7,430,5988	TT,TC,CC		1.4239,7.4219,3.4553	possibly-damaging,possibly-damaging	33/214,33/85	23922281	444,12406	2176	4249	6425	SO:0001583	missense	3543	exon1			TTACCACGGCCAG	X52204	CCDS13809.1, CCDS13810.1	22q11.23	2014-09-17			ENSG00000128322	ENSG00000128322		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	5870	protein-coding gene	gene with protein product		146770		IGLL		3139558, 2511029	Standard	NM_020070		Approved	IGVPB, IGL5, 14.1, CD179B	uc002zxd.3	P15814	OTTHUMG00000150673	ENST00000330377.2:c.97G>A	22.37:g.23922281C>T	ENSP00000329312:p.Val33Met	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_020070	Q0P681	Missense_Mutation	SNP	ENST00000330377.2	37	CCDS13809.1	45	0.020604395604395604	31	0.06300813008130081	7	0.019337016574585635	0	0.0	7	0.009234828496042216	c	0.200	-1.045357	0.01997	0.074219	0.014239	ENSG00000128322	ENST00000249053;ENST00000330377;ENST00000438703	T;T	0.00902	6.87;5.56	1.78	-2.18	0.07037	.	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.09310	N	1	B;B	0.24768	0.025;0.111	B;B	0.14023	0.01;0.01	T	0.40813	-0.9543	9	0.05721	T	0.95	.	3.5367	0.07796	0.0:0.3802:0.1991:0.4207	.	33;33	Q0P681;P15814	.;IGLL1_HUMAN	M	33	ENSP00000329312:V33M;ENSP00000403391:V33M	ENSP00000249053:V33M	V	-	1	0	IGLL1	22252281	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.444000	0.06854	-0.496000	0.06650	-2.956000	0.00083	GTG	C|0.980;T|0.020	0.020	strong		0.721	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1	NM_020070	
CASP8	841	hgsc.bcm.edu	37	2	202149696	202149696	+	Silent	SNP	G	G	A	rs1045487	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:202149696G>A	ENST00000432109.2	+	9	1149	c.960G>A	c.(958-960)aaG>aaA	p.K320K	CASP8_ENST00000323492.7_Silent_p.K305K|CASP8_ENST00000392266.3_3'UTR|CASP8_ENST00000264275.5_Silent_p.K337K|CASP8_ENST00000264274.9_Silent_p.K236K|CASP8_ENST00000392259.2_3'UTR|CASP8_ENST00000358485.4_Silent_p.K379K	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	320					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						ATGGAGACAAGGGCATCATCT	0.478										HNSCC(4;0.00038)			G|||	878	0.175319	0.2602	0.0504	5008	,	,		18997	0.1885		0.0417	False		,,,				2504	0.273				p.K379K	Melanoma(82;831 1348 20716 36952 40159)	Atlas-SNP	.											.	CASP8	272	.	0			c.G1137A						PASS	.	G	,,,,	942,3464	355.9+/-313.2	85,772,1346	174.0	147.0	156.0		915,1137,1011,960,915	0.8	1.0	2	dbSNP_86	156	439,8161	133.8+/-191.2	10,419,3871	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASP8	NM_001080124.1,NM_001080125.1,NM_001228.4,NM_033355.3,NM_033356.3	,,,,	95,1191,5217	AA,AG,GG		5.1047,21.3799,10.6182	,,,,	305/465,379/539,337/497,320/480,305/465	202149696	1381,11625	2203	4300	6503	SO:0001819	synonymous_variant	841	exon8			AGACAAGGGCATC	U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"""Caspases"""	1509	protein-coding gene	gene with protein product		601763	"""caspase 8, apoptosis-related cysteine protease"""			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	ENST00000432109.2:c.960G>A	2.37:g.202149696G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	131	73	0.557252	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Silent	SNP	ENST00000432109.2	37	CCDS2342.1																																																																																			G|0.862;A|0.138	0.138	strong		0.478	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228	
ILK	3611	hgsc.bcm.edu	37	11	6630833	6630833	+	Silent	SNP	G	G	A	rs1043390	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6630833G>A	ENST00000396751.2	+	8	1275	c.819G>A	c.(817-819)ccG>ccA	p.P273P	ILK_ENST00000299421.4_Silent_p.P273P|ILK_ENST00000526711.1_3'UTR|RP11-732A19.2_ENST00000527398.1_RNA|TAF10_ENST00000531760.1_5'Flank|ILK_ENST00000420936.2_Silent_p.P273P|ILK_ENST00000537806.1_Silent_p.P139P|ILK_ENST00000528995.1_Silent_p.P212P	NM_001014795.1	NP_001014795.1	Q13418	ILK_HUMAN	integrin-linked kinase	273	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell junction assembly (GO:0034329)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|extracellular fibril organization (GO:0043206)|fibroblast migration (GO:0010761)|integrin-mediated signaling pathway (GO:0007229)|myelin assembly (GO:0032288)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|peptidyl-serine phosphorylation (GO:0018105)|platelet aggregation (GO:0070527)|positive regulation of axon extension (GO:0045773)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)		ACTGGATGCCGTATGGATCCC	0.507													A|||	1740	0.347444	0.5303	0.2651	5008	,	,		22842	0.3492		0.2555	False		,,,				2504	0.2515				p.P273P		Atlas-SNP	.											.	ILK	41	.	0			c.G819A						PASS	.	A	,,	2088,2314	603.5+/-390.1	482,1124,595	156.0	141.0	146.0		819,819,819	4.4	1.0	11	dbSNP_86	146	2160,6432	713.4+/-405.9	265,1630,2401	no	coding-synonymous,coding-synonymous,coding-synonymous	ILK	NM_001014794.1,NM_001014795.1,NM_004517.2	,,	747,2754,2996	AA,AG,GG		25.1397,47.433,32.692	,,	273/453,273/453,273/453	6630833	4248,8746	2201	4296	6497	SO:0001819	synonymous_variant	3611	exon9			GATGCCGTATGGA	U40282	CCDS7768.1, CCDS60712.1, CCDS60713.1	11p15.4	2014-09-17			ENSG00000166333	ENSG00000166333		"""Ankyrin repeat domain containing"""	6040	protein-coding gene	gene with protein product		602366				8538749	Standard	NM_004517		Approved		uc001mef.3	Q13418	OTTHUMG00000133407	ENST00000396751.2:c.819G>A	11.37:g.6630833G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	243	110	0.452675	NM_001014794	B7Z1I0|B7Z418|D3DQU0|P57043|Q68DZ3	Silent	SNP	ENST00000396751.2	37	CCDS7768.1																																																																																			G|0.669;A|0.331	0.331	strong		0.507	ILK-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384519.1	NM_004517	
PLXNB2	23654	hgsc.bcm.edu	37	22	50722134	50722134	+	Missense_Mutation	SNP	T	T	C	rs11547731	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50722134T>C	ENST00000449103.1	-	15	2607	c.2467A>G	c.(2467-2469)Atc>Gtc	p.I823V	PLXNB2_ENST00000496720.1_5'UTR|PLXNB2_ENST00000359337.4_Missense_Mutation_p.I823V			O15031	PLXB2_HUMAN	plexin B2	823	IPT/TIG 1.		I -> V (in dbSNP:rs11547731).		brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GACCCCAGGATGGTGATGCGG	0.642													T|||	3277	0.654353	0.7602	0.5548	5008	,	,		10260	0.5813		0.6392	False		,,,				2504	0.6728				p.I823V		Atlas-SNP	.											PLXNB2,NS,carcinoma,0,1	PLXNB2	172	1	0			c.A2467G						PASS	.	T	VAL/ILE	2977,931		1140,697,117	30.0	35.0	33.0		2467	4.2	1.0	22	dbSNP_120	33	5334,2918		1745,1844,537	yes	missense	PLXNB2	NM_012401.3	29	2885,2541,654	CC,CT,TT		35.3611,23.8229,31.653	probably-damaging	823/1839	50722134	8311,3849	1954	4126	6080	SO:0001583	missense	23654	exon15			CCAGGATGGTGAT		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.2467A>G	22.37:g.50722134T>C	ENSP00000409171:p.Ile823Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	1382	0.6327838827838828	374	0.7601626016260162	214	0.5911602209944752	306	0.534965034965035	488	0.6437994722955145	T	16.26	3.074368	0.55646	0.761771	0.646389	ENSG00000196576	ENST00000449103;ENST00000359337	T;T	0.64260	-0.09;-0.09	4.22	4.22	0.49857	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.237648	0.28736	N	0.014301	T	0.00012	0.0000	M	0.75264	2.295	0.23620	P	0.99727114	D	0.76494	0.999	D	0.87578	0.998	T	0.42899	-0.9424	9	0.46703	T	0.11	.	11.3529	0.49598	0.0:0.0:0.0:1.0	rs11547731;rs60209269	823	O15031	PLXB2_HUMAN	V	823	ENSP00000409171:I823V;ENSP00000352288:I823V	ENSP00000352288:I823V	I	-	1	0	PLXNB2	49064261	1.000000	0.71417	0.995000	0.50966	0.380000	0.30137	2.064000	0.41432	1.780000	0.52325	0.397000	0.26171	ATC	T|0.360;C|0.640	0.640	strong		0.642	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
DNAH3	55567	hgsc.bcm.edu	37	16	21145648	21145648	+	Silent	SNP	C	C	T	rs11074483	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:21145648C>T	ENST00000261383.3	-	7	1013	c.1014G>A	c.(1012-1014)aaG>aaA	p.K338K	DNAH3_ENST00000415178.1_Silent_p.K338K	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	338	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.K338K(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CCTCGTTCCACTTCTTGGCGC	0.522													C|||	1251	0.2498	0.1853	0.3646	5008	,	,		18455	0.2946		0.2336	False		,,,				2504	0.226				p.K338K		Atlas-SNP	.											DNAH3_ENST00000261383,NS,carcinoma,0,2	DNAH3	1142	2	2	Substitution - coding silent(2)	stomach(2)	c.G1014A						PASS	.	C		915,3487	351.3+/-311.2	97,721,1383	112.0	106.0	108.0		1014	3.9	1.0	16	dbSNP_120	108	2100,6500	363.6+/-333.2	263,1574,2463	no	coding-synonymous	DNAH3	NM_017539.1		360,2295,3846	TT,TC,CC		24.4186,20.786,23.1887		338/4117	21145648	3015,9987	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon7			GTTCCACTTCTTG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1014G>A	16.37:g.21145648C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	86	32	0.372093	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			C|0.759;T|0.241	0.241	strong		0.522	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
CES5A	221223	hgsc.bcm.edu	37	16	55907811	55907811	+	Missense_Mutation	SNP	C	C	T	rs2397965	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:55907811C>T	ENST00000290567.9	-	2	333	c.212G>A	c.(211-213)cGa>cAa	p.R71Q	CES5A_ENST00000520435.1_Missense_Mutation_p.R71Q|CES5A_ENST00000518005.1_5'UTR|CES5A_ENST00000319165.9_Missense_Mutation_p.R71Q|CES5A_ENST00000521992.1_Missense_Mutation_p.R100Q|CES5A_ENST00000541580.1_Intron	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	71			R -> Q (in dbSNP:rs2397965).			extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						GTTCGTAAATCGCAGGGATCC	0.592													C|||	1399	0.279353	0.4349	0.1844	5008	,	,		18934	0.3016		0.1581	False		,,,				2504	0.2382				p.R100Q		Atlas-SNP	.											.	CES5A	206	.	0			c.G299A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	1790,2606	527.6+/-372.2	358,1074,766	74.0	68.0	70.0		212,299,212	5.7	0.0	16	dbSNP_100	70	1346,7254	261.9+/-284.1	113,1120,3067	yes	missense,missense,missense	CES5A	NM_001143685.1,NM_001190158.1,NM_145024.2	43,43,43	471,2194,3833	TT,TC,CC		15.6512,40.7188,24.1305	probably-damaging,probably-damaging,probably-damaging	71/576,100/605,71/526	55907811	3136,9860	2198	4300	6498	SO:0001583	missense	221223	exon3			GTAAATCGCAGGG	AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"""Carboxylesterases"""	26459	protein-coding gene	gene with protein product			"""carboxylesterase 7"""	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.212G>A	16.37:g.55907811C>T	ENSP00000290567:p.Arg71Gln	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	564	0.25824175824175827	190	0.3861788617886179	72	0.19889502762430938	181	0.31643356643356646	121	0.15963060686015831	C	32	5.181060	0.94846	0.407188	0.156512	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000290567;ENST00000520435	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	5.7	5.7	0.88788	Carboxylesterase, type B (1);	0.000000	0.40302	N	0.001129	T	0.00012	0.0000	H	0.99143	4.445	0.22745	P	0.99878859	D;D	0.89917	0.999;1.0	D;D	0.79108	0.958;0.992	T	0.37150	-0.9718	9	0.87932	D	0	.	17.7138	0.88330	0.0:1.0:0.0:0.0	rs2397965;rs52834119;rs61158595;rs2397965	71;71	Q6NT32;Q6NT32-2	EST5A_HUMAN;.	Q	100;71;71;71	ENSP00000428864:R100Q;ENSP00000324271:R71Q;ENSP00000290567:R71Q;ENSP00000428887:R71Q	ENSP00000290567:R71Q	R	-	2	0	CES5A	54465312	0.999000	0.42202	0.033000	0.17914	0.025000	0.11179	5.937000	0.70162	2.861000	0.98227	0.655000	0.94253	CGA	C|0.743;T|0.257	0.257	strong		0.592	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	
CNTNAP5	129684	hgsc.bcm.edu	37	2	125660582	125660582	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:125660582C>T	ENST00000431078.1	+	22	3921	c.3557C>T	c.(3556-3558)gCg>gTg	p.A1186V		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	1186	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCCACTGTCGCGCCTGTGACT	0.537																																					p.A1186V		Atlas-SNP	.											CNTNAP5,caecum,carcinoma,-1,1	CNTNAP5	405	1	0			c.C3557T						PASS	.						62.0	62.0	62.0					2																	125660582		2131	4255	6386	SO:0001583	missense	129684	exon22			CTGTCGCGCCTGT	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.3557C>T	2.37:g.125660582C>T	ENSP00000399013:p.Ala1186Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.578109	0.28180	.	.	ENSG00000155052	ENST00000431078	D	0.88354	-2.37	5.5	3.64	0.41730	Laminin G domain (1);	0.279884	0.24698	N	0.036332	D	0.86932	0.6052	M	0.69248	2.105	0.36478	D	0.867685	P	0.52842	0.956	B	0.40782	0.34	D	0.87606	0.2500	10	0.46703	T	0.11	.	13.6352	0.62219	0.2828:0.7172:0.0:0.0	.	1186	Q8WYK1	CNTP5_HUMAN	V	1186	ENSP00000399013:A1186V	ENSP00000399013:A1186V	A	+	2	0	CNTNAP5	125377052	0.980000	0.34600	0.439000	0.26833	0.015000	0.08874	3.047000	0.49854	0.652000	0.30806	-0.181000	0.13052	GCG	.	.	none		0.537	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
SH3TC2	79628	hgsc.bcm.edu	37	5	148386525	148386525	+	Silent	SNP	T	T	G	rs6871030	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:148386525T>G	ENST00000515425.1	-	16	3695	c.3594A>C	c.(3592-3594)ccA>ccC	p.P1198P	SH3TC2_ENST00000538184.1_3'UTR|SH3TC2_ENST00000512049.1_Silent_p.P1191P|SH3TC2_ENST00000502274.1_Silent_p.P60P	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1198					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTGCAGCCATGGTGGACAGA	0.562													G|||	1920	0.383387	0.4902	0.3055	5008	,	,		19946	0.2222		0.4046	False		,,,				2504	0.4387				p.P1198P		Atlas-SNP	.											.	SH3TC2	178	.	0			c.A3594C						PASS	.	G		2477,1929		478,1521,204	122.0	121.0	122.0		3594	-2.6	0.6	5	dbSNP_116	122	3502,5098		681,2140,1479	no	coding-synonymous	SH3TC2	NM_024577.3		1159,3661,1683	GG,GT,TT		40.7209,43.7812,45.9711		1198/1289	148386525	5979,7027	2203	4300	6503	SO:0001819	synonymous_variant	79628	exon16			CAGCCATGGTGGA	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"""Tetratricopeptide (TTC) repeat domain containing"""	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.3594A>C	5.37:g.148386525T>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	190	93	0.489474	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Silent	SNP	ENST00000515425.1	37	CCDS4293.1																																																																																			C|0.005;G|0.447;T|0.549	0.447	strong		0.562	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577	
KIF19	124602	hgsc.bcm.edu	37	17	72350412	72350412	+	Missense_Mutation	SNP	G	G	A	rs2271535	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72350412G>A	ENST00000389916.4	+	18	2558	c.2420G>A	c.(2419-2421)cGc>cAc	p.R807H	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	807			R -> H (in dbSNP:rs2271535).		ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GCGACAGAGCGCAGCAGCCTG	0.711													G|||	1718	0.343051	0.0756	0.4207	5008	,	,		13893	0.4008		0.4712	False		,,,				2504	0.4581				p.R807H		Atlas-SNP	.											KIF19,NS,carcinoma,0,1	KIF19	102	1	0			c.G2420A						scavenged	.	G	HIS/ARG	571,3475		68,435,1520	16.0	22.0	20.0		2420	1.8	1.0	17	dbSNP_100	20	3907,4455		949,2009,1223	yes	missense	KIF19	NM_153209.3	29	1017,2444,2743	AA,AG,GG		46.7233,14.1127,36.0896	possibly-damaging	807/999	72350412	4478,7930	2023	4181	6204	SO:0001583	missense	124602	exon18			CAGAGCGCAGCAG	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2420G>A	17.37:g.72350412G>A	ENSP00000374566:p.Arg807His	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	37	CCDS32718.2	790	0.3617216117216117	40	0.08130081300813008	149	0.4116022099447514	242	0.4230769230769231	359	0.4736147757255937	G	12.77	2.036734	0.35893	0.141127	0.467233	ENSG00000196169	ENST00000389916	T	0.71817	-0.6	5.06	1.78	0.24846	.	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.41050	P	0.014703000000000022	B	0.13594	0.008	B	0.06405	0.002	T	0.38351	-0.9665	8	0.37606	T	0.19	.	6.784	0.23664	0.2165:0.2365:0.547:0.0	rs2271535;rs58995647	807	Q2TAC6	KIF19_HUMAN	H	807	ENSP00000374566:R807H	ENSP00000374566:R807H	R	+	2	0	KIF19	69862007	1.000000	0.71417	0.967000	0.41034	0.417000	0.31264	1.286000	0.33273	1.141000	0.42275	0.556000	0.70494	CGC	G|0.631;A|0.369	0.369	strong		0.711	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
HLA-C	3107	hgsc.bcm.edu	37	6	31238147	31238147	+	Silent	SNP	C	C	G	rs1050326	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238147C>G	ENST00000376228.5	-	4	749	c.735G>C	c.(733-735)ggG>ggC	p.G245G	HLA-C_ENST00000383329.3_Silent_p.G245G	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	245	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TCTGGTCCTCCCCATCCCGCT	0.637																																					p.G245G		Atlas-SNP	.											.	HLA-C	92	.	0			c.G735C						PASS	.						39.0	36.0	37.0					6																	31238147		2197	4283	6480	SO:0001819	synonymous_variant	3107	exon4			GTCCTCCCCATCC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.735G>C	6.37:g.31238147C>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1																																																																																			G|0.330;C|0.670	0.330	strong		0.637	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
FCGBP	8857	hgsc.bcm.edu	37	19	40408128	40408128	+	Silent	SNP	C	C	T	rs4803310	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40408128C>T	ENST00000221347.6	-	9	4600	c.4593G>A	c.(4591-4593)gaG>gaA	p.E1531E		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1531	Cys-rich.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TCGGAGGGCACTCCATGGCTG	0.657													c|||	953	0.190296	0.3555	0.1383	5008	,	,		17537	0.1319		0.1829	False		,,,				2504	0.0716				p.E1531E		Atlas-SNP	.											FCGBP,NS,malignant_melanoma,0,2	FCGBP	416	2	0			c.G4593A						scavenged	.	C		1295,3111	410.0+/-335.2	208,879,1116	48.0	49.0	49.0		4593	0.1	0.3	19	dbSNP_111	49	1245,7355	234.3+/-267.3	96,1053,3151	no	coding-synonymous	FCGBP	NM_003890.2		304,1932,4267	TT,TC,CC		14.4767,29.3917,19.5294		1531/5406	40408128	2540,10466	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon9			AGGGCACTCCATG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4593G>A	19.37:g.40408128C>T		Somatic	307	3	0.00977199		WXS	Illumina HiSeq	Phase_I	419	206	0.491647	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			C|0.824;T|0.176	0.176	strong		0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
LANCL2	55915	hgsc.bcm.edu	37	7	55433880	55433880	+	Silent	SNP	G	G	C	rs2272262	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:55433880G>C	ENST00000254770.2	+	1	740	c.162G>C	c.(160-162)gcG>gcC	p.A54A		NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	54					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			GTCCCCCGGCGACCACGGATG	0.726													C|||	1451	0.289736	0.4357	0.1988	5008	,	,		12860	0.1558		0.331	False		,,,				2504	0.2526				p.A54A		Atlas-SNP	.											.	LANCL2	54	.	0			c.G162C						PASS	.	C		1722,2634		395,932,851	8.0	11.0	10.0		162	1.4	0.0	7	dbSNP_100	10	2782,5752		515,1752,2000	no	coding-synonymous	LANCL2	NM_018697.3		910,2684,2851	CC,CG,GG		32.599,39.5317,34.9418		54/451	55433880	4504,8386	2178	4267	6445	SO:0001819	synonymous_variant	55915	exon1			CCCGGCGACCACG	AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434			6509	protein-coding gene	gene with protein product	"""testis-specific adriamycin sensitivity protein"", ""G protein-coupled receptor 69B"""	612919	"""LanC (bacterial lantibiotic synthetase component C)-like 2"""	GPR69B		11762191	Standard	NM_018697		Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.162G>C	7.37:g.55433880G>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_018697	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Silent	SNP	ENST00000254770.2	37	CCDS5517.1																																																																																			G|0.685;C|0.315	0.315	strong		0.726	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118236610	118236610	+	Missense_Mutation	SNP	T	T	A	rs2116286	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:118236610T>A	ENST00000369230.3	+	12	1495	c.1349T>A	c.(1348-1350)tTc>tAc	p.F450Y		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	450	PLAT.		F -> Y (in dbSNP:rs2116286).		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		AGATCTACCTTCTGTAGCCAA	0.373													T|||	735	0.146765	0.1188	0.1801	5008	,	,		17279	0.3899		0.0258	False		,,,				2504	0.0348				p.F450Y		Atlas-SNP	.											PNLIPRP3,NS,carcinoma,-1,1	PNLIPRP3	101	1	0			c.T1349A						PASS	.	T	TYR/PHE	482,3924	222.6+/-239.4	30,422,1751	89.0	83.0	85.0		1349	4.8	0.8	10	dbSNP_96	85	87,8513	49.8+/-109.6	0,87,4213	yes	missense	PNLIPRP3	NM_001011709.2	22	30,509,5964	AA,AT,TT		1.0116,10.9396,4.3749	probably-damaging	450/468	118236610	569,12437	2203	4300	6503	SO:0001583	missense	119548	exon12			CTACCTTCTGTAG	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1349T>A	10.37:g.118236610T>A	ENSP00000358232:p.Phe450Tyr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_001011709		Missense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	359	0.16437728937728938	60	0.12195121951219512	49	0.13535911602209943	227	0.3968531468531469	23	0.030343007915567283	T	15.07	2.723258	0.48728	0.109396	0.010116	ENSG00000203837	ENST00000369230	T	0.79247	-1.25	4.8	4.8	0.61643	Lipoxygenase, LH2 (2);Lipase/lipooxygenase, PLAT/LH2 (1);	0.000000	0.52532	D	0.000063	T	0.00012	0.0000	M	0.81497	2.545	0.36846	P	0.11232699999999995	D	0.89917	1.0	D	0.87578	0.998	T	0.01114	-1.1447	9	0.72032	D	0.01	.	12.5183	0.56044	0.0:0.0:0.0:1.0	rs2116286;rs52820680;rs61476440;rs2116286	450	Q17RR3	LIPR3_HUMAN	Y	450	ENSP00000358232:F450Y	ENSP00000358232:F450Y	F	+	2	0	PNLIPRP3	118226600	0.981000	0.34729	0.812000	0.32479	0.180000	0.23129	3.530000	0.53539	2.098000	0.63641	0.528000	0.53228	TTC	T|0.906;A|0.094	0.094	strong		0.373	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
DENND2C	163259	hgsc.bcm.edu	37	1	115164554	115164554	+	Missense_Mutation	SNP	C	C	T	rs56861557	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:115164554C>T	ENST00000393274.1	-	7	1814	c.1189G>A	c.(1189-1191)Ggt>Agt	p.G397S	DENND2C_ENST00000393276.3_Intron|DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393277.1_Missense_Mutation_p.G397S	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	397					positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCAACTTCACCAGCTCGGAAA	0.398													C|||	216	0.043131	0.0552	0.0519	5008	,	,		19072	0.001		0.0497	False		,,,				2504	0.0573				p.G397S		Atlas-SNP	.											.	DENND2C	105	.	0			c.G1189A						PASS	.																																			SO:0001583	missense	163259	exon7			CTTCACCAGCTCG		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"""DENN/MADD domain containing"""	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.1189G>A	1.37:g.115164554C>T	ENSP00000376955:p.Gly397Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	133	73	0.548872	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Missense_Mutation	SNP	ENST00000393274.1	37	CCDS58018.1	75	0.034340659340659344	22	0.044715447154471545	14	0.03867403314917127	1	0.0017482517482517483	38	0.05013192612137203	C	15.74	2.922682	0.52653	.	.	ENSG00000175984	ENST00000393274;ENST00000369540;ENST00000393277	T;T	0.08634	3.71;3.07	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000004	T	0.02610	0.0079	.	.	.	0.32586	N	0.527836	D	0.53151	0.958	B	0.38378	0.272	T	0.50874	-0.8776	9	0.13853	T	0.58	.	19.736	0.96205	0.0:1.0:0.0:0.0	rs56861557	397	Q68D51	DEN2C_HUMAN	S	397	ENSP00000376955:G397S;ENSP00000376958:G397S	ENSP00000358553:G397S	G	-	1	0	DENND2C	114966077	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	5.000000	0.63940	2.732000	0.93576	0.557000	0.71058	GGT	C|0.960;T|0.040	0.040	strong		0.398	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459	
PYGL	5836	hgsc.bcm.edu	37	14	51383432	51383432	+	Silent	SNP	G	G	A	rs2075643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:51383432G>A	ENST00000216392.7	-	9	1352	c.1020C>T	c.(1018-1020)gaC>gaT	p.D340D	PYGL_ENST00000532462.1_Silent_p.D340D|PYGL_ENST00000544180.2_Silent_p.D306D	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	340					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|necroptotic process (GO:0070266)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	AMP binding (GO:0016208)|ATP binding (GO:0005524)|bile acid binding (GO:0032052)|drug binding (GO:0008144)|glucose binding (GO:0005536)|glycogen phosphorylase activity (GO:0008184)|protein homodimerization activity (GO:0042803)|purine nucleobase binding (GO:0002060)|pyridoxal phosphate binding (GO:0030170)|vitamin binding (GO:0019842)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)	CAGGGTGAGTGTCATTCAGCT	0.498													G|||	1179	0.235423	0.0431	0.3501	5008	,	,		19495	0.4365		0.1829	False		,,,				2504	0.2607				p.D340D		Atlas-SNP	.											.	PYGL	77	.	0			c.C1020T						PASS	.	G	,	294,4112	160.3+/-192.7	11,272,1920	115.0	105.0	108.0		918,1020	4.6	1.0	14	dbSNP_96	108	1503,7097	284.6+/-296.7	132,1239,2929	no	coding-synonymous,coding-synonymous	PYGL	NM_001163940.1,NM_002863.4	,	143,1511,4849	AA,AG,GG		17.4767,6.6727,13.8167	,	306/814,340/848	51383432	1797,11209	2203	4300	6503	SO:0001819	synonymous_variant	5836	exon9			GTGAGTGTCATTC		CCDS32080.1, CCDS53894.1	14q11.2-q24.3	2013-03-01	2008-07-31		ENSG00000100504	ENSG00000100504	2.4.1.1	"""Glycogen phosphorylases"""	9725	protein-coding gene	gene with protein product	"""Hers disease"", ""glycogen storage disease type VI"", ""glycogen phosphorylase, liver form"""	613741	"""phosphorylase, glycogen; liver"""			2877458	Standard	NM_002863		Approved		uc001wyu.3	P06737	OTTHUMG00000166596	ENST00000216392.7:c.1020C>T	14.37:g.51383432G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	161	75	0.465839	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Silent	SNP	ENST00000216392.7	37	CCDS32080.1																																																																																			G|0.807;A|0.193	0.193	strong		0.498	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863	
TTN	7273	hgsc.bcm.edu	37	2	179558366	179558366	+	Missense_Mutation	SNP	T	T	C	rs2042995	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179558366T>C	ENST00000591111.1	-	117	30837	c.30613A>G	c.(30613-30615)Att>Gtt	p.I10205V	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.I9278V|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I10522V|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.			I -> V (in Ref. 3; CAD12456 and 9; AAP80791). {ECO:0000305}.	adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTTGGAAATGGCAACGTGA	0.308													C|||	2393	0.477835	0.5877	0.4193	5008	,	,		17705	0.5685		0.2455	False		,,,				2504	0.5164				p.I10522V		Atlas-SNP	.											.	TTN	18412	.	0			c.A31564G						PASS	.	C	,VAL/ILE,,	2003,1581		579,845,368	60.0	62.0	61.0		,27832,,	5.8	1.0	2	dbSNP_94	61	1858,6270		194,1470,2400	yes	intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,29,,	773,2315,2768	CC,CT,TT		22.8593,44.1127,32.9662	,benign,,	,9278/33424,,	179558366	3861,7851	1792	4064	5856	SO:0001583	missense	7273	exon119			TGGAAATGGCAAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30613A>G	2.37:g.179558366T>C	ENSP00000465570:p.Ile10205Val	Somatic	390	1	0.0025641		WXS	Illumina HiSeq	Phase_I	385	164	0.425974	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		910	0.4166666666666667	287	0.5833333333333334	133	0.3674033149171271	306	0.534965034965035	184	0.24274406332453827	C	0.877	-0.730053	0.03135	0.558873	0.228593	ENSG00000155657	ENST00000342992;ENST00000414766;ENST00000473181	T	0.60548	0.18	5.85	5.85	0.93711	.	.	.	.	.	T	0.00012	0.0000	N	0.00960	-1.095	0.09310	P	0.9999999999343484	.	.	.	.	.	.	T	0.29027	-1.0025	6	0.87932	D	0	.	9.3114	0.37908	0.0:0.8379:0.0:0.1621	rs2042995;rs56726642;rs2042995	.	.	.	V	9278;400;32	ENSP00000343764:I9278V	ENSP00000343764:I9278V	I	-	1	0	TTN	179266611	0.947000	0.32204	1.000000	0.80357	0.933000	0.57130	1.140000	0.31516	1.498000	0.48600	-0.128000	0.14901	ATT	T|0.582;C|0.418	0.418	strong		0.308	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MATN2	4147	hgsc.bcm.edu	37	8	99044528	99044528	+	Missense_Mutation	SNP	C	C	T	rs2255317	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:99044528C>T	ENST00000520016.1	+	15	2688	c.2564C>T	c.(2563-2565)aCg>aTg	p.T855M	MATN2_ENST00000521689.1_Missense_Mutation_p.T855M|RPL30_ENST00000518164.1_Intron|MATN2_ENST00000254898.5_Missense_Mutation_p.T855M|MATN2_ENST00000524308.1_Missense_Mutation_p.T814M|MATN2_ENST00000522025.2_Missense_Mutation_p.T571M			O00339	MATN2_HUMAN	matrilin 2	855			T -> M (in dbSNP:rs2255317).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.T855M(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			CTGCCAAAAACGGTCCAACAG	0.458													G|||	633	0.126398	0.1203	0.1182	5008	,	,		18812	0.2163		0.0905	False		,,,				2504	0.0849				p.T855M		Atlas-SNP	.											MATN2_ENST00000520016,NS,carcinoma,0,1	MATN2	165	1	1	Substitution - Missense(1)	stomach(1)	c.C2564T						PASS	.	G	MET/THR,MET/THR	452,3284		16,420,1432	63.0	61.0	62.0		2564,2564	-0.5	0.0	8	dbSNP_100	62	888,7314		53,782,3266	yes	missense,missense	MATN2	NM_002380.3,NM_030583.2	81,81	69,1202,4698	TT,TC,CC		10.8266,12.0985,11.2247	possibly-damaging,possibly-damaging	855/957,855/938	99044528	1340,10598	1868	4101	5969	SO:0001583	missense	4147	exon16			CAAAAACGGTCCA	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.2564C>T	8.37:g.99044528C>T	ENSP00000430487:p.Thr855Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	176	93	0.528409	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	297|297	0.13598901098901098|0.13598901098901098	75|75	0.1524390243902439|0.1524390243902439	42|42	0.11602209944751381|0.11602209944751381	112|112	0.1958041958041958|0.1958041958041958	68|68	0.08970976253298153|0.08970976253298153	G|G	11.66|11.66	1.704563|1.704563	0.30232|0.30232	0.120985|0.120985	0.108266|0.108266	ENSG00000132561|ENSG00000132561	ENST00000519582;ENST00000522135|ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016	.|D;T;D;D;T	.|0.83250	.|-1.64;-0.83;-1.7;-1.64;-0.79	5.9|5.9	-0.47|-0.47	0.12131|0.12131	.|.	.|0.706670	.|0.13358	.|N	.|0.393895	T|T	0.00109|0.00109	0.0003|0.0003	N|N	0.08118|0.08118	0|0	0.58432|0.58432	P|P	5.999999999950489E-6|5.999999999950489E-6	.|B;B;B;B	.|0.18310	.|0.027;0.008;0.01;0.006	.|B;B;B;B	.|0.09377	.|0.003;0.002;0.004;0.002	T|T	0.05022|0.05022	-1.0911|-1.0911	4|9	.|0.46703	.|T	.|0.11	-5.4184|-5.4184	0.3947|0.3947	0.00416|0.00416	0.3082:0.1209:0.2467:0.3242|0.3082:0.1209:0.2467:0.3242	rs2255317;rs52813329;rs60277884;rs2255317|rs2255317;rs52813329;rs60277884;rs2255317	.|814;855;855;855	.|C9JH87;E9PF03;O00339-2;O00339	.|.;.;.;MATN2_HUMAN	W|M	111;18|855;855;814;814;571;855	.|ENSP00000429977:T855M;ENSP00000254898:T855M;ENSP00000430221:T814M;ENSP00000429010:T571M;ENSP00000430487:T855M	.|ENSP00000254898:T855M	R|T	+|+	1|2	2|0	MATN2|MATN2	99113704|99113704	0.633000|0.633000	0.27181|0.27181	0.007000|0.007000	0.13788|0.13788	0.082000|0.082000	0.17680|0.17680	-0.272000|-0.272000	0.08560|0.08560	-0.219000|-0.219000	0.10003|0.10003	-0.127000|-0.127000	0.14921|0.14921	CGG|ACG	C|0.856;T|0.143	0.143	strong		0.458	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
ULK4	54986	hgsc.bcm.edu	37	3	41877414	41877414	+	Missense_Mutation	SNP	T	T	C	rs3774372	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:41877414T>C	ENST00000301831.4	-	18	2168	c.1706A>G	c.(1705-1707)aAa>aGa	p.K569R		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	569			K -> R (in dbSNP:rs3774372).	AIVLLTELIRENFRNSKLKQCLLPTLGE -> TTSSIGIGI LNCLVQHSTPVPRQCLVYV (in Ref. 3; AAH14794). {ECO:0000305}.	cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CTGTTTTAATTTGCTGTTCCT	0.363													T|||	865	0.172724	0.1974	0.1369	5008	,	,		14471	0.1458		0.1849	False		,,,				2504	0.18				p.K569R		Atlas-SNP	.											.	ULK4	150	.	0			c.A1706G						PASS	.	T	ARG/LYS	766,2902		74,618,1142	135.0	134.0	135.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1706	5.5	1.0	3	dbSNP_107	135	1373,6785		118,1137,2824	yes	missense	ULK4	NM_017886.2	26	192,1755,3966	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	16.8301,20.8833,18.0873	possibly-damaging	569/1276	41877414	2139,9687	1834	4079	5913	SO:0001583	missense	54986	exon18			TTTAATTTGCTGT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1706A>G	3.37:g.41877414T>C	ENSP00000301831:p.Lys569Arg	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	263	111	0.422053	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	392	0.1794871794871795	105	0.21341463414634146	51	0.1408839779005525	88	0.15384615384615385	148	0.19525065963060687	T	13.98	2.400184	0.42613	0.208833	0.168301	ENSG00000168038	ENST00000301831	T	0.64438	-0.1	5.48	5.48	0.80851	Armadillo-like helical (1);Armadillo-type fold (2);	0.057123	0.64402	U	0.000002	T	0.00039	0.0001	L	0.33485	1.01	0.09310	P	1.0	P	0.42456	0.78	B	0.39027	0.288	T	0.09100	-1.0690	9	0.14252	T	0.57	.	14.0999	0.65049	0.0:0.0:0.0:1.0	rs3774372;rs17216668;rs56443480;rs3774372	569	Q96C45	ULK4_HUMAN	R	569	ENSP00000301831:K569R	ENSP00000301831:K569R	K	-	2	0	ULK4	41852418	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.095000	0.57728	2.204000	0.70986	0.528000	0.53228	AAA	T|0.818;C|0.182	0.182	strong		0.363	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
CRCT1	54544	hgsc.bcm.edu	37	1	152487979	152487979	+	Silent	SNP	C	C	T	rs2282296	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152487979C>T	ENST00000368790.3	+	2	193	c.120C>T	c.(118-120)tgC>tgT	p.C40C		NM_019060.2	NP_061933.1	Q9UGL9	CRCT1_HUMAN	cysteine-rich C-terminal 1	40	Cys-rich.									lung(1)|ovary(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			cctccTGCTGCGGCTCCGGCA	0.726													C|||	2402	0.479633	0.1611	0.5245	5008	,	,		10685	0.6081		0.6213	False		,,,				2504	0.6002				p.C40C		Atlas-SNP	.											.	CRCT1	6	.	0			c.C120T						PASS	.	C		1227,2513		235,757,878	5.0	7.0	6.0		120	-2.3	0.0	1	dbSNP_100	6	5312,2474		1874,1564,455	no	coding-synonymous	CRCT1	NM_019060.2		2109,2321,1333	TT,TC,CC		31.775,32.8075,43.2674		40/100	152487979	6539,4987	1870	3893	5763	SO:0001819	synonymous_variant	54544	exon2			CTGCTGCGGCTCC	AJ243662	CCDS1012.1	1q21	2008-02-05	2006-12-18	2006-12-18	ENSG00000169509	ENSG00000169509			29875	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 42"""	C1orf42		11230159	Standard	NM_019060		Approved	NICE-1	uc001ezz.3	Q9UGL9	OTTHUMG00000012391	ENST00000368790.3:c.120C>T	1.37:g.152487979C>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_019060	A4QN00|Q6IAD7	Silent	SNP	ENST00000368790.3	37	CCDS1012.1																																																																																			C|0.483;T|0.517	0.517	strong		0.726	CRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034511.1	NM_019060	
KIF21B	23046	hgsc.bcm.edu	37	1	200978422	200978422	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:200978422T>C	ENST00000422435.2	-	2	552	c.236A>G	c.(235-237)tAt>tGt	p.Y79C	KIF21B_ENST00000360529.5_Missense_Mutation_p.Y79C|KIF21B_ENST00000332129.2_Missense_Mutation_p.Y79C|KIF21B_ENST00000461742.2_Missense_Mutation_p.Y79C	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	79	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CGTGGCATTATAGCCCTCGAA	0.557																																					p.Y79C		Atlas-SNP	.											.	KIF21B	208	.	0			c.A236G						PASS	.						106.0	96.0	99.0					1																	200978422		2203	4300	6503	SO:0001583	missense	23046	exon2			GCATTATAGCCCT	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.236A>G	1.37:g.200978422T>C	ENSP00000411831:p.Tyr79Cys	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	211	116	0.549763	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.296788	0.81025	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91	4.67	4.67	0.58626	Kinesin, motor domain (5);	0.000000	0.85682	D	0.000000	D	0.86497	0.5947	M	0.82630	2.6	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;0.999;0.998;0.998	D	0.88783	0.3272	10	0.87932	D	0	.	14.2798	0.66202	0.0:0.0:0.0:1.0	.	79;79;79;79	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	C	79	ENSP00000328494:Y79C;ENSP00000353724:Y79C;ENSP00000433808:Y79C;ENSP00000411831:Y79C	ENSP00000328494:Y79C	Y	-	2	0	KIF21B	199245045	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.841000	0.86834	1.967000	0.57214	0.528000	0.53228	TAT	.	.	none		0.557	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
NCKAP5	344148	hgsc.bcm.edu	37	2	133542574	133542574	+	Missense_Mutation	SNP	C	C	T	rs61995744	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:133542574C>T	ENST00000409261.1	-	14	2183	c.1810G>A	c.(1810-1812)Gtg>Atg	p.V604M	NCKAP5_ENST00000317721.6_Missense_Mutation_p.V604M|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	604										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						GCCAATGACACGTCTGAAGGA	0.493													c|||	896	0.178914	0.0514	0.1844	5008	,	,		20790	0.25		0.2237	False		,,,				2504	0.228				p.V604M		Atlas-SNP	.											.	NCKAP5	322	.	0			c.G1810A						PASS	.	C	MET/VAL,	291,3653		10,271,1691	71.0	72.0	71.0		1810,	-9.8	0.0	2	dbSNP_129	71	1955,6347		213,1529,2409	yes	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	21,	223,1800,4100	TT,TC,CC		23.5485,7.3783,18.3407	benign,	604/1910,	133542574	2246,10000	1972	4151	6123	SO:0001583	missense	344148	exon14			ATGACACGTCTGA	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.1810G>A	2.37:g.133542574C>T	ENSP00000387128:p.Val604Met	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	137	77	0.562044	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	422	0.19322344322344323	31	0.06300813008130081	59	0.16298342541436464	153	0.2674825174825175	179	0.23614775725593667	c	2.054	-0.417081	0.04766	0.073783	0.235485	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.42900	0.96;0.96	5.64	-9.81	0.00487	.	0.745722	0.10216	U	0.701581	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.99999848493	B	0.06786	0.001	B	0.06405	0.002	T	0.15464	-1.0436	9	0.39692	T	0.17	.	3.2691	0.06875	0.1957:0.2621:0.3818:0.1604	.	604	O14513	NCKP5_HUMAN	M	604	ENSP00000387128:V604M;ENSP00000380603:V604M	ENSP00000380603:V604M	V	-	1	0	NCKAP5	133259044	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	-0.453000	0.06778	-2.769000	0.00366	-3.448000	0.00036	GTG	C|0.793;T|0.207	0.207	strong		0.493	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
OGFOD3	79701	hgsc.bcm.edu	37	17	80373452	80373452	+	Silent	SNP	C	C	T	rs4789769	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:80373452C>T	ENST00000313056.5	-	2	277	c.126G>A	c.(124-126)ccG>ccA	p.P42P	Y_RNA_ENST00000364369.1_RNA|OGFOD3_ENST00000329197.5_Silent_p.P42P|HEXDC_ENST00000337014.6_5'Flank	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	42						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)										TCCTTAGCCACGGCCTCTGCC	0.672													C|||	1640	0.327476	0.2678	0.2464	5008	,	,		15837	0.6687		0.2515	False		,,,				2504	0.1922				p.P42P		Atlas-SNP	.											.	.	.	.	0			c.G126A						PASS	.	C	,	1174,3232	395.4+/-329.6	140,894,1169	29.0	32.0	31.0		126,126	-4.3	0.0	17	dbSNP_111	31	1897,6703	325.9+/-317.1	198,1501,2601	no	coding-synonymous,coding-synonymous	C17orf101	NM_024648.2,NM_175902.4	,	338,2395,3770	TT,TC,CC		22.0581,26.6455,23.6122	,	42/320,42/332	80373452	3071,9935	2203	4300	6503	SO:0001819	synonymous_variant	79701	exon2			TAGCCACGGCCTC	BC023602	CCDS11811.1, CCDS11812.1	17q25.3	2012-10-23	2012-10-23	2012-10-23	ENSG00000181396	ENSG00000181396			26174	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 101"""	C17orf101		12477932	Standard	NM_175902		Approved	FLJ22222	uc002keu.2	Q6PK18		ENST00000313056.5:c.126G>A	17.37:g.80373452C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Silent	SNP	ENST00000313056.5	37	CCDS11811.1																																																																																			C|0.728;T|0.272	0.272	strong		0.672	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	
PAMR1	25891	hgsc.bcm.edu	37	11	35456153	35456153	+	Silent	SNP	C	C	T	rs35216474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:35456153C>T	ENST00000378880.2	-	10	1978	c.1533G>A	c.(1531-1533)aaG>aaA	p.K511K	PAMR1_ENST00000378878.3_Silent_p.K400K|PAMR1_ENST00000278360.3_Silent_p.K528K|PAMR1_ENST00000532848.1_Silent_p.K471K	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	511	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						TCATGGTGACCTTCCCCAGGT	0.552													C|||	651	0.129992	0.3343	0.062	5008	,	,		19680	0.001		0.1312	False		,,,				2504	0.0337				p.K528K		Atlas-SNP	.											.	PAMR1	85	.	0			c.G1584A						PASS	.	C	,	1390,3014	457.8+/-351.8	203,984,1015	117.0	103.0	108.0		1533,1584	5.4	1.0	11	dbSNP_126	108	1293,7303	256.5+/-280.9	105,1083,3110	no	coding-synonymous,coding-synonymous	PAMR1	NM_001001991.1,NM_015430.2	,	308,2067,4125	TT,TC,CC		15.0419,31.5622,20.6385	,	511/721,528/738	35456153	2683,10317	2202	4298	6500	SO:0001819	synonymous_variant	25891	exon11			GGTGACCTTCCCC		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.1533G>A	11.37:g.35456153C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	239	239	1	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Silent	SNP	ENST00000378880.2	37	CCDS31460.1																																																																																			C|0.820;T|0.180	0.180	strong		0.552	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430	
GPC1	2817	hgsc.bcm.edu	37	2	241404317	241404317	+	Silent	SNP	C	C	T	rs2229458	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241404317C>T	ENST00000264039.2	+	6	1307	c.1059C>T	c.(1057-1059)ccC>ccT	p.P353P		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	353					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)	p.P353P(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		CCCAGGGCCCCGGGCCTGAGG	0.701													C|||	2588	0.516773	0.6233	0.5274	5008	,	,		16409	0.3026		0.5696	False		,,,				2504	0.5317				p.P353P		Atlas-SNP	.											GPC1,NS,carcinoma,0,1	GPC1	32	1	1	Substitution - coding silent(1)	prostate(1)	c.C1059T						PASS	.	C		2707,1509		895,917,296	13.0	15.0	14.0		1059	-7.8	0.0	2	dbSNP_98	14	4791,3473		1486,1819,827	no	coding-synonymous	GPC1	NM_002081.2		2381,2736,1123	TT,TC,CC		42.0257,35.7922,39.9199		353/559	241404317	7498,4982	2108	4132	6240	SO:0001819	synonymous_variant	2817	exon6			GGGCCCCGGGCCT	AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"""Proteoglycans / Cell Surface : Glypicans"""	4449	protein-coding gene	gene with protein product	"""glypican proteoglycan 1"""	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.1059C>T	2.37:g.241404317C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	51	0.579545	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	1102|1102	0.5045787545787546|0.5045787545787546	310|310	0.6300813008130082|0.6300813008130082	201|201	0.5552486187845304|0.5552486187845304	178|178	0.3111888111888112|0.3111888111888112	413|413	0.5448548812664907|0.5448548812664907	C|C	0.034|0.034	-1.315240|-1.315240	0.01331|0.01331	0.642078|0.642078	0.579743|0.579743	ENSG00000063660|ENSG00000063660	ENST00000425056|ENST00000420138;ENST00000455111	T|.	0.47528|.	0.84|.	3.88|3.88	-7.76|-7.76	0.01232|0.01232	.|.	191.155000|.	0.00357|.	U|.	0.000039|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.21930|0.21930	-1.0231|-1.0231	6|3	0.54805|.	T|.	0.06|.	-2.1006|-2.1006	5.4102|5.4102	0.16344|0.16344	0.325:0.4377:0.0:0.2373|0.325:0.4377:0.0:0.2373	rs2229458;rs13001312;rs17854675|rs2229458;rs13001312;rs17854675	.|.	.|.	.|.	L|W	349|393;105	ENSP00000392629:P349L|.	ENSP00000392629:P349L|.	P|R	+|+	2|1	0|2	GPC1|GPC1	241052990|241052990	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-7.128000|-7.128000	0.00043|0.00043	-2.805000|-2.805000	0.00350|0.00350	-1.239000|-1.239000	0.01543|0.01543	CCG|CGG	C|0.493;T|0.507	0.507	strong		0.701	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
FAM26D	221301	hgsc.bcm.edu	37	6	116875427	116875427	+	Silent	SNP	G	G	A	rs7762318	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:116875427G>A	ENST00000368596.3	+	1	515	c.471G>A	c.(469-471)ctG>ctA	p.L157L	FAM26D_ENST00000416171.2_Intron|FAM26D_ENST00000405399.1_Silent_p.L14L|FAM26D_ENST00000368597.2_Intron			Q5JW98	FA26D_HUMAN	family with sequence similarity 26, member D	157					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				endometrium(1)|lung(5)	6		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0458)|OV - Ovarian serous cystadenocarcinoma(136;0.0694)|Epithelial(106;0.222)		AAGAGATCCTGGCTGGGTTTC	0.438													A|||	3218	0.642572	0.4198	0.7349	5008	,	,		21800	0.8978		0.6123	False		,,,				2504	0.6462				p.L14L		Atlas-SNP	.											.	FAM26D	29	.	0			c.G42A						PASS	.																																			SO:0001819	synonymous_variant	221301	exon3			GATCCTGGCTGGG	AK056801	CCDS5109.1, CCDS59032.1	6q22.31	2008-02-05	2007-03-19	2007-03-19	ENSG00000164451	ENSG00000164451			21094	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 78"""	C6orf78			Standard	NM_153036		Approved	FLJ32239	uc010ked.4	Q5JW98	OTTHUMG00000015443	ENST00000368596.3:c.471G>A	6.37:g.116875427G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	131	127	0.969466	NM_001256887	B0QZ25|B0QZ27|B4DTQ0|Q96MK0	Silent	SNP	ENST00000368596.3	37																																																																																				G|0.359;A|0.641	0.641	strong		0.438	FAM26D-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000041958.1	NM_153036	
RAI1	10743	hgsc.bcm.edu	37	17	17696531	17696531	+	Missense_Mutation	SNP	G	G	C	rs3803763	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17696531G>C	ENST00000353383.1	+	3	738	c.269G>C	c.(268-270)gGc>gCc	p.G90A	RAI1_ENST00000261641.6_Missense_Mutation_p.G90A	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	90			G -> A (in dbSNP:rs3803763).		circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ACACAGCAAGGCCTGCAGGGG	0.701													C|||	3340	0.666933	0.6876	0.5403	5008	,	,		12704	0.9167		0.3509	False		,,,				2504	0.7965				p.G90A		Atlas-SNP	.											RAI1,colon,carcinoma,0,1	RAI1	121	1	0			c.G269C						PASS	.	C	ALA/GLY	2664,1718		830,1004,357	12.0	14.0	13.0		269	1.1	0.9	17	dbSNP_107	13	2677,5899		463,1751,2074	no	missense	RAI1	NM_030665.3	60	1293,2755,2431	CC,CG,GG		31.215,39.2058,41.2178	benign	90/1907	17696531	5341,7617	2191	4288	6479	SO:0001583	missense	10743	exon3			AGCAAGGCCTGCA	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.269G>C	17.37:g.17696531G>C	ENSP00000323074:p.Gly90Ala	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	40	0.645161	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	37	CCDS11188.1	1301	0.5956959706959707	320	0.6504065040650406	179	0.494475138121547	537	0.9388111888111889	265	0.3496042216358839	C	0.005	-2.186931	0.00305	0.607942	0.31215	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.65364	-0.15;2.58;0.47	4.55	1.06	0.20224	.	0.710846	0.12730	N	0.443899	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.19910	-1.0291	9	0.31617	T	0.26	.	3.3322	0.07088	0.2438:0.4093:0.2619:0.0851	rs3803763	90	Q7Z5J4	RAI1_HUMAN	A	90	ENSP00000323074:G90A;ENSP00000379120:G90A;ENSP00000261641:G90A	ENSP00000261641:G90A	G	+	2	0	RAI1	17637256	0.214000	0.23563	0.905000	0.35620	0.238000	0.25445	-0.280000	0.08468	0.029000	0.15352	-0.357000	0.07601	GGC	G|0.503;C|0.497	0.497	strong		0.701	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
SVEP1	79987	hgsc.bcm.edu	37	9	113132221	113132221	+	Missense_Mutation	SNP	G	G	A	rs17204533	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:113132221G>A	ENST00000401783.2	-	47	11012	c.10676C>T	c.(10675-10677)aCg>aTg	p.T3559M	SVEP1_ENST00000374469.1_Missense_Mutation_p.T3536M|SVEP1_ENST00000297826.5_Missense_Mutation_p.T1485M|RNU6-1039P_ENST00000383931.1_RNA	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3559	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.		T -> M (in dbSNP:rs17204533).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GTTATGTCCCGTCCAAGAAGA	0.383													G|||	672	0.134185	0.0129	0.1023	5008	,	,		19726	0.2768		0.168	False		,,,				2504	0.1391				p.T3559M		Atlas-SNP	.											.	SVEP1	326	.	0			c.C10676T						PASS	.	G	MET/THR	118,3602		3,112,1745	91.0	83.0	86.0		10676	4.9	1.0	9	dbSNP_123	86	1303,6891		101,1101,2895	yes	missense	SVEP1	NM_153366.3	81	104,1213,4640	AA,AG,GG		15.9019,3.172,11.9271	probably-damaging	3559/3572	113132221	1421,10493	1860	4097	5957	SO:0001583	missense	79987	exon47			TGTCCCGTCCAAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.10676C>T	9.37:g.113132221G>A	ENSP00000384917:p.Thr3559Met	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	373	0.1707875457875458	9	0.018292682926829267	43	0.11878453038674033	184	0.32167832167832167	137	0.18073878627968337	G	16.25	3.071322	0.55646	0.03172	0.159019	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.25085	1.82;1.82;1.82	5.81	4.91	0.64330	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.374359	0.30547	N	0.009394	T	0.00012	0.0000	M	0.83312	2.635	0.09310	P	0.999999999849264	D	0.65815	0.995	P	0.52514	0.701	T	0.33420	-0.9869	9	0.30854	T	0.27	.	14.6555	0.68831	0.0705:0.0:0.9295:0.0	rs17204533;rs52809365;rs17204533	3559	Q4LDE5	SVEP1_HUMAN	M	3559;3536;1485	ENSP00000384917:T3559M;ENSP00000363593:T3536M;ENSP00000297826:T1485M	ENSP00000297826:T1485M	T	-	2	0	SVEP1	112172042	0.995000	0.38212	0.994000	0.49952	0.583000	0.36354	1.871000	0.39539	1.455000	0.47813	0.650000	0.86243	ACG	G|0.836;A|0.164	0.164	strong		0.383	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
LMLN	89782	hgsc.bcm.edu	37	3	197701913	197701913	+	Splice_Site	SNP	G	G	T	rs7373165	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:197701913G>T	ENST00000330198.4	+	3	340	c.318G>T	c.(316-318)gaG>gaT	p.E106D	LMLN_ENST00000420910.2_Splice_Site_p.E106D|LMLN_ENST00000482695.1_Splice_Site_p.E54D|LMLN_ENST00000332636.5_Splice_Site_p.E54D	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	106			E -> D (in dbSNP:rs7373165).		cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		TTATTTTCAGGTTGCTCCCTG	0.338													G|||	1049	0.209465	0.5197	0.1023	5008	,	,		18661	0.0109		0.1173	False		,,,				2504	0.1656				p.E106D		Atlas-SNP	.											.	LMLN	53	.	0			c.G318T						PASS	.	G	ASP/GLU,ASP/GLU	1969,2437	531.5+/-373.2	443,1083,677	64.0	78.0	74.0		318,318	3.6	1.0	3	dbSNP_116	74	940,7660	204.0+/-246.8	37,866,3397	yes	missense-near-splice,missense-near-splice	LMLN	NM_001136049.2,NM_033029.3	45,45	480,1949,4074	TT,TG,GG		10.9302,44.6891,22.3666	benign,benign	106/693,106/656	197701913	2909,10097	2203	4300	6503	SO:0001630	splice_region_variant	89782	exon3			TTTCAGGTTGCTC	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.318-1G>T	3.37:g.197701913G>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	62	22	0.354839	NM_001136049	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	37	CCDS3332.1	374	0.17124542124542125	243	0.49390243902439024	37	0.10220994475138122	7	0.012237762237762238	87	0.11477572559366754	G	11.75	1.731285	0.30684	0.446891	0.109302	ENSG00000185621	ENST00000482695;ENST00000330198;ENST00000419117;ENST00000420910;ENST00000332636	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	4.44	3.56	0.40772	.	0.259681	0.31233	N	0.008017	T	0.00012	0.0000	N	0.14661	0.345	0.41280	P	0.013098999999999972	B;B;B;B	0.09022	0.001;0.002;0.002;0.0	B;B;B;B	0.15052	0.012;0.005;0.006;0.003	T	0.47699	-0.9097	8	.	.	.	.	8.1783	0.31296	0.1096:0.0:0.8904:0.0	rs7373165;rs52803239;rs58900520;rs7373165	106;54;106;54	Q96KR4;F8WCE5;F8WB28;Q96KR4-2	LMLN_HUMAN;.;.;.	D	54;106;34;106;54	ENSP00000418324:E54D;ENSP00000328829:E106D;ENSP00000390872:E34D;ENSP00000410926:E106D;ENSP00000328611:E54D	.	E	+	3	2	LMLN	199186310	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.868000	0.27982	1.084000	0.41184	0.558000	0.71614	GAG	G|0.784;T|0.216	0.216	strong		0.338	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029	Missense_Mutation
LRRN2	10446	hgsc.bcm.edu	37	1	204587569	204587569	+	Missense_Mutation	SNP	G	G	C	rs3747631	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:204587569G>C	ENST00000367175.1	-	1	3764	c.1552C>G	c.(1552-1554)Ctc>Gtc	p.L518V	LRRN2_ENST00000367176.3_Missense_Mutation_p.L518V|RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367177.3_Missense_Mutation_p.L518V			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	518			L -> V (in dbSNP:rs3747631).		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			GGCTGGAGGAGAGCACGGCCC	0.627													G|||	925	0.184704	0.0575	0.0922	5008	,	,		16939	0.3095		0.2237	False		,,,				2504	0.2536				p.L518V		Atlas-SNP	.											.	LRRN2	81	.	0			c.C1552G						PASS	.	G	VAL/LEU,VAL/LEU	358,4048	184.3+/-211.7	16,326,1861	77.0	73.0	74.0		1552,1552	3.5	0.9	1	dbSNP_107	74	1835,6765	329.0+/-318.6	182,1471,2647	yes	missense,missense	LRRN2	NM_006338.2,NM_201630.1	32,32	198,1797,4508	CC,CG,GG		21.3372,8.1253,16.8614	benign,benign	518/714,518/714	204587569	2193,10813	2203	4300	6503	SO:0001583	missense	10446	exon3			GGAGGAGAGCACG	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.1552C>G	1.37:g.204587569G>C	ENSP00000356143:p.Leu518Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	418	0.19139194139194138	38	0.07723577235772358	39	0.10773480662983426	172	0.3006993006993007	169	0.22295514511873352	G	2.932	-0.220842	0.06061	0.081253	0.213372	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.59906	0.23;0.23;0.23	5.35	3.45	0.39498	.	0.433987	0.17130	N	0.185858	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.26326	-1.0106	9	0.16420	T	0.52	.	10.4948	0.44770	0.0738:0.1345:0.7917:0.0	rs3747631;rs57267382	518	O75325	LRRN2_HUMAN	V	518	ENSP00000356144:L518V;ENSP00000356145:L518V;ENSP00000356143:L518V	ENSP00000356143:L518V	L	-	1	0	LRRN2	202854192	0.998000	0.40836	0.865000	0.33974	0.693000	0.40251	2.784000	0.47774	0.624000	0.30286	-0.386000	0.06593	CTC	G|0.818;C|0.182	0.182	strong		0.627	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
OR8H3	390152	hgsc.bcm.edu	37	11	55890273	55890273	+	Missense_Mutation	SNP	T	T	C	rs61743852	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55890273T>C	ENST00000313472.3	+	1	425	c.425T>C	c.(424-426)cTc>cCc	p.L142P		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					AGGCTCTGCCTCGCTCTCATC	0.443													T|||	195	0.0389377	0.0121	0.0447	5008	,	,		21072	0.001		0.0944	False		,,,				2504	0.0532				p.L142P		Atlas-SNP	.											.	OR8H3	92	.	0			c.T425C						PASS	.	T	PRO/LEU	98,4304	78.3+/-116.7	0,98,2103	166.0	148.0	154.0		425	-5.8	0.0	11	dbSNP_129	154	691,7901	169.6+/-220.9	34,623,3639	no	missense	OR8H3	NM_001005201.1	98	34,721,5742	CC,CT,TT		8.0424,2.2263,6.072	benign	142/313	55890273	789,12205	2201	4296	6497	SO:0001583	missense	390152	exon1			TCTGCCTCGCTCT	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.425T>C	11.37:g.55890273T>C	ENSP00000323928:p.Leu142Pro	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	323	134	0.414861	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	86	0.039377289377289376	4	0.008130081300813009	14	0.03867403314917127	0	0.0	68	0.08970976253298153	T	0.884	-0.727898	0.03158	0.022263	0.080424	ENSG00000181761	ENST00000313472	T	0.39787	1.06	3.44	-5.82	0.02333	GPCR, rhodopsin-like superfamily (1);	1.393450	0.04141	N	0.319642	T	0.02156	0.0067	M	0.83852	2.665	0.09310	N	1	B	0.30634	0.288	B	0.40101	0.319	T	0.42258	-0.9462	10	0.36615	T	0.2	.	0.2506	0.00205	0.2749:0.1759:0.1741:0.375	rs61743852	142	Q8N146	OR8H3_HUMAN	P	142	ENSP00000323928:L142P	ENSP00000323928:L142P	L	+	2	0	OR8H3	55646849	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-2.829000	0.00744	-0.591000	0.05859	-1.603000	0.00810	CTC	T|0.949;C|0.051	0.051	strong		0.443	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
CCDC91	55297	hgsc.bcm.edu	37	12	28605426	28605426	+	Missense_Mutation	SNP	G	G	A	rs10771427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:28605426G>A	ENST00000545336.1	+	14	1359	c.940G>A	c.(940-942)Gtg>Atg	p.V314M	CCDC91_ENST00000381259.1_Missense_Mutation_p.V314M|CCDC91_ENST00000539107.1_Missense_Mutation_p.V278M|CCDC91_ENST00000381256.1_Missense_Mutation_p.V278M|CCDC91_ENST00000306172.5_Missense_Mutation_p.V284M|CCDC91_ENST00000540401.1_3'UTR			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	314	Homodimerization.		V -> M (in dbSNP:rs10771427). {ECO:0000269|PubMed:12808037, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6, ECO:0000269|Ref.7}.		protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					AAAAGAAGCAGTGAAGGATGC	0.313													A|||	3351	0.669129	0.8268	0.6398	5008	,	,		13616	0.4702		0.7475	False		,,,				2504	0.6012				p.V314M		Atlas-SNP	.											.	CCDC91	63	.	0			c.G940A						PASS	.	A	MET/VAL	3626,768	282.8+/-276.7	1495,636,66	56.0	69.0	64.0		940	-5.7	0.2	12	dbSNP_120	64	6544,2038	339.8+/-323.3	2510,1524,257	yes	missense	CCDC91	NM_018318.3	21	4005,2160,323	AA,AG,GG		23.7474,17.4784,21.6245	benign	314/442	28605426	10170,2806	2197	4291	6488	SO:0001583	missense	55297	exon10			GAAGCAGTGAAGG	AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"""GGA binding partner"""					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.940G>A	12.37:g.28605426G>A	ENSP00000438040:p.Val314Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_018318	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Missense_Mutation	SNP	ENST00000545336.1	37	CCDS8716.1	1462	0.6694139194139194	407	0.8272357723577236	235	0.649171270718232	252	0.4405594405594406	568	0.7493403693931399	A	2.110	-0.403863	0.04832	0.825216	0.762526	ENSG00000123106	ENST00000540794;ENST00000536154;ENST00000539107;ENST00000536442;ENST00000545336;ENST00000545737;ENST00000381259;ENST00000381256;ENST00000306172;ENST00000535212	T;T;T;T;T;T;T;T;T;T	0.46063	1.45;1.48;0.97;1.5;1.49;1.5;1.49;0.97;1.49;0.88	5.43	-5.71	0.02413	.	0.735756	0.13394	N	0.391196	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.14578	0.002;0.011;0.002	T	0.43988	-0.9357	9	0.42905	T	0.14	-0.5073	19.6535	0.95827	0.2682:0.0:0.7318:0.0	rs10771427;rs52823249;rs59885605;rs10771427	278;314;284	Q7Z6B0-3;Q7Z6B0;Q7Z6B0-2	.;CCD91_HUMAN;.	M	110;54;278;314;314;314;314;278;284;13	ENSP00000441714:V110M;ENSP00000444440:V54M;ENSP00000440513:V278M;ENSP00000445660:V314M;ENSP00000438040:V314M;ENSP00000442544:V314M;ENSP00000370658:V314M;ENSP00000370655:V278M;ENSP00000305075:V284M;ENSP00000445999:V13M	ENSP00000305075:V284M	V	+	1	0	CCDC91	28496693	0.013000	0.17824	0.203000	0.23512	0.968000	0.65278	-0.271000	0.08572	-1.887000	0.01115	-0.352000	0.07741	GTG	G|0.275;A|0.725	0.725	strong		0.313	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1	NM_018318	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276888	71276888	+	Silent	SNP	T	T	C	rs12793134		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:71276888T>C	ENST00000398531.1	+	1	280	c.255T>C	c.(253-255)ggT>ggC	p.G85G	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	85	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GGGGCTGTGGTTCCTGTGGGG	0.682																																					p.G85G		Atlas-SNP	.											KRTAP5-10,NS,neuroblastoma,0,1	KRTAP5-10	37	1	0			c.T255C						scavenged	.						44.0	64.0	57.0					11																	71276888		2125	4249	6374	SO:0001819	synonymous_variant	387273	exon1			CTGTGGTTCCTGT	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"""Keratin associated proteins"""	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.255T>C	11.37:g.71276888T>C		Somatic	58	3	0.0517241		WXS	Illumina HiSeq	Phase_I	68	7	0.102941	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			T|0.998;C|0.002	0.002	weak		0.682	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
FPR1	2357	hgsc.bcm.edu	37	19	52249680	52249680	+	Missense_Mutation	SNP	T	T	A	rs5030880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52249680T>A	ENST00000595042.1	-	3	709	c.568A>T	c.(568-570)Agg>Tgg	p.R190W	FPR1_ENST00000304748.4_Missense_Mutation_p.R190W	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	190			R -> W (in dbSNP:rs5030880).		activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)	p.R190W(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	ACATTTATCCTCTCTTTAGGG	0.502													T|||	680	0.135783	0.0862	0.0793	5008	,	,		21603	0.2192		0.1153	False		,,,				2504	0.1779				p.R190W		Atlas-SNP	.											FPR1,NS,carcinoma,0,1	FPR1	64	1	1	Substitution - Missense(1)	stomach(1)	c.A568T						PASS	.	T	TRP/ARG,TRP/ARG	372,4034		20,332,1851	114.0	106.0	109.0		568,568	2.6	0.2	19	dbSNP_113	109	1098,7502		82,934,3284	yes	missense,missense	FPR1	NM_001193306.1,NM_002029.3	101,101	102,1266,5135	AA,AT,TT		12.7674,8.443,11.3025	benign,benign	190/351,190/351	52249680	1470,11536	2203	4300	6503	SO:0001583	missense	2357	exon3			TTATCCTCTCTTT	M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"""GPCR / Class A : Formyl peptide receptors"""	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.568A>T	19.37:g.52249680T>A	ENSP00000471493:p.Arg190Trp	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	54	0.964286	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	37	CCDS12839.1	280	0.1282051282051282	60	0.12195121951219512	29	0.08011049723756906	106	0.1853146853146853	85	0.11213720316622691	.	12.16	1.854853	0.32791	0.08443	0.127674	ENSG00000171051	ENST00000304748	T	0.62639	0.01	3.66	2.63	0.31362	GPCR, rhodopsin-like superfamily (1);	0.659654	0.12541	N	0.459864	T	0.00109	0.0003	L	0.41632	1.29	0.54753	P	1.3000000000040757E-5	B	0.09022	0.002	B	0.15870	0.014	T	0.04307	-1.0961	9	0.34782	T	0.22	.	6.5695	0.22531	0.0:0.1219:0.0:0.8781	rs5030880	190	P21462	FPR1_HUMAN	W	190	ENSP00000302707:R190W	ENSP00000302707:R190W	R	-	1	2	FPR1	56941492	0.142000	0.22610	0.152000	0.22495	0.006000	0.05464	1.360000	0.34125	1.596000	0.50062	0.533000	0.62120	AGG	T|0.887;A|0.113	0.113	strong		0.502	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029	
CHDH	55349	hgsc.bcm.edu	37	3	53857676	53857676	+	Silent	SNP	C	C	T	rs17053532	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:53857676C>T	ENST00000315251.6	-	3	797	c.360G>A	c.(358-360)ctG>ctA	p.L120L		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	120					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	GTGGCCAGTACAGCACGCGGC	0.682													C|||	293	0.0585064	0.0068	0.0994	5008	,	,		12278	0.001		0.1779	False		,,,				2504	0.0358				p.L120L		Atlas-SNP	.											.	CHDH	34	.	0			c.G360A						PASS	.	C		96,3886		2,92,1897	7.0	9.0	8.0		360	2.9	1.0	3	dbSNP_123	8	974,6690		56,862,2914	no	coding-synonymous	CHDH	NM_018397.4		58,954,4811	TT,TC,CC		12.7088,2.4108,9.1877		120/595	53857676	1070,10576	1991	3832	5823	SO:0001819	synonymous_variant	55349	exon3			CCAGTACAGCACG	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.360G>A	3.37:g.53857676C>T		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	12	5	0.416667	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																			C|0.905;T|0.095	0.095	strong		0.682	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
KIF23	9493	hgsc.bcm.edu	37	15	69729049	69729049	+	Missense_Mutation	SNP	T	T	C	rs17310879	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:69729049T>C	ENST00000260363.4	+	14	1660	c.1543T>C	c.(1543-1545)Ttt>Ctt	p.F515L	KIF23_ENST00000352331.4_Missense_Mutation_p.F515L|KIF23_ENST00000395392.2_Missense_Mutation_p.F515L|KIF23_ENST00000537891.1_Missense_Mutation_p.F332L|KIF23_ENST00000558585.1_Missense_Mutation_p.F332L|KIF23_ENST00000559279.1_Missense_Mutation_p.F515L	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	515			F -> L (in dbSNP:rs17310879).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						GATTGATGAGTTTAACAAACA	0.338													T|||	32	0.00638978	0.0	0.0101	5008	,	,		17842	0.0		0.0199	False		,,,				2504	0.0051				p.F515L		Atlas-SNP	.											.	KIF23	57	.	0			c.T1543C						PASS	.	T	LEU/PHE,LEU/PHE	12,4386	17.9+/-39.9	0,12,2187	68.0	59.0	62.0		1543,1543	4.0	0.9	15	dbSNP_123	62	126,8470	61.0+/-122.8	2,122,4174	yes	missense,missense	KIF23	NM_004856.5,NM_138555.2	22,22	2,134,6361	CC,CT,TT		1.4658,0.2729,1.062	benign,benign	515/857,515/961	69729049	138,12856	2199	4298	6497	SO:0001583	missense	9493	exon14			GATGAGTTTAACA	X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"""Kinesins"""	6392	protein-coding gene	gene with protein product		605064	"""kinesin-like 5 (mitotic kinesin-like protein 1)"""	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.1543T>C	15.37:g.69729049T>C	ENSP00000260363:p.Phe515Leu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_138555	Q8WVP0	Missense_Mutation	SNP	ENST00000260363.4	37	CCDS32278.1	21	0.009615384615384616	0	0.0	5	0.013812154696132596	0	0.0	16	0.021108179419525065	T	6.643	0.487087	0.12641	0.002729	0.014658	ENSG00000137807	ENST00000260363;ENST00000352331;ENST00000395392;ENST00000537891	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	5.11	3.99	0.46301	.	0.276826	0.41500	N	0.000878	T	0.19565	0.0470	N	0.08118	0	0.38724	D	0.953517	B;B;B	0.14012	0.001;0.009;0.0	B;B;B	0.15484	0.001;0.013;0.001	T	0.18209	-1.0344	10	0.02654	T	1	.	9.3049	0.37870	0.0:0.0866:0.0:0.9134	rs17310879;rs52817803;rs17310879	332;515;515	B4E1K0;Q02241-2;Q02241	.;.;KIF23_HUMAN	L	515;515;515;332	ENSP00000260363:F515L;ENSP00000304978:F515L;ENSP00000378790:F515L;ENSP00000442969:F332L	ENSP00000260363:F515L	F	+	1	0	KIF23	67516103	1.000000	0.71417	0.877000	0.34402	0.953000	0.61014	4.650000	0.61440	0.798000	0.33994	0.459000	0.35465	TTT	T|0.988;C|0.012	0.012	strong		0.338	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
XRCC4	7518	hgsc.bcm.edu	37	5	82648977	82648977	+	Silent	SNP	T	T	G	rs1056503	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:82648977T>G	ENST00000511817.1	+	8	1007	c.927T>G	c.(925-927)tcT>tcG	p.S309S	XRCC4_ENST00000282268.3_Silent_p.S307S|XRCC4_ENST00000338635.6_Silent_p.S309S|XRCC4_ENST00000396027.4_Silent_p.S307S			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	309					cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		CTGAGACGTCTAAAAAGGAGC	0.338								Non-homologous end-joining					G|||	1881	0.375599	0.4758	0.3329	5008	,	,		17355	0.7063		0.1402	False		,,,				2504	0.1718				p.S309S		Atlas-SNP	.											.	XRCC4	37	.	0			c.T927G						PASS	.	G	,,	1942,2464	617.9+/-393.1	424,1094,685	113.0	123.0	120.0		921,927,921	1.1	0.0	5	dbSNP_86	120	1055,7543	768.5+/-407.6	63,929,3307	no	coding-synonymous,coding-synonymous,coding-synonymous	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	,,	487,2023,3992	GG,GT,TT		12.2703,44.0763,23.0468	,,	307/335,309/337,307/335	82648977	2997,10007	2203	4299	6502	SO:0001819	synonymous_variant	7518	exon8			GACGTCTAAAAAG	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.927T>G	5.37:g.82648977T>G		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	297	144	0.484848	NM_022406	A8K3X4|Q9BS72|Q9UP94	Silent	SNP	ENST00000511817.1	37	CCDS4059.1																																																																																			T|0.685;G|0.315	0.315	strong		0.338	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	
SLC5A10	125206	hgsc.bcm.edu	37	17	18923180	18923180	+	Missense_Mutation	SNP	C	C	T	rs12604020	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18923180C>T	ENST00000395645.3	+	13	1583	c.1565C>T	c.(1564-1566)gCa>gTa	p.A522V	SLC5A10_ENST00000395643.2_Missense_Mutation_p.A495V|SLC5A10_ENST00000395647.2_Missense_Mutation_p.A538V|SLC5A10_ENST00000395642.1_Missense_Mutation_p.A492V|SLC5A10_ENST00000317977.6_Missense_Mutation_p.A492V|SLC5A10_ENST00000417251.2_Missense_Mutation_p.A486V	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	522			A -> V (in dbSNP:rs12604020).		sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						GCCCTCTTTGCACTCAGTGGT	0.637													C|||	743	0.148363	0.3064	0.0634	5008	,	,		12943	0.1339		0.0298	False		,,,				2504	0.1319				p.A538V		Atlas-SNP	.											.	SLC5A10	55	.	0			c.C1613T						PASS	.		VAL/ALA,VAL/ALA	1134,3272	395.6+/-329.7	137,860,1206	54.0	47.0	49.0		1565,1613	0.1	0.0	17	dbSNP_120	49	179,8421	80.6+/-143.3	2,175,4123	yes	missense,missense	SLC5A10	NM_001042450.1,NM_152351.3	64,64	139,1035,5329	TT,TC,CC		2.0814,25.7376,10.0953	benign,benign	522/597,538/613	18923180	1313,11693	2203	4300	6503	SO:0001583	missense	125206	exon13			TCTTTGCACTCAG		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"""Solute carriers"""	23155	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 10"""				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.1565C>T	17.37:g.18923180C>T	ENSP00000379007:p.Ala522Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_152351	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Missense_Mutation	SNP	ENST00000395645.3	37	CCDS42275.1	250	0.11446886446886446	127	0.258130081300813	23	0.06353591160220995	81	0.14160839160839161	19	0.025065963060686015	C	5.769	0.326227	0.10900	0.257376	0.020814	ENSG00000154025	ENST00000317977;ENST00000395647;ENST00000395642;ENST00000417251;ENST00000395645;ENST00000395643	D;D;D;D;D;D	0.90197	-2.63;-2.1;-2.63;-2.13;-2.04;-2.12	4.89	0.0898	0.14460	.	1.055510	0.07405	N	0.891408	T	0.00039	0.0001	N	0.12887	0.27	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.001;0.001;0.001;0.001;0.002	T	0.01679	-1.1297	9	0.13470	T	0.59	.	9.1782	0.37125	0.0:0.3832:0.0:0.6168	rs12604020;rs12604020	486;495;522;538;492	B4DPI0;A0PJK1-2;A0PJK1;A0PJK1-4;A0PJK1-3	.;.;SC5AA_HUMAN;.;.	V	492;538;492;486;522;495	ENSP00000324346:A492V;ENSP00000379008:A538V;ENSP00000379004:A492V;ENSP00000401875:A486V;ENSP00000379007:A522V;ENSP00000379005:A495V	ENSP00000324346:A492V	A	+	2	0	SLC5A10	18863905	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.686000	0.05161	-0.206000	0.10203	-1.293000	0.01348	GCA	C|0.885;T|0.115	0.115	strong		0.637	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351	
OVCH1	341350	hgsc.bcm.edu	37	12	29628016	29628016	+	Silent	SNP	G	G	A	rs2043623	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:29628016G>A	ENST00000318184.5	-	14	1577	c.1578C>T	c.(1576-1578)gcC>gcT	p.A526A	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	526	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.A526A(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TGGTAAATCTGGCCTTGAAGC	0.348													A|||	2554	0.509984	0.6687	0.3934	5008	,	,		17713	0.3948		0.5517	False		,,,				2504	0.454				p.A526A		Atlas-SNP	.											OVCH1,NS,carcinoma,0,1	OVCH1	195	1	1	Substitution - coding silent(1)	stomach(1)	c.C1578T						scavenged	.	A		2512,1186		858,796,195	61.0	56.0	57.0		1578	-2.0	0.0	12	dbSNP_94	57	4425,3753		1178,2069,842	no	coding-synonymous	OVCH1	NM_183378.2		2036,2865,1037	AA,AG,GG		45.8914,32.0714,41.5881		526/1135	29628016	6937,4939	1849	4089	5938	SO:0001819	synonymous_variant	341350	exon14			AAATCTGGCCTTG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1578C>T	12.37:g.29628016G>A		Somatic	254	2	0.00787402		WXS	Illumina HiSeq	Phase_I	243	102	0.419753	NM_183378		Silent	SNP	ENST00000318184.5	37																																																																																				G|0.461;A|0.539	0.539	strong		0.348	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
CBS	875	hgsc.bcm.edu	37	21	44485350	44485350	+	Silent	SNP	G	G	A	rs234706	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:44485350G>A	ENST00000398165.3	-	8	958	c.699C>T	c.(697-699)taC>taT	p.Y233Y	CBS_ENST00000470912.1_5'Flank|CBS_ENST00000398168.1_Silent_p.Y233Y|CBS_ENST00000359624.3_Silent_p.Y233Y|CBS_ENST00000398158.1_Silent_p.Y233Y|CBS_ENST00000352178.5_Silent_p.Y233Y|CBS_ENST00000544202.1_Silent_p.Y145Y	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	233					cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	CGGTGGTGTCGTAGTGAGCCA	0.577													G|||	984	0.196486	0.2201	0.1844	5008	,	,		18443	0.0327		0.3062	False		,,,				2504	0.229				p.Y233Y		Atlas-SNP	.											CBS_ENST00000398168,colon,carcinoma,0,2	CBS	85	2	0			c.C699T	GRCh37	CM074081	CBS	M	rs234706	PASS	.	G	,,	1021,3385	378.3+/-322.8	117,787,1299	119.0	93.0	102.0		699,699,699	-1.0	1.0	21	dbSNP_79	102	2960,5640	460.7+/-365.2	499,1962,1839	no	coding-synonymous,coding-synonymous,coding-synonymous	CBS	NM_000071.2,NM_001178008.1,NM_001178009.1	,,	616,2749,3138	AA,AG,GG		34.4186,23.1729,30.6089	,,	233/552,233/552,233/552	44485350	3981,9025	2203	4300	6503	SO:0001819	synonymous_variant	875	exon8			GGTGTCGTAGTGA	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.699C>T	21.37:g.44485350G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Silent	SNP	ENST00000398165.3	37	CCDS13693.1																																																																																			G|0.735;A|0.264	0.264	strong		0.577	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071	
OR8G5	219865	hgsc.bcm.edu	37	11	124135662	124135662	+	Missense_Mutation	SNP	A	A	G	rs2512166	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124135662A>G	ENST00000524943.2	+	1	940	c.940A>G	c.(940-942)Act>Gct	p.T314A	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	314						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		TGTGTTTTATACTATTGTTGT	0.473													A|||	503	0.100439	0.0174	0.1585	5008	,	,		19370	0.13		0.1441	False		,,,				2504	0.0961				p.T314A	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.A940G						PASS	.	A	ALA/THR	161,3897		4,153,1872	83.0	82.0	82.0		940	3.0	0.0	11	dbSNP_100	82	1323,7117		96,1131,2993	no	missense	OR8G5	NM_001005198.1	58	100,1284,4865	GG,GA,AA		15.6754,3.9675,11.8739		314/347	124135662	1484,11014	2029	4220	6249	SO:0001583	missense	219865	exon1			TTTTATACTATTG	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.940A>G	11.37:g.124135662A>G	ENSP00000477014:p.Thr314Ala	Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	293	135	0.460751	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	37																																																																																				A|0.887;G|0.113	0.113	strong		0.473	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
IMP3	55272	hgsc.bcm.edu	37	15	75932129	75932129	+	Silent	SNP	G	G	T	rs13737	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75932129G>T	ENST00000314852.2	-	2	1324	c.381C>A	c.(379-381)gcC>gcA	p.A127A	IMP3_ENST00000565349.1_5'Flank|CTD-2026K11.2_ENST00000564683.1_RNA|IMP3_ENST00000403490.1_Silent_p.A127A			Q8TCT8	SPP2A_HUMAN	IMP3, U3 small nucleolar ribonucleoprotein	118	PA.				membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			large_intestine(1)	1						CAAAGGCCACGGCAGCCTGAA	0.667													G|||	1973	0.39397	0.5151	0.3876	5008	,	,		19460	0.369		0.2704	False		,,,				2504	0.3875				p.A127A		Atlas-SNP	.											IMP3,colon,carcinoma,0,1	IMP3	10	1	0			c.C381A						scavenged	.	G		2100,2294	560.2+/-380.4	504,1092,601	52.0	46.0	48.0		381	-6.3	0.8	15	dbSNP_52	48	2285,6303	373.1+/-336.9	301,1683,2310	no	coding-synonymous	IMP3	NM_018285.3		805,2775,2911	TT,TG,GG		26.6069,47.7924,33.7775		127/185	75932129	4385,8597	2197	4294	6491	SO:0001819	synonymous_variant	55272	exon1			GGCCACGGCAGCC	AB051628	CCDS10282.1	15q24	2014-02-19	2014-02-19	2005-07-14	ENSG00000177971	ENSG00000177971			14497	protein-coding gene	gene with protein product		612980	"""mitochondrial ribosomal protein S4"", ""chromosome 15 open reading frame 12"", ""IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""	MRPS4, C15orf12		11543634, 12655004	Standard	NM_018285		Approved	FLJ10968, BRMS2	uc010bkl.2	Q9NV31	OTTHUMG00000142840	ENST00000314852.2:c.381C>A	15.37:g.75932129G>T		Somatic	71	2	0.028169		WXS	Illumina HiSeq	Phase_I	48	30	0.625	NM_018285	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000314852.2	37	CCDS10282.1																																																																																			G|0.628;T|0.372	0.372	strong		0.667	IMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286476.1	NM_018285	
HERC2	8924	hgsc.bcm.edu	37	15	28422609	28422609	+	Silent	SNP	C	C	T	rs61756153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:28422609C>T	ENST00000261609.7	-	60	9318	c.9210G>A	c.(9208-9210)tcG>tcA	p.S3070S		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CTTCGCCCCACGAAAACACTT	0.473													C|||	773	0.154353	0.0083	0.0836	5008	,	,		18473	0.3929		0.0855	False		,,,				2504	0.227				p.S3070S		Atlas-SNP	.											HERC2,NS,adenoma,-1,1	HERC2	501	1	0			c.G9210A						PASS	.	C		83,4323	67.6+/-105.2	1,81,2121	100.0	88.0	92.0		9210	-8.8	0.6	15	dbSNP_129	92	463,8137	138.4+/-195.2	13,437,3850	no	coding-synonymous	HERC2	NM_004667.4		14,518,5971	TT,TC,CC		5.3837,1.8838,4.1981		3070/4835	28422609	546,12460	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon60			GCCCCACGAAAAC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9210G>A	15.37:g.28422609C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	26	0.351351	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			C|0.932;T|0.068	0.068	strong		0.473	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511873	99511873	+	Missense_Mutation	SNP	G	G	A	rs2715423	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:99511873G>A	ENST00000378919.6	-	5	630	c.425C>T	c.(424-426)gCg>gTg	p.A142V	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_Missense_Mutation_p.A88V	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	142			A -> V (in dbSNP:rs2715423). {ECO:0000269|PubMed:15489334}.				cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						GATGAGTGCCGCGCAGCCCTT	0.542													G|||	638	0.127396	0.0681	0.183	5008	,	,		19533	0.0794		0.2316	False		,,,				2504	0.1104				p.A142V		Atlas-SNP	.											PGPEP1L,NS,carcinoma,-1,2	PGPEP1L	26	2	0			c.C425T						PASS	.	G	VAL/ALA,VAL/ALA	370,3622		16,338,1642	27.0	28.0	28.0		425,263	3.2	0.0	15	dbSNP_100	28	2266,6046		309,1648,2199	yes	missense,missense	PGPEP1L	NM_001102612.2,NM_001167902.1	64,64	325,1986,3841	AA,AG,GG		27.2618,9.2685,21.4239	possibly-damaging,possibly-damaging	142/197,88/143	99511873	2636,9668	1996	4156	6152	SO:0001583	missense	145814	exon5			AGTGCCGCGCAGC		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.425C>T	15.37:g.99511873G>A	ENSP00000368199:p.Ala142Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	121	61	0.504132	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	327	0.14972527472527472	37	0.07520325203252033	72	0.19889502762430938	34	0.05944055944055944	184	0.24274406332453827	G	9.528	1.109957	0.20714	0.092685	0.272618	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.31510	1.49	5.16	3.23	0.37069	.	0.067583	0.56097	D	0.000021	T	0.00012	0.0000	L	0.31157	0.91	0.80722	P	0.0	B	0.26876	0.162	B	0.18561	0.022	T	0.33085	-0.9882	9	0.49607	T	0.09	-16.6381	7.1523	0.25618	0.1471:0.0:0.7136:0.1393	rs2715423;rs60642727;rs2715423	142	A6NFU8	PGPIL_HUMAN	V	142;135	ENSP00000368199:A142V	ENSP00000368199:A142V	A	-	2	0	PGPEP1L	97329396	0.897000	0.30589	0.001000	0.08648	0.002000	0.02628	4.920000	0.63390	0.527000	0.28560	-0.143000	0.13931	GCG	G|0.846;A|0.154	0.154	strong		0.542	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
CCDC171	203238	hgsc.bcm.edu	37	9	15784631	15784631	+	Missense_Mutation	SNP	A	A	G	rs1539172	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:15784631A>G	ENST00000380701.3	+	21	3534	c.3206A>G	c.(3205-3207)aAa>aGa	p.K1069R	CCDC171_ENST00000297641.3_Missense_Mutation_p.K1069R	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	1069			K -> R (in dbSNP:rs1539172). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.														TTGAATTATAAACTTGAATTG	0.368													G|||	2376	0.474441	0.5439	0.3703	5008	,	,		18092	0.3651		0.4742	False		,,,				2504	0.5675				p.K1069R		Atlas-SNP	.											.	.	.	.	0			c.A3206G						PASS	.	G	ARG/LYS	2459,1945	549.6+/-377.8	666,1127,409	84.0	75.0	78.0		3206	4.1	1.0	9	dbSNP_88	78	4297,4303	576.1+/-390.3	1044,2209,1047	yes	missense	C9orf93	NM_173550.2	26	1710,3336,1456	GG,GA,AA		49.9651,44.1644,48.0468	benign	1069/1327	15784631	6756,6248	2202	4300	6502	SO:0001583	missense	203238	exon21			ATTATAAACTTGA	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.3206A>G	9.37:g.15784631A>G	ENSP00000370077:p.Lys1069Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	968|968	0.4432234432234432|0.4432234432234432	264|264	0.5365853658536586|0.5365853658536586	140|140	0.3867403314917127|0.3867403314917127	199|199	0.3479020979020979|0.3479020979020979	365|365	0.4815303430079156|0.4815303430079156	G|G	2.706|2.706	-0.269904|-0.269904	0.05716|0.05716	0.558356|0.558356	0.499651|0.499651	ENSG00000164989|ENSG00000164989	ENST00000297641;ENST00000380689;ENST00000380701|ENST00000449575;ENST00000432954	T;T|.	0.68624|.	-0.34;-0.34|.	5.04|5.04	4.13|4.13	0.48395|0.48395	.|.	0.102710|.	0.64402|.	N|.	0.000004|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04880|0.04880	-0.145|-0.145	0.09310|0.09310	P|P	0.999999999596851|0.999999999596851	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.06405|.	0.0;0.002;0.0|.	T|T	0.42481|0.42481	-0.9449|-0.9449	9|4	0.02654|.	T|.	1|.	-5.4799|-5.4799	7.6667|7.6667	0.28434|0.28434	0.2861:0.0:0.7139:0.0|0.2861:0.0:0.7139:0.0	rs1539172;rs60174439;rs1539172|rs1539172;rs60174439;rs1539172	1077;336;1069|.	B7ZM22;A6NK04;Q6TFL3|.	.;.;CI093_HUMAN|.	R|D	1069;336;1069|309;123	ENSP00000297641:K1069R;ENSP00000370077:K1069R|.	ENSP00000297641:K1069R|.	K|N	+|+	2|1	0|0	C9orf93|C9orf93	15774631|15774631	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.865000|0.865000	0.49528|0.49528	3.377000|3.377000	0.52425|0.52425	1.268000|1.268000	0.44264|0.44264	-0.119000|-0.119000	0.15052|0.15052	AAA|AAC	A|0.511;G|0.489	0.489	strong		0.368	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
AKAP3	10566	hgsc.bcm.edu	37	12	4735737	4735737	+	Silent	SNP	A	A	G	rs2072358	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:4735737A>G	ENST00000545990.2	-	5	2855	c.2331T>C	c.(2329-2331)ctT>ctC	p.L777L	AKAP3_ENST00000228850.1_Silent_p.L777L|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	777					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						CTACCCATTGAAGGACGGCTT	0.493													A|||	1323	0.264177	0.1475	0.3256	5008	,	,		21345	0.3621		0.3022	False		,,,				2504	0.2382				p.L777L		Atlas-SNP	.											.	AKAP3	212	.	0			c.T2331C						PASS	.	A		706,3700	295.0+/-283.4	50,606,1547	155.0	142.0	146.0		2331	-2.0	1.0	12	dbSNP_96	146	2518,6082	414.1+/-351.3	408,1702,2190	no	coding-synonymous	AKAP3	NM_006422.2		458,2308,3737	GG,GA,AA		29.2791,16.0236,24.7886		777/854	4735737	3224,9782	2203	4300	6503	SO:0001819	synonymous_variant	10566	exon4			CCATTGAAGGACG	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.2331T>C	12.37:g.4735737A>G		Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	309	152	0.491909	NM_006422	O75945|Q86X01|Q9UM61	Silent	SNP	ENST00000545990.2	37	CCDS8531.1																																																																																			G|0.259;A|0.741	0.259	strong		0.493	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
YWHAG	7532	hgsc.bcm.edu	37	7	75959188	75959188	+	Silent	SNP	G	G	A	rs2072435	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:75959188G>A	ENST00000307630.3	-	2	672	c.450C>T	c.(448-450)tcC>tcT	p.S150S		NM_012479.3	NP_036611.2	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma	150					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of neuron differentiation (GO:0045664)|regulation of signal transduction (GO:0009966)|regulation of synaptic plasticity (GO:0048167)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	insulin-like growth factor receptor binding (GO:0005159)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)|protein kinase C inhibitor activity (GO:0008426)			endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8						AGGCCTTCTCGGAGGACTCCA	0.562													G|||	1565	0.3125	0.329	0.2896	5008	,	,		17236	0.4454		0.2982	False		,,,				2504	0.184				p.S150S		Atlas-SNP	.											.	YWHAG	24	.	0			c.C450T						PASS	.	G		1334,3072	448.1+/-348.6	198,938,1067	148.0	151.0	150.0		450	-10.8	0.1	7	dbSNP_96	150	2450,6150	405.0+/-348.4	351,1748,2201	no	coding-synonymous	YWHAG	NM_012479.3		549,2686,3268	AA,AG,GG		28.4884,30.2769,29.0943		150/248	75959188	3784,9222	2203	4300	6503	SO:0001819	synonymous_variant	7532	exon2			CTTCTCGGAGGAC	AF142498	CCDS5584.1	7q11.23	2014-06-13	2013-12-03		ENSG00000170027	ENSG00000170027			12852	protein-coding gene	gene with protein product	"""14-3-3 gamma"", ""protein phosphatase 1, regulatory subunit 170"""	605356	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide"""			10486217, 10433554	Standard	NM_012479		Approved	PPP1R170	uc011kgj.1	P61981	OTTHUMG00000022862	ENST00000307630.3:c.450C>T	7.37:g.75959188G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	119	46	0.386555	NM_012479	O70457|P35214|Q6FH52|Q9UDP2|Q9UN99	Silent	SNP	ENST00000307630.3	37	CCDS5584.1																																																																																			G|0.697;A|0.303	0.303	strong		0.562	YWHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253002.1	NM_012479	
ZZEF1	23140	hgsc.bcm.edu	37	17	4017695	4017695	+	Missense_Mutation	SNP	T	T	C	rs138134000	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4017695T>C	ENST00000381638.2	-	4	888	c.764A>G	c.(763-765)tAt>tGt	p.Y255C	snoU13_ENST00000459263.1_RNA|ZZEF1_ENST00000574474.1_5'UTR	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	255	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.						calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						TGTTTCTATATAAGCATAGCA	0.438													T|||	11	0.00219649	0.0	0.0	5008	,	,		17608	0.0		0.005	False		,,,				2504	0.0061				p.Y255C		Atlas-SNP	.											ZZEF1,NS,lymphoid_neoplasm,0,1	ZZEF1	195	1	0			c.A764G						PASS	.	T	CYS/TYR	5,4401	9.9+/-24.2	0,5,2198	180.0	158.0	166.0		764	5.1	1.0	17	dbSNP_134	166	56,8544	35.9+/-90.5	0,56,4244	yes	missense	ZZEF1	NM_015113.3	194	0,61,6442	CC,CT,TT		0.6512,0.1135,0.469	probably-damaging	255/2962	4017695	61,12945	2203	4300	6503	SO:0001583	missense	23140	exon4			TCTATATAAGCAT	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.764A>G	17.37:g.4017695T>C	ENSP00000371051:p.Tyr255Cys	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	234	111	0.474359	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	16.80	3.223085	0.58668	0.001135	0.006512	ENSG00000074755	ENST00000381638	T	0.63580	-0.05	5.12	5.12	0.69794	Anaphase-promoting complex, subunit 10/DOC domain (1);Galactose-binding domain-like (1);	0.367468	0.29028	N	0.013371	T	0.48370	0.1496	N	0.08118	0	0.27369	N	0.955744	D;D	0.63880	0.993;0.967	P;P	0.56788	0.687;0.806	T	0.53892	-0.8374	10	0.41790	T	0.15	-11.0054	14.927	0.70887	0.0:0.0:0.0:1.0	.	255;255	O43149-3;O43149	.;ZZEF1_HUMAN	C	255	ENSP00000371051:Y255C	ENSP00000371051:Y255C	Y	-	2	0	ZZEF1	3964444	1.000000	0.71417	0.981000	0.43875	0.970000	0.65996	3.945000	0.56637	1.912000	0.55364	0.455000	0.32223	TAT	T|0.996;C|0.004	0.004	strong		0.438	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
SDK1	221935	hgsc.bcm.edu	37	7	4213940	4213940	+	Silent	SNP	T	T	C	rs671756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:4213940T>C	ENST00000404826.2	+	33	5026	c.4887T>C	c.(4885-4887)acT>acC	p.T1629T	SDK1_ENST00000389531.3_Silent_p.T1629T	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1629	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GGTCAGGCACTGAGGCCAAGA	0.557													C|||	3334	0.665735	0.5764	0.6902	5008	,	,		20528	0.7659		0.6561	False		,,,				2504	0.6759				p.T1629T		Atlas-SNP	.											.	SDK1	361	.	0			c.T4887C						PASS	.	C		2678,1728	517.8+/-369.5	818,1042,343	202.0	193.0	196.0		4887	-9.8	0.0	7	dbSNP_83	196	5541,3059	469.5+/-367.6	1792,1957,551	no	coding-synonymous	SDK1	NM_152744.3		2610,2999,894	CC,CT,TT		35.5698,39.2192,36.8061		1629/2214	4213940	8219,4787	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon33			AGGCACTGAGGCC	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4887T>C	7.37:g.4213940T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			T|0.351;C|0.649	0.649	strong		0.557	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
ESR1	2099	hgsc.bcm.edu	37	6	152129077	152129077	+	Silent	SNP	T	T	C	rs2077647	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:152129077T>C	ENST00000206249.3	+	1	392	c.30T>C	c.(28-30)tcT>tcC	p.S10S	ESR1_ENST00000338799.5_Silent_p.S10S|ESR1_ENST00000456483.2_Silent_p.S10S|ESR1_ENST00000440973.1_Silent_p.S10S|ESR1_ENST00000427531.2_5'Flank|ESR1_ENST00000406599.1_Silent_p.S10S|ESR1_ENST00000443427.1_Silent_p.S10S	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	10	Modulating (transactivation AF-1); mediates interaction with MACROD1.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	CCAAAGCATCTGGGATGGCCC	0.667													C|||	2336	0.466454	0.5212	0.4654	5008	,	,		14556	0.378		0.4414	False		,,,				2504	0.5102				p.S10S		Atlas-SNP	.											.	ESR1	94	.	0			c.T30C						PASS	.	C	,,,	2127,2279	583.6+/-385.9	519,1089,595	35.0	33.0	34.0		30,30,30,30	-6.6	0.0	6	dbSNP_96	34	4101,4499	579.7+/-390.9	1006,2089,1205	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESR1	NM_000125.3,NM_001122740.1,NM_001122741.1,NM_001122742.1	,,,	1525,3178,1800	CC,CT,TT		47.686,48.2751,47.8856	,,,	10/596,10/596,10/596,10/596	152129077	6228,6778	2203	4300	6503	SO:0001819	synonymous_variant	2099	exon1			AGCATCTGGGATG	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"""Nuclear hormone receptors"""	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.30T>C	6.37:g.152129077T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	120	118	0.983333	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Silent	SNP	ENST00000206249.3	37	CCDS5234.1																																																																																			T|0.538;C|0.462	0.462	strong		0.667	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
ZBTB46	140685	hgsc.bcm.edu	37	20	62407176	62407176	+	Silent	SNP	G	G	A	rs35738769	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62407176G>A	ENST00000245663.4	-	3	1227	c.1077C>T	c.(1075-1077)gaC>gaT	p.D359D	ZBTB46_ENST00000395104.1_Silent_p.D359D|ZBTB46_ENST00000302995.2_Silent_p.D359D	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	359					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GATGCAGGGCGTCGTCCTTCT	0.667													G|||	138	0.0275559	0.0045	0.0476	5008	,	,		16432	0.0		0.0775	False		,,,				2504	0.0215				p.D359D		Atlas-SNP	.											.	ZBTB46	72	.	0			c.C1077T						PASS	.	G		85,4321	71.4+/-109.4	1,83,2119	55.0	57.0	57.0		1077	-11.2	0.0	20	dbSNP_126	57	666,7934	168.0+/-219.6	28,610,3662	no	coding-synonymous	ZBTB46	NM_025224.3		29,693,5781	AA,AG,GG		7.7442,1.9292,5.7743		359/590	62407176	751,12255	2203	4300	6503	SO:0001819	synonymous_variant	140685	exon3			CAGGGCGTCGTCC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1077C>T	20.37:g.62407176G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			G|0.950;A|0.050	0.050	strong		0.667	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
ZP2	7783	hgsc.bcm.edu	37	16	21222672	21222672	+	Missense_Mutation	SNP	C	C	A	rs2075520	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:21222672C>A	ENST00000574002.1	-	3	589	c.107G>T	c.(106-108)gGg>gTg	p.G36V	ZP2_ENST00000574091.1_Missense_Mutation_p.G36V|ZP2_ENST00000219593.4_Missense_Mutation_p.G36V			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	36			G -> V (in dbSNP:rs2075520). {ECO:0000269|PubMed:15489334}.		binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		TATGGAGTTCCCTGAAGTCAC	0.453													A|||	2244	0.448083	0.6717	0.4524	5008	,	,		22005	0.4444		0.2555	False		,,,				2504	0.3446				p.G36V		Atlas-SNP	.											.	ZP2	92	.	0			c.G107T						PASS	.	A	VAL/GLY	2677,1721	516.7+/-369.2	831,1015,353	143.0	142.0	142.0		107	2.4	0.4	16	dbSNP_96	142	2398,6202	700.3+/-405.1	332,1734,2234	yes	missense	ZP2	NM_003460.1	109	1163,2749,2587	AA,AC,CC		27.8837,39.1314,39.0445	benign	36/746	21222672	5075,7923	2199	4300	6499	SO:0001583	missense	7783	exon2			GAGTTCCCTGAAG	M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"""Zona pellucida glycoproteins"""	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.107G>T	16.37:g.21222672C>A	ENSP00000460971:p.Gly36Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	918	0.42032967032967034	319	0.6483739837398373	129	0.356353591160221	263	0.4597902097902098	207	0.27308707124010556	A	0.005	-2.221557	0.00283	0.608686	0.278837	ENSG00000103310	ENST00000219593	T	0.21361	2.01	4.73	2.42	0.29668	.	0.617242	0.15139	N	0.278368	T	0.00012	0.0000	N	0.00049	-2.42	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.40739	-0.9547	9	0.02654	T	1	-3.0493	5.3241	0.15896	0.5579:0.3491:0.093:0.0	rs2075520;rs59742566;rs2075520	36;36;36	B4DEV1;Q4VAP1;Q05996	.;.;ZP2_HUMAN	V	36	ENSP00000219593:G36V	ENSP00000219593:G36V	G	-	2	0	ZP2	21130173	0.012000	0.17670	0.414000	0.26521	0.204000	0.24138	0.668000	0.25127	0.059000	0.16252	-0.256000	0.11100	GGG	C|0.593;A|0.407	0.407	strong		0.453	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
KIF20B	9585	hgsc.bcm.edu	37	10	91498254	91498254	+	Missense_Mutation	SNP	A	A	G	rs1886997	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:91498254A>G	ENST00000371728.3	+	20	3721	c.3656A>G	c.(3655-3657)aAt>aGt	p.N1219S	KIF20B_ENST00000416354.1_Missense_Mutation_p.N1249S|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.N1179S|KIF20B_ENST00000394289.2_Missense_Mutation_p.N1219S	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1219			N -> S (in dbSNP:rs1886997).		ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						AAAGATTTAAATGTAAAGGAA	0.294													G|||	1788	0.357029	0.4796	0.219	5008	,	,		18720	0.3085		0.2326	False		,,,				2504	0.4673				p.N1179S		Atlas-SNP	.											.	KIF20B	191	.	0			c.A3536G						PASS	.	G	SER/ASN	1966,2354		457,1052,651	52.0	57.0	55.0		3536	-0.7	0.9	10	dbSNP_92	55	1972,6594		222,1528,2533	yes	missense	KIF20B	NM_016195.2	46	679,2580,3184	GG,GA,AA		23.0212,45.5093,30.5603	benign	1179/1781	91498254	3938,8948	2160	4283	6443	SO:0001583	missense	9585	exon20			ATTTAAATGTAAA	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"""cancer/testis antigen 90"""	605498	"""M-phase phosphoprotein 1"""	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.3656A>G	10.37:g.91498254A>G	ENSP00000360793:p.Asn1219Ser	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	87	7	0.0804598	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		650	0.2976190476190476	218	0.44308943089430897	86	0.23756906077348067	170	0.2972027972027972	176	0.23218997361477572	G	0.003	-2.536918	0.00143	0.455093	0.230212	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.66638	-0.17;-0.17;-0.22;-0.16	5.82	-0.717	0.11208	.	0.446678	0.21264	N	0.077426	T	0.00012	0.0000	N	0.00554	-1.385	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41395	-0.9511	9	0.02654	T	1	-0.9997	12.5572	0.56261	0.6198:0.0:0.3802:0.0	rs1886997;rs52790182;rs57731638;rs1886997	1219;1179	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	S	1179;1249;1219;1219	ENSP00000260753:N1179S;ENSP00000411545:N1249S;ENSP00000377830:N1219S;ENSP00000360793:N1219S	ENSP00000260753:N1179S	N	+	2	0	KIF20B	91488234	0.986000	0.35501	0.876000	0.34364	0.027000	0.11550	0.107000	0.15375	-0.417000	0.07461	-1.201000	0.01664	AAT	A|0.698;G|0.302	0.302	strong		0.294	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
MYH11	4629	hgsc.bcm.edu	37	16	15818653	15818653	+	Silent	SNP	G	G	A	rs12907|rs587781056	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15818653G>A	ENST00000300036.5	-	30	4076	c.3967C>T	c.(3967-3969)Ctg>Ttg	p.L1323L	NDE1_ENST00000396354.1_3'UTR|NDE1_ENST00000571896.1_3'UTR|NDE1_ENST00000396355.1_3'UTR|NDE1_ENST00000342673.5_3'UTR|AF001548.5_ENST00000574212.1_RNA|MYH11_ENST00000452625.2_Silent_p.L1330L|MYH11_ENST00000396324.3_Silent_p.L1330L|MYH11_ENST00000576790.2_Silent_p.L1323L	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1323					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TCTTGAAGCAGCTCCTGCAAA	0.612			T	CBFB	AML								G|||	509	0.101637	0.3139	0.0317	5008	,	,		18367	0.0387		0.0219	False		,,,				2504	0.0112				p.L1330L		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.C3988T						PASS	.	G	,,,,,	1068,3326	387.7+/-326.6	132,804,1261	114.0	119.0	117.0		3988,3988,,3967,,3967	5.3	1.0	16	dbSNP_52	117	130,8470	67.0+/-129.4	2,126,4172	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous,utr-3,coding-synonymous	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	,,,,,	134,930,5433	AA,AG,GG		1.5116,24.3059,9.2196	,,,,,	1330/1946,1330/1980,,1323/1973,,1323/1939	15818653	1198,11796	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon31			GAAGCAGCTCCTG	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.3967C>T	16.37:g.15818653G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			G|0.897;A|0.103	0.103	strong		0.612	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
GLTSCR1	29998	hgsc.bcm.edu	37	19	48198675	48198675	+	Missense_Mutation	SNP	A	A	G	rs13346368	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48198675A>G	ENST00000396720.3	+	10	3324	c.3130A>G	c.(3130-3132)Acc>Gcc	p.T1044A	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1044			T -> A (in dbSNP:rs13346368).							breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		CAACCTCCCGACCCTGAATGT	0.667													A|||	1509	0.301318	0.3222	0.2983	5008	,	,		9654	0.3185		0.2525	False		,,,				2504	0.3078				p.T1044A		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.A3130G						PASS	.	A	ALA/THR	1065,2803		163,739,1032	13.0	13.0	13.0		3130	-3.2	0.2	19	dbSNP_121	13	2038,6238		282,1474,2382	yes	missense	GLTSCR1	NM_015711.3	58	445,2213,3414	GG,GA,AA		24.6254,27.5336,25.5517	possibly-damaging	1044/1561	48198675	3103,9041	1934	4138	6072	SO:0001583	missense	29998	exon10			CTCCCGACCCTGA	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.3130A>G	19.37:g.48198675A>G	ENSP00000379946:p.Thr1044Ala	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_015711	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	37	CCDS46134.1	600	0.27472527472527475	150	0.3048780487804878	90	0.24861878453038674	166	0.2902097902097902	194	0.2559366754617414	A	3.512	-0.099632	0.07010	0.275336	0.246254	ENSG00000063169	ENST00000396720	T	0.30981	1.51	3.35	-3.15	0.05233	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.42699	-0.9436	8	0.08599	T	0.76	.	5.3333	0.15944	0.2783:0.201:0.5207:0.0	rs13346368;rs61625955;rs13346368	1044	Q9NZM4	GSCR1_HUMAN	A	1044	ENSP00000379946:T1044A	ENSP00000379946:T1044A	T	+	1	0	GLTSCR1	52890487	0.000000	0.05858	0.168000	0.22838	0.416000	0.31233	-0.351000	0.07711	-0.371000	0.08004	0.260000	0.18958	ACC	A|0.713;G|0.287	0.287	strong		0.667	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711	
ZNF470	388566	hgsc.bcm.edu	37	19	57089375	57089375	+	Silent	SNP	A	A	G	rs4570977	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57089375A>G	ENST00000330619.8	+	6	2264	c.1578A>G	c.(1576-1578)caA>caG	p.Q526Q	ZNF470_ENST00000391709.3_Silent_p.Q526Q|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	526					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)			endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		ACCTCGCGCAACATCAGAAAA	0.448													A|||	769	0.153554	0.0847	0.1484	5008	,	,		21970	0.0605		0.2932	False		,,,				2504	0.2025				p.Q526Q		Atlas-SNP	.											.	ZNF470	103	.	0			c.A1578G						PASS	.	A		433,3973	213.5+/-233.1	24,385,1794	69.0	68.0	69.0		1578	-1.8	0.4	19	dbSNP_111	69	2405,6195	400.1+/-346.7	358,1689,2253	no	coding-synonymous	ZNF470	NM_001001668.3		382,2074,4047	GG,GA,AA		27.9651,9.8275,21.8207		526/718	57089375	2838,10168	2203	4300	6503	SO:0001819	synonymous_variant	388566	exon6			CGCGCAACATCAG	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"""Zinc fingers, C2H2-type"", ""-"""	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.1578A>G	19.37:g.57089375A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Silent	SNP	ENST00000330619.8	37	CCDS33122.1																																																																																			A|0.797;G|0.203	0.203	strong		0.448	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668	
KLF12	11278	hgsc.bcm.edu	37	13	74339104	74339104	+	Silent	SNP	G	G	T	rs3764134	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:74339104G>T	ENST00000377669.2	-	5	866	c.840C>A	c.(838-840)ggC>ggA	p.G280G	KLF12_ENST00000377666.4_Silent_p.G280G	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	280					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|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 corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		tcattcgattgccccggaccc	0.358													T|||	2042	0.407748	0.388	0.389	5008	,	,		16354	0.1815		0.5209	False		,,,				2504	0.5644				p.G280G		Atlas-SNP	.											.	KLF12	42	.	0			c.C840A						PASS	.	T		1780,2626	643.4+/-397.8	346,1088,769	95.0	90.0	91.0		840	2.9	1.0	13	dbSNP_107	91	4897,3703	529.4+/-381.6	1404,2089,807	no	coding-synonymous	KLF12	NM_007249.4		1750,3177,1576	TT,TG,GG		43.0581,40.3995,48.6622		280/403	74339104	6677,6329	2203	4300	6503	SO:0001819	synonymous_variant	11278	exon6			TCGATTGCCCCGG	AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6346	protein-coding gene	gene with protein product	"""KLF12 zinc finger transcriptional repressor"", ""AP-2rep transcription factor"", ""AP-2 repressor"""	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.840C>A	13.37:g.74339104G>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	34	33	0.970588	NM_007249	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Silent	SNP	ENST00000377669.2	37	CCDS9449.1																																																																																			G|0.544;T|0.456	0.456	strong		0.358	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249	
LPCAT1	79888	hgsc.bcm.edu	37	5	1494935	1494935	+	Missense_Mutation	SNP	T	T	C	rs28715640	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1494935T>C	ENST00000283415.3	-	3	505	c.373A>G	c.(373-375)Acc>Gcc	p.T125A		NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	125					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		GCCGCCTCGGTGGGCAGCGCC	0.647													T|||	98	0.0195687	0.003	0.0159	5008	,	,		14699	0.001		0.0746	False		,,,				2504	0.0072				p.T125A		Atlas-SNP	.											.	LPCAT1	70	.	0			c.A373G						PASS	.	T	ALA/THR	73,4333	61.7+/-98.7	5,63,2135	43.0	42.0	42.0		373	-0.6	0.3	5	dbSNP_125	42	692,7908	165.5+/-217.6	26,640,3634	yes	missense	LPCAT1	NM_024830.3	58	31,703,5769	CC,CT,TT		8.0465,1.6568,5.8819	benign	125/535	1494935	765,12241	2203	4300	6503	SO:0001583	missense	79888	exon3			CCTCGGTGGGCAG	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"""EF-hand domain containing"""	25718	protein-coding gene	gene with protein product		610472	"""acyltransferase like 2"""	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.373A>G	5.37:g.1494935T>C	ENSP00000283415:p.Thr125Ala	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Missense_Mutation	SNP	ENST00000283415.3	37	CCDS3864.1	68	0.031135531135531136	2	0.0040650406504065045	7	0.019337016574585635	1	0.0017482517482517483	58	0.07651715039577836	T	1.238	-0.622201	0.03636	0.016568	0.080465	ENSG00000153395	ENST00000283415	D	0.92805	-3.11	4.98	-0.643	0.11482	Phospholipid/glycerol acyltransferase (1);	0.525534	0.21815	N	0.068714	T	0.11580	0.0282	N	0.02011	-0.69	0.27461	N	0.953166	B	0.02656	0.0	B	0.04013	0.001	T	0.51888	-0.8648	10	0.07325	T	0.83	-5.7754	1.7637	0.02998	0.1299:0.3057:0.1337:0.4307	rs28715640	125	Q8NF37	PCAT1_HUMAN	A	125	ENSP00000283415:T125A	ENSP00000283415:T125A	T	-	1	0	LPCAT1	1547935	0.000000	0.05858	0.291000	0.24904	0.498000	0.33706	-1.220000	0.02971	-0.378000	0.07918	-1.114000	0.02060	ACC	T|0.954;C|0.046	0.046	strong		0.647	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291639	1291639	+	Silent	SNP	A	A	G	rs1064783		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1291639A>G	ENST00000338844.3	+	4	471	c.438A>G	c.(436-438)tcA>tcG	p.S146S	TPSAB1_ENST00000461509.2_Silent_p.S153S	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	146	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				CCCCTGCCTCAGAGACCTTCC	0.667																																					p.S146S		Atlas-SNP	.											.	TPSAB1	24	.	0			c.A438G						PASS	.						41.0	34.0	36.0					16																	1291639		2199	4298	6497	SO:0001819	synonymous_variant	7177	exon4			TGCCTCAGAGACC	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.438A>G	16.37:g.1291639A>G		Somatic	386	0	0		WXS	Illumina HiSeq	Phase_I	571	41	0.0718039	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Silent	SNP	ENST00000338844.3	37	CCDS10431.1																																																																																			A|0.802;G|0.198	0.198	strong		0.667	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
MCM9	254394	hgsc.bcm.edu	37	6	119137445	119137445	+	Missense_Mutation	SNP	C	C	A	rs78791427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:119137445C>A	ENST00000316316.6	-	13	2260	c.1974G>T	c.(1972-1974)caG>caT	p.Q658H		NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	658					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		GGTGCACACTCTGATTCTGTA	0.408													C|||	14	0.00279553	0.0	0.0	5008	,	,		18273	0.0		0.0119	False		,,,				2504	0.002				p.Q658H		Atlas-SNP	.											MCM9_ENST00000316316,NS,carcinoma,-1,2	MCM9	73	2	0			c.G1974T						PASS	.																																			SO:0001583	missense	254394	exon12			CACACTCTGATTC	BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"""minichromosome maintenance deficient domain containing 1"", ""chromosome 6 open reading frame 61"""	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.1974G>T	6.37:g.119137445C>A	ENSP00000314505:p.Gln658His	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	223	112	0.502242	NM_017696	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Missense_Mutation	SNP	ENST00000316316.6	37	CCDS56447.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	C|C	10.78|10.78	1.446662|1.446662	0.25987|0.25987	.|.	.|.	ENSG00000111877|ENSG00000111877	ENST00000458674|ENST00000316316;ENST00000243218	.|T	.|0.30182	.|1.54	6.17|6.17	0.73|0.73	0.18271|0.18271	.|.	.|4.506090	.|0.00424	.|N	.|0.000066	.|T	.|0.11580	.|0.0282	L|L	0.50333|0.50333	1.59|1.59	0.58432|0.58432	D|D	0.999999|0.999999	.|B	.|0.18741	.|0.03	.|B	.|0.17098	.|0.017	.|T	.|0.45745	.|-0.9240	.|10	.|0.39692	.|T	.|0.17	.|.	1.5623|1.5623	0.02597|0.02597	0.1452:0.4093:0.143:0.3024|0.1452:0.4093:0.143:0.3024	.|.	.|658	.|Q9NXL9	.|MCM9_HUMAN	X|H	150|658;277	.|ENSP00000314505:Q658H	.|ENSP00000243218:Q277H	E|Q	-|-	1|3	0|2	MCM9|MCM9	119244148|119244148	0.956000|0.956000	0.32656|0.32656	0.495000|0.495000	0.27527|0.27527	0.222000|0.222000	0.24845|0.24845	0.344000|0.344000	0.19962|0.19962	0.170000|0.170000	0.19704|0.19704	0.655000|0.655000	0.94253|0.94253	GAG|CAG	C|0.993;A|0.007	0.007	strong		0.408	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	
EPHA5	2044	hgsc.bcm.edu	37	4	66197804	66197804	+	Silent	SNP	C	C	T	rs7349683	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:66197804C>T	ENST00000273854.3	-	17	3495	c.2895G>A	c.(2893-2895)ggG>ggA	p.G965G	EPHA5_ENST00000432638.2_Silent_p.G802G|EPHA5_ENST00000354839.4_Silent_p.G943G|EPHA5_ENST00000511294.1_Silent_p.G966G	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	965	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						ATCTGTAGGCCCCAGATCCTA	0.368										TSP Lung(17;0.13)			C|||	1636	0.326677	0.0893	0.3098	5008	,	,		15856	0.4613		0.3748	False		,,,				2504	0.4714				p.G965G		Atlas-SNP	.											.	EPHA5	315	.	0			c.G2895A						PASS	.	C	,	607,3799	264.1+/-265.8	44,519,1640	75.0	69.0	71.0		2895,2829	3.7	1.0	4	dbSNP_116	71	3073,5527	471.0+/-368.0	550,1973,1777	no	coding-synonymous,coding-synonymous	EPHA5	NM_004439.5,NM_182472.2	,	594,2492,3417	TT,TC,CC		35.7326,13.7767,28.2946	,	965/1038,943/1016	66197804	3680,9326	2203	4300	6503	SO:0001819	synonymous_variant	2044	exon17			GTAGGCCCCAGAT	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3389	protein-coding gene	gene with protein product		600004	"""EphA5"""			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.2895G>A	4.37:g.66197804C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_004439	Q7Z3F2	Silent	SNP	ENST00000273854.3	37	CCDS3513.1																																																																																			C|0.704;T|0.296	0.296	strong		0.368	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439	
TUSC5	286753	hgsc.bcm.edu	37	17	1183347	1183347	+	Missense_Mutation	SNP	G	G	A	rs111701043	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1183347G>A	ENST00000333813.3	+	1	391	c.52G>A	c.(52-54)Gcc>Acc	p.A18T		NM_172367.2	NP_758955.2	Q8IXB3	TUSC5_HUMAN	tumor suppressor candidate 5	18			A -> T (in dbSNP:rs111701043). {ECO:0000269|PubMed:12660825}.		response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|prostate(4)|skin(2)	15				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GCCAGGCTCCGCCGCATTCCT	0.637													G|||	38	0.00758786	0.0023	0.0101	5008	,	,		16485	0.001		0.0229	False		,,,				2504	0.0041				p.A18T		Atlas-SNP	.											.	TUSC5	25	.	0			c.G52A						PASS	.	G	THR/ALA	12,3930		0,12,1959	45.0	50.0	49.0		52	0.5	0.0	17	dbSNP_132	49	198,8098		5,188,3955	yes	missense	TUSC5	NM_172367.2	58	5,200,5914	AA,AG,GG		2.3867,0.3044,1.716	benign	18/178	1183347	210,12028	1971	4148	6119	SO:0001583	missense	286753	exon1			GGCTCCGCCGCAT	AB090231	CCDS42225.1	17p13.3	2009-10-16			ENSG00000184811	ENSG00000184811			29592	protein-coding gene	gene with protein product	"""located at seventeen p thirteen point three 1"", ""interferon induced transmembrane protein domain containing 3"""	612211				12660825	Standard	NM_172367		Approved	LOST1, IFITMD3	uc002fsi.1	Q8IXB3	OTTHUMG00000132196	ENST00000333813.3:c.52G>A	17.37:g.1183347G>A	ENSP00000329548:p.Ala18Thr	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	182	81	0.445055	NM_172367	A6NMK4	Missense_Mutation	SNP	ENST00000333813.3	37	CCDS42225.1	19	0.0086996336996337	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	G	7.327	0.618074	0.14129	0.003044	0.023867	ENSG00000184811	ENST00000333813	T	0.70749	-0.51	5.22	0.456	0.16655	.	0.477465	0.19818	N	0.105387	T	0.25680	0.0625	N	0.17082	0.46	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.17806	-1.0357	10	0.02654	T	1	-6.108	3.8041	0.08770	0.3848:0.2015:0.4137:0.0	.	18	Q8IXB3	TUSC5_HUMAN	T	18	ENSP00000329548:A18T	ENSP00000329548:A18T	A	+	1	0	TUSC5	1130097	0.001000	0.12720	0.026000	0.17262	0.038000	0.13279	0.376000	0.20535	0.099000	0.17552	-0.501000	0.04562	GCC	A|0.014;C|0.000;G|0.986	0.014	strong		0.637	TUSC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255249.1	NM_172367	
C2orf71	388939	hgsc.bcm.edu	37	2	29296870	29296870	+	Silent	SNP	C	C	T	rs62132765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29296870C>T	ENST00000331664.5	-	1	257	c.258G>A	c.(256-258)agG>agA	p.R86R		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	86					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CCATATCTTTCCTTTTGCCTG	0.512													C|||	557	0.111222	0.0129	0.1527	5008	,	,		20671	0.123		0.2137	False		,,,				2504	0.0971				p.R86R		Atlas-SNP	.											C2orf71,rectum,carcinoma,-1,1	C2orf71	146	1	0			c.G258A						PASS	.	C		189,3673		4,181,1746	213.0	196.0	202.0		258	1.3	0.0	2	dbSNP_129	202	1854,6434		192,1470,2482	no	coding-synonymous	C2orf71	NM_001029883.1		196,1651,4228	TT,TC,CC		22.3697,4.8938,16.8148		86/1289	29296870	2043,10107	1931	4144	6075	SO:0001819	synonymous_variant	388939	exon1			ATCTTTCCTTTTG		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.258G>A	2.37:g.29296870C>T		Somatic	491	0	0		WXS	Illumina HiSeq	Phase_I	522	256	0.490421	NM_001029883		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																			C|0.825;T|0.175	0.175	strong		0.512	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
ENTPD8	377841	hgsc.bcm.edu	37	9	140327663	140327663	+	IGR	SNP	C	C	T	rs34155071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140327663C>T	ENST00000472938.1	-	0	1749				NOXA1_ENST00000392815.2_Missense_Mutation_p.P230L|NOXA1_ENST00000341349.2_Missense_Mutation_p.P286L			Q5MY95	ENTP8_HUMAN	ectonucleoside triphosphate diphosphohydrolase 8						nucleoside diphosphate biosynthetic process (GO:0009133)|nucleoside monophosphate biosynthetic process (GO:0009124)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			biliary_tract(1)|lung(4)|prostate(1)|skin(1)	7	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000224)|Epithelial(140;0.000898)		ACAGGGCTGCCGGCAATGGGG	0.667													c|||	1062	0.212061	0.0779	0.1326	5008	,	,		14280	0.247		0.3151	False		,,,				2504	0.3078				p.P286L		Atlas-SNP	.											NOXA1,colon,carcinoma,0,1	NOXA1	32	1	0			c.C857T						scavenged	.	T	LEU/PRO	444,3910		33,378,1766	9.0	11.0	10.0		857	-6.3	0.0	9	dbSNP_126	10	2673,5897		437,1799,2049	yes	missense	NOXA1	NM_006647.1	98	470,2177,3815	TT,TC,CC		31.1902,10.1975,24.1179	benign	286/484	140327663	3117,9807	2177	4285	6462	SO:0001628	intergenic_variant	10811	exon10			GGCTGCCGGCAAT	AY359088	CCDS7043.1, CCDS43913.1	9q34.3	2013-09-20			ENSG00000188833	ENSG00000188833			24860	protein-coding gene	gene with protein product	"""GLSR2492"""					12975309	Standard	NM_198585		Approved	UNQ2492, NTPDase-8	uc004cmw.3	Q5MY95	OTTHUMG00000131831		9.37:g.140327663C>T		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_006647	A2BG17|Q6UVZ0	Missense_Mutation	SNP	ENST00000472938.1	37	CCDS43913.1	479	0.21932234432234432	42	0.08536585365853659	55	0.15193370165745856	141	0.2465034965034965	241	0.3179419525065963	c	5.077	0.199935	0.09652	0.101975	0.311902	ENSG00000188747	ENST00000341349;ENST00000392815	D;D	0.85702	-2.02;-2.01	3.17	-6.34	0.01982	.	3.307570	0.01200	N	0.007549	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.11235	0.003;0.002;0.004	B;B;B	0.06405	0.002;0.001;0.001	T	0.12941	-1.0528	9	0.19147	T	0.46	.	5.8021	0.18420	0.0:0.2326:0.2607:0.5068	rs34155071;rs34155071	230;286;286	Q86UR1-3;Q86UR1;Q86UR1-2	.;NOXA1_HUMAN;.	L	286;230	ENSP00000342848:P286L;ENSP00000376562:P230L	ENSP00000342848:P286L	P	+	2	0	NOXA1	139447484	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.879000	0.00716	-2.169000	0.00777	-0.974000	0.02594	CCG	C|0.795;T|0.205	0.205	strong		0.667	ENTPD8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355991.1	NM_198585	
SULT1A1	6817	hgsc.bcm.edu	37	16	28619911	28619911	+	Silent	SNP	T	T	C	rs1126447	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28619911T>C	ENST00000395607.1	-	3	435	c.162A>G	c.(160-162)gtA>gtG	p.V54V	SULT1A1_ENST00000314752.7_Silent_p.V54V|SULT1A1_ENST00000395609.1_Silent_p.V54V|SULT1A1_ENST00000569554.1_Silent_p.V54V|SULT1A1_ENST00000350842.4_Intron	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	54					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)	p.V54V(1)		endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	GAATCTGGCTTACCCAGGTAG	0.617													.|||	1455	0.290535	0.2284	0.4769	5008	,	,		24736	0.2669		0.335	False		,,,				2504	0.2209				p.V54V		Atlas-SNP	.											SULT1A1,NS,carcinoma,0,1	SULT1A1	53	1	1	Substitution - coding silent(1)	stomach(1)	c.A162G						PASS	.	C	,,,,	880,3514		131,618,1448	101.0	72.0	81.0		162,162,162,162,	0.1	1.0	16	dbSNP_86	81	2909,5691		613,1683,2004	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	SULT1A1	NM_001055.3,NM_177529.2,NM_177530.2,NM_177534.2,NM_177536.3	,,,,	744,2301,3452	CC,CT,TT		33.8256,20.0273,29.1596	,,,,	54/296,54/296,54/296,54/296,	28619911	3789,9205	2197	4300	6497	SO:0001819	synonymous_variant	6817	exon2			CTGGCTTACCCAG	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.162A>G	16.37:g.28619911T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	201	63	0.313433	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Silent	SNP	ENST00000395607.1	37	CCDS32420.1																																																																																			T|0.716;C|0.284	0.284	strong		0.617	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
MOG	4340	hgsc.bcm.edu	37	6	29638101	29638101	+	Silent	SNP	T	T	C	rs112913018	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29638101T>C	ENST00000376917.3	+	6	865	c.636T>C	c.(634-636)ttT>ttC	p.F212F	MOG_ENST00000396701.2_Intron|MOG_ENST00000431798.2_Intron|MOG_ENST00000376891.4_Intron|MOG_ENST00000376898.3_Silent_p.F212F|MOG_ENST00000376894.4_Silent_p.F212F|MOG_ENST00000483013.1_Intron|MOG_ENST00000376888.2_Silent_p.F96F|MOG_ENST00000494692.1_Intron|MOG_ENST00000533330.2_3'UTR|MOG_ENST00000376902.3_3'UTR|MOG_ENST00000396704.3_Intron|MOG_ENST00000490427.1_Intron|MOG_ENST00000416766.2_Silent_p.F174F	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein	212					cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|positive regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034126)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|skin(2)	19						TAACCCTGTTTGTAATTGTGC	0.527													T|||	5	0.000998403	0.0	0.0014	5008	,	,		18756	0.0		0.004	False		,,,				2504	0.0				p.F212F		Atlas-SNP	.											.	MOG	47	.	0			c.T636C						PASS	.						220.0	211.0	214.0					6																	29638101		2203	4300	6503	SO:0001819	synonymous_variant	4340	exon6			CCTGTTTGTAATT		CCDS4667.1, CCDS34366.1, CCDS34367.1, CCDS34368.1, CCDS34369.1, CCDS34370.1, CCDS47394.1, CCDS47395.1, CCDS47395.2, CCDS54977.1	6p22.1	2014-01-16			ENSG00000204655	ENSG00000204655		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	7197	protein-coding gene	gene with protein product		159465					Standard	NM_002433		Approved	BTN6, BTNL11	uc003nne.3	Q16653	OTTHUMG00000031099	ENST00000376917.3:c.636T>C	6.37:g.29638101T>C		Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	423	209	0.49409	NM_002433	A6NDR4|A6NNJ9|A8MY31|B0UZR9|E9PGF0|F8W9D5|O00713|O00714|O00715|Q13054|Q13055|Q14855|Q29ZN8|Q56UY0|Q5JNX7|Q5JNY1|Q5JNY2|Q5JNY4|Q5SSB5|Q5SSB6|Q5STL9|Q5STM0|Q5STM1|Q5STM2|Q5STM5|Q5SUK5|Q5SUK7|Q5SUK8|Q5SUK9|Q5SUL0|Q5SUL1|Q8IYG5|Q92891|Q92892|Q92893|Q92894|Q92895|Q93053|Q96KU9|Q96KV0|Q96KV1|Q99605	Silent	SNP	ENST00000376917.3	37	CCDS34370.1																																																																																			A|0.002;C|0.001;T|0.997	0.001	strong		0.527	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433	
MUC21	394263	hgsc.bcm.edu	37	6	30954414	30954414	+	Missense_Mutation	SNP	C	C	G	rs138015704	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954414C>G	ENST00000376296.3	+	2	703	c.462C>G	c.(460-462)gaC>gaG	p.D154E	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	154	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D154E(1)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAACTCTGACTCCAGCACAA	0.612																																					p.D154E		Atlas-SNP	.											MUC21,NS,carcinoma,0,2	MUC21	98	2	1	Substitution - Missense(1)	prostate(1)	c.C462G						scavenged	.						150.0	141.0	144.0					6																	30954414		2203	4300	6503	SO:0001583	missense	394263	exon2			CTCTGACTCCAGC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.462C>G	6.37:g.30954414C>G	ENSP00000365473:p.Asp154Glu	Somatic	62	5	0.0806452		WXS	Illumina HiSeq	Phase_I	90	18	0.2	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.859428	0.00552	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.01572	4.76	3.52	-7.04	0.01578	.	.	.	.	.	T	0.00178	0.0005	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35276	-0.9795	8	.	.	.	2.0437	7.1844	0.25791	0.108:0.4767:0.3341:0.0812	.	154	Q5SSG8	MUC21_HUMAN	E	154	ENSP00000365473:D154E	.	D	+	3	2	MUC21	31062393	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.637000	0.00407	-4.956000	0.00026	-2.421000	0.00218	GAC	C|0.993;G|0.007	0.007	strong		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
LY6G5B	58496	hgsc.bcm.edu	37	6	31639845	31639845	+	Missense_Mutation	SNP	C	C	A	rs11758242	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31639845C>A	ENST00000375864.4	+	3	1176	c.392C>A	c.(391-393)tCc>tAc	p.S131Y	CSNK2B-LY6G5B-1181_ENST00000375880.2_3'UTR|LY6G5B_ENST00000409525.1_Missense_Mutation_p.S76Y	NM_021221.2	NP_067044.2	Q8NDX9	LY65B_HUMAN	lymphocyte antigen 6 complex, locus G5B	131			S -> Y (in dbSNP:rs11758242).			extracellular region (GO:0005576)				lung(4)	4						CTGTCTGACTCCCAGATTCAG	0.607													C|||	286	0.0571086	0.1316	0.0764	5008	,	,		16595	0.0179		0.0258	False		,,,				2504	0.0153				p.S131Y		Atlas-SNP	.											LY6G5B,NS,carcinoma,0,1	LY6G5B	8	1	0			c.C392A						PASS	.	C	TYR/SER	334,2688		18,298,1195	53.0	50.0	51.0		392	-0.4	0.0	6	dbSNP_120	51	152,5264		1,150,2557	yes	missense	LY6G5B	NM_021221.2	144	19,448,3752	AA,AC,CC		2.8065,11.0523,5.7597	benign	131/202	31639845	486,7952	1511	2708	4219	SO:0001583	missense	58496	exon3			CTGACTCCCAGAT	AF129756	CCDS34400.1	6p21.3	2008-08-01	2002-07-29	2002-08-01	ENSG00000240053	ENSG00000240053			13931	protein-coding gene	gene with protein product		610433	"""chromosome 6 open reading frame 19"""	C6orf19		8812450, 12079290, 17008713	Standard	NM_021221		Approved	G5b		Q8NDX9	OTTHUMG00000031227	ENST00000375864.4:c.392C>A	6.37:g.31639845C>A	ENSP00000365024:p.Ser131Tyr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	70	0.522388	NM_021221	B0UXB2|B0UZ65|B0UZP8|B7ZCA3|Q5SQ62|Q5SST3|Q9UKT0|Q9UMQ0	Missense_Mutation	SNP	ENST00000375864.4	37	CCDS34400.1	139	0.06364468864468864	74	0.15040650406504066	29	0.08011049723756906	16	0.027972027972027972	20	0.026385224274406333	C	0.580	-0.837366	0.02692	0.110523	0.028065	ENSG00000240053	ENST00000409691;ENST00000375864;ENST00000409525	T;T	0.26067	1.76;1.76	3.68	-0.402	0.12404	.	.	.	.	.	T	0.05731	0.0150	L	0.29908	0.895	.	.	.	B	0.28324	0.207	B	0.27715	0.082	T	0.31586	-0.9938	8	0.62326	D	0.03	-0.2784	3.6555	0.08220	0.0:0.4487:0.1881:0.3632	rs11758242;rs52832321;rs11758242	131	Q8NDX9	LY65B_HUMAN	Y	128;131;76	ENSP00000365024:S131Y;ENSP00000386365:S76Y	ENSP00000365024:S131Y	S	+	2	0	LY6G5B	31747824	0.023000	0.18921	0.003000	0.11579	0.123000	0.20343	0.107000	0.15375	-0.100000	0.12241	-0.467000	0.05162	TCC	C|0.932;A|0.068	0.068	strong		0.607	LY6G5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000124389.4		
EPHX2	2053	hgsc.bcm.edu	37	8	27358509	27358509	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27358509A>G	ENST00000521400.1	+	2	598	c.168A>G	c.(166-168)ggA>ggG	p.G56G	EPHX2_ENST00000518379.1_Silent_p.G56G|EPHX2_ENST00000520666.1_3'UTR|EPHX2_ENST00000380476.3_Silent_p.G3G|EPHX2_ENST00000521780.1_Intron|EPHX2_ENST00000517536.1_Silent_p.G56G	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	56	Phosphatase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		TTATGAAAGGAGAGATCACAC	0.527																																					p.G56G		Atlas-SNP	.											EPHX2,scalp,carcinoma,+2,1	EPHX2	57	1	0			c.A168G						PASS	.						101.0	94.0	97.0					8																	27358509		2203	4300	6503	SO:0001819	synonymous_variant	2053	exon2			GAAAGGAGAGATC	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.168A>G	8.37:g.27358509A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Silent	SNP	ENST00000521400.1	37	CCDS6060.1	.	.	.	.	.	.	.	.	.	.	A	6.193	0.403741	0.11754	.	.	ENSG00000120915	ENST00000521684	.	.	.	4.33	0.328	0.15918	.	.	.	.	.	T	0.45418	0.1341	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24404	-1.0161	4	.	.	.	-4.3771	3.8982	0.09149	0.6131:0.1839:0.203:0.0	.	.	.	.	G	56	.	.	E	+	2	0	EPHX2	27414426	0.994000	0.37717	0.854000	0.33618	0.579000	0.36224	0.349000	0.20055	-0.024000	0.13941	0.383000	0.25322	GAG	.	.	none		0.527	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57077464	57077464	+	Silent	SNP	T	T	C	rs10896602	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57077464T>C	ENST00000532437.1	-	5	3032	c.2721A>G	c.(2719-2721)caA>caG	p.Q907Q	TNKS1BP1_ENST00000358252.3_Silent_p.Q907Q|TNKS1BP1_ENST00000530920.1_5'UTR			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	907	Acidic.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TCCCCAAATCTTGGCCCTGCT	0.537													T|||	1661	0.331669	0.4531	0.2522	5008	,	,		19426	0.2827		0.33	False		,,,				2504	0.2761				p.Q907Q		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.A2721G						PASS	.	T		1893,2509	544.2+/-376.5	393,1107,701	190.0	185.0	186.0		2721	-1.2	0.0	11	dbSNP_120	186	2785,5807	442.5+/-360.1	456,1873,1967	no	coding-synonymous	TNKS1BP1	NM_033396.2		849,2980,2668	CC,CT,TT		32.4139,43.0032,36.0012		907/1730	57077464	4678,8316	2201	4296	6497	SO:0001819	synonymous_variant	85456	exon6			CAAATCTTGGCCC	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.2721A>G	11.37:g.57077464T>C		Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	193	193	1	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			T|0.650;C|0.350	0.350	strong		0.537	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
ZNF440	126070	hgsc.bcm.edu	37	19	11942771	11942771	+	Silent	SNP	G	G	A	rs436411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11942771G>A	ENST00000304060.5	+	4	944	c.780G>A	c.(778-780)gaG>gaA	p.E260E		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						AATATCAGGAGTGTGGGAAAG	0.383													a|||	1679	0.335264	0.5272	0.3285	5008	,	,		21077	0.1597		0.3638	False		,,,				2504	0.2321				p.E260E		Atlas-SNP	.											.	ZNF440	56	.	0			c.G780A						PASS	.	A		2221,2177	548.5+/-377.6	565,1091,543	73.0	75.0	75.0		780	0.0	0.0	19	dbSNP_80	75	3337,5251	629.6+/-398.3	615,2107,1572	no	coding-synonymous	ZNF440	NM_152357.2		1180,3198,2115	AA,AG,GG		38.8565,49.4998,42.7999		260/596	11942771	5558,7428	2199	4294	6493	SO:0001819	synonymous_variant	126070	exon4			TCAGGAGTGTGGG	AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"""Zinc fingers, C2H2-type"", ""-"""	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.780G>A	19.37:g.11942771G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_152357	Q8N1R9	Silent	SNP	ENST00000304060.5	37	CCDS42503.1																																																																																			G|0.655;A|0.345	0.345	strong		0.383	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702726	27702726	+	Silent	SNP	G	G	A	rs11015753	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:27702726G>A	ENST00000438700.3	-	1	571	c.454C>T	c.(454-456)Ctg>Ttg	p.L152L		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	152			L -> P (in dbSNP:rs6482626). {ECO:0000269|PubMed:15489334}.		spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						CCGGTGCCCAGCGCGGCTGTC	0.672													G|||	848	0.169329	0.0787	0.1844	5008	,	,		12710	0.0089		0.3062	False		,,,				2504	0.3057				p.L152L		Atlas-SNP	.											.	PTCHD3	140	.	0			c.C454T						PASS	.	G		412,3994	197.1+/-221.3	17,378,1808	61.0	70.0	67.0		454	3.6	0.0	10	dbSNP_120	67	2628,5972	414.5+/-351.5	435,1758,2107	no	coding-synonymous	PTCHD3	NM_001034842.3		452,2136,3915	AA,AG,GG		30.5581,9.3509,23.3738		152/768	27702726	3040,9966	2203	4300	6503	SO:0001819	synonymous_variant	374308	exon1			TGCCCAGCGCGGC	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.454C>T	10.37:g.27702726G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	94	53	0.56383	NM_001034842	I3L499|Q6ZU28	Silent	SNP	ENST00000438700.3	37	CCDS31173.1																																																																																			G|0.786;A|0.214	0.214	strong		0.672	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
FYB	2533	hgsc.bcm.edu	37	5	39141240	39141240	+	Silent	SNP	G	G	A	rs3188386	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:39141240G>A	ENST00000351578.6	-	4	1486	c.1296C>T	c.(1294-1296)agC>agT	p.S432S	FYB_ENST00000512982.1_Silent_p.S432S|FYB_ENST00000505428.1_Silent_p.S432S|FYB_ENST00000515010.1_Silent_p.S432S|FYB_ENST00000540520.1_Silent_p.S442S	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	432	Interaction with SKAP1.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			CATTGACAGGGCTTCTGAAAA	0.338													g|||	611	0.122005	0.1188	0.1369	5008	,	,		20305	0.001		0.2326	False		,,,				2504	0.1268				p.S442S		Atlas-SNP	.											.	FYB	354	.	0			c.C1326T						PASS	.		,	429,3339		29,371,1484	58.0	54.0	56.0		1296,1296	-5.2	0.0	5	dbSNP_126	56	1765,6487		179,1407,2540	no	coding-synonymous,coding-synonymous	FYB	NM_001465.4,NM_199335.3	,	208,1778,4024	AA,AG,GG		21.3888,11.3854,18.2529	,	432/830,432/784	39141240	2194,9826	1884	4126	6010	SO:0001819	synonymous_variant	2533	exon4			GACAGGGCTTCTG	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"""FYN-binding protein (FYB-120/130)"""			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1296C>T	5.37:g.39141240G>A		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	258	113	0.437984	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	37	CCDS47200.1																																																																																			G|0.843;A|0.157	0.157	strong		0.338	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465	
HR	55806	hgsc.bcm.edu	37	8	21978734	21978734	+	Silent	SNP	G	G	A	rs77689228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21978734G>A	ENST00000381418.4	-	10	3691	c.2211C>T	c.(2209-2211)ccC>ccT	p.P737P	HR_ENST00000312841.8_Silent_p.P737P	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	737					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CAGCGGAATCGGGGGTCTCTG	0.632													G|||	33	0.00658946	0.0083	0.0101	5008	,	,		16735	0.0		0.0129	False		,,,				2504	0.002				p.P737P		Atlas-SNP	.											.	HR	71	.	0			c.C2211T						PASS	.	G	,	42,4364	44.6+/-78.6	0,42,2161	59.0	72.0	67.0		2211,2211	-5.9	0.9	8	dbSNP_132	67	120,8480	61.3+/-123.2	0,120,4180	no	coding-synonymous,coding-synonymous	HR	NM_005144.4,NM_018411.4	,	0,162,6341	AA,AG,GG		1.3953,0.9532,1.2456	,	737/1190,737/1135	21978734	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	55806	exon10			GGAATCGGGGGTC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.2211C>T	8.37:g.21978734G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	131	70	0.534351	NM_018411	Q6GS30|Q96H33|Q9NPE1	Silent	SNP	ENST00000381418.4	37	CCDS6022.1																																																																																			G|0.988;A|0.012	0.012	strong		0.632	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
SCN10A	6336	hgsc.bcm.edu	37	3	38768334	38768334	+	Silent	SNP	T	T	C	rs7374804	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:38768334T>C	ENST00000449082.2	-	16	2849	c.2850A>G	c.(2848-2850)aaA>aaG	p.K950K		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	950					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.K950K(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	AGAGTGGGAGTTTCACCACCA	0.607													T|||	681	0.135982	0.1051	0.1037	5008	,	,		20020	0.2599		0.0636	False		,,,				2504	0.1472				p.K950K		Atlas-SNP	.											SCN10A,NS,carcinoma,0,1	SCN10A	359	1	1	Substitution - coding silent(1)	stomach(1)	c.A2850G						PASS	.	T		362,4044	186.0+/-213.0	17,328,1858	68.0	70.0	69.0		2850	-5.9	0.3	3	dbSNP_116	69	557,8043	151.9+/-206.6	17,523,3760	no	coding-synonymous	SCN10A	NM_006514.2		34,851,5618	CC,CT,TT		6.4767,8.2161,7.066		950/1957	38768334	919,12087	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon16			TGGGAGTTTCACC	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.2850A>G	3.37:g.38768334T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	186	85	0.456989	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			T|0.913;C|0.087	0.087	strong		0.607	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
GRIK4	2900	hgsc.bcm.edu	37	11	120827609	120827609	+	Silent	SNP	A	A	G	rs644057	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:120827609A>G	ENST00000527524.2	+	16	2108	c.1821A>G	c.(1819-1821)caA>caG	p.Q607Q	GRIK4_ENST00000438375.2_Silent_p.Q607Q	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	607					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		TCATGCAGCAAGGCTCCACCA	0.657													G|||	3579	0.714657	0.416	0.7709	5008	,	,		15852	0.9911		0.6779	False		,,,				2504	0.8313				p.Q607Q		Atlas-SNP	.											.	GRIK4	149	.	0			c.A1821G						PASS	.	G		1921,2485	622.9+/-394.0	418,1085,700	64.0	50.0	55.0		1821	0.2	1.0	11	dbSNP_83	55	5957,2641	419.9+/-353.2	2078,1801,420	no	coding-synonymous	GRIK4	NM_014619.2		2496,2886,1120	GG,GA,AA		30.7164,43.5996,39.4186		607/957	120827609	7878,5126	2203	4299	6502	SO:0001819	synonymous_variant	2900	exon14			GCAGCAAGGCTCC	S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1821A>G	11.37:g.120827609A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_014619	A8K9L1	Silent	SNP	ENST00000527524.2	37	CCDS8433.1																																																																																			A|0.360;G|0.640	0.640	strong		0.657	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619	
SYK	6850	hgsc.bcm.edu	37	9	93640009	93640009	+	Silent	SNP	G	G	A	rs2290887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:93640009G>A	ENST00000375754.4	+	10	1486	c.1338G>A	c.(1336-1338)ctG>ctA	p.L446L	SYK_ENST00000375747.1_Silent_p.L423L|SYK_ENST00000375751.4_Silent_p.L423L|SYK_ENST00000375746.1_Silent_p.L446L	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	446	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						CCTGGATGCTGGTTATGGAGA	0.502			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								G|||	982	0.196086	0.2095	0.366	5008	,	,		20829	0.2321		0.1362	False		,,,				2504	0.0818				p.L446L		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.G1338A						PASS	.	G	,,,	928,3478	355.1+/-312.9	91,746,1366	138.0	116.0	123.0		1269,1338,1269,1338	3.7	1.0	9	dbSNP_100	123	1215,7385	245.3+/-274.2	88,1039,3173	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	179,1785,4539	AA,AG,GG		14.1279,21.0622,16.477	,,,	423/613,446/636,423/613,446/636	93640009	2143,10863	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon10			GATGCTGGTTATG	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1338G>A	9.37:g.93640009G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	193	95	0.492228	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			G|0.824;A|0.176	0.176	strong		0.502	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
RB1CC1	9821	hgsc.bcm.edu	37	8	53537316	53537316	+	Silent	SNP	A	A	G	rs1129660	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:53537316A>G	ENST00000025008.5	-	23	5191	c.4668T>C	c.(4666-4668)ctT>ctC	p.L1556L	RB1CC1_ENST00000435644.2_Silent_p.L1553L|RB1CC1_ENST00000539297.1_Silent_p.L1553L|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1556					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TTACTTTTCCAAGTACCCAGG	0.328													A|||	1429	0.285343	0.0794	0.3184	5008	,	,		17950	0.6558		0.2058	False		,,,				2504	0.2403				p.L1556L	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.T4668C						PASS	.	A	,	389,4017	194.7+/-219.5	12,365,1826	151.0	140.0	144.0		4659,4668	4.2	1.0	8	dbSNP_86	144	1428,7170	274.1+/-291.0	121,1186,2992	no	coding-synonymous,coding-synonymous	RB1CC1	NM_001083617.1,NM_014781.4	,	133,1551,4818	GG,GA,AA		16.6085,8.8289,13.9726	,	1553/1592,1556/1595	53537316	1817,11187	2203	4299	6502	SO:0001819	synonymous_variant	9821	exon23			TTTTCCAAGTACC	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.4668T>C	8.37:g.53537316A>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	203	96	0.472906	NM_014781	Q86YR4|Q8WVU9|Q92601	Silent	SNP	ENST00000025008.5	37	CCDS34892.1	705	0.3228021978021978	52	0.10569105691056911	103	0.2845303867403315	393	0.6870629370629371	157	0.20712401055408972	A	9.506	1.104580	0.20632	0.088289	0.166085	ENSG00000023287	ENST00000519912	.	.	.	5.37	4.21	0.49690	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48364	-0.9042	5	0.87932	D	0	-12.8495	1.7764	0.03023	0.4551:0.2563:0.08:0.2086	rs1129660;rs3187821;rs17845549;rs17858446	.	.	.	S	96	.	ENSP00000430809:L96S	L	-	2	0	RB1CC1	53699869	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.334000	0.33827	2.154000	0.67381	0.533000	0.62120	TTG	A|0.804;G|0.196	0.196	strong		0.328	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	
IGFN1	91156	hgsc.bcm.edu	37	1	201184275	201184275	+	Silent	SNP	C	C	T	rs2275673	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:201184275C>T	ENST00000335211.4	+	14	9118	c.8988C>T	c.(8986-8988)acC>acT	p.T2996T	IGFN1_ENST00000295591.8_Silent_p.T156T|IGFN1_ENST00000451870.2_Silent_p.T539T	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	539						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CCACCCTGACCGTCCAGGGTA	0.582													T|||	1652	0.329872	0.2383	0.3314	5008	,	,		19691	0.3452		0.3509	False		,,,				2504	0.4151				p.T2996T		Atlas-SNP	.											.	IGFN1	220	.	0			c.C8988T						PASS	.	T		1176,3230	710.0+/-407.8	148,880,1175	56.0	45.0	49.0		8988	-6.3	0.0	1	dbSNP_100	49	2885,5715	670.8+/-402.8	495,1895,1910	no	coding-synonymous	IGFN1	NM_001164586.1		643,2775,3085	TT,TC,CC		33.5465,26.6909,31.2241		2996/3709	201184275	4061,8945	2203	4300	6503	SO:0001819	synonymous_variant	91156	exon14			CCTGACCGTCCAG	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.8988C>T	1.37:g.201184275C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	243	125	0.514403	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	728	0.3333333333333333	129	0.2621951219512195	116	0.32044198895027626	216	0.3776223776223776	267	0.35224274406332456	T	6.988	0.552422	0.13374	0.266909	0.335465	ENSG00000163395	ENST00000412892	.	.	.	4.65	-6.29	0.02013	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.12502	-1.0545	3	.	.	.	.	10.8458	0.46743	0.0948:0.2532:0.0:0.652	rs2275673;rs59363565;rs2275673	.	.	.	C	414	.	.	R	+	1	0	IGFN1	199450898	0.000000	0.05858	0.001000	0.08648	0.201000	0.24016	-1.251000	0.02882	-2.397000	0.00581	-3.288000	0.00047	CGT	C|0.683;T|0.317	0.317	strong		0.582	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
CCDC50	152137	hgsc.bcm.edu	37	3	191093175	191093175	+	Intron	SNP	T	T	A	rs2028574	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:191093175T>A	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Missense_Mutation_p.I258N	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		GAGACTAAGATTAACCATCAG	0.488													A|||	2512	0.501597	0.7231	0.4683	5008	,	,		23143	0.4702		0.4105	False		,,,				2504	0.3517				p.I258N		Atlas-SNP	.											.	CCDC50	39	.	0			c.T773A						PASS	.	A	,ASN/ILE	2955,1451	470.4+/-355.7	985,985,233	92.0	85.0	87.0		,773	-3.5	0.0	3	dbSNP_94	87	3404,5196	640.0+/-399.5	674,2056,1570	yes	intron,missense	CCDC50	NM_174908.3,NM_178335.2	,149	1659,3041,1803	AA,AT,TT		39.5814,32.9324,48.8928	,benign	,258/483	191093175	6359,6647	2203	4300	6503	SO:0001627	intron_variant	152137	exon6			CTAAGATTAACCA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-4773T>A	3.37:g.191093175T>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_178335	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	37	CCDS33913.1	1090	0.4990842490842491	356	0.7235772357723578	165	0.4558011049723757	254	0.44405594405594406	315	0.4155672823218997	A	0.005	-2.181485	0.00308	0.670676	0.395814	ENSG00000152492	ENST00000392456	T	0.27557	1.66	5.48	-3.51	0.04696	.	1.680560	0.03069	N	0.156876	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	8	0.08599	T	0.76	.	0.2695	0.00229	0.3492:0.2346:0.1778:0.2384	rs2028574;rs52816502;rs2028574	258	Q8IVM0-2	.	N	258	ENSP00000376250:I258N	ENSP00000376250:I258N	I	+	2	0	CCDC50	192575869	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.452000	0.06787	-0.512000	0.06505	-0.839000	0.03059	ATT	A|0.494;N|0.000	0.494	strong		0.488	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
LTBP1	4052	hgsc.bcm.edu	37	2	33412077	33412077	+	Silent	SNP	G	G	A	rs1065324	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:33412077G>A	ENST00000404816.2	+	6	1709	c.1356G>A	c.(1354-1356)gcG>gcA	p.A452A	LTBP1_ENST00000402934.1_Silent_p.A126A|LTBP1_ENST00000418533.2_Silent_p.A126A|LTBP1_ENST00000354476.3_Silent_p.A452A|LTBP1_ENST00000407925.1_Silent_p.A126A|LTBP1_ENST00000404525.1_Silent_p.A126A|LTBP1_ENST00000390003.4_Silent_p.A126A			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	452					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CAGGCAAGGCGTTGGGGACGC	0.507													g|||	1842	0.367812	0.2693	0.4496	5008	,	,		20578	0.371		0.4841	False		,,,				2504	0.32				p.A452A		Atlas-SNP	.											.	LTBP1	317	.	0			c.G1356A						PASS	.	A	,,,,	1459,2947	470.5+/-355.8	221,1017,965	113.0	97.0	102.0		378,378,378,378,1356	-10.8	0.0	2	dbSNP_86	102	4299,4301	577.3+/-390.5	1069,2161,1070	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	,,,,	1290,3178,2035	AA,AG,GG		49.9884,33.1139,44.2719	,,,,	126/1396,126/1354,126/1343,126/1301,452/1722	33412077	5758,7248	2203	4300	6503	SO:0001819	synonymous_variant	4052	exon6			CAAGGCGTTGGGG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.1356G>A	2.37:g.33412077G>A		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	161	159	0.987578	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																			G|0.567;A|0.433	0.433	strong		0.507	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183035	11183035	+	Nonsense_Mutation	SNP	C	C	T	rs78820764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11183035C>T	ENST00000390675.2	-	1	971	c.900G>A	c.(898-900)tgG>tgA	p.W300*	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	300					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						CTCCTTTCACCCAGTACCTCA	0.408																																					p.W300X		Atlas-SNP	.											.	TAS2R31	24	.	0			c.G900A						PASS	.																																			SO:0001587	stop_gained	259290	exon1			TTTCACCCAGTAC	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.900G>A	12.37:g.11183035C>T	ENSP00000375093:p.Trp300*	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	263	16	0.0608365	NM_176885	P59547|Q17R84|Q645X5	Nonsense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	.	.	.	.	.	.	.	.	.	.	.	10.72	1.429329	0.25726	.	.	ENSG00000256436	ENST00000390675	.	.	.	2.5	-1.35	0.09114	.	.	.	.	.	.	.	.	.	.	.	0.20196	N	0.99993	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4522	0.16570	0.2085:0.3805:0.4109:0.0	rs3759247	.	.	.	X	300	.	ENSP00000375093:W300X	W	-	3	0	TAS2R31	11074302	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	-2.133000	0.01308	-0.040000	0.13580	-1.271000	0.01417	TGG	C|0.989;T|0.011	0.011	strong		0.408	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
TLR2	7097	hgsc.bcm.edu	37	4	154625042	154625042	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:154625042T>G	ENST00000260010.6	+	1	2391	c.983T>G	c.(982-984)cTg>cGg	p.L328R		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	328					apoptotic process (GO:0006915)|cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to peptidoglycan (GO:0071224)|cellular response to triacyl bacterial lipopeptide (GO:0071727)|central nervous system myelin formation (GO:0032289)|chloramphenicol transport (GO:0042892)|defense response to Gram-positive bacterium (GO:0050830)|detection of diacyl bacterial lipopeptide (GO:0042496)|detection of triacyl bacterial lipopeptide (GO:0042495)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|induction by symbiont of defense-related host nitric oxide production (GO:0052063)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukotriene metabolic process (GO:0006691)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-17 production (GO:0032700)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of Wnt signaling pathway (GO:0030177)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to molecule of fungal origin (GO:0002238)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell body (GO:0044297)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopolysaccharide receptor activity (GO:0001875)|lipoteichoic acid binding (GO:0070891)|peptidoglycan binding (GO:0042834)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)|triacyl lipopeptide binding (GO:0042497)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	29	all_hematologic(180;0.093)	Renal(120;0.117)			OspA lipoprotein(DB00045)	TTTTATGATCTGAGCACTTTA	0.323																																					p.L328R		Atlas-SNP	.											.	TLR2	84	.	0			c.T983G						PASS	.						58.0	63.0	61.0					4																	154625042		2203	4299	6502	SO:0001583	missense	7097	exon3			ATGATCTGAGCAC	U88878	CCDS3784.1	4q32	2008-02-05				ENSG00000137462		"""CD molecules"""	11848	protein-coding gene	gene with protein product		603028				9435236	Standard	XM_005263193		Approved	TIL4, CD282	uc003inq.3	O60603		ENST00000260010.6:c.983T>G	4.37:g.154625042T>G	ENSP00000260010:p.Leu328Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_003264	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	37	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.708432	0.68615	.	.	ENSG00000137462	ENST00000260010	T	0.60424	0.19	6.06	4.88	0.63580	.	0.583671	0.16992	N	0.191252	T	0.72382	0.3453	M	0.77103	2.36	0.09310	N	0.999999	P	0.48407	0.91	P	0.57244	0.816	T	0.65726	-0.6098	10	0.87932	D	0	.	12.394	0.55374	0.0:0.0653:0.0:0.9347	.	328	O60603	TLR2_HUMAN	R	328	ENSP00000260010:L328R	ENSP00000260010:L328R	L	+	2	0	TLR2	154844492	0.709000	0.27886	0.013000	0.15412	0.020000	0.10135	5.184000	0.65070	1.116000	0.41820	-0.263000	0.10527	CTG	.	.	none		0.323	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1		
NEFH	4744	hgsc.bcm.edu	37	22	29885861	29885861	+	Silent	SNP	T	T	C	rs59890097|rs532587474|rs165923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29885861T>C	ENST00000310624.6	+	4	2265	c.2232T>C	c.(2230-2232)gcT>gcC	p.A744A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	750	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAAGAAGCTAAGTCCCCAG	0.552													C|||	4098	0.818291	0.8699	0.7392	5008	,	,		19904	0.7917		0.7694	False		,,,				2504	0.8824				p.A744A		Atlas-SNP	.											.	NEFH	178	.	0			c.T2232C	GRCh37	CD991813	NEFH	D	rs165923	PASS	.	C		3677,729	300.7+/-286.5	1541,595,67	101.0	101.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2232	2.5	0.1	22	dbSNP_79	101	6732,1868	328.2+/-318.2	2636,1460,204	no	coding-synonymous	NEFH	NM_021076.3		4177,2055,271	CC,CT,TT		21.7209,16.5456,19.9677		744/1021	29885861	10409,2597	2203	4300	6503	SO:0001819	synonymous_variant	4744	exon4			AGAAGCTAAGTCC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2232T>C	22.37:g.29885861T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			T|0.192;C|0.808	0.808	strong		0.552	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
SMYD1	150572	hgsc.bcm.edu	37	2	88396120	88396120	+	Silent	SNP	G	G	A	rs2919882	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:88396120G>A	ENST00000419482.2	+	6	790	c.705G>A	c.(703-705)gaG>gaA	p.E235E	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.E222E	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	235	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						TCAGAATTGAGCTCCGGGCCC	0.507													G|||	1572	0.313898	0.4244	0.2579	5008	,	,		20526	0.1627		0.3559	False		,,,				2504	0.317				p.E235E		Atlas-SNP	.											.	SMYD1	95	.	0			c.G705A						PASS	.	G		1785,2621	525.7+/-371.7	357,1071,775	97.0	96.0	96.0		705	1.7	1.0	2	dbSNP_101	96	3132,5468	473.3+/-368.6	569,1994,1737	no	coding-synonymous	SMYD1	NM_198274.3		926,3065,2512	AA,AG,GG		36.4186,40.5129,37.8056		235/491	88396120	4917,8089	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon6			AATTGAGCTCCGG	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.705G>A	2.37:g.88396120G>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	157	76	0.484076	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			G|0.647;A|0.353	0.353	strong		0.507	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
TRIM34	53840	hgsc.bcm.edu	37	11	5664831	5664831	+	Silent	SNP	C	C	A	rs3740998	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5664831C>A	ENST00000514226.1	+	8	1696	c.1359C>A	c.(1357-1359)ggC>ggA	p.G453G	TRIM6-TRIM34_ENST00000457787.2_Silent_p.G453G|TRIM34_ENST00000495668.1_3'UTR|TRIM6-TRIM34_ENST00000354852.5_Silent_p.G807G|TRIM34_ENST00000429814.2_Silent_p.G453G|HBG2_ENST00000380259.2_Intron	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	453	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	17		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;5.72e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAAGCCATGGCTCCCTCATTT	0.463													C|||	1892	0.377796	0.2103	0.438	5008	,	,		20145	0.6458		0.2306	False		,,,				2504	0.4366				p.G807G		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.C2421A						PASS	.	C	,,	1044,3358	383.2+/-324.8	133,778,1290	150.0	145.0	147.0		2421,1359,1359	-1.6	0.5	11	dbSNP_107	147	2042,6552	354.9+/-329.7	252,1538,2507	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM34,TRIM6-TRIM34	NM_001003819.3,NM_001003827.1,NM_021616.5	,,	385,2316,3797	AA,AC,CC		23.7608,23.7165,23.7458	,,	807/843,453/489,453/489	5664831	3086,9910	2201	4297	6498	SO:0001819	synonymous_variant	445372	exon14			CCATGGCTCCCTC	AB039902	CCDS31391.1	11p15	2013-01-09	2011-01-25	2001-11-23		ENSG00000258659		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10063	protein-coding gene	gene with protein product		605684	"""tripartite motif-containing 34"""	RNF21			Standard	NM_130390		Approved			Q9BYJ4	OTTHUMG00000066892	ENST00000514226.1:c.1359C>A	11.37:g.5664831C>A		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	249	125	0.502008	NM_001003819	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Silent	SNP	ENST00000514226.1	37	CCDS31391.1																																																																																			C|0.716;A|0.284	0.284	strong		0.463	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2	NM_001003827	
DNAH14	127602	hgsc.bcm.edu	37	1	225528183	225528183	+	Missense_Mutation	SNP	C	C	A	rs377250670|rs3856145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225528183C>A	ENST00000445597.2	+	47	7770	c.7770C>A	c.(7768-7770)gaC>gaA	p.D2590E	DNAH14_ENST00000439375.2_Missense_Mutation_p.D3393E|DNAH14_ENST00000430092.1_Missense_Mutation_p.D3393E			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2590					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CAGAAATAGACAACCCCCATT	0.318													C|||	2653	0.529752	0.643	0.4697	5008	,	,		17622	0.5089		0.4046	False		,,,				2504	0.5695				p.D3393E		Atlas-SNP	.											.	DNAH14	300	.	0			c.C10179A						PASS	.	C	GLU/ASP	846,538		270,306,116	113.0	99.0	103.0		10179	0.7	1.0	1	dbSNP_108	103	1403,1779		323,757,511	yes	missense	DNAH14	NM_001373.1	45	593,1063,627	AA,AC,CC		44.0918,38.8728,49.2554	possibly-damaging	3393/4516	225528183	2249,2317	692	1591	2283	SO:0001583	missense	127602	exon67			AATAGACAACCCC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.7770C>A	1.37:g.225528183C>A	ENSP00000409472:p.Asp2590Glu	Somatic	380	0	0		WXS	Illumina HiSeq	Phase_I	324	155	0.478395	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1057	0.483974358974359	305	0.6199186991869918	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	C	13.41	2.229518	0.39399	0.611272	0.440918	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.21191	2.02;2.02;2.02	5.22	0.724	0.18236	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999854566	B	0.31817	0.341	B	0.32762	0.152	T	0.33214	-0.9877	7	0.32370	T	0.25	.	1.4675	0.02408	0.2894:0.3987:0.141:0.1709	rs3856145;rs52794541;rs58846503;rs3856145	3393	Q0VDD8-4	.	E	2590;3393;3393	ENSP00000409472:D2590E;ENSP00000414402:D3393E;ENSP00000392061:D3393E	ENSP00000414402:D3393E	D	+	3	2	DNAH14	223594806	1.000000	0.71417	0.981000	0.43875	0.977000	0.68977	0.462000	0.21956	-0.062000	0.13088	0.508000	0.49915	GAC	C|0.498;A|0.500	0.500	strong		0.318	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
CCT6B	10693	hgsc.bcm.edu	37	17	33288363	33288363	+	Missense_Mutation	SNP	C	C	T	rs9635769	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:33288363C>T	ENST00000314144.5	-	1	165	c.50G>A	c.(49-51)cGg>cAg	p.R17Q	CCT6B_ENST00000421975.3_Missense_Mutation_p.R17Q|ZNF830_ENST00000361952.3_5'Flank|CCT6B_ENST00000436961.3_Missense_Mutation_p.R17Q	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	17			R -> Q (in dbSNP:rs9635769). {ECO:0000269|PubMed:15489334}.		chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				CAAAGCTGCCCGGGCCCGCGC	0.557													T|||	2748	0.548722	0.292	0.4813	5008	,	,		18148	0.8353		0.5696	False		,,,				2504	0.6268				p.R17Q		Atlas-SNP	.											CCT6B,caecum,carcinoma,0,3	CCT6B	63	3	0			c.G50A						PASS	.	T	GLN/ARG,GLN/ARG,GLN/ARG	1401,3005	653.7+/-399.6	225,951,1027	37.0	41.0	40.0		50,50,50	0.6	1.0	17	dbSNP_119	40	4973,3627	498.6+/-374.8	1434,2105,761	yes	missense,missense,missense	CCT6B	NM_001193529.1,NM_001193530.1,NM_006584.3	43,43,43	1659,3056,1788	TT,TC,CC		42.1744,31.7975,49.0082	benign,benign,benign	17/494,17/486,17/531	33288363	6374,6632	2203	4300	6503	SO:0001583	missense	10693	exon1			GCTGCCCGGGCCC	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"""Heat Shock Proteins / Chaperonins"""	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.50G>A	17.37:g.33288363C>T	ENSP00000327191:p.Arg17Gln	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_006584	B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	37	CCDS32617.1	1234	0.565018315018315	155	0.3150406504065041	178	0.49171270718232046	467	0.8164335664335665	434	0.5725593667546174	T	3.321	-0.138708	0.06669	0.317975	0.578256	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.11277	2.79;2.79;2.79	5.23	0.553	0.17235	.	0.173536	0.53938	N	0.000060	T	0.00012	0.0000	N	0.05383	-0.06	0.48975	P	2.6199999999998447E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.07177	-1.0786	9	0.22706	T	0.39	0.002	9.5733	0.39442	0.0:0.3838:0.0:0.6162	rs9635769;rs11552271;rs17856746;rs17856769;rs60052983;rs9635769	17;17;17	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	Q	17	ENSP00000398044:R17Q;ENSP00000327191:R17Q;ENSP00000400917:R17Q	ENSP00000327191:R17Q	R	-	2	0	CCT6B	30312476	1.000000	0.71417	0.994000	0.49952	0.350000	0.29205	1.629000	0.37071	-0.266000	0.09339	-0.254000	0.11334	CGG	C|0.481;T|0.519	0.519	strong		0.557	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584	
LAMP5	24141	hgsc.bcm.edu	37	20	9496716	9496716	+	Missense_Mutation	SNP	C	C	G	rs2232264	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:9496716C>G	ENST00000246070.2	+	3	799	c.307C>G	c.(307-309)Cag>Gag	p.Q103E	LAMP5_ENST00000427562.2_Intron|RP5-1119D9.4_ENST00000443469.1_RNA	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5	103			Q -> E (in dbSNP:rs2232264).			cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)											TGGCCACAGCCAGTCGGAGCT	0.622													G|||	1234	0.246406	0.562	0.2003	5008	,	,		15813	0.131		0.1382	False		,,,				2504	0.0828				p.Q103E		Atlas-SNP	.											C20orf103,colon,carcinoma,0,1	.	.	1	0			c.C307G						PASS	.	G	,GLU/GLN	2290,2116	566.0+/-381.8	590,1110,503	35.0	35.0	35.0		,307	6.0	1.0	20	dbSNP_98	35	1424,7176	742.0+/-407.2	111,1202,2987	yes	intron,missense	C20orf103	NM_001199897.1,NM_012261.3	,29	701,2312,3490	GG,GC,CC		16.5581,48.0254,28.5561	,benign	,103/281	9496716	3714,9292	2203	4300	6503	SO:0001583	missense	24141	exon3			CACAGCCAGTCGG	AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"""brain and dendritic cell associated LAMP"""	614641	"""chromosome 20 open reading frame 103"""	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.307C>G	20.37:g.9496716C>G	ENSP00000246070:p.Gln103Glu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	153	81	0.529412	NM_012261	B4DHZ7|B7Z9Z9	Missense_Mutation	SNP	ENST00000246070.2	37	CCDS13106.1	513	0.2348901098901099	249	0.5060975609756098	74	0.20441988950276244	86	0.15034965034965034	104	0.13720316622691292	G	5.673	0.308768	0.10733	0.519746	0.165581	ENSG00000125869	ENST00000246070	T	0.30981	1.51	6.01	6.01	0.97437	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.01352	-0.895	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44314	-0.9336	8	.	.	.	-20.3116	17.5415	0.87849	0.0:0.1238:0.8762:0.0	rs2232264;rs52813663;rs56575354;rs2232264	103	Q9UJQ1	CT103_HUMAN	E	103	ENSP00000246070:Q103E	.	Q	+	1	0	C20orf103	9444716	1.000000	0.71417	0.999000	0.59377	0.934000	0.57294	6.363000	0.73082	1.573000	0.49748	-0.120000	0.15030	CAG	C|0.731;G|0.269	0.269	strong		0.622	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261	
GPRASP2	114928	hgsc.bcm.edu	37	X	101970123	101970123	+	Missense_Mutation	SNP	G	G	A	rs139789934	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:101970123G>A	ENST00000535209.1	+	4	1157	c.326G>A	c.(325-327)cGt>cAt	p.R109H	GPRASP2_ENST00000543253.1_Missense_Mutation_p.R109H|GPRASP2_ENST00000332262.5_Missense_Mutation_p.R109H			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	109						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						GGTGGCGCTCGTTCTAAAACT	0.572													.|||	2	0.000529801	0.0	0.0	3775	,	,		14704	0.0		0.002	False		,,,				2504	0.0				p.R109H		Atlas-SNP	.											.	GPRASP2	89	.	0			c.G326A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,3835		0,0,1632,571	84.0	85.0	84.0		326,326,326,326,326,326	3.9	0.9	X	dbSNP_134	84	12,6716		0,12,2416,1872	yes	missense,missense,missense,missense,missense,missense	GPRASP2,ARMCX5-GPRASP2	NM_001004051.3,NM_001184874.2,NM_001184875.2,NM_001184876.2,NM_001199818.1,NM_138437.5	29,29,29,29,29,29	0,12,4048,2443	AA,AG,GG,G		0.1784,0.0,0.1136	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	109/839,109/839,109/839,109/839,109/839,109/839	101970123	12,10551	2203	4300	6503	SO:0001583	missense	114928	exon4			GCGCTCGTTCTAA	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"""Armadillo repeat containing"""	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.326G>A	X.37:g.101970123G>A	ENSP00000437394:p.Arg109His	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	80	73	0.9125	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	37	CCDS14501.1	2	0.0012055455093429777	0	0.0	0	0.0	0	0.0	1	0.0013227513227513227	G	11.74	1.729796	0.30684	0.0	0.001784	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.08008	3.14;3.14;3.14	4.76	3.89	0.44902	.	0.000000	0.44483	D	0.000442	T	0.05502	0.0145	N	0.14661	0.345	0.18873	N	0.999989	P	0.51240	0.943	B	0.43990	0.438	T	0.28681	-1.0036	10	0.45353	T	0.12	.	6.4019	0.21642	0.1059:0.1825:0.7116:0.0	.	109	Q96D09	GASP2_HUMAN	H	109	ENSP00000437872:R109H;ENSP00000437394:R109H;ENSP00000339057:R109H	ENSP00000339057:R109H	R	+	2	0	GPRASP2	101856779	0.993000	0.37304	0.927000	0.36925	0.006000	0.05464	3.248000	0.51430	1.078000	0.41014	0.600000	0.82982	CGT	G|0.999;A|0.001	0.001	strong		0.572	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
STX16	8675	hgsc.bcm.edu	37	20	57242602	57242602	+	Silent	SNP	G	G	A	rs376636519		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:57242602G>A	ENST00000371141.4	+	3	925	c.201G>A	c.(199-201)gcG>gcA	p.A67A	STX16-NPEPL1_ENST00000530122.1_Silent_p.A67A|STX16_ENST00000371132.4_Silent_p.A46A|STX16_ENST00000361830.3_Silent_p.A67A|STX16_ENST00000359617.4_Silent_p.A14A|STX16_ENST00000361770.5_Silent_p.A50A|STX16_ENST00000355957.5_Silent_p.A50A|STX16_ENST00000496003.1_3'UTR|STX16_ENST00000358029.4_Silent_p.A63A	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	67					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			CAGAAGCAGCGATTGGTGTGA	0.413																																					p.A67A		Atlas-SNP	.											.	STX16	36	.	0			c.G201A						PASS	.	G	,,,,	0,4406		0,0,2203	146.0	135.0	139.0		201,189,150,42,138	-4.6	0.6	20		139	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STX16	NM_001001433.2,NM_001134772.2,NM_001134773.2,NM_001204868.1,NM_003763.5	,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	67/326,63/322,50/309,14/273,46/305	57242602	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8675	exon3			AGCAGCGATTGGT	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.201G>A	20.37:g.57242602G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Silent	SNP	ENST00000371141.4	37	CCDS13468.1																																																																																			.	.	weak		0.413	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433	
NOTCH1	4851	hgsc.bcm.edu	37	9	139418260	139418260	+	Silent	SNP	A	A	G	rs4489420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139418260A>G	ENST00000277541.6	-	3	387	c.312T>C	c.(310-312)aaT>aaC	p.N104N	NOTCH1_ENST00000491649.1_5'UTR	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	104	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGAGGCAGGCATTGTCCAGGG	0.687			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3706	0.740016	0.9523	0.6037	5008	,	,		12414	0.8363		0.505	False		,,,				2504	0.6922				p.N104N		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	0			c.T312C						PASS	.	G		3779,511		1671,437,37	20.0	32.0	28.0		312	-4.3	0.0	9	dbSNP_111	28	4001,4491		956,2089,1201	yes	coding-synonymous	NOTCH1	NM_017617.3		2627,2526,1238	GG,GA,AA		47.1149,11.9114,39.1332		104/2556	139418260	7780,5002	2145	4246	6391	SO:0001819	synonymous_variant	4851	exon3			GCAGGCATTGTCC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.312T>C	9.37:g.139418260A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	137	50	0.364964	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			A|0.323;G|0.677	0.677	strong		0.687	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
OR11H6	122748	hgsc.bcm.edu	37	14	20691888	20691888	+	Missense_Mutation	SNP	C	C	A	rs10140652	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20691888C>A	ENST00000315519.2	+	1	98	c.20C>A	c.(19-21)tCt>tAt	p.S7Y		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	7			S -> Y (in dbSNP:rs10140652).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		attattCATTCTTTGGTTACT	0.373													c|||	498	0.0994409	0.121	0.049	5008	,	,		21282	0.0903		0.0815	False		,,,				2504	0.1339				p.S7Y		Atlas-SNP	.											.	OR11H6	60	.	0			c.C20A						PASS	.	C	TYR/SER	427,3979	198.7+/-222.5	18,391,1794	70.0	75.0	73.0		20	-4.8	0.0	14	dbSNP_119	73	620,7980	153.0+/-207.5	34,552,3714	yes	missense	OR11H6	NM_001004480.1	144	52,943,5508	AA,AC,CC		7.2093,9.6913,8.0501	benign	7/331	20691888	1047,11959	2203	4300	6503	SO:0001583	missense	122748	exon1			TTCATTCTTTGGT		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"""GPCR / Class A : Olfactory receptors"""	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.20C>A	14.37:g.20691888C>A	ENSP00000319071:p.Ser7Tyr	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	170	81	0.476471	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	204	0.09340659340659341	72	0.14634146341463414	17	0.04696132596685083	53	0.09265734265734266	62	0.08179419525065963	c	8.427	0.847651	0.17034	0.096913	0.072093	ENSG00000176219	ENST00000315519	T	0.00554	6.64	4.53	-4.82	0.03171	.	2.033520	0.02979	U	0.145446	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.20671	0.047	B	0.16289	0.015	T	0.39461	-0.9613	9	0.38643	T	0.18	.	7.818	0.29271	0.0:0.2525:0.129:0.6185	rs10140652;rs52838202;rs58829059;rs10140652	7	Q8NGC7	O11H6_HUMAN	Y	7	ENSP00000319071:S7Y	ENSP00000319071:S7Y	S	+	2	0	OR11H6	19761728	0.000000	0.05858	0.001000	0.08648	0.129000	0.20672	-1.346000	0.02634	-0.847000	0.04168	-0.417000	0.06048	TCT	C|0.909;A|0.091	0.091	strong		0.373	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
TCL1B	9623	hgsc.bcm.edu	37	14	96157187	96157187	+	Missense_Mutation	SNP	G	G	A	rs1064017	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:96157187G>A	ENST00000340722.7	+	2	328	c.277G>A	c.(277-279)Ggg>Agg	p.G93R	RP11-1070N10.6_ENST00000461160.1_RNA	NM_004918.3	NP_004909.1	O95988	TCL1B_HUMAN	T-cell leukemia/lymphoma 1B	93			G -> R (in dbSNP:rs1064017). {ECO:0000269|PubMed:10344735, ECO:0000269|PubMed:15489334}.							cervix(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		GCTCTACCCCGGGAGGAAGTA	0.612													G|||	1313	0.262181	0.2413	0.3372	5008	,	,		19471	0.0873		0.4105	False		,,,				2504	0.2648				p.G93R		Atlas-SNP	.											TCL1B,NS,malignant_melanoma,-2,3	TCL1B	30	3	0			c.G277A						PASS	.	G	ARG/GLY	1294,3112	438.2+/-345.2	194,906,1103	65.0	68.0	67.0		277	0.8	0.0	14	dbSNP_86	67	3832,4768	538.4+/-383.4	851,2130,1319	yes	missense	TCL1B	NM_004918.3	125	1045,3036,2422	AA,AG,GG		44.5581,29.369,39.4126	probably-damaging	93/129	96157187	5126,7880	2203	4300	6503	SO:0001583	missense	9623	exon2			TACCCCGGGAGGA	AB018563	CCDS32151.1	14q32.1	2008-09-05			ENSG00000213231	ENSG00000213231			11649	protein-coding gene	gene with protein product		603769				10077617	Standard	NM_004918		Approved	TML1	uc001yez.3	O95988	OTTHUMG00000028912	ENST00000340722.7:c.277G>A	14.37:g.96157187G>A	ENSP00000343223:p.Gly93Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_004918	A6NEK7|Q6IAR7|Q9UBQ4	Missense_Mutation	SNP	ENST00000340722.7	37	CCDS32151.1	612	0.2802197802197802	127	0.258130081300813	117	0.32320441988950277	62	0.10839160839160839	306	0.40369393139841686	G	13.88	2.369441	0.42003	0.29369	0.445581	ENSG00000213231	ENST00000340722;ENST00000538038	T	0.27402	1.67	3.29	0.758	0.18432	.	.	.	.	.	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	P	0.51537	0.946	B	0.41088	0.347	T	0.38735	-0.9647	8	0.06236	T	0.91	-2.7841	2.3513	0.04284	0.232:0.0:0.5016:0.2664	rs1064017;rs1748957;rs3205032;rs17854667;rs52791006;rs58883833;rs1064017	93	O95988	TCL1B_HUMAN	R	93	ENSP00000343223:G93R	ENSP00000343223:G93R	G	+	1	0	TCL1B	95226940	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.137000	0.15995	0.160000	0.19432	0.462000	0.41574	GGG	G|0.658;A|0.342	0.342	strong		0.612	TCL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315123.2		
WRN	7486	hgsc.bcm.edu	37	8	30999280	30999280	+	Missense_Mutation	SNP	G	G	T	rs1801195	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:30999280G>T	ENST00000298139.5	+	26	3471	c.3222G>T	c.(3220-3222)ttG>ttT	p.L1074F		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	1074			L -> F (in dbSNP:rs1801195). {ECO:0000269|PubMed:11161804, ECO:0000269|PubMed:16723399, ECO:0000269|PubMed:8602509, ECO:0000269|PubMed:9450180, ECO:0000269|Ref.3}.		aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		CAAAGAAGTTGCTTCTGCCTA	0.338			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				T|||	2484	0.496006	0.5038	0.5893	5008	,	,		18737	0.6419		0.4404	False		,,,				2504	0.3262				p.L1074F	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.G3222T	GRCh37	CM004850	WRN	M	rs1801195	PASS	.	T	PHE/LEU	2124,2282	597.4+/-388.9	502,1120,581	114.0	113.0	114.0		3222	1.4	0.0	8	dbSNP_89	114	3949,4651	601.3+/-394.3	891,2167,1242	yes	missense	WRN	NM_000553.4	22	1393,3287,1823	TT,TG,GG		45.9186,48.207,46.6938	benign	1074/1433	30999280	6073,6933	2203	4300	6503	SO:0001583	missense	7486	exon26	Familial Cancer Database	WS, Adult Progeria	GAAGTTGCTTCTG		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.3222G>T	8.37:g.30999280G>T	ENSP00000298139:p.Leu1074Phe	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	132	57	0.431818	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	1158	0.5302197802197802	252	0.5121951219512195	224	0.6187845303867403	361	0.6311188811188811	321	0.4234828496042216	T	0.008	-1.924388	0.00493	0.48207	0.459186	ENSG00000165392	ENST00000298139	T	0.31769	1.48	5.51	1.4	0.22301	.	1.213430	0.05612	N	0.578231	T	0.00012	0.0000	N	0.00521	-1.4	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43556	-0.9384	9	0.07325	T	0.83	-0.2835	1.7751	0.03020	0.196:0.1501:0.1066:0.5472	rs1801195;rs2230013;rs2725362;rs3815858;rs17381037;rs17573768;rs60206776;rs2725362	484;1074	Q59F09;Q14191	.;WRN_HUMAN	F	1074	ENSP00000298139:L1074F	ENSP00000298139:L1074F	L	+	3	2	WRN	31118822	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	0.032000	0.13732	0.093000	0.17368	-0.256000	0.11100	TTG	G|0.501;N|0.000	.	strong		0.338	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
METTL21A	151194	hgsc.bcm.edu	37	2	208478055	208478055	+	Silent	SNP	A	A	G	rs17520056	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:208478055A>G	ENST00000411432.1	-	4	588	c.372T>C	c.(370-372)acT>acC	p.T124T	METTL21A_ENST00000448007.2_Silent_p.T124T|METTL21A_ENST00000272839.3_Silent_p.T142T|METTL21A_ENST00000426075.1_Silent_p.T124T|METTL21A_ENST00000448823.2_3'UTR|METTL21A_ENST00000477919.1_5'Flank|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000406927.2_Silent_p.T124T|METTL21A_ENST00000432416.1_Intron|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000442521.1_Silent_p.T124T	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	124					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)	p.T124T(1)		endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						TTTGTCCCCAAGTCAGCTCCT	0.368													A|||	1741	0.347644	0.233	0.3617	5008	,	,		20308	0.372		0.3072	False		,,,				2504	0.5092				p.T124T		Atlas-SNP	.											METTL21A,NS,carcinoma,0,1	METTL21A	24	1	1	Substitution - coding silent(1)	stomach(1)	c.T372C						PASS	.	A	,	1099,3307	392.8+/-328.6	138,823,1242	83.0	83.0	83.0		372,372	-5.0	0.9	2	dbSNP_123	83	2724,5876	432.7+/-357.2	427,1870,2003	no	coding-synonymous,coding-synonymous	METTL21A	NM_001127395.1,NM_145280.4	,	565,2693,3245	GG,GA,AA		31.6744,24.9433,29.3941	,	124/219,124/219	208478055	3823,9183	2203	4300	6503	SO:0001819	synonymous_variant	151194	exon4			TCCCCAAGTCAGC	AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 557b"", ""heat shock protein 70kDa lysine (K) methyltransferase"""	615257	"""family with sequence similarity 119, member A"""	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.372T>C	2.37:g.208478055A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_145280	Q53RV0|Q8N1Z9|Q96GH6	Silent	SNP	ENST00000411432.1	37	CCDS2376.1																																																																																			A|0.705;G|0.295	0.295	strong		0.368	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280	
CCDC28A	25901	hgsc.bcm.edu	37	6	139094937	139094937	+	Silent	SNP	C	C	T	rs11154999	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:139094937C>T	ENST00000332797.6	+	1	281	c.126C>T	c.(124-126)tcC>tcT	p.S42S		NM_015439.2	NP_056254.1	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A	42			S -> Y (in dbSNP:rs34538642).							autonomic_ganglia(1)|large_intestine(3)|lung(8)|ovary(1)	13				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		GGAGCGGGTCCCGGGATGTGA	0.637													C|||	115	0.0229633	0.0136	0.0591	5008	,	,		16196	0.001		0.0507	False		,,,				2504	0.0041				p.S42S		Atlas-SNP	.											.	CCDC28A	34	.	0			c.C126T						PASS	.	C		64,4342	59.3+/-96.0	0,64,2139	83.0	104.0	97.0		126	-4.1	0.0	6	dbSNP_120	97	348,8252	117.9+/-177.5	4,340,3956	no	coding-synonymous	CCDC28A	NM_015439.2		4,404,6095	TT,TC,CC		4.0465,1.4526,3.1678		42/275	139094937	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	25901	exon1			CGGGTCCCGGGAT	AY167571	CCDS5192.1	6q23.1-q24.1	2008-02-05	2005-09-12	2005-09-12	ENSG00000024862	ENSG00000024862			21098	protein-coding gene	gene with protein product		615353	"""chromosome 6 open reading frame 80"""	C6orf80			Standard	NM_015439		Approved	CCRL1AP, DKFZp586D0623	uc003qie.3	Q8IWP9	OTTHUMG00000015683	ENST00000332797.6:c.126C>T	6.37:g.139094937C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_015439	E1P591|Q32NC7|Q66K67|Q96E23|Q9Y430	Silent	SNP	ENST00000332797.6	37	CCDS5192.1																																																																																			C|0.970;T|0.030	0.030	strong		0.637	CCDC28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042444.1	NM_015439	
EFNA3	1944	hgsc.bcm.edu	37	1	155058663	155058663	+	Missense_Mutation	SNP	G	G	A	rs17723260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:155058663G>A	ENST00000368408.3	+	4	638	c.568G>A	c.(568-570)Gtg>Atg	p.V190M	EFNA3_ENST00000418360.2_Intron|EFNA3_ENST00000498667.1_3'UTR|EFNA3_ENST00000556931.1_Missense_Mutation_p.V185M|EFNA3_ENST00000505139.1_Missense_Mutation_p.V185M	NM_004952.4	NP_004943.1	P52797	EFNA3_HUMAN	ephrin-A3	190			V -> M (in dbSNP:rs17723260).		axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|transmembrane-ephrin receptor activity (GO:0005005)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		all cancers(21;5.67e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000284)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGGCCCCAATGTGAAGATCAA	0.687											OREG0013850	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	381	0.0760783	0.0234	0.0994	5008	,	,		13282	0.0109		0.1342	False		,,,				2504	0.138				p.V190M		Atlas-SNP	.											EFNA3,colon,carcinoma,0,1	EFNA3	15	1	0			c.G568A						PASS	.	G	MET/VAL	172,4234	109.9+/-148.2	1,170,2032	44.0	43.0	43.0		568	4.5	1.0	1	dbSNP_123	43	1202,7396	238.8+/-270.1	82,1038,3179	yes	missense	EFNA3	NM_004952.4	21	83,1208,5211	AA,AG,GG		13.98,3.9038,10.566	possibly-damaging	190/239	155058663	1374,11630	2203	4299	6502	SO:0001583	missense	1944	exon4			CCCAATGTGAAGA	BC017722	CCDS1090.1	1q21-q22	2011-03-09			ENSG00000143590	ENSG00000143590		"""Ephrins"""	3223	protein-coding gene	gene with protein product		601381		EPLG3		8660976	Standard	NM_004952		Approved	LERK3, Ehk1-L	uc001fhf.3	P52797	OTTHUMG00000035313	ENST00000368408.3:c.568G>A	1.37:g.155058663G>A	ENSP00000357393:p.Val190Met	Somatic	327	0	0	220	WXS	Illumina HiSeq	Phase_I	292	116	0.39726	NM_004952	B7ZAD3|D3DV85|Q0VGC9|Q5SR70	Missense_Mutation	SNP	ENST00000368408.3	37	CCDS1090.1	165	0.07554945054945054	12	0.024390243902439025	45	0.12430939226519337	3	0.005244755244755245	105	0.13852242744063326	G	16.17	3.046837	0.55110	0.039038	0.1398	ENSG00000143590;ENSG00000143590;ENSG00000251246	ENST00000556931;ENST00000368408;ENST00000505139	D;D;D	0.94897	-3.55;-3.53;-3.55	4.51	4.51	0.55191	.	0.000000	0.33534	N	0.004810	D	0.89326	0.6683	N	0.14661	0.345	0.09310	P	1.0	P;P	0.51351	0.944;0.936	P;P	0.51355	0.667;0.578	D	0.90589	0.4535	9	0.45353	T	0.12	-13.0846	15.1743	0.72899	0.0:0.0:1.0:0.0	rs17723260;rs17723260	185;190	B4DXG7;P52797	.;EFNA3_HUMAN	M	185;190;185	ENSP00000450814:V185M;ENSP00000357393:V190M;ENSP00000426741:V185M	ENSP00000357393:V190M	V	+	1	0	RP11-540D14.8;EFNA3	153325287	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.093000	0.50217	2.525000	0.85131	0.456000	0.33151	GTG	G|0.911;A|0.089	0.089	strong		0.687	EFNA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085429.1	NM_004952	
TRPM6	140803	hgsc.bcm.edu	37	9	77416972	77416972	+	Silent	SNP	C	C	T	rs11144089	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:77416972C>T	ENST00000360774.1	-	16	2088	c.1851G>A	c.(1849-1851)ctG>ctA	p.L617L	RN7SKP47_ENST00000365347.1_RNA|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Silent_p.L612L|TRPM6_ENST00000451710.3_Silent_p.L617L|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000449912.2_Silent_p.L612L|TRPM6_ENST00000376864.4_Silent_p.L617L	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	617					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						GCCTTTTCATCAGCACAGCCC	0.473													C|||	447	0.0892572	0.025	0.1066	5008	,	,		18275	0.1558		0.1074	False		,,,				2504	0.0767				p.L617L		Atlas-SNP	.											.	TRPM6	377	.	0			c.G1851A						PASS	.	C	,,	170,4236	111.2+/-149.4	4,162,2037	124.0	98.0	107.0		1836,1836,1851	-4.8	1.0	9	dbSNP_120	107	798,7802	187.0+/-234.4	36,726,3538	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	40,888,5575	TT,TC,CC		9.2791,3.8584,7.4427	,,	612/2018,612/2018,617/2023	77416972	968,12038	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon16			TTTCATCAGCACA	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.1851G>A	9.37:g.77416972C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	191	80	0.418848	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																			C|0.911;T|0.089	0.089	strong		0.473	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
EHF	26298	hgsc.bcm.edu	37	11	34668143	34668143	+	Silent	SNP	C	C	T	rs2281910	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:34668143C>T	ENST00000533754.1	+	3	472	c.255C>T	c.(253-255)ctC>ctT	p.L85L	EHF_ENST00000530286.1_Silent_p.L85L|EHF_ENST00000531794.1_Silent_p.L107L|EHF_ENST00000527935.1_Silent_p.L85L|EHF_ENST00000450654.2_Silent_p.L85L|EHF_ENST00000257831.3_Silent_p.L85L|EHF_ENST00000531728.1_Silent_p.L85L					ets homologous factor										NFIA/EHF(2)	autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|lung(8)|upper_aerodigestive_tract(1)	17		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			GCGAGCACCTCTGCAGCATGA	0.582													C|||	1158	0.23123	0.1558	0.3213	5008	,	,		21223	0.38		0.1948	False		,,,				2504	0.1534				p.L107L		Atlas-SNP	.											.	EHF	38	.	0			c.C321T						PASS	.	C	,,	688,3716	289.8+/-280.6	48,592,1562	124.0	119.0	120.0		255,321,255	-3.2	1.0	11	dbSNP_100	120	1762,6834	318.4+/-313.7	178,1406,2714	no	coding-synonymous,coding-synonymous,coding-synonymous	EHF	NM_001206615.1,NM_001206616.1,NM_012153.5	,,	226,1998,4276	TT,TC,CC		20.4979,15.6222,18.8462	,,	85/278,107/323,85/301	34668143	2450,10550	2202	4298	6500	SO:0001819	synonymous_variant	26298	exon3			GCACCTCTGCAGC	AF170583	CCDS7894.1, CCDS55752.1, CCDS55753.1	11p12	2008-07-18				ENSG00000135373			3246	protein-coding gene	gene with protein product	"""epithelium-specific ets factor 3"", ""ESE3 transcription factor"""	605439				10527851	Standard	NM_012153		Approved	ESE3, ESEJ	uc021qfu.1	Q9NZC4		ENST00000533754.1:c.255C>T	11.37:g.34668143C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	132	48	0.363636	NM_001206616		Silent	SNP	ENST00000533754.1	37	CCDS7894.1																																																																																			C|0.792;T|0.208	0.208	strong		0.582	EHF-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389855.1	NM_012153	
TAS2R7	50837	hgsc.bcm.edu	37	12	10954258	10954258	+	Missense_Mutation	SNP	C	C	T	rs619381	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:10954258C>T	ENST00000240687.2	-	1	968	c.912G>A	c.(910-912)atG>atA	p.M304I		NM_023919.2	NP_076408.1	Q9NYW3	TA2R7_HUMAN	taste receptor, type 2, member 7	304			M -> I (in dbSNP:rs619381).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.M304I(1)		kidney(1)|large_intestine(1)|lung(3)|skin(2)|stomach(3)	10						TTAGAATAGACATTACTTTCC	0.313													C|||	455	0.0908546	0.0098	0.111	5008	,	,		20774	0.0893		0.0855	False		,,,				2504	0.1933				p.M304I		Atlas-SNP	.											TAS2R7,NS,carcinoma,0,1	TAS2R7	35	1	1	Substitution - Missense(1)	stomach(1)	c.G912A						PASS	.	C	ILE/MET	122,4284	89.7+/-128.4	2,118,2083	81.0	79.0	79.0		912	-0.7	0.0	12	dbSNP_83	79	1043,7557	220.1+/-257.9	65,913,3322	yes	missense	TAS2R7	NM_023919.2	10	67,1031,5405	TT,TC,CC		12.1279,2.769,8.9574	benign	304/319	10954258	1165,11841	2203	4300	6503	SO:0001583	missense	50837	exon1			AATAGACATTACT	AF227133	CCDS8631.1	12p13	2012-08-22			ENSG00000121377	ENSG00000121377		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14913	protein-coding gene	gene with protein product		604793				10761934, 10766242	Standard	NM_023919		Approved	T2R7, TRB4	uc001qyv.3	Q9NYW3	OTTHUMG00000168505	ENST00000240687.2:c.912G>A	12.37:g.10954258C>T	ENSP00000240687:p.Met304Ile	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	51	0.56044	NM_023919	Q645Y1	Missense_Mutation	SNP	ENST00000240687.2	37	CCDS8631.1	152	0.0695970695970696	3	0.006097560975609756	33	0.09116022099447514	55	0.09615384615384616	61	0.08047493403693931	C	11.32	1.603087	0.28534	0.02769	0.121279	ENSG00000121377	ENST00000240687	T	0.36340	1.26	5.72	-0.705	0.11252	.	0.410373	0.21537	N	0.072955	T	0.00210	0.0006	N	0.08118	0	0.80722	P	0.0	B	0.29886	0.26	B	0.27796	0.083	T	0.11108	-1.0601	9	0.87932	D	0	.	4.6703	0.12685	0.2335:0.4905:0.0:0.276	rs619381;rs1663405;rs52812680;rs57496493;rs619381	304	Q9NYW3	TA2R7_HUMAN	I	304	ENSP00000240687:M304I	ENSP00000240687:M304I	M	-	3	0	TAS2R7	10845525	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.526000	0.06207	-0.148000	0.11234	-0.162000	0.13425	ATG	C|0.919;T|0.081	0.081	strong		0.313	TAS2R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399931.1		
ARHGEF28	64283	hgsc.bcm.edu	37	5	73142296	73142296	+	Missense_Mutation	SNP	C	C	T	rs2973571	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:73142296C>T	ENST00000426542.2	+	11	1651	c.1631C>T	c.(1630-1632)tCg>tTg	p.S544L	ARHGEF28_ENST00000287898.5_Missense_Mutation_p.S544L|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.S231L|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.S544L|ARHGEF28_ENST00000513841.1_3'UTR|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.S544L|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.S544L|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.S544L			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	544			S -> L (in dbSNP:rs2973571).		central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										AATCTACAGTCGAAGGTATTC	0.353													C|||	862	0.172125	0.121	0.2522	5008	,	,		18407	0.0764		0.2575	False		,,,				2504	0.1953				p.S544L		Atlas-SNP	.											.	.	.	.	0			c.C1631T						PASS	.	C	LEU/SER,LEU/SER	586,3070		53,480,1295	74.0	68.0	70.0		1631,1631	-0.9	0.0	5	dbSNP_101	70	2232,5942		319,1594,2174	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	145,145	372,2074,3469	TT,TC,CC		27.3061,16.0284,23.8208	benign,benign	544/1732,544/1706	73142296	2818,9012	1828	4087	5915	SO:0001583	missense	64283	exon12			TACAGTCGAAGGT		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.1631C>T	5.37:g.73142296C>T	ENSP00000412175:p.Ser544Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	102	58	0.568627	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	385	0.1762820512820513	54	0.10975609756097561	91	0.2513812154696133	41	0.07167832167832168	199	0.262532981530343	C	11.38	1.623055	0.28889	0.160284	0.273061	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.10668	3.09;3.07;3.08;2.85;3.07;3.08;2.93	5.69	-0.952	0.10366	.	.	.	.	.	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B;B;B;B;B	0.17667	0.001;0.001;0.001;0.023;0.001	B;B;B;B;B	0.12156	0.001;0.001;0.001;0.007;0.002	T	0.49000	-0.8984	8	0.20046	T	0.44	.	10.3084	0.43693	0.0:0.5982:0.0:0.4018	rs2973571;rs17553106;rs52832546;rs2973571	231;544;544;544;544	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-2;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	L	544;544;544;544;544;544;231	ENSP00000296794:S544L;ENSP00000441913:S544L;ENSP00000441436:S544L;ENSP00000287898:S544L;ENSP00000411459:S544L;ENSP00000412175:S544L;ENSP00000296799:S231L	ENSP00000287898:S544L	S	+	2	0	RP11-428C6.1	73178052	0.000000	0.05858	0.008000	0.14137	0.895000	0.52256	0.016000	0.13377	-0.249000	0.09569	0.484000	0.47621	TCG	C|0.829;T|0.171	0.171	strong		0.353	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
HEMGN	55363	hgsc.bcm.edu	37	9	100692330	100692330	+	Silent	SNP	A	A	G	rs35223978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:100692330A>G	ENST00000259456.3	-	4	1490	c.1347T>C	c.(1345-1347)taT>taC	p.Y449Y		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	449					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				NS(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|skin(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(62;0.0559)				GAGGAAAAGTATAAGCATCTT	0.468													A|||	19	0.00379393	0.0	0.0058	5008	,	,		18466	0.0		0.0109	False		,,,				2504	0.0041				p.Y449Y		Atlas-SNP	.											.	HEMGN	55	.	0			c.T1347C						PASS	.	A	,	5,4401	8.1+/-20.4	0,5,2198	221.0	201.0	208.0		1347,1347	0.6	0.0	9	dbSNP_126	208	69,8531	42.2+/-99.7	1,67,4232	no	coding-synonymous,coding-synonymous	HEMGN	NM_018437.3,NM_197978.1	,	1,72,6430	GG,GA,AA		0.8023,0.1135,0.569	,	449/485,449/485	100692330	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	55363	exon3			AAAAGTATAAGCA	AF228713	CCDS6731.1	9q22.33	2014-01-21			ENSG00000136929	ENSG00000136929			17509	protein-coding gene	gene with protein product		610715					Standard	NM_018437		Approved	EDAG, CT155, NDR	uc004axy.4	Q9BXL5	OTTHUMG00000020336	ENST00000259456.3:c.1347T>C	9.37:g.100692330A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	205	89	0.434146	NM_197978	Q6XAR3|Q86XY5|Q9NPC0	Silent	SNP	ENST00000259456.3	37	CCDS6731.1																																																																																			A|0.995;G|0.005	0.005	strong		0.468	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036853	33036853	+	Missense_Mutation	SNP	A	A	C	rs1042308	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33036853A>C	ENST00000419277.1	-	4	700	c.571T>G	c.(571-573)Ttc>Gtc	p.F191V	HLA-DPA1_ENST00000463066.1_5'Flank|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.F191V	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	191	Alpha-2.|Ig-like C1-type.		F -> V (in allele DPA1*02:01, allele DPA1*02:02 and allele DPA1*04:01; dbSNP:rs1042308).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CAGTCATAGAAGTCCTCTGCT	0.547													A|||	2194	0.438099	0.5802	0.2839	5008	,	,		19836	0.6786		0.1889	False		,,,				2504	0.364				p.F191V		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.T571G						PASS	.	A	VAL/PHE,VAL/PHE,VAL/PHE	1427,1593		327,773,410	196.0	217.0	209.0		571,571,571	-3.7	0.0	6	dbSNP_86	209	960,4458		72,816,1821	yes	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	50,50,50	399,1589,2231	CC,CA,AA		17.7187,47.2517,28.2887	benign,benign,benign	191/261,191/261,191/261	33036853	2387,6051	1510	2709	4219	SO:0001583	missense	3113	exon3			CATAGAAGTCCTC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.571T>G	6.37:g.33036853A>C	ENSP00000393566:p.Phe191Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	864|864	0.3956043956043956|0.3956043956043956	275|275	0.5589430894308943|0.5589430894308943	89|89	0.24585635359116023|0.24585635359116023	371|371	0.6486013986013986|0.6486013986013986	129|129	0.17018469656992086|0.17018469656992086	A|A	0.003|0.003	-2.491932|-2.491932	0.00161|0.00161	0.472517|0.472517	0.177187|0.177187	ENSG00000231389|ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337|ENST00000437811	T;T;T|.	0.02579|.	4.24;4.24;4.24|.	3.4|3.4	-3.7|-3.7	0.04437|0.04437	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);|.	0.524360|.	0.17386|.	N|.	0.176127|.	T|T	0.02380|0.02380	0.0073|0.0073	N|N	0.00738|0.00738	-1.235|-1.235	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.43426|0.43426	-0.9392|-0.9392	9|4	0.02654|.	T|.	1|.	.|.	8.0008|8.0008	0.30295|0.30295	0.7188:0.1825:0.0:0.0987|0.7188:0.1825:0.0:0.0987	rs1042308;rs2308933;rs45587632;rs52831627|rs1042308;rs2308933;rs45587632;rs52831627	191|.	P20036|.	DPA1_HUMAN|.	V|R	191;191;158;191|58	ENSP00000393566:F191V;ENSP00000402872:F191V;ENSP00000390929:F191V|.	ENSP00000393566:F191V|.	F|L	-|-	1|2	0|0	HLA-DPA1|HLA-DPA1	33144831|33144831	0.003000|0.003000	0.15002|0.15002	0.003000|0.003000	0.11579|0.11579	0.001000|0.001000	0.01503|0.01503	-0.160000|-0.160000	0.10041|0.10041	-0.501000|-0.501000	0.06605|0.06605	-0.178000|-0.178000	0.13098|0.13098	TTC|CTT	T|0.000;G|0.000;C|0.321;N|0.000;A|0.679	0.321	strong		0.547	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
GOLGB1	2804	hgsc.bcm.edu	37	3	121412892	121412892	+	Silent	SNP	A	A	G	rs11915822	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121412892A>G	ENST00000340645.5	-	13	6588	c.6463T>C	c.(6463-6465)Ttg>Ctg	p.L2155L	GOLGB1_ENST00000393667.3_Silent_p.L2160L	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2155					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		GTCTCTTCCAAGTGGACTTTT	0.438													A|||	609	0.121605	0.1921	0.0576	5008	,	,		22806	0.0685		0.0915	False		,,,				2504	0.1575				p.L2160L		Atlas-SNP	.											.	GOLGB1	319	.	0			c.T6478C						PASS	.	A		875,3531	338.9+/-305.5	88,699,1416	172.0	170.0	171.0		6463	1.8	1.0	3	dbSNP_120	171	864,7736	196.5+/-241.4	49,766,3485	no	coding-synonymous	GOLGB1	NM_004487.3		137,1465,4901	GG,GA,AA		10.0465,19.8593,13.3708		2155/3260	121412892	1739,11267	2203	4300	6503	SO:0001819	synonymous_variant	2804	exon13			CTTCCAAGTGGAC	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.6463T>C	3.37:g.121412892A>G		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	231	94	0.406926	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Silent	SNP	ENST00000340645.5	37	CCDS3004.1																																																																																			A|0.878;G|0.122	0.122	strong		0.438	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
GABRP	2568	hgsc.bcm.edu	37	5	170239112	170239112	+	Missense_Mutation	SNP	C	C	A	rs1063310	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:170239112C>A	ENST00000518525.1	+	11	1637	c.1173C>A	c.(1171-1173)ttC>ttA	p.F391L	GABRP_ENST00000265294.4_Missense_Mutation_p.F391L|GABRP_ENST00000519385.1_3'UTR			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	391			F -> L (in dbSNP:rs1063310). {ECO:0000269|PubMed:15489334}.		signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCGACAAGTTCAAGTTTGTCT	0.403													C|||	1121	0.223842	0.2821	0.1398	5008	,	,		20252	0.2589		0.2565	False		,,,				2504	0.135				p.F391L		Atlas-SNP	.											.	GABRP	65	.	0			c.C1173A						PASS	.	C	LEU/PHE	1338,3068	447.5+/-348.4	207,924,1072	118.0	111.0	113.0		1173	2.9	1.0	5	dbSNP_86	113	2099,6501	362.7+/-332.9	282,1535,2483	yes	missense	GABRP	NM_014211.2	22	489,2459,3555	AA,AC,CC		24.407,30.3677,26.4263	benign	391/441	170239112	3437,9569	2203	4300	6503	SO:0001583	missense	2568	exon10			CAAGTTCAAGTTT	U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4089	protein-coding gene	gene with protein product	"""GABA(A) receptor, pi"""	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.1173C>A	5.37:g.170239112C>A	ENSP00000430100:p.Phe391Leu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	160	90	0.5625	NM_014211	A8KA36|D3DQL2|Q32MJ1	Missense_Mutation	SNP	ENST00000518525.1	37	CCDS4375.1	563	0.25778388278388276	148	0.3008130081300813	55	0.15193370165745856	165	0.28846153846153844	195	0.25725593667546176	C	7.948	0.744234	0.15710	0.303677	0.24407	ENSG00000094755	ENST00000518525;ENST00000265294	T;T	0.80033	-1.33;-1.33	5.74	2.88	0.33553	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.439494	0.27595	N	0.018672	T	0.00012	0.0000	N	0.14661	0.345	0.33623	P	0.39497499999999997	B	0.20164	0.042	B	0.11329	0.006	T	0.07424	-1.0773	9	0.24483	T	0.36	.	6.0236	0.19642	0.0:0.6203:0.1353:0.2443	rs1063310;rs3173007;rs3805457;rs17565897;rs52815531;rs1063310	391	O00591	GBRP_HUMAN	L	391	ENSP00000430100:F391L;ENSP00000265294:F391L	ENSP00000265294:F391L	F	+	3	2	GABRP	170171690	0.998000	0.40836	1.000000	0.80357	0.984000	0.73092	0.331000	0.19733	0.295000	0.22570	0.655000	0.94253	TTC	C|0.739;A|0.261	0.261	strong		0.403	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211	
ZNF17	7565	hgsc.bcm.edu	37	19	57931303	57931303	+	Missense_Mutation	SNP	C	C	A	rs2014827	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57931303C>A	ENST00000601808.1	+	3	656	c.443C>A	c.(442-444)aCa>aAa	p.T148K	AC003002.6_ENST00000596400.1_Missense_Mutation_p.T160K|ZNF17_ENST00000307658.7_Missense_Mutation_p.T150K|AC004076.7_ENST00000597410.1_Intron	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	148			T -> K (in dbSNP:rs2014827).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		AGGAACCTCACATGCATGCAG	0.502													C|||	784	0.15655	0.0106	0.2061	5008	,	,		22289	0.249		0.175	False		,,,				2504	0.2045				p.T148K	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.C443A						PASS	.	C	LYS/THR	182,4222	104.3+/-142.8	4,174,2024	111.0	113.0	112.0		443	-2.3	0.0	19	dbSNP_92	112	1706,6894	300.9+/-305.2	176,1354,2770	yes	missense	ZNF17	NM_006959.2	78	180,1528,4794	AA,AC,CC		19.8372,4.1326,14.5186	probably-damaging	148/663	57931303	1888,11116	2202	4300	6502	SO:0001583	missense	7565	exon3			ACCTCACATGCAT	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"""Zinc fingers, C2H2-type"", ""-"""	12958	protein-coding gene	gene with protein product			"""zinc finger protein 17 (HPF3, KOX 10)"""			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.443C>A	19.37:g.57931303C>A	ENSP00000471905:p.Thr148Lys	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Missense_Mutation	SNP	ENST00000601808.1	37	CCDS42636.1	369	0.16895604395604397	7	0.014227642276422764	70	0.19337016574585636	148	0.25874125874125875	144	0.18997361477572558	C	9.117	1.008038	0.19199	0.041326	0.198372	ENSG00000186272	ENST00000307658	.	.	.	1.46	-2.3	0.06785	.	.	.	.	.	T	0.00012	0.0000	N	0.13272	0.32	0.80722	P	0.0	P;B	0.39480	0.675;0.003	B;B	0.34824	0.19;0.003	T	0.16012	-1.0417	7	0.02654	T	1	.	0.2173	0.00164	0.2081:0.2719:0.2063:0.3137	rs2014827;rs52806689;rs58166306;rs2014827	150;148	P17021-2;P17021	.;ZNF17_HUMAN	K	148	.	ENSP00000302455:T148K	T	+	2	0	ZNF17	62623115	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.039000	0.00308	-0.627000	0.05589	-0.128000	0.14901	ACA	C|0.816;A|0.184	0.184	strong		0.502	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959	
LMF2	91289	hgsc.bcm.edu	37	22	50943010	50943010	+	Silent	SNP	G	G	A	rs762670	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50943010G>A	ENST00000474879.2	-	11	1599	c.1584C>T	c.(1582-1584)cgC>cgT	p.R528R	LMF2_ENST00000216080.5_Silent_p.R503R|LMF2_ENST00000505981.1_5'Flank|LMF2_ENST00000380796.3_Silent_p.R415R	NM_033200.2	NP_149977.2	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	528						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|cervix(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCTGCAGCAGGCGCAAGACCA	0.701													g|||	714	0.142572	0.1641	0.1398	5008	,	,		8932	0.0397		0.2326	False		,,,				2504	0.1288				p.R528R		Atlas-SNP	.											.	LMF2	40	.	0			c.C1584T						PASS	.	G		717,3661		65,587,1537	19.0	20.0	20.0		1584	2.1	1.0	22	dbSNP_86	20	1973,6599		227,1519,2540	no	coding-synonymous	LMF2	NM_033200.2		292,2106,4077	AA,AG,GG		23.0168,16.3773,20.7722		528/708	50943010	2690,10260	2189	4286	6475	SO:0001819	synonymous_variant	91289	exon11			CAGCAGGCGCAAG	BC002942	CCDS14093.1, CCDS14093.2	22q13.33	2008-02-04	2007-11-29	2007-11-29	ENSG00000100258	ENSG00000100258			25096	protein-coding gene	gene with protein product			"""transmembrane protein 153"", ""transmembrane protein 112B"""	TMEM153, TMEM112B		12477932	Standard	NM_033200		Approved		uc003blp.2	Q9BU23	OTTHUMG00000150206	ENST00000474879.2:c.1584C>T	22.37:g.50943010G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_033200	A6NEZ0|Q13392|Q6ZNR2|Q8WU74|Q96C62	Silent	SNP	ENST00000474879.2	37	CCDS14093.2	344	0.1575091575091575	88	0.17886178861788618	58	0.16022099447513813	18	0.03146853146853147	180	0.23746701846965698	G	11.27	1.588451	0.28357	0.163773	0.230168	ENSG00000100258	ENST00000487499	.	.	.	5.46	2.13	0.27403	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999992782	.	.	.	.	.	.	T	0.09465	-1.0673	3	.	.	.	-16.5875	9.5897	0.39539	0.0:0.4122:0.4306:0.1572	rs762670;rs60726771	.	.	.	S	535	.	.	P	-	1	0	LMF2	49289876	1.000000	0.71417	0.983000	0.44433	0.984000	0.73092	0.693000	0.25497	0.233000	0.21120	0.643000	0.83706	CCT	G|0.821;A|0.179	0.179	strong		0.701	LMF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316833.2	NM_033200	
LAMB1	3912	hgsc.bcm.edu	37	7	107603431	107603431	+	Silent	SNP	A	A	C	rs2230156	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:107603431A>C	ENST00000222399.6	-	15	2006	c.1776T>G	c.(1774-1776)ccT>ccG	p.P592P	LAMB1_ENST00000393560.1_Silent_p.P592P|LAMB1_ENST00000393561.1_Silent_p.P616P	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	592	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						AAGCCCCTTCAGGCACTCGGA	0.502													A|||	1431	0.285743	0.3752	0.2968	5008	,	,		15129	0.249		0.2495	False		,,,				2504	0.2321				p.P592P		Atlas-SNP	.											.	LAMB1	185	.	0			c.T1776G						PASS	.	A		1579,2827	492.4+/-362.4	291,997,915	105.0	108.0	107.0		1776	-3.3	0.9	7	dbSNP_98	107	2399,6201	398.2+/-346.0	331,1737,2232	no	coding-synonymous	LAMB1	NM_002291.2		622,2734,3147	CC,CA,AA		27.8953,35.8375,30.5859		592/1787	107603431	3978,9028	2203	4300	6503	SO:0001819	synonymous_variant	3912	exon15			CCCTTCAGGCACT	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.1776T>G	7.37:g.107603431A>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	126	125	0.992063	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	37	CCDS5750.1																																																																																			T|0.137;G|0.054;C|0.234;N|0.000;A|0.575	0.234	strong		0.502	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
MRPS21	54460	hgsc.bcm.edu	37	1	150280546	150280546	+	Missense_Mutation	SNP	C	C	T	rs10480	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:150280546C>T	ENST00000369084.5	+	2	595	c.148C>T	c.(148-150)Cgc>Tgc	p.R50C	MRPS21_ENST00000309092.7_Missense_Mutation_p.R50C	NM_018997.3	NP_061870.1	P82921	RT21_HUMAN	mitochondrial ribosomal protein S21	50			R -> C (in dbSNP:rs10480).		translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(1)|pancreas(1)	4	Lung NSC(24;5.57e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAAGCCATGCCGCCGGCGACA	0.493													C|||	48	0.00958466	0.0008	0.0216	5008	,	,		17027	0.0		0.0249	False		,,,				2504	0.0072				p.R50C		Atlas-SNP	.											.	MRPS21	8	.	0			c.C148T						PASS	.	C	CYS/ARG,CYS/ARG	28,4378	35.2+/-66.4	0,28,2175	50.0	47.0	48.0		148,148	4.9	1.0	1	dbSNP_52	48	289,8311	106.6+/-167.4	8,273,4019	no	missense,missense	MRPS21	NM_018997.2,NM_031901.4	180,180	8,301,6194	TT,TC,CC		3.3605,0.6355,2.4373	benign,benign	50/88,50/88	150280546	317,12689	2203	4300	6503	SO:0001583	missense	54460	exon2			CCATGCCGCCGGC	AB051353	CCDS950.1	1q21	2012-09-13			ENSG00000187145			"""Mitochondrial ribosomal proteins / small subunits"""	14046	protein-coding gene	gene with protein product		611984					Standard	NM_031901		Approved		uc001euk.3	P82921	OTTHUMG00000012544	ENST00000369084.5:c.148C>T	1.37:g.150280546C>T	ENSP00000358080:p.Arg50Cys	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	202	108	0.534653	NM_018997	Q5TB11|Q9BST6	Missense_Mutation	SNP	ENST00000369084.5	37	CCDS950.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	14.33	2.504529	0.44558	0.006355	0.033605	ENSG00000187145	ENST00000309092;ENST00000369084	T;T	0.30182	1.54;1.54	4.93	4.93	0.64822	.	.	.	.	.	T	0.12732	0.0309	.	.	.	0.53005	D	0.999962	B	0.20780	0.048	B	0.15484	0.013	T	0.02991	-1.1085	8	0.36615	T	0.2	.	12.9741	0.58529	0.1618:0.8382:0.0:0.0	rs10480;rs10480	50	P82921	RT21_HUMAN	C	50	ENSP00000312395:R50C;ENSP00000358080:R50C	ENSP00000312395:R50C	R	+	1	0	MRPS21	148547170	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.309000	0.43699	2.567000	0.86603	0.650000	0.86243	CGC	C|0.979;T|0.021	0.021	strong		0.493	MRPS21-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035813.1	NM_018997	
OBP2A	29991	hgsc.bcm.edu	37	9	138440562	138440562	+	Missense_Mutation	SNP	C	C	T	rs3178137	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:138440562C>T	ENST00000539850.1	+	5	423	c.397C>T	c.(397-399)Cct>Tct	p.P133S	OBP2A_ENST00000342114.4_Missense_Mutation_p.P110S|OBP2A_ENST00000371776.1_Missense_Mutation_p.P133S|OBP2A_ENST00000340780.3_Silent_p.I154I			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	133			P -> S (in dbSNP:rs3178137).		response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		AGGTAGGAATCCTAATACCAA	0.582													.|||	913	0.182308	0.1604	0.1398	5008	,	,		15740	0.1567		0.2525	False		,,,				2504	0.1963				p.P133S		Atlas-SNP	.											.	OBP2A	21	.	0			c.C397T						PASS	.	T	SER/PRO	799,3607	320.2+/-296.5	77,645,1481	83.0	76.0	79.0		397	0.5	0.0	9	dbSNP_105	79	2274,6326	381.9+/-340.2	304,1666,2330	yes	missense	OBP2A	NM_014582.2	74	381,2311,3811	TT,TC,CC		26.4419,18.1344,23.6276	benign	133/171	138440562	3073,9933	2203	4300	6503	SO:0001583	missense	29991	exon5			AGGAATCCTAATA	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.397C>T	9.37:g.138440562C>T	ENSP00000441028:p.Pro133Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	175	89	0.508571	NM_014582	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Missense_Mutation	SNP	ENST00000539850.1	37	CCDS6992.1	423	0.1936813186813187	84	0.17073170731707318	63	0.17403314917127072	83	0.1451048951048951	193	0.2546174142480211	c	10.69	1.420551	0.25639	0.181344	0.264419	ENSG00000122136	ENST00000342114;ENST00000371776;ENST00000539850	T;T;T	0.11495	2.77;2.96;2.96	2.49	0.488	0.16848	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.	.	.	.	T	0.00012	0.0000	L	0.41573	1.285	0.80722	P	0.0	P;B	0.44734	0.842;0.054	P;B	0.47981	0.563;0.175	T	0.45323	-0.9269	8	0.42905	T	0.14	-0.5946	5.0378	0.14443	0.0:0.6868:0.0:0.3132	rs3178137;rs7855089	110;133	Q5T8A4;Q9NY56	.;OBP2A_HUMAN	S	110;133;133	ENSP00000340950:P110S;ENSP00000360841:P133S;ENSP00000441028:P133S	ENSP00000340950:P110S	P	+	1	0	OBP2A	137580383	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.113000	0.10774	0.126000	0.18424	-0.359000	0.07587	CCT	C|0.781;T|0.219	0.219	strong		0.582	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582	
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381935	39381935	+	Missense_Mutation	SNP	C	C	T	rs2076110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:39381935C>T	ENST00000333467.3	+	3	338	c.293C>T	c.(292-294)cCg>cTg	p.P98L	APOBEC3B_ENST00000402182.3_Missense_Mutation_p.P98L|APOBEC3B_ENST00000407298.3_Missense_Mutation_p.P98L	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	98	CMP/dCMP deaminase zinc-binding 1.		P -> L (in dbSNP:rs2076110).		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|negative regulation of transposition (GO:0010529)	nucleus (GO:0005634)	deoxycytidine deaminase activity (GO:0047844)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	13	Melanoma(58;0.04)					ACCCCCTGCCCGGACTGTGTG	0.552													C|||	378	0.0754792	0.1717	0.0274	5008	,	,		16108	0.0079		0.0596	False		,,,				2504	0.0654				p.P98L		Atlas-SNP	.											APOBEC3B,colon,carcinoma,0,1	APOBEC3B	32	1	0			c.C293T						PASS	.	C	LEU/PRO	770,3634		53,664,1485	141.0	134.0	136.0		293	-4.2	0.0	22	dbSNP_129	136	519,8077		28,463,3807	no	missense	APOBEC3B	NM_004900.3	98	81,1127,5292	TT,TC,CC		6.0377,17.4841,9.9154	benign	98/383	39381935	1289,11711	2202	4298	6500	SO:0001583	missense	9582	exon3			CCTGCCCGGACTG	AK024854	CCDS13982.1, CCDS58807.1	22q13.1-q13.2	2008-05-15			ENSG00000179750	ENSG00000179750		"""Apolipoprotein B mRNA editing enzymes"""	17352	protein-coding gene	gene with protein product	"""phorbolin 3"""	607110				11863358, 10469298	Standard	NM_004900		Approved	PHRBNL, FLJ21201	uc003awo.2	Q9UH17	OTTHUMG00000151085	ENST00000333467.3:c.293C>T	22.37:g.39381935C>T	ENSP00000327459:p.Pro98Leu	Somatic	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	243	122	0.502058	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Missense_Mutation	SNP	ENST00000333467.3	37	CCDS13982.1	132	0.06043956043956044	83	0.16869918699186992	8	0.022099447513812154	0	0.0	41	0.05408970976253298	.	5.038	0.192766	0.09599	0.174841	0.060377	ENSG00000179750	ENST00000407298;ENST00000402182;ENST00000333467	T;T;T	0.63417	-0.04;-0.04;-0.04	2.12	-4.23	0.03789	APOBEC-like, N-terminal (1);APOBEC/CMP deaminase, zinc-binding (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.00178	0.0005	M	0.62723	1.935	0.80722	P	0.0	B;B	0.33345	0.289;0.409	B;B	0.29785	0.059;0.107	T	0.04178	-1.0971	8	0.21540	T	0.41	.	1.3839	0.02236	0.1397:0.1563:0.2723:0.4317	rs59708943	98;98	B0QYD2;Q9UH17	.;ABC3B_HUMAN	L	98	ENSP00000385068:P98L;ENSP00000385060:P98L;ENSP00000327459:P98L	ENSP00000327459:P98L	P	+	2	0	APOBEC3B	37711881	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-3.926000	0.00333	-1.760000	0.01312	0.184000	0.17185	CCG	C|0.919;T|0.081	0.081	strong		0.552	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
RBM12B	389677	hgsc.bcm.edu	37	8	94746698	94746698	+	Silent	SNP	G	G	T	rs3133974	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:94746698G>T	ENST00000399300.2	-	3	2154	c.1941C>A	c.(1939-1941)ccC>ccA	p.P647P	RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000520961.1_Intron|RBM12B_ENST00000517700.1_Intron	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	647							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			AGTCCTCCTCGGGGAGCTGCC	0.647													G|||	1332	0.265974	0.1755	0.232	5008	,	,		13293	0.3363		0.2843	False		,,,				2504	0.3211				p.P647P		Atlas-SNP	.											.	RBM12B	78	.	0			c.C1941A						PASS	.	G		702,3046		68,566,1240	86.0	89.0	88.0		1941	-8.2	0.0	8	dbSNP_103	88	2304,5910		329,1646,2132	no	coding-synonymous	RBM12B	NM_203390.2		397,2212,3372	TT,TG,GG		28.0497,18.73,25.1296		647/1002	94746698	3006,8956	1874	4107	5981	SO:0001819	synonymous_variant	389677	exon3			CTCCTCGGGGAGC		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.1941C>A	8.37:g.94746698G>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_203390	A8MYB5	Silent	SNP	ENST00000399300.2	37	CCDS43755.1																																																																																			A|0.000;G|0.730;T|0.270	0.270	strong		0.647	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390	
OR2G6	391211	hgsc.bcm.edu	37	1	248685719	248685719	+	Missense_Mutation	SNP	A	A	T	rs9330305	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248685719A>T	ENST00000343414.4	+	1	804	c.772A>T	c.(772-774)Atg>Ttg	p.M258L		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	258			M -> L (in dbSNP:rs9330305).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M258L(1)		NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATCATATTCATGTACCTTCA	0.443													.|||	797	0.159145	0.2973	0.1167	5008	,	,		19802	0.0913		0.1173	False		,,,				2504	0.1155				p.M258L		Atlas-SNP	.											OR2G6,NS,carcinoma,0,1	OR2G6	124	1	1	Substitution - Missense(1)	stomach(1)	c.A772T						PASS	.	A	LEU/MET	1172,3234		147,878,1178	116.0	117.0	117.0		772	3.8	1.0	1	dbSNP_119	117	1049,7551		72,905,3323	yes	missense	OR2G6	NM_001013355.1	15	219,1783,4501	TT,TA,AA		12.1977,26.6001,17.0767	benign	258/317	248685719	2221,10785	2203	4300	6503	SO:0001583	missense	391211	exon1			ATATTCATGTACC		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"""GPCR / Class A : Olfactory receptors"""	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.772A>T	1.37:g.248685719A>T	ENSP00000341291:p.Met258Leu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	160	78	0.4875	NM_001013355	B2RP33	Missense_Mutation	SNP	ENST00000343414.4	37	CCDS31119.1	336	0.15384615384615385	135	0.27439024390243905	48	0.13259668508287292	55	0.09615384615384616	98	0.12928759894459102	N	15.96	2.987563	0.53934	0.266001	0.121977	ENSG00000188558	ENST00000343414	T	0.00115	8.71	3.83	3.83	0.44106	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	U	0.000051	T	0.00012	0.0000	M	0.63169	1.94	0.51767	P	6.499999999998174E-5	P	0.50369	0.934	P	0.50934	0.654	T	0.60480	-0.7255	9	0.66056	D	0.02	.	11.7146	0.51645	1.0:0.0:0.0:0.0	rs9330305;rs52814416;rs9330305	258	Q5TZ20	OR2G6_HUMAN	L	258	ENSP00000341291:M258L	ENSP00000341291:M258L	M	+	1	0	OR2G6	246752342	0.000000	0.05858	0.966000	0.40874	0.615000	0.37417	0.266000	0.18534	1.598000	0.50083	0.329000	0.21502	ATG	A|0.832;T|0.168	0.168	strong		0.443	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842	
AGTPBP1	23287	hgsc.bcm.edu	37	9	88193858	88193858	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:88193858C>T	ENST00000357081.3	-	24	3463	c.3319G>A	c.(3319-3321)Ggc>Agc	p.G1107S	AGTPBP1_ENST00000376083.3_Missense_Mutation_p.G1067S|AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000432218.1_Intron|AGTPBP1_ENST00000376109.3_Missense_Mutation_p.G1119S			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	1107					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						TGATCACAGCCACATAAAGTA	0.348																																					p.G1067S		Atlas-SNP	.											AGTPBP1,NS,carcinoma,+2,1	AGTPBP1	128	1	0			c.G3199A						scavenged	.						158.0	159.0	159.0					9																	88193858		2203	4300	6503	SO:0001583	missense	23287	exon24			CACAGCCACATAA	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 1"", ""tubulinyl-Tyr carboxypeptidase"", ""carboxypeptidase-tubulin"", ""tyrosine carboxypeptidase"", ""soluble carboxypeptidase"""	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.3319G>A	9.37:g.88193858C>T	ENSP00000349592:p.Gly1107Ser	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	129	3	0.0232558	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	C	34	5.393531	0.96009	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109	T;T;T	0.12569	2.67;2.67;2.67	5.52	5.52	0.82312	Peptidase M14, carboxypeptidase A (1);	0.000000	0.85682	D	0.000000	T	0.44052	0.1275	M	0.82923	2.615	0.80722	D	1	D;D;D	0.89917	0.997;1.0;0.999	D;D;D	0.97110	0.966;1.0;0.99	T	0.32079	-0.9920	10	0.51188	T	0.08	-12.9427	19.8254	0.96616	0.0:1.0:0.0:0.0	.	1119;1107;1067	Q9UPW5-3;Q9UPW5;Q9UPW5-2	.;CBPC1_HUMAN;.	S	1107;1067;1119	ENSP00000349592:G1107S;ENSP00000365251:G1067S;ENSP00000365277:G1119S	ENSP00000349592:G1107S	G	-	1	0	AGTPBP1	87383678	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.786000	0.85741	2.773000	0.95371	0.650000	0.86243	GGC	.	.	none		0.348	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239	
GHR	2690	hgsc.bcm.edu	37	5	42719239	42719239	+	Missense_Mutation	SNP	A	A	C	rs6180	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:42719239A>C	ENST00000230882.4	+	10	1820	c.1630A>C	c.(1630-1632)Atc>Ctc	p.I544L	GHR_ENST00000537449.1_Missense_Mutation_p.I357L|GHR_ENST00000357703.3_Missense_Mutation_p.I522L	NM_000163.4|NM_001242399.2|NM_001242400.2|NM_001242401.3|NM_001242402.2|NM_001242403.2|NM_001242404.2|NM_001242405.2|NM_001242406.2	NP_000154.1|NP_001229328.1|NP_001229329.1|NP_001229330.1|NP_001229331.1|NP_001229332.1|NP_001229333.1|NP_001229334.1|NP_001229335.1	P10912	GHR_HUMAN	growth hormone receptor	544			I -> L (polymorphism with a modifier effect on plasma HDL cholesterol levels in familial hypercholesterolemia patients; dbSNP:rs6180). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:12910492, ECO:0000269|PubMed:2813379}.		2-oxoglutarate metabolic process (GO:0006103)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPK activity (GO:0000187)|allantoin metabolic process (GO:0000255)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|endocytosis (GO:0006897)|fatty acid metabolic process (GO:0006631)|growth hormone receptor signaling pathway (GO:0060396)|insulin-like growth factor receptor signaling pathway (GO:0048009)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|multicellular organismal metabolic process (GO:0044236)|oxaloacetate metabolic process (GO:0006107)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|receptor internalization (GO:0031623)|regulation of multicellular organism growth (GO:0040014)|response to cycloheximide (GO:0046898)|response to estradiol (GO:0032355)|succinate metabolic process (GO:0006105)|taurine metabolic process (GO:0019530)|valine metabolic process (GO:0006573)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|growth hormone receptor complex (GO:0070195)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine receptor activity (GO:0004896)|growth factor binding (GO:0019838)|peptide hormone binding (GO:0017046)|proline-rich region binding (GO:0070064)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			NS(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	CAAAAAGTGCATCCCTGTGGC	0.478													A|||	2226	0.444489	0.379	0.4006	5008	,	,		24092	0.5694		0.4185	False		,,,				2504	0.4622				p.I551L		Atlas-SNP	.											.	GHR	94	.	0			c.A1651C	GRCh37	CM032246	GHR	M	rs6180	PASS	.	A	LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,,	1714,2692	515.9+/-369.0	327,1060,816	103.0	87.0	92.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1630,1651,1630,1630,1630,1630,1630,1630,1630,1564,,	3.4	1.0	5	dbSNP_52	92	3961,4639	550.4+/-385.7	903,2155,1242	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,utr-3,utr-3	GHR	NM_000163.4,NM_001242399.2,NM_001242400.2,NM_001242401.3,NM_001242402.2,NM_001242403.2,NM_001242404.2,NM_001242405.2,NM_001242406.2,NM_001242460.1,NM_001242461.1,NM_001242462.1	5,5,5,5,5,5,5,5,5,5,,	1230,3215,2058	CC,CA,AA		46.0581,38.9015,43.6337	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,	544/639,551/646,544/639,544/639,544/639,544/639,544/639,544/639,544/639,522/617,,	42719239	5675,7331	2203	4300	6503	SO:0001583	missense	2690	exon10			AAGTGCATCCCTG		CCDS3940.1, CCDS56364.1, CCDS75239.1, CCDS75240.1	5p14-p12	2013-03-25			ENSG00000112964	ENSG00000112964		"""Fibronectin type III domain containing"""	4263	protein-coding gene	gene with protein product	"""growth hormone binding protein"""	600946					Standard	NM_001242460		Approved	GHBP	uc003jmt.3	P10912	OTTHUMG00000094791	ENST00000230882.4:c.1630A>C	5.37:g.42719239A>C	ENSP00000230882:p.Ile544Leu	Somatic	297	1	0.003367		WXS	Illumina HiSeq	Phase_I	315	315	1	NM_001242399	Q9HCX2	Missense_Mutation	SNP	ENST00000230882.4	37	CCDS3940.1	966	0.4423076923076923	180	0.36585365853658536	147	0.40607734806629836	334	0.583916083916084	305	0.4023746701846966	A	14.26	2.482225	0.44147	0.389015	0.460581	ENSG00000112964	ENST00000230882;ENST00000357703;ENST00000537449	T;T;T	0.35605	1.3;1.3;1.3	6.08	3.43	0.39272	.	0.537042	0.21498	N	0.073576	T	0.00012	0.0000	H	0.94808	3.585	0.49483	P	2.0600000000003948E-4	P	0.50272	0.933	P	0.62014	0.897	T	0.47861	-0.9084	9	0.51188	T	0.08	-7.1042	5.4155	0.16372	0.6692:0.0:0.2016:0.1292	rs6180;rs17231187;rs52796340;rs61155939;rs6180	544	P10912	GHR_HUMAN	L	544;522;357	ENSP00000230882:I544L;ENSP00000350335:I522L;ENSP00000442206:I357L	ENSP00000230882:I544L	I	+	1	0	GHR	42754996	0.991000	0.36638	0.951000	0.38953	0.529000	0.34654	1.574000	0.36482	1.135000	0.42183	0.482000	0.46254	ATC	A|0.548;C|0.448	0.448	strong		0.478	GHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211605.2	NM_000163	
CPA1	1357	hgsc.bcm.edu	37	7	130023539	130023539	+	Silent	SNP	C	C	T	rs12706927	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:130023539C>T	ENST00000011292.3	+	6	750	c.600C>T	c.(598-600)taC>taT	p.Y200Y	CPA1_ENST00000484324.1_Silent_p.Y112Y	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	200					proteolysis (GO:0006508)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(18;0.0435)					CTCAAGACTACGGGCAGGATG	0.587													C|||	384	0.0766773	0.0953	0.0562	5008	,	,		18446	0.006		0.1133	False		,,,				2504	0.1012				p.Y200Y		Atlas-SNP	.											.	CPA1	73	.	0			c.C600T						PASS	.	C		437,3969	212.2+/-232.1	19,399,1785	151.0	129.0	137.0		600	0.6	1.0	7	dbSNP_121	137	1026,7574	219.2+/-257.4	64,898,3338	no	coding-synonymous	CPA1	NM_001868.2		83,1297,5123	TT,TC,CC		11.9302,9.9183,11.2487		200/420	130023539	1463,11543	2203	4300	6503	SO:0001819	synonymous_variant	1357	exon6			AGACTACGGGCAG		CCDS5820.1	7q32	2012-02-10			ENSG00000091704	ENSG00000091704	3.4.17.1		2296	protein-coding gene	gene with protein product	"""pancreatic carboxypeptidase A"""	114850		CPA			Standard	NM_001868		Approved		uc003vpx.3	P15085	OTTHUMG00000157826	ENST00000011292.3:c.600C>T	7.37:g.130023539C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	NM_001868	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	Silent	SNP	ENST00000011292.3	37	CCDS5820.1																																																																																			C|0.903;T|0.097	0.097	strong		0.587	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868	
MYO19	80179	hgsc.bcm.edu	37	17	34871813	34871813	+	Silent	SNP	T	T	C	rs752493	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:34871813T>C	ENST00000431794.3	-	7	957	c.435A>G	c.(433-435)ctA>ctG	p.L145L	MYO19_ENST00000586007.1_Silent_p.L145L|MYO19_ENST00000268852.9_Silent_p.L145L|MYO19_ENST00000544606.1_Silent_p.L11L	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	145	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		AGAACTTCATTAGGCAGCGAG	0.552													t|||	326	0.0650958	0.1702	0.0389	5008	,	,		20726	0.0258		0.0417	False		,,,				2504	0.0061				p.L145L		Atlas-SNP	.											.	MYO19	130	.	0			c.A435G						PASS	.	C	,,	588,3458		42,504,1477	64.0	65.0	64.0		435,435,435	-1.6	1.0	17	dbSNP_86	64	281,8089		2,277,3906	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO19	NM_001033580.2,NM_001163735.1,NM_025109.5	,,	44,781,5383	CC,CT,TT		3.3572,14.5329,6.999	,,	145/318,145/971,145/771	34871813	869,11547	2023	4185	6208	SO:0001819	synonymous_variant	80179	exon8			CTTCATTAGGCAG	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"""Myosins / Myosin superfamily : Class XIX"""	26234	protein-coding gene	gene with protein product			"""myosin head domain containing 1"""	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.435A>G	17.37:g.34871813T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_001163735	Q59GS4|Q9H5X2	Silent	SNP	ENST00000431794.3	37	CCDS54112.1																																																																																			T|0.926;C|0.074	0.074	strong		0.552	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
TTN	7273	hgsc.bcm.edu	37	2	179434516	179434516	+	Missense_Mutation	SNP	C	C	T	rs3813243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179434516C>T	ENST00000591111.1	-	276	71644	c.71420G>A	c.(71419-71421)aGt>aAt	p.S23807N	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S16383N|TTN_ENST00000342992.6_Missense_Mutation_p.S22880N|TTN_ENST00000589042.1_Missense_Mutation_p.S25448N|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S16508N|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S16575N|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23807	Fibronectin type-III 73. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> N. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCACCAACACTCACATCACA	0.368													C|||	397	0.0792732	0.0855	0.0418	5008	,	,		21664	0.1736		0.0328	False		,,,				2504	0.0481				p.S25448N		Atlas-SNP	.											.	TTN	18412	.	0			c.G76343A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER,ASN/SER	241,3527		8,225,1651	146.0	131.0	135.0		49148,68639,49523,49724	5.9	1.0	2	dbSNP_107	135	167,8095		4,159,3968	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	46,46,46,46	12,384,5619	TT,TC,CC		2.0213,6.396,3.3915	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	16383/26927,22880/33424,16508/27052,16575/27119	179434516	408,11622	1884	4131	6015	SO:0001583	missense	7273	exon326			CCAACACTCACAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.71420G>A	2.37:g.179434516C>T	ENSP00000465570:p.Ser23807Asn	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		177	0.08104395604395605	37	0.07520325203252033	16	0.04419889502762431	101	0.17657342657342656	23	0.030343007915567283	C	12.11	1.839419	0.32513	0.06396	0.020213	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	5.92	5.92	0.95590	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00073	0.0002	N	0.17800	0.525	0.28382	P	0.9194971	P;P;P;P	0.43231	0.801;0.801;0.801;0.684	B;B;B;B	0.38106	0.265;0.265;0.265;0.197	T	0.03095	-1.1073	8	0.87932	D	0	.	20.3081	0.98638	0.0:1.0:0.0:0.0	rs3813243;rs52789452;rs3813243	16383;16508;16575;23807	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	22880;16383;16575;16508;16381	ENSP00000343764:S22880N;ENSP00000434586:S16383N;ENSP00000340554:S16575N;ENSP00000352154:S16508N	ENSP00000340554:S16575N	S	-	2	0	TTN	179142762	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.542000	0.53625	2.795000	0.96236	0.655000	0.94253	AGT	C|0.918;T|0.082	0.082	strong		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PRDM2	7799	hgsc.bcm.edu	37	1	14109114	14109114	+	Silent	SNP	A	A	G	rs1203651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14109114A>G	ENST00000235372.7	+	8	5680	c.4824A>G	c.(4822-4824)tcA>tcG	p.S1608S	PRDM2_ENST00000343137.4_Silent_p.S1407S|PRDM2_ENST00000311066.5_Silent_p.S1608S|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Silent_p.S1407S	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1608					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		GCAAAACATCACGGAGCCTGC	0.433													G|||	1828	0.365016	0.2322	0.5418	5008	,	,		20761	0.3988		0.328	False		,,,				2504	0.4223				p.S1608S		Atlas-SNP	.											.	PRDM2	147	.	0			c.A4824G						PASS	.	G	,,,	1163,3243	713.4+/-408.2	156,851,1196	73.0	74.0	73.0		4221,,4824,4824	0.7	0.0	1	dbSNP_87	73	3140,5460	656.3+/-401.3	533,2074,1693	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	,,,	689,2925,2889	GG,GA,AA		36.5116,26.3958,33.0847	,,,	1407/1482,,1608/1719,1608/1683	14109114	4303,8703	2203	4300	6503	SO:0001819	synonymous_variant	7799	exon8			AACATCACGGAGC	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.4824A>G	1.37:g.14109114A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Silent	SNP	ENST00000235372.7	37	CCDS150.1																																																																																			A|0.657;G|0.343	0.343	strong		0.433	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
LRRC52	440699	hgsc.bcm.edu	37	1	165533005	165533005	+	Silent	SNP	C	C	A	rs453717	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:165533005C>A	ENST00000294818.1	+	2	1176	c.886C>A	c.(886-888)Cgg>Agg	p.R296R	RP11-280O1.2_ENST00000438275.1_RNA|RP11-280O1.2_ENST00000421273.1_RNA|RP11-280O1.2_ENST00000416424.1_RNA	NM_001005214.3	NP_001005214.2	Q8N7C0	LRC52_HUMAN	leucine rich repeat containing 52	296					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)	18	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					GGAAGTCAGCCGGCGGATTTT	0.572													A|||	1600	0.319489	0.3767	0.2954	5008	,	,		17171	0.2282		0.3052	False		,,,				2504	0.3681				p.R296R		Atlas-SNP	.											LRRC52,caecum,carcinoma,0,1	LRRC52	50	1	0			c.C886A						PASS	.	A		1511,2895	673.6+/-402.8	261,989,953	62.0	68.0	66.0		886	-0.4	0.0	1	dbSNP_80	66	2460,6140	696.1+/-404.9	336,1788,2176	no	coding-synonymous	LRRC52	NM_001005214.3		597,2777,3129	AA,AC,CC		28.6047,34.2941,30.5321		296/314	165533005	3971,9035	2203	4300	6503	SO:0001819	synonymous_variant	440699	exon2			GTCAGCCGGCGGA	AK098677	CCDS30930.1	1q23.3	2008-02-05			ENSG00000162763	ENSG00000162763			32156	protein-coding gene	gene with protein product		615218					Standard	NM_001005214		Approved	FLJ25811	uc001gde.2	Q8N7C0	OTTHUMG00000034625	ENST00000294818.1:c.886C>A	1.37:g.165533005C>A		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	134	132	0.985075	NM_001005214	A2RUN7|Q5T9K5	Silent	SNP	ENST00000294818.1	37	CCDS30930.1																																																																																			C|0.692;A|0.308	0.308	strong		0.572	LRRC52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083793.1	NM_001005214	
USP35	57558	hgsc.bcm.edu	37	11	77920863	77920863	+	Silent	SNP	C	C	A	rs2512527	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:77920863C>A	ENST00000529308.1	+	10	2223	c.1962C>A	c.(1960-1962)ccC>ccA	p.P654P	USP35_ENST00000530267.1_Silent_p.P222P|USP35_ENST00000530535.1_3'UTR|USP35_ENST00000441408.2_Silent_p.P240P|USP35_ENST00000526425.1_Silent_p.P385P	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	654	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)	p.T655fs*74(1)|p.T411fs*74(1)		endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			ACACCCCCCCCACCAGCCTGT	0.612													c|||	1090	0.217652	0.0605	0.2997	5008	,	,		15520	0.4028		0.1551	False		,,,				2504	0.2454				p.P654P		Atlas-SNP	.											.	USP35	179	.	2	Insertion - Frameshift(2)	ovary(2)	c.C1962A						PASS	.			218,3592		7,204,1694	40.0	51.0	48.0		1962	-9.6	0.0	11	dbSNP_100	48	1065,7147		78,909,3119	no	coding-synonymous	USP35	NM_020798.2		85,1113,4813	AA,AC,CC		12.9688,5.7218,10.6721		654/1019	77920863	1283,10739	1905	4106	6011	SO:0001819	synonymous_variant	57558	exon10			CCCCCCCACCAGC	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.1962C>A	11.37:g.77920863C>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	136	71	0.522059	NM_020798		Silent	SNP	ENST00000529308.1	37	CCDS41693.1																																																																																			C|0.808;A|0.192	0.192	strong		0.612	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
FAM102A	399665	hgsc.bcm.edu	37	9	130710489	130710489	+	Silent	SNP	G	G	A	rs144841491	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:130710489G>A	ENST00000373095.1	-	6	852	c.477C>T	c.(475-477)gcC>gcT	p.A159A	FAM102A_ENST00000373084.4_Silent_p.A17A|FAM102A_ENST00000300434.3_Intron	NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	159	Ser-rich.									breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						AGATGGACTTGGCAGTCGATG	0.597													G|||	7	0.00139776	0.0	0.0	5008	,	,		20006	0.0		0.007	False		,,,				2504	0.0				p.A159A		Atlas-SNP	.											.	FAM102A	32	.	0			c.C477T						PASS	.	G	,	4,4402	8.1+/-20.4	0,4,2199	92.0	82.0	85.0		477,51	3.2	1.0	9	dbSNP_134	85	33,8567	23.4+/-69.3	0,33,4267	no	coding-synonymous,coding-synonymous	FAM102A	NM_001035254.2,NM_203305.2	,	0,37,6466	AA,AG,GG		0.3837,0.0908,0.2845	,	159/385,17/243	130710489	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	399665	exon6			GGACTTGGCAGTC		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"""sym-3 homolog A (C. elegans)"""	610891	"""chromosome 9 open reading frame 132"""	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.477C>T	9.37:g.130710489G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	67	38	0.567164	NM_001035254	A2A329|Q8TEL4	Silent	SNP	ENST00000373095.1	37	CCDS35150.1																																																																																			G|0.997;A|0.003	0.003	strong		0.597	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		
FBXO43	286151	hgsc.bcm.edu	37	8	101153024	101153024	+	Silent	SNP	G	G	A	rs1460934	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:101153024G>A	ENST00000428847.2	-	2	1774	c.1458C>T	c.(1456-1458)atC>atT	p.I486I		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	486					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			TTTTCTTGCCGATCAGTCCTG	0.378													A|||	3296	0.658147	0.7337	0.6888	5008	,	,		18106	0.7292		0.5557	False		,,,				2504	0.5665				p.I486I		Atlas-SNP	.											.	FBXO43	155	.	0			c.C1458T						PASS	.	A		2555,1101		891,773,164	198.0	183.0	188.0		1458	2.5	1.0	8	dbSNP_88	188	4461,3721		1212,2037,842	yes	coding-synonymous	FBXO43	NM_001029860.3		2103,2810,1006	AA,AG,GG		45.4779,30.1149,40.7332		486/709	101153024	7016,4822	1828	4091	5919	SO:0001819	synonymous_variant	286151	exon2			CTTGCCGATCAGT	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"""F-boxes /  ""other"""""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.1458C>T	8.37:g.101153024G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_001029860		Silent	SNP	ENST00000428847.2	37	CCDS47904.1																																																																																			G|0.370;A|0.630	0.630	strong		0.378	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77353973	77353973	+	Missense_Mutation	SNP	G	G	T	rs9930984	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:77353973G>T	ENST00000282849.5	-	16	2723	c.2305C>A	c.(2305-2307)Ctc>Atc	p.L769I		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	769	Spacer.		L -> I (in dbSNP:rs9930984). {ECO:0000269|PubMed:15489334}.		eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GCTGGAATGAGGACCACCGGA	0.488													T|||	3180	0.634984	0.7731	0.6268	5008	,	,		16886	0.8681		0.3648	False		,,,				2504	0.4918				p.L769I		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.C2305A						PASS	.	T	ILE/LEU	3290,1106	395.1+/-329.5	1247,796,155	47.0	53.0	51.0		2305	2.1	0.0	16	dbSNP_119	51	3395,5205	638.9+/-399.4	683,2029,1588	yes	missense	ADAMTS18	NM_199355.2	5	1930,2825,1743	TT,TG,GG		39.4767,25.1592,48.5611	benign	769/1222	77353973	6685,6311	2198	4300	6498	SO:0001583	missense	170692	exon16			GAATGAGGACCAC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2305C>A	16.37:g.77353973G>T	ENSP00000282849:p.Leu769Ile	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	30	16	0.533333	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	1348	0.6172161172161172	368	0.7479674796747967	207	0.5718232044198895	493	0.8618881118881119	280	0.36939313984168864	T	0.356	-0.942285	0.02322	0.748408	0.394767	ENSG00000140873	ENST00000282849	T	0.51574	0.7	5.54	2.08	0.27032	ADAM-TS Spacer 1 (1);	1.032820	0.07672	N	0.935568	T	0.00012	0.0000	N	0.04355	-0.22	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.001	T	0.33497	-0.9866	9	0.46703	T	0.11	.	5.8572	0.18727	0.0:0.2071:0.1293:0.6636	rs9930984;rs17855795;rs52810859;rs59142387;rs9930984	769;769	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	I	769	ENSP00000282849:L769I	ENSP00000282849:L769I	L	-	1	0	ADAMTS18	75911474	0.998000	0.40836	0.004000	0.12327	0.076000	0.17211	2.540000	0.45727	-0.130000	0.11599	-1.221000	0.01599	CTC	G|0.434;T|0.566	0.566	strong		0.488	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
C19orf57	79173	hgsc.bcm.edu	37	19	14000170	14000170	+	Missense_Mutation	SNP	T	T	C	rs3803892	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14000170T>C	ENST00000586783.1	-	5	1498	c.1499A>G	c.(1498-1500)cAg>cGg	p.Q500R	C19orf57_ENST00000591586.1_Intron|C19orf57_ENST00000346736.2_Missense_Mutation_p.Q500R|C19orf57_ENST00000454313.1_Missense_Mutation_p.Q500R			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	500			Q -> R (in dbSNP:rs3803892). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			TGGAATGCCCTGCTGAGCCCC	0.612													T|||	1957	0.390775	0.73	0.2349	5008	,	,		16808	0.3085		0.2117	False		,,,				2504	0.3119				p.Q500R		Atlas-SNP	.											.	C19orf57	34	.	0			c.A1499G						PASS	.	T	ARG/GLN	2888,1518	673.6+/-402.8	948,992,263	67.0	74.0	72.0		1499	-5.5	0.0	19	dbSNP_107	72	1841,6759	329.0+/-318.6	193,1455,2652	yes	missense	C19orf57	NM_024323.3	43	1141,2447,2915	CC,CT,TT		21.407,34.453,36.3601	benign	500/638	14000170	4729,8277	2203	4300	6503	SO:0001583	missense	79173	exon6			ATGCCCTGCTGAG	BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.1499A>G	19.37:g.14000170T>C	ENSP00000465822:p.Gln500Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		780	0.35714285714285715	339	0.6890243902439024	84	0.23204419889502761	196	0.34265734265734266	161	0.21240105540897097	T	9.672	1.146965	0.21288	0.65547	0.21407	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.42131	0.98;0.98	4.17	-5.51	0.02568	.	1.228890	0.06066	N	0.659305	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;B	0.37015	0.578;0.026	B;B	0.38156	0.266;0.01	T	0.39722	-0.9600	9	0.24483	T	0.36	1.4157	1.9501	0.03364	0.2921:0.0973:0.4029:0.2077	rs3803892;rs17850987;rs61282877;rs3803892	500;500	Q0VDD7-2;Q0VDD7	.;CS057_HUMAN	R	500	ENSP00000404382:Q500R;ENSP00000254336:Q500R	ENSP00000254336:Q500R	Q	-	2	0	C19orf57	13861170	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.678000	0.01942	-0.943000	0.03691	-0.314000	0.08810	CAG	T|0.637;C|0.362	0.362	strong		0.612	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	
MRS2	57380	hgsc.bcm.edu	37	6	24418786	24418786	+	Silent	SNP	T	T	C	rs79527965	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:24418786T>C	ENST00000378386.3	+	9	1180	c.1087T>C	c.(1087-1089)Ttg>Ctg	p.L363L	MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000543597.1_Silent_p.L72L|MRS2_ENST00000378353.1_Silent_p.L363L|MRS2_ENST00000274747.7_3'UTR|MRS2_ENST00000535061.1_Silent_p.L313L|MRS2_ENST00000443868.2_Silent_p.L366L	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	363						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	magnesium ion transmembrane transporter activity (GO:0015095)	p.L363L(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12						TGGAATGAATTTGGAATCTTC	0.443													T|||	582	0.116214	0.0159	0.0965	5008	,	,		15455	0.1478		0.1938	False		,,,				2504	0.1534				p.L363L		Atlas-SNP	.											MRS2,NS,carcinoma,0,1	MRS2	31	1	1	Substitution - coding silent(1)	stomach(1)	c.T1087C						PASS	.	T		170,4236	109.5+/-147.8	5,160,2038	158.0	156.0	157.0		1087	1.8	1.0	6	dbSNP_131	157	1234,7366	247.6+/-275.6	84,1066,3150	no	coding-synonymous	MRS2	NM_020662.2		89,1226,5188	CC,CT,TT		14.3488,3.8584,10.795		363/444	24418786	1404,11602	2203	4300	6503	SO:0001819	synonymous_variant	57380	exon9			ATGAATTTGGAAT	AF288288	CCDS4552.1, CCDS69055.1, CCDS69056.1, CCDS75408.1	6p22.3-p22.1	2013-05-03	2013-05-03	2008-01-18	ENSG00000124532	ENSG00000124532			13785	protein-coding gene	gene with protein product			"""MRS2-like, magnesium homeostasis factor (S. cerevisiae)"", ""MRS2 magnesium homeostasis factor homolog (S. cerevisiae)"""	MRS2L			Standard	XM_005249242		Approved		uc003neb.3	Q9HD23	OTTHUMG00000014355	ENST00000378386.3:c.1087T>C	6.37:g.24418786T>C		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	280	142	0.507143	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	37	CCDS4552.1																																																																																			T|0.887;C|0.113	0.113	strong		0.443	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1		
SRRM4	84530	hgsc.bcm.edu	37	12	119554751	119554751	+	Silent	SNP	C	C	G	rs73213764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:119554751C>G	ENST00000267260.4	+	4	763	c.375C>G	c.(373-375)tcC>tcG	p.S125S	RP11-364C11.2_ENST00000537730.1_RNA	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	125	Lys-rich.|Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						GGTCCTCATCCTATAGCCCAT	0.473													C|||	123	0.0245607	0.0408	0.0187	5008	,	,		16293	0.004		0.0219	False		,,,				2504	0.0307				p.S125S		Atlas-SNP	.											SRRM4_ENST00000267260,NS,carcinoma,+1,3	SRRM4	131	3	0			c.C375G						PASS	.	C		162,3536		7,148,1694	79.0	71.0	74.0		375	-1.8	0.7	12	dbSNP_130	74	344,7860		8,328,3766	no	coding-synonymous	SRRM4	NM_194286.3		15,476,5460	GG,GC,CC		4.1931,4.3807,4.2514		125/612	119554751	506,11396	1849	4102	5951	SO:0001819	synonymous_variant	84530	exon4			CTCATCCTATAGC	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.375C>G	12.37:g.119554751C>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	49	32	0.653061	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Silent	SNP	ENST00000267260.4	37	CCDS44994.1																																																																																			C|0.975;G|0.025	0.025	strong		0.473	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
SNCG	6623	hgsc.bcm.edu	37	10	88719789	88719789	+	Silent	SNP	C	C	G	rs760113	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:88719789C>G	ENST00000372017.3	+	3	237	c.195C>G	c.(193-195)gcC>gcG	p.A65A	SNCG_ENST00000483064.1_3'UTR|SNCG_ENST00000348795.4_Missense_Mutation_p.R83G|MMRN2_ENST00000372027.5_5'Flank	NM_003087.2	NP_003078.2	O76070	SYUG_HUMAN	synuclein, gamma (breast cancer-specific protein 1)	65	4 X 11 AA tandem repeats of [EGSA]-K-T-K- [EQ]-[GQ]-V-X(4).				adult locomotory behavior (GO:0008344)|aggressive behavior (GO:0002118)|cellular response to hydrostatic pressure (GO:0071464)|protein secretion (GO:0009306)|regulation of dopamine secretion (GO:0014059)|regulation of neurotransmitter secretion (GO:0046928)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				endometrium(1)|skin(1)	2						AGGCCAACGCCGTGAGCGAGG	0.667													c|||	1152	0.230032	0.2693	0.2262	5008	,	,		18394	0.0615		0.2346	False		,,,				2504	0.3487				p.A65A		Atlas-SNP	.											.	SNCG	8	.	0			c.C195G						PASS	.	C		1208,3198	405.1+/-333.4	175,858,1170	87.0	69.0	75.0		195	-8.2	0.2	10	dbSNP_86	75	2140,6460	349.8+/-327.6	246,1648,2406	no	coding-synonymous	SNCG	NM_003087.2		421,2506,3576	GG,GC,CC		24.8837,27.4172,25.742		65/128	88719789	3348,9658	2203	4300	6503	SO:0001819	synonymous_variant	6623	exon3			CAACGCCGTGAGC	AF044311	CCDS7380.1	10q23.2-q23.3	2006-06-28			ENSG00000173267	ENSG00000173267			11141	protein-coding gene	gene with protein product	"""synoretin"""	602998				9044857, 9700196	Standard	NM_003087		Approved	BCSG1, SR, persyn	uc001keb.2	O76070	OTTHUMG00000018656	ENST00000372017.3:c.195C>G	10.37:g.88719789C>G		Somatic	211	2	0.00947867		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_003087	O15104|Q96P61	Silent	SNP	ENST00000372017.3	37	CCDS7380.1	452	0.20695970695970695	133	0.2703252032520325	96	0.26519337016574585	38	0.06643356643356643	185	0.24406332453825857	C	9.818	1.184969	0.21870	0.274172	0.248837	ENSG00000173267	ENST00000348795	D	0.88664	-2.41	4.93	-8.16	0.01061	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.20821	P	0.999841416	.	.	.	.	.	.	T	0.46789	-0.9166	5	0.87932	D	0	-1.3525	1.0486	0.01575	0.1667:0.2461:0.2358:0.3514	rs760113;rs1048609;rs3188622	.	.	.	G	83	ENSP00000344658:R83G	ENSP00000344658:R83G	R	+	1	0	SNCG	88709769	0.000000	0.05858	0.184000	0.23157	0.666000	0.39218	-1.896000	0.01605	-1.414000	0.02025	-1.157000	0.01802	CGT	C|0.759;G|0.241	0.241	strong		0.667	SNCG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049167.1		
OR5T2	219464	hgsc.bcm.edu	37	11	55999897	55999897	+	Silent	SNP	G	G	A	rs7122000	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55999897G>A	ENST00000313264.4	-	1	840	c.765C>T	c.(763-765)atC>atT	p.I255I		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					AACCATAGGAGATCAGAACAA	0.443													g|||	185	0.0369409	0.003	0.0432	5008	,	,		20939	0.001		0.0944	False		,,,				2504	0.0562				p.I255I		Atlas-SNP	.											OR5T2,NS,carcinoma,0,1	OR5T2	107	1	0			c.C765T						PASS	.	G		58,4344	55.5+/-91.7	0,58,2143	120.0	112.0	115.0		765	-0.2	0.1	11	dbSNP_116	115	690,7902	170.6+/-221.7	34,622,3640	no	coding-synonymous	OR5T2	NM_001004746.1		34,680,5783	AA,AG,GG		8.0307,1.3176,5.7565		255/360	55999897	748,12246	2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			ATAGGAGATCAGA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.765C>T	11.37:g.55999897G>A		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	252	99	0.392857	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	37	CCDS31523.1																																																																																			G|0.952;A|0.048	0.048	strong		0.443	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
ADA	100	hgsc.bcm.edu	37	20	43252915	43252915	+	Silent	SNP	T	T	C	rs244076	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:43252915T>C	ENST00000372874.4	-	6	668	c.534A>G	c.(532-534)gtA>gtG	p.V178V	ADA_ENST00000537820.1_Silent_p.V178V|ADA_ENST00000464097.1_5'UTR	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	178					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	GGTCAATGGCTACCACGGTCT	0.597									Adenosine Deaminase Deficiency				C|||	1331	0.265775	0.4735	0.1585	5008	,	,		19918	0.1548		0.1829	False		,,,				2504	0.2607				p.V178V		Atlas-SNP	.											.	ADA	42	.	0			c.A534G						PASS	.	C		1770,2636	642.7+/-397.7	340,1090,773	103.0	83.0	90.0		534	3.5	1.0	20	dbSNP_79	90	1463,7137	750.6+/-407.4	122,1219,2959	yes	coding-synonymous	ADA	NM_000022.2		462,2309,3732	CC,CT,TT		17.0116,40.1725,24.8578		178/364	43252915	3233,9773	2203	4300	6503	SO:0001819	synonymous_variant	100	exon6	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	AATGGCTACCACG	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.534A>G	20.37:g.43252915T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_000022	Q53F92|Q6LA59	Silent	SNP	ENST00000372874.4	37	CCDS13335.1																																																																																			T|0.751;C|0.249	0.249	strong		0.597	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	
KBTBD7	84078	hgsc.bcm.edu	37	13	41767338	41767338	+	Silent	SNP	A	A	G	rs2039134	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:41767338A>G	ENST00000379483.3	-	1	1364	c.1056T>C	c.(1054-1056)ccT>ccC	p.P352P		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	352										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		AGGGATCTCTAGGATGTCCAA	0.502													.|||	2548	0.508786	0.1029	0.8156	5008	,	,		21033	0.3502		0.832	False		,,,				2504	0.6708				p.P352P		Atlas-SNP	.											KBTBD7,caecum,carcinoma,0,1	KBTBD7	60	1	0			c.T1056C						PASS	.	A		891,3515	325.6+/-299.2	100,691,1412	91.0	58.0	69.0		1056	2.2	0.8	13	dbSNP_94	69	7267,1333	751.6+/-407.4	3084,1099,117	no	coding-synonymous	KBTBD7	NM_032138.4		3184,1790,1529	GG,GA,AA		15.5,20.2224,37.2751		352/685	41767338	8158,4848	2203	4300	6503	SO:0001819	synonymous_variant	84078	exon1			ATCTCTAGGATGT	AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"""BTB/POZ domain containing"""	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.1056T>C	13.37:g.41767338A>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	92	90	0.978261	NM_032138	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Silent	SNP	ENST00000379483.3	37	CCDS9377.1																																																																																			A|0.388;G|0.612	0.612	strong		0.502	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138	
TRIM69	140691	hgsc.bcm.edu	37	15	45048651	45048651	+	Missense_Mutation	SNP	C	C	T	rs3759880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:45048651C>T	ENST00000559390.1	+	4	1497	c.569C>T	c.(568-570)gCt>gTt	p.A190V	TRIM69_ENST00000561043.1_Missense_Mutation_p.A31V|TRIM69_ENST00000338264.4_Missense_Mutation_p.A31V|TRIM69_ENST00000558173.1_5'UTR|TRIM69_ENST00000560442.1_5'UTR|TRIM69_ENST00000558329.1_5'UTR|TRIM69_ENST00000329464.4_Missense_Mutation_p.A190V			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	190			A -> V (in dbSNP:rs3759880).		apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		GAAGCTATTGCTGCTCACAAG	0.473													C|||	686	0.136981	0.2383	0.0764	5008	,	,		20191	0.0685		0.1123	False		,,,				2504	0.1391				p.A190V	Pancreas(84;519 1450 1802 20427 34706)	Atlas-SNP	.											.	TRIM69	47	.	0			c.C569T						PASS	.	C	VAL/ALA,VAL/ALA	703,3241		65,573,1334	41.0	33.0	36.0		92,569	0.1	1.0	15	dbSNP_107	36	694,6652		26,642,3005	yes	missense,missense	TRIM69	NM_080745.3,NM_182985.3	64,64	91,1215,4339	TT,TC,CC		9.4473,17.8245,12.3738	benign,benign	31/342,190/501	45048651	1397,9893	1972	3673	5645	SO:0001583	missense	140691	exon3			CTATTGCTGCTCA	AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	17857	protein-coding gene	gene with protein product			"""ring finger protein 36"", ""tripartite motif-containing 69"""	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.569C>T	15.37:g.45048651C>T	ENSP00000453177:p.Ala190Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_182985	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Missense_Mutation	SNP	ENST00000559390.1	37	CCDS32220.1	270	0.12362637362637363	119	0.241869918699187	32	0.08839779005524862	31	0.05419580419580419	88	0.11609498680738786	C	5.409	0.260660	0.10239	0.178245	0.094473	ENSG00000185880	ENST00000329464;ENST00000338264	T;T	0.56444	1.1;0.46	5.56	0.103	0.14526	.	0.669254	0.13224	N	0.404170	T	0.00012	0.0000	N	0.11106	0.095	0.50632	P	1.2000000000000899E-4	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.002	T	0.26087	-1.0113	9	0.23302	T	0.38	.	5.3173	0.15862	0.0:0.4436:0.2536:0.3028	rs3759880;rs17589120;rs59487609;rs3759880	31;190	Q86WT6-2;Q86WT6	.;TRI69_HUMAN	V	190;31	ENSP00000332284:A190V;ENSP00000342922:A31V	ENSP00000332284:A190V	A	+	2	0	TRIM69	42835943	0.999000	0.42202	0.995000	0.50966	0.061000	0.15899	0.335000	0.19806	0.110000	0.17919	-0.137000	0.14449	GCT	C|0.866;N|0.000	.	strong		0.473	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1		
COL16A1	1307	hgsc.bcm.edu	37	1	32158374	32158374	+	Silent	SNP	T	T	C	rs386630117|rs3818788	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32158374T>C	ENST00000373672.3	-	14	1623	c.1107A>G	c.(1105-1107)ccA>ccG	p.P369P	COL16A1_ENST00000271069.6_Silent_p.P369P|COL16A1_ENST00000373668.3_Silent_p.P369P	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	369	Nonhelical region 10 (NC10).				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TTACCTGAAGTGGGGCATCCG	0.597													C|||	3157	0.630391	0.7663	0.6816	5008	,	,		17205	0.3581		0.6491	False		,,,				2504	0.6718				p.P369P	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.A1107G						PASS	.	C		2904,1054		1071,762,146	53.0	56.0	55.0		1107	-8.9	0.6	1	dbSNP_107	55	5304,2962		1730,1844,559	yes	coding-synonymous	COL16A1	NM_001856.3		2801,2606,705	CC,CT,TT		35.8335,26.6296,32.8534		369/1605	32158374	8208,4016	1979	4133	6112	SO:0001819	synonymous_variant	1307	exon14			CTGAAGTGGGGCA	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.1107A>G	1.37:g.32158374T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	37	CCDS41297.1																																																																																			T|0.401;C|0.599	0.599	strong		0.597	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
METTL20	254013	hgsc.bcm.edu	37	12	31820718	31820718	+	Missense_Mutation	SNP	C	C	G	rs11051523	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:31820718C>G	ENST00000357721.3	+	4	798	c.583C>G	c.(583-585)Ctt>Gtt	p.L195V	METTL20_ENST00000395763.3_Missense_Mutation_p.L195V|METTL20_ENST00000412352.2_Missense_Mutation_p.L195V|METTL20_ENST00000538391.1_3'UTR|METTL20_ENST00000538463.1_Missense_Mutation_p.L195V	NM_001135863.1	NP_001129335.1	Q8IXQ9	MET20_HUMAN	methyltransferase like 20	195						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			lung(2)|stomach(1)	3						TGATGAAGACCTTGCAGATAG	0.433													C|||	8	0.00159744	0.0	0.0058	5008	,	,		18711	0.0		0.002	False		,,,				2504	0.002				p.L195V		Atlas-SNP	.											.	METTL20	23	.	0			c.C583G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU	3,4403	6.2+/-15.9	0,3,2200	118.0	118.0	118.0		583,583,583	5.5	0.7	12	dbSNP_120	118	35,8565	24.6+/-71.5	0,35,4265	yes	missense,missense,missense	METTL20	NM_001135863.1,NM_001135864.1,NM_173802.3	32,32,32	0,38,6465	GG,GC,CC		0.407,0.0681,0.2922	possibly-damaging,possibly-damaging,possibly-damaging	195/263,195/263,195/263	31820718	38,12968	2203	4300	6503	SO:0001583	missense	254013	exon4			GAAGACCTTGCAG	BC039535	CCDS8724.1	12p11.21	2011-03-03	2011-03-03	2011-03-03	ENSG00000139160	ENSG00000139160			28739	protein-coding gene	gene with protein product		615256	"""chromosome 12 open reading frame 72"""	C12orf72			Standard	NM_173802		Approved	DKFZp451L235, MGC50559	uc001rkm.3	Q8IXQ9		ENST00000357721.3:c.583C>G	12.37:g.31820718C>G	ENSP00000350353:p.Leu195Val	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	218	112	0.513761	NM_173802	D3DUW3	Missense_Mutation	SNP	ENST00000357721.3	37	CCDS8724.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	22.2	4.264139	0.80358	6.81E-4	0.00407	ENSG00000139160	ENST00000412352;ENST00000395763;ENST00000538463;ENST00000357721	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.65471	0.2694	M	0.86651	2.83	0.80722	D	1	D	0.55172	0.97	P	0.46796	0.527	T	0.70073	-0.4972	9	0.16896	T	0.51	-21.6458	19.7613	0.96319	0.0:1.0:0.0:0.0	rs11051523	195	Q8IXQ9	MET20_HUMAN	V	195	.	ENSP00000350353:L195V	L	+	1	0	METTL20	31711985	1.000000	0.71417	0.732000	0.30844	0.806000	0.45545	7.160000	0.77495	2.752000	0.94435	0.655000	0.94253	CTT	C|0.998;G|0.002	0.002	strong		0.433	METTL20-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402196.1	NM_173802	
ATG2B	55102	hgsc.bcm.edu	37	14	96769560	96769560	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:96769560G>C	ENST00000359933.4	-	33	5768	c.4875C>G	c.(4873-4875)tgC>tgG	p.C1625W	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1625					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AATCAGGTTTGCATGGCGGGT	0.438																																					p.C1625W		Atlas-SNP	.											.	ATG2B	169	.	0			c.C4875G						PASS	.						88.0	89.0	89.0					14																	96769560		2203	4300	6503	SO:0001583	missense	55102	exon33			AGGTTTGCATGGC	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.4875C>G	14.37:g.96769560G>C	ENSP00000353010:p.Cys1625Trp	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	G	12.66	2.005762	0.35415	.	.	ENSG00000066739	ENST00000359933	T	0.09445	2.98	5.74	3.72	0.42706	.	0.435774	0.22296	N	0.061922	T	0.04227	0.0117	N	0.08118	0	0.23896	N	0.996539	P	0.49358	0.923	B	0.36289	0.221	T	0.33599	-0.9862	10	0.66056	D	0.02	.	4.7681	0.13142	0.3198:0.1534:0.5267:0.0	.	1625	Q96BY7	ATG2B_HUMAN	W	1625	ENSP00000353010:C1625W	ENSP00000261834:C269W	C	-	3	2	ATG2B	95839313	0.002000	0.14202	0.011000	0.14972	0.693000	0.40251	1.215000	0.32431	0.742000	0.32697	0.563000	0.77884	TGC	.	.	none		0.438	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
MXRA5	25878	hgsc.bcm.edu	37	X	3241591	3241591	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:3241591C>T	ENST00000217939.6	-	5	2289	c.2135G>A	c.(2134-2136)aGg>aAg	p.R712K		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	712						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CAGAAGTCTCCTTGAAGTGTT	0.498																																					p.R712K		Atlas-SNP	.											.	MXRA5	815	.	0			c.G2135A						PASS	.						81.0	72.0	75.0					X																	3241591		2203	4300	6503	SO:0001583	missense	25878	exon5			AGTCTCCTTGAAG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2135G>A	X.37:g.3241591C>T	ENSP00000217939:p.Arg712Lys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	81	73	0.901235	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	c	2.192	-0.385056	0.04966	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.62639	0.01	3.49	-0.704	0.11256	.	0.543747	0.15356	N	0.266696	T	0.37598	0.1009	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.13845	-1.0494	10	0.23891	T	0.37	.	5.8602	0.18743	0.0:0.5307:0.2897:0.1795	.	712	Q9NR99	MXRA5_HUMAN	K	712	ENSP00000217939:R712K	ENSP00000217939:R712K	R	-	2	0	MXRA5	3251591	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.256000	0.18351	-0.388000	0.07797	0.529000	0.55759	AGG	.	.	none		0.498	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
Unknown	0	hgsc.bcm.edu	37	7	63680099	63680099	+	IGR	SNP	C	C	A	rs35920205|rs4320434	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:63680099C>A								GUSBP6 (69000 upstream) : ZNF679 (8752 downstream)																							ATCCTTTAACCACTCCTCAAG	0.398													.|||	1119	0.223442	0.1551	0.2205	5008	,	,		19877	0.2679		0.2565	False		,,,				2504	0.2382				p.H224N		Atlas-SNP	.											.	.	.	.	0			c.C670A						PASS	.						42.0	39.0	40.0					7																	63680099		692	1591	2283	SO:0001628	intergenic_variant	730291	exon4			TTTAACCACTCCT																													7.37:g.63680099C>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_001159524		Missense_Mutation	SNP		37																																																																																				C|0.813;A|0.187	0.187	strong	0	0.398								
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036505	33036505	+	Silent	SNP	G	G	C	rs1042434	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33036505G>C	ENST00000419277.1	-	5	834	c.705C>G	c.(703-705)gtC>gtG	p.V235V	HLA-DPA1_ENST00000463066.1_5'Flank|HLA-DPA1_ENST00000428995.1_Silent_p.V235V	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	235					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CGATGATGCCGACTAGGCCCA	0.582													C|||	2381	0.475439	0.7095	0.2997	5008	,	,		18440	0.6796		0.1889	False		,,,				2504	0.3681				p.V235V		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C705G						PASS	.	C	,,	1707,1313		479,749,282	104.0	126.0	118.0		705,705,705	2.5	0.6	6	dbSNP_86	118	968,4450		74,820,1815	yes	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	553,1569,2097	CC,CG,GG		17.8664,43.4768,31.7018	,,	235/261,235/261,235/261	33036505	2675,5763	1510	2709	4219	SO:0001819	synonymous_variant	3113	exon4			GATGCCGACTAGG	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.705C>G	6.37:g.33036505G>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	202	57	0.282178	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1	946	0.43315018315018317	350	0.7113821138211383	96	0.26519337016574585	371	0.6486013986013986	129	0.17018469656992086	C	0.676	-0.800149	0.02841	0.565232	0.178664	ENSG00000231389	ENST00000437811	.	.	.	3.4	2.51	0.30379	.	.	.	.	.	T	0.24624	0.0597	.	.	.	0.09310	P	0.999999832037	.	.	.	.	.	.	T	0.08351	-1.0726	3	.	.	.	.	7.1427	0.25564	0.1821:0.4624:0.3555:0.0	rs1042434;rs3181901;rs17850578	.	.	.	G	103	.	.	R	-	1	2	HLA-DPA1	33144483	0.085000	0.21516	0.599000	0.28851	0.111000	0.19643	0.007000	0.13174	0.212000	0.20703	-0.847000	0.03039	CGG	G|0.663;C|0.337	0.337	strong		0.582	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
DNAH9	1770	hgsc.bcm.edu	37	17	11651057	11651057	+	Missense_Mutation	SNP	A	A	G	rs3744581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:11651057A>G	ENST00000262442.4	+	32	6652	c.6584A>G	c.(6583-6585)aAt>aGt	p.N2195S	DNAH9_ENST00000454412.2_Missense_Mutation_p.N2195S	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2195	AAA 2. {ECO:0000250}.		N -> S (in dbSNP:rs3744581).		cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GGCATCATCAATCCAGCCACA	0.527													A|||	1125	0.224641	0.1543	0.2349	5008	,	,		17290	0.3294		0.2356	False		,,,				2504	0.1933				p.N2195S		Atlas-SNP	.											DNAH9,colon,carcinoma,0,1	DNAH9	695	1	0			c.A6584G	GRCh37	CM065137	DNAH9	M	rs3744581	PASS	.	A	SER/ASN	712,3694	296.4+/-284.2	58,596,1549	58.0	55.0	56.0		6584	3.3	1.0	17	dbSNP_107	56	2099,6501	360.3+/-331.9	250,1599,2451	yes	missense	DNAH9	NM_001372.3	46	308,2195,4000	GG,GA,AA		24.407,16.1598,21.6131	possibly-damaging	2195/4487	11651057	2811,10195	2203	4300	6503	SO:0001583	missense	1770	exon32			TCATCAATCCAGC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6584A>G	17.37:g.11651057A>G	ENSP00000262442:p.Asn2195Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	512	0.23443223443223443	73	0.1483739837398374	71	0.19613259668508287	193	0.3374125874125874	175	0.23087071240105542	A	19.41	3.822547	0.71028	0.161598	0.24407	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	D;D	0.87650	-2.28;-2.28	4.36	3.29	0.37713	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.194965	0.42682	D	0.000662	T	0.00012	0.0000	M	0.82056	2.57	0.09310	P	1.0	P	0.46220	0.874	P	0.53760	0.734	T	0.00000	-1.2947	9	0.51188	T	0.08	.	9.7558	0.40502	0.918:0.0:0.082:0.0	rs3744581;rs58949980;rs3744581	2195	Q9NYC9	DYH9_HUMAN	S	2195;2195;777	ENSP00000262442:N2195S;ENSP00000414874:N2195S	ENSP00000262442:N2195S	N	+	2	0	DNAH9	11591782	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	7.249000	0.78278	0.722000	0.32252	0.455000	0.32223	AAT	A|0.779;G|0.221	0.221	strong		0.527	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
JAG2	3714	hgsc.bcm.edu	37	14	105615648	105615648	+	Missense_Mutation	SNP	C	C	T	rs9972231	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105615648C>T	ENST00000331782.3	-	13	2015	c.1612G>A	c.(1612-1614)Gac>Aac	p.D538N	RP11-44N21.4_ENST00000548203.1_RNA|JAG2_ENST00000347004.2_Missense_Mutation_p.D500N	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	538	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.		D -> N (in dbSNP:rs9972231).		auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)	p.D538N(2)		breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		TCACAAAGGTCGACATCCACC	0.622													c|||	601	0.120008	0.0053	0.1268	5008	,	,		11943	0.1687		0.1312	False		,,,				2504	0.2086				p.D538N		Atlas-SNP	.											JAG2,scalp,carcinoma,0,3	JAG2	69	3	2	Substitution - Missense(2)	lung(1)|skin(1)	c.G1612A						PASS	.		ASN/ASP,ASN/ASP	143,4261	98.9+/-137.6	2,139,2061	68.0	71.0	70.0		1612,1498	3.8	0.0	14	dbSNP_119	70	1119,7481	229.8+/-264.4	82,955,3263	yes	missense,missense	JAG2	NM_002226.3,NM_145159.1	23,23	84,1094,5324	TT,TC,CC		13.0116,3.247,9.7047	possibly-damaging,possibly-damaging	538/1239,500/1201	105615648	1262,11742	2202	4300	6502	SO:0001583	missense	3714	exon13			AAAGGTCGACATC	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.1612G>A	14.37:g.105615648C>T	ENSP00000328169:p.Asp538Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	37	CCDS9998.1	253	0.11584249084249085	5	0.01016260162601626	44	0.12154696132596685	104	0.18181818181818182	100	0.13192612137203166	C	12.41	1.928193	0.34002	0.03247	0.130116	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.83673	-1.75;-1.75	3.8	3.8	0.43715	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.056989	0.64402	D	0.000002	T	0.00412	0.0013	L	0.49455	1.56	0.21020	P	0.999805715	B;B	0.34147	0.438;0.202	B;B	0.29267	0.1;0.025	T	0.30238	-0.9985	9	0.20519	T	0.43	.	13.511	0.61513	0.0:1.0:0.0:0.0	rs9972231;rs57317492;rs9972231	500;538	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	N	538;500	ENSP00000328169:D538N;ENSP00000328566:D500N	ENSP00000328169:D538N	D	-	1	0	JAG2	104686693	0.269000	0.24143	0.038000	0.18304	0.038000	0.13279	0.959000	0.29240	1.830000	0.53286	0.556000	0.70494	GAC	C|0.899;T|0.101	0.101	strong		0.622	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
ELL2	22936	hgsc.bcm.edu	37	5	95236415	95236415	+	Silent	SNP	G	G	A	rs17085249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:95236415G>A	ENST00000237853.4	-	7	1285	c.936C>T	c.(934-936)gaC>gaT	p.D312D	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	312					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.D312D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		AAGATACAGCGTCTCTACTAG	0.413													G|||	1706	0.340655	0.3654	0.2406	5008	,	,		19046	0.4325		0.2793	False		,,,				2504	0.3466				p.D312D		Atlas-SNP	.											ELL2,NS,carcinoma,0,1	ELL2	63	1	1	Substitution - coding silent(1)	prostate(1)	c.C936T						scavenged	.	G		1503,2903	478.5+/-358.2	256,991,956	75.0	73.0	73.0		936	-8.4	0.0	5	dbSNP_123	73	2247,6353	380.4+/-339.6	290,1667,2343	no	coding-synonymous	ELL2	NM_012081.5		546,2658,3299	AA,AG,GG		26.1279,34.1126,28.8328		312/641	95236415	3750,9256	2203	4300	6503	SO:0001819	synonymous_variant	22936	exon7			TACAGCGTCTCTA	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.936C>T	5.37:g.95236415G>A		Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	197	89	0.451777	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	37	CCDS4080.1																																																																																			G|0.697;A|0.303	0.303	strong		0.413	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
KRT73	319101	hgsc.bcm.edu	37	12	53011955	53011955	+	Silent	SNP	G	G	A	rs61736102	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53011955G>A	ENST00000305748.3	-	1	388	c.354C>T	c.(352-354)aaC>aaT	p.N118N	RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	118	Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCAGCTCCACGTTCAGGGGTG	0.592													G|||	1004	0.200479	0.152	0.1023	5008	,	,		16598	0.4454		0.1471	False		,,,				2504	0.138				p.N118N		Atlas-SNP	.											.	KRT73	101	.	0			c.C354T						PASS	.	G		675,3731	285.2+/-278.0	54,567,1582	124.0	125.0	125.0		354	-1.9	1.0	12	dbSNP_129	125	1284,7316	254.1+/-279.5	96,1092,3112	no	coding-synonymous	KRT73	NM_175068.2		150,1659,4694	AA,AG,GG		14.9302,15.32,15.0623		118/541	53011955	1959,11047	2203	4300	6503	SO:0001819	synonymous_variant	319101	exon1			CTCCACGTTCAGG	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.354C>T	12.37:g.53011955G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	173	82	0.473988	NM_175068	Q32MB2	Silent	SNP	ENST00000305748.3	37	CCDS8834.1																																																																																			G|0.827;A|0.173	0.173	strong		0.592	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
TBC1D32	221322	hgsc.bcm.edu	37	6	121602795	121602795	+	Silent	SNP	C	C	T	rs79788801	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:121602795C>T	ENST00000398212.2	-	14	1552	c.1503G>A	c.(1501-1503)ctG>ctA	p.L501L	TBC1D32_ENST00000275159.6_Silent_p.L501L	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	501					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.L501L(1)									TGAGTATCCACAGAACTTCAG	0.294													T|||	273	0.0545128	0.034	0.1196	5008	,	,		14544	0.124		0.0109	False		,,,				2504	0.0092				p.L501L		Atlas-SNP	.											C6orf170,NS,carcinoma,0,1	C6orf170	146	1	1	Substitution - coding silent(1)	stomach(1)	c.G1503A						PASS	.	T		107,3537		3,101,1718	95.0	90.0	92.0		1503	-9.2	0.0	6	dbSNP_131	92	95,8049		0,95,3977	no	coding-synonymous	C6orf170	NM_152730.4		3,196,5695	TT,TC,CC		1.1665,2.9363,1.7136		501/1258	121602795	202,11586	1822	4072	5894	SO:0001819	synonymous_variant	221322	exon14			TATCCACAGAACT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1503G>A	6.37:g.121602795C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	131	69	0.526718	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																			C|0.954;T|0.046	0.046	strong		0.294	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
PCDHGA1	56114	hgsc.bcm.edu	37	5	140712210	140712210	+	Silent	SNP	G	G	T	rs62378403	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140712210G>T	ENST00000517417.1	+	1	1959	c.1959G>T	c.(1957-1959)ccG>ccT	p.P653P	PCDHGA1_ENST00000378105.3_Silent_p.P653P	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	653	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCAGCCCCCGCTCTCCGCCA	0.697													g|||	1021	0.203874	0.2474	0.2032	5008	,	,		14206	0.2401		0.1372	False		,,,				2504	0.1769				p.P653P		Atlas-SNP	.											PCDHGA1_ENST00000517417,NS,carcinoma,0,2	PCDHGA1	397	2	0			c.G1959T						scavenged	.	T	,	312,4048		33,246,1901	31.0	41.0	37.0		1959,1959	-0.2	1.0	5	dbSNP_129	37	439,8145		44,351,3897	no	coding-synonymous,coding-synonymous	PCDHGA1	NM_018912.2,NM_031993.1	,	77,597,5798	TT,TG,GG		5.1142,7.156,5.8019	,	653/932,653/824	140712210	751,12193	2180	4292	6472	SO:0001819	synonymous_variant	56114	exon1			GCCCCCGCTCTCC	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1959G>T	5.37:g.140712210G>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	37	23	0.621622	NM_018912	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	37	CCDS54922.1																																																																																			G|0.826;T|0.174	0.174	strong		0.697	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912	
Unknown	0	hgsc.bcm.edu	37	11	124095647	124095647	+	IGR	SNP	A	A	C	rs2466615	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124095647A>C								OR10D3 (38695 upstream) : OR8G1 (24775 downstream)																							CTTCATTGATATCTGCCATTC	0.458													N|||	3145	0.627995	0.8404	0.5648	5008	,	,		22560	0.4831		0.4831	False		,,,				2504	0.684				p.I84L		Atlas-SNP	.											.	.	.	.	0			c.A250C						PASS	.	C	LEU/ILE	3371,907		1339,693,107	159.0	158.0	159.0		250	0.9	0.1	11	dbSNP_100	159	4180,4386		1032,2116,1135	yes	missense	OR8G2	NM_001007249.1	5	2371,2809,1242	CC,CA,AA		48.7976,21.2015,41.2099	benign	84/305	124095647	7551,5293	2139	4283	6422	SO:0001628	intergenic_variant	26492	exon1			ATTGATATCTGCC																													11.37:g.124095647A>C		Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	209	206	0.985646	NM_001007249		Missense_Mutation	SNP		37																																																																																				A|0.408;C|0.592	0.592	strong	0	0.458								
UTRN	7402	hgsc.bcm.edu	37	6	144743015	144743015	+	Splice_Site	SNP	G	G	A	rs114750149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:144743015G>A	ENST00000367545.3	+	3	143	c.143G>A	c.(142-144)aGt>aAt	p.S48N		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	48	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		CTTTTACAGAGTGGGAAACCA	0.403													G|||	33	0.00658946	0.0038	0.0115	5008	,	,		14452	0.0		0.0159	False		,,,				2504	0.0041				p.S48N		Atlas-SNP	.											.	UTRN	327	.	0			c.G143A						PASS	.	G	ASN/SER	14,4392	22.3+/-47.3	0,14,2189	95.0	82.0	86.0		143	6.0	1.0	6	dbSNP_132	86	133,8467	67.3+/-129.8	1,131,4168	yes	missense-near-splice	UTRN	NM_007124.2	46	1,145,6357	AA,AG,GG		1.5465,0.3177,1.1302	possibly-damaging	48/3434	144743015	147,12859	2203	4300	6503	SO:0001630	splice_region_variant	7402	exon3			TACAGAGTGGGAA	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.142-1G>A	6.37:g.144743015G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	17	0.007783882783882784	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	12	0.0158311345646438	G	16.41	3.114963	0.56505	0.003177	0.015465	ENSG00000152818	ENST00000367529;ENST00000367545;ENST00000421035	D;D	0.95001	-3.58;-3.58	6.03	6.03	0.97812	Calponin homology domain (5);	0.000000	0.56097	D	0.000031	D	0.86879	0.6039	N	0.12569	0.235	0.80722	D	1	P	0.36733	0.567	B	0.40702	0.338	D	0.88088	0.2811	10	0.45353	T	0.12	.	15.973	0.80034	0.0:0.1339:0.8661:0.0	.	48	P46939	UTRO_HUMAN	N	48;48;53	ENSP00000356515:S48N;ENSP00000396276:S53N	ENSP00000356499:S48N	S	+	2	0	UTRN	144784708	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	5.174000	0.65015	2.861000	0.98227	0.655000	0.94253	AGT	G|0.990;A|0.010	0.010	strong		0.403	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		Missense_Mutation
TBC1D4	9882	hgsc.bcm.edu	37	13	76055726	76055726	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:76055726C>T	ENST00000377636.3	-	1	524	c.178G>A	c.(178-180)Gcc>Acc	p.A60T	TBC1D4_ENST00000431480.2_Missense_Mutation_p.A60T|TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000377625.2_Missense_Mutation_p.A60T	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	60	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		CGGATCTCGGCCATGAGCCAG	0.716																																					p.A60T		Atlas-SNP	.											.	TBC1D4	142	.	0			c.G178A						PASS	.						9.0	11.0	11.0					13																	76055726		1891	4103	5994	SO:0001583	missense	9882	exon1			TCTCGGCCATGAG	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.178G>A	13.37:g.76055726C>T	ENSP00000366863:p.Ala60Thr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	52	4	0.0769231	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	C	34	5.373372	0.95923	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625	T;T;T	0.55930	0.49;0.49;0.49	3.95	3.95	0.45737	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.000000	0.49916	D	0.000138	T	0.70386	0.3218	M	0.68593	2.085	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.996	T	0.75459	-0.3310	10	0.72032	D	0.01	-9.0239	16.1706	0.81812	0.0:1.0:0.0:0.0	.	60;60;60	O60343-2;O60343-3;O60343	.;.;TBCD4_HUMAN	T	60	ENSP00000366863:A60T;ENSP00000395986:A60T;ENSP00000366852:A60T	ENSP00000366852:A60T	A	-	1	0	TBC1D4	74953727	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.673000	0.74482	2.017000	0.59298	0.561000	0.74099	GCC	.	.	none		0.716	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
COL4A1	1282	hgsc.bcm.edu	37	13	110804809	110804809	+	Silent	SNP	G	G	A	rs650724	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:110804809G>A	ENST00000375820.4	-	51	4921	c.4800C>T	c.(4798-4800)tcC>tcT	p.S1600S		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1600	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			AGGAGCCGGGGGACGCCAGGG	0.597													G|||	634	0.126597	0.2292	0.2277	5008	,	,		18525	0.0089		0.1074	False		,,,				2504	0.0573				p.S1600S		Atlas-SNP	.											.	COL4A1	372	.	0			c.C4800T						PASS	.	G		893,3513	338.6+/-305.4	91,711,1401	46.0	40.0	42.0		4800	-0.8	0.3	13	dbSNP_83	42	849,7751	189.7+/-236.4	35,779,3486	no	coding-synonymous	COL4A1	NM_001845.4		126,1490,4887	AA,AG,GG		9.8721,20.2678,13.3938		1600/1670	110804809	1742,11264	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon51			GCCGGGGGACGCC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.4800C>T	13.37:g.110804809G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			G|0.870;A|0.130	0.130	strong		0.597	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
SLC6A5	9152	hgsc.bcm.edu	37	11	20623023	20623023	+	Silent	SNP	C	C	T	rs2241941	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:20623023C>T	ENST00000525748.1	+	2	625	c.352C>T	c.(352-354)Ctg>Ttg	p.L118L		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	118					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	CGGCAACGCGCTGCACTGTAA	0.701													C|||	1637	0.326877	0.326	0.3199	5008	,	,		15702	0.3641		0.3489	False		,,,				2504	0.272				p.L118L		Atlas-SNP	.											.	SLC6A5	151	.	0			c.C352T						PASS	.	C		1389,3017		206,977,1020	44.0	44.0	44.0		352	1.7	0.9	11	dbSNP_98	44	2831,5767		472,1887,1940	no	coding-synonymous	SLC6A5	NM_004211.3		678,2864,2960	TT,TC,CC		32.9263,31.5252,32.4516		118/798	20623023	4220,8784	2203	4299	6502	SO:0001819	synonymous_variant	9152	exon2			AACGCGCTGCACT	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.352C>T	11.37:g.20623023C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	37	CCDS7854.1																																																																																			C|0.662;A|0.004	.	strong		0.701	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
HSPG2	3339	hgsc.bcm.edu	37	1	22200998	22200998	+	Missense_Mutation	SNP	C	C	T	rs2229481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22200998C>T	ENST00000374695.3	-	28	3636	c.3557G>A	c.(3556-3558)cGg>cAg	p.R1186Q		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1186	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.		R -> Q (in dbSNP:rs2229481).		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CTGCTCACACCGAGGGCCCTC	0.682													C|||	320	0.0638978	0.1967	0.0432	5008	,	,		17120	0.0		0.0219	False		,,,				2504	0.0082				p.R1186Q		Atlas-SNP	.											.	HSPG2	311	.	0			c.G3557A						PASS	.	C	GLN/ARG	768,3638	290.1+/-280.8	57,654,1492	31.0	31.0	31.0		3557	0.2	1.0	1	dbSNP_98	31	256,8344	96.1+/-157.9	4,248,4048	yes	missense	HSPG2	NM_005529.5	43	61,902,5540	TT,TC,CC		2.9767,17.4308,7.8733	benign	1186/4392	22200998	1024,11982	2203	4300	6503	SO:0001583	missense	3339	exon28			TCACACCGAGGGC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.3557G>A	1.37:g.22200998C>T	ENSP00000363827:p.Arg1186Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	188	91	0.484043	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	152	0.0695970695970696	97	0.19715447154471544	22	0.06077348066298342	6	0.01048951048951049	27	0.03562005277044855	C	11.48	1.651776	0.29336	0.174308	0.029767	ENSG00000142798	ENST00000374695	T	0.61859	0.07	4.93	0.185	0.15096	EGF-like, laminin (4);	0.899723	0.09017	N	0.860725	T	0.00039	0.0001	N	0.04768	-0.165	0.44966	P	0.0020120000000000138	B	0.09022	0.002	B	0.10450	0.005	T	0.14476	-1.0471	9	0.25106	T	0.35	.	8.6369	0.33953	0.0:0.242:0.0:0.758	rs2229481;rs58148193;rs2229481	1186	P98160	PGBM_HUMAN	Q	1186	ENSP00000363827:R1186Q	ENSP00000363827:R1186Q	R	-	2	0	HSPG2	22073585	0.005000	0.15991	0.982000	0.44146	0.734000	0.41952	-0.080000	0.11339	-0.211000	0.10124	-0.480000	0.04831	CGG	C|0.915;T|0.085	0.085	strong		0.682	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
HGFAC	3083	hgsc.bcm.edu	37	4	3444593	3444593	+	Silent	SNP	G	G	A	rs2073504	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:3444593G>A	ENST00000382774.3	+	2	367	c.252G>A	c.(250-252)ccG>ccA	p.P84P	HGFAC_ENST00000511533.1_Silent_p.P84P	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	84					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGGGGCTCCCGCCCCCGCCCA	0.672													G|||	1155	0.230631	0.2057	0.2291	5008	,	,		15322	0.372		0.175	False		,,,				2504	0.1769				p.P84P		Atlas-SNP	.											HGFAC,NS,carcinoma,0,1	HGFAC	69	1	0			c.G252A						PASS	.	G		927,3473	330.4+/-301.5	90,747,1363	43.0	51.0	48.0		252	-1.1	0.0	4	dbSNP_96	48	1407,7191	265.7+/-286.3	119,1169,3011	yes	coding-synonymous	HGFAC	NM_001528.2		209,1916,4374	AA,AG,GG		16.3643,21.0682,17.9566		84/656	3444593	2334,10664	2200	4299	6499	SO:0001819	synonymous_variant	3083	exon2			GCTCCCGCCCCCG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.252G>A	4.37:g.3444593G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	37	CCDS3369.1																																																																																			G|0.806;A|0.194	0.194	strong		0.672	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
CCDC141	285025	hgsc.bcm.edu	37	2	179749720	179749720	+	Missense_Mutation	SNP	G	G	C	rs199718873		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179749720G>C	ENST00000409284.1	-	11	1744	c.1627C>G	c.(1627-1629)Cta>Gta	p.L543V	CCDC141_ENST00000295723.5_5'Flank|CCDC141_ENST00000420890.2_Missense_Mutation_p.L543V			Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	543										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TCTTCTGCTAGCCATCTAGCT	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		20422	0.0		0.001	False		,,,				2504	0.0				p.L543V		Atlas-SNP	.											.	CCDC141	362	.	0			c.C1627G						PASS	.																																			SO:0001583	missense	285025	exon11			CTGCTAGCCATCT	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26821	protein-coding gene	gene with protein product	"""coiled-coil protein associated with myosin II and DISC1"""					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000409284.1:c.1627C>G	2.37:g.179749720G>C	ENSP00000386503:p.Leu543Val	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	266	145	0.545113	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000409284.1	37		.	.	.	.	.	.	.	.	.	.	G	15.06	2.721922	0.48728	.	.	ENSG00000163492	ENST00000420890;ENST00000443758;ENST00000446116;ENST00000409284	T;T	0.63096	-0.02;0.36	5.33	4.42	0.53409	.	.	.	.	.	T	0.53965	0.1829	L	0.59436	1.845	0.80722	D	1	P	0.48294	0.908	B	0.36922	0.236	T	0.58645	-0.7600	8	.	.	.	.	12.621	0.56603	0.0:0.0:0.8349:0.1651	.	543	B8ZZB3	.	V	543;543;478;543	ENSP00000395995:L543V;ENSP00000390190:L543V	.	L	-	1	2	CCDC141	179457965	0.990000	0.36364	0.998000	0.56505	0.327000	0.28475	1.785000	0.38684	2.489000	0.83994	0.591000	0.81541	CTA	G|0.999;C|0.001	0.001	weak		0.393	CCDC141-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000335873.1	NM_173648	
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117359	46117359	+	Silent	SNP	G	G	A	rs183770957	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:46117359G>A	ENST00000400365.3	+	1	273	c.243G>A	c.(241-243)acG>acA	p.T81T	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	81	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						GCTCCTGCACGCCCTCGTGCT	0.672													g|||	11	0.00219649	0.0008	0.0	5008	,	,		17438	0.0		0.0089	False		,,,				2504	0.001				p.T81T		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.G243A						PASS	.	A	,	4,4396		0,4,2196	62.0	71.0	68.0		,243	-6.1	0.0	21		68	70,8514		0,70,4222	no	intron,coding-synonymous	TSPEAR,KRTAP10-12	NM_144991.2,NM_198699.1	,	0,74,6418	AA,AG,GG		0.8155,0.0909,0.5699	,	,81/246	46117359	74,12910	2200	4292	6492	SO:0001819	synonymous_variant	386685	exon1			CTGCACGCCCTCG	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"""Keratin associated proteins"""	20533	protein-coding gene	gene with protein product			"""keratin associated protein 18-12"""	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.243G>A	21.37:g.46117359G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_198699	B2RPA3	Silent	SNP	ENST00000400365.3	37	CCDS42967.1																																																																																			G|0.994;A|0.006	0.006	strong		0.672	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699	
NCKAP5	344148	hgsc.bcm.edu	37	2	133489601	133489601	+	Silent	SNP	A	A	G	rs56284623	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:133489601A>G	ENST00000409261.1	-	17	5525	c.5152T>C	c.(5152-5154)Ttg>Ctg	p.L1718L	NCKAP5_ENST00000317721.6_Silent_p.L1718L|NCKAP5_ENST00000473859.1_5'UTR|NCKAP5_ENST00000405974.3_Silent_p.L399L|NCKAP5_ENST00000409213.1_Silent_p.L399L	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1718										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CCACTGTCCAATGTTCTCATC	0.502													A|||	784	0.15655	0.0492	0.1499	5008	,	,		19816	0.1002		0.2634	False		,,,				2504	0.2546				p.L1718L		Atlas-SNP	.											.	NCKAP5	322	.	0			c.T5152C						PASS	.	A	,	316,3612		15,286,1663	51.0	53.0	52.0		5152,1195	-2.9	0.0	2	dbSNP_129	52	2221,6087		298,1625,2231	no	coding-synonymous,coding-synonymous	NCKAP5	NM_207363.2,NM_207481.3	,	313,1911,3894	GG,GA,AA		26.7333,8.0448,20.7339	,	1718/1910,399/591	133489601	2537,9699	1964	4154	6118	SO:0001819	synonymous_variant	344148	exon17			TGTCCAATGTTCT	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.5152T>C	2.37:g.133489601A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			A|0.822;G|0.178	0.178	strong		0.502	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
GSTZ1	2954	hgsc.bcm.edu	37	14	77793237	77793237	+	Missense_Mutation	SNP	G	G	A	rs7972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77793237G>A	ENST00000556627.1	+	3	255	c.124G>A	c.(124-126)Ggg>Agg	p.G42R	GSTZ1_ENST00000557053.1_5'UTR|GSTZ1_ENST00000393734.1_5'UTR|GSTZ1_ENST00000553586.1_Missense_Mutation_p.G43R|GSTZ1_ENST00000349555.3_Missense_Mutation_p.G42R|GSTZ1_ENST00000216465.5_Missense_Mutation_p.G42R|GSTZ1_ENST00000554279.1_Missense_Mutation_p.G42R|GSTZ1_ENST00000361389.4_5'UTR|GSTZ1_ENST00000557639.1_5'UTR			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	42	GST N-terminal.		R -> G (in allele GSTZ1*B and allele GSTZ1*C; dbSNP:rs7972). {ECO:0000269|PubMed:10373324, ECO:0000269|PubMed:10739172, ECO:0000269|PubMed:12508121, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9417084, ECO:0000269|PubMed:9925947, ECO:0000269|Ref.6, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		cellular nitrogen compound metabolic process (GO:0034641)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|L-phenylalanine catabolic process (GO:0006559)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|maleylacetoacetate isomerase activity (GO:0016034)|protein homodimerization activity (GO:0042803)			lung(2)|prostate(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	CATAAAGGATGGGGGCCAACA	0.567													G|||	153	0.0305511	0.0038	0.0274	5008	,	,		21279	0.0		0.1113	False		,,,				2504	0.0174				p.G42R		Atlas-SNP	.											.	GSTZ1	35	.	0			c.G124A						PASS	.	G	,ARG/GLY,ARG/GLY	78,4326	62.9+/-100.1	0,78,2124	43.0	35.0	37.0		,124,124	5.6	1.0	14	dbSNP_52	37	707,7893	164.3+/-216.7	41,625,3634	yes	utr-5,missense,missense	GSTZ1	NM_001513.3,NM_145870.2,NM_145871.2	,125,125	41,703,5758	AA,AG,GG		8.2209,1.7711,6.0366	,benign,benign	,42/217,42/175	77793237	785,12219	2202	4300	6502	SO:0001583	missense	2954	exon3			AAGGATGGGGGCC	U86529	CCDS9858.1, CCDS9859.1, CCDS9860.1	14q24.3	2012-06-22	2012-06-22		ENSG00000100577	ENSG00000100577	5.2.1.2, 2.5.1.18	"""Glutathione S-transferases / Soluble"""	4643	protein-coding gene	gene with protein product	"""maleylacetoacetate isomerase"""	603758	"""glutathione transferase zeta 1"""			9396740, 9417084	Standard	NM_001513		Approved	GSTZ1-1, MAAI, MAI	uc001xtj.3	O43708	OTTHUMG00000171551	ENST00000556627.1:c.124G>A	14.37:g.77793237G>A	ENSP00000450487:p.Gly42Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	27	0.391304	NM_145871	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	37		109	0.04990842490842491	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	96	0.1266490765171504	G	28.3	4.909294	0.92107	0.017711	0.082209	ENSG00000100577	ENST00000216465;ENST00000554279;ENST00000349555;ENST00000556627;ENST00000553586	T;T;T;T;T	0.18810	4.45;3.14;2.19;2.36;4.44	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.00637	0.0021	.	.	.	0.09310	P	1.0	D	0.89917	1.0	D	0.83275	0.996	T	0.00335	-1.1808	8	0.72032	D	0.01	-6.8373	16.4581	0.84029	0.0:0.0:1.0:0.0	rs7972;rs1128968;rs2266617;rs3177429;rs3186383;rs11551317;rs17353483;rs17750846;rs52835763;rs58270987;rs7972	42	A6NED0	.	R	42;42;42;42;43	ENSP00000216465:G42R;ENSP00000452498:G42R;ENSP00000314404:G42R;ENSP00000450487:G42R;ENSP00000451976:G43R	ENSP00000216465:G42R	G	+	1	0	GSTZ1	76862990	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.705000	0.68355	2.614000	0.88457	0.655000	0.94253	GGG	G|0.949;A|0.051	0.051	strong		0.567	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870	
GATA4	2626	hgsc.bcm.edu	37	8	11614575	11614575	+	Missense_Mutation	SNP	A	A	G	rs3729856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11614575A>G	ENST00000335135.4	+	6	1687	c.1129A>G	c.(1129-1131)Agc>Ggc	p.S377G	GATA4_ENST00000528712.1_Missense_Mutation_p.S171G|GATA4_ENST00000532059.1_Missense_Mutation_p.S378G	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	377			S -> G (in dbSNP:rs3729856).		atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		CTACGGGCACAGCAGCTCCGT	0.657													A|||	215	0.0429313	0.0098	0.0677	5008	,	,		19680	0.001		0.1193	False		,,,				2504	0.0348				p.S377G		Atlas-SNP	.											.	GATA4	29	.	0			c.A1129G						PASS	.	A	GLY/SER	104,4302	82.4+/-120.9	2,100,2101	78.0	60.0	66.0		1129	0.9	1.0	8	dbSNP_107	66	1204,7396	240.7+/-271.3	100,1004,3196	yes	missense	GATA4	NM_002052.3	56	102,1104,5297	GG,GA,AA		14.0,2.3604,10.0569	benign	377/443	11614575	1308,11698	2203	4300	6503	SO:0001583	missense	2626	exon6			GGGCACAGCAGCT	AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574		"""GATA zinc finger domain containing"""	4173	protein-coding gene	gene with protein product		600576	"""GATA-binding protein 4"""			7665171	Standard	NM_002052		Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.1129A>G	8.37:g.11614575A>G	ENSP00000334458:p.Ser377Gly	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	290	130	0.448276	NM_002052	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	Missense_Mutation	SNP	ENST00000335135.4	37	CCDS5983.1	134	0.06135531135531135	6	0.012195121951219513	29	0.08011049723756906	1	0.0017482517482517483	98	0.12928759894459102	A	11.91	1.779594	0.31502	0.023604	0.14	ENSG00000136574	ENST00000528712;ENST00000526716;ENST00000335135;ENST00000259090;ENST00000532059	D;D;D;D	0.98996	-5.31;-5.1;-4.73;-4.73	5.83	0.906	0.19314	.	0.470389	0.23169	N	0.051149	T	0.19485	0.0468	L	0.42245	1.32	0.32041	P	0.59825	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.73538	-0.3951	9	0.18710	T	0.47	-21.9862	1.7073	0.02884	0.4155:0.1484:0.3085:0.1276	rs3729856;rs3729856	378;377	B7ZKZ4;P43694	.;GATA4_HUMAN	G	171;171;377;376;378	ENSP00000435043:S171G;ENSP00000435347:S171G;ENSP00000334458:S377G;ENSP00000435712:S378G	ENSP00000259090:S376G	S	+	1	0	GATA4	11651984	0.849000	0.29639	0.991000	0.47740	0.550000	0.35303	0.243000	0.18106	0.140000	0.18849	-0.256000	0.11100	AGC	A|0.912;G|0.088	0.088	strong		0.657	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207587.2	NM_002052	
NUP107	57122	hgsc.bcm.edu	37	12	69082805	69082805	+	Silent	SNP	G	G	A	rs2259588	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:69082805G>A	ENST00000229179.4	+	2	404	c.72G>A	c.(70-72)cgG>cgA	p.R24R	NUP107_ENST00000378905.2_5'UTR|NUP107_ENST00000539906.1_5'UTR|RP11-637A17.2_ENST00000500695.2_lincRNA	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	24					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			GGACTGCACGGAAACAGAGTG	0.383													G|||	1105	0.220647	0.0582	0.2983	5008	,	,		18358	0.3065		0.2903	False		,,,				2504	0.2249				p.R24R		Atlas-SNP	.											NUP107,NS,carcinoma,+2,1	NUP107	88	1	0			c.G72A						PASS	.	G		404,4002	200.4+/-223.7	20,364,1819	140.0	132.0	135.0		72	-1.5	0.9	12	dbSNP_100	135	2322,6278	390.4+/-343.3	314,1694,2292	no	coding-synonymous	NUP107	NM_020401.2		334,2058,4111	AA,AG,GG		27.0,9.1693,20.9596		24/926	69082805	2726,10280	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon2			TGCACGGAAACAG	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.72G>A	12.37:g.69082805G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			G|0.777;A|0.223	0.223	strong		0.383	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
SPEF2	79925	hgsc.bcm.edu	37	5	35654711	35654711	+	Silent	SNP	C	C	T	rs2270558	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:35654711C>T	ENST00000356031.3	+	7	1015	c.861C>T	c.(859-861)gaC>gaT	p.D287D	SPEF2_ENST00000440995.2_Silent_p.D287D|SPEF2_ENST00000509059.1_Silent_p.D287D|SPEF2_ENST00000282469.6_Silent_p.D287D	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	287					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACTCAGATGACGAGTACATTA	0.368													C|||	3391	0.677117	0.7194	0.683	5008	,	,		16471	0.7401		0.5229	False		,,,				2504	0.7096				p.D287D		Atlas-SNP	.											SPEF2,NS,carcinoma,+2,1	SPEF2	324	1	0			c.C861T						scavenged	.	C	,	3037,1369	672.6+/-402.7	1029,979,195	73.0	75.0	74.0		861,861	-3.9	1.0	5	dbSNP_100	74	4662,3938	602.0+/-394.5	1232,2198,870	no	coding-synonymous,coding-synonymous	SPEF2	NM_024867.3,NM_144722.3	,	2261,3177,1065	TT,TC,CC		45.7907,31.0713,40.8042	,	287/1823,287/515	35654711	7699,5307	2203	4300	6503	SO:0001819	synonymous_variant	79925	exon7			AGATGACGAGTAC	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"""cancer/testis antigen 122"""	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.861C>T	5.37:g.35654711C>T		Somatic	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	144	69	0.479167	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Silent	SNP	ENST00000356031.3	37	CCDS43309.1																																																																																			C|0.379;A|0.004	.	strong		0.368	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
CAMTA2	23125	hgsc.bcm.edu	37	17	4875566	4875566	+	Silent	SNP	T	T	C	rs238230	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4875566T>C	ENST00000348066.3	-	16	2892	c.2769A>G	c.(2767-2769)ccA>ccG	p.P923P	CAMTA2_ENST00000361571.5_Silent_p.P922P|RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000381311.5_Silent_p.P925P|CAMTA2_ENST00000414043.3_Silent_p.P946P|CAMTA2_ENST00000358183.4_Silent_p.P923P|CAMTA2_ENST00000572543.1_Silent_p.P928P	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	923					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						CAGCGTCCTCTGGAGCAGCCC	0.587													T|||	2889	0.576877	0.7882	0.6599	5008	,	,		17313	0.4028		0.5875	False		,,,				2504	0.4008				p.P946P		Atlas-SNP	.											.	CAMTA2	93	.	0			c.A2838G						PASS	.	T	,,,	3428,978	724.0+/-409.5	1338,752,113	67.0	72.0	71.0		2775,2838,2766,2769	-0.5	1.0	17	dbSNP_79	71	5334,3266	642.3+/-399.8	1650,2034,616	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMTA2	NM_001171166.1,NM_001171167.1,NM_001171168.1,NM_015099.3	,,,	2988,2786,729	CC,CT,TT		37.9767,22.197,32.6311	,,,	925/1198,946/1242,922/1202,923/1203	4875566	8762,4244	2203	4300	6503	SO:0001819	synonymous_variant	23125	exon16			GTCCTCTGGAGCA	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.2769A>G	17.37:g.4875566T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Silent	SNP	ENST00000348066.3	37	CCDS11063.1																																																																																			T|0.359;C|0.641	0.641	strong		0.587	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099	
DNAH5	1767	hgsc.bcm.edu	37	5	13780991	13780991	+	Silent	SNP	C	C	T	rs111995400	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13780991C>T	ENST00000265104.4	-	53	9002	c.8898G>A	c.(8896-8898)acG>acA	p.T2966T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2966	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AAGCCAACCTCGTCAGGCTCT	0.463									Kartagener syndrome				C|||	52	0.0103834	0.0015	0.0101	5008	,	,		18879	0.0		0.0398	False		,,,				2504	0.0031				p.T2966T		Atlas-SNP	.											.	DNAH5	868	.	0			c.G8898A						PASS	.	C		22,4384	30.8+/-60.4	0,22,2181	94.0	80.0	85.0		8898	-11.1	0.7	5	dbSNP_132	85	272,8328	104.0+/-165.0	3,266,4031	no	coding-synonymous	DNAH5	NM_001369.2		3,288,6212	TT,TC,CC		3.1628,0.4993,2.2605		2966/4625	13780991	294,12712	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon53	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAACCTCGTCAGG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.8898G>A	5.37:g.13780991C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			C|0.979;T|0.021	0.021	strong		0.463	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
GPR146	115330	hgsc.bcm.edu	37	7	1097183	1097183	+	Missense_Mutation	SNP	G	G	A	rs11761941	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1097183G>A	ENST00000397095.1	+	2	255	c.32G>A	c.(31-33)gGg>gAg	p.G11E	C7orf50_ENST00000397100.2_Intron|GPR146_ENST00000297468.3_Missense_Mutation_p.G11E|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000357429.6_Intron			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	11						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		AACGGCACAGGGCTGGTGGAG	0.677													G|||	345	0.0688898	0.0204	0.0821	5008	,	,		17500	0.0		0.1262	False		,,,				2504	0.137				p.G11E		Atlas-SNP	.											.	GPR146	20	.	0			c.G32A						PASS	.		,,,GLU/GLY	204,4192		2,200,1996	29.0	28.0	28.0		,,,32	-2.5	0.0	7	dbSNP_120	28	1342,7256		105,1132,3062	yes	intron,intron,intron,missense	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,98	107,1332,5058	AA,AG,GG		15.6083,4.6406,11.8978	,,,benign	,,,11/334	1097183	1546,11448	2198	4299	6497	SO:0001583	missense	115330	exon1			GCACAGGGCTGGT	BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"""GPCR / Class A : Orphans"""	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.32G>A	7.37:g.1097183G>A	ENSP00000380283:p.Gly11Glu	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	135	69	0.511111	NM_138445	Q86SP5	Missense_Mutation	SNP	ENST00000397095.1	37	CCDS5321.1	143	0.06547619047619048	10	0.02032520325203252	31	0.0856353591160221	0	0.0	102	0.1345646437994723	G	0.662	-0.805227	0.02819	0.046406	0.156083	ENSG00000164849	ENST00000444847;ENST00000397095;ENST00000427680;ENST00000297468	T;T;T	0.36340	1.26;1.26;1.26	5.12	-2.48	0.06423	.	0.771901	0.12341	N	0.477461	T	0.00073	0.0002	L	0.34521	1.04	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.25117	-1.0141	9	0.06625	T	0.88	-6.8234	0.5541	0.00668	0.3465:0.1291:0.2796:0.2448	rs11761941	11	Q96CH1	GP146_HUMAN	E	11	ENSP00000410743:G11E;ENSP00000380283:G11E;ENSP00000297468:G11E	ENSP00000297468:G11E	G	+	2	0	GPR146	1063709	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.135000	0.15952	-0.364000	0.08088	0.561000	0.74099	GGG	G|0.903;A|0.097	0.097	strong		0.677	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
MAVS	57506	hgsc.bcm.edu	37	20	3844929	3844929	+	Missense_Mutation	SNP	C	C	T	rs45437096	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3844929C>T	ENST00000428216.2	+	6	780	c.652C>T	c.(652-654)Cgt>Tgt	p.R218C	MAVS_ENST00000358134.6_3'UTR|MAVS_ENST00000416600.2_Missense_Mutation_p.R77C	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	218					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						CACACCATCCCGTGGGCCTGT	0.602													C|||	263	0.052516	0.0106	0.0893	5008	,	,		18036	0.0		0.159	False		,,,				2504	0.0276				p.R218C		Atlas-SNP	.											.	MAVS	34	.	0			c.C652T						PASS	.	C	CYS/ARG,CYS/ARG	169,4237	111.6+/-149.8	6,157,2040	91.0	91.0	91.0		229,652	0.3	0.0	20	dbSNP_127	91	1418,7182	272.7+/-290.2	110,1198,2992	yes	missense,missense	MAVS	NM_001206491.1,NM_020746.4	180,180	116,1355,5032	TT,TC,CC		16.4884,3.8357,12.2021	benign,benign	77/400,218/541	3844929	1587,11419	2203	4300	6503	SO:0001583	missense	57506	exon6			CCATCCCGTGGGC	DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"""virus-induced signaling adaptor"", ""IFN-B promoter stimulator 1"", ""CARD adaptor inducing IFN-beta"""	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.652C>T	20.37:g.3844929C>T	ENSP00000401980:p.Arg218Cys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Missense_Mutation	SNP	ENST00000428216.2	37	CCDS33437.1	163	0.07463369963369963	5	0.01016260162601626	38	0.10497237569060773	0	0.0	120	0.158311345646438	C	15.29	2.789708	0.50102	0.038357	0.164884	ENSG00000088888	ENST00000416600;ENST00000428216	T;T	0.34072	1.38;2.34	4.72	0.349	0.16032	.	1.472750	0.03891	N	0.278641	T	0.00109	0.0003	L	0.42245	1.32	0.80722	P	0.0	B	0.15930	0.015	B	0.12837	0.008	T	0.10965	-1.0607	9	0.34782	T	0.22	2.0676	4.4764	0.11746	0.0:0.5479:0.163:0.2891	rs45437096;rs62210536	218	Q7Z434	MAVS_HUMAN	C	77;218	ENSP00000413749:R77C;ENSP00000401980:R218C	ENSP00000413749:R77C	R	+	1	0	MAVS	3792929	0.000000	0.05858	0.012000	0.15200	0.954000	0.61252	-0.940000	0.03929	0.018000	0.15052	0.650000	0.86243	CGT	C|0.888;T|0.112	0.112	strong		0.602	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746	
ABCA2	20	hgsc.bcm.edu	37	9	139911983	139911983	+	Silent	SNP	T	T	G	rs12348881	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139911983T>G	ENST00000371605.3	-	16	2517	c.2370A>C	c.(2368-2370)gcA>gcC	p.A790A	ABCA2_ENST00000341511.6_Silent_p.A791A|ABCA2_ENST00000492260.1_5'Flank|ABCA2_ENST00000265662.5_Silent_p.A791A			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	790					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CCGCGTAGACTGCCAGGAAGA	0.607													G|||	523	0.104433	0.1853	0.0994	5008	,	,		18298	0.0337		0.1074	False		,,,				2504	0.0685				p.A821A		Atlas-SNP	.											.	ABCA2	113	.	0			c.A2463C						PASS	.	G	,	821,3489		92,637,1426	57.0	66.0	63.0		2373,2463	-8.2	0.3	9	dbSNP_120	63	831,7649		38,755,3447	yes	coding-synonymous,coding-synonymous	ABCA2	NM_001606.4,NM_212533.2	,	130,1392,4873	GG,GT,TT		9.7995,19.0487,12.9163	,	791/2437,821/2467	139911983	1652,11138	2155	4240	6395	SO:0001819	synonymous_variant	20	exon17			GTAGACTGCCAGG	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.2370A>C	9.37:g.139911983T>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	87	34	0.390805	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	37																																																																																				T|0.905;G|0.095	0.095	strong		0.607	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	
MUC21	394263	hgsc.bcm.edu	37	6	30954560	30954560	+	Missense_Mutation	SNP	C	C	T	rs531044924	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954560C>T	ENST00000376296.3	+	2	849	c.608C>T	c.(607-609)aCc>aTc	p.T203I	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	203	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGCACAACCTCCAGTGGG	0.617													c|||	192	0.0383387	0.0401	0.0533	5008	,	,		25680	0.0337		0.0308	False		,,,				2504	0.0378				p.T203I		Atlas-SNP	.											.	MUC21	98	.	0			c.C608T						PASS	.						160.0	154.0	156.0					6																	30954560		2203	4300	6503	SO:0001583	missense	394263	exon2			GCACAACCTCCAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.608C>T	6.37:g.30954560C>T	ENSP00000365473:p.Thr203Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	142	13	0.0915493	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	c	9.167	1.020156	0.19433	.	.	ENSG00000204544	ENST00000376296	T	0.11385	2.78	4.1	1.24	0.21308	.	.	.	.	.	T	0.03095	0.0091	L	0.27053	0.805	0.09310	N	1	P	0.44044	0.825	P	0.44897	0.463	T	0.42292	-0.9460	8	.	.	.	.	7.7906	0.29119	0.0:0.7057:0.0:0.2943	.	203	Q5SSG8	MUC21_HUMAN	I	203	ENSP00000365473:T203I	.	T	+	2	0	MUC21	31062539	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.733000	0.04898	0.127000	0.18452	0.491000	0.48974	ACC	.	.	none		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
ZNF512B	57473	hgsc.bcm.edu	37	20	62595547	62595547	+	Missense_Mutation	SNP	C	C	T	rs6062599	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62595547C>T	ENST00000450537.1	-	8	1417	c.1357G>A	c.(1357-1359)Gcc>Acc	p.A453T	ZNF512B_ENST00000369888.1_Missense_Mutation_p.A453T|ZNF512B_ENST00000217130.3_Missense_Mutation_p.A453T			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	453			A -> T (in dbSNP:rs6062599).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					TGAACTCGGGCCTTGTCCTCA	0.652													C|||	385	0.076877	0.0053	0.1153	5008	,	,		17315	0.0149		0.2068	False		,,,				2504	0.0767				p.A453T		Atlas-SNP	.											ZNF512B,caecum,carcinoma,0,1	ZNF512B	72	1	0			c.G1357A						PASS	.	C	THR/ALA	184,4222	118.8+/-156.5	4,176,2023	92.0	98.0	96.0		1357	1.5	0.7	20	dbSNP_114	96	1721,6879	311.7+/-310.5	182,1357,2761	yes	missense	ZNF512B	NM_020713.1	58	186,1533,4784	TT,TC,CC		20.0116,4.1761,14.6471	benign	453/893	62595547	1905,11101	2203	4300	6503	SO:0001583	missense	57473	exon8			CTCGGGCCTTGTC	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.1357G>A	20.37:g.62595547C>T	ENSP00000393795:p.Ala453Thr	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_020713	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	37	CCDS13548.1	222	0.10164835164835165	6	0.012195121951219513	47	0.1298342541436464	11	0.019230769230769232	158	0.20844327176781002	C	11.79	1.742905	0.30865	0.041761	0.200116	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.26660	1.72;1.72;1.72	4.69	1.48	0.22813	.	0.335509	0.28332	N	0.015736	T	0.00012	0.0000	L	0.46157	1.445	0.31149	P	0.7057610000000001	B	0.12630	0.006	B	0.08055	0.003	T	0.22730	-1.0208	9	0.35671	T	0.21	-11.1752	9.4074	0.38471	0.1803:0.7397:0.0:0.08	rs6062599;rs6062599	453	Q96KM6	Z512B_HUMAN	T	453	ENSP00000358904:A453T;ENSP00000393795:A453T;ENSP00000217130:A453T	ENSP00000217130:A453T	A	-	1	0	ZNF512B	62065991	0.919000	0.31177	0.672000	0.29872	0.324000	0.28378	1.378000	0.34328	0.008000	0.14787	0.467000	0.42956	GCC	C|0.882;T|0.118	0.118	strong		0.652	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
OR2T4	127074	hgsc.bcm.edu	37	1	248525647	248525647	+	Silent	SNP	C	C	A	rs28405645	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248525647C>A	ENST00000366475.1	+	1	765	c.765C>A	c.(763-765)ctC>ctA	p.L255L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCATCCTCCTCACCATCCACG	0.517													c|||	1468	0.293131	0.239	0.2709	5008	,	,		22286	0.4256		0.1799	False		,,,				2504	0.362				p.L255L		Atlas-SNP	.											.	OR2T4	126	.	0			c.C765A						PASS	.	C		1061,3345	385.4+/-325.7	140,781,1282	129.0	127.0	128.0		765	-0.0	0.1	1	dbSNP_125	128	1395,7205	269.1+/-288.2	112,1171,3017	no	coding-synonymous	OR2T4	NM_001004696.1		252,1952,4299	AA,AC,CC		16.2209,24.0808,18.8836		255/349	248525647	2456,10550	2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			CCTCCTCACCATC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.765C>A	1.37:g.248525647C>A		Somatic	678	0	0		WXS	Illumina HiSeq	Phase_I	701	325	0.463623	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			C|0.790;A|0.210	0.210	strong		0.517	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
NCOA1	8648	hgsc.bcm.edu	37	2	24980955	24980955	+	Missense_Mutation	SNP	A	A	G	rs150066931	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:24980955A>G	ENST00000406961.1	+	21	4647	c.3995A>G	c.(3994-3996)aAc>aGc	p.N1332S	NCOA1_ENST00000405141.1_Missense_Mutation_p.N1332S|NCOA1_ENST00000348332.3_Missense_Mutation_p.N1332S|NCOA1_ENST00000407230.1_Missense_Mutation_p.N1181S|NCOA1_ENST00000395856.3_Missense_Mutation_p.N1332S|NCOA1_ENST00000538539.1_Missense_Mutation_p.N1332S|NCOA1_ENST00000288599.5_Missense_Mutation_p.N1332S			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	1332					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGAACATGAACCCAATGATG	0.527			T	PAX3	alveolar rhadomyosarcoma								A|||	29	0.00579073	0.0	0.0072	5008	,	,		15823	0.0		0.001	False		,,,				2504	0.0235				p.N1332S		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.A3995G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	161.0	132.0	142.0		3995,3995,3995	3.8	1.0	2	dbSNP_134	142	9,8591	7.1+/-27.0	0,9,4291	yes	missense,missense,missense	NCOA1	NM_003743.4,NM_147223.2,NM_147233.2	46,46,46	0,9,6494	GG,GA,AA		0.1047,0.0,0.0692	probably-damaging,probably-damaging,probably-damaging	1332/1442,1332/1400,1332/1441	24980955	9,12997	2203	4300	6503	SO:0001583	missense	8648	exon19			ACATGAACCCAAT	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.3995A>G	2.37:g.24980955A>G	ENSP00000385216:p.Asn1332Ser	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	272	130	0.477941	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	19.15	3.771069	0.69992	0.0	0.001047	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000407230;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T;T	0.02369	4.44;4.42;4.32;4.42;4.44;4.42;4.44	5.01	3.82	0.43975	.	0.165920	0.53938	D	0.000052	T	0.06872	0.0175	L	0.47716	1.5	0.41217	D	0.986487	D;D;P;D;D	0.61697	0.982;0.99;0.586;0.99;0.982	P;P;B;P;P	0.54889	0.584;0.763;0.28;0.763;0.584	T	0.18085	-1.0348	10	0.62326	D	0.03	.	10.6256	0.45506	0.9228:0.0:0.0771:0.0	.	1332;1332;1332;1332;1181	A8K1V4;Q15788-3;Q15788;Q15788-2;B5MCN7	.;.;NCOA1_HUMAN;.;.	S	1332;1332;1181;1332;1332;1332;1332	ENSP00000385216:N1332S;ENSP00000385097:N1332S;ENSP00000385195:N1181S;ENSP00000444039:N1332S;ENSP00000320940:N1332S;ENSP00000288599:N1332S;ENSP00000379197:N1332S	ENSP00000288599:N1332S	N	+	2	0	NCOA1	24834459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.694000	0.61760	0.897000	0.36392	0.477000	0.44152	AAC	A|0.999;G|0.001	0.001	strong		0.527	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
MUM1	84939	hgsc.bcm.edu	37	19	1370742	1370742	+	Missense_Mutation	SNP	G	G	A	rs34502536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1370742G>A	ENST00000415183.3	+	11	1680	c.1654G>A	c.(1654-1656)Ggg>Agg	p.G552R	MUM1_ENST00000591806.1_Missense_Mutation_p.G552R|MUM1_ENST00000344663.3_Missense_Mutation_p.G552R|MUM1_ENST00000311401.5_Missense_Mutation_p.G483R			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	551					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGCCCCCTGGGGCAGAGGCA	0.662													G|||	35	0.00698882	0.0008	0.013	5008	,	,		13894	0.0		0.0239	False		,,,				2504	0.001				p.G552R		Atlas-SNP	.											.	MUM1	54	.	0			c.G1654A						PASS	.	G	ARG/GLY	17,4093		0,17,2038	7.0	8.0	8.0		1654	2.6	0.0	19	dbSNP_126	8	131,7971		0,131,3920	no	missense	MUM1	NM_032853.3	125	0,148,5958	AA,AG,GG		1.6169,0.4136,1.2119	possibly-damaging	552/712	1370742	148,12064	2055	4051	6106	SO:0001583	missense	84939	exon12			CCCCTGGGGCAGA	AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.1654G>A	19.37:g.1370742G>A	ENSP00000394925:p.Gly552Arg	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	37		26	0.011904761904761904	0	0.0	8	0.022099447513812154	0	0.0	18	0.023746701846965697	G	18.07	3.541037	0.65085	0.004136	0.016169	ENSG00000160953	ENST00000344663;ENST00000311401;ENST00000415183	T;T;T	0.40756	1.02;1.02;1.02	5.07	2.57	0.30868	.	0.460401	0.23351	N	0.049132	T	0.37945	0.1022	M	0.66939	2.045	0.09310	N	1	D;D;D;P	0.89917	0.999;1.0;0.993;0.954	D;D;P;P	0.69307	0.946;0.963;0.898;0.548	T	0.21211	-1.0252	10	0.72032	D	0.01	.	5.3578	0.16071	0.2867:0.0:0.7133:0.0	rs34502536	552;552;483;551	B7ZLY8;D6W5Y8;Q2TAK8-2;Q2TAK8	.;.;.;MUM1_HUMAN	R	552;483;552	ENSP00000345789:G552R;ENSP00000309135:G483R;ENSP00000394925:G552R	ENSP00000309135:G483R	G	+	1	0	MUM1	1321742	0.412000	0.25392	0.009000	0.14445	0.086000	0.17979	2.031000	0.41117	1.253000	0.44018	0.561000	0.74099	GGG	G|0.988;A|0.012	0.012	strong		0.662	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853	
PNPLA3	80339	hgsc.bcm.edu	37	22	44324727	44324727	+	Missense_Mutation	SNP	C	C	G	rs738409	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:44324727C>G	ENST00000216180.3	+	3	617	c.444C>G	c.(442-444)atC>atG	p.I148M	PNPLA3_ENST00000423180.2_Missense_Mutation_p.I144M|PNPLA3_ENST00000478713.1_3'UTR	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	148	Patatin.		I -> M (common polymorphism; fails to hydrolyze emulsified triglycerides; associated with increased hepatic fat content and serum aspartate aminotransferase concentrations; dbSNP:rs738409). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18728122, ECO:0000269|PubMed:18820647, ECO:0000269|PubMed:19224197, ECO:0000269|PubMed:19738004}.		acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)	p.I148M(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				CCTGCTTCATCCCCTTCTACA	0.507													C|||	1313	0.262181	0.118	0.4841	5008	,	,		20458	0.3502		0.2256	False		,,,				2504	0.2464				p.I148M		Atlas-SNP	.											PNPLA3,NS,carcinoma,0,1	PNPLA3	53	1	1	Substitution - Missense(1)	stomach(1)	c.C444G	GRCh37	CM086892	PNPLA3	M	rs738409	PASS	.	C	MET/ILE	639,3767	274.9+/-272.2	58,523,1622	311.0	260.0	277.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	444	-2.0	0.3	22	dbSNP_86	277	1901,6699	335.0+/-321.2	208,1485,2607	yes	missense	PNPLA3	NM_025225.2	10	266,2008,4229	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	22.1047,14.503,19.5294	probably-damaging	148/482	44324727	2540,10466	2203	4300	6503	SO:0001583	missense	80339	exon3			CTTCATCCCCTTC		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"""Patatin-like phospholipase domain containing"""	18590	protein-coding gene	gene with protein product		609567	"""chromosome 22 open reading frame 20"", ""adiponutrin"""	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.444C>G	22.37:g.44324727C>G	ENSP00000216180:p.Ile148Met	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	90	34	0.377778	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Missense_Mutation	SNP	ENST00000216180.3	37	CCDS14054.1	622	0.2847985347985348	59	0.11991869918699187	164	0.4530386740331492	235	0.41083916083916083	164	0.21635883905013192	C	12.12	1.841297	0.32513	0.14503	0.221047	ENSG00000100344	ENST00000216180;ENST00000423180	T;T	0.80738	-1.41;-1.41	5.7	-1.97	0.07503	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.316000	0.28156	N	0.016391	T	0.00012	0.0000	M	0.92026	3.265	0.21355	P	0.999710835	D	0.64830	0.994	D	0.66497	0.944	T	0.20107	-1.0285	9	0.62326	D	0.03	-21.2182	6.3831	0.21546	0.0:0.4064:0.2195:0.3741	rs738409;rs3747205;rs17855952;rs738409	148	Q9NST1	PLPL3_HUMAN	M	148;144	ENSP00000216180:I148M;ENSP00000397987:I144M	ENSP00000216180:I148M	I	+	3	3	PNPLA3	42656060	0.058000	0.20735	0.289000	0.24876	0.080000	0.17528	-0.914000	0.04038	-0.125000	0.11703	-0.136000	0.14681	ATC	C|0.774;G|0.226	0.226	strong		0.507	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225	
PKHD1	5314	hgsc.bcm.edu	37	6	51892977	51892977	+	Silent	SNP	A	A	G	rs141574387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:51892977A>G	ENST00000371117.3	-	30	3812	c.3537T>C	c.(3535-3537)aaT>aaC	p.N1179N	PKHD1_ENST00000340994.4_Silent_p.N1179N	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1179	IPT/TIG 6; atypical.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TGCTGACCCCATTGATAGAGA	0.498													A|||	4	0.000798722	0.0	0.0029	5008	,	,		19364	0.0		0.001	False		,,,				2504	0.001				p.N1179N		Atlas-SNP	.											.	PKHD1	927	.	0			c.T3537C						PASS	.	A	,	0,4406		0,0,2203	144.0	158.0	154.0		3537,3537	2.0	1.0	6	dbSNP_134	154	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	0,15,6488	GG,GA,AA		0.1744,0.0,0.1153	,	1179/4075,1179/3397	51892977	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon30			GACCCCATTGATA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.3537T>C	6.37:g.51892977A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	58	0.604167	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			A|0.999;G|0.001	0.001	strong		0.498	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
CPT1A	1374	hgsc.bcm.edu	37	11	68560787	68560787	+	Silent	SNP	C	C	T	rs2229737	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:68560787C>T	ENST00000265641.5	-	9	1117	c.963G>A	c.(961-963)gaG>gaA	p.E321E	CPT1A_ENST00000539743.1_Silent_p.E321E|CPT1A_ENST00000540367.1_Silent_p.E321E|CPT1A_ENST00000538994.1_Silent_p.E73E|CPT1A_ENST00000376618.2_Silent_p.E321E	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	321					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	ACTCACCTGTCTCCTCTCCTG	0.483													C|||	255	0.0509185	0.0318	0.0663	5008	,	,		16444	0.0198		0.1233	False		,,,				2504	0.0235				p.E321E		Atlas-SNP	.											.	CPT1A	89	.	0			c.G963A						PASS	.	C	,	167,4233	106.9+/-145.3	4,159,2037	52.0	45.0	48.0		963,963	1.1	1.0	11	dbSNP_120	48	910,7678	198.9+/-243.1	56,798,3440	no	coding-synonymous,coding-synonymous	CPT1A	NM_001031847.2,NM_001876.3	,	60,957,5477	TT,TC,CC		10.5962,3.7955,8.2923	,	321/757,321/774	68560787	1077,11911	2200	4294	6494	SO:0001819	synonymous_variant	1374	exon9			ACCTGTCTCCTCT	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.963G>A	11.37:g.68560787C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	128	52	0.40625	NM_001876	Q8TCU0|Q9BWK0	Silent	SNP	ENST00000265641.5	37	CCDS8185.1																																																																																			C|0.914;T|0.086	0.086	strong		0.483	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876	
ZNF250	58500	hgsc.bcm.edu	37	8	146108178	146108178	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:146108178C>T	ENST00000292579.7	-	6	521	c.405G>A	c.(403-405)ccG>ccA	p.P135P	ZNF250_ENST00000543949.1_Intron|ZNF250_ENST00000342660.6_Intron|ZNF250_ENST00000417550.2_Silent_p.P130P	NM_001109689.3|NM_021061.4	NP_001103159.1|NP_066405.1	P15622	ZN250_HUMAN	zinc finger protein 250	135					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)			endometrium(4)|kidney(2)|lung(8)|skin(1)	15	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)		TTAATGGCTTCGGACTCAAGT	0.383																																					p.P135P	NSCLC(16;520 556 24096 40084 43446)	Atlas-SNP	.											ZNF250,NS,carcinoma,0,1	ZNF250	37	1	0			c.G405A						scavenged	.						157.0	163.0	161.0					8																	146108178		2203	4300	6503	SO:0001819	synonymous_variant	58500	exon6			TGGCTTCGGACTC	AK095705	CCDS34972.1, CCDS55282.1	8q24.3	2013-01-08	2004-11-08			ENSG00000196150		"""Zinc fingers, C2H2-type"", ""-"""	13044	protein-coding gene	gene with protein product			"""zinc finger protein 647"""	ZNF647		12477932	Standard	NM_021061		Approved	MGC9718, ZFP647	uc003zer.4	P15622		ENST00000292579.7:c.405G>A	8.37:g.146108178C>T		Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	256	4	0.015625	NM_021061	D3DWP1|Q59HE9|Q8N942|Q96AH9	Silent	SNP	ENST00000292579.7	37	CCDS34972.1																																																																																			.	.	none		0.383	ZNF250-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382968.1	NM_021061	
BLVRA	644	hgsc.bcm.edu	37	7	43830888	43830888	+	Silent	SNP	T	T	C	rs1802846	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:43830888T>C	ENST00000402924.1	+	5	338	c.175T>C	c.(175-177)Ttg>Ctg	p.L59L	BLVRA_ENST00000265523.4_Silent_p.L59L	NM_001253823.1	NP_001240752.1	P53004	BIEA_HUMAN	biliverdin reductase A	59					heme catabolic process (GO:0042167)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	biliverdin reductase activity (GO:0004074)|zinc ion binding (GO:0008270)	p.L59L(1)		endometrium(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(2)	12						GCAGATTTCTTTGGAGGATGC	0.502													T|||	530	0.105831	0.1127	0.1671	5008	,	,		16706	0.0804		0.1213	False		,,,				2504	0.0634				p.L59L		Atlas-SNP	.											BLVRA,NS,carcinoma,0,1	BLVRA	26	1	1	Substitution - coding silent(1)	stomach(1)	c.T175C						PASS	.	T		461,3945	220.0+/-237.6	27,407,1769	127.0	120.0	122.0		175	-2.1	1.0	7	dbSNP_89	122	953,7647	208.4+/-249.9	52,849,3399	no	coding-synonymous	BLVRA	NM_000712.3		79,1256,5168	CC,CT,TT		11.0814,10.463,10.8719		59/297	43830888	1414,11592	2203	4300	6503	SO:0001819	synonymous_variant	644	exon5			ATTTCTTTGGAGG	BC008456	CCDS5472.1	7p13	2012-10-02			ENSG00000106605	ENSG00000106605	1.3.1.24		1062	protein-coding gene	gene with protein product		109750		BLVR			Standard	NM_001253823		Approved		uc003tir.3	P53004	OTTHUMG00000128953	ENST00000402924.1:c.175T>C	7.37:g.43830888T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_001253823	A8K747|O95019|Q86UX0|Q96QL4|Q9BRW8	Silent	SNP	ENST00000402924.1	37	CCDS5472.1																																																																																			T|0.890;C|0.110	0.110	strong		0.502	BLVRA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339006.1	NM_000712	
OR2A25	392138	hgsc.bcm.edu	37	7	143771937	143771937	+	Missense_Mutation	SNP	G	G	C	rs2961135	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143771937G>C	ENST00000408898.2	+	1	663	c.625G>C	c.(625-627)Gcc>Ccc	p.A209P		NM_001004488.1	NP_001004488.1	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A, member 25	209			A -> P (in dbSNP:rs2961135). {ECO:0000269|PubMed:12690205}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(16)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	24	Melanoma(164;0.0783)					GCTGGTGGGAGCCTTCTTTTC	0.458													.|||	3071	0.613219	0.7095	0.7061	5008	,	,		19288	0.6369		0.4761	False		,,,				2504	0.5337				p.A209P		Atlas-SNP	.											.	OR2A25	66	.	0			c.G625C						PASS	.	C	PRO/ALA	2856,1264		986,884,190	128.0	134.0	132.0		625	4.8	0.9	7	dbSNP_101	132	4345,4107		1133,2079,1014	yes	missense	OR2A25	NM_001004488.1	27	2119,2963,1204	CC,CG,GG		48.592,30.6796,42.7219	benign	209/311	143771937	7201,5371	2060	4226	6286	SO:0001583	missense	392138	exon1			GTGGGAGCCTTCT		CCDS43669.1	7q35	2012-08-09		2004-03-10	ENSG00000221933	ENSG00000221933		"""GPCR / Class A : Olfactory receptors"""	19562	protein-coding gene	gene with protein product				OR2A25P, OR2A27			Standard	NM_001004488		Approved		uc011ktx.2	A4D2G3	OTTHUMG00000158013	ENST00000408898.2:c.625G>C	7.37:g.143771937G>C	ENSP00000386167:p.Ala209Pro	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	262	138	0.526718	NM_001004488	B2RNC9	Missense_Mutation	SNP	ENST00000408898.2	37	CCDS43669.1	1309	0.5993589743589743	345	0.7012195121951219	247	0.6823204419889503	368	0.6433566433566433	349	0.4604221635883905	C	0.008	-1.862669	0.00552	0.693204	0.51408	ENSG00000221933	ENST00000408898	T	0.21932	1.98	4.84	4.84	0.62591	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00057	-2.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40270	-0.9572	8	0.02654	T	1	-5.5745	6.7652	0.23562	0.0:0.7262:0.1809:0.0929	rs2961135;rs10366610;rs17735983;rs52811826;rs58464030;rs2961135	209	A4D2G3	O2A25_HUMAN	P	209	ENSP00000386167:A209P	ENSP00000386167:A209P	A	+	1	0	OR2A25	143402870	0.091000	0.21658	0.915000	0.36163	0.193000	0.23685	1.576000	0.36504	1.275000	0.44379	-0.215000	0.12644	GCC	G|0.409;C|0.590	0.590	strong		0.458	OR2A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350000.1		
ITIH4	3700	hgsc.bcm.edu	37	3	52860816	52860816	+	Silent	SNP	C	C	T	rs2276816	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52860816C>T	ENST00000266041.4	-	4	606	c.510G>A	c.(508-510)aaG>aaA	p.K170K	ITIH4-AS1_ENST00000478366.1_RNA|RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000485816.1_Silent_p.K170K|ITIH4_ENST00000406595.1_Silent_p.K170K|ITIH4_ENST00000434759.3_Silent_p.K82K|ITIH4_ENST00000346281.5_Silent_p.K170K	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	170					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CCTGCAGGTGCTTGACCAGCT	0.617													C|||	354	0.0706869	0.0023	0.1037	5008	,	,		19514	0.0575		0.1252	False		,,,				2504	0.0971				p.K170K		Atlas-SNP	.											.	ITIH4	74	.	0			c.G510A						PASS	.	C	,	104,4302	81.9+/-120.4	2,100,2101	42.0	42.0	42.0		510,510	2.4	1.0	3	dbSNP_100	42	975,7625	210.7+/-251.5	68,839,3393	no	coding-synonymous,coding-synonymous	ITIH4	NM_001166449.1,NM_002218.4	,	70,939,5494	TT,TC,CC		11.3372,2.3604,8.2962	,	170/901,170/931	52860816	1079,11927	2203	4300	6503	SO:0001819	synonymous_variant	3700	exon4			CAGGTGCTTGACC	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"""plasma Kallikrein-sensitive glycoprotein"""	600564	"""inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"""	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.510G>A	3.37:g.52860816C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	140	70	0.5	NM_001166449	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Silent	SNP	ENST00000266041.4	37	CCDS2865.1	156	0.07142857142857142	0	0.0	26	0.0718232044198895	38	0.06643356643356643	92	0.12137203166226913	C	9.720	1.159442	0.21454	0.023604	0.113372	ENSG00000055955	ENST00000441637	.	.	.	5.53	2.36	0.29203	.	.	.	.	.	T	0.00815	0.0027	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00844	-1.1543	4	.	.	.	-29.6721	4.3415	0.11112	0.1551:0.4784:0.0:0.3665	rs2276816;rs17419961;rs2276816	.	.	.	T	40	.	.	A	-	1	0	ITIH4	52835856	0.224000	0.23674	1.000000	0.80357	0.977000	0.68977	0.055000	0.14229	0.709000	0.31976	0.655000	0.94253	GCA	C|0.919;T|0.081	0.081	strong		0.617	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
OR51G2	81282	hgsc.bcm.edu	37	11	4935982	4935982	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:4935982G>A	ENST00000322013.3	-	1	940	c.912C>T	c.(910-912)atC>atT	p.I304I	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	304						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTCGATCCCGGATCTGTTTGG	0.473																																					p.I304I		Atlas-SNP	.											OR51G2,right_upper_lobe,carcinoma,-1,1	OR51G2	70	1	0			c.C912T						scavenged	.						93.0	77.0	82.0					11																	4935982		2201	4298	6499	SO:0001819	synonymous_variant	81282	exon1			ATCCCGGATCTGT	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"""GPCR / Class A : Olfactory receptors"""	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.912C>T	11.37:g.4935982G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	148	2	0.0135135	NM_001005238	Q6IFH7	Silent	SNP	ENST00000322013.3	37	CCDS31365.1																																																																																			.	.	none		0.473	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238	
DYX1C1	161582	hgsc.bcm.edu	37	15	55759193	55759193	+	Missense_Mutation	SNP	T	T	C	rs600753	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55759193T>C	ENST00000321149.3	-	5	939	c.572A>G	c.(571-573)gAa>gGa	p.E191G	DYX1C1_ENST00000448430.2_Missense_Mutation_p.E191G|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000380679.1_Missense_Mutation_p.E191G|DYX1C1_ENST00000348518.3_Missense_Mutation_p.E191G|DYX1C1_ENST00000457155.2_Missense_Mutation_p.E191G	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	191			E -> G (in dbSNP:rs600753). {ECO:0000269|PubMed:12954984, ECO:0000269|PubMed:15489334}.		cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		tttttttctttcttctttaat	0.299													T|||	2646	0.528355	0.2806	0.6715	5008	,	,		13485	0.746		0.501	False		,,,				2504	0.5654				p.E191G		Atlas-SNP	.											.	DYX1C1	54	.	0			c.A572G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU	1360,2968		219,922,1023	29.0	28.0	29.0		572,572,572	2.5	0.8	15	dbSNP_83	29	4448,4088		1200,2048,1020	yes	missense,missense,missense	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	98,98,98	1419,2970,2043	CC,CT,TT		47.8913,31.4233,45.1493	possibly-damaging,possibly-damaging,possibly-damaging	191/377,191/382,191/421	55759193	5808,7056	2164	4268	6432	SO:0001583	missense	161582	exon5			TTTCTTTCTTCTT		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.572A>G	15.37:g.55759193T>C	ENSP00000323275:p.Glu191Gly	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	131	126	0.961832	NM_001033560	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	1161	0.5315934065934066	144	0.2926829268292683	233	0.643646408839779	406	0.7097902097902098	378	0.49868073878627966	T	11.06	1.527805	0.27299	0.314233	0.521087	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	T;T;T;T;T	0.49432	2.58;2.58;0.78;3.25;0.78	2.47	2.47	0.30058	.	0.942418	0.08791	N	0.893192	T	0.00012	0.0000	N	0.14661	0.345	0.35594	P	0.19267500000000004	B;B;B	0.21821	0.061;0.041;0.021	B;B;B	0.26094	0.066;0.02;0.016	T	0.42207	-0.9465	9	0.45353	T	0.12	.	6.8751	0.24143	0.0:0.0:0.0:1.0	rs600753;rs17855757;rs52829955;rs59372631;rs600753	191;191;191	Q8WXU2-3;Q8WXU2;Q8WXU2-2	.;DYXC1_HUMAN;.	G	191	ENSP00000403412:E191G;ENSP00000370054:E191G;ENSP00000402640:E191G;ENSP00000323275:E191G;ENSP00000299561:E191G	ENSP00000323275:E191G	E	-	2	0	DYX1C1	53546485	0.896000	0.30565	0.817000	0.32601	0.787000	0.44495	2.440000	0.44855	1.368000	0.46115	0.460000	0.39030	GAA	T|0.503;C|0.497	0.497	strong		0.299	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
GTF2I	2969	hgsc.bcm.edu	37	7	74105424	74105424	+	Silent	SNP	A	A	G	rs143931854	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:74105424A>G	ENST00000324896.4	+	3	608	c.219A>G	c.(217-219)caA>caG	p.Q73Q	GTF2I_ENST00000346152.4_Silent_p.Q73Q|GTF2I_ENST00000443166.1_Silent_p.Q73Q|GTF2I_ENST00000416070.1_Silent_p.Q73Q|GTF2I_ENST00000353920.4_Silent_p.Q73Q|AC083884.8_ENST00000450426.2_RNA	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	73					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						AGGATTTTCAAAAAGATTTTG	0.328													A|||	5	0.000998403	0.0	0.0043	5008	,	,		17800	0.0		0.002	False		,,,				2504	0.0				p.Q73Q		Atlas-SNP	.											.	GTF2I	40	.	0			c.A219G						PASS	.	A	,,,,	2,4404		0,2,2201	68.0	69.0	69.0		219,219,219,219,219	-1.2	1.0	7	dbSNP_134	69	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GTF2I	NM_001163636.1,NM_001518.3,NM_032999.2,NM_033000.2,NM_033001.2	,,,,	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	,,,,	73/977,73/958,73/999,73/979,73/978	74105424	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	2969	exon3			TTTTCAAAAAGAT	U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.219A>G	7.37:g.74105424A>G		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	213	97	0.455399	NM_032999	O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Silent	SNP	ENST00000324896.4	37	CCDS5573.1																																																																																			A|0.999;G|0.001	0.001	strong		0.328	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252708.1	NM_032999	
MELK	9833	hgsc.bcm.edu	37	9	36674842	36674842	+	Silent	SNP	C	C	T	rs2274473	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:36674842C>T	ENST00000298048.2	+	17	1870	c.1686C>T	c.(1684-1686)aaC>aaT	p.N562N	MELK_ENST00000538311.1_Silent_p.N368N|MELK_ENST00000536987.1_Silent_p.N431N|MELK_ENST00000543751.1_Silent_p.N530N|MELK_ENST00000536329.1_Silent_p.N491N|MELK_ENST00000541717.1_Silent_p.N521N|MELK_ENST00000536860.1_Silent_p.N514N|MELK_ENST00000545008.1_Silent_p.N491N	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	562	Autoinhibitory region.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			TTCACTATAACGTGACTACAA	0.343													T|||	3752	0.749201	0.4244	0.8862	5008	,	,		19912	0.8859		0.8887	False		,,,				2504	0.8067				p.N562N	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.C1686T						PASS	.	T		2220,2186	584.7+/-386.1	568,1084,551	63.0	57.0	59.0		1686	2.2	1.0	9	dbSNP_100	59	7721,875	197.2+/-241.9	3465,791,42	no	coding-synonymous	MELK	NM_014791.2		4033,1875,593	TT,TC,CC		10.1792,49.6142,23.5425		562/652	36674842	9941,3061	2203	4298	6501	SO:0001819	synonymous_variant	9833	exon17			CTATAACGTGACT	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1686C>T	9.37:g.36674842C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Silent	SNP	ENST00000298048.2	37	CCDS6606.1																																																																																			C|0.234;T|0.766	0.766	strong		0.343	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791	
HUS1B	135458	hgsc.bcm.edu	37	6	656343	656343	+	Missense_Mutation	SNP	T	T	C	rs17136239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:656343T>C	ENST00000380907.2	-	1	620	c.602A>G	c.(601-603)cAa>cGa	p.Q201R	EXOC2_ENST00000230449.4_Intron|EXOC2_ENST00000448181.3_Intron	NM_148959.3	NP_683762.2	Q8NHY5	HUS1B_HUMAN	HUS1 checkpoint homolog b (S. pombe)	201			Q -> R (in dbSNP:rs17136239).		DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)	checkpoint clamp complex (GO:0030896)|nucleolus (GO:0005730)				endometrium(3)|large_intestine(1)|lung(7)	11	Ovarian(93;0.0733)	Breast(5;0.00139)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.041)|BRCA - Breast invasive adenocarcinoma(62;0.0965)		AAAATAACTTTGAATGGACAC	0.537													T|||	590	0.117812	0.0764	0.0821	5008	,	,		15529	0.1399		0.0825	False		,,,				2504	0.2127				p.Q201R		Atlas-SNP	.											.	HUS1B	26	.	0			c.A602G						PASS	.	T	,ARG/GLN	402,4004	197.7+/-221.8	24,354,1825	95.0	105.0	102.0		,602	-7.2	0.0	6	dbSNP_123	102	668,7932	168.8+/-220.3	21,626,3653	yes	intron,missense	EXOC2,HUS1B	NM_018303.4,NM_148959.3	,43	45,980,5478	CC,CT,TT		7.7674,9.1239,8.227	,benign	,201/279	656343	1070,11936	2203	4300	6503	SO:0001583	missense	135458	exon1			TAACTTTGAATGG	AF508547	CCDS4470.1	6p25.3	2008-08-08	2001-11-28		ENSG00000188996	ENSG00000188996			16485	protein-coding gene	gene with protein product		609713	"""HUS1 (S. pombe) checkpoint homolog b"""			11944979	Standard	NM_148959		Approved		uc003mtg.3	Q8NHY5	OTTHUMG00000090059	ENST00000380907.2:c.602A>G	6.37:g.656343T>C	ENSP00000370293:p.Gln201Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_148959	Q5T4Z2	Missense_Mutation	SNP	ENST00000380907.2	37	CCDS4470.1	207	0.09478021978021978	33	0.06707317073170732	29	0.08011049723756906	88	0.15384615384615385	57	0.07519788918205805	T	9.870	1.198800	0.22121	0.091239	0.077674	ENSG00000188996	ENST00000380907	T	0.11169	2.8	3.73	-7.2	0.01495	.	0.607650	0.14565	N	0.311839	T	0.01092	0.0036	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48210	-0.9055	9	0.16896	T	0.51	.	9.2045	0.37280	0.0:0.1004:0.6757:0.2239	rs17136239;rs17136239	201	Q8NHY5	HUS1B_HUMAN	R	201	ENSP00000370293:Q201R	ENSP00000370293:Q201R	Q	-	2	0	HUS1B	601343	0.405000	0.25336	0.000000	0.03702	0.002000	0.02628	1.547000	0.36190	-1.042000	0.03262	-0.316000	0.08728	CAA	T|0.905;C|0.095	0.095	strong		0.537	HUS1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205617.2	NM_148959	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318741	21318741	+	Silent	SNP	C	C	T	rs75113504	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:21318741C>T	ENST00000583088.1	+	3	982	c.87C>T	c.(85-87)aaC>aaT	p.N29N	KCNJ12_ENST00000331718.5_Silent_p.N29N	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	29					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CGGGCGCCAACGGCTTCGGCA	0.652										Prostate(3;0.18)																											p.N29N		Atlas-SNP	.											KCNJ12,NS,neuroblastoma,0,2	.	.	2	0			c.C87T						PASS	.	C		846,3560		0,846,1357	81.0	69.0	73.0		87	-6.0	0.9	17	dbSNP_131	73	1238,7362		0,1238,3062	no	coding-synonymous	KCNJ12	NM_021012.4		0,2084,4419	TT,TC,CC		14.3953,19.2011,16.0234		29/434	21318741	2084,10922	2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			CGCCAACGGCTTC	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.87C>T	17.37:g.21318741C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	118	20	0.169492	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			C|0.883;T|0.117	0.117	strong		0.652	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
SEC16B	89866	hgsc.bcm.edu	37	1	177923440	177923440	+	Silent	SNP	T	T	G	rs12129817	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:177923440T>G	ENST00000308284.6	-	11	1526	c.1437A>C	c.(1435-1437)ccA>ccC	p.P479P	SEC16B_ENST00000464631.2_Silent_p.P480P|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	479					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						TGTAGGTCTGTGGGTCCATCT	0.532													T|||	836	0.166933	0.1778	0.2032	5008	,	,		19128	0.0288		0.2286	False		,,,				2504	0.2055				p.P479P		Atlas-SNP	.											.	SEC16B	92	.	0			c.A1437C						PASS	.	T		716,3172		74,568,1302	37.0	37.0	37.0		1437	2.1	1.0	1	dbSNP_120	37	1901,6361		213,1475,2443	no	coding-synonymous	SEC16B	NM_033127.2		287,2043,3745	GG,GT,TT		23.009,18.4156,21.5391		479/1061	177923440	2617,9533	1944	4131	6075	SO:0001819	synonymous_variant	89866	exon11			GGTCTGTGGGTCC	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.1437A>C	1.37:g.177923440T>G		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			T|0.822;G|0.178	0.178	strong		0.532	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
POTEE	445582	hgsc.bcm.edu	37	2	132020976	132020976	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:132020976A>G	ENST00000356920.5	+	15	2042	c.1948A>G	c.(1948-1950)Acg>Gcg	p.T650A	POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	650					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											TGAAAATAGTACGTTGCGGGA	0.353																																					p.T650A		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,-1,1	.	.	1	0			c.A1948G						scavenged	.						25.0	26.0	26.0					2																	132020976		1927	4158	6085	SO:0001583	missense	445582	exon15			AATAGTACGTTGC	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.1948A>G	2.37:g.132020976A>G	ENSP00000439189:p.Thr650Ala	Somatic	428	1	0.00233645		WXS	Illumina HiSeq	Phase_I	404	162	0.40099	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	2.826	-0.243795	0.05906	.	.	ENSG00000188219	ENST00000356920	T	0.14144	2.53	0.993	0.993	0.19825	.	.	.	.	.	T	0.07999	0.0200	N	0.19112	0.55	0.09310	N	0.999999	B	0.10296	0.003	B	0.01281	0.0	T	0.31336	-0.9947	9	0.72032	D	0.01	.	4.2424	0.10654	1.0:0.0:0.0:0.0	.	650	Q6S8J3	POTEE_HUMAN	A	650	ENSP00000439189:T650A	ENSP00000439189:T650A	T	+	1	0	AC131180.1	131737446	0.001000	0.12720	0.030000	0.17652	0.008000	0.06430	1.083000	0.30815	0.705000	0.31890	0.155000	0.16302	ACG	.	.	none		0.353	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
NLRP13	126204	hgsc.bcm.edu	37	19	56416409	56416409	+	Silent	SNP	G	G	A	rs28506091	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56416409G>A	ENST00000342929.3	-	8	2516	c.2517C>T	c.(2515-2517)caC>caT	p.H839H	NLRP13_ENST00000588751.1_Silent_p.H839H	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	839							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		ATCGAGTTACGTGTTGGATGC	0.537													G|||	257	0.0513179	0.0741	0.0735	5008	,	,		16374	0.0		0.0954	False		,,,				2504	0.0123				p.H839H		Atlas-SNP	.											.	NLRP13	220	.	0			c.C2517T						PASS	.	G		357,4049	184.7+/-212.0	15,327,1861	157.0	119.0	132.0		2517	-4.6	0.0	19	dbSNP_125	132	735,7865	177.6+/-227.2	26,683,3591	no	coding-synonymous	NLRP13	NM_176810.2		41,1010,5452	AA,AG,GG		8.5465,8.1026,8.3961		839/1044	56416409	1092,11914	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon8			AGTTACGTGTTGG	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2517C>T	19.37:g.56416409G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	139	83	0.597122	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			G|0.922;A|0.078	0.078	strong		0.537	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
DOCK10	55619	hgsc.bcm.edu	37	2	225750861	225750861	+	Silent	SNP	C	C	T	rs2304336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:225750861C>T	ENST00000258390.7	-	6	598	c.531G>A	c.(529-531)gcG>gcA	p.A177A	DOCK10_ENST00000409592.3_Silent_p.A171A	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	177					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		CAGTTCCTCCCGCTCCTCCAC	0.502													c|||	1123	0.224241	0.5272	0.0937	5008	,	,		17262	0.0556		0.1412	False		,,,				2504	0.1667				p.A177A		Atlas-SNP	.											DOCK10,colon,carcinoma,-1,1	DOCK10	308	1	0			c.G531A						PASS	.	T		1820,2040		428,964,538	115.0	117.0	116.0		531	-11.2	0.1	2	dbSNP_100	116	1240,6986		95,1050,2968	no	coding-synonymous	DOCK10	NM_014689.2		523,2014,3506	TT,TC,CC		15.0742,47.1503,25.3186		177/2187	225750861	3060,9026	1930	4113	6043	SO:0001819	synonymous_variant	55619	exon6			TCCTCCCGCTCCT	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.531G>A	2.37:g.225750861C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1																																																																																			C|0.784;T|0.216	0.216	strong		0.502	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
AMPH	273	hgsc.bcm.edu	37	7	38431481	38431481	+	Silent	SNP	C	C	A	rs1058655	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:38431481C>A	ENST00000356264.2	-	19	1961	c.1746G>T	c.(1744-1746)ccG>ccT	p.P582P	AMPH_ENST00000428293.2_Silent_p.P540P|AMPH_ENST00000325590.5_Silent_p.P540P|AMPH_ENST00000471913.1_5'Flank	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	582					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						TAGCCAGCTCCGGTGTCTCGC	0.617													C|||	663	0.132388	0.0401	0.1945	5008	,	,		13936	0.1736		0.1759	False		,,,				2504	0.1258				p.P582P		Atlas-SNP	.											.	AMPH	157	.	0			c.G1746T						PASS	.	C	,	259,4147	149.9+/-184.0	5,249,1949	56.0	51.0	53.0		1746,1620	-10.1	0.0	7	dbSNP_86	53	1851,6749	330.5+/-319.2	193,1465,2642	no	coding-synonymous,coding-synonymous	AMPH	NM_001635.3,NM_139316.2	,	198,1714,4591	AA,AC,CC		21.5233,5.8783,16.2233	,	582/696,540/654	38431481	2110,10896	2203	4300	6503	SO:0001819	synonymous_variant	273	exon19			CAGCTCCGGTGTC		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1746G>T	7.37:g.38431481C>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	142	86	0.605634	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Silent	SNP	ENST00000356264.2	37	CCDS5456.1	337	0.1543040293040293	19	0.03861788617886179	67	0.1850828729281768	108	0.1888111888111888	143	0.18865435356200527	C	5.567	0.289367	0.10513	0.058783	0.215233	ENSG00000078053	ENST00000441628	.	.	.	5.24	-10.1	0.00402	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.5251	9.6967	0.40161	0.0:0.369:0.352:0.279	rs1058655;rs3199301;rs57321987;rs1058655	.	.	.	X	465	.	.	G	-	1	0	AMPH	38398006	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.106000	0.00602	-1.886000	0.01116	-1.937000	0.00501	GGA	C|0.852;A|0.148	0.148	strong		0.617	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
SPPL2C	162540	hgsc.bcm.edu	37	17	43924130	43924130	+	Missense_Mutation	SNP	G	G	A	rs12373139	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43924130G>A	ENST00000329196.5	+	1	1875	c.1858G>A	c.(1858-1860)Ggg>Agg	p.G620R	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	620			G -> R (in dbSNP:rs12373139).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										CATCCCCCCTGGGGCCTCGGA	0.612													G|||	431	0.0860623	0.0151	0.1571	5008	,	,		19919	0.001		0.2396	False		,,,				2504	0.0613				p.G620R		Atlas-SNP	.											.	.	.	.	0			c.G1858A						PASS	.	G	ARG/GLY	201,4205	126.1+/-163.2	5,191,2007	77.0	68.0	71.0		1858	-2.5	0.0	17	dbSNP_120	71	1928,6672	340.7+/-323.7	221,1486,2593	yes	missense	IMP5	NM_175882.2	125	226,1677,4600	AA,AG,GG		22.4186,4.562,16.3694	possibly-damaging	620/685	43924130	2129,10877	2203	4300	6503	SO:0001583	missense	162540	exon1			CCCCCTGGGGCCT		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1858G>A	17.37:g.43924130G>A	ENSP00000332488:p.Gly620Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	3.902	-0.021756	0.07634	0.04562	0.224186	ENSG00000185294	ENST00000329196	T	0.04234	3.67	4.79	-2.5	0.06384	.	1.115670	0.06913	N	0.808070	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.48514	-0.9029	9	0.56958	D	0.05	-35.782	5.2551	0.15542	0.5093:0.1541:0.3366:0.0	rs12373139;rs60853039;rs12373139	620	Q8IUH8	IMP5_HUMAN	R	620	ENSP00000332488:G620R	ENSP00000332488:G620R	G	+	1	0	AC217771.1	41279910	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.187000	0.09656	-0.516000	0.06470	-0.165000	0.13383	GGG	G|0.856;A|0.144	0.144	strong		0.612	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
OR5W2	390148	hgsc.bcm.edu	37	11	55681580	55681580	+	Missense_Mutation	SNP	A	A	G	rs17596519	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55681580A>G	ENST00000344514.1	-	1	478	c.479T>C	c.(478-480)aTg>aCg	p.M160T		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	160			M -> T (in dbSNP:rs17596519).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GGCCAGTGTCATATGTATCAA	0.443													G|||	161	0.0321486	0.0038	0.0331	5008	,	,		20886	0.001		0.0905	False		,,,				2504	0.0419				p.M160T	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.T479C						PASS	.	G	THR/MET	68,4334	819.2+/-416.3	0,68,2133	85.0	75.0	78.0		479	4.1	0.0	11	dbSNP_123	78	683,7909	787.5+/-407.6	34,615,3647	yes	missense	OR5W2	NM_001001960.1	81	34,683,5780	GG,GA,AA		7.9493,1.5448,5.7796	benign	160/311	55681580	751,12243	2201	4296	6497	SO:0001583	missense	390148	exon1			AGTGTCATATGTA	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.479T>C	11.37:g.55681580A>G	ENSP00000342448:p.Met160Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	77	0.035256410256410256	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	67	0.08839050131926121	G	0.001	-2.996641	0.00044	0.015448	0.079493	ENSG00000187612	ENST00000344514	T	0.00016	9.11	5.01	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	N	0.000841	T	0.00012	0.0000	N	0.00016	-2.855	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47328	-0.9126	10	0.02654	T	1	.	4.9705	0.14113	0.1779:0.0:0.6558:0.1663	rs17596519;rs52829451;rs17596519	160	Q8NH69	OR5W2_HUMAN	T	160	ENSP00000342448:M160T	ENSP00000342448:M160T	M	-	2	0	OR5W2	55438156	0.000000	0.05858	0.008000	0.14137	0.008000	0.06430	0.339000	0.19875	0.527000	0.28560	-0.231000	0.12243	ATG	A|0.952;G|0.048	0.048	strong		0.443	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
CCDC86	79080	hgsc.bcm.edu	37	11	60610065	60610065	+	Silent	SNP	G	G	A	rs141728952|rs2074420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:60610065G>A	ENST00000227520.5	+	1	522	c.468G>A	c.(466-468)ccG>ccA	p.P156P	RP11-804A23.4_ENST00000538705.1_RNA|RP11-804A23.2_ENST00000539897.1_RNA	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	156	Pro-rich.				viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						AGCTACCGCCGGTCCCAGGAT	0.662													G|||	1707	0.340855	0.1664	0.2752	5008	,	,		14318	0.6806		0.1899	False		,,,				2504	0.4284				p.P156P		Atlas-SNP	.											CCDC86,NS,carcinoma,0,1	CCDC86	24	1	0			c.G468A						PASS	.						25.0	31.0	29.0					11																	60610065		2196	4289	6485	SO:0001819	synonymous_variant	79080	exon1			ACCGCCGGTCCCA	AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.468G>A	11.37:g.60610065G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_024098	B4DY99	Silent	SNP	ENST00000227520.5	37	CCDS7993.1																																																																																			G|0.725;A|0.275	0.275	strong		0.662	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098	
KIAA1683	80726	hgsc.bcm.edu	37	19	18377761	18377761	+	Missense_Mutation	SNP	A	A	G	rs12609001	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18377761A>G	ENST00000600328.3	-	3	782	c.589T>C	c.(589-591)Tgt>Cgt	p.C197R	KIAA1683_ENST00000392413.4_Missense_Mutation_p.C197R|KIAA1683_ENST00000600359.3_Missense_Mutation_p.C151R			Q9H0B3	K1683_HUMAN	KIAA1683	197			C -> R (in dbSNP:rs12609001). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						AGATTGTCACAGGAAGGGAAC	0.627													A|||	763	0.152356	0.0257	0.1196	5008	,	,		18253	0.3036		0.1292	False		,,,				2504	0.2147				p.C197R		Atlas-SNP	.											.	KIAA1683	190	.	0			c.T589C						PASS	.	A	ARG/CYS,ARG/CYS,ARG/CYS	174,4226	102.5+/-141.1	1,172,2027	36.0	37.0	37.0		589,451,589	-2.6	0.0	19	dbSNP_120	37	1172,7422	228.6+/-263.6	81,1010,3206	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	180,180,180	82,1182,5233	GG,GA,AA		13.6374,3.9545,10.3586	benign,benign,benign	197/1368,151/1135,197/1181	18377761	1346,11648	2200	4297	6497	SO:0001583	missense	80726	exon3			TGTCACAGGAAGG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.589T>C	19.37:g.18377761A>G	ENSP00000470780:p.Cys197Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	311	0.1423992673992674	15	0.03048780487804878	35	0.09668508287292818	167	0.291958041958042	94	0.12401055408970976	A	4.784	0.145746	0.09134	0.039545	0.136374	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000358422;ENST00000411671	T;T;T	0.03496	3.97;3.98;3.91	3.23	-2.62	0.06152	.	2.005360	0.03107	N	0.162000	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P;B	0.39809	0.689;0.0	B;B	0.31337	0.128;0.001	T	0.46233	-0.9206	9	0.11182	T	0.66	2.0952	1.4637	0.02401	0.2975:0.4085:0.1226:0.1714	rs12609001;rs17797876;rs52806099;rs59053306;rs12609001	197;197	E9PDE0;Q9H0B3	.;K1683_HUMAN	R	197;197;151;196;197	ENSP00000376213:C197R;ENSP00000352774:C197R;ENSP00000404501:C151R	ENSP00000351198:C196R	C	-	1	0	KIAA1683	18238761	0.001000	0.12720	0.000000	0.03702	0.098000	0.18820	-0.505000	0.06367	-0.301000	0.08882	0.260000	0.18958	TGT	A|0.874;G|0.126	0.126	strong		0.627	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
SPON2	10417	hgsc.bcm.edu	37	4	1165764	1165764	+	Silent	SNP	C	C	T	rs11538062	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:1165764C>T	ENST00000290902.5	-	2	428	c.96G>A	c.(94-96)gaG>gaA	p.E32E	SPON2_ENST00000431380.1_Silent_p.E32E	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	32	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		AACAGATGGACTCTCCCCCAA	0.682													C|||	674	0.134585	0.1233	0.0965	5008	,	,		12032	0.1815		0.1133	False		,,,				2504	0.1503				p.E32E		Atlas-SNP	.											.	SPON2	22	.	0			c.G96A						PASS	.	C	,,	496,3890		34,428,1731	28.0	39.0	35.0		96,96,96	-1.9	0.0	4	dbSNP_120	35	1132,7418		80,972,3223	no	coding-synonymous,coding-synonymous,coding-synonymous	SPON2	NM_001128325.2,NM_001199021.1,NM_012445.3	,,	114,1400,4954	TT,TC,CC		13.2398,11.3087,12.585	,,	32/332,32/332,32/332	1165764	1628,11308	2193	4275	6468	SO:0001819	synonymous_variant	10417	exon2			GATGGACTCTCCC	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"""Mindin"", ""M-spondin"""	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.96G>A	4.37:g.1165764C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Silent	SNP	ENST00000290902.5	37	CCDS3347.1																																																																																			C|0.870;T|0.130	0.130	strong		0.682	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2		
IKBIP	121457	hgsc.bcm.edu	37	12	99007623	99007623	+	Missense_Mutation	SNP	C	C	T	rs1048906	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:99007623C>T	ENST00000342502.2	-	3	1204	c.793G>A	c.(793-795)Ggt>Agt	p.G265S	IKBIP_ENST00000420861.1_Missense_Mutation_p.G159S|IKBIP_ENST00000393042.3_3'UTR	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein	265			G -> S (in dbSNP:rs1048906).		response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						GCTCTGTCACCTTCTAAGCTT	0.358													T|||	1956	0.390575	0.5295	0.3329	5008	,	,		19240	0.3492		0.2982	False		,,,				2504	0.3814				p.G265S		Atlas-SNP	.											.	IKBIP	46	.	0			c.G793A						PASS	.	T	SER/GLY,	2199,2205	588.1+/-386.8	566,1067,569	127.0	131.0	129.0		793,	1.9	1.0	12	dbSNP_86	129	2699,5899	681.8+/-403.7	424,1851,2024	yes	missense,utr-3	IKBIP	NM_201612.1,NM_201613.1	56,	990,2918,2593	TT,TC,CC		31.391,49.9319,37.6711	,	265/351,	99007623	4898,8104	2202	4299	6501	SO:0001583	missense	121457	exon3			TGTCACCTTCTAA	AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"""I kappa B kinase interacting protein"""	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.793G>A	12.37:g.99007623C>T	ENSP00000343471:p.Gly265Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	160	68	0.425	NM_201612	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Missense_Mutation	SNP	ENST00000342502.2	37	CCDS9067.1	779	0.3566849816849817	243	0.49390243902439024	120	0.3314917127071823	187	0.3269230769230769	229	0.3021108179419525	T	1.750	-0.489406	0.04352	0.499319	0.31391	ENSG00000166130	ENST00000342502;ENST00000420861	T;T	0.38077	1.16;1.3	5.54	1.86	0.25419	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.50632	P	1.1099999999997223E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.47837	-0.9086	8	0.02654	T	1	.	9.8834	0.41247	0.0:0.3942:0.0:0.6058	rs1048906;rs3168530;rs17846476;rs17859535;rs59586369;rs1048906	265	Q70UQ0	IKIP_HUMAN	S	265;159	ENSP00000343471:G265S;ENSP00000398023:G159S	ENSP00000343471:G265S	G	-	1	0	IKBIP	97531754	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	1.688000	0.37690	0.061000	0.16311	-1.213000	0.01624	GGT	C|0.625;T|0.374	0.374	strong		0.358	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687	
PDXDC1	23042	hgsc.bcm.edu	37	16	15129940	15129940	+	Silent	SNP	C	C	T	rs3198697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15129940C>T	ENST00000396410.4	+	23	2272	c.2175C>T	c.(2173-2175)caC>caT	p.H725H	PDXDC1_ENST00000325823.7_Silent_p.H710H|PDXDC1_ENST00000447912.2_Silent_p.H634H|PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000450288.2_Silent_p.H697H|PDXDC1_ENST00000563679.1_Silent_p.H743H|PDXDC1_ENST00000569715.1_Silent_p.H698H	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	725					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CAGTCAGTCACATTGAAGACT	0.567													C|||	813	0.16234	0.0227	0.2133	5008	,	,		18967	0.003		0.3976	False		,,,				2504	0.2372				p.H725H		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C2175T						PASS	.	C		378,4016	190.2+/-216.2	20,338,1839	138.0	134.0	135.0		2175	1.3	0.8	16	dbSNP_105	135	3603,4997	521.2+/-379.8	748,2107,1445	no	coding-synonymous	PDXDC1	NM_015027.2		768,2445,3284	TT,TC,CC		41.8953,8.6026,30.6372		725/789	15129940	3981,9013	2197	4300	6497	SO:0001819	synonymous_variant	23042	exon23			CAGTCACATTGAA	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.2175C>T	16.37:g.15129940C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	37	CCDS32393.1																																																																																			C|0.746;T|0.254	0.254	strong		0.567	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
GBP7	388646	hgsc.bcm.edu	37	1	89599084	89599084	+	Missense_Mutation	SNP	G	G	C	rs79037912		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89599084G>C	ENST00000294671.2	-	10	1657	c.1519C>G	c.(1519-1521)Caa>Gaa	p.Q507E		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	507						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.Q507E(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		TTCTGTTTTTGTCTTAGCAGC	0.458																																					p.Q507E		Atlas-SNP	.											GBP7,extremity,malignant_melanoma,0,1	GBP7	57	1	1	Substitution - Missense(1)	skin(1)	c.C1519G						PASS	.						204.0	189.0	194.0					1																	89599084		2202	4300	6502	SO:0001583	missense	388646	exon10			GTTTTTGTCTTAG	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1519C>G	1.37:g.89599084G>C	ENSP00000294671:p.Gln507Glu	Somatic	415	0	0		WXS	Illumina HiSeq	Phase_I	536	70	0.130597	NM_207398		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	.	.	.	.	.	.	.	.	.	.	G	1.816	-0.473563	0.04445	.	.	ENSG00000213512	ENST00000294671	T	0.01725	4.67	3.6	2.66	0.31614	Guanylate-binding protein, C-terminal (3);	0.212783	0.40554	N	0.001075	T	0.00384	0.0012	N	0.17800	0.525	0.09310	N	1	B	0.20052	0.041	B	0.25405	0.06	T	0.47018	-0.9149	10	0.02654	T	1	.	9.0852	0.36577	0.0:0.2488:0.7512:0.0	.	507	Q8N8V2	GBP7_HUMAN	E	507	ENSP00000294671:Q507E	ENSP00000294671:Q507E	Q	-	1	0	GBP7	89371672	0.436000	0.25586	0.084000	0.20598	0.621000	0.37620	0.585000	0.23879	0.812000	0.34326	0.591000	0.81541	CAA	.	.	weak		0.458	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362104	105362104	+	Silent	SNP	G	G	A	rs111908946|rs11191741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:105362104G>A	ENST00000369774.4	-	15	3147	c.2871C>T	c.(2869-2871)ttC>ttT	p.F957F	SH3PXD2A_ENST00000355946.2_Silent_p.F929F|SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000540321.1_Silent_p.F824F|SH3PXD2A_ENST00000538130.1_Silent_p.F792F|SH3PXD2A_ENST00000427662.2_Intron			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	957					superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		AGGTCTTGCCGAAGCCCCCGG	0.642													G|||	1618	0.323083	0.1067	0.3559	5008	,	,		18050	0.3502		0.3519	False		,,,				2504	0.5348				p.F929F		Atlas-SNP	.											SH3PXD2A,NS,neuroblastoma,0,1	SH3PXD2A	90	1	0			c.C2787T						scavenged	.	G		686,3720	284.9+/-277.9	56,574,1573	58.0	54.0	55.0		2787	1.1	0.5	10	dbSNP_120	55	3046,5554	457.7+/-364.4	553,1940,1807	no	coding-synonymous	SH3PXD2A	NM_014631.2		609,2514,3380	AA,AG,GG		35.4186,15.5697,28.6944		929/1106	105362104	3732,9274	2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			CTTGCCGAAGCCC	AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"""five SH3 domains"""		"""SH3 multiple domains 1"""	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.2871C>T	10.37:g.105362104G>A		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	52	6	0.115385	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		605	0.27701465201465203	61	0.12398373983739837	122	0.3370165745856354	163	0.28496503496503495	259	0.341688654353562	G	0.009	-1.848781	0.00563	0.155697	0.354186	ENSG00000107957	ENST00000420222	.	.	.	5.02	1.13	0.20643	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999883335	.	.	.	.	.	.	T	0.39099	-0.9630	3	.	.	.	-29.7996	8.6238	0.33877	0.544:0.0:0.456:0.0	rs11191741;rs17339506;rs11191741	.	.	.	W	884	.	.	R	-	1	2	SH3PXD2A	105352094	0.074000	0.21230	0.499000	0.27577	0.147000	0.21601	0.484000	0.22308	-0.041000	0.13558	-0.969000	0.02612	CGG	G|0.718;A|0.282	0.282	strong		0.642	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631	
TMEM109	79073	hgsc.bcm.edu	37	11	60689534	60689534	+	Missense_Mutation	SNP	C	C	T	rs75070807	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:60689534C>T	ENST00000227525.3	+	4	1032	c.629C>T	c.(628-630)gCc>gTc	p.A210V	TMEM132A_ENST00000005286.4_5'Flank|TMEM132A_ENST00000453848.2_5'Flank|TMEM109_ENST00000536171.1_Missense_Mutation_p.A210V|RP11-881M11.4_ENST00000543907.1_RNA	NM_024092.2	NP_076997.1	Q9BVC6	TM109_HUMAN	transmembrane protein 109	210					cellular response to gamma radiation (GO:0071480)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell death (GO:0060548)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8						GCCTCTGGGGCCCAACTCGAG	0.706													C|||	48	0.00958466	0.0023	0.0173	5008	,	,		15459	0.0		0.0229	False		,,,				2504	0.0102				p.A210V		Atlas-SNP	.											.	TMEM109	24	.	0			c.C629T						PASS	.	C	VAL/ALA	31,4359		0,31,2164	21.0	25.0	24.0		629	2.8	1.0	11	dbSNP_131	24	237,8333		2,233,4050	yes	missense	TMEM109	NM_024092.2	64	2,264,6214	TT,TC,CC		2.7655,0.7062,2.0679	benign	210/244	60689534	268,12692	2195	4285	6480	SO:0001583	missense	79073	exon4			CTGGGGCCCAACT		CCDS7996.1	11q12.2	2005-12-22				ENSG00000110108			28771	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_024092		Approved	MGC5508	uc001nqg.3	Q9BVC6		ENST00000227525.3:c.629C>T	11.37:g.60689534C>T	ENSP00000227525:p.Ala210Val	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	60	37	0.616667	NM_024092		Missense_Mutation	SNP	ENST00000227525.3	37	CCDS7996.1	27	0.012362637362637362	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	19	0.025065963060686015	C	14.68	2.608134	0.46527	0.007062	0.027655	ENSG00000110108	ENST00000227525;ENST00000536171	.	.	.	4.75	2.82	0.32997	.	0.530146	0.18218	N	0.147992	T	0.11452	0.0279	L	0.34521	1.04	0.26459	N	0.975476	B	0.11235	0.004	B	0.14578	0.011	T	0.09314	-1.0680	9	0.39692	T	0.17	-13.8635	8.6821	0.34214	0.0:0.7661:0.1493:0.0847	.	210	Q9BVC6	TM109_HUMAN	V	210	.	ENSP00000227525:A210V	A	+	2	0	TMEM109	60446110	0.001000	0.12720	1.000000	0.80357	0.164000	0.22412	0.816000	0.27267	0.969000	0.38237	0.555000	0.69702	GCC	C|0.983;T|0.017	0.017	strong		0.706	TMEM109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396343.1	NM_024092	
MLF2	8079	hgsc.bcm.edu	37	12	6858126	6858126	+	Silent	SNP	G	G	A	rs2302371	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6858126G>A	ENST00000203630.5	-	8	1226	c.582C>T	c.(580-582)gaC>gaT	p.D194D	MLF2_ENST00000435120.1_Silent_p.D194D|MLF2_ENST00000539187.1_Silent_p.D194D|MLF2_ENST00000542154.1_Silent_p.D194D|MLF2_ENST00000564181.1_5'Flank			Q15773	MLF2_HUMAN	myeloid leukemia factor 2	194					defense response (GO:0006952)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				kidney(2)|large_intestine(3)|lung(4)	9						GCCGCCACTCGTCATCAAACG	0.677													G|||	426	0.0850639	0.0393	0.1427	5008	,	,		16981	0.119		0.1044	False		,,,				2504	0.0511				p.D194D		Atlas-SNP	.											MLF2,NS,carcinoma,0,3	MLF2	26	3	0			c.C582T						PASS	.	G		239,4151		6,227,1962	15.0	14.0	14.0		582	-1.6	0.8	12	dbSNP_100	14	1069,7493		62,945,3274	no	coding-synonymous	MLF2	NM_005439.2		68,1172,5236	AA,AG,GG		12.4854,5.4442,10.0988		194/249	6858126	1308,11644	2195	4281	6476	SO:0001819	synonymous_variant	8079	exon8			CCACTCGTCATCA	U57342	CCDS8559.1	12p13.31	2014-09-11			ENSG00000089693	ENSG00000089693			7126	protein-coding gene	gene with protein product		601401				8661158	Standard	NM_005439		Approved	NTN4	uc010sfi.2	Q15773	OTTHUMG00000168717	ENST00000203630.5:c.582C>T	12.37:g.6858126G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	134	77	0.574627	NM_005439		Silent	SNP	ENST00000203630.5	37	CCDS8559.1	223	0.1021062271062271	41	0.08333333333333333	42	0.11602209944751381	56	0.0979020979020979	84	0.11081794195250659	G	4.382	0.070542	0.08436	0.054442	0.124854	ENSG00000089693	ENST00000537126	.	.	.	5.21	-1.62	0.08372	.	.	.	.	.	T	0.00845	0.0028	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.36040	-0.9764	4	0.87932	D	0	.	8.2231	0.31554	0.3036:0.0:0.5745:0.1219	rs2302371;rs11538002;rs17630206;rs58054620;rs2302371	.	.	.	M	205	.	ENSP00000439789:T205M	T	-	2	0	MLF2	6728387	0.941000	0.31946	0.775000	0.31657	0.006000	0.05464	0.009000	0.13219	-0.249000	0.09569	-0.218000	0.12543	ACG	G|0.910;A|0.090	0.090	strong		0.677	MLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400733.2		
HNF1A	6927	hgsc.bcm.edu	37	12	121432117	121432117	+	Silent	SNP	G	G	C	rs56348580	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:121432117G>C	ENST00000257555.6	+	4	1090	c.864G>C	c.(862-864)ggG>ggC	p.G288G	HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_Silent_p.G288G|HNF1A_ENST00000541395.1_Silent_p.G288G|HNF1A_ENST00000543427.1_Silent_p.G171G|HNF1A_ENST00000402929.1_Silent_p.G288G|HNF1A_ENST00000400024.2_Silent_p.G288G			P20823	HNF1A_HUMAN	HNF1 homeobox A	288					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CGTACAGCGGGCCCCCCCCAG	0.667									Hepatic Adenoma, Familial Clustering of				g|||	907	0.18111	0.1778	0.415	5008	,	,		17094	0.005		0.3032	False		,,,				2504	0.0757				p.G288G		Atlas-SNP	.											HNF1A,brain,glioma,0,1	HNF1A	302	1	0			c.G864C	GRCh37	CI064741|CM067044	HNF1A	I|M	rs56348580	PASS	.	G		802,3604		95,612,1496	24.0	24.0	24.0		864	2.3	1.0	12	dbSNP_129	24	2264,6334		374,1516,2409	no	coding-synonymous	HNF1A	NM_000545.5		469,2128,3905	CC,CG,GG		26.3317,18.2025,23.5774		288/632	121432117	3066,9938	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon4	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CAGCGGGCCCCCC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.864G>C	12.37:g.121432117G>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.754;C|0.246	0.246	strong		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
ZSCAN12	9753	hgsc.bcm.edu	37	6	28358320	28358320	+	Intron	SNP	A	A	G	rs1361385	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28358320A>G	ENST00000361028.1	-	4	1840				ZSCAN12_ENST00000396827.3_Intron			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|urinary_tract(1)	6						CACTCTTTACATACATAGGTA	0.428													A|||	1935	0.386382	0.5582	0.3271	5008	,	,		21437	0.2996		0.2893	False		,,,				2504	0.3855				p.C583R		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.T1747C						PASS	.	A	ARG/CYS	645,739		147,351,194	298.0	257.0	269.0		1747	2.4	0.2	6	dbSNP_88	269	1003,2179		161,681,749	yes	missense	ZSCAN12	NM_001163391.1	180	308,1032,943	GG,GA,AA		31.5211,46.604,36.0929		583/612	28358320	1648,2918	692	1591	2283	SO:0001627	intron_variant	9753	exon4			CTTTACATACATA	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"""-"", ""Zinc fingers, C2H2-type"""	13172	protein-coding gene	gene with protein product		603978	"""zinc finger protein 305"", ""zinc finger protein 96"""	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.1694+52T>C	6.37:g.28358320A>G		Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	199	105	0.527638	NM_001163391	O43724	Missense_Mutation	SNP	ENST00000361028.1	37																																																																																				A|0.632;G|0.368	0.368	strong		0.428	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724	
BDP1	55814	hgsc.bcm.edu	37	5	70798541	70798541	+	Missense_Mutation	SNP	A	A	G	rs36009281	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:70798541A>G	ENST00000358731.4	+	15	2427	c.2164A>G	c.(2164-2166)Aaa>Gaa	p.K722E	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	722			K -> E (in dbSNP:rs36009281).		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TGCTGAAAGAAAAGAAATTCT	0.423													A|||	163	0.0325479	0.003	0.0432	5008	,	,		16266	0.0		0.0885	False		,,,				2504	0.0409				p.K722E		Atlas-SNP	.											.	BDP1	204	.	0			c.A2164G						PASS	.	A	GLU/LYS	56,3666		0,56,1805	96.0	89.0	91.0		2164	4.7	1.0	5	dbSNP_126	91	682,7490		30,622,3434	yes	missense	BDP1	NM_018429.2	56	30,678,5239	GG,GA,AA		8.3456,1.5046,6.2048	probably-damaging	722/2625	70798541	738,11156	1861	4086	5947	SO:0001583	missense	55814	exon15			GAAAGAAAAGAAA	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.2164A>G	5.37:g.70798541A>G	ENSP00000351575:p.Lys722Glu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	72	0.03296703296703297	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	55	0.07255936675461741	A	15.94	2.980560	0.53827	0.015046	0.083456	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000451951;ENST00000444711	T	0.12255	2.7	4.7	4.7	0.59300	.	0.083784	0.51477	D	0.000094	T	0.01765	0.0056	M	0.64997	1.995	0.80722	D	1	D;D;D	0.71674	0.974;0.998;0.997	P;D;D	0.80764	0.869;0.994;0.946	T	0.00023	-1.2334	10	0.66056	D	0.02	.	10.7286	0.46083	1.0:0.0:0.0:0.0	rs36009281	722;722;722	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	E	722;722;302;722	ENSP00000351575:K722E	ENSP00000351575:K722E	K	+	1	0	BDP1	70834297	0.999000	0.42202	0.993000	0.49108	0.108000	0.19459	1.185000	0.32065	2.109000	0.64355	0.402000	0.26972	AAA	A|0.949;G|0.051	0.051	strong		0.423	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
OR8D4	338662	hgsc.bcm.edu	37	11	123777412	123777412	+	Missense_Mutation	SNP	A	A	G	rs17127950	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:123777412A>G	ENST00000321355.2	+	1	304	c.274A>G	c.(274-276)Atc>Gtc	p.I92V		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	92			I -> V (in dbSNP:rs17127950).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		AGATAGATCCATCTCCTATTC	0.403													A|||	934	0.186502	0.2844	0.1455	5008	,	,		22333	0.0933		0.1829	False		,,,				2504	0.183				p.I92V		Atlas-SNP	.											.	OR8D4	62	.	0			c.A274G						PASS	.	A	VAL/ILE	1081,3323	392.1+/-328.4	140,801,1261	260.0	262.0	261.0		274	3.5	0.1	11	dbSNP_123	261	1635,6963	303.0+/-306.2	164,1307,2828	yes	missense	OR8D4	NM_001005197.1	29	304,2108,4089	GG,GA,AA		19.0161,24.5459,20.8891	possibly-damaging	92/315	123777412	2716,10286	2202	4299	6501	SO:0001583	missense	338662	exon1			AGATCCATCTCCT	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"""GPCR / Class A : Olfactory receptors"""	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.274A>G	11.37:g.123777412A>G	ENSP00000325381:p.Ile92Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	168	80	0.47619	NM_001005197	Q6IFE9	Missense_Mutation	SNP	ENST00000321355.2	37	CCDS31698.1	406	0.1858974358974359	133	0.2703252032520325	57	0.1574585635359116	75	0.13111888111888112	141	0.18601583113456466	A	7.674	0.687645	0.14973	0.245459	0.190161	ENSG00000181518	ENST00000321355	T	0.05580	3.42	5.81	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.138719	0.32901	N	0.005516	T	0.00012	0.0000	M	0.78637	2.42	0.37613	P	0.07899100000000003	B	0.16802	0.019	B	0.21151	0.033	T	0.25222	-1.0138	9	0.72032	D	0.01	.	7.8258	0.29313	0.769:0.0:0.231:0.0	rs17127950;rs52791176;rs58181468;rs17127950	92	Q8NGM9	OR8D4_HUMAN	V	92	ENSP00000325381:I92V	ENSP00000325381:I92V	I	+	1	0	OR8D4	123282622	0.963000	0.33076	0.072000	0.20136	0.270000	0.26580	3.218000	0.51192	0.480000	0.27534	-0.250000	0.11733	ATC	A|0.800;G|0.200	0.200	strong		0.403	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197	
FASTKD2	22868	hgsc.bcm.edu	37	2	207631461	207631461	+	Missense_Mutation	SNP	G	G	A	rs3762568	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:207631461G>A	ENST00000236980.6	+	2	392	c.44G>A	c.(43-45)aGc>aAc	p.S15N	FASTKD2_ENST00000403094.3_Missense_Mutation_p.S15N|FASTKD2_ENST00000402774.3_Missense_Mutation_p.S15N|MDH1B_ENST00000374412.3_5'Flank|MDH1B_ENST00000449792.1_5'Flank|MDH1B_ENST00000392214.2_5'Flank|MDH1B_ENST00000454776.2_5'Flank	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	15			S -> N (in dbSNP:rs3762568).		cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		TCAGTGGAGAGCAAAATGAAT	0.403													G|||	579	0.115615	0.264	0.0562	5008	,	,		16349	0.0516		0.0586	False		,,,				2504	0.0818				p.S15N		Atlas-SNP	.											.	FASTKD2	49	.	0			c.G44A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	1075,3331	379.9+/-323.5	136,803,1264	63.0	68.0	66.0		44,44,44	1.0	0.2	2	dbSNP_107	66	652,7948	164.2+/-216.6	31,590,3679	yes	missense,missense,missense	FASTKD2	NM_001136193.1,NM_001136194.1,NM_014929.3	46,46,46	167,1393,4943	AA,AG,GG		7.5814,24.3985,13.2785	possibly-damaging,possibly-damaging,possibly-damaging	15/711,15/711,15/711	207631461	1727,11279	2203	4300	6503	SO:0001583	missense	22868	exon2			TGGAGAGCAAAAT	BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"""KIAA0971"""	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.44G>A	2.37:g.207631461G>A	ENSP00000236980:p.Ser15Asn	Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	246	246	1	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	37	CCDS2371.1	211	0.09661172161172162	121	0.2459349593495935	23	0.06353591160220995	27	0.0472027972027972	40	0.052770448548812667	G	11.96	1.794198	0.31777	0.243985	0.075814	ENSG00000118246	ENST00000236980;ENST00000418289;ENST00000402774;ENST00000403094	T;T;T;T	0.51325	2.38;0.71;2.38;2.38	4.85	0.971	0.19698	.	0.242367	0.29233	N	0.012757	T	0.00012	0.0000	L	0.46157	1.445	0.48135	P	4.0200000000001346E-4	B;B	0.13594	0.008;0.005	B;B	0.16289	0.015;0.006	T	0.10132	-1.0643	9	0.87932	D	0	-0.4365	4.75	0.13056	0.252:0.0:0.5982:0.1498	rs3762568;rs52824953;rs3762568	15;15	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	N	15	ENSP00000236980:S15N;ENSP00000409927:S15N;ENSP00000385990:S15N;ENSP00000384929:S15N	ENSP00000236980:S15N	S	+	2	0	FASTKD2	207339706	0.686000	0.27661	0.194000	0.23346	0.831000	0.47069	-0.204000	0.09425	-0.001000	0.14495	0.491000	0.48974	AGC	G|0.885;A|0.115	0.115	strong		0.403	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929	
HAPLN4	404037	hgsc.bcm.edu	37	19	19369435	19369435	+	Silent	SNP	A	A	G	rs2074295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19369435A>G	ENST00000291481.7	-	4	777	c.714T>C	c.(712-714)agT>agC	p.S238S	AC138430.4_ENST00000586064.2_RNA	NM_023002.2	NP_075378.1	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4	238	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)	p.S238S(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)	16			Epithelial(12;0.00575)		Hyaluronan(DB08818)	CGCCCCCTGCACTCCCGGTCC	0.701													G|||	1768	0.353035	0.4675	0.3213	5008	,	,		12281	0.2589		0.2117	False		,,,				2504	0.4632				p.S238S		Atlas-SNP	.											HAPLN4,NS,carcinoma,0,3	HAPLN4	44	3	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.T714C						scavenged	.	G		1881,2525	599.7+/-389.3	404,1073,726	30.0	29.0	29.0		714	1.8	0.0	19	dbSNP_96	29	1941,6655	695.8+/-404.8	217,1507,2574	no	coding-synonymous	HAPLN4	NM_023002.2		621,2580,3300	GG,GA,AA		22.5803,42.6918,29.3955		238/403	19369435	3822,9180	2203	4298	6501	SO:0001819	synonymous_variant	404037	exon4			CCCTGCACTCCCG	AB107883	CCDS12398.1	19p13.1	2013-01-11						"""Immunoglobulin superfamily / V-set domain containing"""	31357	protein-coding gene	gene with protein product	"""brain link protein 2"""					12663660	Standard	NM_023002		Approved	BRAL2, KIAA1926	uc002nmb.3	Q86UW8		ENST00000291481.7:c.714T>C	19.37:g.19369435A>G		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_023002	A5PKW5|Q96PW2	Silent	SNP	ENST00000291481.7	37	CCDS12398.1																																																																																			A|0.702;G|0.298	0.298	strong		0.701	HAPLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460117.2	NM_023002	
PTPLAD2	401494	hgsc.bcm.edu	37	9	21029330	21029330	+	Missense_Mutation	SNP	T	T	C	rs2298260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:21029330T>C	ENST00000495827.2	-	2	151	c.106A>G	c.(106-108)Aca>Gca	p.T36A	PTPLAD2_ENST00000513293.2_Missense_Mutation_p.T36A|PTPLAD2_ENST00000488436.1_5'Flank	NM_001010915.3	NP_001010915.2	Q5VWC8	HACD4_HUMAN	protein tyrosine phosphatase-like A domain containing 2	36			T -> A (in dbSNP:rs2298260).		fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)	10				Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10)		GTCATATTTGTAAATATCCAA	0.313													T|||	1723	0.34405	0.2776	0.389	5008	,	,		19330	0.503		0.2883	False		,,,				2504	0.2955				p.T36A		Atlas-SNP	.											.	PTPLAD2	26	.	0			c.A106G						PASS	.	T	ALA/THR	945,2705		130,685,1010	90.0	90.0	90.0		106	4.1	1.0	9	dbSNP_100	90	2226,5926		304,1618,2154	yes	missense	PTPLAD2	NM_001010915.3	58	434,2303,3164	CC,CT,TT		27.3062,25.8904,26.8683	benign	36/233	21029330	3171,8631	1825	4076	5901	SO:0001583	missense	401494	exon2			TATTTGTAAATAT		CCDS43791.1	9p21.3	2008-02-05			ENSG00000188921	ENSG00000188921			20920	protein-coding gene	gene with protein product		615941					Standard	NM_001010915		Approved	Em:AL662879.1, OTTHUMG00000021016	uc010mir.1	Q5VWC8	OTTHUMG00000021016	ENST00000495827.2:c.106A>G	9.37:g.21029330T>C	ENSP00000419503:p.Thr36Ala	Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	250	117	0.468	NM_001010915	Q7Z385	Missense_Mutation	SNP	ENST00000495827.2	37	CCDS43791.1	745	0.3411172161172161	121	0.2459349593495935	130	0.35911602209944754	289	0.5052447552447552	205	0.2704485488126649	T	11.44	1.638463	0.29157	0.258904	0.273062	ENSG00000188921	ENST00000513293;ENST00000495827	T;T	0.21361	2.01;2.01	5.3	4.12	0.48240	.	0.122950	0.53938	N	0.000041	T	0.00012	0.0000	N	0.10733	0.035	0.29235	P	0.873013	B	0.10296	0.003	B	0.10450	0.005	T	0.43909	-0.9362	9	0.17369	T	0.5	-13.4153	10.7399	0.46147	0.0:0.0779:0.0:0.9221	rs2298260;rs57409575;rs2298260	36	Q5VWC8	HACD4_HUMAN	A	36	ENSP00000426475:T36A;ENSP00000419503:T36A	ENSP00000419503:T36A	T	-	1	0	PTPLAD2	21019330	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.608000	0.46308	0.913000	0.36797	0.533000	0.62120	ACA	T|0.655;C|0.345	0.345	strong		0.313	PTPLAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055434.3	NM_001010915	
DEAF1	10522	hgsc.bcm.edu	37	11	653968	653968	+	Silent	SNP	T	T	C	rs10615	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:653968T>C	ENST00000382409.3	-	11	2071	c.1587A>G	c.(1585-1587)caA>caG	p.Q529Q	DEAF1_ENST00000525904.1_5'UTR|DEAF1_ENST00000338675.6_Silent_p.Q454Q	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	529					anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		CTACCTTGCGTTGGCAGAAGG	0.632													C|||	1426	0.284744	0.6263	0.1369	5008	,	,		16402	0.2202		0.1312	False		,,,				2504	0.1524				p.Q529Q		Atlas-SNP	.											.	DEAF1	47	.	0			c.A1587G						PASS	.	C		2383,2023	563.4+/-381.2	659,1065,479	188.0	148.0	161.0		1587	3.5	1.0	11	dbSNP_116	161	1052,7548	771.0+/-407.7	73,906,3321	no	coding-synonymous	DEAF1	NM_021008.2		732,1971,3800	CC,CT,TT		12.2326,45.9147,26.4109		529/566	653968	3435,9571	2203	4300	6503	SO:0001819	synonymous_variant	10522	exon11			CTTGCGTTGGCAG	AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030		"""Zinc fingers, MYND-type"""	14677	protein-coding gene	gene with protein product		602635	"""deformed epidermal autoregulatory factor 1 (Drosophila)"""			9773984	Standard	XR_428838		Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.1587A>G	11.37:g.653968T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_021008	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Silent	SNP	ENST00000382409.3	37	CCDS31327.1																																																																																			T|0.726;C|0.274	0.274	strong		0.632	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383614.3	NM_021008	
EVPL	2125	hgsc.bcm.edu	37	17	74005611	74005611	+	Silent	SNP	G	G	A	rs75019874	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:74005611G>A	ENST00000301607.3	-	22	3928	c.3675C>T	c.(3673-3675)agC>agT	p.S1225S	EVPL_ENST00000586740.1_Silent_p.S1247S	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1225	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TCTCCACACCGCTCCTCTTGC	0.637													G|||	65	0.0129792	0.0015	0.0173	5008	,	,		15968	0.001		0.0258	False		,,,				2504	0.0245				p.S1225S		Atlas-SNP	.											.	EVPL	155	.	0			c.C3675T						PASS	.	G		23,4383	30.8+/-60.4	0,23,2180	109.0	88.0	95.0		3675	-3.5	0.0	17	dbSNP_131	95	206,8394	89.2+/-151.4	3,200,4097	no	coding-synonymous	EVPL	NM_001988.2		3,223,6277	AA,AG,GG		2.3953,0.522,1.7607		1225/2034	74005611	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	2125	exon22			CACACCGCTCCTC	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.3675C>T	17.37:g.74005611G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	134	58	0.432836	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																			G|0.983;A|0.017	0.017	strong		0.637	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
USP29	57663	hgsc.bcm.edu	37	19	57642413	57642413	+	Missense_Mutation	SNP	C	C	A	rs35394887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57642413C>A	ENST00000254181.4	+	4	2824	c.2370C>A	c.(2368-2370)gaC>gaA	p.D790E	USP29_ENST00000598197.1_Missense_Mutation_p.D790E	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	790	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TGGGTTCTGACAACCCAGGAA	0.468													C|||	23	0.00459265	0.0	0.0072	5008	,	,		20144	0.0		0.006	False		,,,				2504	0.0123				p.D790E		Atlas-SNP	.											.	USP29	186	.	0			c.C2370A						PASS	.	C	GLU/ASP	5,4401	9.9+/-24.2	0,5,2198	50.0	43.0	46.0		2370	-1.5	0.0	19	dbSNP_126	46	62,8538	37.8+/-93.5	0,62,4238	yes	missense	USP29	NM_020903.2	45	0,67,6436	AA,AC,CC		0.7209,0.1135,0.5151	probably-damaging	790/923	57642413	67,12939	2203	4300	6503	SO:0001583	missense	57663	exon4			TTCTGACAACCCA		CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"""Ubiquitin-specific peptidases"""	18563	protein-coding gene	gene with protein product		609546	"""ubiquitin specific protease 29"""			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.2370C>A	19.37:g.57642413C>A	ENSP00000254181:p.Asp790Glu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	10.17	1.276210	0.23307	0.001135	0.007209	ENSG00000131864	ENST00000254181	T	0.72942	-0.7	2.05	-1.45	0.08828	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.	.	.	.	T	0.57110	0.2031	L	0.54323	1.7	0.09310	N	1	P	0.47545	0.897	P	0.45946	0.498	T	0.55496	-0.8132	9	0.72032	D	0.01	.	5.8011	0.18414	0.0:0.5297:0.0:0.4703	rs35394887	790	Q9HBJ7	UBP29_HUMAN	E	790	ENSP00000254181:D790E	ENSP00000254181:D790E	D	+	3	2	USP29	62334225	0.862000	0.29867	0.001000	0.08648	0.010000	0.07245	-0.726000	0.04936	-0.484000	0.06763	-0.483000	0.04790	GAC	C|0.996;A|0.004	0.004	strong		0.468	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1		
LRRC55	219527	hgsc.bcm.edu	37	11	56949691	56949691	+	Missense_Mutation	SNP	G	G	A	rs12364102	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56949691G>A	ENST00000497933.1	+	1	471	c.324G>A	c.(322-324)atG>atA	p.M108I		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	78					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						ACCTGCCAATGGACACCCGAA	0.612													G|||	333	0.0664936	0.0144	0.0879	5008	,	,		18285	0.0714		0.1113	False		,,,				2504	0.0706				p.M108I		Atlas-SNP	.											.	LRRC55	52	.	0			c.G324A						PASS	.	G	ILE/MET	136,4266	97.1+/-135.8	2,132,2067	59.0	63.0	62.0		324	4.9	0.9	11	dbSNP_120	62	1052,7540	222.2+/-259.3	75,902,3319	yes	missense	LRRC55	NM_001005210.2	10	77,1034,5386	AA,AG,GG		12.2439,3.0895,9.1427	benign	108/342	56949691	1188,11806	2201	4296	6497	SO:0001583	missense	219527	exon1			GCCAATGGACACC		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.324G>A	11.37:g.56949691G>A	ENSP00000419542:p.Met108Ile	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	175	82	0.468571	NM_001005210	A7E2U7|B2RN81	Missense_Mutation	SNP	ENST00000497933.1	37	CCDS31539.1	162	0.07417582417582418	11	0.022357723577235773	35	0.09668508287292818	42	0.07342657342657342	74	0.09762532981530343	G	15.67	2.901736	0.52227	0.030895	0.122439	ENSG00000183908	ENST00000497933	T	0.41065	1.01	5.8	4.89	0.63831	Leucine-rich repeat-containing N-terminal (1);	0.575233	0.18019	N	0.154310	T	0.00271	0.0008	N	0.01668	-0.77	0.23386	P	0.99778324	B	0.09022	0.002	B	0.09377	0.004	T	0.04053	-1.0981	9	0.46703	T	0.11	.	13.5959	0.61988	0.0752:0.0:0.9248:0.0	rs12364102;rs52808242;rs56765576;rs12364102	78	Q6ZSA7	LRC55_HUMAN	I	108	ENSP00000419542:M108I	ENSP00000419542:M108I	M	+	3	0	LRRC55	56706267	1.000000	0.71417	0.894000	0.35097	0.759000	0.43091	4.049000	0.57397	1.455000	0.47813	0.655000	0.94253	ATG	G|0.920;A|0.080	0.080	strong		0.612	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210	
TMEM17	200728	hgsc.bcm.edu	37	2	62733189	62733189	+	Missense_Mutation	SNP	C	C	T	rs17854454	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:62733189C>T	ENST00000335390.5	-	1	287	c.76G>A	c.(76-78)Ggt>Agt	p.G26S		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	26			G -> S (in dbSNP:rs17854454). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GACTCTGGACCGGTCCGATTG	0.647													C|||	773	0.154353	0.0492	0.134	5008	,	,		12335	0.2302		0.1541	False		,,,				2504	0.2331				p.G26S		Atlas-SNP	.											.	TMEM17	19	.	0			c.G76A						PASS	.	C	SER/GLY	287,4119	151.4+/-185.3	11,265,1927	35.0	36.0	36.0		76	3.9	1.0	2	dbSNP_123	36	1491,7109	271.9+/-289.8	137,1217,2946	yes	missense	TMEM17	NM_198276.2	56	148,1482,4873	TT,TC,CC		17.3372,6.5138,13.6706	benign	26/199	62733189	1778,11228	2203	4300	6503	SO:0001583	missense	200728	exon1			CTGGACCGGTCCG		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.76G>A	2.37:g.62733189C>T	ENSP00000335094:p.Gly26Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	168	107	0.636905	NM_198276	Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	37	CCDS1871.1	344	0.1575091575091575	29	0.05894308943089431	52	0.143646408839779	141	0.2465034965034965	122	0.16094986807387862	C	8.752	0.921567	0.17982	0.065138	0.173372	ENSG00000186889	ENST00000335390	T	0.42513	0.97	4.82	3.92	0.45320	.	0.476121	0.23926	N	0.043188	T	0.00012	0.0000	L	0.27053	0.805	0.30744	P	0.745851	B	0.24368	0.102	B	0.15052	0.012	T	0.13229	-1.0517	9	0.08599	T	0.76	-3.2417	10.6935	0.45886	0.0:0.9078:0.0:0.0922	rs17854454	26	Q86X19	TMM17_HUMAN	S	26	ENSP00000335094:G26S	ENSP00000335094:G26S	G	-	1	0	TMEM17	62586693	1.000000	0.71417	0.991000	0.47740	0.022000	0.10575	2.764000	0.47613	2.525000	0.85131	0.456000	0.33151	GGT	C|0.865;T|0.135	0.135	strong		0.647	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
ATRX	546	hgsc.bcm.edu	37	X	76937963	76937963	+	Missense_Mutation	SNP	G	G	C	rs3088074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:76937963G>C	ENST00000373344.5	-	9	2999	c.2785C>G	c.(2785-2787)Cag>Gag	p.Q929E	ATRX_ENST00000395603.3_Missense_Mutation_p.Q891E|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	929			Q -> E (in dbSNP:rs3088074). {ECO:0000269|Ref.4}.		ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						GTAAAACTCTGCTCTTTCCCA	0.388			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome						C|||	2085	0.552318	0.7209	0.2911	3775	,	,		14097	0.3581		0.2326	False		,,,				2504	0.3425				p.Q929E		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.C2785G						PASS	.	C	GLU/GLN,GLU/GLN	3310,525		1231,361,487,40,84	131.0	131.0	131.0		2785,2671	4.9	0.4	X	dbSNP_102	131	2057,4666		230,1008,589,1189,1280	yes	missense,missense	ATRX	NM_000489.3,NM_138270.2	29,29	1461,1369,1076,1229,1364	CC,CG,C,GG,G		30.5965,13.6897,49.1665	benign,benign	929/2493,891/2455	76937963	5367,5191	2203	4296	6499	SO:0001583	missense	546	exon9			AACTCTGCTCTTT	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.2785C>G	X.37:g.76937963G>C	ENSP00000362441:p.Gln929Glu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	130	121	0.930769	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	846	0.5099457504520796	243	0.8933823529411765	65	0.2195945945945946	143	0.3264840182648402	130	0.2006172839506173	C	0.391	-0.923656	0.02377	0.863103	0.305965	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.90261	-2.55;-2.64	5.79	4.93	0.64822	.	0.479810	0.21799	N	0.068943	T	0.00012	0.0000	N	0.00413	-1.525	0.54753	P	2.0000000000020002E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44251	-0.9340	9	0.02654	T	1	-2.338	9.9408	0.41578	0.0:0.5498:0.3778:0.0724	rs3088074;rs3192074;rs6619935;rs17139638;rs17272202;rs61752454	861;891;929	P46100-6;P46100-4;P46100	.;.;ATRX_HUMAN	E	929;891;856	ENSP00000362441:Q929E;ENSP00000378967:Q891E	ENSP00000362441:Q929E	Q	-	1	0	ATRX	76824619	0.004000	0.15560	0.426000	0.26672	0.158000	0.22134	0.278000	0.18753	0.607000	0.29982	-0.273000	0.10243	CAG	G|0.461;0|0.024	.	strong		0.388	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	
BIRC6	57448	hgsc.bcm.edu	37	2	32690189	32690189	+	Silent	SNP	A	A	G	rs35682129	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:32690189A>G	ENST00000421745.2	+	26	5447	c.5313A>G	c.(5311-5313)caA>caG	p.Q1771Q		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1771					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					ATTTTCTTCAACCTCCGCCTC	0.343													A|||	340	0.0678914	0.0076	0.0879	5008	,	,		13221	0.1498		0.0765	False		,,,				2504	0.0419				p.Q1771Q	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,caecum,carcinoma,0,11	BIRC6	838	11	0			c.A5313G						PASS	.	A		88,4318	70.9+/-108.8	0,88,2115	57.0	57.0	57.0		5313	-7.2	0.7	2	dbSNP_126	57	664,7934	162.3+/-215.1	22,620,3657	no	coding-synonymous	BIRC6	NM_016252.3		22,708,5772	GG,GA,AA		7.7227,1.9973,5.7828		1771/4858	32690189	752,12252	2203	4299	6502	SO:0001819	synonymous_variant	57448	exon26			TCTTCAACCTCCG	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.5313A>G	2.37:g.32690189A>G		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	185	181	0.978378	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			A|0.932;G|0.068	0.068	strong		0.343	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
LCE1F	353137	hgsc.bcm.edu	37	1	152748962	152748962	+	Missense_Mutation	SNP	C	C	T	rs116630978		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152748962C>T	ENST00000334371.2	+	1	115	c.115C>T	c.(115-117)Cct>Tct	p.P39S		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	39	Pro-rich.				keratinization (GO:0031424)			p.P39A(1)		kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			taagtgccctccTGTCTCTTC	0.677													.|||	1	0.000199681	0.0008	0.0	5008	,	,		14646	0.0		0.0	False		,,,				2504	0.0				p.P39S		Atlas-SNP	.											LCE1F,NS,carcinoma,0,2	LCE1F	42	2	1	Substitution - Missense(1)	prostate(1)	c.C115T						PASS	.	C	SER/PRO	1,4405	2.1+/-5.4	0,1,2202	58.0	60.0	59.0		115	4.6	0.9	1	dbSNP_132	59	0,8600		0,0,4300	no	missense	LCE1F	NM_178354.2	74	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	39/119	152748962	1,13005	2203	4300	6503	SO:0001583	missense	353137	exon1			TGCCCTCCTGTCT		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"""Late cornified envelopes"""	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	ENST00000334371.2:c.115C>T	1.37:g.152748962C>T	ENSP00000334187:p.Pro39Ser	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	145	7	0.0482759	NM_178354		Missense_Mutation	SNP	ENST00000334371.2	37	CCDS1023.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	10.13	1.264799	0.23136	2.27E-4	0.0	ENSG00000240386	ENST00000334371	T	0.04119	3.7	4.56	4.56	0.56223	.	.	.	.	.	T	0.02848	0.0085	L	0.39326	1.205	0.24725	N	0.993127	B	0.28760	0.221	B	0.34138	0.176	T	0.30736	-0.9968	9	0.87932	D	0	.	13.0238	0.58804	0.0:1.0:0.0:0.0	.	39	Q5T754	LCE1F_HUMAN	S	39	ENSP00000334187:P39S	ENSP00000334187:P39S	P	+	1	0	LCE1F	151015586	0.776000	0.28616	0.936000	0.37596	0.529000	0.34654	2.029000	0.41098	2.516000	0.84829	0.557000	0.71058	CCT	C|0.998;T|0.002	0.002	strong		0.677	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232534957	232534957	+	Silent	SNP	T	T	C	rs12043251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:232534957T>C	ENST00000366630.1	-	22	5443	c.5085A>G	c.(5083-5085)agA>agG	p.R1695R	SIPA1L2_ENST00000262861.4_Silent_p.R1695R|SIPA1L2_ENST00000308942.4_Silent_p.R751R			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1695					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CCTCCTGCAGTCTCATGTTGT	0.493													C|||	2011	0.401558	0.2564	0.4697	5008	,	,		19239	0.7371		0.2654	False		,,,				2504	0.3436				p.R1695R		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.A5085G						PASS	.	C		1049,3137		147,755,1191	122.0	119.0	120.0		5085	0.7	1.0	1	dbSNP_120	120	2166,6344		268,1630,2357	no	coding-synonymous	SIPA1L2	NM_020808.3		415,2385,3548	CC,CT,TT		25.4524,25.0597,25.3229		1695/1723	232534957	3215,9481	2093	4255	6348	SO:0001819	synonymous_variant	57568	exon21			CTGCAGTCTCATG	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.5085A>G	1.37:g.232534957T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																			T|0.628;C|0.372	0.372	strong		0.493	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
Unknown	0	hgsc.bcm.edu	37	11	124095414	124095414	+	IGR	SNP	C	C	G	rs10893172	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124095414C>G								OR10D3 (38462 upstream) : OR8G1 (25008 downstream)																							TTTCTTTCCTCCGTAGAAACT	0.468													-|||	2254	0.45008	0.6127	0.3429	5008	,	,		16626	0.3165		0.337	False		,,,				2504	0.5603				p.S6C		Atlas-SNP	.											.	.	.	.	0			c.C17G						PASS	.	C	CYS/SER	2055,1735		564,927,404	61.0	61.0	61.0		17	-2.5	0.0	11	dbSNP_120	61	2683,5565		446,1791,1887	yes	missense	OR8G2	NM_001007249.1	112	1010,2718,2291	GG,GC,CC		32.5291,45.7784,39.3587	possibly-damaging	6/305	124095414	4738,7300	1895	4124	6019	SO:0001628	intergenic_variant	26492	exon1			TTTCCTCCGTAGA																													11.37:g.124095414C>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_001007249		Missense_Mutation	SNP		37																																																																																				C|0.606;G|0.394	0.394	strong	0	0.468								
GJB5	2709	hgsc.bcm.edu	37	1	35223345	35223345	+	Silent	SNP	G	G	A	rs3738345	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:35223345G>A	ENST00000338513.1	+	2	587	c.414G>A	c.(412-414)aaG>aaA	p.K138K	GJB4_ENST00000339480.1_5'Flank	NM_005268.3	NP_005259.1	O95377	CXB5_HUMAN	gap junction protein, beta 5, 31.1kDa	138					cell communication (GO:0007154)|epidermis development (GO:0008544)|labyrinthine layer morphogenesis (GO:0060713)|spongiotrophoblast differentiation (GO:0060708)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.K138K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)	10		Myeloproliferative disorder(586;0.0393)				TAGTGTTCAAGGCGAGCGTGG	0.557													G|||	1320	0.263578	0.4826	0.2378	5008	,	,		21205	0.1062		0.2535	False		,,,				2504	0.1585				p.K138K		Atlas-SNP	.											GJB5,NS,carcinoma,0,1	GJB5	35	1	1	Substitution - coding silent(1)	stomach(1)	c.G414A						PASS	.	G		1877,2529	541.7+/-375.8	389,1099,715	129.0	114.0	119.0		414	3.0	1.0	1	dbSNP_107	119	2155,6445	370.3+/-335.8	259,1637,2404	no	coding-synonymous	GJB5	NM_005268.2		648,2736,3119	AA,AG,GG		25.0581,42.601,31.0011		138/274	35223345	4032,8974	2203	4300	6503	SO:0001819	synonymous_variant	2709	exon2			GTTCAAGGCGAGC	BC004379	CCDS382.1	1p34.3	2008-05-14	2007-11-06		ENSG00000189280	ENSG00000189280		"""Ion channels / Gap junction proteins (connexins)"""	4287	protein-coding gene	gene with protein product	"""connexin 31.1"""	604493	"""gap junction protein, beta 5 (connexin 31.1)"", ""gap junction protein, beta 5"""			9843209	Standard	NM_005268		Approved	CX31.1	uc001bxu.4	O95377	OTTHUMG00000004053	ENST00000338513.1:c.414G>A	1.37:g.35223345G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	146	143	0.979452	NM_005268	Q9UPA3	Silent	SNP	ENST00000338513.1	37	CCDS382.1																																																																																			G|0.718;A|0.282	0.282	strong		0.557	GJB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011561.1	NM_005268	
EAPP	55837	hgsc.bcm.edu	37	14	34985645	34985645	+	Silent	SNP	G	G	A	rs7797	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:34985645G>A	ENST00000250454.3	-	6	810	c.729C>T	c.(727-729)gcC>gcT	p.A243A		NM_018453.3	NP_060923.2	Q56P03	EAPP_HUMAN	E2F-associated phosphoprotein	243					negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2)	12	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00342)|Epithelial(34;0.18)	GBM - Glioblastoma multiforme(112;0.0196)		CTGCCTTCTCGGCAGCATCTT	0.448													G|||	1387	0.276957	0.2897	0.219	5008	,	,		18456	0.1905		0.3678	False		,,,				2504	0.2965				p.A243A		Atlas-SNP	.											.	EAPP	28	.	0			c.C729T						PASS	.	G		1303,2659		223,857,901	242.0	239.0	240.0		729	-3.0	0.0	14	dbSNP_52	240	3090,5210		569,1952,1629	no	coding-synonymous	EAPP	NM_018453.3		792,2809,2530	AA,AG,GG		37.2289,32.8874,35.8261		243/286	34985645	4393,7869	1981	4150	6131	SO:0001819	synonymous_variant	55837	exon6			CTTCTCGGCAGCA	AF217512	CCDS41941.1	14q13	2007-03-26	2007-03-26	2007-03-26		ENSG00000129518			19312	protein-coding gene	gene with protein product		609486	"""chromosome 14 open reading frame 11"""	C14orf11		15716352	Standard	NM_018453		Approved	BM036, FLJ20578	uc001wsd.1	Q56P03		ENST00000250454.3:c.729C>T	14.37:g.34985645G>A		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	245	126	0.514286	NM_018453	Q9BVF4|Q9NWV5|Q9NZ86	Silent	SNP	ENST00000250454.3	37	CCDS41941.1																																																																																			G|0.697;A|0.303	0.303	strong		0.448	EAPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409847.1	NM_018453	
MATN2	4147	hgsc.bcm.edu	37	8	99019799	99019799	+	Missense_Mutation	SNP	G	G	A	rs372608950		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:99019799G>A	ENST00000520016.1	+	9	1667	c.1543G>A	c.(1543-1545)Gtg>Atg	p.V515M	MATN2_ENST00000521689.1_Missense_Mutation_p.V515M|MATN2_ENST00000254898.5_Missense_Mutation_p.V515M|MATN2_ENST00000524308.1_Missense_Mutation_p.V474M|MATN2_ENST00000522025.2_Missense_Mutation_p.V231M			O00339	MATN2_HUMAN	matrilin 2	515	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TGAGGGACACGTGCTCCGCAG	0.567																																					p.V515M		Atlas-SNP	.											.	MATN2	165	.	0			c.G1543A						PASS	.						143.0	140.0	141.0					8																	99019799		2145	4249	6394	SO:0001583	missense	4147	exon10			GGACACGTGCTCC	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1543G>A	8.37:g.99019799G>A	ENSP00000430487:p.Val515Met	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.569|6.569	0.473360|0.473360	0.12461|0.12461	.|.	.|.	ENSG00000132561|ENSG00000132561	ENST00000518154|ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016	.|D;D;D;T;D	.|0.87887	.|-2.3;-2.3;-2.31;1.5;-2.3	5.65|5.65	2.57|2.57	0.30868|0.30868	.|Epidermal growth factor-like (1);	.|0.695407	.|0.13029	.|N	.|0.419495	T|T	0.80259|0.80259	0.4590|0.4590	L|L	0.41961|0.41961	1.31|1.31	0.21355|0.21355	N|N	0.999711|0.999711	.|B;B;B;B	.|0.21606	.|0.058;0.026;0.02;0.014	.|B;B;B;B	.|0.11329	.|0.006;0.003;0.005;0.003	T|T	0.68157|0.68157	-0.5483|-0.5483	5|10	.|0.45353	.|T	.|0.12	-6.9692|-6.9692	6.4777|6.4777	0.22045|0.22045	0.4096:0.0:0.5904:0.0|0.4096:0.0:0.5904:0.0	.|.	.|474;515;515;515	.|C9JH87;E9PF03;O00339-2;O00339	.|.;.;.;MATN2_HUMAN	H|M	297|515;515;474;474;231;515	.|ENSP00000429977:V515M;ENSP00000254898:V515M;ENSP00000430221:V474M;ENSP00000429010:V231M;ENSP00000430487:V515M	.|ENSP00000254898:V515M	R|V	+|+	2|1	0|0	MATN2|MATN2	99088975|99088975	0.000000|0.000000	0.05858|0.05858	0.315000|0.315000	0.25238|0.25238	0.144000|0.144000	0.21451|0.21451	-0.333000|-0.333000	0.07894|0.07894	0.577000|0.577000	0.29470|0.29470	-0.126000|-0.126000	0.14955|0.14955	CGT|GTG	.	.	weak		0.567	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
STEAP1B	256227	hgsc.bcm.edu	37	7	22532336	22532336	+	Missense_Mutation	SNP	T	T	C	rs149580813	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:22532336T>C	ENST00000406890.2	-	4	647	c.553A>G	c.(553-555)Aaa>Gaa	p.K185E	STEAP1B_ENST00000404369.4_Missense_Mutation_p.K204E	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	185						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						GCATCTTCTTTATTTTGTTGG	0.408													t|||	302	0.0603035	0.1309	0.0519	5008	,	,		16778	0.0		0.0666	False		,,,				2504	0.0266				p.K204E		Atlas-SNP	.											.	STEAP1B	22	.	0			c.A610G						PASS	.						123.0	108.0	113.0					7																	22532336		692	1590	2282	SO:0001583	missense	256227	exon4			CTTCTTTATTTTG		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.553A>G	7.37:g.22532336T>C	ENSP00000385239:p.Lys185Glu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	201	108	0.537313	NM_001164460	B5MCI2	Missense_Mutation	SNP	ENST00000406890.2	37	CCDS55094.1	125	0.05723443223443223	57	0.11585365853658537	17	0.04696132596685083	0	0.0	51	0.06728232189973615	t	15.21	2.767068	0.49574	.	.	ENSG00000105889	ENST00000406890;ENST00000404369;ENST00000424363;ENST00000439708	T;T;T;T	0.12984	2.68;2.81;2.86;2.63	1.23	1.23	0.21249	Flavoprotein transmembrane component (1);	0.373083	0.16730	U	0.201899	T	0.00241	0.0007	L	0.56280	1.765	0.45806	P	0.001310999999999951	D;P	0.54964	0.969;0.722	P;B	0.51582	0.674;0.393	T	0.09357	-1.0678	9	0.49607	T	0.09	-6.2003	6.6915	0.23174	0.0:0.0:0.0:1.0	.	204;185	B5MCI2;Q6NZ63	.;STEAL_HUMAN	E	185;204;204;204	ENSP00000385239:K185E;ENSP00000384370:K204E;ENSP00000416608:K204E;ENSP00000408954:K204E	ENSP00000384370:K204E	K	-	1	0	STEAP1B	22498861	0.920000	0.31207	0.968000	0.41197	0.370000	0.29829	2.397000	0.44477	0.847000	0.35167	0.102000	0.15555	AAA	T|0.936;C|0.064	0.064	strong		0.408	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		
IL17RD	54756	hgsc.bcm.edu	37	3	57136585	57136585	+	Missense_Mutation	SNP	C	C	T	rs17057718	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:57136585C>T	ENST00000296318.7	-	10	989	c.901G>A	c.(901-903)Gtg>Atg	p.V301M	IL17RD_ENST00000427856.2_Missense_Mutation_p.V277M|IL17RD_ENST00000320057.5_Missense_Mutation_p.V157M|IL17RD_ENST00000463523.1_Missense_Mutation_p.V157M	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	301			V -> M (in dbSNP:rs17057718).		signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		GTGATGGCCACGGCTCTGATG	0.488													C|||	1031	0.205871	0.0408	0.3271	5008	,	,		17270	0.376		0.1471	False		,,,				2504	0.228				p.V301M		Atlas-SNP	.											.	IL17RD	93	.	0			c.G901A						PASS	.	C	MET/VAL	317,4089	168.0+/-198.9	12,293,1898	56.0	58.0	57.0		901	3.6	0.2	3	dbSNP_123	57	1306,7294	257.3+/-281.4	94,1118,3088	yes	missense	IL17RD	NM_017563.3	21	106,1411,4986	TT,TC,CC		15.186,7.1947,12.4789	benign	301/740	57136585	1623,11383	2203	4300	6503	SO:0001583	missense	54756	exon10			TGGCCACGGCTCT	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"""Interleukins and interleukin receptors"""	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.901G>A	3.37:g.57136585C>T	ENSP00000296318:p.Val301Met	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	161	73	0.453416	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Missense_Mutation	SNP	ENST00000296318.7	37	CCDS2880.2	456	0.2087912087912088	23	0.046747967479674794	96	0.26519337016574585	225	0.39335664335664333	112	0.14775725593667546	C	9.731	1.162180	0.21538	0.071947	0.15186	ENSG00000144730	ENST00000296318;ENST00000320057;ENST00000427856;ENST00000463523	T;T;T;T	0.10382	2.88;2.9;2.88;2.9	5.48	3.57	0.40892	.	0.104633	0.64402	D	0.000004	T	0.00012	0.0000	N	0.08118	0	0.27204	P	0.9600953	P;P;P	0.42357	0.669;0.466;0.777	B;B;B	0.31869	0.065;0.052;0.137	T	0.44967	-0.9293	9	0.33940	T	0.23	-19.0964	4.6136	0.12415	0.0:0.6131:0.0:0.3869	rs17057718;rs17057718	157;301;277	B4DXM5;Q8NFM7;Q8NFM7-3	.;I17RD_HUMAN;.	M	301;157;277;157	ENSP00000296318:V301M;ENSP00000322250:V157M;ENSP00000399209:V277M;ENSP00000417516:V157M	ENSP00000296318:V301M	V	-	1	0	IL17RD	57111625	0.894000	0.30519	0.215000	0.23724	0.320000	0.28249	1.488000	0.35551	1.557000	0.49525	-0.136000	0.14681	GTG	C|0.840;T|0.160	0.160	strong		0.488	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563	
CYP39A1	51302	hgsc.bcm.edu	37	6	46609905	46609905	+	Missense_Mutation	SNP	C	C	T	rs2277119	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46609905C>T	ENST00000275016.2	-	2	511	c.308G>A	c.(307-309)cGt>cAt	p.R103H		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	103			R -> H (in dbSNP:rs2277119).		bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						TTTACCTGTACGATAAACGAT	0.328													C|||	1291	0.257788	0.2436	0.1844	5008	,	,		18906	0.2183		0.2505	False		,,,				2504	0.3773				p.R103H		Atlas-SNP	.											.	CYP39A1	41	.	0			c.G308A						PASS	.	C	HIS/ARG	1071,3335	379.7+/-323.4	112,847,1244	65.0	67.0	67.0		308	-8.9	0.0	6	dbSNP_100	67	1960,6632	343.5+/-324.9	230,1500,2566	yes	missense	CYP39A1	NM_016593.3	29	342,2347,3810	TT,TC,CC		22.8119,24.3078,23.319	benign	103/470	46609905	3031,9967	2203	4296	6499	SO:0001583	missense	51302	exon2			CCTGTACGATAAA	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.308G>A	6.37:g.46609905C>T	ENSP00000275016:p.Arg103His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	494	0.2261904761904762	121	0.2459349593495935	64	0.17679558011049723	114	0.1993006993006993	195	0.25725593667546176	C	1.557	-0.537807	0.04082	0.243078	0.228119	ENSG00000146233	ENST00000275016	T	0.68624	-0.34	4.7	-8.93	0.00771	.	1.369710	0.04860	N	0.443911	T	0.15696	0.0378	N	0.01751	-0.74	0.80722	P	0.0	B;B	0.19445	0.036;0.001	B;B	0.10450	0.005;0.002	T	0.11717	-1.0576	9	0.10636	T	0.68	3.4561	19.749	0.96260	0.0:0.1868:0.0:0.8132	rs2277119;rs17216701;rs60948107;rs2277119	103;103	B7Z786;Q9NYL5	.;CP39A_HUMAN	H	103	ENSP00000275016:R103H	ENSP00000275016:R103H	R	-	2	0	CYP39A1	46717864	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.459000	0.06728	-2.709000	0.00395	-1.119000	0.02030	CGT	C|0.767;T|0.232	0.232	strong		0.328	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
CHML	1122	hgsc.bcm.edu	37	1	241798631	241798631	+	Silent	SNP	C	C	T	rs3737604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:241798631C>T	ENST00000366553.1	-	1	601	c.438G>A	c.(436-438)tcG>tcA	p.S146S	OPN3_ENST00000331838.5_Intron|OPN3_ENST00000366554.2_Intron|OPN3_ENST00000469376.1_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	146					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)	p.S146S(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			TATTAAAATACGATAACTGGC	0.398													T|||	1385	0.276558	0.2254	0.2565	5008	,	,		19695	0.2232		0.3241	False		,,,				2504	0.3661				p.S146S		Atlas-SNP	.											CHML,bladder,carcinoma,-1,2	CHML	82	2	1	Substitution - coding silent(1)	stomach(1)	c.G438A						scavenged	.	T	,	1131,3275	707.5+/-407.5	136,859,1208	152.0	153.0	153.0		438,	-6.6	0.0	1	dbSNP_107	153	3007,5591	661.2+/-401.9	539,1929,1831	no	coding-synonymous,intron	CHML,OPN3	NM_001821.3,NM_014322.2	,	675,2788,3039	TT,TC,CC		34.9732,25.6695,31.821	,	146/657,	241798631	4138,8866	2203	4299	6502	SO:0001819	synonymous_variant	1122	exon1			AAAATACGATAAC	X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.438G>A	1.37:g.241798631C>T		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	174	93	0.534483	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Silent	SNP	ENST00000366553.1	37	CCDS31073.1																																																																																			C|0.714;T|0.286	0.286	strong		0.398	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821	
TIAL1	7073	hgsc.bcm.edu	37	10	121336248	121336248	+	Silent	SNP	T	T	C	rs12356865	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:121336248T>C	ENST00000436547.2	-	11	920	c.876A>G	c.(874-876)caA>caG	p.Q292Q	TIAL1_ENST00000369092.4_Silent_p.Q169Q|TIAL1_ENST00000369093.2_Silent_p.Q309Q|TIAL1_ENST00000463089.2_5'UTR	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	292					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)		ATTGGCCCCATTGACTATAGT	0.428													t|||	188	0.0375399	0.0643	0.0548	5008	,	,		19355	0.0		0.0477	False		,,,				2504	0.0174				p.Q309Q		Atlas-SNP	.											TIAL1,NS,carcinoma,-2,2	TIAL1	47	2	0			c.A927G						PASS	.	C	,	238,4168	140.4+/-175.9	4,230,1969	155.0	139.0	145.0		927,876	2.6	1.0	10	dbSNP_120	145	472,8128	138.1+/-194.9	17,438,3845	no	coding-synonymous,coding-synonymous	TIAL1	NM_001033925.1,NM_003252.3	,	21,668,5814	CC,CT,TT		5.4884,5.4017,5.459	,	309/393,292/376	121336248	710,12296	2203	4300	6503	SO:0001819	synonymous_variant	7073	exon11			GCCCCATTGACTA	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.876A>G	10.37:g.121336248T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	144	66	0.458333	NM_001033925	A8K3T0|A8K4L9	Silent	SNP	ENST00000436547.2	37	CCDS7613.1																																																																																			T|0.953;C|0.047	0.047	strong		0.428	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252	
ZNF582	147948	hgsc.bcm.edu	37	19	56895496	56895496	+	Silent	SNP	C	C	T	rs12978696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56895496C>T	ENST00000301310.4	-	5	1448	c.1290G>A	c.(1288-1290)aaG>aaA	p.K430K	ZNF582_ENST00000586929.1_Silent_p.K430K	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		GACTAAAAGCCTTCCCACATT	0.388													C|||	794	0.158546	0.1029	0.0965	5008	,	,		20972	0.3095		0.1382	False		,,,				2504	0.1431				p.K430K	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.G1290A						PASS	.	C		466,3940	219.7+/-237.4	23,420,1760	124.0	119.0	121.0		1290	-5.4	0.0	19	dbSNP_121	121	1094,7506	228.9+/-263.8	76,942,3282	no	coding-synonymous	ZNF582	NM_144690.1		99,1362,5042	TT,TC,CC		12.7209,10.5765,11.9945		430/518	56895496	1560,11446	2203	4300	6503	SO:0001819	synonymous_variant	147948	exon5			AAAAGCCTTCCCA	AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"""Zinc fingers, C2H2-type"", ""-"""	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.1290G>A	19.37:g.56895496C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Silent	SNP	ENST00000301310.4	37	CCDS33121.1																																																																																			C|0.865;T|0.135	0.135	strong		0.388	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690	
TSNARE1	203062	hgsc.bcm.edu	37	8	143413136	143413136	+	Missense_Mutation	SNP	C	C	T	rs10435683	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:143413136C>T	ENST00000307180.3	-	5	919	c.802G>A	c.(802-804)Gtc>Atc	p.V268I	TSNARE1_ENST00000520166.1_Missense_Mutation_p.V268I|TSNARE1_ENST00000524325.1_Missense_Mutation_p.V268I|TSNARE1_ENST00000519651.1_Missense_Mutation_p.V49I	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	268			V -> I (in dbSNP:rs10435683).		intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)	p.V268I(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					ATTCGGAAGACGTTGGCCGAC	0.612													C|||	2160	0.43131	0.5401	0.4424	5008	,	,		19919	0.4742		0.3231	False		,,,				2504	0.3436				p.V268I		Atlas-SNP	.											TSNARE1,NS,carcinoma,0,1	TSNARE1	59	1	1	Substitution - Missense(1)	stomach(1)	c.G802A						PASS	.	C	ILE/VAL	2224,2180		567,1090,545	177.0	123.0	141.0		802	2.4	0.0	8	dbSNP_119	141	2772,5828		443,1886,1971	yes	missense	TSNARE1	NM_145003.3	29	1010,2976,2516	TT,TC,CC		32.2326,49.5005,38.4189	benign	268/514	143413136	4996,8008	2202	4300	6502	SO:0001583	missense	203062	exon5			GGAAGACGTTGGC			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.802G>A	8.37:g.143413136C>T	ENSP00000303437:p.Val268Ile	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	810	0.3708791208791209	194	0.3943089430894309	137	0.3784530386740331	269	0.47027972027972026	210	0.2770448548812665	C	3.809	-0.040197	0.07497	0.504995	0.322326	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	4.23	2.41	0.29592	t-SNARE (1);	0.261153	0.19294	N	0.117812	T	0.00012	0.0000	N	0.17474	0.49	0.52099	P	5.100000000002325E-5	B;B;B;B	0.20671	0.046;0.047;0.046;0.046	B;B;B;B	0.15484	0.013;0.003;0.013;0.013	T	0.46233	-0.9206	9	0.07030	T	0.85	-14.6583	6.5544	0.22452	0.0:0.7704:0.0:0.2296	rs10435683;rs13271812;rs59659999;rs10435683	268;49;268;268	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	I	268;268;268;49	ENSP00000428763:V268I;ENSP00000303437:V268I;ENSP00000427770:V268I;ENSP00000429679:V49I	ENSP00000303437:V268I	V	-	1	0	TSNARE1	143411043	0.273000	0.24181	0.041000	0.18516	0.846000	0.48090	0.430000	0.21428	0.257000	0.21650	0.655000	0.94253	GTC	C|0.605;T|0.395	0.395	strong		0.612	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
TNC	3371	hgsc.bcm.edu	37	9	117803271	117803271	+	Missense_Mutation	SNP	C	C	T	rs2274750	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:117803271C>T	ENST00000350763.4	-	19	5752	c.5341G>A	c.(5341-5343)Gcc>Acc	p.A1781T	TNC_ENST00000537320.1_Missense_Mutation_p.A1144T|TNC_ENST00000340094.3_Missense_Mutation_p.A1417T|TNC_ENST00000535648.1_Missense_Mutation_p.A1326T|TNC_ENST00000341037.4_Missense_Mutation_p.A1599T|TNC_ENST00000345230.3_Missense_Mutation_p.A1144T|TNC_ENST00000346706.3_Missense_Mutation_p.A1235T|TNC_ENST00000423613.2_Missense_Mutation_p.A1508T|TNC_ENST00000542877.1_Missense_Mutation_p.A1418T	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1781	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.		A -> T (in dbSNP:rs2274750).		bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CCCTTCATGGCGATGATGCTG	0.507													C|||	411	0.0820687	0.0983	0.1527	5008	,	,		18369	0.1151		0.0318	False		,,,				2504	0.0276				p.A1781T		Atlas-SNP	.											TNC,NS,carcinoma,+2,1	TNC	282	1	0			c.G5341A	GRCh37	CM067722	TNC	M	rs2274750	scavenged	.	C	THR/ALA	400,4006	200.4+/-223.7	14,372,1817	198.0	166.0	177.0		5341	4.1	0.9	9	dbSNP_100	177	266,8334	102.3+/-163.5	4,258,4038	yes	missense	TNC	NM_002160.3	58	18,630,5855	TT,TC,CC		3.093,9.0785,5.1207	possibly-damaging	1781/2202	117803271	666,12340	2203	4300	6503	SO:0001583	missense	3371	exon19			TCATGGCGATGAT		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5341G>A	9.37:g.117803271C>T	ENSP00000265131:p.Ala1781Thr	Somatic	230	2	0.00869565		WXS	Illumina HiSeq	Phase_I	231	117	0.506494	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	174|174	0.07967032967032966|0.07967032967032966	48|48	0.0975609756097561|0.0975609756097561	44|44	0.12154696132596685|0.12154696132596685	56|56	0.0979020979020979|0.0979020979020979	26|26	0.03430079155672823|0.03430079155672823	C|C	22.7|22.7	4.323493|4.323493	0.81580|0.81580	0.090785|0.090785	0.03093|0.03093	ENSG00000041982|ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877|ENST00000544972	T;T;T;T;T;T;T;T;T|.	0.67523|.	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27|.	6.08|6.08	4.08|4.08	0.47627|0.47627	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.221485|.	0.47455|.	D|.	0.000227|.	T|T	0.04363|0.04363	0.0120|0.0120	M|M	0.89287|0.89287	3.02|3.02	0.53005|0.53005	P|P	3.399999999997849E-5|3.399999999997849E-5	D;P|.	0.61697|.	0.99;0.949|.	P;P|.	0.61132|.	0.884;0.743|.	T|T	0.58869|0.58869	-0.7560|-0.7560	9|4	0.72032|.	D|.	0.01|.	.|.	12.6089|12.6089	0.56540|0.56540	0.5553:0.4447:0.0:0.0|0.5553:0.4447:0.0:0.0	rs2274750;rs52811748;rs2274750|rs2274750;rs52811748;rs2274750	1508;1781|.	E9PC84;P24821|.	.;TENA_HUMAN|.	T|H	1417;1326;1235;1144;1781;1599;1508;1144;1418|343	ENSP00000344400:A1417T;ENSP00000438152:A1326T;ENSP00000344555:A1235T;ENSP00000345861:A1144T;ENSP00000265131:A1781T;ENSP00000339553:A1599T;ENSP00000411406:A1508T;ENSP00000443478:A1144T;ENSP00000442242:A1418T|.	ENSP00000344400:A1417T|.	A|R	-|-	1|2	0|0	TNC|TNC	116843092|116843092	0.997000|0.997000	0.39634|0.39634	0.929000|0.929000	0.37066|0.37066	0.752000|0.752000	0.42762|0.42762	2.473000|2.473000	0.45145|0.45145	1.556000|1.556000	0.49512|0.49512	0.655000|0.655000	0.94253|0.94253	GCC|CGC	C|0.937;T|0.063	0.063	strong		0.507	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
CCDC50	152137	hgsc.bcm.edu	37	3	191093310	191093310	+	Intron	SNP	A	A	G	rs4677728	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:191093310A>G	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Missense_Mutation_p.K303R	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		GAGCACAGAAAAAGGAGACAC	0.532													A|||	2515	0.502196	0.7247	0.4697	5008	,	,		19772	0.4702		0.4105	False		,,,				2504	0.3517				p.K303R		Atlas-SNP	.											.	CCDC50	39	.	0			c.A908G						PASS	.	A	,ARG/LYS	2953,1451	656.2+/-400.0	986,981,235	56.0	57.0	57.0		,908	2.3	1.0	3	dbSNP_111	57	3398,5202	475.0+/-369.0	675,2048,1577	yes	intron,missense	CCDC50	NM_174908.3,NM_178335.2	,26	1661,3029,1812	GG,GA,AA		39.5116,32.9473,48.8388	,benign	,303/483	191093310	6351,6653	2202	4300	6502	SO:0001627	intron_variant	152137	exon6			ACAGAAAAAGGAG	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-4638A>G	3.37:g.191093310A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_178335	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	37	CCDS33913.1	1090	0.4990842490842491	356	0.7235772357723578	165	0.4558011049723757	254	0.44405594405594406	315	0.4155672823218997	A	6.952	0.545436	0.13312	0.670527	0.395116	ENSG00000152492	ENST00000392456	T	0.29655	1.56	5.96	2.32	0.28847	.	0.536798	0.19013	N	0.125006	T	0.00012	0.0000	.	.	.	0.48452	P	3.4199999999995345E-4	B	0.24721	0.11	B	0.19391	0.025	T	0.41520	-0.9504	8	0.02654	T	1	.	7.3769	0.26833	0.752:0.0:0.248:0.0	rs4677728;rs52807307;rs57021632;rs4677728	303	Q8IVM0-2	.	R	303	ENSP00000376250:K303R	ENSP00000376250:K303R	K	+	2	0	CCDC50	192576004	0.999000	0.42202	0.992000	0.48379	0.922000	0.55478	1.352000	0.34033	0.168000	0.19655	0.533000	0.62120	AAA	A|0.502;G|0.498	0.498	strong		0.532	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
COL11A1	1301	hgsc.bcm.edu	37	1	103405892	103405892	+	Silent	SNP	G	G	A	rs17127270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:103405892G>A	ENST00000370096.3	-	43	3687	c.3375C>T	c.(3373-3375)gaC>gaT	p.D1125D	COL11A1_ENST00000512756.1_Silent_p.D1009D|COL11A1_ENST00000353414.4_Silent_p.D1086D|COL11A1_ENST00000358392.2_Silent_p.D1137D	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1125	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCTTGTCTCCGTCTTCCCCAG	0.478													G|||	614	0.122604	0.1989	0.0634	5008	,	,		13676	0.0258		0.1769	False		,,,				2504	0.1053				p.D1137D		Atlas-SNP	.											.	COL11A1	972	.	0			c.C3411T						PASS	.	G	,,,	885,3521	343.1+/-307.5	100,685,1418	53.0	58.0	57.0		3258,3375,3411,3027	-1.0	1.0	1	dbSNP_123	57	1472,7128	280.5+/-294.5	143,1186,2971	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL11A1	NM_001190709.1,NM_001854.3,NM_080629.2,NM_080630.3	,,,	243,1871,4389	AA,AG,GG		17.1163,20.0862,18.1224	,,,	1086/1768,1125/1807,1137/1819,1009/1691	103405892	2357,10649	2203	4300	6503	SO:0001819	synonymous_variant	1301	exon43			GTCTCCGTCTTCC	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3375C>T	1.37:g.103405892G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	37	CCDS778.1																																																																																			G|0.843;A|0.157	0.157	strong		0.478	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
MAML1	9794	hgsc.bcm.edu	37	5	179193598	179193598	+	Silent	SNP	C	C	T	rs3797776	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:179193598C>T	ENST00000292599.3	+	2	1850	c.1587C>T	c.(1585-1587)agC>agT	p.S529S	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCAAGGCAGCCCGGGGTCTG	0.532													C|||	831	0.165935	0.0257	0.2161	5008	,	,		18528	0.1488		0.3231	False		,,,				2504	0.1759				p.S529S		Atlas-SNP	.											.	MAML1	118	.	0			c.C1587T						PASS	.	C		314,4092	168.7+/-199.5	17,280,1906	62.0	61.0	62.0		1587	1.2	0.4	5	dbSNP_107	62	2556,6044	416.9+/-352.3	391,1774,2135	no	coding-synonymous	MAML1	NM_014757.4		408,2054,4041	TT,TC,CC		29.7209,7.1266,22.0667		529/1017	179193598	2870,10136	2203	4300	6503	SO:0001819	synonymous_variant	9794	exon2			AGGCAGCCCGGGG	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1587C>T	5.37:g.179193598C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_014757		Silent	SNP	ENST00000292599.3	37	CCDS34315.1																																																																																			C|0.800;T|0.200	0.200	strong		0.532	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
STK31	56164	hgsc.bcm.edu	37	7	23811822	23811822	+	Silent	SNP	A	A	G	rs147172261		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:23811822A>G	ENST00000355870.3	+	15	2009	c.1890A>G	c.(1888-1890)ctA>ctG	p.L630L	STK31_ENST00000354639.3_Silent_p.L607L|STK31_ENST00000405627.3_3'UTR|STK31_ENST00000433467.2_Silent_p.L630L|STK31_ENST00000428484.1_Silent_p.L607L	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	630						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						ATCACTTGCTATCCATTAAGA	0.313																																					p.L630L		Atlas-SNP	.											STK31,NS,carcinoma,+2,1	STK31	175	1	0			c.A1890G						PASS	.	A	,,	0,4406		0,0,2203	59.0	61.0	60.0		1821,1890,1821	-8.1	0.9	7	dbSNP_134	60	4,8582	3.7+/-12.6	0,4,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	,,	0,4,6492	GG,GA,AA		0.0466,0.0,0.0308	,,	607/997,630/1020,607/997	23811822	4,12988	2203	4293	6496	SO:0001819	synonymous_variant	56164	exon15			CTTGCTATCCATT	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1890A>G	7.37:g.23811822A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	186	93	0.5	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																			A|1.000;G|0.000	0.000	weak		0.313	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
TMEM128	85013	hgsc.bcm.edu	37	4	4239589	4239589	+	Missense_Mutation	SNP	C	C	T	rs202215273		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:4239589C>T	ENST00000382753.4	-	4	481	c.472G>A	c.(472-474)Gtc>Atc	p.V158I	TMEM128_ENST00000538516.1_Intron|TMEM128_ENST00000540397.1_Missense_Mutation_p.V158I|TMEM128_ENST00000254742.2_Missense_Mutation_p.V134I			Q5BJH2	TM128_HUMAN	transmembrane protein 128	158						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)		ATAAACATGACAACCCCCATA	0.358																																					p.V134I		Atlas-SNP	.											TMEM128,NS,carcinoma,+2,1	TMEM128	12	1	0			c.G400A						scavenged	.																																			SO:0001583	missense	85013	exon4			ACATGACAACCCC	BC007729	CCDS3373.1, CCDS75099.1	4p16.3	2008-02-05			ENSG00000132406	ENSG00000132406			28201	protein-coding gene	gene with protein product							Standard	XM_005248034		Approved	MGC13159	uc003ghq.1	Q5BJH2	OTTHUMG00000125475	ENST00000382753.4:c.472G>A	4.37:g.4239589C>T	ENSP00000372201:p.Val158Ile	Somatic	371	1	0.00269542		WXS	Illumina HiSeq	Phase_I	387	30	0.0775194	NM_032927	B4DHS7|D3DVS3|Q5H9U6|Q96I94	Missense_Mutation	SNP	ENST00000382753.4	37		.	.	.	.	.	.	.	.	.	.	C	11.35	1.613970	0.28712	.	.	ENSG00000132406	ENST00000254742;ENST00000382753;ENST00000540397	.	.	.	4.89	0.648	0.17801	.	0.141721	0.45361	D	0.000380	T	0.39253	0.1071	L	0.41415	1.275	0.33775	D	0.623521	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.41270	-0.9518	9	0.30078	T	0.28	-13.7734	10.8272	0.46640	0.0:0.6852:0.0:0.3148	.	158;134	D3DVS1;Q5BJH2-2	.;.	I	134;158;158	.	ENSP00000254742:V134I	V	-	1	0	TMEM128	4290490	0.486000	0.25980	0.400000	0.26346	0.915000	0.54546	1.113000	0.31184	0.151000	0.19162	-0.186000	0.12905	GTC	.	.	weak		0.358	TMEM128-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000246798.2	NM_032927	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149212590	149212590	+	Silent	SNP	C	C	T	rs144195384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149212590C>T	ENST00000309241.5	+	5	986	c.954C>T	c.(952-954)aaC>aaT	p.N318N	PPARGC1B_ENST00000394320.3_Silent_p.N318N|PPARGC1B_ENST00000360453.4_Silent_p.N279N|PPARGC1B_ENST00000403750.1_Silent_p.N254N	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	318					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCTGCAGCAACCCCTCCCAGC	0.627													C|||	12	0.00239617	0.0068	0.0014	5008	,	,		16493	0.0		0.0	False		,,,				2504	0.002				p.N318N		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.C954T						PASS	.	C	,,	25,4381	31.7+/-61.6	0,25,2178	46.0	52.0	50.0		837,762,954	5.6	1.0	5	dbSNP_134	50	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	,,	0,25,6478	TT,TC,CC		0.0,0.5674,0.1922	,,	279/985,254/960,318/1024	149212590	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	133522	exon5			CAGCAACCCCTCC	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.954C>T	5.37:g.149212590C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Silent	SNP	ENST00000309241.5	37	CCDS4298.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	0.907	-0.720352	0.03182	0.005674	0.0	ENSG00000155846	ENST00000434684	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	T	0.69967	0.3170	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71879	-0.4459	4	.	.	.	-7.6835	19.6373	0.95740	0.0:1.0:0.0:0.0	.	.	.	.	S	5	.	.	P	+	1	0	PPARGC1B	149192783	1.000000	0.71417	1.000000	0.80357	0.234000	0.25298	2.309000	0.43699	2.636000	0.89361	0.655000	0.94253	CCC	C|0.998;T|0.002	0.002	strong		0.627	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
F5	2153	hgsc.bcm.edu	37	1	169510233	169510233	+	Silent	SNP	G	G	A	rs9332607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:169510233G>A	ENST00000367797.3	-	13	4296	c.4095C>T	c.(4093-4095)acC>acT	p.T1365T	F5_ENST00000367796.3_Silent_p.T1370T	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1365	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	CTAGAGAAAGGGTTGTATGGC	0.522													N|||	912	0.182109	0.1513	0.2017	5008	,	,		21282	0.001		0.4095	False		,,,				2504	0.1626				p.T1365T		Atlas-SNP	.											.	F5	301	.	0			c.C4095T						PASS	.	G		809,3597		78,653,1472	168.0	186.0	180.0		4095	-3.8	0.0	1	dbSNP_119	180	3471,5129		660,2151,1489	no	coding-synonymous	F5	NM_000130.4		738,2804,2961	AA,AG,GG		40.3605,18.3613,32.9079		1365/2225	169510233	4280,8726	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			AGAAAGGGTTGTA	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.4095C>T	1.37:g.169510233G>A		Somatic	287	1	0.00348432		WXS	Illumina HiSeq	Phase_I	339	169	0.498525	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			G|0.698;A|0.302	0.302	strong		0.522	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
MRO	83876	hgsc.bcm.edu	37	18	48333203	48333203	+	Missense_Mutation	SNP	C	C	G	rs4940019	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:48333203C>G	ENST00000428869.2	-	5	375	c.117G>C	c.(115-117)agG>agC	p.R39S	MRO_ENST00000256425.2_Missense_Mutation_p.R39S|MRO_ENST00000587291.1_Intron|MRO_ENST00000436348.2_Missense_Mutation_p.R53S|MRO_ENST00000588444.1_Missense_Mutation_p.R39S|MRO_ENST00000431965.2_Missense_Mutation_p.R53S|MRO_ENST00000398439.3_Missense_Mutation_p.R39S			Q9BYG7	MSTRO_HUMAN	maestro	39			R -> S (in dbSNP:rs4940019). {ECO:0000269|PubMed:14702039}.			nucleolus (GO:0005730)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|skin(2)	10		Colorectal(6;0.0596)		Colorectal(21;0.082)		GCTTCTGGAACCTCAGTTTCC	0.463													C|||	2319	0.463059	0.1929	0.6816	5008	,	,		19022	0.4673		0.496	False		,,,				2504	0.635				p.R53S		Atlas-SNP	.											.	MRO	36	.	0			c.G159C						PASS	.	C	SER/ARG,SER/ARG,SER/ARG,SER/ARG	1065,3341	387.7+/-326.6	111,843,1249	84.0	87.0	86.0		117,159,159,117	2.6	0.1	18	dbSNP_111	86	4146,4454	565.6+/-388.5	1008,2130,1162	yes	missense,missense,missense,missense	MRO	NM_001127174.1,NM_001127175.1,NM_001127176.1,NM_031939.3	110,110,110,110	1119,2973,2411	GG,GC,CC		48.2093,24.1716,40.0661	benign,benign,benign,benign	39/197,53/211,53/263,39/249	48333203	5211,7795	2203	4300	6503	SO:0001583	missense	83876	exon3			CTGGAACCTCAGT	AK054702	CCDS11947.1, CCDS45867.1, CCDS45868.1, CCDS45869.1	18q21	2012-12-19	2004-06-15		ENSG00000134042	ENSG00000134042		"""maestro heat-like repeat containing"""	24121	protein-coding gene	gene with protein product	"""B29 protein"", ""beside the Ma29 deletion"""	608080	"""chromosome 18 open reading frame 3"""	C18orf3		11401430	Standard	NM_031939		Approved	B29, FLJ30140	uc010dpa.3	Q9BYG7	OTTHUMG00000132692	ENST00000428869.2:c.117G>C	18.37:g.48333203C>G	ENSP00000409509:p.Arg39Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_001127175	B7Z2I5|B7Z3B2|E9PAT5|E9PBI3|K7EKJ8|Q8N6K5	Missense_Mutation	SNP	ENST00000428869.2	37	CCDS11947.1	980	0.44871794871794873	94	0.1910569105691057	230	0.6353591160220995	288	0.5034965034965035	368	0.48548812664907653	C	7.049	0.564038	0.13498	0.241716	0.482093	ENSG00000134042	ENST00000436348;ENST00000431965;ENST00000428869;ENST00000398439;ENST00000256425	T;T;T;T;T	0.31247	2.38;1.98;1.5;1.5;1.5	5.39	2.63	0.31362	Armadillo-type fold (1);	2.863360	0.00855	N	0.001864	T	0.00012	0.0000	M	0.72479	2.2	0.80722	P	0.0	B;P;B;B	0.35774	0.016;0.519;0.024;0.002	B;B;B;B	0.37480	0.006;0.251;0.02;0.007	T	0.47573	-0.9107	9	0.09590	T	0.72	-20.4336	5.1639	0.15075	0.1637:0.6627:0.0:0.1736	rs4940019;rs52818026;rs57216618;rs4940019	39;53;53;39	E9PFU2;E9PBI3;E9PAT5;Q9BYG7	.;.;.;MSTRO_HUMAN	S	53;53;39;39;39	ENSP00000397900:R53S;ENSP00000392614:R53S;ENSP00000409509:R39S;ENSP00000381465:R39S;ENSP00000256425:R39S	ENSP00000256425:R39S	R	-	3	2	MRO	46587201	0.019000	0.18553	0.094000	0.20943	0.732000	0.41865	0.590000	0.23954	0.271000	0.22005	-0.300000	0.09419	AGG	C|0.579;G|0.421	0.421	strong		0.463	MRO-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449478.2	NM_031939	
PLEC	5339	hgsc.bcm.edu	37	8	144992862	144992862	+	Silent	SNP	A	A	G	rs7819099	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144992862A>G	ENST00000322810.4	-	32	11707	c.11538T>C	c.(11536-11538)gcT>gcC	p.A3846A	PLEC_ENST00000398774.2_Silent_p.A3677A|PLEC_ENST00000345136.3_Silent_p.A3709A|PLEC_ENST00000354589.3_Silent_p.A3709A|PLEC_ENST00000354958.2_Silent_p.A3687A|PLEC_ENST00000436759.2_Silent_p.A3736A|PLEC_ENST00000527096.1_Silent_p.A3732A|PLEC_ENST00000356346.3_Silent_p.A3695A|PLEC_ENST00000357649.2_Silent_p.A3713A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3846	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CTTTCTTGAGAGCCTGGTAGA	0.662													G|||	2234	0.446086	0.7844	0.3703	5008	,	,		16512	0.1448		0.4364	False		,,,				2504	0.363				p.A3846A		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	0			c.T11538C						PASS	.	G	,,,,,,,	2861,1041		1085,691,175	25.0	31.0	29.0		11208,11085,11061,11538,11031,11127,11139,11127	-0.3	1.0	8	dbSNP_116	29	3625,4607		868,1889,1359	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	1953,2580,1534	GG,GA,AA		44.0355,26.6786,46.5469	,,,,,,,	3736/4575,3695/4534,3687/4526,3846/4685,3677/4516,3709/4548,3713/4552,3709/4548	144992862	6486,5648	1951	4116	6067	SO:0001819	synonymous_variant	5339	exon32			CTTGAGAGCCTGG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.11538T>C	8.37:g.144992862A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			A|0.555;G|0.445	0.445	strong		0.662	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
OCSTAMP	128506	hgsc.bcm.edu	37	20	45174026	45174026	+	Silent	SNP	A	A	C	rs202396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:45174026A>C	ENST00000279028.2	-	2	1000	c.987T>G	c.(985-987)gcT>gcG	p.A329A		NM_080721.1	NP_542452.1	Q9BR26	OCSTP_HUMAN	osteoclast stimulatory transmembrane protein	329					cellular response to estrogen stimulus (GO:0071391)|cellular response to tumor necrosis factor (GO:0071356)|multinuclear osteoclast differentiation (GO:0072674)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of osteoclast proliferation (GO:0090290)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)	2						AGTCCACAGTAGCCTGTGCCA	0.557													C|||	1266	0.252796	0.5242	0.1052	5008	,	,		19898	0.1577		0.1392	False		,,,				2504	0.2055				p.A329A		Atlas-SNP	.											.	OCSTAMP	34	.	0			c.T987G						PASS	.	C		615,769		142,331,219	17.0	17.0	17.0		987	-7.0	0.1	20	dbSNP_79	17	358,2824		21,316,1254	no	coding-synonymous	C20orf123	NM_080721.1		163,647,1473	CC,CA,AA		11.2508,44.4364,21.3097		329/567	45174026	973,3593	692	1591	2283	SO:0001819	synonymous_variant	128506	exon2			CACAGTAGCCTGT	AL034424	CCDS54468.1	20q13.12	2012-03-27	2012-03-27	2012-03-27	ENSG00000149635	ENSG00000149635			16116	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 123"""	C20orf123		18064667	Standard	NM_080721		Approved	dJ257E24.3	uc010zxu.2	Q9BR26	OTTHUMG00000032652	ENST00000279028.2:c.987T>G	20.37:g.45174026A>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_080721		Silent	SNP	ENST00000279028.2	37	CCDS54468.1																																																																																			A|0.805;C|0.195	0.195	strong		0.557	OCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079573.2	XM_496476	
APOB	338	hgsc.bcm.edu	37	2	21250914	21250914	+	Missense_Mutation	SNP	G	G	A	rs679899	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:21250914G>A	ENST00000233242.1	-	14	1980	c.1853C>T	c.(1852-1854)gCt>gTt	p.A618V	APOB_ENST00000399256.4_Missense_Mutation_p.A618V	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	618	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		A -> V (in dbSNP:rs679899). {ECO:0000269|PubMed:22095935, ECO:0000269|PubMed:3030729, ECO:0000269|PubMed:3759943}.		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCTTTCAGAGCTTCTTTCAC	0.383													G|||	2429	0.485024	0.1301	0.3919	5008	,	,		19326	0.8641		0.4742	False		,,,				2504	0.6513				p.A618V		Atlas-SNP	.											.	APOB	761	.	0			c.C1853T	GRCh37	CM984191	APOB	M	rs679899	PASS	.	G	VAL/ALA	779,3627	312.7+/-292.7	65,649,1489	113.0	117.0	115.0		1853	5.7	1.0	2	dbSNP_83	115	3975,4625	550.9+/-385.8	925,2125,1250	yes	missense	APOB	NM_000384.2	64	990,2774,2739	AA,AG,GG		46.2209,17.6804,36.5524	probably-damaging	618/4564	21250914	4754,8252	2203	4300	6503	SO:0001583	missense	338	exon14			TTCAGAGCTTCTT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1853C>T	2.37:g.21250914G>A	ENSP00000233242:p.Ala618Val	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	173	77	0.445087	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	1072	0.4908424908424908	73	0.1483739837398374	146	0.40331491712707185	483	0.8444055944055944	370	0.48812664907651715	G	29.3	4.993916	0.93167	0.176804	0.462209	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.72051	-0.62;-0.62	5.73	5.73	0.89815	Lipid transport protein, N-terminal (1);Vitellinogen, superhelical (2);	0.071469	0.53938	D	0.000042	T	0.00012	0.0000	M	0.72576	2.205	0.19300	P	0.9999726572	D	0.89917	1.0	D	0.87578	0.998	T	0.45205	-0.9277	9	0.33940	T	0.23	.	20.2886	0.98538	0.0:0.0:1.0:0.0	rs679899;rs1126420;rs3181424;rs17240681;rs52818666;rs57998826;rs679899	618	P04114	APOB_HUMAN	V	618	ENSP00000233242:A618V;ENSP00000382200:A618V	ENSP00000233242:A618V	A	-	2	0	APOB	21104419	1.000000	0.71417	0.965000	0.40720	0.979000	0.70002	6.554000	0.73923	2.882000	0.98803	0.655000	0.94253	GCT	G|0.577;A|0.423	0.423	strong		0.383	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
ANO7	50636	hgsc.bcm.edu	37	2	242129524	242129524	+	Missense_Mutation	SNP	G	G	A	rs34069570	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242129524G>A	ENST00000274979.8	+	2	311	c.208G>A	c.(208-210)Gat>Aat	p.D70N	ANO7_ENST00000402530.3_Missense_Mutation_p.D70N|ANO7_ENST00000402430.3_Missense_Mutation_p.D70N	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	70					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						CGTCCTGATCGATGTGAGCCC	0.662													G|||	41	0.0081869	0.003	0.0159	5008	,	,		16974	0.0		0.0258	False		,,,				2504	0.0				p.D70N		Atlas-SNP	.											.	ANO7	136	.	0			c.G208A						PASS	.	G	ASN/ASP,ASN/ASP	25,4375		0,25,2175	36.0	34.0	35.0		208,208	-2.0	0.0	2	dbSNP_126	35	239,8331		5,229,4051	yes	missense,missense	ANO7	NM_001001666.3,NM_001001891.3	23,23	5,254,6226	AA,AG,GG		2.7888,0.5682,2.0355	benign,benign	70/180,70/934	242129524	264,12706	2200	4285	6485	SO:0001583	missense	50636	exon2			CTGATCGATGTGA	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.208G>A	2.37:g.242129524G>A	ENSP00000274979:p.Asp70Asn	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	240	118	0.491667	NM_001001666	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	28	0.01282051282051282	3	0.006097560975609756	5	0.013812154696132596	0	0.0	20	0.026385224274406333	G	7.485	0.649496	0.14516	0.005682	0.027888	ENSG00000146205	ENST00000274979;ENST00000402530;ENST00000402430	T;T;T	0.72051	-0.62;0.24;-0.62	2.45	-1.97	0.07503	.	3.546690	0.01401	N	0.013599	T	0.29288	0.0729	L	0.28115	0.83	0.09310	N	1	B;B	0.18013	0.001;0.025	B;B	0.10450	0.001;0.005	T	0.13282	-1.0515	10	0.13853	T	0.58	.	5.0463	0.14485	0.3407:0.1573:0.502:0.0	rs34069570	70;70	Q6IWH7;Q6IWH7-2	ANO7_HUMAN;.	N	70	ENSP00000274979:D70N;ENSP00000383985:D70N;ENSP00000385418:D70N	ENSP00000274979:D70N	D	+	1	0	ANO7	241778197	0.000000	0.05858	0.001000	0.08648	0.125000	0.20455	-0.906000	0.04071	-0.982000	0.03515	-1.892000	0.00534	GAT	G|0.983;A|0.017	0.017	strong		0.662	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189616	11189616	+	Missense_Mutation	SNP	G	G	A	rs200495954		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11189616G>A	ENST00000382435.4	+	1	1220	c.1001G>A	c.(1000-1002)gGg>gAg	p.G334E		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	334						integral component of membrane (GO:0016021)											GAGAGGACAGGGAAGGTGGAG	0.498																																					p.G334E		Atlas-SNP	.											AMAC1L2,right_upper_lobe,carcinoma,+1,1	.	.	1	0			c.G1001A						scavenged	.						55.0	58.0	57.0					8																	11189616		2203	4300	6503	SO:0001583	missense	83650	exon1			GGACAGGGAAGGT	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.1001G>A	8.37:g.11189616G>A	ENSP00000371872:p.Gly334Glu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	98	10	0.102041	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	g	5.777	0.327688	0.10956	.	.	ENSG00000177710	ENST00000382435	T	0.38560	1.13	.	.	.	.	0.350088	0.20838	N	0.084754	T	0.26484	0.0647	L	0.50333	1.59	0.28172	N	0.928524	B	0.06786	0.001	B	0.04013	0.001	T	0.35574	-0.9783	8	0.02654	T	1	-1.4658	.	.	.	.	334	Q96KT7	S35G5_HUMAN	E	334	ENSP00000371872:G334E	ENSP00000371872:G334E	G	+	2	0	SLC35G5	11227026	0.086000	0.21541	0.277000	0.24703	0.278000	0.26855	-0.233000	0.09041	0.064000	0.16427	0.064000	0.15345	GGG	G|0.999;A|0.001	0.001	weak		0.498	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
OMA1	115209	hgsc.bcm.edu	37	1	58971831	58971831	+	Silent	SNP	G	G	A	rs3087585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:58971831G>A	ENST00000371226.3	-	8	1379	c.1266C>T	c.(1264-1266)ttC>ttT	p.F422F	OMA1_ENST00000358603.2_Silent_p.F422F|DAB1_ENST00000485760.1_5'UTR	NM_145243.3	NP_660286.1	Q96E52	OMA1_HUMAN	OMA1 zinc metallopeptidase	422					cristae formation (GO:0042407)|diet induced thermogenesis (GO:0002024)|energy homeostasis (GO:0097009)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrial protein processing (GO:0034982)|negative regulation of mitochondrial fusion (GO:0010637)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(1)|large_intestine(6)|liver(2)|lung(6)|prostate(1)|skin(1)	18	all_cancers(7;6.54e-05)					GGCTATCAACGAACTCCATTT	0.433													A|||	1275	0.254593	0.4546	0.2075	5008	,	,		14886	0.0526		0.2922	False		,,,				2504	0.1871				p.F422F		Atlas-SNP	.											.	OMA1	50	.	0			c.C1266T						PASS	.	A		1780,2626	642.4+/-397.6	371,1038,794	123.0	108.0	113.0		1266	-0.1	0.0	1	dbSNP_102	113	2469,6131	695.6+/-404.8	359,1751,2190	no	coding-synonymous	OMA1	NM_145243.3		730,2789,2984	AA,AG,GG		28.7093,40.3995,32.6695		422/525	58971831	4249,8757	2203	4300	6503	SO:0001819	synonymous_variant	115209	exon8			ATCAACGAACTCC	AK091101	CCDS608.1	1p32.2-p32.1	2013-05-03	2013-05-03		ENSG00000162600	ENSG00000162600			29661	protein-coding gene	gene with protein product	"""overlapping activity with M-AAA protease"", ""zinc metallopeptidase OMA1"""		"""OMA1 zinc metallopeptidase homolog (S. cerevisiae)"""			12477932	Standard	NM_145243		Approved	MPRP-1, YKR087C, ZMPOMA1, FLJ33782	uc001cyy.3	Q96E52	OTTHUMG00000010068	ENST00000371226.3:c.1266C>T	1.37:g.58971831G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	140	78	0.557143	NM_145243	D3DQ54|Q5T3G6|Q5T3G7|Q5T3G8|Q5T3G9|Q5T3H0|Q8NBB3	Silent	SNP	ENST00000371226.3	37	CCDS608.1	561	0.25686813186813184	227	0.4613821138211382	82	0.2265193370165746	33	0.057692307692307696	219	0.28891820580474936	A	2.427	-0.331726	0.05314	0.403995	0.287093	ENSG00000162600	ENST00000421528	.	.	.	5.34	-0.0487	0.13837	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.36727	P	0.11849100000000001	.	.	.	.	.	.	T	0.46205	-0.9208	3	.	.	.	-13.7021	1.6752	0.02820	0.3129:0.2556:0.3071:0.1243	rs3087585;rs17117596;rs61504687;rs3087585	.	.	.	C	264	.	.	R	-	1	0	OMA1	58744419	0.000000	0.05858	0.032000	0.17829	0.094000	0.18550	-0.221000	0.09202	-0.102000	0.12197	-0.269000	0.10298	CGT	G|0.701;A|0.299	0.299	strong		0.433	OMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027819.1	NM_145243	
C1orf85	112770	hgsc.bcm.edu	37	1	156264648	156264648	+	Missense_Mutation	SNP	C	C	T	rs1570805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156264648C>T	ENST00000362007.1	-	2	306	c.280G>A	c.(280-282)Gtc>Atc	p.V94I	C1orf85_ENST00000482579.1_5'Flank	NM_001256604.1|NM_001256609.1|NM_144580.2	NP_001243533.1|NP_001243538.1|NP_653181.1	Q8WWB7	NCUG1_HUMAN	chromosome 1 open reading frame 85	94			V -> I (in dbSNP:rs1570805). {ECO:0000269|PubMed:12975309}.		intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(2)|skin(3)	14	Hepatocellular(266;0.158)					CTCCAGTTGACGCTCAGGGTG	0.592													C|||	291	0.058107	0.0113	0.1254	5008	,	,		17017	0.0466		0.1074	False		,,,				2504	0.0348				p.V94I		Atlas-SNP	.											.	C1orf85	41	.	0			c.G280A						PASS	.	C	ILE/VAL	103,4303	82.4+/-120.9	1,101,2101	92.0	100.0	97.0		280	3.2	0.8	1	dbSNP_88	97	908,7692	203.0+/-246.1	51,806,3443	yes	missense	C1orf85	NM_144580.1	29	52,907,5544	TT,TC,CC		10.5581,2.3377,7.7733	possibly-damaging	94/407	156264648	1011,11995	2203	4300	6503	SO:0001583	missense	112770	exon2			AGTTGACGCTCAG	BC011575	CCDS1139.1, CCDS72947.1, CCDS72948.1, CCDS72949.1	1q22	2014-08-07			ENSG00000198715	ENSG00000198715			29436	protein-coding gene	gene with protein product	"""kidney lysosomal membrane protein"""					12975309, 18021396, 19489740	Standard	NM_144580		Approved	MGC31963, NCU-G1	uc001foh.4	Q8WWB7	OTTHUMG00000019789	ENST00000362007.1:c.280G>A	1.37:g.156264648C>T	ENSP00000354553:p.Val94Ile	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	189	92	0.486772	NM_001256608	A6NH16|B4DJN4|Q5SZX4|Q6UX96|Q8IV07|Q96F65	Missense_Mutation	SNP	ENST00000362007.1	37	CCDS1139.1	144	0.06593406593406594	10	0.02032520325203252	29	0.08011049723756906	19	0.033216783216783216	86	0.11345646437994723	C	14.72	2.619989	0.46736	0.023377	0.105581	ENSG00000198715	ENST00000362007	T	0.22336	1.96	5.03	3.15	0.36227	.	0.072496	0.53938	N	0.000046	T	0.10594	0.0259	M	0.75264	2.295	0.09310	P	0.9999999999999845	B	0.27791	0.189	B	0.17722	0.019	T	0.05022	-1.0911	9	0.54805	T	0.06	1.2106	8.546	0.33421	0.0:0.812:0.0:0.188	rs1570805	94	Q8WWB7	NCUG1_HUMAN	I	94	ENSP00000354553:V94I	ENSP00000354553:V94I	V	-	1	0	C1orf85	154531272	0.372000	0.25064	0.810000	0.32431	0.979000	0.70002	0.861000	0.27885	1.118000	0.41863	0.561000	0.74099	GTC	C|0.930;T|0.070	0.070	strong		0.592	C1orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052108.1	NM_144580	
TMEM259	91304	hgsc.bcm.edu	37	19	1014377	1014377	+	Silent	SNP	A	A	G	rs1058506	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1014377A>G	ENST00000356663.3	-	2	442	c.321T>C	c.(319-321)cgT>cgC	p.R107R	TMEM259_ENST00000333175.5_Silent_p.R107R	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	107						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GGATGCCCTCACGCGGCCACT	0.652													a|||	955	0.190695	0.2315	0.121	5008	,	,		17000	0.1141		0.2028	False		,,,				2504	0.2515				p.R107R		Atlas-SNP	.											C19orf6,NS,carcinoma,-1,2	.	.	2	0			c.T321C						PASS	.	A	,	836,3568	316.9+/-294.8	72,692,1438	37.0	36.0	36.0		321,321	-8.4	0.1	19	dbSNP_86	36	1523,7075	281.3+/-295.0	146,1231,2922	no	coding-synonymous,coding-synonymous	C19orf6	NM_001033026.1,NM_033420.3	,	218,1923,4360	GG,GA,AA		17.7134,18.9827,18.1434	,	107/621,107/409	1014377	2359,10643	2202	4299	6501	SO:0001819	synonymous_variant	91304	exon2			GCCCTCACGCGGC	BC008957	CCDS12052.1, CCDS32862.1	19p13.3	2013-02-06	2013-02-06	2013-02-06	ENSG00000182087	ENSG00000182087			17039	protein-coding gene	gene with protein product	"""membralin"", ""aspecific BCL2 ARE-binding protein 1"""	611011	"""chromosome 19 open reading frame 6"""	C19orf6		12638133, 16084606	Standard	XM_005259675		Approved	MGC4022, ASBABP1, MBRL	uc002lqr.1	Q4ZIN3		ENST00000356663.3:c.321T>C	19.37:g.1014377A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	135	48	0.355556	NM_033420	O60392|Q8NF79|Q96H30	Silent	SNP	ENST00000356663.3	37	CCDS32862.1																																																																																			A|0.821;G|0.179	0.179	strong		0.652	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420	
RERE	473	hgsc.bcm.edu	37	1	8425900	8425900	+	Silent	SNP	T	T	C	rs3753275	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:8425900T>C	ENST00000337907.3	-	14	2053	c.1419A>G	c.(1417-1419)acA>acG	p.T473T	RERE_ENST00000460659.1_5'Flank|RERE_ENST00000476556.1_5'UTR|RERE_ENST00000400907.2_Silent_p.T473T|RERE_ENST00000400908.2_Silent_p.T473T|RERE_ENST00000377464.1_Silent_p.T205T	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	473					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GTCTGGAGGGTGTGTTGACGG	0.642													T|||	1243	0.248203	0.413	0.1945	5008	,	,		16536	0.0575		0.1978	False		,,,				2504	0.3119				p.T473T		Atlas-SNP	.											.	RERE	129	.	0			c.A1419G						PASS	.	T	,,	1601,2805	496.7+/-363.6	285,1031,887	90.0	94.0	93.0		1419,,1419	-5.1	1.0	1	dbSNP_107	93	1644,6956	303.8+/-306.6	157,1330,2813	no	coding-synonymous,utr-5,coding-synonymous	RERE	NM_001042681.1,NM_001042682.1,NM_012102.3	,,	442,2361,3700	CC,CT,TT		19.1163,36.3368,24.95	,,	473/1567,,473/1567	8425900	3245,9761	2203	4300	6503	SO:0001819	synonymous_variant	473	exon14			GGAGGGTGTGTTG	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.1419A>G	1.37:g.8425900T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Silent	SNP	ENST00000337907.3	37	CCDS95.1																																																																																			T|0.771;C|0.229	0.229	strong		0.642	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
OR5A1	219982	hgsc.bcm.edu	37	11	59210761	59210761	+	Silent	SNP	C	C	G	rs11605572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:59210761C>G	ENST00000302030.2	+	1	145	c.120C>G	c.(118-120)acC>acG	p.T40T		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						TCTATCTTACCACCCTGGCCT	0.502													.|||	642	0.128195	0.0333	0.1326	5008	,	,		19888	0.1111		0.2525	False		,,,				2504	0.1431				p.T40T		Atlas-SNP	.											OR5A1,right_upper_lobe,carcinoma,+1,1	OR5A1	72	1	0			c.C120G						PASS	.	G		287,4115	799.4+/-415.5	12,263,1926	135.0	129.0	131.0		120	-2.2	0.0	11	dbSNP_120	131	2264,6326	707.1+/-405.6	283,1698,2314	no	coding-synonymous	OR5A1	NM_001004728.1		295,1961,4240	GG,GC,CC		26.3562,6.5198,19.6352		40/316	59210761	2551,10441	2201	4295	6496	SO:0001819	synonymous_variant	219982	exon1			TCTTACCACCCTG	AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"""GPCR / Class A : Olfactory receptors"""	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.120C>G	11.37:g.59210761C>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_001004728	B9EH58|Q6IFF2|Q96RB1	Silent	SNP	ENST00000302030.2	37	CCDS31561.1																																																																																			C|0.809;G|0.191	0.191	strong		0.502	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728	
NANOS3	342977	hgsc.bcm.edu	37	19	13988416	13988416	+	Silent	SNP	A	A	G	rs2016163	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:13988416A>G	ENST00000397555.2	+	2	297	c.297A>G	c.(295-297)acA>acG	p.T99T	NANOS3_ENST00000591727.1_Intron|MIR181D_ENST00000384853.1_RNA|MIR181C_ENST00000384881.1_RNA|NANOS3_ENST00000339133.5_Silent_p.T118T	NM_001098622.2	NP_001092092.1	P60323	NANO3_HUMAN	nanos homolog 3 (Drosophila)	99					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	7			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			GCGGCGCCACACGTGAGCGCG	0.657													G|||	2032	0.405751	0.7587	0.2478	5008	,	,		14719	0.3194		0.2127	False		,,,				2504	0.3282				p.T118T		Atlas-SNP	.											NANOS3,NS,carcinoma,0,1	NANOS3	19	1	0			c.A354G						PASS	.	G		2973,1325		1042,889,218	27.0	33.0	31.0		354	-10.0	0.0	19	dbSNP_92	31	1863,6663		207,1449,2607	no	coding-synonymous	NANOS3	NM_001098622.2		1249,2338,2825	GG,GA,AA		21.8508,30.8283,37.7105		118/193	13988416	4836,7988	2149	4263	6412	SO:0001819	synonymous_variant	342977	exon1			CGCCACACGTGAG	BM702754	CCDS42511.1	19p13.13	2003-12-01				ENSG00000187556			22048	protein-coding gene	gene with protein product		608229					Standard	NM_001098622		Approved	NANOS1L, NOS3	uc002mxj.4	P60323		ENST00000397555.2:c.297A>G	19.37:g.13988416A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_001098622	Q495E5	Silent	SNP	ENST00000397555.2	37																																																																																				A|0.677;G|0.323	0.323	strong		0.657	NANOS3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_292819	
SDK1	221935	hgsc.bcm.edu	37	7	4213975	4213975	+	Missense_Mutation	SNP	A	A	G	rs671694	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:4213975A>G	ENST00000404826.2	+	33	5061	c.4922A>G	c.(4921-4923)cAt>cGt	p.H1641R	SDK1_ENST00000389531.3_Missense_Mutation_p.H1641R	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1641	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.		H -> R (in dbSNP:rs671694). {ECO:0000269|Ref.4}.		cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		ATAGCTTTACATGCTGAGCTC	0.542													G|||	4003	0.799321	0.9803	0.781	5008	,	,		20797	0.7619		0.7266	False		,,,				2504	0.681				p.H1641R		Atlas-SNP	.											.	SDK1	361	.	0			c.A4922G						PASS	.	G	ARG/HIS	4156,250	144.6+/-179.5	1961,234,8	170.0	163.0	165.0		4922	4.9	0.1	7	dbSNP_83	165	6075,2525	413.4+/-351.1	2134,1807,359	yes	missense	SDK1	NM_152744.3	29	4095,2041,367	GG,GA,AA		29.3605,5.6741,21.3363	benign	1641/2214	4213975	10231,2775	2203	4300	6503	SO:0001583	missense	221935	exon33			CTTTACATGCTGA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4922A>G	7.37:g.4213975A>G	ENSP00000385899:p.His1641Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	1754	0.8031135531135531	477	0.9695121951219512	287	0.7928176795580111	433	0.756993006993007	557	0.7348284960422163	G	1.436	-0.568836	0.03910	0.943259	0.706395	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.59906	0.23;0.55	4.91	4.91	0.64330	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.164581	0.40554	N	0.001077	T	0.00012	0.0000	N	0.00170	-1.935	0.54753	P	1.7000000000044757E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.39014	-0.9634	9	0.07644	T	0.81	.	11.7605	0.51900	0.0823:0.0:0.9177:0.0	rs671694;rs9639713;rs17243937;rs59734821;rs671694	1641;128;1641	F8W6X9;F2Z3E9;Q7Z5N4	.;.;SDK1_HUMAN	R	1641	ENSP00000385899:H1641R;ENSP00000374182:H1641R	ENSP00000374182:H1641R	H	+	2	0	SDK1	4180501	0.994000	0.37717	0.086000	0.20670	0.030000	0.12068	3.076000	0.50081	1.073000	0.40885	-0.355000	0.07637	CAT	A|0.203;G|0.797	0.797	strong		0.542	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
TSPAN13	27075	hgsc.bcm.edu	37	7	16823095	16823095	+	Silent	SNP	G	G	A	rs11491	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:16823095G>A	ENST00000262067.4	+	6	1027	c.594G>A	c.(592-594)gcG>gcA	p.A198A		NM_014399.3	NP_055214.1	O95857	TSN13_HUMAN	tetraspanin 13	198						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)		p.A198A(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	7	Lung NSC(10;0.0494)|all_lung(11;0.109)			UCEC - Uterine corpus endometrioid carcinoma (126;0.188)		ACCCCCGCGCGAATCCTAGTG	0.388													G|||	2106	0.420527	0.3056	0.5245	5008	,	,		15724	0.2996		0.5497	False		,,,				2504	0.4939				p.A198A		Atlas-SNP	.											TSPAN13,NS,carcinoma,0,1	TSPAN13	13	1	1	Substitution - coding silent(1)	stomach(1)	c.G594A						PASS	.	G		1390,3016	459.2+/-352.2	238,914,1051	141.0	146.0	144.0		594	-1.4	1.0	7	dbSNP_52	144	4772,3828	611.0+/-395.8	1339,2094,867	no	coding-synonymous	TSPAN13	NM_014399.3		1577,3008,1918	AA,AG,GG		44.5116,31.5479,47.3781		198/205	16823095	6162,6844	2203	4300	6503	SO:0001819	synonymous_variant	27075	exon6			CCGCGCGAATCCT	AF100759	CCDS5363.1	7p21.2	2013-02-14	2005-03-21	2005-03-21	ENSG00000106537	ENSG00000106537		"""Tetraspanins"""	21643	protein-coding gene	gene with protein product		613139	"""transmembrane 4 superfamily member 13"""	TM4SF13			Standard	NM_014399		Approved	NET-6	uc003stq.3	O95857	OTTHUMG00000022968	ENST00000262067.4:c.594G>A	7.37:g.16823095G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_014399		Silent	SNP	ENST00000262067.4	37	CCDS5363.1																																																																																			T|0.000;G|0.537;C|0.000;A|0.463	0.463	strong		0.388	TSPAN13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250178.2	NM_014399	
TBL3	10607	hgsc.bcm.edu	37	16	2026292	2026292	+	Silent	SNP	T	T	C	rs17604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2026292T>C	ENST00000568546.1	+	13	1397	c.1269T>C	c.(1267-1269)agT>agC	p.S423S		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	423					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						ACACACACAGTGTGGGCACCG	0.647													C|||	241	0.048123	0.0643	0.0548	5008	,	,		19431	0.0		0.0984	False		,,,				2504	0.0194				p.S423S	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.T1269C						PASS	.	C		273,4123	793.6+/-415.2	12,249,1937	94.0	65.0	75.0		1269	-1.0	0.7	16	dbSNP_63	75	811,7789	779.5+/-407.7	47,717,3536	no	coding-synonymous	TBL3	NM_006453.2		59,966,5473	CC,CT,TT		9.4302,6.2102,8.341		423/809	2026292	1084,11912	2198	4300	6498	SO:0001819	synonymous_variant	10607	exon13			ACACAGTGTGGGC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1269T>C	16.37:g.2026292T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	159	84	0.528302	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			T|0.923;C|0.077	0.077	strong		0.647	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
CAV3	859	hgsc.bcm.edu	37	3	8775661	8775661	+	Silent	SNP	C	C	T	rs1008642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:8775661C>T	ENST00000343849.2	+	1	176	c.99C>T	c.(97-99)aaC>aaT	p.N33N	SSUH2_ENST00000478513.1_Intron|CAV3_ENST00000397368.2_Silent_p.N33N|CAV3_ENST00000472766.1_3'UTR	NM_001234.4|NM_033337.2	NP_001225.1|NP_203123.1	P56539	CAV3_HUMAN	caveolin 3	33			N -> K (in LGMD1C and MPDT; dbSNP:rs1008642). {ECO:0000269|PubMed:15564037, ECO:0000269|PubMed:15580566}.		actin filament organization (GO:0007015)|cardiac muscle cell development (GO:0055013)|caveola assembly (GO:0070836)|cell differentiation (GO:0030154)|cell growth (GO:0016049)|cholesterol homeostasis (GO:0042632)|cytoplasmic microtubule organization (GO:0031122)|endocytosis (GO:0006897)|establishment of protein localization to plasma membrane (GO:0090002)|glucose homeostasis (GO:0042593)|heart trabecula formation (GO:0060347)|membrane raft organization (GO:0031579)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of cell size (GO:0045792)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sarcomere organization (GO:0060299)|nucleus localization (GO:0051647)|plasma membrane organization (GO:0007009)|plasma membrane repair (GO:0001778)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein localization (GO:0008104)|protein localization to plasma membrane (GO:0072659)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of calcium ion import (GO:0090279)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart contraction (GO:0008016)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of nerve growth factor receptor activity (GO:0051394)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase B signaling (GO:0051896)|regulation of signal transduction by receptor internalization (GO:0038009)|regulation of skeletal muscle contraction (GO:0014819)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|T-tubule organization (GO:0033292)|triglyceride metabolic process (GO:0006641)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|dystrophin-associated glycoprotein complex (GO:0016010)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|connexin binding (GO:0071253)|ion channel binding (GO:0044325)|potassium channel inhibitor activity (GO:0019870)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein complex scaffold (GO:0032947)|sodium channel regulator activity (GO:0017080)			breast(1)|kidney(2)|large_intestine(4)|lung(3)|prostate(1)	11						AGAACATTAACGAGGACATAG	0.577													C|||	1858	0.371006	0.621	0.3055	5008	,	,		15192	0.372		0.2684	False		,,,				2504	0.184				p.N33N		Atlas-SNP	.											.	CAV3	20	.	0			c.C99T	GRCh37	CM043264	CAV3	M	rs1008642	PASS	.	C	,	2409,1997	614.9+/-392.5	652,1105,446	114.0	102.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	99,99	1.6	1.0	3	dbSNP_86	106	2054,6546	356.3+/-330.2	251,1552,2497	no	coding-synonymous,coding-synonymous	CAV3	NM_001234.3,NM_033337.2	,	903,2657,2943	TT,TC,CC		23.8837,45.3246,34.3149	,	33/152,33/152	8775661	4463,8543	2203	4300	6503	SO:0001819	synonymous_variant	859	exon1			CATTAACGAGGAC	AF043101	CCDS2569.1	3p25	2014-09-17			ENSG00000182533	ENSG00000182533			1529	protein-coding gene	gene with protein product	"""M-caveolin"""	601253				9536092, 9537420	Standard	NM_033337		Approved	VIP-21, LGMD1C, VIP21, LQT9	uc003brb.3	P56539	OTTHUMG00000090519	ENST00000343849.2:c.99C>T	3.37:g.8775661C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_033337	A8K777|Q3T1A4	Silent	SNP	ENST00000343849.2	37	CCDS2569.1																																																																																			C|0.636;T|0.364	0.364	strong		0.577	CAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207008.2	NM_033337	
OBP2A	29991	hgsc.bcm.edu	37	9	138440624	138440624	+	Silent	SNP	G	G	C	rs3827835	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:138440624G>C	ENST00000539850.1	+	5	485	c.459G>C	c.(457-459)tcG>tcC	p.S153S	OBP2A_ENST00000342114.4_Silent_p.S130S|OBP2A_ENST00000371776.1_Silent_p.S153S|OBP2A_ENST00000340780.3_Missense_Mutation_p.R175P			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	153					response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		AGGGACTCTCGGAGGAGGACA	0.567													.|||	780	0.155751	0.062	0.1383	5008	,	,		14423	0.1567		0.2515	False		,,,				2504	0.1953				p.S153S		Atlas-SNP	.											.	OBP2A	21	.	0			c.G459C						PASS	.	G		417,3989	202.1+/-225.0	32,353,1818	123.0	113.0	116.0		459	-5.0	0.0	9	dbSNP_107	116	2277,6323	379.4+/-339.3	319,1639,2342	no	coding-synonymous	OBP2A	NM_014582.2		351,1992,4160	CC,CG,GG		26.4767,9.4644,20.7135		153/171	138440624	2694,10312	2203	4300	6503	SO:0001819	synonymous_variant	29991	exon5			ACTCTCGGAGGAG	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.459G>C	9.37:g.138440624G>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	151	75	0.496689	NM_014582	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Silent	SNP	ENST00000539850.1	37	CCDS6992.1	371	0.16987179487179488	32	0.06504065040650407	63	0.17403314917127072	83	0.1451048951048951	193	0.2546174142480211	g	1.241	-0.621429	0.03636	0.094644	0.264767	ENSG00000122136	ENST00000340780	T	0.32988	1.43	2.49	-4.97	0.03029	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35895	-0.9770	7	0.22706	T	0.39	1.1792	6.2524	0.20854	0.4742:0.1358:0.39:0.0	.	175	Q5T8A5	.	P	175	ENSP00000342097:R175P	ENSP00000342097:R175P	R	+	2	0	OBP2A	137580445	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.579000	0.00425	-2.382000	0.00593	-1.546000	0.00904	CGG	A|0.001;C|0.197;G|0.802	0.197	strong		0.567	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582	
SLC8A2	6543	hgsc.bcm.edu	37	19	47969394	47969394	+	Silent	SNP	G	G	A	rs12459087	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:47969394G>A	ENST00000236877.6	-	2	662	c.267C>T	c.(265-267)atC>atT	p.I89I	SLC8A2_ENST00000542837.1_Intron|SLC8A2_ENST00000539381.1_Intron	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	89					blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		AACGGTCGGCGATGATGGACA	0.602													G|||	311	0.0621006	0.0015	0.0634	5008	,	,		16756	0.0655		0.1054	False		,,,				2504	0.0951				p.I89I		Atlas-SNP	.											.	SLC8A2	77	.	0			c.C267T						PASS	.	G		92,4314	75.7+/-113.9	0,92,2111	118.0	82.0	94.0		267	0.8	1.0	19	dbSNP_120	94	940,7660	207.0+/-248.9	59,822,3419	no	coding-synonymous	SLC8A2	NM_015063.2		59,914,5530	AA,AG,GG		10.9302,2.0881,7.9348		89/922	47969394	1032,11974	2203	4300	6503	SO:0001819	synonymous_variant	6543	exon2			GTCGGCGATGATG	AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"""Solute carriers"""	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.267C>T	19.37:g.47969394G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	183	86	0.469945	NM_015063	B4DYQ9	Silent	SNP	ENST00000236877.6	37	CCDS33065.1																																																																																			G|0.927;A|0.073	0.073	strong		0.602	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1		
ACPT	93650	hgsc.bcm.edu	37	19	51297826	51297826	+	Missense_Mutation	SNP	C	C	A	rs55735528|rs386810263	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51297826C>A	ENST00000270593.1	+	9	974	c.974C>A	c.(973-975)gCc>gAc	p.A325D	ACPT_ENST00000270594.3_Missense_Mutation_p.A232D|CTD-2568A17.8_ENST00000594114.1_RNA	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	325						integral component of membrane (GO:0016021)	acid phosphatase activity (GO:0003993)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(3)	11		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GGGAATCCCGCCAAAGATGGA	0.617													A|||	1652	0.329872	0.1309	0.2161	5008	,	,		17428	0.6538		0.3012	False		,,,				2504	0.3753				p.A325D		Atlas-SNP	.											.	ACPT	43	.	0			c.C974A						PASS	.	C	ASP/ALA	673,3733		44,585,1574	39.0	39.0	39.0		974	2.9	0.0	19	dbSNP_129	39	2383,6217		348,1687,2265	yes	missense	ACPT	NM_033068.2	126	392,2272,3839	AA,AC,CC		27.7093,15.2746,23.4968	benign	325/427	51297826	3056,9950	2203	4300	6503	SO:0001583	missense	93650	exon9			ATCCCGCCAAAGA	AF321918	CCDS12802.1	19q13.33	2012-10-02			ENSG00000142513	ENSG00000142513			14376	protein-coding gene	gene with protein product		606362				11414767	Standard	NM_033068		Approved		uc002pta.1	Q9BZG2		ENST00000270593.1:c.974C>A	19.37:g.51297826C>A	ENSP00000270593:p.Ala325Asp	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Missense_Mutation	SNP	ENST00000270593.1	37	CCDS12802.1	640	0.29304029304029305	50	0.1016260162601626	71	0.19613259668508287	329	0.5751748251748252	190	0.25065963060686014	N	3.945	-0.013485	0.07727	0.152746	0.277093	ENSG00000142513	ENST00000270593;ENST00000270594	T;T	0.76709	2.97;-1.04	3.9	2.88	0.33553	.	0.642945	0.14811	N	0.297051	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46638	-0.9177	9	0.14656	T	0.56	-10.0341	8.9577	0.35827	0.8111:0.1889:0.0:0.0	rs55735528;rs61505895	325	Q9BZG2	PPAT_HUMAN	D	325;232	ENSP00000270593:A325D;ENSP00000270594:A232D	ENSP00000270593:A325D	A	+	2	0	ACPT	55989638	0.004000	0.15560	0.017000	0.16124	0.002000	0.02628	1.783000	0.38664	0.688000	0.31529	-0.367000	0.07326	GCC	C|0.752;A|0.248	0.248	strong		0.617	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068	
ZNF696	79943	hgsc.bcm.edu	37	8	144378184	144378184	+	Silent	SNP	C	C	G	rs2235115	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144378184C>G	ENST00000330143.3	+	3	748	c.339C>G	c.(337-339)ggC>ggG	p.G113G		NM_030895.2	NP_112157.2	Q9H7X3	ZN696_HUMAN	zinc finger protein 696	113					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)			lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CAGGCCCCGGCGCAGAGGGCG	0.692													G|||	2537	0.506589	0.2239	0.6499	5008	,	,		14162	0.6726		0.4682	False		,,,				2504	0.6554				p.G113G		Atlas-SNP	.											.	ZNF696	18	.	0			c.C339G						PASS	.	G		989,3259		160,669,1295	6.0	7.0	6.0		339	-5.3	0.0	8	dbSNP_98	6	3578,4716		868,1842,1437	no	coding-synonymous	ZNF696	NM_030895.2		1028,2511,2732	GG,GC,CC		43.1396,23.2815,36.4137		113/375	144378184	4567,7975	2124	4147	6271	SO:0001819	synonymous_variant	79943	exon3			CCCCGGCGCAGAG	AK024191	CCDS6399.1	8q24.3	2013-01-08				ENSG00000185730		"""Zinc fingers, C2H2-type"""	25872	protein-coding gene	gene with protein product							Standard	NM_030895		Approved	FLJ14129	uc003yxy.4	Q9H7X3		ENST00000330143.3:c.339C>G	8.37:g.144378184C>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_030895	A0AVE2	Silent	SNP	ENST00000330143.3	37	CCDS6399.1																																																																																			C|0.518;G|0.482	0.482	strong		0.692	ZNF696-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381164.2	NM_030895	
CACNA1H	8912	hgsc.bcm.edu	37	16	1269029	1269029	+	Silent	SNP	T	T	C	rs2738893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1269029T>C	ENST00000348261.5	+	34	6195	c.5947T>C	c.(5947-5949)Ttg>Ctg	p.L1983L	CACNA1H_ENST00000358590.4_Silent_p.L1977L|CACNA1H_ENST00000565831.1_Silent_p.L1977L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1983					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCAGATCCCATTGGCTGTGTC	0.687													t|||	3464	0.691693	0.6861	0.7075	5008	,	,		11649	0.8681		0.6441	False		,,,				2504	0.5552				p.L1983L		Atlas-SNP	.											.	CACNA1H	317	.	0			c.T5947C						PASS	.		,	2390,1026		866,658,184	7.0	9.0	9.0		5929,5947	-5.6	0.0	16	dbSNP_100	9	4472,2502		1514,1444,529	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	2380,2102,713	CC,CT,TT		35.8761,30.0351,33.9557	,	1977/2348,1983/2354	1269029	6862,3528	1708	3487	5195	SO:0001819	synonymous_variant	8912	exon34			ATCCCATTGGCTG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.5947T>C	16.37:g.1269029T>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	195	195	1	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			T|0.277;C|0.723	0.723	strong		0.687	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
CPSF6	11052	hgsc.bcm.edu	37	12	69646914	69646914	+	Silent	SNP	G	G	A	rs2305641	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:69646914G>A	ENST00000435070.2	+	3	464	c.354G>A	c.(352-354)cgG>cgA	p.R118R	CPSF6_ENST00000456847.3_Silent_p.R118R|CPSF6_ENST00000550987.1_3'UTR|CPSF6_ENST00000551516.1_Intron|CPSF6_ENST00000266679.8_Silent_p.R118R	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa	118	Necessary for interaction with NUDT21/CPSF5.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(7)|lung(8)	16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			TTGAAAATCGGGCAAATGGCC	0.318													G|||	2147	0.428714	0.4607	0.4236	5008	,	,		17172	0.4395		0.4284	False		,,,				2504	0.3783				p.R118R		Atlas-SNP	.											.	CPSF6	96	.	0			c.G354A						PASS	.	G		1972,2432	536.2+/-374.4	456,1060,686	58.0	62.0	61.0		354	0.3	1.0	12	dbSNP_100	61	3769,4827	527.8+/-381.2	826,2117,1355	no	coding-synonymous	CPSF6	NM_007007.2		1282,3177,2041	AA,AG,GG		43.846,44.7775,44.1615		118/552	69646914	5741,7259	2202	4298	6500	SO:0001819	synonymous_variant	11052	exon3			AAATCGGGCAAAT	X67336	CCDS8988.1, CCDS73494.1	12q15	2013-06-18	2002-08-29			ENSG00000111605		"""RNA binding motif (RRM) containing"""	13871	protein-coding gene	gene with protein product	"""cleavage factor Im complex 68 kDa subunit"""	604979	"""cleavage and polyadenylation specific factor 6, 68kD subunit"""			9659921, 17267687	Standard	NM_007007		Approved	CFIM, HPBRII-4, HPBRII-7, CFIM68	uc001sut.4	Q16630		ENST00000435070.2:c.354G>A	12.37:g.69646914G>A		Somatic	341	1	0.00293255		WXS	Illumina HiSeq	Phase_I	356	153	0.429775	NM_007007	A8K7K9|Q53ES1|Q9BSJ7|Q9BW18	Silent	SNP	ENST00000435070.2	37	CCDS8988.1																																																																																			G|0.568;A|0.432	0.432	strong		0.318	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	NM_007007	
POM121L12	285877	hgsc.bcm.edu	37	7	53103794	53103794	+	Missense_Mutation	SNP	C	C	T	rs73357087	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:53103794C>T	ENST00000408890.4	+	1	446	c.430C>T	c.(430-432)Cct>Tct	p.P144S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	144				P -> S (in Ref. 3; CAD38744). {ECO:0000305}.						endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GATCGCGCCCCCTGAGCGTCA	0.711													C|||	720	0.14377	0.2073	0.2133	5008	,	,		11532	0.0982		0.1451	False		,,,				2504	0.0542				p.P144S		Atlas-SNP	.											POM121L12,NS,carcinoma,-1,1	POM121L12	146	1	0			c.C430T						PASS	.	C	SER/PRO	741,3127		76,589,1269	20.0	24.0	23.0		430	0.7	0.0	7	dbSNP_130	23	1083,7119		55,973,3073	yes	missense	POM121L12	NM_182595.3	74	131,1562,4342	TT,TC,CC		13.2041,19.1572,15.1118	probably-damaging	144/297	53103794	1824,10246	1934	4101	6035	SO:0001583	missense	285877	exon1			GCGCCCCCTGAGC		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.430C>T	7.37:g.53103794C>T	ENSP00000386133:p.Pro144Ser	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	29	12	0.413793	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	363	0.1662087912087912	105	0.21341463414634146	72	0.19889502762430938	63	0.11013986013986014	123	0.16226912928759896	C	12.14	1.849414	0.32699	0.191572	0.132041	ENSG00000221900	ENST00000408890	T	0.75477	-0.94	1.76	0.674	0.17946	.	.	.	.	.	T	0.00144	0.0004	L	0.49126	1.545	0.80722	P	0.0	D	0.71674	0.998	P	0.51833	0.681	T	0.04593	-1.0940	8	0.56958	D	0.05	.	6.4991	0.22158	0.0:0.5256:0.4744:0.0	.	144	Q8N7R1	P1L12_HUMAN	S	144	ENSP00000386133:P144S	ENSP00000386133:P144S	P	+	1	0	POM121L12	53071288	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	2.258000	0.43249	0.171000	0.19730	0.455000	0.32223	CCT	C|0.843;T|0.157	0.157	strong		0.711	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
CLK1	1195	hgsc.bcm.edu	37	2	201728858	201728858	+	Intron	SNP	C	C	T	rs140874256	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:201728858C>T	ENST00000321356.4	-	1	136				Y_RNA_ENST00000516950.1_RNA|CLK1_ENST00000434813.2_Missense_Mutation_p.R31H|CLK1_ENST00000492793.1_Intron	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1						cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						GCTTGGCTCACGCACATTCTG	0.587													C|||	6	0.00119808	0.0	0.0029	5008	,	,		15982	0.001		0.002	False		,,,				2504	0.001				p.R31H		Atlas-SNP	.											.	CLK1	103	.	0			c.G92A						PASS	.	C	HIS/ARG,	0,1384		0,0,692	100.0	89.0	92.0		92,	-2.6	0.0	2	dbSNP_134	92	3,3179		0,3,1588	yes	missense,intron	CLK1	NM_001162407.1,NM_004071.3	29,	0,3,2280	TT,TC,CC		0.0943,0.0,0.0657	,	31/527,	201728858	3,4563	692	1591	2283	SO:0001627	intron_variant	1195	exon1			GGCTCACGCACAT	L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"""CDC-like kinases"""	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.0+428G>A	2.37:g.201728858C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	44	0.594595	NM_001162407	B4DFW7|Q0P694|Q8N5V8	Missense_Mutation	SNP	ENST00000321356.4	37	CCDS2331.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	2	0.002638522427440633	C	6.751	0.507366	0.12883	0.0	9.43E-4	ENSG00000013441	ENST00000434813	T	0.70631	-0.5	2.28	-2.64	0.06114	.	.	.	.	.	T	0.43077	0.1231	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11916	-1.0568	9	0.46703	T	0.11	.	2.9621	0.05896	0.1488:0.4118:0.3218:0.1176	.	31	B4DFW7	.	H	31	ENSP00000394734:R31H	ENSP00000394734:R31H	R	-	2	0	CLK1	201437103	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.543000	0.00436	-1.305000	0.02327	-2.739000	0.00128	CGT	C|0.998;T|0.002	0.002	strong		0.587	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2		
AUNIP	79000	hgsc.bcm.edu	37	1	26162313	26162313	+	Missense_Mutation	SNP	T	T	G	rs34449716	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26162313T>G	ENST00000374298.3	-	3	299	c.245A>C	c.(244-246)aAg>aCg	p.K82T	AUNIP_ENST00000481602.1_Intron|AUNIP_ENST00000538789.1_Missense_Mutation_p.K82T	NM_024037.1	NP_076942.1	Q9H7T9	AUNIP_HUMAN	aurora kinase A and ninein interacting protein	82			K -> T (in dbSNP:rs34449716). {ECO:0000269|Ref.3}.		spindle organization (GO:0007051)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)											TGAAACACTCTTCTGGTCACT	0.403													T|||	109	0.0217652	0.0008	0.0259	5008	,	,		21146	0.0		0.0507	False		,,,				2504	0.0399				p.K82T		Atlas-SNP	.											C1orf135,NS,carcinoma,+1,1	AUNIP	1	1	0			c.A245C						PASS	.	T	THR/LYS	55,4351	52.9+/-88.7	0,55,2148	135.0	128.0	130.0		245	-0.6	0.0	1	dbSNP_126	130	501,8099	144.5+/-200.4	14,473,3813	yes	missense	C1orf135	NM_024037.1	78	14,528,5961	GG,GT,TT		5.8256,1.2483,4.275	possibly-damaging	82/358	26162313	556,12450	2203	4300	6503	SO:0001583	missense	79000	exon3			ACACTCTTCTGGT		CCDS266.1, CCDS72731.1	1p36.11	2012-08-07	2012-08-07	2012-08-07	ENSG00000127423	ENSG00000127423			28363	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 135"""	C1orf135		20596670	Standard	NM_001287490		Approved	MGC2603, AIBp	uc001bkw.1	Q9H7T9	OTTHUMG00000007372	ENST00000374298.3:c.245A>C	1.37:g.26162313T>G	ENSP00000363416:p.Lys82Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_024037	C9EI59|Q53F70	Missense_Mutation	SNP	ENST00000374298.3	37	CCDS266.1	51	0.023351648351648352	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	39	0.051451187335092345	T	8.859	0.946394	0.18356	0.012483	0.058256	ENSG00000127423	ENST00000538789;ENST00000374298	T;T	0.48201	0.82;0.82	5.14	-0.644	0.11479	.	0.624103	0.15115	N	0.279730	T	0.03178	0.0093	N	0.24115	0.695	0.09310	N	0.999996	B	0.10296	0.003	B	0.12156	0.007	T	0.06373	-1.0830	10	0.48119	T	0.1	-7.7325	4.9084	0.13809	0.0:0.3653:0.1786:0.4561	rs34449716	82	Q9H7T9	CA135_HUMAN	T	82	ENSP00000443647:K82T;ENSP00000363416:K82T	ENSP00000363416:K82T	K	-	2	0	C1orf135	26034900	0.138000	0.22547	0.036000	0.18154	0.872000	0.50106	0.174000	0.16743	-0.274000	0.09232	-0.334000	0.08254	AAG	T|0.963;G|0.037	0.037	strong		0.403	AUNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019309.2	NM_024037	
D2HGDH	728294	hgsc.bcm.edu	37	2	242690745	242690745	+	Missense_Mutation	SNP	C	C	T	rs1105273	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242690745C>T	ENST00000321264.4	+	8	1291	c.1082C>T	c.(1081-1083)gCg>gTg	p.A361V	D2HGDH_ENST00000403782.1_Missense_Mutation_p.A227V|D2HGDH_ENST00000486953.1_Intron	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	361			A -> V (in dbSNP:rs1105273).		2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		CTGGAGCACGCGCTGGGCTCC	0.617													C|||	1078	0.215256	0.2882	0.3271	5008	,	,		19217	0.2242		0.1133	False		,,,				2504	0.1329				p.A361V		Atlas-SNP	.											D2HGDH,NS,carcinoma,-1,1	D2HGDH	39	1	0			c.C1082T						PASS	.	T	VAL/ALA	1168,3238	408.0+/-334.4	153,862,1188	54.0	51.0	52.0		1082	-7.9	0.0	2	dbSNP_86	52	912,7680	201.8+/-245.2	50,812,3434	yes	missense	D2HGDH	NM_152783.3	64	203,1674,4622	TT,TC,CC		10.6145,26.5093,16.0025	benign	361/522	242690745	2080,10918	2203	4296	6499	SO:0001583	missense	728294	exon8			AGCACGCGCTGGG	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.1082C>T	2.37:g.242690745C>T	ENSP00000315351:p.Ala361Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	158	63	0.398734	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	37	CCDS33426.1	468	0.21428571428571427	134	0.27235772357723576	111	0.30662983425414364	132	0.23076923076923078	91	0.12005277044854881	c	0.048	-1.258655	0.01445	0.265093	0.106145	ENSG00000180902	ENST00000321264;ENST00000403782;ENST00000454048	T;T;T	0.78595	-1.19;-1.19;-1.01	5.1	-7.9	0.01169	FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	0.602385	0.16472	N	0.212932	T	0.00012	0.0000	N	0.20845	0.615	0.27582	P	0.9495508	B	0.13145	0.007	B	0.14023	0.01	T	0.12091	-1.0561	9	0.02654	T	1	-0.5439	16.7058	0.85371	0.0:0.3272:0.0:0.6728	rs1105273	361	Q8N465	D2HDH_HUMAN	V	361;227;62	ENSP00000315351:A361V;ENSP00000384723:A227V;ENSP00000404596:A62V	ENSP00000315351:A361V	A	+	2	0	D2HGDH	242339418	0.045000	0.20229	0.000000	0.03702	0.026000	0.11368	0.251000	0.18257	-1.680000	0.01450	-0.974000	0.02594	GCG	C|0.817;T|0.183	0.183	strong		0.617	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
SMC5	23137	hgsc.bcm.edu	37	9	72897440	72897440	+	Missense_Mutation	SNP	T	T	C	rs1180117	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:72897440T>C	ENST00000361138.5	+	7	980	c.922T>C	c.(922-924)Tgt>Cgt	p.C308R		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	308			C -> R (in dbSNP:rs1180117). {ECO:0000269|PubMed:11408570, ECO:0000269|PubMed:15489334}.		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						TCCTGTAACATGTCGAATTGA	0.353													C|||	1232	0.246006	0.2655	0.1542	5008	,	,		17121	0.2659		0.1928	False		,,,				2504	0.319				p.C308R		Atlas-SNP	.											.	SMC5	96	.	0			c.T922C						PASS	.	C	ARG/CYS	1071,3335	722.2+/-409.3	126,819,1258	93.0	90.0	91.0		922	2.6	0.0	9	dbSNP_87	91	1730,6870	736.5+/-407.0	180,1370,2750	yes	missense	SMC5	NM_015110.3	180	306,2189,4008	CC,CT,TT		20.1163,24.3078,21.5362	benign	308/1102	72897440	2801,10205	2203	4300	6503	SO:0001583	missense	23137	exon7			GTAACATGTCGAA	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.922T>C	9.37:g.72897440T>C	ENSP00000354957:p.Cys308Arg	Somatic	347	1	0.00288184		WXS	Illumina HiSeq	Phase_I	336	167	0.497024	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	491	0.22481684981684982	142	0.2886178861788618	56	0.15469613259668508	146	0.25524475524475526	147	0.19393139841688653	C	0.018	-1.486534	0.01018	0.243078	0.201163	ENSG00000198887	ENST00000361138	T	0.15952	2.38	5.61	2.61	0.31194	RecF/RecN/SMC (1);	0.675701	0.15131	N	0.278842	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46735	-0.9170	9	0.14252	T	0.57	1.4368	3.2463	0.06798	0.3592:0.4049:0.1067:0.1292	rs1180117;rs57413829;rs1180117	308	Q8IY18	SMC5_HUMAN	R	308	ENSP00000354957:C308R	ENSP00000354957:C308R	C	+	1	0	SMC5	72087260	0.000000	0.05858	0.000000	0.03702	0.626000	0.37791	0.328000	0.19681	0.076000	0.16826	-0.128000	0.14901	TGT	T|0.778;C|0.222	0.222	strong		0.353	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	
OR1N2	138882	hgsc.bcm.edu	37	9	125316350	125316350	+	Missense_Mutation	SNP	C	C	T	rs1411272	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:125316350C>T	ENST00000373688.2	+	1	960	c.902C>T	c.(901-903)aCg>aTg	p.T301M		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	301			T -> M (in dbSNP:rs1411272). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T301M(1)		breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						ATTATTCCCACGCTAAACCCA	0.393													T|||	2963	0.591653	0.6362	0.5994	5008	,	,		22233	0.6667		0.5457	False		,,,				2504	0.4959				p.T301M		Atlas-SNP	.											OR1N2,NS,carcinoma,0,1	OR1N2	51	1	1	Substitution - Missense(1)	stomach(1)	c.C902T						scavenged	.	T	MET/THR	2739,1667	507.4+/-366.7	830,1079,294	138.0	138.0	138.0		902	4.6	1.0	9	dbSNP_88	138	4597,4003	553.7+/-386.4	1205,2187,908	yes	missense	OR1N2	NM_001004457.1	81	2035,3266,1202	TT,TC,CC		46.5465,37.8348,43.5953	benign	301/331	125316350	7336,5670	2203	4300	6503	SO:0001583	missense	138882	exon1			TTCCCACGCTAAA		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.902C>T	9.37:g.125316350C>T	ENSP00000362792:p.Thr301Met	Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	176	76	0.431818	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Missense_Mutation	SNP	ENST00000373688.2	37	CCDS35123.1	1269	0.5810439560439561	292	0.5934959349593496	215	0.5939226519337016	355	0.6206293706293706	407	0.5369393139841688	T	0.802	-0.755023	0.03019	0.621652	0.534535	ENSG00000171501	ENST00000373688	T	0.36340	1.26	4.56	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000020	T	0.00012	0.0000	N	0.01464	-0.85	0.51233	P	8.099999999999774E-5	B	0.10296	0.003	B	0.04013	0.001	T	0.45145	-0.9281	9	0.02654	T	1	.	9.4731	0.38856	0.0:0.0857:0.0:0.9143	rs1411272;rs17446467;rs52827441;rs59353884;rs1411272	301	Q8NGR9	OR1N2_HUMAN	M	301	ENSP00000362792:T301M	ENSP00000362792:T301M	T	+	2	0	OR1N2	124356171	0.924000	0.31332	1.000000	0.80357	0.841000	0.47740	3.075000	0.50073	0.800000	0.34041	-0.268000	0.10319	ACG	C|0.431;N|0.000	.	strong		0.393	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
SLC25A29	123096	hgsc.bcm.edu	37	14	100759046	100759046	+	Silent	SNP	C	C	A	rs3825555	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100759046C>A	ENST00000359232.3	-	4	786	c.486G>T	c.(484-486)acG>acT	p.T162T	AL157871.2_ENST00000553954.1_RNA|SLC25A29_ENST00000555927.1_Silent_p.T96T|SLC25A29_ENST00000554912.1_Silent_p.T96T|SLC25A29_ENST00000392908.3_3'UTR|SLC25A29_ENST00000556505.1_Silent_p.T96T|RP11-638I2.6_ENST00000556458.1_lincRNA|SLC25A29_ENST00000539621.1_Silent_p.T96T	NM_001039355.1	NP_001034444.1	Q8N8R3	MCATL_HUMAN	solute carrier family 25 (mitochondrial carnitine/acylcarnitine carrier), member 29	162						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	acyl carnitine transmembrane transporter activity (GO:0015227)			NS(1)|endometrium(1)|ovary(1)	3		Melanoma(154;0.152)			L-Carnitine(DB00583)	CGAAGCTGGGCGTCTCACGCA	0.682													C|||	2656	0.530351	0.3865	0.6081	5008	,	,		13189	0.7083		0.5676	False		,,,				2504	0.4479				p.T162T		Atlas-SNP	.											SLC25A29,NS,carcinoma,0,1	SLC25A29	14	1	0			c.G486T						PASS	.	C		1913,2477		431,1051,713	29.0	19.0	22.0		486	1.1	1.0	14	dbSNP_107	22	4870,3718		1397,2076,821	no	coding-synonymous	SLC25A29	NM_001039355.1		1828,3127,1534	AA,AC,CC		43.293,43.5763,47.7346		162/304	100759046	6783,6195	2195	4294	6489	SO:0001819	synonymous_variant	123096	exon4			GCTGGGCGTCTCA	AK095532	CCDS32156.1	14q32.2	2013-05-22	2012-03-29	2004-01-21	ENSG00000197119	ENSG00000197119		"""Solute carriers"""	20116	protein-coding gene	gene with protein product		615064	"""chromosome 14 open reading frame 69"", ""solute carrier family 25, member 29"""	C14orf69			Standard	XM_005267343		Approved	FLJ38975	uc010twx.2	Q8N8R3	OTTHUMG00000171569	ENST00000359232.3:c.486G>T	14.37:g.100759046C>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_001039355	A3KMR5|Q541V0	Silent	SNP	ENST00000359232.3	37	CCDS32156.1																																																																																			C|0.465;A|0.535	0.535	strong		0.682	SLC25A29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072449.3		
DKK2	27123	hgsc.bcm.edu	37	4	107845794	107845794	+	Missense_Mutation	SNP	C	C	T	rs17037102	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:107845794C>T	ENST00000285311.3	-	3	1142	c.437G>A	c.(436-438)cGg>cAg	p.R146Q	DKK2_ENST00000513208.1_Missense_Mutation_p.R46Q|DKK2_ENST00000510463.1_Missense_Mutation_p.R100Q	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	146			R -> Q (in dbSNP:rs17037102). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.R146Q(2)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		ATCTCTGTGCCGAGTACCATC	0.438													C|||	829	0.165535	0.0053	0.3069	5008	,	,		15707	0.3859		0.1083	False		,,,				2504	0.1135				p.R146Q		Atlas-SNP	.											DKK2,NS,carcinoma,0,3	DKK2	96	3	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.G437A						scavenged	.	C	GLN/ARG	141,4265	98.5+/-137.1	3,135,2065	232.0	211.0	218.0		437	5.8	1.0	4	dbSNP_123	218	881,7719	198.9+/-243.1	45,791,3464	yes	missense	DKK2	NM_014421.2	43	48,926,5529	TT,TC,CC		10.2442,3.2002,7.8579	possibly-damaging	146/260	107845794	1022,11984	2203	4300	6503	SO:0001583	missense	27123	exon3			CTGTGCCGAGTAC	AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"""dickkopf (Xenopus laevis) homolog 2"", ""dickkopf 2 homolog (Xenopus laevis)"""			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.437G>A	4.37:g.107845794C>T	ENSP00000285311:p.Arg146Gln	Somatic	269	2	0.00743494		WXS	Illumina HiSeq	Phase_I	331	4	0.0120846	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Missense_Mutation	SNP	ENST00000285311.3	37	CCDS3675.1	380	0.17399267399267399	3	0.006097560975609756	86	0.23756906077348067	194	0.33916083916083917	97	0.1279683377308707	C	16.95	3.263558	0.59431	0.032002	0.102442	ENSG00000155011	ENST00000285311;ENST00000513208;ENST00000510463	T;T;T	0.44482	0.92;0.94;0.93	5.75	5.75	0.90469	.	0.069405	0.64402	D	0.000020	T	0.00012	0.0000	L	0.29908	0.895	0.27606	P	0.9488256	D;D	0.89917	1.0;0.99	D;D	0.79108	0.992;0.953	T	0.16305	-1.0407	9	0.48119	T	0.1	-20.6321	19.9462	0.97183	0.0:1.0:0.0:0.0	rs17037102;rs17584606;rs52807260;rs58306699;rs17037102	146;146	Q9H3R7;Q9UBU2	.;DKK2_HUMAN	Q	146;46;100	ENSP00000285311:R146Q;ENSP00000421255:R46Q;ENSP00000423797:R100Q	ENSP00000285311:R146Q	R	-	2	0	DKK2	108065243	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.645000	0.46621	2.717000	0.92951	0.585000	0.79938	CGG	C|0.879;T|0.121	0.121	strong		0.438	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4		
SPATA16	83893	hgsc.bcm.edu	37	3	172766822	172766822	+	Silent	SNP	G	G	A	rs508508	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:172766822G>A	ENST00000351008.3	-	3	858	c.675C>T	c.(673-675)agC>agT	p.S225S		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	225					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			AACTTGCCACGCTTGCTATAT	0.383													G|||	859	0.171526	0.2231	0.1801	5008	,	,		17129	0.1379		0.1511	False		,,,				2504	0.1513				p.S225S		Atlas-SNP	.											SPATA16,NS,haematopoietic_neoplasm,-1,2	SPATA16	111	2	0			c.C675T						scavenged	.	G		1031,3375	380.2+/-323.6	131,769,1303	104.0	92.0	96.0		675	-2.7	1.0	3	dbSNP_83	96	1243,7357	249.3+/-276.6	92,1059,3149	no	coding-synonymous	SPATA16	NM_031955.5		223,1828,4452	AA,AG,GG		14.4535,23.3999,17.4842		225/570	172766822	2274,10732	2203	4300	6503	SO:0001819	synonymous_variant	83893	exon3			TGCCACGCTTGCT	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.675C>T	3.37:g.172766822G>A		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	141	76	0.539007	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Silent	SNP	ENST00000351008.3	37	CCDS3221.1																																																																																			G|0.824;A|0.176	0.176	strong		0.383	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955	
RTTN	25914	hgsc.bcm.edu	37	18	67687860	67687860	+	Silent	SNP	T	T	C	rs2304378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:67687860T>C	ENST00000255674.6	-	45	6430	c.6144A>G	c.(6142-6144)gtA>gtG	p.V2048V	RTTN_ENST00000579986.1_5'UTR|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	2048					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CCTTCTGAATTACTCCTTTAC	0.393													T|||	763	0.152356	0.0605	0.1311	5008	,	,		19560	0.1806		0.2286	False		,,,				2504	0.184				p.V2048V		Atlas-SNP	.											.	RTTN	184	.	0			c.A6144G						PASS	.	T		329,3529		12,305,1612	152.0	145.0	147.0		6144	-4.0	1.0	18	dbSNP_100	147	1719,6509		172,1375,2567	no	coding-synonymous	RTTN	NM_173630.3		184,1680,4179	CC,CT,TT		20.8921,8.5277,16.9452		2048/2227	67687860	2048,10038	1929	4114	6043	SO:0001819	synonymous_variant	25914	exon45			CTGAATTACTCCT	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.6144A>G	18.37:g.67687860T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	174	75	0.431034	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Silent	SNP	ENST00000255674.6	37	CCDS42443.1																																																																																			T|0.826;C|0.174	0.174	strong		0.393	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
EID2	163126	hgsc.bcm.edu	37	19	40030704	40030704	+	Missense_Mutation	SNP	C	C	T	rs7252027	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40030704C>T	ENST00000390658.2	-	1	166	c.16G>A	c.(16-18)Gca>Aca	p.A6T		NM_153232.3	NP_694964.3			EP300 interacting inhibitor of differentiation 2											large_intestine(2)|lung(1)|urinary_tract(1)	4	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;3.2e-25)|all cancers(26;8.83e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			CTGCTGTCTGCGGGCAGCTTG	0.687													.|||	995	0.198682	0.0666	0.1686	5008	,	,		11622	0.244		0.2396	False		,,,				2504	0.3098				p.A6T		Atlas-SNP	.											.	EID2	14	.	0			c.G16A						PASS	.	C	THR/ALA	263,2765		12,239,1263	29.0	33.0	32.0		16	0.2	0.3	19	dbSNP_116	32	1280,5000		127,1026,1987	yes	missense	EID2	NM_153232.3	58	139,1265,3250	TT,TC,CC		20.3822,8.6856,16.5771	possibly-damaging	6/237	40030704	1543,7765	1514	3140	4654	SO:0001583	missense	163126	exon1			TGTCTGCGGGCAG	BC030137	CCDS12540.2	19q13.2	2008-10-24	2006-10-12	2006-10-12	ENSG00000176396	ENSG00000176396			28292	protein-coding gene	gene with protein product		609773	"""CREBBP/EP300 inhibitory protein 2"", ""CREBBP/EP300 inhibitor 2"""	CRI2		14585496	Standard	NM_153232		Approved	EID-2, MGC20452	uc002oma.3	Q8N6I1	OTTHUMG00000074073	ENST00000390658.2:c.16G>A	19.37:g.40030704C>T	ENSP00000375073:p.Ala6Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_153232		Missense_Mutation	SNP	ENST00000390658.2	37	CCDS12540.2	443	0.20283882783882784	20	0.04065040650406504	78	0.2154696132596685	149	0.26048951048951047	196	0.25857519788918204	.	17.90	3.503009	0.64298	0.086856	0.203822	ENSG00000176396	ENST00000390658;ENST00000539700	D	0.87412	-2.25	3.64	0.166	0.14999	.	1.449310	0.05067	U	0.480957	T	0.00039	0.0001	L	0.44542	1.39	0.44611	P	0.0024199999999999777	P	0.50710	0.938	B	0.41666	0.363	T	0.04178	-1.0971	9	0.37606	T	0.19	.	3.5746	0.07930	0.0:0.5451:0.2124:0.2426	rs7252027;rs58112765;rs7252027	6	Q8N6I1	EID2_HUMAN	T	6	ENSP00000375073:A6T	ENSP00000375073:A6T	A	-	1	0	EID2	44722544	0.634000	0.27190	0.337000	0.25536	0.424000	0.31475	0.100000	0.15231	0.140000	0.18849	0.485000	0.47835	GCA	C|0.788;T|0.212	0.212	strong		0.687	EID2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157251.1	NM_153232	
ZAK	51776	hgsc.bcm.edu	37	2	174128513	174128513	+	Missense_Mutation	SNP	C	C	T	rs3769148	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:174128513C>T	ENST00000375213.3	+	19	1670	c.1592C>T	c.(1591-1593)tCg>tTg	p.S531L	MLTK_ENST00000409176.2_Missense_Mutation_p.S531L|MLK7-AS1_ENST00000423106.2_RNA|MLK7-AS1_ENST00000422703.1_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		531			S -> L (in dbSNP:rs3769148). {ECO:0000269|PubMed:10924358, ECO:0000269|PubMed:11042189, ECO:0000269|PubMed:11836244, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.6}.		activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										CATGTCCATTCGATTCAGTGG	0.378													C|||	1229	0.245407	0.0219	0.2867	5008	,	,		20916	0.2123		0.4831	False		,,,				2504	0.3078				p.S531L		Atlas-SNP	.											.	ZAK	62	.	0			c.C1592T						PASS	.	C	LEU/SER	354,3406		19,316,1545	119.0	105.0	109.0		1592	0.3	0.0	2	dbSNP_107	109	4058,4184		1005,2048,1068	yes	missense	ZAK	NM_016653.2	145	1024,2364,2613	TT,TC,CC		49.2356,9.4149,36.7605	benign	531/801	174128513	4412,7590	1880	4121	6001	SO:0001583	missense	0	exon19			TCCATTCGATTCA																												ENST00000375213.3:c.1592C>T	2.37:g.174128513C>T	ENSP00000364361:p.Ser531Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	157	88	0.56051	NM_016653	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	37	CCDS42777.1	615	0.2815934065934066	13	0.026422764227642278	111	0.30662983425414364	122	0.21328671328671328	369	0.4868073878627968	C	7.512	0.654931	0.14580	0.094149	0.492356	ENSG00000091436	ENST00000409176;ENST00000375213	T;T	0.75938	-0.98;-0.98	5.74	0.342	0.15996	.	0.899151	0.09761	N	0.759278	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.40776	-0.9545	9	0.25106	T	0.35	.	2.4273	0.04462	0.1168:0.4507:0.2271:0.2054	rs3769148;rs17692053;rs52801304;rs61527137;rs3769148	531	Q9NYL2	MLTK_HUMAN	L	531	ENSP00000387259:S531L;ENSP00000364361:S531L	ENSP00000364361:S531L	S	+	2	0	AC013461.1	173836759	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.555000	0.23422	-0.223000	0.09943	-0.176000	0.13171	TCG	C|0.702;T|0.298	0.298	strong		0.378	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1		
TTN	7273	hgsc.bcm.edu	37	2	179444939	179444939	+	Missense_Mutation	SNP	C	C	T	rs2303838	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179444939C>T	ENST00000591111.1	-	268	62376	c.62152G>A	c.(62152-62154)Gtc>Atc	p.V20718I	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V13294I|TTN_ENST00000342992.6_Missense_Mutation_p.V19791I|TTN_ENST00000589042.1_Missense_Mutation_p.V22359I|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V13419I|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V13486I|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20718	Fibronectin type-III 50. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCACATTGACAGGTGGCCCA	0.348													C|||	1759	0.351238	0.3434	0.2147	5008	,	,		20260	0.631		0.1849	False		,,,				2504	0.3415				p.V22359I		Atlas-SNP	.											.	TTN	18412	.	0			c.G67075A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1207,2467		202,803,832	62.0	60.0	61.0		40456,40255,59371,39880	2.6	0.9	2	dbSNP_100	61	1445,6723		128,1189,2767	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	330,1992,3599	TT,TC,CC		17.691,32.8525,22.3949	benign,benign,benign,benign	13486/27119,13419/27052,19791/33424,13294/26927	179444939	2652,9190	1837	4084	5921	SO:0001583	missense	7273	exon318			CATTGACAGGTGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.62152G>A	2.37:g.179444939C>T	ENSP00000465570:p.Val20718Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	151	64	0.423841	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		710	0.3250915750915751	157	0.31910569105691056	73	0.20165745856353592	344	0.6013986013986014	136	0.17941952506596306	C	9.291	1.050609	0.19827	0.328525	0.17691	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.41	2.61	0.31194	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.54965	1.715	0.27033	P	0.9641858	B;B;B;B	0.10296	0.003;0.003;0.003;0.003	B;B;B;B	0.14578	0.011;0.011;0.011;0.011	T	0.39396	-0.9616	8	0.87932	D	0	.	6.7606	0.23538	0.0:0.6119:0.1229:0.2652	rs2303838;rs52803332;rs59721271;rs2303838	13294;13419;13486;20718	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	19791;13294;13486;13419;13292	ENSP00000343764:V19791I;ENSP00000434586:V13294I;ENSP00000340554:V13486I;ENSP00000352154:V13419I	ENSP00000340554:V13486I	V	-	1	0	TTN	179153185	0.001000	0.12720	0.932000	0.37286	0.972000	0.66771	-0.020000	0.12525	0.261000	0.21753	-0.253000	0.11424	GTC	C|0.677;T|0.323	0.323	strong		0.348	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RP1L1	94137	hgsc.bcm.edu	37	8	10466309	10466309	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:10466309C>T	ENST00000382483.3	-	4	5522	c.5299G>A	c.(5299-5301)Gca>Aca	p.A1767T		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1847					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGAGCCATTGCATCTCCCTCT	0.587																																					p.A1767T		Atlas-SNP	.											RP1L1,right_upper_lobe,carcinoma,0,1	RP1L1	453	1	0			c.G5299A						scavenged	.						173.0	181.0	178.0					8																	10466309		2040	4194	6234	SO:0001583	missense	94137	exon4			CCATTGCATCTCC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5299G>A	8.37:g.10466309C>T	ENSP00000371923:p.Ala1767Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	184	5	0.0271739	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.281256	0.23392	.	.	ENSG00000183638	ENST00000382483	T	0.04317	3.65	4.37	-3.17	0.05202	.	2.250130	0.03055	N	0.155105	T	0.04227	0.0117	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43669	-0.9377	10	0.25106	T	0.35	0.5597	8.6043	0.33764	0.0:0.5114:0.1009:0.3877	.	1767	A6NKC6	.	T	1767	ENSP00000371923:A1767T	ENSP00000371923:A1767T	A	-	1	0	RP1L1	10503719	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.209000	0.09358	-0.578000	0.05959	-1.842000	0.00583	GCA	.	.	none		0.587	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
DENND1A	57706	hgsc.bcm.edu	37	9	126220114	126220114	+	Silent	SNP	C	C	T	rs61736953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:126220114C>T	ENST00000373624.2	-	14	1257	c.1056G>A	c.(1054-1056)agG>agA	p.R352R	DENND1A_ENST00000542603.1_Silent_p.R94R|DENND1A_ENST00000373620.3_Silent_p.R352R|DENND1A_ENST00000394215.2_Silent_p.R322R|DENND1A_ENST00000473039.1_Intron|DENND1A_ENST00000394219.3_Silent_p.R320R|DENND1A_ENST00000373618.1_Silent_p.R320R	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	352	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						GCAGGAACTGCCTCATGGCTC	0.632													C|||	297	0.0593051	0.0946	0.0576	5008	,	,		15802	0.0		0.0686	False		,,,				2504	0.0644				p.R352R		Atlas-SNP	.											.	DENND1A	112	.	0			c.G1056A						PASS	.	C	,	385,4021	187.1+/-213.8	16,353,1834	50.0	44.0	46.0		1056,1056	2.0	1.0	9	dbSNP_129	46	760,7840	177.0+/-226.7	31,698,3571	no	coding-synonymous,coding-synonymous	DENND1A	NM_020946.1,NM_024820.2	,	47,1051,5405	TT,TC,CC		8.8372,8.7381,8.8036	,	352/1010,352/560	126220114	1145,11861	2203	4300	6503	SO:0001819	synonymous_variant	57706	exon14			GAACTGCCTCATG	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.1056G>A	9.37:g.126220114C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	76	45	0.592105	NM_024820	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Silent	SNP	ENST00000373624.2	37	CCDS35133.1																																																																																			C|0.921;T|0.079	0.079	strong		0.632	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
ARHGEF40	55701	hgsc.bcm.edu	37	14	21557021	21557021	+	Silent	SNP	G	G	A	rs74584322	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21557021G>A	ENST00000298694.4	+	23	4678	c.4551G>A	c.(4549-4551)acG>acA	p.T1517T	RP11-998D10.7_ENST00000554733.2_lincRNA|ARHGEF40_ENST00000298693.3_Silent_p.T1469T			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	1517						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T1517T(1)		large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						ACCCCACCACGCCTCTGTGAC	0.522													G|||	194	0.038738	0.0061	0.0216	5008	,	,		18513	0.0327		0.0477	False		,,,				2504	0.092				p.T1517T		Atlas-SNP	.											ARHGEF40,colon,carcinoma,0,1	ARHGEF40	84	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G4551A						scavenged	.	G		71,4335	64.7+/-102.0	0,71,2132	123.0	105.0	111.0		4551	-10.7	0.2	14	dbSNP_132	111	418,8182	130.2+/-188.1	14,390,3896	no	coding-synonymous	ARHGEF40	NM_018071.3		14,461,6028	AA,AG,GG		4.8605,1.6114,3.7598		1517/1520	21557021	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	55701	exon23			CACCACGCCTCTG		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.4551G>A	14.37:g.21557021G>A		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	157	77	0.490446	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	37	CCDS32041.1																																																																																			G|0.965;A|0.035	0.035	strong		0.522	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
AKR1C4	1109	hgsc.bcm.edu	37	10	5242164	5242164	+	Silent	SNP	A	A	G	rs17306779	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:5242164A>G	ENST00000380448.1	+	4	358	c.105A>G	c.(103-105)gtA>gtG	p.V35V	AKR1C4_ENST00000263126.1_Silent_p.V35V|AKR1CL1_ENST00000445191.1_Intron			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	35					androgen metabolic process (GO:0008209)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|bile acid transmembrane transporter activity (GO:0015125)|chlordecone reductase activity (GO:0047743)|electron carrier activity (GO:0009055)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|retinal dehydrogenase activity (GO:0001758)	p.V35V(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	18						ACAGAGCTGTAGAGGTCACCA	0.448													G|||	827	0.165136	0.0961	0.2464	5008	,	,		22801	0.129		0.2207	False		,,,				2504	0.181				p.V35V		Atlas-SNP	.											AKR1C4,NS,carcinoma,0,1	AKR1C4	57	1	1	Substitution - coding silent(1)	stomach(1)	c.A105G						PASS	.	G		487,3919	781.8+/-414.5	26,435,1742	108.0	96.0	100.0		105	-6.9	0.0	10	dbSNP_123	100	1965,6635	723.9+/-406.5	221,1523,2556	no	coding-synonymous	AKR1C4	NM_001818.3		247,1958,4298	GG,GA,AA		22.8488,11.0531,18.8528		35/324	5242164	2452,10554	2203	4300	6503	SO:0001819	synonymous_variant	1109	exon2			AGCTGTAGAGGTC	M33375	CCDS7064.1	10p15.1	2012-12-04	2012-12-04		ENSG00000198610	ENSG00000198610	1.1.1.225	"""Aldo-keto reductases"""	387	protein-coding gene	gene with protein product	"""chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4"""	600451	"""aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)"""	CHDR		7789999	Standard	NM_001818		Approved	DD4, HAKRA, C11, 3-alpha-HSD, CDR, MGC22581	uc001ihw.2	P17516	OTTHUMG00000017591	ENST00000380448.1:c.105A>G	10.37:g.5242164A>G		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	230	113	0.491304	NM_001818	Q5T6A3|Q8WW84|Q9NS54	Silent	SNP	ENST00000380448.1	37	CCDS7064.1																																																																																			A|0.824;G|0.176	0.176	strong		0.448	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818	
DRD2	1813	hgsc.bcm.edu	37	11	113283484	113283484	+	Missense_Mutation	SNP	G	G	C	rs1801028	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:113283484G>C	ENST00000362072.3	-	7	1276	c.932C>G	c.(931-933)tCc>tGc	p.S311C	DRD2_ENST00000355319.2_Missense_Mutation_p.S313C|RP11-159N11.3_ENST00000546284.1_RNA|DRD2_ENST00000346454.3_Missense_Mutation_p.S282C|DRD2_ENST00000538967.1_Missense_Mutation_p.S313C|DRD2_ENST00000542968.1_Missense_Mutation_p.S311C|DRD2_ENST00000544518.1_Missense_Mutation_p.S310C|DRD2_ENST00000535984.1_5'Flank	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	311	Interaction with PPP1R9B. {ECO:0000250}.		S -> C (may be associated with a higher risk for schizophrenia; dbSNP:rs1801028). {ECO:0000269|PubMed:7902708}.		activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	ACCATGGTGGGACGGGTCGGG	0.617													G|||	159	0.0317492	0.0008	0.0173	5008	,	,		13946	0.0367		0.0229	False		,,,				2504	0.0879				p.S311C		Atlas-SNP	.											.	DRD2	98	.	0			c.C932G	GRCh37	CM940365	DRD2	M	rs1801028	PASS	.	G	CYS/SER,CYS/SER	28,4374	33.5+/-64.1	0,28,2173	97.0	84.0	88.0		932,845	5.7	1.0	11	dbSNP_89	88	192,8400	86.3+/-148.7	3,186,4107	yes	missense,missense	DRD2	NM_000795.3,NM_016574.3	112,112	3,214,6280	CC,CG,GG		2.2346,0.6361,1.6931	possibly-damaging,possibly-damaging	311/444,282/415	113283484	220,12774	2201	4296	6497	SO:0001583	missense	1813	exon7			TGGTGGGACGGGT	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"""GPCR / Class A : Dopamine receptors"""	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.932C>G	11.37:g.113283484G>C	ENSP00000354859:p.Ser311Cys	Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	264	135	0.511364	NM_000795	Q9NZR3|Q9UPA9	Missense_Mutation	SNP	ENST00000362072.3	37	CCDS8361.1	50	0.022893772893772892	0	0.0	9	0.024861878453038673	23	0.04020979020979021	18	0.023746701846965697	G	18.42	3.620267	0.66787	0.006361	0.022346	ENSG00000149295	ENST00000355319;ENST00000346454;ENST00000362072;ENST00000544518;ENST00000542968;ENST00000538967	T;T;T;T;T;T	0.74106	-0.78;-0.77;-0.77;-0.81;-0.77;-0.78	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.151757	0.64402	D	0.000009	T	0.55016	0.1894	L	0.41573	1.285	0.46011	D	0.998817	D;B;D	0.63046	0.99;0.036;0.992	P;B;P	0.62649	0.893;0.029;0.905	T	0.72629	-0.4235	10	0.52906	T	0.07	.	19.9025	0.96993	0.0:0.0:1.0:0.0	rs1801028;rs4134622	310;282;311	F8VUV1;P14416-2;P14416	.;.;DRD2_HUMAN	C	313;282;311;310;311;313	ENSP00000347474:S313C;ENSP00000278597:S282C;ENSP00000354859:S311C;ENSP00000441068:S310C;ENSP00000442172:S311C;ENSP00000438215:S313C	ENSP00000278597:S282C	S	-	2	0	DRD2	112788694	1.000000	0.71417	0.994000	0.49952	0.833000	0.47200	6.754000	0.74909	2.722000	0.93159	0.655000	0.94253	TCC	G|0.982;C|0.018	0.018	strong		0.617	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795	
CFAP57	149465	hgsc.bcm.edu	37	1	43652442	43652442	+	Missense_Mutation	SNP	G	G	C	rs11210805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43652442G>C	ENST00000372492.4	+	6	1358	c.1034G>C	c.(1033-1035)tGc>tCc	p.C345S	WDR65_ENST00000528956.1_Missense_Mutation_p.C345S	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		345			C -> S (in dbSNP:rs11210805).							NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTCTGCCTGTGCTTCAGCCCC	0.507													G|||	643	0.128395	0.0098	0.1888	5008	,	,		16964	0.3175		0.0457	False		,,,				2504	0.136				p.C345S		Atlas-SNP	.											.	WDR65	76	.	0			c.G1034C						PASS	.	G	SER/CYS,SER/CYS,SER/CYS	78,4328	69.2+/-107.0	0,78,2125	121.0	106.0	111.0		1034,1034,1034	5.7	1.0	1	dbSNP_120	111	433,8167	133.5+/-191.0	10,413,3877	yes	missense,missense,missense	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	112,112,112	10,491,6002	CC,CG,GG		5.0349,1.7703,3.929	possibly-damaging,possibly-damaging,possibly-damaging	345/699,345/699,345/699	43652442	511,12495	2203	4300	6503	SO:0001583	missense	149465	exon6			GCCTGTGCTTCAG																												ENST00000372492.4:c.1034G>C	1.37:g.43652442G>C	ENSP00000361570:p.Cys345Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	37		270	0.12362637362637363	10	0.02032520325203252	54	0.14917127071823205	169	0.29545454545454547	37	0.048812664907651716	G	16.51	3.143401	0.57044	0.017703	0.050349	ENSG00000243710	ENST00000372492;ENST00000528956	T;T	0.06849	3.25;3.25	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat-like-containing domain (1);	0.047660	0.85682	N	0.000000	T	0.00012	0.0000	M	0.71581	2.175	0.21105	P	0.999789461	B;B	0.33637	0.002;0.42	B;B	0.39876	0.008;0.312	T	0.53940	-0.8367	9	0.19590	T	0.45	.	16.0573	0.80814	0.0:0.134:0.866:0.0	rs11210805	345;345	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	S	345	ENSP00000361570:C345S;ENSP00000435310:C345S	ENSP00000361570:C345S	C	+	2	0	WDR65	43425029	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	6.082000	0.71318	2.649000	0.89929	0.655000	0.94253	TGC	G|0.929;C|0.071	0.071	strong		0.507	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037579	33037579	+	Missense_Mutation	SNP	A	A	T	rs2308912|rs36013091	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33037579A>T	ENST00000419277.1	-	3	314	c.185T>A	c.(184-186)aTg>aAg	p.M62K	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.M62K	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	62	Alpha-1.		M -> K (in dbSNP:rs2308912).|M -> L (in dbSNP:rs2308911).|M -> Q (in allele DPA1*01:06, allele DPA1*02:01, allele DPA1*02:02 and allele DPA1*02:04; requires 2 nucleotide substitutions; dbSNP:rs36013091).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CACATAGAACATCTCATCTTC	0.483													.|||	2159	0.43111	0.5794	0.2795	5008	,	,		19351	0.6508		0.1869	False		,,,				2504	0.363				p.M62K		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.T185A						PASS	.	A	LYS/MET,LYS/MET,LYS/MET	53,2967		2,49,1459	62.0	87.0	78.0		185,185,185	-6.0	0.0	6	dbSNP_126	78	9,5409		0,9,2700	yes	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	95,95,95	2,58,4159	TT,TA,AA		0.1661,1.755,0.7348	possibly-damaging,possibly-damaging,possibly-damaging	62/261,62/261,62/261	33037579	62,8376	1510	2709	4219	SO:0001583	missense	3113	exon2			TAGAACATCTCAT	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.185T>A	6.37:g.33037579A>T	ENSP00000393566:p.Met62Lys	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	166	63	0.379518	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	762	0.3489010989010989	239	0.48577235772357724	78	0.2154696132596685	331	0.5786713286713286	114	0.1503957783641161	A	0.028	-1.354560	0.01256	0.01755	0.001661	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.00737	5.76;5.76;5.76	3.0	-5.99	0.02213	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	2.490280	0.02659	U	0.107291	T	0.00440	0.0014	L	0.41415	1.275	0.80722	P	0.0	B	0.26602	0.154	B	0.42995	0.404	T	0.32719	-0.9896	9	0.30854	T	0.27	.	10.1803	0.42963	0.4129:0.0:0.0:0.5871	rs2308912;rs12722002	62	P20036	DPA1_HUMAN	K	62	ENSP00000393566:M62K;ENSP00000402872:M62K;ENSP00000390929:M62K	ENSP00000393566:M62K	M	-	2	0	HLA-DPA1	33145557	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.558000	0.05978	-3.072000	0.00253	-1.638000	0.00776	ATG	.	.	alt		0.483	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
CCDC69	26112	hgsc.bcm.edu	37	5	150565008	150565008	+	Missense_Mutation	SNP	C	C	T	rs248427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150565008C>T	ENST00000355417.2	-	7	764	c.590G>A	c.(589-591)aGg>aAg	p.R197K	CCDC69_ENST00000521308.1_5'UTR	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	197			R -> K (in dbSNP:rs248427). {ECO:0000269|PubMed:14702039}.							haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GATCAGCCGCCTGTCCAGCTC	0.542													T|||	2048	0.408946	0.4516	0.3991	5008	,	,		21965	0.3492		0.4433	False		,,,				2504	0.3845				p.R197K		Atlas-SNP	.											.	CCDC69	30	.	0			c.G590A						PASS	.	T	LYS/ARG	2034,2372	611.4+/-391.8	467,1100,636	147.0	134.0	138.0		590	2.2	1.0	5	dbSNP_79	138	3892,4708	607.5+/-395.3	882,2128,1290	yes	missense	CCDC69	NM_015621.2	26	1349,3228,1926	TT,TC,CC		45.2558,46.1643,45.5636	benign	197/297	150565008	5926,7080	2203	4300	6503	SO:0001583	missense	26112	exon7			AGCCGCCTGTCCA		CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.590G>A	5.37:g.150565008C>T	ENSP00000347586:p.Arg197Lys	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_015621	A8K9X6	Missense_Mutation	SNP	ENST00000355417.2	37	CCDS4312.1	921	0.4217032967032967	232	0.4715447154471545	152	0.4198895027624309	202	0.3531468531468531	335	0.4419525065963061	T	3.070	-0.191436	0.06299	0.461643	0.452558	ENSG00000198624	ENST00000355417	T	0.08102	3.13	4.92	2.25	0.28309	.	0.199205	0.33253	N	0.005120	T	0.00012	0.0000	N	0.00230	-1.795	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45264	-0.9273	9	0.02654	T	1	-35.1907	7.9554	0.30040	0.0:0.316:0.0:0.684	rs248427;rs1654101;rs52809117;rs248427	197	A6NI79	CCD69_HUMAN	K	197	ENSP00000347586:R197K	ENSP00000347586:R197K	R	-	2	0	CCDC69	150545201	1.000000	0.71417	1.000000	0.80357	0.616000	0.37450	0.830000	0.27462	0.328000	0.23435	-0.521000	0.04368	AGG	A|0.000;C|0.559;G|0.000;N|0.000;T|0.441	0.441	strong		0.542	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621	
UNC13A	23025	hgsc.bcm.edu	37	19	17743622	17743622	+	Missense_Mutation	SNP	C	C	A	rs75595663	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17743622C>A	ENST00000519716.2	-	28	3396	c.3397G>T	c.(3397-3399)Gcc>Tcc	p.A1133S	UNC13A_ENST00000428389.2_Missense_Mutation_p.A1221S|UNC13A_ENST00000552293.1_Missense_Mutation_p.A1133S|UNC13A_ENST00000252773.7_Missense_Mutation_p.A1133S|UNC13A_ENST00000550896.1_Missense_Mutation_p.A1131S|UNC13A_ENST00000551649.1_Missense_Mutation_p.A1133S	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1133	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)	p.A1133T(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						TCCTTGAAGGCGGGAAGTTCC	0.552													C|||	161	0.0321486	0.0038	0.0605	5008	,	,		21853	0.0		0.0875	False		,,,				2504	0.0266				p.A1133S		Atlas-SNP	.											UNC13A_ENST00000519716,colon,carcinoma,0,1	UNC13A	299	1	1	Substitution - Missense(1)	large_intestine(1)	c.G3397T						PASS	.		SER/ALA	42,4218		0,42,2088	107.0	113.0	111.0		3397	-0.7	1.0	19	dbSNP_132	111	740,7768		28,684,3542	yes	missense	UNC13A	NM_001080421.2	99	28,726,5630	AA,AC,CC		8.6977,0.9859,6.1247	benign	1133/1704	17743622	782,11986	2130	4254	6384	SO:0001583	missense	23025	exon27			TGAAGGCGGGAAG	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.3397G>T	19.37:g.17743622C>A	ENSP00000429562:p.Ala1133Ser	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	156	85	0.544872	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	83	0.038003663003663	5	0.01016260162601626	20	0.055248618784530384	0	0.0	58	0.07651715039577836	c	7.186	0.590539	0.13812	0.009859	0.086977	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.80393	-1.36;-1.37;-1.36;-1.23;-1.23;-1.36	3.63	-0.725	0.11174	Munc13 homology 1 (1);	0.684102	0.13889	U	0.355725	T	0.05868	0.0153	L	0.38531	1.155	0.09310	N	0.99999	B	0.06786	0.001	B	0.09377	0.004	T	0.03240	-1.1057	10	0.16420	T	0.52	.	3.8778	0.09064	0.2746:0.472:0.0:0.2533	.	1133	Q9UPW8	UN13A_HUMAN	S	1133;1221;1133;1133;1133;1131	ENSP00000429562:A1133S;ENSP00000400409:A1221S;ENSP00000252773:A1133S;ENSP00000447236:A1133S;ENSP00000447572:A1133S;ENSP00000446831:A1131S	ENSP00000252773:A1133S	A	-	1	0	UNC13A	17604622	0.001000	0.12720	0.987000	0.45799	0.590000	0.36582	-0.016000	0.12613	0.079000	0.16929	0.298000	0.19748	GCC	C|0.950;A|0.050	0.050	strong		0.552	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2929674	2929674	+	Silent	SNP	T	T	C	rs12941934	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:2929674T>C	ENST00000254695.8	+	21	1986	c.1896T>C	c.(1894-1896)cgT>cgC	p.R632R	RAP1GAP2_ENST00000540393.2_Silent_p.R613R|RAP1GAP2_ENST00000542807.1_Silent_p.R632R|RAP1GAP2_ENST00000366401.4_Silent_p.R617R	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	632	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)	p.R632R(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						AAAACGGCCGTGCCATCTCCC	0.672													C|||	2914	0.581869	0.4312	0.6744	5008	,	,		16616	0.6429		0.5606	False		,,,				2504	0.6789				p.R632R		Atlas-SNP	.											RAP1GAP2_ENST00000254695,NS,lymphoid_neoplasm,0,2	RAP1GAP2	90	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.T1896C						PASS	.	C	,	1939,2059		530,879,590	15.0	18.0	17.0		1851,1896	-9.8	0.3	17	dbSNP_121	17	4907,3181		1615,1677,752	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	2145,2556,1342	CC,CT,TT		39.3299,48.4992,43.3559	,	617/716,632/731	2929674	6846,5240	1999	4044	6043	SO:0001819	synonymous_variant	23108	exon21			CGGCCGTGCCATC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1896T>C	17.37:g.2929674T>C		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	217	106	0.488479	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			T|0.421;C|0.579	0.579	strong		0.672	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
OR4D6	219983	hgsc.bcm.edu	37	11	59225221	59225221	+	Missense_Mutation	SNP	T	T	C	rs1453541	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:59225221T>C	ENST00000300127.2	+	1	811	c.788T>C	c.(787-789)aTg>aCg	p.M263T		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	263			M -> T (in dbSNP:rs1453541).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						CGGCCCTTCATGACGCTGCCC	0.527													C|||	1329	0.265375	0.3245	0.2695	5008	,	,		20460	0.1845		0.2972	False		,,,				2504	0.2331				p.M263T		Atlas-SNP	.											OR4D6,NS,carcinoma,-1,2	OR4D6	65	2	0			c.T788C						scavenged	.	T	THR/MET	1469,2933	679.3+/-403.7	238,993,970	114.0	109.0	111.0		788	-2.7	0.0	11	dbSNP_88	111	2714,5876	681.6+/-403.7	417,1880,1998	yes	missense	OR4D6	NM_001004708.1	81	655,2873,2968	CC,CT,TT		31.5949,33.3712,32.1967	benign	263/315	59225221	4183,8809	2201	4295	6496	SO:0001583	missense	219983	exon1			CCTTCATGACGCT	AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"""GPCR / Class A : Olfactory receptors"""	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.788T>C	11.37:g.59225221T>C	ENSP00000300127:p.Met263Thr	Somatic	145	2	0.0137931		WXS	Illumina HiSeq	Phase_I	165	72	0.436364	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	623	0.28525641025641024	159	0.3231707317073171	109	0.3011049723756906	119	0.20804195804195805	236	0.3113456464379947	C	0.001	-3.142940	0.00029	0.333712	0.315949	ENSG00000166884	ENST00000300127	T	0.00054	8.8	6.01	-2.74	0.05932	GPCR, rhodopsin-like superfamily (1);	0.805216	0.11028	N	0.607551	T	0.00012	0.0000	N	0.00055	-2.37	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37126	-0.9719	9	0.02654	T	1	-1.5571	4.6597	0.12636	0.0933:0.5045:0.0917:0.3105	rs1453541;rs17500443;rs59250564;rs1453541	263	Q8NGJ1	OR4D6_HUMAN	T	263	ENSP00000300127:M263T	ENSP00000300127:M263T	M	+	2	0	OR4D6	58981797	0.000000	0.05858	0.001000	0.08648	0.089000	0.18198	-0.221000	0.09202	-0.898000	0.03906	-1.990000	0.00449	ATG	T|0.689;C|0.311	0.311	strong		0.527	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708	
PDZD2	23037	hgsc.bcm.edu	37	5	32093070	32093070	+	Silent	SNP	G	G	A	rs16889442	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:32093070G>A	ENST00000438447.1	+	21	8173	c.7785G>A	c.(7783-7785)tcG>tcA	p.S2595S	PDZD2_ENST00000282493.3_Silent_p.S2595S			O15018	PDZD2_HUMAN	PDZ domain containing 2	2595					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CTGTTTTATCGTCAGTGGGAT	0.393													G|||	587	0.117212	0.0446	0.1398	5008	,	,		18640	0.2381		0.0755	False		,,,				2504	0.1176				p.S2595S		Atlas-SNP	.											.	PDZD2	306	.	0			c.G7785A						PASS	.	G		242,4164	142.7+/-177.9	4,234,1965	80.0	82.0	81.0		7785	-2.3	0.0	5	dbSNP_123	81	766,7834	182.9+/-231.2	33,700,3567	no	coding-synonymous	PDZD2	NM_178140.2		37,934,5532	AA,AG,GG		8.907,5.4925,7.7503		2595/2840	32093070	1008,11998	2203	4300	6503	SO:0001819	synonymous_variant	23037	exon20			TTTATCGTCAGTG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.7785G>A	5.37:g.32093070G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	232	101	0.435345	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			G|0.904;A|0.096	0.096	strong		0.393	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
GDPD4	220032	hgsc.bcm.edu	37	11	76954812	76954812	+	Missense_Mutation	SNP	T	T	C	rs11237145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:76954812T>C	ENST00000376217.2	-	12	1418	c.1168A>G	c.(1168-1170)Att>Gtt	p.I390V	GDPD4_ENST00000315938.4_Missense_Mutation_p.I390V			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	390	GP-PDE.		I -> V (in dbSNP:rs11237145).		glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						AGGGTTTCAATGGATACTAAA	0.413													C|||	1274	0.254393	0.0514	0.1916	5008	,	,		16179	0.256		0.3738	False		,,,				2504	0.4489				p.I390V		Atlas-SNP	.											.	GDPD4	49	.	0			c.A1168G						PASS	.	C	VAL/ILE	458,3942	784.3+/-414.7	30,398,1772	117.0	108.0	111.0		1168	-8.5	0.0	11	dbSNP_120	111	3083,5501	658.5+/-401.6	536,2011,1745	yes	missense	GDPD4	NM_182833.1	29	566,2409,3517	CC,CT,TT		35.9157,10.4091,27.272	benign	390/521	76954812	3541,9443	2200	4292	6492	SO:0001583	missense	220032	exon12			TTTCAATGGATAC	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1168A>G	11.37:g.76954812T>C	ENSP00000365390:p.Ile390Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_182833	Q7Z5B0	Missense_Mutation	SNP	ENST00000376217.2	37		501	0.22939560439560439	25	0.0508130081300813	76	0.20994475138121546	130	0.22727272727272727	270	0.3562005277044855	C	0.016	-1.522396	0.00967	0.104091	0.359157	ENSG00000178795	ENST00000376217;ENST00000315938	T;T	0.10763	2.84;2.84	4.27	-8.54	0.00912	.	0.708347	0.13925	N	0.353264	T	0.00012	0.0000	N	0.05351	-0.065	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.32955	-0.9887	9	0.06099	T	0.92	-2.8135	3.1474	0.06477	0.0959:0.3517:0.1943:0.3581	rs11237145;rs17824220;rs52820078;rs11237145	390	Q6W3E5-2	.	V	390	ENSP00000365390:I390V;ENSP00000320815:I390V	ENSP00000320815:I390V	I	-	1	0	GDPD4	76632460	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.063000	0.00622	-2.006000	0.00958	-1.874000	0.00550	ATT	C|0.254;N|0.000	0.254	strong		0.413	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
CHI3L2	1117	hgsc.bcm.edu	37	1	111778325	111778325	+	Missense_Mutation	SNP	C	C	T	rs11556868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111778325C>T	ENST00000445067.2	+	8	1316	c.545C>T	c.(544-546)gCg>gTg	p.A182V	CHI3L2_ENST00000524472.1_Missense_Mutation_p.A103V|CHI3L2_ENST00000369744.2_Missense_Mutation_p.A172V|CHI3L2_ENST00000369748.4_Missense_Mutation_p.A182V|CHI3L2_ENST00000466741.1_Missense_Mutation_p.A103V			Q15782	CH3L2_HUMAN	chitinase 3-like 2	182			A -> V (in dbSNP:rs11556868). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)	extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		CTCTTGACTGCGGGCGTATCT	0.453													C|||	364	0.0726837	0.0303	0.0634	5008	,	,		22784	0.0089		0.1223	False		,,,				2504	0.1513				p.A182V		Atlas-SNP	.											.	CHI3L2	38	.	0			c.C545T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	183,4223	117.5+/-155.4	2,179,2022	102.0	96.0	98.0		515,308,545	3.4	1.0	1	dbSNP_120	98	1089,7511	228.3+/-263.4	56,977,3267	yes	missense,missense,missense	CHI3L2	NM_001025197.1,NM_001025199.1,NM_004000.2	64,64,64	58,1156,5289	TT,TC,CC		12.6628,4.1534,9.7801	probably-damaging,probably-damaging,probably-damaging	172/381,103/312,182/391	111778325	1272,11734	2203	4300	6503	SO:0001583	missense	1117	exon6			TGACTGCGGGCGT	U49835	CCDS30802.1, CCDS30803.1, CCDS41367.1	1p13.3	2008-02-05			ENSG00000064886	ENSG00000064886			1933	protein-coding gene	gene with protein product		601526				8702629	Standard	NM_001025197		Approved	YKL-39, YKL39	uc001eam.3	Q15782	OTTHUMG00000012174	ENST00000445067.2:c.545C>T	1.37:g.111778325C>T	ENSP00000437082:p.Ala182Val	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	238	116	0.487395	NM_004000	A6NNY3|B4DPR7|Q15749|Q15783|Q5VUV7|Q96F97	Missense_Mutation	SNP	ENST00000445067.2	37	CCDS30802.1	128	0.05860805860805861	12	0.024390243902439025	21	0.058011049723756904	0	0.0	95	0.12532981530343007	C	19.16	3.774289	0.69992	0.041534	0.126628	ENSG00000064886	ENST00000445067;ENST00000528451;ENST00000486561;ENST00000369744;ENST00000369748;ENST00000474304;ENST00000466741;ENST00000477185;ENST00000467038;ENST00000497587;ENST00000524472;ENST00000497220	T;T;T;T;T;T;T;T;T;T;T	0.06608	3.28;3.28;3.28;3.28;3.28;3.28;3.28;3.28;3.28;3.28;3.28	3.39	3.39	0.38822	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.41938	D	0.000786	T	0.10680	0.0261	L	0.60455	1.87	0.21782	P	0.999544656	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.63877	0.919;0.919;0.919	T	0.01440	-1.1354	9	0.66056	D	0.02	-7.4821	12.661	0.56813	0.0:1.0:0.0:0.0	rs11556868;rs17845289;rs17858122;rs59153550;rs11556868	103;172;182	B4DPR7;A6NNY3;Q15782	.;.;CH3L2_HUMAN	V	182;182;182;172;182;163;103;103;84;103;103;36	ENSP00000437082:A182V;ENSP00000436077:A182V;ENSP00000431968:A182V;ENSP00000358759:A172V;ENSP00000358763:A182V;ENSP00000437086:A103V;ENSP00000436272:A103V;ENSP00000431978:A84V;ENSP00000436006:A103V;ENSP00000432049:A103V;ENSP00000435250:A36V	ENSP00000358759:A172V	A	+	2	0	CHI3L2	111579848	0.999000	0.42202	0.993000	0.49108	0.497000	0.33675	1.881000	0.39638	1.857000	0.53885	0.561000	0.74099	GCG	C|0.915;T|0.085	0.085	strong		0.453	CHI3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033669.4	NM_004000	
ZNF682	91120	hgsc.bcm.edu	37	19	20116963	20116963	+	Missense_Mutation	SNP	C	C	T	rs17679334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:20116963C>T	ENST00000397165.2	-	4	1508	c.1348G>A	c.(1348-1350)Gtc>Atc	p.V450I	ZNF682_ENST00000358523.5_Missense_Mutation_p.V418I|ZNF682_ENST00000397162.1_Missense_Mutation_p.V418I|ZNF682_ENST00000596019.1_Intron|ZNF682_ENST00000595736.1_Missense_Mutation_p.V374I|ZNF682_ENST00000597972.1_Missense_Mutation_p.V456I	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	450			V -> I (in dbSNP:rs17679334).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						TAGCGTTTGACGGCAGTATGA	0.388													c|||	975	0.194688	0.2897	0.1931	5008	,	,		20255	0.0754		0.1779	False		,,,				2504	0.2076				p.V450I		Atlas-SNP	.											.	ZNF682	51	.	0			c.G1348A						PASS	.	C	ILE/VAL,ILE/VAL	1183,3155		179,825,1165	88.0	97.0	94.0		1252,1348	-0.4	0.0	19	dbSNP_123	94	1474,7104		135,1204,2950	no	missense,missense	ZNF682	NM_001077349.1,NM_033196.2	29,29	314,2029,4115	TT,TC,CC		17.1835,27.2706,20.5714	benign,benign	418/467,450/499	20116963	2657,10259	2169	4289	6458	SO:0001583	missense	91120	exon4			GTTTGACGGCAGT	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.1348G>A	19.37:g.20116963C>T	ENSP00000380351:p.Val450Ile	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	55	18	0.327273	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	37	CCDS42533.1	398	0.18223443223443223	139	0.28252032520325204	77	0.212707182320442	39	0.06818181818181818	143	0.18865435356200527	c	8.091	0.774465	0.16051	0.272706	0.171835	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000341262;ENST00000358523	T;T;T	0.18502	2.21;2.21;2.21	1.09	-0.422	0.12329	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.26130	0.795	0.58432	P	2.9999999999752447E-6	B	0.11235	0.004	B	0.13407	0.009	T	0.40979	-0.9534	8	0.87932	D	0	.	8.1706	0.31252	0.0:0.8131:0.0:0.1869	rs17679334;rs52819789;rs61436554;rs17679334	450	O95780	ZN682_HUMAN	I	450;418;119;418	ENSP00000380351:V450I;ENSP00000380348:V418I;ENSP00000351324:V418I	ENSP00000340236:V119I	V	-	1	0	ZNF682	19977963	0.147000	0.22687	0.000000	0.03702	0.000000	0.00434	2.720000	0.47252	-1.571000	0.01663	-1.579000	0.00862	GTC	C|0.804;T|0.196	0.196	strong		0.388	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196	
CCDC6	8030	hgsc.bcm.edu	37	10	61552692	61552692	+	Missense_Mutation	SNP	G	G	T	rs1053266	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:61552692G>T	ENST00000263102.6	-	9	1639	c.1408C>A	c.(1408-1410)Ccc>Acc	p.P470T		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	470			P -> T (in dbSNP:rs1053266). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8058316, ECO:0000269|Ref.4}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)	p.P470T(1)	CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		TGGGAGGAGGGGTGCGCCGAA	0.597			T	RET	NSCLC								G|||	2180	0.435304	0.1989	0.598	5008	,	,		16944	0.6121		0.4503	False		,,,				2504	0.4417				p.P470T		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	CCDC6,NS,carcinoma,0,1	CCDC6	44	1	1	Substitution - Missense(1)	stomach(1)	c.C1408A						PASS	.	G	THR/PRO	1164,3242	411.7+/-335.8	177,810,1216	146.0	139.0	142.0		1408	5.6	1.0	10	dbSNP_86	142	4329,4271	579.5+/-390.9	1098,2133,1069	yes	missense	CCDC6	NM_005436.4	38	1275,2943,2285	TT,TG,GG		49.6628,26.4185,42.2344	probably-damaging	470/475	61552692	5493,7513	2203	4300	6503	SO:0001583	missense	8030	exon9			AGGAGGGGTGCGC	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"""DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"""	601985	"""DNA segment on chromosome 10 (unique) 170"""	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.1408C>A	10.37:g.61552692G>T	ENSP00000263102:p.Pro470Thr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	151	77	0.509934	NM_005436	Q15250|Q6GSG7	Missense_Mutation	SNP	ENST00000263102.6	37	CCDS7257.1	1001	0.4583333333333333	109	0.22154471544715448	211	0.5828729281767956	328	0.5734265734265734	353	0.4656992084432718	G	17.13	3.311702	0.60414	0.264185	0.503372	ENSG00000108091	ENST00000263102	T	0.55052	0.54	5.6	5.6	0.85130	.	0.410909	0.25467	N	0.030472	T	0.00012	0.0000	L	0.44542	1.39	0.09310	P	0.999999823558	D	0.71674	0.998	D	0.76071	0.987	T	0.51482	-0.8700	9	0.66056	D	0.02	1.6527	19.9854	0.97342	0.0:0.0:1.0:0.0	rs1053266;rs3193780;rs3750802;rs57560743;rs1053266	470	Q16204	CCDC6_HUMAN	T	470	ENSP00000263102:P470T	ENSP00000263102:P470T	P	-	1	0	CCDC6	61222698	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.852000	0.92215	2.786000	0.95864	0.563000	0.77884	CCC	G|0.577;T|0.423	0.423	strong		0.597	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436	
FLG	2312	hgsc.bcm.edu	37	1	152286126	152286126	+	Silent	SNP	A	A	G	rs11582620	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152286126A>G	ENST00000368799.1	-	3	1271	c.1236T>C	c.(1234-1236)cgT>cgC	p.R412R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	412	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.R412R(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCGGTGTCCACGATCGCTGA	0.587									Ichthyosis				-|||	431	0.0860623	0.0023	0.0778	5008	,	,		20615	0.0992		0.1064	False		,,,				2504	0.1708				p.R412R		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	1	Substitution - coding silent(1)	stomach(1)	c.T1236C						PASS	.	A		93,4313		0,93,2110	236.0	237.0	236.0		1236	-7.0	0.0	1	dbSNP_120	236	1003,7597		66,871,3363	no	coding-synonymous	FLG	NM_002016.1		66,964,5473	GG,GA,AA		11.6628,2.1108,8.4269		412/4062	152286126	1096,11910	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTGTCCACGATCG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1236T>C	1.37:g.152286126A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	173	172	0.99422	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.918;G|0.082	0.082	strong		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PLCB1	23236	hgsc.bcm.edu	37	20	8130943	8130943	+	Silent	SNP	C	C	T	rs16994453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:8130943C>T	ENST00000338037.6	+	2	129	c.102C>T	c.(100-102)gaC>gaT	p.D34D	PLCB1_ENST00000378641.3_Silent_p.D34D|PLCB1_ENST00000378637.2_Silent_p.D34D	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	34				MAGAQPGVHALQLKPVCVSDSLKKGTKFVKWDDD -> MGS LQGIATKILIRILSDALIRKETDLKS (in Ref. 2; AAF86613). {ECO:0000305}.	activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						ATTTCTAGGACTCAACTATTG	0.323													C|||	937	0.187101	0.2542	0.1167	5008	,	,		15402	0.1607		0.1521	False		,,,				2504	0.2096				p.Q34H		Atlas-SNP	.											.	PLCB1	394	.	0			c.A102T						PASS	.	C	,	1088,3318	382.1+/-324.3	147,794,1262	73.0	71.0	71.0		102,102	1.7	1.0	20	dbSNP_123	71	1416,7166	268.5+/-287.9	123,1170,2998	no	coding-synonymous,coding-synonymous	PLCB1	NM_015192.2,NM_182734.1	,	270,1964,4260	TT,TC,CC		16.4997,24.6936,19.2793	,	34/1217,34/1174	8130943	2504,10484	2203	4291	6494	SO:0001819	synonymous_variant	23236	exon2			CTAGGACTCAACT	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.102C>T	20.37:g.8130943C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	201	111	0.552239	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																			C|0.817;T|0.183	0.183	strong		0.323	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
ANO7	50636	hgsc.bcm.edu	37	2	242129487	242129487	+	Silent	SNP	G	G	T	rs11695874	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242129487G>T	ENST00000274979.8	+	2	274	c.171G>T	c.(169-171)cgG>cgT	p.R57R	ANO7_ENST00000402530.3_Silent_p.R57R|ANO7_ENST00000402430.3_Silent_p.R57R	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	57					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						GGATGCTGCGGCGACGGGCCC	0.677													G|||	745	0.148762	0.0968	0.1888	5008	,	,		15980	0.0208		0.3052	False		,,,				2504	0.1616				p.R57R		Atlas-SNP	.											.	ANO7	136	.	0			c.G171T						PASS	.	G	,	571,3819		41,489,1665	29.0	28.0	28.0		171,171	0.4	0.0	2	dbSNP_120	28	2342,6220		335,1672,2274	no	coding-synonymous,coding-synonymous	ANO7	NM_001001666.3,NM_001001891.3	,	376,2161,3939	TT,TG,GG		27.3534,13.0068,22.4907	,	57/180,57/934	242129487	2913,10039	2195	4281	6476	SO:0001819	synonymous_variant	50636	exon2			GCTGCGGCGACGG	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.171G>T	2.37:g.242129487G>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	197	105	0.532995	NM_001001666	Q6IWH6	Silent	SNP	ENST00000274979.8	37	CCDS33423.1																																																																																			G|0.805;T|0.195	0.195	strong		0.677	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
SYT10	341359	hgsc.bcm.edu	37	12	33535289	33535289	+	Silent	SNP	G	G	A	rs10844571	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:33535289G>A	ENST00000228567.3	-	5	1661	c.1365C>T	c.(1363-1365)taC>taT	p.Y455Y	SYT10_ENST00000535526.1_Silent_p.Y274Y	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	455	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					CATACCTATCGTAATCCATGA	0.458													G|||	996	0.198882	0.1619	0.2839	5008	,	,		16125	0.0655		0.2296	False		,,,				2504	0.2945				p.Y455Y		Atlas-SNP	.											.	SYT10	109	.	0			c.C1365T						PASS	.	G		759,3647	309.7+/-291.2	73,613,1517	189.0	164.0	173.0		1365	-7.7	0.1	12	dbSNP_120	173	1975,6625	346.0+/-326.0	231,1513,2556	no	coding-synonymous	SYT10	NM_198992.3		304,2126,4073	AA,AG,GG		22.9651,17.2265,21.0211		455/524	33535289	2734,10272	2203	4300	6503	SO:0001819	synonymous_variant	341359	exon5			CCTATCGTAATCC	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"""Synaptotagmins"""	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.1365C>T	12.37:g.33535289G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	124	59	0.475806	NM_198992	Q495U2	Silent	SNP	ENST00000228567.3	37	CCDS8732.1																																																																																			G|0.800;A|0.200	0.200	strong		0.458	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992	
NBEAL2	23218	hgsc.bcm.edu	37	3	47043538	47043538	+	Silent	SNP	C	C	T	rs2305634	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:47043538C>T	ENST00000450053.3	+	31	5090	c.4911C>T	c.(4909-4911)tcC>tcT	p.S1637S	NBEAL2_ENST00000292309.5_Silent_p.S1453S|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1637					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		ACACCTCTTCCTTGGAGTCAG	0.652													C|||	2362	0.471645	0.2383	0.5216	5008	,	,		18720	0.5387		0.5865	False		,,,				2504	0.5644				p.S1637S		Atlas-SNP	.											NBEAL2_ENST00000450053,NS,carcinoma,0,4	NBEAL2	267	4	0			c.C4911T						PASS	.	C		1134,3064		214,706,1179	6.0	7.0	7.0		4911	-5.6	0.0	3	dbSNP_100	7	4527,3787		1331,1865,961	no	coding-synonymous	NBEAL2	NM_015175.1		1545,2571,2140	TT,TC,CC		45.5497,27.0129,45.2446		1637/2755	47043538	5661,6851	2099	4157	6256	SO:0001819	synonymous_variant	23218	exon31			CTCTTCCTTGGAG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.4911C>T	3.37:g.47043538C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1	1089|1089	0.49862637362637363|0.49862637362637363	143|143	0.29065040650406504|0.29065040650406504	197|197	0.5441988950276243|0.5441988950276243	305|305	0.5332167832167832|0.5332167832167832	444|444	0.5857519788918206|0.5857519788918206	C|C	0.102|0.102	-1.151030|-1.151030	0.01700|0.01700	0.270129|0.270129	0.544503|0.544503	ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000416683	.|.	.|.	.|.	4.62|4.62	-5.57|-5.57	0.02521|0.02521	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	1.999999999946489E-6|1.999999999946489E-6	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.45190|0.45190	-0.9278|-0.9278	3|3	.|.	.|.	.|.	.|.	3.3322|3.3322	0.07088|0.07088	0.1082:0.3229:0.1069:0.4621|0.1082:0.3229:0.1069:0.4621	rs2305634;rs17223724;rs2305634|rs2305634;rs17223724;rs2305634	.|.	.|.	.|.	F|L	6|925	.|.	.|.	L|P	+|+	1|2	0|0	NBEAL2|NBEAL2	47018542|47018542	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.150000|0.150000	0.21749|0.21749	-1.477000|-1.477000	0.02331|0.02331	-1.080000|-1.080000	0.03109|0.03109	-0.145000|-0.145000	0.13849|0.13849	CTT|CCT	C|0.518;G|0.000;T|0.481	0.481	strong		0.652	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
TMEM39B	55116	hgsc.bcm.edu	37	1	32557486	32557486	+	Silent	SNP	A	A	G	rs744455	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32557486A>G	ENST00000336294.5	+	6	947	c.801A>G	c.(799-801)tcA>tcG	p.S267S	TMEM39B_ENST00000487305.1_3'UTR|TMEM39B_ENST00000456834.2_Missense_Mutation_p.T216A|TMEM39B_ENST00000427288.1_Silent_p.S152S|TMEM39B_ENST00000373634.4_Silent_p.S68S	NM_018056.2	NP_060526.2	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	267						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(5)|ovary(1)|prostate(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				GCTGCCTGTCACCCAGCCTCA	0.602													G|||	1120	0.223642	0.2927	0.232	5008	,	,		20192	0.2351		0.0596	False		,,,				2504	0.2812				p.S267S		Atlas-SNP	.											.	TMEM39B	66	.	0			c.A801G						PASS	.	G		1184,3222	710.3+/-407.9	187,810,1206	87.0	73.0	78.0		801	-10.3	0.5	1	dbSNP_86	78	560,8040	794.2+/-407.5	20,520,3760	no	coding-synonymous	TMEM39B	NM_018056.2		207,1330,4966	GG,GA,AA		6.5116,26.8724,13.4092		267/493	32557486	1744,11262	2203	4300	6503	SO:0001819	synonymous_variant	55116	exon6			CCTGTCACCCAGC	AL136695	CCDS351.2	1p35.1	2008-02-05			ENSG00000121775	ENSG00000121775			25510	protein-coding gene	gene with protein product						12477932	Standard	NM_018056		Approved	FLJ10315	uc010ogv.2	Q9GZU3	OTTHUMG00000004020	ENST00000336294.5:c.801A>G	1.37:g.32557486A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_018056	B4DKN8|B4DQE6|B4DTN8|D3DPP4|Q6IA44	Silent	SNP	ENST00000336294.5	37	CCDS351.2	373	0.1707875457875458	147	0.29878048780487804	50	0.13812154696132597	131	0.229020979020979	45	0.059366754617414245	G	13.14	2.148810	0.37923	0.268724	0.065116	ENSG00000121775	ENST00000456834	.	.	.	5.58	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.25710	-1.0124	4	0.87932	D	0	-7.3393	2.6143	0.04900	0.4687:0.2282:0.1626:0.1406	rs744455;rs58248543;rs744455	.	.	.	A	216	.	ENSP00000390889:T188A	T	+	1	0	TMEM39B	32330073	0.002000	0.14202	0.532000	0.27989	0.963000	0.63663	-1.285000	0.02791	-2.042000	0.00914	-0.733000	0.03571	ACC	A|0.849;G|0.151	0.151	strong		0.602	TMEM39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011489.2	NM_018056	
YME1L1	10730	hgsc.bcm.edu	37	10	27434483	27434483	+	Silent	SNP	G	G	A	rs2274634	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:27434483G>A	ENST00000326799.3	-	4	524	c.376C>T	c.(376-378)Cta>Tta	p.L126L	YME1L1_ENST00000477432.1_3'UTR|YME1L1_ENST00000375972.3_Silent_p.L69L|YME1L1_ENST00000376016.3_Silent_p.L69L	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	126					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						CCAATTTTTAGTTCAGATAAT	0.368													A|||	1747	0.348842	0.3132	0.1873	5008	,	,		14029	0.5506		0.2247	False		,,,				2504	0.4315				p.L126L		Atlas-SNP	.											.	YME1L1	71	.	0			c.C376T						PASS	.	A	,	1366,3040	686.8+/-404.8	197,972,1034	94.0	100.0	98.0		205,376	4.6	1.0	10	dbSNP_100	98	1532,7066	745.8+/-407.3	131,1270,2898	no	coding-synonymous,coding-synonymous	YME1L1	NM_014263.2,NM_139312.1	,	328,2242,3932	AA,AG,GG		17.8181,31.0032,22.2855	,	69/717,126/774	27434483	2898,10106	2203	4299	6502	SO:0001819	synonymous_variant	10730	exon4			TTTTTAGTTCAGA	AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"""ATPases / AAA-type"""	12843	protein-coding gene	gene with protein product		607472	"""YME1 (S.cerevisiae)-like 1"", ""YME1-like 1 (S. cerevisiae)"""			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.376C>T	10.37:g.27434483G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	125	48	0.384	NM_139312	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Silent	SNP	ENST00000326799.3	37	CCDS7152.1																																																																																			G|0.727;A|0.273	0.273	strong		0.368	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312	
PCDHA3	56145	hgsc.bcm.edu	37	5	140181734	140181734	+	Missense_Mutation	SNP	A	A	G	rs3733708	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140181734A>G	ENST00000522353.2	+	1	952	c.952A>G	c.(952-954)Atc>Gtc	p.I318V	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.I318V|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	318	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> V (in dbSNP:rs3733708).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCATATGAAATCCAGGTAGA	0.388													.|||	2631	0.525359	0.4788	0.5893	5008	,	,		23136	0.5317		0.5378	False		,,,				2504	0.5235				p.I318V		Atlas-SNP	.											.	PCDHA3	396	.	0			c.A952G						PASS	.	A	,,VAL/ILE,,VAL/ILE	2185,2221	585.5+/-386.3	533,1119,551	143.0	144.0	144.0		,,952,,952	3.5	1.0	5	dbSNP_107	144	4540,4060	594.4+/-393.3	1192,2156,952	yes	intron,intron,missense,intron,missense	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,29,,29	1725,3275,1503	GG,GA,AA		47.2093,49.5915,48.2931	,,,,	,,318/951,,318/825	140181734	6725,6281	2203	4300	6503	SO:0001583	missense	56145	exon1			TATGAAATCCAGG	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.952A>G	5.37:g.140181734A>G	ENSP00000429808:p.Ile318Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	153	78	0.509804	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	1163	0.5325091575091575	252	0.5121951219512195	194	0.5359116022099447	311	0.5437062937062938	406	0.5356200527704486	a	14.17	2.454859	0.43634	0.495915	0.527907	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.52526	0.66;0.66	4.79	3.54	0.40534	Cadherin (4);Cadherin-like (1);	0.000000	0.42172	U	0.000743	T	0.00012	0.0000	M	0.73430	2.235	0.39646	P	0.02960600000000002	P;P	0.35714	0.517;0.472	B;P	0.50825	0.359;0.651	T	0.53180	-0.8475	9	0.87932	D	0	.	10.5422	0.45039	0.7622:0.0:0.0:0.2378	rs3733708;rs13162484;rs17208250;rs17844256;rs52837026;rs57467015;rs3733708	318;318	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	V	318	ENSP00000429808:I318V;ENSP00000434086:I318V	ENSP00000429808:I318V	I	+	1	0	PCDHA3	140161918	0.000000	0.05858	0.985000	0.45067	0.953000	0.61014	-0.509000	0.06336	1.925000	0.55765	0.383000	0.25322	ATC	G|0.521;N|0.000	0.521	strong		0.388	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
C17orf70	80233	hgsc.bcm.edu	37	17	79514129	79514129	+	Missense_Mutation	SNP	G	G	A	rs11552304	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79514129G>A	ENST00000327787.8	-	5	2025	c.1979C>T	c.(1978-1980)cCg>cTg	p.P660L	C17orf70_ENST00000537152.1_Missense_Mutation_p.P509L|C17orf70_ENST00000425898.2_Missense_Mutation_p.P309L			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	660			P -> L (in dbSNP:rs11552304). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			TGTGTGTGGCGGGGCCAGGCC	0.682													G|||	2786	0.55631	0.3858	0.4841	5008	,	,		15044	0.621		0.6342	False		,,,				2504	0.6912				p.P660L		Atlas-SNP	.											.	C17orf70	79	.	0			c.C1979T						PASS	.	G	LEU/PRO	1848,2556		409,1030,763	24.0	32.0	29.0		1979	0.1	0.0	17	dbSNP_120	29	5662,2926		1893,1876,525	yes	missense	C17orf70	NM_025161.5	98	2302,2906,1288	AA,AG,GG		34.0708,41.9619,42.1952	benign	660/882	79514129	7510,5482	2202	4294	6496	SO:0001583	missense	80233	exon5			TGTGGCGGGGCCA	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 100kDa"""	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.1979C>T	17.37:g.79514129G>A	ENSP00000333283:p.Pro660Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	141	87	0.617021	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Missense_Mutation	SNP	ENST00000327787.8	37	CCDS32765.2	1202	0.5503663003663004	185	0.37601626016260165	183	0.505524861878453	346	0.6048951048951049	488	0.6437994722955145	G	11.69	1.714748	0.30413	0.419619	0.659292	ENSG00000185504	ENST00000327787;ENST00000425898;ENST00000537152	T;T;T	0.30448	1.53;1.53;1.53	4.15	0.0692	0.14373	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;P	0.38863	0.394;0.65	B;B	0.29524	0.037;0.103	T	0.40646	-0.9552	8	0.11794	T	0.64	.	4.6267	0.12481	0.3723:0.1653:0.4624:0.0	rs11552304	660;309	Q0VG06;E7EVV8	FP100_HUMAN;.	L	660;309;509	ENSP00000333283:P660L;ENSP00000399674:P309L;ENSP00000440151:P509L	ENSP00000333283:P660L	P	-	2	0	C17orf70	77124582	0.001000	0.12720	0.000000	0.03702	0.197000	0.23852	0.956000	0.29202	0.077000	0.16863	0.655000	0.94253	CCG	G|0.418;A|0.582	0.582	strong		0.682	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161	
CELA3A	10136	hgsc.bcm.edu	37	1	22336308	22336308	+	Silent	SNP	G	G	A	rs12908	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22336308G>A	ENST00000290122.3	+	7	772	c.753G>A	c.(751-753)acG>acA	p.T251T	RN7SL186P_ENST00000466485.2_RNA|RNU6-776P_ENST00000364403.1_RNA	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	251	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GGAAGCCCACGGTGTTCACTC	0.607													G|||	1430	0.285543	0.2307	0.4078	5008	,	,		16710	0.3998		0.2207	False		,,,				2504	0.2219				p.T251T		Atlas-SNP	.											CELA3A,NS,carcinoma,+2,1	CELA3A	35	1	0			c.G753A						PASS	.	G		1140,3266	383.0+/-324.7	180,780,1243	74.0	68.0	70.0		753	-7.3	0.5	1	dbSNP_52	70	1939,6661	311.3+/-310.3	232,1475,2593	no	coding-synonymous	CELA3A	NM_005747.4		412,2255,3836	AA,AG,GG		22.5465,25.8738,23.6737		251/271	22336308	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	10136	exon7			GCCCACGGTGTTC	D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"""protease E"""		"""elastase 3A, pancreatic (protease E)"", ""elastase 3A, pancreatic"""	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.753G>A	1.37:g.22336308G>A		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	248	114	0.459677	NM_005747	B1AQ53|Q9BRW4	Silent	SNP	ENST00000290122.3	37	CCDS220.1																																																																																			G|0.745;A|0.255	0.255	strong		0.607	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747	
MYO15A	51168	hgsc.bcm.edu	37	17	18023897	18023897	+	Missense_Mutation	SNP	G	G	A	rs2955365	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18023897G>A	ENST00000205890.5	+	2	2121	c.1783G>A	c.(1783-1785)Gcc>Acc	p.A595T		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	595				A -> T (in Ref. 2; AAF05903/AF051976). {ECO:0000305}.	inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CAGCCAGAAGGCCCGGGCGGG	0.701													G|||	2772	0.553514	0.503	0.4741	5008	,	,		7970	0.6567		0.3708	False		,,,				2504	0.7597				p.A595T		Atlas-SNP	.											.	MYO15A	268	.	0			c.G1783A						PASS	.	G	THR/ALA	1422,1900		345,732,584	5.0	6.0	6.0		1783	3.6	1.0	17	dbSNP_101	6	2198,5272		395,1408,1932	yes	missense	MYO15A	NM_016239.3	58	740,2140,2516	AA,AG,GG		29.4244,42.8055,33.5434	probably-damaging	595/3531	18023897	3620,7172	1661	3735	5396	SO:0001583	missense	51168	exon2			CAGAAGGCCCGGG	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.1783G>A	17.37:g.18023897G>A	ENSP00000205890:p.Ala595Thr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	1075	0.49221611721611724	267	0.5426829268292683	160	0.4419889502762431	374	0.6538461538461539	274	0.36147757255936674	G	12.28	1.890897	0.33348	0.428055	0.294244	ENSG00000091536	ENST00000205890	D	0.89123	-2.47	4.63	3.58	0.41010	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.9999999881489	P	0.39809	0.689	B	0.34590	0.186	T	0.48937	-0.8990	8	0.56958	D	0.05	.	12.164	0.54119	0.0:0.0:0.8282:0.1718	rs2955365;rs2955365	595	Q9UKN7	MYO15_HUMAN	T	595	ENSP00000205890:A595T	ENSP00000205890:A595T	A	+	1	0	MYO15A	17964622	0.906000	0.30813	0.973000	0.42090	0.175000	0.22909	1.488000	0.35551	2.122000	0.65172	0.448000	0.29417	GCC	G|0.485;A|0.515	0.515	strong		0.701	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
SDK1	221935	hgsc.bcm.edu	37	7	4218155	4218155	+	Missense_Mutation	SNP	G	G	A	rs141831391	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:4218155G>A	ENST00000404826.2	+	35	5174	c.5035G>A	c.(5035-5037)Gcc>Acc	p.A1679T	SDK1_ENST00000389531.3_Missense_Mutation_p.A1659T	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1679	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AATAATGACCGCCTATAACAT	0.547													G|||	8	0.00159744	0.0015	0.0029	5008	,	,		18190	0.0		0.004	False		,,,				2504	0.0				p.A1679T		Atlas-SNP	.											.	SDK1	361	.	0			c.G5035A						PASS	.	G	THR/ALA	5,4401	6.2+/-15.9	1,3,2199	101.0	112.0	108.0		5035	5.1	0.9	7	dbSNP_134	108	50,8550	31.2+/-83.2	0,50,4250	yes	missense	SDK1	NM_152744.3	58	1,53,6449	AA,AG,GG		0.5814,0.1135,0.4229	possibly-damaging	1679/2214	4218155	55,12951	2203	4300	6503	SO:0001583	missense	221935	exon35			ATGACCGCCTATA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.5035G>A	7.37:g.4218155G>A	ENSP00000385899:p.Ala1679Thr	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	6	0.0027472527472527475	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	16.79	3.220897	0.58560	0.001135	0.005814	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.76448	-0.27;-1.02	5.09	5.09	0.68999	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000002	D	0.84570	0.5501	M	0.86864	2.845	0.48452	D	0.999654	D;D;D	0.71674	0.976;0.981;0.998	P;P;P	0.62491	0.526;0.802;0.903	D	0.85799	0.1372	10	0.33141	T	0.24	.	17.0409	0.86489	0.0:0.0:1.0:0.0	.	1659;166;1679	F8W6X9;F2Z3E9;Q7Z5N4	.;.;SDK1_HUMAN	T	1679;1659	ENSP00000385899:A1679T;ENSP00000374182:A1659T	ENSP00000374182:A1659T	A	+	1	0	SDK1	4184681	0.990000	0.36364	0.929000	0.37066	0.213000	0.24496	4.555000	0.60767	2.525000	0.85131	0.655000	0.94253	GCC	G|0.996;A|0.004	0.004	strong		0.547	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
LRRC14B	389257	hgsc.bcm.edu	37	5	192467	192467	+	Missense_Mutation	SNP	G	G	A	rs78454293	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:192467G>A	ENST00000328278.3	+	1	842	c.814G>A	c.(814-816)Gcc>Acc	p.A272T		NM_001080478.1	NP_001073947.1	A6NHZ5	LR14B_HUMAN	leucine rich repeat containing 14B	272										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	10						CGCCTCCATCGCCCGGGAGCT	0.682													G|||	10	0.00199681	0.0008	0.0029	5008	,	,		17788	0.0		0.007	False		,,,				2504	0.0				p.A272T		Atlas-SNP	.											.	LRRC14B	30	.	0			c.G814A						PASS	.	G	THR/ALA	13,4271		0,13,2129	9.0	12.0	11.0		814	4.4	1.0	5	dbSNP_131	11	61,8449		0,61,4194	yes	missense	LRRC14B	NM_001080478.1	58	0,74,6323	AA,AG,GG		0.7168,0.3035,0.5784	possibly-damaging	272/515	192467	74,12720	2142	4255	6397	SO:0001583	missense	389257	exon1			TCCATCGCCCGGG		CCDS47184.1	5p15.33	2010-02-17			ENSG00000185028	ENSG00000185028			37268	protein-coding gene	gene with protein product							Standard	NM_001080478		Approved		uc003jal.1	A6NHZ5	OTTHUMG00000161578	ENST00000328278.3:c.814G>A	5.37:g.192467G>A	ENSP00000327675:p.Ala272Thr	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	189	102	0.539683	NM_001080478		Missense_Mutation	SNP	ENST00000328278.3	37	CCDS47184.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	17.09	3.300830	0.60195	0.003035	0.007168	ENSG00000185028	ENST00000328278	T	0.55052	0.54	5.33	4.43	0.53597	.	0.149049	0.64402	D	0.000010	T	0.42314	0.1197	L	0.38838	1.175	0.36111	D	0.844832	D	0.62365	0.991	P	0.52109	0.69	T	0.51779	-0.8662	10	0.18276	T	0.48	.	12.8535	0.57871	0.0:0.0:0.8357:0.1643	.	272	A6NHZ5	LR14B_HUMAN	T	272	ENSP00000327675:A272T	ENSP00000327675:A272T	A	+	1	0	LRRC14B	245467	1.000000	0.71417	0.987000	0.45799	0.131000	0.20780	7.463000	0.80869	1.185000	0.42971	0.462000	0.41574	GCC	G|0.996;A|0.004	0.004	strong		0.682	LRRC14B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000365393.2	NM_001080478	
C5orf58	133874	hgsc.bcm.edu	37	5	169661994	169661994	+	Missense_Mutation	SNP	G	G	C	rs957998	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:169661994G>C	ENST00000521850.1	+	2	1766	c.77G>C	c.(76-78)cGt>cCt	p.R26P	C5orf58_ENST00000593851.1_Missense_Mutation_p.R26P|C5orf58_ENST00000517575.1_3'UTR			C9J3I9	CE058_HUMAN	chromosome 5 open reading frame 58	26										large_intestine(1)|lung(4)|urinary_tract(1)	6						GGTAAGAAGCGTGTTACTGAT	0.254																																					p.R26P		Atlas-SNP	.											.	C5orf58	13	.	0			c.G77C						PASS	.	G	PRO/ARG	1740,1854		450,840,507	48.0	45.0	46.0		77	3.5	0.0	5	dbSNP_86	46	4070,4038		1024,2022,1008	yes	missense	C5orf58	NM_001102609.1	103	1474,2862,1515	CC,CG,GG		49.8027,48.414,49.6496	benign	26/103	169661994	5810,5892	1797	4054	5851	SO:0001583	missense	133874	exon3			AGAAGCGTGTTAC	BC030767	CCDS47338.1	5q35.1	2009-09-30			ENSG00000234511	ENSG00000234511			37272	protein-coding gene	gene with protein product							Standard	NM_001102609		Approved		uc010jjn.3	C9J3I9	OTTHUMG00000163122	ENST00000521850.1:c.77G>C	5.37:g.169661994G>C	ENSP00000428956:p.Arg26Pro	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_001102609		Missense_Mutation	SNP	ENST00000521850.1	37	CCDS47338.1	1168	0.5347985347985348	238	0.483739837398374	217	0.5994475138121547	318	0.5559440559440559	395	0.521108179419525	G	0.246	-1.010296	0.02095	0.48414	0.501973	ENSG00000234511	ENST00000521850	.	.	.	5.87	3.53	0.40419	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.43540	-0.9385	7	0.34782	T	0.22	.	7.9123	0.29798	0.836:0.0:0.164:0.0	rs957998;rs3761751;rs59509559;rs957998	26	C9J3I9	CE058_HUMAN	P	26	.	ENSP00000428956:R26P	R	+	2	0	C5orf58	169594572	0.725000	0.28048	0.002000	0.10522	0.004000	0.04260	1.242000	0.32755	0.584000	0.29591	-0.302000	0.09304	CGT	G|0.480;C|0.520	0.520	strong		0.254	C5orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371739.1	NM_001102609	
C12orf54	121273	hgsc.bcm.edu	37	12	48888594	48888594	+	Missense_Mutation	SNP	C	C	T	rs11458	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48888594C>T	ENST00000548364.1	+	7	313	c.256C>T	c.(256-258)Cca>Tca	p.P86S	C12orf54_ENST00000314014.2_Missense_Mutation_p.P86S|RP11-722P11.4_ENST00000551847.1_RNA			Q6X4T0	CL054_HUMAN	chromosome 12 open reading frame 54	86			P -> S (in dbSNP:rs11458). {ECO:0000269|Ref.1}.							endometrium(1)|large_intestine(4)	5						CATAAGGCCTCCAGATTCCTT	0.493													C|||	1137	0.227037	0.0371	0.2594	5008	,	,		20088	0.1478		0.4394	False		,,,				2504	0.3241				p.P86S		Atlas-SNP	.											.	C12orf54	11	.	0			c.C256T						PASS	.		SER/PRO	454,3952	216.1+/-234.9	27,400,1776	115.0	117.0	116.0		256	1.7	0.1	12	dbSNP_52	116	3966,4634	552.2+/-386.1	902,2162,1236	yes	missense	C12orf54	NM_152319.3	74	929,2562,3012	TT,TC,CC		46.1163,10.3041,33.9843	benign	86/128	48888594	4420,8586	2203	4300	6503	SO:0001583	missense	121273	exon8			AGGCCTCCAGATT	BC031670	CCDS8764.1	12q13.11	2011-01-31			ENSG00000177627	ENSG00000177627			28553	protein-coding gene	gene with protein product						12477932	Standard	NM_152319		Approved	MGC35033	uc001rrr.3	Q6X4T0	OTTHUMG00000170019	ENST00000548364.1:c.256C>T	12.37:g.48888594C>T	ENSP00000447109:p.Pro86Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	126	52	0.412698	NM_152319	Q6X4S9|Q8N5S2	Missense_Mutation	SNP	ENST00000548364.1	37	CCDS8764.1	594	0.27197802197802196	32	0.06504065040650407	106	0.292817679558011	103	0.18006993006993008	353	0.4656992084432718	C	10.88	1.475188	0.26511	0.103041	0.461163	ENSG00000177627	ENST00000314014;ENST00000548364	T;T	0.61627	0.09;0.09	4.74	1.73	0.24493	.	0.537306	0.15751	N	0.246416	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.21753	0.06	B	0.20184	0.028	T	0.47222	-0.9134	9	0.14252	T	0.57	-2.5036	6.3094	0.21156	0.0:0.6587:0.0:0.3413	rs11458;rs1132190;rs3192741;rs7131975;rs17342728;rs17350393;rs17827594;rs52790501;rs58721339;rs11458	86	Q6X4T0	CL054_HUMAN	S	86	ENSP00000316898:P86S;ENSP00000447109:P86S	ENSP00000316898:P86S	P	+	1	0	C12orf54	47174861	0.725000	0.28048	0.122000	0.21767	0.020000	0.10135	0.025000	0.13577	0.236000	0.21180	0.651000	0.88453	CCA	C|0.697;T|0.303	0.303	strong		0.493	C12orf54-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406875.1	NM_152319	
SYCE1L	100130958	hgsc.bcm.edu	37	16	77246218	77246218	+	Missense_Mutation	SNP	G	G	A	rs13331769	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:77246218G>A	ENST00000378644.4	+	9	588	c.533G>A	c.(532-534)cGg>cAg	p.R178Q	RP11-538I12.2_ENST00000569032.1_RNA	NM_001129979.1	NP_001123451.1	A8MT33	SYC1L_HUMAN	synaptonemal complex central element protein 1-like	178					synaptonemal complex assembly (GO:0007130)	synaptonemal complex (GO:0000795)				breast(1)|prostate(1)	2						GTGGAGCGGCGGCTGCACTCG	0.766													G|||	1815	0.36242	0.2065	0.3833	5008	,	,		11988	0.3065		0.5875	False		,,,				2504	0.3845				p.R178Q		Atlas-SNP	.											SYCE1L,NS,carcinoma,0,1	SYCE1L	10	1	0			c.G533A						PASS	.						3.0	6.0	5.0					16																	77246218		527	1355	1882	SO:0001583	missense	100130958	exon9			AGCGGCGGCTGCA		CCDS45533.1	16q23.1	2009-10-06			ENSG00000205078	ENSG00000205078			37236	protein-coding gene	gene with protein product	"""meiosis-related protein"""					16328886	Standard	NM_001129979		Approved	MRP2	uc010vnh.1	A8MT33		ENST00000378644.4:c.533G>A	16.37:g.77246218G>A	ENSP00000367911:p.Arg178Gln	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_001129979	A6NF23	Missense_Mutation	SNP	ENST00000378644.4	37	CCDS45533.1	873	0.39972527472527475	110	0.22357723577235772	150	0.4143646408839779	178	0.3111888111888112	435	0.5738786279683378	G	3.435	-0.115281	0.06881	.	.	ENSG00000205078	ENST00000378644	T	0.46063	0.88	3.01	0.923	0.19413	.	1.711630	0.04935	U	0.457533	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	D	0.57899	0.981	B	0.43103	0.408	T	0.42120	-0.9470	9	0.09843	T	0.71	.	3.8967	0.09143	0.1317:0.0:0.6355:0.2328	rs13331769	178	A8MT33	SYC1L_HUMAN	Q	178	ENSP00000367911:R178Q	ENSP00000367911:R178Q	R	+	2	0	SYCE1L	75803719	0.005000	0.15991	0.001000	0.08648	0.107000	0.19398	-0.261000	0.08694	0.272000	0.22027	0.471000	0.43371	CGG	G|0.598;A|0.402	0.402	strong		0.766	SYCE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433889.1	NM_001129979	
POTEE	445582	hgsc.bcm.edu	37	2	132021908	132021908	+	Silent	SNP	G	G	A	rs201238743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:132021908G>A	ENST00000356920.5	+	15	2974	c.2880G>A	c.(2878-2880)gcG>gcA	p.A960A	POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	960	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											GCCCCGAGGCGCTCTTCCAGC	0.592																																					p.A960A		Atlas-SNP	.											.	.	.	.	0			c.G2880A						PASS	.						2.0	1.0	1.0					2																	132021908		762	1288	2050	SO:0001819	synonymous_variant	445582	exon15			CGAGGCGCTCTTC	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.2880G>A	2.37:g.132021908G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	184	41	0.222826	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Silent	SNP	ENST00000356920.5	37	CCDS46414.1																																																																																			A|1.000;|0.000	1.000	weak		0.592	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
HID1	283987	hgsc.bcm.edu	37	17	72949146	72949146	+	Silent	SNP	C	C	T	rs2307010	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72949146C>T	ENST00000425042.2	-	16	2084	c.2007G>A	c.(2005-2007)ccG>ccA	p.P669P		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	669					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)											ATGAGGTGGACGGTCGCCGCT	0.692													C|||	984	0.196486	0.0734	0.1859	5008	,	,		13990	0.2698		0.2396	False		,,,				2504	0.2505				p.P669P		Atlas-SNP	.											C17orf28,colon,carcinoma,0,1	.	.	1	0			c.G2007A						PASS	.	C		440,3966		25,390,1788	23.0	20.0	21.0		2007	-1.3	0.8	17	dbSNP_100	21	2060,6536		256,1548,2494	no	coding-synonymous	C17orf28	NM_030630.2		281,1938,4282	TT,TC,CC		23.9646,9.9864,19.2278		669/789	72949146	2500,10502	2203	4298	6501	SO:0001819	synonymous_variant	283987	exon16			GGTGGACGGTCGC		CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"""downregulated in multiple cancer 1"""	605752	"""chromosome 17 open reading frame 28"""	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.2007G>A	17.37:g.72949146C>T		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	179	179	1	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Silent	SNP	ENST00000425042.2	37	CCDS32726.1																																																																																			C|0.809;T|0.191	0.191	strong		0.692	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630	
PTPN7	5778	hgsc.bcm.edu	37	1	202129895	202129895	+	5'Flank	SNP	G	G	A	rs3935295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:202129895G>A	ENST00000308986.5	-	0	0				PTPN7_ENST00000367279.4_5'Flank|PTPN7_ENST00000492977.1_5'Flank|PTPN7_ENST00000543735.1_5'Flank|PTPN7_ENST00000309017.3_Missense_Mutation_p.T14M|PTPN7_ENST00000544762.1_5'Flank			P35236	PTN7_HUMAN	protein tyrosine phosphatase, non-receptor type 7						peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|soft_tissue(1)|urinary_tract(1)	13						CCAAGGCCCCGTTCCCTGGGA	0.667													g|||	874	0.174521	0.0287	0.219	5008	,	,		15828	0.121		0.1938	False		,,,				2504	0.3753				p.T14M		Atlas-SNP	.											.	PTPN7	31	.	0			c.C41T						PASS	.		,MET/THR	64,1576		1,62,757	3.0	3.0	3.0		,41	-5.0	0.0	1	dbSNP_108	3	529,3149		24,481,1334	yes	intron,missense	PTPN7	NM_001199797.1,NM_002832.3	,81	25,543,2091	AA,AG,GG		14.3828,3.9024,11.1508	,	,14/466	202129895	593,4725	820	1839	2659	SO:0001631	upstream_gene_variant	5778	exon1			GGCCCCGTTCCCT	BC001746	CCDS1422.1, CCDS1423.1, CCDS1423.2	1q32.1	2011-06-09			ENSG00000143851	ENSG00000143851		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9659	protein-coding gene	gene with protein product		176889				1510684	Standard	NM_002832		Approved	HEPTP, LC-PTP	uc010ppx.2	P35236	OTTHUMG00000035931		1.37:g.202129895G>A	Exception_encountered	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_002832	B3KXE1|Q53XK4|Q5SXQ0|Q5SXQ1|Q9BV05	Missense_Mutation	SNP	ENST00000308986.5	37		285	0.1304945054945055	12	0.024390243902439025	71	0.19613259668508287	69	0.12062937062937062	133	0.17546174142480211	G	8.548	0.874764	0.17395	0.039024	0.143828	ENSG00000143851	ENST00000309017	T	0.04654	3.58	2.5	-5.01	0.02991	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	4.000000000004E-6	.	.	.	.	.	.	T	0.46911	-0.9157	6	0.87932	D	0	.	0.1815	0.00124	0.2809:0.1647:0.2916:0.2629	rs3935295	.	.	.	M	14	ENSP00000309116:T14M	ENSP00000309116:T14M	T	-	2	0	PTPN7	200396518	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.003000	0.12901	-1.485000	0.01854	-0.643000	0.03959	ACG	G|0.868;A|0.132	0.132	strong		0.667	PTPN7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002832	
FRMPD2	143162	hgsc.bcm.edu	37	10	49383976	49383976	+	Missense_Mutation	SNP	T	T	C	rs200957845		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:49383976T>C	ENST00000374201.3	-	23	3204	c.2902A>G	c.(2902-2904)Att>Gtt	p.I968V	FRMPD2_ENST00000474573.1_5'UTR|FRMPD2_ENST00000463706.1_5'UTR|FRMPD2_ENST00000305531.3_Missense_Mutation_p.I943V|FRMPD2_ENST00000407470.4_Missense_Mutation_p.I936V	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	968	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		CTGGTGTTAATGCCACCCTGA	0.532																																					p.I968V		Atlas-SNP	.											FRMPD2,NS,carcinoma,0,1	FRMPD2	157	1	0			c.A2902G						scavenged	.						3.0	1.0	1.0					10																	49383976		81	163	244	SO:0001583	missense	143162	exon23			TGTTAATGCCACC	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.2902A>G	10.37:g.49383976T>C	ENSP00000363317:p.Ile968Val	Somatic	342	1	0.00292398		WXS	Illumina HiSeq	Phase_I	392	117	0.298469	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.452426	0.01080	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.26810	1.71;1.71;1.71	4.81	-0.335	0.12662	PDZ/DHR/GLGF (4);	.	.	.	.	T	0.10723	0.0262	N	0.03891	-0.335	0.09310	N	1	B;B;B	0.18863	0.006;0.031;0.016	B;B;B	0.23419	0.016;0.046;0.024	T	0.39165	-0.9627	9	0.21540	T	0.41	.	9.0019	0.36088	0.0:0.3679:0.0:0.6321	.	943;968;936	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	V	968;943;936	ENSP00000363317:I968V;ENSP00000307079:I943V;ENSP00000384339:I936V	ENSP00000307079:I943V	I	-	1	0	FRMPD2	49053982	0.623000	0.27094	0.520000	0.27837	0.722000	0.41435	0.524000	0.22940	-0.339000	0.08401	0.528000	0.53228	ATT	T|0.500;C|0.500	0.500	weak		0.532	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
ATP8A2	51761	hgsc.bcm.edu	37	13	26148966	26148966	+	Silent	SNP	C	C	T	rs6491066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:26148966C>T	ENST00000381655.2	+	19	1825	c.1683C>T	c.(1681-1683)ttC>ttT	p.F561F	ATP8A2_ENST00000491840.1_3'UTR|ATP8A2_ENST00000255283.8_Silent_p.F521F	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	521					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		AACAAACATTCGGAATCCTTA	0.333													C|||	2686	0.536342	0.6808	0.6095	5008	,	,		16483	0.1409		0.7147	False		,,,				2504	0.5133				p.F561F		Atlas-SNP	.											.	ATP8A2	181	.	0			c.C1683T						PASS	.	C		2544,1088		906,732,178	128.0	122.0	124.0		1683	1.5	1.0	13	dbSNP_116	124	5800,2348		2069,1662,343	no	coding-synonymous	ATP8A2	NM_016529.4		2975,2394,521	TT,TC,CC		28.8169,29.9559,29.1681		561/1189	26148966	8344,3436	1816	4074	5890	SO:0001819	synonymous_variant	51761	exon19			AACATTCGGAATC	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"""ATPases / P-type"""	13533	protein-coding gene	gene with protein product		605870	"""ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2"", ""ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"""			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.1683C>T	13.37:g.26148966C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Silent	SNP	ENST00000381655.2	37	CCDS41873.1																																																																																			C|0.420;T|0.580	0.580	strong		0.333	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529	
CCDC40	55036	hgsc.bcm.edu	37	17	78073562	78073562	+	Silent	SNP	A	A	G	rs2304854	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78073562A>G	ENST00000397545.4	+	20	3444	c.3417A>G	c.(3415-3417)ccA>ccG	p.P1139P	GAA_ENST00000302262.3_5'Flank|GAA_ENST00000390015.3_5'Flank	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	1139					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TCGAGTCACCAGGGCCCTCCT	0.592													G|||	2512	0.501597	0.6513	0.2911	5008	,	,		16821	0.4355		0.4751	False		,,,				2504	0.544				p.P1139P		Atlas-SNP	.											.	CCDC40	198	.	0			c.A3417G						PASS	.	G		2329,1641		702,925,358	26.0	30.0	29.0		3417	-9.2	0.0	17	dbSNP_100	29	3724,4610		851,2022,1294	no	coding-synonymous	CCDC40	NM_017950.3		1553,2947,1652	GG,GA,AA		44.6844,41.335,49.1954		1139/1143	78073562	6053,6251	1985	4167	6152	SO:0001819	synonymous_variant	55036	exon20			GTCACCAGGGCCC	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.3417A>G	17.37:g.78073562A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	100	56	0.56	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																			A|0.508;G|0.492	0.492	strong		0.592	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082	
ANKRD55	79722	hgsc.bcm.edu	37	5	55407542	55407542	+	Missense_Mutation	SNP	C	C	T	rs321776	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:55407542C>T	ENST00000341048.4	-	10	1184	c.1033G>A	c.(1033-1035)Gtg>Atg	p.V345M	ANKRD55_ENST00000505970.2_5'UTR|ANKRD55_ENST00000504958.2_Missense_Mutation_p.V302M|ANKRD55_ENST00000434982.2_Missense_Mutation_p.V57M	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	345			V -> M (in dbSNP:rs321776). {ECO:0000269|PubMed:15489334}.							breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				TGGTTGAGCACGTTGAACCGT	0.507													T|||	1041	0.207867	0.0658	0.1254	5008	,	,		18687	0.2927		0.2803	False		,,,				2504	0.2965				p.V345M		Atlas-SNP	.											.	ANKRD55	70	.	0			c.G1033A						PASS	.	T	MET/VAL	428,3978		25,378,1800	156.0	152.0	153.0		1033	-3.5	0.0	5	dbSNP_79	153	2313,6287		322,1669,2309	yes	missense	ANKRD55	NM_024669.2	21	347,2047,4109	TT,TC,CC		26.8953,9.714,21.0749	benign	345/615	55407542	2741,10265	2203	4300	6503	SO:0001583	missense	79722	exon10			TGAGCACGTTGAA	AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"""Ankyrin repeat domain containing"""	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.1033G>A	5.37:g.55407542C>T	ENSP00000342295:p.Val345Met	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	170	87	0.511765	NM_024669	B3KVT8|Q3KP45|Q9HAD3	Missense_Mutation	SNP	ENST00000341048.4	37	CCDS34161.1	484	0.2216117216117216	31	0.06300813008130081	61	0.1685082872928177	176	0.3076923076923077	216	0.2849604221635884	.	0.007	-1.993416	0.00439	0.09714	0.268953	ENSG00000164512	ENST00000507283;ENST00000341048;ENST00000504958;ENST00000434982	T;T;T	0.37058	1.41;1.22;1.57	5.49	-3.45	0.04781	.	0.166764	0.50627	N	0.000107	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B;B	0.10296	0.001;0.003	B;B	0.04013	0.001;0.001	T	0.42949	-0.9421	9	0.25106	T	0.35	.	13.7387	0.62833	0.0:0.4255:0.0:0.5745	rs321776;rs52792559;rs61075672;rs321776	345;344	B3KVT8;Q3KP44	.;ANR55_HUMAN	M	345;345;302;57	ENSP00000342295:V345M;ENSP00000424230:V302M;ENSP00000429421:V57M	ENSP00000342295:V345M	V	-	1	0	ANKRD55	55443299	0.001000	0.12720	0.011000	0.14972	0.049000	0.14656	-0.316000	0.08071	-1.167000	0.02779	-2.733000	0.00129	GTG	C|0.786;T|0.214	0.214	strong		0.507	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368510.4	NM_024669	
SNAP91	9892	hgsc.bcm.edu	37	6	84300997	84300997	+	Silent	SNP	A	A	G	rs2273363	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:84300997A>G	ENST00000439399.2	-	22	2263	c.1947T>C	c.(1945-1947)agT>agC	p.S649S	SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000369694.2_Silent_p.S649S|SNAP91_ENST00000521743.1_Silent_p.S649S|SNAP91_ENST00000195649.6_Silent_p.S649S|SNAP91_ENST00000520302.1_Silent_p.S619S|SNAP91_ENST00000521485.1_Silent_p.S649S|SNAP91_ENST00000428679.2_Silent_p.S649S|SNAP91_ENST00000437520.1_Intron	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	649					clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		GTTCAGAAGCACTACTTCCAA	0.368													A|||	835	0.166733	0.0113	0.1354	5008	,	,		15991	0.2381		0.2276	False		,,,				2504	0.2628				p.S649S		Atlas-SNP	.											.	SNAP91	199	.	0			c.T1947C						PASS	.	A	,,,	161,3611		2,157,1727	114.0	111.0	112.0		1947,1857,,1947	3.6	1.0	6	dbSNP_100	112	1943,6273		227,1489,2392	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	SNAP91	NM_001242792.1,NM_001242793.1,NM_001242794.1,NM_014841.2	,,,	229,1646,4119	GG,GA,AA		23.649,4.2683,17.5509	,,,	649/908,619/878,,649/908	84300997	2104,9884	1886	4108	5994	SO:0001819	synonymous_variant	9892	exon21			AGAAGCACTACTT	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"""synaptosomal-associated protein, 91 kDa (mouse) homolog"", ""synaptosomal-associated protein, 91kDa homolog (mouse)"""			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1947T>C	6.37:g.84300997A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Silent	SNP	ENST00000439399.2	37	CCDS47455.1																																																																																			A|0.813;G|0.187	0.187	strong		0.368	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1		
PRRC2C	23215	hgsc.bcm.edu	37	1	171526570	171526570	+	Silent	SNP	G	G	A	rs1687057	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:171526570G>A	ENST00000338920.4	+	19	5550	c.5313G>A	c.(5311-5313)ccG>ccA	p.P1771P	PRRC2C_ENST00000426496.2_Silent_p.P1771P|PRRC2C_ENST00000367742.3_Silent_p.P1773P|PRRC2C_ENST00000392078.3_Silent_p.P1773P	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1771	Ala-rich.		P -> S (in dbSNP:rs1687056).		hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										ctccacttccggcaaccttaa	0.557													A|||	4058	0.810304	0.7474	0.7349	5008	,	,		16772	0.8958		0.8161	False		,,,				2504	0.8548				p.P1771P		Atlas-SNP	.											.	.	.	.	0			c.G5313A						PASS	.	A		2630,730		1040,550,90	114.0	97.0	103.0		5313	0.2	0.0	1	dbSNP_89	103	4976,1054		2056,864,95	no	coding-synonymous	PRRC2C	NM_015172.3		3096,1414,185	AA,AG,GG		17.4793,21.7262,18.9989		1771/2818	171526570	7606,1784	1680	3015	4695	SO:0001819	synonymous_variant	23215	exon19			ACTTCCGGCAACC	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.5313G>A	1.37:g.171526570G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	142	55	0.387324	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2	1784	0.8168498168498168	367	0.7459349593495935	274	0.7569060773480663	513	0.8968531468531469	630	0.8311345646437994	A	3.783	-0.045285	0.07452	0.782738	0.825207	ENSG00000117523	ENST00000495585	.	.	.	0.185	0.185	0.15096	.	.	.	.	.	T	0.13372	0.0324	.	.	.	0.33784	P	0.37531499999999995	.	.	.	.	.	.	T	0.25363	-1.0134	3	.	.	.	.	4.5532	0.12124	0.3714:0.0:0.6286:0.0	rs1687057;rs3737923;rs59443639;rs1687057	.	.	.	Q	319	.	.	R	+	2	0	PRRC2C	169793194	.	.	0.016000	0.15963	0.206000	0.24218	.	.	-0.903000	0.03881	-0.945000	0.02674	CGG	G|0.194;A|0.806	0.806	strong		0.557	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
ROS1	6098	hgsc.bcm.edu	37	6	117725448	117725448	+	Missense_Mutation	SNP	T	T	G	rs1998206	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:117725448T>G	ENST00000368508.3	-	5	631	c.433A>C	c.(433-435)Act>Cct	p.T145P	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.T154P	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	145	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> P (in dbSNP:rs1998206). {ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CATACCTTAGTATAAGTCCAG	0.433			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								T|||	840	0.167732	0.1611	0.1427	5008	,	,		16838	0.1815		0.1501	False		,,,				2504	0.1984				p.T145P		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.A433C						PASS	.	T	PRO/THR	710,3696	298.4+/-285.3	51,608,1544	142.0	141.0	142.0		433	5.4	0.6	6	dbSNP_92	142	1201,7399	243.6+/-273.1	86,1029,3185	yes	missense	ROS1	NM_002944.2	38	137,1637,4729	GG,GT,TT		13.9651,16.1144,14.6932	probably-damaging	145/2348	117725448	1911,11095	2203	4300	6503	SO:0001583	missense	6098	exon5			CCTTAGTATAAGT	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.433A>C	6.37:g.117725448T>G	ENSP00000357494:p.Thr145Pro	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	361	0.1652930402930403	92	0.18699186991869918	55	0.15193370165745856	94	0.16433566433566432	120	0.158311345646438	T	13.59	2.283876	0.40394	0.161144	0.139651	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.58210	0.35;0.35	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000004	T	0.58148	0.2102	L	0.51422	1.61	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.60561	-0.7239	9	0.41790	T	0.15	.	14.6271	0.68629	0.0:0.0:0.0:1.0	rs1998206;rs52812719;rs58941505;rs1998206	145	P08922	ROS1_HUMAN	P	145;154	ENSP00000357494:T145P;ENSP00000357493:T154P	ENSP00000357493:T154P	T	-	1	0	ROS1	117832141	1.000000	0.71417	0.626000	0.29213	0.107000	0.19398	1.604000	0.36804	2.054000	0.61138	0.454000	0.30748	ACT	T|0.852;G|0.148	0.148	strong		0.433	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
CCDC170	80129	hgsc.bcm.edu	37	6	151917660	151917660	+	Missense_Mutation	SNP	G	G	A	rs34430497	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:151917660G>A	ENST00000239374.7	+	9	1757	c.1658G>A	c.(1657-1659)cGa>cAa	p.R553Q	CCDC170_ENST00000367290.5_Missense_Mutation_p.R553Q	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	553			R -> Q (in dbSNP:rs34430497).														AACACGTGTCGAGACTTGCAC	0.517													G|||	78	0.0155751	0.0023	0.0346	5008	,	,		17433	0.002		0.0447	False		,,,				2504	0.0041				p.R553Q		Atlas-SNP	.											C6orf97,colon,carcinoma,+1,1	.	.	1	0			c.G1658A						scavenged	.	G	GLN/ARG	49,4209		0,49,2080	93.0	101.0	98.0		1658	1.9	0.0	6	dbSNP_126	98	512,7964		11,490,3737	yes	missense	C6orf97	NM_025059.3	43	11,539,5817	AA,AG,GG		6.0406,1.1508,4.4055	benign	553/716	151917660	561,12173	2129	4238	6367	SO:0001583	missense	80129	exon9			CGTGTCGAGACTT	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1658G>A	6.37:g.151917660G>A	ENSP00000239374:p.Arg553Gln	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	49	0.022435897435897436	2	0.0040650406504065045	10	0.027624309392265192	1	0.0017482517482517483	36	0.047493403693931395	G	6.579	0.475110	0.12521	0.011508	0.060406	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.77358	2.76;-1.09	5.63	1.89	0.25635	.	0.564673	0.16689	N	0.203618	T	0.29321	0.0730	N	0.16201	0.385	0.09310	N	1	P	0.38677	0.642	B	0.27608	0.081	T	0.15809	-1.0424	10	0.25106	T	0.35	-6.3859	5.0724	0.14613	0.2851:0.0:0.5819:0.1329	rs34430497	553	Q8IYT3	CF097_HUMAN	Q	553	ENSP00000239374:R553Q;ENSP00000356259:R553Q	ENSP00000239374:R553Q	R	+	2	0	C6orf97	151959353	0.029000	0.19370	0.005000	0.12908	0.002000	0.02628	0.592000	0.23984	0.064000	0.16427	-0.150000	0.13652	CGA	G|0.967;A|0.033	0.033	strong		0.517	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
SLC4A5	57835	hgsc.bcm.edu	37	2	74466594	74466594	+	Silent	SNP	G	G	A	rs4853018	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:74466594G>A	ENST00000377634.4	-	21	2586	c.2187C>T	c.(2185-2187)ggC>ggT	p.G729G	SLC4A5_ENST00000394019.2_Silent_p.G729G|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000423644.1_Silent_p.G729G|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Silent_p.G729G|SLC4A5_ENST00000357822.5_Silent_p.G729G|SLC4A5_ENST00000359484.4_Silent_p.G665G|SLC4A5_ENST00000358683.4_Silent_p.G665G|SLC4A5_ENST00000346834.4_Silent_p.G729G					solute carrier family 4 (sodium bicarbonate cotransporter), member 5											breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						GCAGGCGCCCGCCGTAGCTCA	0.537													G|||	1135	0.226637	0.1384	0.2291	5008	,	,		19259	0.1954		0.4304	False		,,,				2504	0.1667				p.G729G		Atlas-SNP	.											SLC4A5_ENST00000377634,colon,carcinoma,0,2	SLC4A5	215	2	0			c.C2187T						PASS	.	G	,	876,3530	340.7+/-306.4	71,734,1398	75.0	74.0	74.0		2187,2187	-9.0	0.7	2	dbSNP_111	74	3620,4980	522.4+/-380.1	757,2106,1437	yes	coding-synonymous,coding-synonymous	SLC4A5	NM_021196.3,NM_133478.2	,	828,2840,2835	AA,AG,GG		42.093,19.882,34.5687	,	729/1138,729/1122	74466594	4496,8510	2203	4300	6503	SO:0001819	synonymous_variant	57835	exon16			GCGCCCGCCGTAG	AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"""Solute carriers"""	18168	protein-coding gene	gene with protein product		606757	"""solute carrier family 4, sodium bicarbonate cotransporter, member 5"""			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.2187C>T	2.37:g.74466594G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	196	129	0.658163	NM_021196		Silent	SNP	ENST00000377634.4	37	CCDS1936.1																																																																																			G|0.694;A|0.306	0.306	strong		0.537	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3		
DCPS	28960	hgsc.bcm.edu	37	11	126174038	126174038	+	Silent	SNP	C	C	T	rs3740915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:126174038C>T	ENST00000263579.4	+	1	392	c.63C>T	c.(61-63)caC>caT	p.H21H	RP11-712L6.5_ENST00000524964.1_Intron	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	21					cellular response to menadione (GO:0036245)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA metabolic process (GO:0016071)|negative regulation of programmed cell death (GO:0043069)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	m7G(5')pppN diphosphatase activity (GO:0050072)|RNA 7-methylguanosine cap binding (GO:0000340)			endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		AGGAGGCCCACGCCGCCAGCA	0.647													C|||	400	0.0798722	0.0015	0.1369	5008	,	,		15968	0.1776		0.0408	False		,,,				2504	0.0849				p.H21H		Atlas-SNP	.											.	DCPS	33	.	0			c.C63T						PASS	.	C		56,4346	55.5+/-91.7	1,54,2146	71.0	54.0	60.0		63	-1.9	0.0	11	dbSNP_107	60	318,8278	112.1+/-172.3	7,304,3987	no	coding-synonymous	DCPS	NM_014026.3		8,358,6133	TT,TC,CC		3.6994,1.2721,2.8774		21/338	126174038	374,12624	2201	4298	6499	SO:0001819	synonymous_variant	28960	exon1			GGCCCACGCCGCC	AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063			29812	protein-coding gene	gene with protein product		610534				12198172, 14523240	Standard	NM_014026		Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.63C>T	11.37:g.126174038C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_014026	Q8NHL8|Q9Y2S5	Silent	SNP	ENST00000263579.4	37	CCDS8473.1																																																																																			C|0.950;T|0.050	0.050	strong		0.647	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
TACC2	10579	hgsc.bcm.edu	37	10	123844503	123844503	+	Missense_Mutation	SNP	C	C	T	rs10887063	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:123844503C>T	ENST00000369005.1	+	4	2828	c.2488C>T	c.(2488-2490)Ctc>Ttc	p.L830F	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.L830F|TACC2_ENST00000515603.1_Missense_Mutation_p.L830F|TACC2_ENST00000515273.1_Missense_Mutation_p.L830F|TACC2_ENST00000334433.3_Missense_Mutation_p.L830F|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	830			L -> F (in dbSNP:rs10887063). {ECO:0000269|PubMed:12620397}.		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGAGAAGCATCTCCAGCCATC	0.557													C|||	922	0.184105	0.2882	0.17	5008	,	,		19229	0.0982		0.1829	False		,,,				2504	0.1431				p.L830F		Atlas-SNP	.											.	TACC2	271	.	0			c.C2488T						PASS	.	C	,PHE/LEU	1381,3025	455.7+/-351.1	210,961,1032	125.0	126.0	126.0		,2488	4.6	0.0	10	dbSNP_120	126	1595,7005	295.9+/-302.6	142,1311,2847	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,22	352,2272,3879	TT,TC,CC		18.5465,31.3436,22.8817	,benign	,830/2949	123844503	2976,10030	2203	4300	6503	SO:0001583	missense	10579	exon4			AAGCATCTCCAGC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.2488C>T	10.37:g.123844503C>T	ENSP00000358001:p.Leu830Phe	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	417	0.19093406593406592	141	0.2865853658536585	73	0.20165745856353592	68	0.11888111888111888	135	0.17810026385224276	C	14.53	2.561552	0.45590	0.313436	0.185465	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.04970	3.62;3.52;3.56;3.62;3.52	5.66	4.57	0.56435	.	0.260219	0.20581	N	0.089522	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P;P;P	0.47106	0.89;0.89;0.89	B;B;B	0.38954	0.286;0.286;0.286	T	0.54866	-0.8229	9	0.46703	T	0.11	-5.2727	12.3263	0.55013	0.0:0.9063:0.0:0.0937	rs10887063;rs52822997;rs10887063	830;830;830	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	F	830;830;830;830;830;820	ENSP00000358001:L830F;ENSP00000424467:L830F;ENSP00000427618:L830F;ENSP00000334280:L830F;ENSP00000395048:L830F	ENSP00000334280:L830F	L	+	1	0	TACC2	123834493	0.001000	0.12720	0.008000	0.14137	0.034000	0.12701	0.982000	0.29539	2.660000	0.90430	0.549000	0.68633	CTC	C|0.791;T|0.209	0.209	strong		0.557	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
RAD51B	5890	hgsc.bcm.edu	37	14	68352672	68352672	+	Missense_Mutation	SNP	A	A	G	rs28910275	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:68352672A>G	ENST00000487270.1	+	6	587	c.539A>G	c.(538-540)tAt>tGt	p.Y180C	RAD51B_ENST00000488612.1_Missense_Mutation_p.Y180C|RAD51B_ENST00000487861.1_Missense_Mutation_p.Y180C|RAD51B_ENST00000390683.3_Missense_Mutation_p.Y180C|RAD51B_ENST00000471583.1_Missense_Mutation_p.Y180C	NM_133509.3	NP_598193.2	O15315	RA51B_HUMAN	RAD51 paralog B	180			Y -> C (in dbSNP:rs28910275). {ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)		HMGA2/RAD51B(11)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11						GTTCATCTTTATCGGGAACTC	0.333								Direct reversal of damage					A|||	15	0.00299521	0.0	0.0	5008	,	,		17500	0.0		0.0149	False		,,,				2504	0.0				p.Y180C		Atlas-SNP	.											.	RAD51B	80	.	0			c.A539G						PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR	3,4403	6.2+/-15.9	0,3,2200	120.0	122.0	121.0		539,539,539	3.5	1.0	14	dbSNP_125	121	36,8564	24.6+/-71.5	0,36,4264	yes	missense,missense,missense	RAD51B	NM_002877.5,NM_133509.3,NM_133510.3	194,194,194	0,39,6464	GG,GA,AA		0.4186,0.0681,0.2999	benign,benign,benign	180/351,180/385,180/351	68352672	39,12967	2203	4300	6503	SO:0001583	missense	5890	exon6			ATCTTTATCGGGA	U84138	CCDS9789.1, CCDS9790.1	14q23-q24.2	2013-07-02	2013-07-02	2011-07-01	ENSG00000182185	ENSG00000182185			9822	protein-coding gene	gene with protein product		602948	"""RAD51 (S. cerevisiae)-like 1"", ""RAD51-like 1 (S. cerevisiae)"", ""RAD51 homolog B (S. cerevisiae)"""	RAD51L1		6261043, 9207106	Standard	NM_002877		Approved	REC2, hREC2, R51H2	uc001xkf.2	O15315	OTTHUMG00000157530	ENST00000487270.1:c.539A>G	14.37:g.68352672A>G	ENSP00000419471:p.Tyr180Cys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_133509	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	Missense_Mutation	SNP	ENST00000487270.1	37	CCDS9789.1	15	0.006868131868131868	0	0.0	0	0.0	0	0.0	15	0.01978891820580475	A	11.67	1.707545	0.30322	6.81E-4	0.004186	ENSG00000182185	ENST00000487861;ENST00000471583;ENST00000487270;ENST00000488612;ENST00000390683;ENST00000402498;ENST00000342389	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	5.77	3.47	0.39725	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.174359	0.39759	N	0.001261	T	0.18593	0.0446	L	0.45285	1.41	0.27025	N	0.964364	B;B;B;B;B;B	0.17268	0.012;0.021;0.005;0.016;0.003;0.001	B;B;B;B;B;B	0.16722	0.016;0.016;0.006;0.007;0.004;0.007	T	0.19614	-1.0300	10	0.59425	D	0.04	-6.2421	7.9405	0.29955	0.8385:0.0:0.1615:0.0	rs28910275	180;180;180;180;180;180	C9JYJ0;C9JSP9;O15315-4;O15315;O15315-1;O15315-2	.;.;.;RA51B_HUMAN;.;.	C	180	ENSP00000419881:Y180C;ENSP00000418859:Y180C;ENSP00000419471:Y180C;ENSP00000420061:Y180C;ENSP00000375101:Y180C	ENSP00000343531:Y180C	Y	+	2	0	RAD51B	67422425	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	1.631000	0.37092	1.036000	0.39998	0.455000	0.32223	TAT	A|0.996;G|0.004	0.004	strong		0.333	RAD51B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349063.1		
PDILT	204474	hgsc.bcm.edu	37	16	20410547	20410547	+	Missense_Mutation	SNP	C	C	T	rs9926580	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20410547C>T	ENST00000302451.4	-	2	324	c.76G>A	c.(76-78)Gcc>Acc	p.A26T		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	26			A -> T (in dbSNP:rs9926580).		cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						GAAACACCGGCGTTAACCTCT	0.602													C|||	1712	0.341853	0.4637	0.3876	5008	,	,		18196	0.1508		0.3091	False		,,,				2504	0.3753				p.A26T		Atlas-SNP	.											.	PDILT	120	.	0			c.G76A						PASS	.	C	THR/ALA	1871,2535	540.4+/-375.5	373,1125,705	142.0	129.0	133.0		76	-2.3	0.0	16	dbSNP_119	133	2463,6137	405.5+/-348.5	325,1813,2162	yes	missense	PDILT	NM_174924.1	58	698,2938,2867	TT,TC,CC		28.6395,42.4648,33.3231	benign	26/585	20410547	4334,8672	2203	4300	6503	SO:0001583	missense	204474	exon2			CACCGGCGTTAAC		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"""Protein disulfide isomerases"""	27338	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 7"", ""protein disulfide isomerase-like protein of the testis"""					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.76G>A	16.37:g.20410547C>T	ENSP00000305465:p.Ala26Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	88	33	0.375	NM_174924	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	677	0.309981684981685	211	0.42886178861788615	143	0.39502762430939226	90	0.15734265734265734	233	0.3073878627968338	C	5.611	0.297465	0.10622	0.424648	0.286395	ENSG00000169340	ENST00000302451	T	0.03004	4.08	3.62	-2.28	0.06826	.	1.496790	0.04333	N	0.352700	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.44757	-0.9307	9	0.11182	T	0.66	.	3.8175	0.08821	0.4809:0.3247:0.0:0.1944	rs9926580;rs9926580	26	Q8N807	PDILT_HUMAN	T	26	ENSP00000305465:A26T	ENSP00000305465:A26T	A	-	1	0	PDILT	20318048	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.759000	0.00100	-0.397000	0.07691	-0.469000	0.05056	GCC	C|0.673;T|0.327	0.327	strong		0.602	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924	
BCL3	602	hgsc.bcm.edu	37	19	45262848	45262848	+	Silent	SNP	C	C	A	rs139295630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:45262848C>A	ENST00000164227.5	+	9	1585	c.1341C>A	c.(1339-1341)ccC>ccA	p.P447P		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	447	Pro/Ser-rich.				antimicrobial humoral response (GO:0019730)|cellular response to DNA damage stimulus (GO:0006974)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|protein import into nucleus, translocation (GO:0000060)|regulation of apoptotic process (GO:0042981)|regulation of DNA binding (GO:0051101)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to UV-C (GO:0010225)|response to virus (GO:0009615)|spleen development (GO:0048536)|T-helper 1 type immune response (GO:0042088)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	Bcl3-Bcl10 complex (GO:0032996)|Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)				CGGTGCCCCCCTCCCCAGCTC	0.672			T	IGH@	CLL								C|||	78	0.0155751	0.0	0.013	5008	,	,		12036	0.0		0.0239	False		,,,				2504	0.046				p.P447P		Atlas-SNP	.		Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	.	BCL3	28	.	0			c.C1341A						PASS	.	C		23,4373		1,21,2176	27.0	34.0	32.0		1341	-1.6	1.0	19	dbSNP_134	32	215,8355		4,207,4074	no	coding-synonymous	BCL3	NM_005178.4		5,228,6250	AA,AC,CC		2.5088,0.5232,1.8356		447/455	45262848	238,12728	2198	4285	6483	SO:0001819	synonymous_variant	602	exon9			GCCCCCCTCCCCA	M31732	CCDS12642.2	19q13.1-q13.2	2013-01-10			ENSG00000069399	ENSG00000069399		"""Ankyrin repeat domain containing"""	998	protein-coding gene	gene with protein product	"""B-cell lymphoma 3-encoded protein"", ""B-cell leukemia/lymphoma 3"", ""chronic lymphatic leukemia protein"""	109560		D19S37, BCL4		1501714, 2180580	Standard	NM_005178		Approved		uc010xxe.2	P20749	OTTHUMG00000151517	ENST00000164227.5:c.1341C>A	19.37:g.45262848C>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	50	30	0.6	NM_005178		Silent	SNP	ENST00000164227.5	37	CCDS12642.2																																																																																			C|0.982;A|0.018	0.018	strong		0.672	BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1	NM_005178	
CAPS2	84698	hgsc.bcm.edu	37	12	75715330	75715330	+	Missense_Mutation	SNP	C	C	A	rs10879901	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:75715330C>A	ENST00000409445.3	-	6	571	c.375G>T	c.(373-375)ttG>ttT	p.L125F	CAPS2_ENST00000393284.3_5'UTR|CAPS2_ENST00000442339.2_5'UTR|CAPS2_ENST00000409799.1_Missense_Mutation_p.L75F	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	125			L -> F (in dbSNP:rs10879901).				calcium ion binding (GO:0005509)	p.L125F(1)		endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						TTGGTGCTGGCAAATTTTCAG	0.299													C|||	997	0.199081	0.1808	0.1686	5008	,	,		18696	0.2321		0.2535	False		,,,				2504	0.1554				p.L125F		Atlas-SNP	.											CAPS2_ENST00000409445,NS,carcinoma,0,1	CAPS2	96	1	1	Substitution - Missense(1)	kidney(1)	c.G375T						PASS	.						226.0	160.0	180.0					12																	75715330		692	1590	2282	SO:0001583	missense	84698	exon6			TGCTGGCAAATTT	AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"""EF-hand domain containing"""	16471	protein-coding gene	gene with protein product		607724	"""calcyphosphine 2"""			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.375G>T	12.37:g.75715330C>A	ENSP00000386959:p.Leu125Phe	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	207	99	0.478261	NM_032606	Q6PH84|Q8N242|Q8NAY5	Missense_Mutation	SNP	ENST00000409445.3	37	CCDS9008.2	394	0.1804029304029304	55	0.11178861788617886	64	0.17679558011049723	104	0.18181818181818182	171	0.22559366754617413	C	15.49	2.848855	0.51164	.	.	ENSG00000180881	ENST00000409799;ENST00000409445;ENST00000552497;ENST00000436898	T;T;T;T	0.61627	1.14;0.55;0.15;0.09	5.15	-1.26	0.09376	.	0.137416	0.33040	N	0.005349	T	0.00039	0.0001	L	0.39245	1.2	0.09310	P	0.9999999999703258	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	T	0.12372	-1.0550	9	0.87932	D	0	0.013	5.7983	0.18399	0.1186:0.532:0.0:0.3495	rs10879901;rs52797522;rs56534596;rs61664370;rs10879901	125;75	Q9BXY5;B9A061	CAYP2_HUMAN;.	F	75;125;20;19	ENSP00000386977:L75F;ENSP00000386959:L125F;ENSP00000449797:L20F;ENSP00000411797:L19F	ENSP00000338474:L20F	L	-	3	2	CAPS2	74001597	0.960000	0.32886	0.960000	0.40013	0.620000	0.37586	-0.135000	0.10420	-0.482000	0.06782	-0.253000	0.11424	TTG	C|0.808;A|0.192	0.192	strong		0.299	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2		
LYZL4	131375	hgsc.bcm.edu	37	3	42448471	42448471	+	Silent	SNP	G	G	A	rs2286720	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:42448471G>A	ENST00000287748.3	-	3	434	c.159C>T	c.(157-159)ttC>ttT	p.F53F	LYZL4_ENST00000441172.1_Silent_p.F53F|LYZL4_ENST00000470991.1_5'UTR	NM_144634.2	NP_653235.1	Q96KX0	LYZL4_HUMAN	lysozyme-like 4	53					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)|nucleus (GO:0005634)	lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(1)|lung(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		ACTTGCTCTCGAAGTAGGCCA	0.572													G|||	560	0.111821	0.0053	0.049	5008	,	,		20438	0.2758		0.1113	False		,,,				2504	0.1319				p.F53F		Atlas-SNP	.											LYZL4,NS,adenoma,0,2	LYZL4	19	2	0			c.C159T						PASS	.	G		90,4316	75.2+/-113.4	1,88,2114	95.0	77.0	83.0	http://www.ncbi.nlm.nih.gov/pubmed?term	159	-3.3	1.0	3	dbSNP_100	83	784,7816	184.7+/-232.6	40,704,3556	yes	coding-synonymous	LYZL4	NM_144634.2		41,792,5670	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	9.1163,2.0427,6.72		53/147	42448471	874,12132	2203	4300	6503	SO:0001819	synonymous_variant	131375	exon3			GCTCTCGAAGTAG	BC016747, AF326749	CCDS2697.1	3p21.33	2006-04-12			ENSG00000157093	ENSG00000157093			28387	protein-coding gene	gene with protein product		612750				12477932	Standard	NM_144634		Approved	MGC26768, LYC4	uc003cle.3	Q96KX0	OTTHUMG00000131793	ENST00000287748.3:c.159C>T	3.37:g.42448471G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_144634		Silent	SNP	ENST00000287748.3	37	CCDS2697.1																																																																																			G|0.901;A|0.099	0.099	strong		0.572	LYZL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254729.2	NM_144634	
CCDC22	28952	hgsc.bcm.edu	37	X	49103224	49103224	+	Silent	SNP	G	G	A	rs2294020	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:49103224G>A	ENST00000376227.3	+	7	917	c.747G>A	c.(745-747)caG>caA	p.Q249Q		NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22	249										NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						AGCGGCTGCAGAAGCAACTGA	0.672													G|||	1760	0.466225	0.4425	0.389	3775	,	,		11394	0.4851		0.2028	False		,,,				2504	0.2168				p.Q249Q		Atlas-SNP	.											.	CCDC22	69	.	0			c.G747A						PASS	.			2100,1688		528,744,300,351,242	9.0	9.0	9.0		747	0.8	0.7	X	dbSNP_100	9	1815,4840		200,917,498,1300,1323	no	coding-synonymous	CCDC22	NM_014008.3		728,1661,798,1651,1565	AA,AG,A,GG,G		27.2727,44.5618,37.4892		249/628	49103224	3915,6528	2165	4238	6403	SO:0001819	synonymous_variant	28952	exon7			GCTGCAGAAGCAA	BC000972	CCDS14322.1	Xp11.23	2008-02-05	2005-07-24	2005-07-24	ENSG00000101997	ENSG00000101997			28909	protein-coding gene	gene with protein product		300859	"""chromosome X open reading frame 37"""	CXorf37		12477932	Standard	NM_014008		Approved	JM1	uc004dnd.2	O60826	OTTHUMG00000024141	ENST00000376227.3:c.747G>A	X.37:g.49103224G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_014008	A8K7G1	Silent	SNP	ENST00000376227.3	37	CCDS14322.1																																																																																			0|0.005;A|0.488	0.488	strong		0.672	CCDC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060822.1	NM_014008	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77323235	77323235	+	Missense_Mutation	SNP	C	C	G	rs3743749	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:77323235C>G	ENST00000282849.5	-	22	3894	c.3476G>C	c.(3475-3477)aGt>aCt	p.S1159T	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1159	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.		S -> T (in dbSNP:rs3743749).		eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GAGCAGACAACTTGAGGAAGG	0.547													C|||	911	0.181909	0.2103	0.1254	5008	,	,		16523	0.2212		0.1451	False		,,,				2504	0.181				p.S1159T		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G3476C						PASS	.	C	THR/SER	923,3473	352.3+/-311.7	94,735,1369	113.0	119.0	117.0		3476	4.8	0.0	16	dbSNP_107	117	1217,7383	247.4+/-275.4	84,1049,3167	yes	missense	ADAMTS18	NM_199355.2	58	178,1784,4536	GG,GC,CC		14.1512,20.9964,16.4666	possibly-damaging	1159/1222	77323235	2140,10856	2198	4300	6498	SO:0001583	missense	170692	exon22			AGACAACTTGAGG	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3476G>C	16.37:g.77323235C>G	ENSP00000282849:p.Ser1159Thr	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	95	37	0.389474	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	366	0.16758241758241757	108	0.21951219512195122	53	0.1464088397790055	105	0.18356643356643357	100	0.13192612137203166	C	19.99	3.928362	0.73327	0.209964	0.141512	ENSG00000140873	ENST00000282849	T	0.61274	0.12	5.77	4.82	0.62117	.	0.154637	0.56097	D	0.000026	T	0.00039	0.0001	L	0.41415	1.275	0.47037	P	7.059999999999844E-4	B	0.25007	0.116	B	0.30401	0.115	T	0.07347	-1.0777	9	0.28530	T	0.3	.	13.7821	0.63089	0.0:0.9264:0.0:0.0736	rs3743749;rs17687094;rs3743749	1159	Q8TE60	ATS18_HUMAN	T	1159	ENSP00000282849:S1159T	ENSP00000282849:S1159T	S	-	2	0	ADAMTS18	75880736	0.197000	0.23362	0.006000	0.13384	0.821000	0.46438	3.104000	0.50306	1.443000	0.47586	0.557000	0.71058	AGT	C|0.827;G|0.173	0.173	strong		0.547	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
MADD	8567	hgsc.bcm.edu	37	11	47298360	47298360	+	Silent	SNP	G	G	A	rs326214	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:47298360G>A	ENST00000311027.5	+	5	1206	c.1041G>A	c.(1039-1041)gaG>gaA	p.E347E	MADD_ENST00000395336.3_Silent_p.E347E|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000395344.3_Silent_p.E347E|MADD_ENST00000342922.4_Silent_p.E347E|MADD_ENST00000406482.1_Silent_p.E347E|MADD_ENST00000402192.2_Silent_p.E347E|MADD_ENST00000402799.1_Silent_p.E347E|MADD_ENST00000349238.3_Silent_p.E347E|MADD_ENST00000407859.3_Silent_p.E347E	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		ACCCACTGGAGTATATGTTTC	0.527													G|||	2354	0.470048	0.3109	0.6369	5008	,	,		22714	0.2738		0.6899	False		,,,				2504	0.5429				p.E347E		Atlas-SNP	.											MADD,colon,carcinoma,+1,1	MADD	172	1	0			c.G1041A						PASS	.	G	,,,,,,,,,	1588,2814	494.5+/-363.0	270,1048,883	255.0	192.0	214.0		1041,1041,1041,1041,1041,1041,1041,1041,1041,1041	4.0	1.0	11	dbSNP_79	214	5952,2644	686.8+/-404.2	2049,1854,395	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MADD	NM_001135943.1,NM_001135944.1,NM_003682.3,NM_130470.2,NM_130471.2,NM_130472.2,NM_130473.2,NM_130474.2,NM_130475.2,NM_130476.2	,,,,,,,,,	2319,2902,1278	AA,AG,GG		30.7585,36.0745,41.9911	,,,,,,,,,	347/1545,347/1542,347/1648,347/1589,347/1566,347/1546,347/1609,347/1480,347/1582,347/1588	47298360	7540,5458	2201	4298	6499	SO:0001819	synonymous_variant	8567	exon5			ACTGGAGTATATG	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1041G>A	11.37:g.47298360G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	129	79	0.612403	NM_130474		Silent	SNP	ENST00000311027.5	37	CCDS7930.1																																																																																			G|0.446;A|0.554	0.554	strong		0.527	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
POM121L12	285877	hgsc.bcm.edu	37	7	53103425	53103425	+	Missense_Mutation	SNP	C	C	A	rs10229800	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:53103425C>A	ENST00000408890.4	+	1	77	c.61C>A	c.(61-63)Ccc>Acc	p.P21T		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	21			P -> T (in dbSNP:rs10229800).							endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GGCGGGAGAACCCCTGCTGCA	0.711													C|||	623	0.124401	0.1354	0.2089	5008	,	,		12664	0.0992		0.1451	False		,,,				2504	0.0542				p.P21T		Atlas-SNP	.											.	POM121L12	146	.	0			c.C61A						PASS	.	C	THR/PRO	482,3566		32,418,1574	14.0	20.0	18.0		61	0.5	0.0	7	dbSNP_119	18	1051,7277		53,945,3166	yes	missense	POM121L12	NM_182595.3	38	85,1363,4740	AA,AC,CC		12.6201,11.9071,12.3869	possibly-damaging	21/297	53103425	1533,10843	2024	4164	6188	SO:0001583	missense	285877	exon1			GGAGAACCCCTGC		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.61C>A	7.37:g.53103425C>A	ENSP00000386133:p.Pro21Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	304	0.1391941391941392	69	0.1402439024390244	70	0.19337016574585636	56	0.0979020979020979	109	0.1437994722955145	C	10.16	1.275119	0.23307	0.119071	0.126201	ENSG00000221900	ENST00000408890	T	0.20881	2.04	1.66	0.497	0.16902	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.31174	0.311	B	0.18561	0.022	T	0.32481	-0.9905	8	0.05833	T	0.94	.	3.1558	0.06504	0.0:0.2723:0.0:0.7277	rs10229800;rs10229800	21	Q8N7R1	P1L12_HUMAN	T	21	ENSP00000386133:P21T	ENSP00000386133:P21T	P	+	1	0	POM121L12	53070919	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	-0.049000	0.11924	0.138000	0.18790	-0.379000	0.06801	CCC	C|0.870;A|0.130	0.130	strong		0.711	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197549	39197549	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39197549G>C	ENST00000306271.4	-	1	164	c.101C>G	c.(100-102)tCc>tGc	p.S34C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	34			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)		p.S34C(6)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCTGGCAGGAGCTGGTCTC	0.612																																					p.S34C		Atlas-SNP	.											KRTAP1-1,NS,carcinoma,0,7	KRTAP1-1	23	7	6	Substitution - Missense(6)	kidney(4)|lung(1)|prostate(1)	c.C101G						scavenged	.						49.0	62.0	58.0					17																	39197549		2018	4199	6217	SO:0001583	missense	81851	exon1			TGGCAGGAGCTGG	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.101C>G	17.37:g.39197549G>C	ENSP00000305975:p.Ser34Cys	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	188	48	0.255319	NM_030967	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	G	0.085	-1.176298	0.01646	.	.	ENSG00000188581	ENST00000306271	T	0.16196	2.36	3.91	1.65	0.23941	.	.	.	.	.	T	0.01835	0.0058	N	0.00010	-3.04	0.22552	N	0.998996	B	0.02656	0.0	B	0.01281	0.0	T	0.40924	-0.9537	9	0.02654	T	1	.	7.8006	0.29172	0.1777:0.6415:0.1808:0.0	.	34	Q07627	KRA11_HUMAN	C	34	ENSP00000305975:S34C	ENSP00000305975:S34C	S	-	2	0	KRTAP1-1	36451075	1.000000	0.71417	0.987000	0.45799	0.816000	0.46133	1.227000	0.32576	0.919000	0.36945	-0.233000	0.12211	TCC	.	.	none		0.612	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
HSPA1L	3305	hgsc.bcm.edu	37	6	31778529	31778529	+	Silent	SNP	C	C	T	rs2075799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31778529C>T	ENST00000375654.4	-	2	1410	c.1221G>A	c.(1219-1221)acG>acA	p.T407T	HSPA1L_ENST00000417199.3_Silent_p.T407T	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	407					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						CGCCCCCAGCCGTCTCCAGCC	0.612													C|||	769	0.153554	0.233	0.1513	5008	,	,		17495	0.1845		0.0875	False		,,,				2504	0.0838				p.T407T		Atlas-SNP	.											HSPA1L,caecum,carcinoma,0,1	HSPA1L	185	1	0			c.G1221A						PASS	.	C		940,3466	358.1+/-314.2	90,760,1353	75.0	71.0	72.0		1221	-10.4	0.0	6	dbSNP_96	72	675,7925	168.8+/-220.3	36,603,3661	yes	coding-synonymous	HSPA1L	NM_005527.3		126,1363,5014	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	7.8488,21.3345,12.4173		407/642	31778529	1615,11391	2203	4300	6503	SO:0001819	synonymous_variant	3305	exon2			CCCAGCCGTCTCC	D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"""Heat shock proteins / HSP70"""	5234	protein-coding gene	gene with protein product		140559	"""heat shock 70kD protein-like 1"""			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.1221G>A	6.37:g.31778529C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_005527	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Silent	SNP	ENST00000375654.4	37	CCDS34413.1																																																																																			C|0.854;T|0.146	0.146	strong		0.612	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2		
TCTE1	202500	hgsc.bcm.edu	37	6	44255387	44255387	+	Missense_Mutation	SNP	C	C	T	rs61742784	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:44255387C>T	ENST00000371505.4	-	2	298	c.176G>A	c.(175-177)cGt>cAt	p.R59H	TCTE1_ENST00000371503.3_5'UTR|RP11-444E17.6_ENST00000505802.1_Intron|TCTE1_ENST00000371504.1_5'Flank|TMEM151B_ENST00000438774.2_Intron	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	59										breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GCGCATCCGACGGATATTGGC	0.552													C|||	278	0.0555112	0.0	0.0403	5008	,	,		21979	0.1746		0.0527	False		,,,				2504	0.0215				p.R59H		Atlas-SNP	.											.	TCTE1	77	.	0			c.G176A						PASS	.	C	HIS/ARG	47,4359	48.9+/-83.8	0,47,2156	157.0	130.0	139.0		176	1.7	0.0	6	dbSNP_129	139	365,8235	122.4+/-181.4	10,345,3945	yes	missense	TCTE1	NM_182539.3	29	10,392,6101	TT,TC,CC		4.2442,1.0667,3.1678	benign	59/502	44255387	412,12594	2203	4300	6503	SO:0001583	missense	202500	exon2			ATCCGACGGATAT	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.176G>A	6.37:g.44255387C>T	ENSP00000360560:p.Arg59His	Somatic	410	1	0.00243902		WXS	Illumina HiSeq	Phase_I	480	262	0.545833	NM_182539	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	37	CCDS4910.1	145	0.06639194139194139	0	0.0	10	0.027624309392265192	99	0.17307692307692307	36	0.047493403693931395	C	10.90	1.481184	0.26598	0.010667	0.042442	ENSG00000146221	ENST00000371505	T	0.23552	1.9	5.5	1.74	0.24563	.	0.669254	0.15523	N	0.257922	T	0.07279	0.0184	L	0.35644	1.08	0.58432	P	1.999999999946489E-6	B	0.23185	0.081	B	0.17098	0.017	T	0.19614	-1.0300	9	0.40728	T	0.16	0.3944	8.3286	0.32173	0.1108:0.6718:0.0:0.2174	.	59	Q5JU00	TCTE1_HUMAN	H	59	ENSP00000360560:R59H	ENSP00000360560:R59H	R	-	2	0	TCTE1	44363365	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-0.388000	0.07352	-0.014000	0.14175	-0.624000	0.04008	CGT	C|0.961;T|0.039	0.039	strong		0.552	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33535060	33535060	+	Missense_Mutation	SNP	G	G	A	rs25754	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:33535060G>A	ENST00000504830.1	-	23	4819	c.4484C>T	c.(4483-4485)aCt>aTt	p.T1495I	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.T1410I	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1495	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.		T -> I (in dbSNP:rs25754). {ECO:0000269|PubMed:11279086}.		cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						ACATTGGACAGTCCTCTTCTG	0.478										HNSCC(64;0.19)			G|||	3003	0.599641	0.6498	0.4986	5008	,	,		17921	0.7688		0.3608	False		,,,				2504	0.6748				p.T1495I		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.C4484T						PASS	.	G	ILE/THR	2673,1733	647.8+/-398.6	811,1051,341	100.0	94.0	96.0		4484	4.1	1.0	5	dbSNP_76	96	3326,5274	495.8+/-374.1	660,2006,1634	yes	missense	ADAMTS12	NM_030955.2	89	1471,3057,1975	AA,AG,GG		38.6744,39.3327,46.1249	benign	1495/1595	33535060	5999,7007	2203	4300	6503	SO:0001583	missense	81792	exon23			TGGACAGTCCTCT	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.4484C>T	5.37:g.33535060G>A	ENSP00000422554:p.Thr1495Ile	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	1186	0.543040293040293	305	0.6199186991869918	177	0.4889502762430939	440	0.7692307692307693	264	0.3482849604221636	G	12.69	2.013407	0.35511	0.606673	0.386744	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.52754	0.65;0.65	4.98	4.1	0.47936	.	0.319926	0.32578	N	0.005912	T	0.00012	0.0000	M	0.76002	2.32	0.09310	P	0.999999999992923	B;B	0.25563	0.129;0.043	B;B	0.26202	0.067;0.043	T	0.42832	-0.9428	9	0.23302	T	0.38	.	8.6185	0.33847	0.1032:0.0:0.8968:0.0	rs25754;rs1697866;rs17566802;rs60616478;rs25754	1410;1495	P58397-3;P58397	.;ATS12_HUMAN	I	1495;1410	ENSP00000422554:T1495I;ENSP00000344847:T1410I	ENSP00000344847:T1410I	T	-	2	0	ADAMTS12	33570817	0.819000	0.29175	0.975000	0.42487	0.853000	0.48598	0.983000	0.29552	2.470000	0.83445	0.563000	0.77884	ACT	G|0.483;A|0.516	0.516	strong		0.478	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
MYH3	4621	hgsc.bcm.edu	37	17	10558267	10558267	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:10558267A>G	ENST00000583535.1	-	3	202	c.115T>C	c.(115-117)Ttc>Ctc	p.F39L	MYH3_ENST00000226209.7_Missense_Mutation_p.F39L	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	39					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TCCACCACGAAGCAATACGTC	0.498																																					p.F39L		Atlas-SNP	.											MYH3,colon,carcinoma,+2,1	MYH3	227	1	0			c.T115C						scavenged	.						233.0	217.0	222.0					17																	10558267		2203	4300	6503	SO:0001583	missense	4621	exon3			CCACGAAGCAATA		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.115T>C	17.37:g.10558267A>G	ENSP00000464317:p.Phe39Leu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	182	4	0.021978	NM_002470	Q15492	Missense_Mutation	SNP	ENST00000583535.1	37	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.022851	0.93462	.	.	ENSG00000109063	ENST00000226209	D	0.82081	-1.57	5.38	5.38	0.77491	Myosin, N-terminal, SH3-like (1);	.	.	.	.	D	0.90205	0.6938	M	0.77103	2.36	0.42626	D	0.993365	B	0.22146	0.065	P	0.48114	0.567	D	0.89920	0.4058	9	0.87932	D	0	.	15.5555	0.76189	1.0:0.0:0.0:0.0	.	39	P11055	MYH3_HUMAN	L	39	ENSP00000226209:F39L	ENSP00000226209:F39L	F	-	1	0	MYH3	10498992	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	8.991000	0.93514	2.255000	0.74692	0.533000	0.62120	TTC	.	.	none		0.498	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
POLR2D	5433	hgsc.bcm.edu	37	2	128608184	128608184	+	Silent	SNP	C	C	T	rs11556864	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:128608184C>T	ENST00000272645.4	-	3	386	c.330G>A	c.(328-330)gaG>gaA	p.E110E	POLR2D_ENST00000487079.1_Intron|POLR2D_ENST00000409955.1_Intron|POLR2D_ENST00000409698.1_Silent_p.E72E	NM_004805.3	NP_004796.1	O15514	RPB4_HUMAN	polymerase (RNA) II (DNA directed) polypeptide D	110					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus in response to heat stress (GO:0031990)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleotide-excision repair (GO:0006289)|positive regulation of translational initiation (GO:0045948)|positive regulation of viral transcription (GO:0050434)|recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (GO:0034402)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)|nucleotide binding (GO:0000166)|translation initiation factor binding (GO:0031369)			large_intestine(1)|lung(4)|urinary_tract(1)	6	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0675)		GAGCCTTGGACTCCTCAGCAG	0.388													C|||	532	0.10623	0.0484	0.0994	5008	,	,		16256	0.1399		0.1014	False		,,,				2504	0.1595				p.E110E		Atlas-SNP	.											.	POLR2D	13	.	0			c.G330A						PASS	.	C		253,4153	146.9+/-181.5	8,237,1958	78.0	86.0	83.0		330	3.4	1.0	2	dbSNP_120	83	789,7811	185.6+/-233.3	45,699,3556	no	coding-synonymous	POLR2D	NM_004805.3		53,936,5514	TT,TC,CC		9.1744,5.7422,8.0117		110/143	128608184	1042,11964	2203	4300	6503	SO:0001819	synonymous_variant	5433	exon3			CTTGGACTCCTCA	U85510	CCDS2151.1	2q21	2013-01-21			ENSG00000144231	ENSG00000144231		"""RNA polymerase subunits"""	9191	protein-coding gene	gene with protein product	"""RNA polymerase II subunit hsRBP4"""	606017				9528765	Standard	NM_004805		Approved	RBP4	uc002tpj.3	O15514	OTTHUMG00000131531	ENST00000272645.4:c.330G>A	2.37:g.128608184C>T		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	312	161	0.516026	NM_004805	Q52LT4	Silent	SNP	ENST00000272645.4	37	CCDS2151.1																																																																																			C|0.907;T|0.093	0.093	strong		0.388	POLR2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254388.3	NM_004805	
ZNF440	126070	hgsc.bcm.edu	37	19	11941221	11941221	+	Missense_Mutation	SNP	T	T	A	rs424132	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11941221T>A	ENST00000304060.5	+	2	291	c.127T>A	c.(127-129)Tta>Ata	p.L43I		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	43	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		L -> I (in dbSNP:rs424132).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CCTGACCTCTTTAGGTAAGGA	0.443													g|||	1609	0.321286	0.4758	0.3271	5008	,	,		19585	0.1597		0.3628	False		,,,				2504	0.2321				p.L43I		Atlas-SNP	.											.	ZNF440	56	.	0			c.T127A						PASS	.						103.0	112.0	109.0					19																	11941221		2203	4297	6500	SO:0001583	missense	126070	exon2			ACCTCTTTAGGTA	AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"""Zinc fingers, C2H2-type"", ""-"""	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.127T>A	19.37:g.11941221T>A	ENSP00000305373:p.Leu43Ile	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_152357	Q8N1R9	Missense_Mutation	SNP	ENST00000304060.5	37	CCDS42503.1	589	0.2696886446886447	168	0.34146341463414637	102	0.281767955801105	79	0.1381118881118881	240	0.316622691292876	a	0.001	-4.623390	0.00000	.	.	ENSG00000171295	ENST00000304060;ENST00000427505;ENST00000414255	T;T;T	0.02446	4.29;4.29;4.29	1.74	-3.49	0.04724	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	N	0.16166	0.38	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45804	-0.9236	8	0.02654	T	1	.	1.758	0.02986	0.3493:0.1726:0.3585:0.1196	rs424132	43	Q8IYI8	ZN440_HUMAN	I	43;46;45	ENSP00000305373:L43I;ENSP00000393489:L46I;ENSP00000411974:L45I	ENSP00000305373:L43I	L	+	1	2	ZNF440	11802221	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-2.264000	0.01173	-4.525000	0.00044	-5.145000	0.00001	TTA	T|0.703;A|0.297	0.297	strong		0.443	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357	
SEC22C	9117	hgsc.bcm.edu	37	3	42610515	42610515	+	Silent	SNP	G	G	A	rs2271187	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:42610515G>A	ENST00000264454.3	-	2	167	c.24C>T	c.(22-24)tgC>tgT	p.C8C	SEC22C_ENST00000493107.1_5'UTR|SEC22C_ENST00000273156.7_Silent_p.C8C|SEC22C_ENST00000536332.1_5'UTR|SEC22C_ENST00000417572.1_Silent_p.C8C|SEC22C_ENST00000423701.2_Silent_p.C8C			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	8	Longin. {ECO:0000255|PROSITE- ProRule:PRU00231}.				ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		CCCGTACCACGCAGGCAAAAA	0.498													G|||	1572	0.313898	0.3956	0.2118	5008	,	,		16034	0.4673		0.1789	False		,,,				2504	0.2566				p.C8C		Atlas-SNP	.											.	SEC22C	27	.	0			c.C24T						PASS	.	G	,,,	1490,2916	471.5+/-356.1	252,986,965	72.0	64.0	67.0		24,24,24,24	-2.3	1.0	3	dbSNP_100	67	1608,6992	297.3+/-303.3	157,1294,2849	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEC22C	NM_001201572.1,NM_001201584.1,NM_004206.3,NM_032970.3	,,,	409,2280,3814	AA,AG,GG		18.6977,33.8175,23.8198	,,,	8/251,8/229,8/251,8/304	42610515	3098,9908	2203	4300	6503	SO:0001819	synonymous_variant	9117	exon2			TACCACGCAGGCA	AF039568	CCDS2699.1, CCDS2700.1, CCDS56246.1	3p24.3-p22.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000093183	ENSG00000093183			16828	protein-coding gene	gene with protein product		604028	"""SEC22 vesicle trafficking protein-like 3 (S. cerevisiae)"""	SEC22L3		9501016, 11001058	Standard	NM_004206		Approved	MGC13261, MGC5373	uc003clj.3	Q9BRL7	OTTHUMG00000131797	ENST00000264454.3:c.24C>T	3.37:g.42610515G>A		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	189	189	1	NM_001201584	O95152|Q68CX3|Q6UW18	Silent	SNP	ENST00000264454.3	37	CCDS2700.1																																																																																			G|0.738;A|0.262	0.262	strong		0.498	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206	
AMPD2	271	hgsc.bcm.edu	37	1	110171333	110171333	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:110171333C>T	ENST00000256578.3	+	12	1998	c.1638C>T	c.(1636-1638)cgC>cgT	p.R546R	RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000358729.4_Silent_p.R471R|AMPD2_ENST00000526301.1_3'UTR|AMPD2_ENST00000528667.1_Silent_p.R546R|AMPD2_ENST00000342115.4_Silent_p.R465R|AMPD2_ENST00000393688.3_Silent_p.R427R|AMPD2_ENST00000528454.1_Silent_p.R428R	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2	546					cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		TTTACGGGCGCTCGAGGGATG	0.617																																					p.R546R		Atlas-SNP	.											AMPD2_ENST00000393689,colon,carcinoma,+2,2	AMPD2	75	2	0			c.C1638T						scavenged	.						38.0	34.0	35.0					1																	110171333		2203	4300	6503	SO:0001819	synonymous_variant	271	exon12			CGGGCGCTCGAGG	S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"""AMPD isoform L"""	102771	"""adenosine monophosphate deaminase 2 (isoform L)"""			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	ENST00000256578.3:c.1638C>T	1.37:g.110171333C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	154	3	0.0194805	NM_004037	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Silent	SNP	ENST00000256578.3	37	CCDS805.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.999020	0.54147	.	.	ENSG00000116337	ENST00000369840	.	.	.	5.08	4.16	0.48862	.	.	.	.	.	T	0.46014	0.1371	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46735	-0.9170	4	.	.	.	-29.4948	8.3688	0.32402	0.1548:0.7618:0.0:0.0834	.	.	.	.	F	517	.	.	L	+	1	0	AMPD2	109972856	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	0.755000	0.26405	1.353000	0.45828	0.655000	0.94253	CTC	.	.	none		0.617	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1		
ICT1	3396	hgsc.bcm.edu	37	17	73016621	73016621	+	Silent	SNP	C	C	T	rs1044228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73016621C>T	ENST00000301585.5	+	5	418	c.405C>T	c.(403-405)ctC>ctT	p.L135L		NM_001545.1	NP_001536.1	Q14197	ICT1_HUMAN	immature colon carcinoma transcript 1	135					mitochondrial translational termination (GO:0070126)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	aminoacyl-tRNA hydrolase activity (GO:0004045)|translation release factor activity, codon nonspecific (GO:0016150)			NS(1)|central_nervous_system(1)|lung(2)|ovary(1)|urinary_tract(1)	6	all_lung(278;0.226)					AGTTGATCCTCACCTCTGAGA	0.473													C|||	1602	0.319888	0.3306	0.4582	5008	,	,		18349	0.1875		0.3618	False		,,,				2504	0.3006				p.L135L		Atlas-SNP	.											.	ICT1	17	.	0			c.C405T						PASS	.	C		1446,2960	457.8+/-351.8	245,956,1002	56.0	58.0	57.0		405	-0.2	1.0	17	dbSNP_86	57	2716,5884	429.3+/-356.2	410,1896,1994	no	coding-synonymous	ICT1	NM_001545.1		655,2852,2996	TT,TC,CC		31.5814,32.8189,32.0006		135/207	73016621	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	3396	exon5			GATCCTCACCTCT	X81788	CCDS11711.1	17q25	2014-02-12				ENSG00000167862			5359	protein-coding gene	gene with protein product		603000				8575443, 20186120	Standard	NM_001545		Approved	DS-1	uc002jmm.3	Q14197		ENST00000301585.5:c.405C>T	17.37:g.73016621C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	135	77	0.57037	NM_001545	B2RAD1|Q53HM7|Q53Y11	Silent	SNP	ENST00000301585.5	37	CCDS11711.1																																																																																			C|0.689;T|0.311	0.311	strong		0.473	ICT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445314.1	NM_001545	
C19orf45	374877	hgsc.bcm.edu	37	19	7573297	7573297	+	Missense_Mutation	SNP	T	T	C	rs608144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7573297T>C	ENST00000361664.2	+	9	1640	c.1499T>C	c.(1498-1500)cTg>cCg	p.L500P	CTD-2207O23.12_ENST00000599312.1_Intron	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	500			L -> P (in dbSNP:rs608144). {ECO:0000269|PubMed:14702039}.							endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						CCTATGTACCTGTGCCCCAGC	0.602													C|||	1507	0.300919	0.3434	0.3847	5008	,	,		17703	0.1746		0.3618	False		,,,				2504	0.2515				p.L500P		Atlas-SNP	.											.	C19orf45	36	.	0			c.T1499C						PASS	.	C	PRO/LEU	1477,2927		254,969,979	26.0	25.0	25.0		1499	2.6	0.6	19	dbSNP_83	25	3056,5544		568,1920,1812	yes	missense	C19orf45	NM_198534.2	98	822,2889,2791	CC,CT,TT		35.5349,33.5377,34.8585	benign	500/506	7573297	4533,8471	2202	4300	6502	SO:0001583	missense	374877	exon9			TGTACCTGTGCCC	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.1499T>C	19.37:g.7573297T>C	ENSP00000355241:p.Leu500Pro	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	724	0.3315018315018315	180	0.36585365853658536	152	0.4198895027624309	112	0.1958041958041958	280	0.36939313984168864	C	0	-2.672641	0.00104	0.335377	0.355349	ENSG00000198723	ENST00000361664	T	0.08008	3.14	3.62	2.58	0.30949	.	0.119789	0.38005	N	0.001860	T	0.00012	0.0000	N	0.00182	-1.905	0.38619	P	0.04891800000000002	B	0.02656	0.0	B	0.01281	0.0	T	0.44236	-0.9341	9	0.02654	T	1	-5.81	4.7376	0.12995	0.2121:0.6759:0.0:0.112	rs608144;rs1133379;rs3178371;rs3195127;rs3745353	500	Q8NA69	CS045_HUMAN	P	500	ENSP00000355241:L500P	ENSP00000355241:L500P	L	+	2	0	C19orf45	7479297	0.161000	0.22892	0.620000	0.29132	0.008000	0.06430	0.574000	0.23714	0.543000	0.28864	-1.294000	0.01345	CTG	T|0.671;C|0.329	0.329	strong		0.602	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
UNC5C	8633	hgsc.bcm.edu	37	4	96256616	96256616	+	Silent	SNP	A	A	G	rs4699423	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:96256616A>G	ENST00000453304.1	-	2	639	c.291T>C	c.(289-291)agT>agC	p.S97S	UNC5C_ENST00000504962.1_Silent_p.S97S|UNC5C_ENST00000506749.1_Silent_p.S97S	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	97	Ig-like.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		GAACCCATTCACTATTACACT	0.408													A|||	2397	0.478634	0.1324	0.5418	5008	,	,		18797	0.8343		0.4573	False		,,,				2504	0.5573				p.S97S		Atlas-SNP	.											.	UNC5C	141	.	0			c.T291C						PASS	.	A		809,3597	322.6+/-297.7	86,637,1480	132.0	126.0	128.0		291	-0.2	1.0	4	dbSNP_111	128	3933,4665	547.2+/-385.1	896,2141,1262	no	coding-synonymous	UNC5C	NM_003728.3		982,2778,2742	GG,GA,AA		45.7432,18.3613,36.4657		97/932	96256616	4742,8262	2203	4299	6502	SO:0001819	synonymous_variant	8633	exon2			CCATTCACTATTA	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.291T>C	4.37:g.96256616A>G		Somatic	287	1	0.00348432		WXS	Illumina HiSeq	Phase_I	298	147	0.493289	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			A|0.582;G|0.418	0.418	strong		0.408	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
LBR	3930	hgsc.bcm.edu	37	1	225600169	225600169	+	Silent	SNP	C	C	T	rs112582692	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225600169C>T	ENST00000338179.2	-	8	1196	c.1071G>A	c.(1069-1071)tcG>tcA	p.S357S	LBR_ENST00000272163.4_Silent_p.S357S|AC092811.1_ENST00000366845.2_5'Flank	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	357					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		AGCTGGCAGGCGACAGGTCAT	0.483													C|||	148	0.0295527	0.0136	0.0259	5008	,	,		15015	0.0208		0.0417	False		,,,				2504	0.0501				p.S357S		Atlas-SNP	.											.	LBR	54	.	0			c.G1071A						PASS	.	C	,	71,4335	63.5+/-100.7	0,71,2132	67.0	68.0	68.0		1071,1071	-12.1	0.0	1	dbSNP_132	68	430,8170	132.6+/-190.3	7,416,3877	no	coding-synonymous,coding-synonymous	LBR	NM_002296.3,NM_194442.2	,	7,487,6009	TT,TC,CC		5.0,1.6114,3.8521	,	357/616,357/616	225600169	501,12505	2203	4300	6503	SO:0001819	synonymous_variant	3930	exon8			GGCAGGCGACAGG	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"""Tudor domain containing"""	6518	protein-coding gene	gene with protein product	"""tudor domain containing 18"""	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.1071G>A	1.37:g.225600169C>T		Somatic	376	0	0		WXS	Illumina HiSeq	Phase_I	437	209	0.478261	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Silent	SNP	ENST00000338179.2	37	CCDS1545.1																																																																																			C|0.965;T|0.035	0.035	strong		0.483	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296	
PPFIBP1	8496	hgsc.bcm.edu	37	12	27788021	27788021	+	Silent	SNP	G	G	A	rs2075378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:27788021G>A	ENST00000318304.8	+	4	526	c.243G>A	c.(241-243)acG>acA	p.T81T	PPFIBP1_ENST00000545334.1_Silent_p.T81T|PPFIBP1_ENST00000228425.6_Silent_p.T81T|PPFIBP1_ENST00000542629.1_Silent_p.T81T|PPFIBP1_ENST00000537927.1_Intron|PPFIBP1_ENST00000535047.1_Silent_p.T81T	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	81					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					CAGCAGAAACGCTTGTTGAAT	0.418													G|||	1745	0.348442	0.2572	0.2997	5008	,	,		18892	0.4008		0.3757	False		,,,				2504	0.4243				p.T81T		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.G243A						PASS	.	G	,,,	1215,3191	425.1+/-340.7	170,875,1158	82.0	87.0	86.0		,243,243,243	-8.6	0.0	12	dbSNP_96	86	3018,5582	466.2+/-366.7	552,1914,1834	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	PPFIBP1	NM_001198915.1,NM_001198916.1,NM_003622.3,NM_177444.2	,,,	722,2789,2992	AA,AG,GG		35.093,27.576,32.5465	,,,	,81/981,81/1006,81/1012	27788021	4233,8773	2203	4300	6503	SO:0001819	synonymous_variant	8496	exon4			AGAAACGCTTGTT	AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.243G>A	12.37:g.27788021G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_003622	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	37	CCDS55812.1																																																																																			G|0.671;A|0.329	0.329	strong		0.418	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
CASS4	57091	hgsc.bcm.edu	37	20	55033713	55033713	+	Silent	SNP	G	G	A	rs3746626	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:55033713G>A	ENST00000360314.3	+	7	2496	c.2271G>A	c.(2269-2271)acG>acA	p.T757T	CASS4_ENST00000371336.3_Silent_p.T757T|AL121914.1_ENST00000390795.2_RNA|CASS4_ENST00000434344.1_Silent_p.T320T	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	757					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						CCGTGCTCACGTACCCCAGCC	0.642													G|||	2632	0.525559	0.413	0.5245	5008	,	,		20324	0.9196		0.34	False		,,,				2504	0.4632				p.T757T		Atlas-SNP	.											.	CASS4	121	.	0			c.G2271A						PASS	.	G	,,,	1768,2636	516.2+/-369.1	370,1028,804	50.0	41.0	44.0		2109,960,2271,2271	-0.1	0.0	20	dbSNP_107	44	2916,5682	448.5+/-361.8	468,1980,1851	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	,,,	838,3008,2655	AA,AG,GG		33.9149,40.1453,36.0252	,,,	703/733,320/350,757/787,757/787	55033713	4684,8318	2202	4299	6501	SO:0001819	synonymous_variant	57091	exon6			GCTCACGTACCCC	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.2271G>A	20.37:g.55033713G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Silent	SNP	ENST00000360314.3	37	CCDS33492.1																																																																																			G|0.575;A|0.425	0.425	strong		0.642	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
DBNDD1	79007	hgsc.bcm.edu	37	16	90075226	90075226	+	Silent	SNP	C	C	T	rs4362387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90075226C>T	ENST00000002501.6	-	3	416	c.285G>A	c.(283-285)tcG>tcA	p.S95S	DBNDD1_ENST00000392973.3_Silent_p.S101S|DBNDD1_ENST00000568838.1_Silent_p.S215S|DBNDD1_ENST00000304733.3_Silent_p.S115S	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	95						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		TCTCGTCGTCCGAGTCAGCAA	0.642													C|||	285	0.0569089	0.0053	0.0706	5008	,	,		20383	0.1587		0.0457	False		,,,				2504	0.0235				p.S115S		Atlas-SNP	.											.	DBNDD1	9	.	0			c.G345A						PASS	.	C	,	47,4035		0,47,1994	40.0	44.0	43.0		285,345	-10.5	0.0	16	dbSNP_111	43	495,7867		14,467,3700	no	coding-synonymous,coding-synonymous	DBNDD1	NM_001042610.1,NM_024043.2	,	14,514,5694	TT,TC,CC		5.9196,1.1514,4.3555	,	95/159,115/179	90075226	542,11902	2041	4181	6222	SO:0001819	synonymous_variant	79007	exon3			GTCGTCCGAGTCA	AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249			28455	protein-coding gene	gene with protein product						12477932	Standard	NM_001288708		Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000002501.6:c.285G>A	16.37:g.90075226C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_024043	B4DQS3|Q69YT2|Q9BW25	Silent	SNP	ENST00000002501.6	37	CCDS42223.1																																																																																			C|0.947;T|0.053	0.053	strong		0.642	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043	
MT-CYB	4519	hgsc.bcm.edu	37	M	14996	14996	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:14996G>A	ENST00000361789.2	+	1	250	c.250G>A	c.(250-252)Gcc>Acc	p.A84T	MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	84					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						GCTACCTTCACGCCAATGGCG	0.483																																					p.A84T		Atlas-SNP	.											.	.	.	.	0			c.G250A						PASS	.																																			SO:0001583	missense	0	exon1			CTTCACGCCAATG			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.250G>A	M.37:g.14996G>A	ENSP00000354554:p.Ala84Thr	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	28	27	0.964286	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.483	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
RHBDF1	64285	hgsc.bcm.edu	37	16	111247	111247	+	Silent	SNP	C	C	T	rs79691782	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:111247C>T	ENST00000262316.6	-	11	1570	c.1428G>A	c.(1426-1428)tcG>tcA	p.S476S	RHBDF1_ENST00000454039.2_Missense_Mutation_p.A511T	NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	476					cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				GCATGCAGGGCGAAAACTTGG	0.726													C|||	120	0.0239617	0.003	0.0331	5008	,	,		9744	0.0		0.0795	False		,,,				2504	0.0133				p.S476S		Atlas-SNP	.											.	RHBDF1	54	.	0			c.G1428A						PASS	.	C		39,3521		0,39,1741	8.0	9.0	9.0		1428	-8.2	1.0	16	dbSNP_131	9	474,6312		14,446,2933	no	coding-synonymous	RHBDF1	NM_022450.3		14,485,4674	TT,TC,CC		6.985,1.0955,4.9584		476/856	111247	513,9833	1780	3393	5173	SO:0001819	synonymous_variant	64285	exon11			GCAGGGCGAAAAC	BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"""chromosome 16 open reading frame 8"", ""rhomboid family 1 (Drosophila)"""	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.1428G>A	16.37:g.111247C>T		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	10	5	0.5	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Silent	SNP	ENST00000262316.6	37	CCDS32344.1	83	0.038003663003663	0	0.0	17	0.04696132596685083	0	0.0	66	0.0870712401055409	.	12.21	1.869066	0.32977	0.010955	0.06985	ENSG00000007384	ENST00000454039	T	0.68025	-0.3	4.72	-8.24	0.01029	.	.	.	.	.	T	0.02649	0.0080	.	.	.	0.23449	N	0.997655	B;B	0.10296	0.003;0.003	B;B	0.06405	0.002;0.001	T	0.38156	-0.9674	8	0.87932	D	0	-13.4212	8.9468	0.35764	0.0:0.1375:0.4469:0.4157	.	511;534	F5GWL4;B4E3Q0	.;.	T	511	ENSP00000392133:A511T	ENSP00000392133:A511T	A	-	1	0	RHBDF1	51247	0.000000	0.05858	0.985000	0.45067	0.558000	0.35554	-2.765000	0.00783	-0.780000	0.04553	0.205000	0.17691	GCC	C|0.961;T|0.039	0.039	strong		0.726	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450	
DNAH5	1767	hgsc.bcm.edu	37	5	13701525	13701525	+	Silent	SNP	T	T	C	rs3734111	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13701525T>C	ENST00000265104.4	-	77	13463	c.13359A>G	c.(13357-13359)acA>acG	p.T4453T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4453					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGAAACCCAGTGTACTAGAAA	0.368									Kartagener syndrome				T|||	2242	0.447684	0.3449	0.4928	5008	,	,		16114	0.4435		0.5398	False		,,,				2504	0.4642				p.T4453T		Atlas-SNP	.											.	DNAH5	868	.	0			c.A13359G						PASS	.	T		1615,2791	484.4+/-360.0	330,955,918	68.0	76.0	73.0		13359	-11.6	0.0	5	dbSNP_107	73	4706,3894	602.6+/-394.5	1263,2180,857	no	coding-synonymous	DNAH5	NM_001369.2		1593,3135,1775	CC,CT,TT		45.2791,36.6546,48.6006		4453/4625	13701525	6321,6685	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon77	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ACCCAGTGTACTA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.13359A>G	5.37:g.13701525T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.537;C|0.463	0.463	strong		0.368	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
SNAPC3	6619	hgsc.bcm.edu	37	9	15453156	15453156	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:15453156C>T	ENST00000380821.3	+	7	1109	c.933C>T	c.(931-933)taC>taT	p.Y311Y	SNAPC3_ENST00000380799.1_Silent_p.Y108Y	NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	311					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		CTTACTTATACTGTCATCAGG	0.368																																					p.Y311Y		Atlas-SNP	.											.	SNAPC3	28	.	0			c.C933T						PASS	.						180.0	175.0	177.0					9																	15453156		2203	4300	6503	SO:0001819	synonymous_variant	6619	exon7			CTTATACTGTCAT	U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"""small nuclear RNA activating complex, polypeptide 3, 50kD"""			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.933C>T	9.37:g.15453156C>T		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	215	91	0.423256	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Silent	SNP	ENST00000380821.3	37	CCDS6478.1																																																																																			.	.	none		0.368	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
PCDHGA10	56106	hgsc.bcm.edu	37	5	140794750	140794750	+	Missense_Mutation	SNP	G	G	A	rs201831693		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140794750G>A	ENST00000398610.2	+	1	2008	c.2008G>A	c.(2008-2010)Gac>Aac	p.D670N	PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB7_ENST00000398594.2_5'Flank|PCDHGB3_ENST00000576222.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA9_ENST00000573521.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	670	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCCGTGGCCGACAGCATCCC	0.652													g|||	1	0.000199681	0.0	0.0014	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.D670N		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.G2008A						PASS	.	G	,,ASN/ASP,,,,,,,,,,,,,,ASN/ASP	0,4400		0,0,2200	48.0	58.0	54.0		,,2008,,,,,,,,,,,,,,2008	5.6	1.0	5		54	5,8583		0,5,4289	no	intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032090.1	,,23,,,,,,,,,,,,,,23	0,5,6489	AA,AG,GG		0.0582,0.0,0.0385	,,,,,,,,,,,,,,,,	,,670/937,,,,,,,,,,,,,,670/851	140794750	5,12983	2200	4294	6494	SO:0001583	missense	56106	exon1			GTGGCCGACAGCA		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"""Cadherins / Protocadherins : Clustered"""	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.2008G>A	5.37:g.140794750G>A	ENSP00000381611:p.Asp670Asn	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	140	69	0.492857	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	37	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	g	12.26	1.885612	0.33255	0.0	5.82E-4	ENSG00000253846	ENST00000398610	D	0.84298	-1.83	5.57	5.57	0.84162	Cadherin (3);Cadherin-like (1);	.	.	.	.	D	0.87916	0.6298	M	0.82630	2.6	0.32335	N	0.560538	P;P	0.39717	0.684;0.557	B;B	0.39119	0.291;0.152	D	0.90719	0.4633	9	0.51188	T	0.08	.	19.1633	0.93543	0.0:0.0:1.0:0.0	.	670;670	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	N	670	ENSP00000381611:D670N	ENSP00000381611:D670N	D	+	1	0	PCDHGA10	140774934	1.000000	0.71417	0.972000	0.41901	0.015000	0.08874	7.703000	0.84585	2.621000	0.88768	0.655000	0.94253	GAC	G|0.999;A|0.001	0.001	weak		0.652	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913	
SUCO	51430	hgsc.bcm.edu	37	1	172579244	172579244	+	Nonsense_Mutation	SNP	C	C	T	rs151013343		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:172579244C>T	ENST00000263688.3	+	24	3829	c.3610C>T	c.(3610-3612)Cga>Tga	p.R1204*	SUCO_ENST00000367723.4_Nonsense_Mutation_p.R1355*|SUCO_ENST00000608151.1_Nonsense_Mutation_p.R1356*|SUCO_ENST00000610051.1_Nonsense_Mutation_p.R833*	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	1204					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											GGCTTTAAAACGAAGACGATC	0.398																																					p.R1204X		Atlas-SNP	.											C1orf9_ENST00000367723,caecum,carcinoma,-1,2	.	.	2	0			c.C3610T						scavenged	.	C	stop/ARG,stop/ARG	0,4406		0,0,2203	61.0	61.0	61.0		3610,3478	4.6	1.0	1	dbSNP_134	61	3,8597	3.0+/-9.4	0,3,4297	yes	stop-gained,stop-gained	C1orf9	NM_014283.3,NM_016227.2	,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,	1204/1255,1160/1211	172579244	3,13003	2203	4300	6503	SO:0001587	stop_gained	51430	exon24			TTAAAACGAAGAC	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.3610C>T	1.37:g.172579244C>T	ENSP00000263688:p.Arg1204*	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	148	2	0.0135135	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Nonsense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	C	41	8.959379	0.99018	0.0	3.49E-4	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.56	4.64	0.57946	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.4768	13.5945	0.61982	0.0:0.9228:0.0:0.0772	.	.	.	.	X	1356;1204	.	ENSP00000263688:R1204X	R	+	1	2	C1orf9	170845867	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.432000	0.44784	2.617000	0.88574	0.650000	0.86243	CGA	C|1.000;T|0.000	0.000	weak		0.398	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227	
FMN2	56776	hgsc.bcm.edu	37	1	240371112	240371112	+	Silent	SNP	G	G	T	rs71646889	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:240371112G>T	ENST00000319653.9	+	5	3230	c.3000G>T	c.(2998-3000)ccG>ccT	p.P1000P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1000	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1143P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACCCCCTCCGCCCCCACTTC	0.716													G|||	1341	0.267772	0.357	0.1873	5008	,	,		4654	0.2927		0.2008	False		,,,				2504	0.2474				p.P1000P		Atlas-SNP	.											FMN2,NS,carcinoma,0,4	FMN2	451	4	1	Substitution - coding silent(1)	prostate(1)	c.G3000T						PASS	.						4.0	6.0	6.0					1																	240371112		1774	3850	5624	SO:0001819	synonymous_variant	56776	exon5			CCCTCCGCCCCCA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3000G>T	1.37:g.240371112G>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	79	20	0.253165	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			A|0.000;G|0.879;T|0.121	0.121	strong		0.716	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
RNF112	7732	hgsc.bcm.edu	37	17	19319374	19319374	+	Silent	SNP	T	T	C	rs76138388	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:19319374T>C	ENST00000461366.1	+	14	1997	c.1782T>C	c.(1780-1782)gcT>gcC	p.A594A	CTB-187M2.2_ENST00000579897.1_RNA|AC004448.2_ENST00000437646.1_lincRNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	594						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	12						CAGGGGCCGCTGTGGTTGGGG	0.687													.|||	1150	0.229633	0.4228	0.085	5008	,	,		10555	0.2847		0.008	False		,,,				2504	0.2423				p.A594A		Atlas-SNP	.											RNF112,NS,haematopoietic_neoplasm,0,1	RNF112	37	1	0			c.T1782C						PASS	.	C		811,2571		72,667,952	3.0	4.0	4.0		1782	-7.5	0.0	17	dbSNP_132	4	89,7169		1,87,3541	no	coding-synonymous	RNF112	NM_007148.4		73,754,4493	CC,CT,TT		1.2262,23.9799,8.4586		594/632	19319374	900,9740	1691	3629	5320	SO:0001819	synonymous_variant	7732	exon14			GGCCGCTGTGGTT	AF054587	CCDS58529.1	17p11.2	2013-01-16	2008-06-13	2008-06-13	ENSG00000128482	ENSG00000128482		"""RING-type (C3HC4) zinc fingers"""	12968	protein-coding gene	gene with protein product		601237	"""zinc finger protein 179"""	ZNF179		8660987, 9806830	Standard	NM_007148		Approved	BFP	uc010vyw.2	Q9ULX5	OTTHUMG00000059601	ENST00000461366.1:c.1782T>C	17.37:g.19319374T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_007148	O60633|Q7Z5V9	Silent	SNP	ENST00000461366.1	37	CCDS58529.1																																																																																			T|0.829;C|0.171	0.171	strong		0.687	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148	
C1orf105	92346	hgsc.bcm.edu	37	1	172431333	172431333	+	Missense_Mutation	SNP	A	A	G	rs16844498	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:172431333A>G	ENST00000367727.4	+	5	487	c.289A>G	c.(289-291)Atg>Gtg	p.M97V	C1orf105_ENST00000367726.1_3'UTR|C1orf105_ENST00000367725.4_Missense_Mutation_p.M87V	NM_139240.3	NP_640333.3	O95561	CA105_HUMAN	chromosome 1 open reading frame 105	97			M -> V (in dbSNP:rs16844498).							large_intestine(1)|lung(12)|prostate(1)|skin(1)	15						ACCAAGAACAATGAAAATCCC	0.318													A|||	220	0.0439297	0.0272	0.049	5008	,	,		20279	0.0		0.0875	False		,,,				2504	0.0634				p.M97V		Atlas-SNP	.											.	C1orf105	24	.	0			c.A289G						PASS	.	A	VAL/MET	137,4269	98.5+/-137.1	2,133,2068	97.0	91.0	93.0		289	-8.5	0.0	1	dbSNP_123	93	515,8085	145.4+/-201.1	19,477,3804	yes	missense	C1orf105	NM_139240.3	21	21,610,5872	GG,GA,AA		5.9884,3.1094,5.0131	benign	97/184	172431333	652,12354	2203	4300	6503	SO:0001583	missense	92346	exon5			AGAACAATGAAAA	AL035295	CCDS1301.1, CCDS72983.1	1q24.3	2012-06-26			ENSG00000180999	ENSG00000180999			29591	protein-coding gene	gene with protein product						12477932	Standard	NM_139240		Approved		uc001gik.3	O95561	OTTHUMG00000034750	ENST00000367727.4:c.289A>G	1.37:g.172431333A>G	ENSP00000356700:p.Met97Val	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	265	119	0.449057	NM_139240	Q8IY02	Missense_Mutation	SNP	ENST00000367727.4	37	CCDS1301.1	102	0.046703296703296704	14	0.028455284552845527	17	0.04696132596685083	0	0.0	71	0.09366754617414248	A	0.006	-2.077666	0.00375	0.031094	0.059884	ENSG00000180999	ENST00000367727;ENST00000488100;ENST00000367725	T;T;T	0.33438	1.41;1.41;1.41	4.26	-8.53	0.00916	.	1.919010	0.02269	N	0.068313	T	0.03390	0.0098	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06162	-1.0842	10	0.33141	T	0.24	0.3528	0.2515	0.00206	0.3358:0.2407:0.1748:0.2487	rs16844498;rs52830958;rs16844498	97	O95561	CA105_HUMAN	V	97;68;87	ENSP00000356700:M97V;ENSP00000431442:M68V;ENSP00000356698:M87V	ENSP00000356698:M87V	M	+	1	0	C1orf105	170697956	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.598000	0.00419	-4.449000	0.00048	-1.937000	0.00501	ATG	A|0.949;G|0.051	0.051	strong		0.318	C1orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084062.2	NM_139240	
AFAP1L1	134265	hgsc.bcm.edu	37	5	148687152	148687152	+	Silent	SNP	G	G	A	rs17854053	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:148687152G>A	ENST00000296721.4	+	7	821	c.723G>A	c.(721-723)acG>acA	p.T241T	AFAP1L1_ENST00000515000.1_Silent_p.T241T|AFAP1L1_ENST00000522492.1_3'UTR	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	241	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCAGCTGACGGTCATCAGGG	0.592													G|||	148	0.0295527	0.0522	0.0346	5008	,	,		18254	0.002		0.0447	False		,,,				2504	0.0082				p.T241T		Atlas-SNP	.											.	AFAP1L1	86	.	0			c.G723A						PASS	.	G	,	243,4163	143.8+/-178.8	4,235,1964	57.0	46.0	49.0		723,723	-9.8	0.0	5	dbSNP_123	49	412,8188	128.2+/-186.4	8,396,3896	no	coding-synonymous,coding-synonymous	AFAP1L1	NM_001146337.1,NM_152406.2	,	12,631,5860	AA,AG,GG		4.7907,5.5152,5.0361	,	241/726,241/769	148687152	655,12351	2203	4300	6503	SO:0001819	synonymous_variant	134265	exon7			GCTGACGGTCATC	AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"""Pleckstrin homology (PH) domain containing"""	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.723G>A	5.37:g.148687152G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_001146337	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Silent	SNP	ENST00000296721.4	37	CCDS34274.1																																																																																			G|0.954;A|0.046	0.046	strong		0.592	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406	
MAGEB18	286514	hgsc.bcm.edu	37	X	26157792	26157792	+	Silent	SNP	C	C	T	rs5944318	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:26157792C>T	ENST00000325250.1	+	2	877	c.690C>T	c.(688-690)gcC>gcT	p.A230A		NM_173699.3	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	230	Interaction with LNX1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(17)|skin(2)|stomach(1)|urinary_tract(2)	33						GTGTATATGCCGATAGGAAGC	0.498													T|||	2795	0.740397	0.6339	0.5519	3775	,	,		15061	0.6935		0.3151	False		,,,				2504	0.5706				p.A230A		Atlas-SNP	.											.	MAGEB18	67	.	0			c.C690T						PASS	.	T		3040,793		1012,548,468,71,103	47.0	41.0	43.0		690	-0.7	0.1	X	dbSNP_114	43	2837,3891		443,1165,786,820,1086	no	coding-synonymous	MAGEB18	NM_173699.3		1455,1713,1254,891,1189	TT,TC,T,CC,C		42.1671,20.6888,44.3519		230/344	26157792	5877,4684	2202	4300	6502	SO:0001819	synonymous_variant	286514	exon2			ATATGCCGATAGG	AK057361	CCDS14216.1	Xp21.3	2008-02-05			ENSG00000176774	ENSG00000176774			28515	protein-coding gene	gene with protein product							Standard	NM_173699		Approved	MGC33889	uc004dbq.2	Q96M61	OTTHUMG00000021282	ENST00000325250.1:c.690C>T	X.37:g.26157792C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	103	101	0.980583	NM_173699		Silent	SNP	ENST00000325250.1	37	CCDS14216.1																																																																																			C|0.368;T|0.632	0.632	strong		0.498	MAGEB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056120.1	NM_173699	
ASPA	443	hgsc.bcm.edu	37	17	3397702	3397702	+	Silent	SNP	C	C	T	rs12948217	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:3397702C>T	ENST00000263080.2	+	5	851	c.693C>T	c.(691-693)taC>taT	p.Y231Y	ASPA_ENST00000456349.2_Silent_p.Y231Y|SPATA22_ENST00000541913.1_Intron	NM_000049.2	NP_000040.1	P45381	ACY2_HUMAN	aspartoacylase	231			Y -> C (in CAND). {ECO:0000269|PubMed:10564886}.		aspartate catabolic process (GO:0006533)|central nervous system myelination (GO:0022010)|positive regulation of oligodendrocyte differentiation (GO:0048714)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminoacylase activity (GO:0004046)|aspartoacylase activity (GO:0019807)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(6)|lung(5)|stomach(1)|urinary_tract(1)	17					L-Aspartic Acid(DB00128)	AAGTTGATTACCCCCGGGATG	0.343													t|||	1020	0.203674	0.2345	0.1844	5008	,	,		20080	0.0496		0.3101	False		,,,				2504	0.2249				p.Y231Y		Atlas-SNP	.											.	ASPA	37	.	0			c.C693T	GRCh37	CM940123	ASPA	M	rs12948217	PASS	.	T	,	1075,3331	722.2+/-409.3	127,821,1255	179.0	200.0	192.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	693,693	3.5	1.0	17	dbSNP_121	192	2687,5913	683.3+/-403.9	446,1795,2059	no	coding-synonymous,coding-synonymous	ASPA	NM_000049.2,NM_001128085.1	,	573,2616,3314	TT,TC,CC		31.2442,24.3985,28.9251	,	231/314,231/314	3397702	3762,9244	2203	4300	6503	SO:0001819	synonymous_variant	443	exon5			TGATTACCCCCGG	S67156	CCDS11028.1	17p13.3	2010-06-24	2010-06-24		ENSG00000108381	ENSG00000108381	3.5.1.15		756	protein-coding gene	gene with protein product	"""aminoacylase 2"", ""Canavan disease"""	608034	"""aspartoacylase (aminoacylase 2, Canavan disease)"""			8252036	Standard	NM_001128085		Approved	ASP, ACY2	uc002fvq.3	P45381	OTTHUMG00000090655	ENST00000263080.2:c.693C>T	17.37:g.3397702C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_000049		Silent	SNP	ENST00000263080.2	37	CCDS11028.1																																																																																			C|0.732;T|0.268	0.268	strong		0.343	ASPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207315.1	NM_000049	
ZNF804B	219578	hgsc.bcm.edu	37	7	88964510	88964510	+	Silent	SNP	T	T	C	rs62469518	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:88964510T>C	ENST00000333190.4	+	4	2823	c.2214T>C	c.(2212-2214)aaT>aaC	p.N738N		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	738							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GCAGAGGTAATTTGCTCTGCT	0.393										HNSCC(36;0.09)			T|||	171	0.0341454	0.0113	0.0605	5008	,	,		20637	0.0		0.0785	False		,,,				2504	0.0358				p.N738N		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T2214C						PASS	.	T		90,4316	73.1+/-111.1	1,88,2114	93.0	88.0	90.0		2214	-1.9	0.0	7	dbSNP_129	90	730,7870	177.5+/-227.1	30,670,3600	no	coding-synonymous	ZNF804B	NM_181646.2		31,758,5714	CC,CT,TT		8.4884,2.0427,6.3048		738/1350	88964510	820,12186	2203	4300	6503	SO:0001819	synonymous_variant	219578	exon4			AGGTAATTTGCTC	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2214T>C	7.37:g.88964510T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	37	CCDS5613.1																																																																																			T|0.939;C|0.061	0.061	strong		0.393	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
MGAM	8972	hgsc.bcm.edu	37	7	141759676	141759676	+	Silent	SNP	T	T	C	rs62477620	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:141759676T>C	ENST00000549489.2	+	33	4064	c.3969T>C	c.(3967-3969)aaT>aaC	p.N1323N	MGAM_ENST00000475668.2_Silent_p.N1323N	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1323	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTTCTGGCAATGAGACACAGC	0.463													t|||	931	0.185903	0.1415	0.2378	5008	,	,		22942	0.1736		0.1938	False		,,,				2504	0.2137				p.N1323N		Atlas-SNP	.											.	MGAM	767	.	0			c.T3969C						PASS	.	T		558,3302		52,454,1424	48.0	41.0	43.0		3969	3.0	1.0	7	dbSNP_129	43	1529,6745		163,1203,2771	no	coding-synonymous	MGAM	NM_004668.2		215,1657,4195	CC,CT,TT		18.4796,14.456,17.1996		1323/1858	141759676	2087,10047	1930	4137	6067	SO:0001819	synonymous_variant	8972	exon33			TGGCAATGAGACA	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.3969T>C	7.37:g.141759676T>C		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	267	261	0.977528	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			T|0.812;C|0.188	0.188	strong		0.463	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
APPL1	26060	hgsc.bcm.edu	37	3	57269608	57269608	+	Silent	SNP	A	A	G	rs11544592	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:57269608A>G	ENST00000288266.3	+	2	216	c.69A>G	c.(67-69)ctA>ctG	p.L23L		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	23	Required for RAB5A binding.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)			breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		GGTCTTTACTAGGTGTATTTG	0.318													A|||	28	0.00559105	0.0	0.0086	5008	,	,		19244	0.0		0.0179	False		,,,				2504	0.0041				p.L23L		Atlas-SNP	.											.	APPL1	59	.	0			c.A69G						PASS	.	A		12,4394	17.9+/-39.9	0,12,2191	112.0	108.0	110.0		69	2.1	1.0	3	dbSNP_123	110	139,8461	69.0+/-131.5	2,135,4163	no	coding-synonymous	APPL1	NM_012096.2		2,147,6354	GG,GA,AA		1.6163,0.2724,1.161		23/710	57269608	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	26060	exon2			TTTACTAGGTGTA	AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"""Pleckstrin homology (PH) domain containing"""	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.69A>G	3.37:g.57269608A>G		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	243	136	0.559671	NM_012096	Q9P2B9	Silent	SNP	ENST00000288266.3	37	CCDS2882.1																																																																																			A|0.987;G|0.013	0.013	strong		0.318	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096	
CARKD	55739	hgsc.bcm.edu	37	13	111290630	111290630	+	Missense_Mutation	SNP	T	T	C	rs41275126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:111290630T>C	ENST00000309957.2	+	10	949	c.935T>C	c.(934-936)aTt>aCt	p.I312T	CARKD_ENST00000458711.2_Intron|CARKD_ENST00000424185.2_Intron|CARKD_ENST00000470164.2_Intron	NM_001242881.1|NM_018210.3	NP_001229810.1|NP_060680.2			carbohydrate kinase domain containing											NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	15						GGTCCTGAGATTGAAACAGGA	0.562													T|||	428	0.0854633	0.059	0.0778	5008	,	,		18537	0.0873		0.165	False		,,,				2504	0.0429				p.I312T		Atlas-SNP	.											.	CARKD	36	.	0			c.T935C						PASS	.	T	,,,THR/ILE	303,4103	163.3+/-195.1	9,285,1909	108.0	126.0	120.0		,,,935	-4.8	0.0	13	dbSNP_127	120	1145,7455	235.3+/-267.9	75,995,3230	no	intron,intron,intron,missense	CARKD	NM_001242881.1,NM_001242882.1,NM_001242883.1,NM_018210.3	,,,89	84,1280,5139	CC,CT,TT		13.314,6.877,11.1333	,,,benign	,,,312/391	111290630	1448,11558	2203	4300	6503	SO:0001583	missense	55739	exon10			CTGAGATTGAAAC	AF151071	CCDS9513.1, CCDS55903.1	13q34	2008-12-19			ENSG00000213995	ENSG00000213995			25576	protein-coding gene	gene with protein product		615910					Standard	NM_018210		Approved	LP3298, FLJ10769	uc001vrc.3	Q8IW45	OTTHUMG00000017345	ENST00000309957.2:c.935T>C	13.37:g.111290630T>C	ENSP00000311984:p.Ile312Thr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	165	68	0.412121	NM_018210		Missense_Mutation	SNP	ENST00000309957.2	37	CCDS9513.1	228	0.1043956043956044	33	0.06707317073170732	27	0.07458563535911603	45	0.07867132867132867	123	0.16226912928759896	T	4.874	0.162543	0.09287	0.06877	0.13314	ENSG00000213995	ENST00000309957	T	0.24538	1.85	2.39	-4.78	0.03209	.	2.105020	0.05192	U	0.503275	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.27732	0.187	B	0.22386	0.039	T	0.22941	-1.0202	8	0.20519	T	0.43	.	5.4941	0.16793	0.0:0.2431:0.5091:0.2478	rs41275126;rs61970490	312	Q8IW45-2	.	T	312	ENSP00000311984:I312T	ENSP00000311984:I312T	I	+	2	0	CARKD	110088631	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.852000	0.04308	-1.456000	0.01921	-0.488000	0.04728	ATT	T|0.892;C|0.108	0.108	strong		0.562	CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210	
AMZ2	51321	hgsc.bcm.edu	37	17	66253095	66253095	+	Silent	SNP	T	T	A	rs7105	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:66253095T>A	ENST00000359904.3	+	7	2200	c.1068T>A	c.(1066-1068)gcT>gcA	p.A356A	ARSG_ENST00000448504.2_5'Flank|AMZ2_ENST00000392720.2_Silent_p.A356A|AMZ2_ENST00000577273.1_3'UTR|AMZ2_ENST00000577866.1_Silent_p.A356A|AMZ2_ENST00000577985.1_Silent_p.A356A|AMZ2_ENST00000580753.1_Silent_p.A356A|AMZ2_ENST00000359783.4_Silent_p.A298A	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	356							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			AATGCCTGGCTGTTCTCCAAA	0.393													.|||	1856	0.370607	0.3048	0.3588	5008	,	,		20327	0.4762		0.3131	False		,,,				2504	0.4182				p.A356A		Atlas-SNP	.											.	AMZ2	15	.	0			c.T1068A						PASS	.	T	,,,,,	1286,3120	437.4+/-345.0	197,892,1114	80.0	79.0	79.0		1068,1068,1068,1068,894,1068	1.1	1.0	17	dbSNP_52	79	2789,5811	441.0+/-359.7	476,1837,1987	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMZ2	NM_001033569.1,NM_001033570.1,NM_001033571.1,NM_001033572.1,NM_001033574.1,NM_016627.4	,,,,,	673,2729,3101	AA,AT,TT		32.4302,29.1875,31.3317	,,,,,	356/361,356/361,356/361,356/361,298/303,356/361	66253095	4075,8931	2203	4300	6503	SO:0001819	synonymous_variant	51321	exon8			CCTGGCTGTTCTC	CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"""archaemetzincin-2"""	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.1068T>A	17.37:g.66253095T>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_001033572	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Silent	SNP	ENST00000359904.3	37	CCDS11674.1																																																																																			T|0.663;A|0.337	0.337	strong		0.393	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627	
RBMXL1	494115	hgsc.bcm.edu	37	1	89448539	89448539	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89448539C>G	ENST00000321792.5	-	2	1398	c.971G>C	c.(970-972)cGa>cCa	p.R324P	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.R324P|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000413769.1_5'Flank|CCBL2_ENST00000370491.3_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	324	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										GTAACTGTCTCGACTTCCACC	0.517																																					p.R324P		Atlas-SNP	.											CCBL2,NS,carcinoma,-1,1	.	.	1	0			c.G971C						scavenged	.						185.0	184.0	184.0					1																	89448539		2203	4300	6503	SO:0001583	missense	494115	exon3			CTGTCTCGACTTC	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.971G>C	1.37:g.89448539C>G	ENSP00000318415:p.Arg324Pro	Somatic	237	5	0.021097		WXS	Illumina HiSeq	Phase_I	296	9	0.0304054	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.844738	0.51164	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.77358	-1.09;-1.09	1.89	0.895	0.19247	.	0.070349	0.64402	D	0.000016	T	0.62925	0.2468	M	0.65498	2.005	0.33162	D	0.547093	D	0.55172	0.97	P	0.46796	0.527	T	0.60667	-0.7218	10	0.52906	T	0.07	-3.2327	6.12	0.20148	0.0:0.8158:0.0:0.1842	.	324	Q96E39	RBMXL_HUMAN	P	324	ENSP00000318415:R324P;ENSP00000446099:R324P	ENSP00000318415:R324P	R	-	2	0	RBMXL1	89221127	1.000000	0.71417	0.995000	0.50966	0.753000	0.42808	4.995000	0.63908	0.128000	0.18479	0.306000	0.20318	CGA	.	.	none		0.517	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
OR11H6	122748	hgsc.bcm.edu	37	14	20692353	20692353	+	Missense_Mutation	SNP	T	T	C	rs146076639	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20692353T>C	ENST00000315519.2	+	1	563	c.485T>C	c.(484-486)cTg>cCg	p.L162P		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		TGTATAATTCTGGTCTGTGTA	0.463													t|||	9	0.00179712	0.0015	0.0029	5008	,	,		21313	0.0		0.004	False		,,,				2504	0.001				p.L162P		Atlas-SNP	.											.	OR11H6	60	.	0			c.T485C						PASS	.	T	PRO/LEU	4,4402	8.1+/-20.4	0,4,2199	101.0	99.0	100.0		485	5.0	1.0	14	dbSNP_134	100	34,8566	23.4+/-69.3	0,34,4266	yes	missense	OR11H6	NM_001004480.1	98	0,38,6465	CC,CT,TT		0.3953,0.0908,0.2922	probably-damaging	162/331	20692353	38,12968	2203	4300	6503	SO:0001583	missense	122748	exon1			TAATTCTGGTCTG		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"""GPCR / Class A : Olfactory receptors"""	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.485T>C	14.37:g.20692353T>C	ENSP00000319071:p.Leu162Pro	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	T	9.989	1.230400	0.22542	9.08E-4	0.003953	ENSG00000176219	ENST00000315519	T	0.45276	0.9	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40818	N	0.001011	T	0.69142	0.3078	H	0.97240	3.965	0.23809	N	0.996783	D	0.89917	1.0	D	0.87578	0.998	T	0.72121	-0.4386	10	0.87932	D	0	.	12.6331	0.56669	0.0:0.0:0.0:1.0	.	162	Q8NGC7	O11H6_HUMAN	P	162	ENSP00000319071:L162P	ENSP00000319071:L162P	L	+	2	0	OR11H6	19762193	0.774000	0.28592	0.996000	0.52242	0.144000	0.21451	4.003000	0.57061	2.077000	0.62373	0.363000	0.22086	CTG	T|0.998;C|0.002	0.002	strong		0.463	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
RREB1	6239	hgsc.bcm.edu	37	6	7246998	7246998	+	Missense_Mutation	SNP	G	G	A	rs2281833	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:7246998G>A	ENST00000349384.6	+	11	4464	c.4150G>A	c.(4150-4152)Ggg>Agg	p.G1384R	RREB1_ENST00000379933.3_Missense_Mutation_p.G1384R|RREB1_ENST00000379938.2_Missense_Mutation_p.G1439R|RREB1_ENST00000334984.6_Intron	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1384			G -> R (in dbSNP:rs2281833).		multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GGCAGGCGCCGGGGGCGCGGC	0.697													G|||	1075	0.214657	0.0809	0.2435	5008	,	,		11963	0.3532		0.1451	False		,,,				2504	0.3037				p.G1439R		Atlas-SNP	.											RREB1_ENST00000379938,NS,carcinoma,0,4	RREB1	242	4	0			c.G4315A						scavenged	.	G	ARG/GLY,ARG/GLY,,ARG/GLY	386,3790		14,358,1716	9.0	11.0	10.0		4150,4315,,4150	0.3	0.0	6	dbSNP_100	10	968,7248		64,840,3204	no	missense,missense,intron,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	125,125,,125	78,1198,4920	AA,AG,GG		11.7819,9.2433,10.9264	probably-damaging,probably-damaging,,probably-damaging	1384/1688,1439/1743,,1384/1688	7246998	1354,11038	2088	4108	6196	SO:0001583	missense	6239	exon12			GGCGCCGGGGGCG	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4150G>A	6.37:g.7246998G>A	ENSP00000305560:p.Gly1384Arg	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	7	3	0.428571	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	407	0.18635531135531136	53	0.10772357723577236	76	0.20994475138121546	167	0.291958041958042	111	0.14643799472295516	G	6.535	0.466891	0.12402	0.092433	0.117819	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384	T;T;T	0.09630	2.97;2.96;2.97	5.25	0.313	0.15842	.	1.071720	0.07262	N	0.867685	T	0.01730	0.0055	N	0.17082	0.46	0.48040	P	4.269999999999552E-4	B;B	0.31274	0.212;0.317	B;B	0.30179	0.052;0.112	T	0.48570	-0.9024	9	0.24483	T	0.36	-2.6678	5.2861	0.15702	0.3033:0.1369:0.5598:0.0	rs2281833	1384;1439	Q92766;Q92766-2	RREB1_HUMAN;.	R	1384;1439;1384	ENSP00000369265:G1384R;ENSP00000369270:G1439R;ENSP00000305560:G1384R	ENSP00000305560:G1384R	G	+	1	0	RREB1	7191997	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.791000	0.26915	-0.024000	0.13941	-0.140000	0.14226	GGG	G|0.815;A|0.185	0.185	strong		0.697	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
SYTL2	54843	hgsc.bcm.edu	37	11	85435730	85435730	+	Intron	SNP	C	C	T	rs550404	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:85435730C>T	ENST00000528231.1	-	7	1737				SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000359152.5_Silent_p.P1114P|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000525423.1_Silent_p.P590P|SYTL2_ENST00000354566.3_Silent_p.P590P	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.P590P(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CAGTTATTAACGGAGCCTCGG	0.438													C|||	3013	0.601637	0.6483	0.5461	5008	,	,		18027	0.6042		0.6541	False		,,,				2504	0.5215				p.P590P		Atlas-SNP	.											.	SYTL2	231	.	1	Substitution - coding silent(1)	prostate(1)	c.G1770A						PASS	.	C	,,,,	2856,1550	664.5+/-401.4	929,998,276	66.0	64.0	65.0		,,,1770,1770	-7.0	0.0	11	dbSNP_83	65	5644,2954	665.0+/-402.2	1877,1890,532	yes	intron,intron,intron,coding-synonymous,coding-synonymous	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,,	2806,2888,808	TT,TC,CC		34.3568,35.1793,34.6355	,,,,	,,,590/1273,590/1257	85435730	8500,4504	2203	4299	6502	SO:0001627	intron_variant	54843	exon1			TATTAACGGAGCC	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+3208G>A	11.37:g.85435730C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	172	170	0.988372	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			C|0.366;T|0.634	0.634	strong		0.438	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
SSTR5	6755	hgsc.bcm.edu	37	16	1129501	1129501	+	Silent	SNP	C	C	T	rs34037914	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1129501C>T	ENST00000293897.4	+	1	721	c.633C>T	c.(631-633)ttC>ttT	p.F211F	SSTR5-AS1_ENST00000569832.1_RNA|SSTR5_ENST00000562758.1_Silent_p.F211F|SSTR5_ENST00000397547.2_Silent_p.F211F	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	211					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytokinesis (GO:0032467)|regulation of insulin secretion (GO:0050796)|somatostatin signaling pathway (GO:0038170)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			endometrium(2)|lung(5)|prostate(1)|skin(1)	9		Hepatocellular(780;0.00369)			Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	TGGGCTTCTTCGCGCCGCTGC	0.711													C|||	162	0.0323482	0.0053	0.0706	5008	,	,		14649	0.001		0.0596	False		,,,				2504	0.046				p.F211F		Atlas-SNP	.											.	SSTR5	36	.	0			c.C633T						PASS	.	C	,	64,4304	58.1+/-94.6	1,62,2121	55.0	56.0	55.0		633,633	-9.4	0.7	16	dbSNP_126	55	550,8038	146.2+/-201.8	20,510,3764	no	coding-synonymous,coding-synonymous	SSTR5	NM_001053.3,NM_001172560.1	,	21,572,5885	TT,TC,CC		6.4043,1.4652,4.7391	,	211/365,211/365	1129501	614,12342	2184	4294	6478	SO:0001819	synonymous_variant	6755	exon2			CTTCTTCGCGCCG	D16827	CCDS10429.1	16p13.3	2012-08-08			ENSG00000162009	ENSG00000162009		"""GPCR / Class A : Somatostatin receptors"""	11334	protein-coding gene	gene with protein product		182455				7607700	Standard	NM_001053		Approved		uc021taf.1	P35346	OTTHUMG00000047842	ENST00000293897.4:c.633C>T	16.37:g.1129501C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_001172560	P34988|Q541E0|Q9UJI5	Silent	SNP	ENST00000293897.4	37	CCDS10429.1																																																																																			C|0.957;T|0.043	0.043	strong		0.711	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1		
GPR139	124274	hgsc.bcm.edu	37	16	20043330	20043330	+	Silent	SNP	T	T	C	rs2147865	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20043330T>C	ENST00000570682.1	-	2	1089	c.789A>G	c.(787-789)gtA>gtG	p.V263V		NM_001002911.2	NP_001002911.1	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	263					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	30						ACATGATGTGTACCAGCCAGC	0.532													C|||	2594	0.517971	0.6029	0.4092	5008	,	,		19887	0.7827		0.328	False		,,,				2504	0.4029				p.V263V		Atlas-SNP	.											.	GPR139	75	.	0			c.A789G						PASS	.	C		2400,2006	561.5+/-380.7	651,1098,454	71.0	74.0	73.0		789	4.8	1.0	16	dbSNP_96	73	2609,5991	689.1+/-404.3	386,1837,2077	no	coding-synonymous	GPR139	NM_001002911.2		1037,2935,2531	CC,CT,TT		30.3372,45.5288,38.513		263/354	20043330	5009,7997	2203	4300	6503	SO:0001819	synonymous_variant	124274	exon2			GATGTGTACCAGC	AY255545	CCDS32398.1	16p13.11	2012-08-21						"""GPCR / Class A : Orphans"""	19995	protein-coding gene	gene with protein product						12679517	Standard	XM_005255114		Approved	PGR3	uc002dgu.1	Q6DWJ6		ENST00000570682.1:c.789A>G	16.37:g.20043330T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	181	180	0.994475	NM_001002911	A8K5R9|Q86SP2|Q8TDU8	Silent	SNP	ENST00000570682.1	37	CCDS32398.1																																																																																			T|0.549;C|0.451	0.451	strong		0.532	GPR139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438522.1	NM_001002911	
ULK4	54986	hgsc.bcm.edu	37	3	41756986	41756986	+	Missense_Mutation	SNP	A	A	T	rs61744385	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:41756986A>T	ENST00000301831.4	-	24	2992	c.2530T>A	c.(2530-2532)Ttg>Atg	p.L844M		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	844					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		GGGAGACACAACTTCAGCTGT	0.433													T|||	1330	0.265575	0.5348	0.1628	5008	,	,		17195	0.1478		0.1839	False		,,,				2504	0.18				p.L844M		Atlas-SNP	.											.	ULK4	150	.	0			c.T2530A						PASS	.	T	MET/LEU	1828,2100		435,958,571	104.0	106.0	105.0		2530	-1.8	0.1	3	dbSNP_129	105	1425,6891		128,1169,2861	yes	missense	ULK4	NM_017886.2	15	563,2127,3432	TT,TA,AA		17.1356,46.5377,26.5681	benign	844/1276	41756986	3253,8991	1964	4158	6122	SO:0001583	missense	54986	exon24			GACACAACTTCAG	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2530T>A	3.37:g.41756986A>T	ENSP00000301831:p.Leu844Met	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	550	0.2518315018315018	262	0.532520325203252	57	0.1574585635359116	86	0.15034965034965034	145	0.19129287598944592	T	2.271	-0.366965	0.05069	0.465377	0.171356	ENSG00000168038	ENST00000301831	T	0.52526	0.66	5.72	-1.82	0.07857	Armadillo-type fold (1);	0.393302	0.27513	N	0.019027	T	0.00012	0.0000	N	0.01109	-1.01	0.36343	P	0.14037200000000005	B	0.06786	0.001	B	0.08055	0.003	T	0.41645	-0.9497	9	0.16896	T	0.51	.	4.4795	0.11760	0.2034:0.0585:0.4211:0.317	rs61744385	844	Q96C45	ULK4_HUMAN	M	844	ENSP00000301831:L844M	ENSP00000301831:L844M	L	-	1	2	ULK4	41731990	0.258000	0.24033	0.069000	0.20011	0.931000	0.56810	0.121000	0.15667	-0.930000	0.03752	-1.147000	0.01851	TTG	A|0.770;T|0.230	0.230	strong		0.433	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
PIP5K1C	23396	hgsc.bcm.edu	37	19	3644220	3644220	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:3644220G>A	ENST00000335312.3	-	12	1463	c.1375C>T	c.(1375-1377)Cgc>Tgc	p.R459C	PIP5K1C_ENST00000537021.1_Missense_Mutation_p.R459C|PIP5K1C_ENST00000539785.1_Missense_Mutation_p.R459C|PIP5K1C_ENST00000589578.1_Missense_Mutation_p.R459C	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	459					actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		GCTCCGCCGCGCCCCTTCTTG	0.687																																					p.R459C	Esophageal Squamous(135;99 1744 12852 27186 39851)	Atlas-SNP	.											.	PIP5K1C	63	.	0			c.C1375T						PASS	.						28.0	34.0	32.0					19																	3644220		2201	4293	6494	SO:0001583	missense	23396	exon12			CGCCGCGCCCCTT	AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.1375C>T	19.37:g.3644220G>A	ENSP00000335333:p.Arg459Cys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	69	42	0.608696	NM_001195733	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Missense_Mutation	SNP	ENST00000335312.3	37	CCDS32872.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990963	0.35131	.	.	ENSG00000186111	ENST00000335312;ENST00000539785;ENST00000537021	T;T;T	0.34275	1.42;1.42;1.37	4.66	3.52	0.40303	.	0.000000	0.85682	D	0.000000	T	0.32882	0.0844	L	0.48642	1.525	0.54753	D	0.999987	B;B	0.32382	0.368;0.252	B;B	0.31614	0.133;0.063	T	0.41378	-0.9512	10	0.87932	D	0	-11.2654	14.5132	0.67802	0.0:0.0:0.843:0.157	.	459;459	O60331-3;O60331	.;PI51C_HUMAN	C	459	ENSP00000335333:R459C;ENSP00000445992:R459C;ENSP00000444779:R459C	ENSP00000335333:R459C	R	-	1	0	PIP5K1C	3595220	1.000000	0.71417	0.785000	0.31869	0.212000	0.24457	6.155000	0.71833	2.146000	0.66826	0.491000	0.48974	CGC	.	.	none		0.687	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2	NM_012398	
SPEG	10290	hgsc.bcm.edu	37	2	220355529	220355529	+	Missense_Mutation	SNP	A	A	G	rs12464085	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:220355529A>G	ENST00000312358.7	+	38	9368	c.9236A>G	c.(9235-9237)cAc>cGc	p.H3079R	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	3079	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.		H -> R (in dbSNP:rs12464085). {ECO:0000269|PubMed:17344846}.		cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CTCCACGGCCACCACGTGCTC	0.592													G|||	2008	0.400958	0.5696	0.3905	5008	,	,		19933	0.1736		0.331	False		,,,				2504	0.4867				p.H3079R		Atlas-SNP	.											.	SPEG	272	.	0			c.A9236G						PASS	.	G	ARG/HIS	2216,2070		584,1048,511	79.0	91.0	87.0		9236	-0.1	1.0	2	dbSNP_120	87	2756,5722		440,1876,1923	yes	missense	SPEG	NM_005876.4	29	1024,2924,2434	GG,GA,AA		32.5077,48.2968,38.9533	benign	3079/3268	220355529	4972,7792	2143	4239	6382	SO:0001583	missense	10290	exon38			ACGGCCACCACGT	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.9236A>G	2.37:g.220355529A>G	ENSP00000311684:p.His3079Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	774	0.3543956043956044	277	0.5630081300813008	146	0.40331491712707185	107	0.18706293706293706	244	0.32189973614775724	G	8.533	0.871477	0.17322	0.517032	0.325077	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.63913	-0.07	4.92	-0.0763	0.13723	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.365604	0.20113	N	0.098961	T	0.00012	0.0000	N	0.11427	0.14	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42699	-0.9436	9	0.02654	T	1	.	11.2813	0.49197	0.4833:0.0:0.5167:0.0	rs12464085;rs57168643;rs12464085	3079	Q15772	SPEG_HUMAN	R	3079	ENSP00000311684:H3079R	ENSP00000265327:H3079R	H	+	2	0	SPEG	220063773	0.842000	0.29525	0.967000	0.41034	0.766000	0.43426	1.359000	0.34113	-0.187000	0.10516	-0.186000	0.12905	CAC	A|0.627;G|0.373	0.373	strong		0.592	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
SORBS1	10580	hgsc.bcm.edu	37	10	97174352	97174352	+	Missense_Mutation	SNP	T	T	C	rs2281939	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:97174352T>C	ENST00000361941.3	-	7	735	c.709A>G	c.(709-711)Acg>Gcg	p.T237A	SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000371249.2_Missense_Mutation_p.T205A|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000393949.1_Missense_Mutation_p.T228A|SORBS1_ENST00000354106.3_Missense_Mutation_p.T228A|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000371227.4_Missense_Mutation_p.T237A|SORBS1_ENST00000277982.5_Missense_Mutation_p.T237A|SORBS1_ENST00000371245.3_Missense_Mutation_p.T168A|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000371247.2_Missense_Mutation_p.T237A|SORBS1_ENST00000353505.5_Missense_Mutation_p.T168A|SORBS1_ENST00000371246.2_Missense_Mutation_p.T237A	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		GATGGTGGCGTCTGGCTAATG	0.637													T|||	802	0.160144	0.3434	0.062	5008	,	,		17833	0.1171		0.0586	False		,,,				2504	0.1309				p.T237A		Atlas-SNP	.											SORBS1_ENST00000371247,NS,carcinoma,+2,2	SORBS1	185	2	0			c.A709G	GRCh37	CM012804	SORBS1	M	rs2281939	PASS	.	T	ALA/THR,ALA/THR,ALA/THR,,,ALA/THR,	1344,3062	420.2+/-338.9	210,924,1069	31.0	32.0	31.0		709,709,502,,,613,	1.8	1.0	10	dbSNP_100	31	444,8154	130.0+/-188.0	13,418,3868	yes	missense,missense,missense,intron,intron,missense,intron	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	58,58,58,,,58,	223,1342,4937	CC,CT,TT		5.164,30.5039,13.7496	possibly-damaging,possibly-damaging,possibly-damaging,,,possibly-damaging,	237/1293,237/1152,168/906,,,205/817,	97174352	1788,11216	2203	4299	6502	SO:0001583	missense	10580	exon7			GTGGCGTCTGGCT	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.709A>G	10.37:g.97174352T>C	ENSP00000355136:p.Thr237Ala	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	66	60	0.909091	NM_001034955		Missense_Mutation	SNP	ENST00000361941.3	37	CCDS31255.1	300	0.13736263736263737	168	0.34146341463414637	21	0.058011049723756904	68	0.11888111888111888	43	0.05672823218997362	T	6.644	0.487361	0.12641	0.305039	0.05164	ENSG00000095637	ENST00000371245;ENST00000371249;ENST00000371247;ENST00000371227;ENST00000371246;ENST00000393949;ENST00000353505;ENST00000361941;ENST00000277982;ENST00000354106	T;T;T;T;T;T;T;T;T;T	0.39056	1.59;1.57;1.1;1.57;1.1;1.1;1.59;1.1;1.1;1.1	5.54	1.8	0.24995	.	0.341205	0.21497	N	0.073592	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	0.999999999036363	P;P;P;B;P;B;P	0.43788	0.817;0.739;0.787;0.038;0.571;0.329;0.514	B;B;B;B;B;B;B	0.39840	0.164;0.225;0.311;0.054;0.121;0.077;0.17	T	0.38112	-0.9676	9	0.34782	T	0.22	-1.483	6.5738	0.22553	0.0:0.138:0.1308:0.7313	rs2281939;rs17849165;rs61182067;rs2281939	435;205;237;205;168;237;237	B7Z9B7;F2Z2S3;Q9BX66-11;Q9BX66-10;Q9BX66-3;Q9BX66;Q9BX66-2	.;.;.;.;.;SRBS1_HUMAN;.	A	168;205;237;237;237;228;168;237;237;228	ENSP00000360291:T168A;ENSP00000360295:T205A;ENSP00000360293:T237A;ENSP00000360271:T237A;ENSP00000360292:T237A;ENSP00000377521:T228A;ENSP00000343998:T168A;ENSP00000355136:T237A;ENSP00000277982:T237A;ENSP00000277984:T228A	ENSP00000277982:T237A	T	-	1	0	SORBS1	97164342	1.000000	0.71417	0.960000	0.40013	0.967000	0.64934	1.022000	0.30052	0.053000	0.16036	0.454000	0.30748	ACG	T|0.860;C|0.140	0.140	strong		0.637	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
ARHGEF40	55701	hgsc.bcm.edu	37	14	21550499	21550499	+	Silent	SNP	G	G	T	rs61746329	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21550499G>T	ENST00000298694.4	+	15	3475	c.3348G>T	c.(3346-3348)acG>acT	p.T1116T	ARHGEF40_ENST00000298693.3_Silent_p.T1116T			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	1116	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						CTGAGCTGACGCCTGAACTTC	0.642													T|||	312	0.0623003	0.0915	0.0303	5008	,	,		17441	0.0337		0.0497	False		,,,				2504	0.0879				p.T1116T		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.G3348T						PASS	.	T		415,3991	751.1+/-412.2	38,339,1826	36.0	37.0	37.0		3348	-2.8	1.0	14	dbSNP_129	37	423,8177	794.5+/-407.5	14,395,3891	no	coding-synonymous	ARHGEF40	NM_018071.3		52,734,5717	TT,TG,GG		4.9186,9.419,6.4432		1116/1520	21550499	838,12168	2203	4300	6503	SO:0001819	synonymous_variant	55701	exon15			GCTGACGCCTGAA		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.3348G>T	14.37:g.21550499G>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	37	CCDS32041.1																																																																																			G|0.943;T|0.057	0.057	strong		0.642	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
OR52N2	390077	hgsc.bcm.edu	37	11	5842356	5842356	+	Missense_Mutation	SNP	A	A	G	rs8181512	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5842356A>G	ENST00000317037.2	+	1	813	c.791A>G	c.(790-792)cAt>cGt	p.H264R	TRIM5_ENST00000380027.1_Intron	NM_001005174.1	NP_001005174.1	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N, member 2	264			H -> R (in dbSNP:rs8181512).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|urinary_tract(1)	32		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.49e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTTTTCACTCATCGTTTTGTA	0.438													A|||	2275	0.454273	0.3411	0.4813	5008	,	,		21883	0.4692		0.5368	False		,,,				2504	0.4877				p.H264R		Atlas-SNP	.											.	OR52N2	58	.	0			c.A791G						PASS	.	A	ARG/HIS	1649,2753	504.4+/-365.8	307,1035,859	203.0	163.0	176.0		791	6.1	0.4	11	dbSNP_117	176	4755,3837	610.9+/-395.7	1293,2169,834	yes	missense	OR52N2	NM_001005174.1	29	1600,3204,1693	GG,GA,AA		44.6578,37.4602,49.2843	probably-damaging	264/322	5842356	6404,6590	2201	4296	6497	SO:0001583	missense	390077	exon1			TCACTCATCGTTT	AB065816	CCDS31399.1	11p15.4	2012-08-09			ENSG00000180988	ENSG00000180988		"""GPCR / Class A : Olfactory receptors"""	15228	protein-coding gene	gene with protein product							Standard	NM_001005174		Approved		uc010qzp.2	Q8NGI0	OTTHUMG00000168801	ENST00000317037.2:c.791A>G	11.37:g.5842356A>G	ENSP00000322801:p.His264Arg	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	281	131	0.466192	NM_001005174	Q6IFF9	Missense_Mutation	SNP	ENST00000317037.2	37	CCDS31399.1	1025	0.4693223443223443	160	0.3252032520325203	180	0.4972375690607735	272	0.4755244755244755	413	0.5448548812664907	A	14.50	2.552601	0.45487	0.374602	0.553422	ENSG00000180988	ENST00000317037	T	0.00084	8.75	6.09	6.09	0.99107	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000032	T	0.00012	0.0000	M	0.90922	3.16	0.28532	P	0.9125249	D	0.62365	0.991	D	0.74674	0.984	T	0.30621	-0.9972	9	0.87932	D	0	.	15.4925	0.75619	1.0:0.0:0.0:0.0	rs8181512;rs56559501;rs57093767;rs8181512	264	Q8NGI0	O52N2_HUMAN	R	264	ENSP00000322801:H264R	ENSP00000322801:H264R	H	+	2	0	OR52N2	5798932	0.457000	0.25752	0.428000	0.26697	0.014000	0.08584	4.960000	0.63673	2.336000	0.79503	0.523000	0.50628	CAT	A|0.522;G|0.478	0.478	strong		0.438	OR52N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401143.1	NM_001005174	
KLK13	26085	hgsc.bcm.edu	37	19	51563265	51563265	+	Missense_Mutation	SNP	G	G	A	rs34089525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51563265G>A	ENST00000595793.1	-	3	367	c.325C>T	c.(325-327)Cac>Tac	p.H109Y	KLK13_ENST00000596955.1_Missense_Mutation_p.H109Y|KLK13_ENST00000335422.3_Intron|KLK13_ENST00000595547.1_Intron	NM_015596.1	NP_056411.1	Q9UKR3	KLK13_HUMAN	kallikrein-related peptidase 13	109	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		H -> Y (in dbSNP:rs34089525).		protein processing (GO:0016485)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)	hydrolase activity (GO:0016787)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	16		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00432)		TATTCAGGGTGGGGGATAGAG	0.582													G|||	56	0.0111821	0.0015	0.0058	5008	,	,		11828	0.0		0.0298	False		,,,				2504	0.0204				p.H109Y		Atlas-SNP	.											.	KLK13	40	.	0			c.C325T						PASS	.	G	TYR/HIS	27,4379	34.3+/-65.2	0,27,2176	88.0	87.0	87.0		325	2.9	1.0	19	dbSNP_126	87	288,8312	106.0+/-166.9	9,270,4021	yes	missense	KLK13	NM_015596.1	83	9,297,6197	AA,AG,GG		3.3488,0.6128,2.422	probably-damaging	109/278	51563265	315,12691	2203	4300	6503	SO:0001583	missense	26085	exon3			CAGGGTGGGGGAT		CCDS12822.1	19q13.33	2008-02-05	2006-10-27			ENSG00000167759		"""Kallikreins"""	6361	protein-coding gene	gene with protein product		605505	"""kallikrein 13"""			16800724, 16800723	Standard	NM_015596		Approved	KLK-L4	uc002pvn.3	Q9UKR3		ENST00000595793.1:c.325C>T	19.37:g.51563265G>A	ENSP00000470555:p.His109Tyr	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	NM_015596	A7UNK6|Q86VI8|Q9Y433	Missense_Mutation	SNP	ENST00000595793.1	37	CCDS12822.1	31	0.014194139194139194	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	26	0.03430079155672823	G	11.51	1.659191	0.29515	0.006128	0.033488	ENSG00000167759	ENST00000156476	.	.	.	3.91	2.86	0.33363	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.132025	0.34700	N	0.003750	T	0.48607	0.1509	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.984	T	0.64820	-0.6317	9	0.87932	D	0	.	7.6127	0.28139	0.1196:0.0:0.8804:0.0	rs34089525	109;109	B5BUM9;Q9UKR3	.;KLK13_HUMAN	Y	109	.	ENSP00000156476:H109Y	H	-	1	0	KLK13	56255077	1.000000	0.71417	0.987000	0.45799	0.002000	0.02628	4.613000	0.61176	1.001000	0.39076	-0.145000	0.13849	CAC	G|0.977;A|0.023	0.023	strong		0.582	KLK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464298.2	NM_015596	
LYST	1130	hgsc.bcm.edu	37	1	235907279	235907279	+	Splice_Site	SNP	A	A	G	rs201045270		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:235907279A>G	ENST00000389794.3	-	30	8325	c.8151T>C	c.(8149-8151)atT>atC	p.I2717I	LYST_ENST00000389793.2_Splice_Site_p.I2717I			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2717					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ATTTACTTACAATAGATACTT	0.279																																					p.I2717I		Atlas-SNP	.											.	LYST	370	.	0			c.T8151C						PASS	.	A		0,4382		0,0,2191	31.0	36.0	34.0		8151	5.5	1.0	1		34	1,8567		0,1,4283	no	coding-synonymous-near-splice	LYST	NM_000081.2		0,1,6474	GG,GA,AA		0.0117,0.0,0.0077		2717/3802	235907279	1,12949	2191	4284	6475	SO:0001630	splice_region_variant	1130	exon30			ACTTACAATAGAT	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.8151+1T>C	1.37:g.235907279A>G		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	196	78	0.397959	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			.	.	weak		0.279	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		Silent
ADAMTS13	11093	hgsc.bcm.edu	37	9	136310908	136310908	+	Missense_Mutation	SNP	C	C	T	rs685523	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:136310908C>T	ENST00000371929.3	+	21	3143	c.2699C>T	c.(2698-2700)gCg>gTg	p.A900V	ADAMTS13_ENST00000355699.2_Missense_Mutation_p.A900V|ADAMTS13_ENST00000536611.1_3'UTR|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000356589.2_Missense_Mutation_p.A869V|ADAMTS13_ENST00000371916.1_3'UTR	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	900	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.		A -> V (in dbSNP:rs685523). {ECO:0000269|PubMed:11557746, ECO:0000269|PubMed:11586351, ECO:0000269|Ref.6}.		cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TGGACCCCTGCGGCAGGGTCG	0.657													C|||	383	0.0764776	0.152	0.0663	5008	,	,		17275	0.002		0.1074	False		,,,				2504	0.0266				p.A900V		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C2699T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	582,3824	249.3+/-256.8	36,510,1657	49.0	48.0	48.0		2699,2606,2699	4.6	0.0	9	dbSNP_83	48	887,7713	196.1+/-241.1	55,777,3468	yes	missense,missense,missense	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	64,64,64	91,1287,5125	TT,TC,CC		10.314,13.2093,11.2948	benign,benign,benign	900/1428,869/1341,900/1372	136310908	1469,11537	2203	4300	6503	SO:0001583	missense	11093	exon21			CCCCTGCGGCAGG	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.2699C>T	9.37:g.136310908C>T	ENSP00000360997:p.Ala900Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	120	68	0.566667	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	188	0.08608058608058608	79	0.16056910569105692	31	0.0856353591160221	0	0.0	78	0.10290237467018469	C	1.573	-0.533746	0.04082	0.132093	0.10314	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589	T;T;T	0.68331	-0.25;-0.32;-0.3	5.69	4.55	0.56014	.	.	.	.	.	T	0.00144	0.0004	N	0.01048	-1.04	0.27682	P	0.9464111	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.04178	-1.0971	8	0.29301	T	0.29	.	6.2823	0.21013	0.0:0.0818:0.1588:0.7594	rs685523;rs36221589;rs56836858;rs685523	900;869;900	Q76LX8;Q76LX8-3;Q76LX8-2	ATS13_HUMAN;.;.	V	900;900;869	ENSP00000360997:A900V;ENSP00000347927:A900V;ENSP00000348997:A869V	ENSP00000347927:A900V	A	+	2	0	ADAMTS13	135300729	0.006000	0.16342	0.041000	0.18516	0.001000	0.01503	1.144000	0.31565	0.971000	0.38288	-0.294000	0.09567	GCG	T|0.098;G|0.006	0.098	strong		0.657	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
OR2T35	403244	hgsc.bcm.edu	37	1	248801897	248801897	+	Silent	SNP	G	G	A	rs79303917	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248801897G>A	ENST00000317450.3	-	1	662	c.663C>T	c.(661-663)atC>atT	p.I221I		NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T, member 35	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I221I(1)		endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CAGTCAGGAGGATGTGCGTGT	0.542																																					p.I221I		Atlas-SNP	.											OR2T35,NS,carcinoma,0,1	OR2T35	19	1	1	Substitution - coding silent(1)	ovary(1)	c.C663T						PASS	.	G		125,3975		2,121,1927	102.0	89.0	93.0		663	-0.2	0.0	1	dbSNP_131	93	877,7621		4,869,3376	no	coding-synonymous	OR2T35	NM_001001827.1		6,990,5303	AA,AG,GG		10.3201,3.0488,7.9536		221/324	248801897	1002,11596	2050	4249	6299	SO:0001819	synonymous_variant	403244	exon1			CAGGAGGATGTGC	BK004475	CCDS31123.1	1q44	2012-08-09			ENSG00000177151	ENSG00000177151		"""GPCR / Class A : Olfactory receptors"""	31257	protein-coding gene	gene with protein product							Standard	NM_001001827		Approved		uc001ies.1	Q8NGX2	OTTHUMG00000040380	ENST00000317450.3:c.663C>T	1.37:g.248801897G>A		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	427	257	0.601874	NM_001001827	Q6IEY7	Silent	SNP	ENST00000317450.3	37	CCDS31123.1																																																																																			G|0.895;A|0.105	0.105	strong		0.542	OR2T35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097130.1	NM_001001827	
VAMP5	10791	hgsc.bcm.edu	37	2	85818886	85818886	+	Silent	SNP	C	C	T	rs14976	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:85818886C>T	ENST00000306384.4	+	2	125	c.42C>T	c.(40-42)aaC>aaT	p.N14N		NM_006634.2	NP_006625.1	O95183	VAMP5_HUMAN	vesicle-associated membrane protein 5	14	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				cell differentiation (GO:0030154)|Golgi to plasma membrane protein transport (GO:0043001)|muscle organ development (GO:0007517)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|large_intestine(3)|lung(1)	5						AGCAGGCGAACGAGGTGACGG	0.607													C|||	963	0.192292	0.152	0.2003	5008	,	,		18936	0.0883		0.2813	False		,,,				2504	0.2566				p.N14N		Atlas-SNP	.											.	VAMP5	13	.	0			c.C42T						PASS	.	C		692,3714	290.7+/-281.1	51,590,1562	132.0	113.0	119.0		42	-3.7	0.5	2	dbSNP_52	119	2410,6190	401.2+/-347.1	335,1740,2225	no	coding-synonymous	VAMP5	NM_006634.2		386,2330,3787	TT,TC,CC		28.0233,15.7059,23.8505		14/117	85818886	3102,9904	2203	4300	6503	SO:0001819	synonymous_variant	10791	exon2			GGCGAACGAGGTG	AF054825	CCDS1980.1	2p11.2	2013-02-13	2012-10-17		ENSG00000168899	ENSG00000168899		"""Vesicle-associated membrane proteins"""	12646	protein-coding gene	gene with protein product	"""myobrevin"""	607029				9725904	Standard	NM_006634		Approved		uc002spu.1	O95183	OTTHUMG00000130169	ENST00000306384.4:c.42C>T	2.37:g.85818886C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	215	106	0.493023	NM_006634	Q9P0T2	Silent	SNP	ENST00000306384.4	37	CCDS1980.1																																																																																			C|0.797;T|0.203	0.203	strong		0.607	VAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252484.2	NM_006634	
LRRC37A2	474170	hgsc.bcm.edu	37	17	44626866	44626866	+	Missense_Mutation	SNP	T	T	C	rs202051157	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44626866T>C	ENST00000576629.1	+	10	4856	c.4361T>C	c.(4360-4362)cTg>cCg	p.L1454P	ARL17A_ENST00000337845.7_Intron|LRRC37A2_ENST00000333412.3_Missense_Mutation_p.L1454P|ARL17A_ENST00000573185.1_Intron|ARL17A_ENST00000329240.4_Intron|ARL17A_ENST00000445552.2_Intron			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	1454						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|pancreas(4)|prostate(2)	15		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		GGCACTGACCTGTCCCCCGAG	0.498																																					p.L1454P		Atlas-SNP	.											LRRC37A2,NS,carcinoid-endocrine_tumour,0,1	LRRC37A2	37	1	0			c.T4361C						scavenged	.						2.0	1.0	1.0					17																	44626866		598	1214	1812	SO:0001583	missense	474170	exon9			CTGACCTGTCCCC	AY386262	CCDS42353.1	17q21.31	2013-05-14			ENSG00000238083	ENSG00000238083			32404	protein-coding gene	gene with protein product	"""c114 SLIT-like testicular protein"""						Standard	NM_001006607		Approved	FLJ45049	uc002ikn.1	A6NM11	OTTHUMG00000178032	ENST00000576629.1:c.4361T>C	17.37:g.44626866T>C	ENSP00000459551:p.Leu1454Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	203	45	0.221675	NM_001006607	B7ZMC3	Missense_Mutation	SNP	ENST00000576629.1	37	CCDS42353.1	.	.	.	.	.	.	.	.	.	.	t	8.780	0.927936	0.18056	.	.	ENSG00000238083	ENST00000333412	T	0.59638	0.25	3.02	-1.85	0.07784	.	.	.	.	.	T	0.62744	0.2453	L	0.59436	1.845	0.09310	N	1	D;D;B	0.69078	0.995;0.997;0.158	D;D;B	0.72982	0.979;0.964;0.074	T	0.52335	-0.8589	9	0.33141	T	0.24	.	3.1977	0.06639	0.0:0.358:0.2285:0.4136	.	1454;415;1454	C9JSP5;B3KRJ4;A6NM11	.;.;L37A2_HUMAN	P	1454	ENSP00000333071:L1454P	ENSP00000333071:L1454P	L	+	2	0	LRRC37A2	41982182	0.000000	0.05858	0.000000	0.03702	0.158000	0.22134	0.101000	0.15251	-0.073000	0.12842	0.147000	0.16070	CTG	.	.	weak		0.498	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607	
IFIH1	64135	hgsc.bcm.edu	37	2	163124637	163124637	+	Missense_Mutation	SNP	T	T	C	rs35667974	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:163124637T>C	ENST00000263642.2	-	14	3162	c.2767A>G	c.(2767-2769)Att>Gtt	p.I923V		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	923					cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						ATTTTCTCAATTACATGGATA	0.398													T|||	12	0.00239617	0.0008	0.0	5008	,	,		18807	0.0		0.0099	False		,,,				2504	0.001				p.I923V		Atlas-SNP	.											.	IFIH1	102	.	0			c.A2767G						PASS	.	T	VAL/ILE	11,4395	17.9+/-39.9	0,11,2192	128.0	128.0	128.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2767	5.1	0.9	2	dbSNP_126	128	140,8460	70.7+/-133.2	4,132,4164	yes	missense	IFIH1	NM_022168.2	29	4,143,6356	CC,CT,TT		1.6279,0.2497,1.161	benign	923/1026	163124637	151,12855	2203	4300	6503	SO:0001583	missense	64135	exon14			TCTCAATTACATG	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.2767A>G	2.37:g.163124637T>C	ENSP00000263642:p.Ile923Val	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	226	103	0.455752	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	17.27	3.347761	0.61183	0.002497	0.016279	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.29917	1.55	5.13	5.13	0.70059	C-terminal domain of RIG-I (1);	0.048848	0.85682	D	0.000000	T	0.29684	0.0741	L	0.50919	1.6	0.50313	D	0.999862	D	0.53151	0.958	P	0.61397	0.888	T	0.09015	-1.0694	10	0.33141	T	0.24	-8.4883	14.9508	0.71071	0.0:0.0:0.0:1.0	rs35667974	923	Q9BYX4	IFIH1_HUMAN	V	923	ENSP00000263642:I923V	ENSP00000263642:I923V	I	-	1	0	IFIH1	162832883	1.000000	0.71417	0.917000	0.36280	0.768000	0.43524	7.427000	0.80284	1.932000	0.55993	0.528000	0.53228	ATT	T|0.991;C|0.009	0.009	strong		0.398	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168	
RBMXL3	139804	hgsc.bcm.edu	37	X	114426385	114426385	+	Missense_Mutation	SNP	G	G	A	rs80194951		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:114426385G>A	ENST00000424776.3	+	1	2423	c.2381G>A	c.(2380-2382)cGc>cAc	p.R794H	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	794	Gly-rich.			R -> H (in Ref. 1; AK097568). {ECO:0000305}.			nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						AGCGGAGGCCGCTCACCCAAT	0.662													G|||	220	0.0582781	0.0038	0.0533	3775	,	,		13082	0.002		0.1123	False		,,,				2504	0.0644				p.R794H		Atlas-SNP	.											.	RBMXL3	83	.	0			c.G2381A						PASS	.	G	HIS/ARG,	34,1175		1,25,7,491,168	30.0	32.0	32.0		2381,	0.9	0.0	X	dbSNP_131	32	387,2004		18,212,139,570,652	yes	missense,intron	LRCH2,RBMXL3	NM_001145346.1,NM_020871.3	29,	19,237,146,1061,820	AA,AG,A,GG,G		16.1857,2.8122,11.6944	possibly-damaging,	794/1068,	114426385	421,3179	692	1591	2283	SO:0001583	missense	139804	exon1			GAGGCCGCTCACC	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.2381G>A	X.37:g.114426385G>A	ENSP00000417451:p.Arg794His	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	215	198	0.92093	NM_001145346	B4DXC0	Missense_Mutation	SNP	ENST00000424776.3	37	CCDS55478.1	117	0.0705244122965642	3	0.006122448979591836	20	0.056179775280898875	2	0.0034965034965034965	53	0.07703488372093023	G	14.93	2.683230	0.47991	0.028122	0.161857	ENSG00000175718	ENST00000424776	T	0.05996	3.36	0.92	0.92	0.19397	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.45567	P	0.0014840000000000408	D	0.56521	0.976	P	0.46629	0.522	T	0.49844	-0.8896	8	0.87932	D	0	.	7.6329	0.28249	1.0E-4:0.0:0.9999:0.0	.	794	Q8N7X1	RMXL3_HUMAN	H	794	ENSP00000417451:R794H	ENSP00000417451:R794H	R	+	2	0	RBMXL3	114332641	0.003000	0.15002	0.013000	0.15412	0.014000	0.08584	0.066000	0.14489	0.179000	0.19938	0.181000	0.17075	CGC	G|0.929;A|0.071	0.071	strong		0.662	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
CRYM	1428	hgsc.bcm.edu	37	16	21272648	21272648	+	Silent	SNP	A	A	G	rs144588424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:21272648A>G	ENST00000219599.3	-	9	1072	c.807T>C	c.(805-807)ttT>ttC	p.F269F	CRYM_ENST00000415987.2_Silent_p.F227F|CRYM_ENST00000396023.2_Silent_p.F269F|CRYM_ENST00000543948.1_Silent_p.F269F	NM_001888.3	NP_001879.1	Q14894	CRYM_HUMAN	crystallin, mu	269					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|sensory perception of sound (GO:0007605)|thyroid hormone metabolic process (GO:0042403)|thyroid hormone transport (GO:0070327)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|thiomorpholine-carboxylate dehydrogenase activity (GO:0047127)|thyroid hormone binding (GO:0070324)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(3)	4				GBM - Glioblastoma multiforme(48;0.0573)		CCAGCTCAGCAAAGATCTCGG	0.507													A|||	9	0.00179712	0.0	0.0043	5008	,	,		17799	0.0		0.004	False		,,,				2504	0.002				p.F269F		Atlas-SNP	.											.	CRYM	13	.	0			c.T807C						PASS	.	A	,	3,4395	4.2+/-10.8	0,3,2196	114.0	94.0	101.0		681,807	-10.2	0.7	16	dbSNP_134	101	51,8549	33.3+/-86.6	1,49,4250	no	coding-synonymous,coding-synonymous	CRYM	NM_001014444.2,NM_001888.3	,	1,52,6446	GG,GA,AA		0.593,0.0682,0.4154	,	227/273,269/315	21272648	54,12944	2199	4300	6499	SO:0001819	synonymous_variant	1428	exon9			CTCAGCAAAGATC		CCDS10597.1	16p12.2	2013-02-14			ENSG00000103316	ENSG00000103316	1.5.1.25		2418	protein-coding gene	gene with protein product	"""thiomorpholine-carboxylate dehydrogenase"""	123740				1478656, 21332720	Standard	NM_001014444		Approved	DFNA40	uc002dim.3	Q14894	OTTHUMG00000090707	ENST00000219599.3:c.807T>C	16.37:g.21272648A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	165	81	0.490909	NM_001888	D5MNX0|Q5HYB7	Silent	SNP	ENST00000219599.3	37	CCDS10597.1																																																																																			A|0.996;G|0.004	0.004	strong		0.507	CRYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207398.1		
C2CD3	26005	hgsc.bcm.edu	37	11	73825503	73825503	+	Silent	SNP	T	T	C	rs10898957	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:73825503T>C	ENST00000334126.7	-	10	1882	c.1656A>G	c.(1654-1656)ccA>ccG	p.P552P	C2CD3_ENST00000313663.7_Silent_p.P552P			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	552					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GAGGACTATCTGGAGGAACTC	0.458													T|||	844	0.16853	0.0915	0.0879	5008	,	,		17889	0.2748		0.17	False		,,,				2504	0.2188				p.P552P		Atlas-SNP	.											.	C2CD3	288	.	0			c.A1656G						PASS	.	T		514,3886	235.2+/-247.8	21,472,1707	138.0	117.0	124.0		1656	4.9	1.0	11	dbSNP_120	124	1514,7072	285.9+/-297.4	139,1236,2918	no	coding-synonymous	C2CD3	NM_015531.4		160,1708,4625	CC,CT,TT		17.6334,11.6818,15.6168		552/1964	73825503	2028,10958	2200	4293	6493	SO:0001819	synonymous_variant	26005	exon10			ACTATCTGGAGGA	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1656A>G	11.37:g.73825503T>C		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	279	278	0.996416	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Silent	SNP	ENST00000334126.7	37																																																																																				T|0.841;C|0.159	0.159	strong		0.458	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
WDR81	124997	hgsc.bcm.edu	37	17	1640793	1640793	+	Silent	SNP	C	C	T	rs587780510|rs8077638	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1640793C>T	ENST00000409644.1	+	10	5640	c.5640C>T	c.(5638-5640)agC>agT	p.S1880S	WDR81_ENST00000545662.1_Silent_p.S511S|WDR81_ENST00000419248.1_Silent_p.S653S|WDR81_ENST00000446363.1_Silent_p.S519S|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Silent_p.S829S|WDR81_ENST00000437219.2_Silent_p.S677S	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1880					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TGTACGGCAGCGAGGTGGTCA	0.597													C|||	1210	0.241613	0.23	0.2075	5008	,	,		22298	0.1865		0.1988	False		,,,				2504	0.3824				p.S1880S		Atlas-SNP	.											WDR81_ENST00000437219,colon,carcinoma,0,6	WDR81	180	6	0			c.C5640T						PASS	.	C	,,,	986,3418	366.8+/-318.0	106,774,1322	229.0	137.0	168.0		2031,5640,1959,2487	2.0	1.0	17	dbSNP_116	168	1799,6801	323.9+/-316.2	186,1427,2687	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	292,2201,4009	TT,TC,CC		20.9186,22.3887,21.4165	,,,	677/739,1880/1942,653/715,829/891	1640793	2785,10219	2202	4300	6502	SO:0001819	synonymous_variant	124997	exon10			CGGCAGCGAGGTG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.5640C>T	17.37:g.1640793C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	191	86	0.450262	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			C|0.789;T|0.211	0.211	strong		0.597	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
OBP2A	29991	hgsc.bcm.edu	37	9	138439809	138439809	+	Missense_Mutation	SNP	T	T	C	rs72766544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:138439809T>C	ENST00000539850.1	+	4	396	c.370T>C	c.(370-372)Tac>Cac	p.Y124H	OBP2A_ENST00000342114.4_Missense_Mutation_p.L79P|OBP2A_ENST00000371776.1_Missense_Mutation_p.Y124H|OBP2A_ENST00000340780.3_Missense_Mutation_p.Y124H			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	124					response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		GGGCCTGCGCTACATGGGAAA	0.617													.|||	773	0.154353	0.0582	0.134	5008	,	,		16945	0.1567		0.2525	False		,,,				2504	0.1953				p.Y124H		Atlas-SNP	.											.	OBP2A	21	.	0			c.T370C						PASS	.	C	HIS/TYR	410,3996	785.5+/-414.8	34,342,1827	41.0	38.0	39.0		370	-0.1	0.0	9	dbSNP_130	39	2253,6347	706.1+/-405.5	302,1649,2349	yes	missense	OBP2A	NM_014582.2	83	336,1991,4176	CC,CT,TT		26.1977,9.3055,20.4752	benign	124/171	138439809	2663,10343	2203	4300	6503	SO:0001583	missense	29991	exon4			CTGCGCTACATGG	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.370T>C	9.37:g.138439809T>C	ENSP00000441028:p.Tyr124His	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	94	54	0.574468	NM_014582	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Missense_Mutation	SNP	ENST00000539850.1	37	CCDS6992.1	369|369	0.16895604395604397|0.16895604395604397	34|34	0.06910569105691057|0.06910569105691057	60|60	0.16574585635359115|0.16574585635359115	82|82	0.14335664335664336|0.14335664335664336	193|193	0.2546174142480211|0.2546174142480211	c|c	0.004|0.004	-2.310517|-2.310517	0.00237|0.00237	0.093055|0.093055	0.261977|0.261977	ENSG00000122136|ENSG00000122136	ENST00000342114|ENST00000340780;ENST00000371776;ENST00000539850	T|T;T;T	0.09073|0.10960	3.02|2.82;3.01;3.01	2.25|2.25	-0.0665|-0.0665	0.13764|0.13764	.|Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.|0.858893	.|0.09691	.|N	.|0.768386	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01048|0.01048	-1.04|-1.04	0.80722|0.80722	P|P	0.0|0.0	B|B;B	0.02656|0.02656	0.0|0.0;0.0	B|B;B	0.01281|0.04013	0.0|0.001;0.001	T|T	0.45205|0.45205	-0.9277|-0.9277	8|9	0.35671|0.10902	T|T	0.21|0.67	-0.9531|-0.9531	1.1399|1.1399	0.01763|0.01763	0.1961:0.3382:0.3111:0.1546|0.1961:0.3382:0.3111:0.1546	.|.	79|124;124	Q5T8A4|Q5T8A5;Q9NY56	.|.;OBP2A_HUMAN	P|H	79|124	ENSP00000340950:L79P|ENSP00000342097:Y124H;ENSP00000360841:Y124H;ENSP00000441028:Y124H	ENSP00000340950:L79P|ENSP00000342097:Y124H	L|Y	+|+	2|1	0|0	OBP2A|OBP2A	137579630|137579630	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-2.078000|-2.078000	0.01370|0.01370	-0.350000|-0.350000	0.08262|0.08262	-1.623000|-1.623000	0.00790|0.00790	CTA|TAC	T|0.804;C|0.196	0.196	strong		0.617	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582	
APEH	327	hgsc.bcm.edu	37	3	49721532	49721532	+	IGR	SNP	G	G	A	rs3197999	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49721532G>A	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Missense_Mutation_p.R703C	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.R689C(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCTGGCCAGCGGGACCTTGCG	0.567													G|||	961	0.191893	0.2179	0.1686	5008	,	,		20686	0.0565		0.3131	False		,,,				2504	0.1881				p.R703C		Atlas-SNP	.											MST1,NS,carcinoma,0,1	MST1	84	1	1	Substitution - Missense(1)	stomach(1)	c.C2107T						PASS	.	G	CYS/ARG	1036,3370	380.4+/-323.7	120,796,1287	64.0	61.0	62.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2107	-2.8	0.1	3	dbSNP_105	62	2525,6075	411.6+/-350.5	385,1755,2160	yes	missense	MST1	NM_020998.3	180	505,2551,3447	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	29.3605,23.5134,27.3797	possibly-damaging	703/726	49721532	3561,9445	2203	4300	6503	SO:0001628	intergenic_variant	4485	exon18			GCCAGCGGGACCT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49721532G>A		Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	379	170	0.448549	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	472|472	0.21611721611721613|0.21611721611721613	119|119	0.241869918699187|0.241869918699187	81|81	0.22375690607734808|0.22375690607734808	37|37	0.06468531468531469|0.06468531468531469	235|235	0.3100263852242744|0.3100263852242744	G|G	17.19|17.19	3.327308|3.327308	0.60743|0.60743	0.235134|0.235134	0.293605|0.293605	ENSG00000173531|ENSG00000173531	ENST00000448220|ENST00000449682	.|D	.|0.89196	.|-2.48	5.59|5.59	-2.82|-2.82	0.05787|0.05787	.|.	.|0.559462	.|0.14941	.|N	.|0.289511	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.74389|0.74389	2.26|2.26	0.46298|0.46298	P|P	0.0010210000000000496|0.0010210000000000496	.|P	.|0.40681	.|0.727	.|B	.|0.40702	.|0.338	T|T	0.21280|0.21280	-1.0250|-1.0250	4|9	.|0.66056	.|D	.|0.02	.|.	12.6939|12.6939	0.56992|0.56992	0.07:0.7015:0.147:0.0815|0.07:0.7015:0.147:0.0815	rs3197999;rs52793577;rs60772290;rs3197999|rs3197999;rs52793577;rs60772290;rs3197999	.|703	.|G3XAK1	.|.	L|C	172|703	.|ENSP00000414287:R703C	.|ENSP00000414287:R703C	P|R	-|-	2|1	0|0	MST1|MST1	49696536|49696536	0.511000|0.511000	0.26179|0.26179	0.123000|0.123000	0.21794|0.21794	0.860000|0.860000	0.49131|0.49131	1.075000|1.075000	0.30716|0.30716	-0.545000|-0.545000	0.06224|0.06224	0.655000|0.655000	0.94253|0.94253	CCG|CGC	G|0.749;A|0.251	0.251	strong		0.567	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
FAT2	2196	hgsc.bcm.edu	37	5	150946773	150946773	+	Missense_Mutation	SNP	G	G	A	rs1432862	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150946773G>A	ENST00000261800.5	-	1	1732	c.1720C>T	c.(1720-1722)Cgc>Tgc	p.R574C		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	574	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> C (in dbSNP:rs1432862).		epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAGTCTTGGCGGATAGACCCT	0.448													G|||	2093	0.417931	0.4365	0.4524	5008	,	,		20289	0.3562		0.4901	False		,,,				2504	0.3579				p.R574C		Atlas-SNP	.											.	FAT2	465	.	0			c.C1720T						PASS	.	G	CYS/ARG	1936,2470	543.6+/-376.3	413,1110,680	73.0	77.0	76.0		1720	4.3	0.0	5	dbSNP_88	76	4501,4099	589.1+/-392.5	1184,2133,983	yes	missense	FAT2	NM_001447.2	180	1597,3243,1663	AA,AG,GG		47.6628,43.9401,49.4925	probably-damaging	574/4350	150946773	6437,6569	2203	4300	6503	SO:0001583	missense	2196	exon1			CTTGGCGGATAGA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.1720C>T	5.37:g.150946773G>A	ENSP00000261800:p.Arg574Cys	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	177	173	0.977401	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	965	0.44184981684981683	234	0.47560975609756095	162	0.44751381215469616	201	0.3513986013986014	368	0.48548812664907653	G	12.72	2.022637	0.35701	0.439401	0.523372	ENSG00000086570	ENST00000261800	T	0.51071	0.72	5.22	4.33	0.51752	Cadherin (3);Cadherin-like (1);	0.788007	0.11570	N	0.550832	T	0.00012	0.0000	M	0.62723	1.935	0.24939	P	0.99186287	D	0.61697	0.99	P	0.51101	0.659	T	0.46952	-0.9154	9	0.66056	D	0.02	.	15.6599	0.77178	0.0:0.1377:0.8623:0.0	rs1432862;rs61018396;rs1432862	574	Q9NYQ8	FAT2_HUMAN	C	574	ENSP00000261800:R574C	ENSP00000261800:R574C	R	-	1	0	FAT2	150926966	1.000000	0.71417	0.027000	0.17364	0.064000	0.16182	6.638000	0.74309	1.148000	0.42385	0.655000	0.94253	CGC	G|0.528;A|0.472	0.472	strong		0.448	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
DCHS2	54798	hgsc.bcm.edu	37	4	155241572	155241572	+	Missense_Mutation	SNP	G	G	A	rs11935573	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:155241572G>A	ENST00000357232.4	-	14	3613	c.3614C>T	c.(3613-3615)tCa>tTa	p.S1205L		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1205	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> L (in dbSNP:rs11935573).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S1205L(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TTCATTTCCTGAGAGGATGCT	0.393													G|||	1317	0.262979	0.0613	0.2997	5008	,	,		22015	0.3552		0.3161	False		,,,				2504	0.3599				p.S1205L		Atlas-SNP	.											DCHS2,NS,carcinoma,0,2	DCHS2	594	2	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.C3614T						PASS	.	G	LEU/SER	461,3945	219.1+/-236.9	25,411,1767	186.0	168.0	174.0		3614	5.6	1.0	4	dbSNP_120	174	2792,5808	442.8+/-360.2	457,1878,1965	yes	missense	DCHS2	NM_017639.3	145	482,2289,3732	AA,AG,GG		32.4651,10.463,25.0115	probably-damaging	1205/2917	155241572	3253,9753	2203	4300	6503	SO:0001583	missense	54798	exon14			TTTCCTGAGAGGA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.3614C>T	4.37:g.155241572G>A	ENSP00000349768:p.Ser1205Leu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	229	116	0.50655	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	597	0.2733516483516483	25	0.0508130081300813	115	0.31767955801104975	210	0.36713286713286714	247	0.3258575197889182	G	24.6	4.548489	0.86127	0.10463	0.324651	ENSG00000197410	ENST00000357232	T	0.43294	0.95	5.56	5.56	0.83823	Cadherin (4);Cadherin-like (1);	0.455087	0.18369	N	0.143322	T	0.00012	0.0000	M	0.76328	2.33	0.09310	P	1.0	D	0.71674	0.998	P	0.61592	0.891	T	0.26643	-1.0097	9	0.54805	T	0.06	.	14.3837	0.66929	0.0:0.0:0.8522:0.1478	rs11935573;rs52822939;rs61644114;rs11935573	1205	Q6V1P9	PCD23_HUMAN	L	1205	ENSP00000349768:S1205L	ENSP00000349768:S1205L	S	-	2	0	DCHS2	155461022	0.953000	0.32496	1.000000	0.80357	0.965000	0.64279	4.281000	0.58965	2.619000	0.88677	0.467000	0.42956	TCA	G|0.746;A|0.254	0.254	strong		0.393	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
BTNL2	56244	hgsc.bcm.edu	37	6	32370835	32370835	+	Missense_Mutation	SNP	T	T	C	rs2076523	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32370835T>C	ENST00000374993.1	-	3	585	c.586A>G	c.(586-588)Aaa>Gaa	p.K196E	BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000454136.3_Missense_Mutation_p.K196E|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000374995.3_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	196	Ig-like V-type 2.		K -> E (in dbSNP:rs2076523). {ECO:0000269|PubMed:14574404}.			integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						AGGCCATCTTTATCTTGGATG	0.582													C|||	1985	0.396366	0.3222	0.4683	5008	,	,		19213	0.4296		0.3738	False		,,,				2504	0.4346				p.K196E		Atlas-SNP	.											.	BTNL2	50	.	0			c.A586G						PASS	.	C	GLU/LYS	918,2104		130,658,723	95.0	85.0	89.0		586	2.6	0.2	6	dbSNP_96	89	2003,3415		355,1293,1061	yes	missense	BTNL2	NM_019602.1	56	485,1951,1784	CC,CT,TT		36.9694,30.3772,34.609	benign	196/456	32370835	2921,5519	1511	2709	4220	SO:0001583	missense	56244	exon3			CATCTTTATCTTG	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.586A>G	6.37:g.32370835T>C	ENSP00000364132:p.Lys196Glu	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	195	94	0.482051	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		809	0.37042124542124544	120	0.24390243902439024	166	0.4585635359116022	240	0.4195804195804196	283	0.3733509234828496	C	0.081	-1.183977	0.01620	0.303772	0.369694	ENSG00000204290	ENST00000468270;ENST00000374993	T	0.73047	-0.71	4.44	2.64	0.31445	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.664405	0.13534	N	0.380721	T	0.07593	0.0191	N	0.00082	-2.215	0.21386	P	0.999700183	B	0.02656	0.0	B	0.01281	0.0	T	0.27191	-1.0081	9	0.02654	T	1	.	7.2001	0.25877	0.0:0.7129:0.0:0.2871	rs2076523;rs17202477;rs17423837;rs52819568;rs61040622;rs2076523	196	Q9UIR0	BTNL2_HUMAN	E	196	ENSP00000364132:K196E	ENSP00000364132:K196E	K	-	1	0	BTNL2	32478813	0.000000	0.05858	0.230000	0.23976	0.377000	0.30045	-0.047000	0.11963	0.244000	0.21351	-0.188000	0.12872	AAA	T|0.648;C|0.352	0.352	strong		0.582	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
ZNF773	374928	hgsc.bcm.edu	37	19	58017754	58017754	+	Silent	SNP	A	A	G	rs386811330|rs61737910	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58017754A>G	ENST00000282292.4	+	4	431	c.291A>G	c.(289-291)gcA>gcG	p.A97A	ZNF773_ENST00000598770.1_Silent_p.A96A|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	97					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)		AGGCTGAGGCAGCTGCTGAGC	0.483													G|||	859	0.171526	0.2716	0.1484	5008	,	,		22829	0.1002		0.2018	False		,,,				2504	0.0951				p.A97A		Atlas-SNP	.											.	ZNF773	62	.	0			c.A291G						PASS	.						84.0	88.0	87.0					19																	58017754		2203	4300	6503	SO:0001819	synonymous_variant	374928	exon4			TGAGGCAGCTGCT	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"""Zinc fingers, C2H2-type"", ""-"""	30487	protein-coding gene	gene with protein product			"""zinc finger protein 419B"""	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.291A>G	19.37:g.58017754A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_198542	Q96DL8	Silent	SNP	ENST00000282292.4	37	CCDS33134.1																																																																																			A|0.834;G|0.166	0.166	strong		0.483	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542	
ANKRD12	23253	hgsc.bcm.edu	37	18	9255982	9255982	+	Missense_Mutation	SNP	A	A	G	rs4798791	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:9255982A>G	ENST00000262126.4	+	9	2957	c.2717A>G	c.(2716-2718)aAg>aGg	p.K906R	ANKRD12_ENST00000383440.2_Missense_Mutation_p.K883R|ANKRD12_ENST00000400020.3_Missense_Mutation_p.K883R	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	906			K -> R (in dbSNP:rs4798791). {ECO:0000269|PubMed:17974005}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						AGTAGAGAAAAGATGGATAGG	0.348													A|||	3072	0.613419	0.3835	0.7104	5008	,	,		17420	0.6607		0.6581	False		,,,				2504	0.7607				p.K906R		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A2717G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	1798,2602		370,1058,772	44.0	45.0	45.0		2648,2648,2717	5.6	1.0	18	dbSNP_111	45	5283,3303		1660,1963,670	yes	missense,missense,missense	ANKRD12	NM_001083625.2,NM_001204056.1,NM_015208.4	26,26,26	2030,3021,1442	GG,GA,AA		38.4696,40.8636,45.472	probably-damaging,probably-damaging,probably-damaging	883/2040,883/2040,906/2063	9255982	7081,5905	2200	4293	6493	SO:0001583	missense	23253	exon9			GAGAAAAGATGGA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.2717A>G	18.37:g.9255982A>G	ENSP00000262126:p.Lys906Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	90	55	0.611111	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	1276	0.5842490842490843	186	0.3780487804878049	238	0.6574585635359116	358	0.6258741258741258	494	0.6517150395778364	A	15.28	2.787958	0.49997	0.408636	0.615304	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.37058	1.22;1.22	5.55	5.55	0.83447	.	0.047619	0.85682	D	0.000000	T	0.00012	0.0000	L	0.34521	1.04	0.18873	P	0.9999845786	P;P	0.45474	0.859;0.779	B;B	0.42555	0.391;0.219	T	0.30031	-0.9992	9	0.51188	T	0.08	-16.5632	15.691	0.77453	1.0:0.0:0.0:0.0	rs4798791;rs17498857;rs59415891;rs4798791	883;906	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	R	883;906	ENSP00000372932:K883R;ENSP00000262126:K906R	ENSP00000262126:K906R	K	+	2	0	ANKRD12	9245982	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	5.872000	0.69636	2.106000	0.64143	0.455000	0.32223	AAG	A|0.446;G|0.554	0.554	strong		0.348	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
FCGBP	8857	hgsc.bcm.edu	37	19	40399383	40399383	+	Silent	SNP	T	T	C	rs138090709		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40399383T>C	ENST00000221347.6	-	13	6319	c.6312A>G	c.(6310-6312)ggA>ggG	p.G2104G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2104	VWFD 5. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCAAGGGTGGTCCGTGGCAGG	0.597																																					p.G2104G		Atlas-SNP	.											FCGBP,NS,carcinoma,-2,2	FCGBP	416	2	0			c.A6312G						scavenged	.	T		120,2044		0,120,962	8.0	11.0	10.0		6312	-6.0	0.0	19	dbSNP_134	10	158,4042		0,158,1942	no	coding-synonymous	FCGBP	NM_003890.2		0,278,2904	CC,CT,TT		3.7619,5.5453,4.3683		2104/5406	40399383	278,6086	1082	2100	3182	SO:0001819	synonymous_variant	8857	exon13			GGGTGGTCCGTGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.6312A>G	19.37:g.40399383T>C		Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	249	43	0.172691	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			T|1.000;C|0.000	0.000	weak		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
THBS4	7060	hgsc.bcm.edu	37	5	79374957	79374957	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:79374957C>T	ENST00000350881.2	+	19	2577	c.2387C>T	c.(2386-2388)gCa>gTa	p.A796V	THBS4_ENST00000504720.1_3'UTR|THBS4_ENST00000511733.1_Missense_Mutation_p.A705V|CTD-2201I18.1_ENST00000503007.1_RNA|CTD-2201I18.1_ENST00000514042.1_RNA	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	796	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		GATGACTATGCAGGCTTTATC	0.473																																					p.A796V		Atlas-SNP	.											.	THBS4	82	.	0			c.C2387T						PASS	.						138.0	128.0	131.0					5																	79374957		2203	4300	6503	SO:0001583	missense	7060	exon19			ACTATGCAGGCTT		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.2387C>T	5.37:g.79374957C>T	ENSP00000339730:p.Ala796Val	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	229	125	0.545852	NM_003248	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	37	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.987130	0.93106	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	D;D	0.94280	-3.39;-3.39	5.06	5.06	0.68205	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.91181	0.7222	N	0.16478	0.41	0.80722	D	1	D	0.71674	0.998	P	0.53266	0.722	D	0.89639	0.3861	10	0.25751	T	0.34	-23.1552	18.977	0.92742	0.0:1.0:0.0:0.0	.	796	P35443	TSP4_HUMAN	V	796;705	ENSP00000339730:A796V;ENSP00000422298:A705V	ENSP00000339730:A796V	A	+	2	0	THBS4	79410713	1.000000	0.71417	0.858000	0.33744	0.991000	0.79684	7.609000	0.82925	2.782000	0.95742	0.655000	0.94253	GCA	.	.	none		0.473	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1		
NEFH	4744	hgsc.bcm.edu	37	22	29886413	29886413	+	Silent	SNP	A	A	G	rs165625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29886413A>G	ENST00000310624.6	+	4	2817	c.2784A>G	c.(2782-2784)gtA>gtG	p.V928V		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	934	Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGACAGAGGTAGCCAAGAAGG	0.517													G|||	4259	0.850439	0.8699	0.7695	5008	,	,		18828	0.9256		0.7694	False		,,,				2504	0.8875				p.V928V		Atlas-SNP	.											.	NEFH	178	.	0			c.A2784G						PASS	.	G		3676,730	299.0+/-285.6	1540,596,67	89.0	88.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2784	3.5	1.0	22	dbSNP_79	88	6740,1860	327.3+/-317.8	2638,1464,198	no	coding-synonymous	NEFH	NM_021076.3		4178,2060,265	GG,GA,AA		21.6279,16.5683,19.9139		928/1021	29886413	10416,2590	2203	4300	6503	SO:0001819	synonymous_variant	4744	exon4			AGAGGTAGCCAAG		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2784A>G	22.37:g.29886413A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	99	96	0.969697	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			A|0.186;G|0.814	0.814	strong		0.517	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
MSGN1	343930	hgsc.bcm.edu	37	2	17998095	17998095	+	Missense_Mutation	SNP	C	C	T	rs35858730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:17998095C>T	ENST00000281047.3	+	1	333	c.310C>T	c.(310-312)Cac>Tac	p.H104Y		NM_001105569.1	NP_001099039.1	A6NI15	MSGN1_HUMAN	mesogenin 1	104			H -> Y (in dbSNP:rs35858730).		cell differentiation (GO:0030154)|segment specification (GO:0007379)|somitogenesis (GO:0001756)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CCAGCCCACCCACCTTCAGGG	0.642													T|||	1482	0.295927	0.1884	0.3429	5008	,	,		18652	0.0278		0.5398	False		,,,				2504	0.4335				p.H104Y	Melanoma(127;325 1712 14802 40657 49130)	Atlas-SNP	.											MSGN1,NS,carcinoma,0,1	MSGN1	39	1	0			c.C310T						PASS	.	T	TYR/HIS	1015,3067		125,765,1151	30.0	38.0	36.0		310	5.8	0.1	2	dbSNP_126	36	4794,3576		1393,2008,784	yes	missense	MSGN1	NM_001105569.1	83	1518,2773,1935	TT,TC,CC		42.724,24.8653,46.6511	benign	104/194	17998095	5809,6643	2041	4185	6226	SO:0001583	missense	343930	exon1			CCCACCCACCTTC		CCDS42657.1	2p24.2	2007-07-23			ENSG00000151379	ENSG00000151379			14907	protein-coding gene	gene with protein product	"""paraxial mesogenin"""	612209				10837126	Standard	NM_001105569		Approved	pMesogenin1	uc010yjt.2	A6NI15	OTTHUMG00000159089	ENST00000281047.3:c.310C>T	2.37:g.17998095C>T	ENSP00000281047:p.His104Tyr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	132	130	0.984848	NM_001105569		Missense_Mutation	SNP	ENST00000281047.3	37	CCDS42657.1	666	0.30494505494505497	96	0.1951219512195122	143	0.39502762430939226	17	0.02972027972027972	410	0.5408970976253298	T	0	-2.614259	0.00120	0.248653	0.57276	ENSG00000151379	ENST00000281047	T	0.16324	2.35	5.77	5.77	0.91146	.	0.301187	0.28901	N	0.013765	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37596	-0.9699	9	0.13470	T	0.59	-25.2315	8.8701	0.35311	0.0:0.2062:0.0:0.7938	rs35858730;rs62130917	104	A6NI15	MSGN1_HUMAN	Y	104	ENSP00000281047:H104Y	ENSP00000281047:H104Y	H	+	1	0	MSGN1	17861576	0.024000	0.19004	0.066000	0.19879	0.062000	0.15995	1.350000	0.34010	1.020000	0.39573	-0.254000	0.11334	CAC	C|0.602;T|0.398	0.398	strong		0.642	MSGN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353253.1	XM_292850	
NXPE1	120400	hgsc.bcm.edu	37	11	114401247	114401247	+	Silent	SNP	A	A	G	rs7941796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:114401247A>G	ENST00000424269.1	-	2	482	c.483T>C	c.(481-483)aaT>aaC	p.N161N	NXPE1_ENST00000536312.1_Silent_p.N161N|NXPE1_ENST00000251921.2_Silent_p.N19N|NXPE1_ENST00000536271.1_5'Flank			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	161						extracellular region (GO:0005576)											GGTAGGTGCCATTGTTGAAGT	0.592													G|||	1301	0.259784	0.5756	0.2493	5008	,	,		18529	0.0		0.1332	False		,,,				2504	0.2382				p.N19N		Atlas-SNP	.											FAM55A,NS,neuroblastoma,-1,1	NXPE1	8	1	0			c.T57C						PASS	.	G		2217,2185	585.8+/-386.3	559,1099,543	81.0	86.0	84.0		57	-8.8	0.4	11	dbSNP_116	84	1193,7399	763.7+/-407.6	97,999,3200	yes	coding-synonymous	FAM55A	NM_152315.2		656,2098,3743	GG,GA,AA		13.885,49.6365,26.2429		19/406	114401247	3410,9584	2201	4296	6497	SO:0001819	synonymous_variant	120400	exon3			GGTGCCATTGTTG	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member A"""	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.483T>C	11.37:g.114401247A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	170	90	0.529412	NM_152315	B0YJ13	Silent	SNP	ENST00000424269.1	37																																																																																				A|0.758;G|0.242	0.242	strong		0.592	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315	
MRPL14	64928	hgsc.bcm.edu	37	6	44081718	44081718	+	Silent	SNP	G	G	A	rs6883	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:44081718G>A	ENST00000372014.3	-	3	431	c.300C>T	c.(298-300)ttC>ttT	p.F100F		NM_032111.2	NP_115487.2	Q6P1L8	RM14_HUMAN	mitochondrial ribosomal protein L14	100					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	12	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0181)			TGTTGGAGTCGAATCTGGGGG	0.587													G|||	3356	0.670128	0.8079	0.719	5008	,	,		18173	0.7857		0.495	False		,,,				2504	0.5102				p.F100F		Atlas-SNP	.											.	MRPL14	15	.	0			c.C300T						PASS	.	G		3349,1057	725.1+/-409.6	1269,811,123	97.0	100.0	99.0		300	-10.0	0.3	6	dbSNP_52	99	4304,4296	578.3+/-390.7	1079,2146,1075	no	coding-synonymous	MRPL14	NM_032111.2		2348,2957,1198	AA,AG,GG		49.9535,23.99,41.1579		100/146	44081718	7653,5353	2203	4300	6503	SO:0001819	synonymous_variant	64928	exon3			GGAGTCGAATCTG	AB051339	CCDS34460.1	6p21.3	2012-09-13			ENSG00000180992	ENSG00000180992		"""Mitochondrial ribosomal proteins / large subunits"""	14279	protein-coding gene	gene with protein product		611827					Standard	XM_005249300		Approved	RPML32, MRP-L32	uc003owp.3	Q6P1L8	OTTHUMG00000014756	ENST00000372014.3:c.300C>T	6.37:g.44081718G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_032111	B2R575|Q96Q72	Silent	SNP	ENST00000372014.3	37	CCDS34460.1																																																																																			G|0.365;A|0.635	0.635	strong		0.587	MRPL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040707.1	NM_032111	
GGT1	2678	hgsc.bcm.edu	37	22	25023893	25023893	+	Missense_Mutation	SNP	G	G	A	rs201313233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25023893G>A	ENST00000400382.1	+	13	2038	c.1283G>A	c.(1282-1284)aGc>aAc	p.S428N	GGT1_ENST00000403838.1_Missense_Mutation_p.S84N|GGT1_ENST00000401885.1_Missense_Mutation_p.S84N|GGT1_ENST00000406383.2_Missense_Mutation_p.S428N|GGT1_ENST00000404532.1_Missense_Mutation_p.S84N|GGT1_ENST00000400380.1_Missense_Mutation_p.S428N|GGT1_ENST00000404223.1_Missense_Mutation_p.S84N|GGT1_ENST00000248923.4_Missense_Mutation_p.S428N|GGT1_ENST00000404920.1_Missense_Mutation_p.S84N|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400383.1_Missense_Mutation_p.S428N			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	428					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.S428N(8)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	AGCTCTCCCAGCATCACCAAC	0.617																																					p.S428N		Atlas-SNP	.											GGT1,scalp,carcinoma,0,10	GGT1	68	10	8	Substitution - Missense(8)	kidney(7)|skin(1)	c.G1283A						scavenged	.						75.0	81.0	79.0					22																	25023893		2203	4300	6503	SO:0001583	missense	2678	exon13			CTCCCAGCATCAC	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1283G>A	22.37:g.25023893G>A	ENSP00000383232:p.Ser428Asn	Somatic	464	0	0		WXS	Illumina HiSeq	Phase_I	472	7	0.0148305	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	0.007	-1.994474	0.00435	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18	3.49	0.971	0.19698	.	0.677608	0.14536	N	0.313585	T	0.01800	0.0057	N	0.00855	-1.145	0.19300	N	0.999979	B	0.02656	0.0	B	0.06405	0.002	T	0.44757	-0.9307	10	0.08179	T	0.78	-26.6577	2.7873	0.05377	0.5605:0.0:0.2509:0.1886	.	428	P19440	GGT1_HUMAN	N	428;428;428;428;428;428;84;84;84;84;84	ENSP00000248923:S428N;ENSP00000393537:S428N;ENSP00000383232:S428N;ENSP00000383233:S428N;ENSP00000383231:S428N;ENSP00000385975:S428N;ENSP00000384381:S84N;ENSP00000385445:S84N;ENSP00000384820:S84N;ENSP00000385016:S84N;ENSP00000385001:S84N	ENSP00000248923:S428N	S	+	2	0	GGT1	23353893	0.005000	0.15991	0.993000	0.49108	0.013000	0.08279	0.113000	0.15499	0.084000	0.17077	-0.708000	0.03648	AGC	G|0.983;A|0.017	0.017	strong		0.617	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
LILRB4	11006	hgsc.bcm.edu	37	19	55178162	55178162	+	Missense_Mutation	SNP	A	A	G	rs11574576	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55178162A>G	ENST00000391736.1	+	12	1318	c.1003A>G	c.(1003-1005)Aac>Gac	p.N335D	LILRB4_ENST00000430952.2_Missense_Mutation_p.N335D|LILRB4_ENST00000391734.3_Missense_Mutation_p.N335D|LILRB4_ENST00000391733.3_Missense_Mutation_p.N336D|LILRB4_ENST00000270452.2_Missense_Mutation_p.N335D	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	335			N -> D (in dbSNP:rs11574576).		immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		TGCCGTGAAGAACACACAGCC	0.612													A|||	2247	0.448682	0.4395	0.3429	5008	,	,		17280	0.5615		0.2903	False		,,,				2504	0.5828				p.N335D		Atlas-SNP	.											.	LILRB4	86	.	0			c.A1003G						PASS	.	A	ASP/ASN,ASP/ASN	1749,2657	521.1+/-370.4	367,1015,821	125.0	113.0	117.0		1003,1003	-3.5	0.0	19	dbSNP_120	117	2451,6149	405.5+/-348.5	339,1773,2188	yes	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	23,23	706,2788,3009	GG,GA,AA		28.5,39.6959,32.2928	benign,benign	335/448,335/449	55178162	4200,8806	2203	4300	6503	SO:0001583	missense	11006	exon10			GTGAAGAACACAC	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1003A>G	19.37:g.55178162A>G	ENSP00000375616:p.Asn335Asp	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	143	59	0.412587	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	895	0.4097985347985348	215	0.4369918699186992	111	0.30662983425414364	337	0.5891608391608392	232	0.30606860158311344	A	0.007	-2.003554	0.00431	0.396959	0.285	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00454	7.33;7.33;7.34;7.32;7.35;7.36	1.9	-3.45	0.04781	.	.	.	.	.	T	0.00012	0.0000	N	0.00332	-1.63	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.001;0.0	T	0.24476	-1.0159	8	0.02654	T	1	.	6.5292	0.22318	0.6493:0.0:0.3507:0.0	rs11574576;rs13343440;rs52815740;rs59068627;rs11574576	335;334;336;335;335	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;.;LIRB4_HUMAN	D	335;335;335;335;336;334	ENSP00000375616:N335D;ENSP00000270452:N335D;ENSP00000408995:N335D;ENSP00000375614:N335D;ENSP00000375613:N336D;ENSP00000401962:N334D	ENSP00000270452:N335D	N	+	1	0	LILRB4	59869974	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	0.001000	0.13038	-0.842000	0.04195	-0.330000	0.08379	AAC	A|0.646;C|0.000;G|0.354	0.354	strong		0.612	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
LAPTM5	7805	hgsc.bcm.edu	37	1	31215364	31215364	+	Silent	SNP	T	T	C	rs1050663	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:31215364T>C	ENST00000294507.3	-	2	194	c.120A>G	c.(118-120)tcA>tcG	p.S40S	LAPTM5_ENST00000476492.1_5'UTR	NM_006762.2	NP_006753.1	Q13571	LAPM5_HUMAN	lysosomal protein transmembrane 5	40					transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)				large_intestine(2)|lung(7)|skin(1)	10		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)		CCACCTCTACTGAGTGCTCGA	0.627													C|||	3028	0.604633	0.6188	0.6873	5008	,	,		20227	0.6716		0.5258	False		,,,				2504	0.5389				p.S40S		Atlas-SNP	.											LAPTM5,NS,carcinoma,0,1	LAPTM5	30	1	0			c.A120G						PASS	.	C		2610,1796	528.7+/-372.5	758,1094,351	80.0	65.0	70.0		120	-10.1	0.0	1	dbSNP_86	70	4194,4406	584.1+/-391.7	1001,2192,1107	no	coding-synonymous	LAPTM5	NM_006762.2		1759,3286,1458	CC,CT,TT		48.7674,40.7626,47.6857		40/263	31215364	6804,6202	2203	4300	6503	SO:0001819	synonymous_variant	7805	exon2			CTCTACTGAGTGC	U51240	CCDS337.1	1p34	2009-07-20	2009-07-20		ENSG00000162511	ENSG00000162511			29612	protein-coding gene	gene with protein product		601476	"""lysosomal multispanning membrane protein 5"""			8661146, 12527926	Standard	NM_006762		Approved		uc001bsc.2	Q13571	OTTHUMG00000003707	ENST00000294507.3:c.120A>G	1.37:g.31215364T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_006762	Q13240|Q14698|Q3KP54	Silent	SNP	ENST00000294507.3	37	CCDS337.1																																																																																			T|0.442;G|0.000;C|0.558	0.558	strong		0.627	LAPTM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010463.1	NM_006762	
EFCAB7	84455	hgsc.bcm.edu	37	1	63999826	63999826	+	Missense_Mutation	SNP	C	C	T	rs6693255	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:63999826C>T	ENST00000371088.4	+	6	989	c.743C>T	c.(742-744)aCa>aTa	p.T248I	RNU7-123P_ENST00000515911.1_RNA	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	248			T -> I (in dbSNP:rs6693255). {ECO:0000269|PubMed:15489334}.				calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						GTTTCCTTCACAGTTACCATG	0.353													C|||	726	0.144968	0.0855	0.1614	5008	,	,		15556	0.1855		0.1441	False		,,,				2504	0.1728				p.T248I		Atlas-SNP	.											EFCAB7,NS,carcinoma,+1,1	EFCAB7	45	1	0			c.C743T						PASS	.	C	ILE/THR	393,4013	195.0+/-219.7	13,367,1823	100.0	98.0	98.0		743	1.5	1.0	1	dbSNP_116	98	1325,7275	260.5+/-283.3	92,1141,3067	yes	missense	EFCAB7	NM_032437.2	89	105,1508,4890	TT,TC,CC		15.407,8.9197,13.2093	benign	248/630	63999826	1718,11288	2203	4300	6503	SO:0001583	missense	84455	exon6			CCTTCACAGTTAC	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.743C>T	1.37:g.63999826C>T	ENSP00000360129:p.Thr248Ile	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	219	100	0.456621	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	325	0.1488095238095238	51	0.10365853658536585	61	0.1685082872928177	105	0.18356643356643357	108	0.1424802110817942	C	3.616	-0.078505	0.07184	0.089197	0.15407	ENSG00000203965	ENST00000371088	T	0.58652	0.32	5.65	1.49	0.22878	.	0.529823	0.23072	N	0.052243	T	0.25269	0.0614	L	0.47716	1.5	0.21719	P	0.999579407	B	0.30763	0.294	B	0.26517	0.07	T	0.06356	-1.0831	9	0.72032	D	0.01	-5.8298	4.209	0.10502	0.1277:0.5984:0.1245:0.1495	rs6693255;rs17856494;rs52831553;rs56659953;rs6693255	248	A8K855	EFCB7_HUMAN	I	248	ENSP00000360129:T248I	ENSP00000360129:T248I	T	+	2	0	EFCAB7	63772414	0.160000	0.22878	0.976000	0.42696	0.393000	0.30537	0.578000	0.23773	0.744000	0.32741	-0.136000	0.14681	ACA	C|0.857;T|0.143	0.143	strong		0.353	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
DNMBP	23268	hgsc.bcm.edu	37	10	101715899	101715899	+	Silent	SNP	G	G	A	rs2862923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:101715899G>A	ENST00000324109.4	-	4	1423	c.1332C>T	c.(1330-1332)ccC>ccT	p.P444P	DNMBP-AS1_ENST00000434409.1_RNA|DNMBP_ENST00000342239.3_Silent_p.P444P	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	444					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		GAAGAAGGTCGGGGTACTGTT	0.502													A|||	2211	0.441494	0.6558	0.4352	5008	,	,		19500	0.2579		0.4175	False		,,,				2504	0.3701				p.P444P		Atlas-SNP	.											.	DNMBP	173	.	0			c.C1332T						PASS	.			2746,1660	506.6+/-366.4	858,1030,315	86.0	92.0	90.0		1332	0.6	0.0	10	dbSNP_101	90	3661,4939	621.1+/-397.1	757,2147,1396	no	coding-synonymous	DNMBP	NM_015221.2		1615,3177,1711	AA,AG,GG		42.5698,37.6759,49.2619		444/1578	101715899	6407,6599	2203	4300	6503	SO:0001819	synonymous_variant	23268	exon4			AAGGTCGGGGTAC	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.1332C>T	10.37:g.101715899G>A		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	102	93	0.911765	NM_015221	Q8IVY3|Q9Y2L3	Silent	SNP	ENST00000324109.4	37	CCDS7485.1																																																																																			G|0.534;A|0.466	0.466	strong		0.502	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
TOLLIP	54472	hgsc.bcm.edu	37	11	1309956	1309956	+	Silent	SNP	C	C	T	rs3750920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1309956C>T	ENST00000317204.6	-	4	540	c.417G>A	c.(415-417)ccG>ccA	p.P139P	TOLLIP_ENST00000527886.1_Silent_p.P70P|TOLLIP_ENST00000527938.1_Intron|TOLLIP_ENST00000542915.1_Silent_p.P89P|TOLLIP_ENST00000263646.7_Silent_p.P111P|TOLLIP_ENST00000528719.1_5'UTR|TOLLIP_ENST00000525159.1_Silent_p.P78P	NM_019009.3	NP_061882.2	Q9H0E2	TOLIP_HUMAN	toll interacting protein	139					autophagy (GO:0006914)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte activation (GO:0045321)|phosphorylation (GO:0016310)|positive regulation of protein sumoylation (GO:0033235)|protein localization to endosome (GO:0036010)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|interleukin-1 receptor complex (GO:0045323)|interleukin-18 receptor complex (GO:0045092)|nuclear body (GO:0016604)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|signal transducer activity (GO:0004871)|Toll-like receptor binding (GO:0035325)			large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	6		all_cancers(49;7.62e-05)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00152)|Lung(200;0.09)|LUSC - Lung squamous cell carcinoma(625;0.107)		TCAGGGACTCCGGGATGGTGA	0.637													c|||	1803	0.360024	0.2761	0.3415	5008	,	,		17466	0.3165		0.4573	False		,,,				2504	0.4315				p.P139P		Atlas-SNP	.											TOLLIP,NS,carcinoma,0,1	TOLLIP	25	1	0			c.G417A						scavenged	.			1317,3087	440.2+/-345.9	205,907,1090	157.0	96.0	117.0		417	-4.6	0.7	11	dbSNP_107	117	3776,4820	535.5+/-382.8	847,2082,1369	no	coding-synonymous	TOLLIP	NM_019009.3		1052,2989,2459	TT,TC,CC		43.9274,29.9046,39.1769		139/275	1309956	5093,7907	2202	4298	6500	SO:0001819	synonymous_variant	54472	exon4			GGACTCCGGGATG	AJ242972	CCDS7723.1	11p	2008-02-05			ENSG00000078902	ENSG00000078902			16476	protein-coding gene	gene with protein product		606277				9426216, 10854325	Standard	NM_019009		Approved	IL-1RAcPIP	uc001lte.3	Q9H0E2	OTTHUMG00000133333	ENST00000317204.6:c.417G>A	11.37:g.1309956C>T		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	128	52	0.40625	NM_019009	B3KXC6|Q9H9E6|Q9UJ69	Silent	SNP	ENST00000317204.6	37	CCDS7723.1																																																																																			C|0.625;T|0.375	0.375	strong		0.637	TOLLIP-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000257162.2	NM_019009	
LILRB1	10859	hgsc.bcm.edu	37	19	55145454	55145454	+	Missense_Mutation	SNP	G	G	A	rs1138736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55145454G>A	ENST00000396331.1	+	10	1699	c.1342G>A	c.(1342-1344)Ggg>Agg	p.G448R	LILRB1_ENST00000434867.2_Missense_Mutation_p.G448R|LILRB1_ENST00000396321.2_Missense_Mutation_p.G448R|LILRB1_ENST00000418536.2_Missense_Mutation_p.G432R|LILRB1_ENST00000396315.1_Missense_Mutation_p.G449R|LILRB1_ENST00000448689.1_Missense_Mutation_p.G448R|LILRB1_ENST00000396332.4_Missense_Mutation_p.G448R|LILRB1_ENST00000427581.2_Missense_Mutation_p.G485R|LILRB1_ENST00000324602.7_Missense_Mutation_p.G449R|LILRB1_ENST00000396317.1_Missense_Mutation_p.G432R|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000396327.3_Missense_Mutation_p.G449R	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	448					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CACCCCCACCGGGTCGGATCC	0.697										HNSCC(37;0.09)			g|||	527	0.105232	0.2012	0.0576	5008	,	,		13562	0.0139		0.1163	False		,,,				2504	0.092				p.G449R		Atlas-SNP	.											.	LILRB1	140	.	0			c.G1345A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	854,3536		90,674,1431	19.0	23.0	22.0		1345,1345,1342,1342	0.6	0.0	19	dbSNP_86	22	1009,7581		50,909,3336	no	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	125,125,125,125	140,1583,4767	AA,AG,GG		11.7462,19.4533,14.3529	benign,benign,benign,benign	449/653,449/652,448/652,448/651	55145454	1863,11117	2195	4295	6490	SO:0001583	missense	10859	exon9			CCCACCGGGTCGG	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1342G>A	19.37:g.55145454G>A	ENSP00000379622:p.Gly448Arg	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	179	101	0.564246	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	234	0.10714285714285714	121	0.2459349593495935	19	0.052486187845303865	9	0.015734265734265736	85	0.11213720316622691	g	0.071	-1.202897	0.01581	0.194533	0.117462	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.00492	7.14;7.06;7.01;7.14;7.09;7.08;7.14;7.14;7.08;7.06;7.08	1.66	0.586	0.17434	.	.	.	.	.	T	0.00012	0.0000	M	0.80183	2.485	0.80722	P	0.0	B;B;B;B;B;B	0.28512	0.023;0.017;0.101;0.11;0.171;0.214	B;B;B;B;B;B	0.21546	0.009;0.004;0.034;0.023;0.035;0.023	T	0.18681	-1.0329	8	0.10636	T	0.68	.	4.2958	0.10901	0.2166:0.0:0.7834:0.0	rs1138736;rs3202773	432;448;449;448;449;448	A8MVE2;D9IDM5;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;.;LIRB1_HUMAN	R	448;432;448;448;449;449;448;448;485;432;449	ENSP00000379614:G448R;ENSP00000391514:G432R;ENSP00000409968:G448R;ENSP00000379622:G448R;ENSP00000379618:G449R;ENSP00000315997:G449R;ENSP00000405243:G448R;ENSP00000379623:G448R;ENSP00000395004:G485R;ENSP00000379610:G432R;ENSP00000379608:G449R	ENSP00000315997:G449R	G	+	1	0	LILRB1	59837266	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.139000	0.10358	0.276000	0.22118	-1.051000	0.02340	GGG	G|0.895;A|0.105	0.105	strong		0.697	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
CACNA2D4	93589	hgsc.bcm.edu	37	12	1965211	1965211	+	Missense_Mutation	SNP	G	G	A	rs369720566		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:1965211G>A	ENST00000382722.5	-	22	2481	c.2119C>T	c.(2119-2121)Cgc>Tgc	p.R707C	CACNA2D4_ENST00000587995.1_Missense_Mutation_p.R682C|CACNA2D4_ENST00000539048.2_5'UTR|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.R643C|CACNA2D4_ENST00000585708.1_Missense_Mutation_p.R643C|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.R707C|CACNA2D4_ENST00000585732.1_Missense_Mutation_p.R568C	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	707					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GTGAGGAAGCGGATCATGGCC	0.547																																					p.R707C	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.C2119T						PASS	.	G	CYS/ARG	0,4086		0,0,2043	66.0	74.0	71.0		2119	3.3	0.8	12		71	1,8377		0,1,4188	no	missense	CACNA2D4	NM_172364.4	180	0,1,6231	AA,AG,GG		0.0119,0.0,0.0080	probably-damaging	707/1138	1965211	1,12463	2043	4189	6232	SO:0001583	missense	93589	exon22			GGAAGCGGATCAT	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.2119C>T	12.37:g.1965211G>A	ENSP00000372169:p.Arg707Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	37	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.188538	0.38609	0.0	1.19E-4	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.31510	1.49	4.2	3.29	0.37713	.	0.257496	0.39909	N	0.001236	T	0.48995	0.1531	M	0.76002	2.32	0.31211	N	0.698629	D;D	0.76494	0.997;0.999	P;P	0.61397	0.888;0.8	T	0.57963	-0.7720	10	0.66056	D	0.02	.	10.5365	0.45007	0.0:0.0:0.6495:0.3505	.	707;707	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	C	643;707;707	ENSP00000372169:R707C	ENSP00000280663:R707C	R	-	1	0	CACNA2D4	1835472	0.445000	0.25657	0.765000	0.31456	0.218000	0.24690	3.494000	0.53273	0.867000	0.35654	0.462000	0.41574	CGC	.	.	weak		0.547	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
PDZRN4	29951	hgsc.bcm.edu	37	12	41946539	41946539	+	Missense_Mutation	SNP	G	G	A	rs285584	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:41946539G>A	ENST00000402685.2	+	6	1293	c.1285G>A	c.(1285-1287)Ggc>Agc	p.G429S	PDZRN4_ENST00000298919.7_Missense_Mutation_p.G169S|PDZRN4_ENST00000539469.2_Missense_Mutation_p.G171S	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	429	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.		G -> S (in dbSNP:rs285584).				ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				AGAAGACACCGGCATTTATGT	0.488													G|||	835	0.166733	0.2557	0.1196	5008	,	,		18129	0.1081		0.159	False		,,,				2504	0.1483				p.G429S		Atlas-SNP	.											.	PDZRN4	346	.	0			c.G1285A						PASS	.	G	SER/GLY,SER/GLY	1055,3351	387.2+/-326.4	137,781,1285	126.0	112.0	116.0		1285,511	5.0	1.0	12	dbSNP_79	116	1387,7213	269.4+/-288.4	120,1147,3033	yes	missense,missense	PDZRN4	NM_001164595.1,NM_013377.3	56,56	257,1928,4318	AA,AG,GG		16.1279,23.9446,18.7759	possibly-damaging,possibly-damaging	429/1037,171/779	41946539	2442,10564	2203	4300	6503	SO:0001583	missense	29951	exon6			GACACCGGCATTT	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1285G>A	12.37:g.41946539G>A	ENSP00000384197:p.Gly429Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	37	CCDS53777.1	343	0.15705128205128205	113	0.22967479674796748	45	0.12430939226519337	61	0.10664335664335664	124	0.16358839050131926	G	35	5.461185	0.96240	0.239446	0.161279	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.56776	0.44;0.44;0.44	5.04	5.04	0.67666	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.62266	1.93	0.09310	P	0.99999786062	D;D;D	0.76494	0.999;0.999;0.998	D;D;P	0.68039	0.955;0.916;0.823	T	0.00209	-1.1917	9	0.87932	D	0	-43.9412	19.2682	0.93998	0.0:0.0:1.0:0.0	rs285584;rs287079;rs17129465;rs57627794;rs285584	429;169;171	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	S	429;171;169	ENSP00000384197:G429S;ENSP00000439990:G171S;ENSP00000298919:G169S	ENSP00000298919:G169S	G	+	1	0	PDZRN4	40232806	1.000000	0.71417	0.971000	0.41717	0.952000	0.60782	6.547000	0.73892	2.715000	0.92844	0.563000	0.77884	GGC	G|0.821;A|0.179	0.179	strong		0.488	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
LONP1	9361	hgsc.bcm.edu	37	19	5711930	5711930	+	Missense_Mutation	SNP	C	C	T	rs11085147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:5711930C>T	ENST00000360614.3	-	4	879	c.722G>A	c.(721-723)cGg>cAg	p.R241Q	LONP1_ENST00000593119.1_Missense_Mutation_p.R177Q|LONP1_ENST00000590729.1_Missense_Mutation_p.R127Q|LONP1_ENST00000540670.2_Missense_Mutation_p.R45Q|LONP1_ENST00000585374.1_Missense_Mutation_p.R127Q	NM_004793.2	NP_004784.2			lon peptidase 1, mitochondrial											breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CTTCTTGCCCCGCTTTGACTT	0.667													C|||	112	0.0223642	0.0008	0.0231	5008	,	,		17751	0.0		0.0865	False		,,,				2504	0.0082				p.M241K		Atlas-SNP	.											.	LONP1	66	.	0			c.T722A						PASS	.	C	GLN/ARG	91,4315	74.7+/-112.8	2,87,2114	42.0	43.0	43.0		722	2.5	0.9	19	dbSNP_120	43	788,7812	184.5+/-232.4	35,718,3547	yes	missense	LONP1	NM_004793.2	43	37,805,5661	TT,TC,CC		9.1628,2.0654,6.7584	possibly-damaging	241/960	5711930	879,12127	2203	4300	6503	SO:0001583	missense	9361	exon4			TTGCCCCGCTTTG	U02389	CCDS12148.1, CCDS62507.1, CCDS62508.1	19p13.2	2014-01-28	2006-10-20	2006-10-20	ENSG00000196365	ENSG00000196365		"""ATPases / AAA-type"", ""Serine peptidases / Serine peptidases"""	9479	protein-coding gene	gene with protein product		605490	"""protease, serine, 15"""	PRSS15		8248235, 8119403	Standard	NM_004793		Approved	LonHS, hLON, PIM1	uc002mcx.4	P36776		ENST00000360614.3:c.722G>A	19.37:g.5711930C>T	ENSP00000353826:p.Arg241Gln	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	88	54	0.613636	NM_004793		Missense_Mutation	SNP	ENST00000360614.3	37	CCDS12148.1	77	0.035256410256410256	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	65	0.08575197889182058	C	11.30	1.598303	0.28445	0.020654	0.091628	ENSG00000196365	ENST00000360614;ENST00000358403;ENST00000540670	T;T	0.24350	2.27;1.86	4.96	2.49	0.30216	Peptidase S16, lon N-terminal (2);	0.470012	0.21298	N	0.076859	T	0.00637	0.0021	L	0.39397	1.21	0.28293	P	0.9234656	B;B;B	0.24483	0.028;0.104;0.063	B;B;B	0.22753	0.041;0.025;0.031	T	0.06570	-1.0819	9	0.21540	T	0.41	-11.665	9.4982	0.39001	0.156:0.6922:0.1519:0.0	rs11085147;rs52791963;rs59635993;rs11085147	241;177;241	E5KMH8;Q8N8K8;P36776	.;.;LONM_HUMAN	Q	241;205;45	ENSP00000353826:R241Q;ENSP00000441523:R45Q	ENSP00000351177:R205Q	R	-	2	0	LONP1	5662930	0.996000	0.38824	0.883000	0.34634	0.042000	0.13812	3.527000	0.53517	2.297000	0.77311	0.555000	0.69702	CGG	C|0.947;T|0.053	0.053	strong		0.667	LONP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451662.1	NM_004793	
PLEC	5339	hgsc.bcm.edu	37	8	144995736	144995736	+	Silent	SNP	G	G	A	rs11777402	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144995736G>A	ENST00000322810.4	-	32	8833	c.8664C>T	c.(8662-8664)aaC>aaT	p.N2888N	PLEC_ENST00000398774.2_Silent_p.N2719N|PLEC_ENST00000345136.3_Silent_p.N2751N|PLEC_ENST00000354589.3_Silent_p.N2751N|PLEC_ENST00000354958.2_Silent_p.N2729N|PLEC_ENST00000436759.2_Silent_p.N2778N|PLEC_ENST00000527096.1_Silent_p.N2774N|PLEC_ENST00000356346.3_Silent_p.N2737N|PLEC_ENST00000357649.2_Silent_p.N2755N	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2888	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TCACAGCCTCGTTGACGGTCA	0.697													G|||	1153	0.230232	0.0272	0.2968	5008	,	,		14387	0.1419		0.4284	False		,,,				2504	0.3446				p.N2888N		Atlas-SNP	.											.	PLEC	1144	.	0			c.C8664T						PASS	.	G	,,,,,,,	365,3783		25,315,1734	28.0	35.0	33.0		8334,8211,8187,8664,8157,8253,8265,8253	-8.6	0.0	8	dbSNP_120	33	3418,4956		715,1988,1484	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	740,2303,3218	AA,AG,GG		40.8168,8.7994,30.2108	,,,,,,,	2778/4575,2737/4534,2729/4526,2888/4685,2719/4516,2751/4548,2755/4552,2751/4548	144995736	3783,8739	2074	4187	6261	SO:0001819	synonymous_variant	5339	exon32			AGCCTCGTTGACG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8664C>T	8.37:g.144995736G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.681;A|0.319	0.319	strong		0.697	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
ARHGEF37	389337	hgsc.bcm.edu	37	5	149008467	149008467	+	Missense_Mutation	SNP	C	C	A	rs3733662	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149008467C>A	ENST00000333677.6	+	12	1919	c.1756C>A	c.(1756-1758)Ccc>Acc	p.P586T		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	586			P -> T (in dbSNP:rs3733662).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GAACAAAGACCCCCGATGTCT	0.602													C|||	803	0.160343	0.0189	0.1412	5008	,	,		17591	0.3333		0.1501	False		,,,				2504	0.1973				p.P586T		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.C1756A						PASS	.	C	THR/PRO	154,3812		0,154,1829	49.0	54.0	52.0		1756	2.9	0.0	5	dbSNP_107	52	1277,7041		87,1103,2969	yes	missense	ARHGEF37	NM_001001669.2	38	87,1257,4798	AA,AC,CC		15.3522,3.883,11.6493	benign	586/676	149008467	1431,10853	1983	4159	6142	SO:0001583	missense	389337	exon12			AAAGACCCCCGAT	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1756C>A	5.37:g.149008467C>A	ENSP00000328083:p.Pro586Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	364	0.16666666666666666	9	0.018292682926829267	59	0.16298342541436464	179	0.3129370629370629	117	0.15435356200527706	C	5.285	0.237941	0.10023	0.03883	0.153522	ENSG00000183111	ENST00000333677	T	0.55052	0.54	5.4	2.86	0.33363	.	0.980252	0.08377	N	0.955147	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.34551	-0.9824	9	0.22706	T	0.39	-0.6438	3.7967	0.08743	0.2349:0.1019:0.0:0.6632	rs3733662;rs58657387;rs3733662	586	A1IGU5	ARH37_HUMAN	T	586	ENSP00000328083:P586T	ENSP00000328083:P586T	P	+	1	0	ARHGEF37	148988660	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	0.583000	0.23849	0.267000	0.21916	-0.339000	0.08088	CCC	C|0.839;A|0.161	0.161	strong		0.602	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
MED13L	23389	hgsc.bcm.edu	37	12	116446355	116446355	+	Silent	SNP	A	A	G	rs61748071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:116446355A>G	ENST00000281928.3	-	10	2069	c.1863T>C	c.(1861-1863)atT>atC	p.I621I		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	621						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TCGAGGGCCTAATCCCACAAT	0.532													A|||	15	0.00299521	0.0	0.0043	5008	,	,		20935	0.0		0.0099	False		,,,				2504	0.002				p.I621I		Atlas-SNP	.											.	MED13L	193	.	0			c.T1863C						PASS	.	A		7,4399	12.9+/-30.5	0,7,2196	62.0	55.0	57.0		1863	-0.3	1.0	12	dbSNP_129	57	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous	MED13L	NM_015335.4		0,53,6450	GG,GA,AA		0.5349,0.1589,0.4075		621/2211	116446355	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	23389	exon10			GGGCCTAATCCCA	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.1863T>C	12.37:g.116446355A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	242	127	0.524793	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																			A|0.996;G|0.004	0.004	strong		0.532	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
JAK1	3716	hgsc.bcm.edu	37	1	65310489	65310489	+	Silent	SNP	T	T	C	rs2230588	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:65310489T>C	ENST00000342505.4	-	16	2447	c.2199A>G	c.(2197-2199)ccA>ccG	p.P733P	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	733	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GCTTGATGAATGGGCCACACT	0.562			Mis		ALL								C|||	1866	0.372604	0.6604	0.3199	5008	,	,		18529	0.2996		0.2525	False		,,,				2504	0.2198				p.P733P		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A2199G						PASS	.	C		2469,1773		752,965,404	93.0	110.0	104.0		2199	-10.0	0.0	1	dbSNP_98	104	1963,6487		242,1479,2504	no	coding-synonymous	JAK1	NM_002227.2		994,2444,2908	CC,CT,TT		23.2308,41.7963,34.9196		733/1155	65310489	4432,8260	2121	4225	6346	SO:0001819	synonymous_variant	3716	exon16			GATGAATGGGCCA	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2199A>G	1.37:g.65310489T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	145	73	0.503448	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																			T|0.670;C|0.330	0.330	strong		0.562	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
ANKDD1A	348094	hgsc.bcm.edu	37	15	65235776	65235776	+	Missense_Mutation	SNP	A	A	G	rs34988193	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:65235776A>G	ENST00000380230.3	+	11	1092	c.1063A>G	c.(1063-1065)Aag>Gag	p.K355E	ANKDD1A_ENST00000395720.1_Missense_Mutation_p.K355E|ANKDD1A_ENST00000357698.3_Missense_Mutation_p.K355E|ANKDD1A_ENST00000395723.1_Missense_Mutation_p.K264E	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	355			K -> E (in dbSNP:rs34988193). {ECO:0000269|PubMed:15489334}.		signal transduction (GO:0007165)			p.K355E(1)		NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						CCTGAGAGATAAGGTACCTct	0.577													A|||	1233	0.246206	0.1263	0.232	5008	,	,		19679	0.127		0.336	False		,,,				2504	0.4489				p.K355E		Atlas-SNP	.											ANKDD1A,NS,carcinoma,0,1	ANKDD1A	47	1	1	Substitution - Missense(1)	prostate(1)	c.A1063G						PASS	.	A	GLU/LYS	757,3647	307.7+/-290.2	72,613,1517	155.0	145.0	148.0		1063	4.3	1.0	15	dbSNP_126	148	2971,5627	462.0+/-365.6	514,1943,1842	yes	missense	ANKDD1A	NM_182703.3	56	586,2556,3359	GG,GA,AA		34.5545,17.1889,28.6725	probably-damaging	355/523	65235776	3728,9274	2202	4299	6501	SO:0001583	missense	348094	exon11			AGAGATAAGGTAC		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"""Ankyrin repeat domain containing"""	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.1063A>G	15.37:g.65235776A>G	ENSP00000369579:p.Lys355Glu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	157	70	0.44586	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Missense_Mutation	SNP	ENST00000380230.3	37	CCDS10197.2	477	0.2184065934065934	73	0.1483739837398374	85	0.23480662983425415	75	0.13111888111888112	244	0.32189973614775724	A	20.9	4.071106	0.76301	0.171889	0.345545	ENSG00000166839	ENST00000380230;ENST00000357698;ENST00000395720;ENST00000395723	T;T;T;T	0.16196	2.38;2.38;2.38;2.36	5.42	4.27	0.50696	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000006	T	0.00012	0.0000	L	0.38649	1.16	0.09310	P	1.0	D	0.76494	0.999	D	0.68483	0.958	T	0.46105	-0.9215	9	0.36615	T	0.2	-48.4158	11.4729	0.50280	0.8492:0.1508:0.0:0.0	rs34988193;rs61079502;rs34988193	355	Q495B1	AKD1A_HUMAN	E	355;355;355;264	ENSP00000369579:K355E;ENSP00000350329:K355E;ENSP00000379070:K355E;ENSP00000379073:K264E	ENSP00000350329:K355E	K	+	1	0	ANKDD1A	63022829	1.000000	0.71417	1.000000	0.80357	0.685000	0.39939	8.227000	0.89787	1.046000	0.40249	0.533000	0.62120	AAG	A|0.742;G|0.258	0.258	strong		0.577	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703	
LPO	4025	hgsc.bcm.edu	37	17	56332327	56332327	+	Missense_Mutation	SNP	G	G	A	rs2301870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:56332327G>A	ENST00000262290.4	+	9	1577	c.1261G>A	c.(1261-1263)Gtg>Atg	p.V421M	LPO_ENST00000543544.1_Missense_Mutation_p.V362M|LPO_ENST00000582328.1_Missense_Mutation_p.V338M|LPO_ENST00000421678.2_Missense_Mutation_p.V338M	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	421			V -> M (in dbSNP:rs2301870). {ECO:0000269|PubMed:19059195, ECO:0000269|PubMed:2222811, ECO:0000269|Ref.3}.		defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)	p.V421M(1)		breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						GGGAGCCTTCGTGCAGGTAGG	0.612													G|||	808	0.161342	0.2526	0.0821	5008	,	,		14954	0.1151		0.1461	False		,,,				2504	0.1575				p.V421M		Atlas-SNP	.											LPO,NS,carcinoma,0,1	LPO	73	1	1	Substitution - Missense(1)	stomach(1)	c.G1261A						PASS	.	G	MET/VAL,MET/VAL	986,3420	369.1+/-318.9	122,742,1339	68.0	68.0	68.0		1012,1261	-6.8	0.1	17	dbSNP_100	68	1169,7431	238.5+/-269.9	77,1015,3208	yes	missense,missense	LPO	NM_001160102.1,NM_006151.2	21,21	199,1757,4547	AA,AG,GG		13.593,22.3786,16.5693	benign,benign	338/630,421/713	56332327	2155,10851	2203	4300	6503	SO:0001583	missense	4025	exon9			GCCTTCGTGCAGG	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1261G>A	17.37:g.56332327G>A	ENSP00000262290:p.Val421Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Missense_Mutation	SNP	ENST00000262290.4	37	CCDS32689.1	309	0.14148351648351648	109	0.22154471544715448	36	0.09944751381215469	63	0.11013986013986014	101	0.13324538258575197	G	10.95	1.497075	0.26861	0.223786	0.13593	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576	T;T;T	0.67865	-0.29;-0.29;-0.29	5.44	-6.83	0.01693	.	1.368490	0.04046	N	0.303995	T	0.00039	0.0001	N	0.05050	-0.12	0.80722	P	0.0	B;P	0.38677	0.042;0.642	B;B	0.36378	0.012;0.223	T	0.04090	-1.0978	9	0.07325	T	0.83	.	16.7414	0.85460	0.8059:0.0:0.1941:0.0	rs2301870;rs57193257;rs2301870	338;421	E7EMJ3;P22079	.;PERL_HUMAN	M	421;338;362;166	ENSP00000262290:V421M;ENSP00000400245:V338M;ENSP00000445344:V362M	ENSP00000262290:V421M	V	+	1	0	LPO	53687326	0.000000	0.05858	0.110000	0.21437	0.974000	0.67602	-0.721000	0.04963	-1.086000	0.03084	-0.768000	0.03414	GTG	G|0.838;A|0.162	0.162	strong		0.612	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1		
ZBBX	79740	hgsc.bcm.edu	37	3	167023738	167023738	+	Splice_Site	SNP	G	G	C	rs13096767	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:167023738G>C	ENST00000392766.2	-	17	1758	c.1418C>G	c.(1417-1419)gCa>gGa	p.A473G	ZBBX_ENST00000392767.2_Splice_Site_p.A473G|ZBBX_ENST00000307529.5_Splice_Site_p.A473G|ZBBX_ENST00000455345.2_Splice_Site_p.A473G|ZBBX_ENST00000392764.1_Splice_Site_p.A444G	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	473			A -> G (in dbSNP:rs13096767). {ECO:0000269|PubMed:14702039}.			intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.A473G(2)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						TGAAGTTTCTGCTGTTAAAAA	0.289													G|||	1676	0.334665	0.3548	0.353	5008	,	,		14218	0.1835		0.4195	False		,,,				2504	0.363				p.A473G		Atlas-SNP	.											ZBBX_ENST00000455345,NS,carcinoma,0,2	ZBBX	299	2	2	Substitution - Missense(2)	stomach(2)	c.C1418G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	1355,2251		257,841,705	35.0	30.0	32.0		1418,1331,1418	4.8	0.9	3	dbSNP_121	32	3450,4668		723,2004,1332	yes	missense-near-splice,missense-near-splice,missense-near-splice	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	60,60,60	980,2845,2037	CC,CG,GG		42.4982,37.5763,40.9843	probably-damaging,probably-damaging,probably-damaging	473/840,444/772,473/801	167023738	4805,6919	1803	4059	5862	SO:0001630	splice_region_variant	79740	exon17			GTTTCTGCTGTTA	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1418-1C>G	3.37:g.167023738G>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	133	54	0.406015	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	730	0.3342490842490842	182	0.3699186991869919	133	0.3674033149171271	103	0.18006993006993008	312	0.41160949868073876	G	8.513	0.866911	0.17250	0.375763	0.424982	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.11385	2.95;2.95;2.96;2.96;2.78	4.76	4.76	0.60689	.	0.377447	0.24642	N	0.036792	T	0.00012	0.0000	L	0.42245	1.32	0.40001	P	0.024836999999999998	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.986	T	0.53816	-0.8385	9	0.36615	T	0.2	.	13.6402	0.62246	0.0:0.0:1.0:0.0	rs13096767;rs52836832;rs13096767	473;473	A8MT70-2;A8MT70	.;ZBBX_HUMAN	G	473;473;473;473;444	ENSP00000376519:A473G;ENSP00000376520:A473G;ENSP00000390232:A473G;ENSP00000305065:A473G;ENSP00000376517:A444G	ENSP00000305065:A473G	A	-	2	0	ZBBX	168506432	0.886000	0.30341	0.891000	0.34965	0.046000	0.14306	0.607000	0.24209	2.332000	0.79248	0.650000	0.86243	GCA	G|0.651;C|0.349	0.349	strong		0.289	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	Missense_Mutation
MUC16	94025	hgsc.bcm.edu	37	19	9056930	9056930	+	Silent	SNP	T	T	G	rs918535	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9056930T>G	ENST00000397910.4	-	3	30719	c.30516A>C	c.(30514-30516)acA>acC	p.T10172T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10174	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGACATGTTTGTCTTCCTAA	0.443													g|||	1218	0.243211	0.3525	0.2867	5008	,	,		22488	0.0258		0.2833	False		,,,				2504	0.2474				p.T10172T		Atlas-SNP	.											.	MUC16	4315	.	0			c.A30516C						PASS	.	G		1268,2662		217,834,914	122.0	121.0	121.0		30516	-6.6	0.0	19	dbSNP_86	121	2525,5781		402,1721,2030	no	coding-synonymous	MUC16	NM_024690.2		619,2555,2944	GG,GT,TT		30.3997,32.2646,30.9987		10172/14508	9056930	3793,8443	1965	4153	6118	SO:0001819	synonymous_variant	94025	exon3			CATGTTTGTCTTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30516A>C	19.37:g.9056930T>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.739;G|0.261	0.261	strong		0.443	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LILRA6	79168	hgsc.bcm.edu	37	19	54745659	54745659	+	Missense_Mutation	SNP	G	G	C	rs200657736		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54745659G>C	ENST00000396365.2	-	4	490	c.451C>G	c.(451-453)Cac>Gac	p.H151D	LILRA6_ENST00000245621.5_Missense_Mutation_p.H151D|LILRA6_ENST00000419410.2_Missense_Mutation_p.H151D|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Missense_Mutation_p.H151D|LILRA6_ENST00000270464.5_Missense_Mutation_p.H151D|LILRA6_ENST00000391735.3_Missense_Mutation_p.H151D	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	151					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACAAAATGGTGATATCCCTTC	0.592																																					p.H151D		Atlas-SNP	.											LILRA6,NS,carcinoma,0,2	LILRA6	75	2	0			c.C451G						scavenged	.						23.0	37.0	32.0					19																	54745659		2100	4266	6366	SO:0001583	missense	79168	exon4			AATGGTGATATCC	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.451C>G	19.37:g.54745659G>C	ENSP00000379651:p.His151Asp	Somatic	675	1	0.00148148		WXS	Illumina HiSeq	Phase_I	652	89	0.136503	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.647560	0.00111	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;4.04;2.82;2.82	2.64	-5.28	0.02755	Immunoglobulin-like fold (1);	2.010510	0.02119	N	0.055507	T	0.01870	0.0059	N	0.00237	-1.79	0.09310	N	1	B;B;B;B;B;B	0.09022	0.002;0.0;0.002;0.0;0.0;0.0	B;B;B;B;B;B	0.08055	0.003;0.0;0.003;0.001;0.002;0.001	T	0.25537	-1.0129	10	0.02654	T	1	.	3.0381	0.06129	0.2388:0.2899:0.373:0.0983	.	151;151;151;151;151;151	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	D	151	ENSP00000390120:H151D;ENSP00000270464:H151D;ENSP00000411227:H151D;ENSP00000375615:H151D;ENSP00000379651:H151D;ENSP00000245621:H151D	ENSP00000245621:H151D	H	-	1	0	LILRA6	59437471	.	.	0.000000	0.03702	0.020000	0.10135	.	.	-3.099000	0.00245	-1.962000	0.00476	CAC	G|0.999;C|0.001	0.001	weak		0.592	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
KIAA0753	9851	hgsc.bcm.edu	37	17	6531648	6531648	+	Silent	SNP	A	A	G	rs2072149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:6531648A>G	ENST00000361413.3	-	3	865	c.507T>C	c.(505-507)tcT>tcC	p.S169S	KIAA0753_ENST00000572370.1_5'UTR|KIAA0753_ENST00000542606.1_5'UTR	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	169						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		CTTTGGCACCAGAGCTGGAGA	0.498													G|||	3491	0.697085	0.8563	0.6801	5008	,	,		17862	0.7103		0.5457	False		,,,				2504	0.636				p.S169S		Atlas-SNP	.											.	KIAA0753	63	.	0			c.T507C						PASS	.	G		3411,805		1390,631,87	100.0	110.0	106.0		507	-6.3	0.9	17	dbSNP_96	106	4870,3570		1416,2038,766	no	coding-synonymous	KIAA0753	NM_014804.2		2806,2669,853	GG,GA,AA		42.2986,19.0939,34.5686		169/968	6531648	8281,4375	2108	4220	6328	SO:0001819	synonymous_variant	9851	exon3			GGCACCAGAGCTG		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.507T>C	17.37:g.6531648A>G		Somatic	285	1	0.00350877		WXS	Illumina HiSeq	Phase_I	311	169	0.543408	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Silent	SNP	ENST00000361413.3	37	CCDS42247.1																																																																																			A|0.332;G|0.668	0.668	strong		0.498	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
ANKRD53	79998	hgsc.bcm.edu	37	2	71211815	71211815	+	Silent	SNP	G	G	A	rs3796098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:71211815G>A	ENST00000360589.3	+	6	1012	c.978G>A	c.(976-978)ctG>ctA	p.L326L	AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000441349.1_3'UTR|ANKRD53_ENST00000272421.6_3'UTR|ANKRD53_ENST00000457410.1_Silent_p.L292L	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	326										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						GCCACTCTCTGGTCTCCAATA	0.577											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	675	0.134784	0.0825	0.1254	5008	,	,		18367	0.1617		0.2276	False		,,,				2504	0.089				p.L326L		Atlas-SNP	.											ANKRD53_ENST00000360589,NS,carcinoma,0,1	ANKRD53	55	1	0			c.G978A						PASS	.	G	,	146,1238		7,132,553	53.0	59.0	58.0		978,	0.8	0.0	2	dbSNP_107	58	690,2492		78,534,979	yes	coding-synonymous,utr-3	ANKRD53	NM_001115116.1,NM_024933.3	,	85,666,1532	AA,AG,GG		21.6845,10.5491,18.3092	,	326/531,	71211815	836,3730	692	1591	2283	SO:0001819	synonymous_variant	79998	exon6			CTCTCTGGTCTCC	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"""Ankyrin repeat domain containing"""	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.978G>A	2.37:g.71211815G>A		Somatic	117	0	0	1128	WXS	Illumina HiSeq	Phase_I	207	59	0.285024	NM_001115116	Q8IYP8	Silent	SNP	ENST00000360589.3	37	CCDS46321.1																																																																																			G|0.837;A|0.163	0.163	strong		0.577	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933	
PKD1L1	168507	hgsc.bcm.edu	37	7	47879049	47879049	+	Missense_Mutation	SNP	G	G	A	rs76100363	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:47879049G>A	ENST00000289672.2	-	36	5814	c.5764C>T	c.(5764-5766)Cgg>Tgg	p.R1922W		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1922					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CCTACCTTCCGGAAGCCGAGT	0.642													G|||	816	0.162939	0.0174	0.2291	5008	,	,		16788	0.2321		0.2078	False		,,,				2504	0.1953				p.R1922W		Atlas-SNP	.											PKD1L1,NS,carcinoma,0,1	PKD1L1	328	1	0			c.C5764T						scavenged	.	G	TRP/ARG	211,4195		3,205,1995	29.0	24.0	26.0		5764	-9.7	0.1	7	dbSNP_131	26	1513,7087		124,1265,2911	yes	missense	PKD1L1	NM_138295.3	101	127,1470,4906	AA,AG,GG		17.593,4.7889,13.2554	benign	1922/2850	47879049	1724,11282	2203	4300	6503	SO:0001583	missense	168507	exon36			CCTTCCGGAAGCC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5764C>T	7.37:g.47879049G>A	ENSP00000289672:p.Arg1922Trp	Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	134	55	0.410448	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	376	0.17216117216117216	11	0.022357723577235773	91	0.2513812154696133	120	0.2097902097902098	154	0.20316622691292877	G	6.846	0.525413	0.13066	0.047889	0.17593	ENSG00000158683	ENST00000289672	T	0.20738	2.05	4.87	-9.73	0.00512	.	1.518000	0.04159	N	0.322748	T	0.00012	0.0000	N	0.11064	0.09	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.28776	-1.0033	9	0.48119	T	0.1	0.0923	8.3591	0.32348	0.6412:0.0:0.1727:0.1862	.	1922	Q8TDX9	PK1L1_HUMAN	W	1922	ENSP00000289672:R1922W	ENSP00000289672:R1922W	R	-	1	2	PKD1L1	47845574	0.000000	0.05858	0.055000	0.19348	0.255000	0.26057	-2.918000	0.00695	-2.336000	0.00628	-0.749000	0.03505	CGG	G|0.859;A|0.141	0.141	strong		0.642	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
JMJD4	65094	hgsc.bcm.edu	37	1	227920357	227920357	+	Silent	SNP	C	C	T	rs4837	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:227920357C>T	ENST00000366758.3	-	6	1127	c.1128G>A	c.(1126-1128)tcG>tcA	p.S376S	SNAP47_ENST00000480897.1_3'UTR|SNAP47_ENST00000366760.1_Intron|JMJD4_ENST00000485807.1_5'UTR|SNAP47_ENST00000315781.5_5'Flank|SNAP47_ENST00000366759.4_5'Flank|JMJD4_ENST00000438896.2_Silent_p.S360S	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	376										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				AGTTGATGCCCGAGCAGGACC	0.587													C|||	466	0.0930511	0.1157	0.0706	5008	,	,		20417	0.0486		0.1074	False		,,,				2504	0.1094				p.S376S		Atlas-SNP	.											.	JMJD4	28	.	0			c.G1128A						PASS	.	C	,	514,3892	234.6+/-247.4	32,450,1721	62.0	56.0	58.0		1080,1128	-10.0	0.0	1	dbSNP_52	58	939,7661	205.8+/-248.1	56,827,3417	no	coding-synonymous,coding-synonymous	JMJD4	NM_001161465.1,NM_023007.2	,	88,1277,5138	TT,TC,CC		10.9186,11.6659,11.1718	,	360/448,376/464	227920357	1453,11553	2203	4300	6503	SO:0001819	synonymous_variant	65094	exon6			GATGCCCGAGCAG	AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692			25724	protein-coding gene	gene with protein product						12477932	Standard	NM_023007		Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.1128G>A	1.37:g.227920357C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_023007	Q5TBZ1|Q5TBZ6|Q9H970	Silent	SNP	ENST00000366758.3	37	CCDS1561.1	202	0.0924908424908425	62	0.12601626016260162	30	0.08287292817679558	30	0.05244755244755245	80	0.10554089709762533	C	6.866	0.529084	0.13127	0.116659	0.109186	ENSG00000081692	ENST00000438896	.	.	.	5.01	-10.0	0.00425	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.9999999999484256	.	.	.	.	.	.	T	0.02184	-1.1199	3	.	.	.	-14.3261	4.112	0.10063	0.2681:0.1906:0.4308:0.1105	rs4837;rs17355133	.	.	.	Q	353	.	.	R	-	2	0	JMJD4	225986980	0.000000	0.05858	0.034000	0.17996	0.956000	0.61745	-5.329000	0.00131	-4.649000	0.00038	-1.779000	0.00650	CGG	C|0.892;T|0.108	0.108	strong		0.587	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007	
CALCOCO2	10241	hgsc.bcm.edu	37	17	46929908	46929908	+	Missense_Mutation	SNP	T	T	C	rs2303015	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:46929908T>C	ENST00000258947.3	+	8	844	c.743T>C	c.(742-744)gTt>gCt	p.V248A	CALCOCO2_ENST00000508679.1_Missense_Mutation_p.V176A|CALCOCO2_ENST00000509507.1_Missense_Mutation_p.V269A|CALCOCO2_ENST00000416445.2_Missense_Mutation_p.V206A|CALCOCO2_ENST00000448105.2_Missense_Mutation_p.V272A	NM_001261390.1|NM_001261391.1|NM_001261393.1|NM_001261395.1|NM_005831.4	NP_001248319.1|NP_001248320.1|NP_001248322.1|NP_001248324.1|NP_005822.1	Q13137	CACO2_HUMAN	calcium binding and coiled-coil domain 2	248			V -> A (in dbSNP:rs2303015). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		response to interferon-gamma (GO:0034341)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	15						GAGAAGCTTGTTCAGGGAGAT	0.378													T|||	756	0.150958	0.3245	0.0533	5008	,	,		20544	0.0675		0.0467	False		,,,				2504	0.1789				p.V272A		Atlas-SNP	.											.	CALCOCO2	29	.	0			c.T815C						PASS	.	T	ALA/VAL	1183,3223	414.6+/-336.9	155,873,1175	74.0	74.0	74.0		743	4.2	0.2	17	dbSNP_100	74	324,8276	114.6+/-174.5	5,314,3981	yes	missense	CALCOCO2	NM_005831.3	64	160,1187,5156	CC,CT,TT		3.7674,26.8498,11.587	possibly-damaging	248/447	46929908	1507,11499	2203	4300	6503	SO:0001583	missense	10241	exon9			AGCTTGTTCAGGG	BC004130	CCDS11538.1, CCDS58558.1, CCDS58559.1, CCDS58560.1, CCDS58561.1	17q21.32	2006-02-09				ENSG00000136436			29912	protein-coding gene	gene with protein product		604587				7540613	Standard	NM_001261390		Approved	MGC17318, NDP52	uc010wlr.3	Q13137		ENST00000258947.3:c.743T>C	17.37:g.46929908T>C	ENSP00000258947:p.Val248Ala	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	277	130	0.469314	NM_001261390	B2RBT0|B4DDC4|B4DDT4|B4DP36|B4E0C0|E7ENK0|E7ETP5|E9PBE5|Q53FQ5|Q53HB5|Q6IBN9|Q9BTF7	Missense_Mutation	SNP	ENST00000258947.3	37	CCDS11538.1	267	0.12225274725274725	181	0.3678861788617886	21	0.058011049723756904	33	0.057692307692307696	32	0.04221635883905013	T	9.801	1.180618	0.21787	0.268498	0.037674	ENSG00000136436	ENST00000258947;ENST00000509507;ENST00000448105;ENST00000513119;ENST00000416445;ENST00000508679	T;T;T;T;T;T	0.17854	2.92;2.92;2.92;2.25;3.04;2.45	5.33	4.22	0.49857	.	1.445420	0.04399	N	0.363956	T	0.00012	0.0000	M	0.70595	2.14	0.80722	P	0.0	B;B;B;B	0.31125	0.309;0.098;0.202;0.095	B;B;B;B	0.31946	0.138;0.076;0.113;0.053	T	0.48559	-0.9025	9	0.09084	T	0.74	0.3295	2.6261	0.04930	0.3817:0.1311:0.0:0.4872	rs2303015;rs52825110;rs58716116;rs2303015	206;272;269;248	E7ETP5;B4DP36;E9PBE5;Q13137	.;.;.;CACO2_HUMAN	A	248;269;272;176;206;176	ENSP00000258947:V248A;ENSP00000424352:V269A;ENSP00000398523:V272A;ENSP00000425090:V176A;ENSP00000406974:V206A;ENSP00000423437:V176A	ENSP00000258947:V248A	V	+	2	0	CALCOCO2	44284907	0.004000	0.15560	0.227000	0.23927	0.963000	0.63663	0.138000	0.16016	2.013000	0.59113	0.528000	0.53228	GTT	T|0.868;G|0.001	.	strong		0.378	CALCOCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360866.1	NM_005831	
SGSM1	129049	hgsc.bcm.edu	37	22	25270455	25270455	+	Silent	SNP	G	G	C	rs9624633	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25270455G>C	ENST00000400359.4	+	13	1372	c.1365G>C	c.(1363-1365)cgG>cgC	p.R455R	SGSM1_ENST00000400358.4_Intron	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	455						Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						CTGCAGGCCGGTCCATGCTGG	0.607													G|||	708	0.141374	0.0825	0.1369	5008	,	,		18657	0.1548		0.0944	False		,,,				2504	0.2587				p.R455R		Atlas-SNP	.											.	SGSM1	150	.	0			c.G1365C						PASS	.	G	,,,	317,3787		14,289,1749	42.0	45.0	44.0		1365,,,1365	1.1	0.2	22	dbSNP_119	44	930,7466		49,832,3317	no	coding-synonymous,intron,intron,coding-synonymous	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	,,,	63,1121,5066	CC,CG,GG		11.0767,7.7242,9.976	,,,	455/1149,,,455/1088	25270455	1247,11253	2052	4198	6250	SO:0001819	synonymous_variant	129049	exon13			AGGCCGGTCCATG	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.1365G>C	22.37:g.25270455G>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	138	77	0.557971	NM_133454	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																			G|0.883;C|0.117	0.117	strong		0.607	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
HCRTR1	3061	hgsc.bcm.edu	37	1	32092525	32092525	+	Missense_Mutation	SNP	A	A	G	rs2271933	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32092525A>G	ENST00000373706.5	+	7	1375	c.1222A>G	c.(1222-1224)Atc>Gtc	p.I408V	HCRTR1_ENST00000468521.1_Intron|HCRTR1_ENST00000373705.1_Intron|HCRTR1_ENST00000403528.2_Missense_Mutation_p.I408V			O43613	OX1R_HUMAN	hypocretin (orexin) receptor 1	408			I -> V (in dbSNP:rs2271933). {ECO:0000269|PubMed:11723285, ECO:0000269|PubMed:14702039}.		feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|orexin receptor activity (GO:0016499)|peptide hormone binding (GO:0017046)			breast(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	7		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)		CCGATGCTCCATCTCCAAAAT	0.652													G|||	2202	0.439696	0.2753	0.5086	5008	,	,		17417	0.244		0.6332	False		,,,				2504	0.6155				p.I408V		Atlas-SNP	.											HCRTR1,caecum,carcinoma,0,1	HCRTR1	20	1	0			c.A1222G	GRCh37	CM056598	HCRTR1	M	rs2271933	PASS	.	G	VAL/ILE	1364,3042	689.8+/-405.2	202,960,1041	106.0	105.0	106.0		1222	3.8	1.0	1	dbSNP_100	106	5281,3319	494.6+/-373.8	1643,1995,662	yes	missense	HCRTR1	NM_001525.2	29	1845,2955,1703	GG,GA,AA		38.593,30.9578,48.9082	benign	408/426	32092525	6645,6361	2203	4300	6503	SO:0001583	missense	3061	exon9			TGCTCCATCTCCA	AF041243	CCDS344.1	1p33	2012-08-08			ENSG00000121764	ENSG00000121764		"""GPCR / Class A : Hypocretin (orexin) receptors"""	4848	protein-coding gene	gene with protein product		602392				9491897	Standard	NM_001525		Approved	OX1R	uc009vtx.2	O43613	OTTHUMG00000003876	ENST00000373706.5:c.1222A>G	1.37:g.32092525A>G	ENSP00000362810:p.Ile408Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001525	A8K3A6|Q9HBV6	Missense_Mutation	SNP	ENST00000373706.5	37	CCDS344.1	939	0.42994505494505497	127	0.258130081300813	192	0.5303867403314917	148	0.25874125874125875	472	0.6226912928759895	G	0.922	-0.715416	0.03206	0.309578	0.61407	ENSG00000121764	ENST00000403528;ENST00000373706	T;T	0.58797	0.31;0.31	4.7	3.78	0.43462	.	0.156920	0.41938	N	0.000795	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45644	-0.9247	9	0.02654	T	1	.	8.2159	0.31511	0.1904:0.0:0.8096:0.0	rs2271933;rs17444652;rs59309008;rs2271933	408	O43613	OX1R_HUMAN	V	408	ENSP00000384387:I408V;ENSP00000362810:I408V	ENSP00000362810:I408V	I	+	1	0	HCRTR1	31865112	0.962000	0.33011	0.965000	0.40720	0.914000	0.54420	1.595000	0.36708	0.690000	0.31570	-0.735000	0.03563	ATC	A|0.531;G|0.469	0.469	strong		0.652	HCRTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011042.1	NM_001525	
TRIM38	10475	hgsc.bcm.edu	37	6	25967068	25967068	+	Silent	SNP	C	C	T	rs2009610	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:25967068C>T	ENST00000357085.3	+	3	794	c.318C>T	c.(316-318)gaC>gaT	p.D106D	TRIM38_ENST00000349458.3_Silent_p.D106D	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	106					negative regulation of defense response to virus (GO:0050687)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						TCTGCGAAGACGAGGGGCAGC	0.557													C|||	479	0.095647	0.0189	0.1153	5008	,	,		19891	0.0665		0.2177	False		,,,				2504	0.09				p.D106D		Atlas-SNP	.											.	TRIM38	50	.	0			c.C318T						PASS	.	C		222,4184		5,212,1986	62.0	60.0	61.0		318	-7.4	0.0	6	dbSNP_92	61	1968,6632		232,1504,2564	no	coding-synonymous	TRIM38	NM_006355.2		237,1716,4550	TT,TC,CC		22.8837,5.0386,16.8384		106/466	25967068	2190,10816	2203	4300	6503	SO:0001819	synonymous_variant	10475	exon3			CGAAGACGAGGGG	U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10059	protein-coding gene	gene with protein product			"""ring finger protein 15"", ""tripartite motif-containing 38"""	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.318C>T	6.37:g.25967068C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_006355	B2R862	Silent	SNP	ENST00000357085.3	37	CCDS4568.1																																																																																			C|0.856;T|0.144	0.144	strong		0.557	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2		
TERT	7015	hgsc.bcm.edu	37	5	1253918	1253918	+	Silent	SNP	C	C	T	rs35033501	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1253918C>T	ENST00000310581.5	-	16	3381	c.3324G>A	c.(3322-3324)ccG>ccA	p.P1108P	TERT_ENST00000334602.6_Silent_p.P1045P|TERT_ENST00000296820.5_3'UTR	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	1108	CTE.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	GCGTCGTCCCCGGGAGCTTCC	0.657									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis				c|||	36	0.0071885	0.0	0.0101	5008	,	,		16253	0.0		0.0288	False		,,,				2504	0.0				p.P1108P		Atlas-SNP	.											.	TERT	2594	.	0			c.G3324A						PASS	.	C	,	23,4331		0,23,2154	22.0	31.0	28.0		3135,3324	-6.8	0.0	5	dbSNP_126	28	208,8314		1,206,4054	no	coding-synonymous,coding-synonymous	TERT	NM_001193376.1,NM_198253.2	,	1,229,6208	TT,TC,CC		2.4407,0.5282,1.794	,	1045/1070,1108/1133	1253918	231,12645	2177	4261	6438	SO:0001819	synonymous_variant	7015	exon16	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	CGTCCCCGGGAGC	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.3324G>A	5.37:g.1253918C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_198253	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	37	CCDS3861.2																																																																																			C|0.985;T|0.015	0.015	strong		0.657	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2		
MUC4	4585	hgsc.bcm.edu	37	3	195505822	195505822	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:195505822G>T	ENST00000463781.3	-	2	13088	c.12629C>A	c.(12628-12630)cCt>cAt	p.P4210H	MUC4_ENST00000475231.1_Missense_Mutation_p.P4210H|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTCGGTGACAGGAAGAGGGGT	0.592																																					p.P4210H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C12629A						scavenged	.						18.0	16.0	17.0					3																	195505822		688	1572	2260	SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12629C>A	3.37:g.195505822G>T	ENSP00000417498:p.Pro4210His	Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	108	5	0.0462963	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	2.410	-0.335654	0.05278	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37058	1.22;1.26	.	.	.	.	.	.	.	.	T	0.32912	0.0845	N	0.14661	0.345	0.09310	N	0.999993	D	0.76494	0.999	D	0.72338	0.977	T	0.14117	-1.0484	7	.	.	.	.	2.6645	0.05037	0.4931:0.0:0.5069:0.0	.	4082	E7ESK3	.	H	4210	ENSP00000417498:P4210H;ENSP00000420243:P4210H	.	P	-	2	0	MUC4	196990601	.	.	0.023000	0.16930	0.027000	0.11550	.	.	0.088000	0.17205	0.089000	0.15464	CCT	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
BAI3	577	hgsc.bcm.edu	37	6	69703767	69703767	+	Silent	SNP	C	C	G	rs144610317	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:69703767C>G	ENST00000370598.1	+	11	2663	c.1842C>G	c.(1840-1842)ggC>ggG	p.G614G		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	614					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TCTATGCAGGCGATCTTCTGA	0.468													C|||	39	0.00778754	0.0008	0.0029	5008	,	,		19026	0.0		0.0129	False		,,,				2504	0.0235				p.G614G		Atlas-SNP	.											.	BAI3	451	.	0			c.C1842G						PASS	.	C		12,4394	19.1+/-41.9	0,12,2191	139.0	144.0	143.0		1842	-12.1	0.1	6	dbSNP_134	143	79,8521	46.3+/-105.2	0,79,4221	no	coding-synonymous	BAI3	NM_001704.2		0,91,6412	GG,GC,CC		0.9186,0.2724,0.6997		614/1523	69703767	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	577	exon11			TGCAGGCGATCTT	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1842C>G	6.37:g.69703767C>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	37	CCDS4968.1																																																																																			C|0.993;G|0.007	0.007	strong		0.468	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
CSPG4	1464	hgsc.bcm.edu	37	15	75981507	75981507	+	Silent	SNP	A	A	G	rs12900539	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75981507A>G	ENST00000308508.5	-	3	1991	c.1899T>C	c.(1897-1899)ggT>ggC	p.G633G		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	633	Globular or compact configuration stabilized by disulfide bonds.|Interaction with COL5A1. {ECO:0000250}.|Interaction with COL6A2. {ECO:0000250}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCTGTGCAGGACCACCGCGGT	0.697													G|||	1870	0.373403	0.2716	0.4986	5008	,	,		16922	0.1865		0.5179	False		,,,				2504	0.4663				p.G633G		Atlas-SNP	.											.	CSPG4	175	.	0			c.T1899C						PASS	.	G		1293,3099		200,893,1103	22.0	23.0	23.0		1899	0.9	0.8	15	dbSNP_121	23	4587,3973		1292,2003,985	no	coding-synonymous	CSPG4	NM_001897.4		1492,2896,2088	GG,GA,AA		46.4136,29.4399,45.3984		633/2323	75981507	5880,7072	2196	4280	6476	SO:0001819	synonymous_variant	1464	exon3			TGCAGGACCACCG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1899T>C	15.37:g.75981507A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			A|0.591;G|0.409	0.409	strong		0.697	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
SLC30A9	10463	hgsc.bcm.edu	37	4	41992677	41992677	+	Silent	SNP	C	C	G	rs2581434	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:41992677C>G	ENST00000264451.7	+	1	189	c.9C>G	c.(7-9)ccC>ccG	p.P3P	RP11-814H16.2_ENST00000608029.1_lincRNA	NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	3					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GGATGTTACCCGGCTTGGCCG	0.682													G|||	3540	0.706869	0.2458	0.8401	5008	,	,		13696	0.9593		0.8151	False		,,,				2504	0.864				p.P3P		Atlas-SNP	.											.	SLC30A9	58	.	0			c.C9G						PASS	.	G		1457,2921		278,901,1010	20.0	20.0	20.0		9	2.8	1.0	4	dbSNP_100	20	7007,1573		2888,1231,171	no	coding-synonymous	SLC30A9	NM_006345.3		3166,2132,1181	GG,GC,CC		18.3333,33.28,34.6813		3/569	41992677	8464,4494	2189	4290	6479	SO:0001819	synonymous_variant	10463	exon1			GTTACCCGGCTTG	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"""Solute carriers"""	1329	protein-coding gene	gene with protein product	"""GRIP1-dependent nuclear receptor coactivator"""	604604	"""chromosome 4 open reading frame 1"""	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.9C>G	4.37:g.41992677C>G		Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_006345	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Silent	SNP	ENST00000264451.7	37	CCDS3465.1																																																																																			C|0.328;G|0.672	0.672	strong		0.682	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3		
ASIP	434	hgsc.bcm.edu	37	20	32856838	32856838	+	Silent	SNP	C	C	A	rs36093428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32856838C>A	ENST00000568305.1	+	4	466	c.264C>A	c.(262-264)ccC>ccA	p.P88P	RP4-785G19.5_ENST00000512005.1_RNA|ASIP_ENST00000374954.3_Silent_p.P88P			P42127	ASIP_HUMAN	agouti signaling protein	88					adult feeding behavior (GO:0008343)|cell-cell signaling (GO:0007267)|generation of precursor metabolites and energy (GO:0006091)|genetic imprinting (GO:0071514)|hormone-mediated signaling pathway (GO:0009755)|melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|regulation of molecular function, epigenetic (GO:0040030)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			central_nervous_system(1)|lung(2)	3						CCCGGACCCCCCTATCTGCGC	0.706													C|||	31	0.0061901	0.0008	0.0144	5008	,	,		11685	0.0		0.0199	False		,,,				2504	0.0				p.P88P		Atlas-SNP	.											.	ASIP	6	.	0			c.C264A						PASS	.	C		3,4325		0,3,2161	9.0	11.0	11.0		264	-1.8	0.0	20	dbSNP_126	11	48,8490		0,48,4221	no	coding-synonymous	ASIP	NM_001672.2		0,51,6382	AA,AC,CC		0.5622,0.0693,0.3964		88/133	32856838	51,12815	2164	4269	6433	SO:0001819	synonymous_variant	434	exon3			GACCCCCCTATCT		CCDS13232.1	20q11.2-q12	2010-06-24	2010-06-24		ENSG00000101440	ENSG00000101440			745	protein-coding gene	gene with protein product	"""nonagouti homolog (mouse)"""	600201	"""agouti (mouse)-signaling protein"", ""agouti signaling protein, nonagouti homolog (mouse)"""	AGTIL		7937887, 7757071	Standard	NM_001672		Approved	ASP	uc002xah.1	P42127	OTTHUMG00000032289	ENST00000568305.1:c.264C>A	20.37:g.32856838C>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	68	48	0.705882	NM_001672	Q3SXL2	Silent	SNP	ENST00000568305.1	37	CCDS13232.1																																																																																			C|0.994;A|0.006	0.006	strong		0.706	ASIP-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430541.1		
RAI1	10743	hgsc.bcm.edu	37	17	17696755	17696755	+	Missense_Mutation	SNP	C	C	A	rs11649804	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17696755C>A	ENST00000353383.1	+	3	962	c.493C>A	c.(493-495)Ccc>Acc	p.P165T	RAI1_ENST00000261641.6_Missense_Mutation_p.P165T	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	165	Gln-rich.		P -> T (in dbSNP:rs11649804).		circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CGCCCAGGTGCCCTTTCGGAC	0.617													C|||	2823	0.563698	0.41	0.5058	5008	,	,		17268	0.8353		0.334	False		,,,				2504	0.7689				p.P165T		Atlas-SNP	.											RAI1,NS,carcinoma,0,1	RAI1	121	1	0			c.C493A						PASS	.	C	THR/PRO	1742,2664	516.5+/-369.2	339,1064,800	58.0	56.0	57.0		493	3.6	1.0	17	dbSNP_120	57	2643,5957	422.3+/-354.0	427,1789,2084	yes	missense	RAI1	NM_030665.3	38	766,2853,2884	AA,AC,CC		30.7326,39.537,33.7152	probably-damaging	165/1907	17696755	4385,8621	2203	4300	6503	SO:0001583	missense	10743	exon3			CAGGTGCCCTTTC	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.493C>A	17.37:g.17696755C>A	ENSP00000323074:p.Pro165Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	37	CCDS11188.1	1094	0.5009157509157509	194	0.3943089430894309	165	0.4558011049723757	479	0.8374125874125874	256	0.33773087071240104	C	16.09	3.025501	0.54683	0.39537	0.307326	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.66995	-0.24;2.48;0.35	4.55	3.58	0.41010	.	0.101091	0.41938	D	0.000800	T	0.00012	0.0000	M	0.62723	1.935	0.34918	P	0.251845	D	0.89917	1.0	D	0.85130	0.997	T	0.31166	-0.9953	9	0.49607	T	0.09	.	11.7853	0.52039	0.0:0.913:0.0:0.087	rs11649804;rs57680432;rs11649804	165	Q7Z5J4	RAI1_HUMAN	T	165	ENSP00000323074:P165T;ENSP00000379120:P165T;ENSP00000261641:P165T	ENSP00000261641:P165T	P	+	1	0	RAI1	17637480	0.775000	0.28604	1.000000	0.80357	0.989000	0.77384	0.679000	0.25291	0.902000	0.36520	0.462000	0.41574	CCC	C|0.584;A|0.415	0.415	strong		0.617	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
DNAH5	1767	hgsc.bcm.edu	37	5	13882841	13882841	+	Silent	SNP	A	A	G	rs10057007	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13882841A>G	ENST00000265104.4	-	21	3362	c.3258T>C	c.(3256-3258)ctT>ctC	p.L1086L	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1086	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					ATTTACCTTGAAGTTCATTTT	0.303									Kartagener syndrome				A|||	1255	0.250599	0.3336	0.2824	5008	,	,		20754	0.12		0.2565	False		,,,				2504	0.2444				p.L1086L		Atlas-SNP	.											.	DNAH5	868	.	0			c.T3258C						PASS	.	A		1398,3008	443.5+/-347.0	226,946,1031	97.0	104.0	102.0		3258	2.2	1.0	5	dbSNP_119	102	2111,6485	356.4+/-330.3	282,1547,2469	no	coding-synonymous	DNAH5	NM_001369.2		508,2493,3500	GG,GA,AA		24.5579,31.7295,26.9882		1086/4625	13882841	3509,9493	2203	4298	6501	SO:0001819	synonymous_variant	1767	exon21	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ACCTTGAAGTTCA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3258T>C	5.37:g.13882841A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	157	78	0.496815	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			A|0.744;G|0.256	0.256	strong		0.303	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
RUVBL2	10856	hgsc.bcm.edu	37	19	49513273	49513273	+	Silent	SNP	C	C	T	rs1062708	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49513273C>T	ENST00000595090.1	+	8	1077	c.613C>T	c.(613-615)Ctg>Ttg	p.L205L	RUVBL2_ENST00000601968.1_Silent_p.L160L|RUVBL2_ENST00000413176.2_Silent_p.L160L	NM_006666.1	NP_006657.1	Q9Y230	RUVB2_HUMAN	RuvB-like AAA ATPase 2	205					ATP catabolic process (GO:0006200)|cellular response to estradiol stimulus (GO:0071392)|cellular response to UV (GO:0034644)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|establishment of protein localization to chromatin (GO:0071169)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of estrogen receptor binding (GO:0071899)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein folding (GO:0006457)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)|transcriptional activation by promoter-enhancer looping (GO:0071733)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Ino80 complex (GO:0031011)|intracellular (GO:0005622)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent DNA helicase activity (GO:0004003)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|unfolded protein binding (GO:0051082)			large_intestine(1)|upper_aerodigestive_tract(1)	2		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		GATCTCCAAGCTGGGCCGCTC	0.662													C|||	1950	0.389377	0.2027	0.4798	5008	,	,		18420	0.3899		0.503	False		,,,				2504	0.4601				p.L205L		Atlas-SNP	.											.	RUVBL2	31	.	0			c.C613T						PASS	.	C		910,3158		113,684,1237	60.0	62.0	62.0		613	3.0	1.0	19	dbSNP_86	62	3994,4320		968,2058,1131	no	coding-synonymous	RUVBL2	NM_006666.1		1081,2742,2368	TT,TC,CC		48.0395,22.3697,39.6059		205/464	49513273	4904,7478	2034	4157	6191	SO:0001819	synonymous_variant	10856	exon8			TCCAAGCTGGGCC	AF155138	CCDS42588.1	19q13.3	2013-09-12	2013-09-12					"""INO80 complex subunits"", ""ATPases / AAA-type"""	10475	protein-coding gene	gene with protein product	"""reptin"", ""INO80 complex subunit J"""	604788	"""RuvB (E coli homolog)-like 2"", ""RuvB-like 2 (E. coli)"""			10428817, 10998447	Standard	XM_005258426		Approved	RVB2, TIP48, TIP49b, Reptin52, ECP51, TIH2, INO80J, Rvb2	uc002plr.1	Q9Y230		ENST00000595090.1:c.613C>T	19.37:g.49513273C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	93	0.96875	NM_006666	B3KQ59|E7ETE5|Q6FIB9|Q6PK27|Q9Y361	Silent	SNP	ENST00000595090.1	37	CCDS42588.1																																																																																			C|0.579;T|0.421	0.421	strong		0.662	RUVBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466235.1		
KDM4C	23081	hgsc.bcm.edu	37	9	7170006	7170006	+	Intron	SNP	G	G	A	rs7022348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:7170006G>A	ENST00000381309.3	+	21	3559				KDM4C_ENST00000428870.2_Intron|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.S1037N	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C						histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						TCTAAAAAAAGCCAATGCAAC	0.398													G|||	667	0.133187	0.1876	0.1369	5008	,	,		19592	0.001		0.2366	False		,,,				2504	0.0869				p.S1037N		Atlas-SNP	.											.	KDM4C	186	.	0			c.G3110A						PASS	.	G	ASN/SER,	232,1152		24,184,484	50.0	44.0	46.0		3110,	0.9	0.0	9	dbSNP_116	46	728,2454		83,562,946	yes	missense,intron	KDM4C	NM_001146694.1,NM_015061.3	46,	107,746,1430	AA,AG,GG		22.8787,16.763,21.025	,	1037/1048,	7170006	960,3606	692	1591	2283	SO:0001627	intron_variant	23081	exon21			AAAAAAGCCAATG	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.2994+116G>A	9.37:g.7170006G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	139	69	0.496403	NM_001146694	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	316	0.1446886446886447	87	0.17682926829268292	56	0.15469613259668508	0	0.0	173	0.22823218997361477	G	11.29	1.595464	0.28445	0.16763	0.228787	ENSG00000107077	ENST00000381306	T	0.16196	2.36	4.15	0.896	0.19253	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.50171	P	1.4300000000000423E-4	B	0.06786	0.001	B	0.09377	0.004	T	0.45556	-0.9253	6	.	.	.	.	6.7317	0.23387	0.3685:0.0:0.6315:0.0	rs7022348;rs7022348	1037	Q9H3R0-2	.	N	1037	ENSP00000370707:S1037N	.	S	+	2	0	KDM4C	7160006	0.000000	0.05858	0.011000	0.14972	0.016000	0.09150	-0.100000	0.10990	0.173000	0.19788	0.467000	0.42956	AGC	G|0.846;A|0.154	0.154	strong		0.398	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
OR5H15	403274	hgsc.bcm.edu	37	3	97887970	97887970	+	Missense_Mutation	SNP	C	C	T	rs72933946	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:97887970C>T	ENST00000356526.2	+	1	427	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W		NM_001005515.1	NP_001005515.1	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H, member 15	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(2)|stomach(1)	35						ACTGTGCATCCGGCTATTAAT	0.373																																					p.R143W		Atlas-SNP	.											OR5H15,NS,carcinoma,-2,1	OR5H15	70	1	0			c.C427T						scavenged	.						73.0	72.0	72.0					3																	97887970		2203	4297	6500	SO:0001583	missense	403274	exon1			TGCATCCGGCTAT		CCDS33799.1	3q11.2	2013-09-23			ENSG00000233412	ENSG00000233412		"""GPCR / Class A : Olfactory receptors"""	31287	protein-coding gene	gene with protein product							Standard	NM_001005515		Approved		uc011bgu.2	A6NDH6	OTTHUMG00000160076	ENST00000356526.2:c.427C>T	3.37:g.97887970C>T	ENSP00000373195:p.Arg143Trp	Somatic	480	2	0.00416667		WXS	Illumina HiSeq	Phase_I	433	6	0.0138568	NM_001005515		Missense_Mutation	SNP	ENST00000356526.2	37	CCDS33799.1	.	.	.	.	.	.	.	.	.	.	-	4.344	0.063283	0.08388	.	.	ENSG00000233412	ENST00000356526;ENST00000454529	T	0.00130	8.69	2.48	-0.601	0.11638	GPCR, rhodopsin-like superfamily (1);	1.476590	0.04503	N	0.381661	T	0.00109	0.0003	L	0.34521	1.04	0.09310	N	1	B	0.18166	0.026	B	0.15870	0.014	T	0.19516	-1.0303	10	0.34782	T	0.22	.	3.5209	0.07741	0.0:0.4065:0.1978:0.3956	.	143	A6NDH6	O5H15_HUMAN	W	143	ENSP00000373195:R143W	ENSP00000373195:R143W	R	+	1	2	OR5H15	99370660	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.931000	0.01556	-0.339000	0.08401	-1.206000	0.01644	CGG	C|0.965;A|0.035	.	alt		0.373	OR5H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359109.1		
DIP2B	57609	hgsc.bcm.edu	37	12	51089734	51089734	+	Silent	SNP	T	T	A	rs11169524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:51089734T>A	ENST00000301180.5	+	16	1951	c.1917T>A	c.(1915-1917)acT>acA	p.T639T		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	639						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						TAATTGTGACTGATGGAGCTA	0.433													T|||	1606	0.320687	0.3298	0.2752	5008	,	,		19751	0.256		0.3449	False		,,,				2504	0.3824				p.T639T		Atlas-SNP	.											.	DIP2B	167	.	0			c.T1917A						PASS	.	T		1416,2990	464.0+/-353.7	219,978,1006	226.0	198.0	207.0		1917	0.2	1.0	12	dbSNP_120	207	3010,5590	466.8+/-366.9	546,1918,1836	no	coding-synonymous	DIP2B	NM_173602.2		765,2896,2842	AA,AT,TT		35.0,32.138,34.0304		639/1577	51089734	4426,8580	2203	4300	6503	SO:0001819	synonymous_variant	57609	exon16			TGTGACTGATGGA	AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.1917T>A	12.37:g.51089734T>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_173602	Q6B011|Q8N1L5|Q8NB38	Silent	SNP	ENST00000301180.5	37	CCDS31799.1																																																																																			T|0.672;A|0.328	0.328	strong		0.433	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602	
ADGB	79747	hgsc.bcm.edu	37	6	146977963	146977963	+	Silent	SNP	A	A	C	rs79354452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:146977963A>C	ENST00000397944.3	+	5	535	c.459A>C	c.(457-459)ggA>ggC	p.G153G	ADGB_ENST00000367493.3_5'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	153	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						TCAATGGAGGAATTTTGAGCA	0.418													A|||	37	0.00738818	0.0	0.0115	5008	,	,		16532	0.0		0.0109	False		,,,				2504	0.0184				p.G153G		Atlas-SNP	.											.	ADGB	93	.	0			c.A459C						PASS	.	A		2,1382		0,2,690	88.0	80.0	82.0		459	-4.7	0.0	6	dbSNP_132	82	73,3109		0,73,1518	no	coding-synonymous	C6orf103	NM_024694.3		0,75,2208	CC,CA,AA		2.2942,0.1445,1.6426		153/1668	146977963	75,4491	692	1591	2283	SO:0001819	synonymous_variant	79747	exon5			TGGAGGAATTTTG	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.459A>C	6.37:g.146977963A>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	183	95	0.519126	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	37																																																																																				A|0.992;C|0.008	0.008	strong		0.418	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
OR1N2	138882	hgsc.bcm.edu	37	9	125315778	125315778	+	Silent	SNP	G	G	C	rs1411271	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:125315778G>C	ENST00000373688.2	+	1	388	c.330G>C	c.(328-330)tcG>tcC	p.S110S		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						AGATCATCTCGTATTCTGGGT	0.483													C|||	2802	0.559505	0.5953	0.5908	5008	,	,		25005	0.6677		0.4791	False		,,,				2504	0.4601				p.S110S		Atlas-SNP	.											.	OR1N2	51	.	0			c.G330C						PASS	.	C		2529,1877	541.3+/-375.7	715,1099,389	232.0	227.0	229.0		330	3.5	1.0	9	dbSNP_88	229	4211,4389	583.4+/-391.5	1011,2189,1100	no	coding-synonymous	OR1N2	NM_001004457.1		1726,3288,1489	CC,CG,GG		48.9651,42.601,48.1778		110/331	125315778	6740,6266	2203	4300	6503	SO:0001819	synonymous_variant	138882	exon1			CATCTCGTATTCT		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.330G>C	9.37:g.125315778G>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	202	91	0.450495	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Silent	SNP	ENST00000373688.2	37	CCDS35123.1																																																																																			G|0.468;C|0.532	0.532	strong		0.483	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
SLC46A3	283537	hgsc.bcm.edu	37	13	29275670	29275670	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:29275670T>C	ENST00000266943.6	-	6	1719	c.1350A>G	c.(1348-1350)atA>atG	p.I450M	RNU6-53P_ENST00000365367.1_RNA|SLC46A3_ENST00000380814.4_Missense_Mutation_p.I450M|SLC46A3_ENST00000475385.1_5'UTR	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	450					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		ATTCTTCTTGTATAAGAAGTT	0.328																																					p.I450M		Atlas-SNP	.											SLC46A3_ENST00000380814,NS,carcinoma,0,2	SLC46A3	86	2	0			c.A1350G						scavenged	.						134.0	125.0	128.0					13																	29275670		2203	4300	6503	SO:0001583	missense	283537	exon6			TTCTTGTATAAGA		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"""Solute carriers"""	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.1350A>G	13.37:g.29275670T>C	ENSP00000266943:p.Ile450Met	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	215	4	0.0186047	NM_181785	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Missense_Mutation	SNP	ENST00000266943.6	37	CCDS9332.1	.	.	.	.	.	.	.	.	.	.	T	5.062	0.197085	0.09599	.	.	ENSG00000139508	ENST00000266943;ENST00000380814	T;T	0.47177	0.86;0.85	4.95	1.03	0.20045	.	1.055720	0.07281	N	0.870702	T	0.42944	0.1225	L	0.54323	1.7	0.22266	N	0.999245	B;B	0.32467	0.372;0.255	B;B	0.27715	0.082;0.037	T	0.31280	-0.9949	10	0.42905	T	0.14	-1.7362	11.5916	0.50949	0.0:0.0:0.5211:0.4789	.	450;450	Q7Z3Q1-2;Q7Z3Q1	.;S46A3_HUMAN	M	450	ENSP00000266943:I450M;ENSP00000370192:I450M	ENSP00000266943:I450M	I	-	3	3	SLC46A3	28173670	0.344000	0.24827	0.140000	0.22221	0.009000	0.06853	0.480000	0.22244	0.096000	0.17463	-0.313000	0.08912	ATA	.	.	none		0.328	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785	
SECISBP2L	9728	hgsc.bcm.edu	37	15	49325289	49325289	+	Silent	SNP	A	A	C	rs11638215	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:49325289A>C	ENST00000559471.1	-	4	800	c.537T>G	c.(535-537)ctT>ctG	p.L179L	SECISBP2L_ENST00000261847.3_Silent_p.L179L	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	179							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						GCTGTTGTAAAAGCTGTTGCT	0.303													A|||	2129	0.42512	0.2292	0.3991	5008	,	,		16480	0.3512		0.6461	False		,,,				2504	0.5573				p.L179L		Atlas-SNP	.											.	SECISBP2L	118	.	0			c.T537G						PASS	.	A	,	1335,3059	441.0+/-346.2	204,927,1066	115.0	105.0	108.0		537,537	5.1	1.0	15	dbSNP_120	108	5381,3209	647.3+/-400.4	1681,2019,595	no	coding-synonymous,coding-synonymous	SECISBP2L	NM_001193489.1,NM_014701.3	,	1885,2946,1661	CC,CA,AA		37.3574,30.3823,48.2748	,	179/1102,179/1057	49325289	6716,6268	2197	4295	6492	SO:0001819	synonymous_variant	9728	exon4			TTGTAAAAGCTGT	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.537T>G	15.37:g.49325289A>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	148	147	0.993243	NM_001193489	Q8N767	Silent	SNP	ENST00000559471.1	37	CCDS53942.1																																																																																			A|0.519;C|0.481	0.481	strong		0.303	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	
GOLGB1	2804	hgsc.bcm.edu	37	3	121414217	121414217	+	Missense_Mutation	SNP	C	C	A	rs35674179	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121414217C>A	ENST00000340645.5	-	13	5263	c.5138G>T	c.(5137-5139)tGt>tTt	p.C1713F	GOLGB1_ENST00000393667.3_Missense_Mutation_p.C1718F	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1713			C -> F (in dbSNP:rs35674179).		Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TGTTTCCATACACTCTTTAGC	0.418													C|||	610	0.121805	0.1921	0.0576	5008	,	,		23271	0.0685		0.0924	False		,,,				2504	0.1575				p.C1718F		Atlas-SNP	.											.	GOLGB1	319	.	0			c.G5153T						PASS	.	C	PHE/CYS	876,3530	339.4+/-305.8	88,700,1415	166.0	164.0	164.0		5138	2.0	0.2	3	dbSNP_126	164	865,7735	196.8+/-241.6	49,767,3484	yes	missense	GOLGB1	NM_004487.3	205	137,1467,4899	AA,AC,CC		10.0581,19.882,13.3861	benign	1713/3260	121414217	1741,11265	2203	4300	6503	SO:0001583	missense	2804	exon13			TCCATACACTCTT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.5138G>T	3.37:g.121414217C>A	ENSP00000341848:p.Cys1713Phe	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	175	94	0.537143	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	213	0.09752747252747253	89	0.18089430894308944	22	0.06077348066298342	34	0.05944055944055944	68	0.08970976253298153	C	1.126	-0.653706	0.03480	0.19882	0.100581	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.13901	2.55;2.55	4.98	2.04	0.26737	.	1.036240	0.07632	N	0.928835	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;P;P;B	0.41569	0.34;0.643;0.755;0.4	B;B;B;B	0.34301	0.116;0.179;0.179;0.169	T	0.41448	-0.9508	9	0.56958	D	0.05	.	3.5049	0.07686	0.1482:0.3887:0.3667:0.0965	rs35674179	1638;1718;1718;1713	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	F	1713;1718	ENSP00000341848:C1713F;ENSP00000377275:C1718F	ENSP00000341848:C1713F	C	-	2	0	GOLGB1	122896907	0.000000	0.05858	0.211000	0.23655	0.862000	0.49288	-0.068000	0.11561	0.660000	0.30964	0.563000	0.77884	TGT	C|0.878;A|0.122	0.122	strong		0.418	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
HR	55806	hgsc.bcm.edu	37	8	21982997	21982997	+	Missense_Mutation	SNP	A	A	G	rs56140348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21982997A>G	ENST00000381418.4	-	5	3057	c.1577T>C	c.(1576-1578)cTg>cCg	p.L526P	HR_ENST00000312841.8_Missense_Mutation_p.L526P	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	526			L -> P (in dbSNP:rs56140348).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CTCCTGCTGCAGCTCCCCTCC	0.682													G|||	762	0.152157	0.3994	0.0893	5008	,	,		15592	0.0149		0.1213	False		,,,				2504	0.0358				p.L526P		Atlas-SNP	.											.	HR	71	.	0			c.T1577C						PASS	.	G	PRO/LEU,PRO/LEU	1708,2696	638.3+/-396.9	341,1026,835	34.0	37.0	36.0		1577,1577	-10.0	0.0	8	dbSNP_129	36	983,7617	767.1+/-407.6	61,861,3378	yes	missense,missense	HR	NM_005144.4,NM_018411.4	98,98	402,1887,4213	GG,GA,AA		11.4302,38.7829,20.6936	benign,benign	526/1190,526/1135	21982997	2691,10313	2202	4300	6502	SO:0001583	missense	55806	exon5			TGCTGCAGCTCCC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1577T>C	8.37:g.21982997A>G	ENSP00000370826:p.Leu526Pro	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	344	0.1575091575091575	208	0.42276422764227645	34	0.09392265193370165	7	0.012237762237762238	95	0.12532981530343007	G	6.680	0.494035	0.12702	0.387829	0.114302	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.72615	-0.67;-0.66	5.0	-9.99	0.00435	.	2.182940	0.02017	N	0.047472	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12091	-1.0561	9	0.27785	T	0.31	3.4699	0.3755	0.00387	0.2398:0.2533:0.2526:0.2543	rs56140348;rs59526019	526;526	O43593-2;O43593	.;HAIR_HUMAN	P	526	ENSP00000370826:L526P;ENSP00000326765:L526P	ENSP00000326765:L526P	L	-	2	0	HR	22038942	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.726000	0.00382	-3.170000	0.00225	-2.971000	0.00081	CTG	A|0.809;G|0.191	0.191	strong		0.682	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
C16orf96	342346	hgsc.bcm.edu	37	16	4625470	4625470	+	Missense_Mutation	SNP	C	C	G	rs77379438	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:4625470C>G	ENST00000444310.4	+	5	989	c.989C>G	c.(988-990)cCt>cGt	p.P330R		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96											NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						gggcctgcacctgggactgaa	0.662													C|||	555	0.110823	0.0015	0.1441	5008	,	,		18099	0.2698		0.0557	False		,,,				2504	0.1278				p.P330R		Atlas-SNP	.											C16orf96,NS,carcinoma,0,1	C16orf96	28	1	0			c.C989G						PASS	.	C	ARG/PRO	21,1363		0,21,671	18.0	23.0	21.0		989	2.1	0.0	16	dbSNP_131	21	178,3004		6,166,1419	yes	missense	C16orf96	NM_001145011.1	103	6,187,2090	GG,GC,CC		5.594,1.5173,4.3583	probably-damaging	330/1142	4625470	199,4367	692	1591	2283	SO:0001583	missense	342346	exon5			CTGCACCTGGGAC		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.989C>G	16.37:g.4625470C>G	ENSP00000415027:p.Pro330Arg	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_001145011		Missense_Mutation	SNP	ENST00000444310.4	37	CCDS53986.1	249	0.11401098901098901	1	0.0020325203252032522	44	0.12154696132596685	168	0.2937062937062937	36	0.047493403693931395	C	13.02	2.112756	0.37242	0.015173	0.05594	ENSG00000205832	ENST00000444310	.	.	.	3.06	2.09	0.27110	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.62365	0.991	P	0.61070	0.883	T	0.13818	-1.0495	7	0.18710	T	0.47	.	6.5083	0.22208	0.0:0.8621:0.0:0.1379	.	330	A6NNT2	CP096_HUMAN	R	330	.	ENSP00000415027:P330R	P	+	2	0	C16orf96	4565471	0.000000	0.05858	0.001000	0.08648	0.093000	0.18481	0.370000	0.20433	0.830000	0.34757	0.407000	0.27541	CCT	C|0.880;G|0.120	0.120	strong		0.662	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432384.1	NM_001145011	
FAT2	2196	hgsc.bcm.edu	37	5	150946436	150946436	+	Missense_Mutation	SNP	A	A	G	rs9324700	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150946436A>G	ENST00000261800.5	-	1	2069	c.2057T>C	c.(2056-2058)tTt>tCt	p.F686S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	686			F -> S (in dbSNP:rs9324700).		epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGCCCAATAAAGTGGAGGAT	0.408													G|||	2103	0.419928	0.4418	0.4539	5008	,	,		22865	0.3571		0.4901	False		,,,				2504	0.3589				p.F686S		Atlas-SNP	.											.	FAT2	465	.	0			c.T2057C						PASS	.	G	SER/PHE	1965,2441	619.5+/-393.4	426,1113,664	113.0	108.0	110.0		2057	4.7	0.0	5	dbSNP_119	110	4503,4097	561.2+/-387.7	1184,2135,981	yes	missense	FAT2	NM_001447.2	155	1610,3248,1645	GG,GA,AA		47.6395,44.5983,49.7309	benign	686/4350	150946436	6468,6538	2203	4300	6503	SO:0001583	missense	2196	exon1			CCAATAAAGTGGA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2057T>C	5.37:g.150946436A>G	ENSP00000261800:p.Phe686Ser	Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	226	226	1	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	969	0.44368131868131866	238	0.483739837398374	162	0.44751381215469616	201	0.3513986013986014	368	0.48548812664907653	G	0.018	-1.477988	0.01035	0.445983	0.523605	ENSG00000086570	ENST00000261800	T	0.39592	1.07	5.57	4.68	0.58851	.	0.188706	0.38164	N	0.001787	T	0.00012	0.0000	N	0.01352	-0.895	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44205	-0.9343	9	0.05833	T	0.94	.	11.0521	0.47896	0.0668:0.0:0.804:0.1292	rs9324700;rs17717795;rs58284682;rs9324700	686	Q9NYQ8	FAT2_HUMAN	S	686	ENSP00000261800:F686S	ENSP00000261800:F686S	F	-	2	0	FAT2	150926629	0.995000	0.38212	0.004000	0.12327	0.587000	0.36485	4.410000	0.59774	0.816000	0.34421	-0.119000	0.15052	TTT	A|0.534;G|0.466	0.466	strong		0.408	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
POMGNT2	84892	hgsc.bcm.edu	37	3	43121559	43121559	+	Silent	SNP	C	C	T	rs604033	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:43121559C>T	ENST00000344697.2	-	2	1710	c.1365G>A	c.(1363-1365)ccG>ccA	p.P455P	POMGNT2_ENST00000441964.1_Silent_p.P455P	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	455					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)										GAATGAGGGACGGGATGTCCA	0.612													C|||	3920	0.782748	0.8275	0.8127	5008	,	,		21590	0.7401		0.7922	False		,,,				2504	0.7352				p.P455P		Atlas-SNP	.											.	.	.	.	0			c.G1365A						PASS	.	C		3589,817	745.7+/-411.7	1450,689,64	41.0	40.0	40.0		1365	-11.1	0.1	3	dbSNP_83	40	6872,1728	732.5+/-406.8	2730,1412,158	no	coding-synonymous	C3orf39	NM_032806.4		4180,2101,222	TT,TC,CC		20.093,18.5429,19.5679		455/581	43121559	10461,2545	2203	4300	6503	SO:0001819	synonymous_variant	84892	exon2			GAGGGACGGGATG	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"""chromosome 3 open reading frame 39"", ""glycosyltransferase-like domain containing 2"""	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.1365G>A	3.37:g.43121559C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	177	175	0.988701	NM_032806	B3KWC3|Q96SY3	Silent	SNP	ENST00000344697.2	37	CCDS2709.1																																																																																			C|0.197;T|0.803	0.803	strong		0.612	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806	
CEP70	80321	hgsc.bcm.edu	37	3	138289163	138289163	+	Silent	SNP	T	T	C	rs1673608	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:138289163T>C	ENST00000264982.3	-	6	728	c.462A>G	c.(460-462)ttA>ttG	p.L154L	CEP70_ENST00000484888.1_Silent_p.L154L|CEP70_ENST00000542237.1_Silent_p.L134L|CEP70_ENST00000481834.1_Silent_p.L154L|CEP70_ENST00000464035.1_Silent_p.L154L|CEP70_ENST00000489254.1_Intron|CEP70_ENST00000478673.1_5'UTR	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	154					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						TCAGTACCTGTAAAGTTTTCT	0.363													T|||	2410	0.48123	0.236	0.6412	5008	,	,		19331	0.5486		0.505	False		,,,				2504	0.6053				p.L154L		Atlas-SNP	.											.	CEP70	51	.	0			c.A462G						PASS	.	T		1172,3232	413.7+/-336.6	139,894,1169	106.0	98.0	101.0		462	5.0	1.0	3	dbSNP_89	101	4534,4064	594.8+/-393.4	1214,2106,979	no	coding-synonymous	CEP70	NM_024491.2		1353,3000,2148	CC,CT,TT		47.2668,26.6122,43.8856		154/598	138289163	5706,7296	2202	4299	6501	SO:0001819	synonymous_variant	80321	exon6			TACCTGTAAAGTT	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.462A>G	3.37:g.138289163T>C		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	221	220	0.995475	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Silent	SNP	ENST00000264982.3	37	CCDS3102.1																																																																																			T|0.549;C|0.451	0.451	strong		0.363	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491	
GPC1	2817	hgsc.bcm.edu	37	2	241405479	241405479	+	Silent	SNP	C	C	T	rs1126920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241405479C>T	ENST00000264039.2	+	9	1697	c.1449C>T	c.(1447-1449)gaC>gaT	p.D483D	GPC1_ENST00000466624.1_3'UTR	NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	483					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		TCCCAGGTGACGACGGCAGCG	0.672													c|||	441	0.0880591	0.1384	0.0793	5008	,	,		15748	0.0228		0.1083	False		,,,				2504	0.0726				p.D483D		Atlas-SNP	.											.	GPC1	32	.	0			c.C1449T						PASS	.			487,3903		24,439,1732	17.0	20.0	19.0		1449	-0.8	1.0	2	dbSNP_86	19	903,7663		31,841,3411	no	coding-synonymous	GPC1	NM_002081.2		55,1280,5143	TT,TC,CC		10.5417,11.0934,10.7286		483/559	241405479	1390,11566	2195	4283	6478	SO:0001819	synonymous_variant	2817	exon9			AGGTGACGACGGC	AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"""Proteoglycans / Cell Surface : Glypicans"""	4449	protein-coding gene	gene with protein product	"""glypican proteoglycan 1"""	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.1449C>T	2.37:g.241405479C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	157	79	0.503185	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	182	0.08333333333333333	57	0.11585365853658537	34	0.09392265193370165	4	0.006993006993006993	87	0.11477572559366754	c	7.885	0.731125	0.15507	0.110934	0.105417	ENSG00000063660	ENST00000420138;ENST00000455111	.	.	.	3.69	-0.751	0.11076	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-30.493	6.8665	0.24096	0.0:0.3043:0.0:0.6957	rs1126920;rs2228328;rs3182276;rs11892101;rs17416393;rs60234710	.	.	.	X	523;235	.	.	R	+	1	2	GPC1	241054152	0.000000	0.05858	0.997000	0.53966	0.879000	0.50718	-1.549000	0.02182	0.018000	0.15052	0.443000	0.29094	CGA	C|0.902;T|0.098	0.098	strong		0.672	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
NPY	4852	hgsc.bcm.edu	37	7	24324879	24324879	+	Missense_Mutation	SNP	T	T	C	rs16139	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:24324879T>C	ENST00000407573.1	+	3	310	c.20T>C	c.(19-21)cTg>cCg	p.L7P	NPY_ENST00000242152.2_Missense_Mutation_p.L7P|NPY_ENST00000405982.1_Missense_Mutation_p.L7P			P01303	NPY_HUMAN	neuropeptide Y	7			L -> P (in dbSNP:rs16139).		adult feeding behavior (GO:0008343)|behavior (GO:0007610)|blood circulation (GO:0008015)|calcium ion transport (GO:0006816)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of appetite (GO:0032100)|regulation of blood pressure (GO:0008217)|synaptic transmission (GO:0007268)	cell (GO:0005623)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			breast(1)|kidney(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	9						AACAAGCGACTGGGGCTGTCC	0.687													T|||	85	0.0169728	0.0023	0.0101	5008	,	,		15851	0.0		0.0398	False		,,,				2504	0.0358				p.L7P		Atlas-SNP	.											.	NPY	25	.	0			c.T20C	GRCh37	CM981392	NPY	M	rs16139	PASS	.	T	PRO/LEU	39,4367	43.1+/-76.7	1,37,2165	95.0	82.0	86.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	20	5.6	1.0	7	dbSNP_54	86	311,8289	111.2+/-171.5	2,307,3991	yes	missense	NPY	NM_000905.3	98	3,344,6156	CC,CT,TT		3.6163,0.8852,2.6911	possibly-damaging	7/98	24324879	350,12656	2203	4300	6503	SO:0001583	missense	4852	exon2			AGCGACTGGGGCT	K01911	CCDS5387.1	7p15.3	2013-02-26			ENSG00000122585	ENSG00000122585		"""Endogenous ligands"""	7955	protein-coding gene	gene with protein product	"""prepro-neuropeptide Y"""	162640					Standard	NM_000905		Approved	PYY4	uc003sww.2	P01303	OTTHUMG00000022973	ENST00000407573.1:c.20T>C	7.37:g.24324879T>C	ENSP00000384364:p.Leu7Pro	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	73	22	0.30137	NM_000905		Missense_Mutation	SNP	ENST00000407573.1	37	CCDS5387.1	38	0.0173992673992674	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	33	0.04353562005277045	T	17.58	3.423959	0.62733	0.008852	0.036163	ENSG00000122585	ENST00000242152;ENST00000407573;ENST00000405982	T;T;T	0.13196	2.61;2.61;2.61	5.57	5.57	0.84162	.	0.247918	0.39475	N	0.001344	T	0.02418	0.0074	.	.	.	0.58432	D	0.999996	B	0.02656	0.0	B	0.04013	0.001	T	0.11131	-1.0600	9	0.39692	T	0.17	-5.0531	11.6261	0.51147	0.0:0.0713:0.0:0.9287	rs16139;rs17313995;rs52829669;rs16139	7	P01303	NPY_HUMAN	P	7	ENSP00000242152:L7P;ENSP00000384364:L7P;ENSP00000385282:L7P	ENSP00000242152:L7P	L	+	2	0	NPY	24291404	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.234000	0.51320	2.119000	0.64992	0.533000	0.62120	CTG	T|0.976;C|0.024	0.024	strong		0.687	NPY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326748.1	NM_000905	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048663	33048663	+	Missense_Mutation	SNP	G	G	A	rs1042153|rs386699871	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33048663G>A	ENST00000418931.2	+	2	431	c.315G>A	c.(313-315)atG>atA	p.M105I	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.M105I	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	105	Beta-1.		M -> I (in allele DPB1*08:02, allele DPB1*09:02, allele DPB1*13:01, allele DPB1*13:02 and allele DPB1*19:01; dbSNP:rs1042153).|M -> V (in allele DPB1*01:01, allele DPB1*03:01, allele DPB1*05:02, allele DPB1*08:01, allele DPB1*09:01, allele DPB1*10:01, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*17:02, allele DPB1*21:02, allele DPB1*22:02, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*29:01, allele DPB1*35:01, allele DPB1*37:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*50:01, allele DPB1*52:01, allele DPB1*54:01, allele DPB1*56:01, allele DPB1*57:01, allele DPB1*65:01, allele DPB1*67:01, allele DPB1*68:01, allele DPB1*70:01, allele DPB1*73:01, allele DPB1*75:01, allele DPB1*76:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*84:01, allele DPB1*88:01, allele DPB1*90:01 and allele DPB1*92:01; dbSNP:rs1042151). {ECO:0000269|PubMed:6330724}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CGGACAGGATGTGCAGACACA	0.701													.|||	1549	0.309305	0.4607	0.2507	5008	,	,		12515	0.2123		0.2296	False		,,,				2504	0.3282				p.M105I		Atlas-SNP	.											HLA-DPB1,NS,lymphoid_neoplasm,+2,1	HLA-DPB1	28	1	0			c.G315A						scavenged	.						29.0	30.0	30.0					6																	33048663		1510	2709	4219	SO:0001583	missense	3115	exon2			CAGGATGTGCAGA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.315G>A	6.37:g.33048663G>A	ENSP00000408146:p.Met105Ile	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	602|602	0.27564102564102566|0.27564102564102566	239|239	0.48577235772357724|0.48577235772357724	82|82	0.2265193370165746|0.2265193370165746	116|116	0.20279720279720279|0.20279720279720279	165|165	0.21767810026385223|0.21767810026385223	G|G	11.30|11.30	1.597043|1.597043	0.28445|0.28445	.|.	.|.	ENSG00000223865|ENSG00000223865	ENST00000416804|ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835	.|T;T;T	.|0.00311	.|8.15;8.15;8.15	4.02|4.02	0.0296|0.0296	0.14163|0.14163	.|MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	.|2.303120	.|0.02598	.|U	.|0.100781	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.02181|0.02181	-0.65|-0.65	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.10450	.|0.001;0.004;0.005	T|T	0.28396|0.28396	-1.0045|-1.0045	4|9	.|0.52906	.|T	.|0.07	.|.	5.9122|5.9122	0.19035|0.19035	0.1929:0.4754:0.3317:0.0|0.1929:0.4754:0.3317:0.0	rs1042153;rs3173290;rs17214748;rs17420330;rs17851009|rs1042153;rs3173290;rs17214748;rs17420330;rs17851009	.|71;115;105	.|A2ALJ6;Q59GY1;P04440	.|.;.;DPB1_HUMAN	Y|I	72|105;105;105;82	.|ENSP00000408146:M105I;ENSP00000439674:M105I;ENSP00000412654:M82I	.|ENSP00000389210:M105I	C|M	+|+	2|3	0|0	HLA-DPB1|HLA-DPB1	33156641|33156641	0.030000|0.030000	0.19436|0.19436	0.450000|0.450000	0.26969|0.26969	0.008000|0.008000	0.06430|0.06430	0.177000|0.177000	0.16801|0.16801	0.105000|0.105000	0.17753|0.17753	-0.134000|-0.134000	0.14843|0.14843	TGT|ATG	G|0.755;A|0.245	0.245	strong		0.701	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
SRPRB	58477	hgsc.bcm.edu	37	3	133524717	133524717	+	Missense_Mutation	SNP	G	G	C	rs1107413	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:133524717G>C	ENST00000466490.2	+	2	310	c.25G>C	c.(25-27)Gtg>Ctg	p.V9L		NM_021203.3	NP_067026.3	Q9Y5M8	SRPRB_HUMAN	signal recognition particle receptor, B subunit	9			V -> L (in dbSNP:rs1107413). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|small GTPase mediated signal transduction (GO:0007264)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|urinary_tract(2)	12						CTCGCGCCGGGTGGCAGATGG	0.677													G|||	867	0.173123	0.0825	0.2363	5008	,	,		15824	0.2262		0.2038	False		,,,				2504	0.1646				p.V9L		Atlas-SNP	.											.	SRPRB	28	.	0			c.G25C						PASS	.	G	LEU/VAL	506,3900	219.4+/-237.2	31,444,1728	43.0	45.0	45.0		25	0.8	0.0	3	dbSNP_86	45	2154,6444	342.7+/-324.6	297,1560,2442	yes	missense	SRPRB	NM_021203.3	32	328,2004,4170	CC,CG,GG		25.0523,11.4843,20.4552	benign	9/272	133524717	2660,10344	2203	4299	6502	SO:0001583	missense	58477	exon2			CGCCGGGTGGCAG	AK075531	CCDS3081.1	3q22.1	2004-01-29			ENSG00000144867	ENSG00000144867			24085	protein-coding gene	gene with protein product						7844142, 10859309	Standard	NM_021203		Approved	APMCF1	uc003epx.2	Q9Y5M8	OTTHUMG00000159753	ENST00000466490.2:c.25G>C	3.37:g.133524717G>C	ENSP00000418401:p.Val9Leu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	138	54	0.391304	NM_021203	Q6P595|Q8N2D8	Missense_Mutation	SNP	ENST00000466490.2	37	CCDS3081.1	402	0.18406593406593408	38	0.07723577235772358	86	0.23756906077348067	126	0.2202797202797203	152	0.20052770448548812	G	4.670	0.124636	0.08931	0.114843	0.250523	ENSG00000144867	ENST00000466490;ENST00000484684	T;T	0.47528	2.54;0.84	4.91	0.767	0.18482	.	3.007370	0.02176	U	0.060084	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10894	-1.0610	9	0.35671	T	0.21	-0.5703	6.6806	0.23117	0.2138:0.164:0.6222:0.0	rs1107413;rs17855773;rs1107413	9	Q9Y5M8	SRPRB_HUMAN	L	9	ENSP00000418401:V9L;ENSP00000417096:V9L	ENSP00000418401:V9L	V	+	1	0	SRPRB	135007407	0.000000	0.05858	0.011000	0.14972	0.111000	0.19643	-1.023000	0.03607	0.256000	0.21614	0.650000	0.86243	GTG	G|0.795;C|0.205	0.205	strong		0.677	SRPRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357170.2		
ZNRF4	148066	hgsc.bcm.edu	37	19	5455800	5455800	+	Missense_Mutation	SNP	G	G	A	rs2240745	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:5455800G>A	ENST00000222033.4	+	1	375	c.298G>A	c.(298-300)Gta>Ata	p.V100I		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	100			V -> I (in dbSNP:rs2240745).			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		GCAGGCAGTGGTACGGGCCGT	0.692													G|||	395	0.0788738	0.0045	0.0259	5008	,	,		15232	0.1845		0.0656	False		,,,				2504	0.1217				p.V100I		Atlas-SNP	.											.	ZNRF4	59	.	0			c.G298A						PASS	.	G	ILE/VAL	60,4196		0,60,2068	46.0	56.0	53.0		298	3.6	0.0	19	dbSNP_98	53	518,7936		9,500,3718	yes	missense	ZNRF4	NM_181710.3	29	9,560,5786	AA,AG,GG		6.1273,1.4098,4.5476	possibly-damaging	100/430	5455800	578,12132	2128	4227	6355	SO:0001583	missense	148066	exon1			GCAGTGGTACGGG	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"""RING-type (C3HC4) zinc fingers"""	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.298G>A	19.37:g.5455800G>A	ENSP00000222033:p.Val100Ile	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	38	37	0.973684	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	37	CCDS42475.1	174	0.07967032967032966	2	0.0040650406504065045	11	0.03038674033149171	115	0.20104895104895104	46	0.06068601583113457	G	8.511	0.866465	0.17250	0.014098	0.061273	ENSG00000105428	ENST00000222033	T	0.04603	3.59	3.63	3.63	0.41609	.	0.563259	0.14220	U	0.333510	T	0.00012	0.0000	N	0.25380	0.74	0.58432	P	1.999999999946489E-6	D	0.61080	0.989	P	0.52343	0.696	T	0.37888	-0.9686	9	0.08179	T	0.78	.	10.79	0.46428	0.0:0.0:1.0:0.0	rs2240745;rs17238641;rs57030663;rs2240745	100	Q8WWF5	ZNRF4_HUMAN	I	100	ENSP00000222033:V100I	ENSP00000222033:V100I	V	+	1	0	ZNRF4	5406800	0.370000	0.25047	0.043000	0.18650	0.006000	0.05464	1.969000	0.40510	1.576000	0.49790	0.313000	0.20887	GTA	G|0.920;A|0.080	0.080	strong		0.692	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
SPATA20	64847	hgsc.bcm.edu	37	17	48628092	48628092	+	Silent	SNP	A	A	G	rs1132414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48628092A>G	ENST00000356488.4	+	10	1232	c.1149A>G	c.(1147-1149)gaA>gaG	p.E383E	SPATA20_ENST00000006658.6_Silent_p.E399E|SPATA20_ENST00000393244.3_Silent_p.E339E|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	383					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			ATAGCGCAGAAGATGCAGACT	0.672											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1497	0.298922	0.68	0.2349	5008	,	,		16897	0.0427		0.2535	False		,,,				2504	0.1401				p.E399E		Atlas-SNP	.											.	SPATA20	59	.	0			c.A1197G						PASS	.	G		2682,1724	489.2+/-361.4	834,1014,355	47.0	59.0	55.0		1197	4.7	1.0	17	dbSNP_86	55	2185,6409	687.2+/-404.2	267,1651,2379	no	coding-synonymous	SPATA20	NM_022827.2		1101,2665,2734	GG,GA,AA		25.4247,39.1285,37.4385		399/803	48628092	4867,8133	2203	4297	6500	SO:0001819	synonymous_variant	64847	exon11			CGCAGAAGATGCA		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1149A>G	17.37:g.48628092A>G		Somatic	89	0	0	119	WXS	Illumina HiSeq	Phase_I	112	48	0.428571	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Silent	SNP	ENST00000356488.4	37	CCDS58563.1																																																																																			A|0.652;G|0.348	0.348	strong		0.672	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
CHAC1	79094	hgsc.bcm.edu	37	15	41245676	41245676	+	Silent	SNP	G	G	A	rs11557249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:41245676G>A	ENST00000446533.3	+	1	330	c.21G>A	c.(19-21)gaG>gaA	p.E7E	CHAC1_ENST00000487220.1_5'Flank|CHAC1_ENST00000444189.2_Silent_p.E7E	NM_001142776.1|NM_024111.3	NP_001136248.1|NP_077016.2	Q9BUX1	CHAC1_HUMAN	ChaC, cation transport regulator homolog 1 (E. coli)	7					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein processing (GO:0010955)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|trans-Golgi network (GO:0005802)	Notch binding (GO:0005112)			endometrium(1)|large_intestine(1)|skin(1)	3		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.66e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.163)		CTCAGCTGGAGCTACCGAGCG	0.701													G|||	1186	0.236821	0.1142	0.3112	5008	,	,		13088	0.2292		0.3907	False		,,,				2504	0.1994				p.E7E		Atlas-SNP	.											CHAC1_ENST00000446533,NS,carcinoma,0,1	CHAC1	25	1	0			c.G21A						PASS	.	G	,	204,1180		10,184,498	14.0	21.0	19.0		21,21	4.0	1.0	15	dbSNP_120	19	1266,1916		250,766,575	no	coding-synonymous,coding-synonymous	CHAC1	NM_001142776.1,NM_024111.3	,	260,950,1073	AA,AG,GG		39.7863,14.7399,32.1945	,	7/220,7/265	41245676	1470,3096	692	1591	2283	SO:0001819	synonymous_variant	79094	exon1			GCTGGAGCTACCG	BC019625	CCDS10070.2, CCDS45233.1	15q15.1	2013-09-12	2006-09-12		ENSG00000128965	ENSG00000128965			28680	protein-coding gene	gene with protein product	"""gamma-GCT acting on glutathione homolog 1"""	614587	"""ChaC, cation transport regulator-like 1 (E. coli)"""			23070364	Standard	NM_024111		Approved	MGC4504	uc001znh.2	Q9BUX1	OTTHUMG00000130208	ENST00000446533.3:c.21G>A	15.37:g.41245676G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	57	5	0.0877193	NM_024111	Q0VIA0	Silent	SNP	ENST00000446533.3	37	CCDS10070.2																																																																																			G|0.742;A|0.258	0.258	strong		0.701	CHAC1-001	KNOWN	downstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252526.3	NM_024111	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596241	48596241	+	Missense_Mutation	SNP	A	A	G	rs11168459	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48596241A>G	ENST00000310248.2	-	1	929	c.835T>C	c.(835-837)Tac>Cac	p.Y279H		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	279			Y -> H (in dbSNP:rs11168459).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y279H(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						ATGATGGTGTACAGGAGGGAG	0.493													A|||	983	0.196286	0.2579	0.1916	5008	,	,		22103	0.1935		0.2117	False		,,,				2504	0.1033				p.Y279H		Atlas-SNP	.											OR10AD1,NS,carcinoma,0,1	OR10AD1	24	1	1	Substitution - Missense(1)	stomach(1)	c.T835C						PASS	.	A	HIS/TYR	1143,3263	405.8+/-333.6	133,877,1193	123.0	122.0	122.0		835	3.8	1.0	12	dbSNP_120	122	1857,6743	331.6+/-319.7	197,1463,2640	yes	missense	OR10AD1	NM_001004134.1	83	330,2340,3833	GG,GA,AA		21.593,25.9419,23.0663	probably-damaging	279/318	48596241	3000,10006	2203	4300	6503	SO:0001583	missense	121275	exon1			TGGTGTACAGGAG		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.835T>C	12.37:g.48596241A>G	ENSP00000308689:p.Tyr279His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	473	0.21657509157509158	125	0.2540650406504065	76	0.20994475138121546	121	0.21153846153846154	151	0.19920844327176782	A	17.45	3.393798	0.62066	0.259419	0.21593	ENSG00000172640	ENST00000310248	T	0.00321	8.11	4.96	3.81	0.43845	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35466	N	0.003189	T	0.00012	0.0000	M	0.90198	3.095	0.31492	P	0.665852	D	0.61697	0.99	P	0.62184	0.899	T	0.43686	-0.9376	9	0.87932	D	0	-26.9109	9.0035	0.36097	0.9115:0.0:0.0885:0.0	rs11168459;rs52836532;rs58095204;rs11168459	279	Q8NGE0	O10AD_HUMAN	H	279	ENSP00000308689:Y279H	ENSP00000308689:Y279H	Y	-	1	0	OR10AD1	46882508	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	8.441000	0.90313	1.030000	0.39839	0.533000	0.62120	TAC	A|0.772;G|0.228	0.228	strong		0.493	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
IRF1	3659	hgsc.bcm.edu	37	5	131822055	131822055	+	Silent	SNP	T	T	C	rs9282762	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:131822055T>C	ENST00000245414.4	-	7	813	c.555A>G	c.(553-555)ccA>ccG	p.P185P	IRF1_ENST00000405885.2_Silent_p.P185P|IRF1_ENST00000463784.1_5'Flank	NM_002198.2	NP_002189.1	P10914	IRF1_HUMAN	interferon regulatory factor 1	185					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell cycle arrest (GO:0007050)|cellular response to interferon-beta (GO:0035458)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000564)|regulation of cell cycle (GO:0051726)|regulation of innate immune response (GO:0045088)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.026)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	LUAD - Lung adenocarcinoma(142;0.247)		TGACAGCACATGGCGACAGTG	0.577													C|||	2036	0.40655	0.4758	0.3588	5008	,	,		19987	0.3829		0.3449	False		,,,				2504	0.4346				p.P185P		Atlas-SNP	.											.	IRF1	26	.	0			c.A555G						PASS	.	C	,	2158,2248	588.0+/-386.8	521,1116,566	72.0	70.0	71.0		,555	-7.7	0.0	5	dbSNP_118	71	2806,5794	672.0+/-402.9	460,1886,1954	no	utr-3,coding-synonymous	IRF1,C5orf56	NM_001207002.1,NM_002198.2	,	981,3002,2520	CC,CT,TT		32.6279,48.9787,38.167	,	,185/326	131822055	4964,8042	2203	4300	6503	SO:0001819	synonymous_variant	3659	exon7			AGCACATGGCGAC		CCDS4155.1	5q23-q31	2008-07-18			ENSG00000125347	ENSG00000125347			6116	protein-coding gene	gene with protein product	"""interferon regulatory factor-1"""	147575				2726461, 1680796	Standard	NM_002198		Approved	MAR	uc003kxa.2	P10914	OTTHUMG00000059497	ENST00000245414.4:c.555A>G	5.37:g.131822055T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_002198	Q96GG7	Silent	SNP	ENST00000245414.4	37	CCDS4155.1																																																																																			T|0.623;C|0.377	0.377	strong		0.577	IRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132340.1	NM_002198	
NFE2L1	4779	hgsc.bcm.edu	37	17	46136133	46136133	+	Silent	SNP	G	G	C	rs2229369	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:46136133G>C	ENST00000362042.3	+	6	2065	c.1449G>C	c.(1447-1449)tcG>tcC	p.S483S	NFE2L1_ENST00000536222.1_Silent_p.S327S|RP5-890E16.4_ENST00000583349.1_RNA|NFE2L1_ENST00000583378.1_Silent_p.S284S|NFE2L1_ENST00000582155.1_Silent_p.S295S|NFE2L1_ENST00000361665.3_Silent_p.S472S|NFE2L1_ENST00000357480.5_Silent_p.S453S|NFE2L1_ENST00000585291.1_Silent_p.S453S	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	483					anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CCTTAGACTCGAGCCATAGCC	0.527													G|||	467	0.0932508	0.0068	0.049	5008	,	,		21212	0.1954		0.1213	False		,,,				2504	0.1074				p.S483S		Atlas-SNP	.											.	NFE2L1	60	.	0			c.G1449C						PASS	.	G		123,4283	90.2+/-128.9	2,119,2082	94.0	94.0	94.0		1449	-8.9	0.9	17	dbSNP_98	94	867,7733	196.8+/-241.6	50,767,3483	no	coding-synonymous	NFE2L1	NM_003204.2		52,886,5565	CC,CG,GG		10.0814,2.7916,7.6119		483/773	46136133	990,12016	2203	4300	6503	SO:0001819	synonymous_variant	4779	exon6			AGACTCGAGCCAT	AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"""basic leucine zipper proteins"""	7781	protein-coding gene	gene with protein product		163260	"""nuclear factor (erythroid-derived 2)-like 1"""	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.1449G>C	17.37:g.46136133G>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	145	67	0.462069	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Silent	SNP	ENST00000362042.3	37	CCDS11524.1																																																																																			G|0.914;C|0.086	0.086	strong		0.527	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204	
HPS6	79803	hgsc.bcm.edu	37	10	103825747	103825747	+	Silent	SNP	G	G	A	rs3737243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:103825747G>A	ENST00000299238.5	+	1	601	c.516G>A	c.(514-516)ggG>ggA	p.G172G		NM_024747.5	NP_079023.2	Q86YV9	HPS6_HUMAN	Hermansky-Pudlak syndrome 6	172					blood coagulation (GO:0007596)|melanocyte differentiation (GO:0030318)|organelle organization (GO:0006996)|protein localization to membrane (GO:0072657)	BLOC-2 complex (GO:0031084)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|Rab GTPase binding (GO:0017137)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)	11		Colorectal(252;0.122)		Epithelial(162;5.93e-08)|all cancers(201;1.03e-06)		AGCCCAGCGGGGAAGCTAGCA	0.697									Hermansky-Pudlak syndrome				G|||	331	0.0660942	0.0076	0.0663	5008	,	,		14141	0.1429		0.1093	False		,,,				2504	0.0215				p.G172G		Atlas-SNP	.											.	HPS6	38	.	0			c.G516A						PASS	.	G		72,4318		1,70,2124	15.0	17.0	16.0		516	-0.3	1.0	10	dbSNP_107	16	847,7743		43,761,3491	no	coding-synonymous	HPS6	NM_024747.5		44,831,5615	AA,AG,GG		9.8603,1.6401,7.0801		172/776	103825747	919,12061	2195	4295	6490	SO:0001819	synonymous_variant	79803	exon1	Familial Cancer Database	HPS, HPS1-8	CAGCGGGGAAGCT	BC009258	CCDS7527.1	10q24.32	2014-06-18			ENSG00000166189	ENSG00000166189			18817	protein-coding gene	gene with protein product		607522				12548288	Standard	NM_024747		Approved	FLJ22501	uc001kuj.3	Q86YV9	OTTHUMG00000018945	ENST00000299238.5:c.516G>A	10.37:g.103825747G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	14	12	0.857143	NM_024747	Q5VV69|Q9H685	Silent	SNP	ENST00000299238.5	37	CCDS7527.1																																																																																			G|0.929;A|0.071	0.071	strong		0.697	HPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050018.2	NM_024747	
C2orf71	388939	hgsc.bcm.edu	37	2	29294629	29294629	+	Silent	SNP	C	C	T	rs34253433	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29294629C>T	ENST00000331664.5	-	1	2498	c.2499G>A	c.(2497-2499)ccG>ccA	p.P833P		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	833					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CTTCCATAGGCGGTGGAGGGA	0.557													c|||	625	0.1248	0.0287	0.1585	5008	,	,		8917	0.1617		0.2137	False		,,,				2504	0.1012				p.P833P		Atlas-SNP	.											.	C2orf71	146	.	0			c.G2499A						PASS	.	C		274,3586		9,256,1665	103.0	102.0	103.0		2499	-10.7	0.3	2	dbSNP_126	103	1857,6439		192,1473,2483	no	coding-synonymous	C2orf71	NM_001029883.1		201,1729,4148	TT,TC,CC		22.3843,7.0984,17.5304		833/1289	29294629	2131,10025	1930	4148	6078	SO:0001819	synonymous_variant	388939	exon1			CATAGGCGGTGGA		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.2499G>A	2.37:g.29294629C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	NM_001029883		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																			C|0.821;T|0.179	0.179	strong		0.557	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
MYH8	4626	hgsc.bcm.edu	37	17	10296486	10296486	+	Silent	SNP	G	G	A	rs33969260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:10296486G>A	ENST00000403437.2	-	36	5302	c.5208C>T	c.(5206-5208)gaC>gaT	p.D1736D	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1736					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GTTGGGAAACGTCATTTTCTA	0.378									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				G|||	478	0.0954473	0.0212	0.1383	5008	,	,		19575	0.002		0.2942	False		,,,				2504	0.0573				p.D1736D		Atlas-SNP	.											.	MYH8	346	.	0			c.C5208T						PASS	.	G		239,4167	140.8+/-176.2	7,225,1971	267.0	240.0	249.0		5208	1.8	1.0	17	dbSNP_126	249	2099,6501	362.3+/-332.7	268,1563,2469	no	coding-synonymous	MYH8	NM_002472.2		275,1788,4440	AA,AG,GG		24.407,5.4244,17.9763		1736/1938	10296486	2338,10668	2203	4300	6503	SO:0001819	synonymous_variant	4626	exon36	Familial Cancer Database	Carney Complex Variant	GGAAACGTCATTT		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.5208C>T	17.37:g.10296486G>A		Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	237	237	1	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																			G|0.826;A|0.174	0.174	strong		0.378	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
MUC16	94025	hgsc.bcm.edu	37	19	9066259	9066259	+	Missense_Mutation	SNP	T	T	C	rs17000770	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9066259T>C	ENST00000397910.4	-	3	21390	c.21187A>G	c.(21187-21189)Act>Gct	p.T7063A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7065	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.T7063A(2)|p.T2696A(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AATCTCTGAGTCAAAGTTGAA	0.498													T|||	1758	0.351038	0.388	0.3746	5008	,	,		22181	0.2768		0.3489	False		,,,				2504	0.363				p.T7063A		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,3	MUC16	4315	3	3	Substitution - Missense(3)	prostate(3)	c.A21187G						PASS	.	T	ALA/THR	1449,2487		279,891,798	137.0	132.0	133.0		21187	-0.1	0.0	19	dbSNP_123	133	3095,5251		606,1883,1684	yes	missense	MUC16	NM_024690.2	58	885,2774,2482	CC,CT,TT		37.0836,36.814,36.9972	possibly-damaging	7063/14508	9066259	4544,7738	1968	4173	6141	SO:0001583	missense	94025	exon3			TCTGAGTCAAAGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21187A>G	19.37:g.9066259T>C	ENSP00000381008:p.Thr7063Ala	Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	746	0.3415750915750916	167	0.3394308943089431	133	0.3674033149171271	174	0.3041958041958042	272	0.35883905013192613	t	4.731	0.136008	0.09032	0.36814	0.370836	ENSG00000181143	ENST00000397910	T	0.26223	1.75	2.54	-0.117	0.13551	.	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	.	.	.	P	0.39424	0.673	P	0.46975	0.533	T	0.45279	-0.9272	8	0.87932	D	0	.	5.3856	0.16216	0.5728:0.0:0.0:0.4272	rs17000770;rs52798269;rs58411266;rs17000770	7063	B5ME49	.	A	7063	ENSP00000381008:T7063A	ENSP00000381008:T7063A	T	-	1	0	MUC16	8927259	0.160000	0.22878	0.001000	0.08648	0.003000	0.03518	1.613000	0.36900	-0.128000	0.11641	0.334000	0.21626	ACT	T|0.643;C|0.357	0.357	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651120	1651120	+	Missense_Mutation	SNP	G	G	T	rs66665994		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1651120G>T	ENST00000399676.2	+	1	88	c.50G>T	c.(49-51)cGt>cTt	p.R17L		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	17				R -> L (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)		p.R17L(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		tgtggaggccgtggctccggc	0.697																																					p.R17L		Atlas-SNP	.											KRTAP5-5,NS,carcinoma,+1,15	KRTAP5-5	86	15	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.G50T						scavenged	.						49.0	62.0	58.0					11																	1651120		2185	4288	6473	SO:0001583	missense	439915	exon1			GAGGCCGTGGCTC	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.50G>T	11.37:g.1651120G>T	ENSP00000382584:p.Arg17Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	65	62	0.953846	NM_001001480	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	1029	0.47115384615384615	280	0.5691056910569106	162	0.44751381215469616	221	0.38636363636363635	366	0.48284960422163586	G	7.595	0.671480	0.14776	.	.	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01005	5.45	2.63	2.63	0.31362	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.49389	P	2.1099999999996122E-4	B	0.24963	0.115	B	0.14023	0.01	T	0.01504	-1.1338	8	0.44086	T	0.13	.	9.323	0.37975	0.0:0.0:1.0:0.0	.	17	Q701N2	KRA55_HUMAN	L	17;15	ENSP00000382584:R17L	ENSP00000382584:R17L	R	+	2	0	KRTAP5-5	1607696	1.000000	0.71417	0.817000	0.32601	0.004000	0.04260	3.925000	0.56484	1.420000	0.47138	0.442000	0.29010	CGT	G|0.527;T|0.473	0.473	strong		0.697	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
SERPINA5	5104	hgsc.bcm.edu	37	14	95053890	95053890	+	Missense_Mutation	SNP	G	G	A	rs6115|rs386780205	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:95053890G>A	ENST00000554866.1	+	2	305	c.191G>A	c.(190-192)aGc>aAc	p.S64N	SERPINA5_ENST00000553780.1_Missense_Mutation_p.S64N|SERPINA5_ENST00000554276.1_Missense_Mutation_p.S64N|SERPINA5_ENST00000329597.7_Missense_Mutation_p.S64N			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	64			S -> N (in dbSNP:rs6115). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1714450, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:2173165, ECO:0000269|PubMed:3027058, ECO:0000269|PubMed:8471250, ECO:0000269|PubMed:8713781, ECO:0000269|Ref.6}.		fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CCCAGCCAGAGCATCTTCTTC	0.627													A|||	3111	0.621206	0.947	0.451	5008	,	,		18313	0.4266		0.6382	False		,,,				2504	0.4847				p.S64N		Atlas-SNP	.											.	SERPINA5	69	.	0			c.G191A						PASS	.	A	ASN/SER	3932,474	195.7+/-220.2	1771,390,42	34.0	35.0	34.0		191	4.1	0.3	14	dbSNP_52	34	5687,2913	444.3+/-360.6	1881,1925,494	yes	missense	SERPINA5	NM_000624.4	46	3652,2315,536	AA,AG,GG		33.8721,10.7581,26.0418	benign	64/407	95053890	9619,3387	2203	4300	6503	SO:0001583	missense	5104	exon3			GCCAGAGCATCTT	M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"""Serine (or cysteine) peptidase inhibitors"""	8723	protein-coding gene	gene with protein product		601841	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"""	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.191G>A	14.37:g.95053890G>A	ENSP00000451126:p.Ser64Asn	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_000624	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	37	CCDS9928.1	1284	0.5879120879120879	414	0.8414634146341463	178	0.49171270718232046	209	0.36538461538461536	483	0.637203166226913	A	0.146	-1.096347	0.01843	0.892419	0.661279	ENSG00000188488	ENST00000554220;ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000553511;ENST00000554633;ENST00000555681;ENST00000554276;ENST00000557598	T;T;T;T;T;T;T;T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6;-0.6	4.11	4.11	0.48088	Serpin domain (3);	0.000000	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00007	-3.165	0.58432	P	4.000000000004E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42849	-0.9427	9	0.02654	T	1	.	9.0791	0.36540	0.912:0.0:0.088:0.0	rs6115;rs17856281;rs57446993;rs6115	64;64	G3V5Q9;P05154	.;IPSP_HUMAN	N	64	ENSP00000450484:S64N;ENSP00000450837:S64N;ENSP00000452469:S64N;ENSP00000451126:S64N;ENSP00000333203:S64N;ENSP00000450745:S64N;ENSP00000451215:S64N;ENSP00000451697:S64N;ENSP00000451650:S64N;ENSP00000451610:S64N;ENSP00000450485:S64N	ENSP00000333203:S64N	S	+	2	0	SERPINA5	94123643	1.000000	0.71417	0.278000	0.24718	0.082000	0.17680	6.683000	0.74533	0.745000	0.32763	-0.361000	0.07541	AGC	G|0.318;A|0.682	0.682	strong		0.627	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
FAM179A	165186	hgsc.bcm.edu	37	2	29259543	29259543	+	Missense_Mutation	SNP	T	T	C	rs72788155	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29259543T>C	ENST00000379558.4	+	18	2906	c.2555T>C	c.(2554-2556)gTt>gCt	p.V852A	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Missense_Mutation_p.V797A	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	852										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						ATCATCACTGTTGCAGACAAC	0.562													T|||	18	0.00359425	0.0008	0.0014	5008	,	,		19875	0.0		0.0129	False		,,,				2504	0.0031				p.V852A		Atlas-SNP	.											.	FAM179A	106	.	0			c.T2555C						PASS	.	T	ALA/VAL	21,4385	29.0+/-57.7	0,21,2182	125.0	94.0	104.0		2555	3.7	0.4	2	dbSNP_130	104	191,8409	84.2+/-146.7	2,187,4111	yes	missense	FAM179A	NM_199280.2	64	2,208,6293	CC,CT,TT		2.2209,0.4766,1.63	benign	852/1020	29259543	212,12794	2203	4300	6503	SO:0001583	missense	165186	exon18			TCACTGTTGCAGA	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.2555T>C	2.37:g.29259543T>C	ENSP00000368876:p.Val852Ala	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	T	15.18	2.757343	0.49468	0.004766	0.022209	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.69040	-0.37;-0.37	6.04	3.68	0.42216	Armadillo-like helical (1);Armadillo-type fold (1);	0.350805	0.24774	N	0.035714	T	0.37839	0.1018	L	0.38531	1.155	0.24198	N	0.995528	B;B;B	0.25390	0.096;0.125;0.082	B;B;B	0.25140	0.039;0.041;0.058	T	0.31024	-0.9958	10	0.34782	T	0.22	.	9.9505	0.41636	0.0:0.128:0.0:0.872	.	797;852;150	F8W8E4;Q6ZUX3;Q6ZUX3-3	.;F179A_HUMAN;.	A	852;797	ENSP00000368876:V852A;ENSP00000384699:V797A	ENSP00000368876:V852A	V	+	2	0	FAM179A	29113047	0.951000	0.32395	0.374000	0.26016	0.893000	0.52053	3.920000	0.56446	0.540000	0.28808	0.459000	0.35465	GTT	T|0.988;C|0.012	0.012	strong		0.562	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
FOXD4	2298	hgsc.bcm.edu	37	9	117696	117696	+	Missense_Mutation	SNP	G	G	A	rs9406415	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:117696G>A	ENST00000382500.2	-	1	721	c.424C>T	c.(424-426)Cgc>Tgc	p.R142C		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	142					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		AACTTGCGGCGGTAGTAGGGG	0.642																																					p.R142C		Atlas-SNP	.											FOXD4_ENST00000382500,brain,glioma,0,1	FOXD4	75	1	0			c.C424T						PASS	.						41.0	68.0	59.0					9																	117696		2097	4163	6260	SO:0001583	missense	2298	exon1			TGCGGCGGTAGTA	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.424C>T	9.37:g.117696G>A	ENSP00000371940:p.Arg142Cys	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	217	85	0.391705	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	477	0.2184065934065934	82	0.16666666666666666	67	0.1850828729281768	135	0.23601398601398602	193	0.2546174142480211	.	15.82	2.945410	0.53079	.	.	ENSG00000170122	ENST00000382500	D	0.96491	-4.03	2.24	2.24	0.28232	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.35870	U	0.002927	T	0.00754	0.0025	M	0.94021	3.485	0.09310	P	0.99999602235	D	0.89917	1.0	D	0.81914	0.995	T	0.00289	-1.1844	9	0.56958	D	0.05	.	4.7852	0.13222	0.0:0.2374:0.5208:0.2418	rs9406415	142	Q12950	FOXD4_HUMAN	C	142	ENSP00000371940:R142C	ENSP00000371940:R142C	R	-	1	0	FOXD4	107696	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	1.314000	0.33597	1.253000	0.44018	0.291000	0.19559	CGC	G|0.778;A|0.222	0.222	strong		0.642	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
LIMA1	51474	hgsc.bcm.edu	37	12	50571069	50571069	+	Silent	SNP	G	G	A	rs35414607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:50571069G>A	ENST00000341247.4	-	11	2207	c.2058C>T	c.(2056-2058)tcC>tcT	p.S686S	LIMA1_ENST00000394943.3_Silent_p.S687S|LIMA1_ENST00000552783.1_Silent_p.S527S|LIMA1_ENST00000552909.1_Silent_p.S525S|LIMA1_ENST00000552491.1_Silent_p.S383S|LIMA1_ENST00000547825.1_Silent_p.S384S|LIMA1_ENST00000552823.1_Silent_p.S526S	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	686					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						CATCTTCATCGGAGTCTGCAC	0.408													G|||	57	0.0113818	0.0401	0.0058	5008	,	,		21645	0.0		0.0	False		,,,				2504	0.0				p.S687S		Atlas-SNP	.											.	LIMA1	67	.	0			c.C2061T						PASS	.	G	,,	121,4285	89.7+/-128.4	2,117,2084	283.0	278.0	279.0		2061,1581,2058	0.0	0.2	12	dbSNP_126	279	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	LIMA1	NM_001113546.1,NM_001113547.1,NM_016357.4	,,	2,118,6383	AA,AG,GG		0.0116,2.7463,0.938	,,	687/761,527/601,686/760	50571069	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	51474	exon11			TTCATCGGAGTCT	AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.2058C>T	12.37:g.50571069G>A		Somatic	590	0	0		WXS	Illumina HiSeq	Phase_I	620	304	0.490323	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Silent	SNP	ENST00000341247.4	37	CCDS8802.1																																																																																			G|0.986;A|0.014	0.014	strong		0.408	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
MRGPRE	116534	hgsc.bcm.edu	37	11	3249984	3249984	+	Missense_Mutation	SNP	C	C	T	rs12295710	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:3249984C>T	ENST00000389832.5	-	2	352	c.46G>A	c.(46-48)Ggc>Agc	p.G16S	MRGPRE_ENST00000436689.2_Missense_Mutation_p.G15S|AC109309.4_ENST00000418995.2_RNA			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	16			G -> S (in dbSNP:rs12295710).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCCTGGGCGCCGTTGGCGGCC	0.672													C|||	1660	0.33147	0.0567	0.3026	5008	,	,		17649	0.4692		0.495	False		,,,				2504	0.4131				p.G16S		Atlas-SNP	.											MRGPRE,colon,carcinoma,+2,1	MRGPRE	35	1	0			c.G46A						PASS	.	C	SER/GLY	484,3440		35,414,1513	31.0	34.0	33.0		43	-2.3	0.0	11	dbSNP_120	33	3932,4356		924,2084,1136	yes	missense	MRGPRE	NM_001039165.2	56	959,2498,2649	TT,TC,CC		47.4421,12.3344,36.1612	benign	15/312	3249984	4416,7796	1962	4144	6106	SO:0001583	missense	116534	exon2			GGGCGCCGTTGGC	AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"""GPCR / Class A : Orphans"""	30694	protein-coding gene	gene with protein product		607232	"""G protein-coupled receptor 167"""	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.46G>A	11.37:g.3249984C>T	ENSP00000374482:p.Gly16Ser	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_001039165	Q2M1V7	Missense_Mutation	SNP	ENST00000389832.5	37		824	0.3772893772893773	34	0.06910569105691057	118	0.3259668508287293	292	0.5104895104895105	380	0.5013192612137203	c	8.567	0.879164	0.17395	0.123344	0.474421	ENSG00000184350	ENST00000436689;ENST00000389832	.	.	.	2.63	-2.32	0.06745	.	0.918531	0.08824	N	0.888287	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45011	-0.9290	8	0.07030	T	0.85	-1.8484	6.7124	0.23284	0.0:0.2466:0.0:0.7534	rs12295710;rs59380296	15	Q86SM8	MRGRE_HUMAN	S	16;15	.	ENSP00000374482:G15S	G	-	1	0	MRGPRE	3206560	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.223000	0.09177	-0.503000	0.06586	-0.350000	0.07774	GGC	C|0.601;T|0.399	0.399	strong		0.672	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536	
CAP2	10486	hgsc.bcm.edu	37	6	17543302	17543302	+	Silent	SNP	A	A	G	rs9256	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:17543302A>G	ENST00000229922.2	+	11	1669	c.1137A>G	c.(1135-1137)aaA>aaG	p.K379K	CAP2_ENST00000378990.2_Silent_p.K353K|CAP2_ENST00000465994.1_Silent_p.K315K|CAP2_ENST00000493172.1_Silent_p.K119K|CAP2_ENST00000489374.1_Silent_p.K267K	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	379	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			ACAACTGTAAAAAACTCGGCC	0.403													G|||	3137	0.626398	0.6233	0.5605	5008	,	,		18074	0.7331		0.6272	False		,,,				2504	0.5665				p.K379K		Atlas-SNP	.											.	CAP2	61	.	0			c.A1137G						PASS	.	G		2882,1524	482.6+/-359.5	949,984,270	176.0	177.0	177.0		1137	2.7	1.0	6	dbSNP_52	177	5516,3084	473.3+/-368.6	1778,1960,562	no	coding-synonymous	CAP2	NM_006366.2		2727,2944,832	GG,GA,AA		35.8605,34.5892,35.4298		379/478	17543302	8398,4608	2203	4300	6503	SO:0001819	synonymous_variant	10486	exon11			CTGTAAAAAACTC	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.1137A>G	6.37:g.17543302A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	174	84	0.482759	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	37	CCDS4539.1																																																																																			A|0.360;G|0.640	0.640	strong		0.403	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
PLBD1	79887	hgsc.bcm.edu	37	12	14664595	14664595	+	Silent	SNP	A	A	G	rs10846013	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:14664595A>G	ENST00000240617.5	-	7	1547	c.895T>C	c.(895-897)Ttg>Ctg	p.L299L		NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	299					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						GTCTGCAGCAATATCAATCCA	0.413													A|||	1420	0.283546	0.1876	0.3919	5008	,	,		20168	0.1925		0.2555	False		,,,				2504	0.4591				p.L299L		Atlas-SNP	.											.	PLBD1	36	.	0			c.T895C						PASS	.	A		859,3547	335.2+/-303.8	68,723,1412	70.0	69.0	69.0		895	-11.6	0.0	12	dbSNP_120	69	2619,5981	424.4+/-354.6	397,1825,2078	no	coding-synonymous	PLBD1	NM_024829.5		465,2548,3490	GG,GA,AA		30.4535,19.4961,26.7415		299/554	14664595	3478,9528	2203	4300	6503	SO:0001819	synonymous_variant	79887	exon7			GCAGCAATATCAA	BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"""PLB homolog 1 (Dictyostelium)"""					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.895T>C	12.37:g.14664595A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_024829	A8K4E9|Q9BVV3|Q9H625	Silent	SNP	ENST00000240617.5	37	CCDS31751.1																																																																																			A|0.734;G|0.266	0.266	strong		0.413	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829	
RSU1	6251	hgsc.bcm.edu	37	10	16794623	16794623	+	Silent	SNP	C	C	T	rs10445	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:16794623C>T	ENST00000377921.3	-	6	814	c.513G>A	c.(511-513)tcG>tcA	p.S171S	RSU1_ENST00000602389.1_Silent_p.S118S|RSU1_ENST00000345264.5_Silent_p.S171S|RSU1_ENST00000464074.2_5'UTR			Q15404	RSU1_HUMAN	Ras suppressor protein 1	171					cell junction assembly (GO:0034329)|positive regulation of neural precursor cell proliferation (GO:2000179)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(1;7.54e-08)		CCTTAGGCAGCGAGATCAGGT	0.478													C|||	518	0.103435	0.0113	0.1599	5008	,	,		19626	0.1538		0.1581	False		,,,				2504	0.0798				p.S171S		Atlas-SNP	.											.	RSU1	31	.	0			c.G513A						PASS	.	C	,	129,4277	93.9+/-132.6	5,119,2079	102.0	96.0	98.0		513,354	-1.4	1.0	10	dbSNP_52	98	1242,7358	249.2+/-276.5	90,1062,3148	no	coding-synonymous,coding-synonymous	RSU1	NM_012425.3,NM_152724.2	,	95,1181,5227	TT,TC,CC		14.4419,2.9278,10.5413	,	171/278,118/225	16794623	1371,11635	2203	4300	6503	SO:0001819	synonymous_variant	6251	exon7			AGGCAGCGAGATC	AK055596	CCDS7112.1, CCDS31157.1	10p13	2012-09-20			ENSG00000148484	ENSG00000148484			10464	protein-coding gene	gene with protein product		179555				8288261	Standard	NM_152724		Approved	RSP-1, FLJ31034	uc001iol.3	Q15404	OTTHUMG00000017740	ENST00000377921.3:c.513G>A	10.37:g.16794623C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_012425	A8KA46|D3DRU3|Q6FI17	Silent	SNP	ENST00000377921.3	37	CCDS7112.1																																																																																			C|0.887;T|0.113	0.113	strong		0.478	RSU1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047006.1	NM_012425, NM_152724	
PRMT2	3275	hgsc.bcm.edu	37	21	48068518	48068518	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:48068518C>T	ENST00000397637.1	+	5	1430	c.476C>T	c.(475-477)gCg>gTg	p.A159V	PRMT2_ENST00000355680.3_Missense_Mutation_p.A159V|PRMT2_ENST00000491389.1_3'UTR|PRMT2_ENST00000440086.1_Missense_Mutation_p.A159V|PRMT2_ENST00000397638.2_Missense_Mutation_p.A159V|PRMT2_ENST00000291705.6_Missense_Mutation_p.A159V|PRMT2_ENST00000458387.2_Missense_Mutation_p.A159V|PRMT2_ENST00000334494.4_Missense_Mutation_p.A159V|PRMT2_ENST00000397628.1_Missense_Mutation_p.A159V|PRMT2_ENST00000451211.2_Missense_Mutation_p.A159V			P55345	ANM2_HUMAN	protein arginine methyltransferase 2	159	Interaction with ESR1.|Interaction with RB1. {ECO:0000250}.|SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				developmental cell growth (GO:0048588)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|protein methylation (GO:0006479)|regulation of androgen receptor signaling pathway (GO:0060765)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (GO:0042054)|histone-arginine N-methyltransferase activity (GO:0008469)|peroxisome proliferator activated receptor binding (GO:0042975)|progesterone receptor binding (GO:0033142)|protein homodimerization activity (GO:0042803)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|retinoic acid receptor binding (GO:0042974)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.A159V(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)		GCACACTATGCGCGGCCTAGA	0.582																																					p.A159V		Atlas-SNP	.											PRMT2,NS,NS,0,1	PRMT2	48	1	1	Substitution - Missense(1)	NS(1)	c.C476T						PASS	.						148.0	133.0	138.0					21																	48068518		2203	4300	6503	SO:0001583	missense	3275	exon5			ACTATGCGCGGCC	U80213	CCDS13737.1, CCDS56219.1, CCDS56220.1, CCDS68230.1, CCDS68231.1, CCDS74806.1	21q22.3	2014-06-12	2006-02-16	2006-02-16	ENSG00000160310	ENSG00000160310	2.1.1.125	"""Protein arginine methyltransferases"""	5186	protein-coding gene	gene with protein product		601961	"""HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 1"", ""HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae)"""	HRMT1L1		9545638	Standard	XM_005261111		Approved	MGC111373	uc002zjy.3	P55345	OTTHUMG00000048806	ENST00000397637.1:c.476C>T	21.37:g.48068518C>T	ENSP00000380759:p.Ala159Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_001242864	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Missense_Mutation	SNP	ENST00000397637.1	37	CCDS13737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.064734|5.064734	0.93898|0.93898	.|.	.|.	ENSG00000160310|ENSG00000160310	ENST00000355680;ENST00000397638;ENST00000458387;ENST00000451211;ENST00000291705;ENST00000397637;ENST00000334494;ENST00000397628;ENST00000440086|ENST00000379844;ENST00000455177	T;T;T;T;T;T;T;T;T|.	0.73152|.	0.82;0.82;-0.54;-0.36;-0.6;0.82;-0.72;-0.71;-0.08|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79747|0.79747	0.4499|0.4499	M|M	0.84846|0.84846	2.72|2.72	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;0.999;1.0;1.0;1.0|.	D;D;P;D;D;D|.	0.81914|.	0.975;0.994;0.904;0.993;0.987;0.995|.	D|D	0.83443|0.83443	0.0044|0.0044	10|6	0.87932|0.87932	D|D	0|0	-9.6393|-9.6393	16.2791|16.2791	0.82664|0.82664	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	159;159;159;159;45;159|.	B7U632;B7U630;B7U631;Q498Y5;Q49AF9;P55345|.	.;.;.;.;.;ANM2_HUMAN|.	V|C	159|45;99	ENSP00000347906:A159V;ENSP00000380760:A159V;ENSP00000407463:A159V;ENSP00000411984:A159V;ENSP00000291705:A159V;ENSP00000380759:A159V;ENSP00000335490:A159V;ENSP00000380752:A159V;ENSP00000397266:A159V|.	ENSP00000291705:A159V|ENSP00000369173:R45C	A|R	+|+	2|1	0|0	PRMT2|PRMT2	46892946|46892946	0.999000|0.999000	0.42202|0.42202	0.035000|0.035000	0.18076|0.18076	0.008000|0.008000	0.06430|0.06430	5.491000|5.491000	0.66887|0.66887	2.531000|2.531000	0.85337|0.85337	0.655000|0.655000	0.94253|0.94253	GCG|CGC	.	.	none		0.582	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535	
SYNPO2	171024	hgsc.bcm.edu	37	4	119947985	119947985	+	Missense_Mutation	SNP	G	G	C	rs12645298	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:119947985G>C	ENST00000429713.2	+	3	643	c.461G>C	c.(460-462)gGc>gCc	p.G154A	SYNPO2_ENST00000434046.2_Missense_Mutation_p.G154A|SYNPO2_ENST00000307142.4_Missense_Mutation_p.G154A|SYNPO2_ENST00000448416.2_Intron	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	154			G -> A (in dbSNP:rs12645298). {ECO:0000269|PubMed:17974005}.			actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GACTGTGCAGGCAGCTTGAAA	0.552													G|||	1288	0.257188	0.0908	0.3876	5008	,	,		17925	0.4196		0.2256	False		,,,				2504	0.2546				p.G154A		Atlas-SNP	.											.	SYNPO2	353	.	0			c.G461C						PASS	.	G	ALA/GLY,ALA/GLY,ALA/GLY	538,3868	227.8+/-242.9	38,462,1703	38.0	41.0	40.0		461,461,461	1.3	0.0	4	dbSNP_120	40	2231,6369	360.3+/-331.9	291,1649,2360	yes	missense,missense,missense	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	60,60,60	329,2111,4063	CC,CG,GG		25.9419,12.2106,21.2902	possibly-damaging,possibly-damaging,possibly-damaging	154/1094,154/1110,154/1262	119947985	2769,10237	2203	4300	6503	SO:0001583	missense	171024	exon3			GTGCAGGCAGCTT	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.461G>C	4.37:g.119947985G>C	ENSP00000395143:p.Gly154Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	598|598	0.27380952380952384|0.27380952380952384	52|52	0.10569105691056911|0.10569105691056911	119|119	0.3287292817679558|0.3287292817679558	244|244	0.42657342657342656|0.42657342657342656	183|183	0.24142480211081793|0.24142480211081793	G|G	3.203|3.203	-0.163297|-0.163297	0.06502|0.06502	0.122106|0.122106	0.259419|0.259419	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.07908|.	3.15;3.18;3.17|.	4.98|4.98	1.33|1.33	0.21861|0.21861	.|.	0.862354|.	0.10111|.	N|.	0.714774|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.64997|0.64997	1.995|1.995	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	P;P;P;P|.	0.46784|.	0.884;0.873;0.805;0.805|.	B;B;B;B|.	0.33454|.	0.142;0.164;0.142;0.142|.	T|T	0.41627|0.41627	-0.9498|-0.9498	9|4	0.40728|.	T|.	0.16|.	-3.3096|-3.3096	8.3309|8.3309	0.32187|0.32187	0.4442:0.0:0.5558:0.0|0.4442:0.0:0.5558:0.0	rs12645298;rs52814983;rs12645298|rs12645298;rs52814983;rs12645298	154;154;154;154|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	A|S	154|105	ENSP00000306015:G154A;ENSP00000395143:G154A;ENSP00000390965:G154A|.	ENSP00000306015:G154A|.	G|R	+|+	2|3	0|2	SYNPO2|SYNPO2	120167433|120167433	0.006000|0.006000	0.16342|0.16342	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.548000|0.548000	0.23314|0.23314	0.032000|0.032000	0.15435|0.15435	-0.262000|-0.262000	0.10625|0.10625	GGC|AGG	G|0.768;C|0.232	0.232	strong		0.552	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
DXO	1797	hgsc.bcm.edu	37	6	31938451	31938451	+	Silent	SNP	T	T	C	rs35337578	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31938451T>C	ENST00000375349.3	-	4	1155	c.744A>G	c.(742-744)ccA>ccG	p.P248P	STK19_ENST00000375331.2_5'Flank|DXO_ENST00000337523.5_Silent_p.P248P|DXO_ENST00000478221.1_5'UTR|DXO_ENST00000375356.3_Silent_p.P248P|STK19_ENST00000375333.2_5'Flank			O77932	DXO_HUMAN	decapping exoribonuclease	248					metabolic process (GO:0008152)|mRNA catabolic process (GO:0006402)|nuclear mRNA surveillance (GO:0071028)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA destabilization (GO:0050779)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|magnesium ion binding (GO:0000287)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA pyrophosphohydrolase activity (GO:0034353)										CATAGCAGGTTGGGGGCTGTG	0.612													C|||	600	0.119808	0.1725	0.0764	5008	,	,		17169	0.0347		0.0994	False		,,,				2504	0.1881				p.P248P		Atlas-SNP	.											.	DOM3Z	20	.	0			c.A744G						PASS	.	C		452,2568		34,384,1092	68.0	75.0	73.0		744	-7.2	0.0	6	dbSNP_126	73	497,4921		35,427,2247	no	coding-synonymous	DOM3Z	NM_005510.3		69,811,3339	CC,CT,TT		9.1731,14.9669,11.2467		248/397	31938451	949,7489	1510	2709	4219	SO:0001819	synonymous_variant	1797	exon4			GCAGGTTGGGGGC	AF059252	CCDS4732.1	6p21.3	2013-09-11	2013-09-11	2013-09-11	ENSG00000204348	ENSG00000204348			2992	protein-coding gene	gene with protein product		605996	"""DOM-3 (C. elegans) homolog Z"", ""dom-3 homolog Z (C. elegans)"""	DOM3Z		9799600, 23523372	Standard	NM_005510		Approved		uc003nyp.1	O77932	OTTHUMG00000031272	ENST00000375349.3:c.744A>G	6.37:g.31938451T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	109	44	0.40367	NM_005510	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Silent	SNP	ENST00000375349.3	37	CCDS4732.1	221	0.10119047619047619	95	0.19308943089430894	26	0.0718232044198895	22	0.038461538461538464	78	0.10290237467018469	C	3.700	-0.061674	0.07317	0.149669	0.091731	ENSG00000204348	ENST00000495340	.	.	.	4.46	-7.15	0.01521	.	.	.	.	.	T	0.03011	0.0089	.	.	.	0.09310	P	0.9999999999990461	.	.	.	.	.	.	T	0.28038	-1.0056	3	.	.	.	-17.4696	0.1015	0.00048	0.3164:0.1726:0.1974:0.3137	rs35337578	.	.	.	R	55	.	.	Q	-	2	0	DOM3Z	32046430	0.000000	0.05858	0.037000	0.18230	0.818000	0.46254	-2.978000	0.00664	-2.191000	0.00756	-2.364000	0.00238	CAA	T|0.893;C|0.107	0.107	strong		0.612	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3		
SNX19	399979	hgsc.bcm.edu	37	11	130784647	130784647	+	Missense_Mutation	SNP	G	G	C	rs1050081	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130784647G>C	ENST00000265909.4	-	1	1757	c.1188C>G	c.(1186-1188)gaC>gaG	p.D396E	SNX19_ENST00000533318.1_Intron|SNX19_ENST00000533214.1_Missense_Mutation_p.D396E|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000530356.1_Intron|SNX19_ENST00000539184.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	396			D -> E (in dbSNP:rs52802589).		protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		CCTGAATCCTGTCAGAGAGAA	0.547													G|||	639	0.127596	0.0492	0.0893	5008	,	,		18749	0.1538		0.1988	False		,,,				2504	0.1605				p.D396E		Atlas-SNP	.											.	SNX19	84	.	0			c.C1188G						PASS	.	G	GLU/ASP	315,4087	168.7+/-199.5	15,285,1901	63.0	62.0	63.0		1188	0.8	0.2	11	dbSNP_86	63	1787,6807	322.6+/-315.6	174,1439,2684	yes	missense	SNX19	NM_014758.2	45	189,1724,4585	CC,CG,GG		20.7936,7.1558,16.1742	benign	396/993	130784647	2102,10894	2201	4297	6498	SO:0001583	missense	399979	exon1			AATCCTGTCAGAG	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1188C>G	11.37:g.130784647G>C	ENSP00000265909:p.Asp396Glu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	37	CCDS31721.1	315	0.14423076923076922	25	0.0508130081300813	35	0.09668508287292818	99	0.17307692307692307	156	0.20580474934036938	G	8.151	0.787417	0.16258	0.071558	0.207936	ENSG00000120451	ENST00000265909;ENST00000533214	T;T	0.20200	2.09;2.09	5.1	0.82	0.18793	.	0.807721	0.11830	N	0.525330	T	0.00012	0.0000	N	0.12746	0.255	0.21984	P	0.999438366	B;B	0.10296	0.003;0.001	B;B	0.09377	0.004;0.002	T	0.41893	-0.9483	9	0.02654	T	1	-2.9451	7.6633	0.28415	0.0689:0.4808:0.3372:0.1132	rs52802589;rs61732897	396;396	E9PKB9;Q92543	.;SNX19_HUMAN	E	396	ENSP00000265909:D396E;ENSP00000435390:D396E	ENSP00000265909:D396E	D	-	3	2	SNX19	130289857	0.000000	0.05858	0.208000	0.23602	0.995000	0.86356	0.207000	0.17395	0.005000	0.14708	0.650000	0.86243	GAC	G|0.838;C|0.162	0.162	strong		0.547	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
MTHFR	4524	hgsc.bcm.edu	37	1	11854476	11854476	+	Missense_Mutation	SNP	T	T	G	rs1801131	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:11854476T>G	ENST00000376592.1	-	7	1414	c.1286A>C	c.(1285-1287)gAa>gCa	p.E429A	MTHFR_ENST00000376585.1_Missense_Mutation_p.E470A|MTHFR_ENST00000376583.3_Missense_Mutation_p.E470A|MTHFR_ENST00000376590.3_Missense_Mutation_p.E429A			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	429			E -> A (common polymorphism; thermolabile; decreased activity; decreased risk for adult acute leukemia; dbSNP:rs1801131). {ECO:0000269|PubMed:10536004, ECO:0000269|PubMed:9545395, ECO:0000269|PubMed:9719624, ECO:0000269|Ref.5}.		blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	AAAGACACTTTCTTCACTGGT	0.537													T|||	1249	0.249401	0.1513	0.1513	5008	,	,		21917	0.2192		0.3131	False		,,,				2504	0.4172				p.E429A		Atlas-SNP	.											.	MTHFR	65	.	0			c.A1286C	GRCh37	CM981315	MTHFR	M	rs1801131	PASS	.	T	ALA/GLU	683,3723	289.8+/-280.6	65,553,1585	103.0	111.0	109.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1286	4.7	0.5	1	dbSNP_89	109	2693,5907	432.0+/-357.0	428,1837,2035	yes	missense	MTHFR	NM_005957.4	107	493,2390,3620	GG,GT,TT		31.314,15.5016,25.9573	benign	429/657	11854476	3376,9630	2203	4300	6503	SO:0001583	missense	4524	exon8			ACACTTTCTTCAC	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.1286A>C	1.37:g.11854476T>G	ENSP00000365777:p.Glu429Ala	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	CCDS137.1	501	0.22939560439560439	83	0.16869918699186992	65	0.17955801104972377	109	0.19055944055944055	244	0.32189973614775724	T	15.29	2.790872	0.50102	0.155016	0.31314	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78	4.74	4.74	0.60224	.	0.095160	0.64402	D	0.000001	T	0.00012	0.0000	L	0.43701	1.375	0.09310	P	0.99999834978	B;P	0.34662	0.021;0.462	B;B	0.25987	0.009;0.065	T	0.07693	-1.0759	9	0.38643	T	0.18	.	13.7416	0.62852	0.0:0.0:0.0:1.0	rs1801131;rs4134712;rs17367365;rs17857426;rs1801131	429;470	P42898;Q5SNW6	MTHR_HUMAN;.	A	429;470;429;470	ENSP00000365777:E429A;ENSP00000365767:E470A;ENSP00000365775:E429A;ENSP00000365770:E470A	ENSP00000365767:E470A	E	-	2	0	MTHFR	11777063	0.968000	0.33430	0.496000	0.27539	0.772000	0.43724	3.792000	0.55476	1.898000	0.54952	0.374000	0.22700	GAA	T|0.722;G|0.238	0.238	strong		0.537	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
VPS54	51542	hgsc.bcm.edu	37	2	64124722	64124722	+	Missense_Mutation	SNP	C	C	A	rs11558741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:64124722C>A	ENST00000272322.4	-	22	2890	c.2736G>T	c.(2734-2736)atG>atT	p.M912I	VPS54_ENST00000409558.4_Missense_Mutation_p.M900I|VPS54_ENST00000354504.3_Missense_Mutation_p.M759I			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	912			M -> I (in dbSNP:rs11558741).		growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						TTAAAAATAACATCTGAAAAA	0.254													C|||	691	0.137979	0.1611	0.1441	5008	,	,		16567	0.0813		0.164	False		,,,				2504	0.1339				p.M912I		Atlas-SNP	.											.	VPS54	57	.	0			c.G2736T						PASS	.	C	ILE/MET,ILE/MET	600,3794		38,524,1635	53.0	55.0	54.0		2700,2736	4.7	1.0	2	dbSNP_120	54	1292,7294		118,1056,3119	yes	missense,missense	VPS54	NM_001005739.1,NM_016516.2	10,10	156,1580,4754	AA,AC,CC		15.0478,13.655,14.5763	benign,benign	900/966,912/978	64124722	1892,11088	2197	4293	6490	SO:0001583	missense	51542	exon22			AAATAACATCTGA	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 164"""	614633	"""vacuolar protein sorting 54 (yeast)"""			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.2736G>T	2.37:g.64124722C>A	ENSP00000272322:p.Met912Ile	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	91	32	0.351648	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Missense_Mutation	SNP	ENST00000272322.4	37	CCDS33208.1	328	0.15018315018315018	96	0.1951219512195122	45	0.12430939226519337	54	0.0944055944055944	133	0.17546174142480211	C	13.89	2.373226	0.42105	0.13655	0.150478	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	T;T;T	0.33438	1.41;1.42;1.42	5.58	4.69	0.59074	.	0.038119	0.85682	D	0.000000	T	0.00039	0.0001	L	0.47716	1.5	0.21652	P	0.999607941	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.08055	0.001;0.0;0.003	T	0.10753	-1.0616	9	0.21540	T	0.41	.	9.7045	0.40207	0.1378:0.7903:0.0:0.072	rs11558741;rs17619976;rs60970434;rs17619976	759;912;900	Q9P1Q0-3;Q9P1Q0;Q9P1Q0-4	.;VPS54_HUMAN;.	I	759;912;900;900;912	ENSP00000346499:M759I;ENSP00000272322:M912I;ENSP00000386980:M900I	ENSP00000272322:M912I	M	-	3	0	VPS54	63978226	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.329000	0.52060	2.611000	0.88343	0.543000	0.68304	ATG	T|0.031;G|0.176	.	strong		0.254	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18681821	18681821	+	Silent	SNP	A	A	G	rs13293151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:18681821A>G	ENST00000380548.4	+	12	1692	c.1353A>G	c.(1351-1353)acA>acG	p.T451T	ADAMTSL1_ENST00000327883.7_Silent_p.T451T|ADAMTSL1_ENST00000276935.6_Silent_p.T451T	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	451	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		GCACAGTGACATGTGGCCAGG	0.478													A|||	1388	0.277157	0.1248	0.3069	5008	,	,		13006	0.2748		0.4185	False		,,,				2504	0.319				p.T451T		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.A1353G						PASS	.	A	,	737,3669	304.9+/-288.7	75,587,1541	171.0	166.0	168.0		1353,1353	-9.6	0.5	9	dbSNP_121	168	3504,5096	512.2+/-377.9	742,2020,1538	no	coding-synonymous,coding-synonymous	ADAMTSL1	NM_001040272.5,NM_052866.4	,	817,2607,3079	GG,GA,AA		40.7442,16.7272,32.608	,	451/1763,451/526	18681821	4241,8765	2203	4300	6503	SO:0001819	synonymous_variant	92949	exon12			AGTGACATGTGGC	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.1353A>G	9.37:g.18681821A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	CCDS47954.1																																																																																			A|0.691;G|0.309	0.309	strong		0.478	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
KIF12	113220	hgsc.bcm.edu	37	9	116856481	116856481	+	Missense_Mutation	SNP	C	C	A	rs35719524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:116856481C>A	ENST00000374118.3	-	10	1116	c.879G>T	c.(877-879)atG>atT	p.M293I	KIF12_ENST00000473174.1_Intron	NM_138424.1	NP_612433.1	Q96FN5	KIF12_HUMAN	kinesin family member 12	426	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	17						CATTCTCTAGCATGAACTCCT	0.627													C|||	485	0.096845	0.1218	0.1052	5008	,	,		16353	0.001		0.164	False		,,,				2504	0.0869				p.M293I		Atlas-SNP	.											.	KIF12	35	.	0			c.G879T						PASS	.	C	ILE/MET	678,3728	286.3+/-278.7	58,562,1583	63.0	66.0	65.0		879	5.6	1.0	9	dbSNP_126	65	1541,7059	289.0+/-299.1	132,1277,2891	yes	missense	KIF12	NM_138424.1	10	190,1839,4474	AA,AC,CC		17.9186,15.3881,17.0614	benign	293/514	116856481	2219,10787	2203	4300	6503	SO:0001583	missense	113220	exon10			CTCTAGCATGAAC	BC010626	CCDS6801.1	9q33.1	2008-02-05			ENSG00000136883	ENSG00000136883		"""Kinesins"""	21495	protein-coding gene	gene with protein product		611278					Standard	NM_138424		Approved		uc004bif.3	Q96FN5	OTTHUMG00000020533	ENST00000374118.3:c.879G>T	9.37:g.116856481C>A	ENSP00000363232:p.Met293Ile	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	83	33	0.39759	NM_138424	Q5TBE0	Missense_Mutation	SNP	ENST00000374118.3	37	CCDS6801.1	236	0.10805860805860806	69	0.1402439024390244	42	0.11602209944751381	1	0.0017482517482517483	124	0.16358839050131926	C	17.41	3.382259	0.61845	0.153881	0.179186	ENSG00000136883	ENST00000374118;ENST00000259410	T	0.73681	-0.77	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000001	T	0.00241	0.0007	L	0.34521	1.04	0.25332	P	0.9890252	B	0.33266	0.404	B	0.32533	0.147	T	0.10132	-1.0643	9	0.36615	T	0.2	.	15.0246	0.71659	0.0:1.0:0.0:0.0	rs35719524;rs62556539	426	Q96FN5	KIF12_HUMAN	I	293;426	ENSP00000363232:M293I	ENSP00000259410:M426I	M	-	3	0	KIF12	115896302	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.060000	0.41394	2.608000	0.88229	0.655000	0.94253	ATG	C|0.851;A|0.149	0.149	strong		0.627	KIF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053751.1	NM_138424	
BBS12	166379	hgsc.bcm.edu	37	4	123664457	123664457	+	Silent	SNP	C	C	T	rs13135445	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:123664457C>T	ENST00000314218.3	+	2	1603	c.1410C>T	c.(1408-1410)tgC>tgT	p.C470C	BBS12_ENST00000542236.1_Silent_p.C470C	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	470					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						ACGGGGTCTGCGTGACCTTCT	0.478									Bardet-Biedl syndrome				T|||	606	0.121006	0.1293	0.1297	5008	,	,		19655	0.0		0.2346	False		,,,				2504	0.1115				p.C470C		Atlas-SNP	.											.	BBS12	63	.	0			c.C1410T						PASS	.	T	,	599,3807	770.2+/-413.7	38,523,1642	80.0	78.0	79.0		1410,1410	-0.7	0.0	4	dbSNP_121	79	2108,6492	716.6+/-406.1	255,1598,2447	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	293,2121,4089	TT,TC,CC		24.5116,13.5951,20.8135	,	470/711,470/711	123664457	2707,10299	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GGTCTGCGTGACC	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1410C>T	4.37:g.123664457C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	150	65	0.433333	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			C|0.818;T|0.182	0.182	strong		0.478	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
TRPV4	59341	hgsc.bcm.edu	37	12	110240838	110240838	+	Silent	SNP	T	T	G	rs3825394	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:110240838T>G	ENST00000418703.2	-	3	764	c.670A>C	c.(670-672)Agg>Cgg	p.R224R	TRPV4_ENST00000392719.2_Silent_p.R224R|TRPV4_ENST00000537083.1_Silent_p.R224R|TRPV4_ENST00000346520.2_Silent_p.R224R|TRPV4_ENST00000536838.1_Silent_p.R190R|TRPV4_ENST00000541794.1_Silent_p.R224R|TRPV4_ENST00000544971.1_Silent_p.R224R|TRPV4_ENST00000261740.2_Silent_p.R224R	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	224					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						ATGAACTCCCTCATGTTGCCG	0.637													G|||	3778	0.754393	0.7284	0.7017	5008	,	,		20128	0.9683		0.5288	False		,,,				2504	0.8384				p.R224R		Atlas-SNP	.											.	TRPV4	88	.	0			c.A670C						PASS	.	G	,,,,	3018,1388	457.6+/-351.7	1054,910,239	108.0	88.0	95.0		670,568,670,670,670	4.5	1.0	12	dbSNP_107	95	4536,4064	558.9+/-387.3	1187,2162,951	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV4	NM_001177428.1,NM_001177431.1,NM_001177433.1,NM_021625.4,NM_147204.2	,,,,	2241,3072,1190	GG,GT,TT		47.2558,31.5025,41.9191	,,,,	224/825,190/838,224/765,224/872,224/812	110240838	7554,5452	2203	4300	6503	SO:0001819	synonymous_variant	59341	exon3			ACTCCCTCATGTT	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18083	protein-coding gene	gene with protein product	"""osmosensitive transient receptor potential channel 4"""	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.670A>C	12.37:g.110240838T>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	101	38	0.376238	NM_001177433	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Silent	SNP	ENST00000418703.2	37	CCDS9134.1																																																																																			T|0.359;G|0.641	0.641	strong		0.637	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625	
SLC39A11	201266	hgsc.bcm.edu	37	17	70645032	70645032	+	Missense_Mutation	SNP	G	G	A	rs61736066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:70645032G>A	ENST00000542342.2	-	9	948	c.860C>T	c.(859-861)gCt>gTt	p.A287V	SLC39A11_ENST00000579988.1_5'UTR|SLC39A11_ENST00000255559.3_Missense_Mutation_p.A280V	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	287					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			endometrium(1)|large_intestine(4)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						GATGGGCTCAGCCAGCACCAC	0.607													G|||	526	0.105032	0.062	0.1412	5008	,	,		18518	0.1647		0.0895	False		,,,				2504	0.092				p.A287V	NSCLC(95;736 1527 12296 39625 41839)	Atlas-SNP	.											.	SLC39A11	32	.	0			c.C860T						PASS	.	G	VAL/ALA,VAL/ALA	283,4123	156.3+/-189.4	11,261,1931	62.0	57.0	59.0		860,839	4.5	0.8	17	dbSNP_129	59	702,7898	173.5+/-223.9	29,644,3627	yes	missense,missense	SLC39A11	NM_001159770.1,NM_139177.3	64,64	40,905,5558	AA,AG,GG		8.1628,6.4231,7.5734	probably-damaging,probably-damaging	287/343,280/336	70645032	985,12021	2203	4300	6503	SO:0001583	missense	201266	exon9			GGCTCAGCCAGCA	AF331643	CCDS11690.1, CCDS54160.1	17q24.3-q25.1	2014-08-12	2013-07-17	2003-10-24	ENSG00000133195	ENSG00000133195		"""Solute carriers"""	14463	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 26"""	C17orf26		11707075	Standard	NM_139177		Approved		uc002jjb.3	Q8N1S5	OTTHUMG00000178306	ENST00000542342.2:c.860C>T	17.37:g.70645032G>A	ENSP00000445829:p.Ala287Val	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_001159770	B2R8H7|Q8WZ81	Missense_Mutation	SNP	ENST00000542342.2	37	CCDS54160.1	246	0.11263736263736264	29	0.05894308943089431	54	0.14917127071823205	95	0.1660839160839161	68	0.08970976253298153	G	13.90	2.375913	0.42105	0.064231	0.081628	ENSG00000133195	ENST00000542342;ENST00000255559	T;T	0.52754	0.65;0.65	5.5	4.5	0.54988	.	0.125962	0.52532	D	0.000072	T	0.00178	0.0005	L	0.31664	0.95	0.09310	P	1.0	D;P	0.54601	0.967;0.92	P;P	0.58391	0.838;0.615	T	0.02064	-1.1220	9	0.06494	T	0.89	.	15.3722	0.74573	0.0:0.0:0.8594:0.1406	.	287;280	Q8N1S5;Q8N1S5-2	S39AB_HUMAN;.	V	287;280	ENSP00000445829:A287V;ENSP00000255559:A280V	ENSP00000255559:A280V	A	-	2	0	SLC39A11	68156627	1.000000	0.71417	0.831000	0.32960	0.996000	0.88848	8.972000	0.93424	1.258000	0.44101	0.655000	0.94253	GCT	G|0.911;A|0.089	0.089	strong		0.607	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1		
C1orf87	127795	hgsc.bcm.edu	37	1	60503762	60503762	+	Silent	SNP	T	T	C	rs17560663	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:60503762T>C	ENST00000371201.3	-	6	872	c.765A>G	c.(763-765)ctA>ctG	p.L255L	C1orf87_ENST00000450089.2_Intron	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	255							calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						AAAACCAGAGTAGCTTTTCAT	0.353													T|||	404	0.0806709	0.0113	0.1282	5008	,	,		17242	0.0218		0.1859	False		,,,				2504	0.093				p.L255L	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.A765G						PASS	.	T		151,4255	102.5+/-141.1	4,143,2056	75.0	69.0	71.0		765	-4.0	0.9	1	dbSNP_123	71	1480,7120	279.8+/-294.2	137,1206,2957	no	coding-synonymous	C1orf87	NM_152377.2		141,1349,5013	CC,CT,TT		17.2093,3.4271,12.5404		255/547	60503762	1631,11375	2203	4300	6503	SO:0001819	synonymous_variant	127795	exon6			CCAGAGTAGCTTT	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"""carcinoma-related EF-hand protein"""					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.765A>G	1.37:g.60503762T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_152377	Q6ZU07|Q8IVS0	Silent	SNP	ENST00000371201.3	37	CCDS614.1																																																																																			T|0.897;C|0.103	0.103	strong		0.353	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377	
LALBA	3906	hgsc.bcm.edu	37	12	48961801	48961801	+	Splice_Site	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48961801C>A	ENST00000301046.2	-	4	394		c.e4-1		LALBA_ENST00000549817.1_3'UTR	NM_002289.2	NP_002280.1	P00709	LALBA_HUMAN	lactalbumin, alpha-						apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|lactose biosynthetic process (GO:0005989)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|lactose synthase activity (GO:0004461)			large_intestine(1)|stomach(2)	3						ATGGGCCAACCTGATAATGGA	0.512																																					.		Atlas-SNP	.											.	LALBA	9	.	0			c.369-1G>T						PASS	.						112.0	85.0	94.0					12																	48961801		2203	4300	6503	SO:0001630	splice_region_variant	3906	exon5			GCCAACCTGATAA		CCDS8765.1	12q13	2012-10-02				ENSG00000167531			6480	protein-coding gene	gene with protein product		149750					Standard	XM_006719395		Approved	LYZL7	uc001rrt.3	P00709	OTTHUMG00000170391	ENST00000301046.2:c.369-1G>T	12.37:g.48961801C>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_002289	Q6FGX0|Q9UDK4	Splice_Site	SNP	ENST00000301046.2	37	CCDS8765.1	.	.	.	.	.	.	.	.	.	.	c	15.72	2.916330	0.52546	.	.	ENSG00000167531	ENST00000301046	.	.	.	4.88	4.88	0.63580	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4099	0.60935	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LALBA	47248068	0.960000	0.32886	0.996000	0.52242	0.794000	0.44872	2.823000	0.48081	2.539000	0.85634	0.461000	0.40582	.	.	.	none		0.512	LALBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408836.1	NM_002289	Intron
PTPRQ	374462	hgsc.bcm.edu	37	12	80936026	80936026	+	Missense_Mutation	SNP	A	A	G	rs17713202	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:80936026A>G	ENST00000266688.5	+	27	3592	c.3592A>G	c.(3592-3594)Aat>Gat	p.N1198D				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1244	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						TACTTCTGATAATTACATAAT	0.328													A|||	571	0.114018	0.1626	0.1354	5008	,	,		16784	0.0		0.175	False		,,,				2504	0.0879				p.N1030D		Atlas-SNP	.											.	PTPRQ	119	.	0			c.A3088G						PASS	.	A	ASP/ASN	197,1187		16,165,511	73.0	62.0	65.0		3150	1.8	1.0	12	dbSNP_123	65	544,2630		47,450,1090	yes	missense	PTPRQ	NM_001145026.1	23	63,615,1601	GG,GA,AA		17.1393,14.2341,16.2571	possibly-damaging	1202/2300	80936026	741,3817	692	1587	2279	SO:0001583	missense	374462	exon19			TCTGATAATTACA	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.3592A>G	12.37:g.80936026A>G	ENSP00000266688:p.Asn1198Asp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	37		266|266	0.12179487179487179|0.12179487179487179	85|85	0.17276422764227642|0.17276422764227642	62|62	0.1712707182320442|0.1712707182320442	0|0	0.0|0.0	119|119	0.15699208443271767|0.15699208443271767	A|A	12.46|12.46	1.944970|1.944970	0.34283|0.34283	0.142341|0.142341	0.171393|0.171393	ENSG00000139304|ENSG00000139304	ENST00000532722|ENST00000266688	.|T	.|0.57107	.|0.42	5.59|5.59	1.79|1.79	0.24919|0.24919	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|.	.|.	.|.	.|.	T|T	0.00144|0.00144	0.0004|0.0004	.|.	.|.	.|.	0.39075|0.39075	P|P	0.039216999999999946|0.039216999999999946	.|P	.|0.42161	.|0.772	.|B	.|0.43123	.|0.409	T|T	0.04427|0.04427	-1.0952|-1.0952	3|7	.|0.28530	.|T	.|0.3	.|.	7.9852|7.9852	0.30207|0.30207	0.6756:0.2573:0.0671:0.0|0.6756:0.2573:0.0671:0.0	rs17713202;rs52824844;rs17713202|rs17713202;rs52824844;rs17713202	.|1244	.|Q9UMZ3	.|PTPRQ_HUMAN	M|D	898|1198	.|ENSP00000266688:N1198D	.|ENSP00000266688:N1198D	I|N	+|+	3|1	3|0	PTPRQ|PTPRQ	79460157|79460157	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.874000|0.874000	0.50279|0.50279	3.769000|3.769000	0.55303|0.55303	0.057000|0.057000	0.16193|0.16193	0.482000|0.482000	0.46254|0.46254	ATA|AAT	A|0.871;G|0.129	0.129	strong		0.328	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056072	26056072	+	Silent	SNP	G	G	C	rs8384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:26056072G>C	ENST00000343677.2	-	1	627	c.585C>G	c.(583-585)ccC>ccG	p.P195P		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	195					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						TAGCGGCCTTGGGCTTCACAG	0.537													G|||	582	0.116214	0.0484	0.121	5008	,	,		16450	0.1627		0.1958	False		,,,				2504	0.0746				p.P195P		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.C585G						PASS	.	G		316,4090	166.9+/-198.0	9,298,1896	73.0	78.0	77.0		585	1.2	1.0	6	dbSNP_52	77	1881,6719	331.9+/-319.9	207,1467,2626	no	coding-synonymous	HIST1H1C	NM_005319.3		216,1765,4522	CC,CG,GG		21.8721,7.172,16.8922		195/214	26056072	2197,10809	2203	4300	6503	SO:0001819	synonymous_variant	3006	exon1			GGCCTTGGGCTTC	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.585C>G	6.37:g.26056072G>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	140	61	0.435714	NM_005319	A8K4I2	Silent	SNP	ENST00000343677.2	37	CCDS4577.1																																																																																			G|0.834;C|0.166	0.166	strong		0.537	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
ARID1B	57492	hgsc.bcm.edu	37	6	157405930	157405930	+	Silent	SNP	G	G	A	rs3734441	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:157405930G>A	ENST00000350026.5	+	5	2134	c.2133G>A	c.(2131-2133)gcG>gcA	p.A711A	ARID1B_ENST00000367148.1_Silent_p.A711A|ARID1B_ENST00000275248.4_Silent_p.A653A|ARID1B_ENST00000346085.5_Silent_p.A724A	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	711	Ser-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CCCCACATGCGTCCCCTCATC	0.607													G|||	2480	0.495208	0.2806	0.6254	5008	,	,		14523	0.5734		0.5239	False		,,,				2504	0.5828				p.A724A		Atlas-SNP	.											ARID1B_ENST00000346085,NS,carcinoma,0,2	ARID1B	320	2	0			c.G2172A						PASS	.	G	,	1512,2894	481.9+/-359.3	253,1006,944	91.0	88.0	89.0		2133,2172	-11.3	0.1	6	dbSNP_107	89	4635,3965	602.5+/-394.5	1260,2115,925	no	coding-synonymous,coding-synonymous	ARID1B	NM_017519.2,NM_020732.3	,	1513,3121,1869	AA,AG,GG		46.1047,34.3168,47.2628	,	711/2237,724/2250	157405930	6147,6859	2203	4300	6503	SO:0001819	synonymous_variant	57492	exon6			ACATGCGTCCCCT	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.2133G>A	6.37:g.157405930G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	37	CCDS5251.2																																																																																			G|0.515;A|0.485	0.485	strong		0.607	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79083120	79083120	+	Missense_Mutation	SNP	G	G	A	rs2127898	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:79083120G>A	ENST00000388820.4	-	6	1130	c.920C>T	c.(919-921)aCg>aTg	p.T307M	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	307	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.		T -> M (in dbSNP:rs2127898). {ECO:0000269|PubMed:15489334}.		cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						TGCATGGTGCGTGATCTTTAG	0.562																																					p.T307M		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C920T						PASS	.	G	MET/THR	1260,3132	429.5+/-342.2	178,904,1114	180.0	139.0	153.0		920	2.8	1.0	15	dbSNP_96	153	2248,6338	378.4+/-338.9	317,1614,2362	no	missense	ADAMTS7	NM_014272.3	81	495,2518,3476	AA,AG,GG		26.1822,28.6885,27.0304	probably-damaging	307/1687	79083120	3508,9470	2196	4293	6489	SO:0001583	missense	11173	exon6			TGGTGCGTGATCT	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.920C>T	15.37:g.79083120G>A	ENSP00000373472:p.Thr307Met	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	547	0.25045787545787546	102	0.2073170731707317	107	0.2955801104972376	163	0.28496503496503495	175	0.23087071240105542	G	16.30	3.084407	0.55861	0.286885	0.261822	ENSG00000136378	ENST00000388820;ENST00000456326	D	0.88277	-2.36	4.86	2.85	0.33270	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.129475	0.49916	D	0.000122	T	0.00039	0.0001	M	0.83483	2.645	0.26834	P	0.9685151	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.73380	0.98;0.969;0.976	T	0.00001	-1.2722	9	0.72032	D	0.01	.	7.9579	0.30053	0.092:0.1618:0.7462:0.0	rs2127898;rs17857516	307;307;307	E7EP58;A8MQ00;Q9UKP4	.;.;ATS7_HUMAN	M	307	ENSP00000373472:T307M	ENSP00000373472:T307M	T	-	2	0	ADAMTS7	76870175	1.000000	0.71417	0.964000	0.40570	0.877000	0.50540	4.633000	0.61318	1.060000	0.40578	-0.643000	0.03959	ACG	G|0.438;A|0.562	0.562	strong		0.562	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
HSPG2	3339	hgsc.bcm.edu	37	1	22158157	22158157	+	Silent	SNP	A	A	G	rs2229488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22158157A>G	ENST00000374695.3	-	82	11419	c.11340T>C	c.(11338-11340)aaT>aaC	p.N3780N	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3780	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GGGAGGTCCCATTGACCGGGG	0.647													g|||	417	0.0832668	0.1687	0.0519	5008	,	,		18250	0.0		0.0666	False		,,,				2504	0.093				p.N3780N		Atlas-SNP	.											.	HSPG2	311	.	0			c.T11340C						PASS	.			760,3646	733.1+/-410.4	67,626,1510	43.0	53.0	50.0		11340	-5.6	0.5	1	dbSNP_98	50	664,7932	771.5+/-407.7	28,608,3662	no	coding-synonymous	HSPG2	NM_005529.5		95,1234,5172	GG,GA,AA		7.7245,17.2492,10.9522		3780/4392	22158157	1424,11578	2203	4298	6501	SO:0001819	synonymous_variant	3339	exon82			GGTCCCATTGACC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.11340T>C	1.37:g.22158157A>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	265	135	0.509434	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			A|0.904;G|0.096	0.096	strong		0.647	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
LAMA1	284217	hgsc.bcm.edu	37	18	6943264	6943264	+	Silent	SNP	G	G	A	rs2016639	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:6943264G>A	ENST00000389658.3	-	62	9075	c.8982C>T	c.(8980-8982)gaC>gaT	p.D2994D		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2994	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.D2994D(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CTGCGTTCCCGTCAACAATCA	0.498													G|||	1433	0.286142	0.0204	0.4006	5008	,	,		20239	0.3413		0.331	False		,,,				2504	0.4611				p.D2994D		Atlas-SNP	.											LAMA1,NS,carcinoma,0,1	LAMA1	458	1	1	Substitution - coding silent(1)	stomach(1)	c.C8982T						PASS	.	G		303,4103	163.6+/-195.4	13,277,1913	308.0	234.0	259.0		8982	-5.8	0.2	18	dbSNP_92	259	2856,5744	448.1+/-361.7	487,1882,1931	no	coding-synonymous	LAMA1	NM_005559.3		500,2159,3844	AA,AG,GG		33.2093,6.877,24.2888		2994/3076	6943264	3159,9847	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon62			GTTCCCGTCAACA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.8982C>T	18.37:g.6943264G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	250	112	0.448	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.755;A|0.245	0.245	strong		0.498	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
GUSB	2990	hgsc.bcm.edu	37	7	65425894	65425894	+	Missense_Mutation	SNP	A	A	G	rs9530	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:65425894A>G	ENST00000304895.4	-	12	2076	c.1946T>C	c.(1945-1947)cTg>cCg	p.L649P	GUSB_ENST00000421103.1_Missense_Mutation_p.L503P|GUSB_ENST00000345660.6_Missense_Mutation_p.L598P	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	649			L -> P (in dbSNP:rs9530). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:3468507, ECO:0000269|PubMed:8089138}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TCAAGTAAACAGGCTGTTTTC	0.512													G|||	2908	0.580671	0.3457	0.562	5008	,	,		18027	0.8323		0.5636	False		,,,				2504	0.6697				p.L649P		Atlas-SNP	.											.	GUSB	52	.	0			c.T1946C						PASS	.	G	PRO/LEU	1628,2778	660.3+/-400.7	299,1030,874	226.0	194.0	205.0		1946	-0.1	0.0	7	dbSNP_52	205	4756,3844	541.4+/-384.0	1327,2102,871	yes	missense	GUSB	NM_000181.3	98	1626,3132,1745	GG,GA,AA		44.6977,36.9496,49.085	benign	649/652	65425894	6384,6622	2203	4300	6503	SO:0001583	missense	2990	exon12			GTAAACAGGCTGT	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1946T>C	7.37:g.65425894A>G	ENSP00000302728:p.Leu649Pro	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	187	94	0.502674	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Missense_Mutation	SNP	ENST00000304895.4	37	CCDS5530.1	1270	0.5815018315018315	145	0.29471544715447157	205	0.5662983425414365	483	0.8444055944055944	437	0.5765171503957783	G	0.010	-1.783147	0.00634	0.369496	0.553023	ENSG00000169919	ENST00000304895;ENST00000421103;ENST00000345660	D;D;D	0.95482	-3.72;-3.6;-3.51	5.6	-0.0658	0.13767	.	1.050190	0.07460	N	0.900468	T	0.00012	0.0000	N	0.16567	0.415	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46762	-0.9168	9	0.35671	T	0.21	.	9.8841	0.41251	0.547:0.0:0.453:0.0	rs9530;rs3202447;rs11559282;rs17784957;rs59194255;rs9530	503;649	E9PCV0;P08236	.;BGLR_HUMAN	P	649;503;598	ENSP00000302728:L649P;ENSP00000391390:L503P;ENSP00000340734:L598P	ENSP00000302728:L649P	L	-	2	0	GUSB	65063329	0.001000	0.12720	0.024000	0.17045	0.015000	0.08874	-0.047000	0.11963	-0.151000	0.11176	-0.766000	0.03442	CTG	G|0.522;N|0.001	0.522	strong		0.512	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
ADPRHL1	113622	hgsc.bcm.edu	37	13	114083316	114083316	+	Silent	SNP	C	C	T	rs9635114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:114083316C>T	ENST00000375418.3	-	4	683	c.597G>A	c.(595-597)gcG>gcA	p.A199A	ADPRHL1_ENST00000356501.4_Silent_p.A117A	NM_138430.3	NP_612439.2	Q8NDY3	ARHL1_HUMAN	ADP-ribosylhydrolase like 1	199					protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	11	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.0195)|GBM - Glioblastoma multiforme(44;0.116)			CCAGAGGCACCGCCCGCAGCA	0.657													C|||	257	0.0513179	0.0	0.0216	5008	,	,		14585	0.1627		0.0318	False		,,,				2504	0.047				p.A199A		Atlas-SNP	.											ADPRHL1,NS,carcinoma,-1,1	ADPRHL1	30	1	0			c.G597A						scavenged	.	C	,	14,4392	20.2+/-43.8	0,14,2189	53.0	48.0	50.0		597,351	-7.7	0.0	13	dbSNP_119	50	77,8523	45.4+/-104.0	1,75,4224	no	coding-synonymous,coding-synonymous	ADPRHL1	NM_138430.3,NM_199162.1	,	1,89,6413	TT,TC,CC		0.8953,0.3177,0.6997	,	199/355,117/273	114083316	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	113622	exon4			AGGCACCGCCCGC	AJ313429	CCDS9535.1, CCDS9536.1	13q34	2003-06-19			ENSG00000153531	ENSG00000153531			21303	protein-coding gene	gene with protein product		610620				12070318	Standard	NM_138430		Approved	ARH2	uc001vtq.1	Q8NDY3	OTTHUMG00000017386	ENST00000375418.3:c.597G>A	13.37:g.114083316C>T		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	74	22	0.297297	NM_138430	Q5JUG2|Q96GD1	Silent	SNP	ENST00000375418.3	37	CCDS9535.1																																																																																			C|0.972;T|0.028	0.028	strong		0.657	ADPRHL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045915.2	NM_138430	
CFAP46	54777	hgsc.bcm.edu	37	10	134736052	134736052	+	Missense_Mutation	SNP	G	G	T	rs4880287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:134736052G>T	ENST00000368586.5	-	12	1517	c.1417C>A	c.(1417-1419)Cgt>Agt	p.R473S	TTC40_ENST00000368582.2_Missense_Mutation_p.R473S	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GTGCACAGACGCAGCCGGGTG	0.701													G|||	1799	0.359225	0.2821	0.4986	5008	,	,		15449	0.3274		0.3459	False		,,,				2504	0.411				p.R473S		Atlas-SNP	.											.	TTC40	100	.	0			c.C1417A						PASS	.																																			SO:0001583	missense	54777	exon12			ACAGACGCAGCCG																												ENST00000368586.5:c.1417C>A	10.37:g.134736052G>T	ENSP00000357575:p.Arg473Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	785	0.35943223443223443	161	0.32723577235772355	164	0.4530386740331492	194	0.33916083916083917	266	0.35092348284960423	G	7.319	0.616533	0.14129	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.44083	2.92;0.93	3.28	3.28	0.37604	.	0.909396	0.09144	N	0.842524	T	0.00012	0.0000	.	.	.	0.50632	P	1.1200000000000099E-4	.	.	.	.	.	.	T	0.47484	-0.9114	6	0.66056	D	0.02	-7.2575	9.937	0.41556	0.0:0.0:0.7961:0.2039	rs4880287	.	.	.	S	473	ENSP00000357575:R473S;ENSP00000357571:R473S	ENSP00000357571:R473S	R	-	1	0	C10orf93	134586042	0.004000	0.15560	0.873000	0.34254	0.025000	0.11179	1.261000	0.32980	1.859000	0.53934	0.462000	0.41574	CGT	G|0.640;T|0.360	0.360	strong		0.701	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
C17orf67	339210	hgsc.bcm.edu	37	17	54872439	54872439	+	Missense_Mutation	SNP	T	T	C	rs72837329	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:54872439T>C	ENST00000575658.1	-	7	1537	c.331A>G	c.(331-333)Att>Gtt	p.I111V	C17orf67_ENST00000397862.2_Missense_Mutation_p.I111V|C17orf67_ENST00000397861.2_Missense_Mutation_p.I87V	NM_001085430.2	NP_001078899.2	Q0P5P2	CQ067_HUMAN	chromosome 17 open reading frame 67	111						extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)	7	Breast(9;2.49e-06)					ACAGGATGAATCCTGTTCCTG	0.597													C|||	632	0.126198	0.1528	0.1124	5008	,	,		21029	0.0179		0.1769	False		,,,				2504	0.1595				p.I87V		Atlas-SNP	.											.	C17orf67	13	.	0			c.A259G						PASS	.	C	VAL/ILE	576,3562		38,500,1531	88.0	101.0	97.0		331	3.7	0.0	17	dbSNP_130	97	1202,7240		83,1036,3102	yes	missense	C17orf67	NM_001085430.1	29	121,1536,4633	CC,CT,TT		14.2383,13.9198,14.1335	benign	111/115	54872439	1778,10802	2069	4221	6290	SO:0001583	missense	339210	exon7			GATGAATCCTGTT	BC041467	CCDS42364.1, CCDS42364.2	17q23.2	2012-10-11			ENSG00000214226	ENSG00000214226			27900	protein-coding gene	gene with protein product						12477932	Standard	NM_001085430		Approved		uc002iuq.4	Q0P5P2	OTTHUMG00000132083	ENST00000575658.1:c.331A>G	17.37:g.54872439T>C	ENSP00000461483:p.Ile111Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_001085430		Missense_Mutation	SNP	ENST00000575658.1	37		284	0.13003663003663005	84	0.17073170731707318	49	0.13535911602209943	14	0.024475524475524476	137	0.18073878627968337	C	2.267	-0.367989	0.05069	0.139198	0.142383	ENSG00000214226	ENST00000397861;ENST00000397862	.	.	.	4.69	3.7	0.42460	.	0.140081	0.28515	N	0.015080	T	0.00039	0.0001	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18777	-1.0326	8	0.02654	T	1	-19.4414	10.6281	0.45519	0.0:0.8372:0.0:0.1628	.	111	Q0P5P2	CQ067_HUMAN	V	111	.	ENSP00000380959:I111V	I	-	1	0	C17orf67	52227438	0.945000	0.32115	0.010000	0.14722	0.022000	0.10575	2.010000	0.40913	0.515000	0.28320	-0.213000	0.12676	ATT	T|0.870;C|0.130	0.130	strong		0.597	C17orf67-202	KNOWN	basic	protein_coding	protein_coding		NM_001085430	
FAM118A	55007	hgsc.bcm.edu	37	22	45723807	45723807	+	Missense_Mutation	SNP	G	G	C	rs11556482	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:45723807G>C	ENST00000216214.3	+	5	1219	c.385G>C	c.(385-387)Gtg>Ctg	p.V129L	FAM118A_ENST00000441876.2_Missense_Mutation_p.V129L|FAM118A_ENST00000405673.1_Missense_Mutation_p.V129L|FAM118A_ENST00000405548.3_5'Flank	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	129			V -> L (in dbSNP:rs11556482). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CCGGAGTCCTGTGGTGCTGCA	0.592													C|||	2691	0.53734	0.8548	0.402	5008	,	,		19525	0.5258		0.2932	False		,,,				2504	0.4673				p.V129L		Atlas-SNP	.											.	FAM118A	32	.	0			c.G385C						PASS	.	C	LEU/VAL,LEU/VAL	3325,1081	392.4+/-328.5	1262,801,140	70.0	59.0	63.0		385,385	-0.0	0.1	22	dbSNP_120	63	2445,6155	697.2+/-404.9	354,1737,2209	yes	missense,missense	FAM118A	NM_001104595.1,NM_017911.2	32,32	1616,2538,2349	CC,CG,GG		28.4302,24.5347,44.3641	benign,benign	129/358,129/358	45723807	5770,7236	2203	4300	6503	SO:0001583	missense	55007	exon4			AGTCCTGTGGTGC	BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 8"""	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.385G>C	22.37:g.45723807G>C	ENSP00000216214:p.Val129Leu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	187	95	0.508021	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Missense_Mutation	SNP	ENST00000216214.3	37	CCDS14065.1	1086	0.49725274725274726	414	0.8414634146341463	153	0.42265193370165743	299	0.5227272727272727	220	0.29023746701846964	C	0.889	-0.726183	0.03158	0.754653	0.284302	ENSG00000100376	ENST00000216214;ENST00000441876;ENST00000405673;ENST00000427777	T;T;T;T	0.42131	1.03;1.03;0.98;0.99	5.12	-0.0348	0.13895	.	0.968722	0.08538	N	0.930981	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36163	-0.9759	9	0.27785	T	0.31	-20.5793	13.0846	0.59133	0.0917:0.3886:0.5197:0.0	rs11556482;rs17845392;rs17858249	129	Q9NWS6	F118A_HUMAN	L	129	ENSP00000216214:V129L;ENSP00000395892:V129L;ENSP00000385231:V129L;ENSP00000395194:V129L	ENSP00000216214:V129L	V	+	1	0	FAM118A	44102471	0.935000	0.31712	0.119000	0.21687	0.190000	0.23558	1.400000	0.34577	0.124000	0.18369	-0.335000	0.08231	GTG	G|0.539;C|0.461	0.461	strong		0.592	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
OVGP1	5016	hgsc.bcm.edu	37	1	111957570	111957570	+	Missense_Mutation	SNP	G	G	C	rs376377993|rs45455292	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111957570G>C	ENST00000369732.3	-	11	1608	c.1553C>G	c.(1552-1554)aCc>aGc	p.T518S		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	518					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		TTCCCCAGGGGTCACAGACTG	0.572													G|||	910	0.181709	0.0643	0.1542	5008	,	,		17214	0.1528		0.2714	False		,,,				2504	0.2975				p.T518S		Atlas-SNP	.											.	OVGP1	177	.	0			c.C1553G						PASS	.						58.0	53.0	55.0					1																	111957570		2194	4297	6491	SO:0001583	missense	5016	exon11			CCAGGGGTCACAG	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1553C>G	1.37:g.111957570G>C	ENSP00000358747:p.Thr518Ser	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	153	36	0.235294	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	284	0.13003663003663005	20	0.04065040650406504	59	0.16298342541436464	62	0.10839160839160839	143	0.18865435356200527	G	12.03	1.816593	0.32145	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.04234	3.67	3.36	2.43	0.29744	.	.	.	.	.	T	0.01454	0.0047	L	0.31578	0.945	0.58432	P	5.000000000032756E-6	B;B	0.17038	0.02;0.02	B;B	0.19148	0.024;0.024	T	0.40459	-0.9562	8	0.62326	D	0.03	.	7.157	0.25643	0.1378:0.0:0.8622:0.0	rs45455292	518;582	Q12889;Q59HH5	OVGP1_HUMAN;.	S	518;582;326	ENSP00000358747:T518S	ENSP00000358743:T582S	T	-	2	0	OVGP1	111759093	0.002000	0.14202	0.003000	0.11579	0.242000	0.25591	0.074000	0.14662	0.696000	0.31696	0.454000	0.30748	ACC	G|0.853;C|0.147	0.147	strong		0.572	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
OR2T6	254879	hgsc.bcm.edu	37	1	248551203	248551203	+	Silent	SNP	T	T	C	rs6700947|rs386642006	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248551203T>C	ENST00000355728.2	+	1	294	c.294T>C	c.(292-294)acT>acC	p.T98T		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCGCCTGCACTGCTCAGTGCT	0.532													t|||	1850	0.369409	0.4962	0.3127	5008	,	,		19053	0.4365		0.1769	False		,,,				2504	0.3671				p.T98T		Atlas-SNP	.											.	OR2T6	101	.	0			c.T294C						PASS	.	C		1893,2513	538.7+/-375.1	423,1047,733	122.0	121.0	121.0		294	-7.1	0.1	1	dbSNP_116	121	1297,7303	256.5+/-280.9	92,1113,3095	no	coding-synonymous	OR2T6	NM_001005471.1		515,2160,3828	CC,CT,TT		15.0814,42.9641,24.5271		98/309	248551203	3190,9816	2203	4300	6503	SO:0001819	synonymous_variant	254879	exon1			CTGCACTGCTCAG	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"""GPCR / Class A : Olfactory receptors"""	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.294T>C	1.37:g.248551203T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	115	64	0.556522	NM_001005471	A6NE36	Silent	SNP	ENST00000355728.2	37	CCDS31114.1																																																																																			T|0.722;C|0.278	0.278	strong		0.532	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471	
DIP2A	23181	hgsc.bcm.edu	37	21	47970581	47970581	+	Silent	SNP	G	G	A	rs2255397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47970581G>A	ENST00000417564.2	+	23	2784	c.2763G>A	c.(2761-2763)acG>acA	p.T921T	DIP2A_ENST00000318711.7_Silent_p.T922T|DIP2A_ENST00000427143.2_Silent_p.T857T|DIP2A_ENST00000400274.1_Silent_p.T917T			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	921					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TGGAAGGGACGCTGCACCCGT	0.532													A|||	1330	0.265575	0.261	0.2795	5008	,	,		21527	0.3452		0.2078	False		,,,				2504	0.2393				p.T921T		Atlas-SNP	.											.	DIP2A	332	.	0			c.G2763A						PASS	.	A	,,	1038,3062		147,744,1159	80.0	79.0	79.0		2571,2751,2763	-9.4	0.1	21	dbSNP_100	79	1760,6658		197,1366,2646	no	coding-synonymous,coding-synonymous,coding-synonymous	DIP2A	NM_001146114.1,NM_001146116.1,NM_015151.3	,,	344,2110,3805	AA,AG,GG		20.9076,25.3171,22.3518	,,	857/1111,917/1568,921/1572	47970581	2798,9720	2050	4209	6259	SO:0001819	synonymous_variant	23181	exon23			AGGGACGCTGCAC	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.2763G>A	21.37:g.47970581G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	185	98	0.52973	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																			G|0.766;A|0.234	0.234	strong		0.532	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
SLC38A10	124565	hgsc.bcm.edu	37	17	79255998	79255998	+	Silent	SNP	G	G	A	rs10871494	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79255998G>A	ENST00000374759.3	-	5	875	c.492C>T	c.(490-492)ttC>ttT	p.F164F	SLC38A10_ENST00000288439.5_Silent_p.F164F|SLC38A10_ENST00000546352.1_5'UTR	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	164					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCACGAACATGAACACGGTGT	0.632													G|||	567	0.113219	0.1157	0.1931	5008	,	,		19566	0.003		0.2207	False		,,,				2504	0.0562				p.F164F		Atlas-SNP	.											SLC38A10_ENST00000374759,NS,carcinoma,0,2	SLC38A10	133	2	0			c.C492T						PASS	.	G	,	567,3839	253.7+/-259.5	35,497,1671	117.0	97.0	104.0		492,492	4.4	1.0	17	dbSNP_120	104	1787,6813	322.2+/-315.5	210,1367,2723	no	coding-synonymous,coding-synonymous	SLC38A10	NM_001037984.1,NM_138570.2	,	245,1864,4394	AA,AG,GG		20.7791,12.8688,18.0993	,	164/1120,164/781	79255998	2354,10652	2203	4300	6503	SO:0001819	synonymous_variant	124565	exon5			GAACATGAACACG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.492C>T	17.37:g.79255998G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	165	90	0.545455	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	37	CCDS42397.1	293	0.13415750915750915	53	0.10772357723577236	73	0.20165745856353592	1	0.0017482517482517483	166	0.21899736147757257	G	11.20	1.569041	0.28003	0.128688	0.207791	ENSG00000157637	ENST00000543204	.	.	.	5.34	4.36	0.52297	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.05115	-1.0905	3	.	.	.	-25.819	11.612	0.51066	0.1424:0.0:0.8576:0.0	rs10871494;rs10871494	.	.	.	Y	23	.	.	H	-	1	0	SLC38A10	76870593	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	3.645000	0.54389	2.485000	0.83878	0.655000	0.94253	CAT	G|0.845;A|0.155	0.155	strong		0.632	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
TTN	7273	hgsc.bcm.edu	37	2	179579093	179579093	+	Missense_Mutation	SNP	T	T	C	rs12693164	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179579093T>C	ENST00000591111.1	-	89	25681	c.25457A>G	c.(25456-25458)aAt>aGt	p.N8486S	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.N7559S|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.N8803S|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12654	Ig-like 67.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTTCCAGCATTGGCTGGTTC	0.393													T|||	1237	0.247005	0.1936	0.1859	5008	,	,		21117	0.4365		0.1561	False		,,,				2504	0.2607				p.N8803S		Atlas-SNP	.											TTN_ENST00000342992,colon,carcinoma,0,1	TTN	18412	1	0			c.A26408G						PASS	.	T	,,,SER/ASN	595,3173		45,505,1334	116.0	113.0	114.0		,,,22676	2.2	1.0	2	dbSNP_121	114	1240,6996		96,1048,2974	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,46	141,1553,4308	CC,CT,TT		15.0559,15.7909,15.2866	,,,benign	,,,7559/33424	179579093	1835,10169	1884	4118	6002	SO:0001583	missense	7273	exon91			CCAGCATTGGCTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25457A>G	2.37:g.179579093T>C	ENSP00000465570:p.Asn8486Ser	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	285	127	0.445614	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		512	0.23443223443223443	98	0.1991869918699187	55	0.15193370165745856	243	0.42482517482517484	116	0.15303430079155672	T	7.990	0.752982	0.15778	0.157909	0.150559	ENSG00000155657	ENST00000342992	T	0.68025	-0.3	5.96	2.25	0.28309	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.999999999999746	B	0.16603	0.018	B	0.09377	0.004	T	0.32025	-0.9922	8	0.87932	D	0	.	12.1749	0.54180	0.0:0.1656:0.0:0.8344	rs12693164;rs52822704;rs58566262;rs12693164	8486	Q8WZ42	TITIN_HUMAN	S	7559	ENSP00000343764:N7559S	ENSP00000343764:N7559S	N	-	2	0	TTN	179287338	1.000000	0.71417	0.983000	0.44433	0.345000	0.29048	0.818000	0.27295	-0.075000	0.12798	-2.240000	0.00288	AAT	T|0.765;C|0.235	0.235	strong		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RBP5	83758	hgsc.bcm.edu	37	12	7277236	7277236	+	Missense_Mutation	SNP	T	T	A	rs2290237	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7277236T>A	ENST00000266560.3	-	3	509	c.343A>T	c.(343-345)Atg>Ttg	p.M115L	C1RL-AS1_ENST00000545775.1_RNA|C1RL-AS1_ENST00000535078.1_RNA|C1RL-AS1_ENST00000541775.1_RNA	NM_031491.2	NP_113679.1	P29762	RABP1_HUMAN	retinol binding protein 5, cellular	118					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoic acid binding (GO:0001972)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			autonomic_ganglia(1)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)	10					Alitretinoin(DB00523)|Tretinoin(DB00755)	AGATACAGCATCTCTCCCTCC	0.582													T|||	1475	0.294529	0.1702	0.4827	5008	,	,		-128	0.1736		0.3738	False		,,,				2504	0.3722				p.M115L		Atlas-SNP	.											.	RBP5	20	.	0			c.A343T						PASS	.	T	LEU/MET	863,3543	335.5+/-303.9	85,693,1425	103.0	103.0	103.0		343	2.0	0.0	12	dbSNP_100	103	3341,5259	496.7+/-374.4	627,2087,1586	yes	missense	RBP5	NM_031491.2	15	712,2780,3011	AA,AT,TT		38.8488,19.5869,32.3235	benign	115/136	7277236	4204,8802	2203	4300	6503	SO:0001583	missense	83758	exon3			ACAGCATCTCTCC	AY007436	CCDS8574.1	12p13.31	2013-03-01	2001-11-28		ENSG00000139194	ENSG00000139194		"""Fatty acid binding protein family"""	15847	protein-coding gene	gene with protein product		611866	"""retinol-binding protein 5, cellular"""			11274389	Standard	NM_031491		Approved	CRBPIII	uc001qsq.3	P82980	OTTHUMG00000168165	ENST00000266560.3:c.343A>T	12.37:g.7277236T>A	ENSP00000266560:p.Met115Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_031491	Q6IAY7|Q8WTV5	Missense_Mutation	SNP	ENST00000266560.3	37	CCDS8574.1	629	0.288003663003663	88	0.17886178861788618	167	0.4613259668508287	87	0.1520979020979021	287	0.3786279683377309	T	9.449	1.090168	0.20390	0.195869	0.388488	ENSG00000139194	ENST00000266560	T	0.07567	3.18	3.19	2.04	0.26737	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	2.671410	0.01367	N	0.012450	T	0.00012	0.0000	N	0.02916	-0.46	0.38416	P	0.053956000000000004	B	0.02656	0.0	B	0.01281	0.0	T	0.46133	-0.9213	9	0.45353	T	0.12	.	5.1611	0.15062	0.0:0.1163:0.3746:0.5091	rs2290237;rs11540814;rs59739778;rs2290237	115	P82980	RET5_HUMAN	L	115	ENSP00000266560:M115L	ENSP00000266560:M115L	M	-	1	0	RBP5	7168510	0.006000	0.16342	0.008000	0.14137	0.539000	0.34962	0.473000	0.22132	0.618000	0.30179	0.379000	0.24179	ATG	T|0.686;A|0.314	0.314	strong		0.582	RBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398554.1	NM_031491	
RBAK	57786	hgsc.bcm.edu	37	7	5096958	5096958	+	Silent	SNP	T	T	C	rs11975068	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:5096958T>C	ENST00000353796.3	+	4	372	c.48T>C	c.(46-48)gaT>gaC	p.D16D	RBAK-RBAKDN_ENST00000396904.2_Silent_p.D16D|RBAK_ENST00000396912.1_Silent_p.D16D|RBAK-RBAKDN_ENST00000407184.1_Silent_p.D16D	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	16	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		TGGCTGTGGATTTCACCCAGG	0.473													T|||	1279	0.255391	0.1687	0.2277	5008	,	,		11943	0.379		0.2724	False		,,,				2504	0.2474				p.D16D		Atlas-SNP	.											RBAK_ENST00000396912,NS,carcinoma,0,1	.	.	1	0			c.T48C						PASS	.	T	,,	808,3598	322.9+/-297.8	75,658,1470	110.0	115.0	113.0		48,48,48	1.9	0.9	7	dbSNP_120	113	2200,6400	374.2+/-337.3	261,1678,2361	no	coding-synonymous,coding-synonymous,coding-synonymous	RBAK,RBAK-LOC389458	NM_001204456.1,NM_001204513.1,NM_021163.3	,,	336,2336,3831	CC,CT,TT		25.5814,18.3386,23.1278	,,	16/715,16/114,16/715	5096958	3008,9998	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGTGGATTTCACC	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"""Zinc fingers, C2H2-type"", ""-"""	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.48T>C	7.37:g.5096958T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	187	96	0.513369	NM_001204513	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Silent	SNP	ENST00000353796.3	37	CCDS5337.1																																																																																			T|0.756;C|0.244	0.244	strong		0.473	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
BTBD10	84280	hgsc.bcm.edu	37	11	13443250	13443250	+	Silent	SNP	C	C	T	rs3789325	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:13443250C>T	ENST00000278174.5	-	3	482	c.237G>A	c.(235-237)acG>acA	p.T79T	BTBD10_ENST00000528120.1_Silent_p.T31T|BTBD10_ENST00000530907.1_Silent_p.T87T|BTBD10_ENST00000532261.1_5'UTR	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10	79						nucleus (GO:0005634)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|prostate(1)	20				Epithelial(150;0.0214)		GCTGAGACTCCGTTCTTTCAT	0.418													T|||	702	0.140176	0.0545	0.2997	5008	,	,		18962	0.1687		0.1481	False		,,,				2504	0.1053				p.T79T		Atlas-SNP	.											.	BTBD10	43	.	0			c.G237A						PASS	.	T		292,4108	799.4+/-415.5	16,260,1924	152.0	125.0	134.0		237	3.8	1.0	11	dbSNP_107	134	1492,7096	747.9+/-407.3	117,1258,2919	no	coding-synonymous	BTBD10	NM_032320.5		133,1518,4843	TT,TC,CC		17.3731,6.6364,13.7358		79/476	13443250	1784,11204	2200	4294	6494	SO:0001819	synonymous_variant	84280	exon3			AGACTCCGTTCTT	AY221959	CCDS7811.1, CCDS73261.1	11p15.2	2013-01-24			ENSG00000148925	ENSG00000148925		"""BTB/POZ domain containing"""	21445	protein-coding gene	gene with protein product		615933				15556295	Standard	XM_005253164		Approved	GMRP1, GMRP-1, MGC13007	uc001mkz.3	Q9BSF8	OTTHUMG00000165787	ENST00000278174.5:c.237G>A	11.37:g.13443250C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_032320	B7Z228|Q86WG1	Silent	SNP	ENST00000278174.5	37	CCDS7811.1																																																																																			C|0.866;T|0.134	0.134	strong		0.418	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320	
Unknown	0	hgsc.bcm.edu	37	11	124096122	124096122	+	IGR	SNP	G	G	A	rs7946182	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124096122G>A								OR10D3 (39170 upstream) : OR8G1 (24300 downstream)																							CTCCGCATTCGCTCCACTGAG	0.498													g|||	2253	0.44988	0.612	0.3429	5008	,	,		20593	0.3155		0.338	False		,,,				2504	0.5603				p.R242H		Atlas-SNP	.											.	.	.	.	0			c.G725A						PASS	.	G	HIS/ARG	1784,2406		550,684,861	87.0	108.0	101.0		725	-3.8	0.0	11	dbSNP_116	101	2151,6399		431,1289,2555	no	missense	OR8G2	NM_001007249.1	29	981,1973,3416	AA,AG,GG		25.1579,42.5776,30.887	benign	242/305	124096122	3935,8805	2095	4275	6370	SO:0001628	intergenic_variant	26492	exon1			GCATTCGCTCCAC																													11.37:g.124096122G>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	208	93	0.447115	NM_001007249		Missense_Mutation	SNP		37																																																																																				G|0.653;A|0.347	0.347	strong	0	0.498								
PRSS12	8492	hgsc.bcm.edu	37	4	119237348	119237348	+	Silent	SNP	T	T	C	rs2292597	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:119237348T>C	ENST00000296498.3	-	6	1563	c.1281A>G	c.(1279-1281)caA>caG	p.Q427Q		NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	427	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.Q427Q(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						TAAATCCCAATTGTCGACAAA	0.378													C|||	2731	0.545327	0.4516	0.5692	5008	,	,		17615	0.5843		0.5626	False		,,,				2504	0.5971				p.Q427Q		Atlas-SNP	.											PRSS12,NS,carcinoma,0,1	PRSS12	71	1	1	Substitution - coding silent(1)	stomach(1)	c.A1281G						PASS	.	C		2088,2318	604.1+/-390.3	516,1056,631	102.0	95.0	97.0		1281	3.5	0.9	4	dbSNP_100	97	4726,3874	544.2+/-384.5	1306,2114,880	no	coding-synonymous	PRSS12	NM_003619.3		1822,3170,1511	CC,CT,TT		45.0465,47.3899,47.6088		427/876	119237348	6814,6192	2203	4300	6503	SO:0001819	synonymous_variant	8492	exon6			TCCCAATTGTCGA	AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"""Serine peptidases / Serine peptidases"""	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.1281A>G	4.37:g.119237348T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_003619	Q9UP16	Silent	SNP	ENST00000296498.3	37	CCDS3709.1																																																																																			T|0.467;C|0.533	0.533	strong		0.378	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2		
PPP1R15A	23645	hgsc.bcm.edu	37	19	49379182	49379182	+	Silent	SNP	G	G	C	rs386810065|rs527	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49379182G>C	ENST00000200453.5	+	3	2246	c.1977G>C	c.(1975-1977)tcG>tcC	p.S659S		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	659					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CTTCCCGCTCGTCTGCTGCTG	0.567													G|||	1786	0.356629	0.5764	0.2896	5008	,	,		16609	0.1984		0.2803	False		,,,				2504	0.3487				p.S659S		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G1977C						PASS	.	G		2273,2133	583.2+/-385.8	569,1135,499	70.0	72.0	71.0		1977	-3.2	0.0	19	dbSNP_36	71	2469,6131	396.7+/-345.5	354,1761,2185	no	coding-synonymous	PPP1R15A	NM_014330.3		923,2896,2684	CC,CG,GG		28.7093,48.4113,36.4601		659/675	49379182	4742,8264	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon3			CCGCTCGTCTGCT	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1977G>C	19.37:g.49379182G>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			G|0.646;C|0.354	0.354	strong		0.567	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
FANCD2	2177	hgsc.bcm.edu	37	3	10138069	10138069	+	Silent	SNP	T	T	G	rs2272125	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:10138069T>G	ENST00000419585.1	+	42	4259	c.4098T>G	c.(4096-4098)ctT>ctG	p.L1366L	FANCD2_ENST00000383807.1_Silent_p.L1366L|FANCD2_ENST00000383806.1_3'UTR|FANCD2_ENST00000287647.3_Silent_p.L1366L|FANCD2OS_ENST00000436517.1_5'Flank|FANCD2OS_ENST00000524279.1_Intron			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	1366					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CCCTGGAACTTTTAGTTTGCA	0.433			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	1213	0.242212	0.5174	0.196	5008	,	,		20261	0.0675		0.1412	False		,,,				2504	0.1871				p.L1366L		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	.	FANCD2	253	.	0			c.T4098G	GRCh37	CM066071	FANCD2	M	rs2272125	PASS	.	G	,,	2077,2329	604.9+/-390.4	491,1095,617	125.0	119.0	121.0		4098,4098,	3.9	0.9	3	dbSNP_100	121	1416,7184	752.7+/-407.4	119,1178,3003	no	coding-synonymous,coding-synonymous,intron	FANCD2,C3orf24	NM_001018115.1,NM_033084.3,NM_173472.1	,,	610,2273,3620	GG,GT,TT		16.4651,47.1403,26.8568	,,	1366/1452,1366/1472,	10138069	3493,9513	2203	4300	6503	SO:0001819	synonymous_variant	2177	exon42	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGAACTTTTAGTT	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.4098T>G	3.37:g.10138069T>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																			T|0.743;G|0.257	0.257	strong		0.433	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
CTTNBP2NL	55917	hgsc.bcm.edu	37	1	112991698	112991698	+	Silent	SNP	T	T	C	rs2256883	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:112991698T>C	ENST00000271277.6	+	4	459	c.234T>C	c.(232-234)aaT>aaC	p.N78N		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	78					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)	p.N78N(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCTGCACAAATCCACTCTCTA	0.458													C|||	2631	0.525359	0.3238	0.5692	5008	,	,		18306	0.4464		0.66	False		,,,				2504	0.7096				p.N78N		Atlas-SNP	.											CTTNBP2NL,NS,carcinoma,0,1	CTTNBP2NL	65	1	1	Substitution - coding silent(1)	stomach(1)	c.T234C						PASS	.	C		1698,2708	653.7+/-399.6	320,1058,825	73.0	70.0	71.0		234	3.8	1.0	1	dbSNP_100	71	5574,3026	465.3+/-366.5	1786,2002,512	no	coding-synonymous	CTTNBP2NL	NM_018704.2		2106,3060,1337	CC,CT,TT		35.186,38.5384,44.0873		78/640	112991698	7272,5734	2203	4300	6503	SO:0001819	synonymous_variant	55917	exon4			CACAAATCCACTC	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.234T>C	1.37:g.112991698T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	162	78	0.481481	NM_018704	B3KMS5|Q96B40	Silent	SNP	ENST00000271277.6	37	CCDS845.1																																																																																			T|0.457;C|0.543	0.543	strong		0.458	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704	
ABCC2	1244	hgsc.bcm.edu	37	10	101604207	101604207	+	Silent	SNP	C	C	T	rs3740066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:101604207C>T	ENST00000370449.4	+	28	4085	c.3972C>T	c.(3970-3972)atC>atT	p.I1324I		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1324	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.I1324I(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CTTGTGACATCGGTAGCATGG	0.542													C|||	1443	0.288139	0.2163	0.3415	5008	,	,		20904	0.247		0.3708	False		,,,				2504	0.3047				p.I1324I		Atlas-SNP	.											ABCC2,NS,carcinoma,0,1	ABCC2	160	1	1	Substitution - coding silent(1)	stomach(1)	c.C3972T	GRCh37	CM080009	ABCC2	M	rs3740066	scavenged	.			1145,3261	407.3+/-334.2	151,843,1209	144.0	126.0	132.0		3972	0.7	0.8	10	dbSNP_107	132	3193,5407	483.7+/-371.2	605,1983,1712	no	coding-synonymous	ABCC2	NM_000392.3		756,2826,2921	TT,TC,CC		37.1279,25.9873,33.3538		1324/1546	101604207	4338,8668	2203	4300	6503	SO:0001819	synonymous_variant	1244	exon28			TGACATCGGTAGC	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.3972C>T	10.37:g.101604207C>T		Somatic	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	23	22	0.956522	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Silent	SNP	ENST00000370449.4	37	CCDS7484.1																																																																																			C|0.678;T|0.322	0.322	strong		0.542	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
KIAA0195	9772	hgsc.bcm.edu	37	17	73493874	73493874	+	Silent	SNP	G	G	C	rs12949173	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73493874G>C	ENST00000314256.7	+	27	3814	c.3420G>C	c.(3418-3420)ctG>ctC	p.L1140L	AC100787.1_ENST00000579379.1_RNA|KIAA0195_ENST00000375248.5_Silent_p.L1150L|KIAA0195_ENST00000579208.1_Silent_p.L791L	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	1140						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCTCTCTGCTGGGGAAGCCCC	0.522													G|||	302	0.0603035	0.0068	0.0994	5008	,	,		18836	0.0		0.1889	False		,,,				2504	0.0348				p.L1140L		Atlas-SNP	.											.	KIAA0195	102	.	0			c.G3420C						PASS	.	G		171,4235	112.9+/-151.0	2,167,2034	87.0	74.0	79.0		3420	3.7	1.0	17	dbSNP_121	79	1884,6716	335.6+/-321.5	217,1450,2633	no	coding-synonymous	KIAA0195	NM_014738.4		219,1617,4667	CC,CG,GG		21.907,3.8811,15.8004		1140/1357	73493874	2055,10951	2203	4300	6503	SO:0001819	synonymous_variant	9772	exon27			TCTGCTGGGGAAG		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.3420G>C	17.37:g.73493874G>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_014738	O75536|Q86XF1	Silent	SNP	ENST00000314256.7	37	CCDS32732.1																																																																																			G|0.863;C|0.137	0.137	strong		0.522	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
GPRC5A	9052	hgsc.bcm.edu	37	12	13061294	13061294	+	Silent	SNP	C	C	T	rs2075288	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:13061294C>T	ENST00000014914.5	+	2	1001	c.111C>T	c.(109-111)gcC>gcT	p.A37A	GPRC5A_ENST00000542056.1_Intron	NM_003979.3	NP_003970.1	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, class C, group 5, member A	37					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	18		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)	TGGCCACAGCCGGGGTTGTGA	0.547													C|||	1811	0.361621	0.0401	0.4481	5008	,	,		20094	0.7173		0.331	False		,,,				2504	0.3998				p.A37A		Atlas-SNP	.											.	GPRC5A	38	.	0			c.C111T						PASS	.	C		323,4083	171.6+/-201.8	12,299,1892	94.0	87.0	89.0		111	-10.7	0.0	12	dbSNP_96	89	2406,6194	401.0+/-347.0	336,1734,2230	no	coding-synonymous	GPRC5A	NM_003979.3		348,2033,4122	TT,TC,CC		27.9767,7.3309,20.9826		37/358	13061294	2729,10277	2203	4300	6503	SO:0001819	synonymous_variant	9052	exon2			CACAGCCGGGGTT	AF095448	CCDS8657.1	12p13-p12.3	2014-01-30	2014-01-30	2005-05-03		ENSG00000013588		"""GPCR / Class C : Orphans"""	9836	protein-coding gene	gene with protein product		604138	"""retinoic acid induced 3"", ""G protein-coupled receptor, family C, group 5, member A"""	RAI3, GPCR5A		9857033	Standard	NM_003979		Approved	RAIG1	uc001rba.3	Q8NFJ5		ENST00000014914.5:c.111C>T	12.37:g.13061294C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_003979	B3KV45|O95357	Silent	SNP	ENST00000014914.5	37	CCDS8657.1																																																																																			C|0.726;T|0.274	0.274	strong		0.547	GPRC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400682.1		
ANKUB1	389161	hgsc.bcm.edu	37	3	149485293	149485293	+	Missense_Mutation	SNP	T	T	C	rs7610425	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:149485293T>C	ENST00000383050.3	-	5	1612	c.1156A>G	c.(1156-1158)Agc>Ggc	p.S386G	ANKUB1_ENST00000446160.1_Missense_Mutation_p.S386G|ANKUB1_ENST00000462519.2_Missense_Mutation_p.S386G			A6NFN9	ANKUB_HUMAN	ankyrin repeat and ubiquitin domain containing 1	386			S -> G (in dbSNP:rs7610425).							breast(1)|kidney(1)|lung(1)|skin(1)	4						GGTTTGCTGCTTGCAGTTTGT	0.458													T|||	1326	0.264776	0.1717	0.2579	5008	,	,		19084	0.247		0.3907	False		,,,				2504	0.2843				p.S386G		Atlas-SNP	.											.	ANKUB1	27	.	0			c.A1156G						PASS	.	T	GLY/SER	285,1099		25,235,432	187.0	133.0	149.0		1156	-1.1	0.0	3	dbSNP_116	149	1266,1916		249,768,574	yes	missense	ANKUB1	NM_001144960.1	56	274,1003,1006	CC,CT,TT		39.7863,20.5925,33.9685	benign	386/545	149485293	1551,3015	692	1591	2283	SO:0001583	missense	389161	exon5			TGCTGCTTGCAGT	AK027233		3q25.1	2013-01-11	2011-05-10	2011-05-10	ENSG00000206199	ENSG00000206199		"""Ankyrin repeat domain containing"""	29642	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 16"""	C3orf16			Standard	NM_001144960		Approved		uc003exl.3	A6NFN9	OTTHUMG00000159615	ENST00000383050.3:c.1156A>G	3.37:g.149485293T>C	ENSP00000372522:p.Ser386Gly	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	220	96	0.436364	NM_001144960	B4E2N8	Missense_Mutation	SNP	ENST00000383050.3	37		614	0.28113553113553114	88	0.17886178861788618	92	0.2541436464088398	123	0.21503496503496503	311	0.4102902374670185	T	11.33	1.607832	0.28623	0.205925	0.397863	ENSG00000206199	ENST00000446160;ENST00000383050;ENST00000462519	T;T;T	0.24908	1.86;1.83;1.86	5.6	-1.11	0.09840	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.49113	-0.8973	8	0.22706	T	0.39	.	6.0018	0.19525	0.0:0.2809:0.126:0.593	rs7610425;rs17788044;rs52792421;rs57468189;rs7610425	386;386	A6NFN9;E9PHT4	ANKUB_HUMAN;.	G	386	ENSP00000387907:S386G;ENSP00000372522:S386G;ENSP00000417635:S386G	ENSP00000372522:S386G	S	-	1	0	ANKUB1	150967983	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	1.012000	0.29924	-0.423000	0.07394	-0.353000	0.07706	AGC	C|0.286;N|0.000	0.286	strong		0.458	ANKUB1-201	KNOWN	basic	protein_coding	protein_coding		NM_001144960	
HLA-B	3106	hgsc.bcm.edu	37	6	31323202	31323202	+	Missense_Mutation	SNP	T	T	C	rs41545916		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323202T>C	ENST00000412585.2	-	4	815	c.787A>G	c.(787-789)Aga>Gga	p.R263G		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	263	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TGGAAGGTTCTATCTCCTGCT	0.582									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.R263G		Atlas-SNP	.											.	HLA-B	54	.	0			c.A787G						PASS	.						93.0	79.0	84.0					6																	31323202		2203	4300	6503	SO:0001583	missense	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	AGGTTCTATCTCC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.787A>G	6.37:g.31323202T>C	ENSP00000399168:p.Arg263Gly	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	179	55	0.307263	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	6.971	0.549058	0.13312	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596	T	0.02323	4.34	3.16	1.33	0.21861	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.165679	0.27881	N	0.017476	T	0.00109	0.0003	N	0.00006	-3.21	0.25657	N	0.986046	B	0.06786	0.001	B	0.04013	0.001	T	0.24764	-1.0151	10	0.02654	T	1	.	7.8568	0.29487	0.0:0.778:0.0:0.222	rs41545916	263	P01889	1B07_HUMAN	G	263;142;142	ENSP00000399168:R263G	ENSP00000399168:R263G	R	-	1	2	HLA-B	31431181	0.310000	0.24527	0.455000	0.27031	0.099000	0.18886	0.951000	0.29135	0.182000	0.20032	-0.549000	0.04216	AGA	.	.	weak		0.582	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
KRT86	3892	hgsc.bcm.edu	37	12	52699033	52699033	+	Missense_Mutation	SNP	G	G	A	rs61914259	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:52699033G>A	ENST00000423955.2	+	7	923	c.745G>A	c.(745-747)Gtt>Att	p.V249I	KRT86_ENST00000544024.1_Missense_Mutation_p.V249I|KRT86_ENST00000293525.5_Missense_Mutation_p.V249I|RP11-845M18.6_ENST00000552441.1_RNA			O43790	KRT86_HUMAN	keratin 86	249	Coil 1B.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		GGAGATCCGCGTTCTCCAGTC	0.567																																					p.V249I		Atlas-SNP	.											KRT86,NS,carcinoma,0,1	KRT86	33	1	0			c.G745A						scavenged	.						146.0	126.0	133.0					12																	52699033		2203	4300	6503	SO:0001583	missense	3892	exon5			ATCCGCGTTCTCC	X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6463	protein-coding gene	gene with protein product	"""hard keratin type II 6"""	601928	"""keratin, hair, basic, 6 (monilethrix)"""	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.745G>A	12.37:g.52699033G>A	ENSP00000444533:p.Val249Ile	Somatic	146	2	0.0136986		WXS	Illumina HiSeq	Phase_I	163	10	0.0613497	NM_002284	P78387	Missense_Mutation	SNP	ENST00000423955.2	37	CCDS41785.1	.	.	.	.	.	.	.	.	.	.	G	9.579	1.123100	0.20959	.	.	ENSG00000170442;ENSG00000170442;ENSG00000170442;ENSG00000258832	ENST00000544024;ENST00000423955;ENST00000293525;ENST00000553310	D;D;D	0.88741	-2.42;-2.42;-2.42	4.69	0.639	0.17747	Filament (1);	0.200519	0.24003	N	0.042444	T	0.79545	0.4464	L	0.39566	1.225	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.61019	-0.7147	10	0.19147	T	0.46	.	5.6128	0.17414	0.3148:0.1288:0.5563:0.0	rs61914259	249	O43790	KRT86_HUMAN	I	249	ENSP00000443169:V249I;ENSP00000444533:V249I;ENSP00000293525:V249I	ENSP00000293525:V249I	V	+	1	0	AC021066.1;KRT86	50985300	0.534000	0.26362	0.012000	0.15200	0.332000	0.28634	2.299000	0.43611	0.091000	0.17302	-0.317000	0.08691	GTT	G|0.695;A|0.305	0.305	strong		0.567	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37438725	37438725	+	Missense_Mutation	SNP	C	C	G	rs200260827	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:37438725C>G	ENST00000602533.1	+	11	1524	c.1425C>G	c.(1423-1425)aaC>aaG	p.N475K	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.N475K|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.N475K			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	531					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N475K(1)		NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						AAATGCAAAACTCTGTTCCAA	0.289													.|||	266	0.053115	0.0666	0.0836	5008	,	,		16587	0.0228		0.0586	False		,,,				2504	0.0389				p.N475K		Atlas-SNP	.											ANKRD30A,trunk,malignant_melanoma,0,1	ANKRD30A	448	1	1	Substitution - Missense(1)	skin(1)	c.C1425G						scavenged	.						108.0	98.0	101.0					10																	37438725		1809	4067	5876	SO:0001583	missense	91074	exon11			GCAAAACTCTGTT	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1425C>G	10.37:g.37438725C>G	ENSP00000473551:p.Asn475Lys	Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	238	33	0.138655	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		21	0.009615384615384616	14	0.028455284552845527	4	0.011049723756906077	2	0.0034965034965034965	1	0.0013192612137203166	.	1.178	-0.639028	0.03557	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.05513	3.43;3.43	1.12	-0.157	0.13387	.	.	.	.	.	T	0.00666	0.0022	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44877	-0.9299	9	0.05525	T	0.97	.	3.0001	0.06011	0.0:0.3069:0.0:0.6931	.	531	Q9BXX3	AN30A_HUMAN	K	475	ENSP00000354432:N475K;ENSP00000363792:N475K	ENSP00000354432:N475K	N	+	3	2	ANKRD30A	37478731	0.020000	0.18652	0.005000	0.12908	0.010000	0.07245	-0.067000	0.11579	-0.051000	0.13334	0.162000	0.16502	AAC	C|0.993;G|0.007	0.007	strong		0.289	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
DACT1	51339	hgsc.bcm.edu	37	14	59113430	59113430	+	Missense_Mutation	SNP	G	G	A	rs698025	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:59113430G>A	ENST00000335867.4	+	4	2113	c.2089G>A	c.(2089-2091)Ggt>Agt	p.G697S	DACT1_ENST00000556859.1_Missense_Mutation_p.G416S|DACT1_ENST00000395153.3_Missense_Mutation_p.G660S|DACT1_ENST00000541264.2_Missense_Mutation_p.G416S			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	697			G -> S (in dbSNP:rs698025).		dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						GGCCCGGCGCGGTCGCCGGGA	0.672													G|||	1353	0.270168	0.4281	0.3343	5008	,	,		11210	0.1508		0.1958	False		,,,				2504	0.2106				p.G697S		Atlas-SNP	.											.	DACT1	119	.	0			c.G2089A						PASS	.	G	SER/GLY,SER/GLY	1574,2826		289,996,915	19.0	22.0	21.0		1978,2089	0.9	0.0	14	dbSNP_86	21	1642,6942		150,1342,2800	yes	missense,missense	DACT1	NM_001079520.1,NM_016651.5	56,56	439,2338,3715	AA,AG,GG		19.1286,35.7727,24.7689	benign,benign	660/800,697/837	59113430	3216,9768	2200	4292	6492	SO:0001583	missense	51339	exon4			CGGCGCGGTCGCC	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.2089G>A	14.37:g.59113430G>A	ENSP00000337439:p.Gly697Ser	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_016651	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	37	CCDS9736.1	548	0.2509157509157509	206	0.4186991869918699	115	0.31767955801104975	80	0.13986013986013987	147	0.19393139841688653	G	0.306	-0.970599	0.02232	0.357727	0.191286	ENSG00000165617	ENST00000556859;ENST00000395151;ENST00000395153;ENST00000335867;ENST00000541264	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	5.32	0.845	0.18950	.	1.464120	0.03992	N	0.294976	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.39522	-0.9610	9	0.10636	T	0.68	-0.416	0.7972	0.01068	0.3771:0.1634:0.2964:0.1632	rs698025	660;697	A8MYJ2;Q9NYF0	.;DACT1_HUMAN	S	416;416;660;697;416	ENSP00000451598:G416S;ENSP00000378581:G416S;ENSP00000378582:G660S;ENSP00000337439:G697S;ENSP00000442850:G416S	ENSP00000337439:G697S	G	+	1	0	DACT1	58183183	0.077000	0.21312	0.000000	0.03702	0.242000	0.25591	1.550000	0.36223	-0.056000	0.13221	-0.244000	0.11960	GGT	G|0.747;T|0.005	.	strong		0.672	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
TAPBPL	55080	hgsc.bcm.edu	37	12	6562836	6562836	+	Silent	SNP	G	G	A	rs2041388	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6562836G>A	ENST00000266556.7	+	3	684	c.519G>A	c.(517-519)ccG>ccA	p.P173P	CD27-AS1_ENST00000545339.1_RNA|TAPBPL_ENST00000544021.1_Silent_p.P96P|CD27-AS1_ENST00000399492.2_RNA|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	173					negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						TCTGGCACCCGACGCTGAACT	0.567													G|||	1016	0.202875	0.0136	0.1599	5008	,	,		18787	0.3224		0.2932	False		,,,				2504	0.273				p.P173P		Atlas-SNP	.											.	TAPBPL	21	.	0			c.G519A						PASS	.	G		249,4157	142.7+/-177.9	8,233,1962	31.0	30.0	31.0		519	-0.2	0.0	12	dbSNP_94	31	2499,6101	401.6+/-347.2	364,1771,2165	no	coding-synonymous	TAPBPL	NM_018009.4		372,2004,4127	AA,AG,GG		29.0581,5.6514,21.1287		173/469	6562836	2748,10258	2203	4300	6503	SO:0001819	synonymous_variant	55080	exon3			GCACCCGACGCTG	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.519G>A	12.37:g.6562836G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	100	41	0.41	NM_018009	Q9NWB8	Silent	SNP	ENST00000266556.7	37	CCDS8546.1																																																																																			G|0.800;A|0.200	0.200	strong		0.567	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
SNX19	399979	hgsc.bcm.edu	37	11	130785304	130785304	+	Silent	SNP	T	T	C	rs3751034	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130785304T>C	ENST00000265909.4	-	1	1100	c.531A>G	c.(529-531)gcA>gcG	p.A177A	SNX19_ENST00000533318.1_Intron|SNX19_ENST00000533214.1_Silent_p.A177A|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000530356.1_Intron|SNX19_ENST00000539184.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	177	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		CATTCTTCCCTGCAGTGGCCT	0.582													T|||	638	0.127396	0.0492	0.0893	5008	,	,		20004	0.1538		0.1988	False		,,,				2504	0.1595				p.A177A		Atlas-SNP	.											.	SNX19	84	.	0			c.A531G						PASS	.	T		315,4087	168.0+/-198.9	15,285,1901	49.0	44.0	46.0		531	-4.3	0.0	11	dbSNP_107	46	1779,6815	320.5+/-314.7	172,1435,2690	no	coding-synonymous	SNX19	NM_014758.2		187,1720,4591	CC,CT,TT		20.7005,7.1558,16.1127		177/993	130785304	2094,10902	2201	4297	6498	SO:0001819	synonymous_variant	399979	exon1			CTTCCCTGCAGTG	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.531A>G	11.37:g.130785304T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_014758	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	37	CCDS31721.1																																																																																			T|0.843;C|0.157	0.157	strong		0.582	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
ZNF395	55893	hgsc.bcm.edu	37	8	28206275	28206275	+	Silent	SNP	G	G	C	rs1046511	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:28206275G>C	ENST00000344423.5	-	10	1634	c.1503C>G	c.(1501-1503)gcC>gcG	p.A501A	ZNF395_ENST00000523095.1_Silent_p.A501A|ZNF395_ENST00000523202.1_Silent_p.A501A	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	501					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		TCCACCGGCAGGCCGTGCACC	0.607													G|||	1578	0.315096	0.1467	0.4928	5008	,	,		16075	0.3879		0.3191	False		,,,				2504	0.3374				p.A501A		Atlas-SNP	.											.	ZNF395	54	.	0			c.C1503G						PASS	.	G		790,3616	314.1+/-293.5	66,658,1479	65.0	64.0	64.0		1503	4.9	1.0	8	dbSNP_86	64	2676,5924	422.8+/-354.1	403,1870,2027	no	coding-synonymous	ZNF395	NM_018660.2		469,2528,3506	CC,CG,GG		31.1163,17.9301,26.6492		501/514	28206275	3466,9540	2203	4300	6503	SO:0001819	synonymous_variant	55893	exon10			CCGGCAGGCCGTG	AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"""Zinc fingers, C2H2-type"""	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.1503C>G	8.37:g.28206275G>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	121	58	0.479339	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Silent	SNP	ENST00000344423.5	37	CCDS6067.1																																																																																			G|0.706;C|0.294	0.294	strong		0.607	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1		
OR2A14	135941	hgsc.bcm.edu	37	7	143826603	143826603	+	Missense_Mutation	SNP	G	G	T	rs2961160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143826603G>T	ENST00000408899.2	+	1	453	c.398G>T	c.(397-399)aGc>aTc	p.S133I		NM_001001659.1	NP_001001659.1	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A, member 14	133			S -> I (in dbSNP:rs2961160). {ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:14983052}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(17)|skin(1)	22	Melanoma(164;0.0783)					CGTTACAATAGCCTCATGAGC	0.517													T|||	3305	0.659944	0.7579	0.7435	5008	,	,		21600	0.7371		0.4841	False		,,,				2504	0.5695				p.S133I		Atlas-SNP	.											OR2A14,NS,carcinoma,+1,1	OR2A14	66	1	0			c.G398T						PASS	.	T	ILE/SER	3225,1095		1205,815,140	191.0	198.0	196.0		398	3.0	0.4	7	dbSNP_101	196	4555,3971		1243,2069,951	yes	missense	OR2A14	NM_001001659.1	142	2448,2884,1091	TT,TG,GG		46.5752,25.3472,39.4364	benign	133/311	143826603	7780,5066	2160	4263	6423	SO:0001583	missense	135941	exon1			ACAATAGCCTCAT		CCDS43672.1	7q35	2013-09-20		2004-03-08	ENSG00000221938	ENSG00000221938		"""GPCR / Class A : Olfactory receptors"""	15084	protein-coding gene	gene with protein product				OR2A14P, OR2A6			Standard	NM_001001659		Approved	OST182	uc011kua.2	Q96R47	OTTHUMG00000158003	ENST00000408899.2:c.398G>T	7.37:g.143826603G>T	ENSP00000386137:p.Ser133Ile	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	252	122	0.484127	NM_001001659	Q6IF41|Q8NGT8	Missense_Mutation	SNP	ENST00000408899.2	37	CCDS43672.1	1408	0.6446886446886447	368	0.7479674796747967	263	0.7265193370165746	427	0.7465034965034965	350	0.46174142480211083	T	1.304	-0.603996	0.03717	0.746528	0.534248	ENSG00000221938	ENST00000408899	T	0.01051	5.4	4.18	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	0.683580	0.11238	U	0.584973	T	0.00012	0.0000	N	0.05306	-0.075	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.04165	-1.0972	9	0.39692	T	0.17	-4.6766	3.667	0.08260	0.0:0.2006:0.1941:0.6053	rs2961160;rs12703584;rs17469079;rs57543916;rs2961160	133	Q96R47	O2A14_HUMAN	I	133	ENSP00000386137:S133I	ENSP00000386137:S133I	S	+	2	0	OR2A14	143457536	0.000000	0.05858	0.381000	0.26106	0.024000	0.10985	-1.556000	0.02168	0.263000	0.21812	-0.363000	0.07495	AGC	G|0.367;T|0.633	0.633	strong		0.517	OR2A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349980.1		
OR10G4	390264	hgsc.bcm.edu	37	11	123886902	123886902	+	Silent	SNP	A	A	G	rs144455396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:123886902A>G	ENST00000320891.4	+	1	621	c.621A>G	c.(619-621)tcA>tcG	p.S207S		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	207						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		TAGTGGCCTCAGGCTGCTTTG	0.557													a|||	4	0.000798722	0.0	0.0014	5008	,	,		22457	0.0		0.003	False		,,,				2504	0.0				p.S207S		Atlas-SNP	.											.	OR10G4	77	.	0			c.A621G						PASS	.	G		4,4398	8.1+/-20.4	0,4,2197	293.0	244.0	261.0		621	-6.4	0.0	11	dbSNP_134	261	18,8580	13.3+/-46.6	0,18,4281	no	coding-synonymous	OR10G4	NM_001004462.1		0,22,6478	GG,GA,AA		0.2094,0.0909,0.1692		207/312	123886902	22,12978	2201	4299	6500	SO:0001819	synonymous_variant	390264	exon1			GGCCTCAGGCTGC	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.621A>G	11.37:g.123886902A>G		Somatic	403	1	0.00248139		WXS	Illumina HiSeq	Phase_I	510	243	0.476471	NM_001004462	Q6IEW0	Silent	SNP	ENST00000320891.4	37	CCDS31702.1																																																																																			A|0.998;G|0.002	0.002	strong		0.557	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
PHKG1	5260	hgsc.bcm.edu	37	7	56149410	56149410	+	Silent	SNP	G	G	A	rs12538444	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:56149410G>A	ENST00000297373.2	-	9	1025	c.831C>T	c.(829-831)taC>taT	p.Y277Y	PHKG1_ENST00000489604.1_5'Flank|PHKG1_ENST00000452681.2_Silent_p.Y309Y|PHKG1_ENST00000537360.1_Silent_p.Y223Y	NM_001258460.1|NM_006213.4	NP_001245389.1|NP_006204.1	Q16816	PHKG1_HUMAN	phosphorylase kinase, gamma 1 (muscle)	277	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|tau-protein kinase activity (GO:0050321)			endometrium(1)|large_intestine(1)|lung(5)	7	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CTTCCGCTGTGTAGCGGTTCT	0.597													G|||	749	0.149561	0.0613	0.2147	5008	,	,		17898	0.0714		0.2237	False		,,,				2504	0.227				p.Y309Y	Melanoma(184;580 2064 5329 24177 35303)	Atlas-SNP	.											.	PHKG1	38	.	0			c.C927T						PASS	.	G		349,4057	179.7+/-208.2	18,313,1872	32.0	32.0	32.0		831	1.6	0.6	7	dbSNP_120	32	1923,6677	330.6+/-319.3	207,1509,2584	no	coding-synonymous	PHKG1	NM_006213.3		225,1822,4456	AA,AG,GG		22.3605,7.921,17.4689		277/388	56149410	2272,10734	2203	4300	6503	SO:0001819	synonymous_variant	5260	exon10			CGCTGTGTAGCGG	X80590	CCDS5525.1, CCDS59057.1	7p11.2	2009-07-10			ENSG00000164776	ENSG00000164776	2.7.11.19		8930	protein-coding gene	gene with protein product		172470		PHKG		8530014	Standard	NM_001258459		Approved		uc011kdb.2	Q16816	OTTHUMG00000023869	ENST00000297373.2:c.831C>T	7.37:g.56149410G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_001258459	B7Z1D0|F5H2S1|Q75LP5	Silent	SNP	ENST00000297373.2	37	CCDS5525.1																																																																																			G|0.840;A|0.160	0.160	strong		0.597	PHKG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251587.1	NM_006213	
LAMTOR5	10542	hgsc.bcm.edu	37	1	110950439	110950439	+	5'Flank	SNP	C	C	T	rs6674775	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:110950439C>T	ENST00000602318.1	-	0	0				LAMTOR5-AS1_ENST00000609512.1_RNA|LAMTOR5_ENST00000602858.1_5'Flank|LAMTOR5-AS1_ENST00000457535.1_RNA|LAMTOR5_ENST00000483260.1_5'Flank|LAMTOR5-AS1_ENST00000608067.1_RNA|LAMTOR5-AS1_ENST00000608499.1_RNA|LAMTOR5-AS1_ENST00000608253.1_RNA|LAMTOR5-AS1_ENST00000598454.1_RNA|LAMTOR5-AS1_ENST00000608602.1_RNA|LAMTOR5-AS1_ENST00000609709.1_RNA|LAMTOR5-AS1_ENST00000610148.1_RNA|LAMTOR5-AS1_ENST00000590826.1_RNA|LAMTOR5-AS1_ENST00000590413.1_RNA|LAMTOR5-AS1_ENST00000609244.1_RNA|LAMTOR5-AS1_ENST00000608486.1_RNA|LAMTOR5_ENST00000474861.2_5'Flank|LAMTOR5-AS1_ENST00000587691.1_RNA|LAMTOR5_ENST00000256644.4_Missense_Mutation_p.S17N			O43504	LTOR5_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5						cellular response to amino acid stimulus (GO:0071230)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)|protein localization to lysosome (GO:0061462)|regulation of cell size (GO:0008361)|response to virus (GO:0009615)|viral genome replication (GO:0019079)	cytosol (GO:0005829)|lysosome (GO:0005764)|Ragulator complex (GO:0071986)											CTGACGAAGGCTTGGGCTCCC	0.617													C|||	1820	0.363419	0.3056	0.379	5008	,	,		17756	0.2758		0.4453	False		,,,				2504	0.4366				p.S17N		Atlas-SNP	.											HBXIP,colon,carcinoma,0,1	.	.	1	0			c.G50A						PASS	.	C	ASN/SER	1534,2872	478.3+/-358.2	255,1024,924	43.0	39.0	41.0		50	-5.0	0.0	1	dbSNP_116	41	4245,4355	566.6+/-388.7	1020,2205,1075	yes	missense	HBXIP	NM_006402.2	46	1275,3229,1999	TT,TC,CC		49.3605,34.8162,44.4333	benign	17/174	110950439	5779,7227	2203	4300	6503	SO:0001631	upstream_gene_variant	10542	exon1			CGAAGGCTTGGGC	AF029890	CCDS824.1	1p12	2012-09-24	2012-09-24	2012-09-24	ENSG00000134248	ENSG00000134248			17955	protein-coding gene	gene with protein product	"""HBx-interacting protein"", ""hepatitis B virus x-interacting protein (9.6kD)"""	608521	"""hepatitis B virus x interacting protein"""	HBXIP		9499022, 22980980	Standard	NM_006402		Approved	XIP, MGC71071	uc001dzr.3	O43504	OTTHUMG00000011568		1.37:g.110950439C>T	Exception_encountered	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	165	162	0.981818	NM_006402	Q6IBD8	Missense_Mutation	SNP	ENST00000602318.1	37		813	0.37225274725274726	173	0.3516260162601626	146	0.40331491712707185	141	0.2465034965034965	353	0.4656992084432718	C	14.27	2.485686	0.44147	0.348162	0.493605	ENSG00000134248	ENST00000256644	.	.	.	2.48	-4.97	0.03029	.	.	.	.	.	T	0.05547	0.0146	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.27839	-1.0062	3	.	.	.	.	1.9189	0.03303	0.1984:0.2224:0.4274:0.1518	rs6674775;rs17627162;rs59054161;rs6674775	.	.	.	N	17	.	.	S	-	2	0	HBXIP	110751962	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.666000	0.05280	-1.854000	0.01163	0.563000	0.77884	AGC	C|0.604;T|0.396	0.396	strong		0.617	LAMTOR5-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467909.1	NM_006402	
VARS2	57176	hgsc.bcm.edu	37	6	30882803	30882803	+	Missense_Mutation	SNP	G	G	A	rs6926723	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30882803G>A	ENST00000321897.5	+	1	822	c.190G>A	c.(190-192)Ggg>Agg	p.G64R	VARS2_ENST00000416670.2_Missense_Mutation_p.G64R|VARS2_ENST00000542001.1_Intron|VARS2_ENST00000541562.1_Missense_Mutation_p.G94R			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	64			G -> R (in dbSNP:rs6926723).		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TGAGATAGCAGGGGAGAGCAA	0.582													G|||	325	0.0648962	0.121	0.0706	5008	,	,		18510	0.0476		0.0358	False		,,,				2504	0.0327				p.G94R		Atlas-SNP	.											.	VARS2	60	.	0			c.G280A						PASS	.	G	,ARG/GLY,ARG/GLY	354,2668		26,302,1183	48.0	58.0	54.0		,280,190	-2.0	0.0	6	dbSNP_116	54	191,5227		8,175,2526	yes	intron,missense,missense	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,125,125	34,477,3709	AA,AG,GG		3.5253,11.7141,6.4573	,benign,benign	,94/1094,64/1064	30882803	545,7895	1511	2709	4220	SO:0001583	missense	57176	exon2			ATAGCAGGGGAGA	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.190G>A	6.37:g.30882803G>A	ENSP00000316092:p.Gly64Arg	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	168	0.07692307692307693	74	0.15040650406504066	35	0.09668508287292818	33	0.057692307692307696	26	0.03430079155672823	G	7.191	0.591455	0.13812	0.117141	0.035253	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000428017;ENST00000413959;ENST00000541562;ENST00000421263	T;T;T;T;T	0.29917	3.59;3.59;1.58;3.59;1.55	4.81	-1.96	0.07525	.	1.526390	0.04112	N	0.314859	T	0.07728	0.0194	L	0.42245	1.32	0.58432	P	5.999999999950489E-6	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.002	T	0.23226	-1.0194	9	0.21540	T	0.41	0.0062	3.5092	0.07701	0.1939:0.4908:0.2028:0.1124	rs6926723;rs52832661;rs6926723	64;94;64	B7ZL25;F5GXJ0;Q5ST30	.;.;SYVM_HUMAN	R	64;64;64;64;94;64	ENSP00000316092:G64R;ENSP00000394802:G64R;ENSP00000403749:G64R;ENSP00000441000:G94R;ENSP00000416390:G64R	ENSP00000316092:G64R	G	+	1	0	VARS2	30990782	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.610000	0.05629	-0.170000	0.10816	-0.781000	0.03364	GGG	G|0.931;A|0.069	0.069	strong		0.582	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
OR7A5	26659	hgsc.bcm.edu	37	19	14938421	14938421	+	Silent	SNP	C	C	G	rs62122652	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14938421C>G	ENST00000322301.3	-	2	720	c.633G>C	c.(631-633)ctG>ctC	p.L211L	OR7A5_ENST00000594432.1_Silent_p.L211L|OR7A5_ENST00000601611.1_Intron			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	211					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						GGATCCCAGTCAGGGGACCTC	0.433													.|||	183	0.0365415	0.0015	0.0231	5008	,	,		21784	0.0337		0.0378	False		,,,				2504	0.0951				p.L211L		Atlas-SNP	.											.	OR7A5	43	.	0			c.G633C						PASS	.	C		59,4347	56.2+/-92.4	0,59,2144	61.0	59.0	60.0		633	-6.3	0.0	19	dbSNP_129	60	501,8099	141.6+/-197.9	21,459,3820	no	coding-synonymous	OR7A5	NM_017506.1		21,518,5964	GG,GC,CC		5.8256,1.3391,4.3057		211/320	14938421	560,12446	2203	4300	6503	SO:0001819	synonymous_variant	26659	exon1			CCCAGTCAGGGGA	X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"""GPCR / Class A : Olfactory receptors"""	8368	protein-coding gene	gene with protein product			"""olfactory receptor, family 7, subfamily A, member 5 pseudogene"""				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.633G>C	19.37:g.14938421C>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	50	0.617284	NM_017506	B2R682|Q6IFP1|Q96R96	Silent	SNP	ENST00000322301.3	37	CCDS12318.1																																																																																			C|0.965;G|0.035	0.035	strong		0.433	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506	
LPAR2	9170	hgsc.bcm.edu	37	19	19737686	19737686	+	Silent	SNP	C	C	T	rs33982830	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19737686C>T	ENST00000542587.1	-	5	1310	c.408G>A	c.(406-408)gtG>gtA	p.V136V	LPAR2_ENST00000407877.3_Silent_p.V136V|LPAR2_ENST00000589311.1_5'Flank|LPAR2_ENST00000586703.1_Silent_p.V136V			Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	136					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of Rho protein signal transduction (GO:0035025)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	10						TGTGCAGCTGCACGGCCATCA	0.706													C|||	868	0.173323	0.0204	0.1758	5008	,	,		14572	0.3323		0.2475	False		,,,				2504	0.138				p.V136V		Atlas-SNP	.											LPAR2,NS,carcinoma,0,1	LPAR2	28	1	0			c.G408A						scavenged	.	C		239,4127		12,215,1956	15.0	13.0	14.0		408	0.7	1.0	19	dbSNP_126	14	2066,6496		231,1604,2446	no	coding-synonymous	LPAR2	NM_004720.5		243,1819,4402	TT,TC,CC		24.1299,5.4741,17.8295		136/352	19737686	2305,10623	2183	4281	6464	SO:0001819	synonymous_variant	9170	exon2			CAGCTGCACGGCC	AF011466	CCDS12407.1	19p12	2012-08-08	2008-04-11	2008-04-11		ENSG00000064547		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	3168	protein-coding gene	gene with protein product		605110	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 4"""	EDG4		9525886, 9804623	Standard	NM_004720		Approved	EDG-4, LPA2	uc002nnb.4	Q9HBW0		ENST00000542587.1:c.408G>A	19.37:g.19737686C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_004720	O00543|O43431	Silent	SNP	ENST00000542587.1	37	CCDS12407.1																																																																																			C|0.828;T|0.172	0.172	strong		0.706	LPAR2-003	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460544.1	NM_004720	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735848	55735848	+	Missense_Mutation	SNP	A	A	G	rs75026138	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55735848A>G	ENST00000312345.2	-	1	142	c.92T>C	c.(91-93)aTg>aCg	p.M31T		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					GCCATTGCACATCAGGATCAT	0.328													A|||	192	0.0383387	0.0129	0.0389	5008	,	,		16339	0.001		0.0944	False		,,,				2504	0.0532				p.M31T		Atlas-SNP	.											.	OR10AG1	100	.	0			c.T92C						PASS	.	A	THR/MET	107,4285		3,101,2092	43.0	50.0	48.0		92	5.3	0.0	11	dbSNP_131	48	678,7900		32,614,3643	yes	missense	OR10AG1	NM_001005491.1	81	35,715,5735	GG,GA,AA		7.9039,2.4362,6.0524	benign	31/302	55735848	785,12185	2196	4289	6485	SO:0001583	missense	282770	exon1			TTGCACATCAGGA	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.92T>C	11.37:g.55735848A>G	ENSP00000311477:p.Met31Thr	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	147	44	0.29932	NM_001005491	B2RNH4|Q6IEU3	Missense_Mutation	SNP	ENST00000312345.2	37	CCDS31514.1	82	0.037545787545787544	4	0.008130081300813009	10	0.027624309392265192	0	0.0	68	0.08970976253298153	A	2.146	-0.395688	0.04899	0.024362	0.079039	ENSG00000174970	ENST00000312345	T	0.00457	7.29	5.27	5.27	0.74061	.	0.922760	0.09098	N	0.848931	T	0.00012	0.0000	N	0.13327	0.33	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.52593	-0.8555	10	0.48119	T	0.1	.	9.5052	0.39042	0.8222:0.1778:0.0:0.0	.	31	Q8NH19	O10AG_HUMAN	T	31	ENSP00000311477:M31T	ENSP00000311477:M31T	M	-	2	0	OR10AG1	55492424	0.003000	0.15002	0.003000	0.11579	0.489000	0.33432	2.073000	0.41519	2.026000	0.59711	0.325000	0.21440	ATG	A|0.950;G|0.050	0.050	strong		0.328	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
ZSCAN5A	79149	hgsc.bcm.edu	37	19	56733425	56733425	+	Missense_Mutation	SNP	C	C	A	rs34187696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56733425C>A	ENST00000587340.1	-	7	1705	c.1010G>T	c.(1009-1011)gGc>gTc	p.G337V	ZSCAN5A_ENST00000592355.1_Missense_Mutation_p.G336V|ZSCAN5A_ENST00000254165.3_Missense_Mutation_p.G220V|ZSCAN5A_ENST00000587492.1_Missense_Mutation_p.G191V|ZSCAN5A_ENST00000391713.1_Missense_Mutation_p.G337V			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	337			G -> V (in dbSNP:rs34187696). {ECO:0000269|PubMed:15489334}.		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.G337V(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GCTCGCAGGGCCTGGGGAATG	0.562													C|||	802	0.160144	0.0454	0.1542	5008	,	,		17258	0.1806		0.2813	False		,,,				2504	0.1738				p.G337V		Atlas-SNP	.											ZSCAN5A,NS,carcinoma,0,1	ZSCAN5A	118	1	1	Substitution - Missense(1)	stomach(1)	c.G1010T						PASS	.	C	VAL/GLY	356,4050	182.2+/-210.1	16,324,1863	73.0	74.0	73.0		1010	0.6	0.0	19	dbSNP_126	73	2492,6108	408.5+/-349.5	363,1766,2171	yes	missense	ZSCAN5A	NM_024303.1	109	379,2090,4034	AA,AC,CC		28.9767,8.0799,21.8976	probably-damaging	337/497	56733425	2848,10158	2203	4300	6503	SO:0001583	missense	79149	exon5			GCAGGGCCTGGGG	AK098700	CCDS12941.1	19q13.43	2013-01-08	2008-06-10	2008-06-10	ENSG00000131848	ENSG00000131848		"""-"", ""Zinc fingers, C2H2-type"""	23710	protein-coding gene	gene with protein product			"""zinc finger protein 495"", ""zinc finger and SCAN domain containing 5"""	ZNF495, ZSCAN5			Standard	NM_024303		Approved	MGC4161	uc002qmq.3	Q9BUG6		ENST00000587340.1:c.1010G>T	19.37:g.56733425C>A	ENSP00000467631:p.Gly337Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	135	58	0.42963	NM_024303	B4DX98|Q49A73|Q53F04|Q8N7B3	Missense_Mutation	SNP	ENST00000587340.1	37	CCDS12941.1	426	0.19505494505494506	32	0.06504065040650407	62	0.1712707182320442	117	0.20454545454545456	215	0.2836411609498681	C	13.15	2.151177	0.38021	0.080799	0.289767	ENSG00000131848	ENST00000391713;ENST00000254165	T;T	0.08193	3.16;3.12	2.05	0.561	0.17285	.	.	.	.	.	T	0.00012	0.0000	M	0.76574	2.34	0.58432	P	1.0000000000287557E-6	D;D	0.63880	0.993;0.993	P;P	0.60949	0.881;0.834	T	0.36138	-0.9760	8	0.26408	T	0.33	.	5.3761	0.16166	0.0:0.7144:0.0:0.2856	rs34187696	220;337	B4DX98;Q9BUG6	.;ZSA5A_HUMAN	V	337;220	ENSP00000375593:G337V;ENSP00000254165:G220V	ENSP00000254165:G220V	G	-	2	0	ZSCAN5A	61425237	0.007000	0.16637	0.000000	0.03702	0.007000	0.05969	-0.082000	0.11304	0.181000	0.19994	0.561000	0.74099	GGC	C|0.792;A|0.208	0.208	strong		0.562	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303	
TNFRSF10D	8793	hgsc.bcm.edu	37	8	23002086	23002086	+	Silent	SNP	G	G	A	rs117862321	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:23002086G>A	ENST00000312584.3	-	7	925	c.831C>T	c.(829-831)aaC>aaT	p.N277N		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	277					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		TCAGGGTCTCGTTGCGGGCAT	0.572													.|||	21	0.00419329	0.0015	0.0014	5008	,	,		21181	0.0		0.0119	False		,,,				2504	0.0061				p.N277N		Atlas-SNP	.											.	TNFRSF10D	21	.	0			c.C831T						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	92.0	87.0	89.0		831	-0.3	0.0	8	dbSNP_132	89	63,8537	38.3+/-94.2	0,63,4237	no	coding-synonymous	TNFRSF10D	NM_003840.3		0,75,6428	AA,AG,GG		0.7326,0.2724,0.5767		277/387	23002086	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	8793	exon7			GGTCTCGTTGCGG	AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.831C>T	8.37:g.23002086G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	174	83	0.477012	NM_003840	B2R8W0|Q9Y6Q4	Silent	SNP	ENST00000312584.3	37	CCDS6038.1																																																																																			G|0.995;A|0.005	0.005	strong		0.572	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1		
VWA5B2	90113	hgsc.bcm.edu	37	3	183951431	183951431	+	Missense_Mutation	SNP	C	C	T	rs902417	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:183951431C>T	ENST00000426955.2	+	4	698	c.598C>T	c.(598-600)Cct>Tct	p.P200S	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_5'UTR	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	211								p.P200S(1)		breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						GCTGGCTGCCCCTCGGGACGT	0.662													C|||	1088	0.217252	0.177	0.2075	5008	,	,		16546	0.2351		0.2485	False		,,,				2504	0.228				p.P200S		Atlas-SNP	.											VWA5B2,NS,carcinoma,0,1	VWA5B2	47	1	1	Substitution - Missense(1)	kidney(1)	c.C598T						PASS	.	C	SER/PRO	241,1143		25,191,476	30.0	37.0	35.0		598	2.0	1.0	3	dbSNP_92	35	724,2458		83,558,950	yes	missense	VWA5B2	NM_138345.1	74	108,749,1426	TT,TC,CC		22.753,17.4133,21.1345	benign	200/1243	183951431	965,3601	692	1591	2283	SO:0001583	missense	90113	exon4			GCTGCCCCTCGGG		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.598C>T	3.37:g.183951431C>T	ENSP00000398688:p.Pro200Ser	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	144	140	0.972222	NM_138345	B9EGN7	Missense_Mutation	SNP	ENST00000426955.2	37	CCDS54686.1	444	0.2032967032967033	88	0.17886178861788618	74	0.20441988950276244	94	0.16433566433566432	188	0.24802110817941952	C	1.623	-0.521080	0.04171	0.174133	0.22753	ENSG00000145198	ENST00000426955	T	0.60424	0.19	3.84	1.99	0.26369	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999633179	B;B	0.27823	0.19;0.004	B;B	0.29267	0.1;0.006	T	0.19160	-1.0314	8	0.33141	T	0.24	-0.1148	4.7979	0.13281	0.2103:0.6742:0.0:0.1154	rs902417;rs1687244;rs3882317;rs59041042;rs902417	200;211	B9EGN7;C9JW99	.;.	S	200	ENSP00000398688:P200S	ENSP00000398688:P200S	P	+	1	0	VWA5B2	185434125	0.999000	0.42202	0.982000	0.44146	0.641000	0.38312	1.678000	0.37586	0.384000	0.24942	0.462000	0.41574	CCT	C|0.788;T|0.212	0.212	strong		0.662	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
IQCG	84223	hgsc.bcm.edu	37	3	197659160	197659160	+	Missense_Mutation	SNP	C	C	G	rs67877771	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:197659160C>G	ENST00000265239.6	-	6	953	c.529G>C	c.(529-531)Gat>Cat	p.D177H	IQCG_ENST00000455191.1_Missense_Mutation_p.D177H|IQCG_ENST00000453254.1_Missense_Mutation_p.D177H	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	177				D -> H (in Ref. 4; AAH04816). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		GCAATCACATCGCTGAAAAAC	0.428													C|||	1411	0.281749	0.5227	0.1715	5008	,	,		16755	0.2262		0.166	False		,,,				2504	0.2106				p.D177H		Atlas-SNP	.											IQCG,rectum,carcinoma,0,1	IQCG	44	1	0			c.G529C						PASS	.	C	HIS/ASP,HIS/ASP	1970,2436	556.1+/-379.4	417,1136,650	107.0	101.0	103.0		529,529	2.9	1.0	3	dbSNP_130	103	1429,7171	275.3+/-291.7	117,1195,2988	yes	missense,missense	IQCG	NM_001134435.1,NM_032263.3	81,81	534,2331,3638	GG,GC,CC		16.6163,44.7118,26.1341	probably-damaging,probably-damaging	177/444,177/444	197659160	3399,9607	2203	4300	6503	SO:0001583	missense	84223	exon6			TCACATCGCTGAA	AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 9"""	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.529G>C	3.37:g.197659160C>G	ENSP00000265239:p.Asp177His	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_032263	Q9BST2|Q9HAG8	Missense_Mutation	SNP	ENST00000265239.6	37	CCDS3331.1	554	0.25366300366300365	256	0.5203252032520326	51	0.1408839779005525	120	0.2097902097902098	127	0.16754617414248021	C	12.96	2.093755	0.36952	0.447118	0.166163	ENSG00000114473	ENST00000265239;ENST00000455191;ENST00000453254;ENST00000416896	T;T;T;T	0.55930	0.74;0.74;0.77;0.49	4.81	2.88	0.33553	.	0.205977	0.38837	N	0.001547	T	0.00012	0.0000	M	0.75264	2.295	0.27204	P	0.9600887	D;D	0.89917	1.0;0.999	D;D	0.70935	0.971;0.948	T	0.47381	-0.9122	9	0.59425	D	0.04	-14.1493	7.1513	0.25612	0.0:0.7581:0.0:0.2419	.	177;177	C9JKX8;Q9H095	.;IQCG_HUMAN	H	177;177;177;158	ENSP00000265239:D177H;ENSP00000407736:D177H;ENSP00000389897:D177H;ENSP00000406411:D158H	ENSP00000265239:D177H	D	-	1	0	IQCG	199143557	0.961000	0.32948	0.987000	0.45799	0.493000	0.33554	1.099000	0.31013	1.073000	0.40885	0.460000	0.39030	GAT	C|0.746;G|0.254	0.254	strong		0.428	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263	
SLC28A1	9154	hgsc.bcm.edu	37	15	85447431	85447431	+	Missense_Mutation	SNP	G	G	A	rs2290272	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:85447431G>A	ENST00000286749.3	+	6	655	c.565G>A	c.(565-567)Gtc>Atc	p.V189I	SLC28A1_ENST00000394573.1_Missense_Mutation_p.V189I|SLC28A1_ENST00000537703.1_Missense_Mutation_p.V111I|SLC28A1_ENST00000538177.1_Missense_Mutation_p.V189I|SLC28A1_ENST00000537216.1_Missense_Mutation_p.V189I|SLC28A1_ENST00000537624.1_Missense_Mutation_p.V189I			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	189			V -> I (in A; dbSNP:rs2290272). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.V189I(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	CTGCGTGTTCGTCGCTCTCCT	0.587													A|||	1919	0.383187	0.1914	0.5058	5008	,	,		20264	0.375		0.3638	False		,,,				2504	0.5838				p.V189I		Atlas-SNP	.											SLC28A1,NS,carcinoma,0,1	SLC28A1	118	1	1	Substitution - Missense(1)	stomach(1)	c.G565A	GRCh37	CM045806	SLC28A1	M	rs2290272	PASS	.	A	ILE/VAL	962,3444	734.2+/-410.6	104,754,1345	171.0	146.0	155.0		565	-5.9	0.0	15	dbSNP_100	155	3013,5585	663.4+/-402.1	524,1965,1810	yes	missense	SLC28A1	NM_004213.3	29	628,2719,3155	AA,AG,GG		35.043,21.8339,30.5675	benign	189/650	85447431	3975,9029	2203	4299	6502	SO:0001583	missense	9154	exon7			GTGTTCGTCGCTC	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.565G>A	15.37:g.85447431G>A	ENSP00000286749:p.Val189Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	762	0.3489010989010989	93	0.18902439024390244	175	0.48342541436464087	208	0.36363636363636365	286	0.37730870712401055	A	0.006	-2.043950	0.00398	0.218339	0.35043	ENSG00000156222	ENST00000537216;ENST00000538177;ENST00000537624;ENST00000286749;ENST00000394573;ENST00000537703	T;T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7;2.7	4.38	-5.87	0.02297	Na dependent nucleoside transporter (1);	0.579854	0.17850	N	0.159890	T	0.00012	0.0000	N	0.02357	-0.585	0.80722	P	0.0	B;B;B;B;B	0.19331	0.005;0.001;0.035;0.001;0.002	B;B;B;B;B	0.19148	0.006;0.003;0.024;0.004;0.006	T	0.16808	-1.0390	9	0.02654	T	1	3.2539	9.4688	0.38829	0.2123:0.2511:0.5366:0.0	rs2290272;rs17222253;rs17536477;rs52799974;rs58773874;rs2290272	189;189;189;111;189	B7Z533;F5H560;B7Z3L6;B7Z3M4;O00337	.;.;.;.;S28A1_HUMAN	I	189;189;189;189;189;111	ENSP00000440546:V189I;ENSP00000443752:V189I;ENSP00000444700:V189I;ENSP00000286749:V189I;ENSP00000378074:V189I;ENSP00000443764:V111I	ENSP00000286749:V189I	V	+	1	0	SLC28A1	83248435	0.142000	0.22610	0.003000	0.11579	0.001000	0.01503	-0.604000	0.05667	-1.600000	0.01603	-1.157000	0.01802	GTC	G|0.674;A|0.326	0.326	strong		0.587	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
CEP192	55125	hgsc.bcm.edu	37	18	13015389	13015389	+	5'UTR	SNP	C	C	G	rs117292623	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:13015389C>G	ENST00000325971.8	+	0	662				CEP192_ENST00000506447.1_Missense_Mutation_p.H194Q			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa						centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ACCTAAGCCACACTAGCTTAT	0.398													C|||	12	0.00239617	0.0008	0.0	5008	,	,		21062	0.0		0.006	False		,,,				2504	0.0051				p.H194Q		Atlas-SNP	.											CEP192_ENST00000506447,colon,carcinoma,+2,1	CEP192	340	1	0			c.C582G						PASS	.	C	GLN/HIS	1,1383		0,1,691	179.0	134.0	147.0		582	0.2	0.2	18	dbSNP_132	147	28,3154		0,28,1563	yes	missense	CEP192	NM_032142.3	24	0,29,2254	GG,GC,CC		0.8799,0.0723,0.6351	possibly-damaging	194/2538	13015389	29,4537	692	1591	2283	SO:0001623	5_prime_UTR_variant	55125	exon6			AAGCCACACTAGC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.-932C>G	18.37:g.13015389C>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	110	59	0.536364	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	9.667	1.145783	0.21288	7.23E-4	0.008799	ENSG00000101639	ENST00000506447	T	0.05855	3.38	4.04	0.238	0.15480	.	.	.	.	.	T	0.02649	0.0080	N	0.24115	0.695	0.21878	N	0.999499	B	0.17268	0.021	B	0.18561	0.022	T	0.43065	-0.9414	9	0.40728	T	0.16	.	3.0221	0.06079	0.0:0.313:0.2373:0.4497	.	194	E9PF99	.	Q	194	ENSP00000427550:H194Q	ENSP00000427550:H194Q	H	+	3	2	CEP192	13005389	0.000000	0.05858	0.151000	0.22473	0.948000	0.59901	0.222000	0.17699	0.037000	0.15575	0.563000	0.77884	CAC	C|0.997;G|0.003	0.003	strong		0.398	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
HLA-B	3106	hgsc.bcm.edu	37	6	31323143	31323143	+	Silent	SNP	T	T	C	rs41546016		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323143T>C	ENST00000412585.2	-	4	874	c.846A>G	c.(844-846)acA>acG	p.T282T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	282	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GTACATGGCATGTGTATCTCT	0.572									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.T282T		Atlas-SNP	.											.	HLA-B	54	.	0			c.A846G						PASS	.						80.0	69.0	73.0					6																	31323143		2203	4300	6503	SO:0001819	synonymous_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	ATGGCATGTGTAT	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.846A>G	6.37:g.31323143T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	178	43	0.241573	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	weak		0.572	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
PAPL	390928	hgsc.bcm.edu	37	19	39590955	39590955	+	Silent	SNP	G	G	A	rs8110736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:39590955G>A	ENST00000331256.5	+	5	868	c.594G>A	c.(592-594)ccG>ccA	p.P198P	PAPL_ENST00000594229.1_Intron	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		198						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										CCAGCCTGCCGTACATGACAT	0.577													g|||	3161	0.63119	0.6914	0.5605	5008	,	,		18009	0.6518		0.6113	False		,,,				2504	0.5992				p.P198P		Atlas-SNP	.											.	.	.	.	0			c.G594A						PASS	.	G		3046,1360	692.4+/-405.5	1053,940,210	123.0	111.0	115.0		594	-9.5	0.6	19	dbSNP_116	115	5315,3285	648.8+/-400.5	1652,2011,637	no	coding-synonymous	PAPL	NM_001004318.2		2705,2951,847	AA,AG,GG		38.1977,30.867,35.7143		198/439	39590955	8361,4645	2203	4300	6503	SO:0001819	synonymous_variant	0	exon5			CCTGCCGTACATG																												ENST00000331256.5:c.594G>A	19.37:g.39590955G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_001004318	B2RN68	Silent	SNP	ENST00000331256.5	37	CCDS33018.1																																																																																			G|0.352;A|0.648	0.648	strong		0.577	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		
SCML4	256380	hgsc.bcm.edu	37	6	108029109	108029109	+	Silent	SNP	T	T	C	rs3734754	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:108029109T>C	ENST00000369020.3	-	7	1325	c.1080A>G	c.(1078-1080)ccA>ccG	p.P360P	SCML4_ENST00000369025.2_Silent_p.P118P|SCML4_ENST00000369022.2_Silent_p.P302P	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	360					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		CCAGAGCCTGTGGGTCGGCGT	0.632													C|||	1125	0.224641	0.1778	0.1354	5008	,	,		18716	0.369		0.1978	False		,,,				2504	0.2301				p.P360P		Atlas-SNP	.											SCML4_ENST00000369020,colon,carcinoma,0,1	SCML4	65	1	0			c.A1080G						PASS	.	C		272,1112		23,226,443	48.0	57.0	54.0		1080	-8.3	0.3	6	dbSNP_107	54	573,2609		54,465,1072	no	coding-synonymous	SCML4	NM_198081.3		77,691,1515	CC,CT,TT		18.0075,19.6532,18.5064		360/415	108029109	845,3721	692	1591	2283	SO:0001819	synonymous_variant	256380	exon7			AGCCTGTGGGTCG		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.1080A>G	6.37:g.108029109T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	121	50	0.413223	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Silent	SNP	ENST00000369020.3	37	CCDS5060.2																																																																																			T|0.784;C|0.216	0.216	strong		0.632	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
WDR11	55717	hgsc.bcm.edu	37	10	122610983	122610983	+	Silent	SNP	G	G	T	rs35692153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122610983G>T	ENST00000263461.6	+	1	297	c.51G>T	c.(49-51)ggG>ggT	p.G17G	WDR11-AS1_ENST00000598981.1_RNA	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					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						CCCTCACGGGGGCCCTCAACG	0.682													G|||	290	0.0579073	0.208	0.0202	5008	,	,		14726	0.0		0.001	False		,,,				2504	0.0				p.G17G		Atlas-SNP	.											.	WDR11	95	.	0			c.G51T						PASS	.	G		707,3685		54,599,1543	18.0	20.0	19.0		51	0.9	1.0	10	dbSNP_126	19	4,8590		0,4,4293	no	coding-synonymous	WDR11	NM_018117.11		54,603,5836	TT,TG,GG		0.0465,16.0974,5.4751		17/1225	122610983	711,12275	2196	4297	6493	SO:0001819	synonymous_variant	55717	exon1			CACGGGGGCCCTC	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.51G>T	10.37:g.122610983G>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	114	44	0.385965	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			G|0.952;T|0.048	0.048	strong		0.682	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
OPRD1	4985	hgsc.bcm.edu	37	1	29189597	29189597	+	Silent	SNP	C	C	T	rs2234918	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:29189597C>T	ENST00000234961.2	+	3	1163	c.921C>T	c.(919-921)ggC>ggT	p.G307G		NM_000911.3	NP_000902.3	P41143	OPRD_HUMAN	opioid receptor, delta 1	307					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adult locomotory behavior (GO:0008344)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|negative regulation of gene expression (GO:0010629)|negative regulation of protein oligomerization (GO:0032460)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein import into nucleus, translocation (GO:0000060)|regulation of calcium ion transport (GO:0051924)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of sensory perception of pain (GO:0051930)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	enkephalin receptor activity (GO:0038046)|opioid receptor activity (GO:0004985)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	TCGCGCTGGGCTACGCCAATA	0.667													C|||	2911	0.58127	0.3056	0.7032	5008	,	,		15581	0.754		0.5726	False		,,,				2504	0.6984				p.G307G		Atlas-SNP	.											OPRD1,rectum,carcinoma,0,1	OPRD1	36	1	0			c.C921T						PASS	.	C		1507,2897		274,959,969	29.0	26.0	27.0	http://www.ncbi.nlm.nih.gov/omim/103780,165195|http://omim.org/entry/165195|http://omim.org/entry/103780	921	3.2	1.0	1	dbSNP_98	27	4618,3982		1248,2122,930	no	coding-synonymous	OPRD1	NM_000911.3		1522,3081,1899	TT,TC,CC		46.3023,34.2189,47.1009		307/373	29189597	6125,6879	2202	4300	6502	SO:0001819	synonymous_variant	4985	exon3			GCTGGGCTACGCC	U10504	CCDS329.1	1p36.1-p34.3	2012-08-08			ENSG00000116329	ENSG00000116329		"""GPCR / Class A : Opioid receptors"""	8153	protein-coding gene	gene with protein product		165195				8415697	Standard	NM_000911		Approved		uc001brf.1	P41143	OTTHUMG00000003646	ENST00000234961.2:c.921C>T	1.37:g.29189597C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	70	67	0.957143	NM_000911	B5B0B8	Silent	SNP	ENST00000234961.2	37	CCDS329.1																																																																																			C|0.504;T|0.496	0.496	strong		0.667	OPRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010330.1	NM_000911	
HYOU1	10525	hgsc.bcm.edu	37	11	118922200	118922200	+	Silent	SNP	G	G	A	rs1804690	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:118922200G>A	ENST00000404233.3	-	13	1600	c.1476C>T	c.(1474-1476)aaC>aaT	p.N492N	HYOU1_ENST00000543287.1_Silent_p.N405N|HYOU1_ENST00000525859.1_Silent_p.N492N|HYOU1_ENST00000529972.1_Silent_p.N492N	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	492					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		TGATGTGGAAGTTGAAATCAT	0.572													G|||	810	0.161741	0.0787	0.0562	5008	,	,		17596	0.2986		0.1133	False		,,,				2504	0.2577				p.N492N		Atlas-SNP	.											.	HYOU1	88	.	0			c.C1476T						PASS	.	G	,	270,4130	152.2+/-185.9	8,254,1938	177.0	160.0	166.0		1476,1476	2.2	1.0	11	dbSNP_89	166	849,7741	193.5+/-239.2	47,755,3493	no	coding-synonymous,coding-synonymous	HYOU1	NM_001130991.1,NM_006389.3	,	55,1009,5431	AA,AG,GG		9.8836,6.1364,8.6143	,	492/1000,492/1000	118922200	1119,11871	2200	4295	6495	SO:0001819	synonymous_variant	10525	exon13			GTGGAAGTTGAAA	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.1476C>T	11.37:g.118922200G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	163	85	0.521472	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Silent	SNP	ENST00000404233.3	37	CCDS8408.1																																																																																			G|0.870;A|0.130	0.130	strong		0.572	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	
TMEM63C	57156	hgsc.bcm.edu	37	14	77703057	77703057	+	Silent	SNP	A	A	G	rs403291	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77703057A>G	ENST00000298351.4	+	9	777	c.633A>G	c.(631-633)gcA>gcG	p.A211A		NM_020431.2	NP_065164.2	Q9P1W3	CSC1_HUMAN	transmembrane protein 63C	211					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)	integral component of membrane (GO:0016021)	calcium activated cation channel activity (GO:0005227)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(1)	23			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		TGGGGTTTGCACCCAGGAATA	0.552													g|||	4019	0.802516	0.8782	0.683	5008	,	,		13712	0.9256		0.7048	False		,,,				2504	0.7587				p.A211A		Atlas-SNP	.											.	TMEM63C	77	.	0			c.A633G						PASS	.			3539,531		1529,481,25	99.0	103.0	102.0		633	1.0	0.8	14	dbSNP_80	102	6025,2335		2174,1677,329	no	coding-synonymous	TMEM63C	NM_020431.2		3703,2158,354	GG,GA,AA		27.9306,13.0467,23.0571		211/807	77703057	9564,2866	2035	4180	6215	SO:0001819	synonymous_variant	57156	exon9			GTTTGCACCCAGG		CCDS45141.1	14q24.3	2014-05-30	2005-07-25	2005-07-25	ENSG00000165548	ENSG00000165548			23787	protein-coding gene	gene with protein product	"""calcium permeable stress-gated cation channel 1 homolog (Arabidopsis)"""		"""chromosome 14 open reading frame 171"""	C14orf171		24503647	Standard	NM_020431		Approved	DKFZp434P0111, CSC1, hsCSC1	uc001xtf.2	Q9P1W3	OTTHUMG00000171557	ENST00000298351.4:c.633A>G	14.37:g.77703057A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_020431	B2RN22|B3KWJ5|Q86TS3|Q86TS4|Q9NSQ4|Q9P1W1	Silent	SNP	ENST00000298351.4	37	CCDS45141.1																																																																																			A|0.231;G|0.769	0.769	strong		0.552	TMEM63C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414193.1		
PZP	5858	hgsc.bcm.edu	37	12	9317885	9317885	+	Silent	SNP	G	G	A	rs2277412	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:9317885G>A	ENST00000261336.2	-	19	2365	c.2337C>T	c.(2335-2337)tcC>tcT	p.S779S	PZP_ENST00000539983.1_5'UTR|PZP_ENST00000381997.2_Silent_p.S648S	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	779					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.S779S(1)|p.S648S(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CAGCATCTTCGGACAGGCAGA	0.567													G|||	1694	0.338259	0.1558	0.3329	5008	,	,		-128	0.4266		0.3956	False		,,,				2504	0.4387				p.S779S	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											PZP_ENST00000381997,NS,carcinoma,0,2	PZP	422	2	2	Substitution - coding silent(2)	stomach(2)	c.C2337T						PASS	.						96.0	82.0	87.0					12																	9317885		2203	4298	6501	SO:0001819	synonymous_variant	5858	exon19			ATCTTCGGACAGG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2337C>T	12.37:g.9317885G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Silent	SNP	ENST00000261336.2	37	CCDS8600.1																																																																																			G|0.167;A|0.833	0.833	weak		0.567	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
FBN3	84467	hgsc.bcm.edu	37	19	8161450	8161450	+	Missense_Mutation	SNP	C	C	T	rs3829817	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8161450C>T	ENST00000600128.1	-	44	5831	c.5417G>A	c.(5416-5418)cGg>cAg	p.R1806Q	FBN3_ENST00000270509.2_Missense_Mutation_p.R1806Q|FBN3_ENST00000601739.1_Missense_Mutation_p.R1806Q			Q75N90	FBN3_HUMAN	fibrillin 3	1806	EGF-like 28. {ECO:0000255|PROSITE- ProRule:PRU00076}.		R -> Q (in dbSNP:rs3829817). {ECO:0000269|PubMed:11347906}.			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						ACACTCATTCCGTCCTGGGGG	0.562													C|||	920	0.183706	0.1346	0.1988	5008	,	,		19629	0.1687		0.2406	False		,,,				2504	0.1963				p.R1806Q		Atlas-SNP	.											.	FBN3	300	.	0			c.G5417A						PASS	.	C	GLN/ARG	673,3733	284.6+/-277.7	60,553,1590	102.0	77.0	85.0		5417	-1.5	0.3	19	dbSNP_107	85	1952,6648	344.1+/-325.2	228,1496,2576	yes	missense	FBN3	NM_032447.3	43	288,2049,4166	TT,TC,CC		22.6977,15.2746,20.183	benign	1806/2810	8161450	2625,10381	2203	4300	6503	SO:0001583	missense	84467	exon43			TCATTCCGTCCTG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5417G>A	19.37:g.8161450C>T	ENSP00000470498:p.Arg1806Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	410	0.18772893772893773	64	0.13008130081300814	70	0.19337016574585636	92	0.16083916083916083	184	0.24274406332453827	C	9.888	1.203326	0.22121	0.152746	0.226977	ENSG00000142449	ENST00000270509	D	0.87179	-2.22	3.63	-1.51	0.08664	Epidermal growth factor-like, type 3 (1);	0.135938	0.50627	N	0.000110	T	0.00073	0.0002	L	0.45352	1.415	0.21984	P	0.999431471	B	0.16396	0.017	B	0.13407	0.009	T	0.05370	-1.0889	9	0.26408	T	0.33	.	8.5647	0.33531	0.0:0.6604:0.0:0.3396	rs3829817;rs52826609;rs56512420;rs59040820;rs3829817	1806	Q75N90	FBN3_HUMAN	Q	1806	ENSP00000270509:R1806Q	ENSP00000270509:R1806Q	R	-	2	0	FBN3	8067450	0.909000	0.30893	0.265000	0.24526	0.173000	0.22820	1.282000	0.33226	-0.474000	0.06862	-0.140000	0.14226	CGG	C|0.810;T|0.190	0.190	strong		0.562	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
SLCO2A1	6578	hgsc.bcm.edu	37	3	133670073	133670073	+	Silent	SNP	T	T	C	rs6767412	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:133670073T>C	ENST00000310926.4	-	6	1113	c.840A>G	c.(838-840)cgA>cgG	p.R280R	SLCO2A1_ENST00000493729.1_Silent_p.R204R	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	280					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)	p.R280R(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	TGGGCATTGCTCGAGGGAAGA	0.488													T|||	1274	0.254393	0.3215	0.2421	5008	,	,		19409	0.2827		0.1909	False		,,,				2504	0.2086				p.R280R		Atlas-SNP	.											SLCO2A1,NS,carcinoma,0,1	SLCO2A1	72	1	1	Substitution - coding silent(1)	stomach(1)	c.A840G						scavenged	.	T		1395,3011	456.5+/-351.3	220,955,1028	87.0	96.0	93.0		840	1.0	0.0	3	dbSNP_116	93	1627,6973	300.6+/-305.0	154,1319,2827	no	coding-synonymous	SLCO2A1	NM_005630.2		374,2274,3855	CC,CT,TT		18.9186,31.6614,23.2354		280/644	133670073	3022,9984	2203	4300	6503	SO:0001819	synonymous_variant	6578	exon6			CATTGCTCGAGGG		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"""Solute carriers"""	10955	protein-coding gene	gene with protein product		601460	"""solute carrier family 21 (prostaglandin transporter), member 2"", ""matrin F/G 1"""	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.840A>G	3.37:g.133670073T>C		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_005630	Q86V98|Q8IUN2	Silent	SNP	ENST00000310926.4	37	CCDS3084.1																																																																																			T|0.773;C|0.227	0.227	strong		0.488	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630	
NMT1	4836	hgsc.bcm.edu	37	17	43176804	43176804	+	Silent	SNP	C	C	T	rs2239923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43176804C>T	ENST00000592782.1	+	9	1047	c.916C>T	c.(916-918)Ctg>Ttg	p.L306L	NMT1_ENST00000258960.2_Silent_p.L306L			P30419	NMT1_HUMAN	N-myristoyltransferase 1	306					apoptotic process (GO:0006915)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	8		Prostate(33;0.155)				CCCACGGAAGCTGATTGAAGT	0.557											OREG0024470	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1122	0.224042	0.059	0.2017	5008	,	,		19639	0.2748		0.2992	False		,,,				2504	0.3333				p.L306L		Atlas-SNP	.											.	NMT1	31	.	0			c.C916T						PASS	.	C		406,4000	199.8+/-223.2	13,380,1810	130.0	109.0	116.0		916	3.3	1.0	17	dbSNP_98	116	2487,6113	409.7+/-349.9	343,1801,2156	no	coding-synonymous	NMT1	NM_021079.3		356,2181,3966	TT,TC,CC		28.9186,9.2147,22.2436		306/497	43176804	2893,10113	2203	4300	6503	SO:0001819	synonymous_variant	4836	exon8			CGGAAGCTGATTG		CCDS11494.1	17q21.31	2012-10-02			ENSG00000136448	ENSG00000136448			7857	protein-coding gene	gene with protein product	"""alternative, short form NMT-S"", ""myristoyl-CoA:protein N-myristoyltransferase"", ""long form, NMT-L"""	160993				1570339	Standard	NM_021079		Approved	NMT	uc002ihz.3	P30419	OTTHUMG00000180003	ENST00000592782.1:c.916C>T	17.37:g.43176804C>T		Somatic	239	1	0.0041841	914	WXS	Illumina HiSeq	Phase_I	331	143	0.432024	NM_021079	A8K7C1|Q9UE09	Silent	SNP	ENST00000592782.1	37	CCDS11494.1																																																																																			C|0.780;T|0.220	0.220	strong		0.557	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079	
PRRC2C	23215	hgsc.bcm.edu	37	1	171556165	171556165	+	Silent	SNP	G	G	C	rs235501	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:171556165G>C	ENST00000338920.4	+	31	8004	c.7767G>C	c.(7765-7767)tcG>tcC	p.S2589S	PRRC2C_ENST00000426496.2_Silent_p.S2524S|PRRC2C_ENST00000367742.3_Silent_p.S2591S|PRRC2C_ENST00000392078.3_Silent_p.S2591S	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2589	Gln-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TACCAGCATCGCAGCTTTCCT	0.418													C|||	3972	0.793131	0.7088	0.732	5008	,	,		19652	0.8958		0.8151	False		,,,				2504	0.8221				p.S2589S		Atlas-SNP	.											.	.	.	.	0			c.G7767C						PASS	.	C		3278,1128	396.7+/-330.2	1227,824,152	88.0	76.0	80.0		7767	2.1	1.0	1	dbSNP_79	80	6971,1629	295.4+/-302.4	2841,1289,170	no	coding-synonymous	PRRC2C	NM_015172.3		4068,2113,322	CC,CG,GG		18.9419,25.6015,21.1979		2589/2818	171556165	10249,2757	2203	4300	6503	SO:0001819	synonymous_variant	23215	exon31			AGCATCGCAGCTT	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.7767G>C	1.37:g.171556165G>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	225	97	0.431111	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2	1766	0.8086080586080586	352	0.7154471544715447	272	0.7513812154696132	513	0.8968531468531469	629	0.8298153034300791	C	9.306	1.054442	0.19907	0.743985	0.810581	ENSG00000117523	ENST00000495585	.	.	.	5.24	2.14	0.27477	.	.	.	.	.	T	0.13372	0.0324	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.19321	-1.0309	3	.	.	.	.	2.8708	0.05616	0.2406:0.4983:0.098:0.1632	rs235501;rs1621096;rs235501	.	.	.	P	1072	.	.	R	+	2	0	PRRC2C	169822789	0.825000	0.29262	1.000000	0.80357	0.942000	0.58702	-0.135000	0.10420	0.308000	0.22923	-0.365000	0.07479	CGC	G|0.203;C|0.797	0.797	strong		0.418	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
SLC38A8	146167	hgsc.bcm.edu	37	16	84067004	84067004	+	Silent	SNP	C	C	T	rs57576928	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84067004C>T	ENST00000299709.3	-	3	458	c.459G>A	c.(457-459)ctG>ctA	p.L153L		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	153					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						AGAGCAGGGGCAGGGTGAAGC	0.672													c|||	471	0.0940495	0.0106	0.0533	5008	,	,		14438	0.1905		0.0845	False		,,,				2504	0.1462				p.L153L		Atlas-SNP	.											.	SLC38A8	60	.	0			c.G459A						PASS	.	G		97,4303	75.7+/-113.9	2,93,2105	60.0	68.0	65.0		459	1.7	0.8	16	dbSNP_129	65	695,7905	169.9+/-221.1	22,651,3627	no	coding-synonymous	SLC38A8	NM_001080442.1		24,744,5732	TT,TC,CC		8.0814,2.2045,6.0923		153/436	84067004	792,12208	2200	4300	6500	SO:0001819	synonymous_variant	146167	exon3			CAGGGGCAGGGTG		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.459G>A	16.37:g.84067004C>T		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	319	155	0.485893	NM_001080442		Silent	SNP	ENST00000299709.3	37	CCDS32495.1																																																																																			C|0.927;T|0.073	0.073	strong		0.672	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
OR4A5	81318	hgsc.bcm.edu	37	11	51411460	51411460	+	Silent	SNP	G	G	A	rs34285763	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:51411460G>A	ENST00000319760.6	-	1	988	c.936C>T	c.(934-936)tcC>tcT	p.S312S		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				ACATGAGGACGGACACTCCTC	0.373													.|||	466	0.0930511	0.0938	0.0706	5008	,	,		17363	0.0863		0.1262	False		,,,				2504	0.0808				p.S312S		Atlas-SNP	.											OR4A5,NS,carcinoma,-1,1	OR4A5	116	1	0			c.C936T						PASS	.	G		385,3967		15,355,1806	18.0	19.0	18.0		936	-1.4	0.0	11	dbSNP_126	18	1029,7543		54,921,3311	no	coding-synonymous	OR4A5	NM_001005272.3		69,1276,5117	AA,AG,GG		12.0042,8.8465,10.9409		312/316	51411460	1414,11510	2176	4286	6462	SO:0001819	synonymous_variant	81318	exon1			GAGGACGGACACT	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.936C>T	11.37:g.51411460G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	37	CCDS31497.1																																																																																			G|0.897;A|0.103	0.103	strong		0.373	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
IL10RA	3587	hgsc.bcm.edu	37	11	117864062	117864062	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:117864062A>G	ENST00000227752.3	+	4	594	c.474A>G	c.(472-474)gaA>gaG	p.E158E	IL10RA_ENST00000545409.1_Silent_p.E9E|IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000541785.1_Silent_p.E138E	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	158					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		ACACATATGAAAGCATCTTCA	0.542																																					p.E158E		Atlas-SNP	.											.	IL10RA	46	.	0			c.A474G						PASS	.						97.0	86.0	90.0					11																	117864062		2200	4296	6496	SO:0001819	synonymous_variant	3587	exon4			ATATGAAAGCATC	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.474A>G	11.37:g.117864062A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	37	CCDS8388.1																																																																																			.	.	none		0.542	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
DOK7	285489	hgsc.bcm.edu	37	4	3494600	3494600	+	Missense_Mutation	SNP	A	A	G	rs6811423	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:3494600A>G	ENST00000340083.5	+	7	952	c.887A>G	c.(886-888)cAg>cGg	p.Q296R	DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR|DOK7_ENST00000389653.2_Missense_Mutation_p.Q296R	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	296	Ser-rich.		Q -> R (in dbSNP:rs6811423). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:22661499}.		neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		AGCACGTCACAGGAGGGGCCT	0.687													.|||	1092	0.218051	0.0272	0.1398	5008	,	,		13805	0.504		0.2286	False		,,,				2504	0.226				p.Q296R		Atlas-SNP	.											DOK7,NS,carcinoma,0,1	DOK7	44	1	0			c.A887G						scavenged	.	A	,ARG/GLN	244,4150		11,222,1964	22.0	20.0	21.0		,887	1.4	0.5	4	dbSNP_116	21	1775,6813		196,1383,2715	yes	utr-3,missense	DOK7	NM_001164673.1,NM_173660.4	,43	207,1605,4679	GG,GA,AA		20.6684,5.553,15.5523	,benign	,296/505	3494600	2019,10963	2197	4294	6491	SO:0001583	missense	285489	exon7			CGTCACAGGAGGG	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.887A>G	4.37:g.3494600A>G	ENSP00000344432:p.Gln296Arg	Somatic	128	2	0.015625		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_173660	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Missense_Mutation	SNP	ENST00000340083.5	37	CCDS3370.2	559	0.25595238095238093	16	0.032520325203252036	60	0.16574585635359115	308	0.5384615384615384	175	0.23087071240105542	A	0.215	-1.032992	0.02029	0.05553	0.206684	ENSG00000175920	ENST00000389653;ENST00000340083	T;T	0.65916	-0.18;-0.09	3.93	1.42	0.22433	.	0.685034	0.14082	N	0.342604	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	P;B	0.34724	0.465;0.0	B;B	0.28011	0.085;0.0	T	0.48514	-0.9029	9	0.18276	T	0.48	-18.3256	5.3934	0.16257	0.5641:0.3427:0.0932:0.0	rs6811423;rs57140233;rs6811423	158;296	Q18PE1-2;Q18PE1	.;DOK7_HUMAN	R	296	ENSP00000374304:Q296R;ENSP00000344432:Q296R	ENSP00000344432:Q296R	Q	+	2	0	DOK7	3464398	0.995000	0.38212	0.462000	0.27118	0.151000	0.21798	1.651000	0.37302	0.123000	0.18342	0.402000	0.26972	CAG	A|0.810;G|0.190	0.190	strong		0.687	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
KRT39	390792	hgsc.bcm.edu	37	17	39123013	39123013	+	Silent	SNP	G	G	A	rs17645930	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39123013G>A	ENST00000355612.2	-	1	131	c.96C>T	c.(94-96)aaC>aaT	p.N32N	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	32	Head.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	17		Breast(137;0.00043)|Ovarian(249;0.15)				GATGGCAGCCGTTGTTAGAAG	0.493													G|||	587	0.117212	0.1452	0.0576	5008	,	,		21091	0.1399		0.1322	False		,,,				2504	0.0828				p.N32N		Atlas-SNP	.											.	KRT39	53	.	0			c.C96T						PASS	.	G		631,3775	274.3+/-271.8	54,523,1626	161.0	161.0	161.0		96	-2.4	0.0	17	dbSNP_123	161	1134,7458	235.0+/-267.7	71,992,3233	no	coding-synonymous	KRT39	NM_213656.3		125,1515,4859	AA,AG,GG		13.1983,14.3214,13.579		32/492	39123013	1765,11233	2203	4296	6499	SO:0001819	synonymous_variant	390792	exon1			GCAGCCGTTGTTA	AJ786657	CCDS11382.1	17q21.2	2013-01-16			ENSG00000196859	ENSG00000196859		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	32971	protein-coding gene	gene with protein product						16831889	Standard	NM_213656		Approved	KA35	uc002hvo.1	Q6A163	OTTHUMG00000133424	ENST00000355612.2:c.96C>T	17.37:g.39123013G>A		Somatic	297	1	0.003367		WXS	Illumina HiSeq	Phase_I	308	163	0.529221	NM_213656	B2RXK6|Q6IFU6	Silent	SNP	ENST00000355612.2	37	CCDS11382.1																																																																																			G|0.868;A|0.132	0.132	strong		0.493	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656	
PROM1	8842	hgsc.bcm.edu	37	4	16020162	16020162	+	Splice_Site	SNP	C	C	T	rs2286455	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:16020162C>T	ENST00000510224.1	-	9	1034	c.786G>A	c.(784-786)gcG>gcA	p.A262A	PROM1_ENST00000502943.1_5'UTR|PROM1_ENST00000508167.1_Splice_Site_p.A253A|PROM1_ENST00000539194.1_Splice_Site_p.A262A|PROM1_ENST00000505450.1_Splice_Site_p.A253A|PROM1_ENST00000540805.1_Splice_Site_p.A262A|PROM1_ENST00000447510.2_Splice_Site_p.A262A|PROM1_ENST00000543373.1_Splice_Site_p.A253A			O43490	PROM1_HUMAN	prominin 1	262					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						TCTCCTTGATCGCTATGGAAA	0.478													C|||	692	0.138179	0.0265	0.1628	5008	,	,		23139	0.2371		0.0944	False		,,,				2504	0.2147				p.A262A		Atlas-SNP	.											.	PROM1	91	.	0			c.G786A						PASS	.	C	,,,,,,	171,3949		5,161,1894	89.0	83.0	85.0		759,759,786,786,759,759,786	-10.8	0.0	4	dbSNP_100	85	879,7529		39,801,3364	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	PROM1	NM_001145847.1,NM_001145848.1,NM_001145849.1,NM_001145850.1,NM_001145851.1,NM_001145852.1,NM_006017.2	,,,,,,	44,962,5258	TT,TC,CC		10.4543,4.1505,8.3812	,,,,,,	253/857,253/857,262/843,262/835,253/834,253/826,262/866	16020162	1050,11478	2060	4204	6264	SO:0001630	splice_region_variant	8842	exon8			CTTGATCGCTATG	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"""CD molecules"""	9454	protein-coding gene	gene with protein product		604365	"""prominin (mouse)-like 1"", ""macular dystrophy, retinal 2"", ""Stargardt disease 4 (autosomal dominant)"""	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.785-1G>A	4.37:g.16020162C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	237	108	0.455696	NM_006017	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Silent	SNP	ENST00000510224.1	37	CCDS47029.1																																																																																			C|0.873;T|0.127	0.127	strong		0.478	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	Silent
FLI1	2313	hgsc.bcm.edu	37	11	128675292	128675292	+	Silent	SNP	T	T	A	rs7113191	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:128675292T>A	ENST00000527786.2	+	6	1176	c.687T>A	c.(685-687)gcT>gcA	p.A229A	FLI1_ENST00000534087.2_Silent_p.A196A|FLI1_ENST00000281428.8_Silent_p.A163A|FLI1_ENST00000344954.6_Silent_p.A196A|FLI1_ENST00000525560.1_Silent_p.A36A	NM_001271010.1|NM_002017.4	NP_001257939.1|NP_002008.2	Q01543	FLI1_HUMAN	Fli-1 proto-oncogene, ETS transcription factor	229					blood circulation (GO:0008015)|cell differentiation (GO:0030154)|hemostasis (GO:0007599)|megakaryocyte development (GO:0035855)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/FLI1(2569)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(2)	31	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		GAAGAGGAGCTTGGGGCAATA	0.398			T	EWSR1	Ewing sarcoma								t|||	877	0.17512	0.2579	0.1254	5008	,	,		21079	0.1706		0.1093	False		,,,				2504	0.1708				p.A229A		Atlas-SNP	.		Dom	yes		11	11q24	2313	Friend leukemia virus integration 1		M	.	FLI1	72	.	0			c.T687A						PASS	.	A	,	916,2778		125,666,1056	77.0	76.0	76.0		588,687	-0.8	0.6	11	dbSNP_116	76	890,7286		47,796,3245	no	coding-synonymous,coding-synonymous	FLI1	NM_001167681.2,NM_002017.3	,	172,1462,4301	AA,AT,TT		10.8855,24.797,15.2148	,	196/420,229/453	128675292	1806,10064	1847	4088	5935	SO:0001819	synonymous_variant	2313	exon6			AGGAGCTTGGGGC	M98833	CCDS44768.1, CCDS53725.1, CCDS59230.1, CCDS59231.1	11q24.1-q24.3	2014-09-17	2013-08-07		ENSG00000151702	ENSG00000151702			3749	protein-coding gene	gene with protein product		193067	"""Friend leukemia virus integration 1"""			1765382	Standard	NM_001167681		Approved	SIC-1, EWSR2	uc010sbu.2	Q01543	OTTHUMG00000165792	ENST00000527786.2:c.687T>A	11.37:g.128675292T>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_002017	B2R8H2|B4DFV4|B4DTC6|G3V183|Q14319|Q92480|Q9UE07	Silent	SNP	ENST00000527786.2	37	CCDS44768.1																																																																																			T|0.855;A|0.145	0.145	strong		0.398	FLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386226.2	NM_002017	
FCAMR	83953	hgsc.bcm.edu	37	1	207134226	207134226	+	Missense_Mutation	SNP	C	C	T	rs3813954	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207134226C>T	ENST00000324852.4	-	6	1469	c.995G>A	c.(994-996)aGc>aAc	p.S332N	FCAMR_ENST00000450945.2_Intron|FCAMR_ENST00000486178.1_5'Flank|FCAMR_ENST00000400962.3_Intron	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	287					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(1)	11						TGTCACCGAGCTTCTGGTGCC	0.537													C|||	67	0.0133786	0.0	0.0	5008	,	,		21949	0.0615		0.0	False		,,,				2504	0.0051				p.S332N	Ovarian(199;1883 2142 16966 44409 45154)	Atlas-SNP	.											.	FCAMR	125	.	0			c.G995A						PASS	.	C	,ASN/SER,	0,1384		0,0,692	156.0	132.0	139.0		,995,	-0.4	0.0	1	dbSNP_107	139	5,3177		0,5,1586	yes	intron,missense,intron	FCAMR	NM_001122979.2,NM_001170631.1,NM_032029.4	,46,	0,5,2278	TT,TC,CC		0.1571,0.0,0.1095	,benign,	,332/578,	207134226	5,4561	692	1591	2283	SO:0001583	missense	83953	exon6			ACCGAGCTTCTGG	AF354295	CCDS41460.1, CCDS53468.1	1q32.1	2013-01-14			ENSG00000162897	ENSG00000162897		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	24692	protein-coding gene	gene with protein product		605484				11779189	Standard	NM_001122979		Approved	FKSG87, FCA/MR, CD351	uc001hfa.4	Q8WWV6	OTTHUMG00000036579	ENST00000324852.4:c.995G>A	1.37:g.207134226C>T	ENSP00000316491:p.Ser332Asn	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	237	110	0.464135	NM_001170631	Q32M82|Q8WWV5|Q96SA2	Missense_Mutation	SNP	ENST00000324852.4	37	CCDS53468.1	24	0.01098901098901099	0	0.0	0	0.0	24	0.04195804195804196	0	0.0	C	11.92	1.781194	0.31502	0.0	0.001571	ENSG00000162897	ENST00000324852;ENST00000367087	T	0.05513	3.43	5.19	-0.41	0.12374	.	0.566370	0.18416	N	0.141910	T	0.00666	0.0022	N	0.21373	0.66	0.09310	N	1	B;B	0.21520	0.057;0.024	B;B	0.18871	0.023;0.012	T	0.43343	-0.9397	10	0.14656	T	0.56	-4.5049	1.4485	0.02369	0.1585:0.3395:0.3089:0.193	rs3813954;rs3813954	307;287	D2KTA8;Q8WWV6	.;FCAMR_HUMAN	N	332;308	ENSP00000316491:S332N	ENSP00000316491:S332N	S	-	2	0	FCAMR	205200849	0.000000	0.05858	0.003000	0.11579	0.257000	0.26127	0.194000	0.17135	0.271000	0.22005	0.556000	0.70494	AGC	C|0.991;T|0.009	0.009	strong		0.537	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029	
C9orf78	51759	hgsc.bcm.edu	37	9	132597021	132597021	+	Silent	SNP	C	C	T	rs3814547	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:132597021C>T	ENST00000372447.3	-	2	161	c.108G>A	c.(106-108)gaG>gaA	p.E36E	USP20_ENST00000315480.4_5'Flank|USP20_ENST00000358355.1_5'Flank|C9orf78_ENST00000461762.1_5'Flank|USP20_ENST00000372429.3_5'Flank	NM_016520.2	NP_057604.1	Q9NZ63	CI078_HUMAN	chromosome 9 open reading frame 78	36						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E36E(1)		kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)	13		Ovarian(14;0.00556)				AGTTCTGTACCTCTCTGGTCT	0.547													C|||	1166	0.232827	0.1997	0.2133	5008	,	,		17649	0.2143		0.2753	False		,,,				2504	0.2669				p.E36E		Atlas-SNP	.											C9orf78,NS,carcinoma,0,1	C9orf78	26	1	1	Substitution - coding silent(1)	stomach(1)	c.G108A						PASS	.	C		912,3494	348.0+/-309.7	91,730,1382	148.0	137.0	141.0		108	-1.2	1.0	9	dbSNP_107	141	2151,6449	368.4+/-335.1	278,1595,2427	no	coding-synonymous	C9orf78	NM_016520.2		369,2325,3809	TT,TC,CC		25.0116,20.699,23.5507		36/290	132597021	3063,9943	2203	4300	6503	SO:0001819	synonymous_variant	51759	exon2			CTGTACCTCTCTG	BC017570	CCDS6931.1	9q34.2	2012-03-16			ENSG00000136819	ENSG00000136819			24932	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 59"""					11042152, 12097419	Standard	NM_016520		Approved	HSPC220, HCA59	uc004byp.3	Q9NZ63	OTTHUMG00000020796	ENST00000372447.3:c.108G>A	9.37:g.132597021C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_016520	B3KPX8|Q8WVU6|Q9NT39	Silent	SNP	ENST00000372447.3	37	CCDS6931.1																																																																																			C|0.765;T|0.235	0.235	strong		0.547	C9orf78-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054625.1	NM_016520	
MADCAM1	8174	hgsc.bcm.edu	37	19	504830	504830	+	Silent	SNP	C	C	G	rs7246543	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:504830C>G	ENST00000215637.3	+	5	1060	c.1014C>G	c.(1012-1014)acC>acG	p.T338T	MADCAM1_ENST00000382683.4_Silent_p.T156T|TPGS1_ENST00000359315.5_5'Flank|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Silent_p.T251T|MADCAM1_ENST00000587541.1_Silent_p.T119T	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	338					aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTTGCCCACCTATCACCTCT	0.662													C|||	1568	0.313099	0.3517	0.4121	5008	,	,		15635	0.2093		0.2763	False		,,,				2504	0.3354				p.T338T		Atlas-SNP	.											.	MADCAM1	29	.	0			c.C1014G						PASS	.	C	,	1435,2971	460.9+/-352.8	222,991,990	46.0	47.0	47.0		1014,753	3.0	0.0	19	dbSNP_116	47	2814,5786	440.1+/-359.4	483,1848,1969	no	coding-synonymous,coding-synonymous	MADCAM1	NM_130760.2,NM_130762.2	,	705,2839,2959	GG,GC,CC		32.7209,32.5692,32.6695	,	338/383,251/296	504830	4249,8757	2203	4300	6503	SO:0001819	synonymous_variant	8174	exon5			GCCCACCTATCAC	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.1014C>G	19.37:g.504830C>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	172	92	0.534884	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Silent	SNP	ENST00000215637.3	37	CCDS12028.1																																																																																			C|0.687;G|0.312;T|0.001	0.312	strong		0.662	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
FAM83B	222584	hgsc.bcm.edu	37	6	54805688	54805688	+	Missense_Mutation	SNP	A	A	C	rs239798	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:54805688A>C	ENST00000306858.7	+	5	2035	c.1919A>C	c.(1918-1920)aAa>aCa	p.K640T	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	640			K -> T (in dbSNP:rs239798). {ECO:0000269|PubMed:15489334}.					p.K640T(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					TATATATATAAAACCTTGGGT	0.373													C|||	1450	0.289537	0.7065	0.1715	5008	,	,		17944	0.0337		0.1511	False		,,,				2504	0.2157				p.K640T		Atlas-SNP	.											FAM83B,NS,carcinoma,0,1	FAM83B	186	1	1	Substitution - Missense(1)	prostate(1)	c.A1919C						PASS	.	C	THR/LYS	2674,1722		823,1028,347	41.0	43.0	42.0		1919	4.7	0.1	6	dbSNP_79	42	1438,7156		105,1228,2964	yes	missense	FAM83B	NM_001010872.1	78	928,2256,3311	CC,CA,AA		16.7326,39.172,31.6551	benign	640/1012	54805688	4112,8878	2198	4297	6495	SO:0001583	missense	222584	exon5			TATATAAAACCTT	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.1919A>C	6.37:g.54805688A>C	ENSP00000304078:p.Lys640Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	548	0.2509157509157509	350	0.7113821138211383	73	0.20165745856353592	13	0.022727272727272728	112	0.14775725593667546	C	0.755	-0.771342	0.02951	0.60828	0.167326	ENSG00000168143	ENST00000306858	T	0.27557	1.66	5.55	4.66	0.58398	.	0.865524	0.10264	N	0.695617	T	0.02342	0.0072	N	0.00146	-1.995	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39683	-0.9602	9	0.09590	T	0.72	-7.5696	15.0301	0.71698	0.2604:0.7396:0.0:0.0	rs239798;rs52808658;rs57244784;rs239798	640	Q5T0W9	FA83B_HUMAN	T	640	ENSP00000304078:K640T	ENSP00000304078:K640T	K	+	2	0	FAM83B	54913647	0.528000	0.26314	0.067000	0.19924	0.901000	0.52897	4.107000	0.57811	0.801000	0.34066	-0.121000	0.15023	AAA	A|0.690;C|0.310	0.310	strong		0.373	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
CERS4	79603	hgsc.bcm.edu	37	19	8326866	8326866	+	Missense_Mutation	SNP	C	C	T	rs17160348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8326866C>T	ENST00000251363.5	+	12	1358	c.1058C>T	c.(1057-1059)gCg>gTg	p.A353V	CERS4_ENST00000558331.1_Missense_Mutation_p.A302V|CERS4_ENST00000559336.1_Missense_Mutation_p.A265V|CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000559450.1_Missense_Mutation_p.A353V	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	353			A -> V (in dbSNP:rs17160348). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AGTGAGGAGGCGGCGGCGGCC	0.637													A|||	634	0.126597	0.1271	0.1772	5008	,	,		13525	0.0883		0.161	False		,,,				2504	0.0941				p.A353V		Atlas-SNP	.											LASS4,caecum,carcinoma,0,1	.	.	1	0			c.C1058T						PASS	.	A	VAL/ALA	589,3817		41,507,1655	27.0	29.0	29.0		1058	3.0	0.0	19	dbSNP_123	29	1411,7189		140,1131,3029	yes	missense	CERS4	NM_024552.2	64	181,1638,4684	TT,TC,CC		16.407,13.3681,15.3775	benign	353/395	8326866	2000,11006	2203	4300	6503	SO:0001583	missense	79603	exon12			AGGAGGCGGCGGC		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.1058C>T	19.37:g.8326866C>T	ENSP00000251363:p.Ala353Val	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	74	44	0.594595	NM_024552	D6W665	Missense_Mutation	SNP	ENST00000251363.5	37	CCDS12197.1	316	0.1446886446886447	77	0.1565040650406504	67	0.1850828729281768	42	0.07342657342657342	130	0.17150395778364116	A	19.15	3.772612	0.69992	0.133681	0.16407	ENSG00000090661	ENST00000251363	T	0.06294	3.32	4.06	3.04	0.35103	.	0.667597	0.15133	N	0.278749	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.46261	-0.9204	9	0.36615	T	0.2	-14.8315	4.4314	0.11529	0.691:0.1999:0.1091:0.0	rs17160348;rs17855412;rs58953975;rs17160348	353;353	Q53HF9;Q9HA82	.;CERS4_HUMAN	V	353	ENSP00000251363:A353V	ENSP00000251363:A353V	A	+	2	0	CERS4	8232866	0.981000	0.34729	0.006000	0.13384	0.061000	0.15899	2.819000	0.48049	0.118000	0.18165	-0.494000	0.04653	GCG	C|0.852;N|0.001	.	strong		0.637	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
A4GALT	53947	hgsc.bcm.edu	37	22	43088971	43088971	+	Silent	SNP	C	C	T	rs9623659	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:43088971C>T	ENST00000401850.1	-	2	1476	c.987G>A	c.(985-987)acG>acA	p.T329T	A4GALT_ENST00000465765.2_5'Flank|A4GALT_ENST00000381278.3_Silent_p.T329T|A4GALT_ENST00000249005.2_Silent_p.T329T			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	329					globoside biosynthetic process (GO:0001576)|glycosphingolipid biosynthetic process (GO:0006688)|plasma membrane organization (GO:0007009)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	galactosyltransferase activity (GO:0008378)|lactosylceramide 4-alpha-galactosyltransferase activity (GO:0050512)|toxic substance binding (GO:0015643)			NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						GTGCCCTGGACGTGGCCTCGA	0.642													C|||	1748	0.349042	0.503	0.3415	5008	,	,		18379	0.1319		0.3817	False		,,,				2504	0.3364				p.T329T		Atlas-SNP	.											.	A4GALT	35	.	0			c.G987A						PASS	.	C		2068,2338	567.8+/-382.2	494,1080,629	66.0	60.0	62.0		987	-2.0	1.0	22	dbSNP_119	62	3189,5411	482.0+/-370.8	597,1995,1708	no	coding-synonymous	A4GALT	NM_017436.4		1091,3075,2337	TT,TC,CC		37.0814,46.936,40.4198		329/354	43088971	5257,7749	2203	4300	6503	SO:0001819	synonymous_variant	53947	exon3			CCTGGACGTGGCC		CCDS14041.1	22q13.2	2014-07-18	2008-07-31		ENSG00000128274	ENSG00000128274	2.4.1.228		18149	protein-coding gene	gene with protein product	"""Gb3 synthase"", ""CD77 synthase"", ""globotriaosylceramide synthase"", ""lactosylceramide 4-alpha-galactosyltransferase"""	607922	"""alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"""			10854428	Standard	XM_005261643		Approved	A14GALT, Gb3S, P(k)	uc003bdb.3	Q9NPC4	OTTHUMG00000150744	ENST00000401850.1:c.987G>A	22.37:g.43088971C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_017436	B2R7C4|Q9P1X5	Silent	SNP	ENST00000401850.1	37	CCDS14041.1																																																																																			C|0.610;T|0.390	0.390	strong		0.642	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436	
CCDC129	223075	hgsc.bcm.edu	37	7	31682601	31682601	+	Silent	SNP	T	T	C	rs38396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:31682601T>C	ENST00000407970.3	+	11	1655	c.1617T>C	c.(1615-1617)caT>caC	p.H539H	CCDC129_ENST00000409210.1_Silent_p.H447H|CCDC129_ENST00000451887.2_Silent_p.H565H|CCDC129_ENST00000319386.3_Silent_p.H391H	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	539										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AAGACAGCCATCTGTGGCAGC	0.552													T|||	682	0.136182	0.0182	0.1556	5008	,	,		20135	0.1806		0.2177	False		,,,				2504	0.1524				p.H565H		Atlas-SNP	.											.	CCDC129	127	.	0			c.T1695C						PASS	.	T		222,4184	132.9+/-169.3	9,204,1990	141.0	135.0	137.0		1617	-10.0	0.0	7	dbSNP_76	137	1730,6870	315.1+/-312.1	183,1364,2753	no	coding-synonymous	CCDC129	NM_194300.2		192,1568,4743	CC,CT,TT		20.1163,5.0386,15.0085		539/1045	31682601	1952,11054	2203	4300	6503	SO:0001819	synonymous_variant	223075	exon11			CAGCCATCTGTGG	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.1617T>C	7.37:g.31682601T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	166	84	0.506024	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Silent	SNP	ENST00000407970.3	37	CCDS5435.2																																																																																			T|0.862;C|0.138	0.138	strong		0.552	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
SECISBP2L	9728	hgsc.bcm.edu	37	15	49285001	49285001	+	Missense_Mutation	SNP	G	G	C	rs34895054	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:49285001G>C	ENST00000559471.1	-	18	3009	c.2746C>G	c.(2746-2748)Cca>Gca	p.P916A	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.P871A	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	916							poly(A) RNA binding (GO:0044822)	p.P871A(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTACCAATTGGGGGTGTGTCA	0.453													G|||	952	0.190096	0.0356	0.1844	5008	,	,		17781	0.2063		0.2823	False		,,,				2504	0.2914				p.P916A		Atlas-SNP	.											SECISBP2L,NS,carcinoma,0,1	SECISBP2L	118	1	1	Substitution - Missense(1)	stomach(1)	c.C2746G						scavenged	.	G	ALA/PRO,ALA/PRO	341,4053	176.6+/-205.7	17,307,1873	174.0	164.0	167.0		2746,2611	-0.6	0.0	15	dbSNP_126	167	2134,6456	367.9+/-334.9	273,1588,2434	yes	missense,missense	SECISBP2L	NM_001193489.1,NM_014701.3	27,27	290,1895,4307	CC,CG,GG		24.8428,7.7606,19.0619	benign,benign	916/1102,871/1057	49285001	2475,10509	2197	4295	6492	SO:0001583	missense	9728	exon18			CAATTGGGGGTGT	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2746C>G	15.37:g.49285001G>C	ENSP00000453854:p.Pro916Ala	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	207	98	0.47343	NM_001193489	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	428	0.19597069597069597	17	0.034552845528455285	72	0.19889502762430938	117	0.20454545454545456	222	0.2928759894459103	G	5.350	0.249933	0.10130	0.077606	0.248428	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.71579	-0.58	4.79	-0.566	0.11767	.	1.036750	0.07555	N	0.916156	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.23249	0.049;0.082	B;B	0.15484	0.01;0.013	T	0.04723	-1.0931	9	0.07990	T	0.79	.	1.6184	0.02708	0.2142:0.1032:0.4026:0.2799	rs34895054	916;871	Q93073;Q93073-2	SBP2L_HUMAN;.	A	871;916	ENSP00000261847:P871A	ENSP00000261847:P871A	P	-	1	0	SECISBP2L	47072293	0.015000	0.18098	0.000000	0.03702	0.811000	0.45836	0.874000	0.28065	-0.169000	0.10834	-0.152000	0.13540	CCA	G|0.812;C|0.188	0.188	strong		0.453	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	
TRDN	10345	hgsc.bcm.edu	37	6	123699042	123699042	+	Splice_Site	SNP	T	T	C	rs6901953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:123699042T>C	ENST00000398178.3	-	17	1209	c.1188A>G	c.(1186-1188)aaA>aaG	p.K396K	TRDN_ENST00000334268.4_Splice_Site_p.K396K	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	396			K -> N (in dbSNP:rs6901953).		cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		TCTTTTCCTGTTCTGAAACAt	0.264													T|||	1363	0.272165	0.3434	0.4251	5008	,	,		14839	0.1012		0.3678	False		,,,				2504	0.1452				p.K397K		Atlas-SNP	.											.	TRDN	88	.	0			c.A1191G						PASS	.	T		1161,2319		219,723,798	14.0	14.0	14.0		1188	3.8	1.0	6	dbSNP_116	14	2890,5060		574,1742,1659	yes	coding-synonymous-near-splice	TRDN	NM_006073.2		793,2465,2457	CC,CT,TT		36.3522,33.3621,35.4418		396/730	123699042	4051,7379	1740	3975	5715	SO:0001630	splice_region_variant	10345	exon17			TTCCTGTTCTGAA	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1187-1A>G	6.37:g.123699042T>C		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Silent	SNP	ENST00000398178.3	37	CCDS55053.1																																																																																			T|0.711;C|0.289	0.289	strong		0.264	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			Silent
SMYD4	114826	hgsc.bcm.edu	37	17	1703543	1703543	+	Missense_Mutation	SNP	G	G	C	rs3809875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1703543G>C	ENST00000305513.7	-	5	1312	c.1145C>G	c.(1144-1146)cCt>cGt	p.P382R		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	382	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		P -> R (in dbSNP:rs3809875).				metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						GTTGCTTTCAGGTAAACAGAT	0.413													G|||	1399	0.279353	0.3926	0.2305	5008	,	,		24591	0.1905		0.2773	False		,,,				2504	0.2546				p.P382R		Atlas-SNP	.											.	SMYD4	50	.	0			c.C1145G						PASS	.	G	ARG/PRO	1733,2673	519.4+/-370.0	336,1061,806	157.0	149.0	152.0		1145	4.8	0.9	17	dbSNP_107	152	2583,6017	419.5+/-353.1	396,1791,2113	yes	missense	SMYD4	NM_052928.2	103	732,2852,2919	CC,CG,GG		30.0349,39.3327,33.1847	probably-damaging	382/805	1703543	4316,8690	2203	4300	6503	SO:0001583	missense	114826	exon5			CTTTCAGGTAAAC	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.1145C>G	17.37:g.1703543G>C	ENSP00000304360:p.Pro382Arg	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	208	95	0.456731	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	612	0.2802197802197802	200	0.4065040650406504	102	0.281767955801105	122	0.21328671328671328	188	0.24802110817941952	G	11.40	1.626284	0.28978	0.393327	0.300349	ENSG00000186532	ENST00000305513	T	0.10005	2.92	5.85	4.83	0.62350	SET domain (2);	0.359538	0.28209	N	0.016186	T	0.00012	0.0000	M	0.69248	2.105	0.80722	P	0.0	D	0.59767	0.986	D	0.65573	0.936	T	0.52503	-0.8567	9	0.16896	T	0.51	-8.5947	16.8524	0.85996	0.0:0.1278:0.8722:0.0	rs3809875;rs61091900;rs3809875	382	Q8IYR2	SMYD4_HUMAN	R	382	ENSP00000304360:P382R	ENSP00000304360:P382R	P	-	2	0	SMYD4	1650293	0.916000	0.31088	0.860000	0.33809	0.075000	0.17131	3.500000	0.53318	2.941000	0.99782	0.655000	0.94253	CCT	G|0.688;C|0.312	0.312	strong		0.413	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
CDHR3	222256	hgsc.bcm.edu	37	7	105621474	105621474	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:105621474C>T	ENST00000317716.9	+	3	390	c.310C>T	c.(310-312)Cag>Tag	p.Q104*	CDHR3_ENST00000478080.1_Nonsense_Mutation_p.Q16*|CDHR3_ENST00000542731.1_Nonsense_Mutation_p.Q104*|CDHR3_ENST00000343407.5_5'UTR|CDHR3_ENST00000541203.1_Nonsense_Mutation_p.Q104*|CDHR3_ENST00000470188.1_3'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	104	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						ATTTGATTTGCAGATTTATGT	0.418																																					p.Q104X		Atlas-SNP	.											.	CDHR3	153	.	0			c.C310T						PASS	.						88.0	82.0	84.0					7																	105621474		1929	4140	6069	SO:0001587	stop_gained	222256	exon3			GATTTGCAGATTT	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.310C>T	7.37:g.105621474C>T	ENSP00000325954:p.Gln104*	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	179	72	0.402235	NM_152750	Q8TCI7	Nonsense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	.	.	.	.	.	.	.	.	.	.	C	36	5.837584	0.97009	.	.	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080;ENST00000541203	.	.	.	5.02	5.02	0.67125	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-3.9079	17.6187	0.88075	0.0:1.0:0.0:0.0	.	.	.	.	X	104;104;16;104	.	ENSP00000325954:Q104X	Q	+	1	0	CDHR3	105408710	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	5.065000	0.64344	2.774000	0.95407	0.561000	0.74099	CAG	.	.	none		0.418	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
RNF123	63891	hgsc.bcm.edu	37	3	49742584	49742584	+	Silent	SNP	G	G	A	rs34539806	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49742584G>A	ENST00000327697.6	+	23	2271	c.2127G>A	c.(2125-2127)acG>acA	p.T709T	RNF123_ENST00000432042.1_Silent_p.T563T	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	709					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		AGGTCCGCACGCTGAGCGTGG	0.647													g|||	22	0.00439297	0.0008	0.0014	5008	,	,		15781	0.0		0.0149	False		,,,				2504	0.0051				p.T709T		Atlas-SNP	.											.	RNF123	100	.	0			c.G2127A						PASS	.			12,4374		0,12,2181	32.0	40.0	37.0		2127	-10.2	0.2	3	dbSNP_126	37	139,8459		1,137,4161	no	coding-synonymous	RNF123	NM_022064.2		1,149,6342	AA,AG,GG		1.6167,0.2736,1.163		709/1315	49742584	151,12833	2193	4299	6492	SO:0001819	synonymous_variant	63891	exon23			CCGCACGCTGAGC	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.2127G>A	3.37:g.49742584G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	162	96	0.592593	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	37	CCDS33758.1																																																																																			G|0.990;A|0.010	0.010	strong		0.647	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
CERS4	79603	hgsc.bcm.edu	37	19	8321937	8321937	+	Silent	SNP	C	C	T	rs1127912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8321937C>T	ENST00000251363.5	+	9	1017	c.717C>T	c.(715-717)caC>caT	p.H239H	CERS4_ENST00000558331.1_Silent_p.H188H|CERS4_ENST00000559336.1_Silent_p.H239H|CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000559450.1_Silent_p.H239H	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	239	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.H239H(1)									TGCTGTTACACGATTCCTCTG	0.602													C|||	1142	0.228035	0.3434	0.2291	5008	,	,		17567	0.1964		0.2117	False		,,,				2504	0.1207				p.H239H		Atlas-SNP	.											LASS4,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C717T						PASS	.	C		1378,3028	455.7+/-351.1	215,948,1040	241.0	226.0	231.0		717	-3.9	0.8	19	dbSNP_86	231	1642,6958	303.2+/-306.3	175,1292,2833	no	coding-synonymous	CERS4	NM_024552.2		390,2240,3873	TT,TC,CC		19.093,31.2755,23.2201		239/395	8321937	3020,9986	2203	4300	6503	SO:0001819	synonymous_variant	79603	exon9			GTTACACGATTCC		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.717C>T	19.37:g.8321937C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	194	79	0.407216	NM_024552	D6W665	Silent	SNP	ENST00000251363.5	37	CCDS12197.1																																																																																			C|0.761;T|0.239	0.239	strong		0.602	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
FREM1	158326	hgsc.bcm.edu	37	9	14776027	14776027	+	Silent	SNP	C	C	T	rs2131880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:14776027C>T	ENST00000380880.3	-	25	5400	c.4617G>A	c.(4615-4617)gcG>gcA	p.A1539A	FREM1_ENST00000422223.2_Silent_p.A1539A|FREM1_ENST00000380881.4_Silent_p.A1540A|FREM1_ENST00000486223.1_5'Flank|FREM1_ENST00000380894.1_Silent_p.A75A			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1539					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TGAGGTTCTCCGCAGGTGTAT	0.597													C|||	533	0.10643	0.1218	0.1138	5008	,	,		18321	0.0238		0.1879	False		,,,				2504	0.0818				p.A1539A		Atlas-SNP	.											.	FREM1	261	.	0			c.G4617A						PASS	.	C	,	515,3505		31,453,1526	140.0	148.0	145.0		225,4617	-10.7	0.0	9	dbSNP_96	145	1478,6870		120,1238,2816	no	coding-synonymous,coding-synonymous	FREM1	NM_001177704.1,NM_144966.5	,	151,1691,4342	TT,TC,CC		17.7048,12.8109,16.1142	,	75/716,1539/2180	14776027	1993,10375	2010	4174	6184	SO:0001819	synonymous_variant	158326	exon26			GTTCTCCGCAGGT	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.4617G>A	9.37:g.14776027C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	147	78	0.530612	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			C|0.882;T|0.118	0.118	strong		0.597	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
SVEP1	79987	hgsc.bcm.edu	37	9	113233720	113233720	+	Silent	SNP	G	G	A	rs10980402	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:113233720G>A	ENST00000401783.2	-	16	3258	c.2922C>T	c.(2920-2922)gcC>gcT	p.A974A	SVEP1_ENST00000374469.1_Silent_p.A951A|SVEP1_ENST00000302728.8_Silent_p.A974A|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	974					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						AATTGCTGTCGGCTATAAGTA	0.433													G|||	959	0.191494	0.0151	0.2579	5008	,	,		16973	0.4206		0.1819	False		,,,				2504	0.1564				p.A974A		Atlas-SNP	.											.	SVEP1	326	.	0			c.C2922T						PASS	.	G		144,3610		3,138,1736	114.0	105.0	108.0		2922	-9.3	0.0	9	dbSNP_120	108	1409,6805		120,1169,2818	no	coding-synonymous	SVEP1	NM_153366.3		123,1307,4554	AA,AG,GG		17.1536,3.8359,12.9763		974/3572	113233720	1553,10415	1877	4107	5984	SO:0001819	synonymous_variant	79987	exon16			GCTGTCGGCTATA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.2922C>T	9.37:g.113233720G>A		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	247	125	0.506073	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			G|0.798;A|0.202	0.202	strong		0.433	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SULT1A2	6799	hgsc.bcm.edu	37	16	28603721	28603721	+	Missense_Mutation	SNP	C	C	T	rs141581853	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28603721C>T	ENST00000395630.1	-	7	988	c.638G>A	c.(637-639)cGc>cAc	p.R213H	SULT1A2_ENST00000335715.4_Missense_Mutation_p.R213H|SULT1A2_ENST00000533150.1_Missense_Mutation_p.R180H	NM_177528.2	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2	213					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine biosynthetic process (GO:0009309)|catecholamine metabolic process (GO:0006584)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|sulfotransferase activity (GO:0008146)	p.R213H(4)		NS(2)|breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|skin(2)	14						TGGCAGGGAGCGCCCCACAAA	0.532													.|||	134	0.0267572	0.0363	0.0677	5008	,	,		20273	0.005		0.0268	False		,,,				2504	0.0072				p.R213H		Atlas-SNP	.											SULT1A2,colon,carcinoma,0,4	SULT1A2	27	4	4	Substitution - Missense(4)	skin(2)|large_intestine(1)|NS(1)	c.G638A						scavenged	.						132.0	119.0	123.0					16																	28603721		2197	4300	6497	SO:0001583	missense	6799	exon7			AGGGAGCGCCCCA	U34804	CCDS10636.1	16p12.1	2008-02-05			ENSG00000197165	ENSG00000197165	2.8.2.1	"""Sulfotransferases, cytosolic"""	11454	protein-coding gene	gene with protein product		601292		STP2		8661000, 8912648	Standard	NM_001054		Approved	HAST4	uc002dqh.2	P50226	OTTHUMG00000048082	ENST00000395630.1:c.638G>A	16.37:g.28603721C>T	ENSP00000378992:p.Arg213His	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	240	10	0.0416667	NM_001054	A9QY25|P78393|Q14CJ7	Missense_Mutation	SNP	ENST00000395630.1	37	CCDS10636.1	.	.	.	.	.	.	.	.	.	.	c	15.21	2.765812	0.49574	.	.	ENSG00000197165	ENST00000533150;ENST00000335715;ENST00000395630	D;D;D	0.82526	-1.62;-1.62;-1.62	4.98	3.0	0.34707	Sulfotransferase domain (1);	0.265029	0.30329	N	0.009878	T	0.81307	0.4795	M	0.85462	2.755	0.22081	N	0.999373	B	0.12013	0.005	B	0.06405	0.002	T	0.73867	-0.3847	10	0.62326	D	0.03	.	6.5172	0.22254	0.0:0.7359:0.0:0.2641	.	213	P50226	ST1A2_HUMAN	H	180;213;213	ENSP00000435271:R180H;ENSP00000338742:R213H;ENSP00000378992:R213H	ENSP00000338742:R213H	R	-	2	0	SULT1A2	28511222	0.000000	0.05858	1.000000	0.80357	0.908000	0.53690	-0.149000	0.10204	2.300000	0.77407	0.456000	0.33151	CGC	C|0.683;T|0.317	0.317	strong		0.532	SULT1A2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109415.2	NM_001054	
LRP2	4036	hgsc.bcm.edu	37	2	170002322	170002322	+	Missense_Mutation	SNP	G	G	A	rs543890594		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:170002322G>A	ENST00000263816.3	-	70	13208	c.12923C>T	c.(12922-12924)aCg>aTg	p.T4308M		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4308					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CACTACCAGCGTTTTCTCTTT	0.388																																					p.T4308M		Atlas-SNP	.											LRP2,right_lower_lobe,carcinoma,+1,1	LRP2	751	1	0			c.C12923T						PASS	.						108.0	100.0	103.0					2																	170002322		2203	4300	6503	SO:0001583	missense	4036	exon70			ACCAGCGTTTTCT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.12923C>T	2.37:g.170002322G>A	ENSP00000263816:p.Thr4308Met	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	69	40	0.57971	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	4.856	0.159199	0.09236	.	.	ENSG00000081479	ENST00000263816	D	0.91894	-2.93	5.38	3.0	0.34707	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.626869	0.17107	N	0.186765	D	0.85084	0.5616	L	0.37507	1.11	0.80722	D	1	B	0.18741	0.03	B	0.06405	0.002	T	0.75399	-0.3331	10	0.31617	T	0.26	.	5.8816	0.18858	0.7744:0.0:0.0793:0.1463	.	4308	P98164	LRP2_HUMAN	M	4308	ENSP00000263816:T4308M	ENSP00000263816:T4308M	T	-	2	0	LRP2	169710568	0.992000	0.36948	0.281000	0.24762	0.093000	0.18481	7.437000	0.80417	0.434000	0.26340	-1.087000	0.02190	ACG	.	.	none		0.388	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
ASIC4	55515	hgsc.bcm.edu	37	2	220399951	220399951	+	Silent	SNP	A	A	G	rs2276643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:220399951A>G	ENST00000347842.3	+	5	1472	c.1458A>G	c.(1456-1458)acA>acG	p.T486T	ASIC4_ENST00000358078.4_Silent_p.T505T	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	486					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										GCAACCTGACACGCTATGGGA	0.607													G|||	1297	0.258986	0.466	0.2723	5008	,	,		16038	0.1468		0.2008	False		,,,				2504	0.1452				p.T486T		Atlas-SNP	.											.	.	.	.	0			c.A1458G						PASS	.	G	,	1906,2500	626.8+/-394.8	412,1082,709	57.0	50.0	52.0		1515,1458	-8.9	0.1	2	dbSNP_100	52	1724,6876	736.5+/-407.0	185,1354,2761	no	coding-synonymous,coding-synonymous	ACCN4	NM_018674.4,NM_182847.2	,	597,2436,3470	GG,GA,AA		20.0465,43.2592,27.9102	,	505/667,486/648	220399951	3630,9376	2203	4300	6503	SO:0001819	synonymous_variant	55515	exon5			CCTGACACGCTAT	AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	21263	protein-coding gene	gene with protein product		606715	"""amiloride-sensitive cation channel 4, pituitary"", ""amiloride-sensitive cation channel family member 4, pituitary"""	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1458A>G	2.37:g.220399951A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Silent	SNP	ENST00000347842.3	37	CCDS2442.1																																																																																			A|0.731;G|0.268	0.268	strong		0.607	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674	
GORAB	92344	hgsc.bcm.edu	37	1	170521376	170521376	+	Missense_Mutation	SNP	G	G	A	rs913257	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:170521376G>A	ENST00000367763.3	+	5	978	c.958G>A	c.(958-960)Gaa>Aaa	p.E320K		NM_152281.2	NP_689494.2	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	320	Necessary for interaction with RCHY1.		E -> K (in dbSNP:rs913257). {ECO:0000269|PubMed:14702039}.			cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|liver(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	17						ATTGCTACACGAACAAGAAGT	0.463													G|||	2968	0.592652	0.5257	0.5865	5008	,	,		20225	0.877		0.4692	False		,,,				2504	0.5215				p.E320K		Atlas-SNP	.											.	GORAB	41	.	0			c.G958A						PASS	.	G	LYS/GLU	2340,2066	607.5+/-391.0	620,1100,483	104.0	93.0	96.0		958	2.7	0.6	1	dbSNP_86	96	3979,4621	553.3+/-386.3	914,2151,1235	yes	missense	GORAB	NM_152281.2	56	1534,3251,1718	AA,AG,GG		46.2674,46.8906,48.5853	possibly-damaging	320/395	170521376	6319,6687	2203	4300	6503	SO:0001583	missense	92344	exon5			CTACACGAACAAG	AK021814	CCDS1289.1, CCDS53428.1	1q24.2	2009-02-13	2009-02-13	2009-02-13	ENSG00000120370	ENSG00000120370			25676	protein-coding gene	gene with protein product	"""gerodermia osteodysplastica"""	607983	"""SCY1-like 1 binding protein 1"""	SCYL1BP1		12783284, 15781263, 18997784	Standard	NM_152281		Approved	FLJ11752, NTKL-BP1, GO	uc001gha.2	Q5T7V8	OTTHUMG00000035228	ENST00000367763.3:c.958G>A	1.37:g.170521376G>A	ENSP00000356737:p.Glu320Lys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	154	74	0.480519	NM_152281	Q49A22|Q6P1P9|Q9HAE6|Q9Y350	Missense_Mutation	SNP	ENST00000367763.3	37	CCDS1289.1	1334	0.6108058608058609	262	0.532520325203252	186	0.5138121546961326	518	0.9055944055944056	368	0.48548812664907653	G	12.55	1.971203	0.34754	0.531094	0.462674	ENSG00000120370	ENST00000367763	T	0.62941	-0.01	5.63	2.65	0.31530	.	0.191109	0.45606	D	0.000353	T	0.33089	0.0851	L	0.57536	1.79	0.19300	P	0.9999718336	P	0.42357	0.777	B	0.30179	0.112	T	0.18335	-1.0340	9	0.49607	T	0.09	-3.2992	9.7822	0.40656	0.0881:0.5253:0.3866:0.0	rs913257;rs52837440;rs56596330;rs59554694;rs913257	320	Q5T7V8	GORAB_HUMAN	K	320	ENSP00000356737:E320K	ENSP00000356737:E320K	E	+	1	0	GORAB	168788000	0.999000	0.42202	0.640000	0.29408	0.012000	0.07955	2.566000	0.45948	0.737000	0.32582	0.655000	0.94253	GAA	G|0.448;A|0.552	0.552	strong		0.463	GORAB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085226.1	NM_152281	
UTP23	84294	hgsc.bcm.edu	37	8	117783975	117783975	+	Missense_Mutation	SNP	C	C	T	rs16888728	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:117783975C>T	ENST00000309822.2	+	3	745	c.644C>T	c.(643-645)cCg>cTg	p.P215L	UTP23_ENST00000517820.1_Intron|UTP23_ENST00000520733.1_Intron|UTP23_ENST00000357148.3_Intron	NM_032334.2	NP_115710.2	Q9BRU9	UTP23_HUMAN	UTP23, small subunit (SSU) processome component, homolog (yeast)	215			P -> L (in dbSNP:rs16888728).		rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	12						AAAAAGGCACCGGACACACAA	0.373													C|||	956	0.190895	0.4614	0.0821	5008	,	,		16387	0.0129		0.1133	False		,,,				2504	0.1656				p.P215L		Atlas-SNP	.											UTP23,NS,carcinoma,0,1	UTP23	38	1	0			c.C644T						PASS	.	C	LEU/PRO	1571,2829		276,1019,905	41.0	45.0	43.0		644	-0.5	0.1	8	dbSNP_123	43	843,7751		46,751,3500	yes	missense	UTP23	NM_032334.2	98	322,1770,4405	TT,TC,CC		9.8092,35.7045,18.5778	benign	215/250	117783975	2414,10580	2200	4297	6497	SO:0001583	missense	84294	exon3			AGGCACCGGACAC		CCDS6320.1	8q24.11	2008-06-12	2008-06-12	2008-06-12		ENSG00000147679			28224	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 53"""	C8orf53		16769905	Standard	NM_032334		Approved	MGC14595	uc003yoc.3	Q9BRU9		ENST00000309822.2:c.644C>T	8.37:g.117783975C>T	ENSP00000308332:p.Pro215Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	36	0.395604	NM_032334	B2RE25|Q96NJ8	Missense_Mutation	SNP	ENST00000309822.2	37	CCDS6320.1	335	0.1533882783882784	206	0.4186991869918699	36	0.09944751381215469	9	0.015734265734265736	84	0.11081794195250659	C	8.050	0.765744	0.15983	0.357045	0.098092	ENSG00000147679	ENST00000309822	T	0.24151	1.87	5.96	-0.543	0.11851	.	0.696157	0.14855	N	0.294442	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.47787	-0.9090	9	0.28530	T	0.3	0.0651	7.2669	0.26234	0.5083:0.3659:0.1257:0.0	rs16888728;rs52795925;rs16888728	215	Q9BRU9	UTP23_HUMAN	L	215	ENSP00000308332:P215L	ENSP00000308332:P215L	P	+	2	0	UTP23	117853156	0.998000	0.40836	0.098000	0.21074	0.567000	0.35839	1.576000	0.36504	-0.081000	0.12662	-0.262000	0.10625	CCG	C|0.812;N|0.001;T|0.186	0.186	strong		0.373	UTP23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381173.1	NM_032334	
LOXL4	84171	hgsc.bcm.edu	37	10	100013438	100013438	+	Silent	SNP	C	C	T	rs17524355	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:100013438C>T	ENST00000260702.3	-	11	1857	c.1707G>A	c.(1705-1707)gcG>gcA	p.A569A	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	569	Lysyl-oxidase like.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		CCATGTGATCCGCAGACTTGG	0.592													C|||	659	0.131589	0.1528	0.1484	5008	,	,		18566	0.0288		0.2207	False		,,,				2504	0.1053				p.A569A		Atlas-SNP	.											LOXL4,caecum,carcinoma,-1,2	LOXL4	60	2	0			c.G1707A						PASS	.	C		767,3639	311.1+/-291.9	75,617,1511	110.0	99.0	102.0		1707	-8.3	0.6	10	dbSNP_123	102	1841,6759	330.9+/-319.4	193,1455,2652	no	coding-synonymous	LOXL4	NM_032211.6		268,2072,4163	TT,TC,CC		21.407,17.4081,20.0523		569/757	100013438	2608,10398	2203	4300	6503	SO:0001819	synonymous_variant	84171	exon11			GTGATCCGCAGAC	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.1707G>A	10.37:g.100013438C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	49	5	0.102041	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Silent	SNP	ENST00000260702.3	37	CCDS7473.1																																																																																			C|0.826;T|0.174	0.174	strong		0.592	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211	
PARP4	143	hgsc.bcm.edu	37	13	25023936	25023936	+	Missense_Mutation	SNP	C	C	T	rs9581043	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25023936C>T	ENST00000381989.3	-	25	3139	c.3034G>A	c.(3034-3036)Gtc>Atc	p.V1012I		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1012	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		V -> I (in dbSNP:rs9581043).		cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		ATCCTTAAGACGTGACGATTT	0.333													t|||	670	0.133786	0.3185	0.0951	5008	,	,		20778	0.0317		0.0974	False		,,,				2504	0.0542				p.V1012I		Atlas-SNP	.											.	PARP4	142	.	0			c.G3034A						PASS	.	T	ILE/VAL	1212,3194	706.4+/-407.4	185,842,1176	70.0	71.0	71.0		3034	-3.8	0.0	13	dbSNP_119	71	1013,7587	772.0+/-407.7	71,871,3358	no	missense	PARP4	NM_006437.3	29	256,1713,4534	TT,TC,CC		11.7791,27.5079,17.1075	benign	1012/1725	25023936	2225,10781	2203	4300	6503	SO:0001583	missense	143	exon25			TTAAGACGTGACG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3034G>A	13.37:g.25023936C>T	ENSP00000371419:p.Val1012Ile	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	251	250	0.996016	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	293	0.13415750915750915	165	0.3353658536585366	37	0.10220994475138122	8	0.013986013986013986	83	0.10949868073878628	T	0.007	-1.973345	0.00452	0.275079	0.117791	ENSG00000102699	ENST00000381989	T	0.07908	3.15	4.64	-3.78	0.04333	von Willebrand factor, type A (3);	0.234215	0.48286	N	0.000184	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B	0.11235	0.004	B	0.11329	0.006	T	0.34153	-0.9840	9	0.02654	T	1	-0.9328	7.7815	0.29068	0.0:0.4459:0.1251:0.429	rs9581043;rs9581043	1012	Q9UKK3	PARP4_HUMAN	I	1012	ENSP00000371419:V1012I	ENSP00000371419:V1012I	V	-	1	0	PARP4	23921936	0.923000	0.31300	0.015000	0.15790	0.247000	0.25773	0.120000	0.15647	-1.306000	0.02324	-1.553000	0.00894	GTC	C|0.848;T|0.152	0.152	strong		0.333	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
KRTAP5-2	440021	hgsc.bcm.edu	37	11	1619202	1619202	+	Silent	SNP	G	G	A	rs61869706|rs59506446		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1619202G>A	ENST00000412090.1	-	1	322	c.279C>T	c.(277-279)ggC>ggT	p.G93G	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	93	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				large_intestine(1)|lung(2)|skin(1)	4		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCCTTGGAGCCCCCACAGG	0.662																																					p.G93G		Atlas-SNP	.											KRTAP5-2,colon,carcinoma,-1,1	KRTAP5-2	38	1	0			c.C279T						PASS	.						40.0	59.0	52.0					11																	1619202		2184	4270	6454	SO:0001819	synonymous_variant	440021	exon1			CTTGGAGCCCCCA	AB126071	CCDS31331.1	11p15.5	2008-02-05				ENSG00000205867		"""Keratin associated proteins"""	23597	protein-coding gene	gene with protein product						15144888	Standard	NM_001004325		Approved	KRTAP5.2, KRTAP5-8	uc001ltv.3	Q701N4		ENST00000412090.1:c.279C>T	11.37:g.1619202G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	72	24	0.333333	NM_001004325	A9JTZ1	Silent	SNP	ENST00000412090.1	37	CCDS31331.1																																																																																			G|0.780;A|0.220	0.220	strong		0.662	KRTAP5-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384775.1	NM_001004325	
PTPRH	5794	hgsc.bcm.edu	37	19	55710074	55710074	+	Missense_Mutation	SNP	G	G	A	rs16986309	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55710074G>A	ENST00000376350.3	-	8	1649	c.1627C>T	c.(1627-1629)Ctc>Ttc	p.L543F	PTPRH_ENST00000263434.5_Missense_Mutation_p.L365F|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	543	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.		L -> F (in dbSNP:rs16986309).		apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CAGACGGTGAGGTGGTACAGG	0.572													G|||	464	0.0926518	0.1278	0.1095	5008	,	,		19650	0.0099		0.1213	False		,,,				2504	0.089				p.L543F		Atlas-SNP	.											.	PTPRH	139	.	0			c.C1627T						PASS	.	G	PHE/LEU,PHE/LEU	595,3811	260.7+/-263.8	41,513,1649	163.0	132.0	142.0		1093,1627	-0.3	0.0	19	dbSNP_123	142	996,7604	214.6+/-254.2	57,882,3361	yes	missense,missense	PTPRH	NM_001161440.1,NM_002842.3	22,22	98,1395,5010	AA,AG,GG		11.5814,13.5043,12.2328	benign,benign	365/938,543/1116	55710074	1591,11415	2203	4300	6503	SO:0001583	missense	5794	exon8			CGGTGAGGTGGTA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.1627C>T	19.37:g.55710074G>A	ENSP00000365528:p.Leu543Phe	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	224	0.10256410256410256	75	0.1524390243902439	50	0.13812154696132597	0	0.0	99	0.13060686015831136	G	0.093	-1.164239	0.01673	0.135043	0.115814	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.52754	0.65;0.65	2.27	-0.302	0.12796	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00109	0.0003	N	0.05124	-0.11	0.80722	P	0.0	B;B;B	0.12630	0.006;0.005;0.004	B;B;B	0.17433	0.018;0.01;0.004	T	0.20207	-1.0282	8	0.12766	T	0.61	.	1.6305	0.02732	0.4856:0.0:0.2259:0.2886	rs16986309;rs52822550;rs58326738;rs16986309	365;365;543	C9JCH2;Q9HD43-2;Q9HD43	.;.;PTPRH_HUMAN	F	543;365	ENSP00000365528:L543F;ENSP00000263434:L365F	ENSP00000263434:L365F	L	-	1	0	PTPRH	60401886	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	0.009000	0.13219	-0.107000	0.12088	0.561000	0.74099	CTC	G|0.884;A|0.116	0.116	strong		0.572	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
C17orf74	201243	hgsc.bcm.edu	37	17	7329134	7329134	+	Missense_Mutation	SNP	G	G	A	rs72842820	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7329134G>A	ENST00000333870.3	+	1	201	c.127G>A	c.(127-129)Gtg>Atg	p.V43M	RP11-104H15.7_ENST00000575310.1_RNA|C17orf74_ENST00000574034.1_Missense_Mutation_p.V43M	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	43						integral component of membrane (GO:0016021)				cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	22		Prostate(122;0.157)				TGGCATCAACGTGGCAACTAT	0.552													G|||	576	0.115016	0.1369	0.0865	5008	,	,		14354	0.002		0.1511	False		,,,				2504	0.1851				p.V43M		Atlas-SNP	.											.	C17orf74	56	.	0			c.G127A						PASS	.	G	MET/VAL	555,3673		37,481,1596	290.0	281.0	284.0		127	-3.8	0.0	17	dbSNP_130	284	1517,6965		162,1193,2886	yes	missense	C17orf74	NM_175734.4	21	199,1674,4482	AA,AG,GG		17.8849,13.1268,16.3021	probably-damaging	43/502	7329134	2072,10638	2114	4241	6355	SO:0001583	missense	201243	exon1			ATCAACGTGGCAA	BC044816	CCDS42255.1	17p13.1	2012-05-30			ENSG00000184560	ENSG00000184560			27315	protein-coding gene	gene with protein product						12477932	Standard	NM_175734		Approved		uc002ggw.3	Q0P670	OTTHUMG00000178190	ENST00000333870.3:c.127G>A	17.37:g.7329134G>A	ENSP00000328061:p.Val43Met	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	270	137	0.507407	NM_175734		Missense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	225	0.10302197802197802	79	0.16056910569105692	30	0.08287292817679558	0	0.0	116	0.15303430079155672	G	10.80	1.453417	0.26161	0.131268	0.178849	ENSG00000184560	ENST00000333870	T	0.56776	0.44	3.8	-3.82	0.04281	.	0.597438	0.13576	N	0.377667	T	0.00073	0.0002	L	0.28556	0.865	0.80722	P	0.0	P	0.41420	0.749	B	0.25506	0.061	T	0.04386	-1.0955	9	0.41790	T	0.15	-13.6248	10.2877	0.43577	0.2277:0.0:0.7723:0.0	.	43	Q0P670	CQ074_HUMAN	M	43	ENSP00000328061:V43M	ENSP00000328061:V43M	V	+	1	0	C17orf74	7269858	0.000000	0.05858	0.002000	0.10522	0.559000	0.35586	-1.738000	0.01842	-0.695000	0.05105	-0.339000	0.08088	GTG	G|0.872;A|0.128	0.128	strong		0.552	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734	
GBP3	2635	hgsc.bcm.edu	37	1	89478868	89478868	+	Splice_Site	SNP	G	G	A	rs113490655	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89478868G>A	ENST00000370481.4	-	6	1088	c.868C>T	c.(868-870)Cgt>Tgt	p.R290C	GBP3_ENST00000475853.2_5'Flank	NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	324	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.R290C(1)		breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		GGGGACTTACGAGGCCCATTG	0.463													.|||	676	0.134984	0.0098	0.1513	5008	,	,		19236	0.1677		0.1879	False		,,,				2504	0.2045				p.R290C		Atlas-SNP	.											GBP3,NS,carcinoma,0,1	GBP3	53	1	1	Substitution - Missense(1)	stomach(1)	c.C868T						PASS	.	G	CYS/ARG	185,4221	119.6+/-157.3	5,175,2023	112.0	102.0	106.0		868	3.8	0.8	1	dbSNP_132	106	1661,6939	308.0+/-308.7	156,1349,2795	yes	missense-near-splice	GBP3	NM_018284.2	180	161,1524,4818	AA,AG,GG		19.314,4.1988,14.1934	possibly-damaging	290/596	89478868	1846,11160	2203	4300	6503	SO:0001630	splice_region_variant	2635	exon6			ACTTACGAGGCCC	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.868+1C>T	1.37:g.89478868G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	208	118	0.567308	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	309	0.14148351648351648	5	0.01016260162601626	58	0.16022099447513813	92	0.16083916083916083	154	0.20316622691292877	G	18.70	3.680847	0.68042	0.041988	0.19314	ENSG00000117226	ENST00000370482;ENST00000370481;ENST00000235878	T	0.02323	4.34	3.85	3.85	0.44370	Guanylate-binding protein, C-terminal (3);	0.289745	0.31188	N	0.008088	T	0.06050	0.0157	M	0.85041	2.73	0.26906	P	0.9670115	D;D	0.58970	0.984;0.965	P;P	0.54210	0.745;0.673	T	0.02632	-1.1131	8	.	.	.	.	11.4749	0.50291	0.0:0.0:1.0:0.0	.	156;290	F6X827;Q9H0R5	.;GBP3_HUMAN	C	258;290;290	ENSP00000359512:R290C	.	R	-	1	0	GBP3	89251456	0.847000	0.29606	0.848000	0.33437	0.401000	0.30781	1.032000	0.30178	2.154000	0.67381	0.514000	0.50259	CGT	G|0.857;A|0.143	0.143	strong		0.463	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	Missense_Mutation
TPO	7173	hgsc.bcm.edu	37	2	1520676	1520676	+	Missense_Mutation	SNP	T	T	C	rs1126799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:1520676T>C	ENST00000345913.4	+	15	2631	c.2540T>C	c.(2539-2541)gTg>gCg	p.V847A	TPO_ENST00000329066.4_Missense_Mutation_p.V847A|TPO_ENST00000346956.3_Missense_Mutation_p.V803A|TPO_ENST00000382201.3_Missense_Mutation_p.V790A|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000337415.3_Missense_Mutation_p.V847A|TPO_ENST00000349624.3_Missense_Mutation_p.V674A|TPO_ENST00000382198.1_Missense_Mutation_p.V674A	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	847			V -> A (in dbSNP:rs1126799). {ECO:0000269|PubMed:12454013, ECO:0000269|PubMed:3453124, ECO:0000269|PubMed:3475693, ECO:0000269|Ref.6}.		cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.V847A(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CTCCCTCGGGTGACTTGGATC	0.592													C|||	3325	0.663938	0.8283	0.6037	5008	,	,		18488	0.5833		0.5417	False		,,,				2504	0.6933				p.V847A		Atlas-SNP	.											TPO,NS,carcinoma,0,1	TPO	224	1	1	Substitution - Missense(1)	stomach(1)	c.T2540C						PASS	.	C	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	3398,1008	373.4+/-320.8	1303,792,108	68.0	71.0	70.0		2540,2540,2369,2369,2408,2021	4.6	0.1	2	dbSNP_86	70	4578,4022	555.0+/-386.6	1207,2164,929	yes	missense,missense,missense,missense,missense,missense	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	64,64,64,64,64,64	2510,2956,1037	CC,CT,TT		46.7674,22.8779,38.6745	benign,benign,benign,benign,benign,benign	847/934,847/934,790/877,790/877,803/890,674/761	1520676	7976,5030	2203	4300	6503	SO:0001583	missense	7173	exon15			CTCGGGTGACTTG		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2540T>C	2.37:g.1520676T>C	ENSP00000318820:p.Val847Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	1334|1334	0.6108058608058609|0.6108058608058609	388|388	0.7886178861788617|0.7886178861788617	209|209	0.5773480662983426|0.5773480662983426	344|344	0.6013986013986014|0.6013986013986014	393|393	0.5184696569920845|0.5184696569920845	C|C	0.007|0.007	-1.960539|-1.960539	0.00465|0.00465	0.771221|0.771221	0.532326|0.532326	ENSG00000115705|ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607;ENST00000425083|ENST00000446278	T;T;T;T;T;T;T;T;T;T|.	0.68025|.	-0.13;-0.12;-0.06;0.16;-0.12;-0.07;0.16;-0.12;0.71;-0.3|.	5.52|5.52	4.6|4.6	0.57074|0.57074	.|.	1.004770|.	0.08016|.	N|.	0.991268|.	T|.	0.00012|.	0.0000|.	N|N	0.00325|0.00325	-1.645|-1.645	0.42496|0.42496	P|P	0.0070829999999999504|0.0070829999999999504	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.0;0.001;0.001;0.0|.	T|.	0.27157|.	-1.0082|.	9|.	0.02654|.	T|.	1|.	-21.4253|-21.4253	8.8585|8.8585	0.35242|0.35242	0.0:0.7477:0.1631:0.0892|0.0:0.7477:0.1631:0.0892	rs1126799;rs2276703;rs3182055;rs17723536;rs52825202;rs57954584;rs1126799|rs1126799;rs2276703;rs3182055;rs17723536;rs52825202;rs57954584;rs1126799	803;674;790;847|.	P07202-4;P07202-5;P07202-2;P07202|.	.;.;.;PERT_HUMAN|.	A|R	847;847;803;674;847;790;674;732;277;68|322	ENSP00000337263:V847A;ENSP00000318820:V847A;ENSP00000263886:V803A;ENSP00000332044:V674A;ENSP00000329869:V847A;ENSP00000371636:V790A;ENSP00000371633:V674A;ENSP00000405788:V732A;ENSP00000419461:V277A;ENSP00000389659:V68A|.	ENSP00000329869:V847A|.	V|X	+|+	2|1	0|0	TPO|TPO	1499683|1499683	0.164000|0.164000	0.22935|0.22935	0.064000|0.064000	0.19789|0.19789	0.001000|0.001000	0.01503|0.01503	0.609000|0.609000	0.24238|0.24238	1.364000|1.364000	0.46038|0.46038	-0.124000|-0.124000	0.14976|0.14976	GTG|TGA	A|0.003;C|0.612	0.612	strong		0.592	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
HSPB2	3316	hgsc.bcm.edu	37	11	111784229	111784229	+	Silent	SNP	C	C	T	rs4252588	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:111784229C>T	ENST00000304298.3	+	2	747	c.159C>T	c.(157-159)gcC>gcT	p.A53A	CRYAB_ENST00000526180.1_5'Flank|HSPB2_ENST00000537382.1_Silent_p.A53A|CRYAB_ENST00000525823.1_5'Flank|CRYAB_ENST00000227251.3_5'Flank|HSPB2-C11orf52_ENST00000534100.1_Intron|CRYAB_ENST00000533280.1_5'Flank|CRYAB_ENST00000531198.1_5'Flank|CRYAB_ENST00000533971.1_5'Flank|CRYAB_ENST00000527950.1_Intron|CRYAB_ENST00000533475.1_Intron	NM_001541.3	NP_001532.1	Q16082	HSPB2_HUMAN	heat shock 27kDa protein 2	53					positive regulation of catalytic activity (GO:0043085)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)	p.A53A(1)		large_intestine(2)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_cancers(61;3.75e-11)|all_epithelial(67;2.33e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;3.57e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.57e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.051)		GGCCTCGGGCCGCCCCAGCTG	0.622													C|||	341	0.0680911	0.1293	0.0461	5008	,	,		16397	0.001		0.0577	False		,,,				2504	0.0808				p.A53A		Atlas-SNP	.											.	HSPB2	20	.	1	Substitution - coding silent(1)	lung(1)	c.C159T						PASS	.	C		504,3898	233.6+/-246.7	33,438,1730	112.0	124.0	120.0		159	-4.8	0.0	11	dbSNP_111	120	608,7986	158.6+/-212.1	22,564,3711	no	coding-synonymous	HSPB2	NM_001541.3		55,1002,5441	TT,TC,CC		7.0747,11.4493,8.5565		53/183	111784229	1112,11884	2201	4297	6498	SO:0001819	synonymous_variant	3316	exon2			TCGGGCCGCCCCA	U75898	CCDS8352.1	11q22-q23	2011-09-02	2002-08-29			ENSG00000170276		"""Heat shock proteins / HSPB"""	5247	protein-coding gene	gene with protein product		602179	"""heat shock 27kD protein 2"""			9344664, 9490724	Standard	NM_001541		Approved	Hs.78846, MKBP	uc001pmg.2	Q16082		ENST00000304298.3:c.159C>T	11.37:g.111784229C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_001541	Q6I9U7	Silent	SNP	ENST00000304298.3	37	CCDS8352.1																																																																																			C|0.914;T|0.086	0.086	strong		0.622	HSPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391669.1		
CFAP70	118491	hgsc.bcm.edu	37	10	75053071	75053071	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:75053071C>T	ENST00000310715.3	-	17	2050	c.1930G>A	c.(1930-1932)Gaa>Aaa	p.E644K	TTC18_ENST00000394865.1_Missense_Mutation_p.E644K|TTC18_ENST00000355577.3_Missense_Mutation_p.E113K|TTC18_ENST00000401621.2_Missense_Mutation_p.E644K|TTC18_ENST00000340329.3_Intron|TTC18_ENST00000493787.1_5'UTR	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		644						extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					ACTTCTGCTTCAAATGCAAAG	0.378																																					p.E644K		Atlas-SNP	.											.	TTC18	106	.	0			c.G1930A						PASS	.						121.0	106.0	111.0					10																	75053071		2203	4300	6503	SO:0001583	missense	118491	exon17			CTGCTTCAAATGC																												ENST00000310715.3:c.1930G>A	10.37:g.75053071C>T	ENSP00000310829:p.Glu644Lys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	113	5	0.0442478	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	C	33	5.207975	0.95033	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23	5.63	5.63	0.86233	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.96191	0.8758	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96140	0.9099	10	0.59425	D	0.04	-0.2715	17.1754	0.86840	0.0:1.0:0.0:0.0	.	644	Q5T0N1	TTC18_HUMAN	K	644;644;644;51;644	ENSP00000310829:E644K;ENSP00000384479:E644K;ENSP00000409527:E51K;ENSP00000378334:E644K	ENSP00000310829:E644K	E	-	1	0	TTC18	74723077	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.093000	0.71422	2.632000	0.89209	0.557000	0.71058	GAA	.	.	none		0.378	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
EIF3F	8665	hgsc.bcm.edu	37	11	8009241	8009241	+	Silent	SNP	C	C	T	rs12421289	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:8009241C>T	ENST00000533626.1	+	3	968	c.342C>T	c.(340-342)gcC>gcT	p.A114A	EIF3F_ENST00000309828.4_Silent_p.A114A|EIF3F_ENST00000537635.1_Silent_p.A129A|EIF3F_ENST00000449102.2_5'UTR					eukaryotic translation initiation factor 3, subunit F											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)	13				Epithelial(150;1.44e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGGGTGCTGCCCGAGTTATCG	0.542											OREG0020726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	338	0.067492	0.0424	0.0994	5008	,	,		19051	0.001		0.1829	False		,,,				2504	0.0286				p.A114A		Atlas-SNP	.											.	EIF3F	23	.	0			c.C342T						PASS	.	C		253,4147		8,237,1955	14.0	15.0	15.0		342	2.9	1.0	11	dbSNP_120	15	1506,7080		132,1242,2919	no	coding-synonymous	EIF3F	NM_003754.2		140,1479,4874	TT,TC,CC		17.5402,5.75,13.5454		114/358	8009241	1759,11227	2200	4293	6493	SO:0001819	synonymous_variant	8665	exon1			TGCTGCCCGAGTT	U94855, AK093511	CCDS7785.1	11p15.4	2010-03-10	2007-07-27	2007-07-27	ENSG00000175390	ENSG00000175390			3275	protein-coding gene	gene with protein product		603914	"""eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa"""	EIF3S5		9341143	Standard	NM_003754		Approved	eIF3-epsilon, eIF3-p47, eIF3f	uc001mfw.3	O00303		ENST00000533626.1:c.342C>T	11.37:g.8009241C>T		Somatic	100	0	0	646	WXS	Illumina HiSeq	Phase_I	111	109	0.981982	NM_003754		Silent	SNP	ENST00000533626.1	37	CCDS7785.1																																																																																			C|0.889;T|0.111	0.111	strong		0.542	EIF3F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385713.2	NM_003754	
PLEC	5339	hgsc.bcm.edu	37	8	144994888	144994888	+	Missense_Mutation	SNP	G	G	A	rs35858667	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144994888G>A	ENST00000322810.4	-	32	9681	c.9512C>T	c.(9511-9513)gCg>gTg	p.A3171V	PLEC_ENST00000398774.2_Missense_Mutation_p.A3002V|PLEC_ENST00000345136.3_Missense_Mutation_p.A3034V|PLEC_ENST00000354589.3_Missense_Mutation_p.A3034V|PLEC_ENST00000354958.2_Missense_Mutation_p.A3012V|PLEC_ENST00000436759.2_Missense_Mutation_p.A3061V|PLEC_ENST00000527096.1_Missense_Mutation_p.A3057V|PLEC_ENST00000356346.3_Missense_Mutation_p.A3020V|PLEC_ENST00000357649.2_Missense_Mutation_p.A3038V	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3171	Globular 2.		A -> V (in dbSNP:rs35858667).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CTTCTGCCCCGCCTCCTCCAG	0.652													G|||	138	0.0275559	0.003	0.0519	5008	,	,		15310	0.0		0.0905	False		,,,				2504	0.0072				p.A3171V		Atlas-SNP	.											.	PLEC	1144	.	0			c.C9512T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	59,4135		0,59,2038	27.0	33.0	31.0		9182,9059,9035,9512,9005,9101,9113,9101	2.8	0.9	8	dbSNP_126	31	611,7749		16,579,3585	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	64,64,64,64,64,64,64,64	16,638,5623	AA,AG,GG		7.3086,1.4068,5.3369	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	3061/4575,3020/4534,3012/4526,3171/4685,3002/4516,3034/4548,3038/4552,3034/4548	144994888	670,11884	2097	4180	6277	SO:0001583	missense	5339	exon32			TGCCCCGCCTCCT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.9512C>T	8.37:g.144994888G>A	ENSP00000323856:p.Ala3171Val	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	89	0.04075091575091575	3	0.006097560975609756	20	0.055248618784530384	2	0.0034965034965034965	64	0.08443271767810026	G	3.399	-0.122623	0.06795	0.014068	0.073086	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68	3.8	2.84	0.33178	.	0.287896	0.26355	U	0.024843	T	0.05960	0.0155	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B;B;B;B	0.22604	0.021;0.072;0.021;0.026;0.021;0.021;0.021;0.021	B;B;B;B;B;B;B;B	0.22601	0.024;0.024;0.024;0.04;0.024;0.024;0.024;0.024	T	0.32798	-0.9893	10	0.72032	D	0.01	.	12.5533	0.56240	0.0:0.2571:0.7429:0.0	rs35858667	3061;3020;3012;3171;3002;3034;3038;3034	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	V	3034;3038;3034;3002;3171;3012;3020;3061;3057	ENSP00000344848:A3034V;ENSP00000350277:A3038V;ENSP00000346602:A3034V;ENSP00000381756:A3002V;ENSP00000323856:A3171V;ENSP00000347044:A3012V;ENSP00000348702:A3020V;ENSP00000388180:A3061V;ENSP00000434583:A3057V	ENSP00000323856:A3171V	A	-	2	0	PLEC	145066876	0.394000	0.25246	0.886000	0.34754	0.194000	0.23727	3.149000	0.50655	1.849000	0.53698	0.448000	0.29417	GCG	G|0.944;A|0.056	0.056	strong		0.652	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
MTO1	25821	hgsc.bcm.edu	37	6	74190448	74190448	+	Silent	SNP	T	T	C	rs2036039	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:74190448T>C	ENST00000370300.4	+	8	1345	c.1255T>C	c.(1255-1257)Ttg>Ctg	p.L419L	MTO1_ENST00000498286.1_Silent_p.L394L|MTO1_ENST00000415954.2_Silent_p.L394L|MTO1_ENST00000370305.1_Silent_p.L345L	NM_012123.3|NM_133645.2	NP_036255.2|NP_598400.1	Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	419					mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)	p.L419L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						CACCCCTTCCTTGGAGACTCA	0.418													C|||	1042	0.208067	0.2693	0.1758	5008	,	,		19156	0.2123		0.1849	False		,,,				2504	0.1677				p.L419L		Atlas-SNP	.											MTO1,NS,carcinoma,0,1	MTO1	59	1	1	Substitution - coding silent(1)	stomach(1)	c.T1255C						PASS	.	C	,,	1141,3265	715.4+/-408.5	149,843,1211	183.0	165.0	171.0		1180,1180,1255	5.2	0.7	6	dbSNP_94	171	1541,7059	746.9+/-407.3	136,1269,2895	no	coding-synonymous,coding-synonymous,coding-synonymous	MTO1	NM_001123226.1,NM_012123.3,NM_133645.2	,,	285,2112,4106	CC,CT,TT		17.9186,25.8965,20.6213	,,	394/733,394/693,419/718	74190448	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	25821	exon8			CCTTCCTTGGAGA	AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297			19261	protein-coding gene	gene with protein product		614667	"""mitochondrial translation optimization 1 homolog (S. cerevisiae)"""			12011058, 22608499	Standard	NM_012123		Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000370300.4:c.1255T>C	6.37:g.74190448T>C		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	192	85	0.442708	NM_133645	B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	Silent	SNP	ENST00000370300.4	37	CCDS4979.1																																																																																			T|0.668;G|0.032;C|0.170;N|0.000;A|0.130	0.170	strong		0.418	MTO1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041215.2	NM_012123	
MICALCL	84953	hgsc.bcm.edu	37	11	12379949	12379949	+	Missense_Mutation	SNP	C	C	T	rs34898047	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:12379949C>T	ENST00000256186.2	+	9	2302	c.2011C>T	c.(2011-2013)Cgc>Tgc	p.R671C		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	671					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		AGAGGAACAACGCATCAGAGA	0.493													C|||	29	0.00579073	0.0008	0.0101	5008	,	,		17452	0.001		0.0189	False		,,,				2504	0.001				p.R671C		Atlas-SNP	.											.	MICALCL	59	.	0			c.C2011T						PASS	.	C	CYS/ARG	7,3929		0,7,1961	225.0	225.0	225.0		2011	4.3	0.7	11	dbSNP_126	225	132,8158		0,132,4013	yes	missense	MICALCL	NM_032867.2	180	0,139,5974	TT,TC,CC		1.5923,0.1778,1.1369	probably-damaging	671/696	12379949	139,12087	1968	4145	6113	SO:0001583	missense	84953	exon9			GAACAACGCATCA	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.2011C>T	11.37:g.12379949C>T	ENSP00000256186:p.Arg671Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	NM_032867	Q7RTP7|Q96JU6	Missense_Mutation	SNP	ENST00000256186.2	37	CCDS41620.1	16	0.007326007326007326	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	10	0.013192612137203167	C	17.09	3.301535	0.60195	0.001778	0.015923	ENSG00000133808	ENST00000256186	T	0.53640	0.61	5.33	4.35	0.52113	Domain of unknown function DUF3585 (1);	0.000000	0.26248	U	0.025469	T	0.58722	0.2142	M	0.92604	3.325	0.40653	D	0.982057	D	0.89917	1.0	D	0.83275	0.996	T	0.74870	-0.3517	10	0.87932	D	0	.	10.2888	0.43584	0.3728:0.6272:0.0:0.0	rs34898047	671	Q6ZW33	MICLK_HUMAN	C	671	ENSP00000256186:R671C	ENSP00000256186:R671C	R	+	1	0	MICALCL	12336525	1.000000	0.71417	0.735000	0.30896	0.623000	0.37688	3.076000	0.50081	2.479000	0.83701	0.655000	0.94253	CGC	C|0.986;T|0.014	0.014	strong		0.493	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
HIPK2	28996	hgsc.bcm.edu	37	7	139415775	139415775	+	Silent	SNP	G	G	C	rs7456421	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:139415775G>C	ENST00000406875.3	-	2	1153	c.1059C>G	c.(1057-1059)gtC>gtG	p.V353V	HIPK2_ENST00000342645.6_Silent_p.V353V|HIPK2_ENST00000428878.2_Silent_p.V353V	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	353	Interaction with DAXX.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					CAGCCTTGGAGACGTGGCTGG	0.512													C|||	1986	0.396565	0.7995	0.4784	5008	,	,		21469	0.2669		0.2127	False		,,,				2504	0.1166				p.V353V		Atlas-SNP	.											.	HIPK2	192	.	0			c.C1059G						PASS	.	C	,	2196,940		777,642,149	93.0	79.0	83.0		1059,1059	3.2	1.0	7	dbSNP_116	83	1421,5743		125,1171,2286	yes	coding-synonymous,coding-synonymous	HIPK2	NM_001113239.2.dup,NM_022740.4.dup	,	902,1813,2435	CC,CG,GG		19.8353,29.9745,35.1165	,	353/368,353/368	139415775	3617,6683	1568	3582	5150	SO:0001819	synonymous_variant	28996	exon2			CTTGGAGACGTGG	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"""homeodomain-interacting protein kinase 2"""			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1059C>G	7.37:g.139415775G>C		Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	252	136	0.539683	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Silent	SNP	ENST00000406875.3	37																																																																																				G|0.630;C|0.370	0.370	strong		0.512	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740	
SMG6	23293	hgsc.bcm.edu	37	17	2203175	2203175	+	Missense_Mutation	SNP	C	C	G	rs1885986	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:2203175C>G	ENST00000263073.6	-	2	922	c.872G>C	c.(871-873)cGa>cCa	p.R291P	SMG6_ENST00000544865.1_Missense_Mutation_p.R260P	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	291	Interaction with telomeric DNA.		R -> P (in dbSNP:rs1885986). {ECO:0000269|PubMed:9872452}.		gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CTTCTTCAGTCGTGGCCTCTC	0.552													C|||	925	0.184704	0.0318	0.4222	5008	,	,		17225	0.0893		0.3569	False		,,,				2504	0.1442				p.R291P	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.G872C						PASS	.	C	PRO/ARG,PRO/ARG	321,4085	169.4+/-200.1	15,291,1897	84.0	74.0	78.0		779,872	5.3	1.0	17	dbSNP_92	78	3091,5509	473.3+/-368.6	554,1983,1763	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	103,103	569,2274,3660	GG,GC,CC		35.9419,7.2855,26.234	probably-damaging,probably-damaging	260/1389,291/1420	2203175	3412,9594	2203	4300	6503	SO:0001583	missense	23293	exon2			TTCAGTCGTGGCC	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.872G>C	17.37:g.2203175C>G	ENSP00000263073:p.Arg291Pro	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	512	0.23443223443223443	21	0.042682926829268296	155	0.4281767955801105	75	0.13111888111888112	261	0.34432717678100266	C	15.57	2.871802	0.51695	0.072855	0.359419	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.10288	2.89;2.89	5.35	5.35	0.76521	.	0.282865	0.34245	N	0.004131	T	0.00012	0.0000	L	0.29908	0.895	0.46011	P	0.0011879999999999669	D	0.71674	0.998	D	0.64042	0.921	T	0.55283	-0.8165	9	0.54805	T	0.06	-3.0807	19.0567	0.93069	0.0:1.0:0.0:0.0	rs1885986;rs3744273;rs1885986	291	Q86US8	EST1A_HUMAN	P	291;260	ENSP00000263073:R291P;ENSP00000443920:R260P	ENSP00000263073:R291P	R	-	2	0	SMG6	2149925	0.963000	0.33076	0.997000	0.53966	0.976000	0.68499	3.931000	0.56529	2.490000	0.84030	0.655000	0.94253	CGA	C|0.743;G|0.257	0.257	strong		0.552	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
C6orf201	404220	hgsc.bcm.edu	37	6	4122249	4122249	+	Missense_Mutation	SNP	C	C	A	rs643232	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:4122249C>A	ENST00000380175.4	+	4	1116	c.351C>A	c.(349-351)aaC>aaA	p.N117K	ECI2_ENST00000413766.2_Intron|ECI2_ENST00000380118.3_Intron|ECI2_ENST00000465828.1_Intron|C6orf201_ENST00000430835.2_Missense_Mutation_p.N117K|ECI2_ENST00000380125.2_Intron|C6orf201_ENST00000333388.5_Missense_Mutation_p.N120K|ECI2_ENST00000361538.2_Intron	NM_001085401.2	NP_001078870.1	Q7Z4U5	CF201_HUMAN	chromosome 6 open reading frame 201	117			N -> K (in dbSNP:rs643232). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.							central_nervous_system(1)|endometrium(3)|lung(2)	6	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				AACTGAGAAACCTGCCAACAA	0.378													A|||	1610	0.321486	0.3404	0.3602	5008	,	,		15599	0.3591		0.332	False		,,,				2504	0.2188				p.N117K		Atlas-SNP	.											.	C6orf201	17	.	0			c.C351A						PASS	.	A	LYS/ASN,,,	1209,2503		203,803,850	78.0	73.0	75.0		351,,,	-1.7	0.0	6	dbSNP_83	75	2488,5730		382,1724,2003	yes	missense,intron,intron,intron	ECI2,C6orf201	NM_001085401.1,NM_001166010.1,NM_006117.2,NM_206836.2	94,,,	585,2527,2853	AA,AC,CC		30.275,32.57,30.9891	benign,,,	117/141,,,	4122249	3697,8233	1856	4109	5965	SO:0001583	missense	404220	exon4			GAGAAACCTGCCA	BC047663	CCDS43419.1	6p25.2	2012-02-21			ENSG00000185689	ENSG00000185689			21620	protein-coding gene	gene with protein product							Standard	NM_001085401		Approved	dJ1013A10.5	uc003mwa.4	Q7Z4U5	OTTHUMG00000014160	ENST00000380175.4:c.351C>A	6.37:g.4122249C>A	ENSP00000420610:p.Asn117Lys	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	234	234	1	NM_001085401	A6NLI6|Q6NXN5	Missense_Mutation	SNP	ENST00000380175.4	37	CCDS43419.1	753|753	0.3447802197802198|0.3447802197802198	153|153	0.31097560975609756|0.31097560975609756	130|130	0.35911602209944754|0.35911602209944754	210|210	0.36713286713286714|0.36713286713286714	260|260	0.34300791556728233|0.34300791556728233	A|A	0.005|0.005	-2.123401|-2.123401	0.00346|0.00346	0.3257|0.3257	0.30275|0.30275	ENSG00000185689|ENSG00000185689	ENST00000333388;ENST00000380175;ENST00000427996;ENST00000451679;ENST00000430835|ENST00000541127	T;T;T;T;T|.	0.50813|.	2.01;2.01;0.73;2.01;1.81|.	2.54|2.54	-1.7|-1.7	0.08159|0.08159	.|.	.|3.055170	.|0.01408	.|N	.|0.013894	T|T	0.02929|0.02929	0.0087|0.0087	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.10428|0.10428	-1.0630|-1.0630	8|6	0.05525|0.02654	T|T	0.97|1	.|.	4.3166|4.3166	0.10997|0.10997	0.3732:0.2021:0.4247:0.0|0.3732:0.2021:0.4247:0.0	rs643232;rs643232|rs643232;rs643232	117;117|.	B4DXB2;Q7Z4U5|.	.;CF201_HUMAN|.	K|T	120;117;120;117;117|192	ENSP00000330777:N120K;ENSP00000420610:N117K;ENSP00000419568:N120K;ENSP00000420763:N117K;ENSP00000396912:N117K|.	ENSP00000330777:N120K|ENSP00000439073:P192T	N|P	+|+	3|1	2|0	C6orf201|C6orf201	4067248|4067248	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	0.085000|0.085000	0.14912|0.14912	-0.784000|-0.784000	0.04528|0.04528	-0.363000|-0.363000	0.07495|0.07495	AAC|CCT	C|0.679;A|0.321	0.321	strong		0.378	C6orf201-001	KNOWN	NMD_exception|basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000314019.2	NM_001085401	
KIAA1551	55196	hgsc.bcm.edu	37	12	32137447	32137447	+	Silent	SNP	C	C	T	rs3759300	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:32137447C>T	ENST00000312561.4	+	4	3972	c.3558C>T	c.(3556-3558)ccC>ccT	p.P1186P	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1186																	AAGGAGTACCCCAGTGTCAGT	0.448													C|||	620	0.123802	0.0106	0.0879	5008	,	,		20430	0.2321		0.1382	False		,,,				2504	0.1759				p.P1186P		Atlas-SNP	.											.	.	.	.	0			c.C3558T						PASS	.	C		133,4273	95.7+/-134.4	0,133,2070	134.0	127.0	130.0		3558	1.4	0.2	12	dbSNP_107	130	1204,7396	243.5+/-273.1	83,1038,3179	no	coding-synonymous	C12orf35	NM_018169.3		83,1171,5249	TT,TC,CC		14.0,3.0186,10.2799		1186/1748	32137447	1337,11669	2203	4300	6503	SO:0001819	synonymous_variant	55196	exon4			AGTACCCCAGTGT	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3558C>T	12.37:g.32137447C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	37	CCDS8725.2																																																																																			C|0.883;T|0.117	0.117	strong		0.448	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
TTC3	7267	hgsc.bcm.edu	37	21	38568308	38568308	+	Silent	SNP	C	C	T	rs6579	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:38568308C>T	ENST00000399017.2	+	42	8297	c.5550C>T	c.(5548-5550)caC>caT	p.H1850H	TTC3_ENST00000355666.1_Silent_p.H1850H|TTC3_ENST00000354749.2_Silent_p.H1850H|TTC3_ENST00000479930.1_3'UTR|TTC3-AS1_ENST00000424733.1_RNA	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1850					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TTATTGAGCACCTGTCAGTGG	0.443													C|||	2965	0.592053	0.6445	0.6282	5008	,	,		19670	0.6032		0.4642	False		,,,				2504	0.6155				p.H1850H	Ovarian(38;194 1649 35661)	Atlas-SNP	.											TTC3,NS,carcinoma,+1,1	TTC3	182	1	0			c.C5550T						PASS	.	C	,	2767,1637	635.0+/-396.3	869,1029,304	46.0	56.0	53.0		5550,5550	1.3	0.6	21	dbSNP_52	53	3845,4755	518.9+/-379.4	898,2049,1353	no	coding-synonymous,coding-synonymous	TTC3	NM_001001894.1,NM_003316.3	,	1767,3078,1657	TT,TC,CC		44.7093,37.1708,49.1541	,	1850/2026,1850/2026	38568308	6612,6392	2202	4300	6502	SO:0001819	synonymous_variant	7267	exon42			TGAGCACCTGTCA	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5550C>T	21.37:g.38568308C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	121	119	0.983471	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1	1238	0.5668498168498168	315	0.6402439024390244	219	0.6049723756906077	357	0.6241258741258742	347	0.4577836411609499	C	8.684	0.905837	0.17760	0.628292	0.447093	ENSG00000182670	ENST00000428693	.	.	.	4.34	1.26	0.21427	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999727439	.	.	.	.	.	.	T	0.42766	-0.9432	3	.	.	.	-3.1681	5.8525	0.18701	0.0:0.5031:0.3875:0.1093	rs6579;rs762138;rs1053981;rs3194540;rs59448802;rs6579	.	.	.	S	142	.	.	P	+	1	0	TTC3	37490178	0.995000	0.38212	0.614000	0.29051	0.859000	0.49053	0.114000	0.15520	0.337000	0.23665	0.467000	0.42956	CCT	C|0.476;T|0.524	0.524	strong		0.443	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
ROCK1	6093	hgsc.bcm.edu	37	18	18534948	18534948	+	Missense_Mutation	SNP	G	G	C	rs201390233		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:18534948G>C	ENST00000399799.2	-	31	4589	c.3649C>G	c.(3649-3651)Caa>Gaa	p.Q1217E		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	1217	Auto-inhibitory.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		Q -> E (in dbSNP:rs2847092). {ECO:0000269|PubMed:17344846}.		actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.Q1217E(1)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TTTTCAGCTTGTTGTACTGGT	0.363																																					p.Q1217E		Atlas-SNP	.											ROCK1_ENST00000399799,NS,carcinoma,0,1	ROCK1	162	1	1	Substitution - Missense(1)	prostate(1)	c.C3649G						scavenged	.						121.0	99.0	107.0					18																	18534948		2203	4300	6503	SO:0001583	missense	6093	exon31			CAGCTTGTTGTAC		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.3649C>G	18.37:g.18534948G>C	ENSP00000382697:p.Gln1217Glu	Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	280	35	0.125	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	G	6.245	0.413238	0.11812	.	.	ENSG00000067900	ENST00000399799	T	0.63255	-0.03	5.43	5.43	0.79202	Pleckstrin homology domain (3);	0.060893	0.64402	D	0.000002	T	0.47248	0.1435	N	0.16903	0.455	0.47659	D	0.999489	B	0.27264	0.173	B	0.32022	0.139	T	0.44711	-0.9310	10	0.02654	T	1	.	19.2276	0.93824	0.0:0.0:1.0:0.0	.	1217	Q13464	ROCK1_HUMAN	E	1217	ENSP00000382697:Q1217E	ENSP00000382697:Q1217E	Q	-	1	0	ROCK1	16788946	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.303000	0.65738	2.530000	0.85305	0.543000	0.68304	CAA	G|0.985;C|0.015	0.015	strong		0.363	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144875979	144875979	+	Silent	SNP	G	G	C	rs71664005	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:144875979G>C	ENST00000369354.3	-	29	4890	c.4701C>G	c.(4699-4701)ctC>ctG	p.L1567L	PDE4DIP_ENST00000530740.1_Silent_p.L1703L|AL138796.1_ENST00000582173.1_RNA|PDE4DIP_ENST00000369356.4_Silent_p.L1567L|PDE4DIP_ENST00000313382.9_Silent_p.L1523L|PDE4DIP_ENST00000369359.4_Silent_p.L1703L|RP4-791M13.5_ENST00000531288.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1567	NBPF. {ECO:0000255|PROSITE- ProRule:PRU00647}.				cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGAATTACCTGAGGGCCAGTG	0.468			T	PDGFRB	MPD																																p.L1567L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C4701G						PASS	.	G	,,	210,4196		0,210,1993	224.0	225.0	225.0		4569,4701,4701	4.2	1.0	1	dbSNP_130	225	1462,7130		0,1462,2834	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,1672,4827	CC,CG,GG		17.0158,4.7662,12.8635	,,	1523/2241,1567/2363,1567/2347	144875979	1672,11326	2203	4296	6499	SO:0001819	synonymous_variant	9659	exon29			TTACCTGAGGGCC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.4701C>G	1.37:g.144875979G>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	136	35	0.257353	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1																																																																																			G|0.216;C|0.784	0.784	strong		0.468	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
COL15A1	1306	hgsc.bcm.edu	37	9	101778272	101778272	+	Missense_Mutation	SNP	A	A	C	rs35250850	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:101778272A>C	ENST00000375001.3	+	11	1941	c.1518A>C	c.(1516-1518)gaA>gaC	p.E506D		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	506	4 X tandem repeats.|Nonhelical region 1 (NC1).		E -> D (in dbSNP:rs35250850).		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CTGGTGATGAAGAAGACTTGG	0.597													A|||	320	0.0638978	0.1135	0.036	5008	,	,		16463	0.001		0.1004	False		,,,				2504	0.044				p.E506D		Atlas-SNP	.											.	COL15A1	211	.	0			c.A1518C						PASS	.	A	ASP/GLU	403,4003	196.0+/-220.5	15,373,1815	57.0	55.0	56.0		1518	-1.0	0.0	9	dbSNP_126	56	705,7895	170.0+/-221.2	30,645,3625	yes	missense	COL15A1	NM_001855.3	45	45,1018,5440	CC,CA,AA		8.1977,9.1466,8.5191	benign	506/1389	101778272	1108,11898	2203	4300	6503	SO:0001583	missense	1306	exon11			TGATGAAGAAGAC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1518A>C	9.37:g.101778272A>C	ENSP00000364140:p.Glu506Asp	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	131	0.059981684981684984	43	0.08739837398373984	15	0.04143646408839779	1	0.0017482517482517483	72	0.09498680738786279	A	4.651	0.121027	0.08881	0.091466	0.081977	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.89681	-2.55	3.08	-1.03	0.10102	.	4.968620	0.01193	N	0.007377	T	0.19765	0.0475	L	0.48642	1.525	0.09310	N	1	B	0.28026	0.198	B	0.24006	0.05	T	0.51764	-0.8664	10	0.16420	T	0.52	.	6.0688	0.19877	0.5556:0.0:0.4444:0.0	rs35250850;rs62561254	506	P39059	COFA1_HUMAN	D	506;476	ENSP00000364140:E506D	ENSP00000364140:E506D	E	+	3	2	COL15A1	100818093	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.241000	0.02911	-0.312000	0.08741	-0.267000	0.10333	GAA	A|0.927;C|0.073	0.073	strong		0.597	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
PCDHGB1	56104	hgsc.bcm.edu	37	5	140731408	140731408	+	Silent	SNP	A	A	G	rs3749777	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140731408A>G	ENST00000523390.1	+	1	1581	c.1581A>G	c.(1579-1581)acA>acG	p.T527T	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	527	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCGAGCTCACACTGCAGGCCA	0.692													.|||	652	0.130192	0.3139	0.0692	5008	,	,		16730	0.0407		0.0875	False		,,,				2504	0.0613				p.T527T		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.A1581G						PASS	.	G	,,,,	1069,3111		131,807,1152	41.0	49.0	46.0		,,,1581,1581	-4.7	0.3	5	dbSNP_107	46	745,7683		29,687,3498	no	intron,intron,intron,coding-synonymous,coding-synonymous	PCDHGB1,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018922.2,NM_032095.1	,,,,	160,1494,4650	GG,GA,AA		8.8396,25.5742,14.3877	,,,,	,,,527/928,527/811	140731408	1814,10794	2090	4214	6304	SO:0001819	synonymous_variant	56104	exon1			GCTCACACTGCAG	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1581A>G	5.37:g.140731408A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	40	14	0.35	NM_018922	Q3SY75|Q9Y5C8	Silent	SNP	ENST00000523390.1	37	CCDS54923.1																																																																																			A|0.882;G|0.118	0.118	strong		0.692	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
PLXNB3	5365	hgsc.bcm.edu	37	X	153042419	153042419	+	Silent	SNP	G	G	A	rs34966902	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153042419G>A	ENST00000361971.5	+	29	5025	c.4911G>A	c.(4909-4911)agG>agA	p.R1637R	PLXNB3_ENST00000538966.1_Silent_p.R1660R|PLXNB3_ENST00000538776.1_Silent_p.R1290R|SRPK3_ENST00000489426.1_5'UTR	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1637					axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGCCCAGAGGTGCCCCTTGG	0.657													G|||	1516	0.401589	0.3707	0.3026	3775	,	,		8007	0.128		0.501	False		,,,				2504	0.1871				p.R1660R		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G4980A						PASS	.	G	,	1987,1832		458,781,290,389,273	35.0	33.0	34.0		4980,4911	3.1	0.6	X	dbSNP_126	34	4446,2273		1089,1048,1220,290,645	no	coding-synonymous,coding-synonymous	PLXNB3	NM_001163257.1,NM_005393.2	,	1547,1829,1510,679,918	AA,AG,A,GG,G		33.8294,47.9707,38.9543	,	1660/1933,1637/1910	153042419	6433,4105	2191	4292	6483	SO:0001819	synonymous_variant	5365	exon30			CCAGAGGTGCCCC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.4911G>A	X.37:g.153042419G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	235	139	0.591489	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Silent	SNP	ENST00000361971.5	37	CCDS14729.1	774	0.4665461121157324	138	0.359375	81	0.2892857142857143	48	0.09302325581395349	265	0.5115830115830116	G	2.424	-0.332388	0.05314	0.520293	0.661706	ENSG00000198753	ENST00000455214	.	.	.	4.92	3.14	0.36123	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999955812	.	.	.	.	.	.	T	0.40175	-0.9577	3	.	.	.	.	4.3884	0.11328	0.0:0.5533:0.1703:0.2764	rs34966902	.	.	.	M	141	.	.	V	+	1	0	PLXNB3	152695613	0.974000	0.33945	0.624000	0.29186	0.156000	0.22039	0.190000	0.17057	0.434000	0.26340	-0.311000	0.09066	GTG	G|0.439;A|0.561	0.561	strong		0.657	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
CR1	1378	hgsc.bcm.edu	37	1	207787796	207787796	+	Missense_Mutation	SNP	T	T	C	rs61822976		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207787796T>C	ENST00000367049.4	+	40	6623	c.6623T>C	c.(6622-6624)aTg>aCg	p.M2208T	CR1_ENST00000367052.1_Missense_Mutation_p.M1758T|CR1_ENST00000367053.1_Missense_Mutation_p.M1758T|CR1_ENST00000400960.2_Missense_Mutation_p.M1758T|CR1_ENST00000367051.1_Missense_Mutation_p.M1758T	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1758					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.M1758T(1)|p.M2208T(1)|p.M1763T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TTGGCTGGAATGAAAGCCCTT	0.408																																					p.M2208T		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,0,4	CR1	354	4	3	Substitution - Missense(3)	prostate(3)	c.T6623C						scavenged	.						128.0	121.0	123.0					1																	207787796		1882	4112	5994	SO:0001583	missense	1378	exon40			CTGGAATGAAAGC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6623T>C	1.37:g.207787796T>C	ENSP00000356016:p.Met2208Thr	Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	260	16	0.0615385	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	T	3.803	-0.041226	0.07452	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96	4.29	-5.87	0.02297	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.09335	0.0230	N	0.20986	0.625	0.09310	N	1	B;P	0.46457	0.043;0.878	B;B	0.42422	0.009;0.387	T	0.19614	-1.0300	9	0.18276	T	0.48	.	1.2481	0.01977	0.4109:0.0944:0.2677:0.2271	rs61822976	1758;2208	P17927;E9PDY4	CR1_HUMAN;.	T	1758;1758;1758;1758;2208	ENSP00000356019:M1758T;ENSP00000356018:M1758T;ENSP00000356020:M1758T;ENSP00000383744:M1758T;ENSP00000356016:M2208T	ENSP00000356016:M2208T	M	+	2	0	CR1	205854419	0.002000	0.14202	0.000000	0.03702	0.554000	0.35429	-0.327000	0.07955	-0.793000	0.04475	0.358000	0.22013	ATG	.	.	weak		0.408	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
LPCAT1	79888	hgsc.bcm.edu	37	5	1494909	1494909	+	Silent	SNP	C	C	T	rs3733796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1494909C>T	ENST00000283415.3	-	3	531	c.399G>A	c.(397-399)gcG>gcA	p.A133A		NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	133					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		ACGAGTGAGGCGCGAGCGTGA	0.647													C|||	1490	0.297524	0.3086	0.2262	5008	,	,		15040	0.4028		0.1869	False		,,,				2504	0.3384				p.A133A		Atlas-SNP	.											LPCAT1,NS,carcinoma,-1,1	LPCAT1	70	1	0			c.G399A						PASS	.	C		1267,3139	432.0+/-343.1	178,911,1114	83.0	72.0	76.0		399	-10.0	0.1	5	dbSNP_107	76	1609,6991	298.7+/-304.1	159,1291,2850	no	coding-synonymous	LPCAT1	NM_024830.3		337,2202,3964	TT,TC,CC		18.7093,28.7562,22.1129		133/535	1494909	2876,10130	2203	4300	6503	SO:0001819	synonymous_variant	79888	exon3			GTGAGGCGCGAGC	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"""EF-hand domain containing"""	25718	protein-coding gene	gene with protein product		610472	"""acyltransferase like 2"""	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.399G>A	5.37:g.1494909C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Silent	SNP	ENST00000283415.3	37	CCDS3864.1																																																																																			C|0.755;T|0.245	0.245	strong		0.647	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830	
METTL22	79091	hgsc.bcm.edu	37	16	8729124	8729124	+	Missense_Mutation	SNP	G	G	A	rs2302607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:8729124G>A	ENST00000381920.3	+	5	913	c.655G>A	c.(655-657)Gct>Act	p.A219T	METTL22_ENST00000568967.1_3'UTR|METTL22_ENST00000561758.1_Missense_Mutation_p.A163T	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	219			A -> T (in dbSNP:rs2302607).			nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			large_intestine(5)|lung(4)	9						CACGGGGCTCGCTAGCATCAT	0.602													G|||	938	0.1873	0.0159	0.1643	5008	,	,		19165	0.3552		0.2694	False		,,,				2504	0.1779				p.A219T		Atlas-SNP	.											.	METTL22	23	.	0			c.G655A						PASS	.	G	THR/ALA	240,3836		6,228,1804	47.0	52.0	50.0		655	-0.7	0.1	16	dbSNP_100	50	2143,6249		266,1611,2319	yes	missense	METTL22	NM_024109.2	58	272,1839,4123	AA,AG,GG		25.5362,5.8881,19.1129	benign	219/405	8729124	2383,10085	2038	4196	6234	SO:0001583	missense	79091	exon5			GGGCTCGCTAGCA	AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"""chromosome 16 open reading frame 68"""	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.655G>A	16.37:g.8729124G>A	ENSP00000371345:p.Ala219Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_024109	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	37	CCDS10533.2	448|448	0.20512820512820512|0.20512820512820512	10|10	0.02032520325203252|0.02032520325203252	64|64	0.17679558011049723|0.17679558011049723	190|190	0.3321678321678322|0.3321678321678322	184|184	0.24274406332453827|0.24274406332453827	G|G	13.75|13.75	2.330758|2.330758	0.41297|0.41297	0.058881|0.058881	0.255362|0.255362	ENSG00000067365|ENSG00000067365	ENST00000381920|ENST00000163678	T|T	0.06218|0.52526	3.33|0.66	4.99|4.99	-0.687|-0.687	0.11320|0.11320	.|.	0.457915|.	0.23067|.	N|.	0.052306|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04768|0.04768	-0.165|-0.165	0.40923|0.40923	P|P	0.015673999999999966|0.015673999999999966	B|.	0.15141|.	0.012|.	B|.	0.17722|.	0.019|.	T|T	0.40270|0.40270	-0.9572|-0.9572	9|6	0.05721|0.87932	T|D	0.95|0	-4.7758|-4.7758	8.9302|8.9302	0.35666|0.35666	0.5304:0.0:0.4696:0.0|0.5304:0.0:0.4696:0.0	rs2302607;rs17673692;rs60311961;rs2302607|rs2302607;rs17673692;rs60311961;rs2302607	219|.	Q9BUU2|.	MET22_HUMAN|.	T|H	219|205	ENSP00000371345:A219T|ENSP00000163678:R205H	ENSP00000371345:A219T|ENSP00000163678:R205H	A|R	+|+	1|2	0|0	METTL22|METTL22	8636625|8636625	0.873000|0.873000	0.30073|0.30073	0.071000|0.071000	0.20095|0.20095	0.122000|0.122000	0.20287|0.20287	1.572000|1.572000	0.36461|0.36461	-0.119000|-0.119000	0.11830|0.11830	-0.136000|-0.136000	0.14681|0.14681	GCT|CGC	G|0.793;A|0.207	0.207	strong		0.602	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109	
OR10A4	283297	hgsc.bcm.edu	37	11	6898495	6898495	+	Missense_Mutation	SNP	T	T	C	rs2595453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6898495T>C	ENST00000379829.2	+	1	640	c.617T>C	c.(616-618)cTa>cCa	p.L206P		NM_207186.2	NP_997069.2	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A, member 4	206			L -> P (in dbSNP:rs2595453). {ECO:0000269|PubMed:11416212, ECO:0000269|PubMed:11705801, ECO:0000269|PubMed:12213199}.		axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|liver(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GCCACTGTCCTATTCATTCTC	0.507													T|||	107	0.0213658	0.0061	0.0375	5008	,	,		21419	0.001		0.0626	False		,,,				2504	0.0092				p.L206P		Atlas-SNP	.											.	OR10A4	65	.	0			c.T617C						PASS	.		PRO/LEU	57,4345	53.6+/-89.4	0,57,2144	159.0	123.0	135.0		617	4.6	1.0	11	dbSNP_100	135	499,8093	144.2+/-200.1	7,485,3804	yes	missense	OR10A4	NM_207186.2	98	7,542,5948	CC,CT,TT		5.8077,1.2949,4.2789	probably-damaging	206/316	6898495	556,12438	2201	4296	6497	SO:0001583	missense	283297	exon1			CTGTCCTATTCAT	AF209506	CCDS7774.1	11p15.4	2012-08-09	2002-11-13	2004-03-10	ENSG00000170782	ENSG00000170782		"""GPCR / Class A : Olfactory receptors"""	15130	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily A, member 4 pseudogene"""	OR10A4P			Standard	NM_207186		Approved		uc010rat.2	Q9H209	OTTHUMG00000165740	ENST00000379829.2:c.617T>C	11.37:g.6898495T>C	ENSP00000369157:p.Leu206Pro	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	221	115	0.520362	NM_207186	B2RNP5|B9EH36|Q96R20	Missense_Mutation	SNP	ENST00000379829.2	37	CCDS7774.1	63	0.028846153846153848	2	0.0040650406504065045	16	0.04419889502762431	1	0.0017482517482517483	44	0.05804749340369393	t	16.79	3.220224	0.58560	0.012949	0.058077	ENSG00000170782	ENST00000379829	T	0.44881	0.91	4.59	4.59	0.56863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34676	N	0.003767	T	0.14485	0.0350	M	0.63208	1.945	0.51233	D	0.99991	D	0.71674	0.998	D	0.76071	0.987	T	0.40232	-0.9574	10	0.87932	D	0	.	12.248	0.54581	0.0:0.0:0.0:1.0	rs2595453;rs52800072;rs58313201;rs2595453	206	Q9H209	O10A4_HUMAN	P	206	ENSP00000369157:L206P	ENSP00000369157:L206P	L	+	2	0	OR10A4	6855071	0.283000	0.24277	0.992000	0.48379	0.995000	0.86356	2.441000	0.44864	2.050000	0.60909	0.529000	0.55759	CTA	T|0.965;C|0.035	0.035	strong		0.507	OR10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385985.1	NM_207186	
DNAJC21	134218	hgsc.bcm.edu	37	5	34954079	34954079	+	Silent	SNP	C	C	G	rs17244979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:34954079C>G	ENST00000342382.4	+	11	1634	c.1407C>G	c.(1405-1407)gtC>gtG	p.V469V	DNAJC21_ENST00000303525.7_Silent_p.V482V|DNAJC21_ENST00000382021.2_Silent_p.V514V			Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21	469					protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			AAAAACCTGTCAGAGTACCTG	0.323													C|||	247	0.0493211	0.003	0.0432	5008	,	,		17475	0.0367		0.0676	False		,,,				2504	0.1104				p.V514V		Atlas-SNP	.											.	DNAJC21	54	.	0			c.C1542G						PASS	.	C	,	64,4342	59.3+/-96.0	2,60,2141	99.0	107.0	104.0		1407,1542	4.9	1.0	5	dbSNP_123	104	720,7880	175.8+/-225.7	33,654,3613	no	coding-synonymous,coding-synonymous	DNAJC21	NM_001012339.2,NM_194283.3	,	35,714,5754	GG,GC,CC		8.3721,1.4526,6.028	,	469/532,514/577	34954079	784,12222	2203	4300	6503	SO:0001819	synonymous_variant	134218	exon12			ACCTGTCAGAGTA		CCDS3907.2, CCDS34144.1	5p13-p12	2012-10-05			ENSG00000168724	ENSG00000168724		"""Heat shock proteins / DNAJ (HSP40)"""	27030	protein-coding gene	gene with protein product	"""JJJ1 DnaJ domain protein homolog (S. cerevisiae)"""					15067379	Standard	XM_005248250		Approved	GS3, DNAJA5, JJJ1	uc003jjc.3	Q5F1R6	OTTHUMG00000074103	ENST00000342382.4:c.1407C>G	5.37:g.34954079C>G		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	239	102	0.426778	NM_194283	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	Silent	SNP	ENST00000342382.4	37	CCDS34144.1																																																																																			C|0.946;G|0.054	0.054	strong		0.323	DNAJC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157337.1	NM_194283	
KIF18B	146909	hgsc.bcm.edu	37	17	43011908	43011908	+	Silent	SNP	G	G	A	rs755547	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43011908G>A	ENST00000593135.1	-	5	751	c.654C>T	c.(652-654)aaC>aaT	p.N218N	KIF18B_ENST00000590129.1_Silent_p.N227N|KIF18B_ENST00000438933.2_Silent_p.N218N|KIF18B_ENST00000339151.4_Silent_p.N218N|KIF18B_ENST00000587309.1_Silent_p.N218N	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	227	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				AGGAAGTCGCGTTGGCATCAG	0.627													g|||	609	0.121605	0.1188	0.1369	5008	,	,		17726	0.0129		0.166	False		,,,				2504	0.181				p.N218N		Atlas-SNP	.											KIF18B,NS,carcinoma,0,2	KIF18B	63	2	0			c.C654T						PASS	.	A		613,3777		31,551,1613	50.0	55.0	54.0		654	-9.8	0.1	17	dbSNP_86	54	1661,6885		163,1335,2775	no	coding-synonymous	KIF18B	NM_001080443.1		194,1886,4388	AA,AG,GG		19.436,13.9636,17.5788		218/856	43011908	2274,10662	2195	4273	6468	SO:0001819	synonymous_variant	146909	exon5			AGTCGCGTTGGCA		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"""Kinesins"""	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.654C>T	17.37:g.43011908G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Silent	SNP	ENST00000593135.1	37	CCDS45709.2																																																																																			G|0.873;T|0.001	.	strong		0.627	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443	
C18orf21	83608	hgsc.bcm.edu	37	18	33557466	33557466	+	Missense_Mutation	SNP	A	A	G	rs2276314	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:33557466A>G	ENST00000592875.1	+	4	1040	c.394A>G	c.(394-396)Aca>Gca	p.T132A	C18orf21_ENST00000333234.5_Missense_Mutation_p.T44A	NM_031446.4	NP_113634.3	Q32NC0	CR021_HUMAN	chromosome 18 open reading frame 21	132			T -> A (in dbSNP:rs2276314). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.							endometrium(1)|kidney(1)|large_intestine(1)|skin(2)	5						TGCCACTCCTACAAGTAAACT	0.438													A|||	1251	0.2498	0.323	0.1859	5008	,	,		18639	0.248		0.2137	False		,,,				2504	0.2352				p.T132A		Atlas-SNP	.											.	C18orf21	15	.	0			c.A394G						PASS	.	A	ALA/THR,ALA/THR,,ALA/THR	1390,3016	457.3+/-351.6	219,952,1032	106.0	95.0	99.0		130,130,,394	-9.5	0.0	18	dbSNP_100	99	1917,6683	339.1+/-323.0	222,1473,2605	yes	missense,missense,intron,missense	C18orf21	NM_001201474.1,NM_001201475.1,NM_001201476.1,NM_031446.4	58,58,,58	441,2425,3637	GG,GA,AA		22.2907,31.5479,25.4267	benign,benign,,benign	44/133,44/133,,132/221	33557466	3307,9699	2203	4300	6503	SO:0001583	missense	83608	exon4			ACTCCTACAAGTA	BC025950	CCDS11916.2, CCDS56064.1, CCDS74212.1	18q12.2	2004-05-05			ENSG00000141428	ENSG00000141428			28802	protein-coding gene	gene with protein product						12477932	Standard	NM_031446		Approved	PNAS-131, PNAS-124, HsT3108	uc002kzc.3	Q32NC0	OTTHUMG00000128531	ENST00000592875.1:c.394A>G	18.37:g.33557466A>G	ENSP00000465517:p.Thr132Ala	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_031446	Q6GW03|Q9BXV6|Q9BXW2	Missense_Mutation	SNP	ENST00000592875.1	37	CCDS11916.2	528	0.24175824175824176	165	0.3353658536585366	56	0.15469613259668508	150	0.26223776223776224	157	0.20712401055408972	A	7.176	0.588546	0.13812	0.315479	0.222907	ENSG00000141428	ENST00000333234;ENST00000269194	T	0.41400	1.0	5.52	-9.47	0.00594	.	1.609950	0.02981	N	0.145670	T	0.00012	0.0000	N	0.16233	0.39	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.32241	-0.9914	9	0.02654	T	1	-2.0526	13.2713	0.60161	0.2449:0.1141:0.641:0.0	rs2276314;rs17845782;rs17858743;rs52824020;rs59707726;rs2276314	132	Q32NC0	CR021_HUMAN	A	132;44	ENSP00000269194:T44A	ENSP00000269194:T44A	T	+	1	0	C18orf21	31811464	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-1.358000	0.02604	-2.144000	0.00802	-0.379000	0.06801	ACA	A|0.742;G|0.258	0.258	strong		0.438	C18orf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250364.1	NM_031446	
SPEG	10290	hgsc.bcm.edu	37	2	220342004	220342004	+	Silent	SNP	G	G	A	rs45519033	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:220342004G>A	ENST00000312358.7	+	20	4698	c.4566G>A	c.(4564-4566)gaG>gaA	p.E1522E	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1522	Ig-like 8.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TGCAGGACGAGGTGCTGCTGA	0.627													G|||	204	0.0407348	0.0091	0.0937	5008	,	,		15120	0.0268		0.0567	False		,,,				2504	0.044				p.E1522E		Atlas-SNP	.											.	SPEG	272	.	0			c.G4566A						PASS	.	G		89,4221		0,89,2066	44.0	49.0	48.0		4566	4.2	1.0	2	dbSNP_127	48	583,7885		17,549,3668	no	coding-synonymous	SPEG	NM_005876.4		17,638,5734	AA,AG,GG		6.8847,2.065,5.259		1522/3268	220342004	672,12106	2155	4234	6389	SO:0001819	synonymous_variant	10290	exon20			GGACGAGGTGCTG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.4566G>A	2.37:g.220342004G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			G|0.945;A|0.055	0.055	strong		0.627	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
OLR1	4973	hgsc.bcm.edu	37	12	10313448	10313448	+	Missense_Mutation	SNP	C	C	G	rs11053646	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:10313448C>G	ENST00000309539.3	-	4	561	c.501G>C	c.(499-501)aaG>aaC	p.K167N	OLR1_ENST00000545927.1_Missense_Mutation_p.K167N|OLR1_ENST00000544577.1_Intron|OLR1_ENST00000432556.2_Intron|OLR1_ENST00000543993.1_Intron	NM_002543.3	NP_002534.1	P78380	OLR1_HUMAN	oxidized low density lipoprotein (lectin-like) receptor 1	167	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		K -> N (common polymorphism; myocardial infarction susceptibility; dbSNP:rs11053646). {ECO:0000269|PubMed:12646194, ECO:0000269|PubMed:14702039}.		blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell death (GO:0008219)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|lipoprotein metabolic process (GO:0042157)|proteolysis (GO:0006508)|response to hydrogen peroxide (GO:0042542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|low-density lipoprotein receptor activity (GO:0005041)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						TCTCTTGGCTCTTTTCCCAGT	0.443													C|||	817	0.163139	0.2209	0.0476	5008	,	,		19453	0.1746		0.0835	False		,,,				2504	0.2372				p.K167N		Atlas-SNP	.											.	OLR1	29	.	0			c.G501C	GRCh37	CM033655	OLR1	M	rs11053646	PASS	.	C	,ASN/LYS,ASN/LYS	919,3487	355.1+/-312.9	95,729,1379	187.0	180.0	182.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,501,501	-0.2	0.6	12	dbSNP_120	182	781,7819	185.3+/-233.1	34,713,3553	yes	intron,missense,missense	OLR1	NM_001172632.1,NM_001172633.1,NM_002543.3	,94,94	129,1442,4932	GG,GC,CC		9.0814,20.8579,13.0709	,possibly-damaging,possibly-damaging	,167/190,167/274	10313448	1700,11306	2203	4300	6503	SO:0001583	missense	4973	exon4			TTGGCTCTTTTCC	D89050	CCDS8618.1, CCDS53745.1, CCDS53746.1	12p13.1-p12.3	2011-08-30	2006-12-07		ENSG00000173391	ENSG00000173391		"""C-type lectin domain containing"""	8133	protein-coding gene	gene with protein product		602601	"""oxidised low density lipoprotein (lectin-like) receptor 1"""			9763655	Standard	NM_002543		Approved	LOX-1, SCARE1, CLEC8A	uc001qxo.1	P78380	OTTHUMG00000168527	ENST00000309539.3:c.501G>C	12.37:g.10313448C>G	ENSP00000309124:p.Lys167Asn	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	167	87	0.520958	NM_001172633	A8K7V9|B4DI48|G3V1I4|Q2PP00|Q7Z484	Missense_Mutation	SNP	ENST00000309539.3	37	CCDS8618.1	288	0.13186813186813187	96	0.1951219512195122	17	0.04696132596685083	109	0.19055944055944055	66	0.0870712401055409	C	0.545	-0.851895	0.02651	0.208579	0.090814	ENSG00000173391	ENST00000309539;ENST00000545927;ENST00000539518;ENST00000538745;ENST00000339968	T;T;T;T;T	0.16743	2.32;2.32;2.32;2.32;2.32	4.98	-0.211	0.13172	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.390912	0.24445	N	0.038462	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	0.999999695872	P	0.38473	0.633	B	0.33339	0.162	T	0.43147	-0.9409	9	0.20519	T	0.43	.	3.5856	0.07970	0.1778:0.2948:0.0:0.5274	rs11053646;rs35996025;rs60209320;rs11053646	167	P78380	OLR1_HUMAN	N	167;167;114;63;63	ENSP00000309124:K167N;ENSP00000439251:K167N;ENSP00000442389:K114N;ENSP00000438925:K63N;ENSP00000340572:K63N	ENSP00000309124:K167N	K	-	3	2	OLR1	10204715	0.952000	0.32445	0.591000	0.28745	0.139000	0.21198	-0.010000	0.12743	-0.143000	0.11334	-0.140000	0.14226	AAG	C|0.862;G|0.138	0.138	strong		0.443	OLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400091.1	NM_002543	
NAGS	162417	hgsc.bcm.edu	37	17	42084067	42084067	+	Silent	SNP	T	T	C	rs55708447	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:42084067T>C	ENST00000293404.3	+	4	1204	c.1086T>C	c.(1084-1086)ttT>ttC	p.F362F	PYY_ENST00000360085.2_5'Flank	NM_153006.2	NP_694551.1	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	362	Amino-acid kinase domain (AAK).				arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial matrix (GO:0005759)	acetyl-CoA:L-glutamate N-acetyltransferase activity (GO:0004042)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		CTGAGCTCTTTAGCAACAAGG	0.682													T|||	535	0.106829	0.0915	0.111	5008	,	,		12642	0.0139		0.2097	False		,,,				2504	0.1145				p.F362F		Atlas-SNP	.											.	NAGS	25	.	0			c.T1086C						PASS	.	T		419,3957		26,367,1795	17.0	16.0	17.0		1086	1.9	1.0	17	dbSNP_129	17	1577,6951		162,1253,2849	no	coding-synonymous	NAGS	NM_153006.2		188,1620,4644	CC,CT,TT		18.492,9.575,15.4681		362/535	42084067	1996,10908	2188	4264	6452	SO:0001819	synonymous_variant	162417	exon4			GCTCTTTAGCAAC	AY116537	CCDS11473.1	17q21.31	2008-02-05				ENSG00000161653			17996	protein-coding gene	gene with protein product		608300				15050968, 12459178	Standard	NM_153006		Approved	AGAS, ARGA, NAT7	uc002ies.3	Q8N159		ENST00000293404.3:c.1086T>C	17.37:g.42084067T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_153006	B2RAZ9|Q8IWR4	Silent	SNP	ENST00000293404.3	37	CCDS11473.1																																																																																			T|0.864;C|0.136	0.136	strong		0.682	NAGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457660.1	NM_153006	
PRRC2C	23215	hgsc.bcm.edu	37	1	171511039	171511039	+	Silent	SNP	C	C	G	rs1687064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:171511039C>G	ENST00000338920.4	+	16	4665	c.4428C>G	c.(4426-4428)tcC>tcG	p.S1476S	PRRC2C_ENST00000426496.2_Silent_p.S1476S|PRRC2C_ENST00000367742.3_Silent_p.S1478S|PRRC2C_ENST00000392078.3_Silent_p.S1478S	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1476					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										GGGATATTTCCGGGAATAAGA	0.428													G|||	4058	0.810304	0.7474	0.7349	5008	,	,		19776	0.8958		0.8161	False		,,,				2504	0.8548				p.S1476S		Atlas-SNP	.											BAT2D1_ENST00000392078,NS,carcinoma,+1,3	.	.	3	0			c.C4428G						PASS	.	G		3402,1004	362.1+/-316.0	1322,758,123	65.0	70.0	68.0		4428	0.3	1.0	1	dbSNP_89	68	6970,1630	288.5+/-298.8	2843,1284,173	no	coding-synonymous	PRRC2C	NM_015172.3		4165,2042,296	GG,GC,CC		18.9535,22.7871,20.2522		1476/2818	171511039	10372,2634	2203	4300	6503	SO:0001819	synonymous_variant	23215	exon16			TATTTCCGGGAAT	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4428C>G	1.37:g.171511039C>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2	1784	0.8168498168498168	367	0.7459349593495935	274	0.7569060773480663	513	0.8968531468531469	630	0.8311345646437994	G	3.033	-0.199301	0.06219	0.772129	0.810465	ENSG00000117523	ENST00000495585	.	.	.	5.65	0.303	0.15791	.	.	.	.	.	T	0.13372	0.0324	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.20907	-1.0261	3	.	.	.	.	4.4843	0.11781	0.2223:0.0663:0.465:0.2465	rs1687064;rs3195721;rs58254582;rs1687064	.	.	.	R	24	.	.	P	+	2	0	PRRC2C	169777663	0.107000	0.21998	0.997000	0.53966	0.928000	0.56348	-0.705000	0.05052	-0.150000	0.11195	-2.870000	0.00099	CCG	C|0.195;G|0.805	0.805	strong		0.428	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
UBP1	7342	hgsc.bcm.edu	37	3	33467112	33467112	+	Missense_Mutation	SNP	G	G	A	rs61751640	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33467112G>A	ENST00000283629.3	-	2	764	c.235C>T	c.(235-237)Cat>Tat	p.H79Y	UBP1_ENST00000283628.5_Missense_Mutation_p.H79Y|UBP1_ENST00000447368.2_Missense_Mutation_p.H79Y	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	79					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						GTTTCATCATGCAGTTTTACT	0.388													G|||	8	0.00159744	0.0	0.0014	5008	,	,		16266	0.0		0.006	False		,,,				2504	0.001				p.H79Y		Atlas-SNP	.											.	UBP1	42	.	0			c.C235T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	11,4395	19.1+/-41.9	0,11,2192	87.0	72.0	77.0		235,235,235	5.9	1.0	3	dbSNP_129	77	89,8511	50.6+/-110.7	0,89,4211	yes	missense,missense,missense	UBP1	NM_001128160.1,NM_001128161.1,NM_014517.4	83,83,83	0,100,6403	AA,AG,GG		1.0349,0.2497,0.7689	benign,benign,benign	79/505,79/541,79/541	33467112	100,12906	2203	4300	6503	SO:0001583	missense	7342	exon2			CATCATGCAGTTT	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.235C>T	3.37:g.33467112G>A	ENSP00000283629:p.His79Tyr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	35	0.406977	NM_001128160	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	37	CCDS2659.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	16.88	3.243954	0.58995	0.002497	0.010349	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628;ENST00000456378	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	5.92	5.92	0.95590	CP2 transcription factor (1);	0.048704	0.85682	D	0.000000	T	0.12646	0.0307	L	0.41573	1.285	0.58432	D	0.999994	B;B	0.13145	0.006;0.007	B;B	0.23852	0.005;0.049	T	0.01587	-1.1318	10	0.56958	D	0.05	-21.3838	13.9369	0.64029	0.0778:0.0:0.9222:0.0	rs61751640	79;79	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	Y	79	ENSP00000283629:H79Y;ENSP00000395558:H79Y;ENSP00000283628:H79Y;ENSP00000401614:H79Y	ENSP00000283628:H79Y	H	-	1	0	UBP1	33442116	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.723000	0.74742	2.810000	0.96702	0.585000	0.79938	CAT	G|0.994;A|0.006	0.006	strong		0.388	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517	
ADAM28	10863	hgsc.bcm.edu	37	8	24167750	24167750	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:24167750T>G	ENST00000265769.4	+	4	412	c.302T>G	c.(301-303)aTt>aGt	p.I101S	RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000540823.1_De_novo_Start_OutOfFrame|ADAM28_ENST00000437154.2_Missense_Mutation_p.I101S|ADAM28_ENST00000397649.3_De_novo_Start_OutOfFrame|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	101					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		AGCCCACAAATTATGGTATAA	0.403																																					p.I101S	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.T302G						PASS	.						84.0	79.0	81.0					8																	24167750		2203	4300	6503	SO:0001583	missense	10863	exon4			CACAAATTATGGT	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.302T>G	8.37:g.24167750T>G	ENSP00000265769:p.Ile101Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.302338	0.60195	.	.	ENSG00000042980	ENST00000265769;ENST00000437154	T;T	0.05786	3.39;3.39	4.97	3.84	0.44239	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.12860	0.0312	L	0.55990	1.75	0.80722	D	1	D;P	0.62365	0.991;0.837	P;P	0.62089	0.898;0.457	T	0.13019	-1.0525	9	0.16420	T	0.52	.	6.8564	0.24042	0.0:0.101:0.0:0.899	.	101;101	Q9UKQ2;Q9UKQ2-2	ADA28_HUMAN;.	S	101	ENSP00000265769:I101S;ENSP00000393699:I101S	ENSP00000265769:I101S	I	+	2	0	ADAM28	24223695	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	2.018000	0.40991	2.222000	0.72286	0.477000	0.44152	ATT	.	.	none		0.403	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
CLEC3A	10143	hgsc.bcm.edu	37	16	78064351	78064351	+	Silent	SNP	C	C	G	rs2293776	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:78064351C>G	ENST00000575655.1	+	3	288	c.207C>G	c.(205-207)ctC>ctG	p.L69L	RP11-281J9.2_ENST00000563114.1_RNA|CLEC3A_ENST00000565808.1_3'UTR|CLEC3A_ENST00000299642.4_Silent_p.L78L	NM_005752.4	NP_005743.4	O75596	CLC3A_HUMAN	C-type lectin domain family 3, member A	69					skeletal system development (GO:0001501)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	18						CAGTCTGTCTCCGAGGCACTA	0.413													C|||	932	0.186102	0.0136	0.2032	5008	,	,		21071	0.1855		0.327	False		,,,				2504	0.2628				p.L78L		Atlas-SNP	.											.	CLEC3A	39	.	0			c.C234G						PASS	.	C		317,4079	165.8+/-197.2	10,297,1891	79.0	74.0	76.0		207	-1.5	1.0	16	dbSNP_100	76	2825,5775	436.4+/-358.3	464,1897,1939	no	coding-synonymous	CLEC3A	NM_005752.4		474,2194,3830	GG,GC,CC		32.8488,7.2111,24.1767		69/198	78064351	3142,9854	2198	4300	6498	SO:0001819	synonymous_variant	10143	exon3			CTGTCTCCGAGGC	AF077345	CCDS10927.1, CCDS10927.2	16q23	2008-02-05	2005-02-09	2005-02-11	ENSG00000166509	ENSG00000166509		"""C-type lectin domain containing"""	2052	protein-coding gene	gene with protein product		613588	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived)"""	CLECSF1		10524194	Standard	NM_001244755		Approved		uc002ffh.5	O75596	OTTHUMG00000137620	ENST00000575655.1:c.207C>G	16.37:g.78064351C>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_005752	B2R8C4|Q3SX91|Q6UXF5	Silent	SNP	ENST00000575655.1	37																																																																																				C|0.771;G|0.229	0.229	strong		0.413	CLEC3A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005752	
TRIM64B	642446	hgsc.bcm.edu	37	11	89608899	89608899	+	Missense_Mutation	SNP	T	T	G	rs201022110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:89608899T>G	ENST00000329862.6	-	1	286	c.287A>C	c.(286-288)gAg>gCg	p.E96A		NM_001136486.1|NM_001164397.1	NP_001129958.1|NP_001157869.1	A6NI03	TR64B_HUMAN	tripartite motif containing 64B	96						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)	2						CTTAGTCTCCTCATGGAGCAC	0.507													t|||	1413	0.282149	0.4433	0.2378	5008	,	,		24915	0.1696		0.2197	False		,,,				2504	0.2761				p.E96A		Atlas-SNP	.											TRIM64B,NS,carcinoma,0,2	TRIM64B	23	2	0			c.A287C						scavenged	.						7.0	7.0	7.0					11																	89608899		495	1394	1889	SO:0001583	missense	642446	exon1			GTCTCCTCATGGA		CCDS53693.1	11q14.3	2014-04-02	2011-01-25		ENSG00000189253	ENSG00000189253		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	37147	protein-coding gene	gene with protein product			"""tripartite motif-containing 64B"""				Standard	NM_001164397		Approved		uc021qoo.1	A6NI03	OTTHUMG00000167638	ENST00000329862.6:c.287A>C	11.37:g.89608899T>G	ENSP00000332969:p.Glu96Ala	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	110	41	0.372727	NM_001164397		Missense_Mutation	SNP	ENST00000329862.6	37	CCDS53693.1	.	.	.	.	.	.	.	.	.	.	.	7.335	0.619740	0.14193	.	.	ENSG00000189253	ENST00000329862	T	0.57436	0.4	2.06	-2.81	0.05805	.	.	.	.	.	T	0.49081	0.1536	M	0.67569	2.06	0.80722	P	0.0	.	.	.	.	.	.	T	0.51733	-0.8668	5	.	.	.	.	3.3853	0.07269	0.0:0.2863:0.2094:0.5043	.	.	.	.	A	96	ENSP00000332969:E96A	.	E	-	2	0	TRIM64B	89248547	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.140000	0.16056	-0.854000	0.04131	0.321000	0.21382	GAG	T|0.500;G|0.500	0.500	strong		0.507	TRIM64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395440.1		
ZNF516	9658	hgsc.bcm.edu	37	18	74092242	74092242	+	Missense_Mutation	SNP	A	A	G	rs117566743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:74092242A>G	ENST00000443185.2	-	4	2145	c.1828T>C	c.(1828-1830)Tgc>Cgc	p.C610R	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	610					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		GAAAAGCAGCAGCGGCGCGGC	0.542													A|||	37	0.00738818	0.0023	0.0086	5008	,	,		18821	0.0		0.0278	False		,,,				2504	0.0				p.C610R		Atlas-SNP	.											ZNF516,NS,carcinoma,0,1	ZNF516	102	1	0			c.T1828C						scavenged	.	A	ARG/CYS	13,3909		0,13,1948	40.0	42.0	41.0		1828	1.7	0.0	18	dbSNP_132	41	215,8073		3,209,3932	yes	missense	ZNF516	NM_014643.3	180	3,222,5880	GG,GA,AA		2.5941,0.3315,1.8673	possibly-damaging	610/1164	74092242	228,11982	1961	4144	6105	SO:0001583	missense	9658	exon4			AGCAGCAGCGGCG	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.1828T>C	18.37:g.74092242A>G	ENSP00000394757:p.Cys610Arg	Somatic	78	2	0.025641		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	37		21	0.009615384615384616	0	0.0	3	0.008287292817679558	0	0.0	18	0.023746701846965697	A	9.811	1.183076	0.21870	0.003315	0.025941	ENSG00000101493	ENST00000443185	T	0.10192	2.9	4.07	1.69	0.24217	.	0.758077	0.12741	N	0.443019	T	0.02688	0.0081	.	.	.	0.31303	N	0.688065	B	0.15473	0.013	B	0.10450	0.005	T	0.10543	-1.0625	9	0.87932	D	0	-11.4753	6.7955	0.23722	0.8108:0.0:0.1892:0.0	.	610	Q92618	ZN516_HUMAN	R	610	ENSP00000394757:C610R	ENSP00000394757:C610R	C	-	1	0	ZNF516	72221230	1.000000	0.71417	0.035000	0.18076	0.137000	0.21094	2.171000	0.42453	0.168000	0.19655	0.533000	0.62120	TGC	A|0.989;G|0.011	0.011	strong		0.542	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
KIF27	55582	hgsc.bcm.edu	37	9	86465131	86465131	+	Missense_Mutation	SNP	T	T	C	rs58077086	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:86465131T>C	ENST00000297814.2	-	16	3582	c.3439A>G	c.(3439-3441)Atg>Gtg	p.M1147V	RP11-575L7.4_ENST00000586206.1_RNA|RP11-575L7.4_ENST00000591217.1_RNA|RP11-575L7.4_ENST00000608866.1_RNA|KIF27_ENST00000334204.2_Missense_Mutation_p.M1050V|RP11-575L7.4_ENST00000589817.1_RNA|RP11-575L7.4_ENST00000590368.1_RNA|RP11-575L7.4_ENST00000590813.1_RNA|KIF27_ENST00000413982.1_Missense_Mutation_p.M1081V	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	1147					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						TCACGAACCATATTATCCCGT	0.393													T|||	659	0.131589	0.034	0.1729	5008	,	,		19611	0.1052		0.2356	False		,,,				2504	0.1544				p.M1147V		Atlas-SNP	.											.	KIF27	103	.	0			c.A3439G						PASS	.	T	VAL/MET	248,4158	142.7+/-177.9	10,228,1965	98.0	91.0	93.0		3439	-0.8	0.3	9	dbSNP_129	93	2071,6525	357.4+/-330.7	266,1539,2493	no	missense	KIF27	NM_017576.1	21	276,1767,4458	CC,CT,TT		24.0926,5.6287,17.8357	benign	1147/1402	86465131	2319,10683	2203	4298	6501	SO:0001583	missense	55582	exon16			GAACCATATTATC	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.3439A>G	9.37:g.86465131T>C	ENSP00000297814:p.Met1147Val	Somatic	584	1	0.00171233		WXS	Illumina HiSeq	Phase_I	616	282	0.457792	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	337	0.1543040293040293	23	0.046747967479674794	60	0.16574585635359115	76	0.13286713286713286	178	0.23482849604221637	T	10.42	1.344925	0.24426	0.056287	0.240926	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.68624	-0.33;-0.34;-0.23	4.58	-0.817	0.10836	.	0.340347	0.27245	N	0.020250	T	0.00039	0.0001	L	0.42245	1.32	0.58432	P	5.999999999950489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.06427	-1.0827	9	0.41790	T	0.15	.	8.8801	0.35370	0.0:0.3374:0.0:0.6626	rs58077086;rs62561946	1050;1081;1147	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	V	1147;1081;1050	ENSP00000297814:M1147V;ENSP00000401688:M1081V;ENSP00000333928:M1050V	ENSP00000297814:M1147V	M	-	1	0	KIF27	85654951	0.027000	0.19231	0.307000	0.25127	0.982000	0.71751	-0.115000	0.10741	-0.311000	0.08754	0.358000	0.22013	ATG	.	.	weak		0.393	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
TSPAN14	81619	hgsc.bcm.edu	37	10	82269158	82269158	+	Silent	SNP	C	C	T	rs145582053		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:82269158C>T	ENST00000429989.3	+	5	604	c.381C>T	c.(379-381)ttC>ttT	p.F127F	TSPAN14_ENST00000481124.1_Intron|TSPAN14_ENST00000372156.1_Silent_p.F127F|TSPAN14_ENST00000372164.3_Silent_p.F110F|TSPAN14_ENST00000341863.6_Intron|TSPAN14_ENST00000372158.1_Silent_p.F127F	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	127					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			GGGAGTTCTTCGAGAGCAACA	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		19378	0.0		0.001	False		,,,				2504	0.0				p.F127F		Atlas-SNP	.											.	TSPAN14	29	.	0			c.C381T						PASS	.	C	,	3,4403	6.2+/-15.9	0,3,2200	109.0	93.0	99.0		,381	-2.1	1.0	10	dbSNP_134	99	7,8593	5.7+/-21.5	0,7,4293	no	intron,coding-synonymous	TSPAN14	NM_001128309.1,NM_030927.2	,	0,10,6493	TT,TC,CC		0.0814,0.0681,0.0769	,	,127/271	82269158	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	81619	exon5			GTTCTTCGAGAGC	AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"""Tetraspanins"""	23303	protein-coding gene	gene with protein product			"""transmembrane 4 superfamily member 14"""	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.381C>T	10.37:g.82269158C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_030927	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Silent	SNP	ENST00000429989.3	37	CCDS7369.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927	
SFT2D1	113402	hgsc.bcm.edu	37	6	166739646	166739646	+	Missense_Mutation	SNP	T	T	C	rs11551053	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:166739646T>C	ENST00000361731.3	-	5	434	c.325A>G	c.(325-327)Ata>Gta	p.I109V	SFT2D1_ENST00000487841.1_5'UTR	NM_145169.1	NP_660152.1			SFT2 domain containing 1									p.I109V(1)		NS(1)|central_nervous_system(1)|large_intestine(3)|upper_aerodigestive_tract(1)	6		Breast(66;0.000148)|Prostate(117;0.109)|Ovarian(120;0.199)		OV - Ovarian serous cystadenocarcinoma(33;2.63e-19)|BRCA - Breast invasive adenocarcinoma(81;4.92e-06)|GBM - Glioblastoma multiforme(31;4.58e-05)		AGGGTAAATATGAAACACAAC	0.413													C|||	557	0.111222	0.0356	0.0793	5008	,	,		18011	0.3313		0.0398	False		,,,				2504	0.0828				p.I109V		Atlas-SNP	.											SFT2D1,colon,carcinoma,+1,2	SFT2D1	12	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.A325G						PASS	.	C	VAL/ILE	147,4259	812.6+/-416.1	1,145,2057	82.0	78.0	79.0		325	-1.3	0.0	6	dbSNP_120	79	304,8296	805.6+/-407.3	5,294,4001	yes	missense	SFT2D1	NM_145169.1	29	6,439,6058	CC,CT,TT		3.5349,3.3364,3.4676	benign	109/160	166739646	451,12555	2203	4300	6503	SO:0001583	missense	113402	exon5			TAAATATGAAACA	AF041429	CCDS5292.1	6q27	2008-02-05	2005-07-25	2005-07-25	ENSG00000198818	ENSG00000198818			21102	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 83"""	C6orf83			Standard	NM_145169		Approved	MGC19825, pRGR1	uc003qux.3	Q8WV19	OTTHUMG00000016001	ENST00000361731.3:c.325A>G	6.37:g.166739646T>C	ENSP00000354590:p.Ile109Val	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	182	92	0.505495	NM_145169		Missense_Mutation	SNP	ENST00000361731.3	37	CCDS5292.1	278	0.12728937728937728	19	0.03861788617886179	26	0.0718232044198895	199	0.3479020979020979	34	0.044854881266490766	C	0	-2.803354	0.00075	0.033364	0.035349	ENSG00000198818	ENST00000361731	T	0.58652	0.32	4.98	-1.34	0.09143	.	0.690574	0.13904	N	0.354704	T	0.07458	0.0188	N	0.03209	-0.39	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.25012	-1.0144	9	0.02654	T	1	-6.1183	5.4909	0.16774	0.1304:0.4651:0.0:0.4045	rs11551053;rs36102427;rs60635309	109	Q8WV19	SFT2A_HUMAN	V	109	ENSP00000354590:I109V	ENSP00000354590:I109V	I	-	1	0	SFT2D1	166659636	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.557000	0.02166	-0.259000	0.09432	-1.008000	0.02478	ATA	T|0.932;C|0.068	0.068	strong		0.413	SFT2D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043061.2	NM_145169	
ATP6V0A1	535	hgsc.bcm.edu	37	17	40632729	40632729	+	Silent	SNP	C	C	T	rs41283429	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:40632729C>T	ENST00000343619.4	+	8	801	c.678C>T	c.(676-678)ggC>ggT	p.G226G	ATP6V0A1_ENST00000544137.1_Intron|ATP6V0A1_ENST00000537728.1_Silent_p.G183G|ATP6V0A1_ENST00000546249.1_Silent_p.G226G|ATP6V0A1_ENST00000264649.6_Silent_p.G233G|ATP6V0A1_ENST00000393829.2_Silent_p.G226G|ATP6V0A1_ENST00000585525.1_Silent_p.G183G	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	226					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		TCTTCCAAGGCGATCAGCTGA	0.443													C|||	88	0.0175719	0.0076	0.0259	5008	,	,		16990	0.0		0.0368	False		,,,				2504	0.0235				p.G233G		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.C699T						PASS	.	C	,,	52,4354	52.3+/-87.9	0,52,2151	95.0	93.0	94.0		699,678,678	-6.6	1.0	17	dbSNP_127	94	348,8252	118.1+/-177.6	8,332,3960	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP6V0A1	NM_001130020.1,NM_001130021.1,NM_005177.3	,,	8,384,6111	TT,TC,CC		4.0465,1.1802,3.0755	,,	233/839,226/838,226/832	40632729	400,12606	2203	4300	6503	SO:0001819	synonymous_variant	535	exon8			CCAAGGCGATCAG	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"""ATPases / V-type"""	865	protein-coding gene	gene with protein product		192130	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 1"", ""ATPase, H+ transporting, lysosomal V0 subunit A1"""	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.678C>T	17.37:g.40632729C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Silent	SNP	ENST00000343619.4	37	CCDS45684.1																																																																																			C|0.969;T|0.031	0.031	strong		0.443	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020	
ZNF292	23036	hgsc.bcm.edu	37	6	87967636	87967636	+	Missense_Mutation	SNP	A	A	G	rs6941356	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:87967636A>G	ENST00000369577.3	+	8	4332	c.4289A>G	c.(4288-4290)aAt>aGt	p.N1430S	ZNF292_ENST00000339907.4_Missense_Mutation_p.N1425S	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1430						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		CTCTCCACAAATGCAGTAAAT	0.428													A|||	423	0.0844649	0.0303	0.0548	5008	,	,		19450	0.1359		0.0954	False		,,,				2504	0.1145				p.N1430S		Atlas-SNP	.											.	ZNF292	479	.	0			c.A4289G						PASS	.	A	SER/ASN	149,3693		2,145,1774	135.0	139.0	138.0		4289	2.6	1.0	6	dbSNP_116	138	769,7513		34,701,3406	yes	missense	ZNF292	NM_015021.1	46	36,846,5180	GG,GA,AA		9.2852,3.8782,7.5718	benign	1430/2724	87967636	918,11206	1921	4141	6062	SO:0001583	missense	23036	exon8			CCACAAATGCAGT	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.4289A>G	6.37:g.87967636A>G	ENSP00000358590:p.Asn1430Ser	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	223	110	0.493274	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	179	0.08195970695970696	13	0.026422764227642278	24	0.06629834254143646	69	0.12062937062937062	73	0.09630606860158311	A	4.306	0.056132	0.08291	0.038782	0.092852	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.06528	3.29;3.3	5.03	2.64	0.31445	.	0.264982	0.31392	N	0.007738	T	0.00998	0.0033	N	0.12182	0.205	0.27326	N	0.956919	B	0.15141	0.012	B	0.12156	0.007	T	0.49000	-0.8984	10	0.20046	T	0.44	.	7.5399	0.27731	0.7564:0.0:0.2436:0.0	rs6941356;rs60552547;rs6941356	1430	O60281	ZN292_HUMAN	S	1430;1425	ENSP00000358590:N1430S;ENSP00000342847:N1425S	ENSP00000342847:N1425S	N	+	2	0	ZNF292	88024355	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.955000	0.40372	0.360000	0.24265	-0.256000	0.11100	AAT	A|0.927;G|0.073	0.073	strong		0.428	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651643	1651643	+	Silent	SNP	C	C	T	rs576867883|rs4752771|rs71025765		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1651643C>T	ENST00000399676.2	+	1	611	c.573C>T	c.(571-573)ccC>ccT	p.P191P		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	191	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.Y182_P191delYCCQSSCCKP(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GCTGTAAGCCCTACTGCTGCC	0.602																																					p.P191P		Atlas-SNP	.											KRTAP5-5,NS,carcinoma,0,1	KRTAP5-5	86	1	1	Deletion - In frame(1)	urinary_tract(1)	c.C573T						PASS	.						67.0	68.0	68.0					11																	1651643		2201	4297	6498	SO:0001819	synonymous_variant	439915	exon1			TAAGCCCTACTGC	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.573C>T	11.37:g.1651643C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			C|0.691;T|0.309	0.309	strong		0.602	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
C6orf201	404220	hgsc.bcm.edu	37	6	4087934	4087934	+	Missense_Mutation	SNP	G	G	C	rs619483	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:4087934G>C	ENST00000380175.4	+	2	824	c.59G>C	c.(58-60)cGc>cCc	p.R20P	FAM217A_ENST00000380188.2_5'Flank|C6orf201_ENST00000430835.2_Missense_Mutation_p.R20P|C6orf201_ENST00000360378.6_3'UTR|C6orf201_ENST00000333388.5_Intron	NM_001085401.2	NP_001078870.1	Q7Z4U5	CF201_HUMAN	chromosome 6 open reading frame 201	20			R -> P (in dbSNP:rs619483). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.							central_nervous_system(1)|endometrium(3)|lung(2)	6	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				CTTTATTCCCGCAAGAGTGAA	0.478													A|||	1348	0.269169	0.3427	0.2896	5008	,	,		16422	0.3591		0.1938	False		,,,				2504	0.1401				p.R20P		Atlas-SNP	.											.	C6orf201	17	.	0			c.G59C						PASS	.	A	PRO/ARG	1246,2576		195,856,860	179.0	191.0	187.0		59	0.2	0.0	6	dbSNP_83	187	1439,6843		128,1183,2830	yes	missense	C6orf201	NM_001085401.1	103	323,2039,3690	CC,CG,GG		17.375,32.6007,22.1827	benign	20/141	4087934	2685,9419	1911	4141	6052	SO:0001583	missense	404220	exon2			ATTCCCGCAAGAG	BC047663	CCDS43419.1	6p25.2	2012-02-21			ENSG00000185689	ENSG00000185689			21620	protein-coding gene	gene with protein product							Standard	NM_001085401		Approved	dJ1013A10.5	uc003mwa.4	Q7Z4U5	OTTHUMG00000014160	ENST00000380175.4:c.59G>C	6.37:g.4087934G>C	ENSP00000420610:p.Arg20Pro	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_001085401	A6NLI6|Q6NXN5	Missense_Mutation	SNP	ENST00000380175.4	37	CCDS43419.1	657	0.3008241758241758	194	0.3943089430894309	97	0.26795580110497236	215	0.3758741258741259	151	0.19920844327176782	A	10.38	1.335190	0.24253	0.326007	0.17375	ENSG00000185689	ENST00000541127;ENST00000380175;ENST00000451679;ENST00000436110;ENST00000430835	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	4.28	0.147	0.14838	.	0.842845	0.09961	N	0.733497	T	0.02649	0.0080	N	0.08118	0	0.80722	P	0.0	B;B	0.10296	0.003;0.003	B;B	0.04013	0.001;0.001	T	0.42310	-0.9459	9	0.48119	T	0.1	.	2.5131	0.04661	0.4552:0.0:0.204:0.3408	rs619483;rs52815722;rs619483	20;20	B4DXB2;Q7Z4U5	.;CF201_HUMAN	P	20	ENSP00000420610:R20P;ENSP00000420763:R20P;ENSP00000417981:R20P;ENSP00000396912:R20P	ENSP00000420610:R20P	R	+	2	0	C6orf201	4032933	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	0.090000	0.15025	-0.010000	0.14271	-0.360000	0.07572	CGC	G|0.746;C|0.254	0.254	strong		0.478	C6orf201-001	KNOWN	NMD_exception|basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000314019.2	NM_001085401	
PIGN	23556	hgsc.bcm.edu	37	18	59814268	59814268	+	Silent	SNP	G	G	A	rs9320000	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:59814268G>A	ENST00000357637.5	-	9	1156	c.741C>T	c.(739-741)caC>caT	p.H247H	PIGN_ENST00000400334.3_Silent_p.H247H	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	247					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				TTCCATAGAAGTGGTTAAACA	0.318													A|||	2958	0.590655	0.3835	0.683	5008	,	,		16107	0.6974		0.6252	False		,,,				2504	0.6595				p.H247H		Atlas-SNP	.											.	PIGN	62	.	0			c.C741T						PASS	.	A	,	1664,2004		362,940,532	97.0	87.0	90.0		741,741	-3.1	0.1	18	dbSNP_119	90	5077,3091		1589,1899,596	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	1951,2839,1128	AA,AG,GG		37.8428,45.3653,43.0466	,	247/932,247/932	59814268	6741,5095	1834	4084	5918	SO:0001819	synonymous_variant	23556	exon9			ATAGAAGTGGTTA	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.741C>T	18.37:g.59814268G>A		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	253	121	0.478261	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			G|0.397;A|0.603	0.603	strong		0.318	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
ACOT4	122970	hgsc.bcm.edu	37	14	74061968	74061968	+	Silent	SNP	T	T	C	rs2010070	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:74061968T>C	ENST00000326303.4	+	3	1130	c.876T>C	c.(874-876)atT>atC	p.I292I		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	292					acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		TCGTGGACATTGTGGATATAA	0.502													C|||	4316	0.861821	0.9887	0.8501	5008	,	,		19104	0.9296		0.7276	False		,,,				2504	0.7669				p.I292I		Atlas-SNP	.											.	ACOT4	25	.	0			c.T876C						PASS	.	C		4164,242	141.9+/-177.2	1965,234,4	89.0	87.0	88.0		876	1.3	1.0	14	dbSNP_92	88	6233,2367	395.6+/-345.1	2263,1707,330	no	coding-synonymous	ACOT4	NM_152331.3		4228,1941,334	CC,CT,TT		27.5233,5.4925,20.06		292/422	74061968	10397,2609	2203	4300	6503	SO:0001819	synonymous_variant	122970	exon3			GGACATTGTGGAT	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.876T>C	14.37:g.74061968T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Silent	SNP	ENST00000326303.4	37	CCDS9817.1																																																																																			T|0.172;C|0.828	0.828	strong		0.502	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
GPSM3	63940	hgsc.bcm.edu	37	6	32159956	32159956	+	Silent	SNP	T	T	C	rs3134605	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32159956T>C	ENST00000375040.3	-	2	506	c.114A>G	c.(112-114)ccA>ccG	p.P38P	PBX2_ENST00000375050.4_5'Flank|GPSM3_ENST00000375043.3_Silent_p.P38P|GPSM3_ENST00000487761.1_Silent_p.P35P	NM_001276501.1	NP_001263430.1	Q9Y4H4	GPSM3_HUMAN	G-protein signaling modulator 3	38	Pro-rich.				regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cytoplasm (GO:0005737)	GDP-dissociation inhibitor activity (GO:0005092)			large_intestine(1)	1						GAGGAGGGGATGGAGGAGCAG	0.627													C|||	1144	0.228435	0.1974	0.1772	5008	,	,		11010	0.2688		0.1918	False		,,,				2504	0.3027				p.P38P		Atlas-SNP	.											GPSM3,colon,carcinoma,0,1	GPSM3	9	1	0			c.A114G						PASS	.	C		812,3594	739.1+/-411.0	76,660,1467	44.0	48.0	47.0		114	-7.0	0.9	6	dbSNP_103	47	1792,6806	727.0+/-406.6	188,1416,2695	yes	coding-synonymous	GPSM3	NM_022107.1		264,2076,4162	CC,CT,TT		20.8421,18.4294,20.0246		38/161	32159956	2604,10400	2203	4299	6502	SO:0001819	synonymous_variant	63940	exon6			AGGGGATGGAGGA	AF155657	CCDS34419.1	6p21.3	2010-06-24	2010-06-24	2004-02-04	ENSG00000213654	ENSG00000213654			13945	protein-coding gene	gene with protein product	"""activator of G-protein signaling 4"""		"""chromosome 6 open reading frame 9"", ""G-protein signalling modulator 3 (AGS3-like, C. elegans)"""	C6orf9		2259622, 15096500	Standard	NM_022107		Approved	NG1, G18, G18.1a, G18.1b, G18.2, AGS4	uc003oaz.3	Q9Y4H4	OTTHUMG00000031244	ENST00000375040.3:c.114A>G	6.37:g.32159956T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_022107	A2BFJ3	Silent	SNP	ENST00000375040.3	37	CCDS34419.1																																																																																			T|0.814;C|0.186	0.186	strong		0.627	GPSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076509.1	NM_022107	
GAS8	2622	hgsc.bcm.edu	37	16	90106746	90106746	+	Silent	SNP	C	C	T	rs61734731	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90106746C>T	ENST00000268699.4	+	9	1172	c.1050C>T	c.(1048-1050)acC>acT	p.T350T	GAS8_ENST00000536122.1_Silent_p.T325T|GAS8_ENST00000540721.1_3'UTR|URAHP_ENST00000517889.1_RNA	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	350					cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		GGAAGTTCACCGCAGCCATCC	0.627													c|||	136	0.0271565	0.0091	0.0115	5008	,	,		19539	0.0446		0.0487	False		,,,				2504	0.0225				p.T350T		Atlas-SNP	.											GAS8,NS,carcinoma,0,1	GAS8	29	1	0			c.C1050T						PASS	.	C		65,4323		0,65,2129	61.0	45.0	51.0		1050	-11.6	0.0	16	dbSNP_129	51	507,8091		15,477,3807	no	coding-synonymous	GAS8	NM_001481.2		15,542,5936	TT,TC,CC		5.8967,1.4813,4.4047		350/479	90106746	572,12414	2194	4299	6493	SO:0001819	synonymous_variant	2622	exon9			GTTCACCGCAGCC	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.1050C>T	16.37:g.90106746C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	39	23	0.589744	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Silent	SNP	ENST00000268699.4	37	CCDS10992.1																																																																																			C|0.963;T|0.037	0.037	strong		0.627	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
TYRP1	7306	hgsc.bcm.edu	37	9	12694255	12694255	+	Silent	SNP	C	C	A	rs34509359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:12694255C>A	ENST00000388918.5	+	2	388	c.259C>A	c.(259-261)Cgg>Agg	p.R87R	TYRP1_ENST00000381136.2_5'Flank|TYRP1_ENST00000381137.2_5'UTR	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	87					acetoacetic acid metabolic process (GO:0043438)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen (GO:0016716)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|stomach(1)	22		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		CAGAGATGATCGGGAGGTCTG	0.592									Oculocutaneous Albinism				C|||	84	0.0167732	0.003	0.0202	5008	,	,		17928	0.0		0.0567	False		,,,				2504	0.0092				p.R87R		Atlas-SNP	.											.	TYRP1	60	.	0			c.C259A						PASS	.	C		73,4333	64.7+/-102.0	0,73,2130	46.0	40.0	42.0		259	3.6	0.9	9	dbSNP_126	42	526,8074	148.0+/-203.3	19,488,3793	no	coding-synonymous	TYRP1	NM_000550.2		19,561,5923	AA,AC,CC		6.1163,1.6568,4.6056		87/538	12694255	599,12407	2203	4300	6503	SO:0001819	synonymous_variant	7306	exon2	Familial Cancer Database		GATGATCGGGAGG	L33830	CCDS34990.1	9p23	2013-01-08			ENSG00000107165	ENSG00000107165			12450	protein-coding gene	gene with protein product		115501		TYRP, CAS2		9434945	Standard	NM_000550		Approved	GP75, CATB, TRP, b-PROTEIN, OCA3	uc003zkv.4	P17643	OTTHUMG00000021034	ENST00000388918.5:c.259C>A	9.37:g.12694255C>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	NM_000550	P78468|P78469|Q13721|Q15679	Silent	SNP	ENST00000388918.5	37	CCDS34990.1																																																																																			C|0.959;A|0.041	0.041	strong		0.592	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550	
XRRA1	143570	hgsc.bcm.edu	37	11	74563077	74563077	+	Silent	SNP	G	G	A	rs2304683	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:74563077G>A	ENST00000340360.6	-	13	1528	c.1197C>T	c.(1195-1197)tgC>tgT	p.C399C	XRRA1_ENST00000321448.8_Silent_p.C124C|XRRA1_ENST00000527087.1_Intron	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						AGACGAACTCGCAGAGAGATG	0.542													G|||	1340	0.267572	0.093	0.4827	5008	,	,		21900	0.506		0.2833	False		,,,				2504	0.089				p.C399C		Atlas-SNP	.											.	XRRA1	46	.	0			c.C1197T						PASS	.	G		507,3555		40,427,1564	139.0	141.0	140.0		1197	-6.4	0.7	11	dbSNP_100	140	2189,6181		286,1617,2282	no	coding-synonymous	XRRA1	NM_182969.1		326,2044,3846	AA,AG,GG		26.1529,12.4815,21.686		399/793	74563077	2696,9736	2031	4185	6216	SO:0001819	synonymous_variant	143570	exon13			GAACTCGCAGAGA	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1197C>T	11.37:g.74563077G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_182969		Silent	SNP	ENST00000340360.6	37	CCDS44680.1																																																																																			G|0.689;A|0.311	0.311	strong		0.542	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969	
GLB1L2	89944	hgsc.bcm.edu	37	11	134226278	134226278	+	Silent	SNP	C	C	T	rs3802928	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:134226278C>T	ENST00000535456.2	+	6	830	c.642C>T	c.(640-642)taC>taT	p.Y214Y	GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Silent_p.Y214Y|GLB1L2_ENST00000389881.3_Silent_p.Y214Y	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	214					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)	p.Y214Y(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		ACATGCCCTACGTCAAGAAGG	0.458													C|||	634	0.126597	0.2027	0.0677	5008	,	,		17955	0.1944		0.0596	False		,,,				2504	0.0644				p.Y214Y		Atlas-SNP	.											GLB1L2,NS,carcinoma,0,1	GLB1L2	79	1	1	Substitution - coding silent(1)	stomach(1)	c.C642T						PASS	.	C		833,3569	330.7+/-301.6	85,663,1453	128.0	135.0	132.0		642	-1.6	0.0	11	dbSNP_107	132	415,8179	130.2+/-188.1	15,385,3897	no	coding-synonymous	GLB1L2	NM_138342.3		100,1048,5350	TT,TC,CC		4.829,18.9232,9.603		214/637	134226278	1248,11748	2201	4297	6498	SO:0001819	synonymous_variant	89944	exon6			GCCCTACGTCAAG		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.642C>T	11.37:g.134226278C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Silent	SNP	ENST00000535456.2	37	CCDS31724.1	264	0.12087912087912088	89	0.18089430894308944	20	0.055248618784530384	115	0.20104895104895104	40	0.052770448548812667	C	0.027	-1.362446	0.01235	0.189232	0.04829	ENSG00000149328	ENST00000525089;ENST00000533324	.	.	.	5.76	-1.59	0.08453	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.22779	P	0.9987403	.	.	.	.	.	.	T	0.17289	-1.0374	3	.	.	.	-11.4588	11.0134	0.47675	0.0:0.4036:0.0:0.5964	rs3802928;rs57061991;rs3802928	.	.	.	C	153;42	.	.	R	+	1	0	GLB1L2	133731488	0.000000	0.05858	0.009000	0.14445	0.018000	0.09664	-1.437000	0.02419	-0.616000	0.05671	-0.137000	0.14449	CGT	C|0.888;T|0.112	0.112	strong		0.458	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	
LPCAT2	54947	hgsc.bcm.edu	37	16	55562359	55562359	+	Missense_Mutation	SNP	G	G	A	rs61739979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:55562359G>A	ENST00000262134.5	+	3	566	c.382G>A	c.(382-384)Gta>Ata	p.V128I		NM_017839.4	NP_060309.2	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	128					glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	12						TATAGTTGCTGTAAAAGGAAA	0.373													G|||	28	0.00559105	0.0	0.013	5008	,	,		15243	0.0		0.0099	False		,,,				2504	0.0092				p.V128I		Atlas-SNP	.											.	LPCAT2	35	.	0			c.G382A						PASS	.	G	ILE/VAL	10,4386	16.8+/-37.8	0,10,2188	169.0	155.0	160.0		382	5.8	1.0	16	dbSNP_129	160	92,8508	51.9+/-112.3	1,90,4209	yes	missense	LPCAT2	NM_017839.4	29	1,100,6397	AA,AG,GG		1.0698,0.2275,0.7849	possibly-damaging	128/545	55562359	102,12894	2198	4300	6498	SO:0001583	missense	54947	exon3			GTTGCTGTAAAAG	AK000488	CCDS10753.1	16q12.2	2013-01-10	2007-12-17	2007-12-17	ENSG00000087253	ENSG00000087253		"""EF-hand domain containing"""	26032	protein-coding gene	gene with protein product		612040	"""acyltransferase like 1"""	AYTL1		16704971	Standard	NM_017839		Approved	FLJ20481	uc002eie.4	Q7L5N7	OTTHUMG00000133238	ENST00000262134.5:c.382G>A	16.37:g.55562359G>A	ENSP00000262134:p.Val128Ile	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	349	151	0.432665	NM_017839	A3KBM1|Q6MZJ6|Q9NX23	Missense_Mutation	SNP	ENST00000262134.5	37	CCDS10753.1	8	0.003663003663003663	0	0.0	5	0.013812154696132596	0	0.0	3	0.00395778364116095	G	18.04	3.534563	0.64972	0.002275	0.010698	ENSG00000087253	ENST00000262134	D	0.92545	-3.06	5.8	5.8	0.92144	Phospholipid/glycerol acyltransferase (1);	0.106957	0.64402	D	0.000007	D	0.90834	0.7121	L	0.47190	1.495	0.80722	D	1	P	0.44521	0.837	P	0.51701	0.677	D	0.89456	0.3733	10	0.32370	T	0.25	-29.6323	20.0553	0.97649	0.0:0.0:1.0:0.0	rs61739979	128	Q7L5N7	PCAT2_HUMAN	I	128	ENSP00000262134:V128I	ENSP00000262134:V128I	V	+	1	0	LPCAT2	54119860	1.000000	0.71417	0.966000	0.40874	0.199000	0.23934	5.400000	0.66320	2.754000	0.94517	0.585000	0.79938	GTA	G|0.994;A|0.006	0.006	strong		0.373	LPCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256977.2	NM_017839	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052743	33052743	+	Silent	SNP	T	T	C	rs1126541	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33052743T>C	ENST00000418931.2	+	3	497	c.381T>C	c.(379-381)aaT>aaC	p.N127N		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	127	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CTAGGGTGAATGTTTCCCCCT	0.493																																					p.N127N		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.T381C						PASS	.						56.0	79.0	71.0					6																	33052743		1508	2708	4216	SO:0001819	synonymous_variant	3115	exon3			GGTGAATGTTTCC		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.381T>C	6.37:g.33052743T>C		Somatic	391	0	0		WXS	Illumina HiSeq	Phase_I	290	87	0.3	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Silent	SNP	ENST00000418931.2	37	CCDS4765.1	.	.	.	.	.	.	.	.	.	.	C	2.747	-0.260959	0.05791	.	.	ENSG00000223865	ENST00000416804	.	.	.	3.85	-3.8	0.04307	.	.	.	.	.	T	0.20007	0.0481	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.18178	-1.0345	3	.	.	.	.	9.3844	0.38333	0.0:0.1988:0.1206:0.6806	rs1126541;rs3176951;rs17434414;rs17851010	.	.	.	T	94	.	.	M	+	2	0	HLA-DPB1	33160721	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.188000	0.00566	-1.277000	0.02411	-0.262000	0.10625	ATG	T|0.706;C|0.294	0.294	strong		0.493	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
HTR6	3362	hgsc.bcm.edu	37	1	19992513	19992513	+	Silent	SNP	C	C	T	rs1805054	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:19992513C>T	ENST00000289753.1	+	1	734	c.267C>T	c.(265-267)taC>taT	p.Y89Y		NM_000871.1	NP_000862.1	P50406	5HT6R_HUMAN	5-hydroxytryptamine (serotonin) receptor 6, G protein-coupled	89					brain development (GO:0007420)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|long-term synaptic potentiation (GO:0060291)|negative regulation of acetylcholine secretion, neurotransmission (GO:0014058)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|synaptic transmission (GO:0007268)	cilium (GO:0005929)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)|serotonin receptor activity (GO:0004993)			endometrium(1)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.81e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00117)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Mianserin(DB06148)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Quetiapine(DB01224)|Sertindole(DB06144)|Ziprasidone(DB00246)	ACGCGCTGTACGGGCGCTGGG	0.657													C|||	864	0.172524	0.202	0.1167	5008	,	,		14788	0.2123		0.1163	False		,,,				2504	0.1892				p.Y89Y	Esophageal Squamous(168;1879 2619 6848 21062)	Atlas-SNP	.											.	HTR6	38	.	0			c.C267T	GRCh37	CM994739	HTR6	M	rs1805054	PASS	.	C		838,3566	324.2+/-298.5	78,682,1442	43.0	42.0	42.0		267	1.2	1.0	1	dbSNP_89	42	1141,7455	231.2+/-265.3	79,983,3236	no	coding-synonymous	HTR6	NM_000871.1		157,1665,4678	TT,TC,CC		13.2736,19.0282,15.2231		89/441	19992513	1979,11021	2202	4298	6500	SO:0001819	synonymous_variant	3362	exon1			GCTGTACGGGCGC	L41147	CCDS197.1	1p36-p35	2012-08-08	2012-02-03		ENSG00000158748	ENSG00000158748		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5301	protein-coding gene	gene with protein product		601109	"""5-hydroxytryptamine (serotonin) receptor 6"""			8522988	Standard	NM_000871		Approved	5-HT6, 5-HT6R	uc001bcl.3	P50406	OTTHUMG00000002713	ENST00000289753.1:c.267C>T	1.37:g.19992513C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	76	48	0.631579	NM_000871	Q13640|Q5TGZ1	Silent	SNP	ENST00000289753.1	37	CCDS197.1																																																																																			C|0.839;T|0.161	0.161	strong		0.657	HTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007704.1	NM_000871	
WNT9A	7483	hgsc.bcm.edu	37	1	228113073	228113073	+	Silent	SNP	C	C	G	rs8192628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:228113073C>G	ENST00000272164.5	-	2	253	c.243G>C	c.(241-243)acG>acC	p.T81T		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	81					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				CCTCCACCAGCGTCTCTGCCA	0.701													C|||	10	0.00199681	0.0	0.0	5008	,	,		16240	0.0		0.008	False		,,,				2504	0.002				p.T81T		Atlas-SNP	.											.	WNT9A	39	.	0			c.G243C						PASS	.	C		8,4394		0,8,2193	17.0	18.0	17.0		243	-6.8	0.9	1	dbSNP_117	17	82,8506		0,82,4212	no	coding-synonymous	WNT9A	NM_003395.2		0,90,6405	GG,GC,CC		0.9548,0.1817,0.6928		81/366	228113073	90,12900	2201	4294	6495	SO:0001819	synonymous_variant	7483	exon2			CACCAGCGTCTCT	AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"""Wingless-type MMTV integration sites"""	12778	protein-coding gene	gene with protein product		602863	"""wingless-type MMTV integration site family, member 14"""	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.243G>C	1.37:g.228113073C>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Silent	SNP	ENST00000272164.5	37	CCDS31045.1																																																																																			G|0.005;C|0.995	0.005	strong		0.701	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395	
IKBKAP	8518	hgsc.bcm.edu	37	9	111679872	111679872	+	Silent	SNP	G	G	A	rs12340246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:111679872G>A	ENST00000374647.5	-	9	1126	c.819C>T	c.(817-819)ctC>ctT	p.L273L	IKBKAP_ENST00000537196.1_5'UTR	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	273					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)	p.L273L(1)		NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						GTCCATGAAGGAGTCCATTTT	0.408													G|||	334	0.0666933	0.0091	0.1513	5008	,	,		18116	0.0933		0.0596	False		,,,				2504	0.0644				p.L273L		Atlas-SNP	.											IKBKAP,NS,carcinoma,0,1	IKBKAP	122	1	1	Substitution - coding silent(1)	stomach(1)	c.C819T						scavenged	.	G		65,4341	60.5+/-97.4	0,65,2138	159.0	160.0	160.0		819	1.4	1.0	9	dbSNP_120	160	384,8216	124.4+/-183.2	7,370,3923	no	coding-synonymous	IKBKAP	NM_003640.3		7,435,6061	AA,AG,GG		4.4651,1.4753,3.4523		273/1333	111679872	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	8518	exon9			ATGAAGGAGTCCA	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.819C>T	9.37:g.111679872G>A		Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	145	72	0.496552	NM_003640	Q5JSV2|Q9H327|Q9UG87	Silent	SNP	ENST00000374647.5	37	CCDS6773.1																																																																																			G|0.952;A|0.048	0.048	strong		0.408	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
ZNF441	126068	hgsc.bcm.edu	37	19	11891003	11891003	+	Missense_Mutation	SNP	G	G	A	rs799193	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11891003G>A	ENST00000357901.4	+	4	466	c.364G>A	c.(364-366)Gtt>Att	p.V122I	ZNF441_ENST00000454339.2_Missense_Mutation_p.V55I	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	122				V -> I (in Ref. 1; BAC04661 and 3; BC144217). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TAATTGCTACGTTAGAGTTGA	0.428													A|||	4476	0.89377	0.969	0.8588	5008	,	,		19072	0.9514		0.7903	False		,,,				2504	0.864				p.V122I		Atlas-SNP	.											.	ZNF441	123	.	0			c.G364A						PASS	.	A	ILE/VAL	4169,237	140.8+/-176.2	1970,229,4	113.0	98.0	103.0		364	0.2	0.0	19	dbSNP_86	103	6791,1809	325.5+/-317.0	2680,1431,189	yes	missense	ZNF441	NM_152355.2	29	4650,1660,193	AA,AG,GG		21.0349,5.379,15.7312	benign	122/694	11891003	10960,2046	2203	4300	6503	SO:0001583	missense	126068	exon4			TGCTACGTTAGAG	AK095956	CCDS12266.2	19p13.13	2013-01-08			ENSG00000197044	ENSG00000197044		"""Zinc fingers, C2H2-type"", ""-"""	20875	protein-coding gene	gene with protein product							Standard	NM_152355		Approved	FLJ38637	uc010dyj.3	Q8N8Z8	OTTHUMG00000154449	ENST00000357901.4:c.364G>A	19.37:g.11891003G>A	ENSP00000350576:p.Val122Ile	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_152355		Missense_Mutation	SNP	ENST00000357901.4	37	CCDS12266.2	1919	0.8786630036630036	470	0.9552845528455285	303	0.8370165745856354	546	0.9545454545454546	600	0.7915567282321899	a	1.130	-0.652644	0.03480	0.94621	0.789651	ENSG00000197044	ENST00000409902;ENST00000357901;ENST00000454339	T;T	0.05513	3.52;3.43	1.22	0.166	0.14999	.	.	.	.	.	T	0.00012	0.0000	N	0.04297	-0.235	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06127	-1.0844	8	0.51188	T	0.08	.	4.2697	0.10780	0.526:0.0:0.474:0.0	rs799193;rs12979868;rs17463947;rs56635883;rs57441506;rs799193	122	Q8N8Z8	ZN441_HUMAN	I	78;122;55	ENSP00000350576:V122I;ENSP00000403738:V55I	ENSP00000350576:V122I	V	+	1	0	ZNF441	11752003	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.300000	0.08243	-0.474000	0.06862	-0.893000	0.02921	GTT	G|0.136;A|0.864	0.864	strong		0.428	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807755	18807755	+	Missense_Mutation	SNP	G	G	A	rs34976233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18807755G>A	ENST00000400664.1	+	1	332	c.280G>A	c.(280-282)Ggc>Agc	p.G94S		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	94			G -> S (in dbSNP:rs34976233).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGCACCACAGGGCTGCAGCTG	0.642													G|||	473	0.0944489	0.1233	0.1239	5008	,	,		17121	0.0377		0.1233	False		,,,				2504	0.0634				p.G94S		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G280A						PASS	.	G	SER/GLY	380,3592		20,340,1626	18.0	21.0	20.0		280	4.2	0.0	1	dbSNP_126	20	1023,7303		64,895,3204	yes	missense	KLHDC7A	NM_152375.2	56	84,1235,4830	AA,AG,GG		12.2868,9.567,11.4084	possibly-damaging	94/778	18807755	1403,10895	1986	4163	6149	SO:0001583	missense	127707	exon1			CCACAGGGCTGCA	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.280G>A	1.37:g.18807755G>A	ENSP00000383505:p.Gly94Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	211	0.09661172161172162	45	0.09146341463414634	48	0.13259668508287292	29	0.050699300699300696	89	0.11741424802110818	G	17.60	3.429416	0.62844	0.09567	0.122868	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.73789	-0.78	5.09	4.18	0.49190	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.80722	P	0.0	B	0.28636	0.218	B	0.21360	0.034	T	0.12604	-1.0541	8	0.42905	T	0.14	.	8.0117	0.30357	0.0884:0.1608:0.7508:0.0	rs34976233	94	Q5VTJ3	KLD7A_HUMAN	S	94;31	ENSP00000383505:G94S	ENSP00000383505:G94S	G	+	1	0	KLHDC7A	18680342	0.021000	0.18746	0.009000	0.14445	0.013000	0.08279	2.183000	0.42565	1.470000	0.48102	0.591000	0.81541	GGC	G|0.895;A|0.105	0.105	strong		0.642	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
SERPINA5	5104	hgsc.bcm.edu	37	14	95058462	95058462	+	Silent	SNP	A	A	C	rs6116	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:95058462A>C	ENST00000554866.1	+	5	1221	c.1107A>C	c.(1105-1107)atA>atC	p.I369I	RP11-986E7.7_ENST00000553947.1_Missense_Mutation_p.Y23S|SERPINA5_ENST00000553780.1_Silent_p.I369I|SERPINA5_ENST00000554276.1_Silent_p.I369I|SERPINA5_ENST00000329597.7_Silent_p.I369I			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	369					fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CGGGGACAATATTCACTTTCA	0.557													C|||	1402	0.279952	0.2731	0.2723	5008	,	,		18114	0.0784		0.4781	False		,,,				2504	0.2986				p.I369I		Atlas-SNP	.											.	SERPINA5	69	.	0			c.A1107C						PASS	.	C		1330,3076	695.9+/-406.0	204,922,1077	189.0	196.0	194.0		1107	1.2	0.0	14	dbSNP_52	194	4213,4387	584.0+/-391.6	1026,2161,1113	no	coding-synonymous	SERPINA5	NM_000624.4		1230,3083,2190	CC,CA,AA		48.9884,30.1861,42.6188		369/407	95058462	5543,7463	2203	4300	6503	SO:0001819	synonymous_variant	5104	exon6			GACAATATTCACT	M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"""Serine (or cysteine) peptidase inhibitors"""	8723	protein-coding gene	gene with protein product		601841	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"""	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.1107A>C	14.37:g.95058462A>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	134	133	0.992537	NM_000624	Q07616|Q9UG30	Silent	SNP	ENST00000554866.1	37	CCDS9928.1																																																																																			A|0.635;C|0.365	0.365	strong		0.557	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
CDCA2	157313	hgsc.bcm.edu	37	8	25364960	25364960	+	Silent	SNP	A	A	G	rs6990278	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:25364960A>G	ENST00000330560.3	+	15	3255	c.2778A>G	c.(2776-2778)acA>acG	p.T926T	CDCA2_ENST00000380665.3_Silent_p.T911T|CDCA2_ENST00000521098.2_3'UTR	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	926					mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		CAATATGTACATTTGACAGCA	0.428													A|||	964	0.192492	0.1687	0.1931	5008	,	,		19672	0.2351		0.2147	False		,,,				2504	0.1575				p.T926T		Atlas-SNP	.											.	CDCA2	78	.	0			c.A2778G						PASS	.	A		769,3637	311.9+/-292.3	73,623,1507	184.0	196.0	192.0		2778	-4.6	0.0	8	dbSNP_116	192	1729,6871	313.5+/-311.4	178,1373,2749	no	coding-synonymous	CDCA2	NM_152562.2		251,1996,4256	GG,GA,AA		20.1047,17.4535,19.2065		926/1024	25364960	2498,10508	2203	4300	6503	SO:0001819	synonymous_variant	157313	exon15			ATGTACATTTGAC	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 81"""					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.2778A>G	8.37:g.25364960A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_152562	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Silent	SNP	ENST00000330560.3	37	CCDS6049.1																																																																																			A|0.800;G|0.200	0.200	strong		0.428	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562	
SLC9C1	285335	hgsc.bcm.edu	37	3	111901099	111901099	+	Missense_Mutation	SNP	T	T	C	rs74840030	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:111901099T>C	ENST00000305815.5	-	21	2782	c.2530A>G	c.(2530-2532)Atg>Gtg	p.M844V	SLC9C1_ENST00000487372.1_Missense_Mutation_p.M796V	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	844					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TTTTTGGCCATGATTAACTAA	0.343													T|||	185	0.0369409	0.0045	0.036	5008	,	,		15999	0.002		0.0537	False		,,,				2504	0.1002				p.M844V		Atlas-SNP	.											.	.	.	.	0			c.A2530G						PASS	.	T	VAL/MET	37,4369	41.6+/-74.8	0,37,2166	75.0	83.0	80.0		2530	4.6	1.0	3	dbSNP_132	80	458,8132	135.4+/-192.6	12,434,3849	yes	missense	SLC9A10	NM_183061.1	21	12,471,6015	CC,CT,TT		5.3318,0.8398,3.8089	benign	844/1178	111901099	495,12501	2203	4295	6498	SO:0001583	missense	285335	exon21			TGGCCATGATTAA	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2530A>G	3.37:g.111901099T>C	ENSP00000306627:p.Met844Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	166	62	0.373494	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	63	0.028846153846153848	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	41	0.05408970976253298	T	8.685	0.906139	0.17760	0.008398	0.053318	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.77750	-1.12;-1.12	5.81	4.59	0.56863	.	0.343378	0.29602	N	0.011697	T	0.29389	0.0732	M	0.64997	1.995	0.25998	N	0.982155	B;B	0.32918	0.39;0.176	B;B	0.37731	0.257;0.037	T	0.58120	-0.7692	10	0.59425	D	0.04	.	9.328	0.38005	0.0:0.0:0.1806:0.8194	.	796;844	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	V	844;796	ENSP00000306627:M844V;ENSP00000420688:M796V	ENSP00000306627:M844V	M	-	1	0	SLC9A10	113383789	0.888000	0.30383	1.000000	0.80357	0.012000	0.07955	1.327000	0.33746	2.215000	0.71742	0.491000	0.48974	ATG	T|0.962;C|0.038	0.038	strong		0.343	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
ASB6	140459	hgsc.bcm.edu	37	9	132400480	132400480	+	Silent	SNP	G	G	A	rs3739851	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:132400480G>A	ENST00000277458.4	-	6	1020	c.855C>T	c.(853-855)gcC>gcT	p.A285A	ASB6_ENST00000277459.4_3'UTR|ASB6_ENST00000450050.2_Silent_p.A206A|RP11-483H20.4_ENST00000455074.1_RNA	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	285					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				NS(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	15		Ovarian(14;0.00556)				AGTTGTAGGCGGCTCCGGACT	0.612													G|||	2311	0.461462	0.3238	0.4899	5008	,	,		19853	0.5129		0.5567	False		,,,				2504	0.4765				p.A285A		Atlas-SNP	.											.	ASB6	31	.	0			c.C855T						PASS	.	G	,,	1622,2784	498.9+/-364.3	297,1028,878	53.0	50.0	51.0		768,855,	-9.3	0.1	9	dbSNP_107	51	5248,3352	643.3+/-399.9	1600,2048,652	no	coding-synonymous,coding-synonymous,utr-3	ASB6	NM_001202403.1,NM_017873.3,NM_177999.2	,,	1897,3076,1530	AA,AG,GG		38.9767,36.8134,47.1782	,,	256/393,285/422,	132400480	6870,6136	2203	4300	6503	SO:0001819	synonymous_variant	140459	exon6			GTAGGCGGCTCCG		CCDS6924.1, CCDS6925.1, CCDS75919.1	9q34.13	2013-01-10	2011-01-25		ENSG00000148331	ENSG00000148331		"""Ankyrin repeat domain containing"""	17181	protein-coding gene	gene with protein product		615051	"""ankyrin repeat and SOCS box-containing 6"""				Standard	NM_017873		Approved		uc004byf.2	Q9NWX5	OTTHUMG00000020787	ENST00000277458.4:c.855C>T	9.37:g.132400480G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_017873	Q5SZB7|Q9BV15	Silent	SNP	ENST00000277458.4	37	CCDS6924.1																																																																																			G|0.503;A|0.497	0.497	strong		0.612	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873	
MUC21	394263	hgsc.bcm.edu	37	6	30954504	30954504	+	Missense_Mutation	SNP	G	G	C	rs200661879		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954504G>C	ENST00000376296.3	+	2	793	c.552G>C	c.(550-552)gaG>gaC	p.E184D	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	184	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAACTCTGAGTCCAGCACAG	0.602																																					p.E184D		Atlas-SNP	.											.	MUC21	98	.	0			c.G552C						PASS	.						171.0	162.0	165.0					6																	30954504		2203	4300	6503	SO:0001583	missense	394263	exon2			CTCTGAGTCCAGC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.552G>C	6.37:g.30954504G>C	ENSP00000365473:p.Glu184Asp	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	158	18	0.113924	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	6.890	0.533768	0.13188	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.01787	4.64	3.49	-3.84	0.04256	.	.	.	.	.	T	0.00356	0.0011	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.42015	-0.9476	8	.	.	.	-1.4131	4.4534	0.11631	0.4451:0.3107:0.2442:0.0	.	184	Q5SSG8	MUC21_HUMAN	D	184	ENSP00000365473:E184D	.	E	+	3	2	MUC21	31062483	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.853000	0.04303	-0.831000	0.04256	-0.410000	0.06199	GAG	.	.	weak		0.602	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
T	6862	hgsc.bcm.edu	37	6	166572045	166572045	+	Missense_Mutation	SNP	C	C	T	rs3127328	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:166572045C>T	ENST00000296946.2	-	9	1534	c.1066G>A	c.(1066-1068)Ggc>Agc	p.G356S	T_ENST00000366871.3_Missense_Mutation_p.G298S	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	356			G -> S (in dbSNP:rs3127328).		anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		GTGACGGCGCCGTTGCTCACA	0.662									Chordoma, Familial Clustering of				C|||	685	0.136781	0.2428	0.0735	5008	,	,		14152	0.0486		0.1193	False		,,,				2504	0.1472				p.G356S		Atlas-SNP	.											.	T	77	.	0			c.G1066A						PASS	.	C	SER/GLY	911,3473		86,739,1367	13.0	17.0	16.0		1066	1.3	0.0	6	dbSNP_103	16	1045,7537		69,907,3315	yes	missense	T	NM_003181.2	56	155,1646,4682	TT,TC,CC		12.1766,20.7801,15.0856	benign	356/436	166572045	1956,11010	2192	4291	6483	SO:0001583	missense	6862	exon9	Familial Cancer Database		CGGCGCCGTTGCT	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"""T-boxes"""	11515	protein-coding gene	gene with protein product		601397	"""T brachyury (mouse) homolog"""			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.1066G>A	6.37:g.166572045C>T	ENSP00000296946:p.Gly356Ser	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_003181	E7ERD6|Q4KMP4	Missense_Mutation	SNP	ENST00000296946.2	37	CCDS5290.1	267	0.12225274725274725	118	0.23983739837398374	33	0.09116022099447514	22	0.038461538461538464	94	0.12401055408970976	C	0.893	-0.724885	0.03158	0.207801	0.121766	ENSG00000164458	ENST00000366876;ENST00000296946;ENST00000366871	T;D	0.81579	-1.48;-1.51	4.68	1.28	0.21552	.	0.612730	0.16544	N	0.209807	T	0.18087	0.0434	N	0.00510	-1.415	0.54753	P	1.6000000000016E-5	B;B;B	0.16802	0.019;0.002;0.009	B;B;B	0.10450	0.004;0.003;0.005	T	0.22103	-1.0226	9	0.02654	T	1	.	5.5945	0.17319	0.0:0.4387:0.0:0.5613	rs3127328;rs3127328	298;356;298	E7ERD6;O15178;Q4KMP4	.;BRAC_HUMAN;.	S	356;356;298	ENSP00000296946:G356S;ENSP00000355836:G298S	ENSP00000296946:G356S	G	-	1	0	T	166492035	1.000000	0.71417	0.006000	0.13384	0.691000	0.40173	1.412000	0.34714	0.478000	0.27488	0.655000	0.94253	GGC	C|0.877;T|0.123	0.123	strong		0.662	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
EPRS	2058	hgsc.bcm.edu	37	1	220156704	220156704	+	Missense_Mutation	SNP	T	T	C	rs5030752	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:220156704T>C	ENST00000366923.3	-	22	3396	c.3127A>G	c.(3127-3129)Ata>Gta	p.I1043V		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1043	Proline--tRNA ligase.		I -> V (in dbSNP:rs5030752). {ECO:0000269|PubMed:17974005}.		cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)	p.I1043V(1)		breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	CAGCCACTTATGTCATGGTAT	0.363													C|||	328	0.0654952	0.0756	0.0389	5008	,	,		17830	0.0536		0.0944	False		,,,				2504	0.0532				p.I1043V		Atlas-SNP	.											EPRS,NS,carcinoma,0,1	EPRS	140	1	1	Substitution - Missense(1)	stomach(1)	c.A3127G						PASS	.	C	VAL/ILE	320,4086	796.1+/-415.3	12,296,1895	55.0	57.0	57.0		3127	4.6	1.0	1	dbSNP_113	57	673,7927	788.6+/-407.6	29,615,3656	yes	missense	EPRS	NM_004446.2	29	41,911,5551	CC,CT,TT		7.8256,7.2628,7.6349	benign	1043/1513	220156704	993,12013	2203	4300	6503	SO:0001583	missense	2058	exon22			CACTTATGTCATG	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"""Aminoacyl tRNA synthetases / Class I"", ""Aminoacyl tRNA synthetases / Class II"""	3418	protein-coding gene	gene with protein product	"""glutamate tRNA ligase"", ""proline tRNA ligase"""	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3127A>G	1.37:g.220156704T>C	ENSP00000355890:p.Ile1043Val	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	234	106	0.452991	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Missense_Mutation	SNP	ENST00000366923.3	37	CCDS31027.1	146	0.06684981684981685	35	0.07113821138211382	18	0.049723756906077346	25	0.043706293706293704	68	0.08970976253298153	C	4.410	0.075691	0.08485	0.072628	0.078256	ENSG00000136628	ENST00000366923	T	0.26810	1.71	5.47	4.56	0.56223	.	0.000000	0.85682	N	0.000000	T	0.00271	0.0008	N	0.00599	-1.345	0.50467	P	1.2999999999996348E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.27054	-1.0085	9	0.02654	T	1	-12.0557	12.1012	0.53785	0.0:0.861:0.0:0.139	rs5030752;rs5030752	1043	P07814	SYEP_HUMAN	V	1043	ENSP00000355890:I1043V	ENSP00000355890:I1043V	I	-	1	0	EPRS	218223327	1.000000	0.71417	0.998000	0.56505	0.706000	0.40770	5.884000	0.69729	0.714000	0.32081	-0.726000	0.03593	ATA	T|0.929;C|0.071	0.071	strong		0.363	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446	
GPER1	2852	hgsc.bcm.edu	37	7	1132260	1132260	+	Missense_Mutation	SNP	G	G	A	rs150960969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1132260G>A	ENST00000297469.3	+	2	1587	c.896G>A	c.(895-897)cGc>cAc	p.R299H	C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|GPER1_ENST00000397088.3_Missense_Mutation_p.R299H|C7orf50_ENST00000357429.6_Intron|GPER1_ENST00000397092.1_Missense_Mutation_p.R299H|GPER1_ENST00000401670.1_Missense_Mutation_p.R299H	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	299					apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										CAGTCTTTCCGCCATGCCCAC	0.627																																					p.R299H		Atlas-SNP	.											.	GPER	25	.	0			c.G896A						PASS	.		HIS/ARG,HIS/ARG,,,HIS/ARG,	1,4405	2.1+/-5.4	0,1,2202	86.0	68.0	74.0		896,896,,,896,	5.7	1.0	7	dbSNP_134	74	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense,intron,intron,missense,intron	GPER,C7orf50	NM_001039966.1,NM_001098201.1,NM_001134395.1,NM_001134396.1,NM_001505.2,NM_032350.5	29,29,,,29,	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	probably-damaging,probably-damaging,,,probably-damaging,	299/376,299/376,,,299/376,	1132260	9,12997	2203	4300	6503	SO:0001583	missense	2852	exon2			CTTTCCGCCATGC	U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"""G protein-coupled receptor 30"""	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.896G>A	7.37:g.1132260G>A	ENSP00000297469:p.Arg299His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Missense_Mutation	SNP	ENST00000297469.3	37	CCDS5322.1	.	.	.	.	.	.	.	.	.	.	G	17.40	3.381327	0.61845	2.27E-4	9.3E-4	ENSG00000164850	ENST00000401670;ENST00000397092;ENST00000297469;ENST00000397088;ENST00000508834	T;T;T;T	0.37411	1.2;1.2;1.2;1.2	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.057131	0.64402	D	0.000001	T	0.51193	0.1660	L	0.37630	1.12	0.54753	D	0.999989	D	0.89917	1.0	D	0.71414	0.973	T	0.39663	-0.9603	10	0.39692	T	0.17	-32.5649	18.7284	0.91724	0.0:0.0:1.0:0.0	.	299	Q99527	GPER_HUMAN	H	299	ENSP00000385151:R299H;ENSP00000380281:R299H;ENSP00000297469:R299H;ENSP00000380277:R299H	ENSP00000297469:R299H	R	+	2	0	GPER	1098786	1.000000	0.71417	1.000000	0.80357	0.371000	0.29859	6.012000	0.70767	2.670000	0.90874	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.627	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966	
YTHDC2	64848	hgsc.bcm.edu	37	5	112899702	112899702	+	Silent	SNP	A	A	G	rs6886628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:112899702A>G	ENST00000161863.4	+	20	2802	c.2589A>G	c.(2587-2589)acA>acG	p.T863T		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	863					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		TTGCTTGCACACTAGCTTATC	0.438													G|||	1662	0.331869	0.6165	0.4265	5008	,	,		15862	0.2004		0.1909	False		,,,				2504	0.1605				p.T863T		Atlas-SNP	.											.	YTHDC2	118	.	0			c.A2589G						PASS	.	G		2532,1872	540.5+/-375.5	747,1038,417	223.0	208.0	213.0		2589	-10.6	0.0	5	dbSNP_116	213	1580,7020	745.2+/-407.3	140,1300,2860	no	coding-synonymous	YTHDC2	NM_022828.3		887,2338,3277	GG,GA,AA		18.3721,42.5068,31.621		863/1431	112899702	4112,8892	2202	4300	6502	SO:0001819	synonymous_variant	64848	exon20			TTGCACACTAGCT	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.2589A>G	5.37:g.112899702A>G		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	301	299	0.993355	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																			A|0.681;G|0.319	0.319	strong		0.438	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
SLC11A2	4891	hgsc.bcm.edu	37	12	51386066	51386066	+	Silent	SNP	A	A	G	rs1048230	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:51386066A>G	ENST00000262051.7	-	13	1341	c.1254T>C	c.(1252-1254)atT>atC	p.I418I	SLC11A2_ENST00000262052.5_Silent_p.I418I|SLC11A2_ENST00000547688.1_Silent_p.I447I|SLC11A2_ENST00000394904.3_Silent_p.I447I|SLC11A2_ENST00000547198.1_Silent_p.I418I|SLC11A2_ENST00000541174.2_Silent_p.I418I|SLC11A2_ENST00000545993.2_Silent_p.I414I|SLC11A2_ENST00000546743.1_Silent_p.I339I	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	418					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						GGATGATGGCAATAGAGCGAG	0.473													A|||	691	0.137979	0.0484	0.1037	5008	,	,		21367	0.1151		0.1809	False		,,,				2504	0.2628				p.I447I		Atlas-SNP	.											.	SLC11A2	51	.	0			c.T1341C						PASS	.	A	,,,,,,	304,4102	166.9+/-198.0	9,286,1908	148.0	117.0	128.0		1254,1341,1254,1254,1254,1254,1242	3.0	1.0	12	dbSNP_86	128	1675,6925	308.4+/-308.9	164,1347,2789	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC11A2	NM_000617.2,NM_001174125.1,NM_001174126.1,NM_001174127.1,NM_001174128.1,NM_001174129.1,NM_001174130.1	,,,,,,	173,1633,4697	GG,GA,AA		19.4767,6.8997,15.2161	,,,,,,	418/562,447/591,418/569,418/569,418/562,418/562,414/558	51386066	1979,11027	2203	4300	6503	SO:0001819	synonymous_variant	4891	exon13			GATGGCAATAGAG	AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"""Solute carriers"""	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.1254T>C	12.37:g.51386066A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Silent	SNP	ENST00000262051.7	37	CCDS53792.1																																																																																			A|0.856;G|0.144	0.144	strong		0.473	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1		
USP44	84101	hgsc.bcm.edu	37	12	95927762	95927762	+	Missense_Mutation	SNP	T	T	C	rs3812813	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:95927762T>C	ENST00000258499.3	-	2	559	c.271A>G	c.(271-273)Aca>Gca	p.T91A	USP44_ENST00000537435.2_Missense_Mutation_p.T91A|USP44_ENST00000552440.1_Missense_Mutation_p.T91A|USP44_ENST00000393091.2_Missense_Mutation_p.T91A	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	91			T -> A (in dbSNP:rs3812813). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						TCTCCAGTTGTGTTATCATTC	0.403											OREG0022039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3586	0.716054	0.8646	0.7089	5008	,	,		24352	0.7242		0.5577	False		,,,				2504	0.6748				p.T91A		Atlas-SNP	.											.	USP44	83	.	0			c.A271G						PASS	.	C	ALA/THR,ALA/THR	3525,881	343.8+/-307.8	1409,707,87	161.0	138.0	146.0		271,271	4.2	1.0	12	dbSNP_107	146	4662,3938	548.2+/-385.3	1281,2100,919	yes	missense,missense	USP44	NM_001042403.1,NM_032147.2	58,58	2690,2807,1006	CC,CT,TT		45.7907,19.9955,37.0521	benign,benign	91/713,91/713	95927762	8187,4819	2203	4300	6503	SO:0001583	missense	84101	exon2			CAGTTGTGTTATC	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.271A>G	12.37:g.95927762T>C	ENSP00000258499:p.Thr91Ala	Somatic	250	0	0	1316	WXS	Illumina HiSeq	Phase_I	273	271	0.992674	NM_032147	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	37	CCDS9053.1	1497	0.6854395604395604	434	0.8821138211382114	246	0.6795580110497238	398	0.6958041958041958	419	0.5527704485488126	C	2.992	-0.207916	0.06180	0.800045	0.542093	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435;ENST00000551837;ENST00000549639	T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;1.61	5.12	4.22	0.49857	Zinc finger, RING/FYVE/PHD-type (1);	0.143807	0.64402	N	0.000006	T	0.00012	0.0000	N	0.00823	-1.155	0.47584	P	5.319999999999769E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.38779	-0.9645	9	0.02654	T	1	.	9.6068	0.39639	0.0:0.7806:0.0:0.2194	rs3812813;rs17845927;rs17858906;rs57133423;rs3812813	91	Q9H0E7	UBP44_HUMAN	A	91	ENSP00000258499:T91A;ENSP00000376806:T91A;ENSP00000448670:T91A;ENSP00000442629:T91A;ENSP00000448601:T91A;ENSP00000449635:T91A	ENSP00000258499:T91A	T	-	1	0	USP44	94451893	0.980000	0.34600	0.971000	0.41717	0.964000	0.63967	1.532000	0.36029	0.647000	0.30713	-0.215000	0.12644	ACA	T|0.338;C|0.662	0.662	strong		0.403	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	
CCDC63	160762	hgsc.bcm.edu	37	12	111342558	111342558	+	Silent	SNP	G	G	T	rs34300256	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:111342558G>T	ENST00000308208.5	+	11	1751	c.1509G>T	c.(1507-1509)gtG>gtT	p.V503V	CCDC63_ENST00000552694.1_Silent_p.V424V|CCDC63_ENST00000545036.1_Silent_p.V463V	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	503										NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						TCCCCCCAGTGCTGGGGGCTG	0.592													G|||	758	0.151358	0.1271	0.3516	5008	,	,		19331	0.002		0.2555	False		,,,				2504	0.089				p.V503V		Atlas-SNP	.											.	CCDC63	89	.	0			c.G1509T						PASS	.	G		640,3766	269.2+/-268.9	49,542,1612	58.0	58.0	58.0		1509	-0.4	0.0	12	dbSNP_126	58	2108,6492	352.9+/-328.9	260,1588,2452	no	coding-synonymous	CCDC63	NM_152591.1		309,2130,4064	TT,TG,GG		24.5116,14.5256,21.1287		503/564	111342558	2748,10258	2203	4300	6503	SO:0001819	synonymous_variant	160762	exon11			CCCAGTGCTGGGG	AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"""outer row dynein assembly 5 homolog (Chlamydomonas)"""						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1509G>T	12.37:g.111342558G>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_152591	B4DY03|Q0P603|Q6P2E1	Silent	SNP	ENST00000308208.5	37	CCDS9151.1																																																																																			G|0.810;T|0.190	0.190	strong		0.592	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591	
CHRNA4	1137	hgsc.bcm.edu	37	20	61981134	61981134	+	Silent	SNP	G	G	A	rs1044396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:61981134G>A	ENST00000370263.4	-	5	1850	c.1629C>T	c.(1627-1629)agC>agT	p.S543S	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	543					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	TGACCGTGGCGCTCGGGGACA	0.687													G|||	1620	0.323482	0.0613	0.4899	5008	,	,		12618	0.2679		0.5288	False		,,,				2504	0.4059				p.S543S		Atlas-SNP	.											.	CHRNA4	98	.	0			c.C1629T						PASS	.	G		657,3745	270.4+/-269.6	57,543,1601	37.0	40.0	39.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1629	-3.1	0.0	20	dbSNP_86	39	4651,3947	582.1+/-391.3	1273,2105,921	no	coding-synonymous	CHRNA4	NM_000744.5		1330,2648,2522	AA,AG,GG		45.906,14.925,40.8308		543/628	61981134	5308,7692	2201	4299	6500	SO:0001819	synonymous_variant	1137	exon5			CGTGGCGCTCGGG		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1958	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 4 (neuronal)"""	118504	"""cholinergic receptor, nicotinic, alpha polypeptide 4"""	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1629C>T	20.37:g.61981134G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	33	24	0.727273	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Silent	SNP	ENST00000370263.4	37	CCDS13517.1																																																																																			G|0.625;A|0.375	0.375	strong		0.687	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3		
HIST1H3C	8352	hgsc.bcm.edu	37	6	26045929	26045929	+	Silent	SNP	T	T	C	rs3752416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:26045929T>C	ENST00000540144.1	+	1	291	c.291T>C	c.(289-291)tgT>tgC	p.C97C	HIST1H2BB_ENST00000357905.2_5'Flank	NM_003531.2	NP_003522.1	P68431	H31_HUMAN	histone cluster 1, H3c	97					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|skin(1)	8						AGGAGGCTTGTGAGGCCTACC	0.582													C|||	3532	0.705272	0.7133	0.6902	5008	,	,		19436	0.8423		0.6531	False		,,,				2504	0.6176				p.C97C		Atlas-SNP	.											.	HIST1H3C	34	.	0			c.T291C						PASS	.	C		3167,1239	425.3+/-340.8	1140,887,176	61.0	57.0	58.0		291	0.5	0.8	6	dbSNP_107	58	5796,2804	441.7+/-359.9	1973,1850,477	no	coding-synonymous	HIST1H3C	NM_003531.2		3113,2737,653	CC,CT,TT		32.6047,28.1207,31.0857		97/137	26045929	8963,4043	2203	4300	6503	SO:0001819	synonymous_variant	8352	exon1			GGCTTGTGAGGCC	X57128	CCDS4576.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196532	ENSG00000278272		"""Histones / Replication-dependent"""	4768	protein-coding gene	gene with protein product		602812	"""H3 histone family, member C"", ""histone 1, H3c"""	H3FC		8227173, 9119399, 12408966	Standard	NM_003531		Approved	H3/c, H3.1	uc003nfv.3	P68431	OTTHUMG00000014416	ENST00000540144.1:c.291T>C	6.37:g.26045929T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_003531	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000540144.1	37	CCDS4576.1																																																																																			T|0.301;C|0.699	0.699	strong		0.582	HIST1H3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040078.1	NM_003531	
SLC3A1	6519	hgsc.bcm.edu	37	2	44547574	44547574	+	Missense_Mutation	SNP	G	G	A	rs698761	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:44547574G>A	ENST00000260649.6	+	10	1930	c.1854G>A	c.(1852-1854)atG>atA	p.M618I	PREPL_ENST00000541738.1_3'UTR|PREPL_ENST00000409411.1_3'UTR|PREPL_ENST00000409957.1_3'UTR|SLC3A1_ENST00000409380.1_Missense_Mutation_p.M340I|SLC3A1_ENST00000409740.3_Missense_Mutation_p.M249I|PREPL_ENST00000409936.1_3'UTR	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	618			M -> I (in dbSNP:rs698761). {ECO:0000269|PubMed:11318953, ECO:0000269|PubMed:11748844, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15913950, ECO:0000269|PubMed:7573036, ECO:0000269|PubMed:8486766, ECO:0000269|PubMed:8663184, ECO:0000269|PubMed:9186880}.		amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	CCGCTAAAATGAGAATAAGGT	0.403													G|||	2308	0.460863	0.2126	0.5447	5008	,	,		20446	0.3214		0.661	False		,,,				2504	0.6748				p.M618I		Atlas-SNP	.											.	SLC3A1	62	.	0			c.G1854A						PASS	.	G	ILE/MET,,,,,,,	1270,3136	431.8+/-343.0	188,894,1121	98.0	89.0	92.0		1854,,,,,,,	-1.4	0.0	2	dbSNP_86	92	5817,2783	677.8+/-403.4	1960,1897,443	yes	missense,utr-3,utr-3,utr-3,utr-3,utr-3,utr-3,utr-3	SLC3A1,PREPL	NM_000341.3,NM_001042385.2,NM_001042386.2,NM_001171603.1,NM_001171606.1,NM_001171613.1,NM_001171617.1,NM_006036.4	10,,,,,,,	2148,2791,1564	AA,AG,GG		32.3605,28.8243,45.5098	benign,,,,,,,	618/686,,,,,,,	44547574	7087,5919	2203	4300	6503	SO:0001583	missense	6519	exon10			TAAAATGAGAATA		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"""Solute carriers"""	11025	protein-coding gene	gene with protein product		104614	"""solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"""			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.1854G>A	2.37:g.44547574G>A	ENSP00000260649:p.Met618Ile	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	155	154	0.993548	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Missense_Mutation	SNP	ENST00000260649.6	37	CCDS1819.1	1000	0.45787545787545786	100	0.2032520325203252	206	0.569060773480663	198	0.34615384615384615	496	0.6543535620052771	G	7.667	0.686183	0.14973	0.288243	0.676395	ENSG00000138079	ENST00000260649;ENST00000540334;ENST00000409380;ENST00000409740	D;D;D	0.99014	-5.33;-4.75;-4.41	5.99	-1.37	0.09056	.	0.561087	0.19190	N	0.120443	T	0.00012	0.0000	L	0.35854	1.095	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.48525	-0.9028	9	0.08179	T;T	0.78;0.78	-1.1288	2.1005	0.03678	0.3431:0.3168:0.233:0.1071	rs698761;rs3172075;rs17580044;rs17845690;rs17858631;rs58800787;rs698761	618	Q07837	SLC31_HUMAN	I	618;554;340;249	ENSP00000260649:M618I;ENSP00000386709:M340I;ENSP00000386677:M249I	ENSP00000260649:M618I;ENSP00000260649:M618I	M	+	3	0	SLC3A1	44401078	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.163000	0.09997	0.140000	0.18849	-0.165000	0.13383	ATG	G|0.505;A|0.495	0.495	strong		0.403	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	
HLA-B	3106	hgsc.bcm.edu	37	6	31324641	31324641	+	Missense_Mutation	SNP	T	T	A	rs1050518	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324641T>A	ENST00000412585.2	-	2	195	c.167A>T	c.(166-168)cAg>cTg	p.Q56L		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	56	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CCTCACGAACTGGGTGTCGTC	0.672									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	995	0.198682	0.1331	0.2262	5008	,	,		9463	0.2054		0.2575	False		,,,				2504	0.2004				p.Q56L		Atlas-SNP	.											.	HLA-B	54	.	0			c.A167T						PASS	.	T	LEU/GLN	165,4137		9,147,1995	38.0	31.0	34.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	167	1.9	1.0	6	dbSNP_86	34	609,7693		62,485,3604	no	missense	HLA-B	NM_005514.6	113	71,632,5599	AA,AT,TT		7.3356,3.8354,6.1409		56/363	31324641	774,11830	2151	4151	6302	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	ACGAACTGGGTGT	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.167A>T	6.37:g.31324641T>A	ENSP00000399168:p.Gln56Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	153	70	0.457516	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	420	0.19230769230769232	63	0.12804878048780488	63	0.17403314917127072	129	0.22552447552447552	165	0.21767810026385223	N	5.247	0.231027	0.09969	0.038354	0.073356	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00014	9.2;9.2	3.2	1.9	0.25705	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	1.192420	0.06747	N	0.779383	T	0.00178	0.0005	M	0.85630	2.765	0.34590	P	0.284578	D;B;D	0.71674	0.998;0.0;0.996	D;B;D	0.80764	0.987;0.003;0.994	T	0.38134	-0.9675	9	0.56958	D	0.05	.	7.6356	0.28264	0.0:0.0:0.213:0.787	rs1050518;rs2308355;rs3175992;rs9266181;rs16896264	56;56;31	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	L	56;67	ENSP00000399168:Q56L;ENSP00000405931:Q67L	ENSP00000399168:Q56L	Q	-	2	0	HLA-B	31432620	0.251000	0.23961	0.999000	0.59377	0.015000	0.08874	0.238000	0.18004	1.476000	0.48215	0.368000	0.22195	CAG	T|0.909;A|0.091	0.091	strong		0.672	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
TBC1D17	79735	hgsc.bcm.edu	37	19	50381802	50381802	+	Silent	SNP	T	T	C	rs373760628		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50381802T>C	ENST00000221543.5	+	3	467	c.168T>C	c.(166-168)gaT>gaC	p.D56D	AKT1S1_ENST00000391831.1_5'Flank|AKT1S1_ENST00000391834.2_5'Flank|AKT1S1_ENST00000344175.5_5'Flank|TBC1D17_ENST00000535102.2_Silent_p.D23D|AKT1S1_ENST00000391835.1_5'Flank|TBC1D17_ENST00000598789.1_3'UTR|AKT1S1_ENST00000391832.3_5'Flank|AKT1S1_ENST00000482622.1_5'Flank	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	56					autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		AGGCTGGAGATTCCACCCAAA	0.552													T|||	1	0.000199681	0.0	0.0	5008	,	,		18217	0.0		0.001	False		,,,				2504	0.0				p.D56D		Atlas-SNP	.											TBC1D17,NS,carcinoma,+2,1	TBC1D17	39	1	0			c.T168C						PASS	.	T	,	0,4406		0,0,2203	105.0	99.0	101.0		69,168	2.2	1.0	19		101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TBC1D17	NM_001168222.1,NM_024682.2	,	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	,	23/616,56/649	50381802	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79735	exon3			TGGAGATTCCACC	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.168T>C	19.37:g.50381802T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_024682	B4DT12|B9A6L8|F5H1W7	Silent	SNP	ENST00000221543.5	37	CCDS12785.1																																																																																			.	.	weak		0.552	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919240	51919240	+	Silent	SNP	C	C	T	rs79484306	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51919240C>T	ENST00000339313.5	-	5	1052	c.936G>A	c.(934-936)ggG>ggA	p.G312G	SIGLEC10_ENST00000432469.2_Silent_p.G229G|SIGLEC10_ENST00000439889.2_Silent_p.G254G|SIGLEC10_ENST00000353836.5_Silent_p.G312G|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Silent_p.G254G|SIGLEC10_ENST00000436984.2_Silent_p.G264G|SIGLEC10_ENST00000356298.5_Silent_p.G312G|SIGLEC10_ENST00000525998.1_Intron|CTD-2616J11.2_ENST00000526996.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	312	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CAGCCTTCACCCCGGGCAGCT	0.672																																					p.G312G		Atlas-SNP	.											SIGLEC12_ENST00000439889,NS,carcinoma,-2,2	SIGLEC10	112	2	0			c.G936A						PASS	.						37.0	42.0	40.0					19																	51919240		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			CTTCACCCCGGGC	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.936G>A	19.37:g.51919240C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	210	47	0.22381	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			C|0.910;T|0.090	0.090	strong		0.672	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
SLC5A11	115584	hgsc.bcm.edu	37	16	24918048	24918048	+	Missense_Mutation	SNP	C	C	T	rs17772929	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:24918048C>T	ENST00000569071.1	+	9	944	c.679C>T	c.(679-681)Cgc>Tgc	p.R227C	SLC5A11_ENST00000539472.1_Silent_p.I295I|SLC5A11_ENST00000565769.1_Silent_p.I295I|SLC5A11_ENST00000347898.3_Silent_p.I359I|SLC5A11_ENST00000424767.2_Silent_p.I324I|SLC5A11_ENST00000449109.2_Missense_Mutation_p.R227C|SLC5A11_ENST00000567758.1_Silent_p.I324I|SLC5A11_ENST00000568579.1_Silent_p.I289I|SLC5A11_ENST00000545376.1_Silent_p.I289I					solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		GTTCGGACATCGCGTATCCCA	0.557											OREG0023688	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1187	0.237021	0.3026	0.2565	5008	,	,		18589	0.0169		0.4254	False		,,,				2504	0.1677				p.R227C		Atlas-SNP	.											SLC5A11,NS,carcinoma,0,1	SLC5A11	97	1	0			c.C679T						scavenged	.	C		1472,2922	472.6+/-356.4	242,988,967	101.0	83.0	89.0		1077	-2.8	0.9	16	dbSNP_123	89	3702,4898	529.3+/-381.6	791,2120,1389	no	coding-synonymous	SLC5A11	NM_052944.2		1033,3108,2356	TT,TC,CC		43.0465,33.5002,39.8184		359/676	24918048	5174,7820	2197	4300	6497	SO:0001583	missense	115584	exon10			GGACATCGCGTAT	AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"""Solute carriers"""	23091	protein-coding gene	gene with protein product		610238	"""solute carrier family 5 (sodium/glucose cotransporter), member 11"""			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000569071.1:c.679C>T	16.37:g.24918048C>T	ENSP00000456376:p.Arg227Cys	Somatic	81	1	0.0123457	775	WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_001258414		Missense_Mutation	SNP	ENST00000569071.1	37	CCDS58440.1	570	0.260989010989011	128	0.2601626016260163	103	0.2845303867403315	9	0.015734265734265736	330	0.43535620052770446	C	15.67	2.903209	0.52333	0.335002	0.430465	ENSG00000158865	ENST00000449109	D	0.83992	-1.79	5.73	-2.83	0.05769	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B	0.13145	0.007	B	0.04013	0.001	T	0.35500	-0.9786	7	0.87932	D	0	.	11.6091	0.51049	0.0:0.3507:0.0:0.6493	rs17772929;rs17854934;rs59135221;rs17772929	227	Q05BF1	.	C	227	ENSP00000389606:R227C	ENSP00000389606:R227C	R	+	1	0	SLC5A11	24825549	0.031000	0.19500	0.939000	0.37840	0.958000	0.62258	-0.908000	0.04063	-0.302000	0.08869	0.563000	0.77884	CGC	C|0.678;T|0.322	0.322	strong		0.557	SLC5A11-006	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435852.1	NM_052944	
CACNA1S	779	hgsc.bcm.edu	37	1	201012484	201012484	+	Missense_Mutation	SNP	C	C	T	rs13374149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:201012484C>T	ENST00000362061.3	-	40	5199	c.4973G>A	c.(4972-4974)cGt>cAt	p.R1658H	CACNA1S_ENST00000367338.3_Missense_Mutation_p.R1639H|RP11-168O16.2_ENST00000415359.1_RNA	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1658			R -> H (in dbSNP:rs13374149).		axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GGTATTGGCACGAGCCAGGGG	0.547											OREG0014067	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	499	0.0996406	0.2867	0.0418	5008	,	,		19713	0.001		0.0577	False		,,,				2504	0.0327				p.R1658H		Atlas-SNP	.											.	CACNA1S	249	.	0			c.G4973A						PASS	.	C	HIS/ARG	1116,3290		137,842,1224	229.0	185.0	200.0		4973	1.6	1.0	1	dbSNP_121	200	456,8144		13,430,3857	yes	missense	CACNA1S	NM_000069.2	29	150,1272,5081	TT,TC,CC		5.3023,25.3291,12.0867	benign	1658/1874	201012484	1572,11434	2203	4300	6503	SO:0001583	missense	779	exon40			TTGGCACGAGCCA	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.4973G>A	1.37:g.201012484C>T	ENSP00000355192:p.Arg1658His	Somatic	166	0	0	2118	WXS	Illumina HiSeq	Phase_I	180	89	0.494444	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	195	0.08928571428571429	135	0.27439024390243905	16	0.04419889502762431	1	0.0017482517482517483	43	0.05672823218997362	.	10.82	1.457511	0.26161	0.253291	0.053023	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.96232	-3.95;-3.88	4.63	1.62	0.23740	.	464.918000	0.00166	U	0.000000	T	0.00144	0.0004	L	0.50333	1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.50030	-0.8875	9	0.26408	T	0.33	.	6.6767	0.23098	0.3124:0.6007:0.0:0.0869	rs13374149;rs52818718;rs13374149	1658	Q13698	CAC1S_HUMAN	H	1658;1639	ENSP00000355192:R1658H;ENSP00000356307:R1639H	ENSP00000355192:R1658H	R	-	2	0	CACNA1S	199279107	0.019000	0.18553	0.958000	0.39756	0.886000	0.51366	-0.316000	0.08071	0.166000	0.19597	0.544000	0.68410	CGT	C|0.890;T|0.110	0.110	strong		0.547	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
SGSM1	129049	hgsc.bcm.edu	37	22	25264353	25264353	+	Silent	SNP	C	C	T	rs61744681	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25264353C>T	ENST00000400359.4	+	11	1012	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G	SGSM1_ENST00000400358.4_Silent_p.G335G	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	335	Required for interaction with RAP family members.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						TTGACAGCGGCGGGACAGTGG	0.642													C|||	16	0.00319489	0.0	0.0101	5008	,	,		16926	0.002		0.007	False		,,,				2504	0.0				p.G335G		Atlas-SNP	.											.	SGSM1	150	.	0			c.C1005T						PASS	.	C	,,,	9,4055		0,9,2023	32.0	37.0	35.0		1005,1005,1005,1005	-9.8	0.5	22	dbSNP_129	35	93,8267		2,89,4089	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	,,,	2,98,6112	TT,TC,CC		1.1124,0.2215,0.821	,,,	335/1149,335/1094,335/1033,335/1088	25264353	102,12322	2032	4180	6212	SO:0001819	synonymous_variant	129049	exon11			CAGCGGCGGGACA	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.1005C>T	22.37:g.25264353C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																			C|0.993;T|0.007	0.007	strong		0.642	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
SPTBN1	6711	hgsc.bcm.edu	37	2	54858511	54858511	+	Silent	SNP	C	C	T	rs1052788	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:54858511C>T	ENST00000356805.4	+	16	3608	c.3327C>T	c.(3325-3327)aaC>aaT	p.N1109N	SPTBN1_ENST00000333896.5_Silent_p.N1096N	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1109					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)	p.N1109N(1)		NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			ACATCAAGAACGAGATCGACA	0.587													C|||	1204	0.240415	0.0431	0.3343	5008	,	,		23981	0.2788		0.336	False		,,,				2504	0.3027				p.N1109N		Atlas-SNP	.											SPTBN1,NS,carcinoma,0,1	SPTBN1	378	1	1	Substitution - coding silent(1)	stomach(1)	c.C3327T						PASS	.	C	,	392,4014	195.3+/-220.0	13,366,1824	173.0	142.0	152.0		3327,3288	-5.8	0.9	2	dbSNP_86	152	2617,5983	424.3+/-354.6	360,1897,2043	no	coding-synonymous,coding-synonymous	SPTBN1	NM_003128.2,NM_178313.2	,	373,2263,3867	TT,TC,CC		30.4302,8.897,23.1355	,	1109/2365,1096/2156	54858511	3009,9997	2203	4300	6503	SO:0001819	synonymous_variant	6711	exon16			CAAGAACGAGATC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3327C>T	2.37:g.54858511C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			C|0.759;T|0.241	0.241	strong		0.587	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
CCDC66	285331	hgsc.bcm.edu	37	3	56653424	56653424	+	Missense_Mutation	SNP	A	A	T	rs199695070|rs61747991	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:56653424A>T	ENST00000394672.3	+	16	2574	c.2504A>T	c.(2503-2505)gAa>gTa	p.E835V	CCDC66_ENST00000436465.2_Missense_Mutation_p.E835V|CCDC66_ENST00000326595.7_Missense_Mutation_p.E801V	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	835					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		AATCAAACAGAATTATCATCT	0.363													A|||	286	0.0571086	0.0726	0.0331	5008	,	,		14948	0.0863		0.0437	False		,,,				2504	0.0368				p.E835V		Atlas-SNP	.											.	CCDC66	145	.	0			c.A2504T						PASS	.	A	VAL/GLU,VAL/GLU	221,4185	134.5+/-170.7	1,219,1983	95.0	104.0	101.0		2402,2504	1.2	0.0	3	dbSNP_129	101	426,8174	131.3+/-189.1	15,396,3889	yes	missense,missense	CCDC66	NM_001012506.4,NM_001141947.1	121,121	16,615,5872	TT,TA,AA		4.9535,5.0159,4.9746	benign,benign	801/915,835/949	56653424	647,12359	2203	4300	6503	SO:0001583	missense	285331	exon16			AAACAGAATTATC	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.2504A>T	3.37:g.56653424A>T	ENSP00000378167:p.Glu835Val	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	235	125	0.531915	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	114	0.0521978021978022	23	0.046747967479674794	11	0.03038674033149171	53	0.09265734265734266	27	0.03562005277044855	A	13.90	2.374788	0.42105	0.050159	0.049535	ENSG00000180376	ENST00000394672;ENST00000326595;ENST00000436465	T;T;T	0.26518	1.73;1.73;1.73	5.23	1.21	0.21127	.	1.051330	0.07418	N	0.893526	T	0.00754	0.0025	L	0.54323	1.7	0.46437	P	9.550000000000392E-4	B	0.28350	0.208	B	0.25291	0.059	T	0.23511	-1.0186	9	0.44086	T	0.13	-1.2667	2.2712	0.04091	0.6016:0.1312:0.1412:0.126	rs61747991	835	A2RUB6	CCD66_HUMAN	V	835;801;835	ENSP00000378167:E835V;ENSP00000326050:E801V;ENSP00000404320:E835V	ENSP00000326050:E801V	E	+	2	0	CCDC66	56628464	0.042000	0.20092	0.016000	0.15963	0.287000	0.27160	1.108000	0.31123	0.391000	0.25143	0.482000	0.46254	GAA	A|0.952;T|0.048	0.048	strong		0.363	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
PNP	4860	hgsc.bcm.edu	37	14	20940626	20940626	+	Silent	SNP	C	C	T	rs1130650	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20940626C>T	ENST00000361505.5	+	2	317	c.171C>T	c.(169-171)ccC>ccT	p.P57P	RP11-203M5.8_ENST00000554678.1_lincRNA	NM_000270.3	NP_000261.2	P01298	PAHO_HUMAN	purine nucleoside phosphorylase	0					digestion (GO:0007586)|protein secretion (GO:0009306)	extracellular region (GO:0005576)	hormone activity (GO:0005179)|receptor binding (GO:0005102)	p.P57P(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|stomach(2)	10						CCAACTTTCCCCGAAGTACAG	0.468													C|||	1024	0.204473	0.2451	0.2104	5008	,	,		20251	0.2083		0.1998	False		,,,				2504	0.1462				p.P57P		Atlas-SNP	.											PNP,NS,carcinoma,+2,2	PNP	21	2	1	Substitution - coding silent(1)	stomach(1)	c.C171T						PASS	.	C		1058,3348	386.3+/-326.1	119,820,1264	63.0	56.0	58.0		171	0.1	0.3	14	dbSNP_86	58	1521,7079	284.4+/-296.6	143,1235,2922	no	coding-synonymous	PNP	NM_000270.3		262,2055,4186	TT,TC,CC		17.686,24.0127,19.8293		57/290	20940626	2579,10427	2203	4300	6503	SO:0001819	synonymous_variant	4860	exon2			CTTTCCCCGAAGT		CCDS9552.1	14q11.2	2014-09-17	2009-12-02	2009-12-02	ENSG00000198805	ENSG00000198805	2.4.2.1		7892	protein-coding gene	gene with protein product		164050	"""nucleoside phosphorylase"""	NP		6087295	Standard	NM_000270		Approved	PUNP	uc001vxo.4	P00491	OTTHUMG00000029546	ENST00000361505.5:c.171C>T	14.37:g.20940626C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	130	71	0.546154	NM_000270		Silent	SNP	ENST00000361505.5	37	CCDS9552.1																																																																																			C|0.786;T|0.214	0.214	strong		0.468	PNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073646.2	NM_000270.2	
ECE2	9718	hgsc.bcm.edu	37	3	183976108	183976108	+	Intron	SNP	T	T	C	rs902415	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:183976108T>C	ENST00000402825.3	+	2	480				EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000324557.4_Silent_p.F171F	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2						brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GAGGCCGGTTTATCTCAATGA	0.552													C|||	1629	0.32528	0.4818	0.2536	5008	,	,		19663	0.3393		0.2455	False		,,,				2504	0.2321				p.F171F		Atlas-SNP	.											.	ECE2	303	.	0			c.T513C						PASS	.	C	,	1812,2594	639.0+/-397.0	394,1024,785	146.0	138.0	141.0		,513	3.2	1.0	3	dbSNP_86	141	1974,6626	723.8+/-406.5	226,1522,2552	no	intron,coding-synonymous	ECE2	NM_014693.3,NM_032331.3	,	620,2546,3337	CC,CT,TT		22.9535,41.1257,29.1096	,	,171/256	183976108	3786,9220	2203	4300	6503	SO:0001627	intron_variant	9718	exon3			CCGGTTTATCTCA	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.480+564T>C	3.37:g.183976108T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	127	125	0.984252	NM_032331	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Silent	SNP	ENST00000402825.3	37	CCDS3256.2																																																																																			T|0.697;C|0.303	0.303	strong		0.552	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
KANSL1	284058	hgsc.bcm.edu	37	17	44110532	44110532	+	Silent	SNP	G	G	A	rs36076725	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44110532G>A	ENST00000262419.6	-	13	3221	c.2751C>T	c.(2749-2751)ttC>ttT	p.F917F	KANSL1_ENST00000574590.1_Silent_p.F917F|KANSL1_ENST00000575318.1_Silent_p.F853F|KANSL1_ENST00000572904.1_Silent_p.F917F|KANSL1_ENST00000432791.1_Silent_p.F917F|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000393476.3_Silent_p.F211F	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	917	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GCAGGGCGGCGAAGGCTGCGT	0.602													G|||	432	0.086262	0.0151	0.1571	5008	,	,		19745	0.001		0.2406	False		,,,				2504	0.0613				p.F917F		Atlas-SNP	.											.	.	.	.	0			c.C2751T						PASS	.	G	,,	201,4205	118.8+/-156.5	5,191,2007	59.0	59.0	59.0		2748,2751,2751	-5.2	0.9	17	dbSNP_126	59	1915,6685	305.0+/-307.2	214,1487,2599	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	219,1678,4606	AA,AG,GG		22.2674,4.562,16.2694	,,	916/1105,917/1106,917/1106	44110532	2116,10890	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon13			GGCGGCGAAGGCT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2751C>T	17.37:g.44110532G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	230	106	0.46087	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.143;C|0.000;G|0.856;T|0.000	0.143	strong		0.602	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
ARVCF	421	hgsc.bcm.edu	37	22	19969587	19969587	+	Silent	SNP	G	G	A	rs372955497		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:19969587G>A	ENST00000263207.3	-	4	529	c.238C>T	c.(238-240)Ctg>Ttg	p.L80L	ARVCF_ENST00000344269.3_Silent_p.L17L|ARVCF_ENST00000401994.1_Silent_p.L17L|ARVCF_ENST00000487793.1_5'UTR|ARVCF_ENST00000406259.1_Silent_p.L80L|ARVCF_ENST00000406522.1_Silent_p.L17L	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	80					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					ATCGTGGCCAGTGAGGCCTGG	0.642																																					p.L80L		Atlas-SNP	.											.	ARVCF	54	.	0			c.C238T						PASS	.	G		0,4404		0,0,2202	71.0	62.0	65.0		238	2.4	0.9	22		65	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ARVCF	NM_001670.2		0,3,6499	AA,AG,GG		0.0349,0.0,0.0231		80/963	19969587	3,13001	2202	4300	6502	SO:0001819	synonymous_variant	421	exon4			TGGCCAGTGAGGC		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"""Armadillo repeat containing"""	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.238C>T	22.37:g.19969587G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_001670	B7WNV2	Silent	SNP	ENST00000263207.3	37	CCDS13771.1																																																																																			.	.	weak		0.642	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
ABHD17A	81926	hgsc.bcm.edu	37	19	1881348	1881348	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1881348C>T	ENST00000292577.7	-	2	651	c.218G>A	c.(217-219)cGt>cAt	p.R73H	ABHD17A_ENST00000590661.1_Missense_Mutation_p.R73H|ABHD17A_ENST00000250974.9_Missense_Mutation_p.R73H	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	73						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										GAAGTCGGCACGCTCCGTCAG	0.716																																					p.R73H		Atlas-SNP	.											FAM108A1,NS,carcinoma,+1,1	FAM108A1	29	1	0			c.G218A						scavenged	.						19.0	21.0	20.0					19																	1881348		2186	4259	6445	SO:0001583	missense	81926	exon2			TCGGCACGCTCCG	BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"""Abhydrolase domain containing"""	28756	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 27"", ""family with sequence similarity 108, member A1"""	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.218G>A	19.37:g.1881348C>T	ENSP00000292577:p.Arg73His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	62	9	0.145161	NM_031213	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Missense_Mutation	SNP	ENST00000292577.7	37	CCDS45902.1	.	.	.	.	.	.	.	.	.	.	c	17.49	3.402578	0.62288	.	.	ENSG00000129968	ENST00000250974;ENST00000292577	T;T	0.48201	0.82;0.95	3.76	3.76	0.43208	.	0.000000	0.85682	D	0.000000	T	0.53883	0.1824	M	0.78344	2.41	0.58432	D	0.999999	B;B;P;D	0.61080	0.014;0.325;0.857;0.989	B;B;B;P	0.45310	0.013;0.139;0.273;0.476	T	0.67031	-0.5773	10	0.87932	D	0	-24.7831	15.1068	0.72326	0.0:1.0:0.0:0.0	.	73;73;73;73	Q96GS6;Q96GS6-2;Q96GS6-3;Q96GS6-4	F18A1_HUMAN;.;.;.	H	73	ENSP00000250974:R73H;ENSP00000292577:R73H	ENSP00000250974:R73H	R	-	2	0	FAM108A1	1832348	1.000000	0.71417	0.927000	0.36925	0.901000	0.52897	7.466000	0.80914	2.108000	0.64289	0.561000	0.74099	CGT	.	.	none		0.716	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213	
C16orf70	80262	hgsc.bcm.edu	37	16	67183867	67183867	+	IGR	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:67183867C>T	ENST00000219139.3	+	0	2865				B3GNT9_ENST00000449549.3_Silent_p.A174A	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70											cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		AGTGGGTTCGCGCGCCCTCCC	0.701																																					p.A174A		Atlas-SNP	.											B3GNT9,NS,carcinoma,-1,1	B3GNT9	25	1	0			c.G522A						scavenged	.						14.0	15.0	14.0					16																	67183867		1889	4052	5941	SO:0001628	intergenic_variant	84752	exon2			GGTTCGCGCGCCC	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 6"""	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510		16.37:g.67183867C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	25	16	0.64	NM_033309	Q9HA86	Silent	SNP	ENST00000219139.3	37	CCDS10828.1																																																																																			.	.	none		0.701	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187	
RALGPS2	55103	hgsc.bcm.edu	37	1	178854330	178854330	+	Missense_Mutation	SNP	C	C	T	rs61758794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:178854330C>T	ENST00000367635.3	+	12	1362	c.1024C>T	c.(1024-1026)Cat>Tat	p.H342Y	RALGPS2_ENST00000477383.1_3'UTR|RALGPS2_ENST00000367634.2_Missense_Mutation_p.H342Y	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	342					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TAGGAAGTGCCATAGTTTGGG	0.393													C|||	10	0.00199681	0.0	0.0014	5008	,	,		15964	0.001		0.007	False		,,,				2504	0.001				p.H342Y		Atlas-SNP	.											.	RALGPS2	69	.	0			c.C1024T						PASS	.	C	TYR/HIS	11,4395	17.9+/-39.9	0,11,2192	75.0	78.0	77.0		1024	5.6	1.0	1	dbSNP_129	77	77,8523	44.9+/-103.4	0,77,4223	yes	missense	RALGPS2	NM_152663.3	83	0,88,6415	TT,TC,CC		0.8953,0.2497,0.6766	benign	342/584	178854330	88,12918	2203	4300	6503	SO:0001583	missense	55103	exon12			AAGTGCCATAGTT	AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"""Pleckstrin homology (PH) domain containing"""	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.1024C>T	1.37:g.178854330C>T	ENSP00000356607:p.His342Tyr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Missense_Mutation	SNP	ENST00000367635.3	37	CCDS1325.1	8|8	0.003663003663003663|0.003663003663003663	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	7|7	0.009234828496042216|0.009234828496042216	C|C	21.5|21.5	4.160216|4.160216	0.78226|0.78226	0.002497|0.002497	0.008953|0.008953	ENSG00000116191|ENSG00000116191	ENST00000367635;ENST00000367634;ENST00000324778|ENST00000415888	T;T;T|.	0.45668|.	0.89;0.89;0.89|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.184745|.	0.47093|.	D|.	0.000242|.	T|T	0.62768|0.62768	0.2455|0.2455	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	B;B|.	0.24823|.	0.069;0.112|.	B;B|.	0.26864|.	0.032;0.074|.	T|T	0.62435|0.62435	-0.6855|-0.6855	10|5	0.19147|.	T|.	0.46|.	.|.	19.2628|19.2628	0.93974|0.93974	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs61758794|rs61758794	342;342|.	B7Z7B1;Q86X27|.	.;RGPS2_HUMAN|.	Y|L	342;342;307|79	ENSP00000356607:H342Y;ENSP00000356606:H342Y;ENSP00000313613:H307Y|.	ENSP00000313613:H307Y|.	H|P	+|+	1|2	0|0	RALGPS2|RALGPS2	177120953|177120953	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.993000|0.993000	0.82548|0.82548	7.318000|7.318000	0.79029|0.79029	2.659000|2.659000	0.90383|0.90383	0.585000|0.585000	0.79938|0.79938	CAT|CCA	C|0.993;T|0.007	0.007	strong		0.393	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663	
MUC16	94025	hgsc.bcm.edu	37	19	9006749	9006749	+	Missense_Mutation	SNP	C	C	T	rs75444444	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9006749C>T	ENST00000397910.4	-	44	39702	c.39499G>A	c.(39499-39501)Gtg>Atg	p.V13167M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13169	SEA 8. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGAATGGCACCAGGAGAGGG	0.428													c|||	993	0.198283	0.2859	0.1153	5008	,	,		20691	0.1399		0.1889	False		,,,				2504	0.2086				p.V13167M		Atlas-SNP	.											.	MUC16	4315	.	0			c.G39499A						PASS	.	T	MET/VAL	976,2894		134,708,1093	185.0	149.0	160.0		39499	-3.6	0.0	19	dbSNP_131	160	1604,6672		161,1282,2695	yes	missense	MUC16	NM_024690.2	21	295,1990,3788	TT,TC,CC		19.3813,25.2196,21.2416	possibly-damaging	13167/14508	9006749	2580,9566	1935	4138	6073	SO:0001583	missense	94025	exon44			ATGGCACCAGGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.39499G>A	19.37:g.9006749C>T	ENSP00000381008:p.Val13167Met	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	150	79	0.526667	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	381|381	0.17445054945054944|0.17445054945054944	136|136	0.2764227642276423|0.2764227642276423	43|43	0.11878453038674033|0.11878453038674033	56|56	0.0979020979020979|0.0979020979020979	146|146	0.19261213720316622|0.19261213720316622	.|.	6.442|6.442	0.449704|0.449704	0.12223|0.12223	0.252196|0.252196	0.193813|0.193813	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000441155|ENST00000542240	T|.	0.42513|.	0.97|.	2.99|2.99	-3.6|-3.6	0.04570|0.04570	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	L|L	0.49640|0.49640	1.575|1.575	.|.	.|.	.|.	P|.	0.50156|.	0.932|.	P|.	0.47134|.	0.539|.	T|.	0.28870|.	-1.0030|.	8|.	0.87932|.	D|.	0|.	-3.4762|-3.4762	3.4755|3.4755	0.07583|0.07583	0.1856:0.3374:0.0:0.477|0.1856:0.3374:0.0:0.477	.|.	13167|.	B5ME49|.	.|.	M|X	13167;298|6	ENSP00000381008:V13167M|.	ENSP00000381008:V13167M|.	V|W	-|-	1|3	0|0	MUC16|MUC16	8867749|8867749	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-3.453000|-3.453000	0.00465|0.00465	-0.648000|-0.648000	0.05437|0.05437	-1.000000|-1.000000	0.02509|0.02509	GTG|TGG	C|0.824;T|0.176	0.176	strong		0.428	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
RADIL	55698	hgsc.bcm.edu	37	7	4874420	4874420	+	Missense_Mutation	SNP	G	G	C	rs2292498	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:4874420G>C	ENST00000399583.3	-	4	1421	c.1234C>G	c.(1234-1236)Cac>Gac	p.H412D	RADIL_ENST00000536091.1_Missense_Mutation_p.H412D|RADIL_ENST00000538469.1_Missense_Mutation_p.H172D	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	412			H -> D (in dbSNP:rs2292498). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		TCCTCCAGGTGGGGCTCAAAC	0.716													G|||	1259	0.251398	0.0401	0.2853	5008	,	,		9176	0.3294		0.2873	False		,,,				2504	0.3957				p.H412D		Atlas-SNP	.											.	RADIL	110	.	0			c.C1234G						PASS	.	G	ASP/HIS	299,3725		19,261,1732	12.0	15.0	14.0		1234	2.6	0.0	7	dbSNP_100	14	2520,5808		397,1726,2041	yes	missense	RADIL	NM_018059.4	81	416,1987,3773	CC,CG,GG		30.2594,7.4304,22.8222	benign	412/1076	4874420	2819,9533	2012	4164	6176	SO:0001583	missense	55698	exon4			CCAGGTGGGGCTC	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.1234C>G	7.37:g.4874420G>C	ENSP00000382492:p.His412Asp	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	526	0.24084249084249085	22	0.044715447154471545	94	0.2596685082872928	195	0.3409090909090909	215	0.2836411609498681	-	0.008	-1.905182	0.00512	0.074304	0.302594	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000536091;ENST00000538469	T;T;T	0.21031	3.45;2.03;3.37	4.45	2.56	0.30785	.	1.666850	0.02995	N	0.147315	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43261	-0.9402	9	0.11794	T	0.64	-5.6915	8.1854	0.31335	0.1638:0.6284:0.2079:0.0	rs2292498;rs2292498	412	Q96JH8	RADIL_HUMAN	D	412;383;146;412;172	ENSP00000382492:H412D;ENSP00000442533:H412D;ENSP00000442966:H172D	ENSP00000320946:H383D	H	-	1	0	RADIL	4840946	0.095000	0.21747	0.004000	0.12327	0.011000	0.07611	1.196000	0.32198	0.291000	0.22468	-0.218000	0.12543	CAC	G|0.754;C|0.246	0.246	strong		0.716	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
CDHR3	222256	hgsc.bcm.edu	37	7	105658451	105658451	+	Missense_Mutation	SNP	G	G	A	rs6967330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:105658451G>A	ENST00000317716.9	+	12	1666	c.1586G>A	c.(1585-1587)tGt>tAt	p.C529Y	CDHR3_ENST00000542731.1_Missense_Mutation_p.C529Y|CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000478080.1_Missense_Mutation_p.C441Y|CDHR3_ENST00000343407.5_Intron	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	529	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		C -> Y (in dbSNP:rs6967330).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						AAAGTGGACTGTGAAACAACC	0.488													A|||	925	0.184704	0.2648	0.1427	5008	,	,		18561	0.0704		0.2078	False		,,,				2504	0.2004				p.C529Y		Atlas-SNP	.											.	CDHR3	153	.	0			c.G1586A						PASS	.	A	TYR/CYS	967,2915		121,725,1095	68.0	67.0	67.0		1586	4.4	0.9	7	dbSNP_116	67	1405,6889		136,1133,2878	yes	missense	CDHR3	NM_152750.4	194	257,1858,3973	AA,AG,GG		16.94,24.9098,19.4809	benign	529/886	105658451	2372,9804	1941	4147	6088	SO:0001583	missense	222256	exon12			TGGACTGTGAAAC	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1586G>A	7.37:g.105658451G>A	ENSP00000325954:p.Cys529Tyr	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	380	0.17399267399267399	127	0.258130081300813	61	0.1685082872928177	39	0.06818181818181818	153	0.20184696569920843	A	0.008	-1.879772	0.00537	0.249098	0.1694	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080	T;T;T	0.47177	0.85;0.85;0.85	5.66	4.39	0.52855	Cadherin (5);Cadherin-like (1);	0.441716	0.23328	N	0.049375	T	0.00012	0.0000	N	0.00033	-2.575	0.09310	P	0.9999999756686	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29427	-1.0012	9	0.02654	T	1	-2.7833	7.8022	0.29180	0.795:0.0:0.073:0.132	rs6967330;rs58478557;rs6967330	516;529	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	Y	529;529;441	ENSP00000439766:C529Y;ENSP00000325954:C529Y;ENSP00000417771:C441Y	ENSP00000325954:C529Y	C	+	2	0	CDHR3	105445687	1.000000	0.71417	0.931000	0.37212	0.057000	0.15508	3.349000	0.52217	0.986000	0.38683	-0.254000	0.11334	TGT	G|0.826;A|0.174	0.174	strong		0.488	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102463407	102463407	+	Silent	SNP	A	A	G	rs12893215	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102463407A>G	ENST00000360184.4	+	16	3764	c.3600A>G	c.(3598-3600)caA>caG	p.Q1200Q		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1200	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.Q1200Q(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TGGAAAAGCAAAGGTTCCAGT	0.413													A|||	1010	0.201677	0.2685	0.1585	5008	,	,		20106	0.251		0.0905	False		,,,				2504	0.2055				p.Q1200Q		Atlas-SNP	.											DYNC1H1,NS,carcinoma,0,1	DYNC1H1	395	1	1	Substitution - coding silent(1)	stomach(1)	c.A3600G						PASS	.	A		1059,3347	380.6+/-323.8	133,793,1277	49.0	50.0	49.0		3600	1.4	1.0	14	dbSNP_121	49	958,7642	208.3+/-249.8	59,840,3401	no	coding-synonymous	DYNC1H1	NM_001376.4		192,1633,4678	GG,GA,AA		11.1395,24.0354,15.5082		1200/4647	102463407	2017,10989	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon16			AAAGCAAAGGTTC	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.3600A>G	14.37:g.102463407A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	176	76	0.431818	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			A|0.836;G|0.164	0.164	strong		0.413	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
AVPI1	60370	hgsc.bcm.edu	37	10	99439673	99439673	+	Splice_Site	SNP	C	C	G	rs3818780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:99439673C>G	ENST00000370626.3	-	2	558		c.e2-1			NM_021732.2	NP_068378.2	Q5T686	AVPI1_HUMAN	arginine vasopressin-induced 1						activation of MAPK activity (GO:0000187)|cell cycle (GO:0007049)					breast(1)|endometrium(1)|large_intestine(2)|skin(1)	5		Colorectal(252;0.162)		Epithelial(162;8.37e-11)|all cancers(201;7.94e-09)		TGTGGATGCTCTGAGGATGCA	0.602													C|||	1064	0.21246	0.1589	0.1729	5008	,	,		17313	0.2153		0.16	False		,,,				2504	0.364				.		Atlas-SNP	.											.	AVPI1	16	.	0			.						PASS	.	C		607,3681		48,511,1585	7.0	7.0	7.0			4.3	0.9	10	dbSNP_107	7	1333,7033		94,1145,2944	yes	splice-3	AVPI1	NM_021732.2		142,1656,4529	GG,GC,CC		15.9335,14.1558,15.3311			99439673	1940,10714	2144	4183	6327	SO:0001630	splice_region_variant	60370	.			GATGCTCTGAGGA	AF131791	CCDS7470.1	10q24.2	2004-04-05			ENSG00000119986	ENSG00000119986			30898	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_021732		Approved	VIP32, PP5395, VIT32	uc001koi.2	Q5T686	OTTHUMG00000018864	ENST00000370626.3:c.10-1G>C	10.37:g.99439673C>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	25	24	0.96	.	Q53G32|Q9H2R9|Q9HBN9	Splice_Site	SNP	ENST00000370626.3	37	CCDS7470.1																																																																																			C|0.822;G|0.178	0.178	strong		0.602	AVPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049736.1	NM_021732	Intron
RSPH4A	345895	hgsc.bcm.edu	37	6	116950734	116950734	+	Missense_Mutation	SNP	G	G	A	rs6927567	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:116950734G>A	ENST00000229554.5	+	4	1804	c.1667G>A	c.(1666-1668)cGc>cAc	p.R556H	RSPH4A_ENST00000368581.4_Intron|RSPH4A_ENST00000368580.4_Missense_Mutation_p.R309H	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	556	Glu-rich.		R -> H (in dbSNP:rs6927567).		axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)				breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						TCCCAGGGTCGCTGTAATTGG	0.378									Kartagener syndrome				G|||	1026	0.204872	0.1089	0.2089	5008	,	,		17994	0.2857		0.2157	False		,,,				2504	0.2372				p.R556H		Atlas-SNP	.											.	RSPH4A	54	.	0			c.G1667A						PASS	.	G	HIS/ARG,	529,3877	240.3+/-251.1	30,469,1704	80.0	80.0	80.0		1667,	5.2	1.0	6	dbSNP_116	80	1679,6921	309.7+/-309.5	167,1345,2788	yes	missense,intron	RSPH4A	NM_001010892.2,NM_001161664.1	29,	197,1814,4492	AA,AG,GG		19.5233,12.0064,16.9768	probably-damaging,	556/717,	116950734	2208,10798	2203	4300	6503	SO:0001583	missense	345895	exon4	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGGGTCGCTGTAA		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"""radial spokehead-like 3"""	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.1667G>A	6.37:g.116950734G>A	ENSP00000229554:p.Arg556His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	29	0.358025	NM_001010892	B4DSI1|Q3KP24|Q5TD95	Missense_Mutation	SNP	ENST00000229554.5	37	CCDS34521.1	464	0.21245421245421245	56	0.11382113821138211	72	0.19889502762430938	166	0.2902097902097902	170	0.22427440633245382	G	20.7	4.027171	0.75390	0.120064	0.195233	ENSG00000111834	ENST00000229554;ENST00000447842;ENST00000368580	T;T	0.38077	1.16;1.16	6.06	5.2	0.72013	.	0.146244	0.64402	N	0.000005	T	0.33030	0.0849	M	0.91768	3.24	0.09310	P	1.0	P	0.43024	0.798	B	0.36608	0.229	T	0.53781	-0.8390	9	0.56958	D	0.05	-4.1885	13.1277	0.59364	0.0768:0.0:0.9232:0.0	rs6927567;rs61322119;rs6927567	556	Q5TD94	RSH4A_HUMAN	H	556;351;309	ENSP00000229554:R556H;ENSP00000357569:R309H	ENSP00000229554:R556H	R	+	2	0	RSPH4A	117057427	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	5.660000	0.68018	1.582000	0.49881	0.650000	0.86243	CGC	G|0.812;A|0.188	0.188	strong		0.378	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892	
IGSF3	3321	hgsc.bcm.edu	37	1	117142707	117142707	+	Missense_Mutation	SNP	G	G	A	rs201515387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:117142707G>A	ENST00000369486.3	-	7	2650	c.1885C>T	c.(1885-1887)Cgc>Tgc	p.R629C	IGSF3_ENST00000369483.1_Missense_Mutation_p.R649C|IGSF3_ENST00000318837.6_Missense_Mutation_p.R649C	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	629	Ig-like C2-type 5.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		ATGCTTAGGCGGACGTTGTTG	0.617																																					p.R649C		Atlas-SNP	.											IGSF3_ENST00000369483,NS,carcinoma,0,2	IGSF3	294	2	0			c.C1945T						scavenged	.						80.0	59.0	66.0					1																	117142707		2203	4300	6503	SO:0001583	missense	3321	exon8			TTAGGCGGACGTT	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.1885C>T	1.37:g.117142707G>A	ENSP00000358498:p.Arg629Cys	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	118	9	0.0762712	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.683765	0.68157	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.02737	4.18;4.18;4.18	4.8	3.86	0.44501	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.141042	0.49916	D	0.000140	T	0.03477	0.0100	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.967;0.995;0.98	T	0.46638	-0.9177	10	0.72032	D	0.01	-38.9912	7.8163	0.29260	0.0:0.1795:0.6349:0.1856	.	649;629;649	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	C	629;649;649	ENSP00000358498:R629C;ENSP00000358495:R649C;ENSP00000321184:R649C	ENSP00000321184:R649C	R	-	1	0	IGSF3	116944230	1.000000	0.71417	0.876000	0.34364	0.961000	0.63080	6.076000	0.71267	1.187000	0.43000	0.455000	0.32223	CGC	G|0.995;A|0.005	0.005	strong		0.617	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
CLEC16A	23274	hgsc.bcm.edu	37	16	11056378	11056378	+	Silent	SNP	C	C	T	rs16957839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:11056378C>T	ENST00000409790.1	+	3	506	c.276C>T	c.(274-276)taC>taT	p.Y92Y	CLEC16A_ENST00000409552.3_Silent_p.Y92Y	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.Y92Y(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CGGGCCGTTACGTGTGCGTTC	0.473													C|||	646	0.128994	0.1324	0.1009	5008	,	,		20644	0.121		0.1352	False		,,,				2504	0.1462				p.Y92Y		Atlas-SNP	.											CLEC16A,NS,carcinoma,0,1	CLEC16A	101	1	1	Substitution - coding silent(1)	stomach(1)	c.C276T						scavenged	.	C		589,3543		47,495,1524	235.0	218.0	224.0		276	-8.5	0.8	16	dbSNP_123	224	1094,7350		67,960,3195	no	coding-synonymous	CLEC16A	NM_015226.2		114,1455,4719	TT,TC,CC		12.9559,14.2546,13.3826		92/1054	11056378	1683,10893	2066	4222	6288	SO:0001819	synonymous_variant	23274	exon3			CCGTTACGTGTGC	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.276C>T	16.37:g.11056378C>T		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	189	84	0.444444	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			C|0.873;T|0.127	0.127	strong		0.473	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
FRAS1	80144	hgsc.bcm.edu	37	4	79443837	79443837	+	Missense_Mutation	SNP	A	A	T	rs931605	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:79443837A>T	ENST00000264895.6	+	69	11123	c.10683A>T	c.(10681-10683)gaA>gaT	p.E3561D		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3557					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CTCTCCCAGAAGTGAAATCTT	0.423													T|||	397	0.0792732	0.0666	0.1023	5008	,	,		19931	0.002		0.1829	False		,,,				2504	0.0532				p.E3561D		Atlas-SNP	.											.	FRAS1	779	.	0			c.A10683T						PASS	.	T	ASP/GLU	290,3446		18,254,1596	52.0	51.0	51.0		10683	-1.1	0.9	4	dbSNP_86	51	1622,6604		166,1290,2657	yes	missense	FRAS1	NM_025074.6	45	184,1544,4253	TT,TA,AA		19.718,7.7623,15.9839	benign	3561/4013	79443837	1912,10050	1868	4113	5981	SO:0001583	missense	80144	exon69			CCCAGAAGTGAAA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.10683A>T	4.37:g.79443837A>T	ENSP00000264895:p.Glu3561Asp	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	114	42	0.368421	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	222|222	0.10164835164835165|0.10164835164835165	41|41	0.08333333333333333|0.08333333333333333	42|42	0.11602209944751381|0.11602209944751381	1|1	0.0017482517482517483|0.0017482517482517483	138|138	0.1820580474934037|0.1820580474934037	T|T	0.082|0.082	-1.182536|-1.182536	0.01620|0.01620	0.077623|0.077623	0.19718|0.19718	ENSG00000138759|ENSG00000138759	ENST00000264895|ENST00000512123	T|.	0.12147|.	2.71|.	6.17|6.17	-1.1|-1.1	0.09872|0.09872	.|.	0.157116|.	0.56097|.	N|.	0.000029|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01188|0.01188	-0.97|-0.97	0.09310|0.09310	P|P	0.9999999999893348|0.9999999999893348	B|.	0.13594|.	0.008|.	B|.	0.17433|.	0.018|.	T|T	0.37731|0.37731	-0.9693|-0.9693	9|4	0.02654|.	T|.	1|.	.|.	2.6921|2.6921	0.05124|0.05124	0.1029:0.2457:0.1071:0.5442|0.1029:0.2457:0.1071:0.5442	rs931605;rs931605|rs931605;rs931605	3561|.	E9PHH6|.	.|.	D|C	3561|1790	ENSP00000264895:E3561D|.	ENSP00000264895:E3561D|.	E|S	+|+	3|1	2|0	FRAS1|FRAS1	79662861|79662861	0.357000|0.357000	0.24938|0.24938	0.859000|0.859000	0.33776|0.33776	0.005000|0.005000	0.04900|0.04900	-0.395000|-0.395000	0.07287|0.07287	-0.299000|-0.299000	0.08909|0.08909	-1.220000|-1.220000	0.01600|0.01600	GAA|AGT	A|0.897;T|0.103	0.103	strong		0.423	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TRPM1	4308	hgsc.bcm.edu	37	15	31329944	31329944	+	Silent	SNP	G	G	A	rs12911350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:31329944G>A	ENST00000256552.6	-	20	2688	c.2541C>T	c.(2539-2541)aaC>aaT	p.N847N	TRPM1_ENST00000397795.2_Silent_p.N825N|RP11-348B17.1_ENST00000561299.1_RNA|RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000542188.1_Silent_p.N864N	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CAATGGGCGCGTTATAGAATT	0.408													g|||	446	0.0890575	0.0983	0.1297	5008	,	,		19983	0.0079		0.1362	False		,,,				2504	0.0828				p.N864N		Atlas-SNP	.											.	TRPM1	183	.	0			c.C2592T						PASS	.	A		435,3371		21,393,1489	166.0	151.0	156.0		2475	-5.7	0.5	15	dbSNP_121	156	1099,7153		75,949,3102	no	coding-synonymous	TRPM1	NM_002420.4		96,1342,4591	AA,AG,GG		13.318,11.4293,12.7218		825/1604	31329944	1534,10524	1903	4126	6029	SO:0001819	synonymous_variant	4308	exon19			GGGCGCGTTATAG	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2541C>T	15.37:g.31329944G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	224	95	0.424107	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			G|0.909;A|0.091	0.091	strong		0.408	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
BRCA2	675	hgsc.bcm.edu	37	13	32906480	32906480	+	Missense_Mutation	SNP	A	A	C	rs766173	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:32906480A>C	ENST00000380152.3	+	10	1098	c.865A>C	c.(865-867)Aat>Cat	p.N289H	BRCA2_ENST00000544455.1_Missense_Mutation_p.N289H			P51587	BRCA2_HUMAN	breast cancer 2, early onset	289			N -> H (common polymorphism; was originally thought to be linked to ovarian cancer; dbSNP:rs766173). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:10978364, ECO:0000269|PubMed:12552570, ECO:0000269|PubMed:15172753, ECO:0000269|PubMed:15365993, ECO:0000269|Ref.3}.		brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		GTCAATGCCAAATGTCCTAGA	0.299			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			A|||	369	0.0736821	0.0325	0.0922	5008	,	,		17587	0.0962		0.0348	False		,,,				2504	0.1329				p.N289H	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.A865C						PASS	.	A	HIS/ASN	89,4315	69.2+/-107.0	0,89,2113	57.0	59.0	58.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	865	1.7	0.0	13	dbSNP_86	58	316,8274	112.1+/-172.3	8,300,3987	yes	missense	BRCA2	NM_000059.3	68	8,389,6100	CC,CA,AA		3.6787,2.0209,3.1168	possibly-damaging	289/3419	32906480	405,12589	2202	4295	6497	SO:0001583	missense	675	exon10	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	ATGCCAAATGTCC	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.865A>C	13.37:g.32906480A>C	ENSP00000369497:p.Asn289His	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	95	81	0.852632	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	127	0.05815018315018315	7	0.014227642276422764	32	0.08839779005524862	60	0.1048951048951049	28	0.036939313984168866	A	12.07	1.828231	0.32329	0.020209	0.036787	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	T;T	0.01043	5.41;5.41	5.6	1.73	0.24493	.	0.724675	0.13345	N	0.394885	T	0.00073	0.0002	L	0.46157	1.445	0.58432	P	4.000000000004E-6	B;D	0.62365	0.278;0.991	B;P	0.49999	0.034;0.628	T	0.51228	-0.8732	9	0.54805	T	0.06	.	1.7973	0.03064	0.4989:0.1565:0.0786:0.266	rs766173;rs1801384;rs52810428;rs766173	289;289	P51587;A1YBP1	BRCA2_HUMAN;.	H	289;289;287	ENSP00000369497:N289H;ENSP00000439902:N289H	ENSP00000369497:N289H	N	+	1	0	BRCA2	31804480	0.222000	0.23652	0.043000	0.18650	0.347000	0.29111	0.478000	0.22212	0.063000	0.16370	0.533000	0.62120	AAT	C|0.046;A|0.954	0.046	strong		0.299	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
COL5A1	1289	hgsc.bcm.edu	37	9	137711997	137711997	+	Silent	SNP	G	G	C	rs2228560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:137711997G>C	ENST00000371817.3	+	58	4896	c.4482G>C	c.(4480-4482)ccG>ccC	p.P1494P		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1494	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TCGGTCCTCCGGGTGAACAGG	0.627													G|||	2044	0.408147	0.5416	0.3256	5008	,	,		21008	0.375		0.3439	False		,,,				2504	0.3865				p.P1494P		Atlas-SNP	.											.	COL5A1	323	.	0			c.G4482C						PASS	.	G		2257,2149		590,1077,536	101.0	95.0	97.0		4482	-9.4	0.0	9	dbSNP_107	97	3273,5327		731,1811,1758	no	coding-synonymous	COL5A1	NM_000093.3		1321,2888,2294	CC,CG,GG		38.0581,48.7744,42.5188		1494/1839	137711997	5530,7476	2203	4300	6503	SO:0001819	synonymous_variant	1289	exon58			TCCTCCGGGTGAA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4482G>C	9.37:g.137711997G>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	125	68	0.544	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			A|0.009;C|0.408;G|0.583	0.408	strong		0.627	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
GABRA5	2558	hgsc.bcm.edu	37	15	27188459	27188459	+	Silent	SNP	C	C	T	rs140685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:27188459C>T	ENST00000335625.5	+	10	1863	c.975C>T	c.(973-975)gcC>gcT	p.A325A	GABRA5_ENST00000355395.5_Silent_p.A325A|GABRA5_ENST00000400081.3_Silent_p.A325A	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	325					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	GGTTCATAGCCGTGTGCTATG	0.572													c|||	2269	0.453075	0.5325	0.5144	5008	,	,		17528	0.3452		0.4742	False		,,,				2504	0.3916				p.A325A		Atlas-SNP	.											.	GABRA5	127	.	0			c.C975T						PASS	.	T	,	2218,2020		616,986,517	29.0	32.0	31.0		975,975	-10.5	0.5	15	dbSNP_78	31	4004,4530		951,2102,1214	no	coding-synonymous,coding-synonymous	GABRA5	NM_000810.3,NM_001165037.1	,	1567,3088,1731	TT,TC,CC		46.9182,47.664,48.7159	,	325/463,325/463	27188459	6222,6550	2119	4267	6386	SO:0001819	synonymous_variant	2558	exon10			CATAGCCGTGTGC		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4079	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 5"""	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.975C>T	15.37:g.27188459C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Silent	SNP	ENST00000335625.5	37	CCDS45194.1																																																																																			C|0.544;T|0.456	0.456	strong		0.572	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1		
DPP8	54878	hgsc.bcm.edu	37	15	65790319	65790319	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:65790319T>C	ENST00000341861.5	-	5	2226	c.646A>G	c.(646-648)Atg>Gtg	p.M216V	DPP8_ENST00000321147.6_Missense_Mutation_p.M216V|DPP8_ENST00000300141.6_Missense_Mutation_p.M200V|DPP8_ENST00000339244.5_Missense_Mutation_p.M216V|DPP8_ENST00000321118.7_Missense_Mutation_p.M216V|DPP8_ENST00000358939.4_Missense_Mutation_p.M200V|DPP8_ENST00000559233.1_Missense_Mutation_p.M216V	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	216					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TTTGGATCCATCCGTATGTTG	0.383																																					p.M216V		Atlas-SNP	.											.	DPP8	78	.	0			c.A646G						PASS	.						158.0	128.0	138.0					15																	65790319		2201	4299	6500	SO:0001583	missense	54878	exon6			GATCCATCCGTAT	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"""dipeptidyl peptidase VIII"", ""dipeptidyl peptidase IV-related protein-1"", ""prolyl dipeptidase DPP8"""	606819	"""dipeptidylpeptidase 8"""			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.646A>G	15.37:g.65790319T>C	ENSP00000339208:p.Met216Val	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	136	59	0.433824	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Missense_Mutation	SNP	ENST00000341861.5	37	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.240676	0.79912	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000339244;ENST00000395652	T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54	5.39	5.39	0.77823	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.51329	0.1668	L	0.61036	1.89	0.25881	N	0.983587	B;P;B;B	0.43578	0.178;0.811;0.178;0.213	B;P;B;B	0.60789	0.108;0.879;0.07;0.173	T	0.45338	-0.9268	10	0.44086	T	0.13	-21.8947	15.4176	0.74983	0.0:0.0:0.0:1.0	.	200;200;216;216	Q6V1X1-3;Q6V1X1-4;Q6V1X1-2;Q6V1X1	.;.;.;DPP8_HUMAN	V	216;200;200;216;216;216;216	ENSP00000339208:M216V;ENSP00000351817:M200V;ENSP00000300141:M200V;ENSP00000318111:M216V;ENSP00000316373:M216V;ENSP00000341230:M216V;ENSP00000379013:M216V	ENSP00000300141:M200V	M	-	1	0	DPP8	63577372	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	7.119000	0.77145	2.027000	0.59764	0.533000	0.62120	ATG	.	.	none		0.383	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743	
CNTLN	54875	hgsc.bcm.edu	37	9	17135115	17135115	+	Silent	SNP	C	C	T	rs41306071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:17135115C>T	ENST00000380647.3	+	1	136	c.52C>T	c.(52-54)Ctg>Ttg	p.L18L	CNTLN_ENST00000380641.4_Silent_p.L18L|CNTLN_ENST00000425824.1_Silent_p.L18L|CNTLN_ENST00000262360.5_Silent_p.L18L|CNTLN_ENST00000484374.1_3'UTR			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	18					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AGCGCGACAGCTGGGCCCCAG	0.697													T|||	658	0.13139	0.0643	0.1484	5008	,	,		14867	0.1548		0.2396	False		,,,				2504	0.0746				p.L18L		Atlas-SNP	.											CNTLN,NS,carcinoma,0,1	CNTLN	128	1	0			c.C52T						PASS	.	T	,	385,3489		26,333,1578	10.0	14.0	13.0		52,52	2.1	0.0	9	dbSNP_127	13	2247,5975		317,1613,2181	no	coding-synonymous,coding-synonymous	CNTLN	NM_001114395.1,NM_017738.2	,	343,1946,3759	TT,TC,CC		27.3291,9.938,21.7593	,	18/392,18/1407	17135115	2632,9464	1937	4111	6048	SO:0001819	synonymous_variant	54875	exon1			CGACAGCTGGGCC	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"""chromosome 9 open reading frame 101"", ""chromosome 9 open reading frame 39"""	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.52C>T	9.37:g.17135115C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	72	44	0.611111	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Silent	SNP	ENST00000380647.3	37	CCDS43789.1																																																																																			C|0.819;T|0.181	0.181	strong		0.697	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738	
ZNF721	170960	hgsc.bcm.edu	37	4	466365	466365	+	Intron	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:466365T>C	ENST00000338977.5	-	1	47				ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Splice_Site_p.L43L|ZNF721_ENST00000507078.1_5'UTR|ZNF721_ENST00000511833.2_Splice_Site_p.L11L			Q8TF20	ZN721_HUMAN	zinc finger protein 721						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L11L(1)		endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						TATCCTCACCTAGGGAGACCA	0.368																																					p.I11M		Atlas-SNP	.											ZNF721_ENST00000511833,NS,carcinoma,0,1	ZNF721	205	1	1	Substitution - coding silent(1)	lung(1)	c.C33G						scavenged	.						79.0	87.0	84.0					4																	466365		2203	4300	6503	SO:0001627	intron_variant	170960	exon2			CTCACCTAGGGAG	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1+26479A>G	4.37:g.466365T>C		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	282	4	0.0141844	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37																																																																																				.	.	none		0.368	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474	
ADAM22	53616	hgsc.bcm.edu	37	7	87754915	87754915	+	Missense_Mutation	SNP	G	G	A	rs17255978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:87754915G>A	ENST00000265727.7	+	8	698	c.619G>A	c.(619-621)Gta>Ata	p.V207I	ADAM22_ENST00000439864.1_Missense_Mutation_p.V207I|ADAM22_ENST00000315984.7_Missense_Mutation_p.V207I|ADAM22_ENST00000398201.4_Missense_Mutation_p.V207I|ADAM22_ENST00000398204.4_Missense_Mutation_p.V207I|ADAM22_ENST00000398209.3_Missense_Mutation_p.V207I			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	207			V -> I (in dbSNP:rs17255978).		adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			ATTTCAGCAAGTAAACATTAC	0.323													G|||	406	0.0810703	0.1203	0.1513	5008	,	,		16506	0.0367		0.0427	False		,,,				2504	0.0634				p.V207I		Atlas-SNP	.											.	ADAM22	280	.	0			c.G619A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	309,3299		17,275,1512	72.0	71.0	71.0		619,619,619,619,619	1.4	1.0	7	dbSNP_123	71	377,7759		7,363,3698	yes	missense,missense,missense,missense,missense	ADAM22	NM_004194.3,NM_016351.4,NM_021721.3,NM_021722.4,NM_021723.3	29,29,29,29,29	24,638,5210	AA,AG,GG		4.6337,8.5643,5.8413	benign,benign,benign,benign,benign	207/860,207/871,207/824,207/900,207/907	87754915	686,11058	1804	4068	5872	SO:0001583	missense	53616	exon8			CAGCAAGTAAACA	AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277		"""ADAM metallopeptidase domain containing"""	201	protein-coding gene	gene with protein product	"""metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2"""	603709	"""a disintegrin and metalloproteinase domain 22"""			9693107, 10524237	Standard	NM_021723		Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.619G>A	7.37:g.87754915G>A	ENSP00000265727:p.Val207Ile	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_021722	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Missense_Mutation	SNP	ENST00000265727.7	37	CCDS47637.1	153	0.07005494505494506	57	0.11585365853658537	43	0.11878453038674033	20	0.03496503496503497	33	0.04353562005277045	G	12.18	1.859660	0.32884	0.085643	0.046337	ENSG00000008277	ENST00000398204;ENST00000439864;ENST00000398201;ENST00000265727;ENST00000315984;ENST00000398209;ENST00000398203	T;T;T;T;T;T;T	0.04234	4.48;3.67;4.48;4.47;4.48;4.48;4.49	5.74	1.35	0.21983	.	0.642574	0.15596	N	0.254151	T	0.00039	0.0001	N	0.08118	0	0.41724	P	0.01047600000000004	B;B;B;B;B;B	0.09022	0.0;0.0;0.0;0.0;0.002;0.0	B;B;B;B;B;B	0.10450	0.002;0.003;0.001;0.005;0.005;0.002	T	0.42799	-0.9430	9	0.37606	T	0.19	.	4.2413	0.10648	0.4614:0.1731:0.3655:0.0	rs17255978;rs17255978	259;207;207;207;207;207	E9PBH5;Q9P0K1-5;Q9P0K1;Q9P0K1-2;E7EPF1;D6W5P7	.;.;ADA22_HUMAN;.;.;.	I	207;207;207;207;207;207;174	ENSP00000381262:V207I;ENSP00000391334:V207I;ENSP00000381260:V207I;ENSP00000265727:V207I;ENSP00000315900:V207I;ENSP00000381267:V207I;ENSP00000381261:V174I	ENSP00000265727:V207I	V	+	1	0	ADAM22	87592851	1.000000	0.71417	0.981000	0.43875	0.979000	0.70002	1.104000	0.31074	0.349000	0.23975	0.655000	0.94253	GTA	G|0.933;A|0.067	0.067	strong		0.323	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723	
CDH23	64072	hgsc.bcm.edu	37	10	73550117	73550117	+	Missense_Mutation	SNP	C	C	G	rs11592462	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:73550117C>G	ENST00000224721.6	+	45	6016	c.6011C>G	c.(6010-6012)aCc>aGc	p.T2004S		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1999	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GCCGTGGTGACCTACCAGCTG	0.632													c|||	1729	0.345248	0.2625	0.317	5008	,	,		17889	0.1597		0.499	False		,,,				2504	0.5102				p.T1999S		Atlas-SNP	.											.	CDH23	365	.	0			c.C5996G						PASS	.		SER/THR	1130,3052		168,794,1129	48.0	54.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5996	4.1	1.0	10	dbSNP_120	52	4091,4325		998,2095,1115	yes	missense	CDH23	NM_022124.5	58	1166,2889,2244	GG,GC,CC		48.6098,27.0206,41.4431	benign	1999/3355	73550117	5221,7377	2091	4208	6299	SO:0001583	missense	64072	exon44			TGGTGACCTACCA	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.6011C>G	10.37:g.73550117C>G	ENSP00000224721:p.Thr2004Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	117	50	0.42735	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		721	0.3301282051282051	115	0.23373983739837398	133	0.3674033149171271	96	0.16783216783216784	377	0.4973614775725594	c	11.52	1.663782	0.29515	0.270206	0.486098	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	5.06	4.14	0.48551	Cadherin (3);Cadherin-like (1);	0.248227	0.38897	N	0.001535	T	0.00012	0.0000	N	0.05534	-0.03	0.09310	P	0.9999999999999997	B	0.02656	0.0	B	0.06405	0.002	T	0.38265	-0.9669	8	0.08837	T	0.75	.	15.6194	0.76793	0.0:0.8623:0.1377:0.0	rs11592462;rs11592462	1999	Q9H251	CAD23_HUMAN	S	2004;1999;2002	.	ENSP00000224721:T2004S	T	+	2	0	CDH23	73220123	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.661000	0.37408	1.096000	0.41439	0.556000	0.70494	ACC	C|0.672;G|0.328	0.328	strong		0.632	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
TSHZ1	10194	hgsc.bcm.edu	37	18	72999359	72999359	+	Missense_Mutation	SNP	T	T	C	rs55679337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:72999359T>C	ENST00000580243.1	+	2	2345	c.1997T>C	c.(1996-1998)cTg>cCg	p.L666P	TSHZ1_ENST00000322038.5_Missense_Mutation_p.L621P			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	666			L -> P (in dbSNP:rs55679337).		anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		AAGAGCTCCCTGGCCAAGGCT	0.557													C|||	1233	0.246206	0.1415	0.317	5008	,	,		19251	0.1726		0.3499	False		,,,				2504	0.3067				p.L621P		Atlas-SNP	.											.	TSHZ1	104	.	0			c.T1862C						PASS	.	C	PRO/LEU	734,3672	755.7+/-412.6	61,612,1530	97.0	86.0	89.0		1862	5.2	0.0	18	dbSNP_129	89	2862,5738	670.7+/-402.8	487,1888,1925	yes	missense	TSHZ1	NM_005786.4	98	548,2500,3455	CC,CT,TT		33.2791,16.6591,27.6488	benign	621/1033	72999359	3596,9410	2203	4300	6503	SO:0001583	missense	10194	exon2			GCTCCCTGGCCAA	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1997T>C	18.37:g.72999359T>C	ENSP00000464391:p.Leu666Pro	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		560	0.2564102564102564	73	0.1483739837398374	132	0.36464088397790057	93	0.16258741258741258	262	0.34564643799472294	C	2.991	-0.208265	0.06180	0.166591	0.332791	ENSG00000179981	ENST00000322038	T	0.36878	1.23	5.22	5.22	0.72569	.	0.263906	0.33959	N	0.004384	T	0.00012	0.0000	N	0.00583	-1.355	0.51012	P	9.80000000000425E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.51919	-0.8644	9	0.31617	T	0.26	-23.6505	14.0235	0.64571	0.0:0.9269:0.0:0.0731	rs55679337	666	Q6ZSZ6	TSH1_HUMAN	P	621	ENSP00000323584:L621P	ENSP00000323584:L621P	L	+	2	0	TSHZ1	71128347	0.956000	0.32656	0.025000	0.17156	0.018000	0.09664	3.627000	0.54252	-1.181000	0.02730	-0.258000	0.10820	CTG	A|0.000;C|0.274;G|0.000;T|0.725	0.274	strong		0.557	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
MINK1	50488	hgsc.bcm.edu	37	17	4794407	4794407	+	Missense_Mutation	SNP	G	G	C	rs200592676	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4794407G>C	ENST00000355280.6	+	15	1924	c.1728G>C	c.(1726-1728)gaG>gaC	p.E576D	MINK1_ENST00000347992.7_Missense_Mutation_p.E576D|MINK1_ENST00000453408.3_Missense_Mutation_p.E576D	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						AGCCCCAGGAGGGACCGCACA	0.647													G|||	3	0.000599042	0.0	0.0	5008	,	,		13597	0.0		0.002	False		,,,				2504	0.001				p.E576D		Atlas-SNP	.											.	MINK1	110	.	0			c.G1728C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	5,3705		0,5,1850	6.0	7.0	6.0		1728,1728,1728,1728	2.5	1.0	17		6	22,7980		0,22,3979	yes	missense,missense,missense,missense	MINK1	NM_001024937.3,NM_015716.4,NM_153827.4,NM_170663.4	45,45,45,45	0,27,5829	CC,CG,GG		0.2749,0.1348,0.2305	benign,benign,benign,benign	576/1313,576/1296,576/1333,576/1304	4794407	27,11685	1855	4001	5856	SO:0001583	missense	50488	exon15			CCAGGAGGGACCG	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.1728G>C	17.37:g.4794407G>C	ENSP00000347427:p.Glu576Asp	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	145	55	0.37931	NM_170663		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.437336	0.25900	0.001348	0.002749	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.73897	-0.79;0.99;-0.79	4.53	2.51	0.30379	.	0.072669	0.53938	D	0.000046	T	0.64918	0.2642	L	0.36672	1.1	0.38630	D	0.951355	P;P;P;P	0.51933	0.949;0.949;0.915;0.949	B;P;B;P	0.49953	0.444;0.627;0.424;0.627	T	0.61342	-0.7082	10	0.16896	T	0.51	.	5.7787	0.18294	0.2429:0.0:0.7571:0.0	.	576;576;576;576	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	D	576	ENSP00000347427:E576D;ENSP00000406487:E576D;ENSP00000269296:E576D	ENSP00000269296:E576D	E	+	3	2	MINK1	4735189	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.254000	0.18314	1.229000	0.43630	0.561000	0.74099	GAG	G|0.995;C|0.005	0.005	weak		0.647	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	
ENDOV	284131	hgsc.bcm.edu	37	17	78395734	78395734	+	Missense_Mutation	SNP	G	G	A	rs34933300	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78395734G>A	ENST00000518137.1	+	3	363	c.335G>A	c.(334-336)cGg>cAg	p.R112Q	ENDOV_ENST00000518907.1_Intron|MIR4730_ENST00000584535.1_RNA|ENDOV_ENST00000518901.1_Intron|ENDOV_ENST00000517795.1_Intron|ENDOV_ENST00000520367.1_Intron|ENDOV_ENST00000517295.2_Missense_Mutation_p.R29Q|ENDOV_ENST00000522751.1_Intron|ENDOV_ENST00000518644.1_Missense_Mutation_p.R29Q|ENDOV_ENST00000323854.5_Intron|ENDOV_ENST00000520284.1_Intron	NM_173627.3	NP_775898.2	Q8N8Q3	ENDOV_HUMAN	endonuclease V	112			R -> Q (in dbSNP:rs34933300). {ECO:0000269|Ref.2}.		DNA repair (GO:0006281)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|magnesium ion binding (GO:0000287)|single-stranded RNA binding (GO:0003727)|structure-specific DNA binding (GO:0043566)			endometrium(1)|lung(1)|pancreas(1)|prostate(1)	4						CAGCAGCTGCGGGAGAAGGAG	0.652								Direct reversal of damage					G|||	620	0.123802	0.0499	0.1729	5008	,	,		17428	0.004		0.2684	False		,,,				2504	0.1636				p.R112Q		Atlas-SNP	.											.	ENDOV	26	.	0			c.G335A						PASS	.	G	,,GLN/ARG	352,3896		14,324,1786	32.0	37.0	35.0		,,335	-3.7	0.0	17	dbSNP_126	35	2156,6316		302,1552,2382	yes	intron,intron,missense	ENDOV	NM_001164637.1,NM_001164638.1,NM_173627.3	,,43	316,1876,4168	AA,AG,GG		25.4485,8.2863,19.717	,,benign	,,112/283	78395734	2508,10212	2124	4236	6360	SO:0001583	missense	284131	exon3			AGCTGCGGGAGAA		CCDS54172.1, CCDS54173.1, CCDS54174.1	17q25.3	2011-05-05			ENSG00000173818	ENSG00000173818			26640	protein-coding gene	gene with protein product						12853604	Standard	NM_001164638		Approved	FLJ35220	uc021ueo.1	Q8N8Q3	OTTHUMG00000164638	ENST00000518137.1:c.335G>A	17.37:g.78395734G>A	ENSP00000429190:p.Arg112Gln	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_173627	I3L3S4|Q6P2G2|Q86X99|Q8NAK0	Missense_Mutation	SNP	ENST00000518137.1	37	CCDS54172.1	307	0.14056776556776557	33	0.06707317073170732	69	0.19060773480662985	0	0.0	205	0.2704485488126649	G	7.998	0.754864	0.15846	0.082863	0.254485	ENSG00000173818	ENST00000518137;ENST00000523228;ENST00000517295	T;T	0.17691	2.26;2.26	4.63	-3.72	0.04411	.	0.635443	0.15397	N	0.264527	T	0.00012	0.0000	N	0.10782	0.045	0.53688	P	2.6999999999999247E-5	B	0.24483	0.104	B	0.19391	0.025	T	0.37314	-0.9711	9	0.06099	T	0.92	-6.2061	11.1273	0.48325	0.4437:0.0:0.5563:0.0	rs34933300	112	Q8N8Q3	ENDOV_HUMAN	Q	112;29;87	ENSP00000429190:R112Q;ENSP00000429603:R29Q	ENSP00000428283:R87Q	R	+	2	0	ENDOV	76010329	0.726000	0.28059	0.005000	0.12908	0.020000	0.10135	-0.103000	0.10940	-1.173000	0.02758	-0.469000	0.05056	CGG	G|0.855;A|0.145	0.145	strong		0.652	ENDOV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379487.1	NM_173627	
HIF3A	64344	hgsc.bcm.edu	37	19	46823702	46823702	+	Missense_Mutation	SNP	A	A	G	rs3764609	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:46823702A>G	ENST00000377670.4	+	9	1059	c.1028A>G	c.(1027-1029)cAg>cGg	p.Q343R	HIF3A_ENST00000244303.6_Missense_Mutation_p.Q274R|HIF3A_ENST00000472815.1_Missense_Mutation_p.Q274R|HIF3A_ENST00000300862.3_Missense_Mutation_p.Q341R|HIF3A_ENST00000420102.2_Missense_Mutation_p.Q292R|HIF3A_ENST00000339613.2_Missense_Mutation_p.Q287R|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000600383.1_Missense_Mutation_p.Q274R	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	343			Q -> R (in dbSNP:rs3764609). {ECO:0000269|PubMed:15489334}.		cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		TACCCCAGCCAGGTGGAAGAG	0.597													G|||	1131	0.225839	0.0408	0.2824	5008	,	,		16275	0.3988		0.1809	False		,,,				2504	0.3037				p.Q343R		Atlas-SNP	.											HIF3A_ENST00000377670,brain,glioma,0,2	HIF3A	154	2	0			c.A1028G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	319,4087	795.8+/-415.3	12,295,1896	75.0	71.0	72.0		821,1022,1028,821	2.7	1.0	19	dbSNP_107	72	1601,6999	742.1+/-407.2	162,1277,2861	yes	missense,missense,missense,missense	HIF3A	NM_022462.4,NM_152794.3,NM_152795.3,NM_152796.2	43,43,43,43	174,1572,4757	GG,GA,AA		18.6163,7.2401,14.7624	benign,benign,benign,benign	274/601,341/668,343/670,274/451	46823702	1920,11086	2203	4300	6503	SO:0001583	missense	64344	exon9			CCAGCCAGGTGGA	AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"""Basic helix-loop-helix proteins"""	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1028A>G	19.37:g.46823702A>G	ENSP00000366898:p.Gln343Arg	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Missense_Mutation	SNP	ENST00000377670.4	37	CCDS12681.2	508	0.2326007326007326	20	0.04065040650406504	88	0.2430939226519337	254	0.44405594405594406	146	0.19261213720316622	G	11.06	1.528818	0.27387	0.072401	0.186163	ENSG00000124440	ENST00000244302;ENST00000377670;ENST00000244303;ENST00000339613;ENST00000291300;ENST00000300862;ENST00000420102	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	4.85	2.68	0.31781	.	0.167273	0.28815	N	0.014058	T	0.00012	0.0000	N	0.01576	-0.805	0.58432	P	9.000000000036756E-6	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.46748	-0.9169	9	0.30078	T	0.28	.	5.1771	0.15141	0.1682:0.0:0.6716:0.1603	rs3764609;rs52805117;rs59819378;rs3764609	292;274;341;287;343;343	F5H884;B4DNA2;Q9Y2N7-2;A8MPQ1;Q9Y2N7;B0M185	.;.;.;.;HIF3A_HUMAN;.	R	343;343;274;287;287;341;292	ENSP00000366898:Q343R;ENSP00000244303:Q274R;ENSP00000341877:Q287R;ENSP00000300862:Q341R;ENSP00000407771:Q292R	ENSP00000244302:Q343R	Q	+	2	0	HIF3A	51515542	0.987000	0.35691	0.980000	0.43619	0.385000	0.30292	0.545000	0.23268	0.208000	0.20626	-0.930000	0.02707	CAG	A|0.820;G|0.180	0.180	strong		0.597	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3		
CA2	760	hgsc.bcm.edu	37	8	86389403	86389403	+	Silent	SNP	T	T	C	rs703	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:86389403T>C	ENST00000285379.5	+	6	792	c.562T>C	c.(562-564)Ttg>Ctg	p.L188L		NM_000067.2	NP_000058.1	P00918	CAH2_HUMAN	carbonic anhydrase II	188					angiotensin-activated signaling pathway (GO:0038166)|bicarbonate transport (GO:0015701)|kidney development (GO:0001822)|morphogenesis of an epithelium (GO:0002009)|odontogenesis of dentin-containing tooth (GO:0042475)|one-carbon metabolic process (GO:0006730)|positive regulation of bone resorption (GO:0045780)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of dipeptide transmembrane transport (GO:2001150)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of anion transport (GO:0044070)|regulation of chloride transport (GO:2001225)|regulation of intracellular pH (GO:0051453)|response to estrogen (GO:0043627)|response to pH (GO:0009268)|response to zinc ion (GO:0010043)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|large_intestine(2)|lung(5)|prostate(1)	11					Acetazolamide(DB00819)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Diclofenamide(DB01144)|Dorzolamide(DB00869)|Ethinamate(DB01031)|Furosemide(DB00695)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Topiramate(DB00273)|Trichlormethiazide(DB01021)|Zonisamide(DB00909)	TCCTGAATCCTTGGATTACTG	0.517													T|||	2893	0.577676	0.7375	0.5476	5008	,	,		18193	0.498		0.6322	False		,,,				2504	0.409				p.L188L		Atlas-SNP	.											.	CA2	28	.	0			c.T562C						PASS	.	T		3074,1332	695.2+/-405.9	1072,930,201	276.0	250.0	259.0		562	-6.1	0.0	8	dbSNP_36	259	5290,3310	645.7+/-400.2	1629,2032,639	no	coding-synonymous	CA2	NM_000067.2		2701,2962,840	CC,CT,TT		38.4884,30.2315,35.6912		188/261	86389403	8364,4642	2203	4300	6503	SO:0001819	synonymous_variant	760	exon6			GAATCCTTGGATT	J03037	CCDS6239.1	8q21.2	2012-10-02			ENSG00000104267	ENSG00000104267	4.2.1.1	"""Carbonic anhydrases"""	1373	protein-coding gene	gene with protein product		611492				3107918	Standard	NM_000067		Approved	Car2, CA-II, CAII	uc003ydk.2	P00918	OTTHUMG00000164944	ENST00000285379.5:c.562T>C	8.37:g.86389403T>C		Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	207	207	1	NM_000067	B2R7G8|Q6FI12|Q96ET9	Silent	SNP	ENST00000285379.5	37	CCDS6239.1																																																																																			T|0.376;C|0.624	0.624	strong		0.517	CA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381097.2	NM_000067	
NRAP	4892	hgsc.bcm.edu	37	10	115422474	115422474	+	Silent	SNP	A	A	G	rs3127122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:115422474A>G	ENST00000359988.3	-	3	463	c.219T>C	c.(217-219)aaT>aaC	p.N73N	NRAP_ENST00000369360.3_Silent_p.N73N|NRAP_ENST00000369358.4_Silent_p.N73N|NRAP_ENST00000360478.3_Silent_p.N73N	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.N73N(2)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TCACATTTAGATTTAATGGAG	0.363													G|||	1448	0.289137	0.289	0.4553	5008	,	,		15795	0.2143		0.3231	False		,,,				2504	0.2137				p.N73N		Atlas-SNP	.											NRAP,NS,carcinoma,0,2	NRAP	208	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.T219C						PASS	.	G	,	1328,3078	696.6+/-406.1	193,942,1068	137.0	129.0	132.0		219,219	0.5	0.4	10	dbSNP_103	132	2944,5656	668.0+/-402.5	502,1940,1858	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	695,2882,2926	GG,GA,AA		34.2326,30.1407,32.8464	,	73/1696,73/1731	115422474	4272,8734	2203	4300	6503	SO:0001819	synonymous_variant	4892	exon3			ATTTAGATTTAAT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.219T>C	10.37:g.115422474A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			A|0.683;G|0.317	0.317	strong		0.363	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
EXOC3L4	91828	hgsc.bcm.edu	37	14	103566785	103566785	+	Missense_Mutation	SNP	C	C	T	rs2297067	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:103566785C>T	ENST00000380069.3	+	1	305	c.229C>T	c.(229-231)Cgg>Tgg	p.R77W	RP11-736N17.8_ENST00000559843.1_RNA	NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	77			R -> W (in dbSNP:rs2297067). {ECO:0000269|PubMed:15489334}.		exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						GGGCCTGTTCCGGCGAAGCTC	0.677													C|||	1068	0.213259	0.0968	0.1974	5008	,	,		17662	0.2579		0.2376	False		,,,				2504	0.3108				p.R77W		Atlas-SNP	.											EXOC3L4,NS,carcinoma,0,1	EXOC3L4	35	1	0			c.C229T						PASS	.	C	TRP/ARG	519,3887	220.0+/-237.6	32,455,1716	24.0	26.0	25.0	http://www.ncbi.nlm.nih.gov/pubmed?term	229	-6.1	0.0	14	dbSNP_100	25	2098,6502	344.1+/-325.2	272,1554,2474	yes	missense	EXOC3L4	NM_001077594.1	101	304,2009,4190	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	24.3953,11.7794,20.1215	probably-damaging	77/723	103566785	2617,10389	2203	4300	6503	SO:0001583	missense	91828	exon1			CTGTTCCGGCGAA	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 73"""	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.229C>T	14.37:g.103566785C>T	ENSP00000369409:p.Arg77Trp	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	211	112	0.530806	NM_001077594	Q14CR2	Missense_Mutation	SNP	ENST00000380069.3	37	CCDS32163.1	439	0.20100732600732601	50	0.1016260162601626	77	0.212707182320442	147	0.256993006993007	165	0.21767810026385223	C	14.43	2.531819	0.45073	0.117794	0.243953	ENSG00000205436	ENST00000380069	T	0.08282	3.11	3.06	-6.12	0.02124	.	0.851266	0.09795	N	0.754920	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	D	0.76494	0.999	P	0.57846	0.828	T	0.04140	-1.0974	9	0.56958	D	0.05	-14.725	6.053	0.19796	0.644:0.1524:0.0:0.2036	rs2297067;rs2297067	77	Q17RC7	EX3L4_HUMAN	W	77	ENSP00000369409:R77W	ENSP00000369409:R77W	R	+	1	2	EXOC3L4	102636538	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.705000	0.05052	-1.798000	0.01250	-1.401000	0.01141	CGG	C|0.804;T|0.196	0.196	strong		0.677	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093	
LEPROTL1	23484	hgsc.bcm.edu	37	8	29961951	29961951	+	Silent	SNP	C	C	T	rs11557703	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:29961951C>T	ENST00000321250.8	+	3	343	c.228C>T	c.(226-228)ggC>ggT	p.G76G	LEPROTL1_ENST00000523116.1_Silent_p.G76G|LEPROTL1_ENST00000518001.1_Silent_p.G15G|LEPROTL1_ENST00000442880.2_Silent_p.G76G|LEPROTL1_ENST00000518192.1_Silent_p.G99G	NM_015344.2	NP_056159.2	O95214	LERL1_HUMAN	leptin receptor overlapping transcript-like 1	76						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)	5				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		TTACAACGGGCATTGTCGTGT	0.378													C|||	601	0.120008	0.0809	0.0692	5008	,	,		18534	0.2312		0.0944	False		,,,				2504	0.1207				p.G76G		Atlas-SNP	.											LEPROTL1_ENST00000523116,NS,carcinoma,+1,2	LEPROTL1	16	2	0			c.C228T						PASS	.	C	,	410,3996	200.4+/-223.7	17,376,1810	204.0	187.0	193.0		228,228	4.0	1.0	8	dbSNP_120	193	692,7908	172.2+/-222.9	22,648,3630	no	coding-synonymous,coding-synonymous	LEPROTL1	NM_001128208.1,NM_015344.2	,	39,1024,5440	TT,TC,CC		8.0465,9.3055,8.473	,	76/170,76/132	29961951	1102,11904	2203	4300	6503	SO:0001819	synonymous_variant	23484	exon3			AACGGGCATTGTC	AF063605	CCDS6075.1, CCDS47834.1	8p12	2014-09-11			ENSG00000104660	ENSG00000104660			6555	protein-coding gene	gene with protein product		607338				11342119	Standard	NM_015344		Approved	my047, Vps55	uc003xhx.2	O95214	OTTHUMG00000163820	ENST00000321250.8:c.228C>T	8.37:g.29961951C>T		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	240	131	0.545833	NM_001128208	E9PHP8|Q9BW48	Silent	SNP	ENST00000321250.8	37	CCDS6075.1	275	0.1259157509157509	48	0.0975609756097561	27	0.07458563535911603	135	0.23601398601398602	65	0.08575197889182058	C	9.414	1.081188	0.20309	0.093055	0.080465	ENSG00000104660	ENST00000519466	.	.	.	5.89	4.04	0.47022	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.08722	-1.0708	3	.	.	.	.	9.4609	0.38785	0.1427:0.7814:0.0:0.0758	rs11557703;rs11557703	.	.	.	V	57	.	.	A	+	2	0	LEPROTL1	30081493	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	2.359000	0.44142	0.772000	0.33382	0.585000	0.79938	GCA	C|0.898;T|0.102	0.102	strong		0.378	LEPROTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375771.2		
SNRNP200	23020	hgsc.bcm.edu	37	2	96944553	96944553	+	Silent	SNP	G	G	A	rs772175	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:96944553G>A	ENST00000323853.5	-	37	5394	c.5317C>T	c.(5317-5319)Ctg>Ttg	p.L1773L	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1773					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						TGACCCTGCAGGTTGTAGTAA	0.547													G|||	1232	0.246006	0.0764	0.3242	5008	,	,		23058	0.4256		0.3101	False		,,,				2504	0.1687				p.L1773L		Atlas-SNP	.											.	SNRNP200	195	.	0			c.C5317T						PASS	.	G		503,3903	233.3+/-246.5	23,457,1723	122.0	106.0	112.0		5317	2.1	1.0	2	dbSNP_86	112	2774,5826	440.5+/-359.5	435,1904,1961	no	coding-synonymous	SNRNP200	NM_014014.4		458,2361,3684	AA,AG,GG		32.2558,11.4163,25.1961		1773/2137	96944553	3277,9729	2203	4300	6503	SO:0001819	synonymous_variant	23020	exon37			CCTGCAGGTTGTA	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5317C>T	2.37:g.96944553G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	235	233	0.991489	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Silent	SNP	ENST00000323853.5	37	CCDS2020.1																																																																																			G|0.733;A|0.267	0.267	strong		0.547	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014	
FZD10	11211	hgsc.bcm.edu	37	12	130649134	130649134	+	Silent	SNP	C	C	T	rs61751357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:130649134C>T	ENST00000229030.4	+	1	2131	c.1647C>T	c.(1645-1647)agC>agT	p.S549S	FZD10-AS1_ENST00000505807.2_RNA|FZD10_ENST00000539839.1_3'UTR			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	549					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		AACCGGCCAGCGTGATCACCA	0.557													c|||	116	0.0231629	0.0015	0.0303	5008	,	,		14181	0.0		0.0696	False		,,,				2504	0.0235				p.S549S		Atlas-SNP	.											.	FZD10	95	.	0			c.C1647T						PASS	.	T		57,4349	54.2+/-90.2	1,55,2147	33.0	38.0	36.0		1647	0.6	0.7	12	dbSNP_129	36	563,8037	150.3+/-205.2	13,537,3750	no	coding-synonymous	FZD10	NM_007197.3		14,592,5897	TT,TC,CC		6.5465,1.2937,4.767		549/582	130649134	620,12386	2203	4300	6503	SO:0001819	synonymous_variant	11211	exon1			GGCCAGCGTGATC	AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"""GPCR / Class F : Frizzled receptors"", ""CD molecules"""	4039	protein-coding gene	gene with protein product		606147	"""frizzled (Drosophila) homolog 10"", ""frizzled homolog 10 (Drosophila)"", ""frizzled 10, seven transmembrane spanning receptor"", ""frizzled family receptor 10"""			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.1647C>T	12.37:g.130649134C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_007197		Silent	SNP	ENST00000229030.4	37	CCDS9267.1																																																																																			C|0.956;T|0.044	0.044	strong		0.557	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SPPL2C	162540	hgsc.bcm.edu	37	17	43923180	43923180	+	Missense_Mutation	SNP	G	G	A	rs242944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43923180G>A	ENST00000329196.5	+	1	925	c.908G>A	c.(907-909)cGc>cAc	p.R303H	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	303			R -> H (in dbSNP:rs242944). {ECO:0000269|PubMed:12139484, ECO:0000269|PubMed:15489334}.			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										CTGGTGTGCCGCCTGTCCCTG	0.607													G|||	3051	0.609225	0.3669	0.6412	5008	,	,		19394	0.7986		0.5557	False		,,,				2504	0.774				p.R303H		Atlas-SNP	.											.	.	.	.	0			c.G908A						PASS	.	G	HIS/ARG	1723,2683	516.2+/-369.1	329,1065,809	71.0	76.0	74.0		908	-8.5	0.0	17	dbSNP_79	74	4803,3797	609.5+/-395.5	1364,2075,861	no	missense	IMP5	NM_175882.2	29	1693,3140,1670	AA,AG,GG		44.1512,39.1058,49.8232	benign	303/685	43923180	6526,6480	2203	4300	6503	SO:0001583	missense	162540	exon1			TGTGCCGCCTGTC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.908G>A	17.37:g.43923180G>A	ENSP00000332488:p.Arg303His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	1287	0.5892857142857143	176	0.35772357723577236	207	0.5718232044198895	470	0.8216783216783217	434	0.5725593667546174	G	3.544	-0.093134	0.07053	0.391058	0.558488	ENSG00000185294	ENST00000329196	T	0.17854	2.25	5.38	-8.51	0.00923	.	.	.	.	.	T	0.00012	0.0000	N	0.16201	0.385	0.53688	P	2.599999999997049E-5	B	0.18166	0.026	B	0.18263	0.021	T	0.24368	-1.0162	8	0.38643	T	0.18	-13.3789	5.449	0.16552	0.3049:0.1053:0.4859:0.1038	rs242944;rs17690422;rs57248845;rs242944	303	Q8IUH8	IMP5_HUMAN	H	303	ENSP00000332488:R303H	ENSP00000332488:R303H	R	+	2	0	AC217771.1	41278960	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.364000	0.07583	-1.677000	0.01455	-1.788000	0.00630	CGC	G|0.466;A|0.534	0.534	strong		0.607	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
CEP112	201134	hgsc.bcm.edu	37	17	64023642	64023642	+	Silent	SNP	A	A	G	rs11079628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:64023642A>G	ENST00000392769.2	-	16	1851	c.1633T>C	c.(1633-1635)Tta>Cta	p.L545L	CEP112_ENST00000537949.1_Silent_p.L503L|CEP112_ENST00000541355.1_Silent_p.L180L|CEP112_ENST00000535342.2_Silent_p.L545L	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	545					receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						ATGTGTTTTAAATGACTTTTC	0.239													A|||	2686	0.536342	0.233	0.6585	5008	,	,		16280	0.873		0.4384	False		,,,				2504	0.6135				p.L545L		Atlas-SNP	.											.	CEP112	192	.	0			c.T1633C						PASS	.	A	,	1082,3192		161,760,1216	40.0	37.0	38.0		1633,1633	5.4	1.0	17	dbSNP_120	38	3290,5132		711,1868,1632	no	coding-synonymous,coding-synonymous	CEP112	NM_001199165.1,NM_145036.3	,	872,2628,2848	GG,GA,AA		39.0644,25.3159,34.436	,	545/956,545/956	64023642	4372,8324	2137	4211	6348	SO:0001819	synonymous_variant	201134	exon16			GTTTTAAATGACT	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"""coiled-coil domain containing 46"""	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.1633T>C	17.37:g.64023642A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	109	101	0.926606	NM_001199165	Q6PIB5|Q8NCR4|Q8NFR4	Silent	SNP	ENST00000392769.2	37	CCDS32710.1																																																																																			A|0.561;G|0.439	0.439	strong		0.239	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	
MBLAC2	153364	hgsc.bcm.edu	37	5	89769999	89769999	+	Silent	SNP	G	G	A	rs2115501	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:89769999G>A	ENST00000316610.6	-	1	586	c.111C>T	c.(109-111)ggC>ggT	p.G37G	MBLAC2_ENST00000514906.1_Silent_p.G37G|POLR3G_ENST00000514483.1_5'Flank|POLR3G_ENST00000399107.1_5'Flank|POLR3G_ENST00000504930.1_5'Flank	NM_203406.1	NP_981951	Q68D91	MBLC2_HUMAN	metallo-beta-lactamase domain containing 2	37						extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			kidney(1)|liver(1)|lung(3)	5						CCTGCTCGGAGCCGCGCACCA	0.607													G|||	348	0.0694888	0.0825	0.0648	5008	,	,		17485	0.006		0.1402	False		,,,				2504	0.0481				p.G37G		Atlas-SNP	.											.	MBLAC2	9	.	0			c.C111T						PASS	.	G		364,4040	178.3+/-207.1	14,336,1852	28.0	25.0	26.0		111	1.3	1.0	5	dbSNP_96	26	885,7715	187.6+/-234.8	44,797,3459	no	coding-synonymous	MBLAC2	NM_203406.1		58,1133,5311	AA,AG,GG		10.2907,8.2652,9.6047		37/280	89769999	1249,11755	2202	4300	6502	SO:0001819	synonymous_variant	153364	exon1			CTCGGAGCCGCGC	BC038230	CCDS4067.1	5q14.3	2009-04-08	2009-04-08		ENSG00000176055	ENSG00000176055			33711	protein-coding gene	gene with protein product							Standard	NM_203406		Approved	DKFZp686P15118, MGC46734	uc003kjp.3	Q68D91	OTTHUMG00000131327	ENST00000316610.6:c.111C>T	5.37:g.89769999G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_203406	D6RJI1|Q8IY16|Q8N8D8	Silent	SNP	ENST00000316610.6	37	CCDS4067.1																																																																																			G|0.911;A|0.089	0.089	strong		0.607	MBLAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254098.2	NM_203406	
IRX3	79191	hgsc.bcm.edu	37	16	54318172	54318172	+	Missense_Mutation	SNP	C	C	A	rs1126960	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:54318172C>A	ENST00000329734.3	-	3	2149	c.1437G>T	c.(1435-1437)caG>caT	p.Q479H		NM_024336.2	NP_077312.2	P78415	IRX3_HUMAN	iroquois homeobox 3	479			Q -> H (in dbSNP:rs1126960).		mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of neuron differentiation (GO:0045666)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	14						TGGGCACGGGCTGGAAAGCTG	0.607													C|||	774	0.154553	0.1732	0.1931	5008	,	,		14474	0.0169		0.2455	False		,,,				2504	0.1503				p.Q479H	GBM(143;1830 1866 4487 4646 37383)	Atlas-SNP	.											.	IRX3	25	.	0			c.G1437T						PASS	.	C	HIS/GLN	850,3546	322.9+/-297.8	83,684,1431	49.0	45.0	46.0		1437	4.1	1.0	16	dbSNP_86	46	2090,6510	346.1+/-326.1	244,1602,2454	yes	missense	IRX3	NM_024336.2	24	327,2286,3885	AA,AC,CC		24.3023,19.3358,22.6223	benign	479/502	54318172	2940,10056	2198	4300	6498	SO:0001583	missense	79191	exon3			CACGGGCTGGAAA	U90308	CCDS10750.1	16q12.2	2011-06-20	2007-07-13		ENSG00000177508	ENSG00000177508		"""Homeoboxes / TALE class"""	14360	protein-coding gene	gene with protein product		612985					Standard	NM_024336		Approved	IRX-1	uc002eht.1	P78415	OTTHUMG00000133200	ENST00000329734.3:c.1437G>T	16.37:g.54318172C>A	ENSP00000331608:p.Gln479His	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_024336	Q7Z4A4|Q7Z4A5|Q8IVC6	Missense_Mutation	SNP	ENST00000329734.3	37	CCDS10750.1	366	0.16758241758241757	87	0.17682926829268292	78	0.2154696132596685	9	0.015734265734265736	192	0.2532981530343008	C	14.42	2.529864	0.45073	0.193358	0.243023	ENSG00000177508	ENST00000329734	T	0.54279	0.58	5.19	4.1	0.47936	.	0.637907	0.15331	N	0.268038	T	0.00012	0.0000	L	0.35854	1.095	0.35136	P	0.23153999999999997	B	0.21225	0.053	B	0.16722	0.016	T	0.07520	-1.0768	9	0.51188	T	0.08	-3.0069	7.686	0.28540	0.0:0.7114:0.0:0.2886	rs1126960;rs3182332;rs16953308;rs17366063;rs17416771	479	P78415	IRX3_HUMAN	H	479	ENSP00000331608:Q479H	ENSP00000331608:Q479H	Q	-	3	2	IRX3	52875673	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.377000	0.20552	1.058000	0.40530	0.555000	0.69702	CAG	T|0.000;G|0.000;C|0.792;A|0.208	0.208	strong		0.607	IRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256910.2		
GPR39	2863	hgsc.bcm.edu	37	2	133174764	133174764	+	Missense_Mutation	SNP	C	C	T	rs2241764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:133174764C>T	ENST00000329321.3	+	1	618	c.149C>T	c.(148-150)gCc>gTc	p.A50V		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	50			A -> V (in dbSNP:rs2241764). {ECO:0000269|PubMed:14702039}.		G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGGAACAGCGCCACCATTCGG	0.532													T|||	1894	0.378195	0.5295	0.3429	5008	,	,		20511	0.2361		0.327	False		,,,				2504	0.3978				p.A50V		Atlas-SNP	.											.	GPR39	60	.	0			c.C149T						PASS	.	T	VAL/ALA	2200,2206	588.0+/-386.8	541,1118,544	150.0	134.0	139.0		149	5.3	1.0	2	dbSNP_98	139	2810,5790	676.5+/-403.3	477,1856,1967	yes	missense	GPR39	NM_001508.2	64	1018,2974,2511	TT,TC,CC		32.6744,49.9319,38.5207	benign	50/454	133174764	5010,7996	2203	4300	6503	SO:0001583	missense	2863	exon1			ACAGCGCCACCAT	AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.149C>T	2.37:g.133174764C>T	ENSP00000327417:p.Ala50Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	252	120	0.47619	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	Missense_Mutation	SNP	ENST00000329321.3	37	CCDS2170.1	786	0.3598901098901099	256	0.5203252032520326	127	0.35082872928176795	151	0.263986013986014	252	0.3324538258575198	T	5.771	0.326541	0.10900	0.499319	0.326744	ENSG00000183840	ENST00000329321	T	0.36157	1.27	5.34	5.34	0.76211	GPCR, rhodopsin-like superfamily (1);	0.264420	0.36628	N	0.002497	T	0.00012	0.0000	N	0.00677	-1.265	0.47123	P	6.789999999999852E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.42999	-0.9418	9	0.06099	T	0.92	.	11.4538	0.50169	0.0:0.0701:0.0:0.9299	rs2241764;rs2241764	50	O43194	GPR39_HUMAN	V	50	ENSP00000327417:A50V	ENSP00000327417:A50V	A	+	2	0	GPR39	132891234	1.000000	0.71417	0.989000	0.46669	0.839000	0.47603	4.958000	0.63660	1.064000	0.40671	-0.391000	0.06502	GCC	C|0.618;T|0.381	0.381	strong		0.532	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1		
ZNF471	57573	hgsc.bcm.edu	37	19	57036012	57036012	+	Missense_Mutation	SNP	G	G	T	rs11667052	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57036012G>T	ENST00000308031.5	+	5	709	c.576G>T	c.(574-576)atG>atT	p.M192I	ZNF471_ENST00000591537.1_Intron|ZNF471_ENST00000593197.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	192			M -> I (in dbSNP:rs11667052). {ECO:0000269|PubMed:10718198}.		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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		AAAATTCTATGGTAATAAAAC	0.299													G|||	920	0.183706	0.2337	0.1398	5008	,	,		18537	0.0526		0.2813	False		,,,				2504	0.182				p.M192I	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.G576T						PASS	.	G	ILE/MET	1006,3392		119,768,1312	26.0	28.0	27.0		576	1.7	0.0	19	dbSNP_120	27	2159,6419		308,1543,2438	yes	missense	ZNF471	NM_020813.2	10	427,2311,3750	TT,TG,GG		25.169,22.874,24.3912	benign	192/627	57036012	3165,9811	2199	4289	6488	SO:0001583	missense	57573	exon5			TTCTATGGTAATA	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"""Zinc fingers, C2H2-type"", ""-"""	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.576G>T	19.37:g.57036012G>T	ENSP00000309161:p.Met192Ile	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	428	0.19597069597069597	120	0.24390243902439024	59	0.16298342541436464	34	0.05944055944055944	215	0.2836411609498681	G	1.290	-0.607754	0.03717	0.22874	0.25169	ENSG00000196263	ENST00000308031	T	0.14516	2.5	3.87	1.71	0.24356	.	.	.	.	.	T	0.00012	0.0000	N	0.00399	-1.545	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46205	-0.9208	8	0.23302	T	0.38	.	6.9352	0.24463	0.3009:0.0:0.6991:0.0	rs11667052;rs52814044;rs58037293;rs11667052	192	Q9BX82	ZN471_HUMAN	I	192	ENSP00000309161:M192I	ENSP00000309161:M192I	M	+	3	0	ZNF471	61727824	.	.	0.001000	0.08648	0.789000	0.44602	.	.	0.427000	0.26145	-0.253000	0.11424	ATG	G|0.792;T|0.208	0.208	strong		0.299	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813	
NACA	4666	hgsc.bcm.edu	37	12	57114435	57114435	+	Silent	SNP	C	C	T	rs376706368		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57114435C>T	ENST00000454682.1	-	3	1160	c.879G>A	c.(877-879)gcG>gcA	p.A293A	NACA_ENST00000546392.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000550952.1_Silent_p.A293A|NACA_ENST00000548563.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000551793.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	293	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						TGTTGGGACCCGCAGTCTTTT	0.502			T	BCL6	NHL																																p.A293A		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.G879A						PASS	.		,,,	0,3136		0,0,1568	61.0	61.0	61.0		,,879,	2.6	0.0	12		61	1,7163		0,1,3581	no	intron,intron,coding-synonymous,intron	NACA	NM_001113201.1,NM_001113202.1,NM_001113203.2,NM_005594.4	,,,	0,1,5149	TT,TC,CC		0.014,0.0,0.0097	,,,	,,293/926,	57114435	1,10299	1568	3582	5150	SO:0001819	synonymous_variant	4666	exon3			GGGACCCGCAGTC	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.879G>A	12.37:g.57114435C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_001113203		Silent	SNP	ENST00000454682.1	37																																																																																				.	.	weak		0.502	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161017556	161017556	+	Silent	SNP	C	C	T	rs2774279	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:161017556C>T	ENST00000368013.3	-	12	3575	c.3255G>A	c.(3253-3255)agG>agA	p.R1085R	ARHGAP30_ENST00000368016.3_Silent_p.R874R|USF1_ENST00000368021.3_5'Flank|USF1_ENST00000435396.1_5'Flank|USF1_ENST00000368020.1_5'Flank|ARHGAP30_ENST00000368015.1_Silent_p.R908R	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	1085					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			ATGCATATGACCTGCGCTGAG	0.552													C|||	1093	0.218251	0.1422	0.2003	5008	,	,		20077	0.1389		0.333	False		,,,				2504	0.2975				p.R1085R		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.G3255A						PASS	.	C	,	846,3560	333.3+/-302.9	80,686,1437	87.0	87.0	87.0		3255,2622	-1.2	0.0	1	dbSNP_100	87	2856,5744	448.2+/-361.8	460,1936,1904	no	coding-synonymous,coding-synonymous	ARHGAP30	NM_001025598.1,NM_181720.2	,	540,2622,3341	TT,TC,CC		33.2093,19.2011,28.4638	,	1085/1102,874/891	161017556	3702,9304	2203	4300	6503	SO:0001819	synonymous_variant	257106	exon12			ATATGACCTGCGC	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.3255G>A	1.37:g.161017556C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Silent	SNP	ENST00000368013.3	37	CCDS30918.1																																																																																			C|0.752;T|0.248	0.248	strong		0.552	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
ARFGEF2	10564	hgsc.bcm.edu	37	20	47630449	47630449	+	Silent	SNP	C	C	T	rs2281582	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:47630449C>T	ENST00000371917.4	+	30	4131	c.4131C>T	c.(4129-4131)atC>atT	p.I1377I		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1377					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)	p.I1377I(1)		breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TGTTCAGAATCGTGTTTCGGA	0.468													C|||	1044	0.208466	0.0416	0.2767	5008	,	,		21107	0.3938		0.1282	False		,,,				2504	0.2771				p.I1377I	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											ARFGEF2,NS,carcinoma,0,1	ARFGEF2	160	1	1	Substitution - coding silent(1)	stomach(1)	c.C4131T						PASS	.	C		293,4113	160.3+/-192.7	7,279,1917	158.0	133.0	141.0		4131	-4.5	0.9	20	dbSNP_100	141	1177,7423	239.9+/-270.8	85,1007,3208	no	coding-synonymous	ARFGEF2	NM_006420.2		92,1286,5125	TT,TC,CC		13.686,6.65,11.3025		1377/1786	47630449	1470,11536	2203	4300	6503	SO:0001819	synonymous_variant	10564	exon30			CAGAATCGTGTTT	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.4131C>T	20.37:g.47630449C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	153	75	0.490196	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																			C|0.847;T|0.153	0.153	strong		0.468	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420	
PDGFC	56034	hgsc.bcm.edu	37	4	157684248	157684248	+	Silent	SNP	T	T	C	rs3815861	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:157684248T>C	ENST00000502773.1	-	6	1522	c.1032A>G	c.(1030-1032)ggA>ggG	p.G344G	PDGFC_ENST00000541126.1_Silent_p.G181G|PDGFC_ENST00000542208.1_Silent_p.G189G|PDGFC_ENST00000422544.2_Silent_p.G281G|PDGFC_ENST00000504672.1_5'UTR	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	344					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)	p.G344G(1)		central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		GCGGCTATCCTCCTGTGCTCC	0.542													T|||	1176	0.234824	0.2307	0.1686	5008	,	,		16765	0.1716		0.165	False		,,,				2504	0.4243				p.G344G		Atlas-SNP	.											PDGFC,NS,carcinoma,0,1	PDGFC	46	1	1	Substitution - coding silent(1)	prostate(1)	c.A1032G						scavenged	.	T		870,3536	337.6+/-304.9	98,674,1431	125.0	94.0	105.0		1032	-2.2	0.9	4	dbSNP_107	105	1329,7271	261.0+/-283.6	113,1103,3084	no	coding-synonymous	PDGFC	NM_016205.2		211,1777,4515	CC,CT,TT		15.4535,19.7458,16.9076		344/346	157684248	2199,10807	2203	4300	6503	SO:0001819	synonymous_variant	56034	exon6			CTATCCTCCTGTG	AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.1032A>G	4.37:g.157684248T>C		Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_016205	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Silent	SNP	ENST00000502773.1	37	CCDS3795.1																																																																																			A|0.000;C|0.171;T|0.829	0.171	strong		0.542	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1		
TG	7038	hgsc.bcm.edu	37	8	134125682	134125682	+	Missense_Mutation	SNP	G	G	A	rs1133076	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:134125682G>A	ENST00000220616.4	+	44	7629	c.7589G>A	c.(7588-7590)cGa>cAa	p.R2530Q	TG_ENST00000542445.1_Missense_Mutation_p.R900Q|TG_ENST00000377869.1_Missense_Mutation_p.R2473Q|TG_ENST00000519543.1_Missense_Mutation_p.R663Q	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2530			R -> Q (in dbSNP:rs1133076). {ECO:0000269|PubMed:10199792}.		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)		GAGGAAAGTCGAGGCCGGACC	0.478													A|||	2691	0.53734	0.8041	0.3516	5008	,	,		18729	0.4028		0.492	False		,,,				2504	0.4939				p.R2530Q		Atlas-SNP	.											.	TG	416	.	0			c.G7589A						PASS	.	A	GLN/ARG	3390,1016	377.3+/-322.4	1301,788,114	67.0	74.0	72.0		7589	4.8	1.0	8	dbSNP_86	72	4078,4522	593.9+/-393.2	968,2142,1190	yes	missense	TG	NM_003235.4	43	2269,2930,1304	AA,AG,GG		47.4186,23.0595,42.5803	benign	2530/2769	134125682	7468,5538	2203	4300	6503	SO:0001583	missense	7038	exon44			AAAGTCGAGGCCG	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.7589G>A	8.37:g.134125682G>A	ENSP00000220616:p.Arg2530Gln	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	1156	0.5293040293040293	406	0.8252032520325203	148	0.4088397790055249	223	0.38986013986013984	379	0.5	A	5.800	0.331826	0.10956	0.769405	0.474186	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	4.83	4.83	0.62350	Carboxylesterase, type B (1);	1.362880	0.04630	N	0.403510	T	0.00012	0.0000	N	0.00483	-1.445	0.49798	P	1.7999999999995797E-4	B;B;B	0.11235	0.001;0.0;0.004	B;B;B	0.04013	0.001;0.0;0.001	T	0.43327	-0.9398	9	0.02654	T	1	.	10.0443	0.42177	0.9198:0.0:0.0802:0.0	rs3194514	663;900;2530	E7EVM0;F5GWW5;P01266	.;.;THYG_HUMAN	Q	2473;1336;2530;900;663	ENSP00000367100:R2473Q;ENSP00000220616:R2530Q;ENSP00000441693:R900Q;ENSP00000430430:R663Q	ENSP00000220616:R2530Q	R	+	2	0	TG	134194864	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	5.139000	0.64801	0.797000	0.33971	-0.254000	0.11334	CGA	G|0.442;A|0.558	0.558	strong		0.478	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
TTN	7273	hgsc.bcm.edu	37	2	179582537	179582537	+	Splice_Site	SNP	G	G	T	rs2627043	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179582537G>T	ENST00000591111.1	-	85	24337	c.24113C>A	c.(24112-24114)gCg>gAg	p.A8038E	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Splice_Site_p.A7111E|TTN_ENST00000589042.1_Splice_Site_p.A8355E|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12230				A -> E (in Ref. 3; CAD12456). {ECO:0000305}.	adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGTTTGCGCGCTGTAAAGAA	0.378													T|||	2228	0.444888	0.4637	0.379	5008	,	,		21070	0.6577		0.2247	False		,,,				2504	0.4734				p.A8355E		Atlas-SNP	.											TTN_ENST00000356127,NS,carcinoma,+1,2	TTN	18412	2	0			c.C25064A						PASS	.	T	GLU/ALA,,,	1507,2191		316,875,658	34.0	34.0	34.0		21332,,,	5.9	1.0	2	dbSNP_100	34	1653,6537		157,1339,2599	yes	missense-near-splice,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	107,,,	473,2214,3257	TT,TG,GG		20.1832,40.7518,26.5814	possibly-damaging,,,	7111/33424,,,	179582537	3160,8728	1849	4095	5944	SO:0001630	splice_region_variant	7273	exon87			TTGCGCGCTGTAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.24113-1C>A	2.37:g.179582537G>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		859	0.3933150183150183	213	0.4329268292682927	113	0.31215469613259667	367	0.6416083916083916	166	0.21899736147757257	T	12.02	1.811212	0.32053	0.407518	0.201832	ENSG00000155657	ENST00000342992	T	0.62639	0.01	5.87	5.87	0.94306	.	.	.	.	.	T	0.00012	0.0000	N	0.01019	-1.045	0.09310	P	1.0	.	.	.	.	.	.	T	0.32666	-0.9898	6	0.87932	D	0	.	13.6839	0.62504	0.0:0.0:0.129:0.871	rs2627043;rs52818239;rs57224311;rs2627043	.	.	.	E	7111	ENSP00000343764:A7111E	ENSP00000343764:A7111E	A	-	2	0	TTN	179290782	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.236000	0.72339	1.157000	0.42530	-0.256000	0.11100	GCG	G|0.606;T|0.394	0.394	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	Missense_Mutation
DFNB31	25861	hgsc.bcm.edu	37	9	117169033	117169033	+	Missense_Mutation	SNP	A	A	G	rs942519	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:117169033A>G	ENST00000362057.3	-	9	2006	c.1838T>C	c.(1837-1839)aTg>aCg	p.M613T	DFNB31_ENST00000374059.3_Missense_Mutation_p.M262T|DFNB31_ENST00000265134.6_Missense_Mutation_p.M230T	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	613	Pro-rich.		M -> T (in dbSNP:rs942519). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCAGGAAGGCATGGAGGAAGG	0.672													G|||	2412	0.481629	0.3585	0.5159	5008	,	,		18367	0.503		0.5149	False		,,,				2504	0.5675				p.M613T		Atlas-SNP	.											.	DFNB31	100	.	0			c.T1838C						PASS	.	G	THR/MET,THR/MET,THR/MET	1703,2703	635.7+/-396.4	337,1029,837	55.0	48.0	50.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	689,1838,1838	0.1	0.0	9	dbSNP_86	50	4695,3903	531.4+/-382.0	1252,2191,856	yes	missense,missense,missense	DFNB31	NM_001083885.2,NM_001173425.1,NM_015404.3	81,81,81	1589,3220,1693	GG,GA,AA		45.3943,38.6518,49.2002	benign,benign,benign	230/525,613/907,613/908	117169033	6398,6606	2203	4299	6502	SO:0001583	missense	25861	exon9			GAAGGCATGGAGG	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"""whirlin"""	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.1838T>C	9.37:g.117169033A>G	ENSP00000354623:p.Met613Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_001173425	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Missense_Mutation	SNP	ENST00000362057.3	37	CCDS6806.1	1062	0.48626373626373626	180	0.36585365853658536	194	0.5359116022099447	301	0.5262237762237763	387	0.5105540897097626	G	0.006	-2.069501	0.00382	0.386518	0.546057	ENSG00000095397	ENST00000265134;ENST00000374059;ENST00000362057	T;T;T	0.06294	4.22;4.2;3.32	4.57	0.0558	0.14316	.	0.410282	0.22939	N	0.053805	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33752	-0.9856	9	0.14656	T	0.56	-1.0976	0.056	0.00013	0.2798:0.192:0.248:0.2803	rs942519;rs60418846;rs942519	613;613;262	B9EGE6;Q9P202;Q9P202-4	.;WHRN_HUMAN;.	T	230;262;613	ENSP00000265134:M230T;ENSP00000363172:M262T;ENSP00000354623:M613T	ENSP00000265134:M230T	M	-	2	0	DFNB31	116208854	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	1.225000	0.32551	-0.207000	0.10187	-1.383000	0.01170	ATG	A|0.511;G|0.489	0.489	strong		0.672	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404	
NSUN4	387338	hgsc.bcm.edu	37	1	46827456	46827456	+	Missense_Mutation	SNP	A	A	G	rs9865	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:46827456A>G	ENST00000474844.1	+	6	1743	c.1093A>G	c.(1093-1095)Ata>Gta	p.I365V	NSUN4_ENST00000498008.1_3'UTR|NSUN4_ENST00000537428.1_Missense_Mutation_p.I316V|NSUN4_ENST00000536062.1_Missense_Mutation_p.I316V	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	365			I -> V (in dbSNP:rs9865). {ECO:0000269|PubMed:14702039}.		rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)			endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					GGAGCTGGTAATACCAAACCT	0.453													A|||	1020	0.203674	0.0552	0.1254	5008	,	,		24169	0.2798		0.1501	False		,,,				2504	0.4366				p.I365V		Atlas-SNP	.											.	NSUN4	26	.	0			c.A1093G						PASS	.	A	VAL/ILE	281,4125	157.4+/-190.3	8,265,1930	172.0	163.0	166.0		1093	3.0	1.0	1	dbSNP_52	166	1160,7440	237.5+/-269.3	76,1008,3216	yes	missense	NSUN4	NM_199044.2	29	84,1273,5146	GG,GA,AA		13.4884,6.3777,11.0795	benign	365/385	46827456	1441,11565	2203	4300	6503	SO:0001583	missense	387338	exon6			CTGGTAATACCAA	AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"""NOP2/Sun domain containing"""	31802	protein-coding gene	gene with protein product	"""sperm head and tail associated protein"""	615394	"""NOL1/NOP2/Sun domain family 4"", ""NOL1/NOP2/Sun domain family, member 4"""				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	ENST00000474844.1:c.1093A>G	1.37:g.46827456A>G	ENSP00000419740:p.Ile365Val	Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	369	203	0.550135	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Missense_Mutation	SNP	ENST00000474844.1	37	CCDS534.1	343	0.15705128205128205	21	0.042682926829268296	50	0.13812154696132597	173	0.30244755244755245	99	0.13060686015831136	A	10.53	1.375749	0.24857	0.063777	0.134884	ENSG00000117481	ENST00000474844;ENST00000536062;ENST00000537428	T;T;T	0.09073	3.02;3.02;3.02	5.43	3.01	0.34805	.	0.293446	0.35407	N	0.003224	T	0.00012	0.0000	L	0.31845	0.965	0.30466	P	0.773765	B;B	0.06786	0.001;0.001	B;B	0.09377	0.002;0.004	T	0.48175	-0.9058	9	0.27082	T	0.32	-9.8212	6.6119	0.22757	0.5345:0.3487:0.0:0.1167	rs9865;rs3170821;rs58670940;rs9865	232;365	B3KUM0;Q96CB9	.;NSUN4_HUMAN	V	365;316;316	ENSP00000419740:I365V;ENSP00000438912:I316V;ENSP00000437758:I316V	ENSP00000419740:I365V	I	+	1	0	NSUN4	46600043	0.991000	0.36638	1.000000	0.80357	0.993000	0.82548	1.173000	0.31920	1.038000	0.40049	0.533000	0.62120	ATA	A|0.862;G|0.138	0.138	strong		0.453	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	
RFPL2	10739	hgsc.bcm.edu	37	22	32589090	32589090	+	Missense_Mutation	SNP	C	C	T	rs8135276	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:32589090C>T	ENST00000400237.1	-	4	1290	c.355G>A	c.(355-357)Gcc>Acc	p.A119T	RFPL2_ENST00000489846.1_5'UTR|RFPL2_ENST00000248983.4_Missense_Mutation_p.A29T|RFPL2_ENST00000248980.4_Missense_Mutation_p.A58T|RFPL2_ENST00000400236.3_Missense_Mutation_p.A29T			O75678	RFPL2_HUMAN	ret finger protein-like 2	119			A -> T (in dbSNP:rs8135276).				zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	21						AGGCAGACGGCGCATCCACAC	0.527													.|||	565	0.112819	0.1543	0.0793	5008	,	,		18441	0.0625		0.1481	False		,,,				2504	0.0961				p.A119T		Atlas-SNP	.											.	RFPL2	81	.	0			c.G355A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	585,3821	258.9+/-262.7	34,517,1652	100.0	97.0	98.0		355,85,85,172	-1.3	0.0	22	dbSNP_116	98	1265,7335	251.4+/-277.9	77,1111,3112	no	missense,missense,missense,missense	RFPL2	NM_001098527.2,NM_001159545.1,NM_001159546.1,NM_006605.3	58,58,58,58	111,1628,4764	TT,TC,CC		14.7093,13.2773,14.2242	benign,benign,benign,benign	119/379,29/289,29/289,58/318	32589090	1850,11156	2203	4300	6503	SO:0001583	missense	10739	exon4			AGACGGCGCATCC	AJ010231	CCDS43009.1, CCDS46694.1, CCDS43009.2	22q12.3	2008-06-12				ENSG00000128253		"""RING-type (C3HC4) zinc fingers"""	9979	protein-coding gene	gene with protein product		605969				10508838	Standard	NM_001098527		Approved	RNF79	uc003amg.3	O75678		ENST00000400237.1:c.355G>A	22.37:g.32589090C>T	ENSP00000383096:p.Ala119Thr	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	209	105	0.502392	NM_001098527		Missense_Mutation	SNP	ENST00000400237.1	37	CCDS43009.2	247	0.1130952380952381	74	0.15040650406504066	31	0.0856353591160221	33	0.057692307692307696	109	0.1437994722955145	C	0.641	-0.813279	0.02798	0.132773	0.147093	ENSG00000128253	ENST00000248980;ENST00000248983;ENST00000400236;ENST00000400237	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	0.636	-1.27	0.09347	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);	.	.	.	.	T	0.00039	0.0001	N	0.01824	-0.7	0.80722	P	0.0	B;B	0.23249	0.082;0.001	B;B	0.15052	0.012;0.001	T	0.29518	-1.0009	7	0.02654	T	1	.	.	.	.	rs8135276	119;58	O75678;O75678-3	RFPL2_HUMAN;.	T	58;29;29;119	ENSP00000248980:A58T;ENSP00000248983:A29T;ENSP00000383095:A29T;ENSP00000383096:A119T	ENSP00000248980:A58T	A	-	1	0	RFPL2	30919090	1.000000	0.71417	0.000000	0.03702	0.002000	0.02628	0.757000	0.26433	-1.220000	0.02594	-1.628000	0.00784	GCC	C|0.875;T|0.125	0.125	strong		0.527	RFPL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075262.2	NM_006605	
CACNA1B	774	hgsc.bcm.edu	37	9	140773504	140773504	+	Splice_Site	SNP	A	A	C	rs140008467|rs77221813		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140773504A>C	ENST00000371372.1	+	2	429		c.e2-1		CACNA1B_ENST00000277549.5_Splice_Site|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371355.4_Intron|CACNA1B_ENST00000371363.1_Splice_Site|CACNA1B_ENST00000277551.2_Splice_Site|CACNA1B_ENST00000371357.1_Splice_Site	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit						calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TAACTCACGCACTCCATTCGA	0.632																																					.		Atlas-SNP	.											CACNA1B,colon,carcinoma,0,1	CACNA1B	266	1	0			c.285-2A>C						scavenged	.						34.0	38.0	37.0					9																	140773504		2144	4242	6386	SO:0001630	splice_region_variant	774	exon2			TCACGCACTCCAT	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.285-1A>C	9.37:g.140773504A>C		Somatic	85	8	0.0941176		WXS	Illumina HiSeq	Phase_I	102	9	0.0882353	NM_001243812	B1AQK5	Splice_Site	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	A	9.642	1.139206	0.21205	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357	.	.	.	4.52	3.37	0.38596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8471	0.41034	0.9182:0.0:0.0818:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1B	139893325	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	8.392000	0.90180	0.597000	0.29811	-0.379000	0.06801	.	.	.	weak		0.632	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	Intron
CNN2	1265	hgsc.bcm.edu	37	19	1036468	1036468	+	Silent	SNP	A	A	G	rs1064411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1036468A>G	ENST00000263097.4	+	6	924	c.561A>G	c.(559-561)agA>agG	p.R187R	CNN2_ENST00000348419.3_Silent_p.R148R|AC011558.5_ENST00000585757.1_RNA|CNN2_ENST00000565096.2_Silent_p.R176R|CNN2_ENST00000606983.1_3'UTR|CNN2_ENST00000562958.2_Silent_p.R208R	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	187				RRHLYDPKNHILPPMD -> AGISMTPRTISCPPWT (in Ref. 6; BAA20887). {ECO:0000305}.	actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGGCACGAGAAGGCATCTCT	0.602													G|||	570	0.113818	0.0855	0.0951	5008	,	,		17403	0.0962		0.1968	False		,,,				2504	0.0982				p.R187R		Atlas-SNP	.											.	CNN2	26	.	0			c.A561G						PASS	.	G	,	446,3960	783.9+/-414.7	24,398,1781	74.0	70.0	71.0		561,444	-0.7	0.0	19	dbSNP_86	71	1807,6793	731.6+/-406.8	178,1451,2671	no	coding-synonymous,coding-synonymous	CNN2	NM_004368.2,NM_201277.1	,	202,1849,4452	GG,GA,AA		21.0116,10.1226,17.3228	,	187/310,148/271	1036468	2253,10753	2203	4300	6503	SO:0001819	synonymous_variant	1265	exon6			CACGAGAAGGCAT	D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.561A>G	19.37:g.1036468A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	154	69	0.448052	NM_004368	A5D8U8|A6NFI4|D6W5X9|Q92578	Silent	SNP	ENST00000263097.4	37	CCDS12053.1																																																																																			A|0.837;G|0.163	0.163	strong		0.602	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368	
FIGLA	344018	hgsc.bcm.edu	37	2	71012734	71012734	+	Missense_Mutation	SNP	C	C	G	rs71647804|rs7566476	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:71012734C>G	ENST00000332372.6	-	3	426	c.422G>C	c.(421-423)aGt>aCt	p.S141T		NM_001004311.3	NP_001004311.2	Q6QHK4	FIGLA_HUMAN	folliculogenesis specific basic helix-loop-helix	141			S -> T (in dbSNP:rs7566476). {ECO:0000269|PubMed:15044608, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)			endometrium(2)|lung(3)	5						TGATTCAGAACTGTTGTTACT	0.403													G|||	3821	0.762979	0.882	0.6873	5008	,	,		19278	0.9077		0.5626	False		,,,				2504	0.7127				p.S141T		Atlas-SNP	.											.	FIGLA	23	.	0			c.G422C						PASS	.	G	THR/SER	3225,739		1309,607,66	414.0	403.0	406.0		422	3.2	0.0	2	dbSNP_116	406	4492,3858		1216,2060,899	yes	missense	FIGLA	NM_001004311.3	58	2525,2667,965	GG,GC,CC		46.2036,18.6428,37.3315	benign	141/220	71012734	7717,4597	1982	4175	6157	SO:0001583	missense	344018	exon3			TCAGAACTGTTGT	BC039536	CCDS46320.1	2p13.3	2013-05-21			ENSG00000183733	ENSG00000183733		"""Basic helix-loop-helix proteins"""	24669	protein-coding gene	gene with protein product	"""factor in the germline alpha"""	608697				12468641	Standard	NM_001004311		Approved	bHLHc8	uc002she.1	Q6QHK4	OTTHUMG00000153440	ENST00000332372.6:c.422G>C	2.37:g.71012734C>G	ENSP00000333097:p.Ser141Thr	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	352	99	0.28125	NM_001004311		Missense_Mutation	SNP	ENST00000332372.6	37	CCDS46320.1	1641	0.7513736263736264	432	0.8780487804878049	238	0.6574585635359116	538	0.9405594405594405	433	0.5712401055408971	G	0.012	-1.681187	0.00745	0.813572	0.537964	ENSG00000183733	ENST00000332372	D	0.95447	-3.71	4.12	3.24	0.37175	Helix-loop-helix DNA-binding (1);	1.058040	0.07402	N	0.890934	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42999	-0.9418	9	0.05721	T	0.95	.	6.0393	0.19726	0.1021:0.191:0.7069:0.0	rs7566476;rs17717676;rs52819463;rs61154013;rs7566476	141	Q6QHK4	FIGLA_HUMAN	T	141	ENSP00000333097:S141T	ENSP00000333097:S141T	S	-	2	0	FIGLA	70866242	0.310000	0.24527	0.010000	0.14722	0.009000	0.06853	1.504000	0.35726	0.701000	0.31803	-0.127000	0.14921	AGT	C|0.255;G|0.745	0.745	strong		0.403	FIGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331214.1	NM_001004311	
SPARCL1	8404	hgsc.bcm.edu	37	4	88416188	88416188	+	Missense_Mutation	SNP	G	G	T	rs13051	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:88416188G>T	ENST00000282470.6	-	3	616	c.146C>A	c.(145-147)gCt>gAt	p.A49D	SPARCL1_ENST00000503414.1_De_novo_Start_OutOfFrame|SPARCL1_ENST00000418378.1_Missense_Mutation_p.A49D	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	49			A -> D (in dbSNP:rs13051). {ECO:0000269|PubMed:7600298}.		signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.A49D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		ATTTTCTTCAGCTTCAGCCCT	0.353													T|||	2881	0.57528	0.882	0.5029	5008	,	,		16934	0.4375		0.3787	False		,,,				2504	0.5562				p.A49D		Atlas-SNP	.											SPARCL1,NS,carcinoma,0,1	SPARCL1	59	1	1	Substitution - Missense(1)	stomach(1)	c.C146A						PASS	.	T	ASP/ALA,ASP/ALA	3556,850	333.3+/-302.9	1435,686,82	155.0	164.0	161.0		146,146	3.0	0.9	4	dbSNP_52	161	3196,5404	653.0+/-401.0	601,1994,1705	yes	missense,missense	SPARCL1	NM_001128310.1,NM_004684.4	126,126	2036,2680,1787	TT,TG,GG		37.1628,19.2919,48.0855	benign,benign	49/665,49/665	88416188	6752,6254	2203	4300	6503	SO:0001583	missense	8404	exon3			TCTTCAGCTTCAG	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.146C>A	4.37:g.88416188G>T	ENSP00000282470:p.Ala49Asp	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	323	153	0.473684	NM_004684	B4E2Z0|E7ESU2|Q14800	Missense_Mutation	SNP	ENST00000282470.6	37	CCDS3622.1	1128	0.5164835164835165	433	0.8800813008130082	189	0.5220994475138122	231	0.40384615384615385	275	0.3627968337730871	T	0.010	-1.742076	0.00675	0.807081	0.371628	ENSG00000152583	ENST00000282470;ENST00000418378;ENST00000509407;ENST00000434434;ENST00000535835;ENST00000512317;ENST00000543631;ENST00000458304	T;T;T;T;T;T;T;T	0.49720	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.77	4.1	3.02	0.34903	.	0.436671	0.23219	N	0.050581	T	0.00012	0.0000	N	0.01168	-0.975	0.53005	P	3.399999999997849E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.31888	-0.9927	9	0.09338	T	0.73	-1.8696	8.876	0.35345	0.0:0.0:0.514:0.486	rs13051;rs1049542;rs3189720;rs7698628;rs17855569;rs60110307;rs13051	49	Q14515	SPRL1_HUMAN	D	49	ENSP00000282470:A49D;ENSP00000414856:A49D;ENSP00000423483:A49D;ENSP00000416971:A49D;ENSP00000438188:A49D;ENSP00000423448:A49D;ENSP00000444832:A49D;ENSP00000406251:A49D	ENSP00000282470:A49D	A	-	2	0	SPARCL1	88635212	0.942000	0.31987	0.909000	0.35828	0.011000	0.07611	0.896000	0.28377	0.458000	0.26988	-0.256000	0.11100	GCT	G|0.474;T|0.526	0.526	strong		0.353	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		
SART3	9733	hgsc.bcm.edu	37	12	108941679	108941679	+	Silent	SNP	G	G	A	rs12579216	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:108941679G>A	ENST00000228284.3	-	3	762	c.528C>T	c.(526-528)gcC>gcT	p.A176A	SART3_ENST00000552221.1_5'UTR|SART3_ENST00000431469.2_Silent_p.A176A	NM_014706.3	NP_055521.1	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T cells 3	176					cell morphogenesis (GO:0000902)|hematopoietic stem cell proliferation (GO:0071425)|homeostasis of number of cells (GO:0048872)|regulation of gene expression (GO:0010468)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A176A(1)		NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|stomach(1)	25						AATCCTTCACGGCTTTCTCAA	0.468									Porokeratosis				G|||	516	0.103035	0.0242	0.0634	5008	,	,		19878	0.1419		0.0964	False		,,,				2504	0.2045				p.A176A		Atlas-SNP	.											SART3,NS,carcinoma,0,1	SART3	64	1	1	Substitution - coding silent(1)	stomach(1)	c.C528T						PASS	.	G		200,4206	125.3+/-162.5	4,192,2007	70.0	66.0	67.0		528	-11.5	0.5	12	dbSNP_120	67	875,7725	198.2+/-242.6	48,779,3473	no	coding-synonymous	SART3	NM_014706.3		52,971,5480	AA,AG,GG		10.1744,4.5393,8.2654		176/964	108941679	1075,11931	2203	4300	6503	SO:0001819	synonymous_variant	9733	exon3	Familial Cancer Database	incl.: Porokeratosis of Mibelli, Disseminated Superficial Actinic Porokertosis, Porokeratosis Palmaris Plantaris et Disseminata, Porokeratosis Punctata Palmaris et Plantaris, Linear Porokeratosis	CTTCACGGCTTTC	AB020880	CCDS9117.1	12q24.11	2013-02-12	2006-12-07			ENSG00000075856		"""RNA binding motif (RRM) containing"""	16860	protein-coding gene	gene with protein product		611684	"""squamous cell carcinoma antigen recognised by T cells 3"""			12032085, 15840095, 20595234	Standard	NM_014706		Approved	KIAA0156, RP11-13G14, TIP110, p110	uc001tmz.1	Q15020	OTTHUMG00000169449	ENST00000228284.3:c.528C>T	12.37:g.108941679G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_014706	A8K2E4|Q2M2H0|Q58F06|Q8IUS1|Q96J95	Silent	SNP	ENST00000228284.3	37	CCDS9117.1																																																																																			G|0.913;A|0.087	0.087	strong		0.468	SART3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404094.1		
TNRC6A	27327	hgsc.bcm.edu	37	16	24788645	24788645	+	Missense_Mutation	SNP	T	T	A	rs11639856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:24788645T>A	ENST00000395799.3	+	5	684	c.555T>A	c.(553-555)aaT>aaA	p.N185K	TNRC6A_ENST00000315183.7_Missense_Mutation_p.N185K	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	185	Interaction with argonaute family proteins.		N -> K (in dbSNP:rs11639856).		cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		AGCCACAAAATAACGGAGAGG	0.413													T|||	844	0.16853	0.2284	0.1484	5008	,	,		19450	0.128		0.162	False		,,,				2504	0.1503				p.N185K		Atlas-SNP	.											.	TNRC6A	171	.	0			c.T555A						PASS	.	T	LYS/ASN	770,3306		77,616,1345	131.0	133.0	132.0		555	2.4	1.0	16	dbSNP_120	132	1574,6846		147,1280,2783	yes	missense	TNRC6A	NM_014494.2	94	224,1896,4128	AA,AT,TT		18.6936,18.8911,18.758	benign	185/1963	24788645	2344,10152	2038	4210	6248	SO:0001583	missense	27327	exon5			ACAAAATAACGGA	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.555T>A	16.37:g.24788645T>A	ENSP00000379144:p.Asn185Lys	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	319	0.14606227106227107	92	0.18699186991869918	56	0.15469613259668508	61	0.10664335664335664	110	0.14511873350923482	T	5.027	0.190761	0.09547	0.188911	0.186936	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.10860	2.83;2.83	5.84	2.44	0.29823	.	0.313190	0.33144	N	0.005233	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.99999840025	B	0.02656	0.0	B	0.01281	0.0	T	0.43556	-0.9384	9	0.06236	T	0.91	-1.0666	4.4847	0.11783	0.1455:0.2438:0.0:0.6107	rs11639856;rs52830311;rs60905112;rs11639856	185	Q8NDV7	TNR6A_HUMAN	K	185	ENSP00000326900:N185K;ENSP00000379144:N185K	ENSP00000326900:N185K	N	+	3	2	TNRC6A	24696146	0.915000	0.31059	1.000000	0.80357	0.998000	0.95712	0.825000	0.27393	1.040000	0.40099	0.482000	0.46254	AAT	T|0.853;A|0.147	0.147	strong		0.413	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
VWA5B2	90113	hgsc.bcm.edu	37	3	183951135	183951135	+	Silent	SNP	C	C	T	rs729377	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:183951135C>T	ENST00000426955.2	+	3	580	c.480C>T	c.(478-480)gcC>gcT	p.A160A	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_5'Flank	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	160										breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						CCCCGCTggccccgccaggcc	0.701													C|||	1498	0.299121	0.3684	0.2608	5008	,	,		14658	0.3165		0.2783	False		,,,				2504	0.2362				p.A160A		Atlas-SNP	.											.	VWA5B2	47	.	0			c.C480T						PASS	.						11.0	15.0	14.0					3																	183951135		692	1591	2283	SO:0001819	synonymous_variant	90113	exon3			GCTGGCCCCGCCA		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.480C>T	3.37:g.183951135C>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	13	12	0.923077	NM_138345	B9EGN7	Silent	SNP	ENST00000426955.2	37	CCDS54686.1																																																																																			C|0.708;T|0.292	0.292	strong		0.701	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
DLK1	8788	hgsc.bcm.edu	37	14	101200860	101200860	+	Missense_Mutation	SNP	G	G	A	rs1058009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:101200860G>A	ENST00000341267.4	+	5	1021	c.779G>A	c.(778-780)aGc>aAc	p.S260N	DLK1_ENST00000331224.6_Intron	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	260			S -> N (in dbSNP:rs1058009).		cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				CGTCTGCCCAGCGGCTATGGG	0.647													G|||	278	0.0555112	0.0091	0.0591	5008	,	,		14798	0.0188		0.0895	False		,,,				2504	0.1186				p.S260N		Atlas-SNP	.											.	DLK1	57	.	0			c.G779A						PASS	.	G	ASN/SER	111,4293	80.9+/-119.3	1,109,2092	34.0	39.0	37.0		779	3.5	0.8	14	dbSNP_86	37	567,8029	146.9+/-202.4	24,519,3755	yes	missense	DLK1	NM_003836.5	46	25,628,5847	AA,AG,GG		6.5961,2.5204,5.2154	possibly-damaging	260/384	101200860	678,12322	2202	4298	6500	SO:0001583	missense	8788	exon5			TGCCCAGCGGCTA	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"""delta-like homolog (Drosophila)"""			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.779G>A	14.37:g.101200860G>A	ENSP00000340292:p.Ser260Asn	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	55	36	0.654545	NM_003836	P15803|Q96DW5	Missense_Mutation	SNP	ENST00000341267.4	37	CCDS9963.1	113	0.051739926739926737	7	0.014227642276422764	20	0.055248618784530384	13	0.022727272727272728	73	0.09630606860158311	G	6.391	0.440273	0.12104	0.025204	0.065961	ENSG00000185559	ENST00000341267	D	0.87256	-2.23	4.46	3.54	0.40534	.	0.880493	0.10000	N	0.728657	T	0.08626	0.0214	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.22800	-1.0206	9	.	.	.	.	4.7591	0.13099	0.1967:0.0:0.6345:0.1688	rs1058009;rs3168825;rs17845129;rs17857930;rs17858266;rs1058009	260	P80370	DLK1_HUMAN	N	260	ENSP00000340292:S260N	.	S	+	2	0	DLK1	100270613	0.001000	0.12720	0.764000	0.31436	0.591000	0.36615	0.337000	0.19841	0.806000	0.34183	0.491000	0.48974	AGC	G|0.948;A|0.052	0.052	strong		0.647	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
UGT2B28	54490	hgsc.bcm.edu	37	4	70152499	70152499	+	Silent	SNP	T	T	A	rs41292341	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:70152499T>A	ENST00000335568.5	+	3	902	c.900T>A	c.(898-900)ggT>ggA	p.G300G	UGT2B28_ENST00000511240.1_Silent_p.G300G	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	300					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						AGAGCTCTGGTGAAAATGGTG	0.413													t|||	142	0.0283546	0.0371	0.036	5008	,	,		10829	0.004		0.0388	False		,,,				2504	0.0256				p.G300G		Atlas-SNP	.											UGT2B28,caecum,carcinoma,0,1	UGT2B28	101	1	0			c.T900A						PASS	.	A	,	93,4047		15,63,1992	140.0	158.0	152.0		900,900	0.7	1.0	4	dbSNP_127	152	305,8197		44,217,3990	no	coding-synonymous,coding-synonymous	UGT2B28	NM_001207004.1,NM_053039.1	,	59,280,5982	AA,AT,TT		3.5874,2.2464,3.1482	,	300/336,300/530	70152499	398,12244	2070	4251	6321	SO:0001819	synonymous_variant	54490	exon3			CTCTGGTGAAAAT	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.900T>A	4.37:g.70152499T>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_053039	B5BUM0|Q9BY62|Q9BY63	Silent	SNP	ENST00000335568.5	37	CCDS3528.1																																																																																			T|0.972;A|0.028	0.028	strong		0.413	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
ALOX15B	247	hgsc.bcm.edu	37	17	7950377	7950377	+	Silent	SNP	C	C	T	rs11541083	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7950377C>T	ENST00000380183.4	+	10	1579	c.1440C>T	c.(1438-1440)atC>atT	p.I480I	ALOX15B_ENST00000380173.2_Silent_p.I451I|ALOX15B_ENST00000572022.1_Silent_p.I480I|ALOX15B_ENST00000573359.1_Silent_p.I451I	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	480	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						GGATGCAGATCTGGGGTGCAG	0.602													C|||	1244	0.248403	0.0711	0.4294	5008	,	,		18794	0.2192		0.3598	False		,,,				2504	0.2751				p.I480I		Atlas-SNP	.											.	ALOX15B	66	.	0			c.C1440T						PASS	.	C	,,	519,3887	238.4+/-249.8	41,437,1725	70.0	69.0	69.0		1353,1353,1440	1.2	1.0	17	dbSNP_120	69	2916,5684	454.5+/-363.5	507,1902,1891	no	coding-synonymous,coding-synonymous,coding-synonymous	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	,,	548,2339,3616	TT,TC,CC		33.907,11.7794,26.4109	,,	451/648,451/603,480/677	7950377	3435,9571	2203	4300	6503	SO:0001819	synonymous_variant	247	exon10			GCAGATCTGGGGT	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1440C>T	17.37:g.7950377C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	79	0.975309	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Silent	SNP	ENST00000380183.4	37	CCDS11128.1																																																																																			C|0.735;T|0.265	0.265	strong		0.602	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
SSFA2	6744	hgsc.bcm.edu	37	2	182792984	182792984	+	Missense_Mutation	SNP	T	T	A	rs2303554	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:182792984T>A	ENST00000431877.2	+	17	3951	c.3772T>A	c.(3772-3774)Tat>Aat	p.Y1258N	SSFA2_ENST00000409001.1_Missense_Mutation_p.Y1236N|SSFA2_ENST00000428267.2_Missense_Mutation_p.Y1083N|SSFA2_ENST00000467172.2_Intron|SSFA2_ENST00000409136.1_Missense_Mutation_p.Y767N|SSFA2_ENST00000320370.7_Intron	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	1258			Y -> N (in dbSNP:rs2303554).			cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			TAAGCAAGATTATCATTAAAC	0.313													A|||	407	0.08127	0.112	0.0403	5008	,	,		16848	0.0843		0.0348	False		,,,				2504	0.1135				p.Y1258N		Atlas-SNP	.											.	SSFA2	130	.	0			c.T3772A						PASS	.						109.0	99.0	102.0					2																	182792984		692	1590	2282	SO:0001583	missense	6744	exon17			CAAGATTATCATT	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"""cleavage signal-1 protein"", ""KRAS-induced actin-interacting protein"", ""sperm associated antigen 13"""	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.3772T>A	2.37:g.182792984T>A	ENSP00000388731:p.Tyr1258Asn	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	210	113	0.538095	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	154	0.07051282051282051	54	0.10975609756097561	15	0.04143646408839779	61	0.10664335664335664	24	0.0316622691292876	A	7.175	0.588424	0.13812	.	.	ENSG00000138434	ENST00000431877;ENST00000409001;ENST00000428267;ENST00000409136	T;T;T;T	0.13657	2.8;2.8;2.8;2.57	5.93	4.78	0.61160	.	1.305430	0.04986	N	0.466525	T	0.00178	0.0005	N	0.08118	0	0.58432	P	9.99999999995449E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.42275	-0.9461	9	0.13470	T	0.59	0.1156	7.1334	0.25515	0.801:0.0:0.0688:0.1302	rs2303554;rs52830405;rs2303554	1083;767;1236;1258	E7END2;E7EUL7;E9PHV5;P28290	.;.;.;SSFA2_HUMAN	N	1258;1236;1083;767	ENSP00000388731:Y1258N;ENSP00000387319:Y1236N;ENSP00000409867:Y1083N;ENSP00000386916:Y767N	ENSP00000387319:Y1236N	Y	+	1	0	SSFA2	182501229	0.993000	0.37304	0.328000	0.25416	0.322000	0.28314	1.886000	0.39688	0.492000	0.27815	-0.257000	0.10917	TAT	T|0.933;A|0.067	0.067	strong		0.313	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751	
ANO10	55129	hgsc.bcm.edu	37	3	43602803	43602803	+	Missense_Mutation	SNP	C	C	T	rs3772165	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:43602803C>T	ENST00000292246.3	-	9	1555	c.1385G>A	c.(1384-1386)cGg>cAg	p.R462Q	ANO10_ENST00000350459.4_Missense_Mutation_p.R272Q|ANO10_ENST00000414522.2_Missense_Mutation_p.R462Q|ANO10_ENST00000396091.3_Missense_Mutation_p.R396Q|ANO10_ENST00000451430.2_Missense_Mutation_p.R351Q	NM_018075.3	NP_060545.3	Q9NW15	ANO10_HUMAN	anoctamin 10	462			R -> Q (in dbSNP:rs3772165). {ECO:0000269|PubMed:14702039}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						CCTCTTCACCCGCACACCATG	0.423													C|||	3321	0.663139	0.4463	0.7334	5008	,	,		16590	0.8849		0.5785	False		,,,				2504	0.7648				p.R462Q		Atlas-SNP	.											.	ANO10	70	.	0			c.G1385A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	2193,2213	586.4+/-386.5	547,1099,557	128.0	120.0	123.0		1385,1187,1052,815,1385	-5.4	0.0	3	dbSNP_107	123	5050,3550	630.8+/-398.4	1511,2028,761	yes	missense,missense,missense,missense,missense	ANO10	NM_001204831.1,NM_001204832.1,NM_001204833.1,NM_001204834.1,NM_018075.3	43,43,43,43,43	2058,3127,1318	TT,TC,CC		41.2791,49.773,44.3103	benign,benign,benign,benign,benign	462/628,396/595,351/550,272/471,462/661	43602803	7243,5763	2203	4300	6503	SO:0001583	missense	55129	exon9			TTCACCCGCACAC	AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	25519	protein-coding gene	gene with protein product		613726	"""transmembrane protein 16K"""	TMEM16K		12477932, 24692353	Standard	NM_001204831		Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000292246.3:c.1385G>A	3.37:g.43602803C>T	ENSP00000292246:p.Arg462Gln	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	241	111	0.460581	NM_018075	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	Missense_Mutation	SNP	ENST00000292246.3	37	CCDS2710.2	1428	0.6538461538461539	208	0.42276422764227645	257	0.7099447513812155	515	0.9003496503496503	448	0.5910290237467019	C	13.89	2.371895	0.42003	0.49773	0.587209	ENSG00000160746	ENST00000292246;ENST00000350459;ENST00000396091;ENST00000414522;ENST00000451430	T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02	5.42	-5.43	0.02632	.	0.506358	0.22536	N	0.058784	T	0.00012	0.0000	L	0.43152	1.355	0.48040	P	4.290000000000127E-4	B;B;P;B;B	0.38420	0.007;0.003;0.63;0.007;0.001	B;B;B;B;B	0.26864	0.009;0.007;0.074;0.009;0.003	T	0.30090	-0.9990	9	0.27082	T	0.32	.	16.2443	0.82434	0.0:0.5744:0.0:0.4255	rs3772165;rs52793486;rs3772165	351;462;272;396;462	Q9NW15-4;C9JHS1;Q9NW15-2;Q9NW15-3;Q9NW15	.;.;.;.;ANO10_HUMAN	Q	462;272;396;462;351	ENSP00000292246:R462Q;ENSP00000327767:R272Q;ENSP00000379398:R396Q;ENSP00000396990:R462Q;ENSP00000394119:R351Q	ENSP00000292246:R462Q	R	-	2	0	ANO10	43577807	0.011000	0.17503	0.017000	0.16124	0.982000	0.71751	-0.139000	0.10358	-0.909000	0.03852	-0.484000	0.04775	CGG	C|0.413;T|0.587	0.587	strong		0.423	ANO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256649.2	NM_018075	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33568687	33568687	+	Silent	SNP	T	T	A	rs7032174	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:33568687T>A	ENST00000290943.6	+	15	2883	c.2787T>A	c.(2785-2787)gcT>gcA	p.A929A	ANKRD18B_ENST00000426460.2_3'UTR	NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	929										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						AGAAAATAGCTGTGATCAGCA	0.373													.|||	717	0.143171	0.1498	0.0951	5008	,	,		18285	0.0903		0.1581	False		,,,				2504	0.2076				p.A928A		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.T2784A						PASS	.																																			SO:0001819	synonymous_variant	441459	exon15			AATAGCTGTGATC			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.2787T>A	9.37:g.33568687T>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				T|0.868;A|0.132	0.132	strong		0.373	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
FAM217A	222826	hgsc.bcm.edu	37	6	4069685	4069685	+	Missense_Mutation	SNP	C	C	T	rs639905	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:4069685C>T	ENST00000274673.3	-	7	1175	c.772G>A	c.(772-774)Gct>Act	p.A258T	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	258			A -> T (in dbSNP:rs639905).														AAGTCTAGAGCACTGAAAGGA	0.418													T|||	1486	0.296725	0.4107	0.2997	5008	,	,		18758	0.3542		0.1889	False		,,,				2504	0.1922				p.A258T		Atlas-SNP	.											.	.	.	.	0			c.G772A						PASS	.	T	THR/ALA	1735,2671	647.9+/-398.6	345,1045,813	82.0	83.0	83.0		772	-1.1	0.0	6	dbSNP_83	83	1508,7092	747.9+/-407.3	138,1232,2930	yes	missense	C6orf146	NM_173563.2	58	483,2277,3743	TT,TC,CC		17.5349,39.3781,24.9346	benign	258/509	4069685	3243,9763	2203	4300	6503	SO:0001583	missense	222826	exon7			CTAGAGCACTGAA	BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 146"""	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.772G>A	6.37:g.4069685C>T	ENSP00000274673:p.Ala258Thr	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	148	145	0.97973	NM_173563	Q5JYK1	Missense_Mutation	SNP	ENST00000274673.3	37	CCDS4489.1	670	0.3067765567765568	210	0.4268292682926829	100	0.27624309392265195	212	0.3706293706293706	148	0.19525065963060687	T	0.078	-1.188431	0.01607	0.393781	0.175349	ENSG00000145975	ENST00000274673;ENST00000538080;ENST00000470599	T	0.19105	2.17	5.43	-1.11	0.09840	.	0.614820	0.16862	N	0.196476	T	0.00695	0.0023	N	0.00104	-2.125	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.35798	-0.9774	9	0.02654	T	1	-1.6331	5.6412	0.17565	0.1471:0.4406:0.0:0.4123	rs639905;rs57001715;rs639905	258	Q8IXS0	CF146_HUMAN	T	258;105;386	ENSP00000274673:A258T	ENSP00000274673:A258T	A	-	1	0	C6orf146	4014684	0.004000	0.15560	0.002000	0.10522	0.672000	0.39443	0.226000	0.17776	-0.624000	0.05611	-2.248000	0.00284	GCT	C|0.732;T|0.268	0.268	strong		0.418	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183832	11183832	+	Missense_Mutation	SNP	G	G	A	rs10845295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11183832G>A	ENST00000390675.2	-	1	174	c.103C>T	c.(103-105)Cgg>Tgg	p.R35W	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	35			R -> W (in dbSNP:rs10845295).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						CTCTTGACCCGCTCAATGGAA	0.388													.|||	1680	0.335463	0.3434	0.4568	5008	,	,		17811	0.1944		0.4801	False		,,,				2504	0.2352				p.R35W		Atlas-SNP	.											TAS2R31,NS,carcinoma,+2,1	TAS2R31	24	1	0			c.C103T						scavenged	.	A	TRP/ARG	1388,2536		252,884,826	58.0	61.0	60.0		103	1.2	0.0	12	dbSNP_120	60	4039,4347		1001,2037,1155	no	missense	TAS2R31	NM_176885.2	101	1253,2921,1981	AA,AG,GG		48.1636,35.3721,44.0861	benign	35/310	11183832	5427,6883	1962	4193	6155	SO:0001583	missense	259290	exon1			TGACCCGCTCAAT	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.103C>T	12.37:g.11183832G>A	ENSP00000375093:p.Arg35Trp	Somatic	271	26	0.095941		WXS	Illumina HiSeq	Phase_I	278	136	0.489209	NM_176885	P59547|Q17R84|Q645X5	Missense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	867	0.39697802197802196	172	0.34959349593495936	157	0.43370165745856354	148	0.25874125874125875	390	0.5145118733509235	A	0.007	-1.952494	0.00470	0.353721	0.481636	ENSG00000256436	ENST00000390675	T	0.00606	6.26	2.45	1.23	0.21249	.	.	.	.	.	T	0.00012	0.0000	N	0.00003	-3.445	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.34428	-0.9829	8	0.02654	T	1	.	4.6954	0.12800	0.6702:0.0:0.3298:0.0	rs10845295	35	P59538	T2R31_HUMAN	W	35	ENSP00000375093:R35W	ENSP00000375093:R35W	R	-	1	2	TAS2R31	11075099	0.004000	0.15560	0.004000	0.12327	0.048000	0.14542	1.722000	0.38042	-0.166000	0.10890	-1.220000	0.01600	CGG	G|0.581;A|0.419	0.419	strong		0.388	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
CAMK2B	816	hgsc.bcm.edu	37	7	44259706	44259706	+	Silent	SNP	G	G	A	rs1065359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:44259706G>A	ENST00000395749.2	-	23	2032	c.1956C>T	c.(1954-1956)aaC>aaT	p.N652N	CAMK2B_ENST00000258682.6_Silent_p.N503N|CAMK2B_ENST00000395747.2_Silent_p.N504N|CAMK2B_ENST00000440254.2_Silent_p.N528N|CAMK2B_ENST00000457475.1_Silent_p.N504N|CAMK2B_ENST00000358707.3_Silent_p.N489N|CAMK2B_ENST00000346990.4_Silent_p.N435N|CAMK2B_ENST00000347193.4_Silent_p.N478N|CAMK2B_ENST00000353625.4_Silent_p.N465N|CAMK2B_ENST00000502837.2_3'UTR|CAMK2B_ENST00000489429.1_5'UTR|CAMK2B_ENST00000350811.3_Silent_p.N528N	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	652					activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						GGAAGTGCACGTTCTGCCACT	0.672													G|||	1698	0.339058	0.1596	0.3213	5008	,	,		16451	0.3879		0.4085	False		,,,				2504	0.4724				p.N652N		Atlas-SNP	.											.	CAMK2B	56	.	0			c.C1956T						PASS	.	G	,,,,,,,	971,3429		119,733,1348	29.0	27.0	28.0		1956,1584,1512,1509,1467,1434,1395,1305	-5.0	0.9	7	dbSNP_86	28	3589,5009		743,2103,1453	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2B	NM_001220.4,NM_172078.2,NM_172079.2,NM_172080.2,NM_172081.2,NM_172082.2,NM_172083.2,NM_172084.2	,,,,,,,	862,2836,2801	AA,AG,GG		41.7423,22.0682,35.0823	,,,,,,,	652/667,528/543,504/519,503/518,489/504,478/493,465/480,435/450	44259706	4560,8438	2200	4299	6499	SO:0001819	synonymous_variant	816	exon23			GTGCACGTTCTGC	U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"""CaM-kinase II beta chain"", ""calcium/calmodulin-dependent protein kinase type II beta chain"", ""CaM kinase II beta subunit"", ""proline rich calmodulin-dependent protein kinase"""	607707	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"""	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.1956C>T	7.37:g.44259706G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_001220	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Silent	SNP	ENST00000395749.2	37	CCDS5483.1																																																																																			G|0.654;A|0.346	0.346	strong		0.672	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084	
KIAA1109	84162	hgsc.bcm.edu	37	4	123229132	123229132	+	Silent	SNP	C	C	T	rs7688384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:123229132C>T	ENST00000264501.4	+	58	10243	c.9870C>T	c.(9868-9870)gcC>gcT	p.A3290A	KIAA1109_ENST00000455637.1_Silent_p.A3290A|KIAA1109_ENST00000388738.3_Silent_p.A3290A			Q2LD37	K1109_HUMAN	KIAA1109	3290					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A3290A(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ATTATAAGGCCGCCTATGACA	0.353													T|||	1388	0.277157	0.0333	0.3084	5008	,	,		18430	0.3611		0.3072	False		,,,				2504	0.4673				p.A3290A		Atlas-SNP	.											KIAA1109,NS,carcinoma,0,1	KIAA1109	424	1	1	Substitution - coding silent(1)	prostate(1)	c.C9870T						scavenged	.	T		304,3376		13,278,1549	155.0	152.0	153.0		9870	4.7	1.0	4	dbSNP_116	153	2662,5532		414,1834,1849	no	coding-synonymous	KIAA1109	NM_015312.3		427,2112,3398	TT,TC,CC		32.4872,8.2609,24.9789		3290/5006	123229132	2966,8908	1840	4097	5937	SO:0001819	synonymous_variant	84162	exon56			TAAGGCCGCCTAT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.9870C>T	4.37:g.123229132C>T		Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	182	84	0.461538	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	571	0.26144688644688646	22	0.044715447154471545	111	0.30662983425414364	199	0.3479020979020979	239	0.3153034300791557	T	9.403	1.078547	0.20227	0.082609	0.324872	ENSG00000138688	ENST00000419325	.	.	.	5.92	4.74	0.60224	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44314	-0.9336	3	.	.	.	.	2.7244	0.05210	0.1185:0.1305:0.1235:0.6276	rs7688384;rs59976925;rs7688384	.	.	.	C	1248	.	.	R	+	1	0	KIAA1109	123448582	0.931000	0.31567	1.000000	0.80357	0.992000	0.81027	-0.047000	0.11963	0.503000	0.28060	-0.254000	0.11334	CGC	C|0.717;T|0.283	0.283	strong		0.353	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
RTKN2	219790	hgsc.bcm.edu	37	10	63977980	63977980	+	Missense_Mutation	SNP	C	C	T	rs61850830	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:63977980C>T	ENST00000373789.3	-	8	958	c.862G>A	c.(862-864)Gca>Aca	p.A288T	RTKN2_ENST00000315289.2_Missense_Mutation_p.A69T|RTKN2_ENST00000395265.1_Missense_Mutation_p.A288T	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	288	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					CCTGCAAATGCATCCTCAGCC	0.408													C|||	535	0.106829	0.0098	0.0735	5008	,	,		15862	0.0982		0.1034	False		,,,				2504	0.274				p.A288T		Atlas-SNP	.											.	RTKN2	68	.	0			c.G862A						PASS	.	C	THR/ALA	101,4305	81.4+/-119.9	2,97,2104	69.0	65.0	66.0		862	5.4	1.0	10	dbSNP_129	66	975,7625	212.5+/-252.8	67,841,3392	yes	missense	RTKN2	NM_145307.2	58	69,938,5496	TT,TC,CC		11.3372,2.2923,8.2731	benign	288/610	63977980	1076,11930	2203	4300	6503	SO:0001583	missense	219790	exon8			CAAATGCATCCTC	BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"""Pleckstrin homology (PH) domain containing"""	19364	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family K member 1"""	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.862G>A	10.37:g.63977980C>T	ENSP00000362894:p.Ala288Thr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_145307	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	Missense_Mutation	SNP	ENST00000373789.3	37	CCDS7263.1	160	0.07326007326007326	5	0.01016260162601626	25	0.06906077348066299	51	0.08916083916083917	79	0.10422163588390501	C	15.85	2.956169	0.53293	0.022923	0.113372	ENSG00000182010	ENST00000315289;ENST00000395265;ENST00000373789	T;T;T	0.43294	0.95;1.54;1.54	5.42	5.42	0.78866	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.315023	0.39687	N	0.001297	T	0.00998	0.0033	L	0.44542	1.39	0.29024	P	0.886098	D;P	0.53462	0.96;0.822	P;B	0.52454	0.699;0.393	T	0.05162	-1.0902	9	0.19590	T	0.45	-6.1534	11.1113	0.48235	0.0:0.8823:0.0:0.1177	rs61850830	69;288	Q5SVY4;Q8IZC4	.;RTKN2_HUMAN	T	69;288;288	ENSP00000325379:A69T;ENSP00000378682:A288T;ENSP00000362894:A288T	ENSP00000325379:A69T	A	-	1	0	RTKN2	63647986	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	2.160000	0.42348	2.711000	0.92665	0.655000	0.94253	GCA	C|0.913;T|0.087	0.087	strong		0.408	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307	
CLHC1	130162	hgsc.bcm.edu	37	2	55404794	55404794	+	Missense_Mutation	SNP	G	G	A	rs14026	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:55404794G>A	ENST00000401408.1	-	12	1853	c.1508C>T	c.(1507-1509)gCa>gTa	p.A503V	CLHC1_ENST00000407122.1_Missense_Mutation_p.A503V|CLHC1_ENST00000494539.1_5'UTR|CLHC1_ENST00000406437.2_Missense_Mutation_p.A54V|CLHC1_ENST00000406076.1_Missense_Mutation_p.A381V	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	503			A -> V (in dbSNP:rs14026). {ECO:0000269|PubMed:15489334}.														TTTCATGTCTGCAGAGAACAG	0.353													A|||	2350	0.469249	0.4796	0.4683	5008	,	,		19202	0.4851		0.5179	False		,,,				2504	0.3896				p.A503V		Atlas-SNP	.											.	.	.	.	0			c.C1508T						PASS	.	A	VAL/ALA,VAL/ALA	2077,2327	606.0+/-390.6	462,1153,587	138.0	132.0	134.0		1142,1508	1.9	0.8	2	dbSNP_52	134	4572,4028	555.6+/-386.7	1222,2128,950	yes	missense,missense	C2orf63	NM_001135598.1,NM_152385.2	64,64	1684,3281,1537	AA,AG,GG		46.8372,47.1617,48.8696	benign,benign	381/465,503/587	55404794	6649,6355	2202	4300	6502	SO:0001583	missense	130162	exon12			ATGTCTGCAGAGA		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.1508C>T	2.37:g.55404794G>A	ENSP00000384869:p.Ala503Val	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	189	90	0.47619	NM_152385	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	37	CCDS33201.1	1101	0.5041208791208791	221	0.4491869918699187	179	0.494475138121547	304	0.5314685314685315	397	0.5237467018469657	A	0.994	-0.693036	0.03303	0.471617	0.531628	ENSG00000162994	ENST00000406437;ENST00000407122;ENST00000401408;ENST00000406076	T;T;T;T	0.30714	1.52;2.27;2.27;2.26	5.64	1.85	0.25348	.	0.796636	0.11310	N	0.577255	T	0.00012	0.0000	N	0.01109	-1.01	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45934	-0.9227	9	0.12430	T	0.62	-1.5454	3.5936	0.07998	0.5868:0.0:0.2574:0.1558	rs14026;rs17528646;rs17845891;rs17858866;rs52824383;rs60025580;rs14026	503	Q8NHS4	CB063_HUMAN	V	54;503;503;381	ENSP00000384810:A54V;ENSP00000385778:A503V;ENSP00000384869:A503V;ENSP00000385512:A381V	ENSP00000384869:A503V	A	-	2	0	C2orf63	55258298	0.009000	0.17119	0.839000	0.33178	0.007000	0.05969	0.430000	0.21428	0.427000	0.26145	-0.381000	0.06696	GCA	G|0.503;A|0.497	0.497	strong		0.353	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	
FLT4	2324	hgsc.bcm.edu	37	5	180057293	180057293	+	Missense_Mutation	SNP	T	T	C	rs34221241	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:180057293T>C	ENST00000261937.6	-	4	523	c.445A>G	c.(445-447)Aac>Gac	p.N149D	FLT4_ENST00000502649.1_Missense_Mutation_p.N149D|FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000393347.3_Missense_Mutation_p.N149D	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	149			N -> D (in dbSNP:rs34221241). {ECO:0000269|PubMed:17344846}.		blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCCTTCCTGTTGACCAAGAGC	0.632													t|||	195	0.0389377	0.0045	0.0331	5008	,	,		17521	0.001		0.1243	False		,,,				2504	0.0409				p.N149D	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.A445G						PASS	.	T	ASP/ASN,ASP/ASN	96,4304	77.8+/-116.1	2,92,2106	112.0	94.0	100.0		445,445	3.0	1.0	5	dbSNP_126	100	838,7760	192.1+/-238.2	49,740,3510	yes	missense,missense	FLT4	NM_002020.4,NM_182925.4	23,23	51,832,5616	CC,CT,TT		9.7465,2.1818,7.1857	benign,benign	149/1299,149/1364	180057293	934,12064	2200	4299	6499	SO:0001583	missense	2324	exon4			TCCTGTTGACCAA	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.445A>G	5.37:g.180057293T>C	ENSP00000261937:p.Asn149Asp	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	146	77	0.527397	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	117	0.05357142857142857	4	0.008130081300813009	15	0.04143646408839779	1	0.0017482517482517483	97	0.1279683377308707	T	9.334	1.061203	0.19987	0.021818	0.097465	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649	T;T;T	0.38722	1.12;1.12;1.12	5.36	2.96	0.34315	Immunoglobulin-like fold (1);	.	.	.	.	T	0.00271	0.0008	L	0.36672	1.1	0.32589	P	0.527408	B;B;B;B	0.15141	0.007;0.012;0.0;0.0	B;B;B;B	0.10450	0.002;0.005;0.003;0.003	T	0.15521	-1.0434	8	0.15066	T	0.55	.	3.9304	0.09283	0.2546:0.1458:0.0:0.5996	rs34221241	149;149;149;149	B5A927;P35916-3;E9PD35;P35916	.;.;.;VGFR3_HUMAN	D	149	ENSP00000261937:N149D;ENSP00000377016:N149D;ENSP00000426057:N149D	ENSP00000261937:N149D	N	-	1	0	FLT4	179989899	1.000000	0.71417	1.000000	0.80357	0.284000	0.27059	1.625000	0.37029	0.440000	0.26502	0.418000	0.28097	AAC	T|0.929;C|0.071	0.071	strong		0.632	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
LILRB4	11006	hgsc.bcm.edu	37	19	55179364	55179364	+	Missense_Mutation	SNP	A	A	G	rs1048801	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55179364A>G	ENST00000391736.1	+	14	1556	c.1241A>G	c.(1240-1242)cAg>cGg	p.Q414R	LILRB4_ENST00000430952.2_Missense_Mutation_p.Q413R|LILRB4_ENST00000391734.3_Missense_Mutation_p.Q361R|LILRB4_ENST00000391733.3_Missense_Mutation_p.Q415R|LILRB4_ENST00000270452.2_Missense_Mutation_p.Q414R	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	414			Q -> R (in dbSNP:rs1048801). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9548455}.		immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		ACCTACGCCCAGCTGCACAGC	0.647													A|||	1888	0.376997	0.4803	0.3818	5008	,	,		15595	0.3155		0.327	False		,,,				2504	0.3487				p.Q414R		Atlas-SNP	.											LILRB4,NS,carcinoma,-1,1	LILRB4	86	1	0			c.A1241G						scavenged	.	A	ARG/GLN,ARG/GLN	1972,2434	555.8+/-379.4	476,1020,707	84.0	88.0	87.0		1238,1241	1.0	0.0	19	dbSNP_86	87	3210,5390	484.2+/-371.3	578,2054,1668	no	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	43,43	1054,3074,2375	GG,GA,AA		37.3256,44.7571,39.8431	possibly-damaging,possibly-damaging	413/448,414/449	55179364	5182,7824	2203	4300	6503	SO:0001583	missense	11006	exon12			ACGCCCAGCTGCA	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1241A>G	19.37:g.55179364A>G	ENSP00000375616:p.Gln414Arg	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	261	116	0.444444	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	788	0.3608058608058608	225	0.4573170731707317	144	0.39779005524861877	171	0.29895104895104896	248	0.32717678100263853	A	10.65	1.410687	0.25465	0.447571	0.373256	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733	T;T;T;T;T	0.01084	5.36;5.36;5.37;6.51;5.37	2.07	0.983	0.19767	.	.	.	.	.	T	0.00012	0.0000	M	0.86864	2.845	0.80722	P	0.0	D;D;D;D	0.65815	0.992;0.995;0.985;0.963	P;P;P;P	0.56563	0.584;0.763;0.801;0.543	T	0.46048	-0.9219	8	0.51188	T	0.08	.	3.8581	0.08984	0.7937:0.0:0.2063:0.0	rs1048801;rs3177732;rs3188849;rs11574595;rs16985517;rs17845809;rs17858774;rs52795380;rs59824494	361;415;413;414	A8MUE1;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	R	414;414;413;361;415	ENSP00000375616:Q414R;ENSP00000270452:Q414R;ENSP00000408995:Q413R;ENSP00000375614:Q361R;ENSP00000375613:Q415R	ENSP00000270452:Q414R	Q	+	2	0	LILRB4	59871176	0.111000	0.22076	0.032000	0.17829	0.331000	0.28603	1.012000	0.29924	0.089000	0.17243	0.334000	0.21626	CAG	A|0.608;G|0.392	0.392	strong		0.647	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
UCK2	7371	hgsc.bcm.edu	37	1	165865478	165865478	+	Silent	SNP	G	G	A	rs11553301	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:165865478G>A	ENST00000367879.4	+	4	711	c.408G>A	c.(406-408)ggG>ggA	p.G136G	UCK2_ENST00000462329.1_3'UTR|UCK2_ENST00000469256.2_5'UTR|RP11-525G13.2_ENST00000455257.2_RNA|UCK2_ENST00000470820.1_5'UTR|UCK2_ENST00000372212.4_Intron	NM_012474.4	NP_036606.2	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2	136					cellular response to oxygen levels (GO:0071453)|CTP salvage (GO:0044211)|feeding behavior (GO:0007631)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to axon injury (GO:0048678)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					TCTTTGAAGGGATCCTGGCCT	0.552													G|||	436	0.0870607	0.0348	0.0836	5008	,	,		21179	0.0823		0.1521	False		,,,				2504	0.0982				p.G136G		Atlas-SNP	.											.	UCK2	31	.	0			c.G408A						PASS	.	G		207,4199	127.8+/-164.7	7,193,2003	218.0	203.0	208.0		408	0.9	1.0	1	dbSNP_120	208	1308,7292	257.7+/-281.7	104,1100,3096	no	coding-synonymous	UCK2	NM_012474.4		111,1293,5099	AA,AG,GG		15.2093,4.6981,11.6485		136/262	165865478	1515,11491	2203	4300	6503	SO:0001819	synonymous_variant	7371	exon4			TGAAGGGATCCTG	AF236637	CCDS1252.1	1p32	2012-10-02	2004-07-13	2004-07-14	ENSG00000143179	ENSG00000143179	2.7.1.48		12562	protein-coding gene	gene with protein product		609329	"""uridine monophosphate kinase"""	UMPK			Standard	NM_012474		Approved		uc001gdp.3	Q9BZX2	OTTHUMG00000040117	ENST00000367879.4:c.408G>A	1.37:g.165865478G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	153	68	0.444444	NM_012474	Q5VV91|Q7KZV3|Q92528|Q96KG5|Q9BU42	Silent	SNP	ENST00000367879.4	37	CCDS1252.1																																																																																			G|0.887;A|0.113	0.113	strong		0.552	UCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096753.1	NM_012474	
BCAM	4059	hgsc.bcm.edu	37	19	45316807	45316807	+	Silent	SNP	C	C	T	rs3810140	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:45316807C>T	ENST00000270233.6	+	6	736	c.714C>T	c.(712-714)gcC>gcT	p.A238A	BCAM_ENST00000589651.1_Silent_p.A238A	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	238	Ig-like V-type 2.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)	p.A238A(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				TCCACTGCGCCGCCCACTACA	0.697													C|||	467	0.0932508	0.0651	0.0836	5008	,	,		14264	0.0466		0.0805	False		,,,				2504	0.1994				p.A238A		Atlas-SNP	.											BCAM,NS,carcinoma,0,1	BCAM	53	1	1	Substitution - coding silent(1)	prostate(1)	c.C714T						PASS	.	C	,	287,4117		11,265,1926	40.0	45.0	43.0		714,714	-5.2	0.0	19	dbSNP_107	43	525,8065		18,489,3788	no	coding-synonymous,coding-synonymous	BCAM	NM_001013257.1,NM_005581.3	,	29,754,5714	TT,TC,CC		6.1118,6.5168,6.249	,	238/589,238/629	45316807	812,12182	2202	4295	6497	SO:0001819	synonymous_variant	4059	exon6			CTGCGCCGCCCAC	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6722	protein-coding gene	gene with protein product		612773	"""Lutheran blood group (Auberger b antigen included)"", ""basal cell adhesion molecule (Lu and Au blood groups)"""	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.714C>T	19.37:g.45316807C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	100	57	0.57	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Silent	SNP	ENST00000270233.6	37	CCDS12644.1																																																																																			C|0.946;T|0.054	0.054	strong		0.697	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	
SETD2	29072	hgsc.bcm.edu	37	3	47125385	47125385	+	Missense_Mutation	SNP	G	G	A	rs4082155	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:47125385G>A	ENST00000409792.3	-	12	5927	c.5885C>T	c.(5884-5886)cCc>cTc	p.P1962L	SETD2_ENST00000492397.1_5'UTR	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1962			P -> L (in dbSNP:rs4082155). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:15489334}.		angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.P1962L(1)|p.P1459L(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GCTCTCTTTGGGCTCTATTTC	0.453			"""N, F, S, Mis"""		clear cell renal carcinoma								G|||	2353	0.469848	0.236	0.5187	5008	,	,		21360	0.5327		0.5825	False		,,,				2504	0.5706				p.P1962L		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	SETD2_ENST00000409792,NS,carcinoma,0,2	SETD2	721	2	2	Substitution - Missense(2)	stomach(2)	c.C5885T						PASS	.	G	LEU/PRO	1261,3145	433.1+/-343.5	201,859,1143	248.0	213.0	225.0		5885	2.9	1.0	3	dbSNP_108	225	4869,3731	618.1+/-396.7	1380,2109,811	yes	missense	SETD2	NM_014159.6	98	1581,2968,1954	AA,AG,GG		43.3837,28.6201,47.1321	benign	1962/2565	47125385	6130,6876	2203	4300	6503	SO:0001583	missense	29072	exon12			TCTTTGGGCTCTA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5885C>T	3.37:g.47125385G>A	ENSP00000386759:p.Pro1962Leu	Somatic	342	1	0.00292398		WXS	Illumina HiSeq	Phase_I	312	146	0.467949	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	1082	0.49542124542124544	143	0.29065040650406504	194	0.5359116022099447	304	0.5314685314685315	441	0.5817941952506597	G	11.54	1.669445	0.29693	0.286201	0.566163	ENSG00000181555	ENST00000451092;ENST00000409792	T	0.21932	1.98	5.69	2.94	0.34122	.	0.827297	0.10610	N	0.654637	T	0.00012	0.0000	N	0.14661	0.345	0.28580	P	0.9101621	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.42207	-0.9465	9	0.13108	T	0.6	.	5.2839	0.15690	0.266:0.0:0.5927:0.1413	rs4082155;rs52814353;rs4082155	1962;1962	F2Z317;Q9BYW2	.;SETD2_HUMAN	L	1962	ENSP00000386759:P1962L	ENSP00000386759:P1962L	P	-	2	0	SETD2	47100389	0.764000	0.28473	0.986000	0.45419	0.925000	0.55904	0.529000	0.23019	0.333000	0.23563	-0.145000	0.13849	CCC	G|0.524;A|0.476	0.476	strong		0.453	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
SPTBN5	51332	hgsc.bcm.edu	37	15	42149472	42149472	+	Missense_Mutation	SNP	T	T	C	rs1456235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:42149472T>C	ENST00000320955.6	-	51	8812	c.8585A>G	c.(8584-8586)cAa>cGa	p.Q2862R		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2862			Q -> R (in dbSNP:rs1456235).		actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		TTCCACATCTTGGGCAAGGCA	0.662													T|||	2626	0.524361	0.0855	0.647	5008	,	,		18275	0.9544		0.5467	False		,,,				2504	0.5644				p.Q2827R		Atlas-SNP	.											.	SPTBN5	171	.	0			c.A8480G						PASS	.	T	ARG/GLN	660,3422		84,492,1465	12.0	15.0	14.0		8480	-3.4	0.0	15	dbSNP_88	14	4536,3818		1273,1990,914	yes	missense	SPTBN5	NM_016642.2	43	1357,2482,2379	CC,CT,TT		45.7027,16.1685,41.7819	benign	2827/3640	42149472	5196,7240	2041	4177	6218	SO:0001583	missense	51332	exon51			ACATCTTGGGCAA	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8585A>G	15.37:g.42149472T>C	ENSP00000317790:p.Gln2862Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		1255	0.5746336996336996	49	0.09959349593495935	231	0.638121546961326	551	0.9632867132867133	424	0.5593667546174143	.	0.024	-1.392953	0.01185	0.161685	0.542973	ENSG00000137877	ENST00000320955	T	0.50548	0.74	3.76	-3.38	0.04883	.	1.017260	0.07908	N	0.973790	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B	0.12630	0.006	B	0.09377	0.004	T	0.31194	-0.9952	9	0.44086	T	0.13	.	1.4134	0.02296	0.128:0.1717:0.2953:0.405	rs1456235;rs17680095;rs57418386;rs1456235	2862	Q9NRC6	SPTN5_HUMAN	R	2862	ENSP00000317790:Q2862R	ENSP00000317790:Q2862R	Q	-	2	0	SPTBN5	39936764	0.003000	0.15002	0.002000	0.10522	0.042000	0.13812	0.010000	0.13242	-0.198000	0.10333	0.383000	0.25322	CAA	T|0.464;C|0.536	0.536	strong		0.662	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
DENND1A	57706	hgsc.bcm.edu	37	9	126520068	126520068	+	Silent	SNP	T	T	C	rs9785285	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:126520068T>C	ENST00000373624.2	-	5	417	c.216A>G	c.(214-216)acA>acG	p.T72T	DENND1A_ENST00000373620.3_Silent_p.T72T|DENND1A_ENST00000394215.2_Silent_p.T42T|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394219.3_Silent_p.T40T|DENND1A_ENST00000373618.1_Silent_p.T40T	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	72	UDENN.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						TGAGCACGAATGTGAAGTTCT	0.453													C|||	1658	0.33107	0.736	0.2161	5008	,	,		20499	0.1121		0.1948	False		,,,				2504	0.2311				p.T72T		Atlas-SNP	.											.	DENND1A	112	.	0			c.A216G						PASS	.	C	,	2886,1520	482.6+/-359.5	962,962,279	85.0	73.0	77.0		216,216	-10.0	0.2	9	dbSNP_119	77	1826,6774	732.0+/-406.8	193,1440,2667	no	coding-synonymous,coding-synonymous	DENND1A	NM_020946.1,NM_024820.2	,	1155,2402,2946	CC,CT,TT		21.2326,34.4984,36.2294	,	72/1010,72/560	126520068	4712,8294	2203	4300	6503	SO:0001819	synonymous_variant	57706	exon5			CACGAATGTGAAG	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.216A>G	9.37:g.126520068T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	107	45	0.420561	NM_024820	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Silent	SNP	ENST00000373624.2	37	CCDS35133.1																																																																																			T|0.658;C|0.342	0.342	strong		0.453	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
CYP4A22	284541	hgsc.bcm.edu	37	1	47611598	47611598	+	Missense_Mutation	SNP	T	T	C	rs2405599	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:47611598T>C	ENST00000371891.3	+	10	1314	c.1283T>C	c.(1282-1284)cTa>cCa	p.L428P	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000294337.3_Missense_Mutation_p.L428P|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000371890.3_Missense_Mutation_p.L330P	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	428			L -> P (in allele CYP4A22*6, allele CYP4A22*9, allele CYP4A22*10, allele CYP4A22*12, allele CYP4A22*13 and allele CYP4A22*15; dbSNP:rs2405599). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGGCCCAACCTAGAGGTATGT	0.512													C|||	1882	0.375799	0.2239	0.2896	5008	,	,		21691	0.6141		0.2237	False		,,,				2504	0.5532				p.L428P	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.T1283C						PASS	.	C	PRO/LEU	1117,3289		132,853,1218	290.0	284.0	286.0		1283	0.6	0.7	1	dbSNP_100	286	1931,6669		221,1489,2590	no	missense	CYP4A22	NM_001010969.2	98	353,2342,3808	CC,CT,TT		22.4535,25.3518,23.4353	benign	428/520	47611598	3048,9958	2203	4300	6503	SO:0001583	missense	284541	exon10			CCAACCTAGAGGT		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.1283T>C	1.37:g.47611598T>C	ENSP00000360958:p.Leu428Pro	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	231	109	0.471861	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	683	0.31272893772893773	97	0.19715447154471544	91	0.2513812154696133	335	0.5856643356643356	160	0.21108179419525067	N	0.023	-1.394920	0.01175	0.253518	0.224535	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.27890	1.64;1.64;1.64	1.59	0.642	0.17765	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00001	-3.695	0.30109	P	0.806743	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.0	T	0.44221	-0.9342	9	0.02654	T	1	.	5.7987	0.18401	0.0:0.6711:0.0:0.3289	rs2405599;rs59295354	330;428	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	P	330;428;428	ENSP00000360957:L330P;ENSP00000360958:L428P;ENSP00000294337:L428P	ENSP00000294337:L428P	L	+	2	0	CYP4A22	47384185	1.000000	0.71417	0.722000	0.30670	0.190000	0.23558	3.694000	0.54742	-0.120000	0.11809	-1.033000	0.02402	CTA	T|0.740;C|0.260	0.260	strong		0.512	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
KIAA0141	9812	hgsc.bcm.edu	37	5	141309265	141309265	+	Silent	SNP	C	C	T	rs10078802	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:141309265C>T	ENST00000432126.2	+	5	665	c.531C>T	c.(529-531)aaC>aaT	p.N177N	KIAA0141_ENST00000194118.4_Silent_p.N177N	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	177					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCACACAACTCTTTGAGAG	0.627													C|||	304	0.0607029	0.0333	0.0447	5008	,	,		17769	0.0099		0.0855	False		,,,				2504	0.136				p.N177N		Atlas-SNP	.											.	KIAA0141	44	.	0			c.C531T						PASS	.	C	,	194,4212	121.3+/-158.8	3,188,2012	61.0	57.0	59.0		531,531	2.3	0.4	5	dbSNP_119	59	718,7882	176.3+/-226.2	25,668,3607	no	coding-synonymous,coding-synonymous	KIAA0141	NM_001142603.1,NM_014773.3	,	28,856,5619	TT,TC,CC		8.3488,4.4031,7.0121	,	177/516,177/516	141309265	912,12094	2203	4300	6503	SO:0001819	synonymous_variant	9812	exon5			ACACAACTCTTTG	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.531C>T	5.37:g.141309265C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	163	83	0.509202	NM_001142603	Q969R4|Q96EU9	Silent	SNP	ENST00000432126.2	37	CCDS4268.1																																																																																			C|0.934;T|0.066	0.066	strong		0.627	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
THRAP3	9967	hgsc.bcm.edu	37	1	36752152	36752152	+	Silent	SNP	C	C	T	rs2242428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:36752152C>T	ENST00000354618.5	+	4	545	c.321C>T	c.(319-321)taC>taT	p.Y107Y	THRAP3_ENST00000469141.2_Silent_p.Y107Y	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	107	Arg-rich.|Required for mRNA splicing activation.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.Y107Y(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ATGGAAACTACCGCTCAAATT	0.522			T	USP6	aneurysmal bone cysts								C|||	1240	0.247604	0.1036	0.2219	5008	,	,		17948	0.0754		0.4205	False		,,,				2504	0.4601				p.Y107Y	Pancreas(129;785 1795 20938 23278 32581)	Atlas-SNP	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	THRAP3,NS,carcinoma,+1,2	THRAP3	93	2	1	Substitution - coding silent(1)	stomach(1)	c.C321T						PASS	.	C		615,3791	268.3+/-268.4	54,507,1642	116.0	117.0	116.0		321	3.9	1.0	1	dbSNP_98	116	3300,5300	493.9+/-373.7	624,2052,1624	no	coding-synonymous	THRAP3	NM_005119.3		678,2559,3266	TT,TC,CC		38.3721,13.9582,30.1015		107/956	36752152	3915,9091	2203	4300	6503	SO:0001819	synonymous_variant	9967	exon4			AAACTACCGCTCA	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.321C>T	1.37:g.36752152C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_005119	D3DPS5|Q5VTK6	Silent	SNP	ENST00000354618.5	37	CCDS405.1																																																																																			C|0.710;T|0.290	0.290	strong		0.522	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119	
FMN2	56776	hgsc.bcm.edu	37	1	240371085	240371085	+	Silent	SNP	A	A	T	rs71646826	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:240371085A>T	ENST00000319653.9	+	5	3203	c.2973A>T	c.(2971-2973)ccA>ccT	p.P991P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	991	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTCCTCCCCCACTTCCCGGAG	0.706													T|||	1028	0.205272	0.2678	0.1427	5008	,	,		5948	0.2054		0.1769	False		,,,				2504	0.1943				p.P991P		Atlas-SNP	.											FMN2,NS,carcinoma,+1,1	FMN2	451	1	0			c.A2973T						PASS	.						10.0	12.0	12.0					1																	240371085		2166	4239	6405	SO:0001819	synonymous_variant	56776	exon5			TCCCCCACTTCCC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2973A>T	1.37:g.240371085A>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	78	12	0.153846	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			A|0.836;T|0.164	0.164	strong		0.706	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
OR51B6	390058	hgsc.bcm.edu	37	11	5372881	5372881	+	Silent	SNP	G	G	A	rs77135024	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5372881G>A	ENST00000380219.1	+	1	144	c.144G>A	c.(142-144)agG>agA	p.R48R	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	48					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTCTCATCAGGAATGATCATA	0.473													G|||	529	0.105631	0.0303	0.1614	5008	,	,		22613	0.0754		0.1541	False		,,,				2504	0.1493				p.R48R		Atlas-SNP	.											OR51B6,NS,carcinoma,+1,1	OR51B6	53	1	0			c.G144A						PASS	.	G		241,4161	141.1+/-176.5	4,233,1964	167.0	135.0	146.0		144	1.6	0.9	11	dbSNP_131	146	1309,7285	259.1+/-282.5	119,1071,3107	no	coding-synonymous	OR51B6	NM_001004750.1		123,1304,5071	AA,AG,GG		15.2316,5.4748,11.9267		48/313	5372881	1550,11446	2201	4297	6498	SO:0001819	synonymous_variant	390058	exon1			CATCAGGAATGAT		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.144G>A	11.37:g.5372881G>A		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	262	128	0.48855	NM_001004750		Silent	SNP	ENST00000380219.1	37	CCDS31379.1																																																																																			G|0.877;A|0.123	0.123	strong		0.473	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
CDCA2	157313	hgsc.bcm.edu	37	8	25364834	25364834	+	Missense_Mutation	SNP	A	A	T	rs3829009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:25364834A>T	ENST00000330560.3	+	15	3129	c.2652A>T	c.(2650-2652)agA>agT	p.R884S	CDCA2_ENST00000380665.3_Missense_Mutation_p.R869S|CDCA2_ENST00000521098.2_3'UTR	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	884			R -> S (in dbSNP:rs3829009). {ECO:0000269|PubMed:15489334}.		mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		TTCAGAGGAGAAATAGTGAAA	0.418													A|||	964	0.192492	0.1687	0.1931	5008	,	,		19130	0.2351		0.2147	False		,,,				2504	0.1575				p.R884S		Atlas-SNP	.											.	CDCA2	78	.	0			c.A2652T						PASS	.	A	SER/ARG	767,3639	303.8+/-288.1	73,621,1509	79.0	84.0	82.0		2652	0.5	0.0	8	dbSNP_107	82	1726,6874	310.0+/-309.6	176,1374,2750	yes	missense	CDCA2	NM_152562.2	110	249,1995,4259	TT,TA,AA		20.0698,17.4081,19.1681	benign	884/1024	25364834	2493,10513	2203	4300	6503	SO:0001583	missense	157313	exon15			GAGGAGAAATAGT	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 81"""					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.2652A>T	8.37:g.25364834A>T	ENSP00000328228:p.Arg884Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_152562	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Missense_Mutation	SNP	ENST00000330560.3	37	CCDS6049.1	457	0.20924908424908426	91	0.18495934959349594	68	0.1878453038674033	135	0.23601398601398602	163	0.21503957783641162	A	1.627	-0.520011	0.04171	0.174081	0.200698	ENSG00000184661	ENST00000330560;ENST00000380665;ENST00000434814	T;T	0.29397	1.57;1.57	5.95	0.538	0.17150	.	1.560230	0.03235	N	0.179576	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.15930	0.015;0.015	B;B	0.15870	0.014;0.014	T	0.21381	-1.0247	9	0.05721	T	0.95	0.2446	8.4248	0.32723	0.5555:0.3775:0.0669:0.0	rs3829009;rs3829009	869;884	E9PEI0;Q69YH5	.;CDCA2_HUMAN	S	884;869;283	ENSP00000328228:R884S;ENSP00000370040:R869S	ENSP00000328228:R884S	R	+	3	2	CDCA2	25420751	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	-0.239000	0.08965	-0.118000	0.11851	0.528000	0.53228	AGA	A|0.802;T|0.198	0.198	strong		0.418	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562	
CBFA2T2	9139	hgsc.bcm.edu	37	20	32210968	32210968	+	Silent	SNP	G	G	A	rs368919989		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32210968G>A	ENST00000346541.3	+	6	1122	c.585G>A	c.(583-585)gcG>gcA	p.A195A	CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000397798.2_Silent_p.A166A|CBFA2T2_ENST00000375279.2_Silent_p.A195A|CBFA2T2_ENST00000397800.1_Silent_p.A166A|CBFA2T2_ENST00000344201.3_Silent_p.A166A|CBFA2T2_ENST00000342704.6_Silent_p.A186A|CBFA2T2_ENST00000359606.3_Silent_p.A205A|CBFA2T2_ENST00000492345.1_Silent_p.A166A	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	195	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						GCGCTCGGGCGGCCAAGCAGA	0.582													G|||	1	0.000199681	0.0008	0.0	5008	,	,		5728	0.0		0.0	False		,,,				2504	0.0				p.A195A	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-SNP	.											.	CBFA2T2	93	.	0			c.G585A						PASS	.						83.0	70.0	75.0					20																	32210968		2203	4300	6503	SO:0001819	synonymous_variant	9139	exon6			TCGGGCGGCCAAG	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"""Zinc fingers, MYND-type"""	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.585G>A	20.37:g.32210968G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	139	67	0.482014	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Silent	SNP	ENST00000346541.3	37	CCDS13221.1																																																																																			.	.	weak		0.582	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999	
GUCY2D	3000	hgsc.bcm.edu	37	17	7907189	7907189	+	Silent	SNP	C	C	T	rs3829789	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7907189C>T	ENST00000254854.4	+	3	891	c.741C>T	c.(739-741)caC>caT	p.H247H		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	247					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				TGGTGATGCACTCGGTGCTGC	0.687													C|||	561	0.112021	0.0605	0.1037	5008	,	,		15826	0.2103		0.1034	False		,,,				2504	0.0951				p.H247H		Atlas-SNP	.											.	GUCY2D	82	.	0			c.C741T						PASS	.	C		351,4055	179.4+/-207.9	12,327,1864	47.0	43.0	44.0		741	-1.2	1.0	17	dbSNP_107	44	1059,7541	220.5+/-258.2	73,913,3314	no	coding-synonymous	GUCY2D	NM_000180.3		85,1240,5178	TT,TC,CC		12.314,7.9664,10.8412		247/1104	7907189	1410,11596	2203	4300	6503	SO:0001819	synonymous_variant	3000	exon3			GATGCACTCGGTG	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"""cone rod dystrophy 6"""	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.741C>T	17.37:g.7907189C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_000180	Q6LEA7	Silent	SNP	ENST00000254854.4	37	CCDS11127.1																																																																																			C|0.893;T|0.107	0.107	strong		0.687	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
DNAH1	25981	hgsc.bcm.edu	37	3	52430526	52430526	+	Missense_Mutation	SNP	G	G	A	rs12163565	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52430526G>A	ENST00000420323.2	+	71	11663	c.11402G>A	c.(11401-11403)gGt>gAt	p.G3801D		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3866	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGTAGCCTTGGTGAAGACTTC	0.602													G|||	831	0.165935	0.0219	0.1239	5008	,	,		17097	0.2927		0.1978	False		,,,				2504	0.227				p.G3801D		Atlas-SNP	.											DNAH1_ENST00000420323,rectum,carcinoma,0,2	DNAH1	534	2	0			c.G11402A						scavenged	.	G	ASP/GLY	203,4047		10,183,1932	52.0	57.0	56.0		11402	2.3	0.7	3	dbSNP_120	56	1603,6875		158,1287,2794	yes	missense	DNAH1	NM_015512.4	94	168,1470,4726	AA,AG,GG		18.9078,4.7765,14.1892	benign	3801/4266	52430526	1806,10922	2125	4239	6364	SO:0001583	missense	25981	exon71			GCCTTGGTGAAGA	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.11402G>A	3.37:g.52430526G>A	ENSP00000401514:p.Gly3801Asp	Somatic	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	126	53	0.420635	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	363	0.1662087912087912	15	0.03048780487804878	52	0.143646408839779	144	0.2517482517482518	152	0.20052770448548812	G	0.006	-2.059211	0.00386	0.047765	0.189078	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.07327	3.2	4.35	2.35	0.29111	.	0.375043	0.26684	N	0.023037	T	0.00012	0.0000	N	0.00602	-1.34	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.0;0.003	T	0.47018	-0.9149	9	0.02654	T	1	.	10.1318	0.42682	0.0878:0.1423:0.7698:0.0	rs12163565;rs52793948;rs57160821;rs12163565	3801;3866	C9JXH6;Q9P2D7-2	.;.	D	3801;554	ENSP00000401514:G3801D	ENSP00000273600:G554D	G	+	2	0	DNAH1	52405566	0.985000	0.35326	0.712000	0.30502	0.148000	0.21650	1.873000	0.39558	1.034000	0.39945	0.491000	0.48974	GGT	G|0.840;A|0.160	0.160	strong		0.602	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
SPATA9	83890	hgsc.bcm.edu	37	5	94994339	94994339	+	Silent	SNP	A	A	G	rs10705	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:94994339A>G	ENST00000274432.8	-	5	894	c.753T>C	c.(751-753)aaT>aaC	p.N251N	SPATA9_ENST00000477047.2_Intron|RFESD_ENST00000508206.1_Intron	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	251					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)	7		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)		AGATTTGCTCATTCATTTCAG	0.348													A|||	640	0.127796	0.0234	0.1614	5008	,	,		17497	0.127		0.2326	False		,,,				2504	0.138				p.N251N		Atlas-SNP	.											.	SPATA9	17	.	0			c.T753C						PASS	.	A		220,4186	127.8+/-164.7	6,208,1989	74.0	76.0	75.0		753	2.9	0.9	5	dbSNP_52	75	1801,6795	321.8+/-315.3	195,1411,2692	no	coding-synonymous	SPATA9	NM_031952.3		201,1619,4681	GG,GA,AA		20.9516,4.9932,15.5438		251/255	94994339	2021,10981	2203	4298	6501	SO:0001819	synonymous_variant	83890	exon5			TTGCTCATTCATT	AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.753T>C	5.37:g.94994339A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	154	77	0.5	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Silent	SNP	ENST00000274432.8	37	CCDS4076.1																																																																																			A|0.846;G|0.154	0.154	strong		0.348	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952	
LRRN2	10446	hgsc.bcm.edu	37	1	204588140	204588140	+	Silent	SNP	G	G	A	rs3747630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:204588140G>A	ENST00000367175.1	-	1	3193	c.981C>T	c.(979-981)caC>caT	p.H327H	LRRN2_ENST00000367176.3_Silent_p.H327H|RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367177.3_Silent_p.H327H			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	327					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			AGGCGCGGGGGTGGATGAAGG	0.602													G|||	1055	0.210663	0.0847	0.1153	5008	,	,		18119	0.3234		0.2545	False		,,,				2504	0.2873				p.H327H		Atlas-SNP	.											.	LRRN2	81	.	0			c.C981T						PASS	.	G	,	486,3920	226.5+/-242.0	27,432,1744	85.0	63.0	71.0		981,981	2.8	1.0	1	dbSNP_107	71	2109,6491	359.4+/-331.5	249,1611,2440	no	coding-synonymous,coding-synonymous	LRRN2	NM_006338.2,NM_201630.1	,	276,2043,4184	AA,AG,GG		24.5233,11.0304,19.9523	,	327/714,327/714	204588140	2595,10411	2203	4300	6503	SO:0001819	synonymous_variant	10446	exon3			GCGGGGGTGGATG	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.981C>T	1.37:g.204588140G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Silent	SNP	ENST00000367175.1	37	CCDS1448.1																																																																																			G|0.800;A|0.200	0.200	strong		0.602	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
FN3KRP	79672	hgsc.bcm.edu	37	17	80684784	80684784	+	Missense_Mutation	SNP	G	G	A	rs142718764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:80684784G>A	ENST00000269373.6	+	6	740	c.667G>A	c.(667-669)Gta>Ata	p.V223I	RP11-388C12.5_ENST00000570919.1_lincRNA|FN3KRP_ENST00000535965.1_Missense_Mutation_p.V173I	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	223							kinase activity (GO:0016301)			breast(1)|large_intestine(2)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	7	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			GGGTGGAAACGTAGCAGAGGA	0.542													G|||	23	0.00459265	0.0008	0.0101	5008	,	,		18038	0.0		0.0139	False		,,,				2504	0.001				p.V223I		Atlas-SNP	.											FN3KRP,NS,lymphoid_neoplasm,0,2	FN3KRP	31	2	0			c.G667A						scavenged	.	G	ILE/VAL	13,4393	20.2+/-43.8	0,13,2190	72.0	76.0	75.0		667	5.8	0.9	17	dbSNP_134	75	170,8430	78.6+/-141.3	2,166,4132	yes	missense	FN3KRP	NM_024619.3	29	2,179,6322	AA,AG,GG		1.9767,0.2951,1.407	probably-damaging	223/310	80684784	183,12823	2203	4300	6503	SO:0001583	missense	79672	exon6			GGAAACGTAGCAG	AY360465	CCDS11817.1	17q25.3	2014-08-12			ENSG00000141560	ENSG00000141560			25700	protein-coding gene	gene with protein product		611683				14633848	Standard	NM_024619		Approved	FLJ12171, FN3KL	uc002kfu.3	Q9HA64	OTTHUMG00000177846	ENST00000269373.6:c.667G>A	17.37:g.80684784G>A	ENSP00000269373:p.Val223Ile	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_024619	Q969F4|Q9H0U7	Missense_Mutation	SNP	ENST00000269373.6	37	CCDS11817.1	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	17.43	3.388490	0.61956	0.002951	0.019767	ENSG00000141560	ENST00000269373;ENST00000535965	T;T	0.39787	1.06;1.06	5.82	5.82	0.92795	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.27098	0.0664	L	0.58354	1.805	0.80722	D	1	P	0.50943	0.94	B	0.40375	0.327	T	0.15321	-1.0441	10	0.31617	T	0.26	-26.0305	19.6844	0.95976	0.0:0.0:1.0:0.0	.	223	Q9HA64	KT3K_HUMAN	I	223;173	ENSP00000269373:V223I;ENSP00000444994:V173I	ENSP00000269373:V223I	V	+	1	0	FN3KRP	78278073	1.000000	0.71417	0.931000	0.37212	0.091000	0.18340	7.773000	0.85462	2.761000	0.94854	0.655000	0.94253	GTA	G|0.987;A|0.013	0.013	strong		0.542	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619	
ESRRA	2101	hgsc.bcm.edu	37	11	64083273	64083273	+	Silent	SNP	C	C	T	rs41294422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64083273C>T	ENST00000405666.1	+	7	1341	c.1107C>T	c.(1105-1107)ccC>ccT	p.P369P	ESRRA_ENST00000406310.1_Silent_p.P368P|PRDX5_ENST00000347941.4_5'Flank|PRDX5_ENST00000265462.4_5'Flank|ESRRA_ENST00000000442.6_Silent_p.P369P|PRDX5_ENST00000352435.4_5'Flank	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	369	Ligand binding domain.				cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						GGGCTGGCCCCGGAGGGGGTG	0.672													C|||	18	0.00359425	0.0008	0.0086	5008	,	,		17322	0.0		0.0109	False		,,,				2504	0.0				p.P369P		Atlas-SNP	.											.	ESRRA	56	.	0			c.C1107T						PASS	.	C		12,3752		0,12,1870	25.0	29.0	28.0		1107	-1.3	1.0	11	dbSNP_127	28	98,8094		1,96,3999	no	coding-synonymous	ESRRA	NM_004451.3		1,108,5869	TT,TC,CC		1.1963,0.3188,0.92		369/424	64083273	110,11846	1882	4096	5978	SO:0001819	synonymous_variant	2101	exon7			TGGCCCCGGAGGG	X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"""Nuclear hormone receptors"""	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.1107C>T	11.37:g.64083273C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	23	0.343284	NM_004451	Q14514	Silent	SNP	ENST00000405666.1	37	CCDS41667.1	15	0.006868131868131868	0	0.0	6	0.016574585635359115	0	0.0	9	0.011873350923482849	C	6.975	0.549876	0.13374	0.003188	0.011963	ENSG00000173153	ENST00000545035	D	0.96396	-4.0	4.36	-1.26	0.09376	.	0.174873	0.28047	N	0.016807	T	0.80221	0.4583	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74523	-0.3637	7	0.05959	T	0.93	.	5.6486	0.17604	0.0:0.4931:0.1729:0.3339	rs41294422;rs61736654	.	.	.	L	150	ENSP00000444710:P150L	ENSP00000444710:P150L	P	+	2	0	ESRRA	63839849	0.165000	0.22948	0.993000	0.49108	0.953000	0.61014	-1.152000	0.03172	-0.298000	0.08921	-0.291000	0.09656	CCG	C|0.991;T|0.009	0.009	strong		0.672	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451	
PTPRB	5787	hgsc.bcm.edu	37	12	70989977	70989977	+	Silent	SNP	T	T	C	rs11178317	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:70989977T>C	ENST00000261266.5	-	3	485	c.456A>G	c.(454-456)caA>caG	p.Q152Q	PTPRB_ENST00000451516.2_Silent_p.Q152Q|PTPRB_ENST00000538708.1_Silent_p.Q152Q|PTPRB_ENST00000334414.6_Silent_p.Q370Q|PTPRB_ENST00000550857.1_Silent_p.Q152Q|PTPRB_ENST00000551525.1_Silent_p.Q369Q|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550358.1_Silent_p.Q370Q	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	152	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CCTGTATCTTTTGGTTATTTT	0.383													T|||	853	0.170327	0.1566	0.2464	5008	,	,		16133	0.2103		0.1272	False		,,,				2504	0.138				p.Q370Q		Atlas-SNP	.											.	PTPRB	676	.	0			c.A1110G						PASS	.	T	,,,	564,3102		47,470,1316	100.0	97.0	98.0		1110,456,456,456	0.6	0.5	12	dbSNP_120	98	894,7278		53,788,3245	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	,,,	100,1258,4561	CC,CT,TT		10.9398,15.3846,12.3163	,,,	370/2216,152/1908,152/1908,152/1998	70989977	1458,10380	1833	4086	5919	SO:0001819	synonymous_variant	5787	exon5			TATCTTTTGGTTA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.456A>G	12.37:g.70989977T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	166	82	0.493976	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	37	CCDS44944.1																																																																																			C|0.170;N|0.000	0.170	strong		0.383	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
WDR87	83889	hgsc.bcm.edu	37	19	38378107	38378107	+	Silent	SNP	G	G	A	rs60704260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:38378107G>A	ENST00000303868.5	-	6	6311	c.6087C>T	c.(6085-6087)agC>agT	p.S2029S	WDR87_ENST00000447313.2_Silent_p.S2068S	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2029	Glu-rich.							p.S2029S(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						TGGCAATTTCGCTTTCCTCCA	0.383													G|||	2005	0.400359	0.5333	0.2911	5008	,	,		20353	0.5764		0.172	False		,,,				2504	0.3517				p.S2029S		Atlas-SNP	.											WDR87,NS,carcinoma,0,1	WDR87	191	1	1	Substitution - coding silent(1)	kidney(1)	c.C6087T						PASS	.	G		633,751		144,345,203	98.0	77.0	83.0		6087	-3.5	0.0	19	dbSNP_129	83	572,2610		49,474,1068	no	coding-synonymous	WDR87	NM_031951.3		193,819,1271	AA,AG,GG		17.9761,45.737,26.3907		2029/2874	38378107	1205,3361	692	1591	2283	SO:0001819	synonymous_variant	83889	exon6			AATTTCGCTTTCC	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.6087C>T	19.37:g.38378107G>A		Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	336	165	0.491071	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			G|0.650;A|0.350	0.350	strong		0.383	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
PINK1	65018	hgsc.bcm.edu	37	1	20960385	20960385	+	Missense_Mutation	SNP	A	A	T	rs45540544|rs45630563|rs148871409	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:20960385A>T	ENST00000321556.4	+	1	438	c.344A>T	c.(343-345)cAg>cTg	p.Q115L		NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	115			Q -> L (in dbSNP:rs148871409). {ECO:0000269|PubMed:15970950, ECO:0000269|PubMed:16009891}.		activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GAGGAAAAACAGGCGGAGAGC	0.721													A|||	74	0.0147764	0.0023	0.0317	5008	,	,		7371	0.0		0.0437	False		,,,				2504	0.0051				p.Q115L	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.A344T						PASS	.	A	LEU/GLN	25,3773		0,25,1874	4.0	5.0	4.0		344	3.9	1.0	1	dbSNP_134	4	360,7636		7,346,3645	yes	missense	PINK1	NM_032409.2	113	7,371,5519	TT,TA,AA		4.5023,0.6582,3.2644	benign	115/582	20960385	385,11409	1899	3998	5897	SO:0001583	missense	65018	exon1			AAAAACAGGCGGA	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"""Parkinson disease"""	14581	protein-coding gene	gene with protein product		608309	"""Parkinson disease (autosomal recessive) 6"""	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.344A>T	1.37:g.20960385A>T	ENSP00000364204:p.Gln115Leu	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	22	7	0.318182	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Missense_Mutation	SNP	ENST00000321556.4	37	CCDS211.1	52	0.023809523809523808	3	0.006097560975609756	15	0.04143646408839779	0	0.0	34	0.044854881266490766	A	13.63	2.294151	0.40594	0.006582	0.045023	ENSG00000158828	ENST00000321556	T	0.73681	-0.77	3.87	3.87	0.44632	.	0.471867	0.20890	N	0.083848	T	0.22742	0.0549	L	0.39633	1.23	0.36789	D	0.884737	B	0.24963	0.115	B	0.20767	0.031	T	0.53878	-0.8376	10	0.37606	T	0.19	-8.0371	9.0005	0.36079	1.0:0.0:0.0:0.0	.	115	Q9BXM7	PINK1_HUMAN	L	115	ENSP00000364204:Q115L	ENSP00000364204:Q115L	Q	+	2	0	PINK1	20832972	1.000000	0.71417	0.990000	0.47175	0.798000	0.45092	1.370000	0.34238	1.614000	0.50241	0.379000	0.24179	CAG	A|0.976;T|0.024	0.024	strong		0.721	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74205878	74205878	+	Silent	SNP	C	C	T	rs17782128	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:74205878C>T	ENST00000286523.5	-	2	1616	c.834G>A	c.(832-834)ccG>ccA	p.P278P	ELMSAN1_ENST00000394071.2_Silent_p.P278P|ELMSAN1_ENST00000486739.1_5'Flank	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	278	Gln-rich.|Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										AGGGTTGCTGCGGCATGGAAT	0.627													c|||	760	0.151757	0.0469	0.1182	5008	,	,		15558	0.1409		0.1839	False		,,,				2504	0.2955				p.P278P		Atlas-SNP	.											C14orf43,bladder,carcinoma,-1,1	.	.	1	0			c.G834A						PASS	.	A	,	275,4131	149.5+/-183.7	12,251,1940	29.0	31.0	30.0		834,834	-1.0	0.9	14	dbSNP_123	30	1666,6934	297.9+/-303.7	162,1342,2796	no	coding-synonymous,coding-synonymous	C14orf43	NM_001043318.1,NM_194278.3	,	174,1593,4736	TT,TC,CC		19.3721,6.2415,14.9239	,	278/1046,278/1046	74205878	1941,11065	2203	4300	6503	SO:0001819	synonymous_variant	91748	exon2			TTGCTGCGGCATG	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.834G>A	14.37:g.74205878C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Silent	SNP	ENST00000286523.5	37	CCDS9819.1																																																																																			C|0.861;T|0.139	0.139	strong		0.627	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278	
RBL2	5934	hgsc.bcm.edu	37	16	53481010	53481010	+	Missense_Mutation	SNP	A	A	G	rs17800727	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:53481010A>G	ENST00000262133.6	+	4	766	c.629A>G	c.(628-630)tAt>tGt	p.Y210C	RP11-44F14.5_ENST00000565073.1_RNA|RBL2_ENST00000544545.1_5'Flank|RBL2_ENST00000379935.4_3'UTR	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	210			Y -> C (in dbSNP:rs17800727).		chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CTTTTTATATATGCAAAAGGT	0.299													A|||	541	0.108027	0.0189	0.2075	5008	,	,		15260	0.001		0.2883	False		,,,				2504	0.0828				p.Y210C		Atlas-SNP	.											.	RBL2	115	.	0			c.A629G						PASS	.	A	CYS/TYR	233,4161	128.2+/-165.1	6,221,1970	50.0	51.0	50.0		629	5.4	1.0	16	dbSNP_123	50	2647,5953	419.1+/-353.0	407,1833,2060	yes	missense	RBL2	NM_005611.3	194	413,2054,4030	GG,GA,AA		30.7791,5.3027,22.1641	benign	210/1140	53481010	2880,10114	2197	4300	6497	SO:0001583	missense	5934	exon4			TTATATATGCAAA	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.629A>G	16.37:g.53481010A>G	ENSP00000262133:p.Tyr210Cys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	87	85	0.977012	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	37	CCDS10748.1	308	0.14102564102564102	14	0.028455284552845527	81	0.22375690607734808	1	0.0017482517482517483	212	0.2796833773087071	A	17.05	3.289226	0.59976	0.053027	0.307791	ENSG00000103479	ENST00000262133;ENST00000544405	T;T	0.73047	-0.71;-0.71	5.38	5.38	0.77491	Domain of unknown function DUF3452, retinoblastoma-associated (1);	0.055127	0.64402	D	0.000001	T	0.00012	0.0000	N	0.11698	0.16	0.09310	P	1.0	B;D	0.69078	0.368;0.997	B;P	0.60173	0.271;0.87	T	0.11665	-1.0578	9	0.37606	T	0.19	-15.9424	15.3883	0.74723	1.0:0.0:0.0:0.0	rs17800727;rs52799983;rs17800727	210;210	Q8NE70;Q08999	.;RBL2_HUMAN	C	210;136	ENSP00000262133:Y210C;ENSP00000443744:Y136C	ENSP00000262133:Y210C	Y	+	2	0	RBL2	52038511	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.903000	0.69877	2.047000	0.60756	0.482000	0.46254	TAT	A|0.828;G|0.172	0.172	strong		0.299	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
KIAA1671	85379	hgsc.bcm.edu	37	22	25573431	25573431	+	Silent	SNP	G	G	A	rs12168578	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25573431G>A	ENST00000406486.4	+	10	5403	c.5016G>A	c.(5014-5016)gaG>gaA	p.E1672E	KIAA1671_ENST00000358431.3_Silent_p.E1672E|KIAA1671_ENST00000401395.1_Silent_p.E179E			Q9BY89	K1671_HUMAN	KIAA1671	1672										autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						GTGAGTCCGAGAGCAGATCAC	0.567													G|||	618	0.123403	0.149	0.0591	5008	,	,		15938	0.0913		0.0805	False		,,,				2504	0.2117				p.E1672E		Atlas-SNP	.											.	KIAA1671	28	.	0			c.G5016A						PASS	.	G		227,1157		15,197,480	82.0	78.0	79.0		5016	0.9	1.0	22	dbSNP_120	79	334,2848		16,302,1273	no	coding-synonymous	KIAA1671	NM_001145206.1		31,499,1753	AA,AG,GG		10.4965,16.4017,12.2865		1672/1807	25573431	561,4005	692	1591	2283	SO:0001819	synonymous_variant	85379	exon7			GTCCGAGAGCAGA		CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077			29345	protein-coding gene	gene with protein product						15289310	Standard	NM_001145206		Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.5016G>A	22.37:g.25573431G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	251	118	0.47012	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			G|0.899;A|0.101	0.101	strong		0.567	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	
TTN	7273	hgsc.bcm.edu	37	2	179393111	179393111	+	Missense_Mutation	SNP	A	A	G	rs16866378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179393111A>G	ENST00000591111.1	-	311	102568	c.102344T>C	c.(102343-102345)gTa>gCa	p.V34115A	TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V26691A|TTN_ENST00000342992.6_Missense_Mutation_p.V33188A|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000587576.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V35756A|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V26816A|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V26883A|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000588804.1_RNA			Q8WZ42	TITIN_HUMAN	titin	34115	Ig-like 151.|Ser-rich.		V -> A. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGGGAGTATACATTTCTGGA	0.398													A|||	461	0.0920527	0.1354	0.0403	5008	,	,		19459	0.1736		0.0318	False		,,,				2504	0.0481				p.V35756A		Atlas-SNP	.											.	TTN	18412	.	0			c.T107267C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	443,3287		29,385,1451	113.0	102.0	105.0		80648,80447,99563,80072	1.2	0.0	2	dbSNP_123	105	170,8040		4,162,3939	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	64,64,64,64	33,547,5390	GG,GA,AA		2.0706,11.8767,5.134	benign,benign,benign,benign	26883/27119,26816/27052,33188/33424,26691/26927	179393111	613,11327	1865	4105	5970	SO:0001583	missense	7273	exon361			GAGTATACATTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.102344T>C	2.37:g.179393111A>G	ENSP00000465570:p.Val34115Ala	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	160	70	0.4375	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		205	0.09386446886446886	68	0.13821138211382114	15	0.04143646408839779	100	0.17482517482517482	22	0.029023746701846966	A	7.782	0.709636	0.15239	0.118767	0.020706	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	5.25	1.24	0.21308	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00210	0.0006	L	0.45744	1.44	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.001	B;B;B;B;B	0.09377	0.001;0.001;0.003;0.004;0.002	T	0.12941	-1.0528	8	0.87932	D	0	.	9.8416	0.41002	0.6746:0.0:0.3254:0.0	rs16866378;rs52835227;rs16866378	26691;26816;26883;34115;33188	D3DPF9;E7EQE6;E7ET18;Q8WZ42;A6NKB1	.;.;.;TITIN_HUMAN;.	A	33188;26691;26883;26816;26688	ENSP00000343764:V33188A;ENSP00000434586:V26691A;ENSP00000340554:V26883A;ENSP00000352154:V26816A	ENSP00000340554:V26883A	V	-	2	0	TTN	179101357	0.258000	0.24033	0.021000	0.16686	0.083000	0.17756	4.288000	0.59007	0.410000	0.25675	0.454000	0.30748	GTA	A|0.906;G|0.094	0.094	strong		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DSG4	147409	hgsc.bcm.edu	37	18	28993183	28993183	+	Silent	SNP	A	A	G	rs12960081	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:28993183A>G	ENST00000308128.4	+	16	2883	c.2748A>G	c.(2746-2748)ccA>ccG	p.P916P	DSG4_ENST00000359747.4_Silent_p.P935P|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	916					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ATGCTGATCCATGTGTGCAAC	0.433													.|||	1970	0.393371	0.1755	0.4856	5008	,	,		22345	0.5139		0.4781	False		,,,				2504	0.411				p.P935P		Atlas-SNP	.											.	DSG4	343	.	0			c.A2805G						PASS	.	A	,	1021,3385	376.8+/-322.2	119,783,1301	178.0	164.0	169.0		2805,2748	0.6	0.1	18	dbSNP_121	169	4074,4526	560.4+/-387.6	947,2180,1173	no	coding-synonymous,coding-synonymous	DSG4	NM_001134453.1,NM_177986.3	,	1066,2963,2474	GG,GA,AA		47.3721,23.1729,39.1742	,	935/1060,916/1041	28993183	5095,7911	2203	4300	6503	SO:0001819	synonymous_variant	147409	exon15			TGATCCATGTGTG	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.2748A>G	18.37:g.28993183A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	200	199	0.995	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Silent	SNP	ENST00000308128.4	37	CCDS11897.1																																																																																			A|0.591;G|0.409	0.409	strong		0.433	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
CC2D1A	54862	hgsc.bcm.edu	37	19	14030689	14030689	+	Silent	SNP	T	T	C	rs10410239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14030689T>C	ENST00000318003.7	+	12	1522	c.1281T>C	c.(1279-1281)ggT>ggC	p.G427G	CC2D1A_ENST00000589606.1_Silent_p.G427G	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	427					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			GTCTGGTGGGTGTCCTGGAGA	0.622													C|||	2110	0.421326	0.8154	0.3256	5008	,	,		14061	0.3016		0.2078	False		,,,				2504	0.2996				p.G427G		Atlas-SNP	.											.	CC2D1A	67	.	0			c.T1281C						PASS	.	C		2729,1057		992,745,156	50.0	58.0	55.0		1281	-9.9	0.4	19	dbSNP_119	55	1706,6544		180,1346,2599	no	coding-synonymous	CC2D1A	NM_017721.4		1172,2091,2755	CC,CT,TT		20.6788,27.9186,36.8478		427/952	14030689	4435,7601	1893	4125	6018	SO:0001819	synonymous_variant	54862	exon12			GGTGGGTGTCCTG	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.1281T>C	19.37:g.14030689T>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	287	146	0.508711	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Silent	SNP	ENST00000318003.7	37	CCDS42512.1																																																																																			T|0.665;C|0.335	0.335	strong		0.622	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
COMMD2	51122	hgsc.bcm.edu	37	3	149468530	149468530	+	Missense_Mutation	SNP	T	T	G	rs9843784	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:149468530T>G	ENST00000473414.1	-	4	391	c.337A>C	c.(337-339)Att>Ctt	p.I113L		NM_016094.3	NP_057178.2	Q86X83	COMD2_HUMAN	COMM domain containing 2	113			I -> L (in dbSNP:rs9843784). {ECO:0000269|PubMed:11042152, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15799966}.							NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TCACTCAGAATCGTTCTGATC	0.358													T|||	1197	0.239018	0.0446	0.268	5008	,	,		16341	0.25		0.4085	False		,,,				2504	0.2955				p.I113L		Atlas-SNP	.											.	COMMD2	21	.	0			c.A337C						PASS	.	T	LEU/ILE	491,3915	229.4+/-244.0	30,431,1742	153.0	148.0	149.0		337	2.7	0.8	3	dbSNP_119	149	3641,4959	523.4+/-380.3	786,2069,1445	yes	missense	COMMD2	NM_016094.3	5	816,2500,3187	GG,GT,TT		42.3372,11.1439,31.77	benign	113/200	149468530	4132,8874	2203	4300	6503	SO:0001583	missense	51122	exon4			TCAGAATCGTTCT	AY542158	CCDS3145.1	3q25.1	2004-02-20			ENSG00000114744	ENSG00000114744			24993	protein-coding gene	gene with protein product						15799966	Standard	NM_016094		Approved	HSPC042	uc003exj.2	Q86X83	OTTHUMG00000159616	ENST00000473414.1:c.337A>C	3.37:g.149468530T>G	ENSP00000419475:p.Ile113Leu	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	246	119	0.48374	NM_016094	Q561V4|Q9H3L5|Q9Y5V1	Missense_Mutation	SNP	ENST00000473414.1	37	CCDS3145.1	563	0.25778388278388276	21	0.042682926829268296	95	0.26243093922651933	130	0.22727272727272727	317	0.4182058047493404	T	14.86	2.662649	0.47572	0.111439	0.423372	ENSG00000114744	ENST00000473414	T	0.08634	3.07	5.36	2.7	0.31948	.	0.147086	0.64402	D	0.000009	T	0.00012	0.0000	L	0.46885	1.475	0.25896	P	0.9834196	B	0.16166	0.016	B	0.14578	0.011	T	0.47315	-0.9127	9	0.27785	T	0.31	-14.4315	11.8066	0.52158	0.0:0.0:0.2777:0.7223	rs9843784;rs17854390;rs52814071;rs59944079;rs9843784	113	Q86X83	COMD2_HUMAN	L	113	ENSP00000419475:I113L	ENSP00000419475:I113L	I	-	1	0	COMMD2	150951220	0.997000	0.39634	0.816000	0.32577	0.834000	0.47266	2.382000	0.44345	0.927000	0.37143	0.528000	0.53228	ATT	T|0.704;G|0.296	0.296	strong		0.358	COMMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356515.1	NM_016094	
TTN	7273	hgsc.bcm.edu	37	2	179404628	179404628	+	Missense_Mutation	SNP	T	T	A	rs72648270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179404628T>A	ENST00000591111.1	-	302	93465	c.93241A>T	c.(93241-93243)Atc>Ttc	p.I31081F	TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I23657F|TTN_ENST00000342992.6_Missense_Mutation_p.I30154F|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I32722F|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I23782F|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000450692.2_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I23849F|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588804.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31081	Ig-like 139.		I -> F. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTAAGTCTGATGACGCCACCT	0.388													T|||	213	0.0425319	0.0015	0.0288	5008	,	,		24155	0.1488		0.0298	False		,,,				2504	0.0112				p.I32722F		Atlas-SNP	.											.	TTN	18412	.	0			c.A98164T						PASS	.	T	PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE	15,3893		0,15,1939	134.0	124.0	127.0		70969,90460,71344,71545	6.2	1.0	2	dbSNP_130	127	141,8173		2,137,4018	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	21,21,21,21	2,152,5957	AA,AT,TT		1.6959,0.3838,1.2764	probably-damaging,probably-damaging,probably-damaging,probably-damaging	23657/26927,30154/33424,23782/27052,23849/27119	179404628	156,12066	1954	4157	6111	SO:0001583	missense	7273	exon352			GTCTGATGACGCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.93241A>T	2.37:g.179404628T>A	ENSP00000465570:p.Ile31081Phe	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	196	94	0.479592	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		115	0.052655677655677656	1	0.0020325203252032522	9	0.024861878453038673	84	0.14685314685314685	21	0.027704485488126648	T	16.63	3.177590	0.57692	0.003838	0.016959	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	6.17	6.17	0.99709	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00524	0.0017	L	0.54323	1.7	0.19575	P	0.9999694415	D;D;D;D	0.71674	0.997;0.997;0.997;0.998	D;D;D;D	0.69824	0.939;0.939;0.939;0.966	T	0.00213	-1.1913	8	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	23657;23782;23849;31081	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	F	30154;23657;23849;23782;23654	ENSP00000343764:I30154F;ENSP00000434586:I23657F;ENSP00000340554:I23849F;ENSP00000352154:I23782F	ENSP00000340554:I23849F	I	-	1	0	TTN	179112874	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.736000	0.47385	2.371000	0.80710	0.533000	0.62120	ATC	T|0.955;A|0.045	0.045	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
HRH1	3269	hgsc.bcm.edu	37	3	11301791	11301791	+	Silent	SNP	A	A	G	rs2067468	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:11301791A>G	ENST00000397056.1	+	3	1259	c.1068A>G	c.(1066-1068)caA>caG	p.Q356Q	HRH1_ENST00000431010.2_Silent_p.Q356Q|HRH1_ENST00000438284.2_Silent_p.Q356Q	NM_000861.3|NM_001098211.1	NP_000852.1|NP_001091681.1	P35367	HRH1_HUMAN	histamine receptor H1	356					cellular response to histamine (GO:0071420)|eosinophil chemotaxis (GO:0048245)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|inositol phosphate-mediated signaling (GO:0048016)|memory (GO:0007613)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|regulation of vascular permeability (GO:0043114)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|histamine receptor activity (GO:0004969)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25					Aceprometazine(DB01615)|Alcaftadine(DB06766)|Alimemazine(DB01246)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Antazoline(DB08799)|Aripiprazole(DB01238)|Asenapine(DB06216)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzatropine(DB00245)|Bepotastine(DB04890)|Betahistine(DB06698)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlorcyclizine(DB08936)|Chloropyramine(DB08800)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clemastine(DB00283)|Clofedanol(DB04837)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Dimetindene(DB08801)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Escitalopram(DB01175)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Iloperidone(DB04946)|Imipramine(DB00458)|Isothipendyl(DB08802)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Loxapine(DB00408)|Maprotiline(DB00934)|Meclizine(DB00737)|Mepyramine(DB06691)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Paliperidone(DB01267)|Phenindamine(DB01619)|Pheniramine(DB01620)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	GTGATAGCCAATCCTTCTCTC	0.522													A|||	113	0.0225639	0.0219	0.0115	5008	,	,		20085	0.0		0.0328	False		,,,				2504	0.044				p.Q356Q		Atlas-SNP	.											.	HRH1	58	.	0			c.A1068G						PASS	.	A	,,,	97,4309	77.3+/-115.6	3,91,2109	142.0	122.0	129.0		1068,1068,1068,1068	-0.2	1.0	3	dbSNP_96	129	339,8261	116.8+/-176.5	7,325,3968	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HRH1	NM_000861.3,NM_001098211.1,NM_001098212.1,NM_001098213.1	,,,	10,416,6077	GG,GA,AA		3.9419,2.2015,3.3523	,,,	356/488,356/488,356/488,356/488	11301791	436,12570	2203	4300	6503	SO:0001819	synonymous_variant	3269	exon3			TAGCCAATCCTTC		CCDS2604.1	3p25	2012-11-12			ENSG00000196639	ENSG00000196639		"""GPCR / Class A : Histamine receptors"""	5182	protein-coding gene	gene with protein product		600167				8003029	Standard	NM_001098211		Approved		uc010hds.3	P35367	OTTHUMG00000129719	ENST00000397056.1:c.1068A>G	3.37:g.11301791A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_000861	A8K047|Q6P9E5	Silent	SNP	ENST00000397056.1	37	CCDS2604.1																																																																																			A|0.971;G|0.029	0.029	strong		0.522	HRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251928.2		
RYR3	6263	hgsc.bcm.edu	37	15	33842400	33842400	+	Silent	SNP	A	A	T	rs41279202	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:33842400A>T	ENST00000389232.4	+	10	925	c.855A>T	c.(853-855)cgA>cgT	p.R285R	RYR3_ENST00000415757.3_Silent_p.R285R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	285	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AGGCTTTCCGACTCCGGCATC	0.483													A|||	68	0.0135783	0.0	0.0187	5008	,	,		17879	0.001		0.0447	False		,,,				2504	0.0092				p.R285R		Atlas-SNP	.											.	RYR3	760	.	0			c.A855T						PASS	.	A		34,4350	34.3+/-65.2	0,34,2158	40.0	42.0	41.0		855	-1.1	1.0	15	dbSNP_127	41	369,8219	120.2+/-179.5	8,353,3933	no	coding-synonymous	RYR3	NM_001036.3		8,387,6091	TT,TA,AA		4.2967,0.7755,3.1067		285/4871	33842400	403,12569	2192	4294	6486	SO:0001819	synonymous_variant	6263	exon10			TTTCCGACTCCGG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.855A>T	15.37:g.33842400A>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			A|0.970;T|0.030	0.030	strong		0.483	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
LYRM2	57226	hgsc.bcm.edu	37	6	90347516	90347516	+	Missense_Mutation	SNP	T	T	A	rs151021837	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:90347516T>A	ENST00000523377.1	-	2	167	c.131A>T	c.(130-132)tAc>tTc	p.Y44F	LYRM2_ENST00000520318.1_Missense_Mutation_p.Y44F|LYRM2_ENST00000517396.1_5'UTR|LYRM2_ENST00000520441.1_Missense_Mutation_p.Y44F	NM_020466.4	NP_065199.1	Q9NU23	LYRM2_HUMAN	LYR motif containing 2	44						mitochondrion (GO:0005739)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(76;2.76e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;3.72e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0131)		ATCTTTCAGGTATTTGCGATC	0.403													T|||	15	0.00299521	0.0008	0.0014	5008	,	,		16864	0.0		0.0129	False		,,,				2504	0.0				p.Y44F		Atlas-SNP	.											.	LYRM2	6	.	0			c.A131T						PASS	.	T	PHE/TYR	8,4398	14.3+/-33.2	0,8,2195	176.0	171.0	173.0		131	4.9	1.0	6	dbSNP_134	173	91,8509	51.5+/-111.7	1,89,4210	no	missense	LYRM2	NM_020466.4	22	1,97,6405	AA,AT,TT		1.0581,0.1816,0.7612	probably-damaging	44/89	90347516	99,12907	2203	4300	6503	SO:0001583	missense	57226	exon2			TTCAGGTATTTGC	BC009782	CCDS5023.1	6q15	2006-09-19			ENSG00000083099	ENSG00000083099		"""LYR motif containing"""	25229	protein-coding gene	gene with protein product						12477932	Standard	NM_020466		Approved	DJ122O8.2	uc003pnm.3	Q9NU23	OTTHUMG00000015203	ENST00000523377.1:c.131A>T	6.37:g.90347516T>A	ENSP00000430025:p.Tyr44Phe	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	318	161	0.506289	NM_020466	B2R4U2|E1P517	Missense_Mutation	SNP	ENST00000523377.1	37	CCDS5023.1	10	0.004578754578754579	0	0.0	0	0.0	0	0.0	10	0.013192612137203167	T	22.3	4.274655	0.80580	0.001816	0.010581	ENSG00000083099	ENST00000520441;ENST00000523377;ENST00000520318	T;T;T	0.72282	-0.64;-0.64;-0.64	6.03	4.86	0.63082	.	0.188192	0.47455	D	0.000240	T	0.49795	0.1578	.	.	.	0.41428	D	0.987849	B	0.14438	0.01	B	0.20767	0.031	T	0.54002	-0.8358	9	0.59425	D	0.04	.	11.4509	0.50151	0.1342:0.0:0.0:0.8658	.	44	Q9NU23	LYRM2_HUMAN	F	44	ENSP00000427859:Y44F;ENSP00000430025:Y44F;ENSP00000428207:Y44F	ENSP00000430316:Y44F	Y	-	2	0	LYRM2	90404237	1.000000	0.71417	0.999000	0.59377	0.787000	0.44495	4.337000	0.59310	1.083000	0.41159	0.455000	0.32223	TAC	T|0.994;A|0.006	0.006	strong		0.403	LYRM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041498.2	NM_020466	
ANKUB1	389161	hgsc.bcm.edu	37	3	149488442	149488442	+	Silent	SNP	A	A	G	rs7630153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:149488442A>G	ENST00000383050.3	-	4	927	c.471T>C	c.(469-471)gaT>gaC	p.D157D	ANKUB1_ENST00000446160.1_Silent_p.D157D|ANKUB1_ENST00000462519.2_Silent_p.D157D			A6NFN9	ANKUB_HUMAN	ankyrin repeat and ubiquitin domain containing 1	157										breast(1)|kidney(1)|lung(1)|skin(1)	4						CATCCCAGACATCCAAGCGAA	0.433													G|||	1645	0.328474	0.6452	0.3573	5008	,	,		18502	0.0248		0.2922	False		,,,				2504	0.2301				p.D157D		Atlas-SNP	.											ANKUB1,NS,carcinoma,-2,1	ANKUB1	27	1	0			c.T471C						PASS	.	G		815,569		246,323,123	164.0	146.0	151.0		471	-3.3	1.0	3	dbSNP_116	151	965,2217		152,661,778	no	coding-synonymous	ANKUB1	NM_001144960.1		398,984,901	GG,GA,AA		30.3268,41.1127,38.9838		157/545	149488442	1780,2786	692	1591	2283	SO:0001819	synonymous_variant	389161	exon4			CCAGACATCCAAG	AK027233		3q25.1	2013-01-11	2011-05-10	2011-05-10	ENSG00000206199	ENSG00000206199		"""Ankyrin repeat domain containing"""	29642	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 16"""	C3orf16			Standard	NM_001144960		Approved		uc003exl.3	A6NFN9	OTTHUMG00000159615	ENST00000383050.3:c.471T>C	3.37:g.149488442A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_001144960	B4E2N8	Silent	SNP	ENST00000383050.3	37																																																																																				A|0.690;G|0.310	0.310	strong		0.433	ANKUB1-201	KNOWN	basic	protein_coding	protein_coding		NM_001144960	
IRS2	8660	hgsc.bcm.edu	37	13	110435231	110435231	+	Missense_Mutation	SNP	C	C	T	rs1805097	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:110435231C>T	ENST00000375856.3	-	1	3684	c.3170G>A	c.(3169-3171)gGc>gAc	p.G1057D		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	1057			G -> D (in dbSNP:rs1805097). {ECO:0000269|PubMed:12687350}.		brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			TGAGGCGGCGCCCGGGCCCTG	0.746													.|||	1419	0.283347	0.0938	0.4107	5008	,	,		7276	0.3929		0.3161	False		,,,				2504	0.3027				p.G1057D	Melanoma(100;613 2409 40847)	Atlas-SNP	.											.	IRS2	44	.	0			c.G3170A	GRCh37	CM003938	IRS2	M	rs1805097	PASS	.	C	ASP/GLY	464,3506		33,398,1554	5.0	5.0	5.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3170	2.1	0.0	13	dbSNP_89	5	2312,5652		359,1594,2029	yes	missense	IRS2	NM_003749.2	94	392,1992,3583	TT,TC,CC		29.0306,11.6877,23.2613	benign	1057/1339	110435231	2776,9158	1985	3982	5967	SO:0001583	missense	8660	exon1			GCGGCGCCCGGGC	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"""Pleckstrin homology (PH) domain containing"""	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.3170G>A	13.37:g.110435231C>T	ENSP00000365016:p.Gly1057Asp	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	37	CCDS9510.1	651	0.2980769230769231	55	0.11178861788617886	134	0.3701657458563536	225	0.39335664335664333	237	0.31266490765171506	C	5.984	0.365448	0.11352	0.116877	0.290306	ENSG00000185950	ENST00000375856	T	0.48522	0.81	4.13	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.23650	0.089	B	0.19946	0.027	T	0.39761	-0.9598	8	0.35671	T	0.21	-3.4542	7.8389	0.29387	0.1819:0.6484:0.1697:0.0	rs1805097;rs17847224	1057	Q9Y4H2	IRS2_HUMAN	D	1057	ENSP00000365016:G1057D	ENSP00000365016:G1057D	G	-	2	0	IRS2	109233232	0.002000	0.14202	0.002000	0.10522	0.006000	0.05464	1.021000	0.30040	0.922000	0.37019	0.644000	0.83932	GGC	C|0.663;T|0.337	0.337	strong		0.746	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749	
PHYH	5264	hgsc.bcm.edu	37	10	13330402	13330402	+	Silent	SNP	T	T	C	rs473407	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:13330402T>C	ENST00000263038.4	-	6	694	c.636A>G	c.(634-636)acA>acG	p.T212T	PHYH_ENST00000396913.2_Silent_p.T112T|PHYH_ENST00000396920.3_Silent_p.T195T	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	212					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|isoprenoid metabolic process (GO:0006720)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|electron carrier activity (GO:0009055)|L-ascorbic acid binding (GO:0031418)|metal ion binding (GO:0046872)|phytanoyl-CoA dioxygenase activity (GO:0048244)			NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	AGCCCTTGTGTGTGCCTGGGA	0.587													T|||	1197	0.239018	0.4312	0.1686	5008	,	,		16570	0.124		0.2286	False		,,,				2504	0.1585				p.T212T		Atlas-SNP	.											.	PHYH	50	.	0			c.A636G						PASS	.	T	,	1709,2697	509.9+/-367.4	339,1031,833	57.0	55.0	56.0		336,636	-5.6	0.3	10	dbSNP_83	56	2192,6408	372.2+/-336.6	278,1636,2386	no	coding-synonymous,coding-synonymous	PHYH	NM_001037537.1,NM_006214.3	,	617,2667,3219	CC,CT,TT		25.4884,38.788,29.9938	,	112/239,212/339	13330402	3901,9105	2203	4300	6503	SO:0001819	synonymous_variant	5264	exon6			CTTGTGTGTGCCT		CCDS7097.1, CCDS41489.1	10p13	2010-04-27	2006-01-09		ENSG00000107537	ENSG00000107537	1.14.11.18		8940	protein-coding gene	gene with protein product	"""Refsum disease"", ""phytanoyl-CoA dioxygenase"""	602026	"""phytanoyl-CoA hydroxylase (Refsum disease)"", ""phytanoyl-CoA hydroxylase"""			9326939	Standard	XM_005252469		Approved	PAHX, RD, PHYH1	uc001imf.3	O14832	OTTHUMG00000017693	ENST00000263038.4:c.636A>G	10.37:g.13330402T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_006214	A8MTS8|B1ALH5	Silent	SNP	ENST00000263038.4	37	CCDS7097.1																																																																																			T|0.728;C|0.272	0.272	strong		0.587	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2		
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2883588	2883588	+	Missense_Mutation	SNP	C	C	A	rs17762452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:2883588C>A	ENST00000254695.8	+	9	694	c.604C>A	c.(604-606)Ctg>Atg	p.L202M	RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.L183M|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.L202M|RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.L187M	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	202			L -> M (in dbSNP:rs17762452).		negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CAGGTCCAAACTGAAGACGGT	0.547													C|||	1488	0.297125	0.1104	0.3112	5008	,	,		1167	0.3313		0.2972	False		,,,				2504	0.5041				p.L202M		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.C604A						PASS	.	C	MET/LEU,MET/LEU	530,3480		43,444,1518	87.0	84.0	85.0		559,604	4.0	1.0	17	dbSNP_123	85	2656,5676		444,1768,1954	yes	missense,missense	RAP1GAP2	NM_001100398.1,NM_015085.4	15,15	487,2212,3472	AA,AC,CC		31.8771,13.217,25.8143	benign,benign	187/716,202/731	2883588	3186,9156	2005	4166	6171	SO:0001583	missense	23108	exon9			TCCAAACTGAAGA	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.604C>A	17.37:g.2883588C>A	ENSP00000254695:p.Leu202Met	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	184	95	0.516304	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	37	CCDS45573.1	594	0.27197802197802196	58	0.11788617886178862	105	0.2900552486187845	204	0.35664335664335667	227	0.2994722955145119	C	11.10	1.540719	0.27563	0.13217	0.318771	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.94138	-3.36;-3.36;-3.36;-3.36	4.99	4.02	0.46733	.	0.484343	0.21364	N	0.075741	T	0.00012	0.0000	N	0.08118	0	0.46149	P	0.0011100000000000554	B;B	0.27264	0.173;0.108	B;B	0.34038	0.174;0.084	T	0.03433	-1.1037	9	0.31617	T	0.26	-8.9204	9.9318	0.41528	0.0:0.3971:0.6029:0.0	rs17762452;rs52833255;rs17762452	187;202	Q684P5-2;Q684P5	.;RPGP2_HUMAN	M	202;187;183;202	ENSP00000254695:L202M;ENSP00000389824:L187M;ENSP00000439688:L183M;ENSP00000444890:L202M	ENSP00000254695:L202M	L	+	1	2	RAP1GAP2	2830338	0.999000	0.42202	1.000000	0.80357	0.953000	0.61014	0.540000	0.23191	1.113000	0.41760	0.555000	0.69702	CTG	C|0.737;A|0.263	0.263	strong		0.547	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
SGMS1	259230	hgsc.bcm.edu	37	10	52103707	52103707	+	Silent	SNP	A	A	G	rs10763354	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:52103707A>G	ENST00000361781.2	-	7	1127	c.168T>C	c.(166-168)aaT>aaC	p.N56N	SGMS1_ENST00000492601.2_5'Flank|SGMS1_ENST00000361543.2_Silent_p.N56N|SGMS1_ENST00000429490.1_Intron	NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	62	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184, ECO:0000305}.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GCCGCTGCCCATTGTCAGAGG	0.512													G|||	2514	0.501997	0.5212	0.6311	5008	,	,		18667	0.4861		0.5298	False		,,,				2504	0.3722				p.N56N		Atlas-SNP	.											.	SGMS1	40	.	0			c.T168C						PASS	.	G		2379,2027	565.8+/-381.8	664,1051,488	80.0	77.0	78.0		168	-3.1	0.9	10	dbSNP_120	78	4551,4049	557.9+/-387.1	1214,2123,963	yes	coding-synonymous	SGMS1	NM_147156.3		1878,3174,1451	GG,GA,AA		47.0814,46.0054,46.7169		56/414	52103707	6930,6076	2203	4300	6503	SO:0001819	synonymous_variant	259230	exon7			CTGCCCATTGTCA	AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	2.7.8.27	"""Sterile alpha motif (SAM) domain containing"""	29799	protein-coding gene	gene with protein product		611573	"""transmembrane protein 23"""	TMEM23		11841947, 14976195	Standard	NM_147156		Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.168T>C	10.37:g.52103707A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	114	111	0.973684	NM_147156	Q68U43|Q6EKK0|Q75SP1	Silent	SNP	ENST00000361781.2	37	CCDS7240.1																																																																																			A|0.473;G|0.527	0.527	strong		0.512	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048074.2	NM_147156	
TPSD1	23430	hgsc.bcm.edu	37	16	1306971	1306971	+	Missense_Mutation	SNP	A	A	G	rs72775466		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306971A>G	ENST00000211076.3	+	3	576	c.428A>G	c.(427-429)cAc>cGc	p.H143R	TPSD1_ENST00000397534.2_Missense_Mutation_p.H136R|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	143	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				ATCTCCAGCCACATCCACACG	0.647																																					p.H143R		Atlas-SNP	.											TPSD1,NS,NS,0,1	TPSD1	47	1	0			c.A428G						scavenged	.						49.0	47.0	47.0					16																	1306971		2198	4299	6497	SO:0001583	missense	23430	exon3			CCAGCCACATCCA	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.428A>G	16.37:g.1306971A>G	ENSP00000211076:p.His143Arg	Somatic	287	2	0.00696864		WXS	Illumina HiSeq	Phase_I	467	94	0.201285	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	.	.	.	.	.	.	.	.	.	.	a	0.006	-2.041578	0.00402	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	T;T	0.81330	-1.48;-1.48	2.55	1.26	0.21427	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.828860	0.02995	N	0.147379	T	0.68035	0.2957	N	0.20304	0.555	0.80722	P	0.0	B;B	0.10296	0.003;0.003	B;B	0.14578	0.011;0.011	T	0.55823	-0.8080	9	0.30078	T	0.28	.	5.9116	0.19031	0.767:0.0:0.0:0.233	.	127;143	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	R	136;143	ENSP00000380668:H136R;ENSP00000211076:H143R	ENSP00000211076:H143R	H	+	2	0	TPSD1	1246972	0.000000	0.05858	0.001000	0.08648	0.073000	0.16967	-0.594000	0.05733	1.156000	0.42514	0.155000	0.16302	CAC	.	.	strong		0.647	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
MUC21	394263	hgsc.bcm.edu	37	6	30955202	30955202	+	Missense_Mutation	SNP	C	C	T	rs2429294	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30955202C>T	ENST00000376296.3	+	2	1491	c.1250C>T	c.(1249-1251)gCc>gTc	p.A417V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	417	28 X 15 AA approximate tandem repeats.|Ser-rich.			A -> I (in Ref. 3; AAQ88781 and 4; CAQ08321). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGTGGGGCCAGCACTGCC	0.622													c|||	404	0.0806709	0.0749	0.1427	5008	,	,		19938	0.0556		0.0805	False		,,,				2504	0.0706				p.A417V		Atlas-SNP	.											.	MUC21	98	.	0			c.C1250T						PASS	.																																			SO:0001583	missense	394263	exon2			GTGGGGCCAGCAC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1250C>T	6.37:g.30955202C>T	ENSP00000365473:p.Ala417Val	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	150	37	0.246667	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	217	0.09935897435897435	48	0.0975609756097561	60	0.16574585635359115	55	0.09615384615384616	54	0.0712401055408971	c	9.220	1.033023	0.19590	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.01804	4.63	3.58	1.78	0.24846	.	.	.	.	.	T	0.00328	0.0010	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.37709	-0.9694	9	0.25106	T	0.35	-0.4275	7.735	0.28808	0.0:0.7843:0.0:0.2157	rs2429294	417	Q5SSG8	MUC21_HUMAN	V	267;417	ENSP00000365473:A417V	ENSP00000365473:A417V	A	+	2	0	MUC21	31063181	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.835000	0.04386	0.325000	0.23359	-0.225000	0.12378	GCC	C|0.901;T|0.099	0.099	strong		0.622	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
DNA2	1763	hgsc.bcm.edu	37	10	70191631	70191631	+	Silent	SNP	C	C	T	rs61855090	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70191631C>T	ENST00000358410.3	-	13	2021	c.1971G>A	c.(1969-1971)acG>acA	p.T657T	DNA2_ENST00000399180.2_Silent_p.T743T|DNA2_ENST00000399179.2_Silent_p.T657T	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	657	Helicase activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						GAGTACATATCGTAGTTGTTT	0.383													C|||	106	0.0211661	0.0038	0.0245	5008	,	,		18377	0.0		0.0457	False		,,,				2504	0.0389				p.T657T		Atlas-SNP	.											.	DNA2	76	.	0			c.G1971A						PASS	.	C		29,3667		0,29,1819	176.0	164.0	168.0		1971	-8.8	0.7	10	dbSNP_129	168	428,7766		18,392,3687	no	coding-synonymous	DNA2	NM_001080449.2		18,421,5506	TT,TC,CC		5.2233,0.7846,3.8436		657/1061	70191631	457,11433	1848	4097	5945	SO:0001819	synonymous_variant	1763	exon13			ACATATCGTAGTT	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"""DNA2 DNA replication helicase 2-like (yeast)"", ""DNA replication helicase 2 homolog (yeast)"""	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.1971G>A	10.37:g.70191631C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				C|0.972;T|0.028	0.028	strong		0.383	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
HELZ2	85441	hgsc.bcm.edu	37	20	62193445	62193445	+	Missense_Mutation	SNP	G	G	A	rs3810481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62193445G>A	ENST00000467148.1	-	10	6578	c.6509C>T	c.(6508-6510)aCg>aTg	p.T2170M	HELZ2_ENST00000427522.2_Missense_Mutation_p.T1601M	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2170	Interaction with THRAP3.		T -> M (in dbSNP:rs3810481).		cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CTGAATGACCGTGAAAGGCTT	0.647													G|||	1038	0.207268	0.0068	0.085	5008	,	,		10051	0.5734		0.16	False		,,,				2504	0.2362				p.T2170M		Atlas-SNP	.											.	.	.	.	0			c.C6509T						PASS	.	G	MET/THR,MET/THR	159,4219		2,155,2032	16.0	19.0	18.0		6509,4802	4.1	0.1	20	dbSNP_107	18	1254,7310		82,1090,3110	yes	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	81,81	84,1245,5142	AA,AG,GG		14.6427,3.6318,10.9179	probably-damaging,probably-damaging	2170/2650,1601/2081	62193445	1413,11529	2189	4282	6471	SO:0001583	missense	85441	exon11			ATGACCGTGAAAG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.6509C>T	20.37:g.62193445G>A	ENSP00000417401:p.Thr2170Met	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	504	0.23076923076923078	6	0.012195121951219513	38	0.10497237569060773	336	0.5874125874125874	124	0.16358839050131926	G	14.03	2.414176	0.42817	0.036318	0.146427	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.84589	-1.87;-1.87	4.06	4.06	0.47325	ATPase, AAA+ type, core (1);	0.191368	0.44483	D	0.000456	T	0.00012	0.0000	M	0.87328	2.875	0.21697	P	0.999589272	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.37957	-0.9683	9	0.72032	D	0.01	-10.5405	11.8752	0.52544	0.0894:0.0:0.9106:0.0	rs3810481;rs60423961;rs3810481	2170;1601	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	M	1601;2170	ENSP00000393257:T1601M;ENSP00000417401:T2170M	ENSP00000393257:T1601M	T	-	2	0	RP4-697K14.7	61663889	1.000000	0.71417	0.078000	0.20375	0.007000	0.05969	5.234000	0.65343	1.830000	0.53286	0.313000	0.20887	ACG	G|0.836;A|0.164	0.164	strong		0.647	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
OR8J1	219477	hgsc.bcm.edu	37	11	56127829	56127829	+	Missense_Mutation	SNP	G	G	T	rs7927015	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56127829G>T	ENST00000303039.3	+	1	139	c.107G>T	c.(106-108)gGg>gTg	p.G36V		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	36			G -> V (in dbSNP:rs7927015).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					GTGCTCTATGGGCTGACCATG	0.498													T|||	195	0.0389377	0.0121	0.0447	5008	,	,		16596	0.001		0.0905	False		,,,				2504	0.0573				p.G36V		Atlas-SNP	.											OR8J1,NS,carcinoma,+1,1	OR8J1	87	1	0			c.G107T						PASS	.	T	VAL/GLY	94,4308	817.6+/-416.3	0,94,2107	133.0	126.0	129.0		107	-0.2	0.1	11	dbSNP_116	129	696,7896	787.7+/-407.6	33,630,3633	no	missense	OR8J1	NM_001005205.2	109	33,724,5740	TT,TG,GG		8.1006,2.1354,6.0797	benign	36/317	56127829	790,12204	2201	4296	6497	SO:0001583	missense	219477	exon1			TCTATGGGCTGAC	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.107G>T	11.37:g.56127829G>T	ENSP00000304060:p.Gly36Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	191	96	0.502618	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	37	CCDS31529.1	87	0.03983516483516483	4	0.008130081300813009	14	0.03867403314917127	0	0.0	69	0.09102902374670185	T	0.021	-1.431938	0.01108	0.021354	0.081006	ENSG00000172487	ENST00000303039	T	0.02812	4.15	4.57	-0.24	0.13047	.	0.834406	0.10664	N	0.648359	T	0.00073	0.0002	N	0.01522	-0.82	0.09310	N	1	B	0.06786	0.001	B	0.15052	0.012	T	0.49214	-0.8963	10	0.20519	T	0.43	.	9.4518	0.38731	0.0:0.2047:0.4521:0.3433	rs7927015;rs17610417;rs52805058;rs7927015	36	Q8NGP2	OR8J1_HUMAN	V	36	ENSP00000304060:G36V	ENSP00000304060:G36V	G	+	2	0	OR8J1	55884405	0.000000	0.05858	0.072000	0.20136	0.001000	0.01503	0.064000	0.14437	-0.157000	0.11059	-2.856000	0.00102	GGG	G|0.947;T|0.053	0.053	strong		0.498	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
SON	6651	hgsc.bcm.edu	37	21	34924243	34924243	+	Silent	SNP	T	T	C	rs16990760	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:34924243T>C	ENST00000356577.4	+	3	3181	c.2706T>C	c.(2704-2706)gaT>gaC	p.D902D	SON_ENST00000300278.4_Silent_p.D902D|SON_ENST00000290239.6_Silent_p.D902D|SON_ENST00000381679.4_Silent_p.D902D|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	902					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						GTACCCAAGATTCTGCTATGT	0.478													T|||	903	0.180312	0.0318	0.2435	5008	,	,		23576	0.1657		0.3101	False		,,,				2504	0.2178				p.D902D		Atlas-SNP	.											SON_ENST00000300278,NS,adenoma,0,2	SON	343	2	0			c.T2706C						PASS	.	T	,	333,4073	175.5+/-204.9	14,305,1884	67.0	66.0	67.0		2706,2706	1.9	1.0	21	dbSNP_123	67	2423,6177	400.5+/-346.8	335,1753,2212	no	coding-synonymous,coding-synonymous	SON	NM_032195.1,NM_138927.1	,	349,2058,4096	CC,CT,TT		28.1744,7.5579,21.1902	,	902/2304,902/2427	34924243	2756,10250	2203	4300	6503	SO:0001819	synonymous_variant	6651	exon3			CCAAGATTCTGCT	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.2706T>C	21.37:g.34924243T>C		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	344	172	0.5	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	37	CCDS13629.1																																																																																			T|0.786;C|0.214	0.214	strong		0.478	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
TSHR	7253	hgsc.bcm.edu	37	14	81562998	81562998	+	Silent	SNP	T	T	C	rs2075179	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:81562998T>C	ENST00000541158.2	+	8	883	c.561T>C	c.(559-561)aaT>aaC	p.N187N	TSHR_ENST00000554435.1_Silent_p.N187N|TSHR_ENST00000298171.2_Silent_p.N187N|TSHR_ENST00000554263.1_Silent_p.N187N|TSHR_ENST00000342443.6_Silent_p.N187N			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	187					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)	p.N187N(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	TGTACAACAATGGCTTTACTT	0.443			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism						C|||	1503	0.30012	0.5953	0.1427	5008	,	,		20379	0.3036		0.1292	False		,,,				2504	0.1851				p.N187N		Atlas-SNP	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	TSHR_ENST00000554435,NS,carcinoma,+2,3	TSHR	462	3	1	Substitution - coding silent(1)	stomach(1)	c.T561C						PASS	.	C	,,	2341,2065	569.7+/-382.7	625,1091,487	154.0	126.0	135.0		561,561,561	0.9	1.0	14	dbSNP_96	135	1167,7433	765.0+/-407.6	78,1011,3211	no	coding-synonymous,coding-synonymous,coding-synonymous	TSHR	NM_000369.2,NM_001018036.2,NM_001142626.2	,,	703,2102,3698	CC,CT,TT		13.5698,46.8679,26.9722	,,	187/765,187/254,187/275	81562998	3508,9498	2203	4300	6503	SO:0001819	synonymous_variant	7253	exon7			CAACAATGGCTTT	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"""GPCR / Class A : Gonadotropin and TSH receptors"""	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.561T>C	14.37:g.81562998T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	177	85	0.480226	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Silent	SNP	ENST00000541158.2	37	CCDS9872.1																																																																																			T|0.711;C|0.289	0.289	strong		0.443	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369	
SSMEM1	136263	hgsc.bcm.edu	37	7	129855837	129855837	+	Missense_Mutation	SNP	C	C	T	rs4728190	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:129855837C>T	ENST00000297819.3	+	3	313	c.262C>T	c.(262-264)Cgg>Tgg	p.R88W		NM_145268.3	NP_660311.1	Q8WWF3	SSMM1_HUMAN	serine-rich single-pass membrane protein 1	88			R -> W (in dbSNP:rs4728190).			integral component of membrane (GO:0016021)											TTCCTGTAAGCGGCAAAGCAA	0.408													C|||	936	0.186901	0.357	0.1499	5008	,	,		22584	0.0069		0.2366	False		,,,				2504	0.1176				p.R88W		Atlas-SNP	.											.	.	.	.	0			c.C262T						PASS	.	C	TRP/ARG	1516,2890	482.6+/-359.5	262,992,949	113.0	103.0	106.0		262	-3.0	0.0	7	dbSNP_111	106	2057,6543	357.1+/-330.6	239,1579,2482	yes	missense	C7orf45	NM_145268.3	101	501,2571,3431	TT,TC,CC		23.9186,34.4076,27.4719	benign	88/245	129855837	3573,9433	2203	4300	6503	SO:0001583	missense	0	exon3			TGTAAGCGGCAAA	AK097635	CCDS5816.1	7q32.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000165120	ENSG00000165120			29580	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 45"""	C7orf45		12477932	Standard	NM_145268		Approved	FLJ40316	uc003vpp.3	Q8WWF3	OTTHUMG00000157844	ENST00000297819.3:c.262C>T	7.37:g.129855837C>T	ENSP00000297819:p.Arg88Trp	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	232	118	0.508621	NM_145268		Missense_Mutation	SNP	ENST00000297819.3	37	CCDS5816.1	425	0.1945970695970696	179	0.3638211382113821	61	0.1685082872928177	1	0.0017482517482517483	184	0.24274406332453827	C	4.155	0.027164	0.08054	0.344076	0.239186	ENSG00000165120	ENST00000297819	T	0.49720	0.77	5.84	-2.95	0.05564	.	0.712332	0.13336	N	0.395538	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.38993	-0.9635	9	0.42905	T	0.14	-0.0013	2.0059	0.03477	0.1078:0.357:0.2119:0.3233	rs4728190;rs52821550;rs57504232;rs4728190	88	Q8WWF3	CG045_HUMAN	W	88	ENSP00000297819:R88W	ENSP00000297819:R88W	R	+	1	2	C7orf45	129643073	0.158000	0.22850	0.000000	0.03702	0.001000	0.01503	-0.011000	0.12721	-0.684000	0.05183	-1.287000	0.01368	CGG	C|0.758;T|0.242	0.242	strong		0.408	SSMEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349768.1	NM_145268	
SBNO1	55206	hgsc.bcm.edu	37	12	123780521	123780521	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:123780521C>T	ENST00000602398.1	-	32	4243	c.4116G>A	c.(4114-4116)gcG>gcA	p.A1372A	SBNO1_ENST00000267176.4_Silent_p.A1371A|SBNO1_ENST00000420886.2_Silent_p.A1372A|SBNO1_ENST00000602750.1_Silent_p.A1371A			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1372					regulation of transcription, DNA-templated (GO:0006355)			p.A1371A(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TCTGTTGGACCGCAAGCTGTT	0.428																																					p.A1372A		Atlas-SNP	.											SBNO1,NS,carcinoma,-1,2	SBNO1	138	2	1	Substitution - coding silent(1)	lung(1)	c.G4116A						scavenged	.						350.0	312.0	325.0					12																	123780521		2203	4300	6503	SO:0001819	synonymous_variant	55206	exon31			TTGGACCGCAAGC	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.4116G>A	12.37:g.123780521C>T		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	272	3	0.0110294	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	37	CCDS53844.1																																																																																			.	.	none		0.428	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
BYSL	705	hgsc.bcm.edu	37	6	41900375	41900375	+	Silent	SNP	C	C	G	rs149587548	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41900375C>G	ENST00000230340.4	+	7	1620	c.1245C>G	c.(1243-1245)ccC>ccG	p.P415P		NM_004053.3	NP_004044.3	Q13895	BYST_HUMAN	bystin-like	415					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|female pregnancy (GO:0007565)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|trophectodermal cell differentiation (GO:0001829)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(5)|skin(1)	8	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			AGCTATCGCCCGAAATCAGGC	0.587													c|||	5	0.000998403	0.0008	0.0	5008	,	,		20952	0.0		0.003	False		,,,				2504	0.001				p.P415P		Atlas-SNP	.											.	BYSL	17	.	0			c.C1245G						PASS	.			4,4402	8.1+/-20.4	0,4,2199	76.0	76.0	76.0		1245	-11.3	0.1	6	dbSNP_134	76	22,8578	15.3+/-51.7	0,22,4278	no	coding-synonymous	BYSL	NM_004053.3		0,26,6477	GG,GC,CC		0.2558,0.0908,0.1999		415/438	41900375	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	705	exon7			ATCGCCCGAAATC	L36720	CCDS34450.1	6p21.1	2008-08-29			ENSG00000112578	ENSG00000112578			1157	protein-coding gene	gene with protein product		603871				9925933, 17381424	Standard	NM_004053		Approved		uc003orl.3	Q13895	OTTHUMG00000014687	ENST00000230340.4:c.1245C>G	6.37:g.41900375C>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_004053	Q6P5W4|Q86W44|Q96IP8	Silent	SNP	ENST00000230340.4	37	CCDS34450.1																																																																																			C|0.998;G|0.002	0.002	strong		0.587	BYSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040535.2		
ZNF527	84503	hgsc.bcm.edu	37	19	37879589	37879589	+	Missense_Mutation	SNP	A	A	G	rs4452075	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:37879589A>G	ENST00000436120.2	+	5	745	c.638A>G	c.(637-639)cAt>cGt	p.H213R	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	213					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAAAGACTCCATGCTGAGAAG	0.343													a|||	1731	0.345647	0.5303	0.2666	5008	,	,		19809	0.3006		0.1581	False		,,,				2504	0.3916				p.H213R		Atlas-SNP	.											.	ZNF527	78	.	0			c.A638G						PASS	.	A	ARG/HIS	1714,1914		406,902,506	52.0	52.0	52.0		638	-0.4	0.0	19	dbSNP_111	52	1372,6754		133,1106,2824	yes	missense	ZNF527	NM_032453.1	29	539,2008,3330	GG,GA,AA		16.8841,47.2437,26.2549	benign	213/610	37879589	3086,8668	1814	4063	5877	SO:0001583	missense	84503	exon5			GACTCCATGCTGA	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"""Zinc fingers, C2H2-type"", ""-"""	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.638A>G	19.37:g.37879589A>G	ENSP00000390179:p.His213Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	180	94	0.522222	NM_032453	B4DVL5	Missense_Mutation	SNP	ENST00000436120.2	37	CCDS42559.1	668	0.3058608058608059	255	0.5182926829268293	108	0.2983425414364641	188	0.32867132867132864	117	0.15435356200527706	a	11.00	1.510539	0.27036	0.472437	0.168841	ENSG00000189164	ENST00000356178;ENST00000317566;ENST00000436120	.	.	.	4.15	-0.451	0.12214	.	0.787147	0.10407	N	0.678369	T	0.00012	0.0000	M	0.61703	1.905	0.48632	P	3.1800000000004047E-4	B;B	0.14012	0.005;0.009	B;B	0.16722	0.007;0.016	T	0.43147	-0.9409	8	0.72032	D	0.01	.	6.3759	0.21507	0.6944:0.1347:0.1709:0.0	rs4452075;rs52804685;rs61429553;rs4452075	213;181	Q8NB42;Q8NB42-2	ZN527_HUMAN;.	R	213;181;161	.	ENSP00000325231:H181R	H	+	2	0	ZNF527	42571429	0.000000	0.05858	0.001000	0.08648	0.304000	0.27724	1.296000	0.33389	-0.407000	0.07576	-1.412000	0.01120	CAT	A|0.698;G|0.302	0.302	strong		0.343	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453	
CFAP69	79846	hgsc.bcm.edu	37	7	89906609	89906609	+	Silent	SNP	C	C	T	rs3761805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:89906609C>T	ENST00000389297.4	+	11	1367	c.1116C>T	c.(1114-1116)aaC>aaT	p.N372N	C7orf63_ENST00000497910.1_Silent_p.N354N|C7orf63_ENST00000316089.8_Silent_p.N372N	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		372										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						TACTATTCAACGTAATTGTGA	0.284													T|||	2022	0.403754	0.4206	0.3905	5008	,	,		16063	0.6855		0.2286	False		,,,				2504	0.2802				p.N372N		Atlas-SNP	.											C7orf63_ENST00000389297,colon,carcinoma,+2,2	C7orf63	158	2	0			c.C1116T						PASS	.	T	,	1262,2320		226,810,755	39.0	41.0	40.0		1116,1062	1.1	1.0	7	dbSNP_107	40	1491,6557		133,1225,2666	no	coding-synonymous,coding-synonymous	C7orf63	NM_001039706.2,NM_001160138.1	,	359,2035,3421	TT,TC,CC		18.5263,35.2317,23.6715	,	372/942,354/924	89906609	2753,8877	1791	4024	5815	SO:0001819	synonymous_variant	79846	exon11			ATTCAACGTAATT																												ENST00000389297.4:c.1116C>T	7.37:g.89906609C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_001039706	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Silent	SNP	ENST00000389297.4	37	CCDS43613.2																																																																																			C|0.602;T|0.398	0.398	strong		0.284	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4		
OTOGL	283310	hgsc.bcm.edu	37	12	80747209	80747209	+	Missense_Mutation	SNP	C	C	G	rs7312569	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:80747209C>G	ENST00000547103.1	+	45	5455	c.5449C>G	c.(5449-5451)Cta>Gta	p.L1817V	OTOGL_ENST00000546620.1_5'Flank|OTOGL_ENST00000458043.2_Missense_Mutation_p.L1829V			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1817					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						CTGTTTGAATCTAAGAGAAGA	0.458													C|||	868	0.173323	0.1846	0.2075	5008	,	,		16401	0.0575		0.1819	False		,,,				2504	0.2444				p.L1829V		Atlas-SNP	.											.	OTOGL	235	.	0			c.C5485G						PASS	.	C	VAL/LEU	688,3198		61,566,1316	72.0	69.0	70.0		5485	0.4	0.1	12	dbSNP_116	70	1621,6675		159,1303,2686	yes	missense	OTOGL	NM_173591.3	32	220,1869,4002	GG,GC,CC		19.5395,17.7046,18.9542		1829/2345	80747209	2309,9873	1943	4148	6091	SO:0001583	missense	283310	exon45			TTGAATCTAAGAG	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5449C>G	12.37:g.80747209C>G	ENSP00000447211:p.Leu1817Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		327|327	0.14972527472527472|0.14972527472527472	86|86	0.17479674796747968|0.17479674796747968	75|75	0.20718232044198895|0.20718232044198895	30|30	0.05244755244755245|0.05244755244755245	136|136	0.17941952506596306|0.17941952506596306	C|C	5.903|5.903	0.350723|0.350723	0.11182|0.11182	0.177046|0.177046	0.195395|0.195395	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043	.|T;T	.|0.55052	.|0.54;0.54	5.74|5.74	0.452|0.452	0.16634|0.16634	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.45285|0.45285	1.41|1.41	0.54753|0.54753	P|P	1.799999999996249E-5|1.799999999996249E-5	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.10847|0.10847	-1.0612|-1.0612	4|6	.|0.31617	.|T	.|0.26	.|.	3.0832|3.0832	0.06269|0.06269	0.1146:0.1279:0.1196:0.6379|0.1146:0.1279:0.1196:0.6379	rs7312569;rs17249560;rs7312569|rs7312569;rs17249560;rs7312569	.|.	.|.	.|.	M|V	271|1817;1829	.|ENSP00000447211:L1817V;ENSP00000400895:L1829V	.|ENSP00000400895:L1829V	I|L	+|+	3|1	3|2	OTOGL|OTOGL	79271340|79271340	0.049000|0.049000	0.20398|0.20398	0.071000|0.071000	0.20095|0.20095	0.298000|0.298000	0.27526|0.27526	0.246000|0.246000	0.18160|0.18160	-0.156000|-0.156000	0.11079|0.11079	-0.294000|-0.294000	0.09567|0.09567	ATC|CTA	C|0.844;G|0.156	0.156	strong		0.458	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
MUC21	394263	hgsc.bcm.edu	37	6	30954309	30954309	+	Silent	SNP	A	A	T	rs150035336		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954309A>T	ENST00000376296.3	+	2	598	c.357A>T	c.(355-357)acA>acT	p.T119T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	119	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GGGCCAGCACAGCCACCAACT	0.597																																					p.T119T		Atlas-SNP	.											.	MUC21	98	.	0			c.A357T						PASS	.						180.0	166.0	171.0					6																	30954309		2203	4298	6501	SO:0001819	synonymous_variant	394263	exon2			CAGCACAGCCACC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.357A>T	6.37:g.30954309A>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	166	15	0.0903614	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			.	.	weak		0.597	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
PCDHA5	56143	hgsc.bcm.edu	37	5	140203432	140203432	+	Missense_Mutation	SNP	C	C	T	rs4141841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140203432C>T	ENST00000529859.1	+	1	2072	c.2072C>T	c.(2071-2073)gCc>gTc	p.A691V	PCDHA5_ENST00000529619.1_Missense_Mutation_p.A691V|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.A691V|PCDHA4_ENST00000512229.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	691			A -> V (in dbSNP:rs4141841).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCGAGGCTGCCCTGGTGGAT	0.677													.|||	2675	0.534145	0.5106	0.5922	5008	,	,		16194	0.5317		0.5378	False		,,,				2504	0.5235				p.A691V		Atlas-SNP	.											.	PCDHA5	361	.	0			c.C2072T						PASS	.	C	,,,,VAL/ALA,,VAL/ALA	2306,2100	588.0+/-386.8	597,1112,494	54.0	57.0	56.0		,,,,2072,,2072	3.9	0.2	5	dbSNP_110	56	4540,4058	580.4+/-391.1	1195,2150,954	no	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,64,,64	1792,3262,1448	TT,TC,CC		47.197,47.6623,47.3547	,,,,,,	,,,,691/937,,691/817	140203432	6846,6158	2203	4299	6502	SO:0001583	missense	56143	exon1			AGGCTGCCCTGGT	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2072C>T	5.37:g.140203432C>T	ENSP00000436557:p.Ala691Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	107	60	0.560748	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	1174	0.5375457875457875	262	0.532520325203252	196	0.5414364640883977	311	0.5437062937062938	405	0.5343007915567283	C	13.21	2.168726	0.38315	0.523377	0.52803	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.51574	0.75;0.7;0.72	3.9	3.9	0.45041	.	.	.	.	.	T	0.00012	0.0000	L	0.58428	1.81	0.80722	P	0.0	B;B;B	0.13145	0.005;0.007;0.007	B;B;B	0.12837	0.004;0.008;0.005	T	0.45011	-0.9290	8	0.45353	T	0.12	.	14.4262	0.67218	0.0:1.0:0.0:0.0	rs4141841;rs17661626;rs17844299;rs58318977;rs4141841	691;691;691	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	V	691	ENSP00000433416:A691V;ENSP00000436557:A691V;ENSP00000367366:A691V	ENSP00000367366:A691V	A	+	2	0	PCDHA5	140183616	0.000000	0.05858	0.173000	0.22940	0.517000	0.34286	-0.140000	0.10342	1.899000	0.54978	0.313000	0.20887	GCC	C|0.471;T|0.529	0.529	strong		0.677	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257266	114257266	+	Missense_Mutation	SNP	C	C	T	rs142136016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:114257266C>T	ENST00000306507.5	+	1	606	c.433C>T	c.(433-435)Cgc>Tgc	p.R145C		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	145					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R145C(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						CCCCTACTACCGCCGCAAGTT	0.642																																					p.R145C		Atlas-SNP	.											FOXD4L1,NS,malignant_melanoma,0,1	FOXD4L1	48	1	1	Substitution - Missense(1)	NS(1)	c.C433T						scavenged	.						23.0	32.0	29.0					2																	114257266		2014	3973	5987	SO:0001583	missense	200350	exon1			TACTACCGCCGCA	AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.433C>T	2.37:g.114257266C>T	ENSP00000302756:p.Arg145Cys	Somatic	360	1	0.00277778		WXS	Illumina HiSeq	Phase_I	496	96	0.193548	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	100	0.045787545787545784	17	0.034552845528455285	16	0.04419889502762431	27	0.0472027972027972	40	0.052770448548812667	.	12.80	2.046891	0.36085	.	.	ENSG00000184492	ENST00000306507	D	0.96491	-4.03	2.57	2.57	0.30868	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.32161	U	0.006487	D	0.84995	0.5596	H	0.95402	3.665	0.58432	D	0.999998	B	0.28350	0.208	B	0.26969	0.075	D	0.88738	0.3241	10	0.72032	D	0.01	.	6.7523	0.23493	0.2797:0.7203:0.0:0.0	.	145	Q9NU39	FX4L1_HUMAN	C	145	ENSP00000302756:R145C	ENSP00000302756:R145C	R	+	1	0	FOXD4L1	113973736	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	1.151000	0.31651	1.452000	0.47756	0.184000	0.17185	CGC	C|0.947;T|0.053	0.053	strong		0.642	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
KBTBD12	166348	hgsc.bcm.edu	37	3	127642814	127642814	+	Missense_Mutation	SNP	G	G	C	rs61268888	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:127642814G>C	ENST00000405109.1	+	2	1377	c.910G>C	c.(910-912)Gta>Cta	p.V304L	KBTBD12_ENST00000343941.4_Intron|KBTBD12_ENST00000407609.3_Intron|KBTBD12_ENST00000405256.1_Missense_Mutation_p.V304L			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	304										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						TTATGATCCTGTATCACGGAA	0.413													G|||	957	0.191094	0.1664	0.085	5008	,	,		17625	0.2331		0.1233	False		,,,				2504	0.3262				p.V304L		Atlas-SNP	.											.	KBTBD12	41	.	0			c.G910C						PASS	.	G	LEU/VAL	649,3191		49,551,1320	134.0	128.0	130.0		910	-1.1	0.0	3	dbSNP_129	130	1054,7168		63,928,3120	yes	missense	KBTBD12	NM_207335.2	32	112,1479,4440	CC,CG,GG		12.8193,16.901,14.1187	benign	304/624	127642814	1703,10359	1920	4111	6031	SO:0001583	missense	166348	exon1			GATCCTGTATCAC		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"""BTB/POZ domain containing"""	25731	protein-coding gene	gene with protein product			"""kelch domain containing 6"""	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.910G>C	3.37:g.127642814G>C	ENSP00000385957:p.Val304Leu	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	246	121	0.49187	NM_207335	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	37	CCDS33848.2	343	0.15705128205128205	89	0.18089430894308944	36	0.09944751381215469	122	0.21328671328671328	96	0.1266490765171504	G	2.653	-0.281515	0.05642	0.16901	0.128193	ENSG00000187715	ENST00000405109;ENST00000405256	T;T	0.66099	-0.19;-0.19	5.47	-1.1	0.09872	Kelch-type beta propeller (1);	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09058	-1.0692	8	0.33141	T	0.24	.	2.4812	0.04587	0.1929:0.1041:0.4764:0.2266	rs61268888;rs61734842	304	Q3ZCT8	KBTBC_HUMAN	L	304	ENSP00000385957:V304L;ENSP00000385879:V304L	ENSP00000385957:V304L	V	+	1	0	KBTBD12	129125504	0.000000	0.05858	0.000000	0.03702	0.971000	0.66376	0.528000	0.23002	0.062000	0.16340	-0.224000	0.12420	GTA	G|0.846;C|0.154	0.154	strong		0.413	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335	
PLEKHG7	440107	hgsc.bcm.edu	37	12	93139348	93139348	+	Missense_Mutation	SNP	A	A	G	rs17790310	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:93139348A>G	ENST00000344636.3	+	5	480	c.296A>G	c.(295-297)gAc>gGc	p.D99G	PLEKHG7_ENST00000549856.1_Missense_Mutation_p.D99G	NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	99	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		D -> G (in dbSNP:rs17790310).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						CAGAGAGATGACTTTGGAATT	0.378													A|||	89	0.0177716	0.0023	0.0274	5008	,	,		18766	0.0		0.0447	False		,,,				2504	0.0225				p.D99G		Atlas-SNP	.											.	PLEKHG7	38	.	0			c.A296G						PASS	.	A	GLY/ASP	54,4352	52.3+/-87.9	0,54,2149	105.0	102.0	103.0		296	5.2	0.9	12	dbSNP_123	103	503,8097	143.7+/-199.7	17,469,3814	yes	missense	PLEKHG7	NM_001004330.2	94	17,523,5963	GG,GA,AA		5.8488,1.2256,4.2826	probably-damaging	99/380	93139348	557,12449	2203	4300	6503	SO:0001583	missense	440107	exon5			GAGATGACTTTGG	AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"""Pleckstrin homology (PH) domain containing"""	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.296A>G	12.37:g.93139348A>G	ENSP00000344961:p.Asp99Gly	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_001004330	B2RNR7	Missense_Mutation	SNP	ENST00000344636.3	37	CCDS31873.1	43	0.019688644688644688	2	0.0040650406504065045	14	0.03867403314917127	0	0.0	27	0.03562005277044855	A	21.9	4.215419	0.79352	0.012256	0.058488	ENSG00000187510	ENST00000344636	T	0.64085	-0.08	5.21	5.21	0.72293	Dbl homology (DH) domain (4);	0.209202	0.50627	D	0.000115	T	0.30792	0.0776	M	0.72894	2.215	0.58432	D	0.999999	D	0.89917	1.0	D	0.79784	0.993	T	0.59101	-0.7517	10	0.25106	T	0.35	-8.9033	15.0379	0.71764	1.0:0.0:0.0:0.0	rs17790310;rs17790310	99	Q6ZR37	PKHG7_HUMAN	G	99	ENSP00000344961:D99G	ENSP00000344961:D99G	D	+	2	0	PLEKHG7	91663479	1.000000	0.71417	0.910000	0.35882	0.897000	0.52465	8.162000	0.89657	2.087000	0.62958	0.528000	0.53228	GAC	A|0.966;G|0.034	0.034	strong		0.378	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330	
CCR4	1233	hgsc.bcm.edu	37	3	32995928	32995928	+	Silent	SNP	C	C	T	rs2228428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:32995928C>T	ENST00000330953.5	+	2	1182	c.1014C>T	c.(1012-1014)taC>taT	p.Y338Y		NM_005508.4	NP_005499.1	P51679	CCR4_HUMAN	chemokine (C-C motif) receptor 4	338					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuron migration (GO:0001764)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of positive chemotaxis (GO:0050927)|response to antibiotic (GO:0046677)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)|tolerance induction (GO:0002507)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			NS(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)|stomach(1)	16						TCCAAATTTACTCTGCTGACA	0.463													C|||	735	0.146765	0.0356	0.2349	5008	,	,		19281	0.0208		0.3141	False		,,,				2504	0.1922				p.Y338Y		Atlas-SNP	.											.	CCR4	36	.	0			c.C1014T						PASS	.	C		348,4054	164.0+/-195.7	14,320,1867	52.0	52.0	52.0		1014	2.1	0.0	3	dbSNP_98	52	2713,5887	421.9+/-353.9	446,1821,2033	no	coding-synonymous	CCR4	NM_005508.4		460,2141,3900	TT,TC,CC		31.5465,7.9055,23.5425		338/361	32995928	3061,9941	2201	4300	6501	SO:0001819	synonymous_variant	1233	exon2			AATTTACTCTGCT	X85740	CCDS2656.1	3p24-p21.3	2012-08-08			ENSG00000183813	ENSG00000183813		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1605	protein-coding gene	gene with protein product		604836				7642634, 8884276	Standard	NM_005508		Approved	CC-CKR-4, CMKBR4, CKR4, k5-5, ChemR13, CD194	uc003cfg.1	P51679	OTTHUMG00000130752	ENST00000330953.5:c.1014C>T	3.37:g.32995928C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	185	77	0.416216	NM_005508	Q9ULY6|Q9ULY7	Silent	SNP	ENST00000330953.5	37	CCDS2656.1																																																																																			C|0.799;T|0.201	0.201	strong		0.463	CCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253252.2		
ST6GAL2	84620	hgsc.bcm.edu	37	2	107459974	107459974	+	Missense_Mutation	SNP	C	C	T	rs3796110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:107459974C>T	ENST00000409382.3	-	2	1070	c.460G>A	c.(460-462)Ggg>Agg	p.G154R	ST6GAL2_ENST00000361686.4_Missense_Mutation_p.G154R|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000409087.3_Missense_Mutation_p.G154R	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	154			G -> R (in dbSNP:rs3796110).		growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						CCTGGCTCCCCGGGGGAAGGG	0.617													C|||	702	0.140176	0.1505	0.147	5008	,	,		14211	0.1369		0.1014	False		,,,				2504	0.1646				p.G154R		Atlas-SNP	.											ST6GAL2,NS,carcinoma,+1,1	ST6GAL2	159	1	0			c.G460A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY	655,3751	268.3+/-268.4	41,573,1589	82.0	99.0	93.0		460,460,460	-2.2	0.0	2	dbSNP_107	93	639,7961	160.4+/-213.5	20,599,3681	yes	missense,missense,missense	ST6GAL2	NM_001142351.1,NM_001142352.1,NM_032528.2	125,125,125	61,1172,5270	TT,TC,CC		7.4302,14.8661,9.9493	benign,benign,benign	154/530,154/467,154/530	107459974	1294,11712	2203	4300	6503	SO:0001583	missense	84620	exon2			GCTCCCCGGGGGA	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"""sialyltransferase 2 (monosialoganglioside sialyltransferase)"""	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.460G>A	2.37:g.107459974C>T	ENSP00000386942:p.Gly154Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	37	CCDS2073.1	263	0.12042124542124542	73	0.1483739837398374	41	0.1132596685082873	73	0.12762237762237763	76	0.10026385224274406	C	4.589	0.109487	0.08780	0.148661	0.074302	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.30981	2.53;2.53;1.51	4.89	-2.16	0.07080	.	1.084480	0.07015	N	0.825771	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B;B	0.21381	0.055;0.01	B;B	0.10450	0.005;0.003	T	0.37911	-0.9685	9	0.13470	T	0.59	-3.3377	13.0284	0.58829	0.0:0.4981:0.0:0.5019	rs3796110;rs61140784;rs3796110	154;154	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	R	154	ENSP00000355273:G154R;ENSP00000386942:G154R;ENSP00000387332:G154R	ENSP00000355273:G154R	G	-	1	0	ST6GAL2	106826406	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	-1.227000	0.02950	-0.671000	0.05274	-1.134000	0.01955	GGG	C|0.893;T|0.107	0.107	strong		0.617	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
MICAL3	57553	hgsc.bcm.edu	37	22	18300879	18300879	+	Silent	SNP	G	G	A	rs11704809	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:18300879G>A	ENST00000441493.2	-	26	4900	c.4548C>T	c.(4546-4548)agC>agT	p.S1516S	MICAL3_ENST00000580469.1_5'Flank	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1516					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		TCTCCTCCACGCTCTCCACAA	0.637													G|||	761	0.151957	0.034	0.1844	5008	,	,		9836	0.0843		0.3161	False		,,,				2504	0.1892				p.S1516S		Atlas-SNP	.											.	MICAL3	53	.	0			c.C4548T						PASS	.	G		287,3845		9,269,1788	45.0	44.0	44.0		4548	-8.1	0.7	22	dbSNP_120	44	2758,5634		453,1852,1891	no	coding-synonymous	MICAL3	NM_015241.2		462,2121,3679	AA,AG,GG		32.8646,6.9458,24.3133		1516/2003	18300879	3045,9479	2066	4196	6262	SO:0001819	synonymous_variant	57553	exon26			CTCCACGCTCTCC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.4548C>T	22.37:g.18300879G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1	372	0.17032967032967034	19	0.03861788617886179	75	0.20718232044198895	49	0.08566433566433566	229	0.3021108179419525	G	2.932	-0.220901	0.06061	0.069458	0.328646	ENSG00000093100	ENST00000252134	.	.	.	4.9	-8.09	0.01090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999519218	.	.	.	.	.	.	T	0.05370	-1.0889	3	.	.	.	.	15.7355	0.77839	0.6563:0.0:0.3437:0.0	rs11704809;rs17339582	.	.	.	V	498	.	.	A	-	2	0	XXbac-B461K10.4	16680879	0.145000	0.22656	0.749000	0.31150	0.370000	0.29829	-0.400000	0.07241	-1.838000	0.01187	-0.291000	0.09656	GCG	G|0.800;A|0.200	0.200	strong		0.637	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
SAG	6295	hgsc.bcm.edu	37	2	234255547	234255547	+	Missense_Mutation	SNP	G	G	A	rs1046974	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:234255547G>A	ENST00000409110.1	+	16	1437	c.1207G>A	c.(1207-1209)Gtt>Att	p.V403I		NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	403			V -> A (in dbSNP:rs1046976). {ECO:0000269|PubMed:3164688, ECO:0000269|PubMed:9020843}.|V -> I (in dbSNP:rs1046974).		cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		CAAGAATGACGTTGATGAGTG	0.453													A|||	1517	0.302915	0.0545	0.245	5008	,	,		20836	0.3988		0.4344	False		,,,				2504	0.4458				p.V403I		Atlas-SNP	.											.	SAG	77	.	0			c.G1207A						PASS	.	A	ILE/VAL	462,3554		25,412,1571	91.0	96.0	95.0		1207	-2.7	0.0	2	dbSNP_86	95	3350,5002		661,2028,1487	yes	missense	SAG	NM_000541.4	29	686,2440,3058	AA,AG,GG		40.1102,11.504,30.8215	benign	403/406	234255547	3812,8556	2008	4176	6184	SO:0001583	missense	6295	exon16			AATGACGTTGATG		CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.1207G>A	2.37:g.234255547G>A	ENSP00000386444:p.Val403Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	88	86	0.977273	NM_000541	A0FDN6|Q53SV3|Q99858	Missense_Mutation	SNP	ENST00000409110.1	37	CCDS46545.1	683	0.31272893772893773	31	0.06300813008130081	104	0.287292817679558	224	0.3916083916083916	324	0.42744063324538256	g	4.826	0.153569	0.09185	0.11504	0.401102	ENSG00000130561	ENST00000252857;ENST00000409110	T	0.06849	3.25	4.39	-2.67	0.06059	.	2.199560	0.02549	N	0.095496	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.48234	-0.9053	9	0.36615	T	0.2	6.8364	6.9618	0.24601	0.5946:0.0:0.2798:0.1255	rs1046974;rs3172176;rs52832638;rs57908936;rs1046974	403	P10523	ARRS_HUMAN	I	403	ENSP00000386444:V403I	ENSP00000252857:V403I	V	+	1	0	SAG	233920286	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.089000	0.15002	-0.720000	0.04935	-0.934000	0.02701	GTT	G|0.696;A|0.304	0.304	strong		0.453	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1	NM_000541	
MUC21	394263	hgsc.bcm.edu	37	6	30954777	30954777	+	Silent	SNP	C	C	T	rs77386732	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954777C>T	ENST00000376296.3	+	2	1066	c.825C>T	c.(823-825)tcC>tcT	p.S275S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	275	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACTCTGAGTCCAGCACAGTGT	0.612																																					p.S275S		Atlas-SNP	.											.	MUC21	98	.	0			c.C825T						PASS	.						188.0	184.0	186.0					6																	30954777		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			TGAGTCCAGCACA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.825C>T	6.37:g.30954777C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	166	41	0.246988	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			C|0.903;T|0.097	0.097	strong		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
MUT	4594	hgsc.bcm.edu	37	6	49415448	49415448	+	Missense_Mutation	SNP	C	C	T	rs2229385	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:49415448C>T	ENST00000274813.3	-	8	1622	c.1495G>A	c.(1495-1497)Gct>Act	p.A499T		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	499			A -> T (in dbSNP:rs2229385). {ECO:0000269|PubMed:11350191, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16281286, ECO:0000269|Ref.4}.		cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACTTCTACAGCGTCTTCTTTT	0.299													C|||	432	0.086262	0.087	0.0706	5008	,	,		14439	0.0675		0.1123	False		,,,				2504	0.089				p.A499T		Atlas-SNP	.											.	MUT	70	.	0			c.G1495A						PASS	.	C	THR/ALA	435,3969	209.5+/-230.2	19,397,1786	107.0	111.0	110.0		1495	-2.1	0.3	6	dbSNP_98	110	908,7686	202.5+/-245.8	43,822,3432	yes	missense	MUT	NM_000255.3	58	62,1219,5218	TT,TC,CC		10.5655,9.8774,10.3324	benign	499/751	49415448	1343,11655	2202	4297	6499	SO:0001583	missense	4594	exon8			CTACAGCGTCTTC		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"""methylmalonyl Coenzyme A mutase"""			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1495G>A	6.37:g.49415448C>T	ENSP00000274813:p.Ala499Thr	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	257	120	0.466926	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Missense_Mutation	SNP	ENST00000274813.3	37	CCDS4924.1	208	0.09523809523809523	51	0.10365853658536585	31	0.0856353591160221	43	0.07517482517482517	83	0.10949868073878628	C	12.17	1.858832	0.32884	0.098774	0.105655	ENSG00000146085	ENST00000274813	D	0.98329	-4.87	5.24	-2.1	0.07210	Cobalamin (vitamin B12)-dependent enzyme, catalytic (1);Cobalamin (vitamin B12)-dependent enzyme, catalytic subdomain (1);Methylmalonyl-CoA mutase, alpha/beta chain, catalytic (1);Methylmalonyl-CoA mutase, alpha chain, catalytic (1);	0.475184	0.23556	N	0.046908	D	0.87641	0.6228	N	0.21324	0.655	0.58432	P	9.000000000036756E-6	B	0.10296	0.003	B	0.17098	0.017	T	0.77544	-0.2548	9	0.49607	T	0.09	-24.5971	0.8215	0.01112	0.3914:0.1122:0.1589:0.3375	rs2229385;rs17851388	499	P22033	MUTA_HUMAN	T	499	ENSP00000274813:A499T	ENSP00000274813:A499T	A	-	1	0	MUT	49523407	0.467000	0.25831	0.322000	0.25334	0.740000	0.42216	0.442000	0.21628	-0.231000	0.09825	-0.516000	0.04426	GCT	C|0.898;T|0.102	0.102	strong		0.299	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1		
ZZEF1	23140	hgsc.bcm.edu	37	17	3979982	3979982	+	Silent	SNP	G	G	A	rs8065185	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:3979982G>A	ENST00000381638.2	-	21	3307	c.3183C>T	c.(3181-3183)ctC>ctT	p.L1061L	ZZEF1_ENST00000574474.1_5'UTR	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1061							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						GGAGTTCTGTGAGGACGCTGA	0.532													G|||	540	0.107827	0.2126	0.1009	5008	,	,		17163	0.0		0.1421	False		,,,				2504	0.047				p.L1061L		Atlas-SNP	.											.	ZZEF1	195	.	0			c.C3183T						PASS	.	G		800,3606	322.1+/-297.4	78,644,1481	48.0	46.0	46.0		3183	-9.4	0.0	17	dbSNP_116	46	1291,7309	255.0+/-280.0	94,1103,3103	no	coding-synonymous	ZZEF1	NM_015113.3		172,1747,4584	AA,AG,GG		15.0116,18.1571,16.0772		1061/2962	3979982	2091,10915	2203	4300	6503	SO:0001819	synonymous_variant	23140	exon21			TTCTGTGAGGACG	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.3183C>T	17.37:g.3979982G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																			G|0.844;A|0.156	0.156	strong		0.532	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
MUC21	394263	hgsc.bcm.edu	37	6	30954573	30954573	+	Silent	SNP	C	C	T	rs372719488		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954573C>T	ENST00000376296.3	+	2	862	c.621C>T	c.(619-621)gcC>gcT	p.A207A	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	207	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAGTGGGGCCAGCACAGCCA	0.627																																					p.A207A		Atlas-SNP	.											MUC21,NS,malignant_melanoma,+1,2	MUC21	98	2	0			c.C621T						scavenged	.						152.0	149.0	150.0					6																	30954573		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			TGGGGCCAGCACA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.621C>T	6.37:g.30954573C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	138	10	0.0724638	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			.	.	weak		0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
DDX20	11218	hgsc.bcm.edu	37	1	112309331	112309331	+	Missense_Mutation	SNP	T	T	C	rs85276	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:112309331T>C	ENST00000369702.4	+	11	2905	c.2285T>C	c.(2284-2286)aTa>aCa	p.I762T	DDX20_ENST00000475700.1_Missense_Mutation_p.I370T	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	762			I -> T (in dbSNP:rs85276).		ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CATAGGGAAATACGTCTGAGT	0.463													C|||	831	0.165935	0.4274	0.0965	5008	,	,		20780	0.003		0.1252	False		,,,				2504	0.0716				p.I762T		Atlas-SNP	.											.	DDX20	50	.	0			c.T2285C						PASS	.	C	THR/ILE	1628,2778	660.4+/-400.7	296,1036,871	104.0	103.0	103.0		2285	4.8	0.0	1	dbSNP_79	103	1099,7501	768.2+/-407.6	69,961,3270	yes	missense	DDX20	NM_007204.4	89	365,1997,4141	CC,CT,TT		12.7791,36.9496,20.9672	benign	762/825	112309331	2727,10279	2203	4300	6503	SO:0001583	missense	11218	exon11			GGGAAATACGTCT	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2285T>C	1.37:g.112309331T>C	ENSP00000358716:p.Ile762Thr	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	200	113	0.565	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	338	0.15476190476190477	213	0.4329268292682927	30	0.08287292817679558	0	0.0	95	0.12532981530343007	C	0.007	-1.996505	0.00435	0.369496	0.127791	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.30714	1.52;2.08	5.82	4.85	0.62838	.	1.043140	0.07424	N	0.894524	T	0.02304	0.0071	N	0.00237	-1.79	0.51482	P	7.100000000004325E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41052	-0.9530	8	.	.	.	-0.4366	8.6229	0.33872	0.1785:0.7366:0.0:0.0849	rs85276;rs697388;rs742793;rs52833651;rs58747656;rs85276	370;762	E9PJ60;Q9UHI6	.;DDX20_HUMAN	T	762;370	ENSP00000358716:I762T;ENSP00000435660:I370T	.	I	+	2	0	DDX20	112110854	0.002000	0.14202	0.002000	0.10522	0.074000	0.17049	0.737000	0.26144	1.489000	0.48450	-0.119000	0.15052	ATA	A|0.004;C|0.196	0.196	strong		0.463	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
RDH5	5959	hgsc.bcm.edu	37	12	56117700	56117700	+	Silent	SNP	C	C	G	rs13193	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56117700C>G	ENST00000257895.5	+	4	752	c.600C>G	c.(598-600)gtC>gtG	p.V200V	RDH5_ENST00000548082.1_Silent_p.V200V|RDH5_ENST00000547072.1_Silent_p.V103V|RP11-644F5.10_ENST00000550412.1_3'UTR	NM_001199771.1|NM_002905.3	NP_001186700.1|NP_002896.2	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis/9-cis)	200				V -> E (in Ref. 2; AAB93668). {ECO:0000305}.	phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)	12					Vitamin A(DB00162)	GGATACGAGTCTCCATCGTGG	0.592													C|||	700	0.139776	0.3616	0.1239	5008	,	,		19146	0.0248		0.0457	False		,,,				2504	0.0665				p.V200V		Atlas-SNP	.											RDH5,NS,carcinoma,0,1	RDH5	25	1	0			c.C600G						PASS	.	C	,	1459,2947	470.5+/-355.8	242,975,986	73.0	67.0	69.0		600,600	5.1	1.0	12	dbSNP_52	69	260,8340	101.2+/-162.5	6,248,4046	no	coding-synonymous,coding-synonymous	RDH5	NM_001199771.1,NM_002905.3	,	248,1223,5032	GG,GC,CC		3.0233,33.1139,13.217	,	200/319,200/319	56117700	1719,11287	2203	4300	6503	SO:0001819	synonymous_variant	5959	exon4			ACGAGTCTCCATC	U89717	CCDS31829.1	12q13-q14	2013-06-03	2006-05-09			ENSG00000135437	1.1.1.105	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	9940	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 9C, member 5"""	601617	"""retinol dehydrogenase 5 (11-cis and 9-cis)"""	RDH1		9115228, 8884265, 19027726	Standard	NM_002905		Approved	HSD17B9, SDR9C5	uc001shl.3	Q92781	OTTHUMG00000170126	ENST00000257895.5:c.600C>G	12.37:g.56117700C>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_001199771	O00179|Q8TAI2	Silent	SNP	ENST00000257895.5	37	CCDS31829.1																																																																																			C|0.876;G|0.124	0.124	strong		0.592	RDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407493.1	NM_002905	
MSGN1	343930	hgsc.bcm.edu	37	2	17998025	17998025	+	Missense_Mutation	SNP	A	A	T	rs34069439	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:17998025A>T	ENST00000281047.3	+	1	263	c.240A>T	c.(238-240)gaA>gaT	p.E80D		NM_001105569.1	NP_001099039.1	A6NI15	MSGN1_HUMAN	mesogenin 1	80			E -> D (in dbSNP:rs34069439).		cell differentiation (GO:0030154)|segment specification (GO:0007379)|somitogenesis (GO:0001756)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GGGGCAGCGAAGGCTGCAGTG	0.642													T|||	1612	0.321885	0.2814	0.3559	5008	,	,		14630	0.0268		0.5398	False		,,,				2504	0.4325				p.E80D	Melanoma(127;325 1712 14802 40657 49130)	Atlas-SNP	.											.	MSGN1	39	.	0			c.A240T						PASS	.	T	ASP/GLU	1369,2541		242,885,828	39.0	44.0	42.0		240	2.3	0.0	2	dbSNP_126	42	4812,3446		1425,1962,742	yes	missense	MSGN1	NM_001105569.1	45	1667,2847,1570	TT,TA,AA		41.7292,35.0128,49.2028	benign	80/194	17998025	6181,5987	1955	4129	6084	SO:0001583	missense	343930	exon1			CAGCGAAGGCTGC		CCDS42657.1	2p24.2	2007-07-23			ENSG00000151379	ENSG00000151379			14907	protein-coding gene	gene with protein product	"""paraxial mesogenin"""	612209				10837126	Standard	NM_001105569		Approved	pMesogenin1	uc010yjt.2	A6NI15	OTTHUMG00000159089	ENST00000281047.3:c.240A>T	2.37:g.17998025A>T	ENSP00000281047:p.Glu80Asp	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	89	81	0.910112	NM_001105569		Missense_Mutation	SNP	ENST00000281047.3	37	CCDS42657.1	720	0.32967032967032966	146	0.2967479674796748	148	0.4088397790055249	16	0.027972027972027972	410	0.5408970976253298	T	0.004	-2.296235	0.00245	0.350128	0.582708	ENSG00000151379	ENST00000281047	T	0.16324	2.35	4.75	2.33	0.28932	.	0.503112	0.16816	N	0.198368	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37430	-0.9706	9	0.11794	T	0.64	-4.0966	0.8901	0.01252	0.1587:0.1728:0.1656:0.5029	rs34069439;rs58519973	80	A6NI15	MSGN1_HUMAN	D	80	ENSP00000281047:E80D	ENSP00000281047:E80D	E	+	3	2	MSGN1	17861506	0.118000	0.22208	0.013000	0.15412	0.169000	0.22640	-0.049000	0.11924	0.087000	0.17167	-0.257000	0.10917	GAA	A|0.586;T|0.414	0.414	strong		0.642	MSGN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353253.1	XM_292850	
PELP1	27043	hgsc.bcm.edu	37	17	4576620	4576620	+	Silent	SNP	C	C	T	rs55677157	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4576620C>T	ENST00000574876.1	-	15	1787	c.1770G>A	c.(1768-1770)ccG>ccA	p.P590P	PELP1_ENST00000269230.7_Intron|PELP1_ENST00000436683.2_Silent_p.P443P|PELP1_ENST00000572293.1_Silent_p.P640P|PELP1_ENST00000301396.4_Silent_p.P734P|AC091153.4_ENST00000441700.2_RNA			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	590					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						AGCGAGGAGACGGGGCCAGCA	0.652													C|||	425	0.0848642	0.0484	0.1282	5008	,	,		16334	0.003		0.2117	False		,,,				2504	0.0573				p.P590P		Atlas-SNP	.											.	PELP1	102	.	0			c.G1770A						PASS	.	C		292,4018		12,268,1875	19.0	30.0	27.0		1770	-3.2	0.9	17	dbSNP_129	27	1899,6647		204,1491,2578	no	coding-synonymous	PELP1	NM_014389.2		216,1759,4453	TT,TC,CC		22.2209,6.7749,17.0426		590/1131	4576620	2191,10665	2155	4273	6428	SO:0001819	synonymous_variant	27043	exon15			AGGAGACGGGGCC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.1770G>A	17.37:g.4576620C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	169	85	0.502959	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			C|0.892;T|0.108	0.108	strong		0.652	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
FANCA	2175	hgsc.bcm.edu	37	16	89857935	89857935	+	Missense_Mutation	SNP	G	G	A	rs11646374	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89857935G>A	ENST00000389301.3	-	14	1265	c.1235C>T	c.(1234-1236)gCg>gTg	p.A412V	FANCA_ENST00000568369.1_Missense_Mutation_p.A412V	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	412			A -> V (in dbSNP:rs11646374). {ECO:0000269|PubMed:18987736}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CATCAAACGCGCCACCCAGTC	0.567			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	353	0.0704872	0.0038	0.0187	5008	,	,		19935	0.254		0.0626	False		,,,				2504	0.0164				p.A412V		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.C1235T						PASS	.	G	VAL/ALA	76,4320	64.7+/-102.0	0,76,2122	65.0	51.0	56.0		1235	5.1	0.1	16	dbSNP_120	56	698,7902	172.5+/-223.2	26,646,3628	yes	missense	FANCA	NM_000135.2	64	26,722,5750	AA,AG,GG		8.1163,1.7288,5.9557	possibly-damaging	412/1456	89857935	774,12222	2198	4300	6498	SO:0001583	missense	2175	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAACGCGCCACCC	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1235C>T	16.37:g.89857935G>A	ENSP00000373952:p.Ala412Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	180	0.08241758241758242	3	0.006097560975609756	10	0.027624309392265192	117	0.20454545454545456	50	0.06596306068601583	G	14.47	2.546014	0.45383	0.017288	0.081163	ENSG00000187741	ENST00000389301	D	0.98585	-5.01	5.13	5.13	0.70059	.	0.801903	0.11032	N	0.607099	T	0.03220	0.0094	M	0.65975	2.015	0.09310	P	0.9999999999981521	P;P	0.52316	0.952;0.952	B;B	0.41174	0.349;0.349	T	0.11155	-1.0599	9	0.46703	T	0.11	-1.967	12.244	0.54560	0.0:0.1854:0.8146:0.0	rs11646374;rs17226204;rs52813493;rs58856001;rs11646374	412;412	B4DRI7;O15360	.;FANCA_HUMAN	V	412	ENSP00000373952:A412V	ENSP00000373952:A412V	A	-	2	0	FANCA	88385436	1.000000	0.71417	0.128000	0.21923	0.016000	0.09150	4.990000	0.63876	2.417000	0.82017	0.650000	0.86243	GCG	G|0.932;A|0.068	0.068	strong		0.567	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
PLEC	5339	hgsc.bcm.edu	37	8	144991176	144991176	+	Silent	SNP	T	T	C	rs6558405	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144991176T>C	ENST00000322810.4	-	32	13393	c.13224A>G	c.(13222-13224)tcA>tcG	p.S4408S	PLEC_ENST00000398774.2_Silent_p.S4239S|PLEC_ENST00000345136.3_Silent_p.S4271S|PLEC_ENST00000354589.3_Silent_p.S4271S|PLEC_ENST00000354958.2_Silent_p.S4249S|PLEC_ENST00000436759.2_Silent_p.S4298S|PLEC_ENST00000527096.1_Silent_p.S4294S|PLEC_ENST00000356346.3_Silent_p.S4257S|PLEC_ENST00000357649.2_Silent_p.S4275S	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4408	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CAGTGGGGTCTGACCAGGAGG	0.667													t|||	2396	0.478435	0.9002	0.3746	5008	,	,		16195	0.1528		0.4423	False		,,,				2504	0.3548				p.S4408S		Atlas-SNP	.											.	PLEC	1144	.	0			c.A13224G						PASS	.	C	,,,,,,,	3321,637		1397,527,55	30.0	38.0	36.0		12894,12771,12747,13224,12717,12813,12825,12813	-10.5	0.1	8	dbSNP_116	36	3608,4686		825,1958,1364	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	2222,2485,1419	CC,CT,TT		43.5013,16.094,43.446	,,,,,,,	4298/4575,4257/4534,4249/4526,4408/4685,4239/4516,4271/4548,4275/4552,4271/4548	144991176	6929,5323	1979	4147	6126	SO:0001819	synonymous_variant	5339	exon32			GGGGTCTGACCAG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.13224A>G	8.37:g.144991176T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			T|0.548;C|0.452	0.452	strong		0.667	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
PLIN1	5346	hgsc.bcm.edu	37	15	90210257	90210257	+	Silent	SNP	G	G	A	rs2304796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:90210257G>A	ENST00000300055.5	-	8	1284	c.1119C>T	c.(1117-1119)gtC>gtT	p.V373V	PLIN1_ENST00000430628.2_Silent_p.V373V	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	373					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						TGGTTGAGGAGACAGCAGGGG	0.607													G|||	1413	0.282149	0.1566	0.219	5008	,	,		19151	0.3472		0.3062	False		,,,				2504	0.4049				p.V373V		Atlas-SNP	.											.	PLIN1	36	.	0			c.C1119T						PASS	.	G	,	793,3607	318.2+/-295.5	72,649,1479	74.0	61.0	65.0		1119,1119	4.2	0.0	15	dbSNP_100	65	2654,5944	426.6+/-355.3	416,1822,2061	no	coding-synonymous,coding-synonymous	PLIN1	NM_001145311.1,NM_002666.4	,	488,2471,3540	AA,AG,GG		30.8676,18.0227,26.5195	,	373/523,373/523	90210257	3447,9551	2200	4299	6499	SO:0001819	synonymous_variant	5346	exon8			TGAGGAGACAGCA	AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"""Perilipins"""	9076	protein-coding gene	gene with protein product		170290	"""perilipin"""	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.1119C>T	15.37:g.90210257G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	195	190	0.974359	NM_001145311	Q8N5Y6	Silent	SNP	ENST00000300055.5	37	CCDS10353.1																																																																																			G|0.730;A|0.270	0.270	strong		0.607	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313424.2	NM_002666	
HEXB	3074	hgsc.bcm.edu	37	5	73992881	73992881	+	Missense_Mutation	SNP	A	A	G	rs10805890	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:73992881A>G	ENST00000261416.7	+	5	736	c.619A>G	c.(619-621)Att>Gtt	p.I207V	HEXB_ENST00000511181.1_5'UTR	NM_000521.3	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B (beta polypeptide)	207			I -> V (probable polymorphism; dbSNP:rs10805890). {ECO:0000269|PubMed:1720305, ECO:0000269|PubMed:8950198}.		astrocyte cell migration (GO:0043615)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|ganglioside catabolic process (GO:0006689)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|lipid storage (GO:0019915)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|male courtship behavior (GO:0008049)|myelination (GO:0042552)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|oogenesis (GO:0048477)|penetration of zona pellucida (GO:0007341)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(3)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		AGGAATTTTGATTGATACATC	0.303													A|||	643	0.128395	0.0091	0.1988	5008	,	,		17389	0.2609		0.1461	False		,,,				2504	0.0849				p.I207V	Melanoma(66;841 1270 13391 18706 27225)	Atlas-SNP	.											.	HEXB	34	.	0			c.A619G	GRCh37	CM910221	HEXB	M	rs10805890	PASS	.	A	VAL/ILE	160,4246	106.0+/-144.5	3,154,2046	92.0	95.0	94.0		619	4.8	1.0	5	dbSNP_120	94	1498,7102	283.2+/-296.0	141,1216,2943	yes	missense	HEXB	NM_000521.3	29	144,1370,4989	GG,GA,AA		17.4186,3.6314,12.748	benign	207/557	73992881	1658,11348	2203	4300	6503	SO:0001583	missense	3074	exon5			ATTTTGATTGATA	M13519	CCDS4022.1	5q13.3	2012-10-02			ENSG00000049860	ENSG00000049860	3.2.1.52		4879	protein-coding gene	gene with protein product		606873				2579389, 3013851	Standard	NM_000521		Approved		uc003kdf.4	P07686	OTTHUMG00000102057	ENST00000261416.7:c.619A>G	5.37:g.73992881A>G	ENSP00000261416:p.Ile207Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_000521		Missense_Mutation	SNP	ENST00000261416.7	37	CCDS4022.1	329	0.15064102564102563	7	0.014227642276422764	64	0.17679558011049723	147	0.256993006993007	111	0.14643799472295516	A	11.93	1.786183	0.31593	0.036314	0.174186	ENSG00000049860	ENST00000261416	D	0.90504	-2.68	6.07	4.85	0.62838	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);Glycoside hydrolase, family 20 (1);	0.055692	0.64402	D	0.000001	T	0.00073	0.0002	L	0.41124	1.26	0.09310	P	1.0	B	0.30482	0.281	B	0.35770	0.21	T	0.06899	-1.0801	9	0.33940	T	0.23	-33.5887	7.9195	0.29837	0.6433:0.2356:0.0:0.1211	rs10805890;rs56696079;rs10805890	207	P07686	HEXB_HUMAN	V	207	ENSP00000261416:I207V	ENSP00000261416:I207V	I	+	1	0	HEXB	74028637	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	1.232000	0.32636	2.330000	0.79161	0.477000	0.44152	ATT	A|0.860;G|0.140	0.140	strong		0.303	HEXB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219859.6	NM_000521	
ZDHHC6	64429	hgsc.bcm.edu	37	10	114200355	114200355	+	Silent	SNP	G	G	A	rs2306159	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:114200355G>A	ENST00000369405.3	-	5	1041	c.618C>T	c.(616-618)acC>acT	p.T206T	ZDHHC6_ENST00000369404.3_Silent_p.T202T	NM_022494.1	NP_071939.1	Q9H6R6	ZDHC6_HUMAN	zinc finger, DHHC-type containing 6	206					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Colorectal(252;0.198)		Epithelial(162;0.0291)|all cancers(201;0.117)		AGGCAAACAAGGTGGTAGCAA	0.443													G|||	2574	0.513978	0.3684	0.5677	5008	,	,		15821	0.4802		0.6014	False		,,,				2504	0.6176				p.T206T		Atlas-SNP	.											.	ZDHHC6	32	.	0			c.C618T						PASS	.	G		1673,2733	509.8+/-367.3	318,1037,848	170.0	154.0	159.0		618	0.5	1.0	10	dbSNP_100	159	4989,3611	625.7+/-397.7	1472,2045,783	no	coding-synonymous	ZDHHC6	NM_022494.1		1790,3082,1631	AA,AG,GG		41.9884,37.9709,48.7775		206/414	114200355	6662,6344	2203	4300	6503	SO:0001819	synonymous_variant	64429	exon5			AAACAAGGTGGTA	AK025605	CCDS7574.1	10q26.11	2008-05-02			ENSG00000023041	ENSG00000023041		"""Zinc fingers, DHHC-type"""	19160	protein-coding gene	gene with protein product							Standard	NM_022494		Approved	ZNF376, FLJ21952	uc001kzv.3	Q9H6R6	OTTHUMG00000019062	ENST00000369405.3:c.618C>T	10.37:g.114200355G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	133	131	0.984962	NM_022494	D3DRB6|Q53G45|Q96IV7|Q9H605	Silent	SNP	ENST00000369405.3	37	CCDS7574.1																																																																																			G|0.496;A|0.504	0.504	strong		0.443	ZDHHC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050393.1	NM_022494	
LRP2	4036	hgsc.bcm.edu	37	2	170175334	170175334	+	Missense_Mutation	SNP	T	T	C	rs2229263	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:170175334T>C	ENST00000263816.3	-	3	533	c.248A>G	c.(247-249)aAc>aGc	p.N83S	LRP2_ENST00000443831.1_Missense_Mutation_p.N83S	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	83	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.		N -> S (in dbSNP:rs2229263). {ECO:0000269|PubMed:8706697}.		cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CACCCAGGAGTTGGGGATGCA	0.473													T|||	1534	0.30631	0.4818	0.2118	5008	,	,		21257	0.2758		0.2783	False		,,,				2504	0.1963				p.N83S		Atlas-SNP	.											.	LRP2	751	.	0			c.A248G						PASS	.	T	SER/ASN	1915,2491	547.0+/-377.2	431,1053,719	144.0	122.0	129.0		248	-6.3	0.0	2	dbSNP_98	129	2524,6076	414.1+/-351.3	363,1798,2139	yes	missense	LRP2	NM_004525.2	46	794,2851,2858	CC,CT,TT		29.3488,43.4635,34.1304	benign	83/4656	170175334	4439,8567	2203	4300	6503	SO:0001583	missense	4036	exon3			CAGGAGTTGGGGA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.248A>G	2.37:g.170175334T>C	ENSP00000263816:p.Asn83Ser	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	164	92	0.560976	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	673	0.30815018315018317	240	0.4878048780487805	83	0.2292817679558011	142	0.24825174825174826	208	0.27440633245382584	T	5.794	0.330732	0.10956	0.434635	0.293488	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.95307	-3.67;-3.67	6.02	-6.27	0.02026	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	2.042490	0.01599	N	0.021945	T	0.00012	0.0000	N	0.04018	-0.295	0.80722	P	0.0	B;B	0.10296	0.0;0.003	B;B	0.10450	0.001;0.005	T	0.33497	-0.9866	8	.	.	.	.	2.1449	0.03784	0.1361:0.3669:0.1931:0.3039	rs2229263;rs2302916;rs6716834;rs17848145;rs52789446;rs58366843;rs6716834	83;83	E9PC35;P98164	.;LRP2_HUMAN	S	83	ENSP00000263816:N83S;ENSP00000409813:N83S	.	N	-	2	0	LRP2	169883580	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.760000	0.04756	-1.027000	0.03325	0.533000	0.62120	AAC	T|0.548;G|0.057	.	strong		0.473	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
WDR81	124997	hgsc.bcm.edu	37	17	1637458	1637458	+	Silent	SNP	G	G	A	rs587780506|rs398088774|rs8065251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1637458G>A	ENST00000409644.1	+	7	5127	c.5127G>A	c.(5125-5127)ccG>ccA	p.P1709P	WDR81_ENST00000545662.1_Silent_p.P340P|WDR81_ENST00000419248.1_Silent_p.P482P|WDR81_ENST00000446363.1_Silent_p.P348P|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Silent_p.P658P|WDR81_ENST00000437219.2_Silent_p.P506P	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1709					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TTGAGGCCCCGCAGCACGTGG	0.672													G|||	1236	0.246805	0.2519	0.2061	5008	,	,		15192	0.1855		0.1978	False		,,,				2504	0.3824				p.P1709P		Atlas-SNP	.											WDR81_ENST00000437219,NS,carcinoma,0,3	WDR81	180	3	0			c.G5127A						scavenged	.	G	,,,	1057,3347		118,821,1263	30.0	32.0	31.0		1518,5127,1446,1974	-8.9	0.1	17	dbSNP_116	31	1802,6794		188,1426,2684	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	306,2247,3947	AA,AG,GG		20.9632,24.0009,21.9923	,,,	506/739,1709/1942,482/715,658/891	1637458	2859,10141	2202	4298	6500	SO:0001819	synonymous_variant	124997	exon7			GGCCCCGCAGCAC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.5127G>A	17.37:g.1637458G>A		Somatic	32	1	0.03125		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			G|0.782;A|0.218	0.218	strong		0.672	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
FAM35A	54537	hgsc.bcm.edu	37	10	88930249	88930249	+	Missense_Mutation	SNP	A	A	T	rs11202365	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:88930249A>T	ENST00000298784.1	+	5	1762	c.1648A>T	c.(1648-1650)Agt>Tgt	p.S550C	FAM35A_ENST00000298786.4_Missense_Mutation_p.S550C	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	550			S -> C (in dbSNP:rs11202365).							endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						CAGTGTAGTTAGTGAAGTTGT	0.358													A|||	1379	0.275359	0.1785	0.255	5008	,	,		17119	0.1607		0.3638	False		,,,				2504	0.4479				p.S550C	Ovarian(175;703 2004 25460 32514 43441)	Atlas-SNP	.											.	FAM35A	48	.	0			c.A1648T						PASS	.	A	CYS/SER	881,3525	336.8+/-304.5	91,699,1413	75.0	70.0	72.0		1648	2.9	0.0	10	dbSNP_120	72	3341,5259	483.5+/-371.2	664,2013,1623	yes	missense	FAM35A	NM_019054.2	112	755,2712,3036	TT,TA,AA		38.8488,19.9955,32.4619	probably-damaging	550/836	88930249	4222,8784	2203	4300	6503	SO:0001583	missense	54537	exon5			GTAGTTAGTGAAG	BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376			28773	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_019054		Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.1648A>T	10.37:g.88930249A>T	ENSP00000298784:p.Ser550Cys	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	54	52	0.962963	NM_019054	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	577|577	0.2641941391941392|0.2641941391941392	103|103	0.20934959349593496|0.20934959349593496	104|104	0.287292817679558|0.287292817679558	85|85	0.1486013986013986|0.1486013986013986	285|285	0.3759894459102902|0.3759894459102902	a|a	11.73|11.73	1.727046|1.727046	0.30593|0.30593	0.199955|0.199955	0.388488|0.388488	ENSG00000122376|ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313|ENST00000342900	T;T;T|.	0.64991|.	-0.13;-0.13;-0.13|.	4.05|4.05	2.92|2.92	0.33932|0.33932	.|.	0.667425|.	0.13796|.	N|.	0.362154|.	T|.	0.00012|.	0.0000|.	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	P|P	0.0|0.0	D|.	0.65815|.	0.995|.	P|.	0.55824|.	0.785|.	T|.	0.44877|.	-0.9299|.	9|.	0.59425|.	D|.	0.04|.	-3.8081|-3.8081	4.8821|4.8821	0.13685|0.13685	0.6758:0.0:0.3242:0.0|0.6758:0.0:0.3242:0.0	rs11202365;rs11202365|rs11202365;rs11202365	550|.	Q86V20|.	FA35A_HUMAN|.	C|L	550|204	ENSP00000298786:S550C;ENSP00000298784:S550C;ENSP00000351064:S550C|.	ENSP00000298784:S550C|.	S|X	+|+	1|2	0|0	FAM35A|FAM35A	88920229|88920229	0.725000|0.725000	0.28048|0.28048	0.017000|0.017000	0.16124|0.16124	0.669000|0.669000	0.39330|0.39330	1.260000|1.260000	0.32968|0.32968	0.630000|0.630000	0.30394|0.30394	0.438000|0.438000	0.28831|0.28831	AGT|TAG	A|0.698;T|0.302	0.302	strong		0.358	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054	
LMF2	91289	hgsc.bcm.edu	37	22	50943232	50943232	+	Splice_Site	SNP	G	G	A	rs8136495	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50943232G>A	ENST00000474879.2	-	10	1451	c.1436C>T	c.(1435-1437)aCg>aTg	p.T479M	LMF2_ENST00000216080.5_Splice_Site_p.T454M|LMF2_ENST00000505981.1_5'Flank|LMF2_ENST00000380796.3_Intron	NM_033200.2	NP_149977.2	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	479			T -> M (in dbSNP:rs8136495).			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|cervix(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		AGGGCTCACCGTCCAGTGGTG	0.677													g|||	711	0.141973	0.1626	0.1398	5008	,	,		11654	0.0387		0.2316	False		,,,				2504	0.1299				p.T479M		Atlas-SNP	.											.	LMF2	40	.	0			c.C1436T						PASS	.	G	MET/THR	696,3684		63,570,1557	16.0	20.0	19.0		1436	1.6	0.8	22	dbSNP_116	19	1960,6604		230,1500,2552	yes	missense-near-splice	LMF2	NM_033200.2	81	293,2070,4109	AA,AG,GG		22.8865,15.8904,20.5192	benign	479/708	50943232	2656,10288	2190	4282	6472	SO:0001630	splice_region_variant	91289	exon10			CTCACCGTCCAGT	BC002942	CCDS14093.1, CCDS14093.2	22q13.33	2008-02-04	2007-11-29	2007-11-29	ENSG00000100258	ENSG00000100258			25096	protein-coding gene	gene with protein product			"""transmembrane protein 153"", ""transmembrane protein 112B"""	TMEM153, TMEM112B		12477932	Standard	NM_033200		Approved		uc003blp.2	Q9BU23	OTTHUMG00000150206	ENST00000474879.2:c.1437+1C>T	22.37:g.50943232G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_033200	A6NEZ0|Q13392|Q6ZNR2|Q8WU74|Q96C62	Missense_Mutation	SNP	ENST00000474879.2	37	CCDS14093.2	341	0.15613553113553114	87	0.17682926829268292	58	0.16022099447513813	18	0.03146853146853147	178	0.23482849604221637	G	12.28	1.889841	0.33348	0.158904	0.228865	ENSG00000100258	ENST00000474879;ENST00000216080	T;T	0.23754	1.89;1.89	4.85	1.58	0.23477	.	0.251286	0.38326	N	0.001725	T	0.00012	0.0000	L	0.58669	1.825	0.09310	P	0.9999999999999691	P;P	0.40032	0.699;0.65	B;B	0.36464	0.225;0.202	T	0.19418	-1.0306	9	0.52906	T	0.07	-0.4637	5.9129	0.19039	0.1699:0.0:0.6769:0.1532	rs8136495;rs56831326	479;454	Q9BU23;Q9BU23-2	LMF2_HUMAN;.	M	479;454	ENSP00000424381:T479M;ENSP00000216080:T454M	ENSP00000216080:T454M	T	-	2	0	LMF2	49290098	1.000000	0.71417	0.765000	0.31456	0.238000	0.25445	2.881000	0.48538	0.120000	0.18254	-0.122000	0.15005	ACG	A|0.183;C|0.000;G|0.816;T|0.000	0.183	strong		0.677	LMF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316833.2	NM_033200	Missense_Mutation
LILRB3	11025	hgsc.bcm.edu	37	19	54725907	54725907	+	Missense_Mutation	SNP	G	G	C	rs55662384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54725907G>C	ENST00000391750.1	-	5	587	c.451C>G	c.(451-453)Cac>Gac	p.H151D	LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.H151D|LILRB3_ENST00000407860.2_Missense_Mutation_p.H151D|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000346401.6_Missense_Mutation_p.H151D|LILRB3_ENST00000424807.1_Missense_Mutation_p.H151D|LILRA6_ENST00000391735.3_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	151	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACAAAATGGTGATATCCCTTC	0.607													.|||	412	0.0822684	0.2844	0.0346	5008	,	,		11604	0.0		0.005	False		,,,				2504	0.0072				p.H151D		Atlas-SNP	.											.	LILRB3	67	.	0			c.C451G						PASS	.						21.0	14.0	17.0					19																	54725907		2080	3877	5957	SO:0001583	missense	11025	exon4			AATGGTGATATCC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.451C>G	19.37:g.54725907G>C	ENSP00000375630:p.His151Asp	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	224	81	0.361607	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	g	0.003	-2.570640	0.00133	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000445347	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;2.82;2.82;5.85	2.87	-4.31	0.03698	Immunoglobulin-like fold (1);	2.010510	0.02119	N	0.055507	T	0.01905	0.0060	N	0.00128	-2.045	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.001;0.0	B;B;B;B;B	0.09377	0.004;0.0;0.003;0.0;0.001	T	0.48570	-0.9024	10	0.02654	T	1	.	8.7737	0.34749	0.1378:0.4079:0.4543:0.0	rs55662384	151;151;151;151;151	B5MCX0;F8WD89;O75022-2;O75022;O75022-3	.;.;.;LIRB3_HUMAN;.	D	151	ENSP00000375630:H151D;ENSP00000412771:H151D;ENSP00000345184:H151D;ENSP00000245620:H151D;ENSP00000384274:H151D;ENSP00000388199:H151D	ENSP00000245620:H151D	H	-	1	0	LILRB3	59417719	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.740000	0.00378	-0.678000	0.05224	-2.793000	0.00115	CAC	G|0.994;C|0.006	0.006	strong		0.607	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
DOCK5	80005	hgsc.bcm.edu	37	8	25222165	25222165	+	Missense_Mutation	SNP	A	A	G	rs2271111	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:25222165A>G	ENST00000276440.7	+	30	3112	c.3068A>G	c.(3067-3069)cAg>cGg	p.Q1023R		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1023			Q -> R (in dbSNP:rs2271111).		positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.Q1023R(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		GCTATAAATCAGTTTGCTGAA	0.418													A|||	1230	0.245607	0.0711	0.304	5008	,	,		18344	0.3562		0.3698	False		,,,				2504	0.1984				p.Q1023R	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											DOCK5,NS,carcinoma,0,1	DOCK5	167	1	1	Substitution - Missense(1)	stomach(1)	c.A3068G						PASS	.	A	ARG/GLN	487,3919	213.8+/-233.3	26,435,1742	137.0	117.0	124.0		3068	4.3	1.0	8	dbSNP_100	124	2886,5714	414.1+/-351.3	498,1890,1912	yes	missense	DOCK5	NM_024940.6	43	524,2325,3654	GG,GA,AA		33.5581,11.0531,25.9342	benign	1023/1871	25222165	3373,9633	2203	4300	6503	SO:0001583	missense	80005	exon30			TAAATCAGTTTGC		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.3068A>G	8.37:g.25222165A>G	ENSP00000276440:p.Gln1023Arg	Somatic	261	2	0.00766284		WXS	Illumina HiSeq	Phase_I	234	234	1	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	634	0.2902930402930403	37	0.07520325203252033	120	0.3314917127071823	189	0.3304195804195804	288	0.37994722955145116	A	10.21	1.287145	0.23478	0.110531	0.335581	ENSG00000147459	ENST00000276440	T	0.23950	1.88	5.62	4.34	0.51931	.	0.058883	0.64402	D	0.000001	T	0.00012	0.0000	L	0.41710	1.295	0.23920	P	0.99646016	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.41858	-0.9485	9	0.08837	T	0.75	.	7.572	0.27913	0.7907:0.0:0.073:0.1362	rs2271111;rs52835832;rs58353884;rs2271111	1013;1023	D3DSS6;Q9H7D0	.;DOCK5_HUMAN	R	1023	ENSP00000276440:Q1023R	ENSP00000276440:Q1023R	Q	+	2	0	DOCK5	25278082	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.300000	0.59079	2.142000	0.66516	0.528000	0.53228	CAG	A|0.749;G|0.251	0.251	strong		0.418	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
WDR31	114987	hgsc.bcm.edu	37	9	116082647	116082647	+	Missense_Mutation	SNP	C	C	G	rs41307479	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:116082647C>G	ENST00000374193.4	-	9	1016	c.770G>C	c.(769-771)tGt>tCt	p.C257S	WDR31_ENST00000341761.4_Missense_Mutation_p.C256S|WDR31_ENST00000374195.3_Missense_Mutation_p.C132S|WDR31_ENST00000461942.1_5'UTR	NM_001012361.2|NM_145241.3	NP_001012361.1|NP_660284.1	Q8NA23	WDR31_HUMAN	WD repeat domain 31	257										NS(1)|large_intestine(1)|lung(2)|prostate(2)	6						CGTGGCTTCACAGCCTTCTCC	0.512													C|||	510	0.101837	0.0098	0.0922	5008	,	,		20961	0.0456		0.1879	False		,,,				2504	0.2025				p.C257S		Atlas-SNP	.											.	WDR31	23	.	0			c.G770C						PASS	.	C	SER/CYS,SER/CYS	203,4203	124.5+/-161.8	6,191,2006	117.0	102.0	107.0		770,767	5.8	1.0	9	dbSNP_127	107	1797,6803	326.3+/-317.3	191,1415,2694	yes	missense,missense	WDR31	NM_001012361.2,NM_145241.3	112,112	197,1606,4700	GG,GC,CC		20.8953,4.6074,15.3775	possibly-damaging,possibly-damaging	257/368,256/367	116082647	2000,11006	2203	4300	6503	SO:0001583	missense	114987	exon9			GCTTCACAGCCTT	BC012352	CCDS6792.1, CCDS35110.1	9q33.1	2013-01-09			ENSG00000148225	ENSG00000148225		"""WD repeat domain containing"""	21421	protein-coding gene	gene with protein product	"""similar to spermatid WD-repeat protein"""						Standard	NM_145241		Approved	FLJ35921	uc004bhb.3	Q8NA23	OTTHUMG00000020525	ENST00000374193.4:c.770G>C	9.37:g.116082647C>G	ENSP00000363308:p.Cys257Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	161	64	0.397516	NM_001012361	Q5W0T9|Q96EG8	Missense_Mutation	SNP	ENST00000374193.4	37	CCDS35110.1	221	0.10119047619047619	4	0.008130081300813009	42	0.11602209944751381	23	0.04020979020979021	152	0.20052770448548812	C	21.9	4.210103	0.79240	0.046074	0.208953	ENSG00000148225	ENST00000374193;ENST00000374195;ENST00000341761	T;T;T	0.05717	3.4;3.4;3.4	5.84	5.84	0.93424	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.81802	2.56	0.09310	P	0.99999999398653	P;P	0.51537	0.91;0.946	P;P	0.51453	0.469;0.67	T	0.45542	-0.9254	9	0.09338	T	0.73	-9.5655	16.2152	0.82206	0.0:0.8673:0.1327:0.0	rs41307479;rs61732662	257;256	Q8NA23;Q8NA23-2	WDR31_HUMAN;.	S	257;132;256	ENSP00000363308:C257S;ENSP00000363310:C132S;ENSP00000345027:C256S	ENSP00000345027:C256S	C	-	2	0	WDR31	115122468	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.162000	0.64942	2.762000	0.94881	0.551000	0.68910	TGT	C|0.850;G|0.150	0.150	strong		0.512	WDR31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053734.2	NM_145241	
TAF15	8148	hgsc.bcm.edu	37	17	34171827	34171827	+	Silent	SNP	C	C	T	rs4251786	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:34171827C>T	ENST00000588240.1	+	15	1639	c.1524C>T	c.(1522-1524)taC>taT	p.Y508Y	TAF15_ENST00000592237.1_Intron|TAF15_ENST00000311979.3_Silent_p.Y505Y	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		gaggaggttacggaggagatc	0.607			T	"""TEC, CHN1, ZNF384"""	"""extraskeletal myxoid chondrosarcomas, ALL"""								C|||	294	0.0587061	0.0053	0.0937	5008	,	,		14946	0.002		0.1571	False		,,,				2504	0.0634				p.Y508Y		Atlas-SNP	.		Dom	yes		17	17q11.1-q11.2	8148	"""TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"""		"""L, M"""	.	TAF15	46	.	0			c.C1524T						PASS	.	C	,	107,4299	84.4+/-122.9	0,107,2096	85.0	75.0	79.0		1515,1524	-4.0	1.0	17	dbSNP_111	79	1128,7472	233.2+/-266.6	76,976,3248	no	coding-synonymous,coding-synonymous	TAF15	NM_003487.2,NM_139215.1	,	76,1083,5344	TT,TC,CC		13.1163,2.4285,9.4956	,	505/590,508/593	34171827	1235,11771	2203	4300	6503	SO:0001819	synonymous_variant	8148	exon15			AGGTTACGGAGGA	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"""RNA binding motif (RRM) containing"""	11547	protein-coding gene	gene with protein product		601574	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"""	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1524C>T	17.37:g.34171827C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_139215	D3DPM5|Q15775|Q5T077	Silent	SNP	ENST00000588240.1	37	CCDS32623.1																																																																																			C|0.917;T|0.083	0.083	strong		0.607	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215	
EMID1	129080	hgsc.bcm.edu	37	22	29630337	29630337	+	Splice_Site	SNP	G	G	A	rs3950176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29630337G>A	ENST00000404820.3	+	12	1200	c.1073G>A	c.(1072-1074)cGg>cAg	p.R358Q	EMID1_ENST00000404755.3_Splice_Site_p.R337Q|EMID1_ENST00000334018.6_Splice_Site_p.R358Q			Q96A84	EMID1_HUMAN	EMI domain containing 1	356	Collagen-like.					collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)|skin(3)	12						GCTGGGCAGCGGGTAAGTGTT	0.607													G|||	724	0.144569	0.1974	0.0605	5008	,	,		19383	0.2302		0.1044	False		,,,				2504	0.0859				p.R358Q		Atlas-SNP	.											.	EMID1	33	.	0			c.G1073A						PASS	.	G	GLN/ARG	837,3569	324.2+/-298.5	82,673,1448	93.0	71.0	78.0		1073	-2.8	0.9	22	dbSNP_108	78	940,7660	203.0+/-246.1	50,840,3410	yes	missense-near-splice	EMID1	NM_133455.2	43	132,1513,4858	AA,AG,GG		10.9302,18.9968,13.6629	benign	358/444	29630337	1777,11229	2203	4300	6503	SO:0001630	splice_region_variant	129080	exon12			GGCAGCGGGTAAG	AJ416090	CCDS33630.1	22q12.2	2009-08-04			ENSG00000186998	ENSG00000186998		"""EMI domain containing"""	18036	protein-coding gene	gene with protein product	"""emilin and multimerin-domain containing protein 1"", ""putative emu1"""	608926				12221002	Standard	NM_001267895		Approved	EMU1, hEmu1, EMI5	uc003aem.4	Q96A84	OTTHUMG00000151013	ENST00000404820.3:c.1074+1G>A	22.37:g.29630337G>A		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_133455	B0QYK6|Q6ICG1|Q86SS7	Missense_Mutation	SNP	ENST00000404820.3	37		355|355	0.16254578754578755|0.16254578754578755	100|100	0.2032520325203252|0.2032520325203252	26|26	0.0718232044198895|0.0718232044198895	143|143	0.25|0.25	86|86	0.11345646437994723|0.11345646437994723	G|G	12.74|12.74	2.028660|2.028660	0.35797|0.35797	0.189968|0.189968	0.109302|0.109302	ENSG00000186998|ENSG00000186998	ENST00000433143|ENST00000334018;ENST00000404755;ENST00000404820	.|D;T;D	.|0.90788	.|-2.73;2.32;-2.73	4.43|4.43	-2.76|-2.76	0.05896|0.05896	.|.	.|0.777093	.|0.11137	.|N	.|0.595736	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.12569|0.12569	0.235|0.235	0.49687|0.49687	P|P	1.8399999999996197E-4|1.8399999999996197E-4	.|B;B;B;B	.|0.19200	.|0.015;0.016;0.034;0.012	.|B;B;B;B	.|0.12156	.|0.007;0.004;0.007;0.004	T|T	0.03394|0.03394	-1.1041|-1.1041	4|9	.|0.11182	.|T	.|0.66	-1.0737|-1.0737	5.4627|5.4627	0.16626|0.16626	0.315:0.2571:0.4278:0.0|0.315:0.2571:0.4278:0.0	rs3950176;rs60629999;rs3950176|rs3950176;rs60629999;rs3950176	.|337;358;356;358	.|B0QYK4;B0QYK5;Q96A84;Q96A84-3	.|.;.;EMID1_HUMAN;.	R|Q	221|358;337;358	.|ENSP00000335481:R358Q;ENSP00000385414:R337Q;ENSP00000384452:R358Q	.|ENSP00000335481:R358Q	G|R	+|+	1|2	0|0	EMID1|EMID1	27960337|27960337	0.564000|0.564000	0.26602|0.26602	0.932000|0.932000	0.37286|0.37286	0.853000|0.853000	0.48598|0.48598	-0.446000|-0.446000	0.06837|0.06837	-1.014000|-1.014000	0.03379|0.03379	-0.797000|-0.797000	0.03246|0.03246	GGG|CGG	G|0.849;A|0.151	0.151	strong		0.607	EMID1-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321075.1	NM_133455	Missense_Mutation
OR8J1	219477	hgsc.bcm.edu	37	11	56128406	56128406	+	Missense_Mutation	SNP	A	A	G	rs62001032	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56128406A>G	ENST00000303039.3	+	1	716	c.684A>G	c.(682-684)atA>atG	p.I228M		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					TTTTAAAAATATGTTCATCAG	0.333													A|||	186	0.0371406	0.0061	0.0432	5008	,	,		20358	0.001		0.0905	False		,,,				2504	0.0573				p.I228M		Atlas-SNP	.											.	OR8J1	87	.	0			c.A684G						PASS	.	A	MET/ILE	56,4346	54.2+/-90.2	0,56,2145	105.0	103.0	104.0		684	-7.1	0.0	11	dbSNP_129	104	693,7897	170.1+/-221.3	32,629,3634	yes	missense	OR8J1	NM_001005205.2	10	32,685,5779	GG,GA,AA		8.0675,1.2721,5.7651	benign	228/317	56128406	749,12243	2201	4295	6496	SO:0001583	missense	219477	exon1			AAAAATATGTTCA	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.684A>G	11.37:g.56128406A>G	ENSP00000304060:p.Ile228Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	140	76	0.542857	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	37	CCDS31529.1	86	0.039377289377289376	5	0.01016260162601626	13	0.03591160220994475	0	0.0	68	0.08970976253298153	A	0.004	-2.313963	0.00235	0.012721	0.080675	ENSG00000172487	ENST00000303039	T	0.00241	8.46	3.9	-7.07	0.01563	GPCR, rhodopsin-like superfamily (1);	0.428210	0.24713	N	0.036203	T	0.00012	0.0000	N	0.17278	0.47	0.09310	N	1	P	0.38565	0.637	P	0.46339	0.513	T	0.41610	-0.9499	10	0.06891	T	0.86	.	10.4867	0.44726	0.1384:0.3514:0.5102:0.0	rs62001032	228	Q8NGP2	OR8J1_HUMAN	M	228	ENSP00000304060:I228M	ENSP00000304060:I228M	I	+	3	3	OR8J1	55884982	0.000000	0.05858	0.003000	0.11579	0.020000	0.10135	-4.819000	0.00182	-1.284000	0.02390	-1.303000	0.01326	ATA	A|0.949;G|0.051	0.051	strong		0.333	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
SAGE1	55511	hgsc.bcm.edu	37	X	134991078	134991078	+	Silent	SNP	A	A	G	rs5974570	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:134991078A>G	ENST00000370709.3	+	12	1497	c.1497A>G	c.(1495-1497)caA>caG	p.Q499Q	SAGE1_ENST00000324447.3_Silent_p.Q499Q|SAGE1_ENST00000537770.1_Intron|SAGE1_ENST00000535938.1_Silent_p.Q499Q			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	499						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					GCAAACCCCAAACTGATAAGG	0.443													a|||	611	0.161854	0.0673	0.1614	3775	,	,		15680	0.1012		0.2058	False		,,,				2504	0.1033				p.Q499Q		Atlas-SNP	.											.	SAGE1	160	.	0			c.A1497G						PASS	.	A		560,3275		31,427,71,1174,500	217.0	154.0	175.0		1497	-2.8	0.0	X	dbSNP_114	175	1754,4974		188,923,455,1317,1417	no	coding-synonymous	SAGE1	NM_018666.2		219,1350,526,2491,1917	GG,GA,G,AA,A		26.0702,14.6023,21.9067		499/905	134991078	2314,8249	2203	4300	6503	SO:0001819	synonymous_variant	55511	exon13			ACCCCAAACTGAT	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.1497A>G	X.37:g.134991078A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	155	14	0.0903226	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			A|0.806;G|0.194	0.194	strong		0.443	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
FAM161A	84140	hgsc.bcm.edu	37	2	62069358	62069358	+	Missense_Mutation	SNP	T	T	C	rs11125895	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:62069358T>C	ENST00000405894.3	-	2	422	c.321A>G	c.(319-321)atA>atG	p.I107M	FAM161A_ENST00000404929.1_Missense_Mutation_p.I107M	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	107			I -> M (in dbSNP:rs11125895). {ECO:0000269|PubMed:17974005}.		cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CCATAGTTTCTATGTGGGCAG	0.388													T|||	802	0.160144	0.1104	0.1787	5008	,	,		19735	0.1508		0.173	False		,,,				2504	0.2106				p.I107M		Atlas-SNP	.											.	FAM161A	200	.	0			c.A321G						PASS	.	T	MET/ILE,MET/ILE	466,3200		23,420,1390	93.0	85.0	88.0		321,321	1.7	0.3	2	dbSNP_120	88	1522,6640		153,1216,2712	yes	missense,missense	FAM161A	NM_001201543.1,NM_032180.2	10,10	176,1636,4102	CC,CT,TT		18.6474,12.7114,16.8076	benign,benign	107/717,107/661	62069358	1988,9840	1833	4081	5914	SO:0001583	missense	84140	exon2			AGTTTCTATGTGG		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.321A>G	2.37:g.62069358T>C	ENSP00000385893:p.Ile107Met	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	210	207	0.985714	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	332	0.152014652014652	44	0.08943089430894309	78	0.2154696132596685	85	0.1486013986013986	125	0.16490765171503957	T	10.85	1.468017	0.26335	0.127114	0.186474	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.66099	-0.19;-0.19	5.95	1.73	0.24493	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.53688	P	2.199999999996649E-5	B;B	0.16396	0.008;0.017	B;B	0.10450	0.002;0.005	T	0.10268	-1.0637	8	0.30854	T	0.27	-6.3985	7.8459	0.29424	0.0:0.5917:0.0:0.4083	rs11125895;rs17573015;rs52802415;rs59431884;rs11125895	107;107	Q3B820;Q3B820-3	F161A_HUMAN;.	M	107	ENSP00000385158:I107M;ENSP00000385893:I107M	ENSP00000385158:I107M	I	-	3	3	FAM161A	61922862	0.996000	0.38824	0.261000	0.24466	0.960000	0.62799	1.338000	0.33873	0.020000	0.15106	0.533000	0.62120	ATA	T|0.833;C|0.167	0.167	strong		0.388	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
TFB2M	64216	hgsc.bcm.edu	37	1	246714587	246714587	+	Silent	SNP	G	G	A	rs10754526	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:246714587G>A	ENST00000366514.4	-	5	908	c.723C>T	c.(721-723)ccC>ccT	p.P241P	TFB2M_ENST00000544618.1_3'UTR	NM_022366.2	NP_071761.1	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	241					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(1)|kidney(12)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)			CTGGATTTCCGGGATCTGCCA	0.318													G|||	2066	0.41254	0.4312	0.4063	5008	,	,		20072	0.3423		0.4702	False		,,,				2504	0.4049				p.P241P		Atlas-SNP	.											.	TFB2M	46	.	0			c.C723T						PASS	.	G		2049,2357	562.1+/-380.9	493,1063,647	69.0	72.0	71.0		723	-4.5	0.0	1	dbSNP_120	71	4096,4504	558.6+/-387.3	1012,2072,1216	no	coding-synonymous	TFB2M	NM_022366.2		1505,3135,1863	AA,AG,GG		47.6279,46.5048,47.2474		241/397	246714587	6145,6861	2203	4300	6503	SO:0001819	synonymous_variant	64216	exon5			ATTTCCGGGATCT	AK026835	CCDS1627.1	1q44	2008-02-05			ENSG00000162851	ENSG00000162851			18559	protein-coding gene	gene with protein product		607055					Standard	NM_022366		Approved	FLJ23182, FLJ22661, Hkp1	uc001ibn.3	Q9H5Q4	OTTHUMG00000040091	ENST00000366514.4:c.723C>T	1.37:g.246714587G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_022366	Q9H626	Silent	SNP	ENST00000366514.4	37	CCDS1627.1																																																																																			G|0.554;A|0.446	0.446	strong		0.318	TFB2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096673.1	NM_022366	
C19orf45	374877	hgsc.bcm.edu	37	19	7569282	7569282	+	Missense_Mutation	SNP	A	A	G	rs484870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7569282A>G	ENST00000361664.2	+	4	908	c.767A>G	c.(766-768)gAt>gGt	p.D256G	CTD-2207O23.12_ENST00000599312.1_5'Flank	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	256			D -> G (in dbSNP:rs484870). {ECO:0000269|PubMed:14702039}.							endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						AGGCCCCAGGATCTGCCTGAA	0.582													N|||	1745	0.348442	0.4992	0.4006	5008	,	,		15898	0.1736		0.3837	False		,,,				2504	0.2515				p.D256G		Atlas-SNP	.											.	C19orf45	36	.	0			c.A767G						PASS	.	G	GLY/ASP	2082,2324		498,1086,619	43.0	45.0	45.0		767	-1.8	0.2	19	dbSNP_83	45	3228,5372		602,2024,1674	yes	missense	C19orf45	NM_198534.2	94	1100,3110,2293	GG,GA,AA		37.5349,47.2537,40.8273	benign	256/506	7569282	5310,7696	2203	4300	6503	SO:0001583	missense	374877	exon4			CCCAGGATCTGCC	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.767A>G	19.37:g.7569282A>G	ENSP00000355241:p.Asp256Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	824	0.3772893772893773	257	0.5223577235772358	157	0.43370165745856354	111	0.19405594405594406	299	0.3944591029023747	N	0.029	-1.348313	0.01266	0.472537	0.375349	ENSG00000198723	ENST00000361664	T	0.13901	2.55	4.37	-1.82	0.07857	.	0.766431	0.11973	N	0.511599	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40327	-0.9569	9	0.02654	T	1	0.0022	4.487	0.11794	0.5052:0.0:0.336:0.1588	rs484870;rs57924778;rs484870	256	Q8NA69	CS045_HUMAN	G	256	ENSP00000355241:D256G	ENSP00000355241:D256G	D	+	2	0	C19orf45	7475282	0.026000	0.19158	0.242000	0.24170	0.232000	0.25224	0.063000	0.14410	-0.612000	0.05701	-0.273000	0.10243	GAT	A|0.620;G|0.380	0.380	strong		0.582	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
SMARCA4	6597	hgsc.bcm.edu	37	19	11098596	11098596	+	Missense_Mutation	SNP	T	T	C	rs140192268	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11098596T>C	ENST00000429416.3	+	7	1395	c.1114T>C	c.(1114-1116)Tac>Cac	p.Y372H	SMARCA4_ENST00000590574.1_Missense_Mutation_p.Y372H|SMARCA4_ENST00000358026.2_Missense_Mutation_p.Y372H|SMARCA4_ENST00000444061.3_Missense_Mutation_p.Y372H|SMARCA4_ENST00000344626.4_Missense_Mutation_p.Y372H|SMARCA4_ENST00000589677.1_Missense_Mutation_p.Y372H|SMARCA4_ENST00000541122.2_Missense_Mutation_p.Y372H|SMARCA4_ENST00000450717.3_Missense_Mutation_p.Y372H|SMARCA4_ENST00000413806.3_Missense_Mutation_p.Y372H	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	372					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GGAGCGCGAGTACAGGTGAGG	0.657			"""F, N, Mis"""		NSCLC								T|||	27	0.00539137	0.0	0.0115	5008	,	,		13036	0.0		0.0169	False		,,,				2504	0.002				p.Y372H		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.T1114C						PASS	.	T	HIS/TYR,HIS/TYR,HIS/TYR,HIS/TYR,HIS/TYR,HIS/TYR,HIS/TYR	12,4306		0,12,2147	22.0	27.0	25.0		1114,1114,1114,1114,1114,1114,1114	4.5	1.0	19	dbSNP_134	25	127,8231		0,127,4052	yes	missense,missense,missense,missense,missense,missense,missense	SMARCA4	NM_001128844.1,NM_001128845.1,NM_001128846.1,NM_001128847.1,NM_001128848.1,NM_001128849.1,NM_003072.3	83,83,83,83,83,83,83	0,139,6199	CC,CT,TT		1.5195,0.2779,1.0966	benign,benign,benign,benign,benign,benign,benign	372/1648,372/1618,372/1617,372/1615,372/1614,372/1680,372/1648	11098596	139,12537	2159	4179	6338	SO:0001583	missense	6597	exon6			CGCGAGTACAGGT	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.1114T>C	19.37:g.11098596T>C	ENSP00000395654:p.Tyr372His	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	154	68	0.441558	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	T	12.15	1.853053	0.32699	0.002779	0.015195	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.08;-2.08;-2.08;-2.08	4.49	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.69611	0.3130	L	0.38531	1.155	0.49483	D	0.99979	B;B;B;B;B;B;B	0.21225	0.04;0.04;0.04;0.053;0.038;0.04;0.04	B;B;B;B;B;B;B	0.26202	0.022;0.022;0.022;0.067;0.022;0.039;0.039	T	0.71573	-0.4552	10	0.20519	T	0.43	-27.0857	12.9367	0.58319	0.0:0.0:0.0:1.0	.	372;372;372;372;372;372;372	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	H	372	ENSP00000395654:Y372H;ENSP00000350720:Y372H;ENSP00000343896:Y372H;ENSP00000445036:Y372H;ENSP00000392837:Y372H;ENSP00000397783:Y372H;ENSP00000414727:Y372H	ENSP00000343896:Y372H	Y	+	1	0	SMARCA4	10959596	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	5.960000	0.70348	1.893000	0.54813	0.533000	0.62120	TAC	T|0.992;C|0.008	0.008	strong		0.657	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
OTOP2	92736	hgsc.bcm.edu	37	17	72927123	72927123	+	Missense_Mutation	SNP	G	G	T	rs6501741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72927123G>T	ENST00000580223.1	+	5	1423	c.1393G>T	c.(1393-1395)Ggg>Tgg	p.G465W	OTOP2_ENST00000331427.4_Missense_Mutation_p.G465W			Q7RTS6	OTOP2_HUMAN	otopetrin 2	465			G -> W (in dbSNP:rs6501741).			integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|prostate(4)|skin(1)|urinary_tract(2)	39	all_lung(278;0.172)|Lung NSC(278;0.207)					ACCCAACCCCGGGCTGGTTAG	0.622													g|||	2728	0.544728	0.2489	0.6571	5008	,	,		16297	0.5645		0.663	False		,,,				2504	0.7229				p.G465W		Atlas-SNP	.											.	OTOP2	81	.	0			c.G1393T						PASS	.	A	TRP/GLY	1422,2984	463.6+/-353.6	240,942,1021	79.0	76.0	77.0		1393	-2.2	0.0	17	dbSNP_116	77	5535,3065	660.6+/-401.8	1783,1969,548	yes	missense	OTOP2	NM_178160.2	184	2023,2911,1569	TT,TG,GG		35.6395,32.2742,46.5093	possibly-damaging	465/563	72927123	6957,6049	2203	4300	6503	SO:0001583	missense	92736	exon6			AACCCCGGGCTGG	BK000567	CCDS11708.1	17q25.3	2006-09-20				ENSG00000183034			19657	protein-coding gene	gene with protein product		607827				12651873	Standard	NM_178160		Approved		uc010wrp.2	Q7RTS6		ENST00000580223.1:c.1393G>T	17.37:g.72927123G>T	ENSP00000463837:p.Gly465Trp	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	144	141	0.979167	NM_178160		Missense_Mutation	SNP	ENST00000580223.1	37	CCDS11708.1	1180	0.5402930402930403	110	0.22357723577235772	220	0.6077348066298343	328	0.5734265734265734	522	0.6886543535620053	g	6.004	0.369093	0.11352	0.322742	0.643605	ENSG00000183034	ENST00000331427	T	0.11277	2.79	5.28	-2.23	0.06930	.	1.174570	0.06075	N	0.660876	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	D	0.63880	0.993	P	0.51229	0.663	T	0.38520	-0.9657	9	0.62326	D	0.03	-8.5625	7.2113	0.25935	0.4975:0.1202:0.3823:0.0	rs6501741;rs12951769;rs61117497;rs6501741	465	Q7RTS6	OTOP2_HUMAN	W	465	ENSP00000332528:G465W	ENSP00000332528:G465W	G	+	1	0	OTOP2	70438718	0.000000	0.05858	0.040000	0.18447	0.004000	0.04260	-0.038000	0.12144	-0.515000	0.06479	-2.867000	0.00100	GGG	A|0.001;G|0.477;T|0.523	0.523	strong		0.622	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160	
PCNT	5116	hgsc.bcm.edu	37	21	47805773	47805773	+	Silent	SNP	T	T	C	rs61735805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47805773T>C	ENST00000359568.5	+	17	3446	c.3339T>C	c.(3337-3339)agT>agC	p.S1113S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1113					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TATCCTTAAGTCACGAGATAG	0.493													T|||	78	0.0155751	0.0008	0.0216	5008	,	,		20050	0.003		0.0398	False		,,,				2504	0.0194				p.S1113S		Atlas-SNP	.											.	PCNT	283	.	0			c.T3339C						PASS	.	T		36,4370	41.6+/-74.8	0,36,2167	124.0	130.0	128.0		3339	-5.8	0.0	21	dbSNP_129	128	383,8217	125.0+/-183.6	10,363,3927	no	coding-synonymous	PCNT	NM_006031.5		10,399,6094	CC,CT,TT		4.4535,0.8171,3.2216		1113/3337	47805773	419,12587	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon17			CTTAAGTCACGAG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.3339T>C	21.37:g.47805773T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	118	49	0.415254	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			T|0.972;C|0.028	0.028	strong		0.493	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
C8orf44	56260	hgsc.bcm.edu	37	8	67592152	67592152	+	Missense_Mutation	SNP	T	T	C	rs1057463	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:67592152T>C	ENST00000519561.1	+	3	594	c.443T>C	c.(442-444)tTc>tCc	p.F148S	C8orf44-SGK3_ENST00000520044.1_3'UTR|C8orf44_ENST00000518860.1_3'UTR|C8orf44_ENST00000390159.3_Missense_Mutation_p.F148S|C8orf44-SGK3_ENST00000519289.1_5'UTR	NM_019607.2	NP_062553.1	Q96CB5	CH044_HUMAN	chromosome 8 open reading frame 44	148			F -> S (in dbSNP:rs1057463). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)				endometrium(1)|kidney(1)|lung(2)	4	Breast(64;0.186)		Epithelial(68;0.000959)|OV - Ovarian serous cystadenocarcinoma(28;0.00318)|all cancers(69;0.00363)|BRCA - Breast invasive adenocarcinoma(89;0.149)			TCCAAAGGCTTCTGGAGTCTT	0.463													T|||	1094	0.21845	0.0514	0.2291	5008	,	,		17882	0.2401		0.2922	False		,,,				2504	0.3384				p.F148S		Atlas-SNP	.											.	C8orf44	18	.	0			c.T443C						PASS	.	T	SER/PHE,	403,4003	194.0+/-219.0	25,353,1825	47.0	50.0	49.0		443,	2.8	0.0	8	dbSNP_86	49	2536,6064	411.1+/-350.4	388,1760,2152	yes	missense,utr-5	C8orf44,C8orf44-SGK3	NM_019607.2,NM_001204173.1	155,	413,2113,3977	CC,CT,TT		29.4884,9.1466,22.5973	possibly-damaging,	148/160,	67592152	2939,10067	2203	4300	6503	SO:0001583	missense	56260	exon3			AAGGCTTCTGGAG	AK002129	CCDS6193.1	8q13.1	2012-05-16		2005-08-09	ENSG00000213865	ENSG00000213865			25646	protein-coding gene	gene with protein product						12477932	Standard	NM_019607		Approved	FLJ11267	uc003xwo.2	Q96CB5	OTTHUMG00000164562	ENST00000519561.1:c.443T>C	8.37:g.67592152T>C	ENSP00000428002:p.Phe148Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_019607	Q9NUM6	Missense_Mutation	SNP	ENST00000519561.1	37	CCDS6193.1	465	0.2129120879120879	26	0.052845528455284556	82	0.2265193370165746	131	0.229020979020979	226	0.29815303430079154	T	14.66	2.602370	0.46423	0.091466	0.294884	ENSG00000213865	ENST00000519561;ENST00000390159	T;T	0.38722	1.12;1.12	3.99	2.84	0.33178	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.40332	0.713	P	0.46629	0.522	T	0.30297	-0.9983	8	0.18276	T	0.48	.	6.239	0.20778	0.0:0.1126:0.0:0.8874	rs1057463;rs3198053;rs17845417;rs17858283;rs60902427;rs1057463	148	Q96CB5	CH044_HUMAN	S	148	ENSP00000428002:F148S;ENSP00000375087:F148S	ENSP00000375087:F148S	F	+	2	0	C8orf44	67754706	0.004000	0.15560	0.020000	0.16555	0.089000	0.18198	1.327000	0.33746	0.893000	0.36288	0.460000	0.39030	TTC	T|0.781;C|0.219	0.219	strong		0.463	C8orf44-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379242.2	NM_019607	
ZFAT	57623	hgsc.bcm.edu	37	8	135649848	135649848	+	Missense_Mutation	SNP	G	G	A	rs12541381	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:135649848G>A	ENST00000377838.3	-	3	478	c.304C>T	c.(304-306)Ccg>Tcg	p.P102S	ZFAT_ENST00000520214.1_Missense_Mutation_p.P90S|ZFAT_ENST00000520356.1_Missense_Mutation_p.P90S|ZFAT_ENST00000523399.1_Missense_Mutation_p.P102S|ZFAT_ENST00000520727.1_Missense_Mutation_p.P90S|ZFAT_ENST00000429442.2_Missense_Mutation_p.P90S	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	102			P -> S (in dbSNP:rs12541381). {ECO:0000269|PubMed:15294872}.		hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			GGAGCCAGCGGGCTGTCCTCA	0.587													G|||	1083	0.216254	0.0628	0.2219	5008	,	,		20089	0.3075		0.2634	False		,,,				2504	0.2771				p.P102S		Atlas-SNP	.											.	ZFAT	265	.	0			c.C304T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO	439,3915		23,393,1761	84.0	89.0	87.0		268,268,304,268,304	1.1	0.0	8	dbSNP_120	87	2113,6437		256,1601,2418	yes	missense,missense,missense,missense,missense	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	74,74,74,74,74	279,1994,4179	AA,AG,GG		24.7135,10.0827,19.7768	benign,benign,benign,benign,benign	90/1232,90/1232,102/1182,90/1146,102/1244	135649848	2552,10352	2177	4275	6452	SO:0001583	missense	57623	exon3			CCAGCGGGCTGTC	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.304C>T	8.37:g.135649848G>A	ENSP00000367069:p.Pro102Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_001174157	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	516	0.23626373626373626	32	0.06504065040650407	93	0.2569060773480663	191	0.3339160839160839	200	0.2638522427440633	G	0.009	-1.839731	0.00573	0.100827	0.247135	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399;ENST00000398946;ENST00000522257;ENST00000518191	T;T;T;T;T;T;T;T	0.41400	3.12;3.05;3.06;3.05;3.05;2.98;1.0;1.57	5.15	1.06	0.20224	.	0.475715	0.20179	N	0.097568	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B	0.17038	0.008;0.02;0.02;0.008	B;B;B;B	0.17433	0.011;0.016;0.018;0.016	T	0.37663	-0.9696	9	0.49607	T	0.09	-2.0869	5.6357	0.17536	0.0725:0.2591:0.5345:0.1339	rs12541381;rs60408772;rs12541381	102;90;90;102	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	S	90;90;90;102;90;90;102;90;40;90	ENSP00000427879:P90S;ENSP00000427831:P90S;ENSP00000394501:P90S;ENSP00000367069:P102S;ENSP00000428483:P90S;ENSP00000429091:P102S;ENSP00000429983:P40S;ENSP00000428192:P90S	ENSP00000326997:P90S	P	-	1	0	ZFAT	135719030	0.159000	0.22864	0.000000	0.03702	0.003000	0.03518	2.410000	0.44592	-0.088000	0.12506	0.561000	0.74099	CCG	G|0.770;A|0.230	0.230	strong		0.587	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
LCN10	414332	hgsc.bcm.edu	37	9	139634495	139634495	+	Nonsense_Mutation	SNP	G	G	A	rs9886752	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139634495G>A	ENST00000474369.1	-	4	441	c.442C>T	c.(442-444)Cag>Tag	p.Q148*	LCN6_ENST00000480584.1_5'Flank|LCN6_ENST00000435202.1_3'UTR|LCN10_ENST00000497771.1_Nonsense_Mutation_p.Q161*|LCN10_ENST00000527229.1_Nonsense_Mutation_p.Q125*			Q6JVE6	LCN10_HUMAN	lipocalin 10	148					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)		GAAACATTCTGCCTATCTGAG	0.542													g|||	998	0.199281	0.1808	0.2421	5008	,	,		19016	0.2698		0.1491	False		,,,				2504	0.1728				p.Q161X		Atlas-SNP	.											.	LCN10	21	.	0			c.C481T						PASS	.		stop/GLN	795,3607		82,631,1488	71.0	57.0	62.0		481	1.7	0.1	9	dbSNP_119	62	1317,7273		105,1107,3083	yes	stop-gained	LCN10	NM_001001712.2		187,1738,4571	AA,AG,GG		15.3318,18.06,16.2562		161/201	139634495	2112,10880	2201	4295	6496	SO:0001587	stop_gained	414332	exon5			CATTCTGCCTATC	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.442C>T	9.37:g.139634495G>A	ENSP00000420564:p.Gln148*	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_001001712	A2RUU3|B0QZ79	Nonsense_Mutation	SNP	ENST00000474369.1	37	CCDS35182.2	438	0.20054945054945056	99	0.20121951219512196	77	0.212707182320442	151	0.263986013986014	111	0.14643799472295516	g	11.56	1.674100	0.29693	0.1806	0.153318	ENSG00000187922	ENST00000527229;ENST00000497771;ENST00000474369	.	.	.	2.66	1.7	0.24286	.	0.672061	0.12237	N	0.486894	.	.	.	.	.	.	0.09310	P	0.999999999541476	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	7.2424	0.26104	0.0:0.2777:0.7222:0.0	rs9886752;rs61671998;rs9886752	.	.	.	X	125;161;148	.	ENSP00000420564:Q148X	Q	-	1	0	LCN10	138754316	0.004000	0.15560	0.055000	0.19348	0.030000	0.12068	1.072000	0.30678	0.657000	0.30906	0.539000	0.68188	CAG	G|0.818;A|0.182	0.182	strong		0.542	LCN10-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318062.2	NM_001001712	
AKAP6	9472	hgsc.bcm.edu	37	14	33293122	33293122	+	Missense_Mutation	SNP	A	A	G	rs1051695	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:33293122A>G	ENST00000280979.4	+	13	6273	c.6103A>G	c.(6103-6105)Aac>Gac	p.N2035D	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2035			N -> D (in dbSNP:rs1051695).		action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TTCTATCAGCAACATTTCCTG	0.413													g|||	3557	0.710264	0.9145	0.6772	5008	,	,		21332	0.6716		0.5308	False		,,,				2504	0.682				p.N2035D	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.A6103G						PASS	.	C	ASP/ASN	3782,624	265.3+/-266.6	1628,526,49	86.0	82.0	83.0		6103	2.2	0.0	14	dbSNP_86	83	4534,4066	558.2+/-387.2	1156,2222,922	yes	missense	AKAP6	NM_004274.4	23	2784,2748,971	GG,GA,AA		47.2791,14.1625,36.0603	benign	2035/2320	33293122	8316,4690	2203	4300	6503	SO:0001583	missense	9472	exon13			ATCAGCAACATTT	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6103A>G	14.37:g.33293122A>G	ENSP00000280979:p.Asn2035Asp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	73	25	0.342466	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	1513	0.6927655677655677	450	0.9146341463414634	243	0.6712707182320442	415	0.7255244755244755	405	0.5343007915567283	g	0.115	-1.133739	0.01756	0.858375	0.527209	ENSG00000151320	ENST00000280979	T	0.04809	3.55	5.96	2.16	0.27623	.	0.699277	0.14515	N	0.314833	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09465	-1.0673	9	0.07644	T	0.81	-0.4192	5.7092	0.17925	0.3465:0.1253:0.5282:0.0	rs1051695;rs17443079;rs52806355;rs60026842;rs1051695	2035	Q13023	AKAP6_HUMAN	D	2035	ENSP00000280979:N2035D	ENSP00000280979:N2035D	N	+	1	0	AKAP6	32362873	0.000000	0.05858	0.003000	0.11579	0.885000	0.51271	-0.005000	0.12855	-0.052000	0.13311	-1.538000	0.00913	AAC	A|0.327;G|0.673	0.673	strong		0.413	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
APOBR	55911	hgsc.bcm.edu	37	16	28507644	28507644	+	Missense_Mutation	SNP	C	C	G	rs180743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28507644C>G	ENST00000431282.1	+	3	1265	c.1255C>G	c.(1255-1257)Ccc>Gcc	p.P419A	CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000328423.5_Missense_Mutation_p.P419A|APOBR_ENST00000564831.1_Missense_Mutation_p.P428A|CLN3_ENST00000569430.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	419	Glu-rich.		P -> A (in dbSNP:rs180743). {ECO:0000269|PubMed:10852956, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15830122}.		cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)	p.P419A(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						CCCCAAACAGCCCCAGGTCCT	0.612													G|||	1508	0.301118	0.4107	0.4308	5008	,	,		17646	0.1042		0.3479	False		,,,				2504	0.2157				p.P428A		Atlas-SNP	.											APOBR,NS,carcinoma,0,1	APOBR	89	1	1	Substitution - Missense(1)	stomach(1)	c.C1282G						PASS	.	G	ALA/PRO	1629,2351		356,917,717	37.0	42.0	40.0		1255	0.5	0.1	16	dbSNP_79	40	3245,5083		660,1925,1579	yes	missense	APOBR	NM_018690.3	27	1016,2842,2296	GG,GC,CC		38.9649,40.9296,39.6003	benign	419/1089	28507644	4874,7434	1990	4164	6154	SO:0001583	missense	55911	exon2			AAACAGCCCCAGG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1255C>G	16.37:g.28507644C>G	ENSP00000416094:p.Pro419Ala	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	37		622	0.2847985347985348	173	0.3516260162601626	125	0.3453038674033149	63	0.11013986013986014	261	0.34432717678100266	G	9.659	1.143564	0.21205	0.409296	0.389649	ENSG00000184730	ENST00000328423;ENST00000431282	T;T	0.41758	0.99;0.99	4.07	0.489	0.16854	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.43147	-0.9409	5	0.06891	T	0.86	0.1921	4.273	0.10796	0.2827:0.3855:0.3317:0.0	rs180743;rs181201;rs180743	.	.	.	A	419	ENSP00000327669:P419A;ENSP00000416094:P419A	ENSP00000327669:P419A	P	+	1	0	APOBR	28415145	0.000000	0.05858	0.097000	0.21041	0.649000	0.38597	-0.438000	0.06905	-0.054000	0.13266	-0.291000	0.09656	CCC	C|0.698;G|0.302	0.302	strong		0.612	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
LHFPL1	340596	hgsc.bcm.edu	37	X	111914244	111914244	+	Silent	SNP	A	A	G	rs7064462	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:111914244A>G	ENST00000371968.3	-	2	614	c.375T>C	c.(373-375)ttT>ttC	p.F125F	LHFPL1_ENST00000536453.1_Silent_p.F125F|LHFPL1_ENST00000478229.1_Intron	NM_178175.3	NP_835469.1	Q86WI0	LHPL1_HUMAN	lipoma HMGIC fusion partner-like 1	125						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)	13						TACCTCCAACAAACTGCGCTG	0.572													G|||	871	0.230728	0.5477	0.0893	3775	,	,		14285	0.0		0.0716	False		,,,				2504	0.0133				p.F125F		Atlas-SNP	.											.	LHFPL1	28	.	0			c.T375C						PASS	.	G		2395,1440		655,732,353,245,218	82.0	62.0	68.0		375	-8.0	0.2	X	dbSNP_116	68	522,6206		11,348,152,2069,1720	no	coding-synonymous	LHFPL1	NM_178175.3		666,1080,505,2314,1938	GG,GA,G,AA,A		7.7586,37.5489,27.6153		125/221	111914244	2917,7646	2203	4300	6503	SO:0001819	synonymous_variant	340596	exon2			TCCAACAAACTGC	AY217350	CCDS14562.1	Xq23	2008-02-05			ENSG00000182508	ENSG00000182508			6587	protein-coding gene	gene with protein product		300566				10329012	Standard	NM_178175		Approved		uc004epq.3	Q86WI0	OTTHUMG00000022214	ENST00000371968.3:c.375T>C	X.37:g.111914244A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	75	73	0.973333	NM_178175	A8K1N1|Q496M9|Q496N0|Q6UXU2	Silent	SNP	ENST00000371968.3	37	CCDS14562.1																																																																																			A|0.714;0|0.003	.	strong		0.572	LHFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057947.1	NM_178175	
OR8J3	81168	hgsc.bcm.edu	37	11	55904331	55904331	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55904331C>T	ENST00000301529.1	-	1	863	c.864G>A	c.(862-864)ttG>ttA	p.L288L		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	288						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					GGCTGTAGATCAAGGGATTCA	0.358																																					p.L288L		Atlas-SNP	.											OR8J3,right_upper_lobe,carcinoma,0,1	OR8J3	112	1	0			c.G864A						scavenged	.						117.0	115.0	116.0					11																	55904331		2201	4296	6497	SO:0001819	synonymous_variant	81168	exon1			GTAGATCAAGGGA		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.864G>A	11.37:g.55904331C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	218	4	0.0183486	NM_001004064	Q6IFB6|Q96RC2	Silent	SNP	ENST00000301529.1	37	CCDS31520.1																																																																																			.	.	none		0.358	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
CNTN3	5067	hgsc.bcm.edu	37	3	74334458	74334458	+	Missense_Mutation	SNP	G	G	A	rs141921900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:74334458G>A	ENST00000263665.6	-	19	2729	c.2702C>T	c.(2701-2703)aCg>aTg	p.T901M		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	901	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		ATACTTACGCGTTTTCTTGGT	0.438													G|||	18	0.00359425	0.0	0.0043	5008	,	,		17726	0.0		0.0139	False		,,,				2504	0.001				p.T901M		Atlas-SNP	.											CNTN3,NS,lymphoid_neoplasm,+1,1	CNTN3	174	1	0			c.C2702T						PASS	.	G	MET/THR	7,4399	12.9+/-30.5	0,7,2196	116.0	124.0	121.0		2702	2.2	0.5	3	dbSNP_134	121	97,8503	54.4+/-115.2	1,95,4204	yes	missense	CNTN3	NM_020872.1	81	1,102,6400	AA,AG,GG		1.1279,0.1589,0.7996	benign	901/1029	74334458	104,12902	2203	4300	6503	SO:0001583	missense	5067	exon19			TTACGCGTTTTCT	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.2702C>T	3.37:g.74334458G>A	ENSP00000263665:p.Thr901Met	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	11.68	1.709735	0.30322	0.001589	0.011279	ENSG00000113805	ENST00000263665	T	0.54675	0.56	5.4	2.15	0.27550	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.290390	0.38720	N	0.001587	T	0.27098	0.0664	N	0.16656	0.425	0.34827	D	0.73933	B	0.11235	0.004	B	0.16289	0.015	T	0.38866	-0.9641	10	0.62326	D	0.03	.	10.8289	0.46649	0.2572:0.0:0.7428:0.0	.	901	Q9P232	CNTN3_HUMAN	M	901	ENSP00000263665:T901M	ENSP00000263665:T901M	T	-	2	0	CNTN3	74417148	1.000000	0.71417	0.483000	0.27378	0.537000	0.34900	4.561000	0.60809	0.762000	0.33152	-0.126000	0.14955	ACG	G|0.995;A|0.005	0.005	strong		0.438	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
MST1L	11223	hgsc.bcm.edu	37	1	17083872	17083872	+	RNA	SNP	G	G	A	rs61635893		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17083872G>A	ENST00000455405.2	-	0	716							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.P642L(1)									GCAGGCAAGTGGGCCCCCGTA	0.562																																					p.P642L		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	endometrium(1)	c.C1925T						scavenged	.																																					11223	exon15			GCAAGTGGGCCCC	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17083872G>A		Somatic	412	5	0.0121359		WXS	Illumina HiSeq	Phase_I	352	62	0.176136	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	13.44	2.237181	0.39498	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41823	D	0.000805	T	0.66197	0.2765	.	.	.	.	.	.	D;D	0.89917	0.999;1.0	D;D	0.97110	0.989;1.0	T	0.72117	-0.4387	6	0.87932	D	0	.	6.7402	0.23431	2.0E-4:0.0:0.9998:0.0	rs61635893	642;668	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	L	642;668	.	ENSP00000439273:P642L	P	-	2	0	MST1P9	16956459	1.000000	0.71417	0.997000	0.53966	0.000000	0.00434	5.900000	0.69853	0.502000	0.28037	0.000000	0.15137	CCA	.	.	weak		0.562	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
PARP4	143	hgsc.bcm.edu	37	13	25033200	25033200	+	Silent	SNP	T	T	A	rs1130941	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25033200T>A	ENST00000381989.3	-	20	2511	c.2406A>T	c.(2404-2406)acA>acT	p.T802T	PARP4_ENST00000480576.1_5'UTR	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	802					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCAGTTCATGTGTATCACTGA	0.333													t|||	454	0.090655	0.1702	0.072	5008	,	,		18224	0.0317		0.0934	False		,,,				2504	0.0542				p.T802T		Atlas-SNP	.											.	PARP4	142	.	0			c.A2406T						PASS	.	T		701,3699	291.3+/-281.4	58,585,1557	93.0	91.0	91.0		2406	2.0	1.0	13	dbSNP_86	91	994,7606	214.2+/-253.9	68,858,3374	no	coding-synonymous	PARP4	NM_006437.3		126,1443,4931	AA,AT,TT		11.5581,15.9318,13.0385		802/1725	25033200	1695,11305	2200	4300	6500	SO:0001819	synonymous_variant	143	exon20			TTCATGTGTATCA	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2406A>T	13.37:g.25033200T>A		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	282	281	0.996454	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			T|0.879;A|0.121	0.121	strong		0.333	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
NAV2	89797	hgsc.bcm.edu	37	11	20065673	20065673	+	Missense_Mutation	SNP	G	G	T	rs3802799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:20065673G>T	ENST00000396087.3	+	14	3222	c.3123G>T	c.(3121-3123)gaG>gaT	p.E1041D	NAV2-AS2_ENST00000533767.1_RNA|NAV2_ENST00000349880.4_Missense_Mutation_p.E1018D|NAV2_ENST00000527559.2_Missense_Mutation_p.E970D|NAV2_ENST00000311043.8_Missense_Mutation_p.E104D|NAV2_ENST00000360655.4_Missense_Mutation_p.E954D|NAV2_ENST00000540292.1_Missense_Mutation_p.E972D|NAV2_ENST00000396085.1_Missense_Mutation_p.E1018D|NAV2_ENST00000533917.1_Missense_Mutation_p.E104D	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1041			E -> D (in dbSNP:rs3802799). {ECO:0000269|PubMed:14702039}.		glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TGTCTGACGAGTCCGACAAAA	0.547													G|||	1354	0.270367	0.0242	0.2709	5008	,	,		17876	0.4504		0.2227	False		,,,				2504	0.4663				p.E1041D		Atlas-SNP	.											.	NAV2	255	.	0			c.G3123T						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	238,4168	140.8+/-176.2	9,220,1974	98.0	87.0	91.0		2862,312,3054,3054	4.5	1.0	11	dbSNP_107	91	1683,6917	309.6+/-309.4	172,1339,2789	yes	missense,missense,missense,missense	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	45,45,45,45	181,1559,4763	TT,TG,GG		19.5698,5.4017,14.7701	probably-damaging,probably-damaging,probably-damaging,probably-damaging	954/2366,104/1494,1018/2430,1018/2433	20065673	1921,11085	2203	4300	6503	SO:0001583	missense	89797	exon14			TGACGAGTCCGAC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.3123G>T	11.37:g.20065673G>T	ENSP00000379396:p.Glu1041Asp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	569	0.26053113553113555	11	0.022357723577235773	103	0.2845303867403315	280	0.48951048951048953	175	0.23087071240105542	G	14.05	2.420641	0.42918	0.054017	0.195698	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000525322;ENST00000530408;ENST00000311043;ENST00000536595	T;T;T;T;T;T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68	5.51	4.5	0.54988	.	0.000000	0.64402	D	0.000015	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.99999173364	D;D;D;B;D	0.76494	0.999;0.996;0.997;0.13;0.999	D;D;D;B;D	0.79784	0.99;0.987;0.99;0.185;0.993	T	0.46233	-0.9206	8	.	.	.	.	10.7967	0.46464	0.2137:0.0:0.7863:0.0	rs3802799;rs52837716;rs57731346;rs3802799	1041;104;104;1018;954	Q8IVL1;Q8IVL1-5;E9PNV5;Q8IVL1-3;Q8IVL1-4	NAV2_HUMAN;.;.;.;.	D	954;1018;1018;1041;970;972;104;104;104;104;104	ENSP00000353871:E954D;ENSP00000379394:E1018D;ENSP00000309577:E1018D;ENSP00000379396:E1041D;ENSP00000435395:E970D;ENSP00000443489:E972D;ENSP00000437316:E104D;ENSP00000437136:E104D;ENSP00000431276:E104D;ENSP00000312169:E104D	.	E	+	3	2	NAV2	20022249	1.000000	0.71417	0.994000	0.49952	0.672000	0.39443	2.664000	0.46783	1.169000	0.42739	0.655000	0.94253	GAG	G|0.806;T|0.194	0.194	strong		0.547	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
RAPSN	5913	hgsc.bcm.edu	37	11	47469439	47469439	+	Silent	SNP	A	A	G	rs7111873	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:47469439A>G	ENST00000298854.2	-	2	669	c.456T>C	c.(454-456)taT>taC	p.Y152Y	RAPSN_ENST00000352508.3_Silent_p.Y152Y|RAPSN_ENST00000529341.1_Silent_p.Y152Y|RAPSN_ENST00000524487.1_Silent_p.Y152Y	NM_005055.4	NP_005046.2	Q13702	RAPSN_HUMAN	receptor-associated protein of the synapse	152					positive regulation of neuron apoptotic process (GO:0043525)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)	acetylcholine receptor binding (GO:0033130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(6)|ovary(2)	12						TGTTGTGGGCATAGCGCAGGG	0.647													G|||	3133	0.625599	0.3472	0.6902	5008	,	,		21049	0.6587		0.7068	False		,,,				2504	0.8384				p.Y152Y		Atlas-SNP	.											.	RAPSN	27	.	0			c.T456C						PASS	.	G	,	1879,2523	621.2+/-393.7	416,1047,738	46.0	37.0	40.0		456,456	-6.8	0.8	11	dbSNP_116	40	6180,2414	393.4+/-344.3	2225,1730,342	no	coding-synonymous,coding-synonymous	RAPSN	NM_005055.4,NM_032645.4	,	2641,2777,1080	GG,GA,AA		28.0894,42.6851,37.9886	,	152/413,152/354	47469439	8059,4937	2201	4297	6498	SO:0001819	synonymous_variant	5913	exon2			GTGGGCATAGCGC		CCDS7936.1, CCDS7937.1	11p11.2	2009-04-28	2007-02-23		ENSG00000165917	ENSG00000165917		"""RING-type (C3HC4) zinc fingers"""	9863	protein-coding gene	gene with protein product	"""rapsyn"""	601592	"""receptor-associated protein of the synapse, 43kD"""			8812503	Standard	NM_005055		Approved	RNF205, CMS1D, CMS1E	uc001nfi.2	Q13702	OTTHUMG00000166891	ENST00000298854.2:c.456T>C	11.37:g.47469439A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_032645	Q8TDF3|Q9BTD9	Silent	SNP	ENST00000298854.2	37	CCDS7936.1																																																																																			A|0.390;G|0.610	0.610	strong		0.647	RAPSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391726.1		
PTPN13	5783	hgsc.bcm.edu	37	4	87690998	87690998	+	Missense_Mutation	SNP	A	A	G	rs2230600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:87690998A>G	ENST00000411767.2	+	29	4629	c.4566A>G	c.(4564-4566)atA>atG	p.I1522M	PTPN13_ENST00000316707.6_Missense_Mutation_p.I1331M|PTPN13_ENST00000427191.2_Missense_Mutation_p.I1503M|PTPN13_ENST00000436978.1_Missense_Mutation_p.I1527M|PTPN13_ENST00000511467.1_Missense_Mutation_p.I1527M			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1522	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.		I -> M (in dbSNP:rs2230600). {ECO:0000269|PubMed:12436199}.		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.I1527M(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		ATAATCTTATACCGGAGCAAA	0.333													A|||	794	0.158546	0.0189	0.2277	5008	,	,		16772	0.3155		0.159	False		,,,				2504	0.136				p.I1527M		Atlas-SNP	.											PTPN13,NS,carcinoma,+1,2	PTPN13	203	2	1	Substitution - Missense(1)	skin(1)	c.A4581G						PASS	.	A	MET/ILE,MET/ILE,MET/ILE,MET/ILE	127,3519		2,123,1698	74.0	72.0	73.0		4509,4566,3993,4581	3.1	1.0	4	dbSNP_98	73	1331,6829		106,1119,2855	yes	missense,missense,missense,missense	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	10,10,10,10	108,1242,4553	GG,GA,AA		16.3113,3.4833,12.3497	benign,benign,benign,benign	1503/2467,1522/2486,1331/2295,1527/2491	87690998	1458,10348	1823	4080	5903	SO:0001583	missense	5783	exon29			TCTTATACCGGAG		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4566A>G	4.37:g.87690998A>G	ENSP00000407249:p.Ile1522Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	124	122	0.983871	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	404	0.184981684981685	10	0.02032520325203252	87	0.24033149171270718	187	0.3269230769230769	120	0.158311345646438	A	11.38	1.622600	0.28889	0.034833	0.163113	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.27402	1.67;1.67;1.67;1.67;1.67	5.74	3.14	0.36123	PDZ/DHR/GLGF (4);	0.501869	0.17902	N	0.158160	T	0.00012	0.0000	L	0.31476	0.935	0.49582	P	1.9800000000003148E-4	B;B;B;B	0.32526	0.374;0.076;0.244;0.134	B;B;B;B	0.39617	0.277;0.121;0.305;0.121	T	0.43130	-0.9410	9	0.34782	T	0.22	.	2.036	0.03540	0.3385:0.1126:0.0836:0.4653	rs2230600;rs2302682;rs10516782;rs17420945;rs56629540;rs61541413;rs2230600	1331;1503;1522;1527	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	M	1503;1527;1331;1522;1527;1471	ENSP00000408368:I1503M;ENSP00000394794:I1527M;ENSP00000322675:I1331M;ENSP00000407249:I1522M;ENSP00000426626:I1527M	ENSP00000322675:I1331M	I	+	3	3	PTPN13	87910022	0.233000	0.23772	0.952000	0.39060	0.992000	0.81027	0.147000	0.16202	0.976000	0.38417	0.533000	0.62120	ATA	A|0.797;G|0.203	0.203	strong		0.333	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
MT-CO3	4514	hgsc.bcm.edu	37	M	9698	9698	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:9698T>C	ENST00000362079.2	+	1	492	c.492T>C	c.(490-492)ctT>ctC	p.L164L	MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-ND4_ENST00000361381.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TS1_ENST00000387416.2_RNA			P00414	COX3_HUMAN	mitochondrially encoded cytochrome c oxidase III	164					aerobic electron transport chain (GO:0019646)|cellular metabolic process (GO:0044237)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(10)|kidney(14)|lung(1)|urinary_tract(1)	27						CAAGCACTGCTTATTACAATT	0.423																																					p.L164L		Atlas-SNP	.											.	.	.	.	0			c.T492C						PASS	.																																			SO:0001819	synonymous_variant	5742	exon1			ACTGCTTATTACA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198938	ENSG00000198938		"""Mitochondrial respiratory chain complex / Complex IV"""	7422	protein-coding gene	gene with protein product		516050	"""cytochrome c oxidase III"""	MTCO3			Standard			Approved	COX3, COIII, CO3		P00414		ENST00000362079.2:c.492T>C	M.37:g.9698T>C		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	ENST00000362079	Q14Y83	Silent	SNP	ENST00000362079.2	37																																																																																				.	.	none		0.423	MT-CO3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024032	
EVC	2121	hgsc.bcm.edu	37	4	5749904	5749904	+	Silent	SNP	T	T	C	rs4688963	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:5749904T>C	ENST00000264956.6	+	8	1153	c.969T>C	c.(967-969)aaT>aaC	p.N323N	EVC_ENST00000509451.1_Silent_p.N323N|EVC_ENST00000382674.2_Silent_p.N323N	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	323					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				AGATGGCAAATATCCAGCACT	0.463													C|||	2361	0.471446	0.4879	0.3098	5008	,	,		20183	0.6171		0.3569	False		,,,				2504	0.5317				p.N323N		Atlas-SNP	.											.	EVC	90	.	0			c.T969C						PASS	.	C		2066,2340	608.3+/-391.1	480,1106,617	112.0	109.0	110.0		969	3.0	1.0	4	dbSNP_111	110	3210,5390	653.2+/-401.0	596,2018,1686	no	coding-synonymous	EVC	NM_153717.2		1076,3124,2303	CC,CT,TT		37.3256,46.8906,40.5659		323/993	5749904	5276,7730	2203	4300	6503	SO:0001819	synonymous_variant	2121	exon8			GGCAAATATCCAG	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.969T>C	4.37:g.5749904T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	118	68	0.576271	NM_153717		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			T|0.559;C|0.441	0.441	strong		0.463	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
SLCO1B3	28234	hgsc.bcm.edu	37	12	21011480	21011480	+	Missense_Mutation	SNP	T	T	G	rs4149117	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:21011480T>G	ENST00000381545.3	+	5	553	c.334T>G	c.(334-336)Tct>Gct	p.S112A	LST3_ENST00000540229.1_Missense_Mutation_p.S112A|SLCO1B3_ENST00000553473.1_Missense_Mutation_p.S112A|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.S112A|LST3_ENST00000381541.3_Missense_Mutation_p.S112A|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.S112A|SLCO1B3_ENST00000545880.1_3'UTR	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	112			S -> A (in dbSNP:rs4149117).		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TATTTTGACATCTTTACCACA	0.328													.|||	3518	0.702476	0.3563	0.8372	5008	,	,		14932	0.6974		0.8648	False		,,,				2504	0.9131				p.S112A		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.T334G						PASS	.	G	ALA/SER	1974,2432	618.1+/-393.1	466,1042,695	167.0	151.0	157.0		334	4.0	1.0	12	dbSNP_110	157	7427,1171	238.1+/-269.7	3210,1007,82	yes	missense	SLCO1B3	NM_019844.2	99	3676,2049,777	GG,GT,TT		13.6194,44.8025,27.7069	benign	112/703	21011480	9401,3603	2203	4299	6502	SO:0001583	missense	28234	exon5			TTGACATCTTTAC		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.334T>G	12.37:g.21011480T>G	ENSP00000370956:p.Ser112Ala	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	164	163	0.993902	NM_019844	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	37	CCDS8684.1	1549	0.7092490842490843	185	0.37601626016260165	310	0.856353591160221	410	0.7167832167832168	644	0.8496042216358839	G	3.999	-0.002855	0.07773	0.448025	0.863806	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046;ENSG00000257046;ENSG00000205754	ENST00000540853;ENST00000261196;ENST00000381545;ENST00000553473;ENST00000381541;ENST00000540229;ENST00000554957	T;T;T;T;T;T;T	0.79845	0.68;0.68;0.68;0.68;-1.31;0.68;-1.31	3.99	3.99	0.46301	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.106603	0.64402	N	0.000006	T	0.00012	0.0000	N	0.00960	-1.095	0.53688	P	2.599999999997049E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.43653	-0.9378	9	0.02654	T	1	.	13.2898	0.60264	0.0:0.0:0.8399:0.1601	rs4149117;rs52800447;rs58702833;rs4149117	112;112;112	F5H094;Q5JAR4;Q9NPD5	.;.;SO1B3_HUMAN	A	112	ENSP00000442000:S112A;ENSP00000261196:S112A;ENSP00000370956:S112A;ENSP00000451758:S112A;ENSP00000370952:S112A;ENSP00000441269:S112A;ENSP00000452013:S112A	ENSP00000370952:S112A	S	+	1	0	SLCO1B3;SLCO1B7;RP11-545J16.1	20902747	0.998000	0.40836	0.987000	0.45799	0.648000	0.38561	5.297000	0.65704	0.797000	0.33971	-0.366000	0.07423	TCT	G|0.702;N|0.000	0.702	strong		0.328	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
EGFL6	25975	hgsc.bcm.edu	37	X	13635937	13635937	+	Silent	SNP	C	C	T	rs5978653	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:13635937C>T	ENST00000361306.1	+	8	1124	c.867C>T	c.(865-867)agC>agT	p.S289S	EGFL6_ENST00000380602.3_Silent_p.S289S	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	289					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						ACAAAAACAGCATGAAAAAGA	0.408													C|||	251	0.0664901	0.0461	0.0346	3775	,	,		13027	0.0962		0.0378	False		,,,				2504	0.0317				p.S289S		Atlas-SNP	.											.	EGFL6	111	.	0			c.C867T						PASS	.	C	,	194,3641		3,156,32,1473,539	103.0	102.0	102.0		867,867	3.7	1.0	X	dbSNP_114	102	429,6299		8,281,132,2139,1740	no	coding-synonymous,coding-synonymous	EGFL6	NM_001167890.1,NM_015507.3	,	11,437,164,3612,2279	TT,TC,T,CC,C		6.3763,5.0587,5.8979	,	289/555,289/554	13635937	623,9940	2203	4300	6503	SO:0001819	synonymous_variant	25975	exon8			AAACAGCATGAAA	AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"""MAM and EGF domain containing"""	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.867C>T	X.37:g.13635937C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	131	6	0.0458015	NM_001167890	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Silent	SNP	ENST00000361306.1	37	CCDS14155.1																																																																																			C|0.938;T|0.062	0.062	strong		0.408	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65349037	65349037	+	Silent	SNP	G	G	A	rs74684453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65349037G>A	ENST00000309295.4	+	9	1159	c.894G>A	c.(892-894)acG>acA	p.T298T		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	298						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CCCAGGACACGGCCCCCACCC	0.677													G|||	34	0.00678914	0.0008	0.0086	5008	,	,		13897	0.0		0.0239	False		,,,				2504	0.0031				p.T298T		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G894A						PASS	.	G		13,3719		0,13,1853	8.0	9.0	9.0		894	3.0	0.8	11	dbSNP_134	9	194,7914		2,190,3862	no	coding-synonymous	EHBP1L1	NM_001099409.1		2,203,5715	AA,AG,GG		2.3927,0.3483,1.7483		298/1524	65349037	207,11633	1866	4054	5920	SO:0001819	synonymous_variant	254102	exon9			GGACACGGCCCCC	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.894G>A	11.37:g.65349037G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	185	89	0.481081	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1																																																																																			G|0.989;A|0.011	0.011	strong		0.677	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
ITGAL	3683	hgsc.bcm.edu	37	16	30507879	30507879	+	Silent	SNP	C	C	T	rs147713219		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30507879C>T	ENST00000356798.6	+	15	2004	c.1824C>T	c.(1822-1824)atC>atT	p.I608I	RP11-297C4.1_ENST00000563751.1_RNA|ITGAL_ENST00000433423.2_Intron|ITGAL_ENST00000358164.5_Silent_p.I525I	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	608					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)	p.I608I(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	GCCAGATGATCGTGCTGAGGT	0.463																																					p.I608I	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											ITGAL,rectum,carcinoma,0,1	ITGAL	149	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C1824T						scavenged	.	C	,	1,4393	2.1+/-5.4	0,1,2196	91.0	77.0	82.0		1575,1824	-0.5	0.9	16	dbSNP_134	82	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ITGAL	NM_001114380.1,NM_002209.2	,	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	,	525/1087,608/1171	30507879	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	3683	exon15			GATGATCGTGCTG		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"""CD molecules"", ""Integrins"""	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1824C>T	16.37:g.30507879C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	88	2	0.0227273	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																			C|1.000;T|0.000	0.000	weak		0.463	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2		
KANSL1	284058	hgsc.bcm.edu	37	17	44110541	44110541	+	Silent	SNP	G	G	A	rs35833914	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44110541G>A	ENST00000262419.6	-	13	3212	c.2742C>T	c.(2740-2742)gaC>gaT	p.D914D	KANSL1_ENST00000574590.1_Silent_p.D914D|KANSL1_ENST00000575318.1_Silent_p.D850D|KANSL1_ENST00000572904.1_Silent_p.D914D|KANSL1_ENST00000432791.1_Silent_p.D914D|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000393476.3_Silent_p.D208D	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	914	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CGAAGGCTGCGTCGGATAGGT	0.592													G|||	432	0.086262	0.0151	0.1571	5008	,	,		19747	0.001		0.2406	False		,,,				2504	0.0613				p.D914D		Atlas-SNP	.											.	.	.	.	0			c.C2742T						PASS	.	G	,,	202,4204		5,192,2006	63.0	62.0	62.0		2739,2742,2742	-3.2	0.8	17	dbSNP_126	62	1914,6686		214,1486,2600	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	219,1678,4606	AA,AG,GG		22.2558,4.5847,16.2694	,,	913/1105,914/1106,914/1106	44110541	2116,10890	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon13			GGCTGCGTCGGAT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2742C>T	17.37:g.44110541G>A		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	231	109	0.471861	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.144;C|0.000;G|0.856;T|0.000	0.144	strong		0.592	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
HLA-C	3107	hgsc.bcm.edu	37	6	31237802	31237802	+	Missense_Mutation	SNP	A	A	G	rs1050147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31237802A>G	ENST00000376228.5	-	5	970	c.956T>C	c.(955-957)gTt>gCt	p.V319A	HLA-C_ENST00000383329.3_Missense_Mutation_p.V319A	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	325					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						AGCTAGGACAACCAGGACAGC	0.597																																					p.V319A		Atlas-SNP	.											.	HLA-C	92	.	0			c.T956C						PASS	.	G	ALA/VAL	3060,1334		1314,432,451	46.0	47.0	47.0		956	-0.2	0.0	6	dbSNP_123	47	5060,3518		1977,1106,1206	yes	missense	HLA-C	NM_002117.5	64	3291,1538,1657	GG,GA,AA		41.0119,30.3596,37.4036	benign	319/367	31237802	8120,4852	2197	4289	6486	SO:0001583	missense	3107	exon5			AGGACAACCAGGA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.956T>C	6.37:g.31237802A>G	ENSP00000365402:p.Val319Ala	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1682	0.7701465201465202	392	0.7967479674796748	291	0.8038674033149171	456	0.7972027972027972	543	0.716358839050132	.	0.012	-1.691464	0.00731	0.696404	0.589881	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00958	5.52;5.5	0.109	-0.218	0.13142	.	0.672928	0.11860	N	0.522519	T	0.00178	0.0005	.	.	.	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.43925	-0.9361	7	0.21540	T	0.41	.	.	.	.	rs17413387;rs35376379;rs41553619	319;319;319;319	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	A	319;319;319;356	ENSP00000365402:V319A;ENSP00000372819:V319A	ENSP00000365402:V319A	V	-	2	0	HLA-C	31345781	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.742000	0.01835	-2.815000	0.00346	-2.811000	0.00111	GTT	A|0.257;G|0.743	0.743	strong		0.597	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
ARFGAP3	26286	hgsc.bcm.edu	37	22	43203137	43203137	+	Silent	SNP	C	C	T	rs738535	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:43203137C>T	ENST00000263245.5	-	14	1572	c.1353G>A	c.(1351-1353)tcG>tcA	p.S451S	ARFGAP3_ENST00000429508.2_Silent_p.S379S|ARFGAP3_ENST00000437119.2_Silent_p.S407S	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	451					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						AGGAACTTGCCGACAGCCTCT	0.522													C|||	1553	0.310104	0.289	0.366	5008	,	,		17906	0.0853		0.4364	False		,,,				2504	0.4008				p.S451S	GBM(58;544 1030 21460 27159 48838)	Atlas-SNP	.											.	ARFGAP3	48	.	0			c.G1353A						PASS	.	C	,	1535,2871	481.0+/-359.0	273,989,941	41.0	35.0	37.0		1221,1353	-6.2	0.0	22	dbSNP_86	37	3892,4708	533.8+/-382.5	907,2078,1315	no	coding-synonymous,coding-synonymous	ARFGAP3	NM_001142293.1,NM_014570.4	,	1180,3067,2256	TT,TC,CC		45.2558,34.8389,41.7269	,	407/473,451/517	43203137	5427,7579	2203	4300	6503	SO:0001819	synonymous_variant	26286	exon14			ACTTGCCGACAGC	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"""ADP-ribosylation factor GTPase activating proteins"""	661	protein-coding gene	gene with protein product		612439	"""ADP-ribosylation factor GTPase activating protein 1"""	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.1353G>A	22.37:g.43203137C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_014570	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Silent	SNP	ENST00000263245.5	37	CCDS14042.1	651	0.2980769230769231	145	0.29471544715447157	149	0.4116022099447514	36	0.06293706293706294	321	0.4234828496042216	C	0.050	-1.253780	0.01457	0.348389	0.452558	ENSG00000242247	ENST00000453516	.	.	.	4.94	-6.15	0.02105	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20403	P	0.9999019985	.	.	.	.	.	.	T	0.48801	-0.9003	3	.	.	.	-8.7248	1.6031	0.02679	0.3155:0.3219:0.2148:0.1478	rs738535;rs1044700;rs3171717;rs17405155;rs17409171;rs17849916;rs60500703;rs738535	.	.	.	S	254	.	.	G	-	1	0	ARFGAP3	41533081	0.156000	0.22821	0.015000	0.15790	0.006000	0.05464	-0.630000	0.05502	-0.428000	0.07339	-0.923000	0.02734	GGC	C|0.641;T|0.359	0.359	strong		0.522	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570	
RASA2	5922	hgsc.bcm.edu	37	3	141327474	141327474	+	Silent	SNP	G	G	A	rs295323	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:141327474G>A	ENST00000452898.1	+	21	2198	c.2163G>A	c.(2161-2163)ctG>ctA	p.L721L	RASA2_ENST00000286364.3_Silent_p.L720L|RASA2_ENST00000509118.1_3'UTR	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	721					intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.L720L(1)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						CTGTGTATCTGAACGGAAATT	0.438													A|||	2256	0.450479	0.7315	0.4625	5008	,	,		21103	0.2937		0.3797	False		,,,				2504	0.2965				p.L720L		Atlas-SNP	.											RASA2_ENST00000286364,NS,carcinoma,0,1	RASA2	169	1	1	Substitution - coding silent(1)	stomach(1)	c.G2160A						PASS	.	A		2958,1448	467.4+/-354.8	999,960,244	123.0	124.0	124.0		2160	-10.8	0.0	3	dbSNP_79	124	3341,5259	643.9+/-400.0	601,2139,1560	no	coding-synonymous	RASA2	NM_006506.2		1600,3099,1804	AA,AG,GG		38.8488,32.8643,48.4315		720/850	141327474	6299,6707	2203	4300	6503	SO:0001819	synonymous_variant	5922	exon21			GTATCTGAACGGA	AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"""Pleckstrin homology (PH) domain containing"""	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.2163G>A	3.37:g.141327474G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	243	119	0.489712	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Silent	SNP	ENST00000452898.1	37																																																																																				G|0.523;A|0.477	0.477	strong		0.438	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506	
AKAP17A	8227	hgsc.bcm.edu	37	X	1719897	1719897	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:1719897C>G	ENST00000313871.3	+	5	1694	c.1498C>G	c.(1498-1500)Ccg>Gcg	p.P500A		NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	500				P -> A (in Ref. 1; AAA61303 and 4; AAI10497). {ECO:0000305}.	B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)	p.P500A(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						CAAGGAGAGCCCGGCCCACCC	0.716													c|||	2672	0.533546	0.447	0.5706	5008	,	,		12421	0.5446		0.6034	False		,,,				2504	0.5409				p.P500A		Atlas-SNP	.											.	AKAP17A	46	.	1	Substitution - Missense(1)	breast(1)	c.C1498G						PASS	.		,ALA/PRO	2001,2381		432,1137,622	14.0	16.0	15.0		,1498	1.6	0.0	X	dbSNP_134	15	4722,3828		1297,2128,850	no	intron,missense	ASMT,AKAP17A	NM_004043.2,NM_005088.2	,27	1729,3265,1472	GG,GC,CC		44.7719,45.6641,48.0127	,benign	,500/696	1719897	6723,6209	2191	4275	6466	SO:0001583	missense	8227	exon5			GAGAGCCCGGCCC	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"""Pseudoautosomal regions / PAR1"", ""A-kinase anchor proteins"""	18783	protein-coding gene	gene with protein product		312095, 465000	"""chromosome X and Y open reading frame 3"", ""splicing factor, arginine/serine-rich 17A"""	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.1498C>G	X.37:g.1719897C>G	ENSP00000324827:p.Pro500Ala	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Missense_Mutation	SNP	ENST00000313871.3	37	CCDS14116.1	1178	0.5393772893772893	203	0.41260162601626016	206	0.569060773480663	306	0.534965034965035	463	0.6108179419525066	c	1.990	-0.432046	0.04669	0.456641	0.552281	ENSG00000197976	ENST00000313871	T	0.41065	1.01	1.56	1.56	0.23342	.	0.494105	0.14634	N	0.307623	T	0.00012	0.0000	.	.	.	0.09310	N	0.999999	B	0.32573	0.376	B	0.25140	0.058	T	0.47661	-0.9100	9	0.08179	T	0.78	.	9.9337	0.41539	0.0:0.6553:0.3447:0.0	.	500	Q02040	AK17A_HUMAN	A	500	ENSP00000324827:P500A	ENSP00000324827:P500A	P	+	1	0	AKAP17A	1679897	0.000000	0.05858	0.029000	0.17559	0.228000	0.25075	-0.095000	0.11077	0.533000	0.28675	0.367000	0.22151	CCG	C|0.459;G|0.541	0.541	strong		0.716	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088	
LSM14A	26065	hgsc.bcm.edu	37	19	34706531	34706531	+	Missense_Mutation	SNP	A	A	G	rs73929373	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:34706531A>G	ENST00000433627.5	+	6	821	c.746A>G	c.(745-747)aAt>aGt	p.N249S	LSM14A_ENST00000544216.3_Missense_Mutation_p.N249S|LSM14A_ENST00000540746.2_Missense_Mutation_p.N208S	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	249					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					AGGCCAGAAAATGAGCAACTC	0.348													A|||	598	0.119409	0.2526	0.1859	5008	,	,		17565	0.0268		0.0249	False		,,,				2504	0.0849				p.N249S		Atlas-SNP	.											.	LSM14A	44	.	0			c.A746G						PASS	.	A	SER/ASN,SER/ASN	942,3464	357.6+/-314.0	111,720,1372	105.0	99.0	101.0		746,746	3.5	1.0	19	dbSNP_130	101	283,8317	105.4+/-166.3	8,267,4025	yes	missense,missense	LSM14A	NM_001114093.1,NM_015578.2	46,46	119,987,5397	GG,GA,AA		3.2907,21.3799,9.4187	benign,benign	249/464,249/464	34706531	1225,11781	2203	4300	6503	SO:0001583	missense	26065	exon6			CAGAAAATGAGCA	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"""chromosome 19 open reading frame 13"", ""family with sequence similarity 61, member A"", ""LSM14 homolog A (SCD6, S. cerevisiae)"""	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.746A>G	19.37:g.34706531A>G	ENSP00000413964:p.Asn249Ser	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	121	49	0.404959	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Missense_Mutation	SNP	ENST00000433627.5	37	CCDS46040.1	203	0.09294871794871795	126	0.25609756097560976	50	0.13812154696132597	10	0.017482517482517484	17	0.022427440633245383	a	11.36	1.614331	0.28712	0.213799	0.032907	ENSG00000257103	ENST00000544216;ENST00000433627;ENST00000540746	T;T;T	0.32988	1.44;1.43;1.51	5.67	3.45	0.39498	.	0.584793	0.21286	N	0.077070	T	0.00012	0.0000	L	0.34521	1.04	0.32771	P	0.503819	B;B;B	0.10296	0.0;0.003;0.001	B;B;B	0.14023	0.002;0.01;0.001	T	0.30995	-0.9959	9	0.07325	T	0.83	-9.8271	7.9304	0.29899	0.6192:0.3076:0.0732:0.0	.	208;249;249	B4DTG6;Q8ND56;Q8ND56-2	.;LS14A_HUMAN;.	S	249;249;208	ENSP00000446271:N249S;ENSP00000413964:N249S;ENSP00000446451:N208S	ENSP00000314768:N249S	N	+	2	0	LSM14A	39398371	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.253000	0.32886	1.085000	0.41206	0.533000	0.62120	AAT	A|0.908;G|0.092	0.092	strong		0.348	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578	
MORC4	79710	hgsc.bcm.edu	37	X	106200202	106200202	+	Missense_Mutation	SNP	G	G	A	rs6622126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:106200202G>A	ENST00000355610.4	-	12	1692	c.1418C>T	c.(1417-1419)aCt>aTt	p.T473I	MORC4_ENST00000255495.7_Missense_Mutation_p.T473I|MORC4_ENST00000535534.1_Missense_Mutation_p.T221I	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	473			T -> I (in dbSNP:rs6622126). {ECO:0000269|PubMed:14702039}.			nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						GTCTTCATCAGTGAGTTCTTG	0.423													A|||	2837	0.751523	0.6589	0.5764	3775	,	,		13471	0.7063		0.3161	False		,,,				2504	0.5481				p.T473I		Atlas-SNP	.											.	MORC4	155	.	0			c.C1418T						PASS	.	A	ILE/THR,ILE/THR	3119,716		1090,486,453,56,118	176.0	158.0	164.0		1418,1418	-3.7	0.1	X	dbSNP_116	164	2890,3838		441,1207,801,780,1071	yes	missense,missense	MORC4	NM_001085354.2,NM_024657.4	89,89	1531,1693,1254,836,1189	AA,AG,A,GG,G		42.9548,18.6701,43.1128	benign,benign	473/901,473/938	106200202	6009,4554	2203	4300	6503	SO:0001583	missense	79710	exon12			TCATCAGTGAGTT	AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 2"", ""zinc finger, CW type with coiled-coil domain 2"""	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.1418C>T	X.37:g.106200202G>A	ENSP00000347821:p.Thr473Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	156	10	0.0641026	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	37	CCDS14525.2	1173	0.7070524412296564	220	0.7692307692307693	127	0.5521739130434783	274	0.9013157894736842	168	0.28187919463087246	A	0.004	-2.304218	0.00240	0.813299	0.429548	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.30714	2.74;1.52;2.74	5.17	-3.74	0.04385	.	1.099420	0.06827	N	0.793253	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.26710	-1.0095	9	0.37606	T	0.19	0.0119	0.387	0.00404	0.2206:0.2629:0.2562:0.2603	rs6622126;rs60963505;rs6622126	221;473;473	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	I	473;221;473	ENSP00000347821:T473I;ENSP00000440359:T221I;ENSP00000255495:T473I	ENSP00000255495:T473I	T	-	2	0	MORC4	106086858	0.027000	0.19231	0.097000	0.21041	0.165000	0.22458	-0.704000	0.05058	-0.938000	0.03714	-3.323000	0.00044	ACT	0|0.012;A|0.648	0.648	strong		0.423	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657	
VWA3B	200403	hgsc.bcm.edu	37	2	98853173	98853173	+	Missense_Mutation	SNP	G	G	A	rs11889349	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:98853173G>A	ENST00000477737.1	+	19	2857	c.2653G>A	c.(2653-2655)Gtg>Atg	p.V885M		NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	885			V -> M (in dbSNP:rs11889349). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.							NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						CAAGCATGTCGTGTCTAAGGT	0.468													g|||	3326	0.664137	0.621	0.4914	5008	,	,		19928	0.7976		0.5447	False		,,,				2504	0.8303				p.V885M		Atlas-SNP	.											.	VWA3B	138	.	0			c.G2653A						PASS	.	G	MET/VAL	2459,1561		749,961,300	138.0	143.0	141.0		2653	0.9	0.0	2	dbSNP_120	141	4564,3812		1250,2064,874	yes	missense	VWA3B	NM_144992.4	21	1999,3025,1174	AA,AG,GG		45.511,38.8308,43.3446	benign	885/1295	98853173	7023,5373	2010	4188	6198	SO:0001583	missense	200403	exon19			CATGTCGTGTCTA	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.2653G>A	2.37:g.98853173G>A	ENSP00000417955:p.Val885Met	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	1320|1320	0.6043956043956044|0.6043956043956044	307|307	0.6239837398373984|0.6239837398373984	181|181	0.5|0.5	440|440	0.7692307692307693|0.7692307692307693	392|392	0.5171503957783641|0.5171503957783641	g|g	0.687|0.687	-0.795959|-0.795959	0.02862|0.02862	0.611692|0.611692	0.54489|0.54489	ENSG00000168658|ENSG00000168658	ENST00000473149|ENST00000477737	.|T	.|0.07327	.|3.2	4.93|4.93	0.946|0.946	0.19549|0.19549	.|.	.|1.329060	.|0.05295	.|N	.|0.521921	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38838|0.38838	1.175|1.175	0.80722|0.80722	P|P	0.0|0.0	.|B;B;P;B	.|0.44139	.|0.029;0.099;0.827;0.056	.|B;B;B;B	.|0.33750	.|0.009;0.02;0.169;0.021	T|T	0.29058|0.29058	-1.0024|-1.0024	4|9	.|0.35671	.|T	.|0.21	.|.	4.4952|4.4952	0.11833|0.11833	0.157:0.1227:0.5949:0.1255|0.157:0.1227:0.5949:0.1255	rs11889349;rs52803499;rs61365735;rs11889349|rs11889349;rs52803499;rs61365735;rs11889349	.|277;885;885;885	.|Q502W6-5;Q502W6;Q502W6-8;Q502W6-6	.|.;VWA3B_HUMAN;.;.	H|M	295|885	.|ENSP00000417955:V885M	.|ENSP00000417955:V885M	R|V	+|+	2|1	0|0	VWA3B|VWA3B	98219605|98219605	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.030000|0.030000	0.12068|0.12068	0.250000|0.250000	0.18235|0.18235	-0.049000|-0.049000	0.13379|0.13379	-1.458000|-1.458000	0.01028|0.01028	CGT|GTG	G|0.380;A|0.620	0.620	strong		0.468	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
ERAP2	64167	hgsc.bcm.edu	37	5	96245439	96245439	+	Silent	SNP	C	C	T	rs1056893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96245439C>T	ENST00000437043.3	+	15	3036	c.2325C>T	c.(2323-2325)tcC>tcT	p.S775S	CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000379904.4_Silent_p.S730S	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	775					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		AACTCTTCTCCCAGTGGATGG	0.473													T|||	2767	0.552516	0.6006	0.5807	5008	,	,		19783	0.5278		0.5199	False		,,,				2504	0.5266				p.S775S		Atlas-SNP	.											.	ERAP2	77	.	0			c.C2325T						PASS	.	T	,	2555,1851	537.9+/-374.9	724,1107,372	69.0	67.0	68.0		2325,2325	-0.9	0.9	5	dbSNP_86	68	4489,4111	563.6+/-388.2	1155,2179,966	yes	coding-synonymous,coding-synonymous	ERAP2	NM_001130140.1,NM_022350.3	,	1879,3286,1338	TT,TC,CC		47.8023,42.0109,45.8404	,	775/961,775/961	96245439	7044,5962	2203	4300	6503	SO:0001819	synonymous_variant	64167	exon15			CTTCTCCCAGTGG	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.2325C>T	5.37:g.96245439C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	191	96	0.502618	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Silent	SNP	ENST00000437043.3	37	CCDS4086.1																																																																																			C|0.452;T|0.548	0.548	strong		0.473	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
PRPF4B	8899	hgsc.bcm.edu	37	6	4044214	4044214	+	Silent	SNP	A	A	G	rs35085092	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:4044214A>G	ENST00000337659.6	+	6	1918	c.1818A>G	c.(1816-1818)tcA>tcG	p.S606S	PRPF4B_ENST00000538861.1_Silent_p.S592S	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	606					mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				TTGAGGCCTCAGTGAAAGCCA	0.418													A|||	270	0.0539137	0.0635	0.0432	5008	,	,		17834	0.006		0.1123	False		,,,				2504	0.0378				p.S606S		Atlas-SNP	.											.	PRPF4B	140	.	0			c.A1818G						PASS	.	A		278,4128	154.4+/-187.8	12,254,1937	94.0	89.0	91.0		1818	-6.6	1.0	6	dbSNP_126	91	809,7791	188.7+/-235.6	34,741,3525	no	coding-synonymous	PRPF4B	NM_003913.4		46,995,5462	GG,GA,AA		9.407,6.3096,8.3577		606/1008	4044214	1087,11919	2203	4300	6503	SO:0001819	synonymous_variant	8899	exon6			GGCCTCAGTGAAA	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"""PRP4 pre-mRNA processing factor 4 homolog B (yeast)"""			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.1818A>G	6.37:g.4044214A>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	199	105	0.527638	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Silent	SNP	ENST00000337659.6	37	CCDS4488.1																																																																																			A|0.925;G|0.075	0.075	strong		0.418	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2		
PKP4	8502	hgsc.bcm.edu	37	2	159517926	159517926	+	Silent	SNP	C	C	T	rs112890651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:159517926C>T	ENST00000389759.3	+	13	2287	c.2175C>T	c.(2173-2175)atC>atT	p.I725I	AC005042.4_ENST00000342892.4_RNA|PKP4_ENST00000389757.3_Silent_p.I725I	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	725					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						TGTATGTGATCCACACGTGTG	0.587										HNSCC(62;0.18)			C|||	18	0.00359425	0.0	0.0058	5008	,	,		20670	0.0		0.0129	False		,,,				2504	0.001				p.I725I		Atlas-SNP	.											.	PKP4	133	.	0			c.C2175T						PASS	.	C	,	5,4401	9.9+/-24.2	0,5,2198	127.0	113.0	118.0		2175,2175	5.7	1.0	2	dbSNP_132	118	103,8497	56.4+/-117.6	2,99,4199	no	coding-synonymous,coding-synonymous	PKP4	NM_001005476.1,NM_003628.3	,	2,104,6397	TT,TC,CC		1.1977,0.1135,0.8304	,	725/1150,725/1193	159517926	108,12898	2203	4300	6503	SO:0001819	synonymous_variant	8502	exon13			TGTGATCCACACG	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"""Armadillo repeat containing"""	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.2175C>T	2.37:g.159517926C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_001005476	Q86W91	Silent	SNP	ENST00000389759.3	37	CCDS33305.1																																																																																			C|0.990;T|0.010	0.010	strong		0.587	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1		
CUX1	1523	hgsc.bcm.edu	37	7	101844851	101844851	+	Silent	SNP	A	A	G	rs60987662	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:101844851A>G	ENST00000292535.7	+	18	2312	c.2274A>G	c.(2272-2274)ccA>ccG	p.P758P	CUX1_ENST00000360264.3_Silent_p.P769P|CUX1_ENST00000549414.2_Silent_p.P736P|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Silent_p.P600P|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000550008.2_Silent_p.P702P|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Silent_p.P656P	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	758					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						CCAGCTACCCACCTCTCGCCA	0.647													G|||	1586	0.316693	0.4206	0.2824	5008	,	,		15026	0.0784		0.3837	False		,,,				2504	0.3773				p.P769P		Atlas-SNP	.											.	CUX1	253	.	0			c.A2307G						PASS	.	G	,,,,,,	1872,2534	630.7+/-395.5	409,1054,740	122.0	131.0	128.0		2307,,,,,,2274	-10.1	0.0	7	dbSNP_129	128	3335,5265	642.8+/-399.9	638,2059,1603	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	CUX1	NM_001202543.1,NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2,NM_181552.3	,,,,,,	1047,3113,2343	GG,GA,AA		38.7791,42.4875,40.0354	,,,,,,	769/1517,,,,,,758/1506	101844851	5207,7799	2203	4300	6503	SO:0001819	synonymous_variant	1523	exon18			CTACCCACCTCTC	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.2274A>G	7.37:g.101844851A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	166	82	0.493976	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	CCDS5721.1																																																																																			A|0.627;G|0.373	0.373	strong		0.647	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
SPPL2C	162540	hgsc.bcm.edu	37	17	43923654	43923654	+	Missense_Mutation	SNP	G	G	C	rs12185233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43923654G>C	ENST00000329196.5	+	1	1399	c.1382G>C	c.(1381-1383)cGc>cCc	p.R461P	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	461			R -> P (in dbSNP:rs12185233).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										TACTGTTGCCGCTTTGATGTG	0.587													G|||	431	0.0860623	0.0151	0.1571	5008	,	,		22035	0.001		0.2396	False		,,,				2504	0.0613				p.R461P		Atlas-SNP	.											IMP5,NS,carcinoma,0,1	.	.	1	0			c.G1382C						PASS	.	G	PRO/ARG	203,4203	127.0+/-164.0	5,193,2005	153.0	117.0	129.0		1382	5.2	1.0	17	dbSNP_120	129	1928,6672	340.3+/-323.5	221,1486,2593	yes	missense	IMP5	NM_175882.2	103	226,1679,4598	CC,CG,GG		22.4186,4.6074,16.3847	possibly-damaging	461/685	43923654	2131,10875	2203	4300	6503	SO:0001583	missense	162540	exon1			GTTGCCGCTTTGA		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1382G>C	17.37:g.43923654G>C	ENSP00000332488:p.Arg461Pro	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	136	59	0.433824	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	15.02	2.709293	0.48517	0.046074	0.224186	ENSG00000185294	ENST00000329196	T	0.27104	1.69	5.2	5.2	0.72013	.	0.000000	0.41823	D	0.000810	T	0.00039	0.0001	M	0.91768	3.24	0.09310	P	0.9999999837478	P	0.36712	0.566	B	0.44133	0.442	T	0.02781	-1.1111	9	0.87932	D	0	-2.5538	16.2754	0.82642	0.0:0.0:1.0:0.0	rs12185233;rs17763711;rs12185233	461	Q8IUH8	IMP5_HUMAN	P	461	ENSP00000332488:R461P	ENSP00000332488:R461P	R	+	2	0	AC217771.1	41279434	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	6.410000	0.73294	2.698000	0.92095	0.563000	0.77884	CGC	G|0.509;C|0.491	0.491	strong		0.587	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
SYCE1	93426	hgsc.bcm.edu	37	10	135370639	135370639	+	Missense_Mutation	SNP	C	C	A	rs8181357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135370639C>A	ENST00000343131.5	-	7	500	c.396G>T	c.(394-396)gaG>gaT	p.E132D	SYCE1_ENST00000432597.2_Missense_Mutation_p.E96D|SPRN_ENST00000541506.1_Intron|SYCE1_ENST00000368517.3_Missense_Mutation_p.E96D	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	132			E -> D (in dbSNP:rs8181357). {ECO:0000269|PubMed:15489334}.		synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.E96D(1)|p.E132D(1)		breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TCTCCTTGCACTCCTGCAACA	0.552													C|||	775	0.154752	0.0454	0.1715	5008	,	,		21943	0.2698		0.1093	False		,,,				2504	0.2188				p.E132D		Atlas-SNP	.											SYCE1_ENST00000343131,NS,carcinoma,0,2	SYCE1	81	2	2	Substitution - Missense(2)	stomach(2)	c.G396T						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	274,4132	151.4+/-185.3	6,262,1935	253.0	239.0	244.0		396,396,288	0.2	0.9	10	dbSNP_117	244	822,7778	189.1+/-236.0	45,732,3523	yes	missense,missense,missense	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	45,45,45	51,994,5458	AA,AC,CC		9.5581,6.2188,8.4269	probably-damaging,probably-damaging,probably-damaging	132/319,132/352,96/283	135370639	1096,11910	2203	4300	6503	SO:0001583	missense	93426	exon7			CTTGCACTCCTGC	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.396G>T	10.37:g.135370639C>A	ENSP00000341282:p.Glu132Asp	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	234	68	0.290598	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	37	CCDS44501.1	329	0.15064102564102563	24	0.04878048780487805	62	0.1712707182320442	153	0.2674825174825175	90	0.11873350923482849	C	12.63	1.996834	0.35226	0.062188	0.095581	ENSG00000171772	ENST00000303903;ENST00000432597;ENST00000368517;ENST00000343131	T;T;T;T	0.32272	1.46;3.12;3.12;3.12	4.3	0.217	0.15264	.	0.389128	0.24176	N	0.040858	T	0.00012	0.0000	L	0.44542	1.39	0.42354	P	0.00761400000000001	B;B;B	0.15930	0.015;0.015;0.015	B;B;B	0.19946	0.016;0.027;0.016	T	0.30822	-0.9965	9	0.38643	T	0.18	-1.8451	5.4635	0.16630	0.0:0.5252:0.306:0.1688	rs8181357;rs11537981;rs17857024;rs52803233;rs8181357	4;132;96	Q8N0S2-3;Q8N0S2;Q8N0S2-2	.;SYCE1_HUMAN;.	D	132;96;96;132	ENSP00000303978:E132D;ENSP00000411779:E96D;ENSP00000357503:E96D;ENSP00000341282:E132D	ENSP00000303978:E132D	E	-	3	2	SYCE1	135220629	0.154000	0.22792	0.912000	0.35992	0.873000	0.50193	-0.666000	0.05280	0.050000	0.15949	0.655000	0.94253	GAG	C|0.892;A|0.108	0.108	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
TECPR1	25851	hgsc.bcm.edu	37	7	97852399	97852399	+	Missense_Mutation	SNP	G	G	A	rs11762014	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:97852399G>A	ENST00000447648.2	-	21	3130	c.2831C>T	c.(2830-2832)cCg>cTg	p.P944L	TECPR1_ENST00000479975.1_5'UTR|TECPR1_ENST00000379795.3_Missense_Mutation_p.P946L			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	944			P -> L (in dbSNP:rs11762014).		autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CTCGGCACCCGGGCTCTCCGG	0.677													G|||	1073	0.214257	0.2368	0.2896	5008	,	,		11014	0.2609		0.1889	False		,,,				2504	0.1084				p.P944L		Atlas-SNP	.											TECPR1,NS,carcinoma,0,1	TECPR1	77	1	0			c.C2831T						PASS	.	G	LEU/PRO	788,3258		72,644,1307	18.0	23.0	22.0		2831	4.1	0.9	7	dbSNP_120	22	1294,7022		103,1088,2967	yes	missense	TECPR1	NM_015395.1	98	175,1732,4274	AA,AG,GG		15.5604,19.476,16.8419	benign	944/1166	97852399	2082,10280	2023	4158	6181	SO:0001583	missense	25851	exon21			GCACCCGGGCTCT		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.2831C>T	7.37:g.97852399G>A	ENSP00000404923:p.Pro944Leu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Missense_Mutation	SNP	ENST00000447648.2	37	CCDS47648.1	516	0.23626373626373626	131	0.266260162601626	89	0.24585635359116023	146	0.25524475524475526	150	0.19788918205804748	G	6.236	0.411705	0.11812	0.19476	0.155604	ENSG00000205356	ENST00000447648;ENST00000379795	T;T	0.29917	1.55;1.55	4.05	4.05	0.47172	.	0.158707	0.30193	N	0.010183	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.9999979686	P	0.39181	0.663	B	0.21708	0.036	T	0.41088	-0.9528	9	0.18710	T	0.47	-12.739	12.3533	0.55161	0.0:0.1706:0.8294:0.0	rs11762014	944	Q7Z6L1	TCPR1_HUMAN	L	944;946	ENSP00000404923:P944L;ENSP00000369121:P946L	ENSP00000369121:P946L	P	-	2	0	TECPR1	97690335	0.473000	0.25878	0.902000	0.35471	0.173000	0.22820	1.236000	0.32683	2.561000	0.86390	0.561000	0.74099	CCG	G|0.777;A|0.223	0.223	strong		0.677	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
ITPR3	3710	hgsc.bcm.edu	37	6	33648144	33648144	+	Silent	SNP	C	C	T	rs11967839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33648144C>T	ENST00000374316.5	+	33	5323	c.4263C>T	c.(4261-4263)taC>taT	p.Y1421Y	ITPR3_ENST00000605930.1_Silent_p.Y1421Y			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1421					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	ACCACTGCTACGTGGACACGG	0.607													C|||	572	0.114217	0.2958	0.0375	5008	,	,		16528	0.0585		0.0447	False		,,,				2504	0.0521				p.Y1421Y		Atlas-SNP	.											.	ITPR3	409	.	0			c.C4263T						PASS	.	C		1037,3369	382.3+/-324.4	121,795,1287	63.0	57.0	59.0		4263	-4.0	0.9	6	dbSNP_120	59	392,8208	126.5+/-185.0	11,370,3919	no	coding-synonymous	ITPR3	NM_002224.3		132,1165,5206	TT,TC,CC		4.5581,23.5361,10.9872		1421/2672	33648144	1429,11577	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon32			CTGCTACGTGGAC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.4263C>T	6.37:g.33648144C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.890;T|0.110	0.110	strong		0.607	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
FAM26D	221301	hgsc.bcm.edu	37	6	116875493	116875493	+	Silent	SNP	T	T	C	rs9387420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:116875493T>C	ENST00000368596.3	+	1	581	c.537T>C	c.(535-537)ctT>ctC	p.L179L	FAM26D_ENST00000416171.2_Silent_p.L35L|FAM26D_ENST00000405399.1_Silent_p.L36L|FAM26D_ENST00000368597.2_Intron			Q5JW98	FA26D_HUMAN	family with sequence similarity 26, member D	179					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				endometrium(1)|lung(5)	6		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0458)|OV - Ovarian serous cystadenocarcinoma(136;0.0694)|Epithelial(106;0.222)		AAATAGCTCTTCTGCACAGAT	0.408													T|||	1127	0.22504	0.1528	0.1542	5008	,	,		21118	0.3482		0.17	False		,,,				2504	0.3027				p.L36L		Atlas-SNP	.											.	FAM26D	29	.	0			c.T108C						PASS	.																																			SO:0001819	synonymous_variant	221301	exon3			AGCTCTTCTGCAC	AK056801	CCDS5109.1, CCDS59032.1	6q22.31	2008-02-05	2007-03-19	2007-03-19	ENSG00000164451	ENSG00000164451			21094	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 78"""	C6orf78			Standard	NM_153036		Approved	FLJ32239	uc010ked.4	Q5JW98	OTTHUMG00000015443	ENST00000368596.3:c.537T>C	6.37:g.116875493T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001256887	B0QZ25|B0QZ27|B4DTQ0|Q96MK0	Silent	SNP	ENST00000368596.3	37																																																																																				C|0.205;N|0.000	0.205	strong		0.408	FAM26D-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000041958.1	NM_153036	
RGS10	6001	hgsc.bcm.edu	37	10	121275099	121275099	+	Silent	SNP	G	G	A	rs11550215	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:121275099G>A	ENST00000369101.3	-	3	324	c.297C>T	c.(295-297)aaC>aaT	p.N99N	RGS10_ENST00000369103.2_Silent_p.N107N|RGS10_ENST00000469575.1_Intron|RGS10_ENST00000392865.1_Silent_p.N93N			O43665	RGS10_HUMAN	regulator of G-protein signaling 10	99	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(2)|large_intestine(1)|lung(3)	6		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00105)|GBM - Glioblastoma multiforme(135;0.195)		GCCCCTCCACGTTGACCTGTG	0.552													G|||	160	0.0319489	0.0227	0.0749	5008	,	,		17708	0.001		0.0527	False		,,,				2504	0.0245				p.N107N		Atlas-SNP	.											.	RGS10	14	.	0			c.C321T						PASS	.	G	,	136,4270	98.0+/-136.7	0,136,2067	215.0	171.0	186.0		321,279	-4.1	1.0	10	dbSNP_120	186	524,8076	146.5+/-202.0	10,504,3786	no	coding-synonymous,coding-synonymous	RGS10	NM_001005339.1,NM_002925.3	,	10,640,5853	AA,AG,GG		6.093,3.0867,5.0746	,	107/182,93/168	121275099	660,12346	2203	4300	6503	SO:0001819	synonymous_variant	6001	exon4			CTCCACGTTGACC	AF045229	CCDS31294.1, CCDS41572.1	10q25	2007-08-14	2007-08-14		ENSG00000148908	ENSG00000148908		"""Regulators of G-protein signaling"""	9992	protein-coding gene	gene with protein product		602856	"""regulator of G-protein signalling 10"""			8774883	Standard	NM_002925		Approved		uc001leg.3	O43665	OTTHUMG00000019150	ENST00000369101.3:c.297C>T	10.37:g.121275099G>A		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	261	129	0.494253	NM_001005339	A8K408|B1AMR8|Q6IAZ6|Q96GN0	Silent	SNP	ENST00000369101.3	37																																																																																				G|0.951;A|0.049	0.049	strong		0.552	RGS10-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050655.1	NM_002925	
PLXND1	23129	hgsc.bcm.edu	37	3	129281718	129281718	+	Silent	SNP	C	C	T	rs2285359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129281718C>T	ENST00000324093.4	-	27	4915	c.4737G>A	c.(4735-4737)acG>acA	p.T1579T	PLXND1_ENST00000393239.1_Silent_p.T1579T	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1579					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.T1579T(1)	PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						CCTGTGTCAGCGTGTCGGTGT	0.607													C|||	461	0.0920527	0.0295	0.0965	5008	,	,		20422	0.2113		0.002	False		,,,				2504	0.1431				p.T1579T	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											PLXND1,NS,carcinoma,0,1	PLXND1	149	1	1	Substitution - coding silent(1)	stomach(1)	c.G4737A						PASS	.	C		69,4337	62.3+/-99.4	0,69,2134	95.0	76.0	83.0		4737	0.5	1.0	3	dbSNP_100	83	43,8557	27.9+/-77.7	0,43,4257	no	coding-synonymous	PLXND1	NM_015103.2		0,112,6391	TT,TC,CC		0.5,1.566,0.8611		1579/1926	129281718	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	23129	exon27			TGTCAGCGTGTCG	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.4737G>A	3.37:g.129281718C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			C|0.966;T|0.034	0.034	strong		0.607	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
PPAPDC1A	196051	hgsc.bcm.edu	37	10	122216862	122216862	+	Silent	SNP	C	C	T	rs67319648	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122216862C>T	ENST00000398250.1	+	1	397	c.45C>T	c.(43-45)ttC>ttT	p.F15F	PPAPDC1A_ENST00000439221.1_Silent_p.F15F|PPAPDC1A_ENST00000541332.1_Silent_p.F15F|PPAPDC1A_ENST00000398248.1_Silent_p.F15F	NM_001030059.1	NP_001025230.1	Q5VZY2	PPC1A_HUMAN	phosphatidic acid phosphatase type 2 domain containing 1A	15					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phospholipid dephosphorylation (GO:0046839)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|urinary_tract(1)	20		Lung NSC(174;0.1)|all_lung(145;0.132)		all cancers(201;0.0117)		CCCTGCTCTTCGGAGTCTTCG	0.677													C|||	981	0.195887	0.1604	0.1916	5008	,	,		10276	0.2986		0.1918	False		,,,				2504	0.1452				p.F15F		Atlas-SNP	.											PPAPDC1A,NS,carcinoma,0,1	PPAPDC1A	48	1	0			c.C45T						PASS	.	C		551,3183		36,479,1352	13.0	17.0	16.0		45	2.9	1.0	10	dbSNP_131	16	1314,6388		116,1082,2653	no	coding-synonymous	PPAPDC1A	NM_001030059.1		152,1561,4005	TT,TC,CC		17.0605,14.7563,16.3081		15/272	122216862	1865,9571	1867	3851	5718	SO:0001819	synonymous_variant	196051	exon1			GCTCTTCGGAGTC	AK098668	CCDS41573.1	10q26.13	2008-02-05		2005-07-15	ENSG00000203805	ENSG00000203805			23531	protein-coding gene	gene with protein product			"""phosphatidic acid phosphatase type 2 domain containing 1"""	PPAPDC1			Standard	XM_005269592		Approved		uc001lev.1	Q5VZY2	OTTHUMG00000019168	ENST00000398250.1:c.45C>T	10.37:g.122216862C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_001030059	A2RU82|Q08EQ2|Q0IIP2|Q495B4|Q5VZY1	Silent	SNP	ENST00000398250.1	37	CCDS41573.1																																																																																			C|0.781;T|0.219	0.219	strong		0.677	PPAPDC1A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_113641	
AGBL4	84871	hgsc.bcm.edu	37	1	49511424	49511424	+	Silent	SNP	A	A	G	rs3934240	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:49511424A>G	ENST00000371839.1	-	5	542	c.426T>C	c.(424-426)caT>caC	p.H142H	AGBL4_ENST00000371838.1_Silent_p.H142H|RP11-141A19.1_ENST00000456002.1_RNA|AGBL4_ENST00000371836.1_Silent_p.H142H	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	142					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.H142H(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		AGTTCTTCCTATGGTCCGGGC	0.403													A|||	1127	0.22504	0.0401	0.2608	5008	,	,		18029	0.4246		0.1889	False		,,,				2504	0.2812				p.H142H		Atlas-SNP	.											AGBL4,NS,carcinoma,0,1	AGBL4	54	1	1	Substitution - coding silent(1)	stomach(1)	c.T426C						PASS	.	A		103,1281		3,97,592	97.0	82.0	87.0		426	-0.5	1.0	1	dbSNP_108	87	703,2479		82,539,970	no	coding-synonymous	AGBL4	NM_032785.3		85,636,1562	GG,GA,AA		22.093,7.4422,17.6522		142/504	49511424	806,3760	692	1591	2283	SO:0001819	synonymous_variant	84871	exon5			CTTCCTATGGTCC	AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 6"""					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.426T>C	1.37:g.49511424A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	175	82	0.468571	NM_032785	B3KT26|B4DG37	Silent	SNP	ENST00000371839.1	37	CCDS44137.1																																																																																			A|0.796;G|0.204	0.204	strong		0.403	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785	
PCDHA4	56144	hgsc.bcm.edu	37	5	140187322	140187322	+	Missense_Mutation	SNP	C	C	T	rs3822346	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140187322C>T	ENST00000530339.1	+	1	550	c.550C>T	c.(550-552)Cct>Tct	p.P184S	PCDHA4_ENST00000356878.4_Missense_Mutation_p.P184S|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.P184S	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	184	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> S (in dbSNP:rs3822346).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAAAAACCACCTGATGACGA	0.478													.|||	2961	0.591254	0.7194	0.6052	5008	,	,		18155	0.5317		0.5388	False		,,,				2504	0.5235				p.P184S		Atlas-SNP	.											.	PCDHA4	419	.	0			c.C550T						PASS	.	T	,,,SER/PRO,,SER/PRO	3099,1307		1101,897,205	46.0	54.0	51.0		,,,550,,550	-0.0	0.0	5	dbSNP_107	51	4537,4063		1192,2153,955	yes	intron,intron,intron,missense,intron,missense	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,74,,74	2293,3050,1160	TT,TC,CC		47.2442,29.6641,41.2886	,,,,,	,,,184/948,,184/799	140187322	7636,5370	2203	4300	6503	SO:0001583	missense	56144	exon1			AAACCACCTGATG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.550C>T	5.37:g.140187322C>T	ENSP00000435300:p.Pro184Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	162	68	0.419753	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	1264	0.5787545787545788	345	0.7012195121951219	202	0.5580110497237569	311	0.5437062937062938	406	0.5356200527704486	N	0.013	-1.639781	0.00799	0.703359	0.527558	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.50001	0.76;0.76;0.76	4.47	-0.0101	0.13998	Cadherin (4);Cadherin-like (1);	0.433605	0.16306	N	0.220228	T	0.00012	0.0000	N	0.00278	-1.715	0.80722	P	0.0	B;B;B	0.09022	0.0;0.001;0.002	B;B;B	0.06405	0.002;0.001;0.001	T	0.34800	-0.9814	9	0.09338	T	0.73	.	5.0772	0.14638	0.5491:0.0893:0.0:0.3616	rs3822346;rs17208285;rs17844277;rs52805413;rs57303265;rs3822346	184;184;184	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	S	184	ENSP00000423470:P184S;ENSP00000349344:P184S;ENSP00000435300:P184S	ENSP00000349344:P184S	P	+	1	0	PCDHA4	140167506	0.000000	0.05858	0.001000	0.08648	0.334000	0.28698	-3.104000	0.00603	-0.113000	0.11958	-0.360000	0.07572	CCT	C|0.417;T|0.583	0.583	strong		0.478	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
ADCK1	57143	hgsc.bcm.edu	37	14	78390880	78390880	+	Silent	SNP	T	T	C	rs2302944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:78390880T>C	ENST00000238561.5	+	8	1038	c.939T>C	c.(937-939)aaT>aaC	p.N313N	ADCK1_ENST00000341211.5_Silent_p.N245N|ADCK1_ENST00000556560.1_3'UTR	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	320	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		ACCCCGGCAATGTACTGGTGC	0.572													T|||	1175	0.234625	0.1626	0.196	5008	,	,		18266	0.2798		0.2127	False		,,,				2504	0.3354				p.N313N		Atlas-SNP	.											.	ADCK1	81	.	0			c.T939C						PASS	.	T	,	775,3631	314.9+/-293.9	66,643,1494	97.0	90.0	92.0		735,939	-8.7	0.6	14	dbSNP_100	92	1829,6771	328.0+/-318.1	187,1455,2658	no	coding-synonymous,coding-synonymous	ADCK1	NM_001142545.1,NM_020421.3	,	253,2098,4152	CC,CT,TT		21.2674,17.5897,20.0215	,	245/456,313/524	78390880	2604,10402	2203	4300	6503	SO:0001819	synonymous_variant	57143	exon8			CGGCAATGTACTG	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.939T>C	14.37:g.78390880T>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Silent	SNP	ENST00000238561.5	37	CCDS9869.1																																																																																			T|0.791;C|0.209	0.209	strong		0.572	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421	
OR1S1	219959	hgsc.bcm.edu	37	11	57982896	57982896	+	Missense_Mutation	SNP	G	G	T	rs2903566	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57982896G>T	ENST00000309433.6	+	1	680	c.680G>T	c.(679-681)aGc>aTc	p.S227I		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	227			S -> I (in dbSNP:rs2903566).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTTACACTCAGCTTCTTTTCC	0.448													T|||	2616	0.522364	0.2814	0.5418	5008	,	,		21979	0.8036		0.4225	False		,,,				2504	0.6472				p.S227I		Atlas-SNP	.											.	OR1S1	139	.	0			c.G680T						PASS	.	T	ILE/SER	1299,3103	697.4+/-406.2	195,909,1097	157.0	124.0	135.0		680	2.1	0.1	11	dbSNP_101	135	3641,4949	623.4+/-397.5	784,2073,1438	yes	missense	OR1S1	NM_001004458.1	142	979,2982,2535	TT,TG,GG		42.3865,29.5093,38.0234	benign	227/326	57982896	4940,8052	2201	4295	6496	SO:0001583	missense	219959	exon1			CACTCAGCTTCTT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.680G>T	11.37:g.57982896G>T	ENSP00000311688:p.Ser227Ile	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1080	0.4945054945054945	146	0.2967479674796748	186	0.5138121546961326	433	0.756993006993007	315	0.4155672823218997	T	0.003	-2.561584	0.00136	0.295093	0.423865	ENSG00000172774	ENST00000309433	T	0.00010	9.43	3.23	2.08	0.27032	GPCR, rhodopsin-like superfamily (1);	0.128568	0.34828	N	0.003657	T	0.00012	0.0000	N	0.00008	-3.13	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46569	-0.9182	9	0.02654	T	1	.	4.0934	0.09980	0.0:0.3043:0.1798:0.516	rs2903566;rs17463613;rs52823244;rs2903566	227	Q8NH92	OR1S1_HUMAN	I	227	ENSP00000311688:S227I	ENSP00000311688:S227I	S	+	2	0	OR1S1	57739472	0.027000	0.19231	0.078000	0.20375	0.442000	0.32017	1.851000	0.39338	-0.026000	0.13895	-0.527000	0.04329	AGC	G|0.565;T|0.435	0.435	strong		0.448	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
MS4A6A	64231	hgsc.bcm.edu	37	11	59940599	59940599	+	Missense_Mutation	SNP	T	T	A	rs7232	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:59940599T>A	ENST00000530839.1	-	7	1045	c.553A>T	c.(553-555)Act>Tct	p.T185S	MS4A6A_ENST00000412309.2_Missense_Mutation_p.T213S|MS4A6A_ENST00000529054.1_Missense_Mutation_p.T213S|MS4A6A_ENST00000420732.2_Missense_Mutation_p.N150I|MS4A6A_ENST00000426738.2_Missense_Mutation_p.T140S|MS4A6A_ENST00000528851.1_Missense_Mutation_p.T185S|MS4A6A_ENST00000323961.3_Missense_Mutation_p.T185S|MS4A6A_ENST00000533023.1_Missense_Mutation_p.N86I	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	185			T -> S (in dbSNP:rs7232). {ECO:0000269|PubMed:11401424}.			integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGAGAGAGAGTTCCCTGAAAG	0.488													T|||	1072	0.214058	0.0401	0.2277	5008	,	,		21441	0.0575		0.3608	False		,,,				2504	0.4499				p.T213S		Atlas-SNP	.											.	MS4A6A	85	.	0			c.A637T	GRCh37	CM067701	MS4A6A	M	rs7232	PASS	.	T	SER/THR,ILE/ASN,SER/THR	428,3974	208.5+/-229.5	15,398,1788	115.0	103.0	107.0		553,449,553	-5.1	0.0	11	dbSNP_52	107	3180,5410	483.3+/-371.1	605,1970,1720	yes	missense,missense,missense	MS4A6A	NM_022349.2,NM_152851.1,NM_152852.1	58,149,58	620,2368,3508	AA,AT,TT		37.0198,9.7229,27.7709	benign,benign,benign	185/226,150/179,185/249	59940599	3608,9384	2201	4295	6496	SO:0001583	missense	64231	exon7			AGAGAGTTCCCTG	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.553A>T	11.37:g.59940599T>A	ENSP00000436979:p.Thr185Ser	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Missense_Mutation	SNP	ENST00000530839.1	37	CCDS7981.1	428|428	0.19597069597069597|0.19597069597069597	19|19	0.03861788617886179|0.03861788617886179	93|93	0.2569060773480663|0.2569060773480663	38|38	0.06643356643356643|0.06643356643356643	278|278	0.36675461741424803|0.36675461741424803	T|T	12.82|12.82	2.051084|2.051084	0.36181|0.36181	0.097229|0.097229	0.370198|0.370198	ENSG00000110077|ENSG00000110077	ENST00000420732;ENST00000533023|ENST00000323961;ENST00000528851;ENST00000530839;ENST00000533989;ENST00000529054;ENST00000426738;ENST00000412309	T;T|T;T;T;T;T;T	0.23552|0.02216	3.09;1.9|4.39;4.39;4.39;4.39;4.39;4.39	4.66|4.66	-5.11|-5.11	0.02901|0.02901	.|.	.|1.816880	.|0.03459	.|N	.|0.211991	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B|P;P;P;P	0.24368|0.44139	0.102|0.626;0.573;0.626;0.827	B|B;B;B;B	0.21151|0.43413	0.033|0.419;0.294;0.419;0.419	T|T	0.35325|0.35325	-0.9793|-0.9793	7|8	0.38643|0.51188	T|T	0.18|0.08	.|.	2.2928|2.2928	0.04143|0.04143	0.1302:0.3935:0.1901:0.2862|0.1302:0.3935:0.1901:0.2862	rs7232;rs1019670;rs1128323;rs3177289;rs3185181;rs17341520;rs17349303;rs17602417;rs17845711;rs17858658;rs52799801;rs56458515;rs1019670|rs7232;rs1019670;rs1128323;rs3177289;rs3185181;rs17341520;rs17349303;rs17602417;rs17845711;rs17858658;rs52799801;rs56458515;rs1019670	150|140;213;213;185	Q9H2W1-3|E7EMT7;F8W9K1;E9PSA9;Q9H2W1	.|.;.;.;M4A6A_HUMAN	I|S	150;86|185;185;185;85;213;140;213	ENSP00000392921:N150I;ENSP00000436172:N86I|ENSP00000315878:T185S;ENSP00000431901:T185S;ENSP00000436979:T185S;ENSP00000435844:T213S;ENSP00000392770:T140S;ENSP00000403212:T213S	ENSP00000392921:N150I|ENSP00000315878:T185S	N|T	-|-	2|1	0|0	MS4A6A|MS4A6A	59697175|59697175	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.131000|0.131000	0.20780|0.20780	-1.954000|-1.954000	0.01525|0.01525	-0.877000|-0.877000	0.04012|0.04012	-0.250000|-0.250000	0.11733|0.11733	AAC|ACT	T|0.641;A|0.359	0.359	strong		0.488	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		
C1orf174	339448	hgsc.bcm.edu	37	1	3807388	3807388	+	Silent	SNP	G	G	A	rs4131373	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:3807388G>A	ENST00000361605.3	-	3	461	c.363C>T	c.(361-363)ctC>ctT	p.L121L	C1orf174_ENST00000486765.1_5'UTR	NM_207356.2	NP_997239.2	Q8IYL3	CA174_HUMAN	chromosome 1 open reading frame 174	121						nucleus (GO:0005634)				endometrium(1)|large_intestine(5)|lung(4)|prostate(1)	11	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)		TGCAGCCACCGAGAGGAAGAC	0.562													G|||	732	0.146166	0.2458	0.1239	5008	,	,		19489	0.0129		0.1829	False		,,,				2504	0.1268				p.L121L		Atlas-SNP	.											.	C1orf174	20	.	0			c.C363T						PASS	.	G		1059,3347	387.5+/-326.5	123,813,1267	60.0	56.0	57.0		363	-8.1	0.0	1	dbSNP_108	57	1527,7073	287.0+/-298.0	140,1247,2913	no	coding-synonymous	C1orf174	NM_207356.2		263,2060,4180	AA,AG,GG		17.7558,24.0354,19.8831		121/244	3807388	2586,10420	2203	4300	6503	SO:0001819	synonymous_variant	339448	exon3			GCCACCGAGAGGA	BC035643	CCDS53.1	1p36.32	2012-07-25			ENSG00000198912	ENSG00000198912			27915	protein-coding gene	gene with protein product						12477932	Standard	NM_207356		Approved	RP13-531C17.2	uc001alf.3	Q8IYL3	OTTHUMG00000003739	ENST00000361605.3:c.363C>T	1.37:g.3807388G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_207356	A8K0C8|A8MUG9|Q5SR20|Q6NX36	Silent	SNP	ENST00000361605.3	37	CCDS53.1																																																																																			G|0.835;A|0.165	0.165	strong		0.562	C1orf174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010539.1	NM_207356	
DNAH3	55567	hgsc.bcm.edu	37	16	20975522	20975522	+	Silent	SNP	A	A	G	rs3826156	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20975522A>G	ENST00000261383.3	-	53	9683	c.9684T>C	c.(9682-9684)agT>agC	p.S3228S	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3228	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TGTTCTTGGCACTTTCCACAA	0.478													G|||	455	0.0908546	0.0424	0.0663	5008	,	,		21974	0.1716		0.0726	False		,,,				2504	0.1094				p.S3228S		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T9684C						PASS	.	G		227,4175	804.3+/-415.8	7,213,1981	145.0	126.0	132.0		9684	-3.5	0.8	16	dbSNP_107	132	667,7933	787.0+/-407.6	23,621,3656	no	coding-synonymous	DNAH3	NM_017539.1		30,834,5637	GG,GA,AA		7.7558,5.1567,6.8759		3228/4117	20975522	894,12108	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon53			CTTGGCACTTTCC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.9684T>C	16.37:g.20975522A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			A|0.925;G|0.075	0.075	strong		0.478	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ZNF860	344787	hgsc.bcm.edu	37	3	32032397	32032397	+	Missense_Mutation	SNP	G	G	T	rs4955216	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:32032397G>T	ENST00000360311.4	+	2	2375	c.1826G>T	c.(1825-1827)cGc>cTc	p.R609L		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	609					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						CATTCACATCGCATTAGACAT	0.398													T|||	2157	0.430711	0.7988	0.3573	5008	,	,		22192	0.3006		0.1928	False		,,,				2504	0.364				p.R609L		Atlas-SNP	.											.	ZNF860	96	.	0			c.G1826T						PASS	.	T	LEU/ARG	935,449		322,291,79	43.0	36.0	38.0		1826	0.3	0.0	3	dbSNP_111	38	610,2572		58,494,1039	no	missense	ZNF860	NM_001137674.2	102	380,785,1118	TT,TG,GG		19.1703,32.4422,33.8371	benign	609/633	32032397	1545,3021	692	1591	2283	SO:0001583	missense	344787	exon2			CACATCGCATTAG	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1826G>T	3.37:g.32032397G>T	ENSP00000373274:p.Arg609Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	836	0.38278388278388276	385	0.782520325203252	125	0.3453038674033149	176	0.3076923076923077	150	0.19788918205804748	T	0.004	-2.318068	0.00235	0.675578	0.191703	ENSG00000197385	ENST00000360311	T	0.06687	3.27	0.314	0.314	0.15847	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00186	-1.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09122	-1.0689	7	.	.	.	.	5.1539	0.15025	0.0:0.0:0.6429:0.357	rs4955216;rs17028702;rs52831549;rs59940424;rs4955216	609	A6NHJ4	ZN860_HUMAN	L	609	ENSP00000373274:R609L	.	R	+	2	0	ZNF860	32007401	0.275000	0.24201	0.001000	0.08648	0.001000	0.01503	1.189000	0.32114	-0.768000	0.04626	-0.930000	0.02707	CGC	G|0.644;T|0.356	0.356	strong		0.398	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
ACOX1	51	hgsc.bcm.edu	37	17	73969835	73969835	+	Missense_Mutation	SNP	C	C	T	rs3744032	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73969835C>T	ENST00000301608.4	-	3	361	c.301G>A	c.(301-303)Ggc>Agc	p.G101S	ACOX1_ENST00000293217.5_Intron|ACOX1_ENST00000537812.1_Intron|ACOX1_ENST00000591857.1_Intron	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	101			G -> S (in dbSNP:rs3744032).		alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	TAATTGAGGCCCACAGGTTCC	0.448													C|||	325	0.0648962	0.0363	0.0548	5008	,	,		18029	0.1399		0.0596	False		,,,				2504	0.0389				p.G101S		Atlas-SNP	.											.	ACOX1	85	.	0			c.G301A						PASS	.	C	,,SER/GLY	158,4248	107.3+/-145.7	5,148,2050	90.0	85.0	87.0		,,301	-0.1	1.0	17	dbSNP_107	87	424,8176	131.8+/-189.6	8,408,3884	yes	intron,intron,missense	ACOX1	NM_001185039.1,NM_004035.6,NM_007292.5	,,56	13,556,5934	TT,TC,CC		4.9302,3.586,4.4749	,,	,,101/661	73969835	582,12424	2203	4300	6503	SO:0001583	missense	51	exon3			TGAGGCCCACAGG	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"""acyl-Coenzyme A oxidase 1, palmitoyl"""			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.301G>A	17.37:g.73969835C>T	ENSP00000301608:p.Gly101Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	37	CCDS11735.1	154	0.07051282051282051	20	0.04065040650406504	17	0.04696132596685083	73	0.12762237762237763	44	0.05804749340369393	C	14.98	2.697390	0.48202	0.03586	0.049302	ENSG00000161533	ENST00000301608	T	0.43688	0.94	5.36	-0.0733	0.13735	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	.	.	.	.	T	0.00300	0.0009	L	0.37507	1.11	0.09310	P	0.9999999999999721	B	0.10296	0.003	B	0.11329	0.006	T	0.23048	-1.0199	8	0.15499	T	0.54	-23.7572	9.8328	0.40952	0.0:0.6531:0.0:0.3469	rs3744032;rs52822122;rs60300640;rs3744032	101	Q15067	ACOX1_HUMAN	S	101	ENSP00000301608:G101S	ENSP00000301608:G101S	G	-	1	0	ACOX1	71481430	0.909000	0.30893	0.957000	0.39632	0.985000	0.73830	0.880000	0.28159	-0.101000	0.12219	-0.149000	0.13747	GGC	C|0.940;T|0.060	0.060	strong		0.448	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1		
ZHX3	23051	hgsc.bcm.edu	37	20	39832628	39832628	+	Missense_Mutation	SNP	T	T	C	rs17265513	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:39832628T>C	ENST00000309060.3	-	4	1344	c.929A>G	c.(928-930)aAt>aGt	p.N310S	ZHX3_ENST00000560361.1_Missense_Mutation_p.N310S|ZHX3_ENST00000559234.1_Missense_Mutation_p.N310S|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000544979.2_Missense_Mutation_p.N310S|ZHX3_ENST00000540170.1_Missense_Mutation_p.N310S|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000432768.2_Missense_Mutation_p.N310S			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	310	Required for homodimerization and interaction with NFYA.|Required for repressor activity.		N -> S (in dbSNP:rs17265513).		cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				CATGGCTGCATTGTACGTTGG	0.557													T|||	295	0.0589058	0.0113	0.0706	5008	,	,		20230	0.001		0.1948	False		,,,				2504	0.0348				p.N310S		Atlas-SNP	.											.	ZHX3	78	.	0			c.A929G						PASS	.	T	SER/ASN	175,4231	114.6+/-152.6	8,159,2036	104.0	95.0	98.0		929	4.8	0.8	20	dbSNP_123	98	1612,6988	299.4+/-304.4	162,1288,2850	yes	missense	ZHX3	NM_015035.3	46	170,1447,4886	CC,CT,TT		18.7442,3.9719,13.7398	probably-damaging	310/957	39832628	1787,11219	2203	4300	6503	SO:0001583	missense	23051	exon3			GCTGCATTGTACG	AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	15935	protein-coding gene	gene with protein product		609598	"""triple homeobox 1"""	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.929A>G	20.37:g.39832628T>C	ENSP00000312222:p.Asn310Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	117	66	0.564103	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	194	0.08882783882783883	4	0.008130081300813009	34	0.09392265193370165	1	0.0017482517482517483	155	0.20448548812664907	T	15.34	2.803175	0.50315	0.039719	0.187442	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262;ENST00000432768	T;T;T;T;T	0.41758	0.99;2.4;2.4;2.16;0.99	5.88	4.79	0.61399	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.044464	0.85682	D	0.000000	T	0.00109	0.0003	M	0.79926	2.475	0.22500	P	0.999041207	D;D;D	0.58268	0.974;0.974;0.982	P;P;P	0.58970	0.829;0.78;0.849	T	0.04165	-1.0972	9	0.36615	T	0.2	-25.1632	11.8515	0.52413	0.0:0.068:0.0:0.932	rs17265513;rs17265513	310;310;310	A8K8Q0;Q9H4I2;F5H820	.;ZHX3_HUMAN;.	S	310;310;310;310;88;310	ENSP00000312222:N310S;ENSP00000362360:N310S;ENSP00000442290:N310S;ENSP00000443783:N310S;ENSP00000415498:N310S	ENSP00000312222:N310S	N	-	2	0	ZHX3	39266042	1.000000	0.71417	0.817000	0.32601	0.778000	0.44026	4.110000	0.57831	1.055000	0.40461	0.533000	0.62120	AAT	T|0.891;C|0.109	0.109	strong		0.557	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035	
TMEM5	10329	hgsc.bcm.edu	37	12	64173807	64173807	+	Missense_Mutation	SNP	G	G	A	rs61935924	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:64173807G>A	ENST00000261234.6	+	1	225	c.67G>A	c.(67-69)Gct>Act	p.A23T	TMEM5_ENST00000537373.1_5'Flank|RP11-415I12.3_ENST00000509615.2_RNA	NM_014254.1	NP_055069.1	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5	23						integral component of plasma membrane (GO:0005887)				breast(1)|large_intestine(3)|liver(2)|lung(7)|prostate(1)|skin(1)	15		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		CTCCCTCTACGCTGCCTACCA	0.716													G|||	262	0.0523163	0.0166	0.0562	5008	,	,		8945	0.0129		0.1044	False		,,,				2504	0.0849				p.A23T		Atlas-SNP	.											.	TMEM5	35	.	0			c.G67A						PASS	.	G	THR/ALA	125,4281	91.1+/-129.8	0,125,2078	51.0	48.0	49.0		67	2.5	1.0	12	dbSNP_129	49	903,7697	200.7+/-244.4	41,821,3438	yes	missense	TMEM5	NM_014254.1	58	41,946,5516	AA,AG,GG		10.5,2.837,7.904	possibly-damaging	23/444	64173807	1028,11978	2203	4300	6503	SO:0001583	missense	10329	exon1			CTCTACGCTGCCT	AB015633	CCDS8966.1, CCDS61179.1	12q14.1	2013-05-07			ENSG00000118600	ENSG00000118600			13530	protein-coding gene	gene with protein product		605862				10072769, 23217329	Standard	NM_014254		Approved	HP10481	uc001srq.2	Q9Y2B1	OTTHUMG00000168730	ENST00000261234.6:c.67G>A	12.37:g.64173807G>A	ENSP00000261234:p.Ala23Thr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_014254	A8K017|Q6PKD6	Missense_Mutation	SNP	ENST00000261234.6	37	CCDS8966.1	121	0.0554029304029304	12	0.024390243902439025	25	0.06906077348066299	6	0.01048951048951049	78	0.10290237467018469	G	24.5	4.540086	0.85917	0.02837	0.105	ENSG00000118600	ENST00000261234	T	0.32023	1.47	3.39	2.5	0.30297	.	0.000000	0.85682	D	0.000000	T	0.01353	0.0044	L	0.49350	1.555	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00123	-1.2026	9	.	.	.	-23.3885	6.7536	0.23501	0.1293:0.0:0.8707:0.0	rs61935924	23	Q9Y2B1	TMEM5_HUMAN	T	23	ENSP00000261234:A23T	.	A	+	1	0	TMEM5	62460074	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.363000	0.59473	1.009000	0.39289	0.462000	0.41574	GCT	G|0.927;A|0.073	0.073	strong		0.716	TMEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400821.1	NM_014254	
SNX29	92017	hgsc.bcm.edu	37	16	12142470	12142470	+	Silent	SNP	C	C	T	rs36013478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:12142470C>T	ENST00000566228.1	+	7	810	c.741C>T	c.(739-741)gtC>gtT	p.V247V	SNX29_ENST00000568359.1_3'UTR	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	247						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						CCAGGAATGTCAGTGCTGGTG	0.562													C|||	48	0.00958466	0.0	0.0346	5008	,	,		21969	0.0		0.0239	False		,,,				2504	0.0				p.V247V		Atlas-SNP	.											.	SNX29	60	.	0			c.C741T						PASS	.	C		19,4375	26.2+/-53.5	1,17,2179	113.0	108.0	110.0		741	2.3	0.0	16	dbSNP_126	110	192,8408	85.3+/-147.7	1,190,4109	no	coding-synonymous	SNX29	NM_032167.3		2,207,6288	TT,TC,CC		2.2326,0.4324,1.6238		247/376	12142470	211,12783	2197	4300	6497	SO:0001819	synonymous_variant	92017	exon7			GAATGTCAGTGCT	AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"""Sorting nexins"""	30542	protein-coding gene	gene with protein product			"""RUN domain containing 2A"""	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.741C>T	16.37:g.12142470C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Silent	SNP	ENST00000566228.1	37	CCDS10553.2																																																																																			C|0.983;T|0.017	0.017	strong		0.562	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
SYNE3	161176	hgsc.bcm.edu	37	14	95918625	95918625	+	Silent	SNP	T	T	C	rs4905318	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:95918625T>C	ENST00000334258.5	-	6	1247	c.1233A>G	c.(1231-1233)ccA>ccG	p.P411P	SYNE3_ENST00000557275.1_Silent_p.P411P|SYNE3_ENST00000554873.1_Silent_p.P168P|SYNE3_ENST00000553340.1_Silent_p.P411P	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	411					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						TATCAGAGAGTGGCTTCAGGT	0.612											OREG0022900	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2308	0.460863	0.382	0.6023	5008	,	,		17704	0.5655		0.4105	False		,,,				2504	0.411				p.P411P		Atlas-SNP	.											.	SYNE3	130	.	0			c.A1233G						PASS	.	T		1715,2691	515.5+/-368.9	338,1039,826	116.0	97.0	104.0		1233	-9.4	0.1	14	dbSNP_111	104	3637,4963	522.0+/-380.0	752,2133,1415	no	coding-synonymous	C14orf49	NM_152592.3		1090,3172,2241	CC,CT,TT		42.2907,38.9242,41.1502		411/976	95918625	5352,7654	2203	4300	6503	SO:0001819	synonymous_variant	161176	exon6			AGAGAGTGGCTTC	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.1233A>G	14.37:g.95918625T>C		Somatic	131	0	0	1316	WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	37	CCDS9935.1																																																																																			T|0.562;C|0.438	0.438	strong		0.612	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
ZFHX3	463	hgsc.bcm.edu	37	16	72992630	72992630	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992630G>T	ENST00000268489.5	-	2	2087	c.1415C>A	c.(1414-1416)gCg>gAg	p.A472E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	472	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				ctcctcctccgcctcttcctc	0.577																																					p.A472E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C1415A						PASS	.						38.0	42.0	41.0					16																	72992630		2198	4300	6498	SO:0001583	missense	463	exon2			TCCTCCGCCTCTT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1415C>A	16.37:g.72992630G>T	ENSP00000268489:p.Ala472Glu	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	53	8	0.150943	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	G	0.252	-1.005988	0.02112	.	.	ENSG00000140836	ENST00000268489	T	0.73258	-0.73	4.63	-9.25	0.00666	.	1.213240	0.06591	N	0.751946	T	0.34048	0.0884	N	0.08118	0	0.54753	D	0.999985	B	0.23490	0.086	B	0.14023	0.01	T	0.29912	-0.9996	10	0.02654	T	1	.	3.1253	0.06405	0.2364:0.0793:0.1273:0.5569	.	472	Q15911	ZFHX3_HUMAN	E	472	ENSP00000268489:A472E	ENSP00000268489:A472E	A	-	2	0	ZFHX3	71550131	0.000000	0.05858	0.020000	0.16555	0.258000	0.26162	-0.323000	0.07997	-1.925000	0.01063	-0.759000	0.03464	GCG	.	.	none		0.577	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
SULF2	55959	hgsc.bcm.edu	37	20	46385955	46385955	+	Silent	SNP	C	C	T	rs61730618	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:46385955C>T	ENST00000359930.4	-	2	1004	c.153G>A	c.(151-153)acG>acA	p.T51T	SULF2_ENST00000361612.4_Silent_p.T51T|SULF2_ENST00000484875.1_Silent_p.T51T|SULF2_ENST00000467815.1_Silent_p.T51T	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	51					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						CCTGGTCGTCCGTCAGCACCA	0.657													C|||	83	0.0165735	0.0008	0.013	5008	,	,		17515	0.0		0.0388	False		,,,				2504	0.0348				p.T51T		Atlas-SNP	.											.	SULF2	131	.	0			c.G153A						PASS	.	C	,,	31,4351		0,31,2160	51.0	37.0	41.0		153,153,153	-9.5	0.1	20	dbSNP_129	41	218,8342		1,216,4063	no	coding-synonymous,coding-synonymous,coding-synonymous	SULF2	NM_001161841.1,NM_018837.3,NM_198596.2	,,	1,247,6223	TT,TC,CC		2.5467,0.7074,1.924	,,	51/871,51/871,51/868	46385955	249,12693	2191	4280	6471	SO:0001819	synonymous_variant	55959	exon2			GTCGTCCGTCAGC	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.153G>A	20.37:g.46385955C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Silent	SNP	ENST00000359930.4	37	CCDS13408.1																																																																																			C|0.982;T|0.018	0.018	strong		0.657	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
PTPN3	5774	hgsc.bcm.edu	37	9	112145799	112145799	+	Silent	SNP	G	G	A	rs2304742	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:112145799G>A	ENST00000374541.2	-	23	2390	c.2286C>T	c.(2284-2286)ccC>ccT	p.P762P	PTPN3_ENST00000446349.1_Silent_p.P586P|PTPN3_ENST00000412145.1_Silent_p.P631P|PTPN3_ENST00000262539.3_Silent_p.P608P|PTPN3_ENST00000394827.3_Silent_p.P230P	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	762	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						TCATGACGTCGGGGGGATCTG	0.557													G|||	258	0.0515176	0.0008	0.1052	5008	,	,		17925	0.1399		0.0268	False		,,,				2504	0.0164				p.P762P		Atlas-SNP	.											.	PTPN3	106	.	0			c.C2286T						PASS	.	G	,,,,,	30,4376	36.0+/-67.5	0,30,2173	127.0	119.0	122.0		2151,1893,1758,1425,1290,2286	-7.5	0.0	9	dbSNP_100	122	277,8323	104.8+/-165.8	6,265,4029	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN3	NM_001145368.1,NM_001145369.1,NM_001145370.1,NM_001145371.1,NM_001145372.1,NM_002829.3	,,,,,	6,295,6202	AA,AG,GG		3.2209,0.6809,2.3604	,,,,,	717/869,631/783,586/738,475/627,430/582,762/914	112145799	307,12699	2203	4300	6503	SO:0001819	synonymous_variant	5774	exon23			GACGTCGGGGGGA		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.2286C>T	9.37:g.112145799G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	153	85	0.555556	NM_002829	A0AUW9|E7EN99|E9PGU7	Silent	SNP	ENST00000374541.2	37	CCDS6776.1																																																																																			G|0.959;A|0.041	0.041	strong		0.557	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
DAOA	267012	hgsc.bcm.edu	37	13	106119446	106119446	+	Missense_Mutation	SNP	G	G	A	rs2391191	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:106119446G>A	ENST00000375936.3	+	2	135	c.89G>A	c.(88-90)aGg>aAg	p.R30K	DAOA_ENST00000329625.5_5'UTR|DAOA-AS1_ENST00000448407.1_RNA	NM_001161812.1|NM_172370.3	NP_001155284.1|NP_758958.3	P59103	DAOA_HUMAN	D-amino acid oxidase activator	30			R -> K (in dbSNP:rs2391191). {ECO:0000269|PubMed:12364586}.		negative regulation of D-amino-acid oxidase activity (GO:1900758)|positive regulation of catalytic activity (GO:0043085)	Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	13	Lung NSC(43;0.01)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					GGTTTTCAAAGGAGCATTCTT	0.299													G|||	1812	0.361821	0.0673	0.4049	5008	,	,		15285	0.626		0.3877	False		,,,				2504	0.4305				p.R30K		Atlas-SNP	.											.	DAOA	26	.	0			c.G89A	GRCh37	CM045704	DAOA	M	rs2391191	PASS	.	G	,,LYS/ARG	411,3175		32,347,1414	85.0	82.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,89	-0.3	0.0	13	dbSNP_100	83	3026,5090		573,1880,1605	yes	utr-5,utr-5,missense	DAOA	NM_001161812.1,NM_001161814.1,NM_172370.3	,,26	605,2227,3019	AA,AG,GG		37.2844,11.4612,29.371	,,	,,30/154	106119446	3437,8265	1793	4058	5851	SO:0001583	missense	267012	exon2			TTCAAAGGAGCAT	AY138547	CCDS41905.1, CCDS53880.1, CCDS59242.1	13q33.2	2011-08-01			ENSG00000182346	ENSG00000182346			21191	protein-coding gene	gene with protein product	"""G72 transcript"""	607408				12364586, 15057823	Standard	NM_001161814		Approved	G72	uc010tjg.2	P59103	OTTHUMG00000041333	ENST00000375936.3:c.89G>A	13.37:g.106119446G>A	ENSP00000365103:p.Arg30Lys	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_172370	A6NKG7|Q0VAE6|Q5VX59|Q86Y17|Q8IWM4	Missense_Mutation	SNP	ENST00000375936.3	37	CCDS41905.1	844	0.38644688644688646	29	0.05894308943089431	143	0.39502762430939226	374	0.6538461538461539	298	0.39313984168865435	G	12.27	1.888219	0.33348	0.114612	0.372844	ENSG00000182346	ENST00000375936	T	0.29142	1.58	3.17	-0.301	0.12800	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.33103	0.397	B	0.28638	0.092	T	0.42865	-0.9426	8	0.09338	T	0.73	.	0.7383	0.00969	0.1871:0.2174:0.3739:0.2216	rs2391191;rs52812974;rs59455029;rs2391191	30	P59103	DAOA_HUMAN	K	30	ENSP00000365103:R30K	ENSP00000365103:R30K	R	+	2	0	DAOA	104917447	0.000000	0.05858	0.000000	0.03702	0.249000	0.25844	0.160000	0.16462	-0.095000	0.12351	0.557000	0.71058	AGG	G|0.570;A|0.430	0.430	strong		0.299	DAOA-005	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099040.2	NM_172370	
MKI67	4288	hgsc.bcm.edu	37	10	129904474	129904474	+	Missense_Mutation	SNP	G	G	A	rs61738284	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:129904474G>A	ENST00000368654.3	-	13	6005	c.5630C>T	c.(5629-5631)cCc>cTc	p.P1877L	MKI67_ENST00000368653.3_Missense_Mutation_p.P1517L	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1877	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GCTTCTCTTGGGCCGTTGCTT	0.468													G|||	515	0.102835	0.0666	0.1556	5008	,	,		20450	0.1359		0.0785	False		,,,				2504	0.1053				p.P1877L		Atlas-SNP	.											.	MKI67	363	.	0			c.C5630T						PASS	.	G	LEU/PRO,LEU/PRO	295,4111	161.8+/-193.9	11,273,1919	257.0	262.0	260.0		4550,5630	-4.0	0.0	10	dbSNP_129	260	771,7829	183.7+/-231.9	39,693,3568	no	missense,missense	MKI67	NM_001145966.1,NM_002417.4	98,98	50,966,5487	AA,AG,GG		8.9651,6.6954,8.1962	probably-damaging,probably-damaging	1517/2897,1877/3257	129904474	1066,11940	2203	4300	6503	SO:0001583	missense	4288	exon13			CTCTTGGGCCGTT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.5630C>T	10.37:g.129904474G>A	ENSP00000357643:p.Pro1877Leu	Somatic	347	1	0.00288184		WXS	Illumina HiSeq	Phase_I	435	186	0.427586	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	209	0.09569597069597069	33	0.06707317073170732	39	0.10773480662983426	79	0.1381118881118881	58	0.07651715039577836	G	7.574	0.667296	0.14710	0.066954	0.089651	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02158	4.42;4.42	3.01	-4.0	0.04057	.	2.514200	0.02262	N	0.067604	T	0.00012	0.0000	N	0.17800	0.525	0.80722	P	0.0	B;B;B	0.29232	0.008;0.118;0.238	B;B;B	0.33890	0.014;0.172;0.085	T	0.43114	-0.9411	9	0.25106	T	0.35	.	4.3421	0.11115	0.3141:0.3137:0.3722:0.0	rs61738284	1876;1517;1877	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	L	1877;1517;1876	ENSP00000357643:P1877L;ENSP00000357642:P1517L	ENSP00000357642:P1517L	P	-	2	0	MKI67	129794464	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.347000	0.07750	-1.098000	0.03038	-0.291000	0.09656	CCC	G|0.915;A|0.085	0.085	strong		0.468	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
PPP2R1B	5519	hgsc.bcm.edu	37	11	111608216	111608216	+	IGR	SNP	T	T	A	rs61756429	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:111608216T>A	ENST00000527614.1	-	0	5587				PPP2R1B_ENST00000426998.2_Missense_Mutation_p.N559Y|PPP2R1B_ENST00000311129.5_Missense_Mutation_p.N623Y|PPP2R1B_ENST00000530787.1_5'Flank	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta						apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		GGGAAGTGGTTCTTGTCAGCC	0.597													T|||	10	0.00199681	0.0	0.0043	5008	,	,		20031	0.0		0.007	False		,,,				2504	0.0				p.N623Y		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A1867T						PASS	.	T	TYR/ASN,TYR/ASN	13,4389	21.2+/-45.6	0,13,2188	155.0	128.0	137.0		1867,1675	4.1	1.0	11	dbSNP_129	137	86,8508	48.9+/-108.6	0,86,4211	yes	missense,missense	PPP2R1B	NM_181699.2,NM_181700.1	143,143	0,99,6399	AA,AT,TT		1.0007,0.2953,0.7618	possibly-damaging,possibly-damaging	623/668,559/604	111608216	99,12897	2201	4297	6498	SO:0001628	intergenic_variant	5519	exon15			AGTGGTTCTTGTC	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9303	protein-coding gene	gene with protein product	"""PP2A-A-beta"", ""protein phosphatase 2A, regulatory subunit A, beta isoform"""	603113	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"""			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741		11.37:g.111608216T>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_181699	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	37	CCDS8349.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	10.82	1.458179	0.26161	0.002953	0.010007	ENSG00000137713	ENST00000311129;ENST00000426998	.	.	.	5.25	4.13	0.48395	.	0.617749	0.15812	N	0.243438	T	0.27933	0.0688	N	0.08118	0	0.80722	D	1	P;D	0.54207	0.94;0.965	P;P	0.51135	0.459;0.66	T	0.18493	-1.0335	9	0.87932	D	0	-10.7806	7.9175	0.29827	0.0:0.0914:0.0:0.9086	rs61756429	559;623	B4DWW5;P30154-2	.;.	Y	623;559	.	ENSP00000311344:N623Y	N	-	1	0	PPP2R1B	111113426	1.000000	0.71417	0.991000	0.47740	0.214000	0.24535	1.866000	0.39489	1.132000	0.42129	0.496000	0.49642	AAC	T|0.992;A|0.008	0.008	strong		0.597	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716	
PXMP2	5827	hgsc.bcm.edu	37	12	133272470	133272470	+	Splice_Site	SNP	G	G	T	rs74727297	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133272470G>T	ENST00000317479.3	+	3	302	c.237G>T	c.(235-237)ggG>ggT	p.G79G	RP13-672B3.2_ENST00000537262.1_Intron|PXMP2_ENST00000428960.2_5'UTR|PXMP2_ENST00000545677.1_Intron|PXMP2_ENST00000543589.1_Intron|PXMP2_ENST00000539093.1_Intron	NM_018663.1	NP_061133.1	Q9NR77	PXMP2_HUMAN	peroxisomal membrane protein 2, 22kDa	79						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|protein complex (GO:0043234)				large_intestine(1)|liver(2)|lung(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.86e-08)|Epithelial(86;2.47e-07)|all cancers(50;6.85e-06)		GGGGCCTCAGGTTCTTCTTCA	0.577													G|||	283	0.0565096	0.0045	0.0447	5008	,	,		16917	0.1032		0.1004	False		,,,				2504	0.0419				p.G79G		Atlas-SNP	.											.	PXMP2	15	.	0			c.G237T						PASS	.	G		70,4336	64.7+/-102.0	0,70,2133	54.0	54.0	54.0		237	-2.4	0.8	12	dbSNP_131	54	920,7680	204.7+/-247.3	60,800,3440	yes	coding-synonymous-near-splice	PXMP2	NM_018663.1		60,870,5573	TT,TG,GG		10.6977,1.5887,7.6119		79/196	133272470	990,12016	2203	4300	6503	SO:0001630	splice_region_variant	5827	exon3			CCTCAGGTTCTTC		CCDS9279.1	12q24	2010-08-18	2002-08-29		ENSG00000176894	ENSG00000176894			9716	protein-coding gene	gene with protein product			"""peroxisomal membrane protein 2 (22kD)"""			11590176	Standard	NM_018663		Approved	PMP22	uc001ukt.3	Q9NR77	OTTHUMG00000168019	ENST00000317479.3:c.237-1G>T	12.37:g.133272470G>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_018663		Silent	SNP	ENST00000317479.3	37	CCDS9279.1																																																																																			G|0.928;T|0.072	0.072	strong		0.577	PXMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397553.1	NM_018663	Silent
GTF2IRD2B	389524	hgsc.bcm.edu	37	7	74563753	74563753	+	Silent	SNP	G	G	A	rs202156190	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:74563753G>A	ENST00000312575.7	+	16	1675	c.1500G>A	c.(1498-1500)tcG>tcA	p.S500S	GTF2IRD2B_ENST00000418185.2_Silent_p.S47S	NM_001003795.2	NP_001003795.1	Q6EKJ0	GTD2B_HUMAN	GTF2I repeat domain containing 2B	500					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S500S(1)		endometrium(1)|ovary(2)|prostate(1)	4						tcttaggctcgtcagacaccg	0.488																																					p.S500S		Atlas-SNP	.											GTF2IRD2B,NS,carcinoma,0,1	GTF2IRD2B	30	1	1	Substitution - coding silent(1)	ovary(1)	c.G1500A						scavenged	.						2.0	1.0	1.0					7																	74563753		845	1893	2738	SO:0001819	synonymous_variant	389524	exon16			AGGCTCGTCAGAC	AY312850	CCDS34659.1	7q11.23	2014-05-06			ENSG00000174428	ENSG00000174428			33125	protein-coding gene	gene with protein product		608900				15100712	Standard	XM_005277580		Approved		uc003ubt.3	Q6EKJ0	OTTHUMG00000181534	ENST00000312575.7:c.1500G>A	7.37:g.74563753G>A		Somatic	688	2	0.00290698		WXS	Illumina HiSeq	Phase_I	907	176	0.194046	NM_001003795	B2RNE9|Q69GU6|Q8N979|Q9H739	Silent	SNP	ENST00000312575.7	37	CCDS34659.1																																																																																			.	.	weak		0.488	GTF2IRD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342728.1	NM_001003795	
EMR3	84658	hgsc.bcm.edu	37	19	14769339	14769339	+	Missense_Mutation	SNP	C	C	G	rs4606855	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14769339C>G	ENST00000253673.5	-	5	479	c.379G>C	c.(379-381)Gag>Cag	p.E127Q	EMR3_ENST00000599900.1_5'UTR|EMR3_ENST00000443157.2_Intron|EMR3_ENST00000344373.4_Missense_Mutation_p.E75Q	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	127			E -> Q (in dbSNP:rs4606855). {ECO:0000269|PubMed:12975309}.		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						TTCCTGCCCTCGGTTGTCTTT	0.498													G|||	4286	0.855831	0.9682	0.7478	5008	,	,		8290	0.8849		0.7227	False		,,,				2504	0.8875				p.E127Q		Atlas-SNP	.											.	EMR3	99	.	0			c.G379C						PASS	.	G	GLN/GLU	4091,315	169.8+/-200.3	1900,291,12	86.0	76.0	80.0		379	-5.8	0.0	19	dbSNP_111	80	6224,2376	394.6+/-344.7	2273,1678,349	yes	missense	EMR3	NM_032571.3	29	4173,1969,361	GG,GC,CC		27.6279,7.1493,20.6905	benign	127/653	14769339	10315,2691	2203	4300	6503	SO:0001583	missense	84658	exon5			TGCCCTCGGTTGT	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"""-"", ""GPCR / Class B : Orphans"""	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.379G>C	19.37:g.14769339C>G	ENSP00000253673:p.Glu127Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_032571		Missense_Mutation	SNP	ENST00000253673.5	37	CCDS12315.1	1753	0.8026556776556777	466	0.9471544715447154	251	0.6933701657458563	479	0.8374125874125874	557	0.7348284960422163	G	0.024	-1.388845	0.01185	0.928507	0.723721	ENSG00000131355	ENST00000253673;ENST00000344373	T;T	0.56275	0.47;2.84	2.93	-5.85	0.02311	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.12630	0.001;0.006	B;B	0.10450	0.001;0.005	T	0.12604	-1.0541	8	0.32370	T	0.25	.	7.9104	0.29787	0.0:0.4:0.4103:0.1897	rs4606855;rs17275227;rs58662049;rs4606855	75;127	Q9BY15-2;Q9BY15	.;EMR3_HUMAN	Q	127;75	ENSP00000253673:E127Q;ENSP00000340758:E75Q	ENSP00000253673:E127Q	E	-	1	0	EMR3	14630339	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.756000	0.04777	-2.680000	0.00409	-1.580000	0.00857	GAG	C|0.200;G|0.800	0.800	strong		0.498	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571	
MGLL	11343	hgsc.bcm.edu	37	3	127413881	127413881	+	Silent	SNP	T	T	C	rs4881	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:127413881T>C	ENST00000434178.2	-	7	1619	c.723A>G	c.(721-723)ctA>ctG	p.L241L	MGLL_ENST00000398104.1_Silent_p.L241L|MGLL_ENST00000398101.3_Silent_p.L215L|MGLL_ENST00000453507.2_Silent_p.L221L|MGLL_ENST00000265052.5_Silent_p.L251L|MGLL_ENST00000476682.1_5'UTR			Q99685	MGLL_HUMAN	monoglyceride lipase	241					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						TGCTGTCACATAGGCGATCGG	0.622													C|||	503	0.100439	0.1974	0.0778	5008	,	,		17787	0.0129		0.0944	False		,,,				2504	0.0818				p.L251L		Atlas-SNP	.											.	MGLL	19	.	0			c.A753G						PASS	.	C	,	652,3480		50,552,1464	50.0	57.0	55.0		723,753	-0.9	1.0	3	dbSNP_52	55	783,7603		42,699,3452	no	coding-synonymous,coding-synonymous	MGLL	NM_001003794.1,NM_007283.5	,	92,1251,4916	CC,CT,TT		9.337,15.7793,11.4635	,	241/304,251/314	127413881	1435,11083	2066	4193	6259	SO:0001819	synonymous_variant	11343	exon7			GTCACATAGGCGA	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.723A>G	3.37:g.127413881T>C		Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	309	150	0.485437	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	ENST00000434178.2	37	CCDS43148.1	199	0.09111721611721611	87	0.17682926829268292	35	0.09668508287292818	7	0.012237762237762238	70	0.09234828496042216	C	11.08	1.534009	0.27387	0.157793	0.09337	ENSG00000074416	ENST00000496306	.	.	.	5.02	-0.899	0.10547	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999997122	.	.	.	.	.	.	T	0.21759	-1.0236	3	.	.	.	-7.5383	5.3013	0.15780	0.2029:0.3099:0.4138:0.0734	rs4881;rs2070258;rs3183250;rs4881	.	.	.	C	147	.	.	Y	-	2	0	MGLL	128896571	0.944000	0.32072	0.975000	0.42487	0.991000	0.79684	-0.074000	0.11450	-0.464000	0.06963	-0.186000	0.12905	TAT	T|0.903;C|0.097	0.097	strong		0.622	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283	
KNSTRN	90417	hgsc.bcm.edu	37	15	40685406	40685406	+	Missense_Mutation	SNP	A	A	T	rs8036457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:40685406A>T	ENST00000416151.2	+	9	950	c.835A>T	c.(835-837)Aat>Tat	p.N279Y	KNSTRN_ENST00000448395.2_Intron|KNSTRN_ENST00000249776.8_Intron|KNSTRN_ENST00000608100.1_Intron	NM_001142761.1	NP_001136233.1			kinetochore-localized astrin/SPAG5 binding protein																		TGCTTGGATGAATCATGGGAT	0.393													A|||	578	0.115415	0.1929	0.0922	5008	,	,		19439	0.0129		0.1431	False		,,,				2504	0.1043				p.N279Y		Atlas-SNP	.											.	.	.	.	0			c.A835T						PASS	.	A	TYR/ASN,,	548,2588		57,434,1077	204.0	179.0	187.0		835,,	0.0	0.0	15	dbSNP_116	187	1050,6114		84,882,2616	yes	missense,intron,intron	C15orf23	NM_001142761.1,NM_001142762.1,NM_033286.3	143,,	141,1316,3693	TT,TA,AA		14.6566,17.4745,15.5146	,,	279/287,,	40685406	1598,8702	1568	3582	5150	SO:0001583	missense	90417	exon9			TGGATGAATCATG	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"""small kinetochore-associated protein"", ""kinetochore-localized astrin-binding protein"", ""TRAF4 associated factor 1"""	614718	"""chromosome 15 open reading frame 23"""	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000416151.2:c.835A>T	15.37:g.40685406A>T	ENSP00000391233:p.Asn279Tyr	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	169	10	0.0591716	NM_001142761		Missense_Mutation	SNP	ENST00000416151.2	37	CCDS45226.1	270	0.12362637362637363	101	0.20528455284552846	35	0.09668508287292818	5	0.008741258741258742	129	0.17018469656992086	A	14.50	2.553931	0.45487	0.174745	0.146566	ENSG00000128944	ENST00000416151	T	0.24908	1.83	3.55	0.0151	0.14103	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.58432	P	1.0000000000287557E-6	D	0.54207	0.965	P	0.51229	0.663	T	0.11131	-1.0600	7	0.87932	D	0	.	5.6657	0.17695	0.6196:0.0:0.3804:0.0	rs8036457;rs8036457	279	Q9Y448-2	.	Y	279	ENSP00000391233:N279Y	ENSP00000391233:N279Y	N	+	1	0	C15orf23	38472698	0.000000	0.05858	0.001000	0.08648	0.104000	0.19210	0.611000	0.24268	-0.014000	0.14175	0.482000	0.46254	AAT	A|0.876;T|0.124	0.124	strong		0.393	KNSTRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000418634.1	NM_001142761	
OPRK1	4986	hgsc.bcm.edu	37	8	54142157	54142157	+	Silent	SNP	T	T	C	rs702764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:54142157T>C	ENST00000265572.3	-	4	1140	c.843A>G	c.(841-843)gcA>gcG	p.A281A	OPRK1_ENST00000524278.1_Silent_p.A192A|RP11-162D9.3_ENST00000524425.1_RNA|OPRK1_ENST00000520287.1_Silent_p.A281A	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	281					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)			NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CGACGAAGACTGCCACCACCA	0.567													C|||	1225	0.244609	0.5416	0.2709	5008	,	,		19584	0.0764		0.1402	False		,,,				2504	0.1053				p.A281A		Atlas-SNP	.											.	OPRK1	90	.	0			c.A843G						PASS	.	C		2062,2344	608.8+/-391.2	485,1092,626	73.0	77.0	76.0		843	-11.6	0.0	8	dbSNP_86	76	1219,7381	762.7+/-407.6	101,1017,3182	no	coding-synonymous	OPRK1	NM_000912.3		586,2109,3808	CC,CT,TT		14.1744,46.7998,25.2268		281/381	54142157	3281,9725	2203	4300	6503	SO:0001819	synonymous_variant	4986	exon4			GAAGACTGCCACC		CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"""GPCR / Class A : Opioid receptors"""	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.843A>G	8.37:g.54142157T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_000912	E5RHC9|Q499G4	Silent	SNP	ENST00000265572.3	37	CCDS6152.1																																																																																			T|0.752;C|0.248	0.248	strong		0.567	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152457795	152457795	+	Silent	SNP	C	C	T	rs118187988	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:152457795C>T	ENST00000367255.5	-	141	26218	c.25617G>A	c.(25615-25617)gaG>gaA	p.E8539E	SYNE1_ENST00000341594.5_Silent_p.E8151E|SYNE1_ENST00000265368.4_Silent_p.E8539E|SYNE1_ENST00000448038.1_Silent_p.E8491E|SYNE1_ENST00000356820.4_Silent_p.E3063E|SYNE1_ENST00000539504.1_Silent_p.E694E|SYNE1_ENST00000423061.1_Silent_p.E8491E|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000354674.4_Silent_p.E717E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8539					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CCCGCCACTCCTCCAGCAGAG	0.602										HNSCC(10;0.0054)			C|||	7	0.00139776	0.0	0.0014	5008	,	,		18729	0.001		0.005	False		,,,				2504	0.0				p.E8539E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G25617A						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	53.0	49.0	50.0		25473,25617	1.8	1.0	6	dbSNP_133	50	16,8584	12.6+/-44.7	0,16,4284	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	,	8491/8750,8539/8798	152457795	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon141			CCACTCCTCCAGC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.25617G>A	6.37:g.152457795C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			C|0.998;T|0.002	0.002	strong		0.602	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
GALNT15	117248	hgsc.bcm.edu	37	3	16217110	16217110	+	Missense_Mutation	SNP	C	C	T	rs11715981	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:16217110C>T	ENST00000339732.5	+	1	955	c.452C>T	c.(451-453)cCg>cTg	p.P151L	GALNT15_ENST00000437509.1_Missense_Mutation_p.P151L|GALNT15_ENST00000470031.1_3'UTR	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	151			P -> L (in dbSNP:rs11715981).		cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										GAGTTGACCCCGTTCAGCCTG	0.642													C|||	164	0.0327476	0.0537	0.0231	5008	,	,		19243	0.0		0.0358	False		,,,				2504	0.0419				p.P151L		Atlas-SNP	.											.	.	.	.	0			c.C452T						PASS	.	C	LEU/PRO	224,4176		5,214,1981	38.0	31.0	33.0		452	2.4	0.0	3	dbSNP_120	33	269,8329		2,265,4032	yes	missense	GALNTL2	NM_054110.4	98	7,479,6013	TT,TC,CC		3.1286,5.0909,3.7929	benign	151/640	16217110	493,12505	2200	4299	6499	SO:0001583	missense	117248	exon1			TGACCCCGTTCAG	AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	21531	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 15"""	615131	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"""	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.452C>T	3.37:g.16217110C>T	ENSP00000344260:p.Pro151Leu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	88	48	0.545455	NM_054110	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	37	CCDS33711.1	70	0.03205128205128205	37	0.07520325203252033	7	0.019337016574585635	0	0.0	26	0.03430079155672823	C	3.127	-0.179357	0.06380	0.050909	0.031286	ENSG00000131386	ENST00000339732;ENST00000437509	T;T	0.56444	0.67;0.46	4.28	2.44	0.29823	.	0.505078	0.19473	N	0.113405	T	0.02304	0.0071	L	0.34521	1.04	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.07347	-1.0777	10	0.72032	D	0.01	.	6.3326	0.21279	0.0:0.6814:0.149:0.1696	rs11715981;rs11715981	151	Q8N3T1	GLTL2_HUMAN	L	151	ENSP00000344260:P151L;ENSP00000395873:P151L	ENSP00000344260:P151L	P	+	2	0	GALNTL2	16192114	0.000000	0.05858	0.007000	0.13788	0.098000	0.18820	-0.328000	0.07945	0.343000	0.23821	-0.932000	0.02703	CCG	C|0.967;T|0.033	0.033	strong		0.642	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110	
CD109	135228	hgsc.bcm.edu	37	6	74497009	74497009	+	Missense_Mutation	SNP	A	A	G	rs2351528	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:74497009A>G	ENST00000287097.5	+	21	2502	c.2390A>G	c.(2389-2391)aAt>aGt	p.N797S	CD109_ENST00000437994.2_Missense_Mutation_p.N797S|CD109_ENST00000422508.2_Missense_Mutation_p.N720S			Q6YHK3	CD109_HUMAN	CD109 molecule	797			N -> S (in dbSNP:rs2351528). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14980714, ECO:0000269|PubMed:16754747, ECO:0000269|PubMed:17974005}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ATGACTTCAAATGAAATAAAT	0.378													G|||	1865	0.372404	0.4675	0.4049	5008	,	,		19371	0.4087		0.339	False		,,,				2504	0.2178				p.N797S		Atlas-SNP	.											CD109,caecum,carcinoma,0,1	CD109	170	1	0			c.A2390G						PASS	.	G	SER/ASN,SER/ASN,SER/ASN	2051,2355	608.2+/-391.1	495,1061,647	65.0	68.0	67.0		2390,2159,2390	1.6	0.1	6	dbSNP_100	67	3057,5543	660.2+/-401.7	552,1953,1795	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	46,46,46	1047,3014,2442	GG,GA,AA		35.5465,46.5502,39.2742	benign,benign,benign	797/1429,720/1369,797/1446	74497009	5108,7898	2203	4300	6503	SO:0001583	missense	135228	exon21			CTTCAAATGAAAT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2390A>G	6.37:g.74497009A>G	ENSP00000287097:p.Asn797Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	879	0.4024725274725275	250	0.508130081300813	143	0.39502762430939226	239	0.4178321678321678	247	0.3258575197889182	G	0.021	-1.425324	0.01126	0.465502	0.355465	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.22945	1.93;2.15;1.93	5.46	1.63	0.23807	.	1.129070	0.06361	N	0.711652	T	0.10380	0.0254	L	0.53671	1.685	0.58432	P	5.000000000032756E-6	B;B;B	0.24618	0.008;0.107;0.004	B;B;B	0.16289	0.014;0.015;0.009	T	0.29119	-1.0022	9	0.30078	T	0.28	.	10.7397	0.46145	0.8168:0.0:0.1832:0.0	rs2351528;rs4632862;rs52791004;rs60212756;rs2351528	720;797;797	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	S	797;720;797	ENSP00000388062:N797S;ENSP00000404475:N720S;ENSP00000287097:N797S	ENSP00000287097:N797S	N	+	2	0	CD109	74553730	1.000000	0.71417	0.079000	0.20413	0.012000	0.07955	1.818000	0.39012	-0.068000	0.12953	-1.874000	0.00550	AAT	A|0.597;G|0.403	0.403	strong		0.378	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
AKAP2	11217	hgsc.bcm.edu	37	9	112900785	112900785	+	Silent	SNP	A	A	G	rs3739456	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:112900785A>G	ENST00000259318.7	+	2	2475	c.2268A>G	c.(2266-2268)tcA>tcG	p.S756S	AKAP2_ENST00000434623.2_Silent_p.S845S|AKAP2_ENST00000510514.5_Silent_p.S987S|PALM2-AKAP2_ENST00000374530.3_Silent_p.S987S|PALM2-AKAP2_ENST00000302798.7_Silent_p.S987S|AKAP2_ENST00000482335.1_3'UTR|AKAP2_ENST00000555236.1_Silent_p.S987S|AKAP2_ENST00000374525.1_Silent_p.S845S	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	756										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						ATGCCCCATCACTGCCCTCCA	0.522													G|||	1635	0.326478	0.1498	0.4107	5008	,	,		20700	0.6587		0.2575	False		,,,				2504	0.2342				p.S987S		Atlas-SNP	.											PALM2-AKAP2,NS,carcinoma,0,2	PALM2-AKAP2	117	2	0			c.A2961G						PASS	.	G	,,,,	738,3668	751.0+/-412.2	68,602,1533	71.0	66.0	68.0		2535,2268,2535,2961,2961	-6.5	0.4	9	dbSNP_107	68	2117,6483	707.9+/-405.6	258,1601,2441	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AKAP2,PALM2-AKAP2	NM_001004065.4,NM_001136562.2,NM_001198656.1,NM_007203.4,NM_147150.2	,,,,	326,2203,3974	GG,GA,AA		24.6163,16.7499,21.9514	,,,,	845/949,756/860,845/962,987/1104,987/1091	112900785	2855,10151	2203	4300	6503	SO:0001819	synonymous_variant	445815	exon8			CCCATCACTGCCC	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.2268A>G	9.37:g.112900785A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Silent	SNP	ENST00000259318.7	37	CCDS48003.1																																																																																			A|0.728;G|0.272	0.272	strong		0.522	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065	
HLA-B	3106	hgsc.bcm.edu	37	6	31324078	31324078	+	Missense_Mutation	SNP	G	G	T	rs1050368	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324078G>T	ENST00000412585.2	-	3	513	c.485C>A	c.(484-486)aCg>aAg	p.T162K		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	162	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CTGAGCCGCCGTGTCCGCGGC	0.697									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.T162K		Atlas-SNP	.											.	HLA-B	54	.	0			c.C485A						PASS	.						30.0	21.0	24.0					6																	31324078		2119	4200	6319	SO:0001583	missense	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	GCCGCCGTGTCCG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.485C>A	6.37:g.31324078G>T	ENSP00000399168:p.Thr162Lys	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	261	67	0.256705	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	89	0.04075091575091575	21	0.042682926829268296	26	0.0718232044198895	1	0.0017482517482517483	41	0.05408970976253298	N	10.62	1.401203	0.25291	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.00010	9.44;9.44	3.18	-5.74	0.02391	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	367.624000	0.00678	U	0.000668	T	0.00073	0.0002	M	0.75777	2.31	0.09310	N	1	P;D	0.55605	0.909;0.972	B;P	0.54924	0.362;0.764	T	0.34403	-0.9830	10	0.66056	D	0.02	.	6.4914	0.22117	0.5326:0.245:0.2225:0.0	rs1050368;rs3176004;rs12721854;rs17851013	162;162	P30480;P01889	1B42_HUMAN;1B07_HUMAN	K	162;41;41;173	ENSP00000399168:T162K;ENSP00000405931:T173K	ENSP00000399168:T162K	T	-	2	0	HLA-B	31432057	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.093000	0.00608	-1.877000	0.01129	-0.873000	0.02984	ACG	T|0.053;G|0.947	0.053	strong		0.697	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
POLR2B	5431	hgsc.bcm.edu	37	4	57881715	57881715	+	Silent	SNP	G	G	A	rs1713982	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:57881715G>A	ENST00000381227.1	+	15	2261	c.1848G>A	c.(1846-1848)acG>acA	p.T616T	POLR2B_ENST00000314595.5_Silent_p.T616T|POLR2B_ENST00000441246.2_Silent_p.T609T|POLR2B_ENST00000431623.2_Silent_p.T541T|POLR2B_ENST00000510355.1_3'UTR			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	616					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					GGATCTATACGGATGCAGGCC	0.333													A|||	1934	0.386182	0.4342	0.2954	5008	,	,		10572	0.2986		0.3469	False		,,,				2504	0.5164				p.T616T		Atlas-SNP	.											POLR2B,colon,carcinoma,0,1	POLR2B	108	1	0			c.G1848A						PASS	.	A		1882,2524	629.0+/-395.2	403,1076,724	119.0	125.0	123.0		1848	-2.7	1.0	4	dbSNP_89	123	2939,5661	667.8+/-402.5	487,1965,1848	no	coding-synonymous	POLR2B	NM_000938.1		890,3041,2572	AA,AG,GG		34.1744,42.7145,37.0675		616/1175	57881715	4821,8185	2203	4300	6503	SO:0001819	synonymous_variant	5431	exon14			CTATACGGATGCA		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"""RNA polymerase subunits"""	9188	protein-coding gene	gene with protein product		180661	"""polymerase (RNA) II (DNA directed) polypeptide B (140kD)"""			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1848G>A	4.37:g.57881715G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_000938	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	37	CCDS3511.1																																																																																			G|0.634;A|0.366	0.366	strong		0.333	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
METTL7B	196410	hgsc.bcm.edu	37	12	56077740	56077740	+	Silent	SNP	C	C	T	rs11615467	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56077740C>T	ENST00000394252.3	+	2	851	c.642C>T	c.(640-642)aaC>aaT	p.N214N		NM_152637.2	NP_689850.2	Q6UX53	MET7B_HUMAN	methyltransferase like 7B	214							methyltransferase activity (GO:0008168)			kidney(1)|large_intestine(1)|lung(4)	6						ATCTTGAGAACGCCCAGTTCT	0.542													C|||	165	0.0329473	0.0265	0.0317	5008	,	,		19829	0.001		0.0646	False		,,,				2504	0.0429				p.N214N		Atlas-SNP	.											.	METTL7B	35	.	0			c.C642T						PASS	.	C		124,4282	92.0+/-130.7	2,120,2081	132.0	110.0	118.0		642	-8.0	0.0	12	dbSNP_120	118	401,8199	127.3+/-185.7	7,387,3906	no	coding-synonymous	METTL7B	NM_152637.2		9,507,5987	TT,TC,CC		4.6628,2.8143,4.0366		214/245	56077740	525,12481	2203	4300	6503	SO:0001819	synonymous_variant	196410	exon2			TGAGAACGCCCAG		CCDS8887.2	12q13.2	2012-06-12			ENSG00000170439	ENSG00000170439			28276	protein-coding gene	gene with protein product	"""associated with lipid droplets 1"""					17004324	Standard	NM_152637		Approved	MGC17301, ALDI	uc010spr.2	Q6UX53	OTTHUMG00000152665	ENST00000394252.3:c.642C>T	12.37:g.56077740C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_152637	A8K247|Q8WUI1	Silent	SNP	ENST00000394252.3	37	CCDS8887.2																																																																																			C|0.959;T|0.041	0.041	strong		0.542	METTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327271.1	NM_152637	
SYTL2	54843	hgsc.bcm.edu	37	11	85456703	85456703	+	Silent	SNP	T	T	C	rs647912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:85456703T>C	ENST00000528231.1	-	3	643	c.366A>G	c.(364-366)gaA>gaG	p.E122E	SYTL2_ENST00000316356.4_Silent_p.E122E|SYTL2_ENST00000527523.1_Silent_p.E74E|SYTL2_ENST00000524452.1_Silent_p.E122E|SYTL2_ENST00000389960.4_Silent_p.E122E	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	122					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		GTGCTGCATCTTCTTCTGGCT	0.532													T|||	2738	0.546725	0.4788	0.5029	5008	,	,		18212	0.6141		0.6342	False		,,,				2504	0.5102				p.E122E		Atlas-SNP	.											.	SYTL2	231	.	0			c.A366G						PASS	.	T	,,	2233,2173	591.1+/-387.5	572,1089,542	167.0	149.0	155.0		366,366,366	-1.5	0.9	11	dbSNP_83	155	5457,3141	656.9+/-401.4	1741,1975,583	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3	,,	2313,3064,1125	CC,CT,TT		36.5318,49.3191,40.8643	,,	122/935,122/936,122/911	85456703	7690,5314	2203	4299	6502	SO:0001819	synonymous_variant	54843	exon4			TGCATCTTCTTCT	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.366A>G	11.37:g.85456703T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_032943	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			T|0.426;C|0.574	0.574	strong		0.532	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
CSF2RA	1438	hgsc.bcm.edu	37	X	1422868	1422868	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:1422868G>A	ENST00000381524.3	+	11	1185	c.999G>A	c.(997-999)gtG>gtA	p.V333V	CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000381500.1_Intron|CSF2RA_ENST00000355432.3_Intron|CSF2RA_ENST00000498153.1_3'UTR|CSF2RA_ENST00000432318.2_Silent_p.V333V|CSF2RA_ENST00000501036.2_Silent_p.V200V|CSF2RA_ENST00000381509.3_Silent_p.V333V|CSF2RA_ENST00000361536.3_Intron|CSF2RA_ENST00000355805.2_Intron|CSF2RA_ENST00000417535.2_Silent_p.V367V|CSF2RA_ENST00000381529.3_Silent_p.V333V			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	333					response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	TCCTAATCGTGGGAACCCTTG	0.537													g|||	1634	0.326278	0.2769	0.3156	5008	,	,		17482	0.3442		0.4056	False		,,,				2504	0.3006				p.V367V	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.G1101A						PASS	.		,,,,,,,,	1242,3164		172,898,1133	514.0	449.0	471.0		999,1101,999,600,999,999,,,	0.8	0.1	X	dbSNP_134	471	3695,4897		800,2095,1401	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,intron	CSF2RA	NM_001161529.1,NM_001161530.1,NM_001161531.1,NM_001161532.1,NM_006140.4,NM_172245.2,NM_172246.2,NM_172247.2,NM_172249.2	,,,,,,,,	972,2993,2534	AA,AG,GG		43.0051,28.1888,37.9828	,,,,,,,,	333/401,367/435,333/411,200/268,333/401,333/401,,,	1422868	4937,8061	2203	4296	6499	SO:0001819	synonymous_variant	1438	exon10			AATCGTGGGAACC	M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"""CD molecules"", ""Pseudoautosomal regions / PAR1"""	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.999G>A	X.37:g.1422868G>A		Somatic	981	0	0		WXS	Illumina HiSeq	Phase_I	496	490	0.987903	NM_001161530	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Silent	SNP	ENST00000381524.3	37	CCDS35191.1																																																																																			G|0.633;A|0.367	0.367	strong		0.537	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2		
ZNF229	7772	hgsc.bcm.edu	37	19	44933706	44933706	+	Missense_Mutation	SNP	C	C	T	rs57014690	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:44933706C>T	ENST00000588931.1	-	6	1683	c.1250G>A	c.(1249-1251)aGc>aAc	p.S417N	ZNF229_ENST00000291187.4_Missense_Mutation_p.S411N|CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	417			S -> N (in dbSNP:rs57014690).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				AAGCACTGAGCTGTAACTGAA	0.522													C|||	814	0.16254	0.1929	0.3213	5008	,	,		20844	0.1558		0.1024	False		,,,				2504	0.0777				p.S417N		Atlas-SNP	.											ZNF229,tonsil,carcinoma,0,1	ZNF229	123	1	0			c.G1250A						scavenged	.	C	ASN/SER	751,3651	285.2+/-278.0	70,611,1520	89.0	100.0	96.0		1250	2.8	0.0	19	dbSNP_129	96	939,7661	203.5+/-246.5	60,819,3421	yes	missense	ZNF229	NM_014518.2	46	130,1430,4941	TT,TC,CC		10.9186,17.0604,12.998	benign	417/826	44933706	1690,11312	2201	4300	6501	SO:0001583	missense	7772	exon6			ACTGAGCTGTAAC	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1250G>A	19.37:g.44933706C>T	ENSP00000466519:p.Ser417Asn	Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	127	75	0.590551	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	363	0.1662087912087912	102	0.2073170731707317	101	0.27900552486187846	83	0.1451048951048951	77	0.10158311345646438	C	11.10	1.539651	0.27563	0.170604	0.109186	ENSG00000167383	ENST00000291187	.	.	.	3.86	2.79	0.32731	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.53561	1.675	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.12553	-1.0543	7	0.24483	T	0.36	.	6.4046	0.21658	0.0:0.6895:0.0:0.3105	rs57014690;rs61740849	417	Q9UJW7	ZN229_HUMAN	N	417	.	ENSP00000291187:S417N	S	-	2	0	ZNF229	49625546	0.000000	0.05858	0.042000	0.18584	0.554000	0.35429	-1.359000	0.02602	1.694000	0.51137	0.609000	0.83330	AGC	C|0.848;T|0.152	0.152	strong		0.522	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60989187	60989187	+	Missense_Mutation	SNP	G	G	T	rs45514096	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60989187G>T	ENST00000252998.1	-	10	1376	c.1220C>A	c.(1219-1221)gCc>gAc	p.A407D		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	407						extracellular space (GO:0005615)											GCCTGCTGCGGCCAGAGCTGC	0.697													G|||	13	0.00259585	0.0008	0.0043	5008	,	,		12734	0.0		0.0089	False		,,,				2504	0.0				p.A407D		Atlas-SNP	.											.	.	.	.	0			c.C1220A						PASS	.	G	ASP/ALA	24,4290		1,22,2134	9.0	10.0	9.0		1220	1.6	0.0	20	dbSNP_127	9	170,8302		3,164,4069	yes	missense	C20orf151	NM_080833.2	126	4,186,6203	TT,TG,GG		2.0066,0.5563,1.5173	possibly-damaging	407/665	60989187	194,12592	2157	4236	6393	SO:0001583	missense	140893	exon10			GCTGCGGCCAGAG	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"""hypothetical protein LOC140893"""		"""chromosome 20 open reading frame 151"""	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.1220C>A	20.37:g.60989187G>T	ENSP00000252998:p.Ala407Asp	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	10	0.004578754578754579	1	0.0020325203252032522	0	0.0	0	0.0	9	0.011873350923482849	G	10.47	1.358863	0.24598	0.005563	0.020066	ENSG00000130701	ENST00000252998	T	0.18960	2.18	2.71	1.57	0.23409	.	1.968570	0.02436	N	0.084087	T	0.09774	0.0240	N	0.25647	0.755	0.09310	N	1	B	0.33494	0.414	B	0.36567	0.228	T	0.27297	-1.0078	10	0.51188	T	0.08	-2.4571	7.5807	0.27963	0.0:0.405:0.595:0.0	rs45514096	407	Q8NC74	CT151_HUMAN	D	407	ENSP00000252998:A407D	ENSP00000252998:A407D	A	-	2	0	C20orf151	60422582	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	0.414000	0.21164	0.295000	0.22570	0.491000	0.48974	GCC	G|0.989;T|0.011	0.011	strong		0.697	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
HS3ST5	222537	hgsc.bcm.edu	37	6	114378970	114378970	+	Silent	SNP	C	C	T	rs2282237	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:114378970C>T	ENST00000312719.5	-	5	1680	c.492G>A	c.(490-492)gaG>gaA	p.E164E	RP3-399L15.3_ENST00000519270.1_RNA|HS3ST5_ENST00000411826.1_Silent_p.E164E|RP3-399L15.3_ENST00000523087.1_RNA|RP3-399L15.3_ENST00000519104.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	164					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)	p.E164E(1)		breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		TTTCTGGAACCTCCTCTGTGA	0.398													C|||	1512	0.301917	0.1604	0.4265	5008	,	,		19184	0.3512		0.3032	False		,,,				2504	0.3528				p.E164E		Atlas-SNP	.											HS3ST5,NS,carcinoma,0,1	HS3ST5	80	1	1	Substitution - coding silent(1)	stomach(1)	c.G492A						PASS	.	C		836,3570	324.8+/-298.8	79,678,1446	154.0	157.0	156.0		492	3.3	1.0	6	dbSNP_100	156	2432,6168	401.0+/-347.0	344,1744,2212	no	coding-synonymous	HS3ST5	NM_153612.3		423,2422,3658	TT,TC,CC		28.2791,18.9741,25.1269		164/347	114378970	3268,9738	2203	4300	6503	SO:0001819	synonymous_variant	222537	exon2			TGGAACCTCCTCT	AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"""Sulfotransferases, membrane-bound"""	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.492G>A	6.37:g.114378970C>T		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	251	120	0.478088	NM_153612	A8K1J2|Q52LI2|Q8N285	Silent	SNP	ENST00000312719.5	37	CCDS34517.1																																																																																			C|0.733;T|0.267	0.267	strong		0.398	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612	
KIAA1549L	25758	hgsc.bcm.edu	37	11	33604960	33604960	+	Silent	SNP	C	C	T	rs2273115	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:33604960C>T	ENST00000321505.4	+	10	3768	c.3588C>T	c.(3586-3588)atC>atT	p.I1196I	KIAA1549L_ENST00000265654.5_Silent_p.I1202I|KIAA1549L_ENST00000389726.3_Silent_p.I1202I			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1196	Poly-Ile.					integral component of membrane (GO:0016021)											TCACGGTCATCATCATCATCA	0.547													C|||	888	0.177316	0.0166	0.2334	5008	,	,		21311	0.3591		0.2187	False		,,,				2504	0.1247				p.I1196I		Atlas-SNP	.											.	.	.	.	0			c.C3588T						PASS	.	C		180,4112		5,170,1971	43.0	46.0	45.0		3588	4.7	1.0	11	dbSNP_100	45	1964,6550		225,1514,2518	no	coding-synonymous	C11orf41	NM_012194.2		230,1684,4489	TT,TC,CC		23.0679,4.1938,16.7422		1196/1850	33604960	2144,10662	2146	4257	6403	SO:0001819	synonymous_variant	25758	exon10			GGTCATCATCATC	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"""chromosome 11 open reading frame 69"", ""chromosome 11 open reading frame 41"""	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.3588C>T	11.37:g.33604960C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2	471	0.21565934065934067	12	0.024390243902439025	79	0.21823204419889503	210	0.36713286713286714	170	0.22427440633245382	C	10.12	1.262125	0.23051	0.041938	0.230679	ENSG00000110427	ENST00000526400	.	.	.	5.57	4.65	0.58169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.42999	-0.9418	3	.	.	.	-25.2471	8.8586	0.35242	0.1496:0.7757:0.0:0.0747	rs2273115	.	.	.	L	594	.	.	S	+	2	0	C11orf41	33561536	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	1.438000	0.35002	2.619000	0.88677	0.561000	0.74099	TCA	C|0.781;T|0.218	0.218	strong		0.547	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
CLEC9A	283420	hgsc.bcm.edu	37	12	10217412	10217412	+	Missense_Mutation	SNP	C	C	T	rs147713876	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:10217412C>T	ENST00000355819.1	+	8	1166	c.553C>T	c.(553-555)Cgc>Tgc	p.R185C		NM_207345.2	NP_997228.1	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A	185	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				positive regulation of cytokine secretion (GO:0050715)|receptor-mediated endocytosis (GO:0006898)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	22						ACACAGCGGACGCTGGCTTTG	0.438																																					p.R185C		Atlas-SNP	.											.	CLEC9A	41	.	0			c.C553T						PASS	.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	125.0	116.0	119.0		553	-3.0	0.0	12	dbSNP_134	119	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CLEC9A	NM_207345.2	180	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging	185/242	10217412	3,13003	2203	4300	6503	SO:0001583	missense	283420	exon8			AGCGGACGCTGGC		CCDS8611.1	12p13.31	2010-04-27				ENSG00000197992		"""C-type lectin domain containing"""	26705	protein-coding gene	gene with protein product		612252					Standard	NM_207345		Approved	UNQ9341, HEEE9341	uc001qxa.3	Q6UXN8		ENST00000355819.1:c.553C>T	12.37:g.10217412C>T	ENSP00000348074:p.Arg185Cys	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_207345	B0ZBM2	Missense_Mutation	SNP	ENST00000355819.1	37	CCDS8611.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.021102	0.54576	2.27E-4	2.33E-4	ENSG00000197992	ENST00000355819	T	0.19394	2.15	5.24	-3.0	0.05480	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.955151	0.08603	N	0.921157	T	0.22551	0.0544	M	0.64997	1.995	0.09310	N	1	D	0.53312	0.959	P	0.48901	0.594	T	0.18903	-1.0322	10	0.59425	D	0.04	.	1.5356	0.02544	0.1565:0.2573:0.1343:0.4519	.	185	Q6UXN8	CLC9A_HUMAN	C	185	ENSP00000348074:R185C	ENSP00000348074:R185C	R	+	1	0	CLEC9A	10108679	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.238000	0.02919	-0.348000	0.08286	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	strong		0.438	CLEC9A-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000399564.1	NM_207345	
SI	6476	hgsc.bcm.edu	37	3	164764719	164764719	+	Silent	SNP	C	C	A	rs9838509	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:164764719C>A	ENST00000264382.3	-	16	1859	c.1797G>T	c.(1795-1797)gcG>gcT	p.A599A		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	599	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.A599A(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	CTAACCAATGCGCAGCATGTC	0.383										HNSCC(35;0.089)			T|||	3048	0.608626	0.4675	0.6225	5008	,	,		13303	0.8284		0.6282	False		,,,				2504	0.5429				p.A599A		Atlas-SNP	.											SI,NS,carcinoma,0,1	SI	500	1	1	Substitution - coding silent(1)	prostate(1)	c.G1797T						PASS	.	T		2137,2269		526,1085,592	93.0	89.0	90.0		1797	-5.7	1.0	3	dbSNP_119	90	5139,3461		1533,2073,694	no	coding-synonymous	SI	NM_001041.3		2059,3158,1286	AA,AC,CC		40.2442,48.502,44.0566		599/1828	164764719	7276,5730	2203	4300	6503	SO:0001819	synonymous_variant	6476	exon16			CCAATGCGCAGCA	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.1797G>T	3.37:g.164764719C>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	254	108	0.425197	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	37	CCDS3196.1																																																																																			C|0.416;A|0.584	0.584	strong		0.383	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
TET2	54790	hgsc.bcm.edu	37	4	106156187	106156187	+	Missense_Mutation	SNP	C	C	T	rs17253672	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:106156187C>T	ENST00000540549.1	+	3	1948	c.1088C>T	c.(1087-1089)cCt>cTt	p.P363L	TET2_ENST00000394764.1_Missense_Mutation_p.P363L|TET2_ENST00000380013.4_Missense_Mutation_p.P363L|TET2_ENST00000413648.2_Missense_Mutation_p.P363L|TET2_ENST00000513237.1_Missense_Mutation_p.P384L|TET2_ENST00000545826.1_Missense_Mutation_p.P363L|TET2_ENST00000305737.2_Missense_Mutation_p.P363L			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	363			P -> L (in dbSNP:rs17253672). {ECO:0000269|PubMed:19483684}.		5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TTGCAAGCTCCTGGTGGCAGC	0.443			"""Mis N, F"""		MDS								C|||	138	0.0275559	0.0023	0.0346	5008	,	,		21283	0.0		0.0696	False		,,,				2504	0.0419				p.P363L		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.C1088T						PASS	.	C	LEU/PRO,LEU/PRO	45,4361	46.0+/-80.4	1,43,2159	63.0	61.0	61.0		1088,1088	5.0	0.9	4	dbSNP_123	61	507,8093	143.6+/-199.6	9,489,3802	yes	missense,missense	TET2	NM_001127208.2,NM_017628.4	98,98	10,532,5961	TT,TC,CC		5.8953,1.0213,4.2442	probably-damaging,probably-damaging	363/2003,363/1166	106156187	552,12454	2203	4300	6503	SO:0001583	missense	54790	exon3			AAGCTCCTGGTGG	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.1088C>T	4.37:g.106156187C>T	ENSP00000442788:p.Pro363Leu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	159	74	0.465409	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	74	0.03388278388278388	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	55	0.07255936675461741	C	16.36	3.101612	0.56183	0.010213	0.058953	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648;ENST00000535110	T;T;T;T;T;T;T	0.03772	3.82;4.48;3.81;4.47;4.48;3.82;3.83	4.97	4.97	0.65823	.	10.901400	0.00166	N	0.000000	T	0.00524	0.0017	N	0.24115	0.695	0.26163	N	0.979979	B;B;P	0.36909	0.421;0.421;0.573	B;B;B	0.39217	0.086;0.086;0.294	T	0.34104	-0.9842	10	0.59425	D	0.04	.	11.1136	0.48247	0.1977:0.8023:0.0:0.0	rs17253672;rs17253672	384;363;363	E7EQS8;Q6N021;Q6N021-2	.;TET2_HUMAN;.	L	363;363;363;384;363;363;363;363	ENSP00000306705:P363L;ENSP00000442788:P363L;ENSP00000442867:P363L;ENSP00000425443:P384L;ENSP00000369351:P363L;ENSP00000378245:P363L;ENSP00000391448:P363L	ENSP00000265149:P363L	P	+	2	0	TET2	106375636	0.910000	0.30920	0.948000	0.38648	0.997000	0.91878	2.144000	0.42197	2.320000	0.78422	0.650000	0.86243	CCT	C|0.964;T|0.036	0.036	strong		0.443	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
MSH6	2956	hgsc.bcm.edu	37	2	48018081	48018081	+	Silent	SNP	A	A	G	rs1800932	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:48018081A>G	ENST00000234420.5	+	2	428	c.276A>G	c.(274-276)ccA>ccG	p.P92P	FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_5'UTR|MSH6_ENST00000540021.1_Intron	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	92	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACTTCTCACCAGGAGATTTGG	0.423			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	434	0.0866613	0.084	0.121	5008	,	,		19522	0.0		0.1789	False		,,,				2504	0.0603				p.P92P		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.A276G						PASS	.	A		513,3893	237.1+/-249.0	33,447,1723	86.0	81.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	276	0.2	1.0	2	dbSNP_89	83	1636,6964	302.2+/-305.8	165,1306,2829	no	coding-synonymous	MSH6	NM_000179.2		198,1753,4552	GG,GA,AA		19.0233,11.6432,16.5231		92/1361	48018081	2149,10857	2203	4300	6503	SO:0001819	synonymous_variant	2956	exon2	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CTCACCAGGAGAT	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"""mutS (E. coli) homolog 6"", ""mutS homolog 6 (E. coli)"""	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.276A>G	2.37:g.48018081A>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	161	69	0.428571	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Silent	SNP	ENST00000234420.5	37	CCDS1836.1																																																																																			A|0.864;G|0.136	0.136	strong		0.423	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
BRCA1	672	hgsc.bcm.edu	37	17	41244000	41244000	+	Missense_Mutation	SNP	T	T	C	rs80357956|rs16942	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:41244000T>C	ENST00000357654.3	-	10	3666	c.3548A>G	c.(3547-3549)aAa>aGa	p.K1183R	BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.K1183R|BRCA1_ENST00000471181.2_Missense_Mutation_p.K1183R|BRCA1_ENST00000309486.4_Missense_Mutation_p.K887R|BRCA1_ENST00000354071.3_Missense_Mutation_p.K1183R|BRCA1_ENST00000493795.1_Missense_Mutation_p.K1136R|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1183			K -> R (common polymorphism; dbSNP:rs16942). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:14722926, ECO:0000269|PubMed:15365993, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7894493, ECO:0000269|Ref.6}.		androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K1183fs*4(1)|p.K1183R(1)		NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		AAGCTCTCCTTTCTGGACGCT	0.428			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			C|||	1766	0.352636	0.2179	0.3746	5008	,	,		20679	0.371		0.3549	False		,,,				2504	0.498				p.K1183R		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	BRCA1,NS,carcinoma,0,1	BRCA1	304	1	2	Substitution - Missense(1)|Deletion - Frameshift(1)	stomach(1)|endometrium(1)	c.A3548G						PASS	.	C	ARG/LYS,ARG/LYS,,,ARG/LYS	1050,3356	721.5+/-409.2	114,822,1267	80.0	74.0	76.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3548,3407,,,3548	-2.3	0.0	17	dbSNP_60	76	2790,5810	673.5+/-403.0	441,1908,1951	yes	missense,missense,intron,intron,missense	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	26,26,,,26	555,2730,3218	CC,CT,TT		32.4419,23.8311,29.5248	benign,benign,,,benign	1183/1864,1136/1817,,,1183/1885	41244000	3840,9166	2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		TCTCCTTTCTGGA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.3548A>G	17.37:g.41244000T>C	ENSP00000350283:p.Lys1183Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	100	58	0.58	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	708	0.3241758241758242	106	0.21544715447154472	143	0.39502762430939226	189	0.3304195804195804	270	0.3562005277044855	C	0.004	-2.282426	0.00251	0.238311	0.324419	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35;-0.35	5.31	-2.35	0.06684	.	0.543999	0.18098	N	0.151790	T	0.00012	0.0000	N	0.00972	-1.085	0.80722	P	0.0	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.0;0.0;0.001;0.002;0.001;0.002	T	0.21586	-1.0241	9	0.02654	T	1	.	7.8272	0.29322	0.1183:0.2486:0.0:0.6331	rs16942;rs17672119;rs52827882;rs59688547;rs16942	1183;1142;1183;1183;1183;1183	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	R	1183;1183;1183;1183;887;1183;1136	ENSP00000350283:K1183R;ENSP00000326002:K1183R;ENSP00000246907:K1183R;ENSP00000310938:K887R;ENSP00000418960:K1183R;ENSP00000418775:K1136R	ENSP00000310938:K887R	K	-	2	0	BRCA1	38497526	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-0.365000	0.07573	-0.437000	0.07243	-0.726000	0.03593	AAA	T|0.695;C|0.305	0.305	strong		0.428	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
NBPF3	84224	hgsc.bcm.edu	37	1	21795388	21795388	+	Missense_Mutation	SNP	A	A	G	rs1827293	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:21795388A>G	ENST00000318249.5	+	3	691	c.341A>G	c.(340-342)tAc>tGc	p.Y114C	NBPF3_ENST00000342104.5_Missense_Mutation_p.Y114C|NBPF3_ENST00000318220.6_Missense_Mutation_p.Y58C|NBPF3_ENST00000454000.2_Intron	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	114			Y -> C (in dbSNP:rs1827293). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CAAAATAATTACGGTAAGTTC	0.448											OREG0013205	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	2123	0.423922	0.1445	0.4755	5008	,	,		19838	0.5804		0.5417	False		,,,				2504	0.4826				p.A114G		Atlas-SNP	.											NBPF3,NS,carcinoma,0,1	NBPF3	55	1	0			c.C341G						PASS	.	A	CYS/TYR	970,3436		104,762,1337	48.0	53.0	51.0		341	-2.2	0.0	1	dbSNP_92	51	4756,3844		1332,2092,876	yes	missense	NBPF3	NM_032264.2	194	1436,2854,2213	GG,GA,AA		44.6977,22.0154,44.0258	probably-damaging	114/634	21795388	5726,7280	2203	4300	6503	SO:0001583	missense	84224	exon3			ATAATTACGGTAA	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.341A>G	1.37:g.21795388A>G	ENSP00000316782:p.Tyr114Cys	Somatic	140	0	0	751	WXS	Illumina HiSeq	Phase_I	168	78	0.464286	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Missense_Mutation	SNP	ENST00000318249.5	37	CCDS216.1	999	0.4574175824175824	88	0.17886178861788618	187	0.5165745856353591	318	0.5559440559440559	406	0.5356200527704486	.	10.34	1.323132	0.24080	0.220154	0.553023	ENSG00000142794	ENST00000318220;ENST00000318249;ENST00000417552;ENST00000342104;ENST00000434838	T;T;T;T	0.04970	3.69;3.52;3.55;3.69	1.08	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	M	0.72353	2.195	0.80722	P	0.0	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.979	T	0.48547	-0.9026	8	0.87932	D	0	.	1.9892	0.03442	0.3991:0.302:0.0:0.2989	rs1827293;rs3738102;rs17420230;rs17856707;rs52824093;rs58179675;rs1827293	114;114	Q9H094-3;Q9H094	.;NBPF3_HUMAN	C	58;114;58;114;58	ENSP00000316739:Y58C;ENSP00000316782:Y114C;ENSP00000340336:Y114C;ENSP00000391865:Y58C	ENSP00000316739:Y58C	Y	+	2	0	NBPF3	21667975	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.056000	0.11787	-0.776000	0.04578	0.327000	0.21459	TAC	A|0.554;G|0.446	0.446	strong		0.448	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
TMCC3	57458	hgsc.bcm.edu	37	12	94976159	94976159	+	Silent	SNP	T	T	C	rs3747551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:94976159T>C	ENST00000261226.4	-	2	365	c.234A>G	c.(232-234)gtA>gtG	p.V78V	TMCC3_ENST00000551457.1_Silent_p.V47V	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	78						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						TCTGCTCTGTTACCTTTAGAA	0.478													T|||	1634	0.326278	0.2421	0.4092	5008	,	,		19343	0.3522		0.3231	False		,,,				2504	0.3579				p.V78V		Atlas-SNP	.											.	TMCC3	63	.	0			c.A234G						PASS	.	T		1146,3260	408.6+/-334.7	161,824,1218	191.0	184.0	186.0		234	-10.6	0.3	12	dbSNP_107	186	2938,5662	458.6+/-364.7	515,1908,1877	no	coding-synonymous	TMCC3	NM_020698.2		676,2732,3095	CC,CT,TT		34.1628,26.01,31.4009		78/478	94976159	4084,8922	2203	4300	6503	SO:0001819	synonymous_variant	57458	exon2			CTCTGTTACCTTT	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"""Transmembrane and coiled-coil domain containing"""	29199	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 3"""			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.234A>G	12.37:g.94976159T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_020698	Q8IWB2	Silent	SNP	ENST00000261226.4	37	CCDS31877.1																																																																																			T|0.673;C|0.327	0.327	strong		0.478	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
TMC2	117532	hgsc.bcm.edu	37	20	2591232	2591232	+	Silent	SNP	C	C	T	rs6050576	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2591232C>T	ENST00000358864.1	+	12	1596	c.1581C>T	c.(1579-1581)gaC>gaT	p.D527D	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	527					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TGATGGATGACGTCCACCTCA	0.448													T|||	1573	0.314097	0.4032	0.2767	5008	,	,		13456	0.2758		0.2356	False		,,,				2504	0.3405				p.D527D		Atlas-SNP	.											.	TMC2	121	.	0			c.C1581T						PASS	.	T		1668,2738	656.8+/-400.1	311,1046,846	86.0	70.0	75.0		1581	-6.3	0.9	20	dbSNP_114	75	2055,6545	718.6+/-406.2	251,1553,2496	no	coding-synonymous	TMC2	NM_080751.2		562,2599,3342	TT,TC,CC		23.8953,37.8575,28.6252		527/907	2591232	3723,9283	2203	4300	6503	SO:0001819	synonymous_variant	117532	exon12			GGATGACGTCCAC	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"""transmembrane, cochlear expressed, 2"""	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1581C>T	20.37:g.2591232C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	147	57	0.387755	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Silent	SNP	ENST00000358864.1	37	CCDS13029.2																																																																																			C|0.710;T|0.290	0.290	strong		0.448	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
MSLN	10232	hgsc.bcm.edu	37	16	814942	814942	+	Missense_Mutation	SNP	G	G	A	rs34695957	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:814942G>A	ENST00000382862.3	+	7	511	c.416G>A	c.(415-417)cGt>cAt	p.R139H	MSLN_ENST00000545450.2_Missense_Mutation_p.R139H|MSLN_ENST00000563941.1_Missense_Mutation_p.R139H|MSLN_ENST00000566549.1_Missense_Mutation_p.R139H	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	139				R -> H (in Ref. 4; AAV87530). {ECO:0000305}.	cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				GCCTGCACCCGTTTCTTCTCC	0.687													G|||	366	0.0730831	0.1899	0.0259	5008	,	,		10513	0.0139		0.007	False		,,,				2504	0.0777				p.R139H		Atlas-SNP	.											.	MSLN	109	.	0			c.G416A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	710,3644	282.8+/-276.7	51,608,1518	28.0	28.0	28.0		416,416,416	-4.4	0.0	16	dbSNP_126	28	94,8488	49.8+/-109.6	1,92,4198	yes	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	29,29,29	52,700,5716	AA,AG,GG		1.0953,16.3068,6.2152	benign,benign,benign	139/623,139/623,139/631	814942	804,12132	2177	4291	6468	SO:0001583	missense	10232	exon8			GCACCCGTTTCTT	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.416G>A	16.37:g.814942G>A	ENSP00000372313:p.Arg139His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	128	0.05860805860805861	100	0.2032520325203252	11	0.03038674033149171	10	0.017482517482517484	7	0.009234828496042216	G	3.067	-0.191983	0.06299	0.163068	0.010953	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.11712	2.75;2.75	2.5	-4.42	0.03579	.	2.137870	0.02352	N	0.075988	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.41520	-0.9504	9	0.30854	T	0.27	0.8303	9.8486	0.41043	0.6383:0.0:0.3617:0.0	rs34695957;rs60393946	138;139;139;139	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	H	139	ENSP00000442965:R139H;ENSP00000372313:R139H	ENSP00000372313:R139H	R	+	2	0	MSLN	754943	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.357000	0.07651	-1.601000	0.01601	-2.110000	0.00354	CGT	G|0.937;A|0.063	0.063	strong		0.687	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
TCEB2	6923	hgsc.bcm.edu	37	16	2821573	2821573	+	3'UTR	SNP	C	C	T	rs8017	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2821573C>T	ENST00000409906.4	-	0	832				AC092117.2_ENST00000581119.1_RNA|TCEB2_ENST00000262306.7_Missense_Mutation_p.S129N|TCEB2_ENST00000409477.1_3'UTR	NM_007108.3	NP_009039.1	Q15370	ELOB_HUMAN	transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B)						cellular response to hypoxia (GO:0071456)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein complex assembly (GO:0006461)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|elongin complex (GO:0070449)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|prostate(1)	3						TGTGTTTCTGCTCTTGGCCAT	0.577													C|||	2072	0.413738	0.2269	0.5533	5008	,	,		16789	0.3591		0.5169	False		,,,				2504	0.5174				p.S129N	GBM(141;5215 5962)	Atlas-SNP	.											.	TCEB2	6	.	0			c.G386A						PASS	.	C	,ASN/SER	1267,3129	432.6+/-343.3	197,873,1128	103.0	95.0	98.0		,386	1.0	0.0	16	dbSNP_52	98	4575,4025	597.1+/-393.7	1224,2127,949	yes	utr-3,missense	TCEB2	NM_007108.3,NM_207013.2	,46	1421,3000,2077	TT,TC,CC		46.8023,28.8217,44.9523	,benign	,129/162	2821573	5842,7154	2198	4300	6498	SO:0001624	3_prime_UTR_variant	6923	exon5			TTTCTGCTCTTGG	L42856	CCDS32374.1, CCDS45387.1	16p12.3	2008-02-05	2002-08-29		ENSG00000103363	ENSG00000103363			11619	protein-coding gene	gene with protein product		600787	"""transcription elongation factor B (SIII), polypeptide 2 (18kD, elongin B)"""			7638163	Standard	NM_007108		Approved	SIII	uc002crm.3	Q15370	OTTHUMG00000154125	ENST00000409906.4:c.*418G>A	16.37:g.2821573C>T		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	141	140	0.992908	NM_207013	B7WPD3	Missense_Mutation	SNP	ENST00000409906.4	37	CCDS45387.1	898	0.41117216117216115	123	0.25	200	0.5524861878453039	194	0.33916083916083917	381	0.5026385224274407	C	9.901	1.206812	0.22205	0.288217	0.531977	ENSG00000103363	ENST00000262306	.	.	.	3.06	1.03	0.20045	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.25105	0.118	B	0.18871	0.023	T	0.44360	-0.9333	7	0.32370	T	0.25	.	3.6722	0.08279	0.2427:0.6226:0.0:0.1347	rs8017;rs1064495;rs3174695;rs8017	129	B7WPD3	.	N	129	.	ENSP00000262306:S129N	S	-	2	0	TCEB2	2761574	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.011000	0.12721	0.323000	0.23307	0.609000	0.83330	AGC	C|0.568;T|0.432	0.432	strong		0.577	TCEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333975.2	NM_007108	
OR2AG2	338755	hgsc.bcm.edu	37	11	6790028	6790028	+	Missense_Mutation	SNP	C	C	G	rs10839616	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6790028C>G	ENST00000338569.2	-	1	258	c.161G>C	c.(160-162)cGg>cCg	p.R54P		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	54			R -> P (in dbSNP:rs10839616).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATGTGGAGCCGGGCTTCTAT	0.542													c|||	1445	0.288538	0.3654	0.1671	5008	,	,		21247	0.2143		0.2157	False		,,,				2504	0.4223				p.R54P		Atlas-SNP	.											OR2AG2,right_upper_lobe,carcinoma,-1,1	OR2AG2	55	1	0			c.G161C						PASS	.	T	PRO/ARG	1501,2901	479.0+/-358.4	246,1009,946	140.0	127.0	132.0		161	0.4	0.0	11	dbSNP_120	132	1890,6702	334.9+/-321.2	231,1428,2637	yes	missense	OR2AG2	NM_001004490.1	103	477,2437,3583	GG,GC,CC		21.9972,34.0981,26.0967	probably-damaging	54/317	6790028	3391,9603	2201	4296	6497	SO:0001583	missense	338755	exon1			TGGAGCCGGGCTT	AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.161G>C	11.37:g.6790028C>G	ENSP00000342697:p.Arg54Pro	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_001004490		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	512	0.23443223443223443	162	0.32926829268292684	74	0.20441988950276244	109	0.19055944055944055	167	0.22031662269129287	c	7.698	0.692473	0.15039	0.340981	0.219972	ENSG00000188124	ENST00000338569	T	0.00449	7.37	4.28	0.401	0.16338	GPCR, rhodopsin-like superfamily (1);	0.497698	0.17054	N	0.188819	T	0.00012	0.0000	M	0.78049	2.395	0.80722	P	0.0	P	0.51147	0.942	P	0.53954	0.738	T	0.49041	-0.8980	9	0.72032	D	0.01	.	8.3017	0.32019	0.0:0.6516:0.0:0.3484	rs10839616;rs52830974;rs10839616	54	A6NM03	O2AG2_HUMAN	P	54	ENSP00000342697:R54P	ENSP00000342697:R54P	R	-	2	0	OR2AG2	6746604	0.000000	0.05858	0.006000	0.13384	0.004000	0.04260	-0.918000	0.04021	0.087000	0.17167	-1.594000	0.00841	CGG	C|0.737;G|0.263	0.263	strong		0.542	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
PLIN1	5346	hgsc.bcm.edu	37	15	90210263	90210263	+	Silent	SNP	A	A	G	rs2304795	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:90210263A>G	ENST00000300055.5	-	8	1278	c.1113T>C	c.(1111-1113)ccT>ccC	p.P371P	PLIN1_ENST00000430628.2_Silent_p.P371P	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	371					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						AGGAGACAGCAGGGGCTGGTG	0.617													A|||	1985	0.396366	0.3707	0.3746	5008	,	,		19066	0.3135		0.3926	False		,,,				2504	0.5358				p.P371P		Atlas-SNP	.											.	PLIN1	36	.	0			c.T1113C						PASS	.	A	,	1749,2651	519.6+/-370.0	352,1045,803	74.0	61.0	65.0		1113,1113	-10.3	0.0	15	dbSNP_100	65	3204,5394	483.4+/-371.1	596,2012,1691	no	coding-synonymous,coding-synonymous	PLIN1	NM_001145311.1,NM_002666.4	,	948,3057,2494	GG,GA,AA		37.2645,39.75,38.1059	,	371/523,371/523	90210263	4953,8045	2200	4299	6499	SO:0001819	synonymous_variant	5346	exon8			GACAGCAGGGGCT	AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"""Perilipins"""	9076	protein-coding gene	gene with protein product		170290	"""perilipin"""	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.1113T>C	15.37:g.90210263A>G		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	203	201	0.990148	NM_001145311	Q8N5Y6	Silent	SNP	ENST00000300055.5	37	CCDS10353.1																																																																																			A|0.623;G|0.377	0.377	strong		0.617	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313424.2	NM_002666	
PRDM2	7799	hgsc.bcm.edu	37	1	14106330	14106330	+	Silent	SNP	C	C	T	rs61747664	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14106330C>T	ENST00000235372.7	+	8	2896	c.2040C>T	c.(2038-2040)caC>caT	p.H680H	PRDM2_ENST00000343137.4_Silent_p.H479H|PRDM2_ENST00000311066.5_Silent_p.H680H|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Silent_p.H479H	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	680					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TGTCTTTCCACAAAGAGAAAA	0.408													T|||	189	0.0377396	0.0015	0.0	5008	,	,		20796	0.0218		0.0169	False		,,,				2504	0.1513				p.H680H		Atlas-SNP	.											.	PRDM2	147	.	0			c.C2040T						PASS	.	T	,,,	12,4394	825.1+/-416.5	0,12,2191	101.0	98.0	99.0		1437,,2040,2040	-0.1	1.0	1	dbSNP_129	99	175,8425	811.7+/-407.1	2,171,4127	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	,,,	2,183,6318	TT,TC,CC		2.0349,0.2724,1.4378	,,,	479/1482,,680/1719,680/1683	14106330	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	7799	exon8			TTTCCACAAAGAG	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.2040C>T	1.37:g.14106330C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	165	75	0.454545	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Silent	SNP	ENST00000235372.7	37	CCDS150.1																																																																																			C|0.983;T|0.017	0.017	strong		0.408	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
GRHL3	57822	hgsc.bcm.edu	37	1	24671418	24671418	+	Missense_Mutation	SNP	A	A	G	rs116396279	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24671418A>G	ENST00000350501.5	+	12	1578	c.1451A>G	c.(1450-1452)aAc>aGc	p.N484S	GRHL3_ENST00000342072.4_Missense_Mutation_p.N391S|GRHL3_ENST00000356046.2_Missense_Mutation_p.N438S|GRHL3_ENST00000236255.4_Missense_Mutation_p.N489S|GRHL3_ENST00000361548.4_Missense_Mutation_p.N484S	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	484					central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		AGCAGCTCCAACAGGTATGGA	0.607													A|||	91	0.0181709	0.0015	0.0231	5008	,	,		13934	0.0		0.0596	False		,,,				2504	0.0133				p.N489S		Atlas-SNP	.											.	GRHL3	69	.	0			c.A1466G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN,SER/ASN	40,4366	41.6+/-74.8	0,40,2163	123.0	116.0	119.0		1451,1451,1466,1313	-0.1	1.0	1	dbSNP_132	119	396,8204	127.0+/-185.4	9,378,3913	yes	missense,missense,missense,missense	GRHL3	NM_198174.2,NM_198173.2,NM_021180.3,NM_001195010.1	46,46,46,46	9,418,6076	GG,GA,AA		4.6047,0.9079,3.3523	benign,benign,benign,benign	484/627,484/603,489/608,438/557	24671418	436,12570	2203	4300	6503	SO:0001583	missense	57822	exon12			GCTCCAACAGGTA	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"""transcription factor CP2-like 4"""	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.1451A>G	1.37:g.24671418A>G	ENSP00000288955:p.Asn484Ser	Somatic	283	1	0.00353357		WXS	Illumina HiSeq	Phase_I	333	159	0.477477	NM_021180	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	54	0.024725274725274724	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	43	0.05672823218997362	A	7.212	0.595687	0.13875	0.009079	0.046047	ENSG00000158055	ENST00000361548;ENST00000342072;ENST00000350501;ENST00000356046;ENST00000236255	T;T;T;T;T	0.10960	3.03;2.82;3.02;3.03;3.03	5.04	-0.14	0.13456	.	0.784158	0.12824	N	0.436214	T	0.00384	0.0012	N	0.01874	-0.695	0.34574	D	0.713724	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.0;0.002;0.001	T	0.48647	-0.9017	10	0.07175	T	0.84	-4.3232	8.0001	0.30291	0.6104:0.0:0.3896:0.0	.	438;489;484	A2A297;Q8TE85-2;G3XAF0	.;.;.	S	484;391;484;438;489	ENSP00000354943:N484S;ENSP00000340543:N391S;ENSP00000288955:N484S;ENSP00000348333:N438S;ENSP00000236255:N489S	ENSP00000236255:N489S	N	+	2	0	GRHL3	24544005	0.999000	0.42202	0.994000	0.49952	0.615000	0.37417	0.882000	0.28186	-0.113000	0.11958	-0.408000	0.06270	AAC	A|0.971;G|0.029	0.029	strong		0.607	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
PM20D1	148811	hgsc.bcm.edu	37	1	205814485	205814485	+	Missense_Mutation	SNP	G	G	A	rs1104899	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:205814485G>A	ENST00000367136.4	-	3	501	c.457C>T	c.(457-459)Cgg>Tgg	p.R153W	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	153			R -> W (in dbSNP:rs1104899). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			AGTGTGCCCCGACCATAGATG	0.562													G|||	1251	0.2498	0.1868	0.2536	5008	,	,		19480	0.255		0.2515	False		,,,				2504	0.3252				p.R153W		Atlas-SNP	.											.	PM20D1	56	.	0			c.C457T						PASS	.	G	TRP/ARG	895,3511	346.2+/-308.9	80,735,1388	103.0	98.0	100.0		457	4.0	0.9	1	dbSNP_86	100	2145,6455	368.8+/-335.2	247,1651,2402	yes	missense	PM20D1	NM_152491.4	101	327,2386,3790	AA,AG,GG		24.9419,20.3132,23.3738	probably-damaging	153/503	205814485	3040,9966	2203	4300	6503	SO:0001583	missense	148811	exon3			TGCCCCGACCATA		CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.457C>T	1.37:g.205814485G>A	ENSP00000356104:p.Arg153Trp	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	505	0.23122710622710624	104	0.21138211382113822	77	0.212707182320442	134	0.23426573426573427	190	0.25065963060686014	G	12.74	2.027395	0.35797	0.203132	0.249419	ENSG00000162877	ENST00000367136	T	0.61980	0.06	5.85	3.96	0.45880	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.93106	3.38	0.19300	P	0.9999726049	D	0.67145	0.996	D	0.69142	0.962	T	0.22382	-1.0218	9	0.72032	D	0.01	.	5.2168	0.15346	0.07:0.1252:0.5523:0.2525	rs1104899;rs4451603;rs17855849;rs52830326;rs60653286;rs1104899	153	Q6GTS8	P20D1_HUMAN	W	153	ENSP00000356104:R153W	ENSP00000356104:R153W	R	-	1	2	PM20D1	204081108	0.998000	0.40836	0.946000	0.38457	0.005000	0.04900	2.648000	0.46647	0.793000	0.33875	-0.254000	0.11334	CGG	G|0.759;A|0.241	0.241	strong		0.562	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
OR51B6	390058	hgsc.bcm.edu	37	11	5373497	5373497	+	Missense_Mutation	SNP	G	G	C	rs7106330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5373497G>C	ENST00000380219.1	+	1	760	c.760G>C	c.(760-762)Gtt>Ctt	p.V254L	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	254			V -> L (in dbSNP:rs7106330).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTCACTGTAGTTTGTCTGAC	0.453													G|||	528	0.105431	0.0303	0.1599	5008	,	,		23552	0.0754		0.1541	False		,,,				2504	0.1493				p.V254L		Atlas-SNP	.											.	OR51B6	53	.	0			c.G760C						PASS	.	G	LEU/VAL	241,4161	141.1+/-176.5	4,233,1964	239.0	212.0	221.0		760	4.0	0.8	11	dbSNP_116	221	1306,7288	258.6+/-282.2	117,1072,3108	yes	missense	OR51B6	NM_001004750.1	32	121,1305,5072	CC,CG,GG		15.1966,5.4748,11.9037	benign	254/313	5373497	1547,11449	2201	4297	6498	SO:0001583	missense	390058	exon1			ACTGTAGTTTGTC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.760G>C	11.37:g.5373497G>C	ENSP00000369568:p.Val254Leu	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	303	144	0.475248	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	261	0.11950549450549451	26	0.052845528455284556	57	0.1574585635359116	50	0.08741258741258741	128	0.16886543535620052	G	11.83	1.757108	0.31137	0.054748	0.151966	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.32023	1.47	4.89	3.98	0.46160	GPCR, rhodopsin-like superfamily (1);	0.278687	0.25453	N	0.030580	T	0.00039	0.0001	N	0.03000	-0.44	0.58432	P	1.999999999946489E-6	B	0.23249	0.082	B	0.29077	0.098	T	0.09885	-1.0654	9	0.59425	D	0.04	.	5.1329	0.14919	0.1815:0.1715:0.647:0.0	rs7106330;rs52837250;rs7106330	254	Q9H340	O51B6_HUMAN	L	253;254	ENSP00000369568:V254L	ENSP00000369568:V254L	V	+	1	0	OR51B6	5330073	0.000000	0.05858	0.793000	0.32043	0.887000	0.51463	-0.090000	0.11163	1.272000	0.44329	0.557000	0.71058	GTT	G|0.883;C|0.117	0.117	strong		0.453	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
CRACR2A	84766	hgsc.bcm.edu	37	12	3782647	3782647	+	Missense_Mutation	SNP	A	A	T	rs36030417	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:3782647A>T	ENST00000252322.1	-	7	1104	c.636T>A	c.(634-636)caT>caA	p.H212Q	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.H212Q|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.H212Q	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		212			H -> Q (in dbSNP:rs36030417).		activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TCTTCTCCTCATGGGCTTCTT	0.488													A|||	855	0.170727	0.115	0.2363	5008	,	,		20099	0.127		0.1471	False		,,,				2504	0.2689				p.H212Q		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.T636A						PASS	.	A	GLN/HIS,GLN/HIS	550,3856	247.5+/-255.7	36,478,1689	151.0	143.0	145.0		636,636	-8.5	0.2	12	dbSNP_126	145	1227,7373	246.9+/-275.2	90,1047,3163	yes	missense,missense	EFCAB4B	NM_001144958.1,NM_032680.3	24,24	126,1525,4852	TT,TA,AA		14.2674,12.483,13.6629	possibly-damaging,possibly-damaging	212/732,212/396	3782647	1777,11229	2203	4300	6503	SO:0001583	missense	84766	exon7			CTCCTCATGGGCT																												ENST00000252322.1:c.636T>A	12.37:g.3782647A>T	ENSP00000252322:p.His212Gln	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	175	72	0.411429	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	332	0.152014652014652	56	0.11382113821138211	86	0.23756906077348067	83	0.1451048951048951	107	0.14116094986807387	A	11.01	1.511825	0.27036	0.12483	0.142674	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.20738	2.05;2.7;2.68	4.55	-8.51	0.00923	.	0.241821	0.41001	D	0.000976	T	0.00012	0.0000	L	0.61218	1.895	0.43203	P	0.004942000000000002	B;P;D	0.56035	0.366;0.949;0.974	B;P;P	0.49140	0.085;0.578;0.601	T	0.04140	-1.0974	9	0.13470	T	0.59	-14.6484	9.6521	0.39904	0.3381:0.0924:0.5695:0.0	rs36030417;rs61907257	212;212;212	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	Q	212	ENSP00000409382:H212Q;ENSP00000412496:H212Q;ENSP00000252322:H212Q	ENSP00000252322:H212Q	H	-	3	2	EFCAB4B	3652908	0.000000	0.05858	0.217000	0.23759	0.545000	0.35147	-3.808000	0.00361	-2.641000	0.00429	-1.844000	0.00574	CAT	A|0.861;T|0.139	0.139	strong		0.488	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
HYLS1	219844	hgsc.bcm.edu	37	11	125769354	125769354	+	Missense_Mutation	SNP	T	T	C	rs667782	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:125769354T>C	ENST00000425380.2	+	3	872	c.91T>C	c.(91-93)Tgt>Cgt	p.C31R	PUS3_ENST00000227474.3_Intron|HYLS1_ENST00000526028.1_Missense_Mutation_p.C31R|HYLS1_ENST00000356438.3_Missense_Mutation_p.C31R	NM_001134793.1	NP_001128265.1	Q96M11	HYLS1_HUMAN	hydrolethalus syndrome 1	31			C -> R (in dbSNP:rs667782). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|skin(3)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		TACCCACATCTGTGCAGGGCA	0.488													T|||	1499	0.299321	0.3177	0.2291	5008	,	,		19753	0.3542		0.2416	False		,,,				2504	0.3272				p.C31R	Esophageal Squamous(172;2590 2636 8884 10471)	Atlas-SNP	.											.	HYLS1	25	.	0			c.T91C						PASS	.	T	ARG/CYS,,ARG/CYS	1325,3077	444.1+/-347.2	212,901,1088	86.0	79.0	81.0		91,,91	6.2	1.0	11	dbSNP_83	81	2046,6552	356.6+/-330.4	255,1536,2508	yes	missense,intron,missense	PUS3,HYLS1	NM_001134793.1,NM_031307.3,NM_145014.2	180,,180	467,2437,3596	CC,CT,TT		23.7962,30.1,25.9308	possibly-damaging,,possibly-damaging	31/300,,31/300	125769354	3371,9629	2201	4299	6500	SO:0001583	missense	219844	exon3			CACATCTGTGCAG	AK057477	CCDS8467.1	11q24	2014-06-18				ENSG00000198331			26558	protein-coding gene	gene with protein product		610693				15843405	Standard	NM_145014		Approved	FLJ32915	uc009zbv.3	Q96M11		ENST00000425380.2:c.91T>C	11.37:g.125769354T>C	ENSP00000414884:p.Cys31Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_001134793	B3KXI8|Q96BX9	Missense_Mutation	SNP	ENST00000425380.2	37	CCDS8467.1	650	0.2976190476190476	171	0.3475609756097561	70	0.19337016574585636	211	0.3688811188811189	198	0.2612137203166227	T	18.54	3.646288	0.67358	0.301	0.237962	ENSG00000198331	ENST00000356438;ENST00000425380;ENST00000526028	T;T;T	0.74106	-0.81;-0.81;-0.81	6.17	6.17	0.99709	.	0.269718	0.30201	N	0.010162	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	1.0	P	0.45212	0.853	P	0.47528	0.549	T	0.04509	-1.0946	9	0.72032	D	0.01	.	15.0521	0.71881	0.0:0.0:0.0:1.0	rs667782;rs17845455;rs17858328;rs52828124;rs59008206;rs667782	31	Q96M11	HYLS1_HUMAN	R	31	ENSP00000348815:C31R;ENSP00000414884:C31R;ENSP00000436833:C31R	ENSP00000348815:C31R	C	+	1	0	HYLS1	125274564	1.000000	0.71417	0.999000	0.59377	0.906000	0.53458	4.052000	0.57420	2.371000	0.80710	0.533000	0.62120	TGT	T|0.719;C|0.281	0.281	strong		0.488	HYLS1-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386733.1	NM_145014	
ETAA1	54465	hgsc.bcm.edu	37	2	67631831	67631831	+	Missense_Mutation	SNP	G	G	A	rs61740794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:67631831G>A	ENST00000272342.5	+	5	2147	c.2017G>A	c.(2017-2019)Gaa>Aaa	p.E673K	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	673						cytoplasm (GO:0005737)		p.E673K(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						TAATAATTCCGAACATGGAGC	0.353													-|||	2282	0.455671	0.348	0.5403	5008	,	,		22167	0.505		0.4692	False		,,,				2504	0.4765				p.E673K		Atlas-SNP	.											ETAA1,NS,carcinoma,0,1	ETAA1	88	1	1	Substitution - Missense(1)	stomach(1)	c.G2017A						scavenged	.	G	LYS/GLU	1494,2910		232,1030,940	82.0	85.0	84.0		2017	2.9	0.0	2	dbSNP_129	84	3874,4726		873,2128,1299	yes	missense	ETAA1	NM_019002.3	56	1105,3158,2239	AA,AG,GG		45.0465,33.9237,41.2796	benign	673/927	67631831	5368,7636	2202	4300	6502	SO:0001583	missense	54465	exon5			AATTCCGAACATG	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.2017G>A	2.37:g.67631831G>A	ENSP00000272342:p.Glu673Lys	Somatic	141	2	0.0141844		WXS	Illumina HiSeq	Phase_I	212	72	0.339623	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	999	0.4574175824175824	173	0.3516260162601626	186	0.5138121546961326	286	0.5	354	0.46701846965699206	-	0.934	-0.711877	0.03206	0.339237	0.450465	ENSG00000143971	ENST00000272342	T	0.15372	2.43	5.37	2.87	0.33458	.	1.006310	0.07982	N	0.985706	T	0.00012	0.0000	N	0.03115	-0.41	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.46345	-0.9198	9	0.02654	T	1	-2.2517	5.7243	0.18004	0.7663:0.0:0.0855:0.1483	rs61740794	673	Q9NY74	ETAA1_HUMAN	K	673	ENSP00000272342:E673K	ENSP00000272342:E673K	E	+	1	0	ETAA1	67485335	0.003000	0.15002	0.001000	0.08648	0.046000	0.14306	0.820000	0.27323	0.998000	0.38996	-0.471000	0.05019	GAA	G|0.590;A|0.410	0.410	strong		0.353	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002	
ZNF658	26149	hgsc.bcm.edu	37	9	40773337	40773337	+	Silent	SNP	C	C	T	rs78487056	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:40773337C>T	ENST00000602553.1	-	5	2232	c.1938G>A	c.(1936-1938)aaG>aaA	p.K646K	ZNF658_ENST00000441795.1_Intron|ZNF658_ENST00000377626.3_Silent_p.K646K			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	646					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)	p.K646K(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TTTGATGTGCCTTGAGAACAG	0.418													C|||	1047	0.209065	0.0424	0.2478	5008	,	,		19384	0.3482		0.2217	False		,,,				2504	0.2505				p.K646K		Atlas-SNP	.											ZNF658,NS,carcinoma,0,1	ZNF658	100	1	1	Substitution - coding silent(1)	ovary(1)	c.G1938A						scavenged	.	C		300,4104	158.9+/-191.5	20,260,1922	120.0	128.0	125.0		1938	-2.4	0.0	9	dbSNP_131	125	1790,6806	315.5+/-312.3	172,1446,2680	no	coding-synonymous	ZNF658	NM_033160.5		192,1706,4602	TT,TC,CC		20.8236,6.812,16.0769		646/1060	40773337	2090,10910	2202	4298	6500	SO:0001819	synonymous_variant	26149	exon5			ATGTGCCTTGAGA	AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"""Zinc fingers, C2H2-type"", ""-"""	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.1938G>A	9.37:g.40773337C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	170	67	0.394118	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Silent	SNP	ENST00000602553.1	37	CCDS35023.1																																																																																			C|0.824;T|0.176	0.176	strong		0.418	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160	
ZNF845	91664	hgsc.bcm.edu	37	19	53856702	53856702	+	Missense_Mutation	SNP	G	G	A	rs200114728	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53856702G>A	ENST00000595091.1	+	5	2993	c.2774G>A	c.(2773-2775)cGt>cAt	p.R925H	ZNF845_ENST00000458035.1_Missense_Mutation_p.R925H			Q96IR2	ZN845_HUMAN	zinc finger protein 845	925					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R925H(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						AAAACCTTCCGTCACAATTCA	0.363													.|||	267	0.0533147	0.0484	0.0562	5008	,	,		21751	0.0466		0.0915	False		,,,				2504	0.0256				p.R925H		Atlas-SNP	.											ZNF845,NS,carcinoma,0,6	ZNF845	101	6	3	Substitution - Missense(3)	kidney(3)	c.G2774A						scavenged	.						33.0	30.0	31.0					19																	53856702		692	1591	2283	SO:0001583	missense	91664	exon4			CCTTCCGTCACAA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2774G>A	19.37:g.53856702G>A	ENSP00000470005:p.Arg925His	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	97	4	0.0412371	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	G	5.812	0.334080	0.11013	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.36157	1.27	2.0	-4.0	0.04057	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42585	0.1209	L	0.58302	1.8	0.09310	N	1	D	0.55800	0.973	P	0.53760	0.734	T	0.43925	-0.9361	9	0.51188	T	0.08	.	10.7803	0.46374	0.0:0.6804:0.1821:0.1375	.	925	Q96IR2	ZN845_HUMAN	H	925;841	ENSP00000388311:R925H	ENSP00000412086:R841H	R	+	2	0	ZNF845	58548514	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-7.662000	0.00032	-1.603000	0.01597	-0.499000	0.04595	CGT	.	.	weak		0.363	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
ITGA9	3680	hgsc.bcm.edu	37	3	37550109	37550109	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:37550109A>G	ENST00000264741.5	+	8	1144	c.888A>G	c.(886-888)tcA>tcG	p.S296S	ITGA9_ENST00000422441.1_Silent_p.S296S	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	296					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		TTCAAGCATCAGGTAAAAAGG	0.338																																					p.S296S		Atlas-SNP	.											.	ITGA9	98	.	0			c.A888G						PASS	.						100.0	105.0	103.0					3																	37550109		2203	4300	6503	SO:0001819	synonymous_variant	3680	exon8			AGCATCAGGTAAA	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.888A>G	3.37:g.37550109A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	160	80	0.5	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																			.	.	none		0.338	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
DISC1	27185	hgsc.bcm.edu	37	1	231954145	231954145	+	Silent	SNP	G	G	A	rs12133766	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:231954145G>A	ENST00000602281.1	+	9	1916	c.1863G>A	c.(1861-1863)ctG>ctA	p.L621L	DISC1_ENST00000366633.3_Silent_p.L621L|DISC1_ENST00000602873.1_3'UTR|DISC1_ENST00000537876.1_Intron|DISC1_ENST00000366636.4_Silent_p.L621L|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000539444.1_3'UTR|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000439617.2_Silent_p.L621L|DISC1_ENST00000535983.1_Silent_p.L621L	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	621	Interaction with ATF4 and ATF5.|Interaction with TRAF3IP1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				GAGAAGGGCTGGAGGGACTCC	0.473													G|||	162	0.0323482	0.0113	0.0403	5008	,	,		21286	0.0337		0.0507	False		,,,				2504	0.0348				p.L653L		Atlas-SNP	.											.	DISC1	207	.	0			c.G1959A						PASS	.	G	,,,,,,,,,,,,,,	84,4322	74.1+/-112.3	2,80,2121	101.0	104.0	103.0		1863,1863,1959,1863,1863,1497,1863,1863,1863,,,,,,1863	4.3	1.0	1	dbSNP_120	103	517,8083	146.9+/-202.4	10,497,3793	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-3,intron,intron,utr-3,utr-3,coding-synonymous	DISC1	NM_001012957.1,NM_001012959.1,NM_001164537.1,NM_001164538.1,NM_001164539.1,NM_001164540.1,NM_001164541.1,NM_001164542.1,NM_001164544.1,NM_001164545.1,NM_001164546.1,NM_001164547.1,NM_001164548.1,NM_001164556.1,NM_018662.2	,,,,,,,,,,,,,,	12,577,5914	AA,AG,GG		6.0116,1.9065,4.6209	,,,,,,,,,,,,,,	621/833,621/679,653/887,621/804,621/756,499/733,621/696,621/682,621/663,,,,,,621/855	231954145	601,12405	2203	4300	6503	SO:0001819	synonymous_variant	27185	exon10			AGGGCTGGAGGGA	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.1863G>A	1.37:g.231954145G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	117	66	0.564103	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Silent	SNP	ENST00000602281.1	37	CCDS59205.1	85	0.03891941391941392	14	0.028455284552845527	20	0.055248618784530384	14	0.024475524475524476	37	0.048812664907651716	G	10.25	1.299074	0.23650	0.019065	0.060116	ENSG00000162946	ENST00000422590	.	.	.	5.23	4.31	0.51392	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.2921	11.297	0.49284	0.0848:0.0:0.9152:0.0	rs12133766;rs57612110;rs12133766	.	.	.	X	24	.	.	W	+	2	0	DISC1	230020768	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.399000	0.52586	1.406000	0.46857	0.591000	0.81541	TGG	G|0.955;A|0.045	0.045	strong		0.473	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662	
IGSF22	283284	hgsc.bcm.edu	37	11	18735570	18735570	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18735570A>G	ENST00000513874.1	-	14	2063	c.1924T>C	c.(1924-1926)Tac>Cac	p.Y642H	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	642	Ig-like 4.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CCATCCTTGTACCATGTCACT	0.597																																					p.Y642H		Atlas-SNP	.											.	IGSF22	211	.	0			c.T1924C						PASS	.						118.0	122.0	121.0					11																	18735570		2176	4259	6435	SO:0001583	missense	283284	exon14			CCTTGTACCATGT	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1924T>C	11.37:g.18735570A>G	ENSP00000421191:p.Tyr642His	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	250	16	0.064	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	A	13.08	2.131488	0.37630	.	.	ENSG00000179057	ENST00000513874	T	0.47528	0.84	4.11	2.99	0.34606	.	0.000000	0.31519	U	0.007518	T	0.54334	0.1852	L	0.58354	1.805	0.22541	N	0.999007	D	0.65815	0.995	D	0.63283	0.913	T	0.42916	-0.9423	10	0.18710	T	0.47	.	7.6466	0.28323	0.9009:0.0:0.0991:0.0	.	642	D6RGV7	.	H	642	ENSP00000421191:Y642H	ENSP00000322422:Y642H	Y	-	1	0	IGSF22	18692146	1.000000	0.71417	0.964000	0.40570	0.991000	0.79684	2.903000	0.48711	0.655000	0.30866	0.450000	0.29827	TAC	.	.	none		0.597	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
SMCHD1	23347	hgsc.bcm.edu	37	18	2656248	2656248	+	Silent	SNP	G	G	C	rs2430853	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:2656248G>C	ENST00000320876.6	+	1	512	c.174G>C	c.(172-174)gcG>gcC	p.A58A	CBX3P2_ENST00000579647.1_RNA|SMCHD1_ENST00000261598.8_Silent_p.A58A	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	58					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GATTTCGCGCGTGTGTGTGTC	0.612													C|||	3158	0.630591	0.9153	0.6009	5008	,	,		13649	0.3274		0.5497	False		,,,				2504	0.6626				p.A58A		Atlas-SNP	.											.	SMCHD1	88	.	0			c.G174C						PASS	.	C		3344,612		1420,504,54	26.0	33.0	31.0		174	-1.8	0.1	18	dbSNP_100	31	4539,3761		1232,2075,843	yes	coding-synonymous	SMCHD1	NM_015295.2		2652,2579,897	CC,CG,GG		45.3133,15.4702,35.6805		58/2006	2656248	7883,4373	1978	4150	6128	SO:0001819	synonymous_variant	23347	exon1			TCGCGCGTGTGTG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.174G>C	18.37:g.2656248G>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			G|0.461;C|0.539	0.539	strong		0.612	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110492352	110492352	+	Missense_Mutation	SNP	C	C	T	rs117952538	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110492352C>T	ENST00000378402.5	+	55	9415	c.9311C>T	c.(9310-9312)aCc>aTc	p.T3104I		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3104	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TTGAATGCTACCTACATATCA	0.333										HNSCC(38;0.096)			C|||	31	0.0061901	0.0008	0.0086	5008	,	,		17368	0.0		0.0179	False		,,,				2504	0.0061				p.T3104I		Atlas-SNP	.											PKHD1L1,NS,carcinoma,-1,1	PKHD1L1	522	1	0			c.C9311T						PASS	.	C	ILE/THR	8,3650		0,8,1821	50.0	49.0	49.0		9311	5.2	1.0	8	dbSNP_132	49	106,8056		0,106,3975	yes	missense	PKHD1L1	NM_177531.4	89	0,114,5796	TT,TC,CC		1.2987,0.2187,0.9645	probably-damaging	3104/4244	110492352	114,11706	1829	4081	5910	SO:0001583	missense	93035	exon55			ATGCTACCTACAT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.9311C>T	8.37:g.110492352C>T	ENSP00000367655:p.Thr3104Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	17	0.007783882783882784	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	13	0.017150395778364115	C	17.97	3.519012	0.64634	0.002187	0.012987	ENSG00000205038	ENST00000378402	D	0.89415	-2.51	5.25	5.25	0.73442	G8 domain (2);	0.139370	0.49305	D	0.000142	D	0.84683	0.5526	M	0.82056	2.57	0.30997	N	0.720711	B	0.29766	0.256	B	0.37989	0.262	D	0.86191	0.1612	10	0.34782	T	0.22	.	16.7128	0.85389	0.0:1.0:0.0:0.0	.	3104	Q86WI1	PKHL1_HUMAN	I	3104	ENSP00000367655:T3104I	ENSP00000367655:T3104I	T	+	2	0	PKHD1L1	110561528	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.752000	0.55172	2.604000	0.88044	0.650000	0.86243	ACC	C|0.992;T|0.008	0.008	strong		0.333	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
DNA2	1763	hgsc.bcm.edu	37	10	70227964	70227964	+	Silent	SNP	C	C	T	rs10998205	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70227964C>T	ENST00000358410.3	-	3	407	c.357G>A	c.(355-357)ctG>ctA	p.L119L	DNA2_ENST00000399180.2_Silent_p.L205L|DNA2_ENST00000399179.2_Silent_p.L119L	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	119	Nuclease activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						TGTCTGGATACAGAATCAAAT	0.398													C|||	697	0.139177	0.0227	0.2277	5008	,	,		16038	0.127		0.1064	False		,,,				2504	0.2802				p.L119L		Atlas-SNP	.											.	DNA2	76	.	0			c.G357A						PASS	.	C		116,3572		3,110,1731	94.0	86.0	89.0		357	-10.8	0.3	10	dbSNP_120	89	717,7483		43,631,3426	no	coding-synonymous	DNA2	NM_001080449.2		46,741,5157	TT,TC,CC		8.7439,3.1453,7.0071		119/1061	70227964	833,11055	1844	4100	5944	SO:0001819	synonymous_variant	1763	exon3			TGGATACAGAATC	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"""DNA2 DNA replication helicase 2-like (yeast)"", ""DNA replication helicase 2 homolog (yeast)"""	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.357G>A	10.37:g.70227964C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	124	71	0.572581	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				C|0.901;T|0.099	0.099	strong		0.398	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
SHMT1	6470	hgsc.bcm.edu	37	17	18232096	18232096	+	Missense_Mutation	SNP	G	G	A	rs1979277	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18232096G>A	ENST00000316694.3	-	12	1554	c.1420C>T	c.(1420-1422)Ctc>Ttc	p.L474F	SHMT1_ENST00000354098.3_Missense_Mutation_p.L435F|SHMT1_ENST00000539052.1_Missense_Mutation_p.L336F|RP1-178F10.3_ENST00000577764.1_lincRNA|SHMT1_ENST00000352886.6_Missense_Mutation_p.L394F	NM_004169.3	NP_004160.3	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	474			L -> F (in dbSNP:rs1979277). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|folic acid metabolic process (GO:0046655)|glycine biosynthetic process from serine (GO:0019264)|L-serine catabolic process (GO:0006565)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase biosynthetic process (GO:0009113)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	amino acid binding (GO:0016597)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)	13					Glycine(DB00145)|Mimosine(DB01055)|Tetrahydrofolic acid(DB00116)	AGAGGGAAGAGAGAGGCGAAG	0.637													G|||	1141	0.227835	0.3313	0.2695	5008	,	,		15016	0.0605		0.3082	False		,,,				2504	0.1483				p.L474F		Atlas-SNP	.											SHMT1,colon,carcinoma,0,1	SHMT1	36	1	0			c.C1420T	GRCh37	CM014391	SHMT1	M	rs1979277	PASS	.	G	PHE/LEU,PHE/LEU	1485,2921		237,1011,955	24.0	24.0	24.0		1420,1303	-4.5	0.0	17	dbSNP_92	24	2608,5988		386,1836,2076	no	missense,missense	SHMT1	NM_004169.3,NM_148918.1	22,22	623,2847,3031	AA,AG,GG		30.3397,33.704,31.4798	benign,benign	474/484,435/445	18232096	4093,8909	2203	4298	6501	SO:0001583	missense	6470	exon12			GGAAGAGAGAGGC		CCDS11196.1, CCDS11197.1, CCDS62112.1	17p11.2	2010-04-23			ENSG00000176974	ENSG00000176974	2.1.2.1		10850	protein-coding gene	gene with protein product	"""cytoplasmic serine hydroxymethyltransferase"", ""14 kDa protein"""	182144				8505317	Standard	NM_004169		Approved	CSHMT, SHMT, MGC15229, MGC24556	uc002gta.3	P34896	OTTHUMG00000059094	ENST00000316694.3:c.1420C>T	17.37:g.18232096G>A	ENSP00000318868:p.Leu474Phe	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_004169	B4DPM9|D3DXD0|Q96HY0|Q9UMD1|Q9UMD2	Missense_Mutation	SNP	ENST00000316694.3	37	CCDS11196.1	538	0.24633699633699635	165	0.3353658536585366	102	0.281767955801105	33	0.057692307692307696	238	0.31398416886543534	G	10.03	1.239397	0.22711	0.33704	0.303397	ENSG00000176974	ENST00000316694;ENST00000395684;ENST00000352886;ENST00000539052;ENST00000354098;ENST00000395685	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.37	-4.52	0.03472	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.898574	0.09830	N	0.750310	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B;B;B	0.27140	0.0;0.169;0.0	B;B;B	0.25140	0.001;0.058;0.0	T	0.45571	-0.9252	9	0.59425	D	0.04	-2.2252	5.6984	0.17869	0.0733:0.4502:0.1512:0.3252	rs1979277;rs2230025;rs3183766;rs17850285;rs57933897;rs1979277	437;435;474	A8MYA6;P34896-2;P34896	.;.;GLYC_HUMAN	F	474;249;394;336;435;437	ENSP00000318868:L474F;ENSP00000345881:L394F;ENSP00000440089:L336F;ENSP00000318805:L435F	ENSP00000318868:L474F	L	-	1	0	SHMT1	18172821	0.000000	0.05858	0.006000	0.13384	0.247000	0.25773	0.542000	0.23222	-0.245000	0.09625	-0.211000	0.12701	CTC	G|0.719;A|0.281	0.281	strong		0.637	SHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130831.2	NM_004169	
CYP2D6	1565	hgsc.bcm.edu	37	22	42523558	42523558	+	Missense_Mutation	SNP	T	T	C	rs202102799		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:42523558T>C	ENST00000360608.5	-	7	1178	c.1064A>G	c.(1063-1065)tAc>tGc	p.Y355C	CYP2D6_ENST00000389970.3_Missense_Mutation_p.Y355C|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.Y304C|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	355					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GGCAGTGGTGTAGGGCATGTG	0.607																																					p.Y355C		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,2	CYP2D6	104	2	0			c.A1064G						scavenged	.						106.0	82.0	90.0					22																	42523558		2202	4300	6502	SO:0001583	missense	1565	exon7			GTGGTGTAGGGCA	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1064A>G	22.37:g.42523558T>C	ENSP00000353820:p.Tyr355Cys	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	323	7	0.0216718	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.884011	0.51908	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.76186	-1.0;-1.0;-1.0	4.93	-8.43	0.00953	.	0.656947	0.15234	N	0.273223	D	0.88265	0.6390	H	0.96518	3.835	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.81914	0.995;0.976;0.995	D	0.91542	0.5250	10	0.87932	D	0	.	18.217	0.89889	0.1595:0.0:0.0:0.8405	.	355;304;355	C1ID54;Q6NXU8;Q6NWU0	.;.;.	C	355;355;301;304;304	ENSP00000353820:Y355C;ENSP00000374620:Y355C;ENSP00000351927:Y304C	ENSP00000351927:Y304C	Y	-	2	0	CYP2D6	40853502	0.995000	0.38212	0.872000	0.34217	0.407000	0.30961	0.270000	0.18607	-1.565000	0.01676	-0.509000	0.04479	TAC	T|0.999;C|0.001	0.001	weak		0.607	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
ALPK2	115701	hgsc.bcm.edu	37	18	56196451	56196451	+	Silent	SNP	C	C	T	rs7236563	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56196451C>T	ENST00000361673.3	-	6	5586	c.5373G>A	c.(5371-5373)aaG>aaA	p.K1791K		NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1791	Ig-like 2.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CAGCTTGGATCTTTTTCAGTA	0.348													C|||	1868	0.373003	0.3169	0.415	5008	,	,		18894	0.2381		0.5815	False		,,,				2504	0.3436				p.K1791K		Atlas-SNP	.											ALPK2_ENST00000361673,colon,carcinoma,0,2	ALPK2	487	2	0			c.G5373A						PASS	.	C		1576,2830	488.3+/-361.2	281,1014,908	92.0	90.0	91.0		5373	2.7	1.0	18	dbSNP_116	91	4617,3983	597.5+/-393.8	1251,2115,934	no	coding-synonymous	ALPK2	NM_052947.3		1532,3129,1842	TT,TC,CC		46.314,35.7694,47.6165		1791/2171	56196451	6193,6813	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon6			TTGGATCTTTTTC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.5373G>A	18.37:g.56196451C>T		Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			C|0.554;T|0.446	0.446	strong		0.348	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
HLA-C	3107	hgsc.bcm.edu	37	6	31238983	31238983	+	Silent	SNP	G	G	T	rs200155513|rs2308585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238983G>T	ENST00000376228.5	-	3	500	c.486C>A	c.(484-486)acC>acA	p.T162T	HLA-C_ENST00000383329.3_Silent_p.T162T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	162	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TCTGAGCCGCGGTGTCCGCGG	0.692																																					p.T162T		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	0			c.C486A						PASS	.						30.0	22.0	25.0					6																	31238983		2142	4169	6311	SO:0001819	synonymous_variant	3107	exon3			AGCCGCGGTGTCC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.486C>A	6.37:g.31238983G>T		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	162	48	0.296296	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	0.028	-1.358296	0.01245	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	-2.02	0.07388	.	.	.	.	.	T	0.25044	0.0608	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.32929	-0.9888	4	.	.	.	.	15.0314	0.71710	0.0:0.2262:0.7738:0.0	rs2308585;rs9264657	.	.	.	S	162	.	.	R	-	1	0	HLA-C	31346962	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.817000	0.00359	-0.877000	0.04012	-0.676000	0.03789	CGC	G|0.514;C|0.486	.	strong		0.692	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
NPSR1	387129	hgsc.bcm.edu	37	7	34818113	34818113	+	Missense_Mutation	SNP	A	A	T	rs324981	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:34818113A>T	ENST00000360581.1	+	3	448	c.320A>T	c.(319-321)aAt>aTt	p.N107I	NPSR1_ENST00000359791.1_Missense_Mutation_p.N107I|NPSR1_ENST00000531252.1_Missense_Mutation_p.N96I|NPSR1_ENST00000381539.3_Missense_Mutation_p.N107I|NPSR1_ENST00000381542.1_Intron|NPSR1_ENST00000381553.3_Missense_Mutation_p.N107I	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	107			N -> I (in dbSNP:rs324981). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15073379, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	ACAGATATTAATTGGCGATTC	0.393													T|||	2341	0.467452	0.559	0.4092	5008	,	,		17830	0.5288		0.4622	False		,,,				2504	0.3272				p.N107I		Atlas-SNP	.											.	NPSR1	134	.	0			c.A320T	GRCh37	CM073245	NPSR1	M	rs324981	PASS	.	T	ILE/ASN,ILE/ASN	2407,1999	559.5+/-380.2	645,1117,441	110.0	98.0	102.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	320,320	5.1	0.1	7	dbSNP_79	102	3962,4638	602.0+/-394.4	920,2122,1258	yes	missense,missense	NPSR1	NM_207172.1,NM_207173.1	149,149	1565,3239,1699	TT,TA,AA		46.0698,45.37,48.9697	benign,benign	107/372,107/378	34818113	6369,6637	2203	4300	6503	SO:0001583	missense	387129	exon3			ATATTAATTGGCG	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.320A>T	7.37:g.34818113A>T	ENSP00000353788:p.Asn107Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	119	66	0.554622	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	37	CCDS5444.1	1052	0.4816849816849817	242	0.491869918699187	162	0.44751381215469616	298	0.5209790209790209	350	0.46174142480211083	T	0.021	-1.424493	0.01126	0.5463	0.460698	ENSG00000187258	ENST00000381553;ENST00000360581;ENST00000359791;ENST00000531252;ENST00000381539	T;T;T;T;T	0.71222	1.56;1.56;1.56;-0.55;1.56	5.14	5.14	0.70334	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000009	T	0.00012	0.0000	N	0.00427	-1.505	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.43376	-0.9395	9	0.02654	T	1	-10.1696	8.6008	0.33742	0.1711:0.0:0.0:0.8289	rs324981;rs56577867;rs57535228;rs324981	96;107;107;107	Q6W5P4-5;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;NPSR1_HUMAN	I	107;107;107;96;107	ENSP00000370965:N107I;ENSP00000353788:N107I;ENSP00000352839:N107I;ENSP00000433258:N96I;ENSP00000370950:N107I	ENSP00000352839:N107I	N	+	2	0	NPSR1	34784638	0.847000	0.29606	0.116000	0.21606	0.191000	0.23601	2.994000	0.49433	0.895000	0.36342	-0.364000	0.07487	AAT	A|0.515;T|0.485	0.485	strong		0.393	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173	
DNHD1	144132	hgsc.bcm.edu	37	11	6554941	6554941	+	Missense_Mutation	SNP	C	C	A	rs4282961	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6554941C>A	ENST00000527990.2	+	12	2536	c.2536C>A	c.(2536-2538)Ctg>Atg	p.L846M	DNHD1_ENST00000254579.6_Missense_Mutation_p.L846M			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	846					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GTACGTCGAGCTGGAGGAGCG	0.532													C|||	1069	0.213458	0.1248	0.2882	5008	,	,		21748	0.131		0.3549	False		,,,				2504	0.2198				p.L846M		Atlas-SNP	.											.	DNHD1	198	.	0			c.C2536A						PASS	.	C	MET/LEU	200,1184		19,162,511	68.0	61.0	63.0		2536	4.1	0.7	11	dbSNP_111	63	1063,2119		181,701,709	yes	missense	DNHD1	NM_144666.2	15	200,863,1220	AA,AC,CC		33.4067,14.4509,27.661	probably-damaging	846/4754	6554941	1263,3303	692	1591	2283	SO:0001583	missense	144132	exon14			GTCGAGCTGGAGG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.2536C>A	11.37:g.6554941C>A	ENSP00000436180:p.Leu846Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	108	40	0.37037	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	521	0.23855311355311357	62	0.12601626016260162	111	0.30662983425414364	90	0.15734265734265734	258	0.3403693931398417	C	15.55	2.865728	0.51588	0.144509	0.334067	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210	T;T	0.37915	1.17;1.17	5.92	4.05	0.47172	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.42629	P	0.006622000000000017	D	0.89917	1.0	D	0.87578	0.998	T	0.31916	-0.9926	8	0.66056	D	0.02	.	8.7938	0.34868	0.0:0.8283:0.0:0.1717	rs4282961;rs17833604;rs60785446;rs4282961	846	Q96M86	DNHD1_HUMAN	M	846;846;112	ENSP00000254579:L846M;ENSP00000436180:L846M	ENSP00000254579:L846M	L	+	1	2	DNHD1	6511517	0.754000	0.28360	0.699000	0.30290	0.467000	0.32768	1.070000	0.30653	0.829000	0.34733	0.655000	0.94253	CTG	C|0.773;A|0.227	0.227	strong		0.532	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
MLXIPL	51085	hgsc.bcm.edu	37	7	73020439	73020439	+	Silent	SNP	C	C	T	rs12539160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:73020439C>T	ENST00000313375.3	-	6	668	c.621G>A	c.(619-621)gcG>gcA	p.A207A	MLXIPL_ENST00000434326.1_Intron|MLXIPL_ENST00000395189.1_Intron|MLXIPL_ENST00000354613.1_Silent_p.A207A|MLXIPL_ENST00000429400.2_Silent_p.A207A|MLXIPL_ENST00000414749.2_Silent_p.A207A	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	207					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				ACCTGCCTTCCGCCTAGGGAG	0.662													C|||	89	0.0177716	0.0151	0.0187	5008	,	,		13931	0.0		0.0388	False		,,,				2504	0.0174				p.A207A		Atlas-SNP	.											.	MLXIPL	54	.	0			c.G621A						PASS	.	C	,,,	106,4248		0,106,2071	10.0	12.0	11.0		621,621,621,621	1.8	0.2	7	dbSNP_120	11	280,8226		2,276,3975	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MLXIPL	NM_032951.2,NM_032952.2,NM_032953.2,NM_032954.2	,,,	2,382,6046	TT,TC,CC		3.2918,2.4345,3.0016	,,,	207/853,207/834,207/851,207/832	73020439	386,12474	2177	4253	6430	SO:0001819	synonymous_variant	51085	exon6			GCCTTCCGCCTAG	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"""carbohydrate response element binding protein"""	605678	"""Williams Beuren syndrome chromosome region 14"""	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.621G>A	7.37:g.73020439C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Silent	SNP	ENST00000313375.3	37	CCDS5553.1																																																																																			C|0.973;T|0.027	0.027	strong		0.662	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187692908	187692908	+	Silent	SNP	T	T	G	rs17852916	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:187692908T>G	ENST00000295131.2	-	9	1744	c.1705A>C	c.(1705-1707)Aga>Cga	p.R569R		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	569					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			AAAGTTGATCTCTTGTTGTCC	0.368													t|||	726	0.144968	0.3154	0.0994	5008	,	,		17199	0.0208		0.1093	False		,,,				2504	0.1115				p.R569R		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.A1705C						PASS	.	G		1331,3075	441.8+/-346.5	205,921,1077	114.0	113.0	113.0		1705	4.3	0.0	2	dbSNP_123	113	972,7628	209.8+/-250.9	45,882,3373	no	coding-synonymous	ZSWIM2	NM_182521.2		250,1803,4450	GG,GT,TT		11.3023,30.2088,17.7072		569/634	187692908	2303,10703	2203	4300	6503	SO:0001819	synonymous_variant	151112	exon9			TTGATCTCTTGTT	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1705A>C	2.37:g.187692908T>G		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	245	107	0.436735	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Silent	SNP	ENST00000295131.2	37	CCDS33348.1																																																																																			T|0.838;G|0.162	0.162	strong		0.368	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
PSG2	5670	hgsc.bcm.edu	37	19	43575905	43575905	+	Missense_Mutation	SNP	C	C	T	rs77035666	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:43575905C>T	ENST00000406487.1	-	4	1009	c.911G>A	c.(910-912)cGt>cAt	p.R304H		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	304	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.R304H(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				GGCTGAGTTACGAACAGAGCA	0.453													C|||	484	0.0966454	0.0651	0.2061	5008	,	,		19273	0.004		0.1103	False		,,,				2504	0.1431				p.R304H		Atlas-SNP	.											PSG2,NS,carcinoma,0,1	PSG2	84	1	1	Substitution - Missense(1)	pancreas(1)	c.G911A						PASS	.	C	HIS/ARG	322,4082	171.9+/-202.1	23,276,1903	176.0	180.0	179.0		911	-2.5	0.0	19	dbSNP_131	179	942,7656	206.8+/-248.7	57,828,3414	yes	missense	PSG2	NM_031246.3	29	80,1104,5317	TT,TC,CC		10.956,7.3115,9.7216		304/336	43575905	1264,11738	2202	4299	6501	SO:0001583	missense	5670	exon4			GAGTTACGAACAG		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.911G>A	19.37:g.43575905C>T	ENSP00000385706:p.Arg304His	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	168	79	0.470238	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	188	0.08608058608058608	32	0.06504065040650407	63	0.17403314917127072	2	0.0034965034965034965	91	0.12005277044854881	c	0.004	-2.267055	0.00259	0.073115	0.10956	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.12774	2.65	1.26	-2.53	0.06326	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00039	0.0001	L	0.33710	1.025	0.80722	P	0.0	B;B	0.24368	0.021;0.102	B;B	0.18263	0.009;0.021	T	0.43196	-0.9406	8	0.09843	T	0.71	.	2.1681	0.03843	0.0:0.2749:0.324:0.4011	.	304;304	B5MCM8;P11465	.;PSG2_HUMAN	H	304	ENSP00000385706:R304H	ENSP00000332984:R304H	R	-	2	0	PSG2	48267745	0.000000	0.05858	0.015000	0.15790	0.005000	0.04900	-0.559000	0.05971	-0.279000	0.09167	-0.507000	0.04495	CGT	C|0.904;T|0.096	0.096	strong		0.453	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
TMEM123	114908	hgsc.bcm.edu	37	11	102272277	102272277	+	Silent	SNP	G	G	T	rs12275185	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:102272277G>T	ENST00000398136.2	-	4	1015	c.595C>A	c.(595-597)Cga>Aga	p.R199R	TMEM123_ENST00000532161.1_Silent_p.R111R|TMEM123_ENST00000361236.3_Silent_p.R180R|TMEM123_ENST00000525577.1_5'Flank	NM_052932.2	NP_443164.2	Q8N131	PORIM_HUMAN	transmembrane protein 123	199					oncosis (GO:0070267)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(3)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		TACATGGTTCGATACCGAATG	0.363													T|||	183	0.0365415	0.062	0.0331	5008	,	,		15076	0.004		0.0626	False		,,,				2504	0.0112				p.R199R		Atlas-SNP	.											.	TMEM123	16	.	0			c.C595A						PASS	.	T		249,3393		5,239,1577	92.0	88.0	89.0		595	4.6	1.0	11	dbSNP_120	89	587,7569		24,539,3515	no	coding-synonymous	TMEM123	NM_052932.2		29,778,5092	TT,TG,GG		7.1972,6.8369,7.0859		199/209	102272277	836,10962	1821	4078	5899	SO:0001819	synonymous_variant	114908	exon4			TGGTTCGATACCG	AL050161	CCDS41702.1	11q22.1	2014-01-02			ENSG00000152558	ENSG00000152558			30138	protein-coding gene	gene with protein product	"""pro oncosis receptor inducing membrane injury gene"""	606356				11481458, 24318988	Standard	NM_052932		Approved	PORIMIN, KCT3	uc001pha.3	Q8N131	OTTHUMG00000167326	ENST00000398136.2:c.595C>A	11.37:g.102272277G>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	76	30	0.394737	NM_052932	Q8IWS2|Q96QV2	Silent	SNP	ENST00000398136.2	37	CCDS41702.1																																																																																			G|0.948;T|0.052	0.052	strong		0.363	TMEM123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394178.1	NM_052932	
DNAH2	146754	hgsc.bcm.edu	37	17	7669761	7669761	+	Missense_Mutation	SNP	G	G	A	rs35788701	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7669761G>A	ENST00000572933.1	+	22	5097	c.3637G>A	c.(3637-3639)Gag>Aag	p.E1213K	DNAH2_ENST00000389173.2_Missense_Mutation_p.E1213K			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1213	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTTCAAGATCGAGCAGCCACC	0.562													G|||	34	0.00678914	0.0023	0.0115	5008	,	,		16931	0.0		0.0129	False		,,,				2504	0.0102				p.E1213K		Atlas-SNP	.											.	DNAH2	498	.	0			c.G3637A						PASS	.	G	LYS/GLU	27,4379	32.6+/-62.9	0,27,2176	71.0	64.0	66.0		3637	5.9	1.0	17	dbSNP_126	66	175,8425	80.1+/-142.7	2,171,4127	yes	missense	DNAH2	NM_020877.2	56	2,198,6303	AA,AG,GG		2.0349,0.6128,1.5531	benign	1213/4428	7669761	202,12804	2203	4300	6503	SO:0001583	missense	146754	exon21			AAGATCGAGCAGC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.3637G>A	17.37:g.7669761G>A	ENSP00000458355:p.Glu1213Lys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	18	0.008241758241758242	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	9	0.011873350923482849	G	19.80	3.895428	0.72639	0.006128	0.020349	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.24151	1.87	5.93	5.93	0.95920	.	0.120623	0.53938	D	0.000048	T	0.16557	0.0398	M	0.75447	2.3	0.80722	D	1	P	0.43826	0.818	B	0.36092	0.217	T	0.03773	-1.1005	10	0.30854	T	0.27	.	17.2605	0.87068	0.0:0.0:1.0:0.0	rs35788701	1213	Q9P225	DYH2_HUMAN	K	1213	ENSP00000373825:E1213K	ENSP00000353818:E1213K	E	+	1	0	DNAH2	7610486	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.495000	0.66912	2.815000	0.96918	0.561000	0.74099	GAG	G|0.986;A|0.014	0.014	strong		0.562	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
DHDDS	79947	hgsc.bcm.edu	37	1	26786627	26786627	+	Missense_Mutation	SNP	G	G	A	rs3816539	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26786627G>A	ENST00000236342.7	+	8	850	c.757G>A	c.(757-759)Gtg>Atg	p.V253M	DHDDS_ENST00000525682.2_Missense_Mutation_p.V219M|DHDDS_ENST00000526219.1_Missense_Mutation_p.V214M|RP3-476K8.3_ENST00000423060.1_RNA|DHDDS_ENST00000360009.2_Missense_Mutation_p.V253M			Q86SQ9	DHDDS_HUMAN	dehydrodolichyl diphosphate synthase	253			V -> M (in dbSNP:rs3816539). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20736409}.		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)	p.V253M(1)		breast(5)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	15		all_cancers(24;2.04e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)		GAACCATAGCGTGCTTCAGGT	0.493													G|||	2280	0.455272	0.4811	0.3069	5008	,	,		21309	0.7093		0.2346	False		,,,				2504	0.4908				p.V253M		Atlas-SNP	.											DHDDS,NS,carcinoma,0,2	DHDDS	33	2	1	Substitution - Missense(1)	stomach(1)	c.G757A						PASS	.	G	MET/VAL,MET/VAL	1958,2448	553.9+/-378.9	436,1086,681	105.0	98.0	101.0		757,757	-1.4	0.6	1	dbSNP_107	101	1781,6819	323.4+/-316.0	183,1415,2702	yes	missense,missense	DHDDS	NM_024887.3,NM_205861.2	21,21	619,2501,3383	AA,AG,GG		20.7093,44.4394,28.7483	benign,benign	253/335,253/334	26786627	3739,9267	2203	4300	6503	SO:0001583	missense	79947	exon8			CATAGCGTGCTTC	AK023164	CCDS281.1, CCDS282.1, CCDS57984.1, CCDS57983.1	1p35.3	2014-01-28			ENSG00000117682	ENSG00000117682			20603	protein-coding gene	gene with protein product		608172				12591616	Standard	NM_024887		Approved	HDS, FLJ13102, DS, RP59	uc001bmk.3	Q86SQ9	OTTHUMG00000003554	ENST00000236342.7:c.757G>A	1.37:g.26786627G>A	ENSP00000236342:p.Val253Met	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_024887	B7Z4B9|B7ZB20|D3DPK7|D3DPK8|D3DPK9|E9KL43|Q5T0A4|Q8NE90|Q9BTG5|Q9BTK3|Q9H905	Missense_Mutation	SNP	ENST00000236342.7	37	CCDS282.1	916|916	0.4194139194139194|0.4194139194139194	212|212	0.43089430894308944|0.43089430894308944	102|102	0.281767955801105|0.281767955801105	421|421	0.736013986013986|0.736013986013986	181|181	0.23878627968337732|0.23878627968337732	G|G	11.04|11.04	1.520802|1.520802	0.27211|0.27211	0.444394|0.444394	0.207093|0.207093	ENSG00000117682|ENSG00000117682	ENST00000416052|ENST00000374192;ENST00000525682;ENST00000236342;ENST00000526219;ENST00000360009;ENST00000430232	.|T;T;T;T;T	.|0.44083	.|0.93;0.93;0.93;0.93;0.94	5.27|5.27	-1.42|-1.42	0.08913|0.08913	.|.	.|0.633953	.|0.18368	.|N	.|0.143355	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B	.|0.09022	.|0.001;0.002;0.001;0.002	.|B;B;B;B	.|0.11329	.|0.006;0.001;0.006;0.005	T|T	0.37526|0.37526	-0.9702|-0.9702	4|9	.|0.54805	.|T	.|0.06	-12.7868|-12.7868	12.0925|12.0925	0.53736|0.53736	0.3764:0.0:0.6236:0.0|0.3764:0.0:0.6236:0.0	rs3816539;rs17849789;rs52803466;rs58359749;rs3816539|rs3816539;rs17849789;rs52803466;rs58359749;rs3816539	.|219;214;253;253	.|B7Z4B9;Q86SQ9-3;Q86SQ9;Q86SQ9-2	.|.;.;DHDDS_HUMAN;.	H|M	129|149;219;253;214;253;214	.|ENSP00000434984:V219M;ENSP00000236342:V253M;ENSP00000434219:V214M;ENSP00000353104:V253M;ENSP00000397584:V214M	.|ENSP00000236342:V253M	R|V	+|+	2|1	0|0	DHDDS|DHDDS	26659214|26659214	0.941000|0.941000	0.31946|0.31946	0.585000|0.585000	0.28666|0.28666	0.801000|0.801000	0.45260|0.45260	0.741000|0.741000	0.26202|0.26202	-0.176000|-0.176000	0.10707|0.10707	0.561000|0.561000	0.74099|0.74099	CGT|GTG	G|0.637;A|0.363	0.363	strong		0.493	DHDDS-011	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392504.1	NM_024887	
CACNA2D4	93589	hgsc.bcm.edu	37	12	1989018	1989018	+	Silent	SNP	T	T	C	rs60945277	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:1989018T>C	ENST00000382722.5	-	14	1877	c.1515A>G	c.(1513-1515)acA>acG	p.T505T	CACNA2D4_ENST00000586184.1_Silent_p.T505T|CACNA2D4_ENST00000587995.1_Silent_p.T505T|CACNA2D4_ENST00000588077.1_Silent_p.T441T|CACNA2D4_ENST00000585732.1_Silent_p.T390T|CACNA2D4_ENST00000585708.1_Silent_p.T441T	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	505	Cache.				calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.T505T(2)		endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		TGGTGAGCAGTGTCAGGCTCT	0.607													C|||	1158	0.23123	0.5688	0.0922	5008	,	,		20455	0.0427		0.1183	False		,,,				2504	0.184				p.T505T	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											CACNA2D4_ENST00000382722,NS,carcinoma,0,2	CACNA2D4	220	2	2	Substitution - coding silent(2)	prostate(2)	c.A1515G						PASS	.	C		1882,2220		422,1038,591	39.0	44.0	42.0		1515	0.1	0.0	12	dbSNP_129	42	900,7446		49,802,3322	no	coding-synonymous	CACNA2D4	NM_172364.4		471,1840,3913	CC,CT,TT		10.7836,45.8801,22.349		505/1138	1989018	2782,9666	2051	4173	6224	SO:0001819	synonymous_variant	93589	exon14			GAGCAGTGTCAGG	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.1515A>G	12.37:g.1989018T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Silent	SNP	ENST00000382722.5	37	CCDS44785.1																																																																																			T|0.817;C|0.183	0.183	strong		0.607	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
NPC1	4864	hgsc.bcm.edu	37	18	21140432	21140432	+	Missense_Mutation	SNP	T	T	C	rs1805081	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:21140432T>C	ENST00000269228.5	-	6	1198	c.644A>G	c.(643-645)cAt>cGt	p.H215R	NPC1_ENST00000412552.2_5'Flank|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	215			H -> R (common polymorphism in Japanese; dbSNP:rs1805081). {ECO:0000269|PubMed:10480349, ECO:0000269|PubMed:11479732, ECO:0000269|PubMed:11754101, ECO:0000269|PubMed:12401890, ECO:0000269|PubMed:12955717, ECO:0000269|PubMed:15774455, ECO:0000269|PubMed:16098014}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CTCCATCCCATGGACTGGAAA	0.423													T|||	1095	0.21865	0.0197	0.2637	5008	,	,		18777	0.256		0.3837	False		,,,				2504	0.2474				p.H215R		Atlas-SNP	.											.	NPC1	114	.	0			c.A644G						PASS	.	T	ARG/HIS	387,4019	193.3+/-218.5	18,351,1834	59.0	54.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	644	-1.1	0.0	18	dbSNP_89	55	3462,5138	507.9+/-376.9	694,2074,1532	yes	missense	NPC1	NM_000271.4	29	712,2425,3366	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	40.2558,8.7835,29.594	benign	215/1279	21140432	3849,9157	2203	4300	6503	SO:0001583	missense	4864	exon6			ATCCCATGGACTG	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.644A>G	18.37:g.21140432T>C	ENSP00000269228:p.His215Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	535	0.24496336996336995	16	0.032520325203252036	89	0.24585635359116023	130	0.22727272727272727	300	0.39577836411609496	T	9.736	1.163509	0.21538	0.087835	0.402558	ENSG00000141458	ENST00000269228;ENST00000540608	D	0.90069	-2.61	5.73	-1.13	0.09775	.	0.802760	0.12270	N	0.483913	T	0.00012	0.0000	N	0.21448	0.665	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16928	-1.0386	9	0.18276	T	0.48	-0.456	0.3945	0.00416	0.2773:0.1416:0.2309:0.3501	rs1805081;rs3745025;rs17878967;rs57242554;rs1805081	215	O15118	NPC1_HUMAN	R	215;60	ENSP00000269228:H215R	ENSP00000269228:H215R	H	-	2	0	NPC1	19394430	0.005000	0.15991	0.000000	0.03702	0.858000	0.48976	0.589000	0.23939	-0.172000	0.10779	0.533000	0.62120	CAT	T|0.733;C|0.267	0.267	strong		0.423	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
LMBR1L	55716	hgsc.bcm.edu	37	12	49495321	49495321	+	Silent	SNP	C	C	A	rs35541634	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:49495321C>A	ENST00000267102.8	-	12	1284	c.942G>T	c.(940-942)gtG>gtT	p.V314V	LMBR1L_ENST00000553204.1_5'Flank|LMBR1L_ENST00000547382.1_Silent_p.V314V|LMBR1L_ENST00000395141.4_Silent_p.V309V	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	314					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CCACAATGAGCACAGACAGGC	0.587													C|||	104	0.0207668	0.003	0.0476	5008	,	,		21686	0.0		0.0606	False		,,,				2504	0.0061				p.V314V		Atlas-SNP	.											.	LMBR1L	61	.	0			c.G942T						PASS	.	C		45,4361	46.0+/-80.4	0,45,2158	62.0	51.0	55.0		942	3.3	1.0	12	dbSNP_126	55	528,8072	146.8+/-202.3	13,502,3785	no	coding-synonymous	LMBR1L	NM_018113.2		13,547,5943	AA,AC,CC		6.1395,1.0213,4.4057		314/490	49495321	573,12433	2203	4300	6503	SO:0001819	synonymous_variant	55716	exon12			AATGAGCACAGAC	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"""limb region 1 homolog (mouse)-like"""			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.942G>T	12.37:g.49495321C>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	103	44	0.427184	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Silent	SNP	ENST00000267102.8	37	CCDS8780.2																																																																																			C|0.963;A|0.037	0.037	strong		0.587	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113	
IQCG	84223	hgsc.bcm.edu	37	3	197665599	197665599	+	Missense_Mutation	SNP	G	G	T	rs9880989	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:197665599G>T	ENST00000265239.6	-	5	759	c.335C>A	c.(334-336)gCc>gAc	p.A112D	IQCG_ENST00000480302.1_5'UTR|IQCG_ENST00000455191.1_Missense_Mutation_p.A112D|IQCG_ENST00000453254.1_Missense_Mutation_p.A112D	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	112			A -> D (in dbSNP:rs9880989). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		GATTGTTGAGGCCATTGGAAG	0.363													G|||	1411	0.281749	0.5197	0.1715	5008	,	,		19781	0.2302		0.166	False		,,,				2504	0.2106				p.A112D		Atlas-SNP	.											.	IQCG	44	.	0			c.C335A						PASS	.	G	ASP/ALA,ASP/ALA	1969,2437	556.0+/-379.4	417,1135,651	234.0	252.0	246.0		335,335	-6.9	0.0	3	dbSNP_119	246	1428,7172	275.3+/-291.7	117,1194,2989	yes	missense,missense	IQCG	NM_001134435.1,NM_032263.3	126,126	534,2329,3640	TT,TG,GG		16.6047,44.6891,26.1187	benign,benign	112/444,112/444	197665599	3397,9609	2203	4300	6503	SO:0001583	missense	84223	exon5			GTTGAGGCCATTG	AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 9"""	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.335C>A	3.37:g.197665599G>T	ENSP00000265239:p.Ala112Asp	Somatic	316	1	0.00316456		WXS	Illumina HiSeq	Phase_I	343	154	0.44898	NM_032263	Q9BST2|Q9HAG8	Missense_Mutation	SNP	ENST00000265239.6	37	CCDS3331.1	554	0.25366300366300365	255	0.5182926829268293	51	0.1408839779005525	121	0.21153846153846154	127	0.16754617414248021	G	7.330	0.618799	0.14129	0.446891	0.166047	ENSG00000114473	ENST00000265239;ENST00000455191;ENST00000453254;ENST00000416896	T;T;T;T	0.44083	0.93;0.93;1.0;0.95	5.14	-6.87	0.01671	.	3.994100	0.00465	N	0.000112	T	0.00012	0.0000	L	0.45581	1.43	0.80722	P	0.0	B;P	0.36959	0.302;0.575	B;B	0.29353	0.101;0.093	T	0.39375	-0.9617	9	0.12103	T	0.63	2.991	5.5736	0.17210	0.1712:0.133:0.5647:0.1311	rs9880989;rs52808997;rs60834300;rs9880989	112;112	C9JKX8;Q9H095	.;IQCG_HUMAN	D	112;112;112;93	ENSP00000265239:A112D;ENSP00000407736:A112D;ENSP00000389897:A112D;ENSP00000406411:A93D	ENSP00000265239:A112D	A	-	2	0	IQCG	199149996	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-1.100000	0.03339	-0.975000	0.03546	0.558000	0.71614	GCC	G|0.736;T|0.264	0.264	strong		0.363	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263	
PLK2	10769	hgsc.bcm.edu	37	5	57755703	57755703	+	Silent	SNP	C	C	T	rs3211270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:57755703C>T	ENST00000274289.3	-	1	384	c.84G>A	c.(82-84)gcG>gcA	p.A28A	PLK2_ENST00000502671.1_5'Flank	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	28				A -> G (in Ref. 1; AAC14573). {ECO:0000305}.	G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		TCTTCGAGTCCGCTCCGCAAC	0.682													C|||	1958	0.390974	0.2572	0.4467	5008	,	,		11602	0.5089		0.3479	False		,,,				2504	0.455				p.A28A		Atlas-SNP	.											.	PLK2	71	.	0			c.G84A						PASS	.	C		1198,3208		159,880,1164	15.0	18.0	17.0		84	2.3	1.0	5	dbSNP_105	17	2885,5701		506,1873,1914	no	coding-synonymous	PLK2	NM_006622.2		665,2753,3078	TT,TC,CC		33.6012,27.1902,31.427		28/686	57755703	4083,8909	2203	4293	6496	SO:0001819	synonymous_variant	10769	exon1			CGAGTCCGCTCCG		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"""serum-inducible kinase"""	607023	"""polo-like kinase 2 (Drosophila)"""				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.84G>A	5.37:g.57755703C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	37	CCDS3974.1																																																																																			C|0.661;T|0.339	0.339	strong		0.682	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622	
SLC29A4	222962	hgsc.bcm.edu	37	7	5327564	5327564	+	Silent	SNP	G	G	A	rs150225311	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:5327564G>A	ENST00000396872.3	+	2	278	c.117G>A	c.(115-117)gcG>gcA	p.A39A	SLC29A4_ENST00000406453.3_Silent_p.A39A|SLC29A4_ENST00000297195.4_Silent_p.A39A			Q7RTT9	S29A4_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 4	39					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			breast(1)|cervix(2)|kidney(7)|large_intestine(1)|liver(1)|lung(7)|urinary_tract(1)	20		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)	Metformin(DB00331)	CGGCGGAGGCGGCTCAGGGCC	0.667													G|||	396	0.0790735	0.1399	0.0115	5008	,	,		18166	0.1409		0.0189	False		,,,				2504	0.0429				p.A39A		Atlas-SNP	.											.	SLC29A4	52	.	0			c.G117A						PASS	.	G	,	516,3884		28,460,1712	21.0	23.0	22.0		117,117	-8.1	0.0	7	dbSNP_134	22	101,8489		1,99,4195	no	coding-synonymous,coding-synonymous	SLC29A4	NM_001040661.1,NM_153247.2	,	29,559,5907	AA,AG,GG		1.1758,11.7273,4.7498	,	39/531,39/531	5327564	617,12373	2200	4295	6495	SO:0001819	synonymous_variant	222962	exon2			GGAGGCGGCTCAG	AK075422	CCDS5340.1, CCDS75561.1	7p22.2	2013-07-17	2013-07-17		ENSG00000164638	ENSG00000164638		"""Solute carriers"""	23097	protein-coding gene	gene with protein product		609149	"""solute carrier family 29 (nucleoside transporters), member 4"""			12838422	Standard	NM_153247		Approved	FLJ34923, ENT4	uc003soc.3	Q7RTT9	OTTHUMG00000023797	ENST00000396872.3:c.117G>A	7.37:g.5327564G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	266	131	0.492481	NM_153247	Q6PJ08|Q86WY8|Q8NAR3|Q8NBM2	Silent	SNP	ENST00000396872.3	37	CCDS5340.1																																																																																			.	.	weak		0.667	SLC29A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060118.6	NM_153247	
THAP8	199745	hgsc.bcm.edu	37	19	36530332	36530332	+	Missense_Mutation	SNP	G	G	A	rs10420353	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:36530332G>A	ENST00000292894.1	-	3	1109	c.565C>T	c.(565-567)Cgg>Tgg	p.R189W	AC002116.7_ENST00000586962.1_RNA|THAP8_ENST00000538849.1_Missense_Mutation_p.R44W|THAP8_ENST00000524106.1_5'Flank	NM_152658.2	NP_689871.1	Q8NA92	THAP8_HUMAN	THAP domain containing 8	189			R -> W (in dbSNP:rs10420353). {ECO:0000269|PubMed:14702039}.				DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TCCTGGCACCGTTGCAGCCTC	0.701													g|||	1294	0.258387	0.2239	0.2233	5008	,	,		15161	0.3274		0.33	False		,,,				2504	0.1851				p.R189W		Atlas-SNP	.											.	THAP8	11	.	0			c.C565T						PASS	.	G	TRP/ARG	909,3421		107,695,1363	7.0	7.0	7.0		565	2.3	0.2	19	dbSNP_119	7	2503,5983		399,1705,2139	no	missense	THAP8	NM_152658.2	101	506,2400,3502	AA,AG,GG		29.4956,20.9931,26.623	benign	189/275	36530332	3412,9404	2165	4243	6408	SO:0001583	missense	199745	exon3			GGCACCGTTGCAG	AK057453	CCDS33000.1	19q13.13	2013-01-25			ENSG00000161277	ENSG00000161277		"""THAP (C2CH-type zinc finger) domain containing"""	23191	protein-coding gene	gene with protein product		612536				12575992	Standard	NM_152658		Approved	FLJ32891	uc002oda.1	Q8NA92	OTTHUMG00000048138	ENST00000292894.1:c.565C>T	19.37:g.36530332G>A	ENSP00000292894:p.Arg189Trp	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	20	15	0.75	NM_152658	Q0P5Z7|Q96M21	Missense_Mutation	SNP	ENST00000292894.1	37	CCDS33000.1	661	0.30265567765567764	122	0.24796747967479674	90	0.24861878453038674	194	0.33916083916083917	255	0.33641160949868076	g	12.94	2.089001	0.36855	0.209931	0.294956	ENSG00000161277	ENST00000292894;ENST00000392182;ENST00000538849	D;T	0.89552	-2.53;1.67	4.54	2.33	0.28932	.	0.571368	0.14254	U	0.331258	T	0.00012	0.0000	N	0.17082	0.46	0.36517	P	0.13008200000000003	B	0.15930	0.015	B	0.08055	0.003	T	0.04915	-1.0918	9	0.32370	T	0.25	-7.5514	5.2732	0.15636	0.1082:0.0:0.6808:0.211	rs10420353;rs10420353	189	Q8NA92	THAP8_HUMAN	W	189;189;44	ENSP00000292894:R189W;ENSP00000445493:R44W	ENSP00000292894:R189W	R	-	1	2	THAP8	41222172	0.988000	0.35896	0.189000	0.23252	0.003000	0.03518	1.634000	0.37123	0.423000	0.26033	0.552000	0.68991	CGG	G|0.699;A|0.301	0.301	strong		0.701	THAP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379036.1	NM_152658	
CADPS	8618	hgsc.bcm.edu	37	3	62543123	62543123	+	Silent	SNP	T	T	C	rs4396888	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:62543123T>C	ENST00000383710.4	-	10	2059	c.1710A>G	c.(1708-1710)ctA>ctG	p.L570L	CADPS_ENST00000357948.3_Silent_p.L570L|CADPS_ENST00000283269.9_Silent_p.L570L	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	570	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		CATCCAATTGTAGAAGTTCCT	0.522													T|||	165	0.0329473	0.0908	0.0202	5008	,	,		18360	0.0		0.0298	False		,,,				2504	0.001				p.L570L		Atlas-SNP	.											.	CADPS	387	.	0			c.A1710G						PASS	.	T	,,	431,3975	208.5+/-229.5	21,389,1793	219.0	207.0	211.0		1710,1710,1710	-12.3	0.0	3	dbSNP_111	211	300,8300	109.8+/-170.3	5,290,4005	no	coding-synonymous,coding-synonymous,coding-synonymous	CADPS	NM_003716.3,NM_183393.2,NM_183394.2	,,	26,679,5798	CC,CT,TT		3.4884,9.7821,5.6205	,,	570/1354,570/1275,570/1315	62543123	731,12275	2203	4300	6503	SO:0001819	synonymous_variant	8618	exon10			CAATTGTAGAAGT	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.1710A>G	3.37:g.62543123T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	37	CCDS46858.1																																																																																			T|0.951;C|0.049	0.049	strong		0.522	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
LDLRAP1	26119	hgsc.bcm.edu	37	1	25889632	25889632	+	Missense_Mutation	SNP	T	T	C	rs386629678|rs6687605	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:25889632T>C	ENST00000374338.4	+	6	723	c.604T>C	c.(604-606)Tcc>Ccc	p.S202P	LDLRAP1_ENST00000488127.1_3'UTR	NM_015627.2	NP_056442.2	Q5SW96	ARH_HUMAN	low density lipoprotein receptor adaptor protein 1	202			S -> H (in ARH; Lebanon; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:11326085}.|S -> P (in dbSNP:rs6687605). {ECO:0000269|PubMed:11326085, ECO:0000269|PubMed:12417523, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		amyloid precursor protein metabolic process (GO:0042982)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|positive regulation of cholesterol metabolic process (GO:0090205)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of signal transduction (GO:0009967)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein binding (GO:0043393)|transport (GO:0006810)	axon (GO:0030424)|basal plasma membrane (GO:0009925)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|neurofilament (GO:0005883)|recycling endosome (GO:0055037)	AP-2 adaptor complex binding (GO:0035612)|beta-amyloid binding (GO:0001540)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphotyrosine binding (GO:0001784)|receptor signaling complex scaffold activity (GO:0030159)|signaling adaptor activity (GO:0035591)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.63e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|GBM - Glioblastoma multiforme(114;0.00914)|READ - Rectum adenocarcinoma(331;0.0649)		CTGCACCCCCTCCTTGAAGAG	0.637													C|||	2178	0.434904	0.3207	0.5101	5008	,	,		14886	0.4425		0.5239	False		,,,				2504	0.4366				p.S202P		Atlas-SNP	.											.	LDLRAP1	28	.	0			c.T604C						PASS	.	C	PRO/SER	1519,2887		290,939,974	35.0	38.0	37.0		604	-2.4	0.0	1	dbSNP_116	37	4583,4013		1231,2121,946	yes	missense	LDLRAP1	NM_015627.2	74	1521,3060,1920	CC,CT,TT		46.6845,34.4757,46.9312	possibly-damaging	202/309	25889632	6102,6900	2203	4298	6501	SO:0001583	missense	26119	exon6			ACCCCCTCCTTGA	BC029770	CCDS30639.1	1p36-p35	2014-09-17			ENSG00000157978	ENSG00000157978			18640	protein-coding gene	gene with protein product		605747					Standard	NM_015627		Approved	ARH, ARH2, FHCB1, FHCB2, MGC34705, DKFZp586D0624	uc001bkl.4	Q5SW96	OTTHUMG00000007386	ENST00000374338.4:c.604T>C	1.37:g.25889632T>C	ENSP00000363458:p.Ser202Pro	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_015627	A2BHI5|Q6TQS9|Q8N2Y0|Q9UFI9	Missense_Mutation	SNP	ENST00000374338.4	37	CCDS30639.1	1002	0.45879120879120877	167	0.3394308943089431	175	0.48342541436464087	286	0.5	374	0.49340369393139843	C	11.22	1.573662	0.28092	0.344757	0.533155	ENSG00000157978	ENST00000374338	T	0.58060	0.36	5.51	-2.44	0.06502	.	0.673517	0.15647	N	0.251599	T	0.00012	0.0000	L	0.52759	1.655	0.80722	P	0.0	B;B	0.23058	0.079;0.079	B;B	0.23716	0.048;0.035	T	0.45205	-0.9277	9	0.28530	T	0.3	-0.4926	2.2127	0.03952	0.1027:0.1987:0.212:0.4866	rs6687605;rs28969503;rs41538216;rs60299789;rs6687605	202;202	B3KR97;Q5SW96	.;ARH_HUMAN	P	202	ENSP00000363458:S202P	ENSP00000363458:S202P	S	+	1	0	LDLRAP1	25762219	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.615000	0.05597	-0.325000	0.08577	-4.093000	0.00011	TCC	T|0.532;C|0.468	0.468	strong		0.637	LDLRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019350.3	NM_015627	
UBASH3A	53347	hgsc.bcm.edu	37	21	43824136	43824136	+	Missense_Mutation	SNP	C	C	T	rs2277800	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:43824136C>T	ENST00000319294.6	+	1	113	c.82C>T	c.(82-84)Ctc>Ttc	p.L28F	UBASH3A_ENST00000291535.6_Missense_Mutation_p.L28F|UBASH3A_ENST00000398367.1_Missense_Mutation_p.L28F|UBASH3A_ENST00000450356.1_Missense_Mutation_p.L28F	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	28	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.		L -> F (in dbSNP:rs2277800). {ECO:0000269|PubMed:15489334}.		negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						CCTGGAGCCCCTCCTGGCCAT	0.692													C|||	338	0.067492	0.0174	0.0159	5008	,	,		14657	0.1716		0.0537	False		,,,				2504	0.0787				p.L28F		Atlas-SNP	.											.	UBASH3A	72	.	0			c.C82T						PASS	.	C	PHE/LEU,PHE/LEU	95,4179		0,95,2042	19.0	17.0	18.0		82,82	4.4	1.0	21	dbSNP_100	18	335,7949		6,323,3813	yes	missense,missense	UBASH3A	NM_001001895.2,NM_018961.3	22,22	6,418,5855	TT,TC,CC		4.0439,2.2227,3.4241	probably-damaging,probably-damaging	28/624,28/662	43824136	430,12128	2137	4142	6279	SO:0001583	missense	53347	exon1			GAGCCCCTCCTGG	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.82C>T	21.37:g.43824136C>T	ENSP00000317327:p.Leu28Phe	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	127	64	0.503937	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Missense_Mutation	SNP	ENST00000319294.6	37	CCDS13687.1	136	0.06227106227106227	9	0.018292682926829267	7	0.019337016574585635	79	0.1381118881118881	41	0.05408970976253298	C	25.1	4.606385	0.87157	0.022227	0.040439	ENSG00000160185	ENST00000291535;ENST00000450356;ENST00000319294;ENST00000398367	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.32	4.43	0.53597	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (1);UBA-like (1);	0.000000	0.52532	D	0.000067	T	0.02380	0.0073	H	0.96111	3.77	0.22648	P	0.9988921	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.997	T	0.58929	-0.7549	9	0.66056	D	0.02	-33.4041	15.3365	0.74260	0.1411:0.8589:0.0:0.0	rs2277800;rs2277800	28;28;28	G5E9E4;P57075-2;P57075	.;.;UBS3A_HUMAN	F	28	ENSP00000291535:L28F;ENSP00000407179:L28F;ENSP00000317327:L28F;ENSP00000381408:L28F	ENSP00000291535:L28F	L	+	1	0	UBASH3A	42697205	1.000000	0.71417	0.990000	0.47175	0.960000	0.62799	5.443000	0.66581	1.222000	0.43521	0.416000	0.27883	CTC	C|0.948;T|0.052	0.052	strong		0.692	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
FDFT1	2222	hgsc.bcm.edu	37	8	11666337	11666337	+	Missense_Mutation	SNP	A	A	G	rs4731	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11666337A>G	ENST00000220584.4	+	2	356	c.134A>G	c.(133-135)aAg>aGg	p.K45R	FDFT1_ENST00000530664.1_5'UTR|FDFT1_ENST00000538689.1_5'UTR|FDFT1_ENST00000443614.2_Missense_Mutation_p.K45R|FDFT1_ENST00000525900.1_Missense_Mutation_p.K38R|FDFT1_ENST00000528812.1_5'UTR|FDFT1_ENST00000446331.2_Intron|FDFT1_ENST00000525777.1_5'Flank|FDFT1_ENST00000528643.1_5'Flank	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	45			K -> R (influences plasma cholesterol levels; associated with increased total cholesterol and non-high-density lipoprotein cholesterol; dbSNP:rs11549147). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18350552}.		cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		ACTTGCTACAAGTATCTCAAT	0.587													A|||	196	0.0391374	0.0144	0.0375	5008	,	,		17093	0.0089		0.0736	False		,,,				2504	0.0695				p.K45R		Atlas-SNP	.											.	FDFT1	25	.	0			c.A134G	GRCh37	CM081612	FDFT1	M	rs11549147	PASS	.	A	ARG/LYS	92,4314	76.2+/-114.5	0,92,2111	84.0	69.0	74.0		134	3.6	1.0	8	dbSNP_120	74	765,7835	180.9+/-229.7	31,703,3566	yes	missense	FDFT1	NM_004462.3	26	31,795,5677	GG,GA,AA		8.8953,2.0881,6.5893	benign	45/418	11666337	857,12149	2203	4300	6503	SO:0001583	missense	2222	exon2			GCTACAAGTATCT	X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"""squalene synthase"""	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.134A>G	8.37:g.11666337A>G	ENSP00000220584:p.Lys45Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Missense_Mutation	SNP	ENST00000220584.4	37	CCDS5985.1	80	0.03663003663003663	6	0.012195121951219513	13	0.03591160220994475	7	0.012237762237762238	54	0.0712401055408971	A	7.731	0.699268	0.15106	0.020881	0.088953	ENSG00000079459	ENST00000530337;ENST00000220584;ENST00000443614;ENST00000525900	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	4.73	3.56	0.40772	Terpenoid synthase (2);	0.596649	0.17759	N	0.162948	T	0.02888	0.0086	L	0.31664	0.95	0.80722	D	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.03259	-1.1055	10	0.13470	T	0.59	-13.7584	3.4786	0.07594	0.6128:0.2112:0.1761:0.0	rs61720710	45;102;38;45	B4DJE5;B4DND3;E9PNM1;P37268	.;.;.;FDFT_HUMAN	R	45;45;45;38	ENSP00000431852:K45R;ENSP00000220584:K45R;ENSP00000390367:K45R;ENSP00000434714:K38R	ENSP00000220584:K45R	K	+	2	0	FDFT1	11703746	0.411000	0.25384	1.000000	0.80357	0.367000	0.29736	0.578000	0.23773	0.825000	0.34637	-0.440000	0.05779	AAG	A|0.942;G|0.058;T|0.000	0.058	strong		0.587	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45993727	45993727	+	Missense_Mutation	SNP	A	A	C	rs148418343	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:45993727A>C	ENST00000400374.3	+	1	122	c.92A>C	c.(91-93)gAc>gCc	p.D31A	TSPEAR_ENST00000397916.1_5'Flank|TSPEAR_ENST00000323084.4_Intron	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	31						keratin filament (GO:0045095)		p.D31A(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CAGGTGGACGACTGCCCAGAG	0.687													.|||	308	0.0615016	0.0484	0.0288	5008	,	,		14764	0.1329		0.0249	False		,,,				2504	0.0665				p.D31A		Atlas-SNP	.											KRTAP10-4,NS,carcinoma,0,1	KRTAP10-4	44	1	1	Substitution - Missense(1)	pancreas(1)	c.A92C						PASS	.	A	,ALA/ASP	231,3929		1,229,1850	60.0	65.0	64.0		,92	3.5	1.0	21	dbSNP_134	64	165,8221		1,163,4029	no	intron,missense	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,126	2,392,5879	CC,CA,AA		1.9676,5.5529,3.1564	,probably-damaging	,31/402	45993727	396,12150	2080	4193	6273	SO:0001583	missense	386672	exon1			TGGACGACTGCCC	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.92A>C	21.37:g.45993727A>C	ENSP00000383225:p.Asp31Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	64	24	0.375	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	106	0.048534798534798536	13	0.026422764227642278	12	0.03314917127071823	70	0.12237762237762238	11	0.014511873350923483	N	13.44	2.238867	0.39598	0.055529	0.019676	ENSG00000215454	ENST00000400374;ENST00000334871	T	0.14893	2.47	4.69	3.52	0.40303	.	.	.	.	.	T	0.00440	0.0014	M	0.63843	1.955	0.40243	P	0.022011000000000003	D	0.67145	0.996	P	0.62740	0.906	T	0.04281	-1.0963	8	0.33141	T	0.24	.	7.9837	0.30198	0.8999:0.0:0.1001:0.0	.	31	P60372	KR104_HUMAN	A	31;20	ENSP00000383225:D31A	ENSP00000333987:D20A	D	+	2	0	KRTAP10-4	44818155	0.911000	0.30947	0.997000	0.53966	0.226000	0.24999	1.128000	0.31369	1.863000	0.54032	0.397000	0.26171	GAC	.	.	weak		0.687	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
SLC39A2	29986	hgsc.bcm.edu	37	14	21469151	21469151	+	Missense_Mutation	SNP	T	T	C	rs2234636	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21469151T>C	ENST00000298681.4	+	4	500	c.343T>C	c.(343-345)Ttt>Ctt	p.F115L	SLC39A2_ENST00000554422.1_3'UTR|RP11-84C10.4_ENST00000557335.1_RNA	NM_014579.3	NP_055394.2	Q9NP94	S39A2_HUMAN	solute carrier family 39 (zinc transporter), member 2	115			F -> L (in dbSNP:rs2234636). {ECO:0000269|PubMed:10681536, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7751801}.		transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	14	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0187)		GGGCTTCTTTTTTGTCTTCTT	0.502													T|||	1602	0.319888	0.1536	0.487	5008	,	,		19450	0.373		0.333	False		,,,				2504	0.3579				p.F115L		Atlas-SNP	.											.	SLC39A2	31	.	0			c.T343C						PASS	.	T	LEU/PHE	810,3596	322.9+/-297.8	67,676,1460	235.0	248.0	243.0		343	-10.9	0.0	14	dbSNP_98	243	3024,5576	465.4+/-366.5	534,1956,1810	yes	missense	SLC39A2	NM_014579.3	22	601,2632,3270	CC,CT,TT		35.1628,18.384,29.4787	benign	115/310	21469151	3834,9172	2203	4300	6503	SO:0001583	missense	29986	exon4			TTCTTTTTTGTCT	AF186081	CCDS9563.1, CCDS58303.1	14q11.1	2013-05-22			ENSG00000165794	ENSG00000165794		"""Solute carriers"""	17127	protein-coding gene	gene with protein product		612166				10681536, 7751801	Standard	NM_014579		Approved	ZIP2	uc001vyr.3	Q9NP94	OTTHUMG00000029616	ENST00000298681.4:c.343T>C	14.37:g.21469151T>C	ENSP00000298681:p.Phe115Leu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_014579	B2RC76|G3V5X2|Q4QQJ1|Q4V9S4|Q96JT6|Q9UD20	Missense_Mutation	SNP	ENST00000298681.4	37	CCDS9563.1	691	0.3163919413919414	64	0.13008130081300814	162	0.44751381215469616	215	0.3758741258741259	250	0.32981530343007914	T	0.533	-0.856861	0.02630	0.18384	0.351628	ENSG00000165794	ENST00000298681	T	0.42513	0.97	5.7	-10.9	0.00192	.	1.098420	0.06882	N	0.802747	T	0.00012	0.0000	N	0.01242	-0.935	0.53005	P	3.399999999997849E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.38045	-0.9679	9	0.02654	T	1	3.531	15.4912	0.75607	0.0:0.632:0.0969:0.2711	rs2234636;rs52810004;rs56686855;rs2234636	115	Q9NP94	S39A2_HUMAN	L	115	ENSP00000298681:F115L	ENSP00000298681:F115L	F	+	1	0	SLC39A2	20538991	0.000000	0.05858	0.001000	0.08648	0.412000	0.31113	-1.414000	0.02471	-2.518000	0.00499	-0.313000	0.08912	TTT	T|0.702;C|0.298	0.298	strong		0.502	SLC39A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073829.2	NM_014579	
CEP89	84902	hgsc.bcm.edu	37	19	33370084	33370084	+	Missense_Mutation	SNP	T	T	A	rs745960	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:33370084T>A	ENST00000305768.5	-	19	2424	c.2336A>T	c.(2335-2337)cAt>cTt	p.H779L	CTD-2085J24.4_ENST00000586628.2_lincRNA	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	779					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						GGTGGGGGCATGAGACTTCAG	0.627													A|||	822	0.164137	0.0703	0.1527	5008	,	,		13330	0.1062		0.334	False		,,,				2504	0.184				p.H779L		Atlas-SNP	.											.	CEP89	82	.	0			c.A2336T						PASS	.	A	LEU/HIS	481,3925	781.6+/-414.5	25,431,1747	72.0	68.0	69.0		2336	-4.7	0.0	19	dbSNP_86	69	3052,5548	661.2+/-401.9	565,1922,1813	yes	missense	CEP89	NM_032816.3	99	590,2353,3560	AA,AT,TT		35.4884,10.9169,27.1644	benign	779/784	33370084	3533,9473	2203	4300	6503	SO:0001583	missense	84902	exon19			GGGGCATGAGACT	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.2336A>T	19.37:g.33370084T>A	ENSP00000306105:p.His779Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	401	0.18360805860805862	31	0.06300813008130081	66	0.18232044198895028	53	0.09265734265734266	251	0.3311345646437995	A	2.187	-0.386125	0.04966	0.109169	0.354884	ENSG00000121289	ENST00000305768	T	0.28666	1.6	4.99	-4.69	0.03299	.	0.823573	0.10428	N	0.675857	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38265	-0.9669	9	0.09843	T	0.71	0.1234	4.7686	0.13144	0.3961:0.0:0.3827:0.2212	rs745960;rs17272260;rs52830747;rs745960	779	Q96ST8	CEP89_HUMAN	L	779	ENSP00000306105:H779L	ENSP00000306105:H779L	H	-	2	0	CEP89	38061924	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.212000	0.17497	-1.325000	0.02269	-2.831000	0.00106	CAT	T|0.761;A|0.239	0.239	strong		0.627	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
GAL3ST3	89792	hgsc.bcm.edu	37	11	65810612	65810612	+	Missense_Mutation	SNP	G	G	T	rs35285455	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65810612G>T	ENST00000312006.4	-	3	943	c.662C>A	c.(661-663)gCc>gAc	p.A221D	GAL3ST3_ENST00000527878.1_Missense_Mutation_p.A221D	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	221			A -> D (in dbSNP:rs35285455).		monosaccharide metabolic process (GO:0005996)|oligosaccharide metabolic process (GO:0009311)|poly-N-acetyllactosamine metabolic process (GO:0030309)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|carbohydrate binding (GO:0030246)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			kidney(1)|lung(9)|ovary(2)|skin(2)	14						CAGGTAGGCGGCGTCGTCGCG	0.657													G|||	66	0.0131789	0.0242	0.0101	5008	,	,		9967	0.0		0.0189	False		,,,				2504	0.0082				p.A221D		Atlas-SNP	.											GAL3ST3,rectum,carcinoma,0,3	GAL3ST3	40	3	0			c.C662A						PASS	.	G	ASP/ALA	81,4313		1,79,2117	31.0	37.0	35.0		662	2.6	1.0	11	dbSNP_126	35	157,8411		1,155,4128	yes	missense	GAL3ST3	NM_033036.2	126	2,234,6245	TT,TG,GG		1.8324,1.8434,1.8361	benign	221/432	65810612	238,12724	2197	4284	6481	SO:0001583	missense	89792	exon3			TAGGCGGCGTCGT	AY026481	CCDS8128.1	11q13.1	2014-08-12			ENSG00000175229	ENSG00000175229		"""Sulfotransferases, membrane-bound"""	24144	protein-coding gene	gene with protein product		608234				11323440, 11356829	Standard	NM_033036		Approved	GAL3ST2	uc001ogw.3	Q96A11	OTTHUMG00000166667	ENST00000312006.4:c.662C>A	11.37:g.65810612G>T	ENSP00000308591:p.Ala221Asp	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	50	38	0.76	NM_033036	Q14D05	Missense_Mutation	SNP	ENST00000312006.4	37	CCDS8128.1	21	0.009615384615384616	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	G	7.938	0.742112	0.15642	0.018434	0.018324	ENSG00000175229	ENST00000312006;ENST00000527878	T;T	0.14391	2.51;2.51	4.51	2.57	0.30868	.	0.445001	0.22406	N	0.060466	T	0.02012	0.0063	N	0.02158	-0.66	0.32668	N	0.517241	B	0.02656	0.0	B	0.01281	0.0	T	0.32375	-0.9909	10	0.14656	T	0.56	-4.5024	9.826	0.40912	0.0:0.0:0.6262:0.3738	rs35285455	221	Q96A11	G3ST3_HUMAN	D	221	ENSP00000308591:A221D;ENSP00000434829:A221D	ENSP00000308591:A221D	A	-	2	0	GAL3ST3	65567188	0.040000	0.19996	0.968000	0.41197	0.996000	0.88848	0.659000	0.24994	0.417000	0.25871	0.561000	0.74099	GCC	G|0.983;T|0.017	0.017	strong		0.657	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391052.1	NM_033036	
PRPF8	10594	hgsc.bcm.edu	37	17	1585130	1585130	+	Silent	SNP	A	A	G	rs11559305	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1585130A>G	ENST00000572621.1	-	4	902	c.637T>C	c.(637-639)Ttg>Ctg	p.L213L	PRPF8_ENST00000304992.6_Silent_p.L213L			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	213					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CTGTCCCTCAACGGCTGGTGG	0.537													A|||	1254	0.250399	0.6029	0.1254	5008	,	,		19508	0.0893		0.1501	False		,,,				2504	0.1319				p.L213L		Atlas-SNP	.											.	PRPF8	169	.	0			c.T637C						PASS	.	A		2264,2142	593.4+/-388.0	584,1096,523	92.0	99.0	97.0		637	0.5	1.0	17	dbSNP_120	97	1504,7096	280.2+/-294.4	126,1252,2922	no	coding-synonymous	PRPF8	NM_006445.3		710,2348,3445	GG,GA,AA		17.4884,48.6155,28.9712		213/2336	1585130	3768,9238	2203	4300	6503	SO:0001819	synonymous_variant	10594	exon5			CCCTCAACGGCTG	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.637T>C	17.37:g.1585130A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	118	68	0.576271	NM_006445	O14547|O75965	Silent	SNP	ENST00000572621.1	37	CCDS11010.1																																																																																			G|0.263;N|0.000	0.263	strong		0.537	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
USP51	158880	hgsc.bcm.edu	37	X	55514818	55514818	+	Silent	SNP	C	C	T	rs3126255	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:55514818C>T	ENST00000500968.3	-	2	637	c.555G>A	c.(553-555)gaG>gaA	p.E185E	USP51_ENST00000586165.1_Intron	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	185					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						CAAACTCGACCTCCAGCAACC	0.587													.|||	1754	0.464636	0.0507	0.3501	3775	,	,		7246	0.4712		0.5149	False		,,,				2504	0.4611				p.E185E		Atlas-SNP	.											.	USP51	71	.	0			c.G555A						PASS	.	C		500,3335		30,369,71,1233,500	35.0	30.0	32.0		555	2.9	1.0	X	dbSNP_103	32	4634,2094		1149,1055,1281,224,591	no	coding-synonymous	USP51	NM_201286.3		1179,1424,1352,1457,1091	TT,TC,T,CC,C		31.1237,13.0378,48.6036		185/712	55514818	5134,5429	2203	4300	6503	SO:0001819	synonymous_variant	158880	exon2			CTCGACCTCCAGC	BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"""Ubiquitin-specific peptidases"""	23086	protein-coding gene	gene with protein product			"""ubiquitin specific protease 51"""			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.555G>A	X.37:g.55514818C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	114	106	0.929825	NM_201286	Q8IWJ8	Silent	SNP	ENST00000500968.3	37	CCDS14370.1																																																																																			C|0.528;T|0.472	0.472	strong		0.587	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286	
EML2	24139	hgsc.bcm.edu	37	19	46133256	46133256	+	Missense_Mutation	SNP	G	G	A	rs7252175	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:46133256G>A	ENST00000245925.3	-	7	609	c.559C>T	c.(559-561)Ctc>Ttc	p.L187F	EML2_ENST00000589876.1_Missense_Mutation_p.L187F|EML2_ENST00000586902.1_5'UTR|EML2_ENST00000587152.1_Missense_Mutation_p.L388F|EML2_ENST00000536630.1_Missense_Mutation_p.L334F	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	187	Tandem atypical propeller in EMLs. {ECO:0000250}.		L -> F (in dbSNP:rs7252175).		negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CACACCGAGAGCATGTGATCA	0.572													G|||	647	0.129193	0.1626	0.1297	5008	,	,		16961	0.1032		0.1083	False		,,,				2504	0.1319				p.L388F		Atlas-SNP	.											EML2,colon,carcinoma,+2,1	EML2	64	1	0			c.C1162T						PASS	.		PHE/LEU,PHE/LEU,PHE/LEU	674,3732	284.6+/-277.7	64,546,1593	195.0	125.0	149.0		1162,1000,559	4.7	1.0	19	dbSNP_116	149	1141,7459	234.0+/-267.1	81,979,3240	yes	missense,missense,missense	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	22,22,22	145,1525,4833	AA,AG,GG		13.2674,15.2973,13.9551	probably-damaging,probably-damaging,probably-damaging	388/851,334/797,187/650	46133256	1815,11191	2203	4300	6503	SO:0001583	missense	24139	exon10			CCGAGAGCATGTG	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.559C>T	19.37:g.46133256G>A	ENSP00000245925:p.Leu187Phe	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	273	0.125	94	0.1910569105691057	48	0.13259668508287292	53	0.09265734265734266	78	0.10290237467018469	G	17.13	3.311155	0.60414	0.152973	0.132674	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055;ENST00000399594	T;T;T	0.50277	0.75;0.75;4.77	4.74	4.74	0.60224	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.00328	0.0010	M	0.93197	3.39	0.09310	P	0.99999586405	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.997;0.999;0.999	T	0.25813	-1.0121	9	0.87932	D	0	-21.5047	15.2691	0.73686	0.0:0.0:1.0:0.0	rs7252175;rs59814666;rs7252175	187;353;334;345;187	B7Z918;B7Z3Q9;B7Z3I2;B7Z872;O95834	.;.;.;.;EMAL2_HUMAN	F	334;187;388;345	ENSP00000442365:L334F;ENSP00000245925:L187F;ENSP00000382503:L345F	ENSP00000245925:L187F	L	-	1	0	EML2	50825096	1.000000	0.71417	0.983000	0.44433	0.792000	0.44763	4.183000	0.58317	2.491000	0.84063	0.305000	0.20034	CTC	G|0.857;A|0.143	0.143	strong		0.572	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
NOP56	10528	hgsc.bcm.edu	37	20	2638882	2638882	+	Missense_Mutation	SNP	T	T	C	rs5856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2638882T>C	ENST00000329276.5	+	12	2243	c.1727T>C	c.(1726-1728)gTt>gCt	p.V576A	SNORD57_ENST00000448188.1_RNA|SNORD56_ENST00000413522.1_RNA|IDH3B_ENST00000488299.1_5'Flank|SNORD86_ENST00000391196.1_RNA|NOP56_ENST00000492135.1_3'UTR	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	576	Lys-rich.		V -> A (in dbSNP:rs5856).		cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						GAAGAGGCGGTTGGCAAGAGC	0.502													C|||	1890	0.377396	0.6188	0.379	5008	,	,		17055	0.255		0.2664	False		,,,				2504	0.2904				p.V576A		Atlas-SNP	.											.	NOP56	73	.	0			c.T1727C						PASS	.	C	ALA/VAL	2180,2120		590,1000,560	8.0	11.0	10.0		1727	1.2	0.0	20	dbSNP_52	10	2163,6351		332,1499,2426	no	missense	NOP56	NM_006392.3	64	922,2499,2986	CC,CT,TT		25.4052,49.3023,33.8926	benign	576/595	2638882	4343,8471	2150	4257	6407	SO:0001583	missense	10528	exon12			AGGCGGTTGGCAA	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.1727T>C	20.37:g.2638882T>C	ENSP00000370589:p.Val576Ala	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	95	54	0.568421	NM_006392	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	775	0.35485347985347987	323	0.6565040650406504	127	0.35082872928176795	132	0.23076923076923078	193	0.2546174142480211	C	0.004	-2.265039	0.00259	0.506977	0.254052	ENSG00000101361	ENST00000329276	T	0.56444	0.46	5.27	1.17	0.20885	.	0.164771	0.36268	N	0.002692	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45818	-0.9235	9	0.02654	T	1	-0.1242	8.327	0.32162	0.0:0.5943:0.0:0.4057	rs5856;rs6754;rs3174890;rs59007437	576	O00567	NOP56_HUMAN	A	576	ENSP00000370589:V576A	ENSP00000370589:V576A	V	+	2	0	NOP56	2586882	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.686000	0.05161	-0.128000	0.11641	-1.026000	0.02426	GTT	T|0.673;C|0.327	0.327	strong		0.502	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
UPK2	7379	hgsc.bcm.edu	37	11	118828942	118828942	+	Silent	SNP	A	A	G	rs623500	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:118828942A>G	ENST00000264031.2	+	5	589	c.554A>G	c.(553-555)tAa>tGa	p.*185*	UPK2_ENST00000534788.1_3'UTR	NM_006760.3	NP_006751.1	O00526	UPK2_HUMAN	uroplakin 2	0					epithelial cell differentiation (GO:0030855)|membrane organization (GO:0061024)|multicellular organismal development (GO:0007275)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)				kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.122)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.47e-05)		TCCCGCAAGTAAGGAGGTCTG	0.662													g|||	1206	0.240815	0.3782	0.1383	5008	,	,		15760	0.0952		0.172	False		,,,				2504	0.3487				p.X185X		Atlas-SNP	.											.	UPK2	12	.	0			c.A554G						PASS	.			1650,2750	500.3+/-364.7	319,1012,869	75.0	60.0	65.0		554	4.5	1.0	11	dbSNP_83	65	1398,7192	270.5+/-289.0	121,1156,3018	no	coding-synonymous	UPK2	NM_006760.3		440,2168,3887	GG,GA,AA		16.2747,37.5,23.4642		185/185	118828942	3048,9942	2200	4295	6495	SO:0001819	synonymous_variant	7379	exon5			GCAAGTAAGGAGG	Y13645	CCDS8404.1	11q23	2008-07-21				ENSG00000110375			12579	protein-coding gene	gene with protein product	"""uroplakin II"", ""uroplakin-2"""	611558				9515818, 9846985	Standard	NM_006760		Approved	UP2, UPII, MGC138598	uc001puh.3	O00526		ENST00000264031.2:c.554A>G	11.37:g.118828942A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_006760	B0YJ92|O00457|Q53YV0	Silent	SNP	ENST00000264031.2	37	CCDS8404.1																																																																																			A|0.788;G|0.212	0.212	strong		0.662	UPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389311.1	NM_006760	
HLTF	6596	hgsc.bcm.edu	37	3	148757864	148757864	+	Missense_Mutation	SNP	C	C	T	rs2229361	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:148757864C>T	ENST00000310053.5	-	21	2649	c.2456G>A	c.(2455-2457)cGt>cAt	p.R819H	HLTF_ENST00000392912.2_Missense_Mutation_p.R819H|HLTF_ENST00000494055.1_Missense_Mutation_p.R819H|HLTF_ENST00000465259.1_Missense_Mutation_p.R818H	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	819			R -> H (in dbSNP:rs2229361).		chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CTCACTGTCACGTGCTAATTC	0.328													C|||	100	0.0199681	0.0008	0.0231	5008	,	,		18149	0.001		0.0278	False		,,,				2504	0.0552				p.R819H		Atlas-SNP	.											.	HLTF	87	.	0			c.G2456A						PASS	.	C	HIS/ARG,HIS/ARG	37,4369	42.3+/-75.8	0,37,2166	136.0	125.0	129.0		2456,2456	1.5	0.0	3	dbSNP_98	129	316,8280	111.6+/-171.8	5,306,3987	yes	missense,missense	HLTF	NM_003071.3,NM_139048.2	29,29	5,343,6153	TT,TC,CC		3.6761,0.8398,2.715	benign,benign	819/1010,819/1010	148757864	353,12649	2203	4298	6501	SO:0001583	missense	6596	exon21			CTGTCACGTGCTA	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"""RING-type (C3HC4) zinc fingers"""	11099	protein-coding gene	gene with protein product		603257	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"""	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.2456G>A	3.37:g.148757864C>T	ENSP00000308944:p.Arg819His	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Missense_Mutation	SNP	ENST00000310053.5	37	CCDS33875.1	35	0.016025641025641024	0	0.0	12	0.03314917127071823	1	0.0017482517482517483	22	0.029023746701846966	C	5.332	0.246511	0.10130	0.008398	0.036761	ENSG00000071794	ENST00000465259;ENST00000310053;ENST00000392912;ENST00000494055;ENST00000467858	D;D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61;-2.36	5.5	1.5	0.22942	.	.	.	.	.	T	0.48223	0.1488	N	0.14661	0.345	0.09310	N	1	B;B	0.30281	0.275;0.275	B;B	0.27170	0.077;0.077	T	0.52852	-0.8520	9	0.28530	T	0.3	0.0404	8.9838	0.35980	0.0:0.4205:0.4351:0.1444	rs2229361;rs17729088;rs52835148;rs2229361	819;819	Q59GQ7;Q14527	.;HLTF_HUMAN	H	818;819;819;819;287	ENSP00000420745:R818H;ENSP00000308944:R819H;ENSP00000376644:R819H;ENSP00000420429:R819H;ENSP00000420106:R287H	ENSP00000308944:R819H	R	-	2	0	HLTF	150240554	0.004000	0.15560	0.004000	0.12327	0.077000	0.17291	0.927000	0.28818	0.296000	0.22592	-0.806000	0.03193	CGT	C|0.976;T|0.024	0.024	strong		0.328	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
TNS1	7145	hgsc.bcm.edu	37	2	218674697	218674697	+	Missense_Mutation	SNP	C	C	T	rs918949	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:218674697C>T	ENST00000171887.4	-	30	5262	c.4810G>A	c.(4810-4812)Gtc>Atc	p.V1604I	TNS1_ENST00000430930.1_Missense_Mutation_p.V1583I|TNS1_ENST00000419504.1_Missense_Mutation_p.V1590I	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1604			V -> I (in dbSNP:rs918949). {ECO:0000269|PubMed:11023826}.		cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		ACAGAGTTGACGAAGAGCACA	0.567													.|||	3056	0.610224	0.8071	0.5922	5008	,	,		20607	0.505		0.5865	False		,,,				2504	0.4898				p.V1604I		Atlas-SNP	.											.	TNS1	251	.	0			c.G4810A						PASS	.		ILE/VAL	3386,1020	727.3+/-409.8	1299,788,116	66.0	65.0	65.0		4810	-4.7	0.4	2	dbSNP_86	65	5251,3349	643.9+/-400.0	1619,2013,668	yes	missense	TNS1	NM_022648.4	29	2918,2801,784	TT,TC,CC		38.9419,23.1502,33.5922	benign	1604/1736	218674697	8637,4369	2203	4300	6503	SO:0001583	missense	7145	exon30			AGTTGACGAAGAG	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4810G>A	2.37:g.218674697C>T	ENSP00000171887:p.Val1604Ile	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	1356	0.6208791208791209	391	0.7947154471544715	225	0.6215469613259669	285	0.4982517482517482	455	0.600263852242744	c	0.884	-0.727836	0.03158	0.768498	0.610581	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	4.44	-4.71	0.03279	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);Tensin phosphotyrosine-binding domain (1);	0.375075	0.25628	N	0.029377	T	0.00012	0.0000	N	0.00298	-1.69	0.09310	P	0.9999999999998628	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.003;0.002	T	0.44205	-0.9343	9	0.12430	T	0.62	.	15.3963	0.74798	0.0:0.2186:0.0:0.7814	rs918949;rs3853996;rs52826748;rs60183014;rs918949	1604;1583;1590	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	I	1604;742;1590;1583	ENSP00000171887:V1604I;ENSP00000394171:V742I;ENSP00000408724:V1590I;ENSP00000406016:V1583I	ENSP00000171887:V1604I	V	-	1	0	TNS1	218382942	1.000000	0.71417	0.368000	0.25939	0.728000	0.41692	0.655000	0.24933	-1.539000	0.01732	-0.401000	0.06369	GTC	C|0.354;T|0.646	0.646	strong		0.567	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
TRAPPC11	60684	hgsc.bcm.edu	37	4	184600571	184600571	+	Silent	SNP	C	C	A	rs62357990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:184600571C>A	ENST00000334690.6	+	9	1099	c.897C>A	c.(895-897)atC>atA	p.I299I	TRAPPC11_ENST00000357207.4_Silent_p.I299I	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	299					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											GAAAACACATCGACTTGTGTA	0.363													C|||	310	0.061901	0.056	0.0389	5008	,	,		17834	0.1319		0.0537	False		,,,				2504	0.0225				p.I299I		Atlas-SNP	.											.	.	.	.	0			c.C897A						PASS	.	C	,	232,4174	138.8+/-174.5	8,216,1979	92.0	93.0	93.0		897,897	-9.0	0.1	4	dbSNP_129	93	573,8027	154.2+/-208.4	22,529,3749	no	coding-synonymous,coding-synonymous	C4orf41	NM_021942.4,NM_199053.1	,	30,745,5728	AA,AC,CC		6.6628,5.2655,6.1895	,	299/1134,299/1087	184600571	805,12201	2203	4300	6503	SO:0001819	synonymous_variant	60684	exon9			ACACATCGACTTG		CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"""Trafficking protein particle complex"""	25751	protein-coding gene	gene with protein product	"""gryzun homolog (Drosophila)"", ""foie gras homolog (zebrafish)"""	614138	"""chromosome 4 open reading frame 41"""	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.897C>A	4.37:g.184600571C>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	87	30	0.344828	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Silent	SNP	ENST00000334690.6	37	CCDS34112.1																																																																																			C|0.939;A|0.061	0.061	strong		0.363	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942	
CDH3	1001	hgsc.bcm.edu	37	16	68719113	68719113	+	Missense_Mutation	SNP	G	G	A	rs34494880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:68719113G>A	ENST00000264012.4	+	11	1974	c.1430G>A	c.(1429-1431)cGc>cAc	p.R477H	CDH3_ENST00000429102.2_Missense_Mutation_p.R477H|CDH3_ENST00000581171.1_Missense_Mutation_p.R422H	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	477	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> H (in dbSNP:rs34494880).		adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		TCCAGCTACCGCATCCTGAGA	0.542													G|||	130	0.0259585	0.0023	0.0173	5008	,	,		20212	0.0		0.0596	False		,,,				2504	0.0562				p.R477H		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.G1430A						PASS	.	G	HIS/ARG	65,4331	61.1+/-98.1	0,65,2133	80.0	70.0	73.0		1430	0.6	1.0	16	dbSNP_126	73	645,7955	166.1+/-218.1	26,593,3681	yes	missense	CDH3	NM_001793.4	29	26,658,5814	AA,AG,GG		7.5,1.4786,5.4632	benign	477/830	68719113	710,12286	2198	4300	6498	SO:0001583	missense	1001	exon11			GCTACCGCATCCT	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.1430G>A	16.37:g.68719113G>A	ENSP00000264012:p.Arg477His	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_001793	B2R6F4|Q05DI6	Missense_Mutation	SNP	ENST00000264012.4	37	CCDS10868.1	63	0.028846153846153848	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	55	0.07255936675461741	G	11.26	1.584836	0.28268	0.014786	0.075	ENSG00000062038	ENST00000429102;ENST00000264012;ENST00000542274	T;T	0.53640	0.61;0.61	5.58	0.567	0.17325	Cadherin (4);Cadherin-like (1);	0.911629	0.09141	N	0.842988	T	0.02193	0.0068	L	0.28014	0.82	0.24544	N	0.994051	B	0.13145	0.007	B	0.12837	0.008	T	0.13548	-1.0505	10	0.35671	T	0.21	.	0.9118	0.01296	0.4382:0.1566:0.2544:0.1508	rs34494880	477	P22223	CADH3_HUMAN	H	477;477;422	ENSP00000398485:R477H;ENSP00000264012:R477H	ENSP00000264012:R477H	R	+	2	0	CDH3	67276614	0.000000	0.05858	0.999000	0.59377	0.725000	0.41563	-0.843000	0.04350	0.072000	0.16694	-0.672000	0.03802	CGC	G|0.953;A|0.047	0.047	strong		0.542	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
ZBTB4	57659	hgsc.bcm.edu	37	17	7366619	7366619	+	Missense_Mutation	SNP	T	T	C	rs34914463	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7366619T>C	ENST00000311403.4	-	4	2021	c.1682A>G	c.(1681-1683)aAt>aGt	p.N561S	ZBTB4_ENST00000380599.4_Missense_Mutation_p.N561S	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	561			N -> S (in dbSNP:rs34914463).		cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		AGCCCGTGGATTCCGGCCCTT	0.701													T|||	140	0.0279553	0.0038	0.0418	5008	,	,		13314	0.0		0.0994	False		,,,				2504	0.0061				p.N561S		Atlas-SNP	.											.	ZBTB4	163	.	0			c.A1682G						PASS	.	T	SER/ASN,SER/ASN	118,4284		3,112,2086	16.0	18.0	18.0		1682,1682	3.9	1.0	17	dbSNP_126	18	1028,7564		77,874,3345	yes	missense,missense	ZBTB4	NM_001128833.1,NM_020899.3	46,46	80,986,5431	CC,CT,TT		11.9646,2.6806,8.8195	possibly-damaging,possibly-damaging	561/1014,561/1014	7366619	1146,11848	2201	4296	6497	SO:0001583	missense	57659	exon4			CGTGGATTCCGGC	AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.1682A>G	17.37:g.7366619T>C	ENSP00000307858:p.Asn561Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Missense_Mutation	SNP	ENST00000311403.4	37	CCDS11107.1	96	0.04395604395604396	5	0.01016260162601626	13	0.03591160220994475	0	0.0	78	0.10290237467018469	T	14.22	2.471484	0.43942	0.026806	0.119646	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.03580	3.88;3.88	4.97	3.86	0.44501	.	0.262110	0.31531	N	0.007500	T	0.00039	0.0001	N	0.19112	0.55	0.26391	N	0.976573	P	0.34977	0.478	B	0.31442	0.13	T	0.45934	-0.9227	10	0.07813	T	0.8	-7.9164	8.5092	0.33206	0.0:0.0:0.1964:0.8036	rs34914463	561	Q9P1Z0	ZBTB4_HUMAN	S	561	ENSP00000307858:N561S;ENSP00000369973:N561S	ENSP00000307858:N561S	N	-	2	0	ZBTB4	7307343	0.033000	0.19621	0.998000	0.56505	0.990000	0.78478	0.346000	0.19997	0.885000	0.36088	0.379000	0.24179	AAT	T|0.942;C|0.058	0.058	strong		0.701	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899	
JADE2	23338	hgsc.bcm.edu	37	5	133887780	133887780	+	Silent	SNP	G	G	A	rs12163993	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:133887780G>A	ENST00000402835.1	+	4	447	c.192G>A	c.(190-192)ccG>ccA	p.P64P	PHF15_ENST00000361895.2_Silent_p.P64P|PHF15_ENST00000395003.1_Silent_p.P64P|PHF15_ENST00000282605.4_Silent_p.P64P																NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGAAGATCCCGGACTCATACC	0.592													G|||	791	0.157947	0.0454	0.2147	5008	,	,		19516	0.2113		0.1571	False		,,,				2504	0.2157				p.P64P		Atlas-SNP	.											.	PHF15	60	.	0			c.G192A						PASS	.	G		231,4175	139.2+/-174.8	8,215,1980	96.0	92.0	93.0		192	-3.9	1.0	5	dbSNP_120	93	1226,7374	248.2+/-276.0	95,1036,3169	no	coding-synonymous	PHF15	NM_015288.4		103,1251,5149	AA,AG,GG		14.2558,5.2429,11.2025		64/791	133887780	1457,11549	2203	4300	6503	SO:0001819	synonymous_variant	23338	exon4			GATCCCGGACTCA																												ENST00000402835.1:c.192G>A	5.37:g.133887780G>A		Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	334	162	0.48503	NM_015288		Silent	SNP	ENST00000402835.1	37																																																																																				G|0.879;A|0.121	0.121	strong		0.592	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1		
ATP13A5	344905	hgsc.bcm.edu	37	3	193080414	193080414	+	Missense_Mutation	SNP	C	C	G	rs6797429	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:193080414C>G	ENST00000342358.4	-	4	514	c.397G>C	c.(397-399)Gaa>Caa	p.E133Q		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	133			E -> Q (in dbSNP:rs6797429).			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TTCTGCACTTCCATGCACCGC	0.483													G|||	2573	0.513778	0.646	0.5259	5008	,	,		21621	0.3859		0.5288	False		,,,				2504	0.4427				p.E133Q		Atlas-SNP	.											.	ATP13A5	171	.	0			c.G397C						PASS	.	G	GLN/GLU	2716,1690	513.1+/-368.2	845,1026,332	142.0	137.0	138.0		397	5.6	0.8	3	dbSNP_116	138	4451,4149	566.6+/-388.7	1179,2093,1028	yes	missense	ATP13A5	NM_198505.2	29	2024,3119,1360	GG,GC,CC		48.2442,38.3568,44.8947	benign	133/1219	193080414	7167,5839	2203	4300	6503	SO:0001583	missense	344905	exon4			GCACTTCCATGCA	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.397G>C	3.37:g.193080414C>G	ENSP00000341942:p.Glu133Gln	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	183	183	1	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	1159	0.5306776556776557	317	0.6443089430894309	202	0.5580110497237569	233	0.40734265734265734	407	0.5369393139841688	G	0.411	-0.913282	0.02415	0.616432	0.517558	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.26223	1.75;1.75	5.6	5.6	0.85130	.	0.268854	0.32548	N	0.005941	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.31392	-0.9945	9	0.09590	T	0.72	-2.1229	13.3521	0.60607	0.0:0.3026:0.6974:0.0	rs6797429;rs59343082;rs6797429	133	Q4VNC0	AT135_HUMAN	Q	133;155	ENSP00000341942:E133Q;ENSP00000389416:E155Q	ENSP00000341942:E133Q	E	-	1	0	ATP13A5	194563108	1.000000	0.71417	0.815000	0.32552	0.069000	0.16628	2.617000	0.46385	1.534000	0.49203	-0.120000	0.15030	GAA	C|0.453;G|0.547	0.547	strong		0.483	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
FRG1	2483	hgsc.bcm.edu	37	4	190878646	190878646	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:190878646G>T	ENST00000226798.4	+	6	748	c.526G>T	c.(526-528)Gaa>Taa	p.E176*	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	176					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.E176*(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		AGGAGAAGAAGAAATGATCAA	0.373																																					p.E176X		Atlas-SNP	.											FRG1,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	FRG1	76	1	1	Substitution - Nonsense(1)	central_nervous_system(1)	c.G526T						scavenged	.						48.0	44.0	45.0					4																	190878646		2179	4274	6453	SO:0001587	stop_gained	2483	exon6			GAAGAAGAAATGA	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.526G>T	4.37:g.190878646G>T	ENSP00000226798:p.Glu176*	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	305	11	0.0360656	NM_004477	A8K775	Nonsense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	34	5.401103	0.96030	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	.	.	.	4.29	3.44	0.39384	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-3.1825	10.4286	0.44393	0.0989:0.0:0.9011:0.0	.	.	.	.	X	176;48;113	.	ENSP00000226798:E176X	E	+	1	0	FRG1	191115640	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	6.376000	0.73141	0.937000	0.37394	0.454000	0.30748	GAA	.	.	none		0.373	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
ZBTB1	22890	hgsc.bcm.edu	37	14	64988830	64988830	+	Missense_Mutation	SNP	C	C	A	rs45512391	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:64988830C>A	ENST00000554015.1	+	4	1039	c.608C>A	c.(607-609)aCt>aAt	p.T203N	ZBTB1_ENST00000394712.2_Missense_Mutation_p.T203N|ZBTB1_ENST00000358738.3_Missense_Mutation_p.T203N|RP11-973N13.4_ENST00000554918.1_RNA			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	203				T -> N (in Ref. 2; BAA76841). {ECO:0000305}.	B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		AAATTATCTACTCCAAAAGAA	0.383													C|||	277	0.0553115	0.0038	0.2334	5008	,	,		21312	0.0		0.0746	False		,,,				2504	0.0358				p.T203N		Atlas-SNP	.											.	ZBTB1	93	.	0			c.C608A						PASS	.	C	ASN/THR,ASN/THR	97,4309	78.8+/-117.2	0,97,2106	93.0	95.0	94.0		608,608	4.2	1.0	14	dbSNP_127	94	837,7763	191.8+/-238.0	39,759,3502	yes	missense,missense	ZBTB1	NM_001123329.1,NM_014950.2	65,65	39,856,5608	AA,AC,CC		9.7326,2.2015,7.1813	benign,benign	203/714,203/645	64988830	934,12072	2203	4300	6503	SO:0001583	missense	22890	exon2			TATCTACTCCAAA	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.608C>A	14.37:g.64988830C>A	ENSP00000451000:p.Thr203Asn	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	187	84	0.449198	NM_014950	A8K6S8|Q86SW8	Missense_Mutation	SNP	ENST00000554015.1	37	CCDS45126.1	148	0.06776556776556776	3	0.006097560975609756	78	0.2154696132596685	0	0.0	67	0.08839050131926121	C	5.368	0.253166	0.10185	0.022015	0.097326	ENSG00000126804	ENST00000554015;ENST00000358738;ENST00000394712	T;T;T	0.10005	2.92;3.5;2.92	6.17	4.24	0.50183	.	0.362622	0.27262	N	0.020169	T	0.00012	0.0000	N	0.01874	-0.695	0.41825	P	0.009951000000000043	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.32587	-0.9901	9	0.48119	T	0.1	-13.1899	8.1138	0.30930	0.2981:0.4844:0.2175:0.0	rs45512391	203;203	Q9Y2K1-2;Q9Y2K1	.;ZBTB1_HUMAN	N	203	ENSP00000451000:T203N;ENSP00000351587:T203N;ENSP00000378201:T203N	ENSP00000351587:T203N	T	+	2	0	ZBTB1	64058583	0.964000	0.33143	1.000000	0.80357	0.999000	0.98932	2.179000	0.42528	2.941000	0.99782	0.655000	0.94253	ACT	C|0.929;A|0.071	0.071	strong		0.383	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1		
KRT81	3887	hgsc.bcm.edu	37	12	52681925	52681925	+	Missense_Mutation	SNP	A	A	C	rs6580873	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:52681925A>C	ENST00000327741.5	-	5	811	c.743T>G	c.(742-744)cTc>cGc	p.L248R	KRT86_ENST00000423955.2_Intron|KRT86_ENST00000544024.1_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	248	Coil 1B.|Rod.		L -> R (in dbSNP:rs6580873). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7556444, ECO:0000269|PubMed:9457912}.			extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		CTGGAGAATGAGGATCTCCTG	0.552													.|||	4688	0.936102	0.9887	0.9207	5008	,	,		18455	0.996		0.8519	False		,,,				2504	0.9008				p.L248R		Atlas-SNP	.											.	KRT81	46	.	0			c.T743G						PASS	.	C	ARG/LEU	4280,126	814.6+/-416.2	2077,126,0	115.0	105.0	108.0		743	2.7	0.3	12	dbSNP_116	108	7134,1466	750.4+/-407.4	2951,1232,117	no	missense	KRT81	NM_002281.3	102	5028,1358,117	CC,CA,AA		17.0465,2.8597,12.2405	benign	248/506	52681925	11414,1592	2203	4300	6503	SO:0001583	missense	3887	exon5			AGAATGAGGATCT	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6458	protein-coding gene	gene with protein product	"""hard keratin type II 1"""	602153	"""keratin, hair, basic, 1"""	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.743T>G	12.37:g.52681925A>C	ENSP00000369349:p.Leu248Arg	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	169	85	0.502959	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Missense_Mutation	SNP	ENST00000327741.5	37	CCDS31805.1	2012	0.9212454212454212	481	0.9776422764227642	318	0.8784530386740331	570	0.9965034965034965	643	0.8482849604221636	a	0.006	-2.118797	0.00346	0.971403	0.829535	ENSG00000205426	ENST00000327741;ENST00000389388	T	0.76839	-1.05	4.59	2.73	0.32206	Filament (1);	0.000000	0.36778	N	0.002409	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45512	-0.9256	8	0.02654	T	1	.	3.3763	0.07238	0.1165:0.4969:0.2328:0.1538	rs6580873;rs17433505;rs52831436;rs59358781;rs6580873	248	Q14533	KRT81_HUMAN	R	248	ENSP00000369349:L248R	ENSP00000369349:L248R	L	-	2	0	KRT81	50968192	0.000000	0.05858	0.330000	0.25442	0.205000	0.24178	-0.476000	0.06591	0.406000	0.25560	-0.224000	0.12420	CTC	A|0.101;C|0.899	0.899	strong		0.552	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281	
APPL2	55198	hgsc.bcm.edu	37	12	105600935	105600935	+	Silent	SNP	G	G	A	rs2293643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:105600935G>A	ENST00000258530.3	-	8	750	c.525C>T	c.(523-525)caC>caT	p.H175H	APPL2_ENST00000549573.1_5'UTR|APPL2_ENST00000539978.2_Silent_p.H132H|APPL2_ENST00000551662.1_Silent_p.H181H	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GGGAGGAGAGGTGCTGCTTCC	0.532													G|||	919	0.183506	0.0787	0.2421	5008	,	,		19223	0.2599		0.1879	False		,,,				2504	0.2004				p.H181H		Atlas-SNP	.											.	APPL2	69	.	0			c.C543T						PASS	.	G		383,4023	192.6+/-218.0	19,345,1839	89.0	80.0	83.0		525	3.0	1.0	12	dbSNP_100	83	1701,6899	312.7+/-311.0	167,1367,2766	no	coding-synonymous	APPL2	NM_018171.3		186,1712,4605	AA,AG,GG		19.7791,8.6927,16.0234		175/665	105600935	2084,10922	2203	4300	6503	SO:0001819	synonymous_variant	55198	exon8			GGAGAGGTGCTGC	AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"""Pleckstrin homology (PH) domain containing"""	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.525C>T	12.37:g.105600935G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_001251904	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Silent	SNP	ENST00000258530.3	37	CCDS9101.1																																																																																			G|0.836;A|0.164	0.164	strong		0.532	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406238.3	NM_018171	
SV2C	22987	hgsc.bcm.edu	37	5	75427935	75427935	+	Silent	SNP	G	G	A	rs10070440	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:75427935G>A	ENST00000502798.2	+	2	802	c.360G>A	c.(358-360)cgG>cgA	p.R120R	SV2C_ENST00000322285.7_Silent_p.R120R	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	120					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		ACAAGGACCGGCGGGAGCTGG	0.552													G|||	2367	0.472644	0.2625	0.4467	5008	,	,		19566	0.3224		0.7396	False		,,,				2504	0.6554				p.R120R		Atlas-SNP	.											SV2C,NS,carcinoma,+2,2	SV2C	97	2	0			c.G360A						scavenged	.	G		1445,2665		271,903,881	98.0	114.0	109.0		360	-11.4	0.0	5	dbSNP_119	109	6388,2022		2426,1536,243	no	coding-synonymous	SV2C	NM_014979.1		2697,2439,1124	AA,AG,GG		24.0428,35.1582,37.4361		120/728	75427935	7833,4687	2055	4205	6260	SO:0001819	synonymous_variant	22987	exon2			GGACCGGCGGGAG	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.360G>A	5.37:g.75427935G>A		Somatic	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_014979	Q496K1|Q9UPU8	Silent	SNP	ENST00000502798.2	37	CCDS43331.1																																																																																			G|0.480;A|0.520	0.520	strong		0.552	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4		
OR2T6	254879	hgsc.bcm.edu	37	1	248551636	248551636	+	Missense_Mutation	SNP	T	T	G	rs954475	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248551636T>G	ENST00000355728.2	+	1	727	c.727T>G	c.(727-729)Tca>Gca	p.S243A		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	243			S -> A (in dbSNP:rs954475).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACCTGCTCTTCACACATGAT	0.507													t|||	1851	0.369609	0.4962	0.3127	5008	,	,		22655	0.4365		0.1769	False		,,,				2504	0.3681				p.S243A		Atlas-SNP	.											.	OR2T6	101	.	0			c.T727G						PASS	.	T	ALA/SER	1921,2485	548.5+/-377.6	423,1075,705	259.0	220.0	234.0		727	2.8	0.0	1	dbSNP_86	234	1297,7303	256.6+/-281.0	92,1113,3095	yes	missense	OR2T6	NM_001005471.1	99	515,2188,3800	GG,GT,TT		15.0814,43.5996,24.7424	probably-damaging	243/309	248551636	3218,9788	2203	4300	6503	SO:0001583	missense	254879	exon1			TGCTCTTCACACA	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"""GPCR / Class A : Olfactory receptors"""	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.727T>G	1.37:g.248551636T>G	ENSP00000347965:p.Ser243Ala	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	269	148	0.550186	NM_001005471	A6NE36	Missense_Mutation	SNP	ENST00000355728.2	37	CCDS31114.1	720	0.32967032967032966	241	0.4898373983739837	94	0.2596685082872928	242	0.4230769230769231	143	0.18865435356200527	T	11.11	1.542475	0.27563	0.435996	0.150814	ENSG00000198104	ENST00000355728	T	0.38887	1.11	4.02	2.85	0.33270	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37219	N	0.002182	T	0.00012	0.0000	M	0.76938	2.355	0.50632	P	1.1300000000002974E-4	D	0.89917	1.0	D	0.97110	1.0	T	0.45381	-0.9265	9	0.87932	D	0	.	6.292	0.21065	0.0:0.089:0.1626:0.7484	rs954475;rs52796985;rs954475	243	Q8NHC8	OR2T6_HUMAN	A	243	ENSP00000347965:S243A	ENSP00000347965:S243A	S	+	1	0	OR2T6	246618259	0.237000	0.23815	0.048000	0.18961	0.377000	0.30045	0.605000	0.24179	0.673000	0.31224	0.523000	0.50628	TCA	T|0.707;G|0.293	0.293	strong		0.507	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471	
CACNA1C	775	hgsc.bcm.edu	37	12	2694638	2694638	+	Silent	SNP	C	C	T	rs215976	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:2694638C>T	ENST00000347598.4	+	17	2436	c.2436C>T	c.(2434-2436)gaC>gaT	p.D812D	CACNA1C_ENST00000399629.1_Silent_p.D812D|CACNA1C_ENST00000399634.1_Silent_p.D812D|CACNA1C_ENST00000399617.1_Silent_p.D812D|CACNA1C_ENST00000406454.3_Silent_p.D812D|CACNA1C_ENST00000399591.1_Silent_p.D812D|CACNA1C_ENST00000399601.1_Silent_p.D812D|CACNA1C_ENST00000402845.3_Silent_p.D812D|CACNA1C_ENST00000399597.1_Silent_p.D812D|CACNA1C_ENST00000399621.1_Silent_p.D812D|CACNA1C_ENST00000344100.3_Silent_p.D812D|CACNA1C_ENST00000399655.1_Silent_p.D812D|CACNA1C_ENST00000399637.1_Silent_p.D812D|CACNA1C_ENST00000399603.1_Silent_p.D812D|CACNA1C_ENST00000399595.1_Silent_p.D812D|CACNA1C_ENST00000480911.1_Silent_p.D812D|CACNA1C_ENST00000399606.1_Silent_p.D812D|CACNA1C_ENST00000399649.1_Silent_p.D812D|CACNA1C_ENST00000399644.1_Silent_p.D812D|CACNA1C_ENST00000327702.7_Silent_p.D812D|CACNA1C_ENST00000399638.1_Silent_p.D812D|CACNA1C_ENST00000335762.5_Silent_p.D837D|CACNA1C_ENST00000399641.1_Silent_p.D812D	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	812					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCACGGCTGACGGAGAGTCTC	0.612													C|||	729	0.145567	0.0877	0.0576	5008	,	,		14849	0.2966		0.0885	False		,,,				2504	0.1892				p.D812D		Atlas-SNP	.											Q6YL47_HUMAN,NS,carcinoma,0,5	CACNA1C	1023	5	0			c.C2436T						scavenged	.	C	,,,,,,,,,,,,,,,,,,,,,,	319,3661		15,289,1686	14.0	19.0	17.0		2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2427,2436,2436,2436,2436,2436	-0.6	0.9	12	dbSNP_79	17	652,7638		26,600,3519	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1C	NM_000719.6,NM_001129827.1,NM_001129829.1,NM_001129830.1,NM_001129831.1,NM_001129832.1,NM_001129833.1,NM_001129834.1,NM_001129835.1,NM_001129836.1,NM_001129837.1,NM_001129838.1,NM_001129839.1,NM_001129840.1,NM_001129841.1,NM_001129842.1,NM_001129843.1,NM_001129844.1,NM_001129846.1,NM_001167623.1,NM_001167624.1,NM_001167625.1,NM_199460.2	,,,,,,,,,,,,,,,,,,,,,,	41,889,5205	TT,TC,CC		7.8649,8.0151,7.9136	,,,,,,,,,,,,,,,,,,,,,,	812/2139,812/2187,812/2180,812/2174,812/2167,812/2159,812/2158,812/2158,812/2158,812/2156,812/2147,812/2147,812/2145,812/2139,812/2139,812/2139,812/2139,809/2136,812/2128,812/2139,812/2174,812/2199,812/2222	2694638	971,11299	1990	4145	6135	SO:0001819	synonymous_variant	775	exon17			GGCTGACGGAGAG	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.2436C>T	12.37:g.2694638C>T		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	83	52	0.626506	NM_001129831	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	37	CCDS44788.1																																																																																			C|0.836;T|0.164	0.164	strong		0.612	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
EML2	24139	hgsc.bcm.edu	37	19	46141845	46141845	+	Missense_Mutation	SNP	T	T	C	rs12151009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:46141845T>C	ENST00000245925.3	-	3	147	c.97A>G	c.(97-99)Atg>Gtg	p.M33V	EML2_ENST00000589876.1_Missense_Mutation_p.M33V|MIR330_ENST00000362196.1_RNA|EML2_ENST00000587152.1_Missense_Mutation_p.M234V|EML2_ENST00000536630.1_Missense_Mutation_p.M180V	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	33	Tandem atypical propeller in EMLs. {ECO:0000250}.		M -> V (in dbSNP:rs12151009).		negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		TCTGGGATCATCATGGGCACA	0.607													T|||	431	0.0860623	0.0061	0.1196	5008	,	,		15465	0.1032		0.1103	False		,,,				2504	0.1278				p.M234V		Atlas-SNP	.											.	EML2	64	.	0			c.A700G						PASS	.		VAL/MET,VAL/MET,VAL/MET	122,4284	89.7+/-128.4	3,116,2084	73.0	67.0	69.0		97,538,700	-4.5	0.9	19	dbSNP_120	69	1138,7462	234.3+/-267.3	81,976,3243	yes	missense,missense,missense	EML2	NM_012155.2,NM_001193269.1,NM_001193268.1	21,21,21	84,1092,5327	CC,CT,TT		13.2326,2.769,9.6878	benign,benign,benign	33/650,180/797,234/851	46141845	1260,11746	2203	4300	6503	SO:0001583	missense	24139	exon6			GGATCATCATGGG	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.97A>G	19.37:g.46141845T>C	ENSP00000245925:p.Met33Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	179	0.08195970695970696	3	0.006097560975609756	44	0.12154696132596685	53	0.09265734265734266	79	0.10422163588390501	T	15.12	2.739504	0.49045	0.02769	0.132326	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055;ENST00000399594	T;T;T	0.26957	1.7;1.7;1.7	4.6	-4.54	0.03452	HELP (1);	0.462809	0.21249	N	0.077664	T	0.00144	0.0004	N	0.22421	0.69	0.54753	P	2.0000000000020002E-5	B;B;B;B;B	0.21821	0.061;0.001;0.001;0.03;0.001	B;B;B;B;B	0.29440	0.102;0.016;0.01;0.034;0.027	T	0.16217	-1.0410	9	0.66056	D	0.02	-5.0507	3.8011	0.08758	0.3982:0.0:0.2021:0.3996	rs12151009;rs57737116;rs12151009	33;199;180;191;33	B7Z918;B7Z3Q9;B7Z3I2;B7Z872;O95834	.;.;.;.;EMAL2_HUMAN	V	180;33;234;191	ENSP00000442365:M180V;ENSP00000245925:M33V;ENSP00000382503:M191V	ENSP00000245925:M33V	M	-	1	0	EML2	50833685	1.000000	0.71417	0.929000	0.37066	0.932000	0.56968	1.910000	0.39927	-0.283000	0.09115	-0.889000	0.02933	ATG	T|0.908;C|0.092	0.092	strong		0.607	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
RAG1	5896	hgsc.bcm.edu	37	11	36597734	36597734	+	Silent	SNP	A	A	G	rs1980131	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:36597734A>G	ENST00000299440.5	+	2	2992	c.2880A>G	c.(2878-2880)gcA>gcG	p.A960A		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	960					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				GGGCATGGGCAAGTGAGGGAA	0.448									Familial Hemophagocytic Lymphohistiocytosis				A|||	313	0.0625	0.0847	0.0677	5008	,	,		20414	0.005		0.0875	False		,,,				2504	0.0624				p.A960A	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.A2880G						PASS	.	A		326,4078	168.0+/-198.9	15,296,1891	91.0	97.0	95.0		2880	-11.3	0.5	11	dbSNP_92	95	695,7901	170.9+/-221.9	28,639,3631	no	coding-synonymous	RAG1	NM_000448.2		43,935,5522	GG,GA,AA		8.0852,7.4024,7.8538		960/1044	36597734	1021,11979	2202	4298	6500	SO:0001819	synonymous_variant	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	ATGGGCAAGTGAG	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"""RING-type (C3HC4) zinc fingers"""	9831	protein-coding gene	gene with protein product	"""recombination activating protein 1"", ""RING finger protein 74"", ""V(D)J recombination-activating protein 1"""	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.2880A>G	11.37:g.36597734A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_000448	E9PPC4|Q8IY72|Q8NER2	Silent	SNP	ENST00000299440.5	37	CCDS7902.1																																																																																			A|0.928;G|0.072	0.072	strong		0.448	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50682865	50682865	+	Silent	SNP	G	G	A	rs5771270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50682865G>A	ENST00000248846.5	-	1	128	c.24C>T	c.(22-24)ttC>ttT	p.F8F	MAPK12_ENST00000497036.1_5'Flank|TUBGCP6_ENST00000439308.2_Silent_p.F8F|HDAC10_ENST00000498366.1_5'Flank			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	8					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		ACAGGTCGTCGAACAGCTGCG	0.657													G|||	1410	0.28155	0.0802	0.2478	5008	,	,		15545	0.3562		0.4026	False		,,,				2504	0.3763				p.F8F		Atlas-SNP	.											TUBGCP6,NS,carcinoma,0,1	TUBGCP6	132	1	0			c.C24T						PASS	.	G		618,3788	242.8+/-252.7	54,510,1639	23.0	26.0	25.0		24	2.1	1.0	22	dbSNP_114	25	3344,5256	465.7+/-366.6	645,2054,1601	no	coding-synonymous	TUBGCP6	NM_020461.3		699,2564,3240	AA,AG,GG		38.8837,14.0263,30.4629		8/1820	50682865	3962,9044	2203	4300	6503	SO:0001819	synonymous_variant	85378	exon1			GTCGTCGAACAGC	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.24C>T	22.37:g.50682865G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																			G|0.710;A|0.290	0.290	strong		0.657	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
RFK	55312	hgsc.bcm.edu	37	9	79003516	79003516	+	Silent	SNP	C	C	G	rs10781358	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:79003516C>G	ENST00000376736.1	-	3	624	c.291G>C	c.(289-291)gtG>gtC	p.V97V	RFK_ENST00000479197.1_5'UTR	NM_018339.5	NP_060809.3	Q969G6	RIFK_HUMAN	riboflavin kinase	97					apoptotic process (GO:0006915)|FMN biosynthetic process (GO:0009398)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|reactive oxygen species metabolic process (GO:0072593)|riboflavin biosynthetic process (GO:0009231)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|riboflavin kinase activity (GO:0008531)			pancreas(1)|prostate(1)|urinary_tract(1)	3					Riboflavin(DB00140)	CAACAATGGCCACATTGAGGA	0.378													C|||	548	0.109425	0.0106	0.1556	5008	,	,		20630	0.0298		0.2356	False		,,,				2504	0.1626				p.V97V		Atlas-SNP	.											.	RFK	13	.	0			c.G291C						PASS	.	C		236,4170	139.6+/-175.2	9,218,1976	115.0	111.0	112.0		291	0.3	1.0	9	dbSNP_120	112	2187,6413	374.4+/-337.4	267,1653,2380	no	coding-synonymous	RFK	NM_018339.5		276,1871,4356	GG,GC,CC		25.4302,5.3563,18.6299		97/156	79003516	2423,10583	2203	4300	6503	SO:0001819	synonymous_variant	55312	exon3			AATGGCCACATTG	AK002011	CCDS35044.1, CCDS35044.2	9q21.31	2010-11-16			ENSG00000135002	ENSG00000135002			30324	protein-coding gene	gene with protein product		613010				14580199	Standard	NM_018339		Approved	FLJ11149, RIFK	uc004akd.2	Q969G6	OTTHUMG00000020040	ENST00000376736.1:c.291G>C	9.37:g.79003516C>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	NM_018339	Q5JSG9|Q9NUT7	Silent	SNP	ENST00000376736.1	37	CCDS35044.2																																																																																			C|0.834;G|0.166	0.166	strong		0.378	RFK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052720.1	NM_018339	
SIRPA	140885	hgsc.bcm.edu	37	20	1895965	1895965	+	Missense_Mutation	SNP	C	C	A	rs17855614|rs373583167|rs386811662	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:1895965C>A	ENST00000358771.4	+	2	452	c.300C>A	c.(298-300)aaC>aaA	p.N100K	SIRPA_ENST00000400068.3_Missense_Mutation_p.N100K|SIRPA_ENST00000356025.3_Missense_Mutation_p.N100K	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	100	Ig-like V-type.		N -> E (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CAAAGAGAAACAACATGGACT	0.517													C|||	480	0.0958466	0.0386	0.1095	5008	,	,		14804	0.1835		0.0537	False		,,,				2504	0.1166				p.N100K	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,brain,glioma,0,4	SIRPA	83	4	0			c.C300A						scavenged	.																																			SO:0001583	missense	140885	exon3			GAGAAACAACATG	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.300C>A	20.37:g.1895965C>A	ENSP00000351621:p.Asn100Lys	Somatic	296	19	0.0641892		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.533326	0.27387	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02158	4.42;4.42;4.42	5.11	0.771	0.18504	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.743450	0.02696	N	0.111247	T	0.04634	0.0126	M	0.65975	2.015	0.09310	N	1	B;B;B	0.33299	0.003;0.407;0.039	B;B;B	0.31812	0.056;0.136;0.082	T	0.44345	-0.9334	10	0.72032	D	0.01	.	8.1767	0.31285	0.0:0.4423:0.4696:0.0881	rs17855614	80;100;100	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	K	100	ENSP00000382941:N100K;ENSP00000348307:N100K;ENSP00000351621:N100K	ENSP00000348307:N100K	N	+	3	2	SIRPA	1843965	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-0.328000	0.07945	0.028000	0.15324	-0.315000	0.08773	AAC	.	.	weak		0.517	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
IGFN1	91156	hgsc.bcm.edu	37	1	201183363	201183363	+	Silent	SNP	C	C	T	rs2282415	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:201183363C>T	ENST00000335211.4	+	13	8917	c.8787C>T	c.(8785-8787)gcC>gcT	p.A2929A	IGFN1_ENST00000295591.8_Silent_p.A89A|IGFN1_ENST00000451870.2_Silent_p.A472A	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	472						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CGGGGGAGGCCGCCACACTCT	0.637													T|||	1628	0.32508	0.2542	0.3184	5008	,	,		15865	0.3095		0.3479	False		,,,				2504	0.4182				p.A2929A		Atlas-SNP	.											.	IGFN1	220	.	0			c.C8787T						PASS	.	T		1188,3218	690.3+/-405.2	151,886,1166	50.0	39.0	43.0		8787	-5.4	0.0	1	dbSNP_100	43	2867,5731	652.2+/-400.9	492,1883,1924	no	coding-synonymous	IGFN1	NM_001164586.1		643,2769,3090	TT,TC,CC		33.345,26.9632,31.1827		2929/3709	201183363	4055,8949	2203	4299	6502	SO:0001819	synonymous_variant	91156	exon13			GGAGGCCGCCACA	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.8787C>T	1.37:g.201183363C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	701	0.320970695970696	132	0.2682926829268293	114	0.3149171270718232	191	0.3339160839160839	264	0.3482849604221636	T	7.400	0.632592	0.14322	0.269632	0.33345	ENSG00000163395	ENST00000412892	.	.	.	3.39	-5.38	0.02673	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.37842	-0.9688	3	.	.	.	.	6.0299	0.19675	0.1971:0.5084:0.0:0.2945	rs2282415;rs17424119;rs58385923;rs2282415	.	.	.	C	347	.	.	R	+	1	0	IGFN1	199449986	0.000000	0.05858	0.009000	0.14445	0.156000	0.22039	-3.675000	0.00396	-1.165000	0.02786	-0.817000	0.03123	CGC	C|0.687;T|0.313	0.313	strong		0.637	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
TXLNB	167838	hgsc.bcm.edu	37	6	139563914	139563914	+	Missense_Mutation	SNP	C	C	G	rs9495391	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:139563914C>G	ENST00000358430.3	-	10	2036	c.1804G>C	c.(1804-1806)Gcg>Ccg	p.A602P	RP1-225E12.3_ENST00000585874.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	602			A -> P (in dbSNP:rs9495391). {ECO:0000269|PubMed:17974005}.			cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		TTCCAGGACGCCTGATCAGCC	0.612													G|||	2423	0.483826	0.9062	0.3588	5008	,	,		18081	0.2351		0.3638	False		,,,				2504	0.3814				p.A602P		Atlas-SNP	.											TXLNB,caecum,carcinoma,+2,2	TXLNB	96	2	0			c.G1804C						PASS	.	G	PRO/ALA	3565,841	325.9+/-299.3	1449,667,87	62.0	72.0	69.0		1804	2.6	0.0	6	dbSNP_119	69	3162,5438	651.3+/-400.8	566,2030,1704	yes	missense	TXLNB	NM_153235.3	27	2015,2697,1791	GG,GC,CC		36.7674,19.0876,48.2777	benign	602/685	139563914	6727,6279	2203	4300	6503	SO:0001583	missense	167838	exon10			AGGACGCCTGATC		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"""chromosome 6 open reading frame 198"""	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.1804G>C	6.37:g.139563914C>G	ENSP00000351206:p.Ala602Pro	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Missense_Mutation	SNP	ENST00000358430.3	37	CCDS34545.1	929	0.42536630036630035	406	0.8252032520325203	129	0.356353591160221	130	0.22727272727272727	264	0.3482849604221636	G	10.58	1.391441	0.25118	0.809124	0.367674	ENSG00000164440	ENST00000358430	T	0.14516	2.5	3.49	2.59	0.31030	.	1.531680	0.03515	N	0.220216	T	0.02267	0.0070	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39121	-0.9629	8	.	.	.	-2.1905	9.6776	0.40050	0.0:0.4166:0.5834:0.0	rs9495391;rs52790733;rs57864218;rs9495391	602	Q8N3L3	TXLNB_HUMAN	P	602	ENSP00000351206:A602P	.	A	-	1	0	TXLNB	139605607	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	-0.219000	0.09228	0.291000	0.22468	-0.120000	0.15030	GCG	C|0.511;G|0.489	0.489	strong		0.612	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235	
MRTO4	51154	hgsc.bcm.edu	37	1	19584004	19584004	+	Silent	SNP	G	G	A	rs1042380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:19584004G>A	ENST00000330263.4	+	5	627	c.330G>A	c.(328-330)gaG>gaA	p.E110E		NM_016183.3	NP_057267.2	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog (S. cerevisiae)	110					ribosome biogenesis (GO:0042254)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|liver(2)|ovary(1)|pancreas(1)|stomach(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GCACAAAGGAGGAGGTGAATG	0.527													G|||	1259	0.251398	0.4932	0.183	5008	,	,		22095	0.1012		0.2266	False		,,,				2504	0.1534				p.E110E	GBM(192;2418 3032 7540 48714)	Atlas-SNP	.											.	MRTO4	17	.	0			c.G330A						PASS	.	G		2091,2315	572.9+/-383.4	505,1081,617	147.0	142.0	144.0		330	-3.3	1.0	1	dbSNP_86	144	2104,6496	363.1+/-333.0	263,1578,2459	no	coding-synonymous	MRTO4	NM_016183.3		768,2659,3076	AA,AG,GG		24.4651,47.458,32.2543		110/240	19584004	4195,8811	2203	4300	6503	SO:0001819	synonymous_variant	51154	exon5			AAAGGAGGAGGTG	AK027569	CCDS191.1	1p36.13	2008-02-05	2006-12-21	2007-01-05	ENSG00000053372	ENSG00000053372			18477	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 33"", ""MRT4, mRNA turnover 4, homolog (S. cerevisiae)"""	C1orf33			Standard	NM_016183		Approved	dJ657E11.4, MRT4	uc001bbs.3	Q9UKD2	OTTHUMG00000002496	ENST00000330263.4:c.330G>A	1.37:g.19584004G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_016183	B3KNB3|Q5TG55|Q96SS6|Q9BPV9	Silent	SNP	ENST00000330263.4	37	CCDS191.1																																																																																			G|0.711;A|0.289	0.289	strong		0.527	MRTO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007075.2	NM_016183	
CHST13	166012	hgsc.bcm.edu	37	3	126260791	126260791	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:126260791C>T	ENST00000319340.2	+	3	446	c.396C>T	c.(394-396)cgC>cgT	p.R132R		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	132					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			central_nervous_system(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(114;0.151)		GCCAAGCCCGCGGCGACCCGC	0.726																																					p.R132R		Atlas-SNP	.											.	CHST13	21	.	0			c.C396T						PASS	.						16.0	13.0	14.0					3																	126260791		2183	4262	6445	SO:0001819	synonymous_variant	166012	exon3			AGCCCGCGGCGAC	AY120869	CCDS3039.1	3q21.3	2008-02-05			ENSG00000180767	ENSG00000180767	2.8.2.5	"""Sulfotransferases, membrane-bound"""	21755	protein-coding gene	gene with protein product		610124				12080076	Standard	NM_152889		Approved	C4ST3	uc003eja.3	Q8NET6	OTTHUMG00000162721	ENST00000319340.2:c.396C>T	3.37:g.126260791C>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_152889	Q3SYA3|Q3SYA5	Silent	SNP	ENST00000319340.2	37	CCDS3039.1																																																																																			.	.	none		0.726	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889	
PCDHGA9	56107	hgsc.bcm.edu	37	5	140784820	140784820	+	Silent	SNP	C	C	T	rs78501291	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140784820C>T	ENST00000573521.1	+	1	2301	c.2301C>T	c.(2299-2301)caC>caT	p.H767H	PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB6_ENST00000520790.1_5'Flank|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	767					homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAAGAGTCACCTGATCTTCC	0.512													.|||	147	0.029353	0.0424	0.036	5008	,	,		17862	0.001		0.0348	False		,,,				2504	0.0307				p.H767H		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.C2301T						PASS	.	C	,,,,,,,,,,,,,,	161,4243	101.2+/-139.8	3,155,2044	113.0	122.0	119.0		,,,,,,,,2301,,,,,,2301	-0.1	0.7	5	dbSNP_132	119	315,8285	109.6+/-170.1	6,303,3991	no	intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032089.1	,,,,,,,,,,,,,,	9,458,6035	TT,TC,CC		3.6628,3.6558,3.6604	,,,,,,,,,,,,,,	,,,,,,,,767/933,,,,,,767/829	140784820	476,12528	2202	4300	6502	SO:0001819	synonymous_variant	56107	exon1			GAGTCACCTGATC	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.2301C>T	5.37:g.140784820C>T		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	278	128	0.460432	NM_032089	A2RU65|Q9Y5C9	Silent	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			C|0.968;T|0.032	0.032	strong		0.512	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
RIN2	54453	hgsc.bcm.edu	37	20	19951534	19951534	+	Missense_Mutation	SNP	T	T	A	rs3803981	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:19951534T>A	ENST00000255006.6	+	7	885	c.736T>A	c.(736-738)Tcg>Acg	p.S246T	RIN2_ENST00000440354.2_Intron|RIN2_ENST00000484638.1_3'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	197					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						AACAGCCAAGTCGGAGGCTCA	0.438													T|||	798	0.159345	0.1679	0.1614	5008	,	,		20069	0.2431		0.1392	False		,,,				2504	0.0808				p.S246T		Atlas-SNP	.											RIN2_ENST00000255006,NS,carcinoma,0,3	RIN2	126	3	0			c.T736A						PASS	.	T	THR/SER,THR/SER	547,3323		39,469,1427	71.0	72.0	72.0		736,589	4.6	1.0	20	dbSNP_107	72	1255,6999		94,1067,2966	yes	missense,missense	RIN2	NM_001242581.1,NM_018993.3	58,58	133,1536,4393	AA,AT,TT		15.2047,14.1344,14.8631	benign,benign	246/945,197/896	19951534	1802,10322	1935	4127	6062	SO:0001583	missense	54453	exon7			GCCAAGTCGGAGG	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.736T>A	20.37:g.19951534T>A	ENSP00000255006:p.Ser246Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	158	70	0.443038	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	37	CCDS56182.1	395	0.18086080586080586	95	0.19308943089430894	54	0.14917127071823205	143	0.25	103	0.1358839050131926	T	6.996	0.553871	0.13374	0.141344	0.152047	ENSG00000132669	ENST00000255006	T	0.49139	0.79	5.66	4.56	0.56223	.	0.049002	0.85682	N	0.000000	T	0.00012	0.0000	N	0.01152	-0.98	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.20042	-1.0287	8	.	.	.	-15.9515	11.5874	0.50927	0.8613:0.0:0.0:0.1387	rs3803981;rs60446832;rs3803981	197	Q8WYP3	RIN2_HUMAN	T	246	ENSP00000255006:S246T	.	S	+	1	0	RIN2	19899534	1.000000	0.71417	0.994000	0.49952	0.971000	0.66376	6.837000	0.75354	0.960000	0.38005	-0.624000	0.04008	TCG	T|0.818;A|0.182	0.182	strong		0.438	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
CCDC157	550631	hgsc.bcm.edu	37	22	30762139	30762139	+	Silent	SNP	C	C	T	rs41281641	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:30762139C>T	ENST00000405659.1	+	3	859	c.150C>T	c.(148-150)ctC>ctT	p.L50L	CCDC157_ENST00000399824.2_Silent_p.L50L|CCDC157_ENST00000338306.3_Silent_p.L50L			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	50										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CCTGTGACCTCGACATGGTGG	0.642													C|||	300	0.0599042	0.1142	0.0389	5008	,	,		20799	0.001		0.0915	False		,,,				2504	0.0297				p.L50L		Atlas-SNP	.											.	CCDC157	86	.	0			c.C150T						PASS	.	C		506,3900	232.6+/-246.1	35,436,1732	152.0	135.0	141.0		150	2.0	1.0	22	dbSNP_127	141	819,7781	189.7+/-236.4	30,759,3511	no	coding-synonymous	CCDC157	NM_001017437.2		65,1195,5243	TT,TC,CC		9.5233,11.4843,10.1876		50/753	30762139	1325,11681	2203	4300	6503	SO:0001819	synonymous_variant	550631	exon3			TGACCTCGACATG	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.150C>T	22.37:g.30762139C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			C|0.931;T|0.069	0.069	strong		0.642	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
ADRA1B	147	hgsc.bcm.edu	37	5	159344461	159344461	+	Silent	SNP	G	G	A	rs3729604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:159344461G>A	ENST00000306675.3	+	1	672	c.549G>A	c.(547-549)ggG>ggA	p.G183G		NM_000679.3	NP_000670.1	P35368	ADA1B_HUMAN	adrenoceptor alpha 1B	183					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|adult heart development (GO:0007512)|behavioral response to cocaine (GO:0048148)|blood vessel remodeling (GO:0001974)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|multicellular organismal development (GO:0007275)|negative regulation of glycogen catabolic process (GO:0045818)|organ growth (GO:0035265)|positive regulation of glycogen catabolic process (GO:0045819)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of the force of heart contraction by epinephrine-norepinephrine (GO:0001997)|regulation of cardiac muscle contraction (GO:0055117)|regulation of vasoconstriction (GO:0019229)|response to amphetamine (GO:0001975)|response to morphine (GO:0043278)|vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure (GO:0001987)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)|protein heterodimerization activity (GO:0046982)	p.G183G(1)		endometrium(3)|large_intestine(6)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acepromazine(DB01614)|Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Dapiprazole(DB00298)|Desipramine(DB01151)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Ziprasidone(DB00246)	CTCTCCTTGGGTGGAAGGAGC	0.607													g|||	1011	0.201877	0.1679	0.1931	5008	,	,		18695	0.3482		0.1759	False		,,,				2504	0.1299				p.G183G		Atlas-SNP	.											ADRA1B,NS,carcinoma,0,1	ADRA1B	39	1	1	Substitution - coding silent(1)	stomach(1)	c.G549A						PASS	.	A		703,3703	293.3+/-282.5	51,601,1551	87.0	84.0	85.0		549	-0.9	1.0	5	dbSNP_107	85	1522,7078	287.5+/-298.3	153,1216,2931	no	coding-synonymous	ADRA1B	NM_000679.3		204,1817,4482	AA,AG,GG		17.6977,15.9555,17.1075		183/521	159344461	2225,10781	2203	4300	6503	SO:0001819	synonymous_variant	147	exon1			CCTTGGGTGGAAG	L31773	CCDS4347.1	5q33.3	2012-08-08	2012-05-09		ENSG00000170214	ENSG00000170214		"""GPCR / Class A : Adrenoceptors : alpha"""	278	protein-coding gene	gene with protein product		104220	"""adrenergic, alpha-1B-, receptor"""				Standard	XM_005265818		Approved		uc003lxt.1	P35368	OTTHUMG00000130327	ENST00000306675.3:c.549G>A	5.37:g.159344461G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	141	82	0.58156	NM_000679	B0LPE1	Silent	SNP	ENST00000306675.3	37	CCDS4347.1																																																																																			G|0.806;A|0.194	0.194	strong		0.607	ADRA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252676.1		
DNAH8	1769	hgsc.bcm.edu	37	6	38851669	38851669	+	Silent	SNP	C	C	T	rs4714192	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:38851669C>T	ENST00000359357.3	+	54	7757	c.7503C>T	c.(7501-7503)taC>taT	p.Y2501Y	DNAH8_ENST00000441566.1_Silent_p.Y2465Y|DNAH8_ENST00000449981.2_Silent_p.Y2718Y			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2501	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.Y2501Y(1)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTGAAAGCTACGTGGATAAGC	0.363													C|||	1220	0.24361	0.1339	0.2262	5008	,	,		12180	0.3512		0.1978	False		,,,				2504	0.3405				p.Y2718Y		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	1	Substitution - coding silent(1)	stomach(1)	c.C8154T						PASS	.	C		651,3755	277.2+/-273.6	63,525,1615	107.0	108.0	107.0		8154	-1.3	1.0	6	dbSNP_111	107	2078,6522	359.5+/-331.6	244,1590,2466	no	coding-synonymous	DNAH8	NM_001206927.1		307,2115,4081	TT,TC,CC		24.1628,14.7753,20.9826		2718/4708	38851669	2729,10277	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon56			AAGCTACGTGGAT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.7503C>T	6.37:g.38851669C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				C|0.782;T|0.218	0.218	strong		0.363	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
TBX21	30009	hgsc.bcm.edu	37	17	45811210	45811210	+	Silent	SNP	A	A	G	rs2074190	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:45811210A>G	ENST00000177694.1	+	1	601	c.390A>G	c.(388-390)ggA>ggG	p.G130G		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	130					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						TACCCGCGGGACTGGAGGTGT	0.672													G|||	1411	0.281749	0.292	0.3429	5008	,	,		11923	0.1121		0.2644	False		,,,				2504	0.4172				p.G130G		Atlas-SNP	.											TBX21,NS,carcinoma,0,1	TBX21	50	1	0			c.A390G						scavenged	.	G		1049,2771		151,747,1012	16.0	18.0	18.0		390	3.5	1.0	17	dbSNP_96	18	2149,6061		257,1635,2213	no	coding-synonymous	TBX21	NM_013351.1		408,2382,3225	GG,GA,AA		26.1754,27.4607,26.5835		130/536	45811210	3198,8832	1910	4105	6015	SO:0001819	synonymous_variant	30009	exon1			CGCGGGACTGGAG	AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"""T-boxes"""	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.390A>G	17.37:g.45811210A>G		Somatic	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_013351		Silent	SNP	ENST00000177694.1	37	CCDS11514.1																																																																																			A|0.750;G|0.250	0.250	strong		0.672	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351	
FCHO1	23149	hgsc.bcm.edu	37	19	17885880	17885880	+	Silent	SNP	C	C	T	rs2287855	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17885880C>T	ENST00000596536.1	+	14	1219	c.936C>T	c.(934-936)ccC>ccT	p.P312P	FCHO1_ENST00000600676.1_Silent_p.P312P|FCHO1_ENST00000389133.4_Silent_p.P312P|FCHO1_ENST00000596951.1_Silent_p.P312P|FCHO1_ENST00000597512.1_Silent_p.P319P|FCHO1_ENST00000252771.7_Silent_p.P312P|FCHO1_ENST00000595033.1_Silent_p.P262P|FCHO1_ENST00000594202.1_Silent_p.P312P|FCHO1_ENST00000539407.1_Silent_p.P312P	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	312	Mediates interaction with the adaptor protein complex AP-2.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						TCCTGGAGCCCGATTCAGGGG	0.582													C|||	473	0.0944489	0.059	0.1369	5008	,	,		17274	0.0337		0.174	False		,,,				2504	0.093				p.P312P		Atlas-SNP	.											.	FCHO1	69	.	0			c.C936T						PASS	.	C	,,,	341,4065	175.9+/-205.1	9,323,1871	55.0	54.0	54.0		936,936,786,936	-6.4	0.0	19	dbSNP_100	54	1245,7355	249.3+/-276.6	94,1057,3149	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCHO1	NM_001161357.1,NM_001161358.1,NM_001161359.1,NM_015122.2	,,,	103,1380,5020	TT,TC,CC		14.4767,7.7394,12.1944	,,,	312/892,312/890,262/840,312/890	17885880	1586,11420	2203	4300	6503	SO:0001819	synonymous_variant	23149	exon13			GGAGCCCGATTCA	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.936C>T	19.37:g.17885880C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	122	58	0.47541	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Silent	SNP	ENST00000596536.1	37	CCDS32955.1																																																																																			C|0.894;T|0.106	0.106	strong		0.582	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122	
SV2B	9899	hgsc.bcm.edu	37	15	91827271	91827271	+	Missense_Mutation	SNP	A	A	G	rs117361551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91827271A>G	ENST00000394232.1	+	11	1998	c.1528A>G	c.(1528-1530)Atc>Gtc	p.I510V	SV2B_ENST00000545111.2_Missense_Mutation_p.I359V|SV2B_ENST00000330276.4_Missense_Mutation_p.I510V	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	510					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			GCACAAGTTCATCAACTGTCG	0.507													A|||	56	0.0111821	0.0008	0.013	5008	,	,		19869	0.0		0.0169	False		,,,				2504	0.0297				p.I510V		Atlas-SNP	.											.	SV2B	98	.	0			c.A1528G						PASS	.	A	VAL/ILE,VAL/ILE	12,4384	19.1+/-41.9	0,12,2186	192.0	184.0	187.0		1075,1528	5.6	1.0	15	dbSNP_132	187	127,8469	64.9+/-127.2	2,123,4173	yes	missense,missense	SV2B	NM_001167580.1,NM_014848.4	29,29	2,135,6359	GG,GA,AA		1.4774,0.273,1.0699	benign,benign	359/533,510/684	91827271	139,12853	2198	4298	6496	SO:0001583	missense	9899	exon12			AAGTTCATCAACT	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1528A>G	15.37:g.91827271A>G	ENSP00000377779:p.Ile510Val	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	178	96	0.539326	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	10.16	1.274723	0.23307	0.00273	0.014774	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.41400	1.0;1.0;1.0	5.61	5.61	0.85477	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.099589	0.64402	D	0.000004	T	0.21145	0.0509	L	0.39245	1.2	0.47584	D	0.999462	B	0.23937	0.094	B	0.31016	0.123	T	0.08911	-1.0699	10	0.12766	T	0.61	-31.4023	14.6867	0.69055	1.0:0.0:0.0:0.0	.	510	Q7L1I2	SV2B_HUMAN	V	359;510;510	ENSP00000443243:I359V;ENSP00000377779:I510V;ENSP00000332818:I510V	ENSP00000332818:I510V	I	+	1	0	SV2B	89628275	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.317000	0.43770	2.152000	0.67230	0.477000	0.44152	ATC	A|0.990;G|0.010	0.010	strong		0.507	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
CCDC153	283152	hgsc.bcm.edu	37	11	119063908	119063908	+	Missense_Mutation	SNP	C	C	T	rs2301574	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:119063908C>T	ENST00000503566.2	-	4	301	c.302G>A	c.(301-303)cGc>cAc	p.R101H	CCDC153_ENST00000415318.1_Missense_Mutation_p.R101H			Q494R4	CC153_HUMAN	coiled-coil domain containing 153	101			R -> H (in dbSNP:rs2301574). {ECO:0000269|PubMed:15489334}.					p.R15H(1)		lung(3)|stomach(1)	4						CTGCTTGCTGCGGGTTTGCAT	0.622													C|||	1227	0.245008	0.2595	0.2089	5008	,	,		17375	0.3542		0.2455	False		,,,				2504	0.138				p.R101H		Atlas-SNP	.											CCDC153,NS,carcinoma,0,1	CCDC153	19	1	1	Substitution - Missense(1)	stomach(1)	c.G302A						PASS	.	C	HIS/ARG	1146,3252	406.2+/-333.8	149,848,1202	87.0	82.0	84.0		302	-0.1	0.0	11	dbSNP_100	84	2131,6459	366.6+/-334.4	264,1603,2428	yes	missense	CCDC153	NM_001145018.1	29	413,2451,3630	TT,TC,CC		24.8079,26.0573,25.231	benign	101/211	119063908	3277,9711	2199	4295	6494	SO:0001583	missense	283152	exon5			TTGCTGCGGGTTT		CCDS44753.1	11q23.3	2011-07-22			ENSG00000248712	ENSG00000248712			27446	protein-coding gene	gene with protein product						12477932	Standard	NM_001145018		Approved	LOC283152	uc010rze.2	Q494R4	OTTHUMG00000156903	ENST00000503566.2:c.302G>A	11.37:g.119063908C>T	ENSP00000423567:p.Arg101His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_001145018		Missense_Mutation	SNP	ENST00000503566.2	37	CCDS44753.1	635	0.2907509157509158	153	0.31097560975609756	83	0.2292817679558011	210	0.36713286713286714	189	0.24934036939313983	C	2.731	-0.264408	0.05754	0.260573	0.248079	ENSG00000248712	ENST00000503566;ENST00000415318	T;T	0.29142	1.58;1.58	4.89	-0.122	0.13531	.	0.545048	0.17907	N	0.157983	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.18013	0.025	B	0.11329	0.006	T	0.48514	-0.9029	9	0.23891	T	0.37	-22.631	7.5928	0.28031	0.0:0.4717:0.0:0.5283	rs2301574;rs52800057;rs58197863;rs2301574	101	Q494R4	CC153_HUMAN	H	101	ENSP00000423567:R101H;ENSP00000445431:R101H	ENSP00000445431:R101H	R	-	2	0	CCDC153	118569118	0.000000	0.05858	0.009000	0.14445	0.068000	0.16541	-0.974000	0.03794	0.088000	0.17205	-0.254000	0.11334	CGC	C|0.728;T|0.272	0.272	strong		0.622	CCDC153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388331.2	NM_001033658	
WDR20	91833	hgsc.bcm.edu	37	14	102675350	102675350	+	Silent	SNP	G	G	C	rs6575900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102675350G>C	ENST00000342702.3	+	3	874	c.843G>C	c.(841-843)ggG>ggC	p.G281G	WDR20_ENST00000424963.2_Silent_p.G157G|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000454394.2_Silent_p.G312G|WDR20_ENST00000499851.2_Silent_p.G24G|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000556511.2_Silent_p.G220G|WDR20_ENST00000556807.1_Silent_p.G220G|WDR20_ENST00000335263.5_Silent_p.G281G|WDR20_ENST00000545563.1_Silent_p.G108G	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	281										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						TGACAGGTGGGGAGGACGACT	0.552													C|||	1722	0.34385	0.761	0.2133	5008	,	,		18621	0.0724		0.2078	False		,,,				2504	0.2924				p.G312G		Atlas-SNP	.											.	WDR20	35	.	0			c.G936C						PASS	.	C	,,,,,,,	3010,1396	460.2+/-352.5	1036,938,229	89.0	66.0	74.0		,,660,936,879,843,843,660	-11.7	0.0	14	dbSNP_116	74	1761,6839	734.8+/-406.9	171,1419,2710	no	utr-3,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR20	NM_001242414.1,NM_001242415.1,NM_001242416.1,NM_001242417.1,NM_001242418.1,NM_144574.3,NM_181291.2,NM_181308.2	,,,,,,,	1207,2357,2939	CC,CG,GG		20.4767,31.6841,36.6831	,,,,,,,	,,220/521,312/601,293/582,281/570,281/582,220/509	102675350	4771,8235	2203	4300	6503	SO:0001819	synonymous_variant	91833	exon4			AGGTGGGGAGGAC	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"""WD repeat domain containing"""	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.843G>C	14.37:g.102675350G>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	154	75	0.487013	NM_001242417	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Silent	SNP	ENST00000342702.3	37	CCDS9969.1	647	0.29624542124542125	372	0.7560975609756098	92	0.2541436464088398	40	0.06993006993006994	143	0.18865435356200527	C	1.987	-0.432810	0.04669	0.683159	0.204767	ENSG00000140153	ENST00000556511	.	.	.	5.83	-11.7	0.00046	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.11470	-1.0586	4	.	.	.	.	11.658	0.51330	0.2768:0.5269:0.1962:0.0	rs6575900;rs6575900	.	.	.	R	212	.	.	G	+	1	0	WDR20	101745103	0.000000	0.05858	0.017000	0.16124	0.929000	0.56500	-2.301000	0.01137	-2.971000	0.00286	-2.098000	0.00363	GGA	G|0.664;C|0.336	0.336	strong		0.552	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291	
IL17RE	132014	hgsc.bcm.edu	37	3	9956279	9956279	+	Silent	SNP	G	G	A	rs455863	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9956279G>A	ENST00000383814.3	+	14	1449	c.1344G>A	c.(1342-1344)ccG>ccA	p.P448P	IL17RE_ENST00000295980.3_Silent_p.P448P|IL17RE_ENST00000454190.2_Missense_Mutation_p.G473R|IL17RE_ENST00000421412.1_Silent_p.P481P|IL17RC_ENST00000413608.1_5'Flank|IL17RC_ENST00000403601.3_5'Flank|IL17RC_ENST00000295981.3_5'Flank|IL17RC_ENST00000416074.2_5'Flank|IL17RC_ENST00000383812.4_5'Flank|IL17RC_ENST00000455057.1_5'Flank	NM_153480.1	NP_705613.1	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E	448					inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(11)|skin(1)	21				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		TCTTGTGTCCGGATGGTGAGT	0.607													G|||	1813	0.362021	0.4054	0.4625	5008	,	,		19167	0.0933		0.5447	False		,,,				2504	0.3211				p.G473R		Atlas-SNP	.											IL17RE,NS,haematopoietic_neoplasm,+1,1	IL17RE	62	1	0			c.G1417A						PASS	.	G	ARG/GLY,,	1829,2577	533.4+/-373.7	391,1047,765	121.0	123.0	122.0		1417,1344,1464	-9.9	0.0	3	dbSNP_80	122	4579,4021	597.6+/-393.8	1205,2169,926	yes	missense,coding-synonymous,coding-synonymous	IL17RE	NM_001193380.1,NM_153480.1,NM_153483.2	125,,	1596,3216,1691	AA,AG,GG		46.7558,41.5116,49.2696	,,	473/534,448/668,488/708	9956279	6408,6598	2203	4300	6503	SO:0001819	synonymous_variant	132014	exon14			GTGTCCGGATGGT	AF458069	CCDS2589.1, CCDS54552.1	3p25.3	2008-02-05			ENSG00000163701	ENSG00000163701		"""Interleukins and interleukin receptors"""	18439	protein-coding gene	gene with protein product		614995					Standard	NM_153480		Approved	FLJ23658	uc003btu.3	Q8NFR9	OTTHUMG00000128649	ENST00000383814.3:c.1344G>A	3.37:g.9956279G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	121	48	0.396694	NM_001193380	B2RB34|B2RNR1|B9EH65|Q6P532|Q8N8H7|Q8N8H8|Q8TEC2	Missense_Mutation	SNP	ENST00000383814.3	37	CCDS2589.1	809	0.37042124542124544	192	0.3902439024390244	168	0.46408839779005523	38	0.06643356643356643	411	0.5422163588390502	G	3.940	-0.014333	0.07681	0.415116	0.532442	ENSG00000163701	ENST00000454190	T	0.30714	1.52	4.94	-9.87	0.00470	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21861	P	0.999502608	B	0.02656	0.0	B	0.01281	0.0	T	0.31724	-0.9933	7	0.87932	D	0	-12.6119	6.2348	0.20756	0.0884:0.1602:0.4815:0.27	rs455863;rs1300549;rs52806952;rs61674331;rs455863	473	Q8NFR9-3	.	R	473	ENSP00000388086:G473R	ENSP00000388086:G473R	G	+	1	0	IL17RE	9931279	0.000000	0.05858	0.011000	0.14972	0.478000	0.33099	-5.110000	0.00150	-4.926000	0.00027	-2.560000	0.00174	GGA	A|0.424;C|0.006	0.424	strong		0.607	IL17RE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250529.1	NM_153480	
TNIP1	10318	hgsc.bcm.edu	37	5	150425467	150425467	+	Silent	SNP	G	G	A	rs2233299	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150425467G>A	ENST00000389378.2	-	9	1479	c.891C>T	c.(889-891)ggC>ggT	p.G297G	TNIP1_ENST00000523338.1_Silent_p.G297G|TNIP1_ENST00000315050.7_Silent_p.G297G|TNIP1_ENST00000518977.1_Silent_p.G297G|TNIP1_ENST00000523200.1_Silent_p.G297G|TNIP1_ENST00000522226.1_Silent_p.G297G|TNIP1_ENST00000520931.1_Silent_p.G244G|TNIP1_ENST00000521591.1_Silent_p.G297G|TNIP1_ENST00000521423.1_Intron|TNIP1_ENST00000524280.1_Silent_p.G297G	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	297	Interacts with Nef.				defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTCGGCTGCGCCCAAGGCCA	0.592													G|||	657	0.13119	0.0673	0.1758	5008	,	,		21120	0.0625		0.2803	False		,,,				2504	0.1033				p.G297G		Atlas-SNP	.											.	TNIP1	51	.	0			c.C891T						PASS	.	G		485,3921	226.5+/-242.0	32,421,1750	106.0	92.0	97.0		891	-5.7	0.6	5	dbSNP_98	97	2374,6226	396.2+/-345.3	351,1672,2277	no	coding-synonymous	TNIP1	NM_006058.3		383,2093,4027	AA,AG,GG		27.6047,11.0077,21.9822		297/637	150425467	2859,10147	2203	4300	6503	SO:0001819	synonymous_variant	10318	exon9			GGCTGCGCCCAAG	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.891C>T	5.37:g.150425467G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Silent	SNP	ENST00000389378.2	37	CCDS34280.1																																																																																			G|0.803;A|0.197	0.197	strong		0.592	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
FUT1	2523	hgsc.bcm.edu	37	19	49254114	49254114	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49254114C>A	ENST00000310160.3	-	4	1399	c.425G>T	c.(424-426)cGg>cTg	p.R142L	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	142					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		CTGCAGCTCCCGCCACGGCGT	0.632																																					p.R142L		Atlas-SNP	.											FUT1,NS,carcinoma,0,1	FUT1	44	1	0			c.G425T						scavenged	.						60.0	74.0	69.0					19																	49254114		2195	4289	6484	SO:0001583	missense	2523	exon4			AGCTCCCGCCACG		CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"""Blood group antigens"", ""Fucosyltransferases"""	4012	protein-coding gene	gene with protein product		211100	"""fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)"", ""fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"""	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.425G>T	19.37:g.49254114C>A	ENSP00000312021:p.Arg142Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	2	0.027027	NM_000148	O14505|O14506|O14507	Missense_Mutation	SNP	ENST00000310160.3	37	CCDS12733.1	.	.	.	.	.	.	.	.	.	.	C	7.797	0.712871	0.15306	.	.	ENSG00000174951	ENST00000310160;ENST00000539428	D	0.96459	-4.02	3.84	-7.67	0.01272	.	1.271890	0.05583	N	0.573202	D	0.91002	0.7170	L	0.31207	0.915	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.81208	-0.1037	10	0.48119	T	0.1	-7.83	8.3401	0.32239	0.1041:0.2338:0.0:0.6621	.	142	P19526	FUT1_HUMAN	L	142;132	ENSP00000312021:R142L	ENSP00000312021:R142L	R	-	2	0	FUT1	53945926	0.000000	0.05858	0.001000	0.08648	0.214000	0.24535	-2.832000	0.00743	-1.782000	0.01275	-0.253000	0.11424	CGG	.	.	none		0.632	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148	
SULT1A1	6817	hgsc.bcm.edu	37	16	28617552	28617552	+	Silent	SNP	C	C	G	rs3176926	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28617552C>G	ENST00000395607.1	-	7	873	c.600G>C	c.(598-600)ccG>ccC	p.P200P	SULT1A1_ENST00000314752.7_Silent_p.P200P|SULT1A1_ENST00000395609.1_Silent_p.P200P|SULT1A1_ENST00000569554.1_Silent_p.P200P|SULT1A1_ENST00000350842.4_Silent_p.P122P	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	200					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)			endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	TCTCCCTTTTCGGGTTCTGAG	0.547																																					p.P200P		Atlas-SNP	.											.	SULT1A1	53	.	0			c.G600C						PASS	.						82.0	61.0	68.0					16																	28617552		2197	4300	6497	SO:0001819	synonymous_variant	6817	exon6			CCTTTTCGGGTTC	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.600G>C	16.37:g.28617552C>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	191	47	0.246073	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Silent	SNP	ENST00000395607.1	37	CCDS32420.1																																																																																			C|0.646;G|0.354	0.354	strong		0.547	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
WRN	7486	hgsc.bcm.edu	37	8	30973957	30973957	+	Silent	SNP	G	G	T	rs1800392	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:30973957G>T	ENST00000298139.5	+	20	2610	c.2361G>T	c.(2359-2361)ctG>ctT	p.L787L		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	787	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TTAGGAAACTGAATCTATCCT	0.383			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				G|||	2360	0.471246	0.4175	0.5764	5008	,	,		18469	0.624		0.4493	False		,,,				2504	0.3344				p.L787L	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.G2361T						PASS	.	G		1810,2596	531.1+/-373.1	364,1082,757	126.0	116.0	119.0		2361	3.8	0.6	8	dbSNP_89	119	4019,4581	556.1+/-386.8	928,2163,1209	yes	coding-synonymous	WRN	NM_000553.4		1292,3245,1966	TT,TG,GG		46.7326,41.0803,44.8178		787/1433	30973957	5829,7177	2203	4300	6503	SO:0001819	synonymous_variant	7486	exon20	Familial Cancer Database	WS, Adult Progeria	GAAACTGAATCTA		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.2361G>T	8.37:g.30973957G>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	152	62	0.407895	NM_000553	A1KYY9	Silent	SNP	ENST00000298139.5	37	CCDS6082.1																																																																																			G|0.509;T|0.491	0.491	strong		0.383	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
OR6C1	390321	hgsc.bcm.edu	37	12	55715048	55715048	+	Missense_Mutation	SNP	C	C	T	rs7132600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:55715048C>T	ENST00000379668.2	+	1	703	c.665C>T	c.(664-666)aCa>aTa	p.T222I		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	222			T -> I (in dbSNP:rs7132600).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						ATTATCAGAACAATTTTGAGA	0.378													C|||	538	0.107428	0.1982	0.0951	5008	,	,		20634	0.0		0.1571	False		,,,				2504	0.0532				p.T222I		Atlas-SNP	.											.	OR6C1	58	.	0			c.C665T						PASS	.	C	ILE/THR	887,3519	343.6+/-307.7	87,713,1403	85.0	77.0	80.0		665	4.6	0.1	12	dbSNP_116	80	1413,7187	271.5+/-289.6	119,1175,3006	yes	missense	OR6C1	NM_001005182.1	89	206,1888,4409	TT,TC,CC		16.4302,20.1316,17.6841	probably-damaging	222/313	55715048	2300,10706	2203	4300	6503	SO:0001583	missense	390321	exon1			TCAGAACAATTTT	AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"""GPCR / Class A : Olfactory receptors"""	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.665C>T	12.37:g.55715048C>T	ENSP00000368990:p.Thr222Ile	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	373	186	0.49866	NM_001005182	B2RNM0	Missense_Mutation	SNP	ENST00000379668.2	37	CCDS31818.1	254	0.1163003663003663	100	0.2032520325203252	36	0.09944751381215469	0	0.0	118	0.15567282321899736	c	12.56	1.974087	0.34848	0.201316	0.164302	ENSG00000205330	ENST00000379668	T	0.00193	8.58	4.62	4.62	0.57501	GPCR, rhodopsin-like superfamily (1);	0.095905	0.46442	D	0.000294	T	0.00012	0.0000	M	0.89715	3.055	0.52099	P	5.100000000002325E-5	D	0.69078	0.997	D	0.74674	0.984	T	0.66131	-0.6000	9	0.87932	D	0	.	17.2438	0.87021	0.0:1.0:0.0:0.0	rs7132600;rs52814756;rs57267122;rs7132600	222	Q96RD1	OR6C1_HUMAN	I	222	ENSP00000368990:T222I	ENSP00000368990:T222I	T	+	2	0	OR6C1	54001315	0.034000	0.19679	0.055000	0.19348	0.267000	0.26476	3.185000	0.50934	2.380000	0.81148	0.563000	0.77884	ACA	C|0.842;T|0.158	0.158	strong		0.378	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182	
DIDO1	11083	hgsc.bcm.edu	37	20	61528271	61528271	+	Missense_Mutation	SNP	C	C	T	rs1883847	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:61528271C>T	ENST00000266070.4	-	7	1991	c.1666G>A	c.(1666-1668)Gcg>Acg	p.A556T	DIDO1_ENST00000395343.1_Missense_Mutation_p.A556T|DIDO1_ENST00000395335.2_Missense_Mutation_p.A556T|DIDO1_ENST00000395340.1_Missense_Mutation_p.A556T	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	556			A -> T (in dbSNP:rs1883847). {ECO:0000269|PubMed:16127461}.		apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A556T(1)		NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					TTGCCCACCGCGGAGCCTGGA	0.562													C|||	1399	0.279353	0.3026	0.3112	5008	,	,		17584	0.3323		0.1948	False		,,,				2504	0.2577				p.A556T	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1,NS,carcinoma,0,1	DIDO1	321	1	1	Substitution - Missense(1)	stomach(1)	c.G1666A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	1135,3271	396.0+/-329.9	149,837,1217	35.0	37.0	36.0		1666,1666,1666,1666	-8.2	0.0	20	dbSNP_92	36	1838,6762	318.6+/-313.7	205,1428,2667	yes	missense,missense,missense,missense	DIDO1	NM_001193369.1,NM_001193370.1,NM_033081.2,NM_080797.3	58,58,58,58	354,2265,3884	TT,TC,CC		21.3721,25.7603,22.8587	benign,benign,benign,benign	556/2241,556/1190,556/2241,556/1190	61528271	2973,10033	2203	4300	6503	SO:0001583	missense	11083	exon7			CCACCGCGGAGCC	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.1666G>A	20.37:g.61528271C>T	ENSP00000266070:p.Ala556Thr	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	185	77	0.416216	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	560	0.2564102564102564	136	0.2764227642276423	112	0.30939226519337015	178	0.3111888111888112	134	0.17678100263852242	C	10.19	1.281329	0.23392	0.257603	0.213721	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.12672	3.04;3.04;2.66;2.66	5.71	-8.25	0.01025	.	1.786570	0.03882	N	0.277200	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;B	0.15930	0.014;0.015	B;B	0.08055	0.003;0.003	T	0.44937	-0.9295	9	0.06757	T	0.87	0.9897	12.6879	0.56958	0.1107:0.5888:0.0:0.3005	rs1883847;rs57309326;rs1883847	556;556	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	T	556	ENSP00000266070:A556T;ENSP00000378752:A556T;ENSP00000378749:A556T;ENSP00000378744:A556T	ENSP00000266070:A556T	A	-	1	0	DIDO1	60998716	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.603000	0.02077	-1.541000	0.01727	-0.222000	0.12452	GCG	C|0.752;T|0.248	0.248	strong		0.562	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
OR8H1	219469	hgsc.bcm.edu	37	11	56058474	56058474	+	Missense_Mutation	SNP	T	T	A	rs17540861	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56058474T>A	ENST00000313022.2	-	1	92	c.65A>T	c.(64-66)gAg>gTg	p.E22V		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	22			E -> V (in dbSNP:rs17540861).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					CATCTGGACCTCTTCAGAATC	0.418													t|||	195	0.0389377	0.0121	0.0447	5008	,	,		18755	0.001		0.0924	False		,,,				2504	0.0552				p.E22V		Atlas-SNP	.											.	OR8H1	89	.	0			c.A65T						PASS	.	T	VAL/GLU	96,4306	77.3+/-115.6	0,96,2105	115.0	111.0	112.0		65	-0.1	0.0	11	dbSNP_123	112	685,7907	169.9+/-221.1	33,619,3644	yes	missense	OR8H1	NM_001005199.1	121	33,715,5749	AA,AT,TT		7.9725,2.1808,6.0105	benign	22/312	56058474	781,12213	2201	4296	6497	SO:0001583	missense	219469	exon1			TGGACCTCTTCAG	AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"""GPCR / Class A : Olfactory receptors"""	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.65A>T	11.37:g.56058474T>A	ENSP00000323595:p.Glu22Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_001005199	B2RNI7|Q6IFC5	Missense_Mutation	SNP	ENST00000313022.2	37	CCDS31526.1	88	0.040293040293040296	4	0.008130081300813009	14	0.03867403314917127	0	0.0	70	0.09234828496042216	T	14.04	2.415981	0.42817	0.021808	0.079725	ENSG00000181693	ENST00000313022;ENST00000395186	T	0.00446	7.39	3.77	-0.0985	0.13628	.	0.126774	0.36374	N	0.002634	T	0.00039	0.0001	M	0.78223	2.4	0.09310	N	1	P	0.38110	0.618	P	0.44811	0.461	T	0.45687	-0.9244	10	0.72032	D	0.01	.	8.1275	0.31008	0.0:0.2596:0.0:0.7404	rs17540861;rs17540861	22	Q8NGG4	OR8H1_HUMAN	V	22;18	ENSP00000323595:E22V	ENSP00000323595:E22V	E	-	2	0	OR8H1	55815050	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.002000	0.12924	-0.126000	0.11682	0.472000	0.43445	GAG	T|0.950;A|0.050	0.050	strong		0.418	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199	
PTPN21	11099	hgsc.bcm.edu	37	14	88935925	88935925	+	Silent	SNP	A	A	G	rs2297129	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:88935925A>G	ENST00000556564.1	-	17	3437	c.3153T>C	c.(3151-3153)acT>acC	p.T1051T	PTPN21_ENST00000328736.3_Silent_p.T1051T	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	1051	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TCTCTTGCCCAGTAAGGAGGT	0.507													G|||	1979	0.395168	0.5219	0.2781	5008	,	,		17864	0.38		0.2962	False		,,,				2504	0.4243				p.T1051T		Atlas-SNP	.											.	PTPN21	113	.	0			c.T3153C						PASS	.	G		2231,2175	585.0+/-386.2	556,1119,528	111.0	103.0	106.0		3153	-5.3	0.8	14	dbSNP_100	106	2932,5668	669.1+/-402.6	490,1952,1858	no	coding-synonymous	PTPN21	NM_007039.3		1046,3071,2386	GG,GA,AA		34.093,49.3645,39.6971		1051/1175	88935925	5163,7843	2203	4300	6503	SO:0001819	synonymous_variant	11099	exon17			TTGCCCAGTAAGG	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.3153T>C	14.37:g.88935925A>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	185	88	0.475676	NM_007039		Silent	SNP	ENST00000556564.1	37	CCDS9884.1																																																																																			A|0.610;G|0.390	0.390	strong		0.507	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		
SLC12A5	57468	hgsc.bcm.edu	37	20	44680493	44680493	+	Silent	SNP	G	G	A	rs17344810	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:44680493G>A	ENST00000454036.2	+	18	2479	c.2430G>A	c.(2428-2430)acG>acA	p.T810T	SLC12A5_ENST00000243964.3_Silent_p.T787T	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	810					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	ATCATCAGACGTGGAGGAACT	0.617													G|||	461	0.0920527	0.0688	0.0634	5008	,	,		11640	0.0149		0.1183	False		,,,				2504	0.1963				p.T810T		Atlas-SNP	.											.	SLC12A5	181	.	0			c.G2430A						PASS	.	G	,	382,4024	191.6+/-217.2	21,340,1842	45.0	48.0	47.0		2430,2361	-6.7	1.0	20	dbSNP_123	47	960,7640	204.9+/-247.5	48,864,3388	no	coding-synonymous,coding-synonymous	SLC12A5	NM_001134771.1,NM_020708.4	,	69,1204,5230	AA,AG,GG		11.1628,8.67,10.3183	,	810/1140,787/1117	44680493	1342,11664	2203	4300	6503	SO:0001819	synonymous_variant	57468	exon18			TCAGACGTGGAGG	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"""Solute carriers"""	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.2430G>A	20.37:g.44680493G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	37	CCDS46610.1																																																																																			G|0.909;A|0.091	0.091	strong		0.617	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
EPHB1	2047	hgsc.bcm.edu	37	3	134898742	134898742	+	Silent	SNP	C	C	T	rs1042787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:134898742C>T	ENST00000398015.3	+	10	2170	c.1800C>T	c.(1798-1800)taC>taT	p.Y600Y	EPHB1_ENST00000493838.1_Silent_p.Y161Y	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	600					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						CCTTCACTTACGAGGATCCCA	0.488													T|||	2694	0.537939	0.5166	0.5	5008	,	,		22244	0.7282		0.3797	False		,,,				2504	0.5603				p.Y600Y		Atlas-SNP	.											.	EPHB1	519	.	0			c.C1800T						PASS	.	T		1879,2053		457,965,544	217.0	203.0	208.0		1800	-0.7	1.0	3	dbSNP_107	208	3256,5138		643,1970,1584	yes	coding-synonymous	EPHB1	NM_004441.4		1100,2935,2128	TT,TC,CC		38.7896,47.7874,41.6599		600/985	134898742	5135,7191	1966	4197	6163	SO:0001819	synonymous_variant	2047	exon10			CACTTACGAGGAT	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.1800C>T	3.37:g.134898742C>T		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	292	137	0.469178	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Silent	SNP	ENST00000398015.3	37	CCDS46921.1																																																																																			C|0.508;T|0.492	0.492	strong		0.488	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
VANGL1	81839	hgsc.bcm.edu	37	1	116206423	116206423	+	Missense_Mutation	SNP	G	G	A	rs4839469	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:116206423G>A	ENST00000355485.2	+	4	617	c.346G>A	c.(346-348)Gcc>Acc	p.A116T	VANGL1_ENST00000369509.1_Missense_Mutation_p.A116T|VANGL1_ENST00000369510.4_Missense_Mutation_p.A114T|VANGL1_ENST00000310260.3_Missense_Mutation_p.A116T	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	116			A -> T (in dbSNP:rs4839469). {ECO:0000269|PubMed:15952208}.		multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		CCTCACCGTCGCCTCTTTTCT	0.542													G|||	576	0.115016	0.0416	0.2176	5008	,	,		17906	0.122		0.162	False		,,,				2504	0.0859				p.A116T		Atlas-SNP	.											.	VANGL1	65	.	0			c.G346A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	299,4107	162.9+/-194.8	9,281,1913	171.0	157.0	162.0		340,346,346	3.9	0.1	1	dbSNP_111	162	1315,7285	260.1+/-283.0	101,1113,3086	yes	missense,missense,missense	VANGL1	NM_001172411.1,NM_001172412.1,NM_138959.2	58,58,58	110,1394,4999	AA,AG,GG		15.2907,6.7862,12.4097	benign,benign,benign	114/523,116/525,116/525	116206423	1614,11392	2203	4300	6503	SO:0001583	missense	81839	exon4			ACCGTCGCCTCTT	AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"""vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)"", ""vang-like 1 (van gogh, Drosophila)"""			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.346G>A	1.37:g.116206423G>A	ENSP00000347672:p.Ala116Thr	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	242	232	0.958678	NM_138959	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	290	0.13278388278388278	25	0.0508130081300813	76	0.20994475138121546	78	0.13636363636363635	111	0.14643799472295516	G	10.79	1.450629	0.26074	0.067862	0.152907	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	4.81	3.9	0.45041	.	0.174068	0.51477	D	0.000100	T	0.51466	0.1676	N	0.21324	0.655	0.35814	P	0.17590799999999995	B;B	0.15930	0.012;0.015	B;B	0.10450	0.003;0.005	T	0.42999	-0.9418	9	0.19147	T	0.46	-15.4084	13.4342	0.61073	0.076:0.0:0.924:0.0	rs4839469;rs17500370;rs61579604;rs4839469	114;116	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	T	116;114;116;116	ENSP00000347672:A116T;ENSP00000358523:A114T;ENSP00000310800:A116T;ENSP00000358522:A116T	ENSP00000310800:A116T	A	+	1	0	VANGL1	116007946	0.932000	0.31603	0.060000	0.19600	0.717000	0.41224	3.690000	0.54713	1.397000	0.46682	-0.142000	0.14014	GCC	A|0.122;C|0.001;G|0.877;N|0.000	0.122	strong		0.542	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1		
BRD2	6046	hgsc.bcm.edu	37	6	32944094	32944094	+	Silent	SNP	G	G	C	rs15912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32944094G>C	ENST00000374825.4	+	6	2379	c.678G>C	c.(676-678)ctG>ctC	p.L226L	BRD2_ENST00000443797.2_Silent_p.L106L|BRD2_ENST00000395287.1_Silent_p.L226L|BRD2_ENST00000374831.4_Silent_p.L226L|BRD2_ENST00000449085.2_Silent_p.L179L|BRD2_ENST00000395289.2_Silent_p.L226L	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	226					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						ACACAGCCCTGTATACTCCTC	0.512													G|||	239	0.0477236	0.0068	0.0548	5008	,	,		20224	0.0208		0.0805	False		,,,				2504	0.092				p.L226L		Atlas-SNP	.											.	BRD2	70	.	0			c.G678C						PASS	.	G	,,,	62,2960		1,60,1450	125.0	109.0	115.0		678,678,537,678	1.4	1.0	6	dbSNP_52	115	419,4999		12,395,2302	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BRD2	NM_001113182.2,NM_001199455.1,NM_001199456.1,NM_005104.3	,,,	13,455,3752	CC,CG,GG		7.7335,2.0516,5.6991	,,,	226/802,226/837,179/755,226/802	32944094	481,7959	1511	2709	4220	SO:0001819	synonymous_variant	6046	exon6			AGCCCTGTATACT	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.678G>C	6.37:g.32944094G>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	98	0.04487179487179487	3	0.006097560975609756	20	0.055248618784530384	14	0.024475524475524476	61	0.08047493403693931	G	7.849	0.723590	0.15439	0.020516	0.077335	ENSG00000204256	ENST00000456339;ENST00000449025	.	.	.	5.33	1.43	0.22495	.	.	.	.	.	T	0.35653	0.0939	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.18178	-1.0345	4	.	.	.	-10.1803	5.1342	0.14926	0.2501:0.0:0.6055:0.1444	rs15912;rs17430759;rs52789941;rs15912	.	.	.	S	228;232	.	.	C	+	2	0	BRD2	33052072	0.539000	0.26402	0.999000	0.59377	0.998000	0.95712	-0.195000	0.09546	0.141000	0.18875	0.643000	0.83706	TGT	G|0.946;C|0.054	0.054	strong		0.512	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
COPE	11316	hgsc.bcm.edu	37	19	19023853	19023853	+	Silent	SNP	T	T	C	rs3177137	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19023853T>C	ENST00000262812.4	-	2	177	c.129A>G	c.(127-129)ctA>ctG	p.L43L	COPE_ENST00000349893.4_Silent_p.L43L|COPE_ENST00000351079.4_Silent_p.L43L|COPE_ENST00000598969.1_5'UTR|AC002985.3_ENST00000596918.1_3'UTR|COPE_ENST00000600932.1_Silent_p.L43L	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	43					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						CTGGGCTTGATAGCTGTGGGA	0.617													C|||	1753	0.35004	0.3222	0.5836	5008	,	,		18947	0.1925		0.4871	False		,,,				2504	0.2434				p.L43L		Atlas-SNP	.											COPE,NS,adenoma,0,1	COPE	26	1	0			c.A129G						PASS	.	C	,,	1594,2812	663.6+/-401.2	303,988,912	127.0	91.0	103.0		129,129,129	-9.8	0.0	19	dbSNP_105	103	4168,4432	585.7+/-391.9	997,2174,1129	no	coding-synonymous,coding-synonymous,coding-synonymous	COPE	NM_007263.3,NM_199442.1,NM_199444.1	,,	1300,3162,2041	CC,CT,TT		48.4651,36.1779,44.3026	,,	43/309,43/258,43/257	19023853	5762,7244	2203	4300	6503	SO:0001819	synonymous_variant	11316	exon2			GCTTGATAGCTGT	AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669			2234	protein-coding gene	gene with protein product		606942				10469566	Standard	NM_007263		Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.129A>G	19.37:g.19023853T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_007263	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	Silent	SNP	ENST00000262812.4	37	CCDS12387.1																																																																																			T|0.586;C|0.414	0.414	strong		0.617	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464801.1	NM_007263	
NLRP4	147945	hgsc.bcm.edu	37	19	56369314	56369314	+	Silent	SNP	G	G	A	rs16986718	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56369314G>A	ENST00000301295.6	+	3	977	c.555G>A	c.(553-555)acG>acA	p.T185T	NLRP4_ENST00000587891.1_Silent_p.T110T|NLRP4_ENST00000346986.5_Silent_p.T185T	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	185	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TCCTGTACACGTTCTATTTCT	0.498													A|||	1229	0.245407	0.3222	0.2651	5008	,	,		19870	0.2391		0.2575	False		,,,				2504	0.1217				p.T185T		Atlas-SNP	.											NLRP4_ENST00000301295,colon,carcinoma,0,1	NLRP4	331	1	0			c.G555A						PASS	.	A		1434,2972	466.4+/-354.5	233,968,1002	109.0	108.0	108.0		555	-8.5	0.0	19	dbSNP_123	108	2243,6357	380.1+/-339.5	291,1661,2348	yes	coding-synonymous	NLRP4	NM_134444.4		524,2629,3350	AA,AG,GG		26.0814,32.5465,28.2716		185/995	56369314	3677,9329	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			GTACACGTTCTAT	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.555G>A	19.37:g.56369314G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	187	184	0.983957	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			G|0.718;A|0.281	0.281	strong		0.498	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
DDX11	1663	hgsc.bcm.edu	37	12	31253995	31253995	+	Silent	SNP	C	C	T	rs1046456	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:31253995C>T	ENST00000407793.2	+	20	2234	c.1983C>T	c.(1981-1983)ctC>ctT	p.L661L	DDX11_ENST00000545668.1_Silent_p.L661L|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000228264.6_Silent_p.L635L|DDX11_ENST00000542838.1_Silent_p.L661L|DDX11_ENST00000350437.4_Silent_p.L661L	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	661					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					TCCTGCCCCTCGTCATCTGCA	0.597										Multiple Myeloma(12;0.14)			T|||	3147	0.628395	0.6861	0.6124	5008	,	,		17036	0.8065		0.4394	False		,,,				2504	0.5726				p.L661L		Atlas-SNP	.											.	DDX11	188	.	0			c.C1983T						PASS	.	T	,,	2942,1464	472.6+/-356.4	986,970,247	87.0	96.0	93.0		1983,1983,1983	-7.5	0.0	12	dbSNP_86	93	3916,4684	604.9+/-394.9	909,2098,1293	no	coding-synonymous,coding-synonymous,coding-synonymous	DDX11	NM_004399.2,NM_030653.3,NM_152438.1	,,	1895,3068,1540	TT,TC,CC		45.5349,33.2274,47.2705	,,	661/857,661/907,661/971	31253995	6858,6148	2203	4300	6503	SO:0001819	synonymous_variant	1663	exon20			GCCCCTCGTCATC	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1983C>T	12.37:g.31253995C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	37	CCDS44856.1																																																																																			C|0.466;T|0.534	0.534	strong		0.597	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291160	1291160	+	Missense_Mutation	SNP	G	G	T	rs141519544		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1291160G>T	ENST00000338844.3	+	3	101	c.68G>T	c.(67-69)gGc>gTc	p.G23V	TPSAB1_ENST00000461509.2_Missense_Mutation_p.G30V	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	23			G -> V (in allele alpha; dbSNP:rs1141965). {ECO:0000269|PubMed:10898108}.		defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G23V(1)		NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				CCAGCCCCAGGCCAGGCCCTG	0.711																																					p.G23V		Atlas-SNP	.											TPSAB1,NS,lymphoid_neoplasm,0,2	TPSAB1	24	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G68T						scavenged	.						21.0	23.0	22.0					16																	1291160		2193	4291	6484	SO:0001583	missense	7177	exon3			CCCCAGGCCAGGC	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.68G>T	16.37:g.1291160G>T	ENSP00000343577:p.Gly23Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	76	11	0.144737	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	37	CCDS10431.1	745	0.3411172161172161	111	0.22560975609756098	106	0.292817679558011	262	0.458041958041958	266	0.35092348284960423	G	9.934	1.215703	0.22373	.	.	ENSG00000172236	ENST00000338844;ENST00000461509	D;D	0.86497	-2.13;-2.13	2.84	0.752	0.18398	.	0.709020	0.11654	N	0.542536	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	D	0.56287	0.975	P	0.45660	0.489	T	0.17868	-1.0355	9	0.39692	T	0.17	.	4.3463	0.11134	0.1498:0.3033:0.5468:0.0	.	23	Q15661	TRYB1_HUMAN	V	23;30	ENSP00000343577:G23V;ENSP00000418247:G30V	ENSP00000343577:G23V	G	+	2	0	TPSAB1	1231161	0.001000	0.12720	0.035000	0.18076	0.629000	0.37895	0.668000	0.25127	0.237000	0.21200	0.479000	0.44913	GGC	G|0.658;T|0.342	0.342	strong		0.711	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
TTN	7273	hgsc.bcm.edu	37	2	179398509	179398509	+	Missense_Mutation	SNP	C	C	A	rs3731752	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179398509C>A	ENST00000591111.1	-	308	98134	c.97910G>T	c.(97909-97911)gGa>gTa	p.G32637V	TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G25213V|TTN_ENST00000342992.6_Missense_Mutation_p.G31710V|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G34278V|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G25338V|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G25405V|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000588804.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32637	Ig-like 144.		G -> V. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATAGTTACTCCAAACCGGAC	0.423													C|||	391	0.0780751	0.0847	0.0403	5008	,	,		21817	0.1716		0.0318	False		,,,				2504	0.047				p.G34278V		Atlas-SNP	.											.	TTN	18412	.	0			c.G102833T						PASS	.	C	VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY	245,3561		8,229,1666	97.0	89.0	92.0		75638,95129,76013,76214	5.6	1.0	2	dbSNP_107	92	163,8059		4,155,3952	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	109,109,109,109	12,384,5618	AA,AC,CC		1.9825,6.4372,3.3921	probably-damaging,probably-damaging,probably-damaging,probably-damaging	25213/26927,31710/33424,25338/27052,25405/27119	179398509	408,11620	1903	4111	6014	SO:0001583	missense	7273	exon358			GTTACTCCAAACC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.97910G>T	2.37:g.179398509C>A	ENSP00000465570:p.Gly32637Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	152	71	0.467105	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		175	0.08012820512820513	38	0.07723577235772358	15	0.04143646408839779	100	0.17482517482517482	22	0.029023746701846966	C	15.09	2.730452	0.48939	0.064372	0.019825	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.6	5.6	0.85130	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Protein kinase-like domain (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.00300	0.0009	N	0.01874	-0.695	0.09310	P	0.9999999839552	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.73380	0.98;0.98;0.98;0.98	T	0.51647	-0.8679	8	0.87932	D	0	.	13.8517	0.63501	0.0:0.9246:0.0:0.0754	rs3731752;rs52831571;rs57847880;rs3731752	25213;25338;25405;32637	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	31710;25213;25405;25338;25210	ENSP00000343764:G31710V;ENSP00000434586:G25213V;ENSP00000340554:G25405V;ENSP00000352154:G25338V	ENSP00000340554:G25405V	G	-	2	0	TTN	179106755	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.794000	0.85869	2.641000	0.89580	0.491000	0.48974	GGA	C|0.922;A|0.078	0.078	strong		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
NEK2	4751	hgsc.bcm.edu	37	1	211848807	211848807	+	Silent	SNP	A	A	C	rs55635245	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:211848807A>C	ENST00000366999.4	-	1	153	c.15T>G	c.(13-15)gcT>gcG	p.A5A	NEK2_ENST00000540251.1_Intron|NEK2_ENST00000366998.3_Silent_p.A5A|RP11-122M14.1_ENST00000415202.1_RNA	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	5					blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		CATAGTCCTCAGCCCGGGAAG	0.642													A|||	162	0.0323482	0.0015	0.1066	5008	,	,		16073	0.0		0.0636	False		,,,				2504	0.0225				p.A5A		Atlas-SNP	.											.	NEK2	49	.	0			c.T15G						PASS	.	A	,,	69,4337	59.3+/-96.0	0,69,2134	54.0	55.0	55.0		15,15,15	2.5	1.0	1	dbSNP_129	55	530,8070	141.9+/-198.1	14,502,3784	no	coding-synonymous,coding-synonymous,coding-synonymous	NEK2	NM_001204182.1,NM_001204183.1,NM_002497.3	,,	14,571,5918	CC,CA,AA		6.1628,1.566,4.6056	,,	5/389,5/385,5/446	211848807	599,12407	2203	4300	6503	SO:0001819	synonymous_variant	4751	exon1			GTCCTCAGCCCGG	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"""HsPK 21"", ""protein phosphatase 1, regulatory subunit 111"""	604043	"""NIMA (never in mitosis gene a)-related kinase 2"""			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.15T>G	1.37:g.211848807A>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Silent	SNP	ENST00000366999.4	37	CCDS1500.1																																																																																			A|0.959;C|0.041	0.041	strong		0.642	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497	
PDGFRA	5156	hgsc.bcm.edu	37	4	55143577	55143577	+	Silent	SNP	G	G	A	rs10028020	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55143577G>A	ENST00000257290.5	+	13	2140	c.1809G>A	c.(1807-1809)gcG>gcA	p.A603A	FIP1L1_ENST00000507166.1_Silent_p.A363A	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	603	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	GGTCTGGAGCGTTTGGGAAGG	0.532			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)			G|||	1142	0.228035	0.3366	0.2666	5008	,	,		16391	0.1726		0.1064	False		,,,				2504	0.2362				p.A603A	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	.	PDGFRA	1583	.	0			c.G1809A						PASS	.	G		1306,3100	441.2+/-346.3	179,948,1076	141.0	145.0	144.0		1809	-11.3	0.1	4	dbSNP_119	144	855,7745	193.8+/-239.4	54,747,3499	no	coding-synonymous	PDGFRA	NM_006206.4		233,1695,4575	AA,AG,GG		9.9419,29.6414,16.6154		603/1090	55143577	2161,10845	2203	4300	6503	SO:0001819	synonymous_variant	5156	exon13	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	TGGAGCGTTTGGG	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1809G>A	4.37:g.55143577G>A		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	267	117	0.438202	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																			A|0.170;C|0.000;G|0.830	0.170	strong		0.532	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
OR5A1	219982	hgsc.bcm.edu	37	11	59211421	59211421	+	Silent	SNP	C	C	T	rs17591107	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:59211421C>T	ENST00000302030.2	+	1	805	c.780C>T	c.(778-780)ttC>ttT	p.F260F		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						CAGCCCTTTTCGTGTACTTGC	0.537													C|||	630	0.125799	0.0242	0.1326	5008	,	,		21088	0.1111		0.2525	False		,,,				2504	0.1431				p.F260F		Atlas-SNP	.											OR5A1,NS,adenoma,0,1	OR5A1	72	1	0			c.C780T						PASS	.	C		251,4151	146.9+/-181.5	10,231,1960	265.0	215.0	232.0		780	6.0	1.0	11	dbSNP_123	232	2264,6326	383.3+/-340.7	283,1698,2314	no	coding-synonymous	OR5A1	NM_001004728.1		293,1929,4274	TT,TC,CC		26.3562,5.702,19.3581		260/316	59211421	2515,10477	2201	4295	6496	SO:0001819	synonymous_variant	219982	exon1			CCTTTTCGTGTAC	AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"""GPCR / Class A : Olfactory receptors"""	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.780C>T	11.37:g.59211421C>T		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	310	146	0.470968	NM_001004728	B9EH58|Q6IFF2|Q96RB1	Silent	SNP	ENST00000302030.2	37	CCDS31561.1																																																																																			C|0.815;T|0.185	0.185	strong		0.537	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728	
EPHA8	2046	hgsc.bcm.edu	37	1	22923873	22923873	+	Missense_Mutation	SNP	G	G	C	rs999765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22923873G>C	ENST00000166244.3	+	10	1906	c.1834G>C	c.(1834-1836)Gaa>Caa	p.E612Q		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	612	Mediates interaction with PIK3CG and required for endocytosis. {ECO:0000250}.		E -> Q (in dbSNP:rs999765). {ECO:0000269|PubMed:10819331}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GTTCTATGCGGAACCCCACAC	0.647													G|||	459	0.0916534	0.1021	0.1066	5008	,	,		13142	0.0774		0.1024	False		,,,				2504	0.0706				p.E612Q		Atlas-SNP	.											.	EPHA8	221	.	0			c.G1834C						PASS	.	G	GLN/GLU	467,3939	218.1+/-236.3	30,407,1766	58.0	71.0	66.0		1834	4.6	0.5	1	dbSNP_86	66	900,7700	200.0+/-243.9	37,826,3437	yes	missense	EPHA8	NM_020526.3	29	67,1233,5203	CC,CG,GG		10.4651,10.5992,10.5105	possibly-damaging	612/1006	22923873	1367,11639	2203	4300	6503	SO:0001583	missense	2046	exon10			TATGCGGAACCCC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.1834G>C	1.37:g.22923873G>C	ENSP00000166244:p.Glu612Gln	Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	238	120	0.504202	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	37	CCDS225.1	217	0.09935897435897435	45	0.09146341463414634	35	0.09668508287292818	60	0.1048951048951049	77	0.10158311345646438	G	13.65	2.301585	0.40694	0.105992	0.104651	ENSG00000070886	ENST00000166244	T	0.11277	2.79	4.63	4.63	0.57726	Protein kinase-like domain (1);	0.061308	0.64402	D	0.000007	T	0.00210	0.0006	N	0.22421	0.69	0.09310	P	1.0	B	0.27559	0.181	B	0.29267	0.1	T	0.26326	-1.0106	9	0.87932	D	0	.	16.2101	0.82150	0.0:0.0:1.0:0.0	rs999765;rs16827315;rs999765	612	P29322	EPHA8_HUMAN	Q	612	ENSP00000166244:E612Q	ENSP00000166244:E612Q	E	+	1	0	EPHA8	22796460	1.000000	0.71417	0.462000	0.27118	0.061000	0.15899	7.803000	0.85983	2.412000	0.81896	0.491000	0.48974	GAA	G|0.893;C|0.107	0.107	strong		0.647	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
EPHA6	285220	hgsc.bcm.edu	37	3	97194242	97194242	+	Silent	SNP	C	C	T	rs16838751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:97194242C>T	ENST00000514100.1	+	5	359	c.117C>T	c.(115-117)acC>acT	p.T39T	EPHA6_ENST00000442602.2_Silent_p.T13T|EPHA6_ENST00000502694.1_Silent_p.T39T|EPHA6_ENST00000389672.5_Silent_p.T647T	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	553	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						TGATAGCCACCGCCGCTGTTG	0.418													C|||	1054	0.210463	0.4327	0.2695	5008	,	,		17156	0.0992		0.0885	False		,,,				2504	0.1084				p.T647T		Atlas-SNP	.											.	EPHA6	439	.	0			c.C1941T						PASS	.	C	,	1407,2405		270,867,769	78.0	80.0	79.0		1941,117	-9.1	0.4	3	dbSNP_123	79	749,7499		29,691,3404	no	coding-synonymous,coding-synonymous	EPHA6	NM_001080448.2,NM_173655.2	,	299,1558,4173	TT,TC,CC		9.081,36.9098,17.8773	,	647/1131,39/335	97194242	2156,9904	1906	4124	6030	SO:0001819	synonymous_variant	285220	exon8			AGCCACCGCCGCT	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000514100.1:c.117C>T	3.37:g.97194242C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_001080448	D6RAL5	Silent	SNP	ENST00000514100.1	37																																																																																				C|0.804;T|0.196	0.196	strong		0.418	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448	
COL6A6	131873	hgsc.bcm.edu	37	3	130380710	130380710	+	Silent	SNP	C	C	T	rs201325545	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:130380710C>T	ENST00000358511.6	+	34	6091	c.6060C>T	c.(6058-6060)ttC>ttT	p.F2020F	COL6A6_ENST00000453409.2_Silent_p.F2020F	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	2020	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CCCCCGACTTCCTACCCAACA	0.512													C|||	2	0.000399361	0.0	0.0	5008	,	,		18044	0.0		0.0	False		,,,				2504	0.002				p.F2020F		Atlas-SNP	.											.	COL6A6	497	.	0			c.C6060T						PASS	.	C		1,3759		0,1,1879	56.0	54.0	55.0		6060	4.1	1.0	3		55	10,8210		0,10,4100	no	coding-synonymous	COL6A6	NM_001102608.1		0,11,5979	TT,TC,CC		0.1217,0.0266,0.0918		2020/2264	130380710	11,11969	1880	4110	5990	SO:0001819	synonymous_variant	131873	exon34			CGACTTCCTACCC	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.6060C>T	3.37:g.130380710C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	141	58	0.411348	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																			C|0.996;T|0.004	0.004	strong		0.512	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
TAOK2	9344	hgsc.bcm.edu	37	16	29989416	29989416	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:29989416G>A	ENST00000308893.4	+	3	1182	c.139G>A	c.(139-141)Gat>Aat	p.D47N	TAOK2_ENST00000279394.3_Missense_Mutation_p.D47N|TAOK2_ENST00000416441.2_5'Flank|TAOK2_ENST00000543033.1_Missense_Mutation_p.D47N	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	47	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						CTAGGCCCGGGATGTCCGGAA	0.577																																					p.D47N		Atlas-SNP	.											TAOK2_ENST00000308893,NS,carcinoma,0,2	TAOK2	142	2	0			c.G139A						scavenged	.						90.0	75.0	80.0					16																	29989416		2197	4300	6497	SO:0001583	missense	9344	exon3			GCCCGGGATGTCC	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.139G>A	16.37:g.29989416G>A	ENSP00000310094:p.Asp47Asn	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	142	4	0.028169	NM_004783	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Missense_Mutation	SNP	ENST00000308893.4	37	CCDS10663.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.582620	0.65992	.	.	ENSG00000149930	ENST00000416441;ENST00000308893;ENST00000543033;ENST00000279394	T;T;T	0.65178	-0.14;-0.14;-0.14	5.33	5.33	0.75918	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.58018	0.2093	N	0.21097	0.63	0.80722	D	1	B;B;B;B	0.30686	0.174;0.161;0.077;0.29	B;B;B;B	0.42593	0.228;0.117;0.115;0.392	T	0.53415	-0.8442	9	.	.	.	.	17.7937	0.88562	0.0:0.0:1.0:0.0	.	231;47;47;47	Q86V37;Q9UL54-2;A0PJ48;Q9UL54	.;.;.;TAOK2_HUMAN	N	47	ENSP00000310094:D47N;ENSP00000440336:D47N;ENSP00000279394:D47N	.	D	+	1	0	TAOK2	29896917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.649000	0.83500	2.497000	0.84241	0.561000	0.74099	GAT	.	.	none		0.577	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151	
HELZ	9931	hgsc.bcm.edu	37	17	65104666	65104666	+	Silent	SNP	T	T	G	rs11657929	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:65104666T>G	ENST00000358691.5	-	30	4832	c.4666A>C	c.(4666-4668)Agg>Cgg	p.R1556R	HELZ_ENST00000580168.1_Silent_p.R1557R	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1556						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					CAGTCTGCCCTCACTGGCGGC	0.577													G|||	3599	0.71865	0.7761	0.6239	5008	,	,		17114	0.881		0.5189	False		,,,				2504	0.7464				p.R1556R		Atlas-SNP	.											.	HELZ	160	.	0			c.A4666C						PASS	.	G		3044,1158		1115,814,172	68.0	82.0	77.0		4666	3.0	1.0	17	dbSNP_120	77	4093,4377		999,2095,1141	no	coding-synonymous	HELZ	NM_014877.3		2114,2909,1313	GG,GT,TT		48.3235,27.5583,43.679		1556/1943	65104666	7137,5535	2101	4235	6336	SO:0001819	synonymous_variant	9931	exon30			CTGCCCTCACTGG	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.4666A>C	17.37:g.65104666T>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_014877	I6L9H4	Silent	SNP	ENST00000358691.5	37	CCDS42374.1																																																																																			T|0.382;G|0.618	0.618	strong		0.577	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	
MUC16	94025	hgsc.bcm.edu	37	19	9075346	9075346	+	Missense_Mutation	SNP	T	T	A	rs2591592	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9075346T>A	ENST00000397910.4	-	3	12303	c.12100A>T	c.(12100-12102)Att>Ttt	p.I4034F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4036	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAAGAGATAATACTTGTTTGT	0.473													t|||	2195	0.438299	0.4115	0.4683	5008	,	,		21847	0.2579		0.5755	False		,,,				2504	0.498				p.I4034F		Atlas-SNP	.											.	MUC16	4315	.	0			c.A12100T						PASS	.	T	PHE/ILE	1807,2223		407,993,615	119.0	113.0	115.0		12100	-1.0	0.0	19	dbSNP_100	115	4917,3395		1445,2027,684	yes	missense	MUC16	NM_024690.2	21	1852,3020,1299	AA,AT,TT		40.8446,44.8387,45.5194	probably-damaging	4034/14508	9075346	6724,5618	2015	4156	6171	SO:0001583	missense	94025	exon3			AGATAATACTTGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.12100A>T	19.37:g.9075346T>A	ENSP00000381008:p.Ile4034Phe	Somatic	295	1	0.00338983		WXS	Illumina HiSeq	Phase_I	256	255	0.996094	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	936	0.42857142857142855	194	0.3943089430894309	180	0.4972375690607735	127	0.22202797202797203	435	0.5738786279683378	-	5.432	0.264864	0.10294	0.448387	0.591554	ENSG00000181143	ENST00000397910	T	0.02709	4.19	2.33	-1.05	0.10036	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	.	.	.	D	0.59767	0.986	P	0.53912	0.737	T	0.43605	-0.9381	8	0.87932	D	0	.	2.0719	0.03615	0.2508:0.3189:0.0:0.4302	rs2591592;rs52799163;rs2591592	4034	B5ME49	.	F	4034	ENSP00000381008:I4034F	ENSP00000381008:I4034F	I	-	1	0	MUC16	8936346	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.602000	0.05680	-0.363000	0.08101	0.260000	0.18958	ATT	T|0.558;A|0.442	0.442	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
STEAP1B	256227	hgsc.bcm.edu	37	7	22532986	22532986	+	Missense_Mutation	SNP	C	C	A	rs16881812	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:22532986C>A	ENST00000406890.2	-	3	591	c.497G>T	c.(496-498)aGg>aTg	p.R166M	STEAP1B_ENST00000404369.4_Missense_Mutation_p.R185M	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	166			R -> M (in dbSNP:rs16881812).			integral component of membrane (GO:0016021)		p.R166M(1)|p.R185M(1)		endometrium(1)|kidney(1)|lung(2)	4						GTAGGATCGCCTCATTGCGTA	0.378													c|||	302	0.0603035	0.1309	0.0519	5008	,	,		19663	0.0		0.0666	False		,,,				2504	0.0266				p.R185M		Atlas-SNP	.											STEAP1B,NS,carcinoma,0,2	STEAP1B	22	2	2	Substitution - Missense(2)	endometrium(2)	c.G554T						scavenged	.	C	MET/ARG,MET/ARG	186,1198		15,156,521	131.0	105.0	113.0		554,497	1.2	1.0	7	dbSNP_123	113	290,2892		14,262,1315	no	missense,missense	STEAP1B	NM_001164460.1,NM_207342.2	91,91	29,418,1836	AA,AC,CC		9.1138,13.4393,10.4249	probably-damaging,probably-damaging	185/343,166/246	22532986	476,4090	692	1591	2283	SO:0001583	missense	256227	exon3			GATCGCCTCATTG		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.497G>T	7.37:g.22532986C>A	ENSP00000385239:p.Arg166Met	Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	222	91	0.40991	NM_001164460	B5MCI2	Missense_Mutation	SNP	ENST00000406890.2	37	CCDS55094.1	128	0.05860805860805861	60	0.12195121951219512	17	0.04696132596685083	0	0.0	51	0.06728232189973615	c	11.87	1.768335	0.31320	0.134393	0.091138	ENSG00000105889	ENST00000406890;ENST00000404369;ENST00000424363;ENST00000439708	D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91	1.23	1.23	0.21249	Flavoprotein transmembrane component (1);	0.000000	0.47852	U	0.000220	T	0.22360	0.0539	M	0.80332	2.49	0.33646	P	0.392123	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.67027	-0.5774	9	0.87932	D	0	-15.5027	8.5117	0.33222	0.0:1.0:0.0:0.0	rs16881812;rs16881812	185;166	B5MCI2;Q6NZ63	.;STEAL_HUMAN	M	166;185;185;185	ENSP00000385239:R166M;ENSP00000384370:R185M;ENSP00000416608:R185M;ENSP00000408954:R185M	ENSP00000384370:R185M	R	-	2	0	STEAP1B	22499511	1.000000	0.71417	0.995000	0.50966	0.185000	0.23345	5.802000	0.69122	1.022000	0.39626	0.121000	0.15741	AGG	C|0.933;A|0.067	0.067	strong		0.378	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		
MANBA	4126	hgsc.bcm.edu	37	4	103555992	103555992	+	Silent	SNP	A	A	G	rs2272697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:103555992A>G	ENST00000226578.4	-	16	2467	c.2368T>C	c.(2368-2370)Ttg>Ctg	p.L790L	MANBA_ENST00000505239.1_Silent_p.L733L	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	790					cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)	p.L790L(1)		cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		GGTGAGGACAAGAAGTGGTAG	0.567													G|||	2753	0.54972	0.6619	0.6542	5008	,	,		19905	0.5198		0.493	False		,,,				2504	0.4131				p.L790L		Atlas-SNP	.											MANBA,NS,carcinoma,0,2	MANBA	78	2	1	Substitution - coding silent(1)	prostate(1)	c.T2368C						PASS	.	G		2720,1686	511.1+/-367.7	851,1018,334	87.0	79.0	82.0		2368	3.7	1.0	4	dbSNP_100	82	4413,4187	568.4+/-389.0	1120,2173,1007	no	coding-synonymous	MANBA	NM_005908.3		1971,3191,1341	GG,GA,AA		48.686,38.266,45.1561		790/880	103555992	7133,5873	2203	4300	6503	SO:0001819	synonymous_variant	4126	exon16			AGGACAAGAAGTG		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.2368T>C	4.37:g.103555992A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_005908	Q96BC3|Q9NYX9	Silent	SNP	ENST00000226578.4	37	CCDS3658.1																																																																																			A|0.447;G|0.553	0.553	strong		0.567	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
BBS12	166379	hgsc.bcm.edu	37	4	123664919	123664919	+	Silent	SNP	A	A	G	rs13102440	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:123664919A>G	ENST00000314218.3	+	2	2065	c.1872A>G	c.(1870-1872)caA>caG	p.Q624Q	BBS12_ENST00000542236.1_Silent_p.Q624Q	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	624					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						ATCATCTGCAAAATGCCACAG	0.353									Bardet-Biedl syndrome				A|||	460	0.091853	0.0484	0.1052	5008	,	,		20993	0.0		0.2127	False		,,,				2504	0.1115				p.Q624Q		Atlas-SNP	.											.	BBS12	63	.	0			c.A1872G						PASS	.	A	,	289,4117	159.6+/-192.1	15,259,1929	85.0	82.0	83.0		1872,1872	-1.3	0.1	4	dbSNP_121	83	1940,6660	341.7+/-324.1	230,1480,2590	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	245,1739,4519	GG,GA,AA		22.5581,6.5592,17.1382	,	624/711,624/711	123664919	2229,10777	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TCTGCAAAATGCC	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1872A>G	4.37:g.123664919A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			A|0.856;G|0.144	0.144	strong		0.353	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
HIST1H4B	8366	hgsc.bcm.edu	37	6	26027433	26027433	+	Silent	SNP	G	G	A	rs3752419	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:26027433G>A	ENST00000377364.3	-	1	47	c.48C>T	c.(46-48)gcC>gcT	p.A16A		NM_003544.2	NP_003535.1	P62805	H4_HUMAN	histone cluster 1, H4b	16					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			large_intestine(4)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	13						GGTGACGCTTGGCACCTCCCT	0.542													G|||	1975	0.394369	0.1309	0.4524	5008	,	,		16190	0.7123		0.3956	False		,,,				2504	0.3804				p.A16A		Atlas-SNP	.											.	HIST1H4B	27	.	0			c.C48T						PASS	.	G		847,3559	333.6+/-303.0	82,683,1438	67.0	61.0	63.0		48	-9.1	0.1	6	dbSNP_107	63	3484,5116	509.7+/-377.3	735,2014,1551	no	coding-synonymous	HIST1H4B	NM_003544.2		817,2697,2989	AA,AG,GG		40.5116,19.2238,33.3		16/104	26027433	4331,8675	2203	4300	6503	SO:0001819	synonymous_variant	8366	exon1			ACGCTTGGCACCT	X67081	CCDS4572.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124529	ENSG00000278705		"""Histones / Replication-dependent"""	4789	protein-coding gene	gene with protein product		602829	"""H4 histone family, member I"", ""histone 1, H4b"""	H4FI		9119399, 12408966	Standard	NM_003544		Approved	H4/I	uc003nfr.3	P62805	OTTHUMG00000014417	ENST00000377364.3:c.48C>T	6.37:g.26027433G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	NM_003544	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377364.3	37	CCDS4572.1																																																																																			G|0.628;A|0.372	0.372	strong		0.542	HIST1H4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040079.2	NM_003544	
MICA	100507436	hgsc.bcm.edu	37	6	31382893	31382893	+	3'UTR	SNP	A	A	G	rs41545814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31382893A>G	ENST00000449934.2	+	0	1187				HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				TCTTGGGTCCACTGGCTCCAC	0.572													a|||	77	0.0153754	0.0182	0.0533	5008	,	,		14019	0.001		0.0149	False		,,,				2504	0.0				p.T377A		Atlas-SNP	.											.	MICA	21	.	0			c.A1129G						PASS	.	A		28,1356		1,26,665	146.0	135.0	138.0			-1.9	0.0	6	dbSNP_127	138	99,3083		4,91,1496	yes	utr-3	MICA	NM_001177519.1		5,117,2161	GG,GA,AA		3.1113,2.0231,2.7814			31382893	127,4439	692	1591	2283	SO:0001624	3_prime_UTR_variant	100507436	exon7			GGGTCCACTGGCT	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.*134A>G	6.37:g.31382893A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_000247		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			A|0.976;G|0.024	0.024	strong		0.572	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
PCDHGA4	56111	hgsc.bcm.edu	37	5	140735215	140735215	+	Missense_Mutation	SNP	G	G	A	rs11575949	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140735215G>A	ENST00000571252.1	+	1	448	c.448G>A	c.(448-450)Gca>Aca	p.A150T	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	150	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> T (in dbSNP:rs11575949).		homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAATCCTGGGGCAAGATTTCC	0.448													.|||	650	0.129792	0.3124	0.0692	5008	,	,		19460	0.0407		0.0875	False		,,,				2504	0.0613				p.A150T		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.G448A						PASS	.	A	,,,THR/ALA,,THR/ALA	1017,2739		127,763,988	67.0	69.0	68.0		,,,448,,448	2.1	0.9	5	dbSNP_120	68	741,7485		29,683,3401	yes	intron,intron,intron,missense,intron,missense	PCDHGB1,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018922.2,NM_032053.1	,,,58,,58	156,1446,4389	AA,AG,GG		9.008,27.0767,14.672	,,,,,	,,,150/932,,150/821	140735215	1758,10224	1878	4113	5991	SO:0001583	missense	56111	exon1			CCTGGGGCAAGAT	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.448G>A	5.37:g.140735215G>A	ENSP00000458570:p.Ala150Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			G|0.880;A|0.120	0.120	strong		0.448	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
CEP57	9702	hgsc.bcm.edu	37	11	95546138	95546138	+	Missense_Mutation	SNP	G	G	A	rs140149031		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:95546138G>A	ENST00000325542.5	+	3	483	c.245G>A	c.(244-246)cGc>cAc	p.R82H	CEP57_ENST00000538658.1_Missense_Mutation_p.R82H|CEP57_ENST00000541150.1_Missense_Mutation_p.R73H|CEP57_ENST00000325486.5_Missense_Mutation_p.R82H|CEP57_ENST00000536587.1_3'UTR|CEP57_ENST00000537677.1_Missense_Mutation_p.R55H	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	82	centrosome localization domain (CLD). {ECO:0000250}.				fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AAGATTCGACGCTTGGAACTT	0.373									Mosaic Variegated Aneuploidy Syndrome																												p.R82H		Atlas-SNP	.											CEP57,NS,carcinoma,+1,1	CEP57	40	1	0			c.G245A						scavenged	.	G	HIS/ARG	0,4402		0,0,2201	87.0	90.0	89.0		245	5.1	1.0	11	dbSNP_134	89	1,8595	1.2+/-3.3	0,1,4297	no	missense	CEP57	NM_014679.4	29	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	82/501	95546138	1,12997	2201	4298	6499	SO:0001583	missense	9702	exon3	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	TTCGACGCTTGGA	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.245G>A	11.37:g.95546138G>A	ENSP00000317902:p.Arg82His	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	171	2	0.0116959	NM_001243777	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Missense_Mutation	SNP	ENST00000325542.5	37	CCDS8304.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111143	0.77210	0.0	1.16E-4	ENSG00000166037	ENST00000537677;ENST00000325542;ENST00000325486;ENST00000544522;ENST00000541365;ENST00000538658;ENST00000541150	T;T;T;T;D;T;T	0.83506	0.61;0.61;0.61;0.61;-1.73;0.61;0.61	5.98	5.07	0.68467	.	0.155218	0.45867	D	0.000334	D	0.85327	0.5671	L	0.45137	1.4	0.35174	D	0.771824	D;D;D;D	0.71674	0.997;0.998;0.998;0.992	P;D;P;P	0.64144	0.847;0.922;0.905;0.759	D	0.88480	0.3068	10	0.87932	D	0	-6.3413	10.0787	0.42377	0.1966:0.0:0.8034:0.0	.	73;82;82;82	F5H5F7;Q86XR8-2;Q86XR8;Q86XR8-3	.;.;CEP57_HUMAN;.	H	55;82;82;73;55;82;73	ENSP00000441392:R55H;ENSP00000317902:R82H;ENSP00000317487:R82H;ENSP00000438065:R73H;ENSP00000445821:R55H;ENSP00000445706:R82H;ENSP00000443436:R73H	ENSP00000317487:R82H	R	+	2	0	CEP57	95185786	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.964000	0.40462	2.838000	0.97847	0.591000	0.81541	CGC	G|1.000;A|0.000	0.000	weak		0.373	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679	
SERPINA5	5104	hgsc.bcm.edu	37	14	95054176	95054176	+	Silent	SNP	T	T	C	rs6112	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:95054176T>C	ENST00000554866.1	+	2	591	c.477T>C	c.(475-477)ccT>ccC	p.P159P	SERPINA5_ENST00000553780.1_Silent_p.P159P|SERPINA5_ENST00000554276.1_Silent_p.P159P|SERPINA5_ENST00000329597.7_Silent_p.P159P			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	159					fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	ACACTTTCCCTACCAACTTTA	0.512													C|||	3095	0.618011	0.9486	0.4524	5008	,	,		20789	0.4087		0.6372	False		,,,				2504	0.4847				p.P159P		Atlas-SNP	.											.	SERPINA5	69	.	0			c.T477C						PASS	.	C		3954,452	218.1+/-236.3	1778,398,27	88.0	78.0	81.0		477	1.8	0.0	14	dbSNP_52	81	5701,2899	453.5+/-363.3	1882,1937,481	no	coding-synonymous	SERPINA5	NM_000624.4		3660,2335,508	CC,CT,TT		33.7093,10.2587,25.765		159/407	95054176	9655,3351	2203	4300	6503	SO:0001819	synonymous_variant	5104	exon3			TTTCCCTACCAAC	M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"""Serine (or cysteine) peptidase inhibitors"""	8723	protein-coding gene	gene with protein product		601841	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"""	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.477T>C	14.37:g.95054176T>C		Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	224	221	0.986607	NM_000624	Q07616|Q9UG30	Silent	SNP	ENST00000554866.1	37	CCDS9928.1																																																																																			T|0.312;C|0.688	0.688	strong		0.512	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
MUC5B	727897	hgsc.bcm.edu	37	11	1267502	1267502	+	Missense_Mutation	SNP	C	C	T	rs141653894	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1267502C>T	ENST00000529681.1	+	31	9450	c.9392C>T	c.(9391-9393)aCg>aTg	p.T3131M	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.T3134M	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3131	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACTCCGGGGACGACCTGGATC	0.657													c|||	133	0.0265575	0.003	0.062	5008	,	,		15581	0.003		0.0726	False		,,,				2504	0.0102				p.T3131M		Atlas-SNP	.											MUC5AC,mouth,carcinoma,-1,1	MUC5B	473	1	0			c.C9392T						PASS	.	C	MET/THR	43,4095		1,41,2027	74.0	97.0	89.0		9392	1.6	0.0	11	dbSNP_134	89	477,7895		26,425,3735	no	missense	MUC5B	NM_002458.2	81	27,466,5762	TT,TC,CC		5.6976,1.0391,4.1567	probably-damaging	3131/5763	1267502	520,11990	2069	4186	6255	SO:0001583	missense	727897	exon31			CGGGGACGACCTG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.9392C>T	11.37:g.1267502C>T	ENSP00000436812:p.Thr3131Met	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	238	119	0.5	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	80	0.03663003663003663	2	0.0040650406504065045	30	0.08287292817679558	1	0.0017482517482517483	47	0.06200527704485488	c	5.268	0.234962	0.09969	0.010391	0.056976	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000538459	T;T	0.20332	2.08;2.26	1.56	1.56	0.23342	.	.	.	.	.	T	0.01558	0.0050	L	0.34521	1.04	0.80722	P	0.0	D;D	0.89917	1.0;1.0	D;D	0.68943	0.912;0.961	T	0.10382	-1.0632	8	0.87932	D	0	.	7.4725	0.27357	0.0:0.7277:0.2723:0.0	.	3714;3134	A7Y9J9;E9PBJ0	.;.	M	3131;3134;3103;3091;21	ENSP00000436812:T3131M;ENSP00000415793:T3134M	ENSP00000343037:T3103M	T	+	2	0	MUC5B	1224078	0.000000	0.05858	0.004000	0.12327	0.039000	0.13416	0.370000	0.20433	1.204000	0.43247	0.186000	0.17326	ACG	C|0.962;T|0.038	0.038	strong		0.657	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
DGKE	8526	hgsc.bcm.edu	37	17	54940127	54940127	+	Missense_Mutation	SNP	A	A	G	rs61751972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:54940127A>G	ENST00000284061.3	+	12	1859	c.1679A>G	c.(1678-1680)cAa>cGa	p.Q560R		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	560					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					ACTTCGGATCAAGAAGATATA	0.393													A|||	4	0.000798722	0.0	0.0	5008	,	,		18984	0.0		0.004	False		,,,				2504	0.0				p.Q560R		Atlas-SNP	.											.	DGKE	47	.	0			c.A1679G						PASS	.	A	ARG/GLN	2,4404	4.2+/-10.8	0,2,2201	77.0	70.0	72.0		1679	0.8	1.0	17	dbSNP_129	72	21,8579	16.0+/-53.3	0,21,4279	yes	missense	DGKE	NM_003647.2	43	0,23,6480	GG,GA,AA		0.2442,0.0454,0.1768	benign	560/568	54940127	23,12983	2203	4300	6503	SO:0001583	missense	8526	exon12			CGGATCAAGAAGA	U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"""diacylglycerol kinase, epsilon (64kD)"""			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.1679A>G	17.37:g.54940127A>G	ENSP00000284061:p.Gln560Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_003647	Q8TBM4|Q9UKQ3	Missense_Mutation	SNP	ENST00000284061.3	37	CCDS11590.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	15.11	2.734675	0.48939	4.54E-4	0.002442	ENSG00000153933	ENST00000284061	T	0.16897	2.31	5.92	0.807	0.18714	.	0.762462	0.13392	N	0.391343	T	0.13114	0.0318	L	0.36672	1.1	0.80722	D	1	B	0.19583	0.037	B	0.19391	0.025	T	0.10753	-1.0616	10	0.27082	T	0.32	.	10.1281	0.42663	0.5593:0.3798:0.061:0.0	rs61751972	560	P52429	DGKE_HUMAN	R	560	ENSP00000284061:Q560R	ENSP00000284061:Q560R	Q	+	2	0	DGKE	52295126	0.990000	0.36364	0.996000	0.52242	0.993000	0.82548	1.290000	0.33319	0.120000	0.18254	0.524000	0.50904	CAA	A|0.998;G|0.002	0.002	strong		0.393	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647	
MEP1A	4224	hgsc.bcm.edu	37	6	46793175	46793175	+	Silent	SNP	G	G	A	rs6920863	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46793175G>A	ENST00000230588.4	+	8	732	c.723G>A	c.(721-723)caG>caA	p.Q241Q		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	241	Metalloprotease.				digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			TTATCGGACAGCGCCTGGATT	0.443													G|||	1995	0.398363	0.5272	0.428	5008	,	,		15507	0.2153		0.3777	False		,,,				2504	0.4131				p.Q241Q		Atlas-SNP	.											.	MEP1A	93	.	0			c.G723A						PASS	.	G		2223,2183	589.9+/-387.2	551,1121,531	131.0	116.0	121.0		723	0.7	1.0	6	dbSNP_116	121	3417,5183	504.6+/-376.2	686,2045,1569	no	coding-synonymous	MEP1A	NM_005588.2		1237,3166,2100	AA,AG,GG		39.7326,49.5461,43.3646		241/747	46793175	5640,7366	2203	4300	6503	SO:0001819	synonymous_variant	4224	exon8			CGGACAGCGCCTG		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.723G>A	6.37:g.46793175G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	234	111	0.474359	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Silent	SNP	ENST00000230588.4	37	CCDS4918.1																																																																																			G|0.598;A|0.402	0.402	strong		0.443	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588	
RALGAPB	57148	hgsc.bcm.edu	37	20	37203571	37203571	+	Silent	SNP	A	A	G	rs143567036	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:37203571A>G	ENST00000262879.6	+	30	4730	c.4446A>G	c.(4444-4446)tcA>tcG	p.S1482S	RALGAPB_ENST00000490114.1_3'UTR|RALGAPB_ENST00000397042.3_Silent_p.S1479S|RALGAPB_ENST00000397038.1_Silent_p.S1261S|RALGAPB_ENST00000397040.1_Silent_p.S1482S			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1482					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TTTATACTTCACTTTTCCAGG	0.463																																					p.S1482S		Atlas-SNP	.											.	RALGAPB	134	.	0			c.A4446G						PASS	.	A		0,4406		0,0,2203	84.0	89.0	87.0		4446	2.4	1.0	20	dbSNP_134	87	3,8597	4.3+/-15.6	0,3,4297	no	coding-synonymous	RALGAPB	NM_020336.2		0,3,6500	GG,GA,AA		0.0349,0.0,0.0231		1482/1495	37203571	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	57148	exon30			TACTTCACTTTTC	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.4446A>G	20.37:g.37203571A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	144	57	0.395833	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Silent	SNP	ENST00000262879.6	37	CCDS13305.1																																																																																			A|0.999;G|0.001	0.001	strong		0.463	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
ACIN1	22985	hgsc.bcm.edu	37	14	23549785	23549785	+	Missense_Mutation	SNP	T	T	C	rs3811182	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23549785T>C	ENST00000262710.1	-	6	1260	c.933A>G	c.(931-933)atA>atG	p.I311M	ACIN1_ENST00000555053.1_Missense_Mutation_p.I311M|ACIN1_ENST00000457657.1_Missense_Mutation_p.I271M|ACIN1_ENST00000605057.1_Missense_Mutation_p.I253M|ACIN1_ENST00000555352.1_5'Flank	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	311	Glu-rich.		I -> M (in dbSNP:rs3811182).		apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		TTACTCTAGGTATCTCTTCCC	0.458													C|||	2508	0.500799	0.6914	0.3689	5008	,	,		20323	0.4554		0.3777	False		,,,				2504	0.5102				p.I311M		Atlas-SNP	.											.	ACIN1	147	.	0			c.A933G						PASS	.	C	MET/ILE,MET/ILE,MET/ILE	2869,1537	486.4+/-360.6	935,999,269	245.0	214.0	224.0		933,813,933	0.1	0.0	14	dbSNP_107	224	3543,5057	630.5+/-398.4	721,2101,1478	yes	missense,missense,missense	ACIN1	NM_001164814.1,NM_001164815.1,NM_014977.3	10,10,10	1656,3100,1747	CC,CT,TT		41.1977,34.8842,49.3003	benign,benign,benign	311/1329,271/1302,311/1342	23549785	6412,6594	2203	4300	6503	SO:0001583	missense	22985	exon6			TCTAGGTATCTCT	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.933A>G	14.37:g.23549785T>C	ENSP00000262710:p.Ile311Met	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	323	322	0.996904	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	989	0.45283882783882784	320	0.6504065040650406	136	0.3756906077348066	259	0.4527972027972028	274	0.36147757255936674	C	0.001	-3.379418	0.00015	0.651158	0.411977	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.16457	2.34;2.34;2.34	4.16	0.113	0.14631	.	0.806596	0.10782	N	0.634812	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.25433	-1.0132	9	0.32370	T	0.25	3.4746	3.2091	0.06676	0.2982:0.3234:0.0:0.3784	rs3811182;rs57721090;rs3811182	311;311	G3V3M7;Q9UKV3	.;ACINU_HUMAN	M	311;271;311	ENSP00000262710:I311M;ENSP00000405677:I271M;ENSP00000451328:I311M	ENSP00000262710:I311M	I	-	3	3	ACIN1	22619625	0.000000	0.05858	0.000000	0.03702	0.185000	0.23345	-3.042000	0.00632	-0.194000	0.10399	-2.211000	0.00300	ATA	T|0.512;C|0.488	0.488	strong		0.458	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
PKD1L2	114780	hgsc.bcm.edu	37	16	81248716	81248716	+	RNA	SNP	C	C	T	rs12933806	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81248716C>T	ENST00000525539.1	-	0	546				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CGCCCGTAGACGGCATCCTGG	0.642											OREG0023964	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1122	0.224042	0.1641	0.1844	5008	,	,		16096	0.3423		0.1948	False		,,,				2504	0.2413				p.V183I		Atlas-SNP	.											.	PKD1L2	361	.	0			c.G547A						PASS	.	C	ILE/VAL,ILE/VAL	584,3354		48,488,1433	20.0	25.0	23.0		547,547	-9.5	0.0	16	dbSNP_121	23	1779,6497		178,1423,2537	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	29,29	226,1911,3970	TT,TC,CC		21.4959,14.8299,19.3467	benign,benign	183/992,183/2460	81248716	2363,9851	1969	4138	6107			114780	exon3			CGTAGACGGCATC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81248716C>T		Somatic	135	0	0	1204	WXS	Illumina HiSeq	Phase_I	133	133	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		497	0.22756410256410256	72	0.14634146341463414	67	0.1850828729281768	202	0.3531468531468531	156	0.20580474934036938	C	0.778	-0.763459	0.02996	0.148299	0.214959	ENSG00000166473	ENST00000337114	T	0.16897	2.31	4.77	-9.53	0.00575	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.554186	0.18461	N	0.140537	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.34900	-0.9810	8	0.21014	T	0.42	-0.1932	3.3061	0.07001	0.238:0.2075:0.0622:0.4924	rs12933806;rs58907852;rs12933806	183;183	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	I	183	ENSP00000337397:V183I	ENSP00000337397:V183I	V	-	1	0	PKD1L2	79806217	0.534000	0.26362	0.038000	0.18304	0.029000	0.11900	0.549000	0.23329	-1.943000	0.01039	-1.103000	0.02113	GTC	C|0.780;T|0.220	0.220	strong		0.642	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
BRWD1	54014	hgsc.bcm.edu	37	21	40670460	40670460	+	Missense_Mutation	SNP	G	G	C	rs2056844	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:40670460G>C	ENST00000333229.2	-	5	574	c.247C>G	c.(247-249)Cag>Gag	p.Q83E	BRWD1_ENST00000342449.3_Missense_Mutation_p.Q83E|BRWD1_ENST00000470108.1_5'UTR|BRWD1_ENST00000341322.4_Missense_Mutation_p.Q83E|BRWD1_ENST00000380800.3_Missense_Mutation_p.Q83E	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	83			Q -> E (in dbSNP:rs2056844). {ECO:0000269|Ref.3}.		cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				CCGATGCGCTGGCAGATTTGC	0.403													G|||	2396	0.478435	0.4342	0.5663	5008	,	,		17108	0.4355		0.4831	False		,,,				2504	0.5153				p.Q83E	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.C247G						PASS	.	G	GLU/GLN,GLU/GLN,GLU/GLN	1998,2408	559.6+/-380.3	444,1110,649	120.0	125.0	124.0		247,247,247	4.7	1.0	21	dbSNP_94	124	3949,4651	550.2+/-385.7	900,2149,1251	yes	missense,missense,missense	BRWD1	NM_001007246.2,NM_018963.4,NM_033656.3	29,29,29	1344,3259,1900	CC,CG,GG		45.9186,45.3473,45.725	benign,benign,benign	83/121,83/2321,83/2270	40670460	5947,7059	2203	4300	6503	SO:0001583	missense	54014	exon5			TGCGCTGGCAGAT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.247C>G	21.37:g.40670460G>C	ENSP00000330753:p.Gln83Glu	Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	297	141	0.474747	NM_001007246	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	1023	0.4684065934065934	203	0.41260162601626016	206	0.569060773480663	244	0.42657342657342656	370	0.48812664907651715	G	7.794	0.712263	0.15306	0.453473	0.459186	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800;ENST00000341322	T;T;T;T	0.21191	2.02;2.02;2.02;2.02	5.55	4.65	0.58169	.	0.180087	0.38548	N	0.001650	T	0.00012	0.0000	N	0.11341	0.13	0.41000	P	0.015075999999999978	B;P;B	0.35481	0.001;0.504;0.003	B;B;B	0.36534	0.001;0.227;0.002	T	0.25537	-1.0129	9	0.21014	T	0.42	-6.51	10.8709	0.46883	0.0:0.1187:0.6989:0.1824	rs2056844;rs3194833;rs17017337;rs52804097;rs2056844	83;83;83	Q6P2D1;Q9NSI6-2;Q9NSI6	.;.;BRWD1_HUMAN	E	83	ENSP00000330753:Q83E;ENSP00000344333:Q83E;ENSP00000370178:Q83E;ENSP00000342106:Q83E	ENSP00000330753:Q83E	Q	-	1	0	BRWD1	39592330	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.501000	0.53325	1.320000	0.45209	0.467000	0.42956	CAG	G|0.542;C|0.458	0.458	strong		0.403	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
OR2T12	127064	hgsc.bcm.edu	37	1	248458760	248458760	+	Missense_Mutation	SNP	C	C	A	rs12135684	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248458760C>A	ENST00000317996.1	-	1	120	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	41			A -> S (in dbSNP:rs12135684).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			ATCATGAGGGCATTGCTAAAC	0.517													-|||	1258	0.251198	0.1316	0.2651	5008	,	,		15579	0.3591		0.1849	False		,,,				2504	0.3599				p.A41S		Atlas-SNP	.											OR2T12,caecum,carcinoma,0,1	OR2T12	113	1	0			c.G121T						PASS	.	C	SER/ALA	581,3825	248.4+/-256.2	45,491,1667	108.0	96.0	100.0		121	-3.1	0.0	1	dbSNP_120	100	1560,7040	288.6+/-298.9	144,1272,2884	yes	missense	OR2T12	NM_001004692.1	99	189,1763,4551	AA,AC,CC		18.1395,13.1866,16.4616	benign	41/321	248458760	2141,10865	2203	4300	6503	SO:0001583	missense	127064	exon1			TGAGGGCATTGCT	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.121G>T	1.37:g.248458760C>A	ENSP00000324583:p.Ala41Ser	Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	342	146	0.426901	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	523	0.23946886446886448	86	0.17479674796747968	86	0.23756906077348067	198	0.34615384615384615	153	0.20184696569920843	c	5.228	0.227590	0.09916	0.131866	0.181395	ENSG00000177201	ENST00000317996	T	0.00922	5.54	1.55	-3.09	0.05331	GPCR, rhodopsin-like superfamily (1);	0.508381	0.14656	U	0.306246	T	0.00012	0.0000	N	0.16066	0.365	0.80722	P	0.0	B	0.06786	0.001	B	0.12837	0.008	T	0.20306	-1.0279	9	0.09084	T	0.74	.	6.1685	0.20404	0.0:0.5253:0.3187:0.156	rs12135684	41	Q8NG77	O2T12_HUMAN	S	41	ENSP00000324583:A41S	ENSP00000324583:A41S	A	-	1	0	OR2T12	246525383	0.000000	0.05858	0.016000	0.15963	0.239000	0.25481	-7.823000	0.00029	-0.223000	0.09943	0.175000	0.17021	GCC	C|0.817;A|0.183	0.183	strong		0.517	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
MUC21	394263	hgsc.bcm.edu	37	6	30954347	30954347	+	Missense_Mutation	SNP	C	C	T	rs144625089		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954347C>T	ENST00000376296.3	+	2	636	c.395C>T	c.(394-396)gCc>gTc	p.A132V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	132	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A132V(2)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGTGGGGCCAGCACAGCC	0.612																																					p.A132V		Atlas-SNP	.											MUC21,colon,carcinoma,0,2	MUC21	98	2	2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	c.C395T						PASS	.						164.0	154.0	157.0					6																	30954347		2203	4300	6503	SO:0001583	missense	394263	exon2			GTGGGGCCAGCAC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.395C>T	6.37:g.30954347C>T	ENSP00000365473:p.Ala132Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	142	10	0.0704225	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	C	10.74	1.435486	0.25813	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.04119	3.7	3.01	2.1	0.27182	.	.	.	.	.	T	0.00784	0.0026	N	0.08118	0	0.09310	N	1	B	0.20988	0.05	B	0.20767	0.031	T	0.47598	-0.9105	8	.	.	.	.	7.2947	0.26387	0.2628:0.7372:0.0:0.0	.	132	Q5SSG8	MUC21_HUMAN	V	132	ENSP00000365473:A132V	.	A	+	2	0	MUC21	31062326	0.000000	0.05858	0.003000	0.11579	0.140000	0.21249	0.351000	0.20096	0.799000	0.34018	0.485000	0.47835	GCC	C|0.999;T|0.001	0.001	weak		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
POLQ	10721	hgsc.bcm.edu	37	3	121252048	121252048	+	Missense_Mutation	SNP	T	T	G	rs73179915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121252048T>G	ENST00000264233.5	-	6	877	c.749A>C	c.(748-750)gAt>gCt	p.D250A	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	250	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		ACTGGCTAGATCTGCCTGACT	0.368								DNA polymerases (catalytic subunits)					T|||	3	0.000599042	0.0	0.0	5008	,	,		18003	0.0		0.003	False		,,,				2504	0.0				p.D250A	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A749C						PASS	.	T	ALA/ASP	1,4405	2.1+/-5.4	0,1,2202	78.0	77.0	77.0		749	1.6	0.9	3	dbSNP_130	77	19,8581	14.0+/-48.4	0,19,4281	yes	missense	POLQ	NM_199420.3	126	0,20,6483	GG,GT,TT		0.2209,0.0227,0.1538	benign	250/2591	121252048	20,12986	2203	4300	6503	SO:0001583	missense	10721	exon6			GCTAGATCTGCCT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.749A>C	3.37:g.121252048T>G	ENSP00000264233:p.Asp250Ala	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	139	65	0.467626	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	5.065	0.197617	0.09652	2.27E-4	0.002209	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.49139	0.79	5.3	1.56	0.23342	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	1.695750	0.02414	N	0.081944	T	0.29749	0.0743	N	0.11364	0.135	0.09310	N	1	B	0.21452	0.056	B	0.24394	0.053	T	0.20505	-1.0273	10	0.12103	T	0.63	.	8.008	0.30336	0.0:0.3139:0.0:0.6861	.	250	O75417	DPOLQ_HUMAN	A	250;385	ENSP00000264233:D250A	ENSP00000264233:D250A	D	-	2	0	POLQ	122734738	0.029000	0.19370	0.855000	0.33649	0.438000	0.31896	0.913000	0.28611	0.393000	0.25203	0.383000	0.25322	GAT	T|0.999;G|0.001	0.001	strong		0.368	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
CHRNG	1146	hgsc.bcm.edu	37	2	233410294	233410294	+	Silent	SNP	C	C	T	rs2099489	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233410294C>T	ENST00000389494.3	+	12	1443	c.1422C>T	c.(1420-1422)cgC>cgT	p.R474R	CHRNG_ENST00000389492.3_Silent_p.R422R	NM_005199.4	NP_005190.4	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma (muscle)	474					muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)			breast(2)|endometrium(3)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)	Galantamine(DB00674)	TGCTGGACCGCGTCTGCTTCC	0.647													C|||	761	0.151957	0.1051	0.134	5008	,	,		17988	0.1181		0.1928	False		,,,				2504	0.2209				p.R474R		Atlas-SNP	.											.	CHRNG	54	.	0			c.C1422T						PASS	.	C		551,3855	247.8+/-255.9	43,465,1695	111.0	81.0	91.0		1422	-9.1	0.8	2	dbSNP_96	91	1744,6856	318.2+/-313.6	182,1380,2738	no	coding-synonymous	CHRNG	NM_005199.4		225,1845,4433	TT,TC,CC		20.2791,12.5057,17.6457		474/518	233410294	2295,10711	2203	4300	6503	SO:0001819	synonymous_variant	1146	exon12			GGACCGCGTCTGC	X01715	CCDS33400.1	2q37.1	2012-10-02	2012-02-07		ENSG00000196811	ENSG00000196811		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1967	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, gamma (muscle)"""	100730	"""cholinergic receptor, nicotinic, gamma"""	ACHRG			Standard	NM_005199		Approved		uc002vsx.1	P07510	OTTHUMG00000153327	ENST00000389494.3:c.1422C>T	2.37:g.233410294C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_005199	B3KWM8|Q14DU4|Q53RG2	Silent	SNP	ENST00000389494.3	37	CCDS33400.1																																																																																			C|0.836;T|0.164	0.164	strong		0.647	CHRNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330743.1	NM_005199	
BMP3	651	hgsc.bcm.edu	37	4	81967240	81967240	+	Missense_Mutation	SNP	C	C	T	rs34505126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:81967240C>T	ENST00000282701.2	+	2	985	c.665C>T	c.(664-666)aCg>aTg	p.T222M		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	222			T -> M (in dbSNP:rs34505126).		cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						TTTAACATTACGTCCAAGGGA	0.433													C|||	125	0.0249601	0.0847	0.0115	5008	,	,		20614	0.0		0.001	False		,,,				2504	0.0041				p.T222M		Atlas-SNP	.											.	BMP3	59	.	0			c.C665T						PASS	.	C	MET/THR	273,4133	154.4+/-187.8	5,263,1935	115.0	123.0	120.0		665	5.1	0.3	4	dbSNP_126	120	6,8594	4.3+/-15.6	0,6,4294	yes	missense	BMP3	NM_001201.2	81	5,269,6229	TT,TC,CC		0.0698,6.1961,2.1452	probably-damaging	222/473	81967240	279,12727	2203	4300	6503	SO:0001583	missense	651	exon2			ACATTACGTCCAA	M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"""Bone morphogenetic proteins"""	1070	protein-coding gene	gene with protein product	"""osteogenin"""	112263	"""bone morphogenetic protein 3 (osteogenic)"""				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.665C>T	4.37:g.81967240C>T	ENSP00000282701:p.Thr222Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	43	0.019688644688644688	38	0.07723577235772358	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.519	1.107725	0.20714	0.061961	6.98E-4	ENSG00000152785	ENST00000282701	T	0.74632	-0.86	5.08	5.08	0.68730	.	0.361129	0.33610	N	0.004726	T	0.27349	0.0671	M	0.68952	2.095	0.09310	N	1	D	0.89917	1.0	D	0.69307	0.963	T	0.54866	-0.8229	10	0.56958	D	0.05	.	14.6465	0.68764	0.1459:0.8541:0.0:0.0	rs34505126;rs61679463	222	P12645	BMP3_HUMAN	M	222	ENSP00000282701:T222M	ENSP00000282701:T222M	T	+	2	0	BMP3	82186264	0.293000	0.24371	0.254000	0.24359	0.004000	0.04260	2.015000	0.40961	2.806000	0.96561	0.655000	0.94253	ACG	C|0.975;T|0.025	0.025	strong		0.433	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1		
NOL10	79954	hgsc.bcm.edu	37	2	10712278	10712278	+	Silent	SNP	C	C	T	rs3732114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:10712278C>T	ENST00000381685.5	-	21	2091	c.1986G>A	c.(1984-1986)ctG>ctA	p.L662L	NOL10_ENST00000538384.1_Silent_p.L636L|NOL10_ENST00000542668.1_Silent_p.L612L|NOL10_ENST00000345985.3_Silent_p.L612L	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	662						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		CTTGTCGATGCAGTTTCTCAG	0.443													C|||	1535	0.30651	0.5	0.3156	5008	,	,		19280	0.4335		0.1183	False		,,,				2504	0.1012				p.L662L		Atlas-SNP	.											.	NOL10	22	.	0			c.G1986A						PASS	.	C		2024,2382	563.2+/-381.1	482,1060,661	222.0	216.0	218.0		1986	4.0	1.0	2	dbSNP_107	218	955,7645	208.2+/-249.7	55,845,3400	no	coding-synonymous	NOL10	NM_024894.2		537,1905,4061	TT,TC,CC		11.1047,45.9374,22.9048		662/689	10712278	2979,10027	2203	4300	6503	SO:0001819	synonymous_variant	79954	exon21			TCGATGCAGTTTC	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1986G>A	2.37:g.10712278C>T		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	307	155	0.504886	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Silent	SNP	ENST00000381685.5	37	CCDS1673.2																																																																																			C|0.730;T|0.270	0.270	strong		0.443	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
OR51B4	79339	hgsc.bcm.edu	37	11	5322520	5322520	+	Silent	SNP	G	G	A	rs12283334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5322520G>A	ENST00000380224.1	-	1	706	c.657C>T	c.(655-657)ctC>ctT	p.L219L	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	219					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCACTGTCTTGAGGATTAGTA	0.373													G|||	986	0.196885	0.1354	0.2651	5008	,	,		21963	0.1458		0.2565	False		,,,				2504	0.2229				p.L219L		Atlas-SNP	.											.	OR51B4	64	.	0			c.C657T						PASS	.	G		631,3771	272.5+/-270.8	48,535,1618	72.0	69.0	70.0		657	-8.8	0.0	11	dbSNP_120	70	2408,6186	399.7+/-346.5	328,1752,2217	no	coding-synonymous	OR51B4	NM_033179.2		376,2287,3835	AA,AG,GG		28.0195,14.3344,23.3841		219/311	5322520	3039,9957	2201	4297	6498	SO:0001819	synonymous_variant	79339	exon1			TGTCTTGAGGATT	BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"""GPCR / Class A : Olfactory receptors"""	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.657C>T	11.37:g.5322520G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_033179	A7MAV5|Q6NTD7	Silent	SNP	ENST00000380224.1	37	CCDS7757.1																																																																																			G|0.775;A|0.225	0.225	strong		0.373	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179	
OR6C74	254783	hgsc.bcm.edu	37	12	55641920	55641920	+	Silent	SNP	G	G	A	rs73322883	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:55641920G>A	ENST00000343870.4	+	1	939	c.849G>A	c.(847-849)ttG>ttA	p.L283L		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	12						CCCCCATGTTGAATCCCTTTA	0.358													G|||	360	0.071885	0.1082	0.0375	5008	,	,		17899	0.0476		0.0318	False		,,,				2504	0.1135				p.L283L		Atlas-SNP	.											.	OR6C74	52	.	0			c.G849A						PASS	.	G		443,3961	192.6+/-218.0	25,393,1784	47.0	52.0	50.0		849	2.5	1.0	12	dbSNP_130	50	227,8369	89.9+/-152.1	0,227,4071	no	coding-synonymous	OR6C74	NM_001005490.1		25,620,5855	AA,AG,GG		2.6408,10.059,5.1538		283/313	55641920	670,12330	2202	4298	6500	SO:0001819	synonymous_variant	254783	exon1			CATGTTGAATCCC		CCDS31816.1	12q13.13	2012-08-09			ENSG00000197706	ENSG00000197706		"""GPCR / Class A : Olfactory receptors"""	31303	protein-coding gene	gene with protein product							Standard	NM_001005490		Approved		uc010spg.2	A6NCV1	OTTHUMG00000165162	ENST00000343870.4:c.849G>A	12.37:g.55641920G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	NM_001005490		Silent	SNP	ENST00000343870.4	37	CCDS31816.1																																																																																			G|0.949;A|0.051	0.051	strong		0.358	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1		
APOBR	55911	hgsc.bcm.edu	37	16	28508447	28508447	+	Silent	SNP	A	A	G	rs40831	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28508447A>G	ENST00000431282.1	+	3	2068	c.2058A>G	c.(2056-2058)gcA>gcG	p.A686A	CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000328423.5_Silent_p.A686A|APOBR_ENST00000564831.1_Silent_p.A695A|CLN3_ENST00000569430.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	686	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						AGGGAGAGGCATCTGTCTCAG	0.612													G|||	2463	0.491813	0.5605	0.5317	5008	,	,		16515	0.373		0.3678	False		,,,				2504	0.6207				p.A695A		Atlas-SNP	.											.	APOBR	89	.	0			c.A2085G						PASS	.	G		2138,2056		584,970,543	22.0	28.0	26.0		2058	0.4	0.0	16	dbSNP_76	26	3458,4958		747,1964,1497	no	coding-synonymous	APOBR	NM_018690.3		1331,2934,2040	GG,GA,AA		41.0884,49.0224,44.3775		686/1089	28508447	5596,7014	2097	4208	6305	SO:0001819	synonymous_variant	55911	exon2			AGAGGCATCTGTC	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.2058A>G	16.37:g.28508447A>G		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	37																																																																																				A|0.584;G|0.416	0.416	strong		0.612	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
HIVEP1	3096	hgsc.bcm.edu	37	6	12124855	12124855	+	Missense_Mutation	SNP	G	G	A	rs2228213	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:12124855G>A	ENST00000379388.2	+	4	5159	c.4827G>A	c.(4825-4827)atG>atA	p.M1609I	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1609			M -> I (in dbSNP:rs2228213). {ECO:0000269|PubMed:2108316}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.M1609I(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TTGACAGCATGTCTAATTCGC	0.458													G|||	1087	0.217053	0.0628	0.245	5008	,	,		22560	0.2232		0.333	False		,,,				2504	0.2802				p.M1609I		Atlas-SNP	.											HIVEP1,NS,carcinoma,0,1	HIVEP1	242	1	1	Substitution - Missense(1)	prostate(1)	c.G4827A						PASS	.	G	ILE/MET	375,3739		21,333,1703	127.0	127.0	127.0		4827	1.5	0.0	6	dbSNP_98	127	2879,5513		496,1887,1813	yes	missense	HIVEP1	NM_002114.2	10	517,2220,3516	AA,AG,GG		34.3065,9.1152,26.0195	benign	1609/2719	12124855	3254,9252	2057	4196	6253	SO:0001583	missense	3096	exon4			CAGCATGTCTAAT	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.4827G>A	6.37:g.12124855G>A	ENSP00000368698:p.Met1609Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	513	0.2348901098901099	42	0.08536585365853659	87	0.24033149171270718	134	0.23426573426573427	250	0.32981530343007914	G	8.067	0.769364	0.15983	0.091152	0.343065	ENSG00000095951	ENST00000379388	T	0.08282	3.11	5.77	1.51	0.23008	.	.	.	.	.	T	0.02848	0.0085	L	0.47716	1.5	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.36114	-0.9761	7	.	.	.	0.3363	12.2002	0.54321	0.2588:0.0:0.7412:0.0	rs2228213;rs3823451;rs17609202;rs52803833;rs58502243;rs2228213	1609	P15822	ZEP1_HUMAN	I	1609	ENSP00000368698:M1609I	.	M	+	3	0	HIVEP1	12232841	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.624000	0.24462	0.369000	0.24510	0.650000	0.86243	ATG	G|0.757;A|0.241	0.241	strong		0.458	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
IRX4	50805	hgsc.bcm.edu	37	5	1880891	1880891	+	Missense_Mutation	SNP	C	C	T	rs2232376	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1880891C>T	ENST00000505790.1	-	4	811	c.355G>A	c.(355-357)Gct>Act	p.A119T	IRX4_ENST00000505938.1_5'UTR|IRX4_ENST00000231357.2_Missense_Mutation_p.A119T|IRX4_ENST00000513692.1_Missense_Mutation_p.A119T	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	119			A -> T (in dbSNP:rs2232376). {ECO:0000269|PubMed:15489334}.		establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		TAGGCGGCAGCGGCTGGTGCC	0.632													C|||	687	0.137181	0.2156	0.1599	5008	,	,		13055	0.0139		0.2058	False		,,,				2504	0.0716				p.A119T		Atlas-SNP	.											IRX4,colon,carcinoma,0,1	IRX4	45	1	0			c.G355A						scavenged	.	C	THR/ALA	1014,3390	372.5+/-320.4	107,800,1295	71.0	75.0	74.0		355	4.0	0.0	5	dbSNP_98	74	1742,6858	315.1+/-312.1	175,1392,2733	yes	missense	IRX4	NM_016358.2	58	282,2192,4028	TT,TC,CC		20.2558,23.0245,21.1935	benign	119/520	1880891	2756,10248	2202	4300	6502	SO:0001583	missense	50805	exon3			CGGCAGCGGCTGG	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"""Homeoboxes / TALE class"""	6129	protein-coding gene	gene with protein product		606199	"""iroquois homeobox protein 4"""			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.355G>A	5.37:g.1880891C>T	ENSP00000423161:p.Ala119Thr	Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Missense_Mutation	SNP	ENST00000505790.1	37	CCDS3867.1	346	0.15842490842490842	112	0.22764227642276422	70	0.19337016574585636	10	0.017482517482517484	154	0.20316622691292877	C	6.313	0.425811	0.11987	0.230245	0.202558	ENSG00000113430	ENST00000231357;ENST00000505790;ENST00000513692;ENST00000511126	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.04	4.03	4.03	0.46877	.	0.359172	0.28332	N	0.015722	T	0.00012	0.0000	N	0.16478	0.41	0.29531	P	0.852752	P	0.37061	0.58	B	0.26310	0.068	T	0.10428	-1.0630	9	0.21014	T	0.42	-14.4145	14.9752	0.71267	0.0:1.0:0.0:0.0	rs2232376;rs60328712;rs2232376	119	P78413	IRX4_HUMAN	T	119	ENSP00000231357:A119T;ENSP00000423161:A119T;ENSP00000424235:A119T;ENSP00000421772:A119T	ENSP00000231357:A119T	A	-	1	0	IRX4	1933891	0.997000	0.39634	0.014000	0.15608	0.013000	0.08279	3.640000	0.54350	1.801000	0.52704	0.557000	0.71058	GCT	T|0.195;G|0.006	0.195	strong		0.632	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358	
MAN2A1	4124	hgsc.bcm.edu	37	5	109117171	109117171	+	Silent	SNP	A	A	G	rs13189822	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:109117171A>G	ENST00000261483.4	+	9	2501	c.1449A>G	c.(1447-1449)caA>caG	p.Q483Q		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	483					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		ACAAGGGCCAATCGATGTTCC	0.368													A|||	1396	0.278754	0.0575	0.2435	5008	,	,		15756	0.6151		0.1541	False		,,,				2504	0.3845				p.Q483Q		Atlas-SNP	.											.	MAN2A1	136	.	0			c.A1449G						PASS	.	A		316,4088	169.1+/-199.8	17,282,1903	130.0	124.0	126.0		1449	-3.0	0.0	5	dbSNP_121	126	1480,7120	281.2+/-294.9	137,1206,2957	no	coding-synonymous	MAN2A1	NM_002372.2		154,1488,4860	GG,GA,AA		17.2093,7.1753,13.8111		483/1145	109117171	1796,11208	2202	4300	6502	SO:0001819	synonymous_variant	4124	exon9			GGGCCAATCGATG		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.1449A>G	5.37:g.109117171A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_002372	Q16767	Silent	SNP	ENST00000261483.4	37	CCDS34209.1																																																																																			A|0.799;G|0.201	0.201	strong		0.368	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
HECW1	23072	hgsc.bcm.edu	37	7	43547692	43547692	+	Silent	SNP	G	G	A	rs17172219	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:43547692G>A	ENST00000395891.2	+	23	4433	c.3828G>A	c.(3826-3828)caG>caA	p.Q1276Q	AC011738.4_ENST00000436105.1_RNA|HECW1_ENST00000453890.1_Silent_p.Q1242Q	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1276	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						AAGAGCTCCAGCGAAACAAGC	0.547													G|||	20	0.00399361	0.0151	0.0	5008	,	,		20717	0.0		0.0	False		,,,				2504	0.0				p.Q1276Q		Atlas-SNP	.											.	HECW1	540	.	0			c.G3828A						PASS	.	G		74,3858		1,72,1893	76.0	78.0	77.0		3828	5.8	1.0	7	dbSNP_123	77	1,8287		0,1,4143	no	coding-synonymous	HECW1	NM_015052.3		1,73,6036	AA,AG,GG		0.0121,1.882,0.6137		1276/1607	43547692	75,12145	1966	4144	6110	SO:0001819	synonymous_variant	23072	exon23			GCTCCAGCGAAAC	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3828G>A	7.37:g.43547692G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	116	66	0.568965	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			G|0.995;A|0.005	0.005	strong		0.547	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
GAB2	9846	hgsc.bcm.edu	37	11	77930345	77930345	+	Silent	SNP	T	T	C	rs2450122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:77930345T>C	ENST00000361507.4	-	10	2089	c.2004A>G	c.(2002-2004)tcA>tcG	p.S668S	GAB2_ENST00000340149.2_Silent_p.S630S	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	668					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			TGGAAGGCTCTGAGGACTGCC	0.612													C|||	1325	0.264577	0.1989	0.3156	5008	,	,		19086	0.3978		0.1779	False		,,,				2504	0.2689				p.S668S		Atlas-SNP	.											.	GAB2	63	.	0			c.A2004G						PASS	.	C	,	794,3606	750.6+/-412.1	79,636,1485	112.0	93.0	100.0		1890,2004	-8.8	0.7	11	dbSNP_100	100	1387,7197	753.7+/-407.5	117,1153,3022	no	coding-synonymous,coding-synonymous	GAB2	NM_012296.3,NM_080491.2	,	196,1789,4507	CC,CT,TT		16.158,18.0455,16.7976	,	630/639,668/677	77930345	2181,10803	2200	4292	6492	SO:0001819	synonymous_variant	9846	exon10			AGGCTCTGAGGAC	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"""Pleckstrin homology (PH) domain containing"""	14458	protein-coding gene	gene with protein product	"""Grb2-associated binder 2"""	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.2004A>G	11.37:g.77930345T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Silent	SNP	ENST00000361507.4	37	CCDS8259.1																																																																																			T|0.789;C|0.211	0.211	strong		0.612	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491	
RANBP9	10048	hgsc.bcm.edu	37	6	13711279	13711279	+	Silent	SNP	A	A	G	rs6905991	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:13711279A>G	ENST00000011619.3	-	1	517	c.459T>C	c.(457-459)cgT>cgC	p.R153R		NM_005493.2	NP_005484.2	Q96S59	RANB9_HUMAN	RAN binding protein 9	153	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				axon guidance (GO:0007411)|microtubule nucleation (GO:0007020)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	16	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			CCGGGTAGAGACGCTTCAGCC	0.677													G|||	2173	0.433906	0.4796	0.4179	5008	,	,		7364	0.2847		0.4622	False		,,,				2504	0.5082				p.R153R		Atlas-SNP	.											RANBP9,NS,carcinoma,0,1	RANBP9	42	1	0			c.T459C						scavenged	.	G		1906,2464		464,978,743	12.0	14.0	13.0		459	2.6	1.0	6	dbSNP_116	13	3907,4663		916,2075,1294	no	coding-synonymous	RANBP9	NM_005493.2		1380,3053,2037	GG,GA,AA		45.5893,43.6156,44.9227		153/730	13711279	5813,7127	2185	4285	6470	SO:0001819	synonymous_variant	10048	exon1			GTAGAGACGCTTC	AB008515	CCDS4529.1	6p23	2010-05-25			ENSG00000010017	ENSG00000010017			13727	protein-coding gene	gene with protein product	"""Ran Binding Protein in the Microtubule organizing center"""	603854				9817760	Standard	NM_005493		Approved	RanBPM	uc003nbb.3	Q96S59	OTTHUMG00000015642	ENST00000011619.3:c.459T>C	6.37:g.13711279A>G		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	139	80	0.57554	NM_005493	A0PJA2|B2R8E1|O94764|Q6P3T7|Q7LBR2|Q7Z7F9	Silent	SNP	ENST00000011619.3	37	CCDS4529.1																																																																																			A|0.575;C|0.000;G|0.424;T|0.000	0.424	strong		0.677	RANBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042373.1		
ZSWIM2	151112	hgsc.bcm.edu	37	2	187697883	187697883	+	Missense_Mutation	SNP	A	A	G	rs10164815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:187697883A>G	ENST00000295131.2	-	7	944	c.905T>C	c.(904-906)aTt>aCt	p.I302T		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	302				I -> T (in Ref. 4; AAH31094). {ECO:0000305}.	apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			CTTTTCTTCAATCTCATTTTT	0.294													A|||	872	0.174121	0.4213	0.1066	5008	,	,		13175	0.0208		0.1113	False		,,,				2504	0.1104				p.I302T		Atlas-SNP	.											ZSWIM2,NS,carcinoma,-1,1	ZSWIM2	119	1	0			c.T905C						PASS	.	A	THR/ILE	1740,2658	500.1+/-364.6	342,1056,801	113.0	108.0	110.0		905	-4.1	0.1	2	dbSNP_119	110	970,7618	203.8+/-246.7	44,882,3368	yes	missense	ZSWIM2	NM_182521.2	89	386,1938,4169	GG,GA,AA		11.2948,39.5634,20.8686	benign	302/634	187697883	2710,10276	2199	4294	6493	SO:0001583	missense	151112	exon7			TCTTCAATCTCAT	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.905T>C	2.37:g.187697883A>G	ENSP00000295131:p.Ile302Thr	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	359	183	0.509749	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	326	0.14926739926739926	193	0.39227642276422764	41	0.1132596685082873	10	0.017482517482517484	82	0.10817941952506596	A	5.584	0.292590	0.10567	0.395634	0.112948	ENSG00000163012	ENST00000295131	T	0.22743	1.94	5.28	-4.09	0.03951	.	0.950517	0.08736	N	0.901379	T	0.00012	0.0000	L	0.31926	0.97	0.80722	P	0.0	B	0.10296	0.003	B	0.09377	0.004	T	0.47598	-0.9105	9	0.02654	T	1	0.2256	0.3454	0.00340	0.2072:0.265:0.1812:0.3466	rs10164815;rs17845944;rs17858925;rs52821540;rs59170533;rs10164815	302	Q8NEG5	ZSWM2_HUMAN	T	302	ENSP00000295131:I302T	ENSP00000295131:I302T	I	-	2	0	ZSWIM2	187406128	0.035000	0.19736	0.059000	0.19551	0.932000	0.56968	-0.045000	0.12003	-0.275000	0.09219	0.477000	0.44152	ATT	A|0.809;G|0.191	0.191	strong		0.294	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
ABTB1	80325	hgsc.bcm.edu	37	3	127395817	127395817	+	Silent	SNP	G	G	A	rs35834653	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:127395817G>A	ENST00000232744.8	+	7	620	c.534G>A	c.(532-534)ctG>ctA	p.L178L	ABTB1_ENST00000453791.2_Silent_p.L36L|ABTB1_ENST00000468137.1_Silent_p.L36L|ABTB1_ENST00000393363.3_Silent_p.L36L					ankyrin repeat and BTB (POZ) domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	10						CAGGCCGCCTGGACATTGGCG	0.642													G|||	97	0.019369	0.0008	0.0418	5008	,	,		19736	0.001		0.0596	False		,,,				2504	0.0061				p.L178L		Atlas-SNP	.											.	ABTB1	36	.	0			c.G534A						PASS	.	G	,	56,4350	50.9+/-86.3	0,56,2147	40.0	39.0	40.0		108,534	2.5	1.0	3	dbSNP_126	40	547,8053	149.5+/-204.6	15,517,3768	no	coding-synonymous,coding-synonymous	ABTB1	NM_032548.3,NM_172027.2	,	15,573,5915	AA,AG,GG		6.3605,1.271,4.6363	,	36/337,178/479	127395817	603,12403	2203	4300	6503	SO:0001819	synonymous_variant	80325	exon7			CCGCCTGGACATT	AB053324	CCDS3045.1, CCDS46901.1	3q21	2013-01-10			ENSG00000114626	ENSG00000114626		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	18275	protein-coding gene	gene with protein product		608308				10891360, 11494141	Standard	NM_172027		Approved	BPOZ, EF1ABP, Btb3, BTBD21	uc003ejt.3	Q969K4	OTTHUMG00000159636	ENST00000232744.8:c.534G>A	3.37:g.127395817G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_172027		Silent	SNP	ENST00000232744.8	37	CCDS3045.1																																																																																			G|0.962;A|0.038	0.038	strong		0.642	ABTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356595.1	NM_172027	
C6orf165	154313	hgsc.bcm.edu	37	6	88126423	88126423	+	Missense_Mutation	SNP	G	G	C	rs16879281	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:88126423G>C	ENST00000507897.1	+	6	592	c.509G>C	c.(508-510)gGg>gCg	p.G170A	C6ORF165_ENST00000369562.4_Missense_Mutation_p.G170A			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	170			G -> A (in dbSNP:rs16879281).							NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		GCAGAGCTTGGGACATTTCTA	0.348													G|||	507	0.101238	0.0862	0.0692	5008	,	,		16632	0.1042		0.1193	False		,,,				2504	0.1227				p.G170A		Atlas-SNP	.											.	C6orf165	116	.	0			c.G509C						PASS	.	G	ALA/GLY	442,3964	211.2+/-231.4	22,398,1783	73.0	73.0	73.0		509	2.9	0.7	6	dbSNP_123	73	943,7657	207.5+/-249.2	47,849,3404	yes	missense	C6orf165	NM_001031743.2	60	69,1247,5187	CC,CG,GG		10.9651,10.0318,10.6489	benign	170/623	88126423	1385,11621	2203	4300	6503	SO:0001583	missense	154313	exon6			AGCTTGGGACATT	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.509G>C	6.37:g.88126423G>C	ENSP00000426769:p.Gly170Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	212	0.09706959706959707	37	0.07520325203252033	29	0.08011049723756906	56	0.0979020979020979	90	0.11873350923482849	G	8.024	0.760261	0.15914	0.100318	0.109651	ENSG00000213204	ENST00000369562;ENST00000480123	T;T	0.28255	1.62;1.62	5.7	2.88	0.33553	.	0.336335	0.33895	N	0.004444	T	0.07458	0.0188	L	0.45051	1.395	0.30376	P	0.782449	B;B	0.27351	0.176;0.01	B;B	0.22601	0.04;0.025	T	0.24941	-1.0146	9	0.05833	T	0.94	.	10.5196	0.44912	0.0:0.34:0.4274:0.2326	rs16879281;rs52801747;rs16879281	170;170	Q8IYR0;E1P509	CF165_HUMAN;.	A	170	ENSP00000358575:G170A;ENSP00000422494:G170A	ENSP00000358575:G170A	G	+	2	0	C6orf165	88183142	0.948000	0.32251	0.744000	0.31058	0.781000	0.44180	1.409000	0.34680	0.291000	0.22468	0.655000	0.94253	GGG	G|0.903;C|0.097	0.097	strong		0.348	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823	
AGAP2	116986	hgsc.bcm.edu	37	12	58126234	58126234	+	Silent	SNP	C	C	A	rs17852479	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:58126234C>A	ENST00000547588.1	-	7	1745	c.1746G>T	c.(1744-1746)ctG>ctT	p.L582L	AGAP2_ENST00000257897.3_Silent_p.L246L	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	582					axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						GGGAGCTGGGCAGGGACTTGC	0.622													C|||	1080	0.215655	0.0401	0.3141	5008	,	,		17999	0.1379		0.4523	False		,,,				2504	0.2198				p.L582L		Atlas-SNP	.											AGAP2_ENST00000547588,NS,carcinoma,0,2	AGAP2	167	2	0			c.G1746T						PASS	.	C	,	438,3964		27,384,1790	26.0	22.0	23.0		1746,738	2.2	1.0	12	dbSNP_123	23	3695,4895		805,2085,1405	no	coding-synonymous,coding-synonymous	AGAP2	NM_001122772.2,NM_014770.3	,	832,2469,3195	AA,AC,CC		43.0151,9.95,31.8119	,	582/1193,246/837	58126234	4133,8859	2201	4295	6496	SO:0001819	synonymous_variant	116986	exon7			GCTGGGCAGGGAC	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16921	protein-coding gene	gene with protein product		605476	"""centaurin, gamma 1"""	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.1746G>T	12.37:g.58126234C>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	89	70	0.786517	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Silent	SNP	ENST00000547588.1	37	CCDS44932.1	533	0.24404761904761904	31	0.06300813008130081	128	0.35359116022099446	46	0.08041958041958042	328	0.43271767810026385	C	9.421	1.082920	0.20309	0.0995	0.430151	ENSG00000135439	ENST00000328568	.	.	.	5.06	2.19	0.27852	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47100	-0.9143	3	.	.	.	.	6.4328	0.21807	0.0:0.6607:0.1395:0.1998	rs17852479	.	.	.	S	446	.	.	A	-	1	0	AGAP2	56412501	0.972000	0.33761	1.000000	0.80357	0.999000	0.98932	0.103000	0.15292	0.256000	0.21614	0.655000	0.94253	GCC	A|0.274;C|0.726;G|0.000	0.274	strong		0.622	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770	
DSP	1832	hgsc.bcm.edu	37	6	7577260	7577260	+	Silent	SNP	C	C	T	rs2064217	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:7577260C>T	ENST00000379802.3	+	20	3203	c.2862C>T	c.(2860-2862)tgC>tgT	p.C954C	DSP_ENST00000418664.2_Silent_p.C954C	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	954	Globular 1.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.C954C(1)		biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		CTGAACTTTGCGCCAATTCAA	0.323													C|||	1378	0.27516	0.4039	0.2363	5008	,	,		18325	0.1915		0.2266	False		,,,				2504	0.2648				p.C954C		Atlas-SNP	.											DSP,NS,carcinoma,0,1	DSP	306	1	1	Substitution - coding silent(1)	stomach(1)	c.C2862T						PASS	.	C	,	1640,2766	502.2+/-365.2	310,1020,873	88.0	84.0	85.0		2862,2862	2.1	1.0	6	dbSNP_94	85	1856,6742	329.9+/-319.0	194,1468,2637	no	coding-synonymous,coding-synonymous	DSP	NM_001008844.1,NM_004415.2	,	504,2488,3510	TT,TC,CC		21.5864,37.222,26.884	,	954/2273,954/2872	7577260	3496,9508	2203	4299	6502	SO:0001819	synonymous_variant	1832	exon20			ACTTTGCGCCAAT	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.2862C>T	6.37:g.7577260C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	176	83	0.471591	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																			C|0.737;T|0.263	0.263	strong		0.323	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
BLM	641	hgsc.bcm.edu	37	15	91341535	91341535	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91341535T>A	ENST00000355112.3	+	17	3444	c.3326T>A	c.(3325-3327)tTt>tAt	p.F1109Y	BLM_ENST00000560509.1_Missense_Mutation_p.F1109Y|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1109					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TCTGGAAGATTTACTATGAAT	0.313			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.F1109Y		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.T3326A						PASS	.						131.0	131.0	131.0					15																	91341535		2198	4296	6494	SO:0001583	missense	641	exon17	Familial Cancer Database		GAAGATTTACTAT	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3326T>A	15.37:g.91341535T>A	ENSP00000347232:p.Phe1109Tyr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	137	48	0.350365	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	37	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	T	14.42	2.529829	0.45073	.	.	ENSG00000197299	ENST00000355112;ENST00000536925;ENST00000543977	T	0.51325	0.71	5.36	5.36	0.76844	RQC domain (2);	0.134612	0.52532	D	0.000066	T	0.37758	0.1015	N	0.25380	0.74	0.31109	N	0.710145	B;B	0.24882	0.113;0.113	B;B	0.30401	0.115;0.115	T	0.42464	-0.9450	10	0.33141	T	0.24	-20.8792	13.2993	0.60315	0.0:0.0:0.0:1.0	.	1109;1109	B2RAN0;P54132	.;BLM_HUMAN	Y	1109;739;296	ENSP00000347232:F1109Y	ENSP00000347232:F1109Y	F	+	2	0	BLM	89142539	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.846000	0.62860	2.037000	0.60232	0.477000	0.44152	TTT	.	.	none		0.313	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
HDAC6	10013	hgsc.bcm.edu	37	X	48681187	48681187	+	Missense_Mutation	SNP	G	G	A	rs61735967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:48681187G>A	ENST00000334136.5	+	24	2673	c.2495G>A	c.(2494-2496)cGc>cAc	p.R832H	HDAC6_ENST00000376619.2_Missense_Mutation_p.R832H|HDAC6_ENST00000444343.2_Missense_Mutation_p.R846H			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	832					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	AGATACTGGCGCAGCTTACGG	0.622													G|||	31	0.00821192	0.0	0.0072	3775	,	,		13125	0.0		0.0229	False		,,,				2504	0.0031				p.R832H	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.G2495A						PASS	.	G	HIS/ARG	20,3815		0,16,4,1616,567	37.0	34.0	35.0		2495	2.8	1.0	X	dbSNP_129	35	219,6509		3,153,60,2272,1812	yes	missense	HDAC6	NM_006044.2	29	3,169,64,3888,2379	AA,AG,A,GG,G		3.2551,0.5215,2.2626	probably-damaging	832/1216	48681187	239,10324	2203	4300	6503	SO:0001583	missense	10013	exon24			ACTGGCGCAGCTT	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 90"""	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.2495G>A	X.37:g.48681187G>A	ENSP00000334061:p.Arg832His	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	125	120	0.96	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	37	CCDS14306.1	20	0.012055455093429777	0	0.0	1	0.002793296089385475	0	0.0	18	0.023872679045092837	G	18.61	3.661801	0.67700	0.005215	0.032551	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619	T;T;T	0.60424	0.19;0.19;0.19	5.89	2.84	0.33178	Histone deacetylase domain (1);	0.340463	0.28859	N	0.013918	T	0.42966	0.1226	M	0.64997	1.995	0.40692	D	0.982406	D;D;D;D	0.76494	0.972;0.999;0.998;0.972	B;P;D;B	0.66351	0.406;0.891;0.943;0.406	T	0.57087	-0.7871	10	0.48119	T	0.1	-16.5194	7.4397	0.27176	0.3456:0.0:0.6544:0.0	rs61735967	822;195;480;832	B4DZN1;B3KY98;B3KVK5;Q9UBN7	.;.;.;HDAC6_HUMAN	H	846;832;832	ENSP00000398566:R846H;ENSP00000334061:R832H;ENSP00000365804:R832H	ENSP00000334061:R832H	R	+	2	0	HDAC6	48566131	0.328000	0.24687	0.970000	0.41538	0.966000	0.64601	1.046000	0.30354	0.633000	0.30452	0.600000	0.82982	CGC	G|0.983;A|0.017	0.017	strong		0.622	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044	
PTPRQ	374462	hgsc.bcm.edu	37	12	80878310	80878310	+	Missense_Mutation	SNP	C	C	G	rs61729287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:80878310C>G	ENST00000266688.5	+	14	1273	c.1273C>G	c.(1273-1275)Caa>Gaa	p.Q425E				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	471	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						AATTATTAACCAATACCGAGT	0.368													C|||	48	0.00958466	0.0	0.013	5008	,	,		15111	0.0		0.0249	False		,,,				2504	0.0143				p.Q257E		Atlas-SNP	.											.	PTPRQ	119	.	0			c.C769G						PASS	.	C	GLU/GLN	8,1376		0,8,684	114.0	103.0	106.0		831	6.1	1.0	12	dbSNP_129	106	89,3093		0,89,1502	yes	missense	PTPRQ	NM_001145026.1	29	0,97,2186	GG,GC,CC		2.797,0.578,2.1244	possibly-damaging	429/2300	80878310	97,4469	692	1591	2283	SO:0001583	missense	374462	exon6			ATTAACCAATACC	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.1273C>G	12.37:g.80878310C>G	ENSP00000266688:p.Gln425Glu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	37		28	0.01282051282051282	0	0.0	7	0.019337016574585635	0	0.0	21	0.027704485488126648	C	18.99	3.740500	0.69304	0.00578	0.02797	ENSG00000139304	ENST00000266688	T	0.52526	0.66	6.06	6.06	0.98353	Fibronectin, type III (3);Immunoglobulin-like fold (1);	.	.	.	.	T	0.15349	0.0370	.	.	.	0.36172	D	0.848855	P	0.50369	0.934	P	0.44422	0.449	T	0.15954	-1.0419	8	0.02654	T	1	.	20.6397	0.99537	0.0:1.0:0.0:0.0	rs61729287	471	Q9UMZ3	PTPRQ_HUMAN	E	425	ENSP00000266688:Q425E	ENSP00000266688:Q425E	Q	+	1	0	PTPRQ	79402441	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.276000	0.65580	2.880000	0.98712	0.650000	0.86243	CAA	C|0.987;G|0.013	0.013	strong		0.368	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
ACOT13	55856	hgsc.bcm.edu	37	6	24698215	24698215	+	Silent	SNP	G	G	A	rs7765904	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:24698215G>A	ENST00000230048.4	+	2	379	c.186G>A	c.(184-186)acG>acA	p.T62T	ACOT13_ENST00000537591.1_Silent_p.T39T|RP1-30M3.5_ENST00000607014.1_RNA|ACOT13_ENST00000476436.1_3'UTR	NM_018473.3	NP_060943.1	Q9NPJ3	ACO13_HUMAN	acyl-CoA thioesterase 13	62					metabolic process (GO:0008152)|protein homotetramerization (GO:0051289)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA hydrolase activity (GO:0047617)			large_intestine(1)	1						TGACAGCCACGTTAGTAGATA	0.453													G|||	738	0.147364	0.1316	0.1643	5008	,	,		17513	0.0605		0.2475	False		,,,				2504	0.1431				p.T62T		Atlas-SNP	.											.	ACOT13	12	.	0			c.G186A						PASS	.	G	,	702,3704	292.7+/-282.2	54,594,1555	107.0	91.0	97.0		117,186	-2.9	0.0	6	dbSNP_116	97	2197,6403	374.8+/-337.5	293,1611,2396	no	coding-synonymous,coding-synonymous	ACOT13	NM_001160094.1,NM_018473.3	,	347,2205,3951	AA,AG,GG		25.5465,15.9328,22.2897	,	39/118,62/141	24698215	2899,10107	2203	4300	6503	SO:0001819	synonymous_variant	55856	exon2			AGCCACGTTAGTA	AF220186	CCDS4558.1, CCDS54972.1	6p22.1	2009-11-20	2009-05-05	2009-05-05	ENSG00000112304	ENSG00000112304		"""Acyl CoA thioesterases"""	20999	protein-coding gene	gene with protein product		615652	"""thioesterase superfamily member 2"""	THEM2		16934754, 19405909	Standard	NM_018473		Approved	HT012	uc003nek.3	Q9NPJ3	OTTHUMG00000014359	ENST00000230048.4:c.186G>A	6.37:g.24698215G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	128	79	0.617188	NM_018473	F5H2L4|O95549	Silent	SNP	ENST00000230048.4	37	CCDS4558.1																																																																																			G|0.812;A|0.188	0.188	strong		0.453	ACOT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040010.2	NM_018473	
COG4	25839	hgsc.bcm.edu	37	16	70546234	70546234	+	Silent	SNP	G	G	A	rs3762171	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:70546234G>A	ENST00000323786.5	-	5	667	c.646C>T	c.(646-648)Ctg>Ttg	p.L216L	COG4_ENST00000564653.1_Silent_p.I173I|COG4_ENST00000393612.4_Silent_p.L212L	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	212					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				ACCTGGGGCAGATCACCTTCC	0.507													G|||	2355	0.470248	0.2859	0.415	5008	,	,		23036	0.5813		0.4175	False		,,,				2504	0.6984				p.L216L		Atlas-SNP	.											.	COG4	64	.	0			c.C646T						PASS	.	G	,	1313,3083	440.8+/-346.1	195,923,1080	96.0	84.0	88.0		646,646	2.4	1.0	16	dbSNP_107	88	3649,4951	524.2+/-380.5	788,2073,1439	no	coding-synonymous,coding-synonymous	COG4	NM_001195139.1,NM_015386.2	,	983,2996,2519	AA,AG,GG		42.4302,29.8681,38.181	,	216/769,216/790	70546234	4962,8034	2198	4300	6498	SO:0001819	synonymous_variant	25839	exon5			GGGGCAGATCACC	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"""Components of oligomeric golgi complex"""	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.646C>T	16.37:g.70546234G>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	242	111	0.458678	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Silent	SNP	ENST00000323786.5	37	CCDS10892.2																																																																																			G|0.578;A|0.422	0.422	strong		0.507	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3		
DACT2	168002	hgsc.bcm.edu	37	6	168709385	168709385	+	Missense_Mutation	SNP	T	T	C	rs374278981|rs6925614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168709385T>C	ENST00000366795.3	-	4	1140	c.1052A>G	c.(1051-1053)gAg>gGg	p.E351G	DACT2_ENST00000610183.1_Missense_Mutation_p.E181G|DACT2_ENST00000607983.1_Splice_Site|DACT2_ENST00000366796.3_Intron	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	351			E -> G (in dbSNP:rs6925614).		epithelial cell morphogenesis (GO:0003382)|hematopoietic progenitor cell differentiation (GO:0002244)|inner medullary collecting duct development (GO:0072061)|negative regulation of cell adhesion (GO:0007162)|negative regulation of nodal signaling pathway (GO:1900108)|skin development (GO:0043588)	mitochondrion (GO:0005739)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)|transcription factor binding (GO:0008134)			endometrium(1)	1		Breast(66;1.46e-05)|Ovarian(120;0.0728)		OV - Ovarian serous cystadenocarcinoma(33;5.33e-21)|BRCA - Breast invasive adenocarcinoma(81;1.18e-06)|GBM - Glioblastoma multiforme(31;0.000957)		CTGTTCTCCCTCGCTACCCTT	0.652													C|||	1879	0.3752	0.4592	0.3804	5008	,	,		17919	0.246		0.3678	False		,,,				2504	0.3988				p.E351G		Atlas-SNP	.											DACT2_ENST00000366795,NS,carcinoma,-1,1	DACT2	46	1	0			c.A1052G						PASS	.	C	GLY/GLU	663,721		169,325,198	40.0	38.0	38.0		1052	-8.5	0.0	6	dbSNP_116	38	1132,2050		206,720,665	yes	missense	DACT2	NM_214462.3	98	375,1045,863	CC,CT,TT		35.5751,47.9046,39.3123	benign	351/775	168709385	1795,2771	692	1591	2283	SO:0001583	missense	168002	exon4			TCTCCCTCGCTAC	AF318336	CCDS47519.1, CCDS69241.1, CCDS75554.1	6q27	2013-05-15	2013-05-15	2003-09-17	ENSG00000164488	ENSG00000164488			21231	protein-coding gene	gene with protein product		608966	"""chromosome 6 open reading frame 116"", ""dapper homolog 2, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 2 (Xenopus laevis)"""	C6orf116			Standard	NM_001286351		Approved	bA503C24.7, DAPPER2	uc003qwq.3	Q5SW24	OTTHUMG00000016046	ENST00000366795.3:c.1052A>G	6.37:g.168709385T>C	ENSP00000355760:p.Glu351Gly	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	33	12	0.363636	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Missense_Mutation	SNP	ENST00000366795.3	37	CCDS47519.1	772	0.3534798534798535	200	0.4065040650406504	138	0.3812154696132597	165	0.28846153846153844	269	0.3548812664907652	C	5.583	0.292297	0.10567	0.479046	0.355751	ENSG00000164488	ENST00000366795	T	0.39787	1.06	4.24	-8.48	0.00935	.	0.728918	0.12437	N	0.469055	T	0.04272	0.0118	N	0.03115	-0.41	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.27673	-1.0067	9	0.46703	T	0.11	-3.1909	4.4404	0.11572	0.1424:0.5155:0.1504:0.1917	rs6925614;rs61543421;rs6925614	351	Q5SW24	DACT2_HUMAN	G	351	ENSP00000355760:E351G	ENSP00000355760:E351G	E	-	2	0	DACT2	168452234	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.232000	0.09055	-1.890000	0.01111	-2.330000	0.00249	GAG	T|0.628;C|0.372	0.372	strong		0.652	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
CCDC132	55610	hgsc.bcm.edu	37	7	92900576	92900576	+	Splice_Site	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:92900576T>G	ENST00000305866.5	+	10	830		c.e10+2		CCDC132_ENST00000544910.1_Splice_Site|CCDC132_ENST00000535481.1_Intron|CCDC132_ENST00000251739.5_Splice_Site|CCDC132_ENST00000541136.1_Splice_Site|CCDC132_ENST00000317751.6_Splice_Site	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132							extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			CAGATTGAGGTAAGAAGTATT	0.294																																					.		Atlas-SNP	.											.	CCDC132	136	.	0			c.702+2T>G						PASS	.						121.0	129.0	126.0					7																	92900576		2203	4298	6501	SO:0001630	splice_region_variant	55610	exon10			TTGAGGTAAGAAG	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.702+2T>G	7.37:g.92900576T>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	111	43	0.387387	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Splice_Site	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.030563	0.75504	.	.	ENSG00000004766	ENST00000251739;ENST00000305866;ENST00000544910;ENST00000541136;ENST00000458707	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3837	0.74681	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCDC132	92738512	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.413000	0.80104	2.367000	0.80283	0.528000	0.53228	.	.	.	none		0.294	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	Intron
EPG5	57724	hgsc.bcm.edu	37	18	43481075	43481075	+	Missense_Mutation	SNP	G	G	A	rs1893523	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:43481075G>A	ENST00000282041.5	-	26	4566	c.4532C>T	c.(4531-4533)gCt>gTt	p.A1511V	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1511			A -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|A -> V (in dbSNP:rs1893523).		autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CGGGTGCAGAGCAAGGGGAGG	0.488													A|||	1604	0.320288	0.4523	0.3329	5008	,	,		20661	0.3046		0.169	False		,,,				2504	0.3047				p.A1511V		Atlas-SNP	.											EPG5,NS,carcinoma,-1,1	EPG5	199	1	0			c.C4532T						PASS	.	A	VAL/ALA	1602,2422		306,990,716	64.0	72.0	69.0		4532	-3.1	0.0	18	dbSNP_92	69	1183,7147		85,1013,3067	yes	missense	EPG5	NM_020964.2	64	391,2003,3783	AA,AG,GG		14.2017,39.8111,22.5433	benign	1511/2580	43481075	2785,9569	2012	4165	6177	SO:0001583	missense	57724	exon26			TGCAGAGCAAGGG	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.4532C>T	18.37:g.43481075G>A	ENSP00000282041:p.Ala1511Val	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	626	0.2866300366300366	209	0.4247967479674797	113	0.31215469613259667	177	0.3094405594405594	127	0.16754617414248021	A	4.836	0.155387	0.09236	0.398111	0.142017	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.09538	2.97	5.59	-3.12	0.05282	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46048	-0.9219	8	0.24483	T	0.36	0.359	5.9743	0.19369	0.2483:0.1136:0.5183:0.1197	rs1893523;rs3744994;rs52830351;rs61517336;rs1893523	1511	Q9HCE0	EPG5_HUMAN	V	1511;386	ENSP00000282041:A1511V	ENSP00000282041:A1511V	A	-	2	0	EPG5	41735073	0.000000	0.05858	0.005000	0.12908	0.075000	0.17131	0.057000	0.14279	-1.280000	0.02402	-1.204000	0.01649	GCT	G|0.748;A|0.252	0.252	strong		0.488	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
CASC5	57082	hgsc.bcm.edu	37	15	40898643	40898643	+	Missense_Mutation	SNP	G	G	C	rs7177192	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:40898643G>C	ENST00000346991.5	+	4	518	c.128G>C	c.(127-129)aGa>aCa	p.R43T	CASC5_ENST00000527044.1_Missense_Mutation_p.R43T|CASC5_ENST00000399668.2_Missense_Mutation_p.R43T|snoU13_ENST00000459027.1_RNA			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	43	Interaction with BUB1 and BUB1B.		R -> T (in dbSNP:rs7177192). {ECO:0000269|PubMed:12087463}.		acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.R43T(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GGGAATGAAAGAGTTCAGGTA	0.323													C|||	3274	0.653754	0.7307	0.6124	5008	,	,		17975	0.3542		0.8559	False		,,,				2504	0.68				p.R43T		Atlas-SNP	.											CASC5,NS,carcinoma,0,1	CASC5	269	1	1	Substitution - Missense(1)	stomach(1)	c.G128C						PASS	.	C	THR/ARG,THR/ARG	2788,820		1077,634,93	70.0	69.0	69.0		128,128	-4.8	0.0	15	dbSNP_116	69	6866,1268		2903,1060,104	yes	missense,missense	CASC5	NM_144508.3,NM_170589.3	71,71	3980,1694,197	CC,CG,GG		15.5889,22.7273,17.7823	benign,benign	43/2317,43/2343	40898643	9654,2088	1804	4067	5871	SO:0001583	missense	57082	exon4			ATGAAAGAGTTCA	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.128G>C	15.37:g.40898643G>C	ENSP00000335463:p.Arg43Thr	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_144508	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	1439	0.6588827838827839	364	0.7398373983739838	238	0.6574585635359116	183	0.31993006993006995	654	0.862796833773087	C	0.545	-0.852082	0.02651	0.772727	0.844111	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000527044;ENST00000399668	T;T;T	0.22945	1.93;1.93;1.93	4.65	-4.84	0.03151	.	1.988660	0.02241	N	0.065785	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.37957	-0.9683	9	0.02654	T	1	.	2.2862	0.04127	0.1184:0.1675:0.2349:0.4793	rs7177192;rs7177192	43;43;43	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	T	43	ENSP00000335463:R43T;ENSP00000432654:R43T;ENSP00000382576:R43T	ENSP00000260369:R43T	R	+	2	0	CASC5	38685935	0.001000	0.12720	0.001000	0.08648	0.000000	0.00434	-0.480000	0.06559	-1.200000	0.02662	-1.123000	0.02005	AGA	G|0.308;C|0.692	0.692	strong		0.323	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
NFATC1	4772	hgsc.bcm.edu	37	18	77170477	77170477	+	Missense_Mutation	SNP	C	C	A	rs1051978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:77170477C>A	ENST00000427363.2	+	2	202	c.202C>A	c.(202-204)Ccg>Acg	p.P68T	NFATC1_ENST00000329101.4_Missense_Mutation_p.P55T|NFATC1_ENST00000592223.1_Missense_Mutation_p.P55T|NFATC1_ENST00000587635.1_Missense_Mutation_p.P68T|NFATC1_ENST00000591814.1_Missense_Mutation_p.P68T|NFATC1_ENST00000545796.1_Intron|NFATC1_ENST00000586434.1_Missense_Mutation_p.P55T|NFATC1_ENST00000397790.2_Intron|NFATC1_ENST00000318065.5_Missense_Mutation_p.P55T|NFATC1_ENST00000542384.1_Missense_Mutation_p.P68T|NFATC1_ENST00000253506.5_Missense_Mutation_p.P68T			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	68			P -> T (in dbSNP:rs1051978).		calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	CCTGCCGGCCCCGTGCCACAA	0.652													C|||	234	0.0467252	0.0068	0.1527	5008	,	,		14100	0.0		0.0934	False		,,,				2504	0.0256				p.P68T	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C202A						PASS	.	C	THR/PRO,THR/PRO,,THR/PRO,THR/PRO	100,4306	77.8+/-116.1	1,98,2104	59.0	68.0	65.0		202,163,,163,202	3.5	0.0	18	dbSNP_86	65	935,7663	205.9+/-248.2	54,827,3418	yes	missense,missense,intron,missense,missense	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	38,38,,38,38	55,925,5522	AA,AC,CC		10.8746,2.2696,7.9591	possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	68/826,55/931,,55/813,68/717	77170477	1035,11969	2203	4299	6502	SO:0001583	missense	4772	exon2			CCGGCCCCGTGCC	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.202C>A	18.37:g.77170477C>A	ENSP00000389377:p.Pro68Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		128	0.05860805860805861	4	0.008130081300813009	50	0.13812154696132597	0	0.0	74	0.09762532981530343	C	10.32	1.318656	0.23994	0.022696	0.108746	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000542384;ENST00000329101;ENST00000427363;ENST00000397794	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	4.39	3.49	0.39957	.	0.118056	0.64402	D	0.000016	T	0.00328	0.0010	M	0.70275	2.135	0.09310	P	1.0	B;B;B;B;B;B;B	0.34181	0.306;0.306;0.306;0.306;0.306;0.44;0.306	B;B;B;B;B;B;B	0.30646	0.08;0.118;0.05;0.08;0.08;0.08;0.05	T	0.10543	-1.0625	9	0.66056	D	0.02	-10.9661	8.6371	0.33955	0.0:0.7533:0.1611:0.0856	rs1051978;rs2230114;rs16958940;rs1051978	55;55;68;68;68;55;68	B5B2M7;B5B2N1;B5B2M6;O95644;B5B2M4;B5B2M5;Q2M1S3	.;.;.;NFAC1_HUMAN;.;.;.	T	68;68;68;55;55;32	ENSP00000316553:P68T;ENSP00000253506:P68T;ENSP00000442435:P68T;ENSP00000327850:P55T	ENSP00000253506:P68T	P	+	1	0	NFATC1	75271465	0.236000	0.23804	0.006000	0.13384	0.137000	0.21094	2.714000	0.47202	1.013000	0.39391	0.561000	0.74099	CCG	C|0.931;A|0.069	0.069	strong		0.652	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
SLC52A3	113278	hgsc.bcm.edu	37	20	746098	746098	+	Silent	SNP	G	G	A	rs3746808	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:746098G>A	ENST00000217254.7	-	2	562	c.321C>T	c.(319-321)gcC>gcT	p.A107A	SLC52A3_ENST00000473664.1_5'UTR|SLC52A3_ENST00000381944.3_Silent_p.A107A	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	107					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										GGACCAAGAAGGCGATGCTGT	0.592													G|||	1284	0.25639	0.1362	0.3401	5008	,	,		19825	0.2014		0.3082	False		,,,				2504	0.363				p.A107A		Atlas-SNP	.											.	.	.	.	0			c.C321T						PASS	.	G		692,3714	275.4+/-272.5	54,584,1565	62.0	48.0	53.0		321	3.7	0.7	20	dbSNP_107	53	2633,5967	403.1+/-347.7	420,1793,2087	no	coding-synonymous	C20orf54	NM_033409.3		474,2377,3652	AA,AG,GG		30.6163,15.7059,25.5651		107/470	746098	3325,9681	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon2			CAAGAAGGCGATG	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.321C>T	20.37:g.746098G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			G|0.754;A|0.246	0.246	strong		0.592	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
ANO4	121601	hgsc.bcm.edu	37	12	101520689	101520689	+	Silent	SNP	A	A	G	rs1055734	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:101520689A>G	ENST00000392977.3	+	27	2919	c.2709A>G	c.(2707-2709)tcA>tcG	p.S903S	ANO4_ENST00000550015.1_Silent_p.S423S|ANO4_ENST00000299222.9_Silent_p.S423S|ANO4_ENST00000392979.3_Silent_p.S868S			Q32M45	ANO4_HUMAN	anoctamin 4	903					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						ACCTCATTTCATATCTGATCC	0.443										HNSCC(74;0.22)			A|||	737	0.147165	0.0968	0.1182	5008	,	,		23218	0.1895		0.1302	False		,,,				2504	0.2096				p.S868S		Atlas-SNP	.											ANO4,NS,carcinoma,+1,1	ANO4	183	1	0			c.A2604G						scavenged	.	A		469,3937	222.6+/-239.4	26,417,1760	100.0	90.0	94.0		2604	-2.5	1.0	12	dbSNP_86	94	1317,7283	259.8+/-282.9	97,1123,3080	no	coding-synonymous	ANO4	NM_178826.3		123,1540,4840	GG,GA,AA		15.314,10.6446,13.7321		868/921	101520689	1786,11220	2203	4300	6503	SO:0001819	synonymous_variant	121601	exon26			CATTTCATATCTG	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	23837	protein-coding gene	gene with protein product		610111	"""transmembrane protein 16D"""	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.2709A>G	12.37:g.101520689A>G		Somatic	270	2	0.00740741		WXS	Illumina HiSeq	Phase_I	279	121	0.433692	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Silent	SNP	ENST00000392977.3	37																																																																																				A|0.860;G|0.140	0.140	strong		0.443	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826	
CACNA1H	8912	hgsc.bcm.edu	37	16	1252259	1252259	+	Silent	SNP	A	A	G	rs9934839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1252259A>G	ENST00000348261.5	+	9	2057	c.1809A>G	c.(1807-1809)agA>agG	p.R603R	CACNA1H_ENST00000358590.4_Silent_p.R603R|CACNA1H_ENST00000565831.1_Silent_p.R603R	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	603					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCAGCCTCAGACTGGCCACAG	0.677													G|||	1986	0.396565	0.5877	0.379	5008	,	,		14978	0.119		0.4901	False		,,,				2504	0.3405				p.R603R		Atlas-SNP	.											.	CACNA1H	317	.	0			c.A1809G	GRCh37	CM071579	CACNA1H	M	rs9934839	PASS	.	G	,	2248,1408		734,780,314	5.0	6.0	6.0		1809,1809	2.3	0.9	16	dbSNP_119	6	4058,3834		1155,1748,1043	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	1889,2528,1357	GG,GA,AA		48.5808,38.512,45.3931	,	603/2348,603/2354	1252259	6306,5242	1828	3946	5774	SO:0001819	synonymous_variant	8912	exon9			CCTCAGACTGGCC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1809A>G	16.37:g.1252259A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			A|0.594;G|0.406	0.406	strong		0.677	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
HMCN1	83872	hgsc.bcm.edu	37	1	186120800	186120800	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:186120800A>G	ENST00000271588.4	+	95	15050	c.14821A>G	c.(14821-14823)Ata>Gta	p.I4941V	HMCN1_ENST00000367492.2_Missense_Mutation_p.I4941V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4941	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AGCAAAGGAAATAGGAGAAGC	0.343																																					p.I4941V		Atlas-SNP	.											HMCN1,NS,malignant_melanoma,0,1	HMCN1	797	1	0			c.A14821G						scavenged	.						125.0	132.0	129.0					1																	186120800		2203	4300	6503	SO:0001583	missense	83872	exon95			AAGGAAATAGGAG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.14821A>G	1.37:g.186120800A>G	ENSP00000271588:p.Ile4941Val	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	339	5	0.0147493	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	3.573	-0.087243	0.07097	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.30182	1.54;1.54	5.43	3.1	0.35709	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.240486	0.49305	N	0.000159	T	0.16769	0.0403	N	0.17674	0.51	0.32143	N	0.585257	B	0.09022	0.002	B	0.14578	0.011	T	0.13791	-1.0496	10	0.27785	T	0.31	.	6.0342	0.19697	0.7403:0.0:0.1375:0.1222	.	4941	Q96RW7	HMCN1_HUMAN	V	4941	ENSP00000271588:I4941V;ENSP00000356462:I4941V	ENSP00000271588:I4941V	I	+	1	0	HMCN1	184387423	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.535000	0.36061	0.363000	0.24346	0.528000	0.53228	ATA	.	.	none		0.343	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
TTC38	55020	hgsc.bcm.edu	37	22	46669924	46669924	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:46669924G>A	ENST00000381031.3	+	4	399	c.323G>A	c.(322-324)cGg>cAg	p.R108Q	TTC38_ENST00000445282.2_Missense_Mutation_p.R108Q	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	108						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						CTGACAAGGCGGGAGCAGCTG	0.602																																					p.R108Q		Atlas-SNP	.											.	TTC38	40	.	0			c.G323A						PASS	.						46.0	52.0	50.0					22																	46669924		2080	4217	6297	SO:0001583	missense	55020	exon4			CAAGGCGGGAGCA		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"""Tetratricopeptide (TTC) repeat domain containing"""	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.323G>A	22.37:g.46669924G>A	ENSP00000370419:p.Arg108Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	37	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.249754	0.80024	.	.	ENSG00000075234	ENST00000381031;ENST00000445282;ENST00000421359	T;T;T	0.67865	0.97;0.24;-0.29	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.85710	2.77	0.24599	N	0.993783	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	T	0.78427	-0.2208	10	0.62326	D	0.03	-0.2222	18.5029	0.90888	0.0:0.0:1.0:0.0	.	108;108	E7ES35;Q5R3I4	.;TTC38_HUMAN	Q	108	ENSP00000370419:R108Q;ENSP00000393960:R108Q;ENSP00000410095:R108Q	ENSP00000370419:R108Q	R	+	2	0	TTC38	45048588	1.000000	0.71417	0.595000	0.28798	0.086000	0.17979	9.017000	0.93651	2.596000	0.87737	0.650000	0.86243	CGG	.	.	none		0.602	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
COX11	1353	hgsc.bcm.edu	37	17	53042208	53042208	+	Silent	SNP	A	A	G	rs145197312	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:53042208A>G	ENST00000299335.3	-	2	510	c.372T>C	c.(370-372)acT>acC	p.T124T	COX11_ENST00000571584.1_Silent_p.T124T	NM_004375.3	NP_004366.1	Q9Y6N1	COX11_HUMAN	cytochrome c oxidase assembly homolog 11 (yeast)	124					hydrogen ion transmembrane transport (GO:1902600)|negative regulation of glucokinase activity (GO:0033132)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|prostate(1)	9						CTCCAAGTCCAGTAGTCTAGA	0.313													A|||	4	0.000798722	0.0	0.0014	5008	,	,		20429	0.0		0.003	False		,,,				2504	0.0				p.T124T		Atlas-SNP	.											.	COX11	16	.	0			c.T372C						PASS	.	A	,,	4,4402	8.1+/-20.4	0,4,2199	80.0	73.0	75.0		372,372,372	-1.6	1.0	17	dbSNP_134	75	38,8562	25.7+/-73.6	0,38,4262	no	coding-synonymous,coding-synonymous,coding-synonymous	COX11	NM_001162861.1,NM_001162862.1,NM_004375.3	,,	0,42,6461	GG,GA,AA		0.4419,0.0908,0.3229	,,	124/231,124/232,124/277	53042208	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	1353	exon2			AAGTCCAGTAGTC	AF044321	CCDS11583.1, CCDS58579.1	17q22	2012-10-15	2012-10-15			ENSG00000166260		"""Mitochondrial respiratory chain complex assembly factors"""	2261	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit 11"", ""cytochrome c oxidase assembly protein COX11"""	603648	"""COX11 (yeast) homolog, cytochrome c oxidase assembly protein"", ""COX11 cytochrome c oxidase assembly homolog (yeast)"""			9878253	Standard	NM_004375		Approved	COX11P	uc010wng.1	Q9Y6N1		ENST00000299335.3:c.372T>C	17.37:g.53042208A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001162861	D3DTY5|I3L220|Q6FHB7|Q9BRX0|Q9UME8	Silent	SNP	ENST00000299335.3	37	CCDS11583.1																																																																																			A|0.998;G|0.002	0.002	strong		0.313	COX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439182.1	NM_004375	
ZNF548	147694	hgsc.bcm.edu	37	19	57909827	57909827	+	Missense_Mutation	SNP	G	G	T	rs17856896	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57909827G>T	ENST00000366197.5	+	3	422	c.172G>T	c.(172-174)Gca>Tca	p.A58S	AC003002.6_ENST00000596400.1_Intron|AC004076.7_ENST00000597410.1_Intron|ZNF548_ENST00000336128.7_Missense_Mutation_p.A70S|ZNF548_ENST00000597400.1_3'UTR|AC003002.4_ENST00000597658.1_Missense_Mutation_p.A61S|AC003002.6_ENST00000600421.1_Intron	NM_152909.3	NP_690873.2	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	58	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		A -> S (in dbSNP:rs17856896). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GGATGAGGAGGCACCTTCACA	0.522													G|||	443	0.0884585	0.0106	0.0663	5008	,	,		21716	0.0784		0.1302	False		,,,				2504	0.1769				p.A70S		Atlas-SNP	.											.	ZNF548	64	.	0			c.G208T						PASS	.	G	SER/ALA,SER/ALA	114,4238	76.8+/-115.0	2,110,2064	115.0	111.0	112.0		208,172	-1.9	0.0	19	dbSNP_123	112	1151,7435	230.3+/-264.7	83,985,3225	yes	missense,missense	ZNF548	NM_001172773.1,NM_152909.3	99,99	85,1095,5289	TT,TG,GG		13.4055,2.6195,9.7774	benign,benign	70/546,58/534	57909827	1265,11673	2176	4293	6469	SO:0001583	missense	147694	exon4			GAGGAGGCACCTT	AK057494	CCDS46209.1, CCDS54324.1	19q13.43	2013-01-08				ENSG00000188785		"""Zinc fingers, C2H2-type"", ""-"""	26561	protein-coding gene	gene with protein product						12477932	Standard	NM_152909		Approved	FLJ32932	uc002qon.3	Q8NEK5		ENST00000366197.5:c.172G>T	19.37:g.57909827G>T	ENSP00000379482:p.Ala58Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_001172773	Q96M05	Missense_Mutation	SNP	ENST00000366197.5	37	CCDS46209.1	182	0.08333333333333333	10	0.02032520325203252	28	0.07734806629834254	39	0.06818181818181818	105	0.13852242744063326	G	16.16	3.043681	0.55003	0.026195	0.134055	ENSG00000188785	ENST00000336128;ENST00000366197	T;T	0.00717	5.79;5.79	3.08	-1.9	0.07665	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	N	0.11789	0.175	0.80722	P	0.0	B;B	0.34290	0.447;0.319	B;B	0.29598	0.104;0.048	T	0.32134	-0.9918	8	0.11182	T	0.66	.	3.9551	0.09387	0.3705:0.3585:0.271:0.0	rs17856896;rs17856896	70;58	Q8NEK5-2;Q8NEK5	.;ZN548_HUMAN	S	70;58	ENSP00000337555:A70S;ENSP00000379482:A58S	ENSP00000337555:A70S	A	+	1	0	ZNF548	62601639	0.000000	0.05858	0.000000	0.03702	0.432000	0.31715	-0.034000	0.12225	-0.177000	0.10690	-0.515000	0.04445	GCA	G|0.913;T|0.087	0.087	strong		0.522	ZNF548-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465937.1	NM_152909	
CNGB3	54714	hgsc.bcm.edu	37	8	87588248	87588248	+	Silent	SNP	T	T	C	rs3735970	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:87588248T>C	ENST00000320005.5	-	18	2261	c.2214A>G	c.(2212-2214)gaA>gaG	p.E738E		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	738					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						TATCTTTAtcttcattttctt	0.363													T|||	412	0.0822684	0.0696	0.085	5008	,	,		18686	0.1022		0.0885	False		,,,				2504	0.0706				p.E738E		Atlas-SNP	.											.	CNGB3	176	.	0			c.A2214G						PASS	.	T		302,4104	146.1+/-180.8	11,280,1912	199.0	202.0	201.0		2214	2.8	0.2	8	dbSNP_107	201	718,7882	162.7+/-215.4	32,654,3614	no	coding-synonymous	CNGB3	NM_019098.4		43,934,5526	CC,CT,TT		8.3488,6.8543,7.8425		738/810	87588248	1020,11986	2203	4300	6503	SO:0001819	synonymous_variant	54714	exon18			TTTATCTTCATTT	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2153	protein-coding gene	gene with protein product		605080	"""achromatopsia (rod monochromacy) 3"", ""achromatopsia (rod monochromacy) 1"""	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.2214A>G	8.37:g.87588248T>C		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	253	120	0.474308	NM_019098	C9JA51|Q9NRE9	Silent	SNP	ENST00000320005.5	37	CCDS6244.1																																																																																			T|0.918;C|0.082	0.082	strong		0.363	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098	
DAGLA	747	hgsc.bcm.edu	37	11	61487690	61487690	+	Silent	SNP	G	G	A	rs198430	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61487690G>A	ENST00000257215.5	+	2	179	c.63G>A	c.(61-63)ccG>ccA	p.P21P		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	21					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		TCGTCCTACCGGCCATCTTCC	0.642													G|||	1503	0.30012	0.2269	0.3213	5008	,	,		18461	0.4643		0.2416	False		,,,				2504	0.2751				p.P21P		Atlas-SNP	.											DAGLA,NS,carcinoma,0,1	DAGLA	109	1	0			c.G63A						PASS	.	G		991,3413	368.3+/-318.6	107,777,1318	113.0	101.0	105.0		63	-6.5	1.0	11	dbSNP_79	105	2179,6419	372.6+/-336.7	266,1647,2386	no	coding-synonymous	DAGLA	NM_006133.2		373,2424,3704	AA,AG,GG		25.3431,22.5023,24.3809		21/1043	61487690	3170,9832	2202	4299	6501	SO:0001819	synonymous_variant	747	exon2			CCTACCGGCCATC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.63G>A	11.37:g.61487690G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	112	110	0.982143	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	37	CCDS31578.1																																																																																			G|0.742;A|0.258	0.258	strong		0.642	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
OR6C3	254786	hgsc.bcm.edu	37	12	55725690	55725690	+	Missense_Mutation	SNP	C	C	T	rs4318060	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:55725690C>T	ENST00000379667.1	+	1	206	c.206C>T	c.(205-207)tCa>tTa	p.S69L		NM_054104.1	NP_473445.1	Q9NZP0	OR6C3_HUMAN	olfactory receptor, family 6, subfamily C, member 3	69			S -> L (in dbSNP:rs4318060).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						TTAGAAATCTCATTTACAACC	0.418													C|||	540	0.107827	0.1997	0.0951	5008	,	,		18408	0.0		0.1571	False		,,,				2504	0.0532				p.S69L		Atlas-SNP	.											.	OR6C3	36	.	0			c.C206T						PASS	.		LEU/SER	882,3524	333.1+/-302.8	85,712,1406	99.0	109.0	106.0		206	4.8	1.0	12	dbSNP_111	106	1414,7186	271.6+/-289.6	120,1174,3006	yes	missense	OR6C3	NM_054104.1	145	205,1886,4412	TT,TC,CC		16.4419,20.0182,17.6534	benign	69/312	55725690	2296,10710	2203	4300	6503	SO:0001583	missense	254786	exon1			AAATCTCATTTAC	AF179770	CCDS31819.1	12q13.2	2013-09-23			ENSG00000205329	ENSG00000205329		"""GPCR / Class A : Olfactory receptors"""	15437	protein-coding gene	gene with protein product							Standard	NM_054104		Approved	OST709	uc010spj.2	Q9NZP0	OTTHUMG00000169861	ENST00000379667.1:c.206C>T	12.37:g.55725690C>T	ENSP00000368989:p.Ser69Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_054104		Missense_Mutation	SNP	ENST00000379667.1	37	CCDS31819.1	254	0.1163003663003663	100	0.2032520325203252	36	0.09944751381215469	0	0.0	118	0.15567282321899736	C	11.61	1.690093	0.29962	0.200182	0.164419	ENSG00000205329	ENST00000379667	T	0.19250	2.16	4.82	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.374600	0.19516	N	0.112395	T	0.00012	0.0000	L	0.37850	1.14	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.12400	-1.0549	9	0.41790	T	0.15	.	14.1168	0.65159	0.0:0.807:0.193:0.0	rs4318060;rs52816488;rs60237450;rs4318060	69	Q9NZP0	OR6C3_HUMAN	L	69	ENSP00000368989:S69L	ENSP00000368989:S69L	S	+	2	0	OR6C3	54011957	0.000000	0.05858	0.988000	0.46212	0.894000	0.52154	0.936000	0.28938	2.665000	0.90641	0.461000	0.40582	TCA	C|0.845;T|0.155	0.155	strong		0.418	OR6C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406309.1		
CIT	11113	hgsc.bcm.edu	37	12	120156141	120156141	+	Silent	SNP	G	G	A	rs278102	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:120156141G>A	ENST00000261833.7	-	31	4003	c.3951C>T	c.(3949-3951)tcC>tcT	p.S1317S	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Silent_p.S1359S	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1317					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		GCACGATGGCGGACATGGCGA	0.642													G|||	914	0.182508	0.2383	0.1916	5008	,	,		13978	0.0109		0.2843	False		,,,				2504	0.1728				p.S1359S		Atlas-SNP	.											.	CIT	535	.	0			c.C4077T						PASS	.	G	,	1056,3350	385.6+/-325.8	134,788,1281	69.0	79.0	76.0		4077,3951	-8.0	0.9	12	dbSNP_79	76	2485,6113	407.8+/-349.3	358,1769,2172	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	492,2557,3453	AA,AG,GG		28.9021,23.9673,27.2301	,	1359/2070,1317/2028	120156141	3541,9463	2203	4299	6502	SO:0001819	synonymous_variant	11113	exon32			GATGGCGGACATG	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.3951C>T	12.37:g.120156141G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	50	0.595238	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	409	0.18727106227106227	115	0.23373983739837398	73	0.20165745856353592	5	0.008741258741258742	216	0.2849604221635884	G	11.45	1.641188	0.29157	0.239673	0.289021	ENSG00000122966	ENST00000392520	.	.	.	5.74	-8.01	0.01122	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17410	-1.0370	3	.	.	.	.	8.9636	0.35863	0.439:0.1088:0.4522:0.0	rs278102;rs17409026;rs278102	.	.	.	L	930	.	.	P	-	2	0	CIT	118640524	0.307000	0.24500	0.876000	0.34364	0.986000	0.74619	-0.263000	0.08670	-1.770000	0.01295	-0.345000	0.07892	CCG	G|0.760;A|0.240	0.240	strong		0.642	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
ATHL1	80162	hgsc.bcm.edu	37	11	290891	290891	+	Silent	SNP	T	T	C	rs72636977	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:290891T>C	ENST00000409548.2	+	4	799	c.684T>C	c.(682-684)taT>taC	p.Y228Y	RP11-326C3.2_ENST00000525217.1_RNA|ATHL1_ENST00000409479.1_Silent_p.Y228Y|ATHL1_ENST00000409655.1_Silent_p.Y51Y|RP11-326C3.2_ENST00000534742.1_RNA|RP11-326C3.2_ENST00000533924.1_RNA	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	228					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		GAGCTCTGTATACGGCTCACG	0.677													C|||	926	0.184904	0.1672	0.2219	5008	,	,		19198	0.3075		0.0596	False		,,,				2504	0.1851				p.Y228Y		Atlas-SNP	.											ATHL1_ENST00000409548,NS,carcinoma,0,2	ATHL1	88	2	0			c.T684C						PASS	.	C		648,3758	272.2+/-270.6	43,562,1598	46.0	49.0	48.0		684	-0.5	0.0	11	dbSNP_130	48	467,8133	134.1+/-191.5	13,441,3846	no	coding-synonymous	ATHL1	NM_025092.4		56,1003,5444	CC,CT,TT		5.4302,14.7072,8.573		228/738	290891	1115,11891	2203	4300	6503	SO:0001819	synonymous_variant	80162	exon4			TCTGTATACGGCT	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.684T>C	11.37:g.290891T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	170	96	0.564706	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																			T|0.894;C|0.106	0.106	strong		0.677	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
ZNF618	114991	hgsc.bcm.edu	37	9	116770776	116770776	+	Silent	SNP	C	C	T	rs3748183	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:116770776C>T	ENST00000374126.5	+	9	795	c.696C>T	c.(694-696)gtC>gtT	p.V232V	ZNF618_ENST00000288466.7_Silent_p.V200V			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	232					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						ACCAAGGTGTCGTGGCCACGG	0.657													C|||	1519	0.303315	0.062	0.2565	5008	,	,		17346	0.5962		0.3439	False		,,,				2504	0.319				p.V200V		Atlas-SNP	.											.	ZNF618	184	.	0			c.C600T						PASS	.	C		424,3478		25,374,1552	49.0	57.0	55.0		600	-5.7	0.8	9	dbSNP_107	55	2698,5554		451,1796,1879	no	coding-synonymous	ZNF618	NM_133374.2		476,2170,3431	TT,TC,CC		32.6951,10.8662,25.687		200/862	116770776	3122,9032	1951	4126	6077	SO:0001819	synonymous_variant	114991	exon8			AGGTGTCGTGGCC	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.696C>T	9.37:g.116770776C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	113	111	0.982301	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				C|0.649;T|0.351	0.351	strong		0.657	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
TMCC3	57458	hgsc.bcm.edu	37	12	94976084	94976084	+	Silent	SNP	T	T	C	rs3747552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:94976084T>C	ENST00000261226.4	-	2	440	c.309A>G	c.(307-309)gcA>gcG	p.A103A	TMCC3_ENST00000551457.1_Silent_p.A72A	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	103						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						GCTGCTTGTCTGCGTTGTTCA	0.453													C|||	3502	0.699281	0.9266	0.6095	5008	,	,		19833	0.6002		0.5775	False		,,,				2504	0.683				p.A103A		Atlas-SNP	.											.	TMCC3	63	.	0			c.A309G						PASS	.	C		3795,611	267.7+/-268.0	1645,505,53	155.0	142.0	146.0		309	-11.2	0.0	12	dbSNP_107	146	4855,3745	533.1+/-382.3	1393,2069,838	no	coding-synonymous	TMCC3	NM_020698.2		3038,2574,891	CC,CT,TT		43.5465,13.8675,33.4922		103/478	94976084	8650,4356	2203	4300	6503	SO:0001819	synonymous_variant	57458	exon2			CTTGTCTGCGTTG	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"""Transmembrane and coiled-coil domain containing"""	29199	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 3"""			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.309A>G	12.37:g.94976084T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_020698	Q8IWB2	Silent	SNP	ENST00000261226.4	37	CCDS31877.1																																																																																			T|0.335;C|0.665	0.665	strong		0.453	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
OR5H1	26341	hgsc.bcm.edu	37	3	97851900	97851900	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:97851900A>G	ENST00000354565.2	+	1	359	c.359A>G	c.(358-360)tAt>tGt	p.Y120C	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	120						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						ACGATGGCATATGATCGCTAT	0.393																																					p.Y120C		Atlas-SNP	.											OR5H1,NS,carcinoma,0,1	OR5H1	71	1	0			c.A359G						scavenged	.						135.0	132.0	133.0					3																	97851900		2201	4299	6500	SO:0001583	missense	26341	exon1			TGGCATATGATCG	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"""GPCR / Class A : Olfactory receptors"""	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.359A>G	3.37:g.97851900A>G	ENSP00000346575:p.Tyr120Cys	Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	551	24	0.0435572	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	37	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	A	5.647	0.304060	0.10678	.	.	ENSG00000231192	ENST00000354565	T	0.01347	4.99	3.57	3.57	0.40892	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42682	D	0.000670	T	0.03783	0.0107	M	0.91090	3.175	0.23238	N	0.998065	B	0.33280	0.405	B	0.30782	0.12	T	0.12682	-1.0538	10	0.87932	D	0	.	10.1009	0.42504	1.0:0.0:0.0:0.0	.	120	A6NKK0	OR5H1_HUMAN	C	120	ENSP00000346575:Y120C	ENSP00000346575:Y120C	Y	+	2	0	OR5H1	99334590	1.000000	0.71417	0.997000	0.53966	0.092000	0.18411	2.069000	0.41481	1.481000	0.48307	0.164000	0.16699	TAT	.	.	none		0.393	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338	
GAS8	2622	hgsc.bcm.edu	37	16	90095597	90095597	+	Intron	SNP	T	T	C	rs61118444|rs71137702	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90095597T>C	ENST00000268699.4	+	2	212				GAS8_ENST00000536122.1_Intron|GAS8_ENST00000540721.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.I52V	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		gggcaggctatggggcagcct	0.662													t|||	2317	0.46266	0.3767	0.4611	5008	,	,		15322	0.63		0.3757	False		,,,				2504	0.4969				p.I52V		Atlas-SNP	.											.	C16orf3	14	.	0			c.A154G						PASS	.						20.0	23.0	22.0					16																	90095597		2197	4299	6496	SO:0001627	intron_variant	750	exon1			AGGCTATGGGGCA	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1467T>C	16.37:g.90095597T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	6	0.0740741	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	t	0.096	-1.158920	0.01686	.	.	ENSG00000221819	ENST00000408886	T	0.47177	0.85	.	.	.	.	.	.	.	.	T	0.17408	0.0418	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14117	-1.0484	5	.	.	.	.	.	.	.	rs61118444;rs62640378	60	O95177	CP003_HUMAN	V	52	ENSP00000386218:I52V	.	I	-	1	0	C16orf3	88623098	0.005000	0.15991	0.000000	0.03702	0.009000	0.06853	-2.049000	0.01405	-2.579000	0.00463	-1.976000	0.00459	ATA	T|0.361;C|0.639	0.639	strong		0.662	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
COL4A1	1282	hgsc.bcm.edu	37	13	110813709	110813709	+	Silent	SNP	G	G	A	rs1133219	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:110813709G>A	ENST00000375820.4	-	49	4591	c.4470C>T	c.(4468-4470)gcC>gcT	p.A1490A	COL4A1_ENST00000467182.1_5'UTR	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1490	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.			A -> T (in Ref. 17; ABE73157). {ECO:0000305}.	axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			GGCAGCTGCCGGCCGTGCCTA	0.438													G|||	1542	0.307907	0.3563	0.2536	5008	,	,		21124	0.2123		0.3419	False		,,,				2504	0.3446				p.A1490A		Atlas-SNP	.											.	COL4A1	372	.	0			c.C4470T						PASS	.	G		1661,2745	497.6+/-363.9	305,1051,847	70.0	55.0	60.0		4470	-8.6	0.9	13	dbSNP_86	60	2979,5621	451.5+/-362.7	549,1881,1870	no	coding-synonymous	COL4A1	NM_001845.4		854,2932,2717	AA,AG,GG		34.6395,37.6986,35.6758		1490/1670	110813709	4640,8366	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon49			GCTGCCGGCCGTG	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.4470C>T	13.37:g.110813709G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			G|0.664;A|0.336	0.336	strong		0.438	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807953	18807953	+	Missense_Mutation	SNP	C	C	A	rs11261022	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18807953C>A	ENST00000400664.1	+	1	530	c.478C>A	c.(478-480)Cgc>Agc	p.R160S		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	160			R -> S (in dbSNP:rs11261022).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CCATTTCCCCCGCTTGGGCAG	0.642													C|||	1400	0.279553	0.2534	0.3401	5008	,	,		17782	0.2321		0.3628	False		,,,				2504	0.2352				p.R160S		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C478A						PASS	.	C	SER/ARG	1039,3127		137,765,1181	32.0	37.0	35.0		478	-4.0	0.0	1	dbSNP_120	35	2972,5484		509,1954,1765	yes	missense	KLHDC7A	NM_152375.2	110	646,2719,2946	AA,AC,CC		35.1466,24.94,31.7778	benign	160/778	18807953	4011,8611	2083	4228	6311	SO:0001583	missense	127707	exon1			TTCCCCCGCTTGG	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.478C>A	1.37:g.18807953C>A	ENSP00000383505:p.Arg160Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	670	0.3067765567765568	140	0.2845528455284553	105	0.2900552486187845	139	0.243006993006993	286	0.37730870712401055	C	11.86	1.764864	0.31228	0.2494	0.351466	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.72051	-0.62	4.65	-3.99	0.04069	.	3.517270	0.05457	U	0.550465	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.18166	0.026	B	0.12837	0.008	T	0.13926	-1.0491	9	0.12430	T	0.62	.	2.446	0.04506	0.1147:0.3232:0.3378:0.2243	rs11261022	160	Q5VTJ3	KLD7A_HUMAN	S	160;97	ENSP00000383505:R160S	ENSP00000383505:R160S	R	+	1	0	KLHDC7A	18680540	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-4.138000	0.00287	-0.507000	0.06549	-0.216000	0.12614	CGC	C|0.671;A|0.329	0.329	strong		0.642	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
MUC16	94025	hgsc.bcm.edu	37	19	9060059	9060059	+	Missense_Mutation	SNP	A	A	C	rs12977368	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9060059A>C	ENST00000397910.4	-	3	27590	c.27387T>G	c.(27385-27387)gaT>gaG	p.D9129E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9131	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCCATGGCACATCTCCAGGAG	0.483													A|||	897	0.179113	0.1445	0.2061	5008	,	,		23138	0.0099		0.3121	False		,,,				2504	0.2444				p.D9129E		Atlas-SNP	.											.	MUC16	4315	.	0			c.T27387G						PASS	.	A	GLU/ASP	610,3382		40,530,1426	79.0	75.0	76.0		27387	-1.2	0.0	19	dbSNP_121	76	2806,5520		497,1812,1854	yes	missense	MUC16	NM_024690.2	45	537,2342,3280	CC,CA,AA		33.7017,15.2806,27.7318	possibly-damaging	9129/14508	9060059	3416,8902	1996	4163	6159	SO:0001583	missense	94025	exon3			TGGCACATCTCCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27387T>G	19.37:g.9060059A>C	ENSP00000381008:p.Asp9129Glu	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	180	180	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	390	0.17857142857142858	68	0.13821138211382114	78	0.2154696132596685	5	0.008741258741258742	239	0.3153034300791557	a	6.593	0.477708	0.12521	0.152806	0.337017	ENSG00000181143	ENST00000397910	T	0.23348	1.91	2.34	-1.19	0.09585	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	.	.	.	P	0.41041	0.736	B	0.44224	0.444	T	0.40887	-0.9539	8	0.87932	D	0	.	2.9933	0.05990	0.4644:0.2373:0.2983:0.0	rs12977368;rs12977368	9129	B5ME49	.	E	9129	ENSP00000381008:D9129E	ENSP00000381008:D9129E	D	-	3	2	MUC16	8921059	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-2.522000	0.00950	-0.409000	0.07553	-0.775000	0.03384	GAT	A|0.794;C|0.206	0.206	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LMO7	4008	hgsc.bcm.edu	37	13	76370783	76370783	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:76370783A>G	ENST00000341547.4	+	7	1776	c.516A>G	c.(514-516)acA>acG	p.T172T	LMO7_ENST00000357063.3_Silent_p.T172T|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000526202.1_Silent_p.T81T|LMO7_ENST00000321797.8_5'UTR|LMO7_ENST00000465261.2_5'UTR|LMO7_ENST00000377534.3_Silent_p.T172T	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	172					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T172T(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		TTTTGATAACATTGTACTGGC	0.363																																					p.T172T		Atlas-SNP	.											LMO7_ENST00000357063,NS,carcinoma,0,2	LMO7	334	2	2	Substitution - coding silent(2)	breast(2)	c.A516G						PASS	.						80.0	75.0	77.0					13																	76370783		2203	4300	6503	SO:0001819	synonymous_variant	4008	exon7			GATAACATTGTAC	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000341547.4:c.516A>G	13.37:g.76370783A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Silent	SNP	ENST00000341547.4	37	CCDS9454.1																																																																																			.	.	none		0.363	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358	
MAP9	79884	hgsc.bcm.edu	37	4	156289917	156289917	+	Missense_Mutation	SNP	G	G	A	rs3733391	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:156289917G>A	ENST00000311277.4	-	5	792	c.529C>T	c.(529-531)Cgg>Tgg	p.R177W	AC097467.2_ENST00000596165.1_RNA|MAP9_ENST00000515654.1_Missense_Mutation_p.R177W|AC097467.2_ENST00000600928.1_RNA|AC097467.2_ENST00000598890.1_RNA|MAP9_ENST00000379248.2_Missense_Mutation_p.R104W|AC097467.2_ENST00000597831.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	177			R -> W (in dbSNP:rs3733391). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16049101}.		cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		CTCCTTGGCCGAGGTGATGGT	0.378													G|||	849	0.169529	0.0197	0.1282	5008	,	,		19316	0.2054		0.2406	False		,,,				2504	0.2914				p.R177W		Atlas-SNP	.											MAP9,NS,carcinoma,+1,2	MAP9	79	2	0			c.C529T						PASS	.	G	TRP/ARG	225,4181	134.1+/-170.4	3,219,1981	129.0	121.0	124.0		529	3.1	0.9	4	dbSNP_107	124	1777,6823	320.7+/-314.7	187,1403,2710	yes	missense	MAP9	NM_001039580.1	101	190,1622,4691	AA,AG,GG		20.6628,5.1067,15.3929	probably-damaging	177/648	156289917	2002,11004	2203	4300	6503	SO:0001583	missense	79884	exon5			TTGGCCGAGGTGA	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"""aster-associated protein"""	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.529C>T	4.37:g.156289917G>A	ENSP00000310593:p.Arg177Trp	Somatic	491	1	0.00203666		WXS	Illumina HiSeq	Phase_I	497	226	0.454728	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	37	CCDS35493.1	344	0.1575091575091575	8	0.016260162601626018	50	0.13812154696132597	119	0.20804195804195805	167	0.22031662269129287	G	12.54	1.968422	0.34754	0.051067	0.206628	ENSG00000164114	ENST00000311277;ENST00000515654;ENST00000433024;ENST00000393836;ENST00000379248	T;T;T;T	0.40476	1.92;1.98;1.17;1.03	5.06	3.12	0.35913	.	0.869549	0.09941	N	0.735941	T	0.00039	0.0001	M	0.66939	2.045	0.30004	P	0.815778	B;B;B	0.25007	0.035;0.116;0.116	B;B;B	0.14578	0.006;0.011;0.011	T	0.05582	-1.0876	9	0.59425	D	0.04	4.7887	6.3104	0.21161	0.1036:0.0:0.7217:0.1747	rs3733391;rs52822019;rs60246226;rs3733391	104;177;177	A8MSM7;B9EJB6;Q49MG5	.;.;MAP9_HUMAN	W	177;177;176;177;104	ENSP00000310593:R177W;ENSP00000427402:R177W;ENSP00000394048:R176W;ENSP00000368550:R104W	ENSP00000310593:R177W	R	-	1	2	MAP9	156509367	0.995000	0.38212	0.925000	0.36789	0.779000	0.44077	2.687000	0.46976	0.496000	0.27904	0.467000	0.42956	CGG	G|0.847;A|0.153	0.153	strong		0.378	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	
KRT74	121391	hgsc.bcm.edu	37	12	52966390	52966390	+	Missense_Mutation	SNP	A	A	T	rs11170176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:52966390A>T	ENST00000305620.2	-	2	580	c.533T>A	c.(532-534)cTg>cAg	p.L178Q	KRT74_ENST00000549343.1_Missense_Mutation_p.L178Q	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	178	Linker 1.|Rod.		L -> Q (in dbSNP:rs11170176).		intermediate filament cytoskeleton organization (GO:0045104)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	keratin filament binding (GO:1990254)|structural molecule activity (GO:0005198)			kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	28				BRCA - Breast invasive adenocarcinoma(357;0.191)		GTTCAGGTCCAGCTGCTGCAG	0.557													A|||	1108	0.221246	0.2761	0.098	5008	,	,		20769	0.376		0.1193	False		,,,				2504	0.18				p.L178Q		Atlas-SNP	.											.	KRT74	67	.	0			c.T533A						PASS	.	A	GLN/LEU	1196,3210	417.4+/-337.9	170,856,1177	129.0	118.0	122.0		533	4.7	1.0	12	dbSNP_120	122	1086,7514	227.1+/-262.6	68,950,3282	no	missense	KRT74	NM_175053.3	113	238,1806,4459	TT,TA,AA		12.6279,27.1448,17.5457	benign	178/530	52966390	2282,10724	2203	4300	6503	SO:0001583	missense	121391	exon2			AGGTCCAGCTGCT	BK000977	CCDS8832.1	12q13.13	2013-06-25			ENSG00000170484	ENSG00000170484		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28929	protein-coding gene	gene with protein product		608248				12648212, 16831889	Standard	NM_175053		Approved	K6IRS4, KRT5C, KRT6IRS4	uc001sap.1	Q7RTS7	OTTHUMG00000169658	ENST00000305620.2:c.533T>A	12.37:g.52966390A>T	ENSP00000307240:p.Leu178Gln	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	223	118	0.529148	NM_175053	B5MD61|Q86Y45	Missense_Mutation	SNP	ENST00000305620.2	37	CCDS8832.1	456	0.2087912087912088	126	0.25609756097560976	42	0.11602209944751381	189	0.3304195804195804	99	0.13060686015831136	A	15.55	2.865720	0.51588	0.271448	0.126279	ENSG00000170484	ENST00000549343;ENST00000305620	D;D	0.87491	-2.26;-2.26	4.71	4.71	0.59529	Filament (1);	0.324202	0.17383	N	0.176247	T	0.00012	0.0000	N	0.00113	-2.09	0.29642	P	0.844674	P	0.40578	0.722	P	0.46452	0.517	T	0.48547	-0.9026	9	0.02654	T	1	.	5.812	0.18471	0.6142:0.1334:0.0:0.2524	rs11170176	178	Q7RTS7	K2C74_HUMAN	Q	178	ENSP00000447447:L178Q;ENSP00000307240:L178Q	ENSP00000307240:L178Q	L	-	2	0	KRT74	51252657	0.974000	0.33945	1.000000	0.80357	0.981000	0.71138	2.808000	0.47963	2.066000	0.61787	0.528000	0.53228	CTG	A|0.812;T|0.188	0.188	strong		0.557	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053	
MLLT4	4301	hgsc.bcm.edu	37	6	168317816	168317816	+	Silent	SNP	A	A	C	rs6906754	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168317816A>C	ENST00000447894.2	+	19	2592	c.2592A>C	c.(2590-2592)ccA>ccC	p.P864P	MLLT4_ENST00000366806.2_Silent_p.P864P|MLLT4_ENST00000400822.3_Silent_p.P863P|MLLT4_ENST00000392108.3_Silent_p.P864P|MLLT4_ENST00000392112.1_Silent_p.P848P|MLLT4_ENST00000351017.4_Silent_p.P871P|MLLT4_ENST00000344191.4_Silent_p.P864P			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	864	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		ATGACATTCCAAATATAAACA	0.348			T	MLL	AL								A|||	964	0.192492	0.2247	0.2118	5008	,	,		16930	0.1935		0.0775	False		,,,				2504	0.2526				p.P864P		Atlas-SNP	.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	.	MLLT4	351	.	0			c.A2592C						PASS	.	A	,	798,3608	317.7+/-295.3	65,668,1470	136.0	129.0	131.0		2592,2544	-11.0	0.0	6	dbSNP_116	131	680,7920	169.0+/-220.4	26,628,3646	no	coding-synonymous,coding-synonymous	MLLT4	NM_001040000.2,NM_001207008.1	,	91,1296,5116	CC,CA,AA		7.907,18.1117,11.364	,	864/1652,848/1744	168317816	1478,11528	2203	4300	6503	SO:0001819	synonymous_variant	4301	exon19			CATTCCAAATATA	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.2592A>C	6.37:g.168317816A>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	198	93	0.469697	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				A|0.869;C|0.131	0.131	strong		0.348	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
ZSCAN25	221785	hgsc.bcm.edu	37	7	99217424	99217424	+	Silent	SNP	G	G	A	rs10282706	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99217424G>A	ENST00000394152.2	+	4	522	c.195G>A	c.(193-195)gaG>gaA	p.E65E	ZSCAN25_ENST00000466948.1_3'UTR|ZSCAN25_ENST00000262941.6_Silent_p.E65E|ZSCAN25_ENST00000334715.3_Silent_p.E65E	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	65	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				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)										AGCTCCAGGAGCTCTGTCGTC	0.612													A|||	1722	0.34385	0.6914	0.1916	5008	,	,		18685	0.2817		0.0596	False		,,,				2504	0.3384				p.E65E		Atlas-SNP	.											.	.	.	.	0			c.G195A						PASS	.	A		2514,1892	542.5+/-376.0	714,1086,403	71.0	79.0	77.0		195	-0.9	1.0	7	dbSNP_119	77	674,7926	788.3+/-407.6	32,610,3658	no	coding-synonymous	ZNF498	NM_145115.2		746,1696,4061	AA,AG,GG		7.8372,42.9414,24.5118		65/545	99217424	3188,9818	2203	4300	6503	SO:0001819	synonymous_variant	221785	exon4			CCAGGAGCTCTGT	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"""-"", ""Zinc fingers, C2H2-type"""	21961	protein-coding gene	gene with protein product			"""zinc finger protein 498"""	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.195G>A	7.37:g.99217424G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	92	47	0.51087	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Silent	SNP	ENST00000394152.2	37	CCDS5671.2																																																																																			G|0.735;A|0.265	0.265	strong		0.612	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115	
OR5F1	338674	hgsc.bcm.edu	37	11	55761786	55761786	+	Missense_Mutation	SNP	A	A	C	rs61888467	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55761786A>C	ENST00000278409.1	-	1	315	c.316T>G	c.(316-318)Tcc>Gcc	p.S106A		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	106					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					GTCGCCAGGGAGATAAAGAAG	0.468													C|||	204	0.0407348	0.0219	0.0389	5008	,	,		18550	0.002		0.0934	False		,,,				2504	0.0532				p.S106A		Atlas-SNP	.											.	OR5F1	116	.	0			c.T316G						PASS	.	C	ALA/SER	122,4280	812.3+/-416.1	3,116,2082	89.0	86.0	87.0		316	-3.5	0.0	11	dbSNP_129	87	669,7923	786.0+/-407.6	34,601,3661	no	missense	OR5F1	NM_003697.1	99	37,717,5743	CC,CA,AA		7.7863,2.7715,6.0874	benign	106/315	55761786	791,12203	2201	4296	6497	SO:0001583	missense	338674	exon1			CCAGGGAGATAAA	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"""GPCR / Class A : Olfactory receptors"""	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.316T>G	11.37:g.55761786A>C	ENSP00000278409:p.Ser106Ala	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	220	80	0.363636	NM_003697	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	37	CCDS31515.1	84	0.038461538461538464	11	0.022357723577235773	10	0.027624309392265192	1	0.0017482517482517483	62	0.08179419525065963	C	0.001	-2.926568	0.00054	0.027715	0.077863	ENSG00000149133	ENST00000278409	T	0.00922	5.54	3.03	-3.49	0.04724	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	N	0.04090	-0.28	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41805	-0.9488	9	0.02654	T	1	.	0.8715	0.01215	0.2324:0.2934:0.1152:0.359	rs61888467	106	O95221	OR5F1_HUMAN	A	106	ENSP00000278409:S106A	ENSP00000278409:S106A	S	-	1	0	OR5F1	55518362	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-4.178000	0.00279	-0.761000	0.04670	-1.872000	0.00552	TCC	A|0.961;C|0.039	0.039	strong		0.468	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697	
MT-ND5	4540	hgsc.bcm.edu	37	M	14037	14037	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:14037A>G	ENST00000361567.2	+	1	1701	c.1701A>G	c.(1699-1701)tcA>tcG	p.S567S	MT-TE_ENST00000387459.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	567					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AAAACAATTTCACAGCACCAA	0.448																																					p.S567S		Atlas-SNP	.											.	.	.	.	0			c.A1701G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			AATTTCACAGCAC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1701A>G	M.37:g.14037A>G		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	28	27	0.964286	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.448	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
BRICD5	283870	hgsc.bcm.edu	37	16	2260567	2260567	+	Missense_Mutation	SNP	C	C	T	rs26857	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2260567C>T	ENST00000562360.1	-	2	135	c.136G>A	c.(136-138)Gtt>Att	p.V46I	BRICD5_ENST00000328540.3_Missense_Mutation_p.V46I|RP11-304L19.8_ENST00000561544.1_lincRNA|BRICD5_ENST00000566018.1_Missense_Mutation_p.V46I			Q6PL45	BRID5_HUMAN	BRICHOS domain containing 5	46			V -> I (in dbSNP:rs26857). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)		p.V46I(1)									CCAGCCACAACCCCCACAGCG	0.662													C|||	2582	0.515575	0.497	0.4841	5008	,	,		16452	0.6032		0.4702	False		,,,				2504	0.5194				p.V46I		Atlas-SNP	.											C16orf79,NS,lymphoid_neoplasm,0,1	.	.	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G136A						PASS	.	C	ILE/VAL	2185,2205		554,1077,564	22.0	27.0	25.0		136	1.2	0.0	16	dbSNP_76	25	4030,4558		965,2100,1229	yes	missense	C16orf79	NM_182563.3	29	1519,3177,1793	TT,TC,CC		46.9259,49.7722,47.8887	benign	46/229	2260567	6215,6763	2195	4294	6489	SO:0001583	missense	283870	exon2			CCACAACCCCCAC	BC039154	CCDS10463.1	16p13.3	2012-10-10	2012-10-10	2012-10-10	ENSG00000182685	ENSG00000182685		"""BRICHOS domain containing"""	28309	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 79"""	C16orf79		12477932	Standard	NM_182563		Approved	MGC21830	uc002cpi.2	Q6PL45	OTTHUMG00000128831	ENST00000562360.1:c.136G>A	16.37:g.2260567C>T	ENSP00000455052:p.Val46Ile	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	NM_182563	C9J7K2|Q8IXU9	Missense_Mutation	SNP	ENST00000562360.1	37	CCDS10463.1	1127	0.5160256410256411	252	0.5121951219512195	168	0.46408839779005523	349	0.6101398601398601	358	0.47229551451187335	C	0.024	-1.388868	0.01185	0.497722	0.469259	ENSG00000182685	ENST00000328540	T	0.24151	1.87	5.48	1.17	0.20885	.	0.645519	0.15632	N	0.252357	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.11235	0.004;0.003	B;B	0.13407	0.002;0.009	T	0.43845	-0.9366	9	0.05525	T	0.97	-1.5005	4.4636	0.11678	0.0:0.5028:0.1556:0.3417	rs26857;rs1640774;rs4018449;rs12931243;rs17853879;rs59033835;rs26857	46;46	Q6PL45;Q6PL45-2	CP079_HUMAN;.	I	46	ENSP00000332389:V46I	ENSP00000332389:V46I	V	-	1	0	C16orf79	2200568	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	0.241000	0.18065	0.298000	0.22638	-0.137000	0.14449	GTT	C|0.523;T|0.477	0.477	strong		0.662	BRICD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435091.1	NM_182563	
FMO3	2328	hgsc.bcm.edu	37	1	171083174	171083174	+	Silent	SNP	C	C	T	rs909530	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:171083174C>T	ENST00000367755.4	+	7	966	c.855C>T	c.(853-855)aaC>aaT	p.N285N	FMO3_ENST00000392085.2_Silent_p.N285N|FMO3_ENST00000542847.1_Silent_p.N265N|FMO3_ENST00000538429.1_Silent_p.N222N	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	285					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)	p.N285N(1)		endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CTGTATTTAACGATGAGCTCC	0.413													T|||	1671	0.333666	0.4576	0.3487	5008	,	,		19836	0.3452		0.2356	False		,,,				2504	0.2444				p.N285N		Atlas-SNP	.											FMO3,NS,carcinoma,0,1	FMO3	73	1	1	Substitution - coding silent(1)	stomach(1)	c.C855T						PASS	.	T	,	1905,2501	627.8+/-395.0	406,1093,704	84.0	76.0	79.0		855,855	0.8	1.0	1	dbSNP_86	79	2094,6506	717.2+/-406.1	263,1568,2469	no	coding-synonymous,coding-synonymous	FMO3	NM_001002294.2,NM_006894.5	,	669,2661,3173	TT,TC,CC		24.3488,43.2365,30.7473	,	285/533,285/533	171083174	3999,9007	2203	4300	6503	SO:0001819	synonymous_variant	2328	exon7			ATTTAACGATGAG	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.855C>T	1.37:g.171083174C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	192	192	1	NM_006894	B2R816|Q14854|Q8N5N5	Silent	SNP	ENST00000367755.4	37	CCDS1292.1																																																																																			C|0.665;T|0.335	0.335	strong		0.413	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	
OR2AG1	144125	hgsc.bcm.edu	37	11	6806496	6806496	+	Silent	SNP	T	T	C	rs11041022	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6806496T>C	ENST00000307401.4	+	1	249	c.228T>C	c.(226-228)gtT>gtC	p.V76V		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	76						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TCACATCTGTTGTCACTCCCA	0.567													T|||	967	0.193091	0.1059	0.2032	5008	,	,		21659	0.1825		0.328	False		,,,				2504	0.1759				p.V76V		Atlas-SNP	.											OR2AG1,NS,carcinoma,+1,1	OR2AG1	57	1	0			c.T228C						PASS	.	T		573,3829	255.5+/-260.7	35,503,1663	157.0	143.0	148.0		228	1.6	1.0	11	dbSNP_120	148	2885,5703	452.9+/-363.1	504,1877,1913	no	coding-synonymous	OR2AG1	NM_001004489.2		539,2380,3576	CC,CT,TT		33.5934,13.0168,26.6205		76/317	6806496	3458,9532	2201	4294	6495	SO:0001819	synonymous_variant	144125	exon1			ATCTGTTGTCACT	AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"""GPCR / Class A : Olfactory receptors"""	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.228T>C	11.37:g.6806496T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	200	110	0.55	NM_001004489	B9EKV7|Q6IFG7|Q96R26	Silent	SNP	ENST00000307401.4	37	CCDS31414.1																																																																																			T|0.789;C|0.211	0.211	strong		0.567	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385980.1	NM_001004489	
GAA	2548	hgsc.bcm.edu	37	17	78078656	78078656	+	Missense_Mutation	SNP	G	G	A	rs1800299	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78078656G>A	ENST00000302262.3	+	2	490	c.271G>A	c.(271-273)Gat>Aat	p.D91N	GAA_ENST00000390015.3_Missense_Mutation_p.D91N	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	91	P-type. {ECO:0000255|PROSITE- ProRule:PRU00779}.		D -> N (in allele GAA*2; lower affinity for glycogen and starch but not for lower-molecular weight substrates; dbSNP:rs1800299). {ECO:0000269|PubMed:21109266, ECO:0000269|PubMed:2203258, ECO:0000269|PubMed:9521422}.		cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	CAGCCGCTTCGATTGCGCCCC	0.692													G|||	58	0.0115815	0.0053	0.0173	5008	,	,		15176	0.001		0.0278	False		,,,				2504	0.0102				p.D91N		Atlas-SNP	.											.	GAA	66	.	0			c.G271A	GRCh37	CD983801	GAA	D	rs1800299	PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP	29,4377	34.3+/-65.2	0,29,2174	35.0	33.0	34.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	271,271,271	4.9	1.0	17	dbSNP_89	34	271,8329	100.8+/-162.1	6,259,4035	yes	missense,missense,missense	GAA	NM_000152.3,NM_001079803.1,NM_001079804.1	23,23,23	6,288,6209	AA,AG,GG		3.1512,0.6582,2.3066	probably-damaging,probably-damaging,probably-damaging	91/953,91/953,91/953	78078656	300,12706	2203	4300	6503	SO:0001583	missense	2548	exon3			CGCTTCGATTGCG		CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"""Pompe disease"", ""glycogen storage disease type II"""	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.271G>A	17.37:g.78078656G>A	ENSP00000305692:p.Asp91Asn	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	122	72	0.590164	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Missense_Mutation	SNP	ENST00000302262.3	37	CCDS32760.1	34	0.015567765567765568	4	0.008130081300813009	8	0.022099447513812154	0	0.0	22	0.029023746701846966	G	16.20	3.054964	0.55325	0.006582	0.031512	ENSG00000171298	ENST00000302262;ENST00000390015	T;T	0.58210	0.35;0.35	4.94	4.94	0.65067	P-type trefoil, conserved site (1);P-type trefoil (4);	0.000000	0.85682	D	0.000000	T	0.41811	0.1175	L	0.45051	1.395	0.53688	D	0.99997	D	0.89917	1.0	D	0.91635	0.999	T	0.56836	-0.7913	10	0.41790	T	0.15	-47.1701	16.922	0.86166	0.0:0.0:1.0:0.0	rs1800299;rs52818006	91	P10253	LYAG_HUMAN	N	91	ENSP00000305692:D91N;ENSP00000374665:D91N	ENSP00000305692:D91N	D	+	1	0	GAA	75693251	1.000000	0.71417	0.992000	0.48379	0.213000	0.24496	9.466000	0.97665	2.279000	0.76181	0.655000	0.94253	GAT	G|0.979;A|0.021	0.021	strong		0.692	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		
ANLN	54443	hgsc.bcm.edu	37	7	36459076	36459076	+	Silent	SNP	G	G	A	rs17213431	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:36459076G>A	ENST00000265748.2	+	10	2078	c.1857G>A	c.(1855-1857)gtG>gtA	p.V619V	ANLN_ENST00000396068.2_Silent_p.V582V	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	619	Interaction with F-actin.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						CAGTTGGTGTGGTAAGTCCAG	0.418													G|||	357	0.0712859	0.0045	0.0677	5008	,	,		20963	0.0337		0.1382	False		,,,				2504	0.1339				p.V619V		Atlas-SNP	.											.	ANLN	101	.	0			c.G1857A						PASS	.	G		143,4263	99.8+/-138.5	7,129,2067	90.0	83.0	85.0		1857	1.0	0.4	7	dbSNP_123	85	1135,7465	234.9+/-267.6	60,1015,3225	no	coding-synonymous	ANLN	NM_018685.2		67,1144,5292	AA,AG,GG		13.1977,3.2456,9.8262		619/1125	36459076	1278,11728	2203	4300	6503	SO:0001819	synonymous_variant	54443	exon10			TGGTGTGGTAAGT	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"""Pleckstrin homology (PH) domain containing"""	14082	protein-coding gene	gene with protein product			"""anillin (Drosophila Scraps homolog), actin binding protein"", ""anillin, actin binding protein (scraps homolog, Drosophila)"""			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.1857G>A	7.37:g.36459076G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Silent	SNP	ENST00000265748.2	37	CCDS5447.1																																																																																			G|0.916;A|0.084	0.084	strong		0.418	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685	
SCARA3	51435	hgsc.bcm.edu	37	8	27516323	27516323	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27516323G>A	ENST00000301904.3	+	5	656	c.636G>A	c.(634-636)gaG>gaA	p.E212E	SCARA3_ENST00000337221.4_Silent_p.E212E	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	212					receptor-mediated endocytosis (GO:0006898)|response to oxidative stress (GO:0006979)|UV protection (GO:0009650)	collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)			breast(1)|large_intestine(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	9		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		TCACCCAGGAGTGCTACGATG	0.612																																					p.E212E		Atlas-SNP	.											.	SCARA3	93	.	0			c.G636A						PASS	.						38.0	39.0	39.0					8																	27516323		2203	4300	6503	SO:0001819	synonymous_variant	51435	exon5			CCAGGAGTGCTAC	AB007829	CCDS34870.1, CCDS34871.1	8p21	2010-03-24			ENSG00000168077	ENSG00000168077			19000	protein-coding gene	gene with protein product	"""macrophage scavenger receptor-like 1"""	602728				9747040, 9580669	Standard	NM_182826		Approved	CSR1, CSR, MSLR1, APC7, MSRL1	uc003xga.1	Q6AZY7	OTTHUMG00000163898	ENST00000301904.3:c.636G>A	8.37:g.27516323G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_182826	Q9UM15|Q9UM16	Silent	SNP	ENST00000301904.3	37	CCDS34871.1																																																																																			.	.	none		0.612	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240	
DNAI2	64446	hgsc.bcm.edu	37	17	72301432	72301432	+	Silent	SNP	A	A	G	rs8073660	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72301432A>G	ENST00000311014.6	+	9	1129	c.1062A>G	c.(1060-1062)gaA>gaG	p.E354E	DNAI2_ENST00000579490.1_Silent_p.E411E|DNAI2_ENST00000446837.2_Silent_p.E354E|RP11-647F2.2_ENST00000585167.1_RNA|AC103809.1_ENST00000516976.1_RNA|DNAI2_ENST00000307504.5_Silent_p.E211E|DNAI2_ENST00000582036.1_Silent_p.E354E			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	354					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						CGTCAGCTGAAAAGATTGTGT	0.592									Kartagener syndrome				G|||	1997	0.398762	0.2965	0.3732	5008	,	,		18768	0.254		0.6103	False		,,,				2504	0.4867				p.E354E		Atlas-SNP	.											.	DNAI2	102	.	0			c.A1062G						PASS	.	G	,	1607,2799	664.0+/-401.3	316,975,912	107.0	87.0	94.0		1062,1062	5.0	1.0	17	dbSNP_116	94	5345,3255	489.4+/-372.6	1675,1995,630	no	coding-synonymous,coding-synonymous	DNAI2	NM_001172810.1,NM_023036.4	,	1991,2970,1542	GG,GA,AA		37.8488,36.473,46.5477	,	354/594,354/606	72301432	6952,6054	2203	4300	6503	SO:0001819	synonymous_variant	64446	exon9	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGCTGAAAAGATT	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"""Axonemal dyneins"", ""WD repeat domain containing"""	18744	protein-coding gene	gene with protein product	"""dynein intermediate chain 2"""	605483	"""dynein, axonemal, intermediate polypeptide 2"""			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.1062A>G	17.37:g.72301432A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																			A|0.535;G|0.465	0.465	strong		0.592	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
COL6A1	1291	hgsc.bcm.edu	37	21	47423507	47423507	+	Silent	SNP	G	G	A	rs71336107|rs1053315	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47423507G>A	ENST00000361866.3	+	35	2781	c.2667G>A	c.(2665-2667)gcG>gcA	p.A889A	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	889	C-terminal globular domain.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)	p.A889A(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		CAGAGCGGGCGTCGCTGCAGT	0.682													G|||	1343	0.268171	0.4077	0.281	5008	,	,		14817	0.1379		0.2734	False		,,,				2504	0.1994				p.A889A		Atlas-SNP	.											COL6A1,NS,carcinoma,0,2	COL6A1	101	2	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2667A						PASS	.	G		1718,2686		346,1026,830	29.0	29.0	29.0		2667	-2.6	0.0	21	dbSNP_86	29	2667,5931		438,1791,2070	no	coding-synonymous	COL6A1	NM_001848.2		784,2817,2900	AA,AG,GG		31.0188,39.01,33.7256		889/1029	47423507	4385,8617	2202	4299	6501	SO:0001819	synonymous_variant	1291	exon35			GCGGGCGTCGCTG	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2667G>A	21.37:g.47423507G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Silent	SNP	ENST00000361866.3	37	CCDS13727.1																																																																																			ATC|0.500;GTT|0.500	.	alt		0.682	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
MTRR	4552	hgsc.bcm.edu	37	5	7892933	7892933	+	Silent	SNP	A	A	G	rs35890938	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7892933A>G	ENST00000264668.2	+	11	1575	c.1545A>G	c.(1543-1545)gtA>gtG	p.V515V	MTRR_ENST00000440940.2_Silent_p.V488V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	515	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GGAAGGGAGTATGTACAGGCT	0.473													G|||	40	0.00798722	0.0015	0.0245	5008	,	,		18051	0.0		0.0189	False		,,,				2504	0.002				p.V515V		Atlas-SNP	.											.	MTRR	74	.	0			c.A1545G						PASS	.	G	,	46,4360	822.1+/-416.4	0,46,2157	150.0	129.0	136.0		1464,1545	0.7	0.5	5	dbSNP_126	136	207,8393	810.1+/-407.1	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,249,6252	GG,GA,AA		2.407,1.044,1.9453	,	488/699,515/726	7892933	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			GGGAGTATGTACA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1545A>G	5.37:g.7892933A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	186	93	0.5	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
SLC7A7	9056	hgsc.bcm.edu	37	14	23248112	23248112	+	Silent	SNP	A	A	G	rs1805061	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23248112A>G	ENST00000397532.3	-	4	1185	c.660T>C	c.(658-660)ggT>ggC	p.G220G	SLC7A7_ENST00000397529.2_Silent_p.G220G|SLC7A7_ENST00000554517.1_5'UTR|SLC7A7_ENST00000555702.1_Silent_p.G220G|SLC7A7_ENST00000554061.1_5'UTR|SLC7A7_ENST00000285850.7_Silent_p.G220G|SLC7A7_ENST00000397528.4_Silent_p.G220G			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7	220					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		CAAATGATGAACCCTCAAAGG	0.488													A|||	1191	0.237819	0.2874	0.268	5008	,	,		20311	0.3373		0.1392	False		,,,				2504	0.1483				p.G220G		Atlas-SNP	.											.	SLC7A7	36	.	0			c.T660C						PASS	.	A	,,	1132,3274	406.2+/-333.8	145,842,1216	106.0	94.0	98.0		660,660,660	-4.1	1.0	14	dbSNP_89	98	1125,7475	231.7+/-265.6	70,985,3245	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC7A7	NM_001126105.2,NM_001126106.2,NM_003982.3	,,	215,1827,4461	GG,GA,AA		13.0814,25.6922,17.3535	,,	220/512,220/512,220/512	23248112	2257,10749	2203	4300	6503	SO:0001819	synonymous_variant	9056	exon5			TGATGAACCCTCA	AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"""Solute carriers"""	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692	ENST00000397532.3:c.660T>C	14.37:g.23248112A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	149	70	0.469799	NM_001126105	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	Silent	SNP	ENST00000397532.3	37	CCDS9574.1																																																																																			A|0.800;G|0.200	0.200	strong		0.488	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3		
MT-CO3	4514	hgsc.bcm.edu	37	M	9716	9716	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:9716T>C	ENST00000362079.2	+	1	510	c.510T>C	c.(508-510)ggT>ggC	p.G170G	MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-ND4_ENST00000361381.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TS1_ENST00000387416.2_RNA			P00414	COX3_HUMAN	mitochondrially encoded cytochrome c oxidase III	170					aerobic electron transport chain (GO:0019646)|cellular metabolic process (GO:0044237)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(10)|kidney(14)|lung(1)|urinary_tract(1)	27						ATTTTACTGGGTCTCTATTTT	0.428																																					p.G170G		Atlas-SNP	.											.	.	.	.	0			c.T510C						PASS	.																																			SO:0001819	synonymous_variant	5742	exon1			ACTGGGTCTCTAT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198938	ENSG00000198938		"""Mitochondrial respiratory chain complex / Complex IV"""	7422	protein-coding gene	gene with protein product		516050	"""cytochrome c oxidase III"""	MTCO3			Standard			Approved	COX3, COIII, CO3		P00414		ENST00000362079.2:c.510T>C	M.37:g.9716T>C		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	ENST00000362079	Q14Y83	Silent	SNP	ENST00000362079.2	37																																																																																				.	.	none		0.428	MT-CO3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024032	
HIF1A	3091	hgsc.bcm.edu	37	14	62194239	62194239	+	Silent	SNP	G	G	A	rs17099141	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:62194239G>A	ENST00000337138.4	+	6	904	c.639G>A	c.(637-639)aaG>aaA	p.K213K	HIF1A_ENST00000557538.1_Silent_p.K154K|HIF1A-AS2_ENST00000554254.1_lincRNA|HIF1A_ENST00000394997.1_Silent_p.K214K|HIF1A_ENST00000323441.6_Silent_p.K213K|HIF1A_ENST00000539097.1_Silent_p.K237K|HIF1A_ENST00000557206.1_3'UTR	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	213	Interaction with TSGA10. {ECO:0000250}.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	GTGGGTATAAGAAACCACCTA	0.408													G|||	121	0.0241613	0.062	0.0173	5008	,	,		18532	0.0		0.0229	False		,,,				2504	0.0041				p.K237K		Atlas-SNP	.											HIF1A,brain,glioma,+2,27	HIF1A	120	27	0			c.G711A						PASS	.	G	,	274,4132	154.4+/-187.8	11,252,1940	173.0	147.0	156.0		639,639	5.0	1.0	14	dbSNP_123	156	159,8441	76.0+/-138.7	0,159,4141	no	coding-synonymous,coding-synonymous	HIF1A	NM_001530.3,NM_181054.2	,	11,411,6081	AA,AG,GG		1.8488,6.2188,3.3292	,	213/827,213/736	62194239	433,12573	2203	4300	6503	SO:0001819	synonymous_variant	3091	exon6			GTATAAGAAACCA	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"""Basic helix-loop-helix proteins"""	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.639G>A	14.37:g.62194239G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	120	50	0.416667	NM_001243084	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Silent	SNP	ENST00000337138.4	37	CCDS9753.1																																																																																			G|0.967;A|0.033	0.033	strong		0.408	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530	
DOLPP1	57171	hgsc.bcm.edu	37	9	131848488	131848488	+	Missense_Mutation	SNP	G	G	A	rs149976737	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:131848488G>A	ENST00000372546.4	+	6	564	c.532G>A	c.(532-534)Gcc>Acc	p.A178T	DOLPP1_ENST00000406974.3_Intron|DOLPP1_ENST00000540102.1_Intron	NM_020438.4	NP_065171.2	Q86YN1	DOPP1_HUMAN	dolichyldiphosphatase 1	178					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|lipid biosynthetic process (GO:0008610)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	dolichyldiphosphatase activity (GO:0047874)			endometrium(3)|kidney(2)|lung(7)|skin(1)	13						CATGGCCATCGCCTGGTTCAT	0.622													G|||	5	0.000998403	0.0	0.0	5008	,	,		20902	0.0		0.005	False		,,,				2504	0.0				p.A178T		Atlas-SNP	.											.	DOLPP1	17	.	0			c.G532A						PASS	.	G	,THR/ALA	0,4406		0,0,2203	103.0	80.0	87.0		,532	5.5	1.0	9	dbSNP_134	87	5,8595	4.3+/-15.6	0,5,4295	yes	intron,missense	DOLPP1	NM_001135917.1,NM_020438.4	,58	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	,benign	,178/239	131848488	5,13001	2203	4300	6503	SO:0001583	missense	57171	exon6			GCCATCGCCTGGT	BC009493	CCDS6918.1, CCDS48039.1	9q34.1	2013-05-21	2013-05-21		ENSG00000167130	ENSG00000167130	3.6.1.43		29565	protein-coding gene	gene with protein product	"""linked to Surfeit genes in Fugu rubripes 2"""	614516	"""dolichyl pyrophosphate phosphatase 1"""			10369878, 12198133	Standard	NM_020438		Approved	LSFR2	uc004bxc.3	Q86YN1	OTTHUMG00000020771	ENST00000372546.4:c.532G>A	9.37:g.131848488G>A	ENSP00000361625:p.Ala178Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_020438	A8K3U8|B0QZG4|Q96GF8|Q9Y3G1	Missense_Mutation	SNP	ENST00000372546.4	37	CCDS6918.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	17.16	3.317356	0.60524	0.0	5.81E-4	ENSG00000167130	ENST00000372546	T	0.75589	-0.95	5.51	5.51	0.81932	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.107308	0.64402	D	0.000004	T	0.70316	0.3210	L	0.49256	1.55	0.80722	D	1	P	0.50710	0.938	B	0.41571	0.36	T	0.68969	-0.5269	10	0.24483	T	0.36	-10.1792	18.4662	0.90755	0.0:0.0:1.0:0.0	.	178	Q86YN1	DOPP1_HUMAN	T	178	ENSP00000361625:A178T	ENSP00000361625:A178T	A	+	1	0	DOLPP1	130888309	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	7.230000	0.78097	2.604000	0.88044	0.456000	0.33151	GCC	G|0.999;A|0.001	0.001	strong		0.622	DOLPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054548.4	NM_020438	
RYR1	6261	hgsc.bcm.edu	37	19	38956803	38956803	+	Silent	SNP	G	G	A	rs2228069	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:38956803G>A	ENST00000359596.3	+	24	2943	c.2943G>A	c.(2941-2943)acG>acA	p.T981T	RYR1_ENST00000360985.3_Silent_p.T981T|RYR1_ENST00000355481.4_Silent_p.T981T			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	981	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CGGCGCAGACGACACTGGTGG	0.657													G|||	2732	0.545527	0.5212	0.6599	5008	,	,		15571	0.5298		0.6412	False		,,,				2504	0.4151				p.T981T		Atlas-SNP	.											.	RYR1	708	.	0			c.G2943A						PASS	.	G	,	2462,1938	602.3+/-389.9	704,1054,442	34.0	35.0	35.0		2943,2943	-7.6	0.1	19	dbSNP_98	35	5299,3299	624.8+/-397.6	1663,1973,663	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	2367,3027,1105	AA,AG,GG		38.3694,44.0455,40.2908	,	981/5039,981/5034	38956803	7761,5237	2200	4299	6499	SO:0001819	synonymous_variant	6261	exon24			GCAGACGACACTG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.2943G>A	19.37:g.38956803G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			A|0.594;C|0.000;G|0.406	0.594	strong		0.657	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
COPS2	9318	hgsc.bcm.edu	37	15	49429410	49429410	+	Silent	SNP	A	A	G	rs17473148	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:49429410A>G	ENST00000388901.5	-	6	550	c.477T>C	c.(475-477)taT>taC	p.Y159Y	Y_RNA_ENST00000363250.1_RNA|COPS2_ENST00000299259.6_Silent_p.Y166Y|COPS2_ENST00000542928.1_Silent_p.Y95Y	NM_001143887.1|NM_004236.3	NP_001137359.1|NP_004227.1	P61201	CSN2_HUMAN	COP9 signalosome subunit 2	159					cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(2)	18		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		CTCGTTCTAAATATAATTTTC	0.328													A|||	553	0.110423	0.0174	0.1441	5008	,	,		13666	0.006		0.2356	False		,,,				2504	0.1912				p.Y166Y	NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)	Atlas-SNP	.											.	COPS2	41	.	0			c.T498C						PASS	.	A	,	194,4196	110.8+/-149.0	6,182,2007	38.0	41.0	40.0		498,477	3.2	1.0	15	dbSNP_123	40	1717,6871	306.4+/-307.9	178,1361,2755	no	coding-synonymous,coding-synonymous	COPS2	NM_001143887.1,NM_004236.3	,	184,1543,4762	GG,GA,AA		19.993,4.4191,14.7249	,	166/451,159/444	49429410	1911,11067	2195	4294	6489	SO:0001819	synonymous_variant	9318	exon6			TTCTAAATATAAT	AF212227	CCDS32235.1, CCDS45257.1	15q21.2	2013-03-14	2013-03-14						30747	protein-coding gene	gene with protein product		604508	"""COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)"""			7776974, 9535219	Standard	NM_004236		Approved	TRIP15, ALIEN, CSN2	uc001zxh.3	P61201		ENST00000388901.5:c.477T>C	15.37:g.49429410A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_001143887	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Silent	SNP	ENST00000388901.5	37	CCDS32235.1																																																																																			A|0.868;G|0.132	0.132	strong		0.328	COPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417840.1	NM_004236	
SCN7A	6332	hgsc.bcm.edu	37	2	167313451	167313451	+	Missense_Mutation	SNP	T	T	C	rs11888208	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:167313451T>C	ENST00000409855.1	-	10	1345	c.1219A>G	c.(1219-1221)Ata>Gta	p.I407V		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	407			I -> V (in dbSNP:rs11888208).		membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TTCTTAGATATTTCACCAACT	0.333													T|||	593	0.118411	0.177	0.0692	5008	,	,		5681	0.0208		0.1362	False		,,,				2504	0.1564				p.I407V		Atlas-SNP	.											.	SCN7A	410	.	0			c.A1219G						PASS	.	T	VAL/ILE	552,3072		45,462,1305	70.0	62.0	64.0		1219	3.0	0.0	2	dbSNP_120	64	1238,6908		100,1038,2935	yes	missense	SCN7A	NM_002976.3	29	145,1500,4240	CC,CT,TT		15.1976,15.2318,15.2082	benign	407/1683	167313451	1790,9980	1812	4073	5885	SO:0001583	missense	6332	exon10			TAGATATTTCACC	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.1219A>G	2.37:g.167313451T>C	ENSP00000386796:p.Ile407Val	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	192	96	0.5	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	217	0.09935897435897435	74	0.15040650406504066	29	0.08011049723756906	12	0.02097902097902098	102	0.1345646437994723	T	12.48	1.952025	0.34471	0.152318	0.151976	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992	D;D	0.96554	-4.03;-4.05	5.35	3.01	0.34805	.	1.133800	0.06559	N	0.746436	T	0.06325	0.0163	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.66035	-0.6023	9	0.72032	D	0.01	.	4.7931	0.13259	0.0:0.4109:0.0:0.5891	rs11888208;rs52816781;rs60443139;rs11888208	407	Q01118	SCN7A_HUMAN	V	407	ENSP00000386796:I407V;ENSP00000413699:I407V	ENSP00000259060:I407V	I	-	1	0	SCN7A	167021697	0.429000	0.25530	0.003000	0.11579	0.002000	0.02628	2.172000	0.42463	0.868000	0.35678	0.454000	0.30748	ATA	T|0.896;C|0.104	0.104	strong		0.333	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
NSF	4905	hgsc.bcm.edu	37	17	44828931	44828931	+	Silent	SNP	G	G	A	rs199533	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44828931G>A	ENST00000398238.4	+	19	2213	c.2106G>A	c.(2104-2106)aaG>aaA	p.K702K	NSF_ENST00000575068.1_Silent_p.K697K|NSF_ENST00000225282.8_Silent_p.K608K	NM_006178.3	NP_006169.2	P46459	NSF_HUMAN	N-ethylmaleimide-sensitive factor	702					exocytosis (GO:0006887)|plasma membrane fusion (GO:0045026)|positive regulation of receptor recycling (GO:0001921)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|syntaxin-1 binding (GO:0017075)			kidney(2)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		AAGGGAAGAAGGTCTGGATAG	0.408													G|||	396	0.0790735	0.0106	0.1513	5008	,	,		17691	0.001		0.2227	False		,,,				2504	0.0532				p.K702K	Ovarian(25;472 742 1472 36813 50223)	Atlas-SNP	.											.	NSF	27	.	0			c.G2106A						PASS	.	G		146,3720		4,138,1791	115.0	107.0	110.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2106	0.6	1.0	17	dbSNP_79	110	1742,6542		181,1380,2581	yes	coding-synonymous	NSF	NM_006178.3		185,1518,4372	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	21.0285,3.7765,15.5391		702/745	44828931	1888,10262	1933	4142	6075	SO:0001819	synonymous_variant	4905	exon19			GAAGAAGGTCTGG		CCDS42354.1	17q21	2010-04-21			ENSG00000073969	ENSG00000073969		"""ATPases / AAA-type"""	8016	protein-coding gene	gene with protein product	"""N-ethylmaleimide-sensitive factor-like protein"""	601633				1315316, 8875895	Standard	NM_006178		Approved	SKD2	uc002iku.3	P46459	OTTHUMG00000134315	ENST00000398238.4:c.2106G>A	17.37:g.44828931G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_006178	A8K2D9|B4DFA2|Q8N6D7|Q9UKZ2	Silent	SNP	ENST00000398238.4	37	CCDS42354.1																																																																																			G|0.874;A|0.126	0.126	strong		0.408	NSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259348.2	NM_006178	
MT-ATP6	4508	hgsc.bcm.edu	37	M	9055	9055	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:9055G>A	ENST00000361899.2	+	1	529	c.529G>A	c.(529-531)Gcc>Acc	p.A177T	MT-TG_ENST00000387429.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TS1_ENST00000387416.2_RNA			P00846	ATP6_HUMAN	mitochondrially encoded ATP synthase 6	177			A -> T (in dbSNP:rs9645429).		ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(7)|kidney(8)|prostate(1)	18						TAATTGGAAGCGCCACCCTAG	0.453																																					p.A177T		Atlas-SNP	.											.	.	.	.	0			c.G529A						PASS	.																																			SO:0001583	missense	0	exon1			GGAAGCGCCACCC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198899	ENSG00000198899		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7414	protein-coding gene	gene with protein product		516060	"""ATP synthase 6"", ""spicular retinitis pigmentosa with dementia, seizures, ataxia, proximal muscle weakness and sensory deficit"""	MTATP6, RP		7219534	Standard			Approved	ATP6, ATPase-6, Su6m		P00846		ENST00000361899.2:c.529G>A	M.37:g.9055G>A	ENSP00000354632:p.Ala177Thr	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	ENST00000361899	Q34772|Q5S8W5|Q5S9E7|Q5S9I6|Q5SA31|Q6RPB7|Q6VHC0|Q6VHE0|Q6WQF4|Q7YCC1|Q7YCF8|Q7YCG1|Q85KU8|Q85KX1|Q85L05|Q8HNQ4|Q8HNQ8|Q8WCX6|Q9B2U5|Q9B2Z2	Missense_Mutation	SNP	ENST00000361899.2	37																																																																																				.	.	none		0.453	MT-ATP6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024031	
TRAK2	66008	hgsc.bcm.edu	37	2	202252478	202252478	+	Silent	SNP	A	A	G	rs35620793	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:202252478A>G	ENST00000332624.3	-	13	2072	c.1644T>C	c.(1642-1644)agT>agC	p.S548S		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	548					protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						CTCGAAGGCAACTGGCACTGC	0.493													A|||	103	0.0205671	0.0038	0.0519	5008	,	,		19358	0.0		0.0586	False		,,,				2504	0.0031				p.S548S		Atlas-SNP	.											.	TRAK2	62	.	0			c.T1644C						PASS	.	A		41,4365	45.3+/-79.5	0,41,2162	99.0	103.0	102.0		1644	0.8	1.0	2	dbSNP_126	102	536,8064	147.7+/-203.1	16,504,3780	no	coding-synonymous	TRAK2	NM_015049.2		16,545,5942	GG,GA,AA		6.2326,0.9305,4.4364		548/915	202252478	577,12429	2203	4300	6503	SO:0001819	synonymous_variant	66008	exon13			AAGGCAACTGGCA	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"""gamma-aminobutyric acid(A) receptor-interacting factor"", ""milton homolog 2 (Drosophila)"", ""O-linked N-acetylglucosamine transferase interacting protein 98"""	607334	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"""	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.1644T>C	2.37:g.202252478A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	206	97	0.470874	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Silent	SNP	ENST00000332624.3	37	CCDS2347.1																																																																																			A|0.959;G|0.041	0.041	strong		0.493	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049	
IGSF10	285313	hgsc.bcm.edu	37	3	151155248	151155248	+	Silent	SNP	A	A	C	rs16863390	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:151155248A>C	ENST00000282466.3	-	6	7100	c.7101T>G	c.(7099-7101)ccT>ccG	p.P2367P	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2367	Ig-like C2-type 10.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGATTATTTCAGGTGGTGGGT	0.373													A|||	181	0.0361422	0.0008	0.0216	5008	,	,		21975	0.0843		0.0298	False		,,,				2504	0.0511				p.P2367P		Atlas-SNP	.											.	IGSF10	279	.	0			c.T7101G						PASS	.	A	,,	10,4396	17.9+/-39.9	0,10,2193	132.0	132.0	132.0		1182,1038,7101	-7.1	0.8	3	dbSNP_123	132	198,8402	86.9+/-149.2	4,190,4106	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	4,200,6299	CC,CA,AA		2.3023,0.227,1.5993	,,	394/651,346/603,2367/2624	151155248	208,12798	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			TATTTCAGGTGGT	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.7101T>G	3.37:g.151155248A>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	146	79	0.541096	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			A|0.969;C|0.031	0.031	strong		0.373	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
TCN1	6947	hgsc.bcm.edu	37	11	59623378	59623378	+	Missense_Mutation	SNP	C	C	A	rs34324219	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:59623378C>A	ENST00000257264.3	-	6	1005	c.901G>T	c.(901-903)Gat>Tat	p.D301Y	TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	301	Globular N-terminal alpha domain.		D -> Y (in dbSNP:rs34324219).		cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTGTTAATATCCAAGAAGGTC	0.448													c|||	262	0.0523163	0.0454	0.0663	5008	,	,		17482	0.0		0.1153	False		,,,				2504	0.0409				p.D301Y		Atlas-SNP	.											TCN1,lymph_node,lymphoid_neoplasm,0,2	TCN1	64	2	0			c.G901T						PASS	.		TYR/ASP	303,4099	164.4+/-196.0	12,279,1910	124.0	124.0	124.0		901	1.8	0.5	11	dbSNP_126	124	985,7605	212.8+/-253.0	50,885,3360	yes	missense	TCN1	NM_001062.3	160	62,1164,5270	AA,AC,CC		11.4668,6.8832,9.9138	probably-damaging	301/434	59623378	1288,11704	2201	4295	6496	SO:0001583	missense	6947	exon6			TAATATCCAAGAA	J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"""haptocorin"", ""haptocorrin"""	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.901G>T	11.37:g.59623378C>A	ENSP00000257264:p.Asp301Tyr	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_001062	A8KAC5|Q8WV77	Missense_Mutation	SNP	ENST00000257264.3	37	CCDS7978.1	150	0.06868131868131869	26	0.052845528455284556	29	0.08011049723756906	0	0.0	95	0.12532981530343007	c	13.24	2.178076	0.38511	0.068832	0.114668	ENSG00000134827	ENST00000257264	T	0.50548	0.74	4.83	1.77	0.24775	.	0.214249	0.30658	N	0.009141	T	0.00608	0.0020	M	0.80746	2.51	0.20563	N	0.999888	P	0.42961	0.795	B	0.43950	0.437	T	0.04115	-1.0976	10	0.72032	D	0.01	.	3.5864	0.07973	0.1709:0.5693:0.1655:0.0943	rs34324219	301	P20061	TCO1_HUMAN	Y	301	ENSP00000257264:D301Y	ENSP00000257264:D301Y	D	-	1	0	TCN1	59379954	0.117000	0.22190	0.479000	0.27329	0.688000	0.40055	-0.220000	0.09215	0.072000	0.16694	0.580000	0.79431	GAT	C|0.914;A|0.086	0.086	strong		0.448	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062	
IL17RA	23765	hgsc.bcm.edu	37	22	17589246	17589246	+	Silent	SNP	G	G	A	rs879576	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:17589246G>A	ENST00000319363.6	+	13	1270	c.1137G>A	c.(1135-1137)aaG>aaA	p.K379K		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	379	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		AGCCCAGGAAGGTCTGGATCA	0.637													G|||	608	0.121406	0.2466	0.0893	5008	,	,		18073	0.0		0.1173	False		,,,				2504	0.1043				p.K379K		Atlas-SNP	.											.	IL17RA	62	.	0			c.G1137A						PASS	.	G		999,3407	371.7+/-320.1	123,753,1327	63.0	65.0	64.0		1137	2.1	1.0	22	dbSNP_86	64	1065,7535	224.7+/-261.0	78,909,3313	yes	coding-synonymous	IL17RA	NM_014339.5		201,1662,4640	AA,AG,GG		12.3837,22.6736,15.8696		379/867	17589246	2064,10942	2203	4300	6503	SO:0001819	synonymous_variant	23765	exon13			CAGGAAGGTCTGG	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"""Interleukins and interleukin receptors"", ""CD molecules"""	5985	protein-coding gene	gene with protein product		605461	"""interleukin 17 receptor"""	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.1137G>A	22.37:g.17589246G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	122	71	0.581967	NM_014339	O43844|Q20WK1	Silent	SNP	ENST00000319363.6	37	CCDS13739.1																																																																																			G|0.856;A|0.144	0.144	strong		0.637	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291622	1291622	+	Missense_Mutation	SNP	A	A	G	rs149113013	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1291622A>G	ENST00000338844.3	+	4	454	c.421A>G	c.(421-423)Acc>Gcc	p.T141A	TPSAB1_ENST00000461509.2_Missense_Mutation_p.T148A	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	141	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		T -> A (in dbSNP:rs1800992). {ECO:0000269|PubMed:10898108}.|T -> M (in allele alpha).		defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				CCACACGGTCACCCTGCCCCC	0.662													A|||	1009	0.201478	0.2874	0.2695	5008	,	,		17793	0.1171		0.1918	False		,,,				2504	0.1339				p.T141A		Atlas-SNP	.											.	TPSAB1	24	.	0			c.A421G						PASS	.						30.0	25.0	26.0					16																	1291622		2198	4297	6495	SO:0001583	missense	7177	exon4			ACGGTCACCCTGC	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.421A>G	16.37:g.1291622A>G	ENSP00000343577:p.Thr141Ala	Somatic	426	1	0.00234742		WXS	Illumina HiSeq	Phase_I	560	156	0.278571	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	37	CCDS10431.1	448	0.20512820512820512	154	0.3130081300813008	86	0.23756906077348067	75	0.13111888111888112	133	0.17546174142480211	A	0.171	-1.071903	0.01918	.	.	ENSG00000172236	ENST00000338844;ENST00000461509	T;T	0.80994	-1.44;-1.44	3.74	0.17	0.15021	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.872655	0.09671	N	0.771165	T	0.00012	0.0000	N	0.03268	-0.37	0.45477	P	0.0015540000000000553	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.06463	-1.0825	9	0.33141	T	0.24	.	7.8036	0.29189	0.3416:0.0:0.0:0.6584	.	132;141	Q15661-2;Q15661	.;TRYB1_HUMAN	A	141;148	ENSP00000343577:T141A;ENSP00000418247:T148A	ENSP00000343577:T141A	T	+	1	0	TPSAB1	1231623	0.000000	0.05858	0.458000	0.27068	0.169000	0.22640	0.545000	0.23268	0.161000	0.19458	0.392000	0.25879	ACC	G|1.000;|0.000	1.000	weak		0.662	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
ITIH4	3700	hgsc.bcm.edu	37	3	52864584	52864584	+	Silent	SNP	A	A	G	rs2071042|rs200128168	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52864584A>G	ENST00000266041.4	-	1	171	c.75T>C	c.(73-75)acT>acC	p.T25T	RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000485816.1_Silent_p.T25T|RP5-966M1.6_ENST00000513520.1_5'UTR|ITIH4_ENST00000406595.1_Silent_p.T25T|ITIH4_ENST00000434759.3_5'UTR|ITIH4_ENST00000346281.5_Silent_p.T25T	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	25					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CGGCAGTAGTAGTCTGGTGGA	0.607													G|||	2546	0.508387	0.7042	0.5576	5008	,	,		19086	0.372		0.4046	False		,,,				2504	0.456				p.T25T		Atlas-SNP	.											.	ITIH4	74	.	0			c.T75C						PASS	.	G	,	2881,1525	480.8+/-358.9	915,1051,237	137.0	128.0	131.0		75,75	-0.4	0.0	3	dbSNP_96	131	3303,5297	646.7+/-400.3	634,2035,1631	no	coding-synonymous,coding-synonymous	ITIH4	NM_001166449.1,NM_002218.4	,	1549,3086,1868	GG,GA,AA		38.407,34.6119,47.5473	,	25/901,25/931	52864584	6184,6822	2203	4300	6503	SO:0001819	synonymous_variant	3700	exon1			AGTAGTAGTCTGG	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"""plasma Kallikrein-sensitive glycoprotein"""	600564	"""inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"""	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.75T>C	3.37:g.52864584A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_001166449	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Silent	SNP	ENST00000266041.4	37	CCDS2865.1																																																																																			A|0.509;G|0.491	0.491	strong		0.607	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
CAMK1G	57172	hgsc.bcm.edu	37	1	209785206	209785206	+	Missense_Mutation	SNP	G	G	A	rs11119315	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:209785206G>A	ENST00000009105.1	+	11	1230	c.985G>A	c.(985-987)Gtc>Atc	p.V329I	CAMK1G_ENST00000494990.1_3'UTR|CAMK1G_ENST00000361322.2_Missense_Mutation_p.V329I			Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	329			V -> I (in dbSNP:rs11119315). {ECO:0000269|PubMed:10645953, ECO:0000269|PubMed:17344846}.			calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|central_nervous_system(1)|large_intestine(8)|lung(8)|stomach(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		CAGCCCGGGCGTCCGCCCAGA	0.592													G|||	917	0.183107	0.3064	0.1859	5008	,	,		16967	0.1062		0.1819	False		,,,				2504	0.0951				p.V329I	Ovarian(163;530 1939 9680 28669 48710)	Atlas-SNP	.											.	CAMK1G	49	.	0			c.G985A						PASS	.	G	ILE/VAL	1284,3122	436.4+/-344.6	196,892,1115	83.0	91.0	88.0		985	-1.1	0.0	1	dbSNP_120	88	1541,7059	288.9+/-299.0	141,1259,2900	yes	missense	CAMK1G	NM_020439.2	29	337,2151,4015	AA,AG,GG		17.9186,29.1421,21.7207	benign	329/477	209785206	2825,10181	2203	4300	6503	SO:0001583	missense	57172	exon11			CCGGGCGTCCGCC		CCDS1486.1	1q32.2	2012-09-20			ENSG00000008118	ENSG00000008118			14585	protein-coding gene	gene with protein product		614994				12637513	Standard	NM_020439		Approved	VWS1, CLICKIII, dJ272L16.1	uc001hhd.3	Q96NX5	OTTHUMG00000036361	ENST00000009105.1:c.985G>A	1.37:g.209785206G>A	ENSP00000009105:p.Val329Ile	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_020439	Q86UH5|Q9Y3J7	Missense_Mutation	SNP	ENST00000009105.1	37	CCDS1486.1	443	0.20283882783882784	147	0.29878048780487804	72	0.19889502762430938	77	0.1346153846153846	147	0.19393139841688653	G	11.15	1.555376	0.27739	0.291421	0.179186	ENSG00000008118	ENST00000009105;ENST00000361322	T;T	0.68025	-0.3;-0.3	5.46	-1.06	0.10002	Protein kinase-like domain (1);	1.859790	0.02680	N	0.109614	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.13594	0.008;0.001	B;B	0.11329	0.006;0.003	T	0.07693	-1.0759	9	0.37606	T	0.19	.	5.3832	0.16204	0.4188:0.1366:0.4446:0.0	rs11119315;rs58071130;rs11119315	329;329	Q96NX5-2;Q96NX5	.;KCC1G_HUMAN	I	329	ENSP00000009105:V329I;ENSP00000354861:V329I	ENSP00000009105:V329I	V	+	1	0	CAMK1G	207851829	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-1.582000	0.02117	-0.529000	0.06358	-0.343000	0.07986	GTC	G|0.792;A|0.208	0.208	strong		0.592	CAMK1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088526.1	NM_020439	
ZNF251	90987	hgsc.bcm.edu	37	8	145979138	145979138	+	Silent	SNP	C	C	T	rs35571769	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:145979138C>T	ENST00000292562.7	-	4	482	c.207G>A	c.(205-207)caG>caA	p.Q69Q	ZNF251_ENST00000524394.1_Intron	NM_138367.1	NP_612376.1	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|kidney(1)|large_intestine(5)|lung(9)|stomach(1)	17	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		GTTCCTTCCCCTGCTCCAGCT	0.552													C|||	153	0.0305511	0.003	0.0418	5008	,	,		19660	0.001		0.0825	False		,,,				2504	0.0368				p.Q69Q		Atlas-SNP	.											.	ZNF251	80	.	0			c.G207A						PASS	.	C		47,3885		0,47,1919	42.0	42.0	42.0		207	1.6	0.8	8	dbSNP_126	42	610,7726		23,564,3581	no	coding-synonymous	ZNF251	NM_138367.1		23,611,5500	TT,TC,CC		7.3177,1.1953,5.3554		69/672	145979138	657,11611	1966	4168	6134	SO:0001819	synonymous_variant	90987	exon4			CTTCCCCTGCTCC	AK000435	CCDS47944.1	8q24.3	2013-01-08			ENSG00000198169	ENSG00000198169		"""Zinc fingers, C2H2-type"", ""-"""	13045	protein-coding gene	gene with protein product							Standard	NM_138367		Approved		uc003zdv.4	Q9BRH9	OTTHUMG00000165189	ENST00000292562.7:c.207G>A	8.37:g.145979138C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_138367	Q2M219	Silent	SNP	ENST00000292562.7	37	CCDS47944.1	78	0.03571428571428571	1	0.0020325203252032522	15	0.04143646408839779	1	0.0017482517482517483	61	0.08047493403693931	C	3.833	-0.035391	0.07497	0.011953	0.073177	ENSG00000198169	ENST00000525191	.	.	.	2.85	1.63	0.23807	.	.	.	.	.	T	0.05364	0.0142	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01824	-1.1266	4	.	.	.	-10.9154	6.4363	0.21825	0.0:0.129:0.0:0.871	rs35571769;rs61748663	.	.	.	R	107	.	.	G	-	1	0	ZNF251	145949943	0.004000	0.15560	0.762000	0.31397	0.643000	0.38383	-0.045000	0.12003	0.515000	0.28320	-0.281000	0.10026	GGG	C|0.961;T|0.039	0.039	strong		0.552	ZNF251-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382541.1	NM_138367	
RB1	5925	hgsc.bcm.edu	37	13	49039405	49039405	+	Nonsense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:49039405T>A	ENST00000267163.4	+	23	2528	c.2390T>A	c.(2389-2391)tTa>tAa	p.L797*		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	797	Domain C; mediates interaction with E4F1.|Interaction with LIMD1.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(11)|p.L797fs*1(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	AGTTCACCCTTACGGATTCCT	0.403		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.L797X		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	.	RB1	1068	.	27	Whole gene deletion(15)|Unknown(11)|Deletion - Frameshift(1)	bone(11)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|lung(1)|ovary(1)|liver(1)	c.T2390A	GRCh37	CM023820	RB1	M		PASS	.						131.0	133.0	133.0					13																	49039405		2203	4300	6503	SO:0001587	stop_gained	5925	exon23	Familial Cancer Database		CACCCTTACGGAT	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2390T>A	13.37:g.49039405T>A	ENSP00000267163:p.Leu797*	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	80	7	0.0875	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Nonsense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	T	39	7.903488	0.98554	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	5.87	5.87	0.94306	.	0.091849	0.44902	D	0.000409	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7061	0.51597	0.0:0.0:0.158:0.842	.	.	.	.	X	776;797	.	ENSP00000267163:L797X	L	+	2	0	RB1	47937406	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.593000	0.67550	2.242000	0.73789	0.482000	0.46254	TTA	.	.	none		0.403	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
SMC5	23137	hgsc.bcm.edu	37	9	72933774	72933774	+	Missense_Mutation	SNP	A	A	G	rs11142365	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:72933774A>G	ENST00000361138.5	+	15	2103	c.2045A>G	c.(2044-2046)cAt>cGt	p.H682R		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	682			H -> R (in dbSNP:rs11142365).		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						ACAAGCAAACATCTGGAGCAC	0.318													A|||	436	0.0870607	0.1664	0.0821	5008	,	,		16017	0.0139		0.1044	False		,,,				2504	0.0409				p.H682R		Atlas-SNP	.											.	SMC5	96	.	0			c.A2045G						PASS	.	A	ARG/HIS	670,3726		53,564,1581	48.0	50.0	49.0		2045	0.2	0.0	9	dbSNP_120	49	1012,7584		62,888,3348	no	missense	SMC5	NM_015110.3	29	115,1452,4929	GG,GA,AA		11.7729,15.2411,12.9464	benign	682/1102	72933774	1682,11310	2198	4298	6496	SO:0001583	missense	23137	exon15			GCAAACATCTGGA	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.2045A>G	9.37:g.72933774A>G	ENSP00000354957:p.His682Arg	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	138	50	0.362319	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	210	0.09615384615384616	93	0.18902439024390244	32	0.08839779005524862	5	0.008741258741258742	80	0.10554089709762533	A	3.138	-0.176891	0.06380	0.152411	0.117729	ENSG00000198887	ENST00000361138	T	0.16196	2.36	5.3	0.161	0.14977	RecF/RecN/SMC (1);	1.282520	0.04800	N	0.433287	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.39375	-0.9617	9	0.17832	T	0.49	-0.7879	4.1705	0.10327	0.4124:0.0:0.2134:0.3742	rs11142365	682	Q8IY18	SMC5_HUMAN	R	682	ENSP00000354957:H682R	ENSP00000354957:H682R	H	+	2	0	SMC5	72123594	0.000000	0.05858	0.005000	0.12908	0.889000	0.51656	0.330000	0.19715	0.008000	0.14787	0.472000	0.43445	CAT	A|0.888;G|0.112	0.112	strong		0.318	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	
HLA-C	3107	hgsc.bcm.edu	37	6	31239585	31239585	+	Missense_Mutation	SNP	C	C	T	rs1050437	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239585C>T	ENST00000376228.5	-	2	148	c.134G>A	c.(133-135)cGc>cAc	p.R45H	HLA-C_ENST00000383329.3_Missense_Mutation_p.R45H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	45	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TGAGATGAAGCGGGGCTCTCC	0.716													t|||	1128	0.22524	0.1808	0.2032	5008	,	,		12192	0.3333		0.2048	False		,,,				2504	0.2106				p.R45H		Atlas-SNP	.											.	HLA-C	92	.	0			c.G134A						PASS	.						27.0	26.0	27.0					6																	31239585		1508	2700	4208	SO:0001583	missense	3107	exon2			ATGAAGCGGGGCT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.134G>A	6.37:g.31239585C>T	ENSP00000365402:p.Arg45His	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	449	0.20558608058608058	73	0.1483739837398374	63	0.17403314917127072	167	0.291958041958042	146	0.19261213720316622	N	7.459	0.644270	0.14451	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00011	9.34;9.34	2.49	-0.367	0.12541	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.753997	0.10398	N	0.679503	T	0.00073	0.0002	M	0.91510	3.215	0.80722	P	0.0	B;B;B;B	0.17667	0.023;0.002;0.009;0.001	B;B;B;B	0.14578	0.011;0.002;0.004;0.002	T	0.38887	-0.9640	9	0.52906	T	0.07	.	5.2636	0.15588	0.0:0.5579:0.0:0.4421	rs34483041;rs41563919	45;45;45;45	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	H	45;45;45;82	ENSP00000365402:R45H;ENSP00000372819:R45H	ENSP00000365402:R45H	R	-	2	0	HLA-C	31347564	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.698000	0.01908	-0.110000	0.12022	-0.679000	0.03777	CGC	C|0.826;T|0.174	0.174	strong		0.716	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
PLCG2	5336	hgsc.bcm.edu	37	16	81929488	81929488	+	Silent	SNP	C	C	T	rs1143688	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81929488C>T	ENST00000359376.3	+	13	1363	c.1149C>T	c.(1147-1149)gaC>gaT	p.D383D		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	383	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						TCAAGTTTGACGACGTCGTGC	0.577													C|||	2036	0.40655	0.1029	0.5994	5008	,	,		19362	0.7113		0.3549	False		,,,				2504	0.4192				p.D383D		Atlas-SNP	.											.	PLCG2	276	.	0			c.C1149T						PASS	.	C		616,3574		56,504,1535	159.0	170.0	166.0		1149	-9.9	0.1	16	dbSNP_86	166	3035,5431		557,1921,1755	no	coding-synonymous	PLCG2	NM_002661.3		613,2425,3290	TT,TC,CC		35.8493,14.7017,28.848		383/1266	81929488	3651,9005	2095	4233	6328	SO:0001819	synonymous_variant	5336	exon13			GTTTGACGACGTC		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1149C>T	16.37:g.81929488C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	122	63	0.516393	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			C|0.594;N|0.000	.	strong		0.577	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
FHL5	9457	hgsc.bcm.edu	37	6	97058574	97058574	+	Missense_Mutation	SNP	G	G	A	rs2252816	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:97058574G>A	ENST00000326771.2	+	6	1011	c.631G>A	c.(631-633)Gtg>Atg	p.V211M	FHL5_ENST00000541107.1_Missense_Mutation_p.V211M	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	211	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.		V -> M (in dbSNP:rs2252816). {ECO:0000269|PubMed:11327716, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		TCCATTCTGCGTGGACTGCTA	0.438													G|||	1692	0.337859	0.0371	0.4971	5008	,	,		18493	0.5625		0.3887	False		,,,				2504	0.3476				p.V211M		Atlas-SNP	.											.	FHL5	73	.	0			c.G631A						PASS	.	G	MET/VAL,MET/VAL	428,3978	208.2+/-229.3	16,396,1791	230.0	212.0	218.0		631,631	-11.8	0.0	6	dbSNP_100	218	3248,5352	488.2+/-372.3	597,2054,1649	yes	missense,missense	FHL5	NM_001170807.1,NM_020482.4	21,21	613,2450,3440	AA,AG,GG		37.7674,9.714,28.2639	benign,benign	211/285,211/285	97058574	3676,9330	2203	4300	6503	SO:0001583	missense	9457	exon6			TTCTGCGTGGACT	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.631G>A	6.37:g.97058574G>A	ENSP00000326022:p.Val211Met	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	242	106	0.438017	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	37	CCDS5035.1	795	0.364010989010989	20	0.04065040650406504	163	0.45027624309392267	309	0.5402097902097902	303	0.3997361477572559	G	17.66	3.445731	0.63178	0.09714	0.377674	ENSG00000112214	ENST00000541107;ENST00000326771	D;D	0.87334	-2.24;-2.24	5.88	-11.8	0.00035	Zinc finger, LIM-type (4);	0.456393	0.16131	N	0.228209	T	0.73110	0.3545	M	0.82716	2.605	0.58432	P	5.999999999950489E-6	P	0.35107	0.484	B	0.36666	0.23	T	0.56757	-0.7926	9	0.54805	T	0.06	.	8.8785	0.35360	0.1348:0.5335:0.2361:0.0955	rs2252816;rs17851932;rs17856840;rs52821839;rs2252816	211	Q5TD97	FHL5_HUMAN	M	211	ENSP00000442357:V211M;ENSP00000326022:V211M	ENSP00000326022:V211M	V	+	1	0	FHL5	97165295	0.000000	0.05858	0.044000	0.18714	0.988000	0.76386	-1.087000	0.03383	-2.198000	0.00749	-0.271000	0.10264	GTG	G|0.688;A|0.312	0.312	strong		0.438	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
MYO15A	51168	hgsc.bcm.edu	37	17	18057167	18057167	+	Missense_Mutation	SNP	A	A	T	rs712270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18057167A>T	ENST00000205890.5	+	43	8383	c.8045A>T	c.(8044-8046)tAc>tTc	p.Y2682F	MYO15A_ENST00000585180.1_5'Flank|MYO15A_ENST00000418233.3_De_novo_Start_OutOfFrame	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2682	Tail.		Y -> F (in dbSNP:rs712270).		inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CCCAACTTCTACGGCTATCAG	0.667													A|||	1066	0.212859	0.1732	0.2968	5008	,	,		8448	0.0704		0.3907	False		,,,				2504	0.1708				p.Y2682F		Atlas-SNP	.											MYO15A,NS,carcinoma,0,1	MYO15A	268	1	0			c.A8045T						PASS	.	A	PHE/TYR	861,2937		86,689,1124	44.0	45.0	45.0		8045	5.1	0.5	17	dbSNP_86	45	3348,4886		696,1956,1465	yes	missense	MYO15A	NM_016239.3	22	782,2645,2589	TT,TA,AA		40.6607,22.6698,34.9817	probably-damaging	2682/3531	18057167	4209,7823	1899	4117	6016	SO:0001583	missense	51168	exon42			ACTTCTACGGCTA	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8045A>T	17.37:g.18057167A>T	ENSP00000205890:p.Tyr2682Phe	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	267	115	0.430712	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	538	0.24633699633699635	84	0.17073170731707318	107	0.2955801104972376	42	0.07342657342657342	305	0.4023746701846966	A	17.13	3.311675	0.60414	0.226698	0.406607	ENSG00000091536	ENST00000205890	D	0.87571	-2.27	5.07	5.07	0.68467	.	.	.	.	.	T	0.00012	0.0000	L	0.33485	1.01	0.09310	P	1.0	D	0.76494	0.999	D	0.63283	0.913	T	0.22452	-1.0216	8	0.19147	T	0.46	.	8.7972	0.34887	0.9117:0.0:0.0883:0.0	rs712270;rs1671919;rs52825480;rs57683381;rs712270	2682	Q9UKN7	MYO15_HUMAN	F	2682	ENSP00000205890:Y2682F	ENSP00000205890:Y2682F	Y	+	2	0	MYO15A	17997892	1.000000	0.71417	0.513000	0.27749	0.804000	0.45430	5.142000	0.64820	1.915000	0.55452	0.460000	0.39030	TAC	A|0.723;T|0.277	0.277	strong		0.667	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
ELL2	22936	hgsc.bcm.edu	37	5	95236459	95236459	+	Missense_Mutation	SNP	C	C	T	rs3815768	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:95236459C>T	ENST00000237853.4	-	7	1241	c.892G>A	c.(892-894)Gca>Aca	p.A298T	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	298			A -> T (in dbSNP:rs3815768). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9108030}.		regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		CTGGTGCCTGCAGCATTCTGA	0.393													C|||	1711	0.341653	0.3699	0.2392	5008	,	,		18726	0.4325		0.2803	False		,,,				2504	0.3456				p.A298T		Atlas-SNP	.											.	ELL2	63	.	0			c.G892A						PASS	.	C	THR/ALA	1538,2868	483.0+/-359.6	271,996,936	68.0	68.0	68.0		892	3.7	1.0	5	dbSNP_107	68	2248,6352	380.4+/-339.6	291,1666,2343	yes	missense	ELL2	NM_012081.5	58	562,2662,3279	TT,TC,CC		26.1395,34.9069,29.1096	benign	298/641	95236459	3786,9220	2203	4300	6503	SO:0001583	missense	22936	exon7			TGCCTGCAGCATT	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.892G>A	5.37:g.95236459C>T	ENSP00000237853:p.Ala298Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	165	71	0.430303	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	37	CCDS4080.1	725	0.33195970695970695	174	0.35365853658536583	84	0.23204419889502761	246	0.43006993006993005	221	0.29155672823219	C	9.940	1.217350	0.22373	0.349069	0.261395	ENSG00000118985	ENST00000237853;ENST00000513343	T;T	0.28454	2.06;1.61	5.7	3.65	0.41850	.	0.261711	0.43110	N	0.000615	T	0.00012	0.0000	N	0.00392	-1.555	0.09310	P	0.9999999999999996	B	0.02656	0.0	B	0.08055	0.003	T	0.46470	-0.9189	9	0.02654	T	1	-0.7066	4.8931	0.13737	0.0:0.6493:0.0:0.3507	rs3815768;rs17855530;rs61132053;rs3815768	298	O00472	ELL2_HUMAN	T	298;116	ENSP00000237853:A298T;ENSP00000423915:A116T	ENSP00000237853:A298T	A	-	1	0	ELL2	95262215	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	1.128000	0.31369	1.374000	0.46228	0.561000	0.74099	GCA	C|0.695;T|0.305	0.305	strong		0.393	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
RAI1	10743	hgsc.bcm.edu	37	17	17697099	17697099	+	Silent	SNP	G	G	A	rs587780429|rs398124422|rs35068024|rs11078398|rs587780431	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17697099G>A	ENST00000353383.1	+	3	1306	c.837G>A	c.(835-837)caG>caA	p.Q279Q	RAI1_ENST00000261641.6_Silent_p.Q279Q	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	279	Gln-rich.|Poly-Gln.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ATGACcagcagcagcagcagc	0.637													G|||	2748	0.548722	0.4047	0.5	5008	,	,		14895	0.8333		0.333	False		,,,				2504	0.7065				p.Q279Q		Atlas-SNP	.											.	RAI1	121	.	0			c.G837A						PASS	.	G		1437,2657		231,975,841	20.0	25.0	23.0		837	0.2	0.5	17	dbSNP_120	23	2226,5860		298,1630,2115	no	coding-synonymous	RAI1	NM_030665.3		529,2605,2956	AA,AG,GG		27.5291,35.1001,30.0739		279/1907	17697099	3663,8517	2047	4043	6090	SO:0001819	synonymous_variant	10743	exon3			CCAGCAGCAGCAG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.837G>A	17.37:g.17697099G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			G|0.495;A|0.505	0.505	strong		0.637	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
NACA	4666	hgsc.bcm.edu	37	12	57106660	57106660	+	Silent	SNP	A	A	T	rs4788	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57106660A>T	ENST00000454682.1	-	8	6413	c.6132T>A	c.(6130-6132)atT>atA	p.I2044I	NACA_ENST00000546392.1_Silent_p.I181I|NACA_ENST00000356769.3_Silent_p.I181I|NACA_ENST00000393891.4_Silent_p.I181I|NACA_ENST00000550952.1_Silent_p.I891I|NACA_ENST00000548563.1_Silent_p.I102I|NACA_ENST00000552540.1_Silent_p.I181I|NACA_ENST00000551793.1_5'Flank	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	2044	UBA.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						TGACCAATTCAATGTCCTTAA	0.408			T	BCL6	NHL								T|||	3984	0.795527	0.8623	0.755	5008	,	,		22146	0.745		0.7316	False		,,,				2504	0.8517				p.I891I		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.T2673A						PASS	.	T	,,,	3717,689	289.2+/-280.3	1571,575,57	177.0	161.0	167.0		543,543,2673,543	3.0	1.0	12	dbSNP_52	167	6215,2385	396.3+/-345.4	2254,1707,339	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NACA	NM_001113201.1,NM_001113202.1,NM_001113203.2,NM_005594.4	,,,	3825,2282,396	TT,TA,AA		27.7326,15.6378,23.6352	,,,	181/216,181/216,891/926,181/216	57106660	9932,3074	2203	4300	6503	SO:0001819	synonymous_variant	4666	exon10			CAATTCAATGTCC	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.6132T>A	12.37:g.57106660A>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	181	90	0.497238	NM_001113203		Silent	SNP	ENST00000454682.1	37																																																																																				A|0.235;T|0.765	0.765	strong		0.408	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
CAPN5	726	hgsc.bcm.edu	37	11	76826545	76826545	+	Silent	SNP	A	A	G	rs143460583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:76826545A>G	ENST00000278559.3	+	6	993	c.804A>G	c.(802-804)ctA>ctG	p.L268L	CAPN5_ENST00000456580.2_Silent_p.L308L|CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000529629.1_Silent_p.L268L	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	268	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						GCCACGGCCTACTGGCCTTCT	0.657													a|||	7	0.00139776	0.0008	0.0043	5008	,	,		20264	0.0		0.003	False		,,,				2504	0.0				p.L268L		Atlas-SNP	.											CAPN5,NS,carcinoma,0,1	CAPN5	67	1	0			c.A804G						PASS	.			0,4400		0,0,2200	43.0	41.0	42.0		804	2.0	1.0	11	dbSNP_134	42	29,8555	21.0+/-64.5	0,29,4263	no	coding-synonymous	CAPN5	NM_004055.4		0,29,6463	GG,GA,AA		0.3378,0.0,0.2234		268/641	76826545	29,12955	2200	4292	6492	SO:0001819	synonymous_variant	726	exon6			CGGCCTACTGGCC		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"""vitreoretinopathy, neovascular inflammatory"""	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.804A>G	11.37:g.76826545A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	168	72	0.428571	NM_004055	O00263	Silent	SNP	ENST00000278559.3	37	CCDS8248.1																																																																																			A|0.997;G|0.003	0.003	strong		0.657	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055	
COL3A1	1281	hgsc.bcm.edu	37	2	189855742	189855742	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:189855742C>T	ENST00000304636.3	+	11	981	c.811C>T	c.(811-813)Cga>Tga	p.R271*	COL3A1_ENST00000317840.5_Nonsense_Mutation_p.R271*	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	271	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	CTTCGATGGACGAAATGGAGA	0.284																																					p.R271X		Atlas-SNP	.											COL3A1,face,carcinoma,-1,1	COL3A1	292	1	0			c.C811T						scavenged	.						99.0	113.0	109.0					2																	189855742		2203	4297	6500	SO:0001587	stop_gained	1281	exon11			GATGGACGAAATG	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.811C>T	2.37:g.189855742C>T	ENSP00000304408:p.Arg271*	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	257	3	0.0116732	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Nonsense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	C	38	7.041164	0.98021	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	.	.	.	5.98	5.98	0.97165	.	0.000000	0.43416	D	0.000575	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	13.3447	0.60566	0.2587:0.7413:0.0:0.0	.	.	.	.	X	271	.	ENSP00000304408:R271X	R	+	1	2	COL3A1	189563987	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.434000	0.34958	2.838000	0.97847	0.591000	0.81541	CGA	.	.	none		0.284	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
FOXP4	116113	hgsc.bcm.edu	37	6	41566580	41566580	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41566580C>T	ENST00000307972.4	+	16	1961	c.1949C>T	c.(1948-1950)cCc>cTc	p.P650L	FOXP4_ENST00000373057.3_Missense_Mutation_p.P648L|FOXP4_ENST00000373063.3_Missense_Mutation_p.P637L|MIR4641_ENST00000578353.1_RNA|FOXP4_ENST00000373060.1_Missense_Mutation_p.P650L|FOXP4_ENST00000409208.1_Missense_Mutation_p.P638L			Q8IVH2	FOXP4_HUMAN	forkhead box P4	650					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GACAGGCAGCCCGGGCCTCCC	0.667																																					p.P650L		Atlas-SNP	.											FOXP4_ENST00000373060,colon,carcinoma,-1,2	FOXP4	83	2	0			c.C1949T						scavenged	.						15.0	18.0	17.0					6																	41566580		2186	4271	6457	SO:0001583	missense	116113	exon17			GGCAGCCCGGGCC	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.1949C>T	6.37:g.41566580C>T	ENSP00000309823:p.Pro650Leu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	203	3	0.0147783	NM_001012426	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	C	19.47	3.832911	0.71258	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	D;D;D;D;D	0.91011	-2.76;-2.76;-2.77;-2.77;-2.76	4.36	4.36	0.52297	.	0.149049	0.43919	D	0.000516	D	0.93566	0.7946	M	0.68317	2.08	0.80722	D	1	P;P;D	0.76494	0.906;0.906;0.999	B;B;D	0.91635	0.42;0.42;0.999	D	0.94172	0.7424	10	0.87932	D	0	.	15.206	0.73180	0.0:1.0:0.0:0.0	.	637;648;650	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	L	650;637;638;648;650	ENSP00000362151:P650L;ENSP00000362154:P637L;ENSP00000386958:P638L;ENSP00000362148:P648L;ENSP00000309823:P650L	ENSP00000309823:P650L	P	+	2	0	FOXP4	41674558	1.000000	0.71417	0.967000	0.41034	0.352000	0.29268	4.885000	0.63142	2.435000	0.82474	0.462000	0.41574	CCC	.	.	none		0.667	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457	
BRCA1	672	hgsc.bcm.edu	37	17	41245466	41245466	+	Silent	SNP	G	G	A	rs1799949	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:41245466G>A	ENST00000357654.3	-	10	2200	c.2082C>T	c.(2080-2082)agC>agT	p.S694S	BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Silent_p.S694S|BRCA1_ENST00000471181.2_Silent_p.S694S|BRCA1_ENST00000309486.4_Silent_p.S398S|BRCA1_ENST00000354071.3_Silent_p.S694S|BRCA1_ENST00000493795.1_Silent_p.S647S|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	694					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S694S(1)		NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GGAAAGTATCGCTGTCATGTC	0.408			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			G|||	1685	0.336462	0.2103	0.353	5008	,	,		20322	0.371		0.3002	False		,,,				2504	0.4969				p.S694S		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	BRCA1,NS,carcinoma,0,1	BRCA1	304	1	1	Substitution - coding silent(1)	stomach(1)	c.C2082T						PASS	.	G	,,,,	1055,3349	385.6+/-325.8	114,827,1261	116.0	104.0	108.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2082,1941,,,2082	0.6	0.0	17	dbSNP_89	108	2790,5810	442.1+/-360.0	443,1904,1953	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	,,,,	557,2731,3214	AA,AG,GG		32.4419,23.9555,29.5678	,,,,	694/1864,647/1817,,,694/1885	41245466	3845,9159	2202	4300	6502	SO:0001819	synonymous_variant	672	exon10	Familial Cancer Database		AGTATCGCTGTCA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.2082C>T	17.37:g.41245466G>A		Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	271	131	0.483395	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	37	CCDS11453.1																																																																																			G|0.697;A|0.303	0.303	strong		0.408	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
FAM20A	54757	hgsc.bcm.edu	37	17	66533655	66533655	+	Missense_Mutation	SNP	A	A	G	rs2907373	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:66533655A>G	ENST00000592554.1	-	11	2311	c.1589T>C	c.(1588-1590)tTg>tCg	p.L530S	FAM20A_ENST00000226094.5_5'UTR|PRKAR1A_ENST00000588188.2_Intron	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	530			L -> S (in dbSNP:rs2907373). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					GTCTGGGGCCAACTGTTCCAC	0.577													G|||	3992	0.797125	0.8744	0.7608	5008	,	,		18350	0.8958		0.6789	False		,,,				2504	0.7382				p.L530S		Atlas-SNP	.											.	FAM20A	35	.	0			c.T1589C						PASS	.	G	SER/LEU	3667,739	302.7+/-287.5	1536,595,72	60.0	50.0	54.0		1589	1.1	0.0	17	dbSNP_101	54	5694,2906	454.4+/-363.5	1877,1940,483	yes	missense	FAM20A	NM_017565.3	145	3413,2535,555	GG,GA,AA		33.7907,16.7726,28.0255	benign	530/542	66533655	9361,3645	2203	4300	6503	SO:0001583	missense	54757	exon11			GGGGCCAACTGTT	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.1589T>C	17.37:g.66533655A>G	ENSP00000468308:p.Leu530Ser	Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_017565	B2RN47|B2RN49|Q9UF95	Missense_Mutation	SNP	ENST00000592554.1	37	CCDS11679.1	1720	0.7875457875457875	418	0.8495934959349594	262	0.7237569060773481	523	0.9143356643356644	517	0.6820580474934037	G	0.802	-0.755110	0.03019	0.832274	0.662093	ENSG00000108950	ENST00000226094;ENST00000375556	.	.	.	5.54	1.13	0.20643	.	1.170840	0.06023	N	0.651583	T	0.00012	0.0000	N	0.00419	-1.52	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29912	-0.9996	8	0.08599	T	0.76	2.3105	2.2353	0.04006	0.2033:0.1934:0.4637:0.1396	rs2907373;rs3169744;rs17701893;rs2907373	530;385	Q96MK3;B7Z4Y3	FA20A_HUMAN;.	S	530;134	.	ENSP00000226094:L530S	L	-	2	0	FAM20A	64045250	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	0.360000	0.20250	0.023000	0.15187	-0.338000	0.08134	TTG	A|0.254;G|0.746	0.746	strong		0.577	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565	
CEACAM18	729767	hgsc.bcm.edu	37	19	51984656	51984656	+	Missense_Mutation	SNP	G	G	A	rs62115071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51984656G>A	ENST00000396477.4	+	3	431	c.410G>A	c.(409-411)aGc>aAc	p.S137N	CEACAM18_ENST00000451626.1_Missense_Mutation_p.S198N	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	137										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GAGTTGGGAAGCAATCTGGGC	0.527													g|||	674	0.134585	0.0787	0.111	5008	,	,		20642	0.1091		0.1839	False		,,,				2504	0.2025				p.S198N		Atlas-SNP	.											.	CEACAM18	96	.	0			c.G593A						PASS	.	G	ASN/SER	372,3574		19,334,1620	52.0	49.0	50.0		593	-5.3	0.0	19	dbSNP_129	50	1563,6741		148,1267,2737	yes	missense	CEACAM18	NM_001080405.1	46	167,1601,4357	AA,AG,GG		18.8223,9.4273,15.7959	possibly-damaging	198/399	51984656	1935,10315	1973	4152	6125	SO:0001583	missense	729767	exon4			TGGGAAGCAATCT			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.410G>A	19.37:g.51984656G>A	ENSP00000379738:p.Ser137Asn	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		274	0.12545787545787546	41	0.08333333333333333	44	0.12154696132596685	56	0.0979020979020979	133	0.17546174142480211	.	5.067	0.197947	0.09652	0.094273	0.188223	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.06142	3.34	2.63	-5.27	0.02763	.	.	.	.	.	T	0.00012	0.0000	M	0.73430	2.235	0.80722	P	0.0	B	0.12013	0.005	B	0.19148	0.024	T	0.41448	-0.9508	8	0.44086	T	0.13	.	1.1296	0.01743	0.3907:0.2791:0.1895:0.1408	rs62115071	198	A8MTB9	CEA18_HUMAN	N	198;137;137	ENSP00000402203:S198N	ENSP00000379738:S137N	S	+	2	0	CEACAM18	56676468	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.583000	0.02115	-1.933000	0.01052	0.558000	0.71614	AGC	G|0.862;A|0.138	0.138	strong		0.527	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
PCNT	5116	hgsc.bcm.edu	37	21	47847700	47847700	+	Silent	SNP	C	C	T	rs61735817	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47847700C>T	ENST00000359568.5	+	34	7592	c.7485C>T	c.(7483-7485)atC>atT	p.I2495I	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2495					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AGAAGATCATCCGTGAGCAGG	0.582													c|||	92	0.0183706	0.0008	0.0259	5008	,	,		19242	0.001		0.0676	False		,,,				2504	0.0041				p.I2495I		Atlas-SNP	.											.	PCNT	283	.	0			c.C7485T						PASS	.	T		60,4346	56.8+/-93.2	1,58,2144	57.0	57.0	57.0		7485	0.3	0.0	21	dbSNP_129	57	523,8077	146.3+/-201.9	10,503,3787	no	coding-synonymous	PCNT	NM_006031.5		11,561,5931	TT,TC,CC		6.0814,1.3618,4.4825		2495/3337	47847700	583,12423	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon34			GATCATCCGTGAG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7485C>T	21.37:g.47847700C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	43	17	0.395349	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.958;T|0.042	0.042	strong		0.582	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
SLC17A3	10786	hgsc.bcm.edu	37	6	25849620	25849620	+	Silent	SNP	A	A	G	rs942379	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:25849620A>G	ENST00000360657.3	-	10	1395	c.1110T>C	c.(1108-1110)agT>agC	p.S370S	SLC17A3_ENST00000361703.6_Silent_p.S370S|SLC17A3_ENST00000397060.4_Silent_p.S448S			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	370					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						GAAGAAATCCACTGACAGTGG	0.418													G|||	3521	0.703075	0.9198	0.6902	5008	,	,		15514	0.8105		0.5388	False		,,,				2504	0.4775				p.S448S		Atlas-SNP	.											.	SLC17A3	95	.	0			c.T1344C						PASS	.	G	,	3764,642	275.2+/-272.4	1612,540,51	74.0	71.0	72.0		1344,1110	-0.8	0.1	6	dbSNP_86	72	4553,4047	554.6+/-386.5	1190,2173,937	no	coding-synonymous,coding-synonymous	SLC17A3	NM_001098486.1,NM_006632.3	,	2802,2713,988	GG,GA,AA		47.0581,14.571,36.0526	,	448/499,370/421	25849620	8317,4689	2203	4300	6503	SO:0001819	synonymous_variant	10786	exon11			AAATCCACTGACA	U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"""Solute carriers"""	10931	protein-coding gene	gene with protein product		611034	"""solute carrier family 17 (sodium phosphate), member 3"""			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.1110T>C	6.37:g.25849620A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_001098486	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Silent	SNP	ENST00000360657.3	37	CCDS4566.2	1584	0.7252747252747253	454	0.9227642276422764	247	0.6823204419889503	476	0.8321678321678322	407	0.5369393139841688	G	4.510	0.094579	0.08632	0.85429	0.529419	ENSG00000124564	ENST00000481949	.	.	.	4.55	-0.836	0.10770	.	.	.	.	.	T	0.12732	0.0309	.	.	.	0.25770	P	0.9848456	.	.	.	.	.	.	T	0.23762	-1.0179	3	.	.	.	.	4.0301	0.09705	0.5185:0.1813:0.3002:0.0	rs942379;rs1747553;rs3736878;rs17270953;rs17851585;rs57863386;rs942379	.	.	.	A	49	.	.	V	-	2	0	SLC17A3	25957599	0.000000	0.05858	0.128000	0.21923	0.014000	0.08584	-1.080000	0.03407	-0.075000	0.12798	-0.266000	0.10368	GTG	A|0.326;G|0.674	0.674	strong		0.418	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2		
MMS22L	253714	hgsc.bcm.edu	37	6	97599674	97599674	+	Missense_Mutation	SNP	G	G	A	rs138146580	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:97599674G>A	ENST00000275053.4	-	23	3720	c.3455C>T	c.(3454-3456)cCt>cTt	p.P1152L	MMS22L_ENST00000369251.2_Missense_Mutation_p.P1112L	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1152					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						CTGGGAGGAAGGTTCTTCTTC	0.433													G|||	37	0.00738818	0.0023	0.0058	5008	,	,		15425	0.0		0.0239	False		,,,				2504	0.0061				p.P1152L		Atlas-SNP	.											.	MMS22L	102	.	0			c.C3455T						PASS	.	G	LEU/PRO	17,4389	24.3+/-50.5	0,17,2186	204.0	203.0	203.0		3455	3.6	1.0	6	dbSNP_134	203	155,8445	73.5+/-136.2	2,151,4147	yes	missense	MMS22L	NM_198468.2	98	2,168,6333	AA,AG,GG		1.8023,0.3858,1.3225	benign	1152/1244	97599674	172,12834	2203	4300	6503	SO:0001583	missense	253714	exon23			GAGGAAGGTTCTT		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"""chromosome 6 open reading frame 167"""	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3455C>T	6.37:g.97599674G>A	ENSP00000275053:p.Pro1152Leu	Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	187	100	0.534759	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	37	CCDS5039.1	26	0.011904761904761904	3	0.006097560975609756	4	0.011049723756906077	0	0.0	19	0.025065963060686015	G	9.389	1.074903	0.20227	0.003858	0.018023	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.29655	3.93;1.56	5.44	3.59	0.41128	.	0.290094	0.38492	N	0.001666	T	0.09202	0.0227	L	0.56769	1.78	0.44966	D	0.997984	B;B	0.31548	0.328;0.082	B;B	0.27380	0.079;0.036	T	0.13255	-1.0516	10	0.14252	T	0.57	.	3.4047	0.07336	0.1576:0.1261:0.5698:0.1465	.	1112;1152	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	L	1152;1112	ENSP00000275053:P1152L;ENSP00000358254:P1112L	ENSP00000275053:P1152L	P	-	2	0	MMS22L	97706395	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.175000	0.31944	0.606000	0.29965	0.650000	0.86243	CCT	G|0.987;A|0.013	0.013	strong		0.433	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468	
CAPN9	10753	hgsc.bcm.edu	37	1	230923313	230923313	+	Missense_Mutation	SNP	C	C	T	rs12731961	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:230923313C>T	ENST00000271971.2	+	13	1677	c.1564C>T	c.(1564-1566)Cgg>Tgg	p.R522W	RP11-99J16__A.2_ENST00000412344.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000452640.1_RNA|CAPN9_ENST00000354537.1_Missense_Mutation_p.R496W|CAPN9_ENST00000366666.2_Missense_Mutation_p.R459W	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	522	Domain IV.|EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.		R -> W (in dbSNP:rs12731961). {ECO:0000269|Ref.3}.		digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				GGAGGAGCAGCGGTTTCGGGC	0.522													C|||	982	0.196086	0.3207	0.1542	5008	,	,		19755	0.0813		0.1819	False		,,,				2504	0.1902				p.R522W		Atlas-SNP	.											.	CAPN9	116	.	0			c.C1564T						PASS	.	C	TRP/ARG,TRP/ARG	1255,3151	430.1+/-342.5	191,873,1139	118.0	99.0	105.0		1564,1486	3.2	0.4	1	dbSNP_121	105	1661,6939	306.2+/-307.8	158,1345,2797	yes	missense,missense	CAPN9	NM_006615.2,NM_016452.1	101,101	349,2218,3936	TT,TC,CC		19.314,28.4839,22.4204	possibly-damaging,possibly-damaging	522/691,496/665	230923313	2916,10090	2203	4300	6503	SO:0001583	missense	10753	exon13			GAGCAGCGGTTTC	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1564C>T	1.37:g.230923313C>T	ENSP00000271971:p.Arg522Trp	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	37	CCDS1586.1	381	0.17445054945054944	150	0.3048780487804878	56	0.15469613259668508	35	0.06118881118881119	140	0.18469656992084432	C	8.961	0.970662	0.18659	0.284839	0.19314	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	D;D;D	0.95103	-3.61;-3.61;-3.61	5.17	3.18	0.36537	EF-hand-like domain (1);	0.641175	0.17553	N	0.170097	T	0.00039	0.0001	L	0.34521	1.04	0.80722	P	0.0	P;P;P	0.52061	0.917;0.95;0.917	B;P;B	0.45138	0.28;0.471;0.28	T	0.00000	-1.3148	9	0.72032	D	0.01	.	12.7937	0.57549	0.0:0.6867:0.3133:0.0	rs12731961;rs52797755;rs56556331;rs58840974;rs12731961	459;496;522	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	W	522;496;459	ENSP00000271971:R522W;ENSP00000346538:R496W;ENSP00000355626:R459W	ENSP00000271971:R522W	R	+	1	2	CAPN9	228989936	0.185000	0.23213	0.373000	0.26003	0.052000	0.14988	0.780000	0.26760	1.128000	0.42052	0.655000	0.94253	CGG	C|0.793;T|0.207	0.207	strong		0.522	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
LBX2	85474	hgsc.bcm.edu	37	2	74725178	74725178	+	Missense_Mutation	SNP	G	G	A	rs17009998	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:74725178G>A	ENST00000377566.4	-	2	651	c.473C>T	c.(472-474)tCc>tTc	p.S158F	AC005041.17_ENST00000479098.1_RNA|LBX2_ENST00000341396.2_3'UTR|LBX2_ENST00000460508.3_Missense_Mutation_p.S154F|LBX2_ENST00000550249.1_5'UTR	NM_001282430.1	NP_001269359.1	Q6XYB7	LBX2_HUMAN	ladybird homeobox 2	158			S -> F (in dbSNP:rs17009998).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(1)	4						GACTTCCGGGGACAACGCGCG	0.687													G|||	1668	0.333067	0.1399	0.2579	5008	,	,		15440	0.8204		0.1551	False		,,,				2504	0.3282				p.S154F		Atlas-SNP	.											.	LBX2	13	.	0			c.C461T						PASS	.	G	PHE/SER	662,3744	276.3+/-273.0	54,554,1595	49.0	48.0	48.0		461	3.0	0.2	2	dbSNP_123	48	1139,7459	227.9+/-263.1	77,985,3237	yes	missense	LBX2	NM_001009812.1	155	131,1539,4832	AA,AG,GG		13.2473,15.025,13.8496	probably-damaging	154/195	74725178	1801,11203	2203	4299	6502	SO:0001583	missense	85474	exon2			TCCGGGGACAACG	AC005041	CCDS33228.1, CCDS62938.1	2p13.1	2014-05-06	2007-02-15		ENSG00000179528	ENSG00000179528		"""Homeoboxes / ANTP class : NKL subclass"""	15525	protein-coding gene	gene with protein product		607164	"""ladybird homeobox homolog 2 (Drosophila)"""			11386758	Standard	NM_001282430		Approved		uc002slw.3	Q6XYB7	OTTHUMG00000170595	ENST00000377566.4:c.473C>T	2.37:g.74725178G>A	ENSP00000366789:p.Ser158Phe	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	229	149	0.650655	NM_001009812	Q7Z5Y8	Missense_Mutation	SNP	ENST00000377566.4	37		718	0.32875457875457875	63	0.12804878048780488	72	0.19889502762430938	471	0.8234265734265734	112	0.14775725593667546	G	15.19	2.759678	0.49468	0.15025	0.132473	ENSG00000179528	ENST00000377566;ENST00000460508	D;D	0.91945	-2.82;-2.94	4.76	2.95	0.34219	.	0.647217	0.13712	N	0.367991	T	0.00012	0.0000	L	0.29908	0.895	0.20563	P	0.999885927	B;B	0.12630	0.006;0.002	B;B	0.19148	0.024;0.002	T	0.44174	-0.9345	9	0.66056	D	0.02	.	7.3598	0.26739	0.0893:0.0:0.7431:0.1677	rs17009998;rs60339187;rs17009998	154;158	Q6XYB7-2;Q6XYB7	.;LBX2_HUMAN	F	158;154	ENSP00000366789:S158F;ENSP00000417116:S154F	ENSP00000366789:S158F	S	-	2	0	LBX2	74578686	0.000000	0.05858	0.178000	0.23040	0.034000	0.12701	0.297000	0.19101	0.605000	0.29947	0.561000	0.74099	TCC	G|0.774;A|0.226	0.226	strong		0.687	LBX2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328490.1	NM_001009812	
KIAA0020	9933	hgsc.bcm.edu	37	9	2812282	2812282	+	Missense_Mutation	SNP	A	A	T	rs142216382	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:2812282A>T	ENST00000397885.2	-	14	1556	c.1350T>A	c.(1348-1350)gaT>gaA	p.D450E		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	450	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		TATGTGCAGGATCTCTGGGGC	0.358																																					p.D450E		Atlas-SNP	.											.	KIAA0020	56	.	0			c.T1350A						PASS	.	A	GLU/ASP	1,4405	2.1+/-5.4	0,1,2202	215.0	193.0	200.0		1350	0.9	1.0	9	dbSNP_134	200	6,8594	5.0+/-18.6	0,6,4294	yes	missense	KIAA0020	NM_014878.4	45	0,7,6496	TT,TA,AA		0.0698,0.0227,0.0538	possibly-damaging	450/649	2812282	7,12999	2203	4300	6503	SO:0001583	missense	9933	exon14			TGCAGGATCTCTG	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1350T>A	9.37:g.2812282A>T	ENSP00000380982:p.Asp450Glu	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	229	115	0.502183	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	A	21.3	4.134740	0.77662	2.27E-4	6.98E-4	ENSG00000080608	ENST00000397885	T	0.52754	0.65	5.5	0.953	0.19590	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.134559	0.64402	D	0.000003	T	0.62208	0.2409	M	0.80746	2.51	0.54753	D	0.999989	D;D	0.54397	0.966;0.966	P;P	0.61874	0.861;0.895	T	0.59894	-0.7368	10	0.35671	T	0.21	-21.8403	10.3652	0.44019	0.613:0.0:0.387:0.0	.	310;450	B2RDG4;Q15397	.;K0020_HUMAN	E	450	ENSP00000380982:D450E	ENSP00000380982:D450E	D	-	3	2	KIAA0020	2802282	0.947000	0.32204	1.000000	0.80357	0.997000	0.91878	0.103000	0.15292	0.093000	0.17368	0.482000	0.46254	GAT	A|0.999;T|0.001	0.001	strong		0.358	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
ANXA4	307	hgsc.bcm.edu	37	2	70033584	70033584	+	Missense_Mutation	SNP	C	C	T	rs2228203	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:70033584C>T	ENST00000394295.4	+	5	508	c.260C>T	c.(259-261)aCg>aTg	p.T87M	ANXA4_ENST00000536030.1_Missense_Mutation_p.T3M|ANXA4_ENST00000409920.1_Intron	NM_001153.3	NP_001144.1	P09525	ANXA4_HUMAN	annexin A4	85					epithelial cell differentiation (GO:0030855)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phospholipase inhibitor activity (GO:0004859)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11						GGGATGATGACGCCCACGGTG	0.537													C|||	1005	0.200679	0.3169	0.17	5008	,	,		21921	0.1736		0.1958	False		,,,				2504	0.0982				p.T87M		Atlas-SNP	.											.	ANXA4	34	.	0			c.C260T						PASS	.	C	MET/THR	1367,3039	453.6+/-350.4	227,913,1063	207.0	145.0	166.0		260	-1.3	0.7	2	dbSNP_98	166	1628,6972	301.4+/-305.4	155,1318,2827	yes	missense	ANXA4	NM_001153.3	81	382,2231,3890	TT,TC,CC		18.9302,31.0259,23.0278	benign	87/322	70033584	2995,10011	2203	4300	6503	SO:0001583	missense	307	exon5			TGATGACGCCCAC	M82809	CCDS1894.1	2p13.3	2008-02-05			ENSG00000196975	ENSG00000196975		"""Annexins"""	542	protein-coding gene	gene with protein product		106491		ANX4		1346776	Standard	NM_001153		Approved		uc002sfr.4	P09525	OTTHUMG00000129649	ENST00000394295.4:c.260C>T	2.37:g.70033584C>T	ENSP00000377833:p.Thr87Met	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	362	136	0.375691	NM_001153	B4DDF9|Q96F33|Q9BWK1	Missense_Mutation	SNP	ENST00000394295.4	37	CCDS1894.1	491	0.22481684981684982	162	0.32926829268292684	61	0.1685082872928177	112	0.1958041958041958	156	0.20580474934036938	C	0.114	-1.134746	0.01742	0.310259	0.189302	ENSG00000196975	ENST00000394295;ENST00000536030	T;T	0.11930	2.73;2.73	4.97	-1.3	0.09259	.	0.184470	0.56097	N	0.000028	T	0.00012	0.0000	N	0.05078	-0.115	0.30952	P	0.724574	B;B	0.20671	0.023;0.047	B;B	0.17098	0.004;0.017	T	0.49485	-0.8935	8	.	.	.	.	10.5802	0.45250	0.0:0.5408:0.0:0.4592	rs2228203;rs11549470;rs17355624;rs52832365;rs61061911;rs11549470	85;87	P09525;Q6LES2	ANXA4_HUMAN;.	M	87;3	ENSP00000377833:T87M;ENSP00000441931:T3M	.	T	+	2	0	ANXA4	69887088	0.129000	0.22400	0.707000	0.30419	0.004000	0.04260	0.043000	0.13971	-0.232000	0.09811	-1.056000	0.02311	ACG	C|0.770;A|0.001	.	strong		0.537	ANXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251848.2	NM_001153	
TARS	6897	hgsc.bcm.edu	37	5	33461355	33461355	+	Silent	SNP	G	G	A	rs2270905	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:33461355G>A	ENST00000265112.3	+	13	1817	c.1506G>A	c.(1504-1506)ccG>ccA	p.P502P	TARS_ENST00000455217.2_Silent_p.P535P|TARS_ENST00000414361.2_Silent_p.P381P|TARS_ENST00000509410.1_3'UTR|TARS_ENST00000541634.1_Silent_p.P398P|TARS_ENST00000502553.1_Silent_p.P502P	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	502					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)			NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	CTACTCGCCCGGAAAAATTCC	0.353													G|||	692	0.138179	0.1256	0.1441	5008	,	,		18644	0.127		0.2356	False		,,,				2504	0.0624				p.P535P		Atlas-SNP	.											TARS,NS,carcinoma,+1,1	TARS	66	1	0			c.G1605A						PASS	.	G		624,3782	262.5+/-264.9	43,538,1622	85.0	91.0	89.0		1506	-4.8	1.0	5	dbSNP_100	89	1892,6708	331.8+/-319.8	201,1490,2609	no	coding-synonymous	TARS	NM_152295.3		244,2028,4231	AA,AG,GG		22.0,14.1625,19.3449		502/724	33461355	2516,10490	2203	4300	6503	SO:0001819	synonymous_variant	6897	exon14			TCGCCCGGAAAAA	AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	11572	protein-coding gene	gene with protein product	"""threonine tRNA ligase 1, cytoplasmic"""	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.1506G>A	5.37:g.33461355G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	179	93	0.519553	NM_001258438	A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Silent	SNP	ENST00000265112.3	37	CCDS3899.1																																																																																			G|0.816;A|0.184	0.184	strong		0.353	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295	
LILRA6	79168	hgsc.bcm.edu	37	19	54744182	54744182	+	Missense_Mutation	SNP	A	A	T	rs3193485	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54744182A>T	ENST00000396365.2	-	6	1265	c.1226T>A	c.(1225-1227)tTc>tAc	p.F409Y	LILRA6_ENST00000245621.5_Missense_Mutation_p.F409Y|LILRA6_ENST00000419410.2_Missense_Mutation_p.F409Y|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	409					immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.F409Y(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CTCACTGGGGAAAGACAGCAG	0.622																																					p.F409Y		Atlas-SNP	.											LILRA6,nipple,malignant_melanoma,0,1	LILRA6	75	1	1	Substitution - Missense(1)	skin(1)	c.T1226A						scavenged	.						97.0	135.0	122.0					19																	54744182		2197	4300	6497	SO:0001583	missense	79168	exon6			CTGGGGAAAGACA	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.1226T>A	19.37:g.54744182A>T	ENSP00000379651:p.Phe409Tyr	Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	325	30	0.0923077	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.262301	0.00021	.	.	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.00717	5.79;5.79;5.79	2.71	-5.43	0.02632	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	12.755800	0.00166	N	0.000006	T	0.00845	0.0028	L	0.56199	1.76	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.002	B;B;B	0.06405	0.0;0.0;0.002	T	0.53641	-0.8410	10	0.09338	T	0.73	.	2.0397	0.03547	0.4944:0.1022:0.2479:0.1555	rs3193485	409;409;409	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	Y	409	ENSP00000411227:F409Y;ENSP00000379651:F409Y;ENSP00000245621:F409Y	ENSP00000245621:F409Y	F	-	2	0	LILRA6	59435994	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.946000	0.00167	-4.280000	0.00059	-3.764000	0.00021	TTC	.	.	alt		0.622	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
DTHD1	401124	hgsc.bcm.edu	37	4	36340753	36340753	+	Missense_Mutation	SNP	G	G	A	rs9654132	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:36340753G>A	ENST00000456874.2	+	8	2043	c.1985G>A	c.(1984-1986)cGt>cAt	p.R662H	DTHD1_ENST00000357504.3_Missense_Mutation_p.R497H|RP11-431M7.2_ENST00000504344.1_RNA|DTHD1_ENST00000503528.1_Intron|DTHD1_ENST00000507598.1_Missense_Mutation_p.R702H	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	662			R -> H (in dbSNP:rs9654132). {ECO:0000269|PubMed:14702039}.		signal transduction (GO:0007165)			p.R497H(3)|p.R662H(2)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						TTAATCAACCGTCCACAGAGT	0.348													g|||	984	0.196486	0.1831	0.1873	5008	,	,		17837	0.127		0.2624	False		,,,				2504	0.2249				p.R662H		Atlas-SNP	.											DTHD1_ENST00000456874,NS,carcinoma,0,5	DTHD1	63	5	5	Substitution - Missense(5)	kidney(4)|stomach(1)	c.G1985A						PASS	.	A	HIS/ARG,HIS/ARG	277,1107		32,213,447	232.0	186.0	200.0		1490,1985	2.2	1.0	4	dbSNP_119	200	733,2449		77,579,935	yes	missense,missense	DTHD1	NM_001136536.3,NM_001170700.1	29,29	109,792,1382	AA,AG,GG		23.0358,20.0145,22.12	benign,benign	497/617,662/782	36340753	1010,3556	692	1591	2283	SO:0001583	missense	401124	exon8			TCAACCGTCCACA	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.1985G>A	4.37:g.36340753G>A	ENSP00000401597:p.Arg662His	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_001170700	B2RXK4|B4E2N7	Missense_Mutation	SNP	ENST00000456874.2	37	CCDS54754.1	405	0.18543956043956045	80	0.16260162601626016	54	0.14917127071823205	72	0.1258741258741259	199	0.262532981530343	g	12.44	1.937584	0.34189	0.200145	0.230358	ENSG00000197057	ENST00000357504;ENST00000507598;ENST00000456874	T;T;T	0.78816	-1.21;-1.21;-1.21	5.04	2.18	0.27775	.	0.329059	0.32503	N	0.006013	T	0.00012	0.0000	L	0.27053	0.805	0.39370	P	0.03393400000000002	B	0.31640	0.333	B	0.25506	0.061	T	0.05099	-1.0906	9	0.46703	T	0.11	-2.3523	9.6835	0.40085	0.2531:0.0:0.7469:0.0	rs9654132;rs57110323;rs9654132	497	Q6ZMT9-2	.	H	497;702;662	ENSP00000350103:R497H;ENSP00000424426:R702H;ENSP00000401597:R662H	ENSP00000350103:R497H	R	+	2	0	DTHD1	36017148	0.984000	0.35163	1.000000	0.80357	0.975000	0.68041	0.817000	0.27281	0.732000	0.32470	-0.215000	0.12644	CGT	G|0.809;A|0.191	0.191	strong		0.348	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
NECAB3	63941	hgsc.bcm.edu	37	20	32248163	32248163	+	Silent	SNP	C	C	T	rs3746460	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32248163C>T	ENST00000246190.6	-	6	481	c.426G>A	c.(424-426)acG>acA	p.T142T	C20orf144_ENST00000375222.3_5'Flank|NECAB3_ENST00000375238.4_Silent_p.T142T|RP1-63M2.6_ENST00000607224.1_RNA|NECAB3_ENST00000606525.1_5'UTR	NM_031232.3	NP_112509.3	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	142					protein metabolic process (GO:0019538)|protein secretion (GO:0009306)|regulation of amyloid precursor protein biosynthetic process (GO:0042984)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|Golgi cis cisterna (GO:0000137)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			large_intestine(3)|lung(5)|skin(2)	10						GCAGGAAGCGCGTCACAAACT	0.652													c|||	1479	0.295327	0.2769	0.2104	5008	,	,		19779	0.3909		0.3181	False		,,,				2504	0.2587				p.T142T		Atlas-SNP	.											.	NECAB3	27	.	0			c.G426A						PASS	.	T	,	1104,3052		145,814,1119	49.0	55.0	53.0		426,426	-10.2	0.3	20	dbSNP_107	53	2492,5940		385,1722,2109	no	coding-synonymous,coding-synonymous	NECAB3	NM_031231.3,NM_031232.3	,	530,2536,3228	TT,TC,CC		29.5541,26.564,28.5669	,	142/363,142/397	32248163	3596,8992	2078	4216	6294	SO:0001819	synonymous_variant	63941	exon6			GAAGCGCGTCACA	AB039947	CCDS42866.1, CCDS42867.1	20q11.21	2013-01-10	2007-12-06	2007-12-06	ENSG00000125967	ENSG00000125967		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	15851	protein-coding gene	gene with protein product	"""EF-hand calcium binding protein 3"""	612478	"""amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein"""	SYTIP2, APBA2BP		10833507	Standard	NM_031232		Approved	XB51, dJ63M2.4, NIP1, dJ63M2.5, EFCBP3	uc002wzn.4	Q96P71	OTTHUMG00000032264	ENST00000246190.6:c.426G>A	20.37:g.32248163C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	36	0.6	NM_031232	A8K780|E1P5N2|Q5JWF5|Q5JWF6|Q5JWF7|Q86VV1|Q9H433|Q9H8G8|Q9HBW7|Q9HCQ9	Silent	SNP	ENST00000246190.6	37	CCDS42866.1																																																																																			C|0.701;T|0.299	0.299	strong		0.652	NECAB3-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078724.2		
PLEKHM1	9842	hgsc.bcm.edu	37	17	43545893	43545893	+	Silent	SNP	T	T	C	rs1879581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43545893T>C	ENST00000430334.3	-	5	1123	c.990A>G	c.(988-990)acA>acG	p.T330T	RN7SL730P_ENST00000583727.1_RNA|PLEKHM1_ENST00000421073.2_Silent_p.T241T	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	330					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					TGGGGATCTCTGTTTCTTGGC	0.537													C|||	412	0.0822684	0.0378	0.1556	5008	,	,		19822	0.001		0.1958	False		,,,				2504	0.0573				p.T330T		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.A990G						PASS	.	C		281,4125	800.6+/-415.6	10,261,1932	140.0	137.0	138.0		990	-5.9	0.0	17	dbSNP_92	138	1646,6954	741.1+/-407.1	155,1336,2809	no	coding-synonymous	PLEKHM1	NM_014798.2		165,1597,4741	CC,CT,TT		19.1395,6.3777,14.8162		330/1057	43545893	1927,11079	2203	4300	6503	SO:0001819	synonymous_variant	9842	exon5			GATCTCTGTTTCT	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.990A>G	17.37:g.43545893T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	131	73	0.557252	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			T|0.863;C|0.137	0.137	strong		0.537	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
OR2AG2	338755	hgsc.bcm.edu	37	11	6789929	6789929	+	Missense_Mutation	SNP	C	C	A	rs11828782	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6789929C>A	ENST00000338569.2	-	1	357	c.260G>T	c.(259-261)cGc>cTc	p.R87L		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	87			R -> L (in dbSNP:rs11828782).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R87L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GTTTTCTCTGCGCAGAAAGTC	0.552													C|||	1036	0.206869	0.1467	0.2104	5008	,	,		22024	0.1538		0.3509	False		,,,				2504	0.1922				p.R87L		Atlas-SNP	.											OR2AG2,NS,carcinoma,0,1	OR2AG2	55	1	1	Substitution - Missense(1)	stomach(1)	c.G260T						PASS	.	C	LEU/ARG	777,3625	316.3+/-294.6	67,643,1491	106.0	96.0	100.0		260	-8.7	0.0	11	dbSNP_120	100	3018,5574	467.2+/-367.0	523,1972,1801	yes	missense	OR2AG2	NM_001004490.1	102	590,2615,3292	AA,AC,CC		35.1257,17.6511,29.2058	benign	87/317	6789929	3795,9199	2201	4296	6497	SO:0001583	missense	338755	exon1			TCTCTGCGCAGAA	AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.260G>T	11.37:g.6789929C>A	ENSP00000342697:p.Arg87Leu	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	212	90	0.424528	NM_001004490		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	538	0.24633699633699635	77	0.1565040650406504	82	0.2265193370165746	112	0.1958041958041958	267	0.35224274406332456	C	0.019	-1.454107	0.01071	0.176511	0.351257	ENSG00000188124	ENST00000338569	T	0.01335	5.0	4.47	-8.66	0.00866	GPCR, rhodopsin-like superfamily (1);	1.383410	0.04762	N	0.426471	T	0.00012	0.0000	N	0.02345	-0.59	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48525	-0.9028	9	0.09338	T	0.73	.	1.2451	0.01971	0.2921:0.2242:0.0924:0.3914	rs11828782;rs52797581;rs11828782	87	A6NM03	O2AG2_HUMAN	L	87	ENSP00000342697:R87L	ENSP00000342697:R87L	R	-	2	0	OR2AG2	6746505	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-1.751000	0.01821	-2.027000	0.00932	-0.136000	0.14681	CGC	C|0.744;A|0.256	0.256	strong		0.552	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
TPMT	7172	hgsc.bcm.edu	37	6	18130918	18130918	+	Missense_Mutation	SNP	T	T	C	rs1142345	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:18130918T>C	ENST00000309983.4	-	9	804	c.719A>G	c.(718-720)tAt>tGt	p.Y240C		NM_000367.2	NP_000358.1	P51580	TPMT_HUMAN	thiopurine S-methyltransferase	240			Y -> C (in TPMT deficiency; allele TPMT*3B and allele TPMT*3C; reduced activity; protein shows enhanced degradation; TPMT*3C is the most common mutant in African-Americans and the only allele in the Japanese and Taiwanese individuals; TPMT*3C frequencies are 7.6% in Ghanaian and 0.3% in Caucasian individuals; dbSNP:rs1142345). {ECO:0000269|PubMed:10208641, ECO:0000269|PubMed:10751626, ECO:0000269|PubMed:15819814, ECO:0000269|PubMed:16220112, ECO:0000269|PubMed:16476125, ECO:0000269|PubMed:16789994, ECO:0000269|PubMed:8561894, ECO:0000269|PubMed:8644731, ECO:0000269|PubMed:9246020, ECO:0000269|PubMed:9336428, ECO:0000269|PubMed:9931345}.		methylation (GO:0032259)|nucleobase-containing compound metabolic process (GO:0006139)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	thiopurine S-methyltransferase activity (GO:0008119)			large_intestine(2)|lung(1)	3	Ovarian(93;0.016)|Breast(50;0.0245)	all_hematologic(90;0.146)	all cancers(50;0.06)|Epithelial(50;0.0654)		Azathioprine(DB00993)|Bendroflumethiazide(DB00436)|Cefazolin(DB01327)|Mercaptopurine(DB01033)|Olsalazine(DB01250)|Trichlormethiazide(DB01021)	TGTAAGTAGATATAACTTTTC	0.303													T|||	196	0.0391374	0.0666	0.0576	5008	,	,		17798	0.0218		0.0288	False		,,,				2504	0.0174				p.Y240C	Colon(190;1381 2791 16728 32493)	Atlas-SNP	.											.	TPMT	17	.	0			c.A719G	GRCh37	CM961383	TPMT	M	rs1142345	PASS	.	T	CYS/TYR	232,4174	134.5+/-170.7	4,224,1975	75.0	76.0	76.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	719	5.9	1.0	6	dbSNP_86	76	358,8224	119.7+/-179.0	13,332,3946	yes	missense	TPMT	NM_000367.2	194	17,556,5921	CC,CT,TT		4.1715,5.2655,4.5427	probably-damaging	240/246	18130918	590,12398	2203	4291	6494	SO:0001583	missense	7172	exon9			AGTAGATATAACT		CCDS4543.1	6p22.3	2014-09-17			ENSG00000137364	ENSG00000137364	2.1.1.67		12014	protein-coding gene	gene with protein product		187680				8316220	Standard	NM_000367		Approved		uc003ncm.3	P51580	OTTHUMG00000014317	ENST00000309983.4:c.719A>G	6.37:g.18130918T>C	ENSP00000312304:p.Tyr240Cys	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	254	254	1	NM_000367	O14806|O15423|O15424|O15425|O15426|O15515|O15548|O43213|Q5VUK6|Q9UBE6|Q9UBT8|Q9UE62	Missense_Mutation	SNP	ENST00000309983.4	37	CCDS4543.1	101	0.04624542124542125	47	0.09552845528455285	24	0.06629834254143646	10	0.017482517482517484	20	0.026385224274406333	T	19.88	3.909025	0.72868	0.052655	0.041715	ENSG00000137364	ENST00000309983	T	0.66460	-0.21	5.92	5.92	0.95590	.	0.130199	0.56097	D	0.000036	D	0.82875	0.5132	M	0.91717	3.235	0.09310	P	0.999999794745	D	0.89917	1.0	D	0.91635	0.999	D	0.87055	0.2149	9	0.72032	D	0.01	-27.1591	15.1814	0.72962	0.0:0.0:0.0:1.0	rs1142345;rs1801205;rs16880254;rs29001646;rs52798150;rs61510596;rs1142345	240	P51580	TPMT_HUMAN	C	240	ENSP00000312304:Y240C	ENSP00000312304:Y240C	Y	-	2	0	TPMT	18238897	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	4.763000	0.62257	2.270000	0.75569	0.477000	0.44152	TAT	T|0.956;C|0.044	0.044	strong		0.303	TPMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039960.1		
KMT2D	8085	hgsc.bcm.edu	37	12	49425978	49425978	+	Silent	SNP	T	T	C	rs3741622	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:49425978T>C	ENST00000301067.7	-	39	12509	c.12510A>G	c.(12508-12510)ccA>ccG	p.P4170P		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4170	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.P3900P(1)									TGGGAGGTTGTGGCCCTGTAT	0.592													T|||	1379	0.275359	0.0234	0.2363	5008	,	,		18835	0.4454		0.3022	False		,,,				2504	0.4407				p.P4170P		Atlas-SNP	.											MLL2,NS,carcinoma,0,1	MLL2	1173	1	1	Substitution - coding silent(1)	stomach(1)	c.A12510G						PASS	.	T		288,3676		10,268,1704	90.0	80.0	83.0		12510	1.8	1.0	12	dbSNP_107	83	2787,5517		480,1827,1845	no	coding-synonymous	MLL2	NM_003482.3		490,2095,3549	CC,CT,TT		33.5621,7.2654,25.0652		4170/5538	49425978	3075,9193	1982	4152	6134	SO:0001819	synonymous_variant	8085	exon39			AGGTTGTGGCCCT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.12510A>G	12.37:g.49425978T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	130	48	0.369231	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			T|0.725;C|0.275	0.275	strong		0.592	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
PCDHA3	56145	hgsc.bcm.edu	37	5	140181892	140181892	+	Silent	SNP	T	T	C	rs3733707	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140181892T>C	ENST00000522353.2	+	1	1110	c.1110T>C	c.(1108-1110)gcT>gcC	p.A370A	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Silent_p.A370A|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	370	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGTCATCGCTCTGATCAGCG	0.478													.|||	3011	0.601238	0.7572	0.6052	5008	,	,		22120	0.5317		0.5388	False		,,,				2504	0.5235				p.A370A		Atlas-SNP	.											PCDHA3_ENST00000522353,rectum,carcinoma,+2,2	PCDHA3	396	2	0			c.T1110C						PASS	.	C	,,,,	3224,1182		1184,856,163	124.0	120.0	122.0		,,1110,,1110	3.9	1.0	5	dbSNP_107	122	4542,4058		1193,2156,951	no	intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,,,	2377,3012,1114	CC,CT,TT		47.186,26.8271,40.2891	,,,,	,,370/951,,370/825	140181892	7766,5240	2203	4300	6503	SO:0001819	synonymous_variant	56145	exon1			CATCGCTCTGATC	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1110T>C	5.37:g.140181892T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	139	68	0.489209	NM_031497	O75286	Silent	SNP	ENST00000522353.2	37	CCDS54915.1																																																																																			T|0.403;C|0.597	0.597	strong		0.478	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
TPSD1	23430	hgsc.bcm.edu	37	16	1306973	1306973	+	Missense_Mutation	SNP	A	A	G	rs79313952		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1306973A>G	ENST00000211076.3	+	3	578	c.430A>G	c.(430-432)Atc>Gtc	p.I144V	TPSD1_ENST00000397534.2_Missense_Mutation_p.I137V|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	144	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CTCCAGCCACATCCACACGGT	0.642																																					p.I144V		Atlas-SNP	.											TPSD1,NS,NS,0,1	TPSD1	47	1	0			c.A430G						PASS	.						49.0	47.0	47.0					16																	1306973		2198	4299	6497	SO:0001583	missense	23430	exon3			AGCCACATCCACA	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.430A>G	16.37:g.1306973A>G	ENSP00000211076:p.Ile144Val	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	457	88	0.19256	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	761	0.3484432234432234	140	0.2845528455284553	110	0.30386740331491713	250	0.4370629370629371	261	0.34432717678100266	a	0.001	-2.882799	0.00061	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.85702	-2.02;-2.02	2.55	-5.1	0.02911	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.756136	0.11242	N	0.584558	T	0.00012	0.0000	N	0.04043	-0.29	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.13407	0.009;0.009	T	0.23404	-1.0189	9	0.02654	T	1	.	0.0994	0.00046	0.3174:0.1569:0.211:0.3148	.	128;144	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	V	137;144	ENSP00000380668:I137V;ENSP00000211076:I144V	ENSP00000211076:I144V	I	+	1	0	TPSD1	1246974	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-1.101000	0.03336	-1.132000	0.02907	-1.639000	0.00775	ATC	A|0.652;G|0.348	0.348	strong		0.642	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
ZNF460	10794	hgsc.bcm.edu	37	19	57802806	57802806	+	Silent	SNP	C	C	T	rs2041109	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57802806C>T	ENST00000360338.3	+	3	1219	c.897C>T	c.(895-897)aaC>aaT	p.N299N	ZNF460_ENST00000537645.1_Silent_p.N258N	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	299					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TCTTGCATAACAAGAGCCACA	0.468													c|||	923	0.184305	0.0908	0.3084	5008	,	,		22596	0.1657		0.2515	False		,,,				2504	0.1728				p.N299N		Atlas-SNP	.											.	ZNF460	59	.	0			c.C897T						PASS	.	C		494,3912	229.4+/-244.0	27,440,1736	95.0	85.0	89.0		897	-0.9	0.0	19	dbSNP_94	89	2199,6401	375.0+/-337.6	295,1609,2396	no	coding-synonymous	ZNF460	NM_006635.3		322,2049,4132	TT,TC,CC		25.5698,11.212,20.7058		299/563	57802806	2693,10313	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			GCATAACAAGAGC	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.897C>T	19.37:g.57802806C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			C|0.799;T|0.201	0.201	strong		0.468	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
SLC22A18	5002	hgsc.bcm.edu	37	11	2943671	2943671	+	Missense_Mutation	SNP	G	G	C	rs1129782	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:2943671G>C	ENST00000380574.1	+	10	1403	c.972G>C	c.(970-972)tgG>tgC	p.W324C	SLC22A18_ENST00000449793.2_Missense_Mutation_p.W226C|SLC22A18_ENST00000441077.1_3'UTR|SLC22A18_ENST00000312221.5_Missense_Mutation_p.W324C|SLC22A18_ENST00000347936.2_Missense_Mutation_p.W324C			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	324			W -> C (in dbSNP:rs1129782).		drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		CCCAGGCCTGGATGTCCAGCG	0.657													G|||	647	0.129193	0.0076	0.134	5008	,	,		11711	0.123		0.2018	False		,,,				2504	0.2219				p.W324C		Atlas-SNP	.											.	SLC22A18	20	.	0			c.G972C						PASS	.	G	CYS/TRP,CYS/TRP	166,4234	103.8+/-142.4	5,156,2039	65.0	45.0	52.0		972,972	2.5	0.7	11	dbSNP_86	52	1778,6820	297.4+/-303.4	173,1432,2694	yes	missense,missense	SLC22A18	NM_002555.5,NM_183233.2	215,215	178,1588,4733	CC,CG,GG		20.6792,3.7727,14.9561	benign,benign	324/425,324/425	2943671	1944,11054	2200	4299	6499	SO:0001583	missense	5002	exon10			GGCCTGGATGTCC	AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"""Solute carriers"""	10964	protein-coding gene	gene with protein product		602631	"""solute carrier family 22 (organic cation transporter), member 1-like"""	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.972G>C	11.37:g.2943671G>C	ENSP00000369948:p.Trp324Cys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	274	0.12545787545787546	7	0.014227642276422764	43	0.11878453038674033	71	0.12412587412587413	153	0.20184696569920843	G	4.917	0.170328	0.09339	0.037727	0.206792	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574	T;T;T;T	0.80994	0.28;0.28;-1.44;0.28	4.56	2.49	0.30216	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.874893	0.09614	N	0.778444	T	0.00073	0.0002	N	0.03608	-0.345	0.29262	P	0.871274	B;B	0.13145	0.007;0.002	B;B	0.09377	0.004;0.0	T	0.04855	-1.0922	9	0.62326	D	0.03	-8.7963	11.9756	0.53089	0.0:0.3348:0.6652:0.0	rs1129782;rs3177634;rs3188051;rs11559226;rs1129782	226;324	E9PRM7;Q96BI1	.;S22AI_HUMAN	C	324;324;226;324	ENSP00000307859:W324C;ENSP00000311139:W324C;ENSP00000392072:W226C;ENSP00000369948:W324C	ENSP00000311139:W324C	W	+	3	0	SLC22A18	2900247	0.533000	0.26354	0.749000	0.31150	0.286000	0.27126	0.687000	0.25407	0.867000	0.35654	0.549000	0.68633	TGG	G|0.866;C|0.134	0.134	strong		0.657	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233	
PMS2	5395	hgsc.bcm.edu	37	7	6026988	6026988	+	Missense_Mutation	SNP	G	G	A	rs1805321	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:6026988G>A	ENST00000265849.7	-	11	1513	c.1408C>T	c.(1408-1410)Cct>Tct	p.P470S	PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Missense_Mutation_p.P470S|PMS2_ENST00000441476.2_Missense_Mutation_p.P364S|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	470			P -> S (in dbSNP:rs1805321). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TCTTTCTGAGGTCTCAGGACG	0.567			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				G|||	1794	0.358227	0.2723	0.428	5008	,	,		16764	0.3601		0.4374	False		,,,				2504	0.3415				p.P470S		Atlas-SNP	.	yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2	88	.	0			c.C1408T						PASS	.	G	SER/PRO	1242,3164	428.7+/-342.0	177,888,1138	106.0	102.0	103.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1408	0.6	0.0	7	dbSNP_98	103	3620,4980	523.7+/-380.4	743,2134,1423	no	missense	PMS2	NM_000535.5	74	920,3022,2561	AA,AG,GG		42.093,28.1888,37.3827	benign	470/863	6026988	4862,8144	2203	4300	6503	SO:0001583	missense	5395	exon11	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TCTGAGGTCTCAG		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.1408C>T	7.37:g.6026988G>A	ENSP00000265849:p.Pro470Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	861	0.3942307692307692	148	0.3008130081300813	153	0.42265193370165743	223	0.38986013986013984	337	0.4445910290237467	g	1.779	-0.482327	0.04383	0.281888	0.42093	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;D	0.84944	1.14;1.14;-1.92	5.84	0.572	0.17357	.	2.392390	0.01199	N	0.007524	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B;B;B	0.16603	0.018;0.002;0.006	B;B;B	0.10450	0.005;0.001;0.005	T	0.29212	-1.0019	9	0.09084	T	0.74	-5.0156	2.3347	0.04244	0.2519:0.1234:0.4861:0.1386	rs1805321;rs57467937;rs1805321	470;470;364	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	S	470;423;364;470	ENSP00000265849:P470S;ENSP00000392843:P364S;ENSP00000384308:P470S	ENSP00000265849:P470S	P	-	1	0	PMS2	5993514	0.001000	0.12720	0.006000	0.13384	0.004000	0.04260	0.265000	0.18515	0.386000	0.24997	-0.145000	0.13849	CCT	G|0.639;A|0.361	0.361	strong		0.567	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
KREMEN1	83999	hgsc.bcm.edu	37	22	29521353	29521353	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29521353G>A	ENST00000407188.1	+	5	574	c.574G>A	c.(574-576)Ggg>Agg	p.G192R	KREMEN1_ENST00000400335.4_Missense_Mutation_p.G194R|KREMEN1_ENST00000400338.2_Missense_Mutation_p.G194R|KREMEN1_ENST00000327813.5_Missense_Mutation_p.G194R			Q96MU8	KREM1_HUMAN	kringle containing transmembrane protein 1	192	WSC. {ECO:0000255|PROSITE- ProRule:PRU00558}.				cell communication (GO:0007154)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	20						CGTCTGCTTCGGGGATCACAC	0.552																																					p.G194R		Atlas-SNP	.											.	KREMEN1	46	.	0			c.G580A						PASS	.						165.0	170.0	168.0					22																	29521353		2146	4261	6407	SO:0001583	missense	83999	exon5			TGCTTCGGGGATC	AB059618	CCDS43000.1, CCDS13849.1, CCDS43000.2	22q12.1	2008-03-27	2002-11-13	2002-11-15	ENSG00000183762	ENSG00000183762			17550	protein-coding gene	gene with protein product		609898	"""kringle containing transmembrane protein"""	KREMEN		11267660	Standard	NM_001039570		Approved	KRM1	uc011akm.1	Q96MU8	OTTHUMG00000030987	ENST00000407188.1:c.574G>A	22.37:g.29521353G>A	ENSP00000385431:p.Gly192Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	146	67	0.458904	NM_001039570	B0QY46|B0QY47|B1AJR5|Q5TIB9|Q6P3X6|Q9BY70|Q9UGS5|Q9UGU1	Missense_Mutation	SNP	ENST00000407188.1	37	CCDS43000.2	.	.	.	.	.	.	.	.	.	.	G	23.7	4.442407	0.83993	.	.	ENSG00000183762	ENST00000400335;ENST00000400338;ENST00000327813;ENST00000407188	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.74	4.73	0.59995	Carbohydrate-binding WSC (2);	0.000000	0.64402	D	0.000006	D	0.84906	0.5576	M	0.92970	3.365	0.58432	D	0.999999	D;D;B	0.89917	1.0;1.0;0.357	D;D;B	0.97110	1.0;1.0;0.072	D	0.88314	0.2958	10	0.87932	D	0	.	12.87	0.57960	0.079:0.0:0.921:0.0	.	192;194;194	Q96MU8;Q96MU8-2;Q96MU8-3	KREM1_HUMAN;.;.	R	194;194;194;192	ENSP00000383189:G194R;ENSP00000383192:G194R;ENSP00000331242:G194R;ENSP00000385431:G192R	ENSP00000331242:G194R	G	+	1	0	KREMEN1	27851353	1.000000	0.71417	0.997000	0.53966	0.790000	0.44656	9.146000	0.94640	1.579000	0.49836	0.650000	0.86243	GGG	.	.	none		0.552	KREMEN1-004	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320947.1		
OR2M3	127062	hgsc.bcm.edu	37	1	248366792	248366792	+	Silent	SNP	T	T	C	rs12562957	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248366792T>C	ENST00000456743.1	+	1	461	c.423T>C	c.(421-423)tgT>tgC	p.C141C		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	141						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CTAAAATTTGTGGACTTATGA	0.453													T|||	1232	0.246006	0.171	0.255	5008	,	,		19737	0.3542		0.1451	False		,,,				2504	0.3333				p.C141C		Atlas-SNP	.											.	OR2M3	116	.	0			c.T423C						PASS	.	T		688,3718	290.4+/-280.9	61,566,1576	208.0	208.0	208.0		423	-0.0	0.0	1	dbSNP_120	208	1258,7342	251.1+/-277.7	90,1078,3132	no	coding-synonymous	OR2M3	NM_001004689.1		151,1644,4708	CC,CT,TT		14.6279,15.6151,14.9623		141/313	248366792	1946,11060	2203	4300	6503	SO:0001819	synonymous_variant	127062	exon1			AATTTGTGGACTT		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"""GPCR / Class A : Olfactory receptors"""	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.423T>C	1.37:g.248366792T>C		Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	369	166	0.449865	NM_001004689	B9EH06|Q6IEY0	Silent	SNP	ENST00000456743.1	37	CCDS31107.1																																																																																			T|0.828;C|0.172	0.172	strong		0.453	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689	
CACNA2D3	55799	hgsc.bcm.edu	37	3	54880461	54880461	+	Silent	SNP	A	A	G	rs3773603	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:54880461A>G	ENST00000474759.1	+	17	1641	c.1593A>G	c.(1591-1593)ggA>ggG	p.G531G	CACNA2D3_ENST00000415676.2_Silent_p.G531G|CACNA2D3_ENST00000490478.1_Silent_p.G437G|CACNA2D3_ENST00000288197.5_Silent_p.G531G	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	531	Cache.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CAAATAATGGATATATCCTGA	0.383													A|||	837	0.167133	0.112	0.1873	5008	,	,		17618	0.1786		0.1938	False		,,,				2504	0.1881				p.G531G		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.A1593G						PASS	.	A		497,3269		34,429,1420	86.0	82.0	83.0		1593	1.2	1.0	3	dbSNP_107	83	1533,6683		142,1249,2717	no	coding-synonymous	CACNA2D3	NM_018398.2		176,1678,4137	GG,GA,AA		18.6587,13.197,16.9421		531/1092	54880461	2030,9952	1883	4108	5991	SO:0001819	synonymous_variant	55799	exon17			TAATGGATATATC	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"""Calcium channel subunits"""	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.1593A>G	3.37:g.54880461A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	147	59	0.401361	NM_018398	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	37	CCDS54598.1																																																																																			A|0.825;G|0.175	0.175	strong		0.383	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		
SLC6A15	55117	hgsc.bcm.edu	37	12	85277561	85277561	+	Intron	SNP	T	T	A	rs17183577	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:85277561T>A	ENST00000266682.5	-	5	1298				SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000552192.1_Intron|SLC6A15_ENST00000450363.3_Missense_Mutation_p.D278V	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15						amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						CCCACAGAAATCTGTAACAGA	0.348													T|||	374	0.0746805	0.0053	0.1599	5008	,	,		18044	0.0		0.2266	False		,,,				2504	0.0286				p.D278V		Atlas-SNP	.											.	SLC6A15	159	.	0			c.A833T						PASS	.	T	,VAL/ASP,	191,4215	121.3+/-158.8	7,177,2019	73.0	71.0	72.0		,833,	-0.4	0.0	12	dbSNP_123	72	1788,6812	314.9+/-312.0	196,1396,2708	yes	intron,missense,intron	SLC6A15	NM_001146335.1,NM_018057.5,NM_182767.4	,152,	203,1573,4727	AA,AT,TT		20.7907,4.335,15.2161	,,	,278/290,	85277561	1979,11027	2203	4300	6503	SO:0001627	intron_variant	55117	exon5			CAGAAATCTGTAA	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"""Solute carriers"""	13621	protein-coding gene	gene with protein product	"""homolog of rat orphan transporter v7-3"", ""sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"""	607971	"""solute carrier family 6 (neurotransmitter transporter), member 15"""			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.756+76A>T	12.37:g.85277561T>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	181	88	0.486188	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	238	0.10897435897435898	2	0.0040650406504065045	59	0.16298342541436464	0	0.0	177	0.23350923482849603	T	7.764	0.705915	0.15172	0.04335	0.207907	ENSG00000072041	ENST00000450363	T	0.68479	-0.33	4.95	-0.422	0.12329	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09907	-1.0653	7	0.87932	D	0	.	1.2642	0.02007	0.2154:0.1912:0.1092:0.4842	rs17183577;rs52796771;rs17183577	278	Q9H9F5	.	V	278	ENSP00000390706:D278V	ENSP00000390706:D278V	D	-	2	0	SLC6A15	83801692	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.510000	0.22723	-0.439000	0.07222	-1.427000	0.01099	GAT	T|0.862;A|0.138	0.138	strong		0.348	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
STPG1	90529	hgsc.bcm.edu	37	1	24706269	24706269	+	Silent	SNP	A	A	G	rs1064842	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24706269A>G	ENST00000374409.1	-	5	590	c.336T>C	c.(334-336)aaT>aaC	p.N112N	STPG1_ENST00000003583.8_Silent_p.N65N|STPG1_ENST00000468303.1_5'UTR|STPG1_ENST00000337248.4_Silent_p.N112N|STPG1_ENST00000440416.1_Silent_p.N65N	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	112					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											TAGTGTATGCATTCGCTGCAG	0.418													G|||	2099	0.419129	0.4894	0.5101	5008	,	,		20086	0.4444		0.3618	False		,,,				2504	0.2924				p.N112N		Atlas-SNP	.											C1orf201_ENST00000374409,colon,carcinoma,0,2	.	.	2	0			c.T336C						PASS	.	G	,,,	2182,2224	589.8+/-387.2	536,1110,557	100.0	100.0	100.0		336,336,60,195	-7.3	0.0	1	dbSNP_86	100	2936,5664	668.7+/-402.6	467,2002,1831	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C1orf201	NM_001199012.1,NM_001199013.1,NM_001199014.1,NM_178122.4	,,,	1003,3112,2388	GG,GA,AA		34.1395,49.5234,39.3511	,,,	112/335,112/335,20/243,65/288	24706269	5118,7888	2203	4300	6503	SO:0001819	synonymous_variant	90529	exon5			GTATGCATTCGCT	BC047705	CCDS253.1, CCDS55581.1	1p36.11	2012-10-31	2012-07-30	2012-07-30	ENSG00000001460	ENSG00000001460			28070	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 2"""	615826	"""chromosome 1 open reading frame 201"""	C1orf201		23028632	Standard	NM_001199012		Approved	FLJ33340, MAPO2	uc001bjc.3	Q5TH74	OTTHUMG00000003297	ENST00000374409.1:c.336T>C	1.37:g.24706269A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	154	58	0.376623	NM_001199012	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Silent	SNP	ENST00000374409.1	37	CCDS55581.1	947	0.4336080586080586	241	0.4898373983739837	172	0.47513812154696133	249	0.4353146853146853	285	0.3759894459102902	G	1.081	-0.667099	0.03428	0.495234	0.341395	ENSG00000001460	ENST00000435187	.	.	.	5.9	-7.34	0.01427	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	8.000000000008E-6	.	.	.	.	.	.	T	0.02081	-1.1217	3	.	.	.	-27.1846	18.1247	0.89581	0.3522:0.0:0.6478:0.0	rs1064842;rs3765429;rs10314500;rs59501254;rs1064842	.	.	.	T	89	.	.	M	-	2	0	C1orf201	24578856	0.010000	0.17322	0.000000	0.03702	0.270000	0.26580	-1.203000	0.03019	-1.966000	0.01009	-2.223000	0.00295	ATG	A|0.589;G|0.411	0.411	strong		0.418	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122	
RNF133	168433	hgsc.bcm.edu	37	7	122338970	122338970	+	Start_Codon_SNP	SNP	C	C	T	rs71574716	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:122338970C>T	ENST00000340112.2	-	1	240	c.3G>A	c.(1-3)atG>atA	p.M1I	CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000334010.7_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	1					protein autoubiquitination (GO:0051865)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21						TGAGTAGATGCATCTCTCTCT	0.398													C|||	91	0.0181709	0.0015	0.0331	5008	,	,		19518	0.0		0.0517	False		,,,				2504	0.0143				p.M1I	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.G3A						PASS	.	C	,,,ILE/MET	29,4373		0,29,2172	48.0	48.0	48.0		,,,3	4.8	0.4	7	dbSNP_130	48	363,8175		5,353,3911	yes	intron,intron,intron,missense	CADPS2,RNF133	NM_001009571.3,NM_001167940.1,NM_017954.10,NM_139175.1	,,,10	5,382,6083	TT,TC,CC		4.2516,0.6588,3.0294	,,,possibly-damaging	,,,1/377	122338970	392,12548	2201	4269	6470	SO:0001582	initiator_codon_variant	168433	exon1			TAGATGCATCTCT	AF447589	CCDS5784.1	7q31.33	2013-01-09			ENSG00000188050	ENSG00000188050		"""RING-type (C3HC4) zinc fingers"""	21154	protein-coding gene	gene with protein product							Standard	NM_139175		Approved		uc003vkj.1	Q8WVZ7	OTTHUMG00000157092	ENST00000340112.2:c.3G>A	7.37:g.122338970C>T	ENSP00000344489:p.Met1Ile	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	168	97	0.577381	NM_139175	A4D0W2|Q8N7G7	Missense_Mutation	SNP	ENST00000340112.2	37	CCDS5784.1	48	0.02197802197802198	0	0.0	10	0.027624309392265192	0	0.0	38	0.05013192612137203	C	15.43	2.832133	0.50845	0.006588	0.042516	ENSG00000188050	ENST00000340112	T	0.13420	2.59	5.72	4.84	0.62591	.	0.844884	0.09999	U	0.728693	T	0.02193	0.0068	.	.	.	0.80722	D	1	B	0.20550	0.046	B	0.14578	0.011	T	0.04128	-1.0975	9	0.87932	D	0	.	13.2124	0.59832	0.1594:0.8406:0.0:0.0	.	1	Q8WVZ7	RN133_HUMAN	I	1	ENSP00000344489:M1I	ENSP00000344489:M1I	M	-	3	0	RNF133	122126206	1.000000	0.71417	0.403000	0.26384	0.449000	0.32228	4.183000	0.58317	1.406000	0.46857	0.655000	0.94253	ATG	C|0.972;T|0.028	0.028	strong		0.398	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175	Missense_Mutation
AASDH	132949	hgsc.bcm.edu	37	4	57237683	57237683	+	Silent	SNP	G	G	A	rs6554354	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:57237683G>A	ENST00000205214.6	-	5	975	c.795C>T	c.(793-795)tcC>tcT	p.S265S	AASDH_ENST00000451613.1_Silent_p.S265S|AASDH_ENST00000602986.1_Silent_p.S112S|AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000502617.1_Silent_p.S265S|AASDH_ENST00000513376.1_Silent_p.S165S|AASDH_ENST00000510762.1_Intron	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	265					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.S265S(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				GCAACTTGACGGAAGTTGGTA	0.408													G|||	1392	0.277955	0.2829	0.2939	5008	,	,		18504	0.0724		0.4155	False		,,,				2504	0.3303				p.S265S		Atlas-SNP	.											AASDH,NS,carcinoma,0,1	AASDH	101	1	1	Substitution - coding silent(1)	prostate(1)	c.C795T						PASS	.	G		1284,3122	436.8+/-344.8	170,944,1089	104.0	92.0	96.0		795	-1.7	1.0	4	dbSNP_116	96	3664,4936	526.6+/-381.0	759,2146,1395	no	coding-synonymous	AASDH	NM_181806.2		929,3090,2484	AA,AG,GG		42.6047,29.1421,38.044		265/1099	57237683	4948,8058	2203	4300	6503	SO:0001819	synonymous_variant	132949	exon5			CTTGACGGAAGTT	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.795C>T	4.37:g.57237683G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	116	114	0.982759	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Silent	SNP	ENST00000205214.6	37	CCDS3504.1																																																																																			G|0.663;A|0.337	0.337	strong		0.408	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
OR2T2	401992	hgsc.bcm.edu	37	1	248616749	248616749	+	Silent	SNP	C	C	G	rs151176830		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248616749C>G	ENST00000342927.3	+	1	673	c.651C>G	c.(649-651)gtC>gtG	p.V217V		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCATCTCTGTCTCCTACACGC	0.542																																					p.V217V		Atlas-SNP	.											OR2T2,NS,carcinoma,0,1	OR2T2	73	1	0			c.C651G						scavenged	.						255.0	173.0	201.0					1																	248616749		2189	4267	6456	SO:0001819	synonymous_variant	401992	exon1			CTCTGTCTCCTAC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.651C>G	1.37:g.248616749C>G		Somatic	436	6	0.0137615		WXS	Illumina HiSeq	Phase_I	553	9	0.0162749	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			C|0.500;G|0.500	0.500	strong		0.542	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
FAM135A	57579	hgsc.bcm.edu	37	6	71269459	71269459	+	Silent	SNP	C	C	T	rs16869371	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:71269459C>T	ENST00000418814.2	+	22	4997	c.4383C>T	c.(4381-4383)ccC>ccT	p.P1461P	FAM135A_ENST00000361499.3_Silent_p.P1265P|FAM135A_ENST00000505769.1_Silent_p.P1041P|FAM135A_ENST00000370479.3_Silent_p.P1248P|FAM135A_ENST00000457062.2_Silent_p.P1248P	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1461										breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						TGCTTCGACCCGTTCTGCAAA	0.383													c|||	776	0.154952	0.1702	0.2061	5008	,	,		14788	0.0863		0.159	False		,,,				2504	0.1646				p.P1461P		Atlas-SNP	.											.	FAM135A	181	.	0			c.C4383T						PASS	.	G	,,	774,3632	313.0+/-292.9	74,626,1503	92.0	86.0	88.0		3795,4383,3744	0.3	1.0	6	dbSNP_123	88	1381,7219	268.9+/-288.1	126,1129,3045	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	200,1755,4548	TT,TC,CC		16.0581,17.567,16.5693	,,	1265/1320,1461/1516,1248/1303	71269459	2155,10851	2203	4300	6503	SO:0001819	synonymous_variant	57579	exon20			TCGACCCGTTCTG	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"""KIAA1411"""	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.4383C>T	6.37:g.71269459C>T		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			C|0.841;T|0.159	0.159	strong		0.383	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
KNDC1	85442	hgsc.bcm.edu	37	10	135010568	135010568	+	Missense_Mutation	SNP	G	G	A	rs35152544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135010568G>A	ENST00000304613.3	+	11	1762	c.1741G>A	c.(1741-1743)Ggc>Agc	p.G581S	KNDC1_ENST00000368571.2_Missense_Mutation_p.G516S|KNDC1_ENST00000368572.2_Missense_Mutation_p.G581S			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	581	KIND 2. {ECO:0000255|PROSITE- ProRule:PRU00709}.		G -> S (in dbSNP:rs35152544).		cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CCAGGTGTGCGGCAGCTACCT	0.642													G|||	240	0.0479233	0.0938	0.0418	5008	,	,		15259	0.001		0.0586	False		,,,				2504	0.0276				p.G581S		Atlas-SNP	.											.	KNDC1	155	.	0			c.G1741A						PASS	.	G	SER/GLY	367,4039	187.8+/-214.3	14,339,1850	72.0	55.0	61.0		1741	-5.0	0.0	10	dbSNP_126	61	577,8023	154.9+/-209.1	23,531,3746	yes	missense	KNDC1	NM_152643.6	56	37,870,5596	AA,AG,GG		6.7093,8.3296,7.2582	benign	581/1750	135010568	944,12062	2203	4300	6503	SO:0001583	missense	85442	exon11			GTGTGCGGCAGCT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.1741G>A	10.37:g.135010568G>A	ENSP00000304437:p.Gly581Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	153	152	0.993464	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	110	0.05036630036630037	48	0.0975609756097561	15	0.04143646408839779	1	0.0017482517482517483	46	0.06068601583113457	G	3.258	-0.151765	0.06585	0.083296	0.067093	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.09073	3.02;3.02;3.02	3.76	-4.98	0.03019	KIND (2);	0.822927	0.10555	N	0.660916	T	0.00039	0.0001	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.20671	0.038;0.047	B;B	0.14023	0.01;0.007	T	0.30327	-0.9982	9	0.02654	T	1	-9.1876	4.8634	0.13596	0.4145:0.2857:0.2998:0.0	rs35152544	516;581	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	S	581;581;516	ENSP00000304437:G581S;ENSP00000357561:G581S;ENSP00000357560:G516S	ENSP00000304437:G581S	G	+	1	0	KNDC1	134860558	0.000000	0.05858	0.000000	0.03702	0.312000	0.27988	-0.475000	0.06599	-1.124000	0.02936	0.467000	0.42956	GGC	G|0.933;A|0.067	0.067	strong		0.642	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
ZNF414	84330	hgsc.bcm.edu	37	19	8578118	8578118	+	Silent	SNP	A	A	G	rs1064009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8578118A>G	ENST00000255616.8	-	2	212	c.111T>C	c.(109-111)ccT>ccC	p.P37P	ZNF414_ENST00000393927.4_Silent_p.P37P	NM_032370.2	NP_115746.2	Q96IQ9	ZN414_HUMAN	zinc finger protein 414	37					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(2)	2						TGGAGGAGGAAGGGGCTGCAG	0.672													G|||	1034	0.20647	0.3086	0.1686	5008	,	,		16266	0.1746		0.1978	False		,,,				2504	0.137				p.P37P		Atlas-SNP	.											.	ZNF414	25	.	0			c.T111C						PASS	.	G	,	1098,3304		179,740,1282	14.0	16.0	15.0		111,111	-2.7	0.0	19	dbSNP_86	15	1370,7230		141,1088,3071	no	coding-synonymous,coding-synonymous	ZNF414	NM_001146175.1,NM_032370.2	,	320,1828,4353	GG,GA,AA		15.9302,24.9432,18.9817	,	37/391,37/313	8578118	2468,10534	2201	4300	6501	SO:0001819	synonymous_variant	84330	exon2			GGAGGAAGGGGCT	AK074191	CCDS12205.1, CCDS54211.1	19p13.2	2008-02-05				ENSG00000133250		"""Zinc fingers, C2H2-type"""	20630	protein-coding gene	gene with protein product							Standard	NM_032370		Approved	MGC15716, Zfp414	uc002mke.4	Q96IQ9		ENST00000255616.8:c.111T>C	19.37:g.8578118A>G		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_032370	A8MY94	Silent	SNP	ENST00000255616.8	37	CCDS12205.1																																																																																			A|0.795;G|0.205	0.205	strong		0.672	ZNF414-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460199.2	NM_032370	
DKKL1	27120	hgsc.bcm.edu	37	19	49869051	49869051	+	Splice_Site	SNP	T	T	G	rs2303759	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49869051T>G	ENST00000221498.2	+	4	731	c.326T>G	c.(325-327)aTg>aGg	p.M109R	AC010524.2_ENST00000599433.1_RNA|DKKL1_ENST00000594268.1_Intron	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	109			M -> R (in dbSNP:rs2303759).		anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		TCCTCACAGATGACCGACAAC	0.562													T|||	1594	0.318291	0.292	0.2464	5008	,	,		17401	0.3373		0.2396	False		,,,				2504	0.4663				p.M109R		Atlas-SNP	.											.	DKKL1	23	.	0			c.T326G						PASS	.	T	,ARG/MET,ARG/MET	1266,3140	430.6+/-342.6	182,902,1119	102.0	89.0	93.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,101,326	4.3	1.0	19	dbSNP_100	93	2278,6322	384.0+/-341.0	302,1674,2324	no	intron,missense-near-splice,missense-near-splice	DKKL1	NM_001197301.1,NM_001197302.1,NM_014419.3	,91,91	484,2576,3443	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	26.4884,28.7335,27.249	,benign,benign	,34/168,109/243	49869051	3544,9462	2203	4300	6503	SO:0001630	splice_region_variant	27120	exon4			CACAGATGACCGA	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"""cancer/testis antigen 34"", ""soggy"""	605418	"""dickkopf-like 1 (soggy)"""			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.325-1T>G	19.37:g.49869051T>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	37	CCDS12762.1	590	0.27014652014652013	134	0.27235772357723576	90	0.24861878453038674	186	0.32517482517482516	180	0.23746701846965698	T	10.98	1.504113	0.26949	0.287335	0.264884	ENSG00000104901	ENST00000221498	T	0.11930	2.73	4.35	4.35	0.52113	.	0.503678	0.16898	N	0.195029	T	0.00012	0.0000	N	0.08118	0	0.20764	P	0.99985795	B	0.32620	0.378	B	0.29353	0.101	T	0.43245	-0.9403	9	0.72032	D	0.01	-11.7793	10.1284	0.42663	0.0:0.0:0.0:1.0	rs2303759;rs52827084;rs59086630;rs2303759	109	Q9UK85	DKKL1_HUMAN	R	109	ENSP00000221498:M109R	ENSP00000221498:M109R	M	+	2	0	DKKL1	54560863	1.000000	0.71417	1.000000	0.80357	0.376000	0.30014	3.671000	0.54576	1.980000	0.57719	0.459000	0.35465	ATG	T|0.710;G|0.290	0.290	strong		0.562	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419	Missense_Mutation
LLGL2	3993	hgsc.bcm.edu	37	17	73570718	73570718	+	Silent	SNP	C	C	G	rs1126939	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73570718C>G	ENST00000392550.3	+	25	3141	c.3024C>G	c.(3022-3024)gcC>gcG	p.A1008A	LLGL2_ENST00000167462.5_Missense_Mutation_p.P994R|LLGL2_ENST00000577200.1_Silent_p.A1008A	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	1008					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CACATCGAGCCGCCGTGGGGT	0.677													G|||	1579	0.315296	0.6112	0.245	5008	,	,		13176	0.1508		0.2823	False		,,,				2504	0.1687				p.P994R		Atlas-SNP	.											.	LLGL2	155	.	0			c.C2981G						PASS	.	G	,ARG/PRO	2545,1861		755,1035,413	23.0	27.0	26.0		3024,2981	0.0	0.0	17	dbSNP_86	26	2533,6067		399,1735,2166	yes	coding-synonymous,missense	LLGL2	NM_001031803.1,NM_004524.2	,103	1154,2770,2579	GG,GC,CC		29.4535,42.2379,39.0435	,	1008/1021,994/1016	73570718	5078,7928	2203	4300	6503	SO:0001819	synonymous_variant	3993	exon24			TCGAGCCGCCGTG	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.3024C>G	17.37:g.73570718C>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	723	0.33104395604395603	334	0.6788617886178862	88	0.2430939226519337	81	0.14160839160839161	220	0.29023746701846964	G	8.672	0.903015	0.17760	0.577621	0.294535	ENSG00000073350	ENST00000167462;ENST00000545227	T	0.04917	3.53	4.66	0.0224	0.14133	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15896	-1.0421	7	0.87932	D	0	0.7107	4.422	0.11484	0.3008:0.3105:0.3886:0.0	rs1126939;rs1671017;rs3211300;rs11554115;rs17846684;rs17859783;rs61184994;rs1126939	983;994	G3V1I9;Q6P1M3-2	.;.	R	994;983	ENSP00000167462:P994R	ENSP00000167462:P994R	P	+	2	0	LLGL2	71082313	0.000000	0.05858	0.000000	0.03702	0.271000	0.26615	-0.116000	0.10724	-0.271000	0.09272	-0.293000	0.09583	CCG	C|0.621;G|0.379	0.379	strong		0.677	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
TGM6	343641	hgsc.bcm.edu	37	20	2380323	2380323	+	Silent	SNP	G	G	A	rs6114033	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2380323G>A	ENST00000202625.2	+	6	850	c.789G>A	c.(787-789)aaG>aaA	p.K263K	TGM6_ENST00000381423.1_Silent_p.K263K|TGM6_ENST00000477505.1_3'UTR	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	263					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	AGTGGCTCAAGGGCAGGTACA	0.662													G|||	912	0.182109	0.1982	0.1974	5008	,	,		12837	0.1498		0.1153	False		,,,				2504	0.2515				p.K263K		Atlas-SNP	.											TGM6,NS,carcinoma,0,1	TGM6	126	1	0			c.G789A						PASS	.	G		845,3561	315.2+/-294.0	72,701,1430	42.0	45.0	44.0		789	5.0	1.0	20	dbSNP_114	44	815,7785	179.2+/-228.4	45,725,3530	no	coding-synonymous	TGM6	NM_198994.2		117,1426,4960	AA,AG,GG		9.4767,19.1784,12.7633		263/707	2380323	1660,11346	2203	4300	6503	SO:0001819	synonymous_variant	343641	exon6			GCTCAAGGGCAGG	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.789G>A	20.37:g.2380323G>A		Somatic	261	1	0.00383142		WXS	Illumina HiSeq	Phase_I	221	214	0.968326	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	37	CCDS13025.1																																																																																			G|0.857;A|0.143	0.143	strong		0.662	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
ACKR2	1238	hgsc.bcm.edu	37	3	42907112	42907112	+	Missense_Mutation	SNP	A	A	C	rs2228468	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:42907112A>C	ENST00000422265.1	+	3	1293	c.1118A>C	c.(1117-1119)tAc>tCc	p.Y373S	RP11-141M3.5_ENST00000471537.1_RNA|CYP8B1_ENST00000437102.1_Intron|KRBOX1_ENST00000426937.1_Intron|ACKR2_ENST00000273145.2_Missense_Mutation_p.Y373S|ACKR2_ENST00000442925.1_Missense_Mutation_p.Y373S	NM_001296.4	NP_001287.2	O00590	ACKR2_HUMAN	atypical chemokine receptor 2	373	C-terminal cytoplasmic tail.		Y -> S (in dbSNP:rs2228468). {ECO:0000269|PubMed:14702039}.		chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|multicellular organismal development (GO:0007275)|neutrophil activation (GO:0042119)|receptor-mediated endocytosis (GO:0006898)	actin filament (GO:0005884)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-X-C chemokine receptor activity (GO:0016494)|chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)										TCTGAGAACTACCCTAACAAG	0.498													C|||	2209	0.441094	0.2292	0.5807	5008	,	,		18899	0.6776		0.4006	False		,,,				2504	0.4264				p.Y373S		Atlas-SNP	.											CCBP2,caecum,carcinoma,0,1	CCBP2	49	1	0			c.A1118C						PASS	.	C	SER/TYR	1123,3283	713.6+/-408.3	135,853,1215	83.0	84.0	84.0		1118	0.7	0.0	3	dbSNP_98	84	3397,5203	634.2+/-398.8	687,2023,1590	yes	missense	CCBP2	NM_001296.4	144	822,2876,2805	CC,CA,AA		39.5,25.488,34.7532	benign	373/385	42907112	4520,8486	2203	4300	6503	SO:0001583	missense	1238	exon3			AGAACTACCCTAA	U94888	CCDS2706.1	3p21.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144648	ENSG00000144648		"""GPCR / Class A : Chemokine receptors : Atypical"""	1565	protein-coding gene	gene with protein product		602648	"""chemokine binding protein 2"""	CMKBR9, CCBP2		9364936, 9405404, 16148	Standard	NM_001296		Approved	CCR10, D6, CCR9	uc003cme.3	O00590	OTTHUMG00000133040	ENST00000422265.1:c.1118A>C	3.37:g.42907112A>C	ENSP00000416996:p.Tyr373Ser	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	189	186	0.984127	NM_001296	B2R8Y8|O00537|Q53YA1|Q86UN9|Q96A02	Missense_Mutation	SNP	ENST00000422265.1	37	CCDS2706.1	1012	0.4633699633699634	116	0.23577235772357724	202	0.5580110497237569	388	0.6783216783216783	306	0.40369393139841686	C	0.007	-2.000847	0.00431	0.25488	0.395	ENSG00000144648	ENST00000442925;ENST00000422265;ENST00000273145	T;T;T	0.70869	-0.52;-0.52;-0.52	3.45	0.689	0.18033	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43228	-0.9404	7	.	.	.	.	3.1046	0.06337	0.1894:0.4907:0.0:0.3199	rs2228468;rs17318440;rs52817687;rs57779279;rs2228468	373	O00590	CCBP2_HUMAN	S	373	ENSP00000396150:Y373S;ENSP00000416996:Y373S;ENSP00000273145:Y373S	.	Y	+	2	0	CCBP2	42882116	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-0.129000	0.10515	-0.082000	0.12640	-1.623000	0.00790	TAC	A|0.607;C|0.392;T|0.001	0.392	strong		0.498	ACKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256645.2	NM_001296	
OR8B2	26595	hgsc.bcm.edu	37	11	124252718	124252718	+	Silent	SNP	G	G	A	rs886201	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124252718G>A	ENST00000375013.2	-	1	540	c.522C>T	c.(520-522)atC>atT	p.I174I		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		AGTAATGGTTGATGATATTAG	0.488																																					p.I174I		Atlas-SNP	.											.	OR8B2	42	.	0			c.C522T						PASS	.						29.0	29.0	29.0					11																	124252718		2200	4279	6479	SO:0001819	synonymous_variant	26595	exon1			ATGGTTGATGATA	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"""GPCR / Class A : Olfactory receptors"""	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.522C>T	11.37:g.124252718G>A		Somatic	452	0	0		WXS	Illumina HiSeq	Phase_I	504	186	0.369048	NM_001005468	Q8NGH2	Silent	SNP	ENST00000375013.2	37	CCDS31708.1																																																																																			G|0.836;A|0.164	0.164	strong		0.488	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468	
CSPG4	1464	hgsc.bcm.edu	37	15	75982085	75982085	+	Missense_Mutation	SNP	C	C	T	rs79463888	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75982085C>T	ENST00000308508.5	-	3	1413	c.1321G>A	c.(1321-1323)Gag>Aag	p.E441K		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	441	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GTGCCCCCCTCGGCCACCACC	0.637																																					p.E441K		Atlas-SNP	.											CSPG4,NS,haematopoietic_neoplasm,0,1	CSPG4	175	1	0			c.G1321A						scavenged	.						43.0	42.0	43.0					15																	75982085		2197	4292	6489	SO:0001583	missense	1464	exon3			CCCCCTCGGCCAC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1321G>A	15.37:g.75982085C>T	ENSP00000312506:p.Glu441Lys	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	203	16	0.0788177	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	18.26	3.584924	0.65992	.	.	ENSG00000173546	ENST00000308508	T	0.31510	1.49	5.26	5.26	0.73747	.	0.170667	0.41001	D	0.000974	T	0.48642	0.1511	M	0.78049	2.395	0.80722	D	1	D	0.71674	0.998	P	0.56278	0.795	T	0.52041	-0.8628	10	0.59425	D	0.04	.	11.3564	0.49617	0.0:0.9168:0.0:0.0831	.	441	Q6UVK1	CSPG4_HUMAN	K	441	ENSP00000312506:E441K	ENSP00000312506:E441K	E	-	1	0	CSPG4	73769140	1.000000	0.71417	0.998000	0.56505	0.513000	0.34164	4.634000	0.61325	2.463000	0.83235	0.555000	0.69702	GAG	C|0.878;T|0.122	0.122	strong		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
TRIOBP	11078	hgsc.bcm.edu	37	22	38130459	38130459	+	Missense_Mutation	SNP	G	G	T	rs8140207	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38130459G>T	ENST00000406386.3	+	9	4371	c.4116G>T	c.(4114-4116)gaG>gaT	p.E1372D		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1372			E -> D (in dbSNP:rs8140207).		actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GCCAAGCAGAGCCCCCTCATC	0.652													G|||	1322	0.263978	0.0401	0.2968	5008	,	,		16877	0.3016		0.3241	False		,,,				2504	0.4427				p.E1372D		Atlas-SNP	.											.	TRIOBP	262	.	0			c.G4116T						PASS	.	G	ASP/GLU	295,3593		11,273,1660	31.0	35.0	34.0		4116	0.9	0.0	22	dbSNP_116	34	2442,5822		337,1768,2027	yes	missense	TRIOBP	NM_001039141.2	45	348,2041,3687	TT,TG,GG		29.5499,7.5874,22.523	benign	1372/2366	38130459	2737,9415	1944	4132	6076	SO:0001583	missense	11078	exon9			AGCAGAGCCCCCT	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.4116G>T	22.37:g.38130459G>T	ENSP00000384312:p.Glu1372Asp	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	169	165	0.976331	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	585	0.26785714285714285	25	0.0508130081300813	109	0.3011049723756906	201	0.3513986013986014	250	0.32981530343007914	G	10.95	1.496753	0.26861	0.075874	0.295499	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.28454	1.61	5.45	0.937	0.19494	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	1.999999999946489E-6	B	0.21071	0.051	B	0.17979	0.02	T	0.46789	-0.9166	8	0.22109	T	0.4	.	3.1706	0.06551	0.3631:0.0:0.4543:0.1825	rs8140207;rs8140207	1372	Q9H2D6	TARA_HUMAN	D	1372;1333	ENSP00000384312:E1372D	ENSP00000384312:E1372D	E	+	3	2	TRIOBP	36460405	0.008000	0.16893	0.010000	0.14722	0.219000	0.24729	-0.109000	0.10840	0.228000	0.21019	0.563000	0.77884	GAG	G|0.726;T|0.274	0.274	strong		0.652	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
ARHGAP44	9912	hgsc.bcm.edu	37	17	12862170	12862170	+	Silent	SNP	C	C	T	rs3213687	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:12862170C>T	ENST00000379672.5	+	16	1779	c.1479C>T	c.(1477-1479)agC>agT	p.S493S	ARHGAP44_ENST00000262444.9_Silent_p.S493S|ARHGAP44_ENST00000340825.3_Silent_p.S493S	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	493					exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						GGCCCCTCAGCGTCGCCACGG	0.582													C|||	406	0.0810703	0.0045	0.1153	5008	,	,		15614	0.0863		0.0934	False		,,,				2504	0.1421				p.S493S		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.C1479T						PASS	.	C		82,4088		0,82,2003	15.0	17.0	16.0		1479	-7.7	0.3	17	dbSNP_106	16	744,7690		29,686,3502	no	coding-synonymous	ARHGAP44	NM_014859.4		29,768,5505	TT,TC,CC		8.8214,1.9664,6.5535		493/819	12862170	826,11778	2085	4217	6302	SO:0001819	synonymous_variant	9912	exon16			CCTCAGCGTCGCC		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"""Rho GTPase activating proteins"""	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.1479C>T	17.37:g.12862170C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	77	46	0.597403	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Silent	SNP	ENST00000379672.5	37	CCDS45616.1																																																																																			C|0.926;T|0.074	0.074	strong		0.582	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859	
LTBP1	4052	hgsc.bcm.edu	37	2	33447202	33447202	+	Silent	SNP	C	C	T	rs2290448	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:33447202C>T	ENST00000404816.2	+	9	2213	c.1860C>T	c.(1858-1860)aaC>aaT	p.N620N	LTBP1_ENST00000402934.1_Silent_p.N294N|LTBP1_ENST00000418533.2_Silent_p.N294N|LTBP1_ENST00000354476.3_Silent_p.N620N|LTBP1_ENST00000407925.1_Silent_p.N294N|LTBP1_ENST00000404525.1_Silent_p.N294N|LTBP1_ENST00000390003.4_Silent_p.N294N			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	620					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AGCGGGTTAACAACACCTTTT	0.383													C|||	1666	0.332668	0.1936	0.4337	5008	,	,		19452	0.3323		0.4861	False		,,,				2504	0.2914				p.N620N		Atlas-SNP	.											.	LTBP1	317	.	0			c.C1860T						PASS	.	C	,,,,	1019,3387	375.6+/-321.7	109,801,1293	117.0	101.0	106.0		882,882,882,882,1860	2.2	1.0	2	dbSNP_100	106	4214,4386	570.6+/-389.4	1021,2172,1107	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	,,,,	1130,2973,2400	TT,TC,CC		49.0,23.1276,40.2353	,,,,	294/1396,294/1354,294/1343,294/1301,620/1722	33447202	5233,7773	2203	4300	6503	SO:0001819	synonymous_variant	4052	exon9			GGTTAACAACACC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.1860C>T	2.37:g.33447202C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																			C|0.608;T|0.392	0.392	strong		0.383	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
MT-ND4	4538	hgsc.bcm.edu	37	M	11467	11467	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:11467A>G	ENST00000361381.2	+	1	708	c.708A>G	c.(706-708)ttA>ttG	p.L236L	MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	236					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						GCAGTACTCTTAAAACTAGGC	0.463																																					p.L236L		Atlas-SNP	.											.	.	.	.	0			c.A708G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ACTCTTAAAACTA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.708A>G	M.37:g.11467A>G		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	alt		0.463	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
SEPT12	124404	hgsc.bcm.edu	37	16	4837545	4837545	+	Silent	SNP	A	A	G	rs9673735	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:4837545A>G	ENST00000268231.8	-	2	365	c.102T>C	c.(100-102)gcT>gcC	p.A34A	SEPT12_ENST00000591861.1_5'UTR|SMIM22_ENST00000589721.1_5'Flank|SMIM22_ENST00000589327.1_5'Flank|SEPT12_ENST00000396693.5_Silent_p.A34A	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	34					cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)	p.A34A(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						GGTCCAGCACAGCCTCAATGC	0.627													A|||	1520	0.303514	0.1536	0.3458	5008	,	,		18187	0.3026		0.328	False		,,,				2504	0.4519				p.A34A		Atlas-SNP	.											SEPT12,colon,carcinoma,0,2	SEPT12	40	2	1	Substitution - coding silent(1)	stomach(1)	c.T102C						PASS	.	A	,	704,3690	293.6+/-282.7	56,592,1549	200.0	146.0	164.0		102,102	-9.9	0.5	16	dbSNP_119	164	2371,6229	394.7+/-344.8	340,1691,2269	no	coding-synonymous,coding-synonymous	SEPT12	NM_001154458.2,NM_144605.4	,	396,2283,3818	GG,GA,AA		27.5698,16.0218,23.6648	,	34/313,34/359	4837545	3075,9919	2197	4300	6497	SO:0001819	synonymous_variant	124404	exon2			CAGCACAGCCTCA	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.102T>C	16.37:g.4837545A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	109	65	0.59633	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Silent	SNP	ENST00000268231.8	37	CCDS10522.1																																																																																			A|0.743;G|0.257	0.257	strong		0.627	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605	
SI	6476	hgsc.bcm.edu	37	3	164783165	164783165	+	Missense_Mutation	SNP	T	T	C	rs9283633	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:164783165T>C	ENST00000264382.3	-	7	753	c.691A>G	c.(691-693)Acc>Gcc	p.T231A		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	231	Isomaltase.		T -> A (in dbSNP:rs9283633). {ECO:0000269|PubMed:1353958, ECO:0000269|PubMed:14724820, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16329100, ECO:0000269|PubMed:2962903}.		carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	GGAAGACGGGTTGAGATCTGT	0.343										HNSCC(35;0.089)			T|||	3085	0.616014	0.4622	0.621	5008	,	,		10113	0.8323		0.6312	False		,,,				2504	0.5818				p.T231A		Atlas-SNP	.											.	SI	500	.	0			c.A691G						PASS	.	T	ALA/THR	2110,2296	574.6+/-383.8	501,1108,594	59.0	59.0	59.0		691	1.0	0.6	3	dbSNP_119	59	5150,3450	634.3+/-398.8	1539,2072,689	yes	missense	SI	NM_001041.3	58	2040,3180,1283	CC,CT,TT		40.1163,47.8892,44.1796	benign	231/1828	164783165	7260,5746	2203	4300	6503	SO:0001583	missense	6476	exon7			GACGGGTTGAGAT	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.691A>G	3.37:g.164783165T>C	ENSP00000264382:p.Thr231Ala	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	163	73	0.447853	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	1390	0.6364468864468864	216	0.43902439024390244	214	0.5911602209944752	478	0.8356643356643356	482	0.6358839050131926	T	10.86	1.468408	0.26335	0.478892	0.598837	ENSG00000090402	ENST00000264382	D	0.87256	-2.23	5.9	1.05	0.20165	Glycoside hydrolase-type carbohydrate-binding (1);	0.297149	0.42682	N	0.000672	T	0.00012	0.0000	L	0.52905	1.665	0.37249	P	0.09354399999999996	B	0.11235	0.004	B	0.12837	0.008	T	0.39165	-0.9627	9	0.45353	T	0.12	.	8.956	0.35818	0.0:0.2896:0.0:0.7104	rs9283633;rs58773922;rs9283633	231	P14410	SUIS_HUMAN	A	231	ENSP00000264382:T231A	ENSP00000264382:T231A	T	-	1	0	SI	166265859	0.913000	0.31002	0.596000	0.28811	0.347000	0.29111	0.966000	0.29331	0.164000	0.19529	0.528000	0.53228	ACC	T|0.416;C|0.584	0.584	strong		0.343	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
UNC13A	23025	hgsc.bcm.edu	37	19	17728572	17728572	+	Silent	SNP	C	C	T	rs56174023	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17728572C>T	ENST00000519716.2	-	41	4496	c.4497G>A	c.(4495-4497)tcG>tcA	p.S1499S	UNC13A_ENST00000428389.2_Silent_p.S1587S|UNC13A_ENST00000552293.1_Silent_p.S1474S|UNC13A_ENST00000252773.7_Silent_p.S1499S|UNC13A_ENST00000550896.1_Silent_p.S1472S|UNC13A_ENST00000551649.1_Silent_p.S1499S	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1499	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						GCGTGTAGAGCGACAGGGCAT	0.607													C|||	449	0.0896565	0.031	0.1052	5008	,	,		19100	0.001		0.2515	False		,,,				2504	0.0828				p.S1499S		Atlas-SNP	.											.	UNC13A	299	.	0			c.G4497A						PASS	.	C		205,3971		3,199,1886	103.0	112.0	109.0		4497	-4.5	1.0	19	dbSNP_129	109	2033,6449		245,1543,2453	no	coding-synonymous	UNC13A	NM_001080421.2		248,1742,4339	TT,TC,CC		23.9684,4.909,17.6805		1499/1704	17728572	2238,10420	2088	4241	6329	SO:0001819	synonymous_variant	23025	exon39			GTAGAGCGACAGG	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.4497G>A	19.37:g.17728572C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	113	67	0.59292	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																			C|0.861;T|0.139	0.139	strong		0.607	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183108	11183108	+	Missense_Mutation	SNP	G	G	C	rs12318612	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11183108G>C	ENST00000390675.2	-	1	898	c.827C>G	c.(826-828)cCa>cGa	p.P276R	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	276			P -> R (in dbSNP:rs12318612).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						CAGGATGAATGGGTGGATTGA	0.423													.|||	614	0.122604	0.1051	0.2161	5008	,	,		19158	0.0		0.2734	False		,,,				2504	0.0511				p.P276R		Atlas-SNP	.											.	TAS2R31	24	.	0			c.C827G						PASS	.	G	ARG/PRO	499,3503		40,419,1542	192.0	194.0	193.0		827	2.4	0.0	12	dbSNP_120	193	2122,6246		286,1550,2348	no	missense	TAS2R31	NM_176885.2	103	326,1969,3890	CC,CG,GG		25.3585,12.4688,21.1884	possibly-damaging	276/310	11183108	2621,9749	2001	4184	6185	SO:0001583	missense	259290	exon1			ATGAATGGGTGGA	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.827C>G	12.37:g.11183108G>C	ENSP00000375093:p.Pro276Arg	Somatic	385	0	0		WXS	Illumina HiSeq	Phase_I	372	176	0.473118	NM_176885	P59547|Q17R84|Q645X5	Missense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	354	0.1620879120879121	71	0.1443089430894309	74	0.20441988950276244	0	0.0	209	0.2757255936675462	.	9.268	1.044890	0.19748	0.124688	0.253585	ENSG00000256436	ENST00000390675	T	0.64085	-0.08	2.41	2.41	0.29592	.	.	.	.	.	T	0.00012	0.0000	M	0.64404	1.975	0.80722	P	0.0	P	0.41188	0.741	B	0.41412	0.356	T	0.07385	-1.0775	8	0.87932	D	0	.	8.3448	0.32266	0.0:0.0:1.0:0.0	rs12318612	276	P59538	T2R31_HUMAN	R	276	ENSP00000375093:P276R	ENSP00000375093:P276R	P	-	2	0	TAS2R31	11074375	0.007000	0.16637	0.014000	0.15608	0.032000	0.12392	1.677000	0.37576	1.376000	0.46267	0.184000	0.17185	CCA	.	.	weak		0.423	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
SLC5A10	125206	hgsc.bcm.edu	37	17	18918396	18918396	+	Silent	SNP	G	G	C	rs2074279	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18918396G>C	ENST00000395645.3	+	11	1143	c.1125G>C	c.(1123-1125)gcG>gcC	p.A375A	SLC5A10_ENST00000395643.2_Silent_p.A348A|SLC5A10_ENST00000395647.2_Silent_p.A391A|SLC5A10_ENST00000395642.1_Silent_p.A308A|SLC5A10_ENST00000317977.6_Silent_p.A308A|SLC5A10_ENST00000417251.2_Silent_p.A339A	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	375					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						TGATGCTGGCGGCGCTCATGT	0.677													C|||	997	0.199081	0.3336	0.0663	5008	,	,		12776	0.3413		0.0288	False		,,,				2504	0.1401				p.A391A		Atlas-SNP	.											.	SLC5A10	55	.	0			c.G1173C						PASS	.	C	,	1209,3197	706.8+/-407.4	151,907,1145	60.0	49.0	53.0		1125,1173	-4.3	0.8	17	dbSNP_96	53	187,8413	810.1+/-407.1	2,183,4115	no	coding-synonymous,coding-synonymous	SLC5A10	NM_001042450.1,NM_152351.3	,	153,1090,5260	CC,CG,GG		2.1744,27.4399,10.7335	,	375/597,391/613	18918396	1396,11610	2203	4300	6503	SO:0001819	synonymous_variant	125206	exon11			GCTGGCGGCGCTC		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"""Solute carriers"""	23155	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 10"""				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.1125G>C	17.37:g.18918396G>C		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	258	131	0.507752	NM_152351	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Silent	SNP	ENST00000395645.3	37	CCDS42275.1																																																																																			G|0.872;C|0.128	0.128	strong		0.677	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351	
SORBS1	10580	hgsc.bcm.edu	37	10	97106165	97106165	+	Silent	SNP	T	T	C	rs726176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:97106165T>C	ENST00000361941.3	-	24	2453	c.2427A>G	c.(2425-2427)ctA>ctG	p.L809L	SORBS1_ENST00000306402.6_Silent_p.L556L|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000607232.1_Silent_p.L1069L|SORBS1_ENST00000371249.2_Silent_p.L591L|SORBS1_ENST00000371239.1_Silent_p.L586L|SORBS1_ENST00000393949.1_Silent_p.L779L|SORBS1_ENST00000354106.3_Silent_p.L779L|SORBS1_ENST00000371241.1_Silent_p.L459L|SORBS1_ENST00000371227.4_Silent_p.L763L|SORBS1_ENST00000277982.5_Silent_p.L831L|SORBS1_ENST00000371245.3_Silent_p.L660L|SORBS1_ENST00000347291.4_Silent_p.L621L|SORBS1_ENST00000371247.2_Silent_p.L809L|SORBS1_ENST00000353505.5_Silent_p.L660L|SORBS1_ENST00000371246.2_Silent_p.L831L	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		GCACTTACTTTAGTGTCTGAG	0.343													T|||	2043	0.407947	0.205	0.451	5008	,	,		19496	0.6696		0.3241	False		,,,				2504	0.4683				p.L831L		Atlas-SNP	.											.	SORBS1	185	.	0			c.A2493G						PASS	.	T	,,,,,,	915,3491	351.6+/-311.3	95,725,1383	85.0	85.0	85.0		2427,2493,1980,1545,1377,1773,1668	2.1	1.0	10	dbSNP_86	85	2392,6208	398.1+/-346.0	331,1730,2239	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	,,,,,,	426,2455,3622	CC,CT,TT		27.814,20.7671,25.4267	,,,,,,	809/1293,831/1152,660/906,515/741,459/685,591/817,556/782	97106165	3307,9699	2203	4300	6503	SO:0001819	synonymous_variant	10580	exon24			TTACTTTAGTGTC	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.2427A>G	10.37:g.97106165T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	37	35	0.945946	NM_001034955		Silent	SNP	ENST00000361941.3	37	CCDS31255.1																																																																																			A|0.002;C|0.320	0.320	strong		0.343	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
OAT	4942	hgsc.bcm.edu	37	10	126089434	126089434	+	Silent	SNP	G	G	A	rs11461	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:126089434G>A	ENST00000368845.5	-	9	1226	c.1134C>T	c.(1132-1134)aaC>aaT	p.N378N	OAT_ENST00000467675.1_5'Flank|OAT_ENST00000539214.1_Silent_p.N240N	NM_000274.3	NP_000265.1	P04181	OAT_HUMAN	ornithine aminotransferase	378					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-proline biosynthetic process (GO:0055129)|protein hexamerization (GO:0034214)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ornithine-oxo-acid transaminase activity (GO:0004587)|pyridoxal phosphate binding (GO:0030170)			endometrium(2)|large_intestine(1)|lung(2)	5		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)	TGACAATAGCGTTTAATAATC	0.308													G|||	2053	0.409944	0.1445	0.5259	5008	,	,		16380	0.6369		0.3648	False		,,,				2504	0.499				p.N378N		Atlas-SNP	.											.	OAT	25	.	0			c.C1134T						PASS	.	G	,	765,3641	309.1+/-290.9	71,623,1509	87.0	80.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1134,720	-4.0	0.5	10	dbSNP_52	82	3334,5262	493.7+/-373.6	620,2094,1584	no	coding-synonymous,coding-synonymous	OAT	NM_000274.3,NM_001171814.1	,	691,2717,3093	AA,AG,GG		38.7855,17.3627,31.5259	,	378/440,240/302	126089434	4099,8903	2203	4298	6501	SO:0001819	synonymous_variant	4942	exon9			AATAGCGTTTAAT	BC016928	CCDS7639.1, CCDS53586.1	10q26	2014-09-17	2010-01-20		ENSG00000065154	ENSG00000065154	2.6.1.13		8091	protein-coding gene	gene with protein product	"""Ornithine aminotransferase"", ""ornithine aminotransferase precursor"", ""gyrate atrophy"""	613349				1682785	Standard	NM_000274		Approved	HOGA	uc001lhp.3	P04181	OTTHUMG00000019213	ENST00000368845.5:c.1134C>T	10.37:g.126089434G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	149	63	0.422819	NM_000274	D3DRF0|Q16068|Q16069|Q68CS0|Q6IAV9|Q9UD03	Silent	SNP	ENST00000368845.5	37	CCDS7639.1																																																																																			G|0.648;A|0.352	0.352	strong		0.308	OAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050863.1	NM_000274	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693044	187693044	+	Silent	SNP	C	C	T	rs17852915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:187693044C>T	ENST00000295131.2	-	9	1608	c.1569G>A	c.(1567-1569)gtG>gtA	p.V523V		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	523					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			CAGTGGGACACACAATATTCT	0.403													T|||	872	0.174121	0.4213	0.1066	5008	,	,		17252	0.0208		0.1103	False		,,,				2504	0.1115				p.V523V		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.G1569A						PASS	.	T		1758,2648	644.2+/-398.0	344,1070,789	72.0	69.0	70.0		1569	-7.5	0.0	2	dbSNP_123	70	978,7622	772.8+/-407.7	44,890,3366	no	coding-synonymous	ZSWIM2	NM_182521.2		388,1960,4155	TT,TC,CC		11.3721,39.9001,21.0364		523/634	187693044	2736,10270	2203	4300	6503	SO:0001819	synonymous_variant	151112	exon9			GGGACACACAATA	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1569G>A	2.37:g.187693044C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	171	75	0.438596	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Silent	SNP	ENST00000295131.2	37	CCDS33348.1																																																																																			C|0.809;T|0.191	0.191	strong		0.403	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
ZFC3H1	196441	hgsc.bcm.edu	37	12	72024662	72024662	+	Silent	SNP	C	C	G	rs186434284	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:72024662C>G	ENST00000378743.3	-	17	3901	c.3543G>C	c.(3541-3543)ccG>ccC	p.P1181P		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1181					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AACACTGATCCGGTTCAATCA	0.348													C|||	16	0.00319489	0.0	0.0043	5008	,	,		16884	0.0		0.008	False		,,,				2504	0.0051				p.P1181P		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.G3543C						PASS	.	C		8,3930		0,8,1961	111.0	105.0	107.0		3543	-9.6	0.8	12		107	72,8274		0,72,4101	no	coding-synonymous	ZFC3H1	NM_144982.4		0,80,6062	GG,GC,CC		0.8627,0.2031,0.6513		1181/1990	72024662	80,12204	1969	4173	6142	SO:0001819	synonymous_variant	196441	exon17			CTGATCCGGTTCA	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.3543G>C	12.37:g.72024662C>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	164	75	0.457317	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Silent	SNP	ENST00000378743.3	37	CCDS41813.1																																																																																			C|0.993;G|0.007	0.007	strong		0.348	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
SPRR3	6707	hgsc.bcm.edu	37	1	152975810	152975810	+	Missense_Mutation	SNP	G	G	A	rs72704847|rs527966074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152975810G>A	ENST00000295367.4	+	2	356	c.314G>A	c.(313-315)gGc>gAc	p.G105D	SPRR3_ENST00000331860.3_Missense_Mutation_p.G105D|SPRR3_ENST00000542696.1_Missense_Mutation_p.G97D	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	105	14 X 8 AA approximate tandem repeats.		Missing.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCTGAGCCAGGCTACACCAAG	0.572													-|||	33	0.00658946	0.0008	0.0159	5008	,	,		20523	0.0		0.0209	False		,,,				2504	0.0				p.G105D		Atlas-SNP	.											.	SPRR3	45	.	0			c.G314A						PASS	.	G	ASP/GLY,ASP/GLY	27,4379	32.6+/-62.9	0,27,2176	99.0	80.0	87.0		314,314	1.0	0.0	1	dbSNP_131	87	142,8458	71.0+/-133.6	1,140,4159	yes	missense,missense	SPRR3	NM_001097589.1,NM_005416.2	94,94	1,167,6335	AA,AG,GG		1.6512,0.6128,1.2994	probably-damaging,probably-damaging	105/170,105/170	152975810	169,12837	2203	4300	6503	SO:0001583	missense	6707	exon2			AGCCAGGCTACAC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.314G>A	1.37:g.152975810G>A	ENSP00000295367:p.Gly105Asp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	154	65	0.422078	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Missense_Mutation	SNP	ENST00000295367.4	37	CCDS1033.1	21	0.009615384615384616	0	0.0	8	0.022099447513812154	0	0.0	13	0.017150395778364115	G	10.84	1.465063	0.26335	0.006128	0.016512	ENSG00000163209	ENST00000331860;ENST00000443178;ENST00000295367;ENST00000542696	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	5.31	0.967	0.19674	.	.	.	.	.	T	0.05823	0.0152	L	0.31664	0.95	0.09310	N	1	D;P	0.62365	0.991;0.606	D;B	0.65233	0.933;0.177	T	0.29912	-0.9996	9	0.12766	T	0.61	.	8.245	0.31682	0.0767:0.0:0.5068:0.4165	.	97;105	F5GZ12;Q9UBC9	.;SPRR3_HUMAN	D	105;105;105;97	ENSP00000330391:G105D;ENSP00000402016:G105D;ENSP00000295367:G105D;ENSP00000441477:G97D	ENSP00000295367:G105D	G	+	2	0	SPRR3	151242434	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.009000	0.12765	0.242000	0.21303	-0.321000	0.08615	GGC	G|0.988;A|0.012	0.012	strong		0.572	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
TXNDC15	79770	hgsc.bcm.edu	37	5	134223593	134223593	+	Silent	SNP	A	A	G	rs3733897	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:134223593A>G	ENST00000358387.4	+	2	937	c.312A>G	c.(310-312)aaA>aaG	p.K104K	TXNDC15_ENST00000546290.1_Silent_p.K81K	NM_024715.3	NP_078991.3	Q96J42	TXD15_HUMAN	thioredoxin domain containing 15	104					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGAGGACAAAGTGAGTTCAG	0.597													A|||	779	0.155551	0.0401	0.1398	5008	,	,		18547	0.2748		0.1491	False		,,,				2504	0.2065				p.K104K		Atlas-SNP	.											.	TXNDC15	37	.	0			c.A312G						PASS	.	A		231,4175	136.9+/-172.8	12,207,1984	109.0	97.0	101.0		312	-2.9	0.0	5	dbSNP_107	101	1162,7438	239.3+/-270.5	74,1014,3212	no	coding-synonymous	TXNDC15	NM_024715.3		86,1221,5196	GG,GA,AA		13.5116,5.2429,10.7104		104/361	134223593	1393,11613	2203	4300	6503	SO:0001819	synonymous_variant	79770	exon2			GGACAAAGTGAGT	AK026278	CCDS4180.1	5q31.1	2008-02-05	2007-08-16	2007-08-16	ENSG00000113621	ENSG00000113621			20652	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 14"""	C5orf14			Standard	NM_024715		Approved	2310047H23Rik, FLJ22625	uc003lac.1	Q96J42	OTTHUMG00000129115	ENST00000358387.4:c.312A>G	5.37:g.134223593A>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	154	84	0.545455	NM_024715	D3DQA9|Q96MT2|Q9H639	Silent	SNP	ENST00000358387.4	37	CCDS4180.1	336	0.15384615384615385	15	0.03048780487804878	43	0.11878453038674033	166	0.2902097902097902	112	0.14775725593667546	A	3.787	-0.044405	0.07452	0.052429	0.135116	ENSG00000113621	ENST00000508779	T	0.44482	0.92	5.61	-2.92	0.05615	.	0.939495	0.09190	N	0.836199	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.34079	-0.9843	6	0.16420	T	0.52	-13.9406	12.8157	0.57665	0.3788:0.0:0.6212:0.0	rs3733897;rs17695387;rs17846002;rs17858986;rs3733897	.	.	.	R	88	ENSP00000423513:K88R	ENSP00000423513:K88R	K	+	2	0	TXNDC15	134251492	0.000000	0.05858	0.012000	0.15200	0.417000	0.31264	-0.505000	0.06367	-0.425000	0.07371	-0.472000	0.04984	AAG	A|0.872;G|0.128	0.128	strong		0.597	TXNDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251160.1	NM_024715	
GMEB2	26205	hgsc.bcm.edu	37	20	62221766	62221766	+	Silent	SNP	C	C	T	rs2297428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62221766C>T	ENST00000266068.1	-	9	1747	c.1269G>A	c.(1267-1269)ccG>ccA	p.P423P	GMEB2_ENST00000370069.1_Silent_p.P372P|GMEB2_ENST00000370077.1_Silent_p.P423P			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	423					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			GCGGGGAGGCCGGGGAGCTGG	0.692													C|||	1126	0.22484	0.0091	0.1066	5008	,	,		15223	0.5159		0.2127	False		,,,				2504	0.3129				p.P423P		Atlas-SNP	.											.	GMEB2	44	.	0			c.G1269A						PASS	.	C		224,4138		12,200,1969	12.0	13.0	12.0		1269	-8.9	0.2	20	dbSNP_100	12	1750,6810		175,1400,2705	no	coding-synonymous	GMEB2	NM_012384.3		187,1600,4674	TT,TC,CC		20.4439,5.1353,15.2763		423/531	62221766	1974,10948	2181	4280	6461	SO:0001819	synonymous_variant	26205	exon10			GGAGGCCGGGGAG	AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216			4371	protein-coding gene	gene with protein product		607451				10523663, 11743720	Standard	NM_012384		Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000266068.1:c.1269G>A	20.37:g.62221766C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_012384	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	Silent	SNP	ENST00000266068.1	37	CCDS13528.1																																																																																			C|0.763;T|0.237	0.237	strong		0.692	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	NM_012384	
IL12RB1	3594	hgsc.bcm.edu	37	19	18191664	18191664	+	Silent	SNP	C	C	G	rs11086087	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18191664C>G	ENST00000600835.2	-	5	685	c.387G>C	c.(385-387)gtG>gtC	p.V129V	IL12RB1_ENST00000593993.2_Silent_p.V129V|IL12RB1_ENST00000322153.7_Silent_p.V129V			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	129	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						GCTGCAGGGTCACCTCAGGAG	0.572													C|||	651	0.129992	0.0537	0.0807	5008	,	,		18656	0.2857		0.1193	False		,,,				2504	0.1186				p.V129V		Atlas-SNP	.											.	IL12RB1	92	.	0			c.G387C						PASS	.	C	,	244,4162	141.9+/-177.2	5,234,1964	100.0	91.0	94.0		387,387	-4.7	0.0	19	dbSNP_120	94	991,7609	215.0+/-254.5	55,881,3364	no	coding-synonymous,coding-synonymous	IL12RB1	NM_005535.1,NM_153701.1	,	60,1115,5328	GG,GC,CC		11.5233,5.5379,9.4956	,	129/663,129/382	18191664	1235,11771	2203	4300	6503	SO:0001819	synonymous_variant	3594	exon4			CAGGGTCACCTCA	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.387G>C	19.37:g.18191664C>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Silent	SNP	ENST00000600835.2	37	CCDS54232.1																																																																																			G|0.108;C|0.892	0.108	strong		0.572	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
ZZEF1	23140	hgsc.bcm.edu	37	17	3947533	3947533	+	Missense_Mutation	SNP	G	G	A	rs1006954	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:3947533G>A	ENST00000381638.2	-	38	6275	c.6151C>T	c.(6151-6153)Cct>Tct	p.P2051S		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2051			P -> S (in dbSNP:rs1006954).				calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						AGTCCTGTAGGTGGGCTAGCA	0.418													G|||	393	0.0784744	0.1324	0.0793	5008	,	,		20481	0.0		0.1282	False		,,,				2504	0.0348				p.P2051S		Atlas-SNP	.											.	ZZEF1	195	.	0			c.C6151T						PASS	.	G	SER/PRO	560,3846	252.4+/-258.8	35,490,1678	205.0	189.0	195.0		6151	1.3	0.0	17	dbSNP_86	195	1183,7417	241.0+/-271.5	81,1021,3198	yes	missense	ZZEF1	NM_015113.3	74	116,1511,4876	AA,AG,GG		13.7558,12.7099,13.4015	probably-damaging	2051/2962	3947533	1743,11263	2203	4300	6503	SO:0001583	missense	23140	exon38			CTGTAGGTGGGCT	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.6151C>T	17.37:g.3947533G>A	ENSP00000371051:p.Pro2051Ser	Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	303	135	0.445545	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	206	0.09432234432234432	68	0.13821138211382114	32	0.08839779005524862	0	0.0	106	0.13984168865435356	G	0.014	-1.585389	0.00872	0.127099	0.137558	ENSG00000074755	ENST00000381638	T	0.19532	2.14	4.43	1.29	0.21616	.	0.640341	0.16694	N	0.203411	T	0.00073	0.0002	N	0.17082	0.46	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.002	T	0.26155	-1.0111	9	0.35671	T	0.21	-1.3534	3.8494	0.08948	0.2002:0.0:0.6103:0.1895	rs1006954;rs52814193;rs59412953;rs1006954	2051;2051	O43149-2;O43149	.;ZZEF1_HUMAN	S	2051	ENSP00000371051:P2051S	ENSP00000371051:P2051S	P	-	1	0	ZZEF1	3894282	0.020000	0.18652	0.027000	0.17364	0.009000	0.06853	0.450000	0.21762	0.345000	0.23873	0.655000	0.94253	CCT	G|0.875;A|0.125	0.125	strong		0.418	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
C12orf5	57103	hgsc.bcm.edu	37	12	4461485	4461485	+	Silent	SNP	G	G	A	rs7133330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:4461485G>A	ENST00000179259.4	+	6	508	c.441G>A	c.(439-441)gcG>gcA	p.A147A	C12orf5_ENST00000537251.1_3'UTR	NM_020375.2	NP_065108.1	Q9NQ88	TIGAR_HUMAN	chromosome 12 open reading frame 5	147					intestinal epithelial cell development (GO:0060576)|negative regulation of macromitophagy (GO:1901525)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|response to gamma radiation (GO:0010332)|response to xenobiotic stimulus (GO:0009410)	intracellular (GO:0005622)	fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			endometrium(1)|large_intestine(1)|lung(5)|skin(3)	10			all cancers(3;1.15e-07)|Colorectal(7;0.00165)|OV - Ovarian serous cystadenocarcinoma(31;0.00596)|COAD - Colon adenocarcinoma(12;0.0229)|GBM - Glioblastoma multiforme(3;0.0266)|STAD - Stomach adenocarcinoma(119;0.206)			TGAAAGAAGCGGATCAAAAAG	0.333													G|||	918	0.183307	0.0832	0.2839	5008	,	,		19855	0.1577		0.2714	False		,,,				2504	0.183				p.A147A	Colon(1;100 192 35375 49454 52532)	Atlas-SNP	.											.	C12orf5	28	.	0			c.G441A						PASS	.	G		494,3912	223.6+/-240.1	32,430,1741	56.0	57.0	57.0		441	-1.5	0.1	12	dbSNP_116	57	2302,6298	383.6+/-340.8	306,1690,2304	no	coding-synonymous	C12orf5	NM_020375.2		338,2120,4045	AA,AG,GG		26.7674,11.212,21.4978		147/271	4461485	2796,10210	2203	4300	6503	SO:0001819	synonymous_variant	57103	exon6			AGAAGCGGATCAA	AJ272206	CCDS8525.1	12p13.32	2014-05-29	2009-11-24	2009-11-24	ENSG00000078237	ENSG00000078237	3.1.3.46		1185	protein-coding gene	gene with protein product	"""TP53-induced glycolysis and apoptosis regulator"""	610775				16140933, 16839880, 18945750, 19713938	Standard	NM_020375		Approved	TIGAR	uc001qmp.3	Q9NQ88		ENST00000179259.4:c.441G>A	12.37:g.4461485G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_020375	B2R840	Silent	SNP	ENST00000179259.4	37	CCDS8525.1																																																																																			G|0.799;A|0.201	0.201	strong		0.333	C12orf5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398290.1	NM_020375	
MDM1	56890	hgsc.bcm.edu	37	12	68709892	68709892	+	Missense_Mutation	SNP	C	C	T	rs17224810	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:68709892C>T	ENST00000303145.7	-	8	1233	c.1147G>A	c.(1147-1149)Gtt>Att	p.V383I	MDM1_ENST00000411698.2_Missense_Mutation_p.V348I|MDM1_ENST00000540418.1_Missense_Mutation_p.V103I	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	383			V -> I (in dbSNP:rs17224810).		retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		TTGCTACTAACGGTTCCTTCT	0.408													C|||	687	0.137181	0.059	0.3098	5008	,	,		19331	0.1131		0.1859	False		,,,				2504	0.0951				p.V383I		Atlas-SNP	.											MDM1,caecum,carcinoma,+1,1	MDM1	74	1	0			c.G1147A						PASS	.	C	ILE/VAL,ILE/VAL	396,4010	197.1+/-221.3	19,358,1826	86.0	80.0	82.0		1042,1147	-6.2	0.0	12	dbSNP_123	82	1678,6922	307.6+/-308.5	189,1300,2811	yes	missense,missense	MDM1	NM_001205028.1,NM_017440.4	29,29	208,1658,4637	TT,TC,CC		19.5116,8.9877,15.9465	benign,benign	348/680,383/715	68709892	2074,10932	2203	4300	6503	SO:0001583	missense	56890	exon8			TACTAACGGTTCC	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"""Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"""			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.1147G>A	12.37:g.68709892C>T	ENSP00000302537:p.Val383Ile	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	167	91	0.54491	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	37	CCDS8983.1	320	0.14652014652014653	26	0.052845528455284556	94	0.2596685082872928	66	0.11538461538461539	134	0.17678100263852242	C	0.004	-2.246298	0.00271	0.089877	0.195116	ENSG00000111554	ENST00000540418;ENST00000303145;ENST00000411698	T;T;T	0.19105	2.17;2.17;2.17	5.77	-6.15	0.02105	.	0.637167	0.15333	N	0.267906	T	0.00012	0.0000	N	0.04203	-0.255	0.34656	P	0.27787300000000004	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.41413	-0.9510	8	.	.	.	-2.47	15.5588	0.76223	0.0:0.5298:0.0:0.4702	rs17224810;rs52820856;rs56563436;rs56944808;rs17224810	348;383	E7EPQ3;Q8TC05	.;MDM1_HUMAN	I	103;383;348	ENSP00000443815:V103I;ENSP00000302537:V383I;ENSP00000391006:V348I	.	V	-	1	0	MDM1	66996159	0.310000	0.24527	0.043000	0.18650	0.010000	0.07245	-0.243000	0.08915	-1.379000	0.02118	-2.048000	0.00412	GTT	C|0.857;T|0.143	0.143	strong		0.408	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128	
WDR64	128025	hgsc.bcm.edu	37	1	241929542	241929542	+	Missense_Mutation	SNP	G	G	A	rs12095445	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:241929542G>A	ENST00000366552.2	+	15	2147	c.1940G>A	c.(1939-1941)cGa>cAa	p.R647Q	WDR64_ENST00000437684.2_Missense_Mutation_p.R647Q	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	647			R -> Q (in dbSNP:rs12095445).							breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GATTTATTACGAGTGAACTGC	0.373													G|||	551	0.110024	0.2194	0.1225	5008	,	,		16781	0.003		0.1541	False		,,,				2504	0.0184				p.R647Q		Atlas-SNP	.											WDR64_ENST00000366552,NS,carcinoma,+1,2	WDR64	234	2	0			c.G1940A						PASS	.	G	GLN/ARG	952,3454	360.1+/-315.1	94,764,1345	131.0	128.0	129.0		1940	0.7	0.2	1	dbSNP_120	129	1408,7192	271.6+/-289.6	121,1166,3013	yes	missense	WDR64	NM_144625.4	43	215,1930,4358	AA,AG,GG		16.3721,21.6069,18.1455	benign	647/1082	241929542	2360,10646	2203	4300	6503	SO:0001583	missense	128025	exon15			TATTACGAGTGAA	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"""WD repeat domain containing"""	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1940G>A	1.37:g.241929542G>A	ENSP00000355510:p.Arg647Gln	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_144625	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	37		262|262	0.11996336996336997|0.11996336996336997	101|101	0.20528455284552846|0.20528455284552846	51|51	0.1408839779005525|0.1408839779005525	2|2	0.0034965034965034965|0.0034965034965034965	108|108	0.1424802110817942|0.1424802110817942	G|G	7.315|7.315	0.615699|0.615699	0.14129|0.14129	0.216069|0.216069	0.163721|0.163721	ENSG00000162843|ENSG00000162843	ENST00000425826|ENST00000366552;ENST00000437684;ENST00000414635	.|T;T;T	.|0.39787	.|1.06;1.06;1.06	4.47|4.47	0.735|0.735	0.18300|0.18300	.|WD40 repeat-like-containing domain (1);	.|0.943557	.|0.08769	.|N	.|0.896536	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.48452|0.48452	P|P	3.4999999999996145E-4|3.4999999999996145E-4	.|B;B	.|0.23591	.|0.088;0.062	.|B;B	.|0.18871	.|0.023;0.005	T|T	0.31779|0.31779	-0.9931|-0.9931	4|9	.|0.22109	.|T	.|0.4	-0.0022|-0.0022	3.7563|3.7563	0.08586|0.08586	0.5957:0.1885:0.2158:0.0|0.5957:0.1885:0.2158:0.0	rs12095445;rs52808464;rs58881118;rs12095445|rs12095445;rs52808464;rs58881118;rs12095445	.|647;367	.|B1ANS9;D1MPS4	.|WDR64_HUMAN;.	K|Q	126|647;647;418	.|ENSP00000355510:R647Q;ENSP00000402446:R647Q;ENSP00000406656:R418Q	.|ENSP00000355510:R647Q	E|R	+|+	1|2	0|0	WDR64|WDR64	239996165|239996165	1.000000|1.000000	0.71417|0.71417	0.228000|0.228000	0.23943|0.23943	0.031000|0.031000	0.12232|0.12232	2.437000|2.437000	0.44828|0.44828	-0.072000|-0.072000	0.12864|0.12864	-1.283000|-1.283000	0.01379|0.01379	GAG|CGA	G|0.839;A|0.161	0.161	strong		0.373	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625	
ITGA9	3680	hgsc.bcm.edu	37	3	37574951	37574951	+	Missense_Mutation	SNP	G	G	A	rs267561	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:37574951G>A	ENST00000264741.5	+	14	1776	c.1520G>A	c.(1519-1521)gGa>gAa	p.G507E	ITGA9_ENST00000422441.1_Missense_Mutation_p.G507E	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	507			G -> E (in dbSNP:rs267561). {ECO:0000269|PubMed:8245132, ECO:0000269|PubMed:8290272}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		CACGTTCCAGGAGAGATTGGT	0.547													G|||	2800	0.559105	0.4486	0.6844	5008	,	,		21440	0.8046		0.5427	False		,,,				2504	0.3834				p.G507E		Atlas-SNP	.											.	ITGA9	98	.	0			c.G1520A						PASS	.	G	GLU/GLY	2077,2329	570.8+/-382.9	493,1091,619	74.0	54.0	61.0		1520	5.9	1.0	3	dbSNP_79	61	4991,3609	624.8+/-397.6	1455,2081,764	yes	missense	ITGA9	NM_002207.2	98	1948,3172,1383	AA,AG,GG		41.9651,47.1403,45.6559	probably-damaging	507/1036	37574951	7068,5938	2203	4300	6503	SO:0001583	missense	3680	exon14			TTCCAGGAGAGAT	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.1520G>A	3.37:g.37574951G>A	ENSP00000264741:p.Gly507Glu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_002207	Q14638	Missense_Mutation	SNP	ENST00000264741.5	37	CCDS2669.1	1340	0.6135531135531136	208	0.42276422764227645	253	0.6988950276243094	470	0.8216783216783217	409	0.5395778364116095	G	19.23	3.787460	0.70337	0.471403	0.580349	ENSG00000144668	ENST00000422441;ENST00000264741	T;T	0.47177	0.85;0.85	5.86	5.86	0.93980	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.75777	2.31	0.09310	P	0.99999999975383	B;P	0.35944	0.003;0.529	B;B	0.44163	0.02;0.443	T	0.18241	-1.0343	9	0.25106	T	0.35	.	20.1865	0.98220	0.0:0.0:1.0:0.0	rs267561;rs572520;rs1223424;rs17036593;rs17852740;rs60380953;rs267561	507;507	Q13797;E9PDS3	ITA9_HUMAN;.	E	507	ENSP00000397258:G507E;ENSP00000264741:G507E	ENSP00000264741:G507E	G	+	2	0	ITGA9	37549955	1.000000	0.71417	0.999000	0.59377	0.481000	0.33189	7.753000	0.85153	2.775000	0.95449	0.655000	0.94253	GGA	G|0.424;T|0.003	.	strong		0.547	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
MRPL22	29093	hgsc.bcm.edu	37	5	154346325	154346325	+	Silent	SNP	G	G	A	rs7965	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:154346325G>A	ENST00000523037.1	+	7	530	c.489G>A	c.(487-489)aaG>aaA	p.K163K	MRPL22_ENST00000265229.8_Silent_p.K83K|MRPL22_ENST00000518364.1_3'UTR|MRPL22_ENST00000522038.1_Silent_p.K169K|MRPL22_ENST00000439747.3_Silent_p.K189K	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	163					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCATGGAGAAGGTTTATTGCC	0.522													G|||	305	0.0609026	0.0484	0.0648	5008	,	,		19357	0.002		0.1392	False		,,,				2504	0.0552				p.K163K		Atlas-SNP	.											.	MRPL22	18	.	0			c.G489A						PASS	.	G	,	267,4139	151.4+/-185.3	9,249,1945	152.0	140.0	144.0		249,489	2.0	1.0	5	dbSNP_52	144	1128,7472	232.9+/-266.4	82,964,3254	no	coding-synonymous,coding-synonymous	MRPL22	NM_001014990.2,NM_014180.3	,	91,1213,5199	AA,AG,GG		13.1163,6.0599,10.7258	,	83/127,163/207	154346325	1395,11611	2203	4300	6503	SO:0001819	synonymous_variant	29093	exon7			GGAGAAGGTTTAT	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"""Mitochondrial ribosomal proteins / large subunits"""	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.489G>A	5.37:g.154346325G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	147	70	0.47619	NM_014180	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Silent	SNP	ENST00000523037.1	37	CCDS4331.1																																																																																			G|0.908;A|0.092	0.092	strong		0.522	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2		
REV1	51455	hgsc.bcm.edu	37	2	100058870	100058870	+	Missense_Mutation	SNP	C	C	T	rs3087403	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:100058870C>T	ENST00000258428.3	-	5	640	c.412G>A	c.(412-414)Gtg>Atg	p.V138M	REV1_ENST00000393445.3_Missense_Mutation_p.V138M|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	138			V -> M (in dbSNP:rs3087403).		DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCTTTCTGCACACTGGACTGC	0.453								Direct reversal of damage					.|||	1131	0.225839	0.2995	0.3415	5008	,	,		17072	0.0625		0.2833	False		,,,				2504	0.1534				p.V138M		Atlas-SNP	.											.	REV1	100	.	0			c.G412A						PASS	.	C	MET/VAL,MET/VAL	1246,3160	428.7+/-342.0	166,914,1123	138.0	122.0	127.0		412,412	1.8	0.0	2	dbSNP_102	127	2396,6204	397.5+/-345.8	310,1776,2214	yes	missense,missense	REV1	NM_001037872.1,NM_016316.2	21,21	476,2690,3337	TT,TC,CC		27.8605,28.2796,28.0025	benign,benign	138/1251,138/1252	100058870	3642,9364	2203	4300	6503	SO:0001583	missense	51455	exon5			TCTGCACACTGGA	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"""DNA polymerases"""	14060	protein-coding gene	gene with protein product		606134	"""REV1 (yeast homolog)- like"", ""REV1-like (yeast)"", ""REV1 homolog (S. cerevisiae)"""	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.412G>A	2.37:g.100058870C>T	ENSP00000258428:p.Val138Met	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	182	97	0.532967	NM_001037872	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	521	0.23855311355311357	151	0.30691056910569103	123	0.3397790055248619	31	0.05419580419580419	216	0.2849604221635884	C	12.34	1.908171	0.33721	0.282796	0.278605	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.28895	1.59;1.59	5.59	1.76	0.24704	.	0.501568	0.22005	N	0.065958	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B;B;B	0.19706	0.038;0.003;0.019	B;B;B	0.20577	0.03;0.01;0.029	T	0.31024	-0.9958	9	0.46703	T	0.11	.	6.6283	0.22843	0.0:0.6148:0.1185:0.2667	rs3087403;rs17713429;rs52807598;rs58647355;rs3087403	117;138;138	Q9UBZ9-3;Q9UBZ9;Q9UBZ9-2	.;REV1_HUMAN;.	M	138	ENSP00000377091:V138M;ENSP00000258428:V138M	ENSP00000258428:V138M	V	-	1	0	REV1	99425302	0.005000	0.15991	0.004000	0.12327	0.997000	0.91878	1.136000	0.31467	0.052000	0.16007	0.655000	0.94253	GTG	C|0.747;T|0.253	0.253	strong		0.453	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	
OTUD7A	161725	hgsc.bcm.edu	37	15	31793930	31793930	+	Silent	SNP	A	A	G	rs7164569	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:31793930A>G	ENST00000307050.4	-	8	1205	c.1113T>C	c.(1111-1113)ctT>ctC	p.L371L	OTUD7A_ENST00000382902.1_Silent_p.L378L	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	371	Catalytic. {ECO:0000250}.|OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding. {ECO:0000250}.				protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		CCATGGACACAAGGGCAGAGA	0.572													a|||	1657	0.330871	0.5061	0.3429	5008	,	,		20439	0.2212		0.339	False		,,,				2504	0.1902				p.L371L		Atlas-SNP	.											.	OTUD7A	89	.	0			c.T1113C						PASS	.	A		2080,2324	571.9+/-383.2	480,1120,602	158.0	138.0	145.0		1113	-9.7	0.2	15	dbSNP_116	145	3028,5572	467.5+/-367.1	550,1928,1822	no	coding-synonymous	OTUD7A	NM_130901.1		1030,3048,2424	GG,GA,AA		35.2093,47.2298,39.2802		371/927	31793930	5108,7896	2202	4300	6502	SO:0001819	synonymous_variant	161725	exon8			GGACACAAGGGCA	AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918		"""OTU domain containing"""	20718	protein-coding gene	gene with protein product		612024	"""chromosome 15 open reading frame 16"", ""OTU domain containing 7"", ""OTU domain containing 7A"""	C15orf16, OTUD7		23827681	Standard	NM_130901		Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.1113T>C	15.37:g.31793930A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	174	87	0.5	NM_130901	Q8IWK5	Silent	SNP	ENST00000307050.4	37	CCDS10026.1																																																																																			A|0.632;G|0.368	0.368	strong		0.572	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901	
SPAG1	6674	hgsc.bcm.edu	37	8	101252680	101252680	+	Missense_Mutation	SNP	T	T	C	rs6511	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:101252680T>C	ENST00000388798.2	+	18	2521	c.2330T>C	c.(2329-2331)aTg>aCg	p.M777T	SPAG1_ENST00000251809.3_Missense_Mutation_p.M777T	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	777			M -> T (in dbSNP:rs6511). {ECO:0000269|PubMed:11517287}.		axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.M777T(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GAGGTCTCCATGGGATGCCTT	0.483													C|||	3142	0.627396	0.7179	0.7233	5008	,	,		17979	0.5327		0.6193	False		,,,				2504	0.5429				p.M777T		Atlas-SNP	.											SPAG1,pharynx,carcinoma,-1,2	SPAG1	80	2	1	Substitution - Missense(1)	stomach(1)	c.T2330C						PASS	.	C	THR/MET,THR/MET	3051,1355	438.2+/-345.2	1073,905,225	82.0	90.0	87.0		2330,2330	-3.7	0.0	8	dbSNP_52	87	5241,3359	495.6+/-374.1	1599,2043,658	yes	missense,missense	SPAG1	NM_003114.4,NM_172218.2	81,81	2672,2948,883	CC,CT,TT		39.0581,30.7535,36.2448	benign,benign	777/927,777/927	101252680	8292,4714	2203	4300	6503	SO:0001583	missense	6674	exon18			TCTCCATGGGATG	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"""Tetratricopeptide (TTC) repeat domain containing"""	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.2330T>C	8.37:g.101252680T>C	ENSP00000373450:p.Met777Thr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	37	CCDS34930.1	1387	0.63507326007326	353	0.717479674796748	259	0.7154696132596685	294	0.513986013986014	481	0.6345646437994723	C	0.080	-1.186039	0.01620	0.692465	0.609419	ENSG00000104450	ENST00000251809;ENST00000388798	T;T	0.59502	0.26;0.26	5.77	-3.7	0.04437	.	1.659360	0.03303	N	0.189258	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31641	-0.9936	9	0.06494	T	0.89	2.3277	4.5629	0.12168	0.0974:0.2617:0.0968:0.5441	rs6511;rs1631163;rs52789688;rs61672000;rs6511	777	Q07617	SPAG1_HUMAN	T	777	ENSP00000251809:M777T;ENSP00000373450:M777T	ENSP00000251809:M777T	M	+	2	0	SPAG1	101321856	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.164000	0.09983	-1.149000	0.02843	-0.215000	0.12644	ATG	T|0.369;C|0.631	0.631	strong		0.483	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218	
TENM2	57451	hgsc.bcm.edu	37	5	167689296	167689296	+	Silent	SNP	C	C	T	rs17632540	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:167689296C>T	ENST00000518659.1	+	29	7845	c.7806C>T	c.(7804-7806)aaC>aaT	p.N2602N	TENM2_ENST00000519204.1_Silent_p.N2481N|TENM2_ENST00000545108.1_Silent_p.N2601N|TENM2_ENST00000520394.1_Silent_p.N2363N|TENM2_ENST00000403607.2_Silent_p.N2426N	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2602					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TGCTGAACAACGCCTACTACC	0.562													C|||	999	0.199481	0.1536	0.1556	5008	,	,		20212	0.002		0.3022	False		,,,				2504	0.3906				p.N2593N		Atlas-SNP	.											.	.	.	.	0			c.C7779T						PASS	.	C		684,3574		58,568,1503	43.0	48.0	47.0		7779	0.5	1.0	5	dbSNP_123	47	2524,5976		397,1730,2123	no	coding-synonymous	ODZ2	NM_001122679.1		455,2298,3626	TT,TC,CC		29.6941,16.0639,25.145		2593/2766	167689296	3208,9550	2129	4250	6379	SO:0001819	synonymous_variant	57451	exon29			GAACAACGCCTAC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.7806C>T	5.37:g.167689296C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				C|0.820;T|0.180	0.180	strong		0.562	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
PRIM1	5557	hgsc.bcm.edu	37	12	57133140	57133140	+	Silent	SNP	T	T	G	rs1131514	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57133140T>G	ENST00000338193.6	-	10	1026	c.990A>C	c.(988-990)atA>atC	p.I330I		NM_000946.2	NP_000937.1	P49642	PRI1_HUMAN	primase, DNA, polypeptide 1 (49kDa)	330					DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			kidney(1)|lung(6)|prostate(1)	8						TAGGCACAGATATGCGACCTG	0.328													T|||	3043	0.607628	0.3343	0.6657	5008	,	,		18766	0.7401		0.6252	False		,,,				2504	0.7812				p.I330I		Atlas-SNP	.											PRIM1,NS,carcinoma,0,1	PRIM1	22	1	0			c.A990C						PASS	.	T		1591,2143		348,895,624	79.0	70.0	73.0		990	2.9	1.0	12	dbSNP_86	73	5095,3095		1594,1907,594	no	coding-synonymous	PRIM1	NM_000946.2		1942,2802,1218	GG,GT,TT		37.79,42.6085,43.9282		330/421	57133140	6686,5238	1867	4095	5962	SO:0001819	synonymous_variant	5557	exon10			CACAGATATGCGA	BC005266	CCDS44926.1	12q13.3	2007-06-19	2007-06-19			ENSG00000198056			9369	protein-coding gene	gene with protein product		176635				8530050	Standard	NM_000946		Approved		uc001smd.3	P49642	OTTHUMG00000170034	ENST00000338193.6:c.990A>C	12.37:g.57133140T>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_000946		Silent	SNP	ENST00000338193.6	37	CCDS44926.1																																																																																			T|0.243;G|0.376	0.376	strong		0.328	PRIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406956.1	NM_000946	
CNTNAP4	85445	hgsc.bcm.edu	37	16	76587202	76587202	+	Missense_Mutation	SNP	T	T	G	rs7202925	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:76587202T>G	ENST00000476707.1	+	21	3613	c.3474T>G	c.(3472-3474)gaT>gaG	p.D1158E	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.D1154E|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.D1082E|RP11-58C22.1_ENST00000563764.1_5'Flank|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.D1106E			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	1155	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)		p.D1082E(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						TGGACCAGGATACTGCACTGG	0.517													G|||	1504	0.300319	0.3449	0.196	5008	,	,		18787	0.2847		0.2773	False		,,,				2504	0.3538				p.D1082E		Atlas-SNP	.											CNTNAP4_ENST00000478060,NS,carcinoma,0,1	CNTNAP4	600	1	1	Substitution - Missense(1)	stomach(1)	c.T3246G						PASS	.	G	GLU/ASP,GLU/ASP	1309,2613		209,891,861	28.0	30.0	29.0		3464,3246	3.3	1.0	16	dbSNP_116	29	2328,6014		317,1694,2160	yes	missense,missense	CNTNAP4	NM_033401.3,NM_138994.3	45,45	526,2585,3021	GG,GT,TT		27.907,33.3758,29.6559	benign,benign	1155/1309,1082/1236	76587202	3637,8627	1961	4171	6132	SO:0001583	missense	85445	exon21			CCAGGATACTGCA	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.3474T>G	16.37:g.76587202T>G	ENSP00000417628:p.Asp1158Glu	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	211	95	0.450237	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		619	0.2834249084249084	162	0.32926829268292684	76	0.20994475138121546	168	0.2937062937062937	213	0.28100263852242746	G	1.370	-0.586320	0.03827	0.333758	0.27907	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.32	3.32	0.38043	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.41938	N	0.000790	T	0.00012	0.0000	.	.	.	0.58432	P	4.000000000004E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.002;0.001;0.004	T	0.35968	-0.9767	8	0.02654	T	1	.	10.8875	0.46976	0.0:0.1204:0.5057:0.374	rs7202925;rs60336736;rs7202925	1082;1158;1155	E9PFZ6;E9PDN6;Q9C0A0	.;.;CNTP4_HUMAN	E	1154;1106;1082;1158	ENSP00000306893:D1154E;ENSP00000439733:D1106E;ENSP00000418741:D1082E;ENSP00000417628:D1158E	ENSP00000306893:D1154E	D	+	3	2	CNTNAP4	75144703	0.998000	0.40836	0.996000	0.52242	0.464000	0.32679	0.388000	0.20735	0.366000	0.24427	-0.121000	0.15023	GAT	T|0.706;G|0.294	0.294	strong		0.517	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	
SLFN5	162394	hgsc.bcm.edu	37	17	33592725	33592725	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:33592725G>A	ENST00000299977.4	+	5	2642	c.2494G>A	c.(2494-2496)Gcg>Acg	p.A832T	SLFN5_ENST00000542451.1_3'UTR	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	832					cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		GATCGGTGATGCGTCGGATGT	0.443																																					p.A832T		Atlas-SNP	.											SLFN5,colon,carcinoma,-1,1	SLFN5	92	1	0			c.G2494A						scavenged	.						96.0	85.0	88.0					17																	33592725		2203	4300	6503	SO:0001583	missense	162394	exon5			GGTGATGCGTCGG	BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.2494G>A	17.37:g.33592725G>A	ENSP00000299977:p.Ala832Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	170	2	0.0117647	NM_144975	Q08AF2|Q8WU54|Q96A82	Missense_Mutation	SNP	ENST00000299977.4	37	CCDS32619.1	.	.	.	.	.	.	.	.	.	.	g	13.86	2.361771	0.41801	.	.	ENSG00000166750	ENST00000299977	D	0.81996	-1.56	2.54	1.56	0.23342	.	0.739382	0.11087	N	0.601231	T	0.61135	0.2323	N	0.08118	0	0.09310	N	1	B	0.33528	0.416	B	0.23018	0.043	T	0.54741	-0.8248	10	0.62326	D	0.03	.	5.3307	0.15930	0.1639:0.0:0.8361:0.0	.	832	Q08AF3	SLFN5_HUMAN	T	832	ENSP00000299977:A832T	ENSP00000299977:A832T	A	+	1	0	SLFN5	30616838	0.018000	0.18449	0.002000	0.10522	0.001000	0.01503	2.196000	0.42686	0.634000	0.30469	-0.140000	0.14226	GCG	.	.	none		0.443	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975	
SPTB	6710	hgsc.bcm.edu	37	14	65245956	65245956	+	Silent	SNP	C	C	T	rs1741488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:65245956C>T	ENST00000389721.5	-	21	4514	c.4482G>A	c.(4480-4482)gtG>gtA	p.V1494V	SPTB_ENST00000542895.1_Silent_p.V1494V|SPTB_ENST00000389722.3_Silent_p.V1494V|SPTB_ENST00000389720.3_Silent_p.V1494V|SPTB_ENST00000556626.1_Silent_p.V1494V	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1494					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GCCTCTCCTCCACCCAAAGCT	0.572													C|||	2061	0.411542	0.7012	0.1657	5008	,	,		14786	0.3532		0.2445	False		,,,				2504	0.4264				p.V1494V		Atlas-SNP	.											.	SPTB	378	.	0			c.G4482A						PASS	.	C	,	2672,1734	635.9+/-396.5	813,1046,344	57.0	61.0	60.0		4482,4482	5.2	1.0	14	dbSNP_89	60	2059,6541	350.6+/-327.9	249,1561,2490	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	1062,2607,2834	TT,TC,CC		23.9419,39.3554,36.3755	,	1494/2138,1494/2329	65245956	4731,8275	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon21			CTCCTCCACCCAA		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4482G>A	14.37:g.65245956C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	160	69	0.43125	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			C|0.634;T|0.366	0.366	strong		0.572	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
PDCD6IP	10015	hgsc.bcm.edu	37	3	33877626	33877626	+	Missense_Mutation	SNP	G	G	A	rs3792594	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33877626G>A	ENST00000307296.3	+	8	1302	c.925G>A	c.(925-927)Gct>Act	p.A309T	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.A314T			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	309	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.|Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.		A -> T (in dbSNP:rs3792594). {ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						TCGTGCCCTTGCTGCAGCAAA	0.388													A|||	1639	0.327276	0.2912	0.402	5008	,	,		18899	0.4067		0.2326	False		,,,				2504	0.3384				p.A314T		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.G940A						PASS	.	A	THR/ALA,THR/ALA	1309,3097	697.2+/-406.2	175,959,1069	161.0	165.0	164.0		940,925	2.7	1.0	3	dbSNP_107	164	2278,6322	707.5+/-405.6	280,1718,2302	yes	missense,missense	PDCD6IP	NM_001162429.1,NM_013374.4	58,58	455,2677,3371	AA,AG,GG		26.4884,29.7095,27.5796	benign,benign	314/874,309/869	33877626	3587,9419	2203	4300	6503	SO:0001583	missense	10015	exon8			GCCCTTGCTGCAG	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.925G>A	3.37:g.33877626G>A	ENSP00000307387:p.Ala309Thr	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	222	113	0.509009	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	737	0.3374542124542125	156	0.3170731707317073	155	0.4281767955801105	246	0.43006993006993005	180	0.23746701846965698	A	7.300	0.612793	0.14066	0.297095	0.264884	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.16743	2.32;2.32	5.18	2.68	0.31781	BRO1 domain (3);	0.048164	0.85682	N	0.000000	T	0.00012	0.0000	N	0.05534	-0.03	0.41888	P	0.009646999999999961	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.15484	0.013;0.001;0.001	T	0.48736	-0.9009	9	0.17832	T	0.49	-7.0423	10.1043	0.42524	0.7313:0.0:0.2687:0.0	rs3792594;rs52810638;rs57922878;rs3792594	90;314;309	B7Z5C1;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	T	309;314	ENSP00000307387:A309T;ENSP00000411825:A314T	ENSP00000307387:A309T	A	+	1	0	PDCD6IP	33852630	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	2.195000	0.42677	0.272000	0.22027	-0.269000	0.10298	GCT	G|0.698;A|0.302	0.302	strong		0.388	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
IL24	11009	hgsc.bcm.edu	37	1	207076321	207076321	+	Splice_Site	SNP	T	T	G	rs150080259	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207076321T>G	ENST00000294984.2	+	7	812	c.538T>G	c.(538-540)Ttg>Gtg	p.L180V	FAIM3_ENST00000528654.1_5'Flank|IL24_ENST00000391929.3_Splice_Site_p.L181V|IL24_ENST00000367093.3_Splice_Site_p.L128V|IL24_ENST00000491169.1_3'UTR	NM_001185156.1|NM_006850.3	NP_001172085.1|NP_006841.1	Q13007	IL24_HUMAN	interleukin 24	180					apoptotic process (GO:0006915)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|serine phosphorylation of STAT3 protein (GO:0033136)|wound healing (GO:0042060)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)				endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12	Breast(84;0.201)					TTCCCTTTAGTTGGACGTAGA	0.473													T|||	35	0.00698882	0.0	0.0	5008	,	,		22265	0.0308		0.0	False		,,,				2504	0.0041				p.L181V		Atlas-SNP	.											.	IL24	20	.	0			c.T541G						PASS	.	T	VAL/LEU,VAL/LEU,ARG/SER,VAL/LEU	1,4405	2.1+/-5.4	0,1,2202	218.0	217.0	217.0		541,382,183,538	-0.8	0.5	1	dbSNP_134	217	13,8587	10.5+/-38.8	0,13,4287	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	IL24	NM_001185156.1,NM_001185157.1,NM_001185158.1,NM_006850.3	32,32,110,32	0,14,6489	GG,GT,TT		0.1512,0.0227,0.1076	benign,benign,benign,benign	181/208,128/155,61/64,180/207	207076321	14,12992	2203	4300	6503	SO:0001630	splice_region_variant	11009	exon7			CTTTAGTTGGACG	U16261	CCDS1471.1, CCDS53465.1, CCDS53466.1, CCDS73021.1	1q32	2011-07-15		2001-06-29	ENSG00000162892	ENSG00000162892		"""Interleukins and interleukin receptors"""	11346	protein-coding gene	gene with protein product	"""melanoma differentiation association protein 7"", ""suppression of tumorigenicity 16 (melanoma differentiation)"", ""IL-4-induced secreted protein"""	604136		ST16		8545104, 8799171	Standard	NM_001185156		Approved	mda-7, IL10B, Mob-5, C49A, FISP, IL-24	uc001heu.2	Q13007	OTTHUMG00000036459	ENST00000294984.2:c.538-1T>G	1.37:g.207076321T>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_001185156	Q2YHE5|Q53XZ7|Q5YLN8|Q96DB0|Q96KG4	Missense_Mutation	SNP	ENST00000294984.2	37	CCDS1471.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	T	13.60	2.286193	0.40394	2.27E-4	0.001512	ENSG00000162892	ENST00000391929;ENST00000294984;ENST00000367093	T;T;T	0.24151	1.87;1.87;1.87	4.45	-0.763	0.11030	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.000000	0.64402	D	0.000011	T	0.33585	0.0868	.	.	.	0.33498	D	0.589509	D;P;P	0.76494	0.999;0.897;0.897	D;B;B	0.83275	0.996;0.432;0.432	T	0.46162	-0.9211	8	.	.	.	.	7.6215	0.28187	0.0:0.473:0.0:0.527	.	128;181;180	Q2YHE5;Q53XZ7;Q13007	.;.;IL24_HUMAN	V	181;180;128	ENSP00000375795:L181V;ENSP00000294984:L180V;ENSP00000356060:L128V	.	L	+	1	2	IL24	205142944	0.862000	0.29867	0.462000	0.27118	0.493000	0.33554	-0.631000	0.05496	-0.279000	0.09167	-0.376000	0.06991	TTG	T|0.998;G|0.002	0.002	strong		0.473	IL24-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088680.2	NM_006850	Missense_Mutation
PCNX	22990	hgsc.bcm.edu	37	14	71500217	71500217	+	Silent	SNP	C	C	T	rs71425297	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:71500217C>T	ENST00000304743.2	+	17	4076	c.3630C>T	c.(3628-3630)taC>taT	p.Y1210Y	PCNX_ENST00000238570.5_Silent_p.Y1210Y|PCNX_ENST00000439984.3_Silent_p.Y1099Y	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1210						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		CAGTGTCTTACCATCTCAGCC	0.338													C|||	18	0.00359425	0.0	0.0	5008	,	,		15944	0.0		0.0179	False		,,,				2504	0.0				p.Y1210Y		Atlas-SNP	.											.	PCNX	198	.	0			c.C3630T						PASS	.	C		10,4396	16.8+/-37.8	1,8,2194	153.0	138.0	143.0		3630	0.5	1.0	14	dbSNP_130	143	87,8513	49.4+/-109.1	0,87,4213	no	coding-synonymous	PCNX	NM_014982.2		1,95,6407	TT,TC,CC		1.0116,0.227,0.7458		1210/2342	71500217	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	22990	exon17			GTCTTACCATCTC	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.3630C>T	14.37:g.71500217C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	187	82	0.438503	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	37	CCDS9806.1	14	0.00641025641025641	0	0.0	0	0.0	0	0.0	14	0.018469656992084433	C	8.208	0.799745	0.16397	0.00227	0.010116	ENSG00000100731	ENST00000554691	.	.	.	5.72	0.525	0.17072	.	.	.	.	.	T	0.39886	0.1095	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38286	-0.9668	4	.	.	.	.	9.1872	0.37178	0.0:0.3569:0.0:0.6431	.	.	.	.	I	269	.	.	T	+	2	0	PCNX	70569970	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	1.090000	0.30902	0.105000	0.17753	-0.300000	0.09419	ACC	C|0.992;T|0.008	0.008	strong		0.338	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319185	21319185	+	Silent	SNP	T	T	A	rs149832249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:21319185T>A	ENST00000583088.1	+	3	1426	c.531T>A	c.(529-531)atT>atA	p.I177I	KCNJ12_ENST00000331718.5_Silent_p.I177I	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	177					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CCTTCATGATTGGTGCCATCA	0.637										Prostate(3;0.18)																											p.I177I		Atlas-SNP	.											.	.	.	.	0			c.T531A						PASS	.	T		2,4404		0,2,2201	87.0	81.0	83.0		531	-4.0	0.9	17	dbSNP_134	83	18,8582	5.7+/-21.5	0,18,4282	no	coding-synonymous	KCNJ12	NM_021012.4		0,20,6483	AA,AT,TT		0.2093,0.0454,0.1538		177/434	21319185	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			CATGATTGGTGCC	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.531T>A	17.37:g.21319185T>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	212	23	0.108491	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			T|0.999;A|0.001	0.001	strong		0.637	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
DOCK6	57572	hgsc.bcm.edu	37	19	11319491	11319491	+	Silent	SNP	G	G	A	rs8409	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11319491G>A	ENST00000294618.7	-	39	4970	c.4959C>T	c.(4957-4959)aaC>aaT	p.N1653N	DOCK6_ENST00000319867.7_Silent_p.N992N|CTC-510F12.2_ENST00000588634.1_RNA	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1653	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						CCTCTAGCACGTTGGATGAGA	0.647													G|||	2212	0.441693	0.264	0.4741	5008	,	,		17093	0.4633		0.6044	False		,,,				2504	0.4693				p.N1653N		Atlas-SNP	.											.	DOCK6	104	.	0			c.C4959T						PASS	.			1280,2982		202,876,1053	65.0	74.0	71.0		4959	0.1	1.0	19	dbSNP_52	71	4940,3504		1448,2044,730	yes	coding-synonymous	DOCK6	NM_020812.2		1650,2920,1783	AA,AG,GG		41.4969,30.0328,48.9533		1653/2048	11319491	6220,6486	2131	4222	6353	SO:0001819	synonymous_variant	57572	exon39			TAGCACGTTGGAT		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.4959C>T	19.37:g.11319491G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			G|0.533;A|0.467	0.467	strong		0.647	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
MID2	11043	hgsc.bcm.edu	37	X	107159291	107159291	+	Missense_Mutation	SNP	C	C	A	rs12849510	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:107159291C>A	ENST00000262843.6	+	6	1681	c.1133C>A	c.(1132-1134)gCc>gAc	p.A378D	MID2_ENST00000443968.2_Missense_Mutation_p.A378D|RP6-191P20.4_ENST00000430140.1_RNA	NM_012216.3|NM_052817.2	NP_036348.2|NP_438112.2	Q9UJV3	TRIM1_HUMAN	midline 2	378	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.		A -> D (in dbSNP:rs12849510).		innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein localization to microtubule (GO:0035372)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)	19						TTTAATGATGCCTTTGAAAAC	0.343													C|||	110	0.0291391	0.0091	0.0245	3775	,	,		10993	0.002		0.0497	False		,,,				2504	0.0297				p.A378D		Atlas-SNP	.											.	MID2	122	.	0			c.C1133A						PASS	.	C	ASP/ALA,ASP/ALA	59,3776		1,50,7,1581,564	119.0	116.0	117.0		1133,1133	5.2	1.0	X	dbSNP_121	117	342,6385		6,218,112,2204,1759	yes	missense,missense	MID2	NM_012216.3,NM_052817.2	126,126	7,268,119,3785,2323	AA,AC,A,CC,C		5.084,1.5385,3.7966	benign,benign	378/736,378/706	107159291	401,10161	2203	4299	6502	SO:0001583	missense	11043	exon6			ATGATGCCTTTGA		CCDS14532.2, CCDS14533.2	Xq22.1-q22.2	2013-02-11			ENSG00000080561	ENSG00000080561		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	7096	protein-coding gene	gene with protein product		300204				10400986	Standard	NM_012216		Approved	FXY2, TRIM1, RNF60	uc004enl.3	Q9UJV3	OTTHUMG00000022171	ENST00000262843.6:c.1133C>A	X.37:g.107159291C>A	ENSP00000262843:p.Ala378Asp	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	NM_012216	A6NEL8|A6PVI5|Q5JYF5|Q8WWK1|Q9UJR9	Missense_Mutation	SNP	ENST00000262843.6	37	CCDS14532.2	48	0.028933092224231464	4	0.008130081300813009	4	0.011299435028248588	1	0.0017482517482517483	22	0.030054644808743168	C	15.48	2.847537	0.51164	0.015385	0.05084	ENSG00000080561	ENST00000262843;ENST00000443968	T;T	0.59638	0.25;0.28	5.23	5.23	0.72850	COS domain (1);	0.109652	0.64402	D	0.000008	T	0.15046	0.0363	L	0.40543	1.245	0.09310	P	0.9999999747693	B;B	0.28552	0.215;0.022	B;B	0.32465	0.146;0.037	T	0.52873	-0.8517	9	0.51188	T	0.08	.	15.1546	0.72730	0.0:1.0:0.0:0.0	rs12849510;rs52815338;rs57540397;rs12849510	378;378	Q9UJV3;Q9UJV3-2	TRIM1_HUMAN;.	D	378	ENSP00000262843:A378D;ENSP00000413976:A378D	ENSP00000262843:A378D	A	+	2	0	MID2	107045947	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.166000	0.68216	0.600000	0.82982	GCC	C|0.965;A|0.035	0.035	strong		0.343	MID2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057852.2	NM_012216	
LONRF3	79836	hgsc.bcm.edu	37	X	118108785	118108785	+	Silent	SNP	T	T	C	rs3813933	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:118108785T>C	ENST00000371628.3	+	1	73	c.42T>C	c.(40-42)gcT>gcC	p.A14A	LONRF3_ENST00000304778.7_Silent_p.A14A|LONRF3_ENST00000422289.2_5'Flank	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	14							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						GCTTGCCCGCTGAGGTCAGCA	0.647													C|||	1898	0.502781	0.2247	0.464	3775	,	,		12076	0.5923		0.327	False		,,,				2504	0.3609				p.A14A		Atlas-SNP	.											.	LONRF3	138	.	0			c.T42C						PASS	.	C	,	1211,2620		174,681,182,777,385	24.0	19.0	20.0		42,42	-1.1	0.5	X	dbSNP_107	20	2862,3854		444,1178,796,804,1068	no	coding-synonymous,coding-synonymous	LONRF3	NM_001031855.1,NM_024778.4	,	618,1859,978,1581,1453	CC,CT,C,TT,T		42.6147,31.6105,38.6176	,	14/760,14/719	118108785	4073,6474	2199	4290	6489	SO:0001819	synonymous_variant	79836	exon1			GCCCGCTGAGGTC	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"""RING-type (C3HC4) zinc fingers"""	21152	protein-coding gene	gene with protein product			"""ring finger protein 127"""	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.42T>C	X.37:g.118108785T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Silent	SNP	ENST00000371628.3	37	CCDS35374.1																																																																																			T|0.560;C|0.440	0.440	strong		0.647	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778	
MICALL1	85377	hgsc.bcm.edu	37	22	38323507	38323507	+	Missense_Mutation	SNP	G	G	T	rs9610875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38323507G>T	ENST00000215957.6	+	9	1681	c.1555G>T	c.(1555-1557)Gcc>Tcc	p.A519S	MICALL1_ENST00000402631.1_3'UTR	NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	519	Pro-rich.		A -> S (in dbSNP:rs9610875). {ECO:0000269|PubMed:17974005}.		endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					GTCTGAGAGCGCCAGCCAGAC	0.677													G|||	840	0.167732	0.0265	0.2637	5008	,	,		15751	0.1349		0.2336	False		,,,				2504	0.2566				p.A519S		Atlas-SNP	.											.	MICALL1	53	.	0			c.G1555T						PASS	.	G	SER/ALA	252,4154	146.1+/-180.8	10,232,1961	67.0	61.0	63.0		1555	1.6	0.2	22	dbSNP_119	63	2080,6520	359.8+/-331.7	267,1546,2487	yes	missense	MICALL1	NM_033386.3	99	277,1778,4448	TT,TG,GG		24.186,5.7195,17.9302	benign	519/864	38323507	2332,10674	2203	4300	6503	SO:0001583	missense	85377	exon9			GAGAGCGCCAGCC	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"""molecule interacting with Rab13"""					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.1555G>T	22.37:g.38323507G>T	ENSP00000215957:p.Ala519Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	37	CCDS13961.1	380|380	0.17399267399267399|0.17399267399267399	11|11	0.022357723577235773|0.022357723577235773	103|103	0.2845303867403315|0.2845303867403315	84|84	0.14685314685314685|0.14685314685314685	182|182	0.24010554089709762|0.24010554089709762	G|G	3.806|3.806	-0.040672|-0.040672	0.07497|0.07497	0.057195|0.057195	0.24186|0.24186	ENSG00000100139|ENSG00000100139	ENST00000215957|ENST00000454685	T|.	0.47177|.	0.85|.	4.99|4.99	1.63|1.63	0.23807|0.23807	.|.	0.441509|.	0.21510|.	N|.	0.073393|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00082|0.00082	-2.215|-2.215	0.23174|0.23174	P|P	0.99817006|0.99817006	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.41378|0.41378	-0.9512|-0.9512	9|4	0.02654|.	T|.	1|.	.|.	7.7553|7.7553	0.28921|0.28921	0.0:0.0694:0.2627:0.6679|0.0:0.0694:0.2627:0.6679	rs9610875;rs57936345;rs9610875|rs9610875;rs57936345;rs9610875	519|.	Q8N3F8|.	MILK1_HUMAN|.	S|L	519|96	ENSP00000215957:A519S|.	ENSP00000215957:A519S|.	A|R	+|+	1|2	0|0	MICALL1|MICALL1	36653453|36653453	0.620000|0.620000	0.27068|0.27068	0.236000|0.236000	0.24074|0.24074	0.259000|0.259000	0.26198|0.26198	2.468000|2.468000	0.45102|0.45102	-0.039000|-0.039000	0.13602|0.13602	-0.385000|-0.385000	0.06624|0.06624	GCC|CGC	G|0.829;T|0.171	0.171	strong		0.677	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386	
ACSM1	116285	hgsc.bcm.edu	37	16	20635418	20635418	+	Splice_Site	SNP	C	C	T	rs3743690	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20635418C>T	ENST00000307493.4	-	12	1714	c.1647G>A	c.(1645-1647)aaG>aaA	p.K549K	ACSM1_ENST00000219151.4_Splice_Site_p.K200K|ACSM1_ENST00000520010.1_Splice_Site_p.K549K	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	549				K -> N (in Ref. 1; BAB64535/BAB68363). {ECO:0000305}.	benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						CCTCACTCACCTTCCTTGGGT	0.547													C|||	920	0.183706	0.0295	0.1297	5008	,	,		21557	0.499		0.1461	False		,,,				2504	0.1442				p.K549K		Atlas-SNP	.											.	ACSM1	118	.	0			c.G1647A						PASS	.	C		199,4203	125.3+/-162.5	6,187,2008	256.0	199.0	218.0		1647	3.9	1.0	16	dbSNP_107	218	1065,7535	224.4+/-260.8	72,921,3307	yes	coding-synonymous-near-splice	ACSM1	NM_052956.2		78,1108,5315	TT,TC,CC		12.3837,4.5207,9.7216		549/578	20635418	1264,11738	2201	4300	6501	SO:0001630	splice_region_variant	116285	exon12			ACTCACCTTCCTT	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"""Acyl-CoA synthetase family"""	18049	protein-coding gene	gene with protein product		614357	"""butyryl Coenzyme A synthetase 1"""	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.1647+1G>A	16.37:g.20635418C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	135	74	0.548148	NM_052956	Q08AH2|Q96A20	Silent	SNP	ENST00000307493.4	37	CCDS10587.1	481	0.22023809523809523	20	0.04065040650406504	52	0.143646408839779	305	0.5332167832167832	104	0.13720316622691292	c	5.565	0.289098	0.10513	0.045207	0.123837	ENSG00000166743	ENST00000524149	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.52064	-0.8625	3	.	.	.	.	15.1985	0.73116	0.0:1.0:0.0:0.0	rs3743690;rs3743690	.	.	.	K	221	.	.	R	-	2	0	ACSM1	20542919	1.000000	0.71417	1.000000	0.80357	0.197000	0.23852	5.528000	0.67129	2.183000	0.69458	0.609000	0.83330	AGG	C|0.852;T|0.148	0.148	strong		0.547	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956	Silent
LRRC36	55282	hgsc.bcm.edu	37	16	67381383	67381383	+	Intron	SNP	G	G	C	rs79636320	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:67381383G>C	ENST00000329956.6	+	4	410				LRRC36_ENST00000290940.7_5'UTR|LRRC36_ENST00000541146.1_5'UTR|LRRC36_ENST00000563303.1_Intron|LRRC36_ENST00000435835.3_Missense_Mutation_p.R5P|LRRC36_ENST00000563189.1_Missense_Mutation_p.R5P	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36											endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	24		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		CTCAGACCACGGTTTTTGCCT	0.408													G|||	166	0.033147	0.0038	0.0447	5008	,	,		19532	0.001		0.0924	False		,,,				2504	0.0368				p.R5P		Atlas-SNP	.											.	LRRC36	68	.	0			c.G14C						PASS	.	G	PRO/ARG,	98,4298	77.3+/-115.6	0,98,2100	97.0	94.0	95.0		14,	-1.2	0.1	16	dbSNP_132	95	912,7688	203.1+/-246.2	44,824,3432	yes	missense,intron	LRRC36	NM_001161575.1,NM_018296.5	103,	44,922,5532	CC,CG,GG		10.6047,2.2293,7.7716	,	5/634,	67381383	1010,11986	2198	4300	6498	SO:0001627	intron_variant	55282	exon1			GACCACGGTTTTT	BC026156	CCDS32467.1, CCDS58474.1	16q22.1	2008-02-05				ENSG00000159708			25615	protein-coding gene	gene with protein product						12477932	Standard	NM_001161575		Approved	FLJ11004	uc002esv.3	Q1X8D7		ENST00000329956.6:c.392-15G>C	16.37:g.67381383G>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	NM_001161575	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Missense_Mutation	SNP	ENST00000329956.6	37	CCDS32467.1	94	0.04304029304029304	3	0.006097560975609756	22	0.06077348066298342	0	0.0	69	0.09102902374670185	G	11.44	1.640532	0.29157	0.022293	0.106047	ENSG00000159708	ENST00000435835	T	0.32515	1.45	5.41	-1.24	0.09435	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	0.58432	P	4.000000000004E-6	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.24012	-1.0172	8	0.66056	D	0.02	.	1.8701	0.03207	0.1927:0.3625:0.3013:0.1434	.	5;5	B7Z7B3;Q1X8D7-2	.;.	P	5	ENSP00000411122:R5P	ENSP00000411122:R5P	R	+	2	0	LRRC36	65938884	0.001000	0.12720	0.149000	0.22428	0.983000	0.72400	-0.132000	0.10467	0.035000	0.15519	0.655000	0.94253	CGG	G|0.945;C|0.055	0.055	strong		0.408	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296	
NPAP1	23742	hgsc.bcm.edu	37	15	24923283	24923283	+	Missense_Mutation	SNP	G	G	A	rs36032407	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:24923283G>A	ENST00000329468.2	+	1	2743	c.2269G>A	c.(2269-2271)Gct>Act	p.A757T		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	757			A -> T (in dbSNP:rs36032407).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CAGGGCACCAGCTACAGCTTC	0.582													A|||	74	0.0147764	0.0045	0.0259	5008	,	,		16883	0.0		0.0318	False		,,,				2504	0.0184				p.A757T		Atlas-SNP	.											.	.	.	.	0			c.G2269A						PASS	.	A	THR/ALA	55,4351		0,55,2148	120.0	128.0	126.0		2269	-2.0	0.0	15	dbSNP_126	126	328,8272		8,312,3980	yes	missense	C15orf2	NM_018958.2	58	8,367,6128	AA,AG,GG		3.814,1.2483,2.9448	benign	757/1157	24923283	383,12623	2203	4300	6503	SO:0001583	missense	23742	exon1			GCACCAGCTACAG	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2269G>A	15.37:g.24923283G>A	ENSP00000333735:p.Ala757Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	117	60	0.512821	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	41	0.018772893772893772	3	0.006097560975609756	9	0.024861878453038673	0	0.0	29	0.03825857519788918	.	0.013	-1.618879	0.00828	0.012483	0.03814	ENSG00000185823	ENST00000329468	T	0.06528	3.29	2.14	-1.98	0.07480	.	3.179220	0.01097	N	0.005281	T	0.00580	0.0019	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40384	-0.9566	10	0.02654	T	1	.	7.9136	0.29806	0.389:0.0:0.611:0.0	rs36032407	757	Q9NZP6	CO002_HUMAN	T	757	ENSP00000333735:A757T	ENSP00000333735:A757T	A	+	1	0	C15orf2	22474376	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.134000	0.03228	-1.045000	0.03250	-1.298000	0.01336	GCT	G|0.972;A|0.028	0.028	strong		0.582	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
ELFN2	114794	hgsc.bcm.edu	37	22	37770630	37770630	+	Silent	SNP	G	G	A	rs2071856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:37770630G>A	ENST00000402918.2	-	3	1730	c.945C>T	c.(943-945)atC>atT	p.I315I	RP1-63G5.8_ENST00000609322.1_RNA|RP1-63G5.5_ENST00000430883.1_RNA|ELFN2_ENST00000435824.1_5'Flank	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	315	Fibronectin type-III.				negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)	p.I315I(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					AGGGGTGTGGGATGATGACCA	0.602													G|||	1609	0.321286	0.2375	0.1758	5008	,	,		19473	0.3988		0.325	False		,,,				2504	0.454				p.I315I		Atlas-SNP	.											ELFN2,NS,carcinoma,0,1	ELFN2	89	1	1	Substitution - coding silent(1)	stomach(1)	c.C945T						PASS	.	G		1031,3375	381.6+/-324.1	119,793,1291	327.0	294.0	305.0		945	4.2	1.0	22	dbSNP_96	305	2562,6038	417.6+/-352.5	409,1744,2147	no	coding-synonymous	ELFN2	NM_052906.3		528,2537,3438	AA,AG,GG		29.7907,23.3999,27.6257		315/821	37770630	3593,9413	2203	4300	6503	SO:0001819	synonymous_variant	114794	exon3			GTGTGGGATGATG	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	29396	protein-coding gene	gene with protein product			"""leucine rich repeat containing 62"", ""extracellular leucine-rich repeat and fibronectin type III containing 2"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 2"", ""protein phosphatase 1, regulatory subunit 29"""	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.945C>T	22.37:g.37770630G>A		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	285	140	0.491228	NM_052906	Q96PY3	Silent	SNP	ENST00000402918.2	37	CCDS33642.1																																																																																			G|0.709;A|0.291	0.291	strong		0.602	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906	
PLEC	5339	hgsc.bcm.edu	37	8	145001031	145001031	+	Missense_Mutation	SNP	T	T	C	rs55895668	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:145001031T>C	ENST00000322810.4	-	30	4545	c.4376A>G	c.(4375-4377)cAc>cGc	p.H1459R	PLEC_ENST00000398774.2_Missense_Mutation_p.H1290R|PLEC_ENST00000345136.3_Missense_Mutation_p.H1322R|PLEC_ENST00000354589.3_Missense_Mutation_p.H1322R|PLEC_ENST00000354958.2_Missense_Mutation_p.H1300R|PLEC_ENST00000436759.2_Missense_Mutation_p.H1349R|PLEC_ENST00000527096.1_Missense_Mutation_p.H1345R|PLEC_ENST00000356346.3_Missense_Mutation_p.H1308R|PLEC_ENST00000357649.2_Missense_Mutation_p.H1326R	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1459	Globular 1.		H -> R (in dbSNP:rs55895668).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.H1349R(1)|p.H1459R(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CTCGCTGTAGTGCGTACGCAG	0.622													C|||	2337	0.466653	0.8782	0.3674	5008	,	,		15191	0.1429		0.4344	False		,,,				2504	0.3476				p.H1459R		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,2	PLEC	1144	2	2	Substitution - Missense(2)	stomach(2)	c.A4376G						PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	3556,766		1479,598,84	106.0	116.0	112.0		3965,3977,3965,3869,4376,3899,3923,4046	3.9	0.9	8	dbSNP_129	112	3666,4872		820,2026,1423	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_201384.1,NM_201383.1,NM_201382.2,NM_201381.1,NM_201380.2,NM_201379.1,NM_201378.2,NM_000445.3	29,29,29,29,29,29,29,29	2299,2624,1507	CC,CT,TT		42.9375,17.7233,43.8414	benign,benign,benign,benign,benign,benign,benign,benign	1322/4548,1326/4552,1322/4548,1290/4516,1459/4685,1300/4526,1308/4534,1349/4575	145001031	7222,5638	2161	4269	6430	SO:0001583	missense	5339	exon30			CTGTAGTGCGTAC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.4376A>G	8.37:g.145001031T>C	ENSP00000323856:p.His1459Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	974|974	0.445970695970696|0.445970695970696	421|421	0.8556910569105691|0.8556910569105691	137|137	0.3784530386740331|0.3784530386740331	94|94	0.16433566433566432|0.16433566433566432	322|322	0.42480211081794195|0.42480211081794195	C|C	8.506|8.506	0.865407|0.865407	0.17250|0.17250	0.822767|0.822767	0.429375|0.429375	ENSG00000178209|ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096|ENST00000527303	T;T;T;T;T;T;T;T;T|.	0.26810|.	1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71|.	4.79|4.79	3.9|3.9	0.45041|0.45041	.|.	0.084010|.	0.44688|.	N|.	0.000425|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00170|0.00170	-1.935|-1.935	0.47819|0.47819	P|P	4.709999999999992E-4|4.709999999999992E-4	B;B;B;B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0|.	T|T	0.29882|0.29882	-0.9997|-0.9997	9|4	0.02654|.	T|.	1|.	.|.	7.4776|7.4776	0.27385|0.27385	0.0:0.697:0.0:0.303|0.0:0.697:0.0:0.303	rs55895668;rs61296353;rs62522551|rs55895668;rs61296353;rs62522551	1349;1308;1300;1459;1290;1322;1326;1322|.	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4|.	.;.;.;PLEC_HUMAN;.;.;.;.|.	R|A	1322;1326;1322;1290;1459;1300;1308;1349;1345|19	ENSP00000344848:H1322R;ENSP00000350277:H1326R;ENSP00000346602:H1322R;ENSP00000381756:H1290R;ENSP00000323856:H1459R;ENSP00000347044:H1300R;ENSP00000348702:H1308R;ENSP00000388180:H1349R;ENSP00000434583:H1345R|.	ENSP00000323856:H1459R|.	H|T	-|-	2|1	0|0	PLEC|PLEC	145073019|145073019	0.981000|0.981000	0.34729|0.34729	0.870000|0.870000	0.34147|0.34147	0.410000|0.410000	0.31052|0.31052	1.623000|1.623000	0.37008|0.37008	1.009000|1.009000	0.39289|0.39289	-0.380000|-0.380000	0.06706|0.06706	CAC|ACT	T|0.550;C|0.450	0.450	strong		0.622	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
HIST1H4C	8364	hgsc.bcm.edu	37	6	26104280	26104280	+	Silent	SNP	T	T	C	rs2229768	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:26104280T>C	ENST00000377803.2	+	1	177	c.105T>C	c.(103-105)atT>atC	p.I35I		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	35					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7						AACCGGCTATTCGCCGTTTGG	0.547													T|||	881	0.175919	0.2587	0.1398	5008	,	,		17436	0.1667		0.1998	False		,,,				2504	0.0746				p.I35I		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.T105C						PASS	.	T		1075,3331		122,831,1250	62.0	63.0	63.0		105	-3.0	0.6	6	dbSNP_98	63	1877,6723		201,1475,2624	no	coding-synonymous	HIST1H4C	NM_003542.3		323,2306,3874	CC,CT,TT		21.8256,24.3985,22.6972		35/104	26104280	2952,10054	2203	4300	6503	SO:0001819	synonymous_variant	8364	exon1			GGCTATTCGCCGT	X60486	CCDS4583.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000197061	ENSG00000197061		"""Histones / Replication-dependent"""	4787	protein-coding gene	gene with protein product		602827	"""H4 histone family, member G"", ""histone 1, H4c"""	H4FG		9119399, 12408966	Standard	NM_003542		Approved	H4/g, dJ221C16.1	uc003ngi.3	P62805	OTTHUMG00000014429	ENST00000377803.2:c.105T>C	6.37:g.26104280T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377803.2	37	CCDS4583.1																																																																																			T|0.790;C|0.210	0.210	strong		0.547	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542	
ARID3B	10620	hgsc.bcm.edu	37	15	74836319	74836319	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:74836319A>G	ENST00000346246.5	+	2	273	c.42A>G	c.(40-42)caA>caG	p.Q14Q		NM_006465.2	NP_006456.1	Q8IVW6	ARI3B_HUMAN	AT rich interactive domain 3B (BRIGHT-like)	14	Gln-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(2)	14						agcagcaacaacagaagcagc	0.562																																					p.Q14Q		Atlas-SNP	.											ARID3B,right_lower_lobe,carcinoma,0,1	ARID3B	35	1	0			c.A42G						scavenged	.						18.0	21.0	20.0					15																	74836319		2196	4294	6490	SO:0001819	synonymous_variant	10620	exon2			GCAACAACAGAAG		CCDS10264.1	15q24	2013-02-07	2006-11-08		ENSG00000179361	ENSG00000179361		"""-"""	14350	protein-coding gene	gene with protein product		612457	"""AT rich interactive domain 3B (BRIGHT- like)"""				Standard	NM_006465		Approved	BDP, DRIL2	uc002ayd.3	Q8IVW6	OTTHUMG00000141321	ENST00000346246.5:c.42A>G	15.37:g.74836319A>G		Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	167	8	0.0479042	NM_006465	O95443|Q59HC9|Q6P9C9	Silent	SNP	ENST00000346246.5	37	CCDS10264.1																																																																																			.	.	none		0.562	ARID3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280688.2	NM_006465	
DEGS2	123099	hgsc.bcm.edu	37	14	100615665	100615665	+	Silent	SNP	T	T	C	rs4905936	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100615665T>C	ENST00000305631.5	-	2	1040	c.465A>G	c.(463-465)acA>acG	p.T155T	DEGS2_ENST00000553834.1_Intron|DEGS2_ENST00000557117.1_5'UTR	NM_206918.2	NP_996801.2			delta(4)-desaturase, sphingolipid 2											breast(1)|lung(6)|skin(1)	8		Melanoma(154;0.212)				TGCGGGCGGGTGTGCAGAAGA	0.662													C|||	4493	0.897165	0.851	0.9207	5008	,	,		16285	0.996		0.8926	False		,,,				2504	0.8456				p.T155T		Atlas-SNP	.											.	DEGS2	25	.	0			c.A465G						PASS	.	C		3798,608	244.7+/-253.9	1641,516,46	30.0	31.0	31.0		465	-2.4	1.0	14	dbSNP_111	31	7531,1065	212.8+/-253.0	3314,903,81	no	coding-synonymous	DEGS2	NM_206918.2		4955,1419,127	CC,CT,TT		12.3895,13.7994,12.8673		155/324	100615665	11329,1673	2203	4298	6501	SO:0001819	synonymous_variant	123099	exon2			GGCGGGTGTGCAG		CCDS9956.1	14q32.2	2013-09-02	2011-12-09	2004-12-14	ENSG00000168350	ENSG00000168350		"""Fatty acid desaturases"""	20113	protein-coding gene	gene with protein product	"""sphingolipid delta(4)-desaturase 2"", ""dihydroceramide desaturase 2"""	610862	"""chromosome 14 open reading frame 66"", ""degenerative spermatocyte homolog 2, lipid desaturase (Drosophila)"""	C14orf66			Standard	NM_206918		Approved	DES2, FADS8	uc001ygx.2	Q6QHC5	OTTHUMG00000171537	ENST00000305631.5:c.465A>G	14.37:g.100615665T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_206918		Silent	SNP	ENST00000305631.5	37	CCDS9956.1																																																																																			T|0.116;C|0.884	0.884	strong		0.662	DEGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414003.1	NM_206918	
PHF12	57649	hgsc.bcm.edu	37	17	27277200	27277200	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:27277200T>A	ENST00000332830.4	-	2	941	c.131A>T	c.(130-132)gAg>gTg	p.E44V	PHF12_ENST00000577226.1_Missense_Mutation_p.E44V|PHF12_ENST00000268756.3_Missense_Mutation_p.E44V	NM_001033561.1	NP_001028733.1			PHD finger protein 12											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			GGGCTCCTTCTCAGGCTTCCG	0.622																																					p.E44V		Atlas-SNP	.											.	PHF12	69	.	0			c.A131T						PASS	.						69.0	66.0	67.0					17																	27277200		2203	4300	6503	SO:0001583	missense	57649	exon2			TCCTTCTCAGGCT	AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"""Zinc fingers, PHD-type"""	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.131A>T	17.37:g.27277200T>A	ENSP00000329933:p.Glu44Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_020889		Missense_Mutation	SNP	ENST00000332830.4	37	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.766609	0.31228	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.94576	-3.45;-3.46;-3.46	4.43	4.43	0.53597	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.187807	0.45867	D	0.000333	D	0.90383	0.6990	L	0.44542	1.39	0.58432	D	0.999998	B;B;B;B;B	0.31611	0.128;0.331;0.202;0.03;0.01	B;B;B;B;B	0.25884	0.026;0.064;0.058;0.012;0.012	D	0.89168	0.3535	10	0.40728	T	0.16	-1.4833	12.955	0.58421	0.0:0.0:0.0:1.0	.	26;44;44;44;44	B4DFE2;A8K5V5;Q96QT6-2;Q2TAK2;Q96QT6	.;.;.;.;PHF12_HUMAN	V	44	ENSP00000329933:E44V;ENSP00000368157:E44V;ENSP00000268756:E44V	ENSP00000268756:E44V	E	-	2	0	PHF12	24301326	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.609000	0.61148	1.978000	0.57642	0.533000	0.62120	GAG	.	.	none		0.622	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889	
FAM83F	113828	hgsc.bcm.edu	37	22	40417780	40417780	+	Silent	SNP	C	C	T	rs5995793	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:40417780C>T	ENST00000333407.6	+	4	1360	c.1266C>T	c.(1264-1266)aaC>aaT	p.N422N	FAM83F_ENST00000473717.1_Silent_p.N254N	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	422										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						CCAGCCGAAACGGCATGGGAG	0.667													T|||	1443	0.288139	0.3979	0.1628	5008	,	,		15282	0.0853		0.2873	False		,,,				2504	0.4387				p.N422N		Atlas-SNP	.											.	FAM83F	29	.	0			c.C1266T						PASS	.	T		1481,2919		256,969,975	21.0	20.0	21.0		1266	-6.0	0.1	22	dbSNP_114	21	2483,6113		342,1799,2157	no	coding-synonymous	FAM83F	NM_138435.2		598,2768,3132	TT,TC,CC		28.8855,33.6591,30.5017		422/501	40417780	3964,9032	2200	4298	6498	SO:0001819	synonymous_variant	113828	exon4			CCGAAACGGCATG		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.1266C>T	22.37:g.40417780C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	102	37	0.362745	NM_138435	Q96FD6	Silent	SNP	ENST00000333407.6	37	CCDS14000.2																																																																																			C|0.719;T|0.281	0.281	strong		0.667	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
PTGFRN	5738	hgsc.bcm.edu	37	1	117529458	117529458	+	Missense_Mutation	SNP	G	G	A	rs10801922	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:117529458G>A	ENST00000393203.2	+	9	2656	c.2509G>A	c.(2509-2511)Gtc>Atc	p.V837I		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	837			V -> I (in dbSNP:rs10801922).		lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		GCTGATCGGCGTCGGTCTGTC	0.617													G|||	2494	0.498003	0.3018	0.5951	5008	,	,		18613	0.6597		0.4364	False		,,,				2504	0.591				p.V837I		Atlas-SNP	.											PTGFRN,NS,carcinoma,-2,1	PTGFRN	91	1	0			c.G2509A						PASS	.	G	ILE/VAL	1378,3028	454.4+/-350.6	235,908,1060	111.0	96.0	101.0		2509	0.1	0.7	1	dbSNP_120	101	3825,4775	539.9+/-383.7	853,2119,1328	yes	missense	PTGFRN	NM_020440.2	29	1088,3027,2388	AA,AG,GG		44.4767,31.2755,40.0046	benign	837/880	117529458	5203,7803	2203	4300	6503	SO:0001583	missense	5738	exon9			ATCGGCGTCGGTC	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9601	protein-coding gene	gene with protein product		601204	"""prostaglandin F2 receptor negative regulator"""			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.2509G>A	1.37:g.117529458G>A	ENSP00000376899:p.Val837Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_020440	Q5VVU9|Q8N2K6	Missense_Mutation	SNP	ENST00000393203.2	37	CCDS890.1	1078	0.4935897435897436	159	0.3231707317073171	190	0.5248618784530387	382	0.6678321678321678	347	0.4577836411609499	G	8.889	0.953437	0.18431	0.312755	0.444767	ENSG00000134247	ENST00000393203;ENST00000544471	T	0.04360	3.64	6.17	0.122	0.14702	.	0.456264	0.23245	N	0.050303	T	0.00552	0.0018	N	0.02539	-0.55	0.58432	P	5.000000000032756E-6	B	0.12013	0.005	B	0.08055	0.003	T	0.44436	-0.9328	9	0.07175	T	0.84	-16.8037	11.6594	0.51337	0.3447:0.0:0.6553:0.0	rs10801922;rs17579898;rs52822596;rs61548861;rs10801922	837	Q9P2B2	FPRP_HUMAN	I	837;696	ENSP00000376899:V837I	ENSP00000376899:V837I	V	+	1	0	PTGFRN	117330981	0.796000	0.28864	0.726000	0.30738	0.976000	0.68499	0.593000	0.23999	0.115000	0.18071	-0.137000	0.14449	GTC	G|0.560;A|0.440	0.440	strong		0.617	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
MUC21	394263	hgsc.bcm.edu	37	6	30954489	30954489	+	Silent	SNP	A	A	T	rs143989844	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954489A>T	ENST00000376296.3	+	2	778	c.537A>T	c.(535-537)acA>acT	p.T179T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	179	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GGGCCAGCACAGCCACCAACT	0.612													a|||	398	0.0794728	0.0711	0.1225	5008	,	,		26872	0.0685		0.0865	False		,,,				2504	0.0644				p.T179T		Atlas-SNP	.											.	MUC21	98	.	0			c.A537T						PASS	.						156.0	148.0	151.0					6																	30954489		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			CAGCACAGCCACC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.537A>T	6.37:g.30954489A>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	143	16	0.111888	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			A|0.999;T|0.001	0.001	weak		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
CEP128	145508	hgsc.bcm.edu	37	14	81251255	81251255	+	Missense_Mutation	SNP	T	T	C	rs327463	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:81251255T>C	ENST00000555265.1	-	15	2570	c.2195A>G	c.(2194-2196)cAt>cGt	p.H732R	CEP128_ENST00000281129.3_Missense_Mutation_p.H732R			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	732			H -> R (in dbSNP:rs327463).			centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)		p.H732R(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						AGTCCTGATATGATTCTCAGC	0.373													T|||	1664	0.332268	0.2383	0.3602	5008	,	,		20879	0.1806		0.3827	False		,,,				2504	0.544				p.H732R		Atlas-SNP	.											CEP128,NS,carcinoma,0,1	CEP128	146	1	1	Substitution - Missense(1)	stomach(1)	c.A2195G						PASS	.	T	ARG/HIS	1182,3224	413.5+/-336.5	154,874,1175	108.0	102.0	104.0		2195	4.9	1.0	14	dbSNP_79	104	3475,5125	505.0+/-376.3	698,2079,1523	yes	missense	CEP128	NM_152446.3	29	852,2953,2698	CC,CT,TT		40.407,26.8271,35.8066	probably-damaging	732/1095	81251255	4657,8349	2203	4300	6503	SO:0001583	missense	145508	exon14			CTGATATGATTCT	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 61"", ""chromosome 14 open reading frame 145"""	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2195A>G	14.37:g.81251255T>C	ENSP00000451162:p.His732Arg	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	318	318	1	NM_152446	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	634	0.2902930402930403	112	0.22764227642276422	128	0.35359116022099446	106	0.1853146853146853	288	0.37994722955145116	T	11.43	1.637792	0.29157	0.268271	0.40407	ENSG00000100629	ENST00000281129;ENST00000555265;ENST00000393619	T;T	0.29917	1.55;1.55	6.06	4.88	0.63580	.	0.163302	0.42548	D	0.000692	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	1.0	D	0.67145	0.996	P	0.61533	0.89	T	0.47315	-0.9127	9	0.17832	T	0.49	.	12.7799	0.57471	0.1224:0.0:0.0:0.8776	rs327463;rs328219;rs57357691;rs327463	732	Q6ZU80	CE128_HUMAN	R	732	ENSP00000281129:H732R;ENSP00000451162:H732R	ENSP00000281129:H732R	H	-	2	0	CEP128	80321008	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.088000	0.41663	2.326000	0.78906	0.472000	0.43445	CAT	T|0.657;C|0.343	0.343	strong		0.373	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	
CCHCR1	54535	hgsc.bcm.edu	37	6	31122315	31122315	+	Missense_Mutation	SNP	G	G	C	rs130066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31122315G>C	ENST00000376266.5	-	4	614	c.492C>G	c.(490-492)agC>agG	p.S164R	CCHCR1_ENST00000396263.2_Missense_Mutation_p.S164R|CCHCR1_ENST00000396268.3_Missense_Mutation_p.S253R|CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000451521.2_Missense_Mutation_p.S217R	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	164			S -> R (in dbSNP:rs130066). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:10888604, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						GCTCCCGCTGGCTCCCCTCTT	0.607													G|||	1974	0.394169	0.3449	0.4697	5008	,	,		17834	0.3839		0.4115	False		,,,				2504	0.3998				p.S253R		Atlas-SNP	.											CCHCR1_ENST00000396268,colon,carcinoma,0,2	CCHCR1	68	2	0			c.C759G						PASS	.	G	ARG/SER,ARG/SER,ARG/SER	1140,1880		206,728,576	283.0	356.0	330.0		651,759,492	3.5	1.0	6	dbSNP_78	330	2323,3095		502,1319,888	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	110,110,110	708,2047,1464	CC,CG,GG		42.8756,37.7483,41.0405	benign,benign,benign	217/836,253/872,164/783	31122315	3463,4975	1510	2709	4219	SO:0001583	missense	54535	exon4			CCGCTGGCTCCCC	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.492C>G	6.37:g.31122315G>C	ENSP00000365442:p.Ser164Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	149	66	0.442953	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	858	0.39285714285714285	180	0.36585365853658536	165	0.4558011049723757	193	0.3374125874125874	320	0.42216358839050133	G	9.768	1.171833	0.21704	0.377483	0.428756	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521;ENST00000448141;ENST00000508683;ENST00000448162;ENST00000513222	T;T;T;T;T;T;T;T	0.03553	3.89;3.89;3.89;3.89;3.89;3.89;3.89;3.89	5.33	3.49	0.39957	.	0.644615	0.15641	N	0.251901	T	0.01189	0.0039	L	0.46157	1.445	0.47862	P	4.690000000000527E-4	B;B;B;B;B	0.13594	0.0;0.0;0.0;0.008;0.004	B;B;B;B;B	0.14023	0.004;0.002;0.003;0.01;0.006	T	0.45011	-0.9290	9	0.15499	T	0.54	-4.4865	7.2484	0.26135	0.0924:0.171:0.7367:0.0	rs130066;rs3173363;rs17400873;rs57866586;rs130066	164;164;164;217;253	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	R	253;164;164;164;217;128;128;164;138	ENSP00000379566:S253R;ENSP00000365442:S164R;ENSP00000379561:S164R;ENSP00000401039:S217R;ENSP00000414323:S128R;ENSP00000421393:S128R;ENSP00000390027:S164R;ENSP00000425682:S138R	ENSP00000365442:S164R	S	-	3	2	CCHCR1	31230294	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	2.837000	0.48191	0.596000	0.29794	0.638000	0.83543	AGC	G|0.595;C|0.405	0.405	strong		0.607	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
ZC3H3	23144	hgsc.bcm.edu	37	8	144522388	144522388	+	Missense_Mutation	SNP	A	A	T	rs2272753	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144522388A>T	ENST00000262577.5	-	11	2669	c.2638T>A	c.(2638-2640)Tca>Aca	p.S880T		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	880	Poly-Ser.				mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			ggaggggatgaggaggaggag	0.652													A|||	560	0.111821	0.0363	0.1167	5008	,	,		16934	0.2431		0.1461	False		,,,				2504	0.0399				p.S880T		Atlas-SNP	.											.	ZC3H3	75	.	0			c.T2638A						PASS	.	A	THR/SER	208,4198		8,192,2003	29.0	28.0	29.0		2638	-8.5	0.0	8	dbSNP_100	29	945,7653		118,709,3472	no	missense	ZC3H3	NM_015117.2	58	126,901,5475	TT,TA,AA		10.9909,4.7208,8.8665	possibly-damaging	880/949	144522388	1153,11851	2203	4299	6502	SO:0001583	missense	23144	exon11			GGGATGAGGAGGA	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"""Zinc fingers, CCCH-type domain containing"""	28972	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 3"""	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.2638T>A	8.37:g.144522388A>T	ENSP00000262577:p.Ser880Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	273	0.125	24	0.04878048780487805	42	0.11602209944751381	124	0.21678321678321677	83	0.10949868073878628	A	10.21	1.288569	0.23478	0.047208	0.109909	ENSG00000014164	ENST00000262577	T	0.44083	0.93	4.25	-8.5	0.00927	.	2.759650	0.01499	N	0.017425	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.23650	0.089	B	0.18263	0.021	T	0.07927	-1.0747	9	0.11794	T	0.64	2.0487	4.56	0.12156	0.1813:0.3576:0.3664:0.0948	rs2272753	880	Q8IXZ2	ZC3H3_HUMAN	T	880	ENSP00000262577:S880T	ENSP00000262577:S880T	S	-	1	0	ZC3H3	144593531	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-4.369000	0.00245	-2.892000	0.00315	-0.605000	0.04089	TCA	A|0.879;T|0.121	0.121	strong		0.652	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
MRPL53	116540	hgsc.bcm.edu	37	2	74699778	74699778	+	Missense_Mutation	SNP	C	C	A	rs1047911	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:74699778C>A	ENST00000258105.7	-	1	671	c.10G>T	c.(10-12)Gcc>Tcc	p.A4S	MRPL53_ENST00000409710.1_Missense_Mutation_p.A4S	NM_053050.4	NP_444278.1	Q96EL3	RM53_HUMAN	mitochondrial ribosomal protein L53	4			A -> S (in dbSNP:rs1047911).			mitochondrion (GO:0005739)|ribosome (GO:0005840)				central_nervous_system(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5						CGAGCCAAGGCAGCTGCCATG	0.602													C|||	2588	0.516773	0.8064	0.3098	5008	,	,		20314	0.8214		0.1581	False		,,,				2504	0.3272				p.A4S		Atlas-SNP	.											.	MRPL53	13	.	0			c.G10T						PASS	.	C	SER/ALA	3112,1294	679.3+/-403.7	1106,900,197	55.0	52.0	53.0		10	2.3	0.2	2	dbSNP_86	53	1187,7411	228.6+/-263.6	88,1011,3200	yes	missense	MRPL53	NM_053050.4	99	1194,1911,3397	AA,AC,CC		13.8055,29.369,33.0591	benign	4/113	74699778	4299,8705	2203	4299	6502	SO:0001583	missense	116540	exon1			CCAAGGCAGCTGC	BC012163	CCDS1944.1	2p13.1	2012-09-13			ENSG00000204822	ENSG00000204822		"""Mitochondrial ribosomal proteins / large subunits"""	16684	protein-coding gene	gene with protein product		611857				11551941	Standard	NM_053050		Approved		uc002sln.3	Q96EL3	OTTHUMG00000129961	ENST00000258105.7:c.10G>T	2.37:g.74699778C>A	ENSP00000258105:p.Ala4Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	205	134	0.653659	NM_053050		Missense_Mutation	SNP	ENST00000258105.7	37	CCDS1944.1	1092	0.5	396	0.8048780487804879	99	0.27348066298342544	474	0.8286713286713286	123	0.16226912928759896	C	5.013	0.188132	0.09547	0.70631	0.138055	ENSG00000204822	ENST00000258105;ENST00000409710	T;T	0.57595	0.76;0.39	5.09	2.26	0.28386	.	0.532852	0.21296	N	0.076882	T	0.00012	0.0000	N	0.14661	0.345	0.52099	P	5.900000000003125E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.38866	-0.9641	9	0.07482	T	0.82	-14.3176	3.6041	0.08035	0.1827:0.5686:0.1584:0.0903	rs1047911;rs3210341;rs11554618;rs56805532;rs1047911	4	Q96EL3	RM53_HUMAN	S	4	ENSP00000258105:A4S;ENSP00000386920:A4S	ENSP00000258105:A4S	A	-	1	0	MRPL53	74553286	0.793000	0.28825	0.169000	0.22859	0.002000	0.02628	0.255000	0.18333	0.280000	0.22209	-0.137000	0.14449	GCC	C|0.587;A|0.413	0.413	strong		0.602	MRPL53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252225.2	NM_053050	
HLA-C	3107	hgsc.bcm.edu	37	6	31239407	31239407	+	Missense_Mutation	SNP	G	G	T	rs17408553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239407G>T	ENST00000376228.5	-	2	326	c.312C>A	c.(310-312)aaC>aaA	p.N104K	HLA-C_ENST00000383329.3_Missense_Mutation_p.N104K	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	104	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						AGCCGCGCAGGTTCCGCAGGC	0.716													g|||	1938	0.386981	0.5408	0.3862	5008	,	,		10850	0.1399		0.4115	False		,,,				2504	0.409				p.N104K		Atlas-SNP	.											.	HLA-C	92	.	0			c.C312A						PASS	.	G	LYS/ASN	1618,1404		435,748,328	40.0	41.0	41.0		312	-0.2	0.0	6	dbSNP_123	41	2036,3382		372,1292,1045	no	missense	HLA-C	NM_002117.5	94	807,2040,1373	TT,TG,GG		37.5784,46.4593,43.2938	benign	104/367	31239407	3654,4786	1511	2709	4220	SO:0001583	missense	3107	exon2			GCGCAGGTTCCGC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.312C>A	6.37:g.31239407G>T	ENSP00000365402:p.Asn104Lys	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	186	96	0.516129	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	792|792	0.3626373626373626|0.3626373626373626	263|263	0.5345528455284553|0.5345528455284553	141|141	0.38950276243093923|0.38950276243093923	80|80	0.13986013986013987|0.13986013986013987	308|308	0.40633245382585753|0.40633245382585753	N|N	7.072|7.072	0.568503|0.568503	0.13560|0.13560	0.535407|0.535407	0.375784|0.375784	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00686|.	5.85;5.85|.	2.81|2.81	-0.203|-0.203	0.13204|0.13204	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	1.795410|.	0.05622|.	U|.	0.580150|.	T|T	0.33381|0.33381	0.0861|0.0861	M|M	0.76838|0.76838	2.35|2.35	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.21688|.	0.059;0.017;0.017;0.008|.	B;B;B;B|.	0.33890|.	0.172;0.066;0.097;0.045|.	T|T	0.23833|0.23833	-1.0177|-1.0177	9|4	0.37606|.	T|.	0.19|.	.|.	3.4973|3.4973	0.07659|0.07659	0.2649:0.2124:0.5227:0.0|0.2649:0.2124:0.5227:0.0	rs17408553;rs28393247;rs52821555|rs17408553;rs28393247;rs52821555	104;104;104;104|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	K|T	104;104;104;141|104	ENSP00000365402:N104K;ENSP00000372819:N104K|.	ENSP00000365402:N104K|.	N|P	-|-	3|1	2|0	HLA-C|HLA-C	31347386|31347386	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.046000|-0.046000	0.11983|0.11983	-0.060000|-0.060000	0.13132|0.13132	0.305000|0.305000	0.20034|0.20034	AAC|CCT	T|0.398;G|0.602	0.398	strong		0.716	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
ABCC1	4363	hgsc.bcm.edu	37	16	16139714	16139714	+	Silent	SNP	T	T	C	rs35587	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:16139714T>C	ENST00000399410.3	+	9	1237	c.1062T>C	c.(1060-1062)aaT>aaC	p.N354N	ABCC1_ENST00000349029.5_Silent_p.N354N|ABCC1_ENST00000346370.5_Silent_p.N354N|ABCC1_ENST00000351154.5_Silent_p.N354N|ABCC1_ENST00000399408.2_Silent_p.N354N|ABCC1_ENST00000345148.5_Silent_p.N354N	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	354	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	AGTTCGTGAATGACACGAAGG	0.562											OREG0023639	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	2118	0.422923	0.711	0.3573	5008	,	,		21507	0.4415		0.3131	False		,,,				2504	0.1738				p.N354N		Atlas-SNP	.											.	ABCC1	156	.	0			c.T1062C						PASS	.	C	,,,,	2564,1580		821,922,329	47.0	51.0	50.0		1062,1062,1062,1062,1062	-6.0	0.2	16	dbSNP_76	50	2447,5985		348,1751,2117	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	1169,2673,2446	CC,CT,TT		29.0204,38.1274,39.8457	,,,,	354/1532,354/1473,354/1476,354/1417,354/1467	16139714	5011,7565	2072	4216	6288	SO:0001819	synonymous_variant	4363	exon9			CGTGAATGACACG	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.1062T>C	16.37:g.16139714T>C		Somatic	87	0	0	708	WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			T|0.576;C|0.424	0.424	strong		0.562	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
CD2	914	hgsc.bcm.edu	37	1	117311147	117311147	+	Missense_Mutation	SNP	C	C	A	rs699738	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:117311147C>A	ENST00000369478.3	+	5	906	c.798C>A	c.(796-798)caC>caA	p.H266Q		NM_001767.3	NP_001758.2	P06729	CD2_HUMAN	CD2 molecule	266			H -> Q (in dbSNP:rs699738). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2437578, ECO:0000269|PubMed:2901953}.		apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|heterotypic cell-cell adhesion (GO:0034113)|leukocyte migration (GO:0050900)|membrane raft polarization (GO:0001766)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of myeloid dendritic cell activation (GO:0030887)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of T cell differentiation (GO:0045580)|single organismal cell-cell adhesion (GO:0016337)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)	p.H266Q(1)		NS(1)|breast(2)|large_intestine(3)|liver(1)|lung(8)|skin(2)|stomach(1)	18	Lung SC(450;0.225)	all_cancers(81;3.15e-06)|Acute lymphoblastic leukemia(138;1.7e-08)|all_epithelial(167;8.38e-07)|all_lung(203;3.37e-06)|Lung NSC(69;2.31e-05)		Epithelial(280;6.71e-26)|OV - Ovarian serous cystadenocarcinoma(397;4.74e-24)|all cancers(265;1.93e-22)|Lung(183;0.0543)|Kidney(133;0.0813)|Colorectal(144;0.174)|KIRC - Kidney renal clear cell carcinoma(1967;0.176)|LUSC - Lung squamous cell carcinoma(189;0.189)|BRCA - Breast invasive adenocarcinoma(282;0.201)	Alefacept(DB00092)	GGAAGCCCCACCAAATTCCAG	0.547													C|||	1475	0.294529	0.6293	0.245	5008	,	,		16465	0.2877		0.1004	False		,,,				2504	0.0838				p.H266Q	NSCLC(14;263 555 26380 43512 51332)	Atlas-SNP	.											CD2,NS,carcinoma,0,1	CD2	43	1	1	Substitution - Missense(1)	stomach(1)	c.C798A						PASS	.	C	GLN/HIS	2258,2148	595.4+/-388.4	605,1048,550	76.0	67.0	70.0		798	-3.0	0.0	1	dbSNP_86	70	728,7872	176.9+/-226.6	42,644,3614	yes	missense	CD2	NM_001767.3	24	647,1692,4164	AA,AC,CC		8.4651,48.7517,22.9586	benign	266/352	117311147	2986,10020	2203	4300	6503	SO:0001583	missense	914	exon5			GCCCCACCAAATT	BC033583	CCDS889.1	1p13	2013-01-11	2006-03-28		ENSG00000116824	ENSG00000116824		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1639	protein-coding gene	gene with protein product		186990	"""CD2 antigen (p50), sheep red blood cell receptor"""	SRBC		2437578	Standard	NM_001767		Approved		uc001egu.4	P06729	OTTHUMG00000022750	ENST00000369478.3:c.798C>A	1.37:g.117311147C>A	ENSP00000358490:p.His266Gln	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	159	77	0.484277	NM_001767	Q96TE5	Missense_Mutation	SNP	ENST00000369478.3	37	CCDS889.1	586	0.2683150183150183	280	0.5691056910569106	79	0.21823204419889503	159	0.27797202797202797	68	0.08970976253298153	C	6.631	0.484852	0.12641	0.512483	0.084651	ENSG00000116824	ENST00000369478	T	0.43294	0.95	5.14	-2.99	0.05497	.	1.870040	0.02393	N	0.079913	T	0.08044	0.0201	L	0.38838	1.175	0.58432	P	1.999999999946489E-6	B	0.23442	0.085	B	0.14023	0.01	T	0.05818	-1.0862	9	0.10377	T	0.69	0.4668	0.3605	0.00363	0.2725:0.2438:0.1336:0.3501	rs699738;rs2228148;rs3192062;rs17846047;rs17859038;rs61507076;rs699738	266	P06729	CD2_HUMAN	Q	266	ENSP00000358490:H266Q	ENSP00000358490:H266Q	H	+	3	2	CD2	117112670	0.000000	0.05858	0.000000	0.03702	0.127000	0.20565	-0.485000	0.06520	-0.389000	0.07786	0.655000	0.94253	CAC	C|0.731;A|0.269	0.269	strong		0.547	CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059039.2	NM_001767	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798237	55798237	+	Silent	SNP	C	C	T	rs17528782	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55798237C>T	ENST00000313555.1	+	1	343	c.343C>T	c.(343-345)Ctg>Ttg	p.L115L		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	115						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					GTGCCTTATCCTGGCAGCAAT	0.478													C|||	192	0.0383387	0.0129	0.0403	5008	,	,		20050	0.001		0.0934	False		,,,				2504	0.0532				p.L115L		Atlas-SNP	.											OR5AS1,NS,carcinoma,-1,1	OR5AS1	121	1	0			c.C343T						PASS	.	C		111,4291	84.8+/-123.5	3,105,2093	116.0	97.0	103.0		343	1.5	0.9	11	dbSNP_123	103	692,7900	171.0+/-222.0	34,624,3638	no	coding-synonymous	OR5AS1	NM_001001921.1		37,729,5731	TT,TC,CC		8.054,2.5216,6.1798		115/325	55798237	803,12191	2201	4296	6497	SO:0001819	synonymous_variant	219447	exon1			CTTATCCTGGCAG	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.343C>T	11.37:g.55798237C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	250	116	0.464	NM_001001921	Q6IFB8	Silent	SNP	ENST00000313555.1	37	CCDS31516.1																																																																																			C|0.948;T|0.052	0.052	strong		0.478	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
BRCA2	675	hgsc.bcm.edu	37	13	32910721	32910721	+	Silent	SNP	T	T	C	rs1801499	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:32910721T>C	ENST00000380152.3	+	11	2462	c.2229T>C	c.(2227-2229)caT>caC	p.H743H	BRCA2_ENST00000544455.1_Silent_p.H743H			P51587	BRCA2_HUMAN	breast cancer 2, early onset	743	Interaction with NPM1.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		CAGTACAACATTCAAAAGTGG	0.383			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			T|||	368	0.0734824	0.0325	0.0922	5008	,	,		18927	0.0952		0.0348	False		,,,				2504	0.1329				p.H743H	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.T2229C						PASS	.	T		89,4317	73.6+/-111.7	0,89,2114	67.0	69.0	68.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2229	2.8	0.0	13	dbSNP_89	68	318,8282	113.5+/-173.5	8,302,3990	no	coding-synonymous	BRCA2	NM_000059.3		8,391,6104	CC,CT,TT		3.6977,2.02,3.1293		743/3419	32910721	407,12599	2203	4300	6503	SO:0001819	synonymous_variant	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	ACAACATTCAAAA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.2229T>C	13.37:g.32910721T>C		Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	116	98	0.844828	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																			T|0.956;C|0.044	0.044	strong		0.383	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
PI4KA	5297	hgsc.bcm.edu	37	22	21065645	21065645	+	Silent	SNP	A	A	G	rs444310		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:21065645A>G	ENST00000572273.1	-	51	5963	c.5733T>C	c.(5731-5733)ggT>ggC	p.G1911G	PI4KA_ENST00000255882.6_Silent_p.G1969G|PI4KA_ENST00000414196.3_Silent_p.G721G			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1911	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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)	p.G1911G(1)		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)			GGATGATATGACCCTTCTTGT	0.587																																					p.G1969G	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,0,1	PI4KA	313	1	1	Substitution - coding silent(1)	stomach(1)	c.T5907C						scavenged	.	G	,	1543,2565		564,415,1075	105.0	128.0	120.0		2163,5733	1.5	1.0	22	dbSNP_80	120	936,7236		280,376,3430	no	coding-synonymous,coding-synonymous	PI4KA	NM_002650.2,NM_058004.3	,	844,791,4505	GG,GA,AA		11.4537,37.5609,20.1873	,	721/855,1911/2045	21065645	2479,9801	2054	4086	6140	SO:0001819	synonymous_variant	5297	exon51			GATATGACCCTTC	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.5733T>C	22.37:g.21065645A>G		Somatic	546	2	0.003663		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				A|1.000;|0.000	.	weak		0.587	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
MAN2B1	4125	hgsc.bcm.edu	37	19	12772165	12772165	+	Missense_Mutation	SNP	G	G	A	rs1054487	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12772165G>A	ENST00000456935.2	-	7	975	c.935C>T	c.(934-936)aCt>aTt	p.T312I	MAN2B1_ENST00000221363.4_Missense_Mutation_p.T312I|MAN2B1_ENST00000495617.1_5'Flank	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	312			T -> I (in dbSNP:rs1054487). {ECO:0000269|PubMed:22161967, ECO:0000269|PubMed:9915946}.		cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGTCATCACAGTGTGGTTGGT	0.527													A|||	1642	0.327875	0.584	0.281	5008	,	,		20649	0.0615		0.4036	False		,,,				2504	0.2117				p.T312I		Atlas-SNP	.											MAN2B1,NS,adenoma,0,1	MAN2B1	91	1	0			c.C935T						PASS	.	A	ILE/THR,ILE/THR	2366,2040	561.6+/-380.8	647,1072,484	210.0	173.0	186.0		935,935	-2.2	0.0	19	dbSNP_86	186	3533,5067	632.4+/-398.6	703,2127,1470	yes	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	89,89	1350,3199,1954	AA,AG,GG		41.0814,46.3005,45.356	benign,benign	312/1012,312/1011	12772165	5899,7107	2203	4300	6503	SO:0001583	missense	4125	exon7			ATCACAGTGTGGT		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.935C>T	19.37:g.12772165G>A	ENSP00000395473:p.Thr312Ile	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	200	97	0.485	NM_001173498	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	705	0.3228021978021978	264	0.5365853658536586	114	0.3149171270718232	30	0.05244755244755245	297	0.391820580474934	A	0.054	-1.240886	0.01493	0.536995	0.410814	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	T;T	0.75704	-0.96;-0.96	5.51	-2.19	0.07015	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.587060	0.15426	N	0.262975	T	0.00012	0.0000	N	0.00162	-1.95	0.43852	P	0.0035570000000000324	B;B	0.10296	0.001;0.003	B;B	0.18871	0.008;0.023	T	0.39292	-0.9621	9	0.02654	T	1	-4.9597	11.2538	0.49041	0.6457:0.0:0.3543:0.0	rs1054487;rs2070086;rs3195022;rs17421591;rs52803796;rs60126972;rs1054487	312;312	G5E928;O00754	.;MA2B1_HUMAN	I	312;251;312	ENSP00000395473:T312I;ENSP00000221363:T312I	ENSP00000221363:T312I	T	-	2	0	MAN2B1	12633165	0.971000	0.33674	0.015000	0.15790	0.286000	0.27126	1.938000	0.40203	-0.506000	0.06558	-1.214000	0.01621	ACT	T|0.000;G|0.602;A|0.398	0.398	strong		0.527	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
ICOSLG	23308	hgsc.bcm.edu	37	21	45656774	45656774	+	Missense_Mutation	SNP	C	C	T	rs11558819	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:45656774C>T	ENST00000407780.3	-	3	509	c.382G>A	c.(382-384)Gtt>Att	p.V128I	ICOSLG_ENST00000344330.4_Missense_Mutation_p.V128I|ICOSLG_ENST00000400379.3_Missense_Mutation_p.V128I|ICOSLG_ENST00000400377.3_Intron	NM_001283052.1	NP_001269981.1	O75144	ICOSL_HUMAN	inducible T-cell co-stimulator ligand	128	Ig-like V-type.		V -> I (in dbSNP:rs11558819).		B cell activation (GO:0042113)|defense response (GO:0006952)|hyperosmotic response (GO:0006972)|positive regulation of activated T cell proliferation (GO:0042104)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.V128I(1)		endometrium(2)|lung(1)|stomach(1)|urinary_tract(1)	5				Colorectal(79;0.0163)|READ - Rectum adenocarcinoma(84;0.0772)		GTAACCTCAACGCTCAAAACC	0.572													c|||	1348	0.269169	0.3427	0.3271	5008	,	,		18992	0.1438		0.2873	False		,,,				2504	0.2393				p.V128I		Atlas-SNP	.											ICOSLG,NS,carcinoma,0,1	ICOSLG	20	1	1	Substitution - Missense(1)	stomach(1)	c.G382A						PASS	.	T	ILE/VAL	1318,2860		210,898,981	101.0	113.0	109.0		382	1.0	0.0	21	dbSNP_120	109	2320,6132		329,1662,2235	yes	missense	ICOSLG	NM_015259.4	29	539,2560,3216	TT,TC,CC		27.4491,31.5462,28.8044	possibly-damaging	128/303	45656774	3638,8992	2089	4226	6315	SO:0001583	missense	23308	exon3			CCTCAACGCTCAA	AB014553	CCDS42952.1, CCDS63377.1, CCDS63379.1	21q22.3	2014-01-30		2005-01-12	ENSG00000160223	ENSG00000160223		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Endogenous ligands"""	17087	protein-coding gene	gene with protein product	"""B7-related protein 1"", ""B7 homologue 2"", ""B7 homolog 2"""	605717		ICOSL		9734811, 11007762	Standard	NM_001283050		Approved	KIAA0653, GL50, B7-H2, B7RP-1, B7H2, B7RP1, ICOS-L, CD275	uc002zee.3	O75144	OTTHUMG00000086920	ENST00000407780.3:c.382G>A	21.37:g.45656774C>T	ENSP00000384432:p.Val128Ile	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_015259	A8MUZ1|Q9HD18|Q9NRQ1	Missense_Mutation	SNP	ENST00000407780.3	37	CCDS42952.1	547	0.25045787545787546	150	0.3048780487804878	105	0.2900552486187845	77	0.1346153846153846	215	0.2836411609498681	c	8.707	0.911038	0.17833	0.315462	0.274491	ENSG00000160223	ENST00000344330;ENST00000407780;ENST00000400379	T;T;T	0.27557	1.66;1.66;1.66	5.01	1.05	0.20165	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.262160	0.05654	N	0.585727	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	P;P	0.39903	0.694;0.694	B;B	0.37550	0.253;0.253	T	0.32079	-0.9920	9	0.24483	T	0.36	.	4.0371	0.09735	0.0:0.5387:0.1755:0.2858	rs11558819;rs11575872	128;128	A0N0L8;O75144	.;ICOSL_HUMAN	I	128	ENSP00000339477:V128I;ENSP00000384432:V128I;ENSP00000383230:V128I	ENSP00000339477:V128I	V	-	1	0	ICOSLG	44481202	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.355000	0.07671	0.332000	0.23536	-0.766000	0.03442	GTT	C|0.738;T|0.262	0.262	strong		0.572	ICOSLG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195838.1	NM_015259	
PLXNA2	5362	hgsc.bcm.edu	37	1	208391254	208391254	+	Missense_Mutation	SNP	C	C	T	rs2782948	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:208391254C>T	ENST00000367033.3	-	2	771	c.14G>A	c.(13-15)cGg>cAg	p.R5Q		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	5			R -> Q (in dbSNP:rs2782948). {ECO:0000269|PubMed:12975309}.		axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.R5Q(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GGGCCAGGGCCGCCTCTGTTC	0.667													C|||	1826	0.364617	0.3601	0.3314	5008	,	,		14354	0.4018		0.3022	False		,,,				2504	0.4202				p.R5Q		Atlas-SNP	.											PLXNA2,NS,carcinoma,0,1	PLXNA2	178	1	1	Substitution - Missense(1)	prostate(1)	c.G14A						PASS	.	C	GLN/ARG	1475,2785		301,873,956	14.0	18.0	17.0		14	5.5	1.0	1	dbSNP_100	17	2702,5660		522,1658,2001	yes	missense	PLXNA2	NM_025179.3	43	823,2531,2957	TT,TC,CC		32.3128,34.6244,33.093	probably-damaging	5/1895	208391254	4177,8445	2130	4181	6311	SO:0001583	missense	5362	exon2			CAGGGCCGCCTCT	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.14G>A	1.37:g.208391254C>T	ENSP00000356000:p.Arg5Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	787	0.36034798534798534	172	0.34959349593495936	127	0.35082872928176795	261	0.4562937062937063	227	0.2994722955145119	C	12.54	1.969753	0.34754	0.346244	0.323128	ENSG00000076356	ENST00000367033	T	0.00902	5.56	5.5	5.5	0.81552	.	1.704600	0.03240	N	0.180311	T	0.00012	0.0000	N	0.19112	0.55	0.36191	P	0.14992899999999998	P;B	0.46706	0.883;0.029	B;B	0.34038	0.174;0.011	T	0.48570	-0.9024	9	0.66056	D	0.02	.	13.6821	0.62491	0.0:0.9266:0.0:0.0734	rs2782948;rs3748736;rs2782948	59;5	O75051-2;O75051	.;PLXA2_HUMAN	Q	5	ENSP00000356000:R5Q	ENSP00000356000:R5Q	R	-	2	0	PLXNA2	206457877	0.994000	0.37717	0.985000	0.45067	0.023000	0.10783	0.519000	0.22862	2.588000	0.87417	0.650000	0.86243	CGG	C|0.660;T|0.340	0.340	strong		0.667	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
CORO2B	10391	hgsc.bcm.edu	37	15	69011119	69011119	+	Silent	SNP	C	C	T	rs33913544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:69011119C>T	ENST00000566799.1	+	9	1079	c.1050C>T	c.(1048-1050)atC>atT	p.I350I	CORO2B_ENST00000540068.1_Silent_p.I345I|CORO2B_ENST00000543950.1_Silent_p.I345I|CORO2B_ENST00000261861.5_Silent_p.I345I			Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B	350					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			kidney(3)|large_intestine(13)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						AGGGCCTGATCGAGCCCATCT	0.622													c|||	630	0.125799	0.0817	0.1787	5008	,	,		16956	0.0496		0.2485	False		,,,				2504	0.1002				p.I350I		Atlas-SNP	.											.	CORO2B	68	.	0			c.C1050T						PASS	.	T	,,	395,4005	196.0+/-220.5	20,355,1825	79.0	59.0	66.0		1035,1035,1050	-11.0	0.1	15	dbSNP_126	66	2056,6540	356.9+/-330.5	258,1540,2500	no	coding-synonymous,coding-synonymous,coding-synonymous	CORO2B	NM_001190456.1,NM_001190457.1,NM_006091.4	,,	278,1895,4325	TT,TC,CC		23.9181,8.9773,18.8596	,,	345/476,345/476,350/481	69011119	2451,10545	2200	4298	6498	SO:0001819	synonymous_variant	10391	exon9			CCTGATCGAGCCC	AB010098	CCDS53952.1, CCDS10229.2	15q22.31	2013-01-10	2001-11-28		ENSG00000103647	ENSG00000103647		"""Coronins"", ""WD repeat domain containing"""	2256	protein-coding gene	gene with protein product	"""clipin C"", ""coronin, actin-binding, 2B"""	605002	"""coronin, actin-binding protein, 2B"""			10224093, 10231032	Standard	NM_001190456		Approved	ClipinC, KIAA0925	uc021spj.1	Q9UQ03	OTTHUMG00000133288	ENST00000566799.1:c.1050C>T	15.37:g.69011119C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_006091	A8K0W3|O94767|Q8TAN1	Silent	SNP	ENST00000566799.1	37	CCDS10229.2																																																																																			C|0.820;T|0.180	0.180	strong		0.622	CORO2B-203	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006091	
SMCR8	140775	hgsc.bcm.edu	37	17	18220674	18220674	+	Missense_Mutation	SNP	C	C	T	rs8080966	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18220674C>T	ENST00000406438.3	+	1	2051	c.1571C>T	c.(1570-1572)cCc>cTc	p.P524L	TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank|TOP3A_ENST00000582230.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	524			P -> L (in dbSNP:rs8080966). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						AGTACCTGCCCCTCTGAGGCC	0.537													C|||	894	0.178514	0.1604	0.2421	5008	,	,		20664	0.0605		0.3062	False		,,,				2504	0.1483				p.P524L		Atlas-SNP	.											.	SMCR8	62	.	0			c.C1571T						PASS	.	C	LEU/PRO	916,3490	349.3+/-310.3	87,742,1374	90.0	89.0	90.0		1571	5.9	1.0	17	dbSNP_116	90	2594,6006	418.1+/-352.7	382,1830,2088	yes	missense	SMCR8	NM_144775.2	98	469,2572,3462	TT,TC,CC		30.1628,20.7898,26.9875	probably-damaging	524/938	18220674	3510,9496	2203	4300	6503	SO:0001583	missense	140775	exon1			CCTGCCCCTCTGA	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.1571C>T	17.37:g.18220674C>T	ENSP00000385025:p.Pro524Leu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	37	CCDS11195.2	440	0.20146520146520147	79	0.16056910569105692	91	0.2513812154696133	33	0.057692307692307696	237	0.31266490765171506	C	9.135	1.012468	0.19277	0.207898	0.301628	ENSG00000176994	ENST00000406438	T	0.71934	-0.61	5.91	5.91	0.95273	.	0.151452	0.46442	D	0.000294	T	0.00012	0.0000	L	0.32530	0.975	0.09310	P	0.99999898358	D	0.89917	1.0	D	0.85130	0.997	T	0.06935	-1.0799	9	0.14656	T	0.56	-56.313	20.2983	0.98569	0.0:1.0:0.0:0.0	rs8080966;rs52799159;rs59228353;rs8080966	524	Q8TEV9	SMCR8_HUMAN	L	524	ENSP00000385025:P524L	ENSP00000385025:P524L	P	+	2	0	SMCR8	18161399	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.311000	0.65786	2.802000	0.96397	0.655000	0.94253	CCC	C|0.770;T|0.230	0.230	strong		0.537	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
FBXW10	10517	hgsc.bcm.edu	37	17	18681913	18681913	+	Missense_Mutation	SNP	G	G	A	rs77288131	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18681913G>A	ENST00000395665.4	+	14	2682	c.2461G>A	c.(2461-2463)Gcc>Acc	p.A821T	FBXW10_ENST00000308799.4_Missense_Mutation_p.A830T|FBXW10_ENST00000301938.4_Missense_Mutation_p.A768T|TVP23B_ENST00000574226.1_5'Flank|TVP23B_ENST00000307767.8_5'Flank|FBXW10_ENST00000395667.1_Missense_Mutation_p.A820T|TVP23B_ENST00000476139.1_5'Flank			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	821			A -> T (in dbSNP:rs1026259). {ECO:0000269|PubMed:11230166}.							NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GACTGTTAGCGCCCTGCAGCA	0.478													N|||	437	0.0872604	0.1263	0.0648	5008	,	,		16718	0.0635		0.0805	False		,,,				2504	0.0818				p.A821T		Atlas-SNP	.											.	FBXW10	82	.	0			c.G2461A						PASS	.	G	THR/ALA	480,3924	218.4+/-236.5	20,440,1742	43.0	45.0	44.0		2458	2.8	0.6	17	dbSNP_131	44	639,7957	162.2+/-214.9	20,599,3679	no	missense	FBXW10	NM_031456.3	58	40,1039,5421	AA,AG,GG		7.4337,10.8992,8.6077	benign	820/1052	18681913	1119,11881	2202	4298	6500	SO:0001583	missense	10517	exon14			GTTAGCGCCCTGC	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.2461G>A	17.37:g.18681913G>A	ENSP00000379025:p.Ala821Thr	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	224	114	0.508929	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	197	0.0902014652014652	72	0.14634146341463414	28	0.07734806629834254	37	0.06468531468531469	60	0.079155672823219	G	3.176	-0.168987	0.06461	0.108992	0.074337	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.62105	0.05;0.29;0.09;0.16	3.88	2.81	0.32909	.	0.000000	0.35378	U	0.003241	T	0.00328	0.0010	L	0.38175	1.15	0.39205	P	0.03678199999999998	B;B;B;B	0.21821	0.025;0.056;0.008;0.061	B;B;B;B	0.17433	0.007;0.018;0.002;0.007	T	0.09773	-1.0659	9	0.33940	T	0.23	.	10.2526	0.43377	0.0:0.0:0.789:0.2109	.	768;830;821;820	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	T	820;830;768;821	ENSP00000379026:A820T;ENSP00000310382:A830T;ENSP00000306937:A768T;ENSP00000379025:A821T	ENSP00000306937:A768T	A	+	1	0	FBXW10	18622638	0.007000	0.16637	0.617000	0.29091	0.211000	0.24417	0.897000	0.28390	1.963000	0.57068	0.404000	0.27445	GCC	G|0.912;A|0.088	0.088	strong		0.478	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249125	71249125	+	Silent	SNP	A	A	G	rs537752041|rs113379698|rs55848980	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:71249125A>G	ENST00000398534.3	+	1	55	c.24A>G	c.(22-24)ggA>ggG	p.G8G		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	8						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						GCTGCTCTGGAGGCTGTGGCT	0.652																																					p.G8G		Atlas-SNP	.											KRTAP5-8,rectum,carcinoma,0,2	KRTAP5-8	28	2	0			c.A24G						PASS	.						47.0	66.0	60.0					11																	71249125		2189	4280	6469	SO:0001819	synonymous_variant	57830	exon1			CTCTGGAGGCTGT	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.24A>G	11.37:g.71249125A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	102	10	0.0980392	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																			A|0.500;G|0.500	0.500	weak		0.652	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
CDCP1	64866	hgsc.bcm.edu	37	3	45153708	45153708	+	Silent	SNP	G	G	A	rs35501071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:45153708G>A	ENST00000296129.1	-	3	656	c.522C>T	c.(520-522)atC>atT	p.I174I	CDCP1_ENST00000490471.1_5'Flank|CDCP1_ENST00000425231.2_Silent_p.I174I	NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	174						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		AGAAGGTTCCGATCCTGACCA	0.577													G|||	689	0.13758	0.1301	0.1614	5008	,	,		18945	0.0456		0.1928	False		,,,				2504	0.1687				p.I174I		Atlas-SNP	.											CDCP1,colon,carcinoma,0,1	CDCP1	61	1	0			c.C522T						PASS	.	G	,	475,3931	223.0+/-239.6	30,415,1758	161.0	149.0	153.0		522,522	-2.3	0.6	3	dbSNP_126	153	1520,7080	288.0+/-298.5	112,1296,2892	no	coding-synonymous,coding-synonymous	CDCP1	NM_022842.3,NM_178181.1	,	142,1711,4650	AA,AG,GG		17.6744,10.7808,15.3391	,	174/837,174/344	45153708	1995,11011	2203	4300	6503	SO:0001819	synonymous_variant	64866	exon3			GGTTCCGATCCTG	AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"""CD molecules"""	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.522C>T	3.37:g.45153708G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_178181	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Silent	SNP	ENST00000296129.1	37	CCDS2727.1																																																																																			G|0.844;A|0.156	0.156	strong		0.577	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842	
DSCAM	1826	hgsc.bcm.edu	37	21	41725630	41725630	+	Missense_Mutation	SNP	G	G	C	rs2297270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:41725630G>C	ENST00000400454.1	-	5	1173	c.696C>G	c.(694-696)gaC>gaG	p.D232E		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	232	Ig-like C2-type 3.		D -> E (in dbSNP:rs2297270).		cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CTTTGCGATGGTCAAACCCAT	0.537													G|||	714	0.142572	0.2065	0.1499	5008	,	,		17892	0.2093		0.0755	False		,,,				2504	0.0511				p.D232E	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C696G						PASS	.	G	GLU/ASP	630,3164		55,520,1322	24.0	24.0	24.0		696	-10.1	0.7	21	dbSNP_100	24	638,7626		29,580,3523	yes	missense	DSCAM	NM_001389.3	45	84,1100,4845	CC,CG,GG		7.7202,16.6052,10.5158	benign	232/2013	41725630	1268,10790	1897	4132	6029	SO:0001583	missense	1826	exon5			GCGATGGTCAAAC	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.696C>G	21.37:g.41725630G>C	ENSP00000383303:p.Asp232Glu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	42	40	0.952381	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	347	0.15888278388278387	95	0.19308943089430894	56	0.15469613259668508	139	0.243006993006993	57	0.07519788918205805	G	1.753	-0.488713	0.04352	0.166052	0.077202	ENSG00000171587	ENST00000400454	T	0.65916	-0.18	5.31	-10.1	0.00402	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.164825	0.53938	D	0.000058	T	0.00012	0.0000	N	0.01267	-0.92	0.44635	P	0.0023809999999999665	B	0.02656	0.0	B	0.04013	0.001	T	0.07177	-1.0786	9	0.02654	T	1	.	12.5074	0.55989	0.0941:0.1349:0.6959:0.0751	rs2297270;rs2297270	232	O60469	DSCAM_HUMAN	E	232	ENSP00000383303:D232E	ENSP00000383303:D232E	D	-	3	2	DSCAM	40647500	0.193000	0.23313	0.690000	0.30148	0.975000	0.68041	-0.492000	0.06467	-1.752000	0.01325	-0.806000	0.03193	GAC	G|0.854;C|0.146	0.146	strong		0.537	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
MATN2	4147	hgsc.bcm.edu	37	8	99006748	99006748	+	Silent	SNP	C	C	T	rs11559201	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:99006748C>T	ENST00000520016.1	+	6	1246	c.1122C>T	c.(1120-1122)caC>caT	p.H374H	MATN2_ENST00000521689.1_Silent_p.H374H|MATN2_ENST00000254898.5_Silent_p.H374H|MATN2_ENST00000524308.1_Intron|MATN2_ENST00000522025.2_Silent_p.H90H			O00339	MATN2_HUMAN	matrilin 2	374	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			GATGTCAGCACGAGTGTGTTA	0.423													C|||	610	0.121805	0.1513	0.1052	5008	,	,		18606	0.0774		0.1471	False		,,,				2504	0.1135				p.H374H		Atlas-SNP	.											.	MATN2	165	.	0			c.C1122T						PASS	.	C	,	518,3382		29,460,1461	176.0	173.0	174.0		1122,1122	-11.5	0.0	8	dbSNP_120	174	1436,6846		126,1184,2831	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	155,1644,4292	TT,TC,CC		17.3388,13.2821,16.0401	,	374/957,374/938	99006748	1954,10228	1950	4141	6091	SO:0001819	synonymous_variant	4147	exon7			TCAGCACGAGTGT	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1122C>T	8.37:g.99006748C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	263	0.12042124542124542	74	0.15040650406504066	42	0.11602209944751381	37	0.06468531468531469	110	0.14511873350923482	C	3.537	-0.094593	0.07053	0.132821	0.173388	ENSG00000132561	ENST00000518154;ENST00000521041	.	.	.	5.73	-11.5	0.00074	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999863628	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.0438	8.8597	0.35249	0.0652:0.1537:0.1297:0.6513	rs11559201;rs17850660;rs17858379;rs58845670;rs11559201	.	.	.	X	157;129	.	.	R	+	1	2	MATN2	99075924	0.000000	0.05858	0.048000	0.18961	0.667000	0.39255	-2.725000	0.00808	-3.721000	0.00115	-1.595000	0.00837	CGA	C|0.872;T|0.128	0.128	strong		0.423	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
MICA	100507436	hgsc.bcm.edu	37	6	31378358	31378358	+	Missense_Mutation	SNP	T	T	G	rs1063630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31378358T>G	ENST00000449934.2	+	2	163	c.109T>G	c.(109-111)Tgg>Ggg	p.W37G	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				GGTGCTGTCCTGGGATGGATC	0.512													c|||	1343	0.268171	0.3797	0.3386	5008	,	,		20004	0.1786		0.1928	False		,,,				2504	0.2372				p.W37G		Atlas-SNP	.											.	MICA	21	.	0			c.T109G						PASS	.	C	GLY/TRP	476,908		97,282,313	9.0	10.0	10.0		109	-2.2	0.0	6	dbSNP_86	10	534,2640		46,442,1099	no	missense	MICA	NM_001177519.1	184	143,724,1412	GG,GT,TT		16.8242,34.3931,22.1588	benign	37/333	31378358	1010,3548	692	1587	2279	SO:0001583	missense	100507436	exon2			CTGTCCTGGGATG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.109T>G	6.37:g.31378358T>G	ENSP00000413079:p.Trp37Gly	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	215	91	0.423256	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	575	0.2632783882783883	179	0.3638211382113821	140	0.3867403314917127	95	0.1660839160839161	161	0.21240105540897097	N	6.451	0.451312	0.12223	0.343931	0.168242	ENSG00000204520	ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.00682	5.86;5.86	2.89	-2.15	0.07102	.	2.042530	0.02822	N	0.125645	T	0.00271	0.0008	N	0.16903	0.455	0.80722	P	0.0	B	0.32071	0.355	B	0.36845	0.234	T	0.41805	-0.9488	9	0.56958	D	0.05	.	4.6738	0.12701	0.1467:0.4801:0.0:0.3732	rs1063630;rs17206511;rs17882548;rs59366444	37	Q96QC4	.	G	37;37;37;24	ENSP00000413079:W37G;ENSP00000402410:W24G	ENSP00000365394:W37G	W	+	1	0	MICA	31486337	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.968000	0.03817	-0.789000	0.04498	-3.462000	0.00035	TGG	C|0.003;G|0.250;T|0.747	0.250	strong		0.512	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
CPAMD8	27151	hgsc.bcm.edu	37	19	17108098	17108098	+	Silent	SNP	C	C	T	rs112680414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17108098C>T	ENST00000443236.1	-	11	1090	c.1059G>A	c.(1057-1059)gcG>gcA	p.A353A	CPAMD8_ENST00000388925.4_Silent_p.A306A	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	306						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CAGGGACGTCCGCTGGGATCA	0.632													c|||	254	0.0507188	0.0976	0.0447	5008	,	,		19796	0.0		0.0487	False		,,,				2504	0.046				p.A353A		Atlas-SNP	.											CPAMD8,colon,carcinoma,-2,1	CPAMD8	192	1	0			c.G1059A						PASS	.	C		312,3586		11,290,1648	13.0	15.0	14.0		1059	-6.0	0.0	19	dbSNP_132	14	345,7923		9,327,3798	no	coding-synonymous	CPAMD8	NM_015692.2		20,617,5446	TT,TC,CC		4.1727,8.0041,5.4003		353/1933	17108098	657,11509	1949	4134	6083	SO:0001819	synonymous_variant	27151	exon11			GACGTCCGCTGGG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1059G>A	19.37:g.17108098C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	171	74	0.432749	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	99	0.04532967032967033	47	0.09552845528455285	12	0.03314917127071823	0	0.0	40	0.052770448548812667	c	1.322	-0.599146	0.03744	0.080041	0.041727	ENSG00000160111	ENST00000443236	.	.	.	3.0	-6.01	0.02199	.	.	.	.	.	T	0.00412	0.0013	.	.	.	0.20563	P	0.99988098	.	.	.	.	.	.	T	0.21552	-1.0242	3	.	.	.	.	1.6364	0.02743	0.1984:0.1044:0.2767:0.4205	.	.	.	.	Q	364	.	.	R	-	2	0	CPAMD8	16969098	0.026000	0.19158	0.006000	0.13384	0.207000	0.24258	-0.649000	0.05384	-0.960000	0.03613	-0.266000	0.10368	CGG	C|0.838;T|0.162	0.162	strong		0.632	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
KMT2D	8085	hgsc.bcm.edu	37	12	49444545	49444545	+	Silent	SNP	G	G	A	rs2241726	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:49444545G>A	ENST00000301067.7	-	11	2825	c.2826C>T	c.(2824-2826)atC>atT	p.I942I		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	942	Pro-rich.			Missing (in Ref. 1; AAC51734). {ECO:0000305}.	chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.?(1)									CAGCTGTGATGATGGGTGAGA	0.542													A|||	2021	0.403554	0.4297	0.2911	5008	,	,		19639	0.4306		0.3479	False		,,,				2504	0.4775				p.I942I		Atlas-SNP	.											MLL2,NS,carcinoma,0,1	MLL2	1173	1	1	Unknown(1)	stomach(1)	c.C2826T						PASS	.	A		1612,2248		346,920,664	45.0	52.0	49.0		2826	2.4	1.0	12	dbSNP_98	49	3053,5191		577,1899,1646	no	coding-synonymous	MLL2	NM_003482.3		923,2819,2310	AA,AG,GG		37.033,41.7617,38.541		942/5538	49444545	4665,7439	1930	4122	6052	SO:0001819	synonymous_variant	8085	exon11			TGTGATGATGGGT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.2826C>T	12.37:g.49444545G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			G|0.624;A|0.376	0.376	strong		0.542	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
PFKP	5214	hgsc.bcm.edu	37	10	3172121	3172121	+	Silent	SNP	C	C	T	rs1052333	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:3172121C>T	ENST00000381125.4	+	17	1870	c.1794C>T	c.(1792-1794)gcC>gcT	p.A598A	PFKP_ENST00000381072.1_Silent_p.A16A|PFKP_ENST00000381075.2_Silent_p.A590A	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	598	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		GGCTCGCGGCCGGAGCTGATG	0.632													c|||	2065	0.41234	0.469	0.3761	5008	,	,		15467	0.37		0.3936	False		,,,				2504	0.4243				p.A598A		Atlas-SNP	.											PFKP_ENST00000381075,NS,carcinoma,0,2	PFKP	182	2	0			c.C1794T						scavenged	.	G	,	1979,2427		448,1083,672	45.0	44.0	45.0		1770,1794	-9.0	0.0	10	dbSNP_86	45	3119,5481		571,1977,1752	no	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	1019,3060,2424	TT,TC,CC		36.2674,44.916,39.1973	,	590/777,598/785	3172121	5098,7908	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon17			CGCGGCCGGAGCT	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1794C>T	10.37:g.3172121C>T		Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	885	0.4052197802197802	221	0.4491869918699187	149	0.4116022099447514	210	0.36713286713286714	305	0.4023746701846966	N	0.036	-1.304876	0.01353	0.44916	0.362674	ENSG00000067057	ENST00000413079	.	.	.	4.49	-8.98	0.00754	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999936	.	.	.	.	.	.	T	0.31806	-0.9930	3	.	.	.	.	0.6695	0.00856	0.2114:0.1981:0.2652:0.3253	rs1052333;rs17845873;rs17858848;rs61479798;rs1052333	.	.	.	W	162	.	.	R	+	1	2	PFKP	3162121	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-4.635000	0.00205	-3.442000	0.00162	-1.465000	0.01017	CGG	C|0.611;T|0.389	0.389	strong		0.632	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
CD4	920	hgsc.bcm.edu	37	12	6926363	6926363	+	Silent	SNP	T	T	C	rs1055141	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6926363T>C	ENST00000011653.4	+	7	1281	c.1023T>C	c.(1021-1023)agT>agC	p.S341S		NM_000616.4|NM_001195015.2|NM_001195016.2|NM_001195017.2	NP_000607.1|NP_001181944.1|NP_001181945.1|NP_001181946.1	P01730	CD4_HUMAN	CD4 molecule	341	Ig-like C2-type 3.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cytokine production (GO:0001816)|defense response to Gram-negative bacterium (GO:0050829)|entry into host cell (GO:0030260)|enzyme linked receptor protein signaling pathway (GO:0007167)|immune response (GO:0006955)|induction by virus of host cell-cell fusion (GO:0006948)|innate immune response (GO:0045087)|maintenance of protein location in cell (GO:0032507)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase activity (GO:0045860)|protein palmitoleylation (GO:0045234)|regulation of defense response to virus by virus (GO:0050690)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|T cell selection (GO:0045058)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|enzyme binding (GO:0019899)|extracellular matrix structural constituent (GO:0005201)|glycoprotein binding (GO:0001948)|MHC class II protein binding (GO:0042289)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	23		Myeloproliferative disorder(1001;0.0122)			Antithymocyte globulin(DB00098)	TGATGCTGAGTTTGAAACTGG	0.567													C|||	3740	0.746805	0.792	0.6686	5008	,	,		-128	0.9137		0.5696	False		,,,				2504	0.7515				p.S341S		Atlas-SNP	.											.	CD4	47	.	0			c.T1023C						PASS	.	C	,,,,	3275,1131	402.8+/-332.5	1228,819,156	86.0	67.0	74.0		1023,486,204,204,204	-0.9	0.0	12	dbSNP_86	74	4669,3931	548.0+/-385.3	1277,2115,908	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD4	NM_000616.4,NM_001195014.2,NM_001195015.2,NM_001195016.2,NM_001195017.2	,,,,	2505,2934,1064	CC,CT,TT		45.7093,25.6695,38.9205	,,,,	341/459,162/280,68/186,68/186,68/186	6926363	7944,5062	2203	4300	6503	SO:0001819	synonymous_variant	920	exon7			GCTGAGTTTGAAA	M35160	CCDS8562.1	12p13.31	2013-01-11	2006-03-28		ENSG00000010610	ENSG00000010610		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1678	protein-coding gene	gene with protein product		186940	"""CD4 antigen (p55)"", ""T-cell surface glycoprotein CD4"""				Standard	NM_000616		Approved		uc001qqv.2	P01730	OTTHUMG00000168514	ENST00000011653.4:c.1023T>C	12.37:g.6926363T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_000616	B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5	Silent	SNP	ENST00000011653.4	37	CCDS8562.1																																																																																			T|0.328;C|0.672	0.672	strong		0.567	CD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399978.1	NM_000616	
BAG3	9531	hgsc.bcm.edu	37	10	121429394	121429394	+	Missense_Mutation	SNP	G	G	T	rs35434411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:121429394G>T	ENST00000369085.3	+	2	518	c.212G>T	c.(211-213)cGg>cTg	p.R71L		NM_004281.3	NP_004272.2	O95817	BAG3_HUMAN	BCL2-associated athanogene 3	71			R -> Q (in dbSNP:rs35434411). {ECO:0000269|PubMed:21459883}.|R -> W (in CMD1HH). {ECO:0000269|PubMed:21353195}.		brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of apoptotic process (GO:0043066)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|Z disc (GO:0030018)				endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(5)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	20		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00187)|BRCA - Breast invasive adenocarcinoma(275;0.148)		GGCCCTTCCCGGGAGGGCTCT	0.577																																					p.R71L		Atlas-SNP	.											.	BAG3	42	.	0			c.G212T						PASS	.						83.0	87.0	85.0					10																	121429394		2203	4300	6503	SO:0001583	missense	9531	exon2			CTTCCCGGGAGGG	AF095193	CCDS7615.1	10q25.2-q26.2	2014-09-17			ENSG00000151929	ENSG00000151929			939	protein-coding gene	gene with protein product		603883				9873016, 18094623	Standard	XM_005270287		Approved		uc001lem.3	O95817	OTTHUMG00000019155	ENST00000369085.3:c.212G>T	10.37:g.121429394G>T	ENSP00000358081:p.Arg71Leu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	115	66	0.573913	NM_004281	A8K5L8|Q3B763|Q9NT20|Q9P120	Missense_Mutation	SNP	ENST00000369085.3	37	CCDS7615.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967365	0.53507	.	.	ENSG00000151929	ENST00000369085;ENST00000450186	T;T	0.75367	-0.93;-0.91	5.4	3.12	0.35913	.	0.417057	0.28219	N	0.016148	T	0.65101	0.2659	L	0.57536	1.79	0.09310	N	1	P;P	0.37276	0.589;0.589	B;B	0.29524	0.103;0.103	T	0.61657	-0.7018	10	0.59425	D	0.04	-12.1508	10.3289	0.43809	0.3064:0.0:0.6936:0.0	.	71;71	O95817;Q53GY1	BAG3_HUMAN;.	L	71;13	ENSP00000358081:R71L;ENSP00000410036:R13L	ENSP00000358081:R71L	R	+	2	0	BAG3	121419384	0.073000	0.21202	0.995000	0.50966	0.981000	0.71138	1.137000	0.31479	1.217000	0.43442	0.561000	0.74099	CGG	G|0.979;A|0.021	.	alt		0.577	BAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050662.1	NM_004281	
Unknown	0	hgsc.bcm.edu	37	11	124095884	124095884	+	IGR	SNP	A	A	G	rs2466614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124095884A>G								OR10D3 (38932 upstream) : OR8G1 (24538 downstream)																							GGGAGTTTACATTTTAGGCAT	0.433													a|||	504	0.100639	0.0174	0.1585	5008	,	,		23282	0.131		0.1441	False		,,,				2504	0.0961				p.I163V		Atlas-SNP	.											.	.	.	.	0			c.A487G						PASS	.	A	VAL/ILE	168,4040		4,160,1940	255.0	264.0	261.0		487	-4.2	0.0	11	dbSNP_100	261	1339,7207		97,1145,3031	yes	missense	OR8G2	NM_001007249.1	29	101,1305,4971	GG,GA,AA		15.6681,3.9924,11.8159	benign	163/305	124095884	1507,11247	2104	4273	6377	SO:0001628	intergenic_variant	26492	exon1			GTTTACATTTTAG																													11.37:g.124095884A>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	222	101	0.454955	NM_001007249		Missense_Mutation	SNP		37																																																																																				A|0.893;G|0.107	0.107	strong	0	0.433								
SIRPG	55423	hgsc.bcm.edu	37	20	1617069	1617069	+	Silent	SNP	A	A	G	rs2277761	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:1617069A>G	ENST00000303415.3	-	3	577	c.513T>C	c.(511-513)caT>caC	p.H171H	SIRPG_ENST00000344103.4_Intron|SIRPG_ENST00000381583.2_Silent_p.H171H|SIRPG_ENST00000216927.4_Silent_p.H171H|RP11-77C3.3_ENST00000437384.1_RNA|RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000381580.1_Silent_p.H138H	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	171	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						GAGAGAAGCCATGGGACTCAC	0.557													a|||	1148	0.229233	0.1619	0.366	5008	,	,		19683	0.2103		0.2376	False		,,,				2504	0.2342				p.H171H		Atlas-SNP	.											SIRPG,NS,carcinoma,-1,1	SIRPG	61	1	0			c.T513C						PASS	.	A	,,	726,3680		54,618,1531	149.0	133.0	138.0		513,513,	-4.2	0.0	20	dbSNP_100	138	2134,6466		266,1602,2432	no	coding-synonymous,coding-synonymous,intron	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	320,2220,3963	GG,GA,AA		24.814,16.4775,21.9899	,,	171/277,171/388,	1617069	2860,10146	2203	4300	6503	SO:0001819	synonymous_variant	55423	exon3			GAAGCCATGGGAC	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.513T>C	20.37:g.1617069A>G		Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	369	367	0.99458	NM_001039508	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			A|0.776;G|0.224	0.224	strong		0.557	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
SERPINB8	5271	hgsc.bcm.edu	37	18	61650865	61650865	+	Silent	SNP	G	G	A	rs11537989	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:61650865G>A	ENST00000397985.2	+	5	733	c.477G>A	c.(475-477)ctG>ctA	p.L159L	SERPINB8_ENST00000397988.3_Silent_p.L159L|SERPINB8_ENST00000353706.2_Silent_p.L159L|SERPINB8_ENST00000542677.1_5'UTR	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	159					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				TGACAAAGCTGGTCCTTGTGA	0.408													G|||	1082	0.216054	0.0393	0.2795	5008	,	,		16519	0.3224		0.3002	False		,,,				2504	0.2137				p.L159L		Atlas-SNP	.											.	SERPINB8	42	.	0			c.G477A						PASS	.	G	,,	466,3940	219.7+/-237.4	26,414,1763	133.0	124.0	127.0		477,477,477	3.9	1.0	18	dbSNP_120	127	2651,5949	427.8+/-355.7	445,1761,2094	no	coding-synonymous,coding-synonymous,coding-synonymous	SERPINB8	NM_001031848.1,NM_002640.3,NM_198833.1	,,	471,2175,3857	AA,AG,GG		30.8256,10.5765,23.9659	,,	159/243,159/375,159/375	61650865	3117,9889	2203	4300	6503	SO:0001819	synonymous_variant	5271	exon5			AAAGCTGGTCCTT	L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"""Serine (or cysteine) peptidase inhibitors"""	8952	protein-coding gene	gene with protein product	"""cytoplasmic antiproteinase 2"""	601697	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"""	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.477G>A	18.37:g.61650865G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	119	48	0.403361	NM_001031848	B4DTW2|Q7Z2V6|Q8N178	Silent	SNP	ENST00000397985.2	37	CCDS11991.1	523	0.23946886446886448	32	0.06504065040650407	112	0.30939226519337015	159	0.27797202797202797	220	0.29023746701846964	G	3.867	-0.028764	0.07589	0.105765	0.308256	ENSG00000166401	ENST00000295211	.	.	.	5.65	3.87	0.44632	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7681	0.28991	0.1418:0.0:0.7254:0.1327	rs11537989;rs17846092;rs17859094	.	.	.	X	101	.	.	W	+	2	0	SERPINB8	59801845	0.654000	0.27367	0.998000	0.56505	0.357000	0.29423	-0.225000	0.09151	0.942000	0.37525	0.655000	0.94253	TGG	G|0.763;A|0.237	0.237	strong		0.408	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848	
F13A1	2162	hgsc.bcm.edu	37	6	6318795	6318795	+	Missense_Mutation	SNP	C	C	A	rs5985	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:6318795C>A	ENST00000264870.3	-	2	368	c.103G>T	c.(103-105)Gtg>Ttg	p.V35L		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	35			V -> L (higher specific activity; dbSNP:rs5985). {ECO:0000269|PubMed:10391209, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	CGGGGCACCACGCCCTGAAGC	0.622													C|||	740	0.147764	0.1641	0.2695	5008	,	,		15212	0.002		0.2416	False		,,,				2504	0.093				p.V35L		Atlas-SNP	.											.	F13A1	135	.	0			c.G103T	GRCh37	CM950376	F13A1	M	rs5985	PASS	.	C	LEU/VAL	804,3602	322.1+/-297.4	69,666,1468	136.0	119.0	125.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	103	1.9	0.0	6	dbSNP_52	125	2163,6437	371.9+/-336.4	278,1607,2415	yes	missense	F13A1	NM_000129.3	32	347,2273,3883	AA,AC,CC		25.1512,18.2478,22.8125	benign	35/733	6318795	2967,10039	2203	4300	6503	SO:0001583	missense	2162	exon2			GCACCACGCCCTG	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.103G>T	6.37:g.6318795C>A	ENSP00000264870:p.Val35Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	CCDS4496.1	342	0.1565934065934066	77	0.1565040650406504	83	0.2292817679558011	0	0.0	182	0.24010554089709762	C	0.015	-1.562909	0.00903	0.182478	0.251512	ENSG00000124491	ENST00000264870;ENST00000441301;ENST00000414279;ENST00000431222	D;D	0.86030	-2.06;-2.06	4.64	1.89	0.25635	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.784671	0.11580	N	0.549870	T	0.34106	0.0886	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04017	-1.0984	9	0.08179	T	0.78	.	4.1972	0.10448	0.0869:0.1605:0.5922:0.1605	rs5985;rs60452761;rs5985	35;35	F5H080;P00488	.;F13A_HUMAN	L	35;35;35;73	ENSP00000264870:V35L;ENSP00000413334:V35L	ENSP00000264870:V35L	V	-	1	0	F13A1	6263794	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.249000	0.08842	0.212000	0.20703	-0.802000	0.03209	GTG	C|0.805;A|0.195	0.195	strong		0.622	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
MOV10L1	54456	hgsc.bcm.edu	37	22	50528916	50528916	+	Intron	SNP	C	C	T	rs9617018	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50528916C>T	ENST00000262794.5	+	1	180				MOV10L1_ENST00000475190.1_Intron|MOV10L1_ENST00000395843.1_Intron|MOV10L1_ENST00000395858.3_Intron|MOV10L1_ENST00000540615.1_Silent_p.L4L|MOV10L1_ENST00000545383.1_Intron	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1						ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGTCGTTCCTCCCTGTCCGCA	0.617													c|||	825	0.164736	0.0946	0.3127	5008	,	,		15244	0.1944		0.1352	False		,,,				2504	0.1544				p.L4L		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C12T						PASS	.		,,	333,2803		20,293,1255	47.0	49.0	48.0		,12,	0.5	0.0	22	dbSNP_119	48	1056,6108		84,888,2610	no	intron,coding-synonymous,intron	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	104,1181,3865	TT,TC,CC		14.7404,10.6186,13.4854	,,	,4/1166,	50528916	1389,8911	1568	3582	5150	SO:0001627	intron_variant	54456	exon1			GTTCCTCCCTGTC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.97+302C>T	22.37:g.50528916C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_001164105	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			C|0.844;T|0.156	0.156	strong		0.617	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
LYZL1	84569	hgsc.bcm.edu	37	10	29578084	29578084	+	Missense_Mutation	SNP	A	A	G	rs2532753	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:29578084A>G	ENST00000375500.3	+	1	95	c.38A>G	c.(37-39)aAg>aGg	p.K13R		NM_032517.4	NP_115906.3	Q6UWQ5	LYZL1_HUMAN	lysozyme-like 1	0					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			central_nervous_system(1)|cervix(2)|large_intestine(2)|lung(5)|skin(1)	11		Breast(68;0.203)				TCACCGACTAAGTGGAGCAGT	0.507													A|||	3390	0.676917	0.6006	0.7421	5008	,	,		15766	0.7897		0.6153	False		,,,				2504	0.681				p.K13R		Atlas-SNP	.											.	LYZL1	25	.	0			c.A38G						PASS	.						40.0	35.0	37.0					10																	29578084		2203	4298	6501	SO:0001583	missense	84569	exon1			CGACTAAGTGGAG		CCDS31174.1	10p12.1	2004-08-02			ENSG00000120563	ENSG00000120563	3.2.1.1		30502	protein-coding gene	gene with protein product						12477932	Standard	XM_005252627		Approved	MGC33408, LYC2	uc001iul.3	Q6UWQ5	OTTHUMG00000017880	ENST00000375500.3:c.38A>G	10.37:g.29578084A>G	ENSP00000364650:p.Lys13Arg	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	NM_032517	Q5T921|Q8WW16	Missense_Mutation	SNP	ENST00000375500.3	37	CCDS31174.1	1430	0.6547619047619048	287	0.5833333333333334	232	0.6408839779005525	456	0.7972027972027972	455	0.600263852242744	A	12.59	1.982645	0.34942	.	.	ENSG00000120563	ENST00000375500	T	0.68903	-0.36	4.04	4.04	0.47022	.	6.432820	0.00541	N	0.000231	T	0.00012	0.0000	.	.	.	0.42321	P	0.007746000000000031	P	0.46395	0.877	P	0.44811	0.461	T	0.40232	-0.9574	8	0.22109	T	0.4	-9.5578	9.6607	0.39954	1.0:0.0:0.0:0.0	rs17851935	13	Q6UWQ5-2	.	R	13	ENSP00000364650:K13R	ENSP00000364650:K13R	K	+	2	0	LYZL1	29618090	1.000000	0.71417	0.999000	0.59377	0.017000	0.09413	2.028000	0.41088	2.058000	0.61347	0.459000	0.35465	AAG	A|1.000;|0.000	.	weak		0.507	LYZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047381.1	NM_032517	
PNPLA3	80339	hgsc.bcm.edu	37	22	44322970	44322970	+	Missense_Mutation	SNP	G	G	T	rs2076212	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:44322970G>T	ENST00000216180.3	+	2	516	c.343G>T	c.(343-345)Ggc>Tgc	p.G115C	PNPLA3_ENST00000423180.2_Missense_Mutation_p.G111C|PNPLA3_ENST00000478713.1_3'UTR	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	115	Patatin.		G -> C (in dbSNP:rs2076212). {ECO:0000269|PubMed:14702039}.		acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				CGGCAAAATAGGCATCTCTCT	0.502													T|||	610	0.121805	0.1513	0.1095	5008	,	,		22640	0.0694		0.1262	False		,,,				2504	0.1401				p.G115C		Atlas-SNP	.											.	PNPLA3	53	.	0			c.G343T						PASS	.	T	CYS/GLY	697,3709	760.4+/-413.0	49,599,1555	88.0	78.0	81.0		343	-6.8	0.0	22	dbSNP_96	81	1155,7445	765.9+/-407.6	78,999,3223	yes	missense	PNPLA3	NM_025225.2	159	127,1598,4778	TT,TG,GG		13.4302,15.8193,14.2396	benign	115/482	44322970	1852,11154	2203	4300	6503	SO:0001583	missense	80339	exon2			AAAATAGGCATCT		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"""Patatin-like phospholipase domain containing"""	18590	protein-coding gene	gene with protein product		609567	"""chromosome 22 open reading frame 20"", ""adiponutrin"""	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.343G>T	22.37:g.44322970G>T	ENSP00000216180:p.Gly115Cys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	166	86	0.518072	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Missense_Mutation	SNP	ENST00000216180.3	37	CCDS14054.1	240	0.10989010989010989	70	0.14227642276422764	47	0.1298342541436464	36	0.06293706293706294	87	0.11477572559366754	T	1.886	-0.456571	0.04540	0.158193	0.134302	ENSG00000100344	ENST00000216180;ENST00000423180	T;T	0.77229	-1.08;-1.08	5.5	-6.85	0.01681	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	1.730350	0.03006	N	0.148858	T	0.00241	0.0007	N	0.02357	-0.585	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03898	-1.0994	9	0.27785	T	0.31	-4.7916	6.1878	0.20508	0.1592:0.0569:0.4581:0.3258	rs2076212;rs17493969;rs59332912;rs2076212	115	Q9NST1	PLPL3_HUMAN	C	115;111	ENSP00000216180:G115C;ENSP00000397987:G111C	ENSP00000216180:G115C	G	+	1	0	PNPLA3	42654303	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.199000	0.09491	-1.567000	0.01671	-0.269000	0.10298	GGC	G|0.867;T|0.132	0.132	strong		0.502	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225	
OTOF	9381	hgsc.bcm.edu	37	2	26699855	26699855	+	Silent	SNP	G	G	C	rs2272069	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:26699855G>C	ENST00000272371.2	-	22	2706	c.2580C>G	c.(2578-2580)gtC>gtG	p.V860V	OTOF_ENST00000403946.3_Silent_p.V860V|OTOF_ENST00000339598.3_Silent_p.V113V|OTOF_ENST00000402415.3_Silent_p.V170V|OTOF_ENST00000338581.6_Silent_p.V113V	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	860					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGCATAGGCGACACGCTTGT	0.602													G|||	2512	0.501597	0.2617	0.5418	5008	,	,		7767	0.8542		0.4225	False		,,,				2504	0.5153				p.V860V	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C2580G						PASS	.	G	,,,	1188,3192	408.9+/-334.8	169,850,1171	69.0	54.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	339,2580,510,339	1.6	1.0	2	dbSNP_100	60	3269,5315	486.2+/-371.8	600,2069,1623	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	769,2919,2794	CC,CG,GG		38.0825,27.1233,34.3798	,,,	113/1231,860/1998,170/1308,113/1231	26699855	4457,8507	2190	4292	6482	SO:0001819	synonymous_variant	9381	exon22			ATAGGCGACACGC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2580C>G	2.37:g.26699855G>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	137	61	0.445255	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			G|0.597;C|0.403	0.403	strong		0.602	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
MUC2	4583	hgsc.bcm.edu	37	11	1092624	1092624	+	Silent	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1092624C>A	ENST00000441003.2	+	30	4470	c.4443C>A	c.(4441-4443)acC>acA	p.T1481T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1482T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4216	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gccctccaaccaccactccca	0.627																																					p.T1481T		Atlas-SNP	.											MUC2_ENST00000441003,extremity,malignant_melanoma,+2,2	MUC2	614	2	0			c.C4443A						scavenged	.						223.0	336.0	297.0					11																	1092624		1558	2939	4497	SO:0001819	synonymous_variant	4583	exon30			TCCAACCACCACT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4443C>A	11.37:g.1092624C>A		Somatic	167	5	0.0299401		WXS	Illumina HiSeq	Phase_I	164	16	0.097561	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
HELB	92797	hgsc.bcm.edu	37	12	66704098	66704098	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:66704098A>G	ENST00000247815.4	+	4	1449	c.1390A>G	c.(1390-1392)Atg>Gtg	p.M464V		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	464					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		TGCTTTGGAAATGATTTGCTC	0.428																																					p.M464V		Atlas-SNP	.											HELB,NS,carcinoma,-2,1	HELB	90	1	0			c.A1390G						PASS	.						90.0	90.0	90.0					12																	66704098		2203	4300	6503	SO:0001583	missense	92797	exon4			TTGGAAATGATTT	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.1390A>G	12.37:g.66704098A>G	ENSP00000247815:p.Met464Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.589061	0.46110	.	.	ENSG00000127311	ENST00000247815	T	0.40476	1.03	6.04	6.04	0.98038	.	0.083556	0.85682	D	0.000000	T	0.34629	0.0904	L	0.28344	0.845	0.28916	N	0.892402	P	0.40144	0.704	B	0.42462	0.388	T	0.28964	-1.0027	9	.	.	.	-27.9413	13.0143	0.58749	0.8657:0.1343:0.0:0.0	.	464	Q8NG08	HELB_HUMAN	V	464	ENSP00000247815:M464V	.	M	+	1	0	HELB	64990365	1.000000	0.71417	0.993000	0.49108	0.790000	0.44656	5.571000	0.67404	2.317000	0.78254	0.459000	0.35465	ATG	.	.	none		0.428	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
MUC2	4583	hgsc.bcm.edu	37	11	1104123	1104123	+	Silent	SNP	C	C	T	rs12270802	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1104123C>T	ENST00000441003.2	+	49	8341	c.8314C>T	c.(8314-8316)Ctg>Ttg	p.L2772L		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5134					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.L2772L(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TGAGGTGGTCCTGAGCTGCCC	0.672													C|||	778	0.155351	0.4039	0.072	5008	,	,		14321	0.0357		0.0934	False		,,,				2504	0.0654				p.L2768L		Atlas-SNP	.											MUC2_ENST00000441003,NS,lymphoid_neoplasm,0,1	MUC2	614	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C8302T						PASS	.	C		1294,2806		202,890,958	14.0	20.0	18.0		8299	1.6	0.0	11	dbSNP_120	18	690,7674		27,636,3519	no	coding-synonymous	MUC2	NM_002457.2		229,1526,4477	TT,TC,CC		8.2496,31.561,15.9178		2767/2813	1104123	1984,10480	2050	4182	6232	SO:0001819	synonymous_variant	4583	exon50			GTGGTCCTGAGCT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.8314C>T	11.37:g.1104123C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	161	78	0.484472	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.894;T|0.106	0.106	strong		0.672	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR11H12	440153	hgsc.bcm.edu	37	14	19378395	19378395	+	Missense_Mutation	SNP	A	A	G	rs201551285		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:19378395A>G	ENST00000550708.1	+	1	874	c.802A>G	c.(802-804)Agc>Ggc	p.S268G		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ACTGTGCTATAGCTCTCTTAT	0.468																																					p.S268G		Atlas-SNP	.											OR11H12,NS,carcinoma,0,1	OR11H12	58	1	0			c.A802G						scavenged	.						6.0	1.0	2.0					14																	19378395		83	207	290	SO:0001583	missense	440153	exon1			TGCTATAGCTCTC		CCDS32017.1	14q11.2	2013-01-25			ENSG00000257115	ENSG00000257115		"""GPCR / Class A : Olfactory receptors"""	30738	protein-coding gene	gene with protein product							Standard	NM_001013354		Approved		uc010tkp.2	B2RN74	OTTHUMG00000170298	ENST00000550708.1:c.802A>G	14.37:g.19378395A>G	ENSP00000449002:p.Ser268Gly	Somatic	608	3	0.00493421		WXS	Illumina HiSeq	Phase_I	791	259	0.327434	NM_001013354		Missense_Mutation	SNP	ENST00000550708.1	37	CCDS32017.1	.	.	.	.	.	.	.	.	.	.	a	0.004	-2.378550	0.00205	.	.	ENSG00000257115	ENST00000550708	T	0.35236	1.32	0.585	0.585	0.17428	GPCR, rhodopsin-like superfamily (1);	0.161607	0.28252	N	0.016023	T	0.05593	0.0147	N	0.00146	-1.995	0.19945	N	0.999944	B	0.02656	0.0	B	0.01281	0.0	T	0.31586	-0.9938	9	0.02654	T	1	.	4.1147	0.10076	0.5146:0.0:0.4853:0.0	.	268	B2RN74	O11HC_HUMAN	G	268	ENSP00000449002:S268G	ENSP00000449002:S268G	S	+	1	0	CR383656.1	18448395	0.000000	0.05858	0.815000	0.32552	0.031000	0.12232	0.077000	0.14738	-1.164000	0.02790	-2.094000	0.00368	AGC	A|0.500;G|0.500	0.500	weak		0.468	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354	
XDH	7498	hgsc.bcm.edu	37	2	31590917	31590917	+	Missense_Mutation	SNP	T	T	C	rs17011368	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:31590917T>C	ENST00000379416.3	-	20	2155	c.2107A>G	c.(2107-2109)Ata>Gta	p.I703V		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	703			I -> V (in dbSNP:rs17011368). {ECO:0000269|Ref.6}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	TTGTTCTTTATAGCATCCTGA	0.428													T|||	260	0.0519169	0.1195	0.0317	5008	,	,		20601	0.004		0.0477	False		,,,				2504	0.0286				p.I703V	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.A2107G	GRCh37	CM080637	XDH	M	rs17011368	PASS	.	T	VAL/ILE	508,3898	235.2+/-247.8	33,442,1728	143.0	135.0	138.0		2107	4.8	1.0	2	dbSNP_123	138	294,8306	107.4+/-168.2	4,286,4010	yes	missense	XDH	NM_000379.3	29	37,728,5738	CC,CT,TT		3.4186,11.5297,6.1664	possibly-damaging	703/1334	31590917	802,12204	2203	4300	6503	SO:0001583	missense	7498	exon20			TCTTTATAGCATC	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.2107A>G	2.37:g.31590917T>C	ENSP00000368727:p.Ile703Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	198	97	0.489899	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	37	CCDS1775.1	106	0.048534798534798536	68	0.13821138211382114	12	0.03314917127071823	0	0.0	26	0.03430079155672823	T	16.30	3.084344	0.55861	0.115297	0.034186	ENSG00000158125	ENST00000379416	T	0.39229	1.09	6.02	4.8	0.61643	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.044294	0.85682	D	0.000000	T	0.00356	0.0011	L	0.53561	1.675	0.09310	P	0.99999870301	B	0.15473	0.013	B	0.28638	0.092	T	0.13361	-1.0512	9	0.87932	D	0	.	11.1748	0.48593	0.0:0.0:0.1538:0.8462	rs17011368;rs52829758;rs58778509;rs17011368	703	P47989	XDH_HUMAN	V	703	ENSP00000368727:I703V	ENSP00000368727:I703V	I	-	1	0	XDH	31444421	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	3.383000	0.52471	2.311000	0.77944	0.533000	0.62120	ATA	T|0.942;C|0.058	0.058	strong		0.428	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
ZNF845	91664	hgsc.bcm.edu	37	19	53856730	53856730	+	Silent	SNP	G	G	A	rs201351032	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53856730G>A	ENST00000595091.1	+	5	3021	c.2802G>A	c.(2800-2802)aaG>aaA	p.K934K	ZNF845_ENST00000458035.1_Silent_p.K934K			Q96IR2	ZN845_HUMAN	zinc finger protein 845	934					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K934K(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TAATTCATAAGACAATTCATA	0.368													.|||	271	0.0541134	0.0507	0.0576	5008	,	,		22260	0.0456		0.0924	False		,,,				2504	0.0256				p.K934K		Atlas-SNP	.											ZNF845,NS,carcinoma,0,5	ZNF845	101	5	3	Substitution - coding silent(3)	kidney(3)	c.G2802A						scavenged	.																																			SO:0001819	synonymous_variant	91664	exon4			TCATAAGACAATT	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2802G>A	19.37:g.53856730G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	95	4	0.0421053	NM_138374		Silent	SNP	ENST00000595091.1	37	CCDS46170.1																																																																																			.	.	weak		0.368	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
CACNA1H	8912	hgsc.bcm.edu	37	16	1252441	1252441	+	Missense_Mutation	SNP	T	T	C	rs4984636	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1252441T>C	ENST00000348261.5	+	9	2239	c.1991T>C	c.(1990-1992)gTc>gCc	p.V664A	CACNA1H_ENST00000358590.4_Missense_Mutation_p.V664A|CACNA1H_ENST00000565831.1_Missense_Mutation_p.V664A	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	664			V -> A (in dbSNP:rs4984636). {ECO:0000269|PubMed:11751928, ECO:0000269|PubMed:12891677, ECO:0000269|PubMed:9670923}.		aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCGCATGTGGTCGGGGAGCAT	0.682													T|||	530	0.105831	0.0091	0.1744	5008	,	,		16513	0.002		0.2863	False		,,,				2504	0.1094				p.V664A		Atlas-SNP	.											CACNA1H_ENST00000358590,rectum,carcinoma,0,2	CACNA1H	317	2	0			c.T1991C						scavenged	.	T	ALA/VAL,ALA/VAL	178,3466		11,156,1655	4.0	5.0	5.0		1991,1991	4.5	0.2	16	dbSNP_111	5	1823,5663		248,1327,2168	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	64,64	259,1483,3823	CC,CT,TT		24.3521,4.8847,17.9784	possibly-damaging,possibly-damaging	664/2348,664/2354	1252441	2001,9129	1822	3743	5565	SO:0001583	missense	8912	exon9			ATGTGGTCGGGGA	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1991T>C	16.37:g.1252441T>C	ENSP00000334198:p.Val664Ala	Somatic	26	1	0.0384615		WXS	Illumina HiSeq	Phase_I	24	16	0.666667	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	287	0.13141025641025642	8	0.016260162601626018	63	0.17403314917127072	1	0.0017482517482517483	215	0.2836411609498681	T	17.49	3.403103	0.62288	0.048847	0.243521	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96619	-4.07;-4.01	4.47	4.47	0.54385	.	157.429000	0.00166	N	0.000000	T	0.00178	0.0005	L	0.50333	1.59	0.36796	P	0.11489499999999997	P;D	0.53151	0.571;0.958	B;P	0.46026	0.288;0.501	T	0.54669	-0.8259	9	0.51188	T	0.08	.	13.0686	0.59048	0.0:0.0:0.0:1.0	rs4984636;rs57010276;rs4984636	664;664	O95180-2;O95180	.;CAC1H_HUMAN	A	664	ENSP00000334198:V664A;ENSP00000351401:V664A	ENSP00000334198:V664A	V	+	2	0	CACNA1H	1192442	1.000000	0.71417	0.174000	0.22961	0.858000	0.48976	4.766000	0.62279	1.864000	0.54056	0.533000	0.62120	GTC	T|0.874;C|0.126	0.126	strong		0.682	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
ZNF214	7761	hgsc.bcm.edu	37	11	7022717	7022717	+	Missense_Mutation	SNP	T	T	C	rs1156526	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7022717T>C	ENST00000278314.4	-	3	512	c.197A>G	c.(196-198)tAc>tGc	p.Y66C	ZNF214_ENST00000536068.1_Missense_Mutation_p.Y66C|ZNF214_ENST00000531083.1_5'UTR	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		Y -> C (in dbSNP:rs1156526).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		GCCTTGCCAGTAGGAAAAATT	0.393													C|||	2968	0.592652	0.416	0.6354	5008	,	,		17954	0.7073		0.6223	False		,,,				2504	0.6524				p.Y66C	Ovarian(22;251 657 736 21522 46864)	Atlas-SNP	.											.	ZNF214	65	.	0			c.A197G						PASS	.	C	CYS/TYR	1818,2584	629.4+/-395.3	368,1082,751	121.0	127.0	125.0		197	-0.0	0.1	11	dbSNP_87	125	5328,3262	475.1+/-369.0	1670,1988,637	yes	missense	ZNF214	NM_013249.2	194	2038,3070,1388	CC,CT,TT		37.9744,41.2994,44.9969	benign	66/607	7022717	7146,5846	2201	4295	6496	SO:0001583	missense	7761	exon3			TGCCAGTAGGAAA	AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"""Zinc fingers, C2H2-type"", ""-"""	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.197A>G	11.37:g.7022717T>C	ENSP00000278314:p.Tyr66Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	109	60	0.550459	NM_013249	B2R8Q1	Missense_Mutation	SNP	ENST00000278314.4	37	CCDS31418.1	1286	0.5888278388278388	204	0.4146341463414634	222	0.6132596685082873	388	0.6783216783216783	472	0.6226912928759895	C	0.003	-2.540209	0.00143	0.412994	0.620256	ENSG00000149050	ENST00000278314;ENST00000536068	T;T	0.05139	3.49;3.49	4.14	-0.00722	0.14010	Krueppel-associated box (1);	0.520211	0.16344	N	0.218548	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13098	-1.0522	9	0.23891	T	0.37	.	0.8929	0.01257	0.152:0.2747:0.2967:0.2767	rs1156526;rs17193385;rs52834751;rs60011445;rs1156526	66	Q9UL59	ZN214_HUMAN	C	66	ENSP00000278314:Y66C;ENSP00000445373:Y66C	ENSP00000278314:Y66C	Y	-	2	0	ZNF214	6979293	0.000000	0.05858	0.082000	0.20525	0.161000	0.22273	-0.816000	0.04477	-0.081000	0.12662	-0.119000	0.15052	TAC	C|0.558;N|0.000	0.558	strong		0.393	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1		
EMILIN3	90187	hgsc.bcm.edu	37	20	39990614	39990614	+	Missense_Mutation	SNP	C	C	T	rs2235592	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:39990614C>T	ENST00000332312.3	-	4	1787	c.1595G>A	c.(1594-1596)aGc>aAc	p.S532N		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	532			S -> N (in dbSNP:rs2235592). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				TGCCACGAGGCTGTCCAGGAT	0.647													T|||	1418	0.283147	0.3139	0.3012	5008	,	,		18066	0.4772		0.2127	False		,,,				2504	0.1012				p.S532N		Atlas-SNP	.											.	EMILIN3	63	.	0			c.G1595A						PASS	.	T	ASN/SER	1419,2987	678.0+/-403.5	227,965,1011	58.0	59.0	58.0		1595	0.3	1.0	20	dbSNP_98	58	1628,6970	736.7+/-407.0	165,1298,2836	yes	missense	EMILIN3	NM_052846.1	46	392,2263,3847	TT,TC,CC		18.9346,32.2061,23.4313	benign	532/767	39990614	3047,9957	2203	4299	6502	SO:0001583	missense	90187	exon4			ACGAGGCTGTCCA	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1595G>A	20.37:g.39990614C>T	ENSP00000332806:p.Ser532Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Missense_Mutation	SNP	ENST00000332312.3	37	CCDS13316.1	687	0.31456043956043955	143	0.29065040650406504	99	0.27348066298342544	274	0.479020979020979	171	0.22559366754617413	T	0.015	-1.566276	0.00903	0.322061	0.189346	ENSG00000183798	ENST00000332312	T	0.13778	2.56	4.56	0.312	0.15837	.	0.972341	0.08500	N	0.936658	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44892	-0.9298	8	.	.	.	-6.6365	2.2658	0.04078	0.1108:0.2638:0.3711:0.2543	rs2235592	532	Q9NT22	EMIL3_HUMAN	N	532	ENSP00000332806:S532N	.	S	-	2	0	EMILIN3	39424028	0.054000	0.20591	0.964000	0.40570	0.647000	0.38526	-0.098000	0.11024	-0.055000	0.13244	-0.361000	0.07541	AGC	C|0.743;T|0.257	0.257	strong		0.647	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
COL6A1	1291	hgsc.bcm.edu	37	21	47423636	47423636	+	Silent	SNP	C	C	T	rs1053320	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47423636C>T	ENST00000361866.3	+	35	2910	c.2796C>T	c.(2794-2796)tcC>tcT	p.S932S	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	932	C-terminal globular domain.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		AGGCCTCGTCCGGCGCTGCCA	0.657													C|||	1323	0.264177	0.4251	0.2752	5008	,	,		17479	0.1329		0.2555	False		,,,				2504	0.183				p.S932S		Atlas-SNP	.											COL6A1,NS,carcinoma,0,1	COL6A1	101	1	0			c.C2796T						scavenged	.	C		1773,2631		363,1047,792	28.0	24.0	25.0		2796	-9.5	0.0	21	dbSNP_86	25	2479,6115		383,1713,2201	no	coding-synonymous	COL6A1	NM_001848.2		746,2760,2993	TT,TC,CC		28.8457,40.2589,32.7127		932/1029	47423636	4252,8746	2202	4297	6499	SO:0001819	synonymous_variant	1291	exon35			CTCGTCCGGCGCT	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2796C>T	21.37:g.47423636C>T		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	197	95	0.482233	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Silent	SNP	ENST00000361866.3	37	CCDS13727.1																																																																																			C|0.700;T|0.300	0.300	strong		0.657	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489766	32489766	+	Missense_Mutation	SNP	A	A	T	rs41562819		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32489766A>T	ENST00000374975.3	-	2	348	c.286T>A	c.(286-288)Ttc>Atc	p.F96I		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						TCTTCCAGGAAGTCCTTCTGG	0.647																																					p.F96I		Atlas-SNP	.											HLA-DRB5,brain,glioma,0,2	HLA-DRB5	31	2	0			c.T286A						scavenged	.						39.0	34.0	36.0					6																	32489766		2125	4114	6239	SO:0001583	missense	3127	exon2			CCAGGAAGTCCTT		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.286T>A	6.37:g.32489766A>T	ENSP00000364114:p.Phe96Ile	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	24	17	0.708333	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	2.149	-0.394867	0.04899	.	.	ENSG00000198502	ENST00000374975	T	0.00302	8.2	4.72	-9.43	0.00607	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	1.726360	0.03614	N	0.235269	T	0.00012	0.0000	N	0.03154	-0.405	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42344	-0.9457	10	0.06099	T	0.92	.	2.9274	0.05788	0.4968:0.1765:0.2165:0.1102	rs41562819	23;96	Q29973;Q30154	.;DRB5_HUMAN	I	96	ENSP00000364114:F96I	ENSP00000364114:F96I	F	-	1	0	HLA-DRB5	32597744	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-11.144000	0.00004	-5.435000	0.00014	-4.131000	0.00010	TTC	G|0.474;A|0.526	.	strong		0.647	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
CCDC144NL	339184	hgsc.bcm.edu	37	17	20798992	20798992	+	Silent	SNP	C	C	T	rs8073465	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:20798992C>T	ENST00000327925.5	-	1	461	c.342G>A	c.(340-342)aaG>aaA	p.K114K	RP11-344E13.3_ENST00000582324.1_RNA|RP11-344E13.3_ENST00000577860.1_RNA|RP11-344E13.3_ENST00000439794.2_RNA|RP11-344E13.3_ENST00000583962.1_RNA|RP11-344E13.3_ENST00000417232.2_RNA|RNU6-1178P_ENST00000516674.1_RNA|RP11-344E13.3_ENST00000577537.1_RNA	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	114										large_intestine(3)|lung(3)|skin(1)	7						GCCATTACCTCTTCTTCCTAT	0.652													c|||	497	0.0992412	0.0212	0.0865	5008	,	,		14967	0.1766		0.1501	False		,,,				2504	0.0818				p.K114K		Atlas-SNP	.											.	CCDC144NL	34	.	0			c.G342A						PASS	.	C		228,4178	130.2+/-166.9	12,204,1987	74.0	79.0	77.0		342	-1.8	0.0	17	dbSNP_116	77	1217,7383	229.0+/-263.8	74,1069,3157	no	coding-synonymous	CCDC144NL	NM_001004306.1		86,1273,5144	TT,TC,CC		14.1512,5.1748,11.1103		114/222	20798992	1445,11561	2203	4300	6503	SO:0001819	synonymous_variant	339184	exon1			TTACCTCTTCTTC		CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212			33735	protein-coding gene	gene with protein product							Standard	NM_001004306		Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.342G>A	17.37:g.20798992C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	162	76	0.469136	NM_001004306		Silent	SNP	ENST00000327925.5	37	CCDS32591.1																																																																																			C|0.883;T|0.117	0.117	strong		0.652	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255361.2	NM_001004306	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45502758	45502758	+	Missense_Mutation	SNP	G	G	A	rs367993178		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:45502758G>A	ENST00000291574.4	+	14	1988	c.1813G>A	c.(1813-1815)Gtt>Att	p.V605I		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	605					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)	p.V605F(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						CGTGGGCGGCGTTTTGTGCGT	0.483																																					p.V605I		Atlas-SNP	.											TRAPPC10,colon,carcinoma,0,1	TRAPPC10	109	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1813A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	194.0	163.0	173.0		1813	-3.0	0.0	21		173	1,8599	1.2+/-3.3	0,1,4299	no	missense	TRAPPC10	NM_003274.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	605/1260	45502758	1,13005	2203	4300	6503	SO:0001583	missense	7109	exon14			GGCGGCGTTTTGT	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.1813G>A	21.37:g.45502758G>A	ENSP00000291574:p.Val605Ile	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	177	72	0.40678	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	37	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	G	6.340	0.430748	0.12045	0.0	1.16E-4	ENSG00000160218	ENST00000291574	T	0.40756	1.02	5.58	-2.99	0.05497	.	0.845087	0.10694	N	0.644857	T	0.22666	0.0547	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.21965	-1.0230	10	0.23891	T	0.37	.	8.3648	0.32380	0.6995:0.0:0.1746:0.1259	.	605	P48553	TPC10_HUMAN	I	605	ENSP00000291574:V605I	ENSP00000291574:V605I	V	+	1	0	TRAPPC10	44327186	0.001000	0.12720	0.000000	0.03702	0.031000	0.12232	1.285000	0.33261	-0.457000	0.07033	-0.768000	0.03414	GTT	.	.	weak		0.483	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
COL9A3	1299	hgsc.bcm.edu	37	20	61463522	61463522	+	Missense_Mutation	SNP	C	C	A	rs751557	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:61463522C>A	ENST00000343916.3	+	25	1307	c.1304C>A	c.(1303-1305)gCa>gAa	p.A435E		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	435	Triple-helical region 3 (COL3).		A -> E (in dbSNP:rs751557). {ECO:0000269|PubMed:11565064, ECO:0000269|PubMed:8586434}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					GGAGGTGCCGCAGGCCCTAAG	0.602													C|||	1066	0.212859	0.447	0.1729	5008	,	,		20947	0.0496		0.2177	False		,,,				2504	0.0879				p.A435E		Atlas-SNP	.											COL9A3,caecum,carcinoma,0,1	COL9A3	70	1	0			c.C1304A						PASS	.	C	GLU/ALA	1747,2659	513.9+/-368.5	338,1071,794	58.0	61.0	60.0		1304	4.2	0.4	20	dbSNP_86	60	1774,6826	317.9+/-313.4	185,1404,2711	yes	missense	COL9A3	NM_001853.3	107	523,2475,3505	AA,AC,CC		20.6279,39.6505,27.0721	probably-damaging	435/685	61463522	3521,9485	2203	4300	6503	SO:0001583	missense	1299	exon25			GTGCCGCAGGCCC	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.1304C>A	20.37:g.61463522C>A	ENSP00000341640:p.Ala435Glu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	167	89	0.532934	NM_001853	Q13681|Q9H4G9|Q9UPE2	Missense_Mutation	SNP	ENST00000343916.3	37	CCDS13505.1	464	0.21245421245421245	204	0.4146341463414634	66	0.18232044198895028	32	0.055944055944055944	162	0.21372031662269128	C	10.51	1.371130	0.24771	0.396505	0.206279	ENSG00000092758	ENST00000343916	D	0.93712	-3.27	5.2	4.23	0.50019	.	0.843935	0.10592	N	0.656672	T	0.00012	0.0000	N	0.05078	-0.115	0.80722	P	0.0	B	0.23185	0.081	B	0.25506	0.061	T	0.04664	-1.0935	9	0.07325	T	0.83	.	12.5103	0.56002	0.0:0.868:0.0:0.132	rs751557;rs59729765;rs751557	435	Q14050	CO9A3_HUMAN	E	435	ENSP00000341640:A435E	ENSP00000341640:A435E	A	+	2	0	COL9A3	60933967	0.003000	0.15002	0.425000	0.26659	0.227000	0.25037	0.934000	0.28910	2.584000	0.87258	0.462000	0.41574	GCA	T|0.003;G|0.006	.	strong		0.602	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
DNMBP	23268	hgsc.bcm.edu	37	10	101639796	101639796	+	Silent	SNP	G	G	A	rs2255901	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:101639796G>A	ENST00000324109.4	-	16	4411	c.4320C>T	c.(4318-4320)tcC>tcT	p.S1440S	DNMBP_ENST00000540316.1_Silent_p.S376S|DNMBP_ENST00000342239.3_Silent_p.S1464S|DNMBP_ENST00000543621.1_Silent_p.S686S	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1440	Ser-rich.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		GCTGGGAGGTGGAGTCTGGGT	0.532													A|||	2326	0.464457	0.5386	0.4798	5008	,	,		21013	0.2679		0.5388	False		,,,				2504	0.4796				p.S1440S		Atlas-SNP	.											DNMBP,NS,adenoma,0,1	DNMBP	173	1	0			c.C4320T						PASS	.			2356,2050	568.5+/-382.4	629,1098,476	154.0	150.0	151.0		4320	-1.7	0.0	10	dbSNP_100	151	4503,4097	562.1+/-387.9	1190,2123,987	no	coding-synonymous	DNMBP	NM_015221.2		1819,3221,1463	AA,AG,GG		47.6395,46.5275,47.2628		1440/1578	101639796	6859,6147	2203	4300	6503	SO:0001819	synonymous_variant	23268	exon16			GGAGGTGGAGTCT	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.4320C>T	10.37:g.101639796G>A		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	154	143	0.928571	NM_015221	Q8IVY3|Q9Y2L3	Silent	SNP	ENST00000324109.4	37	CCDS7485.1																																																																																			G|0.502;A|0.498	0.498	strong		0.532	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056549	26056549	+	Silent	SNP	A	A	G	rs10425	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:26056549A>G	ENST00000343677.2	-	1	150	c.108T>C	c.(106-108)tcT>tcC	p.S36S		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	36	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						CCGGGGGACCAGACGCCTTAC	0.632													G|||	3810	0.760783	0.9281	0.6744	5008	,	,		14394	0.8552		0.6372	False		,,,				2504	0.6258				p.S36S		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.T108C						PASS	.	G		3896,510		1730,436,37	44.0	52.0	50.0		108	-10.2	0.1	6	dbSNP_52	50	5650,2950		1879,1892,529	no	coding-synonymous	HIST1H1C	NM_005319.3		3609,2328,566	GG,GA,AA		34.3023,11.5751,26.6031		36/214	26056549	9546,3460	2203	4300	6503	SO:0001819	synonymous_variant	3006	exon1			GGGACCAGACGCC	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.108T>C	6.37:g.26056549A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	87	85	0.977012	NM_005319	A8K4I2	Silent	SNP	ENST00000343677.2	37	CCDS4577.1																																																																																			A|0.253;G|0.747	0.747	strong		0.632	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
ARL13A	392509	hgsc.bcm.edu	37	X	100243459	100243459	+	Intron	SNP	G	G	T	rs3934462	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:100243459G>T	ENST00000450049.2	+	7	857					NM_001162491.1	NP_001155963.1	Q5H913	AR13A_HUMAN	ADP-ribosylation factor-like 13A						small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(1)|ovary(1)	2						CTAGGAGAATGAGAGCTCAGA	0.378													T|||	3448	0.913377	0.6551	0.6859	3775	,	,		14730	0.7321		0.6918	False		,,,				2504	0.6871				p.M279I		Atlas-SNP	.											.	ARL13A	7	.	0			c.G837T						PASS	.	T	ILE/MET,ILE/MET,	2725,439		963,315,484,19,86	48.0	43.0	45.0		837,837,	-5.2	0.0	X	dbSNP_108	45	5876,549		1952,348,1624,18,165	yes	missense,missense,intron	ARL13A	NM_001012990.3,NM_001162490.1,NM_001162491.1	10,10,	2915,663,2108,37,251	TT,TG,T,GG,G		8.5447,13.8748,10.3035	benign,benign,	279/291,279/291,	100243459	8601,988	1867	4107	5974	SO:0001627	intron_variant	392509	exon8			GAGAATGAGAGCT		CCDS55463.1	Xq22.1	2014-05-09	2005-11-18	2005-11-18	ENSG00000174225	ENSG00000174225		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	31709	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 13"""	ARL13			Standard	NM_001162491		Approved		uc011mrf.2	Q5H913	OTTHUMG00000022013	ENST00000450049.2:c.744+187G>T	X.37:g.100243459G>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	184	183	0.994565	NM_001162490	B2RTT6|B4DX50	Missense_Mutation	SNP	ENST00000450049.2	37	CCDS55463.1																																																																																			G|0.109;T|0.891	0.891	strong		0.378	ARL13A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000057504.2	XM_373358	
ZNF860	344787	hgsc.bcm.edu	37	3	32031643	32031643	+	Missense_Mutation	SNP	A	A	G	rs386659897|rs13065048	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:32031643A>G	ENST00000360311.4	+	2	1621	c.1072A>G	c.(1072-1074)Aca>Gca	p.T358A		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	358					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						TTCACACCTCACACAACACAC	0.403													a|||	2357	0.470647	0.7988	0.3602	5008	,	,		21395	0.4534		0.1968	False		,,,				2504	0.4049				p.T358A		Atlas-SNP	.											.	ZNF860	96	.	0			c.A1072G						PASS	.	G	ALA/THR	933,451		325,283,84	48.0	50.0	49.0		1072	-0.7	0.0	3	dbSNP_121	49	608,2574		57,494,1040	no	missense	ZNF860	NM_001137674.2	58	382,777,1124	GG,GA,AA		19.1075,32.5867,33.7495	benign	358/633	32031643	1541,3025	692	1591	2283	SO:0001583	missense	344787	exon2			CACCTCACACAAC	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1072A>G	3.37:g.32031643A>G	ENSP00000373274:p.Thr358Ala	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	254	74	0.291339	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	913	0.41804029304029305	385	0.782520325203252	126	0.34806629834254144	249	0.4353146853146853	153	0.20184696569920843	a	0.001	-2.874949	0.00062	0.674133	0.191075	ENSG00000197385	ENST00000360311	T	0.06849	3.25	0.345	-0.691	0.11305	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.22034	-1.0228	7	.	.	.	.	2.7881	0.05379	0.2503:0.0:0.5021:0.2476	rs13065048;rs52806446;rs60333482;rs13065048	358	A6NHJ4	ZN860_HUMAN	A	358	ENSP00000373274:T358A	.	T	+	1	0	ZNF860	32006647	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.246000	0.18160	-2.012000	0.00950	-2.005000	0.00442	ACA	A|0.615;G|0.385	0.385	strong		0.403	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
CTNNA1	1495	hgsc.bcm.edu	37	5	138266552	138266552	+	Silent	SNP	C	C	G	rs11552052	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:138266552C>G	ENST00000302763.7	+	16	2316	c.2226C>G	c.(2224-2226)gtC>gtG	p.V742V	CTNNA1_ENST00000540387.1_Silent_p.V372V|CTNNA1_ENST00000355078.5_Silent_p.V639V|CTNNA1_ENST00000518825.1_Silent_p.V742V	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	742					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)			CATCGGATGTCATCAGTGCTG	0.473													C|||	46	0.0091853	0.0008	0.0202	5008	,	,		20074	0.0		0.0288	False		,,,				2504	0.002				p.V742V		Atlas-SNP	.											.	CTNNA1	114	.	0			c.C2226G						PASS	.	C		25,4381	31.7+/-61.6	0,25,2178	86.0	88.0	87.0		2226	2.3	1.0	5	dbSNP_120	87	259,8341	101.0+/-162.3	1,257,4042	no	coding-synonymous	CTNNA1	NM_001903.2		1,282,6220	GG,GC,CC		3.0116,0.5674,2.1836		742/907	138266552	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	1495	exon16			GGATGTCATCAGT	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.2226C>G	5.37:g.138266552C>G		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	235	88	0.374468	NM_001903	Q12795|Q8N1C0	Silent	SNP	ENST00000302763.7	37	CCDS34243.1																																																																																			C|0.983;G|0.017	0.017	strong		0.473	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	
OR51Q1	390061	hgsc.bcm.edu	37	11	5443700	5443700	+	Silent	SNP	C	C	T	rs2736588	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5443700C>T	ENST00000300778.4	+	1	360	c.270C>T	c.(268-270)aaC>aaT	p.N90N	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	90						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCTGGTTCAACGTTCGTAGAA	0.517													C|||	2272	0.453674	0.2799	0.3991	5008	,	,		23503	0.7024		0.3986	False		,,,				2504	0.5276				p.N90N		Atlas-SNP	.											.	OR51Q1	79	.	0			c.C270T						PASS	.	C		1332,3070	447.3+/-348.3	203,926,1072	158.0	141.0	147.0		270	-2.3	0.0	11	dbSNP_100	147	3373,5221	499.6+/-375.0	676,2021,1600	no	coding-synonymous	OR51Q1	NM_001004757.2		879,2947,2672	TT,TC,CC		39.2483,30.259,36.2034		90/318	5443700	4705,8291	2201	4297	6498	SO:0001819	synonymous_variant	390061	exon1			GTTCAACGTTCGT	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.270C>T	11.37:g.5443700C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	191	102	0.534031	NM_001004757	B2RNN1	Silent	SNP	ENST00000300778.4	37	CCDS31381.1																																																																																			C|0.602;T|0.398	0.398	strong		0.517	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
HKDC1	80201	hgsc.bcm.edu	37	10	70992664	70992664	+	Missense_Mutation	SNP	C	C	T	rs874556	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70992664C>T	ENST00000354624.5	+	3	504	c.371C>T	c.(370-372)aCa>aTa	p.T124I	RP11-227H15.4_ENST00000450995.1_RNA|HKDC1_ENST00000395086.2_Missense_Mutation_p.T124I	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	124	Hexokinase type-1 1.		T -> I (in dbSNP:rs874556).		carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						GGGAACGGCACAGAGGTACCT	0.577													C|||	2674	0.533946	0.5545	0.4539	5008	,	,		19703	0.7361		0.4135	False		,,,				2504	0.4785				p.T124I		Atlas-SNP	.											.	HKDC1	98	.	0			c.C371T						PASS	.	C	ILE/THR	2330,2076	605.6+/-390.6	624,1082,497	149.0	132.0	138.0		371	1.7	0.0	10	dbSNP_86	138	3568,5032	518.8+/-379.3	770,2028,1502	yes	missense	HKDC1	NM_025130.3	89	1394,3110,1999	TT,TC,CC		41.4884,47.1176,45.3483	benign	124/918	70992664	5898,7108	2203	4300	6503	SO:0001583	missense	80201	exon3			ACGGCACAGAGGT		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.371C>T	10.37:g.70992664C>T	ENSP00000346643:p.Thr124Ile	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	1194	0.5467032967032966	288	0.5853658536585366	147	0.40607734806629836	442	0.7727272727272727	317	0.4182058047493404	C	12.55	1.972198	0.34754	0.528824	0.414884	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.99042	-5.36;-5.36	4.6	1.69	0.24217	Hexokinase, N-terminal (1);	0.820588	0.11075	N	0.602464	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.44190	-0.9344	9	0.44086	T	0.13	0.2826	5.6728	0.17731	0.2742:0.5743:0.0:0.1514	rs874556;rs11555769;rs17475150;rs52817419;rs57880774;rs874556	124	Q2TB90	HKDC1_HUMAN	I	124	ENSP00000346643:T124I;ENSP00000378521:T124I	ENSP00000346643:T124I	T	+	2	0	HKDC1	70662670	0.000000	0.05858	0.001000	0.08648	0.226000	0.24999	1.080000	0.30779	0.168000	0.19655	0.561000	0.74099	ACA	C|0.493;T|0.507	0.507	strong		0.577	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130	
FMO3	2328	hgsc.bcm.edu	37	1	171083242	171083242	+	Missense_Mutation	SNP	A	A	G	rs2266780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:171083242A>G	ENST00000367755.4	+	7	1034	c.923A>G	c.(922-924)gAg>gGg	p.E308G	FMO3_ENST00000392085.2_Missense_Mutation_p.E308G|FMO3_ENST00000542847.1_Missense_Mutation_p.E288G|FMO3_ENST00000538429.1_Missense_Mutation_p.E245G	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	308			E -> G (16% reduction in catalytic efficiency toward trimethylamine and 40% increase toward benzydamine and methyl p- tolyl sulfide; dbSNP:rs2266780). {ECO:0000269|PubMed:10479479, ECO:0000269|PubMed:17050781, ECO:0000269|PubMed:9536088, ECO:0000269|Ref.4}.		drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	GAATTCACAGAGACCTCGGCC	0.463													A|||	458	0.0914537	0.0189	0.0821	5008	,	,		19038	0.1687		0.172	False		,,,				2504	0.0337				p.E308G		Atlas-SNP	.											.	FMO3	73	.	0			c.A923G	GRCh37	CM992885	FMO3	M	rs2266780	PASS	.	A	GLY/GLU,GLY/GLU	189,4217	118.8+/-156.5	6,177,2020	149.0	131.0	137.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	923,923	3.6	1.0	1	dbSNP_100	137	1619,6981	300.5+/-305.0	157,1305,2838	yes	missense,missense	FMO3	NM_001002294.2,NM_006894.5	98,98	163,1482,4858	GG,GA,AA		18.8256,4.2896,13.9013	benign,benign	308/533,308/533	171083242	1808,11198	2203	4300	6503	SO:0001583	missense	2328	exon7			TCACAGAGACCTC	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.923A>G	1.37:g.171083242A>G	ENSP00000356729:p.Glu308Gly	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	205	97	0.473171	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	37	CCDS1292.1	283	0.1295787545787546	9	0.018292682926829267	29	0.08011049723756906	106	0.1853146853146853	139	0.18337730870712401	A	15.62	2.887923	0.52014	0.042896	0.188256	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.62498	0.02;0.02;0.02;0.02	4.73	3.58	0.41010	.	0.153914	0.64402	D	0.000020	T	0.57213	0.2038	L	0.45470	1.425	0.20403	P	0.9999083861	D;P;P	0.89917	1.0;0.713;0.939	D;P;P	0.80764	0.994;0.673;0.859	T	0.55976	-0.8055	9	0.18710	T	0.47	-22.3006	11.4047	0.49892	0.8481:0.1519:0.0:0.0	rs2266780;rs17564742;rs57076237;rs2266780	245;288;308	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	G	308;308;288;245	ENSP00000356729:E308G;ENSP00000375935:E308G;ENSP00000444073:E288G;ENSP00000439500:E245G	ENSP00000356729:E308G	E	+	2	0	FMO3	169349866	1.000000	0.71417	0.959000	0.39883	0.591000	0.36615	5.276000	0.65580	0.728000	0.32382	0.528000	0.53228	GAG	A|0.877;G|0.123	0.123	strong		0.463	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	
TNXB	7148	hgsc.bcm.edu	37	6	32025980	32025980	+	Silent	SNP	G	G	A	rs12196385	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32025980G>A	ENST00000375244.3	-	22	7881	c.7680C>T	c.(7678-7680)gaC>gaT	p.D2560D	TNXB_ENST00000375247.2_Silent_p.D2560D			P22105	TENX_HUMAN	tenascin XB	2620	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GGGGCCGCCCGTCCCTGTCCT	0.652													G|||	564	0.11262	0.1626	0.0432	5008	,	,		15128	0.0347		0.0994	False		,,,				2504	0.1881				p.D2560D		Atlas-SNP	.											.	TNXB	553	.	0			c.C7680T						PASS	.	G		418,2146		33,352,897	55.0	63.0	60.0		7680	-8.4	0.1	6	dbSNP_120	60	448,4642		25,398,2122	no	coding-synonymous	TNXB	NM_019105.6		58,750,3019	AA,AG,GG		8.8016,16.3027,11.3143		2560/4243	32025980	866,6788	1282	2545	3827	SO:0001819	synonymous_variant	7148	exon22			CCGCCCGTCCCTG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7680C>T	6.37:g.32025980G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				G|0.900;A|0.100	0.100	strong		0.652	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
HIST3H3	8290	hgsc.bcm.edu	37	1	228612892	228612892	+	Silent	SNP	G	G	A	rs56336130	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:228612892G>A	ENST00000366696.1	-	1	134	c.135C>T	c.(133-135)ggC>ggT	p.G45G		NM_003493.2	NP_003484.1	Q16695	H31T_HUMAN	histone cluster 3, H3	45					telomere maintenance (GO:0000723)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(2)|prostate(2)|skin(1)	6		Prostate(94;0.0724)				GCGCCACCGTGCCGGGCCGGT	0.677													g|||	217	0.0433307	0.0061	0.0519	5008	,	,		13044	0.0139		0.0746	False		,,,				2504	0.0859				p.G45G		Atlas-SNP	.											.	HIST3H3	20	.	0			c.C135T						PASS	.	G		76,4330	61.1+/-98.1	1,74,2128	52.0	58.0	56.0		135	-0.3	0.3	1	dbSNP_129	56	746,7854	172.5+/-223.2	39,668,3593	no	coding-synonymous	HIST3H3	NM_003493.2		40,742,5721	AA,AG,GG		8.6744,1.7249,6.3202		45/137	228612892	822,12184	2203	4300	6503	SO:0001819	synonymous_variant	8290	exon1			CACCGTGCCGGGC	Z49861	CCDS1572.1	1q42.13	2012-09-19	2006-10-11	2003-02-21	ENSG00000168148	ENSG00000168148		"""Histones / Replication-dependent"""	4778	protein-coding gene	gene with protein product		602820	"""H3 histone family, member T"", ""histone 3, H3"""	H3FT		8834248, 12408966	Standard	NM_003493		Approved	H3t, H3/g, H3.4	uc001hsx.1	Q16695	OTTHUMG00000040044	ENST00000366696.1:c.135C>T	1.37:g.228612892G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_003493	B2R5K3|Q6FGU4	Silent	SNP	ENST00000366696.1	37	CCDS1572.1																																																																																			G|0.942;A|0.058	0.058	strong		0.677	HIST3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096595.2	NM_003493	
RAB11FIP2	22841	hgsc.bcm.edu	37	10	119774598	119774598	+	Missense_Mutation	SNP	T	T	A	rs58533443	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:119774598T>A	ENST00000355624.3	-	4	1728	c.1289A>T	c.(1288-1290)aAt>aTt	p.N430I	RAB11FIP2_ENST00000369199.3_Missense_Mutation_p.N450I|RAB11FIP2_ENST00000476207.1_5'UTR|RP11-354M20.3_ENST00000451610.2_RNA|RP11-354M20.3_ENST00000595446.1_RNA	NM_014904.2	NP_055719.1	Q7L804	RFIP2_HUMAN	RAB11 family interacting protein 2 (class I)	430					establishment of cell polarity (GO:0030010)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(8)	19		Colorectal(252;0.235)		all cancers(201;0.0238)		GAGGTCTTCATTGCTTGTTGG	0.358													T|||	309	0.0617013	0.0431	0.072	5008	,	,		17272	0.1806		0.006	False		,,,				2504	0.0143				p.N430I		Atlas-SNP	.											.	RAB11FIP2	39	.	0			c.A1289T						PASS	.	T	ILE/ASN	188,4218	118.8+/-156.5	4,180,2019	90.0	85.0	87.0		1289	-3.6	1.0	10	dbSNP_129	87	42,8558	27.9+/-77.7	0,42,4258	yes	missense	RAB11FIP2	NM_014904.2	149	4,222,6277	AA,AT,TT		0.4884,4.2669,1.7684	benign	430/513	119774598	230,12776	2203	4300	6503	SO:0001583	missense	22841	exon4			TCTTCATTGCTTG	AY037299	CCDS7602.1	10q26.12	2004-07-22			ENSG00000107560	ENSG00000107560			29152	protein-coding gene	gene with protein product		608599				11994279, 10231032	Standard	NM_014904		Approved	KIAA0941, nRip11, Rab11-FIP2	uc001ldj.2	Q7L804	OTTHUMG00000019128	ENST00000355624.3:c.1289A>T	10.37:g.119774598T>A	ENSP00000347839:p.Asn430Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	NM_014904	A6NEI4|Q3I768|Q9Y2F0	Missense_Mutation	SNP	ENST00000355624.3	37	CCDS7602.1	149	0.06822344322344322	16	0.032520325203252036	18	0.049723756906077346	112	0.1958041958041958	3	0.00395778364116095	T	14.14	2.446920	0.43429	0.042669	0.004884	ENSG00000107560	ENST00000355624;ENST00000369199	T;T	0.63913	-0.07;-0.05	5.92	-3.59	0.04583	.	1.103000	0.06527	N	0.740675	T	0.00039	0.0001	N	0.14661	0.345	0.39854	P	0.02671100000000004	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09143	-1.0688	9	0.49607	T	0.09	-0.1284	9.1794	0.37131	0.0:0.5334:0.2088:0.2578	rs58533443	450;430	Q3I768;Q7L804	.;RFIP2_HUMAN	I	430;450	ENSP00000347839:N430I;ENSP00000358200:N450I	ENSP00000347839:N430I	N	-	2	0	RAB11FIP2	119764588	0.296000	0.24398	0.979000	0.43373	0.990000	0.78478	-0.870000	0.04228	-0.270000	0.09285	0.528000	0.53228	AAT	T|0.967;A|0.033	0.033	strong		0.358	RAB11FIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050583.1	NM_014904	
CCDC107	203260	hgsc.bcm.edu	37	9	35660901	35660901	+	Missense_Mutation	SNP	C	C	T	rs2275420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35660901C>T	ENST00000426546.2	+	5	635	c.569C>T	c.(568-570)tCt>tTt	p.S190F	ARHGEF39_ENST00000378395.2_3'UTR|RMRP_ENST00000602361.1_lincRNA|CCDC107_ENST00000378406.1_3'UTR|CCDC107_ENST00000378409.3_Intron|ARHGEF39_ENST00000343259.3_3'UTR|CCDC107_ENST00000378407.3_3'UTR|ARHGEF39_ENST00000378387.3_3'UTR|CCDC107_ENST00000327351.2_Intron|ARHGEF39_ENST00000490970.1_5'Flank|CCDC107_ENST00000421582.2_3'UTR	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	190			S -> F (in dbSNP:rs2275420).			integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GACAAAGTCTCTGAAACTGGA	0.542													C|||	758	0.151358	0.3336	0.0879	5008	,	,		19570	0.0427		0.1312	False		,,,				2504	0.0828				p.S190F		Atlas-SNP	.											.	CCDC107	12	.	0			c.C569T						PASS	.	C	PHE/SER,,,,	1323,3083	445.1+/-347.6	206,911,1086	120.0	128.0	126.0		569,,,,	1.2	0.0	9	dbSNP_100	126	1168,7432	238.5+/-269.9	79,1010,3211	yes	missense,intron,intron,utr-3,utr-3	C9orf100,CCDC107	NM_174923.2,NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2	155,,,,	285,1921,4297	TT,TC,CC		13.5814,30.0272,19.1527	probably-damaging,,,,	190/284,,,,	35660901	2491,10515	2203	4300	6503	SO:0001583	missense	203260	exon5			AAGTCTCTGAAAC	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.569C>T	9.37:g.35660901C>T	ENSP00000414964:p.Ser190Phe	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Missense_Mutation	SNP	ENST00000426546.2	37	CCDS6583.1	327	0.14972527472527472	163	0.3313008130081301	32	0.08839779005524862	26	0.045454545454545456	106	0.13984168865435356	C	9.796	1.179221	0.21787	0.300272	0.135814	ENSG00000159884	ENST00000426546	T	0.25085	1.82	5.44	1.16	0.20824	.	1.492810	0.03871	N	0.275557	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	D	0.55605	0.972	P	0.53549	0.729	T	0.25187	-1.0139	9	0.59425	D	0.04	-0.0036	3.0663	0.06215	0.3277:0.434:0.15:0.0883	rs2275420;rs52801812;rs59963800;rs2275420	190	Q8WV48	CC107_HUMAN	F	190	ENSP00000414964:S190F	ENSP00000414964:S190F	S	+	2	0	CCDC107	35650901	0.000000	0.05858	0.000000	0.03702	0.248000	0.25809	0.104000	0.15313	0.358000	0.24211	0.655000	0.94253	TCT	C|0.831;T|0.169	0.169	strong		0.542	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923	
GAS8	2622	hgsc.bcm.edu	37	16	90095596	90095596	+	Intron	SNP	A	A	G	rs55742939	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90095596A>G	ENST00000268699.4	+	2	212				GAS8_ENST00000536122.1_Intron|GAS8_ENST00000540721.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.I52T	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		ggggcaggctatggggcagcc	0.662													a|||	2317	0.46266	0.3767	0.4611	5008	,	,		15261	0.63		0.3757	False		,,,				2504	0.4969				p.I52T		Atlas-SNP	.											.	C16orf3	14	.	0			c.T155C						PASS	.						20.0	22.0	22.0					16																	90095596		2196	4299	6495	SO:0001627	intron_variant	750	exon1			CAGGCTATGGGGC	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1466A>G	16.37:g.90095596A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	6	0.075	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	a	0.042	-1.279284	0.01410	.	.	ENSG00000221819	ENST00000408886	T	0.51817	0.69	.	.	.	.	.	.	.	.	T	0.17280	0.0415	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14531	-1.0469	6	.	.	.	.	.	.	.	rs55742939	60	O95177	CP003_HUMAN	T	52	ENSP00000386218:I52T	.	I	-	2	0	C16orf3	88623097	0.006000	0.16342	0.000000	0.03702	0.009000	0.06853	-1.935000	0.01550	-2.550000	0.00480	-1.973000	0.00462	ATA	A|0.500;G|0.500	0.500	weak		0.662	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
ELSPBP1	64100	hgsc.bcm.edu	37	19	48525466	48525466	+	Missense_Mutation	SNP	C	C	T	rs35700000	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48525466C>T	ENST00000339841.2	+	6	732	c.554C>T	c.(553-555)cCg>cTg	p.P185L	ELSPBP1_ENST00000597519.1_Missense_Mutation_p.P37L	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	185	Fibronectin type-II 4. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		TGTCACTTTCCGTTCAACTAT	0.443													c|||	69	0.013778	0.0023	0.0072	5008	,	,		20502	0.0		0.0288	False		,,,				2504	0.0327				p.P185L		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.C554T						PASS	.	C	LEU/PRO	19,4387	27.2+/-55.0	0,19,2184	192.0	171.0	178.0		554	3.7	0.9	19	dbSNP_126	178	252,8348	99.5+/-161.0	5,242,4053	yes	missense	ELSPBP1	NM_022142.4	98	5,261,6237	TT,TC,CC		2.9302,0.4312,2.0837	probably-damaging	185/224	48525466	271,12735	2203	4300	6503	SO:0001583	missense	64100	exon6			ACTTTCCGTTCAA	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.554C>T	19.37:g.48525466C>T	ENSP00000340660:p.Pro185Leu	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	202	108	0.534653	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	35	0.016025641025641024	4	0.008130081300813009	7	0.019337016574585635	0	0.0	24	0.0316622691292876	C	15.92	2.973836	0.53720	0.004312	0.029302	ENSG00000169393	ENST00000339841	D	0.93488	-3.23	3.66	3.66	0.41972	Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.000000	0.48286	D	0.000187	D	0.92593	0.7647	H	0.94658	3.565	0.39211	D	0.963313	D	0.89917	1.0	D	0.87578	0.998	D	0.91856	0.5495	10	0.87932	D	0	.	7.6915	0.28571	0.0:0.8769:0.0:0.1231	rs35700000	185	Q96BH3	ESPB1_HUMAN	L	185	ENSP00000340660:P185L	ENSP00000340660:P185L	P	+	2	0	ELSPBP1	53217278	0.967000	0.33354	0.940000	0.37924	0.712000	0.41017	2.829000	0.48128	1.968000	0.57251	0.609000	0.83330	CCG	C|0.980;T|0.020	0.020	strong		0.443	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
NID1	4811	hgsc.bcm.edu	37	1	236208773	236208773	+	Missense_Mutation	SNP	C	C	T	rs10733133	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:236208773C>T	ENST00000264187.6	-	3	818	c.736G>A	c.(736-738)Gtt>Att	p.V246I	NID1_ENST00000366595.3_Missense_Mutation_p.V246I	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	246	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.		V -> I (in dbSNP:rs10733133). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2574658, ECO:0000269|PubMed:7557988, ECO:0000269|Ref.6}.		basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	AAATTTTCAACTGATTCCCTG	0.363													T|||	2941	0.58726	0.6369	0.5562	5008	,	,		17367	0.7063		0.4334	False		,,,				2504	0.5777				p.V246I		Atlas-SNP	.											.	NID1	196	.	0			c.G736A						PASS	.	T	ILE/VAL	2717,1689	509.9+/-367.4	824,1069,310	77.0	83.0	81.0		736	-1.0	0.0	1	dbSNP_120	81	3699,4901	619.4+/-396.9	801,2097,1402	yes	missense	NID1	NM_002508.2	29	1625,3166,1712	TT,TC,CC		43.0116,38.3341,49.3311	benign	246/1248	236208773	6416,6590	2203	4300	6503	SO:0001583	missense	4811	exon3			TTTCAACTGATTC	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.736G>A	1.37:g.236208773C>T	ENSP00000264187:p.Val246Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	123	47	0.382114	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	1220	0.5586080586080586	310	0.6300813008130082	186	0.5138121546961326	394	0.6888111888111889	330	0.43535620052770446	T	0.212	-1.035412	0.02029	0.616659	0.430116	ENSG00000116962	ENST00000264187;ENST00000366595	T;T	0.73258	-0.73;-0.73	5.79	-0.963	0.10330	Nidogen, extracellular domain (3);	0.272597	0.43579	N	0.000544	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.39272	-0.9622	9	0.02654	T	1	.	7.3445	0.26656	0.0:0.2555:0.3858:0.3587	rs10733133;rs12725765;rs16833218;rs17846375;rs17859412;rs52819413;rs59472471;rs10733133	246;246	P14543-2;P14543	.;NID1_HUMAN	I	246	ENSP00000264187:V246I;ENSP00000355554:V246I	ENSP00000264187:V246I	V	-	1	0	NID1	234275396	0.000000	0.05858	0.016000	0.15963	0.196000	0.23810	-1.229000	0.02945	-0.363000	0.08101	-0.254000	0.11334	GTT	C|0.469;N|0.000	.	strong		0.363	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
SMCHD1	23347	hgsc.bcm.edu	37	18	2750477	2750477	+	Silent	SNP	A	A	G	rs2304859	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:2750477A>G	ENST00000320876.6	+	32	4475	c.4137A>G	c.(4135-4137)gcA>gcG	p.A1379A	SMCHD1_ENST00000261598.8_Silent_p.A1379A|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1379					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						ACAAAGATGCATCCTTCTTAG	0.313													G|||	1933	0.385982	0.2685	0.4467	5008	,	,		17899	0.5218		0.2634	False		,,,				2504	0.4877				p.A1379A		Atlas-SNP	.											SMCHD1,colon,carcinoma,+1,3	SMCHD1	88	3	0			c.A4137G						PASS	.	G		955,2687		126,703,992	45.0	42.0	43.0		4137	0.8	1.0	18	dbSNP_100	43	2297,5879		311,1675,2102	no	coding-synonymous	SMCHD1	NM_015295.2		437,2378,3094	GG,GA,AA		28.0944,26.2219,27.5173		1379/2006	2750477	3252,8566	1821	4088	5909	SO:0001819	synonymous_variant	23347	exon32			AGATGCATCCTTC	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.4137A>G	18.37:g.2750477A>G		Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			G|0.336;N|0.000	0.336	strong		0.313	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
ZNF454	285676	hgsc.bcm.edu	37	5	178391902	178391902	+	Missense_Mutation	SNP	A	A	C	rs12719860	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:178391902A>C	ENST00000320129.3	+	5	800	c.497A>C	c.(496-498)gAt>gCt	p.D166A	ZNF454_ENST00000519564.1_Missense_Mutation_p.D166A	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	166			D -> A (in dbSNP:rs12719860). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		CTTCACAGTGATCAAAGTCAG	0.433													C|||	3306	0.660144	0.6437	0.6931	5008	,	,		19744	0.6597		0.6869	False		,,,				2504	0.6319				p.D166A		Atlas-SNP	.											.	ZNF454	99	.	0			c.A497C						PASS	.	C	ALA/ASP,ALA/ASP,ALA/ASP	2820,1586	495.1+/-363.2	908,1004,291	72.0	71.0	71.0		497,497,497	0.7	0.0	5	dbSNP_121	71	5867,2733	436.0+/-358.2	1990,1887,423	yes	missense,missense,missense	ZNF454	NM_001178089.1,NM_001178090.1,NM_182594.2	126,126,126	2898,2891,714	CC,CA,AA		31.7791,35.9964,33.2078	benign,benign,benign	166/523,166/523,166/523	178391902	8687,4319	2203	4300	6503	SO:0001583	missense	285676	exon5			ACAGTGATCAAAG	AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"""Zinc fingers, C2H2-type"", ""-"""	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.497A>C	5.37:g.178391902A>C	ENSP00000326249:p.Asp166Ala	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	158	61	0.386076	NM_001178089	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	CCDS4441.1	1461	0.6689560439560439	321	0.6524390243902439	258	0.712707182320442	364	0.6363636363636364	518	0.683377308707124	C	0.255	-1.003612	0.02128	0.640036	0.682209	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.07114	3.22;3.22	4.55	0.689	0.18033	.	2582.400000	0.00166	N	0.000014	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37572	-0.9700	9	0.15499	T	0.54	-0.0278	0.8264	0.01121	0.1675:0.3:0.1733:0.3592	rs12719860;rs52822914;rs60625225;rs12719860	166	Q8N9F8	ZN454_HUMAN	A	166	ENSP00000326249:D166A;ENSP00000430354:D166A	ENSP00000326249:D166A	D	+	2	0	ZNF454	178324508	0.026000	0.19158	0.000000	0.03702	0.000000	0.00434	-0.173000	0.09854	0.063000	0.16370	-1.104000	0.02111	GAT	A|0.334;C|0.666	0.666	strong		0.433	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037557	33037557	+	Silent	SNP	C	C	T	rs1042177	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33037557C>T	ENST00000419277.1	-	3	336	c.207G>A	c.(205-207)aaG>aaA	p.K69K	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Silent_p.K69K	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	69	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CGGTCTCCTTCTTGTCCAGAT	0.453													.|||	1181	0.235823	0.3775	0.2363	5008	,	,		19499	0.1022		0.1551	False		,,,				2504	0.2648				p.K69K		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G207A						PASS	.	C	,,	807,2215		129,549,833	69.0	91.0	83.0		207,207,207	3.0	0.8	6	dbSNP_86	83	718,4700		45,628,2036	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	174,1177,2869	TT,TC,CC		13.2521,26.7042,18.0687	,,	69/261,69/261,69/261	33037557	1525,6915	1511	2709	4220	SO:0001819	synonymous_variant	3113	exon2			CTCCTTCTTGTCC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.207G>A	6.37:g.33037557C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	173	67	0.387283	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1																																																																																			C|0.814;T|0.186	0.186	strong		0.453	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
DEF8	54849	hgsc.bcm.edu	37	16	90025640	90025640	+	Intron	SNP	G	G	C	rs8166	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90025640G>C	ENST00000268676.7	+	6	786				DEF8_ENST00000418391.2_Missense_Mutation_p.M197I|DEF8_ENST00000563795.1_Intron|DEF8_ENST00000567874.1_Intron|DEF8_ENST00000563594.1_Intron|DEF8_ENST00000563848.1_Intron|DEF8_ENST00000569453.1_Intron|DEF8_ENST00000570182.1_Intron	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)						intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		acattcAGATGtgagctatcc	0.507													C|||	609	0.121605	0.1021	0.0303	5008	,	,		20366	0.2688		0.0557	False		,,,				2504	0.1288				p.M197I		Atlas-SNP	.											.	DEF8	28	.	0			c.G591C						PASS	.	C	,,,,,ILE/MET,ILE/MET,ILE/MET,	278,2366		14,250,1058	23.0	33.0	29.0		,,,,,591,591,591,	-0.3	0.0	16	dbSNP_52	29	314,4304		9,296,2004	yes	intron,intron,intron,intron,intron,missense,missense,missense,intron	DEF8	NM_001242816.1,NM_001242817.1,NM_001242818.1,NM_001242819.1,NM_001242820.1,NM_001242821.1,NM_001242822.1,NM_017702.3,NM_207514.2	,,,,,10,10,10,	23,546,3062	CC,CG,GG		6.7995,10.5144,8.152	,,,,,,,,	,,,,,197/198,197/198,197/198,	90025640	592,6670	1322	2309	3631	SO:0001627	intron_variant	54849	exon6			TCAGATGTGAGCT	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.697+77G>C	16.37:g.90025640G>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_001242822	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Missense_Mutation	SNP	ENST00000268676.7	37	CCDS10989.1	235	0.10760073260073261	55	0.11178861788617886	13	0.03591160220994475	122	0.21328671328671328	45	0.059366754617414245	C	2.530	-0.308796	0.05458	0.105144	0.067995	ENSG00000140995	ENST00000418391	T	0.40476	1.03	1.8	-0.313	0.12754	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30090	-0.9990	6	.	.	.	.	2.9572	0.05881	0.0:0.4513:0.242:0.3067	rs8166;rs1130141;rs3188708	197	Q6ZN54-2	.	I	197	ENSP00000412784:M197I	.	M	+	3	0	DEF8	88553141	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.291000	0.02775	-0.402000	0.07633	-0.501000	0.04562	ATG	G|0.888;C|0.112	0.112	strong		0.507	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514	
HNF1A	6927	hgsc.bcm.edu	37	12	121437114	121437114	+	Silent	SNP	G	G	A	rs55834942	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:121437114G>A	ENST00000257555.6	+	8	1771	c.1545G>A	c.(1543-1545)acG>acA	p.T515T	RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Silent_p.T515T|HNF1A_ENST00000541395.1_Silent_p.T515T			P20823	HNF1A_HUMAN	HNF1 homeobox A	515					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ACACCCACACGGGCCTGCTCC	0.677									Hepatic Adenoma, Familial Clustering of				.|||	315	0.0628994	0.0121	0.1095	5008	,	,		16172	0.001		0.1988	False		,,,				2504	0.0225				p.T515T		Atlas-SNP	.											HNF1A,brain,glioma,0,4	HNF1A	302	4	0			c.G1545A						scavenged	.	G		175,4231	113.3+/-151.4	4,167,2032	68.0	70.0	70.0		1545	-7.7	0.9	12	dbSNP_129	70	1654,6944	303.3+/-306.4	156,1342,2801	yes	coding-synonymous	HNF1A	NM_000545.5		160,1509,4833	AA,AG,GG		19.237,3.9719,14.0649		515/632	121437114	1829,11175	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCACACGGGCCTG	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1545G>A	12.37:g.121437114G>A		Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	175	80	0.457143	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.860;A|0.140	0.140	strong		0.677	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
PDPR	55066	hgsc.bcm.edu	37	16	70180088	70180088	+	Missense_Mutation	SNP	A	A	T	rs2287978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:70180088A>T	ENST00000288050.4	+	16	2876	c.1919A>T	c.(1918-1920)tAt>tTt	p.Y640F	PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000398122.3_Missense_Mutation_p.Y540F|PDPR_ENST00000542659.1_De_novo_Start_InFrame|PDPR_ENST00000568530.1_Missense_Mutation_p.Y640F|PDPR_ENST00000567046.1_De_novo_Start_OutOfFrame	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	640					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		GAGTTGTCCTATGCCCCTATG	0.468													.|||	559	0.111621	0.0091	0.0893	5008	,	,		24813	0.1865		0.1173	False		,,,				2504	0.183				p.Y640F		Atlas-SNP	.											.	PDPR	66	.	0			c.A1919T						PASS	.	A	PHE/TYR	106,3632		4,98,1767	115.0	116.0	115.0		1919	5.0	1.0	16	dbSNP_134	115	956,7278		43,870,3204	no	missense	PDPR	NM_017990.3	22	47,968,4971	TT,TA,AA		11.6104,2.8357,8.8707	possibly-damaging	640/880	70180088	1062,10910	1869	4117	5986	SO:0001583	missense	55066	exon16			TGTCCTATGCCCC		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1919A>T	16.37:g.70180088A>T	ENSP00000288050:p.Tyr640Phe	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	148	55	0.371622	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.851062	0.71719	0.028357	0.116104	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055	D;D	0.83163	-1.69;-1.69	5.02	5.02	0.67125	Glycine cleavage T-protein, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.06096	0.0158	N	0.14661	0.345	0.09310	P	1.0	D;D	0.64830	0.994;0.965	D;P	0.63033	0.91;0.845	T	0.64097	-0.6487	9	0.59425	D	0.04	.	13.9208	0.63930	1.0:0.0:0.0:0.0	.	368;640	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	F	640;540;368	ENSP00000288050:Y640F;ENSP00000381190:Y540F	ENSP00000205055:Y368F	Y	+	2	0	PDPR	68737589	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.097000	0.94193	1.898000	0.54952	0.379000	0.24179	TAT	A|0.750;T|0.250	0.250	weak		0.468	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
RAB3IL1	5866	hgsc.bcm.edu	37	11	61669946	61669946	+	Missense_Mutation	SNP	G	G	A	rs3815045	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61669946G>A	ENST00000394836.2	-	8	1124	c.967C>T	c.(967-969)Cat>Tat	p.H323Y	RAB3IL1_ENST00000301773.5_Missense_Mutation_p.H297Y	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	323			H -> Y (in dbSNP:rs3815045).		positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						ATGTAGTAATGGCTTTTGGAG	0.627													G|||	723	0.144369	0.0023	0.0965	5008	,	,		15368	0.3264		0.0288	False		,,,				2504	0.3016				p.H323Y		Atlas-SNP	.											.	RAB3IL1	39	.	0			c.C967T						PASS	.	G	TYR/HIS	38,4362		0,38,2162	51.0	48.0	49.0		967	3.5	1.0	11	dbSNP_107	49	200,8396		1,198,4099	yes	missense	RAB3IL1	NM_013401.2	83	1,236,6261	AA,AG,GG		2.3267,0.8636,1.8313	benign	323/383	61669946	238,12758	2200	4298	6498	SO:0001583	missense	5866	exon8			AGTAATGGCTTTT	AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.967C>T	11.37:g.61669946G>A	ENSP00000378313:p.His323Tyr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_013401	Q86V32|Q9P1Q8	Missense_Mutation	SNP	ENST00000394836.2	37	CCDS8014.1	247	0.1130952380952381	3	0.006097560975609756	44	0.12154696132596685	177	0.3094405594405594	23	0.030343007915567283	G	1.709	-0.499563	0.04291	0.008636	0.023267	ENSG00000167994	ENST00000394836;ENST00000301773	T;T	0.37584	1.19;1.19	4.45	3.53	0.40419	.	0.059127	0.64402	D	0.000001	T	0.00012	0.0000	N	0.01824	-0.7	0.25508	P	0.9874804	B;B	0.13145	0.007;0.001	B;B	0.12156	0.007;0.002	T	0.43376	-0.9395	9	0.02654	T	1	-7.1268	4.2305	0.10601	0.3235:0.0:0.6765:0.0	rs3815045;rs61261385;rs3815045	297;323	Q8TBN0-2;Q8TBN0	.;R3GEF_HUMAN	Y	323;297	ENSP00000378313:H323Y;ENSP00000301773:H297Y	ENSP00000301773:H297Y	H	-	1	0	RAB3IL1	61426522	1.000000	0.71417	0.976000	0.42696	0.386000	0.30323	6.324000	0.72896	2.411000	0.81874	0.561000	0.74099	CAT	G|0.922;A|0.078	0.078	strong		0.627	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401	
AKAP3	10566	hgsc.bcm.edu	37	12	4736569	4736569	+	Missense_Mutation	SNP	A	A	G	rs12366671	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:4736569A>G	ENST00000545990.2	-	5	2023	c.1499T>C	c.(1498-1500)aTt>aCt	p.I500T	AKAP3_ENST00000228850.1_Missense_Mutation_p.I500T|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	500			I -> T (in dbSNP:rs12366671). {ECO:0000269|PubMed:10529264}.		acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						GAGGTTGCCAATATCTTCAGG	0.468													A|||	442	0.0882588	0.0098	0.1037	5008	,	,		21478	0.0774		0.1431	False		,,,				2504	0.138				p.I500T		Atlas-SNP	.											.	AKAP3	212	.	0			c.T1499C						PASS	.	A	THR/ILE	137,4269	97.1+/-135.8	3,131,2069	67.0	64.0	65.0		1499	0.4	0.0	12	dbSNP_120	65	1350,7250	261.9+/-284.1	108,1134,3058	yes	missense	AKAP3	NM_006422.2	89	111,1265,5127	GG,GA,AA		15.6977,3.1094,11.4332	benign	500/854	4736569	1487,11519	2203	4300	6503	SO:0001583	missense	10566	exon4			TTGCCAATATCTT	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.1499T>C	12.37:g.4736569A>G	ENSP00000440994:p.Ile500Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	99	54	0.545455	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	193	0.08836996336996338	8	0.016260162601626018	46	0.1270718232044199	37	0.06468531468531469	102	0.1345646437994723	A	0.020	-1.442911	0.01089	0.031094	0.156977	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.07021	3.23;3.23	5.65	0.433	0.16534	A-kinase anchor 110kDa, C-terminal (1);	0.867679	0.10101	N	0.715909	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43972	-0.9358	9	0.02654	T	1	0.3055	4.2907	0.10878	0.3284:0.0:0.5238:0.1477	rs12366671;rs52799632;rs58734502;rs12366671	500	O75969	AKAP3_HUMAN	T	500	ENSP00000228850:I500T;ENSP00000440994:I500T	ENSP00000228850:I500T	I	-	2	0	AKAP3	4606830	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.545000	0.23268	-0.080000	0.12685	-0.177000	0.13119	ATT	A|0.899;G|0.101	0.101	strong		0.468	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
NFKBIZ	64332	hgsc.bcm.edu	37	3	101576175	101576175	+	Silent	SNP	T	T	C	rs14134	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:101576175T>C	ENST00000326172.5	+	11	2090	c.1975T>C	c.(1975-1977)Ttg>Ctg	p.L659L	NFKBIZ_ENST00000394054.2_Silent_p.L559L|NFKBIZ_ENST00000326151.5_Silent_p.L537L	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	659	Interaction with NFKB1/p50. {ECO:0000250}.				inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						TGCTGCCAGCTTGCAGTATCG	0.478													C|||	2676	0.534345	0.497	0.6772	5008	,	,		21394	0.4405		0.6282	False		,,,				2504	0.4836				p.L659L		Atlas-SNP	.											.	NFKBIZ	55	.	0			c.T1975C						PASS	.	C	,	2288,2118	577.4+/-384.4	609,1070,524	103.0	97.0	99.0		1675,1975	6.0	1.0	3	dbSNP_52	99	5408,3192	481.0+/-370.5	1662,2084,554	no	coding-synonymous,coding-synonymous	NFKBIZ	NM_001005474.2,NM_031419.3	,	2271,3154,1078	CC,CT,TT		37.1163,48.0708,40.8273	,	559/619,659/719	101576175	7696,5310	2203	4300	6503	SO:0001819	synonymous_variant	64332	exon11			GCCAGCTTGCAGT	AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"""Ankyrin repeat domain containing"""	29805	protein-coding gene	gene with protein product	"""IL-1 inducible nuclear ankyrin-repeat protein"""	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.1975T>C	3.37:g.101576175T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_031419	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Silent	SNP	ENST00000326172.5	37	CCDS2946.1																																																																																			T|0.427;C|0.573	0.573	strong		0.478	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419	
ZNF446	55663	hgsc.bcm.edu	37	19	58989495	58989495	+	Missense_Mutation	SNP	A	A	C	rs893185	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58989495A>C	ENST00000594369.1	+	4	955	c.574A>C	c.(574-576)Aac>Cac	p.N192H	CTD-2619J13.23_ENST00000598051.1_RNA|ZNF446_ENST00000335841.4_Missense_Mutation_p.N192H|ZNF446_ENST00000596341.1_Missense_Mutation_p.N192H	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	192			N -> H (in dbSNP:rs893185).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CCCTGAGGGGAACCATGGACA	0.607													C|||	2205	0.440296	0.6089	0.3545	5008	,	,		18796	0.3175		0.4702	False		,,,				2504	0.3691				p.N192H		Atlas-SNP	.											.	ZNF446	22	.	0			c.A574C						PASS	.	C	HIS/ASN	2720,1686	510.3+/-367.5	841,1038,324	137.0	104.0	115.0		574	1.0	0.0	19	dbSNP_86	115	3935,4665	603.7+/-394.7	922,2091,1287	yes	missense	ZNF446	NM_017908.2	68	1763,3129,1611	CC,CA,AA		45.7558,38.266,48.8313	benign	192/451	58989495	6655,6351	2203	4300	6503	SO:0001583	missense	55663	exon4			GAGGGGAACCATG		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.574A>C	19.37:g.58989495A>C	ENSP00000472802:p.Asn192His	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_017908		Missense_Mutation	SNP	ENST00000594369.1	37	CCDS12982.1	995	0.4555860805860806	328	0.6666666666666666	139	0.3839779005524862	175	0.30594405594405594	353	0.4656992084432718	C	1.839	-0.468001	0.04476	0.61734	0.457558	ENSG00000083838	ENST00000335841;ENST00000540481	T	0.04603	3.59	4.31	1.05	0.20165	.	0.370024	0.19780	N	0.106248	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07347	-1.0777	9	0.20046	T	0.44	-4.4839	3.4022	0.07328	0.1795:0.5304:0.0:0.2901	rs893185;rs17319584;rs17856530;rs57843950;rs893185	192;192	F5H201;Q9NWS9	.;ZN446_HUMAN	H	192	ENSP00000336565:N192H	ENSP00000336565:N192H	N	+	1	0	ZNF446	63681307	0.000000	0.05858	0.014000	0.15608	0.260000	0.26232	0.137000	0.15995	0.087000	0.17167	-0.217000	0.12591	AAC	T|0.002;G|0.001	.	strong		0.607	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908	
B4GALNT2	124872	hgsc.bcm.edu	37	17	47210506	47210506	+	Missense_Mutation	SNP	C	C	A	rs7207403	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:47210506C>A	ENST00000300404.2	+	1	178	c.119C>A	c.(118-120)gCt>gAt	p.A40D	B4GALNT2_ENST00000504681.1_Intron|B4GALNT2_ENST00000393354.2_Intron	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	40			A -> D (in dbSNP:rs7207403). {ECO:0000269|PubMed:12678917, ECO:0000269|PubMed:14688233, ECO:0000269|PubMed:15489334}.		lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			GGCTTCGGGGCTCTCTGCTTG	0.687													c|||	2159	0.43111	0.5242	0.4914	5008	,	,		11092	0.129		0.5348	False		,,,				2504	0.4673				p.A40D	GBM(124;244 1635 8663 18097 33175)	Atlas-SNP	.											.	B4GALNT2	67	.	0			c.C119A						PASS	.		,,ASP/ALA	2350,2038		653,1044,497	10.0	11.0	11.0		,,119	-1.4	0.0	17	dbSNP_116	11	4861,3723		1392,2077,823	yes	intron,intron,missense	B4GALNT2	NM_001159387.1,NM_001159388.1,NM_153446.2	,,126	2045,3121,1320	AA,AC,CC		43.3714,46.4448,44.411	,,benign	,,40/567	47210506	7211,5761	2194	4292	6486	SO:0001583	missense	124872	exon1			TCGGGGCTCTCTG	AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	24136	protein-coding gene	gene with protein product		111730	"""UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"""	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.119C>A	17.37:g.47210506C>A	ENSP00000300404:p.Ala40Asp	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	35	33	0.942857	NM_153446	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	ENST00000300404.2	37	CCDS11544.1	947	0.4336080586080586	268	0.5447154471544715	199	0.5497237569060773	73	0.12762237762237763	407	0.5369393139841688	-	10.62	1.400523	0.25291	0.535552	0.566286	ENSG00000167080	ENST00000300404	T	0.20738	2.05	2.04	-1.38	0.09027	.	2.814070	0.01939	N	0.041783	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46400	-0.9194	9	0.12766	T	0.61	0.0011	0.8699	0.01212	0.2381:0.3704:0.2339:0.1576	rs7207403;rs52830075;rs56661869;rs7207403	40	Q8NHY0	B4GN2_HUMAN	D	40	ENSP00000300404:A40D	ENSP00000300404:A40D	A	+	2	0	B4GALNT2	44565505	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.254000	0.18314	-0.291000	0.09012	-0.284000	0.09977	GCT	C|0.573;A|0.427	0.427	strong		0.687	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446	
FREM1	158326	hgsc.bcm.edu	37	9	14819370	14819370	+	Missense_Mutation	SNP	G	G	T	rs7023244	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:14819370G>T	ENST00000380880.3	-	14	3191	c.2408C>A	c.(2407-2409)tCt>tAt	p.S803Y	FREM1_ENST00000422223.2_Missense_Mutation_p.S803Y|FREM1_ENST00000380881.4_Missense_Mutation_p.S804Y			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	803			S -> Y (in dbSNP:rs7023244).		cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		ATCTGCATCAGAAATTAGAAT	0.478													G|||	822	0.164137	0.0832	0.255	5008	,	,		18171	0.0794		0.2525	False		,,,				2504	0.2055				p.S803Y		Atlas-SNP	.											.	FREM1	261	.	0			c.C2408A						PASS	.	G	TYR/SER	455,3437		31,393,1522	114.0	109.0	111.0		2408	5.9	1.0	9	dbSNP_116	111	2046,6238		276,1494,2372	yes	missense	FREM1	NM_144966.5	144	307,1887,3894	TT,TG,GG		24.6982,11.6906,20.5404	possibly-damaging	803/2180	14819370	2501,9675	1946	4142	6088	SO:0001583	missense	158326	exon15			GCATCAGAAATTA	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.2408C>A	9.37:g.14819370G>T	ENSP00000370262:p.Ser803Tyr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	374	0.17124542124542125	37	0.07520325203252033	89	0.24585635359116023	55	0.09615384615384616	193	0.2546174142480211	G	20.5	4.005732	0.74932	0.116906	0.246982	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.27256	1.68;1.68;1.68	5.86	5.86	0.93980	.	0.225793	0.47852	D	0.000210	T	0.00012	0.0000	M	0.85041	2.73	0.09310	P	0.9999956479	D	0.65815	0.995	P	0.62649	0.905	T	0.00071	-1.2130	9	0.87932	D	0	-15.0418	20.1931	0.98233	0.0:0.0:1.0:0.0	rs7023244;rs56569639;rs7023244	803	Q5H8C1	FREM1_HUMAN	Y	804;803;803	ENSP00000370263:S804Y;ENSP00000412940:S803Y;ENSP00000370262:S803Y	ENSP00000370257:S806Y	S	-	2	0	FREM1	14809370	1.000000	0.71417	0.993000	0.49108	0.383000	0.30230	8.582000	0.90791	2.771000	0.95319	0.563000	0.77884	TCT	G|0.830;T|0.170	0.170	strong		0.478	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
BAZ1A	11177	hgsc.bcm.edu	37	14	35242828	35242828	+	Silent	SNP	G	G	A	rs2275145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:35242828G>A	ENST00000382422.2	-	19	3429	c.3102C>T	c.(3100-3102)gaC>gaT	p.D1034D	BAZ1A_ENST00000360310.1_Silent_p.D1034D|BAZ1A_ENST00000358716.4_Silent_p.D1002D			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1034					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		TCTCTTCTACGTCTTCATTCA	0.343													G|||	2581	0.515375	0.4387	0.5461	5008	,	,		16749	0.4911		0.5318	False		,,,				2504	0.6053				p.D1034D		Atlas-SNP	.											.	BAZ1A	128	.	0			c.C3102T						PASS	.	G	,	2076,2330	571.5+/-383.1	501,1074,628	175.0	160.0	165.0		3102,3006	3.2	0.6	14	dbSNP_100	165	4352,4246	579.9+/-391.0	1080,2192,1027	yes	coding-synonymous,coding-synonymous	BAZ1A	NM_013448.2,NM_182648.1	,	1581,3266,1655	AA,AG,GG		49.3836,47.1176,49.4309	,	1034/1557,1002/1525	35242828	6428,6576	2203	4299	6502	SO:0001819	synonymous_variant	11177	exon20			TTCTACGTCTTCA	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.3102C>T	14.37:g.35242828G>A		Somatic	339	0	0		WXS	Illumina HiSeq	Phase_I	275	273	0.992727	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1																																																																																			G|0.500;A|0.500	0.500	strong		0.343	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
MUC2	4583	hgsc.bcm.edu	37	11	1088815	1088815	+	Silent	SNP	A	A	G	rs7103978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1088815A>G	ENST00000441003.2	+	26	3627	c.3600A>G	c.(3598-3600)gcA>gcG	p.A1200A	MUC2_ENST00000359061.5_Silent_p.A1200A	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1200					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CACCTGGAGCATCGGTTCCCA	0.592													G|||	326	0.0650958	0.053	0.0591	5008	,	,		22307	0.0556		0.0974	False		,,,				2504	0.0624				p.A1200A		Atlas-SNP	.											.	MUC2	614	.	0			c.A3600G						PASS	.	G		223,3987		5,213,1887	59.0	64.0	62.0		3600	-7.2	0.0	11	dbSNP_116	62	784,7636		37,710,3463	no	coding-synonymous	MUC2	NM_002457.2		42,923,5350	GG,GA,AA		9.3112,5.2969,7.9731		1200/2813	1088815	1007,11623	2105	4210	6315	SO:0001819	synonymous_variant	4583	exon26			TGGAGCATCGGTT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3600A>G	11.37:g.1088815A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				A|0.939;G|0.061	0.061	strong		0.592	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR5M3	219482	hgsc.bcm.edu	37	11	56237609	56237609	+	Missense_Mutation	SNP	A	A	G	rs200070203	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56237609A>G	ENST00000312240.2	-	1	405	c.365T>C	c.(364-366)aTg>aCg	p.M122T		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					CCCAATTGCCATGTATCTATC	0.383													a|||	26	0.00519169	0.0	0.0058	5008	,	,		20815	0.0		0.0169	False		,,,				2504	0.0051				p.M122T		Atlas-SNP	.											.	OR5M3	103	.	0			c.T365C						PASS	.						92.0	86.0	88.0					11																	56237609		2201	4280	6481	SO:0001583	missense	219482	exon1			ATTGCCATGTATC	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"""GPCR / Class A : Olfactory receptors"""	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.365T>C	11.37:g.56237609A>G	ENSP00000312208:p.Met122Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	85	9	0.105882	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	37	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	A	7.717	0.696444	0.15106	.	.	ENSG00000174937	ENST00000312240	T	0.01323	5.01	5.13	4.0	0.46444	GPCR, rhodopsin-like superfamily (1);	0.215738	0.32852	N	0.005578	T	0.01870	0.0059	L	0.43646	1.37	0.28098	N	0.931539	B	0.06786	0.001	B	0.10450	0.005	T	0.30995	-0.9959	10	0.56958	D	0.05	-7.874	9.9755	0.41781	0.9186:0.0:0.0814:0.0	.	122	Q8NGP4	OR5M3_HUMAN	T	122	ENSP00000312208:M122T	ENSP00000312208:M122T	M	-	2	0	OR5M3	55994185	0.001000	0.12720	0.975000	0.42487	0.077000	0.17291	1.595000	0.36708	0.794000	0.33899	-0.536000	0.04276	ATG	.	.	weak		0.383	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742	
LHCGR	3973	hgsc.bcm.edu	37	2	48915871	48915871	+	Silent	SNP	A	A	G	rs11125179	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:48915871A>G	ENST00000294954.7	-	11	1086	c.1065T>C	c.(1063-1065)gaT>gaC	p.D355D	STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000344775.3_Silent_p.D293D|LHCGR_ENST00000405626.1_Silent_p.D328D|LHCGR_ENST00000401907.1_Intron|LHCGR_ENST00000403273.1_Intron	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	355					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	AGCCCATAATATCTTCACAGG	0.438													A|||	2966	0.592252	0.2542	0.6643	5008	,	,		19323	0.9236		0.6382	False		,,,				2504	0.6094				p.D355D		Atlas-SNP	.											.	LHCGR	154	.	0			c.T1065C						PASS	.	A	,	1382,3024	454.9+/-350.8	224,934,1045	134.0	134.0	134.0		1065,	-0.9	1.0	2	dbSNP_120	134	5078,3522	631.5+/-398.5	1497,2084,719	no	coding-synonymous,intron	LHCGR,STON1-GTF2A1L	NM_000233.3,NM_001198593.1	,	1721,3018,1764	GG,GA,AA		40.9535,31.3663,49.6694	,	355/700,	48915871	6460,6546	2203	4300	6503	SO:0001819	synonymous_variant	3973	exon11			CATAATATCTTCA		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"""GPCR / Class A : Gonadotropin and TSH receptors"""	6585	protein-coding gene	gene with protein product		152790	"""hypergonadotropic hypogonadism"""	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.1065T>C	2.37:g.48915871A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	183	79	0.431694	NM_000233	Q14751|Q15996|Q9UEW9	Silent	SNP	ENST00000294954.7	37	CCDS1842.1																																																																																			A|0.453;G|0.547	0.547	strong		0.438	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3	
MAGEC1	9947	hgsc.bcm.edu	37	X	140993926	140993926	+	Missense_Mutation	SNP	C	C	G	rs76335605		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:140993926C>G	ENST00000285879.4	+	4	1022	c.736C>G	c.(736-738)Ctg>Gtg	p.L246V	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	246										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CTCCACTTTACTGAGTCTTTT	0.498										HNSCC(15;0.026)			-|||	287	0.0760265	0.0424	0.0476	3775	,	,		11837	0.0347		0.0795	False		,,,				2504	0.0849				p.L246V		Atlas-SNP	.											.	MAGEC1	317	.	0			c.C736G						PASS	.	C	VAL/LEU	23,3776		0,20,3,1603,550	70.0	57.0	62.0		736		0.1	X	dbSNP_131	62	140,6372		0,119,21,2271,1711	no	missense	MAGEC1	NM_005462.4	32	0,139,24,3874,2261	GG,GC,G,CC,C		2.1499,0.6054,1.5808	possibly-damaging	246/1143	140993926	163,10148	2176	4122	6298	SO:0001583	missense	9947	exon4			ACTTTACTGAGTC	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.736C>G	X.37:g.140993926C>G	ENSP00000285879:p.Leu246Val	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	77	24	0.311688	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	6	0.003616636528028933	0	0.0	0	0.0	0	0.0	2	0.002652519893899204	t	2.032	-0.422182	0.04734	0.006054	0.021499	ENSG00000155495	ENST00000285879;ENST00000370511;ENST00000370510	T;T	0.13657	3.61;2.57	.	.	.	.	.	.	.	.	T	0.03739	0.0106	N	0.08118	0	0.09310	P	0.9999999835082	P	0.34587	0.458	B	0.41691	0.364	T	0.30592	-0.9973	7	0.87932	D	0	.	5.8503	0.18689	0.0:0.9991:0.0:9.0E-4	.	246	O60732	MAGC1_HUMAN	V	246;48;47	ENSP00000285879:L246V;ENSP00000359542:L48V	ENSP00000285879:L246V	L	+	1	2	MAGEC1	140821592	0.000000	0.05858	0.128000	0.21923	0.128000	0.20619	-2.616000	0.00881	0.054000	0.16065	0.054000	0.15206	CTG	C|0.996;G|0.003;T|0.001	0.003	strong		0.498	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
ARHGEF40	55701	hgsc.bcm.edu	37	14	21553004	21553004	+	Silent	SNP	C	C	T	rs749731	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21553004C>T	ENST00000298694.4	+	18	4009	c.3882C>T	c.(3880-3882)ttC>ttT	p.F1294F	ARHGEF40_ENST00000298693.3_Silent_p.F1294F			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	1294	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						TCTTTCTCTTCGAGCATCTCC	0.522													T|||	365	0.0728834	0.1286	0.036	5008	,	,		20298	0.0337		0.0497	False		,,,				2504	0.0879				p.F1294F		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.C3882T						PASS	.	T		603,3803	770.2+/-413.7	40,523,1640	158.0	146.0	150.0		3882	1.7	1.0	14	dbSNP_86	150	424,8176	800.6+/-407.4	14,396,3890	no	coding-synonymous	ARHGEF40	NM_018071.3		54,919,5530	TT,TC,CC		4.9302,13.6859,7.8964		1294/1520	21553004	1027,11979	2203	4300	6503	SO:0001819	synonymous_variant	55701	exon18			TCTCTTCGAGCAT		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.3882C>T	14.37:g.21553004C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	37	CCDS32041.1																																																																																			C|0.932;T|0.068	0.068	strong		0.522	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
WARS2	10352	hgsc.bcm.edu	37	1	119584949	119584949	+	Silent	SNP	G	G	A	rs33960696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:119584949G>A	ENST00000235521.4	-	4	479	c.453C>T	c.(451-453)caC>caT	p.H151H	WARS2_ENST00000537870.1_Silent_p.H57H|WARS2_ENST00000369426.5_Silent_p.H151H	NM_015836.3|NM_201263.2	NP_056651.1|NP_957715.1	Q9UGM6	SYWM_HUMAN	tryptophanyl tRNA synthetase 2, mitochondrial	151				H -> R (in Ref. 3; BAD96917). {ECO:0000305}.	gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)|vasculogenesis (GO:0001570)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(2)	15	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	CCGTGCCATCGTGCTTCTGCT	0.453													G|||	290	0.0579073	0.0522	0.0403	5008	,	,		16602	0.004		0.0706	False		,,,				2504	0.1207				p.H151H		Atlas-SNP	.											.	WARS2	69	.	0			c.C453T						PASS	.	G	,	215,4191	129.4+/-166.1	4,207,1992	148.0	134.0	139.0		453,453	-11.3	0.0	1	dbSNP_126	139	647,7953	164.8+/-217.1	27,593,3680	no	coding-synonymous,coding-synonymous	WARS2	NM_015836.3,NM_201263.2	,	31,800,5672	AA,AG,GG		7.5233,4.8797,6.6277	,	151/361,151/221	119584949	862,12144	2203	4300	6503	SO:0001819	synonymous_variant	10352	exon4			GCCATCGTGCTTC	BC021722	CCDS900.1, CCDS30817.1	1p12	2011-07-01	2007-02-23		ENSG00000116874	ENSG00000116874	6.1.1.2	"""Aminoacyl tRNA synthetases / Class I"""	12730	protein-coding gene	gene with protein product	"""tryptophan tRNA ligase 2, mitochondrial"""	604733				10072595, 10828066	Standard	NM_201263		Approved	TrpRS	uc001ehn.3	Q9UGM6	OTTHUMG00000012335	ENST00000235521.4:c.453C>T	1.37:g.119584949G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	204	97	0.47549	NM_015836	B1ALR1|B2R9D4|Q53FT4|Q5VUD2|Q86TQ0	Silent	SNP	ENST00000235521.4	37	CCDS900.1																																																																																			G|0.937;A|0.063	0.063	strong		0.453	WARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034362.1	NM_015836	
CAPN9	10753	hgsc.bcm.edu	37	1	230916260	230916260	+	Silent	SNP	C	C	T	rs28359687	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:230916260C>T	ENST00000271971.2	+	11	1400	c.1287C>T	c.(1285-1287)gaC>gaT	p.D429D	RP11-99J16__A.2_ENST00000412344.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000452640.1_RNA|CAPN9_ENST00000354537.1_Silent_p.D403D|CAPN9_ENST00000366666.2_Silent_p.D366D	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	429	Domain III.				digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				CTGACAAAGACGAACACCTGA	0.517													C|||	540	0.107827	0.087	0.1297	5008	,	,		16813	0.0813		0.1481	False		,,,				2504	0.1063				p.D429D		Atlas-SNP	.											.	CAPN9	116	.	0			c.C1287T						PASS	.	C	,	424,3982	206.2+/-227.9	21,382,1800	84.0	82.0	83.0		1287,1209	-8.1	0.0	1	dbSNP_125	83	1327,7273	260.8+/-283.4	94,1139,3067	no	coding-synonymous,coding-synonymous	CAPN9	NM_006615.2,NM_016452.1	,	115,1521,4867	TT,TC,CC		15.4302,9.6232,13.463	,	429/691,403/665	230916260	1751,11255	2203	4300	6503	SO:0001819	synonymous_variant	10753	exon11			CAAAGACGAACAC	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1287C>T	1.37:g.230916260C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_006615	B1APS1|B1AQI0|Q9NS74	Silent	SNP	ENST00000271971.2	37	CCDS1586.1																																																																																			C|0.878;T|0.122	0.122	strong		0.517	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
SLC41A3	54946	hgsc.bcm.edu	37	3	125726048	125726048	+	Silent	SNP	G	G	C	rs2279819	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:125726048G>C	ENST00000315891.6	-	11	1513	c.1275C>G	c.(1273-1275)ctC>ctG	p.L425L	SLC41A3_ENST00000346785.5_Silent_p.L389L|SLC41A3_ENST00000508835.1_Silent_p.L308L|SLC41A3_ENST00000383598.2_Silent_p.L399L|SLC41A3_ENST00000360370.4_Silent_p.L425L	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	425						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		TCACTTCTGCGAGGTACAGCA	0.552													C|||	3334	0.665735	0.9395	0.5461	5008	,	,		21833	0.503		0.6203	False		,,,				2504	0.5951				p.L425L		Atlas-SNP	.											.	SLC41A3	80	.	0			c.C1275G						PASS	.	C	,,,,	3927,479	223.6+/-240.1	1749,429,25	63.0	58.0	60.0		1275,1167,1197,924,1275	4.6	1.0	3	dbSNP_100	60	5407,3193	483.1+/-371.0	1711,1985,604	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC41A3	NM_001008485.1,NM_001008486.1,NM_001008487.1,NM_001164475.1,NM_017836.3	,,,,	3460,2414,629	CC,CG,GG		37.1279,10.8715,28.2331	,,,,	425/508,389/472,399/462,308/371,425/488	125726048	9334,3672	2203	4300	6503	SO:0001819	synonymous_variant	54946	exon11			TTCTGCGAGGTAC		CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544		"""Solute carriers"""	31046	protein-coding gene	gene with protein product		610803					Standard	NM_001164475		Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000315891.6:c.1275C>G	3.37:g.125726048G>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	122	63	0.516393	NM_017836	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Silent	SNP	ENST00000315891.6	37	CCDS33843.1																																																																																			G|0.309;C|0.691	0.691	strong		0.552	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836	
DEGS2	123099	hgsc.bcm.edu	37	14	100625902	100625902	+	Missense_Mutation	SNP	C	C	T	rs7157599	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100625902C>T	ENST00000553834.1	-	1	30	c.23G>A	c.(22-24)aGc>aAc	p.S8N	DEGS2_ENST00000305631.5_Missense_Mutation_p.S8N					delta(4)-desaturase, sphingolipid 2											breast(1)|lung(6)|skin(1)	8		Melanoma(154;0.212)				CTCGAAGTCGCTGCGGCTCGC	0.766													c|||	3842	0.767173	0.8661	0.768	5008	,	,		8798	0.7282		0.6948	False		,,,				2504	0.7474				p.S8N		Atlas-SNP	.											.	DEGS2	25	.	0			c.G23A						PASS	.	T	ASN/SER	2896,464		1254,388,38	8.0	7.0	8.0	http://www.ncbi.nlm.nih.gov/pubmed?term	23	0.5	1.0	14	dbSNP_116	8	4583,1505		1740,1103,201	yes	missense	DEGS2	NM_206918.2	46	2994,1491,239	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	24.7208,13.8095,20.8404	benign	8/324	100625902	7479,1969	1680	3044	4724	SO:0001583	missense	123099	exon1			AAGTCGCTGCGGC		CCDS9956.1	14q32.2	2013-09-02	2011-12-09	2004-12-14	ENSG00000168350	ENSG00000168350		"""Fatty acid desaturases"""	20113	protein-coding gene	gene with protein product	"""sphingolipid delta(4)-desaturase 2"", ""dihydroceramide desaturase 2"""	610862	"""chromosome 14 open reading frame 66"", ""degenerative spermatocyte homolog 2, lipid desaturase (Drosophila)"""	C14orf66			Standard	NM_206918		Approved	DES2, FADS8	uc001ygx.2	Q6QHC5	OTTHUMG00000171537	ENST00000553834.1:c.23G>A	14.37:g.100625902C>T	ENSP00000450637:p.Ser8Asn	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_206918		Missense_Mutation	SNP	ENST00000553834.1	37		1662	0.760989010989011	431	0.8760162601626016	274	0.7569060773480663	424	0.7412587412587412	533	0.7031662269129287	.	9.769	1.172237	0.21704	0.861905	0.752792	ENSG00000168350	ENST00000305631;ENST00000553834	T;T	0.40476	1.03;1.03	4.72	0.456	0.16655	Sphingolipid delta4-desaturase, N-terminal (1);	0.817312	0.11149	N	0.594331	T	0.00012	0.0000	N	0.13003	0.285	0.58432	P	9.000000000036756E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.21827	-1.0234	9	0.17369	T	0.5	-1.5775	5.1779	0.15145	0.1384:0.5173:0.2681:0.0762	rs7157599;rs60508435;rs7157599	8	Q6QHC5	DEGS2_HUMAN	N	8	ENSP00000307126:S8N;ENSP00000450637:S8N	ENSP00000307126:S8N	S	-	2	0	DEGS2	99695655	0.085000	0.21516	0.990000	0.47175	0.532000	0.34746	-0.317000	0.08060	-0.209000	0.10156	-0.336000	0.08194	AGC	C|0.235;T|0.765	0.765	strong		0.766	DEGS2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414004.1	NM_206918	
WDR90	197335	hgsc.bcm.edu	37	16	709001	709001	+	Missense_Mutation	SNP	C	C	A	rs4984906	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:709001C>A	ENST00000293879.4	+	24	3001	c.3001C>A	c.(3001-3003)Cct>Act	p.P1001T	LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Missense_Mutation_p.P1001T			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1001			P -> T (in dbSNP:rs4984906). {ECO:0000269|PubMed:14702039}.							endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				TGTCCTGGCCCCTACTGAGAG	0.647													G|||	3523	0.703474	0.9024	0.6052	5008	,	,		16851	0.9802		0.3718	False		,,,				2504	0.5603				p.P1001T		Atlas-SNP	.											.	WDR90	107	.	0			c.C3001A						PASS	.	G	THR/PRO	3390,816		1376,638,89	81.0	100.0	94.0		3001	-9.6	0.0	16	dbSNP_111	94	3087,5335		584,1919,1708	yes	missense	WDR90	NM_145294.4	38	1960,2557,1797	AA,AC,CC		36.654,19.4009,48.7092	benign	1001/1749	709001	6477,6151	2103	4211	6314	SO:0001583	missense	197335	exon24			CTGGCCCCTACTG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.3001C>A	16.37:g.709001C>A	ENSP00000293879:p.Pro1001Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	141	137	0.971631	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	1473	0.6744505494505495	430	0.8739837398373984	199	0.5497237569060773	560	0.9790209790209791	284	0.37467018469656993	G	0.007	-1.973176	0.00452	0.805991	0.36654	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.51574	0.7;1.54	4.79	-9.58	0.00559	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	17.628600	0.03178	N	0.171711	T	0.00012	0.0000	N	0.13235	0.315	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25641	-1.0126	9	0.10377	T	0.69	.	6.7898	0.23693	0.1519:0.2458:0.4772:0.1251	rs4984906;rs60133024;rs4984906	1001;1001	F8VUX9;Q96KV7	.;WDR90_HUMAN	T	1001	ENSP00000448122:P1001T;ENSP00000293879:P1001T	ENSP00000293879:P1001T	P	+	1	0	WDR90	649002	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.228000	0.02948	-2.099000	0.00849	-3.030000	0.00073	CCT	C|0.379;A|0.621	0.621	strong		0.647	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
MICAL2	9645	hgsc.bcm.edu	37	11	12246233	12246233	+	Silent	SNP	G	G	C	rs3816921	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:12246233G>C	ENST00000256194.4	+	13	1842	c.1554G>C	c.(1552-1554)cgG>cgC	p.R518R	MICAL2_ENST00000527546.1_Silent_p.R518R|MICAL2_ENST00000342902.5_Silent_p.R518R|MICAL2_ENST00000537344.1_Silent_p.R518R|MICAL2_ENST00000379612.3_Silent_p.R518R	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	518	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		CAGATATCCGGCCCAGCAAGC	0.612													G|||	1375	0.274561	0.0159	0.4035	5008	,	,		18524	0.5387		0.1382	False		,,,				2504	0.4008				p.R518R		Atlas-SNP	.											.	MICAL2	114	.	0			c.G1554C						PASS	.	G		199,4203	122.1+/-159.5	7,185,2009	103.0	92.0	96.0		1554	0.9	1.0	11	dbSNP_107	96	1142,7446	233.7+/-266.9	84,974,3236	no	coding-synonymous	MICAL2	NM_014632.2		91,1159,5245	CC,CG,GG		13.2976,4.5207,10.3233		518/1125	12246233	1341,11649	2201	4294	6495	SO:0001819	synonymous_variant	9645	exon13			TATCCGGCCCAGC	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.1554G>C	11.37:g.12246233G>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	183	88	0.480874	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																			G|0.832;C|0.168	0.168	strong		0.612	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
CATSPER3	347732	hgsc.bcm.edu	37	5	134332143	134332143	+	Missense_Mutation	SNP	G	G	A	rs114447625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:134332143G>A	ENST00000282611.6	+	3	519	c.433G>A	c.(433-435)Gct>Act	p.A145T		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	145					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCTGTATATCGCTGATGGCAT	0.547													G|||	43	0.00858626	0.0008	0.0101	5008	,	,		20081	0.0		0.0258	False		,,,				2504	0.0092				p.A145T		Atlas-SNP	.											.	CATSPER3	38	.	0			c.G433A						PASS	.	G	THR/ALA	20,4386	27.2+/-55.0	0,20,2183	135.0	117.0	123.0		433	4.1	0.0	5	dbSNP_132	123	264,8336	102.9+/-164.1	6,252,4042	yes	missense	CATSPER3	NM_178019.2	58	6,272,6225	AA,AG,GG		3.0698,0.4539,2.1836	probably-damaging	145/399	134332143	284,12722	2203	4300	6503	SO:0001583	missense	347732	exon3			TATATCGCTGATG	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.433G>A	5.37:g.134332143G>A	ENSP00000282611:p.Ala145Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	G	13.19	2.164341	0.38217	0.004539	0.030698	ENSG00000152705	ENST00000282611	D	0.98550	-4.99	4.14	4.14	0.48551	Ion transport (1);	0.256502	0.27886	N	0.017445	D	0.91676	0.7369	M	0.63843	1.955	0.09310	N	1	P	0.51537	0.946	B	0.41174	0.349	D	0.88435	0.3038	10	0.66056	D	0.02	-7.0009	12.2204	0.54431	0.0:0.0:1.0:0.0	.	145	Q86XQ3	CTSR3_HUMAN	T	145	ENSP00000282611:A145T	ENSP00000282611:A145T	A	+	1	0	CATSPER3	134360042	0.001000	0.12720	0.008000	0.14137	0.158000	0.22134	1.002000	0.29796	2.587000	0.87381	0.561000	0.74099	GCT	G|0.981;A|0.019	0.019	strong		0.547	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
OR8H3	390152	hgsc.bcm.edu	37	11	55890571	55890571	+	Silent	SNP	C	C	T	rs61743017	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55890571C>T	ENST00000313472.3	+	1	723	c.723C>T	c.(721-723)tgC>tgT	p.C241C		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TCTCTACTTGCGTCTCTCATC	0.403													C|||	191	0.038139	0.0091	0.0447	5008	,	,		20555	0.001		0.0944	False		,,,				2504	0.0532				p.C241C		Atlas-SNP	.											.	OR8H3	92	.	0			c.C723T						PASS	.	C		86,4316	71.4+/-109.4	0,86,2115	120.0	115.0	116.0		723	1.2	0.8	11	dbSNP_129	116	693,7899	171.3+/-222.3	34,625,3637	no	coding-synonymous	OR8H3	NM_001005201.1		34,711,5752	TT,TC,CC		8.0656,1.9537,5.9951		241/313	55890571	779,12215	2201	4296	6497	SO:0001819	synonymous_variant	390152	exon1			TACTTGCGTCTCT	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.723C>T	11.37:g.55890571C>T		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	265	113	0.426415	NM_001005201	Q6IFB7	Silent	SNP	ENST00000313472.3	37	CCDS31519.1																																																																																			C|0.950;T|0.050	0.050	strong		0.403	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
MCM7	4176	hgsc.bcm.edu	37	7	99696797	99696797	+	Missense_Mutation	SNP	T	T	C	rs2070215	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99696797T>C	ENST00000303887.5	-	5	1076	c.431A>G	c.(430-432)aAc>aGc	p.N144S	MCM7_ENST00000343023.6_Missense_Mutation_p.N144S|AP4M1_ENST00000429084.1_5'Flank|AP4M1_ENST00000359593.4_5'Flank|AP4M1_ENST00000422582.1_5'Flank|MCM7_ENST00000354230.3_5'UTR|AP4M1_ENST00000421755.1_5'Flank	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	144			N -> S (in dbSNP:rs2070215). {ECO:0000269|PubMed:8626784}.		cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)	p.N144S(1)		endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACGAGGCTTGTTGCTGCTAGG	0.512													T|||	981	0.195887	0.0129	0.1902	5008	,	,		20215	0.2758		0.2734	False		,,,				2504	0.2853				p.N144S		Atlas-SNP	.											MCM7_ENST00000303887,NS,carcinoma,0,1	MCM7	136	1	1	Substitution - Missense(1)	stomach(1)	c.A431G						PASS	.	T	SER/ASN,	287,4119	158.5+/-191.2	7,273,1923	110.0	105.0	107.0		431,	-3.6	0.9	7	dbSNP_96	107	2459,6141	405.7+/-348.6	355,1749,2196	yes	missense,utr-5	MCM7	NM_005916.3,NM_182776.1	46,	362,2022,4119	CC,CT,TT		28.593,6.5138,21.1133	benign,	144/720,	99696797	2746,10260	2203	4300	6503	SO:0001583	missense	4176	exon5			GGCTTGTTGCTGC		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 104"""	600592	"""minichromosome maintenance deficient (S. cerevisiae) 7"", ""MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"""	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.431A>G	7.37:g.99696797T>C	ENSP00000307288:p.Asn144Ser	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	148	75	0.506757	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	37	CCDS5683.1	435	0.19917582417582416	10	0.02032520325203252	73	0.20165745856353592	147	0.256993006993007	205	0.2704485488126649	T	2.044	-0.419462	0.04766	0.065138	0.28593	ENSG00000166508	ENST00000343023;ENST00000303887;ENST00000542483;ENST00000362082;ENST00000425308	T;T;T	0.10382	2.88;2.88;2.88	4.58	-3.6	0.04570	Nucleic acid-binding, OB-fold-like (1);	0.790345	0.12308	N	0.480423	T	0.00012	0.0000	N	0.00729	-1.24	0.53005	P	3.2000000000032E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40572	-0.9556	9	0.06494	T	0.89	-10.0949	7.4761	0.27376	0.0:0.4978:0.2936:0.2086	rs2070215;rs17447420;rs17845219;rs17858032;rs57620700;rs2070215	144	P33993	MCM7_HUMAN	S	144;144;81;37;37	ENSP00000344006:N144S;ENSP00000307288:N144S;ENSP00000411295:N37S	ENSP00000307288:N144S	N	-	2	0	MCM7	99534733	0.002000	0.14202	0.910000	0.35882	0.915000	0.54546	-0.062000	0.11674	-0.576000	0.05974	0.379000	0.24179	AAC	T|0.798;C|0.202	0.202	strong		0.512	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3		
SPATA31D1	389763	hgsc.bcm.edu	37	9	84607758	84607758	+	Silent	SNP	T	T	A	rs10867826	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:84607758T>A	ENST00000344803.2	+	4	2420	c.2373T>A	c.(2371-2373)acT>acA	p.T791T		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	791					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GTCCGGAGACTTCTTCAGACA	0.473													A|||	3126	0.624201	0.975	0.4294	5008	,	,		20246	0.7024		0.4473	False		,,,				2504	0.3896				p.T791T		Atlas-SNP	.											.	.	.	.	0			c.T2373A						PASS	.	A		3408,420		1525,358,31	106.0	102.0	103.0		2373	-4.7	0.0	9	dbSNP_120	103	3519,4719		754,2011,1354	no	coding-synonymous	FAM75D1	NM_001001670.2		2279,2369,1385	AA,AT,TT		42.7167,10.9718,42.5908		791/1577	84607758	6927,5139	1914	4119	6033	SO:0001819	synonymous_variant	389763	exon4			GGAGACTTCTTCA		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.2373T>A	9.37:g.84607758T>A		Somatic	407	1	0.002457		WXS	Illumina HiSeq	Phase_I	516	515	0.998062	NM_001001670		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																			T|0.426;A|0.574	0.574	strong		0.473	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
MAPT	4137	hgsc.bcm.edu	37	17	44067400	44067400	+	Missense_Mutation	SNP	T	T	C	rs10445337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44067400T>C	ENST00000571987.1	+	7	1339	c.1339T>C	c.(1339-1341)Tcc>Ccc	p.S447P	MAPT_ENST00000576518.1_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.S447P|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.S447P|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.S447P|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	447			S -> P (in dbSNP:rs10445337). {ECO:0000269|PubMed:9629852}.		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	TTCTGTCACTTCCCGAACTGG	0.532													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		17709	0.001		0.2406	False		,,,				2504	0.0613				p.S447P		Atlas-SNP	.											.	MAPT	135	.	0			c.T1339C						PASS	.	C	PRO/SER,,,,,,PRO/SER,	225,4181	804.2+/-415.7	6,213,1984	125.0	126.0	125.0		1339,,,,,,1339,	4.1	1.0	17	dbSNP_119	125	1917,6683	721.4+/-406.4	220,1477,2603	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	74,,,,,,74,	226,1690,4587	CC,CT,TT		22.2907,5.1067,16.4693	benign,,,,,,benign,	447/777,,,,,,447/759,	44067400	2142,10864	2203	4300	6503	SO:0001583	missense	4137	exon8			GTCACTTCCCGAA	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1339T>C	17.37:g.44067400T>C	ENSP00000458742:p.Ser447Pro	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	4.363	0.066874	0.08388	0.051067	0.222907	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.22539	1.95;1.95;1.95	5.17	4.14	0.48551	.	0.000000	0.41396	N	0.000891	T	0.00012	0.0000	N	0.00436	-1.5	0.09310	P	0.9999999999986787	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37842	-0.9688	9	0.02654	T	1	-9.971	6.5764	0.22569	0.0:0.7842:0.0:0.2158	rs10445337;rs52822487;rs10445337	447;447	P10636-9;P10636	.;TAU_HUMAN	P	447	ENSP00000340820:S447P;ENSP00000262410:S447P;ENSP00000410838:S447P	ENSP00000262410:S447P	S	+	1	0	MAPT	41423237	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.033000	0.30191	1.427000	0.47276	-0.320000	0.08662	TCC	T|0.856;C|0.144	0.144	strong		0.532	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
TNRC6A	27327	hgsc.bcm.edu	37	16	24802325	24802325	+	Missense_Mutation	SNP	C	C	T	rs3803716	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:24802325C>T	ENST00000395799.3	+	6	2491	c.2362C>T	c.(2362-2364)Cct>Tct	p.P788S	TNRC6A_ENST00000315183.7_Missense_Mutation_p.P788S	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	788	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.		P -> S (in dbSNP:rs3803716).		cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		CGATCCCAAACCTGCTCTGAG	0.502													C|||	788	0.157348	0.1884	0.1455	5008	,	,		17985	0.126		0.162	False		,,,				2504	0.1513				p.P788S		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C2362T						PASS	.	C	SER/PRO	767,3621		67,633,1494	36.0	39.0	38.0		2362	5.8	1.0	16	dbSNP_107	38	1632,6966		155,1322,2822	yes	missense	TNRC6A	NM_014494.2	74	222,1955,4316	TT,TC,CC		18.9812,17.4795,18.4737	benign	788/1963	24802325	2399,10587	2194	4299	6493	SO:0001583	missense	27327	exon6			CCCAAACCTGCTC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.2362C>T	16.37:g.24802325C>T	ENSP00000379144:p.Pro788Ser	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	56	20	0.357143	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	301	0.13782051282051283	77	0.1565040650406504	55	0.15193370165745856	59	0.10314685314685315	110	0.14511873350923482	C	6.894	0.534394	0.13188	0.174795	0.189812	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.12569	2.67;2.68	5.85	5.85	0.93711	.	0.242162	0.39146	N	0.001457	T	0.00012	0.0000	N	0.10809	0.05	0.09310	P	1.0	B;B;B	0.19706	0.002;0.011;0.038	B;B;B	0.17979	0.02;0.013;0.018	T	0.42849	-0.9427	9	0.13853	T	0.58	-9.2271	7.6837	0.28528	0.0:0.8077:0.0:0.1923	rs3803716;rs17771305;rs61587441;rs3803716	535;788;788	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	S	788	ENSP00000326900:P788S;ENSP00000379144:P788S	ENSP00000326900:P788S	P	+	1	0	TNRC6A	24709826	1.000000	0.71417	0.969000	0.41365	0.862000	0.49288	2.213000	0.42844	2.768000	0.95171	0.655000	0.94253	CCT	C|0.850;T|0.150	0.150	strong		0.502	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
HNF4G	3174	hgsc.bcm.edu	37	8	76452313	76452313	+	Intron	SNP	G	G	A	rs2943549	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:76452313G>A	ENST00000354370.1	+	3	247				HNF4G_ENST00000396423.2_Missense_Mutation_p.S29N			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma						endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			TATAATTCAAGTGGTGAGTTA	0.363													A|||	3064	0.611821	0.9516	0.4827	5008	,	,		19333	0.3938		0.5785	False		,,,				2504	0.5031				p.S29N		Atlas-SNP	.											.	HNF4G	111	.	0			c.G86A						PASS	.	A	ASN/SER	3282,388		1470,342,23	100.0	101.0	101.0		86	3.6	1.0	8	dbSNP_101	101	4662,3496		1321,2020,738	yes	missense	HNF4G	NM_004133.4	46	2791,2362,761	AA,AG,GG		42.8536,10.5722,32.8373	benign	29/446	76452313	7944,3884	1835	4079	5914	SO:0001627	intron_variant	3174	exon1			ATTCAAGTGGTGA		CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749		"""Nuclear hormone receptors"""	5026	protein-coding gene	gene with protein product		605966				8622695, 12220494	Standard	NM_004133		Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.-23-3733G>A	8.37:g.76452313G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	37		1353	0.6195054945054945	475	0.9654471544715447	181	0.5	254	0.44405594405594406	443	0.5844327176781002	A	0.007	-1.980060	0.00448	0.894278	0.571464	ENSG00000164749	ENST00000396423	D	0.91996	-2.95	4.71	3.58	0.41010	.	0.406903	0.24750	N	0.035912	T	0.00012	0.0000	N	0.11064	0.09	0.53005	P	3.6999999999953737E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.42361	-0.9456	9	0.02654	T	1	.	8.0755	0.30714	0.7686:0.0:0.2314:0.0	rs2943549;rs61555353;rs2943549	29	F1D8Q4	.	N	29	ENSP00000379701:S29N	ENSP00000379701:S29N	S	+	2	0	HNF4G	76614868	1.000000	0.71417	1.000000	0.80357	0.074000	0.17049	1.740000	0.38228	0.925000	0.37094	-0.332000	0.08345	AGT	G|0.377;A|0.623	0.623	strong		0.363	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133	
TMEM17	200728	hgsc.bcm.edu	37	2	62733201	62733201	+	Missense_Mutation	SNP	A	A	T	rs78110679	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:62733201A>T	ENST00000335390.5	-	1	275	c.64T>A	c.(64-66)Tcc>Acc	p.S22T		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	22					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GTCCGATTGGAATCACTGAAC	0.662													A|||	335	0.066893	0.1233	0.0403	5008	,	,		12266	0.0069		0.0656	False		,,,				2504	0.0726				p.S22T		Atlas-SNP	.											.	TMEM17	19	.	0			c.T64A						PASS	.	A	THR/SER	524,3882	226.9+/-242.2	35,454,1714	34.0	36.0	35.0		64	3.6	1.0	2	dbSNP_131	35	650,7950	159.1+/-212.4	24,602,3674	yes	missense	TMEM17	NM_198276.2	58	59,1056,5388	TT,TA,AA		7.5581,11.8929,9.0266	benign	22/199	62733201	1174,11832	2203	4300	6503	SO:0001583	missense	200728	exon1			GATTGGAATCACT		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.64T>A	2.37:g.62733201A>T	ENSP00000335094:p.Ser22Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	165	102	0.618182	NM_198276	Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	37	CCDS1871.1	122	0.055860805860805864	56	0.11382113821138211	12	0.03314917127071823	2	0.0034965034965034965	52	0.06860158311345646	A	3.916	-0.019007	0.07681	0.118929	0.075581	ENSG00000186889	ENST00000335390	T	0.42900	0.96	4.82	3.59	0.41128	.	0.548588	0.18807	N	0.130637	T	0.00271	0.0008	N	0.12182	0.205	0.25286	N	0.989391	B	0.11235	0.004	B	0.06405	0.002	T	0.12268	-1.0554	10	0.11182	T	0.66	-5.5351	7.1569	0.25643	0.7408:0.0:0.0:0.2592	.	22	Q86X19	TMM17_HUMAN	T	22	ENSP00000335094:S22T	ENSP00000335094:S22T	S	-	1	0	TMEM17	62586705	1.000000	0.71417	1.000000	0.80357	0.096000	0.18686	2.292000	0.43549	2.043000	0.60533	0.374000	0.22700	TCC	A|0.925;T|0.075	0.075	strong		0.662	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
LYZL2	119180	hgsc.bcm.edu	37	10	30918549	30918549	+	Missense_Mutation	SNP	G	G	C	rs201069868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:30918549G>C	ENST00000375318.2	-	1	142	c.86C>G	c.(85-87)gCg>gGg	p.A29G		NM_183058.2	NP_898881.2	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	0					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			NS(2)|central_nervous_system(1)|large_intestine(1)|lung(14)|prostate(1)	19		Prostate(175;0.151)				GGTGCCTGCCGCAGAGGCTGA	0.527																																					p.A29G		Atlas-SNP	.											LYZL2,NS,adenoma,0,2	LYZL2	33	2	0			c.C86G						PASS	.						79.0	71.0	74.0					10																	30918549		2203	4300	6503	SO:0001583	missense	119180	exon1			CCTGCCGCAGAGG	AF139543	CCDS7167.2	10p11.23	2009-12-04			ENSG00000151033	ENSG00000151033			29613	protein-coding gene	gene with protein product		612748					Standard	NM_183058		Approved		uc001ivk.3	Q7Z4W2	OTTHUMG00000017898	ENST00000375318.2:c.86C>G	10.37:g.30918549G>C	ENSP00000364467:p.Ala29Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	155	29	0.187097	NM_183058	Q6NZ69	Missense_Mutation	SNP	ENST00000375318.2	37	CCDS7167.2	.	.	.	.	.	.	.	.	.	.	g	0.233	-1.019814	0.02078	.	.	ENSG00000151033	ENST00000375318	T	0.68025	-0.3	2.33	-0.854	0.10705	.	2.470750	0.01887	N	0.038284	T	0.45776	0.1359	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16958	-1.0385	9	0.15499	T	0.54	0.1998	4.5545	0.12130	0.0:0.3972:0.4547:0.1482	.	29	Q7Z4W2-2	.	G	29	ENSP00000364467:A29G	ENSP00000364467:A29G	A	-	2	0	LYZL2	30958555	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.110000	0.10824	-0.224000	0.09928	-0.381000	0.06696	GCG	G|0.894;C|0.106	0.106	strong		0.527	LYZL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047434.1	NM_183058	
NRROS	375387	hgsc.bcm.edu	37	3	196388099	196388099	+	Missense_Mutation	SNP	G	G	C	rs62623661	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:196388099G>C	ENST00000328557.4	+	3	1788	c.1585G>C	c.(1585-1587)Gcg>Ccg	p.A529P		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	529					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CAGCTTTATGGCGTTGGACTT	0.582													G|||	242	0.0483227	0.0083	0.0836	5008	,	,		18830	0.0		0.1392	False		,,,				2504	0.0337				p.A529P		Atlas-SNP	.											LRRC33,colon,carcinoma,-1,2	LRRC33	91	2	0			c.G1585C						PASS	.	G	PRO/ALA	117,4289	87.3+/-125.9	4,109,2090	127.0	125.0	126.0		1585	3.2	0.0	3	dbSNP_129	126	1093,7507	229.3+/-264.0	64,965,3271	yes	missense	LRRC33	NM_198565.1	27	68,1074,5361	CC,CG,GG		12.7093,2.6555,9.3034	benign	529/693	196388099	1210,11796	2203	4300	6503	SO:0001583	missense	375387	exon3			TTTATGGCGTTGG	AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"""leucine rich repeat containing 33"""	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.1585G>C	3.37:g.196388099G>C	ENSP00000328625:p.Ala529Pro	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	239	129	0.539749	NM_198565		Missense_Mutation	SNP	ENST00000328557.4	37	CCDS3319.1	126	0.057692307692307696	7	0.014227642276422764	28	0.07734806629834254	0	0.0	91	0.12005277044854881	G	2.087	-0.409399	0.04799	0.026555	0.127093	ENSG00000174004	ENST00000328557	T	0.52057	0.68	5.97	3.23	0.37069	.	0.288824	0.37095	N	0.002260	T	0.00241	0.0007	N	0.08118	0	0.18873	N	0.999988	B	0.20550	0.046	B	0.17722	0.019	T	0.05632	-1.0873	10	0.31617	T	0.26	.	6.9554	0.24568	0.2497:0.0:0.6374:0.1128	rs62623661	529	Q86YC3	LRC33_HUMAN	P	529	ENSP00000328625:A529P	ENSP00000328625:A529P	A	+	1	0	LRRC33	197872496	0.783000	0.28701	0.009000	0.14445	0.012000	0.07955	1.444000	0.35068	0.877000	0.35895	-0.137000	0.14449	GCG	G|0.915;C|0.085	0.085	strong		0.582	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565	
P2RX7	5027	hgsc.bcm.edu	37	12	121622304	121622304	+	Missense_Mutation	SNP	A	A	C	rs3751143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:121622304A>C	ENST00000546057.1	+	13	1630	c.1487A>C	c.(1486-1488)gAg>gCg	p.E496A	P2RX7_ENST00000535250.1_Missense_Mutation_p.E406A|P2RX7_ENST00000541446.1_Missense_Mutation_p.E207A|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000328963.5_Missense_Mutation_p.E326A	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	496			E -> A (polymorphism that results in a loss of function; dbSNP:rs3751143). {ECO:0000269|PubMed:11150303, ECO:0000269|PubMed:15489334}.		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGCCTGGAGGAGCTGTGCTGC	0.607													A|||	1039	0.207468	0.0847	0.1916	5008	,	,		16659	0.2669		0.2087	False		,,,				2504	0.3221				p.E496A		Atlas-SNP	.											.	P2RX7	53	.	0			c.A1487C	GRCh37	CM021316	P2RX7	M	rs3751143	PASS	.	A	ALA/GLU	396,4010	194.7+/-219.5	19,358,1826	41.0	40.0	40.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1487	5.2	1.0	12	dbSNP_107	40	1590,7010	294.4+/-301.9	151,1288,2861	yes	missense	P2RX7	NM_002562.5	107	170,1646,4687	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	18.4884,8.9877,15.2699	probably-damaging	496/596	121622304	1986,11020	2203	4300	6503	SO:0001583	missense	5027	exon13			TGGAGGAGCTGTG	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.1487A>C	12.37:g.121622304A>C	ENSP00000442349:p.Glu496Ala	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	421	0.19276556776556777	43	0.08739837398373984	77	0.212707182320442	146	0.25524475524475526	155	0.20448548812664907	A	25.1	4.606826	0.87157	0.089877	0.184884	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.05580	4.32;3.93;4.1;3.42	5.21	5.21	0.72293	.	0.000000	0.45867	D	0.000340	T	0.00012	0.0000	M	0.80982	2.52	0.27905	P	0.9388482	D;D;D;D	0.71674	0.986;0.998;0.986;0.991	P;D;P;P	0.81914	0.84;0.995;0.84;0.831	T	0.13710	-1.0499	9	0.87932	D	0	-30.5986	12.4464	0.55653	1.0:0.0:0.0:0.0	rs3751143;rs17850236;rs58839176;rs3751143	326;207;406;496	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	A	496;326;406;207	ENSP00000442349:E496A;ENSP00000330696:E326A;ENSP00000442572:E406A;ENSP00000437471:E207A	ENSP00000330696:E326A	E	+	2	0	P2RX7	120106687	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.490000	0.73645	1.967000	0.57214	0.482000	0.46254	GAG	A|0.826;C|0.174	0.174	strong		0.607	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
TBL3	10607	hgsc.bcm.edu	37	16	2025411	2025411	+	Silent	SNP	G	G	C	rs12925447	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2025411G>C	ENST00000568546.1	+	9	905	c.777G>C	c.(775-777)ggG>ggC	p.G259G		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	259					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						AGTCCCCAGGGCTGTACTTTC	0.627													C|||	260	0.0519169	0.0787	0.0576	5008	,	,		18960	0.0		0.0964	False		,,,				2504	0.0194				p.G259G	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.G777C						PASS	.	C		330,4066	794.5+/-415.3	19,292,1887	100.0	104.0	103.0		777	3.0	0.9	16	dbSNP_121	103	808,7792	782.3+/-407.6	47,714,3539	no	coding-synonymous	TBL3	NM_006453.2		66,1006,5426	CC,CG,GG		9.3953,7.5068,8.7565		259/809	2025411	1138,11858	2198	4300	6498	SO:0001819	synonymous_variant	10607	exon9			CCCAGGGCTGTAC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.777G>C	16.37:g.2025411G>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			G|0.918;C|0.082	0.082	strong		0.627	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
CR2	1380	hgsc.bcm.edu	37	1	207646923	207646923	+	Intron	SNP	G	G	A	rs17616	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207646923G>A	ENST00000367058.3	+	11	2167				CR2_ENST00000367057.3_Missense_Mutation_p.R671H|CR2_ENST00000367059.3_Intron|CR2_ENST00000458541.2_Intron	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2						B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CACCATGGTCGTCATACAGGT	0.453													G|||	1290	0.257588	0.4228	0.2017	5008	,	,		21002	0.1071		0.2903	False		,,,				2504	0.1953				p.R671H		Atlas-SNP	.											CR2,NS,carcinoma,+1,1	CR2	164	1	0			c.G2012A						PASS	.	G	HIS/ARG,	1672,2734	508.4+/-367.0	334,1004,865	126.0	126.0	126.0		2012,	-8.6	0.0	1	dbSNP_63	126	2707,5893	433.4+/-357.4	420,1867,2013	yes	missense,intron	CR2	NM_001006658.2,NM_001877.4	29,	754,2871,2878	AA,AG,GG		31.4767,37.9483,33.6691	,	671/1093,	207646923	4379,8627	2203	4300	6503	SO:0001627	intron_variant	1380	exon11			ATGGTCGTCATAC	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1979-223G>A	1.37:g.207646923G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	279	116	0.415771	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	584	0.2673992673992674	205	0.4166666666666667	90	0.24861878453038674	65	0.11363636363636363	224	0.2955145118733509	G	18.79	3.697997	0.68386	0.379483	0.314767	ENSG00000117322	ENST00000367057	T	0.64803	-0.12	5.11	-8.57	0.00900	.	.	.	.	.	T	0.00012	0.0000	L	0.31664	0.95	0.80722	P	0.0	D	0.63046	0.992	P	0.51582	0.674	T	0.04165	-1.0972	8	0.40728	T	0.16	.	9.1856	0.37168	0.6537:0.0:0.2436:0.1026	rs17616;rs4328074;rs52802875;rs61243177;rs17616	671	P20023-3	.	H	671	ENSP00000356024:R671H	ENSP00000356024:R671H	R	+	2	0	CR2	205713546	0.000000	0.05858	0.000000	0.03702	0.347000	0.29111	-1.366000	0.02585	-1.688000	0.01435	-1.127000	0.01993	CGT	G|0.694;A|0.306	0.306	strong		0.453	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
COL21A1	81578	hgsc.bcm.edu	37	6	55924962	55924962	+	Missense_Mutation	SNP	A	A	G	rs12209452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:55924962A>G	ENST00000244728.5	-	28	2859	c.2462T>C	c.(2461-2463)cTg>cCg	p.L821P	COL21A1_ENST00000370819.1_Missense_Mutation_p.L818P|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000535941.1_Missense_Mutation_p.L821P|COL21A1_ENST00000370808.2_Intron	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	821			L -> P (in dbSNP:rs12209452).		extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.L821P(2)		breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			ATGTTGGGACAGGCAATGATC	0.493													A|||	89	0.0177716	0.0038	0.0245	5008	,	,		13156	0.001		0.0497	False		,,,				2504	0.0164				p.L821P		Atlas-SNP	.											COL21A1_ENST00000244728,NS,carcinoma,0,2	COL21A1	201	2	2	Substitution - Missense(2)	prostate(2)	c.T2462C						PASS	.	A	PRO/LEU	32,3664		0,32,1816	48.0	47.0	47.0		2462	0.0	0.2	6	dbSNP_120	47	411,7767		6,399,3684	yes	missense	COL21A1	NM_030820.3	98	6,431,5500	GG,GA,AA		5.0257,0.8658,3.7308	benign	821/958	55924962	443,11431	1848	4089	5937	SO:0001583	missense	81578	exon28			TGGGACAGGCAAT	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.2462T>C	6.37:g.55924962A>G	ENSP00000244728:p.Leu821Pro	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	58	0.026556776556776556	1	0.0020325203252032522	11	0.03038674033149171	1	0.0017482517482517483	45	0.059366754617414245	A	8.779	0.927742	0.18056	0.008658	0.050257	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811	D;D;D	0.89617	-2.53;-2.49;-2.54	5.33	-0.0045	0.14022	.	0.877447	0.09643	N	0.774756	T	0.50939	0.1645	N	0.08118	0	0.09310	P	0.9999999658888	B;B;B	0.24533	0.031;0.105;0.105	B;B;B	0.16722	0.016;0.016;0.016	T	0.17868	-1.0355	8	.	.	.	.	2.1255	0.03737	0.1274:0.1496:0.132:0.591	rs12209452;rs52799557;rs12209452	821;821;178	B7ZLK3;Q96P44;B3KU30	.;COLA1_HUMAN;.	P	821;818;821;818	ENSP00000244728:L821P;ENSP00000359855:L818P;ENSP00000444384:L821P	.	L	-	2	0	COL21A1	56032921	0.988000	0.35896	0.180000	0.23079	0.989000	0.77384	1.732000	0.38146	-0.235000	0.09767	-0.270000	0.10280	CTG	A|0.970;G|0.030	0.030	strong		0.493	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
ODF3B	440836	hgsc.bcm.edu	37	22	50969647	50969647	+	Missense_Mutation	SNP	C	C	G	rs139023197	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50969647C>G	ENST00000428989.2	-	3	390	c.391G>C	c.(391-393)Ggt>Cgt	p.G131R	TYMP_ENST00000252029.3_5'Flank|TYMP_ENST00000395680.1_5'Flank|ODF3B_ENST00000405135.1_Missense_Mutation_p.G146A|ODF3B_ENST00000401779.1_Missense_Mutation_p.G107A|TYMP_ENST00000395678.3_5'Flank|ODF3B_ENST00000329363.4_Missense_Mutation_p.G131R|ODF3B_ENST00000403326.1_Missense_Mutation_p.G63R|TYMP_ENST00000395681.1_5'Flank			A8MYP8	ODF3B_HUMAN	outer dense fiber of sperm tails 3B	131										lung(2)	2						GCCTGGACACCCCAGTTTCGG	0.682													C|||	101	0.0201677	0.0015	0.0202	5008	,	,		13778	0.0079		0.0437	False		,,,				2504	0.0337				p.G131R		Atlas-SNP	.											.	ODF3B	6	.	0			c.G391C						PASS	.	C	ARG/GLY	21,3985		0,21,1982	31.0	35.0	34.0		391	4.2	1.0	22	dbSNP_134	34	324,8002		11,302,3850	yes	missense	ODF3B	NM_001014440.3	125	11,323,5832	GG,GC,CC		3.8914,0.5242,2.7976	probably-damaging	131/254	50969647	345,11987	2003	4163	6166	SO:0001583	missense	440836	exon4			GGACACCCCAGTT		CCDS43039.1	22q13.33	2008-10-24			ENSG00000177989	ENSG00000177989			34388	protein-coding gene	gene with protein product							Standard	NM_001014440		Approved		uc003bmh.2	A8MYP8	OTTHUMG00000150334	ENST00000428989.2:c.391G>C	22.37:g.50969647C>G	ENSP00000390712:p.Gly131Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	140	76	0.542857	NM_001014440	A0PK18	Missense_Mutation	SNP	ENST00000428989.2	37	CCDS43039.1	41|41	0.018772893772893772|0.018772893772893772	0|0	0.0|0.0	5|5	0.013812154696132596|0.013812154696132596	4|4	0.006993006993006993|0.006993006993006993	32|32	0.04221635883905013|0.04221635883905013	C|C	12.83|12.83	2.055725|2.055725	0.36277|0.36277	0.005242|0.005242	0.038914|0.038914	ENSG00000177989|ENSG00000177989	ENST00000401779;ENST00000405135|ENST00000329363;ENST00000403326;ENST00000428989	T|T;T;T	0.52295|0.29917	0.67|1.55;1.6;1.55	4.21|4.21	4.21|4.21	0.49690|0.49690	.|.	.|.	.|.	.|.	.|.	T|T	0.11281|0.11281	0.0275|0.0275	L|L	0.47716|0.47716	1.5|1.5	0.32204|0.32204	N|N	0.57746|0.57746	D|D	0.60160|0.58268	0.987|0.982	P|P	0.61328|0.55011	0.887|0.766	T|T	0.04723|0.04723	-1.0931|-1.0931	9|9	0.59425|0.16420	D|T	0.04|0.52	-2.6159|-2.6159	12.2401|12.2401	0.54538|0.54538	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	107|131	B5MD02|A8MYP8	.|ODF3B_HUMAN	A|R	107;146|131;63;131	ENSP00000384012:G146A|ENSP00000382804:G131R;ENSP00000385123:G63R;ENSP00000390712:G131R	ENSP00000384310:G107A|ENSP00000382804:G131R	G|G	-|-	2|1	0|0	ODF3B|ODF3B	49316513|49316513	0.579000|0.579000	0.26725|0.26725	0.996000|0.996000	0.52242|0.52242	0.471000|0.471000	0.32888|0.32888	1.708000|1.708000	0.37899|0.37899	2.329000|2.329000	0.79093|0.79093	0.561000|0.561000	0.74099|0.74099	GGG|GGT	C|0.969;G|0.031	0.031	strong		0.682	ODF3B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317626.2		
ZNF407	55628	hgsc.bcm.edu	37	18	72347482	72347482	+	Silent	SNP	T	T	C	rs12327359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:72347482T>C	ENST00000299687.5	+	1	4507	c.4507T>C	c.(4507-4509)Tta>Cta	p.L1503L	ZNF407_ENST00000582337.1_Silent_p.L1503L|ZNF407_ENST00000577538.1_Silent_p.L1503L|ZNF407_ENST00000309902.6_Silent_p.L1503L	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1503					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L1503L(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAATTTATTTTTACATATTAA	0.473													C|||	2123	0.423922	0.7201	0.3271	5008	,	,		19354	0.1845		0.4175	False		,,,				2504	0.3456				p.L1503L		Atlas-SNP	.											ZNF407,NS,carcinoma,0,1	ZNF407	231	1	1	Substitution - coding silent(1)	prostate(1)	c.T4507C						PASS	.	C	,,	2571,1165		885,801,182	41.0	43.0	43.0		4507,4507,4507	4.8	0.9	18	dbSNP_120	43	3538,4686		754,2030,1328	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	1639,2831,1510	CC,CT,TT		43.0204,31.1831,48.9214	,,	1503/1816,1503/1661,1503/2249	72347482	6109,5851	1868	4112	5980	SO:0001819	synonymous_variant	55628	exon1			TTATTTTTACATA	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.4507T>C	18.37:g.72347482T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			T|0.567;C|0.433	0.433	strong		0.473	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
EVC2	132884	hgsc.bcm.edu	37	4	5570221	5570221	+	Silent	SNP	G	G	A	rs12511039	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:5570221G>A	ENST00000344408.5	-	20	3560	c.3507C>T	c.(3505-3507)caC>caT	p.H1169H	EVC2_ENST00000310917.2_Silent_p.H1089H|EVC2_ENST00000344938.1_Silent_p.H1169H	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	1169					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.H1169H(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TCTCAGCTGCGTGGTCCACAT	0.697													G|||	2208	0.440895	0.1566	0.3703	5008	,	,		13114	0.876		0.3111	False		,,,				2504	0.5603				p.H1169H		Atlas-SNP	.											EVC2,NS,lymphoid_neoplasm,0,1	EVC2	202	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C3507T						PASS	.	G	,	749,3653		74,601,1526	24.0	24.0	24.0		3267,3507	3.5	0.0	4	dbSNP_120	24	2584,6014		374,1836,2089	no	coding-synonymous,coding-synonymous	EVC2	NM_001166136.1,NM_147127.4	,	448,2437,3615	AA,AG,GG		30.0535,17.015,25.6385	,	1089/1229,1169/1309	5570221	3333,9667	2201	4299	6500	SO:0001819	synonymous_variant	132884	exon20			AGCTGCGTGGTCC	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.3507C>T	4.37:g.5570221G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	48	0.607595	NM_147127	Q86YT3|Q86YT4|Q8NG49	Silent	SNP	ENST00000344408.5	37	CCDS3382.2																																																																																			G|0.656;A|0.344	0.344	strong		0.697	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121653177	121653177	+	Silent	SNP	A	A	G	rs61732006	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:121653177A>G	ENST00000393386.2	+	12	4488	c.4077A>G	c.(4075-4077)acA>acG	p.T1359T	PTPRZ1_ENST00000483028.1_3'UTR|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1359					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						CTTCTGATACATTTGTATCTA	0.378													A|||	528	0.105431	0.1528	0.0562	5008	,	,		22427	0.2093		0.0557	False		,,,				2504	0.0204				p.T1359T		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.A4077G						PASS	.	A	,,	698,3708	292.7+/-282.2	63,572,1568	179.0	179.0	179.0		,,4077	-1.4	0.0	7	dbSNP_129	179	650,7950	165.9+/-218.0	23,604,3673	no	intron,intron,coding-synonymous	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,	86,1176,5241	GG,GA,AA		7.5581,15.842,10.3644	,,	,,1359/2316	121653177	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			TGATACATTTGTA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.4077A>G	7.37:g.121653177A>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	247	99	0.40081	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			A|0.902;G|0.098	0.098	strong		0.378	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
FAM83B	222584	hgsc.bcm.edu	37	6	54806489	54806489	+	Missense_Mutation	SNP	C	C	A	rs9475077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:54806489C>A	ENST00000306858.7	+	5	2836	c.2720C>A	c.(2719-2721)aCc>aAc	p.T907N	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	907			T -> N (in dbSNP:rs9475077). {ECO:0000269|PubMed:15489334}.							autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					GCAGTTGTTACCCCTGAAAGA	0.463													C|||	1449	0.289337	0.7057	0.1715	5008	,	,		19602	0.0337		0.1511	False		,,,				2504	0.2157				p.T907N		Atlas-SNP	.											.	FAM83B	186	.	0			c.C2720A						PASS	.	C	ASN/THR	2682,1724	650.0+/-399.0	825,1032,346	103.0	94.0	97.0		2720	-0.4	0.0	6	dbSNP_119	97	1443,7157	276.7+/-292.4	100,1243,2957	yes	missense	FAM83B	NM_001010872.1	65	925,2275,3303	AA,AC,CC		16.7791,39.1285,31.7161	benign	907/1012	54806489	4125,8881	2203	4300	6503	SO:0001583	missense	222584	exon5			TTGTTACCCCTGA	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.2720C>A	6.37:g.54806489C>A	ENSP00000304078:p.Thr907Asn	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	547	0.25045787545787546	349	0.709349593495935	73	0.20165745856353592	13	0.022727272727272728	112	0.14775725593667546	C	11.68	1.710954	0.30322	0.608715	0.167791	ENSG00000168143	ENST00000306858	T	0.31769	1.48	5.63	-0.417	0.12347	.	1.021330	0.07821	N	0.959732	T	0.08670	0.0215	L	0.29908	0.895	0.80722	P	0.0	B	0.20671	0.047	B	0.19148	0.024	T	0.34254	-0.9836	9	0.54805	T	0.06	-0.0157	7.8902	0.29674	0.0:0.5634:0.0989:0.3378	rs9475077;rs52817191;rs58256665;rs9475077	907	Q5T0W9	FA83B_HUMAN	N	907	ENSP00000304078:T907N	ENSP00000304078:T907N	T	+	2	0	FAM83B	54914448	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.247000	0.18179	-0.133000	0.11537	-0.136000	0.14681	ACC	C|0.694;A|0.306	0.306	strong		0.463	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
ST6GALNAC1	55808	hgsc.bcm.edu	37	17	74625715	74625715	+	Silent	SNP	T	T	C	rs8081258	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:74625715T>C	ENST00000156626.7	-	2	409	c.210A>G	c.(208-210)gcA>gcG	p.A70A	ST6GALNAC1_ENST00000590878.1_5'UTR	NM_018414.3	NP_060884.1	Q9NSC7	SIA7A_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	70					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	22						TTGTCCTCCTTGCCCTTGTGG	0.537													T|||	383	0.0764776	0.1271	0.0634	5008	,	,		19270	0.001		0.0924	False		,,,				2504	0.0787				p.A70A		Atlas-SNP	.											.	ST6GALNAC1	42	.	0			c.A210G						PASS	.	T		498,3908	232.6+/-246.1	27,444,1732	168.0	150.0	156.0		210	-2.6	0.0	17	dbSNP_116	156	864,7736	195.6+/-240.8	41,782,3477	no	coding-synonymous	ST6GALNAC1	NM_018414.3		68,1226,5209	CC,CT,TT		10.0465,11.3028,10.4721		70/601	74625715	1362,11644	2203	4300	6503	SO:0001819	synonymous_variant	55808	exon2			CCTCCTTGCCCTT	Y11339	CCDS11748.1	17q25.3	2013-03-01	2005-02-07	2005-02-07	ENSG00000070526	ENSG00000070526		"""Sialyltransferases"""	23614	protein-coding gene	gene with protein product		610138	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) A"""	SIAT7A			Standard	NM_001289107		Approved	ST6GalNAcI	uc002jsh.3	Q9NSC7	OTTHUMG00000180369	ENST00000156626.7:c.210A>G	17.37:g.74625715T>C		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	374	193	0.516043	NM_018414	Q6UW90|Q9NSC6	Silent	SNP	ENST00000156626.7	37	CCDS11748.1																																																																																			T|0.901;C|0.099	0.099	strong		0.537	ST6GALNAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450974.1	NM_018414	
GABRA4	2557	hgsc.bcm.edu	37	4	46995366	46995366	+	Missense_Mutation	SNP	G	G	T	rs2229940	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:46995366G>T	ENST00000264318.3	-	1	1058	c.76C>A	c.(76-78)Ctg>Atg	p.L26M	GABRA4_ENST00000509316.1_5'UTR	NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	26			L -> M (in dbSNP:rs2229940).		central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.L26M(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	CAAACCGCCAGGCACAGGAAG	0.607													G|||	1506	0.300719	0.2526	0.2968	5008	,	,		16875	0.3879		0.3668	False		,,,				2504	0.2106				p.L26M	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											GABRA4,NS,carcinoma,0,1	GABRA4	129	1	1	Substitution - Missense(1)	prostate(1)	c.C76A						PASS	.	G	MET/LEU,,	1132,3274	403.5+/-332.8	127,878,1198	109.0	105.0	106.0		76,,	3.0	1.0	4	dbSNP_98	106	3154,5446	479.1+/-370.0	599,1956,1745	yes	missense,intron,intron	GABRA4	NM_000809.3,NM_001204266.1,NM_001204267.1	15,,	726,2834,2943	TT,TG,GG		36.6744,25.6922,32.954	probably-damaging,,	26/555,,	46995366	4286,8720	2203	4300	6503	SO:0001583	missense	2557	exon1			CCGCCAGGCACAG		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4078	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 4"""	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.76C>A	4.37:g.46995366G>T	ENSP00000264318:p.Leu26Met	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	204	95	0.465686	NM_000809	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	742	0.33974358974358976	138	0.2804878048780488	107	0.2955801104972376	214	0.3741258741258741	283	0.3733509234828496	G	13.24	2.178732	0.38511	0.256922	0.366744	ENSG00000109158	ENST00000264318	D	0.81996	-1.56	4.72	2.98	0.34508	.	0.473208	0.19701	N	0.108022	T	0.00012	0.0000	N	0.24115	0.695	0.35598	P	0.19235199999999997	B	0.23806	0.091	B	0.29524	0.103	T	0.13045	-1.0524	9	0.49607	T	0.09	.	6.8007	0.23750	0.2113:0.0:0.7887:0.0	rs2229940;rs2280071;rs16859834;rs52790560;rs2229940	26	P48169	GBRA4_HUMAN	M	26	ENSP00000264318:L26M	ENSP00000264318:L26M	L	-	1	2	GABRA4	46690123	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	2.533000	0.45667	0.588000	0.29660	0.585000	0.79938	CTG	G|0.672;T|0.328	0.328	strong		0.607	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1		
PRAMEF1	65121	hgsc.bcm.edu	37	1	12854401	12854401	+	Nonsense_Mutation	SNP	G	G	T	rs201717831		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:12854401G>T	ENST00000332296.7	+	3	728	c.625G>T	c.(625-627)Gag>Tag	p.E209*	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	209					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TAGTATTCAAGAGCTGGAAAT	0.398																																					p.E209X		Atlas-SNP	.											PRAMEF1,NS,carcinoma,0,2	PRAMEF1	78	2	0			c.G625T						scavenged	.						363.0	333.0	343.0					1																	12854401		2203	4300	6503	SO:0001587	stop_gained	65121	exon3			ATTCAAGAGCTGG	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"""-"""	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.625G>T	1.37:g.12854401G>T	ENSP00000332134:p.Glu209*	Somatic	478	22	0.0460251		WXS	Illumina HiSeq	Phase_I	579	44	0.0759931	NM_023013	Q9UQP2	Nonsense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	16.09	3.023241	0.54683	.	.	ENSG00000116721	ENST00000332296	.	.	.	1.74	0.76	0.18442	.	0.742629	0.12834	N	0.435382	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	3.5875	0.07977	0.2694:0.0:0.7306:0.0	.	.	.	.	X	209	.	ENSP00000332134:E209X	E	+	1	0	PRAMEF1	12776988	0.002000	0.14202	0.001000	0.08648	0.004000	0.04260	0.426000	0.21363	0.256000	0.21614	0.543000	0.68304	GAG	G|0.500;C|0.500	.	alt		0.398	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
ZNF419	79744	hgsc.bcm.edu	37	19	58003488	58003488	+	Silent	SNP	A	A	G	rs2074070	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58003488A>G	ENST00000221735.7	+	4	393	c.207A>G	c.(205-207)gcA>gcG	p.A69A	ZNF419_ENST00000518999.1_Silent_p.A70A|ZNF419_ENST00000354197.4_Silent_p.A57A|ZNF419_ENST00000347466.6_Intron|ZNF419_ENST00000442920.2_Silent_p.A56A|ZNF419_ENST00000520540.1_Silent_p.A57A|ZNF419_ENST00000426954.2_Silent_p.A57A|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000415379.2_Intron|ZNF419_ENST00000424930.2_Silent_p.A70A			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		TAGGACTTGCATCTTCCAAGA	0.468													A|||	2157	0.430711	0.2995	0.4611	5008	,	,		18486	0.5764		0.3161	False		,,,				2504	0.5542				p.A70A		Atlas-SNP	.											.	ZNF419	134	.	0			c.A210G						PASS	.						63.0	60.0	61.0					19																	58003488		2202	4280	6482	SO:0001819	synonymous_variant	79744	exon4			ACTTGCATCTTCC	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.207A>G	19.37:g.58003488A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	137	55	0.40146	NM_001098491	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	37	CCDS54326.1																																																																																			A|0.647;G|0.353	0.353	strong		0.468	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	
FREM2	341640	hgsc.bcm.edu	37	13	39263023	39263023	+	Silent	SNP	C	C	T	rs12874397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:39263023C>T	ENST00000280481.7	+	1	1758	c.1542C>T	c.(1540-1542)gcC>gcT	p.A514A		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	514					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AGCTGGCAGCCGGCCAGGTGG	0.602													C|||	422	0.0842652	0.0061	0.1239	5008	,	,		14684	0.004		0.2634	False		,,,				2504	0.0603				p.A514A		Atlas-SNP	.											.	FREM2	385	.	0			c.C1542T						PASS	.	C		190,4216	115.9+/-153.8	4,182,2017	25.0	25.0	25.0		1542	-9.4	0.2	13	dbSNP_121	25	2241,6357	355.9+/-330.1	314,1613,2372	no	coding-synonymous	FREM2	NM_207361.4		318,1795,4389	TT,TC,CC		26.0642,4.3123,18.6942		514/3170	39263023	2431,10573	2203	4299	6502	SO:0001819	synonymous_variant	341640	exon1			GGCAGCCGGCCAG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.1542C>T	13.37:g.39263023C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	48	44	0.916667	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|0.841;T|0.159	0.159	strong		0.602	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
SERPINA1	5265	hgsc.bcm.edu	37	14	94849201	94849201	+	Missense_Mutation	SNP	C	C	T	rs709932	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:94849201C>T	ENST00000448921.1	-	4	946	c.374G>A	c.(373-375)cGt>cAt	p.R125H	SERPINA1_ENST00000393088.4_Missense_Mutation_p.R125H|SERPINA1_ENST00000555289.1_5'Flank|SERPINA1_ENST00000440909.1_Missense_Mutation_p.R125H|SERPINA1_ENST00000404814.4_Missense_Mutation_p.R125H|SERPINA1_ENST00000402629.1_Missense_Mutation_p.R125H|SERPINA1_ENST00000393087.4_Missense_Mutation_p.R125H|SERPINA1_ENST00000355814.4_Missense_Mutation_p.R125H|SERPINA1_ENST00000437397.1_Missense_Mutation_p.R125H|SERPINA1_ENST00000449399.3_Missense_Mutation_p.R125H	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	125			R -> H (in M2; associated with D-400; dbSNP:rs709932).		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		GTTGAGGGTACGGAGGAGTTC	0.552													C|||	804	0.160543	0.0197	0.1138	5008	,	,		17932	0.2282		0.1561	False		,,,				2504	0.319				p.R125H		Atlas-SNP	.											.	SERPINA1	51	.	0			c.G374A	GRCh37	CM900182	SERPINA1	M	rs709932	PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	160,4246	109.1+/-147.4	1,158,2044	58.0	57.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	374,374,374,374,374,374,374,374,374,374,374	-2.8	0.0	14	dbSNP_86	57	1421,7179	273.7+/-290.8	117,1187,2996	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	SERPINA1	NM_000295.4,NM_001002235.2,NM_001002236.2,NM_001127700.1,NM_001127701.1,NM_001127702.1,NM_001127703.1,NM_001127704.1,NM_001127705.1,NM_001127706.1,NM_001127707.1	29,29,29,29,29,29,29,29,29,29,29	118,1345,5040	TT,TC,CC		16.5233,3.6314,12.1559	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	125/419,125/419,125/419,125/419,125/419,125/419,125/419,125/419,125/419,125/419,125/419	94849201	1581,11425	2203	4300	6503	SO:0001583	missense	5265	exon4			AGGGTACGGAGGA	X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"""Serine (or cysteine) peptidase inhibitors"""	8941	protein-coding gene	gene with protein product	"""protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"""	107400	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"""	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.374G>A	14.37:g.94849201C>T	ENSP00000416066:p.Arg125His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_001127701	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Missense_Mutation	SNP	ENST00000448921.1	37	CCDS9925.1	285	0.1304945054945055	9	0.018292682926829267	48	0.13259668508287292	124	0.21678321678321677	104	0.13720316622691292	C	1.988	-0.432510	0.04669	0.036314	0.165233	ENSG00000197249	ENST00000440909;ENST00000448921;ENST00000437397;ENST00000355814;ENST00000393087;ENST00000393088;ENST00000404814;ENST00000449399;ENST00000402629;ENST00000554720;ENST00000556091;ENST00000557492	D;D;D;D;D;D;D;D;D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77	5.62	-2.82	0.05787	Serpin domain (3);	1.216040	0.05869	N	0.624379	T	0.00039	0.0001	N	0.02674	-0.535	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.07424	-1.0773	9	0.05525	T	0.97	.	7.3598	0.26739	0.0:0.2499:0.1816:0.5685	rs709932;rs3189606;rs52795514;rs57636922;rs709932	125;125	P01009-2;P01009	.;A1AT_HUMAN	H	125;125;125;125;125;125;125;125;125;39;125;125	ENSP00000390299:R125H;ENSP00000416066:R125H;ENSP00000408474:R125H;ENSP00000348068:R125H;ENSP00000376802:R125H;ENSP00000376803:R125H;ENSP00000385960:R125H;ENSP00000416354:R125H;ENSP00000386094:R125H;ENSP00000450561:R39H;ENSP00000452169:R125H;ENSP00000452452:R125H	ENSP00000348068:R125H	R	-	2	0	SERPINA1	93918954	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	-0.755000	0.04782	-0.129000	0.11620	-1.199000	0.01669	CGT	T|0.129;G|0.004	0.129	strong		0.552	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235	
FMN2	56776	hgsc.bcm.edu	37	1	240341268	240341268	+	Silent	SNP	A	A	G	rs3765588	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:240341268A>G	ENST00000319653.9	+	3	2060	c.1830A>G	c.(1828-1830)tcA>tcG	p.S610S	RP11-567G24.3_ENST00000412311.1_RNA|RP11-567G24.3_ENST00000444308.1_RNA	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	610					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCACACACTCATTGGACTATT	0.418													G|||	1194	0.238419	0.3283	0.1138	5008	,	,		14859	0.2232		0.1789	False		,,,				2504	0.2822				p.S610S		Atlas-SNP	.											.	FMN2	451	.	0			c.A1830G						PASS	.	G		1286,3120	700.0+/-406.6	196,894,1113	98.0	95.0	96.0		1830	-11.0	0.4	1	dbSNP_107	96	1657,6943	740.4+/-407.1	160,1337,2803	no	coding-synonymous	FMN2	NM_020066.4		356,2231,3916	GG,GA,AA		19.2674,29.1875,22.628		610/1723	240341268	2943,10063	2203	4300	6503	SO:0001819	synonymous_variant	56776	exon3			ACACTCATTGGAC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1830A>G	1.37:g.240341268A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			A|0.768;G|0.232	0.232	strong		0.418	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
HLA-C	3107	hgsc.bcm.edu	37	6	31238930	31238930	+	Missense_Mutation	SNP	A	A	C	rs79636386	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238930A>C	ENST00000376228.5	-	3	553	c.539T>G	c.(538-540)cTg>cGg	p.L180R	HLA-C_ENST00000383329.3_Missense_Mutation_p.L180R	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	180	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GTAGGCTCTCAGCTGCTCCGC	0.687													a|||	1859	0.371206	0.3396	0.3833	5008	,	,		11518	0.372		0.3857	False		,,,				2504	0.3896				p.L180R		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	0			c.T539G						PASS	.						44.0	31.0	35.0					6																	31238930		2196	4292	6488	SO:0001583	missense	3107	exon3			GCTCTCAGCTGCT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.539T>G	6.37:g.31238930A>C	ENSP00000365402:p.Leu180Arg	Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	187	85	0.454545	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	659	0.3017399267399267	127	0.258130081300813	121	0.3342541436464088	176	0.3076923076923077	235	0.3100263852242744	.	0.350	-0.945417	0.02304	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00010	9.43;9.43	2.81	-5.62	0.02481	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	115.764000	0.00166	N	0.000008	T	0.00012	0.0000	N	0.04335	-0.225	0.80722	P	0.0	B;B;B;B	0.19331	0.035;0.01;0.023;0.01	B;B;B;B	0.22601	0.035;0.018;0.04;0.018	T	0.33599	-0.9862	9	0.15499	T	0.54	.	0.7503	0.00989	0.3702:0.2557:0.1128:0.2613	rs2308592;rs9264655;rs17839942;rs28367578	180;180;180;180	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	R	180;180;180;217	ENSP00000365402:L180R;ENSP00000372819:L180R	ENSP00000365402:L180R	L	-	2	0	HLA-C	31346909	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.015000	0.00160	-3.815000	0.00103	-3.321000	0.00044	CTG	T|0.001;C|0.301;A|0.698	0.301	weak		0.687	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
WWC1	23286	hgsc.bcm.edu	37	5	167850748	167850748	+	Silent	SNP	A	A	G	rs12054944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:167850748A>G	ENST00000265293.4	+	11	1987	c.1485A>G	c.(1483-1485)tcA>tcG	p.S495S	WWC1_ENST00000521089.1_Silent_p.S495S	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	495					cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		TCCGGCCCTCAGGCTGCATCA	0.632													G|||	3339	0.666733	0.6657	0.6383	5008	,	,		16221	0.9921		0.4473	False		,,,				2504	0.5787				p.S495S		Atlas-SNP	.											WWC1,NS,carcinoma,0,2	WWC1	98	2	0			c.A1485G						PASS	.	G	,,	2774,1632	500.0+/-364.6	861,1052,290	55.0	57.0	56.0		1485,1485,1485	-10.4	0.2	5	dbSNP_120	56	3727,4873	614.4+/-396.2	815,2097,1388	no	coding-synonymous,coding-synonymous,coding-synonymous	WWC1	NM_001161661.1,NM_001161662.1,NM_015238.2	,,	1676,3149,1678	GG,GA,AA		43.3372,37.0404,49.9846	,,	495/1120,495/1119,495/1114	167850748	6501,6505	2203	4300	6503	SO:0001819	synonymous_variant	23286	exon11			GCCCTCAGGCTGC	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"""WW, C2 and coiled-coil domain containing"""	29435	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 168"""	610533	"""WW, C2 and coiled-coil domain containing 1"""			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.1485A>G	5.37:g.167850748A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	86	0.966292	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Silent	SNP	ENST00000265293.4	37	CCDS4366.1	1438	0.6584249084249084	329	0.6686991869918699	213	0.5883977900552486	571	0.9982517482517482	325	0.4287598944591029	G	7.670	0.686728	0.14973	0.629596	0.433372	ENSG00000113645	ENST00000393895;ENST00000524228	.	.	.	5.22	-10.4	0.00318	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999049553	.	.	.	.	.	.	T	0.16867	-1.0388	3	.	.	.	.	2.1271	0.03741	0.3239:0.2652:0.0693:0.3416	rs12054944;rs17633374;rs59077503;rs12054944	.	.	.	G	457;272	.	.	R	+	1	2	WWC1	167783326	0.000000	0.05858	0.173000	0.22940	0.734000	0.41952	-4.861000	0.00177	-2.954000	0.00292	-0.119000	0.15052	AGG	A|0.448;G|0.552	0.552	strong		0.632	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	
OR12D2	26529	hgsc.bcm.edu	37	6	29364835	29364835	+	Missense_Mutation	SNP	T	T	G	rs2073153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29364835T>G	ENST00000383555.2	+	1	420	c.359T>G	c.(358-360)cTc>cGc	p.L120R	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	120			L -> R (in dbSNP:rs2073153).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						GCATTTGACCTCTCTGTGGCT	0.493													G|||	1597	0.31889	0.1921	0.3458	5008	,	,		21217	0.3641		0.4523	False		,,,				2504	0.2873				p.L120R		Atlas-SNP	.											.	OR12D2	42	.	0			c.T359G	GRCh37	CM035845	OR12D2	M	rs2073153	PASS	.	G	ARG/LEU	669,2353		75,519,917	94.0	94.0	94.0		359	3.0	0.9	6	dbSNP_96	94	2409,3009		534,1341,834	yes	missense	OR12D2	NM_013936.3	102	609,1860,1751	GG,GT,TT		44.4629,22.1377,36.4692	benign	120/308	29364835	3078,5362	1511	2709	4220	SO:0001583	missense	26529	exon1			TTGACCTCTCTGT		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.359T>G	6.37:g.29364835T>G	ENSP00000373047:p.Leu120Arg	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	295	121	0.410169	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	787	0.36034798534798534	101	0.20528455284552846	123	0.3397790055248619	208	0.36363636363636365	355	0.4683377308707124	G	0.013	-1.637038	0.00806	0.221377	0.444629	ENSG00000168787	ENST00000383555	T	0.04809	3.55	3.94	3.05	0.35203	GPCR, rhodopsin-like superfamily (1);	0.200095	0.35772	N	0.002997	T	0.00144	0.0004	N	0.00000	-4.03	0.45295	P	0.0017089999999999606	B	0.02656	0.0	B	0.01281	0.0	T	0.35076	-0.9803	9	0.02654	T	1	.	9.9552	0.41661	0.0:0.151:0.692:0.1569	rs2073153;rs58214000	120	P58182	O12D2_HUMAN	R	120	ENSP00000373047:L120R	ENSP00000373047:L120R	L	+	2	0	OR12D2	29472814	0.936000	0.31750	0.926000	0.36857	0.003000	0.03518	4.857000	0.62939	0.329000	0.23460	-0.982000	0.02568	CTC	T|0.650;G|0.350	0.350	strong		0.493	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
KY	339855	hgsc.bcm.edu	37	3	134322814	134322814	+	Silent	SNP	G	G	C	rs2293294	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:134322814G>C	ENST00000423778.2	-	11	1654	c.1593C>G	c.(1591-1593)ggC>ggG	p.G531G	KY_ENST00000503669.1_3'UTR|KY_ENST00000508956.1_Silent_p.G510G	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	531					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)	p.G531G(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGGCAAACTTGCCTGCATGGG	0.527													G|||	1482	0.295927	0.413	0.2349	5008	,	,		20559	0.1101		0.33	False		,,,				2504	0.3374				p.G531G		Atlas-SNP	.											KY_ENST00000423778,NS,carcinoma,0,1	KY	92	1	1	Substitution - coding silent(1)	stomach(1)	c.C1593G						PASS	.	G		1556,2496		331,894,801	79.0	81.0	80.0		1593	3.8	1.0	3	dbSNP_100	80	2993,5407		564,1865,1771	no	coding-synonymous	KY	NM_178554.4		895,2759,2572	CC,CG,GG		35.631,38.4008,36.5323		531/662	134322814	4549,7903	2026	4200	6226	SO:0001819	synonymous_variant	339855	exon11			AAACTTGCCTGCA	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.1593C>G	3.37:g.134322814G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			G|0.694;C|0.306	0.306	strong		0.527	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
COL2A1	1280	hgsc.bcm.edu	37	12	48391416	48391416	+	Silent	SNP	G	G	T	rs3737548	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48391416G>T	ENST00000380518.3	-	7	668	c.504C>A	c.(502-504)ggC>ggA	p.G168G	COL2A1_ENST00000337299.6_Silent_p.G99G	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	168					axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	gaccaggggggccgggaggac	0.562													G|||	1098	0.219249	0.146	0.2277	5008	,	,		17261	0.3036		0.2356	False		,,,				2504	0.2086				p.G168G		Atlas-SNP	.											.	COL2A1	368	.	0			c.C504A						PASS	.	G	,	693,3713	269.8+/-269.2	52,589,1562	31.0	35.0	34.0		504,297	-0.7	1.0	12	dbSNP_107	34	1927,6673	319.5+/-314.2	209,1509,2582	no	coding-synonymous,coding-synonymous	COL2A1	NM_001844.4,NM_033150.2	,	261,2098,4144	TT,TG,GG		22.407,15.7286,20.1445	,	168/1488,99/1419	48391416	2620,10386	2203	4300	6503	SO:0001819	synonymous_variant	1280	exon7			AGGGGGGCCGGGA	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.504C>A	12.37:g.48391416G>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	96	58	0.604167	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	37	CCDS41778.1																																																																																			G|0.784;T|0.216	0.216	strong		0.562	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
SPATS1	221409	hgsc.bcm.edu	37	6	44310854	44310854	+	Missense_Mutation	SNP	G	G	A	rs10948132	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:44310854G>A	ENST00000288390.2	+	1	369	c.22G>A	c.(22-24)Gga>Aga	p.G8R	RP11-444E17.6_ENST00000505802.1_Intron|SPATS1_ENST00000323108.8_Missense_Mutation_p.G8R			Q496A3	SPAS1_HUMAN	spermatogenesis associated, serine-rich 1	8			G -> R (in dbSNP:rs10948132). {ECO:0000269|PubMed:15489334}.							NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(5)|skin(1)|urinary_tract(1)	14	all_lung(25;0.00469)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CATGCTCACTGGAAACAGTCC	0.498													G|||	1776	0.354633	0.0983	0.5058	5008	,	,		16358	0.6151		0.3022	False		,,,				2504	0.3793				p.G8R		Atlas-SNP	.											.	SPATS1	61	.	0			c.G22A						PASS	.	G	ARG/GLY	579,3827	257.0+/-261.6	37,505,1661	62.0	58.0	60.0		22	2.5	0.0	6	dbSNP_120	60	2417,6183	401.6+/-347.2	319,1779,2202	yes	missense	SPATS1	NM_145026.3	125	356,2284,3863	AA,AG,GG		28.1047,13.1412,23.0355	probably-damaging	8/301	44310854	2996,10010	2203	4300	6503	SO:0001583	missense	221409	exon2			CTCACTGGAAACA	AK058171	CCDS4911.1	6p21.1	2003-08-08			ENSG00000249481	ENSG00000249481			22957	protein-coding gene	gene with protein product							Standard	NM_145026		Approved	SPATA8, FLJ25442, SRSP1	uc021yzz.1	Q496A3	OTTHUMG00000014764	ENST00000288390.2:c.22G>A	6.37:g.44310854G>A	ENSP00000424400:p.Gly8Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_145026	Q496A2|Q496A5|Q96LJ0	Missense_Mutation	SNP	ENST00000288390.2	37	CCDS4911.1	807	0.3695054945054945	44	0.08943089430894309	169	0.46685082872928174	349	0.6101398601398601	245	0.3232189973614776	G	14.21	2.466907	0.43839	0.131412	0.281047	ENSG00000249481	ENST00000323108;ENST00000288390	T;T	0.55413	0.52;0.52	3.43	2.55	0.30701	.	0.233763	0.22137	N	0.064107	T	0.53722	0.1814	L	0.57536	1.79	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.58278	-0.7664	9	0.87932	D	0	.	8.293	0.31969	0.0:0.0:0.7659:0.2341	rs10948132;rs52794200;rs59695445;rs10948132	8	Q496A3	SPAS1_HUMAN	R	8	ENSP00000437552:G8R;ENSP00000424400:G8R	ENSP00000424400:G8R	G	+	1	0	SPATS1	44418832	0.008000	0.16893	0.013000	0.15412	0.017000	0.09413	0.755000	0.26405	0.998000	0.38996	0.563000	0.77884	GGA	G|0.713;A|0.286	0.286	strong		0.498	SPATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040738.2	NM_145026	
TNR	7143	hgsc.bcm.edu	37	1	175335234	175335234	+	Silent	SNP	C	C	T	rs1385541	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:175335234C>T	ENST00000367674.2	-	11	2802	c.2094G>A	c.(2092-2094)tcG>tcA	p.S698S	TNR_ENST00000263525.2_Silent_p.S698S			Q92752	TENR_HUMAN	tenascin R	698	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TGGAGGTCTCCGAGGAGGCTG	0.522													C|||	832	0.166134	0.1483	0.1974	5008	,	,		22079	0.1042		0.2445	False		,,,				2504	0.1513				p.S698S		Atlas-SNP	.											.	TNR	399	.	0			c.G2094A						PASS	.	C		604,3802	264.1+/-265.8	53,498,1652	116.0	94.0	102.0		2094	-11.8	0.5	1	dbSNP_88	102	2089,6511	360.6+/-332.0	258,1573,2469	no	coding-synonymous	TNR	NM_003285.2		311,2071,4121	TT,TC,CC		24.2907,13.7086,20.7058		698/1359	175335234	2693,10313	2203	4300	6503	SO:0001819	synonymous_variant	7143	exon11			GGTCTCCGAGGAG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.2094G>A	1.37:g.175335234C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	237	132	0.556962	NM_003285	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																			C|0.809;T|0.191	0.191	strong		0.522	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
DNHD1	144132	hgsc.bcm.edu	37	11	6561270	6561270	+	Silent	SNP	A	A	G	rs10839577	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6561270A>G	ENST00000527990.2	+	16	3585	c.3585A>G	c.(3583-3585)caA>caG	p.Q1195Q	DNHD1_ENST00000254579.6_Silent_p.Q1195Q			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1195					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GCAGCCCCCAATGGGAGGTAG	0.607													a|||	1260	0.251597	0.1785	0.3156	5008	,	,		16066	0.1329		0.3807	False		,,,				2504	0.2945				p.Q1195Q		Atlas-SNP	.											.	DNHD1	198	.	0			c.A3585G						PASS	.	A		272,1112		28,216,448	30.0	38.0	36.0		3585	-2.8	0.1	11	dbSNP_120	36	1106,2076		196,714,681	no	coding-synonymous	DNHD1	NM_144666.2		224,930,1129	GG,GA,AA		34.758,19.6532,30.1796		1195/4754	6561270	1378,3188	692	1591	2283	SO:0001819	synonymous_variant	144132	exon18			CCCCCAATGGGAG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.3585A>G	11.37:g.6561270A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			A|0.739;G|0.261	0.261	strong		0.607	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
USP7	7874	hgsc.bcm.edu	37	16	9057083	9057083	+	Silent	SNP	G	G	A	rs374020920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:9057083G>A	ENST00000344836.4	-	1	258	c.60C>T	c.(58-60)ccC>ccT	p.P20P	RP11-77H9.8_ENST00000564485.1_lincRNA	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	20	Interaction with TSPYL5.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						CCATGTCCTCGGGCTCGCTCA	0.756													G|||	12	0.00239617	0.0	0.0014	5008	,	,		3991	0.0		0.004	False		,,,				2504	0.0072				p.P20P		Atlas-SNP	.											.	USP7	116	.	0			c.C60T						PASS	.	G		7,2427		0,7,1210	5.0	6.0	6.0		60	1.3	1.0	16		6	26,4274		0,26,2124	no	coding-synonymous	USP7	NM_003470.2		0,33,3334	AA,AG,GG		0.6047,0.2876,0.4901		20/1103	9057083	33,6701	1217	2150	3367	SO:0001819	synonymous_variant	7874	exon1			GTCCTCGGGCTCG	Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"""Ubiquitin-specific peptidases"""	12630	protein-coding gene	gene with protein product		602519	"""ubiquitin specific protease 7 (herpes virus-associated)"""	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.60C>T	16.37:g.9057083G>A		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	15	11	0.733333	NM_003470	A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	37	CCDS32385.1																																																																																			.	.	weak		0.756	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2		
MCPH1	79648	hgsc.bcm.edu	37	8	6302671	6302671	+	Silent	SNP	C	C	T	rs2920676	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:6302671C>T	ENST00000344683.5	+	8	1504	c.1428C>T	c.(1426-1428)ttC>ttT	p.F476F	MCPH1_ENST00000522905.1_Silent_p.F428F|MCPH1_ENST00000519480.1_Silent_p.F476F	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	476					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		TTACCAATTTCACAGCAAAAA	0.443													C|||	1042	0.208067	0.4849	0.062	5008	,	,		21877	0.1667		0.0348	False		,,,				2504	0.1585				p.F476F	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.C1428T						PASS	.	C	,,	1457,2249		283,891,679	72.0	71.0	72.0		1428,1284,1428	-9.9	0.0	8	dbSNP_101	72	148,8060		0,148,3956	no	coding-synonymous,coding-synonymous,coding-synonymous	MCPH1	NM_001172574.1,NM_001172575.1,NM_024596.3	,,	283,1039,4635	TT,TC,CC		1.8031,39.3146,13.4715	,,	476/611,428/563,476/836	6302671	1605,10309	1853	4104	5957	SO:0001819	synonymous_variant	79648	exon8			CAATTTCACAGCA	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1428C>T	8.37:g.6302671C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	37	CCDS43689.1																																																																																			C|0.841;T|0.159	0.159	strong		0.443	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
COL11A1	1301	hgsc.bcm.edu	37	1	103548497	103548497	+	Missense_Mutation	SNP	A	A	C	rs11164663	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:103548497A>C	ENST00000370096.3	-	2	450	c.138T>G	c.(136-138)gaT>gaG	p.D46E	COL11A1_ENST00000512756.1_Missense_Mutation_p.D46E|COL11A1_ENST00000353414.4_Missense_Mutation_p.D46E|COL11A1_ENST00000358392.2_Missense_Mutation_p.D46E	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	46			D -> E (in dbSNP:rs11164663).		cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		AATTGTGAAAATCTAGTGCTT	0.333													A|||	317	0.0632987	0.1241	0.0447	5008	,	,		14822	0.0208		0.0835	False		,,,				2504	0.0174				p.D46E		Atlas-SNP	.											.	COL11A1	972	.	0			c.T138G						PASS	.	A	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	580,3826	252.1+/-258.6	36,508,1659	95.0	96.0	96.0		138,138,138,138	3.0	1.0	1	dbSNP_120	96	705,7895	171.6+/-222.5	30,645,3625	yes	missense,missense,missense,missense	COL11A1	NM_080630.3,NM_080629.2,NM_001854.3,NM_001190709.1	45,45,45,45	66,1153,5284	CC,CA,AA		8.1977,13.1639,9.8801	benign,benign,benign,benign	46/1691,46/1819,46/1807,46/1768	103548497	1285,11721	2203	4300	6503	SO:0001583	missense	1301	exon2			GTGAAAATCTAGT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.138T>G	1.37:g.103548497A>C	ENSP00000359114:p.Asp46Glu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	174	94	0.54023	NM_001854	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	136	0.06227106227106227	46	0.09349593495934959	17	0.04696132596685083	13	0.022727272727272728	60	0.079155672823219	A	6.808	0.518173	0.13005	0.131639	0.081977	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239	T;T;T;T;T	0.02140	4.43;4.43;4.43;4.43;4.43	5.7	2.99	0.34606	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.226724	0.44285	D	0.000473	T	0.00328	0.0010	N	0.10972	0.075	0.38472	P	0.05249499999999996	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.48547	-0.9026	9	0.06625	T	0.88	.	0.5818	0.00713	0.3431:0.2659:0.1208:0.2701	rs11164663;rs61468253;rs11164663	46;46;46;46	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	E	46	ENSP00000359114:D46E;ENSP00000351163:D46E;ENSP00000302551:D46E;ENSP00000426533:D46E;ENSP00000408640:D46E	ENSP00000302551:D46E	D	-	3	2	COL11A1	103321085	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.159000	0.31749	2.175000	0.68902	0.383000	0.25322	GAT	A|0.918;C|0.082	0.082	strong		0.333	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
FGF13	2258	hgsc.bcm.edu	37	X	137715056	137715056	+	Silent	SNP	G	G	A	rs374129615		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:137715056G>A	ENST00000315930.6	-	5	1354	c.693C>T	c.(691-693)ggC>ggT	p.G231G	FGF13_ENST00000541469.1_Silent_p.G185G|FGF13_ENST00000370603.3_Silent_p.G241G|FGF13_ENST00000305414.4_Silent_p.G178G|FGF13_ENST00000441825.2_Silent_p.G212G	NM_004114.3	NP_004105.1	Q92913	FGF13_HUMAN	fibroblast growth factor 13	231					cell-cell signaling (GO:0007267)|cerebral cortex cell migration (GO:0021795)|establishment of neuroblast polarity (GO:0045200)|hippocampus development (GO:0021766)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|microtubule polymerization (GO:0046785)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of microtubule depolymerization (GO:0007026)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|positive regulation of protein kinase activity (GO:0045860)|protein localization to plasma membrane (GO:0072659)|signal transduction (GO:0007165)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|filopodium (GO:0030175)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|microtubule (GO:0005874)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-tubulin binding (GO:0048487)|growth factor activity (GO:0008083)|ion channel binding (GO:0044325)|microtubule binding (GO:0008017)|protein kinase activator activity (GO:0030295)|sodium channel regulator activity (GO:0017080)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	24	Acute lymphoblastic leukemia(192;0.000127)					CGTTCAGCACGCCAGAGACAC	0.537													G|||	2	0.000529801	0.0	0.0	3775	,	,		12666	0.0		0.001	False		,,,				2504	0.001				p.G241G		Atlas-SNP	.											.	FGF13	135	.	0			c.C723T						PASS	.	G	,,,,,	0,3835		0,0,1632,571	215.0	165.0	182.0		555,723,636,636,693,534	-4.1	0.9	X		182	1,6727		0,1,2427,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FGF13	NM_001139498.1,NM_001139500.1,NM_001139501.1,NM_001139502.1,NM_004114.3,NM_033642.2	,,,,,	0,1,4059,2443	AA,AG,GG,G		0.0149,0.0,0.0095	,,,,,	185/200,241/256,212/227,212/227,231/246,178/193	137715056	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	2258	exon7			CAGCACGCCAGAG	BC034340	CCDS14664.1, CCDS14665.1, CCDS55511.1	Xq26.3	2008-02-05			ENSG00000129682	ENSG00000129682			3670	protein-coding gene	gene with protein product	"""fibroblast growth factor homologous factor 2"""	300070				8790420	Standard	NM_033642		Approved	FHF2, FGF2	uc011mwj.2	Q92913	OTTHUMG00000022532	ENST00000315930.6:c.693C>T	X.37:g.137715056G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	44	38	0.863636	NM_001139500	B1AK18|B7Z4M7|B7Z8N0|D3DWH4|O95830|Q9NZH9|Q9NZI0	Silent	SNP	ENST00000315930.6	37	CCDS14665.1																																																																																			.	.	weak		0.537	FGF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058534.2	NM_004114	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377086	49377086	+	Missense_Mutation	SNP	T	T	C	rs611251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49377086T>C	ENST00000200453.5	+	2	865	c.596T>C	c.(595-597)gTa>gCa	p.V199A		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	199	Glu-rich.		V -> A (in dbSNP:rs611251).		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		GAAGAAGCTGTAAAGAAAGAA	0.532													T|||	1368	0.273163	0.534	0.2262	5008	,	,		18625	0.0933		0.1521	False		,,,				2504	0.2638				p.V199A		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.T596C						PASS	.	T	ALA/VAL	2102,2304	573.6+/-383.6	513,1076,614	149.0	161.0	157.0		596	0.4	0.0	19	dbSNP_83	157	1245,7355	249.3+/-276.6	74,1097,3129	yes	missense	PPP1R15A	NM_014330.3	64	587,2173,3743	CC,CT,TT		14.4767,47.7077,25.7343	probably-damaging	199/675	49377086	3347,9659	2203	4300	6503	SO:0001583	missense	23645	exon2			AAGCTGTAAAGAA	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.596T>C	19.37:g.49377086T>C	ENSP00000200453:p.Val199Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	66	42	0.636364	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	513	0.2348901098901099	259	0.5264227642276422	81	0.22375690607734808	57	0.09965034965034965	116	0.15303430079155672	T	10.91	1.483851	0.26598	0.477077	0.144767	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.04194	3.68	4.06	0.39	0.16275	.	1.686450	0.03645	N	0.240170	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B	0.26363	0.147	B	0.19666	0.026	T	0.44159	-0.9346	9	0.02654	T	1	-1.0388	2.3232	0.04216	0.2168:0.2659:0.0:0.5173	rs611251;rs3177847;rs3826819;rs52819950;rs58000193;rs611251	199	O75807	PR15A_HUMAN	A	199;39;157	ENSP00000200453:V199A	ENSP00000200453:V199A	V	+	2	0	PPP1R15A	54068898	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.145000	0.16157	0.236000	0.21180	0.418000	0.28097	GTA	T|0.735;G|0.004	.	strong		0.532	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
CFAP46	54777	hgsc.bcm.edu	37	10	134736026	134736026	+	Silent	SNP	G	G	A	rs4880286	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:134736026G>A	ENST00000368586.5	-	12	1543	c.1443C>T	c.(1441-1443)gcC>gcT	p.A481A	TTC40_ENST00000368582.2_Silent_p.A481A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CGCGCTCAGGGGCCTGGTATA	0.701													G|||	1798	0.359026	0.2821	0.4986	5008	,	,		15308	0.3264		0.3459	False		,,,				2504	0.411				p.A481A		Atlas-SNP	.											.	TTC40	100	.	0			c.C1443T						PASS	.																																			SO:0001819	synonymous_variant	54777	exon12			CTCAGGGGCCTGG																												ENST00000368586.5:c.1443C>T	10.37:g.134736026G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			G|0.640;A|0.360	0.360	strong		0.701	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
VCAN	1462	hgsc.bcm.edu	37	5	82786194	82786194	+	Silent	SNP	T	T	C	rs12332199	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:82786194T>C	ENST00000265077.3	+	3	913	c.348T>C	c.(346-348)acT>acC	p.T116T	VCAN_ENST00000342785.4_Silent_p.T116T|VCAN_ENST00000513984.1_Silent_p.T116T|VCAN_ENST00000512590.2_Silent_p.T68T|VCAN_ENST00000343200.5_Silent_p.T116T|VCAN_ENST00000502527.2_Silent_p.T116T	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	116	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CCTCCCTCACTGTGGTCAAGC	0.532													C|||	1714	0.342252	0.5	0.3775	5008	,	,		19796	0.2034		0.3936	False		,,,				2504	0.1943				p.T116T		Atlas-SNP	.											.	VCAN	498	.	0			c.T348C						PASS	.	C	,,,	2057,2349	608.2+/-391.1	468,1121,614	146.0	137.0	140.0		348,348,348,348	0.9	0.1	5	dbSNP_120	140	3247,5353	649.2+/-400.6	601,2045,1654	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	1069,3166,2268	CC,CT,TT		37.7558,46.6863,40.7812	,,,	116/656,116/2410,116/1643,116/3397	82786194	5304,7702	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon3			CCTCACTGTGGTC	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.348T>C	5.37:g.82786194T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			T|0.613;C|0.387	0.387	strong		0.532	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
KIAA0922	23240	hgsc.bcm.edu	37	4	154388363	154388363	+	Splice_Site	SNP	C	C	T	rs78441178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:154388363C>T	ENST00000409663.3	+	2	177	c.125C>T	c.(124-126)gCg>gTg	p.A42V	KIAA0922_ENST00000409959.3_Splice_Site_p.A42V|KIAA0922_ENST00000440693.1_Splice_Site_p.A42V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	42						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				GTTCCTGCAGCGATTGAGCCG	0.577													c|||	2	0.000399361	0.0	0.0	5008	,	,		18938	0.0		0.002	False		,,,				2504	0.0				p.A42V		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C125T						PASS	.		VAL/ALA,VAL/ALA	1,1383		0,1,691	198.0	177.0	183.0		125,125	4.2	1.0	4	dbSNP_131	183	15,3167		0,15,1576	yes	missense-near-splice,missense-near-splice	KIAA0922	NM_001131007.1,NM_015196.3	64,64	0,16,2267	TT,TC,CC		0.4714,0.0723,0.3504	benign,benign	42/1611,42/1610	154388363	16,4550	692	1591	2283	SO:0001630	splice_region_variant	23240	exon2			CTGCAGCGATTGA	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.125-1C>T	4.37:g.154388363C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	218	104	0.477064	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	c	15.31	2.796674	0.50208	7.23E-4	0.004714	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959	T;T;T	0.28255	1.89;1.62;1.9	5.23	4.19	0.49359	.	.	.	.	.	T	0.27798	0.0684	L	0.55481	1.735	0.27301	N	0.957589	B;B	0.32526	0.374;0.257	B;B	0.29942	0.109;0.051	T	0.08827	-1.0703	8	.	.	.	.	10.079	0.42377	0.0:0.8247:0.0:0.1753	.	42;42	A2VDJ0-5;A2VDJ0	.;T131L_HUMAN	V	42	ENSP00000386574:A42V;ENSP00000409663:A42V;ENSP00000386787:A42V	.	A	+	2	0	KIAA0922	154607813	0.991000	0.36638	1.000000	0.80357	0.988000	0.76386	1.197000	0.32211	2.442000	0.82660	0.550000	0.68814	GCG	.	.	weak		0.577	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	Missense_Mutation
SALL4	57167	hgsc.bcm.edu	37	20	50407502	50407502	+	Missense_Mutation	SNP	A	A	C	rs6126344	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:50407502A>C	ENST00000217086.4	-	2	1631	c.1520T>G	c.(1519-1521)cTg>cGg	p.L507R	SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000395997.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	507			L -> R (in dbSNP:rs6126344). {ECO:0000269|PubMed:12395297}.		embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CCCAGGCTGCAGGTCACCGGG	0.582													A|||	1797	0.358826	0.1218	0.3386	5008	,	,		18800	0.5962		0.335	False		,,,				2504	0.4734				p.L507R		Atlas-SNP	.											.	SALL4	168	.	0			c.T1520G						PASS	.	A	ARG/LEU	660,3746	275.4+/-272.5	47,566,1590	96.0	103.0	101.0		1520	1.9	1.0	20	dbSNP_114	101	2957,5643	453.1+/-363.1	519,1919,1862	yes	missense	SALL4	NM_020436.3	102	566,2485,3452	CC,CA,AA		34.3837,14.9796,27.8102	possibly-damaging	507/1054	50407502	3617,9389	2203	4300	6503	SO:0001583	missense	57167	exon2			GGCTGCAGGTCAC	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1520T>G	20.37:g.50407502A>C	ENSP00000217086:p.Leu507Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	765	0.35027472527472525	65	0.13211382113821138	130	0.35911602209944754	327	0.5716783216783217	243	0.32058047493403696	A	3.845	-0.033053	0.07543	0.149796	0.343837	ENSG00000101115	ENST00000217086	T	0.10382	2.88	5.34	1.9	0.25705	.	0.226097	0.22773	N	0.055811	T	0.00012	0.0000	M	0.61703	1.905	0.19775	P	0.9999563645	B	0.17852	0.024	B	0.10450	0.005	T	0.38564	-0.9655	9	0.10636	T	0.68	-2.9243	8.6398	0.33970	0.7793:0.0:0.2207:0.0	rs6126344	507	Q9UJQ4	SALL4_HUMAN	R	507	ENSP00000217086:L507R	ENSP00000217086:L507R	L	-	2	0	SALL4	49840909	0.998000	0.40836	0.979000	0.43373	0.486000	0.33341	2.155000	0.42301	0.343000	0.23821	-0.322000	0.08575	CTG	A|0.697;C|0.303	0.303	strong		0.582	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
STARD3	10948	hgsc.bcm.edu	37	17	37815304	37815304	+	Splice_Site	SNP	G	G	C	rs11556624	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:37815304G>C	ENST00000336308.5	+	8	865	c.647G>C	c.(646-648)gGg>gCg	p.G216A	STARD3_ENST00000578232.1_3'UTR|STARD3_ENST00000544210.2_Splice_Site_p.G216A|STARD3_ENST00000580611.1_Splice_Site_p.G190A|STARD3_ENST00000394250.4_Splice_Site_p.G198A	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	216	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.		G -> A (in dbSNP:rs11556624). {ECO:0000269|PubMed:15489334}.		cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)	p.G216V(2)		endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TTTTCTGCAGGGTCTGACAAT	0.527													G|||	26	0.00519169	0.0	0.0072	5008	,	,		16711	0.0		0.0199	False		,,,				2504	0.001				p.G216A		Atlas-SNP	.											.	STARD3	33	.	2	Substitution - Missense(2)	lung(2)	c.G647C						PASS	.	G	ALA/GLY,ALA/GLY,ALA/GLY	17,4389	23.3+/-48.9	0,17,2186	222.0	216.0	218.0		647,593,647	5.0	1.0	17	dbSNP_120	218	210,8390	88.1+/-150.5	2,206,4092	yes	missense-near-splice,missense-near-splice,missense-near-splice	STARD3	NM_001165937.1,NM_001165938.1,NM_006804.3	60,60,60	2,223,6278	CC,CG,GG		2.4419,0.3858,1.7453	probably-damaging,probably-damaging,probably-damaging	216/446,198/428,216/446	37815304	227,12779	2203	4300	6503	SO:0001630	splice_region_variant	10948	exon8			CTGCAGGGTCTGA		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"""StAR-related lipid transfer (START) domain containing"""	17579	protein-coding gene	gene with protein product		607048	"""START domain containing 3"""				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.647-1G>C	17.37:g.37815304G>C		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	198	88	0.444444	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Missense_Mutation	SNP	ENST00000336308.5	37	CCDS11341.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	0	0.0	11	0.014511873350923483	G	24.2	4.505510	0.85282	0.003858	0.024419	ENSG00000131748	ENST00000336308;ENST00000544210;ENST00000394250	D;D;D	0.85629	-1.93;-2.01;-1.9	5.0	5.0	0.66597	MENTAL domain (1);START-like domain (1);	0.111430	0.64402	D	0.000010	D	0.83161	0.5194	L	0.50333	1.59	0.80722	D	1	D;D;D;D	0.76494	0.999;0.97;0.999;0.998	D;P;D;P	0.72338	0.977;0.83;0.929;0.888	D	0.87250	0.2272	10	0.72032	D	0.01	.	15.4337	0.75125	0.0:0.0:1.0:0.0	rs11556624	216;216;198;216	F5H0G2;B4DUY1;A8MXA4;Q14849	.;.;.;STAR3_HUMAN	A	216;216;198	ENSP00000337446:G216A;ENSP00000439869:G216A;ENSP00000377794:G198A	ENSP00000337446:G216A	G	+	2	0	STARD3	35068830	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.323000	0.59221	2.314000	0.78098	0.655000	0.94253	GGG	G|0.985;C|0.015	0.015	strong		0.527	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1		Missense_Mutation
FUCA1	2517	hgsc.bcm.edu	37	1	24180962	24180962	+	Missense_Mutation	SNP	T	T	C	rs13551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24180962T>C	ENST00000374479.3	-	5	864	c.857A>G	c.(856-858)cAg>cGg	p.Q286R		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	286			Q -> R (in allele FUCA1*2; dbSNP:rs13551). {ECO:0000269|PubMed:12408193, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7815431, ECO:0000269|PubMed:8399358, ECO:0000269|PubMed:8504303}.		fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		TGGCAAGCTCTGTGGCTTGAA	0.463													t|||	1058	0.211262	0.1021	0.2464	5008	,	,		17166	0.2808		0.332	False		,,,				2504	0.138				p.Q286R		Atlas-SNP	.											.	FUCA1	24	.	0			c.A857G						PASS	.		ARG/GLN	643,3763	276.9+/-273.4	46,551,1606	140.0	133.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	857	3.6	0.0	1	dbSNP_52	135	2845,5755	447.0+/-361.4	457,1931,1912	yes	missense	FUCA1	NM_000147.4	43	503,2482,3518	CC,CT,TT		33.0814,14.5937,26.8184	benign	286/467	24180962	3488,9518	2203	4300	6503	SO:0001583	missense	2517	exon5			AAGCTCTGTGGCT	BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.857A>G	1.37:g.24180962T>C	ENSP00000363603:p.Gln286Arg	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	248	113	0.455645	NM_000147	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Missense_Mutation	SNP	ENST00000374479.3	37	CCDS244.2	549	0.25137362637362637	63	0.12804878048780488	97	0.26795580110497236	141	0.2465034965034965	248	0.32717678100263853	t	7.821	0.717720	0.15372	0.145937	0.330814	ENSG00000179163	ENST00000374479;ENST00000374475	T	0.56444	0.46	4.74	3.6	0.41247	Glycoside hydrolase, family 29, conserved site (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	1.038340	0.07550	N	0.915237	T	0.00012	0.0000	L	0.35487	1.065	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.22871	-1.0204	9	0.87932	D	0	-18.2834	3.1357	0.06438	0.0:0.2037:0.2751:0.5212	rs13551;rs1126515;rs2228423;rs3181585;rs11549094;rs52796281;rs13551	286	P04066	FUCO_HUMAN	R	286;75	ENSP00000363603:Q286R	ENSP00000363599:Q75R	Q	-	2	0	FUCA1	24053549	0.000000	0.05858	0.002000	0.10522	0.148000	0.21650	0.652000	0.24888	0.839000	0.34971	0.515000	0.50301	CAG	.	.	none		0.463	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147	
HLA-B	3106	hgsc.bcm.edu	37	6	31324547	31324547	+	Missense_Mutation	SNP	G	G	C	rs1065386|rs281864604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324547G>C	ENST00000412585.2	-	2	289	c.261C>G	c.(259-261)aaC>aaG	p.N87K		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	87	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)	p.N87K(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						AGATCTGTGTGTTCCGGTCCC	0.662									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	2278	0.454872	0.3676	0.4179	5008	,	,		6866	0.5853		0.3936	False		,,,				2504	0.5276				p.N87K		Atlas-SNP	.											HLA-B,NS,lymphoid_neoplasm,-2,2	HLA-B	54	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C261G						PASS	.	C	LYS/ASN	834,3406		230,374,1516	66.0	64.0	65.0		261	-1.2	0.0	6	dbSNP_86	65	1737,6553		553,631,2961	no	missense	HLA-B	NM_005514.6	94	783,1005,4477	CC,CG,GG		20.953,19.6698,20.5188		87/363	31324547	2571,9959	2120	4145	6265	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CTGTGTGTTCCGG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.261C>G	6.37:g.31324547G>C	ENSP00000399168:p.Asn87Lys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	760	0.34798534798534797	120	0.24390243902439024	97	0.26795580110497236	301	0.5262237762237763	242	0.31926121372031663	N	7.741	0.701384	0.15172	0.196698	0.20953	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00705	5.81;5.81	3.2	-1.24	0.09435	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.715036	0.10428	U	0.675817	T	0.01421	0.0046	M	0.87758	2.905	0.80722	P	0.0	B;B;D	0.54207	0.147;0.334;0.965	B;B;D	0.63192	0.119;0.185;0.912	T	0.17745	-1.0359	9	0.66056	D	0.02	.	7.0496	0.25065	0.0:0.4051:0.4134:0.1816	rs1131200;rs2308411;rs3177919;rs3190898	87;87;62	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	K	87;98	ENSP00000399168:N87K;ENSP00000405931:N98K	ENSP00000399168:N87K	N	-	3	2	HLA-B	31432526	0.013000	0.17824	0.000000	0.03702	0.000000	0.00434	-1.228000	0.02948	-0.885000	0.03971	-1.610000	0.00802	AAC	G|0.668;C|0.332	0.332	strong		0.662	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
PTCD1	26024	hgsc.bcm.edu	37	7	99032458	99032458	+	Silent	SNP	C	C	T	rs940336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99032458C>T	ENST00000292478.4	-	2	658	c.408G>A	c.(406-408)ccG>ccA	p.P136P	ATP5J2-PTCD1_ENST00000437572.1_5'Flank|PTCD1_ENST00000485746.1_5'UTR|ATP5J2-PTCD1_ENST00000413834.1_Silent_p.P185P|PTCD1_ENST00000555673.1_Silent_p.P185P	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	136					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			AGTACCAGTACGGGGTGTTTC	0.552													C|||	800	0.159744	0.1029	0.0893	5008	,	,		16719	0.3026		0.0199	False		,,,				2504	0.2832				p.P185P		Atlas-SNP	.											.	.	.	.	0			c.G555A						PASS	.	C	,	390,4016	196.4+/-220.7	20,350,1833	159.0	166.0	163.0		555,408	-1.3	0.4	7	dbSNP_86	163	197,8403	85.6+/-148.0	3,191,4106	no	coding-synonymous,coding-synonymous	PTCD1,ATP5J2-PTCD1	NM_001198879.1,NM_015545.3	,	23,541,5939	TT,TC,CC		2.2907,8.8516,4.5133	,	185/750,136/701	99032458	587,12419	2203	4300	6503	SO:0001819	synonymous_variant	100526740	exon3			CCAGTACGGGGTG	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.408G>A	7.37:g.99032458C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	214	104	0.485981	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	37	CCDS34691.1																																																																																			C|0.928;T|0.072	0.072	strong		0.552	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
PLEC	5339	hgsc.bcm.edu	37	8	144992103	144992103	+	Silent	SNP	T	T	C	rs6558406	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144992103T>C	ENST00000322810.4	-	32	12466	c.12297A>G	c.(12295-12297)acA>acG	p.T4099T	PLEC_ENST00000398774.2_Silent_p.T3930T|PLEC_ENST00000345136.3_Silent_p.T3962T|PLEC_ENST00000354589.3_Silent_p.T3962T|PLEC_ENST00000354958.2_Silent_p.T3940T|PLEC_ENST00000436759.2_Silent_p.T3989T|PLEC_ENST00000527096.1_Silent_p.T3985T|PLEC_ENST00000356346.3_Silent_p.T3948T|PLEC_ENST00000357649.2_Silent_p.T3966T	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4099	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCTCAAAGGCTGTGCCGGGGC	0.627													C|||	2456	0.490415	0.916	0.3775	5008	,	,		18721	0.1538		0.4563	False		,,,				2504	0.3773				p.T4099T		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	0			c.A12297G						PASS	.	C	,,,,,,,	3615,601		1558,499,51	28.0	34.0	32.0		11967,11844,11820,12297,11790,11886,11898,11886	-8.6	0.4	8	dbSNP_116	32	3834,4614		903,2028,1293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	2461,2527,1344	CC,CT,TT		45.3835,14.2552,41.1797	,,,,,,,	3989/4575,3948/4534,3940/4526,4099/4685,3930/4516,3962/4548,3966/4552,3962/4548	144992103	7449,5215	2108	4224	6332	SO:0001819	synonymous_variant	5339	exon32			AAAGGCTGTGCCG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.12297A>G	8.37:g.144992103T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	161	77	0.478261	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			T|0.520;C|0.480	0.480	strong		0.627	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
RSBN1	54665	hgsc.bcm.edu	37	1	114354942	114354942	+	Silent	SNP	T	T	G	rs3789604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:114354942T>G	ENST00000261441.5	-	1	156	c.93A>C	c.(91-93)cgA>cgC	p.R31R	RP5-1073O3.2_ENST00000418238.1_RNA|RP5-1073O3.2_ENST00000429398.1_RNA	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	31						nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CGTCCGCGCATCGCGCAAGCG	0.672													T|||	670	0.133786	0.0461	0.1369	5008	,	,		12587	0.2282		0.1879	False		,,,				2504	0.0971				p.R31R		Atlas-SNP	.											RSBN1,rectum,carcinoma,0,2	RSBN1	71	2	0			c.A93C	GRCh37	CR053507	PTPN22	R	rs3789604	PASS	.	T		350,4042		13,324,1859	21.0	29.0	27.0	http://omim.org/entry/177900	93	-10.1	0.1	1	dbSNP_107	27	1581,7007		145,1291,2858	yes	coding-synonymous	RSBN1	NM_018364.3		158,1615,4717	GG,GT,TT		18.4094,7.969,14.8767		31/803	114354942	1931,11049	2196	4294	6490	SO:0001819	synonymous_variant	54665	exon1			CGCGCATCGCGCA	AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.93A>C	1.37:g.114354942T>G		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_018364	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Silent	SNP	ENST00000261441.5	37	CCDS862.1																																																																																			T|0.851;G|0.149	0.149	strong		0.672	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364	
OTOR	56914	hgsc.bcm.edu	37	20	16729138	16729138	+	Missense_Mutation	SNP	T	T	C	rs6135876	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:16729138T>C	ENST00000246081.2	+	1	136	c.92T>C	c.(91-93)cTc>cCc	p.L31P		NM_020157.2	NP_064542.1	Q9NRC9	OTOR_HUMAN	otoraplin	31			L -> P (in dbSNP:rs6135876). {ECO:0000269|Ref.6}.		cartilage condensation (GO:0001502)|sensory perception of sound (GO:0007605)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(1)|liver(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	10						TCCAAGAAGCTCTGTGCAGAT	0.363													T|||	974	0.194489	0.0545	0.1239	5008	,	,		18794	0.3165		0.16	False		,,,				2504	0.3436				p.L31P		Atlas-SNP	.											.	OTOR	22	.	0			c.T92C						PASS	.	T	PRO/LEU	345,4061	179.0+/-207.6	12,321,1870	216.0	215.0	215.0		92	5.9	1.0	20	dbSNP_114	215	1503,7097	285.8+/-297.4	142,1219,2939	yes	missense	OTOR	NM_020157.2	98	154,1540,4809	CC,CT,TT		17.4767,7.8302,14.2088	probably-damaging	31/129	16729138	1848,11158	2203	4300	6503	SO:0001583	missense	56914	exon1			AGAAGCTCTGTGC	AF233261	CCDS13124.1	20p12.1-p11.23	2005-11-14			ENSG00000125879	ENSG00000125879			8517	protein-coding gene	gene with protein product		606067				10873378	Standard	NM_020157		Approved	MIAL, MIAL1, FDP	uc002wpj.3	Q9NRC9	OTTHUMG00000031931	ENST00000246081.2:c.92T>C	20.37:g.16729138T>C	ENSP00000246081:p.Leu31Pro	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	237	236	0.995781	NM_020157	D3DW22|Q3MIU6	Missense_Mutation	SNP	ENST00000246081.2	37	CCDS13124.1	381	0.17445054945054944	31	0.06300813008130081	53	0.1464088397790055	172	0.3006993006993007	125	0.16490765171503957	T	20.9	4.074316	0.76415	0.078302	0.174767	ENSG00000125879	ENST00000246081	D	0.83506	-1.73	5.93	5.93	0.95920	Src homology-3 domain (1);	0.145914	0.49916	D	0.000140	T	0.00039	0.0001	L	0.43152	1.355	0.09310	P	0.999999999207977	D	0.76494	0.999	D	0.67231	0.95	T	0.00054	-1.2181	9	0.72032	D	0.01	-13.0638	14.9654	0.71188	0.0:0.0:0.0:1.0	rs6135876;rs52799694;rs58763389;rs6135876	31	Q9NRC9	OTOR_HUMAN	P	31	ENSP00000246081:L31P	ENSP00000246081:L31P	L	+	2	0	OTOR	16677138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.835000	0.69368	2.281000	0.76405	0.533000	0.62120	CTC	T|0.844;C|0.156	0.156	strong		0.363	OTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078108.2		
MERTK	10461	hgsc.bcm.edu	37	2	112786357	112786357	+	Silent	SNP	G	G	A	rs10205793	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:112786357G>A	ENST00000295408.4	+	19	3173	c.2916G>A	c.(2914-2916)tcG>tcA	p.S972S	MERTK_ENST00000409780.1_Silent_p.S796S|MERTK_ENST00000421804.2_Silent_p.S972S			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	972					apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						GGTCCCATTCGAGCATGCTGC	0.537													G|||	254	0.0507188	0.1293	0.0346	5008	,	,		17084	0.002		0.0408	False		,,,				2504	0.0164				p.S972S		Atlas-SNP	.											.	MERTK	112	.	0			c.G2916A						PASS	.	G		522,3884	238.0+/-249.6	23,476,1704	49.0	46.0	47.0		2916	-11.7	0.0	2	dbSNP_119	47	309,8291	111.6+/-171.8	3,303,3994	no	coding-synonymous	MERTK	NM_006343.2		26,779,5698	AA,AG,GG		3.593,11.8475,6.3894		972/1000	112786357	831,12175	2203	4300	6503	SO:0001819	synonymous_variant	10461	exon19			CCATTCGAGCATG	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.2916G>A	2.37:g.112786357G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	115	66	0.573913	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	37	CCDS2094.1																																																																																			G|0.944;A|0.056	0.056	strong		0.537	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
ATP13A2	23400	hgsc.bcm.edu	37	1	17314942	17314942	+	Silent	SNP	G	G	A	rs9435662	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17314942G>A	ENST00000326735.8	-	24	2670	c.2637C>T	c.(2635-2637)ggC>ggT	p.G879G	ATP13A2_ENST00000452699.1_Silent_p.G874G|ATP13A2_ENST00000341676.5_Silent_p.G835G|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2	879					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGTCATTGGCGCCGTCTCCGC	0.617													G|||	1696	0.338658	0.1369	0.4568	5008	,	,		14687	0.2599		0.508	False		,,,				2504	0.4346				p.G879G		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C2637T						PASS	.	G	,,	912,3494	352.3+/-311.7	101,710,1392	85.0	84.0	84.0		2622,2505,2637	-7.5	0.6	1	dbSNP_119	84	4491,4109	590.3+/-392.7	1154,2183,963	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	1255,2893,2355	AA,AG,GG		47.7791,20.699,41.5424	,,	874/1176,835/1159,879/1181	17314942	5403,7603	2203	4300	6503	SO:0001819	synonymous_variant	23400	exon24			ATTGGCGCCGTCT	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2637C>T	1.37:g.17314942G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	166	164	0.987952	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			G|0.606;A|0.394	0.394	strong		0.617	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
ANO1	55107	hgsc.bcm.edu	37	11	70007311	70007311	+	Silent	SNP	A	A	G	rs2276066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:70007311A>G	ENST00000355303.5	+	17	1928	c.1623A>G	c.(1621-1623)agA>agG	p.R541R	ANO1_ENST00000316296.5_Silent_p.R483R|ANO1_ENST00000531349.1_Silent_p.R250R|ANO1_ENST00000530676.1_Silent_p.R395R|ANO1_ENST00000538023.1_Silent_p.R541R|ANO1_ENST00000398543.2_Silent_p.R395R	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	541					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	TCATCTACAGAATCTCCATGG	0.617													A|||	3021	0.603235	0.3986	0.5807	5008	,	,		20089	0.7798		0.6501	False		,,,				2504	0.6656				p.R541R		Atlas-SNP	.											.	ANO1	156	.	0			c.A1623G						PASS	.	A		1872,2378		415,1042,668	69.0	73.0	71.0		1623	-2.7	1.0	11	dbSNP_100	71	5568,2866		1856,1856,505	no	coding-synonymous	ANO1	NM_018043.5		2271,2898,1173	GG,GA,AA		33.9815,44.0471,41.3434		541/987	70007311	7440,5244	2125	4217	6342	SO:0001819	synonymous_variant	55107	exon17			CTACAGAATCTCC	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.1623A>G	11.37:g.70007311A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Silent	SNP	ENST00000355303.5	37	CCDS44663.1																																																																																			A|0.393;G|0.607	0.607	strong		0.617	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043	
PIFO	128344	hgsc.bcm.edu	37	1	111891192	111891192	+	Missense_Mutation	SNP	C	C	A	rs2184884	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111891192C>A	ENST00000369738.4	+	4	678	c.313C>A	c.(313-315)Cac>Aac	p.H105N	PIFO_ENST00000369737.4_Missense_Mutation_p.H72N|PIFO_ENST00000484512.1_3'UTR	NM_181643.4	NP_857594.2	Q8TCI5	PIFO_HUMAN	primary cilia formation	105			H -> N (in dbSNP:rs2184884). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20643351}.		cell projection organization (GO:0030030)|positive regulation of kinase activity (GO:0033674)|regulation of cell projection organization (GO:0031344)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	beta-tubulin binding (GO:0048487)|gamma-tubulin binding (GO:0043015)|kinesin binding (GO:0019894)|protein kinase binding (GO:0019901)|Rab GTPase binding (GO:0017137)										GCAGGAAAAACACAAACAAAA	0.398													C|||	413	0.0824681	0.1082	0.0793	5008	,	,		19315	0.0		0.1193	False		,,,				2504	0.0971				p.H105N		Atlas-SNP	.											.	.	.	.	0			c.C313A						PASS	.	C	ASN/HIS	493,3913	226.9+/-242.2	14,465,1724	269.0	290.0	283.0		313	-1.5	0.0	1	dbSNP_96	283	1082,7518	225.2+/-261.4	66,950,3284	yes	missense	C1orf88	NM_181643.4	68	80,1415,5008	AA,AC,CC		12.5814,11.1893,12.1098	benign	105/192	111891192	1575,11431	2203	4300	6503	SO:0001583	missense	128344	exon4			GAAAAACACAAAC	BC050319	CCDS833.1, CCDS72836.1	1p13.2	2012-10-10	2012-10-10	2012-10-10	ENSG00000173947	ENSG00000173947			27009	protein-coding gene	gene with protein product		614234	"""chromosome 1 open reading frame 88"""	C1orf88		20643351	Standard	XM_005270472		Approved	FLJ23853, pitchfork	uc001eaw.2	Q8TCI5	OTTHUMG00000011168	ENST00000369738.4:c.313C>A	1.37:g.111891192C>A	ENSP00000358753:p.His105Asn	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	134	62	0.462687	NM_181643	D9J0A2|D9J0A3|Q4G0K4|Q52LJ6|Q5T5D5|Q5T5D6|Q8N310	Missense_Mutation	SNP	ENST00000369738.4	37	CCDS833.1	177	0.08104395604395605	47	0.09552845528455285	33	0.09116022099447514	0	0.0	97	0.1279683377308707	C	9.920	1.211873	0.22289	0.111893	0.125814	ENSG00000173947	ENST00000369738;ENST00000369737	T;T	0.30714	1.95;1.52	4.36	-1.47	0.08772	.	1.113020	0.06724	N	0.775499	T	0.10895	0.0266	M	0.70595	2.14	0.80722	P	0.0	P;P	0.41848	0.763;0.634	B;B	0.39027	0.288;0.215	T	0.19582	-1.0301	9	0.30078	T	0.28	-0.0016	0.3377	0.00328	0.342:0.2674:0.1679:0.2226	rs2184884;rs52832382;rs56928069;rs2184884	72;105	Q8TCI5-3;Q8TCI5	.;PIFO_HUMAN	N	105;72	ENSP00000358753:H105N;ENSP00000358752:H72N	ENSP00000358752:H72N	H	+	1	0	C1orf88	111692715	0.000000	0.05858	0.001000	0.08648	0.245000	0.25701	-0.888000	0.04148	-0.124000	0.11724	0.449000	0.29647	CAC	C|0.891;A|0.109	0.109	strong		0.398	PIFO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030718.1	NM_181643	
IRS4	8471	hgsc.bcm.edu	37	X	107979475	107979475	+	Missense_Mutation	SNP	G	G	A	rs1801162	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:107979475G>A	ENST00000372129.2	-	1	176	c.100C>T	c.(100-102)Ctt>Ttt	p.L34F	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	34			L -> F (in dbSNP:rs1801162).		positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GAGGAAAGAAGCGGGGTGGTC	0.642													g|||	185	0.0490066	0.0499	0.0562	3775	,	,		8286	0.002		0.0408	False		,,,				2504	0.0378				p.L34F		Atlas-SNP	.											.	IRS4	253	.	0			c.C100T						PASS	.		PHE/LEU	256,3579		6,206,38,1420,533	28.0	30.0	29.0		100	0.4	0.2	X	dbSNP_89	29	392,6332		7,258,120,2163,1748	yes	missense	IRS4	NM_003604.2	22	13,464,158,3583,2281	AA,AG,A,GG,G		5.8299,6.6754,6.1369	benign	34/1258	107979475	648,9911	2203	4296	6499	SO:0001583	missense	8471	exon1			AAAGAAGCGGGGT	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.100C>T	X.37:g.107979475G>A	ENSP00000361202:p.Leu34Phe	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	94	85	0.904255	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	84	0.05063291139240506	29	0.06016597510373444	14	0.03977272727272727	0	0.0	20	0.02717391304347826	g	10.04	1.241221	0.22711	0.066754	0.058299	ENSG00000133124	ENST00000372129	T	0.38887	1.11	3.24	0.359	0.16088	.	1.235780	0.06363	N	0.712073	T	0.01489	0.0048	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.14200	-1.0481	9	0.30854	T	0.27	-0.1263	3.9713	0.09454	0.2496:0.385:0.3654:0.0	rs1801162;rs52823369	34	O14654	IRS4_HUMAN	F	34	ENSP00000361202:L34F	ENSP00000361202:L34F	L	-	1	0	IRS4	107866131	0.154000	0.22792	0.238000	0.24106	0.652000	0.38707	0.194000	0.17135	-0.030000	0.13804	0.431000	0.28591	CTT	G|0.943;A|0.057	0.057	strong		0.642	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
EPS15	2060	hgsc.bcm.edu	37	1	51829575	51829575	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:51829575C>T	ENST00000371733.3	-	23	2418	c.2322G>A	c.(2320-2322)aaG>aaA	p.K774K	EPS15_ENST00000371730.2_Silent_p.K640K|EPS15_ENST00000396122.4_Silent_p.K451K	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	774	15 X 3 AA repeats of D-P-F.|Pro-rich.				cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						GAGTTCCGATCTTTGGTGGCA	0.448			T	MLL	ALL																																p.K774K		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	EPS15,right_upper_lobe,carcinoma,0,1	EPS15	72	1	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.G2322A						PASS	.						215.0	194.0	201.0					1																	51829575		2203	4300	6503	SO:0001819	synonymous_variant	2060	exon23			TCCGATCTTTGGT	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"""EF-hand domain containing"""	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.2322G>A	1.37:g.51829575C>T		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	236	106	0.449153	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Silent	SNP	ENST00000371733.3	37	CCDS557.1																																																																																			.	.	none		0.448	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	
FZD6	8323	hgsc.bcm.edu	37	8	104337096	104337096	+	Silent	SNP	A	A	G	rs3808554	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:104337096A>G	ENST00000358755.4	+	4	1079	c.762A>G	c.(760-762)ctA>ctG	p.L254L	FZD6_ENST00000523739.1_Silent_p.L222L|FZD6_ENST00000540287.1_Intron|FZD6_ENST00000522566.1_Silent_p.L254L	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	254					angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			GATTTTTGCTAGGCGATAGCA	0.398													A|||	2249	0.449081	0.2988	0.5086	5008	,	,		22099	0.6379		0.4573	False		,,,				2504	0.407				p.L254L		Atlas-SNP	.											.	FZD6	61	.	0			c.A762G						PASS	.	A	,,	1341,3065	444.7+/-347.4	192,957,1054	110.0	95.0	100.0		762,666,762	-0.8	1.0	8	dbSNP_107	100	4009,4591	551.8+/-386.0	951,2107,1242	no	coding-synonymous,coding-synonymous,coding-synonymous	FZD6	NM_001164615.1,NM_001164616.1,NM_003506.3	,,	1143,3064,2296	GG,GA,AA		46.6163,30.4358,41.1349	,,	254/707,222/675,254/707	104337096	5350,7656	2203	4300	6503	SO:0001819	synonymous_variant	8323	exon4			TTTGCTAGGCGAT	AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"""GPCR / Class F : Frizzled receptors"""	4044	protein-coding gene	gene with protein product		603409	"""frizzled (Drosophila) homolog 6"", ""frizzled homolog 6 (Drosophila)"", ""frizzled 6, seven transmembrane spanning receptor"", ""frizzled family receptor 6"""			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.762A>G	8.37:g.104337096A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	139	54	0.388489	NM_003506	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Silent	SNP	ENST00000358755.4	37	CCDS6298.1																																																																																			A|0.576;G|0.424	0.424	strong		0.398	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506	
COL9A3	1299	hgsc.bcm.edu	37	20	61460124	61460124	+	Silent	SNP	G	G	A	rs2249903	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:61460124G>A	ENST00000343916.3	+	18	912	c.909G>A	c.(907-909)ccG>ccA	p.P303P		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	303	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					AGGGCATGCCGGGCAAGGACG	0.682													G|||	422	0.0842652	0.0363	0.1167	5008	,	,		19021	0.0308		0.1889	False		,,,				2504	0.0736				p.P303P		Atlas-SNP	.											COL9A3,right_lower_lobe,carcinoma,+1,1	COL9A3	70	1	0			c.G909A						PASS	.	G		276,4126	150.3+/-184.3	11,254,1936	51.0	47.0	48.0		909	-7.8	1.0	20	dbSNP_100	48	1507,7091	281.8+/-295.3	135,1237,2927	no	coding-synonymous	COL9A3	NM_001853.3		146,1491,4863	AA,AG,GG		17.5273,6.2699,13.7154		303/685	61460124	1783,11217	2201	4299	6500	SO:0001819	synonymous_variant	1299	exon18			CATGCCGGGCAAG	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.909G>A	20.37:g.61460124G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_001853	Q13681|Q9H4G9|Q9UPE2	Silent	SNP	ENST00000343916.3	37	CCDS13505.1																																																																																			G|0.833;A|0.167	0.167	strong		0.682	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
AR	367	hgsc.bcm.edu	37	X	66765627	66765627	+	Silent	SNP	G	G	A	rs6152	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:66765627G>A	ENST00000374690.3	+	1	1163	c.639G>A	c.(637-639)gaG>gaA	p.E213E	AR_ENST00000396044.3_Silent_p.E213E|AR_ENST00000504326.1_Silent_p.E213E|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	211	Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	GAGCGAGGGAGGCCTCGGGGG	0.572									Androgen Insensitivity Syndrome				g|||	901	0.238675	0.4932	0.1023	3775	,	,		13539	0.002		0.1083	False		,,,				2504	0.0685				p.E213E		Atlas-SNP	.											.	AR	249	.	0			c.G639A	GRCh37	CM051843	AR	M	rs6152	PASS	.			2312,1523		588,793,343,251,228	34.0	34.0	34.0	http://omim.org/entry/300710	639	3.0	1.0	X	dbSNP_52	34	1057,5671		56,625,320,1747,1552	no	coding-synonymous	AR	NM_000044.3		644,1418,663,1998,1780	AA,AG,A,GG,G		15.7105,39.7132,31.8943		213/921	66765627	3369,7194	2203	4300	6503	SO:0001819	synonymous_variant	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GAGGGAGGCCTCG	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.639G>A	X.37:g.66765627G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	50	45	0.9	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent	SNP	ENST00000374690.3	37	CCDS14387.1																																																																																			G|0.700;A|0.300	0.300	strong		0.572	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
FERMT1	55612	hgsc.bcm.edu	37	20	6088265	6088265	+	Missense_Mutation	SNP	G	G	A	rs62200482	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:6088265G>A	ENST00000217289.4	-	6	1551	c.763C>T	c.(763-765)Cgc>Tgc	p.R255C	FERMT1_ENST00000536936.1_De_novo_Start_OutOfFrame	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	255	FERM.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						ATAAGGGAGCGTGAGGAGTCT	0.333													G|||	256	0.0511182	0.003	0.0418	5008	,	,		16905	0.0804		0.0875	False		,,,				2504	0.0552				p.R255C		Atlas-SNP	.											.	FERMT1	106	.	0			c.C763T						PASS	.	G	CYS/ARG	86,4320	70.3+/-108.2	2,82,2119	55.0	54.0	55.0		763	4.5	0.8	20	dbSNP_129	55	743,7857	179.9+/-228.9	25,693,3582	yes	missense	FERMT1	NM_017671.4	180	27,775,5701	AA,AG,GG		8.6395,1.9519,6.374	probably-damaging	255/678	6088265	829,12177	2203	4300	6503	SO:0001583	missense	55612	exon6			GGGAGCGTGAGGA	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.763C>T	20.37:g.6088265G>A	ENSP00000217289:p.Arg255Cys	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	188	71	0.37766	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Missense_Mutation	SNP	ENST00000217289.4	37	CCDS13098.1	124	0.056776556776556776	3	0.006097560975609756	14	0.03867403314917127	45	0.07867132867132867	62	0.08179419525065963	G	16.82	3.229469	0.58777	0.019519	0.086395	ENSG00000101311	ENST00000217289;ENST00000339538	T	0.78126	-1.15	5.5	4.54	0.55810	FERM, N-terminal (1);Band 4.1 domain (1);	0.050080	0.85682	D	0.000000	T	0.29684	0.0741	M	0.83384	2.64	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.97110	0.993;1.0	T	0.72711	-0.4211	9	0.87932	D	0	-9.0744	13.859	0.63548	0.0:0.0:0.7233:0.2767	rs62200482	255;255	Q9BQL6-4;Q9BQL6	.;FERM1_HUMAN	C	255	ENSP00000217289:R255C	ENSP00000217289:R255C	R	-	1	0	FERMT1	6036265	1.000000	0.71417	0.803000	0.32268	0.360000	0.29518	4.367000	0.59498	1.438000	0.47492	0.650000	0.86243	CGC	G|0.936;A|0.064	0.064	strong		0.333	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
ALOX15B	247	hgsc.bcm.edu	37	17	7948175	7948175	+	Silent	SNP	C	C	T	rs6503070	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7948175C>T	ENST00000380183.4	+	6	844	c.705C>T	c.(703-705)gaC>gaT	p.D235D	ALOX15B_ENST00000380173.2_Silent_p.D235D|ALOX15B_ENST00000572022.1_Silent_p.D235D|ALOX15B_ENST00000573359.1_Silent_p.D235D	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	235	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)	p.D235D(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						GGCAGGAGGACGCCTTCTTCG	0.617													T|||	2991	0.597244	0.8699	0.5403	5008	,	,		12415	0.4087		0.4404	False		,,,				2504	0.6247				p.D235D		Atlas-SNP	.											ALOX15B,NS,carcinoma,0,1	ALOX15B	66	1	1	Substitution - coding silent(1)	stomach(1)	c.C705T						PASS	.	T	,,	3486,920	351.6+/-311.3	1380,726,97	94.0	63.0	73.0		705,705,705	-4.8	0.2	17	dbSNP_116	73	3723,4877	616.5+/-396.5	817,2089,1394	no	coding-synonymous,coding-synonymous,coding-synonymous	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	,,	2197,2815,1491	TT,TC,CC		43.2907,20.8806,44.5717	,,	235/648,235/603,235/677	7948175	7209,5797	2203	4300	6503	SO:0001819	synonymous_variant	247	exon6			GGAGGACGCCTTC	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.705C>T	17.37:g.7948175C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	154	151	0.980519	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Silent	SNP	ENST00000380183.4	37	CCDS11128.1																																																																																			A|0.000;C|0.449;T|0.551	0.551	strong		0.617	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
MAP1B	4131	hgsc.bcm.edu	37	5	71494931	71494931	+	Missense_Mutation	SNP	A	A	C	rs13153166	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:71494931A>C	ENST00000296755.7	+	5	6047	c.5749A>C	c.(5749-5751)Agt>Cgt	p.S1917R		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1917			S -> R (in dbSNP:rs13153166).		axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		AAAATCTCCAAGTGACAGTGG	0.443													A|||	70	0.0139776	0.0008	0.0144	5008	,	,		19524	0.0		0.0437	False		,,,				2504	0.0153				p.S1917R	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A5749C						PASS	.	A	ARG/SER	35,4369	38.4+/-70.7	0,35,2167	61.0	64.0	63.0		5749	-6.4	0.0	5	dbSNP_121	63	405,8195	120.4+/-179.7	14,377,3909	yes	missense	MAP1B	NM_005909.3	110	14,412,6076	CC,CA,AA		4.7093,0.7947,3.3836	possibly-damaging	1917/2469	71494931	440,12564	2202	4300	6502	SO:0001583	missense	4131	exon5			TCTCCAAGTGACA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.5749A>C	5.37:g.71494931A>C	ENSP00000296755:p.Ser1917Arg	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	41	0.018772893772893772	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	32	0.04221635883905013	A	7.818	0.717223	0.15372	0.007947	0.047093	ENSG00000131711	ENST00000296755	T	0.03358	3.96	5.25	-6.42	0.01932	.	1.069650	0.07205	N	0.858174	T	0.00271	0.0008	N	0.08118	0	0.09310	N	1	B;B	0.27625	0.183;0.001	B;B	0.24394	0.053;0.004	T	0.48547	-0.9026	10	0.15066	T	0.55	0.3559	1.5602	0.02593	0.2865:0.2001:0.3763:0.1371	rs13153166;rs52835272;rs60281324;rs13153166	1791;1917	A2BDK6;P46821	.;MAP1B_HUMAN	R	1917	ENSP00000296755:S1917R	ENSP00000296755:S1917R	S	+	1	0	MAP1B	71530687	0.000000	0.05858	0.003000	0.11579	0.867000	0.49689	-0.116000	0.10724	-0.676000	0.05238	-0.490000	0.04691	AGT	A|0.974;C|0.026	0.026	strong		0.443	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65349756	65349756	+	Missense_Mutation	SNP	T	T	G	rs6591182	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65349756T>G	ENST00000309295.4	+	9	1878	c.1613T>G	c.(1612-1614)gTg>gGg	p.V538G		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	538			V -> G (in dbSNP:rs6591182). {ECO:0000269|PubMed:14702039}.			membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						AGGCCCCAGGTGAGCAGCTGG	0.632													T|||	2133	0.425919	0.3101	0.3775	5008	,	,		16959	0.4514		0.506	False		,,,				2504	0.5082				p.V538G		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.T1613G						PASS	.	T	GLY/VAL	1180,2562		196,788,887	12.0	14.0	13.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1613	3.8	1.0	11	dbSNP_116	13	3862,4282		984,1894,1194	yes	missense	EHBP1L1	NM_001099409.1	109	1180,2682,2081	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	47.4214,31.5339,42.4197	probably-damaging	538/1524	65349756	5042,6844	1871	4072	5943	SO:0001583	missense	254102	exon9			CCCAGGTGAGCAG	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.1613T>G	11.37:g.65349756T>G	ENSP00000312671:p.Val538Gly	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	174	78	0.448276	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	37	CCDS44649.1	942	0.43131868131868134	162	0.32926829268292684	138	0.3812154696132597	260	0.45454545454545453	382	0.503957783641161	T	16.66	3.184620	0.57909	0.315339	0.474214	ENSG00000173442	ENST00000309295	T	0.73258	-0.73	5.03	3.82	0.43975	.	0.000000	0.43919	D	0.000510	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	0.99999999893969	P	0.52842	0.956	P	0.50082	0.63	T	0.46843	-0.9162	9	0.87932	D	0	.	8.8901	0.35427	0.1672:0.0:0.0:0.8328	rs6591182;rs57588931;rs6591182	538	Q8N3D4	EH1L1_HUMAN	G	538	ENSP00000312671:V538G	ENSP00000312671:V538G	V	+	2	0	EHBP1L1	65106332	0.995000	0.38212	1.000000	0.80357	0.709000	0.40893	0.116000	0.15561	1.890000	0.54733	0.459000	0.35465	GTG	T|0.577;G|0.423	0.423	strong		0.632	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
SSUH2	51066	hgsc.bcm.edu	37	3	8675539	8675539	+	Missense_Mutation	SNP	G	G	A	rs2276800	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:8675539G>A	ENST00000317371.4	-	11	1311	c.86C>T	c.(85-87)cCg>cTg	p.P29L	SSUH2_ENST00000341795.3_Missense_Mutation_p.P29L|SSUH2_ENST00000544814.1_Intron|SSUH2_ENST00000415132.1_Missense_Mutation_p.P29L			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	29			P -> L (in dbSNP:rs2276800).			cytoplasm (GO:0005737)											GGACTCACGCGGGCCAGCCAG	0.657													A|||	1671	0.333666	0.6838	0.2651	5008	,	,		10609	0.1984		0.1829	False		,,,				2504	0.2035				p.P29L		Atlas-SNP	.											C3orf32,NS,carcinoma,0,2	.	.	2	0			c.C86T						scavenged	.	A	LEU/PRO	2615,1791	503.9+/-365.7	793,1029,381	27.0	30.0	29.0		86	-4.0	0.0	3	dbSNP_100	29	1528,7072	728.5+/-406.7	120,1288,2892	yes	missense	C3orf32	NM_015931.1	98	913,2317,3273	AA,AG,GG		17.7674,40.6491,31.8545	probably-damaging	29/354	8675539	4143,8863	2203	4300	6503	SO:0001583	missense	51066	exon4			TCACGCGGGCCAG	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.86C>T	3.37:g.8675539G>A	ENSP00000324551:p.Pro29Leu	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	145	138	0.951724	NM_015931	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	37	CCDS2568.1	636	0.29120879120879123	323	0.6565040650406504	89	0.24585635359116023	86	0.15034965034965034	138	0.1820580474934037	A	6.834	0.522996	0.13066	0.593509	0.177674	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132	T;T;T	0.51817	0.74;0.74;0.69	3.97	-4.02	0.04034	.	0.656465	0.14884	N	0.292819	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33085	-0.9882	9	0.07813	T	0.8	0.3753	6.2471	0.20825	0.3373:0.0:0.5156:0.147	rs2276800;rs57482921;rs2276800	29	Q9Y2M2	CC032_HUMAN	L	29	ENSP00000339150:P29L;ENSP00000324551:P29L;ENSP00000410757:P29L	ENSP00000324551:P29L	P	-	2	0	C3orf32	8650539	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.643000	0.05421	-1.368000	0.02149	-0.893000	0.02921	CCG	G|0.689;A|0.311	0.311	strong		0.657	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931	
ZNF418	147686	hgsc.bcm.edu	37	19	58437773	58437773	+	Silent	SNP	T	T	C	rs184676943	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58437773T>C	ENST00000396147.1	-	4	2067	c.1776A>G	c.(1774-1776)gaA>gaG	p.E592E	ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000595830.1_Silent_p.E592E|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599852.1_Silent_p.E507E|ZNF418_ENST00000425570.3_Silent_p.E613E	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	592					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		ATTCCCTGCATTCATAAGGCC	0.453																																					p.E592E		Atlas-SNP	.											.	ZNF418	76	.	0			c.A1776G						PASS	.	T		10,4390		0,10,2190	84.0	87.0	86.0		1776	-0.9	0.0	19		86	109,8491		1,107,4192	no	coding-synonymous	ZNF418	NM_133460.1		1,117,6382	CC,CT,TT		1.2674,0.2273,0.9154		592/677	58437773	119,12881	2200	4300	6500	SO:0001819	synonymous_variant	147686	exon4			CCTGCATTCATAA	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1776A>G	19.37:g.58437773T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	87	15	0.172414	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			T|0.988;C|0.012	0.012	strong		0.453	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807536	18807536	+	Missense_Mutation	SNP	G	G	T	rs7512414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18807536G>T	ENST00000400664.1	+	1	113	c.61G>T	c.(61-63)Gtg>Ttg	p.V21L		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	21			V -> L (in dbSNP:rs7512414).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GACCGGCAAGGTGGTGCTGTC	0.627													G|||	473	0.0944489	0.1233	0.1239	5008	,	,		18132	0.0377		0.1233	False		,,,				2504	0.0634				p.V21L		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G61T						PASS	.	G	LEU/VAL	401,3739		18,365,1687	47.0	54.0	52.0		61	3.9	1.0	1	dbSNP_116	52	1033,7421		60,913,3254	yes	missense	KLHDC7A	NM_152375.2	32	78,1278,4941	TT,TG,GG		12.2191,9.686,11.3864	benign	21/778	18807536	1434,11160	2070	4227	6297	SO:0001583	missense	127707	exon1			GGCAAGGTGGTGC	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.61G>T	1.37:g.18807536G>T	ENSP00000383505:p.Val21Leu	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	326	149	0.457055	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	213	0.09752747252747253	45	0.09146341463414634	48	0.13259668508287292	29	0.050699300699300696	91	0.12005277044854881	G	9.454	1.091325	0.20471	0.09686	0.122191	ENSG00000179023	ENST00000400664	T	0.74209	-0.82	5.82	3.89	0.44902	.	.	.	.	.	T	0.00724	0.0024	N	0.12182	0.205	0.34395	P	0.30533699999999997	B	0.14012	0.009	B	0.10450	0.005	T	0.10268	-1.0637	8	0.02654	T	1	.	13.8326	0.63391	0.0:0.5191:0.4809:0.0	rs7512414;rs7512414	21	Q5VTJ3	KLD7A_HUMAN	L	21	ENSP00000383505:V21L	ENSP00000383505:V21L	V	+	1	0	KLHDC7A	18680123	1.000000	0.71417	0.999000	0.59377	0.075000	0.17131	1.846000	0.39289	1.452000	0.47756	0.591000	0.81541	GTG	G|0.888;T|0.112	0.112	strong		0.627	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
ZNF655	79027	hgsc.bcm.edu	37	7	99159522	99159522	+	Intron	SNP	C	C	G	rs141089610	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99159522C>G	ENST00000394163.2	+	2	319				ZNF655_ENST00000440391.1_Intron|ZNF655_ENST00000252713.4_Intron|ZNF655_ENST00000449244.1_Missense_Mutation_p.P50A|GS1-259H13.10_ENST00000455905.1_Intron|ZNF655_ENST00000493277.1_Intron|GS1-259H13.10_ENST00000486324.1_Intron|ZNF655_ENST00000424881.1_Intron|ZNF655_ENST00000357864.2_Intron|ZNF655_ENST00000425063.1_Missense_Mutation_p.P50A|ZNF655_ENST00000320583.5_Missense_Mutation_p.P50A|ZNF655_ENST00000454654.1_Missense_Mutation_p.P50A	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655						negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					TCCACCTGTTCCTCAGGTGCC	0.612													C|||	38	0.00758786	0.0015	0.013	5008	,	,		19086	0.0		0.0179	False		,,,				2504	0.0092				p.P50A		Atlas-SNP	.											ZNF655_ENST00000320583,NS,lymphoid_neoplasm,0,1	ZNF655	75	1	0			c.C148G						PASS	.	C	,,,,ALA/PRO,,ALA/PRO,	20,4386	25.3+/-52.1	0,20,2183	55.0	39.0	44.0		,,,,148,,148,	0.8	1.0	7	dbSNP_134	44	166,8434	71.0+/-133.6	2,162,4136	yes	intron,intron,intron,intron,missense,intron,missense,intron	ZNF655	NM_001009958.1,NM_001009960.1,NM_001083956.1,NM_001085366.1,NM_001085367.1,NM_001085368.1,NM_024061.3,NM_138494.2	,,,,27,,27,	2,182,6319	GG,GC,CC		1.9302,0.4539,1.4301	,,,,,,,	,,,,50/182,,50/182,	99159522	186,12820	2203	4300	6503	SO:0001627	intron_variant	79027	exon3			CCTGTTCCTCAGG	AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"""Zinc fingers, C2H2-type"", ""-"""	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.136+1204C>G	7.37:g.99159522C>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	102	31	0.303922	NM_024061	A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Missense_Mutation	SNP	ENST00000394163.2	37	CCDS5669.1	16	0.007326007326007326	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	10	0.013192612137203167	C	13.24	2.179346	0.38511	0.004539	0.019302	ENSG00000197343	ENST00000320583;ENST00000454654;ENST00000449244;ENST00000425063	T	0.01287	5.05	4.98	0.824	0.18818	.	.	.	.	.	T	0.00524	0.0017	N	0.22421	0.69	0.80722	D	1	B	0.15141	0.012	B	0.14578	0.011	T	0.52793	-0.8528	9	0.09590	T	0.72	.	7.1925	0.25834	0.0:0.598:0.0:0.402	.	50	Q8N720-2	.	A	50	ENSP00000322363:P50A	ENSP00000322363:P50A	P	+	1	0	ZNF655	98997458	0.996000	0.38824	0.994000	0.49952	0.996000	0.88848	0.445000	0.21677	0.048000	0.15891	0.563000	0.77884	CCT	C|0.988;G|0.012	0.012	strong		0.612	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1	NM_138494	
PLEKHO2	80301	hgsc.bcm.edu	37	15	65157482	65157482	+	Missense_Mutation	SNP	C	C	T	rs2010875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:65157482C>T	ENST00000323544.4	+	6	996	c.868C>T	c.(868-870)Ccg>Tcg	p.P290S	AC069368.3_ENST00000437723.1_Intron	NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	290	Pro-rich.		P -> S (in dbSNP:rs2010875). {ECO:0000269|PubMed:15498874}.							NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						GAGTGCAGAACCGTCCCAGGC	0.617													C|||	1518	0.303115	0.1581	0.2983	5008	,	,		17993	0.7589		0.1461	False		,,,				2504	0.1943				p.P290S		Atlas-SNP	.											.	PLEKHO2	50	.	0			c.C868T						PASS	.	C	SER/PRO,SER/PRO	673,3731	275.7+/-272.7	50,573,1579	49.0	52.0	51.0		718,868	1.8	0.0	15	dbSNP_92	51	1310,7286	250.0+/-277.0	100,1110,3088	yes	missense,missense	PLEKHO2	NM_001195059.1,NM_025201.4	74,74	150,1683,4667	TT,TC,CC		15.2396,15.2816,15.2538	benign,benign	240/441,290/491	65157482	1983,11017	2202	4298	6500	SO:0001583	missense	80301	exon6			GCAGAACCGTCCC	AF318373	CCDS10196.1, CCDS73739.1	15q22.31	2013-01-10	2007-12-14	2007-12-14	ENSG00000241839	ENSG00000241839		"""Pleckstrin homology (PH) domain containing"""	30026	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family Q member 1"""	PLEKHQ1		12477932	Standard	NM_025201		Approved	DKFZp761K2312, PP1628, pp9099	uc002anv.3	Q8TD55	OTTHUMG00000133050	ENST00000323544.4:c.868C>T	15.37:g.65157482C>T	ENSP00000326706:p.Pro290Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_025201	Q7L4H4|Q8WYS8	Missense_Mutation	SNP	ENST00000323544.4	37	CCDS10196.1	730	0.3342490842490842	69	0.1402439024390244	97	0.26795580110497236	451	0.7884615384615384	113	0.14907651715039577	C	0.003	-2.482521	0.00163	0.152816	0.152396	ENSG00000241839	ENST00000323544	T	0.29142	1.58	5.33	1.78	0.24846	.	1.654450	0.02961	N	0.143106	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.40059	-0.9583	9	0.06236	T	0.91	.	2.3278	0.04227	0.1592:0.2521:0.4516:0.1371	rs2010875;rs3809502;rs12911443;rs16948324;rs52791051;rs57577084;rs2010875	240;290	Q8TD55-2;Q8TD55	.;PKHO2_HUMAN	S	290	ENSP00000326706:P290S	ENSP00000326706:P290S	P	+	1	0	PLEKHO2	62944535	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	0.212000	0.17497	0.593000	0.29745	0.655000	0.94253	CCG	T|0.220;G|0.000;C|0.779	0.220	strong		0.617	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1	NM_025201	
CPPED1	55313	hgsc.bcm.edu	37	16	12897578	12897578	+	Missense_Mutation	SNP	G	G	T	rs3748976	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:12897578G>T	ENST00000381774.4	-	1	296	c.56C>A	c.(55-57)gCc>gAc	p.A19D	CPPED1_ENST00000261660.4_Missense_Mutation_p.A19D|CPPED1_ENST00000433677.2_Missense_Mutation_p.A19D	NM_018340.2	NP_060810.2	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain containing 1	19			A -> D (in dbSNP:rs3748976). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15991289}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|urinary_tract(1)	18						GGGAAACGCGGCCAGGGTCCT	0.667													T|||	1858	0.371006	0.7345	0.2637	5008	,	,		11981	0.4018		0.1421	False		,,,				2504	0.1595				p.A19D		Atlas-SNP	.											.	CPPED1	41	.	0			c.C56A						PASS	.	T	ASP/ALA,ASP/ALA	2226,1526		666,894,316	14.0	17.0	16.0		56,56	4.8	1.0	16	dbSNP_107	16	1428,6730		124,1180,2775	no	missense,missense	CPPED1	NM_001099455.1,NM_018340.2	126,126	790,2074,3091	TT,TG,GG		17.5043,40.6716,30.6801	benign,benign	19/173,19/315	12897578	3654,8256	1876	4079	5955	SO:0001583	missense	55313	exon1			AACGCGGCCAGGG	AK022710	CCDS42119.1, CCDS42120.1	16p13.12	2014-02-12	2009-03-13		ENSG00000103381	ENSG00000103381			25632	protein-coding gene	gene with protein product	"""complete S transactivated protein 1"""	615603				12477932	Standard	NM_018340		Approved	CSTP1, FLJ11151	uc002dca.4	Q9BRF8	OTTHUMG00000167711	ENST00000381774.4:c.56C>A	16.37:g.12897578G>T	ENSP00000371193:p.Ala19Asp	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_001099455	B4DQ68|Q6MZY9|Q9H9M9|Q9NUT6	Missense_Mutation	SNP	ENST00000381774.4	37	CCDS42120.1	757	0.3466117216117216	348	0.7073170731707317	93	0.2569060773480663	205	0.3583916083916084	111	0.14643799472295516	T	7.138	0.581246	0.13686	0.593284	0.175043	ENSG00000103381	ENST00000381774;ENST00000433677;ENST00000261660	T;T;T	0.03065	4.06;4.13;4.06	4.81	4.81	0.61882	.	0.343849	0.32852	N	0.005578	T	0.00012	0.0000	N	0.00538	-1.39	0.49687	P	1.8499999999999073E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10132	-1.0643	9	0.08599	T	0.76	-17.4724	8.6703	0.34145	0.0:0.0:0.1934:0.8066	rs3748976;rs58899350;rs3748976	19;19	Q9BRF8-2;Q9BRF8	.;CPPED_HUMAN	D	19	ENSP00000371193:A19D;ENSP00000411127:A19D;ENSP00000261660:A19D	ENSP00000261660:A19D	A	-	2	0	CPPED1	12805079	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	1.878000	0.39608	0.870000	0.35726	-0.534000	0.04291	GCC	G|0.651;T|0.349	0.349	strong		0.667	CPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395795.2	NM_018340	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037580	33037580	+	Missense_Mutation	SNP	T	T	G	rs36013091|rs2308911	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33037580T>G	ENST00000419277.1	-	3	313	c.184A>C	c.(184-186)Atg>Ctg	p.M62L	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.M62L	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	62	Alpha-1.		M -> K (in dbSNP:rs2308912).|M -> L (in dbSNP:rs2308911).|M -> Q (in allele DPA1*01:06, allele DPA1*02:01, allele DPA1*02:02 and allele DPA1*02:04; requires 2 nucleotide substitutions; dbSNP:rs36013091).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						ACATAGAACATCTCATCTTCA	0.488													.|||	2159	0.43111	0.5794	0.2795	5008	,	,		19572	0.6508		0.1869	False		,,,				2504	0.363				p.M62L		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.A184C						PASS	.	T	LEU/MET,LEU/MET,LEU/MET	45,2975		3,39,1468	62.0	87.0	78.0		184,184,184	-6.0	0.0	6	dbSNP_126	78	7,5411		0,7,2702	no	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	15,15,15	3,46,4170	GG,GT,TT		0.1292,1.4901,0.6163	benign,benign,benign	62/261,62/261,62/261	33037580	52,8386	1510	2709	4219	SO:0001583	missense	3113	exon2			AGAACATCTCATC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.184A>C	6.37:g.33037580T>G	ENSP00000393566:p.Met62Leu	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	165	63	0.381818	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	760	0.34798534798534797	239	0.48577235772357724	78	0.2154696132596685	329	0.5751748251748252	114	0.1503957783641161	T	0.001	-3.735704	0.00005	0.014901	0.001292	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.00623	6.15;6.15;6.15	3.0	-5.99	0.02213	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	2.490280	0.02659	U	0.107291	T	0.00109	0.0003	N	0.13003	0.285	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48502	-0.9030	9	0.02654	T	1	.	2.9736	0.05930	0.092:0.1781:0.3519:0.378	rs2308911;rs12722001;rs52808337	62	P20036	DPA1_HUMAN	L	62	ENSP00000393566:M62L;ENSP00000402872:M62L;ENSP00000390929:M62L	ENSP00000393566:M62L	M	-	1	0	HLA-DPA1	33145558	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	-2.357000	0.01086	-3.633000	0.00129	-1.423000	0.01107	ATG	T|0.716;G|0.284	0.284	strong		0.488	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
CSMD3	114788	hgsc.bcm.edu	37	8	113841971	113841971	+	Silent	SNP	A	A	G	rs142880481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:113841971A>G	ENST00000297405.5	-	12	2047	c.1803T>C	c.(1801-1803)gaT>gaC	p.D601D	CSMD3_ENST00000343508.3_Silent_p.D561D|CSMD3_ENST00000352409.3_Silent_p.D601D|CSMD3_ENST00000455883.2_Silent_p.D497D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	601	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTGTCAAGGTATCATAGCCAA	0.403										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	6	0.00119808	0.0	0.0014	5008	,	,		15247	0.0		0.005	False		,,,				2504	0.0				p.D601D		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T1803C						PASS	.	A	,,	1,4405	2.1+/-5.4	0,1,2202	108.0	97.0	100.0		1491,1803,1683	-3.2	0.9	8	dbSNP_134	100	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	0,19,6484	GG,GA,AA		0.2093,0.0227,0.1461	,,	497/3539,601/3708,561/3668	113841971	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon12			CAAGGTATCATAG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1803T>C	8.37:g.113841971A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.999;G|0.001	0.001	strong		0.403	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
HLA-B	3106	hgsc.bcm.edu	37	6	31324664	31324664	+	Silent	SNP	T	T	G	rs9266184	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324664T>G	ENST00000412585.2	-	2	172	c.144A>C	c.(142-144)tcA>tcC	p.S48S		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	48	Alpha-1.		S -> A (in dbSNP:rs713031).|S -> P (in dbSNP:rs713031).|S -> T (in dbSNP:rs713031).		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CGTAGCCCACTGAGATGAAGC	0.697									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	1128	0.22524	0.149	0.2277	5008	,	,		10041	0.2629		0.2833	False		,,,				2504	0.228				p.S48S		Atlas-SNP	.											.	HLA-B	54	.	0			c.A144C						PASS	.	T		84,4162		5,74,2044	29.0	23.0	25.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	144	-2.6	0.0	6	dbSNP_118	25	338,7908		44,250,3829	no	coding-synonymous	HLA-B	NM_005514.6		49,324,5873	GG,GT,TT		4.099,1.9783,3.3782		48/363	31324664	422,12070	2123	4123	6246	SO:0001819	synonymous_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	GCCCACTGAGATG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.144A>C	6.37:g.31324664T>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			G|0.111;T|0.889	0.111	strong		0.697	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
PMFBP1	83449	hgsc.bcm.edu	37	16	72184566	72184566	+	Missense_Mutation	SNP	C	C	T	rs35370634	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72184566C>T	ENST00000237353.10	-	5	838	c.577G>A	c.(577-579)Gag>Aag	p.E193K	PMFBP1_ENST00000355636.6_Missense_Mutation_p.E48K|PMFBP1_ENST00000537465.1_Missense_Mutation_p.E193K	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	193			E -> K (in dbSNP:rs35370634).			cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TCTAGTAACTCGATGTTGCTC	0.532													C|||	439	0.0876597	0.0151	0.0634	5008	,	,		20294	0.0218		0.162	False		,,,				2504	0.1943				p.E193K		Atlas-SNP	.											.	PMFBP1	101	.	0			c.G577A						PASS	.	C	LYS/GLU,LYS/GLU	158,4238	107.3+/-145.7	6,146,2046	166.0	152.0	157.0		142,577	6.2	1.0	16	dbSNP_126	157	1404,7196	271.1+/-289.3	127,1150,3023	yes	missense,missense	PMFBP1	NM_001160213.1,NM_031293.2	56,56	133,1296,5069	TT,TC,CC		16.3256,3.5942,12.0191	probably-damaging,probably-damaging	48/883,193/1008	72184566	1562,11434	2198	4300	6498	SO:0001583	missense	83449	exon5			GTAACTCGATGTT	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.577G>A	16.37:g.72184566C>T	ENSP00000237353:p.Glu193Lys	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	184	73	0.396739	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	37	CCDS32483.1	178	0.0815018315018315	8	0.016260162601626018	27	0.07458563535911603	11	0.019230769230769232	132	0.1741424802110818	C	33	5.203928	0.95033	0.035942	0.163256	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.79247	-1.25;-1.25;2.47	6.17	6.17	0.99709	.	0.000000	0.52532	D	0.000062	T	0.00666	0.0022	N	0.24115	0.695	0.29957	P	0.819727	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.989;0.989	T	0.33727	-0.9857	9	0.08837	T	0.75	-33.6909	16.3795	0.83443	0.0:1.0:0.0:0.0	rs35370634	193;193;193	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	K	193;193;48	ENSP00000443817:E193K;ENSP00000237353:E193K;ENSP00000347854:E48K	ENSP00000237353:E193K	E	-	1	0	PMFBP1	70742067	0.830000	0.29337	0.996000	0.52242	0.917000	0.54804	3.761000	0.55242	2.941000	0.99782	0.655000	0.94253	GAG	C|0.891;T|0.109	0.109	strong		0.532	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293	
SON	6651	hgsc.bcm.edu	37	21	34945721	34945721	+	Silent	SNP	T	T	C	rs3174808	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:34945721T>C	ENST00000356577.4	+	9	7468	c.6993T>C	c.(6991-6993)aaT>aaC	p.N2331N	SON_ENST00000470533.1_3'UTR|SON_ENST00000290239.6_3'UTR|SON_ENST00000381692.2_Silent_p.N359N	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	2331	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						AAGAAGGCAATAAGGAACCCA	0.383													T|||	1450	0.289537	0.2474	0.3242	5008	,	,		18499	0.249		0.328	False		,,,				2504	0.3241				p.N2331N		Atlas-SNP	.											.	SON	343	.	0			c.T6993C						PASS	.	T		1129,3277	401.3+/-331.9	141,847,1215	113.0	110.0	111.0		6993	1.8	1.0	21	dbSNP_105	111	2805,5791	441.8+/-359.9	460,1885,1953	yes	coding-synonymous	SON	NM_138927.1		601,2732,3168	CC,CT,TT		32.6315,25.6241,30.2569		2331/2427	34945721	3934,9068	2203	4298	6501	SO:0001819	synonymous_variant	6651	exon9			AGGCAATAAGGAA	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.6993T>C	21.37:g.34945721T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	117	63	0.538462	NM_138927	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	37	CCDS13629.1	629	0.288003663003663	121	0.2459349593495935	102	0.281767955801105	150	0.26223776223776224	256	0.33773087071240104	T	5.834	0.338035	0.11013	0.256241	0.326315	ENSG00000159140	ENST00000436227	.	.	.	5.44	1.81	0.25067	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999137549	.	.	.	.	.	.	T	0.32640	-0.9899	3	.	.	.	.	9.5434	0.39266	0.0:0.2748:0.0:0.7252	rs3174808;rs16839001	.	.	.	T	1326	.	.	I	+	2	0	SON	33867591	0.956000	0.32656	1.000000	0.80357	0.976000	0.68499	0.026000	0.13599	0.447000	0.26695	0.477000	0.44152	ATA	T|0.696;C|0.304	0.304	strong		0.383	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
VN1R2	317701	hgsc.bcm.edu	37	19	53761740	53761740	+	Missense_Mutation	SNP	T	T	C	rs386810659|rs2965249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53761740T>C	ENST00000341702.3	+	1	196	c.112T>C	c.(112-114)Tgc>Cgc	p.C38R		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	38			C -> R (in dbSNP:rs2965249). {ECO:0000269|PubMed:12123587, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		taaatatcagtgcagcctggc	0.493													t|||	1575	0.314497	0.3321	0.2738	5008	,	,		17084	0.3671		0.2952	False		,,,				2504	0.2853				p.C38R		Atlas-SNP	.											.	VN1R2	71	.	0			c.T112C						PASS	.						11.0	12.0	12.0					19																	53761740		1888	3577	5465	SO:0001583	missense	317701	exon1			TATCAGTGCAGCC	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.112T>C	19.37:g.53761740T>C	ENSP00000351244:p.Cys38Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	37	CCDS12862.1	696	0.31868131868131866	150	0.3048780487804878	117	0.32320441988950277	219	0.38286713286713286	210	0.2770448548812665	t	0.969	-0.700889	0.03255	.	.	ENSG00000196131	ENST00000341702	T	0.11604	2.76	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.399999999995849E-5	P	0.39520	0.676	B	0.42343	0.384	T	0.49263	-0.8958	6	0.87932	D	0	.	.	.	.	rs2965249	38	Q8NFZ6	VN1R2_HUMAN	R	38	ENSP00000351244:C38R	ENSP00000351244:C38R	C	+	1	0	VN1R2	58453552	0.173000	0.23056	0.192000	0.23308	0.193000	0.23685	0.000000	0.12993	0.064000	0.16427	0.063000	0.15292	TGC	T|0.678;C|0.322	0.322	strong		0.493	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856	
CRIP1	1396	hgsc.bcm.edu	37	14	105954705	105954705	+	Missense_Mutation	SNP	C	C	T	rs55633823	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105954705C>T	ENST00000330233.7	+	3	1116	c.173C>T	c.(172-174)gCa>gTa	p.A58V	CRIP1_ENST00000392531.3_Missense_Mutation_p.A58V|C14orf80_ENST00000334656.7_5'Flank|C14orf80_ENST00000329886.7_5'Flank|C14orf80_ENST00000392527.1_5'Flank|C14orf80_ENST00000392523.4_5'Flank|CRIP1_ENST00000409393.2_Missense_Mutation_p.A58V|C14orf80_ENST00000354560.6_5'Flank|C14orf80_ENST00000392522.3_5'Flank|CRIP1_ENST00000551180.1_Silent_p.R26R			P50238	CRIP1_HUMAN	cysteine-rich protein 1 (intestinal)	58	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.			A -> V (in Ref. 1; AAA64537). {ECO:0000305}.	cell proliferation (GO:0008283)|cellular response to antibiotic (GO:0071236)|cellular response to UV-B (GO:0071493)|heart development (GO:0007507)|immune response (GO:0006955)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|prostate gland stromal morphogenesis (GO:0060741)|regulation of gene expression (GO:0010468)|response to organic substance (GO:0010033)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)	AT DNA binding (GO:0003680)|DNA binding, bending (GO:0008301)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)						Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.235)		CCCTGCTACGCAGCCATGTTT	0.632													C|||	390	0.0778754	0.0076	0.121	5008	,	,		9817	0.0		0.2177	False		,,,				2504	0.0787				p.A58V		Atlas-SNP	.											.	CRIP1	1	.	0			c.C173T						PASS	.	C	VAL/ALA	220,4184	129.8+/-166.5	7,206,1989	47.0	61.0	56.0		173	3.3	0.0	14	dbSNP_129	56	2111,6489	358.8+/-331.3	260,1591,2449	yes	missense	CRIP1	NM_001311.4	64	267,1797,4438	TT,TC,CC		24.5465,4.9955,17.9253	benign	58/78	105954705	2331,10673	2202	4300	6502	SO:0001583	missense	1396	exon4			GCTACGCAGCCAT		CCDS10004.1	14q32.33	2004-06-18			ENSG00000213145	ENSG00000213145			2360	protein-coding gene	gene with protein product		123875				9480758	Standard	NM_001311		Approved	CRIP	uc001yri.4	P50238	OTTHUMG00000029908	ENST00000330233.7:c.173C>T	14.37:g.105954705C>T	ENSP00000332449:p.Ala58Val	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	232	147	0.633621	NM_001311	H3BPI2|Q13628|Q53XY7|Q96J34	Missense_Mutation	SNP	ENST00000330233.7	37	CCDS10004.1	225	0.10302197802197802	8	0.016260162601626018	46	0.1270718232044199	0	0.0	171	0.22559366754617413	C	8.914	0.959358	0.18507	0.049955	0.245465	ENSG00000213145	ENST00000330233;ENST00000409393;ENST00000392531	D;D;D	0.87179	-2.22;-2.22;-2.22	4.24	3.35	0.38373	Zinc finger, LIM-type (3);	0.239612	0.24508	U	0.037904	T	0.00073	0.0002	.	.	.	0.58432	P	9.99999999995449E-6	B	0.17465	0.022	B	0.29440	0.102	T	0.19844	-1.0293	8	0.72032	D	0.01	-11.1404	6.9571	0.24578	0.0:0.727:0.1761:0.0969	rs7824;rs1128313;rs3185152;rs3185188;rs11544872;rs12882865;rs17029668;rs17029674;rs17294933	58	P50238	CRIP1_HUMAN	V	58	ENSP00000332449:A58V;ENSP00000386340:A58V;ENSP00000376315:A58V	ENSP00000447493:A58V	A	+	2	0	CRIP1	105025750	0.004000	0.15560	0.045000	0.18777	0.001000	0.01503	1.652000	0.37313	1.000000	0.39049	-0.142000	0.14014	GCA	C|0.838;T|0.162	0.162	strong		0.632	CRIP1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335466.2	NM_001311	
ODF4	146852	hgsc.bcm.edu	37	17	8243598	8243598	+	Missense_Mutation	SNP	C	C	T	rs73250854	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:8243598C>T	ENST00000328248.2	+	1	417	c.229C>T	c.(229-231)Cgc>Tgc	p.R77C	ODF4_ENST00000584943.1_Intron|RP11-849F2.4_ENST00000585275.1_lincRNA	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	77					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)				endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						ACACAGCTTCCGCTGGATGGC	0.567													C|||	492	0.0982428	0.1694	0.098	5008	,	,		18973	0.0139		0.1024	False		,,,				2504	0.0849				p.R77C		Atlas-SNP	.											ODF4,colon,carcinoma,0,1	ODF4	23	1	0			c.C229T						PASS	.	C	CYS/ARG	627,3779	273.1+/-271.2	48,531,1624	71.0	63.0	66.0		229	2.8	0.0	17	dbSNP_130	66	961,7639	210.0+/-251.0	51,859,3390	yes	missense	ODF4	NM_153007.4	180	99,1390,5014	TT,TC,CC		11.1744,14.2306,12.2097	probably-damaging	77/258	8243598	1588,11418	2203	4300	6503	SO:0001583	missense	146852	exon1			AGCTTCCGCTGGA	AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650			19056	protein-coding gene	gene with protein product	"""cancer/testis antigen 136"""	610097					Standard	NM_153007		Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000328248.2:c.229C>T	17.37:g.8243598C>T	ENSP00000331086:p.Arg77Cys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_153007	Q8J021	Missense_Mutation	SNP	ENST00000328248.2	37	CCDS11140.1	208	0.09523809523809523	85	0.17276422764227642	35	0.09668508287292818	9	0.015734265734265736	79	0.10422163588390501	C	12.36	1.916018	0.33815	0.142306	0.111744	ENSG00000184650	ENST00000328248	T	0.41758	0.99	4.89	2.84	0.33178	.	0.778936	0.11350	N	0.573108	T	0.00178	0.0005	L	0.42245	1.32	0.58432	P	1.0000000000287557E-6	D	0.69078	0.997	P	0.58130	0.833	T	0.06481	-1.0824	9	0.87932	D	0	-6.3939	5.6501	0.17612	0.1938:0.7066:0.0:0.0996	.	77	Q2M2E3	ODFP4_HUMAN	C	77	ENSP00000331086:R77C	ENSP00000331086:R77C	R	+	1	0	ODF4	8184323	0.013000	0.17824	0.001000	0.08648	0.003000	0.03518	0.702000	0.25631	0.615000	0.30124	0.655000	0.94253	CGC	C|0.881;T|0.119	0.119	strong		0.567	ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1		
SPPL2C	162540	hgsc.bcm.edu	37	17	43923683	43923683	+	Missense_Mutation	SNP	A	A	G	rs12185268	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43923683A>G	ENST00000329196.5	+	1	1428	c.1411A>G	c.(1411-1413)Atc>Gtc	p.I471V	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	471			I -> V (in dbSNP:rs12185268).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										CTCCCGTCAGATCTACTTCGT	0.582													G|||	432	0.086262	0.0151	0.1585	5008	,	,		22310	0.001		0.2396	False		,,,				2504	0.0613				p.I471V		Atlas-SNP	.											.	.	.	.	0			c.A1411G						PASS	.	G	VAL/ILE	203,4203	807.6+/-415.9	5,193,2005	134.0	101.0	112.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1411	0.8	0.3	17	dbSNP_120	112	1928,6672	726.4+/-406.6	221,1486,2593	yes	missense	IMP5	NM_175882.2	29	226,1679,4598	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	22.4186,4.6074,16.3847	benign	471/685	43923683	2131,10875	2203	4300	6503	SO:0001583	missense	162540	exon1			CGTCAGATCTACT		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1411A>G	17.37:g.43923683A>G	ENSP00000332488:p.Ile471Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	134	56	0.41791	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	0	-2.736907	0.00088	0.046074	0.224186	ENSG00000185294	ENST00000329196	T	0.17213	2.29	5.2	0.828	0.18841	.	0.406531	0.17861	N	0.159532	T	0.00012	0.0000	N	0.00869	-1.13	0.58432	P	8.000000000008E-6	B	0.11235	0.004	B	0.15484	0.013	T	0.41431	-0.9509	9	0.02654	T	1	-17.3089	4.7545	0.13077	0.3353:0.3144:0.3503:0.0	rs12185268;rs17763723;rs60640757;rs12185268	471	Q8IUH8	IMP5_HUMAN	V	471	ENSP00000332488:I471V	ENSP00000332488:I471V	I	+	1	0	AC217771.1	41279463	0.049000	0.20398	0.302000	0.25058	0.000000	0.00434	0.337000	0.19841	-0.152000	0.11156	-0.971000	0.02607	ATC	A|0.853;G|0.147	0.147	strong		0.582	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735813	55735813	+	Missense_Mutation	SNP	G	G	C	rs80245253	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55735813G>C	ENST00000312345.2	-	1	177	c.127C>G	c.(127-129)Cac>Gac	p.H43D		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	43						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					AGAGCGGGGTGAATTTTTATT	0.338													C|||	191	0.038139	0.0129	0.0389	5008	,	,		16236	0.001		0.0934	False		,,,				2504	0.0532				p.H43D		Atlas-SNP	.											.	OR10AG1	100	.	0			c.C127G						PASS	.	C	ASP/HIS	106,4290	757.3+/-412.7	3,100,2095	48.0	55.0	53.0		127	2.4	0.0	11	dbSNP_132	53	683,7903	763.3+/-407.6	33,617,3643	yes	missense	OR10AG1	NM_001005491.1	81	36,717,5738	CC,CG,GG		7.9548,2.4113,6.0776	benign	43/302	55735813	789,12193	2198	4293	6491	SO:0001583	missense	282770	exon1			CGGGGTGAATTTT	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.127C>G	11.37:g.55735813G>C	ENSP00000311477:p.His43Asp	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	155	49	0.316129	NM_001005491	B2RNH4|Q6IEU3	Missense_Mutation	SNP	ENST00000312345.2	37	CCDS31514.1	82	0.037545787545787544	4	0.008130081300813009	10	0.027624309392265192	0	0.0	68	0.08970976253298153	C	0	-2.681134	0.00102	0.024113	0.079548	ENSG00000174970	ENST00000312345	T	0.00327	8.09	5.27	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	0.283271	0.24766	N	0.035761	T	0.00012	0.0000	N	0.00027	-2.645	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	10	0.02654	T	1	.	4.2571	0.10722	0.0:0.4979:0.1616:0.3406	.	43	Q8NH19	O10AG_HUMAN	D	43	ENSP00000311477:H43D	ENSP00000311477:H43D	H	-	1	0	OR10AG1	55492389	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-2.021000	0.01440	0.251000	0.21505	-2.090000	0.00372	CAC	G|0.951;C|0.049	0.049	strong		0.338	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
ZNF385D	79750	hgsc.bcm.edu	37	3	21462880	21462880	+	Silent	SNP	A	A	G	rs4455340	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:21462880A>G	ENST00000281523.2	-	8	1532	c.1014T>C	c.(1012-1014)aaT>aaC	p.N338N		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	338						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						ctgctAGAGGATTTGGTAGAA	0.453													A|||	1233	0.246206	0.1029	0.2133	5008	,	,		10928	0.3462		0.325	False		,,,				2504	0.2791				p.N338N		Atlas-SNP	.											.	ZNF385D	93	.	0			c.T1014C						PASS	.	A		627,3779	263.4+/-265.5	42,543,1618	39.0	43.0	42.0		1014	-3.0	0.0	3	dbSNP_111	42	2605,5995	407.1+/-349.0	400,1805,2095	no	coding-synonymous	ZNF385D	NM_024697.2		442,2348,3713	GG,GA,AA		30.2907,14.2306,24.8501		338/396	21462880	3232,9774	2203	4300	6503	SO:0001819	synonymous_variant	79750	exon8			TAGAGGATTTGGT	BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"""zinc finger protein 659"""	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.1014T>C	3.37:g.21462880A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	49	29	0.591837	NM_024697		Silent	SNP	ENST00000281523.2	37	CCDS2636.1																																																																																			A|0.722;G|0.278	0.278	strong		0.453	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697	
GPR75	10936	hgsc.bcm.edu	37	2	54081548	54081548	+	Missense_Mutation	SNP	C	C	T	rs34000641	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:54081548C>T	ENST00000394705.2	-	2	616	c.346G>A	c.(346-348)Gct>Act	p.A116T	ASB3_ENST00000406625.2_Intron|GPR75-ASB3_ENST00000352846.3_Intron|ASB3_ENST00000498475.2_Intron	NM_006794.3	NP_006785.1	O95800	GPR75_HUMAN	G protein-coupled receptor 75	116	Phe-rich.		A -> T (in dbSNP:rs34000641). {ECO:0000269|PubMed:11466257}.		chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of neuron death (GO:1901214)	integral component of plasma membrane (GO:0005887)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AAGCAGAAAGCATCCGGGATA	0.517													C|||	82	0.0163738	0.0015	0.0331	5008	,	,		22590	0.0		0.0358	False		,,,				2504	0.0215				p.A116T		Atlas-SNP	.											.	GPR75	55	.	0			c.G346A						PASS	.	C	,THR/ALA	25,4381	30.8+/-60.4	0,25,2178	78.0	79.0	79.0		,346	1.9	0.0	2	dbSNP_126	79	288,8312	107.0+/-167.8	4,280,4016	yes	intron,missense	GPR75,GPR75-ASB3	NM_001164165.1,NM_006794.3	,58	4,305,6194	TT,TC,CC		3.3488,0.5674,2.4066	,benign	,116/541	54081548	313,12693	2203	4300	6503	SO:0001583	missense	10936	exon2			AGAAAGCATCCGG	AF101472	CCDS1849.1	2p16	2012-08-21			ENSG00000119737	ENSG00000119737		"""GPCR / Class A : Orphans"""	4526	protein-coding gene	gene with protein product		606704				10381362	Standard	NM_006794		Approved	WI-31133	uc002rxo.3	O95800	OTTHUMG00000129280	ENST00000394705.2:c.346G>A	2.37:g.54081548C>T	ENSP00000378195:p.Ala116Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	154	77	0.5	NM_006794	B2RC02|Q6NWR2	Missense_Mutation	SNP	ENST00000394705.2	37	CCDS1849.1	41	0.018772893772893772	3	0.006097560975609756	13	0.03591160220994475	0	0.0	25	0.032981530343007916	C	11.13	1.546930	0.27652	0.005674	0.033488	ENSG00000119737	ENST00000394705	T	0.73789	-0.78	5.75	1.93	0.25924	GPCR, rhodopsin-like superfamily (1);	0.420647	0.28057	N	0.016775	T	0.23926	0.0579	.	.	.	0.26102	N	0.980802	B	0.02656	0.0	B	0.09377	0.004	T	0.10177	-1.0641	9	0.17369	T	0.5	0.8186	10.2743	0.43501	0.0:0.6632:0.0:0.3368	rs34000641	116	O95800	GPR75_HUMAN	T	116	ENSP00000378195:A116T	ENSP00000378195:A116T	A	-	1	0	GPR75	53935052	0.005000	0.15991	0.026000	0.17262	0.978000	0.69477	0.367000	0.20382	0.073000	0.16731	0.561000	0.74099	GCT	C|0.975;T|0.025	0.025	strong		0.517	GPR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251403.2		
MMP27	64066	hgsc.bcm.edu	37	11	102562700	102562700	+	Missense_Mutation	SNP	C	C	T	rs2509010	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:102562700C>T	ENST00000260229.4	-	10	1430	c.1339G>A	c.(1339-1341)Gac>Aac	p.D447N		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	447			D -> N (in dbSNP:rs2509010). {ECO:0000269|PubMed:12975309}.		collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	GTCTTAATGTCGTATTCAAAT	0.333													C|||	820	0.163738	0.0696	0.2435	5008	,	,		17366	0.1081		0.2744	False		,,,				2504	0.1779				p.D447N		Atlas-SNP	.											.	MMP27	84	.	0			c.G1339A						PASS	.	C	ASN/ASP	475,3931	223.6+/-240.1	26,423,1754	89.0	80.0	83.0		1339	3.9	1.0	11	dbSNP_100	83	2437,6155	402.7+/-347.6	353,1731,2212	yes	missense	MMP27	NM_022122.2	23	379,2154,3966	TT,TC,CC		28.3636,10.7808,22.4034	benign	447/514	102562700	2912,10086	2203	4296	6499	SO:0001583	missense	64066	exon10			TAATGTCGTATTC	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.1339G>A	11.37:g.102562700C>T	ENSP00000260229:p.Asp447Asn	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	85	26	0.305882	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	393	0.17994505494505494	32	0.06504065040650407	78	0.2154696132596685	60	0.1048951048951049	223	0.2941952506596306	C	14.06	2.422247	0.43020	0.107808	0.283636	ENSG00000137675	ENST00000260229	T	0.14144	2.53	5.96	3.86	0.44501	Hemopexin/matrixin (2);	0.085303	0.50627	D	0.000108	T	0.00012	0.0000	L	0.41079	1.255	0.30645	P	0.75601	P	0.36974	0.576	B	0.20767	0.031	T	0.48514	-0.9029	9	0.18710	T	0.47	.	10.2161	0.43168	0.0:0.7788:0.1407:0.0804	rs2509010;rs52836586;rs2509010	447	Q9H306	MMP27_HUMAN	N	447	ENSP00000260229:D447N	ENSP00000260229:D447N	D	-	1	0	MMP27	102067910	0.990000	0.36364	0.980000	0.43619	0.808000	0.45660	1.080000	0.30779	2.819000	0.97034	0.585000	0.79938	GAC	C|0.800;T|0.200	0.200	strong		0.333	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
LONRF2	164832	hgsc.bcm.edu	37	2	100916306	100916306	+	Silent	SNP	A	A	G	rs2033748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:100916306A>G	ENST00000393437.3	-	5	1779	c.1140T>C	c.(1138-1140)ttT>ttC	p.F380F	LONRF2_ENST00000409647.1_Silent_p.F137F	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	380							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						TATCCTCTTCAAAGTGTAGAC	0.418													A|||	3863	0.771366	0.8911	0.7349	5008	,	,		13826	0.9405		0.673	False		,,,				2504	0.5624				p.F380F		Atlas-SNP	.											.	LONRF2	62	.	0			c.T1140C						PASS	.	A		3669,737	757.4+/-412.7	1525,619,59	69.0	67.0	68.0		1140	-4.1	0.0	2	dbSNP_94	68	5543,3057	662.6+/-402.0	1797,1949,554	no	coding-synonymous	LONRF2	NM_198461.3		3322,2568,613	GG,GA,AA		35.5465,16.7272,29.1712		380/755	100916306	9212,3794	2203	4300	6503	SO:0001819	synonymous_variant	164832	exon5			CTCTTCAAAGTGT	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"""RING-type (C3HC4) zinc fingers"""	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1140T>C	2.37:g.100916306A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	131	53	0.40458	NM_198461	B9A006|Q6ZSR4	Silent	SNP	ENST00000393437.3	37	CCDS2046.2																																																																																			A|0.270;G|0.730	0.730	strong		0.418	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461	
CFAP57	149465	hgsc.bcm.edu	37	1	43649393	43649393	+	Silent	SNP	T	T	C	rs663336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43649393T>C	ENST00000372492.4	+	4	930	c.606T>C	c.(604-606)gcT>gcC	p.A202A	WDR65_ENST00000528956.1_Silent_p.A202A	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		202										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				ACTATCTAGCTCACACCTGGG	0.493													C|||	1322	0.263978	0.3949	0.2637	5008	,	,		18592	0.3185		0.0666	False		,,,				2504	0.2342				p.A202A		Atlas-SNP	.											.	WDR65	76	.	0			c.T606C						PASS	.	C	,,	1611,2795	663.1+/-401.2	290,1031,882	110.0	107.0	108.0		606,606,606	0.5	1.0	1	dbSNP_83	108	662,7938	789.2+/-407.6	32,598,3670	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	322,1629,4552	CC,CT,TT		7.6977,36.5638,17.4765	,,	202/699,202/699,202/699	43649393	2273,10733	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon4			TCTAGCTCACACC																												ENST00000372492.4:c.606T>C	1.37:g.43649393T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				T|0.801;C|0.199	0.199	strong		0.493	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
GAB2	9846	hgsc.bcm.edu	37	11	77936166	77936166	+	Silent	SNP	A	A	G	rs1385600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:77936166A>G	ENST00000361507.4	-	5	1375	c.1290T>C	c.(1288-1290)gtT>gtC	p.V430V	GAB2_ENST00000526030.1_5'Flank|GAB2_ENST00000340149.2_Silent_p.V392V	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	430					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			GGAAAGAGCCAACTCCATCAC	0.532													G|||	1734	0.346246	0.4924	0.3357	5008	,	,		20447	0.4008		0.1829	False		,,,				2504	0.2679				p.V430V		Atlas-SNP	.											.	GAB2	63	.	0			c.T1290C						PASS	.	G	,	1879,2521	630.1+/-395.4	410,1059,731	133.0	126.0	129.0		1176,1290	2.3	0.0	11	dbSNP_88	129	1413,7171	752.5+/-407.4	125,1163,3004	no	coding-synonymous,coding-synonymous	GAB2	NM_012296.3,NM_080491.2	,	535,2222,3735	GG,GA,AA		16.4609,42.7045,25.3543	,	392/639,430/677	77936166	3292,9692	2200	4292	6492	SO:0001819	synonymous_variant	9846	exon5			AGAGCCAACTCCA	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"""Pleckstrin homology (PH) domain containing"""	14458	protein-coding gene	gene with protein product	"""Grb2-associated binder 2"""	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.1290T>C	11.37:g.77936166A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	49	0.550562	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Silent	SNP	ENST00000361507.4	37	CCDS8259.1																																																																																			A|0.691;G|0.309	0.309	strong		0.532	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491	
NIN	51199	hgsc.bcm.edu	37	14	51192659	51192659	+	Silent	SNP	G	G	A	rs1983764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:51192659G>A	ENST00000382041.3	-	30	6394	c.6204C>T	c.(6202-6204)ccC>ccT	p.P2068P	RP11-248J18.3_ENST00000602615.1_RNA|NIN_ENST00000245441.5_Intron|NIN_ENST00000389868.3_Intron|NIN_ENST00000382043.4_Silent_p.P1355P|NIN_ENST00000324330.9_3'UTR|NIN_ENST00000530997.2_Intron	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	2068					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					AGAGATGACCGGGTAGGCTCA	0.398			T	PDGFRB	MPD								G|||	1225	0.244609	0.0303	0.2507	5008	,	,		20594	0.2966		0.3469	False		,,,				2504	0.3712				p.P2068P		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C6204T						PASS	.	G	,,	384,4022	195.7+/-220.2	17,350,1836	233.0	203.0	213.0		4065,,6204	-4.4	0.0	14	dbSNP_92	213	3053,5547	470.4+/-367.8	530,1993,1777	no	coding-synonymous,intron,coding-synonymous	NIN	NM_016350.4,NM_020921.3,NM_182946.1	,,	547,2343,3613	AA,AG,GG		35.5,8.7154,26.4263	,,	1355/1378,,2068/2091	51192659	3437,9569	2203	4300	6503	SO:0001819	synonymous_variant	51199	exon30			ATGACCGGGTAGG	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"""EF-hand domain containing"""	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.6204C>T	14.37:g.51192659G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	246	126	0.512195	NM_182946	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	37	CCDS32079.1	564	0.25824175824175827	24	0.04878048780487805	86	0.23756906077348067	183	0.31993006993006995	271	0.3575197889182058	G	6.376	0.437532	0.12104	0.087154	0.355	ENSG00000100503	ENST00000389869	.	.	.	5.93	-4.4	0.03600	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44298	-0.9337	3	.	.	.	.	1.1314	0.01746	0.3536:0.2034:0.297:0.146	rs1983764;rs52794699;rs59283049;rs1983764	.	.	.	W	1559	.	.	R	-	1	2	NIN	50262409	0.000000	0.05858	0.001000	0.08648	0.213000	0.24496	-1.297000	0.02759	-1.103000	0.03019	-1.004000	0.02495	CGG	G|0.744;A|0.256	0.256	strong		0.398	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
TMCC3	57458	hgsc.bcm.edu	37	12	94972290	94972290	+	Silent	SNP	C	C	T	rs2270893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:94972290C>T	ENST00000261226.4	-	3	1142	c.1011G>A	c.(1009-1011)gaG>gaA	p.E337E	TMCC3_ENST00000551457.1_Silent_p.E306E	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	337						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						GCAGCTGGTCCTCCAGTCGCT	0.542													C|||	2604	0.519968	0.5234	0.5634	5008	,	,		16768	0.4653		0.5378	False		,,,				2504	0.5225				p.E337E		Atlas-SNP	.											TMCC3,NS,carcinoma,0,1	TMCC3	63	1	0			c.G1011A						PASS	.	C		2276,2130	598.6+/-389.1	590,1096,517	71.0	57.0	62.0		1011	-1.1	1.0	12	dbSNP_100	62	4626,3974	600.1+/-394.2	1263,2100,937	no	coding-synonymous	TMCC3	NM_020698.2		1853,3196,1454	TT,TC,CC		46.2093,48.3432,46.9322		337/478	94972290	6902,6104	2203	4300	6503	SO:0001819	synonymous_variant	57458	exon3			CTGGTCCTCCAGT	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"""Transmembrane and coiled-coil domain containing"""	29199	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 3"""			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.1011G>A	12.37:g.94972290C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_020698	Q8IWB2	Silent	SNP	ENST00000261226.4	37	CCDS31877.1																																																																																			C|0.474;T|0.526	0.526	strong		0.542	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110447469	110447469	+	Missense_Mutation	SNP	G	G	A	rs376326343		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110447469G>A	ENST00000378402.5	+	29	3495	c.3391G>A	c.(3391-3393)Gtt>Att	p.V1131I		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1131	IPT/TIG 4.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ACATGCCCCCGTTGCTGTGTC	0.413										HNSCC(38;0.096)			G|||	1	0.000199681	0.0	0.0	5008	,	,		19159	0.0		0.001	False		,,,				2504	0.0				p.V1131I		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G3391A						PASS	.	G	ILE/VAL	0,3716		0,0,1858	173.0	171.0	172.0		3391	4.3	0.0	8		172	3,8233		0,3,4115	no	missense	PKHD1L1	NM_177531.4	29	0,3,5973	AA,AG,GG		0.0364,0.0,0.0251	probably-damaging	1131/4244	110447469	3,11949	1858	4118	5976	SO:0001583	missense	93035	exon29			GCCCCCGTTGCTG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.3391G>A	8.37:g.110447469G>A	ENSP00000367655:p.Val1131Ile	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	173	80	0.462428	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	5.667	0.307710	0.10733	0.0	3.64E-4	ENSG00000205038	ENST00000378402	T	0.80033	-1.33	6.07	4.28	0.50868	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.146172	0.44902	N	0.000403	T	0.73133	0.3548	L	0.52759	1.655	0.22142	N	0.999333	B	0.12630	0.006	B	0.12156	0.007	T	0.59279	-0.7484	10	0.28530	T	0.3	.	9.7436	0.40433	0.1605:0.0:0.8395:0.0	.	1131	Q86WI1	PKHL1_HUMAN	I	1131	ENSP00000367655:V1131I	ENSP00000367655:V1131I	V	+	1	0	PKHD1L1	110516645	0.934000	0.31675	0.041000	0.18516	0.005000	0.04900	2.374000	0.44274	0.883000	0.36040	-0.150000	0.13652	GTT	.	.	weak		0.413	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
EPHA10	284656	hgsc.bcm.edu	37	1	38186189	38186189	+	Missense_Mutation	SNP	C	C	T	rs6671088	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:38186189C>T	ENST00000373048.4	-	13	2245	c.2246G>A	c.(2245-2247)gGg>gAg	p.G749E	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000330210.7_Missense_Mutation_p.G244E|EPHA10_ENST00000427468.2_Missense_Mutation_p.G749E|EPHA10_ENST00000540011.1_3'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	749	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		G -> E (in dbSNP:rs6671088).		ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGGCAGCAACCCCATCAGTTG	0.632													C|||	561	0.112021	0.1785	0.0879	5008	,	,		17125	0.001		0.1551	False		,,,				2504	0.1094				p.G749E		Atlas-SNP	.											EPHA10,NS,carcinoma,0,2	EPHA10	120	2	0			c.G2246A						PASS	.	C	GLU/GLY	729,3437		60,609,1414	20.0	25.0	23.0		2246	4.0	1.0	1	dbSNP_116	23	1367,7027		112,1143,2942	yes	missense	EPHA10	NM_001099439.1	98	172,1752,4356	TT,TC,CC		16.2854,17.4988,16.6879	probably-damaging	749/1009	38186189	2096,10464	2083	4197	6280	SO:0001583	missense	284656	exon13			AGCAACCCCATCA	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2246G>A	1.37:g.38186189C>T	ENSP00000362139:p.Gly749Glu	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	301	142	0.471761	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	238	0.10897435897435898	88	0.17886178861788618	36	0.09944751381215469	0	0.0	114	0.1503957783641161	C	20.3	3.971582	0.74246	0.174988	0.162854	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000373048	D;D;D	0.81739	-1.53;-1.53;-1.53	4.93	4.0	0.46444	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38111	N	0.001809	T	0.00300	0.0009	N	0.20530	0.585	0.09310	P	0.9999999999999999	P	0.46277	0.875	B	0.40477	0.33	T	0.30592	-0.9973	9	0.87932	D	0	.	14.3163	0.66452	0.0:0.7191:0.2809:0.0	rs6671088;rs59740185;rs6671088	749	Q5JZY3	EPHAA_HUMAN	E	244;749;749	ENSP00000330379:G244E;ENSP00000397746:G749E;ENSP00000362139:G749E	ENSP00000330379:G244E	G	-	2	0	EPHA10	37958776	0.964000	0.33143	0.990000	0.47175	0.974000	0.67602	2.038000	0.41184	1.059000	0.40554	0.467000	0.42956	GGG	C|0.875;T|0.125	0.125	strong		0.632	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
LTA	4049	hgsc.bcm.edu	37	6	31540556	31540556	+	Missense_Mutation	SNP	T	T	C	rs2229094	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31540556T>C	ENST00000454783.1	+	2	295	c.37T>C	c.(37-39)Tgt>Cgt	p.C13R	LTA_ENST00000418386.2_Missense_Mutation_p.C13R|TNF_ENST00000449264.2_5'Flank	NM_001159740.2	NP_001153212.1	P01374	TNFB_HUMAN	lymphotoxin alpha	13			C -> R (in dbSNP:rs2229094). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.10, ECO:0000269|Ref.11}.		apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|humoral immune response (GO:0006959)|lymph node development (GO:0048535)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of interferon-gamma production (GO:0032729)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|membrane (GO:0016020)	receptor binding (GO:0005102)			endometrium(2)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9					Etanercept(DB00005)	CCCAAGGGTGTGTGGCACCAC	0.647													C|||	1374	0.274361	0.2685	0.2738	5008	,	,		16761	0.1974		0.2873	False		,,,				2504	0.3487				p.C13R		Atlas-SNP	.											.	LTA	18	.	0			c.T37C						PASS	.	C	ARG/CYS,ARG/CYS	849,2171		110,629,771	92.0	92.0	92.0		37,37	1.3	0.0	6	dbSNP_98	92	1465,3953		183,1099,1427	yes	missense,missense	LTA	NM_000595.2,NM_001159740.1	180,180	293,1728,2198	CC,CT,TT		27.0395,28.1126,27.4236	benign,benign	13/206,13/206	31540556	2314,6124	1510	2709	4219	SO:0001583	missense	4049	exon2			AGGGTGTGTGGCA	X01393	CCDS4701.1	6p21.3	2013-05-22	2013-05-22		ENSG00000226979	ENSG00000226979		"""Tumor necrosis factor (ligand) superfamily"""	6709	protein-coding gene	gene with protein product	"""TNF superfamily member 1"""	153440	"""lymphotoxin alpha (TNF superfamily, member 1)"""	TNFB		2995927, 3001529	Standard	NM_001159740		Approved	TNFSF1, LT	uc011dnu.2	P01374	OTTHUMG00000031135	ENST00000454783.1:c.37T>C	6.37:g.31540556T>C	ENSP00000403495:p.Cys13Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_001159740	Q8N4C3|Q9UKS8	Missense_Mutation	SNP	ENST00000454783.1	37	CCDS4701.1	586	0.2683150183150183	137	0.2784552845528455	109	0.3011049723756906	110	0.19230769230769232	230	0.3034300791556728	C	0.052	-1.248400	0.01469	0.281126	0.270395	ENSG00000226979	ENST00000454783;ENST00000418386;ENST00000436827	T;T	0.15603	2.41;2.41	4.32	1.26	0.21427	.	0.907619	0.09501	N	0.793658	T	0.02455	0.0075	N	0.03115	-0.41	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.43114	-0.9411	9	0.48119	T	0.1	1.3306	9.5912	0.39548	0.0:0.7643:0.0:0.2357	rs2229094;rs2857713;rs3888136;rs4080102;rs17840074;rs17846103;rs17859106;rs56749012;rs2229094	13	P01374	TNFB_HUMAN	R	13	ENSP00000403495:C13R;ENSP00000413450:C13R	ENSP00000413450:C13R	C	+	1	0	LTA	31648535	0.001000	0.12720	0.027000	0.17364	0.399000	0.30720	-0.648000	0.05391	-0.174000	0.10743	-0.119000	0.15052	TGT	T|0.737;C|0.263	0.263	strong		0.647	LTA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259097.1		
GNA13	10672	hgsc.bcm.edu	37	17	63010494	63010494	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:63010494G>A	ENST00000439174.2	-	4	1260	c.1015C>T	c.(1015-1017)Cag>Tag	p.Q339*	GNA13_ENST00000541118.1_Nonsense_Mutation_p.Q244*	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	339					activation of phospholipase D activity (GO:0031584)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|in utero embryonic development (GO:0001701)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(14)|kidney(2)|large_intestine(4)|lung(6)|urinary_tract(1)	34						AAGGGCTTCTGTTGCTGGTCC	0.473																																					p.Q339X		Atlas-SNP	.											.	GNA13	69	.	0			c.C1015T						PASS	.						133.0	107.0	116.0					17																	63010494		2203	4300	6503	SO:0001587	stop_gained	10672	exon4			GCTTCTGTTGCTG	L22075	CCDS11661.1, CCDS62302.1	17q24.1	2014-09-04			ENSG00000120063	ENSG00000120063			4381	protein-coding gene	gene with protein product		604406				7791744	Standard	NM_006572		Approved	G13, MGC46138	uc002jfc.3	Q14344	OTTHUMG00000179316	ENST00000439174.2:c.1015C>T	17.37:g.63010494G>A	ENSP00000400717:p.Gln339*	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	147	127	0.863946	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Nonsense_Mutation	SNP	ENST00000439174.2	37	CCDS11661.1	.	.	.	.	.	.	.	.	.	.	G	36	5.876075	0.97055	.	.	ENSG00000120063	ENST00000439174;ENST00000541118;ENST00000239138	.	.	.	5.93	5.93	0.95920	.	0.048927	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	19.949	0.97192	0.0:0.0:1.0:0.0	.	.	.	.	X	339;244;314	.	ENSP00000239138:Q314X	Q	-	1	0	GNA13	60440956	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.664000	0.74437	2.826000	0.97356	0.655000	0.94253	CAG	.	.	none		0.473	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572	
MYO16	23026	hgsc.bcm.edu	37	13	109793246	109793246	+	Silent	SNP	G	G	C	rs80260507	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:109793246G>C	ENST00000357550.2	+	31	4661	c.4620G>C	c.(4618-4620)ccG>ccC	p.P1540P	MYO16_ENST00000356711.2_Silent_p.P1540P	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CGCTGTCCCCGCAGTACTCCA	0.711													G|||	231	0.0461262	0.0272	0.0648	5008	,	,		5556	0.0		0.1083	False		,,,				2504	0.0419				p.P1562P		Atlas-SNP	.											MYO16,NS,carcinoma,0,2	MYO16	285	2	0			c.G4686C						PASS	.	G	,	129,4247		2,125,2061	16.0	20.0	18.0		4686,4620	-7.8	0.0	13	dbSNP_131	18	799,7773		42,715,3529	no	coding-synonymous,coding-synonymous	MYO16	NM_001198950.1,NM_015011.1	,	44,840,5590	CC,CG,GG		9.321,2.9479,7.1671	,	1562/1881,1540/1859	109793246	928,12020	2188	4286	6474	SO:0001819	synonymous_variant	23026	exon32			GTCCCCGCAGTAC		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4620G>C	13.37:g.109793246G>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_001198950		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																			G|0.933;C|0.067	0.067	strong		0.711	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
FAT2	2196	hgsc.bcm.edu	37	5	150945862	150945862	+	Silent	SNP	A	A	G	rs3734057	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150945862A>G	ENST00000261800.5	-	1	2643	c.2631T>C	c.(2629-2631)gtT>gtC	p.V877V		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	877	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGTGTCCTGTAACAACCAGTT	0.567													A|||	2102	0.419728	0.441	0.4539	5008	,	,		15603	0.3571		0.4901	False		,,,				2504	0.3589				p.V877V		Atlas-SNP	.											.	FAT2	465	.	0			c.T2631C						PASS	.	A		1960,2446	555.1+/-379.2	423,1114,666	97.0	93.0	94.0		2631	2.7	0.9	5	dbSNP_107	94	4499,4101	592.7+/-393.0	1183,2133,984	no	coding-synonymous	FAT2	NM_001447.2		1606,3247,1650	GG,GA,AA		47.686,44.4848,49.6617		877/4350	150945862	6459,6547	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			TCCTGTAACAACC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2631T>C	5.37:g.150945862A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	202	201	0.995049	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			A|0.526;G|0.474	0.474	strong		0.567	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651199	1651199	+	Silent	SNP	A	A	G	rs71025763|rs144216147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1651199A>G	ENST00000399676.2	+	1	167	c.129A>G	c.(127-129)ggA>ggG	p.G43G		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	43				G -> GGCGS (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ccggctgtggaggctgtgggg	0.711													N|||	2130	0.425319	0.5333	0.3703	5008	,	,		5729	0.2897		0.4135	False		,,,				2504	0.4703				p.G43G		Atlas-SNP	.											KRTAP5-5,NS,neuroblastoma,0,1	KRTAP5-5	86	1	0			c.A129G						scavenged	.						12.0	19.0	17.0					11																	1651199		1824	3748	5572	SO:0001819	synonymous_variant	439915	exon1			CTGTGGAGGCTGT	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.129A>G	11.37:g.1651199A>G		Somatic	53	5	0.0943396		WXS	Illumina HiSeq	Phase_I	20	16	0.8	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			.	.	weak		0.711	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
KRT74	121391	hgsc.bcm.edu	37	12	52966428	52966428	+	Missense_Mutation	SNP	G	G	C	rs11170177	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:52966428G>C	ENST00000305620.2	-	2	542	c.495C>G	c.(493-495)aaC>aaG	p.N165K	KRT74_ENST00000549343.1_Missense_Mutation_p.N165K	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	165	Coil 1A.|Rod.		N -> K (in dbSNP:rs11170177).		intermediate filament cytoskeleton organization (GO:0045104)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	keratin filament binding (GO:1990254)|structural molecule activity (GO:0005198)			kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	28				BRCA - Breast invasive adenocarcinoma(357;0.191)		CTAGAACCTGGTTCTGCTGCT	0.552													G|||	489	0.0976438	0.0053	0.0259	5008	,	,		21114	0.3175		0.0517	False		,,,				2504	0.0941				p.N165K		Atlas-SNP	.											.	KRT74	67	.	0			c.C495G						PASS	.	G	LYS/ASN	60,4346	58.1+/-94.6	1,58,2144	98.0	89.0	92.0		495	3.8	1.0	12	dbSNP_120	92	472,8128	139.0+/-195.8	12,448,3840	yes	missense	KRT74	NM_175053.3	94	13,506,5984	CC,CG,GG		5.4884,1.3618,4.0904	probably-damaging	165/530	52966428	532,12474	2203	4300	6503	SO:0001583	missense	121391	exon2			AACCTGGTTCTGC	BK000977	CCDS8832.1	12q13.13	2013-06-25			ENSG00000170484	ENSG00000170484		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28929	protein-coding gene	gene with protein product		608248				12648212, 16831889	Standard	NM_175053		Approved	K6IRS4, KRT5C, KRT6IRS4	uc001sap.1	Q7RTS7	OTTHUMG00000169658	ENST00000305620.2:c.495C>G	12.37:g.52966428G>C	ENSP00000307240:p.Asn165Lys	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	176	92	0.522727	NM_175053	B5MD61|Q86Y45	Missense_Mutation	SNP	ENST00000305620.2	37	CCDS8832.1	227	0.10393772893772894	1	0.0020325203252032522	8	0.022099447513812154	172	0.3006993006993007	46	0.06068601583113457	G	22.6	4.306532	0.81247	0.013618	0.054884	ENSG00000170484	ENST00000549343;ENST00000305620	D;D	0.97959	-4.63;-4.63	4.71	3.82	0.43975	Filament (1);	0.000000	0.38663	N	0.001605	T	0.00468	0.0015	H	0.99783	4.775	0.20873	P	0.999830008	D	0.89917	1.0	D	0.97110	1.0	T	0.00000	-1.8587	9	0.87932	D	0	.	13.466	0.61254	0.0771:0.0:0.9229:0.0	rs11170177	165	Q7RTS7	K2C74_HUMAN	K	165	ENSP00000447447:N165K;ENSP00000307240:N165K	ENSP00000307240:N165K	N	-	3	2	KRT74	51252695	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.695000	0.74593	1.297000	0.44761	0.650000	0.86243	AAC	G|0.933;C|0.067	0.067	strong		0.552	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053	
PNISR	25957	hgsc.bcm.edu	37	6	99848998	99848998	+	Silent	SNP	A	A	C	rs369239036		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:99848998A>C	ENST00000369239.5	-	12	2040	c.1836T>G	c.(1834-1836)ccT>ccG	p.P612P	PNISR_ENST00000438806.1_Silent_p.P612P	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	612						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						TCTCTCGGGAAGGACTCCGAT	0.428																																					p.P612P		Atlas-SNP	.											.	PNISR	74	.	0			c.T1836G						PASS	.	A	,	0,4406		0,0,2203	110.0	98.0	102.0		1836,1836	4.2	1.0	6		102	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	PNISR	NM_015491.1,NM_032870.2	,	0,2,6501	CC,CA,AA		0.0233,0.0,0.0154	,	612/806,612/806	99848998	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	25957	exon11			TCGGGAAGGACTC	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 111"", ""splicing factor, arginine/serine-rich 18"""	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.1836T>G	6.37:g.99848998A>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	164	83	0.506098	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Silent	SNP	ENST00000369239.5	37	CCDS5043.1																																																																																			.	.	weak		0.428	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870	
GFER	2671	hgsc.bcm.edu	37	16	2035907	2035907	+	Missense_Mutation	SNP	T	T	C	rs36041021	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2035907T>C	ENST00000248114.6	+	3	502	c.496T>C	c.(496-498)Ttc>Ctc	p.F166L	AC005606.14_ENST00000564438.1_lincRNA|GFER_ENST00000567719.1_Missense_Mutation_p.F91L|GFER_ENST00000569451.1_Missense_Mutation_p.L100P	NM_005262.2	NP_005253.3	P55789	ALR_HUMAN	growth factor, augmenter of liver regeneration	166	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.		F -> L (in dbSNP:rs36041021).		cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|protein disulfide oxidoreductase activity (GO:0015035)|thiol oxidase activity (GO:0016972)			endometrium(1)|large_intestine(1)|lung(3)	5					Flavin adenine dinucleotide(DB03147)	CCGGGCATGCTTCACACAGTG	0.612													T|||	166	0.033147	0.0106	0.0548	5008	,	,		21910	0.0		0.0944	False		,,,				2504	0.0194				p.F166L		Atlas-SNP	.											.	GFER	8	.	0			c.T496C						PASS	.	T	LEU/PHE	90,4306	73.6+/-111.7	0,90,2108	95.0	95.0	95.0		496	2.1	0.3	16	dbSNP_126	95	781,7817	183.7+/-231.9	43,695,3561	yes	missense	GFER	NM_005262.2	22	43,785,5669	CC,CT,TT		9.0835,2.0473,6.7031	benign	166/206	2035907	871,12123	2198	4299	6497	SO:0001583	missense	2671	exon3			GCATGCTTCACAC	BC002429	CCDS32368.1	16p13.3-p13.12	2011-06-22	2008-08-01		ENSG00000127554	ENSG00000127554			4236	protein-coding gene	gene with protein product	"""ERV1 homolog (S. cerevisiae)"""	600924	"""growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)"""			8575761	Standard	NM_005262		Approved	HSS, ERV1, ALR, HERV1, HPO1, HPO2	uc002cob.3	P55789		ENST00000248114.6:c.496T>C	16.37:g.2035907T>C	ENSP00000248114:p.Phe166Leu	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	NM_005262	Q53YM6|Q8TAH6|Q9H290|Q9UK40	Missense_Mutation	SNP	ENST00000248114.6	37	CCDS32368.1	94	0.04304029304029304	5	0.01016260162601626	21	0.058011049723756904	0	0.0	68	0.08970976253298153	T	3.575	-0.086827	0.07097	0.020473	0.090835	ENSG00000127554	ENST00000248114;ENST00000425414	T	0.48201	0.82	4.43	2.12	0.27331	Erv1/Alr (3);ERV/ALR sulphydryl oxidase (1);	0.222700	0.43416	N	0.000561	T	0.00666	0.0022	N	0.04508	-0.205	0.41513	D	0.988359	B;B	0.16603	0.01;0.018	B;B	0.23018	0.038;0.043	T	0.08513	-1.0718	10	0.05833	T	0.94	-5.0624	7.8859	0.29651	0.0:0.1771:0.0:0.8229	rs36041021	92;166	Q9UQK8;P55789	.;ALR_HUMAN	L	166;86	ENSP00000248114:F166L	ENSP00000248114:F166L	F	+	1	0	GFER	1975908	0.870000	0.30015	0.305000	0.25099	0.006000	0.05464	1.382000	0.34374	0.652000	0.30806	-0.558000	0.04189	TTC	T|0.938;C|0.062	0.062	strong		0.612	GFER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434243.1	NM_005262	
ACSBG1	23205	hgsc.bcm.edu	37	15	78471110	78471110	+	Silent	SNP	G	G	A	rs17850484	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:78471110G>A	ENST00000258873.4	-	11	1753	c.1548C>T	c.(1546-1548)ggC>ggT	p.G516G	ACSBG1_ENST00000541759.1_Silent_p.G274G|ACSBG1_ENST00000560817.1_Silent_p.G274G	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	516					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						GGCAGATCTCGCCAATGCCCT	0.632													G|||	444	0.0886581	0.0832	0.0418	5008	,	,		17055	0.0327		0.0696	False		,,,				2504	0.2065				p.G516G		Atlas-SNP	.											.	ACSBG1	79	.	0			c.C1548T						PASS	.	G	,	314,4078	169.4+/-200.1	13,288,1895	102.0	70.0	81.0		1536,1548	-11.0	0.1	15	dbSNP_123	81	575,8011	154.6+/-208.8	19,537,3737	no	coding-synonymous,coding-synonymous	ACSBG1	NM_001199377.1,NM_015162.4	,	32,825,5632	AA,AG,GG		6.6969,7.1494,6.8501	,	512/721,516/725	78471110	889,12089	2196	4293	6489	SO:0001819	synonymous_variant	23205	exon11			GATCTCGCCAATG	AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"""Acyl-CoA synthetase family"""	29567	protein-coding gene	gene with protein product	"""bubblegum"", ""very long-chain acyl-CoA synthetase"", ""lipidosin"""	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.1548C>T	15.37:g.78471110G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_015162	B2RB61|O75126|Q76N27|Q9HC26	Silent	SNP	ENST00000258873.4	37	CCDS10298.1																																																																																			G|0.936;A|0.064	0.064	strong		0.632	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162	
FRG1	2483	hgsc.bcm.edu	37	4	190878626	190878626	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:190878626G>A	ENST00000226798.4	+	6	728	c.506G>A	c.(505-507)aGt>aAt	p.S169N	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	169					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.S169N(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		GAAGCAAAAAGTAAAACAGCA	0.363																																					p.S169N		Atlas-SNP	.											FRG1,NS,carcinoma,+1,3	FRG1	76	3	1	Substitution - Missense(1)	skin(1)	c.G506A						scavenged	.						49.0	46.0	47.0					4																	190878626		2184	4282	6466	SO:0001583	missense	2483	exon6			CAAAAAGTAAAAC	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.506G>A	4.37:g.190878626G>A	ENSP00000226798:p.Ser169Asn	Somatic	290	1	0.00344828		WXS	Illumina HiSeq	Phase_I	317	15	0.0473186	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	14.80	2.642895	0.47153	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.48522	1.77;0.81	4.19	2.41	0.29592	Actin cross-linking (1);	0.160510	0.64402	N	0.000002	T	0.36552	0.0971	N	0.17723	0.515	0.45777	D	0.998661	P	0.35982	0.531	P	0.45406	0.479	T	0.07578	-1.0765	10	0.30854	T	0.27	0.1847	7.6816	0.28518	0.219:0.0:0.781:0.0	.	169	Q14331	FRG1_HUMAN	N	169;41;106	ENSP00000226798:S169N;ENSP00000435943:S106N	ENSP00000226798:S169N	S	+	2	0	FRG1	191115620	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	1.784000	0.38674	0.340000	0.23745	0.454000	0.30748	AGT	G|0.500;A|0.500	0.500	weak		0.363	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
OR2T2	401992	hgsc.bcm.edu	37	1	248616764	248616764	+	Silent	SNP	C	C	T	rs376553658		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248616764C>T	ENST00000342927.3	+	1	688	c.666C>T	c.(664-666)atC>atT	p.I222I		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	222						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACACGCACATCCTCCTGACTG	0.542																																					p.I222I		Atlas-SNP	.											OR2T2,NS,carcinoma,0,1	OR2T2	73	1	0			c.C666T						scavenged	.						182.0	125.0	144.0					1																	248616764		2186	4264	6450	SO:0001819	synonymous_variant	401992	exon1			GCACATCCTCCTG	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.666C>T	1.37:g.248616764C>T		Somatic	429	1	0.002331		WXS	Illumina HiSeq	Phase_I	539	14	0.025974	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			C|0.500;T|0.500	0.500	strong		0.542	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
C19orf45	374877	hgsc.bcm.edu	37	19	7570990	7570990	+	Silent	SNP	A	A	G	rs685048	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7570990A>G	ENST00000361664.2	+	7	1287	c.1146A>G	c.(1144-1146)agA>agG	p.R382R	CTD-2207O23.12_ENST00000599312.1_5'Flank	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	382										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						CAGAGTGGAGACAGGTGCAGA	0.617													G|||	1717	0.342851	0.4894	0.3963	5008	,	,		9929	0.1736		0.3718	False		,,,				2504	0.2515				p.R382R		Atlas-SNP	.											.	C19orf45	36	.	0			c.A1146G						PASS	.	G		2057,2349	607.5+/-391.0	490,1077,636	69.0	64.0	65.0		1146	-0.2	0.0	19	dbSNP_83	65	3182,5418	653.5+/-401.1	586,2010,1704	no	coding-synonymous	C19orf45	NM_198534.2		1076,3087,2340	GG,GA,AA		37.0,46.6863,40.2814		382/506	7570990	5239,7767	2203	4300	6503	SO:0001819	synonymous_variant	374877	exon7			GTGGAGACAGGTG	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.1146A>G	19.37:g.7570990A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	99	38	0.383838	NM_198534	Q8N115	Silent	SNP	ENST00000361664.2	37	CCDS12179.2																																																																																			A|0.618;G|0.382	0.382	strong		0.617	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
EFCAB12	90288	hgsc.bcm.edu	37	3	129137127	129137127	+	Silent	SNP	G	G	A	rs3796392	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129137127G>A	ENST00000505956.1	-	3	813	c.651C>T	c.(649-651)acC>acT	p.T217T	EFCAB12_ENST00000326085.3_Silent_p.T217T	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	217	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)										ACTCCTCCCTGGTGATTCTCT	0.547													G|||	758	0.151358	0.1309	0.1239	5008	,	,		16983	0.4603		0.002	False		,,,				2504	0.0337				p.T217T		Atlas-SNP	.											.	.	.	.	0			c.C651T						PASS	.	G		405,3589		22,361,1614	55.0	52.0	53.0		651	3.7	1.0	3	dbSNP_107	53	33,8279		1,31,4124	no	coding-synonymous	C3orf25	NM_207307.1		23,392,5738	AA,AG,GG		0.397,10.1402,3.5592		217/573	129137127	438,11868	1997	4156	6153	SO:0001819	synonymous_variant	90288	exon3			CTCCCTGGTGATT	AK096099	CCDS54638.1	3q21.3	2013-01-10	2012-07-20	2012-07-20	ENSG00000172771	ENSG00000172771		"""EF-hand domain containing"""	28061	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 25"""	C3orf25			Standard	NM_207307		Approved		uc003emg.3	Q6NXP0	OTTHUMG00000159464	ENST00000505956.1:c.651C>T	3.37:g.129137127G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_207307	Q69YX4	Silent	SNP	ENST00000505956.1	37	CCDS54638.1																																																																																			G|0.851;A|0.149	0.149	strong		0.547	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	
LINS	55180	hgsc.bcm.edu	37	15	101110302	101110302	+	Missense_Mutation	SNP	C	C	G	rs2411837	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:101110302C>G	ENST00000314742.8	-	7	1637	c.1415G>C	c.(1414-1416)aGc>aCc	p.S472T	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	472			S -> T (in dbSNP:rs2411837).					p.S472T(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						CTGAGTCAAGCTTTCAGTGGC	0.338													C|||	1276	0.254792	0.115	0.2219	5008	,	,		17645	0.2252		0.4215	False		,,,				2504	0.3262				p.S472T		Atlas-SNP	.											LINS,NS,carcinoma,0,1	LINS	62	1	1	Substitution - Missense(1)	stomach(1)	c.G1415C						scavenged	.	C	THR/SER	691,3715	263.8+/-265.7	61,569,1573	56.0	55.0	56.0		1415	1.5	0.0	15	dbSNP_100	56	3716,4882	488.7+/-372.4	815,2086,1398	yes	missense	LINS	NM_001040616.2	58	876,2655,2971	GG,GC,CC		43.2194,15.6832,33.8896	benign	472/758	101110302	4407,8597	2203	4299	6502	SO:0001583	missense	55180	exon7			GTCAAGCTTTCAG	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"""lines homolog 1 (Drosophila)"""	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1415G>C	15.37:g.101110302C>G	ENSP00000318423:p.Ser472Thr	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	5	3	0.6	NM_001040616	Q96FW2|Q9NVQ3	Missense_Mutation	SNP	ENST00000314742.8	37	CCDS10385.1	616	0.28205128205128205	69	0.1402439024390244	92	0.2541436464088398	132	0.23076923076923078	323	0.4261213720316623	C	6.256	0.415431	0.11870	0.156832	0.432194	ENSG00000140471	ENST00000314742	T	0.18338	2.22	5.48	1.52	0.23074	.	1.019250	0.07759	N	0.949715	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.32467	0.372	B	0.30316	0.114	T	0.47394	-0.9121	9	0.52906	T	0.07	0.0722	8.2917	0.31960	0.0:0.5925:0.0:0.4075	rs2411837;rs17777920;rs52833524;rs2411837	472	Q8NG48	LINES_HUMAN	T	472	ENSP00000318423:S472T	ENSP00000318423:S472T	S	-	2	0	LINS	98927825	0.000000	0.05858	0.025000	0.17156	0.670000	0.39368	-0.174000	0.09839	0.285000	0.22329	0.655000	0.94253	AGC	C|0.688;G|0.310	0.310	strong		0.338	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148	
CFAP58	159686	hgsc.bcm.edu	37	10	106152111	106152111	+	Missense_Mutation	SNP	T	T	A	rs11192036	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:106152111T>A	ENST00000369704.3	+	10	1620	c.1486T>A	c.(1486-1488)Tca>Aca	p.S496T		NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		496			S -> T (in dbSNP:rs11192036).			extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		AGCTGTGAGATCAGACAGAAA	0.303													T|||	1104	0.220447	0.2042	0.1945	5008	,	,		16246	0.2341		0.2634	False		,,,				2504	0.2025				p.S496T		Atlas-SNP	.											.	CCDC147	137	.	0			c.T1486A						PASS	.	T	THR/SER	872,3532	315.2+/-294.0	93,686,1423	54.0	61.0	59.0		1486	5.5	1.0	10	dbSNP_120	59	2203,6393	358.1+/-331.0	281,1641,2376	yes	missense	CCDC147	NM_001008723.1	58	374,2327,3799	AA,AT,TT		25.6282,19.8002,23.6538	benign	496/873	106152111	3075,9925	2202	4298	6500	SO:0001583	missense	159686	exon10			GTGAGATCAGACA																												ENST00000369704.3:c.1486T>A	10.37:g.106152111T>A	ENSP00000358718:p.Ser496Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	33	30	0.909091	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	37	CCDS31282.1	519	0.23763736263736263	98	0.1991869918699187	75	0.20718232044198895	149	0.26048951048951047	197	0.2598944591029024	T	12.33	1.905796	0.33628	0.198002	0.256282	ENSG00000120051	ENST00000369704	T	0.44482	0.92	5.49	5.49	0.81192	.	0.260201	0.38897	N	0.001522	T	0.00012	0.0000	L	0.31804	0.96	0.09310	P	1.0	B	0.25521	0.128	B	0.25405	0.06	T	0.28396	-1.0045	9	0.17832	T	0.49	-4.5368	11.393	0.49825	0.1433:0.0:0.0:0.8567	rs11192036;rs17755504;rs52829473;rs11192036	496	Q5T655	CC147_HUMAN	T	496	ENSP00000358718:S496T	ENSP00000358718:S496T	S	+	1	0	CCDC147	106142101	0.999000	0.42202	0.994000	0.49952	0.920000	0.55202	2.502000	0.45398	2.093000	0.63338	0.533000	0.62120	TCA	T|0.767;A|0.233	0.233	strong		0.303	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1		
FAM120B	84498	hgsc.bcm.edu	37	6	170627651	170627651	+	Silent	SNP	G	G	A	rs9460113	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:170627651G>A	ENST00000476287.1	+	2	1281	c.1173G>A	c.(1171-1173)acG>acA	p.T391T	FAM120B_ENST00000540480.1_Silent_p.T403T|FAM120B_ENST00000252510.9_Intron|FAM120B_ENST00000537664.1_Silent_p.T414T	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	391					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		AAGTTCCCACGTGTACAGGCC	0.542													G|||	2500	0.499201	0.5749	0.5951	5008	,	,		20319	0.124		0.671	False		,,,				2504	0.5389				p.T391T		Atlas-SNP	.											.	FAM120B	108	.	0			c.G1173A						PASS	.	G		2524,1882	629.5+/-395.3	716,1092,395	177.0	185.0	182.0		1173	-0.5	0.0	6	dbSNP_119	182	5736,2864	672.2+/-402.9	1940,1856,504	no	coding-synonymous	FAM120B	NM_032448.1		2656,2948,899	AA,AG,GG		33.3023,42.7145,36.4909		391/911	170627651	8260,4746	2203	4300	6503	SO:0001819	synonymous_variant	84498	exon2			TCCCACGTGTACA	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.1173G>A	6.37:g.170627651G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_032448	B4DL34|Q86V68|Q96JI9	Silent	SNP	ENST00000476287.1	37	CCDS5314.1																																																																																			G|0.427;A|0.573	0.573	strong		0.542	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
DNAH14	127602	hgsc.bcm.edu	37	1	225534348	225534348	+	Missense_Mutation	SNP	G	G	A	rs7535953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225534348G>A	ENST00000445597.2	+	49	8600	c.8600G>A	c.(8599-8601)aGa>aAa	p.R2867K	DNAH14_ENST00000439375.2_Missense_Mutation_p.R3670K|DNAH14_ENST00000430092.1_Missense_Mutation_p.R3670K			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2867					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TCCCAGTCTAGACTTACTAGT	0.338													G|||	2650	0.529153	0.6407	0.4697	5008	,	,		17939	0.5089		0.4046	False		,,,				2504	0.5695				p.R3670K		Atlas-SNP	.											.	DNAH14	300	.	0			c.G11009A						PASS	.						48.0	44.0	45.0					1																	225534348		692	1585	2277	SO:0001583	missense	127602	exon69			AGTCTAGACTTAC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.8600G>A	1.37:g.225534348G>A	ENSP00000409472:p.Arg2867Lys	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	167	83	0.497006	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	G	1.991	-0.431729	0.04669	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.39997	1.05;1.05;1.05	4.94	-3.81	0.04294	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.40213	-0.9575	7	0.02654	T	1	.	6.7277	0.23365	0.6059:0.0:0.272:0.1221	rs7535953;rs17522510;rs52812222;rs58063527;rs7535953	3670	Q0VDD8-4	.	K	2867;3670;3670	ENSP00000409472:R2867K;ENSP00000414402:R3670K;ENSP00000392061:R3670K	ENSP00000414402:R3670K	R	+	2	0	DNAH14	223600971	0.000000	0.05858	0.000000	0.03702	0.463000	0.32649	-0.207000	0.09384	-0.823000	0.04301	-0.357000	0.07601	AGA	G|0.499;A|0.501	0.501	strong		0.338	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
MGAM	8972	hgsc.bcm.edu	37	7	141755358	141755358	+	Splice_Site	SNP	T	T	C	rs67998329	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:141755358T>C	ENST00000549489.2	+	28	3410	c.3315T>C	c.(3313-3315)atT>atC	p.I1105I	MGAM_ENST00000475668.2_Splice_Site_p.I1105I	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1105	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGTGTTTCAGTTGGGACTCTC	0.453													t|||	1160	0.231629	0.2852	0.2522	5008	,	,		20345	0.1984		0.1958	False		,,,				2504	0.2157				p.I1105I		Atlas-SNP	.											.	MGAM	767	.	0			c.T3315C						PASS	.	T		884,2952		113,658,1147	142.0	130.0	134.0		3315	-2.2	0.9	7	dbSNP_130	134	1521,6753		162,1197,2778	yes	coding-synonymous-near-splice	MGAM	NM_004668.2		275,1855,3925	CC,CT,TT		18.3829,23.0448,19.8596		1105/1858	141755358	2405,9705	1918	4137	6055	SO:0001630	splice_region_variant	8972	exon28			TTTCAGTTGGGAC	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.3315-1T>C	7.37:g.141755358T>C		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			T|0.776;C|0.224	0.224	strong		0.453	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		Silent
BEGAIN	57596	hgsc.bcm.edu	37	14	101005215	101005215	+	Silent	SNP	T	T	C	rs12893951	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:101005215T>C	ENST00000355173.2	-	7	944	c.873A>G	c.(871-873)gcA>gcG	p.A291A	CTD-2062F14.3_ENST00000553301.1_lincRNA|BEGAIN_ENST00000556751.1_Silent_p.A227A|BEGAIN_ENST00000443071.2_Silent_p.A291A	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	291						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				GCAGTGAGCCTGCGTAGCTGG	0.706													C|||	3260	0.650958	0.969	0.6254	5008	,	,		13674	0.7093		0.4274	False		,,,				2504	0.409				p.A291A	NSCLC(159;1889 2010 9965 27479 40101)	Atlas-SNP	.											.	BEGAIN	32	.	0			c.A873G						PASS	.	C	,	3873,527		1715,443,42	23.0	26.0	25.0		873,873	1.5	0.9	14	dbSNP_121	25	3508,5090		752,2004,1543	no	coding-synonymous,coding-synonymous	BEGAIN	NM_001159531.1,NM_020836.3	,	2467,2447,1585	CC,CT,TT		40.8002,11.9773,43.2143	,	291/594,291/594	101005215	7381,5617	2200	4299	6499	SO:0001819	synonymous_variant	57596	exon7			TGAGCCTGCGTAG	BC002607	CCDS9962.1	14q32.2	2012-12-07	2012-12-07			ENSG00000183092			24163	protein-coding gene	gene with protein product			"""brain-enriched guanylate kinase-associated homolog (rat)"""			10819331	Standard	NM_020836		Approved	KIAA1446	uc010txa.2	Q9BUH8		ENST00000355173.2:c.873A>G	14.37:g.101005215T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	36	13	0.361111	NM_020836	Q9NPU3|Q9P282	Silent	SNP	ENST00000355173.2	37	CCDS9962.1																																																																																			T|0.388;C|0.612	0.612	strong		0.706	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836	
UGT2A1	10941	hgsc.bcm.edu	37	4	70462042	70462042	+	Missense_Mutation	SNP	C	C	T	rs4148301	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:70462042C>T	ENST00000503640.1	-	3	977	c.922G>A	c.(922-924)Gga>Aga	p.G308R	UGT2A1_ENST00000502343.1_Intron|UGT2A1_ENST00000512704.1_Intron|UGT2A2_ENST00000457664.2_Missense_Mutation_p.G317R|UGT2A1_ENST00000514019.1_Intron|UGT2A1_ENST00000286604.4_Intron	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	308			G -> R (in dbSNP:rs4148301).		cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						ACCATTGATCCCAGAGAAAAC	0.408													C|||	351	0.0700879	0.0567	0.0908	5008	,	,		17128	0.0565		0.0974	False		,,,				2504	0.0593				p.G317R		Atlas-SNP	.											.	.	.	.	0			c.G949A						PASS	.	C	ARG/GLY,ARG/GLY	336,4070	177.6+/-206.5	16,304,1883	119.0	111.0	114.0		949,922	5.4	1.0	4	dbSNP_110	114	858,7742	195.4+/-240.6	37,784,3479	yes	missense,missense	UGT2A1,UGT2A2	NM_001105677.2,NM_006798.2	125,125	53,1088,5362	TT,TC,CC		9.9767,7.626,9.1804	probably-damaging,probably-damaging	317/537,308/528	70462042	1194,11812	2203	4300	6503	SO:0001583	missense	574537	exon3			TTGATCCCAGAGA	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"""UDP glucuronosyltransferases"""	12542	protein-coding gene	gene with protein product		604716	"""UDP glycosyltransferase 2 family, polypeptide A1"", ""UDP glucuronosyltransferase 2 family, polypeptide A1"""			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.922G>A	4.37:g.70462042C>T	ENSP00000424478:p.Gly308Arg	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_001105677	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	167	0.07646520146520147	28	0.056910569105691054	37	0.10220994475138122	29	0.050699300699300696	73	0.09630606860158311	C	29.9	5.046584	0.93740	0.07626	0.099767	ENSG00000173610	ENST00000457664;ENST00000503640	D;D	0.96136	-3.92;-3.92	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.76702	0.4024	H	0.97516	4.02	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73652	-0.3915	9	0.87932	D	0	.	16.687	0.85311	0.0:1.0:0.0:0.0	rs4148301;rs56544392;rs58191288;rs4148301	317;308	Q9Y4X1-2;Q9Y4X1	.;UD2A1_HUMAN	R	317;308	ENSP00000387888:G317R;ENSP00000424478:G308R	ENSP00000387888:G317R	G	-	1	0	UGT2A1	70496631	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.517000	0.81783	2.530000	0.85305	0.591000	0.81541	GGA	C|0.916;T|0.084	0.084	strong		0.408	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
NEFH	4744	hgsc.bcm.edu	37	22	29885564	29885564	+	Silent	SNP	A	A	G	rs202065964|rs371230849		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29885564A>G	ENST00000310624.6	+	4	1968	c.1935A>G	c.(1933-1935)gaA>gaG	p.E645E		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CGAAGGAGGAAGCAAAGTCCC	0.562																																					p.E645E		Atlas-SNP	.											NEFH,rectum,carcinoma,0,1	NEFH	178	1	0			c.A1935G						scavenged	.						83.0	89.0	87.0					22																	29885564		2203	4300	6503	SO:0001819	synonymous_variant	4744	exon4			GGAGGAAGCAAAG		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1935A>G	22.37:g.29885564A>G		Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	42	15	0.357143	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			.	.	weak		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39907036	39907036	+	Silent	SNP	C	C	T	rs2277743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:39907036C>T	ENST00000409794.3	+	5	1378	c.528C>T	c.(526-528)gcC>gcT	p.A176A	PLEKHG2_ENST00000409797.2_Silent_p.A176A|PLEKHG2_ENST00000378550.1_Silent_p.A176A|PLEKHG2_ENST00000458508.2_Silent_p.A117A|PLEKHG2_ENST00000425673.1_Silent_p.A176A	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	176	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GGGGTATTGCCGAGTGCTTCG	0.657													C|||	883	0.176318	0.2163	0.1974	5008	,	,		13310	0.0387		0.1859	False		,,,				2504	0.2393				p.A176A		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C528T						PASS	.	C		977,3429	355.4+/-313.0	113,751,1339	62.0	71.0	68.0		528	-4.2	1.0	19	dbSNP_100	68	1533,7067	280.8+/-294.7	135,1263,2902	no	coding-synonymous	PLEKHG2	NM_022835.2		248,2014,4241	TT,TC,CC		17.8256,22.1743,19.2988		176/1387	39907036	2510,10496	2203	4300	6503	SO:0001819	synonymous_variant	64857	exon5			TATTGCCGAGTGC	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.528C>T	19.37:g.39907036C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	359	0.16437728937728938	114	0.23170731707317074	86	0.23756906077348067	14	0.024475524475524476	145	0.19129287598944592	C	10.86	1.469971	0.26423	0.221743	0.178256	ENSG00000090924	ENST00000205135	.	.	.	4.68	-4.25	0.03766	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999842	.	.	.	.	.	.	T	0.35226	-0.9797	3	.	.	.	.	2.0945	0.03665	0.1055:0.2325:0.2962:0.3659	rs2277743;rs17206567;rs60635542;rs2277743	.	.	.	L	73	.	.	P	+	2	0	PLEKHG2	44598876	0.000000	0.05858	0.959000	0.39883	0.945000	0.59286	-6.192000	0.00076	-0.551000	0.06175	0.491000	0.48974	CCG	C|0.826;T|0.174	0.174	strong		0.657	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
CCAR1	55749	hgsc.bcm.edu	37	10	70502288	70502288	+	Silent	SNP	G	G	A	rs1300253	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70502288G>A	ENST00000265872.6	+	6	599	c.480G>A	c.(478-480)acG>acA	p.T160T	CCAR1_ENST00000543719.1_Silent_p.T145T|CCAR1_ENST00000535016.1_Silent_p.T145T	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	160					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						TACATGATACGTTTGGATTTG	0.403													A|||	4314	0.861422	0.9297	0.9222	5008	,	,		21254	0.7401		0.8618	False		,,,				2504	0.8507				p.T160T		Atlas-SNP	.											CCAR1,NS,carcinoma,+1,1	CCAR1	118	1	0			c.G480A						PASS	.	A		4067,339	174.8+/-204.3	1875,317,11	247.0	234.0	238.0		480	-11.3	0.4	10	dbSNP_87	238	7393,1207	244.7+/-273.8	3169,1055,76	no	coding-synonymous	CCAR1	NM_018237.2		5044,1372,87	AA,AG,GG		14.0349,7.6941,11.8868		160/1151	70502288	11460,1546	2203	4300	6503	SO:0001819	synonymous_variant	55749	exon6			TGATACGTTTGGA	AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.480G>A	10.37:g.70502288G>A		Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	291	291	1	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Silent	SNP	ENST00000265872.6	37	CCDS7282.1																																																																																			G|0.135;A|0.865	0.865	strong		0.403	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237	
UBA6	55236	hgsc.bcm.edu	37	4	68500171	68500171	+	Silent	SNP	A	A	G	rs10008910	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:68500171A>G	ENST00000322244.5	-	21	1967	c.1908T>C	c.(1906-1908)caT>caC	p.H636H		NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	636					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						ACTGTATGGTATGTTCAATAG	0.333													A|||	783	0.15635	0.1581	0.1182	5008	,	,		15380	0.1052		0.165	False		,,,				2504	0.2249				p.H636H		Atlas-SNP	.											.	UBA6	98	.	0			c.T1908C						PASS	.	A		748,3656	282.8+/-276.7	73,602,1527	65.0	73.0	70.0		1908	0.7	1.0	4	dbSNP_119	70	1202,7394	238.5+/-269.9	80,1042,3176	no	coding-synonymous	UBA6	NM_018227.5		153,1644,4703	GG,GA,AA		13.9832,16.9846,15.0		636/1053	68500171	1950,11050	2202	4298	6500	SO:0001819	synonymous_variant	55236	exon21			TATGGTATGTTCA	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"""Ubiquitin-like modifier activating enzymes"""	25581	protein-coding gene	gene with protein product	"""UBA6, ubiquitin-activating enzyme E1"""	611361	"""ubiquitin-activating enzyme E1-like 2"""	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.1908T>C	4.37:g.68500171A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Silent	SNP	ENST00000322244.5	37	CCDS3516.1	325	0.1488095238095238	77	0.1565040650406504	48	0.13259668508287292	72	0.1258741258741259	128	0.16886543535620052	A	8.494	0.862714	0.17178	0.169846	0.139832	ENSG00000033178	ENST00000505673	.	.	.	5.79	0.723	0.18231	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.10451	-1.0629	3	.	.	.	-16.826	9.1465	0.36937	0.7147:0.0:0.2853:0.0	rs10008910	.	.	.	T	170	.	.	I	-	2	0	UBA6	68182766	0.996000	0.38824	0.998000	0.56505	0.920000	0.55202	0.482000	0.22276	-0.075000	0.12798	0.482000	0.46254	ATA	A|0.851;G|0.149	0.149	strong		0.333	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256920	140256920	+	Silent	SNP	G	G	C	rs115718636	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140256920G>C	ENST00000398631.2	+	1	1863	c.1863G>C	c.(1861-1863)ccG>ccC	p.P621P	PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	621	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCACATCCCGTTCCACGTGG	0.672													.|||	111	0.0221645	0.0129	0.0303	5008	,	,		17234	0.0		0.0656	False		,,,				2504	0.0072				p.P621P	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,colon,carcinoma,0,2	PCDHA12	196	2	0			c.G1863C						scavenged	.	G	,,,,,,,,,,,,,,,	117,4289	87.8+/-126.4	0,117,2086	228.0	205.0	213.0		,,,1863,,,,,,,,,,,,1863	-0.7	0.9	5	dbSNP_132	213	437,8161	133.5+/-191.0	11,415,3873	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031864.1	,,,,,,,,,,,,,,,	11,532,5959	CC,CG,GG		5.0826,2.6555,4.2602	,,,,,,,,,,,,,,,	,,,621/942,,,,,,,,,,,,621/793	140256920	554,12450	2203	4299	6502	SO:0001819	synonymous_variant	56137	exon1			CATCCCGTTCCAC	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1863G>C	5.37:g.140256920G>C		Somatic	282	4	0.0141844		WXS	Illumina HiSeq	Phase_I	230	110	0.478261	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			G|0.959;C|0.041	0.041	strong		0.672	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
PARP4	143	hgsc.bcm.edu	37	13	25075859	25075859	+	Silent	SNP	C	C	T	rs1539096	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25075859C>T	ENST00000381989.3	-	3	351	c.246G>A	c.(244-246)agG>agA	p.R82R		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	82	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GTCTCTTTTCCCTGATAGATT	0.398													.|||	3031	0.605232	0.618	0.6037	5008	,	,		16368	0.6062		0.5119	False		,,,				2504	0.684				p.R82R		Atlas-SNP	.											.	PARP4	142	.	0			c.G246A						PASS	.	T		2558,1848	536.5+/-374.5	738,1082,383	125.0	130.0	128.0		246	1.5	0.3	13	dbSNP_88	128	4634,3966	551.8+/-386.0	1240,2154,906	no	coding-synonymous	PARP4	NM_006437.3		1978,3236,1289	TT,TC,CC		46.1163,41.9428,44.7024		82/1725	25075859	7192,5814	2203	4300	6503	SO:0001819	synonymous_variant	143	exon3			CTTTTCCCTGATA	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.246G>A	13.37:g.25075859C>T		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			C|0.431;T|0.569	0.569	strong		0.398	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
TMTC4	84899	hgsc.bcm.edu	37	13	101266580	101266580	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:101266580G>A	ENST00000376234.3	-	15	2073	c.1884C>T	c.(1882-1884)ctC>ctT	p.L628L	TMTC4_ENST00000342624.5_Silent_p.L647L|TMTC4_ENST00000328767.5_Silent_p.L517L	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	628						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CTGTATTGTCGAGGAGTATAA	0.463																																					p.L647L		Atlas-SNP	.											.	TMTC4	103	.	0			c.C1941T						PASS	.						166.0	143.0	151.0					13																	101266580		2203	4300	6503	SO:0001819	synonymous_variant	84899	exon16			ATTGTCGAGGAGT		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1884C>T	13.37:g.101266580G>A		Somatic	288	1	0.00347222		WXS	Illumina HiSeq	Phase_I	305	141	0.462295	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	CCDS41904.1																																																																																			.	.	none		0.463	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
SLCO1B3	28234	hgsc.bcm.edu	37	12	21015760	21015760	+	Missense_Mutation	SNP	G	G	A	rs7311358	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:21015760G>A	ENST00000381545.3	+	8	918	c.699G>A	c.(697-699)atG>atA	p.M233I	LST3_ENST00000540229.1_Missense_Mutation_p.M233I|SLCO1B3_ENST00000553473.1_Missense_Mutation_p.M233I|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.M233I|LST3_ENST00000381541.3_Intron|SLCO1B7_ENST00000554957.1_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	233			M -> I (in dbSNP:rs7311358).		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TTGCTAAAATGTACGTGGATA	0.353													.|||	3518	0.702476	0.3555	0.8372	5008	,	,		15110	0.6984		0.8648	False		,,,				2504	0.9131				p.M233I		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.G699A						PASS	.	G	ILE/MET	1972,2434	555.5+/-379.3	464,1044,695	169.0	144.0	153.0		699	-2.0	0.1	12	dbSNP_116	153	7429,1171	764.5+/-407.6	3210,1009,81	yes	missense	SLCO1B3	NM_019844.2	10	3674,2053,776	AA,AG,GG		13.6163,44.7571,27.718	benign	233/703	21015760	9401,3605	2203	4300	6503	SO:0001583	missense	28234	exon8			TAAAATGTACGTG		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.699G>A	12.37:g.21015760G>A	ENSP00000370956:p.Met233Ile	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	192	192	1	NM_019844	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	37	CCDS8684.1	1550	0.7097069597069597	185	0.37601626016260165	310	0.856353591160221	411	0.7185314685314685	644	0.8496042216358839	G	11.67	1.706783	0.30232	0.447571	0.863837	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046	ENST00000540853;ENST00000261196;ENST00000381545;ENST00000553473;ENST00000544370;ENST00000540229	T;T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31;1.31	3.9	-2.0	0.07433	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.365415	0.31145	N	0.008175	T	0.00012	0.0000	N	0.04994	-0.135	0.09310	P	0.999999826979	B;B	0.23854	0.092;0.007	B;B	0.20577	0.03;0.007	T	0.14896	-1.0456	9	0.23891	T	0.37	.	4.723	0.12927	0.3524:0.277:0.3706:0.0	rs7311358;rs60001963;rs7311358	233;233	Q5JAR4;Q9NPD5	.;SO1B3_HUMAN	I	233;233;233;233;57;233	ENSP00000442000:M233I;ENSP00000261196:M233I;ENSP00000370956:M233I;ENSP00000451758:M233I;ENSP00000443225:M57I;ENSP00000441269:M233I	ENSP00000441269:M233I	M	+	3	0	SLCO1B3;RP11-545J16.1	20907027	0.001000	0.12720	0.065000	0.19835	0.847000	0.48162	-1.540000	0.02200	-0.125000	0.11703	0.460000	0.39030	ATG	G|0.289;A|0.711	0.711	strong		0.353	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
N4BP2	55728	hgsc.bcm.edu	37	4	40122453	40122453	+	Missense_Mutation	SNP	C	C	T	rs78417585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:40122453C>T	ENST00000261435.6	+	9	3138	c.2722C>T	c.(2722-2724)Ccc>Tcc	p.P908S		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	908					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)	p.P908S(1)		breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TTTAAGTGAGCCCAACCTAGA	0.398													C|||	14	0.00279553	0.0	0.0058	5008	,	,		22081	0.0		0.0099	False		,,,				2504	0.0				p.P908S		Atlas-SNP	.											N4BP2,NS,carcinoma,0,1	N4BP2	166	1	1	Substitution - Missense(1)	pancreas(1)	c.C2722T						PASS	.	C	SER/PRO	13,4393	19.1+/-41.9	0,13,2190	50.0	48.0	49.0		2722	1.6	0.2	4	dbSNP_131	49	82,8518	46.3+/-105.2	1,80,4219	yes	missense	N4BP2	NM_018177.4	74	1,93,6409	TT,TC,CC		0.9535,0.2951,0.7304	benign	908/1771	40122453	95,12911	2203	4300	6503	SO:0001583	missense	55728	exon9			AGTGAGCCCAACC	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.2722C>T	4.37:g.40122453C>T	ENSP00000261435:p.Pro908Ser	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	263	132	0.501901	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	C|C	0.446|0.446	-0.896370|-0.896370	0.02472|0.02472	0.002951|0.002951	0.009535|0.009535	ENSG00000078177|ENSG00000078177	ENST00000513269|ENST00000261435;ENST00000381804	.|T	.|0.14391	.|2.51	5.48|5.48	1.64|1.64	0.23874|0.23874	.|.	.|0.866997	.|0.10353	.|N	.|0.684921	T|T	0.06962|0.06962	0.0177|0.0177	L|L	0.45581|0.45581	1.43|1.43	0.09310|0.09310	N|N	1|1	.|B;B	.|0.14438	.|0.01;0.006	.|B;B	.|0.08055	.|0.003;0.001	T|T	0.41928|0.41928	-0.9481|-0.9481	5|10	.|0.10636	.|T	.|0.68	-0.6285|-0.6285	4.8249|4.8249	0.13410|0.13410	0.0:0.4947:0.1599:0.3453|0.0:0.4947:0.1599:0.3453	.|.	.|908;908	.|Q86UW6-2;Q86UW6	.|.;N4BP2_HUMAN	V|S	554|908;828	.|ENSP00000261435:P908S	.|ENSP00000261435:P908S	A|P	+|+	2|1	0|0	N4BP2|N4BP2	39798848|39798848	0.000000|0.000000	0.05858|0.05858	0.230000|0.230000	0.23976|0.23976	0.286000|0.286000	0.27126|0.27126	0.125000|0.125000	0.15749|0.15749	0.803000|0.803000	0.34113|0.34113	0.655000|0.655000	0.94253|0.94253	GCC|CCC	C|0.992;T|0.008	0.008	strong		0.398	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
CEACAM16	388551	hgsc.bcm.edu	37	19	45206695	45206695	+	Silent	SNP	G	G	A	rs894189	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:45206695G>A	ENST00000405314.2	+	2	211	c.114G>A	c.(112-114)acG>acA	p.T38T	CEACAM16_ENST00000587331.1_Silent_p.T38T|CTB-171A8.1_ENST00000590796.1_RNA			Q2WEN9	CEA16_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 16	38					sensory perception of sound (GO:0007605)	extracellular region (GO:0005576)|stereocilium bundle tip (GO:0032426)				endometrium(3)|large_intestine(2)|lung(3)|ovary(1)	9	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)				ACAACGTCACGCTGGTCGTCC	0.617													G|||	683	0.136382	0.2723	0.1873	5008	,	,		18500	0.0506		0.0487	False		,,,				2504	0.0951				p.T38T		Atlas-SNP	.											.	CEACAM16	56	.	0			c.G114A						PASS	.	G		951,3193		108,735,1229	38.0	41.0	40.0		114	-10.3	0.4	19	dbSNP_86	40	424,7942		15,394,3774	no	coding-synonymous	CEACAM16	NM_001039213.2		123,1129,5003	AA,AG,GG		5.0681,22.9488,10.9912		38/426	45206695	1375,11135	2072	4183	6255	SO:0001819	synonymous_variant	388551	exon3			CGTCACGCTGGTC		CCDS54278.1	19q13.31	2014-01-27			ENSG00000213892	ENSG00000213892		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31948	protein-coding gene	gene with protein product		614591				21368133	Standard	NM_001039213		Approved	DFNA4B	uc010xxd.2	Q2WEN9	OTTHUMG00000151519	ENST00000405314.2:c.114G>A	19.37:g.45206695G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	169	91	0.538462	NM_001039213	A7LI12	Silent	SNP	ENST00000405314.2	37	CCDS54278.1																																																																																			G|0.889;A|0.111	0.111	strong		0.617	CEACAM16-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		XM_371177	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052768	33052768	+	Silent	SNP	T	T	C	rs1042187	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33052768T>C	ENST00000418931.2	+	3	522	c.406T>C	c.(406-408)Ttg>Ctg	p.L136L		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	136	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)	p.L136L(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GAAGGGGCCCTTGCAGCACCA	0.502													.|||	2322	0.463658	0.5976	0.3314	5008	,	,		18424	0.621		0.3151	False		,,,				2504	0.3671				p.L136L		Atlas-SNP	.											HLA-DPB1,rectum,carcinoma,0,1	HLA-DPB1	28	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T406C						scavenged	.						74.0	95.0	87.0					6																	33052768		1510	2709	4219	SO:0001819	synonymous_variant	3115	exon3			GGGCCCTTGCAGC		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.406T>C	6.37:g.33052768T>C		Somatic	430	2	0.00465116		WXS	Illumina HiSeq	Phase_I	351	119	0.339031	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Silent	SNP	ENST00000418931.2	37	CCDS4765.1																																																																																			A|0.000;C|0.386;G|0.000;T|0.614	0.386	strong		0.502	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
ATF7IP	55729	hgsc.bcm.edu	37	12	14577892	14577892	+	Missense_Mutation	SNP	A	A	T	rs2231909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:14577892A>T	ENST00000540793.1	+	1	1198	c.1043A>T	c.(1042-1044)aAt>aTt	p.N348I	ATF7IP_ENST00000544627.1_Missense_Mutation_p.N356I|ATF7IP_ENST00000536444.1_Missense_Mutation_p.N348I|ATF7IP_ENST00000261168.4_Missense_Mutation_p.N348I|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000543189.1_Missense_Mutation_p.N348I			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	348			N -> I (in dbSNP:rs2231909). {ECO:0000269|PubMed:12665582}.		DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						ATTGATGCTAATGAAGAAACT	0.318													A|||	1609	0.321286	0.0953	0.4928	5008	,	,		19484	0.3284		0.3867	False		,,,				2504	0.4305				p.N348I		Atlas-SNP	.											.	ATF7IP	136	.	0			c.A1043T						PASS	.	A	ILE/ASN	581,3825	231.7+/-245.5	37,507,1659	60.0	67.0	65.0		1043	1.8	0.2	12	dbSNP_98	65	3422,5178	488.8+/-372.5	691,2040,1569	yes	missense	ATF7IP	NM_018179.3	149	728,2547,3228	TT,TA,AA		39.7907,13.1866,30.7781	benign	348/1271	14577892	4003,9003	2203	4300	6503	SO:0001583	missense	55729	exon2			ATGCTAATGAAGA	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.1043A>T	12.37:g.14577892A>T	ENSP00000444589:p.Asn348Ile	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	698	0.31959706959706957	53	0.10772357723577236	161	0.4447513812154696	186	0.32517482517482516	298	0.39313984168865435	A	10.03	1.239961	0.22711	0.131866	0.397907	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000396279;ENST00000540793	T;T;T;T;T;T	0.24350	2.19;2.18;2.19;2.19;1.86;2.19	5.55	1.82	0.25136	.	0.907720	0.09489	N	0.795183	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.16802	0.019;0.001;0.001;0.001	B;B;B;B	0.09377	0.004;0.001;0.001;0.002	T	0.46484	-0.9188	9	0.44086	T	0.13	-1.0045	1.3118	0.02099	0.5136:0.1269:0.1384:0.2211	rs2231909;rs17403090;rs57622137;rs2231909	348;348;348;348	B4DRL6;G3V1U0;Q6VMQ6;Q6VMQ6-2	.;.;MCAF1_HUMAN;.	I	348;348;348;356;348;348	ENSP00000261168:N348I;ENSP00000443179:N348I;ENSP00000445955:N348I;ENSP00000440440:N356I;ENSP00000379575:N348I;ENSP00000444589:N348I	ENSP00000261168:N348I	N	+	2	0	ATF7IP	14469159	0.001000	0.12720	0.234000	0.24042	0.967000	0.64934	0.257000	0.18369	0.117000	0.18138	-0.256000	0.11100	AAT	A|0.678;T|0.322	0.322	strong		0.318	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
SARDH	1757	hgsc.bcm.edu	37	9	136561367	136561367	+	Silent	SNP	G	G	A	rs2502740	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:136561367G>A	ENST00000371872.4	-	14	2042	c.1785C>T	c.(1783-1785)tcC>tcT	p.S595S	SARDH_ENST00000371868.1_Silent_p.S23S|SARDH_ENST00000439388.1_Silent_p.S595S|SARDH_ENST00000422262.2_Silent_p.S427S	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	595					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		TGACATCTGCGGAGAAGAGCC	0.617																																					p.S595S		Atlas-SNP	.											SARDH,NS,carcinoma,0,1	SARDH	112	1	0			c.C1785T						PASS	.	A	,	656,3750	276.0+/-272.9	77,502,1624	61.0	56.0	58.0		1785,1785	-10.0	0.0	9	dbSNP_100	58	2932,5668	458.5+/-364.6	508,1916,1876	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	585,2418,3500	AA,AG,GG		34.093,14.8888,27.5873	,	595/919,595/919	136561367	3588,9418	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon14			ATCTGCGGAGAAG		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1785C>T	9.37:g.136561367G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			G|0.744;A|0.256	0.256	strong		0.617	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
CHRD	8646	hgsc.bcm.edu	37	3	184102396	184102396	+	Silent	SNP	C	C	T	rs16858778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:184102396C>T	ENST00000204604.1	+	13	1758	c.1512C>T	c.(1510-1512)aaC>aaT	p.N504N	EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000450923.1_Silent_p.N504N|CHRD_ENST00000348986.3_Silent_p.N464N|CHRD_ENST00000545352.1_Silent_p.N134N	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	504	CHRD 3. {ECO:0000255|PROSITE- ProRule:PRU00230}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCTTCCTGAACGTGGGCACCA	0.642													C|||	602	0.120208	0.0227	0.2522	5008	,	,		18257	0.2024		0.0507	False		,,,				2504	0.1452				p.N504N		Atlas-SNP	.											.	CHRD	149	.	0			c.C1512T						PASS	.	C		182,4224	115.9+/-153.8	3,176,2024	79.0	78.0	78.0		1512	-3.9	1.0	3	dbSNP_123	78	707,7893	173.3+/-223.8	35,637,3628	no	coding-synonymous	CHRD	NM_003741.2		38,813,5652	TT,TC,CC		8.2209,4.1307,6.8353		504/956	184102396	889,12117	2203	4300	6503	SO:0001819	synonymous_variant	8646	exon13			CCTGAACGTGGGC	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.1512C>T	3.37:g.184102396C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	70	27	0.385714	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Silent	SNP	ENST00000204604.1	37	CCDS3266.1																																																																																			C|0.909;T|0.091	0.091	strong		0.642	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
GRIK2	2898	hgsc.bcm.edu	37	6	102483356	102483356	+	Silent	SNP	C	C	A	rs3213607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:102483356C>A	ENST00000421544.1	+	14	2716	c.2226C>A	c.(2224-2226)atC>atA	p.I742I	GRIK2_ENST00000369137.3_Silent_p.I666I|GRIK2_ENST00000369134.4_Silent_p.I693I|GRIK2_ENST00000318991.6_Silent_p.I742I|GRIK2_ENST00000413795.1_Silent_p.I742I|GRIK2_ENST00000369138.1_Silent_p.I742I	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	742					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	CAACAACCATCGAGTTTGTTA	0.468													C|||	312	0.0623003	0.0961	0.049	5008	,	,		13586	0.0446		0.0537	False		,,,				2504	0.0532				p.I742I		Atlas-SNP	.											.	GRIK2	487	.	0			c.C2226A						PASS	.	C	,,	340,4066	178.3+/-207.1	13,314,1876	184.0	186.0	185.0		2226,2226,2226	-10.4	0.2	6	dbSNP_106	185	515,8085	146.0+/-201.7	16,483,3801	no	coding-synonymous,coding-synonymous,coding-synonymous	GRIK2	NM_001166247.1,NM_021956.4,NM_175768.3	,,	29,797,5677	AA,AC,CC		5.9884,7.7167,6.5739	,,	742/893,742/909,742/870	102483356	855,12151	2203	4300	6503	SO:0001819	synonymous_variant	2898	exon14			AACCATCGAGTTT		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2226C>A	6.37:g.102483356C>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	240	234	0.975	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Silent	SNP	ENST00000421544.1	37	CCDS5048.1																																																																																			C|0.933;A|0.067	0.067	strong		0.468	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1		
TBC1D2B	23102	hgsc.bcm.edu	37	15	78317679	78317679	+	Silent	SNP	C	C	T	rs148026593		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:78317679C>T	ENST00000300584.3	-	5	1007	c.1008G>A	c.(1006-1008)ccG>ccA	p.P336P	TBC1D2B_ENST00000409931.3_Silent_p.P336P	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	336							Rab GTPase activator activity (GO:0005097)	p.P336P(2)		breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						TTTCGGAGGCCGGCTTCCTGA	0.502													c|||	1	0.000199681	0.0	0.0	5008	,	,		13209	0.0		0.001	False		,,,				2504	0.0				p.P336P		Atlas-SNP	.											TBC1D2B_ENST00000300584,NS,carcinoma,0,2	TBC1D2B	104	2	2	Substitution - coding silent(2)	endometrium(2)	c.G1008A						PASS	.	T	,	0,4392		0,0,2196	110.0	99.0	103.0		1008,1008	-8.8	0.0	15	dbSNP_134	103	4,8582	3.7+/-12.6	0,4,4289	no	coding-synonymous,coding-synonymous	TBC1D2B	NM_015079.5,NM_144572.1	,	0,4,6485	TT,TC,CC		0.0466,0.0,0.0308	,	336/915,336/964	78317679	4,12974	2196	4293	6489	SO:0001819	synonymous_variant	23102	exon5			GGAGGCCGGCTTC	AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.1008G>A	15.37:g.78317679C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	112	66	0.589286	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Silent	SNP	ENST00000300584.3	37	CCDS45314.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	5.989	0.366325	0.11352	0.0	4.66E-4	ENSG00000167202	ENST00000418039	.	.	.	5.61	-8.8	0.00817	.	.	.	.	.	T	0.15998	0.0385	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.21177	-1.0253	4	.	.	.	.	3.3969	0.07310	0.0858:0.2262:0.2483:0.4397	.	.	.	.	Q	218	.	.	R	-	2	0	TBC1D2B	76104734	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.861000	0.00177	-1.282000	0.02396	-1.027000	0.02421	CGG	C|0.999;T|0.001	0.001	strong		0.502	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079	
SLX4	84464	hgsc.bcm.edu	37	16	3656482	3656482	+	Silent	SNP	C	C	T	rs8061528	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:3656482C>T	ENST00000294008.3	-	3	1393	c.753G>A	c.(751-753)gcG>gcA	p.A251A		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	251	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TACCATTCCCCGCCATCATCT	0.507								Direct reversal of damage					C|||	1156	0.230831	0.2466	0.1902	5008	,	,		19972	0.2808		0.1978	False		,,,				2504	0.2209				p.A251A		Atlas-SNP	.											.	SLX4	173	.	0			c.G753A						PASS	.	C		1099,3295	395.4+/-329.6	135,829,1233	237.0	230.0	233.0		753	-8.8	0.0	16	dbSNP_116	233	1746,6854	318.3+/-313.6	183,1380,2737	no	coding-synonymous	SLX4	NM_032444.2		318,2209,3970	TT,TC,CC		20.3023,25.0114,21.8947		251/1835	3656482	2845,10149	2197	4300	6497	SO:0001819	synonymous_variant	84464	exon3			ATTCCCCGCCATC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.753G>A	16.37:g.3656482C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	189	105	0.555556	NM_032444	Q69YT8|Q8TF15|Q96JP1	Silent	SNP	ENST00000294008.3	37	CCDS10506.2																																																																																			C|0.767;T|0.233	0.233	strong		0.507	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
DAGLA	747	hgsc.bcm.edu	37	11	61505168	61505168	+	Silent	SNP	G	G	A	rs198444	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61505168G>A	ENST00000257215.5	+	15	1640	c.1524G>A	c.(1522-1524)gcG>gcA	p.A508A		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	508					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		GTGAGGATGCGATGGAGTATT	0.622													G|||	2461	0.491414	0.3631	0.4986	5008	,	,		15387	0.7986		0.4284	False		,,,				2504	0.408				p.A508A		Atlas-SNP	.											DAGLA,NS,carcinoma,+1,1	DAGLA	109	1	0			c.G1524A						PASS	.	G		1586,2818	492.9+/-362.5	275,1036,891	160.0	131.0	141.0		1524	-3.4	1.0	11	dbSNP_79	141	3767,4831	535.2+/-382.8	819,2129,1351	no	coding-synonymous	DAGLA	NM_006133.2		1094,3165,2242	AA,AG,GG		43.8125,36.0127,41.1706		508/1043	61505168	5353,7649	2202	4299	6501	SO:0001819	synonymous_variant	747	exon15			GGATGCGATGGAG	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.1524G>A	11.37:g.61505168G>A		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	37	CCDS31578.1																																																																																			G|0.536;A|0.464	0.464	strong		0.622	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
PARP15	165631	hgsc.bcm.edu	37	3	122345870	122345870	+	Silent	SNP	C	C	T	rs17208928	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:122345870C>T	ENST00000464300.2	+	9	1494	c.1428C>T	c.(1426-1428)tcC>tcT	p.S476S	PARP15_ENST00000493645.1_Intron|PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000310366.4_Silent_p.S242S|PARP15_ENST00000483793.1_Intron	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	476					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		CCACATTCTCCATGACTACAT	0.348													C|||	417	0.0832668	0.0091	0.0922	5008	,	,		20261	0.0089		0.2177	False		,,,				2504	0.1155				p.S476S		Atlas-SNP	.											.	PARP15	115	.	0			c.C1428T						PASS	.	C	,	165,4241	106.9+/-145.3	5,155,2043	68.0	66.0	67.0		1428,726	1.8	0.0	3	dbSNP_123	67	1683,6917	308.0+/-308.7	166,1351,2783	no	coding-synonymous,coding-synonymous	PARP15	NM_001113523.1,NM_152615.1	,	171,1506,4826	TT,TC,CC		19.5698,3.7449,14.2088	,	476/679,242/445	122345870	1848,11158	2203	4300	6503	SO:0001819	synonymous_variant	165631	exon9			ATTCTCCATGACT	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1428C>T	3.37:g.122345870C>T		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	253	107	0.422925	NM_001113523	J3KR47|Q8N1K3	Silent	SNP	ENST00000464300.2	37	CCDS46893.1																																																																																			C|0.878;T|0.122	0.122	strong		0.348	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
HLA-C	3107	hgsc.bcm.edu	37	6	31238135	31238135	+	Silent	SNP	G	G	A	rs1050317	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238135G>A	ENST00000376228.5	-	4	761	c.747C>T	c.(745-747)acC>acT	p.T249T	HLA-C_ENST00000383329.3_Silent_p.T249T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	249	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CGGTGTCCTGGGTCTGGTCCT	0.622													A|||	3889	0.776558	0.8056	0.8112	5008	,	,		15060	0.8046		0.7197	False		,,,				2504	0.7423				p.T249T		Atlas-SNP	.											.	HLA-C	92	.	0			c.C747T						PASS	.						43.0	38.0	40.0					6																	31238135		2201	4293	6494	SO:0001819	synonymous_variant	3107	exon4			GTCCTGGGTCTGG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.747C>T	6.37:g.31238135G>A		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	102	99	0.970588	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1																																																																																			G|0.266;A|0.734	0.734	strong		0.622	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
FAM20A	54757	hgsc.bcm.edu	37	17	66539847	66539847	+	Silent	SNP	C	C	T	rs2286562	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:66539847C>T	ENST00000592554.1	-	5	1457	c.735G>A	c.(733-735)gaG>gaA	p.E245E	FAM20A_ENST00000226094.5_5'UTR|PRKAR1A_ENST00000588188.2_Intron|AC079210.1_ENST00000600820.1_Missense_Mutation_p.L36F	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	245					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)		p.E245E(1)		cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					CTGGTGTCTCCTCATCTCGCT	0.527													C|||	1172	0.234026	0.0764	0.3372	5008	,	,		20373	0.4534		0.1819	False		,,,				2504	0.2014				p.E245E		Atlas-SNP	.											FAM20A,NS,carcinoma,0,1	FAM20A	35	1	1	Substitution - coding silent(1)	stomach(1)	c.G735A						PASS	.	C		430,3976	208.5+/-229.5	15,400,1788	171.0	149.0	157.0		735	-4.4	1.0	17	dbSNP_100	157	1577,7023	294.0+/-301.7	140,1297,2863	no	coding-synonymous	FAM20A	NM_017565.3		155,1697,4651	TT,TC,CC		18.3372,9.7594,15.4313		245/542	66539847	2007,10999	2203	4300	6503	SO:0001819	synonymous_variant	54757	exon5			TGTCTCCTCATCT	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.735G>A	17.37:g.66539847C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	164	75	0.457317	NM_017565	B2RN47|B2RN49|Q9UF95	Silent	SNP	ENST00000592554.1	37	CCDS11679.1																																																																																			C|0.814;T|0.186	0.186	strong		0.527	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565	
ZNF366	167465	hgsc.bcm.edu	37	5	71756102	71756102	+	Silent	SNP	G	G	A	rs7721922	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:71756102G>A	ENST00000318442.5	-	2	1712	c.1222C>T	c.(1222-1224)Ctg>Ttg	p.L408L		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	408					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TGGTTCTGCAGCTGGCTCGGG	0.602													G|||	2642	0.527556	0.5008	0.4135	5008	,	,		18509	0.8621		0.335	False		,,,				2504	0.498				p.L408L		Atlas-SNP	.											ZNF366,NS,adenoma,0,1	ZNF366	108	1	0			c.C1222T						PASS	.	G		2249,2157	595.3+/-388.4	599,1051,553	130.0	100.0	110.0		1222	4.9	1.0	5	dbSNP_116	110	2813,5787	446.1+/-361.2	448,1917,1935	no	coding-synonymous	ZNF366	NM_152625.1		1047,2968,2488	AA,AG,GG		32.7093,48.956,38.9205		408/745	71756102	5062,7944	2203	4300	6503	SO:0001819	synonymous_variant	167465	exon2			TCTGCAGCTGGCT	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.1222C>T	5.37:g.71756102G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	253	133	0.525692	NM_152625	Q5HYI9|Q7RTV4	Silent	SNP	ENST00000318442.5	37	CCDS4015.1																																																																																			G|0.553;A|0.447	0.447	strong		0.602	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
NOX5	79400	hgsc.bcm.edu	37	15	69328226	69328226	+	Missense_Mutation	SNP	C	C	T	rs12907196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:69328226C>T	ENST00000388866.3	+	7	1179	c.1138C>T	c.(1138-1140)Ctc>Ttc	p.L380F	NOX5_ENST00000448182.3_Missense_Mutation_p.L334F|NOX5_ENST00000530406.2_Missense_Mutation_p.L352F|NOX5_ENST00000455873.3_Missense_Mutation_p.L345F|NOX5_ENST00000260364.5_Missense_Mutation_p.L362F|RP11-809H16.4_ENST00000559495.1_RNA	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	380	Ferric oxidoreductase.|Poly-Leu.			L -> F (in Ref. 2; BAB84884/BAB84897, 3; BAB15319/BAG37241, 6; EAW77830 and 7; AAI25098/AAI25099). {ECO:0000305}.	angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						GCTGCTCCTCCTCATGTTCAT	0.607													C|||	1358	0.271166	0.1135	0.33	5008	,	,		18072	0.124		0.5358	False		,,,				2504	0.3221				p.L380F		Atlas-SNP	.											.	NOX5	60	.	0			c.C1138T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU	756,3644	309.1+/-290.9	69,618,1513	130.0	105.0	113.0		1054,1033,1138	1.2	0.4	15	dbSNP_121	113	4772,3824	611.8+/-395.9	1312,2148,838	yes	missense,missense,missense	NOX5	NM_001184779.1,NM_001184780.1,NM_024505.3	22,22,22	1381,2766,2351	TT,TC,CC		44.4858,17.1818,42.5362	possibly-damaging,possibly-damaging,possibly-damaging	352/738,345/731,380/766	69328226	5528,7468	2200	4298	6498	SO:0001583	missense	79400	exon7			CTCCTCCTCATGT	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"""EF-hand domain containing"""	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.1138C>T	15.37:g.69328226C>T	ENSP00000373518:p.Leu380Phe	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	108	62	0.574074	NM_024505	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Missense_Mutation	SNP	ENST00000388866.3	37	CCDS32276.2	673	0.30815018315018317	54	0.10975609756097561	128	0.35359116022099446	79	0.1381118881118881	412	0.5435356200527705	C	14.65	2.599053	0.46318	0.171818	0.555142	ENSG00000255346	ENST00000455873;ENST00000448182;ENST00000388866;ENST00000530406	D;D;D	0.92965	-3.14;-3.14;-3.14	3.38	1.18	0.20946	Flavoprotein transmembrane component (1);	0.376029	0.24347	N	0.039319	T	0.00012	0.0000	M	0.69248	2.105	0.24350	P	0.99492859	B;D;P	0.56287	0.303;0.975;0.886	B;P;P	0.56088	0.158;0.791;0.598	T	0.22312	-1.0220	9	0.45353	T	0.12	-12.2301	6.6006	0.22699	0.1777:0.5554:0.2669:0.0	rs12907196;rs35425174;rs60520952;rs12907196	345;380;352	Q96PH1-6;Q96PH1;Q96PH1-3	.;NOX5_HUMAN;.	F	345;362;380;352	ENSP00000416828:L345F;ENSP00000373518:L380F;ENSP00000432440:L352F	ENSP00000373518:L380F	L	+	1	0	NOX5	67115280	0.609000	0.26975	0.434000	0.26772	0.448000	0.32197	0.984000	0.29565	1.433000	0.47394	0.313000	0.20887	CTC	C|0.650;T|0.350	0.350	strong		0.607	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505	
ACAD9	28976	hgsc.bcm.edu	37	3	128614185	128614185	+	Silent	SNP	A	A	C	rs1680778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:128614185A>C	ENST00000308982.7	+	4	460	c.379A>C	c.(379-381)Aga>Cga	p.R127R		NM_014049.4	NP_054768.2	Q9H845	ACAD9_HUMAN	acyl-CoA dehydrogenase family, member 9	127						dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	30						CATGTACTCAAGACTAGGGGA	0.552													C|||	2721	0.543331	0.851	0.428	5008	,	,		19128	0.623		0.2932	False		,,,				2504	0.3845				p.R127R		Atlas-SNP	.											.	ACAD9	51	.	0			c.A379C						PASS	.	C		3267,1139	401.0+/-331.8	1218,831,154	107.0	88.0	94.0		379	5.5	0.0	3	dbSNP_89	94	2589,6011	683.9+/-403.9	399,1791,2110	no	coding-synonymous	ACAD9	NM_014049.4		1617,2622,2264	CC,CA,AA		30.1047,25.8511,45.0254		127/622	128614185	5856,7150	2203	4300	6503	SO:0001819	synonymous_variant	28976	exon4			TACTCAAGACTAG	AF078854	CCDS3053.1	3q21.3	2013-05-24	2010-04-30		ENSG00000177646	ENSG00000177646		"""Mitochondrial respiratory chain complex assembly factors"""	21497	protein-coding gene	gene with protein product		611103	"""acyl-Coenzyme A dehydrogenase family, member 9"""			12359260, 21057504, 20816094	Standard	NM_014049		Approved	NPD002, MGC14452	uc003ela.4	Q9H845	OTTHUMG00000159942	ENST00000308982.7:c.379A>C	3.37:g.128614185A>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	182	96	0.527473	NM_014049	D3DNB8|Q8WXX3	Silent	SNP	ENST00000308982.7	37	CCDS3053.1																																																																																			A|0.502;C|0.498	0.498	strong		0.552	ACAD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358405.1	NM_014049	
ATHL1	80162	hgsc.bcm.edu	37	11	290918	290918	+	Silent	SNP	G	G	A	rs72636978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:290918G>A	ENST00000409548.2	+	4	826	c.711G>A	c.(709-711)caG>caA	p.Q237Q	RP11-326C3.2_ENST00000525217.1_RNA|ATHL1_ENST00000409479.1_Silent_p.Q237Q|ATHL1_ENST00000409655.1_Silent_p.Q60Q|RP11-326C3.2_ENST00000534742.1_RNA|RP11-326C3.2_ENST00000533924.1_RNA	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	237					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		CCTGGGCCCAGCTCTGGGTAG	0.692													A|||	906	0.180911	0.1543	0.2219	5008	,	,		18156	0.3056		0.0586	False		,,,				2504	0.1851				p.Q237Q		Atlas-SNP	.											.	ATHL1	88	.	0			c.G711A						PASS	.	A		607,3799	756.2+/-412.6	36,535,1632	45.0	50.0	48.0		711	1.6	1.0	11	dbSNP_130	48	479,8121	790.2+/-407.6	13,453,3834	no	coding-synonymous	ATHL1	NM_025092.4		49,988,5466	AA,AG,GG		5.5698,13.7767,8.35		237/738	290918	1086,11920	2203	4300	6503	SO:0001819	synonymous_variant	80162	exon4			GGCCCAGCTCTGG	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.711G>A	11.37:g.290918G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	205	112	0.546341	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																			G|0.895;A|0.105	0.105	strong		0.692	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
NRAP	4892	hgsc.bcm.edu	37	10	115411598	115411598	+	Silent	SNP	C	C	A	rs4918861	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:115411598C>A	ENST00000359988.3	-	7	883	c.639G>T	c.(637-639)ctG>ctT	p.L213L	NRAP_ENST00000369360.3_Silent_p.L213L|NRAP_ENST00000369358.4_Silent_p.L213L|NRAP_ENST00000360478.3_Silent_p.L213L	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TGCTCCGTAGCAGCTCAGGAG	0.522													C|||	1325	0.264577	0.3306	0.2248	5008	,	,		20859	0.2163		0.2684	False		,,,				2504	0.2495				p.L213L		Atlas-SNP	.											.	NRAP	208	.	0			c.G639T						PASS	.	C	,	1511,2895	482.8+/-359.5	263,985,955	105.0	81.0	89.0		639,639	2.9	1.0	10	dbSNP_111	89	2389,6211	397.4+/-345.7	335,1719,2246	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	598,2704,3201	AA,AC,CC		27.7791,34.2941,29.9862	,	213/1696,213/1731	115411598	3900,9106	2203	4300	6503	SO:0001819	synonymous_variant	4892	exon7			CCGTAGCAGCTCA		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.639G>T	10.37:g.115411598C>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			C|0.712;A|0.288	0.288	strong		0.522	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
CPAMD8	27151	hgsc.bcm.edu	37	19	17108136	17108136	+	Missense_Mutation	SNP	G	G	A	rs61744196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17108136G>A	ENST00000443236.1	-	11	1052	c.1021C>T	c.(1021-1023)Cgg>Tgg	p.R341W	CPAMD8_ENST00000388925.4_Missense_Mutation_p.R294W	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	294						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						TCGAAGTCCCGGGAGCCGAGG	0.602													g|||	99	0.0197684	0.0023	0.036	5008	,	,		19204	0.0		0.0457	False		,,,				2504	0.0256				p.R341W		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C1021T						PASS	.	G	TRP/ARG	23,4013		0,23,1995	12.0	15.0	14.0		1021	1.7	0.9	19	dbSNP_129	14	322,8026		6,310,3858	yes	missense	CPAMD8	NM_015692.2	101	6,333,5853	AA,AG,GG		3.8572,0.5699,2.7859	probably-damaging	341/1933	17108136	345,12039	2018	4174	6192	SO:0001583	missense	27151	exon11			AGTCCCGGGAGCC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1021C>T	19.37:g.17108136G>A	ENSP00000402505:p.Arg341Trp	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	134	56	0.41791	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	50	0.022893772893772892	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	38	0.05013192612137203	g	12.88	2.070194	0.36566	0.005699	0.038572	ENSG00000160111	ENST00000291440;ENST00000388925	T;T	0.53206	0.63;0.65	3.0	1.71	0.24356	.	0.186387	0.32488	U	0.006027	T	0.02848	0.0085	N	0.08118	0	0.23758	N	0.996929	P	0.41498	0.752	B	0.20955	0.032	T	0.15723	-1.0427	10	0.72032	D	0.01	.	9.7544	0.40494	0.0:0.6086:0.3914:0.0	.	294	Q8IZJ3	CPMD8_HUMAN	W	341;294	ENSP00000291440:R341W;ENSP00000373577:R294W	ENSP00000291440:R341W	R	-	1	2	CPAMD8	16969136	1.000000	0.71417	0.943000	0.38184	0.758000	0.43043	4.855000	0.62925	1.423000	0.47198	0.555000	0.69702	CGG	G|0.969;A|0.031	0.031	strong		0.602	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209815	84209815	+	Missense_Mutation	SNP	C	C	G	rs2288021	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84209815C>G	ENST00000378553.5	+	11	2099	c.1975C>G	c.(1975-1977)Cta>Gta	p.L659V	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	659			L -> P (in dbSNP:rs2288022). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.|L -> V (in dbSNP:rs2288021).		axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						CTCTGGCCAGCTACTGATGCC	0.557													C|||	658	0.13139	0.0068	0.2406	5008	,	,		16998	0.0972		0.2078	False		,,,				2504	0.1789				p.L659V		Atlas-SNP	.											.	DNAAF1	81	.	0			c.C1975G						PASS	.	C	VAL/LEU	192,4208	119.2+/-156.9	6,180,2014	35.0	33.0	34.0		1975	0.3	0.0	16	dbSNP_100	34	1878,6722	329.9+/-319.0	234,1410,2656	yes	missense	DNAAF1	NM_178452.4	32	240,1590,4670	GG,GC,CC		21.8372,4.3636,15.9231	benign	659/726	84209815	2070,10930	2200	4300	6500	SO:0001583	missense	123872	exon11			GGCCAGCTACTGA	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1975C>G	16.37:g.84209815C>G	ENSP00000367815:p.Leu659Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	305	0.13965201465201466	5	0.01016260162601626	94	0.2596685082872928	50	0.08741258741258741	156	0.20580474934036938	C	9.473	1.096043	0.20552	0.043636	0.218372	ENSG00000154099	ENST00000378553	T	0.24350	1.86	4.67	0.294	0.15747	.	1.269100	0.05886	N	0.627428	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B;B	0.15473	0.013;0.013	B;B	0.21917	0.025;0.037	T	0.41270	-0.9518	9	0.40728	T	0.16	1.8768	2.8722	0.05620	0.1997:0.4697:0.0:0.3306	rs2288021	423;659	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	V	659	ENSP00000367815:L659V	ENSP00000367815:L659V	L	+	1	2	DNAAF1	82767316	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.449000	0.06812	0.214000	0.20742	-0.360000	0.07572	CTA	C|0.848;G|0.152	0.152	strong		0.557	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
ASB5	140458	hgsc.bcm.edu	37	4	177138061	177138061	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:177138061G>T	ENST00000296525.3	-	6	883	c.770C>A	c.(769-771)gCa>gAa	p.A257E	ASB5_ENST00000512254.1_Missense_Mutation_p.A204E	NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	257					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.A257E(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		ATTGATATCTGCTCCAAATTC	0.408																																					p.A257E		Atlas-SNP	.											ASB5,NS,carcinoma,0,1	ASB5	88	1	1	Substitution - Missense(1)	lung(1)	c.C770A						scavenged	.						201.0	189.0	193.0					4																	177138061		2203	4300	6503	SO:0001583	missense	140458	exon6			ATATCTGCTCCAA	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"""Ankyrin repeat domain containing"""	17180	protein-coding gene	gene with protein product		615050	"""ankyrin repeat and SOCS box-containing 5"""				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.770C>A	4.37:g.177138061G>T	ENSP00000296525:p.Ala257Glu	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	225	4	0.0177778	NM_080874	Q8N7B5	Missense_Mutation	SNP	ENST00000296525.3	37	CCDS3827.1	.	.	.	.	.	.	.	.	.	.	G	32	5.125222	0.94429	.	.	ENSG00000164122	ENST00000296525;ENST00000512254	T;T	0.80994	-0.01;-1.44	5.45	5.45	0.79879	Ankyrin repeat-containing domain (4);	0.048013	0.85682	D	0.000000	D	0.93012	0.7776	H	0.94964	3.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.94409	0.7630	10	0.87932	D	0	-25.6897	19.6512	0.95812	0.0:0.0:1.0:0.0	.	257;204	Q8WWX0;Q8N7B5	ASB5_HUMAN;.	E	257;204	ENSP00000296525:A257E;ENSP00000422877:A204E	ENSP00000296525:A257E	A	-	2	0	ASB5	177375055	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.016000	0.93645	2.712000	0.92718	0.591000	0.81541	GCA	.	.	none		0.408	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1		
KL	9365	hgsc.bcm.edu	37	13	33634983	33634983	+	Silent	SNP	C	C	T	rs564481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:33634983C>T	ENST00000380099.3	+	4	1775	c.1767C>T	c.(1765-1767)caC>caT	p.H589H	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	589	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		AGGAAATGCACGTTACACATT	0.517													C|||	1248	0.249201	0.0401	0.5086	5008	,	,		22365	0.1637		0.3618	False		,,,				2504	0.32				p.H589H		Atlas-SNP	.											.	KL	106	.	0			c.C1767T						PASS	.	C		434,3972	208.5+/-229.5	25,384,1794	168.0	142.0	151.0		1767	-3.8	0.0	13	dbSNP_83	151	3520,5080	512.8+/-378.0	748,2024,1528	no	coding-synonymous	KL	NM_004795.3		773,2408,3322	TT,TC,CC		40.9302,9.8502,30.4014		589/1013	33634983	3954,9052	2203	4300	6503	SO:0001819	synonymous_variant	9365	exon4			AATGCACGTTACA	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1767C>T	13.37:g.33634983C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	37	CCDS9347.1																																																																																			C|0.704;T|0.296	0.296	strong		0.517	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13719022	13719022	+	Silent	SNP	T	T	G	rs30169	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13719022T>G	ENST00000265104.4	-	72	12572	c.12468A>C	c.(12466-12468)ggA>ggC	p.G4156G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4156	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTGCCCGGAGTCCTTGTGGAG	0.428									Kartagener syndrome				G|||	2099	0.419129	0.3858	0.4107	5008	,	,		17429	0.4405		0.3966	False		,,,				2504	0.4714				p.G4156G		Atlas-SNP	.											DNAH5,head_neck,malignant_melanoma,-2,1	DNAH5	868	1	0			c.A12468C						PASS	.	G		1713,2693	650.7+/-399.1	358,997,848	118.0	119.0	118.0		12468	2.8	1.0	5	dbSNP_76	118	3649,4951	623.3+/-397.4	759,2131,1410	no	coding-synonymous	DNAH5	NM_001369.2		1117,3128,2258	GG,GT,TT		42.4302,38.8788,41.2271		4156/4625	13719022	5362,7644	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon72	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCGGAGTCCTTGT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12468A>C	5.37:g.13719022T>G		Somatic	224	2	0.00892857		WXS	Illumina HiSeq	Phase_I	239	238	0.995816	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.596;G|0.404	0.404	strong		0.428	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
MGAM	8972	hgsc.bcm.edu	37	7	141796215	141796215	+	Splice_Site	SNP	T	T	C	rs199885850		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:141796215T>C	ENST00000549489.2	+	42	5099	c.5004T>C	c.(5002-5004)cgT>cgC	p.R1668R	MGAM_ENST00000475668.2_Splice_Site_p.R2564R	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1668	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.R1668R(2)|p.R2565R(1)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCCTGGAGCGTGTGAGTATGG	0.582																																					p.R1668R		Atlas-SNP	.											MGAM_ENST00000549489,NS,carcinoma,+2,6	MGAM	767	6	3	Substitution - coding silent(3)	prostate(3)	c.T5004C						scavenged	.						88.0	83.0	85.0					7																	141796215		1950	4132	6082	SO:0001630	splice_region_variant	8972	exon42			GGAGCGTGTGAGT	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.5004+1T>C	7.37:g.141796215T>C		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	295	8	0.0271186	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			.	.	weak		0.582	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		Silent
ZNF333	84449	hgsc.bcm.edu	37	19	14829749	14829749	+	Missense_Mutation	SNP	C	C	T	rs3764626	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14829749C>T	ENST00000292530.6	+	12	1701	c.1610C>T	c.(1609-1611)gCg>gTg	p.A537V	ZNF333_ENST00000536363.1_Missense_Mutation_p.A428V|ZNF333_ENST00000540689.2_Intron	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	537			A -> V (in dbSNP:rs3764626).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						TATGAGTGCGCGACTTGCGGT	0.532													G|||	2410	0.48123	0.438	0.4914	5008	,	,		22164	0.619		0.3022	False		,,,				2504	0.5746				p.A537V	NSCLC(60;75 1281 16985 25154 29885)	Atlas-SNP	.											.	ZNF333	76	.	0			c.C1610T						PASS	.	G	VAL/ALA	1769,2637		362,1045,796	103.0	81.0	89.0		1610	0.3	0.0	19	dbSNP_107	89	2553,6047		394,1765,2141	yes	missense	ZNF333	NM_032433.2	64	756,2810,2937	TT,TC,CC		29.686,40.1498,33.2308	possibly-damaging	537/666	14829749	4322,8684	2203	4300	6503	SO:0001583	missense	84449	exon12			AGTGCGCGACTTG		CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"""Zinc fingers, C2H2-type"", ""-"""	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.1610C>T	19.37:g.14829749C>T	ENSP00000292530:p.Ala537Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	99	53	0.535354	NM_032433	Q6P2E6|Q86WS6|Q8TDL0	Missense_Mutation	SNP	ENST00000292530.6	37	CCDS12316.1	944	0.43223443223443225	212	0.43089430894308944	149	0.4116022099447514	338	0.5909090909090909	245	0.3232189973614776	G	16.10	3.028610	0.54790	0.401498	0.29686	ENSG00000160961	ENST00000536363;ENST00000292530	T;T	0.07688	3.17;3.17	2.54	0.305	0.15801	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.20401	0.57	0.80722	P	0.0	B	0.32507	0.373	B	0.26094	0.066	T	0.16988	-1.0384	8	0.36615	T	0.2	.	12.1716	0.54161	0.0:0.5749:0.4251:0.0	rs3764626;rs59099264;rs3764626	537	Q96JL9	ZN333_HUMAN	V	428;537	ENSP00000439749:A428V;ENSP00000292530:A537V	ENSP00000292530:A537V	A	+	2	0	ZNF333	14690749	0.000000	0.05858	0.000000	0.03702	0.889000	0.51656	-0.446000	0.06837	-0.096000	0.12329	-0.120000	0.15030	GCG	C|0.613;T|0.387	0.387	strong		0.532	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433	
FCGBP	8857	hgsc.bcm.edu	37	19	40364280	40364280	+	Missense_Mutation	SNP	G	G	A	rs113103150	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40364280G>A	ENST00000221347.6	-	31	14369	c.14362C>T	c.(14362-14364)Ccc>Tcc	p.P4788S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4788	TIL 11.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TGGCCCACGGGTACGCAGGTG	0.662													G|||	58	0.0115815	0.0008	0.0216	5008	,	,		18350	0.0		0.0408	False		,,,				2504	0.001				p.P4788S		Atlas-SNP	.											.	FCGBP	416	.	0			c.C14362T						PASS	.	G	SER/PRO	31,4375	36.0+/-67.5	0,31,2172	57.0	54.0	55.0		14362	4.1	0.7	19	dbSNP_132	55	321,8279	110.2+/-170.6	8,305,3987	yes	missense	FCGBP	NM_003890.2	74	8,336,6159	AA,AG,GG		3.7326,0.7036,2.7064	probably-damaging	4788/5406	40364280	352,12654	2203	4300	6503	SO:0001583	missense	8857	exon31			CCACGGGTACGCA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.14362C>T	19.37:g.40364280G>A	ENSP00000221347:p.Pro4788Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	164	82	0.5	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	40	0.018315018315018316	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	30	0.0395778364116095	G	13.59	2.281674	0.40394	0.007036	0.037326	ENSG00000090920	ENST00000221347	D	0.91577	-2.87	5.14	4.09	0.47781	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	0.000000	0.64402	U	0.000001	D	0.82518	0.5054	M	0.75777	2.31	0.40992	D	0.98486	D	0.61697	0.99	D	0.69824	0.966	D	0.84949	0.0870	10	0.31617	T	0.26	.	12.3322	0.55046	0.0842:0.0:0.9158:0.0	.	4788	Q9Y6R7	FCGBP_HUMAN	S	4788	ENSP00000221347:P4788S	ENSP00000221347:P4788S	P	-	1	0	FCGBP	45056120	1.000000	0.71417	0.718000	0.30602	0.055000	0.15305	2.964000	0.49192	2.567000	0.86603	0.313000	0.20887	CCC	G|0.977;A|0.023	0.023	strong		0.662	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
NKAPL	222698	hgsc.bcm.edu	37	6	28227436	28227436	+	Missense_Mutation	SNP	A	A	G	rs12000	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28227436A>G	ENST00000343684.3	+	1	339	c.287A>G	c.(286-288)tAc>tGc	p.Y96C	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	96			Y -> C (in dbSNP:rs12000). {ECO:0000269|PubMed:15489334}.							breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						GGATATCGCTACCATCGTCAC	0.572													A|||	2217	0.442692	0.6959	0.353	5008	,	,		19456	0.4444		0.2167	False		,,,				2504	0.3947				p.Y96C		Atlas-SNP	.											.	NKAPL	72	.	0			c.A287G						PASS	.	A	CYS/TYR	2555,1851	634.6+/-396.2	755,1045,403	61.0	61.0	61.0		287	1.9	0.0	6	dbSNP_52	61	1757,6843	317.8+/-313.4	171,1415,2714	yes	missense	NKAPL	NM_001007531.1	194	926,2460,3117	GG,GA,AA		20.4302,42.0109,33.1539	benign	96/403	28227436	4312,8694	2203	4300	6503	SO:0001583	missense	222698	exon1			ATCGCTACCATCG	BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 194"""	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.287A>G	6.37:g.28227436A>G	ENSP00000345716:p.Tyr96Cys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_001007531	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	883	0.4043040293040293	350	0.7113821138211383	135	0.3729281767955801	248	0.43356643356643354	150	0.19788918205804748	A	10.43	1.347619	0.24426	0.579891	0.204302	ENSG00000189134	ENST00000343684	T	0.14516	2.5	4.31	1.87	0.25490	.	0.882652	0.09597	N	0.780706	T	0.02494	0.0076	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.43734	-0.9373	9	0.39692	T	0.17	-1.0519	3.6366	0.08151	0.7037:0.0:0.1045:0.1918	rs12000;rs1133598;rs1679733;rs3195472;rs3734565;rs52814218;rs56901220;rs12000	96	Q5M9Q1	NKAPL_HUMAN	C	96	ENSP00000345716:Y96C	ENSP00000345716:Y96C	Y	+	2	0	NKAPL	28335415	0.000000	0.05858	0.004000	0.12327	0.022000	0.10575	-0.091000	0.11146	0.302000	0.22762	0.533000	0.62120	TAC	A|0.613;G|0.387	0.387	strong		0.572	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1		
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919302	51919302	+	Missense_Mutation	SNP	T	T	C	rs201376644	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51919302T>C	ENST00000339313.5	-	5	990	c.874A>G	c.(874-876)Aac>Gac	p.N292D	SIGLEC10_ENST00000432469.2_Missense_Mutation_p.N209D|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.N234D|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.N292D|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.N234D|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.N244D|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.N292D|SIGLEC10_ENST00000525998.1_Intron|CTD-2616J11.2_ENST00000526996.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	292	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		AGGACTCTGTTCTGCAGGACC	0.652																																					p.N292D		Atlas-SNP	.											SIGLEC12_ENST00000439889,rectum,carcinoma,0,2	SIGLEC10	112	2	0			c.A874G						PASS	.						19.0	24.0	22.0					19																	51919302		2201	4299	6500	SO:0001583	missense	89790	exon5			CTCTGTTCTGCAG	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.874A>G	19.37:g.51919302T>C	ENSP00000345243:p.Asn292Asp	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	108	17	0.157407	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	7.755	0.704152	0.15172	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;T;T;T;T;T;T	0.40476	1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.03	4.37	1.07	0.20283	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.427133	0.19965	N	0.102128	T	0.13841	0.0335	N	0.02854	-0.475	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001	T	0.33701	-0.9858	10	0.02654	T	1	.	7.7519	0.28903	0.0:0.684:0.0:0.316	.	244;292;292;234;234;292	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	D	292;209;292;234;234;244;292;106	ENSP00000342389:N292D;ENSP00000396742:N209D;ENSP00000348646:N292D;ENSP00000408387:N234D;ENSP00000389132:N234D;ENSP00000414324:N244D;ENSP00000345243:N292D;ENSP00000435281:N106D	ENSP00000345243:N292D	N	-	1	0	SIGLEC10	56611114	0.000000	0.05858	0.002000	0.10522	0.047000	0.14425	0.182000	0.16900	-0.072000	0.12864	-1.945000	0.00491	AAC	T|0.998;C|0.002	0.002	strong		0.652	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
SPAG17	200162	hgsc.bcm.edu	37	1	118644524	118644524	+	Missense_Mutation	SNP	T	T	A	rs17185492	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:118644524T>A	ENST00000336338.5	-	5	538	c.473A>T	c.(472-474)gAa>gTa	p.E158V		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	158	Lys-rich.		E -> V (in dbSNP:rs17185492).			cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TTTATCCTTTTCTAACTTAGG	0.428													T|||	580	0.115815	0.0212	0.147	5008	,	,		20034	0.1329		0.2078	False		,,,				2504	0.1094				p.E158V		Atlas-SNP	.											SPAG17,NS,adenoma,0,1	SPAG17	263	1	0			c.A473T						scavenged	.	T	VAL/GLU	219,4187	132.5+/-169.0	7,205,1991	130.0	126.0	128.0		473	5.4	0.9	1	dbSNP_123	128	1714,6886	308.9+/-309.1	172,1370,2758	yes	missense	SPAG17	NM_206996.2	121	179,1575,4749	AA,AT,TT		19.9302,4.9705,14.8624	probably-damaging	158/2224	118644524	1933,11073	2203	4300	6503	SO:0001583	missense	200162	exon5			TCCTTTTCTAACT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.473A>T	1.37:g.118644524T>A	ENSP00000337804:p.Glu158Val	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	150	56	0.373333	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	300	0.13736263736263737	7	0.014227642276422764	60	0.16574585635359115	70	0.12237762237762238	163	0.21503957783641162	T	18.97	3.734811	0.69189	0.049705	0.199302	ENSG00000155761	ENST00000336338	T	0.62788	-0.0	5.39	5.39	0.77823	.	0.060022	0.64402	D	0.000005	T	0.71762	0.3378	M	0.72118	2.19	0.33071	P	0.46462800000000004	D	0.89917	1.0	D	0.87578	0.998	T	0.77378	-0.2610	9	0.72032	D	0.01	.	13.0669	0.59038	0.0:0.0:0.0:1.0	rs17185492;rs52810700;rs17185492	158	Q6Q759	SPG17_HUMAN	V	158	ENSP00000337804:E158V	ENSP00000337804:E158V	E	-	2	0	SPAG17	118446047	1.000000	0.71417	0.946000	0.38457	0.628000	0.37860	3.050000	0.49877	2.168000	0.68352	0.533000	0.62120	GAA	T|0.860;A|0.140	0.140	strong		0.428	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240729	39240729	+	Missense_Mutation	SNP	A	A	G	rs200532954	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240729A>G	ENST00000391417.4	+	1	271	c.271A>G	c.(271-273)Atg>Gtg	p.M91V		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	116	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						cagctgctgtatgtccagctg	0.677													g|||	366	0.0730831	0.0272	0.0663	5008	,	,		17277	0.1012		0.1431	False		,,,				2504	0.0389				p.M91V		Atlas-SNP	.											KRTAP4-9_ENST00000377734,bladder,carcinoma,0,4	KRTAP4-7	49	4	0			c.A271G						scavenged	.						11.0	17.0	15.0					17																	39240729		684	1582	2266	SO:0001583	missense	100132476	exon1			TGCTGTATGTCCA	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.271A>G	17.37:g.39240729A>G	ENSP00000375236:p.Met91Val	Somatic	38	3	0.0789474		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.030	-1.342089	0.01277	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00567	6.54	3.74	-2.07	0.07276	.	5.393590	0.01146	N	0.006314	T	0.00300	0.0009	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46679	-0.9174	9	0.05959	T	0.93	.	9.7653	0.40557	0.3807:0.0:0.6193:0.0	.	91	Q9BYR0	KRA47_HUMAN	V	91;82	ENSP00000375236:M91V	ENSP00000375236:M91V	M	+	1	0	KRTAP4-9;KRTAP4-7	36494255	0.000000	0.05858	0.006000	0.13384	0.872000	0.50106	-4.081000	0.00299	-0.949000	0.03663	-0.374000	0.07098	ATG	.	.	weak		0.677	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
ZNF470	388566	hgsc.bcm.edu	37	19	57085769	57085769	+	Missense_Mutation	SNP	G	G	C	rs10421285	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57085769G>C	ENST00000330619.8	+	4	753	c.67G>C	c.(67-69)Gtg>Ctg	p.V23L	ZNF470_ENST00000391709.3_Missense_Mutation_p.V23L|ZNF470_ENST00000601902.1_Missense_Mutation_p.V23L	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	23	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> L (in dbSNP:rs10421285). {ECO:0000269|PubMed:15302581}.		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)	p.V23L(1)		endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		TTAGGGTTCAGTGACTTTCAC	0.403													G|||	2123	0.423922	0.6657	0.3357	5008	,	,		20025	0.2788		0.3698	False		,,,				2504	0.365				p.V23L		Atlas-SNP	.											ZNF470,NS,carcinoma,0,1	ZNF470	103	1	1	Substitution - Missense(1)	stomach(1)	c.G67C						PASS	.	G	LEU/VAL	2705,1701	652.9+/-399.5	827,1051,325	182.0	166.0	171.0		67	-3.1	0.0	19	dbSNP_119	171	3139,5461	478.2+/-369.8	605,1929,1766	yes	missense	ZNF470	NM_001001668.3	32	1432,2980,2091	CC,CG,GG		36.5,38.6064,44.9331	benign	23/718	57085769	5844,7162	2203	4300	6503	SO:0001583	missense	388566	exon4			GGTTCAGTGACTT	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"""Zinc fingers, C2H2-type"", ""-"""	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.67G>C	19.37:g.57085769G>C	ENSP00000333223:p.Val23Leu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	144	68	0.472222	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	37	CCDS33122.1	867	0.39697802197802196	317	0.6443089430894309	127	0.35082872928176795	147	0.256993006993007	276	0.3641160949868074	G	7.600	0.672565	0.14776	0.613936	0.365	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.04862	3.54;3.54	3.58	-3.06	0.05379	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	L	0.53671	1.685	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.31364	-0.9946	8	0.21540	T	0.41	.	4.4059	0.11409	0.4026:0.3162:0.2812:0.0	rs10421285;rs56621387;rs10421285	23	Q6ECI4	ZN470_HUMAN	L	23	ENSP00000375590:V23L;ENSP00000333223:V23L	ENSP00000333223:V23L	V	+	1	0	ZNF470	61777581	0.661000	0.27430	0.034000	0.17996	0.830000	0.47004	0.740000	0.26188	-0.621000	0.05633	-0.182000	0.12963	GTG	G|0.566;C|0.434	0.434	strong		0.403	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668	
SLC25A22	79751	hgsc.bcm.edu	37	11	793588	793588	+	Silent	SNP	G	G	A	rs80335370	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:793588G>A	ENST00000320230.5	-	5	715	c.234C>T	c.(232-234)ccC>ccT	p.P78P	SLC25A22_ENST00000531214.1_Silent_p.P78P	NM_001191061.1|NM_024698.5	NP_001177990.1|NP_078974.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22	78					L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGCCTTCTCGGGGGTGACGA	0.632													g|||	334	0.0666933	0.0318	0.0648	5008	,	,		18508	0.0456		0.1183	False		,,,				2504	0.0838				p.P78P	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											SLC25A22,NS,carcinoma,0,1	SLC25A22	19	1	0			c.C234T						PASS	.	A	,,	176,4230	113.8+/-151.8	2,172,2029	85.0	71.0	76.0		234,234,234	-6.9	0.7	11	dbSNP_132	76	1051,7547	222.7+/-259.7	60,931,3308	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC25A22	NM_001191060.1,NM_001191061.1,NM_024698.5	,,	62,1103,5337	AA,AG,GG		12.2238,3.9946,9.4356	,,	78/324,78/324,78/324	793588	1227,11777	2203	4299	6502	SO:0001819	synonymous_variant	79751	exon5			CTTCTCGGGGGTG	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310	ENST00000320230.5:c.234C>T	11.37:g.793588G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_001191061	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Silent	SNP	ENST00000320230.5	37	CCDS7715.1																																																																																			G|0.918;A|0.082	0.082	strong		0.632	SLC25A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257107.2		
VAV2	7410	hgsc.bcm.edu	37	9	136643994	136643994	+	Missense_Mutation	SNP	T	T	C	rs602990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:136643994T>C	ENST00000371850.3	-	22	1811	c.1780A>G	c.(1780-1782)Atg>Gtg	p.M594V	VAV2_ENST00000406606.3_Missense_Mutation_p.M584V|VAV2_ENST00000371851.1_Missense_Mutation_p.M584V	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	594	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.		M -> V (in dbSNP:rs602990). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7762982}.		angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.M584V(1)		breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		TAATTCTGCATGGCCACCATC	0.632													C|||	2480	0.495208	0.8404	0.4798	5008	,	,		15534	0.0645		0.5189	False		,,,				2504	0.4591				p.M594V		Atlas-SNP	.											VAV2,NS,carcinoma,0,1	VAV2	165	1	1	Substitution - Missense(1)	stomach(1)	c.A1780G						scavenged	.	C	VAL/MET,VAL/MET	3543,863	334.9+/-303.7	1426,691,86	61.0	56.0	58.0		1780,1750	1.9	0.3	9	dbSNP_83	58	4549,4051	556.6+/-386.9	1186,2177,937	yes	missense,missense	VAV2	NM_001134398.1,NM_003371.3	21,21	2612,2868,1023	CC,CT,TT		47.1047,19.5869,37.7826	benign,benign	594/879,584/840	136643994	8092,4914	2203	4300	6503	SO:0001583	missense	7410	exon22			TCTGCATGGCCAC		CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12658	protein-coding gene	gene with protein product		600428	"""vav 2 oncogene"""			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.1780A>G	9.37:g.136643994T>C	ENSP00000360916:p.Met594Val	Somatic	58	1	0.0172414		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001134398	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Missense_Mutation	SNP	ENST00000371850.3	37	CCDS48053.1	1007	0.4610805860805861	413	0.8394308943089431	175	0.48342541436464087	18	0.03146853146853147	401	0.5290237467018469	C	0.795	-0.757601	0.03019	0.804131	0.528953	ENSG00000160293	ENST00000371850;ENST00000371851;ENST00000406606;ENST00000325440	T;T;T	0.06068	3.35;3.35;3.35	4.8	1.91	0.25777	Src homology-3 domain (3);Variant SH3 (1);	0.290997	0.33075	N	0.005314	T	0.00012	0.0000	N	0.02539	-0.55	0.54753	P	1.799999999996249E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.19128	-1.0315	9	0.08179	T	0.78	.	13.6487	0.62297	0.0:0.8398:0.0:0.1602	rs602990;rs61232391;rs602990	584;594;584	P52735-2;P52735;P52735-3	.;VAV2_HUMAN;.	V	594;584;584;584	ENSP00000360916:M594V;ENSP00000360917:M584V;ENSP00000385362:M584V	ENSP00000317258:M584V	M	-	1	0	VAV2	135633815	0.339000	0.24784	0.298000	0.25002	0.741000	0.42261	0.920000	0.28705	0.116000	0.18110	-2.599000	0.00162	ATG	T|0.441;C|0.559	0.559	strong		0.632	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1		
FAT2	2196	hgsc.bcm.edu	37	5	150946132	150946132	+	Silent	SNP	G	G	A	rs3734059	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150946132G>A	ENST00000261800.5	-	1	2373	c.2361C>T	c.(2359-2361)atC>atT	p.I787I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	787	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTACATTGAGGATGTAGAAAT	0.502													G|||	2101	0.419529	0.441	0.4539	5008	,	,		21698	0.3562		0.4901	False		,,,				2504	0.3589				p.I787I		Atlas-SNP	.											.	FAT2	465	.	0			c.C2361T						PASS	.	G		1960,2446	554.6+/-379.1	423,1114,666	74.0	71.0	72.0		2361	3.0	1.0	5	dbSNP_107	72	4497,4103	592.2+/-392.9	1182,2133,985	no	coding-synonymous	FAT2	NM_001447.2		1605,3247,1651	AA,AG,GG		47.7093,44.4848,49.6463		787/4350	150946132	6457,6549	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			ATTGAGGATGTAG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2361C>T	5.37:g.150946132G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.527;A|0.473	0.473	strong		0.502	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
TRPM3	80036	hgsc.bcm.edu	37	9	73240431	73240431	+	Silent	SNP	T	T	G	rs73451725	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:73240431T>G	ENST00000357533.2	-	13	1640	c.1641A>C	c.(1639-1641)cgA>cgC	p.R547R	TRPM3_ENST00000377105.1_Silent_p.R392R|TRPM3_ENST00000396280.5_Silent_p.R392R|TRPM3_ENST00000358082.3_Intron|TRPM3_ENST00000396292.4_Intron|TRPM3_ENST00000377110.3_Intron|TRPM3_ENST00000408909.2_Silent_p.R392R|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396285.1_Intron|TRPM3_ENST00000423814.3_Intron|TRPM3_ENST00000360823.2_Intron|TRPM3_ENST00000377106.1_Intron			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	569					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						CTGGATACTCTCGCTTGGAAA	0.294													T|||	701	0.139976	0.1498	0.1167	5008	,	,		19826	0.2302		0.0885	False		,,,				2504	0.1033				p.R392R		Atlas-SNP	.											.	TRPM3	700	.	0			c.A1176C						PASS	.	T	,,,,,,	713,3693	291.3+/-281.4	60,593,1550	61.0	66.0	65.0		,,1176,,1176,,	6.0	1.0	9	dbSNP_130	65	846,7754	193.7+/-239.3	43,760,3497	no	intron,intron,coding-synonymous,intron,coding-synonymous,intron,intron	TRPM3	NM_001007471.2,NM_020952.4,NM_024971.5,NM_206944.3,NM_206945.3,NM_206946.3,NM_206947.3	,,,,,,	103,1353,5047	GG,GT,TT		9.8372,16.1825,11.9868	,,,,,,	,,392/1567,,392/1557,,	73240431	1559,11447	2203	4300	6503	SO:0001819	synonymous_variant	80036	exon13			ATACTCTCGCTTG	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000357533.2:c.1641A>C	9.37:g.73240431T>G		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	218	107	0.490826	NM_206945	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000357533.2	37																																																																																				T|0.873;G|0.127	0.127	strong		0.294	TRPM3-014	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000214163.1	NM_206945	
MS4A12	54860	hgsc.bcm.edu	37	11	60265002	60265002	+	Nonsense_Mutation	SNP	C	C	T	rs2298553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:60265002C>T	ENST00000016913.4	+	2	268	c.211C>T	c.(211-213)Caa>Taa	p.Q71*	MS4A12_ENST00000525951.1_3'UTR|MS4A12_ENST00000537076.1_Nonsense_Mutation_p.Q71*	NM_017716.2	NP_060186.2	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member 12	71						integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)	17						AGGAAATATACAAATGATAAA	0.428													C|||	2395	0.478235	0.534	0.4914	5008	,	,		18593	0.4802		0.4334	False		,,,				2504	0.4376				p.Q71X		Atlas-SNP	.											.	MS4A12	44	.	0			c.C211T	GRCh37	CM068011	MS4A12	M	rs2298553	PASS	.	C	stop/GLN,stop/GLN	2063,2343	569.7+/-382.7	480,1103,620	56.0	56.0	56.0		211,211	4.0	0.0	11	dbSNP_100	56	3821,4779	538.7+/-383.5	861,2099,1340	yes	stop-gained,stop-gained	MS4A12	NM_001164470.1,NM_017716.2	,	1341,3202,1960	TT,TC,CC		44.4302,46.8225,45.2407	,	71/222,71/268	60265002	5884,7122	2203	4300	6503	SO:0001587	stop_gained	54860	exon2			AATATACAAATGA	AK000224	CCDS7988.1, CCDS53638.1	11q12	2008-03-25				ENSG00000071203			13370	protein-coding gene	gene with protein product		606550				11401424, 11486273	Standard	NM_017716		Approved	Ms4a10, FLJ20217	uc001npr.3	Q9NXJ0		ENST00000016913.4:c.211C>T	11.37:g.60265002C>T	ENSP00000016913:p.Gln71*	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_017716	F5GX98|Q8N6L4	Nonsense_Mutation	SNP	ENST00000016913.4	37	CCDS7988.1	993	0.45467032967032966	246	0.5	165	0.4558011049723757	243	0.42482517482517484	339	0.4472295514511873	C	15.75	2.925047	0.52759	0.468225	0.444302	ENSG00000071203	ENST00000537076;ENST00000526784;ENST00000016913;ENST00000530007	.	.	.	4.95	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999765913	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	.	10.6965	0.45903	0.1911:0.8089:0.0:0.0	rs2298553;rs52837052;rs60199962;rs2298553	.	.	.	X	71	.	ENSP00000016913:Q71X	Q	+	1	0	MS4A12	60021578	0.026000	0.19158	0.002000	0.10522	0.082000	0.17680	3.079000	0.50104	1.121000	0.41925	0.462000	0.41574	CAA	C|0.541;N|0.000	.	strong		0.428	MS4A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383627.1		
ILF2	3608	hgsc.bcm.edu	37	1	153635022	153635022	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:153635022A>G	ENST00000361891.4	-	14	1148	c.1023T>C	c.(1021-1023)tcT>tcC	p.S341S	ILF2_ENST00000480213.1_5'UTR	NM_001267809.1|NM_004515.3	NP_001254738.1|NP_004506.2	Q12905	ILF2_HUMAN	interleukin enhancer binding factor 2	341	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				immune response (GO:0006955)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			cervix(1)|kidney(1)|lung(4)|skin(1)	7	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TAGATATTTCAGAAGCAAGAT	0.393																																					p.S341S		Atlas-SNP	.											.	ILF2	25	.	0			c.T1023C						PASS	.						121.0	120.0	120.0					1																	153635022		2203	4300	6503	SO:0001819	synonymous_variant	3608	exon14			TATTTCAGAAGCA	U10323	CCDS1050.1, CCDS72919.1	1q21.3	2012-12-04	2012-12-04		ENSG00000143621	ENSG00000143621			6037	protein-coding gene	gene with protein product		603181	"""interleukin enhancer binding factor 2, 45kD"", ""interleukin enhancer binding factor 2, 45kDa"""			7519613	Standard	NM_004515		Approved	NF45	uc001fcr.4	Q12905	OTTHUMG00000037087	ENST00000361891.4:c.1023T>C	1.37:g.153635022A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	152	71	0.467105	NM_004515	A6NDB0|B2R8G7|Q5SR10|Q5SR11|Q7L7R3|Q9BWD4|Q9P1N0	Silent	SNP	ENST00000361891.4	37	CCDS1050.1																																																																																			.	.	none		0.393	ILF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090040.1	NM_004515	
C9	735	hgsc.bcm.edu	37	5	39364554	39364554	+	Missense_Mutation	SNP	G	G	A	rs700233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:39364554G>A	ENST00000263408.4	-	1	108	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	C9_ENST00000509186.1_Intron	NM_001737.3	NP_001728.1	P02748	CO9_HUMAN	complement component 9	5			R -> W (in dbSNP:rs700233).		complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|hemolysis by symbiont of host erythrocytes (GO:0019836)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane attack complex (GO:0005579)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)			GCAAAGCTCCGGCAGGCTGAC	0.517													G|||	1433	0.286142	0.2413	0.3718	5008	,	,		18252	0.0714		0.4235	False		,,,				2504	0.3661				p.R5W		Atlas-SNP	.											.	C9	116	.	0			c.C13T						PASS	.	G	TRP/ARG	1121,3285	402.6+/-332.4	158,805,1240	82.0	71.0	75.0		13	-8.7	0.0	5	dbSNP_86	75	3563,5037	515.9+/-378.7	730,2103,1467	yes	missense	C9	NM_001737.3	101	888,2908,2707	AA,AG,GG		41.4302,25.4426,36.0141	benign	5/560	39364554	4684,8322	2203	4300	6503	SO:0001583	missense	735	exon1			AGCTCCGGCAGGC		CCDS3929.1	5p14-p12	2014-09-17			ENSG00000113600	ENSG00000113600		"""Complement system"""	1358	protein-coding gene	gene with protein product		120940					Standard	NM_001737		Approved		uc003jlv.4	P02748	OTTHUMG00000094767	ENST00000263408.4:c.13C>T	5.37:g.39364554G>A	ENSP00000263408:p.Arg5Trp	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_001737		Missense_Mutation	SNP	ENST00000263408.4	37	CCDS3929.1	644	0.2948717948717949	129	0.2621951219512195	143	0.39502762430939226	46	0.08041958041958042	326	0.43007915567282323	G	10.63	1.405274	0.25378	0.254426	0.414302	ENSG00000113600	ENST00000263408	T	0.34072	1.38	4.45	-8.66	0.00866	.	3.427000	0.00687	N	0.000708	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26224	-1.0109	9	0.37606	T	0.19	5.1937	0.3149	0.00294	0.2623:0.2207:0.2768:0.2401	rs700233;rs1631129;rs3854893;rs17385752;rs58690123;rs700233	5	P02748	CO9_HUMAN	W	5	ENSP00000263408:R5W	ENSP00000263408:R5W	R	-	1	2	C9	39400311	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	-2.551000	0.00928	-1.634000	0.01537	-1.233000	0.01565	CGG	G|0.675;A|0.325	0.325	strong		0.517	C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211576.3		
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808526	18808526	+	Missense_Mutation	SNP	A	A	C	rs2992752	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18808526A>C	ENST00000400664.1	+	1	1103	c.1051A>C	c.(1051-1053)Aca>Cca	p.T351P		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	351			T -> P (in dbSNP:rs2992752). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CTCCCCGCAGACAGGGCCGTG	0.677													C|||	3369	0.672724	0.6611	0.7277	5008	,	,		15380	0.8948		0.6113	False		,,,				2504	0.4836				p.T351P		Atlas-SNP	.											KLHDC7A,NS,carcinoma,0,1	KLHDC7A	60	1	0			c.A1051C						PASS	.	C	PRO/THR	2798,1418		971,856,281	12.0	16.0	15.0		1051	0.7	0.0	1	dbSNP_101	15	5294,3114		1724,1846,634	yes	missense	KLHDC7A	NM_152375.2	38	2695,2702,915	CC,CA,AA		37.0362,33.6338,35.8999	benign	351/778	18808526	8092,4532	2108	4204	6312	SO:0001583	missense	127707	exon1			CCGCAGACAGGGC	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.1051A>C	1.37:g.18808526A>C	ENSP00000383505:p.Thr351Pro	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	1574	0.7206959706959707	330	0.6707317073170732	254	0.7016574585635359	523	0.9143356643356644	467	0.6160949868073878	C	0.317	-0.963986	0.02249	0.663662	0.629638	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.71461	-0.57	5.01	0.69	0.18039	.	1.313680	0.05153	N	0.496434	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37776	-0.9691	9	0.02654	T	1	.	3.8663	0.09018	0.4101:0.3546:0.0:0.2353	rs2992752;rs58275241	351	Q5VTJ3	KLD7A_HUMAN	P	351;288	ENSP00000383505:T351P	ENSP00000383505:T351P	T	+	1	0	KLHDC7A	18681113	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.198000	0.03035	-0.075000	0.12798	-1.961000	0.00478	ACA	A|0.310;C|0.690	0.690	strong		0.677	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
PTPN23	25930	hgsc.bcm.edu	37	3	47452786	47452786	+	Silent	SNP	G	G	A	rs1531875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:47452786G>A	ENST00000265562.4	+	20	3575	c.3498G>A	c.(3496-3498)gaG>gaA	p.E1166E	PTPN23_ENST00000431726.1_Silent_p.E1040E	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1166					cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACCCCTATGAGCATCCTGAGA	0.672													G|||	2298	0.458866	0.2405	0.5202	5008	,	,		15089	0.4633		0.6024	False		,,,				2504	0.5583				p.E1166E		Atlas-SNP	.											PTPN23,colon,carcinoma,0,1	PTPN23	85	1	0			c.G3498A						PASS	.	G		1234,3168		196,842,1163	25.0	26.0	26.0		3498	2.0	0.9	3	dbSNP_88	26	5072,3522		1520,2032,745	no	coding-synonymous	PTPN23	NM_015466.2		1716,2874,1908	AA,AG,GG		40.9821,28.0327,48.5226		1166/1637	47452786	6306,6690	2201	4297	6498	SO:0001819	synonymous_variant	25930	exon20			CTATGAGCATCCT	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.3498G>A	3.37:g.47452786G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Silent	SNP	ENST00000265562.4	37	CCDS2754.1																																																																																			G|0.529;A|0.471	0.471	strong		0.672	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
ARSH	347527	hgsc.bcm.edu	37	X	2928125	2928125	+	Silent	SNP	C	C	T	rs79487908	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:2928125C>T	ENST00000381130.2	+	2	147	c.147C>T	c.(145-147)ctC>ctT	p.L49L		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	49					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CCCAGCATCTCGCAGCTGCTT	0.517													C|||	101	0.026755	0.0045	0.0159	3775	,	,		12432	0.0079		0.0507	False		,,,				2504	0.0256				p.L49L		Atlas-SNP	.											.	ARSH	72	.	0			c.C147T						PASS	.	C		58,3777		0,45,13,1587,558	87.0	68.0	74.0		147	0.7	0.1	X	dbSNP_131	74	444,6284		7,312,118,2109,1754	no	coding-synonymous	ARSH	NM_001011719.1		7,357,131,3696,2312	TT,TC,T,CC,C		6.5993,1.5124,4.7524		49/563	2928125	502,10061	2203	4300	6503	SO:0001819	synonymous_variant	347527	exon2			GCATCTCGCAGCT	AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"""Arylsulfatase family"""	32488	protein-coding gene	gene with protein product		300586	"""arylsulfatase H"""			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.147C>T	X.37:g.2928125C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	134	125	0.932836	NM_001011719		Silent	SNP	ENST00000381130.2	37	CCDS35198.1																																																																																			C|0.959;T|0.041	0.041	strong		0.517	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
FBXW10	10517	hgsc.bcm.edu	37	17	18682399	18682399	+	Missense_Mutation	SNP	A	A	G	rs1318979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18682399A>G	ENST00000395665.4	+	14	3168	c.2947A>G	c.(2947-2949)Act>Gct	p.T983A	FBXW10_ENST00000308799.4_Missense_Mutation_p.T992A|FBXW10_ENST00000301938.4_Missense_Mutation_p.T930A|TVP23B_ENST00000574226.1_5'Flank|TVP23B_ENST00000307767.8_5'Flank|FBXW10_ENST00000395667.1_Missense_Mutation_p.T982A|TVP23B_ENST00000476139.1_5'Flank			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	983								p.T982A(1)		NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						TAGAGTGAACACTGAGTTCGT	0.527																																					p.T983A		Atlas-SNP	.											FBXW10,extremity,malignant_melanoma,0,1	FBXW10	82	1	1	Substitution - Missense(1)	skin(1)	c.A2947G						scavenged	.						61.0	55.0	57.0					17																	18682399		2015	3877	5892	SO:0001583	missense	10517	exon14			GTGAACACTGAGT	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.2947A>G	17.37:g.18682399A>G	ENSP00000379025:p.Thr983Ala	Somatic	531	3	0.00564972		WXS	Illumina HiSeq	Phase_I	367	20	0.0544959	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	409	0.18727106227106227	97	0.19715447154471544	81	0.22375690607734808	71	0.12412587412587413	160	0.21108179419525067	A	10.59	1.393102	0.25118	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	3.38	3.38	0.38709	.	0.586804	0.12753	U	0.441979	T	0.00210	0.0006	M	0.61703	1.905	0.47276	P	6.270000000000442E-4	D;D;D;D	0.71674	0.99;0.998;0.984;0.998	D;D;D;D	0.80764	0.98;0.994;0.956;0.994	T	0.05273	-1.0895	9	0.35671	T	0.21	.	9.7578	0.40513	1.0:0.0:0.0:0.0	.	930;992;983;982	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	A	982;992;930;983	ENSP00000379026:T982A;ENSP00000310382:T992A;ENSP00000306937:T930A;ENSP00000379025:T983A	ENSP00000306937:T930A	T	+	1	0	FBXW10	18623124	0.422000	0.25473	0.559000	0.28332	0.113000	0.19764	1.755000	0.38379	1.381000	0.46364	0.338000	0.21704	ACT	A|0.813;G|0.187	0.187	strong		0.527	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
SDK2	54549	hgsc.bcm.edu	37	17	71380062	71380062	+	Missense_Mutation	SNP	G	G	A	rs35467001	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:71380062G>A	ENST00000392650.3	-	33	4658	c.4658C>T	c.(4657-4659)aCg>aTg	p.T1553M	SDK2_ENST00000388726.3_Missense_Mutation_p.T1553M	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1553	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.			T -> M (in Ref. 3; AAH45763/AAH66363). {ECO:0000305}.	cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GCCTCGAAGCGTGAAGCCCCT	0.612													G|||	342	0.0682907	0.1029	0.0504	5008	,	,		18626	0.0069		0.0666	False		,,,				2504	0.0992				p.T1553M		Atlas-SNP	.											.	SDK2	219	.	0			c.C4658T						PASS	.	G	MET/THR	362,4044	185.0+/-212.2	19,324,1860	122.0	100.0	107.0		4658	5.5	1.0	17	dbSNP_126	107	465,8135	138.9+/-195.6	13,439,3848	yes	missense	SDK2	NM_001144952.1	81	32,763,5708	AA,AG,GG		5.407,8.2161,6.3586	possibly-damaging	1553/2173	71380062	827,12179	2203	4300	6503	SO:0001583	missense	54549	exon33			CGAAGCGTGAAGC	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.4658C>T	17.37:g.71380062G>A	ENSP00000376421:p.Thr1553Met	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	168	78	0.464286	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	109	0.04990842490842491	46	0.09349593495934959	16	0.04419889502762431	1	0.0017482517482517483	46	0.06068601583113457	G	16.75	3.210154	0.58343	0.082161	0.05407	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893	T;T;T	0.60299	0.2;0.41;0.41	5.47	5.47	0.80525	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.192213	0.44902	D	0.000406	T	0.08044	0.0201	M	0.61703	1.905	0.27686	P	0.946283	P;P;P	0.50066	0.931;0.87;0.843	P;P;P	0.54401	0.636;0.751;0.636	T	0.30504	-0.9976	9	0.48119	T	0.1	.	18.9149	0.92501	0.0:0.0:1.0:0.0	rs35467001	1553;1553;1553	Q58EX2-2;Q58EX2;Q58EX2-3	.;SDK2_HUMAN;.	M	1177;1553;1553;729;1553	ENSP00000376421:T1553M;ENSP00000373378:T1553M;ENSP00000407098:T729M	ENSP00000324967:T1553M	T	-	2	0	SDK2	68891657	1.000000	0.71417	0.957000	0.39632	0.899000	0.52679	3.137000	0.50562	2.565000	0.86533	0.561000	0.74099	ACG	G|0.944;A|0.056	0.056	strong		0.612	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
SEC63	11231	hgsc.bcm.edu	37	6	108222673	108222673	+	Missense_Mutation	SNP	G	G	A	rs192072257		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:108222673G>A	ENST00000369002.4	-	13	1437	c.1258C>T	c.(1258-1260)Cgt>Tgt	p.R420C		NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	420	SEC63 1.				liver development (GO:0001889)|multicellular organismal aging (GO:0010259)|nitrogen compound metabolic process (GO:0006807)|posttranslational protein targeting to membrane (GO:0006620)|posttranslational protein targeting to membrane, translocation (GO:0031204)|protein targeting to membrane (GO:0006612)|renal system development (GO:0072001)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		AGAGTGTGACGATCTGATTCT	0.328													G|||	1	0.000199681	0.0	0.0	5008	,	,		15042	0.0		0.001	False		,,,				2504	0.0				p.R420C		Atlas-SNP	.											SEC63,NS,carcinoma,0,2	SEC63	79	2	0			c.C1258T						PASS	.						77.0	73.0	74.0					6																	108222673		2203	4300	6503	SO:0001583	missense	11231	exon13			TGTGACGATCTGA	BC048287	CCDS5061.1	6q21	2011-09-05	2006-09-12		ENSG00000025796	ENSG00000025796		"""Heat shock proteins / DNAJ (HSP40)"""	21082	protein-coding gene	gene with protein product		608648	"""SEC63-like (S. cerevisiae)"""			10219736, 10543453	Standard	NM_007214		Approved	SEC63L, PRO2507, ERdj2, DNAJC23	uc003psc.4	Q9UGP8	OTTHUMG00000015316	ENST00000369002.4:c.1258C>T	6.37:g.108222673G>A	ENSP00000357998:p.Arg420Cys	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	237	115	0.485232	NM_007214	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	Missense_Mutation	SNP	ENST00000369002.4	37	CCDS5061.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	23.3	4.400712	0.83120	.	.	ENSG00000025796	ENST00000369002;ENST00000437345;ENST00000423697	T	0.63255	-0.03	5.78	5.78	0.91487	Sec63 domain (3);	0.000000	0.85682	D	0.000000	T	0.80449	0.4625	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.82436	-0.0458	10	0.87932	D	0	-8.1434	19.9981	0.97395	0.0:0.0:1.0:0.0	.	420;420	Q9UGP8;B3KQF0	SEC63_HUMAN;.	C	420;71;280	ENSP00000357998:R420C	ENSP00000357998:R420C	R	-	1	0	SEC63	108329366	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.952000	0.75989	2.733000	0.93635	0.561000	0.74099	CGT	G|1.000;A|0.000	0.000	strong		0.328	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214	
BAI2	576	hgsc.bcm.edu	37	1	32196647	32196647	+	Silent	SNP	C	C	G	rs909001|rs35020949	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32196647C>G	ENST00000373658.3	-	29	4475	c.4134G>C	c.(4132-4134)ccG>ccC	p.P1378P	BAI2_ENST00000527361.1_Silent_p.P1345P|BAI2_ENST00000398547.1_Silent_p.P1311P|BAI2_ENST00000398538.1_Silent_p.P1366P|BAI2_ENST00000257070.4_Silent_p.P1345P|BAI2_ENST00000398556.3_Silent_p.P1293P|BAI2_ENST00000398542.1_Silent_p.P1278P|BAI2_ENST00000373655.2_Silent_p.P1378P|BAI2_ENST00000440175.2_Silent_p.P987P|BAI2_ENST00000465256.1_5'UTR	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1378					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GGGTCCCCTCCGGCCGGGCCC	0.711													G|||	1930	0.385383	0.7579	0.2594	5008	,	,		12912	0.2331		0.159	False		,,,				2504	0.3609				p.P1378P		Atlas-SNP	.											.	BAI2	128	.	0			c.G4134C						PASS	.	G		2507,1833		741,1025,404	8.0	11.0	10.0		4134	-10.9	0.0	1	dbSNP_86	10	1364,7136		119,1126,3005	no	coding-synonymous	BAI2	NM_001703.2		860,2151,3409	GG,GC,CC		16.0471,42.235,30.148		1378/1586	32196647	3871,8969	2170	4250	6420	SO:0001819	synonymous_variant	576	exon29			CCCCTCCGGCCGG	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.4134G>C	1.37:g.32196647C>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	37	CCDS346.2																																																																																			C|0.675;G|0.325	0.325	strong		0.711	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
KCNA4	3739	hgsc.bcm.edu	37	11	30033191	30033191	+	Silent	SNP	G	G	A	rs3802914	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:30033191G>A	ENST00000328224.6	-	2	2268	c.1035C>T	c.(1033-1035)ggC>ggT	p.G345G	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	345					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	CACCATGCCCGCCAGCACTCA	0.498													g|||	855	0.170727	0.3154	0.1801	5008	,	,		19509	0.0357		0.171	False		,,,				2504	0.1074				p.G345G		Atlas-SNP	.											.	KCNA4	158	.	0			c.C1035T						PASS	.	A		1191,2871		182,827,1022	84.0	77.0	79.0		1035	-10.9	0.1	11	dbSNP_107	79	1368,7020		118,1132,2944	no	coding-synonymous	KCNA4	NM_002233.3		300,1959,3966	AA,AG,GG		16.309,29.3205,20.5542		345/654	30033191	2559,9891	2031	4194	6225	SO:0001819	synonymous_variant	3739	exon2			ATGCCCGCCAGCA	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6222	protein-coding gene	gene with protein product		176266	"""potassium voltage-gated channel, shaker-related subfamily, member 4-like"""	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1035C>T	11.37:g.30033191G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_002233		Silent	SNP	ENST00000328224.6	37	CCDS41629.1																																																																																			G|0.833;A|0.167	0.167	strong		0.498	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233	
SLC43A2	124935	hgsc.bcm.edu	37	17	1479963	1479963	+	Silent	SNP	G	G	A	rs142934102		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1479963G>A	ENST00000301335.5	-	13	1564	c.1476C>T	c.(1474-1476)agC>agT	p.S492S	SLC43A2_ENST00000412517.3_Silent_p.S355S|SLC43A2_ENST00000571650.1_Silent_p.S496S|SLC43A2_ENST00000382147.4_Silent_p.S496S	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	492					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CGAAGAGCGCGCTGATCAGAG	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		14140	0.0		0.001	False		,,,				2504	0.0				p.S492S		Atlas-SNP	.											.	SLC43A2	37	.	0			c.C1476T						PASS	.	G		0,4406		0,0,2203	46.0	44.0	45.0		1476	-10.0	0.1	17	dbSNP_134	45	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	SLC43A2	NM_152346.1		0,6,6497	AA,AG,GG		0.0698,0.0,0.0461		492/570	1479963	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	124935	exon13			GAGCGCGCTGATC	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.1476C>T	17.37:g.1479963G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	25	14	0.56	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																			G|1.000;A|0.000	0.000	weak		0.637	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346	
FBXO36	130888	hgsc.bcm.edu	37	2	230861519	230861519	+	Missense_Mutation	SNP	G	G	T	rs1035834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:230861519G>T	ENST00000283946.3	+	3	276	c.258G>T	c.(256-258)ttG>ttT	p.L86F	FBXO36_ENST00000409992.1_Intron|FBXO36_ENST00000373652.3_Missense_Mutation_p.L55F	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	86			L -> F (in dbSNP:rs1035834). {ECO:0000269|PubMed:15489334}.					p.L86F(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		TCATCAATTTGTGCAAAGGTA	0.358													G|||	900	0.179712	0.1959	0.268	5008	,	,		20240	0.1042		0.2654	False		,,,				2504	0.0849				p.L86F		Atlas-SNP	.											FBXO36_ENST00000283946,NS,carcinoma,0,1	FBXO36	22	1	1	Substitution - Missense(1)	stomach(1)	c.G258T						PASS	.	G	PHE/LEU	833,3573	326.9+/-299.8	69,695,1439	172.0	166.0	168.0		258	1.0	1.0	2	dbSNP_86	168	2064,6536	358.1+/-331.0	275,1514,2511	no	missense	FBXO36	NM_174899.4	22	344,2209,3950	TT,TG,GG		24.0,18.906,22.2743	probably-damaging	86/189	230861519	2897,10109	2203	4300	6503	SO:0001583	missense	130888	exon3			CAATTTGTGCAAA	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"""F-boxes /  ""other"""""	27020	protein-coding gene	gene with protein product		609105	"""F-box only protein 36"""			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.258G>T	2.37:g.230861519G>T	ENSP00000283946:p.Leu86Phe	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	227	92	0.405286	NM_174899	B3KVQ6|Q53TE6|Q8WWD4	Missense_Mutation	SNP	ENST00000283946.3	37	CCDS2472.1	465	0.2129120879120879	97	0.19715447154471544	106	0.292817679558011	61	0.10664335664335664	201	0.26517150395778366	G	13.49	2.254163	0.39896	0.18906	0.24	ENSG00000153832	ENST00000373652;ENST00000283946	T;T	0.57907	0.37;0.44	5.37	0.962	0.19643	.	0.000000	0.64402	D	0.000008	T	0.00012	0.0000	M	0.81682	2.555	0.09310	P	0.9999999999885822	D;D	0.60160	0.987;0.987	P;P	0.59825	0.864;0.864	T	0.11203	-1.0597	9	0.56958	D	0.05	-18.3118	12.425	0.55542	0.1911:0.0:0.8089:0.0	rs1035834;rs17846077;rs17859075;rs52834785;rs1035834	55;86	B3KVQ6;Q8NEA4	.;FBX36_HUMAN	F	55;86	ENSP00000362756:L55F;ENSP00000283946:L86F	ENSP00000283946:L86F	L	+	3	2	FBXO36	230569763	1.000000	0.71417	0.959000	0.39883	0.083000	0.17756	0.765000	0.26546	0.125000	0.18397	0.561000	0.74099	TTG	G|0.789;T|0.211	0.211	strong		0.358	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899	
CCT5	22948	hgsc.bcm.edu	37	5	10256161	10256161	+	Silent	SNP	T	T	C	rs1042392	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:10256161T>C	ENST00000280326.4	+	4	846	c.426T>C	c.(424-426)cgT>cgC	p.R142R	CCT5_ENST00000506600.1_Silent_p.R49R|CCT5_ENST00000515390.1_Silent_p.R87R|CCT5_ENST00000515676.1_Silent_p.R104R|CCT5_ENST00000503026.1_Silent_p.R121R	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	142					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						AGGCTGCTCGTGTTGCTATTG	0.517													C|||	3468	0.692492	0.4039	0.7767	5008	,	,		19668	0.8839		0.8579	False		,,,				2504	0.6554				p.R142R		Atlas-SNP	.											.	CCT5	49	.	0			c.T426C						PASS	.	C		2043,2363	610.4+/-391.6	474,1095,634	96.0	73.0	81.0		426	1.5	1.0	5	dbSNP_86	81	7417,1183	240.4+/-271.1	3195,1027,78	no	coding-synonymous	CCT5	NM_012073.3		3669,2122,712	CC,CT,TT		13.7558,46.3686,27.2643		142/542	10256161	9460,3546	2203	4300	6503	SO:0001819	synonymous_variant	22948	exon4			TGCTCGTGTTGCT	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"""Heat Shock Proteins / Chaperonins"""	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.426T>C	5.37:g.10256161T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	136	132	0.970588	NM_012073	A8JZY8|A8K2X8|B4DYD8	Silent	SNP	ENST00000280326.4	37	CCDS3877.1																																																																																			T|0.255;C|0.745	0.745	strong		0.517	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2		
BPIFB3	359710	hgsc.bcm.edu	37	20	31652292	31652292	+	Missense_Mutation	SNP	G	G	A	rs4911290	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:31652292G>A	ENST00000375494.3	+	7	682	c.682G>A	c.(682-684)Gtg>Atg	p.V228M		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	228	Leu-rich.		V -> M (in dbSNP:rs4911290).		innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCTTGGGTCCGTGGAATTCTC	0.557													G|||	2454	0.490016	0.3464	0.4755	5008	,	,		18488	0.756		0.3867	False		,,,				2504	0.5266				p.V228M		Atlas-SNP	.											.	.	.	.	0			c.G682A						PASS	.	G	MET/VAL	1447,2959	470.2+/-355.7	245,957,1001	97.0	77.0	84.0		682	2.6	0.8	20	dbSNP_111	84	3141,5459	478.1+/-369.8	585,1971,1744	yes	missense	BPIFB3	NM_182658.1	21	830,2928,2745	AA,AG,GG		36.5233,32.8416,35.276	benign	228/477	31652292	4588,8418	2203	4300	6503	SO:0001583	missense	359710	exon7			GGGTCCGTGGAAT	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.682G>A	20.37:g.31652292G>A	ENSP00000364643:p.Val228Met	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	37	CCDS13212.1	1061	0.4858058608058608	178	0.3617886178861789	161	0.4447513812154696	430	0.7517482517482518	292	0.38522427440633245	G	8.111	0.778703	0.16120	0.328416	0.365233	ENSG00000186190	ENST00000375494	T	0.06687	3.27	4.58	2.63	0.31362	.	0.282354	0.24960	N	0.034221	T	0.00012	0.0000	M	0.70275	2.135	0.45035	P	0.001943000000000028	P	0.34837	0.472	B	0.34385	0.181	T	0.02339	-1.1174	9	0.87932	D	0	-12.5412	13.1368	0.59413	0.0:0.1717:0.8283:0.0	rs4911290;rs52793725;rs58138039;rs4911290	228	P59826	BPIB3_HUMAN	M	228	ENSP00000364643:V228M	ENSP00000364643:V228M	V	+	1	0	BPIFB3	31115953	0.921000	0.31238	0.833000	0.33012	0.052000	0.14988	1.284000	0.33249	0.569000	0.29329	-0.853000	0.03031	GTG	G|0.588;A|0.412	0.412	strong		0.557	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
GPR111	222611	hgsc.bcm.edu	37	6	47649574	47649574	+	Missense_Mutation	SNP	A	A	G	rs10807372|rs71538333	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:47649574A>G	ENST00000296862.1	+	6	1279	c.1279A>G	c.(1279-1281)Aaa>Gaa	p.K427E	GPR111_ENST00000507065.1_Missense_Mutation_p.K359E|GPR111_ENST00000398742.2_Missense_Mutation_p.K359E			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	427	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.			K -> E (in Ref. 3; ABC41928). {ECO:0000305}.	G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						TAGGCCAAGCAAATTGTTTAC	0.443													A|||	2551	0.509385	0.4448	0.4323	5008	,	,		22627	0.3085		0.6272	False		,,,				2504	0.7372				p.K359E		Atlas-SNP	.											.	GPR111	123	.	0			c.A1075G						PASS	.	A	GLU/LYS	1754,2104		397,960,572	139.0	131.0	134.0		1075	1.6	0.5	6	dbSNP_120	134	5326,2926		1739,1848,539	yes	missense	GPR111	NM_153839.6	56	2136,2808,1111	GG,GA,AA		35.4581,45.464,41.5359	benign	359/643	47649574	7080,5030	1929	4126	6055	SO:0001583	missense	222611	exon7			CCAAGCAAATTGT	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.1279A>G	6.37:g.47649574A>G	ENSP00000296862:p.Lys427Glu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	37		839	0.3841575091575092	161	0.32723577235772355	158	0.43646408839779005	148	0.25874125874125875	372	0.49076517150395776	A	8.406	0.843036	0.16963	0.45464	0.645419	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.35789	2.06;2.04;1.29	5.53	1.64	0.23874	GPS domain (2);	0.720175	0.13186	N	0.407111	T	0.06872	0.0175	N	0.19112	0.55	0.80722	P	0.0	B;B	0.14012	0.002;0.009	B;B	0.16289	0.006;0.015	T	0.24261	-1.0165	9	0.39692	T	0.17	.	1.3446	0.02161	0.4879:0.2189:0.1677:0.1255	rs10807372;rs52833782;rs60948975;rs10807372	359;427	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	E	359;427;359	ENSP00000422934:K359E;ENSP00000296862:K427E;ENSP00000381727:K359E	ENSP00000296862:K427E	K	+	1	0	GPR111	47757533	0.000000	0.05858	0.493000	0.27502	0.973000	0.67179	0.485000	0.22324	0.401000	0.25424	0.482000	0.46254	AAA	A|0.519;G|0.481	0.481	strong		0.443	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
BEST3	144453	hgsc.bcm.edu	37	12	70091452	70091452	+	Missense_Mutation	SNP	A	A	G	rs1025016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:70091452A>G	ENST00000330891.5	-	2	353	c.127T>C	c.(127-129)Tat>Cat	p.Y43H	BEST3_ENST00000551160.1_Intron|BEST3_ENST00000476098.1_Intron|BEST3_ENST00000393365.1_5'UTR|BEST3_ENST00000533674.1_Intron|BEST3_ENST00000331471.4_Missense_Mutation_p.Y43H|BEST3_ENST00000553096.1_Intron|BEST3_ENST00000266661.4_Intron	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	43			Y -> H (in dbSNP:rs1025016).		negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			ATTGCTGTATAAAGAACAGCA	0.348													A|||	292	0.0583067	0.0121	0.0591	5008	,	,		20704	0.0278		0.0795	False		,,,				2504	0.1299				p.Y43H		Atlas-SNP	.											BEST3_ENST00000330891,lymph_node,lymphoid_neoplasm,0,1	BEST3	129	1	0			c.T127C						PASS	.	A	HIS/TYR	88,3610		1,86,1762	89.0	86.0	87.0		127	5.8	1.0	12	dbSNP_86	87	722,7468		28,666,3401	yes	missense	BEST3	NM_032735.2	83	29,752,5163	GG,GA,AA		8.8156,2.3797,6.8136	probably-damaging	43/669	70091452	810,11078	1849	4095	5944	SO:0001583	missense	144453	exon2			CTGTATAAAGAAC	AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17105	protein-coding gene	gene with protein product		607337	"""vitelliform macular dystrophy 2-like 3"""	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.127T>C	12.37:g.70091452A>G	ENSP00000332413:p.Tyr43His	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	177	95	0.536723	NM_032735	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Missense_Mutation	SNP	ENST00000330891.5	37	CCDS8992.2	93	0.042582417582417584	7	0.014227642276422764	17	0.04696132596685083	15	0.026223776223776224	54	0.0712401055408971	A	25.2	4.609058	0.87258	0.023797	0.088156	ENSG00000127325	ENST00000331471;ENST00000330891;ENST00000548658	D;D;D	0.98747	-5.11;-5.11;-5.11	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.90466	0.7014	H	0.96943	3.91	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	T	0.72537	-0.4263	10	0.87932	D	0	-20.4712	16.226	0.82293	1.0:0.0:0.0:0.0	rs1025016;rs52800017;rs59138198;rs1025016	43;43	Q8N1M1;Q8N1M1-1	BEST3_HUMAN;.	H	43	ENSP00000329064:Y43H;ENSP00000332413:Y43H;ENSP00000446575:Y43H	ENSP00000332413:Y43H	Y	-	1	0	BEST3	68377719	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.576000	0.82467	2.230000	0.72887	0.528000	0.53228	TAT	A|0.941;G|0.059	0.059	strong		0.348	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439	
POLR1E	64425	hgsc.bcm.edu	37	9	37503087	37503087	+	Missense_Mutation	SNP	G	G	A	rs10814571	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:37503087G>A	ENST00000377798.4	+	12	1261	c.1148G>A	c.(1147-1149)aGg>aAg	p.R383K	POLR1E_ENST00000442009.2_Missense_Mutation_p.R313K|POLR1E_ENST00000377792.3_Missense_Mutation_p.R445K	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	0					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		TCCAAAAGAAGGGTGTCTGTG	0.557													G|||	1075	0.214657	0.1694	0.3112	5008	,	,		18191	0.2431		0.2018	False		,,,				2504	0.1912				p.R383K	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.G1148A						PASS	.	G	LYS/ARG	806,3600	320.2+/-296.5	71,664,1468	102.0	108.0	106.0		1148	-7.7	0.0	9	dbSNP_120	106	1874,6726	334.6+/-321.1	201,1472,2627	yes	missense	POLR1E	NM_022490.1	26	272,2136,4095	AA,AG,GG		21.7907,18.2932,20.6059	benign	383/420	37503087	2680,10326	2203	4300	6503	SO:0001583	missense	64425	exon12			AAAGAAGGGTGTC	AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"""RNA polymerase subunits"""	17631	protein-coding gene	gene with protein product	"""RNA polymerase I associated factor 53"""		"""polymerase (RNA) I associated factor 1"""	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.1148G>A	9.37:g.37503087G>A	ENSP00000367029:p.Arg383Lys	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	153	77	0.503268	NM_022490	O75395|Q5JTE3	Missense_Mutation	SNP	ENST00000377798.4	37	CCDS6611.1	465	0.2129120879120879	93	0.18902439024390244	95	0.26243093922651933	126	0.2202797202797203	151	0.19920844327176782	G	5.831	0.337637	0.11013	0.182932	0.217907	ENSG00000137054	ENST00000377798;ENST00000442009;ENST00000377792	T;T;T	0.19806	2.12;2.12;2.12	5.69	-7.71	0.01254	.	0.707197	0.14585	N	0.310629	T	0.00012	0.0000	N	0.00146	-1.995	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.46148	-0.9212	9	0.12103	T	0.63	-2.4041	11.0644	0.47966	0.6452:0.2582:0.0967:0.0	rs10814571;rs17851139;rs52796836;rs59896159;rs10814571	313;445;383	E7EX70;Q9GZS1;Q9GZS1-2	.;RPA49_HUMAN;.	K	383;313;445	ENSP00000367029:R383K;ENSP00000399887:R313K;ENSP00000367023:R445K	ENSP00000367023:R445K	R	+	2	0	POLR1E	37493087	0.008000	0.16893	0.011000	0.14972	0.928000	0.56348	-0.392000	0.07314	-0.965000	0.03591	0.655000	0.94253	AGG	G|0.798;A|0.202	0.202	strong		0.557	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129933	175129933	+	Missense_Mutation	SNP	T	T	C	rs150137790		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:175129933T>C	ENST00000423313.1	-	4	753	c.217A>G	c.(217-219)Aag>Gag	p.K73E	KIAA0040_ENST00000545251.2_Missense_Mutation_p.K73E|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000444639.1_Missense_Mutation_p.K73E	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	tccttcttcttcttcttcttc	0.502																																					p.K73E		Atlas-SNP	.											KIAA0040,colon,carcinoma,0,1	KIAA0040	2	1	0			c.A217G						PASS	.						107.0	90.0	95.0					1																	175129933		692	1591	2283	SO:0001583	missense	9674	exon3			TCTTCTTCTTCTT	D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.217A>G	1.37:g.175129933T>C	ENSP00000462172:p.Lys73Glu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	124	11	0.0887097	NM_001162895	A8K9H6|Q2NKQ0	Missense_Mutation	SNP	ENST00000423313.1	37																																																																																				.	.	none		0.502	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
PHF14	9678	hgsc.bcm.edu	37	7	11022230	11022230	+	Missense_Mutation	SNP	A	A	G	rs218966	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:11022230A>G	ENST00000403050.3	+	3	796	c.344A>G	c.(343-345)aAg>aGg	p.K115R	PHF14_ENST00000445996.2_Intron	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	115	Glu/Lys-rich.		K -> R (in dbSNP:rs218966). {ECO:0000269|PubMed:9872452}.		lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		AGAaagaaaaaggagaaagag	0.338													A|||	3126	0.624201	0.789	0.562	5008	,	,		19534	0.4831		0.6581	False		,,,				2504	0.5562				p.K115R		Atlas-SNP	.											.	PHF14	90	.	0			c.A344G						PASS	.	A	ARG/LYS	2717,787		1073,571,108	10.0	10.0	10.0		344	4.0	1.0	7	dbSNP_79	10	5234,2642		1775,1684,479	yes	missense	PHF14	NM_014660.3	26	2848,2255,587	GG,GA,AA		33.5449,22.46,30.1318	benign	115/889	11022230	7951,3429	1752	3938	5690	SO:0001583	missense	9678	exon3			AGAAAAAGGAGAA	AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"""Zinc fingers, PHD-type"""	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.344A>G	7.37:g.11022230A>G	ENSP00000385795:p.Lys115Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_014660	A7MCZ3|B4DI82	Missense_Mutation	SNP	ENST00000403050.3	37	CCDS47542.1	1363	0.6240842490842491	371	0.7540650406504065	212	0.585635359116022	289	0.5052447552447552	491	0.6477572559366754	A	8.260	0.810894	0.16537	0.7754	0.664551	ENSG00000106443	ENST00000403050	T	0.66638	-0.22	5.11	3.96	0.45880	.	0.597682	0.18157	N	0.149898	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.9999999999997332	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35992	-0.9766	9	0.37606	T	0.19	.	10.3673	0.44033	0.9224:0.0:0.0776:0.0	rs62652325	115;115	A8MSQ1;O94880	.;PHF14_HUMAN	R	115	ENSP00000385795:K115R	ENSP00000385795:K115R	K	+	2	0	PHF14	10988755	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.987000	0.56944	0.969000	0.38237	0.477000	0.44152	AAG	A|0.369;G|0.631	0.631	strong		0.338	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660	
OR2AE1	81392	hgsc.bcm.edu	37	7	99474427	99474427	+	Missense_Mutation	SNP	A	A	G	rs2572023	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99474427A>G	ENST00000316368.2	-	1	253	c.230T>C	c.(229-231)aTc>aCc	p.I77T		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	77			I -> T (in dbSNP:rs2572023).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					CTTCAGGATGATTGTGGAGAC	0.483													G|||	2781	0.555312	0.9107	0.4251	5008	,	,		23726	0.2907		0.4851	False		,,,				2504	0.5123				p.I77T		Atlas-SNP	.											.	OR2AE1	32	.	0			c.T230C						PASS	.	G	THR/ILE	3687,719	296.7+/-284.4	1546,595,62	114.0	97.0	103.0		230	0.8	0.1	7	dbSNP_100	103	4489,4111	562.2+/-387.9	1165,2159,976	yes	missense	OR2AE1	NM_001005276.1	89	2711,2754,1038	GG,GA,AA		47.8023,16.3187,37.1367	benign	77/324	99474427	8176,4830	2203	4300	6503	SO:0001583	missense	81392	exon1			AGGATGATTGTGG	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"""GPCR / Class A : Olfactory receptors"""	15087	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily AE, member 2"""	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.230T>C	7.37:g.99474427A>G	ENSP00000313936:p.Ile77Thr	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_001005276	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	1152	0.5274725274725275	455	0.9247967479674797	171	0.4723756906077348	148	0.25874125874125875	378	0.49868073878627966	G	0.001	-3.109683	0.00032	0.836813	0.521977	ENSG00000244623	ENST00000316368	T	0.01139	5.28	3.63	0.807	0.18714	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41396	N	0.000891	T	0.00012	0.0000	N	0.04669	-0.19	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28554	-1.0040	9	0.02654	T	1	.	7.1689	0.25706	0.5367:0.0:0.4633:0.0	rs2572023;rs17277317;rs58768647;rs2572023	77	Q8NHA4	O2AE1_HUMAN	T	77	ENSP00000313936:I77T	ENSP00000313936:I77T	I	-	2	0	OR2AE1	99312363	0.000000	0.05858	0.126000	0.21872	0.014000	0.08584	-0.121000	0.10643	-0.055000	0.13244	-0.299000	0.09455	ATC	G|0.588;N|0.000	0.588	strong		0.483	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1		
ANXA11	311	hgsc.bcm.edu	37	10	81926702	81926702	+	Missense_Mutation	SNP	G	G	A	rs1049550	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:81926702G>A	ENST00000438331.1	-	8	1170	c.688C>T	c.(688-690)Cgc>Tgc	p.R230C	ANXA11_ENST00000537102.1_Missense_Mutation_p.R197C|ANXA11_ENST00000535999.1_Missense_Mutation_p.R230C|ANXA11_ENST00000372231.3_Missense_Mutation_p.R230C|ANXA11_ENST00000265447.4_Missense_Mutation_p.R230C|ANXA11_ENST00000422982.3_Missense_Mutation_p.R230C|ANXA11_ENST00000360615.4_Missense_Mutation_p.R230C	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	230			R -> C (in dbSNP:rs1049550).		cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			TTGTTGGAGCGACTCCCCAGG	0.637													.|||	1964	0.392173	0.1551	0.4654	5008	,	,		14900	0.6429		0.4503	False		,,,				2504	0.3425				p.R230C		Atlas-SNP	.											.	ANXA11	32	.	0			c.C688T	GRCh37	CM064971	ANXA11	M	rs1049550	PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	891,3515		93,705,1405	58.0	49.0	52.0	http://omim.org/entry/612388	688,688,688	4.3	1.0	10	dbSNP_86	52	3521,5079		740,2041,1519	yes	missense,missense,missense	ANXA11	NM_001157.2,NM_145868.1,NM_145869.1	180,180,180	833,2746,2924	AA,AG,GG		40.9419,20.2224,33.9228	probably-damaging,probably-damaging,probably-damaging	230/506,230/506,230/506	81926702	4412,8594	2203	4300	6503	SO:0001583	missense	311	exon7			TGGAGCGACTCCC	L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"""Annexins"""	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.688C>T	10.37:g.81926702G>A	ENSP00000398610:p.Arg230Cys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_145868	B4DVE7	Missense_Mutation	SNP	ENST00000438331.1	37	CCDS7364.1	927	0.42445054945054944	72	0.14634146341463414	152	0.4198895027624309	370	0.6468531468531469	333	0.4393139841688654	.	24.1	4.488911	0.84962	0.202224	0.409419	ENSG00000122359	ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000424188;ENST00000537102	T;T;T;T;T;T;T	0.12879	2.64;2.64;2.64;2.64;2.64;2.64;2.64	5.26	4.35	0.52113	Annexin repeat, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.96833	3.89	0.09310	P	0.9999999781241	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.996	T	0.45026	-0.9289	9	0.72032	D	0.01	.	9.1797	0.37134	0.0:0.16:0.6742:0.1658	rs1049550;rs1802933;rs2070070;rs2228426;rs3189725;rs17676239;rs52830790;rs1049550	330;230;230	B7Z6L0;Q5T0G8;P50995	.;.;ANX11_HUMAN	C	230;230;230;230;230;230;230;137;197	ENSP00000361305:R230C;ENSP00000404412:R230C;ENSP00000398610:R230C;ENSP00000353827:R230C;ENSP00000265447:R230C;ENSP00000441748:R230C;ENSP00000441400:R197C	ENSP00000265447:R230C	R	-	1	0	ANXA11	81916682	1.000000	0.71417	0.974000	0.42286	0.984000	0.73092	7.474000	0.81024	1.360000	0.45960	0.561000	0.74099	CGC	G|0.630;T|0.004	.	strong		0.637	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869	
CNGB3	54714	hgsc.bcm.edu	37	8	87588198	87588198	+	Missense_Mutation	SNP	T	T	C	rs3735972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:87588198T>C	ENST00000320005.5	-	18	2311	c.2264A>G	c.(2263-2265)gAa>gGa	p.E755G		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	755			E -> G (in dbSNP:rs3735972). {ECO:0000269|PubMed:10958649, ECO:0000269|PubMed:15712225}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						TGCTGTACATTCAGGTCTGTC	0.398													T|||	412	0.0822684	0.0696	0.085	5008	,	,		18346	0.1022		0.0885	False		,,,				2504	0.0706				p.E755G		Atlas-SNP	.											CNGB3,NS,carcinoma,-1,1	CNGB3	176	1	0			c.A2264G						PASS	.	T	GLY/GLU	310,4096	167.6+/-198.6	11,288,1904	242.0	243.0	243.0		2264	3.0	0.0	8	dbSNP_107	243	743,7857	179.5+/-228.6	32,679,3589	yes	missense	CNGB3	NM_019098.4	98	43,967,5493	CC,CT,TT		8.6395,7.0359,8.0963	benign	755/810	87588198	1053,11953	2203	4300	6503	SO:0001583	missense	54714	exon18			GTACATTCAGGTC	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2153	protein-coding gene	gene with protein product		605080	"""achromatopsia (rod monochromacy) 3"", ""achromatopsia (rod monochromacy) 1"""	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.2264A>G	8.37:g.87588198T>C	ENSP00000316605:p.Glu755Gly	Somatic	354	1	0.00282486		WXS	Illumina HiSeq	Phase_I	291	143	0.491409	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	177	0.08104395604395605	29	0.05894308943089431	33	0.09116022099447514	48	0.08391608391608392	67	0.08839050131926121	T	10.79	1.449535	0.26074	0.070359	0.086395	ENSG00000170289	ENST00000320005	D	0.97186	-4.28	5.37	2.97	0.34412	.	0.666605	0.14178	N	0.336259	T	0.38665	0.1049	N	0.14661	0.345	0.80722	P	0.0	B;B	0.27732	0.187;0.118	B;B	0.27500	0.08;0.037	T	0.73808	-0.3866	9	0.28530	T	0.3	.	6.4711	0.22009	0.0:0.0817:0.1575:0.7608	rs3735972;rs52818605;rs56540041;rs57600088;rs3735972	750;755	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	G	755	ENSP00000316605:E755G	ENSP00000316605:E755G	E	-	2	0	CNGB3	87657314	0.002000	0.14202	0.000000	0.03702	0.022000	0.10575	1.196000	0.32198	0.426000	0.26116	0.383000	0.25322	GAA	T|0.921;C|0.079	0.079	strong		0.398	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098	
TTC7A	57217	hgsc.bcm.edu	37	2	47177617	47177617	+	Silent	SNP	C	C	T	rs61738825	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:47177617C>T	ENST00000319190.5	+	2	668	c.300C>T	c.(298-300)agC>agT	p.S100S	TTC7A_ENST00000461601.1_3'UTR|TTC7A_ENST00000394850.2_Silent_p.S100S|TTC7A_ENST00000263737.6_5'UTR|TTC7A_ENST00000536057.1_Silent_p.S100S|TTC7A_ENST00000409245.1_Silent_p.S66S	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	100					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			CGAAGATGAGCGAAGCCAAAA	0.507													C|||	254	0.0507188	0.0242	0.0576	5008	,	,		21040	0.0		0.1153	False		,,,				2504	0.0675				p.S100S		Atlas-SNP	.											.	TTC7A	80	.	0			c.C300T						PASS	.	C		157,4249	105.2+/-143.6	5,147,2051	110.0	99.0	103.0		300	-0.4	0.4	2	dbSNP_129	103	846,7754	194.9+/-240.2	42,762,3496	no	coding-synonymous	TTC7A	NM_020458.2		47,909,5547	TT,TC,CC		9.8372,3.5633,7.7118		100/859	47177617	1003,12003	2203	4300	6503	SO:0001819	synonymous_variant	57217	exon2			GATGAGCGAAGCC	AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"""Tetratricopeptide (TTC) repeat domain containing"""	19750	protein-coding gene	gene with protein product		609332	"""tetratricopeptide repeat domain 7"""	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.300C>T	2.37:g.47177617C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																			C|0.928;T|0.072	0.072	strong		0.507	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
WNK2	65268	hgsc.bcm.edu	37	9	96052295	96052295	+	Silent	SNP	C	C	G	rs4744216	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:96052295C>G	ENST00000297954.4	+	21	5013	c.5013C>G	c.(5011-5013)gcC>gcG	p.A1671A	WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000427277.2_Silent_p.A1246A|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000349097.3_Silent_p.A1283A|WNK2_ENST00000395477.2_Silent_p.A1634A	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1671					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CTCGAGGGGCCGTGATGGAGC	0.557													C|||	508	0.101438	0.0567	0.1931	5008	,	,		18250	0.0794		0.165	False		,,,				2504	0.0542				p.A1634A		Atlas-SNP	.											.	WNK2	277	.	0			c.C4902G						PASS	.	C		287,4111		8,271,1920	56.0	43.0	47.0		4902	-7.8	0.0	9	dbSNP_111	47	1109,7465		87,935,3265	no	coding-synonymous	WNK2	NM_006648.3		95,1206,5185	GG,GC,CC		12.9345,6.5257,10.7616		1634/2218	96052295	1396,11576	2199	4287	6486	SO:0001819	synonymous_variant	65268	exon20			AGGGGCCGTGATG	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.5013C>G	9.37:g.96052295C>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		285|285	0.1304945054945055|0.1304945054945055	35|35	0.07113821138211382|0.07113821138211382	66|66	0.18232044198895028|0.18232044198895028	60|60	0.1048951048951049|0.1048951048951049	124|124	0.16358839050131926|0.16358839050131926	C|C	4.351|4.351	0.064678|0.064678	0.08388|0.08388	0.065257|0.065257	0.129345|0.129345	ENSG00000165238|ENSG00000165238	ENST00000432730;ENST00000448251;ENST00000453718|ENST00000411624	.|.	.|.	.|.	3.88|3.88	-7.75|-7.75	0.01236|0.01236	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.58432|0.58432	P|P	9.000000000036756E-6|9.000000000036756E-6	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.14172|0.14172	-1.0482|-1.0482	3|3	.|.	.|.	.|.	.|.	4.9979|4.9979	0.14249|0.14249	0.0956:0.5305:0.1214:0.2525|0.0956:0.5305:0.1214:0.2525	rs4744216;rs17342460;rs59448703|rs4744216;rs17342460;rs59448703	.|.	.|.	.|.	R|G	1630;431;157|1238	.|.	.|.	P|R	+|+	2|1	0|0	WNK2|WNK2	95092116|95092116	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.063000|0.063000	0.16089|0.16089	-2.141000|-2.141000	0.01300|0.01300	-2.184000|-2.184000	0.00762|0.00762	-1.267000|-1.267000	0.01435|0.01435	CCG|CGT	C|0.887;G|0.112	0.112	strong		0.557	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
MUC20	200958	hgsc.bcm.edu	37	3	195452991	195452991	+	Missense_Mutation	SNP	C	C	T	rs3828411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:195452991C>T	ENST00000447234.2	+	2	1643	c.1517C>T	c.(1516-1518)aCa>aTa	p.T506I	MUC20_ENST00000445522.2_Missense_Mutation_p.T471I|MUC20_ENST00000436408.1_Missense_Mutation_p.T506I|MUC20_ENST00000320736.6_Missense_Mutation_p.T335I	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	506	Involved in oligomerization.		Missing. {ECO:0000269|PubMed:14702039}.	AT -> TI (in Ref. 5; AAH29267). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		AACAGCGCCACAGAAAGAGAA	0.607																																					p.T335I		Atlas-SNP	.											.	MUC20	84	.	0			c.C1004T						PASS	.						58.0	51.0	53.0					3																	195452991		2160	4257	6417	SO:0001583	missense	200958	exon3			GCGCCACAGAAAG	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1517C>T	3.37:g.195452991C>T	ENSP00000414350:p.Thr506Ile	Somatic	366	0	0		WXS	Illumina HiSeq	Phase_I	396	94	0.237374	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	C	11.97	1.798091	0.31777	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.35605	1.82;2.14;1.97;1.3	3.86	-1.52	0.08637	.	1.053130	0.07525	N	0.911171	T	0.20088	0.0483	L	0.34521	1.04	0.09310	N	1	P	0.35844	0.524	B	0.35353	0.201	T	0.17899	-1.0354	10	0.17832	T	0.49	4.1971	0.5998	0.00742	0.1743:0.3375:0.1705:0.3177	rs3828411;rs52818607;rs3828411	335	E9PH32	.	I	506;335;506;471	ENSP00000414350:T506I;ENSP00000325431:T335I;ENSP00000396774:T506I;ENSP00000405629:T471I	ENSP00000325431:T335I	T	+	2	0	MUC20	196938662	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.792000	0.04594	-0.191000	0.10448	-0.279000	0.10071	ACA	C|0.942;T|0.058	0.058	strong		0.607	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
GRHL3	57822	hgsc.bcm.edu	37	1	24658063	24658063	+	Missense_Mutation	SNP	C	C	G	rs2486668	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24658063C>G	ENST00000350501.5	+	2	292	c.165C>G	c.(163-165)gaC>gaG	p.D55E	GRHL3_ENST00000530984.1_3'UTR|GRHL3_ENST00000342072.4_5'UTR|GRHL3_ENST00000356046.2_Missense_Mutation_p.D9E|GRHL3_ENST00000236255.4_Missense_Mutation_p.D60E|GRHL3_ENST00000361548.4_Missense_Mutation_p.D55E	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	55	Transcription activation.		D -> E (in dbSNP:rs2486668).		central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.D60E(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		GAGATGATGACAGTGTTGCGG	0.498													C|||	894	0.178514	0.2277	0.1311	5008	,	,		21488	0.1944		0.164	False		,,,				2504	0.1442				p.D60E		Atlas-SNP	.											GRHL3,NS,carcinoma,0,1	GRHL3	69	1	1	Substitution - Missense(1)	stomach(1)	c.C180G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	911,3495	350.5+/-310.9	79,753,1371	228.0	184.0	199.0		165,165,180,27	0.3	1.0	1	dbSNP_100	199	1414,7186	272.2+/-289.9	121,1172,3007	yes	missense,missense,missense,missense	GRHL3	NM_198174.2,NM_198173.2,NM_021180.3,NM_001195010.1	45,45,45,45	200,1925,4378	GG,GC,CC		16.4419,20.6764,17.8764	benign,benign,benign,benign	55/627,55/603,60/608,9/557	24658063	2325,10681	2203	4300	6503	SO:0001583	missense	57822	exon2			TGATGACAGTGTT	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"""transcription factor CP2-like 4"""	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.165C>G	1.37:g.24658063C>G	ENSP00000288955:p.Asp55Glu	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	220	101	0.459091	NM_021180	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	381	0.17445054945054944	96	0.1951219512195122	54	0.14917127071823205	101	0.17657342657342656	130	0.17150395778364116	C	16.02	3.004367	0.54254	0.206764	0.164419	ENSG00000158055	ENST00000361548;ENST00000350501;ENST00000356046;ENST00000524724;ENST00000236255	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67	5.93	0.337	0.15966	.	0.081063	0.53938	N	0.000042	T	0.00039	0.0001	L	0.47016	1.485	0.09310	P	1.0	B;B	0.10296	0.003;0.001	B;B	0.14578	0.01;0.011	T	0.06716	-1.0811	9	0.39692	T	0.17	-29.9612	2.9343	0.05809	0.2248:0.4219:0.2306:0.1228	rs2486668;rs17256946;rs52824550;rs2486668	60;55	Q8TE85-2;G3XAF0	.;.	E	55;55;9;9;60	ENSP00000354943:D55E;ENSP00000288955:D55E;ENSP00000348333:D9E;ENSP00000431290:D9E;ENSP00000236255:D60E	ENSP00000236255:D60E	D	+	3	2	GRHL3	24530650	0.998000	0.40836	0.997000	0.53966	0.996000	0.88848	0.647000	0.24812	0.353000	0.24079	0.655000	0.94253	GAC	C|0.823;G|0.177	0.177	strong		0.498	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
OR13H1	347468	hgsc.bcm.edu	37	X	130678596	130678596	+	Silent	SNP	C	C	G	rs17316625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:130678596C>G	ENST00000338616.3	+	1	647	c.549C>G	c.(547-549)ctC>ctG	p.L183L		NM_001004486.1	NP_001004486.1	Q8NG92	O13H1_HUMAN	olfactory receptor, family 13, subfamily H, member 1	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15	Acute lymphoblastic leukemia(192;0.000636)					TTCTCTCCCTCATTAAGCTGA	0.473													C|||	684	0.181192	0.0151	0.1369	3775	,	,		17026	0.0446		0.2654	False		,,,				2504	0.2628				p.L183L		Atlas-SNP	.											.	OR13H1	41	.	0			c.C549G						PASS	.	C		209,3626		6,171,26,1455,545	256.0	220.0	232.0		549	0.6	0.0	X	dbSNP_123	232	2432,4296		293,1132,714,1003,1158	no	coding-synonymous	OR13H1	NM_001004486.1		299,1303,740,2458,1703	GG,GC,G,CC,C		36.1474,5.4498,25.0024		183/309	130678596	2641,7922	2203	4300	6503	SO:0001819	synonymous_variant	347468	exon1			CTCCCTCATTAAG		CCDS35396.1	Xq26.2	2012-08-23			ENSG00000171054	ENSG00000171054		"""GPCR / Class A : Olfactory receptors"""	14755	protein-coding gene	gene with protein product							Standard	NM_001004486		Approved		uc011muw.2	Q8NG92	OTTHUMG00000022411	ENST00000338616.3:c.549C>G	X.37:g.130678596C>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	199	199	1	NM_001004486	B2RNQ3|Q6IET8|Q96R12	Silent	SNP	ENST00000338616.3	37	CCDS35396.1																																																																																			C|0.787;0|0.015	.	strong		0.473	OR13H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058297.1		
SCN7A	6332	hgsc.bcm.edu	37	2	167263065	167263065	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:167263065A>G	ENST00000409855.1	-	25	4200	c.4074T>C	c.(4072-4074)cgT>cgC	p.R1358R		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1358					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	CTTTTCCAAGACGCAGCATGT	0.463																																					p.R1358R		Atlas-SNP	.											SCN7A_ENST00000409855,NS,carcinoma,-1,2	SCN7A	410	2	0			c.T4074C						scavenged	.						118.0	112.0	114.0					2																	167263065		1983	4155	6138	SO:0001819	synonymous_variant	6332	exon25			TCCAAGACGCAGC	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.4074T>C	2.37:g.167263065A>G		Somatic	261	1	0.00383142		WXS	Illumina HiSeq	Phase_I	272	3	0.0110294	NM_002976		Silent	SNP	ENST00000409855.1	37	CCDS46442.1																																																																																			.	.	none		0.463	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
ZNF521	25925	hgsc.bcm.edu	37	18	22775185	22775185	+	Silent	SNP	C	C	T	rs1140026	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:22775185C>T	ENST00000361524.3	-	5	3745	c.3597G>A	c.(3595-3597)aaG>aaA	p.K1199K	ZNF521_ENST00000584787.1_Silent_p.K979K|ZNF521_ENST00000538137.2_Silent_p.K1199K	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1199					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CCATCTGACACTTGATGCATT	0.323			T	PAX5	ALL								C|||	1135	0.226637	0.1316	0.2089	5008	,	,		19650	0.2768		0.2535	False		,,,				2504	0.2883				p.K1199K		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.G3597A						PASS	.	C		631,3773	271.6+/-270.3	33,565,1604	145.0	126.0	133.0		3597	5.6	1.0	18	dbSNP_86	133	2084,6516	357.9+/-330.9	254,1576,2470	no	coding-synonymous	ZNF521	NM_015461.2		287,2141,4074	TT,TC,CC		24.2326,14.3279,20.8782		1199/1312	22775185	2715,10289	2202	4300	6502	SO:0001819	synonymous_variant	25925	exon5			CTGACACTTGATG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3597G>A	18.37:g.22775185C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																			C|0.786;T|0.214	0.214	strong		0.323	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
PCMTD1	115294	hgsc.bcm.edu	37	8	52746153	52746153	+	Silent	SNP	C	C	T	rs9298462	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:52746153C>T	ENST00000360540.5	-	5	913	c.507G>A	c.(505-507)gtG>gtA	p.V169V	PCMTD1_ENST00000544451.1_Silent_p.V93V|PCMTD1_ENST00000522514.1_Silent_p.V169V|PCMTD1_ENST00000519559.1_5'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	169						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				GGTCTTTCTGCACTCCAGCTC	0.388													G|||	2233	0.445887	0.0514	0.6268	5008	,	,		13567	0.4802		0.6292	False		,,,				2504	0.6268				p.V169V		Atlas-SNP	.											.	PCMTD1	73	.	0			c.G507A						PASS	.	G		720,3686		74,572,1557	147.0	130.0	135.0		507	0.4	1.0	8	dbSNP_119	135	5829,2771		1978,1873,449	no	coding-synonymous	PCMTD1	NM_052937.2		2052,2445,2006	TT,TC,CC		32.2209,16.3414,49.6463		169/358	52746153	6549,6457	2203	4300	6503	SO:0001819	synonymous_variant	115294	exon4			TTTCTGCACTCCA		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.507G>A	8.37:g.52746153C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_052937	Q96FK9	Silent	SNP	ENST00000360540.5	37	CCDS6148.1	967	0.44276556776556775	29	0.05894308943089431	222	0.6132596685082873	254	0.44405594405594406	462	0.6094986807387863	G	15.40	2.822254	0.50739	0.163414	0.677791	ENSG00000168300	ENST00000519554	.	.	.	5.48	0.404	0.16355	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.36529	-0.9744	3	.	.	.	-30.2887	1.6916	0.02853	0.2412:0.1038:0.4422:0.2129	rs9298462;rs17853080;rs9298462	.	.	.	Y	61	.	.	C	-	2	0	PCMTD1	52908706	0.864000	0.29904	0.968000	0.41197	0.937000	0.57800	-0.023000	0.12456	-0.486000	0.06744	-0.934000	0.02701	TGC	C|0.530;T|0.470	0.470	strong		0.388	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
NPLOC4	55666	hgsc.bcm.edu	37	17	79596811	79596811	+	Silent	SNP	C	C	T	rs9894429	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79596811C>T	ENST00000331134.6	-	2	251	c.36G>A	c.(34-36)ccG>ccA	p.P12P	NPLOC4_ENST00000539314.1_5'UTR|NPLOC4_ENST00000374747.5_Silent_p.P12P	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	12					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			TCACTCCATCCGGGGACTGGA	0.448													C|||	3376	0.674121	0.8147	0.6758	5008	,	,		19563	0.7768		0.4115	False		,,,				2504	0.6472				p.P12P		Atlas-SNP	.											.	NPLOC4	27	.	0			c.G36A						PASS	.	C		3042,974		1162,718,128	199.0	200.0	200.0	http://www.ncbi.nlm.nih.gov/pubmed?term	36	-9.1	0.5	17	dbSNP_119	200	3859,4497		901,2057,1220	yes	coding-synonymous	NPLOC4	NM_017921.2		2063,2775,1348	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	46.1824,24.253,44.2208		12/609	79596811	6901,5471	2008	4178	6186	SO:0001819	synonymous_variant	55666	exon2			TCCATCCGGGGAC	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.36G>A	17.37:g.79596811C>T		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	232	112	0.482759	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Silent	SNP	ENST00000331134.6	37	CCDS45812.1																																																																																			C|0.375;T|0.625	0.625	strong		0.448	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1		
EXOC3L4	91828	hgsc.bcm.edu	37	14	103576395	103576395	+	Silent	SNP	G	G	A	rs729185	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:103576395G>A	ENST00000380069.3	+	11	2080	c.2004G>A	c.(2002-2004)gcG>gcA	p.A668A		NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	668					exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						CCATTCTGGCGCTGCGCCGAC	0.687													A|||	1568	0.313099	0.3487	0.4236	5008	,	,		12324	0.4196		0.1322	False		,,,				2504	0.2628				p.A668A		Atlas-SNP	.											.	EXOC3L4	35	.	0			c.G2004A						PASS	.	A		1276,3076		173,930,1073	10.0	10.0	10.0		2004	-8.1	0.1	14	dbSNP_86	10	989,7495		69,851,3322	no	coding-synonymous	EXOC3L4	NM_001077594.1		242,1781,4395	AA,AG,GG		11.6572,29.3199,17.6457		668/723	103576395	2265,10571	2176	4242	6418	SO:0001819	synonymous_variant	91828	exon11			TCTGGCGCTGCGC	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 73"""	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.2004G>A	14.37:g.103576395G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	160	79	0.49375	NM_001077594	Q14CR2	Silent	SNP	ENST00000380069.3	37	CCDS32163.1																																																																																			G|0.764;A|0.236	0.236	strong		0.687	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093	
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28331127	28331127	+	Missense_Mutation	SNP	A	A	G	rs13201752|rs371085669	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28331127A>G	ENST00000377255.3	+	5	895	c.598A>G	c.(598-600)Aaa>Gaa	p.K200E	ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.K200E|ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.K52E	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	200			K -> A (requires 2 nucleotide substitutions; dbSNP:rs13201752). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.|K -> E (in dbSNP:rs45505399). {ECO:0000269|PubMed:14702039}.|K -> T (in dbSNP:rs13201753).		autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						CAGAGAAGATAAAGTGGTAGC	0.542													G|||	1952	0.389776	0.5825	0.3213	5008	,	,		16796	0.2986		0.2843	False		,,,				2504	0.3804				p.K200E		Atlas-SNP	.											ZKSCAN3,NS,other,-2,1	ZKSCAN3	50	1	0			c.A598G						PASS	.	G	GLU/LYS,GLU/LYS,GLU/LYS	2170,2236		549,1072,582	97.0	83.0	88.0		598,154,598	-6.0	0.0	6	dbSNP_121	88	2549,6051		401,1747,2152	yes	missense,missense,missense	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	56,56,56	950,2819,2734	GG,GA,AA		29.6395,49.251,36.2833	benign,benign,benign	200/539,52/391,200/539	28331127	4719,8287	2203	4300	6503	SO:0001583	missense	80317	exon4			GAAGATAAAGTGG	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.598A>G	6.37:g.28331127A>G	ENSP00000366465:p.Lys200Glu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	584	0.2673992673992674	201	0.40853658536585363	103	0.2845303867403315	128	0.22377622377622378	152	0.20052770448548812	.	0.001	-2.933332	0.00053	0.49251	0.296395	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.13901	2.55;2.55;2.55	2.99	-5.98	0.02220	.	.	.	.	.	T	0.01029	0.0034	N	0.08118	0	0.80722	P	0.0	B	0.21520	0.057	B	0.15870	0.014	T	0.37150	-0.9718	8	0.02654	T	1	.	9.4241	0.38570	0.37:0.1121:0.5179:0.0	rs45505399;rs58188640;rs61741931	200	Q9BRR0	ZKSC3_HUMAN	E	200;52;200	ENSP00000252211:K200E;ENSP00000341883:K52E;ENSP00000366465:K200E	ENSP00000252211:K200E	K	+	1	0	ZKSCAN3	28439106	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.587000	0.02108	-2.492000	0.00516	-2.444000	0.00210	AAA	A|0.648;G|0.352	0.352	alt		0.542	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
IRAK1	3654	hgsc.bcm.edu	37	X	153284192	153284192	+	Missense_Mutation	SNP	A	A	G	rs1059702	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153284192A>G	ENST00000369980.3	-	5	754	c.587T>C	c.(586-588)tTt>tCt	p.F196S	IRAK1_ENST00000393682.1_Missense_Mutation_p.F222S|IRAK1_ENST00000477274.1_5'Flank|IRAK1_ENST00000393687.2_Missense_Mutation_p.F196S|MIR718_ENST00000390190.2_RNA|IRAK1_ENST00000429936.2_Missense_Mutation_p.F222S|IRAK1_ENST00000369974.2_Missense_Mutation_p.F196S	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	196	ProST region.		F -> S (in dbSNP:rs1059702). {ECO:0000269|PubMed:8599092}.		activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCAAAACGGAAAGGGGCGGGC	0.642													G|||	2374	0.628874	0.7337	0.4337	3775	,	,		12789	0.1667		0.6491	False		,,,				2504	0.2883				p.F196S		Atlas-SNP	.											.	IRAK1	107	.	0			c.T587C						PASS	.	G	SER/PHE,SER/PHE,SER/PHE	3663,172		1491,139,542,2,29	40.0	39.0	39.0		587,587,587	3.7	0.0	X	dbSNP_86	39	5783,945		1800,578,1605,50,267	yes	missense,missense,missense	IRAK1	NM_001025242.1,NM_001025243.1,NM_001569.3	155,155,155	3291,717,2147,52,296	GG,GA,G,AA,A		14.0458,4.485,10.5746	benign,benign,benign	196/683,196/634,196/713	153284192	9446,1117	2203	4300	6503	SO:0001583	missense	3654	exon5			AACGGAAAGGGGC	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.587T>C	X.37:g.153284192A>G	ENSP00000358997:p.Phe196Ser	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	365	226	0.619178	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Missense_Mutation	SNP	ENST00000369980.3	37	CCDS14740.1	1126	0.6787221217600965	256	0.9552238805970149	116	0.48333333333333334	53	0.10474308300395258	339	0.7635135135135135	.	8.005	0.756226	0.15846	0.95515	0.859542	ENSG00000184216	ENST00000369980;ENST00000369974;ENST00000393682;ENST00000393687;ENST00000429936	T;D;D;T;T	0.92858	1.44;-3.12;-3.12;1.44;1.44	4.57	3.68	0.42216	Protein kinase-like domain (1);	0.475758	0.17848	N	0.159961	T	0.00012	0.0000	N	0.00116	-2.08	0.80722	P	0.0	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.44034	-0.9354	9	0.20046	T	0.44	-1.92	6.4293	0.21788	0.1022:0.3457:0.5521:0.0	rs1059702;rs17856471;rs58363670;rs1059702	196;196;196	P51617-4;P51617;P51617-2	.;IRAK1_HUMAN;.	S	196;196;222;196;222	ENSP00000358997:F196S;ENSP00000358991:F196S;ENSP00000377287:F222S;ENSP00000377291:F196S;ENSP00000392662:F222S	ENSP00000358990:F222S	F	-	2	0	IRAK1	152937386	0.053000	0.20554	0.002000	0.10522	0.090000	0.18270	0.487000	0.22356	0.235000	0.21160	-0.252000	0.11476	TTT	0|0.003;G|0.794	0.794	strong		0.642	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3		
MERTK	10461	hgsc.bcm.edu	37	2	112786049	112786049	+	Missense_Mutation	SNP	G	G	A	rs2230517	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:112786049G>A	ENST00000295408.4	+	19	2865	c.2608G>A	c.(2608-2610)Gtt>Att	p.V870I	MERTK_ENST00000409780.1_Missense_Mutation_p.V694I|MERTK_ENST00000421804.2_Missense_Mutation_p.V870I			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	870			V -> I (in dbSNP:rs2230517). {ECO:0000269|PubMed:17344846}.		apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						CCAAGCAGACGTTATTTACGT	0.512													G|||	361	0.0720847	0.2073	0.0389	5008	,	,		18361	0.002		0.0417	False		,,,				2504	0.0164				p.V870I		Atlas-SNP	.											.	MERTK	112	.	0			c.G2608A						PASS	.	G	ILE/VAL	856,3550	336.8+/-304.5	81,694,1428	120.0	124.0	122.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2608	-3.0	0.0	2	dbSNP_98	122	314,8286	113.3+/-173.4	4,306,3990	yes	missense	MERTK	NM_006343.2	29	85,1000,5418	AA,AG,GG		3.6512,19.4281,8.9958	benign	870/1000	112786049	1170,11836	2203	4300	6503	SO:0001583	missense	10461	exon19			GCAGACGTTATTT	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.2608G>A	2.37:g.112786049G>A	ENSP00000295408:p.Val870Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_006343	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	147	0.0673076923076923	103	0.20934959349593496	14	0.03867403314917127	0	0.0	30	0.0395778364116095	G	0.011	-1.730664	0.00687	0.194281	0.036512	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000393237;ENST00000409780;ENST00000449344	T;T;T;T	0.62105	0.05;0.05;0.05;0.05	5.95	-3.0	0.05480	Protein kinase-like domain (1);	0.970607	0.08337	N	0.961494	T	0.00039	0.0001	N	0.13235	0.315	0.80722	P	0.0	B	0.11235	0.004	B	0.08055	0.003	T	0.22382	-1.0218	9	0.09084	T	0.74	-8.8934	14.4689	0.67501	0.7085:0.0:0.2915:0.0	rs2230517;rs17838485;rs2230517	870	Q12866	MERTK_HUMAN	I	870;870;529;694;194	ENSP00000295408:V870I;ENSP00000389152:V870I;ENSP00000387277:V694I;ENSP00000412660:V194I	ENSP00000295408:V870I	V	+	1	0	MERTK	112502520	0.071000	0.21146	0.001000	0.08648	0.011000	0.07611	0.527000	0.22987	-0.674000	0.05253	-0.345000	0.07892	GTT	G|0.921;A|0.079	0.079	strong		0.512	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
EPC1	80314	hgsc.bcm.edu	37	10	32635834	32635834	+	Silent	SNP	G	G	A	rs11597888	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:32635834G>A	ENST00000263062.8	-	1	279	c.10C>T	c.(10-12)Ctg>Ttg	p.L4L	EPC1_ENST00000319778.6_Silent_p.L4L|RP11-135A24.2_ENST00000417447.1_RNA|EPC1_ENST00000375110.2_Intron|EPC1_ENST00000480402.1_5'UTR|AL391839.1_ENST00000410377.1_RNA|RP11-135A24.4_ENST00000412085.1_RNA	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	4					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				CGAAACGACAGTTTACTCATC	0.642													G|||	943	0.188299	0.062	0.2061	5008	,	,		11636	0.2103		0.1521	False		,,,				2504	0.3609				p.L4L		Atlas-SNP	.											.	EPC1	74	.	0			c.C10T						PASS	.	G		358,4048	181.5+/-209.5	8,342,1853	40.0	43.0	42.0		10	3.7	1.0	10	dbSNP_120	42	1419,7181	271.1+/-289.3	114,1191,2995	no	coding-synonymous	EPC1	NM_025209.2		122,1533,4848	AA,AG,GG		16.5,8.1253,13.6629		4/837	32635834	1777,11229	2203	4300	6503	SO:0001819	synonymous_variant	80314	exon1			ACGACAGTTTACT	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.10C>T	10.37:g.32635834G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Silent	SNP	ENST00000263062.8	37	CCDS7172.1																																																																																			G|0.859;A|0.141	0.141	strong		0.642	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1		
CFAP45	25790	hgsc.bcm.edu	37	1	159850401	159850401	+	Silent	SNP	C	C	G	rs7550537	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:159850401C>G	ENST00000368099.4	-	8	1051	c.987G>C	c.(985-987)ctG>ctC	p.L329L	CCDC19_ENST00000426543.2_Silent_p.L244L|CCDC19_ENST00000476696.1_5'UTR	NM_012337.2	NP_036469.2														endometrium(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	26	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			CCTGAGCCAGCAGTTCTGCTT	0.463													C|||	616	0.123003	0.146	0.062	5008	,	,		22368	0.1071		0.0984	False		,,,				2504	0.1769				p.L329L		Atlas-SNP	.											.	CCDC19	79	.	0			c.G987C						PASS	.	C		641,3765	276.6+/-273.2	43,555,1605	172.0	148.0	156.0		987	0.6	0.9	1	dbSNP_116	156	841,7759	194.4+/-239.8	47,747,3506	no	coding-synonymous	CCDC19	NM_012337.2		90,1302,5111	GG,GC,CC		9.7791,14.5483,11.3947		329/552	159850401	1482,11524	2203	4300	6503	SO:0001819	synonymous_variant	25790	exon8			AGCCAGCAGTTCT																												ENST00000368099.4:c.987G>C	1.37:g.159850401C>G		Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	324	156	0.481481	NM_012337		Silent	SNP	ENST00000368099.4	37	CCDS30914.1																																																																																			C|0.888;G|0.112	0.112	strong		0.463	CCDC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085979.1		
OR1S2	219958	hgsc.bcm.edu	37	11	57971171	57971171	+	Silent	SNP	C	C	T	rs200697120	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57971171C>T	ENST00000302592.6	-	1	482	c.483G>A	c.(481-483)tcG>tcA	p.S161S		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	161						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				TGAGGAACCACGAGATGACTG	0.498																																					p.S161S		Atlas-SNP	.											.	OR1S2	119	.	0			c.G483A						PASS	.						209.0	196.0	200.0					11																	57971171		2201	4296	6497	SO:0001819	synonymous_variant	219958	exon1			GAACCACGAGATG	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.483G>A	11.37:g.57971171C>T		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	285	28	0.0982456	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	37	CCDS31545.1																																																																																			C|0.928;T|0.072	0.072	strong		0.498	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
DNAH8	1769	hgsc.bcm.edu	37	6	38750888	38750888	+	Missense_Mutation	SNP	A	A	G	rs3823430	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:38750888A>G	ENST00000359357.3	+	15	1971	c.1717A>G	c.(1717-1719)Atc>Gtc	p.I573V	DNAH8_ENST00000441566.1_Missense_Mutation_p.I573V|DNAH8_ENST00000449981.2_Missense_Mutation_p.I790V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	573			I -> V (in dbSNP:rs3823430). {ECO:0000269|PubMed:12297094}.		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CACAGCCTGGATCAGAGAGAT	0.433													A|||	908	0.18131	0.1074	0.1585	5008	,	,		17777	0.37		0.1093	False		,,,				2504	0.1769				p.I790V		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A2368G						PASS	.	A	VAL/ILE	397,4009	197.1+/-221.3	19,359,1825	138.0	126.0	130.0		2368	1.4	1.0	6	dbSNP_107	130	1193,7407	242.5+/-272.5	70,1053,3177	yes	missense	DNAH8	NM_001206927.1	29	89,1412,5002	GG,GA,AA		13.8721,9.0104,12.2251	benign	790/4708	38750888	1590,11416	2203	4300	6503	SO:0001583	missense	1769	exon17			GCCTGGATCAGAG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.1717A>G	6.37:g.38750888A>G	ENSP00000352312:p.Ile573Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		400	0.18315018315018314	53	0.10772357723577236	54	0.14917127071823205	214	0.3741258741258741	79	0.10422163588390501	A	4.702	0.130510	0.08981	0.090104	0.138721	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.54866	0.55;0.55;0.55	5.83	1.44	0.22558	Dynein heavy chain, domain-1 (1);	0.769510	0.12095	N	0.500051	T	0.06600	0.0169	N	0.03000	-0.44	0.43095	P	0.005229000000000039	B	0.02656	0.0	B	0.04013	0.001	T	0.31668	-0.9935	9	0.07813	T	0.8	.	4.3906	0.11339	0.479:0.0:0.3697:0.1513	rs3823430;rs52804056;rs58149215;rs3823430	573	Q96JB1	DYH8_HUMAN	V	778;778;573;573	ENSP00000333363:I778V;ENSP00000352312:I573V;ENSP00000402294:I573V	ENSP00000333363:I778V	I	+	1	0	DNAH8	38858866	0.995000	0.38212	0.996000	0.52242	0.605000	0.37080	0.254000	0.18314	-0.050000	0.13356	-0.408000	0.06270	ATC	A|0.848;G|0.152	0.152	strong		0.433	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33568763	33568763	+	Missense_Mutation	SNP	C	C	T	rs41313967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:33568763C>T	ENST00000290943.6	+	15	2959	c.2863C>T	c.(2863-2865)Cca>Tca	p.P955S	ANKRD18B_ENST00000426460.2_3'UTR	NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	955										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						gaggccagACCCAGAGTTACC	0.388													.|||	297	0.0593051	0.056	0.0346	5008	,	,		16961	0.0437		0.0616	False		,,,				2504	0.0951				p.P954S		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.C2860T						PASS	.																																			SO:0001583	missense	441459	exon15			CCAGACCCAGAGT			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.2863C>T	9.37:g.33568763C>T	ENSP00000290943:p.Pro955Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_001244752		Missense_Mutation	SNP	ENST00000290943.6	37		106	0.048534798534798536	29	0.05894308943089431	14	0.03867403314917127	16	0.027972027972027972	47	0.06200527704485488	C	10.39	1.336581	0.24253	.	.	ENSG00000230453	ENST00000290943;ENST00000357927	T;T	0.29655	1.56;1.56	1.6	0.667	0.17907	.	.	.	.	.	T	0.03434	0.0099	.	.	.	0.22366	N	0.999163	.	.	.	.	.	.	T	0.20974	-1.0259	5	0.66056	D	0.02	.	3.9938	0.09549	0.0:0.7692:0.0:0.2308	rs41313967	.	.	.	S	955;336	ENSP00000290943:P955S;ENSP00000350607:P336S	ENSP00000290943:P955S	P	+	1	0	ANKRD18B	33558763	0.003000	0.15002	0.005000	0.12908	0.014000	0.08584	0.286000	0.18902	0.236000	0.21180	0.454000	0.30748	CCA	C|0.944;T|0.056	0.056	strong		0.388	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
LARGE	9215	hgsc.bcm.edu	37	22	33679238	33679238	+	Silent	SNP	T	T	C	rs11913417	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:33679238T>C	ENST00000354992.2	-	14	2398	c.1827A>G	c.(1825-1827)tcA>tcG	p.S609S	LARGE_ENST00000402320.1_Silent_p.S557S|LARGE_ENST00000452586.2_Silent_p.S408S|LARGE_ENST00000337431.2_Silent_p.S557S|LARGE_ENST00000437602.2_Intron|LARGE_ENST00000397394.2_Silent_p.S609S	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	609					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				ACTCCGCTTTTGACTTGGGGA	0.547													C|||	182	0.0363419	0.0756	0.0086	5008	,	,		19914	0.005		0.004	False		,,,				2504	0.0685				p.S609S	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											.	LARGE	98	.	0			c.A1827G						PASS	.	C	,	280,4126	800.8+/-415.6	9,262,1932	138.0	119.0	126.0		1827,1827	-10.8	0.0	22	dbSNP_120	126	44,8556	817.3+/-406.9	0,44,4256	no	coding-synonymous,coding-synonymous	LARGE	NM_004737.4,NM_133642.3	,	9,306,6188	CC,CT,TT		0.5116,6.355,2.4912	,	609/757,609/757	33679238	324,12682	2203	4300	6503	SO:0001819	synonymous_variant	9215	exon14			CGCTTTTGACTTG	AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1827A>G	22.37:g.33679238T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	152	65	0.427632	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	37	CCDS13912.1																																																																																			T|0.970;C|0.030	0.030	strong		0.547	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642	
SLC39A14	23516	hgsc.bcm.edu	37	8	22273687	22273687	+	Silent	SNP	T	T	C	rs6558052	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22273687T>C	ENST00000381237.1	+	7	1160	c.1041T>C	c.(1039-1041)caT>caC	p.H347H	SLC39A14_ENST00000359741.5_Silent_p.H347H|SLC39A14_ENST00000289952.5_Silent_p.H347H|SLC39A14_ENST00000240095.6_Silent_p.H347H	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	347					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		ACGGCCTCCATAATTTCATCG	0.557													C|||	1434	0.286342	0.7247	0.121	5008	,	,		21035	0.1915		0.0517	False		,,,				2504	0.1503				p.H347H		Atlas-SNP	.											SLC39A14_ENST00000381237,NS,malignant_melanoma,+2,2	SLC39A14	59	2	0			c.T1041C						PASS	.	C	,,,	2620,1786	527.4+/-372.1	791,1038,374	103.0	96.0	99.0		1041,1041,1041,1041	4.2	1.0	8	dbSNP_116	99	465,8135	798.8+/-407.4	10,445,3845	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC39A14	NM_001128431.2,NM_001135153.1,NM_001135154.1,NM_015359.4	,,,	801,1483,4219	CC,CT,TT		5.407,40.5356,23.7198	,,,	347/493,347/493,347/482,347/493	22273687	3085,9921	2203	4300	6503	SO:0001819	synonymous_variant	23516	exon7			CCTCCATAATTTC	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"""Solute carriers"""	20858	protein-coding gene	gene with protein product		608736	"""solute carrier family 39 (metal ion transporter), member 14"""			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.1041T>C	8.37:g.22273687T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	203	94	0.463054	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Silent	SNP	ENST00000381237.1	37	CCDS47823.1																																																																																			T|0.748;C|0.252	0.252	strong		0.557	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677	
SVIL	6840	hgsc.bcm.edu	37	10	29779936	29779936	+	Silent	SNP	G	G	A	rs45519332	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:29779936G>A	ENST00000355867.4	-	22	4784	c.4032C>T	c.(4030-4032)tcC>tcT	p.S1344S	SVIL_ENST00000535393.1_Silent_p.S258S|SVIL_ENST00000375400.3_Silent_p.S918S|SVIL_ENST00000375398.2_Silent_p.S1344S|SVIL_ENST00000538146.1_Silent_p.S136S	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1344					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GCTCGGCCACGGAAGACGTCA	0.587													A|||	409	0.0816693	0.0976	0.1527	5008	,	,		19089	0.0347		0.0825	False		,,,				2504	0.0573				p.S1344S		Atlas-SNP	.											.	SVIL	226	.	0			c.C4032T						PASS	.	A	,	415,3991	779.2+/-414.3	10,395,1798	27.0	27.0	27.0		2754,4032	-8.2	0.0	10	dbSNP_127	27	629,7971	783.4+/-407.6	3,623,3674	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	13,1018,5472	AA,AG,GG		7.314,9.419,8.0271	,	918/1789,1344/2215	29779936	1044,11962	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon22			GGCCACGGAAGAC	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.4032C>T	10.37:g.29779936G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	90	30	0.333333	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			G|0.928;A|0.072	0.072	strong		0.587	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
ASZ1	136991	hgsc.bcm.edu	37	7	117024820	117024820	+	Missense_Mutation	SNP	T	T	G	rs1029396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:117024820T>G	ENST00000284629.2	-	6	709	c.647A>C	c.(646-648)aAg>aCg	p.K216T		NM_130768.2	NP_570124.1			ankyrin repeat, SAM and basic leucine zipper domain containing 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(3)|skin(1)	24	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)			ACTTGGCATCTTTCCATCTTT	0.348													T|||	1123	0.224241	0.0764	0.2478	5008	,	,		17556	0.4157		0.0775	False		,,,				2504	0.3609				p.K216T		Atlas-SNP	.											.	ASZ1	56	.	0			c.A647C						PASS	.	T	THR/LYS	306,4100	166.9+/-198.0	13,280,1910	168.0	151.0	156.0		647	3.1	1.0	7	dbSNP_86	156	675,7925	170.1+/-221.3	26,623,3651	yes	missense	ASZ1	NM_130768.2	78	39,903,5561	GG,GT,TT		7.8488,6.9451,7.5427	benign	216/476	117024820	981,12025	2203	4300	6503	SO:0001583	missense	136991	exon6			GGCATCTTTCCAT	AF461259	CCDS5772.1	7q31.2	2013-01-10	2005-03-15	2004-07-16	ENSG00000154438	ENSG00000154438		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	1350	protein-coding gene	gene with protein product		605797	"""ankyrin-like 1"""	C7orf7, ANKL1		12040005, 11279520	Standard	NM_130768		Approved	Orf3, GASZ, ALP1, CT1.19	uc003vjb.2	Q8WWH4	OTTHUMG00000064565	ENST00000284629.2:c.647A>C	7.37:g.117024820T>G	ENSP00000284629:p.Lys216Thr	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	235	114	0.485106	NM_130768		Missense_Mutation	SNP	ENST00000284629.2	37	CCDS5772.1	400	0.18315018315018314	33	0.06707317073170732	73	0.20165745856353592	225	0.39335664335664333	69	0.09102902374670185	T	13.96	2.391736	0.42410	0.069451	0.078488	ENSG00000154438	ENST00000284629	T	0.72394	-0.65	5.83	3.1	0.35709	Ankyrin repeat-containing domain (3);	0.245619	0.47455	D	0.000233	T	0.00012	0.0000	M	0.61703	1.905	0.28069	P	0.9326477	B;P	0.37914	0.381;0.611	B;B	0.30029	0.11;0.11	T	0.21109	-1.0255	9	0.44086	T	0.13	-8.1857	8.1602	0.31194	0.0:0.205:0.0:0.795	rs1029396;rs52830819;rs59010785;rs1029396	216;216	B7ZM20;Q8WWH4	.;ASZ1_HUMAN	T	216	ENSP00000284629:K216T	ENSP00000284629:K216T	K	-	2	0	ASZ1	116812056	1.000000	0.71417	0.992000	0.48379	0.789000	0.44602	2.902000	0.48703	0.337000	0.23665	0.533000	0.62120	AAG	T|0.868;G|0.132	0.132	strong		0.348	ASZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000138907.7	NM_130768	
PPFIA2	8499	hgsc.bcm.edu	37	12	81769581	81769581	+	Silent	SNP	C	C	T	rs10862301	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:81769581C>T	ENST00000549396.1	-	10	1285	c.1125G>A	c.(1123-1125)ctG>ctA	p.L375L	PPFIA2_ENST00000333447.7_Silent_p.L357L|PPFIA2_ENST00000550584.2_Silent_p.L375L|PPFIA2_ENST00000552948.1_Silent_p.L375L|PPFIA2_ENST00000407050.4_Silent_p.L301L|RP11-315E17.1_ENST00000546936.1_RNA|PPFIA2_ENST00000443686.3_Silent_p.L276L|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000549325.1_Silent_p.L357L|PPFIA2_ENST00000550359.2_Silent_p.L222L|PPFIA2_ENST00000548586.1_Silent_p.L375L	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	375	Glu-rich.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						GAACCTGCCGCAGGATAGCTT	0.403													T|||	2232	0.445687	0.5673	0.402	5008	,	,		16197	0.5387		0.2724	False		,,,				2504	0.3947				p.L375L		Atlas-SNP	.											.	PPFIA2	207	.	0			c.G1125A						PASS	.	T	,,,,,,	1778,2016		402,974,521	150.0	147.0	148.0		1125,1071,1125,1125,903,828,1125	-5.7	0.8	12	dbSNP_120	148	2059,6149		257,1545,2302	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPFIA2	NM_001220473.1,NM_001220474.1,NM_001220475.1,NM_001220476.1,NM_001220477.1,NM_001220478.1,NM_003625.3	,,,,,,	659,2519,2823	TT,TC,CC		25.0853,46.8635,31.9697	,,,,,,	375/1248,357/1233,375/1237,375/1252,301/1157,276/1153,375/1258	81769581	3837,8165	1897	4104	6001	SO:0001819	synonymous_variant	8499	exon9			CTGCCGCAGGATA	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9246	protein-coding gene	gene with protein product	"""Liprin-alpha2"""	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.1125G>A	12.37:g.81769581C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	221	109	0.493213	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Silent	SNP	ENST00000549396.1	37	CCDS55857.1	955	0.43727106227106227	287	0.5833333333333334	138	0.3812154696132597	323	0.5646853146853147	207	0.27308707124010556	T	6.490	0.458611	0.12342	0.468635	0.250853	ENSG00000139220	ENST00000548790	.	.	.	5.45	-5.72	0.02406	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999899829	.	.	.	.	.	.	T	0.44817	-0.9303	3	.	.	.	-3.6027	3.7466	0.08551	0.0904:0.3488:0.2767:0.2841	rs10862301;rs52801936;rs57160712;rs10862301	.	.	.	Y	193	.	.	C	-	2	0	PPFIA2	80293712	0.378000	0.25114	0.806000	0.32338	0.739000	0.42172	-0.501000	0.06398	-1.195000	0.02680	-1.811000	0.00612	TGC	C|0.573;N|0.000	.	strong		0.403	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1		
ALCAM	214	hgsc.bcm.edu	37	3	105260518	105260518	+	Silent	SNP	G	G	A	rs579565	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:105260518G>A	ENST00000306107.5	+	8	1400	c.900G>A	c.(898-900)ctG>ctA	p.L300L	ALCAM_ENST00000389927.4_Intron|ALCAM_ENST00000481337.1_3'UTR|ALCAM_ENST00000472644.2_Silent_p.L300L|ALCAM_ENST00000486979.2_Silent_p.L249L	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	300	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CTTACACACTGACGGATGTGA	0.423													G|||	1186	0.236821	0.3041	0.3084	5008	,	,		19891	0.1548		0.2366	False		,,,				2504	0.18				p.L300L		Atlas-SNP	.											.	ALCAM	71	.	0			c.G900A						PASS	.	G		1260,3146	428.7+/-342.0	184,892,1127	163.0	131.0	142.0		900	5.3	1.0	3	dbSNP_83	142	1903,6697	335.4+/-321.4	219,1465,2616	no	coding-synonymous	ALCAM	NM_001627.3		403,2357,3743	AA,AG,GG		22.1279,28.5974,24.3195		300/584	105260518	3163,9843	2203	4300	6503	SO:0001819	synonymous_variant	214	exon8			CACACTGACGGAT	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.900G>A	3.37:g.105260518G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	130	60	0.461538	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Silent	SNP	ENST00000306107.5	37	CCDS33810.1																																																																																			G|0.759;A|0.241	0.241	strong		0.423	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
ZNF653	115950	hgsc.bcm.edu	37	19	11598600	11598600	+	Silent	SNP	C	C	T	rs184960221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11598600C>T	ENST00000293771.5	-	4	814	c.678G>A	c.(676-678)acG>acA	p.T226T	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	226					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						GGCTGGTGGGCGTCGCTGCCG	0.672													C|||	240	0.0479233	0.0393	0.0994	5008	,	,		9045	0.0397		0.0408	False		,,,				2504	0.0389				p.T226T	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											ZNF653,NS,carcinoma,0,1	ZNF653	48	1	0			c.G678A						PASS	.						25.0	24.0	24.0					19																	11598600		2175	4227	6402	SO:0001819	synonymous_variant	115950	exon4			GGTGGGCGTCGCT	AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.678G>A	19.37:g.11598600C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_138783	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			C|0.959;T|0.041	0.041	strong		0.672	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
SAGE1	55511	hgsc.bcm.edu	37	X	134986700	134986700	+	Silent	SNP	T	T	C	rs12014884	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:134986700T>C	ENST00000370709.3	+	3	285	c.285T>C	c.(283-285)aaT>aaC	p.N95N	SAGE1_ENST00000324447.3_Silent_p.N95N|SAGE1_ENST00000537770.1_Silent_p.N95N|SAGE1_ENST00000535938.1_Silent_p.N95N			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	95						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					TAGCTGATAATGTCTTGTCAA	0.423													N|||	610	0.161589	0.0673	0.1614	3775	,	,		15712	0.1002		0.2058	False		,,,				2504	0.1033				p.N95N		Atlas-SNP	.											.	SAGE1	160	.	0			c.T285C						PASS	.	C		557,3278		30,426,71,1176,500	167.0	132.0	144.0		285	1.4	0.0	X	dbSNP_120	144	1755,4973		188,924,455,1316,1417	no	coding-synonymous	SAGE1	NM_018666.2		218,1350,526,2492,1917	CC,CT,C,TT,T		26.085,14.5241,21.8877		95/905	134986700	2312,8251	2203	4300	6503	SO:0001819	synonymous_variant	55511	exon4			TGATAATGTCTTG	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.285T>C	X.37:g.134986700T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	278	12	0.0431655	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			T|0.806;C|0.194	0.194	strong		0.423	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
GYS1	2997	hgsc.bcm.edu	37	19	49485548	49485548	+	Silent	SNP	G	G	A	rs5464	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49485548G>A	ENST00000323798.3	-	7	1222	c.1026C>T	c.(1024-1026)ttC>ttT	p.F342F	GYS1_ENST00000544287.1_5'UTR|GYS1_ENST00000541188.1_Silent_p.F262F|GYS1_ENST00000540532.1_Missense_Mutation_p.S223F|GYS1_ENST00000263276.6_Silent_p.F278F	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	342					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		ATGCCTCCAGGAAGACGTCAG	0.517													G|||	1275	0.254593	0.2943	0.2608	5008	,	,		17958	0.2183		0.2922	False		,,,				2504	0.1953				p.F342F		Atlas-SNP	.											.	GYS1	59	.	0			c.C1026T						PASS	.	G	,	1243,3163	431.0+/-342.8	197,849,1157	110.0	101.0	104.0		834,1026	4.2	1.0	19	dbSNP_52	104	2535,6065	415.4+/-351.8	365,1805,2130	no	coding-synonymous,coding-synonymous	GYS1	NM_001161587.1,NM_002103.4	,	562,2654,3287	AA,AG,GG		29.4767,28.2115,29.0481	,	278/674,342/738	49485548	3778,9228	2203	4300	6503	SO:0001819	synonymous_variant	2997	exon7			CTCCAGGAAGACG		CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.1026C>T	19.37:g.49485548G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_002103	Q9BTT9	Silent	SNP	ENST00000323798.3	37	CCDS12747.1	589	0.2696886446886447	156	0.3170731707317073	100	0.27624309392265195	134	0.23426573426573427	199	0.262532981530343	G	12.39	1.922336	0.33908	0.282115	0.294767	ENSG00000104812	ENST00000540532	T	0.26373	1.74	5.21	4.16	0.48862	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.39974	P	0.025175999999999976	.	.	.	.	.	.	T	0.43669	-0.9377	4	.	.	.	-31.0172	8.5832	0.33642	0.1731:0.0:0.8269:0.0	rs5464;rs2228476;rs8192706;rs13306416;rs16981011;rs16981013;rs17206756;rs5464	.	.	.	F	223	ENSP00000445197:S223F	.	S	-	2	0	GYS1	54177360	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.703000	0.37846	2.613000	0.88420	0.650000	0.86243	TCC	G|0.713;A|0.287	0.287	strong		0.517	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103	
PRRC2A	7916	hgsc.bcm.edu	37	6	31599594	31599594	+	Silent	SNP	A	A	G	rs10947220	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31599594A>G	ENST00000376033.2	+	16	3378	c.3144A>G	c.(3142-3144)ggA>ggG	p.G1048G	PRRC2A_ENST00000376007.4_Silent_p.G1048G	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1048	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GAGGGCGGGGAGCCCGAAGCC	0.647													A|||	233	0.0465256	0.1006	0.0634	5008	,	,		12424	0.0179		0.0219	False		,,,				2504	0.0164				p.G1048G		Atlas-SNP	.											PRRC2A,NS,neuroblastoma,0,1	PRRC2A	152	1	0			c.A3144G						PASS	.	A	,	170,2840		4,162,1339	15.0	16.0	15.0		3144,3144	-0.8	1.0	6	dbSNP_120	15	114,5284		0,114,2585	no	coding-synonymous,coding-synonymous	PRRC2A	NM_004638.3,NM_080686.2	,	4,276,3924	GG,GA,AA		2.1119,5.6478,3.3777	,	1048/2158,1048/2158	31599594	284,8124	1505	2699	4204	SO:0001819	synonymous_variant	7916	exon16			GCGGGGAGCCCGA	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3144A>G	6.37:g.31599594A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																			A|0.949;G|0.050;T|0.000	0.050	strong		0.647	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
MRPS9	64965	hgsc.bcm.edu	37	2	105705507	105705507	+	Silent	SNP	C	C	T	rs11538198	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:105705507C>T	ENST00000258455.3	+	6	665	c.555C>T	c.(553-555)ctC>ctT	p.L185L		NM_182640.2	NP_872578.1	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9	185					DNA damage response, detection of DNA damage (GO:0042769)|peptide biosynthetic process (GO:0043043)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						AAAGTCTGCTCCCAGAAAAAA	0.308													T|||	836	0.166933	0.1339	0.2781	5008	,	,		14945	0.1091		0.2247	False		,,,				2504	0.1329				p.L185L		Atlas-SNP	.											.	MRPS9	32	.	0			c.C555T						PASS	.	T		639,3767	759.9+/-412.9	33,573,1597	83.0	88.0	87.0		555	-5.4	0.0	2	dbSNP_120	87	2070,6526	714.8+/-406.0	231,1608,2459	no	coding-synonymous	MRPS9	NM_182640.2		264,2181,4056	TT,TC,CC		24.081,14.503,20.8353		185/397	105705507	2709,10293	2203	4298	6501	SO:0001819	synonymous_variant	64965	exon6			TCTGCTCCCAGAA		CCDS2065.1	2q12.1	2012-09-13			ENSG00000135972	ENSG00000135972		"""Mitochondrial ribosomal proteins / small subunits"""	14501	protein-coding gene	gene with protein product	"""28S ribosomal protein S9, mitochondrial"""	611975				11279123	Standard	NM_182640		Approved	RPMS9, MRP-S9, S9mt	uc002tcn.4	P82933	OTTHUMG00000130807	ENST00000258455.3:c.555C>T	2.37:g.105705507C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_182640	Q6PG40	Silent	SNP	ENST00000258455.3	37	CCDS2065.1																																																																																			C|0.797;T|0.203	0.203	strong		0.308	MRPS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253352.1	NM_182640	
DNAH14	127602	hgsc.bcm.edu	37	1	225521101	225521101	+	Intron	SNP	G	G	C	rs41268715	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225521101G>C	ENST00000445597.2	+	45	7485				DNAH14_ENST00000439375.2_Missense_Mutation_p.E3232Q|DNAH14_ENST00000430092.1_Missense_Mutation_p.E3232Q			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TTTAACACCAGAATTTCGCCA	0.338													G|||	133	0.0265575	0.003	0.0245	5008	,	,		14751	0.001		0.0547	False		,,,				2504	0.0573				p.E3232Q		Atlas-SNP	.											.	DNAH14	300	.	0			c.G9694C						PASS	.	G	GLN/GLU	10,1374		0,10,682	123.0	107.0	112.0		9694	4.7	1.0	1	dbSNP_127	112	161,3021		3,155,1433	yes	missense	DNAH14	NM_001373.1	29	3,165,2115	CC,CG,GG		5.0597,0.7225,3.7451	possibly-damaging	3232/4516	225521101	171,4395	692	1591	2283	SO:0001627	intron_variant	127602	exon64			ACACCAGAATTTC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.7486-3867G>C	1.37:g.225521101G>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		50	0.022893772893772892	3	0.006097560975609756	9	0.024861878453038673	0	0.0	38	0.05013192612137203	G	13.68	2.309067	0.40895	0.007225	0.050597	ENSG00000185842	ENST00000430092;ENST00000439375	T;T	0.74315	-0.83;-0.83	5.62	4.71	0.59529	.	0.258285	0.20213	N	0.096852	T	0.29158	0.0725	L	0.39020	1.185	0.80722	D	1	P	0.48016	0.904	P	0.48227	0.571	T	0.51204	-0.8735	10	0.10636	T	0.68	.	13.473	0.61292	0.0772:0.0:0.9228:0.0	rs41268715	3232	Q0VDD8-4	.	Q	3232	ENSP00000414402:E3232Q;ENSP00000392061:E3232Q	ENSP00000414402:E3232Q	E	+	1	0	DNAH14	223587724	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.510000	0.60455	1.370000	0.46153	0.603000	0.83216	GAA	G|0.968;C|0.032	0.032	strong		0.338	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
MAP7D3	79649	hgsc.bcm.edu	37	X	135310785	135310785	+	Missense_Mutation	SNP	T	T	C	rs2273221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:135310785T>C	ENST00000316077.9	-	11	2103	c.1883A>G	c.(1882-1884)cAa>cGa	p.Q628R	MAP7D3_ENST00000370661.1_Missense_Mutation_p.Q593R|MAP7D3_ENST00000495432.1_5'UTR|MAP7D3_ENST00000370663.5_Missense_Mutation_p.Q610R	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	628			Q -> R (in dbSNP:rs2273221). {ECO:0000269|PubMed:15489334}.		microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.Q925R(1)		central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					TGCTGACCTTTGCTGCATTTC	0.398													C|||	1846	0.489007	0.2126	0.3501	3775	,	,		12628	0.5427		0.4076	False		,,,				2504	0.3732				p.Q628R		Atlas-SNP	.											.	MAP7D3	102	.	1	Substitution - Missense(1)	prostate(1)	c.A1883G						PASS	.	C	ARG/GLN,ARG/GLN,ARG/GLN	937,2175		112,522,191,637,379	148.0	126.0	133.0		1829,1778,1883	-5.9	0.0	X	dbSNP_100	133	3433,2942		704,1087,938,509,837	yes	missense,missense,missense	MAP7D3	NM_001173516.1,NM_001173517.1,NM_024597.3	43,43,43	816,1609,1129,1146,1216	CC,CT,C,TT,T		46.149,30.1093,46.063	benign,benign,benign	610/859,593/842,628/877	135310785	4370,5117	1841	4075	5916	SO:0001583	missense	79649	exon11			GACCTTTGCTGCA	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1883A>G	X.37:g.135310785T>C	ENSP00000318086:p.Gln628Arg	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	874	0.5268233875828813	75	0.1736111111111111	90	0.3409090909090909	202	0.543010752688172	224	0.4072727272727273	C	7.976	0.750132	0.15778	0.301093	0.53851	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.44	-5.9	0.02275	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.0;0.0;0.001	B;B;B;B	0.08055	0.002;0.001;0.002;0.003	T	0.44682	-0.9312	8	0.25751	T	0.34	.	6.02	0.19625	0.1559:0.0717:0.0997:0.6727	rs2273221;rs17330808;rs17846287;rs17859311;rs52825916;rs61380364;rs2273221	610;587;628;593	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	R	593;628;610;587	ENSP00000359695:Q593R;ENSP00000318086:Q628R;ENSP00000359697:Q610R;ENSP00000359694:Q587R	ENSP00000318086:Q628R	Q	-	2	0	MAP7D3	135138451	0.001000	0.12720	0.000000	0.03702	0.021000	0.10359	-0.479000	0.06567	-2.118000	0.00828	-0.879000	0.02964	CAA	0|0.030;C|0.478	0.478	strong		0.398	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
TENM2	57451	hgsc.bcm.edu	37	5	167674370	167674370	+	Silent	SNP	C	C	T	rs3733988	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:167674370C>T	ENST00000518659.1	+	27	6465	c.6426C>T	c.(6424-6426)atC>atT	p.I2142I	TENM2_ENST00000519204.1_Silent_p.I2021I|TENM2_ENST00000545108.1_Silent_p.I2141I|TENM2_ENST00000520394.1_Silent_p.I1903I|TENM2_ENST00000403607.2_Silent_p.I1966I	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2142					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.I1975I(1)									TCAACCAGATCATCACCACTG	0.502													T|||	2181	0.435503	0.4418	0.4496	5008	,	,		22119	0.1726		0.5408	False		,,,				2504	0.5798				p.I2133I		Atlas-SNP	.											ODZ2,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C6399T						PASS	.	T		1689,2371		343,1003,684	131.0	128.0	129.0		6399	4.7	1.0	5	dbSNP_107	129	4405,3949		1191,2023,963	no	coding-synonymous	ODZ2	NM_001122679.1		1534,3026,1647	TT,TC,CC		47.2708,41.601,49.0897		2133/2766	167674370	6094,6320	2030	4177	6207	SO:0001819	synonymous_variant	57451	exon27			CCAGATCATCACC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.6426C>T	5.37:g.167674370C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				C|0.592;T|0.408	0.408	strong		0.502	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
TRAPPC5	126003	hgsc.bcm.edu	37	19	7747445	7747445	+	Silent	SNP	G	G	A	rs1053363	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7747445G>A	ENST00000317378.5	+	2	493	c.306G>A	c.(304-306)gcG>gcA	p.A102A	TRAPPC5_ENST00000596148.1_Silent_p.A102A|CTD-3214H19.16_ENST00000597959.1_3'UTR|TRAPPC5_ENST00000426877.2_Silent_p.A102A|TRAPPC5_ENST00000595985.1_Silent_p.A35A	NM_174894.2	NP_777554.1	Q8IUR0	TPPC5_HUMAN	trafficking protein particle complex 5	102					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|TRAPP complex (GO:0030008)				NS(1)|lung(2)	3						GCAAGGAGGCGGACAAGCTGG	0.632													G|||	1217	0.243011	0.4274	0.1326	5008	,	,		13972	0.127		0.174	False		,,,				2504	0.2628				p.A102A		Atlas-SNP	.											.	TRAPPC5	11	.	0			c.G306A						PASS	.	G	,,	1729,2653		355,1019,817	37.0	41.0	39.0		306,306,306	-8.2	0.6	19	dbSNP_86	39	1408,7148		106,1196,2976	no	coding-synonymous,coding-synonymous,coding-synonymous	TRAPPC5	NM_001042461.1,NM_001042462.1,NM_174894.1	,,	461,2215,3793	AA,AG,GG		16.4563,39.4569,24.2464	,,	102/189,102/189,102/189	7747445	3137,9801	2191	4278	6469	SO:0001819	synonymous_variant	126003	exon2			GGAGGCGGACAAG	BC042161	CCDS42490.1	19p13.3	2011-10-10				ENSG00000181029		"""Trafficking protein particle complex"""	23067	protein-coding gene	gene with protein product							Standard	NM_001042462		Approved	MGC52424, TRS31	uc002mhj.2	Q8IUR0		ENST00000317378.5:c.306G>A	19.37:g.7747445G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_001042461	A8K7I6	Silent	SNP	ENST00000317378.5	37	CCDS42490.1																																																																																			T|0.000;G|0.798;C|0.000;A|0.202	0.202	strong		0.632	TRAPPC5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461252.1	XM_058961	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036959	33036959	+	Silent	SNP	G	G	A	rs201076982|rs2308929	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33036959G>A	ENST00000419277.1	-	4	594	c.465C>T	c.(463-465)aaC>aaT	p.N155N	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Silent_p.N155N	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	155	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CCAGCTCCCCGTTGCACAGCC	0.567													G|||	2199	0.439097	0.5802	0.2839	5008	,	,		18975	0.6796		0.1899	False		,,,				2504	0.3671				p.N155N		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C465T						PASS	.	G	,,	1420,1600		327,766,417	156.0	180.0	172.0		465,465,465	-6.8	0.0	6	dbSNP_126	172	962,4454		72,818,1818	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	399,1584,2235	AA,AG,GG		17.7622,47.0199,28.2361	,,	155/261,155/261,155/261	33036959	2382,6054	1510	2708	4218	SO:0001819	synonymous_variant	3113	exon3			CTCCCCGTTGCAC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.465C>T	6.37:g.33036959G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	121	52	0.429752	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1	864	0.3956043956043956	274	0.556910569105691	89	0.24585635359116023	371	0.6486013986013986	130	0.17150395778364116	G	3.309	-0.141181	0.06669	0.470199	0.177622	ENSG00000231389	ENST00000437811	.	.	.	3.4	-6.81	0.01704	.	.	.	.	.	T	0.19604	0.0471	.	.	.	0.18873	P	0.9999892507	.	.	.	.	.	.	T	0.14755	-1.0461	3	.	.	.	.	11.6574	0.51325	0.4795:0.0:0.5205:0.0	rs2308929;rs17850580	.	.	.	W	23	.	.	R	-	1	2	HLA-DPA1	33144937	0.958000	0.32768	0.019000	0.16419	0.560000	0.35617	0.053000	0.14184	-1.606000	0.01591	-0.481000	0.04817	CGG	G|0.695;A|0.305	0.305	strong		0.567	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
MCM3AP	8888	hgsc.bcm.edu	37	21	47666744	47666744	+	Missense_Mutation	SNP	G	G	T	rs17183220	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47666744G>T	ENST00000397708.1	-	22	4601	c.4347C>A	c.(4345-4347)gaC>gaA	p.D1449E	MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.D1449E|MCM3AP-AS1_ENST00000455567.1_RNA|AP001469.7_ENST00000444966.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1449			D -> E (in dbSNP:rs17183220). {ECO:0000269|Ref.2}.		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)					CTCCCAGGAGGTCCTTCTGTG	0.587													G|||	105	0.0209665	0.0045	0.0375	5008	,	,		19253	0.001		0.0666	False		,,,				2504	0.0051				p.D1449E		Atlas-SNP	.											.	MCM3AP	146	.	0			c.C4347A						PASS	.	G	GLU/ASP	72,4334	63.5+/-100.7	1,70,2132	109.0	105.0	107.0		4347	0.8	1.0	21	dbSNP_123	107	568,8032	152.7+/-207.2	13,542,3745	yes	missense	MCM3AP	NM_003906.3	45	14,612,5877	TT,TG,GG		6.6047,1.6341,4.9208	benign	1449/1981	47666744	640,12366	2203	4300	6503	SO:0001583	missense	8888	exon21			CAGGAGGTCCTTC	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.4347C>A	21.37:g.47666744G>T	ENSP00000380820:p.Asp1449Glu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	228	103	0.451754	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	81	0.03708791208791209	6	0.012195121951219513	19	0.052486187845303865	1	0.0017482517482517483	55	0.07255936675461741	G	9.045	0.990724	0.18966	0.016341	0.066047	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.03212	4.01;4.01	5.68	0.83	0.18854	.	0.187758	0.56097	N	0.000033	T	0.00178	0.0005	N	0.11927	0.2	0.37779	D	0.926956	B	0.09022	0.002	B	0.09377	0.004	T	0.55547	-0.8124	10	0.18710	T	0.47	-9.1595	0.8098	0.01091	0.217:0.2784:0.2857:0.2189	rs17183220;rs17183220	1449	O60318	MCM3A_HUMAN	E	1449	ENSP00000380820:D1449E;ENSP00000291688:D1449E	ENSP00000291688:D1449E	D	-	3	2	MCM3AP	46491172	0.997000	0.39634	0.998000	0.56505	0.655000	0.38815	0.417000	0.21214	0.080000	0.16959	0.650000	0.86243	GAC	G|0.957;T|0.043	0.043	strong		0.587	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
BDP1	55814	hgsc.bcm.edu	37	5	70809169	70809169	+	Missense_Mutation	SNP	A	A	G	rs1698063	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:70809169A>G	ENST00000358731.4	+	19	4668	c.4405A>G	c.(4405-4407)Aag>Gag	p.K1469E	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	1469			K -> E (in dbSNP:rs1698063). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:15489334}.		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		ATCAGAAACCAAGAAAATGGA	0.368													A|||	2001	0.399561	0.3797	0.3055	5008	,	,		15547	0.3621		0.4583	False		,,,				2504	0.4714				p.K1469E		Atlas-SNP	.											.	BDP1	204	.	0			c.A4405G						PASS	.	A	GLU/LYS	1320,2304		247,826,739	146.0	149.0	148.0		4405	2.1	0.0	5	dbSNP_89	148	3734,4404		882,1970,1217	yes	missense	BDP1	NM_018429.2	56	1129,2796,1956	GG,GA,AA		45.8835,36.4238,42.9689	benign	1469/2625	70809169	5054,6708	1812	4069	5881	SO:0001583	missense	55814	exon19			GAAACCAAGAAAA	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.4405A>G	5.37:g.70809169A>G	ENSP00000351575:p.Lys1469Glu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	872	0.3992673992673993	184	0.37398373983739835	121	0.3342541436464088	216	0.3776223776223776	351	0.4630606860158311	A	8.146	0.786380	0.16189	0.364238	0.458835	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.09163	3.01	5.0	2.1	0.27182	.	0.958392	0.08637	N	0.916186	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	2.9999999999752447E-6	B;B	0.27416	0.001;0.178	B;B	0.22386	0.002;0.039	T	0.46062	-0.9218	9	0.23891	T	0.37	.	4.0483	0.09783	0.2052:0.0:0.6035:0.1913	rs1698063;rs3748041;rs17275387;rs58039781;rs3748041	1469;1469	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	E	1469;1049	ENSP00000351575:K1469E	ENSP00000351575:K1469E	K	+	1	0	BDP1	70844925	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.269000	0.18589	0.193000	0.20303	-0.425000	0.05940	AAG	A|0.595;G|0.405	0.405	strong		0.368	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
LONRF2	164832	hgsc.bcm.edu	37	2	100915772	100915772	+	Missense_Mutation	SNP	A	A	G	rs4851287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:100915772A>G	ENST00000393437.3	-	6	1916	c.1277T>C	c.(1276-1278)cTt>cCt	p.L426P	LONRF2_ENST00000409647.1_Missense_Mutation_p.L183P	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	426			L -> P (in dbSNP:rs4851287). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.				ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						GCTCCTTTGAAGTGAGAGATC	0.433													G|||	3865	0.771765	0.8903	0.7363	5008	,	,		15374	0.9405		0.675	False		,,,				2504	0.5624				p.L426P		Atlas-SNP	.											.	LONRF2	62	.	0			c.T1277C						PASS	.	G	PRO/LEU	3671,735	299.3+/-285.7	1528,615,60	77.0	77.0	77.0		1277	4.0	0.0	2	dbSNP_111	77	5539,3061	465.4+/-366.5	1793,1953,554	yes	missense	LONRF2	NM_198461.3	98	3321,2568,614	GG,GA,AA		35.593,16.6818,29.1865	benign	426/755	100915772	9210,3796	2203	4300	6503	SO:0001583	missense	164832	exon6			CTTTGAAGTGAGA	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"""RING-type (C3HC4) zinc fingers"""	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1277T>C	2.37:g.100915772A>G	ENSP00000377086:p.Leu426Pro	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	195	81	0.415385	NM_198461	B9A006|Q6ZSR4	Missense_Mutation	SNP	ENST00000393437.3	37	CCDS2046.2	1709	0.7825091575091575	418	0.8495934959349594	245	0.6767955801104972	544	0.951048951048951	502	0.662269129287599	G	0.236	-1.017352	0.02078	0.833182	0.64407	ENSG00000170500	ENST00000393437;ENST00000409647	D;D	0.85556	-1.85;-2.0	3.96	3.96	0.45880	.	2.046660	0.02244	N	0.066060	T	0.00012	0.0000	N	0.00436	-1.5	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.50725	-0.8794	9	0.28530	T	0.3	-0.3994	7.1311	0.25502	0.0942:0.1715:0.7343:0.0	rs4851287;rs17438333;rs52819330;rs60152501;rs4851287	426	Q1L5Z9	LONF2_HUMAN	P	426;183	ENSP00000377086:L426P;ENSP00000386823:L183P	ENSP00000377086:L426P	L	-	2	0	LONRF2	100282204	0.972000	0.33761	0.014000	0.15608	0.001000	0.01503	1.729000	0.38115	0.878000	0.35920	-0.227000	0.12334	CTT	A|0.253;G|0.747	0.747	strong		0.433	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461	
SLC30A9	10463	hgsc.bcm.edu	37	4	42003671	42003671	+	Missense_Mutation	SNP	A	A	G	rs1047626	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:42003671A>G	ENST00000264451.7	+	2	328	c.148A>G	c.(148-150)Atg>Gtg	p.M50V		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	50			M -> V (in dbSNP:rs1047626). {ECO:0000269|PubMed:10409434, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CTTTTCAAACATGGTTCCCTG	0.358													A|||	3147	0.628395	0.1051	0.768	5008	,	,		13831	0.9484		0.7565	False		,,,				2504	0.7751				p.M50V		Atlas-SNP	.											.	SLC30A9	58	.	0			c.A148G						PASS	.	A	VAL/MET	939,3467	355.1+/-312.9	105,729,1369	113.0	104.0	107.0		148	-2.8	0.0	4	dbSNP_86	107	6546,2054	716.9+/-406.1	2479,1588,233	yes	missense	SLC30A9	NM_006345.3	21	2584,2317,1602	GG,GA,AA		23.8837,21.3118,42.4496	benign	50/569	42003671	7485,5521	2203	4300	6503	SO:0001583	missense	10463	exon2			TCAAACATGGTTC	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"""Solute carriers"""	1329	protein-coding gene	gene with protein product	"""GRIP1-dependent nuclear receptor coactivator"""	604604	"""chromosome 4 open reading frame 1"""	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.148A>G	4.37:g.42003671A>G	ENSP00000264451:p.Met50Val	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	191	191	1	NM_006345	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Missense_Mutation	SNP	ENST00000264451.7	37	CCDS3465.1	1460	0.6684981684981685	57	0.11585365853658537	273	0.7541436464088398	545	0.9527972027972028	585	0.7717678100263852	A	0.007	-2.015140	0.00422	0.213118	0.761163	ENSG00000014824	ENST00000264451	T	0.20598	2.06	4.66	-2.85	0.05734	.	0.711210	0.14166	N	0.337003	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41805	-0.9488	9	0.02654	T	1	0.1043	4.5984	0.12341	0.4612:0.0:0.3868:0.152	rs1047626;rs1801961;rs3187632;rs17412165;rs17530086;rs17845128;rs17856522;rs17857929;rs61370393;rs1047626	50	Q6PML9	ZNT9_HUMAN	V	50	ENSP00000264451:M50V	ENSP00000264451:M50V	M	+	1	0	SLC30A9	41698428	0.000000	0.05858	0.000000	0.03702	0.400000	0.30750	-0.933000	0.03959	-0.527000	0.06374	-0.316000	0.08728	ATG	A|0.395;G|0.605	0.605	strong		0.358	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3		
CCDC77	84318	hgsc.bcm.edu	37	12	547683	547683	+	Missense_Mutation	SNP	T	T	C	rs735295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:547683T>C	ENST00000239830.4	+	10	1183	c.1004T>C	c.(1003-1005)aTg>aCg	p.M335T	CCDC77_ENST00000412006.2_Missense_Mutation_p.M303T|CCDC77_ENST00000422000.1_Missense_Mutation_p.M303T|CCDC77_ENST00000540180.1_Missense_Mutation_p.M303T	NM_032358.3	NP_115734.1	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77	335			M -> T (in dbSNP:rs735295).			centrosome (GO:0005813)|membrane (GO:0016020)				cervix(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			TTGCCCGTTATGCATGAGAGT	0.348													t|||	1617	0.322883	0.2943	0.4107	5008	,	,		20941	0.3433		0.2594	False		,,,				2504	0.3436				p.M335T		Atlas-SNP	.											.	CCDC77	35	.	0			c.T1004C						PASS	.		THR/MET,THR/MET,THR/MET,THR/MET	1275,3131	434.9+/-344.1	188,899,1116	107.0	113.0	111.0		908,908,908,1004	-0.7	0.0	12	dbSNP_86	111	2262,6338	381.6+/-340.1	327,1608,2365	yes	missense,missense,missense,missense	CCDC77	NM_001130146.1,NM_001130147.1,NM_001130148.1,NM_032358.3	81,81,81,81	515,2507,3481	CC,CT,TT		26.3023,28.9378,27.1951	benign,benign,benign,benign	303/457,303/457,303/457,335/489	547683	3537,9469	2203	4300	6503	SO:0001583	missense	84318	exon10			CCGTTATGCATGA	AK027638	CCDS8503.1, CCDS44781.1	12p13.33	2006-02-16			ENSG00000120647	ENSG00000120647			28203	protein-coding gene	gene with protein product						12477932	Standard	NM_001130148		Approved	MGC13183	uc001qig.3	Q9BR77	OTTHUMG00000129214	ENST00000239830.4:c.1004T>C	12.37:g.547683T>C	ENSP00000239830:p.Met335Thr	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	206	109	0.529126	NM_032358	B4DDE8	Missense_Mutation	SNP	ENST00000239830.4	37	CCDS8503.1	656	0.30036630036630035	135	0.27439024390243905	131	0.36187845303867405	210	0.36713286713286714	180	0.23746701846965698	t	1.210	-0.629996	0.03610	0.289378	0.263023	ENSG00000120647	ENST00000540180;ENST00000422000;ENST00000543504;ENST00000239830;ENST00000412006	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	5.04	-0.73	0.11154	.	1.631020	0.03648	N	0.240587	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.36962	-0.9726	9	0.14252	T	0.57	1.6004	1.8436	0.03155	0.3208:0.0781:0.3264:0.2747	rs735295;rs3764877;rs56454173;rs59893558;rs735295	335	Q9BR77	CCD77_HUMAN	T	303;303;303;335;303	ENSP00000440554:M303T;ENSP00000391870:M303T;ENSP00000445873:M303T;ENSP00000239830:M335T;ENSP00000412925:M303T	ENSP00000239830:M335T	M	+	2	0	CCDC77	417944	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-0.569000	0.05902	0.008000	0.14787	-0.438000	0.05819	ATG	C|0.291;N|0.001	0.291	strong		0.348	CCDC77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251296.1	NM_032358	
CASS4	57091	hgsc.bcm.edu	37	20	55033476	55033476	+	Silent	SNP	C	C	G	rs3746623	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:55033476C>G	ENST00000360314.3	+	7	2259	c.2034C>G	c.(2032-2034)ctC>ctG	p.L678L	CASS4_ENST00000371336.3_Silent_p.L678L|AL121914.1_ENST00000390795.2_RNA|CASS4_ENST00000434344.1_Silent_p.L241L	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	678					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						ACTGCCGGCTCTACTTTGGGG	0.547													G|||	2634	0.525958	0.416	0.5231	5008	,	,		14490	0.9196		0.339	False		,,,				2504	0.4632				p.L678L		Atlas-SNP	.											.	CASS4	121	.	0			c.C2034G						PASS	.	G	,,,	1783,2623	643.2+/-397.8	374,1035,794	58.0	59.0	59.0		1872,723,2034,2034	-1.1	1.0	20	dbSNP_107	59	2924,5676	669.8+/-402.7	469,1986,1845	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	,,,	843,3021,2639	GG,GC,CC		34.0,40.4675,36.191	,,,	624/733,241/350,678/787,678/787	55033476	4707,8299	2203	4300	6503	SO:0001819	synonymous_variant	57091	exon6			CCGGCTCTACTTT	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.2034C>G	20.37:g.55033476C>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Silent	SNP	ENST00000360314.3	37	CCDS33492.1																																																																																			C|0.588;G|0.412	0.412	strong		0.547	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808069	18808069	+	Silent	SNP	A	A	G	rs7528572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18808069A>G	ENST00000400664.1	+	1	646	c.594A>G	c.(592-594)ggA>ggG	p.G198G		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	198						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGCATCCAGGACTGGGGCAAC	0.602													G|||	473	0.0944489	0.1233	0.1239	5008	,	,		17039	0.0377		0.1233	False		,,,				2504	0.0634				p.G198G		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.A594G						PASS	.	G		451,3955	781.1+/-414.5	22,407,1774	47.0	48.0	48.0		594	1.5	0.0	1	dbSNP_116	48	1063,7537	767.3+/-407.6	62,939,3299	no	coding-synonymous	KLHDC7A	NM_152375.2		84,1346,5073	GG,GA,AA		12.3605,10.236,11.6408		198/778	18808069	1514,11492	2203	4300	6503	SO:0001819	synonymous_variant	127707	exon1			TCCAGGACTGGGG	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.594A>G	1.37:g.18808069A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																			A|0.893;G|0.107	0.107	strong		0.602	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
LMTK3	114783	hgsc.bcm.edu	37	19	49013809	49013809	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49013809G>T	ENST00000600059.1	-	2	344	c.117C>A	c.(115-117)taC>taA	p.Y39*	CTC-273B12.10_ENST00000598924.1_lincRNA|LMTK3_ENST00000270238.3_Nonsense_Mutation_p.Y68*			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	39					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		GGACCACAGCGTAGGGAGGAG	0.627																																					p.Y68X		Atlas-SNP	.											LMTK3_ENST00000270238,caecum,carcinoma,-1,3	LMTK3	125	3	0			c.C204A						PASS	.						41.0	57.0	51.0					19																	49013809		2064	4205	6269	SO:0001587	stop_gained	114783	exon3			CACAGCGTAGGGA	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 101"""						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.117C>A	19.37:g.49013809G>T	ENSP00000472020:p.Tyr39*	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	152	67	0.440789	NM_001080434	Q4G0U1	Nonsense_Mutation	SNP	ENST00000600059.1	37		.	.	.	.	.	.	.	.	.	.	g	20.9	4.066456	0.76187	.	.	ENSG00000142235	ENST00000270238	.	.	.	3.95	-2.25	0.06888	.	0.000000	0.64402	U	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	8.747	0.34591	0.6394:0.0:0.3606:0.0	.	.	.	.	X	68	.	ENSP00000270238:Y68X	Y	-	3	2	LMTK3	53705621	0.797000	0.28877	0.989000	0.46669	0.972000	0.66771	-0.150000	0.10189	-0.406000	0.07588	0.282000	0.19409	TAC	.	.	none		0.627	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895	
IKBKAP	8518	hgsc.bcm.edu	37	9	111659439	111659439	+	Missense_Mutation	SNP	T	T	C	rs2230794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:111659439T>C	ENST00000374647.5	-	23	2797	c.2490A>G	c.(2488-2490)atA>atG	p.I830M	IKBKAP_ENST00000537196.1_Missense_Mutation_p.I481M	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	830			I -> M (in dbSNP:rs2230794).		chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)	p.I830M(1)		NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TATGAGGATTTATGCTCTCCA	0.473													T|||	328	0.0654952	0.0083	0.1527	5008	,	,		21060	0.0863		0.0596	False		,,,				2504	0.0654				p.I830M		Atlas-SNP	.											IKBKAP,NS,carcinoma,0,1	IKBKAP	122	1	1	Substitution - Missense(1)	stomach(1)	c.A2490G						PASS	.	T	MET/ILE	69,4337	62.9+/-100.1	0,69,2134	212.0	172.0	185.0		2490	-1.9	0.1	9	dbSNP_98	185	402,8198	127.5+/-185.8	7,388,3905	yes	missense	IKBKAP	NM_003640.3	10	7,457,6039	CC,CT,TT		4.6744,1.566,3.6214	probably-damaging	830/1333	111659439	471,12535	2203	4300	6503	SO:0001583	missense	8518	exon23			AGGATTTATGCTC	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.2490A>G	9.37:g.111659439T>C	ENSP00000363779:p.Ile830Met	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	196	87	0.443878	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	37	CCDS6773.1	174	0.07967032967032966	8	0.016260162601626018	63	0.17403314917127072	62	0.10839160839160839	41	0.05408970976253298	T	10.94	1.493424	0.26774	0.01566	0.046744	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.26660	1.72;1.72	5.35	-1.86	0.07760	.	0.130671	0.64402	D	0.000018	T	0.00039	0.0001	M	0.73598	2.24	0.34877	P	0.255788	P	0.36789	0.57	B	0.33960	0.173	T	0.06826	-1.0805	9	0.33141	T	0.24	-7.4114	3.1982	0.06640	0.1124:0.1528:0.4721:0.2627	rs2230794;rs2230794	830	O95163	ELP1_HUMAN	M	830;481	ENSP00000363779:I830M;ENSP00000439367:I481M	ENSP00000363779:I830M	I	-	3	3	IKBKAP	110699260	0.626000	0.27120	0.127000	0.21898	0.660000	0.38997	-0.202000	0.09451	-0.500000	0.06614	0.383000	0.25322	ATA	T|0.950;C|0.050	0.050	strong		0.473	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
FAM66D	100132923	hgsc.bcm.edu	37	8	11990882	11990882	+	RNA	SNP	C	C	T	rs9720235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11990882C>T	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		GTGTCTGAAACGCCGTGGCAG	0.498													t|||	2043	0.407947	0.2897	0.5187	5008	,	,		24947	0.4077		0.4513	False		,,,				2504	0.4448				p.V213I		Atlas-SNP	.											.	.	.	.	0			c.G637A						PASS	.																																					392197	exon1			CTGAAACGCCGTG			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11990882C>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001256869		Missense_Mutation	SNP	ENST00000434078.2	37																																																																																				C|0.499;T|0.501	0.501	strong		0.498	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
OR10G7	390265	hgsc.bcm.edu	37	11	123908971	123908971	+	Silent	SNP	C	C	T	rs142080661	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:123908971C>T	ENST00000330487.5	-	1	746	c.738G>A	c.(736-738)gtG>gtA	p.V246V		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	246						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AGCAAAGGACCACGATACAGT	0.567													C|||	12	0.00239617	0.0	0.0	5008	,	,		18724	0.0		0.0	False		,,,				2504	0.0123				p.V246V		Atlas-SNP	.											.	OR10G7	103	.	0			c.G738A						PASS	.	C		0,4400		0,0,2200	110.0	95.0	100.0		738	2.4	1.0	11	dbSNP_134	100	8,8590	6.4+/-24.3	0,8,4291	no	coding-synonymous	OR10G7	NM_001004463.1		0,8,6491	TT,TC,CC		0.093,0.0,0.0615		246/312	123908971	8,12990	2200	4299	6499	SO:0001819	synonymous_variant	390265	exon1			AAGGACCACGATA	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.738G>A	11.37:g.123908971C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	196	103	0.52551	NM_001004463	Q6IFE8	Silent	SNP	ENST00000330487.5	37	CCDS31705.1																																																																																			C|1.000;T|0.000	0.000	strong		0.567	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
RANBP17	64901	hgsc.bcm.edu	37	5	170626735	170626735	+	Silent	SNP	A	A	G	rs35724654	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:170626735A>G	ENST00000523189.1	+	19	2264	c.2100A>G	c.(2098-2100)gtA>gtG	p.V700V	RANBP17_ENST00000521759.1_3'UTR	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	700					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTGAAACAGTATTACAAATAT	0.333			T	TRD@	ALL								A|||	323	0.0644968	0.0098	0.0634	5008	,	,		18777	0.001		0.173	False		,,,				2504	0.093				p.V700V		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.A2100G						PASS	.	A		141,4265	98.9+/-137.6	4,133,2066	122.0	121.0	121.0		2100	-3.7	0.9	5	dbSNP_126	121	1398,7202	269.3+/-288.3	138,1122,3040	no	coding-synonymous	RANBP17	NM_022897.3		142,1255,5106	GG,GA,AA		16.2558,3.2002,11.833		700/1089	170626735	1539,11467	2203	4300	6503	SO:0001819	synonymous_variant	64901	exon19			AACAGTATTACAA	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.2100A>G	5.37:g.170626735A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_022897	Q8IU74	Silent	SNP	ENST00000523189.1	37	CCDS34287.1																																																																																			A|0.890;G|0.110	0.110	strong		0.333	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897	
P2RY13	53829	hgsc.bcm.edu	37	3	151046604	151046604	+	Silent	SNP	G	G	T	rs3732757	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:151046604G>T	ENST00000325602.5	-	2	259	c.240C>A	c.(238-240)atC>atA	p.I80I	MED12L_ENST00000491549.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_176894.2	NP_795713.2	Q9BPV8	P2Y13_HUMAN	purinergic receptor P2Y, G-protein coupled, 13	80					negative regulation of adenylate cyclase activity (GO:0007194)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(72;0.0189)|Lung(72;0.0278)			TTTTGAGGTAGATGATGAAGG	0.502													G|||	300	0.0599042	0.0106	0.0331	5008	,	,		17897	0.127		0.0457	False		,,,				2504	0.091				p.I80I		Atlas-SNP	.											.	P2RY13	80	.	0			c.C240A						PASS	.	G	,	94,4312	77.8+/-116.1	0,94,2109	108.0	104.0	105.0		,240	3.0	1.0	3	dbSNP_107	105	413,8187	130.0+/-188.0	13,387,3900	no	intron,coding-synonymous	P2RY13,MED12L	NM_053002.4,NM_176894.2	,	13,481,6009	TT,TG,GG		4.8023,2.1335,3.8982	,	,80/355	151046604	507,12499	2203	4300	6503	SO:0001819	synonymous_variant	53829	exon2			GAGGTAGATGATG	AF295368	CCDS3158.2	3q24	2012-08-08	2004-07-12	2004-07-14	ENSG00000181631	ENSG00000181631		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	4537	protein-coding gene	gene with protein product		606380	"""G protein-coupled receptor 86"""	GPR94, GPR86		11273702, 11574155	Standard	NM_176894		Approved	FKSG77, P2Y13	uc003eyv.2	Q9BPV8	OTTHUMG00000155745	ENST00000325602.5:c.240C>A	3.37:g.151046604G>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	170	82	0.482353	NM_176894	B2R827|Q05C50|Q6DKN4|Q8IUT5|Q8TDU7|Q9BY61	Silent	SNP	ENST00000325602.5	37	CCDS3158.2																																																																																			G|0.951;T|0.049	0.049	strong		0.502	P2RY13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341468.1	NM_023914	
SMG6	23293	hgsc.bcm.edu	37	17	2202323	2202323	+	Missense_Mutation	SNP	T	T	C	rs34047637	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:2202323T>C	ENST00000263073.6	-	2	1774	c.1724A>G	c.(1723-1725)aAc>aGc	p.N575S	SMG6_ENST00000544865.1_Missense_Mutation_p.N544S	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	575			N -> S (in dbSNP:rs34047637).		gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TTGCTGCAGGTTCCTCATGTG	0.602													T|||	80	0.0159744	0.003	0.0432	5008	,	,		17211	0.0		0.0427	False		,,,				2504	0.0031				p.N575S	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A1724G						PASS	.	T	SER/ASN,SER/ASN	37,4369	41.6+/-74.8	0,37,2166	199.0	183.0	189.0		1631,1724	5.7	1.0	17	dbSNP_126	189	450,8150	135.1+/-192.4	10,430,3860	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	46,46	10,467,6026	CC,CT,TT		5.2326,0.8398,3.7444	benign,benign	544/1389,575/1420	2202323	487,12519	2203	4300	6503	SO:0001583	missense	23293	exon2			TGCAGGTTCCTCA	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.1724A>G	17.37:g.2202323T>C	ENSP00000263073:p.Asn575Ser	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	191	95	0.497382	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	52	0.023809523809523808	1	0.0020325203252032522	22	0.06077348066298342	0	0.0	29	0.03825857519788918	t	5.872	0.345025	0.11126	0.008398	0.052326	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.07567	3.18;3.18	5.67	5.67	0.87782	.	0.222297	0.47455	D	0.000239	T	0.00496	0.0016	N	0.19112	0.55	0.27924	N	0.938129	B	0.11235	0.004	B	0.11329	0.006	T	0.43507	-0.9387	10	0.05721	T	0.95	-11.7455	7.1522	0.25616	0.0:0.0736:0.1482:0.7782	rs34047637	575	Q86US8	EST1A_HUMAN	S	575;544	ENSP00000263073:N575S;ENSP00000443920:N544S	ENSP00000263073:N575S	N	-	2	0	SMG6	2149073	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	2.910000	0.48766	2.158000	0.67659	0.524000	0.50904	AAC	T|0.966;C|0.034	0.034	strong		0.602	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
TRIM51	84767	hgsc.bcm.edu	37	11	55655597	55655597	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55655597A>G	ENST00000449290.2	+	4	689	c.597A>G	c.(595-597)gaA>gaG	p.E199E	TRIM51_ENST00000244891.3_Silent_p.E56E	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	199						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										ATCACTTGGAAAGGCTGCGAA	0.433																																					p.E199E		Atlas-SNP	.											SPRYD5_ENST00000327733,NS,carcinoma,+2,2	.	.	2	0			c.A597G						scavenged	.						61.0	58.0	59.0					11																	55655597		2201	4296	6497	SO:0001819	synonymous_variant	84767	exon4			CTTGGAAAGGCTG	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19023	protein-coding gene	gene with protein product			"""SPRY domain containing 5"""	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.597A>G	11.37:g.55655597A>G		Somatic	502	18	0.0358566		WXS	Illumina HiSeq	Phase_I	584	26	0.0445205	NM_032681	A6NMG2	Silent	SNP	ENST00000449290.2	37																																																																																				.	.	none		0.433	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
CARD14	79092	hgsc.bcm.edu	37	17	78177680	78177680	+	Missense_Mutation	SNP	G	G	A	rs143600438		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78177680G>A	ENST00000573882.1	+	18	2815	c.2279G>A	c.(2278-2280)cGc>cAc	p.R760H	RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000576824.1_RNA|CARD14_ENST00000392434.2_3'UTR|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|CARD14_ENST00000344227.2_Missense_Mutation_p.R760H|RP11-334C17.5_ENST00000573346.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	760					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			ACCGTGACCCGCAAGGTGAGG	0.672													G|||	1	0.000199681	0.0	0.0	5008	,	,		16335	0.001		0.0	False		,,,				2504	0.0				p.R760H		Atlas-SNP	.											.	CARD14	98	.	0			c.G2279A						PASS	.	G	HIS/ARG	2,4390		0,2,2194	22.0	21.0	21.0		2279	4.1	1.0	17	dbSNP_134	21	0,8592		0,0,4296	no	missense	CARD14	NM_024110.3	29	0,2,6490	AA,AG,GG		0.0,0.0455,0.0154	probably-damaging	760/1005	78177680	2,12982	2196	4296	6492	SO:0001583	missense	79092	exon16			TGACCCGCAAGGT	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2279G>A	17.37:g.78177680G>A	ENSP00000458715:p.Arg760His	Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	319	148	0.46395	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.859093	0.51376	4.55E-4	0.0	ENSG00000141527	ENST00000344227	T	0.05855	3.38	4.12	4.12	0.48240	.	6.592470	0.00481	U	0.000120	T	0.18635	0.0447	M	0.76328	2.33	0.80722	D	1	P	0.42584	0.784	B	0.44224	0.444	T	0.16482	-1.0401	10	0.44086	T	0.13	-13.3243	15.1676	0.72840	0.0:0.0:1.0:0.0	.	760	Q9BXL6	CAR14_HUMAN	H	760	ENSP00000344549:R760H	ENSP00000344549:R760H	R	+	2	0	CARD14	75792275	1.000000	0.71417	1.000000	0.80357	0.276000	0.26787	3.682000	0.54656	1.865000	0.54081	0.485000	0.47835	CGC	G|1.000;A|0.000	0.000	weak		0.672	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
ALKBH4	54784	hgsc.bcm.edu	37	7	102098010	102098010	+	Missense_Mutation	SNP	G	G	A	rs41275227	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:102098010G>A	ENST00000292566.3	-	3	779	c.740C>T	c.(739-741)gCg>gTg	p.A247V		NM_017621.3	NP_060091.1	Q9NXW9	ALKB4_HUMAN	alkB, alkylation repair homolog 4 (E. coli)	247			A -> V (in dbSNP:rs41275227).		actomyosin structure organization (GO:0031032)|cleavage furrow ingression (GO:0036090)|protein demethylation (GO:0006482)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	contractile ring (GO:0070938)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)	actin binding (GO:0003779)|demethylase activity (GO:0032451)|metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			kidney(1)|lung(5)|skin(2)	8						GTGCCGTGCCGCCCCGGTGAG	0.672													G|||	639	0.127596	0.0068	0.1153	5008	,	,		15013	0.1478		0.165	False		,,,				2504	0.2403				p.A247V		Atlas-SNP	.											.	ALKBH4	21	.	0			c.C740T						PASS	.	G	VAL/ALA	158,4242	96.7+/-135.4	1,156,2043	27.0	24.0	25.0		740	3.3	0.0	7	dbSNP_127	25	1337,7261	243.9+/-273.3	95,1147,3057	yes	missense	ALKBH4	NM_017621.3	64	96,1303,5100	AA,AG,GG		15.5501,3.5909,11.5018	benign	247/303	102098010	1495,11503	2200	4299	6499	SO:0001583	missense	54784	exon3			CGTGCCGCCCCGG	BC017096	CCDS5723.1	7q22.1	2006-02-09			ENSG00000160993	ENSG00000160993		"""Alkylation repair homologs"""	21900	protein-coding gene	gene with protein product		613302					Standard	NM_017621		Approved	FLJ20013	uc003uzl.3	Q9NXW9	OTTHUMG00000157720	ENST00000292566.3:c.740C>T	7.37:g.102098010G>A	ENSP00000292566:p.Ala247Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_017621	Q53H92|Q9H6A4	Missense_Mutation	SNP	ENST00000292566.3	37	CCDS5723.1	250	0.11446886446886446	7	0.014227642276422764	46	0.1270718232044199	75	0.13111888111888112	122	0.16094986807387862	G	7.498	0.652085	0.14580	0.035909	0.155501	ENSG00000160993	ENST00000292566	T	0.76448	-1.02	5.08	3.26	0.37387	Oxoglutarate/iron-dependent oxygenase (1);	0.381387	0.28312	N	0.015810	T	0.00412	0.0013	L	0.40543	1.245	0.80722	P	0.0	B	0.29862	0.259	B	0.22601	0.04	T	0.10428	-1.0630	9	0.39692	T	0.17	-13.0381	3.6021	0.08028	0.0854:0.1346:0.5029:0.2771	rs41275227	247	Q9NXW9	ALKB4_HUMAN	V	247	ENSP00000292566:A247V	ENSP00000292566:A247V	A	-	2	0	ALKBH4	101885015	0.903000	0.30736	0.001000	0.08648	0.010000	0.07245	2.765000	0.47621	0.534000	0.28695	0.561000	0.74099	GCG	G|0.892;A|0.108	0.108	strong		0.672	ALKBH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349503.1	NM_017621	
TBC1D1	23216	hgsc.bcm.edu	37	4	37904089	37904089	+	Missense_Mutation	SNP	C	C	T	rs35859249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:37904089C>T	ENST00000261439.4	+	2	728	c.373C>T	c.(373-375)Cgg>Tgg	p.R125W	TBC1D1_ENST00000402522.1_Missense_Mutation_p.R125W|TBC1D1_ENST00000508802.1_Missense_Mutation_p.R125W	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	125			R -> W (may be associated with risk of familial obesity; dbSNP:rs35859249). {ECO:0000269|PubMed:16893906, ECO:0000269|PubMed:18325908}.		membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						CGCTGTCCACCGGCAGAGTAT	0.438													C|||	422	0.0842652	0.0136	0.0648	5008	,	,		19784	0.124		0.1004	False		,,,				2504	0.136				p.R125W		Atlas-SNP	.											.	TBC1D1	94	.	0			c.C373T	GRCh37	CM064293	TBC1D1	M	rs35859249	PASS	.	C	TRP/ARG	130,4276	91.6+/-130.3	4,122,2077	76.0	77.0	77.0	http://omim.org/entry/608410	373	3.2	0.0	4	dbSNP_126	77	831,7769	189.1+/-236.0	41,749,3510	yes	missense	TBC1D1	NM_015173.2	101	45,871,5587	TT,TC,CC		9.6628,2.9505,7.3889	probably-damaging	125/1169	37904089	961,12045	2203	4300	6503	SO:0001583	missense	23216	exon2			GTCCACCGGCAGA	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.373C>T	4.37:g.37904089C>T	ENSP00000261439:p.Arg125Trp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	37	CCDS33972.1	176	0.08058608058608059	5	0.01016260162601626	23	0.06353591160220995	68	0.11888111888111888	80	0.10554089709762533	C	15.27	2.783590	0.49891	0.029505	0.096628	ENSG00000065882	ENST00000508802;ENST00000261439;ENST00000402522	T;T;T	0.23950	3.59;3.98;1.88	6.07	3.15	0.36227	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	1.202460	0.06320	N	0.704358	T	0.00300	0.0009	N	0.08118	0	0.44275	P	0.0028650000000000064	D;D	0.63046	0.992;0.958	B;P	0.44860	0.332;0.462	T	0.35822	-0.9773	9	0.66056	D	0.02	-6.0566	15.2101	0.73214	0.4489:0.5511:0.0:0.0	rs35859249;rs61752237	125;125	E9PGH8;Q86TI0	.;TBCD1_HUMAN	W	125	ENSP00000423651:R125W;ENSP00000261439:R125W;ENSP00000383994:R125W	ENSP00000261439:R125W	R	+	1	2	TBC1D1	37580484	0.002000	0.14202	0.005000	0.12908	0.417000	0.31264	0.851000	0.27751	0.271000	0.22005	0.585000	0.79938	CGG	C|0.922;T|0.078	0.078	strong		0.438	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
PPT2	9374	hgsc.bcm.edu	37	6	32122472	32122472	+	Missense_Mutation	SNP	C	C	A	rs3096696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32122472C>A	ENST00000324816.6	+	2	669	c.101C>A	c.(100-102)gCg>gAg	p.A34E	PPT2-EGFL8_ENST00000422437.1_Missense_Mutation_p.A34E|PPT2_ENST00000437001.2_5'UTR|PRRT1_ENST00000211413.5_5'Flank|PPT2-EGFL8_ENST00000453656.2_3'UTR|PPT2_ENST00000395523.1_Missense_Mutation_p.A34E|PPT2_ENST00000375143.2_Missense_Mutation_p.A34E|PPT2_ENST00000375137.2_Missense_Mutation_p.A34E|PRRT1_ENST00000375150.2_5'Flank|PPT2_ENST00000361568.2_Missense_Mutation_p.A40E|PRRT1_ENST00000375152.2_5'Flank|PPT2_ENST00000493548.1_3'UTR|PPT2_ENST00000445576.2_Missense_Mutation_p.A34E			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	34			A -> E (in dbSNP:rs3096696). {ECO:0000269|PubMed:10051407, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14656967}.		cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						CCCCACCGCGCGTCCTACAAG	0.662													C|||	781	0.15595	0.2103	0.1023	5008	,	,		14262	0.0377		0.2018	False		,,,				2504	0.1953				p.A40E		Atlas-SNP	.											.	PPT2	19	.	0			c.C119A						PASS	.	C	GLU/ALA,GLU/ALA,GLU/ALA	574,2442		54,466,988	50.0	56.0	54.0		101,101,119	2.6	0.1	6	dbSNP_103	54	1143,4271		112,919,1676	yes	missense,missense,missense	PPT2	NM_001204103.1,NM_005155.6,NM_138717.2	107,107,107	166,1385,2664	AA,AC,CC		21.1119,19.0318,20.3677	benign,benign,benign	34/303,34/303,40/309	32122472	1717,6713	1508	2707	4215	SO:0001583	missense	9374	exon2			ACCGCGCGTCCTA	AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	3.1.2.22		9326	protein-coding gene	gene with protein product		603298				9341199, 10051407	Standard	NM_138717		Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.101C>A	6.37:g.32122472C>A	ENSP00000320528:p.Ala34Glu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_138717	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	Missense_Mutation	SNP	ENST00000324816.6	37	CCDS4742.1	312	0.14285714285714285	105	0.21341463414634146	33	0.09116022099447514	23	0.04020979020979021	151	0.19920844327176782	C	10.98	1.504887	0.26949	0.190318	0.211119	ENSG00000221988	ENST00000414204;ENST00000361568;ENST00000395523;ENST00000445576;ENST00000324816;ENST00000375137;ENST00000375143;ENST00000424499;ENST00000436118;ENST00000453656	D;D;D;D;D;D;D;D;T	0.94092	-3.35;-3.35;-3.35;-3.35;-3.35;-3.35;-3.35;-3.35;1.42	4.63	2.61	0.31194	.	1.033790	0.07631	N	0.928533	T	0.68732	0.3033	N	0.14661	0.345	0.46458	P	9.460000000000024E-4	P;B;B	0.35226	0.491;0.209;0.116	B;B;B	0.31614	0.133;0.125;0.095	T	0.60367	-0.7277	9	0.02654	T	1	-2.8103	6.931	0.24442	0.0:0.6957:0.1926:0.1117	rs3096696;rs17208035;rs61155654	34;34;40	Q9UMR5-2;Q9UMR5;B0S872	.;PPT2_HUMAN;.	E	34;40;34;34;34;34;34;34;34;34	ENSP00000398847:A34E;ENSP00000354608:A40E;ENSP00000378894:A34E;ENSP00000412381:A34E;ENSP00000320528:A34E;ENSP00000364279:A34E;ENSP00000364285:A34E;ENSP00000409877:A34E;ENSP00000395456:A34E	ENSP00000320528:A34E	A	+	2	0	PPT2	32230450	0.006000	0.16342	0.052000	0.19188	0.733000	0.41908	0.937000	0.28951	1.107000	0.41642	0.484000	0.47621	GCG	C|0.825;A|0.175	0.175	strong		0.662	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076552.4	NM_138717	
FLG	2312	hgsc.bcm.edu	37	1	152277657	152277657	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152277657A>G	ENST00000368799.1	-	3	9740	c.9705T>C	c.(9703-9705)gcT>gcC	p.A3235A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3235	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGTTTCTGGAAGCAGACCCAG	0.597									Ichthyosis																												p.A3235A		Atlas-SNP	.											FLG,NS,carcinoma,-2,1	FLG	900	1	0			c.T9705C						scavenged	.						179.0	190.0	186.0					1																	152277657		2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCTGGAAGCAGAC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9705T>C	1.37:g.152277657A>G		Somatic	206	2	0.00970874		WXS	Illumina HiSeq	Phase_I	243	4	0.0164609	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			.	.	none		0.597	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
KBTBD7	84078	hgsc.bcm.edu	37	13	41767341	41767341	+	Silent	SNP	A	A	G	rs2039135	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:41767341A>G	ENST00000379483.3	-	1	1361	c.1053T>C	c.(1051-1053)caT>caC	p.H351H		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	351										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		GATCTCTAGGATGTCCAAAGA	0.502													.|||	2548	0.508786	0.1029	0.8156	5008	,	,		20807	0.3502		0.832	False		,,,				2504	0.6708				p.H351H		Atlas-SNP	.											.	KBTBD7	60	.	0			c.T1053C						PASS	.	G		875,3531	726.9+/-409.8	99,677,1427	93.0	57.0	69.0		1053	-3.2	0.5	13	dbSNP_94	69	7230,1370	238.5+/-269.9	3083,1064,153	no	coding-synonymous	KBTBD7	NM_032138.4		3182,1741,1580	GG,GA,AA		15.9302,19.8593,37.6826		351/685	41767341	8105,4901	2203	4300	6503	SO:0001819	synonymous_variant	84078	exon1			TCTAGGATGTCCA	AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"""BTB/POZ domain containing"""	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.1053T>C	13.37:g.41767341A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	86	84	0.976744	NM_032138	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Silent	SNP	ENST00000379483.3	37	CCDS9377.1																																																																																			A|0.378;G|0.622	0.622	strong		0.502	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138	
KTI12	112970	hgsc.bcm.edu	37	1	52498861	52498861	+	Missense_Mutation	SNP	A	A	T	rs2783175	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:52498861A>T	ENST00000371614.1	-	1	627	c.573T>A	c.(571-573)gaT>gaA	p.D191E	TXNDC12_ENST00000371626.4_Intron|RP11-91A18.4_ENST00000425802.1_RNA	NM_138417.2	NP_612426.1	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated (S. cerevisiae)	191			D -> E (in dbSNP:rs2783175).				ATP binding (GO:0005524)	p.D191E(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						ATTTCTCTGAATCCGGAGTCA	0.572													T|||	355	0.0708866	0.0802	0.0735	5008	,	,		16217	0.1379		0.0268	False		,,,				2504	0.0327				p.D191E		Atlas-SNP	.											KTI12,NS,carcinoma,0,1	KTI12	30	1	1	Substitution - Missense(1)	stomach(1)	c.T573A						PASS	.	T	,GLU/ASP	319,4087	793.0+/-415.2	11,297,1895	55.0	61.0	59.0		,573	-5.7	0.0	1	dbSNP_100	59	398,8202	798.7+/-407.4	7,384,3909	yes	intron,missense	TXNDC12,KTI12	NM_015913.2,NM_138417.2	,45	18,681,5804	TT,TA,AA		4.6279,7.2401,5.5128	,benign	,191/355	52498861	717,12289	2203	4300	6503	SO:0001583	missense	112970	exon1			CTCTGAATCCGGA		CCDS562.1	1p32.3	2008-02-05			ENSG00000198841	ENSG00000198841			25160	protein-coding gene	gene with protein product						11929532	Standard	NM_138417		Approved	TOT4, MGC20419, SBBI81	uc001ctj.1	Q96EK9	OTTHUMG00000008630	ENST00000371614.1:c.573T>A	1.37:g.52498861A>T	ENSP00000360676:p.Asp191Glu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	119	58	0.487395	NM_138417		Missense_Mutation	SNP	ENST00000371614.1	37	CCDS562.1	173	0.07921245421245421	46	0.09349593495934959	25	0.06906077348066299	74	0.12937062937062938	28	0.036939313984168866	T	3.931	-0.016193	0.07681	0.072401	0.046279	ENSG00000198841	ENST00000371614	T	0.46819	0.86	4.39	-5.73	0.02398	.	.	.	.	.	T	0.00144	0.0004	N	0.02736	-0.51	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10109	-1.0644	8	0.02654	T	1	.	7.0787	0.25219	0.2012:0.6352:0.0:0.1636	rs2783175;rs61455582;rs2783175	191	Q96EK9	KTI12_HUMAN	E	191	ENSP00000360676:D191E	ENSP00000360676:D191E	D	-	3	2	KTI12	52271449	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.454000	0.00465	-1.842000	0.01181	-1.250000	0.01514	GAT	A|0.934;T|0.066	0.066	strong		0.572	KTI12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023821.1	NM_138417	
GBP4	115361	hgsc.bcm.edu	37	1	89652078	89652078	+	Missense_Mutation	SNP	A	A	T	rs608339	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89652078A>T	ENST00000355754.6	-	10	1742	c.1645T>A	c.(1645-1647)Ttg>Atg	p.L549M	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	549			L -> M (in dbSNP:rs608339).	LEE -> MER (in Ref. 1; AAL02054 and 3; BAC85144). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		TCCTCCTCCAACTTCTTCTCC	0.488													A|||	1800	0.359425	0.1445	0.3141	5008	,	,		18963	0.3988		0.4891	False		,,,				2504	0.5082				p.L549M		Atlas-SNP	.											.	GBP4	89	.	0			c.T1645A						PASS	.	A	MET/LEU	889,3517		121,647,1435	186.0	127.0	147.0		1645	-6.2	0.0	1	dbSNP_83	147	4032,4562		1093,1846,1358	yes	missense	GBP4	NM_052941.4	15	1214,2493,2793	TT,TA,AA		46.9165,20.177,37.8538	benign	549/641	89652078	4921,8079	2203	4297	6500	SO:0001583	missense	115361	exon10			CCTCCAACTTCTT	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1645T>A	1.37:g.89652078A>T	ENSP00000359490:p.Leu549Met	Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	679	0.3108974358974359	43	0.08739837398373984	117	0.32320441988950277	188	0.32867132867132864	331	0.4366754617414248	A	0.182	-1.061175	0.01950	0.20177	0.469165	ENSG00000162654	ENST00000355754	T	0.02421	4.3	4.29	-6.25	0.02039	Guanylate-binding protein, C-terminal (3);	0.381500	0.29737	N	0.011330	T	0.00300	0.0009	N	0.03253	-0.375	0.53688	P	2.8999999999945736E-5	B	0.14805	0.011	B	0.25614	0.062	T	0.26916	-1.0089	9	0.02654	T	1	.	7.3538	0.26706	0.5342:0.0:0.1115:0.3542	rs608339;rs1142891;rs3180077;rs3206373;rs608339	549	Q96PP9	GBP4_HUMAN	M	549	ENSP00000359490:L549M	ENSP00000359490:L549M	L	-	1	2	GBP4	89424666	0.001000	0.12720	0.007000	0.13788	0.003000	0.03518	-0.767000	0.04720	-1.293000	0.02362	-1.750000	0.00680	TTG	A|0.658;T|0.342	0.342	strong		0.488	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
PPL	5493	hgsc.bcm.edu	37	16	4935636	4935636	+	Missense_Mutation	SNP	G	G	A	rs2075639	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:4935636G>A	ENST00000345988.2	-	22	3109	c.3020C>T	c.(3019-3021)gCg>gTg	p.A1007V	PPL_ENST00000590782.2_Missense_Mutation_p.A1005V	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1007			A -> V (in dbSNP:rs2075639).		keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						GACCTCATCCGCCTGGGCCCT	0.697													G|||	598	0.119409	0.0061	0.1888	5008	,	,		17164	0.2242		0.0785	False		,,,				2504	0.1575				p.A1007V		Atlas-SNP	.											.	PPL	168	.	0			c.C3020T						PASS	.	G	VAL/ALA	108,4286	80.4+/-118.8	1,106,2090	76.0	79.0	78.0		3020	-2.7	0.0	16	dbSNP_96	78	701,7897	165.1+/-217.3	30,641,3628	yes	missense	PPL	NM_002705.4	64	31,747,5718	AA,AG,GG		8.1531,2.4579,6.2269	benign	1007/1757	4935636	809,12183	2197	4299	6496	SO:0001583	missense	5493	exon22			TCATCCGCCTGGG	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3020C>T	16.37:g.4935636G>A	ENSP00000340510:p.Ala1007Val	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	168	83	0.494048	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	258	0.11813186813186813	7	0.014227642276422764	61	0.1685082872928177	132	0.23076923076923078	58	0.07651715039577836	G	10.45	1.354545	0.24512	0.024579	0.081531	ENSG00000118898	ENST00000345988	T	0.46063	0.88	4.89	-2.67	0.06059	.	0.297452	0.31531	N	0.007490	T	0.00012	0.0000	L	0.51422	1.61	0.58432	P	5.000000000032756E-6	B	0.29253	0.239	B	0.14023	0.01	T	0.09164	-1.0687	9	0.51188	T	0.08	.	3.0003	0.06011	0.1392:0.1079:0.2588:0.4941	rs2075639;rs52834399;rs57621226;rs2075639	1007	O60437	PEPL_HUMAN	V	1007	ENSP00000340510:A1007V	ENSP00000340510:A1007V	A	-	2	0	PPL	4875637	0.970000	0.33590	0.020000	0.16555	0.202000	0.24057	1.726000	0.38085	-0.515000	0.06479	0.484000	0.47621	GCG	G|0.915;A|0.085	0.085	strong		0.697	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
HMOX1	3162	hgsc.bcm.edu	37	22	35777185	35777185	+	Missense_Mutation	SNP	G	G	C	rs2071747	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:35777185G>C	ENST00000216117.8	+	1	358	c.19G>C	c.(19-21)Gac>Cac	p.D7H		NM_002133.2	NP_002124.1	P09601	HMOX1_HUMAN	heme oxygenase (decycling) 1	7			D -> H (in dbSNP:rs2071747). {ECO:0000269|Ref.3}.		angiogenesis (GO:0001525)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to cadmium ion (GO:0071276)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient (GO:0031670)|endothelial cell proliferation (GO:0001935)|erythrocyte homeostasis (GO:0034101)|excretion (GO:0007588)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|iron ion homeostasis (GO:0055072)|low-density lipoprotein particle clearance (GO:0034383)|negative regulation of DNA binding (GO:0043392)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smooth muscle cell proliferation (GO:0048662)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|protein homooligomerization (GO:0051260)|regulation of angiogenesis (GO:0045765)|regulation of blood pressure (GO:0008217)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to estrogen (GO:0043627)|response to hydrogen peroxide (GO:0042542)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|smooth muscle hyperplasia (GO:0014806)|transmembrane transport (GO:0055085)|wound healing involved in inflammatory response (GO:0002246)	caveola (GO:0005901)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)|phospholipase D activity (GO:0004630)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16					Vitamin E(DB00163)	TCCGCAACCCGACAGGCAAGC	0.721													G|||	182	0.0363419	0.0287	0.0216	5008	,	,		11362	0.0536		0.0586	False		,,,				2504	0.0164				p.D7H		Atlas-SNP	.											.	HMOX1	32	.	0			c.G19C						PASS	.	G	HIS/ASP	60,3634		1,58,1788	4.0	5.0	5.0		19	2.4	1.0	22	dbSNP_96	5	276,7250		2,272,3489	no	missense	HMOX1	NM_002133.2	81	3,330,5277	CC,CG,GG		3.6673,1.6243,2.9947	benign	7/289	35777185	336,10884	1847	3763	5610	SO:0001583	missense	3162	exon1			CAACCCGACAGGC		CCDS13914.1	22q12	2003-10-13			ENSG00000100292	ENSG00000100292	1.14.99.3		5013	protein-coding gene	gene with protein product		141250				10591208	Standard	NM_002133		Approved	bK286B10, HO-1	uc003ant.2	P09601	OTTHUMG00000150960	ENST00000216117.8:c.19G>C	22.37:g.35777185G>C	ENSP00000216117:p.Asp7His	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	11	5	0.454545	NM_002133		Missense_Mutation	SNP	ENST00000216117.8	37	CCDS13914.1	110	0.05036630036630037	22	0.044715447154471545	8	0.022099447513812154	36	0.06293706293706294	44	0.05804749340369393	G	10.07	1.249851	0.22880	0.016243	0.036673	ENSG00000100292	ENST00000412893;ENST00000216117	T;T	0.18502	2.21;2.26	3.44	2.43	0.29744	Haem oxygenase-like, multi-helical (1);	1.539270	0.03633	N	0.238258	T	0.01029	0.0034	N	0.08118	0	0.29095	N	0.88183	B	0.06786	0.001	B	0.04013	0.001	T	0.18366	-1.0339	10	0.62326	D	0.03	-14.9887	6.7633	0.23552	0.1276:0.0:0.8724:0.0	rs2071747;rs11555831;rs17879005;rs2071747	7	P09601	HMOX1_HUMAN	H	7	ENSP00000413316:D7H;ENSP00000216117:D7H	ENSP00000216117:D7H	D	+	1	0	HMOX1	34107185	0.604000	0.26932	0.996000	0.52242	0.335000	0.28730	0.359000	0.20233	1.033000	0.39918	0.650000	0.86243	GAC	G|0.952;C|0.048	0.048	strong		0.721	HMOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320657.1		
RNF166	115992	hgsc.bcm.edu	37	16	88767769	88767769	+	Silent	SNP	G	G	C	rs2306049	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:88767769G>C	ENST00000312838.4	-	2	308	c.213C>G	c.(211-213)ctC>ctG	p.L71L	RNF166_ENST00000567844.1_Intron|RP5-1142A6.5_ENST00000561699.1_RNA|RNF166_ENST00000537718.2_5'Flank|RNF166_ENST00000568683.1_5'Flank|RNF166_ENST00000562499.1_5'UTR|RNF166_ENST00000541206.2_5'UTR	NM_178841.3	NP_849163.1	Q96A37	RN166_HUMAN	ring finger protein 166	71							zinc ion binding (GO:0008270)			endometrium(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0476)		GCAGGCGGCAGAGTGGGCACA	0.662													G|||	1945	0.388379	0.2995	0.4265	5008	,	,		14677	0.3194		0.5417	False		,,,				2504	0.3947				p.L71L		Atlas-SNP	.											.	RNF166	3	.	0			c.C213G						PASS	.	G	,,	1501,2893	473.5+/-356.7	248,1005,944	67.0	62.0	64.0		,,213	1.2	1.0	16	dbSNP_100	64	4917,3683	618.8+/-396.8	1433,2051,816	no	intron,utr-5,coding-synonymous	RNF166	NM_001171815.1,NM_001171816.1,NM_178841.3	,,	1681,3056,1760	CC,CG,GG		42.8256,34.1602,49.392	,,	,,71/238	88767769	6418,6576	2197	4300	6497	SO:0001819	synonymous_variant	115992	exon2			GCGGCAGAGTGGG	AK057106	CCDS10969.1, CCDS54056.1, CCDS54057.1	16q24.3	2013-01-09			ENSG00000158717	ENSG00000158717		"""RING-type (C3HC4) zinc fingers"""	28856	protein-coding gene	gene with protein product						12477932	Standard	NM_178841		Approved	MGC2647, MGC14381	uc002flk.3	Q96A37	OTTHUMG00000137863	ENST00000312838.4:c.213C>G	16.37:g.88767769G>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_178841	B3KQ03|D3DX75|H3BTU8|Q96DM0	Silent	SNP	ENST00000312838.4	37	CCDS10969.1																																																																																			G|0.537;C|0.463	0.463	strong		0.662	RNF166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269544.1	NM_178841	
CHRDL2	25884	hgsc.bcm.edu	37	11	74419378	74419378	+	Silent	SNP	C	C	T	rs7948433	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:74419378C>T	ENST00000376332.3	-	5	991	c.495G>A	c.(493-495)ccG>ccA	p.P165P	CHRDL2_ENST00000534159.1_5'UTR|CHRDL2_ENST00000263671.5_Silent_p.P165P	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	165	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cartilage development (GO:0051216)|cell differentiation (GO:0030154)|ossification (GO:0001503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)|skin(2)	15	Hepatocellular(1;0.098)					AGTCTGGCAGCGGGAGGGGTG	0.627													C|||	1672	0.333866	0.1346	0.5677	5008	,	,		18016	0.5357		0.3807	False		,,,				2504	0.181				p.P165P		Atlas-SNP	.											.	CHRDL2	47	.	0			c.G495A						PASS	.	C		772,3620		80,612,1504	38.0	35.0	36.0		495	-9.7	0.2	11	dbSNP_116	36	3230,5354		601,2028,1663	no	coding-synonymous	CHRDL2	NM_015424.3		681,2640,3167	TT,TC,CC		37.6281,17.5774,30.8416		165/452	74419378	4002,8974	2196	4292	6488	SO:0001819	synonymous_variant	25884	exon5			TGGCAGCGGGAGG	AL110168	CCDS8234.1, CCDS60893.1	11q13.4	2013-09-20			ENSG00000054938	ENSG00000054938			24168	protein-coding gene	gene with protein product		613127				12853144, 12975309	Standard	NM_015424		Approved	BNF1	uc001ovh.3	Q6WN34	OTTHUMG00000165623	ENST00000376332.3:c.495G>A	11.37:g.74419378C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_015424	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Silent	SNP	ENST00000376332.3	37																																																																																				C|0.675;T|0.325	0.325	strong		0.627	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1		
HERC5	51191	hgsc.bcm.edu	37	4	89391771	89391771	+	Silent	SNP	C	C	T	rs55990584	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:89391771C>T	ENST00000264350.3	+	10	1398	c.1245C>T	c.(1243-1245)atC>atT	p.I415I	HERC5_ENST00000508159.1_Silent_p.I53I	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	415					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		ATAGGGAAATCCAAGAGATAT	0.299													C|||	25	0.00499201	0.0015	0.0086	5008	,	,		15624	0.0		0.0169	False		,,,				2504	0.0				p.I415I	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-SNP	.											.	HERC5	114	.	0			c.C1245T						PASS	.	C		20,4386	25.3+/-52.1	0,20,2183	107.0	122.0	117.0		1245	1.0	1.0	4	dbSNP_129	117	144,8452	69.7+/-132.2	1,142,4155	no	coding-synonymous	HERC5	NM_016323.2		1,162,6338	TT,TC,CC		1.6752,0.4539,1.2613		415/1025	89391771	164,12838	2203	4298	6501	SO:0001819	synonymous_variant	51191	exon10			GGAAATCCAAGAG	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"""hect domain and RLD 5"""			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1245C>T	4.37:g.89391771C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	153	55	0.359477	NM_016323	B2RTQ1|Q69G20	Silent	SNP	ENST00000264350.3	37	CCDS3630.1																																																																																			C|0.989;T|0.011	0.011	strong		0.299	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323	
TUBB8	347688	hgsc.bcm.edu	37	10	95167	95167	+	Silent	SNP	G	G	A	rs202227666	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:95167G>A	ENST00000309812.4	-	1	74	c.12C>T	c.(10-12)atC>atT	p.I4I	TUBB8_ENST00000447903.2_Intron|TUBB8_ENST00000413237.3_Intron|TUBB8_ENST00000332708.5_Silent_p.I4I	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	4					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		GCGTGAGCACGATCTCCCTCA	0.667																																					p.I4I	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,colon,carcinoma,-2,2	TUBB8	62	2	0			c.C12T						scavenged	.						18.0	17.0	17.0					10																	95167		2197	4294	6491	SO:0001819	synonymous_variant	347688	exon1			GAGCACGATCTCC	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.12C>T	10.37:g.95167G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	116	8	0.0689655	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1																																																																																			G|0.980;A|0.019	0.019	strong		0.667	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
MDH1B	130752	hgsc.bcm.edu	37	2	207603221	207603221	+	Missense_Mutation	SNP	T	T	C	rs2287632	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:207603221T>C	ENST00000374412.3	-	12	1818	c.1543A>G	c.(1543-1545)Acc>Gcc	p.T515A	MDH1B_ENST00000449792.1_Missense_Mutation_p.T417A|MDH1B_ENST00000454776.2_Missense_Mutation_p.T514A	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	515			T -> A (in dbSNP:rs2287632).		carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		GATTCCACGGTTTTGCCTTCA	0.269													T|||	509	0.101637	0.1861	0.0764	5008	,	,		20164	0.0595		0.0716	False		,,,				2504	0.0798				p.T515A	Pancreas(76;29 1355 28675 37177 51207)	Atlas-SNP	.											.	MDH1B	89	.	0			c.A1543G						PASS	.	T	ALA/THR	708,3692	274.3+/-271.8	63,582,1555	81.0	84.0	83.0		1543	-3.5	0.0	2	dbSNP_100	83	763,7829	174.6+/-224.8	34,695,3567	yes	missense	MDH1B	NM_001039845.1	58	97,1277,5122	CC,CT,TT		8.8804,16.0909,11.3224	benign	515/519	207603221	1471,11521	2200	4296	6496	SO:0001583	missense	130752	exon12			CCACGGTTTTGCC		CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.1543A>G	2.37:g.207603221T>C	ENSP00000363533:p.Thr515Ala	Somatic	212	2	0.00943396		WXS	Illumina HiSeq	Phase_I	180	179	0.994444	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	37	CCDS33365.1	197	0.0902014652014652	90	0.18292682926829268	28	0.07734806629834254	33	0.057692307692307696	46	0.06068601583113457	T	8.539	0.872777	0.17322	0.160909	0.088804	ENSG00000138400	ENST00000374412;ENST00000449792;ENST00000454776	T;T;T	0.31510	1.51;1.49;1.5	4.02	-3.49	0.04724	.	2.417000	0.02095	N	0.053436	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.30090	-0.9990	9	0.87932	D	0	1.2602	5.4946	0.16795	0.0:0.1904:0.4747:0.3349	rs2287632;rs2287632	514;515	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	A	515;417;514	ENSP00000363533:T515A;ENSP00000416577:T417A;ENSP00000389916:T514A	ENSP00000363533:T515A	T	-	1	0	MDH1B	207311466	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	-0.209000	0.09358	-0.586000	0.05898	-0.478000	0.04885	ACC	T|0.898;C|0.102	0.102	strong		0.269	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845	
TAS2R50	259296	hgsc.bcm.edu	37	12	11138935	11138935	+	Silent	SNP	T	T	C	rs66679979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11138935T>C	ENST00000506868.1	-	1	576	c.525A>G	c.(523-525)tcA>tcG	p.S175S	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	175					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)	17						CAGTCAAATATGAAAGATGTA	0.388													T|||	493	0.0984425	0.1346	0.0908	5008	,	,		20092	0.002		0.1252	False		,,,				2504	0.1268				p.S175S		Atlas-SNP	.											.	TAS2R50	37	.	0			c.A525G						PASS	.	T		631,3775	272.5+/-270.8	52,527,1624	150.0	130.0	137.0		525	-3.1	0.0	12	dbSNP_130	137	1309,7291	257.9+/-281.7	111,1087,3102	no	coding-synonymous	TAS2R50	NM_176890.2		163,1614,4726	CC,CT,TT		15.2209,14.3214,14.9162		175/300	11138935	1940,11066	2203	4300	6503	SO:0001819	synonymous_variant	259296	exon1			CAAATATGAAAGA	AF494235	CCDS8638.1	12p13.2	2012-08-22			ENSG00000212126	ENSG00000212126		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18882	protein-coding gene	gene with protein product		609627				12379855, 12584440, 16175505	Standard	NM_176890		Approved	T2R51	uc001qzl.2	P59544	OTTHUMG00000162719	ENST00000506868.1:c.525A>G	12.37:g.11138935T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	141	54	0.382979	NM_176890	P59545|Q2M255|Q645Y0	Silent	SNP	ENST00000506868.1	37	CCDS8638.1																																																																																			T|0.870;C|0.130	0.130	strong		0.388	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890	
MUC21	394263	hgsc.bcm.edu	37	6	30954327	30954327	+	Silent	SNP	C	C	T	rs149194643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954327C>T	ENST00000376296.3	+	2	616	c.375C>T	c.(373-375)tcC>tcT	p.S125S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	125	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACTCTGAGTCCAGCACACCCT	0.592																																					p.S125S		Atlas-SNP	.											.	MUC21	98	.	0			c.C375T						PASS	.						174.0	162.0	166.0					6																	30954327		2203	4299	6502	SO:0001819	synonymous_variant	394263	exon2			TGAGTCCAGCACA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.375C>T	6.37:g.30954327C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	151	12	0.0794702	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			C|0.989;T|0.011	0.011	strong		0.592	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
PRRC2C	23215	hgsc.bcm.edu	37	1	171514731	171514731	+	Missense_Mutation	SNP	C	C	G	rs235468	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:171514731C>G	ENST00000338920.4	+	17	5108	c.4871C>G	c.(4870-4872)tCt>tGt	p.S1624C	PRRC2C_ENST00000426496.2_Missense_Mutation_p.S1624C|PRRC2C_ENST00000367742.3_Missense_Mutation_p.S1626C|PRRC2C_ENST00000392078.3_Missense_Mutation_p.S1626C	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1624			S -> C (in dbSNP:rs235468). {ECO:0000269|PubMed:10470851}.		hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TCCAAAGATTCTACTGGGAAA	0.448													C|||	4030	0.804712	0.7277	0.7305	5008	,	,		11348	0.8968		0.8161	False		,,,				2504	0.8548				p.S1624C		Atlas-SNP	.											.	.	.	.	0			c.C4871G						PASS	.	C	CYS/SER	3337,1069	714.8+/-408.4	1269,799,135	67.0	66.0	66.0		4871	3.3	0.1	1	dbSNP_79	66	6975,1625	731.2+/-406.8	2842,1291,167	yes	missense	PRRC2C	NM_015172.3	112	4111,2090,302	GG,GC,CC		18.8953,24.2624,20.7135	possibly-damaging	1624/2818	171514731	10312,2694	2203	4300	6503	SO:0001583	missense	23215	exon17			AAGATTCTACTGG	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4871C>G	1.37:g.171514731C>G	ENSP00000343629:p.Ser1624Cys	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	262	127	0.484733	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	1777|1777	0.8136446886446886|0.8136446886446886	361|361	0.733739837398374|0.733739837398374	273|273	0.7541436464088398|0.7541436464088398	513|513	0.8968531468531469|0.8968531468531469	630|630	0.8311345646437994|0.8311345646437994	C|C	9.741|9.741	1.164748|1.164748	0.21538|0.21538	0.757376|0.757376	0.811047|0.811047	ENSG00000117523|ENSG00000117523	ENST00000495585|ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	.|T;T;T;T	.|0.02050	.|4.48;4.48;4.48;4.48	5.23|5.23	3.27|3.27	0.37495|0.37495	.|.	.|0.896358	.|0.09167	.|N	.|0.839392	T|T	0.01061|0.01061	0.0035|0.0035	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	.|P	.|0.36315	.|0.547	.|B	.|0.43331	.|0.416	T|T	0.54523|0.54523	-0.8281|-0.8281	4|9	.|0.44086	.|T	.|0.13	.|.	11.4197|11.4197	0.49974|0.49974	0.0:0.8498:0.0:0.1502|0.0:0.8498:0.0:0.1502	rs235468;rs1687065;rs3817771;rs52827513;rs235468|rs235468;rs1687065;rs3817771;rs52827513;rs235468	.|1624	.|Q9Y520-4	.|.	V|C	172|1626;1625;1624;1626;1624;1381	.|ENSP00000375928:S1626C;ENSP00000410219:S1624C;ENSP00000356716:S1626C;ENSP00000343629:S1624C	.|ENSP00000343629:S1624C	L|S	+|+	1|2	2|0	PRRC2C|PRRC2C	169781355|169781355	0.003000|0.003000	0.15002|0.15002	0.092000|0.092000	0.20876|0.20876	0.989000|0.989000	0.77384|0.77384	1.489000|1.489000	0.35562|0.35562	1.156000|1.156000	0.42514|0.42514	0.552000|0.552000	0.68991|0.68991	CTA|TCT	C|0.196;G|0.804	0.804	strong		0.448	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
NCOA4	8031	hgsc.bcm.edu	37	10	51568378	51568378	+	Intron	SNP	T	T	G	rs10761581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:51568378T>G	ENST00000374087.4	+	1	70				NCOA4_ENST00000430396.2_Intron|NCOA4_ENST00000452682.1_Missense_Mutation_p.F8V|NCOA4_ENST00000438493.1_Missense_Mutation_p.F8V|NCOA4_ENST00000414907.2_Intron|NCOA4_ENST00000498586.1_Intron	NM_001145263.1	NP_001138735.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4						androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)	p.F8V(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						GTTGACCACTTTTGCTCTAGC	0.418			T	RET	papillary thyroid								g|||	2302	0.459665	0.3222	0.3228	5008	,	,		16941	0.5119		0.4433	False		,,,				2504	0.7055				p.F8V		Atlas-SNP	.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	NCOA4_ENST00000452682,NS,carcinoma,0,1	NCOA4	58	1	1	Substitution - Missense(1)	stomach(1)	c.T22G						PASS	.	G	VAL/PHE,VAL/PHE,	492,892		87,318,287	94.0	87.0	89.0		22,22,	0.9	0.0	10	dbSNP_120	89	1396,1786		306,784,501	yes	missense,missense,intron	NCOA4	NM_001145260.1,NM_001145261.1,NM_001145263.1	50,50,	393,1102,788	GG,GT,TT		43.8718,35.5491,41.3491	benign,benign,	8/651,8/631,	51568378	1888,2678	692	1591	2283	SO:0001627	intron_variant	8031	exon2			ACCACTTTTGCTC	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"""RET-activating gene ELE1"""	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000374087.4:c.-15+3082T>G	10.37:g.51568378T>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_001145261	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Missense_Mutation	SNP	ENST00000374087.4	37	CCDS7237.1	895	0.4097985347985348	146	0.2967479674796748	119	0.3287292817679558	301	0.5262237762237763	329	0.4340369393139842	G	0.006	-2.037693	0.00402	0.355491	0.438718	ENSG00000138293	ENST00000438493;ENST00000452682	T;T	0.12465	2.71;2.68	2.02	0.858	0.19030	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45352	-0.9267	7	0.02654	T	1	.	6.7255	0.23355	0.0:0.0:0.2523:0.7477	rs10761581;rs17720176;rs10761581	8	E9PAV7	.	V	8	ENSP00000405146:F8V;ENSP00000395465:F8V	ENSP00000405146:F8V	F	+	1	0	NCOA4	51238384	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.060000	0.11712	-0.120000	0.11809	-1.509000	0.00949	TTT	T|0.572;G|0.428	0.428	strong		0.418	NCOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048050.1	NM_005437	
FAM181A	90050	hgsc.bcm.edu	37	14	94391699	94391699	+	Missense_Mutation	SNP	G	G	A	rs10141024	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:94391699G>A	ENST00000267594.5	+	2	389	c.82G>A	c.(82-84)Gcg>Acg	p.A28T	FAM181A_ENST00000556222.1_5'Flank|FAM181A_ENST00000557000.2_5'Flank|FAM181A-AS1_ENST00000554742.1_RNA|FAM181A_ENST00000557719.1_Intron	NM_001207073.1|NM_001207074.1|NM_138344.4	NP_001194002.1|NP_001194003.1|NP_612353.3	Q8N9Y4	F181A_HUMAN	family with sequence similarity 181, member A	28			A -> T (in dbSNP:rs10141024). {ECO:0000269|PubMed:14702039}.							cervix(1)|endometrium(2)|large_intestine(8)|lung(4)|prostate(1)|skin(2)	18						GGAGAAAAGGGCGAGCACAGC	0.532													G|||	2513	0.501797	0.4327	0.3963	5008	,	,		21989	0.6409		0.5427	False		,,,				2504	0.4847				p.A28T		Atlas-SNP	.											FAM181A,NS,malignant_melanoma,0,3	FAM181A	42	3	0			c.G82A						PASS	.	G	,THR/ALA	2029,2377	563.5+/-381.2	447,1135,621	79.0	71.0	74.0		,82	-0.6	0.0	14	dbSNP_119	74	4565,4035	596.2+/-393.6	1206,2153,941	yes	intron,missense	FAM181A	NM_001207071.1,NM_138344.4	,58	1653,3288,1562	AA,AG,GG		46.9186,46.0508,49.3003	,benign	,28/355	94391699	6594,6412	2203	4300	6503	SO:0001583	missense	90050	exon2			AAAAGGGCGAGCA	BC009073	CCDS9914.1, CCDS55939.1	14q32.12	2011-11-30	2008-07-22	2008-07-22	ENSG00000140067	ENSG00000140067			20491	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 152"""	C14orf152			Standard	NM_138344		Approved		uc021saz.1	Q8N9Y4	OTTHUMG00000171297	ENST00000267594.5:c.82G>A	14.37:g.94391699G>A	ENSP00000267594:p.Ala28Thr	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_138344	B2RD39|Q96GY1	Missense_Mutation	SNP	ENST00000267594.5	37	CCDS9914.1	1178	0.5393772893772893	232	0.4715447154471545	160	0.4419889502762431	382	0.6678321678321678	404	0.5329815303430079	G	9.206	1.029758	0.19512	0.460508	0.530814	ENSG00000140067	ENST00000267594	T	0.34859	1.34	2.15	-0.574	0.11738	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35076	-0.9803	8	0.36615	T	0.2	.	4.632	0.12506	0.5191:0.0:0.4809:0.0	rs10141024;rs52827633;rs59807175;rs10141024	28	Q8N9Y4	F181A_HUMAN	T	28	ENSP00000267594:A28T	ENSP00000267594:A28T	A	+	1	0	FAM181A	93461452	0.001000	0.12720	0.002000	0.10522	0.029000	0.11900	0.410000	0.21098	-0.170000	0.10816	0.462000	0.41574	GCG	G|0.475;A|0.525	0.525	strong		0.532	FAM181A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412840.1	NM_138344	
RAB3A	5864	hgsc.bcm.edu	37	19	18311199	18311199	+	Silent	SNP	A	A	G	rs1046565	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18311199A>G	ENST00000222256.4	-	3	463	c.285T>C	c.(283-285)gcT>gcC	p.A95A	RAB3A_ENST00000464076.3_5'UTR	NM_002866.4	NP_002857.1	P20336	RAB3A_HUMAN	RAB3A, member RAS oncogene family	95					axonogenesis (GO:0007409)|constitutive secretory pathway (GO:0045054)|glutamate secretion (GO:0014047)|GTP catabolic process (GO:0006184)|lung development (GO:0030324)|maintenance of presynaptic active zone structure (GO:0048790)|mitochondrion organization (GO:0007005)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|post-embryonic development (GO:0009791)|protein transport (GO:0015031)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|respiratory system process (GO:0003016)|response to electrical stimulus (GO:0051602)|sensory perception of touch (GO:0050975)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle recycling (GO:0036465)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)	p.A95A(1)		NS(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	8						TGAAGCCCATAGCGCCCCGGT	0.517													A|||	809	0.161542	0.0287	0.2363	5008	,	,		20724	0.0923		0.3658	False		,,,				2504	0.1493				p.A95A		Atlas-SNP	.											RAB3A,colon,carcinoma,0,2	RAB3A	23	2	1	Substitution - coding silent(1)	stomach(1)	c.T285C						scavenged	.	A		336,4070	174.4+/-204.0	20,296,1887	221.0	176.0	191.0		285	1.7	1.0	19	dbSNP_86	191	2923,5677	456.4+/-364.1	494,1935,1871	no	coding-synonymous	RAB3A	NM_002866.4		514,2231,3758	GG,GA,AA		33.9884,7.626,25.0577		95/221	18311199	3259,9747	2203	4300	6503	SO:0001819	synonymous_variant	5864	exon3			GCCCATAGCGCCC		CCDS12372.1	19p13.2	2008-07-17			ENSG00000105649	ENSG00000105649		"""RAB, member RAS oncogene"""	9777	protein-coding gene	gene with protein product	"""RAS-associated protein RAB3A"""	179490				2687157, 7532276	Standard	NM_002866		Approved		uc002nie.2	P20336	OTTHUMG00000137378	ENST00000222256.4:c.285T>C	19.37:g.18311199A>G		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	251	114	0.454183	NM_002866	A8K0J4|Q9NYE1	Silent	SNP	ENST00000222256.4	37	CCDS12372.1																																																																																			A|0.782;G|0.218	0.218	strong		0.517	RAB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268056.2	NM_002866	
AHNAK	79026	hgsc.bcm.edu	37	11	62296601	62296601	+	Missense_Mutation	SNP	T	T	C	rs74853209	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62296601T>C	ENST00000378024.4	-	5	5562	c.5288A>G	c.(5287-5289)aAg>aGg	p.K1763R	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1763					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GCCTTTCAACTTTCCTTCTGG	0.458													T|||	222	0.0443291	0.1051	0.0303	5008	,	,		20127	0.0119		0.0258	False		,,,				2504	0.0245				p.K1763R		Atlas-SNP	.											.	AHNAK	532	.	0			c.A5288G						PASS	.	T	ARG/LYS,	423,3981	206.5+/-228.1	18,387,1797	111.0	125.0	120.0		5288,	2.4	0.0	11	dbSNP_131	120	220,8378	91.1+/-153.3	4,212,4083	yes	missense,intron	AHNAK	NM_001620.1,NM_024060.2	26,	22,599,5880	CC,CT,TT		2.5587,9.6049,4.9454	possibly-damaging,	1763/5891,	62296601	643,12359	2202	4299	6501	SO:0001583	missense	79026	exon5			TTCAACTTTCCTT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.5288A>G	11.37:g.62296601T>C	ENSP00000367263:p.Lys1763Arg	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	162	85	0.524691	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	98	0.04487179487179487	59	0.11991869918699187	15	0.04143646408839779	7	0.012237762237762238	17	0.022427440633245383	T	10.27	1.304694	0.23736	0.096049	0.025587	ENSG00000124942	ENST00000378024	T	0.26518	1.73	3.55	2.39	0.29439	.	.	.	.	.	T	0.01156	0.0038	M	0.94142	3.5	0.28349	N	0.920975	D	0.71674	0.998	D	0.66084	0.941	T	0.01824	-1.1266	9	0.33940	T	0.23	.	8.3557	0.32329	0.0:0.1004:0.0:0.8996	.	1763	Q09666	AHNK_HUMAN	R	1763	ENSP00000367263:K1763R	ENSP00000367263:K1763R	K	-	2	0	AHNAK	62053177	0.996000	0.38824	0.008000	0.14137	0.002000	0.02628	3.041000	0.49807	0.370000	0.24538	0.254000	0.18369	AAG	T|0.950;C|0.050	0.050	strong		0.458	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
INADL	10207	hgsc.bcm.edu	37	1	62579891	62579891	+	Missense_Mutation	SNP	G	G	T	rs12140153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:62579891G>T	ENST00000371158.2	+	35	4742	c.4628G>T	c.(4627-4629)gGc>gTc	p.G1543V	INADL_ENST00000545929.1_Missense_Mutation_p.G188V|INADL_ENST00000543708.1_Missense_Mutation_p.G357V|INADL_ENST00000316485.6_Missense_Mutation_p.G1573V	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1543	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GCTGGCCGGGGCCTGGGCCTG	0.542													G|||	133	0.0265575	0.0038	0.0216	5008	,	,		18042	0.0		0.0666	False		,,,				2504	0.047				p.G1543V		Atlas-SNP	.											.	INADL	179	.	0			c.G4628T						PASS	.	G	VAL/GLY	64,4342	60.5+/-97.4	0,64,2139	58.0	62.0	61.0		4628	5.5	1.0	1	dbSNP_120	61	757,7843	182.2+/-230.7	36,685,3579	yes	missense	INADL	NM_176877.2	109	36,749,5718	TT,TG,GG		8.8023,1.4526,6.3125	probably-damaging	1543/1802	62579891	821,12185	2203	4300	6503	SO:0001583	missense	10207	exon35			GCCGGGGCCTGGG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4628G>T	1.37:g.62579891G>T	ENSP00000360200:p.Gly1543Val	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	195	91	0.466667	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	66	0.03021978021978022	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	55	0.07255936675461741	G	25.5	4.645815	0.87958	0.014526	0.088023	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000543708;ENST00000545929	T;T;T;T	0.34859	1.69;2.61;1.69;1.34	5.5	5.5	0.81552	PDZ/DHR/GLGF (4);	0.080609	0.47093	D	0.000244	T	0.07999	0.0200	M	0.90369	3.11	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999;0.999	D;D;D;D;D;D	0.97110	1.0;0.99;0.998;0.998;0.995;0.996	T	0.54576	-0.8273	10	0.87932	D	0	.	19.425	0.94737	0.0:0.0:1.0:0.0	rs12140153	188;357;1002;1573;1543;1515	F5GY89;B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;.;INADL_HUMAN;.	V	1543;1573;1573;1515;357;188	ENSP00000360200:G1543V;ENSP00000326199:G1573V;ENSP00000445790:G357V;ENSP00000440094:G188V	ENSP00000326199:G1573V	G	+	2	0	INADL	62352479	1.000000	0.71417	0.999000	0.59377	0.662000	0.39071	9.772000	0.98984	2.584000	0.87258	0.563000	0.77884	GGC	G|0.943;T|0.057	0.057	strong		0.542	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
LEPR	3953	hgsc.bcm.edu	37	1	66067109	66067109	+	Silent	SNP	T	T	C	rs1805134	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:66067109T>C	ENST00000349533.6	+	9	1214	c.1029T>C	c.(1027-1029)agT>agC	p.S343S	LEPR_ENST00000406510.3_Intron|LEPR_ENST00000371059.3_Silent_p.S343S|LEPR_ENST00000371058.1_Silent_p.S343S|LEPR_ENST00000371060.3_Silent_p.S343S|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000344610.8_Silent_p.S343S	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TTCTGACAAGTGTTGGGTCTA	0.343													T|||	1272	0.253994	0.382	0.1455	5008	,	,		19654	0.0675		0.2227	False		,,,				2504	0.3824				p.S343S		Atlas-SNP	.											.	LEPR	284	.	0			c.T1029C	GRCh37	CM030473	LEPR	M	rs1805134	PASS	.	T	,,,,,	1394,3012	455.5+/-351.0	226,942,1035	107.0	105.0	106.0		1029,1029,1029,1029,1029,1029	-2.8	0.0	1	dbSNP_89	106	1776,6824	318.3+/-313.6	166,1444,2690	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LEPR	NM_001003679.3,NM_001003680.3,NM_001198687.1,NM_001198688.1,NM_001198689.1,NM_002303.5	,,,,,	392,2386,3725	CC,CT,TT		20.6512,31.6387,24.3734	,,,,,	343/897,343/959,343/959,343/907,343/897,343/1166	66067109	3170,9836	2203	4300	6503	SO:0001819	synonymous_variant	3953	exon9			GACAAGTGTTGGG	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.1029T>C	1.37:g.66067109T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	60	0.555556	NM_001003680	Q6FHL5	Silent	SNP	ENST00000349533.6	37	CCDS631.1																																																																																			C|0.231;N|0.000	0.231	strong		0.343	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
GRK5	2869	hgsc.bcm.edu	37	10	121196335	121196335	+	Missense_Mutation	SNP	G	G	A	rs2230349	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:121196335G>A	ENST00000392870.2	+	9	1240	c.911G>A	c.(910-912)cGt>cAt	p.R304H	GRK5_ENST00000369108.3_Missense_Mutation_p.R199H	NM_005308.2	NP_005299.1	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5	304	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs2230349). {ECO:0000269|PubMed:17344846}.		adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|phospholipid binding (GO:0005543)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(5)|lung(15)|skin(3)|stomach(1)|urinary_tract(1)	27		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		GACCTCCACCGTGAGAACACC	0.597													G|||	630	0.125799	0.0023	0.0951	5008	,	,		20562	0.2827		0.0755	False		,,,				2504	0.2045				p.R304H		Atlas-SNP	.											.	GRK5	58	.	0			c.G911A						PASS	.	G	HIS/ARG	100,4306	81.4+/-119.9	1,98,2104	73.0	62.0	65.0		911	3.5	0.9	10	dbSNP_98	65	858,7742	194.7+/-240.0	38,782,3480	yes	missense	GRK5	NM_005308.2	29	39,880,5584	AA,AG,GG		9.9767,2.2696,7.3658	probably-damaging	304/591	121196335	958,12048	2203	4300	6503	SO:0001583	missense	2869	exon9			TCCACCGTGAGAA	L15388	CCDS7612.1	10q26.11	2013-09-19	2004-02-04	2004-02-06	ENSG00000198873	ENSG00000198873			4544	protein-coding gene	gene with protein product		600870		GPRK5		7685906	Standard	NM_005308		Approved		uc001led.3	P34947	OTTHUMG00000019149	ENST00000392870.2:c.911G>A	10.37:g.121196335G>A	ENSP00000376609:p.Arg304His	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	117	59	0.504274	NM_005308	D3DRD0|Q5T059	Missense_Mutation	SNP	ENST00000392870.2	37	CCDS7612.1	260	0.11904761904761904	4	0.008130081300813009	36	0.09944751381215469	159	0.27797202797202797	61	0.08047493403693931	G	21.6	4.170418	0.78452	0.022696	0.099767	ENSG00000198873	ENST00000392870;ENST00000369108	T;T	0.25250	1.81;1.81	5.43	3.52	0.40303	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.199423	0.32314	N	0.006278	T	0.00012	0.0000	L	0.42686	1.345	0.19775	P	0.9999570022	B;B	0.22346	0.028;0.068	B;B	0.14023	0.01;0.01	T	0.26677	-1.0096	9	0.59425	D	0.04	-9.8627	9.713	0.40256	0.075:0.0:0.7849:0.1401	rs2230349;rs2275041;rs12718341;rs12718341	304;304	B2R7K0;P34947	.;GRK5_HUMAN	H	304;199	ENSP00000376609:R304H;ENSP00000358104:R199H	ENSP00000358104:R199H	R	+	2	0	GRK5	121186325	0.996000	0.38824	0.873000	0.34254	0.987000	0.75469	3.386000	0.52492	0.606000	0.29965	0.563000	0.77884	CGT	A|0.093;C|0.000;G|0.907	0.093	strong		0.597	GRK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050652.2	NM_005308	
UBE3D	90025	hgsc.bcm.edu	37	6	83667045	83667045	+	Missense_Mutation	SNP	C	C	T	rs7739323	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:83667045C>T	ENST00000369747.3	-	9	1257	c.1135G>A	c.(1135-1137)Gtg>Atg	p.V379M		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	379	HECT-like.		V -> M (in dbSNP:rs7739323).		protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										AAGGAATTCACACGGCGAAGG	0.463													T|||	791	0.157947	0.1838	0.1427	5008	,	,		17847	0.126		0.1571	False		,,,				2504	0.1677				p.V379M		Atlas-SNP	.											.	.	.	.	0			c.G1135A						PASS	.	T	MET/VAL	794,3612	751.1+/-412.2	77,640,1486	117.0	96.0	103.0		1135	5.6	0.8	6	dbSNP_116	103	1310,7290	758.2+/-407.5	100,1110,3090	yes	missense	UBE2CBP	NM_198920.1	21	177,1750,4576	TT,TC,CC		15.2326,18.0209,16.1771	benign	379/390	83667045	2104,10902	2203	4300	6503	SO:0001583	missense	90025	exon9			AATTCACACGGCG	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"""UBCH10 binding protein with a hect-like domain"""	612495	"""chromosome 6 open reading frame 157"", ""ubiquitin-conjugating enzyme E2C binding protein"""	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.1135G>A	6.37:g.83667045C>T	ENSP00000358762:p.Val379Met	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_198920	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	37	CCDS34491.1	361	0.1652930402930403	112	0.22764227642276422	57	0.1574585635359116	71	0.12412587412587413	121	0.15963060686015831	T	0.011	-1.692513	0.00731	0.180209	0.152326	ENSG00000118420	ENST00000369747	T	0.28069	1.63	5.57	5.57	0.84162	.	0.000000	0.85682	N	0.000000	T	0.01558	0.0050	N	0.00170	-1.935	0.09310	P	0.9999999999999759	B	0.06786	0.001	B	0.06405	0.002	T	0.41538	-0.9503	9	0.02654	T	1	-17.7087	9.4496	0.38719	0.0:0.0819:0.0:0.9181	rs7739323;rs17214717;rs7739323	379	Q7Z6J8	UB2CB_HUMAN	M	379	ENSP00000358762:V379M	ENSP00000358762:V379M	V	-	1	0	UBE2CBP	83723764	0.943000	0.32029	0.764000	0.31436	0.036000	0.12997	1.450000	0.35134	0.953000	0.37825	-0.521000	0.04368	GTG	C|0.843;T|0.157	0.157	strong		0.463	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920	
ADAMTS8	11095	hgsc.bcm.edu	37	11	130284668	130284668	+	Missense_Mutation	SNP	G	G	A	rs36124917	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130284668G>A	ENST00000257359.6	-	5	2030	c.1324C>T	c.(1324-1326)Cgc>Tgc	p.R442C		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	442	Disintegrin.				negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		AGGGCCATGCGGCCCGGGAGG	0.652													G|||	6	0.00119808	0.0	0.0029	5008	,	,		18271	0.0		0.004	False		,,,				2504	0.0				p.R442C		Atlas-SNP	.											.	ADAMTS8	172	.	0			c.C1324T						PASS	.	G	CYS/ARG	2,3864		0,2,1931	23.0	27.0	26.0		1324	3.7	0.2	11	dbSNP_126	26	44,8208		0,44,4082	yes	missense	ADAMTS8	NM_007037.4	180	0,46,6013	AA,AG,GG		0.5332,0.0517,0.3796	possibly-damaging	442/890	130284668	46,12072	1933	4126	6059	SO:0001583	missense	11095	exon5			CCATGCGGCCCGG	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	224	protein-coding gene	gene with protein product		605175	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"""			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.1324C>T	11.37:g.130284668G>A	ENSP00000257359:p.Arg442Cys	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_007037	Q9NZS0	Missense_Mutation	SNP	ENST00000257359.6	37	CCDS41732.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	10.03	1.238816	0.22711	5.17E-4	0.005332	ENSG00000134917	ENST00000257359;ENST00000414575	T	0.03717	3.83	5.59	3.66	0.41972	.	0.515138	0.23185	N	0.050966	T	0.04003	0.0112	L	0.58101	1.795	0.34062	D	0.657465	B	0.15719	0.014	B	0.11329	0.006	T	0.03750	-1.1007	10	0.87932	D	0	.	12.4808	0.55842	0.0:0.1281:0.7384:0.1334	rs36124917	442	Q9UP79	ATS8_HUMAN	C	442;471	ENSP00000257359:R442C	ENSP00000257359:R442C	R	-	1	0	ADAMTS8	129789878	0.998000	0.40836	0.213000	0.23690	0.145000	0.21501	2.672000	0.46850	0.661000	0.30985	0.655000	0.94253	CGC	G|0.998;A|0.002	0.002	strong		0.652	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037	
NRG2	9542	hgsc.bcm.edu	37	5	139422232	139422232	+	Silent	SNP	G	G	A	rs144634106	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:139422232G>A	ENST00000361474.1	-	1	647	c.423C>T	c.(421-423)gcC>gcT	p.A141A	NRG2_ENST00000289409.4_Silent_p.A141A|NRG2_ENST00000289422.7_Silent_p.A141A|NRG2_ENST00000541337.1_Silent_p.A141A|NRG2_ENST00000394770.1_Silent_p.A141A|NRG2_ENST00000358522.3_Silent_p.A141A|NRG2_ENST00000545385.1_Silent_p.A141A	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	141					embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAGCCGCCGGCTGGGACCA	0.697													G|||	134	0.0267572	0.0272	0.0403	5008	,	,		7889	0.0		0.0616	False		,,,				2504	0.0082				p.A141A		Atlas-SNP	.											.	NRG2	69	.	0			c.C423T						PASS	.	G	,,,,	145,4055		4,137,1959	6.0	8.0	7.0		423,423,423,423,423	-0.9	1.0	5	dbSNP_134	7	503,7855		16,471,3692	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRG2	NM_001184935.1,NM_004883.2,NM_013981.3,NM_013982.2,NM_013983.2	,,,,	20,608,5651	AA,AG,GG		6.0182,3.4524,5.1601	,,,,	141/785,141/851,141/845,141/859,141/853	139422232	648,11910	2100	4179	6279	SO:0001819	synonymous_variant	9542	exon1			GCCGCCGGCTGGG		CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"""Immunoglobulin superfamily / I-set domain containing"""	7998	protein-coding gene	gene with protein product	"""neural- and thymus-derived activator for ErbB kinases"", ""divergent of neuregulin-1"""	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.423C>T	5.37:g.139422232G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_013982		Silent	SNP	ENST00000361474.1	37	CCDS4217.1																																																																																			G|0.965;A|0.035	0.035	strong		0.697	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982	
SUGP1	57794	hgsc.bcm.edu	37	19	19390185	19390185	+	Silent	SNP	G	G	A	rs11555053	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19390185G>A	ENST00000247001.5	-	10	1712	c.1365C>T	c.(1363-1365)taC>taT	p.Y455Y		NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	455	Gln/Met-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						TGATCATGTCGTACATCTGCT	0.642													G|||	747	0.149161	0.295	0.1268	5008	,	,		19295	0.0		0.167	False		,,,				2504	0.1033				p.Y455Y		Atlas-SNP	.											SUGP1,NS,carcinoma,0,1	SUGP1	63	1	0			c.C1365T						PASS	.	G		1242,3162	411.7+/-335.8	171,900,1131	67.0	44.0	52.0		1365	-2.3	1.0	19	dbSNP_120	52	1363,7237	257.9+/-281.7	106,1151,3043	no	coding-synonymous	SUGP1	NM_172231.3		277,2051,4174	AA,AG,GG		15.8488,28.2016,20.0323		455/646	19390185	2605,10399	2202	4300	6502	SO:0001819	synonymous_variant	57794	exon10			CATGTCGTACATC	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"""G patch domain containing"""	18643	protein-coding gene	gene with protein product		607992	"""splicing factor 4"""	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.1365C>T	19.37:g.19390185G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Silent	SNP	ENST00000247001.5	37	CCDS12399.1																																																																																			G|0.805;A|0.195	0.195	strong		0.642	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164	
CP	1356	hgsc.bcm.edu	37	3	148904434	148904434	+	Silent	SNP	T	T	G	rs1053709	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:148904434T>G	ENST00000264613.6	-	11	2212	c.1950A>C	c.(1948-1950)ggA>ggC	p.G650G	CP_ENST00000462336.1_5'UTR	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	650	F5/8 type A 2.|Plastocyanin-like 4.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CGGCCTCATTTCCGGCGCTGA	0.458													T|||	98	0.0195687	0.0008	0.036	5008	,	,		20261	0.001		0.0457	False		,,,				2504	0.0256				p.G650G		Atlas-SNP	.											.	CP	112	.	0			c.A1950C						PASS	.	T		59,4347	55.5+/-91.7	1,57,2145	154.0	139.0	144.0		1950	2.2	1.0	3	dbSNP_86	144	520,8080	146.2+/-201.8	10,500,3790	no	coding-synonymous	CP	NM_000096.3		11,557,5935	GG,GT,TT		6.0465,1.3391,4.4518		650/1066	148904434	579,12427	2203	4300	6503	SO:0001819	synonymous_variant	1356	exon11			CTCATTTCCGGCG	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1950A>C	3.37:g.148904434T>G		Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	266	129	0.484962	NM_000096	Q14063|Q2PP18|Q9UKS4	Silent	SNP	ENST00000264613.6	37	CCDS3141.1																																																																																			T|0.962;G|0.038	0.038	strong		0.458	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096	
GLI2	2736	hgsc.bcm.edu	37	2	121742124	121742124	+	Silent	SNP	G	G	A	rs61732852	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:121742124G>A	ENST00000452319.1	+	12	1821	c.1761G>A	c.(1759-1761)acG>acA	p.T587T	GLI2_ENST00000314490.11_Silent_p.T259T|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000361492.4_Silent_p.T587T					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				ATGTGAAAACGGTCCACGGCC	0.597													G|||	22	0.00439297	0.0	0.0043	5008	,	,		19759	0.0		0.0139	False		,,,				2504	0.0051				p.T587T		Atlas-SNP	.											.	GLI2	187	.	0			c.G1761A						PASS	.	G		13,4393	19.1+/-41.9	0,13,2190	154.0	147.0	149.0		1761	-9.0	0.3	2	dbSNP_129	149	117,8483	61.7+/-123.6	0,117,4183	no	coding-synonymous	GLI2	NM_005270.4		0,130,6373	AA,AG,GG		1.3605,0.2951,0.9995		587/1587	121742124	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	2736	exon11			GAAAACGGTCCAC		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.1761G>A	2.37:g.121742124G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	199	82	0.41206	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			G|0.991;A|0.009	0.009	strong		0.597	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
CYP2D6	1565	hgsc.bcm.edu	37	22	42523528	42523528	+	Missense_Mutation	SNP	C	C	T	rs1058172	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:42523528C>T	ENST00000360608.5	-	7	1208	c.1094G>A	c.(1093-1095)cGc>cAc	p.R365H	CYP2D6_ENST00000389970.3_Missense_Mutation_p.R365H|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.R314H|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	365			R -> H (in dbSNP:rs1058172).		alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GTCCCCAAAGCGCTGCACCTC	0.602																																					p.R365H		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,2	CYP2D6	104	2	0			c.G1094A						scavenged	.						106.0	85.0	92.0					22																	42523528		2202	4300	6502	SO:0001583	missense	1565	exon7			CCAAAGCGCTGCA	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1094G>A	22.37:g.42523528C>T	ENSP00000353820:p.Arg365His	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	381	163	0.427822	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	154	0.07051282051282051	11	0.022357723577235773	39	0.10773480662983426	0	0.0	104	0.13720316622691292	C	34	5.359243	0.95854	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	D;D;D	0.97505	-4.41;-4.41;-4.41	4.93	4.93	0.64822	.	0.000000	0.64402	D	0.000001	T	0.61800	0.2376	H	0.99545	4.62	0.09310	P	0.99999999622316	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.978;0.999	T	0.49943	-0.8885	9	0.87932	D	0	.	17.7329	0.88383	0.0:1.0:0.0:0.0	rs1058172;rs1974456;rs4134603;rs17002850	365;314;365	C1ID54;Q6NXU8;Q6NWU0	.;.;.	H	365;365;311;314;314	ENSP00000353820:R365H;ENSP00000374620:R365H;ENSP00000351927:R314H	ENSP00000351927:R314H	R	-	2	0	CYP2D6	40853472	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.610000	0.82949	2.283000	0.76528	0.555000	0.69702	CGC	C|0.908;T|0.092	0.092	strong		0.602	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
NPHP4	261734	hgsc.bcm.edu	37	1	5935162	5935162	+	Splice_Site	SNP	A	A	T	rs1287637	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:5935162A>T	ENST00000378156.4	-	21	3083		c.e21-2		NPHP4_ENST00000478423.2_Splice_Site	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4						actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CTGCTGCGCCAGCAGACAAGA	0.637													t|||	4223	0.843251	0.91	0.8401	5008	,	,		17793	0.7907		0.8111	False		,,,				2504	0.8425				.		Atlas-SNP	.											.	NPHP4	119	.	0			c.2818-2T>A						PASS	.			3888,462		1741,406,28	25.0	30.0	28.0			4.9	0.2	1	dbSNP_87	28	6953,1555		2846,1261,147	yes	splice-3	NPHP4	NM_015102.3		4587,1667,175	TT,TA,AA		18.2769,10.6207,15.6867			5935162	10841,2017	2175	4254	6429	SO:0001630	splice_region_variant	261734	exon22			TGCGCCAGCAGAC	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.2818-2T>A	1.37:g.5935162A>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	43	26	0.604651	NM_015102	Q8IWC0	Splice_Site	SNP	ENST00000378156.4	37	CCDS44052.1	1821	0.8337912087912088	435	0.8841463414634146	295	0.8149171270718232	476	0.8321678321678322	615	0.8113456464379947	t	8.681	0.905064	0.17760	0.893793	0.817231	ENSG00000131697	ENST00000378156	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.5729	0.22549	0.1387:0.0778:0.0:0.7835	rs1287637;rs60394218;rs1287637	.	.	.	.	-1	.	.	.	-	.	.	NPHP4	5857749	0.036000	0.19791	0.202000	0.23494	0.005000	0.04900	0.452000	0.21795	0.745000	0.32763	-0.557000	0.04193	.	A|0.171;T|0.829	0.829	strong		0.637	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		Intron
ZZEF1	23140	hgsc.bcm.edu	37	17	3953083	3953083	+	Silent	SNP	T	T	C	rs781853	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:3953083T>C	ENST00000381638.2	-	37	6058	c.5934A>G	c.(5932-5934)ccA>ccG	p.P1978P		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1978							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						GCACAGTGACTGGTAGGGCCT	0.512													T|||	2319	0.463059	0.7769	0.4078	5008	,	,		18878	0.2431		0.4026	False		,,,				2504	0.3671				p.P1978P		Atlas-SNP	.											ZZEF1,colon,carcinoma,0,1	ZZEF1	195	1	0			c.A5934G						PASS	.	T		3198,1208	708.6+/-407.6	1176,846,181	117.0	107.0	110.0		5934	0.9	0.0	17	dbSNP_86	110	3383,5217	501.4+/-375.4	647,2089,1564	no	coding-synonymous	ZZEF1	NM_015113.3		1823,2935,1745	CC,CT,TT		39.3372,27.4172,49.4003		1978/2962	3953083	6581,6425	2203	4300	6503	SO:0001819	synonymous_variant	23140	exon37			AGTGACTGGTAGG	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.5934A>G	17.37:g.3953083T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	144	61	0.423611	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																			T|0.502;C|0.498	0.498	strong		0.512	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
LPCAT3	10162	hgsc.bcm.edu	37	12	7091918	7091918	+	Silent	SNP	C	C	T	rs3764031	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7091918C>T	ENST00000261407.4	-	3	370	c.285G>A	c.(283-285)ctG>ctA	p.L95L	U47924.30_ENST00000606112.1_lincRNA|LPCAT3_ENST00000535021.1_5'Flank	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	95					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						GCACAATACACAGCAGGGAGT	0.483													T|||	921	0.183906	0.4788	0.0994	5008	,	,		-128	0.0506		0.0845	False		,,,				2504	0.0849				p.L95L		Atlas-SNP	.											.	LPCAT3	33	.	0			c.G285A						PASS	.	T		1791,2615	641.9+/-397.6	379,1033,791	153.0	133.0	140.0		285	-7.4	0.1	12	dbSNP_107	140	698,7902	788.0+/-407.6	32,634,3634	no	coding-synonymous	LPCAT3	NM_005768.5		411,1667,4425	TT,TC,CC		8.1163,40.6491,19.1373		95/488	7091918	2489,10517	2203	4300	6503	SO:0001819	synonymous_variant	10162	exon3			AATACACAGCAGG	U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"""O-acyltransferase (membrane bound) domain containing 5"", ""membrane bound O-acyltransferase domain containing 5"""	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970	ENST00000261407.4:c.285G>A	12.37:g.7091918C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	162	87	0.537037	NM_005768	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Silent	SNP	ENST00000261407.4	37	CCDS8572.1																																																																																			C|0.809;T|0.191	0.191	strong		0.483	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768	
PLCB1	23236	hgsc.bcm.edu	37	20	8703060	8703060	+	Missense_Mutation	SNP	A	A	T	rs138851178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:8703060A>T	ENST00000338037.6	+	15	1600	c.1573A>T	c.(1573-1575)Atg>Ttg	p.M525L	PLCB1_ENST00000378641.3_Missense_Mutation_p.M525L|PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378637.2_Missense_Mutation_p.M525L	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	525					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						AAAATCTTCAATGGATGAGGT	0.448																																					p.E525X		Atlas-SNP	.											.	PLCB1	394	.	0			c.G1573T						PASS	.						201.0	160.0	174.0					20																	8703060		2203	4300	6503	SO:0001583	missense	23236	exon15			TCTTCAATGGATG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.1573A>T	20.37:g.8703060A>T	ENSP00000338185:p.Met525Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Nonsense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.190382	0.58017	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.49432	0.78;0.78;0.78	5.96	5.96	0.96718	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.157283	0.37906	U	0.001882	T	0.42245	0.1194	L	0.44542	1.39	0.52501	D	0.999952	B;B	0.13145	0.0;0.007	B;B	0.16289	0.001;0.015	T	0.19516	-1.0303	10	0.28530	T	0.3	.	15.6296	0.76893	1.0:0.0:0.0:0.0	.	525;525	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	L	525;525;525;445;445	ENSP00000367908:M525L;ENSP00000338185:M525L;ENSP00000367904:M525L	ENSP00000338185:M525L	M	+	1	0	PLCB1	8651060	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.524000	0.81866	2.285000	0.76669	0.533000	0.62120	ATG	A|1.000;G|0.000	.	alt		0.448	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
GM2A	2760	hgsc.bcm.edu	37	5	150647012	150647012	+	Silent	SNP	A	A	G	rs1048723	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150647012A>G	ENST00000357164.3	+	4	907	c.582A>G	c.(580-582)taA>taG	p.*194*		NM_000405.4|NM_001167607.1	NP_000396.2|NP_001161079.1	P17900	SAP3_HUMAN	GM2 ganglioside activator	0					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|learning or memory (GO:0007611)|lipid storage (GO:0019915)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	apical cortex (GO:0045179)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|mitochondrion (GO:0005739)	beta-N-acetylhexosaminidase activity (GO:0004563)|lipid transporter activity (GO:0005319)|phospholipase activator activity (GO:0016004)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|upper_aerodigestive_tract(2)	8		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGGCATATAACATGGCATCT	0.552													A|||	1330	0.265575	0.0885	0.4524	5008	,	,		21786	0.2698		0.3171	False		,,,				2504	0.3149				p.X194X		Atlas-SNP	.											.	GM2A	24	.	0			c.A582G						PASS	.	A	,	585,3821	256.1+/-261.0	41,503,1659	94.0	93.0	93.0		582,	-2.1	0.0	5	dbSNP_86	93	2395,6205	397.7+/-345.9	338,1719,2243	no	coding-synonymous,intron	GM2A	NM_000405.4,NM_001167607.1	,	379,2222,3902	GG,GA,AA		27.8488,13.2773,22.9125	,	194/194,	150647012	2980,10026	2203	4300	6503	SO:0001819	synonymous_variant	2760	exon4			CATATAACATGGC		CCDS4313.1	5q33.1	2010-03-17	2004-05-20		ENSG00000196743	ENSG00000196743			4367	protein-coding gene	gene with protein product	"""cerebroside sulfate activator protein"", ""sphingolipid activator protein 3"""	613109	"""GM2 ganglioside activator protein"""			115863, 1915857	Standard	NM_000405		Approved	SAP-3	uc003ltr.4	P17900	OTTHUMG00000130124	ENST00000357164.3:c.582A>G	5.37:g.150647012A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	150	84	0.56	NM_000405	B2R699|D3DQH6|Q14426|Q14428|Q6LBL5	Silent	SNP	ENST00000357164.3	37	CCDS4313.1																																																																																			A|0.762;G|0.238;T|0.000	0.238	strong		0.552	GM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252432.1	NM_000405	
KIAA1279	26128	hgsc.bcm.edu	37	10	70748784	70748784	+	Missense_Mutation	SNP	G	G	A	rs2255607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70748784G>A	ENST00000361983.4	+	1	298	c.196G>A	c.(196-198)Ggc>Agc	p.G66S		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	66			G -> S (in dbSNP:rs2255607). {ECO:0000269|PubMed:10574462}.		cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						GGCCGAGGACGGCCCGGGTGC	0.701													G|||	1772	0.353834	0.329	0.3156	5008	,	,		14045	0.3562		0.4811	False		,,,				2504	0.2812				p.G66S		Atlas-SNP	.											.	KIAA1279	35	.	0			c.G196A						PASS	.	G	SER/GLY	1507,2899		265,977,961	30.0	37.0	35.0		196	-0.1	0.0	10	dbSNP_100	35	4153,4441		1010,2133,1154	no	missense	KIAA1279	NM_015634.3	56	1275,3110,2115	AA,AG,GG		48.3244,34.2034,43.5385	possibly-damaging	66/622	70748784	5660,7340	2203	4297	6500	SO:0001583	missense	26128	exon1			GAGGACGGCCCGG	BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954			23419	protein-coding gene	gene with protein product		609367					Standard	NM_015634		Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.196G>A	10.37:g.70748784G>A	ENSP00000354848:p.Gly66Ser	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Missense_Mutation	SNP	ENST00000361983.4	37	CCDS7284.1	880	0.40293040293040294	168	0.34146341463414637	133	0.3674033149171271	221	0.38636363636363635	358	0.47229551451187335	G	1.857	-0.463542	0.04476	0.342034	0.483244	ENSG00000198954	ENST00000361983	T	0.41400	1.0	5.24	-0.111	0.13576	.	0.508915	0.22554	N	0.058552	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45293	-0.9271	9	0.08837	T	0.75	-22.3659	3.8437	0.08925	0.2493:0.0:0.4709:0.2798	rs2255607;rs57824932	66	Q96EK5	KBP_HUMAN	S	66	ENSP00000354848:G66S	ENSP00000354848:G66S	G	+	1	0	KIAA1279	70418790	0.000000	0.05858	0.002000	0.10522	0.047000	0.14425	0.211000	0.17474	-0.053000	0.13289	-0.158000	0.13435	GGC	G|0.584;A|0.416	0.416	strong		0.701	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634	
COL13A1	1305	hgsc.bcm.edu	37	10	71647223	71647223	+	Silent	SNP	A	A	C	rs11816811	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:71647223A>C	ENST00000398978.3	+	7	990	c.498A>C	c.(496-498)ggA>ggC	p.G166G	COL13A1_ENST00000398968.3_Silent_p.G166G|COL13A1_ENST00000356340.3_Silent_p.G166G|COL13A1_ENST00000398972.3_Silent_p.G166G|COL13A1_ENST00000398966.3_Silent_p.G166G|COL13A1_ENST00000398964.3_Silent_p.G137G|COL13A1_ENST00000398973.3_Silent_p.G166G|COL13A1_ENST00000357811.3_Silent_p.G166G|COL13A1_ENST00000398969.3_Silent_p.G128G|COL13A1_ENST00000517713.1_Silent_p.G166G|COL13A1_ENST00000398971.3_Silent_p.G166G|COL13A1_ENST00000354547.3_Silent_p.G166G|COL13A1_ENST00000520133.1_Silent_p.G137G|COL13A1_ENST00000398974.3_Silent_p.G154G|COL13A1_ENST00000522165.1_Silent_p.G166G|COL13A1_ENST00000520267.1_Silent_p.G128G	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						GTCAACCAGGAACTAGAGGTT	0.483													C|||	443	0.0884585	0.0953	0.0692	5008	,	,		18412	0.0784		0.1213	False		,,,				2504	0.0695				p.G166G		Atlas-SNP	.											.	COL13A1	133	.	0			c.A498C						PASS	.	C	,,,,,	361,3401		17,327,1537	115.0	124.0	121.0		498,384,498,498,498,411	1.9	0.4	10	dbSNP_120	121	900,7336		45,810,3263	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL13A1	NM_001130103.1,NM_080798.3,NM_080800.3,NM_080801.3,NM_080802.3,NM_080805.3	,,,,,	62,1137,4800	CC,CA,AA		10.9276,9.596,10.5101	,,,,,	166/718,128/646,166/687,166/696,166/669,137/611	71647223	1261,10737	1881	4118	5999	SO:0001819	synonymous_variant	1305	exon7			ACCAGGAACTAGA	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"""Collagens"""	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.498A>C	10.37:g.71647223A>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_080802		Silent	SNP	ENST00000398978.3	37	CCDS44419.1																																																																																			A|0.897;C|0.102	0.102	strong		0.483	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203	
EFCAB7	84455	hgsc.bcm.edu	37	1	63991267	63991267	+	Silent	SNP	T	T	C	rs217478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:63991267T>C	ENST00000371088.4	+	2	270	c.24T>C	c.(22-24)gaT>gaC	p.D8D	ITGB3BP_ENST00000371092.3_5'Flank|ITGB3BP_ENST00000283568.8_5'Flank|ITGB3BP_ENST00000271002.10_5'Flank	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	8							calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						CACGAAGCGATGCAACTTTCT	0.353													T|||	2012	0.401757	0.3026	0.4741	5008	,	,		14553	0.4812		0.326	False		,,,				2504	0.4806				p.D8D		Atlas-SNP	.											EFCAB7,colon,carcinoma,+2,1	EFCAB7	45	1	0			c.T24C						PASS	.	T		1444,2962	456.9+/-351.5	237,970,996	72.0	79.0	77.0		24	0.2	0.3	1	dbSNP_79	77	2736,5864	434.9+/-357.9	436,1864,2000	no	coding-synonymous	EFCAB7	NM_032437.2		673,2834,2996	CC,CT,TT		31.814,32.7735,32.139		8/630	63991267	4180,8826	2203	4300	6503	SO:0001819	synonymous_variant	84455	exon2			AAGCGATGCAACT	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.24T>C	1.37:g.63991267T>C		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	219	93	0.424658	NM_032437	Q658P0|Q96B95|Q96JM6	Silent	SNP	ENST00000371088.4	37	CCDS30737.1																																																																																			C|0.347;N|0.000	0.347	strong		0.353	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
MYH8	4626	hgsc.bcm.edu	37	17	10304261	10304261	+	Silent	SNP	G	G	A	rs3744552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:10304261G>A	ENST00000403437.2	-	26	3364	c.3270C>T	c.(3268-3270)atC>atT	p.I1090I	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1090					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TCAAATTGCTGATTTCAAATT	0.328									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				A|||	2372	0.473642	0.7292	0.4841	5008	,	,		17387	0.124		0.6272	False		,,,				2504	0.3231				p.I1090I		Atlas-SNP	.											.	MYH8	346	.	0			c.C3270T						PASS	.	A		3062,1344	446.7+/-348.1	1058,946,199	71.0	68.0	69.0		3270	1.0	1.0	17	dbSNP_107	69	4997,3603	518.7+/-379.3	1466,2065,769	no	coding-synonymous	MYH8	NM_002472.2		2524,3011,968	AA,AG,GG		41.8953,30.5039,38.0363		1090/1938	10304261	8059,4947	2203	4300	6503	SO:0001819	synonymous_variant	4626	exon26	Familial Cancer Database	Carney Complex Variant	ATTGCTGATTTCA		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.3270C>T	17.37:g.10304261G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																			G|0.433;A|0.567	0.567	strong		0.328	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
FANCA	2175	hgsc.bcm.edu	37	16	89807233	89807233	+	Silent	SNP	C	C	G	rs11649210	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89807233C>G	ENST00000389301.3	-	38	3837	c.3807G>C	c.(3805-3807)ctG>ctC	p.L1269L	FANCA_ENST00000568369.1_Silent_p.L1269L|ZNF276_ENST00000289816.5_3'UTR	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1269					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GATGTGACGACAGCAGGCCCA	0.463			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	691	0.137979	0.1543	0.0346	5008	,	,		17285	0.2629		0.0736	False		,,,				2504	0.1268				p.L1269L		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.G3807C						PASS	.	G	,,	629,3767	764.9+/-413.3	38,553,1607	84.0	77.0	79.0		3807,,	-7.2	0.1	16	dbSNP_120	79	774,7826	781.2+/-407.6	32,710,3558	no	coding-synonymous,utr-3,utr-3	FANCA,ZNF276	NM_000135.2,NM_001113525.1,NM_152287.3	,,	70,1263,5165	GG,GC,CC		9.0,14.3085,10.7956	,,	1269/1456,,	89807233	1403,11593	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon38	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGACGACAGCAGG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3807G>C	16.37:g.89807233C>G		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	234	114	0.487179	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			C|0.892;G|0.108	0.108	strong		0.463	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
DVL2	1856	hgsc.bcm.edu	37	17	7133162	7133162	+	Silent	SNP	G	G	A	rs222836	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7133162G>A	ENST00000005340.5	-	5	903	c.621C>T	c.(619-621)agC>agT	p.S207S	DVL2_ENST00000575458.1_Silent_p.S201S|DVL2_ENST00000574642.1_5'UTR	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	207					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						AGTCCCCCAGGCTGGTACTCT	0.657													G|||	2264	0.452077	0.3018	0.451	5008	,	,		18255	0.4712		0.5109	False		,,,				2504	0.5757				p.S207S		Atlas-SNP	.											.	DVL2	49	.	0			c.C621T						PASS	.	G		1510,2896	479.2+/-358.4	248,1014,941	80.0	86.0	84.0		621	3.1	1.0	17	dbSNP_79	84	4449,4151	587.6+/-392.2	1154,2141,1005	no	coding-synonymous	DVL2	NM_004422.2		1402,3155,1946	AA,AG,GG		48.2674,34.2714,45.8173		207/737	7133162	5959,7047	2203	4300	6503	SO:0001819	synonymous_variant	1856	exon5			CCCCAGGCTGGTA	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.621C>T	17.37:g.7133162G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	73	25	0.342466	NM_004422	D3DTN3|Q53XM0	Silent	SNP	ENST00000005340.5	37	CCDS11091.1																																																																																			G|0.552;A|0.448	0.448	strong		0.657	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
GRIN2A	2903	hgsc.bcm.edu	37	16	9943666	9943666	+	Silent	SNP	C	C	T	rs2229193	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:9943666C>T	ENST00000396573.2	-	6	1584	c.1275G>A	c.(1273-1275)ctG>ctA	p.L425L	GRIN2A_ENST00000535259.1_Silent_p.L268L|GRIN2A_ENST00000330684.3_Silent_p.L425L|GRIN2A_ENST00000562109.1_Silent_p.L425L|GRIN2A_ENST00000396575.2_Silent_p.L425L|GRIN2A_ENST00000404927.2_Silent_p.L425L	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	425					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ACGTCTCGGTCAGGGGGTCTA	0.547													C|||	1131	0.225839	0.2988	0.2089	5008	,	,		18934	0.0754		0.2992	False		,,,				2504	0.2188				p.L425L		Atlas-SNP	.											.	GRIN2A	366	.	0			c.G1275A						PASS	.	C	,,	1310,3084	444.1+/-347.2	187,936,1074	179.0	139.0	153.0		1275,1275,1275	3.2	1.0	16	dbSNP_116	153	2543,6057	415.2+/-351.7	346,1851,2103	no	coding-synonymous,coding-synonymous,coding-synonymous	GRIN2A	NM_000833.3,NM_001134407.1,NM_001134408.1	,,	533,2787,3177	TT,TC,CC		29.5698,29.8134,29.6521	,,	425/1465,425/1465,425/1282	9943666	3853,9141	2197	4300	6497	SO:0001819	synonymous_variant	2903	exon6			CTCGGTCAGGGGG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.1275G>A	16.37:g.9943666C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	182	84	0.461538	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																			C|0.736;T|0.264	0.264	strong		0.547	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
EVC	2121	hgsc.bcm.edu	37	4	5749961	5749961	+	Silent	SNP	G	G	C	rs4688962	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:5749961G>C	ENST00000264956.6	+	8	1210	c.1026G>C	c.(1024-1026)ctG>ctC	p.L342L	EVC_ENST00000509451.1_Silent_p.L342L|EVC_ENST00000382674.2_Silent_p.L342L	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	342					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				CCCGACAGCTGATGATGACTC	0.507													C|||	2919	0.582867	0.7776	0.3905	5008	,	,		17601	0.6181		0.4245	False		,,,				2504	0.5828				p.L342L		Atlas-SNP	.											.	EVC	90	.	0			c.G1026C						PASS	.	C		3138,1268	434.9+/-344.1	1125,888,190	97.0	94.0	95.0		1026	3.3	0.5	4	dbSNP_111	95	3787,4813	615.5+/-396.4	836,2115,1349	no	coding-synonymous	EVC	NM_153717.2		1961,3003,1539	CC,CG,GG		44.0349,28.7789,46.7553		342/993	5749961	6925,6081	2203	4300	6503	SO:0001819	synonymous_variant	2121	exon8			ACAGCTGATGATG	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.1026G>C	4.37:g.5749961G>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	NM_153717		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			G|0.459;C|0.541	0.541	strong		0.507	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
OR7A10	390892	hgsc.bcm.edu	37	19	14952560	14952560	+	Missense_Mutation	SNP	G	G	T	rs12985894	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14952560G>T	ENST00000248058.1	-	1	129	c.130C>A	c.(130-132)Ctc>Atc	p.L44I		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					AGGATGATGAGCAGGTTCCCG	0.512													.|||	618	0.123403	0.143	0.1196	5008	,	,		18213	0.0903		0.1541	False		,,,				2504	0.1022				p.L44I		Atlas-SNP	.											.	OR7A10	33	.	0			c.C130A						PASS	.	G	ILE/LEU	675,3731	285.7+/-278.4	58,559,1586	70.0	66.0	67.0		130	2.8	1.0	19	dbSNP_121	67	1455,7139	277.4+/-292.8	140,1175,2982	no	missense	OR7A10	NM_001005190.1	5	198,1734,4568	TT,TG,GG		16.9304,15.32,16.3846	possibly-damaging	44/310	14952560	2130,10870	2203	4297	6500	SO:0001583	missense	390892	exon1			TGATGAGCAGGTT		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.130C>A	19.37:g.14952560G>T	ENSP00000248058:p.Leu44Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	260	0.11904761904761904	69	0.1402439024390244	48	0.13259668508287292	27	0.0472027972027972	116	0.15303430079155672	g	9.293	1.051138	0.19827	0.1532	0.169304	ENSG00000127515	ENST00000248058	T	0.02606	4.23	2.79	2.79	0.32731	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34133	U	0.004236	T	0.00039	0.0001	L	0.60904	1.88	0.48452	P	3.4199999999995345E-4	P	0.46327	0.876	P	0.54238	0.746	T	0.25293	-1.0136	9	0.72032	D	0.01	.	7.1625	0.25672	0.0:0.0:0.7333:0.2667	rs12985894	44	O76100	OR7AA_HUMAN	I	44	ENSP00000248058:L44I	ENSP00000248058:L44I	L	-	1	0	OR7A10	14813560	0.000000	0.05858	1.000000	0.80357	0.286000	0.27126	-0.617000	0.05584	1.572000	0.49736	0.430000	0.28490	CTC	G|0.856;T|0.144	0.144	strong		0.512	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
FANCA	2175	hgsc.bcm.edu	37	16	89866043	89866043	+	Missense_Mutation	SNP	T	T	C	rs7190823	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89866043T>C	ENST00000389301.3	-	9	826	c.796A>G	c.(796-798)Acg>Gcg	p.T266A	FANCA_ENST00000534992.1_Missense_Mutation_p.T266A|FANCA_ENST00000563673.1_Missense_Mutation_p.T266A|FANCA_ENST00000568369.1_Missense_Mutation_p.T266A|FANCA_ENST00000389302.3_Missense_Mutation_p.T266A|FANCA_ENST00000543736.1_Missense_Mutation_p.T234A	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	266			T -> A (in dbSNP:rs7190823). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:9399890, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		ACATCAACCGTGACCTGTCAA	0.358			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	3458	0.690495	0.7625	0.6037	5008	,	,		21218	0.9871		0.3956	False		,,,				2504	0.6524				p.T266A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,colon,carcinoma,+1,1	FANCA	99	1	0			c.A796G						scavenged	.	C	ALA/THR,ALA/THR	3190,1206	421.5+/-339.4	1151,888,159	147.0	127.0	134.0		796,796	1.9	0.1	16	dbSNP_116	134	3386,5214	640.8+/-399.6	677,2032,1591	yes	missense,missense	FANCA	NM_000135.2,NM_001018112.1	58,58	1828,2920,1750	CC,CT,TT		39.3721,27.434,49.3998	benign,benign	266/1456,266/298	89866043	6576,6420	2198	4300	6498	SO:0001583	missense	2175	exon9	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CAACCGTGACCTG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.796A>G	16.37:g.89866043T>C	ENSP00000373952:p.Thr266Ala	Somatic	142	2	0.0140845		WXS	Illumina HiSeq	Phase_I	151	73	0.483444	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	1435	0.657051282051282	370	0.7520325203252033	199	0.5497237569060773	564	0.986013986013986	302	0.39841688654353563	C	0.399	-0.919409	0.02396	0.72566	0.393721	ENSG00000187741	ENST00000389301;ENST00000389302;ENST00000534992;ENST00000543736	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	4.1	1.85	0.25348	.	0.674836	0.13063	N	0.416735	T	0.00012	0.0000	N	0.00162	-1.95	0.80722	P	0.0	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.29397	-1.0013	9	0.02654	T	1	-13.3596	5.1091	0.14800	0.4757:0.4147:0.0:0.1096	rs7190823;rs17232400;rs17669765;rs52833740;rs57464202;rs7190823	266;234;266;266;266;266	B4DRI7;Q0VAP4;A0PJU8;F5H8D5;O15360-2;O15360	.;.;.;.;.;FANCA_HUMAN	A	266;266;266;234	ENSP00000373952:T266A;ENSP00000373953:T266A;ENSP00000443675:T266A;ENSP00000443409:T234A	ENSP00000373952:T266A	T	-	1	0	FANCA	88393544	0.007000	0.16637	0.078000	0.20375	0.146000	0.21551	0.402000	0.20965	0.381000	0.24851	-0.222000	0.12452	ACG	T|0.408;C|0.592	0.592	strong		0.358	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
POM121	9883	hgsc.bcm.edu	37	7	72413779	72413779	+	Missense_Mutation	SNP	G	G	A	rs140060630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:72413779G>A	ENST00000434423.2	+	11	3247	c.3247G>A	c.(3247-3249)Ggg>Agg	p.G1083R	POM121_ENST00000446813.1_Missense_Mutation_p.G818R|POM121_ENST00000257622.4_Missense_Mutation_p.G818R|POM121_ENST00000395270.1_Missense_Mutation_p.G818R|POM121_ENST00000358357.3_Missense_Mutation_p.G818R			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	1083	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CGCCAGCAGCGGGAGCAGCAG	0.652													.|||	18	0.00359425	0.0098	0.0043	5008	,	,		20902	0.0		0.002	False		,,,				2504	0.0				p.G818R		Atlas-SNP	.											.	POM121	131	.	0			c.G2452A						PASS	.	G	ARG/GLY	24,4310		1,22,2144	12.0	15.0	14.0		2452	3.0	0.9	7	dbSNP_134	14	1,8471		0,1,4235	no	missense	POM121	NM_172020.2	125	1,23,6379	AA,AG,GG		0.0118,0.5538,0.1952	probably-damaging	818/985	72413779	25,12781	2167	4236	6403	SO:0001583	missense	9883	exon11			AGCAGCGGGAGCA	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.3247G>A	7.37:g.72413779G>A	ENSP00000405562:p.Gly1083Arg	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	247	134	0.54251	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		.	.	.	.	.	.	.	.	.	.	G	8.813	0.935612	0.18206	0.005538	1.18E-4	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.07800	3.21;3.16;3.21;3.16;3.37	3.01	3.01	0.34805	.	0.000000	0.40222	N	0.001143	T	0.16769	0.0403	M	0.83223	2.63	0.18873	N	0.999987	D;D	0.76494	0.999;0.999	D;D	0.64237	0.923;0.923	T	0.02385	-1.1167	10	0.72032	D	0.01	.	5.5665	0.17173	0.169:0.0:0.831:0.0	.	818;1083	A8MXF9;Q96HA1	.;P121A_HUMAN	R	818;818;818;818;1083	ENSP00000393020:G818R;ENSP00000257622:G818R;ENSP00000378687:G818R;ENSP00000351124:G818R;ENSP00000405562:G1083R	ENSP00000257622:G818R	G	+	1	0	POM121	72051715	0.793000	0.28825	0.904000	0.35570	0.083000	0.17756	1.592000	0.36676	1.684000	0.51022	0.391000	0.25812	GGG	G|0.998;A|0.002	0.002	strong		0.652	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
BAZ2A	11176	hgsc.bcm.edu	37	12	57004268	57004268	+	Silent	SNP	G	G	A	rs34393899	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57004268G>A	ENST00000551812.1	-	8	1903	c.1710C>T	c.(1708-1710)agC>agT	p.S570S	BAZ2A_ENST00000179765.5_Silent_p.S538S|BAZ2A_ENST00000549884.1_Silent_p.S568S|BAZ2A_ENST00000379441.3_Silent_p.S540S	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	570	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.				chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						GCCATCGGTGGCTGCCCTTCT	0.562													G|||	74	0.0147764	0.0015	0.0245	5008	,	,		19468	0.0		0.0437	False		,,,				2504	0.0112				p.S570S		Atlas-SNP	.											.	BAZ2A	263	.	0			c.C1710T						PASS	.	G		26,4122		0,26,2048	53.0	57.0	56.0		1710	4.0	1.0	12	dbSNP_126	56	351,8077		8,335,3871	no	coding-synonymous	BAZ2A	NM_013449.3		8,361,5919	AA,AG,GG		4.1647,0.6268,2.9978		570/1906	57004268	377,12199	2074	4214	6288	SO:0001819	synonymous_variant	11176	exon8			TCGGTGGCTGCCC	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"""Zinc fingers, PHD-type"""	962	protein-coding gene	gene with protein product	"""TTF-I interacting peptide 5"""	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.1710C>T	12.37:g.57004268G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	167	84	0.502994	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Silent	SNP	ENST00000551812.1	37	CCDS44924.1																																																																																			G|0.974;A|0.026	0.026	strong		0.562	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	
SNX19	399979	hgsc.bcm.edu	37	11	130784616	130784616	+	Missense_Mutation	SNP	T	T	C	rs3190345	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130784616T>C	ENST00000265909.4	-	1	1788	c.1219A>G	c.(1219-1221)Agt>Ggt	p.S407G	SNX19_ENST00000533318.1_Intron|SNX19_ENST00000533214.1_Missense_Mutation_p.S407G|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000530356.1_5'UTR|SNX19_ENST00000539184.1_5'UTR	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	407			S -> G (in dbSNP:rs3190345).		protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GCCTGGGAACTCTCTAGGGCA	0.567													C|||	639	0.127596	0.0492	0.0893	5008	,	,		18306	0.1538		0.1988	False		,,,				2504	0.1605				p.S407G		Atlas-SNP	.											.	SNX19	84	.	0			c.A1219G						PASS	.	C	GLY/SER	315,4087	797.1+/-415.4	15,285,1901	58.0	56.0	57.0		1219	3.0	0.0	11	dbSNP_105	57	1786,6808	732.6+/-406.8	174,1438,2685	no	missense	SNX19	NM_014758.2	56	189,1723,4586	CC,CT,TT		20.7819,7.1558,16.1665	benign	407/993	130784616	2101,10895	2201	4297	6498	SO:0001583	missense	399979	exon1			GGGAACTCTCTAG	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1219A>G	11.37:g.130784616T>C	ENSP00000265909:p.Ser407Gly	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	37	CCDS31721.1	314	0.14377289377289376	25	0.0508130081300813	35	0.09668508287292818	99	0.17307692307692307	155	0.20448548812664907	C	0.021	-1.422840	0.01126	0.071558	0.207819	ENSG00000120451	ENST00000265909;ENST00000533214	T;T	0.15256	2.44;2.44	5.1	2.97	0.34412	.	1.048190	0.07300	N	0.873937	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41980	-0.9478	9	0.02654	T	1	-0.0564	4.9645	0.14083	0.0:0.5692:0.1475:0.2833	rs3190345	407;407	E9PKB9;Q92543	.;SNX19_HUMAN	G	407	ENSP00000265909:S407G;ENSP00000435390:S407G	ENSP00000265909:S407G	S	-	1	0	SNX19	130289826	0.000000	0.05858	0.000000	0.03702	0.752000	0.42762	0.546000	0.23284	0.208000	0.20626	-0.128000	0.14901	AGT	T|0.844;C|0.156	0.156	strong		0.567	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
TMEM17	200728	hgsc.bcm.edu	37	2	62733253	62733253	+	Silent	SNP	C	C	T	rs11676567	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:62733253C>T	ENST00000335390.5	-	1	223	c.12G>A	c.(10-12)ccG>ccA	p.P4P		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	4					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GCACCGGATCCGGCAGCTCCA	0.672													C|||	2167	0.432708	0.4433	0.4568	5008	,	,		13268	0.5248		0.3569	False		,,,				2504	0.3845				p.P4P		Atlas-SNP	.											TMEM17,NS,carcinoma,0,1	TMEM17	19	1	0			c.G12A						PASS	.	C		1912,2494		431,1050,722	23.0	25.0	25.0		12	-1.9	1.0	2	dbSNP_120	25	3217,5383		619,1979,1702	no	coding-synonymous	TMEM17	NM_198276.2		1050,3029,2424	TT,TC,CC		37.407,43.3954,39.4356		4/199	62733253	5129,7877	2203	4300	6503	SO:0001819	synonymous_variant	200728	exon1			CGGATCCGGCAGC		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.12G>A	2.37:g.62733253C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	104	58	0.557692	NM_198276	Q53QP7|Q53R98	Silent	SNP	ENST00000335390.5	37	CCDS1871.1																																																																																			C|0.598;T|0.402	0.402	strong		0.672	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
POLR2B	5431	hgsc.bcm.edu	37	4	57876955	57876955	+	Silent	SNP	G	G	A	rs1718878	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:57876955G>A	ENST00000381227.1	+	13	2003	c.1590G>A	c.(1588-1590)gcG>gcA	p.A530A	POLR2B_ENST00000314595.5_Silent_p.A530A|POLR2B_ENST00000441246.2_Silent_p.A523A|POLR2B_ENST00000431623.2_Silent_p.A455A|POLR2B_ENST00000510355.1_3'UTR			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	530					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					CCTTGATGGCGTATATTTCAG	0.353													A|||	1937	0.386781	0.4365	0.2954	5008	,	,		16271	0.2986		0.3469	False		,,,				2504	0.5164				p.A530A		Atlas-SNP	.											.	POLR2B	108	.	0			c.G1590A						PASS	.	A		1880,2526	624.5+/-394.3	400,1080,723	117.0	124.0	121.0		1590	2.0	1.0	4	dbSNP_89	121	2935,5661	666.9+/-402.4	487,1961,1850	no	coding-synonymous	POLR2B	NM_000938.1		887,3041,2573	AA,AG,GG		34.1438,42.6691,37.0328		530/1175	57876955	4815,8187	2203	4298	6501	SO:0001819	synonymous_variant	5431	exon12			GATGGCGTATATT		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"""RNA polymerase subunits"""	9188	protein-coding gene	gene with protein product		180661	"""polymerase (RNA) II (DNA directed) polypeptide B (140kD)"""			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1590G>A	4.37:g.57876955G>A		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	281	112	0.398576	NM_000938	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	37	CCDS3511.1																																																																																			G|0.635;A|0.365	0.365	strong		0.353	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
DKKL1	27120	hgsc.bcm.edu	37	19	49867913	49867913	+	Missense_Mutation	SNP	G	G	A	rs919364	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49867913G>A	ENST00000221498.2	+	2	490	c.85G>A	c.(85-87)Gct>Act	p.A29T	DKKL1_ENST00000594268.1_Intron|TEAD2_ENST00000311227.2_5'Flank|TEAD2_ENST00000601519.1_5'Flank|TEAD2_ENST00000593945.1_5'Flank|TEAD2_ENST00000539846.1_5'Flank	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	29			A -> T (in dbSNP:rs919364).		anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		GATCCCCTCCGCTGCAGCTCC	0.627													A|||	1300	0.259585	0.3457	0.2104	5008	,	,		15578	0.1766		0.3111	False		,,,				2504	0.2106				p.A29T		Atlas-SNP	.											.	DKKL1	23	.	0			c.G85A						PASS	.	A	THR/ALA,,THR/ALA	1429,2977	683.3+/-404.2	252,925,1026	58.0	51.0	54.0		85,,85	-0.6	0.1	19	dbSNP_86	54	2728,5872	680.6+/-403.7	423,1882,1995	yes	missense,utr-5,missense	DKKL1	NM_001197301.1,NM_001197302.1,NM_014419.3	58,,58	675,2807,3021	AA,AG,GG		31.7209,32.433,31.9622	benign,,benign	29/212,,29/243	49867913	4157,8849	2203	4300	6503	SO:0001583	missense	27120	exon2			CCCTCCGCTGCAG	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"""cancer/testis antigen 34"", ""soggy"""	605418	"""dickkopf-like 1 (soggy)"""			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.85G>A	19.37:g.49867913G>A	ENSP00000221498:p.Ala29Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	166	81	0.487952	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	37	CCDS12762.1	587	0.26877289377289376	172	0.34959349593495936	85	0.23480662983425415	108	0.1888111888111888	222	0.2928759894459103	A	6.302	0.423838	0.11928	0.32433	0.317209	ENSG00000104901	ENST00000221498	T	0.12879	2.64	3.36	-0.557	0.11800	.	1.217580	0.06218	N	0.686307	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43572	-0.9383	9	0.02654	T	1	1.3103	0.2643	0.00223	0.2897:0.1597:0.283:0.2677	rs919364;rs60520264;rs919364	29	Q9UK85	DKKL1_HUMAN	T	29	ENSP00000221498:A29T	ENSP00000221498:A29T	A	+	1	0	DKKL1	54559725	0.000000	0.05858	0.107000	0.21349	0.832000	0.47134	-1.722000	0.01868	-0.298000	0.08921	-0.361000	0.07541	GCT	G|0.704;A|0.296	0.296	strong		0.627	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419	
IPO8	10526	hgsc.bcm.edu	37	12	30823971	30823971	+	Silent	SNP	A	A	G	rs1054426	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:30823971A>G	ENST00000256079.4	-	9	1307	c.969T>C	c.(967-969)ctT>ctC	p.L323L	IPO8_ENST00000544829.1_Silent_p.L118L	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	323					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					ATGCTTGCTGAAGAACACGGG	0.378													G|||	2474	0.49401	0.702	0.2911	5008	,	,		13803	0.4484		0.5089	False		,,,				2504	0.3885				p.L323L		Atlas-SNP	.											.	IPO8	105	.	0			c.T969C						PASS	.	G	,	2902,1504	477.0+/-357.8	951,1000,252	154.0	158.0	157.0		354,969	0.4	1.0	12	dbSNP_86	157	4449,4151	564.8+/-388.4	1146,2157,997	no	coding-synonymous,coding-synonymous	IPO8	NM_001190995.1,NM_006390.3	,	2097,3157,1249	GG,GA,AA		48.2674,34.1353,43.4799	,	118/833,323/1038	30823971	7351,5655	2203	4300	6503	SO:0001819	synonymous_variant	10526	exon9			TTGCTGAAGAACA	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"""Importins"""	9853	protein-coding gene	gene with protein product		605600	"""RAN binding protein 8"""	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.969T>C	12.37:g.30823971A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	185	80	0.432432	NM_006390	B7Z7M3	Silent	SNP	ENST00000256079.4	37	CCDS8719.1																																																																																			A|0.447;G|0.553	0.553	strong		0.378	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390	
MAP7D3	79649	hgsc.bcm.edu	37	X	135313034	135313034	+	Missense_Mutation	SNP	T	T	G	rs1055497	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:135313034T>G	ENST00000316077.9	-	9	1725	c.1505A>C	c.(1504-1506)gAa>gCa	p.E502A	MAP7D3_ENST00000370661.1_Missense_Mutation_p.E467A|MAP7D3_ENST00000495432.1_5'Flank|MAP7D3_ENST00000370663.5_Missense_Mutation_p.E484A	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	502			E -> A (in dbSNP:rs1055497). {ECO:0000269|PubMed:15489334}.		microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					ACAAGCATTTTCAGGAGATGA	0.413													g|||	2070	0.548344	0.3676	0.3732	3775	,	,		12866	0.5427		0.4105	False		,,,				2504	0.3732				p.E502A		Atlas-SNP	.											.	MAP7D3	102	.	0			c.A1505C						PASS	.		ALA/GLU,ALA/GLU,ALA/GLU	1761,1645		385,701,290,332,280	162.0	143.0	149.0		1451,1400,1505	1.0	0.0	X	dbSNP_86	149	3552,2957		744,1111,953,501,844	yes	missense,missense,missense	MAP7D3	NM_001173516.1,NM_001173517.1,NM_024597.3	107,107,107	1129,1812,1243,833,1124	GG,GT,G,TT,T		45.4294,48.2971,46.4145	benign,benign,benign	484/859,467/842,502/877	135313034	5313,4602	1988	4153	6141	SO:0001583	missense	79649	exon9			GCATTTTCAGGAG	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1505A>C	X.37:g.135313034T>G	ENSP00000318086:p.Glu502Ala	Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	943	0.568414707655214	112	0.2916666666666667	95	0.35984848484848486	202	0.543010752688172	227	0.4127272727272727	g	0.095	-1.160453	0.01686	0.517029	0.545706	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.04317	4.28;3.65;3.65;3.82	5.8	1.03	0.20045	.	0.900171	0.09038	N	0.857688	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.41998	-0.9477	9	0.02654	T	1	-0.5443	3.6492	0.08196	0.3154:0.0:0.4123:0.2723	rs1055497;rs3174434;rs17846288;rs17859312;rs52828368;rs60930052;rs1055497	484;461;502;467	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	A	467;502;484;461	ENSP00000359695:E467A;ENSP00000318086:E502A;ENSP00000359697:E484A;ENSP00000359694:E461A	ENSP00000318086:E502A	E	-	2	0	MAP7D3	135140700	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.932000	0.28884	-0.527000	0.06374	-1.902000	0.00527	GAA	0|0.026;G|0.527	0.527	strong		0.413	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
LRRC4C	57689	hgsc.bcm.edu	37	11	40136151	40136151	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:40136151C>T	ENST00000278198.2	-	2	3655	c.1692G>A	c.(1690-1692)agG>agA	p.R564R	LRRC4C_ENST00000527150.1_Silent_p.R564R|LRRC4C_ENST00000528697.1_Silent_p.R564R|LRRC4C_ENST00000530763.1_Silent_p.R564R			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	564					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TTTCAACAGTCCTTGTTGGGG	0.488																																					p.R564R		Atlas-SNP	.											LRRC4C,NS,carcinoma,0,1	LRRC4C	190	1	0			c.G1692A						scavenged	.						179.0	171.0	173.0					11																	40136151		2203	4300	6503	SO:0001819	synonymous_variant	57689	exon7			AACAGTCCTTGTT	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1692G>A	11.37:g.40136151C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	262	3	0.0114504	NM_001258419	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	37	CCDS31464.1																																																																																			.	.	none		0.488	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
GPR111	222611	hgsc.bcm.edu	37	6	47646842	47646842	+	Missense_Mutation	SNP	A	A	G	rs6907125	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:47646842A>G	ENST00000296862.1	+	4	443	c.443A>G	c.(442-444)cAg>cGg	p.Q148R	GPR111_ENST00000507065.1_Missense_Mutation_p.Q80R|GPR111_ENST00000398742.2_Missense_Mutation_p.Q80R			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	148			Q -> R (in dbSNP:rs6907125).		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						GACACCTGCCAGACTCTTAAT	0.458													G|||	2589	0.516973	0.472	0.4366	5008	,	,		22238	0.3085		0.6272	False		,,,				2504	0.7362				p.Q80R		Atlas-SNP	.											.	GPR111	123	.	0			c.A239G						PASS	.	G	ARG/GLN	1885,2091		444,997,547	122.0	117.0	118.0		239	-1.8	0.0	6	dbSNP_116	118	5388,2946		1756,1876,535	yes	missense	GPR111	NM_153839.6	43	2200,2873,1082	GG,GA,AA		35.3492,47.4095,40.918	benign	80/643	47646842	7273,5037	1988	4167	6155	SO:0001583	missense	222611	exon5			CCTGCCAGACTCT	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.443A>G	6.37:g.47646842A>G	ENSP00000296862:p.Gln148Arg	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	175	85	0.485714	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	37		1057	0.483974358974359	239	0.48577235772357724	178	0.49171270718232046	171	0.29895104895104896	469	0.6187335092348285	G	0.897	-0.723488	0.03158	0.474095	0.646508	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.35048	2.1;2.06;1.33	4.69	-1.76	0.08006	.	1.198910	0.06180	N	0.679354	T	0.03827	0.0108	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33343	-0.9872	9	0.38643	T	0.18	.	6.4296	0.21788	0.537:0.1727:0.2903:0.0	rs6907125;rs60689810;rs6907125	80;148	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	R	80;148;80	ENSP00000422934:Q80R;ENSP00000296862:Q148R;ENSP00000381727:Q80R	ENSP00000296862:Q148R	Q	+	2	0	GPR111	47754801	0.167000	0.22975	0.044000	0.18714	0.397000	0.30659	0.159000	0.16442	-0.415000	0.07484	-0.760000	0.03462	CAG	A|0.480;G|0.520	0.520	strong		0.458	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
ERBB2	2064	hgsc.bcm.edu	37	17	37879588	37879588	+	Missense_Mutation	SNP	A	A	G	rs1136201	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:37879588A>G	ENST00000269571.5	+	17	2122	c.1963A>G	c.(1963-1965)Atc>Gtc	p.I655V	ERBB2_ENST00000541774.1_Missense_Mutation_p.I640V|ERBB2_ENST00000584601.1_Missense_Mutation_p.I625V|ERBB2_ENST00000445658.2_Missense_Mutation_p.I379V|ERBB2_ENST00000584450.1_Missense_Mutation_p.I655V|ERBB2_ENST00000406381.2_Missense_Mutation_p.I625V|ERBB2_ENST00000540147.1_Missense_Mutation_p.I625V			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	655			I -> V (in allele B2 and allele B3; dbSNP:rs1136201). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8095488, ECO:0000269|Ref.3}.		axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GACGTCCATCATCTCTGCGGT	0.612		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)			A|||	608	0.121406	0.0098	0.1369	5008	,	,		13960	0.124		0.2455	False		,,,				2504	0.1309				p.I655V		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	ERBB2	429	.	0			c.A1963G	GRCh37	CM004332	ERBB2	M	rs1136201	PASS	.	A	VAL/ILE,VAL/ILE	212,4194	132.1+/-168.6	5,202,1996	113.0	103.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1873,1963	5.0	1.0	17	dbSNP_86	106	1980,6620	346.8+/-326.3	223,1534,2543	yes	missense,missense	ERBB2	NM_001005862.1,NM_004448.2	29,29	228,1736,4539	GG,GA,AA		23.0233,4.8116,16.8538	benign,benign	625/1226,655/1256	37879588	2192,10814	2203	4300	6503	SO:0001583	missense	2064	exon17			TCCATCATCTCTG	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1963A>G	17.37:g.37879588A>G	ENSP00000269571:p.Ile655Val	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	204	106	0.519608	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	339	0.15521978021978022	5	0.01016260162601626	58	0.16022099447513813	83	0.1451048951048951	193	0.2546174142480211	A	13.67	2.306999	0.40795	0.048116	0.230233	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.76316	-1.01;-1.01;-0.99;-1.01;-1.01	4.97	4.97	0.65823	Cytochrome c1, transmembrane anchor, C-terminal (1);	.	.	.	.	T	0.00039	0.0001	N	0.25485	0.75	0.09310	P	1.0	B;P;B	0.39576	0.406;0.679;0.406	B;B;B	0.37650	0.108;0.255;0.108	T	0.05920	-1.0856	8	0.22706	T	0.39	.	8.987	0.35999	0.9164:0.0:0.0836:0.0	rs1136201;rs1801200;rs2006406;rs2230699;rs17606815;rs59955961;rs1801200	379;640;655	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	V	625;640;379;655;625	ENSP00000385185:I625V;ENSP00000446466:I640V;ENSP00000404047:I379V;ENSP00000269571:I655V;ENSP00000443562:I625V	ENSP00000269571:I655V	I	+	1	0	ERBB2	35133114	1.000000	0.71417	0.995000	0.50966	0.892000	0.51952	4.008000	0.57103	1.880000	0.54463	0.459000	0.35465	ATC	A|0.845;G|0.155;N|0.000;T|0.000	0.155	strong		0.612	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
MUC21	394263	hgsc.bcm.edu	37	6	30955201	30955201	+	Missense_Mutation	SNP	G	G	A	rs2508018	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30955201G>A	ENST00000376296.3	+	2	1490	c.1249G>A	c.(1249-1251)Gcc>Acc	p.A417T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	417	28 X 15 AA approximate tandem repeats.|Ser-rich.			A -> I (in Ref. 3; AAQ88781 and 4; CAQ08321). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GTCCAGTGGGGCCAGCACTGC	0.627													g|||	404	0.0806709	0.0749	0.1427	5008	,	,		20374	0.0556		0.0805	False		,,,				2504	0.0706				p.A417T		Atlas-SNP	.											.	MUC21	98	.	0			c.G1249A						PASS	.						140.0	136.0	137.0					6																	30955201		2203	4300	6503	SO:0001583	missense	394263	exon2			AGTGGGGCCAGCA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1249G>A	6.37:g.30955201G>A	ENSP00000365473:p.Ala417Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	147	37	0.251701	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	217	0.09935897435897435	48	0.0975609756097561	60	0.16574585635359115	55	0.09615384615384616	54	0.0712401055408971	g	0.076	-1.192559	0.01607	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.01287	5.05	3.58	-7.16	0.01516	.	.	.	.	.	T	0.00178	0.0005	N	0.04508	-0.205	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.45026	-0.9289	9	0.06625	T	0.88	-0.4275	6.7193	0.23321	0.1341:0.0:0.3783:0.4876	rs2508018;rs2508018	417	Q5SSG8	MUC21_HUMAN	T	267;417	ENSP00000365473:A417T	ENSP00000365473:A417T	A	+	1	0	MUC21	31063180	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-1.607000	0.02070	-2.884000	0.00318	0.586000	0.80456	GCC	G|0.917;A|0.083	0.083	strong		0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
PIGO	84720	hgsc.bcm.edu	37	9	35091880	35091880	+	Silent	SNP	C	C	T	rs10814196	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35091880C>T	ENST00000378617.3	-	7	2398	c.2004G>A	c.(2002-2004)ttG>ttA	p.L668L	PIGO_ENST00000341666.3_Silent_p.L668L|PIGO_ENST00000298004.5_Intron|PIGO_ENST00000361778.2_Intron	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	668					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CTCCATACCACAAATTCTTGG	0.592													C|||	981	0.195887	0.1891	0.2046	5008	,	,		17772	0.0774		0.2048	False		,,,				2504	0.3119				p.L668L		Atlas-SNP	.											.	PIGO	86	.	0			c.G2004A						PASS	.	C	,,	835,3571	331.2+/-301.9	82,671,1450	49.0	51.0	50.0		,2004,	2.5	1.0	9	dbSNP_120	50	1748,6852	316.2+/-312.6	181,1386,2733	no	intron,coding-synonymous,intron	PIGO	NM_001201484.1,NM_032634.3,NM_152850.3	,,	263,2057,4183	TT,TC,CC		20.3256,18.9514,19.8601	,,	,668/1090,	35091880	2583,10423	2203	4300	6503	SO:0001819	synonymous_variant	84720	exon7			ATACCACAAATTC	AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"""Phosphatidylinositol glycan anchor biosynthesis"""	23215	protein-coding gene	gene with protein product		614730	"""phosphatidylinositol glycan, class O"""			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.2004G>A	9.37:g.35091880C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_032634	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Silent	SNP	ENST00000378617.3	37	CCDS6575.1																																																																																			C|0.816;T|0.184	0.184	strong		0.592	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	NM_032634	
CASC5	57082	hgsc.bcm.edu	37	15	40916237	40916237	+	Missense_Mutation	SNP	A	A	G	rs17747633	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:40916237A>G	ENST00000346991.5	+	11	4243	c.3853A>G	c.(3853-3855)Aaa>Gaa	p.K1285E	CASC5_ENST00000399668.2_Missense_Mutation_p.K1259E			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1285			K -> E (in dbSNP:rs17747633). {ECO:0000269|PubMed:10980622}.		acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.K1285E(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GGTCATAGGGAAAGTTGTAGA	0.378													a|||	1019	0.203474	0.0257	0.2565	5008	,	,		20762	0.0992		0.4573	False		,,,				2504	0.2526				p.K1285E		Atlas-SNP	.											CASC5_ENST00000346991,colon,carcinoma,0,3	CASC5	269	3	1	Substitution - Missense(1)	stomach(1)	c.A3853G						scavenged	.	C	GLU/LYS,GLU/LYS	357,3341		26,305,1518	86.0	78.0	81.0		3775,3853	3.4	0.2	15	dbSNP_123	81	3546,4648		750,2046,1301	yes	missense,missense	CASC5	NM_144508.3,NM_170589.3	56,56	776,2351,2819	GG,GA,AA		43.2756,9.6539,32.8204	probably-damaging,probably-damaging	1259/2317,1285/2343	40916237	3903,7989	1849	4097	5946	SO:0001583	missense	57082	exon11			ATAGGGAAAGTTG	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.3853A>G	15.37:g.40916237A>G	ENSP00000335463:p.Lys1285Glu	Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	48	47	0.979167	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	496	0.2271062271062271	15	0.03048780487804878	108	0.2983425414364641	40	0.06993006993006994	333	0.4393139841688654	a	11.70	1.718008	0.30413	0.096539	0.432756	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.20200	2.09;2.09	4.57	3.44	0.39384	.	0.301070	0.23627	N	0.046177	T	0.00012	0.0000	M	0.63843	1.955	0.44168	P	0.0030210000000000514	D;D;D	0.60160	0.987;0.987;0.974	D;D;P	0.63597	0.916;0.916;0.854	T	0.47471	-0.9115	9	0.37606	T	0.19	.	10.2596	0.43419	0.8335:0.1665:0.0:0.0	rs17747633;rs17747633	1259;1285;1259	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	E	1285;1259;1259	ENSP00000335463:K1285E;ENSP00000382576:K1259E	ENSP00000260369:K1259E	K	+	1	0	CASC5	38703529	0.000000	0.05858	0.158000	0.22627	0.387000	0.30353	0.183000	0.16919	0.877000	0.35895	-0.264000	0.10439	AAA	A|0.758;G|0.242	0.242	strong		0.378	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
SERPINB3	6317	hgsc.bcm.edu	37	18	61322995	61322995	+	Missense_Mutation	SNP	T	T	C	rs1065205	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:61322995T>C	ENST00000283752.5	-	8	1212	c.1069A>G	c.(1069-1071)Act>Gct	p.T357A	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.T305A	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	357			T -> A (in dbSNP:rs1065205). {ECO:0000269|PubMed:1958219, ECO:0000269|Ref.3, ECO:0000269|Ref.9}.		negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TTAGTTGAAGTAGGTGATGAT	0.473													T|||	964	0.192492	0.0825	0.2017	5008	,	,		20327	0.4405		0.0865	False		,,,				2504	0.1881				p.T357A		Atlas-SNP	.											.	SERPINB3	90	.	0			c.A1069G						PASS	.	T	ALA/THR	375,4031	190.2+/-216.2	32,311,1860	147.0	148.0	148.0		1069	-5.9	0.0	18	dbSNP_86	148	731,7869	177.8+/-227.3	26,679,3595	no	missense	SERPINB3	NM_006919.2	58	58,990,5455	CC,CT,TT		8.5,8.5111,8.5038	benign	357/391	61322995	1106,11900	2203	4300	6503	SO:0001583	missense	6317	exon8			TTGAAGTAGGTGA	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1069A>G	18.37:g.61322995T>C	ENSP00000283752:p.Thr357Ala	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	338	156	0.461538	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	417	0.19093406593406592	50	0.1016260162601626	70	0.19337016574585636	228	0.3986013986013986	69	0.09102902374670185	T	0.531	-0.857900	0.02610	0.085111	0.085	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.82344	-1.6;-1.6	2.96	-5.92	0.02261	Serpin domain (3);	.	.	.	.	T	0.00012	0.0000	N	0.01809	-0.71	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.07947	-1.0746	8	0.05833	T	0.94	.	0.8688	0.01210	0.3065:0.2008:0.1067:0.386	rs1065205;rs3169980;rs52799665;rs56795109;rs1065205	305;357	P29508-2;P29508	.;SPB3_HUMAN	A	357;305	ENSP00000283752:T357A;ENSP00000329498:T305A	ENSP00000283752:T357A	T	-	1	0	SERPINB3	59473975	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-7.571000	0.00034	-1.670000	0.01468	-1.855000	0.00564	ACT	T|0.864;C|0.136	0.136	strong		0.473	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
TTC4	7268	hgsc.bcm.edu	37	1	55182300	55182300	+	Missense_Mutation	SNP	T	T	A	rs1147990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:55182300T>A	ENST00000371281.3	+	2	226	c.139T>A	c.(139-141)Tcg>Acg	p.S47T	MROH7-TTC4_ENST00000414150.2_Nonsense_Mutation_p.C1282*|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	47			S -> T (in dbSNP:rs1147990). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.							breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						CCTATTTATGTCGAGAGCGCC	0.408													A|||	3347	0.668331	0.5038	0.6081	5008	,	,		20068	0.9683		0.5477	False		,,,				2504	0.7485				p.S47T		Atlas-SNP	.											TTC4,NS,carcinoma,-2,1	TTC4	21	1	0			c.T139A						PASS	.	A	THR/SER	2432,1974	555.1+/-379.2	673,1086,444	89.0	89.0	89.0		139	4.9	1.0	1	dbSNP_87	89	4395,4205	570.7+/-389.4	1119,2157,1024	yes	missense	TTC4	NM_004623.4	58	1792,3243,1468	AA,AT,TT		48.8953,44.8025,47.5088	benign	47/388	55182300	6827,6179	2203	4300	6503	SO:0001583	missense	7268	exon2			TTTATGTCGAGAG		CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"""Tetratricopeptide (TTC) repeat domain containing"""	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.139T>A	1.37:g.55182300T>A	ENSP00000360329:p.Ser47Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	69	40	0.57971	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Missense_Mutation	SNP	ENST00000371281.3	37	CCDS596.1	1449	0.6634615384615384	277	0.5630081300813008	214	0.5911602209944752	556	0.972027972027972	402	0.5303430079155673	A	10.97	1.502706	0.26949	0.551975	0.511047	ENSG00000243725	ENST00000371281;ENST00000371284	T	0.12569	2.67	4.92	4.92	0.64577	.	.	.	.	.	T	0.00012	0.0000	N	0.03050	-0.425	0.52099	P	5.599999999994498E-5	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.38714	-0.9648	8	0.02654	T	1	-7.8097	9.6171	0.39698	0.8434:0.0:0.0:0.1566	rs1147990;rs1623164;rs17856041;rs56423771;rs56930428;rs1147990	47;58	O95801;Q5TA95	TTC4_HUMAN;.	T	47;58	ENSP00000360329:S47T	ENSP00000360329:S47T	S	+	1	0	TTC4	54954888	1.000000	0.71417	0.996000	0.52242	0.591000	0.36615	5.925000	0.70062	1.011000	0.39340	-0.257000	0.10917	TCG	T|0.395;A|0.605	0.605	strong		0.408	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623	
MTERF2	80298	hgsc.bcm.edu	37	12	107372277	107372277	+	Silent	SNP	C	C	T	rs1043156	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:107372277C>T	ENST00000552029.1	-	2	2284	c.216G>A	c.(214-216)gaG>gaA	p.E72E	MTERFD3_ENST00000240050.4_Silent_p.E72E|C12orf23_ENST00000551237.1_3'UTR|MTERFD3_ENST00000392830.2_Silent_p.E72E			Q49AM1	MTEF2_HUMAN		72					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	transcription regulatory region DNA binding (GO:0044212)			breast(1)|kidney(1)|large_intestine(2)|lung(3)	7						AGGTTTCATCCTCTAAAAGTA	0.383													C|||	588	0.117412	0.149	0.0922	5008	,	,		19062	0.0099		0.1252	False		,,,				2504	0.1953				p.E72E		Atlas-SNP	.											.	MTERFD3	32	.	0			c.G216A						PASS	.	C	,	620,3786	267.1+/-267.6	48,524,1631	118.0	115.0	116.0		216,216	1.6	0.4	12	dbSNP_86	116	1129,7471	232.1+/-265.8	63,1003,3234	no	coding-synonymous,coding-synonymous	MTERFD3	NM_001033050.1,NM_025198.3	,	111,1527,4865	TT,TC,CC		13.1279,14.0717,13.4476	,	72/386,72/386	107372277	1749,11257	2203	4300	6503	SO:0001819	synonymous_variant	80298	exon3			TTCATCCTCTAAA																												ENST00000552029.1:c.216G>A	12.37:g.107372277C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	193	102	0.528497	NM_001033050	Q53HM2|Q9H4L6|Q9H7Y9	Silent	SNP	ENST00000552029.1	37	CCDS9111.1																																																																																			C|0.884;T|0.116	0.116	strong		0.383	MTERFD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406835.1		
CLPB	81570	hgsc.bcm.edu	37	11	72006559	72006559	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:72006559C>T	ENST00000294053.3	-	13	1726	c.1553G>A	c.(1552-1554)cGt>cAt	p.R518H	CLPB_ENST00000543042.1_Missense_Mutation_p.R317H|CLPB_ENST00000437826.2_Missense_Mutation_p.R473H|CLPB_ENST00000538021.1_Missense_Mutation_p.R126H|CLPB_ENST00000340729.5_Missense_Mutation_p.R459H|CLPB_ENST00000538039.1_Missense_Mutation_p.R488H	NM_001258394.1|NM_030813.4	NP_001245323.1|NP_110440.1	Q9H078	CLPB_HUMAN	ClpB caseinolytic peptidase B homolog (E. coli)	518					cellular response to heat (GO:0034605)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	19						AATACGGTTACGGCTCATCTC	0.582																																					p.R518H		Atlas-SNP	.											CLPB,NS,carcinoma,-1,1	CLPB	45	1	0			c.G1553A						scavenged	.						127.0	89.0	102.0					11																	72006559		2200	4293	6493	SO:0001583	missense	81570	exon13			CGGTTACGGCTCA	BC006404	CCDS8215.1, CCDS58152.1, CCDS58153.1, CCDS58154.1	11q13.4	2013-01-10			ENSG00000162129	ENSG00000162129		"""Ankyrin repeat domain containing"""	30664	protein-coding gene	gene with protein product	"""suppressor of potassium transport defect 3"""					11230166, 7835694	Standard	NM_030813		Approved	HSP78, SKD3, FLJ13152	uc010rqy.3	Q9H078	OTTHUMG00000167902	ENST00000294053.3:c.1553G>A	11.37:g.72006559C>T	ENSP00000294053:p.Arg518His	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	215	3	0.0139535	NM_030813	B4DXJ7|B4DXP7|E7EWN6|F8W7P6|Q8ND11|Q9H8Y0	Missense_Mutation	SNP	ENST00000294053.3	37	CCDS8215.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.51|13.51	2.259714|2.259714	0.39995|0.39995	.|.	.|.	ENSG00000162129|ENSG00000162129	ENST00000294053;ENST00000538039;ENST00000535990;ENST00000340729;ENST00000437826;ENST00000543042;ENST00000538021|ENST00000544382	T;T;T;T;T;T|.	0.66280|.	1.86;1.07;2.08;-0.2;2.34;0.39|.	4.8|4.8	0.0813|0.0813	0.14424|0.14424	ATPase, AAA-2 (1);ATPase, AAA+ type, core (1);|.	0.539313|.	0.18628|.	N|.	0.135645|.	T|T	0.26376|0.26376	0.0644|0.0644	N|N	0.17474|0.17474	0.49|0.49	0.27902|0.27902	N|N	0.938955|0.938955	B;B;B;B;B;B|.	0.15141|.	0.0;0.003;0.012;0.003;0.01;0.004|.	B;B;B;B;B;B|.	0.14023|.	0.002;0.002;0.01;0.002;0.007;0.003|.	T|T	0.29027|0.29027	-1.0025|-1.0025	10|5	0.44086|.	T|.	0.13|.	-0.7747|-0.7747	9.1849|9.1849	0.37165|0.37165	0.0:0.5309:0.0:0.4691|0.0:0.5309:0.0:0.4691	.|.	317;459;473;488;518;126|.	B4DXW4;F8W7P6;E7EWN6;Q9H078-2;Q9H078;Q7Z777|.	.;.;.;.;CLPB_HUMAN;.|.	H|I	518;488;523;459;473;317;126|296	ENSP00000294053:R518H;ENSP00000441518:R488H;ENSP00000443822:R523H;ENSP00000340385:R459H;ENSP00000407296:R473H;ENSP00000439746:R317H|.	ENSP00000294053:R518H|.	R|V	-|-	2|1	0|0	CLPB|CLPB	71684207|71684207	0.268000|0.268000	0.24133|0.24133	0.992000|0.992000	0.48379|0.48379	0.998000|0.998000	0.95712|0.95712	0.242000|0.242000	0.18087|0.18087	0.037000|0.037000	0.15575|0.15575	0.561000|0.561000	0.74099|0.74099	CGT|GTA	.	.	none		0.582	CLPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396889.1	NM_030813	
TACSTD2	4070	hgsc.bcm.edu	37	1	59042311	59042311	+	Missense_Mutation	SNP	T	T	G	rs35075952	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:59042311T>G	ENST00000371225.2	-	1	855	c.518A>C	c.(517-519)gAc>gCc	p.D173A		NM_002353.2	NP_002344.2	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	173			D -> A (in dbSNP:rs35075952). {ECO:0000269|PubMed:11687514}.		cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell motility (GO:2000146)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of stem cell differentiation (GO:2000738)|regulation of epithelial cell proliferation (GO:0050678)|ureteric bud morphogenesis (GO:0060675)|visual perception (GO:0007601)	basal plasma membrane (GO:0009925)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)					all_cancers(7;6.54e-05)					CAGCTCGGCGTCCAGGTCTGA	0.677													T|||	521	0.104034	0.2262	0.0908	5008	,	,		15486	0.003		0.1133	False		,,,				2504	0.0429				p.D173A		Atlas-SNP	.											.	TACSTD2	6	.	0			c.A518C						PASS	.	T	ALA/ASP	705,3689		51,603,1543	15.0	19.0	18.0		518	2.8	1.0	1	dbSNP_126	18	885,7701		45,795,3453	yes	missense	TACSTD2	NM_002353.2	126	96,1398,4996	GG,GT,TT		10.3075,16.0446,12.2496	benign	173/324	59042311	1590,11390	2197	4293	6490	SO:0001583	missense	4070	exon1			TCGGCGTCCAGGT	X77753	CCDS609.1	1p32	2008-02-05			ENSG00000184292	ENSG00000184292			11530	protein-coding gene	gene with protein product		137290		M1S1		8382772, 11306819	Standard	NM_002353		Approved	TROP2, GA733-1, EGP-1	uc001cyz.4	P09758	OTTHUMG00000010067	ENST00000371225.2:c.518A>C	1.37:g.59042311T>G	ENSP00000360269:p.Asp173Ala	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	37	10	0.27027	NM_002353	Q15658|Q6FG48|Q7Z7Q4|Q96QD2	Missense_Mutation	SNP	ENST00000371225.2	37	CCDS609.1	228	0.1043956043956044	108	0.21951219512195122	40	0.11049723756906077	0	0.0	80	0.10554089709762533	T	2.461	-0.324174	0.05350	0.160446	0.103075	ENSG00000184292	ENST00000371225	T	0.76060	-0.99	5.26	2.81	0.32909	.	0.459579	0.25104	N	0.033111	T	0.00039	0.0001	L	0.41236	1.265	0.41557	P	0.01139100000000004	B	0.09022	0.002	B	0.09377	0.004	T	0.03259	-1.1055	9	0.07990	T	0.79	-20.1605	7.4616	0.27298	0.0:0.0812:0.2488:0.67	rs35075952;rs61779293	173	P09758	TACD2_HUMAN	A	173	ENSP00000360269:D173A	ENSP00000360269:D173A	D	-	2	0	TACSTD2	58814899	0.737000	0.28175	0.962000	0.40283	0.337000	0.28794	1.254000	0.32897	1.975000	0.57531	0.459000	0.35465	GAC	T|0.894;G|0.106	0.106	strong		0.677	TACSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027818.1	NM_002353	
ZNF33A	7581	hgsc.bcm.edu	37	10	38345465	38345465	+	Missense_Mutation	SNP	G	G	C	rs10508862	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:38345465G>C	ENST00000458705.2	+	5	2568	c.2410G>C	c.(2410-2412)Gat>Cat	p.D804H	ZNF33A_ENST00000307441.9_Missense_Mutation_p.D804H|ZNF33A_ENST00000432900.2_Missense_Mutation_p.D811H|ZNF33A_ENST00000374618.3_Missense_Mutation_p.D805H|ZNF33A_ENST00000469037.2_Intron			Q06730	ZN33A_HUMAN	zinc finger protein 33A	804			D -> H (in dbSNP:rs10508862).		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)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AGAAAGCCCTGATGACATCCT	0.383													G|||	159	0.0317492	0.0015	0.0648	5008	,	,		18726	0.0		0.1034	False		,,,				2504	0.0082				p.D805H		Atlas-SNP	.											.	ZNF33A	103	.	0			c.G2413C						PASS	.	G	HIS/ASP,HIS/ASP	78,4328	65.8+/-103.3	1,76,2126	58.0	56.0	57.0		2413,2410	-1.4	0.0	10	dbSNP_119	57	753,7845	176.3+/-226.2	31,691,3577	yes	missense,missense	ZNF33A	NM_006954.1,NM_006974.2	81,81	32,767,5703	CC,CG,GG		8.7579,1.7703,6.3903	benign,benign	805/812,804/811	38345465	831,12173	2203	4299	6502	SO:0001583	missense	7581	exon5			AGCCCTGATGACA	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.2410G>C	10.37:g.38345465G>C	ENSP00000387713:p.Asp804His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	53	20	0.377358	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	108	0.04945054945054945	1	0.0020325203252032522	32	0.08839779005524862	0	0.0	75	0.09894459102902374	G	0.577	-0.838757	0.02692	0.017703	0.087579	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.06528	3.3;3.29;3.29;3.29	2.14	-1.36	0.09085	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.80722	P	0.0	B;B;B	0.28783	0.222;0.044;0.073	B;B;B	0.19391	0.025;0.011;0.025	T	0.44832	-0.9302	8	0.59425	D	0.04	.	2.3013	0.04162	0.4573:0.0:0.3056:0.2371	rs10508862;rs17663822;rs56465645;rs10508862	811;804;805	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	H	805;811;804;804	ENSP00000363747:D805H;ENSP00000402467:D811H;ENSP00000387713:D804H;ENSP00000304268:D804H	ENSP00000304268:D804H	D	+	1	0	ZNF33A	38385471	0.037000	0.19845	0.003000	0.11579	0.003000	0.03518	-0.229000	0.09098	-0.196000	0.10366	-0.657000	0.03884	GAT	G|0.940;C|0.060	0.060	strong		0.383	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
WDFY4	57705	hgsc.bcm.edu	37	10	50025446	50025446	+	Missense_Mutation	SNP	G	G	T	rs12268007	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50025446G>T	ENST00000325239.5	+	31	5524	c.5497G>T	c.(5497-5499)Gcc>Tcc	p.A1833S	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1833						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CCCCCTGGGAGCCCAAAAGGT	0.622													G|||	833	0.166334	0.2905	0.1542	5008	,	,		18222	0.1071		0.1223	False		,,,				2504	0.1135				p.A1833S		Atlas-SNP	.											.	WDFY4	205	.	0			c.G5497T						PASS	.	G	SER/ALA	397,987		60,277,355	24.0	31.0	29.0		5497	-1.6	0.0	10	dbSNP_120	29	338,2844		18,302,1271	yes	missense	WDFY4	NM_020945.1	99	78,579,1626	TT,TG,GG		10.6223,28.685,16.0972	benign	1833/3185	50025446	735,3831	692	1591	2283	SO:0001583	missense	57705	exon32			CTGGGAGCCCAAA	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.5497G>T	10.37:g.50025446G>T	ENSP00000320563:p.Ala1833Ser	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	339|339	0.15521978021978022|0.15521978021978022	124|124	0.25203252032520324|0.25203252032520324	52|52	0.143646408839779|0.143646408839779	71|71	0.12412587412587413|0.12412587412587413	92|92	0.12137203166226913|0.12137203166226913	G|G	1.092|1.092	-0.663764|-0.663764	0.03428|0.03428	0.28685|0.28685	0.106223|0.106223	ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239|ENST00000312002;ENST00000374161	T|.	0.55760|.	0.5|.	5.24|5.24	-1.59|-1.59	0.08453|0.08453	.|.	0.981883|.	0.08311|.	N|.	0.965312|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02011|0.02011	-0.69|-0.69	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.12630|.	0.006;0.0|.	B;B|.	0.08055|.	0.003;0.001|.	T|T	0.42548|0.42548	-0.9445|-0.9445	8|4	.|.	.|.	.|.	.|.	5.3947|5.3947	0.16263|0.16263	0.3875:0.2776:0.335:0.0|0.3875:0.2776:0.335:0.0	rs12268007;rs12268007|rs12268007;rs12268007	361;1833|.	F2Z372;Q6ZS81|.	.;WDFY4_HUMAN|.	S|I	1833|923;379	ENSP00000320563:A1833S|.	.|.	A|S	+|+	1|2	0|0	WDFY4|WDFY4	49695452|49695452	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.080000|0.080000	0.17528|0.17528	-1.238000|-1.238000	0.02919|0.02919	-0.578000|-0.578000	0.05959|0.05959	-0.302000|-0.302000	0.09304|0.09304	GCC|AGC	G|0.836;T|0.164	0.164	strong		0.622	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
OR1S1	219959	hgsc.bcm.edu	37	11	57982620	57982620	+	Missense_Mutation	SNP	A	A	G	rs1966834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57982620A>G	ENST00000309433.6	+	1	404	c.404A>G	c.(403-405)cAc>cGc	p.H135R		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	135			H -> R (in dbSNP:rs1966834).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				GCCTATGACCACTTTGTGGCG	0.438													G|||	2598	0.51877	0.2844	0.5418	5008	,	,		22010	0.8036		0.4205	False		,,,				2504	0.6268				p.H135R		Atlas-SNP	.											.	OR1S1	139	.	0			c.A404G	GRCh37	CM035848	OR1S1	M	rs1966834	PASS	.	G	ARG/HIS	1324,3078	695.1+/-405.9	197,930,1074	182.0	173.0	176.0		404	3.5	1.0	11	dbSNP_92	176	3621,4971	625.0+/-397.7	779,2063,1454	yes	missense	OR1S1	NM_001004458.1	29	976,2993,2528	GG,GA,AA		42.1439,30.0772,38.056	benign	135/326	57982620	4945,8049	2201	4296	6497	SO:0001583	missense	219959	exon1			ATGACCACTTTGT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.404A>G	11.37:g.57982620A>G	ENSP00000311688:p.His135Arg	Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	345	155	0.449275	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1083	0.4958791208791209	148	0.3008130081300813	187	0.5165745856353591	433	0.756993006993007	315	0.4155672823218997	G	0.809	-0.752849	0.03041	0.300772	0.421439	ENSG00000172774	ENST00000309433	T	0.04809	3.55	3.45	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	N	0.000173	T	0.00012	0.0000	N	0.00006	-3.19	0.46458	P	9.470000000000312E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.32107	-0.9919	9	0.02654	T	1	.	10.0632	0.42288	0.102:0.0:0.898:0.0	rs1966834;rs52803988;rs1966834	135	Q8NH92	OR1S1_HUMAN	R	135	ENSP00000311688:H135R	ENSP00000311688:H135R	H	+	2	0	OR1S1	57739196	1.000000	0.71417	1.000000	0.80357	0.381000	0.30169	6.004000	0.70709	0.671000	0.31185	-0.348000	0.07805	CAC	A|0.569;G|0.431	0.431	strong		0.438	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
PDCL3	79031	hgsc.bcm.edu	37	2	101186088	101186088	+	Silent	SNP	C	C	T	rs1052117	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:101186088C>T	ENST00000264254.6	+	4	651	c.273C>T	c.(271-273)ttC>ttT	p.F91F		NM_024065.4	NP_076970.1	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	91	Thioredoxin fold. {ECO:0000250}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|protein folding (GO:0006457)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|viral process (GO:0016032)	cytoplasm (GO:0005737)	protein binding involved in protein folding (GO:0044183)			endometrium(3)|large_intestine(2)|liver(1)|lung(6)	12						AGAATAAATTCGGAGAAGTTT	0.453													T|||	3271	0.653155	0.6286	0.4236	5008	,	,		16729	0.9772		0.4404	False		,,,				2504	0.7342				p.F91F		Atlas-SNP	.											.	PDCL3	27	.	0			c.C273T						PASS	.	T		2674,1732		807,1060,336	77.0	80.0	79.0		273	4.6	1.0	2	dbSNP_86	79	3594,5002		758,2078,1462	yes	coding-synonymous	PDCL3	NM_024065.4		1565,3138,1798	TT,TC,CC		41.8101,39.31,48.208		91/240	101186088	6268,6734	2203	4298	6501	SO:0001819	synonymous_variant	79031	exon4			TAAATTCGGAGAA	AF267853	CCDS33261.1	2q12	2008-02-05			ENSG00000115539	ENSG00000115539			28860	protein-coding gene	gene with protein product		611678					Standard	NM_024065		Approved	VIAF1	uc002tao.2	Q9H2J4	OTTHUMG00000153141	ENST00000264254.6:c.273C>T	2.37:g.101186088C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	177	87	0.491525	NM_024065	B2RA00|Q53S68	Silent	SNP	ENST00000264254.6	37	CCDS33261.1	1335	0.6112637362637363	299	0.6077235772357723	152	0.4198895027624309	561	0.9807692307692307	323	0.4261213720316623	.	9.720	1.159365	0.21454	0.6069	0.418101	ENSG00000115539	ENST00000450127	.	.	.	4.59	4.59	0.56863	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.21930	-1.0231	3	.	.	.	-29.9739	9.3103	0.37900	0.0:0.154:0.0:0.846	rs1052117;rs3192512;rs11549304;rs1052117	.	.	.	L	39	.	.	S	+	2	0	PDCL3	100552520	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	3.013000	0.49582	0.705000	0.31890	-0.381000	0.06696	TCG	C|0.467;T|0.533	0.533	strong		0.453	PDCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329734.1	NM_024065	
IL31RA	133396	hgsc.bcm.edu	37	5	55210702	55210702	+	Silent	SNP	C	C	T	rs17701253	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:55210702C>T	ENST00000447346.2	+	14	1829	c.1764C>T	c.(1762-1764)acC>acT	p.T588T	IL31RA_ENST00000354961.4_Silent_p.T569T|IL31RA_ENST00000396834.1_Silent_p.T569T|IL31RA_ENST00000359040.5_Silent_p.T588T|IL31RA_ENST00000490985.1_Silent_p.T446T	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	556					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				GTTGGCCCACCGTTCCCAACC	0.418													C|||	147	0.029353	0.0038	0.0706	5008	,	,		22559	0.006		0.0497	False		,,,				2504	0.0378				p.T588T		Atlas-SNP	.											.	IL31RA	84	.	0			c.C1764T						PASS	.	C	,,,,	61,4345	58.1+/-94.6	0,61,2142	120.0	106.0	111.0		1707,1764,1707,1338,1764	-5.7	0.0	5	dbSNP_123	111	513,8087	145.3+/-201.0	15,483,3802	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL31RA	NM_001242636.1,NM_001242637.1,NM_001242638.1,NM_001242639.1,NM_139017.5	,,,,	15,544,5944	TT,TC,CC		5.9651,1.3845,4.4133	,,,,	569/746,588/682,569/663,446/623,588/765	55210702	574,12432	2203	4300	6503	SO:0001819	synonymous_variant	133396	exon14			GCCCACCGTTCCC	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.1764C>T	5.37:g.55210702C>T		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	282	142	0.503546	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Silent	SNP	ENST00000447346.2	37	CCDS3970.2																																																																																			C|0.962;T|0.038	0.038	strong		0.418	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
COL17A1	1308	hgsc.bcm.edu	37	10	105793750	105793750	+	Missense_Mutation	SNP	T	T	C	rs17116350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:105793750T>C	ENST00000353479.5	-	52	4399	c.4109A>G	c.(4108-4110)gAt>gGt	p.D1370G	COL17A1_ENST00000369733.3_Missense_Mutation_p.D1288G	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1370	Triple-helical region.		D -> G (in dbSNP:rs17116350). {ECO:0000269|PubMed:9012408}.		cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GTAATCCAGATCTCCAGCAAA	0.582													C|||	1295	0.258586	0.3865	0.245	5008	,	,		16412	0.1359		0.2366	False		,,,				2504	0.2444				p.D1370G		Atlas-SNP	.											COL17A1,colon,carcinoma,0,1	COL17A1	149	1	0			c.A4109G						PASS	.	C	GLY/ASP	1649,2757	659.9+/-400.6	321,1007,875	119.0	116.0	117.0		4109	-0.4	1.0	10	dbSNP_123	117	2126,6474	715.4+/-406.1	256,1614,2430	yes	missense	COL17A1	NM_000494.3	94	577,2621,3305	CC,CT,TT		24.7209,37.4262,29.0251	benign	1370/1498	105793750	3775,9231	2203	4300	6503	SO:0001583	missense	1308	exon52			TCCAGATCTCCAG	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"""Collagens"""	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.4109A>G	10.37:g.105793750T>C	ENSP00000340937:p.Asp1370Gly	Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	37	CCDS7554.1	510	0.23351648351648352	177	0.3597560975609756	77	0.212707182320442	81	0.14160839160839161	175	0.23087071240105542	C	0.946	-0.708078	0.03230	0.374262	0.247209	ENSG00000065618	ENST00000353479;ENST00000369733	D;D	0.90955	-2.76;-2.76	4.87	-0.367	0.12541	.	0.941840	0.08723	N	0.903109	T	0.00012	0.0000	N	0.16266	0.395	0.20196	P	0.9999218909	B	0.02656	0.0	B	0.01281	0.0	T	0.03278	-1.1053	9	0.27082	T	0.32	-0.1527	6.4563	0.21932	0.0:0.1656:0.2387:0.5957	rs17116350;rs17879742;rs17116350	1370	Q9UMD9	COHA1_HUMAN	G	1370;1288	ENSP00000340937:D1370G;ENSP00000358748:D1288G	ENSP00000340937:D1370G	D	-	2	0	COL17A1	105783740	0.003000	0.15002	0.989000	0.46669	0.578000	0.36192	0.142000	0.16096	0.017000	0.15025	-0.974000	0.02594	GAT	C|0.269;N|0.000	0.269	strong		0.582	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	
CELSR1	9620	hgsc.bcm.edu	37	22	46786315	46786315	+	Missense_Mutation	SNP	T	T	C	rs4044210	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:46786315T>C	ENST00000262738.3	-	17	6318	c.6319A>G	c.(6319-6321)Atc>Gtc	p.I2107V		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2107			I -> V (in dbSNP:rs4044210).		anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		ACGAAGGAGATGGTGGTACAG	0.602											OREG0026656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1385	0.276558	0.7315	0.1412	5008	,	,		17117	0.0179		0.163	False		,,,				2504	0.1411				p.I2107V		Atlas-SNP	.											.	CELSR1	242	.	0			c.A6319G						PASS	.	T	VAL/ILE	2851,1555	656.2+/-400.0	913,1025,265	68.0	61.0	63.0		6319	-2.9	0.0	22	dbSNP_108	63	1380,7220	265.0+/-285.9	90,1200,3010	yes	missense	CELSR1	NM_014246.1	29	1003,2225,3275	CC,CT,TT		16.0465,35.2928,32.5311	benign	2107/3015	46786315	4231,8775	2203	4300	6503	SO:0001583	missense	9620	exon17			AGGAGATGGTGGT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.6319A>G	22.37:g.46786315T>C	ENSP00000262738:p.Ile2107Val	Somatic	66	0	0	941	WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	541	0.24771062271062272	355	0.7215447154471545	54	0.14917127071823205	9	0.015734265734265736	123	0.16226912928759896	T	1.740	-0.491935	0.04322	0.647072	0.160465	ENSG00000075275	ENST00000262738	T	0.66995	-0.24	4.34	-2.9	0.05648	GPCR, family 2, extracellular hormone receptor domain (2);	1.387560	0.05247	N	0.513246	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.14012	0.009;0.0	B;B	0.17098	0.017;0.006	T	0.42515	-0.9447	9	0.17832	T	0.49	.	1.6957	0.02861	0.1714:0.3139:0.1045:0.4102	rs4044210;rs60899189;rs4044210	428;2107	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	V	2107	ENSP00000262738:I2107V	ENSP00000262738:I2107V	I	-	1	0	CELSR1	45164979	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-1.005000	0.03674	-0.298000	0.08921	-0.177000	0.13119	ATC	T|0.693;C|0.307	0.307	strong		0.602	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
OR2A5	393046	hgsc.bcm.edu	37	7	143748257	143748257	+	Missense_Mutation	SNP	G	G	A	rs6464574	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143748257G>A	ENST00000408906.2	+	1	797	c.763G>A	c.(763-765)Gcc>Acc	p.A255T		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	255			A -> T (in dbSNP:rs6464574).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A255T(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					CTTTGGCAGCGCCATTGTCAT	0.587													.|||	1198	0.239217	0.3533	0.2493	5008	,	,		19374	0.0079		0.2873	False		,,,				2504	0.2669				p.A255T		Atlas-SNP	.											OR2A5,NS,carcinoma,0,1	OR2A5	78	1	1	Substitution - Missense(1)	lung(1)	c.G763A						PASS	.	G	THR/ALA	1296,2754		229,838,958	95.0	95.0	95.0		763	5.4	1.0	7	dbSNP_116	95	2613,5763		401,1811,1976	no	missense	OR2A5	NM_012365.1	58	630,2649,2934	AA,AG,GG		31.1963,32.0,31.4582	benign	255/312	143748257	3909,8517	2025	4188	6213	SO:0001583	missense	393046	exon1			GGCAGCGCCATTG	U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"""GPCR / Class A : Olfactory receptors"""	8232	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 5"""	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.763G>A	7.37:g.143748257G>A	ENSP00000386208:p.Ala255Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_012365	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	444	0.2032967032967033	146	0.2967479674796748	94	0.2596685082872928	0	0.0	204	0.2691292875989446	G	17.51	3.407798	0.62399	0.32	0.311963	ENSG00000221836	ENST00000408906	T	0.00169	8.63	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31872	U	0.006933	T	0.00012	0.0000	L	0.41356	1.27	0.43110	P	0.005184999999999995	D	0.65815	0.995	P	0.53006	0.715	T	0.67469	-0.5663	9	0.72032	D	0.01	.	11.5247	0.50573	0.0:0.0:0.8216:0.1784	rs6464574	255	Q96R48	OR2A5_HUMAN	T	255	ENSP00000386208:A255T	ENSP00000386208:A255T	A	+	1	0	OR2A5	143379190	0.001000	0.12720	0.986000	0.45419	0.966000	0.64601	1.051000	0.30417	2.797000	0.96272	0.650000	0.86243	GCC	G|0.752;A|0.248	0.248	strong		0.587	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1		
NTN4	59277	hgsc.bcm.edu	37	12	96131895	96131895	+	Missense_Mutation	SNP	A	A	G	rs17288108	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:96131895A>G	ENST00000343702.4	-	3	1061	c.613T>C	c.(613-615)Tac>Cac	p.Y205H	NTN4_ENST00000344911.4_Missense_Mutation_p.Y168H|NTN4_ENST00000553059.1_Missense_Mutation_p.Y205H|NTN4_ENST00000538383.1_Missense_Mutation_p.Y168H|NTN4_ENST00000552603.1_5'UTR	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	205	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.		Y -> H (in dbSNP:rs17288108).		axon guidance (GO:0007411)|extracellular matrix organization (GO:0030198)|neuron remodeling (GO:0016322)|regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling (GO:0060668)	basement membrane (GO:0005604)|plasma membrane (GO:0005886)				NS(2)|breast(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						TCTGTATCGTATGGTGGTGAC	0.458													A|||	367	0.0732827	0.0038	0.0908	5008	,	,		17826	0.0238		0.1849	False		,,,				2504	0.091				p.Y205H		Atlas-SNP	.											NTN4,colon,carcinoma,+2,1	NTN4	67	1	0			c.T613C						PASS	.	A	HIS/TYR	137,4269	97.1+/-135.8	1,135,2067	152.0	142.0	145.0		613	1.6	0.0	12	dbSNP_123	145	1507,7093	285.5+/-297.2	127,1253,2920	yes	missense	NTN4	NM_021229.3	83	128,1388,4987	GG,GA,AA		17.5233,3.1094,12.6403	benign	205/629	96131895	1644,11362	2203	4300	6503	SO:0001583	missense	59277	exon3			TATCGTATGGTGG	AF119916	CCDS9054.1	12q22	2013-03-01			ENSG00000074527	ENSG00000074527		"""Netrins"""	13658	protein-coding gene	gene with protein product	"""beta-netrin"", ""Netrin-4"""	610401				11038171	Standard	NM_021229		Approved		uc001tei.3	Q9HB63	OTTHUMG00000170290	ENST00000343702.4:c.613T>C	12.37:g.96131895A>G	ENSP00000340998:p.Tyr205His	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	123	68	0.552846	NM_021229	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Missense_Mutation	SNP	ENST00000343702.4	37	CCDS9054.1	188	0.08608058608058608	1	0.0020325203252032522	38	0.10497237569060773	7	0.012237762237762238	142	0.18733509234828497	A	4.879	0.163335	0.09287	0.031094	0.175233	ENSG00000074527	ENST00000343702;ENST00000344911;ENST00000538383;ENST00000553059;ENST00000547980	T;T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9;-0.9	5.51	1.57	0.23409	Laminin, N-terminal (3);	0.390669	0.28436	N	0.015352	T	0.00073	0.0002	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.04041	-1.0982	9	0.15066	T	0.55	.	4.6958	0.12802	0.5194:0.0:0.1166:0.364	rs17288108;rs52829375;rs59573535;rs17288108	205;205	Q9HB63-2;Q9HB63	.;NET4_HUMAN	H	205;168;168;205;168	ENSP00000340998:Y205H;ENSP00000339436:Y168H;ENSP00000444432:Y168H;ENSP00000447292:Y205H;ENSP00000447594:Y168H	ENSP00000340998:Y205H	Y	-	1	0	NTN4	94656026	0.000000	0.05858	0.043000	0.18650	0.748000	0.42578	-0.014000	0.12656	0.895000	0.36342	0.454000	0.30748	TAC	A|0.893;G|0.107	0.107	strong		0.458	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	156287	156287	+	Silent	SNP	G	G	A	rs6554830	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:156287G>A	ENST00000283426.6	+	8	1292	c.1242G>A	c.(1240-1242)gcG>gcA	p.A414A		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	414							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		CCGTCCTGGCGCGGCTGAGGA	0.612													G|||	737	0.147165	0.3767	0.0951	5008	,	,		17550	0.0129		0.1233	False		,,,				2504	0.0368				p.A414A		Atlas-SNP	.											PLEKHG4B_ENST00000283426,rectum,carcinoma,0,1	PLEKHG4B	167	1	0			c.G1242A						PASS	.	G		1579,2827	492.9+/-362.5	290,999,914	61.0	57.0	59.0		1242	-7.3	0.1	5	dbSNP_116	59	1065,7535	224.5+/-260.9	61,943,3296	no	coding-synonymous	PLEKHG4B	NM_052909.3		351,1942,4210	AA,AG,GG		12.3837,35.8375,20.3291		414/1272	156287	2644,10362	2203	4300	6503	SO:0001819	synonymous_variant	153478	exon8			CCTGGCGCGGCTG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1242G>A	5.37:g.156287G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_052909		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																			G|0.820;A|0.180	0.180	strong		0.612	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
OR10G3	26533	hgsc.bcm.edu	37	14	22038731	22038731	+	Missense_Mutation	SNP	C	C	G	rs12886819	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:22038731C>G	ENST00000303532.1	-	1	144	c.145G>C	c.(145-147)Gtc>Ctc	p.V49L		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	49						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)	15	all_cancers(95;0.000987)			GBM - Glioblastoma multiforme(265;0.0139)		TCTGCCCAGACAGTGATTAAA	0.463													C|||	42	0.00838658	0.0023	0.0101	5008	,	,		21952	0.0		0.0298	False		,,,				2504	0.002				p.V49L		Atlas-SNP	.											.	OR10G3	40	.	0			c.G145C						PASS	.	C	LEU/VAL	28,4378	34.3+/-65.2	0,28,2175	75.0	73.0	74.0		145	3.4	1.0	14	dbSNP_121	74	231,8369	95.2+/-157.0	2,227,4071	yes	missense	OR10G3	NM_001005465.1	32	2,255,6246	GG,GC,CC		2.686,0.6355,1.9914	benign	49/314	22038731	259,12747	2203	4300	6503	SO:0001583	missense	26533	exon1			CCCAGACAGTGAT		CCDS32046.1	14q11.2	2013-09-24			ENSG00000169208	ENSG00000169208		"""GPCR / Class A : Olfactory receptors"""	8171	protein-coding gene	gene with protein product						8188290	Standard	NM_001005465		Approved		uc010tmb.2	Q8NGC4	OTTHUMG00000168886	ENST00000303532.1:c.145G>C	14.37:g.22038731C>G	ENSP00000302437:p.Val49Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_001005465	Q6IET7|Q96R77	Missense_Mutation	SNP	ENST00000303532.1	37	CCDS32046.1	27	0.012362637362637362	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	21	0.027704485488126648	C	11.04	1.521943	0.27211	0.006355	0.02686	ENSG00000169208	ENST00000303532	T	0.03124	4.04	4.33	3.44	0.39384	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42053	D	0.000763	T	0.02342	0.0072	M	0.84846	2.72	0.23070	N	0.99835	B	0.22346	0.068	B	0.27380	0.079	T	0.16719	-1.0393	10	0.87932	D	0	-33.6789	7.2391	0.26086	0.0:0.7924:0.0:0.2076	rs12886819;rs12886819	49	Q8NGC4	O10G3_HUMAN	L	49	ENSP00000302437:V49L	ENSP00000302437:V49L	V	-	1	0	OR10G3	21108571	0.014000	0.17966	0.997000	0.53966	0.860000	0.49131	0.027000	0.13621	0.943000	0.37553	-0.224000	0.12420	GTC	C|0.975;G|0.025	0.025	strong		0.463	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
MYO1E	4643	hgsc.bcm.edu	37	15	59453384	59453384	+	Silent	SNP	T	T	C	rs2306791	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:59453384T>C	ENST00000288235.4	-	24	3072	c.2673A>G	c.(2671-2673)gcA>gcG	p.A891A		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	891	Myosin tail. {ECO:0000255}.			WSAG -> GVQGA (in Ref. 1; AAA62667). {ECO:0000305}.	actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		GGGAGCCCCCTGCACTCCAGG	0.567											OREG0023156	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1279	0.255391	0.5424	0.2147	5008	,	,		15978	0.0843		0.1759	False		,,,				2504	0.1544				p.A891A		Atlas-SNP	.											.	MYO1E	99	.	0			c.A2673G						PASS	.	C		2173,2209	584.2+/-386.0	547,1079,565	45.0	47.0	46.0		2673	-10.1	0.2	15	dbSNP_100	46	1478,7104	740.6+/-407.1	130,1218,2943	no	coding-synonymous	MYO1E	NM_004998.2		677,2297,3508	CC,CT,TT		17.2221,49.5892,28.1626		891/1109	59453384	3651,9313	2191	4291	6482	SO:0001819	synonymous_variant	4643	exon24			GCCCCCTGCACTC	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"""Myosins / Myosin superfamily : Class I"""	7599	protein-coding gene	gene with protein product	"""myosin-IC"""	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.2673A>G	15.37:g.59453384T>C		Somatic	75	0	0	1038	WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_004998	Q14778	Silent	SNP	ENST00000288235.4	37	CCDS32254.1																																																																																			T|0.727;C|0.273	0.273	strong		0.567	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998	
PLXND1	23129	hgsc.bcm.edu	37	3	129275206	129275206	+	Silent	SNP	C	C	T	rs11920311	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129275206C>T	ENST00000324093.4	-	36	5905	c.5727G>A	c.(5725-5727)caG>caA	p.Q1909Q	PLXND1_ENST00000393239.1_3'UTR|PLXND1_ENST00000504689.1_Intron	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1909					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						AAGCCACCACCTGCTCAAACT	0.617													T|||	1165	0.232628	0.3306	0.2046	5008	,	,		19032	0.2103		0.1402	False		,,,				2504	0.2382				p.Q1909Q	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.G5727A						PASS	.	T		1236,3170	705.9+/-407.3	162,912,1129	206.0	184.0	192.0		5727	2.8	1.0	3	dbSNP_120	192	1147,7453	766.4+/-407.6	67,1013,3220	no	coding-synonymous	PLXND1	NM_015103.2		229,1925,4349	TT,TC,CC		13.3372,28.0527,18.3223		1909/1926	129275206	2383,10623	2203	4300	6503	SO:0001819	synonymous_variant	23129	exon36			CACCACCTGCTCA	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.5727G>A	3.37:g.129275206C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	223	112	0.502242	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			C|0.790;T|0.210	0.210	strong		0.617	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
KIAA1551	55196	hgsc.bcm.edu	37	12	32137852	32137852	+	Silent	SNP	C	C	G	rs3759297	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:32137852C>G	ENST00000312561.4	+	4	4377	c.3963C>G	c.(3961-3963)acC>acG	p.T1321T	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1321																	CTCAGGAAACCCGACAGAAGA	0.363													C|||	729	0.145567	0.1014	0.1282	5008	,	,		20068	0.0833		0.1879	False		,,,				2504	0.2382				p.T1321T		Atlas-SNP	.											C12orf35,NS,lymphoid_neoplasm,+1,1	.	.	1	0			c.C3963G						PASS	.	C		501,3905	232.0+/-245.7	25,451,1727	88.0	92.0	91.0		3963	-4.3	0.0	12	dbSNP_107	91	1747,6853	317.4+/-313.2	171,1405,2724	no	coding-synonymous	C12orf35	NM_018169.3		196,1856,4451	GG,GC,CC		20.314,11.3709,17.2843		1321/1748	32137852	2248,10758	2203	4300	6503	SO:0001819	synonymous_variant	55196	exon4			GGAAACCCGACAG	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3963C>G	12.37:g.32137852C>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	37	CCDS8725.2																																																																																			C|0.840;G|0.160	0.160	strong		0.363	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
TLR8	51311	hgsc.bcm.edu	37	X	12937804	12937804	+	Silent	SNP	C	C	T	rs5744080	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:12937804C>T	ENST00000218032.6	+	2	732	c.645C>T	c.(643-645)caC>caT	p.H215H	TLR8_ENST00000311912.5_Silent_p.H233H	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	215					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.H233H(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CTCTTTCACACGTGCCACCCA	0.363													c|||	2556	0.677086	0.6157	0.513	3775	,	,		13833	0.6121		0.2843	False		,,,				2504	0.4939				p.H215H		Atlas-SNP	.											.	TLR8	134	.	1	Substitution - coding silent(1)	stomach(1)	c.C645T						PASS	.	T		2877,958		918,610,431,104,140	65.0	70.0	69.0		645	-4.9	0.0	X	dbSNP_114	69	2640,4087		388,1130,734,910,1137	no	coding-synonymous	TLR8	NM_138636.4		1306,1740,1165,1014,1277	TT,TC,T,CC,C		39.2448,24.9804,47.7656		215/1042	12937804	5517,5045	2203	4299	6502	SO:0001819	synonymous_variant	51311	exon2			TTCACACGTGCCA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.645C>T	X.37:g.12937804C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	140	129	0.921429	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	37	CCDS14152.1																																																																																			C|0.402;0|0.003	.	strong		0.363	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
ZBTB21	49854	hgsc.bcm.edu	37	21	43413651	43413651	+	Missense_Mutation	SNP	T	T	C	rs871545	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:43413651T>C	ENST00000310826.5	-	3	737	c.554A>G	c.(553-555)aAt>aGt	p.N185S	ZBTB21_ENST00000398505.3_Missense_Mutation_p.N185S|ZBTB21_ENST00000398499.1_Missense_Mutation_p.N185S|ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398511.3_Missense_Mutation_p.N185S	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	185			N -> S (in dbSNP:rs871545).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										CTTATTGGTATTGGCCTTGAC	0.418													T|||	498	0.0994409	0.0378	0.0764	5008	,	,		20866	0.0655		0.1938	False		,,,				2504	0.137				p.N185S		Atlas-SNP	.											ZNF295,NS,carcinoma,+1,1	.	.	1	0			c.A554G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	271,4135	154.0+/-187.5	7,257,1939	187.0	174.0	179.0		554,554,554	-3.0	0.0	21	dbSNP_86	179	1625,6975	301.0+/-305.2	152,1321,2827	yes	missense,missense,missense	ZNF295	NM_001098402.1,NM_001098403.1,NM_020727.4	46,46,46	159,1578,4766	CC,CT,TT		18.8953,6.1507,14.5779	benign,benign,benign	185/1067,185/866,185/1067	43413651	1896,11110	2203	4300	6503	SO:0001583	missense	49854	exon3			TTGGTATTGGCCT	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.554A>G	21.37:g.43413651T>C	ENSP00000308759:p.Asn185Ser	Somatic	434	0	0		WXS	Illumina HiSeq	Phase_I	444	225	0.506757	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Missense_Mutation	SNP	ENST00000310826.5	37	CCDS13678.1	237	0.10851648351648352	15	0.03048780487804878	27	0.07458563535911603	35	0.06118881118881119	160	0.21108179419525067	T	3.401	-0.122323	0.06795	0.061507	0.188953	ENSG00000173276	ENST00000398505;ENST00000310826;ENST00000398499;ENST00000398511	T;T;T;T	0.06768	3.52;3.26;3.26;3.26	5.81	-2.96	0.05547	.	0.698049	0.13293	N	0.398833	T	0.00012	0.0000	N	0.01800	-0.715	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.43196	-0.9406	9	0.02654	T	1	-3.3374	8.3118	0.32075	0.0:0.4223:0.1033:0.4744	rs871545;rs52802180;rs871545	185;185	Q9ULJ3-2;Q9ULJ3	.;ZN295_HUMAN	S	185	ENSP00000381517:N185S;ENSP00000308759:N185S;ENSP00000381512:N185S;ENSP00000381523:N185S	ENSP00000308759:N185S	N	-	2	0	ZNF295	42286720	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.417000	0.07088	-0.353000	0.08224	-0.256000	0.11100	AAT	T|0.878;C|0.122	0.122	strong		0.418	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727	
PTPRS	5802	hgsc.bcm.edu	37	19	5210782	5210782	+	Silent	SNP	G	G	A	rs1143698	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:5210782G>A	ENST00000587303.1	-	33	5368	c.5269C>T	c.(5269-5271)Ctg>Ttg	p.L1757L	PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Silent_p.L1737L|PTPRS_ENST00000372412.4_Silent_p.L1758L|PTPRS_ENST00000357368.4_Silent_p.L1757L|PTPRS_ENST00000588012.1_Silent_p.L1719L|PTPRS_ENST00000592099.1_Silent_p.L1310L|PTPRS_ENST00000348075.2_Silent_p.L1719L|PTPRS_ENST00000353284.2_Silent_p.L1310L			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1757	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.L1757L(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GTCTCCGCCAGCGGCCCCTGT	0.642													G|||	1678	0.335064	0.5545	0.3516	5008	,	,		18919	0.0992		0.2714	False		,,,				2504	0.3354				p.L1757L		Atlas-SNP	.											PTPRS,NS,carcinoma,0,1	PTPRS	169	1	1	Substitution - coding silent(1)	stomach(1)	c.C5269T						scavenged	.	G	,,,	2056,2350	567.1+/-382.1	483,1090,630	76.0	61.0	66.0		5269,3928,5155,3940	2.6	0.9	19	dbSNP_86	66	2348,6252	391.5+/-343.7	314,1720,2266	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRS	NM_002850.3,NM_130853.2,NM_130854.2,NM_130855.2	,,,	797,2810,2896	AA,AG,GG		27.3023,46.6636,33.8613	,,,	1757/1949,1310/1502,1719/1911,1314/1506	5210782	4404,8602	2203	4300	6503	SO:0001819	synonymous_variant	5802	exon34			CCGCCAGCGGCCC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.5269C>T	19.37:g.5210782G>A		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	100	40	0.4	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																			G|0.667;A|0.333	0.333	strong		0.642	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
ZNF439	90594	hgsc.bcm.edu	37	19	11979164	11979164	+	Missense_Mutation	SNP	T	T	C	rs10500209	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11979164T>C	ENST00000304030.2	+	3	1480	c.1280T>C	c.(1279-1281)tTg>tCg	p.L427S	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Missense_Mutation_p.L291S	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	427			L -> S (in dbSNP:rs10500209). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						AATCTTCAATTGCATGGTAGG	0.453													-|||	502	0.10024	0.0091	0.2017	5008	,	,		19620	0.004		0.2604	False		,,,				2504	0.0859				p.L427S		Atlas-SNP	.											.	ZNF439	67	.	0			c.T1280C						PASS	.	T	SER/LEU	234,4172	138.4+/-174.2	3,228,1972	71.0	66.0	68.0		1280	-0.7	0.0	19	dbSNP_119	68	2358,6242	392.9+/-344.2	303,1752,2245	no	missense	ZNF439	NM_152262.2	145	306,1980,4217	CC,CT,TT		27.4186,5.3109,19.9293	benign	427/500	11979164	2592,10414	2203	4300	6503	SO:0001583	missense	90594	exon3			TTCAATTGCATGG	AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"""Zinc fingers, C2H2-type"", ""-"""	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.1280T>C	19.37:g.11979164T>C	ENSP00000305077:p.Leu427Ser	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_152262	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	295	0.13507326007326007	9	0.018292682926829267	76	0.20994475138121546	4	0.006993006993006993	206	0.2717678100263852	t	0.012	-1.684349	0.00745	0.053109	0.274186	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.07021	3.23;3.23	0.575	-0.71	0.11234	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.03253	-0.375	0.80722	P	0.0	B	0.26602	0.154	B	0.31101	0.124	T	0.45644	-0.9247	8	0.10636	T	0.68	.	3.2351	0.06762	0.0:0.4434:0.2616:0.295	rs10500209;rs17705609;rs17855566;rs52803841;rs56466712;rs59470711;rs10500209	427	Q8NDP4	ZN439_HUMAN	S	291;427	ENSP00000395632:L291S;ENSP00000305077:L427S	ENSP00000305077:L427S	L	+	2	0	ZNF439	11840164	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	-10.396000	0.00006	-0.375000	0.07955	0.163000	0.16589	TTG	T|0.842;C|0.158	0.158	strong		0.453	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1		
MNS1	55329	hgsc.bcm.edu	37	15	56736681	56736681	+	Missense_Mutation	SNP	A	A	G	rs35775595	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:56736681A>G	ENST00000260453.3	-	5	811	c.647T>C	c.(646-648)aTt>aCt	p.I216T	TEX9_ENST00000352903.2_Intron|TEX9_ENST00000537232.1_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	216	Glu-rich.		I -> T (in dbSNP:rs35775595).		cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		AATTTCATCAATCATGAGTTT	0.328													A|||	30	0.00599042	0.0008	0.013	5008	,	,		18617	0.0		0.0169	False		,,,				2504	0.0031				p.I216T		Atlas-SNP	.											.	MNS1	39	.	0			c.T647C						PASS	.	A	THR/ILE,	23,4361	29.9+/-59.1	0,23,2169	114.0	107.0	110.0		647,	5.4	1.0	15	dbSNP_126	110	234,8348	95.6+/-157.4	0,234,4057	yes	missense,intron	MNS1,TEX9	NM_018365.2,NM_198524.1	89,	0,257,6226	GG,GA,AA		2.7266,0.5246,1.9821	possibly-damaging,	216/496,	56736681	257,12709	2192	4291	6483	SO:0001583	missense	55329	exon5			TCATCAATCATGA	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"""spermatogenesis associated 40"""	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.647T>C	15.37:g.56736681A>G	ENSP00000260453:p.Ile216Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	168	74	0.440476	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	37	CCDS10158.1	20	0.009157509157509158	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	15	0.01978891820580475	A	24.5	4.537928	0.85917	0.005246	0.027266	ENSG00000138587	ENST00000260453	T	0.11385	2.78	5.43	5.43	0.79202	.	0.154112	0.56097	D	0.000023	T	0.10594	0.0259	M	0.81497	2.545	0.50171	D	0.99985	D	0.52996	0.957	P	0.54431	0.752	T	0.00583	-1.1659	10	0.42905	T	0.14	-5.7208	14.6574	0.68844	1.0:0.0:0.0:0.0	rs35775595	216	Q8NEH6	MNS1_HUMAN	T	216	ENSP00000260453:I216T	ENSP00000260453:I216T	I	-	2	0	MNS1	54523973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.070000	0.93974	2.053000	0.61076	0.523000	0.50628	ATT	A|0.984;G|0.016	0.016	strong		0.328	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365	
AHNAK	79026	hgsc.bcm.edu	37	11	62297447	62297447	+	Missense_Mutation	SNP	T	T	C	rs75436331	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62297447T>C	ENST00000378024.4	-	5	4716	c.4442A>G	c.(4441-4443)aAa>aGa	p.K1481R	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1481					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				ATCAGGAGCTTTTATCTCTCC	0.418													t|||	163	0.0325479	0.062	0.0274	5008	,	,		20307	0.0119		0.0258	False		,,,				2504	0.0245				p.K1481R		Atlas-SNP	.											.	AHNAK	532	.	0			c.A4442G						PASS	.	T	ARG/LYS,	308,4096		11,286,1905	165.0	171.0	169.0		4442,	4.5	0.2	11	dbSNP_131	169	220,8378		4,212,4083	yes	missense,intron	AHNAK	NM_001620.1,NM_024060.2	26,	15,498,5988	CC,CT,TT		2.5587,6.9936,4.0609	possibly-damaging,	1481/5891,	62297447	528,12474	2202	4299	6501	SO:0001583	missense	79026	exon5			GGAGCTTTTATCT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.4442A>G	11.37:g.62297447T>C	ENSP00000367263:p.Lys1481Arg	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	229	114	0.497817	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	73	0.033424908424908424	36	0.07317073170731707	13	0.03591160220994475	7	0.012237762237762238	17	0.022427440633245383	N	13.79	2.342406	0.41498	0.069936	0.025587	ENSG00000124942	ENST00000378024	T	0.01068	5.38	4.47	4.47	0.54385	.	.	.	.	.	T	0.00300	0.0009	M	0.86953	2.85	0.34690	D	0.725662	P	0.37061	0.58	B	0.38755	0.281	T	0.39522	-0.9610	9	0.33940	T	0.23	.	13.4741	0.61297	0.0:0.0:0.0:1.0	.	1481	Q09666	AHNK_HUMAN	R	1481	ENSP00000367263:K1481R	ENSP00000367263:K1481R	K	-	2	0	AHNAK	62054023	.	.	0.221000	0.23827	0.011000	0.07611	.	.	1.663000	0.50791	0.449000	0.29647	AAA	T|0.958;C|0.042	0.042	strong		0.418	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
MDC1	9656	hgsc.bcm.edu	37	6	30672342	30672342	+	Missense_Mutation	SNP	A	A	G	rs3130645	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30672342A>G	ENST00000376406.3	-	10	5265	c.4618T>C	c.(4618-4620)Tcc>Ccc	p.S1540P	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Missense_Mutation_p.S1276P	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1540	Interaction with the PRKDC complex.		S -> P (in dbSNP:rs3130645). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18669648, ECO:0000269|PubMed:8724849, ECO:0000269|Ref.3}.		DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						GTGGAGGTGGAAGGCTGGAGC	0.577								Other conserved DNA damage response genes					A|||	657	0.13119	0.3056	0.134	5008	,	,		21158	0.0635		0.0596	False		,,,				2504	0.0368				p.S1540P		Atlas-SNP	.											.	MDC1	218	.	0			c.T4618C						PASS	.	A	PRO/SER	1223,3183	409.3+/-334.9	174,875,1154	119.0	139.0	132.0		4618	-8.4	0.0	6	dbSNP_103	132	519,8081	141.9+/-198.1	21,477,3802	no	missense	MDC1	NM_014641.2	74	195,1352,4956	GG,GA,AA		6.0349,27.7576,13.3938	probably-damaging	1540/2090	30672342	1742,11264	2203	4300	6503	SO:0001583	missense	9656	exon10			AGGTGGAAGGCTG	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.4618T>C	6.37:g.30672342A>G	ENSP00000365588:p.Ser1540Pro	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	276	121	0.438406	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	269	0.12316849816849818	136	0.2764227642276423	52	0.143646408839779	43	0.07517482517482517	38	0.05013192612137203	A	10.58	1.389410	0.25118	0.277576	0.060349	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.11169	2.8;2.8	4.26	-8.4	0.00965	.	.	.	.	.	T	0.02455	0.0075	M	0.68593	2.085	0.80722	P	0.0	B;B	0.17852	0.024;0.002	B;B	0.18561	0.022;0.001	T	0.39603	-0.9606	8	0.30078	T	0.28	.	2.3277	0.04227	0.2323:0.1232:0.4035:0.241	rs3130645;rs13219132;rs52796082;rs61323254;rs3130645	1276;1540	Q14676-2;Q14676	.;MDC1_HUMAN	P	1540;1276;1253;1106	ENSP00000365588:S1540P;ENSP00000365587:S1276P	ENSP00000365587:S1276P	S	-	1	0	MDC1	30780321	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.052000	0.00305	-1.785000	0.01271	-1.251000	0.01509	TCC	A|0.872;G|0.128	0.128	strong		0.577	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
C20orf203	284805	hgsc.bcm.edu	37	20	31238627	31238627	+	lincRNA	SNP	C	C	T	rs7272020	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:31238627C>T	ENST00000608990.1	-	0	764							Q8NBC4	CT203_HUMAN	chromosome 20 open reading frame 203							cytoplasm (GO:0005737)											TCCTCCTTCCCGCCCCACCGC	0.602													C|||	610	0.121805	0.0484	0.147	5008	,	,		11617	0.0		0.2714	False		,,,				2504	0.1748				p.A64A		Atlas-SNP	.											.	.	.	.	0			c.G192A						PASS	.																																					284805	exon3			CCTTCCCGCCCCA	AK091025		20q11.21	2013-12-06			ENSG00000198547	ENSG00000198547			26592	protein-coding gene	gene with protein product						20376170	Standard	NM_182584		Approved	FLJ33706	uc021wbx.1	Q8NBC4	OTTHUMG00000032224		20.37:g.31238627C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_182584	B8JHY2	Silent	SNP	ENST00000608990.1	37																																																																																				C|0.860;T|0.140	0.140	strong		0.602	C20orf203-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000078641.3	NM_182584	
RBM43	375287	hgsc.bcm.edu	37	2	152112161	152112161	+	Missense_Mutation	SNP	C	C	G	rs147060862	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:152112161C>G	ENST00000331426.5	-	2	251	c.100G>C	c.(100-102)Gta>Cta	p.V34L		NM_198557.2	NP_940959.1	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	34	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.131)		TTCACTAATACGGCCAATAAT	0.408													C|||	72	0.014377	0.0151	0.0245	5008	,	,		13812	0.001		0.0288	False		,,,				2504	0.0051				p.V34L		Atlas-SNP	.											RBM43,colon,carcinoma,0,1	RBM43	35	1	0			c.G100C						PASS	.	C	LEU/VAL	60,4346	56.8+/-93.2	0,60,2143	131.0	130.0	130.0		100	-1.3	0.0	2	dbSNP_134	130	251,8349	99.5+/-161.0	5,241,4054	yes	missense	RBM43	NM_198557.2	32	5,301,6197	GG,GC,CC		2.9186,1.3618,2.3912	benign	34/358	152112161	311,12695	2203	4300	6503	SO:0001583	missense	375287	exon2			CTAATACGGCCAA	AK127552	CCDS2191.1	2q23.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000184898	ENSG00000184898		"""RNA binding motif (RRM) containing"""	24790	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 38"""	C2orf38			Standard	NM_198557		Approved	FLJ45645	uc002txh.3	Q6ZSC3	OTTHUMG00000131866	ENST00000331426.5:c.100G>C	2.37:g.152112161C>G	ENSP00000331211:p.Val34Leu	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	213	111	0.521127	NM_198557	B2RMT5	Missense_Mutation	SNP	ENST00000331426.5	37	CCDS2191.1	34	0.015567765567765568	6	0.012195121951219513	9	0.024861878453038673	1	0.0017482517482517483	18	0.023746701846965697	C	2.210	-0.380974	0.05000	0.013618	0.029186	ENSG00000184898	ENST00000331426	T	0.42131	0.98	4.25	-1.31	0.09230	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.899723	0.09370	N	0.811424	T	0.05593	0.0147	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23119	-1.0197	10	0.09843	T	0.71	-0.7126	4.1354	0.10169	0.0:0.414:0.209:0.377	.	34	Q6ZSC3	RBM43_HUMAN	L	34	ENSP00000331211:V34L	ENSP00000331211:V34L	V	-	1	0	RBM43	151820407	0.000000	0.05858	0.025000	0.17156	0.004000	0.04260	0.426000	0.21363	-0.071000	0.12886	-2.222000	0.00295	GTA	C|0.974;G|0.026	0.026	strong		0.408	RBM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254816.2	NM_198557	
NACA	4666	hgsc.bcm.edu	37	12	57114100	57114100	+	Missense_Mutation	SNP	A	A	G	rs2926743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57114100A>G	ENST00000454682.1	-	3	1495	c.1214T>C	c.(1213-1215)tTt>tCt	p.F405S	NACA_ENST00000546392.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.F405S|NACA_ENST00000548563.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000551793.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	405	Pro-rich.		F -> S (in dbSNP:rs2926743). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						AGATAATGAAAAAGAGGTAGC	0.463			T	BCL6	NHL								g|||	4050	0.808706	0.9092	0.7594	5008	,	,		19862	0.745		0.7316	False		,,,				2504	0.8528				p.F405S		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.T1214C						PASS	.	-	,,,SER/PHE	2815,321		1267,281,20	91.0	82.0	85.0		,,,1214	0.5	0.0	12	dbSNP_101	85	5171,1993		1871,1429,282	yes	intron,intron,intron,missense	NACA	NM_001113201.1,NM_001113202.1,NM_005594.4,NM_001113203.2	,,,155	3138,1710,302	GG,GA,AA		27.8197,10.236,22.466	,,,benign	,,,405/926	57114100	7986,2314	1568	3582	5150	SO:0001583	missense	4666	exon3			AATGAAAAAGAGG	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.1214T>C	12.37:g.57114100A>G	ENSP00000403817:p.Phe405Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	37		1710	0.782967032967033	443	0.9004065040650406	284	0.7845303867403315	430	0.7517482517482518	553	0.7295514511873351	N	4.329	0.060360	0.08339	0.89764	0.721803	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.44881	0.91;1.01	3.62	0.525	0.17072	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12477	-1.0546	8	0.87932	D	0	.	4.1106	0.10057	0.3336:0.1724:0.494:0.0	rs2926743;rs61076464;rs2926743	405;405	E9PAV3;F8VU71	.;.	S	405	ENSP00000403817:F405S;ENSP00000448035:F405S	ENSP00000403817:F405S	F	-	2	0	NACA	55400367	0.000000	0.05858	0.015000	0.15790	0.163000	0.22366	0.063000	0.14410	-0.202000	0.10268	-0.701000	0.03672	TTT	A|0.212;G|0.788	0.788	strong		0.463	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238453	71238453	+	Missense_Mutation	SNP	G	G	C	rs147685834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:71238453G>C	ENST00000398536.4	+	1	141	c.107G>C	c.(106-108)tGt>tCt	p.C36S		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	36	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						TCCAGCTGCTGTGTGCCCGTC	0.682													g|||	1257	0.250998	0.2088	0.2233	5008	,	,		10723	0.2877		0.1918	False		,,,				2504	0.3507				p.C36S		Atlas-SNP	.											KRTAP5-7,NS,carcinoma,0,1	KRTAP5-7	23	1	0			c.G107C						PASS	.	G	SER/CYS	856,3544		65,726,1409	69.0	90.0	83.0		107	1.8	1.0	11	dbSNP_134	83	1314,7270		110,1094,3088	no	missense	KRTAP5-7	NM_001012503.1	112	175,1820,4497	CC,CG,GG		15.3075,19.4545,16.7129	possibly-damaging	36/166	71238453	2170,10814	2200	4292	6492	SO:0001583	missense	440050	exon1			GCTGCTGTGTGCC	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"""Keratin associated proteins"""	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.107G>C	11.37:g.71238453G>C	ENSP00000417330:p.Cys36Ser	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	182	91	0.5	NM_001012503	B2RNM3|Q701N5	Missense_Mutation	SNP	ENST00000398536.4	37	CCDS41682.1	497	0.22756410256410256	100	0.2032520325203252	86	0.23756906077348067	173	0.30244755244755245	138	0.1820580474934037	N	6.704	0.498625	0.12762	0.194545	0.153075	ENSG00000244411	ENST00000398536	T	0.01397	4.94	1.8	1.8	0.24995	.	.	.	.	.	T	0.00012	0.0000	M	0.89658	3.05	0.43608	P	0.004022999999999999	P	0.47106	0.89	P	0.54965	0.765	T	0.33624	-0.9861	8	0.54805	T	0.06	.	7.1256	0.25469	0.0:0.0:1.0:0.0	.	36	Q6L8G8	KRA57_HUMAN	S	36	ENSP00000417330:C36S	ENSP00000417330:C36S	C	+	2	0	KRTAP5-7	70916101	1.000000	0.71417	0.978000	0.43139	0.179000	0.23085	3.185000	0.50934	1.345000	0.45676	0.281000	0.19383	TGT	G|0.807;C|0.193	0.193	strong		0.682	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1		
MUC21	394263	hgsc.bcm.edu	37	6	30954909	30954909	+	Missense_Mutation	SNP	C	C	G	rs9262380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954909C>G	ENST00000376296.3	+	2	1198	c.957C>G	c.(955-957)gaC>gaG	p.D319E	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	319	28 X 15 AA approximate tandem repeats.|Ser-rich.		D -> E (in dbSNP:rs9262380). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404}.		cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAACTCTGACTCCAGCACAA	0.607																																					p.D319E		Atlas-SNP	.											MUC21,NS,carcinoma,+2,1	MUC21	98	1	0			c.C957G						scavenged	.						152.0	150.0	150.0					6																	30954909		2203	4300	6503	SO:0001583	missense	394263	exon2			CTCTGACTCCAGC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.957C>G	6.37:g.30954909C>G	ENSP00000365473:p.Asp319Glu	Somatic	75	3	0.04		WXS	Illumina HiSeq	Phase_I	86	17	0.197674	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	c	0.044	-1.272035	0.01421	.	.	ENSG00000204544	ENST00000376296	T	0.01572	4.76	4.3	-8.61	0.00885	.	.	.	.	.	T	0.00241	0.0007	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45308	-0.9270	8	.	.	.	1.3828	7.9638	0.30087	0.1168:0.5304:0.2677:0.0851	rs9262380	319	Q5SSG8	MUC21_HUMAN	E	319	ENSP00000365473:D319E	.	D	+	3	2	MUC21	31062888	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.701000	0.00389	-3.309000	0.00190	-2.881000	0.00097	GAC	C|0.971;G|0.029	0.029	strong		0.607	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
RNASET2	8635	hgsc.bcm.edu	37	6	167369650	167369650	+	Silent	SNP	G	G	A	rs12193095	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:167369650G>A	ENST00000508775.1	-	1	540	c.21C>T	c.(19-21)cgC>cgT	p.R7R	RNASET2_ENST00000366855.6_5'UTR|RNASET2_ENST00000476238.2_Silent_p.R7R|RP11-514O12.4_ENST00000507747.1_5'Flank	NM_003730.4	NP_003721.2	O00584	RNT2_HUMAN	ribonuclease T2	7					RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	ribonuclease activity (GO:0004540)|ribonuclease T2 activity (GO:0033897)|RNA binding (GO:0003723)			large_intestine(4)|lung(4)	8		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)		GCAGGGCCCCGCGCAGGGCTG	0.697													G|||	116	0.0231629	0.003	0.0389	5008	,	,		12533	0.0		0.0775	False		,,,				2504	0.0072				p.R7R		Atlas-SNP	.											RNASET2,NS,carcinoma,0,1	RNASET2	18	1	0			c.C21T						scavenged	.	G		53,3937		0,53,1942	9.0	9.0	9.0		21	-2.0	0.0	6	dbSNP_120	9	561,7163		13,535,3314	no	coding-synonymous	RNASET2	NM_003730.4		13,588,5256	AA,AG,GG		7.2631,1.3283,5.2416		7/257	167369650	614,11100	1995	3862	5857	SO:0001819	synonymous_variant	8635	exon1			GGCCCCGCGCAGG	AJ419866	CCDS5295.1	6q27	2014-05-20			ENSG00000026297	ENSG00000026297			21686	protein-coding gene	gene with protein product		612944				9192857	Standard	NM_003730		Approved	RNASE6PL, FLJ10907, bA514O12.3	uc003qve.3	O00584	OTTHUMG00000016009	ENST00000508775.1:c.21C>T	6.37:g.167369650G>A		Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	59	36	0.610169	NM_003730	B2RDA7|E1P5C3|Q5T8Q0|Q8TCU2|Q9BZ46|Q9BZ47	Silent	SNP	ENST00000508775.1	37	CCDS5295.1																																																																																			G|0.973;A|0.027	0.027	strong		0.697	RNASET2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043089.2	NM_003730	
GSAP	54103	hgsc.bcm.edu	37	7	76984572	76984572	+	Silent	SNP	G	G	A	rs2037753	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:76984572G>A	ENST00000257626.7	-	16	1374	c.1296C>T	c.(1294-1296)tgC>tgT	p.C432C		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	432					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										AGTAGAGCGCGCAGTGCAACG	0.478													A|||	2664	0.531949	0.8253	0.4798	5008	,	,		19035	0.504		0.2962	False		,,,				2504	0.4438				p.C432C		Atlas-SNP	.											.	PION	74	.	0			c.C1296T						PASS	.	A		3255,1151	408.2+/-334.5	1219,817,167	75.0	74.0	74.0		1296	-2.2	0.0	7	dbSNP_94	74	2729,5871	681.2+/-403.7	418,1893,1989	no	coding-synonymous	PION	NM_017439.3		1637,2710,2156	AA,AG,GG		31.7326,26.1235,46.0095		432/855	76984572	5984,7022	2203	4300	6503	SO:0001819	synonymous_variant	54103	exon16			GAGCGCGCAGTGC		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"""pigeon homolog (Drosophila)"""	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.1296C>T	7.37:g.76984572G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	153	66	0.431373	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Silent	SNP	ENST00000257626.7	37	CCDS34672.2																																																																																			G|0.528;A|0.472	0.472	strong		0.478	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
SLC27A5	10998	hgsc.bcm.edu	37	19	59012675	59012675	+	Missense_Mutation	SNP	C	C	T	rs142672241	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:59012675C>T	ENST00000263093.2	-	4	1269	c.1160G>A	c.(1159-1161)cGg>cAg	p.R387Q	SLC27A5_ENST00000601355.1_Missense_Mutation_p.R303Q|SLC27A5_ENST00000594786.1_5'Flank|SLC27A5_ENST00000599700.1_5'Flank	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	387					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		ACACAAGTACCGCAGGAGCTC	0.527													C|||	5	0.000998403	0.0	0.0029	5008	,	,		16011	0.0		0.003	False		,,,				2504	0.0				p.R387Q		Atlas-SNP	.											SLC27A5,NS,carcinoma,0,1	SLC27A5	58	1	0			c.G1160A						scavenged	.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	128.0	131.0	130.0		1160	3.8	1.0	19	dbSNP_134	130	25,8575	18.5+/-59.3	0,25,4275	yes	missense	SLC27A5	NM_012254.2	43	0,27,6476	TT,TC,CC		0.2907,0.0454,0.2076	probably-damaging	387/691	59012675	27,12979	2203	4300	6503	SO:0001583	missense	10998	exon4			AAGTACCGCAGGA	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.1160G>A	19.37:g.59012675C>T	ENSP00000263093:p.Arg387Gln	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	31	2	0.0645161	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	25.5	4.648722	0.87958	4.54E-4	0.002907	ENSG00000083807	ENST00000263093	T	0.44482	0.92	4.9	3.85	0.44370	AMP-dependent synthetase/ligase (1);	0.135756	0.49305	N	0.000150	T	0.58119	0.2100	M	0.91038	3.17	0.35105	D	0.765588	D	0.76494	0.999	P	0.62184	0.899	T	0.76852	-0.2806	10	0.87932	D	0	-32.5211	9.865	0.41138	0.0:0.9026:0.0:0.0974	.	387	Q9Y2P5	S27A5_HUMAN	Q	387	ENSP00000263093:R387Q	ENSP00000263093:R387Q	R	-	2	0	SLC27A5	63704487	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	4.953000	0.63624	1.188000	0.43014	0.563000	0.77884	CGG	C|0.997;T|0.003	0.003	strong		0.527	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
S100A13	6284	hgsc.bcm.edu	37	1	153598904	153598904	+	Silent	SNP	G	G	C	rs113541380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:153598904G>C	ENST00000392623.1	-	2	235	c.45C>G	c.(43-45)acC>acG	p.T15T	S100A1_ENST00000368696.3_5'Flank|S100A1_ENST00000292169.1_5'Flank|S100A1_ENST00000368698.3_5'Flank|S100A13_ENST00000392622.1_Silent_p.T15T|S100A13_ENST00000368699.1_Silent_p.T15T|S100A13_ENST00000440685.2_Silent_p.T15T|S100A13_ENST00000339556.4_Silent_p.T15T|RP1-178F15.5_ENST00000497086.1_RNA|S100A13_ENST00000491177.1_5'UTR	NM_001024212.1	NP_001019383.1	Q99584	S10AD_HUMAN	S100 calcium binding protein A13	15					cytokine secretion (GO:0050663)|interleukin-1 alpha secretion (GO:0050703)|mast cell degranulation (GO:0043303)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of cell shape (GO:0008360)|response to copper ion (GO:0046688)|response to electrical stimulus (GO:0051602)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mast cell granule (GO:0042629)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|RAGE receptor binding (GO:0050786)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)	7	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)		Amlexanox(DB01025)|Olopatadine(DB00768)	TGGTGACCACGGTCTCAATGG	0.562													G|||	36	0.0071885	0.0008	0.0086	5008	,	,		20114	0.0		0.0288	False		,,,				2504	0.0				p.T15T	NSCLC(156;1296 1989 17590 30930 49554)	Atlas-SNP	.											.	S100A13	10	.	0			c.C45G						PASS	.	G	,,,,	15,4391	22.3+/-47.3	0,15,2188	185.0	170.0	175.0		45,45,45,45,45	-10.0	0.1	1	dbSNP_132	175	124,8476	65.6+/-127.9	0,124,4176	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	S100A13	NM_001024210.1,NM_001024211.1,NM_001024212.1,NM_001024213.1,NM_005979.2	,,,,	0,139,6364	CC,CG,GG		1.4419,0.3404,1.0687	,,,,	15/99,15/99,15/99,15/99,15/99	153598904	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	6284	exon2			GACCACGGTCTCA	AK097132	CCDS30874.1	1q21	2008-02-05	2001-11-28		ENSG00000189171	ENSG00000189171		"""S100 calcium binding proteins"""	10490	protein-coding gene	gene with protein product		601989	"""S100 calcium-binding protein A13"""			8985590	Standard	XM_005245434		Approved		uc001fch.3	Q99584	OTTHUMG00000036641	ENST00000392623.1:c.45C>G	1.37:g.153598904G>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	141	78	0.553191	NM_001024213	Q52PI9|Q6FGF8	Silent	SNP	ENST00000392623.1	37	CCDS30874.1																																																																																			G|0.990;C|0.010	0.010	strong		0.562	S100A13-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089109.3	NM_005979	
TIGD2	166815	hgsc.bcm.edu	37	4	90035549	90035549	+	Missense_Mutation	SNP	A	A	G	rs2280099	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:90035549A>G	ENST00000317005.2	+	1	1582	c.1424A>G	c.(1423-1425)cAt>cGt	p.H475R	FAM13A_ENST00000502459.1_5'Flank|RP11-84C13.1_ENST00000603357.1_lincRNA	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	475			H -> R (in dbSNP:rs2280099).			nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	14		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)		CCAGAGAAGCATATTAGCCAT	0.423													A|||	611	0.122005	0.0121	0.1066	5008	,	,		18799	0.1647		0.1918	False		,,,				2504	0.1656				p.H475R		Atlas-SNP	.											.	TIGD2	36	.	0			c.A1424G						PASS	.	A	ARG/HIS	191,4215	119.6+/-157.3	6,179,2018	52.0	52.0	52.0		1424	3.3	1.0	4	dbSNP_100	52	1522,7078	281.8+/-295.3	137,1248,2915	yes	missense	TIGD2	NM_145715.2	29	143,1427,4933	GG,GA,AA		17.6977,4.335,13.1708	probably-damaging	475/526	90035549	1713,11293	2203	4300	6503	SO:0001583	missense	166815	exon1			AGAAGCATATTAG	AK027653	CCDS3633.1	4q21.3	2013-02-21			ENSG00000180346	ENSG00000180346			18333	protein-coding gene	gene with protein product		612973					Standard	NM_145715		Approved		uc003hsk.3	Q4W5G0	OTTHUMG00000130946	ENST00000317005.2:c.1424A>G	4.37:g.90035549A>G	ENSP00000317170:p.His475Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	151	65	0.430464	NM_145715		Missense_Mutation	SNP	ENST00000317005.2	37	CCDS3633.1	274	0.12545787545787546	7	0.014227642276422764	38	0.10497237569060773	96	0.16783216783216784	133	0.17546174142480211	A	13.12	2.141726	0.37825	0.04335	0.176977	ENSG00000180346	ENST00000317005	T	0.22539	1.95	4.49	3.28	0.37604	.	0.479025	0.17418	N	0.174951	T	0.00039	0.0001	L	0.50333	1.59	0.37050	P	0.10244699999999995	D	0.53462	0.96	P	0.51701	0.677	T	0.10428	-1.0630	9	0.10377	T	0.69	-1.9981	7.153	0.25622	0.801:0.0:0.0:0.199	rs2280099;rs17821016;rs58960369;rs2280099	475	Q4W5G0	TIGD2_HUMAN	R	475	ENSP00000317170:H475R	ENSP00000317170:H475R	H	+	2	0	TIGD2	90254572	0.886000	0.30341	1.000000	0.80357	0.942000	0.58702	0.941000	0.29005	0.729000	0.32403	0.383000	0.25322	CAT	G|0.132;N|0.000	0.132	strong		0.423	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715	
CCDC154	645811	hgsc.bcm.edu	37	16	1484528	1484528	+	Missense_Mutation	SNP	G	G	A	rs61744665	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1484528G>A	ENST00000389176.3	-	17	2072	c.1906C>T	c.(1906-1908)Cgc>Tgc	p.R636C	CCDC154_ENST00000409671.1_Missense_Mutation_p.R484C	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	636						endosome (GO:0005768)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						GCCTTCCAGCGCAGCCACCTG	0.711													G|||	574	0.114617	0.2814	0.0504	5008	,	,		8608	0.0516		0.0447	False		,,,				2504	0.0716				p.R629C		Atlas-SNP	.											.	CCDC154	27	.	0			c.C1885T						PASS	.						48.0	43.0	44.0					16																	1484528		692	1591	2283	SO:0001583	missense	645811	exon17			TCCAGCGCAGCCA			16p13.3	2012-12-13			ENSG00000197599	ENSG00000197599			34454	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 29"""	C16orf29			Standard	NM_001143980		Approved	LOC645811	uc010uve.2	A6NI56	OTTHUMG00000154097	ENST00000389176.3:c.1906C>T	16.37:g.1484528G>A	ENSP00000373828:p.Arg636Cys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_001143980	G9JV18	Missense_Mutation	SNP	ENST00000389176.3	37		212	0.09706959706959707	137	0.2784552845528455	14	0.03867403314917127	29	0.050699300699300696	32	0.04221635883905013	G	16.40	3.111505	0.56398	.	.	ENSG00000197599	ENST00000409671;ENST00000389176	.	.	.	4.88	2.8	0.32819	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.47350	0.894	B	0.36186	0.219	T	0.29150	-1.0021	7	0.87932	D	0	-2.2298	11.1302	0.48343	0.0:0.0:0.6666:0.3334	.	636	A6NI56	CC154_HUMAN	C	484;636	.	ENSP00000373828:R636C	R	-	1	0	CCDC154	1424529	0.013000	0.17824	0.213000	0.23690	0.089000	0.18198	0.611000	0.24268	1.038000	0.40049	0.491000	0.48974	CGC	G|0.901;A|0.099	0.099	strong		0.711	CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
CDHR2	54825	hgsc.bcm.edu	37	5	176011444	176011444	+	Missense_Mutation	SNP	C	C	T	rs115050587	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:176011444C>T	ENST00000510636.1	+	19	2436	c.2162C>T	c.(2161-2163)gCg>gTg	p.A721V	CDHR2_ENST00000506348.1_Missense_Mutation_p.A721V|CDHR2_ENST00000261944.5_Missense_Mutation_p.A721V	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	721	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						GCCTGGGACGCGGACCAGACG	0.637													C|||	9	0.00179712	0.0015	0.0014	5008	,	,		18356	0.0		0.005	False		,,,				2504	0.001				p.A721V		Atlas-SNP	.											.	CDHR2	152	.	0			c.C2162T						PASS	.	C	VAL/ALA,VAL/ALA	14,4392	21.2+/-45.6	0,14,2189	93.0	96.0	95.0		2162,2162	4.2	0.1	5	dbSNP_132	95	119,8481	61.0+/-122.8	0,119,4181	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	64,64	0,133,6370	TT,TC,CC		1.3837,0.3177,1.0226	probably-damaging,probably-damaging	721/1311,721/1311	176011444	133,12873	2203	4300	6503	SO:0001583	missense	54825	exon19			GGGACGCGGACCA	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"""Cadherins / Cadherin-related"""	18231	protein-coding gene	gene with protein product	"""protocadherin LKC"""		"""protocadherin 24"""	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.2162C>T	5.37:g.176011444C>T	ENSP00000424565:p.Ala721Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	136	76	0.558824	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	13.57	2.277159	0.40294	0.003177	0.013837	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.55413	0.52;0.52;0.52	5.12	4.24	0.50183	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.66470	0.2792	M	0.91920	3.255	0.33621	D	0.604834	D	0.67145	0.996	P	0.59546	0.859	T	0.81061	-0.1103	9	0.36615	T	0.2	-11.2568	12.946	0.58373	0.2944:0.7056:0.0:0.0	.	721	Q9BYE9	CDHR2_HUMAN	V	721	ENSP00000424565:A721V;ENSP00000261944:A721V;ENSP00000421078:A721V	ENSP00000261944:A721V	A	+	2	0	CDHR2	175944050	0.874000	0.30092	0.079000	0.20413	0.097000	0.18754	1.646000	0.37249	1.248000	0.43934	0.549000	0.68633	GCG	C|0.991;T|0.009	0.009	strong		0.637	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
MYSM1	114803	hgsc.bcm.edu	37	1	59125683	59125683	+	Missense_Mutation	SNP	C	C	T	rs232777	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:59125683C>T	ENST00000472487.1	-	20	2512	c.2473G>A	c.(2473-2475)Gaa>Aaa	p.E825K	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	825			E -> K (in dbSNP:rs232777).		chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.E825K(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					ATTAACAATTCCTTTGTACAG	0.294													C|||	1515	0.302516	0.4599	0.2666	5008	,	,		18527	0.2143		0.2018	False		,,,				2504	0.3098				p.E825K		Atlas-SNP	.											MYSM1,NS,carcinoma,+2,2	MYSM1	50	2	1	Substitution - Missense(1)	stomach(1)	c.G2473A						PASS	.	C	LYS/GLU	1406,2204		273,860,672	78.0	76.0	76.0		2473	1.3	0.6	1	dbSNP_79	76	1396,6748		119,1158,2795	yes	missense	MYSM1	NM_001085487.2	56	392,2018,3467	TT,TC,CC		17.1415,38.9474,23.8387	possibly-damaging	825/829	59125683	2802,8952	1805	4072	5877	SO:0001583	missense	114803	exon20			ACAATTCCTTTGT	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.2473G>A	1.37:g.59125683C>T	ENSP00000418734:p.Glu825Lys	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	257	110	0.428016	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Missense_Mutation	SNP	ENST00000472487.1	37	CCDS41343.1	565	0.2586996336996337	213	0.4329268292682927	84	0.23204419889502761	112	0.1958041958041958	156	0.20580474934036938	C	15.55	2.865960	0.51588	0.389474	0.171415	ENSG00000162601	ENST00000472487	T	0.26518	1.73	5.46	1.26	0.21427	.	0.862293	0.10295	N	0.691878	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.43782	-0.9370	9	0.72032	D	0.01	-8.4071	3.8643	0.09010	0.1179:0.4841:0.2537:0.1443	rs232777;rs593577;rs52823386;rs60284479;rs232777	825	Q5VVJ2	MYSM1_HUMAN	K	825	ENSP00000418734:E825K	ENSP00000418734:E825K	E	-	1	0	MYSM1	58898271	0.025000	0.19082	0.630000	0.29268	0.985000	0.73830	0.117000	0.15583	0.413000	0.25759	0.591000	0.81541	GAA	C|0.742;T|0.258	0.258	strong		0.294	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481	
MYSM1	114803	hgsc.bcm.edu	37	1	59142713	59142713	+	Silent	SNP	T	T	C	rs579110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:59142713T>C	ENST00000472487.1	-	9	1314	c.1275A>G	c.(1273-1275)ccA>ccG	p.P425P	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	425	SWIRM. {ECO:0000255|PROSITE- ProRule:PRU00247}.				chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					TTAAGTATTTTGGTTTGCATA	0.333													C|||	3242	0.647364	0.7133	0.6686	5008	,	,		15179	0.629		0.5875	False		,,,				2504	0.6237				p.P425P		Atlas-SNP	.											.	MYSM1	50	.	0			c.A1275G						PASS	.	C		2476,1222		812,852,185	162.0	159.0	160.0		1275	3.3	1.0	1	dbSNP_83	160	4738,3446		1394,1950,748	no	coding-synonymous	MYSM1	NM_001085487.2		2206,2802,933	CC,CT,TT		42.1065,33.0449,39.2863		425/829	59142713	7214,4668	1849	4092	5941	SO:0001819	synonymous_variant	114803	exon9			GTATTTTGGTTTG	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.1275A>G	1.37:g.59142713T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Silent	SNP	ENST00000472487.1	37	CCDS41343.1																																																																																			T|0.386;C|0.614	0.614	strong		0.333	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481	
MDC1	9656	hgsc.bcm.edu	37	6	30672326	30672326	+	Missense_Mutation	SNP	T	T	C	rs17292678	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30672326T>C	ENST00000376406.3	-	10	5281	c.4634A>G	c.(4633-4635)cAa>cGa	p.Q1545R	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Missense_Mutation_p.Q1281R	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1545	Interaction with the PRKDC complex.		Q -> R (in dbSNP:rs17292678). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16702430, ECO:0000269|PubMed:8724849, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.		DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						GGTGACAGGTTGGTCTGTGGA	0.567								Other conserved DNA damage response genes					T|||	253	0.0505192	0.0825	0.0648	5008	,	,		21855	0.0417		0.0258	False		,,,				2504	0.0317				p.Q1545R		Atlas-SNP	.											.	MDC1	218	.	0			c.A4634G						PASS	.	T	ARG/GLN	338,4068	175.1+/-204.6	9,320,1874	120.0	139.0	132.0		4634	3.1	0.0	6	dbSNP_123	132	244,8356	95.9+/-157.7	3,238,4059	no	missense	MDC1	NM_014641.2	43	12,558,5933	CC,CT,TT		2.8372,7.6714,4.4749	possibly-damaging	1545/2090	30672326	582,12424	2203	4300	6503	SO:0001583	missense	9656	exon10			ACAGGTTGGTCTG	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.4634A>G	6.37:g.30672326T>C	ENSP00000365588:p.Gln1545Arg	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	283	127	0.448763	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	105	0.04807692307692308	34	0.06910569105691057	27	0.07458563535911603	25	0.043706293706293704	19	0.025065963060686015	T	8.733	0.917038	0.17907	0.076714	0.028372	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.08458	3.09;3.09	4.26	3.11	0.35812	.	.	.	.	.	T	0.04634	0.0126	M	0.72894	2.215	0.80722	P	0.0	B;B	0.30482	0.281;0.009	B;B	0.36534	0.227;0.004	T	0.23691	-1.0181	8	0.30078	T	0.28	.	6.4195	0.21736	0.0:0.1087:0.0:0.8913	rs17292678;rs57435770	1281;1545	Q14676-2;Q14676	.;MDC1_HUMAN	R	1545;1281;1258;1111	ENSP00000365588:Q1545R;ENSP00000365587:Q1281R	ENSP00000365587:Q1281R	Q	-	2	0	MDC1	30780305	0.001000	0.12720	0.012000	0.15200	0.006000	0.05464	-0.038000	0.12144	0.994000	0.38892	0.369000	0.22263	CAA	T|0.957;C|0.043	0.043	strong		0.567	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
ZNF708	7562	hgsc.bcm.edu	37	19	21477379	21477379	+	Missense_Mutation	SNP	C	C	T	rs504280	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:21477379C>T	ENST00000356929.3	-	4	586	c.389G>A	c.(388-390)cGg>cAg	p.R130Q		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	66					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						TGTCACACACCGGTTAAGTCC	0.378													C|||	929	0.185503	0.1755	0.1816	5008	,	,		18026	0.1091		0.2624	False		,,,				2504	0.2014				p.R130Q		Atlas-SNP	.											.	ZNF708	66	.	0			c.G389A						PASS	.	C	GLN/ARG	791,3615		67,657,1479	176.0	158.0	164.0		389	-0.9	0.0	19	dbSNP_83	164	2114,6486		258,1598,2444	yes	missense	ZNF708	NM_021269.2	43	325,2255,3923	TT,TC,CC		24.5814,17.9528,22.3358	benign	130/564	21477379	2905,10101	2203	4300	6503	SO:0001583	missense	7562	exon4			ACACACCGGTTAA	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"""Zinc fingers, C2H2-type"", ""-"""	12945	protein-coding gene	gene with protein product			"""zinc finger protein 15-like 1 (KOX 8)"", ""zinc finger protein 708"", ""zinc finger protein 708 (KOX8)"""	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.389G>A	19.37:g.21477379C>T	ENSP00000349401:p.Arg130Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	94	54	0.574468	NM_021269	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	422	0.19322344322344323	85	0.17276422764227642	72	0.19889502762430938	56	0.0979020979020979	209	0.2757255936675462	.	0.005	-2.169809	0.00315	0.179528	0.245814	ENSG00000182141	ENST00000356929	T	0.32988	1.43	0.449	-0.883	0.10600	.	.	.	.	.	T	0.00012	0.0000	N	0.00043	-2.465	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28396	-1.0045	7	0.02654	T	1	.	.	.	.	rs504280;rs17618630;rs52789772;rs504280	130	P17019	ZN708_HUMAN	Q	130	ENSP00000349401:R130Q	ENSP00000349401:R130Q	R	-	2	0	ZNF708	21269219	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.722000	0.04958	-0.737000	0.04824	-0.811000	0.03165	CGG	C|0.780;T|0.220	0.220	strong		0.378	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138764741	138764741	+	Missense_Mutation	SNP	T	T	G	rs142490389	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:138764741T>G	ENST00000242351.5	-	4	1262	c.946A>C	c.(946-948)Act>Cct	p.T316P	ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.T316P|ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.T316P	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	316					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						CCAAGATCAGTAGCCTTGGAC	0.582													T|||	2	0.000399361	0.0	0.0	5008	,	,		19261	0.0		0.002	False		,,,				2504	0.0				p.T316P		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.A946C						PASS	.	T	PRO/THR,PRO/THR	4,4402	8.1+/-20.4	0,4,2199	51.0	51.0	51.0		946,946	-8.9	0.0	7	dbSNP_134	51	22,8578	16.0+/-53.3	0,22,4278	yes	missense,missense	ZC3HAV1	NM_020119.3,NM_024625.3	38,38	0,26,6477	GG,GT,TT		0.2558,0.0908,0.1999	benign,benign	316/903,316/700	138764741	26,12980	2203	4300	6503	SO:0001583	missense	56829	exon4			GATCAGTAGCCTT	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.946A>C	7.37:g.138764741T>G	ENSP00000242351:p.Thr316Pro	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	63	38	0.603175	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	11.79	1.745165	0.30955	9.08E-4	0.002558	ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652;ENST00000540247	T;T;T	0.30448	1.53;1.53;1.53	4.47	-8.94	0.00768	.	1.426730	0.04367	N	0.358508	T	0.16896	0.0406	L	0.36672	1.1	0.09310	N	1	B;B	0.21225	0.053;0.001	B;B	0.15484	0.013;0.002	T	0.17592	-1.0364	10	0.48119	T	0.1	.	0.8161	0.01103	0.3267:0.2947:0.2199:0.1588	.	316;316	Q7Z2W4-2;Q7Z2W4	.;ZCCHV_HUMAN	P	316;316;316;76	ENSP00000242351:T316P;ENSP00000418385:T316P;ENSP00000419855:T316P	ENSP00000242351:T316P	T	-	1	0	ZC3HAV1	138415281	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-4.989000	0.00162	-1.691000	0.01430	0.528000	0.53228	ACT	T|0.999;G|0.001	0.001	strong		0.582	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
PEF1	553115	hgsc.bcm.edu	37	1	32096265	32096265	+	Silent	SNP	A	A	G	rs1061770	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32096265A>G	ENST00000373703.4	-	5	826	c.804T>C	c.(802-804)atT>atC	p.I268I	PEF1_ENST00000492061.1_5'Flank|HCRTR1_ENST00000373705.1_Intron	NM_012392.3	NP_036524.1	Q9UBV8	PEF1_HUMAN	penta-EF-hand domain containing 1	268	EF-hand 5. {ECO:0000255|PROSITE- ProRule:PRU00448}.|Required for interaction with PDCD6.				proteolysis (GO:0006508)|response to calcium ion (GO:0051592)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|poly(A) RNA binding (GO:0044822)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)|all_neural(195;0.186)		STAD - Stomach adenocarcinoma(196;0.0546)		AGCTGAGCCGAATGTTGCCTT	0.572													A|||	1787	0.356829	0.0794	0.4741	5008	,	,		2811	0.248		0.5676	False		,,,				2504	0.544				p.I268I		Atlas-SNP	.											.	PEF1	20	.	0			c.T804C						PASS	.	A		730,3676	301.0+/-286.6	77,576,1550	113.0	83.0	93.0		804	0.1	1.0	1	dbSNP_86	93	4811,3789	613.4+/-396.1	1352,2107,841	no	coding-synonymous	PEF1	NM_012392.3		1429,2683,2391	GG,GA,AA		44.0581,16.5683,42.6034		268/285	32096265	5541,7465	2203	4300	6503	SO:0001819	synonymous_variant	553115	exon5			GAGCCGAATGTTG		CCDS345.1	1p34	2013-01-10			ENSG00000162517	ENSG00000162517		"""EF-hand domain containing"""	30009	protein-coding gene	gene with protein product	"""peflin"""	610033				10486255, 11883899	Standard	NM_012392		Approved	PEF1A	uc001bth.2	Q9UBV8	OTTHUMG00000003877	ENST00000373703.4:c.804T>C	1.37:g.32096265A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_012392		Silent	SNP	ENST00000373703.4	37	CCDS345.1																																																																																			A|0.587;G|0.413	0.413	strong		0.572	PEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011046.1	NM_012392	
PARP15	165631	hgsc.bcm.edu	37	3	122354716	122354716	+	Silent	SNP	C	C	T	rs61754895	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:122354716C>T	ENST00000464300.2	+	12	1872	c.1806C>T	c.(1804-1806)gaC>gaT	p.D602D	PARP15_ENST00000493645.1_Silent_p.D299D|PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000310366.4_Silent_p.D368D|PARP15_ENST00000483793.1_Silent_p.D407D	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	602	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		CTGCCAAGGACACCTACTCCA	0.443													C|||	538	0.107428	0.0567	0.1297	5008	,	,		22138	0.0099		0.2465	False		,,,				2504	0.1176				p.D602D		Atlas-SNP	.											.	PARP15	115	.	0			c.C1806T						PASS	.	C	,	313,4093	168.0+/-198.9	11,291,1901	144.0	128.0	133.0		1806,1104	-2.7	0.0	3	dbSNP_129	133	2006,6594	352.0+/-328.5	244,1518,2538	no	coding-synonymous,coding-synonymous	PARP15	NM_001113523.1,NM_152615.1	,	255,1809,4439	TT,TC,CC		23.3256,7.1039,17.8302	,	602/679,368/445	122354716	2319,10687	2203	4300	6503	SO:0001819	synonymous_variant	165631	exon12			CAAGGACACCTAC	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1806C>T	3.37:g.122354716C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	99	57	0.575758	NM_001113523	J3KR47|Q8N1K3	Silent	SNP	ENST00000464300.2	37	CCDS46893.1																																																																																			C|0.834;T|0.166	0.166	strong		0.443	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
AQP12A	375318	hgsc.bcm.edu	37	2	241631665	241631665	+	Silent	SNP	C	C	T	rs76463197	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241631665C>T	ENST00000337801.4	+	2	367	c.298C>T	c.(298-300)Ctg>Ttg	p.L100L	AQP12A_ENST00000429564.1_Silent_p.L112L|AC011298.2_ENST00000407635.2_lincRNA	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	100						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(3)|large_intestine(2)|lung(7)	14		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		GCCTGGCACGCTGTTGAAGCT	0.682													c|||	546	0.109026	0.0303	0.1326	5008	,	,		13526	0.003		0.2565	False		,,,				2504	0.1564				p.L100L		Atlas-SNP	.											.	AQP12A	32	.	0			c.C298T						PASS	.			342,3798		71,200,1799	27.0	36.0	33.0		298	2.6	0.7	2	dbSNP_131	33	2063,6445		366,1331,2557	no	coding-synonymous	AQP12A	NM_198998.1		437,1531,4356	TT,TC,CC		24.2478,8.2609,19.0149		100/296	241631665	2405,10243	2070	4254	6324	SO:0001819	synonymous_variant	375318	exon2			GGCACGCTGTTGA	AB040748		2q37.3	2013-06-03	2005-05-26	2005-05-26	ENSG00000184945	ENSG00000184945		"""Ion channels / Aquaporins"""	19941	protein-coding gene	gene with protein product		609789	"""aquaporin 12"""	AQP12			Standard	NM_198998		Approved		uc002vzu.3	Q8IXF9	OTTHUMG00000183906	ENST00000337801.4:c.298C>T	2.37:g.241631665C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_198998		Silent	SNP	ENST00000337801.4	37																																																																																				C|0.836;T|0.164	0.164	strong		0.682	AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998	
MOB3A	126308	hgsc.bcm.edu	37	19	2078488	2078488	+	Silent	SNP	T	T	C	rs2074894	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:2078488T>C	ENST00000357066.3	-	3	451	c.72A>G	c.(70-72)ccA>ccG	p.P24P	MOB3A_ENST00000592143.1_Intron|MOB3A_ENST00000592280.1_Silent_p.P24P	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	24						intracellular (GO:0005622)	metal ion binding (GO:0046872)										GCTGGGTGCCTGGCTCAAACT	0.627													C|||	1973	0.39397	0.6528	0.2507	5008	,	,		16431	0.1835		0.329	False		,,,				2504	0.4294				p.P24P		Atlas-SNP	.											MOBKL2A,rectum,carcinoma,0,1	.	.	1	0			c.A72G						PASS	.	C		2793,1613	497.7+/-363.9	887,1019,297	55.0	57.0	56.0		72	-8.5	0.0	19	dbSNP_96	56	2932,5668	665.8+/-402.3	506,1920,1874	no	coding-synonymous	MOB3A	NM_130807.2		1393,2939,2171	CC,CT,TT		34.093,36.6092,44.0181		24/218	2078488	5725,7281	2203	4300	6503	SO:0001819	synonymous_variant	126308	exon3			GGTGCCTGGCTCA	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.72A>G	19.37:g.2078488T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			T|0.597;C|0.403	0.403	strong		0.627	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
JAK2	3717	hgsc.bcm.edu	37	9	5081828	5081828	+	Missense_Mutation	SNP	G	G	C	rs150221602	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:5081828G>C	ENST00000381652.3	+	19	3032	c.2538G>C	c.(2536-2538)gaG>gaC	p.E846D	JAK2_ENST00000539801.1_Missense_Mutation_p.E846D|JAK2_ENST00000544510.1_Missense_Mutation_p.E697D|AL161450.1_ENST00000601793.1_Intron	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	846					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	AGTTTGAAGAGAGACATTTGA	0.358		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																												p.E846D		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.G2538C						PASS	.	G	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	104.0	104.0	104.0		2538	0.0	1.0	9	dbSNP_134	104	5,8595	4.3+/-15.6	0,5,4295	yes	missense	JAK2	NM_004972.3	45	0,6,6497	CC,CG,GG		0.0581,0.0227,0.0461	benign	846/1133	5081828	6,13000	2203	4300	6503	SO:0001583	missense	3717	exon19	Familial Cancer Database		TGAAGAGAGACAT		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.2538G>C	9.37:g.5081828G>C	ENSP00000371067:p.Glu846Asp	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	120	54	0.45	NM_004972	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.648097	0.47258	2.27E-4	5.81E-4	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	D;D;D	0.89123	-2.47;-2.47;-2.47	5.42	0.0118	0.14089	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.85948	0.5816	M	0.73962	2.25	0.47245	D	0.999367	B	0.31100	0.308	B	0.27076	0.076	T	0.79249	-0.1881	10	0.62326	D	0.03	-17.9695	10.7256	0.46066	0.6272:0.0:0.3728:0.0	.	846	O60674	JAK2_HUMAN	D	846;846;697	ENSP00000440387:E846D;ENSP00000371067:E846D;ENSP00000443103:E697D	ENSP00000371067:E846D	E	+	3	2	JAK2	5071828	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	0.585000	0.23879	-0.298000	0.08921	0.655000	0.94253	GAG	G|0.999;C|0.001	0.001	strong		0.358	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
HLA-B	3106	hgsc.bcm.edu	37	6	31323215	31323215	+	Silent	SNP	T	T	C	rs41541216	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323215T>C	ENST00000412585.2	-	4	802	c.774A>G	c.(772-774)agA>agG	p.R258R		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	258	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CTCCTGCTGGTCTGGTCTCCA	0.582									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.R258R		Atlas-SNP	.											.	HLA-B	54	.	0			c.A774G						PASS	.						103.0	88.0	93.0					6																	31323215		2203	4300	6503	SO:0001819	synonymous_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	TGCTGGTCTGGTC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.774A>G	6.37:g.31323215T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	188	61	0.324468	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			T|0.774;C|0.226	0.226	strong		0.582	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382453	24382453	+	IGR	SNP	G	G	C	rs112697166		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:24382453G>C								AC004552.1 (15430 upstream) : PDK3 (100884 downstream)																							agctgctgctgctgctcctgc	0.627																																					p.A526P		Atlas-SNP	.											.	.	.	.	0			c.G1576C						PASS	.						2.0	2.0	2.0					X																	24382453		966	2386	3352	SO:0001628	intergenic_variant	100130302	exon1			GCTGCTGCTGCTC																													X.37:g.24382453G>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	76	21	0.276316	NM_001136234		Missense_Mutation	SNP		37																																																																																				G|0.500;C|0.500	0.500	weak	0	0.627								
MYO15A	51168	hgsc.bcm.edu	37	17	18058521	18058521	+	Silent	SNP	C	C	T	rs712272	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18058521C>T	ENST00000205890.5	+	46	8660	c.8322C>T	c.(8320-8322)tcC>tcT	p.S2774S	MYO15A_ENST00000585180.1_Silent_p.S38S|MYO15A_ENST00000418233.3_Silent_p.S38S	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2774	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TCTACTTCTCCCGCATCTTCC	0.602													C|||	1078	0.215256	0.1846	0.2983	5008	,	,		17398	0.0675		0.3907	False		,,,				2504	0.1697				p.S2774S		Atlas-SNP	.											.	MYO15A	268	.	0			c.C8322T						PASS	.	C		956,3260		106,744,1258	40.0	49.0	46.0		8322	-0.5	1.0	17	dbSNP_86	46	3446,4990		723,2000,1495	no	coding-synonymous	MYO15A	NM_016239.3		829,2744,2753	TT,TC,CC		40.8487,22.6755,34.7929		2774/3531	18058521	4402,8250	2108	4218	6326	SO:0001819	synonymous_variant	51168	exon45			CTTCTCCCGCATC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8322C>T	17.37:g.18058521C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	98	53	0.540816	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																			C|0.696;T|0.304	0.304	strong		0.602	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
BAG3	9531	hgsc.bcm.edu	37	10	121436362	121436362	+	Silent	SNP	A	A	G	rs196295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:121436362A>G	ENST00000369085.3	+	4	1602	c.1296A>G	c.(1294-1296)gtA>gtG	p.V432V		NM_004281.3	NP_004272.2	O95817	BAG3_HUMAN	BCL2-associated athanogene 3	432	BAG. {ECO:0000255|PROSITE- ProRule:PRU00369}.				brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of apoptotic process (GO:0043066)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|Z disc (GO:0030018)				endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(5)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	20		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00187)|BRCA - Breast invasive adenocarcinoma(275;0.148)		TGGAGAAGGTACAGGGGCTGG	0.532													G|||	3538	0.70647	0.7534	0.7219	5008	,	,		19654	0.4881		0.8012	False		,,,				2504	0.7597				p.V432V		Atlas-SNP	.											.	BAG3	42	.	0			c.A1296G						PASS	.	G		3318,1088	389.6+/-327.4	1263,792,148	45.0	48.0	47.0		1296	1.4	1.0	10	dbSNP_79	47	6701,1899	334.5+/-321.0	2613,1475,212	no	coding-synonymous	BAG3	NM_004281.3		3876,2267,360	GG,GA,AA		22.0814,24.6936,22.9663		432/576	121436362	10019,2987	2203	4300	6503	SO:0001819	synonymous_variant	9531	exon4			GAAGGTACAGGGG	AF095193	CCDS7615.1	10q25.2-q26.2	2014-09-17			ENSG00000151929	ENSG00000151929			939	protein-coding gene	gene with protein product		603883				9873016, 18094623	Standard	XM_005270287		Approved		uc001lem.3	O95817	OTTHUMG00000019155	ENST00000369085.3:c.1296A>G	10.37:g.121436362A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_004281	A8K5L8|Q3B763|Q9NT20|Q9P120	Silent	SNP	ENST00000369085.3	37	CCDS7615.1																																																																																			A|0.263;G|0.737	0.737	strong		0.532	BAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050662.1	NM_004281	
LRRC37A2	474170	hgsc.bcm.edu	37	17	44626347	44626347	+	Missense_Mutation	SNP	T	T	C	rs62073349		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44626347T>C	ENST00000576629.1	+	10	4337	c.3842T>C	c.(3841-3843)aTt>aCt	p.I1281T	ARL17A_ENST00000337845.7_Intron|LRRC37A2_ENST00000333412.3_Missense_Mutation_p.I1281T|ARL17A_ENST00000573185.1_Intron|ARL17A_ENST00000329240.4_Intron|ARL17A_ENST00000445552.2_Intron			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	1281			I -> T (in dbSNP:rs62073349). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|pancreas(4)|prostate(2)	15		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		GCTATTTCCATTTTAGAAAGT	0.473																																					p.I1281T		Atlas-SNP	.											.	LRRC37A2	37	.	0			c.T3842C						PASS	.	T	THR/ILE,	188,4164		0,188,1988	42.0	72.0	62.0		3842,	0.6	0.1	17	dbSNP_129	62	1695,6885		5,1685,2600	no	missense,intron	ARL17A,LRRC37A2	NM_001006607.2,NM_016632.2	89,	5,1873,4588	CC,CT,TT		19.7552,4.3199,14.5608	benign,	1281/1701,	44626347	1883,11049	2176	4290	6466	SO:0001583	missense	474170	exon9			TTTCCATTTTAGA	AY386262	CCDS42353.1	17q21.31	2013-05-14			ENSG00000238083	ENSG00000238083			32404	protein-coding gene	gene with protein product	"""c114 SLIT-like testicular protein"""						Standard	NM_001006607		Approved	FLJ45049	uc002ikn.1	A6NM11	OTTHUMG00000178032	ENST00000576629.1:c.3842T>C	17.37:g.44626347T>C	ENSP00000459551:p.Ile1281Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	169	69	0.408284	NM_001006607	B7ZMC3	Missense_Mutation	SNP	ENST00000576629.1	37	CCDS42353.1	.	.	.	.	.	.	.	.	.	.	t	7.146	0.582772	0.13749	0.043199	0.197552	ENSG00000238083	ENST00000333412	T	0.58652	0.32	2.91	0.618	0.17624	.	.	.	.	.	T	0.00073	0.0002	L	0.44542	1.39	0.09310	N	1	B;B;B	0.31680	0.064;0.335;0.025	B;B;B	0.31751	0.012;0.135;0.008	T	0.02115	-1.1211	9	0.37606	T	0.19	.	4.4111	0.11434	0.0:0.3258:0.0:0.6742	.	1281;242;1281	C9JSP5;B3KRJ4;A6NM11	.;.;L37A2_HUMAN	T	1281	ENSP00000333071:I1281T	ENSP00000333071:I1281T	I	+	2	0	LRRC37A2	41981663	0.746000	0.28272	0.099000	0.21106	0.015000	0.08874	0.854000	0.27791	0.341000	0.23771	0.147000	0.16070	ATT	.	.	weak		0.473	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607	
DSG3	1830	hgsc.bcm.edu	37	18	29054294	29054294	+	Missense_Mutation	SNP	C	C	T	rs111986709	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:29054294C>T	ENST00000257189.4	+	15	2395	c.2312C>T	c.(2311-2313)tCc>tTc	p.S771F		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	771					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACAAGGCATTCCACTGGAGGA	0.493													C|||	58	0.0115815	0.0015	0.013	5008	,	,		18033	0.0		0.0249	False		,,,				2504	0.0225				p.S771F		Atlas-SNP	.											.	DSG3	172	.	0			c.C2312T						PASS	.	C	PHE/SER	40,4366	43.1+/-76.7	0,40,2163	130.0	127.0	128.0		2312	6.1	1.0	18	dbSNP_132	128	309,8291	111.4+/-171.7	4,301,3995	yes	missense	DSG3	NM_001944.2	155	4,341,6158	TT,TC,CC		3.593,0.9079,2.6834	probably-damaging	771/1000	29054294	349,12657	2203	4300	6503	SO:0001583	missense	1830	exon15			GGCATTCCACTGG	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2312C>T	18.37:g.29054294C>T	ENSP00000257189:p.Ser771Phe	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	170	94	0.552941	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	27	0.012362637362637362	0	0.0	4	0.011049723756906077	0	0.0	23	0.030343007915567283	C	16.16	3.045378	0.55110	0.009079	0.03593	ENSG00000134757	ENST00000257189	T	0.63255	-0.03	6.06	6.06	0.98353	.	0.000000	0.50627	D	0.000110	T	0.37732	0.1014	M	0.71581	2.175	0.41681	D	0.989299	P	0.35700	0.516	B	0.41174	0.349	T	0.60712	-0.7209	10	0.59425	D	0.04	.	18.8049	0.92032	0.0:1.0:0.0:0.0	.	771	P32926	DSG3_HUMAN	F	771	ENSP00000257189:S771F	ENSP00000257189:S771F	S	+	2	0	DSG3	27308292	0.993000	0.37304	1.000000	0.80357	0.130000	0.20726	3.179000	0.50887	2.879000	0.98667	0.650000	0.86243	TCC	C|0.975;T|0.025	0.025	strong		0.493	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
NEDD4	4734	hgsc.bcm.edu	37	15	56243766	56243766	+	Silent	SNP	C	C	T	rs61732704	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:56243766C>T	ENST00000435532.3	-	3	331	c.141G>A	c.(139-141)acG>acA	p.T47T		NM_006154.2	NP_006145.2	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	0					adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		GGTCATATAACGTCACTCTCA	0.289													C|||	324	0.0646965	0.0166	0.1542	5008	,	,		11341	0.0347		0.0646	False		,,,				2504	0.0971				p.T47T		Atlas-SNP	.											.	NEDD4	167	.	0			c.G141A						PASS	.	C		102,3418		3,96,1661	54.0	49.0	51.0		141	-10.3	0.1	15	dbSNP_129	51	453,7407		7,439,3484	no	coding-synonymous	NEDD4	NM_006154.2		10,535,5145	TT,TC,CC		5.7634,2.8977,4.877		47/901	56243766	555,10825	1760	3930	5690	SO:0001819	synonymous_variant	4734	exon3			ATATAACGTCACT	D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"""receptor-potentiating factor 1"""	602278	"""neural precursor cell expressed, developmentally down-regulated 4"""			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000435532.3:c.141G>A	15.37:g.56243766C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	111	108	0.972973	NM_006154	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Silent	SNP	ENST00000435532.3	37	CCDS45265.1																																																																																			C|0.943;T|0.057	0.057	strong		0.289	NEDD4-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359821.2	NM_198400	
OR5R1	219479	hgsc.bcm.edu	37	11	56185401	56185401	+	Missense_Mutation	SNP	C	C	T	rs7123108	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56185401C>T	ENST00000312253.1	-	1	307	c.308G>A	c.(307-309)tGt>tAt	p.C103Y		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	103			C -> Y (in dbSNP:rs7123108).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					GGTGAGAAAACAACCCAGTTG	0.458													C|||	186	0.0371406	0.003	0.0432	5008	,	,		21443	0.001		0.0944	False		,,,				2504	0.0573				p.C103Y		Atlas-SNP	.											.	OR5R1	83	.	0			c.G308A						PASS	.	C	TYR/CYS	56,4346	54.2+/-90.2	0,56,2145	99.0	94.0	96.0		308	2.6	1.0	11	dbSNP_116	96	695,7897	171.6+/-222.5	33,629,3634	yes	missense	OR5R1	NM_001004744.1	194	33,685,5779	TT,TC,CC		8.0889,1.2721,5.7796	probably-damaging	103/325	56185401	751,12243	2201	4296	6497	SO:0001583	missense	219479	exon1			AGAAAACAACCCA	AB065504	CCDS31530.1	11q11	2012-08-09		2004-03-10	ENSG00000174942	ENSG00000174942		"""GPCR / Class A : Olfactory receptors"""	14841	protein-coding gene	gene with protein product				OR5R1P			Standard	NM_001004744		Approved		uc010rji.2	Q8NH85	OTTHUMG00000154219	ENST00000312253.1:c.308G>A	11.37:g.56185401C>T	ENSP00000308595:p.Cys103Tyr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	37	CCDS31530.1	85	0.03891941391941392	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	71	0.09366754617414248	C	13.19	2.163974	0.38217	0.012721	0.080889	ENSG00000174942	ENST00000312253	T	0.00237	8.47	5.78	2.59	0.31030	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35495	U	0.003163	T	0.00012	0.0000	L	0.31476	0.935	0.09310	N	1	D	0.55172	0.97	P	0.52066	0.689	T	0.60444	-0.7262	10	0.87932	D	0	-6.7475	14.8151	0.70028	0.4182:0.5818:0.0:0.0	rs7123108;rs17544570;rs52823358;rs7123108	103	Q8NH85	OR5R1_HUMAN	Y	103	ENSP00000308595:C103Y	ENSP00000308595:C103Y	C	-	2	0	OR5R1	55941977	0.000000	0.05858	0.959000	0.39883	0.673000	0.39480	0.269000	0.18589	1.436000	0.47453	0.478000	0.44815	TGT	C|0.951;T|0.049	0.049	strong		0.458	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744	
CUX2	23316	hgsc.bcm.edu	37	12	111785586	111785586	+	Silent	SNP	T	T	C	rs3803167	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:111785586T>C	ENST00000261726.6	+	22	4072	c.3918T>C	c.(3916-3918)gaT>gaC	p.D1306D		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1306					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						TGGAGGAGGATGCTGAGGAAG	0.612													C|||	2644	0.527955	0.6195	0.451	5008	,	,		14602	0.7639		0.2435	False		,,,				2504	0.5082				p.D1306D		Atlas-SNP	.											.	CUX2	145	.	0			c.T3918C						PASS	.	C		2298,1986		614,1070,458	47.0	55.0	52.0		3918	-8.0	0.0	12	dbSNP_107	52	1843,6617		209,1425,2596	no	coding-synonymous	CUX2	NM_015267.3		823,2495,3054	CC,CT,TT		21.7849,46.3585,32.4937		1306/1487	111785586	4141,8603	2142	4230	6372	SO:0001819	synonymous_variant	23316	exon22			GGAGGATGCTGAG	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"""Homeoboxes / CUT class"""	19347	protein-coding gene	gene with protein product		610648	"""cut-like 2 (Drosophila)"""	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.3918T>C	12.37:g.111785586T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_015267	A7E2Y4	Silent	SNP	ENST00000261726.6	37	CCDS41837.1																																																																																			T|0.524;C|0.476	0.476	strong		0.612	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	
EXD3	54932	hgsc.bcm.edu	37	9	140243880	140243880	+	Missense_Mutation	SNP	G	G	A	rs35097575	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140243880G>A	ENST00000340951.4	-	15	1793	c.1598C>T	c.(1597-1599)aCg>aTg	p.T533M	EXD3_ENST00000342129.4_Missense_Mutation_p.T213M	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CAGCTGCTGCGTCTTGTCCAG	0.711													g|||	69	0.013778	0.0023	0.0187	5008	,	,		15457	0.001		0.0417	False		,,,				2504	0.0102				p.T533M		Atlas-SNP	.											EXD3_ENST00000340951,NS,carcinoma,0,2	EXD3	86	2	0			c.C1598T						PASS	.		MET/THR	43,4201		0,43,2079	18.0	24.0	22.0		1598	0.6	0.0	9	dbSNP_126	22	422,8020		10,402,3809	yes	missense	EXD3	NM_017820.3	81	10,445,5888	AA,AG,GG		4.9988,1.0132,3.6655	probably-damaging	533/877	140243880	465,12221	2122	4221	6343	SO:0001583	missense	54932	exon15			TGCTGCGTCTTGT		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.1598C>T	9.37:g.140243880G>A	ENSP00000340474:p.Thr533Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	38	0.0173992673992674	3	0.006097560975609756	5	0.013812154696132596	0	0.0	30	0.0395778364116095	g	9.747	1.166369	0.21621	0.010132	0.049988	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.64991	-0.13;-0.13	3.9	0.646	0.17789	-5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2);	1.821850	0.03484	U	0.215568	T	0.17323	0.0416	M	0.62723	1.935	0.09310	N	1	D;P	0.53312	0.959;0.903	B;B	0.36959	0.237;0.202	T	0.39354	-0.9618	10	0.41790	T	0.15	.	7.4036	0.26977	0.0972:0.3149:0.5879:0.0	rs35097575	213;533	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	M	213;533	ENSP00000343705:T213M;ENSP00000340474:T533M	ENSP00000340474:T533M	T	-	2	0	EXD3	139363701	0.001000	0.12720	0.001000	0.08648	0.059000	0.15707	0.710000	0.25748	0.138000	0.18790	0.282000	0.19409	ACG	G|0.982;A|0.018	0.018	strong		0.711	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
REV1	51455	hgsc.bcm.edu	37	2	100055506	100055506	+	Missense_Mutation	SNP	A	A	G	rs3087386	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:100055506A>G	ENST00000258428.3	-	6	998	c.770T>C	c.(769-771)tTt>tCt	p.F257S	REV1_ENST00000393445.3_Missense_Mutation_p.F257S|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	257			F -> S (in dbSNP:rs3087386).		DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTCCTGGGAAAAGGCTGGAGA	0.498								Direct reversal of damage					.|||	2906	0.580272	0.7315	0.7003	5008	,	,		19504	0.3611		0.5666	False		,,,				2504	0.5307				p.F257S		Atlas-SNP	.											.	REV1	100	.	0			c.T770C						PASS	.	G	SER/PHE,SER/PHE	3115,1291	436.8+/-344.8	1099,917,187	57.0	55.0	56.0		770,770	-0.0	0.0	2	dbSNP_102	56	4708,3892	544.8+/-384.7	1283,2142,875	yes	missense,missense	REV1	NM_001037872.1,NM_016316.2	155,155	2382,3059,1062	GG,GA,AA		45.2558,29.301,39.8508	benign,benign	257/1251,257/1252	100055506	7823,5183	2203	4300	6503	SO:0001583	missense	51455	exon6			TGGGAAAAGGCTG	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"""DNA polymerases"""	14060	protein-coding gene	gene with protein product		606134	"""REV1 (yeast homolog)- like"", ""REV1-like (yeast)"", ""REV1 homolog (S. cerevisiae)"""	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.770T>C	2.37:g.100055506A>G	ENSP00000258428:p.Phe257Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_001037872	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	1254	0.5741758241758241	355	0.7215447154471545	253	0.6988950276243094	204	0.35664335664335667	442	0.58311345646438	G	0.727	-0.781505	0.02929	0.70699	0.547442	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.25414	1.8;1.8	5.54	-0.0271	0.13927	.	1.017110	0.07806	N	0.957370	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35450	-0.9788	9	0.08179	T	0.78	.	6.4404	0.21847	0.4589:0.1197:0.4214:0.0	rs3087386;rs3749086;rs58019413;rs3087386	236;257;257	Q9UBZ9-3;Q9UBZ9;Q9UBZ9-2	.;REV1_HUMAN;.	S	257	ENSP00000377091:F257S;ENSP00000258428:F257S	ENSP00000258428:F257S	F	-	2	0	REV1	99421938	0.164000	0.22935	0.000000	0.03702	0.074000	0.17049	0.717000	0.25851	-0.622000	0.05626	-1.653000	0.00756	TTT	A|0.422;G|0.578	0.578	strong		0.498	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	
PARP4	143	hgsc.bcm.edu	37	13	25074490	25074490	+	Missense_Mutation	SNP	C	C	T	rs9578751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25074490C>T	ENST00000381989.3	-	4	470	c.365G>A	c.(364-366)aGt>aAt	p.S122N		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	122			S -> N (in dbSNP:rs9578751).		cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CTCTGTGGCACTGTCCGGGCA	0.398													.|||	320	0.0638978	0.0772	0.0591	5008	,	,		14701	0.0317		0.0924	False		,,,				2504	0.0532				p.S122N		Atlas-SNP	.											.	PARP4	142	.	0			c.G365A						PASS	.	C	ASN/SER	390,4016	196.7+/-221.0	22,346,1835	121.0	116.0	118.0		365	-3.5	0.0	13	dbSNP_119	118	983,7617	213.4+/-253.3	66,851,3383	yes	missense	PARP4	NM_006437.3	46	88,1197,5218	TT,TC,CC		11.4302,8.8516,10.5567	benign	122/1725	25074490	1373,11633	2203	4300	6503	SO:0001583	missense	143	exon4			GTGGCACTGTCCG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.365G>A	13.37:g.25074490C>T	ENSP00000371419:p.Ser122Asn	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	154	0.07051282051282051	44	0.08943089430894309	24	0.06629834254143646	8	0.013986013986013986	78	0.10290237467018469	C	1.648	-0.514674	0.04200	0.088516	0.114302	ENSG00000102699	ENST00000381989	T	0.44482	0.92	3.38	-3.55	0.04639	.	1.369470	0.04747	N	0.423829	T	0.00328	0.0010	N	0.02736	-0.51	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13522	-1.0506	10	0.10377	T	0.69	-4.6393	9.1088	0.36714	0.0:0.5451:0.0:0.4549	rs9578751;rs17470431;rs52802969;rs9578751	122	Q9UKK3	PARP4_HUMAN	N	122	ENSP00000371419:S122N	ENSP00000371419:S122N	S	-	2	0	PARP4	23972490	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.085000	0.01362	-0.749000	0.04747	-1.427000	0.01099	AGT	C|0.909;T|0.091	0.091	strong		0.398	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
MORF4L1	10933	hgsc.bcm.edu	37	15	79185898	79185898	+	Silent	SNP	C	C	A	rs1435163	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:79185898C>A	ENST00000331268.5	+	10	879	c.675C>A	c.(673-675)gcC>gcA	p.A225A	MORF4L1_ENST00000558502.1_Silent_p.A98A|MORF4L1_ENST00000559345.1_Silent_p.A98A|MORF4L1_ENST00000561171.1_Intron|MORF4L1_ENST00000558746.1_Silent_p.A159A|MORF4L1_ENST00000379535.4_Silent_p.A211A|MORF4L1_ENST00000426013.2_Silent_p.A186A	NM_206839.2	NP_996670.1	Q9UBU8	MO4L1_HUMAN	mortality factor 4 like 1	225	Interaction with RB1-1.|MRG. {ECO:0000255|PROSITE- ProRule:PRU00972}.|Sufficient for interaction with PHF12.|Sufficient for interaction with SIN3A.				cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|double-strand break repair via homologous recombination (GO:0000724)|histone deacetylation (GO:0016575)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|Sin3 complex (GO:0016580)	chromatin binding (GO:0003682)|protein N-terminus binding (GO:0047485)			breast(1)|large_intestine(3)|lung(4)|prostate(1)|urinary_tract(1)	10						ATCTTCCTGCCAAGAAGAATG	0.303													C|||	701	0.139976	0.1127	0.1326	5008	,	,		18954	0.254		0.1262	False		,,,				2504	0.0787				p.A225A		Atlas-SNP	.											.	MORF4L1	26	.	0			c.C675A						PASS	.	C	,	479,3911	204.8+/-226.9	26,427,1742	67.0	72.0	71.0		558,675	0.5	1.0	15	dbSNP_88	71	1087,7493	220.8+/-258.4	70,947,3273	no	coding-synonymous,coding-synonymous	MORF4L1	NM_006791.2,NM_206839.1	,	96,1374,5015	AA,AC,CC		12.669,10.9112,12.074	,	186/324,225/363	79185898	1566,11404	2195	4290	6485	SO:0001819	synonymous_variant	10933	exon10			TCCTGCCAAGAAG	AF100615	CCDS10307.1, CCDS32304.1, CCDS58393.1	15q25.1	2009-07-13			ENSG00000185787	ENSG00000185787			16989	protein-coding gene	gene with protein product	"""MORF-related gene on chromosome 15"", ""Esa1p-associated factor 3 homolog (S. cerevisiae)"""	607303				8619474, 9110174	Standard	NM_006791		Approved	MRG15, MORFRG15, HsT17725, Eaf3, MEAF3	uc002bel.4	Q9UBU8	OTTHUMG00000143865	ENST00000331268.5:c.675C>A	15.37:g.79185898C>A		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	221	105	0.475113	NM_206839	B4DKN6|B7Z6R1|D3DW88|O95899|Q5QTS1|Q6NVX8|Q86YT7|Q9HBP6|Q9NSW5	Silent	SNP	ENST00000331268.5	37	CCDS10307.1																																																																																			C|0.877;A|0.123	0.123	strong		0.303	MORF4L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000290131.4	NM_006791	
THAP6	152815	hgsc.bcm.edu	37	4	76452302	76452302	+	Missense_Mutation	SNP	T	T	A	rs150566447		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:76452302T>A	ENST00000311638.3	+	5	615	c.547T>A	c.(547-549)Ttg>Atg	p.L183M	THAP6_ENST00000380837.3_Missense_Mutation_p.L141M|THAP6_ENST00000507885.1_Intron|THAP6_ENST00000514480.1_Missense_Mutation_p.L183M|THAP6_ENST00000507557.1_Intron|THAP6_ENST00000504190.1_Intron|THAP6_ENST00000507556.1_Intron|THAP6_ENST00000502620.1_Intron	NM_144721.4	NP_653322.1	Q8TBB0	THAP6_HUMAN	THAP domain containing 6	183						microtubule cytoskeleton (GO:0015630)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(5)	5			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TCAGAAATCATTGAGGAAGAC	0.398													T|||	1	0.000199681	0.0	0.0	5008	,	,		19622	0.0		0.001	False		,,,				2504	0.0				p.L183M		Atlas-SNP	.											.	THAP6	14	.	0			c.T547A						PASS	.	T	MET/LEU	1,4405	2.1+/-5.4	0,1,2202	114.0	118.0	117.0		547	-3.8	0.7	4	dbSNP_134	117	27,8573	18.5+/-59.3	0,27,4273	yes	missense	THAP6	NM_144721.4	15	0,28,6475	AA,AT,TT		0.314,0.0227,0.2153	probably-damaging	183/223	76452302	28,12978	2203	4300	6503	SO:0001583	missense	152815	exon5			AAATCATTGAGGA	BC022989	CCDS3568.1	4q21.21	2013-01-25			ENSG00000174796	ENSG00000174796		"""THAP (C2CH-type zinc finger) domain containing"""	23189	protein-coding gene	gene with protein product		612535				12575992	Standard	NM_144721		Approved	MGC30052	uc003him.3	Q8TBB0	OTTHUMG00000130108	ENST00000311638.3:c.547T>A	4.37:g.76452302T>A	ENSP00000309007:p.Leu183Met	Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	250	129	0.516	NM_144721	B4E146|Q5HYJ7|Q5JPC6	Missense_Mutation	SNP	ENST00000311638.3	37	CCDS3568.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	17.57	3.422570	0.62622	2.27E-4	0.00314	ENSG00000174796	ENST00000311638;ENST00000380837;ENST00000514480	D;D;D	0.98666	-5.06;-2.37;-5.06	4.67	-3.82	0.04281	.	0.149661	0.28828	N	0.014010	D	0.97102	0.9053	N	0.19112	0.55	0.21445	N	0.999684	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.963	D	0.93524	0.6864	10	0.33141	T	0.24	-10.7559	11.1423	0.48411	0.0:0.5762:0.0:0.4238	.	141;183	Q8TBB0-2;Q8TBB0	.;THAP6_HUMAN	M	183;141;183	ENSP00000309007:L183M;ENSP00000370217:L141M;ENSP00000423720:L183M	ENSP00000309007:L183M	L	+	1	2	THAP6	76671326	0.071000	0.21146	0.716000	0.30569	0.983000	0.72400	-1.212000	0.02994	-0.636000	0.05524	0.533000	0.62120	TTG	T|0.998;A|0.002	0.002	strong		0.398	THAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252414.1	NM_144721	
UTRN	7402	hgsc.bcm.edu	37	6	144758799	144758799	+	Silent	SNP	A	A	G	rs4895642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:144758799A>G	ENST00000367545.3	+	10	1158	c.1158A>G	c.(1156-1158)gaA>gaG	p.E386E		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	386	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.E386E(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		CAGACGAAGAAGAATTTGAGA	0.512													G|||	2327	0.464657	0.795	0.562	5008	,	,		19112	0.4365		0.2237	False		,,,				2504	0.226				p.E386E		Atlas-SNP	.											UTRN,NS,carcinoma,0,1	UTRN	327	1	1	Substitution - coding silent(1)	stomach(1)	c.A1158G						PASS	.	G		3108,1298	437.6+/-345.0	1098,912,193	109.0	98.0	102.0		1158	1.1	1.0	6	dbSNP_111	102	2096,6504	717.8+/-406.2	255,1586,2459	yes	coding-synonymous	UTRN	NM_007124.2		1353,2498,2652	GG,GA,AA		24.3721,29.4598,40.0123		386/3434	144758799	5204,7802	2203	4300	6503	SO:0001819	synonymous_variant	7402	exon10			CGAAGAAGAATTT	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.1158A>G	6.37:g.144758799A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	37	CCDS34547.1																																																																																			A|0.563;G|0.437	0.437	strong		0.512	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
HAUS7	55559	hgsc.bcm.edu	37	X	152735959	152735959	+	Silent	SNP	C	C	T	rs2032436	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:152735959C>T	ENST00000370211.4	-	1	130	c.87G>A	c.(85-87)gaG>gaA	p.E29E	TREX2_ENST00000330912.2_5'UTR|TREX2_ENST00000338525.2_5'UTR|HAUS7_ENST00000370212.3_Silent_p.E29E|TREX2_ENST00000370232.1_5'UTR|HAUS7_ENST00000370210.1_Silent_p.E19E|HAUS7_ENST00000421080.2_5'UTR|TREX2_ENST00000334497.2_5'UTR	NM_017518.7	NP_059988.3	Q99871	HAUS7_HUMAN	HAUS augmin-like complex, subunit 7	29					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	thioesterase binding (GO:0031996)			endometrium(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)	19						TGCTGTCGCCCTCGTCCTCTG	0.711													C|||	308	0.0815894	0.0053	0.0764	3775	,	,		5361	0.0		0.2177	False		,,,				2504	0.0297				p.E29E		Atlas-SNP	.											.	HAUS7	44	.	0			c.G87A						PASS	.	C		131,3688		3,116,9,1510,552	27.0	21.0	23.0		87	3.5	0.0	X	dbSNP_94	23	1644,5076		149,886,460,1392,1406	no	coding-synonymous	HAUS7	NM_017518.6		152,1002,469,2902,1958	TT,TC,T,CC,C		24.4643,3.4302,16.8422		29/369	152735959	1775,8764	2190	4293	6483	SO:0001819	synonymous_variant	55559	exon1			GTCGCCCTCGTCC	AF267739	CCDS35438.1	Xq28	2011-10-24	2009-04-20	2009-04-20		ENSG00000213397		"""HAUS augmin-like complex subunits"""	32979	protein-coding gene	gene with protein product	"""UCH37 interacting protein 1"", ""26S proteasome-associated UCH interacting protein 1"""	300540	"""UCHL5 interacting protein"""	UCHL5IP		11163772, 16395595, 19427217	Standard	NM_017518		Approved	UIP1	uc004fho.2	Q99871		ENST00000370211.4:c.87G>A	X.37:g.152735959C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_017518	B4DUH6|D3DWT9|Q96HS8|Q9NP54|Q9UFH9	Silent	SNP	ENST00000370211.4	37	CCDS35438.1																																																																																			C|0.857;T|0.143	0.143	strong		0.711	HAUS7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060963.2	NM_017518	
TF	7018	hgsc.bcm.edu	37	3	133494354	133494354	+	Missense_Mutation	SNP	C	C	T	rs1049296	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:133494354C>T	ENST00000402696.3	+	15	2250	c.1765C>T	c.(1765-1767)Cct>Tct	p.P589S	TF_ENST00000264998.3_Missense_Mutation_p.P462S	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	589	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.		P -> S (in allele TF*C2; dbSNP:rs1049296). {ECO:0000269|PubMed:11702220, ECO:0000269|PubMed:11703331, ECO:0000269|PubMed:9272172, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	TACCAGGAAACCTGTGGAGGA	0.493													C|||	783	0.15635	0.0605	0.121	5008	,	,		22741	0.256		0.1382	False		,,,				2504	0.227				p.P589S		Atlas-SNP	.											TF,colon,carcinoma,-1,1	TF	116	1	0			c.C1765T	GRCh37	CM033984	TF	M	rs1049296	PASS	.	C	SER/PRO	339,4067	178.0+/-206.8	11,317,1875	182.0	179.0	180.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1765	-6.9	0.0	3	dbSNP_86	180	1358,7242	266.5+/-286.8	101,1156,3043	yes	missense	TF	NM_001063.3	74	112,1473,4918	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	15.7907,7.6941,13.0478	benign	589/699	133494354	1697,11309	2203	4300	6503	SO:0001583	missense	7018	exon15			AGGAAACCTGTGG		CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.1765C>T	3.37:g.133494354C>T	ENSP00000385834:p.Pro589Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Missense_Mutation	SNP	ENST00000402696.3	37	CCDS3080.1	325	0.1488095238095238	32	0.06504065040650407	52	0.143646408839779	137	0.2395104895104895	104	0.13720316622691292	C	9.645	1.139976	0.21205	0.076941	0.157907	ENSG00000091513	ENST00000402696;ENST00000264998	T;T	0.07908	3.15;3.15	5.01	-6.91	0.01649	.	1.463040	0.03931	N	0.285272	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.09022	0.002	B	0.14578	0.011	T	0.42916	-0.9423	9	0.44086	T	0.13	-0.967	6.2687	0.20943	0.0788:0.4316:0.3239:0.1658	rs1049296;rs56624236;rs59474673;rs1049296	589	P02787	TRFE_HUMAN	S	589;462	ENSP00000385834:P589S;ENSP00000264998:P462S	ENSP00000264998:P462S	P	+	1	0	TF	134977044	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-2.546000	0.00932	-1.250000	0.02497	-1.267000	0.01435	CCT	C|0.855;T|0.145	0.145	strong		0.493	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
SPATA4	132851	hgsc.bcm.edu	37	4	177113836	177113836	+	Silent	SNP	C	C	T	rs6832177	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:177113836C>T	ENST00000280191.2	-	4	738	c.630G>A	c.(628-630)gcG>gcA	p.A210A	SPATA4_ENST00000515234.1_Silent_p.A37A	NM_144644.2	NP_653245.2	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	210						cytoplasm (GO:0005737)				NS(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)	22		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)		TGAGGAACTCCGCTTTAAGTT	0.373													c|||	1416	0.282748	0.2239	0.3646	5008	,	,		17787	0.255		0.3708	False		,,,				2504	0.2423				p.A210A		Atlas-SNP	.											SPATA4,NS,carcinoma,-1,1	SPATA4	44	1	0			c.G630A						PASS	.	C		1120,3286	398.3+/-330.8	147,826,1230	88.0	91.0	90.0		630	-3.7	0.0	4	dbSNP_116	90	3042,5558	466.9+/-366.9	551,1940,1809	no	coding-synonymous	SPATA4	NM_144644.2		698,2766,3039	TT,TC,CC		35.3721,25.4199,32.0006		210/306	177113836	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	132851	exon4			GAACTCCGCTTTA	AY040204	CCDS3826.1	4q34.2	2008-02-05			ENSG00000150628	ENSG00000150628			17333	protein-coding gene	gene with protein product		609879					Standard	NM_144644		Approved	TSARG2, SPEF1B	uc003iuo.1	Q8NEY3	OTTHUMG00000160788	ENST00000280191.2:c.630G>A	4.37:g.177113836C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	202	92	0.455446	NM_144644	Q8NCS5|Q8WW15	Silent	SNP	ENST00000280191.2	37	CCDS3826.1																																																																																			C|0.701;T|0.299	0.299	strong		0.373	SPATA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362326.1	NM_144644	
Unknown	0	hgsc.bcm.edu	37	11	124096277	124096277	+	IGR	SNP	G	G	A	rs2466612	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124096277G>A								OR10D3 (39325 upstream) : OR8G1 (24145 downstream)																							TTATACTATTGTTGTGCCCAT	0.438													g|||	494	0.0986422	0.0174	0.1527	5008	,	,		20206	0.13		0.1412	False		,,,				2504	0.0941				p.V294I		Atlas-SNP	.											.	.	.	.	0			c.G880A						PASS	.						73.0	67.0	69.0					11																	124096277		1925	4152	6077	SO:0001628	intergenic_variant	26492	exon1			ACTATTGTTGTGC																													11.37:g.124096277G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	180	75	0.416667	NM_001007249		Missense_Mutation	SNP		37																																																																																				G|0.888;A|0.112	0.112	strong	0	0.438								
TNFRSF19	55504	hgsc.bcm.edu	37	13	24242165	24242165	+	Silent	SNP	C	C	T	rs61745191	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:24242165C>T	ENST00000382258.4	+	8	987	c.783C>T	c.(781-783)agC>agT	p.S261S	TNFRSF19_ENST00000248484.4_Silent_p.S261S|TNFRSF19_ENST00000382263.3_Silent_p.S261S|TNFRSF19_ENST00000403372.2_Silent_p.S129S	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	261					apoptotic process (GO:0006915)|hair follicle development (GO:0001942)|JNK cascade (GO:0007254)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)	tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	22		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		AGGCCTGCAGCCCCAACCCGG	0.567													C|||	123	0.0245607	0.0053	0.0447	5008	,	,		16006	0.0		0.0815	False		,,,				2504	0.0031				p.S261S		Atlas-SNP	.											.	TNFRSF19	52	.	0			c.C783T						PASS	.	C	,,,	52,4354	51.6+/-87.1	0,52,2151	54.0	48.0	50.0		783,387,783,783	3.9	0.0	13	dbSNP_129	50	517,8083	143.4+/-199.5	20,477,3803	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TNFRSF19	NM_001204458.1,NM_001204459.1,NM_018647.3,NM_148957.3	,,,	20,529,5954	TT,TC,CC		6.0116,1.1802,4.3749	,,,	261/418,129/286,261/424,261/418	24242165	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	55504	exon8			CTGCAGCCCCAAC	AB040434	CCDS9301.1, CCDS9302.1, CCDS55893.1	13q12.11-q12.3	2008-07-18			ENSG00000127863	ENSG00000127863		"""Tumor necrosis factor receptor superfamily"""	11915	protein-coding gene	gene with protein product	"""toxicity and JNK inducer"""	606122				10764796, 10809768	Standard	NM_018647		Approved	TAJ-alpha, TROY, TAJ, TRADE	uc001uov.2	Q9NS68	OTTHUMG00000016568	ENST00000382258.4:c.783C>T	13.37:g.24242165C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_018647	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Silent	SNP	ENST00000382258.4	37	CCDS9302.1																																																																																			C|0.955;T|0.045	0.045	strong		0.567	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647	
PKD1	5310	hgsc.bcm.edu	37	16	2159405	2159405	+	Silent	SNP	C	C	T	rs2575313	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2159405C>T	ENST00000262304.4	-	15	5971	c.5763G>A	c.(5761-5763)ctG>ctA	p.L1921L	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Silent_p.L1921L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1921	PKD 15. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CGCCGACCTGCAGGCGGAAGG	0.697													c|||	60	0.0119808	0.0008	0.0159	5008	,	,		15667	0.0		0.0467	False		,,,				2504	0.001				p.L1921L		Atlas-SNP	.											.	PKD1	184	.	0			c.G5763A						PASS	.	C	,	39,4067		0,39,2014	9.0	12.0	11.0		5763,5763	-1.0	0.7	16	dbSNP_100	11	387,7875		7,373,3751	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	7,412,5765	TT,TC,CC		4.6841,0.9498,3.4444	,	1921/4303,1921/4304	2159405	426,11942	2053	4131	6184	SO:0001819	synonymous_variant	5310	exon15			GACCTGCAGGCGG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.5763G>A	16.37:g.2159405C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	10	6	0.6	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			C|0.977;T|0.023	0.023	strong		0.697	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
CLLU1	574028	hgsc.bcm.edu	37	12	92818482	92818482	+	Missense_Mutation	SNP	C	C	T	rs12580153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:92818482C>T	ENST00000378485.1	+	1	748	c.26C>T	c.(25-27)tCc>tTc	p.S9F	CLLU1_ENST00000472839.2_Intron|CLLU1OS_ENST00000378487.2_Intron|RP11-693J15.4_ENST00000508671.1_RNA|CLLU1OS_ENST00000538965.1_Intron	NM_001025233.1	NP_001020404.1	Q5K131	CLLU1_HUMAN	chronic lymphocytic leukemia up-regulated 1	9			S -> F (in dbSNP:rs12580153).			cytoplasm (GO:0005737)				NS(1)|breast(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	7						TCCTTTCATTCCTCTATTTAC	0.378													C|||	820	0.163738	0.0658	0.1787	5008	,	,		16184	0.1379		0.2793	False		,,,				2504	0.1933				p.S9F		Atlas-SNP	.											.	CLLU1	12	.	0			c.C26T						PASS	.	C	,PHE/SER	325,3321		15,295,1513	34.0	31.0	32.0		,26	0.2	0.0	12	dbSNP_120	32	2191,5975		306,1579,2198	yes	intron,missense	CLLU1OS,CLLU1	NM_001025232.1,NM_001025233.1	,155	321,1874,3711	TT,TC,CC		26.8308,8.9139,21.3004	,	,9/122	92818482	2516,9296	1823	4083	5906	SO:0001583	missense	574028	exon1			TTCATTCCTCTAT	AJ845162		12q22	2012-04-19			ENSG00000257127	ENSG00000257127			29841	protein-coding gene	gene with protein product						19726446	Standard	NR_027932		Approved		uc001tcg.1	Q5K131	OTTHUMG00000170103	ENST00000378485.1:c.26C>T	12.37:g.92818482C>T	ENSP00000367746:p.Ser9Phe	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_001025233		Missense_Mutation	SNP	ENST00000378485.1	37		407	0.18635531135531136	43	0.08739837398373984	74	0.20441988950276244	84	0.14685314685314685	206	0.2717678100263852	C	2.161	-0.392163	0.04932	0.089139	0.268308	ENSG00000257127	ENST00000378485	T	0.51071	0.72	2.22	0.23	0.15372	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.28586	-1.0039	6	0.87932	D	0	.	2.7444	0.05263	0.2754:0.5574:0.0:0.1671	rs12580153;rs17790214;rs60279934;rs12580153	.	.	.	F	9	ENSP00000367746:S9F	ENSP00000367746:S9F	S	+	2	0	AC063949.1	91342613	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.423000	0.07034	0.039000	0.15632	-0.149000	0.13747	TCC	C|0.805;T|0.195	0.195	strong		0.378	CLLU1-003	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000366643.1	NM_001025233	
XRCC4	7518	hgsc.bcm.edu	37	5	82491674	82491674	+	Missense_Mutation	SNP	T	T	C	rs28360135	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:82491674T>C	ENST00000511817.1	+	4	481	c.401T>C	c.(400-402)aTt>aCt	p.I134T	XRCC4_ENST00000282268.3_Missense_Mutation_p.I134T|XRCC4_ENST00000509268.1_3'UTR|XRCC4_ENST00000338635.6_Missense_Mutation_p.I134T|XRCC4_ENST00000396027.4_Missense_Mutation_p.I134T			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	134			I -> T (in dbSNP:rs28360135). {ECO:0000269|Ref.6}.		cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		TTGGACACCATTGCAGAAAAT	0.383								Non-homologous end-joining					T|||	72	0.014377	0.0015	0.0288	5008	,	,		16080	0.0		0.0348	False		,,,				2504	0.0153				p.I134T		Atlas-SNP	.											.	XRCC4	37	.	0			c.T401C	GRCh37	CM067727	XRCC4	M	rs28360135	PASS	.	T	THR/ILE,THR/ILE,THR/ILE	42,4364	44.6+/-78.6	0,42,2161	76.0	77.0	77.0		401,401,401	5.6	0.8	5	dbSNP_125	77	349,8251	117.7+/-177.3	5,339,3956	yes	missense,missense,missense	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	89,89,89	5,381,6117	CC,CT,TT		4.0581,0.9532,3.0063	benign,benign,benign	134/335,134/337,134/335	82491674	391,12615	2203	4300	6503	SO:0001583	missense	7518	exon4			ACACCATTGCAGA	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.401T>C	5.37:g.82491674T>C	ENSP00000421491:p.Ile134Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	119	70	0.588235	NM_003401	A8K3X4|Q9BS72|Q9UP94	Missense_Mutation	SNP	ENST00000511817.1	37	CCDS4059.1	36	0.016483516483516484	0	0.0	16	0.04419889502762431	0	0.0	20	0.026385224274406333	T	16.23	3.064029	0.55432	0.009532	0.040581	ENSG00000152422	ENST00000282268;ENST00000338635;ENST00000396027;ENST00000511817	T;T;T;T	0.12039	2.72;2.72;2.72;2.72	5.56	5.56	0.83823	DNA double-strand break repair and VJ recombination XRCC4, C-terminal (1);	0.265189	0.37437	N	0.002090	T	0.03783	0.0107	L	0.43757	1.38	0.27800	N	0.942505	P;D;P	0.53745	0.953;0.962;0.699	B;P;P	0.51615	0.407;0.675;0.465	T	0.05818	-1.0862	10	0.13108	T	0.6	.	10.1016	0.42509	0.0:0.076:0.0:0.924	rs28360135;rs28360135	134;134;134	Q13426-2;Q13426;Q13426-3	.;XRCC4_HUMAN;.	T	134	ENSP00000282268:I134T;ENSP00000342011:I134T;ENSP00000379344:I134T;ENSP00000421491:I134T	ENSP00000282268:I134T	I	+	2	0	XRCC4	82527430	0.992000	0.36948	0.836000	0.33094	0.918000	0.54935	2.552000	0.45828	2.238000	0.73509	0.477000	0.44152	ATT	T|0.973;C|0.027	0.027	strong		0.383	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	
BSN	8927	hgsc.bcm.edu	37	3	49688155	49688155	+	Silent	SNP	C	C	T	rs139787101	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49688155C>T	ENST00000296452.4	+	4	1743	c.1629C>T	c.(1627-1629)gcC>gcT	p.A543A		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	543					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CTGTAGGGGCCCCTCACCGTG	0.672													C|||	11	0.00219649	0.0008	0.0014	5008	,	,		13139	0.0		0.0089	False		,,,				2504	0.0				p.A543A		Atlas-SNP	.											.	BSN	272	.	0			c.C1629T						PASS	.	C		8,4394		0,8,2193	59.0	73.0	68.0		1629	1.4	1.0	3	dbSNP_134	68	82,8516		0,82,4217	no	coding-synonymous	BSN	NM_003458.3		0,90,6410	TT,TC,CC		0.9537,0.1817,0.6923		543/3927	49688155	90,12910	2201	4299	6500	SO:0001819	synonymous_variant	8927	exon4			AGGGGCCCCTCAC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.1629C>T	3.37:g.49688155C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	159	78	0.490566	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			C|0.994;T|0.006	0.006	strong		0.672	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
H1FOO	132243	hgsc.bcm.edu	37	3	129262077	129262077	+	Missense_Mutation	SNP	G	G	A	rs118098064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129262077G>A	ENST00000324382.2	+	1	21	c.16G>A	c.(16-18)Gtc>Atc	p.V6I		NM_153833.1	NP_722575.1	Q8IZA3	H1FOO_HUMAN	H1 histone family, member O, oocyte-specific	6					meiotic nuclear division (GO:0007126)|negative regulation of stem cell differentiation (GO:2000737)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of DNA methylation (GO:0044030)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|female germ cell nucleus (GO:0001674)|nucleosome (GO:0000786)|nucleus (GO:0005634)	nucleosomal DNA binding (GO:0031492)			endometrium(1)|lung(4)|skin(1)	6						TCCTGGGAGCGTCACCAGCGA	0.612													G|||	426	0.0850639	0.0219	0.0461	5008	,	,		17169	0.2173		0.002	False		,,,				2504	0.1472				p.V6I		Atlas-SNP	.											.	H1FOO	20	.	0			c.G16A						PASS	.	G	ILE/VAL	58,4348	55.5+/-91.7	0,58,2145	80.0	59.0	66.0		16	0.7	0.0	3	dbSNP_132	66	41,8559	25.7+/-73.6	0,41,4259	yes	missense	H1FOO	NM_153833.1	29	0,99,6404	AA,AG,GG		0.4767,1.3164,0.7612	benign	6/347	129262077	99,12907	2203	4300	6503	SO:0001583	missense	132243	exon1			GGGAGCGTCACCA	AY158091	CCDS3064.1	3q21.3	2011-01-27			ENSG00000178804	ENSG00000178804		"""Histones / Replication-independent"""	18463	protein-coding gene	gene with protein product						12408966	Standard	NM_153833		Approved		uc003emu.3	Q8IZA3	OTTHUMG00000159541	ENST00000324382.2:c.16G>A	3.37:g.129262077G>A	ENSP00000319799:p.Val6Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	151	69	0.456954	NM_153833	Q86WT7	Missense_Mutation	SNP	ENST00000324382.2	37	CCDS3064.1	172	0.07875457875457875	18	0.036585365853658534	20	0.055248618784530384	133	0.23251748251748253	1	0.0013192612137203166	G	11.22	1.574957	0.28092	0.013164	0.004767	ENSG00000178804	ENST00000324382	T	0.48522	0.81	3.46	0.688	0.18027	.	1.526110	0.04283	N	0.344254	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.29612	0.251	B	0.18561	0.022	T	0.11591	-1.0581	9	0.56958	D	0.05	-0.6684	5.6342	0.17528	0.3619:0.0:0.6381:0.0	.	6	Q8IZA3	H1FOO_HUMAN	I	6	ENSP00000319799:V6I	ENSP00000319799:V6I	V	+	1	0	H1FOO	130744767	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-2.439000	0.01016	0.131000	0.18576	-0.291000	0.09656	GTC	G|0.971;A|0.029	0.029	strong		0.612	H1FOO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356100.3	NM_153833	
SULT1A2	6799	hgsc.bcm.edu	37	16	28603655	28603655	+	Missense_Mutation	SNP	T	T	G	rs1059491	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28603655T>G	ENST00000395630.1	-	7	1054	c.704A>C	c.(703-705)aAc>aCc	p.N235T	SULT1A2_ENST00000335715.4_Missense_Mutation_p.N235T|SULT1A2_ENST00000533150.1_Missense_Mutation_p.N202T	NM_177528.2	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2	235			N -> T (in dbSNP:rs1059491). {ECO:0000269|PubMed:10762004, ECO:0000269|PubMed:8697101, ECO:0000269|PubMed:8912648, ECO:0000269|PubMed:9119390}.		3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine biosynthetic process (GO:0009309)|catecholamine metabolic process (GO:0006584)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|sulfotransferase activity (GO:0008146)			NS(2)|breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|skin(2)	14						GGTCATAGGGTTCTTCTTCAT	0.567													.|||	1126	0.22484	0.2209	0.3977	5008	,	,		18966	0.0744		0.3171	False		,,,				2504	0.1677				p.N235T		Atlas-SNP	.											SULT1A2,lymph_node,lymphoid_neoplasm,0,1	SULT1A2	27	1	0			c.A704C						scavenged	.	T	THR/ASN,THR/ASN	1083,3311	390.0+/-327.5	145,793,1259	224.0	198.0	207.0		704,704	5.0	1.0	16	dbSNP_86	207	3103,5497	474.1+/-368.8	573,1957,1770	yes	missense,missense	SULT1A2	NM_001054.3,NM_177528.2	65,65	718,2750,3029	GG,GT,TT		36.0814,24.6472,32.2149	probably-damaging,probably-damaging	235/296,235/296	28603655	4186,8808	2197	4300	6497	SO:0001583	missense	6799	exon7			ATAGGGTTCTTCT	U34804	CCDS10636.1	16p12.1	2008-02-05			ENSG00000197165	ENSG00000197165	2.8.2.1	"""Sulfotransferases, cytosolic"""	11454	protein-coding gene	gene with protein product		601292		STP2		8661000, 8912648	Standard	NM_001054		Approved	HAST4	uc002dqh.2	P50226	OTTHUMG00000048082	ENST00000395630.1:c.704A>C	16.37:g.28603655T>G	ENSP00000378992:p.Asn235Thr	Somatic	203	5	0.0246305		WXS	Illumina HiSeq	Phase_I	285	141	0.494737	NM_001054	A9QY25|P78393|Q14CJ7	Missense_Mutation	SNP	ENST00000395630.1	37	CCDS10636.1	527	0.2413003663003663	106	0.21544715447154472	117	0.32320441988950277	53	0.09265734265734266	251	0.3311345646437995	t	20.2	3.950088	0.73787	0.246472	0.360814	ENSG00000197165	ENST00000533150;ENST00000335715;ENST00000395630	T;T;T	0.02103	4.45;4.45;4.45	4.98	4.98	0.66077	Sulfotransferase domain (1);	0.068979	0.64402	D	0.000019	T	0.00012	0.0000	M	0.86502	2.82	0.29114	P	0.880686	D	0.89917	1.0	D	0.97110	1.0	T	0.42599	-0.9442	9	0.72032	D	0.01	.	12.659	0.56803	0.0:0.0:0.0:1.0	rs1059491;rs3174702;rs16940488	235	P50226	ST1A2_HUMAN	T	202;235;235	ENSP00000435271:N202T;ENSP00000338742:N235T;ENSP00000378992:N235T	ENSP00000338742:N235T	N	-	2	0	SULT1A2	28511156	1.000000	0.71417	0.997000	0.53966	0.624000	0.37722	7.957000	0.87870	1.864000	0.54056	0.374000	0.22700	AAC	T|0.705;G|0.295	0.295	strong		0.567	SULT1A2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109415.2	NM_001054	
CCT5	22948	hgsc.bcm.edu	37	5	10254817	10254817	+	Silent	SNP	A	A	G	rs2578617	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:10254817A>G	ENST00000280326.4	+	3	618	c.198A>G	c.(196-198)ggA>ggG	p.G66G	CCT5_ENST00000506600.1_Intron|CCT5_ENST00000515390.1_Intron|CCT5_ENST00000515676.1_Silent_p.G28G|CCT5_ENST00000503026.1_Silent_p.G45G	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	66					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						ATAAGGATGGAGATGTGACTG	0.413													A|||	3435	0.685903	0.388	0.7752	5008	,	,		20357	0.879		0.8539	False		,,,				2504	0.6534				p.G66G		Atlas-SNP	.											.	CCT5	49	.	0			c.A198G						PASS	.	A		1995,2411	559.2+/-380.2	451,1093,659	166.0	145.0	152.0		198	-9.3	0.2	5	dbSNP_100	152	7352,1248	761.4+/-407.6	3140,1072,88	no	coding-synonymous	CCT5	NM_012073.3		3591,2165,747	GG,GA,AA		14.5116,45.2792,28.1332		66/542	10254817	9347,3659	2203	4300	6503	SO:0001819	synonymous_variant	22948	exon3			GGATGGAGATGTG	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"""Heat Shock Proteins / Chaperonins"""	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.198A>G	5.37:g.10254817A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_012073	A8JZY8|A8K2X8|B4DYD8	Silent	SNP	ENST00000280326.4	37	CCDS3877.1																																																																																			A|0.264;G|0.736	0.736	strong		0.413	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2		
TOX4	9878	hgsc.bcm.edu	37	14	21960816	21960816	+	Silent	SNP	T	T	C	rs1060722	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21960816T>C	ENST00000405508.1	+	8	1317	c.1041T>C	c.(1039-1041)ctT>ctC	p.L347L	TOX4_ENST00000262709.3_Silent_p.L347L|TOX4_ENST00000448790.2_Silent_p.L324L			O94842	TOX4_HUMAN	TOX high mobility group box family member 4	347						chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)			large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		ACTCCACCCTTTCATCCTATG	0.493													T|||	2482	0.495607	0.4281	0.3746	5008	,	,		18322	0.6488		0.503	False		,,,				2504	0.5072				p.L347L		Atlas-SNP	.											.	TOX4	50	.	0			c.T1041C						PASS	.	T		2066,2340	570.7+/-382.9	476,1114,613	114.0	116.0	116.0		1041	1.4	1.0	14	dbSNP_86	116	4318,4282	578.9+/-390.8	1124,2070,1106	no	coding-synonymous	TOX4	NM_014828.2		1600,3184,1719	CC,CT,TT		49.7907,46.8906,49.085		347/622	21960816	6384,6622	2203	4300	6503	SO:0001819	synonymous_variant	9878	exon7			CACCCTTTCATCC	AB018280	CCDS32043.1	14q11.2	2007-03-20	2007-03-20	2007-03-20	ENSG00000092203	ENSG00000092203			20161	protein-coding gene	gene with protein product		614032	"""chromosome 14 open reading frame 92"", ""KIAA0737"""	C14orf92, KIAA0737			Standard	NM_014828		Approved	LCP1	uc001waz.3	O94842	OTTHUMG00000150278	ENST00000405508.1:c.1041T>C	14.37:g.21960816T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_014828	B4DPY8|B4DSM0|E7EV69	Silent	SNP	ENST00000405508.1	37	CCDS32043.1																																																																																			T|0.514;C|0.486	0.486	strong		0.493	TOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317287.2	NM_014828	
CDH12	1010	hgsc.bcm.edu	37	5	21752050	21752050	+	Silent	SNP	A	A	G	rs6451992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:21752050A>G	ENST00000382254.1	-	15	3267	c.2181T>C	c.(2179-2181)gaT>gaC	p.D727D	RP11-804N13.1_ENST00000522350.1_RNA|CDH12_ENST00000522262.1_Silent_p.D687D|CDH12_ENST00000504376.2_Silent_p.D727D|CDH12_ENST00000521384.1_5'UTR	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	727					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D727D(1)		NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						GGGCAGTTGGATCCACATCAT	0.493										HNSCC(59;0.17)			G|||	2748	0.548722	0.3782	0.6268	5008	,	,		15734	0.4355		0.7475	False		,,,				2504	0.636				p.D727D		Atlas-SNP	.											CDH12,NS,carcinoma,0,1	CDH12	238	1	1	Substitution - coding silent(1)	stomach(1)	c.T2181C						scavenged	.	G		2006,2400	614.5+/-392.4	454,1098,651	243.0	207.0	219.0		2181	0.3	0.6	5	dbSNP_116	219	6327,2273	383.0+/-340.6	2333,1661,306	no	coding-synonymous	CDH12	NM_004061.3		2787,2759,957	GG,GA,AA		26.4302,45.5288,35.9296		727/795	21752050	8333,4673	2203	4300	6503	SO:0001819	synonymous_variant	1010	exon15			AGTTGGATCCACA	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"""Cadherins / Major cadherins"""	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.2181T>C	5.37:g.21752050A>G		Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	221	103	0.466063	NM_004061	B2RBT1|B7Z2U6|Q86UD2	Silent	SNP	ENST00000382254.1	37	CCDS3890.1																																																																																			A|0.382;G|0.618	0.618	strong		0.493	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061	
CCDC9	26093	hgsc.bcm.edu	37	19	47770032	47770032	+	Silent	SNP	C	C	T	rs60383222	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:47770032C>T	ENST00000221922.6	+	8	1107	c.885C>T	c.(883-885)gcC>gcT	p.A295A		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	295							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		AGTGGGATGCCGAGAAGACCG	0.617													C|||	694	0.138578	0.1278	0.0865	5008	,	,		15709	0.0754		0.1471	False		,,,				2504	0.2464				p.A295A		Atlas-SNP	.											.	CCDC9	37	.	0			c.C885T						PASS	.	C		521,3881		34,453,1714	45.0	33.0	37.0		885	-8.6	0.1	19	dbSNP_129	37	1312,7288		110,1092,3098	no	coding-synonymous	CCDC9	NM_015603.2		144,1545,4812	TT,TC,CC		15.2558,11.8355,14.0978		295/532	47770032	1833,11169	2201	4300	6501	SO:0001819	synonymous_variant	26093	exon8			GGATGCCGAGAAG	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.885C>T	19.37:g.47770032C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	146	48	0.328767	NM_015603		Silent	SNP	ENST00000221922.6	37	CCDS12698.1																																																																																			C|0.880;T|0.120	0.120	strong		0.617	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
PRSS54	221191	hgsc.bcm.edu	37	16	58327646	58327646	+	Silent	SNP	A	A	G	rs2288012	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:58327646A>G	ENST00000219301.4	-	3	469	c.75T>C	c.(73-75)taT>taC	p.Y25Y	PRSS54_ENST00000567164.1_Silent_p.Y25Y|PRSS54_ENST00000543437.1_5'UTR	NM_001080492.1	NP_001073961.1	Q6PEW0	PRS54_HUMAN	protease, serine, 54	25						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.Y25Y(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TGGTGGAAGAATAGAGAAGGC	0.572													G|||	3673	0.733427	0.9115	0.6167	5008	,	,		17036	0.631		0.7773	False		,,,				2504	0.636				p.Y25Y		Atlas-SNP	.											PRSS54,NS,carcinoma,0,1	PRSS54	48	1	1	Substitution - coding silent(1)	stomach(1)	c.T75C						PASS	.	G		3899,497	224.3+/-240.5	1736,427,35	94.0	66.0	75.0		75	-0.2	0.0	16	dbSNP_100	75	6669,1931	333.7+/-320.7	2607,1455,238	no	coding-synonymous	PRSS54	NM_001080492.1		4343,1882,273	GG,GA,AA		22.4535,11.3057,18.6827		25/396	58327646	10568,2428	2198	4300	6498	SO:0001819	synonymous_variant	221191	exon3			GGAAGAATAGAGA	AK058068	CCDS32463.1	16q21	2010-05-07			ENSG00000103023	ENSG00000103023		"""Serine peptidases / Serine peptidases"""	26336	protein-coding gene	gene with protein product	"""cancer/testis antigen 67"""					17521433	Standard	NM_001080492		Approved	FLJ25339, KLKBL4, CT67	uc002enf.3	Q6PEW0		ENST00000219301.4:c.75T>C	16.37:g.58327646A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_001080492	Q96LN9|Q9NT77	Silent	SNP	ENST00000219301.4	37	CCDS32463.1																																																																																			A|0.224;G|0.776	0.776	strong		0.572	PRSS54-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422556.1	NM_001080492	
HIVEP3	59269	hgsc.bcm.edu	37	1	42046613	42046613	+	Silent	SNP	G	G	T	rs12132697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:42046613G>T	ENST00000372583.1	-	4	4741	c.3856C>A	c.(3856-3858)Cgg>Agg	p.R1286R	HIVEP3_ENST00000372584.1_Silent_p.R1286R|HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000429157.2_Silent_p.R1286R|HIVEP3_ENST00000247584.5_Silent_p.R1286R	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1286					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GGGGGTAGCCGGATGTCACTG	0.617													G|||	607	0.121206	0.0204	0.1311	5008	,	,		17803	0.0446		0.2505	False		,,,				2504	0.1963				p.R1286R		Atlas-SNP	.											HIVEP3,NS,carcinoma,0,1	HIVEP3	235	1	0			c.C3856A						scavenged	.	G	,	275,4131	151.8+/-185.6	13,249,1941	44.0	47.0	46.0		3856,3856	5.2	0.4	1	dbSNP_120	46	2176,6424	368.8+/-335.2	297,1582,2421	no	coding-synonymous,coding-synonymous	HIVEP3	NM_001127714.2,NM_024503.4	,	310,1831,4362	TT,TG,GG		25.3023,6.2415,18.8451	,	1286/2406,1286/2407	42046613	2451,10555	2203	4300	6503	SO:0001819	synonymous_variant	59269	exon4			GTAGCCGGATGTC	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.3856C>A	1.37:g.42046613G>T		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	89	49	0.550562	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																			G|0.838;T|0.162	0.162	strong		0.617	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
CNTROB	116840	hgsc.bcm.edu	37	17	7847955	7847955	+	Splice_Site	SNP	C	C	A	rs11650083	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7847955C>A	ENST00000563694.1	+	12	2658	c.1733C>A	c.(1732-1734)cCa>cAa	p.P578Q	CNTROB_ENST00000565740.1_Splice_Site_p.P578Q|CNTROB_ENST00000380255.3_Intron|CNTROB_ENST00000380262.3_Splice_Site_p.P578Q	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	578	Pro-rich.|Required for centrosome localization.		P -> Q (in dbSNP:rs11650083). {ECO:0000269|PubMed:11984006, ECO:0000269|PubMed:14702039}.		centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				CCCAACCCTCCAGTACGCCTT	0.557													C|||	3028	0.604633	0.447	0.6614	5008	,	,		4301	0.8016		0.4493	False		,,,				2504	0.7342				p.P578Q		Atlas-SNP	.											CNTROB,colon,carcinoma,0,1	CNTROB	61	1	0			c.C1733A						PASS	.	C	GLN/PRO,GLN/PRO	2082,2324	571.4+/-383.1	501,1080,622	99.0	91.0	94.0		1733,1733	-2.4	0.0	17	dbSNP_120	94	3952,4648	547.5+/-385.2	914,2124,1262	yes	missense-near-splice,missense-near-splice	CNTROB	NM_001037144.5,NM_053051.3	76,76	1415,3204,1884	AA,AC,CC		45.9535,47.2537,46.394	benign,benign	578/926,578/904	7847955	6034,6972	2203	4300	6503	SO:0001630	splice_region_variant	116840	exon12			ACCCTCCAGTACG	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.1734+1C>A	17.37:g.7847955C>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	29	0.386667	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Missense_Mutation	SNP	ENST00000563694.1	37	CCDS11126.1	1225	0.5608974358974359	234	0.47560975609756095	220	0.6077348066298343	424	0.7412587412587412	347	0.4577836411609499	C	8.908	0.957899	0.18507	0.472537	0.459535	ENSG00000170037	ENST00000380262	T	0.38077	1.16	4.56	-2.37	0.06643	.	1.024840	0.07770	N	0.951533	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B;B	0.12013	0.001;0.001;0.005	B;B;B	0.12156	0.001;0.001;0.007	T	0.40757	-0.9546	9	0.10902	T	0.67	-1.0583	4.5619	0.12165	0.5422:0.2684:0.0:0.1895	rs11650083;rs52795073;rs57150255;rs11650083	578;578;578	Q8N137-3;Q8N137;Q8N137-2	.;CNTRB_HUMAN;.	Q	578	ENSP00000369614:P578Q	ENSP00000369614:P578Q	P	+	2	0	CNTROB	7788680	0.021000	0.18746	0.002000	0.10522	0.010000	0.07245	-0.104000	0.10923	-0.113000	0.11958	0.561000	0.74099	CCA	C|0.491;A|0.509	0.509	strong		0.557	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	Missense_Mutation
MAPK1IP1L	93487	hgsc.bcm.edu	37	14	55529860	55529860	+	Silent	SNP	A	A	G	rs17851309	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:55529860A>G	ENST00000395468.4	+	3	720	c.543A>G	c.(541-543)caA>caG	p.Q181Q		NM_144578.3	NP_653179.1	Q8NDC0	MISSL_HUMAN	mitogen-activated protein kinase 1 interacting protein 1-like	181	Pro-rich.									endometrium(2)|large_intestine(1)|lung(3)	6						CTCCTCCCCAAGCCCCTGGGG	0.612													A|||	199	0.0397364	0.0484	0.0346	5008	,	,		17398	0.0069		0.0398	False		,,,				2504	0.0654				p.Q181Q		Atlas-SNP	.											.	MAPK1IP1L	14	.	0			c.A543G						PASS	.	A		188,4218		8,172,2023	57.0	55.0	55.0		543	1.4	1.0	14	dbSNP_123	55	345,8255		10,325,3965	no	coding-synonymous	MAPK1IP1L	NM_144578.3		18,497,5988	GG,GA,AA		4.0116,4.2669,4.0981		181/246	55529860	533,12473	2203	4300	6503	SO:0001819	synonymous_variant	93487	exon3			TCCCCAAGCCCCT	AK025580	CCDS32085.1	14q22.1	2008-01-30	2008-01-30	2008-01-16		ENSG00000168175			19840	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 32"", ""mitogen activated protein kinase 1 interacting protein 1-like"""	C14orf32		12011110	Standard	NM_144578		Approved		uc001xbq.1	Q8NDC0		ENST00000395468.4:c.543A>G	14.37:g.55529860A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	137	69	0.50365	NM_144578	B2RDD8|Q96BG5	Silent	SNP	ENST00000395468.4	37	CCDS32085.1																																																																																			A|0.960;G|0.040	0.040	strong		0.612	MAPK1IP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411302.2	NM_144578	
SLC4A7	9497	hgsc.bcm.edu	37	3	27472936	27472936	+	Missense_Mutation	SNP	C	C	T	rs3755652	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:27472936C>T	ENST00000295736.5	-	7	1046	c.976G>A	c.(976-978)Gag>Aag	p.E326K	SLC4A7_ENST00000440156.1_Missense_Mutation_p.E322K|SLC4A7_ENST00000428386.1_Intron|SLC4A7_ENST00000445684.1_Missense_Mutation_p.E322K|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000454389.1_Missense_Mutation_p.E335K|SLC4A7_ENST00000425128.2_Missense_Mutation_p.E318K|SLC4A7_ENST00000446700.1_Missense_Mutation_p.E318K|SLC4A7_ENST00000435667.2_Intron|SLC4A7_ENST00000455077.1_Intron|SLC4A7_ENST00000437179.1_Intron	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	326			E -> K (in dbSNP:rs3755652). {ECO:0000269|PubMed:10347222, ECO:0000269|Ref.4}.		auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CGCTGACTCTCTTGGGAACTT	0.542													c|||	647	0.129193	0.0461	0.1643	5008	,	,		15813	0.0565		0.2266	False		,,,				2504	0.1912				p.E326K		Atlas-SNP	.											.	SLC4A7	119	.	0			c.G976A						PASS	.	C	LYS/GLU	359,4047	184.3+/-211.7	10,339,1854	108.0	113.0	111.0		976	5.1	0.8	3	dbSNP_107	111	2159,6441	369.3+/-335.4	270,1619,2411	yes	missense	SLC4A7	NM_003615.3	56	280,1958,4265	TT,TC,CC		25.1047,8.148,19.3603	benign	326/1215	27472936	2518,10488	2203	4300	6503	SO:0001583	missense	9497	exon7			GACTCTCTTGGGA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.976G>A	3.37:g.27472936C>T	ENSP00000295736:p.Glu326Lys	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	218	217	0.995413	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	276	0.12637362637362637	21	0.042682926829268296	70	0.19337016574585636	19	0.033216783216783216	166	0.21899736147757257	c	4.815	0.151530	0.09185	0.08148	0.251047	ENSG00000033867	ENST00000295736;ENST00000454389;ENST00000440156;ENST00000446700;ENST00000445684;ENST00000425128	T;T;T;T;T;T	0.77489	-1.01;-1.02;-1.1;-1.1;-1.1;0.42	5.98	5.12	0.69794	Bicarbonate transporter, cytoplasmic (1);	0.315954	0.28284	N	0.015915	T	0.00039	0.0001	N	0.11560	0.145	0.38427	P	0.053651000000000004	B;B;B;B;B	0.15141	0.012;0.012;0.012;0.012;0.005	B;B;B;B;B	0.21917	0.037;0.037;0.037;0.037;0.025	T	0.03576	-1.1023	9	0.06757	T	0.87	.	15.793	0.78380	0.0:0.2578:0.7422:0.0	rs3755652;rs17682585;rs56593324;rs57811624;rs3755652	322;318;322;335;326	E9PFN4;E9PGC1;B5M453;E9PDL9;Q9Y6M7	.;.;.;.;S4A7_HUMAN	K	326;335;322;318;322;318	ENSP00000295736:E326K;ENSP00000390394:E335K;ENSP00000414797:E322K;ENSP00000406605:E318K;ENSP00000406804:E322K;ENSP00000401949:E318K	ENSP00000295736:E326K	E	-	1	0	SLC4A7	27447940	0.996000	0.38824	0.793000	0.32043	0.844000	0.47949	2.454000	0.44979	1.560000	0.49568	-0.191000	0.12829	GAG	C|0.843;T|0.157	0.157	strong		0.542	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
SIVA1	10572	hgsc.bcm.edu	37	14	105222037	105222037	+	Silent	SNP	C	C	T	rs1132975	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105222037C>T	ENST00000329967.6	+	2	291	c.189C>T	c.(187-189)gcC>gcT	p.A63A	SIVA1_ENST00000347067.5_Intron	NM_006427.3	NP_006418.2	O15304	SIVA_HUMAN	SIVA1, apoptosis-inducing factor	63					activation-induced cell death of T cells (GO:0006924)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	CD27 receptor binding (GO:0005175)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|prostate(1)	3		all_cancers(154;0.14)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.173)		AAGGCTGTGCCGTCGTTCACC	0.622													C|||	2170	0.433307	0.2398	0.5014	5008	,	,		18850	0.624		0.34	False		,,,				2504	0.546				p.A63A		Atlas-SNP	.											.	SIVA1	12	.	0			c.C189T						PASS	.	C	,	1189,3217	416.5+/-337.6	169,851,1183	79.0	76.0	77.0		189,	0.0	0.0	14	dbSNP_86	77	2917,5683	455.5+/-363.8	501,1915,1884	no	coding-synonymous,intron	SIVA1	NM_006427.3,NM_021709.2	,	670,2766,3067	TT,TC,CC		33.9186,26.9859,31.57	,	63/176,	105222037	4106,8900	2203	4300	6503	SO:0001819	synonymous_variant	10572	exon2			CTGTGCCGTCGTT	U82938	CCDS9992.1, CCDS9993.1	14q32.33	2007-03-19							17712	protein-coding gene	gene with protein product		605567				9177220	Standard	NM_006427		Approved	SIVA, Siva-1, Siva-2, CD27BP	uc001yph.3	O15304		ENST00000329967.6:c.189C>T	14.37:g.105222037C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_006427	Q96P98|Q9UPD6	Silent	SNP	ENST00000329967.6	37	CCDS9992.1	905	0.4143772893772894	140	0.2845528455284553	168	0.46408839779005523	345	0.6031468531468531	252	0.3324538258575198	C	8.528	0.870369	0.17322	0.269859	0.339186	ENSG00000184990	ENST00000556195	.	.	.	5.03	0.00199	0.14048	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47341	P	6.099999999999994E-4	.	.	.	.	.	.	T	0.46498	-0.9187	3	.	.	.	-12.2268	8.0122	0.30359	0.0:0.5495:0.0:0.4505	rs1132975;rs3194340;rs3803306;rs59682710;rs1132975	.	.	.	L	81	.	.	P	+	2	0	SIVA1	104293082	0.000000	0.05858	0.002000	0.10522	0.873000	0.50193	-0.220000	0.09215	-0.046000	0.13446	-0.251000	0.11542	CCG	C|0.646;T|0.354	0.354	strong		0.622	SIVA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410541.1	NM_006427	
SNX19	399979	hgsc.bcm.edu	37	11	130784488	130784488	+	Silent	SNP	A	A	G	rs61734874	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130784488A>G	ENST00000265909.4	-	1	1916	c.1347T>C	c.(1345-1347)atT>atC	p.I449I	SNX19_ENST00000533318.1_Intron|SNX19_ENST00000533214.1_Silent_p.I449I|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000530356.1_Intron|SNX19_ENST00000539184.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	449					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		CTGCTGTGTCAATATGGATCT	0.557													G|||	639	0.127596	0.0492	0.0893	5008	,	,		19499	0.1538		0.1988	False		,,,				2504	0.1605				p.I449I		Atlas-SNP	.											.	SNX19	84	.	0			c.T1347C						PASS	.	G		315,4087	797.4+/-415.4	15,285,1901	105.0	103.0	103.0		1347	-0.4	1.0	11	dbSNP_129	103	1788,6806	732.8+/-406.9	174,1440,2683	no	coding-synonymous	SNX19	NM_014758.2		189,1725,4584	GG,GA,AA		20.8052,7.1558,16.1819		449/993	130784488	2103,10893	2201	4297	6498	SO:0001819	synonymous_variant	399979	exon1			TGTGTCAATATGG	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1347T>C	11.37:g.130784488A>G		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	198	87	0.439394	NM_014758	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	37	CCDS31721.1																																																																																			A|0.842;G|0.158	0.158	strong		0.557	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
USP4	7375	hgsc.bcm.edu	37	3	49362369	49362369	+	Silent	SNP	C	C	T	rs56038006	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49362369C>T	ENST00000265560.4	-	5	637	c.591G>A	c.(589-591)aaG>aaA	p.K197K	USP4_ENST00000415188.1_Silent_p.K197K|USP4_ENST00000416417.1_Silent_p.K197K|USP4_ENST00000351842.4_Silent_p.K197K	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	197	Necessary for interaction with SART3. {ECO:0000269|PubMed:20595234}.|Ubiquitin-like 1.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.K197K(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		TGTTGTCTAGCTTGCTCAACT	0.557													C|||	461	0.0920527	0.0651	0.098	5008	,	,		21404	0.0546		0.1988	False		,,,				2504	0.0532				p.K197K		Atlas-SNP	.											USP4,NS,carcinoma,0,1	USP4	72	1	1	Substitution - coding silent(1)	stomach(1)	c.G591A						PASS	.	C	,	428,3978	208.2+/-229.3	17,394,1792	170.0	170.0	170.0		591,591	-0.3	0.3	3	dbSNP_129	170	1489,7111	283.7+/-296.3	130,1229,2941	no	coding-synonymous,coding-synonymous	USP4	NM_003363.3,NM_199443.2	,	147,1623,4733	TT,TC,CC		17.314,9.714,14.7394	,	197/964,197/917	49362369	1917,11089	2203	4300	6503	SO:0001819	synonymous_variant	7375	exon5			GTCTAGCTTGCTC	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"""Ubiquitin-specific peptidases"""	12627	protein-coding gene	gene with protein product		603486	"""ubiquitin specific protease 4 (proto-oncogene)"""	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.591G>A	3.37:g.49362369C>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	262	114	0.435115	NM_001251877	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	37	CCDS2793.1																																																																																			C|0.855;T|0.145	0.145	strong		0.557	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443	
C9orf129	445577	hgsc.bcm.edu	37	9	96097662	96097662	+	Missense_Mutation	SNP	G	G	A	rs4744219	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:96097662G>A	ENST00000375419.1	-	3	722	c.359C>T	c.(358-360)gCg>gTg	p.A120V		NM_001098808.1	NP_001092278.1	Q5T035	CI129_HUMAN	chromosome 9 open reading frame 129	120										endometrium(2)|large_intestine(1)|lung(1)|ovary(2)	6						TCACTTTGTCGCCCCTCCGCT	0.632													G|||	315	0.0628994	0.0219	0.0749	5008	,	,		18181	0.0337		0.1481	False		,,,				2504	0.0521				p.A120V		Atlas-SNP	.											.	C9orf129	18	.	0			c.C359T						PASS	.						14.0	16.0	15.0					9																	96097662		2197	4286	6483	SO:0001583	missense	445577	exon3			TTTGTCGCCCCTC		CCDS43850.1	9q22.31	2012-04-02			ENSG00000204352	ENSG00000204352			31116	protein-coding gene	gene with protein product							Standard	NM_001098808		Approved	bA165J3.3	uc010mre.3	Q5T035	OTTHUMG00000020248	ENST00000375419.1:c.359C>T	9.37:g.96097662G>A	ENSP00000364568:p.Ala120Val	Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	344	153	0.444767	NM_001098808		Missense_Mutation	SNP	ENST00000375419.1	37	CCDS43850.1	182	0.08333333333333333	14	0.028455284552845527	30	0.08287292817679558	22	0.038461538461538464	116	0.15303430079155672	G	13.09	2.132457	0.37630	.	.	ENSG00000204352	ENST00000375419	T	0.51325	0.71	2.56	2.56	0.30785	.	.	.	.	.	T	0.00178	0.0005	N	0.24115	0.695	0.35885	P	0.17073799999999995	P	0.39920	0.695	B	0.27500	0.08	T	0.12915	-1.0529	8	0.72032	D	0.01	.	13.5524	0.61740	0.0:0.0:1.0:0.0	rs4744219	120	Q5T035	CI129_HUMAN	V	120	ENSP00000364568:A120V	ENSP00000364568:A120V	A	-	2	0	C9orf129	95137483	1.000000	0.71417	0.993000	0.49108	0.423000	0.31445	7.245000	0.78237	1.438000	0.47492	0.298000	0.19748	GCG	.	.	weak		0.632	C9orf129-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053147.1	NM_001098808	
WRN	7486	hgsc.bcm.edu	37	8	30938704	30938704	+	Missense_Mutation	SNP	G	G	A	rs1800391	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:30938704G>A	ENST00000298139.5	+	9	1410	c.1161G>A	c.(1159-1161)atG>atA	p.M387I		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	387			M -> I (in dbSNP:rs1800391). {ECO:0000269|PubMed:10206685, ECO:0000269|PubMed:11161804, ECO:0000269|PubMed:9450180, ECO:0000269|Ref.4}.		aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		AAGAGAATATGGAAAGAGCTT	0.333			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				G|||	235	0.0469249	0.0015	0.0821	5008	,	,		20232	0.002		0.0765	False		,,,				2504	0.0992				p.M387I	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.G1161A						PASS	.	G	ILE/MET	67,4339	60.5+/-97.4	1,65,2137	108.0	111.0	110.0		1161	3.8	0.4	8	dbSNP_89	110	681,7919	171.4+/-222.4	34,613,3653	yes	missense	WRN	NM_000553.4	10	35,678,5790	AA,AG,GG		7.9186,1.5207,5.7512	benign	387/1433	30938704	748,12258	2203	4300	6503	SO:0001583	missense	7486	exon9	Familial Cancer Database	WS, Adult Progeria	GAATATGGAAAGA		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1161G>A	8.37:g.30938704G>A	ENSP00000298139:p.Met387Ile	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	194	83	0.427835	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	90	0.04120879120879121	3	0.006097560975609756	23	0.06353591160220995	1	0.0017482517482517483	63	0.08311345646437995	G	8.120	0.780662	0.16120	0.015207	0.079186	ENSG00000165392	ENST00000298139	T	0.43294	0.95	5.73	3.82	0.43975	.	1.819620	0.02116	N	0.055182	T	0.01940	0.0061	L	0.38175	1.15	0.09310	N	1	B	0.28233	0.204	B	0.21151	0.033	T	0.07195	-1.0785	10	0.24483	T	0.36	16.2097	5.6983	0.17867	0.4971:0.0:0.5029:0.0	rs1800391;rs17571733;rs52820535;rs57324259;rs1800391	387	Q14191	WRN_HUMAN	I	387	ENSP00000298139:M387I	ENSP00000298139:M387I	M	+	3	0	WRN	31058246	0.030000	0.19436	0.361000	0.25849	0.086000	0.17979	0.114000	0.15520	0.646000	0.30693	0.650000	0.86243	ATG	G|0.944;A|0.056	0.056	strong		0.333	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
COL4A2	1284	hgsc.bcm.edu	37	13	111121620	111121620	+	Missense_Mutation	SNP	C	C	T	rs9583500	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:111121620C>T	ENST00000360467.5	+	28	2458	c.2152C>T	c.(2152-2154)Ccc>Tcc	p.P718S		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	718	Triple-helical region.		P -> S (polymorphism that does not affect COL4A2 and COL4A1 secretion; dbSNP:rs9583500). {ECO:0000269|PubMed:21527998, ECO:0000269|PubMed:22209247}.		angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			AGGACCAGGGCCCAGGGGCTT	0.602													C|||	956	0.190895	0.3578	0.2176	5008	,	,		16522	0.0208		0.2167	False		,,,				2504	0.0951				p.P718S		Atlas-SNP	.											.	COL4A2	178	.	0			c.C2152T						PASS	.	C	SER/PRO	1150,2674		161,828,923	65.0	64.0	64.0		2152	5.6	1.0	13	dbSNP_119	64	1637,6601		154,1329,2636	yes	missense	COL4A2	NM_001846.2	74	315,2157,3559	TT,TC,CC		19.8713,30.0732,23.1056	probably-damaging	718/1713	111121620	2787,9275	1912	4119	6031	SO:0001583	missense	1284	exon28			CCAGGGCCCAGGG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.2152C>T	13.37:g.111121620C>T	ENSP00000353654:p.Pro718Ser	Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	182	176	0.967033	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	37	CCDS41907.1	418	0.19139194139194138	160	0.3252032520325203	83	0.2292817679558011	12	0.02097902097902098	163	0.21503957783641162	C	0.613	-0.824320	0.02755	0.300732	0.198713	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.94793	-3.52	5.57	5.57	0.84162	.	0.136981	0.33327	N	0.005022	T	0.00012	0.0000	M	0.66297	2.02	0.42507	P	0.007041999999999993	B	0.28400	0.21	B	0.28991	0.097	T	0.31971	-0.9924	9	0.08599	T	0.76	.	9.8067	0.40797	0.0:0.8463:0.0:0.1537	rs9583500;rs52830583;rs57845568;rs9583500	718	P08572	CO4A2_HUMAN	S	718	ENSP00000353654:P718S	ENSP00000257309:P718S	P	+	1	0	COL4A2	109919621	0.938000	0.31826	0.972000	0.41901	0.002000	0.02628	1.281000	0.33214	2.618000	0.88619	0.563000	0.77884	CCC	C|0.812;T|0.188	0.188	strong		0.602	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
STYK1	55359	hgsc.bcm.edu	37	12	10782115	10782115	+	Missense_Mutation	SNP	T	T	C	rs3759259	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:10782115T>C	ENST00000075503.3	-	6	1130	c.610A>G	c.(610-612)Agc>Ggc	p.S204G		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	204	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> G (in dbSNP:rs3759259). {ECO:0000269|PubMed:12841579, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.6}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						CAGAGAAAGCTGAGCAGGTCC	0.527										HNSCC(73;0.22)			T|||	2998	0.598642	0.3457	0.7032	5008	,	,		17885	0.7917		0.6431	False		,,,				2504	0.6217				p.S204G		Atlas-SNP	.											.	STYK1	55	.	0			c.A610G						PASS	.	T	GLY/SER	1674,2732	508.3+/-366.9	336,1002,865	55.0	45.0	49.0		610	5.6	1.0	12	dbSNP_107	49	5065,3535	631.7+/-398.5	1486,2093,721	yes	missense	STYK1	NM_018423.2	56	1822,3095,1586	CC,CT,TT		41.1047,37.9936,48.1855	benign	204/423	10782115	6739,6267	2203	4300	6503	SO:0001583	missense	55359	exon6			GAAAGCTGAGCAG	AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.610A>G	12.37:g.10782115T>C	ENSP00000075503:p.Ser204Gly	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_018423	B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Missense_Mutation	SNP	ENST00000075503.3	37	CCDS8629.1	1351	0.6185897435897436	173	0.3516260162601626	241	0.6657458563535912	451	0.7884615384615384	486	0.6411609498680739	T	10.93	1.490929	0.26774	0.379936	0.588953	ENSG00000060140	ENST00000075503	T	0.69806	-0.43	5.58	5.58	0.84498	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.427798	0.26369	N	0.024770	T	0.00012	0.0000	N	0.13371	0.34	0.46279	P	0.0010379999999999834	B	0.06786	0.001	B	0.14023	0.01	T	0.40701	-0.9549	9	0.62326	D	0.03	-8.2332	10.0973	0.42482	0.0:0.0:0.1684:0.8316	rs3759259;rs17809572;rs58022630;rs3759259	204	Q6J9G0	STYK1_HUMAN	G	204	ENSP00000075503:S204G	ENSP00000075503:S204G	S	-	1	0	STYK1	10673382	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.496000	0.53288	2.244000	0.73946	0.533000	0.62120	AGC	T|0.438;C|0.562	0.562	strong		0.527	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423	
RRP36	88745	hgsc.bcm.edu	37	6	42995211	42995211	+	Silent	SNP	A	A	G	rs1138141	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:42995211A>G	ENST00000244496.5	+	6	649	c.639A>G	c.(637-639)aaA>aaG	p.K213K		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	213					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						ACTTCCTGAAAAAATGTGAGT	0.572													G|||	1566	0.3127	0.5953	0.2378	5008	,	,		16765	0.2123		0.1233	False		,,,				2504	0.2822				p.K213K		Atlas-SNP	.											.	RRP36	20	.	0			c.A639G						PASS	.	G		2388,2018	549.6+/-377.8	646,1096,461	64.0	63.0	64.0		639	5.3	1.0	6	dbSNP_86	64	1116,7484	754.9+/-407.5	70,976,3254	no	coding-synonymous	RRP36	NM_033112.2		716,2072,3715	GG,GA,AA		12.9767,45.8012,26.9414		213/260	42995211	3504,9502	2203	4300	6503	SO:0001819	synonymous_variant	88745	exon6			CCTGAAAAAATGT	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"""chromosome 6 open reading frame 153"""	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.639A>G	6.37:g.42995211A>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	162	68	0.419753	NM_033112	Q9BRF6|Q9P0C8	Silent	SNP	ENST00000244496.5	37	CCDS34453.1																																																																																			A|0.725;G|0.275	0.275	strong		0.572	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112	
CLEC4C	170482	hgsc.bcm.edu	37	12	7894056	7894056	+	Missense_Mutation	SNP	G	G	A	rs73056605	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7894056G>A	ENST00000542353.1	-	4	686	c.196C>T	c.(196-198)Cca>Tca	p.P66S	CLEC4C_ENST00000540085.1_Missense_Mutation_p.P35S|CLEC4C_ENST00000354629.5_Missense_Mutation_p.P35S|CLEC4C_ENST00000360345.3_Missense_Mutation_p.P66S	NM_130441.2	NP_569708.1	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C	66				P -> S (in Ref. 3; AAQ88590). {ECO:0000305}.	innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.P66S(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				Kidney(36;0.0915)		GTCAGGCTTGGATGATACTGT	0.428													G|||	936	0.186901	0.0446	0.3285	5008	,	,		-128	0.1994		0.2962	False		,,,				2504	0.1534				p.P66S		Atlas-SNP	.											CLEC4C,NS,carcinoma,+2,2	CLEC4C	44	2	1	Substitution - Missense(1)	stomach(1)	c.C196T						PASS	.	G	SER/PRO,SER/PRO	398,4008	197.1+/-221.3	21,356,1826	206.0	173.0	184.0		196,103	-1.3	0.0	12	dbSNP_130	184	2458,6142	406.9+/-349.0	375,1708,2217	yes	missense,missense	CLEC4C	NM_130441.2,NM_203503.1	74,74	396,2064,4043	AA,AG,GG		28.5814,9.0331,21.9591	benign,benign	66/214,35/183	7894056	2856,10150	2203	4300	6503	SO:0001583	missense	170482	exon4			GGCTTGGATGATA	AF325460	CCDS8583.1, CCDS8584.1	12p13.2-p12.3	2008-02-05	2004-02-13	2005-02-11	ENSG00000198178	ENSG00000198178		"""C-type lectin domain containing"", ""CD molecules"""	13258	protein-coding gene	gene with protein product		606677	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7"""	CLECSF11, CLECSF7		11031109, 11536172	Standard	NM_130441		Approved	HECL, DLEC, BDCA2, CD303	uc001qth.1	Q8WTT0	OTTHUMG00000168441	ENST00000542353.1:c.196C>T	12.37:g.7894056G>A	ENSP00000440428:p.Pro66Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	139	70	0.503597	NM_130441	D3DUU3|Q3T1C3|Q6UXS8|Q8WXX8	Missense_Mutation	SNP	ENST00000542353.1	37	CCDS8583.1	499	0.22847985347985347	24	0.04878048780487805	123	0.3397790055248619	132	0.23076923076923078	220	0.29023746701846964	G	0.005	-2.238978	0.00274	0.090331	0.285814	ENSG00000198178	ENST00000542353;ENST00000354629;ENST00000540085;ENST00000360345	T;T;T;T	0.02121	4.49;4.44;4.44;4.49	1.79	-1.29	0.09288	.	.	.	.	.	T	0.00012	0.0000	N	0.00162	-1.95	0.80722	P	0.0	B;B	0.19583	0.0;0.037	B;B	0.14023	0.004;0.01	T	0.36432	-0.9748	8	0.05620	T	0.96	.	4.8437	0.13503	0.5335:0.0:0.4665:0.0	.	35;66	Q8WTT0-2;Q8WTT0	.;CLC4C_HUMAN	S	66;35;35;66	ENSP00000440428:P66S;ENSP00000346648:P35S;ENSP00000445338:P35S;ENSP00000353500:P66S	ENSP00000346648:P35S	P	-	1	0	CLEC4C	7785323	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-0.053000	0.11846	-0.356000	0.08187	-0.351000	0.07748	CCA	G|0.766;A|0.234	0.234	strong		0.428	CLEC4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399750.1	NM_203503	
NLRP4	147945	hgsc.bcm.edu	37	19	56369908	56369908	+	Missense_Mutation	SNP	G	G	C	rs17857373	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56369908G>C	ENST00000301295.6	+	3	1571	c.1149G>C	c.(1147-1149)gaG>gaC	p.E383D	NLRP4_ENST00000587891.1_Missense_Mutation_p.E308D|NLRP4_ENST00000346986.5_Missense_Mutation_p.E383D	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	383	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		E -> D (in dbSNP:rs17857373). {ECO:0000269|PubMed:15489334}.		inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TCACACCTGAGGGTGCCGAGG	0.552													G|||	67	0.0133786	0.0015	0.0274	5008	,	,		17533	0.0		0.0358	False		,,,				2504	0.0102				p.E383D		Atlas-SNP	.											.	NLRP4	331	.	0			c.G1149C						PASS	.	G	ASP/GLU	49,4357	51.6+/-87.1	1,47,2155	54.0	50.0	52.0		1149	-8.2	0.0	19	dbSNP_123	52	517,8083	144.5+/-200.4	14,489,3797	yes	missense	NLRP4	NM_134444.4	45	15,536,5952	CC,CG,GG		6.0116,1.1121,4.3518	benign	383/995	56369908	566,12440	2203	4300	6503	SO:0001583	missense	147945	exon3			ACCTGAGGGTGCC	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1149G>C	19.37:g.56369908G>C	ENSP00000301295:p.Glu383Asp	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	40	0.018315018315018316	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	26	0.03430079155672823	G	6.573	0.474120	0.12521	0.011121	0.060116	ENSG00000160505	ENST00000301295;ENST00000346986	D;D	0.84146	-1.81;-1.81	4.1	-8.19	0.01049	.	.	.	.	.	T	0.14356	0.0347	N	0.05124	-0.11	0.09310	N	1	B;B;B	0.14012	0.009;0.001;0.0	B;B;B	0.17722	0.019;0.002;0.001	T	0.38200	-0.9672	9	0.16896	T	0.51	.	3.2706	0.06880	0.3205:0.4181:0.1559:0.1055	rs17857373;rs17857373	383;308;383	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	D	383	ENSP00000301295:E383D;ENSP00000344787:E383D	ENSP00000301295:E383D	E	+	3	2	NLRP4	61061720	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.860000	0.00348	-1.277000	0.02411	-0.150000	0.13652	GAG	G|0.963;C|0.037	0.037	strong		0.552	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
KAZALD1	81621	hgsc.bcm.edu	37	10	102824349	102824349	+	Missense_Mutation	SNP	G	G	C	rs807037	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:102824349G>C	ENST00000370200.5	+	4	1090	c.764G>C	c.(763-765)gGc>gCc	p.G255A		NM_030929.4	NP_112191.2	Q96I82	KAZD1_HUMAN	Kazal-type serine peptidase inhibitor domain 1	255	Ig-like C2-type.		G -> A (in dbSNP:rs807037). {ECO:0000269|Ref.6}.		cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|regulation of cell growth (GO:0001558)	interstitial matrix (GO:0005614)				endometrium(1)|ovary(1)|prostate(2)	4				Epithelial(162;6.21e-09)|all cancers(201;3.14e-07)		CGCTGCCTTGGCCGCAATGCC	0.617													C|||	2983	0.595647	0.6241	0.549	5008	,	,		19776	0.4921		0.6461	False		,,,				2504	0.6452				p.G255A		Atlas-SNP	.											.	KAZALD1	14	.	0			c.G764C						PASS	.	C	ALA/GLY	2781,1625	501.7+/-365.1	896,989,318	58.0	52.0	54.0		764	5.5	1.0	10	dbSNP_86	54	5697,2903	452.9+/-363.1	1898,1901,501	yes	missense	KAZALD1	NM_030929.4	60	2794,2890,819	CC,CG,GG		33.7558,36.8815,34.8147	benign	255/305	102824349	8478,4528	2203	4300	6503	SO:0001583	missense	81621	exon4			GCCTTGGCCGCAA	AF333487	CCDS7509.1	10q24.32	2013-01-11	2005-08-17		ENSG00000107821	ENSG00000107821		"""Immunoglobulin superfamily / I-set domain containing"""	25460	protein-coding gene	gene with protein product		609208	"""Kazal-type serine protease inhibitor domain 1"""			12975309	Standard	NM_030929		Approved	FKSG40, FKSG28	uc001ksr.3	Q96I82	OTTHUMG00000018918	ENST00000370200.5:c.764G>C	10.37:g.102824349G>C	ENSP00000359219:p.Gly255Ala	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	37	36	0.972973	NM_030929	D3DR74|Q6ZMB1|Q9BQ73	Missense_Mutation	SNP	ENST00000370200.5	37	CCDS7509.1	1272	0.5824175824175825	312	0.6341463414634146	215	0.5939226519337016	249	0.4353146853146853	496	0.6543535620052771	C	8.866	0.948041	0.18356	0.631185	0.662442	ENSG00000107821	ENST00000370200	T	0.53857	0.6	5.53	5.53	0.82687	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00096	-2.155	0.41455	P	0.011998999999999982	B	0.02656	0.0	B	0.01281	0.0	T	0.46456	-0.9190	9	0.02654	T	1	-1.4851	16.5874	0.84731	0.0:0.8695:0.1305:0.0	rs807037;rs1767658;rs807037	255	Q96I82	KAZD1_HUMAN	A	255	ENSP00000359219:G255A	ENSP00000359219:G255A	G	+	2	0	KAZALD1	102814339	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	6.064000	0.71169	1.349000	0.45751	-0.216000	0.12614	GGC	G|0.373;C|0.627	0.627	strong		0.617	KAZALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049891.2	NM_030929	
TNFAIP8L3	388121	hgsc.bcm.edu	37	15	51350429	51350429	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:51350429G>A	ENST00000327536.5	-	3	627	c.528C>T	c.(526-528)atC>atT	p.I176I	RP11-108K3.1_ENST00000559909.1_lincRNA	NM_207381.2	NP_997264.2	Q5GJ75	TP8L3_HUMAN	tumor necrosis factor, alpha-induced protein 8-like 3	176								p.I176I(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	11				all cancers(107;0.000389)|GBM - Glioblastoma multiforme(94;0.00338)		AGAGGATCCCGATTTTGATCG	0.468																																					p.I176I		Atlas-SNP	.											TNFAIP8L3,caecum,carcinoma,0,1	TNFAIP8L3	30	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C528T						scavenged	.						296.0	234.0	255.0					15																	51350429		2196	4293	6489	SO:0001819	synonymous_variant	388121	exon3			GATCCCGATTTTG	AK123281	CCDS32241.1	15q21.2	2005-08-09				ENSG00000183578			20620	protein-coding gene	gene with protein product							Standard	XM_005254367		Approved	FLJ41287	uc001zyy.3	Q5GJ75		ENST00000327536.5:c.528C>T	15.37:g.51350429G>A		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	247	4	0.0161943	NM_207381	Q6ZWD1	Silent	SNP	ENST00000327536.5	37	CCDS32241.1																																																																																			.	.	none		0.468	TNFAIP8L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418661.1	NM_207381	
UPF2	26019	hgsc.bcm.edu	37	10	12071397	12071397	+	Silent	SNP	G	G	A	rs11257490	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:12071397G>A	ENST00000356352.2	-	2	965	c.492C>T	c.(490-492)ctC>ctT	p.L164L	UPF2_ENST00000357604.5_Silent_p.L164L|UPF2_ENST00000397053.2_Silent_p.L164L			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	164					gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				AACTTGAGTCGAGGCGGCTGA	0.403													A|||	1311	0.261781	0.2814	0.2507	5008	,	,		16409	0.4435		0.161	False		,,,				2504	0.1595				p.L164L		Atlas-SNP	.											.	UPF2	111	.	0			c.C492T						PASS	.	A	,	1166,3240	703.9+/-407.1	145,876,1182	102.0	111.0	108.0		492,492	-3.3	1.0	10	dbSNP_120	108	1443,7157	746.8+/-407.3	132,1179,2989	no	coding-synonymous,coding-synonymous	UPF2	NM_015542.2,NM_080599.1	,	277,2055,4171	AA,AG,GG		16.7791,26.4639,20.06	,	164/1273,164/1273	12071397	2609,10397	2203	4300	6503	SO:0001819	synonymous_variant	26019	exon3			TGAGTCGAGGCGG	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"""smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.492C>T	10.37:g.12071397G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	153	64	0.418301	NM_080599	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Silent	SNP	ENST00000356352.2	37	CCDS7086.1																																																																																			G|0.765;A|0.235	0.235	strong		0.403	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1		
APOBEC1	339	hgsc.bcm.edu	37	12	7803646	7803646	+	Silent	SNP	G	G	A	rs10431309	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7803646G>A	ENST00000229304.4	-	4	554	c.534C>T	c.(532-534)taC>taT	p.Y178Y		NM_001644.3	NP_001635.2	P41238	ABEC1_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	178					cellular response to insulin stimulus (GO:0032869)|cytidine deamination (GO:0009972)|cytidine to uridine editing (GO:0016554)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|gene expression (GO:0010467)|lipid metabolic process (GO:0006629)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein transport (GO:0042953)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to osmotic stress (GO:0006970)|response to zinc ion (GO:0010043)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	AU-rich element binding (GO:0017091)|cytidine deaminase activity (GO:0004126)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.Y178Y(1)		kidney(2)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|stomach(1)	17						GCTCCAGTGCGTACAACATCA	0.433													G|||	1212	0.242013	0.1483	0.1916	5008	,	,		-128	0.2312		0.2594	False		,,,				2504	0.3978				p.Y178Y	Pancreas(135;929 1826 4531 10527 41012)	Atlas-SNP	.											APOBEC1,caecum,carcinoma,0,2	APOBEC1	43	2	1	Substitution - coding silent(1)	stomach(1)	c.C534T						PASS	.	G		629,3777	270.7+/-269.8	51,527,1625	154.0	139.0	144.0		534	-3.2	0.5	12	dbSNP_119	144	2082,6518	360.6+/-332.0	236,1610,2454	no	coding-synonymous	APOBEC1	NM_001644.3		287,2137,4079	AA,AG,GG		24.2093,14.276,20.8442		178/237	7803646	2711,10295	2203	4300	6503	SO:0001819	synonymous_variant	339	exon4			CAGTGCGTACAAC	U72891	CCDS8579.1	12p13.1	2007-02-01			ENSG00000111701	ENSG00000111701		"""Apolipoprotein B mRNA editing enzymes"""	604	protein-coding gene	gene with protein product		600130					Standard	XM_005253355		Approved	BEDP, CDAR1, APOBEC-1, HEPR	uc001qtb.3	P41238	OTTHUMG00000141288	ENST00000229304.4:c.534C>T	12.37:g.7803646G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_001644	Q9UE64|Q9UM71	Silent	SNP	ENST00000229304.4	37	CCDS8579.1																																																																																			G|0.779;A|0.221	0.221	strong		0.433	APOBEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280523.1	NM_001644	
HRH3	11255	hgsc.bcm.edu	37	20	60791404	60791404	+	Silent	SNP	C	C	T	rs3787429	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60791404C>T	ENST00000340177.5	-	3	1280	c.996G>A	c.(994-996)tcG>tcA	p.S332S	HRH3_ENST00000317393.6_Silent_p.S332S	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	332					brain development (GO:0007420)|drinking behavior (GO:0042756)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of serotonin secretion (GO:0014063)|neurotransmitter secretion (GO:0007269)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of norepinephrine secretion (GO:0014061)|response to organic cyclic compound (GO:0014070)	integral component of plasma membrane (GO:0005887)|myelin sheath (GO:0043209)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|histamine receptor activity (GO:0004969)			breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Betahistine(DB06698)|Histamine Phosphate(DB00667)|Mirtazapine(DB00370)	GCTTCTCCAGCGAGGCCGAGG	0.657													C|||	2456	0.490415	0.5825	0.4986	5008	,	,		15426	0.3671		0.4056	False		,,,				2504	0.5746				p.S332S		Atlas-SNP	.											.	HRH3	25	.	0			c.G996A						PASS	.	C		2403,1991		657,1089,451	15.0	15.0	15.0		996	-9.2	0.2	20	dbSNP_107	15	3387,5197		676,2035,1581	no	coding-synonymous	HRH3	NM_007232.2		1333,3124,2032	TT,TC,CC		39.4571,45.3118,44.614		332/446	60791404	5790,7188	2197	4292	6489	SO:0001819	synonymous_variant	11255	exon3			CTCCAGCGAGGCC	AF140538	CCDS13493.1	20q13.33	2013-09-19			ENSG00000101180	ENSG00000101180		"""GPCR / Class A : Histamine receptors"""	5184	protein-coding gene	gene with protein product		604525				10347254	Standard	NM_007232		Approved	GPCR97	uc002ycf.2	Q9Y5N1	OTTHUMG00000032899	ENST00000340177.5:c.996G>A	20.37:g.60791404C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_007232	Q4QRI7|Q9GZX2|Q9H4K8	Silent	SNP	ENST00000340177.5	37	CCDS13493.1																																																																																			C|0.531;T|0.469	0.469	strong		0.657	HRH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079994.1	NM_007232	
MOK	5891	hgsc.bcm.edu	37	14	102729881	102729881	+	Splice_Site	SNP	A	A	G	rs56377169	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102729881A>G	ENST00000361847.2	-	4	515		c.e4+1		MOK_ENST00000524214.1_Splice_Site|MOK_ENST00000522874.1_Splice_Site|MOK_ENST00000193029.6_Splice_Site	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase						protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)										TATTCTACGTACCTCGTATTA	0.318													A|||	278	0.0555112	0.0166	0.049	5008	,	,		18341	0.003		0.0785	False		,,,				2504	0.1431				.		Atlas-SNP	.											.	.	.	.	0			c.283+2T>C						PASS	.	A		121,4281	87.3+/-125.9	1,119,2081	108.0	109.0	108.0			5.8	1.0	14	dbSNP_129	108	613,7987	157.7+/-211.4	17,579,3704	yes	splice-5	MOK	NM_014226.1		18,698,5785	GG,GA,AA		7.1279,2.7488,5.6453			102729881	734,12268	2201	4300	6501	SO:0001630	splice_region_variant	5891	exon5			CTACGTACCTCGT	AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"""renal tumor antigen"""	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.283+1T>C	14.37:g.102729881A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Splice_Site	SNP	ENST00000361847.2	37	CCDS9971.1	80	0.03663003663003663	10	0.02032520325203252	20	0.055248618784530384	2	0.0034965034965034965	48	0.0633245382585752	A	19.54	3.847364	0.71603	0.027488	0.071279	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3848	0.66938	1.0:0.0:0.0:0.0	rs56377169	.	.	.	.	-1	.	.	.	-	.	.	RAGE	101799634	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	7.256000	0.78350	2.209000	0.71365	0.533000	0.62120	.	A|0.954;G|0.046	0.046	strong		0.318	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		Intron
GRAMD1C	54762	hgsc.bcm.edu	37	3	113594377	113594377	+	Silent	SNP	A	A	G	rs13079383	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:113594377A>G	ENST00000358160.4	+	4	798	c.306A>G	c.(304-306)ctA>ctG	p.L102L	GRAMD1C_ENST00000479212.1_3'UTR|GRAMD1C_ENST00000452134.2_5'UTR	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	102	GRAM.					integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						AGGGACGACTATACCTTTCAG	0.328													A|||	1213	0.242212	0.0651	0.3314	5008	,	,		17431	0.2738		0.3638	False		,,,				2504	0.2607				p.L102L		Atlas-SNP	.											.	GRAMD1C	71	.	0			c.A306G						PASS	.	A		470,3936	223.9+/-240.3	23,424,1756	158.0	154.0	155.0		306	-11.6	0.6	3	dbSNP_121	155	3211,5389	485.0+/-371.5	607,1997,1696	no	coding-synonymous	GRAMD1C	NM_017577.4		630,2421,3452	GG,GA,AA		37.3372,10.6673,28.3023		102/663	113594377	3681,9325	2203	4300	6503	SO:0001819	synonymous_variant	54762	exon4			ACGACTATACCTT		CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.306A>G	3.37:g.113594377A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_017577	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Silent	SNP	ENST00000358160.4	37	CCDS33826.1																																																																																			A|0.724;G|0.276	0.276	strong		0.328	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577	
KIF1A	547	hgsc.bcm.edu	37	2	241713646	241713646	+	Silent	SNP	A	A	G	rs1063353	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241713646A>G	ENST00000320389.7	-	12	1149	c.991T>C	c.(991-993)Ttg>Ctg	p.L331L	KIF1A_ENST00000498729.2_Silent_p.L331L	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	331	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		GCAGGACTCAAGGCTGCCACC	0.592													G|||	2572	0.513578	0.7428	0.3631	5008	,	,		13128	0.622		0.3618	False		,,,				2504	0.3548				p.L331L		Atlas-SNP	.											.	KIF1A	152	.	0			c.T991C						PASS	.	G		2789,1501		909,971,265	72.0	77.0	75.0		991	4.3	1.0	2	dbSNP_86	75	2940,5542		516,1908,1817	no	coding-synonymous	KIF1A	NM_004321.5		1425,2879,2082	GG,GA,AA		34.6616,34.9883,44.8559		331/1691	241713646	5729,7043	2145	4241	6386	SO:0001819	synonymous_variant	547	exon12			GACTCAAGGCTGC	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.991T>C	2.37:g.241713646A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	246	129	0.52439	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Silent	SNP	ENST00000320389.7	37	CCDS46561.1	1092	0.5	354	0.7195121951219512	115	0.31767955801104975	349	0.6101398601398601	274	0.36147757255936674	G	5.440	0.266237	0.10294	0.650117	0.346616	ENSG00000130294	ENST00000428768	.	.	.	4.33	4.33	0.51752	.	0.000000	0.64402	U	0.000002	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40403	-0.9565	4	.	.	.	.	12.0657	0.53586	0.0862:0.0:0.9138:0.0	rs1063353;rs3204419	.	.	.	P	138	.	.	L	-	2	0	KIF1A	241362319	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	6.463000	0.73530	0.820000	0.34516	-0.374000	0.07098	CTT	A|0.528;G|0.472	0.472	strong		0.592	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
ACAA1	30	hgsc.bcm.edu	37	3	38170810	38170810	+	Missense_Mutation	SNP	C	C	G	rs156265	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:38170810C>G	ENST00000333167.8	-	6	688	c.516G>C	c.(514-516)gaG>gaC	p.E172D	ACAA1_ENST00000480865.1_5'UTR|ACAA1_ENST00000444607.2_3'UTR|ACAA1_ENST00000301810.7_Intron|ACAA1_ENST00000450296.1_Missense_Mutation_p.E131D|ACAA1_ENST00000544624.1_Missense_Mutation_p.E20D	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	172			E -> D (in dbSNP:rs156265).		alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		CTCTGGCCTTCTCCTTCTCCA	0.552													C|||	685	0.136781	0.025	0.1326	5008	,	,		21211	0.3244		0.1431	False		,,,				2504	0.091				p.E172D		Atlas-SNP	.											.	ACAA1	32	.	0			c.G516C						PASS	.	C	,ASP/GLU	206,4200	129.4+/-166.1	3,200,2000	173.0	138.0	150.0		,516	1.7	0.9	3	dbSNP_79	150	1251,7349	251.0+/-277.6	95,1061,3144	yes	intron,missense	ACAA1	NM_001130410.1,NM_001607.3	,45	98,1261,5144	GG,GC,CC		14.5465,4.6754,11.2025	,benign	,172/425	38170810	1457,11549	2203	4300	6503	SO:0001583	missense	30	exon6			GGCCTTCTCCTTC	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"""peroxisomal 3-oxoacyl-Coenzyme A thiolase"""	604054	"""acetyl-Coenzyme A acyltransferase 1"""				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087	ENST00000333167.8:c.516G>C	3.37:g.38170810C>G	ENSP00000333664:p.Glu172Asp	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	230	119	0.517391	NM_001607	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	37	CCDS2673.1	361|361	0.1652930402930403|0.1652930402930403	15|15	0.03048780487804878|0.03048780487804878	49|49	0.13535911602209943|0.13535911602209943	188|188	0.32867132867132864|0.32867132867132864	109|109	0.1437994722955145|0.1437994722955145	C|C	11.98|11.98	1.800208|1.800208	0.31869|0.31869	0.046754|0.046754	0.145465|0.145465	ENSG00000060971|ENSG00000060971	ENST00000333167;ENST00000450296;ENST00000358122;ENST00000544624|ENST00000452171	D;D;D|.	0.90444|.	-2.67;-2.67;-2.67|.	5.96|5.96	1.68|1.68	0.24146|0.24146	Thiolase, N-terminal (1);Thiolase-like (1);|.	0.830821|.	0.11392|.	N|.	0.568720|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04705|0.04705	-0.18|-0.18	0.24790|0.24790	P|P	0.9927613|0.9927613	B;B;B|.	0.06786|.	0.0;0.001;0.0|.	B;B;B|.	0.08055|.	0.0;0.003;0.0|.	T|T	0.45396|0.45396	-0.9264|-0.9264	9|4	0.22706|.	T|.	0.39|.	-15.202|-15.202	3.3169|3.3169	0.07036|0.07036	0.3401:0.2881:0.2935:0.0783|0.3401:0.2881:0.2935:0.0783	rs156265;rs52826071;rs156265|rs156265;rs52826071;rs156265	104;131;172|.	F5GXL8;C9JDE9;P09110|.	.;.;THIK_HUMAN|.	D|T	172;131;104;20|45	ENSP00000333664:E172D;ENSP00000395183:E131D;ENSP00000445710:E20D|.	ENSP00000333664:E172D|.	E|R	-|-	3|2	2|0	ACAA1|ACAA1	38145814|38145814	0.024000|0.024000	0.19004|0.19004	0.907000|0.907000	0.35723|0.35723	0.765000|0.765000	0.43378|0.43378	0.247000|0.247000	0.18179|0.18179	0.791000|0.791000	0.33826|0.33826	-0.175000|-0.175000	0.13238|0.13238	GAG|AGA	C|0.865;G|0.135	0.135	strong		0.552	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607	
ZNRF4	148066	hgsc.bcm.edu	37	19	5455735	5455735	+	Missense_Mutation	SNP	G	G	A	rs2240744	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:5455735G>A	ENST00000222033.4	+	1	310	c.233G>A	c.(232-234)cGa>cAa	p.R78Q		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	78			R -> Q (in dbSNP:rs2240744). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		CGGCCGGGCCGAGCCCTCGTG	0.677													G|||	989	0.197484	0.0272	0.1326	5008	,	,		15803	0.3958		0.2157	False		,,,				2504	0.2505				p.R78Q		Atlas-SNP	.											.	ZNRF4	59	.	0			c.G233A						PASS	.	G	GLN/ARG	221,3965		4,213,1876	44.0	54.0	50.0		233	-6.7	0.0	19	dbSNP_98	50	1604,6758		161,1282,2738	yes	missense	ZNRF4	NM_181710.3	43	165,1495,4614	AA,AG,GG		19.182,5.2795,14.5442	benign	78/430	5455735	1825,10723	2093	4181	6274	SO:0001583	missense	148066	exon1			CGGGCCGAGCCCT	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"""RING-type (C3HC4) zinc fingers"""	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.233G>A	19.37:g.5455735G>A	ENSP00000222033:p.Arg78Gln	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	37	CCDS42475.1	457	0.20924908424908426	16	0.032520325203252036	56	0.15469613259668508	226	0.3951048951048951	159	0.20976253298153033	G	6.622	0.483220	0.12581	0.052795	0.19182	ENSG00000105428	ENST00000222033	T	0.04275	3.66	3.33	-6.66	0.01789	.	5.956070	0.02111	N	0.054827	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46610	-0.9179	9	0.28530	T	0.3	.	0.5923	0.00730	0.2607:0.2955:0.1335:0.3103	rs2240744;rs17238634;rs17845551;rs17858448;rs60227294;rs2240744	78	Q8WWF5	ZNRF4_HUMAN	Q	78	ENSP00000222033:R78Q	ENSP00000222033:R78Q	R	+	2	0	ZNRF4	5406735	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-2.987000	0.00659	-1.706000	0.01404	-2.122000	0.00348	CGA	G|0.785;A|0.215	0.215	strong		0.677	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
SLC16A8	23539	hgsc.bcm.edu	37	22	38478666	38478666	+	Splice_Site	SNP	C	C	G	rs77968014	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38478666C>G	ENST00000320521.5	-	2	323		c.e2+1		SLC16A8_ENST00000469516.1_Intron	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8						blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|lactate transmembrane transport (GO:0035873)|lactate transport (GO:0015727)|leukocyte migration (GO:0050900)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			kidney(1)|large_intestine(1)|prostate(1)	3	Melanoma(58;0.045)				Pyruvic acid(DB00119)	GGGACACTGACCCGTGCCGTA	0.701													C|||	17	0.00339457	0.0	0.0058	5008	,	,		12685	0.0		0.0119	False		,,,				2504	0.001				.		Atlas-SNP	.											.	SLC16A8	13	.	0			c.214+1G>C						PASS	.	C		5,4307		0,5,2151	7.0	9.0	8.0			4.2	1.0	22	dbSNP_132	8	51,8433		0,51,4191	yes	splice-5	SLC16A8	NM_013356.2		0,56,6342	GG,GC,CC		0.6011,0.116,0.4376			38478666	56,12740	2156	4242	6398	SO:0001630	splice_region_variant	23539	exon3			CACTGACCCGTGC	AF132610	CCDS13966.1	22q12.3-q13.2	2013-07-18	2013-07-18		ENSG00000100156	ENSG00000100156		"""Solute carriers"""	16270	protein-coding gene	gene with protein product	"""monocarboxylate transporter 3"""	610409	"""solute carrier 16 (monocarboxylic acid transporters), member 8"""			10493836	Standard	NM_013356		Approved	MCT3, REMP	uc003auu.3	O95907	OTTHUMG00000151196	ENST00000320521.5:c.214+1G>C	22.37:g.38478666C>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_013356	Q9UBE2	Splice_Site	SNP	ENST00000320521.5	37	CCDS13966.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	21.4	4.146560	0.77888	0.00116	0.006011	ENSG00000100156	ENST00000320521;ENST00000427592	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0149	0.86415	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC16A8	36808612	1.000000	0.71417	0.975000	0.42487	0.835000	0.47333	7.622000	0.83099	2.094000	0.63399	0.485000	0.47835	.	C|0.997;G|0.003	0.003	strong		0.701	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356	Intron
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084787	31084787	+	Intron	SNP	A	A	G	rs707913	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31084787A>G	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Missense_Mutation_p.F202S	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GGATACCCCAAAGGTCTGGGA	0.572													A|||	1407	0.28095	0.4009	0.3314	5008	,	,		19609	0.3403		0.2336	False		,,,				2504	0.0706				p.F202S		Atlas-SNP	.											.	CDSN	48	.	0			c.T605C						PASS	.	A	,SER/PHE	1578,2828	492.9+/-362.5	271,1036,896	90.0	99.0	96.0		,605	1.4	0.0	6	dbSNP_86	96	1876,6724	335.3+/-321.3	195,1486,2619	yes	intron,missense	CDSN,PSORS1C1	NM_014068.2,NM_001264.4	,155	466,2522,3515	GG,GA,AA		21.814,35.8148,26.557	,benign	,202/530	31084787	3454,9552	2203	4300	6503	SO:0001627	intron_variant	1041	exon2			ACCCCAAAGGTCT	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2119A>G	6.37:g.31084787A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	100	98	0.98	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	653	0.298992673992674	182	0.3699186991869919	123	0.3397790055248619	180	0.3146853146853147	168	0.22163588390501318	A	0.044	-1.272710	0.01421	0.358148	0.21814	ENSG00000204539	ENST00000376288	T	0.03745	3.82	3.33	1.41	0.22369	.	1.761040	0.04336	N	0.353243	T	0.00815	0.0027	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47315	-0.9127	6	0.19590	T	0.45	0.705	6.0849	0.19962	0.2711:0.0:0.7289:0.0	rs707913;rs3203540;rs3869104;rs707913	.	.	.	S	202	ENSP00000365465:F202S	ENSP00000365465:F202S	F	-	2	0	CDSN	31192766	0.055000	0.20627	0.002000	0.10522	0.003000	0.03518	2.133000	0.42093	0.413000	0.25759	-0.562000	0.04174	TTT	A|0.728;G|0.272	0.272	strong		0.572	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
ZNF366	167465	hgsc.bcm.edu	37	5	71756670	71756670	+	Silent	SNP	C	C	T	rs2278600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:71756670C>T	ENST00000318442.5	-	2	1144	c.654G>A	c.(652-654)gaG>gaA	p.E218E		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	218					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TCTCCTGGGGCTCGGCTTTCC	0.647													C|||	1385	0.276558	0.3775	0.2046	5008	,	,		18159	0.4077		0.1332	False		,,,				2504	0.2035				p.E218E		Atlas-SNP	.											ZNF366,NS,carcinoma,-2,1	ZNF366	108	1	0			c.G654A						PASS	.	C		1601,2805	491.7+/-362.2	310,981,912	73.0	75.0	74.0		654	3.1	0.4	5	dbSNP_100	74	1198,7402	242.2+/-272.3	85,1028,3187	no	coding-synonymous	ZNF366	NM_152625.1		395,2009,4099	TT,TC,CC		13.9302,36.3368,21.5208		218/745	71756670	2799,10207	2203	4300	6503	SO:0001819	synonymous_variant	167465	exon2			CTGGGGCTCGGCT	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.654G>A	5.37:g.71756670C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	80	32	0.4	NM_152625	Q5HYI9|Q7RTV4	Silent	SNP	ENST00000318442.5	37	CCDS4015.1																																																																																			C|0.757;T|0.243	0.243	strong		0.647	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
NLRC3	197358	hgsc.bcm.edu	37	16	3613263	3613263	+	RNA	SNP	C	C	T	rs142571279	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:3613263C>T	ENST00000301749.7	-	0	2080				NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000359128.5_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GCACAGACTGCGGCATCGGGG	0.701													C|||	27	0.00539137	0.0008	0.0101	5008	,	,		16218	0.0		0.0159	False		,,,				2504	0.0031				p.A559T		Atlas-SNP	.											NLRC3,NS,carcinoma,0,1	NLRC3	103	1	0			c.G1675A						PASS	.	C	THR/ALA	16,4184		0,16,2084	11.0	14.0	13.0		1675	0.9	0.0	16	dbSNP_134	13	124,8260		2,120,4070	yes	missense	NLRC3	NM_178844.2	58	2,136,6154	TT,TC,CC		1.479,0.381,1.1125	benign	559/1066	3613263	140,12444	2100	4192	6292			197358	exon5			AGACTGCGGCATC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613263C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		16	0.007326007326007326	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	C	2.055	-0.416723	0.04766	0.00381	0.01479	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81	5.2	0.91	0.19337	.	0.691974	0.14232	N	0.332666	T	0.47525	0.1450	.	.	.	0.09310	N	1	B	0.23058	0.079	B	0.15052	0.012	T	0.36187	-0.9758	9	0.13470	T	0.59	.	0.7685	0.01020	0.1727:0.3899:0.1676:0.2699	.	606	C9JLH9	.	T	559;559;559;606;541	ENSP00000301749:A559T;ENSP00000352039:A559T;ENSP00000414415:A606T;ENSP00000323897:A541T	ENSP00000301749:A559T	A	-	1	0	NLRC3	3553264	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.683000	0.25349	1.182000	0.42928	0.655000	0.94253	GCA	C|0.993;T|0.007	0.007	strong		0.701	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
PMFBP1	83449	hgsc.bcm.edu	37	16	72156842	72156842	+	Missense_Mutation	SNP	T	T	G	rs16973716	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72156842T>G	ENST00000537792.1	-	3	236	c.237A>C	c.(235-237)aaA>aaC	p.K79N	PMFBP1_ENST00000237353.10_Missense_Mutation_p.K913N|PMFBP1_ENST00000355636.6_Missense_Mutation_p.K768N|PMFBP1_ENST00000537465.1_Missense_Mutation_p.K918N			Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	918						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TGGCAATGTATTTCACCTGCT	0.537													T|||	2412	0.481629	0.6263	0.3112	5008	,	,		20099	0.3413		0.4105	False		,,,				2504	0.6247				p.K913N		Atlas-SNP	.											.	PMFBP1	101	.	0			c.A2739C						PASS	.	T	ASN/LYS,ASN/LYS	2428,1968	619.0+/-393.3	681,1066,451	90.0	87.0	88.0		2304,2739	3.8	1.0	16	dbSNP_123	88	3631,4969	522.4+/-380.1	781,2069,1450	yes	missense,missense	PMFBP1	NM_001160213.1,NM_031293.2	94,94	1462,3135,1901	GG,GT,TT		42.2209,44.768,46.622	probably-damaging,probably-damaging	768/883,913/1008	72156842	6059,6937	2198	4300	6498	SO:0001583	missense	83449	exon19			AATGTATTTCACC	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000537792.1:c.237A>C	16.37:g.72156842T>G	ENSP00000443366:p.Lys79Asn	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000537792.1	37		939	0.42994505494505497	291	0.5914634146341463	126	0.34806629834254144	203	0.3548951048951049	319	0.420844327176781	T	17.71	3.456390	0.63401	0.55232	0.422209	ENSG00000118557	ENST00000537792;ENST00000537465;ENST00000237353;ENST00000355636	T;T;T;T	0.58506	0.33;2.27;2.3;2.11	4.87	3.78	0.43462	.	0.000000	0.51477	D	0.000097	T	0.00012	0.0000	M	0.68317	2.08	0.36865	P	0.11140700000000003	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.83275	0.996;0.948;0.994	T	0.50162	-0.8860	9	0.54805	T	0.06	-21.4562	7.1271	0.25477	0.0:0.1004:0.0:0.8996	rs16973716;rs16973716	918;913;918	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	N	79;918;913;768	ENSP00000443366:K79N;ENSP00000443817:K918N;ENSP00000237353:K913N;ENSP00000347854:K768N	ENSP00000237353:K913N	K	-	3	2	PMFBP1	70714343	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	1.490000	0.35573	0.893000	0.36288	0.477000	0.44152	AAA	T|0.542;G|0.458	0.458	strong		0.537	PMFBP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000396523.1	NM_031293	
ZFHX3	463	hgsc.bcm.edu	37	16	72992221	72992221	+	Silent	SNP	G	G	A	rs61735550	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992221G>A	ENST00000268489.5	-	2	2496	c.1824C>T	c.(1822-1824)agC>agT	p.S608S	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	608					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CACCCTCTGTGCTTTCATTTG	0.617													G|||	416	0.0830671	0.0174	0.098	5008	,	,		18070	0.0		0.2306	False		,,,				2504	0.0951				p.S608S		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C1824T						PASS	.	G	,	239,4157	140.4+/-175.9	9,221,1968	102.0	95.0	97.0		,1824	4.3	1.0	16	dbSNP_129	97	2109,6491	364.6+/-333.6	259,1591,2450	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	268,1812,4418	AA,AG,GG		24.5233,5.4368,18.0671	,	,608/3704	72992221	2348,10648	2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCTGTGCTTTCA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1824C>T	16.37:g.72992221G>A		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	261	258	0.988506	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			G|0.830;A|0.170	0.170	strong		0.617	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
OR4D11	219986	hgsc.bcm.edu	37	11	59271637	59271637	+	Missense_Mutation	SNP	T	T	C	rs7120079	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:59271637T>C	ENST00000313253.1	+	1	589	c.589T>C	c.(589-591)Ttc>Ctc	p.F197L		NM_001004706.1	NP_001004706.1	Q8NGI4	OR4DB_HUMAN	olfactory receptor, family 4, subfamily D, member 11	197			F -> L (in dbSNP:rs7120079).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F197L(1)		endometrium(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29						TGCTCTTGAGTTCTTGATGAT	0.498													N|||	1515	0.302516	0.289	0.2219	5008	,	,		21137	0.2758		0.3091	False		,,,				2504	0.3988				p.F197L		Atlas-SNP	.											OR4D11,NS,carcinoma,0,1	OR4D11	62	1	1	Substitution - Missense(1)	stomach(1)	c.T589C						PASS	.	C	LEU/PHE	1225,3177		173,879,1149	221.0	211.0	214.0		589	1.1	0.7	11	dbSNP_116	214	2595,5995		396,1803,2096	yes	missense	OR4D11	NM_001004706.1	22	569,2682,3245	CC,CT,TT		30.2095,27.8283,29.4027	benign	197/312	59271637	3820,9172	2201	4295	6496	SO:0001583	missense	219986	exon1			CTTGAGTTCTTGA	AB065810	CCDS31563.1	11q12.1	2012-08-09		2004-03-10	ENSG00000176200	ENSG00000176200		"""GPCR / Class A : Olfactory receptors"""	15174	protein-coding gene	gene with protein product				OR4D11P			Standard	NM_001004706		Approved		uc001noa.1	Q8NGI4	OTTHUMG00000167342	ENST00000313253.1:c.589T>C	11.37:g.59271637T>C	ENSP00000320077:p.Phe197Leu	Somatic	368	1	0.00271739		WXS	Illumina HiSeq	Phase_I	382	381	0.997382	NM_001004706		Missense_Mutation	SNP	ENST00000313253.1	37	CCDS31563.1	646	0.2957875457875458	178	0.3617886178861789	89	0.24585635359116023	151	0.263986013986014	228	0.3007915567282322	N	0.008	-1.881657	0.00532	0.278283	0.302095	ENSG00000176200	ENST00000313253	T	0.00027	8.93	5.44	1.12	0.20585	GPCR, rhodopsin-like superfamily (1);	0.310617	0.23135	N	0.051532	T	0.00012	0.0000	N	0.00188	-1.89	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33240	-0.9876	9	0.02654	T	1	-13.1729	5.4471	0.16541	0.4598:0.3596:0.1128:0.0679	rs7120079;rs52793081;rs60254438;rs7120079	197	Q8NGI4	OR4DB_HUMAN	L	197	ENSP00000320077:F197L	ENSP00000320077:F197L	F	+	1	0	OR4D11	59028213	0.000000	0.05858	0.686000	0.30086	0.074000	0.17049	-0.412000	0.07132	-0.284000	0.09102	-0.226000	0.12346	TTC	T|0.696;C|0.304	0.304	strong		0.498	OR4D11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394236.1	NM_001004706	
SLC4A1AP	22950	hgsc.bcm.edu	37	2	27908005	27908005	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:27908005A>G	ENST00000326019.6	+	10	2259	c.1977A>G	c.(1975-1977)aaA>aaG	p.K659K		NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	659	Glu-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					aagaagagaaagaaaaggagg	0.493																																					p.K659K		Atlas-SNP	.											SLC4A1AP,NS,carcinoma,+2,1	SLC4A1AP	63	1	0			c.A1977G						scavenged	.						55.0	56.0	56.0					2																	27908005		2203	4297	6500	SO:0001819	synonymous_variant	22950	exon10			AGAGAAAGAAAAG		CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"""lung cancer oncogene 3"""	602655	"""solute carrier family 4 (anion exchanger), member 1, adapter protein"""			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.1977A>G	2.37:g.27908005A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	120	3	0.025	NM_018158	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Silent	SNP	ENST00000326019.6	37	CCDS33166.1																																																																																			.	.	none		0.493	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1	NM_018158	
SLC9C1	285335	hgsc.bcm.edu	37	3	111887788	111887788	+	Missense_Mutation	SNP	A	A	G	rs73853324	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:111887788A>G	ENST00000305815.5	-	25	3425	c.3173T>C	c.(3172-3174)gTa>gCa	p.V1058A	SLC9C1_ENST00000487372.1_Missense_Mutation_p.V1010A	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	1058					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										ACAATCTTCTACAGCTCCATG	0.308													A|||	266	0.053115	0.0666	0.0418	5008	,	,		20809	0.002		0.0547	False		,,,				2504	0.0941				p.V1058A		Atlas-SNP	.											.	.	.	.	0			c.T3173C						PASS	.	A	ALA/VAL	256,4148	146.5+/-181.1	12,232,1958	124.0	130.0	128.0		3173	2.4	1.0	3	dbSNP_130	128	457,8141	135.7+/-192.9	11,435,3853	yes	missense	SLC9A10	NM_183061.1	64	23,667,5811	GG,GA,AA		5.3152,5.8129,5.4838	benign	1058/1178	111887788	713,12289	2202	4299	6501	SO:0001583	missense	285335	exon25			TCTTCTACAGCTC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.3173T>C	3.37:g.111887788A>G	ENSP00000306627:p.Val1058Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	181	88	0.486188	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	95	0.043498168498168496	32	0.06504065040650407	22	0.06077348066298342	0	0.0	41	0.05408970976253298	A	12.92	2.082593	0.36758	0.058129	0.053152	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.79653	-1.29;-1.29	6.06	2.42	0.29668	.	0.333153	0.25807	N	0.028179	T	0.18299	0.0439	L	0.38175	1.15	0.23320	N	0.997917	B;B	0.22541	0.071;0.006	B;B	0.33750	0.169;0.005	T	0.40553	-0.9557	10	0.36615	T	0.2	-0.1852	7.4468	0.27215	0.7407:0.0:0.2593:0.0	.	1010;1058	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	A	1058;1010	ENSP00000306627:V1058A;ENSP00000420688:V1010A	ENSP00000306627:V1058A	V	-	2	0	SLC9A10	113370478	0.992000	0.36948	0.997000	0.53966	0.865000	0.49528	1.593000	0.36686	0.556000	0.29098	0.528000	0.53228	GTA	A|0.946;G|0.054	0.054	strong		0.308	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411260	105411260	+	Missense_Mutation	SNP	A	A	G	rs2819425	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105411260A>G	ENST00000333244.5	-	7	10647	c.10528T>C	c.(10528-10530)Tcc>Ccc	p.S3510P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3510						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGCATGGAGGAGAGGCTCACG	0.637													.|||	103	0.0205671	0.0371	0.013	5008	,	,		18098	0.003		0.0278	False		,,,				2504	0.0143				p.S3510P		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,+1,1	AHNAK2	719	1	0			c.T10528C						PASS	.	A	PRO/SER	96,3774		4,88,1843	124.0	134.0	131.0		10528	1.1	0.0	14	dbSNP_100	131	134,8102		1,132,3985	no	missense	AHNAK2	NM_138420.2	74	5,220,5828	GG,GA,AA		1.627,2.4806,1.8999	benign	3510/5796	105411260	230,11876	1935	4118	6053	SO:0001583	missense	113146	exon7			TGGAGGAGAGGCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.10528T>C	14.37:g.105411260A>G	ENSP00000353114:p.Ser3510Pro	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	169	75	0.443787	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	54	0.024725274725274724	26	0.052845528455284556	5	0.013812154696132596	6	0.01048951048951049	17	0.022427440633245383	a	0.017	-1.504266	0.00992	0.024806	0.01627	ENSG00000185567	ENST00000333244	T	0.00543	6.68	4.08	1.14	0.20703	.	.	.	.	.	T	0.00012	0.0000	N	0.00008	-3.105	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43475	-0.9389	9	0.02654	T	1	.	3.7815	0.08682	0.091:0.2962:0.4609:0.1519	rs2819425	3510	Q8IVF2	AHNK2_HUMAN	P	3510	ENSP00000353114:S3510P	ENSP00000353114:S3510P	S	-	1	0	AHNAK2	104482305	0.105000	0.21958	0.000000	0.03702	0.004000	0.04260	0.097000	0.15168	-0.074000	0.12820	-1.216000	0.01612	TCC	A|0.978;G|0.022	0.022	strong		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
DCHS2	54798	hgsc.bcm.edu	37	4	155298432	155298432	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:155298432A>G	ENST00000357232.4	-	3	398	c.399T>C	c.(397-399)taT>taC	p.Y133Y	DCHS2_ENST00000339452.1_Silent_p.Y739Y	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	133	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CCAGGAGATCATAGGTAGCTG	0.443																																					p.Y739Y		Atlas-SNP	.											.	DCHS2	594	.	0			c.T2217C						PASS	.						134.0	121.0	126.0					4																	155298432		2203	4300	6503	SO:0001819	synonymous_variant	54798	exon2			GAGATCATAGGTA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.399T>C	4.37:g.155298432A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			.	.	none		0.443	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
TPM1	7168	hgsc.bcm.edu	37	15	63351873	63351873	+	Silent	SNP	T	T	C	rs11558747	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:63351873T>C	ENST00000403994.3	+	4	566	c.486T>C	c.(484-486)taT>taC	p.Y162Y	TPM1_ENST00000559556.1_Silent_p.Y162Y|TPM1_ENST00000267996.7_Silent_p.Y162Y|TPM1_ENST00000317516.7_Silent_p.Y126Y|TPM1_ENST00000559397.1_Silent_p.Y162Y|TPM1_ENST00000404484.4_Silent_p.Y126Y|TPM1_ENST00000334895.5_Silent_p.Y126Y|TPM1_ENST00000357980.4_Silent_p.Y204Y|TPM1_ENST00000358278.3_Silent_p.Y162Y|TPM1_ENST00000560959.1_Silent_p.Y126Y|TPM1_ENST00000560445.1_Intron|TPM1_ENST00000288398.6_Silent_p.Y162Y|TPM1_ENST00000559281.1_Silent_p.Y126Y	NM_001018005.1	NP_001018005.1	P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	162					cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						ACCGCAAATATGAAGAGGTCA	0.502													T|||	121	0.0241613	0.0015	0.0447	5008	,	,		19741	0.0		0.0676	False		,,,				2504	0.0204				p.Y162Y		Atlas-SNP	.											.	TPM1	59	.	0			c.T486C						PASS	.	T	,,,,,,	49,4357	50.2+/-85.5	1,47,2155	60.0	59.0	59.0		486,486,486,486,486,378,486	4.7	1.0	15	dbSNP_120	59	613,7987	161.1+/-214.1	26,561,3713	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPM1	NM_000366.5,NM_001018004.1,NM_001018005.1,NM_001018006.1,NM_001018007.1,NM_001018008.1,NM_001018020.1	,,,,,,	27,608,5868	CC,CT,TT		7.1279,1.1121,5.09	,,,,,,	162/285,162/285,162/285,162/285,162/285,126/246,162/285	63351873	662,12344	2203	4300	6503	SO:0001819	synonymous_variant	7168	exon4			CAAATATGAAGAG	AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416		"""Tropomyosins"""	12010	protein-coding gene	gene with protein product		191010	"""chromosome 15 open reading frame 13"", ""cardiomyopathy, hypertrophic 3"""	C15orf13, CMH3		10343096, 8205619	Standard	XM_005254637		Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000403994.3:c.486T>C	15.37:g.63351873T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_001018007	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Silent	SNP	ENST00000403994.3	37	CCDS45273.1																																																																																			T|0.951;C|0.049	0.049	strong		0.502	TPM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417083.2	NM_001018004	
OAS3	4940	hgsc.bcm.edu	37	12	113386779	113386779	+	Missense_Mutation	SNP	C	C	G	rs2285933	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:113386779C>G	ENST00000228928.7	+	6	1322	c.1143C>G	c.(1141-1143)agC>agG	p.S381R	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	381	Linker.		S -> R (in dbSNP:rs2285933). {ECO:0000269|PubMed:15489334}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						GAGCAGGGAGCAAACCTCCCT	0.607													C|||	1405	0.280551	0.4092	0.379	5008	,	,		19978	0.1577		0.2565	False		,,,				2504	0.1881				p.S381R		Atlas-SNP	.											OAS3,brain,glioma,0,1	OAS3	63	1	0			c.C1143G						PASS	.	C	ARG/SER	1450,2514		249,952,781	37.0	41.0	40.0		1143	0.0	0.0	12	dbSNP_100	40	2178,6156		291,1596,2280	yes	missense	OAS3	NM_006187.2	110	540,2548,3061	GG,GC,CC		26.1339,36.5792,29.5007	benign	381/1088	113386779	3628,8670	1982	4167	6149	SO:0001583	missense	4940	exon6			AGGGAGCAAACCT	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.1143C>G	12.37:g.113386779C>G	ENSP00000228928:p.Ser381Arg	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	166	84	0.506024	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	621	0.28434065934065933	194	0.3943089430894309	117	0.32320441988950277	105	0.18356643356643357	205	0.2704485488126649	C	2.291	-0.362396	0.05103	0.365792	0.261339	ENSG00000111331	ENST00000228928;ENST00000323881	T	0.06687	3.27	3.0	0.0313	0.14170	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.26002	0.139	B	0.12156	0.007	T	0.47623	-0.9103	8	0.51188	T	0.08	.	3.3881	0.07278	0.0:0.52:0.2178:0.2622	rs2285933;rs2285933	381	Q9Y6K5	OAS3_HUMAN	R	381	ENSP00000228928:S381R	ENSP00000228928:S381R	S	+	3	2	OAS3	111871162	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.993000	0.03720	-0.002000	0.14469	-0.145000	0.13849	AGC	C|0.724;G|0.276	0.276	strong		0.607	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
GALNS	2588	hgsc.bcm.edu	37	16	88884466	88884466	+	Silent	SNP	C	C	T	rs2303271	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:88884466C>T	ENST00000268695.5	-	13	1519	c.1431G>A	c.(1429-1431)gaG>gaA	p.E477E	GALNS_ENST00000542788.1_Silent_p.E402E	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	477					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		GGACCAAGGCCTCCTGGTGCT	0.672													C|||	2375	0.474241	0.4947	0.4265	5008	,	,		16578	0.627		0.3827	False		,,,				2504	0.4172				p.E477E	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											.	GALNS	37	.	0			c.G1431A						PASS	.	C		2024,2324		475,1074,625	61.0	45.0	51.0		1431	-0.9	0.0	16	dbSNP_100	51	3140,5450		563,2014,1718	no	coding-synonymous	GALNS	NM_000512.4		1038,3088,2343	TT,TC,CC		36.5541,46.5501,39.9134		477/523	88884466	5164,7774	2174	4295	6469	SO:0001819	synonymous_variant	2588	exon13			CAAGGCCTCCTGG	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"""Arylsulfatase family"""	4122	protein-coding gene	gene with protein product	"""Morquio syndrome"", ""mucopolysaccharidosis type IVA"""	612222	"""galactosamine (N-acetyl)-6-sulfate sulfatase"""			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.1431G>A	16.37:g.88884466C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_000512	Q86VK3	Silent	SNP	ENST00000268695.5	37	CCDS10970.1																																																																																			C|0.573;T|0.427	0.427	strong		0.672	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1		
TMEM86A	144110	hgsc.bcm.edu	37	11	18728650	18728650	+	IGR	SNP	T	T	C	rs2289965	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18728650T>C	ENST00000280734.2	+	0	3595				IGSF22_ENST00000513874.1_Missense_Mutation_p.I1131V|IGSF22_ENST00000510673.1_5'Flank|RP11-1081L13.4_ENST00000527285.1_RNA	NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A							integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						TTCATGATGATGTAGTGAGCC	0.582													C|||	947	0.189097	0.0166	0.3429	5008	,	,		20413	0.1339		0.3976	False		,,,				2504	0.1554				p.I1131V		Atlas-SNP	.											.	IGSF22	211	.	0			c.A3391G						PASS	.	C	VAL/ILE	104,1280		8,88,596	176.0	140.0	151.0		3391	2.5	0.3	11	dbSNP_100	151	1267,1915		245,777,569	yes	missense	IGSF22	NM_173588.3	29	253,865,1165	CC,CT,TT		39.8177,7.5145,30.0263	benign	1131/1327	18728650	1371,3195	692	1591	2283	SO:0001628	intergenic_variant	283284	exon21			TGATGATGTAGTG	BC035692	CCDS7844.1	11p15.1	2005-10-28				ENSG00000151117			26890	protein-coding gene	gene with protein product							Standard	NM_153347		Approved	FLJ90119	uc001moz.1	Q8N2M4			11.37:g.18728650T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_173588	Q96AJ0	Missense_Mutation	SNP	ENST00000280734.2	37	CCDS7844.1	511	0.23397435897435898	13	0.026422764227642278	133	0.3674033149171271	68	0.11888111888111888	297	0.391820580474934	C	8.429	0.848099	0.17034	0.075145	0.398177	ENSG00000179057	ENST00000513874	T	0.56444	0.46	3.57	2.53	0.30540	.	.	.	.	.	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	8	0.08179	T	0.78	.	4.9575	0.14050	0.0:0.612:0.1654:0.2226	rs2289965;rs17400035;rs52807214;rs60072054;rs2289965	1131	D6RGV7	.	V	1131	ENSP00000421191:I1131V	ENSP00000421191:I1131V	I	-	1	0	IGSF22	18685226	0.000000	0.05858	0.252000	0.24328	0.490000	0.33462	-0.206000	0.09398	0.218000	0.20820	-0.213000	0.12676	ATC	T|0.800;C|0.200	0.200	strong		0.582	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1	NM_153347	
TUT1	64852	hgsc.bcm.edu	37	11	62343667	62343667	+	Silent	SNP	A	A	T	rs118073625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62343667A>T	ENST00000476907.1	-	9	2215	c.1524T>A	c.(1522-1524)cgT>cgA	p.R508R	EEF1G_ENST00000378019.3_5'Flank|EEF1G_ENST00000532986.1_5'Flank|EEF1G_ENST00000329251.4_5'Flank|MIR3654_ENST00000496634.2_Intron|TUT1_ENST00000308436.7_Silent_p.R546R			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	508	PAP-associated.				mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GCAGGGAGCCACGAAGATCCC	0.612													A|||	9	0.00179712	0.0	0.0014	5008	,	,		18897	0.0		0.007	False		,,,				2504	0.001				p.R546R		Atlas-SNP	.											.	TUT1	122	.	0			c.T1638A						PASS	.	A		4,4374		0,4,2185	18.0	20.0	19.0		1638	-0.2	1.0	11	dbSNP_133	19	81,8511		0,81,4215	no	coding-synonymous	TUT1	NM_022830.2		0,85,6400	TT,TA,AA		0.9427,0.0914,0.6554		546/913	62343667	85,12885	2189	4296	6485	SO:0001819	synonymous_variant	64852	exon9			GGAGCCACGAAGA	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"""RNA binding motif (RRM) containing"""	26184	protein-coding gene	gene with protein product	"""RNA uridylyltransferase"", ""U6 TUTase"", ""TUTase 6"""	610641	"""RNA binding motif protein 21"""	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.1524T>A	11.37:g.62343667A>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	52	17	0.326923	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Silent	SNP	ENST00000476907.1	37																																																																																				A|0.995;T|0.005	0.005	strong		0.612	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830	
ZNF286A	57335	hgsc.bcm.edu	37	17	15604485	15604485	+	Silent	SNP	T	T	C	rs78494624	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:15604485T>C	ENST00000464847.2	+	2	610	c.57T>C	c.(55-57)tcT>tcC	p.S19S	ZNF286A_ENST00000581529.1_Silent_p.S9S|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000395894.2_Silent_p.S19S|ZNF286A_ENST00000593105.1_Silent_p.S9S|ZNF286A_ENST00000395893.2_Silent_p.S19S|ZNF286A_ENST00000472486.1_Silent_p.S9S|ZNF286A_ENST00000580259.1_Silent_p.S19S|ZNF286A_ENST00000421016.1_Silent_p.S19S|ZNF286A_ENST00000585194.1_Silent_p.S19S|ZNF286A_ENST00000583566.1_Silent_p.S19S|ZNF286A_ENST00000413242.2_Silent_p.S19S			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	19					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)	p.S19S(1)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		CCCAGGATTCTCCCCATTTCC	0.473																																					p.S19S		Atlas-SNP	.											ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	1	Substitution - coding silent(1)	pancreas(1)	c.T57C						PASS	.						275.0	242.0	253.0					17																	15604485		2203	4300	6503	SO:0001819	synonymous_variant	57335	exon3			GGATTCTCCCCAT	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"""Zinc fingers, C2H2-type"", ""-"""	13501	protein-coding gene	gene with protein product			"""zinc finger protein 286"""	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.57T>C	17.37:g.15604485T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	263	61	0.231939	NM_020652	B4DKF9|Q96JF3	Silent	SNP	ENST00000464847.2	37	CCDS11172.1																																																																																			T|0.895;C|0.105	0.105	strong		0.473	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652	
CENPF	1063	hgsc.bcm.edu	37	1	214830617	214830617	+	Missense_Mutation	SNP	A	A	G	rs438034	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:214830617A>G	ENST00000366955.3	+	18	8995	c.8827A>G	c.(8827-8829)Aga>Gga	p.R2943G		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	3039	Sufficient for centromere localization.|Sufficient for nuclear localization.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GGAGAATGGTAGAGGACCAAC	0.448													A|||	3097	0.618411	0.354	0.6383	5008	,	,		18995	0.8879		0.5606	False		,,,				2504	0.7434				p.R2943G	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A8827G						PASS	.	A	GLY/ARG	1750,2656	521.2+/-370.5	351,1048,804	68.0	65.0	66.0	http://www.ncbi.nlm.nih.gov/pubmed?term	8827	2.5	0.0	1	dbSNP_80	66	4649,3951	602.8+/-394.6	1236,2177,887	yes	missense	CENPF	NM_016343.3	125	1587,3225,1691	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	45.9419,39.7186,49.2004	benign	2943/3115	214830617	6399,6607	2203	4300	6503	SO:0001583	missense	1063	exon18			AATGGTAGAGGAC	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8827A>G	1.37:g.214830617A>G	ENSP00000355922:p.Arg2943Gly	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	78	32	0.410256	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	1357	0.6213369963369964	171	0.3475609756097561	222	0.6132596685082873	525	0.9178321678321678	439	0.579155672823219	A	11.90	1.777316	0.31411	0.397186	0.540581	ENSG00000117724	ENST00000366955	T	0.02763	4.17	5.5	2.52	0.30459	.	0.924044	0.08889	N	0.878910	T	0.00012	0.0000	N	0.01705	-0.755	0.53688	P	2.599999999997049E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.11084	-1.0602	9	0.22706	T	0.39	.	7.8784	0.29608	0.1505:0.1331:0.7163:0.0	rs438034;rs3190325;rs17799902;rs60119608;rs438034	3039	P49454	CENPF_HUMAN	G	2943	ENSP00000355922:R2943G	ENSP00000355922:R2943G	R	+	1	2	CENPF	212897240	0.274000	0.24191	0.000000	0.03702	0.469000	0.32828	1.447000	0.35101	0.331000	0.23511	-0.248000	0.11899	AGA	T|0.003;G|0.549	0.549	strong		0.448	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
HLA-C	3107	hgsc.bcm.edu	37	6	31239430	31239430	+	Missense_Mutation	SNP	C	C	T	rs41543814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239430C>T	ENST00000376228.5	-	2	303	c.289G>A	c.(289-291)Gct>Act	p.A97T	HLA-C_ENST00000383329.3_Missense_Mutation_p.A97T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	97	Alpha-1.		A -> T (in dbSNP:rs41543814).		antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)	p.A97T(2)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACTCGGTCAGCCTGTGCCTGG	0.706													c|||	2314	0.462061	0.3797	0.5202	5008	,	,		11727	0.6567		0.4404	False		,,,				2504	0.3538				p.A97T		Atlas-SNP	.											HLA-C_ENST00000383329,NS,lymphoid_neoplasm,0,2	HLA-C	92	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G289A						scavenged	.						46.0	46.0	46.0					6																	31239430		1511	2709	4220	SO:0001583	missense	3107	exon2			GGTCAGCCTGTGC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.289G>A	6.37:g.31239430C>T	ENSP00000365402:p.Ala97Thr	Somatic	192	4	0.0208333		WXS	Illumina HiSeq	Phase_I	216	213	0.986111	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1058|1058	0.48443223443223443|0.48443223443223443	181|181	0.3678861788617886|0.3678861788617886	183|183	0.505524861878453|0.505524861878453	369|369	0.6451048951048951|0.6451048951048951	325|325	0.4287598944591029|0.4287598944591029	N|N	7.393|7.393	0.631156|0.631156	0.14322|0.14322	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.54;9.54|.	2.81|2.81	-5.5|-5.5	0.02576|0.02576	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	14.671800|.	0.01100|.	N|.	0.005358|.	T|T	0.05135|0.05135	0.0137|0.0137	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.09022|.	0.002;0.0;0.0;0.0|.	B;B;B;B|.	0.12837|.	0.008;0.004;0.008;0.003|.	T|T	0.31641|0.31641	-0.9936|-0.9936	8|3	0.02654|.	T|.	1|.	.|.	0.9604|0.9604	0.01394|0.01394	0.1547:0.2311:0.1576:0.4566|0.1547:0.2311:0.1576:0.4566	rs41543814|rs41543814	97;97;97;97|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	T|D	97;97;97;134|96	ENSP00000365402:A97T;ENSP00000372819:A97T|.	ENSP00000365402:A97T|.	A|G	-|-	1|2	0|0	HLA-C|HLA-C	31347409|31347409	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-6.348000|-6.348000	0.00069|0.00069	-1.130000|-1.130000	0.02914|0.02914	-2.495000|-2.495000	0.00193|0.00193	GCT|GGC	C|0.546;T|0.454	0.454	strong		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74206658	74206658	+	Silent	SNP	G	G	A	rs758773	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:74206658G>A	ENST00000286523.5	-	2	836	c.54C>T	c.(52-54)ttC>ttT	p.F18F	ELMSAN1_ENST00000394071.2_Silent_p.F18F|ELMSAN1_ENST00000486739.1_5'Flank	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	18					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										CCTGGCCCCCGAAGAGGCAAC	0.647													G|||	766	0.152955	0.0507	0.1182	5008	,	,		18910	0.1419		0.1839	False		,,,				2504	0.2955				p.F18F		Atlas-SNP	.											.	.	.	.	0			c.C54T						PASS	.	G	,	286,4120	150.7+/-184.7	12,262,1929	43.0	47.0	46.0		54,54	0.1	1.0	14	dbSNP_86	46	1665,6935	290.1+/-299.6	163,1339,2798	no	coding-synonymous,coding-synonymous	C14orf43	NM_001043318.1,NM_194278.3	,	175,1601,4727	AA,AG,GG		19.3605,6.4911,15.0008	,	18/1046,18/1046	74206658	1951,11055	2203	4300	6503	SO:0001819	synonymous_variant	91748	exon2			GCCCCCGAAGAGG	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.54C>T	14.37:g.74206658G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Silent	SNP	ENST00000286523.5	37	CCDS9819.1																																																																																			G|0.859;A|0.141	0.141	strong		0.647	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278	
LAMTOR5	10542	hgsc.bcm.edu	37	1	110950277	110950277	+	5'UTR	SNP	G	G	A	rs6698159	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:110950277G>A	ENST00000602318.1	-	0	53				LAMTOR5-AS1_ENST00000609512.1_RNA|LAMTOR5_ENST00000602858.1_5'Flank|LAMTOR5-AS1_ENST00000457535.1_RNA|LAMTOR5_ENST00000483260.1_5'UTR|LAMTOR5-AS1_ENST00000608067.1_RNA|LAMTOR5-AS1_ENST00000608499.1_RNA|LAMTOR5-AS1_ENST00000608253.1_RNA|LAMTOR5-AS1_ENST00000598454.1_RNA|LAMTOR5-AS1_ENST00000608602.1_RNA|LAMTOR5-AS1_ENST00000609709.1_RNA|LAMTOR5-AS1_ENST00000610148.1_RNA|LAMTOR5-AS1_ENST00000590826.1_RNA|LAMTOR5-AS1_ENST00000590413.1_RNA|LAMTOR5-AS1_ENST00000609244.1_RNA|LAMTOR5-AS1_ENST00000608486.1_RNA|LAMTOR5_ENST00000474861.2_5'UTR|LAMTOR5-AS1_ENST00000587691.1_RNA|LAMTOR5_ENST00000256644.4_Missense_Mutation_p.P71L			O43504	LTOR5_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5						cellular response to amino acid stimulus (GO:0071230)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)|protein localization to lysosome (GO:0061462)|regulation of cell size (GO:0008361)|response to virus (GO:0009615)|viral genome replication (GO:0019079)	cytosol (GO:0005829)|lysosome (GO:0005764)|Ragulator complex (GO:0071986)											AGAACCCAGCGGCACGGCACG	0.632													G|||	489	0.0976438	0.1377	0.0562	5008	,	,		16882	0.0476		0.1083	False		,,,				2504	0.1135				p.P71L		Atlas-SNP	.											.	.	.	.	0			c.C212T						PASS	.	G	LEU/PRO	582,3824	257.7+/-262.0	32,518,1653	78.0	66.0	70.0		212	-3.2	0.0	1	dbSNP_116	70	1077,7523	226.2+/-262.0	55,967,3278	yes	missense	HBXIP	NM_006402.2	98	87,1485,4931	AA,AG,GG		12.5233,13.2093,12.7557		71/174	110950277	1659,11347	2203	4300	6503	SO:0001623	5_prime_UTR_variant	10542	exon1			CCCAGCGGCACGG	AF029890	CCDS824.1	1p12	2012-09-24	2012-09-24	2012-09-24	ENSG00000134248	ENSG00000134248			17955	protein-coding gene	gene with protein product	"""HBx-interacting protein"", ""hepatitis B virus x-interacting protein (9.6kD)"""	608521	"""hepatitis B virus x interacting protein"""	HBXIP		9499022, 22980980	Standard	NM_006402		Approved	XIP, MGC71071	uc001dzr.3	O43504	OTTHUMG00000011568	ENST00000602318.1:c.-35C>T	1.37:g.110950277G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	NM_006402	Q6IBD8	Missense_Mutation	SNP	ENST00000602318.1	37		223	0.1021062271062271	88	0.17886178861788618	20	0.055248618784530384	25	0.043706293706293704	90	0.11873350923482849	G	7.173	0.588085	0.13812	0.132093	0.125233	ENSG00000134248	ENST00000256644	.	.	.	4.05	-3.2	0.05156	.	6.096850	0.01218	N	0.008001	T	0.02119	0.0066	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.18116	-1.0347	5	0.02654	T	1	11.6479	4.793	0.13257	0.422:0.2918:0.2863:0.0	rs6698159;rs52819665;rs6698159	.	.	.	L	71	.	ENSP00000256644:P71L	P	-	2	0	HBXIP	110751800	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.505000	0.06367	-0.594000	0.05836	-0.300000	0.09419	CCG	G|0.880;A|0.120	0.120	strong		0.632	LAMTOR5-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467909.1	NM_006402	
MYOM2	9172	hgsc.bcm.edu	37	8	2050519	2050519	+	Silent	SNP	C	C	T	rs2294071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:2050519C>T	ENST00000262113.4	+	21	2823	c.2682C>T	c.(2680-2682)ggC>ggT	p.G894G	MYOM2_ENST00000523438.1_Silent_p.G319G	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	894	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		ATGCAAATGGCGTGGGGAAGC	0.512													C|||	524	0.104633	0.1384	0.062	5008	,	,		20417	0.0754		0.0636	False		,,,				2504	0.1616				p.G894G		Atlas-SNP	.											.	MYOM2	251	.	0			c.C2682T						PASS	.	C		632,3774	271.9+/-270.5	41,550,1612	79.0	69.0	72.0		2682	-10.5	0.0	8	dbSNP_100	72	577,8023	154.9+/-209.1	26,525,3749	no	coding-synonymous	MYOM2	NM_003970.2		67,1075,5361	TT,TC,CC		6.7093,14.3441,9.2957		894/1466	2050519	1209,11797	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon21			AAATGGCGTGGGG		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.2682C>T	8.37:g.2050519C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			C|0.901;T|0.099	0.099	strong		0.512	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
MALL	7851	hgsc.bcm.edu	37	2	110849222	110849222	+	Silent	SNP	G	G	A	rs141095578	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:110849222G>A	ENST00000272462.2	-	2	1004	c.231C>T	c.(229-231)taC>taT	p.Y77Y	MALL_ENST00000427178.1_Intron	NM_005434.4	NP_005425.1	Q13021	MALL_HUMAN	mal, T-cell differentiation protein-like	77	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cholesterol homeostasis (GO:0042632)	clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)		p.Y77Y(1)		kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	9				Epithelial(1;0.0546)|STAD - Stomach adenocarcinoma(1;0.18)		ATCCAAACAAGTAAGACAACA	0.483																																					p.Y77Y		Atlas-SNP	.											MALL,NS,carcinoma,0,1	MALL	14	1	1	Substitution - coding silent(1)	stomach(1)	c.C231T						scavenged	.						65.0	60.0	61.0					2																	110849222		2201	4296	6497	SO:0001819	synonymous_variant	7851	exon2			AAACAAGTAAGAC	U17077	CCDS2085.1	2q13	2008-02-05			ENSG00000144063	ENSG00000144063			6818	protein-coding gene	gene with protein product		602022				9326933	Standard	NM_005434		Approved	BENE	uc002tfk.3	Q13021	OTTHUMG00000131196	ENST00000272462.2:c.231C>T	2.37:g.110849222G>A		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	132	26	0.19697	NM_005434	B3KWR6|Q9BTU0	Silent	SNP	ENST00000272462.2	37	CCDS2085.1																																																																																			G|0.884;A|0.116	0.116	strong		0.483	MALL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253921.1	NM_005434	
SMYD4	114826	hgsc.bcm.edu	37	17	1703982	1703982	+	Missense_Mutation	SNP	C	C	T	rs9913923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1703982C>T	ENST00000305513.7	-	5	873	c.706G>A	c.(706-708)Ggc>Agc	p.G236S		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	236	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		G -> S (in dbSNP:rs9913923).				metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						ACGCATAAGCCGATGGATGAT	0.502													C|||	654	0.130591	0.2451	0.0735	5008	,	,		12317	0.0635		0.0805	False		,,,				2504	0.137				p.G236S		Atlas-SNP	.											.	SMYD4	50	.	0			c.G706A						PASS	.	C	SER/GLY	976,3430	367.1+/-318.1	107,762,1334	171.0	165.0	167.0		706	-6.1	0.2	17	dbSNP_119	167	828,7772	190.7+/-237.1	35,758,3507	yes	missense	SMYD4	NM_052928.2	56	142,1520,4841	TT,TC,CC		9.6279,22.1516,13.8705	benign	236/805	1703982	1804,11202	2203	4300	6503	SO:0001583	missense	114826	exon5			ATAAGCCGATGGA	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.706G>A	17.37:g.1703982C>T	ENSP00000304360:p.Gly236Ser	Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	226	126	0.557522	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	266	0.12179487179487179	134	0.27235772357723576	31	0.0856353591160221	48	0.08391608391608392	53	0.06992084432717678	C	0.014	-1.582771	0.00879	0.221516	0.096279	ENSG00000186532	ENST00000305513	T	0.08896	3.04	5.99	-6.05	0.02172	SET domain (1);	0.750916	0.14769	N	0.299484	T	0.00012	0.0000	N	0.02103	-0.685	0.58432	P	1.999999999946489E-6	B	0.12630	0.006	B	0.04013	0.001	T	0.34428	-0.9829	9	0.02654	T	1	-0.033	10.6048	0.45388	0.0:0.2418:0.5253:0.2329	rs9913923;rs52828951;rs56419688;rs59448424;rs9913923	236	Q8IYR2	SMYD4_HUMAN	S	236	ENSP00000304360:G236S	ENSP00000304360:G236S	G	-	1	0	SMYD4	1650732	0.002000	0.14202	0.177000	0.23020	0.001000	0.01503	-0.797000	0.04570	-0.727000	0.04888	-0.302000	0.09304	GGC	C|0.863;T|0.137	0.137	strong		0.502	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
SCN9A	6335	hgsc.bcm.edu	37	2	167144995	167144995	+	Silent	SNP	T	T	C	rs13402180	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:167144995T>C	ENST00000409435.1	-	9	1265	c.1266A>G	c.(1264-1266)gaA>gaG	p.E422E	SCN9A_ENST00000303354.6_Silent_p.E423E|SCN9A_ENST00000375387.4_Silent_p.E423E|SCN9A_ENST00000409672.1_Silent_p.E422E|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	422					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCTGTTGAAATTCTAATTCTT	0.363													T|||	1775	0.354433	0.357	0.3242	5008	,	,		14756	0.3065		0.4036	False		,,,				2504	0.3712				p.E422E		Atlas-SNP	.											.	SCN9A	296	.	0			c.A1266G						PASS	.	T		1403,2275		281,841,717	143.0	150.0	148.0		1266	4.6	1.0	2	dbSNP_121	148	3184,5004		600,1984,1510	no	coding-synonymous	SCN9A	NM_002977.3		881,2825,2227	CC,CT,TT		38.8862,38.1457,38.6567		422/1978	167144995	4587,7279	1839	4094	5933	SO:0001819	synonymous_variant	6335	exon10			TTGAAATTCTAAT	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1266A>G	2.37:g.167144995T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			C|0.338;T|0.662	0.338	strong		0.363	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
LRRC34	151827	hgsc.bcm.edu	37	3	169514585	169514585	+	Missense_Mutation	SNP	A	A	T	rs10936600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:169514585A>T	ENST00000316515.7	-	7	997	c.721T>A	c.(721-723)Tta>Ata	p.L241I	LRRC34_ENST00000522830.1_Missense_Mutation_p.L225I|LRRC34_ENST00000522526.2_Missense_Mutation_p.L254I|LRRC34_ENST00000524327.1_5'UTR|RP11-362K14.6_ENST00000602835.1_RNA|LRRC34_ENST00000446859.1_Missense_Mutation_p.L286I|RP11-362K14.7_ENST00000602913.1_RNA	NM_153353.4	NP_699184.2	Q8IZ02	LRC34_HUMAN	leucine rich repeat containing 34	241			L -> I (in dbSNP:rs10936600).							breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(2)	10	all_cancers(22;4.12e-22)|all_epithelial(15;7.54e-27)|all_lung(20;1.63e-16)|Lung NSC(18;6.92e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			GCATCACATAACTGTTGTATA	0.368													A|||	1367	0.272963	0.0598	0.353	5008	,	,		17676	0.5784		0.2425	False		,,,				2504	0.2209				p.L286I		Atlas-SNP	.											.	LRRC34	30	.	0			c.T856A						PASS	.	A	ILE/LEU,ILE/LEU,ILE/LEU	422,3984	204.5+/-226.7	19,384,1800	140.0	118.0	125.0		856,856,760	-0.4	0.0	3	dbSNP_120	125	2129,6471	365.8+/-334.1	281,1567,2452	yes	missense,missense,missense	LRRC34	NM_001172779.1,NM_001172780.1,NM_153353.4	5,5,5	300,1951,4252	TT,TA,AA		24.7558,9.5778,19.614	probably-damaging,probably-damaging,probably-damaging	286/465,286/362,254/433	169514585	2551,10455	2203	4300	6503	SO:0001583	missense	151827	exon8			CACATAACTGTTG	AK095125	CCDS3208.1, CCDS3208.2, CCDS54672.1	3q26.2	2014-03-18			ENSG00000171757	ENSG00000171757			28408	protein-coding gene	gene with protein product						12477932	Standard	NM_153353		Approved	MGC27085	uc003ffy.3	Q8IZ02	OTTHUMG00000164419	ENST00000316515.7:c.721T>A	3.37:g.169514585A>T	ENSP00000326150:p.Leu241Ile	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	262	147	0.561069	NM_001172779	B4DEJ7|E9PBH2|G5E9T7	Missense_Mutation	SNP	ENST00000316515.7	37		674	0.3086080586080586	43	0.08739837398373984	104	0.287292817679558	335	0.5856643356643356	192	0.2532981530343008	A	12.07	1.827537	0.32329	0.095778	0.247558	ENSG00000171757	ENST00000446859;ENST00000316515;ENST00000522830;ENST00000522526;ENST00000528597	T;T;T;T;T	0.61627	0.09;0.09;0.09;0.09;0.29	5.97	-0.438	0.12268	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.49778	1.585	0.38734	P	0.046262000000000025	D;D;D;D;D	0.89917	0.998;0.999;0.998;1.0;0.999	D;D;D;D;D	0.80764	0.947;0.994;0.969;0.992;0.994	T	0.46484	-0.9188	9	0.20046	T	0.44	-12.371	12.0559	0.53536	0.4398:0.0:0.5602:0.0	rs10936600;rs52820542;rs56578627;rs59898455;rs10936600	273;225;225;286;241	B4DHF2;B3KT77;G3V115;G5E9T7;Q8IZ02	.;.;.;.;LRC34_HUMAN	I	286;241;225;254;35	ENSP00000414635:L286I;ENSP00000326150:L241I;ENSP00000429593:L225I;ENSP00000429278:L254I;ENSP00000436883:L35I	ENSP00000326150:L241I	L	-	1	2	LRRC34	170997279	0.759000	0.28416	0.001000	0.08648	0.001000	0.01503	1.045000	0.30341	-0.269000	0.09298	-0.923000	0.02734	TTA	A|0.759;T|0.241	0.241	strong		0.368	LRRC34-201	KNOWN	basic	protein_coding	protein_coding		NM_153353	
BACE1	23621	hgsc.bcm.edu	37	11	117163824	117163824	+	Silent	SNP	C	C	G	rs638405	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:117163824C>G	ENST00000313005.6	-	5	1246	c.786G>C	c.(784-786)gtG>gtC	p.V262V	BACE1_ENST00000445823.2_Silent_p.V218V|BACE1_ENST00000428381.2_Silent_p.V193V|BACE1_ENST00000392937.6_Silent_p.V162V|BACE1_ENST00000510630.1_Silent_p.V137V|BACE1_ENST00000513780.1_Silent_p.V237V|BACE1_ENST00000514464.1_5'Flank|BACE1_ENST00000528053.1_Silent_p.V262V	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	262					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		GCACAATGATCACCTCATAAT	0.507													C|||	2772	0.553514	0.5363	0.549	5008	,	,		17135	0.6498		0.4076	False		,,,				2504	0.6309				p.V262V		Atlas-SNP	.											.	BACE1	33	.	0			c.G786C						PASS	.	C	,,,,,	2289,2113	601.2+/-389.7	589,1111,501	250.0	238.0	242.0		486,411,786,654,711,579	0.6	1.0	11	dbSNP_83	242	3400,5192	502.6+/-375.7	683,2034,1579	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BACE1	NM_001207048.1,NM_001207049.1,NM_012104.4,NM_138971.3,NM_138972.3,NM_138973.3	,,,,,	1272,3145,2080	GG,GC,CC		39.5717,48.0009,43.7817	,,,,,	162/402,137/377,262/502,218/458,237/477,193/433	117163824	5689,7305	2201	4296	6497	SO:0001819	synonymous_variant	23621	exon5			AATGATCACCTCA	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"""beta-site APP-cleaving enzyme"""	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.786G>C	11.37:g.117163824C>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	146	62	0.424658	NM_012104	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Silent	SNP	ENST00000313005.6	37	CCDS8383.1	1119	0.5123626373626373	278	0.5650406504065041	190	0.5248618784530387	354	0.6188811188811189	297	0.391820580474934	C	10.34	1.322171	0.23994	0.519991	0.395717	ENSG00000186318	ENST00000530844;ENST00000504995	.	.	.	6.07	0.58	0.17402	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40553	-0.9557	3	.	.	.	.	1.3856	0.02240	0.1254:0.3307:0.2724:0.2714	rs638405;rs60889749;rs638405	.	.	.	H	132;192	.	.	D	-	1	0	BACE1	116669034	0.957000	0.32711	1.000000	0.80357	0.977000	0.68977	0.011000	0.13264	0.414000	0.25790	-0.768000	0.03414	GAT	C|0.533;G|0.467	0.467	strong		0.507	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1		
TONSL	4796	hgsc.bcm.edu	37	8	145661320	145661320	+	Silent	SNP	G	G	A	rs2721140	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:145661320G>A	ENST00000409379.3	-	17	2525	c.2496C>T	c.(2494-2496)gcC>gcT	p.A832A	AC084125.4_ENST00000442850.1_RNA|AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	832					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						GCCAGTCCCCGGCCAGGCACT	0.741													g|||	2347	0.46865	0.4115	0.438	5008	,	,		13786	0.4246		0.4662	False		,,,				2504	0.6155				p.A832A		Atlas-SNP	.											TONSL_ENST00000409379,rectum,carcinoma,0,2	TONSL	128	2	0			c.C2496T						scavenged	.			1747,2459		402,943,758	8.0	11.0	10.0		2496	-8.9	0.0	8	dbSNP_100	10	3725,4593		923,1879,1357	no	coding-synonymous	TONSL	NM_013432.4		1325,2822,2115	AA,AG,GG		44.7824,41.5359,43.6921		832/1379	145661320	5472,7052	2103	4159	6262	SO:0001819	synonymous_variant	4796	exon17			GTCCCCGGCCAGG		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"""Ankyrin repeat domain containing"""	7801	protein-coding gene	gene with protein product		604546	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"""	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.2496C>T	8.37:g.145661320G>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Silent	SNP	ENST00000409379.3	37	CCDS34968.2																																																																																			G|0.603;A|0.397	0.397	strong		0.741	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432	
HMGXB3	22993	hgsc.bcm.edu	37	5	149404179	149404179	+	Missense_Mutation	SNP	G	G	T	rs35341726	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149404179G>T	ENST00000502717.1	+	7	1860	c.1396G>T	c.(1396-1398)Gta>Tta	p.V466L	HMGXB3_ENST00000503427.1_Missense_Mutation_p.V434L	NM_014983.2	NP_055798	Q12766	HMGX3_HUMAN	HMG box domain containing 3	712					phosphorylation (GO:0016310)	nucleus (GO:0005634)	DNA binding (GO:0003677)|kinase activity (GO:0016301)			central_nervous_system(1)|endometrium(3)|kidney(3)|skin(2)	9						TGGAGCAGACGTACCAACACC	0.502													G|||	349	0.0696885	0.1097	0.0303	5008	,	,		19101	0.0704		0.0487	False		,,,				2504	0.0644				p.V466L		Atlas-SNP	.											.	HMGXB3	31	.	0			c.G1396T						PASS	.	G	LEU/VAL	131,1253		5,121,566	60.0	58.0	59.0		1396	-6.3	0.0	5	dbSNP_126	59	185,2997		7,171,1413	yes	missense	HMGXB3	NM_014983.2	32	12,292,1979	TT,TG,GG		5.814,9.4653,6.9207	benign	466/1293	149404179	316,4250	692	1591	2283	SO:0001583	missense	22993	exon7			GCAGACGTACCAA	D83778	CCDS54935.1	5q33.1	2011-07-01		2009-01-05	ENSG00000113716	ENSG00000113716		"""High mobility group / Non-canonical"""	28982	protein-coding gene	gene with protein product				HMGX3		8724849	Standard	NM_014983		Approved	SMF, KIAA0194	uc003lrk.4	Q12766	OTTHUMG00000163493	ENST00000502717.1:c.1396G>T	5.37:g.149404179G>T	ENSP00000421917:p.Val466Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_014983	G5E9Y4|Q86UG3|Q9UMF4	Missense_Mutation	SNP	ENST00000502717.1	37	CCDS54935.1	151	0.06913919413919414	63	0.12804878048780488	11	0.03038674033149171	40	0.06993006993006994	37	0.048812664907651716	G	3.932	-0.016051	0.07681	0.094653	0.05814	ENSG00000113716	ENST00000503427;ENST00000502717	.	.	.	5.94	-6.34	0.01982	.	0.983709	0.08350	N	0.959441	T	0.00241	0.0007	N	0.25647	0.755	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30149	-0.9988	8	0.87932	D	0	0.0752	5.8724	0.18810	0.3456:0.0998:0.4571:0.0975	rs35341726;rs61748730	712	Q12766	HMGX3_HUMAN	L	434;466	.	ENSP00000421917:V466L	V	+	1	0	HMGXB3	149384372	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.180000	0.01258	-0.672000	0.05266	-1.027000	0.02421	GTA	G|0.934;T|0.066	0.066	strong		0.502	HMGXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373771.1	XM_001717202	
SI	6476	hgsc.bcm.edu	37	3	164773057	164773057	+	Silent	SNP	G	G	A	rs9290257	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:164773057G>A	ENST00000264382.3	-	13	1499	c.1437C>T	c.(1435-1437)aaC>aaT	p.N479N		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	479	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TGCAGTTTGGGTTAGTGAAAT	0.323										HNSCC(35;0.089)			A|||	3100	0.61901	0.4735	0.6225	5008	,	,		13975	0.8313		0.6312	False		,,,				2504	0.5818				p.N479N		Atlas-SNP	.											.	SI	500	.	0			c.C1437T						PASS	.	A		2160,2246	593.3+/-388.0	529,1102,572	124.0	120.0	121.0		1437	2.7	0.9	3	dbSNP_119	121	5149,3451	507.6+/-376.9	1538,2073,689	no	coding-synonymous	SI	NM_001041.3		2067,3175,1261	AA,AG,GG		40.1279,49.0241,43.8029		479/1828	164773057	7309,5697	2203	4300	6503	SO:0001819	synonymous_variant	6476	exon13			GTTTGGGTTAGTG	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.1437C>T	3.37:g.164773057G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	37	CCDS3196.1																																																																																			G|0.403;A|0.597	0.597	strong		0.323	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
ZAP70	7535	hgsc.bcm.edu	37	2	98354511	98354511	+	Silent	SNP	G	G	A	rs3192177	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:98354511G>A	ENST00000264972.5	+	13	1892	c.1677G>A	c.(1675-1677)gaG>gaA	p.E559E	ZAP70_ENST00000451498.2_Silent_p.E252E|ZAP70_ENST00000442208.1_Silent_p.E433E|ZAP70_ENST00000463643.1_3'UTR	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	559	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						AGCGGATGGAGTGCCCACCAG	0.612													G|||	743	0.148363	0.087	0.2075	5008	,	,		17953	0.0109		0.3618	False		,,,				2504	0.1115				p.E559E		Atlas-SNP	.											.	ZAP70	77	.	0			c.G1677A						PASS	.	G	,	555,3851	245.0+/-254.1	39,477,1687	91.0	87.0	89.0		1677,756	1.6	1.0	2	dbSNP_105	89	2939,5661	444.1+/-360.6	510,1919,1871	no	coding-synonymous,coding-synonymous	ZAP70	NM_001079.3,NM_207519.1	,	549,2396,3558	AA,AG,GG		34.1744,12.5965,26.8645	,	559/620,252/313	98354511	3494,9512	2203	4300	6503	SO:0001819	synonymous_variant	7535	exon13			GATGGAGTGCCCA	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"""SH2 domain containing"""	12858	protein-coding gene	gene with protein product		176947	"""zeta-chain (TCR) associated protein kinase (70 kD)"""	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.1677G>A	2.37:g.98354511G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	200	103	0.515	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Silent	SNP	ENST00000264972.5	37	CCDS33254.1																																																																																			G|0.786;A|0.214	0.214	strong		0.612	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1		
C15orf27	123591	hgsc.bcm.edu	37	15	76496232	76496232	+	Missense_Mutation	SNP	G	G	A	rs937732	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:76496232G>A	ENST00000388942.3	+	11	1448	c.1172G>A	c.(1171-1173)cGc>cAc	p.R391H		NM_152335.2	NP_689548.2	Q2M3C6	CO027_HUMAN	chromosome 15 open reading frame 27	391			R -> H (in dbSNP:rs937732). {ECO:0000269|PubMed:14702039}.		calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|membrane depolarization during action potential (GO:0086010)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|large_intestine(1)|lung(10)|pancreas(1)	13						AGTGCCTCCCGCAGCTCAGTC	0.657													G|||	1874	0.374201	0.2284	0.3256	5008	,	,		17152	0.5794		0.2684	False		,,,				2504	0.5031				p.R391H		Atlas-SNP	.											.	C15orf27	32	.	0			c.G1172A						PASS	.	G	HIS/ARG	1063,3331	388.2+/-326.8	111,841,1245	77.0	74.0	75.0		1172	0.9	0.3	15	dbSNP_86	75	2242,6346	380.3+/-339.6	289,1664,2341	yes	missense	C15orf27	NM_152335.2	29	400,2505,3586	AA,AG,GG		26.1062,24.1921,25.4583	benign	391/532	76496232	3305,9677	2197	4294	6491	SO:0001583	missense	123591	exon11			CCTCCCGCAGCTC	AK095509	CCDS10289.2	15q23-q24.1	2012-09-27			ENSG00000169758	ENSG00000169758			26763	protein-coding gene	gene with protein product						14702039, 22020278	Standard	NM_152335		Approved	FLJ38190	uc002bbq.3	Q2M3C6	OTTHUMG00000142918	ENST00000388942.3:c.1172G>A	15.37:g.76496232G>A	ENSP00000373594:p.Arg391His	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_152335	Q8N993|Q96LL5	Missense_Mutation	SNP	ENST00000388942.3	37	CCDS10289.2	761	0.3484432234432234	119	0.241869918699187	124	0.3425414364640884	316	0.5524475524475524	202	0.26649076517150394	G	11.20	1.569114	0.28003	0.241921	0.261062	ENSG00000169758	ENST00000388942	T	0.37752	1.18	4.9	0.87	0.19102	.	1.238380	0.05458	N	0.550598	T	0.00012	0.0000	L	0.38531	1.155	0.28268	P	0.9245182	B;B	0.21309	0.054;0.003	B;B	0.14023	0.01;0.003	T	0.48031	-0.9070	9	0.38643	T	0.18	-16.2618	7.5721	0.27913	0.3391:0.0:0.6609:0.0	rs937732;rs61128976;rs937732	355;391	Q2M3C6-2;Q2M3C6	.;CO027_HUMAN	H	391	ENSP00000373594:R391H	ENSP00000373594:R391H	R	+	2	0	C15orf27	74283287	0.035000	0.19736	0.343000	0.25615	0.398000	0.30690	0.749000	0.26320	-0.104000	0.12154	0.455000	0.32223	CGC	G|0.704;A|0.296	0.296	strong		0.657	C15orf27-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286637.2	NM_152335	
TTLL2	83887	hgsc.bcm.edu	37	6	167753691	167753691	+	Silent	SNP	C	C	T	rs877653	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:167753691C>T	ENST00000239587.5	+	3	391	c.303C>T	c.(301-303)agC>agT	p.S101S		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	101	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		TGGTGCAAAGCGTCCTCCTGG	0.542													C|||	1552	0.309904	0.1679	0.2824	5008	,	,		20342	0.5079		0.2664	False		,,,				2504	0.362				p.S101S		Atlas-SNP	.											.	TTLL2	82	.	0			c.C303T						PASS	.	C		840,3566	329.6+/-301.1	80,680,1443	62.0	57.0	59.0		303	-6.0	0.2	6	dbSNP_86	59	2537,6063	415.1+/-351.7	364,1809,2127	no	coding-synonymous	TTLL2	NM_031949.4		444,2489,3570	TT,TC,CC		29.5,19.0649,25.9649		101/593	167753691	3377,9629	2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			GCAAAGCGTCCTC	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.303C>T	6.37:g.167753691C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	37	CCDS5301.1																																																																																			C|0.724;T|0.276	0.276	strong		0.542	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
CELSR2	1952	hgsc.bcm.edu	37	1	109810544	109810544	+	Silent	SNP	C	C	A	rs2281894	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:109810544C>A	ENST00000271332.3	+	17	6241	c.6180C>A	c.(6178-6180)cgC>cgA	p.R2060R		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2060					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TGCTCCTGCGCAACGCCACGC	0.677													C|||	1131	0.225839	0.0537	0.2205	5008	,	,		18633	0.4206		0.1928	False		,,,				2504	0.2955				p.R2060R	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.C6180A						PASS	.	C		313,4093	152.9+/-186.6	17,279,1907	29.0	29.0	29.0		6180	0.1	1.0	1	dbSNP_100	29	1603,6997	272.4+/-290.1	169,1265,2866	no	coding-synonymous	CELSR2	NM_001408.2		186,1544,4773	AA,AC,CC		18.6395,7.1039,14.7317		2060/2924	109810544	1916,11090	2203	4300	6503	SO:0001819	synonymous_variant	1952	exon17			CCTGCGCAACGCC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.6180C>A	1.37:g.109810544C>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	165	163	0.987879	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			C|0.824;A|0.176	0.176	strong		0.677	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
SLC6A13	6540	hgsc.bcm.edu	37	12	332362	332362	+	Silent	SNP	C	C	T	rs2289954	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:332362C>T	ENST00000343164.4	-	12	1402	c.1350G>A	c.(1348-1350)gcG>gcA	p.A450A	SLC6A13_ENST00000445055.2_Silent_p.A358A|SLC6A13_ENST00000539668.1_5'UTR	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	450					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			TGCCACTGGCCGCATAGTAGT	0.512													C|||	871	0.173922	0.2224	0.1455	5008	,	,		20321	0.1359		0.173	False		,,,				2504	0.1687				p.A450A		Atlas-SNP	.											SLC6A13,NS,carcinoma,-1,1	SLC6A13	62	1	0			c.G1350A						PASS	.	C	,	1044,3362	383.2+/-324.8	119,806,1278	158.0	129.0	139.0		1074,1350	-6.7	0.6	12	dbSNP_100	139	1709,6891	312.1+/-310.7	171,1367,2762	no	coding-synonymous,coding-synonymous	SLC6A13	NM_001190997.2,NM_016615.4	,	290,2173,4040	TT,TC,CC		19.8721,23.695,21.1672	,	358/511,450/603	332362	2753,10253	2203	4300	6503	SO:0001819	synonymous_variant	6540	exon12			ACTGGCCGCATAG	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1350G>A	12.37:g.332362C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Silent	SNP	ENST00000343164.4	37	CCDS8502.1																																																																																			C|0.802;T|0.198	0.198	strong		0.512	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615	
HCLS1	3059	hgsc.bcm.edu	37	3	121361787	121361787	+	Silent	SNP	G	G	A	rs2070178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121361787G>A	ENST00000314583.3	-	6	532	c.441C>T	c.(439-441)caC>caT	p.H147H	HCLS1_ENST00000428394.2_Silent_p.H147H|HCLS1_ENST00000473883.1_5'UTR	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	147					actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		TCTGAGATGTGTGCTTCTCCA	0.473													G|||	1157	0.23103	0.1838	0.1744	5008	,	,		19684	0.2768		0.2197	False		,,,				2504	0.2996				p.H147H		Atlas-SNP	.											.	HCLS1	78	.	0			c.C441T						PASS	.	G		924,3482	354.9+/-312.8	94,736,1373	198.0	197.0	198.0		441	1.7	0.2	3	dbSNP_96	198	1959,6641	345.6+/-325.8	234,1491,2575	no	coding-synonymous	HCLS1	NM_005335.4		328,2227,3948	AA,AG,GG		22.7791,20.9714,22.1667		147/487	121361787	2883,10123	2203	4300	6503	SO:0001819	synonymous_variant	3059	exon6			AGATGTGTGCTTC		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"""cortactin-like"""	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.441C>T	3.37:g.121361787G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	32	0.380952	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Silent	SNP	ENST00000314583.3	37	CCDS3003.1																																																																																			G|0.772;A|0.228	0.228	strong		0.473	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335	
SIRPG	55423	hgsc.bcm.edu	37	20	1610918	1610918	+	Silent	SNP	T	T	A	rs34442420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:1610918T>A	ENST00000303415.3	-	5	1180	c.1116A>T	c.(1114-1116)atA>atT	p.I372I	SIRPG_ENST00000344103.4_Silent_p.I155I|SIRPG_ENST00000381583.2_Silent_p.I261I|SIRPG_ENST00000216927.4_Silent_p.I261I|SIRPG_ENST00000478145.2_5'UTR|SIRPG_ENST00000381580.1_Silent_p.I339I	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	372					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						GGAGGACAGCTATGAGGAGCA	0.582													t|||	21	0.00419329	0.0	0.0072	5008	,	,		19098	0.0		0.0159	False		,,,				2504	0.0				p.I372I		Atlas-SNP	.											.	SIRPG	61	.	0			c.A1116T						PASS	.	T	,,	10,4390		0,10,2190	61.0	55.0	57.0		783,1116,465	-2.1	0.0	20	dbSNP_126	57	114,8474		1,112,4181	no	coding-synonymous,coding-synonymous,coding-synonymous	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	1,122,6371	AA,AT,TT		1.3274,0.2273,0.9547	,,	261/277,372/388,155/171	1610918	124,12864	2200	4294	6494	SO:0001819	synonymous_variant	55423	exon5			GACAGCTATGAGG	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.1116A>T	20.37:g.1610918T>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_018556	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			T|0.991;A|0.009	0.009	strong		0.582	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
ADSSL1	122622	hgsc.bcm.edu	37	14	105211221	105211221	+	Silent	SNP	C	C	T	rs12432802	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105211221C>T	ENST00000330877.2	+	11	1231	c.1146C>T	c.(1144-1146)aaC>aaT	p.N382N	ADSSL1_ENST00000554657.1_3'UTR|ADSSL1_ENST00000556623.1_5'Flank|ADSSL1_ENST00000332972.5_Silent_p.N425N|ADSSL1_ENST00000555674.1_5'Flank	NM_152328.3	NP_689541.1			adenylosuccinate synthase like 1											central_nervous_system(1)|cervix(1)|kidney(1)|lung(5)|ovary(2)|prostate(1)	11		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)		ACAAGCTGAACGGGAAAAGGA	0.532													C|||	1020	0.203674	0.0658	0.2046	5008	,	,		20645	0.5228		0.0656	False		,,,				2504	0.2025				p.N425N		Atlas-SNP	.											.	ADSSL1	37	.	0			c.C1275T						PASS	.	C	,	261,4145	149.2+/-183.4	8,245,1950	84.0	78.0	80.0		1146,1275	-1.4	0.8	14	dbSNP_120	80	559,8041	152.2+/-206.8	16,527,3757	no	coding-synonymous,coding-synonymous	ADSSL1	NM_152328.3,NM_199165.1	,	24,772,5707	TT,TC,CC		6.5,5.9237,6.3048	,	382/458,425/501	105211221	820,12186	2203	4300	6503	SO:0001819	synonymous_variant	122622	exon11			GCTGAACGGGAAA	AK095921	CCDS9990.1, CCDS9991.1	14q32.33	2010-08-05			ENSG00000185100	ENSG00000185100			20093	protein-coding gene	gene with protein product		612498					Standard	NM_199165		Approved	FLJ38602	uc001ype.3	Q8N142		ENST00000330877.2:c.1146C>T	14.37:g.105211221C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_199165		Silent	SNP	ENST00000330877.2	37	CCDS9990.1																																																																																			C|0.882;T|0.118	0.118	strong		0.532	ADSSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410529.1		
PGM5	5239	hgsc.bcm.edu	37	9	70993219	70993219	+	Silent	SNP	C	C	T	rs147720326	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:70993219C>T	ENST00000396396.1	+	2	595	c.366C>T	c.(364-366)agC>agT	p.S122S	PGM5_ENST00000604870.2_3'UTR|PGM5_ENST00000396392.1_Silent_p.S122S	NM_021965.3	NP_068800.2	Q15124	PGM5_HUMAN	phosphoglucomutase 5	122	Substrate binding. {ECO:0000250|UniProtKB:P00949}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)	cell-cell adherens junction (GO:0005913)|costamere (GO:0043034)|cytoplasmic side of plasma membrane (GO:0009898)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|sarcolemma (GO:0042383)|spot adherens junction (GO:0005914)|stress fiber (GO:0001725)|Z disc (GO:0030018)	intramolecular transferase activity, phosphotransferases (GO:0016868)|magnesium ion binding (GO:0000287)|structural molecule activity (GO:0005198)			endometrium(5)|kidney(1)|large_intestine(5)|liver(2)|lung(15)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	34						TAACAGCCAGCCACTGCCCTG	0.473													c|||	167	0.0333466	0.0537	0.0519	5008	,	,		18546	0.0109		0.0378	False		,,,				2504	0.0112				p.S122S		Atlas-SNP	.											.	PGM5	80	.	0			c.C366T						PASS	.						26.0	27.0	27.0					9																	70993219		2202	4280	6482	SO:0001819	synonymous_variant	5239	exon2			AGCCAGCCACTGC	L40933	CCDS6622.2	9q13	2008-02-05			ENSG00000154330	ENSG00000154330			8908	protein-coding gene	gene with protein product	"""phosphoglucomutase-related protein"""	600981				8586438, 8631316	Standard	NM_021965		Approved	PGMRP	uc004agr.3	Q15124	OTTHUMG00000019966	ENST00000396396.1:c.366C>T	9.37:g.70993219C>T		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	360	168	0.466667	NM_021965	B1AM46|B4DLQ6|Q5VYV3|Q8N527|Q9UDH4	Silent	SNP	ENST00000396396.1	37	CCDS6622.2																																																																																			.	.	weak		0.473	PGM5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052548.2	NM_021965	
HLA-B	3106	hgsc.bcm.edu	37	6	31324110	31324110	+	Silent	SNP	G	G	A	rs12721849	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324110G>A	ENST00000412585.2	-	3	481	c.453C>T	c.(451-453)aaC>aaT	p.N151N		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	151	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GCAGGTCCTCGTTCAGGGCGA	0.701									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.N151N		Atlas-SNP	.											.	HLA-B	54	.	0			c.C453T						PASS	.						31.0	23.0	26.0					6																	31324110		2125	4205	6330	SO:0001819	synonymous_variant	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	GTCCTCGTTCAGG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.453C>T	6.37:g.31324110G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	174	39	0.224138	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			T|0.000;G|0.957;A|0.043	0.043	strong		0.701	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
MSGN1	343930	hgsc.bcm.edu	37	2	17998331	17998331	+	Silent	SNP	T	T	C	rs13001625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:17998331T>C	ENST00000281047.3	+	1	569	c.546T>C	c.(544-546)ctT>ctC	p.L182L		NM_001105569.1	NP_001099039.1	A6NI15	MSGN1_HUMAN	mesogenin 1	182					cell differentiation (GO:0030154)|segment specification (GO:0007379)|somitogenesis (GO:0001756)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CAGACCTCCTTAACCGCGGCA	0.572													C|||	1475	0.294529	0.2027	0.3501	5008	,	,		18695	0.0278		0.5378	False		,,,				2504	0.4039				p.L182L	Melanoma(127;325 1712 14802 40657 49130)	Atlas-SNP	.											.	MSGN1	39	.	0			c.T546C						PASS	.	C		1054,3016		144,766,1125	37.0	40.0	39.0		546	3.0	1.0	2	dbSNP_121	39	4775,3595		1379,2017,789	no	coding-synonymous	MSGN1	NM_001105569.1		1523,2783,1914	CC,CT,TT		42.951,25.8968,46.8569		182/194	17998331	5829,6611	2035	4185	6220	SO:0001819	synonymous_variant	343930	exon1			CCTCCTTAACCGC		CCDS42657.1	2p24.2	2007-07-23			ENSG00000151379	ENSG00000151379			14907	protein-coding gene	gene with protein product	"""paraxial mesogenin"""	612209				10837126	Standard	NM_001105569		Approved	pMesogenin1	uc010yjt.2	A6NI15	OTTHUMG00000159089	ENST00000281047.3:c.546T>C	2.37:g.17998331T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001105569		Silent	SNP	ENST00000281047.3	37	CCDS42657.1																																																																																			T|0.585;C|0.415	0.415	strong		0.572	MSGN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353253.1	XM_292850	
PRKCB	5579	hgsc.bcm.edu	37	16	24202458	24202458	+	Silent	SNP	C	C	T	rs3729904	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:24202458C>T	ENST00000321728.7	+	16	1945	c.1770C>T	c.(1768-1770)ggC>ggT	p.G590G	PRKCB_ENST00000303531.7_Silent_p.G590G	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	590	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	GACCTGAAGGCGAACGTGATA	0.428													C|||	1259	0.251398	0.3343	0.1974	5008	,	,		19955	0.0942		0.2535	False		,,,				2504	0.3374				p.G590G		Atlas-SNP	.											PRKCB_ENST00000321728,NS,carcinoma,+2,3	PRKCB	383	3	0			c.C1770T						PASS	.	C	,	1274,3120	437.4+/-345.0	179,916,1102	104.0	102.0	102.0		1770,1770	-10.5	0.9	16	dbSNP_107	102	2111,6489	363.5+/-333.2	265,1581,2454	no	coding-synonymous,coding-synonymous	PRKCB	NM_002738.6,NM_212535.2	,	444,2497,3556	TT,TC,CC		24.5465,28.9941,26.0505	,	590/674,590/672	24202458	3385,9609	2197	4300	6497	SO:0001819	synonymous_variant	5579	exon16			TGAAGGCGAACGT	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"""protein kinase C, beta 1"""	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.1770C>T	16.37:g.24202458C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Silent	SNP	ENST00000321728.7	37	CCDS10618.1																																																																																			C|0.765;T|0.235	0.235	strong		0.428	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
CEP135	9662	hgsc.bcm.edu	37	4	56820412	56820412	+	Missense_Mutation	SNP	G	G	A	rs77591659	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:56820412G>A	ENST00000257287.4	+	4	459	c.335G>A	c.(334-336)cGt>cAt	p.R112H	CEP135_ENST00000422247.2_Missense_Mutation_p.R112H	NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	112					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					AAATGTGCACGTGAAACAGCT	0.313													G|||	62	0.0123802	0.0015	0.0115	5008	,	,		17116	0.0		0.0437	False		,,,				2504	0.0082				p.R112H		Atlas-SNP	.											.	CEP135	115	.	0			c.G335A						PASS	.	G	HIS/ARG	38,4368	42.3+/-75.8	0,38,2165	66.0	64.0	64.0		335	-0.4	0.1	4	dbSNP_131	64	364,8236	121.0+/-180.1	8,348,3944	yes	missense	CEP135	NM_025009.3	29	8,386,6109	AA,AG,GG		4.2326,0.8625,3.0909	benign	112/1141	56820412	402,12604	2203	4300	6503	SO:0001583	missense	9662	exon4			GTGCACGTGAAAC	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"""KIAA0635"", ""centrosomal protein 4"""	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.335G>A	4.37:g.56820412G>A	ENSP00000257287:p.Arg112His	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	233	116	0.497854	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	36	0.016483516483516484	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	27	0.03562005277044855	G	2.889	-0.230142	0.05983	0.008625	0.042326	ENSG00000174799	ENST00000422247;ENST00000257287	T	0.41065	1.01	5.54	-0.452	0.12205	.	0.308339	0.34411	N	0.003985	T	0.03053	0.0090	N	0.02315	-0.6	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.13124	-1.0521	10	0.36615	T	0.2	.	5.3337	0.15945	0.5636:0.0:0.2894:0.147	.	112;112	Q66GS9;Q66GS9-2	CP135_HUMAN;.	H	112	ENSP00000257287:R112H	ENSP00000257287:R112H	R	+	2	0	CEP135	56515169	0.961000	0.32948	0.104000	0.21259	0.321000	0.28281	2.063000	0.41423	0.061000	0.16311	-0.229000	0.12294	CGT	G|0.973;A|0.027	0.027	strong		0.313	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552000	32552000	+	Missense_Mutation	SNP	C	C	T	rs17880292	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32552000C>T	ENST00000360004.5	-	2	361	c.256G>A	c.(256-258)Gac>Aac	p.D86N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	86	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TACTCAGCGTCAGGCCGCCCC	0.632										Multiple Myeloma(14;0.17)			C|||	334	0.0666933	0.0938	0.0591	5008	,	,		7793	0.1002		0.0487	False		,,,				2504	0.0194				p.D86N		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G256A						PASS	.																																			SO:0001583	missense	3123	exon2			CAGCGTCAGGCCG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.256G>A	6.37:g.32552000C>T	ENSP00000353099:p.Asp86Asn	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	50	16	0.32	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	13.25	2.179960	0.38511	.	.	ENSG00000196126	ENST00000360004	T	0.00224	8.51	3.52	-1.57	0.08506	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	11.458300	0.00979	N	0.003354	T	0.00073	0.0002	M	0.63428	1.95	0.09310	N	1	B	0.21606	0.058	B	0.28385	0.089	T	0.33777	-0.9855	10	0.72032	D	0.01	.	3.0064	0.06030	0.3359:0.2318:0.0:0.4323	rs17880292	86	P01911	2B1F_HUMAN	N	86	ENSP00000353099:D86N	ENSP00000353099:D86N	D	-	1	0	HLA-DRB1	32659978	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.770000	0.00188	-0.268000	0.09312	0.453000	0.30009	GAC	C|0.989;T|0.011	0.011	strong		0.632	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
GNAI1	2770	hgsc.bcm.edu	37	7	79842157	79842157	+	Silent	SNP	T	T	C	rs10241877	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:79842157T>C	ENST00000351004.3	+	7	1219	c.846T>C	c.(844-846)ccT>ccC	p.P282P	GNAI1_ENST00000457358.2_Silent_p.P230P	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	282					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						AAAAGAGCCCTCTCACTATAT	0.333													T|||	533	0.10643	0.0098	0.1196	5008	,	,		16091	0.0843		0.1233	False		,,,				2504	0.2331				p.P282P		Atlas-SNP	.											.	GNAI1	44	.	0			c.T846C						PASS	.	T		129,4277	87.8+/-126.4	1,127,2075	66.0	74.0	71.0		846	-1.8	1.0	7	dbSNP_119	71	888,7698	189.4+/-236.2	40,808,3445	no	coding-synonymous	GNAI1	NM_002069.5		41,935,5520	CC,CT,TT		10.3424,2.9278,7.8279		282/355	79842157	1017,11975	2203	4293	6496	SO:0001819	synonymous_variant	2770	exon7			GAGCCCTCTCACT	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"""Gi1 protein alpha subunit"""	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.846T>C	7.37:g.79842157T>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	216	94	0.435185	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Silent	SNP	ENST00000351004.3	37	CCDS5595.1																																																																																			T|0.917;C|0.083	0.083	strong		0.333	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069	
ARIH2	10425	hgsc.bcm.edu	37	3	48965102	48965102	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:48965102C>T	ENST00000356401.4	+	3	450	c.111C>T	c.(109-111)gaC>gaT	p.D37D	ARIH2_ENST00000490095.1_Intron|ARIH2_ENST00000449376.1_Silent_p.D37D	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	37	Asp/Glu-rich (acidic).				developmental cell growth (GO:0048588)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organismal development (GO:0007275)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		ACATAGAGGACTATTACGTGG	0.512																																					p.D37D		Atlas-SNP	.											ARIH2,NS,carcinoma,+2,1	ARIH2	32	1	0			c.C111T						scavenged	.						74.0	76.0	75.0					3																	48965102		2203	4300	6503	SO:0001819	synonymous_variant	10425	exon3			AGAGGACTATTAC	AF099149	CCDS2780.1	3p21	2013-10-03	2013-10-03		ENSG00000177479	ENSG00000177479			690	protein-coding gene	gene with protein product	"""all-trans retinoic acid inducible RING finger"""	605615	"""ariadne (Drosophila) homolog 2"", ""ariadne homolog 2 (Drosophila)"""			10422847, 24058416	Standard	XM_005264798		Approved	TRIAD1	uc003cvb.3	O95376	OTTHUMG00000133547	ENST00000356401.4:c.111C>T	3.37:g.48965102C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	136	2	0.0147059	NM_006321	Q9HBZ6|Q9UEM9	Silent	SNP	ENST00000356401.4	37	CCDS2780.1																																																																																			.	.	none		0.512	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257525.1	NM_006321	
JAG2	3714	hgsc.bcm.edu	37	14	105611282	105611282	+	Silent	SNP	A	A	G	rs2272591	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105611282A>G	ENST00000331782.3	-	24	3472	c.3069T>C	c.(3067-3069)gcT>gcC	p.A1023A	JAG2_ENST00000347004.2_Silent_p.A985A	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	1023					auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		CCACCTCCACAGCACTGGCCC	0.682													G|||	3389	0.676717	0.8918	0.6484	5008	,	,		3772	0.502		0.6581	False		,,,				2504	0.6053				p.A1023A		Atlas-SNP	.											.	JAG2	69	.	0			c.T3069C						PASS	.	G	,	3649,713		1525,599,57	22.0	28.0	26.0		3069,2955	-8.7	0.0	14	dbSNP_100	26	5644,2932		1884,1876,528	no	coding-synonymous,coding-synonymous	JAG2	NM_002226.3,NM_145159.1	,	3409,2475,585	GG,GA,AA		34.1884,16.3457,28.1728	,	1023/1239,985/1201	105611282	9293,3645	2181	4288	6469	SO:0001819	synonymous_variant	3714	exon24			CTCCACAGCACTG	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.3069T>C	14.37:g.105611282A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	CCDS9998.1																																																																																			A|0.300;G|0.700	0.700	strong		0.682	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
SVIL	6840	hgsc.bcm.edu	37	10	29783885	29783885	+	Silent	SNP	A	A	G	rs1056782	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:29783885A>G	ENST00000355867.4	-	20	4551	c.3799T>C	c.(3799-3801)Ttg>Ctg	p.L1267L	SVIL_ENST00000535393.1_Silent_p.L181L|SVIL_ENST00000375400.3_Silent_p.L841L|SVIL_ENST00000375398.2_Silent_p.L1267L|SVIL_ENST00000538146.1_Silent_p.L59L	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1267					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				AGCCTGTCCAACTTCAGGTCC	0.448																																					p.L1267L		Atlas-SNP	.											.	SVIL	226	.	0			c.T3799C						PASS	.	A	,	1110,3296		84,942,1177	185.0	180.0	181.0		2521,3799	-2.0	1.0	10	dbSNP_86	181	3424,5176		495,2434,1371	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	579,3376,2548	GG,GA,AA		39.814,25.1929,34.8608	,	841/1789,1267/2215	29783885	4534,8472	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon20			TGTCCAACTTCAG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.3799T>C	10.37:g.29783885A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	208	71	0.341346	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			A|0.589;G|0.411	0.411	strong		0.448	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
SBNO2	22904	hgsc.bcm.edu	37	19	1113701	1113701	+	Missense_Mutation	SNP	G	G	A	rs2302110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1113701G>A	ENST00000361757.3	-	19	2317	c.2080C>T	c.(2080-2082)Ccc>Tcc	p.P694S	SBNO2_ENST00000587024.1_Missense_Mutation_p.P684S|SBNO2_ENST00000438103.2_Missense_Mutation_p.P637S	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	694				P -> S (in Ref. 1; BAA76807 and 4; BAB84928). {ECO:0000305}.	bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGCACAGGGGTCCTAGGGAG	0.682													G|||	773	0.154353	0.0567	0.2075	5008	,	,		14613	0.125		0.2406	False		,,,				2504	0.1902				p.P694S		Atlas-SNP	.											.	SBNO2	112	.	0			c.C2080T						PASS	.	G	SER/PRO,SER/PRO	290,3482		18,254,1614	8.0	10.0	9.0		1909,2080	3.2	0.0	19	dbSNP_100	9	1691,6451		183,1325,2563	yes	missense,missense	SBNO2	NM_001100122.1,NM_014963.2	74,74	201,1579,4177	AA,AG,GG		20.7689,7.6882,16.6275	benign,benign	637/1310,694/1367	1113701	1981,9933	1886	4071	5957	SO:0001583	missense	22904	exon19			ACAGGGGTCCTAG	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.2080C>T	19.37:g.1113701G>A	ENSP00000354733:p.Pro694Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	134	85	0.634328	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Missense_Mutation	SNP	ENST00000361757.3	37	CCDS45894.1	360	0.16483516483516483	29	0.05894308943089431	75	0.20718232044198895	75	0.13111888111888112	181	0.23878627968337732	G	9.380	1.072723	0.20147	0.076882	0.207689	ENSG00000064932	ENST00000361757;ENST00000438103;ENST00000250872	.	.	.	4.3	3.23	0.37069	.	0.570312	0.15263	N	0.271669	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.09377	0.002;0.004	T	0.18840	-1.0324	8	0.07030	T	0.85	-22.0912	6.9838	0.24718	0.2122:0.0:0.7878:0.0	.	694;637	Q9Y2G9;Q9Y2G9-3	SBNO2_HUMAN;.	S	694;637;701	.	ENSP00000250872:P701S	P	-	1	0	SBNO2	1064701	0.017000	0.18338	0.033000	0.17914	0.030000	0.12068	0.584000	0.23864	0.991000	0.38814	0.561000	0.74099	CCC	A|0.162;G|0.838	0.162	strong		0.682	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
ESPNL	339768	hgsc.bcm.edu	37	2	239039183	239039183	+	Missense_Mutation	SNP	G	G	A	rs73102303	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:239039183G>A	ENST00000343063.3	+	9	2091	c.1828G>A	c.(1828-1830)Gtg>Atg	p.V610M	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.V242M|ESPNL_ENST00000409169.1_Missense_Mutation_p.V566M	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	610				V -> M (in Ref. 1; BAC85884 and 3; AAH42051). {ECO:0000305}.						endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GCTGAAGGGCGTGCATGGGCT	0.711													G|||	658	0.13139	0.2413	0.085	5008	,	,		16293	0.0526		0.1113	False		,,,				2504	0.1176				p.V610M		Atlas-SNP	.											ESPNL,NS,carcinoma,0,1	ESPNL	63	1	0			c.G1828A						PASS	.	G	MET/VAL	862,3504		81,700,1402	10.0	11.0	11.0		1828	-2.3	0.3	2	dbSNP_130	11	920,7564		49,822,3371	yes	missense	ESPNL	NM_194312.2	21	130,1522,4773	AA,AG,GG		10.8439,19.7435,13.8677	benign	610/1006	239039183	1782,11068	2183	4242	6425	SO:0001583	missense	339768	exon9			AAGGGCGTGCATG	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.1828G>A	2.37:g.239039183G>A	ENSP00000339115:p.Val610Met	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	249	0.11401098901098901	97	0.19715447154471544	35	0.09668508287292818	41	0.07167832167832168	76	0.10026385224274406	G	0.031	-1.332649	0.01298	0.197435	0.108439	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.63580	-0.05;1.04;0.61	3.78	-2.26	0.06867	.	0.423150	0.21191	N	0.078648	T	0.00039	0.0001	N	0.05124	-0.11	0.80722	P	0.0	B;B	0.33494	0.414;0.291	B;B	0.20384	0.029;0.013	T	0.19031	-1.0318	9	0.19147	T	0.46	-12.2189	9.0509	0.36376	0.6378:0.0:0.3622:0.0	.	566;610	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	M	610;566;242	ENSP00000339115:V610M;ENSP00000386577:V566M;ENSP00000386579:V242M	ENSP00000339115:V610M	V	+	1	0	ESPNL	238703922	0.016000	0.18221	0.297000	0.24988	0.220000	0.24768	-0.513000	0.06305	-0.396000	0.07703	0.205000	0.17691	GTG	G|0.871;A|0.129	0.129	strong		0.711	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
TRIM2	23321	hgsc.bcm.edu	37	4	154216710	154216710	+	Silent	SNP	G	G	A	rs893805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:154216710G>A	ENST00000437508.2	+	6	1152	c.951G>A	c.(949-951)acG>acA	p.T317T	TRIM2_ENST00000494872.1_3'UTR|TRIM2_ENST00000338700.5_Silent_p.T344T	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	317					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T317T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		ACCTCGGGACGATCTTAACCA	0.622													G|||	2280	0.455272	0.6536	0.4049	5008	,	,		19242	0.1786		0.4563	False		,,,				2504	0.5072				p.T344T		Atlas-SNP	.											TRIM2,NS,carcinoma,0,1	TRIM2	105	1	1	Substitution - coding silent(1)	prostate(1)	c.G1032A						PASS	.	G	,	2770,1636	659.6+/-400.6	871,1028,304	69.0	61.0	63.0		951,1032	-4.9	0.0	4	dbSNP_86	63	4120,4480	563.6+/-388.2	984,2152,1164	no	coding-synonymous,coding-synonymous	TRIM2	NM_001130067.1,NM_015271.3	,	1855,3180,1468	AA,AG,GG		47.907,37.1312,47.0245	,	317/745,344/772	154216710	6890,6116	2203	4300	6503	SO:0001819	synonymous_variant	23321	exon6			CGGGACGATCTTA	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	15974	protein-coding gene	gene with protein product		614141	"""tripartite motif-containing 2"""			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.951G>A	4.37:g.154216710G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_015271	D3DP09|O60272|Q9BSI9|Q9UFZ1	Silent	SNP	ENST00000437508.2	37	CCDS47147.1																																																																																			G|0.511;A|0.489	0.489	strong		0.622	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1		
PRSS53	339105	hgsc.bcm.edu	37	16	31097689	31097689	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31097689C>T	ENST00000280606.6	-	5	785	c.632G>A	c.(631-633)gGc>gAc	p.G211D		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	211	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						AGGCTGGGGGCCCCCACATAG	0.642																																					p.G211D		Atlas-SNP	.											.	PRSS53	29	.	0			c.G632A						PASS	.						42.0	48.0	46.0					16																	31097689		1877	4102	5979	SO:0001583	missense	339105	exon5			TGGGGGCCCCCAC		CCDS42153.1	16p11.2	2010-05-07			ENSG00000151006	ENSG00000151006		"""Serine peptidases / Serine peptidases"""	34407	protein-coding gene	gene with protein product	"""polyserase 3"""	610561				16566820	Standard	NM_001039503		Approved	POL3S	uc002eaq.3	Q2L4Q9	OTTHUMG00000047358	ENST00000280606.6:c.632G>A	16.37:g.31097689C>T	ENSP00000280606:p.Gly211Asp	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	100	39	0.39	NM_001039503		Missense_Mutation	SNP	ENST00000280606.6	37	CCDS42153.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.109734	0.77096	.	.	ENSG00000151006	ENST00000280606	D	0.90133	-2.62	5.77	5.77	0.91146	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.36778	U	0.002401	D	0.95385	0.8502	M	0.84773	2.715	0.53688	D	0.999979	D	0.89917	1.0	D	0.97110	1.0	D	0.95533	0.8605	10	0.87932	D	0	.	13.1188	0.59314	0.0:0.8394:0.1606:0.0	.	211	Q2L4Q9	PRS53_HUMAN	D	211	ENSP00000280606:G211D	ENSP00000280606:G211D	G	-	2	0	PRSS53	31005190	0.992000	0.36948	1.000000	0.80357	0.946000	0.59487	3.137000	0.50562	2.723000	0.93209	0.655000	0.94253	GGC	.	.	none		0.642	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268	
ZZEF1	23140	hgsc.bcm.edu	37	17	3916823	3916823	+	Silent	SNP	G	G	A	rs8075562	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:3916823G>A	ENST00000381638.2	-	52	8623	c.8499C>T	c.(8497-8499)ggC>ggT	p.G2833G		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2833							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						GACAGGCCACGCCCACCAGCC	0.537													G|||	1011	0.201877	0.3033	0.2061	5008	,	,		14586	0.0734		0.2048	False		,,,				2504	0.1912				p.G2833G		Atlas-SNP	.											.	ZZEF1	195	.	0			c.C8499T						PASS	.	G		1143,3263	406.6+/-333.9	156,831,1216	82.0	77.0	78.0		8499	-10.9	0.4	17	dbSNP_116	78	1659,6941	306.1+/-307.8	156,1347,2797	no	coding-synonymous	ZZEF1	NM_015113.3		312,2178,4013	AA,AG,GG		19.2907,25.9419,21.5439		2833/2962	3916823	2802,10204	2203	4300	6503	SO:0001819	synonymous_variant	23140	exon52			GGCCACGCCCACC	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.8499C>T	17.37:g.3916823G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	27	0.375	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																			G|0.778;A|0.222	0.222	strong		0.537	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
CNTNAP1	8506	hgsc.bcm.edu	37	17	40842762	40842762	+	Silent	SNP	C	C	A	rs1553469	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:40842762C>A	ENST00000264638.4	+	13	2078	c.1861C>A	c.(1861-1863)Cga>Aga	p.R621R	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	621	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				axon cargo transport (GO:0008088)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|neuron projection morphogenesis (GO:0048812)|neuronal action potential propagation (GO:0019227)|paranodal junction assembly (GO:0030913)|positive regulation of signal transduction (GO:0009967)|protein localization to paranode region of axon (GO:0002175)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|voltage-gated potassium channel complex (GO:0008076)	receptor activity (GO:0004872)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		GCCAGAGAACCGAGCGTGGAC	0.597													C|||	198	0.0395367	0.0242	0.1196	5008	,	,		18736	0.0		0.0497	False		,,,				2504	0.0337				p.R621R		Atlas-SNP	.											.	CNTNAP1	116	.	0			c.C1861A						PASS	.	C		121,4285	88.2+/-126.9	2,117,2084	107.0	104.0	105.0		1861	2.6	1.0	17	dbSNP_88	105	607,7993	159.2+/-212.6	19,569,3712	no	coding-synonymous	CNTNAP1	NM_003632.2		21,686,5796	AA,AC,CC		7.0581,2.7463,5.5974		621/1385	40842762	728,12278	2203	4300	6503	SO:0001819	synonymous_variant	8506	exon13			GAGAACCGAGCGT	U87223	CCDS11436.1	17q21	2008-07-18				ENSG00000108797			8011	protein-coding gene	gene with protein product	"""neurexin 4"""	602346		NRXN4		9118959	Standard	NM_003632		Approved	p190, Caspr, CNTNAP	uc002iay.3	P78357		ENST00000264638.4:c.1861C>A	17.37:g.40842762C>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_003632		Silent	SNP	ENST00000264638.4	37	CCDS11436.1																																																																																			T|0.000;G|0.005	.	strong		0.597	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632	
REEP6	92840	hgsc.bcm.edu	37	19	1489817	1489817	+	5'Flank	SNP	C	C	T	rs12972390	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1489817C>T	ENST00000233596.3	+	0	0				PCSK4_ENST00000300954.5_Missense_Mutation_p.R90H|PCSK4_ENST00000587784.1_Intron	NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6						regulation of intracellular transport (GO:0032386)	apical part of cell (GO:0045177)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				lung(1)|ovary(1)	2		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGTGCAGGCGGTGGCCCCA	0.677													C|||	60	0.0119808	0.0015	0.0231	5008	,	,		14349	0.0		0.0268	False		,,,				2504	0.0153				p.R90H		Atlas-SNP	.											.	PCSK4	44	.	0			c.G269A						PASS	.	C	HIS/ARG	21,4373		0,21,2176	21.0	24.0	23.0		269	2.0	1.0	19	dbSNP_121	23	316,8284		6,304,3990	yes	missense	PCSK4	NM_017573.3	29	6,325,6166	TT,TC,CC		3.6744,0.4779,2.5935	benign	90/756	1489817	337,12657	2197	4300	6497	SO:0001631	upstream_gene_variant	54760	exon2			TGCAGGCGGTGGC	BC008201	CCDS12070.1	19p13.3	2012-12-20	2006-02-08	2006-02-07	ENSG00000115255	ENSG00000115255		"""Receptor accessory proteins"""	30078	protein-coding gene	gene with protein product	"""polyposis locus protein 1-like 1"", ""deleted in polyposis 1-like 1"""	609346	"""chromosome 19 open reading frame 32"""	C19orf32		16271481, 15550249	Standard	NM_138393		Approved	DP1L1, FLJ25383	uc002ltc.3	Q96HR9	OTTHUMG00000180072		19.37:g.1489817C>T	Exception_encountered	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	172	96	0.55814	NM_017573	B2RE01|D6W5Z0|Q96LM0	Missense_Mutation	SNP	ENST00000233596.3	37	CCDS12070.1	32	0.014652014652014652	0	0.0	10	0.027624309392265192	0	0.0	22	0.029023746701846966	C	2.756	-0.259014	0.05791	0.004779	0.036744	ENSG00000115257	ENST00000300954	T	0.27720	1.65	3.13	2.03	0.26663	Proteinase inhibitor, propeptide (1);	0.604415	0.14044	N	0.345214	T	0.01976	0.0062	N	0.04203	-0.255	0.28129	N	0.930294	B	0.21688	0.059	B	0.09377	0.004	T	0.32052	-0.9921	10	0.02654	T	1	.	5.578	0.17235	0.0:0.7484:0.0:0.2516	rs12972390;rs12972390	90	Q6UW60	PCSK4_HUMAN	H	90	ENSP00000300954:R90H	ENSP00000300954:R90H	R	-	2	0	PCSK4	1440817	0.000000	0.05858	1.000000	0.80357	0.837000	0.47467	0.348000	0.20031	1.606000	0.50161	0.561000	0.74099	CGC	C|0.980;T|0.020	0.020	strong		0.677	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393	
PKP2	5318	hgsc.bcm.edu	37	12	33021917	33021917	+	Missense_Mutation	SNP	C	C	G	rs200586695		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:33021917C>G	ENST00000070846.6	-	4	1138	c.1114G>C	c.(1114-1116)Gct>Cct	p.A372P	PKP2_ENST00000340811.4_Missense_Mutation_p.A372P	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	372			A -> P. {ECO:0000269|PubMed:20031617, ECO:0000269|PubMed:21062920}.		adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GTAGCTGCAGCAGAAATCCTG	0.498																																					p.A372P		Atlas-SNP	.											.	PKP2	110	.	0			c.G1114C						PASS	.	C	PRO/ALA,PRO/ALA	0,4406		0,0,2203	118.0	106.0	110.0		1114,1114	4.2	0.0	12		110	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	PKP2	NM_001005242.2,NM_004572.3	27,27	0,6,6497	GG,GC,CC		0.0698,0.0,0.0461	benign,benign	372/838,372/882	33021917	6,13000	2203	4300	6503	SO:0001583	missense	5318	exon4			CTGCAGCAGAAAT	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.1114G>C	12.37:g.33021917C>G	ENSP00000070846:p.Ala372Pro	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.703879	0.30232	0.0	6.98E-4	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.52754	0.65;0.65	5.09	4.2	0.49525	Armadillo-like helical (1);Armadillo-type fold (1);	2.116220	0.01794	N	0.032478	T	0.55940	0.1952	L	0.55481	1.735	0.31883	N	0.618224	P;P;P	0.43662	0.676;0.548;0.814	P;B;P	0.47015	0.506;0.309;0.534	T	0.41556	-0.9502	10	0.30854	T	0.27	-1.899	11.5273	0.50586	0.0:0.9155:0.0:0.0845	.	372;372;372	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	P	372	ENSP00000342800:A372P;ENSP00000070846:A372P	ENSP00000070846:A372P	A	-	1	0	PKP2	32913184	0.805000	0.28982	0.017000	0.16124	0.333000	0.28666	2.159000	0.42339	1.136000	0.42199	0.650000	0.86243	GCT	C|0.999;G|0.001	0.001	weak		0.498	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
ZFPM2	23414	hgsc.bcm.edu	37	8	106813518	106813518	+	Missense_Mutation	SNP	C	C	G	rs11993776	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:106813518C>G	ENST00000407775.2	+	8	1458	c.1208C>G	c.(1207-1209)gCa>gGa	p.A403G	RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|ZFPM2_ENST00000517361.1_Missense_Mutation_p.A271G|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000524045.2_RNA|ZFPM2_ENST00000378472.4_Missense_Mutation_p.A134G|ZFPM2_ENST00000522296.1_3'UTR|ZFPM2_ENST00000520492.1_Missense_Mutation_p.A271G|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000521622.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	403			A -> G (in dbSNP:rs11993776). {ECO:0000269|PubMed:24549039}.		blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			TCTCCAAGTGCAACTGAAGAC	0.517													G|||	968	0.193291	0.441	0.1023	5008	,	,		19753	0.131		0.1024	False		,,,				2504	0.0808				p.A403G		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C1208G						PASS	.	G	GLY/ALA	1423,2563		257,909,827	87.0	86.0	86.0		1208	4.0	0.0	8	dbSNP_120	86	787,7573		40,707,3433	yes	missense	ZFPM2	NM_012082.3	60	297,1616,4260	GG,GC,CC		9.4139,35.6999,17.9005	benign	403/1152	106813518	2210,10136	1993	4180	6173	SO:0001583	missense	23414	exon8			CAAGTGCAACTGA	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.1208C>G	8.37:g.106813518C>G	ENSP00000384179:p.Ala403Gly	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	154	153	0.993506	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	410	0.18772893772893773	209	0.4247967479674797	34	0.09392265193370165	83	0.1451048951048951	84	0.11081794195250659	G	0.020	-1.443220	0.01089	0.356999	0.094139	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.19532	2.14;2.63;2.63;3.84	5.87	4.01	0.46588	.	0.152514	0.64402	N	0.000017	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	8.000000000008E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46965	-0.9153	9	0.06625	T	0.88	.	13.3304	0.60483	0.0:0.388:0.4991:0.1129	rs11993776;rs57100171;rs11993776	403	Q8WW38	FOG2_HUMAN	G	403;271;271;134	ENSP00000384179:A403G;ENSP00000430757:A271G;ENSP00000428720:A271G;ENSP00000367733:A134G	ENSP00000367733:A134G	A	+	2	0	ZFPM2	106882694	1.000000	0.71417	0.024000	0.17045	0.590000	0.36582	4.021000	0.57196	0.318000	0.23185	-0.120000	0.15030	GCA	C|0.817;G|0.183	0.183	strong		0.517	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
HS3ST1	9957	hgsc.bcm.edu	37	4	11401087	11401087	+	Silent	SNP	A	A	G	rs1047389	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:11401087A>G	ENST00000002596.5	-	2	1717	c.543T>C	c.(541-543)gaT>gaC	p.D181D		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	181					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						TGAGCCTGCCATCGCGCACCA	0.582													G|||	1262	0.251997	0.3192	0.1945	5008	,	,		19159	0.1885		0.1978	False		,,,				2504	0.3231				p.D181D		Atlas-SNP	.											.	HS3ST1	41	.	0			c.T543C						PASS	.	G		1287,3119	700.4+/-406.6	196,895,1112	83.0	76.0	78.0		543	0.1	0.8	4	dbSNP_86	78	1820,6780	731.5+/-406.8	189,1442,2669	no	coding-synonymous	HS3ST1	NM_005114.2		385,2337,3781	GG,GA,AA		21.1628,29.2102,23.889		181/308	11401087	3107,9899	2203	4300	6503	SO:0001819	synonymous_variant	9957	exon2			CCTGCCATCGCGC	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.543T>C	4.37:g.11401087A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	205	92	0.44878	NM_005114	B3KUA6|Q6PEY8	Silent	SNP	ENST00000002596.5	37	CCDS3408.1																																																																																			G|0.241;N|0.000	0.241	strong		0.582	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114	
MEFV	4210	hgsc.bcm.edu	37	16	3304654	3304654	+	Silent	SNP	T	T	C	rs224224	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:3304654T>C	ENST00000219596.1	-	2	453	c.414A>G	c.(412-414)ggA>ggG	p.G138G	MEFV_ENST00000541159.1_Intron|MEFV_ENST00000339854.4_Intron|MEFV_ENST00000536379.1_Intron	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	138			G -> A (association with renal amyloidosis). {ECO:0000269|PubMed:11139244}.		inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GGCTGGCAGCTCCGCCCCCGT	0.716													C|||	1936	0.386581	0.5257	0.5937	5008	,	,		11024	0.1587		0.4742	False		,,,				2504	0.1963				p.G138G		Atlas-SNP	.											MEFV,colon,carcinoma,-2,1	MEFV	170	1	0			c.A414G						scavenged	.	C	,	2119,2193		569,981,606	13.0	15.0	14.0		414,	-2.9	0.0	16	dbSNP_79	14	3830,4614		944,1942,1336	no	coding-synonymous,intron	MEFV	NM_000243.2,NM_001198536.1	,	1513,2923,1942	CC,CT,TT		45.3577,49.1419,46.6369	,	138/782,	3304654	5949,6807	2156	4222	6378	SO:0001819	synonymous_variant	4210	exon2			GGCAGCTCCGCCC	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.414A>G	16.37:g.3304654T>C		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	11	5	0.454545	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																			T|0.550;C|0.450	0.450	strong		0.716	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
ABCA2	20	hgsc.bcm.edu	37	9	139905141	139905141	+	Silent	SNP	G	G	A	rs112887513	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139905141G>A	ENST00000371605.3	-	39	6249	c.6102C>T	c.(6100-6102)gcC>gcT	p.A2034A	ABCA2_ENST00000341511.6_Silent_p.A2035A|ABCA2_ENST00000265662.5_Silent_p.A2035A			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	2034					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GCCGCTCACTGGCCACGTCCA	0.637													g|||	329	0.0656949	0.0234	0.0447	5008	,	,		5333	0.0437		0.0586	False		,,,				2504	0.1677				p.A2065A		Atlas-SNP	.											.	ABCA2	113	.	0			c.C6195T						PASS	.	C	,	105,4197		4,97,2050	99.0	111.0	107.0		6105,6195	0.7	0.3	9	dbSNP_132	107	572,7938		15,542,3698	yes	coding-synonymous,coding-synonymous	ABCA2	NM_001606.4,NM_212533.2	,	19,639,5748	AA,AG,GG		6.7215,2.4407,5.2841	,	2035/2437,2065/2467	139905141	677,12135	2151	4255	6406	SO:0001819	synonymous_variant	20	exon40			CTCACTGGCCACG	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.6102C>T	9.37:g.139905141G>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	339	164	0.483776	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	37																																																																																				A|0.055;C|0.000;G|0.945	0.055	strong		0.637	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	
TMEM132C	92293	hgsc.bcm.edu	37	12	128899673	128899673	+	Missense_Mutation	SNP	A	A	G	rs11059681	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:128899673A>G	ENST00000435159.2	+	2	482	c.482A>G	c.(481-483)cAc>cGc	p.H161R		NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	161			H -> R (in dbSNP:rs11059681).			integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(2)|prostate(2)|skin(1)	13						TGGGATGACCACGGCGCCGGG	0.597													G|||	1890	0.377396	0.416	0.3487	5008	,	,		16224	0.3998		0.4672	False		,,,				2504	0.2301				p.H161R		Atlas-SNP	.											.	TMEM132C	142	.	0			c.A482G						PASS	.	G	ARG/HIS	590,794		133,324,235	15.0	18.0	17.0		482	-9.1	0.0	12	dbSNP_120	17	1477,1705		340,797,454	yes	missense	TMEM132C	NM_001136103.2	29	473,1121,689	GG,GA,AA		46.4173,42.6301,45.2694	benign	161/1109	128899673	2067,2499	692	1591	2283	SO:0001583	missense	92293	exon2			ATGACCACGGCGC	AK126715		12q24.32	2014-06-13				ENSG00000181234			25436	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 152"""						Standard	NM_001136103		Approved	DKFZp761O2018, PPP1R152	uc021rgn.1	Q8N3T6		ENST00000435159.2:c.482A>G	12.37:g.128899673A>G	ENSP00000410852:p.His161Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	123	65	0.528455	NM_001136103	Q69YX8	Missense_Mutation	SNP	ENST00000435159.2	37		935	0.4281135531135531	215	0.4369918699186992	138	0.3812154696132597	229	0.40034965034965037	353	0.4656992084432718	G	3.437	-0.114890	0.06881	0.426301	0.464173	ENSG00000181234	ENST00000435159	T	0.10573	2.86	4.96	-9.14	0.00701	.	.	.	.	.	T	0.00012	0.0000	N	0.16903	0.455	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46414	-0.9193	8	0.19147	T	0.46	.	8.8075	0.34948	0.3934:0.2616:0.345:0.0	rs11059681;rs11059681	161	Q8N3T6	T132C_HUMAN	R	161	ENSP00000410852:H161R	ENSP00000410852:H161R	H	+	2	0	TMEM132C	127465626	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	0.354000	0.20146	-2.580000	0.00462	-1.096000	0.02151	CAC	A|0.571;G|0.429	0.429	strong		0.597	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3425749	3425749	+	Missense_Mutation	SNP	C	C	T	rs145733257		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:3425749C>T	ENST00000324266.5	+	4	1457	c.1262C>T	c.(1261-1263)aCg>aTg	p.T421M	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.T421M	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	421					vesicle-mediated transport (GO:0016192)												ACCAGCCACACGACAGATTCA	0.587													C|||	1	0.000199681	0.0	0.0	5008	,	,		20473	0.0		0.001	False		,,,				2504	0.0				p.T421M		Atlas-SNP	.											.	.	.	.	0			c.C1262T						PASS	.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	28.0	27.0	28.0		1262	4.7	0.8	2	dbSNP_134	28	19,8581	12.6+/-44.7	0,19,4281	yes	missense	TTC15	NM_016030.5	81	0,20,6483	TT,TC,CC		0.2209,0.0227,0.1538	probably-damaging	421/736	3425749	20,12986	2203	4300	6503	SO:0001583	missense	51112	exon4			GCCACACGACAGA	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1262C>T	2.37:g.3425749C>T	ENSP00000324318:p.Thr421Met	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	161	74	0.459627	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	24.4|24.4	4.524474|4.524474	0.85600|0.85600	2.27E-4|2.27E-4	0.002209|0.002209	ENSG00000171853|ENSG00000171853	ENST00000441983|ENST00000382110;ENST00000304601;ENST00000324266	.|T;T	.|0.54866	.|0.55;0.55	4.72|4.72	4.72|4.72	0.59763|0.59763	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.72906	.|0.3519	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.73380	.|0.964;0.98	.|T	.|0.76942	.|-0.2772	.|10	.|0.66056	.|D	.|0.02	.|.	16.8604|16.8604	0.86016|0.86016	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|404;421	.|E7ENL7;Q8WVT3	.|.;TPC12_HUMAN	X|M	101|421;404;421	.|ENSP00000371544:T421M;ENSP00000324318:T421M	.|ENSP00000303612:T404M	R|T	+|+	1|2	2|0	TTC15|TTC15	3404756|3404756	1.000000|1.000000	0.71417|0.71417	0.841000|0.841000	0.33234|0.33234	0.976000|0.976000	0.68499|0.68499	7.133000|7.133000	0.77259|0.77259	2.439000|2.439000	0.82584|0.82584	0.563000|0.563000	0.77884|0.77884	CGA|ACG	C|0.999;T|0.001	0.001	strong		0.587	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
SCAMP2	10066	hgsc.bcm.edu	37	15	75146371	75146371	+	Silent	SNP	C	C	T	rs77456595	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75146371C>T	ENST00000268099.9	-	3	325	c.216G>A	c.(214-216)ccG>ccA	p.P72P		NM_005697.3	NP_005688.2	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2	72					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)|trans-Golgi network membrane (GO:0032588)|transport vesicle (GO:0030133)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	9						CCTGGGGGGTCGGCTGGGTTG	0.572													C|||	74	0.0147764	0.0023	0.0216	5008	,	,		17320	0.001		0.0487	False		,,,				2504	0.0061				p.P72P		Atlas-SNP	.											.	SCAMP2	18	.	0			c.G216A						PASS	.	C		43,4351	45.3+/-79.5	0,43,2154	88.0	85.0	86.0		216	-3.6	0.0	15	dbSNP_131	86	386,8204	125.5+/-184.1	13,360,3922	no	coding-synonymous	SCAMP2	NM_005697.3		13,403,6076	TT,TC,CC		4.4936,0.9786,3.3041		72/330	75146371	429,12555	2197	4295	6492	SO:0001819	synonymous_variant	10066	exon3			GGGGGTCGGCTGG	AF005038	CCDS10271.1	15q23-q25	2013-02-21			ENSG00000140497	ENSG00000140497		"""Secretory carrier membrane proteins"""	10564	protein-coding gene	gene with protein product		606912				9378760	Standard	NM_005697		Approved		uc002azb.1	O15127	OTTHUMG00000142817	ENST00000268099.9:c.216G>A	15.37:g.75146371C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_005697	B2RDF0|Q9BQE8	Silent	SNP	ENST00000268099.9	37	CCDS10271.1																																																																																			C|0.967;T|0.033	0.033	strong		0.572	SCAMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286403.3	NM_005697	
WDR60	55112	hgsc.bcm.edu	37	7	158715219	158715219	+	Silent	SNP	A	A	G	rs2730238	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:158715219A>G	ENST00000407559.3	+	16	2231	c.2073A>G	c.(2071-2073)aaA>aaG	p.K691K		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	691					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		GGCCACAGAAAGTTCTGATAT	0.547													G|||	4438	0.886182	0.9115	0.9135	5008	,	,		19651	0.9464		0.8121	False		,,,				2504	0.8466				p.K691K		Atlas-SNP	.											WDR60,right_lower_lobe,carcinoma,+1,1	WDR60	94	1	0			c.A2073G						PASS	.			3880,404		1756,368,18	59.0	59.0	59.0		2073	4.3	1.0	7	dbSNP_100	59	6968,1522		2852,1264,129	no	coding-synonymous	WDR60	NM_018051.4		4608,1632,147	GG,GA,AA		17.927,9.4304,15.0775		691/1067	158715219	10848,1926	2142	4245	6387	SO:0001819	synonymous_variant	55112	exon16			ACAGAAAGTTCTG		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"""WD repeat domain containing"""	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.2073A>G	7.37:g.158715219A>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	232	231	0.99569	NM_018051	Q9NW58	Silent	SNP	ENST00000407559.3	37	CCDS47757.1																																																																																			A|0.178;G|0.822	0.822	strong		0.547	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051	
HLA-C	3107	hgsc.bcm.edu	37	6	31239100	31239100	+	Silent	SNP	A	A	G	rs1131114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239100A>G	ENST00000376228.5	-	3	383	c.369T>C	c.(367-369)tcT>tcC	p.S123S	HLA-C_ENST00000383329.3_Silent_p.S123S	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	123	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GGTCGCAGCCAGACATCCTCT	0.716													a|||	406	0.0810703	0.1051	0.062	5008	,	,		10861	0.0516		0.0626	False		,,,				2504	0.1115				p.S123S		Atlas-SNP	.											HLA-C_ENST00000383329,colon,carcinoma,-2,2	HLA-C	92	2	0			c.T369C						scavenged	.						22.0	20.0	21.0					6																	31239100		2156	4197	6353	SO:0001819	synonymous_variant	3107	exon3			GCAGCCAGACATC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.369T>C	6.37:g.31239100A>G		Somatic	69	7	0.101449		WXS	Illumina HiSeq	Phase_I	95	36	0.378947	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	10.59	1.393588	0.25205	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	-4.37	0.03633	.	.	.	.	.	T	0.44540	0.1298	.	.	.	0.38381	D	0.945134	.	.	.	.	.	.	T	0.57429	-0.7813	5	0.87932	D	0	.	7.4106	0.27016	0.2497:0.1736:0.5767:0.0	rs1131114;rs1140413;rs2308570;rs3177881;rs3190680;rs3204470	.	.	.	R	123	.	ENSP00000365412:W118R	W	-	1	0	HLA-C	31347079	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-3.666000	0.00399	-1.022000	0.03346	-0.952000	0.02654	TGG	G|0.048;A|0.952	0.048	strong		0.716	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
MTG2	26164	hgsc.bcm.edu	37	20	60768615	60768615	+	Missense_Mutation	SNP	G	G	A	rs6062133	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60768615G>A	ENST00000370823.3	+	2	157	c.139G>A	c.(139-141)Ggc>Agc	p.G47S	MTG2_ENST00000536470.1_Intron|MTG2_ENST00000436421.2_Missense_Mutation_p.G47S	NM_015666.3	NP_056481.1	Q9H4K7	MTG2_HUMAN	mitochondrial ribosome-associated GTPase 2	47	Localized in the mitochondria.|Not localized in the mitochondria.		G -> S (in dbSNP:rs6062133).		GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)										GCTCTCGGTCGGCCGTGCGGA	0.622													G|||	452	0.0902556	0.1399	0.0821	5008	,	,		16510	0.0228		0.1352	False		,,,				2504	0.0521				p.G47S		Atlas-SNP	.											.	GTPBP5	43	.	0			c.G139A						PASS	.	G	SER/GLY	608,3798	265.6+/-266.7	47,514,1642	45.0	48.0	47.0		139	-0.7	0.0	20	dbSNP_114	47	1233,7367	246.8+/-275.1	88,1057,3155	yes	missense	GTPBP5	NM_015666.3	56	135,1571,4797	AA,AG,GG		14.3372,13.7994,14.155	benign	47/407	60768615	1841,11165	2203	4300	6503	SO:0001583	missense	26164	exon2			TCGGTCGGCCGTG	AK001603	CCDS13492.1	20q13.33	2013-05-24	2013-05-24	2013-05-24	ENSG00000101181	ENSG00000101181			16239	protein-coding gene	gene with protein product		610919	"""GTP-binding protein 5 (putative)"", ""GTP binding protein 5 (putative)"""	GTPBP5		17054726, 23396448	Standard	NM_015666		Approved	FLJ10741, dJ1005F21.2, ObgH1		Q9H4K7	OTTHUMG00000032897	ENST00000370823.3:c.139G>A	20.37:g.60768615G>A	ENSP00000359859:p.Gly47Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_015666	A6NDR3|B4DR85|Q96I17|Q9NVG9|Q9UFR4	Missense_Mutation	SNP	ENST00000370823.3	37	CCDS13492.1	201	0.09203296703296704	56	0.11382113821138211	28	0.07734806629834254	15	0.026223776223776224	102	0.1345646437994723	G	11.27	1.590005	0.28357	0.137994	0.143372	ENSG00000101181	ENST00000436421;ENST00000370823;ENST00000448254	T;T;T	0.19532	2.14;2.9;2.39	5.17	-0.701	0.11269	.	0.473596	0.24158	N	0.041007	T	0.00073	0.0002	N	0.03948	-0.315	0.58432	P	1.0000000000287557E-6	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.41998	-0.9477	9	0.12766	T	0.61	-30.959	10.6978	0.45909	0.8491:0.0:0.1509:0.0	rs6062133;rs6062133	47;47;47	Q5JXJ0;E7EU10;Q9H4K7	.;.;GTPB5_HUMAN	S	47	ENSP00000392267:G47S;ENSP00000359859:G47S;ENSP00000414693:G47S	ENSP00000359859:G47S	G	+	1	0	GTPBP5	60202010	0.013000	0.17824	0.001000	0.08648	0.000000	0.00434	-0.049000	0.11924	-0.378000	0.07918	-1.723000	0.00705	GGC	A|0.128;C|0.000;G|0.872	0.128	strong		0.622	MTG2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079989.1	NM_015666	
MYH11	4629	hgsc.bcm.edu	37	16	15809117	15809117	+	Silent	SNP	C	C	T	rs28505375|rs587781069	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15809117C>T	ENST00000300036.5	-	39	5626	c.5517G>A	c.(5515-5517)gcG>gcA	p.A1839A	NDE1_ENST00000396354.1_Intron|NDE1_ENST00000396355.1_Intron|NDE1_ENST00000342673.5_Intron|MYH11_ENST00000452625.2_Silent_p.A1846A|MYH11_ENST00000396324.3_Silent_p.A1846A|MYH11_ENST00000576790.2_Silent_p.A1839A	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1839					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						ACTTGGTGGCCGCCTGTTTCT	0.557			T	CBFB	AML								C|||	461	0.0920527	0.2784	0.0274	5008	,	,		15333	0.0387		0.0229	False		,,,				2504	0.0123				p.A1846A		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.G5538A						PASS	.	C	,,,,,	942,3452	357.1+/-313.8	99,744,1354	77.0	73.0	75.0		5538,5538,,5517,,5517	-5.5	0.0	16	dbSNP_125	75	136,8464	69.0+/-131.5	3,130,4167	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	,,,,,	102,874,5521	TT,TC,CC		1.5814,21.4383,8.2961	,,,,,	1846/1946,1846/1980,,1839/1973,,1839/1939	15809117	1078,11916	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon40			GGTGGCCGCCTGT	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5517G>A	16.37:g.15809117C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	153	77	0.503268	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			C|0.920;T|0.080	0.080	strong		0.557	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
EMILIN3	90187	hgsc.bcm.edu	37	20	39991171	39991171	+	Silent	SNP	G	G	A	rs61739307	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:39991171G>A	ENST00000332312.3	-	4	1230	c.1038C>T	c.(1036-1038)gcC>gcT	p.A346A		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	346						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				TCCGGCTGGCGGCCTGACCCT	0.672													G|||	405	0.0808706	0.059	0.1225	5008	,	,		14633	0.003		0.1799	False		,,,				2504	0.0593				p.A346A		Atlas-SNP	.											EMILIN3,rectum,carcinoma,0,1	EMILIN3	63	1	0			c.C1038T						PASS	.	G		390,4012		16,358,1827	15.0	17.0	16.0		1038	-10.3	0.2	20	dbSNP_129	16	1433,7165		130,1173,2996	no	coding-synonymous	EMILIN3	NM_052846.1		146,1531,4823	AA,AG,GG		16.6667,8.8596,14.0231		346/767	39991171	1823,11177	2201	4299	6500	SO:0001819	synonymous_variant	90187	exon4			GCTGGCGGCCTGA	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1038C>T	20.37:g.39991171G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																			G|0.883;A|0.117	0.117	strong		0.672	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
MRC2	9902	hgsc.bcm.edu	37	17	60767594	60767594	+	Silent	SNP	C	C	A	rs147759673		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:60767594C>A	ENST00000303375.5	+	26	4222	c.3820C>A	c.(3820-3822)Cgg>Agg	p.R1274R	MRC2_ENST00000446119.2_Silent_p.R140R	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1274	C-type lectin 8. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						GATTCCCTTCCGGGAGCACTG	0.617																																					p.R1274R		Atlas-SNP	.											.	MRC2	126	.	0			c.C3820A						PASS	.	C		0,4406		0,0,2203	36.0	44.0	42.0		3820	3.8	1.0	17	dbSNP_134	42	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	MRC2	NM_006039.3		0,6,6497	AA,AC,CC		0.0698,0.0,0.0461		1274/1480	60767594	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	9902	exon26			CCCTTCCGGGAGC	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"""CD molecules"", ""C-type lectin domain containing"""	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3820C>A	17.37:g.60767594C>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	227	116	0.511013	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	37	CCDS11634.1																																																																																			C|1.000;A|0.000	0.000	weak		0.617	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
SACS	26278	hgsc.bcm.edu	37	13	23930055	23930055	+	Missense_Mutation	SNP	A	A	T	rs2031640	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:23930055A>T	ENST00000382292.3	-	7	969	c.696T>A	c.(694-696)aaT>aaA	p.N232K	SACS_ENST00000476776.1_5'Flank|SACS_ENST00000402364.1_5'UTR|SACS_ENST00000382298.3_Missense_Mutation_p.N232K			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	232			N -> K (in dbSNP:rs2031640).		cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CATCTTTGAGATTCCAACATT	0.393													A|||	433	0.0864617	0.0068	0.0922	5008	,	,		18517	0.121		0.1292	False		,,,				2504	0.1104				p.N232K		Atlas-SNP	.											.	SACS	871	.	0			c.T696A						PASS	.	A	LYS/ASN	103,4303	79.9+/-118.3	2,99,2102	87.0	81.0	83.0		696	0.7	1.0	13	dbSNP_94	83	1002,7598	216.2+/-255.3	49,904,3347	yes	missense	SACS	NM_014363.4	94	51,1003,5449	TT,TA,AA		11.6512,2.3377,8.4961	probably-damaging	232/4580	23930055	1105,11901	2203	4300	6503	SO:0001583	missense	26278	exon8			TTTGAGATTCCAA	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.696T>A	13.37:g.23930055A>T	ENSP00000371729:p.Asn232Lys	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	313	162	0.517572	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	208|208	0.09523809523809523|0.09523809523809523	2|2	0.0040650406504065045|0.0040650406504065045	32|32	0.08839779005524862|0.08839779005524862	74|74	0.12937062937062938|0.12937062937062938	100|100	0.13192612137203166|0.13192612137203166	A|A	19.71|19.71	3.877814|3.877814	0.72294|0.72294	0.023377|0.023377	0.116512|0.116512	ENSG00000151835|ENSG00000151835	ENST00000382292;ENST00000382298|ENST00000455470	D;D|.	0.84146|.	-1.81;-1.81|.	5.94|5.94	0.714|0.714	0.18180|0.18180	ATPase-like, ATP-binding domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00300|0.00300	0.0009|0.0009	L|L	0.31420|0.31420	0.93|0.93	0.27070|0.27070	P|P	0.9633483|0.9633483	D;P;P|.	0.54601|.	0.967;0.767;0.787|.	P;P;B|.	0.57101|.	0.813;0.661;0.345|.	T|T	0.16217|0.16217	-1.0410|-1.0410	9|4	0.22706|.	T|.	0.39|.	.|.	5.7211|5.7211	0.17988|0.17988	0.6049:0.1294:0.2657:0.0|0.6049:0.1294:0.2657:0.0	rs2031640;rs17378785;rs2031640|rs2031640;rs17378785;rs2031640	131;19;232|.	B2REB1;E9PAL4;Q9NZJ4|.	.;.;SACS_HUMAN|.	K|T	232|132	ENSP00000371729:N232K;ENSP00000371735:N232K|.	ENSP00000371729:N232K|.	N|S	-|-	3|1	2|0	SACS|SACS	22828055|22828055	0.995000|0.995000	0.38212|0.38212	0.998000|0.998000	0.56505|0.56505	0.997000|0.997000	0.91878|0.91878	0.536000|0.536000	0.23129|0.23129	-0.073000|-0.073000	0.12842|0.12842	0.528000|0.528000	0.53228|0.53228	AAT|TCT	A|0.907;T|0.093	0.093	strong		0.393	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32925226	32925226	+	Silent	SNP	T	T	G	rs77143444	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:32925226T>G	ENST00000361627.3	+	9	1874	c.1152T>G	c.(1150-1152)tcT>tcG	p.S384S	ARHGAP11A_ENST00000563864.1_Intron|ARHGAP11A_ENST00000565905.1_Silent_p.S195S|ARHGAP11A_ENST00000543522.1_Silent_p.S195S|ARHGAP11A_ENST00000567348.1_Silent_p.S384S	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	384					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		GTTCACTCTCTCCTGTACTCA	0.393													T|||	15	0.00299521	0.0	0.0014	5008	,	,		16649	0.0		0.0129	False		,,,				2504	0.001				p.S384S	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.T1152G						PASS	.	T	,	5,4397		0,5,2196	159.0	154.0	156.0		1152,1152	2.1	1.0	15	dbSNP_131	156	63,8537		1,61,4238	no	coding-synonymous,coding-synonymous	ARHGAP11A	NM_014783.3,NM_199357.1	,	1,66,6434	GG,GT,TT		0.7326,0.1136,0.523	,	384/1024,384/502	32925226	68,12934	2201	4300	6501	SO:0001819	synonymous_variant	9824	exon9			ACTCTCTCCTGTA	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1152T>G	15.37:g.32925226T>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	165	81	0.490909	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	37	CCDS10028.1																																																																																			T|0.995;G|0.005	0.005	strong		0.393	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	
OR8B3	390271	hgsc.bcm.edu	37	11	124266927	124266927	+	Silent	SNP	A	A	G	rs142812088		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124266927A>G	ENST00000354597.3	-	1	337	c.321T>C	c.(319-321)ttT>ttC	p.F107F		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CAGAGATGACAAAAAAGAGAA	0.388																																					p.F107F		Atlas-SNP	.											OR8B3,NS,carcinoma,0,1	OR8B3	36	1	0			c.T321C						scavenged	.						78.0	76.0	77.0					11																	124266927		2201	4299	6500	SO:0001819	synonymous_variant	390271	exon1			GATGACAAAAAAG	AB065827	CCDS31709.1	11q24.1	2012-08-09			ENSG00000196661	ENSG00000196661		"""GPCR / Class A : Olfactory receptors"""	8472	protein-coding gene	gene with protein product							Standard	NM_001005467		Approved		uc010saj.2	Q8NGG8	OTTHUMG00000165983	ENST00000354597.3:c.321T>C	11.37:g.124266927A>G		Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	347	16	0.0461095	NM_001005467	Q6IFQ8|Q8NGH1	Silent	SNP	ENST00000354597.3	37	CCDS31709.1																																																																																			A|1.000;G|0.000	0.000	weak		0.388	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467	
KIAA1429	25962	hgsc.bcm.edu	37	8	95538708	95538708	+	Silent	SNP	G	G	A	rs7835534	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:95538708G>A	ENST00000297591.5	-	8	1839	c.1764C>T	c.(1762-1764)caC>caT	p.H588H	KIAA1429_ENST00000437199.1_Silent_p.H588H|KIAA1429_ENST00000421249.2_Silent_p.H588H	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	588					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			CATCTGTGTCGTGATCAGGTT	0.388													G|||	139	0.0277556	0.0325	0.049	5008	,	,		20615	0.0		0.0388	False		,,,				2504	0.0235				p.H588H		Atlas-SNP	.											.	KIAA1429	176	.	0			c.C1764T						PASS	.	G	,	180,4226	117.1+/-155.0	4,172,2027	153.0	149.0	150.0		1764,1764	-0.7	1.0	8	dbSNP_116	150	513,8087	145.1+/-200.9	15,483,3802	no	coding-synonymous,coding-synonymous	KIAA1429	NM_015496.4,NM_183009.2	,	19,655,5829	AA,AG,GG		5.9651,4.0853,5.3283	,	588/1813,588/1148	95538708	693,12313	2203	4300	6503	SO:0001819	synonymous_variant	25962	exon8			TGTGTCGTGATCA	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.1764C>T	8.37:g.95538708G>A		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	268	134	0.5	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	37	CCDS34923.1																																																																																			G|0.958;A|0.042	0.042	strong		0.388	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
ATP8B3	148229	hgsc.bcm.edu	37	19	1783261	1783261	+	Silent	SNP	C	C	T	rs2385387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1783261C>T	ENST00000310127.6	-	29	3907	c.3669G>A	c.(3667-3669)aaG>aaA	p.K1223K	ATP8B3_ENST00000539485.1_Silent_p.K1233K|ATP8B3_ENST00000525591.1_Silent_p.K1186K	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1223					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTCCTCCACCTTCTCCTCCT	0.592													.|||	1508	0.301118	0.1505	0.3343	5008	,	,		17351	0.3095		0.4105	False		,,,				2504	0.3599				p.K1223K		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G3669A						PASS	.	C	,	681,3309		71,539,1385	19.0	20.0	20.0		3558,3669	0.6	0.0	19	dbSNP_100	20	3481,4787		744,1993,1397	no	coding-synonymous,coding-synonymous	ATP8B3	NM_001178002.1,NM_138813.2	,	815,2532,2782	TT,TC,CC		42.1021,17.0677,33.9533	,	1186/1264,1223/1301	1783261	4162,8096	1995	4134	6129	SO:0001819	synonymous_variant	148229	exon29			CTCCACCTTCTCC	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.3669G>A	19.37:g.1783261C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Silent	SNP	ENST00000310127.6	37	CCDS45901.1																																																																																			C|0.687;T|0.313	0.313	strong		0.592	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
SERPINH1	871	hgsc.bcm.edu	37	11	75277992	75277992	+	Silent	SNP	C	C	T	rs651581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:75277992C>T	ENST00000524558.1	+	2	2033	c.598C>T	c.(598-600)Cta>Tta	p.L200L	SERPINH1_ENST00000358171.3_Silent_p.L200L|SERPINH1_ENST00000530284.1_Silent_p.L200L|SERPINH1_ENST00000533603.1_Silent_p.L200L|SERPINH1_ENST00000525876.1_5'Flank			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	200					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					CGGCGCCCTGCTAGTCAACGC	0.667													C|||	1499	0.299321	0.0847	0.3213	5008	,	,		17900	0.2976		0.5417	False		,,,				2504	0.3262				p.L200L		Atlas-SNP	.											.	SERPINH1	33	.	0			c.C598T						PASS	.	C	,	757,3633		68,621,1506	28.0	27.0	27.0		598,598	2.6	1.0	11	dbSNP_83	27	4755,3803		1324,2107,848	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	1392,2728,2354	TT,TC,CC		44.438,17.2437,42.5703	,	200/419,200/419	75277992	5512,7436	2195	4279	6474	SO:0001819	synonymous_variant	871	exon2			GCCCTGCTAGTCA	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.598C>T	11.37:g.75277992C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	28	12	0.428571	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																			C|0.626;T|0.374	0.374	strong		0.667	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
LRRC42	115353	hgsc.bcm.edu	37	1	54432019	54432019	+	Silent	SNP	G	G	A	rs2294514	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:54432019G>A	ENST00000371370.3	+	8	1499	c.978G>A	c.(976-978)gaG>gaA	p.E326E	LRRC42_ENST00000477905.1_3'UTR|LRRC42_ENST00000319223.4_Silent_p.E326E	NM_001256409.1	NP_001243338.1	Q9Y546	LRC42_HUMAN	leucine rich repeat containing 42	326										breast(2)|kidney(1)|large_intestine(1)|lung(5)	9						AGCCACGGGAGACCTCGGAGC	0.443													A|||	1301	0.259784	0.7163	0.1254	5008	,	,		19363	0.0605		0.1451	False		,,,				2504	0.0613				p.E326E		Atlas-SNP	.											.	LRRC42	29	.	0			c.G978A						PASS	.	A		2618,1788	526.7+/-371.9	781,1056,366	90.0	95.0	93.0		978	1.2	0.0	1	dbSNP_100	93	1291,7309	759.0+/-407.5	105,1081,3114	yes	coding-synonymous	LRRC42	NM_052940.3		886,2137,3480	AA,AG,GG		15.0116,40.581,30.0554		326/429	54432019	3909,9097	2203	4300	6503	SO:0001819	synonymous_variant	115353	exon7			ACGGGAGACCTCG	AK075201	CCDS585.1	1p33-p32.1	2014-02-12			ENSG00000116212	ENSG00000116212			28792	protein-coding gene	gene with protein product						12477932	Standard	NM_001256409		Approved	MGC8974	uc001cwj.2	Q9Y546	OTTHUMG00000008436	ENST00000371370.3:c.978G>A	1.37:g.54432019G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	191	112	0.586387	NM_052940	D3DQ46|Q8N2Q8	Silent	SNP	ENST00000371370.3	37	CCDS585.1																																																																																			G|0.708;A|0.292	0.292	strong		0.443	LRRC42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023250.1	NM_052940	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118236218	118236218	+	Silent	SNP	C	C	T	rs61729315	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:118236218C>T	ENST00000369230.3	+	11	1373	c.1227C>T	c.(1225-1227)aaC>aaT	p.N409N		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	409	PLAT.				lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		CAGATGTTAACGTTGGAAACA	0.363													C|||	174	0.0347444	0.0212	0.072	5008	,	,		18369	0.0476		0.0278	False		,,,				2504	0.0204				p.N409N		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.C1227T						PASS	.	C		71,4335	63.5+/-100.7	1,69,2133	124.0	121.0	122.0		1227	-8.3	0.0	10	dbSNP_129	122	78,8522	46.3+/-105.2	0,78,4222	no	coding-synonymous	PNLIPRP3	NM_001011709.2		1,147,6355	TT,TC,CC		0.907,1.6114,1.1456		409/468	118236218	149,12857	2203	4300	6503	SO:0001819	synonymous_variant	119548	exon11			TGTTAACGTTGGA	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1227C>T	10.37:g.118236218C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	168	79	0.470238	NM_001011709		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																			C|0.982;T|0.018	0.018	strong		0.363	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110510964	110510964	+	Missense_Mutation	SNP	A	A	C	rs191412861	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110510964A>C	ENST00000378402.5	+	67	10896	c.10792A>C	c.(10792-10794)Agt>Cgt	p.S3598R		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3598					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AGGAATCATGAGTTACAATGC	0.408										HNSCC(38;0.096)			A|||	28	0.00559105	0.0008	0.0072	5008	,	,		16193	0.0		0.005	False		,,,				2504	0.0174				p.S3598R		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A10792C						PASS	.	A	ARG/SER	2,3744		0,2,1871	81.0	77.0	78.0		10792	6.0	1.0	8		78	48,8134		1,46,4044	yes	missense	PKHD1L1	NM_177531.4	110	1,48,5915	CC,CA,AA		0.5867,0.0534,0.4192	probably-damaging	3598/4244	110510964	50,11878	1873	4091	5964	SO:0001583	missense	93035	exon67			ATCATGAGTTACA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.10792A>C	8.37:g.110510964A>C	ENSP00000367655:p.Ser3598Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	158	59	0.373418	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	A	26.4	4.731514	0.89390	5.34E-4	0.005867	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.86865	-2.18;-1.99	6.02	6.02	0.97574	.	0.109105	0.64402	D	0.000010	D	0.83723	0.5316	M	0.78637	2.42	0.40619	D	0.981744	B	0.25719	0.132	B	0.22601	0.04	D	0.84175	0.0436	10	0.59425	D	0.04	.	14.5014	0.67724	1.0:0.0:0.0:0.0	.	3598	Q86WI1	PKHL1_HUMAN	R	3598;526	ENSP00000367655:S3598R;ENSP00000437376:S526R	ENSP00000367655:S3598R	S	+	1	0	PKHD1L1	110580140	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.683000	0.84093	2.299000	0.77371	0.528000	0.53228	AGT	A|0.997;C|0.003	0.003	strong		0.408	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
STAB2	55576	hgsc.bcm.edu	37	12	104092996	104092996	+	Silent	SNP	T	T	C	rs697210	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:104092996T>C	ENST00000388887.2	+	34	3909	c.3705T>C	c.(3703-3705)caT>caC	p.H1235H		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TCTTTCTCCATAATGACCAGG	0.468													.|||	1772	0.353834	0.4168	0.3804	5008	,	,		22002	0.37		0.3121	False		,,,				2504	0.2761				p.H1235H		Atlas-SNP	.											.	STAB2	370	.	0			c.T3705C						PASS	.	C		1729,2677	649.2+/-398.8	341,1047,815	191.0	162.0	172.0		3705	-3.1	0.0	12	dbSNP_86	172	2548,6052	691.5+/-404.5	357,1834,2109	no	coding-synonymous	STAB2	NM_017564.9		698,2881,2924	CC,CT,TT		29.6279,39.2419,32.8848		1235/2552	104092996	4277,8729	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon34			TCTCCATAATGAC	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.3705T>C	12.37:g.104092996T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	192	92	0.479167	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			T|0.664;C|0.336	0.336	strong		0.468	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
OR4A5	81318	hgsc.bcm.edu	37	11	51411740	51411740	+	Missense_Mutation	SNP	A	A	T	rs35083184	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:51411740A>T	ENST00000319760.6	-	1	708	c.656T>A	c.(655-657)cTa>cAa	p.L219Q		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	219			L -> Q (in dbSNP:rs35083184).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				AAGGGAGCTTAGGATGACTCC	0.438													.|||	406	0.0810703	0.056	0.0591	5008	,	,		19988	0.0863		0.1252	False		,,,				2504	0.0798				p.L219Q		Atlas-SNP	.											.	OR4A5	116	.	0			c.T656A						PASS	.	A	GLN/LEU	240,4162		7,226,1968	60.0	60.0	60.0		656	0.7	0.3	11	dbSNP_126	60	1040,7550		60,920,3315	yes	missense	OR4A5	NM_001005272.3	113	67,1146,5283	TT,TA,AA		12.1071,5.4521,9.8522	possibly-damaging	219/316	51411740	1280,11712	2201	4295	6496	SO:0001583	missense	81318	exon1			GAGCTTAGGATGA	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.656T>A	11.37:g.51411740A>T	ENSP00000367664:p.Leu219Gln	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	185	0.08470695970695971	30	0.06097560975609756	28	0.07734806629834254	35	0.06118881118881119	92	0.12137203166226913	.	8.099	0.776258	0.16051	0.054521	0.121071	ENSG00000221840	ENST00000319760	T	0.00249	8.44	1.93	0.659	0.17861	GPCR, rhodopsin-like superfamily (1);	0.204155	0.24258	N	0.040117	T	0.00012	0.0000	H	0.96576	3.845	0.80722	P	0.0	P	0.38370	0.628	P	0.53689	0.732	T	0.08848	-1.0702	9	0.87932	D	0	.	6.1148	0.20120	0.7386:0.2614:0.0:0.0	rs35083184	219	Q8NH83	OR4A5_HUMAN	Q	219	ENSP00000367664:L219Q	ENSP00000367664:L219Q	L	-	2	0	OR4A5	51268316	0.004000	0.15560	0.262000	0.24481	0.026000	0.11368	1.313000	0.33585	0.166000	0.19597	0.136000	0.15936	CTA	A|0.903;T|0.097	0.097	strong		0.438	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
CAMKK1	84254	hgsc.bcm.edu	37	17	3775848	3775848	+	Splice_Site	SNP	T	T	C	rs7214723|rs17855558	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:3775848T>C	ENST00000348335.2	-	12	1272	c.1124A>G	c.(1123-1125)gAg>gGg	p.E375G	CAMKK1_ENST00000381769.2_Splice_Site_p.E402G|CAMKK1_ENST00000158166.5_Splice_Site_p.E413G|CAMKK1_ENST00000381771.2_Splice_Site_p.E413G	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	375	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> G (in dbSNP:rs7214723). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	11				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		GACAACTCACTCCTCAGGAAA	0.577													T|||	1980	0.395367	0.1044	0.5418	5008	,	,		18215	0.4028		0.4433	False		,,,				2504	0.6278				p.E413G		Atlas-SNP	.											.	CAMKK1	70	.	0			c.A1238G	GRCh37	CM067356	CAMKK1	M	rs7214723	PASS	.		GLY/GLU,GLY/GLU,GLY/GLU	756,3650	308.6+/-290.6	71,614,1518	102.0	90.0	94.0		1124,1124,1238	4.1	1.0	17	dbSNP_116	94	3836,4764	538.9+/-383.5	860,2116,1324	yes	missense-near-splice,missense-near-splice,missense-near-splice	CAMKK1	NM_032294.2,NM_172206.1,NM_172207.2	98,98,98	931,2730,2842	CC,CT,TT		44.6047,17.1584,35.3068	benign,benign,benign	375/506,375/506,413/521	3775848	4592,8414	2203	4300	6503	SO:0001630	splice_region_variant	84254	exon13			ACTCACTCCTCAG	AL136576	CCDS11038.1, CCDS11039.1	17p13.3	2004-02-18			ENSG00000004660	ENSG00000004660			1469	protein-coding gene	gene with protein product		611411				11230166	Standard	NM_172207		Approved	DKFZp761M0423, CAMKKA, MGC34095	uc002fwt.3	Q8N5S9	OTTHUMG00000090725	ENST00000348335.2:c.1124+1A>G	17.37:g.3775848T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_172207	Q9BQH3	Missense_Mutation	SNP	ENST00000348335.2	37	CCDS11038.1	777	0.3557692307692308	45	0.09146341463414634	186	0.5138121546961326	221	0.38636363636363635	325	0.4287598944591029	T	13.54	2.268221	0.40095	0.171584	0.446047	ENSG00000004660	ENST00000381769;ENST00000348335;ENST00000381771;ENST00000158166	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.23	4.1	0.47936	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.505696	0.21230	N	0.077994	T	0.00012	0.0000	L	0.28694	0.88	0.21822	P	0.99952029	B;B	0.14805	0.008;0.011	B;B	0.28305	0.009;0.088	T	0.46076	-0.9217	8	.	.	.	-23.4052	10.7485	0.46194	0.1418:0.0:0.0:0.8582	rs7214723;rs17709051;rs59070130;rs7214723	413;375	F8W9H1;Q8N5S9	.;KKCC1_HUMAN	G	402;375;413;413	ENSP00000371188:E402G;ENSP00000323118:E375G;ENSP00000371190:E413G;ENSP00000158166:E413G	.	E	-	2	0	CAMKK1	3722597	0.998000	0.40836	0.993000	0.49108	0.770000	0.43624	2.666000	0.46799	1.987000	0.57996	0.524000	0.50904	GAG	T|0.644;C|0.356	0.356	strong		0.577	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207	Missense_Mutation
TBL3	10607	hgsc.bcm.edu	37	16	2026891	2026891	+	Missense_Mutation	SNP	T	T	C	rs17605	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2026891T>C	ENST00000568546.1	+	14	1497	c.1369T>C	c.(1369-1371)Tcc>Ccc	p.S457P		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	457			S -> P (in dbSNP:rs17605). {ECO:0000269|Ref.2}.		G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						AGCCTTGCTGTCCAAGAACAC	0.602													T|||	241	0.048123	0.0643	0.0548	5008	,	,		20858	0.0		0.0984	False		,,,				2504	0.0194				p.S457P	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.T1369C						PASS	.	T	PRO/SER	273,4123	153.7+/-187.2	12,249,1937	110.0	89.0	96.0		1369	-0.4	0.0	16	dbSNP_63	96	811,7789	187.4+/-234.7	47,717,3536	yes	missense	TBL3	NM_006453.2	74	59,966,5473	CC,CT,TT		9.4302,6.2102,8.341	possibly-damaging	457/809	2026891	1084,11912	2198	4300	6498	SO:0001583	missense	10607	exon14			TTGCTGTCCAAGA	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1369T>C	16.37:g.2026891T>C	ENSP00000454836:p.Ser457Pro	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	96	54	0.5625	NM_006453	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	37	CCDS10453.1	124	0.056776556776556776	37	0.07520325203252033	20	0.055248618784530384	0	0.0	67	0.08839050131926121	T	9.925	1.213264	0.22289	0.062102	0.094302	ENSG00000183751	ENST00000332704	.	.	.	5.27	-0.37	0.12530	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.886090	0.01880	N	0.037799	T	0.00845	0.0028	N	0.17474	0.49	0.52501	P	4.099999999995774E-5	P;P	0.44309	0.736;0.832	B;B	0.38106	0.193;0.265	T	0.11397	-1.0589	8	0.30854	T	0.27	-15.4021	9.1598	0.37016	0.1268:0.0:0.5215:0.3517	rs17605;rs17135737;rs17605	219;457	A0JLS5;Q12788	.;TBL3_HUMAN	P	457	.	ENSP00000331815:S457P	S	+	1	0	TBL3	1966892	0.080000	0.21391	0.004000	0.12327	0.713000	0.41058	0.223000	0.17719	-0.039000	0.13602	0.459000	0.35465	TCC	T|0.925;C|0.075	0.075	strong		0.602	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
SF3B3	23450	hgsc.bcm.edu	37	16	70569215	70569215	+	Silent	SNP	A	A	T	rs33910368	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:70569215A>T	ENST00000302516.5	+	6	928	c.717A>T	c.(715-717)ccA>ccT	p.P239P	SNORD111_ENST00000408139.1_RNA	NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	239					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				TCACAGTTCCAGGAGGGTCAG	0.428													A|||	2355	0.470248	0.2874	0.4135	5008	,	,		18512	0.5804		0.4155	False		,,,				2504	0.7004				p.P239P		Atlas-SNP	.											.	SF3B3	99	.	0			c.A717T						PASS	.	A		1292,3104	437.0+/-344.8	190,912,1096	207.0	212.0	210.0		717	-9.7	0.8	16	dbSNP_126	210	3632,4968	522.8+/-380.2	780,2072,1448	no	coding-synonymous	SF3B3	NM_012426.4		970,2984,2544	TT,TA,AA		42.2326,29.3904,37.8886		239/1218	70569215	4924,8072	2198	4300	6498	SO:0001819	synonymous_variant	23450	exon6			AGTTCCAGGAGGG	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"""splicing factor 3b, subunit 3, 130kD"""			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.717A>T	16.37:g.70569215A>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	190	102	0.536842	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Silent	SNP	ENST00000302516.5	37	CCDS10894.1																																																																																			A|0.596;T|0.404	0.404	strong		0.428	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426	
MRGPRE	116534	hgsc.bcm.edu	37	11	3249552	3249552	+	Missense_Mutation	SNP	C	C	T	rs4391795	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:3249552C>T	ENST00000389832.5	-	2	784	c.478G>A	c.(478-480)Ggc>Agc	p.G160S	MRGPRE_ENST00000436689.2_Missense_Mutation_p.G159S|AC109309.4_ENST00000418995.2_RNA			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	160			G -> S (in dbSNP:rs4391795).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTGCAGGCGCCGCTGAGCAGC	0.692													C|||	1467	0.292931	0.0953	0.2392	5008	,	,		13177	0.378		0.4523	False		,,,				2504	0.3466				p.G160S		Atlas-SNP	.											.	MRGPRE	35	.	0			c.G478A						PASS	.	C	SER/GLY	481,3647		34,413,1617	5.0	9.0	8.0		475	0.8	0.0	11	dbSNP_111	8	3172,5086		621,1930,1578	yes	missense	MRGPRE	NM_001039165.2	56	655,2343,3195	TT,TC,CC		38.4112,11.6521,29.493	probably-damaging	159/312	3249552	3653,8733	2064	4129	6193	SO:0001583	missense	116534	exon2			AGGCGCCGCTGAG	AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"""GPCR / Class A : Orphans"""	30694	protein-coding gene	gene with protein product		607232	"""G protein-coupled receptor 167"""	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.478G>A	11.37:g.3249552C>T	ENSP00000374482:p.Gly160Ser	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	25	14	0.56	NM_001039165	Q2M1V7	Missense_Mutation	SNP	ENST00000389832.5	37		712	0.326007326007326	37	0.07520325203252033	100	0.27624309392265195	229	0.40034965034965037	346	0.45646437994722955	c	7.476	0.647610	0.14516	0.116521	0.384112	ENSG00000184350	ENST00000436689;ENST00000389832	.	.	.	3.75	0.817	0.18773	GPCR, rhodopsin-like superfamily (1);	0.506640	0.14301	U	0.328254	T	0.00012	0.0000	L	0.39397	1.21	0.80722	P	0.0	D	0.61080	0.989	P	0.55455	0.776	T	0.44697	-0.9311	8	0.24483	T	0.36	-11.0184	5.6296	0.17504	0.0:0.6298:0.0:0.3702	rs4391795;rs4990224	159	Q86SM8	MRGRE_HUMAN	S	160;159	.	ENSP00000374482:G159S	G	-	1	0	MRGPRE	3206128	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	0.733000	0.26087	-0.017000	0.14103	-0.229000	0.12294	GGC	C|0.673;T|0.327	0.327	strong		0.692	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536	
DNAI2	64446	hgsc.bcm.edu	37	17	72295966	72295966	+	Silent	SNP	C	C	T	rs34159194	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72295966C>T	ENST00000311014.6	+	7	901	c.834C>T	c.(832-834)acC>acT	p.T278T	DNAI2_ENST00000579490.1_Silent_p.T335T|DNAI2_ENST00000446837.2_Silent_p.T278T|DNAI2_ENST00000307504.5_Silent_p.T135T|DNAI2_ENST00000582036.1_Silent_p.T278T			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	278					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						AGACGGGCACCGAGTGCTTCT	0.612									Kartagener syndrome				C|||	370	0.0738818	0.0129	0.0865	5008	,	,		16936	0.003		0.171	False		,,,				2504	0.1207				p.T278T		Atlas-SNP	.											.	DNAI2	102	.	0			c.C834T						PASS	.	C	,	205,4201	126.1+/-163.2	5,195,2003	64.0	47.0	53.0		834,834	-10.3	0.8	17	dbSNP_126	53	1612,6988	298.9+/-304.1	152,1308,2840	no	coding-synonymous,coding-synonymous	DNAI2	NM_001172810.1,NM_023036.4	,	157,1503,4843	TT,TC,CC		18.7442,4.6527,13.9705	,	278/594,278/606	72295966	1817,11189	2203	4300	6503	SO:0001819	synonymous_variant	64446	exon7	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGGCACCGAGTGC	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"""Axonemal dyneins"", ""WD repeat domain containing"""	18744	protein-coding gene	gene with protein product	"""dynein intermediate chain 2"""	605483	"""dynein, axonemal, intermediate polypeptide 2"""			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.834C>T	17.37:g.72295966C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																			C|0.883;T|0.117	0.117	strong		0.612	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
DBF4	10926	hgsc.bcm.edu	37	7	87537183	87537183	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:87537183A>G	ENST00000265728.1	+	12	2234	c.1730A>G	c.(1729-1731)aAa>aGa	p.K577R		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	577					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				ATACATCGAAAAGTGAAAATA	0.333																																					p.K577R		Atlas-SNP	.											.	DBF4	67	.	0			c.A1730G						PASS	.						48.0	55.0	52.0					7																	87537183		2201	4266	6467	SO:0001583	missense	10926	exon12			ATCGAAAAGTGAA	AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634		"""Zinc fingers, DBF-type"""	17364	protein-coding gene	gene with protein product	"""activator of S phase kinase"", ""chiffon homolog (Drosophila)"", ""zinc finger, DBF-type containing 1"", ""DBF4 zinc finger A"""	604281	"""DBF4 homolog (S. cerevisiae)"""			10373557, 10517317	Standard	NM_006716		Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.1730A>G	7.37:g.87537183A>G	ENSP00000265728:p.Lys577Arg	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	297	158	0.531987	NM_006716	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Missense_Mutation	SNP	ENST00000265728.1	37	CCDS5611.1	.	.	.	.	.	.	.	.	.	.	A	16.90	3.250022	0.59212	.	.	ENSG00000006634	ENST00000265728	T	0.52295	0.67	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000002	T	0.46718	0.1407	M	0.63843	1.955	0.47905	D	0.999544	P;P	0.52463	0.953;0.802	B;B	0.41036	0.346;0.277	T	0.55798	-0.8084	10	0.87932	D	0	-13.7887	13.5232	0.61580	1.0:0.0:0.0:0.0	.	353;577	B7Z8C6;Q9UBU7	.;DBF4A_HUMAN	R	577	ENSP00000265728:K577R	ENSP00000265728:K577R	K	+	2	0	DBF4	87375119	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.326000	0.59241	1.934000	0.56057	0.528000	0.53228	AAA	.	.	none		0.333	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716	
REP15	387849	hgsc.bcm.edu	37	12	27849795	27849795	+	Silent	SNP	C	C	T	rs929948|rs386761425	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:27849795C>T	ENST00000310791.2	+	1	368	c.300C>T	c.(298-300)tcC>tcT	p.S100S	RP11-1060J15.4_ENST00000536922.1_RNA|RP11-1060J15.4_ENST00000536317.1_RNA|RP11-1060J15.4_ENST00000542660.1_RNA	NM_001029874.1	NP_001025045.1	Q6BDI9	REP15_HUMAN	RAB15 effector protein	100					receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	endosome membrane (GO:0010008)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)				breast(1)|cervix(1)|large_intestine(2)|lung(4)|ovary(1)	9	Lung SC(9;0.0873)					TTTGGGGATCCAACAAGCAAA	0.488													C|||	2985	0.596046	0.6399	0.6888	5008	,	,		20554	0.5268		0.6262	False		,,,				2504	0.5112				p.S100S		Atlas-SNP	.											.	REP15	13	.	0			c.C300T						PASS	.	C		2775,1631	661.2+/-400.9	873,1029,301	83.0	80.0	81.0		300	-9.8	0.0	12	dbSNP_86	81	5305,3295	646.4+/-400.3	1624,2057,619	no	coding-synonymous	REP15	NM_001029874.1		2497,3086,920	TT,TC,CC		38.314,37.0177,37.8748		100/237	27849795	8080,4926	2203	4300	6503	SO:0001819	synonymous_variant	387849	exon1			GGGATCCAACAAG	BC140921	CCDS31762.1	12p11.22	2010-09-02			ENSG00000174236	ENSG00000174236			33748	protein-coding gene	gene with protein product		610848				16195351	Standard	NM_001029874		Approved	RAB15EP	uc001rig.1	Q6BDI9		ENST00000310791.2:c.300C>T	12.37:g.27849795C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_001029874	B2RU16	Silent	SNP	ENST00000310791.2	37	CCDS31762.1																																																																																			C|0.408;T|0.592	0.592	strong		0.488	REP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402894.1	NM_001029874	
PSEN2	5664	hgsc.bcm.edu	37	1	227069677	227069677	+	Silent	SNP	T	T	C	rs11405	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:227069677T>C	ENST00000366783.3	+	4	505	c.69T>C	c.(67-69)gcT>gcC	p.A23A	PSEN2_ENST00000366782.1_Silent_p.A56A|PSEN2_ENST00000391872.2_Silent_p.A56A|PSEN2_ENST00000340188.4_Silent_p.A23A|PSEN2_ENST00000422240.2_Silent_p.A23A|PSEN2_ENST00000472139.2_5'Flank	NM_000447.2|NM_012486.2	NP_000438.2|NP_036618.2	P49810	PSN2_HUMAN	presenilin 2	23					amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|brain morphogenesis (GO:0048854)|calcium ion transport (GO:0006816)|cardiac muscle contraction (GO:0060048)|cell fate specification (GO:0001708)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|forebrain development (GO:0030900)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|locomotion (GO:0040011)|lung alveolus development (GO:0048286)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|memory (GO:0007613)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of protein phosphorylation (GO:0001933)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of synaptic plasticity (GO:0048167)|response to hypoxia (GO:0001666)|somitogenesis (GO:0001756)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear inner membrane (GO:0005637)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|urinary_tract(1)	20		Prostate(94;0.0771)				TAATGTCGGCTGAGAGCCCCA	0.622													C|||	3684	0.735623	0.8313	0.7176	5008	,	,		19714	0.5427		0.8022	False		,,,				2504	0.7495				p.A23A		Atlas-SNP	.											.	PSEN2	55	.	0			c.T69C						PASS	.	C	,	3606,800	319.6+/-296.2	1479,648,76	66.0	62.0	63.0		69,69	-5.7	0.5	1	dbSNP_52	63	6709,1891	335.8+/-321.6	2603,1503,194	no	coding-synonymous,coding-synonymous	PSEN2	NM_000447.2,NM_012486.2	,	4082,2151,270	CC,CT,TT		21.9884,18.1571,20.6905	,	23/449,23/448	227069677	10315,2691	2203	4300	6503	SO:0001819	synonymous_variant	5664	exon4			GTCGGCTGAGAGC	BC006365	CCDS1556.1, CCDS44324.1	1q42.13	2014-09-17	2014-02-24		ENSG00000143801	ENSG00000143801			9509	protein-coding gene	gene with protein product		600759	"""Alzheimer disease 4"""	AD4		7638621	Standard	NM_000447		Approved	AD3L, STM2, PS2	uc009xeo.1	P49810	OTTHUMG00000037563	ENST00000366783.3:c.69T>C	1.37:g.227069677T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	125	123	0.984	NM_012486	A8K8D4|B1AP21|Q96P32	Silent	SNP	ENST00000366783.3	37	CCDS1556.1																																																																																			T|0.227;C|0.773	0.773	strong		0.622	PSEN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091539.1	NM_000447	
MC1R	4157	hgsc.bcm.edu	37	16	89986608	89986608	+	Silent	SNP	A	A	G	rs2228478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89986608A>G	ENST00000555147.1	+	1	2322	c.942A>G	c.(940-942)acA>acG	p.T314T	RP11-566K11.7_ENST00000570217.1_RNA|MC1R_ENST00000555427.1_Silent_p.T314T|TUBB3_ENST00000554444.1_5'Flank|TUBB3_ENST00000556922.1_Silent_p.T314T|RP11-566K11.4_ENST00000554623.1_RNA	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	314					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		AGGTGCTGACATGCTCCTGGT	0.592									Melanoma, Familial Clustering of				G|||	1297	0.258986	0.4871	0.0836	5008	,	,		19553	0.2927		0.0924	False		,,,				2504	0.2117				p.T314T		Atlas-SNP	.											.	MC1R	20	.	0			c.A942G						PASS	.	G		1731,2511		347,1037,737	67.0	66.0	66.0		942	0.6	0.8	16	dbSNP_98	66	914,7554		55,804,3375	no	coding-synonymous	MC1R	NM_002386.3		402,1841,4112	GG,GA,AA		10.7936,40.8062,20.8104		314/318	89986608	2645,10065	2121	4234	6355	SO:0001819	synonymous_variant	4157	exon1	Familial Cancer Database		GCTGACATGCTCC		CCDS56011.1	16q24.3	2012-10-05			ENSG00000258839	ENSG00000258839		"""GPCR / Class A : Melanocortin receptors"""	6929	protein-coding gene	gene with protein product		155555				8458079	Standard	NM_002386		Approved	MSH-R		Q01726		ENST00000555147.1:c.942A>G	16.37:g.89986608A>G		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	227	120	0.528634	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Silent	SNP	ENST00000555147.1	37	CCDS56011.1																																																																																			A|0.821;G|0.179	0.179	strong		0.592	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
OR8H3	390152	hgsc.bcm.edu	37	11	55890320	55890320	+	Missense_Mutation	SNP	G	G	C	rs61743838	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55890320G>C	ENST00000313472.3	+	1	472	c.472G>C	c.(472-474)Gtc>Ctc	p.V158L		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	158						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					GGACTCCTTTGTCAATGTGGT	0.443													G|||	195	0.0389377	0.0121	0.0447	5008	,	,		21844	0.001		0.0944	False		,,,				2504	0.0532				p.V158L		Atlas-SNP	.											.	OR8H3	92	.	0			c.G472C						PASS	.	G	LEU/VAL	98,4304	78.3+/-116.7	0,98,2103	224.0	199.0	207.0		472	-3.2	0.0	11	dbSNP_129	207	692,7900	171.2+/-222.1	34,624,3638	yes	missense	OR8H3	NM_001005201.1	32	34,722,5741	CC,CG,GG		8.054,2.2263,6.0797	benign	158/313	55890320	790,12204	2201	4296	6497	SO:0001583	missense	390152	exon1			TCCTTTGTCAATG	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.472G>C	11.37:g.55890320G>C	ENSP00000323928:p.Val158Leu	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	316	132	0.417722	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	86	0.039377289377289376	4	0.008130081300813009	14	0.03867403314917127	0	0.0	68	0.08970976253298153	G	7.598	0.672168	0.14776	0.022263	0.08054	ENSG00000181761	ENST00000313472	T	0.35421	1.31	3.62	-3.17	0.05202	GPCR, rhodopsin-like superfamily (1);	1.117260	0.06780	N	0.785094	T	0.01029	0.0034	L	0.31157	0.91	0.09310	N	1	P	0.35307	0.494	B	0.41666	0.363	T	0.25606	-1.0127	10	0.49607	T	0.09	.	5.4437	0.16523	0.6729:0.0:0.1649:0.1622	rs61743838	158	Q8N146	OR8H3_HUMAN	L	158	ENSP00000323928:V158L	ENSP00000323928:V158L	V	+	1	0	OR8H3	55646896	0.000000	0.05858	0.000000	0.03702	0.240000	0.25518	-1.869000	0.01643	-0.461000	0.06993	0.173000	0.16961	GTC	G|0.948;C|0.052	0.052	strong		0.443	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
TAS2R30	259293	hgsc.bcm.edu	37	12	11286790	11286790	+	Silent	SNP	A	A	C	rs2600355	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11286790A>C	ENST00000539585.1	-	1	453	c.54T>G	c.(52-54)gtT>gtG	p.V18V	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	18					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						AATTTCCAATAACAAATATAA	0.338													a|||	1761	0.351637	0.357	0.4712	5008	,	,		20113	0.1944		0.5109	False		,,,				2504	0.2577				p.V18V		Atlas-SNP	.											.	TAS2R30	28	.	0			c.T54G						PASS	.						39.0	37.0	38.0					12																	11286790		1874	4131	6005	SO:0001819	synonymous_variant	259293	exon1			TCCAATAACAAAT	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19112	protein-coding gene	gene with protein product		613963	"""taste receptor, type 2, member 47"""	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.54T>G	12.37:g.11286790A>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	194	83	0.427835	NM_001097643	Q645X7	Silent	SNP	ENST00000539585.1	37	CCDS53750.1																																																																																			A|0.635;C|0.365	0.365	strong		0.338	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643	
EBF1	1879	hgsc.bcm.edu	37	5	158204425	158204425	+	Silent	SNP	A	A	G	rs1368298	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:158204425A>G	ENST00000313708.6	-	10	1314	c.1032T>C	c.(1030-1032)taT>taC	p.Y344Y	EBF1_ENST00000380654.4_Silent_p.Y313Y|EBF1_ENST00000517373.1_Silent_p.Y336Y|EBF1_ENST00000518836.1_5'UTR	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	344	IPT/TIG.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|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)	p.Y344Y(1)	HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCTTACCTGTATAAATGAATC	0.458			T	HMGA2	lipoma								G|||	2972	0.59345	0.854	0.6138	5008	,	,		19972	0.6151		0.4513	False		,,,				2504	0.3507				p.Y344Y		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	EBF1,NS,carcinoma,0,1	EBF1	110	1	1	Substitution - coding silent(1)	prostate(1)	c.T1032C						PASS	.	G		3494,912	350.3+/-310.7	1407,680,116	157.0	143.0	148.0		1032	1.9	1.0	5	dbSNP_88	148	3828,4772	610.7+/-395.7	870,2088,1342	no	coding-synonymous	EBF1	NM_024007.3		2277,2768,1458	GG,GA,AA		44.5116,20.699,43.7029		344/592	158204425	7322,5684	2203	4300	6503	SO:0001819	synonymous_variant	1879	exon10			ACCTGTATAAATG	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"""early B-cell factor"""	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1032T>C	5.37:g.158204425A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	214	213	0.995327	NM_024007	Q8IW11	Silent	SNP	ENST00000313708.6	37	CCDS4343.1																																																																																			A|0.408;G|0.592	0.592	strong		0.458	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007	
ZNF490	57474	hgsc.bcm.edu	37	19	12691497	12691497	+	Silent	SNP	G	G	A	rs140620156	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12691497G>A	ENST00000311437.6	-	5	1514	c.1392C>T	c.(1390-1392)caC>caT	p.H464H	ZNF490_ENST00000465656.1_5'Flank|CTD-2192J16.20_ENST00000593682.1_Missense_Mutation_p.T98M	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	464					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						GACTTCTTTCGTGCCTTCGAA	0.418													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		20275	0.0		0.003	False		,,,				2504	0.0				p.H464H		Atlas-SNP	.											.	ZNF490	42	.	0			c.C1392T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	129.0	128.0	128.0		1392	-1.5	0.0	19	dbSNP_134	128	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	ZNF490	NM_020714.2		0,40,6463	AA,AG,GG		0.407,0.1135,0.3076		464/530	12691497	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	57474	exon5			TCTTTCGTGCCTT	AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"""Zinc fingers, C2H2-type"", ""-"""	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.1392C>T	19.37:g.12691497G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	102	42	0.411765	NM_020714		Silent	SNP	ENST00000311437.6	37	CCDS12272.1																																																																																			G|0.997;A|0.003	0.003	strong		0.418	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714	
EVA1C	59271	hgsc.bcm.edu	37	21	33887131	33887131	+	Silent	SNP	G	G	A	rs1129157	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:33887131G>A	ENST00000300255.2	+	8	1430	c.957G>A	c.(955-957)ccG>ccA	p.P319P	EVA1C_ENST00000485488.1_3'UTR|EVA1C_ENST00000401402.3_Silent_p.P271P|EVA1C_ENST00000382699.3_Silent_p.P316P	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	319						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										CAGCCCACCCGGAGAGAGCTG	0.617													G|||	2458	0.490815	0.5976	0.5072	5008	,	,		17369	0.631		0.2922	False		,,,				2504	0.3947				p.P319P		Atlas-SNP	.											.	.	.	.	0			c.G957A						PASS	.	G		2457,1949	584.9+/-386.1	698,1061,444	38.0	39.0	39.0		957	-11.2	0.2	21	dbSNP_105	39	2363,6237	365.7+/-334.0	328,1707,2265	no	coding-synonymous	C21orf63	NM_058187.3		1026,2768,2709	AA,AG,GG		27.4767,44.2351,37.0598		319/442	33887131	4820,8186	2203	4300	6503	SO:0001819	synonymous_variant	59271	exon8			CCACCCGGAGAGA	AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 64"", ""chromosome 21 open reading frame 63"", ""family with sequence similarity 176, member C"""	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.957G>A	21.37:g.33887131G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_058187	A6ND58|Q8IXZ0	Silent	SNP	ENST00000300255.2	37	CCDS13614.1																																																																																			G|0.575;A|0.425	0.425	strong		0.617	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187	
CLASP2	23122	hgsc.bcm.edu	37	3	33543195	33543195	+	Silent	SNP	C	C	T	rs111990025	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33543195C>T	ENST00000468888.2	-	38	4453	c.4407G>A	c.(4405-4407)gcG>gcA	p.A1469A	CLASP2_ENST00000307312.7_Silent_p.A950A|CLASP2_ENST00000480013.1_Silent_p.A1248A|CLASP2_ENST00000359576.5_Silent_p.A1460A|CLASP2_ENST00000539981.1_3'UTR|CLASP2_ENST00000461133.3_Silent_p.A1228A|CLASP2_ENST00000399362.4_Silent_p.A1468A			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1249					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						CACCAATTACCGCATGAACAG	0.443													C|||	57	0.0113818	0.0008	0.0072	5008	,	,		19135	0.001		0.0219	False		,,,				2504	0.0286				p.A1470A		Atlas-SNP	.											.	CLASP2	138	.	0			c.G4410A						PASS	.	C	,	24,3892		0,24,1934	141.0	135.0	137.0		3747,4410	-6.2	0.4	3	dbSNP_132	137	206,8106		3,200,3953	no	coding-synonymous,coding-synonymous	CLASP2	NM_001207044.1,NM_015097.2	,	3,224,5887	TT,TC,CC		2.4783,0.6129,1.8809	,	1249/1295,1470/1516	33543195	230,11998	1958	4156	6114	SO:0001819	synonymous_variant	23122	exon38			AATTACCGCATGA	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.4407G>A	3.37:g.33543195C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37		22	0.010073260073260074	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	20	0.026385224274406333	C	6.469	0.454728	0.12283	0.006129	0.024783	ENSG00000163539	ENST00000487553	.	.	.	5.7	-6.15	0.02105	.	.	.	.	.	T	0.29126	0.0724	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52953	-0.8506	4	.	.	.	-6.566	11.4283	0.50025	0.085:0.3006:0.0:0.6144	.	.	.	.	S	175	.	.	G	-	1	0	CLASP2	33518199	0.000000	0.05858	0.395000	0.26283	0.793000	0.44817	-2.319000	0.01120	-1.720000	0.01380	-2.945000	0.00085	GGT	C|0.987;T|0.013	0.013	strong		0.443	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	
SLC6A18	348932	hgsc.bcm.edu	37	5	1244425	1244425	+	Missense_Mutation	SNP	C	C	T	rs4073918	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1244425C>T	ENST00000324642.3	+	10	1556	c.1433C>T	c.(1432-1434)cCg>cTg	p.P478L	SLC6A18_ENST00000296821.4_Missense_Mutation_p.P376L	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	478			P -> L (in dbSNP:rs4073918). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:19033659}.		amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			GCCGCTTCCCCGAACCTGCTC	0.582													T|||	3386	0.676118	0.9009	0.696	5008	,	,		14095	0.2728		0.7744	False		,,,				2504	0.6728				p.P478L		Atlas-SNP	.											.	SLC6A18	84	.	0			c.C1433T						PASS	.	T	LEU/PRO	3803,603	261.9+/-264.6	1636,531,36	155.0	155.0	155.0		1433	4.9	0.0	5	dbSNP_108	155	6571,2029	352.4+/-328.6	2502,1567,231	yes	missense	SLC6A18	NM_182632.2	98	4138,2098,267	TT,TC,CC		23.593,13.6859,20.2368	benign	478/629	1244425	10374,2632	2203	4300	6503	SO:0001583	missense	348932	exon10			CTTCCCCGAACCT	AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"""Solute carriers"""	26441	protein-coding gene	gene with protein product		610300	"""solute carrier family 6 (neurotransmitter transporter), member 18"", ""solute carrier family 6, member 18"""			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.1433C>T	5.37:g.1244425C>T	ENSP00000323549:p.Pro478Leu	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	187	85	0.454545	NM_182632		Missense_Mutation	SNP	ENST00000324642.3	37	CCDS3860.1	1453	0.6652930402930403	446	0.9065040650406504	263	0.7265193370165746	161	0.28146853146853146	583	0.7691292875989446	T	0.647	-0.810981	0.02798	0.863141	0.76407	ENSG00000164363	ENST00000324642;ENST00000296821	T;T	0.72282	-0.64;-0.64	4.87	4.87	0.63330	.	0.313451	0.26859	N	0.022133	T	0.00012	0.0000	N	0.00165	-1.945	0.35260	P	0.22053500000000004	B	0.06786	0.001	B	0.04013	0.001	T	0.39961	-0.9588	9	0.11182	T	0.66	.	8.4287	0.32744	0.0:0.0922:0.0:0.9078	rs4073918;rs52796423;rs58973522;rs4073918	478	Q96N87	S6A18_HUMAN	L	478;376	ENSP00000323549:P478L;ENSP00000296821:P376L	ENSP00000296821:P376L	P	+	2	0	SLC6A18	1297425	0.980000	0.34600	0.005000	0.12908	0.030000	0.12068	4.148000	0.58085	0.722000	0.32252	-0.361000	0.07541	CCG	C|0.254;T|0.746	0.746	strong		0.582	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632	
OR52N1	79473	hgsc.bcm.edu	37	11	5809548	5809548	+	Missense_Mutation	SNP	G	G	A	rs7948009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5809548G>A	ENST00000317078.1	-	1	498	c.499C>T	c.(499-501)Cgc>Tgc	p.R167C	TRIM5_ENST00000380027.1_Intron	NM_001001913.1	NP_001001913.1	Q8NH53	O52N1_HUMAN	olfactory receptor, family 52, subfamily N, member 1	167			R -> C (in dbSNP:rs7948009).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(15)|prostate(2)|skin(3)	31		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		TATGGAAGGCGCTTGGTGAGG	0.478													G|||	2763	0.551717	0.2458	0.5908	5008	,	,		22784	0.7054		0.6382	False		,,,				2504	0.6902				p.R167C		Atlas-SNP	.											.	OR52N1	70	.	0			c.C499T						PASS	.	G	CYS/ARG	1436,2966	466.6+/-354.6	240,956,1005	135.0	115.0	122.0		499	1.4	1.0	11	dbSNP_116	122	5686,2906	671.1+/-402.8	1876,1934,486	yes	missense	OR52N1	NM_001001913.1	180	2116,2890,1491	AA,AG,GG		33.8222,32.6215,45.1901	benign	167/321	5809548	7122,5872	2201	4296	6497	SO:0001583	missense	79473	exon1			GAAGGCGCTTGGT	AB065538	CCDS31398.1	11p15.4	2012-08-09			ENSG00000181001	ENSG00000181001		"""GPCR / Class A : Olfactory receptors"""	14853	protein-coding gene	gene with protein product							Standard	NM_001001913		Approved		uc010qzo.2	Q8NH53	OTTHUMG00000168800	ENST00000317078.1:c.499C>T	11.37:g.5809548G>A	ENSP00000322823:p.Arg167Cys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	165	74	0.448485	NM_001001913	Q6IFF6	Missense_Mutation	SNP	ENST00000317078.1	37	CCDS31398.1	1248	0.5714285714285714	113	0.22967479674796748	230	0.6353591160220995	414	0.7237762237762237	491	0.6477572559366754	G	7.954	0.745558	0.15710	0.326215	0.661778	ENSG00000181001	ENST00000317078	T	0.00188	8.59	4.59	1.38	0.22167	GPCR, rhodopsin-like superfamily (1);	0.134990	0.31177	N	0.008107	T	0.00012	0.0000	M	0.75085	2.285	0.34260	P	0.320248	B	0.23128	0.08	B	0.27715	0.082	T	0.43829	-0.9367	9	0.72032	D	0.01	.	3.8534	0.08965	0.0884:0.1355:0.5257:0.2504	rs7948009;rs52796900;rs61678687;rs7948009	167	Q8NH53	O52N1_HUMAN	C	167	ENSP00000322823:R167C	ENSP00000322823:R167C	R	-	1	0	OR52N1	5766124	0.000000	0.05858	0.979000	0.43373	0.182000	0.23217	-2.131000	0.01311	0.618000	0.30179	0.609000	0.83330	CGC	G|0.440;A|0.560	0.560	strong		0.478	OR52N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401142.1	NM_001001913	
ZNF74	7625	hgsc.bcm.edu	37	22	20761063	20761063	+	Silent	SNP	G	G	A	rs2228236	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:20761063G>A	ENST00000400451.2	+	5	2254	c.1740G>A	c.(1738-1740)gaG>gaA	p.E580E	ZNF74_ENST00000357502.5_3'UTR|ZNF74_ENST00000405993.1_Silent_p.E548E|ZNF74_ENST00000403682.3_3'UTR|ZNF74_ENST00000356671.5_Silent_p.E580E	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	580					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			TGCACAGCGAGGGGAAGCCCT	0.572													G|||	547	0.109225	0.1899	0.1066	5008	,	,		20956	0.002		0.164	False		,,,				2504	0.0562				p.E580E		Atlas-SNP	.											.	ZNF74	54	.	0			c.G1740A						PASS	.	G		751,3543		63,625,1459	49.0	55.0	53.0		1740	-8.5	0.0	22	dbSNP_98	53	1315,7225		102,1111,3057	no	coding-synonymous	ZNF74	NM_003426.2		165,1736,4516	AA,AG,GG		15.3981,17.4895,16.0979		580/645	20761063	2066,10768	2147	4270	6417	SO:0001819	synonymous_variant	7625	exon5			CAGCGAGGGGAAG	X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"""Zinc fingers, C2H2-type"", ""-"""	13144	protein-coding gene	gene with protein product		194548	"""zinc finger protein 74 (Cos52)"""			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.1740G>A	22.37:g.20761063G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_003426	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Silent	SNP	ENST00000400451.2	37	CCDS42982.1																																																																																			G|0.859;A|0.141	0.141	strong		0.572	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426	
KIAA1683	80726	hgsc.bcm.edu	37	19	18377274	18377274	+	Missense_Mutation	SNP	A	A	G	rs3746186	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18377274A>G	ENST00000600328.3	-	3	1269	c.1076T>C	c.(1075-1077)aTg>aCg	p.M359T	KIAA1683_ENST00000392413.4_Missense_Mutation_p.M359T|KIAA1683_ENST00000600359.3_Missense_Mutation_p.M313T			Q9H0B3	K1683_HUMAN	KIAA1683	359	Thr-rich.		M -> T (in dbSNP:rs3746186). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GGTGGTGGTCATCGTGGACGC	0.547													a|||	2723	0.54373	0.6929	0.5908	5008	,	,		16555	0.5496		0.4294	False		,,,				2504	0.4202				p.M359T		Atlas-SNP	.											.	KIAA1683	190	.	0			c.T1076C						PASS	.	A	THR/MET,THR/MET,THR/MET	2963,1443	682.0+/-404.1	1009,945,249	98.0	89.0	92.0		1076,938,1076	-2.6	0.0	19	dbSNP_107	92	3665,4935	526.1+/-380.9	788,2089,1423	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	81,81,81	1797,3034,1672	GG,GA,AA		42.6163,32.7508,49.0389	benign,benign,benign	359/1368,313/1135,359/1181	18377274	6628,6378	2203	4300	6503	SO:0001583	missense	80726	exon3			GTGGTCATCGTGG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1076T>C	19.37:g.18377274A>G	ENSP00000470780:p.Met359Thr	Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	274	139	0.507299	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	1158	0.5302197802197802	340	0.6910569105691057	193	0.5331491712707183	298	0.5209790209790209	327	0.4313984168865435	a	3.325	-0.137994	0.06711	0.672492	0.426163	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000358422	T;T;T	0.03889	3.86;3.84;3.77	4.1	-2.6	0.06190	.	1.688340	0.03444	N	0.209661	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26292	-1.0107	9	0.23891	T	0.37	.	4.4187	0.11470	0.6279:0.0:0.2104:0.1616	rs3746186;rs58006576;rs3746186	359;359	E9PDE0;Q9H0B3	.;K1683_HUMAN	T	359;359;313;358	ENSP00000376213:M359T;ENSP00000352774:M359T;ENSP00000404501:M313T	ENSP00000351198:M358T	M	-	2	0	KIAA1683	18238274	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.495000	0.06443	-0.751000	0.04734	-3.011000	0.00075	ATG	A|0.485;G|0.515	0.515	strong		0.547	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
CACHD1	57685	hgsc.bcm.edu	37	1	65016302	65016302	+	Missense_Mutation	SNP	C	C	G	rs61731118	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:65016302C>G	ENST00000371073.2	+	2	224	c.224C>G	c.(223-225)aCt>aGt	p.T75S	CACHD1_ENST00000290039.5_Missense_Mutation_p.T24S|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	75					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						TTTGTTTACACTGAGAAAATC	0.358													C|||	23	0.00459265	0.0038	0.0043	5008	,	,		17088	0.0		0.0149	False		,,,				2504	0.0				p.T24S		Atlas-SNP	.											.	CACHD1	125	.	0			c.C71G						PASS	.	C	SER/THR	20,3722		0,20,1851	90.0	84.0	86.0		71	6.0	1.0	1	dbSNP_129	86	89,8093		2,85,4004	yes	missense	CACHD1	NM_020925.2	58	2,105,5855	GG,GC,CC		1.0878,0.5345,0.9141	possibly-damaging	24/1224	65016302	109,11815	1871	4091	5962	SO:0001583	missense	57685	exon2			TTTACACTGAGAA	AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.224C>G	1.37:g.65016302C>G	ENSP00000360113:p.Thr75Ser	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	329	157	0.477204	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		15	0.006868131868131868	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	14.52	2.558856	0.45590	0.005345	0.010878	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.22539	1.95;1.96	6.02	6.02	0.97574	.	0.049317	0.85682	D	0.000000	T	0.13329	0.0323	N	0.19112	0.55	0.58432	D	0.999995	P	0.40332	0.713	P	0.51742	0.678	T	0.01800	-1.1271	10	0.06891	T	0.86	-24.6272	19.3726	0.94495	0.0:1.0:0.0:0.0	rs61731118	75	Q5VU97	CAHD1_HUMAN	S	75;24	ENSP00000360113:T75S;ENSP00000290039:T24S	ENSP00000290039:T24S	T	+	2	0	CACHD1	64788890	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.373000	0.66162	2.878000	0.98634	0.650000	0.86243	ACT	C|0.991;G|0.009	0.009	strong		0.358	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
KIAA1683	80726	hgsc.bcm.edu	37	19	18376407	18376407	+	Missense_Mutation	SNP	T	T	A	rs8110972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18376407T>A	ENST00000600328.3	-	3	2136	c.1943A>T	c.(1942-1944)tAt>tTt	p.Y648F	KIAA1683_ENST00000392413.4_Missense_Mutation_p.Y648F|KIAA1683_ENST00000600359.3_Missense_Mutation_p.Y602F			Q9H0B3	K1683_HUMAN	KIAA1683	648			Y -> F (in dbSNP:rs8110972). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TACAGGCACATACACGTGAGG	0.572													T|||	2725	0.544129	0.6929	0.5908	5008	,	,		18450	0.5516		0.4294	False		,,,				2504	0.4202				p.Y648F		Atlas-SNP	.											.	KIAA1683	190	.	0			c.A1943T						PASS	.	T	PHE/TYR,PHE/TYR,PHE/TYR	2960,1446	681.7+/-404.0	1008,944,251	72.0	65.0	67.0		1943,1805,1943	-8.1	0.0	19	dbSNP_116	67	3662,4938	525.3+/-380.7	783,2096,1421	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	22,22,22	1791,3040,1672	AA,AT,TT		42.5814,32.8189,49.085	probably-damaging,probably-damaging,probably-damaging	648/1368,602/1135,648/1181	18376407	6622,6384	2203	4300	6503	SO:0001583	missense	80726	exon3			GGCACATACACGT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1943A>T	19.37:g.18376407T>A	ENSP00000470780:p.Tyr648Phe	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	135	62	0.459259	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	1158	0.5302197802197802	340	0.6910569105691057	193	0.5331491712707183	298	0.5209790209790209	327	0.4313984168865435	T	7.458	0.644115	0.14451	0.671811	0.425814	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634	T;T;T	0.05025	3.62;3.58;3.51	4.36	-8.1	0.01086	.	1.477180	0.04788	N	0.431124	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.003	T	0.40776	-0.9545	9	0.12103	T	0.63	0.4876	0.4597	0.00514	0.2348:0.2779:0.2375:0.2498	rs8110972;rs17711424;rs8110972	648;648	E9PDE0;Q9H0B3	.;K1683_HUMAN	F	648;648;602	ENSP00000376213:Y648F;ENSP00000352774:Y648F;ENSP00000404501:Y602F	ENSP00000352774:Y648F	Y	-	2	0	KIAA1683	18237407	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.546000	0.06062	-1.462000	0.01907	-1.402000	0.01139	TAT	T|0.486;A|0.514	0.514	strong		0.572	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
PREB	10113	hgsc.bcm.edu	37	2	27355991	27355991	+	Silent	SNP	G	G	T	rs2289358	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:27355991G>T	ENST00000260643.2	-	3	793	c.540C>A	c.(538-540)gtC>gtA	p.V180V	PREB_ENST00000416802.1_Intron|PREB_ENST00000406567.3_Silent_p.V180V	NM_013388.4	NP_037520.1	Q9HCU5	PREB_HUMAN	prolactin regulatory element binding	180					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACACCTTCCAGACACGGACGT	0.493													G|||	965	0.192692	0.2708	0.1772	5008	,	,		22022	0.1736		0.162	False		,,,				2504	0.1493				p.V180V		Atlas-SNP	.											.	PREB	37	.	0			c.C540A						PASS	.	G		1012,3394	377.3+/-322.4	120,772,1311	160.0	170.0	166.0		540	3.4	1.0	2	dbSNP_100	166	1332,7268	261.2+/-283.7	108,1116,3076	no	coding-synonymous	PREB	NM_013388.4		228,1888,4387	TT,TG,GG		15.4884,22.9687,18.0225		180/418	27355991	2344,10662	2203	4300	6503	SO:0001819	synonymous_variant	10113	exon3			CTTCCAGACACGG		CCDS1738.1	2p23	2013-01-10			ENSG00000138073	ENSG00000138073		"""WD repeat domain containing"""	9356	protein-coding gene	gene with protein product		606395				10194769, 12735795	Standard	NM_013388		Approved	SEC12	uc002rix.1	Q9HCU5	OTTHUMG00000097076	ENST00000260643.2:c.540C>A	2.37:g.27355991G>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	105	56	0.533333	NM_013388	Q53SZ8|Q9UH94	Silent	SNP	ENST00000260643.2	37	CCDS1738.1																																																																																			G|0.800;T|0.200	0.200	strong		0.493	PREB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214195.1	NM_013388	
MORC1	27136	hgsc.bcm.edu	37	3	108703587	108703587	+	Missense_Mutation	SNP	C	C	T	rs2290057	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:108703587C>T	ENST00000483760.1	-	22	2280	c.2237G>A	c.(2236-2238)aGc>aAc	p.S746N	MORC1_ENST00000232603.5_Missense_Mutation_p.S767N					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						TAATGAAGAGCTTCTTTTCAT	0.343													C|||	1369	0.273363	0.0113	0.2968	5008	,	,		18376	0.6399		0.1869	False		,,,				2504	0.3221				p.S767N		Atlas-SNP	.											.	MORC1	211	.	0			c.G2300A						PASS	.	C	ASN/SER	179,4227	115.4+/-153.4	4,171,2028	107.0	96.0	100.0		2300	-0.1	0.1	3	dbSNP_100	100	1649,6949	303.4+/-306.4	172,1305,2822	yes	missense	MORC1	NM_014429.3	46	176,1476,4850	TT,TC,CC		19.1789,4.0626,14.0572	benign	767/985	108703587	1828,11176	2203	4299	6502	SO:0001583	missense	27136	exon23			GAAGAGCTTCTTT	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2237G>A	3.37:g.108703587C>T	ENSP00000417282:p.Ser746Asn	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	135	76	0.562963	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	37		618	0.28296703296703296	9	0.018292682926829267	89	0.24585635359116023	385	0.6730769230769231	135	0.17810026385224276	C	0	-2.608932	0.00121	0.040626	0.191789	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.04603	3.61;3.59	5.49	-0.0644	0.13772	.	0.342268	0.25425	N	0.030765	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28586	-1.0039	9	0.02654	T	1	-3.8754	0.8362	0.01140	0.1531:0.2097:0.1593:0.478	rs2290057;rs52821386;rs57469576;rs2290057	746;767	E7ERX1;Q86VD1	.;MORC1_HUMAN	N	767;746	ENSP00000232603:S767N;ENSP00000417282:S746N	ENSP00000232603:S767N	S	-	2	0	MORC1	110186277	0.062000	0.20869	0.094000	0.20943	0.040000	0.13550	-0.439000	0.06897	-0.157000	0.11059	-1.251000	0.01509	AGC	C|0.801;T|0.199	0.199	strong		0.343	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
TUBGCP2	10844	hgsc.bcm.edu	37	10	135098621	135098621	+	Silent	SNP	G	G	A	rs35736540	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135098621G>A	ENST00000252936.3	-	12	2031	c.1992C>T	c.(1990-1992)acC>acT	p.T664T	TUBGCP2_ENST00000368563.2_Silent_p.T664T|TUBGCP2_ENST00000543663.1_Silent_p.T692T|TUBGCP2_ENST00000368562.1_Silent_p.T257T|TUBGCP2_ENST00000417178.2_Silent_p.T534T			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	664					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		GCTGCTTGGCGGTTTTGTTGC	0.617													G|||	64	0.0127796	0.0045	0.0231	5008	,	,		17397	0.0		0.0229	False		,,,				2504	0.0194				p.T692T		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.C2076T						PASS	.	G		27,4379	35.2+/-66.4	0,27,2176	111.0	82.0	92.0		1992	-10.9	0.0	10	dbSNP_126	92	153,8447	73.8+/-136.5	2,149,4149	no	coding-synonymous	TUBGCP2	NM_006659.2		2,176,6325	AA,AG,GG		1.7791,0.6128,1.384		664/903	135098621	180,12826	2203	4300	6503	SO:0001819	synonymous_variant	10844	exon14			CTTGGCGGTTTTG	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.1992C>T	10.37:g.135098621G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	140	60	0.428571	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	37	CCDS7676.1																																																																																			G|0.986;A|0.014	0.014	strong		0.617	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1		
MARCH1	55016	hgsc.bcm.edu	37	4	164466824	164466824	+	Silent	SNP	C	C	T	rs13130399	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:164466824C>T	ENST00000503008.1	-	7	1471	c.495G>A	c.(493-495)gcG>gcA	p.A165A	MARCH1_ENST00000274056.7_Silent_p.A165A|MARCH1_ENST00000514618.1_Silent_p.A421A|MARCH1_ENST00000339875.5_Silent_p.A148A	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase	165					antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A148A(2)		endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				CACAGGTGATCGCGATTACGT	0.428													C|||	1933	0.385982	0.2776	0.6037	5008	,	,		19890	0.3482		0.4583	False		,,,				2504	0.3425				p.A165A		Atlas-SNP	.											MARCH1,NS,carcinoma,0,2	MARCH1	83	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.G495A						PASS	.	C	,	1242,3164	428.5+/-341.9	173,896,1134	301.0	226.0	252.0		495,444	0.3	1.0	4	dbSNP_121	252	4042,4558	557.0+/-387.0	965,2112,1223	no	coding-synonymous,coding-synonymous	MARCH1	NM_001166373.1,NM_017923.3	,	1138,3008,2357	TT,TC,CC		47.0,28.1888,40.6274	,	165/290,148/273	164466824	5284,7722	2203	4300	6503	SO:0001819	synonymous_variant	55016	exon7			GGTGATCGCGATT	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	26077	protein-coding gene	gene with protein product		613331	"""membrane-associated ring finger (C3HC4) 1"""			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.495G>A	4.37:g.164466824C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	248	119	0.479839	NM_001166373	D3DP29|Q9NWR0	Silent	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																			C|0.612;T|0.388	0.388	strong		0.428	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923	
KIAA1614	57710	hgsc.bcm.edu	37	1	180905448	180905448	+	Missense_Mutation	SNP	G	G	T	rs3795504	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:180905448G>T	ENST00000367588.4	+	5	2458	c.2403G>T	c.(2401-2403)ttG>ttT	p.L801F	KIAA1614_ENST00000367587.1_Missense_Mutation_p.L422F	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	801			L -> F (in dbSNP:rs3795504). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039}.							NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CAGCTTCCTTGTGTCCTGAAG	0.612													T|||	2021	0.403554	0.3548	0.428	5008	,	,		19313	0.2748		0.4533	False		,,,				2504	0.5337				p.L801F		Atlas-SNP	.											.	KIAA1614	75	.	0			c.G2403T						PASS	.	T	PHE/LEU	1469,2525		285,899,813	67.0	71.0	69.0		2403	2.4	0.0	1	dbSNP_107	69	3670,4648		807,2056,1296	yes	missense	KIAA1614	NM_020950.1	22	1092,2955,2109	TT,TG,GG		44.1212,36.7802,41.7398	benign	801/1191	180905448	5139,7173	1997	4159	6156	SO:0001583	missense	57710	exon5			TTCCTTGTGTCCT	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2403G>T	1.37:g.180905448G>T	ENSP00000356560:p.Leu801Phe	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	130	65	0.5	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	37	CCDS41442.1	842	0.38553113553113555	181	0.3678861788617886	175	0.48342541436464087	146	0.25524475524475526	340	0.44854881266490765	T	2.589	-0.295649	0.05532	0.367802	0.441212	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.42513	0.97;0.97	4.3	2.38	0.29361	.	0.948451	0.08769	N	0.896507	T	0.00012	0.0000	N	0.11560	0.145	0.20821	P	0.999844	B	0.02656	0.0	B	0.04013	0.001	T	0.48468	-0.9033	9	0.14252	T	0.57	-0.1445	4.419	0.11470	0.0:0.5393:0.1748:0.2859	rs3795504;rs17302221;rs59561360;rs3795504	801	Q5VZ46	K1614_HUMAN	F	801;422	ENSP00000356560:L801F;ENSP00000356559:L422F	ENSP00000356559:L422F	L	+	3	2	KIAA1614	179172071	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.066000	0.14489	0.277000	0.22141	-1.202000	0.01658	TTG	G|0.614;T|0.386	0.386	strong		0.612	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
MTUS1	57509	hgsc.bcm.edu	37	8	17612694	17612694	+	Missense_Mutation	SNP	C	C	G	rs73206291	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:17612694C>G	ENST00000262102.6	-	2	847	c.623G>C	c.(622-624)tGg>tCg	p.W208S	MTUS1_ENST00000519263.1_Missense_Mutation_p.W208S|MTUS1_ENST00000381862.3_Missense_Mutation_p.W208S|MTUS1_ENST00000381869.3_Missense_Mutation_p.W208S	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	208					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		GGAAGATGTCCAAGTGGAATA	0.448													C|||	140	0.0279553	0.0083	0.0533	5008	,	,		22393	0.0		0.0865	False		,,,				2504	0.0051				p.W208S		Atlas-SNP	.											.	MTUS1	144	.	0			c.G623C						PASS	.	C	SER/TRP,SER/TRP	60,3784		0,60,1862	159.0	138.0	145.0		623,623	-3.6	0.0	8	dbSNP_130	145	714,7542		31,652,3445	yes	missense,missense	MTUS1	NM_001001924.2,NM_001001925.2	177,177	31,712,5307	GG,GC,CC		8.6483,1.5609,6.3967	benign,benign	208/1271,208/1217	17612694	774,11326	1922	4128	6050	SO:0001583	missense	57509	exon2			GATGTCCAAGTGG	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.623G>C	8.37:g.17612694C>G	ENSP00000262102:p.Trp208Ser	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	125	70	0.56	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	101	0.04624542124542125	10	0.02032520325203252	21	0.058011049723756904	0	0.0	70	0.09234828496042216	C	11.00	1.509672	0.27036	0.015609	0.086483	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.18016	3.21;3.23;3.21;2.24	4.32	-3.56	0.04626	.	2.590450	0.01463	N	0.015961	T	0.00328	0.0010	N	0.14661	0.345	0.09310	N	1	B;B;B	0.25169	0.119;0.068;0.068	B;B;B	0.26416	0.069;0.035;0.035	T	0.18745	-1.0327	9	.	.	.	14.9121	3.2553	0.06830	0.3723:0.4085:0.112:0.1073	.	208;208;208	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	S	208	ENSP00000371293:W208S;ENSP00000262102:W208S;ENSP00000430167:W208S;ENSP00000371286:W208S	.	W	-	2	0	MTUS1	17656974	0.000000	0.05858	0.000000	0.03702	0.694000	0.40290	-0.681000	0.05191	-0.684000	0.05183	0.563000	0.77884	TGG	C|0.943;G|0.057	0.057	strong		0.448	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
EIF5B	9669	hgsc.bcm.edu	37	2	99995517	99995517	+	Silent	SNP	C	C	T	rs11896520	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:99995517C>T	ENST00000289371.6	+	11	2080	c.1878C>T	c.(1876-1878)acC>acT	p.T626T		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	626					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATGTAAACACCGAAAAGCTAA	0.299													C|||	758	0.151358	0.09	0.3012	5008	,	,		14631	0.0149		0.2753	False		,,,				2504	0.1411				p.T626T	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											EIF5B,caecum,carcinoma,0,1	EIF5B	95	1	0			c.C1878T						PASS	.	C		362,3280		12,338,1471	75.0	66.0	69.0		1878	-3.9	1.0	2	dbSNP_120	69	2231,5933		284,1663,2135	no	coding-synonymous	EIF5B	NM_015904.3		296,2001,3606	TT,TC,CC		27.3273,9.9396,21.9634		626/1221	99995517	2593,9213	1821	4082	5903	SO:0001819	synonymous_variant	9669	exon11			AAACACCGAAAAG	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"""translation initiation factor IF2"""	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.1878C>T	2.37:g.99995517C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	37	CCDS42721.1																																																																																			C|0.813;T|0.187	0.187	strong		0.299	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904	
OR12D2	26529	hgsc.bcm.edu	37	6	29364838	29364838	+	Missense_Mutation	SNP	C	C	G	rs2073152	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29364838C>G	ENST00000383555.2	+	1	423	c.362C>G	c.(361-363)tCt>tGt	p.S121C	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	121			S -> C (in dbSNP:rs2073152).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						TTTGACCTCTCTGTGGCTATC	0.498													C|||	873	0.174321	0.1044	0.1455	5008	,	,		21158	0.2381		0.3052	False		,,,				2504	0.089				p.S121C		Atlas-SNP	.											.	OR12D2	42	.	0			c.C362G						PASS	.	C	CYS/SER	400,2622		27,346,1138	95.0	95.0	95.0		362	1.4	1.0	6	dbSNP_96	95	1588,3830		251,1086,1372	no	missense	OR12D2	NM_013936.3	112	278,1432,2510	GG,GC,CC		29.3097,13.2363,23.5545	benign	121/308	29364838	1988,6452	1511	2709	4220	SO:0001583	missense	26529	exon1			ACCTCTCTGTGGC		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.362C>G	6.37:g.29364838C>G	ENSP00000373047:p.Ser121Cys	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	289	119	0.411765	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	500	0.22893772893772893	62	0.12601626016260162	56	0.15469613259668508	146	0.25524475524475526	236	0.3113456464379947	C	3.829	-0.036169	0.07497	0.132363	0.293097	ENSG00000168787	ENST00000383555	T	0.01369	4.97	3.94	1.42	0.22433	GPCR, rhodopsin-like superfamily (1);	0.312384	0.27807	N	0.017778	T	0.00210	0.0006	N	0.01257	-0.925	0.48901	P	2.7800000000000047E-4	B	0.24186	0.099	B	0.14578	0.011	T	0.47249	-0.9132	9	0.72032	D	0.01	.	4.3245	0.11034	0.4926:0.0982:0.0:0.4092	rs2073152;rs52828595;rs57122758;rs2073152	121	P58182	O12D2_HUMAN	C	121	ENSP00000373047:S121C	ENSP00000373047:S121C	S	+	2	0	OR12D2	29472817	0.118000	0.22208	0.954000	0.39281	0.013000	0.08279	0.184000	0.16939	0.093000	0.17368	-1.328000	0.01277	TCT	C|0.763;G|0.237	0.237	strong		0.498	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
SLC5A10	125206	hgsc.bcm.edu	37	17	18880268	18880268	+	Silent	SNP	C	C	A	rs2472715	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18880268C>A	ENST00000395645.3	+	9	966	c.948C>A	c.(946-948)atC>atA	p.I316I	SLC5A10_ENST00000395643.2_Silent_p.I289I|SLC5A10_ENST00000395647.2_Silent_p.I316I|FAM83G_ENST00000345041.4_Intron|FAM83G_ENST00000585154.2_Intron|SLC5A10_ENST00000395642.1_Silent_p.I233I|SLC5A10_ENST00000317977.6_Silent_p.I233I|SLC5A10_ENST00000417251.2_Silent_p.I316I|FAM83G_ENST00000388995.6_Intron	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	316					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						GCCTGATCATCATGCCGGGCA	0.637													C|||	1346	0.26877	0.1725	0.2781	5008	,	,		20325	0.3671		0.3837	False		,,,				2504	0.1728				p.I316I		Atlas-SNP	.											.	SLC5A10	55	.	0			c.C948A						PASS	.	C	,,	884,3522	343.1+/-307.5	95,694,1414	111.0	90.0	97.0		,948,948	2.9	1.0	17	dbSNP_100	97	3246,5354	488.4+/-372.4	621,2004,1675	no	intron,coding-synonymous,coding-synonymous	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	,,	716,2698,3089	AA,AC,CC		37.7442,20.0635,31.7546	,,	,316/597,316/613	18880268	4130,8876	2203	4300	6503	SO:0001819	synonymous_variant	125206	exon9			GATCATCATGCCG		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"""Solute carriers"""	23155	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 10"""				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.948C>A	17.37:g.18880268C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_001042450	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Silent	SNP	ENST00000395645.3	37	CCDS42275.1																																																																																			C|0.687;A|0.313	0.313	strong		0.637	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351	
SLFN5	162394	hgsc.bcm.edu	37	17	33586111	33586111	+	Silent	SNP	G	G	A	rs141928271	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:33586111G>A	ENST00000299977.4	+	2	550	c.402G>A	c.(400-402)ctG>ctA	p.L134L	SLFN5_ENST00000542451.1_Silent_p.L134L|SLFN5_ENST00000592325.1_Silent_p.L134L	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	134					cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		AGGAAGCTCTGGCATTCCTCA	0.458													G|||	12	0.00239617	0.0008	0.0	5008	,	,		21328	0.0		0.0089	False		,,,				2504	0.002				p.L134L		Atlas-SNP	.											.	SLFN5	92	.	0			c.G402A						PASS	.	G		8,4398	15.5+/-35.6	0,8,2195	115.0	113.0	114.0		402	2.7	0.0	17	dbSNP_134	114	68,8532	41.2+/-98.3	0,68,4232	no	coding-synonymous	SLFN5	NM_144975.3		0,76,6427	AA,AG,GG		0.7907,0.1816,0.5843		134/892	33586111	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	162394	exon2			AGCTCTGGCATTC	BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.402G>A	17.37:g.33586111G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	198	96	0.484848	NM_144975	Q08AF2|Q8WU54|Q96A82	Silent	SNP	ENST00000299977.4	37	CCDS32619.1																																																																																			G|0.994;A|0.006	0.006	strong		0.458	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975	
POLQ	10721	hgsc.bcm.edu	37	3	121208176	121208176	+	Missense_Mutation	SNP	T	T	C	rs3218651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121208176T>C	ENST00000264233.5	-	16	3730	c.3602A>G	c.(3601-3603)cAt>cGt	p.H1201R		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1201					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TGTCTGTTCATGAGATTGCTT	0.343								DNA polymerases (catalytic subunits)					T|||	1451	0.289736	0.1203	0.2954	5008	,	,		20581	0.5496		0.1511	False		,,,				2504	0.3896				p.H1201R	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A3602G						PASS	.	T	ARG/HIS	462,3944	218.7+/-236.7	27,408,1768	203.0	208.0	206.0		3602	4.2	0.0	3	dbSNP_106	206	1261,7339	251.4+/-277.9	106,1049,3145	yes	missense	POLQ	NM_199420.3	29	133,1457,4913	CC,CT,TT		14.6628,10.4857,13.2477	benign	1201/2591	121208176	1723,11283	2203	4300	6503	SO:0001583	missense	10721	exon16			TGTTCATGAGATT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.3602A>G	3.37:g.121208176T>C	ENSP00000264233:p.His1201Arg	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	194	79	0.407216	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	620	0.2838827838827839	69	0.1402439024390244	92	0.2541436464088398	331	0.5786713286713286	128	0.16886543535620052	T	3.626	-0.076630	0.07184	0.104857	0.146628	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.45276	0.9	5.45	4.24	0.50183	.	0.659014	0.14910	N	0.291263	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.20780	0.048;0.001	B;B	0.15870	0.014;0.0	T	0.42155	-0.9468	9	0.15499	T	0.54	.	10.3646	0.44015	0.156:0.0:0.0:0.844	rs3218651;rs52826086;rs60671312;rs3218651	1201;373	O75417;O75417-2	DPOLQ_HUMAN;.	R	824;1201;1337	ENSP00000264233:H1201R	ENSP00000264233:H1201R	H	-	2	0	POLQ	122690866	0.000000	0.05858	0.016000	0.15963	0.038000	0.13279	-0.078000	0.11375	2.289000	0.77006	0.460000	0.39030	CAT	T|0.779;C|0.221	0.221	strong		0.343	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
HLA-DOA	3111	hgsc.bcm.edu	37	6	32975257	32975257	+	Silent	SNP	C	C	T	rs365066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32975257C>T	ENST00000229829.5	-	3	519	c.444G>A	c.(442-444)ctG>ctA	p.L148L	HLA-DOA_ENST00000450833.2_Silent_p.L118L|HLA-DOA_ENST00000495532.1_5'UTR	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	148	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						GGCCGTTGCGCAGCCAGGTGA	0.582													C|||	1964	0.392173	0.3071	0.3501	5008	,	,		20061	0.5496		0.4294	False		,,,				2504	0.3364				p.L148L		Atlas-SNP	.											.	HLA-DOA	22	.	0			c.G444A						PASS	.	C		1074,1948		193,688,630	179.0	169.0	173.0		444	1.7	1.0	6	dbSNP_80	173	2330,3088		504,1322,883	no	coding-synonymous	HLA-DOA	NM_002119.3		697,2010,1513	TT,TC,CC		43.0048,35.5394,40.3318		148/251	32975257	3404,5036	1511	2709	4220	SO:0001819	synonymous_variant	3111	exon3			GTTGCGCAGCCAG	M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA		2370084	Standard	XM_005272804		Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.444G>A	6.37:g.32975257C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_002119	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Silent	SNP	ENST00000229829.5	37	CCDS4763.1																																																																																			C|0.605;T|0.395	0.395	strong		0.582	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119	
THEM5	284486	hgsc.bcm.edu	37	1	151820324	151820324	+	Missense_Mutation	SNP	T	T	C	rs6587625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:151820324T>C	ENST00000368817.5	-	5	721	c.590A>G	c.(589-591)gAc>gGc	p.D197G	AL450992.2_ENST00000434182.1_RNA	NM_182578.3	NP_872384	Q8N1Q8	ACO15_HUMAN	thioesterase superfamily member 5	197			D -> G (in dbSNP:rs6587625).		cardiolipin acyl-chain remodeling (GO:0035965)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)	mitochondrial matrix (GO:0005759)	palmitoyl-CoA hydrolase activity (GO:0016290)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AACCAGAGAGTCCACGGGGAT	0.532													C|||	3896	0.777955	0.8752	0.8674	5008	,	,		15489	0.6815		0.833	False		,,,				2504	0.6258				p.D197G		Atlas-SNP	.											.	THEM5	41	.	0			c.A590G						PASS	.	C	GLY/ASP	3782,624	271.0+/-269.9	1625,532,46	94.0	89.0	91.0		590	4.2	1.0	1	dbSNP_116	91	6954,1646	304.6+/-307.0	2819,1316,165	yes	missense	THEM5	NM_182578.3	94	4444,1848,211	CC,CT,TT		19.1395,14.1625,17.4535	benign	197/248	151820324	10736,2270	2203	4300	6503	SO:0001583	missense	284486	exon5			AGAGAGTCCACGG	AK095283	CCDS1005.1	1q21.3	2008-02-05			ENSG00000196407	ENSG00000196407			26755	protein-coding gene	gene with protein product		615653					Standard	NM_182578		Approved	FLJ37964	uc021oyw.1	Q8N1Q8	OTTHUMG00000013070	ENST00000368817.5:c.590A>G	1.37:g.151820324T>C	ENSP00000357807:p.Asp197Gly	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_182578	Q5T1C3	Missense_Mutation	SNP	ENST00000368817.5	37	CCDS1005.1	1746|1746	0.7994505494505495|0.7994505494505495	426|426	0.8658536585365854|0.8658536585365854	309|309	0.8535911602209945|0.8535911602209945	379|379	0.6625874125874126|0.6625874125874126	632|632	0.8337730870712401|0.8337730870712401	C|C	0.017|0.017	-1.506755|-1.506755	0.00992|0.00992	0.858375|0.858375	0.808605|0.808605	ENSG00000196407|ENSG00000196407	ENST00000368817|ENST00000453881	T|.	0.12147|.	2.71|.	5.09|5.09	4.17|4.17	0.49024|0.49024	Thioesterase superfamily (1);|.	0.207171|.	0.40818|.	N|.	0.001017|.	T|T	0.02888|0.02888	0.0086|0.0086	N|N	0.00670|0.00670	-1.27|-1.27	0.51012|0.51012	P|P	9.40000000000385E-5|9.40000000000385E-5	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.38714|0.38714	-0.9648|-0.9648	9|4	0.02654|.	T|.	1|.	-13.1518|-13.1518	7.1408|7.1408	0.25554|0.25554	0.0:0.8002:0.0:0.1998|0.0:0.8002:0.0:0.1998	rs6587625;rs52794777;rs57310650;rs6587625|rs6587625;rs52794777;rs57310650;rs6587625	197|.	Q8N1Q8|.	THEM5_HUMAN|.	G|A	197|144	ENSP00000357807:D197G|.	ENSP00000357807:D197G|.	D|T	-|-	2|1	0|0	THEM5|THEM5	150086948|150086948	0.999000|0.999000	0.42202|0.42202	0.998000|0.998000	0.56505|0.56505	0.053000|0.053000	0.15095|0.15095	0.635000|0.635000	0.24629|0.24629	1.160000|1.160000	0.42584|0.42584	-0.119000|-0.119000	0.15052|0.15052	GAC|ACT	T|0.206;C|0.794	0.794	strong		0.532	THEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036678.2	NM_182578	
SAMD9L	219285	hgsc.bcm.edu	37	7	92763720	92763720	+	Missense_Mutation	SNP	G	G	A	rs151304501	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:92763720G>A	ENST00000318238.4	-	5	2781	c.1565C>T	c.(1564-1566)gCt>gTt	p.A522V	SAMD9L_ENST00000411955.1_Missense_Mutation_p.A522V|SAMD9L_ENST00000437805.1_Missense_Mutation_p.A522V	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	522					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			GACTTCTGAAGCTCTTTCTCT	0.383													G|||	35	0.00698882	0.0015	0.0187	5008	,	,		17823	0.0		0.0139	False		,,,				2504	0.0061				p.A522V		Atlas-SNP	.											.	SAMD9L	227	.	0			c.C1565T						PASS	.	G	VAL/ALA	21,4385	25.3+/-52.1	0,21,2182	65.0	71.0	69.0		1565	4.6	1.0	7	dbSNP_134	69	190,8410	78.9+/-141.6	3,184,4113	yes	missense	SAMD9L	NM_152703.2	64	3,205,6295	AA,AG,GG		2.2093,0.4766,1.6223	possibly-damaging	522/1585	92763720	211,12795	2203	4300	6503	SO:0001583	missense	219285	exon5			TCTGAAGCTCTTT	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"""Sterile alpha motif (SAM) domain containing"""	1349	protein-coding gene	gene with protein product		611170	"""chromosome 7 open reading frame 6"""	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.1565C>T	7.37:g.92763720G>A	ENSP00000326247:p.Ala522Val	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	15	0.006868131868131868	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	7	0.009234828496042216	G	18.36	3.606454	0.66445	0.004766	0.022093	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.17370	2.28;2.28;2.28	4.59	4.59	0.56863	.	0.083768	0.46758	D	0.000268	T	0.22859	0.0552	M	0.63843	1.955	0.39926	D	0.97422	D	0.67145	0.996	D	0.64776	0.929	T	0.14587	-1.0467	10	0.72032	D	0.01	-8.7019	17.1609	0.86803	0.0:0.0:1.0:0.0	.	522	Q8IVG5	SAM9L_HUMAN	V	522	ENSP00000326247:A522V;ENSP00000405760:A522V;ENSP00000408796:A522V	ENSP00000326247:A522V	A	-	2	0	SAMD9L	92601656	0.170000	0.23016	1.000000	0.80357	0.694000	0.40290	1.276000	0.33156	2.384000	0.81235	0.460000	0.39030	GCT	G|0.987;A|0.013	0.013	strong		0.383	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703	
TRIM29	23650	hgsc.bcm.edu	37	11	119998151	119998151	+	Missense_Mutation	SNP	C	C	G	rs146343820	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:119998151C>G	ENST00000341846.5	-	3	1448	c.1027G>C	c.(1027-1029)Gtg>Ctg	p.V343L	TRIM29_ENST00000529044.1_Missense_Mutation_p.V82L|TRIM29_ENST00000528870.1_5'Flank|TRIM29_ENST00000541857.1_Missense_Mutation_p.V76L	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	343					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		ATCACCTTCACTTGGTCCACA	0.587																																					p.V343L		Atlas-SNP	.											.	TRIM29	78	.	0			c.G1027C						PASS	.	C	LEU/VAL	4,4394	8.1+/-20.4	0,4,2195	181.0	148.0	159.0		1027	4.2	0.9	11	dbSNP_134	159	9,8581	7.1+/-27.0	0,9,4286	yes	missense	TRIM29	NM_012101.3	32	0,13,6481	GG,GC,CC		0.1048,0.091,0.1001	benign	343/589	119998151	13,12975	2199	4295	6494	SO:0001583	missense	23650	exon3			CCTTCACTTGGTC	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"""Tripartite motif containing / Tripartite motif containing"""	17274	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM29"", ""ataxia-telangiectasia group D-associated protein"""	610658	"""tripartite motif-containing 29"""			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.1027G>C	11.37:g.119998151C>G	ENSP00000343129:p.Val343Leu	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	197	90	0.456853	NM_012101	Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	37	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.840150	0.51057	9.1E-4	0.001048	ENSG00000137699	ENST00000341846;ENST00000541857;ENST00000529044	T	0.35605	1.3	5.14	4.23	0.50019	.	0.220732	0.32147	N	0.006505	T	0.20659	0.0497	N	0.19112	0.55	0.36728	D	0.881557	B;B;B	0.21452	0.003;0.011;0.056	B;B;B	0.17433	0.009;0.017;0.018	T	0.14035	-1.0487	9	.	.	.	.	8.188	0.31350	0.0:0.7621:0.0:0.2379	.	76;82;343	B7Z8U9;E9PRL4;Q14134	.;.;TRI29_HUMAN	L	343;76;82	ENSP00000343129:V343L	.	V	-	1	0	TRIM29	119503361	0.533000	0.26354	0.908000	0.35775	0.971000	0.66376	0.465000	0.22004	1.183000	0.42943	0.655000	0.94253	GTG	C|0.999;G|0.001	0.001	strong		0.587	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101	
GSTM5	2949	hgsc.bcm.edu	37	1	110260040	110260040	+	Missense_Mutation	SNP	A	A	G	rs113130058	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:110260040A>G	ENST00000256593.3	+	8	707	c.649A>G	c.(649-651)Agc>Ggc	p.S217G	GSTM5_ENST00000492718.1_3'UTR|GSTM5_ENST00000369813.1_3'UTR|GSTM5_ENST00000369812.5_Missense_Mutation_p.S236G	NM_000851.3	NP_000842.2	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5	217					glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)			NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	TACATGGAACAGCAAATAGGG	0.557													A|||	12	0.00239617	0.0	0.0029	5008	,	,		18649	0.0		0.0089	False		,,,				2504	0.001				p.S217G		Atlas-SNP	.											.	GSTM5	89	.	0			c.A649G						PASS	.	A	GLY/SER	9,4397	16.8+/-37.8	0,9,2194	92.0	83.0	86.0		649	3.1	0.0	1	dbSNP_132	86	67,8533	40.8+/-97.7	0,67,4233	yes	missense	GSTM5	NM_000851.3	56	0,76,6427	GG,GA,AA		0.7791,0.2043,0.5843	benign	217/219	110260040	76,12930	2203	4300	6503	SO:0001583	missense	2949	exon8			TGGAACAGCAAAT	L02321	CCDS811.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134201	ENSG00000134201	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4637	protein-coding gene	gene with protein product		138385	"""glutathione S-transferase M5"""			8473333	Standard	NM_000851		Approved		uc001dyn.3	P46439	OTTHUMG00000011644	ENST00000256593.3:c.649A>G	1.37:g.110260040A>G	ENSP00000256593:p.Ser217Gly	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	32	0.395062	NM_000851	A8K0V8|Q6PD78	Missense_Mutation	SNP	ENST00000256593.3	37	CCDS811.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	A	12.54	1.968184	0.34754	0.002043	0.007791	ENSG00000134201	ENST00000256593;ENST00000369812	T;T	0.03413	3.94;3.94	5.42	3.08	0.35506	.	0.068378	0.53938	U	0.000043	T	0.00580	0.0019	N	0.12182	0.205	0.18873	N	0.999982	B	0.02656	0.0	B	0.04013	0.001	T	0.47086	-0.9144	10	0.08599	T	0.76	.	6.8806	0.24170	0.8:0.0:0.2:0.0	.	217	P46439	GSTM5_HUMAN	G	217;236	ENSP00000256593:S217G;ENSP00000358827:S236G	ENSP00000256593:S217G	S	+	1	0	GSTM5	110061563	0.010000	0.17322	0.001000	0.08648	0.003000	0.03518	0.854000	0.27791	0.993000	0.38866	0.533000	0.62120	AGC	A|0.995;G|0.005	0.005	strong		0.557	GSTM5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032200.1	NM_000851	
ZNF211	10520	hgsc.bcm.edu	37	19	58153465	58153465	+	Nonsense_Mutation	SNP	T	T	A	rs146505315	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58153465T>A	ENST00000347302.3	+	3	1790	c.1611T>A	c.(1609-1611)taT>taA	p.Y537*	ZNF211_ENST00000299871.5_Nonsense_Mutation_p.Y602*|ZNF211_ENST00000544273.1_Nonsense_Mutation_p.Y549*|ZNF211_ENST00000391703.3_Nonsense_Mutation_p.Y476*|ZNF211_ENST00000254182.7_Nonsense_Mutation_p.Y528*|ZNF211_ENST00000420680.1_Nonsense_Mutation_p.Y541*|ZNF211_ENST00000541801.1_Nonsense_Mutation_p.Y528*|ZNF211_ENST00000240731.4_Nonsense_Mutation_p.Y550*	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	537					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AAAGGCCTTATCAGTGCAGTC	0.453													T|||	6	0.00119808	0.0008	0.0014	5008	,	,		21540	0.0		0.004	False		,,,				2504	0.0				p.Y602X		Atlas-SNP	.											.	ZNF211	78	.	0			c.T1806A						PASS	.	T	stop/TYR,stop/TYR	10,4396	16.8+/-37.8	0,10,2193	105.0	102.0	103.0		1650,1611	-4.0	0.0	19	dbSNP_134	103	49,8551	31.2+/-83.2	0,49,4251	yes	stop-gained,stop-gained	ZNF211	NM_006385.3,NM_198855.2	,	0,59,6444	AA,AT,TT		0.5698,0.227,0.4536	,	550/578,537/565	58153465	59,12947	2203	4300	6503	SO:0001587	stop_gained	10520	exon5			GCCTTATCAGTGC	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.1611T>A	19.37:g.58153465T>A	ENSP00000339562:p.Tyr537*	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	53	20	0.377358	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Nonsense_Mutation	SNP	ENST00000347302.3	37	CCDS12957.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	t|t	37|37	5.990100|5.990100	0.97179|0.97179	0.00227|0.00227	0.005698|0.005698	ENSG00000121417|ENSG00000121417	ENST00000407202|ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731	.|.	.|.	.|.	2.37|2.37	-4.02|-4.02	0.04034|0.04034	.|.	.|.	.|.	.|.	.|.	T|.	0.10809|.	0.0264|.	.|.	.|.	.|.	0.41247|0.41247	D|D	0.986684|0.986684	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.41484|.	-0.9506|.	4|.	.|0.02654	.|T	.|1	.|.	1.7708|1.7708	0.03011|0.03011	0.1459:0.3803:0.1482:0.3256|0.1459:0.3803:0.1482:0.3256	.|.	.|.	.|.	.|.	T|X	541|541;537;528;476;528;602;549;550	.|.	.|ENSP00000240731:Y550X	S|Y	+|+	1|3	0|2	ZNF211|ZNF211	62845277|62845277	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.940000|0.940000	0.58332|0.58332	-0.503000|-0.503000	0.06383|0.06383	-1.154000|-1.154000	0.02825|0.02825	0.477000|0.477000	0.44152|0.44152	TCA|TAT	T|0.996;A|0.004	0.004	strong		0.453	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
MBD4	8930	hgsc.bcm.edu	37	3	129155451	129155451	+	Missense_Mutation	SNP	C	C	T	rs140693	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129155451C>T	ENST00000249910.1	-	3	1211	c.1036G>A	c.(1036-1038)Gag>Aag	p.E346K	MBD4_ENST00000503197.1_Missense_Mutation_p.E346K|MBD4_ENST00000393278.2_Intron|MBD4_ENST00000507208.1_Missense_Mutation_p.E346K|MBD4_ENST00000509587.1_Intron|MBD4_ENST00000429544.2_Missense_Mutation_p.E346K	NM_003925.1	NP_003916.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	346			E -> K (in dbSNP:rs140693). {ECO:0000269|Ref.8}.		base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						TCATACTTCTCGTTGTGTTCT	0.333								Base excision repair (BER), DNA glycosylases					C|||	554	0.110623	0.0166	0.111	5008	,	,		21106	0.4187		0.002	False		,,,				2504	0.0317				p.E346K		Atlas-SNP	.											.	MBD4	53	.	0			c.G1036A	GRCh37	CM067695	MBD4	M	rs140693	PASS	.	C	LYS/GLU	97,4309	77.8+/-116.1	0,97,2106	111.0	117.0	115.0		1036	-3.7	0.0	3	dbSNP_78	115	32,8568	21.0+/-64.5	1,30,4269	yes	missense	MBD4	NM_003925.1	56	1,127,6375	TT,TC,CC		0.3721,2.2015,0.9918	benign	346/581	129155451	129,12877	2203	4300	6503	SO:0001583	missense	8930	exon3			ACTTCTCGTTGTG	AF072250	CCDS3058.1, CCDS63766.1, CCDS63767.1, CCDS63768.1, CCDS63769.1	3q21.3	2004-03-02			ENSG00000129071	ENSG00000129071			6919	protein-coding gene	gene with protein product		603574				9774669, 10097147	Standard	NM_003925		Approved	MED1	uc003emh.2	O95243	OTTHUMG00000159463	ENST00000249910.1:c.1036G>A	3.37:g.129155451C>T	ENSP00000249910:p.Glu346Lys	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	228	102	0.447368	NM_003925	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000249910.1	37	CCDS3058.1	273	0.125	11	0.022357723577235773	35	0.09668508287292818	225	0.39335664335664333	2	0.002638522427440633	C	9.301	1.052994	0.19907	0.022015	0.003721	ENSG00000129071	ENST00000429544;ENST00000249910;ENST00000503197;ENST00000507208	D;D;D;D	0.93953	-3.11;-3.11;-3.32;-3.32	4.85	-3.74	0.04385	.	1.322790	0.05363	N	0.534022	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.15141	0.006;0.006;0.012;0.003	B;B;B;B	0.10450	0.003;0.004;0.005;0.002	T	0.08249	-1.0731	9	0.09084	T	0.74	0.1894	9.8936	0.41304	0.0:0.7613:0.1205:0.1181	rs140693;rs3733143;rs16859514;rs52837417;rs60793507;rs140693	346;346;346;346	E9PEE4;O95243-2;O95243-3;O95243	.;.;.;MBD4_HUMAN	K	346	ENSP00000394080:E346K;ENSP00000249910:E346K;ENSP00000424873:E346K;ENSP00000422327:E346K	ENSP00000249910:E346K	E	-	1	0	MBD4	130638141	0.000000	0.05858	0.000000	0.03702	0.107000	0.19398	-1.958000	0.01519	-1.333000	0.02247	-0.355000	0.07637	GAG	C|0.939;T|0.061	0.061	strong		0.333	MBD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355529.1	NM_003925	
DNAH6	1768	hgsc.bcm.edu	37	2	84861723	84861723	+	Silent	SNP	C	C	T	rs7570005	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:84861723C>T	ENST00000237449.6	+	29	4619	c.4611C>T	c.(4609-4611)atC>atT	p.I1537I	DNAH6_ENST00000398278.2_Silent_p.I1537I|DNAH6_ENST00000389394.3_Silent_p.I1537I			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1537	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TGTCCGTCATCGCGCAGCAAC	0.468													T|||	867	0.173123	0.4622	0.0937	5008	,	,		18058	0.0129		0.0775	False		,,,				2504	0.1022				p.I1537I		Atlas-SNP	.											.	DNAH6	194	.	0			c.C4611T						PASS	.	T		600,784		116,368,208	76.0	67.0	70.0		4611	-5.5	0.7	2	dbSNP_116	70	251,2931		8,235,1348	no	coding-synonymous	DNAH6	NM_001370.1		124,603,1556	TT,TC,CC		7.8881,43.3526,18.6378		1537/4159	84861723	851,3715	692	1591	2283	SO:0001819	synonymous_variant	1768	exon30			CGTCATCGCGCAG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.4611C>T	2.37:g.84861723C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			C|0.843;T|0.157	0.157	strong		0.468	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
C1S	716	hgsc.bcm.edu	37	12	7171620	7171620	+	Silent	SNP	C	C	T	rs7965055	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7171620C>T	ENST00000406697.1	+	8	1069	c.441C>T	c.(439-441)tgC>tgT	p.C147C	C1S_ENST00000402681.3_5'UTR|C1S_ENST00000328916.3_Silent_p.C147C|C1S_ENST00000360817.5_Silent_p.C147C			P09871	C1S_HUMAN	complement component 1, s subcomponent	147	EGF-like; calcium-binding.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GCCACTTCTGCAACAATTTCA	0.448													C|||	455	0.0908546	0.1717	0.0677	5008	,	,		-128	0.003		0.0865	False		,,,				2504	0.093				p.C147C	GBM(156;750 1943 12971 24779 31015)	Atlas-SNP	.											.	C1S	93	.	0			c.C441T						PASS	.	C	,	640,3766	275.2+/-272.4	42,556,1605	176.0	173.0	174.0		441,441	3.0	1.0	12	dbSNP_116	174	666,7934	168.0+/-219.6	32,602,3666	no	coding-synonymous,coding-synonymous	C1S	NM_001734.3,NM_201442.2	,	74,1158,5271	TT,TC,CC		7.7442,14.5256,10.0415	,	147/689,147/689	7171620	1306,11700	2203	4300	6503	SO:0001819	synonymous_variant	716	exon5			CTTCTGCAACAAT		CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"""Complement system"""	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.441C>T	12.37:g.7171620C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	185	183	0.989189	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Silent	SNP	ENST00000406697.1	37	CCDS31735.1																																																																																			C|0.903;T|0.097	0.097	strong		0.448	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734	
CHST10	9486	hgsc.bcm.edu	37	2	101010082	101010082	+	Silent	SNP	G	G	C	rs3748930	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:101010082G>C	ENST00000264249.3	-	7	1081	c.696C>G	c.(694-696)acC>acG	p.T232T	CHST10_ENST00000542617.1_Silent_p.T280T|CHST10_ENST00000409701.1_Silent_p.T232T	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	232					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						GGATCCCCCGGGTCTCTGTCC	0.507													G|||	3034	0.605831	0.6263	0.5778	5008	,	,		18067	0.8065		0.499	False		,,,				2504	0.501				p.T232T		Atlas-SNP	.											.	CHST10	42	.	0			c.C696G						PASS	.	G		2762,1644	659.5+/-400.6	862,1038,303	194.0	188.0	190.0		696	5.1	1.0	2	dbSNP_107	190	4260,4340	576.1+/-390.3	1073,2114,1113	no	coding-synonymous	CHST10	NM_004854.4		1935,3152,1416	CC,CG,GG		49.5349,37.3128,46.0095		232/357	101010082	7022,5984	2203	4300	6503	SO:0001819	synonymous_variant	9486	exon7			CCCCCGGGTCTCT	BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"""Sulfotransferases, membrane-bound"""	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.696C>G	2.37:g.101010082G>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	NM_004854	Q53T18	Silent	SNP	ENST00000264249.3	37	CCDS2047.1																																																																																			G|0.426;C|0.574	0.574	strong		0.507	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854	
AOC2	314	hgsc.bcm.edu	37	17	40996656	40996656	+	Missense_Mutation	SNP	A	A	G	rs34230945	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:40996656A>G	ENST00000253799.3	+	1	40	c.13A>G	c.(13-15)Ata>Gta	p.I5V	AOC2_ENST00000452774.2_Missense_Mutation_p.I5V	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	5			I -> V (in dbSNP:rs34230945). {ECO:0000269|Ref.4}.		amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(14)|ovary(4)|skin(2)	30		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		GCATCTCAAGATAGTCCTGGC	0.527													A|||	26	0.00519169	0.0	0.0086	5008	,	,		21798	0.0		0.0169	False		,,,				2504	0.0031				p.I5V		Atlas-SNP	.											.	AOC2	61	.	0			c.A13G						PASS	.	A	VAL/ILE,VAL/ILE	26,4380	32.6+/-62.9	0,26,2177	279.0	260.0	266.0		13,13	2.2	1.0	17	dbSNP_126	266	238,8362	96.3+/-158.1	5,228,4067	yes	missense,missense	AOC2	NM_001158.3,NM_009590.2	29,29	5,254,6244	GG,GA,AA		2.7674,0.5901,2.0298	benign,benign	5/730,5/757	40996656	264,12742	2203	4300	6503	SO:0001583	missense	314	exon1			CTCAAGATAGTCC	AF081363	CCDS11443.1, CCDS45690.1	17q21	2012-07-13				ENSG00000131480	1.4.3.21		549	protein-coding gene	gene with protein product		602268				9119395, 9722954	Standard	NM_001158		Approved	RAO, DAO2	uc002ibu.3	O75106		ENST00000253799.3:c.13A>G	17.37:g.40996656A>G	ENSP00000253799:p.Ile5Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	174	92	0.528736	NM_009590	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	37	CCDS11443.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	0.087	-1.172883	0.01646	0.005901	0.027674	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.01787	4.64;4.64	5.3	2.18	0.27775	.	1.298320	0.04973	N	0.464182	T	0.00384	0.0012	N	0.08118	0	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.43327	-0.9398	10	0.02654	T	1	-30.1472	3.5251	0.07756	0.4707:0.0:0.3498:0.1795	rs34230945	5;5	O75106;O75106-2	AOC2_HUMAN;.	V	5	ENSP00000253799:I5V;ENSP00000406134:I5V	ENSP00000253799:I5V	I	+	1	0	AOC2	38250182	0.908000	0.30866	0.983000	0.44433	0.986000	0.74619	1.238000	0.32707	0.327000	0.23409	0.533000	0.62120	ATA	A|0.984;G|0.016	0.016	strong		0.527	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158	
LIPK	643414	hgsc.bcm.edu	37	10	90512306	90512306	+	Missense_Mutation	SNP	G	G	C	rs1214464	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:90512306G>C	ENST00000404190.1	+	9	993	c.993G>C	c.(991-993)atG>atC	p.M331I		NM_001080518.1	NP_001073987.1	Q5VXJ0	LIPK_HUMAN	lipase, family member K	331			M -> I (in dbSNP:rs1214464).		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	12		Colorectal(252;0.0381)		Colorectal(12;7.03e-05)|COAD - Colon adenocarcinoma(12;8.33e-05)		TTACTAAGATGGAAGTTCCAA	0.323													G|||	927	0.185104	0.0068	0.2781	5008	,	,		18940	0.2877		0.2097	False		,,,				2504	0.229				p.M331I		Atlas-SNP	.											.	LIPK	50	.	0			c.G993C						PASS	.	G	ILE/MET	181,3549		7,167,1691	39.0	36.0	37.0		993	3.7	1.0	10	dbSNP_87	37	1687,6529		201,1285,2622	yes	missense	LIPK	NM_001080518.1	10	208,1452,4313	CC,CG,GG		20.5331,4.8525,15.637	possibly-damaging	331/400	90512306	1868,10078	1865	4108	5973	SO:0001583	missense	643414	exon9			TAAGATGGAAGTT		CCDS44455.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000204021	ENSG00000204021			23444	protein-coding gene	gene with protein product		613922	"""lipase-like, ab-hydrolase domain containing 2"""	LIPL2			Standard	NM_001080518		Approved	bA186O14.2	uc010qmv.2	Q5VXJ0	OTTHUMG00000018693	ENST00000404190.1:c.993G>C	10.37:g.90512306G>C	ENSP00000383900:p.Met331Ile	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	57	52	0.912281	NM_001080518	A7KIH8	Missense_Mutation	SNP	ENST00000404190.1	37	CCDS44455.1	404	0.184981684981685	4	0.008130081300813009	79	0.21823204419889503	168	0.2937062937062937	153	0.20184696569920843	G	14.84	2.655169	0.47467	0.048525	0.205331	ENSG00000204021	ENST00000404190	T	0.62498	0.02	5.65	3.69	0.42338	Alpha/beta hydrolase fold-1 (1);	0.373592	0.26991	N	0.021464	T	0.00012	0.0000	N	0.12920	0.275	0.30831	P	0.7366900000000001	B	0.30281	0.275	B	0.35899	0.213	T	0.11665	-1.0578	9	0.09590	T	0.72	-12.5189	10.4283	0.44391	0.0:0.1445:0.7055:0.15	rs1214464;rs56611384;rs1214464	331	Q5VXJ0	LIPK_HUMAN	I	331	ENSP00000383900:M331I	ENSP00000383900:M331I	M	+	3	0	LIPK	90502286	0.997000	0.39634	0.997000	0.53966	0.991000	0.79684	2.593000	0.46180	1.583000	0.49898	0.655000	0.94253	ATG	G|0.809;C|0.191	0.191	strong		0.323	LIPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049253.2	XM_061222	
ABCA1	19	hgsc.bcm.edu	37	9	107602666	107602666	+	Silent	SNP	C	C	T	rs2246841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:107602666C>T	ENST00000374736.3	-	9	1342	c.948G>A	c.(946-948)ggG>ggA	p.G316G		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	316					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	TGATCTTCAGCCCCCCTCCCT	0.512													C|||	764	0.152556	0.2685	0.1859	5008	,	,		19626	0.0377		0.0944	False		,,,				2504	0.1503				p.G316G		Atlas-SNP	.											.	ABCA1	244	.	0			c.G948A						PASS	.	C		978,3428	367.1+/-318.1	121,736,1346	117.0	89.0	98.0		948	-3.4	1.0	9	dbSNP_100	98	965,7635	210.4+/-251.3	49,867,3384	no	coding-synonymous	ABCA1	NM_005502.3		170,1603,4730	TT,TC,CC		11.2209,22.197,14.9393		316/2262	107602666	1943,11063	2203	4300	6503	SO:0001819	synonymous_variant	19	exon9			CTTCAGCCCCCCT	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.948G>A	9.37:g.107602666C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	242	113	0.466942	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			C|0.866;T|0.134	0.134	strong		0.512	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
OR5H1	26341	hgsc.bcm.edu	37	3	97851659	97851659	+	Missense_Mutation	SNP	A	A	T	rs199787047	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:97851659A>T	ENST00000354565.2	+	1	118	c.118A>T	c.(118-120)Atg>Ttg	p.M40L	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M40L(3)		breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						CATCACCATCATGGGGAATCT	0.413																																					p.M40L		Atlas-SNP	.											OR5H1,NS,carcinoma,-2,7	OR5H1	71	7	3	Substitution - Missense(3)	kidney(2)|endometrium(1)	c.A118T						scavenged	.						45.0	49.0	48.0					3																	97851659		2174	4242	6416	SO:0001583	missense	26341	exon1			ACCATCATGGGGA	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"""GPCR / Class A : Olfactory receptors"""	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.118A>T	3.37:g.97851659A>T	ENSP00000346575:p.Met40Leu	Somatic	512	3	0.00585938		WXS	Illumina HiSeq	Phase_I	680	11	0.0161765	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	37	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	A	3.067	-0.192020	0.06299	.	.	ENSG00000231192	ENST00000354565	T	0.00241	8.46	3.63	-0.16	0.13375	.	0.578292	0.14348	N	0.325303	T	0.00073	0.0002	N	0.04116	-0.275	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04976	-1.0914	10	0.33940	T	0.23	.	7.0903	0.25279	0.5661:0.0:0.4339:0.0	.	40	A6NKK0	OR5H1_HUMAN	L	40	ENSP00000346575:M40L	ENSP00000346575:M40L	M	+	1	0	OR5H1	99334349	0.000000	0.05858	0.016000	0.15963	0.102000	0.19082	-3.263000	0.00535	-0.297000	0.08934	0.164000	0.16699	ATG	A|0.978;T|0.022	0.022	strong		0.413	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338	
CD72	971	hgsc.bcm.edu	37	9	35612978	35612978	+	Missense_Mutation	SNP	G	G	A	rs34791102	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35612978G>A	ENST00000396757.1	-	7	865	c.701C>T	c.(700-702)cCg>cTg	p.P234L	CD72_ENST00000490239.1_5'UTR|CD72_ENST00000259633.4_Missense_Mutation_p.P234L			P21854	CD72_HUMAN	CD72 molecule	234	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		P -> L (in dbSNP:rs34791102).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor binding (GO:0005102)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(5)|liver(1)|lung(6)	12			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CCATCCCGACGGACAGCAGGT	0.423													g|||	309	0.0617013	0.1377	0.0216	5008	,	,		22020	0.005		0.0646	False		,,,				2504	0.0429				p.P234L		Atlas-SNP	.											.	CD72	20	.	0			c.C701T						PASS	.	A	LEU/PRO	553,3853	248.1+/-256.1	39,475,1689	128.0	115.0	119.0		701	3.8	0.3	9	dbSNP_126	119	459,8141	137.1+/-194.1	13,433,3854	yes	missense	CD72	NM_001782.2	98	52,908,5543	AA,AG,GG		5.3372,12.5511,7.781	probably-damaging	234/360	35612978	1012,11994	2203	4300	6503	SO:0001583	missense	971	exon6			CCCGACGGACAGC		CCDS6581.1	9p	2008-07-21	2006-03-28		ENSG00000137101	ENSG00000137101		"""CD molecules"""	1696	protein-coding gene	gene with protein product		107272	"""CD72 antigen"""			2044654, 1711157	Standard	NM_001782		Approved	LYB2, CD72b	uc003zxb.2	P21854	OTTHUMG00000019870	ENST00000396757.1:c.701C>T	9.37:g.35612978G>A	ENSP00000379980:p.Pro234Leu	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	186	100	0.537634	NM_001782		Missense_Mutation	SNP	ENST00000396757.1	37	CCDS6581.1	113	0.051739926739926737	53	0.10772357723577236	4	0.011049723756906077	3	0.005244755244755245	53	0.06992084432717678	g	6.100	0.386632	0.11524	0.125511	0.053372	ENSG00000137101	ENST00000396757;ENST00000396759;ENST00000259633	T;T	0.61158	0.13;0.13	5.64	3.81	0.43845	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (1);	0.306603	0.28414	N	0.015435	T	0.00724	0.0024	M	0.78637	2.42	0.38189	D	0.939854	P;P	0.45986	0.87;0.87	B;B	0.31812	0.136;0.136	T	0.00883	-1.1528	10	0.59425	D	0.04	-8.2535	11.3314	0.49479	0.1584:0.0:0.8416:0.0	rs34791102;rs34791102	234;234	Q5TLG3;P21854	.;CD72_HUMAN	L	234	ENSP00000379980:P234L;ENSP00000259633:P234L	ENSP00000259633:P234L	P	-	2	0	CD72	35602978	0.735000	0.28153	0.325000	0.25375	0.008000	0.06430	0.807000	0.27140	0.352000	0.24053	-0.713000	0.03633	CCG	G|0.929;A|0.071	0.071	strong		0.423	CD72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052336.1	NM_001782	
MCCD1	401250	hgsc.bcm.edu	37	6	31496915	31496915	+	Missense_Mutation	SNP	G	G	A	rs2259435	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31496915G>A	ENST00000376191.2	+	1	422	c.124G>A	c.(124-126)Gag>Aag	p.E42K	DDX39B_ENST00000462421.1_5'Flank	NM_001011700.2	NP_001011700.2	P59942	MCCD1_HUMAN	mitochondrial coiled-coil domain 1	42			E -> K (in dbSNP:rs2259435). {ECO:0000269|PubMed:14574404}.			mitochondrion (GO:0005739)				skin(1)	1						AAGCATGGAAGAGCAGACCAG	0.577													g|||	856	0.170927	0.1437	0.1556	5008	,	,		12182	0.1647		0.159	False		,,,				2504	0.2372				p.E42K		Atlas-SNP	.											.	MCCD1	3	.	0			c.G124A						PASS	.	G	LYS/GLU	442,2580		23,396,1092	117.0	102.0	107.0		124	-0.6	0.0	6	dbSNP_100	107	926,4492		83,760,1866	yes	missense	MCCD1	NM_001011700.2	56	106,1156,2958	AA,AG,GG		17.0912,14.6261,16.2085	probably-damaging	42/120	31496915	1368,7072	1511	2709	4220	SO:0001583	missense	401250	exon1			ATGGAAGAGCAGA		CCDS34396.1	6p21.3	2003-10-17				ENSG00000204511			20668	protein-coding gene	gene with protein product		609624				14527716	Standard	NM_001011700		Approved		uc003ntp.1	P59942		ENST00000376191.2:c.124G>A	6.37:g.31496915G>A	ENSP00000365362:p.Glu42Lys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_001011700	A2AB29|A2RUP7|B0UZB2|Q7RTY2	Missense_Mutation	SNP	ENST00000376191.2	37	CCDS34396.1	368	0.1684981684981685	85	0.17276422764227642	66	0.18232044198895028	91	0.1590909090909091	126	0.1662269129287599	-	10.03	1.239623	0.22711	0.146261	0.170912	ENSG00000204511	ENST00000376191	T	0.26223	1.75	3.5	-0.639	0.11497	.	0.488362	0.16931	N	0.193658	T	0.04182	0.0116	N	0.14661	0.345	0.80722	P	0.0	B	0.19200	0.034	B	0.24155	0.051	T	0.33111	-0.9881	9	0.51188	T	0.08	-2.4108	3.7777	0.08667	0.3422:0.1843:0.4735:0.0	rs2259435;rs59557207;rs2259435	42	P59942	MCCD1_HUMAN	K	42	ENSP00000365362:E42K	ENSP00000365362:E42K	E	+	1	0	MCCD1	31604894	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	0.035000	0.13797	-0.269000	0.09298	-0.263000	0.10527	GAG	G|0.837;A|0.163	0.163	strong		0.577	MCCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259099.1		
VPS4A	27183	hgsc.bcm.edu	37	16	69355155	69355155	+	Silent	SNP	G	G	A	rs1127232	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:69355155G>A	ENST00000254950.11	+	9	1209	c.1053G>A	c.(1051-1053)tcG>tcA	p.S351S	VPS4A_ENST00000564399.1_3'UTR|COG8_ENST00000564419.1_Intron	NM_013245.2	NP_037377.1			vacuolar protein sorting 4 homolog A (S. cerevisiae)											NS(1)|central_nervous_system(1)|large_intestine(2)|lung(3)	7		Ovarian(137;0.101)				AGGTGCAGTCGGCCACACACT	0.567													G|||	251	0.0501198	0.0514	0.0562	5008	,	,		17910	0.0159		0.0527	False		,,,				2504	0.0767				p.S351S		Atlas-SNP	.											.	VPS4A	18	.	0			c.G1053A						PASS	.	G		202,3920		5,192,1864	11.0	12.0	12.0		1053	-9.6	0.4	16	dbSNP_86	12	443,7803		6,431,3686	no	coding-synonymous	VPS4A	NM_013245.2		11,623,5550	AA,AG,GG		5.3723,4.9005,5.2151		351/438	69355155	645,11723	2061	4123	6184	SO:0001819	synonymous_variant	27183	exon9			GCAGTCGGCCACA	AF112215	CCDS45517.1	16q23.1	2010-04-21	2006-04-04		ENSG00000132612	ENSG00000132612		"""ATPases / AAA-type"""	13488	protein-coding gene	gene with protein product		609982	"""vacuolar protein sorting 4A (yeast homolog)"", ""vacuolar protein sorting 4A (yeast)"""			10637304, 11563910	Standard	NM_013245		Approved	VPS4, VPS4-1, FLJ22197, SKD2, SKD1, SKD1A	uc002eww.3	Q9UN37		ENST00000254950.11:c.1053G>A	16.37:g.69355155G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_013245		Silent	SNP	ENST00000254950.11	37	CCDS45517.1																																																																																			A|0.047;C|0.000;G|0.953	0.047	strong		0.567	VPS4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430563.3	NM_013245	
MT-ND5	4540	hgsc.bcm.edu	37	M	14053	14053	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:14053A>G	ENST00000361567.2	+	1	1717	c.1717A>G	c.(1717-1719)Acc>Gcc	p.T573A	MT-TE_ENST00000387459.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	573					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ACCAAATCTCCACCTCCATCA	0.423																																					p.T573A		Atlas-SNP	.											.	.	.	.	0			c.A1717G						PASS	.																																			SO:0001583	missense	0	exon1			ATCTCCACCTCCA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1717A>G	M.37:g.14053A>G	ENSP00000354813:p.Thr573Ala	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	30	29	0.966667	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.423	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
AGGF1	55109	hgsc.bcm.edu	37	5	76359024	76359024	+	Missense_Mutation	SNP	C	C	A	rs34400049	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:76359024C>A	ENST00000312916.7	+	14	2474	c.2092C>A	c.(2092-2094)Cct>Act	p.P698T		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	698			P -> T (in dbSNP:rs34400049). {ECO:0000269|PubMed:14961121}.		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		AGAAACTAAGCCTCAAAAAGA	0.378													C|||	1027	0.205072	0.0802	0.3199	5008	,	,		16784	0.2728		0.2952	False		,,,				2504	0.1299				p.P698T		Atlas-SNP	.											.	AGGF1	71	.	0			c.C2092A						PASS	.	C	THR/PRO	440,3966	210.8+/-231.2	31,378,1794	83.0	88.0	86.0		2092	1.6	0.9	5	dbSNP_126	86	2499,6101	409.6+/-349.9	366,1767,2167	yes	missense	AGGF1	NM_018046.4	38	397,2145,3961	AA,AC,CC		29.0581,9.9864,22.5973	benign	698/715	76359024	2939,10067	2203	4300	6503	SO:0001583	missense	55109	exon14			ACTAAGCCTCAAA	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"""G patch domain containing"""	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.2092C>A	5.37:g.76359024C>A	ENSP00000316109:p.Pro698Thr	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	190	78	0.410526	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	CCDS4035.1	514	0.23534798534798534	47	0.09552845528455285	107	0.2955801104972376	143	0.25	217	0.2862796833773087	C	0.081	-1.184419	0.01620	0.099864	0.290581	ENSG00000164252	ENST00000312916	T	0.35421	1.31	5.47	1.61	0.23674	.	0.795454	0.12324	N	0.478965	T	0.00012	0.0000	L	0.29908	0.895	0.29291	P	0.869337	B	0.28713	0.22	B	0.19148	0.024	T	0.33497	-0.9866	9	0.02654	T	1	-18.1993	1.31	0.02096	0.1414:0.3459:0.1383:0.3744	rs34400049	698	Q8N302	AGGF1_HUMAN	T	698	ENSP00000316109:P698T	ENSP00000316109:P698T	P	+	1	0	AGGF1	76394780	0.008000	0.16893	0.924000	0.36721	0.903000	0.53119	-0.210000	0.09345	0.003000	0.14656	-0.145000	0.13849	CCT	A|0.225;C|0.775	0.225	strong		0.378	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
MYPN	84665	hgsc.bcm.edu	37	10	69959242	69959242	+	Missense_Mutation	SNP	C	C	A	rs7079481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:69959242C>A	ENST00000358913.5	+	17	3891	c.3403C>A	c.(3403-3405)Cca>Aca	p.P1135T	MYPN_ENST00000540630.1_Missense_Mutation_p.P1135T|MYPN_ENST00000354393.2_Missense_Mutation_p.P860T	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	1135	Ig-like 4.|Interaction with ACTN.		P -> T (in dbSNP:rs7079481). {ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						GCTCATTGACCCACTCACTCA	0.542													C|||	1704	0.340256	0.2163	0.402	5008	,	,		19149	0.2391		0.4841	False		,,,				2504	0.4202				p.P1135T		Atlas-SNP	.											.	MYPN	189	.	0			c.C3403A						PASS	.	C	THR/PRO	1163,3243	410.6+/-335.4	136,891,1176	126.0	102.0	110.0		3403	5.4	1.0	10	dbSNP_116	110	4116,4484	563.8+/-388.2	1033,2050,1217	yes	missense	MYPN	NM_032578.2	38	1169,2941,2393	AA,AC,CC		47.8605,26.3958,40.589	probably-damaging	1135/1321	69959242	5279,7727	2203	4300	6503	SO:0001583	missense	84665	exon17			ATTGACCCACTCA	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.3403C>A	10.37:g.69959242C>A	ENSP00000351790:p.Pro1135Thr	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	250	131	0.524	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	786	0.3598901098901099	117	0.23780487804878048	156	0.430939226519337	146	0.25524475524475526	367	0.4841688654353562	C	27.0	4.791076	0.90367	0.263958	0.478605	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.72394	-0.65;-0.65;-0.65	5.38	5.38	0.77491	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.35414	1.06	0.09310	P	0.999999999312082	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	T	0.44081	-0.9351	8	.	.	.	.	19.3311	0.94288	0.0:1.0:0.0:0.0	rs7079481;rs52819321;rs58442467;rs7079481	1135;860;1135	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	T	860;860;1135;1135	ENSP00000346369:P860T;ENSP00000351790:P1135T;ENSP00000441668:P1135T	.	P	+	1	0	MYPN	69629248	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	7.595000	0.82710	2.813000	0.96785	0.655000	0.94253	CCA	C|0.623;A|0.377	0.377	strong		0.542	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
PRKCDBP	112464	hgsc.bcm.edu	37	11	6340525	6340525	+	Silent	SNP	A	A	T	rs12570	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6340525A>T	ENST00000303927.3	-	2	824	c.654T>A	c.(652-654)gcT>gcA	p.A218A	PRKCDBP_ENST00000530979.1_Silent_p.A250A	NM_145040.2	NP_659477.2	Q969G5	PRDBP_HUMAN	protein kinase C, delta binding protein	218					cortical actin cytoskeleton organization (GO:0030866)|negative regulation of fermentation (GO:1901003)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	caveola (GO:0005901)|protein complex (GO:0043234)				large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GCTGGGCTTCAGCGCTCCGGC	0.721													A|||	3279	0.654752	0.5537	0.5937	5008	,	,		14486	0.7341		0.7097	False		,,,				2504	0.6963				p.A218A		Atlas-SNP	.											PRKCDBP,NS,carcinoma,0,1	PRKCDBP	19	1	0			c.T654A						PASS	.	A		2461,1937		689,1083,427	33.0	40.0	38.0		654	-2.9	0.0	11	dbSNP_52	38	5896,2690		2025,1846,422	no	coding-synonymous	PRKCDBP	NM_145040.2		2714,2929,849	TT,TA,AA		31.3301,44.0427,35.6362		218/262	6340525	8357,4627	2199	4293	6492	SO:0001819	synonymous_variant	112464	exon2			GGCTTCAGCGCTC	AF339881	CCDS7762.1	11p15.4	2011-04-20			ENSG00000170955	ENSG00000170955			9400	protein-coding gene	gene with protein product	"""sdr-related gene product that binds to c-kinase"""					9054438	Standard	NM_145040		Approved	SRBC, HSRBC, MGC20400, cavin-3, CAVIN3	uc001mcu.1	Q969G5	OTTHUMG00000133378	ENST00000303927.3:c.654T>A	11.37:g.6340525A>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	19	9	0.473684	NM_145040		Silent	SNP	ENST00000303927.3	37	CCDS7762.1																																																																																			A|0.354;T|0.646	0.646	strong		0.721	PRKCDBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257228.2	NM_145040	
ZZEF1	23140	hgsc.bcm.edu	37	17	3953102	3953102	+	Missense_Mutation	SNP	A	A	G	rs781852	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:3953102A>G	ENST00000381638.2	-	37	6039	c.5915T>C	c.(5914-5916)cTa>cCa	p.L1972P		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1972			L -> P (in dbSNP:rs781852). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9455477}.				calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						CTGATCTTCTAGGCTCGAGTC	0.507													G|||	2379	0.47504	0.8154	0.4092	5008	,	,		18550	0.247		0.4026	False		,,,				2504	0.3712				p.L1972P		Atlas-SNP	.											ZZEF1,colon,carcinoma,0,1	ZZEF1	195	1	0			c.T5915C						PASS	.	G	PRO/LEU	3341,1065	387.9+/-326.7	1287,767,149	105.0	98.0	100.0		5915	5.5	0.5	17	dbSNP_86	100	3384,5216	641.0+/-399.6	645,2094,1561	yes	missense	ZZEF1	NM_015113.3	98	1932,2861,1710	GG,GA,AA		39.3488,24.1716,48.2931	benign	1972/2962	3953102	6725,6281	2203	4300	6503	SO:0001583	missense	23140	exon37			TCTTCTAGGCTCG	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.5915T>C	17.37:g.3953102A>G	ENSP00000371051:p.Leu1972Pro	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	1019	0.4665750915750916	403	0.8191056910569106	159	0.43922651933701656	154	0.2692307692307692	303	0.3997361477572559	G	10.46	1.357175	0.24598	0.758284	0.393488	ENSG00000074755	ENST00000381638	T	0.20069	2.1	5.46	5.46	0.80206	.	0.180691	0.50627	N	0.000117	T	0.00012	0.0000	N	0.03608	-0.345	0.48696	P	3.049999999999997E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.13098	-1.0522	9	0.30078	T	0.28	0.0053	11.8912	0.52630	0.0817:0.0:0.9183:0.0	rs781852;rs3786013;rs52816057;rs57619552;rs781852	1972;1972	O43149-2;O43149	.;ZZEF1_HUMAN	P	1972	ENSP00000371051:L1972P	ENSP00000371051:L1972P	L	-	2	0	ZZEF1	3899851	0.190000	0.23276	0.524000	0.27887	0.007000	0.05969	3.513000	0.53414	1.470000	0.48102	-0.176000	0.13171	CTA	T|0.003;G|0.504	0.504	strong		0.507	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
C1orf162	128346	hgsc.bcm.edu	37	1	112018657	112018657	+	Missense_Mutation	SNP	G	G	A	rs6703267	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:112018657G>A	ENST00000343534.5	+	2	257	c.7G>A	c.(7-9)Ggc>Agc	p.G3S	C1orf162_ENST00000464591.1_3'UTR|C1orf162_ENST00000369718.3_Missense_Mutation_p.G3S	NM_174896.2	NP_777556.1	Q8NEQ5	CA162_HUMAN	chromosome 1 open reading frame 162	3			G -> S (in dbSNP:rs6703267).			integral component of membrane (GO:0016021)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5		all_cancers(81;0.00116)|all_epithelial(167;0.000761)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0236)|Colorectal(144;0.0286)|all cancers(265;0.0572)|Epithelial(280;0.0862)|COAD - Colon adenocarcinoma(174;0.112)|LUSC - Lung squamous cell carcinoma(189;0.134)		CAGCATGGGAGGCAATGGCTC	0.463													G|||	952	0.190096	0.2042	0.1398	5008	,	,		20843	0.1379		0.2386	False		,,,				2504	0.2106				p.G3S		Atlas-SNP	.											.	C1orf162	14	.	0			c.G7A						PASS	.	G	SER/GLY	883,3523	344.4+/-308.1	88,707,1408	76.0	73.0	74.0		7	-1.9	0.0	1	dbSNP_116	74	2300,6300	387.6+/-342.3	288,1724,2288	yes	missense	C1orf162	NM_174896.2	56	376,2431,3696	AA,AG,GG		26.7442,20.0409,24.4733	probably-damaging	3/156	112018657	3183,9823	2203	4300	6503	SO:0001583	missense	128346	exon2			ATGGGAGGCAATG	BC017973	CCDS837.1, CCDS72837.1	1p13.2	2008-02-05			ENSG00000143110	ENSG00000143110			28344	protein-coding gene	gene with protein product						12477932	Standard	XM_005270475		Approved	MGC24133	uc001ebe.3	Q8NEQ5	OTTHUMG00000011750	ENST00000343534.5:c.7G>A	1.37:g.112018657G>A	ENSP00000344218:p.Gly3Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_174896	Q5QNZ1	Missense_Mutation	SNP	ENST00000343534.5	37	CCDS837.1	408	0.18681318681318682	98	0.1991869918699187	60	0.16574585635359115	74	0.12937062937062938	176	0.23218997361477572	G	15.93	2.978115	0.53720	0.200409	0.267442	ENSG00000143110	ENST00000343534;ENST00000369718	T;T	0.46451	0.87;0.88	4.55	-1.89	0.07689	.	1.560890	0.03861	N	0.274047	T	0.04182	0.0116	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B	0.33318	0.408	B	0.23275	0.045	T	0.04191	-1.0970	9	0.02654	T	1	0.769	0.9459	0.01365	0.3879:0.1551:0.2983:0.1587	rs6703267;rs52796710;rs56712920;rs6703267	3	Q8NEQ5	CA162_HUMAN	S	3	ENSP00000344218:G3S;ENSP00000358732:G3S	ENSP00000344218:G3S	G	+	1	0	C1orf162	111820180	0.000000	0.05858	0.008000	0.14137	0.089000	0.18198	-1.138000	0.03216	-0.329000	0.08527	-0.165000	0.13383	GGC	G|0.782;A|0.218	0.218	strong		0.463	C1orf162-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032471.1	NM_174896	
TLE3	7090	hgsc.bcm.edu	37	15	70346923	70346923	+	Silent	SNP	C	C	T	rs2228178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:70346923C>T	ENST00000558939.1	-	16	3066	c.1689G>A	c.(1687-1689)tcG>tcA	p.S563S	TLE3_ENST00000558201.1_Silent_p.S569S|TLE3_ENST00000539550.1_Silent_p.S490S|TLE3_ENST00000442299.2_Silent_p.S555S|TLE3_ENST00000440567.3_Silent_p.S553S|TLE3_ENST00000559048.1_Silent_p.S563S|TLE3_ENST00000557907.1_Silent_p.S555S|TLE3_ENST00000317509.8_Silent_p.S551S|TLE3_ENST00000557997.1_Silent_p.S555S|TLE3_ENST00000560589.1_Silent_p.S507S|TLE3_ENST00000559191.1_Silent_p.S144S|TLE3_ENST00000560939.1_Silent_p.S565S|TLE3_ENST00000559929.1_Silent_p.S573S|TLE3_ENST00000558379.1_Silent_p.S558S|TLE3_ENST00000451782.2_Silent_p.S560S	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	563					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						GGGGCGTGGGCGAGGCCAGGT	0.657													C|||	1816	0.36262	0.2284	0.4726	5008	,	,		18079	0.255		0.4781	False		,,,				2504	0.4581				p.S563S		Atlas-SNP	.											TLE3,bladder,carcinoma,-1,1	TLE3	104	1	0			c.G1689A						PASS	.	C	,,	1199,3183		179,841,1171	30.0	35.0	33.0		1680,1689,1653	-9.1	0.7	15	dbSNP_98	33	4037,4549		969,2099,1225	no	coding-synonymous,coding-synonymous,coding-synonymous	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	,,	1148,2940,2396	TT,TC,CC		47.0184,27.3619,40.3763	,,	560/770,563/773,551/761	70346923	5236,7732	2191	4293	6484	SO:0001819	synonymous_variant	7090	exon16			CGTGGGCGAGGCC	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.1689G>A	15.37:g.70346923C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	97	60	0.618557	NM_005078	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Silent	SNP	ENST00000558939.1	37	CCDS45293.1																																																																																			C|0.629;T|0.371	0.371	strong		0.657	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
CFAP97	57587	hgsc.bcm.edu	37	4	186097045	186097045	+	Silent	SNP	C	C	T	rs6855305	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:186097045C>T	ENST00000458385.2	-	3	1334	c.1215G>A	c.(1213-1215)ccG>ccA	p.P405P	KIAA1430_ENST00000296775.6_Silent_p.P405P|KIAA1430_ENST00000514798.1_Silent_p.P405P|KIAA1430_ENST00000502992.1_5'UTR	NM_020827.1	NP_065878.1	Q9P2B7	K1430_HUMAN		405										endometrium(3)|kidney(2)|large_intestine(5)|upper_aerodigestive_tract(1)	11		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)		TTTTGCTTCCCGGCTTTTCCG	0.448													T|||	2532	0.505591	0.6573	0.464	5008	,	,		16644	0.3998		0.505	False		,,,				2504	0.4397				p.P405P		Atlas-SNP	.											.	KIAA1430	55	.	0			c.G1215A						PASS	.	T		2252,1430		694,864,283	143.0	134.0	136.0		1215	0.6	1.0	4	dbSNP_116	136	3818,4346		893,2032,1157	no	coding-synonymous	KIAA1430	NM_020827.1		1587,2896,1440	TT,TC,CC		46.7663,38.8376,48.7591		405/533	186097045	6070,5776	1841	4082	5923	SO:0001819	synonymous_variant	57587	exon3			GCTTCCCGGCTTT																												ENST00000458385.2:c.1215G>A	4.37:g.186097045C>T		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	201	110	0.547264	NM_020827	B3KRP7|D3DP60|Q05CU1|Q4W5M4|Q8N6E7|Q9UF45	Silent	SNP	ENST00000458385.2	37	CCDS47168.1																																																																																			C|0.502;N|0.000	.	strong		0.448	KIAA1430-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360717.2		
SYTL1	84958	hgsc.bcm.edu	37	1	27676925	27676925	+	Silent	SNP	G	G	A	rs6702341	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:27676925G>A	ENST00000543823.1	+	9	1416	c.954G>A	c.(952-954)aaG>aaA	p.K318K	SYTL1_ENST00000318074.5_Silent_p.K306K|SYTL1_ENST00000490170.1_3'UTR			Q8IYJ3	SYTL1_HUMAN	synaptotagmin-like 1	318	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|melanosome (GO:0042470)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)			NS(1)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	12		Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0908)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.0013)|KIRC - Kidney renal clear cell carcinoma(1967;0.00158)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GCAAGCGCAAGACGGCGGTGA	0.597													G|||	1226	0.244808	0.1392	0.2089	5008	,	,		15790	0.1786		0.3787	False		,,,				2504	0.3436				p.K318K		Atlas-SNP	.											.	SYTL1	57	.	0			c.G954A						PASS	.	G	,	745,3661	304.6+/-288.6	66,613,1524	115.0	101.0	106.0		954,918	3.9	1.0	1	dbSNP_116	106	3233,5367	488.6+/-372.4	618,1997,1685	no	coding-synonymous,coding-synonymous	SYTL1	NM_001193308.1,NM_032872.2	,	684,2610,3209	AA,AG,GG		37.593,16.9088,30.5859	,	318/563,306/551	27676925	3978,9028	2203	4300	6503	SO:0001819	synonymous_variant	84958	exon10			GCGCAAGACGGCG	AK027902	CCDS298.1, CCDS53286.1	1p35.3	2008-02-05			ENSG00000142765	ENSG00000142765			15584	protein-coding gene	gene with protein product		608042				12137562	Standard	NM_032872		Approved	SLP1, JFC1, FLJ14996, exophilin-7	uc001bnw.2	Q8IYJ3	OTTHUMG00000005770	ENST00000543823.1:c.954G>A	1.37:g.27676925G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_001193308	Q5SSC9|Q96BB6|Q96GU6|Q96S89|Q96SI0	Silent	SNP	ENST00000543823.1	37	CCDS53286.1	546	0.25	72	0.14634146341463414	78	0.2154696132596685	100	0.17482517482517482	296	0.39050131926121373	G	11.12	1.546023	0.27652	0.169088	0.37593	ENSG00000142765	ENST00000496001	.	.	.	3.87	3.87	0.44632	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46789	-0.9166	3	.	.	.	-18.2362	6.0715	0.19891	0.2147:0.0:0.7853:0.0	rs6702341	.	.	.	K	166	.	.	R	+	2	0	SYTL1	27549512	1.000000	0.71417	0.999000	0.59377	0.962000	0.63368	0.998000	0.29744	2.155000	0.67459	0.462000	0.41574	AGA	G|0.711;A|0.289	0.289	strong		0.597	SYTL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032872	
HLA-B	3106	hgsc.bcm.edu	37	6	31324154	31324154	+	Missense_Mutation	SNP	G	G	A	rs1050379	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324154G>A	ENST00000412585.2	-	3	437	c.409C>T	c.(409-411)Cat>Tat	p.H137Y		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	137	Alpha-2.		H -> Y (in dbSNP:rs1050379).		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TACTGGTCATGCCCGCGGAGG	0.706									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				A|||	1320	0.263578	0.2746	0.2896	5008	,	,		8205	0.2133		0.3221	False		,,,				2504	0.2219				p.H137Y		Atlas-SNP	.											.	HLA-B	54	.	0			c.C409T						PASS	.						23.0	19.0	21.0					6																	31324154		2045	4160	6205	SO:0001583	missense	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	GGTCATGCCCGCG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.409C>T	6.37:g.31324154G>A	ENSP00000399168:p.His137Tyr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	48	46	0.958333	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	590	0.27014652014652013	130	0.26422764227642276	115	0.31767955801104975	116	0.20279720279720279	229	0.3021108179419525	N	6.838	0.523788	0.13066	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.00608	6.25;6.25	3.18	0.609	0.17575	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.533784	0.13653	N	0.372115	T	0.00039	0.0001	N	0.00011	-2.985	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.15484	0.0;0.013	T	0.13980	-1.0489	10	0.02654	T	1	.	3.2669	0.06868	0.6106:0.0:0.2156:0.1738	rs1050379;rs3173353;rs3175997;rs9266152;rs16896605	137;137	P30480;P01889	1B42_HUMAN;1B07_HUMAN	Y	137;16;16;148	ENSP00000399168:H137Y;ENSP00000405931:H148Y	ENSP00000399168:H137Y	H	-	1	0	HLA-B	31432133	0.000000	0.05858	0.080000	0.20451	0.011000	0.07611	0.998000	0.29744	-0.269000	0.09298	-0.891000	0.02926	CAT	G|0.731;A|0.269	0.269	strong		0.706	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
MYPN	84665	hgsc.bcm.edu	37	10	69933921	69933921	+	Missense_Mutation	SNP	G	G	A	rs10997975	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:69933921G>A	ENST00000358913.5	+	11	2560	c.2072G>A	c.(2071-2073)aGc>aAc	p.S691N	MYPN_ENST00000540630.1_Missense_Mutation_p.S691N|MYPN_ENST00000354393.2_Missense_Mutation_p.S416N	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	691			S -> N (in dbSNP:rs10997975). {ECO:0000269|PubMed:11309420, ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						TTTCCTTTCAGCATGACTGTT	0.488													A|||	1682	0.335863	0.1762	0.4035	5008	,	,		17477	0.2649		0.4851	False		,,,				2504	0.4233				p.S691N		Atlas-SNP	.											.	MYPN	189	.	0			c.G2072A						PASS	.	A	ASN/SER	976,3430	733.0+/-410.4	109,758,1336	163.0	139.0	148.0		2072	3.2	0.4	10	dbSNP_120	148	4128,4472	589.8+/-392.6	1043,2042,1215	yes	missense	MYPN	NM_032578.2	46	1152,2800,2551	AA,AG,GG		48.0,22.1516,39.2434	benign	691/1321	69933921	5104,7902	2203	4300	6503	SO:0001583	missense	84665	exon11			CTTTCAGCATGAC	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2072G>A	10.37:g.69933921G>A	ENSP00000351790:p.Ser691Asn	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	303	141	0.465347	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	783	0.3585164835164835	100	0.2032520325203252	153	0.42265193370165743	162	0.28321678321678323	368	0.48548812664907653	A	1.120	-0.655690	0.03480	0.221516	0.48	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.58797	0.31;0.42;0.4	5.51	3.21	0.36854	.	0.510690	0.22191	N	0.063361	T	0.00012	0.0000	N	0.00841	-1.15	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.46925	-0.9156	8	.	.	.	.	8.0938	0.30816	0.7773:0.0:0.2227:0.0	rs10997975;rs17458172;rs52815281;rs59577198;rs10997975	691;416;691	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	N	416;416;691;691	ENSP00000346369:S416N;ENSP00000351790:S691N;ENSP00000441668:S691N	.	S	+	2	0	MYPN	69603927	0.491000	0.26019	0.353000	0.25747	0.906000	0.53458	0.428000	0.21395	0.088000	0.17205	-0.254000	0.11334	AGC	A|0.370;G|0.630	0.370	strong		0.488	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
AIMP2	7965	hgsc.bcm.edu	37	7	6063283	6063283	+	Silent	SNP	C	C	T	rs4560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:6063283C>T	ENST00000223029.3	+	4	1043	c.924C>T	c.(922-924)aaC>aaT	p.N308N	AIMP2_ENST00000395236.2_Silent_p.N239N|EIF2AK1_ENST00000536084.1_3'UTR|EIF2AK1_ENST00000199389.6_3'UTR|AIMP2_ENST00000400479.2_Silent_p.N230N	NM_006303.3	NP_006294.2	Q13155	AIMP2_HUMAN	aminoacyl tRNA synthetase complex-interacting multifunctional protein 2	308	GST C-terminal.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|tRNA aminoacylation for protein translation (GO:0006418)|Type II pneumocyte differentiation (GO:0060510)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						CTTGTGAAAACCTGGCTCCTT	0.483													c|||	1642	0.327875	0.1611	0.3977	5008	,	,		18782	0.369		0.4563	False		,,,				2504	0.3292				p.N308N		Atlas-SNP	.											.	AIMP2	32	.	0			c.C924T						PASS	.	C	,,	844,3562	332.5+/-302.5	88,668,1447	96.0	80.0	86.0		,924,	4.5	1.0	7	dbSNP_52	86	3699,4901	530.0+/-381.7	779,2141,1380	no	utr-3,coding-synonymous,utr-3	AIMP2,EIF2AK1	NM_001134335.1,NM_006303.3,NM_014413.3	,,	867,2809,2827	TT,TC,CC		43.0116,19.1557,34.93	,,	,308/321,	6063283	4543,8463	2203	4300	6503	SO:0001819	synonymous_variant	7965	exon4			TGAAAACCTGGCT	U24169	CCDS5344.1	7p22.1	2009-05-29			ENSG00000106305	ENSG00000106305			20609	protein-coding gene	gene with protein product		600859				8666379, 18695251	Standard	NM_006303		Approved	p38, PRO0992, JTV-1, JTV1	uc003spo.3	Q13155	OTTHUMG00000122077	ENST00000223029.3:c.924C>T	7.37:g.6063283C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	213	212	0.995305	NM_006303	Q75MR1|Q96CZ5|Q9P1L2	Silent	SNP	ENST00000223029.3	37	CCDS5344.1																																																																																			C|0.643;T|0.357	0.357	strong		0.483	AIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242834.2	NM_006303	
PRSS35	167681	hgsc.bcm.edu	37	6	84234144	84234144	+	Silent	SNP	C	C	T	rs3812141	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:84234144C>T	ENST00000369700.3	+	2	1161	c.984C>T	c.(982-984)tcC>tcT	p.S328S	PRSS35_ENST00000536636.1_Silent_p.S328S	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	328	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		GCAGTGTGTCCGACGAATCCA	0.478													C|||	1027	0.205072	0.2632	0.111	5008	,	,		19495	0.2242		0.1332	False		,,,				2504	0.2474				p.S328S		Atlas-SNP	.											.	PRSS35	60	.	0			c.C984T						PASS	.	C	,	1043,3363	383.5+/-324.9	128,787,1288	124.0	124.0	124.0		984,984	-11.8	0.0	6	dbSNP_107	124	1302,7298	258.4+/-282.1	81,1140,3079	no	coding-synonymous,coding-synonymous	PRSS35	NM_001170423.1,NM_153362.2	,	209,1927,4367	TT,TC,CC		15.1395,23.6723,18.0301	,	328/414,328/414	84234144	2345,10661	2203	4300	6503	SO:0001819	synonymous_variant	167681	exon2			TGTGTCCGACGAA	BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"""Serine peptidases / Serine peptidases"""	21387	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 158"""	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.984C>T	6.37:g.84234144C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	54	0.580645	NM_153362	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	37	CCDS4999.1																																																																																			C|0.813;T|0.187	0.187	strong		0.478	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362	
OR4C15	81309	hgsc.bcm.edu	37	11	55322099	55322099	+	Missense_Mutation	SNP	C	C	G	rs17496724	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55322099C>G	ENST00000314644.2	+	1	317	c.317C>G	c.(316-318)gCt>gGt	p.A106G		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						AGCAGCCCTGCTCTTCTGGTG	0.443										HNSCC(20;0.049)																											p.A106G		Atlas-SNP	.											.	OR4C15	145	.	0			c.C317G						PASS	.						172.0	137.0	149.0					11																	55322099		2201	4296	6497	SO:0001583	missense	81309	exon1			GCCCTGCTCTTCT	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"""GPCR / Class A : Olfactory receptors"""	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.317C>G	11.37:g.55322099C>G	ENSP00000324958:p.Ala106Gly	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	77	36	0.467532	NM_001001920	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.417099	0.25552	.	.	ENSG00000181939	ENST00000314644	T	0.01092	5.35	4.79	4.79	0.61399	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01523	0.0049	N	0.20881	0.62	0.09310	N	1	B	0.34264	0.446	B	0.35813	0.211	T	0.54344	-0.8308	9	0.62326	D	0.03	.	15.7279	0.77777	0.0:1.0:0.0:0.0	.	52	Q8NGM1	OR4CF_HUMAN	G	106	ENSP00000324958:A106G	ENSP00000324958:A106G	A	+	2	0	OR4C15	55078675	0.000000	0.05858	0.765000	0.31456	0.191000	0.23601	-0.885000	0.04161	2.665000	0.90641	0.385000	0.25706	GCT	C|0.966;A|0.034	.	alt		0.443	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920	
VGLL2	245806	hgsc.bcm.edu	37	6	117591755	117591755	+	Silent	SNP	T	T	C	rs13194610	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:117591755T>C	ENST00000326274.5	+	3	631	c.441T>C	c.(439-441)aaT>aaC	p.N147N	VGLL2_ENST00000352536.3_Intron	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	147					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|kidney(1)|lung(3)	5				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)		CCTTCTGGAATAGCGCGTACC	0.711													C|||	893	0.178315	0.3752	0.0951	5008	,	,		7610	0.1319		0.1054	False		,,,				2504	0.0941				p.N147N		Atlas-SNP	.											.	VGLL2	18	.	0			c.T441C						PASS	.	C	,	1283,3091		171,941,1075	10.0	12.0	11.0		,441	4.1	1.0	6	dbSNP_121	11	904,7648		52,800,3424	yes	intron,coding-synonymous	VGLL2	NM_153453.1,NM_182645.2	,	223,1741,4499	CC,CT,TT		10.5706,29.3324,16.9194	,	,147/318	117591755	2187,10739	2187	4276	6463	SO:0001819	synonymous_variant	245806	exon3			CTGGAATAGCGCG	AY056583	CCDS5114.1, CCDS5115.1	6q22.31	2014-03-03	2014-03-03		ENSG00000170162	ENSG00000170162			20232	protein-coding gene	gene with protein product		609979	"""vestigial like 2 (Drosophila)"""			12376544	Standard	NM_153453		Approved		uc003pxn.3	Q8N8G2	OTTHUMG00000015451	ENST00000326274.5:c.441T>C	6.37:g.117591755T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	32	19	0.59375	NM_182645	Q8WWX1	Silent	SNP	ENST00000326274.5	37	CCDS5115.1																																																																																			T|0.831;C|0.169	0.169	strong		0.711	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453	
OXGR1	27199	hgsc.bcm.edu	37	13	97639414	97639414	+	Silent	SNP	C	C	T	rs9284174	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:97639414C>T	ENST00000298440.1	-	4	843	c.600G>A	c.(598-600)ctG>ctA	p.L200L	OXGR1_ENST00000543457.1_Silent_p.L200L	NM_080818.3	NP_543008.3	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	200					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			CAGTCAAAATCAGGTTGTACC	0.463													T|||	2618	0.522764	0.587	0.3487	5008	,	,		24354	0.4544		0.5358	False		,,,				2504	0.6166				p.L200L		Atlas-SNP	.											.	OXGR1	46	.	0			c.G600A						PASS	.	T		2509,1897	544.3+/-376.5	706,1097,400	189.0	164.0	173.0		600	-11.7	0.0	13	dbSNP_119	173	4595,4005	554.5+/-386.5	1206,2183,911	no	coding-synonymous	OXGR1	NM_080818.3		1912,3280,1311	TT,TC,CC		46.5698,43.0549,45.3791		200/338	97639414	7104,5902	2203	4300	6503	SO:0001819	synonymous_variant	27199	exon4			CAAAATCAGGTTG	AF411109	CCDS9482.1	13q32.2	2014-04-09	2004-07-08	2004-07-09	ENSG00000165621	ENSG00000165621		"""GPCR / Class A : Orphans"""	4531	protein-coding gene	gene with protein product	"""2-oxoglutarate receptor 1"", ""alpha-ketoglutarate receptor 1"""	606922	"""G protein-coupled receptor 80"""	GPR99, GPR80		15141213, 12098360	Standard	NM_080818		Approved	P2RY15, P2Y15, aKGR	uc001vmx.1	Q96P68	OTTHUMG00000017236	ENST00000298440.1:c.600G>A	13.37:g.97639414C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	170	74	0.435294	NM_080818	Q5T5A7|Q86TL1	Silent	SNP	ENST00000298440.1	37	CCDS9482.1																																																																																			C|0.476;T|0.524	0.524	strong		0.463	OXGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045521.3	NM_080818	
MADCAM1	8174	hgsc.bcm.edu	37	19	501767	501767	+	Missense_Mutation	SNP	C	C	T	rs78245161		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:501767C>T	ENST00000215637.3	+	4	812	c.766C>T	c.(766-768)Cct>Tct	p.P256S	MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.P37S	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	256	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCCCAGGAGCCTCCCGACAC	0.726																																					p.P256S		Atlas-SNP	.											MADCAM1,NS,carcinoma,0,1	MADCAM1	29	1	0			c.C766T						PASS	.						31.0	35.0	33.0					19																	501767		2194	4286	6480	SO:0001583	missense	8174	exon4			CAGGAGCCTCCCG	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.766C>T	19.37:g.501767C>T	ENSP00000215637:p.Pro256Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	15	0.157895	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	c	5.207	0.223693	0.09863	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.09538	2.97	2.86	2.86	0.33363	.	.	.	.	.	T	0.06188	0.0160	N	0.12182	0.205	0.54753	D	0.999986	D	0.63046	0.992	P	0.45577	0.486	T	0.38045	-0.9679	9	0.08837	T	0.75	.	9.9622	0.41704	0.0:1.0:0.0:0.0	.	256	Q13477	MADCA_HUMAN	S	280;272;264;256	ENSP00000215637:P256S	ENSP00000215637:P256S	P	+	1	0	MADCAM1	452767	0.000000	0.05858	0.008000	0.14137	0.003000	0.03518	-0.228000	0.09114	1.548000	0.49413	0.638000	0.83543	CCT	C|0.500;T|0.500	0.500	weak		0.726	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
CEP290	80184	hgsc.bcm.edu	37	12	88500847	88500847	+	Missense_Mutation	SNP	T	T	C	rs11104738	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:88500847T>C	ENST00000552810.1	-	24	2855	c.2512A>G	c.(2512-2514)Aaa>Gaa	p.K838E	CEP290_ENST00000309041.7_Missense_Mutation_p.K840E|CEP290_ENST00000397838.3_5'UTR|CEP290_ENST00000547691.2_5'Flank	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	838			K -> E (in dbSNP:rs11104738). {ECO:0000269|PubMed:17564967}.		cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTTATTGTTTTAGATTCTGTT	0.259													T|||	486	0.0970447	0.0098	0.1499	5008	,	,		15730	0.2133		0.0487	False		,,,				2504	0.1074				p.K838E		Atlas-SNP	.											.	CEP290	195	.	0			c.A2512G						PASS	.	T	GLU/LYS	56,3500		1,54,1723	93.0	81.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2512	4.8	1.0	12	dbSNP_120	85	324,7750		7,310,3720	yes	missense	CEP290	NM_025114.3	56	8,364,5443	CC,CT,TT		4.0129,1.5748,3.2674	benign	838/2480	88500847	380,11250	1778	4037	5815	SO:0001583	missense	80184	exon24			TTGTTTTAGATTC	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.2512A>G	12.37:g.88500847T>C	ENSP00000448012:p.Lys838Glu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	124	38	0.306452	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	231	0.10576923076923077	2	0.0040650406504065045	47	0.1298342541436464	141	0.2465034965034965	41	0.05408970976253298	T	1.605	-0.525563	0.04141	0.015748	0.040129	ENSG00000198707	ENST00000552810;ENST00000309041	T;T	0.16743	2.32;2.32	5.67	4.77	0.60923	.	0.183752	0.47455	N	0.000228	T	0.00012	0.0000	N	0.02802	-0.49	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37979	-0.9682	9	0.02654	T	1	.	8.9454	0.35756	0.147:0.777:0.0:0.0759	rs11104738;rs11104738	838	O15078	CE290_HUMAN	E	838;840	ENSP00000448012:K838E;ENSP00000308021:K840E	ENSP00000308021:K840E	K	-	1	0	CEP290	87024978	1.000000	0.71417	0.998000	0.56505	0.606000	0.37113	2.903000	0.48711	1.356000	0.45884	-0.467000	0.05162	AAA	T|0.898;C|0.102	0.102	strong		0.259	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
KRTAP10-5	386680	hgsc.bcm.edu	37	21	45999908	45999908	+	Missense_Mutation	SNP	A	A	C	rs380585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:45999908A>C	ENST00000400372.1	-	1	573	c.548T>G	c.(547-549)tTc>tGc	p.F183C	TSPEAR_ENST00000323084.4_Intron	NM_198694.2	NP_941967.2	P60370	KR105_HUMAN	keratin associated protein 10-5	183	22 X 5 AA repeats of C-C-X(3).		F -> C (in dbSNP:rs380585).			keratin filament (GO:0045095)				endometrium(2)|kidney(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	14						GATGGGTTTGAAGCAGACAGG	0.602													.|||	730	0.145767	0.2489	0.0692	5008	,	,		22219	0.1964		0.0378	False		,,,				2504	0.1196				p.F183C		Atlas-SNP	.											.	KRTAP10-5	43	.	0			c.T548G						PASS	.	C	,CYS/PHE	944,3462	734.8+/-410.6	116,712,1375	190.0	196.0	194.0		,548	0.9	0.1	21	dbSNP_80	194	264,8336	806.2+/-407.2	4,256,4040	no	intron,missense	TSPEAR,KRTAP10-5	NM_144991.2,NM_198694.2	,205	120,968,5415	CC,CA,AA		3.0698,21.4253,9.288	,benign	,183/272	45999908	1208,11798	2203	4300	6503	SO:0001583	missense	386680	exon1			GGTTTGAAGCAGA	AJ566384	CCDS42958.1	21q22.3	2007-10-05			ENSG00000241123	ENSG00000241123		"""Keratin associated proteins"""	22969	protein-coding gene	gene with protein product				KRTAP18-5			Standard	NM_198694		Approved	KAP10.5, KAP18.5	uc002zfl.1	P60370	OTTHUMG00000057638	ENST00000400372.1:c.548T>G	21.37:g.45999908A>C	ENSP00000383223:p.Phe183Cys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_198694	Q0VAR7|Q0VAR8|Q70LJ3	Missense_Mutation	SNP	ENST00000400372.1	37	CCDS42958.1	286	0.13095238095238096	119	0.241869918699187	27	0.07458563535911603	119	0.20804195804195805	21	0.027704485488126648	c	0.001	-3.150025	0.00029	0.214253	0.030698	ENSG00000241123	ENST00000400372	T	0.00768	5.72	2.89	0.948	0.19561	.	.	.	.	.	T	0.00012	0.0000	N	0.00016	-2.86	0.53005	P	3.100000000000325E-5	B	0.12013	0.005	B	0.01281	0.0	T	0.39961	-0.9588	8	0.02654	T	1	.	2.2902	0.04136	0.1834:0.3404:0.3598:0.1164	rs380585	183	P60370	KR105_HUMAN	C	183	ENSP00000383223:F183C	ENSP00000383223:F183C	F	-	2	0	KRTAP10-5	44824336	0.053000	0.20554	0.129000	0.21949	0.017000	0.09413	-0.206000	0.09398	-0.183000	0.10585	-0.677000	0.03784	TTC	A|0.902;C|0.098	0.098	strong		0.602	KRTAP10-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128042.1		
BPIFB6	128859	hgsc.bcm.edu	37	20	31627291	31627291	+	Missense_Mutation	SNP	A	A	G	rs4911287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:31627291A>G	ENST00000349552.1	+	10	1039	c.1039A>G	c.(1039-1041)Agc>Ggc	p.S347G		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	347			S -> G (in dbSNP:rs4911287).			extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCGGTGGCGGAGCAAGGCTCC	0.532													G|||	3037	0.60643	0.7716	0.4827	5008	,	,		20088	0.7421		0.3917	False		,,,				2504	0.5521				p.S347G		Atlas-SNP	.											BPIL3,NS,carcinoma,-2,1	.	.	1	0			c.A1039G						PASS	.	G	GLY/SER	3060,1346	446.5+/-348.0	1092,876,235	105.0	112.0	109.0		1039	2.0	0.0	20	dbSNP_111	109	3244,5356	650.1+/-400.7	612,2020,1668	yes	missense	BPIFB6	NM_174897.2	56	1704,2896,1903	GG,GA,AA		37.7209,30.5493,48.4699	benign	347/454	31627291	6304,6702	2203	4300	6503	SO:0001583	missense	128859	exon10			TGGCGGAGCAAGG	AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"""BPI fold containing"""	16504	protein-coding gene	gene with protein product		614110	"""bactericidal/permeability-increasing protein-like 3"""	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.1039A>G	20.37:g.31627291A>G	ENSP00000344929:p.Ser347Gly	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_174897		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	1268	0.5805860805860806	394	0.8008130081300813	165	0.4558011049723757	414	0.7237762237762237	295	0.3891820580474934	G	0.460	-0.889715	0.02511	0.694507	0.377209	ENSG00000167104	ENST00000349552	T	0.06687	3.27	4.43	2.02	0.26589	.	0.707366	0.12342	N	0.477386	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09228	-1.0684	9	0.10902	T	0.67	.	5.9577	0.19283	0.39:0.0:0.61:0.0	rs4911287;rs57352515;rs4911287	347	Q8NFQ5	BPIB6_HUMAN	G	347	ENSP00000344929:S347G	ENSP00000344929:S347G	S	+	1	0	BPIFB6	31090952	0.500000	0.26091	0.015000	0.15790	0.003000	0.03518	0.538000	0.23160	0.396000	0.25283	-0.227000	0.12334	AGC	A|0.477;G|0.523	0.523	strong		0.532	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897	
CEP290	80184	hgsc.bcm.edu	37	12	88505633	88505633	+	Silent	SNP	A	A	G	rs45465996	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:88505633A>G	ENST00000552810.1	-	21	2398	c.2055T>C	c.(2053-2055)gcT>gcC	p.A685A	CEP290_ENST00000309041.7_Silent_p.A687A|CEP290_ENST00000397838.3_5'UTR	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	685					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTGATTCTATAGCCTAGCAAA	0.318													A|||	345	0.0688898	0.0227	0.1023	5008	,	,		12512	0.001		0.2008	False		,,,				2504	0.0419				p.A685A		Atlas-SNP	.											.	CEP290	195	.	0			c.T2055C						PASS	.	A		177,3379		7,163,1608	21.0	19.0	19.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2055	0.6	1.0	12	dbSNP_127	19	1438,6672		137,1164,2754	no	coding-synonymous	CEP290	NM_025114.3		144,1327,4362	GG,GA,AA		17.7312,4.9775,13.8436		685/2480	88505633	1615,10051	1778	4055	5833	SO:0001819	synonymous_variant	80184	exon21			TTCTATAGCCTAG	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.2055T>C	12.37:g.88505633A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Silent	SNP	ENST00000552810.1	37	CCDS55858.1	188	0.08608058608058608	6	0.012195121951219513	34	0.09392265193370165	1	0.0017482517482517483	147	0.19393139841688653	A	13.61	2.288974	0.40494	0.049775	0.177312	ENSG00000198707	ENST00000545139	.	.	.	5.79	0.62	0.17637	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17992	-1.0351	4	0.56958	D	0.05	.	0.5596	0.00676	0.2812:0.3026:0.2014:0.2148	rs45465996;rs62638181	.	.	.	H	540	.	ENSP00000444813:Y540H	Y	-	1	0	CEP290	87029764	0.971000	0.33674	0.996000	0.52242	0.956000	0.61745	0.004000	0.13106	-0.126000	0.11682	0.477000	0.44152	TAT	A|0.892;G|0.108	0.108	strong		0.318	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
CCDC155	147872	hgsc.bcm.edu	37	19	49894152	49894152	+	Silent	SNP	C	C	T	rs7256629	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49894152C>T	ENST00000447857.3	+	2	217	c.12C>T	c.(10-12)ccC>ccT	p.P4P	AC010524.2_ENST00000599433.1_RNA|CCDC155_ENST00000593725.1_3'UTR	NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	4						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						TGGACCTGCCCGAGGGCCCGG	0.677													C|||	2543	0.507788	0.4637	0.3934	5008	,	,		14434	0.5129		0.493	False		,,,				2504	0.6585				p.P4P		Atlas-SNP	.											.	CCDC155	46	.	0			c.C12T						PASS	.	C		1730,2044		396,938,553	21.0	26.0	25.0		12	-6.5	0.0	19	dbSNP_116	25	4150,4058		1057,2036,1011	no	coding-synonymous	CCDC155	NM_144688.4		1453,2974,1564	TT,TC,CC		49.4396,45.84,49.0736		4/563	49894152	5880,6102	1887	4104	5991	SO:0001819	synonymous_variant	147872	exon2			CCTGCCCGAGGGC		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.12C>T	19.37:g.49894152C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_144688	Q96MC3	Silent	SNP	ENST00000447857.3	37	CCDS46140.1																																																																																			C|0.523;T|0.477	0.477	strong		0.677	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688	
FZD6	8323	hgsc.bcm.edu	37	8	104343686	104343686	+	Silent	SNP	G	G	A	rs1053917	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:104343686G>A	ENST00000358755.4	+	7	2387	c.2070G>A	c.(2068-2070)ccG>ccA	p.P690P	FZD6_ENST00000523739.1_Silent_p.P658P|FZD6_ENST00000540287.1_Silent_p.P385P|FZD6_ENST00000522566.1_Silent_p.P690P	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	690					angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			TTGTTCACCCGGTTTCAGGAG	0.458													g|||	2193	0.437899	0.2829	0.5043	5008	,	,		18114	0.627		0.4493	False		,,,				2504	0.3937				p.P690P		Atlas-SNP	.											.	FZD6	61	.	0			c.G2070A						PASS	.	A	,,	1291,3115	436.4+/-344.6	174,943,1086	115.0	108.0	110.0		2070,1974,2070	-11.4	0.0	8	dbSNP_86	110	3992,4608	552.9+/-386.2	940,2112,1248	no	coding-synonymous,coding-synonymous,coding-synonymous	FZD6	NM_001164615.1,NM_001164616.1,NM_003506.3	,,	1114,3055,2334	AA,AG,GG		46.4186,29.301,40.6197	,,	690/707,658/675,690/707	104343686	5283,7723	2203	4300	6503	SO:0001819	synonymous_variant	8323	exon7			TCACCCGGTTTCA	AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"""GPCR / Class F : Frizzled receptors"""	4044	protein-coding gene	gene with protein product		603409	"""frizzled (Drosophila) homolog 6"", ""frizzled homolog 6 (Drosophila)"", ""frizzled 6, seven transmembrane spanning receptor"", ""frizzled family receptor 6"""			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.2070G>A	8.37:g.104343686G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_003506	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Silent	SNP	ENST00000358755.4	37	CCDS6298.1																																																																																			G|0.585;A|0.415	0.415	strong		0.458	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506	
ECI1	1632	hgsc.bcm.edu	37	16	2294549	2294549	+	Missense_Mutation	SNP	C	C	T	rs145543160		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2294549C>T	ENST00000301729.4	-	4	346	c.299G>A	c.(298-300)cGc>cAc	p.R100H	ECI1_ENST00000562238.1_Missense_Mutation_p.R100H|ECI1_ENST00000570258.1_Missense_Mutation_p.R41H|RP11-304L19.11_ENST00000565709.1_RNA	NM_001919.3	NP_001910.2	P42126	ECI1_HUMAN	enoyl-CoA delta isomerase 1	100					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|intramolecular oxidoreductase activity (GO:0016860)			endometrium(1)|large_intestine(2)|lung(6)	9						GACACCCGGGCGGTCCTGCAG	0.692													C|||	1	0.000199681	0.0	0.0	5008	,	,		16248	0.0		0.001	False		,,,				2504	0.0				p.R100H		Atlas-SNP	.											ECI1,NS,carcinoma,-1,1	ECI1	20	1	0			c.G299A						PASS	.	C	HIS/ARG,HIS/ARG	3,4349		0,3,2173	20.0	19.0	19.0		299,299	3.1	0.0	16	dbSNP_134	19	14,8564		0,14,4275	yes	missense,missense	ECI1	NM_001178029.1,NM_001919.3	29,29	0,17,6448	TT,TC,CC		0.1632,0.0689,0.1315	possibly-damaging,possibly-damaging	100/286,100/303	2294549	17,12913	2176	4289	6465	SO:0001583	missense	1632	exon4			CCCGGGCGGTCCT		CCDS10464.1, CCDS58410.1	16p13.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000167969	ENSG00000167969	5.3.3.8		2703	protein-coding gene	gene with protein product	"""3,2 trans-enoyl-CoA isomerase"""	600305	"""dodecenoyl-Coenzyme A delta isomerase (3,2 trans-enoyl-Coenzyme A isomerase)"", ""dodecenoyl-CoA isomerase"""	DCI		7829074	Standard	NM_001178029		Approved		uc002cpr.3	P42126	OTTHUMG00000128830	ENST00000301729.4:c.299G>A	16.37:g.2294549C>T	ENSP00000301729:p.Arg100His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	109	42	0.385321	NM_001178029	A8K512|Q13290|Q7Z2L6|Q7Z2L7|Q9BUB8|Q9BW05|Q9UDG6	Missense_Mutation	SNP	ENST00000301729.4	37	CCDS10464.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.396	1.076878	0.20227	6.89E-4	0.001632	ENSG00000167969	ENST00000301729	D	0.85702	-2.02	5.1	3.08	0.35506	Crotonase, core (1);	1.086010	0.06745	N	0.778936	T	0.78502	0.4293	L	0.52573	1.65	0.09310	N	1	P;B	0.40476	0.718;0.084	B;B	0.30105	0.111;0.024	T	0.63892	-0.6534	10	0.35671	T	0.21	-4.2812	8.5437	0.33408	0.1653:0.5146:0.3201:0.0	.	100;100	P42126-2;P42126	.;ECI1_HUMAN	H	100	ENSP00000301729:R100H	ENSP00000301729:R100H	R	-	2	0	ECI1	2234550	0.000000	0.05858	0.047000	0.18901	0.030000	0.12068	-0.936000	0.03946	0.697000	0.31718	0.650000	0.86243	CGC	C|0.998;T|0.002	0.002	strong		0.692	ECI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250768.1		
C4orf33	132321	hgsc.bcm.edu	37	4	130032843	130032843	+	Missense_Mutation	SNP	A	A	G	rs17351999	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:130032843A>G	ENST00000281146.5	+	6	1218	c.497A>G	c.(496-498)cAt>cGt	p.H166R	C4orf33_ENST00000425929.1_Missense_Mutation_p.H166R	NM_173487.2	NP_775758.2	Q8N1A6	CD033_HUMAN	chromosome 4 open reading frame 33	166			H -> R (in dbSNP:rs17351999). {ECO:0000269|PubMed:14702039}.							endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	10						GCTTTTAGCCATTGCCTAGAA	0.353													A|||	483	0.0964457	0.0083	0.1311	5008	,	,		16238	0.0655		0.161	False		,,,				2504	0.1564				p.H166R		Atlas-SNP	.											C4orf33,NS,carcinoma,+1,1	C4orf33	15	1	0			c.A497G						PASS	.	A	ARG/HIS,ARG/HIS	152,4254	105.6+/-144.1	6,140,2057	111.0	105.0	107.0		497,497	5.8	1.0	4	dbSNP_123	107	1299,7301	254.3+/-279.6	120,1059,3121	yes	missense,missense	C4orf33	NM_001099783.1,NM_173487.2	29,29	126,1199,5178	GG,GA,AA		15.1047,3.4498,11.1564	probably-damaging,probably-damaging	166/200,166/200	130032843	1451,11555	2203	4300	6503	SO:0001583	missense	132321	exon6			TTAGCCATTGCCT	AK091022	CCDS3741.1	4q28.2	2008-02-05			ENSG00000151470	ENSG00000151470			27025	protein-coding gene	gene with protein product						12477932	Standard	NM_001099783		Approved	FLJ33703	uc010iod.3	Q8N1A6	OTTHUMG00000133347	ENST00000281146.5:c.497A>G	4.37:g.130032843A>G	ENSP00000281146:p.His166Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	183	97	0.530055	NM_001099783	D3DNY2|Q6PJF3|Q8NBC5	Missense_Mutation	SNP	ENST00000281146.5	37	CCDS3741.1	222	0.10164835164835165	6	0.012195121951219513	54	0.14917127071823205	46	0.08041958041958042	116	0.15303430079155672	A	20.2	3.955322	0.73902	0.034498	0.151047	ENSG00000151470	ENST00000281146;ENST00000425929	T;T	0.47528	0.84;0.84	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.00936	0.0031	M	0.86651	2.83	0.09310	P	0.99999999004049	D	0.89917	1.0	D	0.85130	0.997	T	0.30119	-0.9989	9	0.66056	D	0.02	-20.028	15.0534	0.71894	1.0:0.0:0.0:0.0	rs17351999;rs52811016;rs17351999	166	Q8N1A6	CD033_HUMAN	R	166	ENSP00000281146:H166R;ENSP00000401090:H166R	ENSP00000281146:H166R	H	+	2	0	C4orf33	130252293	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	8.045000	0.89436	2.198000	0.70561	0.528000	0.53228	CAT	A|0.892;G|0.108	0.108	strong		0.353	C4orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257177.2	NM_173487	
MUC16	94025	hgsc.bcm.edu	37	19	8987218	8987218	+	Missense_Mutation	SNP	G	G	T	rs3764556	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8987218G>T	ENST00000397910.4	-	68	42072	c.41869C>A	c.(41869-41871)Cag>Aag	p.Q13957K	MUC16_ENST00000380951.5_Missense_Mutation_p.Q598K	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13982	SEA 13. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ACCAGGTGCTGCATGACGTTG	0.602													g|||	2179	0.435104	0.5885	0.2824	5008	,	,		12369	0.4286		0.2734	False		,,,				2504	0.5092				p.Q13957K		Atlas-SNP	.											.	MUC16	4315	.	0			c.C41869A						PASS	.	G	LYS/GLN	2175,2061		549,1077,492	100.0	102.0	101.0		41869	1.4	0.7	19	dbSNP_107	101	2313,6177		320,1673,2252	yes	missense	MUC16	NM_024690.2	53	869,2750,2744	TT,TG,GG		27.2438,48.6544,35.2664	benign	13957/14508	8987218	4488,8238	2118	4245	6363	SO:0001583	missense	94025	exon68			GGTGCTGCATGAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.41869C>A	19.37:g.8987218G>T	ENSP00000381008:p.Gln13957Lys	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	260	126	0.484615	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	807|807	0.3695054945054945|0.3695054945054945	290|290	0.5894308943089431|0.5894308943089431	97|97	0.26795580110497236|0.26795580110497236	215|215	0.3758741258741259|0.3758741258741259	205|205	0.2704485488126649|0.2704485488126649	G|G	6.661|6.661	0.490582|0.490582	0.12702|0.12702	0.513456|0.513456	0.272438|0.272438	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.27256	.|1.68;1.68	3.61|3.61	1.37|1.37	0.22104|0.22104	.|.	.|0.000000	.|0.34314	.|N	.|0.004068	.|T	.|0.00012	.|0.0000	M|M	0.88031|0.88031	2.925|2.925	.|.	.|.	.|.	.|B	.|0.22541	.|0.071	.|B	.|0.38616	.|0.277	.|T	.|0.35822	.|-0.9773	.|9	.|0.49607	.|T	.|0.09	.|.	8.3481|8.3481	0.32286|0.32286	0.0:0.0:0.5708:0.4292|0.0:0.0:0.5708:0.4292	rs3764556;rs52835054;rs57189590;rs3764556|rs3764556;rs52835054;rs57189590;rs3764556	.|13957	.|B5ME49	.|.	X|K	796|13957;598	.|ENSP00000381008:Q13957K;ENSP00000370338:Q598K	.|ENSP00000370338:Q598K	C|Q	-|-	3|1	2|0	MUC16|MUC16	8848218|8848218	0.666000|0.666000	0.27475|0.27475	0.680000|0.680000	0.29994|0.29994	0.004000|0.004000	0.04260|0.04260	1.684000|1.684000	0.37649|0.37649	0.472000|0.472000	0.27344|0.27344	-0.291000|-0.291000	0.09656|0.09656	TGC|CAG	G|0.618;T|0.382	0.382	strong		0.602	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LRP4	4038	hgsc.bcm.edu	37	11	46893108	46893108	+	Missense_Mutation	SNP	T	T	C	rs2306029	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:46893108T>C	ENST00000378623.1	-	31	4902	c.4660A>G	c.(4660-4662)Agc>Ggc	p.S1554G	LRP4-AS1_ENST00000531719.1_RNA|LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1554			S -> G (in dbSNP:rs2306029). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9693030, ECO:0000269|Ref.1}.		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)		GACACATGGCTGACCAAGACC	0.532													T|||	1841	0.367612	0.1142	0.4841	5008	,	,		17882	0.2569		0.5417	False		,,,				2504	0.5624				p.S1554G		Atlas-SNP	.											.	LRP4	160	.	0			c.A4660G						PASS	.	T	GLY/SER	858,3544		99,660,1442	113.0	91.0	98.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4660	5.8	1.0	11	dbSNP_100	98	4671,3927		1285,2101,913	yes	missense	LRP4	NM_002334.3	56	1384,2761,2355	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	45.6734,19.4911,42.5308	benign	1554/1906	46893108	5529,7471	2201	4299	6500	SO:0001583	missense	4038	exon31			CATGGCTGACCAA	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.4660A>G	11.37:g.46893108T>C	ENSP00000367888:p.Ser1554Gly	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	767	0.35119047619047616	52	0.10569105691056911	163	0.45027624309392267	153	0.2674825174825175	399	0.5263852242744064	.	18.48	3.633739	0.67130	0.194911	0.543266	ENSG00000134569	ENST00000378623	D	0.95788	-3.81	5.81	5.81	0.92471	Six-bladed beta-propeller, TolB-like (1);	0.185823	0.64402	D	0.000020	T	0.00012	0.0000	M	0.65975	2.015	0.21290	P	0.999738373	B	0.29115	0.233	B	0.39465	0.3	T	0.02358	-1.1171	9	0.59425	D	0.04	.	12.391	0.55358	0.1258:0.0:0.0:0.8742	rs2306029;rs17787852;rs17848230;rs59459638;rs2306029	1554	O75096	LRP4_HUMAN	G	1554	ENSP00000367888:S1554G	ENSP00000367888:S1554G	S	-	1	0	LRP4	46849684	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.437000	0.80417	2.210000	0.71456	0.533000	0.62120	AGC	C|0.383;N|0.000	0.383	strong		0.532	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
MYSM1	114803	hgsc.bcm.edu	37	1	59147926	59147926	+	Missense_Mutation	SNP	T	T	C	rs12139511	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:59147926T>C	ENST00000472487.1	-	8	829	c.790A>G	c.(790-792)Act>Gct	p.T264A	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	264			T -> A (in dbSNP:rs12139511). {ECO:0000269|PubMed:11572484, ECO:0000269|PubMed:14702039}.		chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					CTGTCAGAAGTAATGAATTCT	0.393													C|||	3165	0.631989	0.6589	0.6643	5008	,	,		18269	0.629		0.5875	False		,,,				2504	0.6217				p.T264A		Atlas-SNP	.											.	MYSM1	50	.	0			c.A790G						PASS	.	C	ALA/THR	2270,1390		693,884,253	138.0	129.0	132.0		790	0.9	0.0	1	dbSNP_120	132	4735,3439		1394,1947,746	yes	missense	MYSM1	NM_001085487.2	58	2087,2831,999	CC,CT,TT		42.0724,37.9781,40.8062	benign	264/829	59147926	7005,4829	1830	4087	5917	SO:0001583	missense	114803	exon8			CAGAAGTAATGAA	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.790A>G	1.37:g.59147926T>C	ENSP00000418734:p.Thr264Ala	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Missense_Mutation	SNP	ENST00000472487.1	37	CCDS41343.1	1335	0.6112637362637363	300	0.6097560975609756	240	0.6629834254143646	352	0.6153846153846154	443	0.5844327176781002	C	0.005	-2.129199	0.00342	0.620219	0.579276	ENSG00000162601	ENST00000472487	T	0.21361	2.01	4.11	0.948	0.19561	.	1.029490	0.07656	N	0.932742	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42292	-0.9460	9	0.07813	T	0.8	.	0.6661	0.00851	0.1711:0.3473:0.1642:0.3174	rs12139511;rs52807153;rs59603957;rs12139511	264	Q5VVJ2	MYSM1_HUMAN	A	264	ENSP00000418734:T264A	ENSP00000418734:T264A	T	-	1	0	MYSM1	58920514	0.001000	0.12720	0.007000	0.13788	0.500000	0.33767	0.198000	0.17217	0.077000	0.16863	-0.197000	0.12766	ACT	T|0.407;C|0.593	0.593	strong		0.393	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481	
AP4B1	10717	hgsc.bcm.edu	37	1	114443899	114443899	+	Silent	SNP	G	G	A	rs17464525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:114443899G>A	ENST00000369569.1	-	4	856	c.576C>T	c.(574-576)ggC>ggT	p.G192G	AP4B1_ENST00000369566.3_Intron|AP4B1_ENST00000256658.4_Silent_p.G192G|AP4B1_ENST00000369567.1_Intron|AP4B1-AS1_ENST00000419536.1_RNA	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit	192					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|trans-Golgi network (GO:0005802)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|prostate(3)	25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGATGACAACGCCTCCTTCCT	0.433													G|||	613	0.122404	0.0605	0.1124	5008	,	,		17226	0.1776		0.1819	False		,,,				2504	0.0951				p.G192G		Atlas-SNP	.											.	AP4B1	72	.	0			c.C576T						PASS	.	G		417,3989	204.5+/-226.7	20,377,1806	113.0	110.0	111.0		576	-4.8	0.9	1	dbSNP_123	111	1635,6965	303.4+/-306.4	148,1339,2813	no	coding-synonymous	AP4B1	NM_006594.2		168,1716,4619	AA,AG,GG		19.0116,9.4644,15.7773		192/740	114443899	2052,10954	2203	4300	6503	SO:0001819	synonymous_variant	10717	exon5			GACAACGCCTCCT	AF092094	CCDS865.1	1p13.2	2012-03-30			ENSG00000134262	ENSG00000134262			572	protein-coding gene	gene with protein product	"""beta 4 subunit of AP-4"""	607245	"""spastic paraplegia 47"""	SPG47		10066790	Standard	NM_006594		Approved	BETA-4	uc001eeb.3	Q9Y6B7	OTTHUMG00000011943	ENST00000369569.1:c.576C>T	1.37:g.114443899G>A		Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	297	148	0.498316	NM_006594	B7Z4X3|Q59EJ4|Q96CL6	Silent	SNP	ENST00000369569.1	37	CCDS865.1																																																																																			G|0.856;A|0.144	0.144	strong		0.433	AP4B1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033037.1	NM_006594	
TRIM6	117854	hgsc.bcm.edu	37	11	5625784	5625784	+	Silent	SNP	A	A	G	rs3751005	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5625784A>G	ENST00000278302.5	+	3	584	c.444A>G	c.(442-444)ctA>ctG	p.L148L	TRIM6_ENST00000507320.1_5'UTR|HBG2_ENST00000380259.2_Intron|TRIM6_ENST00000445329.1_5'UTR|TRIM6_ENST00000506134.1_5'UTR|AC015691.13_ENST00000394793.2_RNA|TRIM6_ENST00000380097.3_Silent_p.L176L|TRIM6_ENST00000515022.1_Intron|TRIM6-TRIM34_ENST00000354852.5_Silent_p.L176L|TRIM6_ENST00000380107.1_Silent_p.L122L	NM_001198645.1|NM_058166.4	NP_001185574.1|NP_477514.1	Q9C030	TRIM6_HUMAN	tripartite motif containing 6	148					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|prostate(2)|stomach(1)	22		Lung NSC(207;2.23e-07)|all_lung(207;1.81e-06)|Medulloblastoma(188;0.00225)|Breast(177;0.0101)|all_neural(188;0.0212)		Epithelial(150;1.12e-45)|BRCA - Breast invasive adenocarcinoma(625;0.00101)|LUSC - Lung squamous cell carcinoma(625;0.192)		AGGAGTCTCTAAAGAAGCTGA	0.438													A|||	431	0.0860623	0.0598	0.0836	5008	,	,		20410	0.1756		0.0109	False		,,,				2504	0.1084				p.L176L		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.A528G						PASS	.	A	,,,,	306,4096	165.8+/-197.2	9,288,1904	127.0	131.0	130.0		528,528,,,444	2.6	1.0	11	dbSNP_107	130	124,8470	64.9+/-127.2	3,118,4176	no	coding-synonymous,coding-synonymous,utr-5,intron,coding-synonymous	TRIM6,TRIM6-TRIM34	NM_001003818.2,NM_001003819.3,NM_001198644.1,NM_001198645.1,NM_058166.4	,,,,	12,406,6080	GG,GA,AA		1.4429,6.9514,3.3087	,,,,	176/517,176/843,,,148/489	5625784	430,12566	2201	4297	6498	SO:0001819	synonymous_variant	445372	exon3			GTCTCTAAAGAAG	AF220030	CCDS31389.1, CCDS31390.1, CCDS55738.1	11p15	2013-01-09	2011-01-25		ENSG00000121236	ENSG00000121236		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16277	protein-coding gene	gene with protein product		607564	"""tripartite motif-containing 6"""			11331580	Standard	NM_058166		Approved	RNF89		Q9C030	OTTHUMG00000150029	ENST00000278302.5:c.444A>G	11.37:g.5625784A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_001003819	A8K2A7|B4DDQ5|Q86WZ8|Q9HCR1	Silent	SNP	ENST00000278302.5	37	CCDS31390.1																																																																																			A|0.949;G|0.051	0.051	strong		0.438	TRIM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143376.2	NM_001003818	
R3HCC1	203069	hgsc.bcm.edu	37	8	23152334	23152334	+	Silent	SNP	A	A	G	rs15946	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:23152334A>G	ENST00000411463.1	+	8	1269	c.1269A>G	c.(1267-1269)acA>acG	p.T423T	R3HCC1_ENST00000265806.6_Silent_p.T196T|R3HCC1_ENST00000518454.1_Silent_p.T196T|R3HCC1_ENST00000522012.1_3'UTR			Q9Y3T6	R3HC1_HUMAN	R3H domain and coiled-coil containing 1	423							nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)			central_nervous_system(1)|skin(2)	3						GGCCCCTCACACAGGGAACCA	0.597													G|||	3892	0.777157	0.8109	0.6988	5008	,	,		16126	0.9613		0.7018	False		,,,				2504	0.6748				p.T196T		Atlas-SNP	.											.	R3HCC1	11	.	0			c.A588G						PASS	.	G		1114,270		449,216,27	49.0	49.0	49.0		588	-9.6	0.4	8	dbSNP_52	49	2345,837		861,623,107	no	coding-synonymous	R3HCC1	NM_001136108.1		1310,839,134	GG,GA,AA		26.3042,19.5087,24.2444		196/254	23152334	3459,1107	692	1591	2283	SO:0001819	synonymous_variant	203069	exon7			CCTCACACAGGGA		CCDS47826.1	8p21.3	2012-05-23		2005-11-20	ENSG00000104679	ENSG00000104679			27329	protein-coding gene	gene with protein product						12477932	Standard	XM_005273427		Approved	DKFZp564N123	uc003xdf.3	Q9Y3T6	OTTHUMG00000163786	ENST00000411463.1:c.1269A>G	8.37:g.23152334A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_001136108	B7ZLI1	Silent	SNP	ENST00000411463.1	37																																																																																				A|0.205;C|0.000;G|0.795	0.795	strong		0.597	R3HCC1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001136108	
THAP8	199745	hgsc.bcm.edu	37	19	36530428	36530428	+	Missense_Mutation	SNP	G	G	A	rs34250145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:36530428G>A	ENST00000292894.1	-	3	1013	c.469C>T	c.(469-471)Cct>Tct	p.P157S	AC002116.7_ENST00000586962.1_RNA|THAP8_ENST00000538849.1_Missense_Mutation_p.P12S|THAP8_ENST00000524106.1_5'Flank	NM_152658.2	NP_689871.1	Q8NA92	THAP8_HUMAN	THAP domain containing 8	157			P -> S (in dbSNP:rs34250145). {ECO:0000269|PubMed:15489334}.				DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GACCGCTCAGGAGTTGGCGCA	0.692													g|||	446	0.0890575	0.0318	0.2622	5008	,	,		15842	0.0367		0.0964	False		,,,				2504	0.09				p.P157S		Atlas-SNP	.											.	THAP8	11	.	0			c.C469T						PASS	.	G	SER/PRO	169,4231		2,165,2033	15.0	15.0	15.0		469	-0.7	0.0	19	dbSNP_126	15	824,7764		27,770,3497	yes	missense	THAP8	NM_152658.2	74	29,935,5530	AA,AG,GG		9.5948,3.8409,7.6455	possibly-damaging	157/275	36530428	993,11995	2200	4294	6494	SO:0001583	missense	199745	exon3			GCTCAGGAGTTGG	AK057453	CCDS33000.1	19q13.13	2013-01-25			ENSG00000161277	ENSG00000161277		"""THAP (C2CH-type zinc finger) domain containing"""	23191	protein-coding gene	gene with protein product		612536				12575992	Standard	NM_152658		Approved	FLJ32891	uc002oda.1	Q8NA92	OTTHUMG00000048138	ENST00000292894.1:c.469C>T	19.37:g.36530428G>A	ENSP00000292894:p.Pro157Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	112	46	0.410714	NM_152658	Q0P5Z7|Q96M21	Missense_Mutation	SNP	ENST00000292894.1	37	CCDS33000.1	189	0.08653846153846154	23	0.046747967479674794	77	0.212707182320442	16	0.027972027972027972	73	0.09630606860158311	g	11.30	1.596797	0.28445	0.038409	0.095948	ENSG00000161277	ENST00000292894;ENST00000392182;ENST00000538849	D;T	0.90069	-2.61;1.82	4.54	-0.702	0.11265	.	1.768490	0.05563	U	0.569616	T	0.00210	0.0006	L	0.27053	0.805	0.80722	P	0.0	B	0.18461	0.028	B	0.15052	0.012	T	0.10177	-1.0641	9	0.09338	T	0.73	-13.0061	6.1343	0.20223	0.186:0.2854:0.5286:0.0	rs34250145;rs34250145	157	Q8NA92	THAP8_HUMAN	S	157;157;12	ENSP00000292894:P157S;ENSP00000445493:P12S	ENSP00000292894:P157S	P	-	1	0	THAP8	41222268	0.000000	0.05858	0.005000	0.12908	0.007000	0.05969	-0.644000	0.05415	0.093000	0.17368	0.552000	0.68991	CCT	G|0.931;A|0.069	0.069	strong		0.692	THAP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379036.1	NM_152658	
KIF5B	3799	hgsc.bcm.edu	37	10	32306151	32306151	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:32306151C>T	ENST00000302418.4	-	24	3138	c.2681G>A	c.(2680-2682)cGc>cAc	p.R894H	KIF5B_ENST00000493889.1_5'UTR	NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	894					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)		KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				TTGCTGATAGCGTTTGCGATC	0.428			T	"""RET, ALK"""	NSCLC																																p.R894H		Atlas-SNP	.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	KIF5B,rectum,carcinoma,-1,1	KIF5B	81	1	0			c.G2681A						scavenged	.						308.0	271.0	283.0					10																	32306151		2203	4300	6503	SO:0001583	missense	3799	exon24			TGATAGCGTTTGC	X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"""Kinesins"""	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.2681G>A	10.37:g.32306151C>T	ENSP00000307078:p.Arg894His	Somatic	301	1	0.00332226		WXS	Illumina HiSeq	Phase_I	355	4	0.0112676	NM_004521	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	C	31	5.090879	0.94149	.	.	ENSG00000170759	ENST00000302418	T	0.77750	-1.12	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.90290	0.6963	M	0.88570	2.965	0.58432	D	0.999999	D	0.89917	1.0	D	0.72625	0.978	D	0.91641	0.5327	10	0.87932	D	0	.	19.5519	0.95324	0.0:1.0:0.0:0.0	.	894	P33176	KINH_HUMAN	H	894	ENSP00000307078:R894H	ENSP00000307078:R894H	R	-	2	0	KIF5B	32346157	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.747000	0.85070	2.623000	0.88846	0.467000	0.42956	CGC	.	.	none		0.428	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521	
DHX58	79132	hgsc.bcm.edu	37	17	40255812	40255812	+	Missense_Mutation	SNP	C	C	T	rs2074160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:40255812C>T	ENST00000251642.3	-	12	1790	c.1568G>A	c.(1567-1569)cGg>cAg	p.R523Q		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	523	Repressor domain.		R -> Q (in dbSNP:rs2074160).		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CTGCAGATCCCGGATCTGGGG	0.612													C|||	685	0.136781	0.3086	0.0231	5008	,	,		18710	0.1667		0.0239	False		,,,				2504	0.0706				p.R523Q		Atlas-SNP	.											.	DHX58	39	.	0			c.G1568A						PASS	.	C	GLN/ARG	1225,3181		167,891,1145	33.0	32.0	32.0		1568	-5.6	0.1	17	dbSNP_96	32	165,8435		2,161,4137	yes	missense	DHX58	NM_024119.2	43	169,1052,5282	TT,TC,CC		1.9186,27.803,10.6874	benign	523/679	40255812	1390,11616	2203	4300	6503	SO:0001583	missense	79132	exon12			AGATCCCGGATCT	BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"""RNA helicase LGP2"""	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.1568G>A	17.37:g.40255812C>T	ENSP00000251642:p.Arg523Gln	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_024119	Q9HAM6	Missense_Mutation	SNP	ENST00000251642.3	37	CCDS11416.1	255	0.11675824175824176	159	0.3231707317073171	6	0.016574585635359115	76	0.13286713286713286	14	0.018469656992084433	C	5.340	0.248132	0.10130	0.27803	0.019186	ENSG00000108771	ENST00000251642	T	0.04551	3.6	5.62	-5.56	0.02529	.	1.612920	0.03016	N	0.150031	T	0.00012	0.0000	N	0.16066	0.365	0.80722	P	0.0	B;B	0.14438	0.006;0.01	B;B	0.06405	0.002;0.002	T	0.48525	-0.9028	9	0.11182	T	0.66	.	7.5574	0.27833	0.134:0.3672:0.0:0.4988	rs2074160;rs52795470;rs2074160	516;523	B7Z455;Q96C10	.;DHX58_HUMAN	Q	523	ENSP00000251642:R523Q	ENSP00000251642:R523Q	R	-	2	0	DHX58	37509338	0.000000	0.05858	0.079000	0.20413	0.553000	0.35397	-2.754000	0.00790	-0.693000	0.05121	-0.749000	0.03505	CGG	C|0.886;T|0.114	0.114	strong		0.612	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119	
TCF4	6925	hgsc.bcm.edu	37	18	52895531	52895531	+	Silent	SNP	T	T	C	rs8766	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:52895531T>C	ENST00000356073.4	-	19	2540	c.1929A>G	c.(1927-1929)tcA>tcG	p.S643S	TCF4_ENST00000568740.1_Silent_p.S618S|TCF4_ENST00000537856.3_Silent_p.S513S|TCF4_ENST00000543082.1_Silent_p.S601S|TCF4_ENST00000568673.1_Silent_p.S623S|TCF4_ENST00000561831.3_Silent_p.S483S|TCF4_ENST00000570287.2_Silent_p.S483S|TCF4_ENST00000457482.3_Silent_p.S487S|TCF4_ENST00000544241.2_Silent_p.S576S|TCF4_ENST00000537578.1_Silent_p.S623S|TCF4_ENST00000570177.2_Silent_p.S513S|TCF4_ENST00000540999.1_Silent_p.S619S|TCF4_ENST00000564999.1_Silent_p.S643S|TCF4_ENST00000566279.1_Silent_p.S587S|TCF4_ENST00000561992.1_Silent_p.S513S|TCF4_ENST00000564228.1_Silent_p.S572S|TCF4_ENST00000354452.3_Silent_p.S647S|TCF4_ENST00000565018.2_Silent_p.S647S|TCF4_ENST00000566286.1_Silent_p.S640S|TCF4_ENST00000567880.1_Silent_p.S583S|TCF4_ENST00000564403.2_Silent_p.S653S|TCF4_ENST00000398339.1_Silent_p.S749S	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	643					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GGGGAGGCTCTGAGGACACCT	0.498													C|||	1715	0.342452	0.2965	0.366	5008	,	,		17666	0.4008		0.4155	False		,,,				2504	0.2526				p.S749S		Atlas-SNP	.											.	TCF4	178	.	0			c.A2247G						PASS	.	C	,	1401,3005	687.2+/-404.8	221,959,1023	125.0	114.0	118.0		1941,1929	-5.4	0.5	18	dbSNP_52	118	3342,5258	643.2+/-399.9	658,2026,1616	no	coding-synonymous,coding-synonymous	TCF4	NM_001083962.1,NM_003199.2	,	879,2985,2639	CC,CT,TT		38.8605,31.7975,36.4678	,	647/672,643/668	52895531	4743,8263	2203	4300	6503	SO:0001819	synonymous_variant	6925	exon20			AGGCTCTGAGGAC	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"""Basic helix-loop-helix proteins"""	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1929A>G	18.37:g.52895531T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Silent	SNP	ENST00000356073.4	37	CCDS11960.1																																																																																			T|0.626;C|0.374	0.374	strong		0.498	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	
CTSW	1521	hgsc.bcm.edu	37	11	65650883	65650883	+	Silent	SNP	A	A	G	rs35841983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65650883A>G	ENST00000307886.3	+	9	1054	c.1008A>G	c.(1006-1008)caA>caG	p.Q336Q	CTSW_ENST00000528419.1_Silent_p.Q336Q|FIBP_ENST00000426652.2_5'Flank	NM_001335.3	NP_001326	P56202	CATW_HUMAN	cathepsin W	336					immune response (GO:0006955)	membrane (GO:0016020)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)	9				READ - Rectum adenocarcinoma(159;0.168)		GGGGGGCCCAATGGGGAGAGA	0.602													A|||	89	0.0177716	0.0416	0.0159	5008	,	,		14914	0.0		0.0229	False		,,,				2504	0.0				p.Q336Q		Atlas-SNP	.											.	CTSW	18	.	0			c.A1008G						PASS	.	A		125,4277	94.8+/-133.5	3,119,2079	67.0	73.0	71.0		1008	-10.0	0.0	11	dbSNP_126	71	243,8349	97.7+/-159.3	3,237,4056	no	coding-synonymous	CTSW	NM_001335.3		6,356,6135	GG,GA,AA		2.8282,2.8396,2.8321		336/377	65650883	368,12626	2201	4296	6497	SO:0001819	synonymous_variant	1521	exon9			GGCCCAATGGGGA	AF055903	CCDS8117.1	11q13.1	2008-02-01	2006-12-05		ENSG00000172543	ENSG00000172543		"""Cathepsins"""	2546	protein-coding gene	gene with protein product		602364	"""cathepsin W (lymphopain)"""			9108299, 9675123	Standard	NM_001335		Approved		uc001ogc.1	P56202	OTTHUMG00000166663	ENST00000307886.3:c.1008A>G	11.37:g.65650883A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_001335	Q86VT4	Silent	SNP	ENST00000307886.3	37	CCDS8117.1																																																																																			A|0.975;G|0.025	0.025	strong		0.602	CTSW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391042.1	NM_001335	
GLI1	2735	hgsc.bcm.edu	37	12	57861785	57861785	+	Silent	SNP	T	T	C	rs61734545	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57861785T>C	ENST00000228682.2	+	10	1177	c.1086T>C	c.(1084-1086)taT>taC	p.Y362Y	GLI1_ENST00000546141.1_Silent_p.Y321Y|GLI1_ENST00000543426.1_Silent_p.Y234Y	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	362					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			AGAAGCCGTATGTATGTAAGC	0.507													T|||	76	0.0151757	0.0023	0.0144	5008	,	,		23089	0.0		0.0249	False		,,,				2504	0.0389				p.Y362Y	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											GLI1,NS,carcinoma,+1,1	GLI1	141	1	0			c.T1086C						PASS	.	T	,,	38,4368	43.1+/-76.7	1,36,2166	69.0	53.0	58.0		702,963,1086	-4.7	0.1	12	dbSNP_129	58	287,8313	105.0+/-166.0	4,279,4017	no	coding-synonymous,coding-synonymous,coding-synonymous	GLI1	NM_001160045.1,NM_001167609.1,NM_005269.2	,,	5,315,6183	CC,CT,TT		3.3372,0.8625,2.4988	,,	234/979,321/1066,362/1107	57861785	325,12681	2203	4300	6503	SO:0001819	synonymous_variant	2735	exon10			GCCGTATGTATGT		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.1086T>C	12.37:g.57861785T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Silent	SNP	ENST00000228682.2	37	CCDS8940.1																																																																																			T|0.978;C|0.022	0.022	strong		0.507	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
SKP2	6502	hgsc.bcm.edu	37	5	36163858	36163858	+	Splice_Site	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:36163858C>T	ENST00000274255.6	+	3	588	c.392C>T	c.(391-393)gCg>gTg	p.A131V	SKP2_ENST00000508514.1_Intron|SKP2_ENST00000546211.1_Intron|SKP2_ENST00000274254.5_Splice_Site_p.A131V	NM_005983.3	NP_005974.2	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase	131	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|cellular response to cell-matrix adhesion (GO:0071460)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	identical protein binding (GO:0042802)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|ovary(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TATCGCCTAGCGTAAGTATTT	0.458																																					p.A131V		Atlas-SNP	.											.	SKP2	70	.	0			c.C392T						PASS	.						118.0	101.0	107.0					5																	36163858		2203	4300	6503	SO:0001630	splice_region_variant	6502	exon3			GCCTAGCGTAAGT	U33761	CCDS3915.1, CCDS3916.1, CCDS58944.1	5p13	2012-02-23	2012-02-23		ENSG00000145604	ENSG00000145604		"""F-boxes / Leucine-rich repeats"""	10901	protein-coding gene	gene with protein product		601436	"""S-phase kinase-associated protein 2 (p45)"""			8646875	Standard	NM_005983		Approved	FBXL1, FBL1, p45	uc003jkc.2	Q13309	OTTHUMG00000131106	ENST00000274255.6:c.392+1C>T	5.37:g.36163858C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	185	95	0.513514	NM_032637	A8K5E0|B4DJT4|Q8TDZ0|Q8TDZ1|Q9BV69	Missense_Mutation	SNP	ENST00000274255.6	37	CCDS3916.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.565020	0.45694	.	.	ENSG00000145604	ENST00000274254;ENST00000274255;ENST00000308927;ENST00000513151	T;T;T	0.55930	0.49;0.49;0.49	4.92	4.05	0.47172	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.382188	0.30723	N	0.009015	T	0.37376	0.1001	N	0.24115	0.695	0.80722	D	1	B;B	0.23806	0.059;0.091	B;B	0.09377	0.003;0.004	T	0.31223	-0.9951	10	0.72032	D	0.01	-7.66	11.5359	0.50636	0.0:0.9161:0.0:0.0839	.	131;131	Q13309-2;Q13309	.;SKP2_HUMAN	V	131;131;97;131	ENSP00000274254:A131V;ENSP00000274255:A131V;ENSP00000423188:A131V	ENSP00000274254:A131V	A	+	2	0	SKP2	36199615	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.113000	0.57851	1.437000	0.47472	0.650000	0.86243	GCG	.	.	none		0.458	SKP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253769.2	NM_005983	Missense_Mutation
SMPD4	55627	hgsc.bcm.edu	37	2	130912778	130912778	+	Silent	SNP	A	A	G	rs149268431	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:130912778A>G	ENST00000409031.1	-	15	2609	c.1461T>C	c.(1459-1461)ttT>ttC	p.F487F	SMPD4_ENST00000426662.2_Silent_p.F123F|SMPD4_ENST00000453750.1_Silent_p.F236F|SMPD4_ENST00000431183.2_Silent_p.F385F|SMPD4_ENST00000351288.6_Silent_p.F458F|SMPD4_ENST00000443958.2_Silent_p.F151F|SMPD4_ENST00000473720.1_5'Flank|SMPD4_ENST00000452225.2_Silent_p.F228F|SMPD4_ENST00000339679.7_Silent_p.F345F	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	448					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	CGCGGTTCAGAAAGCCCACAA	0.607																																					p.F487F		Atlas-SNP	.											SMPD4,NS,adenoma,0,1	SMPD4	67	1	0			c.T1461C						PASS	.						97.0	89.0	92.0					2																	130912778		2203	4300	6503	SO:0001819	synonymous_variant	55627	exon15			GTTCAGAAAGCCC	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.1461T>C	2.37:g.130912778A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	153	15	0.0980392	NM_017951	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Silent	SNP	ENST00000409031.1	37	CCDS42751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	2.815|2.815	-0.246012|-0.246012	0.05906|0.05906	.|.	.|.	ENSG00000136699|ENSG00000136699	ENST00000439886|ENST00000430682	.|.	.|.	.|.	4.24|4.24	0.732|0.732	0.18283|0.18283	.|.	0.052113|.	0.85682|.	D|.	0.000000|.	T|T	0.57373|0.57373	0.2049|0.2049	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49854|0.49854	-0.8895|-0.8895	6|4	0.54805|.	T|.	0.06|.	.|.	9.4799|9.4799	0.38895|0.38895	0.3955:0.0:0.6045:0.0|0.3955:0.0:0.6045:0.0	.|.	.|.	.|.	.|.	S|P	362|169	.|.	ENSP00000401648:F362S|.	F|S	-|-	2|1	0|0	SMPD4|SMPD4	130629248|130629248	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.078000|0.078000	0.17371|0.17371	1.128000|1.128000	0.31369|0.31369	-0.037000|-0.037000	0.13646|0.13646	-0.684000|-0.684000	0.03749|0.03749	TTC|TCT	A|0.998;G|0.002	0.002	strong		0.607	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751	
OBP2A	29991	hgsc.bcm.edu	37	9	138440554	138440554	+	Splice_Site	SNP	G	G	C	rs55695858	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:138440554G>C	ENST00000539850.1	+	5	415	c.389G>C	c.(388-390)gGt>gCt	p.G130A	OBP2A_ENST00000342114.4_Missense_Mutation_p.G107A|OBP2A_ENST00000371776.1_Splice_Site_p.G130A|OBP2A_ENST00000340780.3_Missense_Mutation_p.V152L			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	130			G -> A (in dbSNP:rs55695858).		response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		TCACCTGCAGGTAGGAATCCT	0.582													.|||	869	0.173522	0.1286	0.1369	5008	,	,		15862	0.1567		0.2525	False		,,,				2504	0.1963				p.G130A		Atlas-SNP	.											.	OBP2A	21	.	0			c.G389C						PASS	.	G	ALA/GLY	661,3745	280.5+/-275.4	58,545,1600	76.0	69.0	71.0		389	2.5	0.1	9	dbSNP_129	71	2275,6325	381.9+/-340.2	305,1665,2330	yes	missense-near-splice	OBP2A	NM_014582.2	60	363,2210,3930	CC,CG,GG		26.4535,15.0023,22.5742	probably-damaging	130/171	138440554	2936,10070	2203	4300	6503	SO:0001630	splice_region_variant	29991	exon5			CTGCAGGTAGGAA	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.389-1G>C	9.37:g.138440554G>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	179	90	0.502793	NM_014582	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Missense_Mutation	SNP	ENST00000539850.1	37	CCDS6992.1	410|410	0.18772893772893773|0.18772893772893773	69|69	0.1402439024390244|0.1402439024390244	63|63	0.17403314917127072|0.17403314917127072	84|84	0.14685314685314685|0.14685314685314685	194|194	0.2559366754617414|0.2559366754617414	g|g	14.94|14.94	2.685917|2.685917	0.47991|0.47991	0.150023|0.150023	0.264535|0.264535	ENSG00000122136|ENSG00000122136	ENST00000342114;ENST00000371776;ENST00000539850|ENST00000340780	T;T;T|T	0.10382|0.28895	2.88;3.14;3.14|1.59	2.49|2.49	2.49|2.49	0.30216|0.30216	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.83483|0.83483	2.645|2.645	0.45979|0.45979	P|P	0.0012010000000000076|0.0012010000000000076	D;P|P	0.76494|0.36222	0.999;0.845|0.544	D;P|B	0.87578|0.34873	0.998;0.585|0.191	T|T	0.14671|0.14671	-1.0464|-1.0464	8|8	0.40728|0.27785	T|T	0.16|0.31	-1.3376|-1.3376	8.6552|8.6552	0.34060|0.34060	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs55695858;rs61739461|rs55695858;rs61739461	107;130|152	Q5T8A4;Q9NY56|Q5T8A5	.;OBP2A_HUMAN|.	A|L	107;130;130|152	ENSP00000340950:G107A;ENSP00000360841:G130A;ENSP00000441028:G130A|ENSP00000342097:V152L	ENSP00000340950:G107A|ENSP00000342097:V152L	G|V	+|+	2|1	0|0	OBP2A|OBP2A	137580375|137580375	0.056000|0.056000	0.20664|0.20664	0.127000|0.127000	0.21898|0.21898	0.498000|0.498000	0.33706|0.33706	1.149000|1.149000	0.31626|0.31626	1.711000|1.711000	0.51337|0.51337	0.480000|0.480000	0.44947|0.44947	GGT|GTA	G|0.790;C|0.210	0.210	strong		0.582	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582	Missense_Mutation
DYDC2	84332	hgsc.bcm.edu	37	10	82126541	82126541	+	Missense_Mutation	SNP	C	C	G	rs36027713	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:82126541C>G	ENST00000372199.1	+	6	966	c.368C>G	c.(367-369)cCa>cGa	p.P123R	DYDC2_ENST00000372197.1_Missense_Mutation_p.P123R|DYDC2_ENST00000372198.1_Missense_Mutation_p.P137R|DYDC2_ENST00000256039.2_Missense_Mutation_p.P123R|DYDC2_ENST00000444807.2_Missense_Mutation_p.P123R			Q96IM9	DYDC2_HUMAN	DPY30 domain containing 2	123										breast(1)|large_intestine(3)|lung(6)|skin(1)	11			Colorectal(32;0.229)			GAATTCCTGCCAGGTACTTCC	0.468													C|||	43	0.00858626	0.0	0.0144	5008	,	,		18616	0.0		0.0308	False		,,,				2504	0.002				p.P137R		Atlas-SNP	.											DYDC2,NS,carcinoma,+1,1	DYDC2	18	1	0			c.C410G						PASS	.	C	ARG/PRO	24,4382	31.7+/-61.6	0,24,2179	108.0	111.0	110.0		368	3.8	0.0	10	dbSNP_126	110	215,8385	90.4+/-152.6	2,211,4087	yes	missense	DYDC2	NM_032372.4	103	2,235,6266	GG,GC,CC		2.5,0.5447,1.8376	possibly-damaging	123/178	82126541	239,12767	2203	4300	6503	SO:0001583	missense	84332	exon4			TCCTGCCAGGTAC	BC018606	CCDS7367.1, CCDS58088.1	10q23.1	2006-06-16			ENSG00000133665	ENSG00000133665			23468	protein-coding gene	gene with protein product						12477932	Standard	NM_032372		Approved	bA36D19.6, MGC16186	uc031pwk.1	Q96IM9	OTTHUMG00000018610	ENST00000372199.1:c.368C>G	10.37:g.82126541C>G	ENSP00000361273:p.Pro123Arg	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_001270042	D3DWD6|Q5QP07|Q5QP11	Missense_Mutation	SNP	ENST00000372199.1	37	CCDS7367.1	31	0.014194139194139194	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	25	0.032981530343007916	C	14.26	2.481710	0.44147	0.005447	0.025	ENSG00000133665	ENST00000372199;ENST00000372198;ENST00000372197;ENST00000444807;ENST00000411538;ENST00000256039	T;T;T;T;T	0.67698	-0.17;-0.28;-0.17;-0.17;-0.17	4.68	3.77	0.43336	.	0.122835	0.37623	N	0.002007	T	0.26629	0.0651	L	0.32530	0.975	0.09310	N	1	B	0.34329	0.449	B	0.26864	0.074	T	0.38394	-0.9663	10	0.54805	T	0.06	-9.1269	10.9297	0.47211	0.0:0.7898:0.2102:0.0	rs36027713;rs61859208	123	Q96IM9	DYDC2_HUMAN	R	123;137;123;123;123;123	ENSP00000361273:P123R;ENSP00000361272:P137R;ENSP00000361271:P123R;ENSP00000410285:P123R;ENSP00000256039:P123R	ENSP00000256039:P123R	P	+	2	0	DYDC2	82116521	0.006000	0.16342	0.014000	0.15608	0.001000	0.01503	1.492000	0.35594	1.558000	0.49541	-0.211000	0.12701	CCA	C|0.982;G|0.018	0.018	strong		0.468	DYDC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049063.1	NM_032372	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052958	33052958	+	Missense_Mutation	SNP	C	C	T	rs1042335	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33052958C>T	ENST00000418931.2	+	3	712	c.596C>T	c.(595-597)aCc>aTc	p.T199I		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	199	Beta-2.|Ig-like C1-type.		T -> I (in allele DPB1*01:01, allele DPB1*03:01, allele DPB1*05:01, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*09:01, allele DPB1*09:02, allele DPB1*13:01, allele DPB1*14:01, allele DPB1*15:01, allele DPB1*18:01, allele DPB1*19:01, allele DPB1*20:01, allele DPB1*26:01, allele DPB1*45:01 and allele DPB1*85:01; dbSNP:rs1042335). {ECO:0000269|PubMed:6330724}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GATGTCTACACCTGCCAAGTG	0.577													.|||	2322	0.463658	0.5976	0.3314	5008	,	,		19045	0.621		0.3151	False		,,,				2504	0.3671				p.T199I		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.C596T						PASS	.	T	ILE/THR	1688,1332		460,768,282	91.0	92.0	92.0		596	0.8	0.8	6	dbSNP_86	92	1607,3809		234,1139,1335	no	missense	HLA-DPB1	NM_002121.5	89	694,1907,1617	TT,TC,CC		29.6713,44.106,39.0588	benign	199/259	33052958	3295,5141	1510	2708	4218	SO:0001583	missense	3115	exon3			TCTACACCTGCCA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.596C>T	6.37:g.33052958C>T	ENSP00000408146:p.Thr199Ile	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	249	106	0.425703	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	960|960	0.43956043956043955|0.43956043956043955	290|290	0.5894308943089431|0.5894308943089431	110|110	0.30386740331491713|0.30386740331491713	327|327	0.5716783216783217|0.5716783216783217	233|233	0.3073878627968338|0.3073878627968338	T|T	12.07|12.07	1.827253|1.827253	0.32329|0.32329	0.55894|0.55894	0.296713|0.296713	ENSG00000223865|ENSG00000223865	ENST00000416804|ENST00000418931;ENST00000411942;ENST00000422592;ENST00000428835	.|T;T	.|0.03468	.|3.92;3.92	3.74|3.74	0.814|0.814	0.18756|0.18756	.|Immunoglobulin/major histocompatibility complex, conserved site (1);Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	.|0.320608	.|0.29273	.|N	.|0.012630	T|T	0.02767|0.02767	0.0083|0.0083	M|M	0.85710|0.85710	2.77|2.77	0.09310|0.09310	P|P	0.9999999915136|0.9999999915136	.|B;B;B	.|0.27910	.|0.023;0.193;0.023	.|B;B;B	.|0.35899	.|0.081;0.213;0.044	T|T	0.11397|0.11397	-1.0589|-1.0589	4|9	.|0.48119	.|T	.|0.1	.|.	5.5056|5.5056	0.16852|0.16852	0.0:0.6367:0.164:0.1992|0.0:0.6367:0.164:0.1992	rs1042335;rs3173287;rs17406024;rs17845374;rs17858227;rs59491258|rs1042335;rs3173287;rs17406024;rs17845374;rs17858227;rs59491258	.|165;209;199	.|A2ALJ6;Q59GY1;P04440	.|.;.;DPB1_HUMAN	S|I	166|199;169;10;176	.|ENSP00000408146:T199I;ENSP00000412654:T176I	.|ENSP00000389210:T169I	P|T	+|+	1|2	0|0	HLA-DPB1|HLA-DPB1	33160936|33160936	0.012000|0.012000	0.17670|0.17670	0.794000|0.794000	0.32065|0.32065	0.976000|0.976000	0.68499|0.68499	-0.014000|-0.014000	0.12656|0.12656	0.036000|0.036000	0.15547|0.15547	-0.256000|-0.256000	0.11100|0.11100	CCT|ACC	C|0.607;T|0.393	0.393	strong		0.577	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
ZNF839	55778	hgsc.bcm.edu	37	14	102792631	102792631	+	Missense_Mutation	SNP	G	G	A	rs7158139	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102792631G>A	ENST00000558850.1	+	2	600	c.250G>A	c.(250-252)Gat>Aat	p.D84N	ZNF839_ENST00000442396.2_Missense_Mutation_p.D200N|ZNF839_ENST00000559185.1_Missense_Mutation_p.D84N|ZNF839_ENST00000262236.5_Missense_Mutation_p.D84N	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	84							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						CAAGGCTCCAGATGAACAGGG	0.537													A|||	2094	0.418131	0.73	0.415	5008	,	,		17657	0.3403		0.171	False		,,,				2504	0.3333				p.D200N		Atlas-SNP	.											.	ZNF839	41	.	0			c.G598A						PASS	.	A	ASN/ASP	2371,1407		726,919,244	30.0	31.0	30.0		598	-6.3	0.0	14	dbSNP_116	30	1401,6823		129,1143,2840	yes	missense	ZNF839	NM_018335.3	23	855,2062,3084	AA,AG,GG		17.0355,37.2419,31.4281	benign	200/928	102792631	3772,8230	1889	4112	6001	SO:0001583	missense	55778	exon2			GCTCCAGATGAAC	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.250G>A	14.37:g.102792631G>A	ENSP00000453363:p.Asp84Asn	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Missense_Mutation	SNP	ENST00000558850.1	37	CCDS58336.1	811	0.37133699633699635	348	0.7073170731707317	150	0.4143646408839779	200	0.34965034965034963	113	0.14907651715039577	A	0.964	-0.702287	0.03255	0.627581	0.170355	ENSG00000022976	ENST00000442396;ENST00000262236	T;T	0.35605	1.3;1.3	5.08	-6.29	0.02013	.	1.489540	0.06200	N	0.683141	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.32745	-0.9895	9	0.02654	T	1	.	6.9775	0.24683	0.3301:0.3395:0.3304:0.0	rs7158139;rs52827842;rs7158139	200;84;84	A8K0R7-5;A8K0R7-2;A8K0R7	.;.;ZN839_HUMAN	N	200;84	ENSP00000399863:D200N;ENSP00000262236:D84N	ENSP00000262236:D84N	D	+	1	0	ZNF839	101862384	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.150000	0.10189	-2.202000	0.00745	-3.173000	0.00056	GAT	G|0.622;A|0.378	0.378	strong		0.537	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
TRPM6	140803	hgsc.bcm.edu	37	9	77436641	77436641	+	Silent	SNP	G	G	A	rs7018994	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:77436641G>A	ENST00000360774.1	-	8	1191	c.954C>T	c.(952-954)ggC>ggT	p.G318G	TRPM6_ENST00000376872.3_Silent_p.G318G|TRPM6_ENST00000361255.3_Silent_p.G313G|TRPM6_ENST00000451710.3_Silent_p.G318G|TRPM6_ENST00000483186.1_5'UTR|TRPM6_ENST00000376871.3_Silent_p.G318G|TRPM6_ENST00000449912.2_Silent_p.G313G|TRPM6_ENST00000376864.4_Silent_p.G318G	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	318					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						CCCTACCTGTGCCCTCACACA	0.572													G|||	1797	0.358826	0.0673	0.4438	5008	,	,		17635	0.5536		0.3787	False		,,,				2504	0.4714				p.G318G		Atlas-SNP	.											.	TRPM6	377	.	0			c.C954T						PASS	.	G	,,	512,3894	234.6+/-247.4	26,460,1717	143.0	105.0	118.0		939,939,954	4.6	1.0	9	dbSNP_116	118	3043,5557	467.6+/-367.1	549,1945,1806	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	575,2405,3523	AA,AG,GG		35.3837,11.6205,27.3335	,,	313/2018,313/2018,318/2023	77436641	3555,9451	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon8			ACCTGTGCCCTCA	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.954C>T	9.37:g.77436641G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	40	0.555556	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																			G|0.701;A|0.299	0.299	strong		0.572	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
ZNF12	7559	hgsc.bcm.edu	37	7	6731672	6731672	+	Missense_Mutation	SNP	G	G	C	rs61731528	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:6731672G>C	ENST00000405858.1	-	5	1442	c.901C>G	c.(901-903)Cag>Gag	p.Q301E	AC073343.13_ENST00000366167.2_RNA|ZNF12_ENST00000404360.1_Missense_Mutation_p.Q227E|AC073343.2_ENST00000577401.1_RNA|ZNF12_ENST00000342651.5_Missense_Mutation_p.Q263E	NM_006956.2|NM_016265.3	NP_008887.2|NP_057349.2	P17014	ZNF12_HUMAN	zinc finger protein 12	301					negative regulation of transcription, DNA-templated (GO:0045892)|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(2)|endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(3)	16		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)		TTCCCACACTGATTACATTCG	0.423													G|||	93	0.0185703	0.003	0.036	5008	,	,		20118	0.0		0.0427	False		,,,				2504	0.0215				p.Q301E		Atlas-SNP	.											.	ZNF12	53	.	0			c.C901G						PASS	.	G	GLU/GLN,GLU/GLN	45,4353	44.6+/-78.6	1,43,2155	77.0	85.0	82.0		787,901	-0.1	0.0	7	dbSNP_129	82	297,8299	106.2+/-167.1	3,291,4004	yes	missense,missense	ZNF12	NM_006956.2,NM_016265.3	29,29	4,334,6159	CC,CG,GG		3.4551,1.0232,2.632	possibly-damaging,possibly-damaging	263/660,301/698	6731672	342,12652	2199	4298	6497	SO:0001583	missense	7559	exon5			CACACTGATTACA	X52334, AB021643	CCDS47538.1, CCDS47539.1	7p21.1	2013-01-08	2005-06-09		ENSG00000164631	ENSG00000164631		"""Zinc fingers, C2H2-type"", ""-"""	12902	protein-coding gene	gene with protein product		194536	"""zinc finger protein 325"""	ZNF325			Standard	NM_016265		Approved	KOX3, GIOT-3	uc003sqt.1	P17014	OTTHUMG00000151910	ENST00000405858.1:c.901C>G	7.37:g.6731672G>C	ENSP00000385939:p.Gln301Glu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	30	0.38961	NM_016265	A8MYC4|A8WFQ8|B2RNQ7|B4DF45|Q6N016|Q8NHZ0|Q9H9P0|Q9ULZ6	Missense_Mutation	SNP	ENST00000405858.1	37	CCDS47538.1	51	0.023351648351648352	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	32	0.04221635883905013	G	8.928	0.962772	0.18583	0.010232	0.034551	ENSG00000164631	ENST00000404360;ENST00000405858;ENST00000342651;ENST00000399476;ENST00000330442	T;T;T	0.00792	5.69;5.69;5.69	4.03	-0.0473	0.13844	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.379769	0.19455	N	0.113860	T	0.00109	0.0003	N	0.03903	-0.33	0.09310	N	1	P;B	0.43431	0.807;0.007	P;B	0.45276	0.475;0.004	T	0.42447	-0.9451	10	0.02654	T	1	.	10.7549	0.46230	0.0:0.5707:0.293:0.1363	rs61731528	301;263	P17014;P17014-5	ZNF12_HUMAN;.	E	227;301;263;359;265	ENSP00000384405:Q227E;ENSP00000385939:Q301E;ENSP00000344745:Q263E	ENSP00000331039:Q265E	Q	-	1	0	ZNF12	6698197	0.000000	0.05858	0.030000	0.17652	0.993000	0.82548	-0.485000	0.06520	-0.016000	0.14127	0.563000	0.77884	CAG	G|0.952;C|0.048	0.048	strong		0.423	ZNF12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324373.2	NM_016265	
CEACAM20	125931	hgsc.bcm.edu	37	19	45016116	45016116	+	RNA	SNP	A	A	G	rs8100718	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:45016116A>G	ENST00000454753.1	-	0	1813							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)		p.C511R(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				GATATATTGCAATACTCAGGA	0.507													A|||	1925	0.384385	0.1679	0.4078	5008	,	,		18720	0.3919		0.4612	False		,,,				2504	0.5736				p.C512R		Atlas-SNP	.											CEACAM20,NS,carcinoma,0,1	CEACAM20	31	1	1	Substitution - Missense(1)	prostate(1)	c.T1534C						PASS	.	A	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	917,3079		106,705,1187	46.0	46.0	46.0		1535,1256,1256,1535	0.9	0.0	19	dbSNP_116	46	4182,4158		1069,2044,1057	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	180,180,180,180	1175,2749,2244	GG,GA,AA		49.8561,22.9479,41.3343	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	512/597,419/492,419/504,512/585	45016116	5099,7237	1998	4170	6168			125931	exon10			TATTGCAATACTC	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45016116A>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	184	95	0.516304	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				A|0.633;G|0.366	0.366	strong		0.507	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
ATG7	10533	hgsc.bcm.edu	37	3	11596302	11596302	+	Silent	SNP	T	T	C	rs8154	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:11596302T>C	ENST00000354449.3	+	19	2122	c.2097T>C	c.(2095-2097)gaT>gaC	p.D699D	ATG7_ENST00000354956.5_Silent_p.D672D|ATG7_ENST00000446450.2_Silent_p.D619D	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7	699					adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)	p.D699D(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						ACATGAGCGATGATGAGACCA	0.637													C|||	1275	0.254593	0.3419	0.2277	5008	,	,		17980	0.1389		0.3201	False		,,,				2504	0.2076				p.D699D		Atlas-SNP	.											ATG7,NS,adenoma,0,2	ATG7	56	2	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.T2097C						PASS	.	C	,,	1417,2989	685.6+/-404.6	218,981,1004	89.0	79.0	82.0		2016,1857,2097	1.4	0.9	3	dbSNP_100	82	2776,5824	678.6+/-403.5	459,1858,1983	no	coding-synonymous,coding-synonymous,coding-synonymous	ATG7	NM_001136031.2,NM_001144912.1,NM_006395.2	,,	677,2839,2987	CC,CT,TT		32.2791,32.1607,32.239	,,	672/677,619/624,699/704	11596302	4193,8813	2203	4300	6503	SO:0001819	synonymous_variant	10533	exon19			GAGCGATGATGAG	AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"""Ubiquitin-like modifier activating enzymes"""	16935	protein-coding gene	gene with protein product	"""ubiquitin-activating enzyme E1-like protein"""	608760	"""APG7 autophagy 7-like (S. cerevisiae)"", ""ATG7 autophagy related 7 homolog (S. cerevisiae)"""	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740	ENST00000354449.3:c.2097T>C	3.37:g.11596302T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_006395	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Silent	SNP	ENST00000354449.3	37	CCDS2605.1																																																																																			T|0.705;C|0.295	0.295	strong		0.637	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702744	27702744	+	Silent	SNP	A	A	G	rs11015754	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:27702744A>G	ENST00000438700.3	-	1	553	c.436T>C	c.(436-438)Ttg>Ctg	p.L146L		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	146					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						GTCAGCATCAAGGGCGCCAGC	0.662													A|||	506	0.101038	0.0492	0.121	5008	,	,		11744	0.004		0.2008	False		,,,				2504	0.1544				p.L146L		Atlas-SNP	.											.	PTCHD3	140	.	0			c.T436C						PASS	.	A		228,4178	127.4+/-164.3	8,212,1983	47.0	54.0	52.0		436	-7.8	0.0	10	dbSNP_120	52	1677,6923	292.4+/-300.8	174,1329,2797	no	coding-synonymous	PTCHD3	NM_001034842.3		182,1541,4780	GG,GA,AA		19.5,5.1748,14.6471		146/768	27702744	1905,11101	2203	4300	6503	SO:0001819	synonymous_variant	374308	exon1			GCATCAAGGGCGC	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.436T>C	10.37:g.27702744A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	46	0.597403	NM_001034842	I3L499|Q6ZU28	Silent	SNP	ENST00000438700.3	37	CCDS31173.1																																																																																			A|0.865;G|0.135	0.135	strong		0.662	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
ABCC1	4363	hgsc.bcm.edu	37	16	16138322	16138322	+	Silent	SNP	T	T	C	rs246221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:16138322T>C	ENST00000399410.3	+	8	1000	c.825T>C	c.(823-825)gtT>gtC	p.V275V	ABCC1_ENST00000349029.5_Silent_p.V275V|ABCC1_ENST00000346370.5_Silent_p.V275V|ABCC1_ENST00000351154.5_Silent_p.V275V|ABCC1_ENST00000399408.2_Silent_p.V275V|ABCC1_ENST00000345148.5_Silent_p.V275V	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	275					arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CGGTGAAGGTTGTGTACTCCT	0.582													C|||	2127	0.42472	0.7118	0.3617	5008	,	,		17677	0.4425		0.3171	False		,,,				2504	0.1738				p.V275V		Atlas-SNP	.											.	ABCC1	156	.	0			c.T825C						PASS	.	C	,,,,	2485,1507		792,901,303	63.0	63.0	63.0		825,825,825,825,825	-5.3	0.0	16	dbSNP_79	63	2451,5883		345,1761,2061	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	1137,2662,2364	CC,CT,TT		29.4096,37.7505,40.0454	,,,,	275/1532,275/1473,275/1476,275/1417,275/1467	16138322	4936,7390	1996	4167	6163	SO:0001819	synonymous_variant	4363	exon8			GAAGGTTGTGTAC	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.825T>C	16.37:g.16138322T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			T|0.563;C|0.437	0.437	strong		0.582	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
NUP62	23636	hgsc.bcm.edu	37	19	50412217	50412217	+	Missense_Mutation	SNP	C	C	G	rs1062798	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50412217C>G	ENST00000596217.1	-	2	2735	c.848G>C	c.(847-849)aGc>aCc	p.S283T	NUP62_ENST00000422090.2_Missense_Mutation_p.S283T|NUP62_ENST00000413454.1_Missense_Mutation_p.S283T|NUP62_ENST00000597723.1_Intron|NUP62_ENST00000600583.1_5'Flank|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000352066.3_Missense_Mutation_p.S283T|NUP62_ENST00000597029.1_Missense_Mutation_p.S283T|IL4I1_ENST00000341114.3_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	283	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.		S -> T (in dbSNP:rs1062798). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:1915414}.		carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		gctgctgctgctggtggtggt	0.627													C|||	1584	0.316294	0.2383	0.379	5008	,	,		15105	0.3938		0.3827	False		,,,				2504	0.229				p.S283T		Atlas-SNP	.											NUP62,NS,carcinoma,0,2	NUP62	50	2	0			c.G848C						PASS	.	C	THR/SER,THR/SER,THR/SER,THR/SER,THR/SER,	997,3405		118,761,1322	31.0	29.0	30.0		848,848,848,848,848,	0.8	0.0	19	dbSNP_86	30	3113,5481		577,1959,1761	yes	missense,missense,missense,missense,missense,intron	NUP62,IL4I1	NM_001193357.1,NM_012346.4,NM_016553.4,NM_153718.3,NM_153719.3,NM_172374.1	58,58,58,58,58,	695,2720,3083	GG,GC,CC		36.2229,22.6488,31.6251	benign,benign,benign,benign,benign,	283/523,283/523,283/523,283/523,283/523,	50412217	4110,8886	2201	4297	6498	SO:0001583	missense	23636	exon3			CTGCTGCTGGTGG	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"""nuclear pore glycoprotein p62"""	605815	"""nucleoporin 62kD"""			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.848G>C	19.37:g.50412217C>G	ENSP00000471191:p.Ser283Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Missense_Mutation	SNP	ENST00000596217.1	37	CCDS12788.1	763	0.34935897435897434	103	0.20934959349593496	134	0.3701657458563536	230	0.4020979020979021	296	0.39050131926121373	C	0.016	-1.533751	0.00951	0.226488	0.362229	ENSG00000213024	ENST00000352066;ENST00000422090;ENST00000413454	T;T;T	0.36157	1.27;1.27;1.27	4.24	0.801	0.18679	Nucleoporin, NSP1-like, C-terminal (1);	1.330530	0.05670	N	0.588508	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45366	-0.9266	8	.	.	.	-2.1099	13.4683	0.61268	0.0:0.2452:0.7548:0.0	rs1062798;rs3203778;rs3745497;rs4009638;rs5828420;rs17844993;rs17857752;rs52814004	283	P37198	NUP62_HUMAN	T	283	ENSP00000305503:S283T;ENSP00000407331:S283T;ENSP00000387991:S283T	.	S	-	2	0	NUP62	55104029	0.050000	0.20438	0.000000	0.03702	0.004000	0.04260	1.221000	0.32503	0.190000	0.20209	-1.162000	0.01777	AGC	C|0.677;G|0.323	0.323	strong		0.627	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719	
SLC14A2	8170	hgsc.bcm.edu	37	18	43246156	43246156	+	Missense_Mutation	SNP	G	G	A	rs9960464	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:43246156G>A	ENST00000255226.6	+	12	2345	c.1529G>A	c.(1528-1530)cGa>cAa	p.R510Q	SLC14A2_ENST00000586448.1_Missense_Mutation_p.R510Q|SLC14A2_ENST00000589658.1_5'UTR	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	510			R -> Q (in dbSNP:rs9960464). {ECO:0000269|PubMed:11502588, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)	p.R510Q(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTTCCCTATCGATACCGGAAG	0.512											OREG0024946	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	1870	0.373403	0.2867	0.4712	5008	,	,		17597	0.3423		0.4314	False		,,,				2504	0.3937				p.R510Q		Atlas-SNP	.											SLC14A2,NS,carcinoma,0,1	SLC14A2	121	1	1	Substitution - Missense(1)	stomach(1)	c.G1529A						PASS	.	G	GLN/ARG,GLN/ARG	1446,2960	469.2+/-355.4	225,996,982	160.0	126.0	138.0		1529,1529	-11.7	0.0	18	dbSNP_119	138	3848,4752	541.7+/-384.0	826,2196,1278	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	43,43	1051,3192,2260	AA,AG,GG		44.7442,32.8189,40.7043	benign,benign	510/921,510/921	43246156	5294,7712	2203	4300	6503	SO:0001583	missense	8170	exon13			CCTATCGATACCG	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.1529G>A	18.37:g.43246156G>A	ENSP00000255226:p.Arg510Gln	Somatic	138	0	0	914	WXS	Illumina HiSeq	Phase_I	117	47	0.401709	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	839	0.3841575091575092	138	0.2804878048780488	175	0.48342541436464087	192	0.3356643356643357	334	0.44063324538258575	g	7.576	0.667826	0.14710	0.328189	0.447442	ENSG00000132874	ENST00000255226	T	0.32515	1.45	6.04	-11.7	0.00046	.	1.340750	0.04528	N	0.385873	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40924	-0.9537	9	0.13108	T	0.6	3.2061	6.7344	0.23401	0.1347:0.579:0.0671:0.2192	rs9960464;rs52828182;rs59892831;rs9960464	510	Q15849	UT2_HUMAN	Q	510	ENSP00000255226:R510Q	ENSP00000255226:R510Q	R	+	2	0	SLC14A2	41500154	0.000000	0.05858	0.000000	0.03702	0.146000	0.21551	-0.763000	0.04740	-1.612000	0.01579	-0.405000	0.06341	CGA	G|0.615;A|0.385	0.385	strong		0.512	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
CHTF18	63922	hgsc.bcm.edu	37	16	840378	840378	+	Missense_Mutation	SNP	A	A	G	rs3765263	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:840378A>G	ENST00000262315.9	+	6	794	c.731A>G	c.(730-732)aAg>aGg	p.K244R	CHTF18_ENST00000455171.2_Missense_Mutation_p.K272R|RPUSD1_ENST00000007264.2_5'Flank|CHTF18_ENST00000317063.6_Missense_Mutation_p.K441R|RPUSD1_ENST00000565809.1_5'Flank|RPUSD1_ENST00000561734.1_5'Flank|RPUSD1_ENST00000567114.1_5'Flank|CHTF18_ENST00000491530.1_3'UTR	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	244			K -> R (in dbSNP:rs3765263). {ECO:0000269|PubMed:14702039}.		cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				GAGGCCCAGAAGCTTTCAGAC	0.652													G|||	2476	0.494409	0.643	0.3833	5008	,	,		12625	0.5704		0.2296	False		,,,				2504	0.5665				p.K244R		Atlas-SNP	.											CHTF18,NS,carcinoma,0,1	CHTF18	52	1	0			c.A731G						scavenged	.	G	ARG/LYS	1991,1853		544,903,475	19.0	23.0	21.0		731	-5.4	0.1	16	dbSNP_107	21	2009,6221		254,1501,2360	yes	missense	CHTF18	NM_022092.2	26	798,2404,2835	GG,GA,AA		24.4107,48.205,33.129	benign	244/976	840378	4000,8074	1922	4115	6037	SO:0001583	missense	63922	exon6			CCCAGAAGCTTTC	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"""ATPases / AAA-type"""	18435	protein-coding gene	gene with protein product		613201	"""chromosome 16 open reading frame 41"""	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.731A>G	16.37:g.840378A>G	ENSP00000262315:p.Lys244Arg	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	951	0.43543956043956045	322	0.6544715447154471	124	0.3425414364640884	333	0.5821678321678322	172	0.22691292875989447	G	0.009	-1.816330	0.00595	0.51795	0.244107	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.09445	2.98;2.98;3.0	4.3	-5.39	0.02664	.	16.147100	0.00166	N	0.000001	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.43940	-0.9360	9	0.08381	T	0.77	-8.9345	16.0123	0.80411	0.8404:0.0:0.1596:0.0	rs3765263;rs17856178;rs60467149;rs3765263	272;244	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	R	441;272;244	ENSP00000313029:K441R;ENSP00000406252:K272R;ENSP00000262315:K244R	ENSP00000262315:K244R	K	+	2	0	CHTF18	780379	0.000000	0.05858	0.081000	0.20488	0.007000	0.05969	-3.390000	0.00487	-1.724000	0.01373	-1.451000	0.01035	AAG	A|0.564;G|0.436	0.436	strong		0.652	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
SPATA2	9825	hgsc.bcm.edu	37	20	48522330	48522330	+	Silent	SNP	G	G	A	rs495337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:48522330G>A	ENST00000422556.1	-	3	1738	c.1389C>T	c.(1387-1389)tgC>tgT	p.C463C	SPATA2_ENST00000543716.1_Silent_p.C326C|SPATA2_ENST00000289431.5_Silent_p.C463C	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	463					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	20	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			CTGGGCGGTTGCAGAAGCCAC	0.602													G|||	1793	0.358027	0.0991	0.464	5008	,	,		18237	0.3403		0.3976	False		,,,				2504	0.6104				p.C463C		Atlas-SNP	.											.	SPATA2	36	.	0			c.C1389T						PASS	.	G	,	602,3804	264.1+/-265.8	40,522,1641	91.0	85.0	87.0	http://omim.org/entry/612950|http://www.ncbi.nlm.nih.gov/pubmed?term	1389,1389	-3.2	1.0	20	dbSNP_83	87	3551,5049	516.4+/-378.8	729,2093,1478	yes	coding-synonymous,coding-synonymous	SPATA2	NM_001135773.1,NM_006038.3	,	769,2615,3119	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	41.2907,13.6632,31.9314	,	463/521,463/521	48522330	4153,8853	2203	4300	6503	SO:0001819	synonymous_variant	9825	exon3			GCGGTTGCAGAAG	AB018300	CCDS13422.1	20q13.13	2014-06-13			ENSG00000158480	ENSG00000158480			14681	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 145"""	607662					Standard	NM_001135773		Approved	KIAA0757, PD1, tamo, PPP1R145	uc002xuw.3	Q9UM82	OTTHUMG00000032704	ENST00000422556.1:c.1389C>T	20.37:g.48522330G>A		Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	273	129	0.472527	NM_006038	E1P626|O94857	Silent	SNP	ENST00000422556.1	37	CCDS13422.1																																																																																			G|0.679;A|0.321	0.321	strong		0.602	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038	
GMNN	51053	hgsc.bcm.edu	37	6	24780944	24780944	+	Silent	SNP	A	A	C	rs2307300	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:24780944A>C	ENST00000230056.3	+	3	437	c.105A>C	c.(103-105)ggA>ggC	p.G35G	GMNN_ENST00000356509.3_Silent_p.G35G	NM_015895.4	NP_056979.1	O75496	GEMI_HUMAN	geminin, DNA replication inhibitor	35					mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	10						CTGCATCTGGATCTCTTGTTG	0.368													A|||	73	0.0145767	0.0038	0.0259	5008	,	,		18564	0.003		0.0427	False		,,,				2504	0.0041				p.G35G		Atlas-SNP	.											.	GMNN	19	.	0			c.A105C						PASS	.	A		55,4351	52.3+/-87.9	1,53,2149	122.0	118.0	119.0		105	-5.5	0.9	6	dbSNP_100	119	428,8172	132.3+/-190.0	5,418,3877	no	coding-synonymous	GMNN	NM_015895.3		6,471,6026	CC,CA,AA		4.9767,1.2483,3.7137		35/210	24780944	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	51053	exon3			ATCTGGATCTCTT	AF067855	CCDS4560.1	6p21.32	2008-10-31			ENSG00000112312	ENSG00000112312			17493	protein-coding gene	gene with protein product		602842				9635433	Standard	NM_001251989		Approved	Gem	uc003nem.3	O75496	OTTHUMG00000014363	ENST00000230056.3:c.105A>C	6.37:g.24780944A>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	NM_001251991	B3KMM8|Q9H1Z1	Silent	SNP	ENST00000230056.3	37	CCDS4560.1																																																																																			A|0.969;C|0.031	0.031	strong		0.368	GMNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040021.2	NM_015895	
ALPK2	115701	hgsc.bcm.edu	37	18	56204410	56204410	+	Silent	SNP	C	C	T	rs55910046|rs59392360|rs386803723	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56204410C>T	ENST00000361673.3	-	5	3222	c.3009G>A	c.(3007-3009)agG>agA	p.R1003R	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1003						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCTCAGTCTCCCTGGTCGCTT	0.483													C|||	2025	0.404353	0.4304	0.4294	5008	,	,		21047	0.2371		0.5736	False		,,,				2504	0.3497				p.R1003R		Atlas-SNP	.											ALPK2_ENST00000361673,colon,carcinoma,0,1	ALPK2	487	1	0			c.G3009A						PASS	.	C		1713,2693		444,825,934	110.0	92.0	98.0		3009	-2.2	0.0	18	dbSNP_129	98	3942,4656		1219,1504,1576	no	coding-synonymous	ALPK2	NM_052947.3		1663,2329,2510	TT,TC,CC		45.8479,38.8788,43.4866		1003/2171	56204410	5655,7349	2203	4299	6502	SO:0001819	synonymous_variant	115701	exon5			AGTCTCCCTGGTC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.3009G>A	18.37:g.56204410C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	181	43	0.237569	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			C|0.535;T|0.465	0.465	strong		0.483	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
POM121L2	94026	hgsc.bcm.edu	37	6	27277051	27277051	+	Missense_Mutation	SNP	C	C	T	rs41269255	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:27277051C>T	ENST00000444565.1	-	1	2898	c.2899G>A	c.(2899-2901)Gcc>Acc	p.A967T	POM121L2_ENST00000377451.2_Missense_Mutation_p.A903T	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	967										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						GCAATGGGGGCCATAGTCTTT	0.572													C|||	537	0.107228	0.0817	0.1009	5008	,	,		17356	0.0813		0.1392	False		,,,				2504	0.1401				p.A967T		Atlas-SNP	.											POM121L2,colon,carcinoma,0,1	POM121L2	61	1	0			c.G2899A						PASS	.	C	THR/ALA	109,1275		6,97,589	51.0	51.0	51.0		2899	-0.0	0.0	6	dbSNP_127	51	359,2823		21,317,1253	yes	missense	POM121L2	NM_033482.3	58	27,414,1842	TT,TC,CC		11.2822,7.8757,10.2497	possibly-damaging	967/1036	27277051	468,4098	692	1591	2283	SO:0001583	missense	94026	exon1			TGGGGGCCATAGT	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.2899G>A	6.37:g.27277051C>T	ENSP00000392726:p.Ala967Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	231	0.10576923076923077	47	0.09552845528455285	37	0.10220994475138122	41	0.07167832167832168	106	0.13984168865435356	C	7.174	0.588193	0.13812	0.078757	0.112822	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.12984	2.65;2.63	3.68	-0.0238	0.13941	.	.	.	.	.	T	0.02230	0.0069	L	0.29908	0.895	0.80722	P	0.0	B	0.25312	0.123	B	0.16289	0.015	T	0.46843	-0.9162	8	0.23891	T	0.37	.	4.333	0.11073	0.0:0.5773:0.2256:0.1971	rs41269255;rs61736080	967	C9J1I7	.	T	903;967	ENSP00000366671:A903T;ENSP00000392726:A967T	ENSP00000366671:A903T	A	-	1	0	POM121L2	27385030	0.001000	0.12720	0.000000	0.03702	0.076000	0.17211	-0.104000	0.10923	-0.014000	0.14175	0.305000	0.20034	GCC	C|0.891;T|0.109	0.109	strong		0.572	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
SBNO2	22904	hgsc.bcm.edu	37	19	1119019	1119019	+	Silent	SNP	C	C	T	rs2074920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1119019C>T	ENST00000361757.3	-	14	1755	c.1518G>A	c.(1516-1518)gcG>gcA	p.A506A	SBNO2_ENST00000587024.1_Silent_p.A506A|SBNO2_ENST00000438103.2_Silent_p.A449A	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	506					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGCAGGGCCGCGCGGTTGT	0.672													C|||	2449	0.489018	0.6793	0.6138	5008	,	,		14934	0.2371		0.4642	False		,,,				2504	0.4284				p.A506A		Atlas-SNP	.											.	SBNO2	112	.	0			c.G1518A						PASS	.	C	,	2913,1375		1020,873,251	22.0	29.0	26.0		1347,1518	-7.8	0.3	19	dbSNP_96	26	3934,4528		930,2074,1227	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	1950,2947,1478	TT,TC,CC		46.4902,32.0662,46.298	,	449/1310,506/1367	1119019	6847,5903	2144	4231	6375	SO:0001819	synonymous_variant	22904	exon14			CAGGGCCGCGCGG	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.1518G>A	19.37:g.1119019C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			C|0.519;T|0.481	0.481	strong		0.672	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
PAMR1	25891	hgsc.bcm.edu	37	11	35456061	35456061	+	Splice_Site	SNP	T	T	C	rs61736408	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:35456061T>C	ENST00000378880.2	-	10	2070	c.1625A>G	c.(1624-1626)cAg>cGg	p.Q542R	PAMR1_ENST00000378878.3_Splice_Site_p.Q431R|PAMR1_ENST00000278360.3_Splice_Site_p.Q559R|PAMR1_ENST00000532848.1_Splice_Site_p.Q502R	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	542	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.			Q -> R (in Ref. 3; CAB43317/CAI46203/ CAE45808). {ECO:0000305}.		extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						CTCTCTTACCTGTAGGCTCTG	0.512													C|||	651	0.129992	0.3343	0.062	5008	,	,		18863	0.001		0.1312	False		,,,				2504	0.0337				p.Q559R		Atlas-SNP	.											.	PAMR1	85	.	0			c.A1676G						PASS	.	C	ARG/GLN,ARG/GLN	1391,3013	688.3+/-405.0	204,983,1015	98.0	88.0	91.0		1625,1676	5.5	1.0	11	dbSNP_129	91	1295,7301	758.7+/-407.5	105,1085,3108	yes	missense-near-splice,missense-near-splice	PAMR1	NM_001001991.1,NM_015430.2	43,43	309,2068,4123	CC,CT,TT		15.0651,31.5849,20.6615	benign,benign	542/721,559/738	35456061	2686,10314	2202	4298	6500	SO:0001630	splice_region_variant	25891	exon11			CTTACCTGTAGGC		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.1626+1A>G	11.37:g.35456061T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	164	162	0.987805	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	286	0.13095238095238096	163	0.3313008130081301	26	0.0718232044198895	1	0.0017482517482517483	96	0.1266490765171504	C	6.139	0.393910	0.11638	0.315849	0.150651	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605	D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4	5.52	5.52	0.82312	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.055729	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00788	-1.185	0.54753	P	1.799999999996249E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.11641	-1.0579	9	0.87932	D	0	.	10.7685	0.46308	0.0:0.8547:0.0:0.1453	rs61736408	431;542;559	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	R	559;542;431;502;519	ENSP00000278360:Q559R;ENSP00000368158:Q542R;ENSP00000368156:Q431R;ENSP00000433868:Q502R;ENSP00000432591:Q519R	ENSP00000278360:Q559R	Q	-	2	0	PAMR1	35412637	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	2.667000	0.46808	1.353000	0.45828	-0.227000	0.12334	CAG	T|0.819;C|0.181	0.181	strong		0.512	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430	Missense_Mutation
KANK4	163782	hgsc.bcm.edu	37	1	62732421	62732421	+	Missense_Mutation	SNP	T	T	C	rs11207949	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:62732421T>C	ENST00000371153.4	-	6	2680	c.2302A>G	c.(2302-2304)Acc>Gcc	p.T768A	KANK4_ENST00000371150.1_Missense_Mutation_p.T124A|KANK4_ENST00000354381.3_Missense_Mutation_p.T140A	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	768			T -> A (in dbSNP:rs11207949).			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						TGGTCTGTGGTGGTCCCAGTT	0.408													T|||	1530	0.305511	0.2095	0.3977	5008	,	,		20974	0.5873		0.2654	False		,,,				2504	0.1207				p.T768A		Atlas-SNP	.											.	KANK4	135	.	0			c.A2302G						PASS	.	T	ALA/THR	982,3424	367.8+/-318.4	110,762,1331	109.0	114.0	112.0		2302	3.6	0.0	1	dbSNP_120	112	2106,6494	363.6+/-333.2	286,1534,2480	yes	missense	KANK4	NM_181712.4	58	396,2296,3811	CC,CT,TT		24.4884,22.2878,23.7429	benign	768/996	62732421	3088,9918	2203	4300	6503	SO:0001583	missense	163782	exon6			CTGTGGTGGTCCC	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.2302A>G	1.37:g.62732421T>C	ENSP00000360195:p.Thr768Ala	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	166	67	0.403614	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	37	CCDS620.1	772	0.3534798534798535	115	0.23373983739837398	134	0.3701657458563536	321	0.5611888111888111	202	0.26649076517150394	T	3.448	-0.112649	0.06881	0.222878	0.244884	ENSG00000132854	ENST00000371153;ENST00000354381;ENST00000371150	T;T;T	0.45668	0.9;0.89;0.9	4.73	3.57	0.40892	.	0.198316	0.25247	N	0.032045	T	0.00012	0.0000	L	0.49640	1.575	0.80722	P	0.0	B;B	0.12630	0.001;0.006	B;B	0.14578	0.01;0.011	T	0.44019	-0.9355	9	0.32370	T	0.25	-6.4429	12.177	0.54190	0.0:0.0:0.1429:0.8571	rs11207949;rs17379933;rs52816310;rs56522827;rs61507558;rs11207949	140;768	Q5T7N3-2;Q5T7N3	.;KANK4_HUMAN	A	768;140;124	ENSP00000360195:T768A;ENSP00000346352:T140A;ENSP00000360192:T124A	ENSP00000346352:T140A	T	-	1	0	KANK4	62505009	0.935000	0.31712	0.040000	0.18447	0.454000	0.32378	2.380000	0.44327	0.867000	0.35654	0.482000	0.46254	ACC	T|0.722;C|0.278	0.278	strong		0.408	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
GRIN2B	2904	hgsc.bcm.edu	37	12	13715975	13715975	+	Silent	SNP	A	A	G	rs1805247	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:13715975A>G	ENST00000609686.1	-	13	4406	c.4197T>C	c.(4195-4197)caT>caC	p.H1399H		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	1399					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ATTTGCTGCCATGGAGCAAGC	0.632													A|||	1088	0.217252	0.3805	0.1196	5008	,	,		17467	0.1835		0.0815	False		,,,				2504	0.2403				p.H1399H		Atlas-SNP	.											GRIN2B,NS,carcinoma,-2,1	GRIN2B	303	1	0			c.T4197C						scavenged	.	A		1406,3000	459.6+/-352.3	225,956,1022	43.0	42.0	43.0		4197	-0.3	1.0	12	dbSNP_92	43	755,7845	181.3+/-230.0	29,697,3574	no	coding-synonymous	GRIN2B	NM_000834.3		254,1653,4596	GG,GA,AA		8.7791,31.911,16.6154		1399/1485	13715975	2161,10845	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon13			GCTGCCATGGAGC		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.4197T>C	12.37:g.13715975A>G		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			A|0.815;G|0.185	0.185	strong		0.632	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
BAI3	577	hgsc.bcm.edu	37	6	70071173	70071173	+	Silent	SNP	G	G	A	rs913543	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:70071173G>A	ENST00000370598.1	+	29	4829	c.4008G>A	c.(4006-4008)ccG>ccA	p.P1336P	BAI3_ENST00000546190.1_Silent_p.P300P|BAI3_ENST00000238918.8_Silent_p.P542P	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1336					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				AAACCTTGCCGCATGAAAGGC	0.403													G|||	2435	0.486222	0.1747	0.4568	5008	,	,		20805	0.8304		0.4463	False		,,,				2504	0.6145				p.P1336P		Atlas-SNP	.											.	BAI3	451	.	0			c.G4008A						PASS	.	G		1019,3387	373.7+/-320.9	120,779,1304	76.0	72.0	73.0		4008	-2.2	1.0	6	dbSNP_86	73	3768,4830	533.9+/-382.5	832,2104,1363	no	coding-synonymous	BAI3	NM_001704.2		952,2883,2667	AA,AG,GG		43.8241,23.1276,36.8118		1336/1523	70071173	4787,8217	2203	4299	6502	SO:0001819	synonymous_variant	577	exon29			CTTGCCGCATGAA	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.4008G>A	6.37:g.70071173G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	37	CCDS4968.1																																																																																			G|0.585;A|0.415	0.415	strong		0.403	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
MROH7	374977	hgsc.bcm.edu	37	1	55119534	55119534	+	Missense_Mutation	SNP	C	C	T	rs17399810	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:55119534C>T	ENST00000421030.2	+	3	1220	c.935C>T	c.(934-936)tCc>tTc	p.S312F	MROH7_ENST00000545244.1_Intron|MROH7_ENST00000454855.2_Intron|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.S312F|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000409996.1_Intron|MROH7_ENST00000395690.2_Missense_Mutation_p.S312F|MROH7_ENST00000339553.5_Missense_Mutation_p.S312F	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	312	Ser-rich.		S -> F (in dbSNP:rs17399810). {ECO:0000269|PubMed:14702039}.			extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											AGCCTGCACTCCAGCACCCAT	0.557													C|||	515	0.102835	0.0855	0.1369	5008	,	,		21469	0.002		0.2237	False		,,,				2504	0.0818				p.S312F		Atlas-SNP	.											.	.	.	.	0			c.C935T						PASS	.	C	PHE/SER	491,3833		24,443,1695	123.0	119.0	120.0		935	3.9	0.0	1	dbSNP_123	120	2035,6483		253,1529,2477	yes	missense	HEATR8	NM_001039464.2	155	277,1972,4172	TT,TC,CC		23.8906,11.3552,19.6698	probably-damaging	312/1324	55119534	2526,10316	2162	4259	6421	SO:0001583	missense	374977	exon3			TGCACTCCAGCAC	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"""maestro heat-like repeat containing"""	24802	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 175"", ""HEAT repeat containing 8"""	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.935C>T	1.37:g.55119534C>T	ENSP00000396622:p.Ser312Phe	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	169	85	0.502959	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	273	0.125	41	0.08333333333333333	60	0.16574585635359115	1	0.0017482517482517483	171	0.22559366754617413	C	15.16	2.751855	0.49362	0.113552	0.238906	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000339553;ENST00000395690	T;T;T	0.05258	3.47;3.47;3.47	3.89	3.89	0.44902	.	0.705640	0.11885	N	0.520120	T	0.00012	0.0000	L	0.29908	0.895	0.25689	P	0.9857195	D;D;D	0.89917	0.998;0.998;1.0	D;D;D	0.80764	0.971;0.971;0.994	T	0.46289	-0.9202	9	0.62326	D	0.03	.	11.6674	0.51381	0.0:1.0:0.0:0.0	rs17399810;rs17399810	312;312;312	F8W8P2;Q68CQ1;Q68CQ1-4	.;HEAT8_HUMAN;.	F	312	ENSP00000396622:S312F;ENSP00000343211:S312F;ENSP00000379044:S312F	ENSP00000343211:S312F	S	+	2	0	HEATR8	54892122	0.163000	0.22920	0.020000	0.16555	0.006000	0.05464	1.680000	0.37607	2.471000	0.83476	0.655000	0.94253	TCC	C|0.855;T|0.145	0.145	strong		0.557	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144921924	144921924	+	Silent	SNP	G	G	A	rs71664015	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:144921924G>A	ENST00000369354.3	-	9	1294	c.1105C>T	c.(1105-1107)Ctg>Ttg	p.L369L	PDE4DIP_ENST00000369351.3_Silent_p.L369L|PDE4DIP_ENST00000369349.3_Silent_p.L369L|PDE4DIP_ENST00000529945.1_Silent_p.L532L|PDE4DIP_ENST00000530740.1_Silent_p.L506L|PDE4DIP_ENST00000369356.4_Silent_p.L369L|PDE4DIP_ENST00000313382.9_Silent_p.L435L|PDE4DIP_ENST00000479408.2_Silent_p.L156L|PDE4DIP_ENST00000369359.4_Silent_p.L506L|PDE4DIP_ENST00000313431.9_Silent_p.L532L			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	369					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GCATCAGCCAGTTGGCGCTCT	0.463			T	PDGFRB	MPD																																p.L532L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C1594T						PASS	.	G	,,,,	203,4203		0,203,2000	375.0	388.0	384.0		1594,1105,1303,1105,1105	5.8	1.0	1	dbSNP_130	384	1431,7161		0,1431,2865	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001002811.1,NM_001002812.1,NM_001198832.1,NM_001198834.2,NM_014644.4	,,,,	0,1634,4865	AA,AG,GG		16.655,4.6074,12.5712	,,,,	532/1133,369/970,435/2241,369/2363,369/2347	144921924	1634,11364	2203	4296	6499	SO:0001819	synonymous_variant	9659	exon5			CAGCCAGTTGGCG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.1105C>T	1.37:g.144921924G>A		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	302	64	0.211921	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1																																																																																			A|0.001;C|0.795	0.001	strong		0.463	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
OLA1	29789	hgsc.bcm.edu	37	2	174946760	174946760	+	Missense_Mutation	SNP	T	T	C	rs11558990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:174946760T>C	ENST00000409546.1	-	8	1451	c.821A>G	c.(820-822)tAt>tGt	p.Y274C	OLA1_ENST00000392560.2_5'UTR|OLA1_ENST00000428402.2_Intron|OLA1_ENST00000344357.5_Missense_Mutation_p.Y96C|OLA1_ENST00000284719.3_Missense_Mutation_p.Y254C					Obg-like ATPase 1											breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						ACCTGGGTCATACTTGTCCAC	0.418													T|||	482	0.096246	0.0703	0.1254	5008	,	,		16705	0.0159		0.1998	False		,,,				2504	0.0869				p.Y254C		Atlas-SNP	.											.	OLA1	37	.	0			c.A761G						PASS	.	T	CYS/TYR,CYS/TYR	426,3980	209.8+/-230.5	23,380,1800	103.0	99.0	101.0		287,761	3.1	1.0	2	dbSNP_120	101	1753,6845	319.0+/-313.9	198,1357,2744	yes	missense,missense	OLA1	NM_001011708.1,NM_013341.3	194,194	221,1737,4544	CC,CT,TT		20.3885,9.6686,16.7564	benign,benign	96/239,254/397	174946760	2179,10825	2203	4299	6502	SO:0001583	missense	29789	exon8			GGGTCATACTTGT		CCDS2255.1, CCDS42779.1	2q31.1	2014-06-24	2007-07-27	2007-07-27	ENSG00000138430	ENSG00000138430			28833	protein-coding gene	gene with protein product		611175	"""GTP-binding protein 9 (putative)"""	GTPBP9		17430889, 24486488	Standard	NM_013341		Approved	PTD004	uc002uih.3	Q9NTK5	OTTHUMG00000132335	ENST00000409546.1:c.821A>G	2.37:g.174946760T>C	ENSP00000386350:p.Tyr274Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	83	51	0.614458	NM_013341		Missense_Mutation	SNP	ENST00000409546.1	37		253	0.11584249084249085	39	0.07926829268292683	56	0.15469613259668508	10	0.017482517482517484	148	0.19525065963060687	T	8.292	0.817935	0.16607	0.096686	0.203885	ENSG00000138430	ENST00000284719;ENST00000344357;ENST00000409546;ENST00000429575	T;T	0.43294	0.95;0.95	5.58	3.11	0.35812	.	0.110120	0.64402	D	0.000010	T	0.00039	0.0001	L	0.27053	0.805	0.28177	P	0.9283201	B;P	0.36010	0.445;0.532	B;B	0.40134	0.32;0.06	T	0.11470	-1.0586	9	0.56958	D	0.05	.	12.6576	0.56795	0.0:0.0:0.2598:0.7402	rs11558990	96;254	Q9NTK5-2;Q9NTK5	.;OLA1_HUMAN	C	254;96;274;96	ENSP00000284719:Y254C;ENSP00000386350:Y274C	ENSP00000284719:Y254C	Y	-	2	0	OLA1	174655006	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.888000	0.48594	0.360000	0.24265	0.533000	0.62120	TAT	T|0.841;C|0.159	0.159	strong		0.418	OLA1-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333877.1	NM_013341	
GRM6	2916	hgsc.bcm.edu	37	5	178415937	178415937	+	Splice_Site	SNP	A	A	G	rs2067011	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:178415937A>G	ENST00000517717.1	-	7	1391	c.1353T>C	c.(1351-1353)aaT>aaC	p.N451N	GRM6_ENST00000231188.5_Splice_Site_p.N451N|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	451					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		CCCACTCACCATTGAAGCGGA	0.637													A|||	2539	0.506989	0.388	0.5317	5008	,	,		13198	0.5913		0.5547	False		,,,				2504	0.5143				p.N451N		Atlas-SNP	.											.	GRM6	149	.	0			c.T1353C						PASS	.	A		1806,2600	523.5+/-371.1	382,1042,779	38.0	37.0	38.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1353	-4.4	1.0	5	dbSNP_96	38	4625,3975	592.2+/-392.9	1195,2235,870	yes	coding-synonymous-near-splice	GRM6	NM_000843.3		1577,3277,1649	GG,GA,AA		46.2209,40.9896,49.4464		451/878	178415937	6431,6575	2203	4300	6503	SO:0001630	splice_region_variant	2916	exon6			CTCACCATTGAAG	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1354+1T>C	5.37:g.178415937A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	219	121	0.552511	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1	1153	0.5279304029304029	219	0.4451219512195122	180	0.4972375690607735	336	0.5874125874125874	418	0.5514511873350924	A	11.88	1.769401	0.31320	0.409896	0.537791	ENSG00000113262	ENST00000319065	.	.	.	5.29	-4.44	0.03557	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46020	-0.9221	4	0.87932	D	0	.	15.2442	0.73493	0.2527:0.0:0.7473:0.0	rs2067011;rs17839799;rs52803732;rs61390692;rs2067011	.	.	.	R	491	.	ENSP00000325675:W491R	W	-	1	0	GRM6	178348543	0.002000	0.14202	0.973000	0.42090	0.937000	0.57800	-1.561000	0.02158	-0.676000	0.05238	0.459000	0.35465	TGG	A|0.500;G|0.500	0.500	strong		0.637	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		Silent
AP1M2	10053	hgsc.bcm.edu	37	19	10692000	10692000	+	Silent	SNP	T	T	C	rs1045361	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10692000T>C	ENST00000250244.6	-	6	697	c.615A>G	c.(613-615)tcA>tcG	p.S205S	AP1M2_ENST00000590923.1_Silent_p.S205S	NM_005498.4	NP_005489.2	Q9Y6Q5	AP1M2_HUMAN	adaptor-related protein complex 1, mu 2 subunit	205	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein targeting (GO:0006605)|regulation of defense response to virus by virus (GO:0050690)|vesicle targeting (GO:0006903)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				endometrium(4)|large_intestine(1)|lung(1)|ovary(2)|urinary_tract(1)	9			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)			CTGGCATTCCTGACAGAAACA	0.557											OREG0025241	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	1866	0.372604	0.2557	0.5115	5008	,	,		19255	0.6627		0.1779	False		,,,				2504	0.3333				p.S205S		Atlas-SNP	.											AP1M2,colon,carcinoma,0,1	AP1M2	35	1	0			c.A615G						scavenged	.	T		924,3180		101,722,1229	51.0	54.0	53.0		615	-10.6	0.0	19	dbSNP_86	53	1683,6737		165,1353,2692	yes	coding-synonymous	AP1M2	NM_005498.4		266,2075,3921	CC,CT,TT		19.9881,22.5146,20.816		205/424	10692000	2607,9917	2052	4210	6262	SO:0001819	synonymous_variant	10053	exon6			CATTCCTGACAGA	AF020797	CCDS45964.1	19p13.2	2008-10-07				ENSG00000129354			558	protein-coding gene	gene with protein product		607309				10338135	Standard	NM_005498		Approved	HSMU1B, mu2, AP1-mu2	uc002mpc.3	Q9Y6Q5		ENST00000250244.6:c.615A>G	19.37:g.10692000T>C		Somatic	124	1	0.00806452	666	WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_005498	B2RDV5|Q9BSI8	Silent	SNP	ENST00000250244.6	37	CCDS45964.1																																																																																			T|0.749;C|0.251	0.251	strong		0.557	AP1M2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452034.1		
CUX1	1523	hgsc.bcm.edu	37	7	101837149	101837149	+	Silent	SNP	G	G	A	rs11540899|rs2230104	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:101837149G>A	ENST00000292535.7	+	13	1142	c.1104G>A	c.(1102-1104)ccG>ccA	p.P368P	CUX1_ENST00000360264.3_Silent_p.P379P|CUX1_ENST00000549414.2_Silent_p.P368P|CUX1_ENST00000547394.2_Silent_p.P363P|CUX1_ENST00000425244.2_Silent_p.P333P|CUX1_ENST00000556210.1_Silent_p.P368P|CUX1_ENST00000292538.4_Silent_p.P379P|CUX1_ENST00000393824.3_Silent_p.P340P|CUX1_ENST00000437600.4_Silent_p.P377P|CUX1_ENST00000550008.2_Silent_p.P368P|SNORA48_ENST00000517015.1_RNA|CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000546411.2_Silent_p.P368P	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	368					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						AGTTTGCACCGTCCGAGGGCG	0.527													G|||	1495	0.298522	0.3646	0.2738	5008	,	,		19932	0.0675		0.3857	False		,,,				2504	0.3753				p.P379P		Atlas-SNP	.											CUX1_ENST00000292538,rectum,carcinoma,0,2	CUX1	253	2	0			c.G1137A						PASS	.	G	,,,,,,	1667,2739	507.1+/-366.6	331,1005,867	82.0	69.0	73.0		1137,1089,999,1020,1137,1131,1104	-8.6	0.0	7	dbSNP_120	73	3374,5226	499.2+/-374.9	652,2070,1578	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CUX1	NM_001202543.1,NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2,NM_181552.3	,,,,,,	983,3075,2445	AA,AG,GG		39.2326,37.8348,38.759	,,,,,,	379/1517,363/663,333/633,340/640,379/679,377/677,368/1506	101837149	5041,7965	2203	4300	6503	SO:0001819	synonymous_variant	1523	exon13			TGCACCGTCCGAG	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1104G>A	7.37:g.101837149G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	CCDS5721.1																																																																																			G|0.655;A|0.345	0.345	strong		0.527	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
TBXAS1	6916	hgsc.bcm.edu	37	7	139715645	139715645	+	Missense_Mutation	SNP	C	C	A	rs5763	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:139715645C>A	ENST00000336425.5	+	15	1738	c.1349C>A	c.(1348-1350)aCc>aAc	p.T450N	TBXAS1_ENST00000425687.1_Missense_Mutation_p.T383N|TBXAS1_ENST00000462275.1_3'UTR|TBXAS1_ENST00000411653.1_Missense_Mutation_p.T450N|TBXAS1_ENST00000448866.1_Missense_Mutation_p.T450N|TBXAS1_ENST00000416849.2_Missense_Mutation_p.T497N|TBXAS1_ENST00000414508.2_Missense_Mutation_p.T451N|TBXAS1_ENST00000263552.6_Missense_Mutation_p.T451N|TBXAS1_ENST00000458722.1_Missense_Mutation_p.T496N|TBXAS1_ENST00000436047.2_Missense_Mutation_p.T451N			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	450			T -> N (in allele CYP5A1*8; dbSNP:rs5763). {ECO:0000269|PubMed:11465543}.		arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	AGCCCGGAGACCTTCAACCCT	0.602													C|||	27	0.00539137	0.0015	0.0072	5008	,	,		16586	0.0		0.0149	False		,,,				2504	0.0051				p.T497N		Atlas-SNP	.											.	TBXAS1	121	.	0			c.C1490A	GRCh37	CM054133	TBXAS1	M	rs5763	PASS	.	C	ASN/THR,ASN/THR,ASN/THR,ASN/THR,ASN/THR	15,4391	22.3+/-47.3	0,15,2188	53.0	52.0	53.0		1352,1352,1490,1148,1352	0.3	0.1	7	dbSNP_52	53	178,8422	78.6+/-141.3	3,172,4125	yes	missense,missense,missense,missense,missense	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	65,65,65,65,65	3,187,6313	AA,AC,CC		2.0698,0.3404,1.4839	benign,benign,benign,benign,benign	451/535,451/535,497/581,383/467,451/461	139715645	193,12813	2203	4300	6503	SO:0001583	missense	6916	exon12			CGGAGACCTTCAA	L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"""Cytochrome P450s"""	11609	protein-coding gene	gene with protein product	"""cytochrome P450, family 5, subfamily A, polypeptide 1"""	274180	"""thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"""			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000336425.5:c.1349C>A	7.37:g.139715645C>A	ENSP00000338087:p.Thr450Asn	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000336425.5	37		14	0.00641025641025641	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	3.350	-0.132775	0.06711	0.003404	0.020698	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000414508;ENST00000448866;ENST00000458722;ENST00000411653	T;T;T;T;T;T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4	4.52	0.297	0.15762	.	0.380726	0.27577	N	0.018760	T	0.37293	0.0998	L	0.47190	1.495	0.80722	D	1	B;B;B;B;B;B;B	0.14805	0.011;0.009;0.003;0.002;0.002;0.004;0.004	B;B;B;B;B;B;B	0.26517	0.025;0.01;0.014;0.007;0.07;0.014;0.009	T	0.33497	-0.9866	10	0.52906	T	0.07	.	4.2042	0.10481	0.459:0.3493:0.0:0.1916	rs5763;rs52807031;rs61074508;rs5763	431;497;402;383;451;451;450	B4DVP1;E7EP08;B4E0M5;E7ESB5;E7EMU9;Q53F23;P24557	.;.;.;.;.;.;THAS_HUMAN	N	383;451;450;497;451;451;450;496;450	ENSP00000388736:T383N;ENSP00000263552:T451N;ENSP00000338087:T450N;ENSP00000389414:T497N;ENSP00000392361:T451N;ENSP00000392702:T451N;ENSP00000402536:T450N;ENSP00000411274:T496N;ENSP00000411326:T450N	ENSP00000263552:T451N	T	+	2	0	TBXAS1	139362114	0.703000	0.27826	0.050000	0.19076	0.020000	0.10135	-0.032000	0.12266	0.039000	0.15632	-0.379000	0.06801	ACC	C|0.988;A|0.012	0.012	strong		0.602	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13894894	13894894	+	Missense_Mutation	SNP	T	T	A	rs4701997	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13894894T>A	ENST00000265104.4	-	16	2400	c.2296A>T	c.(2296-2298)Ata>Tta	p.I766L	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	766	Stem. {ECO:0000250}.		I -> L (in dbSNP:rs4701997).		cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I766L(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GCAGCAGGTATTTTTGACTTC	0.408									Kartagener syndrome				T|||	2443	0.487819	0.5681	0.4654	5008	,	,		18015	0.249		0.5	False		,,,				2504	0.6288				p.I766L		Atlas-SNP	.											DNAH5,NS,carcinoma,0,1	DNAH5	868	1	1	Substitution - Missense(1)	stomach(1)	c.A2296T						PASS	.	T	LEU/ILE	2349,2057	609.7+/-391.4	615,1119,469	175.0	164.0	168.0		2296	4.4	1.0	5	dbSNP_111	168	4368,4232	582.7+/-391.4	1127,2114,1059	yes	missense	DNAH5	NM_001369.2	5	1742,3233,1528	AA,AT,TT		49.2093,46.6863,48.3546	benign	766/4625	13894894	6717,6289	2203	4300	6503	SO:0001583	missense	1767	exon16	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAGGTATTTTTGA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.2296A>T	5.37:g.13894894T>A	ENSP00000265104:p.Ile766Leu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	965	0.44184981684981683	281	0.5711382113821138	175	0.48342541436464087	140	0.24475524475524477	369	0.4868073878627968	T	11.42	1.634972	0.29068	0.533137	0.507907	ENSG00000039139	ENST00000265104	T	0.47869	0.83	5.53	4.37	0.52481	Dynein heavy chain, domain-1 (1);	0.227351	0.51477	D	0.000098	T	0.00012	0.0000	M	0.64404	1.975	0.30184	P	0.800164	B	0.06786	0.001	B	0.20955	0.032	T	0.44967	-0.9293	9	0.13470	T	0.59	.	8.5314	0.33337	0.0:0.1491:0.0:0.8509	rs4701997;rs17210254;rs52819664;rs4701997	766	Q8TE73	DYH5_HUMAN	L	766	ENSP00000265104:I766L	ENSP00000265104:I766L	I	-	1	0	DNAH5	13947894	1.000000	0.71417	1.000000	0.80357	0.421000	0.31385	3.012000	0.49575	0.935000	0.37341	0.459000	0.35465	ATA	T|0.517;A|0.483	0.483	strong		0.408	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28331128	28331128	+	Missense_Mutation	SNP	A	A	C	rs13201753|rs371085669	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28331128A>C	ENST00000377255.3	+	5	896	c.599A>C	c.(598-600)aAa>aCa	p.K200T	ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.K200T|ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.K52T	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	200			K -> A (requires 2 nucleotide substitutions; dbSNP:rs13201752). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.|K -> E (in dbSNP:rs45505399). {ECO:0000269|PubMed:14702039}.|K -> T (in dbSNP:rs13201753).		autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						AGAGAAGATAAAGTGGTAGCT	0.537													C|||	1952	0.389776	0.5825	0.3213	5008	,	,		16779	0.2986		0.2843	False		,,,				2504	0.3804				p.K200T		Atlas-SNP	.											ZKSCAN3,NS,other,-1,1	ZKSCAN3	50	1	0			c.A599C						PASS	.	C	THR/LYS,THR/LYS,THR/LYS	2170,2236		549,1072,582	97.0	83.0	88.0		599,155,599	-0.1	0.0	6	dbSNP_121	88	2534,6066		400,1734,2166	yes	missense,missense,missense	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	78,78,78	949,2806,2748	CC,CA,AA		29.4651,49.251,36.1679	benign,benign,benign	200/539,52/391,200/539	28331128	4704,8302	2203	4300	6503	SO:0001583	missense	80317	exon4			AAGATAAAGTGGT	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.599A>C	6.37:g.28331128A>C	ENSP00000366465:p.Lys200Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	579	0.2651098901098901	199	0.40447154471544716	101	0.27900552486187846	129	0.22552447552447552	150	0.19788918205804748	.	0.016	-1.538627	0.00942	0.49251	0.294651	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.14022	2.54;2.54;2.54	2.99	-0.126	0.13515	.	.	.	.	.	T	0.01353	0.0044	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.49418	-0.8942	8	0.19147	T	0.46	.	6.7841	0.23664	0.3054:0.3751:0.3196:0.0	rs13201753;rs58899552;rs13201753	200	Q9BRR0	ZKSC3_HUMAN	T	200;52;200	ENSP00000252211:K200T;ENSP00000341883:K52T;ENSP00000366465:K200T	ENSP00000252211:K200T	K	+	2	0	ZKSCAN3	28439107	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.151000	0.10175	-0.315000	0.08703	-1.122000	0.02009	AAA	.	.	alt		0.537	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
ADCK4	79934	hgsc.bcm.edu	37	19	41220529	41220529	+	Silent	SNP	C	C	T	rs11673492	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:41220529C>T	ENST00000324464.3	-	2	310	c.9G>A	c.(7-9)ctG>ctA	p.L3L	ITPKC_ENST00000263370.2_5'Flank|ADCK4_ENST00000450541.1_Silent_p.L3L|ADCK4_ENST00000243583.6_Silent_p.L3L	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	3						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CCCCCACCTTCAGCCACATTG	0.637													C|||	497	0.0992412	0.1324	0.0922	5008	,	,		12878	0.003		0.1978	False		,,,				2504	0.0573				p.L3L		Atlas-SNP	.											.	ADCK4	92	.	0			c.G9A						PASS	.	C	,	572,3834		42,488,1673	30.0	35.0	33.0		9,9	2.4	0.9	19	dbSNP_120	33	1656,6932		171,1314,2809	no	coding-synonymous,coding-synonymous	ADCK4	NM_001142555.2,NM_024876.3	,	213,1802,4482	TT,TC,CC		19.2827,12.9823,17.1464	,	3/504,3/545	41220529	2228,10766	2203	4294	6497	SO:0001819	synonymous_variant	79934	exon2			CACCTTCAGCCAC	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.9G>A	19.37:g.41220529C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_001142555	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	37	CCDS12562.1																																																																																			C|0.854;T|0.146	0.146	strong		0.637	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
IDO2	169355	hgsc.bcm.edu	37	8	39872935	39872935	+	Nonsense_Mutation	SNP	T	T	A	rs4503083	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:39872935T>A	ENST00000389060.4	+	10	1038	c.1038T>A	c.(1036-1038)taT>taA	p.Y346*	IDO2_ENST00000502986.2_Nonsense_Mutation_p.Y359*|IDO2_ENST00000343295.4_3'UTR			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	346					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						TGCGGAGCTATCACATCACCA	0.542													T|||	1151	0.229832	0.112	0.317	5008	,	,		19406	0.3601		0.2107	False		,,,				2504	0.2127				p.Y359X		Atlas-SNP	.											.	IDO2	78	.	0			c.T1077A						PASS	.	T	stop/TYR	458,3716		22,414,1651	80.0	79.0	79.0		1077	-2.2	1.0	8	dbSNP_111	79	1743,6659		175,1393,2633	yes	stop-gained	IDO2	NM_194294.2		197,1807,4284	AA,AT,TT		20.7451,10.9727,17.5016		359/421	39872935	2201,10375	2087	4201	6288	SO:0001587	stop_gained	169355	exon11			GAGCTATCACATC	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"""indoleamine-pyrrole 2,3 dioxygenase-like 1"""	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.1038T>A	8.37:g.39872935T>A	ENSP00000426447:p.Tyr346*	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	204	91	0.446078	NM_194294	A4UD41	Nonsense_Mutation	SNP	ENST00000389060.4	37		540	0.24725274725274726	46	0.09349593495934959	106	0.292817679558011	228	0.3986013986013986	160	0.21108179419525067	T	18.77	3.694799	0.68386	0.109727	0.207451	ENSG00000188676	ENST00000502986;ENST00000389060	.	.	.	5.74	-2.22	0.06952	.	0.257128	0.39210	N	0.001422	.	.	.	.	.	.	0.09310	P	0.9999999999991586	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0548	0.71904	0.0:0.7555:0.0:0.2445	rs4503083;rs56452642;rs4503083	.	.	.	X	359;346	.	.	Y	+	3	2	IDO2	39992092	0.996000	0.38824	0.988000	0.46212	0.680000	0.39746	0.394000	0.20834	-0.380000	0.07894	-0.256000	0.11100	TAT	T|0.758;A|0.242	0.242	strong		0.542	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
MERTK	10461	hgsc.bcm.edu	37	2	112751928	112751928	+	Missense_Mutation	SNP	G	G	A	rs386649210|rs7604639	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:112751928G>A	ENST00000295408.4	+	9	1654	c.1397G>A	c.(1396-1398)aGa>aAa	p.R466K	MERTK_ENST00000409780.1_Missense_Mutation_p.R290K|MERTK_ENST00000421804.2_Missense_Mutation_p.R466K			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	466	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> K (in dbSNP:rs7604639). {ECO:0000269|PubMed:11062461, ECO:0000269|PubMed:17344846}.		apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						GCCGTCACCAGAGGGGGAGTT	0.532													A|||	2812	0.561502	0.6664	0.6037	5008	,	,		19456	0.2758		0.6243	False		,,,				2504	0.6196				p.R466K		Atlas-SNP	.											.	MERTK	112	.	0			c.G1397A						PASS	.	A	LYS/ARG	2858,1548	488.1+/-361.1	928,1002,273	151.0	145.0	147.0		1397	-3.2	0.0	2	dbSNP_116	147	5388,3212	484.9+/-371.5	1704,1980,616	yes	missense	MERTK	NM_006343.2	26	2632,2982,889	AA,AG,GG		37.3488,35.1339,36.5985	benign	466/1000	112751928	8246,4760	2203	4300	6503	SO:0001583	missense	10461	exon9			TCACCAGAGGGGG	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1397G>A	2.37:g.112751928G>A	ENSP00000295408:p.Arg466Lys	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	239	236	0.987448	NM_006343	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	1130	0.5173992673992674	318	0.6463414634146342	218	0.6022099447513812	124	0.21678321678321677	470	0.6200527704485488	A	0.056	-1.237453	0.01493	0.648661	0.626512	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000393237;ENST00000409780	T;T;T	0.52754	0.65;0.65;0.65	5.1	-3.17	0.05202	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.221135	0.22473	N	0.059590	T	0.00012	0.0000	N	0.02665	-0.54	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38243	-0.9670	9	0.02654	T	1	-1.1242	12.5621	0.56288	0.4085:0.0:0.5915:0.0	rs7604639;rs17809673;rs52817844;rs58591742;rs7604639	466	Q12866	MERTK_HUMAN	K	466;466;61;290	ENSP00000295408:R466K;ENSP00000389152:R466K;ENSP00000387277:R290K	ENSP00000295408:R466K	R	+	2	0	MERTK	112468399	0.000000	0.05858	0.009000	0.14445	0.104000	0.19210	-1.465000	0.02357	-0.861000	0.04094	-0.360000	0.07572	AGA	G|0.415;A|0.585	0.585	strong		0.532	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
CARKD	55739	hgsc.bcm.edu	37	13	111279817	111279817	+	Missense_Mutation	SNP	A	A	G	rs3742191	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:111279817A>G	ENST00000309957.2	+	5	432	c.418A>G	c.(418-420)Aag>Gag	p.K140E	CARKD_ENST00000397191.4_Missense_Mutation_p.K77E|CARKD_ENST00000458711.2_Intron|CARKD_ENST00000424185.2_Missense_Mutation_p.K30E|CARKD_ENST00000470164.2_3'UTR	NM_001242881.1|NM_018210.3	NP_001229810.1|NP_060680.2			carbohydrate kinase domain containing											NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	15						TGAGGTGGAGAAGTGGCTGCC	0.478													A|||	311	0.0621006	0.0204	0.0922	5008	,	,		16742	0.1091		0.0358	False		,,,				2504	0.0757				p.K140E		Atlas-SNP	.											.	CARKD	36	.	0			c.A418G						PASS	.	A	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	121,4285	91.1+/-129.8	2,117,2084	117.0	98.0	104.0		418,364,88,418	-0.2	0.0	13	dbSNP_107	104	315,8285	112.0+/-172.2	5,305,3990	no	missense,missense,missense,missense	CARKD	NM_001242881.1,NM_001242882.1,NM_001242883.1,NM_018210.3	56,56,56,56	7,422,6074	GG,GA,AA		3.6628,2.7463,3.3523	benign,benign,benign,benign	140/348,122/330,30/238,140/391	111279817	436,12570	2203	4300	6503	SO:0001583	missense	55739	exon5			GTGGAGAAGTGGC	AF151071	CCDS9513.1, CCDS55903.1	13q34	2008-12-19			ENSG00000213995	ENSG00000213995			25576	protein-coding gene	gene with protein product		615910					Standard	NM_018210		Approved	LP3298, FLJ10769	uc001vrc.3	Q8IW45	OTTHUMG00000017345	ENST00000309957.2:c.418A>G	13.37:g.111279817A>G	ENSP00000311984:p.Lys140Glu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	163	67	0.411043	NM_018210		Missense_Mutation	SNP	ENST00000309957.2	37	CCDS9513.1	115	0.052655677655677656	11	0.022357723577235773	28	0.07734806629834254	45	0.07867132867132867	31	0.040897097625329816	A	4.322	0.059086	0.08339	0.027463	0.036628	ENSG00000213995	ENST00000424185;ENST00000439607;ENST00000397191;ENST00000309957	T;T;T	0.20200	2.15;2.09;2.15	5.13	-0.227	0.13102	Uncharacterised domain, carbohydrate kinase-related (3);	0.276420	0.39274	N	0.001406	T	0.00356	0.0011	N	0.05259	-0.085	0.09310	N	0.999997	B;B;B;B;B	0.19445	0.002;0.001;0.034;0.036;0.001	B;B;B;B;B	0.21360	0.011;0.006;0.034;0.021;0.006	T	0.32851	-0.9891	10	0.06494	T	0.89	-0.249	5.5108	0.16880	0.6381:0.1353:0.2266:0.0	rs3742191;rs3742191	30;122;77;140;140	Q8IW45-4;B4DKX7;B7Z3Q0;Q8IW45-2;Q8IW45	.;.;.;.;CARKD_HUMAN	E	30;122;77;140	ENSP00000413191:K30E;ENSP00000380375:K77E;ENSP00000311984:K140E	ENSP00000311984:K140E	K	+	1	0	CARKD	110077818	0.887000	0.30362	0.000000	0.03702	0.324000	0.28378	1.784000	0.38674	-0.259000	0.09432	0.459000	0.35465	AAG	A|0.955;G|0.045	0.045	strong		0.478	CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210	
SYDE2	84144	hgsc.bcm.edu	37	1	85666156	85666156	+	Missense_Mutation	SNP	T	T	G	rs12121540	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:85666156T>G	ENST00000341460.5	-	1	573	c.524A>C	c.(523-525)cAg>cCg	p.Q175P		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	175				Q -> P (in Ref. 3; BAB14711). {ECO:0000305}.	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)		GGGGCCTTCCTGGCGGTCTCC	0.622													T|||	1525	0.304513	0.1543	0.379	5008	,	,		16400	0.4683		0.2376	False		,,,				2504	0.3548				p.Q175P		Atlas-SNP	.											.	SYDE2	135	.	0			c.A524C						PASS	.	T	PRO/GLN	628,3240		42,544,1348	54.0	57.0	56.0		524	-9.1	0.0	1	dbSNP_120	56	1975,6311		244,1487,2412	yes	missense	SYDE2	NM_032184.1	76	286,2031,3760	GG,GT,TT		23.8354,16.2358,21.4168	benign	175/1195	85666156	2603,9551	1934	4143	6077	SO:0001583	missense	84144	exon1			CCTTCCTGGCGGT	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.524A>C	1.37:g.85666156T>G	ENSP00000340594:p.Gln175Pro	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	CCDS44169.1	657	0.3008241758241758	82	0.16666666666666666	131	0.36187845303867405	278	0.486013986013986	166	0.21899736147757257	T	2.467	-0.322733	0.05350	0.162358	0.238354	ENSG00000097096	ENST00000341460	T	0.06294	3.32	5.07	-9.1	0.00714	.	0.566434	0.15454	N	0.261471	T	0.00524	0.0017	N	0.11201	0.11	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.45175	-0.9279	9	0.09843	T	0.71	.	1.9173	0.03300	0.1694:0.1286:0.2964:0.4057	rs12121540	175;175	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	P	175	ENSP00000340594:Q175P	ENSP00000340594:Q175P	Q	-	2	0	SYDE2	85438744	0.001000	0.12720	0.028000	0.17463	0.036000	0.12997	-0.785000	0.04628	-1.318000	0.02289	-1.843000	0.00578	CAG	T|0.705;G|0.295	0.295	strong		0.622	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2		
MPDZ	8777	hgsc.bcm.edu	37	9	13176312	13176312	+	Silent	SNP	C	C	T	rs2274856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:13176312C>T	ENST00000319217.7	-	20	3001	c.2754G>A	c.(2752-2754)tcG>tcA	p.S918S	MPDZ_ENST00000447879.1_Silent_p.S918S|MPDZ_ENST00000381022.2_Silent_p.S918S|MPDZ_ENST00000546205.1_Silent_p.S918S|MPDZ_ENST00000541718.1_Silent_p.S918S|MPDZ_ENST00000381015.4_Silent_p.S918S|MPDZ_ENST00000536827.1_Silent_p.S918S	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	918					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TTATGTCCACCGAAGGTGTAT	0.388													C|||	1969	0.393171	0.5257	0.3012	5008	,	,		18249	0.495		0.2594	False		,,,				2504	0.3119				p.S918S		Atlas-SNP	.											.	MPDZ	324	.	0			c.G2754A						PASS	.	C		1657,2057		373,911,573	92.0	79.0	83.0		2754	-11.6	0.0	9	dbSNP_100	83	2132,6068		295,1542,2263	no	coding-synonymous	MPDZ	NM_003829.3		668,2453,2836	TT,TC,CC		26.0,44.615,31.8029		918/2042	13176312	3789,8125	1857	4100	5957	SO:0001819	synonymous_variant	8777	exon20			GTCCACCGAAGGT	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2754G>A	9.37:g.13176312C>T		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	260	258	0.992308	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																				C|0.613;T|0.387	0.387	strong		0.388	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
CCT6B	10693	hgsc.bcm.edu	37	17	33269648	33269648	+	Missense_Mutation	SNP	C	C	G	rs2230553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:33269648C>G	ENST00000314144.5	-	7	855	c.740G>C	c.(739-741)gGt>gCt	p.G247A	CCT6B_ENST00000421975.3_Missense_Mutation_p.G210A|CCT6B_ENST00000436961.3_Missense_Mutation_p.G202A	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	247			G -> A (in dbSNP:rs2230553). {ECO:0000269|PubMed:8812458}.		chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				ATAAAAGAAACCAGAGTTCAC	0.328													C|||	1218	0.243211	0.149	0.1859	5008	,	,		14931	0.2639		0.3728	False		,,,				2504	0.2566				p.G247A		Atlas-SNP	.											.	CCT6B	63	.	0			c.G740C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY	765,3635	276.0+/-272.9	73,619,1508	48.0	47.0	48.0		629,605,740	4.1	1.0	17	dbSNP_98	48	3152,5434	452.4+/-362.9	585,1982,1726	yes	missense,missense,missense	CCT6B	NM_001193529.1,NM_001193530.1,NM_006584.3	60,60,60	658,2601,3234	GG,GC,CC		36.7109,17.3864,30.1633	possibly-damaging,possibly-damaging,possibly-damaging	210/494,202/486,247/531	33269648	3917,9069	2200	4293	6493	SO:0001583	missense	10693	exon7			AAGAAACCAGAGT	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"""Heat Shock Proteins / Chaperonins"""	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.740G>C	17.37:g.33269648C>G	ENSP00000327191:p.Gly247Ala	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_006584	B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	37	CCDS32617.1	582	0.2664835164835165	87	0.17682926829268292	75	0.20718232044198895	131	0.229020979020979	289	0.3812664907651715	C	16.88	3.244978	0.59103	0.173864	0.367109	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.67523	-0.27;-0.27;-0.27	4.06	4.06	0.47325	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.91920	3.255	0.09310	P	0.9999999860995	B;B;P	0.37233	0.155;0.248;0.588	B;B;P	0.44696	0.276;0.303;0.458	T	0.08006	-1.0743	9	0.62326	D	0.03	-9.8571	14.0935	0.65006	0.0:1.0:0.0:0.0	rs2230553;rs16970466;rs52825862;rs2230553	202;210;247	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	A	210;247;202	ENSP00000398044:G210A;ENSP00000327191:G247A;ENSP00000400917:G202A	ENSP00000327191:G247A	G	-	2	0	CCT6B	30293761	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	7.019000	0.76412	2.220000	0.72140	0.591000	0.81541	GGT	C|0.717;G|0.283	0.283	strong		0.328	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584	
KIAA1683	80726	hgsc.bcm.edu	37	19	18375882	18375882	+	Missense_Mutation	SNP	G	G	C	rs12608777	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18375882G>C	ENST00000600328.3	-	3	2661	c.2468C>G	c.(2467-2469)cCg>cGg	p.P823R	KIAA1683_ENST00000392413.4_Missense_Mutation_p.P823R|KIAA1683_ENST00000600359.3_Missense_Mutation_p.P777R			Q9H0B3	K1683_HUMAN	KIAA1683	823			P -> R (in dbSNP:rs12608777). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						ACAGGCTGCCGGGCATGGTCC	0.677													G|||	761	0.151957	0.0257	0.1196	5008	,	,		16464	0.3036		0.1292	False		,,,				2504	0.2127				p.P823R		Atlas-SNP	.											KIAA1683,NS,carcinoma,-1,1	KIAA1683	190	1	0			c.C2468G						PASS	.	G	ARG/PRO,ARG/PRO,ARG/PRO	178,4228	112.1+/-150.2	1,176,2026	60.0	59.0	59.0		2468,2330,2468	-1.3	0.0	19	dbSNP_120	59	1177,7417	225.8+/-261.7	82,1013,3202	no	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	103,103,103	83,1189,5228	CC,CG,GG		13.6956,4.0399,10.4231	possibly-damaging,possibly-damaging,possibly-damaging	823/1368,777/1135,823/1181	18375882	1355,11645	2203	4297	6500	SO:0001583	missense	80726	exon3			GCTGCCGGGCATG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2468C>G	19.37:g.18375882G>C	ENSP00000470780:p.Pro823Arg	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	311	0.1423992673992674	15	0.03048780487804878	35	0.09668508287292818	167	0.291958041958042	94	0.12401055408970976	G	9.122	1.009200	0.19277	0.040399	0.136956	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000411671	T;T;T	0.03580	3.96;3.96;3.88	3.87	-1.29	0.09288	.	1.359350	0.05345	N	0.530918	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P;D	0.64830	0.924;0.994	B;P	0.60886	0.269;0.88	T	0.45818	-0.9235	9	0.29301	T	0.29	-3.4881	3.2366	0.06766	0.2478:0.0:0.3126:0.4396	rs12608777;rs17797810;rs12608777	823;823	E9PDE0;Q9H0B3	.;K1683_HUMAN	R	823;823;777;437	ENSP00000376213:P823R;ENSP00000352774:P823R;ENSP00000404501:P777R	ENSP00000352774:P823R	P	-	2	0	KIAA1683	18236882	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.023000	0.12456	0.016000	0.14998	-0.373000	0.07131	CCG	G|0.879;C|0.121	0.121	strong		0.677	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
ZNF705A	440077	hgsc.bcm.edu	37	12	8329833	8329833	+	Missense_Mutation	SNP	G	G	A	rs11043758	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:8329833G>A	ENST00000359286.4	+	5	646	c.557G>A	c.(556-558)cGc>cAc	p.R186H	FAM66C_ENST00000544214.1_RNA|FAM66C_ENST00000456135.2_RNA|FAM66C_ENST00000454799.2_RNA	NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	186			R -> H (in dbSNP:rs11043758).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R186H(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		AATTGCTTTCGCCTTAGACGG	0.393																																					p.R186H		Atlas-SNP	.											ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	1	Substitution - Missense(1)	stomach(1)	c.G557A						scavenged	.						85.0	86.0	86.0					12																	8329833		2198	4290	6488	SO:0001583	missense	440077	exon5			GCTTTCGCCTTAG	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"""Zinc fingers, C2H2-type"", ""-"""	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.557G>A	12.37:g.8329833G>A	ENSP00000352233:p.Arg186His	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	191	69	0.361257	NM_001004328		Missense_Mutation	SNP	ENST00000359286.4	37	CCDS31737.1	992	0.4542124542124542	174	0.35365853658536583	165	0.4558011049723757	275	0.4807692307692308	378	0.49868073878627966	.	0.017	-1.494887	0.01009	.	.	ENSG00000196946	ENST00000396570;ENST00000359286	T;T	0.03920	3.76;3.76	1.35	-2.7	0.06004	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.01624	-0.795	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34976	-0.9807	7	.	.	.	.	2.8848	0.05658	0.3359:0.0:0.3342:0.3299	rs11043758	186	Q6ZN79	Z705A_HUMAN	H	186	ENSP00000379816:R186H;ENSP00000352233:R186H	.	R	+	2	0	ZNF705A	8221100	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.401000	0.01048	-2.388000	0.00588	-0.724000	0.03597	CGC	G|0.506;A|0.494	0.494	strong		0.393	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328	
C4orf51	646603	hgsc.bcm.edu	37	4	146653620	146653620	+	Missense_Mutation	SNP	G	G	A	rs10008599	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:146653620G>A	ENST00000438731.1	+	6	517	c.517G>A	c.(517-519)Gat>Aat	p.D173N	C4orf51_ENST00000508981.1_3'UTR	NM_001080531.1	NP_001074000.1	C9J302	CD051_HUMAN	chromosome 4 open reading frame 51	173										haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)	6						TGGACGGTGCGATTCTGAAAG	0.473													G|||	386	0.0770767	0.1362	0.0778	5008	,	,		13978	0.001		0.1183	False		,,,				2504	0.0327				p.D173N		Atlas-SNP	.											.	C4orf51	18	.	0			c.G517A						PASS	.	G	ASN/ASP	473,3461		36,401,1530	58.0	61.0	60.0		517	-0.4	0.0	4	dbSNP_119	60	1010,7298		64,882,3208	yes	missense	C4orf51	NM_001080531.1	23	100,1283,4738	AA,AG,GG		12.157,12.0234,12.114	possibly-damaging	173/203	146653620	1483,10759	1967	4154	6121	SO:0001583	missense	646603	exon6			CGGTGCGATTCTG		CCDS47140.1	4q31.21	2009-09-09			ENSG00000237136	ENSG00000237136			37264	protein-coding gene	gene with protein product							Standard	NM_001080531		Approved		uc003ikk.3	C9J302	OTTHUMG00000161367	ENST00000438731.1:c.517G>A	4.37:g.146653620G>A	ENSP00000391404:p.Asp173Asn	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	149	67	0.449664	NM_001080531		Missense_Mutation	SNP	ENST00000438731.1	37	CCDS47140.1	188	0.08608058608058608	63	0.12804878048780488	32	0.08839779005524862	1	0.0017482517482517483	92	0.12137203166226913	G	16.17	3.046140	0.55110	0.120234	0.12157	ENSG00000237136	ENST00000438731	.	.	.	3.77	-0.356	0.12583	.	.	.	.	.	T	0.00241	0.0007	N	0.24115	0.695	0.80722	P	0.0	B	0.21688	0.059	B	0.12837	0.008	T	0.13176	-1.0519	7	0.87932	D	0	.	2.3842	0.04362	0.1325:0.1847:0.4956:0.1872	rs10008599	173	C9J302	CD051_HUMAN	N	173	.	ENSP00000391404:D173N	D	+	1	0	C4orf51	146873070	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.031000	0.12287	-0.097000	0.12307	0.555000	0.69702	GAT	G|0.908;A|0.092	0.092	strong		0.473	C4orf51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080531	
WDR66	144406	hgsc.bcm.edu	37	12	122396395	122396395	+	Missense_Mutation	SNP	C	C	T	rs17852561	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:122396395C>T	ENST00000288912.4	+	12	2802	c.1948C>T	c.(1948-1950)Ctt>Ttt	p.L650F	WDR66_ENST00000397454.2_Missense_Mutation_p.L650F	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	650				L -> F (in Ref. 2; AAH28421 and 4; CAD38786). {ECO:0000305}.			calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		TGAGAAGGGGCTTGGAGTCCA	0.468													C|||	1392	0.277955	0.0159	0.3602	5008	,	,		20010	0.4821		0.3111	False		,,,				2504	0.3292				p.L650F	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C1948T						PASS	.	C	PHE/LEU,PHE/LEU	212,3546		11,190,1678	217.0	211.0	213.0		1948,1948	2.9	0.9	12	dbSNP_123	213	2481,5733		384,1713,2010	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	22,22	395,1903,3688	TT,TC,CC		30.2045,5.6413,22.4942	benign,benign	650/942,650/1150	122396395	2693,9279	1879	4107	5986	SO:0001583	missense	144406	exon12			AAGGGGCTTGGAG	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.1948C>T	12.37:g.122396395C>T	ENSP00000288912:p.Leu650Phe	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	163	86	0.527607	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	664	0.304029304029304	15	0.03048780487804878	123	0.3397790055248619	286	0.5	240	0.316622691292876	C	10.60	1.395987	0.25205	0.056413	0.302045	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.62941	3.45;-0.01	4.79	2.94	0.34122	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.725385	0.13466	N	0.385742	T	0.00012	0.0000	M	0.61703	1.905	0.80722	P	0.0	B	0.18310	0.027	B	0.13407	0.009	T	0.41431	-0.9509	9	0.30078	T	0.28	.	4.2331	0.10613	0.1409:0.4138:0.3589:0.0865	rs17852561	650	Q8TBY9	WDR66_HUMAN	F	650	ENSP00000288912:L650F;ENSP00000380595:L650F	ENSP00000288912:L650F	L	+	1	0	WDR66	120880778	0.969000	0.33509	0.889000	0.34880	0.953000	0.61014	0.530000	0.23036	0.588000	0.29660	0.555000	0.69702	CTT	C|0.702;T|0.298	0.298	strong		0.468	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
FFAR2	2867	hgsc.bcm.edu	37	19	35941248	35941248	+	Missense_Mutation	SNP	T	T	A	rs409093	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:35941248T>A	ENST00000599180.2	+	2	712	c.632T>A	c.(631-633)cTt>cAt	p.L211H	FFAR2_ENST00000601590.1_Intron|FFAR2_ENST00000246549.2_Missense_Mutation_p.L211H			O15552	FFAR2_HUMAN	free fatty acid receptor 2	211			L -> H (in dbSNP:rs409093).		cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TCCCAGCCCCTTGTGGGGGCC	0.627													A|||	241	0.048123	0.0151	0.0173	5008	,	,		16792	0.0		0.0795	False		,,,				2504	0.1319				p.L211H	GBM(40;139 809 9833 23358 48736)	Atlas-SNP	.											.	FFAR2	39	.	0			c.T632A						PASS	.	A	HIS/LEU	142,4264	809.3+/-416.0	3,136,2064	80.0	77.0	78.0		632	5.5	1.0	19	dbSNP_80	78	623,7977	786.6+/-407.6	30,563,3707	yes	missense	FFAR2	NM_005306.2	99	33,699,5771	AA,AT,TT		7.2442,3.2229,5.8819	benign	211/331	35941248	765,12241	2203	4300	6503	SO:0001583	missense	2867	exon1			AGCCCCTTGTGGG	AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"""GPCR / Class A : Fatty acid receptors"""	4501	protein-coding gene	gene with protein product		603823	"""G protein-coupled receptor 43"""	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.632T>A	19.37:g.35941248T>A	ENSP00000473159:p.Leu211His	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	127	53	0.417323	NM_005306	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Missense_Mutation	SNP	ENST00000599180.2	37	CCDS12461.1	79	0.036172161172161175	7	0.014227642276422764	8	0.022099447513812154	0	0.0	64	0.08443271767810026	A	3.298	-0.143577	0.06627	0.032229	0.072442	ENSG00000126262	ENST00000246549	T	0.36520	1.25	5.49	5.49	0.81192	GPCR, rhodopsin-like superfamily (1);	0.199219	0.51477	N	0.000086	T	0.00552	0.0018	N	0.00656	-1.285	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.11717	-1.0576	9	0.09843	T	0.71	-16.2679	10.4718	0.44642	0.8542:0.0:0.0:0.1458	rs409093;rs52811194;rs409093	211	O15552	FFAR2_HUMAN	H	211	ENSP00000246549:L211H	ENSP00000246549:L211H	L	+	2	0	FFAR2	40633088	0.649000	0.27322	0.958000	0.39756	0.808000	0.45660	4.376000	0.59556	1.031000	0.39867	-0.364000	0.07487	CTT	T|0.950;A|0.050	0.050	strong		0.627	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306	
MAML2	84441	hgsc.bcm.edu	37	11	95825797	95825797	+	Silent	SNP	A	A	G	rs7931870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:95825797A>G	ENST00000524717.1	-	2	2682	c.1398T>C	c.(1396-1398)tcT>tcC	p.S466S		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	466					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				GTCCAGCAGAAGAGGGCAAGG	0.587			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid								A|||	2531	0.505391	0.7224	0.464	5008	,	,		19396	0.2014		0.5736	False		,,,				2504	0.4847				p.S466S		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.T1398C						PASS	.	A		3061,1279		1112,837,221	59.0	62.0	61.0		1398	-8.5	0.0	11	dbSNP_116	61	4951,3611		1461,2029,791	no	coding-synonymous	MAML2	NM_032427.1		2573,2866,1012	GG,GA,AA		42.1747,29.47,37.9011		466/1157	95825797	8012,4890	2170	4281	6451	SO:0001819	synonymous_variant	84441	exon2			AGCAGAAGAGGGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1398T>C	11.37:g.95825797A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	173	83	0.479769	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			A|0.486;G|0.514	0.514	strong		0.587	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
CYP4Z1	199974	hgsc.bcm.edu	37	1	47571902	47571902	+	Silent	SNP	C	C	T	rs4926802	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:47571902C>T	ENST00000334194.3	+	9	1173	c.1170C>T	c.(1168-1170)atC>atT	p.I390I	CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_178134.2	NP_835235.1	Q86W10	CP4Z1_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 1	390						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			cervix(1)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	11						ACAAACCCATCACCTTTCCAG	0.443													T|||	2953	0.589657	0.5121	0.4683	5008	,	,		17743	0.9563		0.34	False		,,,				2504	0.6595				p.I390I		Atlas-SNP	.											.	CYP4Z1	43	.	0			c.C1170T						PASS	.	T		2180,2226	582.0+/-385.5	552,1076,575	95.0	88.0	91.0		1170	-6.5	0.4	1	dbSNP_111	91	2807,5793	670.8+/-402.8	419,1969,1912	no	coding-synonymous	CYP4Z1	NM_178134.2		971,3045,2487	TT,TC,CC		32.6395,49.478,38.3438		390/506	47571902	4987,8019	2203	4300	6503	SO:0001819	synonymous_variant	199974	exon9			ACCCATCACCTTT	AY262056	CCDS545.1	1p33	2008-02-05			ENSG00000186160	ENSG00000186160		"""Cytochrome P450s"""	20583	protein-coding gene	gene with protein product						15059886	Standard	NM_178134		Approved	CYP4A20	uc001cqu.1	Q86W10	OTTHUMG00000008019	ENST00000334194.3:c.1170C>T	1.37:g.47571902C>T		Somatic	363	1	0.00275482		WXS	Illumina HiSeq	Phase_I	363	144	0.396694	NM_178134	Q5VVE4	Silent	SNP	ENST00000334194.3	37	CCDS545.1																																																																																			.	.	weak		0.443	CYP4Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022020.1	NM_178134	
C1QTNF6	114904	hgsc.bcm.edu	37	22	37578579	37578579	+	Silent	SNP	C	C	T	rs229519	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:37578579C>T	ENST00000337843.2	-	3	561	c.486G>A	c.(484-486)acG>acA	p.T162T	C1QTNF6_ENST00000397110.2_Silent_p.T162T|RP1-151B14.6_ENST00000419128.1_RNA|C1QTNF6_ENST00000470655.1_5'UTR|C1QTNF6_ENST00000255836.6_Silent_p.T38T	NM_031910.3	NP_114116.3	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	143	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				protein heterotrimerization (GO:0070208)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)		p.T162T(1)		breast(1)|large_intestine(2)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)	11						CGAAGAGCAGCGTCTGGAAGT	0.627													T|||	2327	0.464657	0.6339	0.4769	5008	,	,		19745	0.495		0.2763	False		,,,				2504	0.3896				p.T162T		Atlas-SNP	.											C1QTNF6,NS,adenoma,0,2	C1QTNF6	32	2	1	Substitution - coding silent(1)	stomach(1)	c.G486A						scavenged	.	T	,	2520,1886	542.2+/-376.0	720,1080,403	56.0	59.0	58.0		486,486	-6.5	0.9	22	dbSNP_79	58	2273,6327	706.2+/-405.5	304,1665,2331	no	coding-synonymous,coding-synonymous	C1QTNF6	NM_031910.3,NM_182486.1	,	1024,2745,2734	TT,TC,CC		26.4302,42.8053,36.8522	,	162/279,162/279	37578579	4793,8213	2203	4300	6503	SO:0001819	synonymous_variant	114904	exon3			GAGCAGCGTCTGG	AF329842	CCDS13943.1	22q13.1	2014-02-21			ENSG00000133466	ENSG00000133466			14343	protein-coding gene	gene with protein product		614910				12975309	Standard	NM_031910		Approved	CTRP6, ZACRP6	uc003aqy.1	Q9BXI9	OTTHUMG00000150538	ENST00000337843.2:c.486G>A	22.37:g.37578579C>T		Somatic	80	2	0.025		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_182486	Q5H9G8|Q6ZRM7	Silent	SNP	ENST00000337843.2	37	CCDS13943.1																																																																																			C|0.580;T|0.420	0.420	strong		0.627	C1QTNF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318807.1	NM_182486	
OR12D2	26529	hgsc.bcm.edu	37	6	29365241	29365241	+	Silent	SNP	T	T	C	rs2073150	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29365241T>C	ENST00000383555.2	+	1	826	c.765T>C	c.(763-765)ctT>ctC	p.L255L	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CACCTGTTCTTTTCACCTATA	0.458													C|||	1651	0.329673	0.2254	0.3588	5008	,	,		21296	0.3641		0.4533	False		,,,				2504	0.2873				p.L255L		Atlas-SNP	.											.	OR12D2	42	.	0			c.T765C						PASS	.	C		768,2254		96,576,839	212.0	210.0	210.0		765	-1.6	0.0	6	dbSNP_96	210	2419,2997		538,1343,827	no	coding-synonymous	OR12D2	NM_013936.3		634,1919,1666	CC,CT,TT		44.664,25.4136,37.7696		255/308	29365241	3187,5251	1511	2708	4219	SO:0001819	synonymous_variant	26529	exon1			TGTTCTTTTCACC		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.765T>C	6.37:g.29365241T>C		Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	261	124	0.475096	NM_013936	B0S862|Q5SUN9|Q6IET9	Silent	SNP	ENST00000383555.2	37	CCDS4659.1																																																																																			T|0.623;C|0.377	0.377	strong		0.458	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
VCAN	1462	hgsc.bcm.edu	37	5	82836241	82836241	+	Silent	SNP	C	C	T	rs61754536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:82836241C>T	ENST00000265077.3	+	8	7984	c.7419C>T	c.(7417-7419)agC>agT	p.S2473S	VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000343200.5_Silent_p.S1486S|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2473	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AGGTGCCAAGCGCTAAAGCTG	0.468													C|||	25	0.00499201	0.0	0.0086	5008	,	,		18881	0.0		0.0139	False		,,,				2504	0.0051				p.S2473S		Atlas-SNP	.											VCAN,colon,carcinoma,0,1	VCAN	498	1	0			c.C7419T						PASS	.	C	,,,	7,4399	12.9+/-30.5	0,7,2196	91.0	88.0	89.0		,4458,,7419	-7.8	0.0	5	dbSNP_129	89	64,8536	39.8+/-96.3	0,64,4236	no	intron,coding-synonymous,intron,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	0,71,6432	TT,TC,CC		0.7442,0.1589,0.5459	,,,	,1486/2410,,2473/3397	82836241	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			GCCAAGCGCTAAA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7419C>T	5.37:g.82836241C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	177	91	0.514124	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			C|0.993;G|0.000;T|0.006	0.006	strong		0.468	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
FN3K	64122	hgsc.bcm.edu	37	17	80708607	80708607	+	Silent	SNP	C	C	T	rs149413139	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:80708607C>T	ENST00000300784.7	+	6	968	c.906C>T	c.(904-906)ggC>ggT	p.G302G	TBCD_ENST00000355528.4_5'Flank|TBCD_ENST00000397466.2_5'Flank|TBCD_ENST00000539345.2_5'Flank	NM_022158.3	NP_071441.1	Q9H479	FN3K_HUMAN	fructosamine 3 kinase	302					epithelial cell differentiation (GO:0030855)|fructoselysine metabolic process (GO:0030393)		fructosamine-3-kinase activity (GO:0030387)			central_nervous_system(1)|kidney(1)|lung(1)|urinary_tract(1)	4	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			CTTCCTTGGGCACCATGCGAA	0.667													C|||	24	0.00479233	0.0015	0.0101	5008	,	,		8415	0.0		0.0139	False		,,,				2504	0.001				p.G302G	Melanoma(10;391 597 14592 32548 32749)	Atlas-SNP	.											.	FN3K	17	.	0			c.C906T						PASS	.	C		13,4393	20.2+/-43.8	0,13,2190	52.0	60.0	57.0		906	-1.1	1.0	17	dbSNP_134	57	169,8431	78.1+/-140.7	2,165,4133	no	coding-synonymous	FN3K	NM_022158.3		2,178,6323	TT,TC,CC		1.9651,0.2951,1.3994		302/310	80708607	182,12824	2203	4300	6503	SO:0001819	synonymous_variant	64122	exon6			CTTGGGCACCATG	AJ404615	CCDS11818.1	17q25	2008-02-05				ENSG00000167363			24822	protein-coding gene	gene with protein product		608425				11522682, 14641062	Standard	NM_022158		Approved		uc010wvs.1	Q9H479		ENST00000300784.7:c.906C>T	17.37:g.80708607C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_022158		Silent	SNP	ENST00000300784.7	37	CCDS11818.1																																																																																			C|0.988;T|0.012	0.012	strong		0.667	FN3K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439229.1	NM_022158	
WDFY4	57705	hgsc.bcm.edu	37	10	49998780	49998780	+	Missense_Mutation	SNP	G	G	A	rs41282009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:49998780G>A	ENST00000325239.5	+	22	4102	c.4075G>A	c.(4075-4077)Gta>Ata	p.V1359I	WDFY4_ENST00000413659.2_Intron	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1359						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						AGGGGTGAGGGTATTCCACTC	0.547													G|||	585	0.116813	0.0076	0.1354	5008	,	,		21810	0.3075		0.0378	False		,,,				2504	0.136				p.V1359I		Atlas-SNP	.											.	WDFY4	205	.	0			c.G4075A						PASS	.	G	ILE/VAL	22,1362		1,20,671	89.0	77.0	81.0		4075	4.3	1.0	10	dbSNP_127	81	128,3054		3,122,1466	yes	missense	WDFY4	NM_020945.1	29	4,142,2137	AA,AG,GG		4.0226,1.5896,3.2852	benign	1359/3185	49998780	150,4416	692	1591	2283	SO:0001583	missense	57705	exon23			GTGAGGGTATTCC	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.4075G>A	10.37:g.49998780G>A	ENSP00000320563:p.Val1359Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	136	70	0.514706	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	271|271	0.12408424908424909|0.12408424908424909	9|9	0.018292682926829267|0.018292682926829267	37|37	0.10220994475138122|0.10220994475138122	197|197	0.34440559440559443|0.34440559440559443	28|28	0.036939313984168866|0.036939313984168866	G|G	12.79|12.79	2.043021|2.043021	0.36085|0.36085	0.015896|0.015896	0.040226|0.040226	ENSG00000128815|ENSG00000128815	ENST00000312002|ENST00000426033;ENST00000325239	.|T	.|0.57907	.|0.37	5.18|5.18	4.28|4.28	0.50868|0.50868	.|.	.|0.317537	.|0.30383	.|N	.|0.009757	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.52573|0.52573	1.65|1.65	0.09310|0.09310	P|P	0.9999999999999167|0.9999999999999167	.|P	.|0.34864	.|0.473	.|B	.|0.28553	.|0.091	T|T	0.33599|0.33599	-0.9862|-0.9862	4|8	.|.	.|.	.|.	.|.	11.738|11.738	0.51775|0.51775	0.0825:0.0:0.9175:0.0|0.0825:0.0:0.9175:0.0	rs41282009|rs41282009	.|1359	.|Q6ZS81	.|WDFY4_HUMAN	D|I	449|1359	.|ENSP00000320563:V1359I	.|.	G|V	+|+	2|1	0|0	WDFY4|WDFY4	49668786|49668786	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.571000|0.571000	0.35966|0.35966	3.911000|3.911000	0.56378|0.56378	1.319000|1.319000	0.45190|0.45190	-0.232000|-0.232000	0.12228|0.12228	GGT|GTA	G|0.892;A|0.108	0.108	strong		0.547	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
CR1	1378	hgsc.bcm.edu	37	1	207782707	207782707	+	Missense_Mutation	SNP	A	A	G	rs17259045	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207782707A>G	ENST00000367049.4	+	37	5969	c.5969A>G	c.(5968-5970)aAt>aGt	p.N1990S	CR1_ENST00000367052.1_Missense_Mutation_p.N1540S|CR1_ENST00000367053.1_Missense_Mutation_p.N1540S|CR1_ENST00000400960.2_Missense_Mutation_p.N1540S|CR1_ENST00000367051.1_Missense_Mutation_p.N1540S|RP11-78B10.2_ENST00000597497.1_RNA|RP11-78B10.2_ENST00000596003.1_RNA	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1540					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TCTTTTCACAATGGAACGGTG	0.438													A|||	286	0.0571086	0.0083	0.1585	5008	,	,		18757	0.002		0.0954	False		,,,				2504	0.0685				p.N1990S		Atlas-SNP	.											.	CR1	354	.	0			c.A5969G						PASS	.	A	SER/ASN,SER/ASN	96,3838		0,96,1871	109.0	106.0	107.0		4619,5969	1.5	0.0	1	dbSNP_123	107	861,7445		48,765,3340	yes	missense,missense	CR1	NM_000573.3,NM_000651.4	46,46	48,861,5211	GG,GA,AA		10.366,2.4403,7.8186	benign,benign	1540/2040,1990/2490	207782707	957,11283	1967	4153	6120	SO:0001583	missense	1378	exon37			TTCACAATGGAAC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.5969A>G	1.37:g.207782707A>G	ENSP00000356016:p.Asn1990Ser	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	210	101	0.480952	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	129	0.059065934065934064	8	0.016260162601626018	52	0.143646408839779	1	0.0017482517482517483	68	0.08970976253298153	A	2.820	-0.244986	0.05906	0.024403	0.10366	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;-0.06	2.66	1.51	0.23008	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00271	0.0008	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.10296	0.0;0.0;0.003	B;B;B	0.08055	0.0;0.001;0.003	T	0.07214	-1.0784	8	0.25106	T	0.35	.	6.7686	0.23581	0.8656:0.0:0.1344:0.0	rs17259045;rs17259045	1540;1540;1990	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	S	1540;1540;1540;1540;1090;1990	ENSP00000356019:N1540S;ENSP00000356018:N1540S;ENSP00000356020:N1540S;ENSP00000383744:N1540S;ENSP00000436139:N1090S;ENSP00000356016:N1990S	ENSP00000356016:N1990S	N	+	2	0	CR1	205849330	0.642000	0.27260	0.001000	0.08648	0.005000	0.04900	-0.140000	0.10342	0.022000	0.15160	-1.477000	0.00996	AAT	A|0.938;G|0.062	0.062	strong		0.438	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
OR4E2	26686	hgsc.bcm.edu	37	14	22134018	22134018	+	Missense_Mutation	SNP	C	C	T	rs61732411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:22134018C>T	ENST00000408935.1	+	1	722	c.722C>T	c.(721-723)tCg>tTg	p.S241L		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		TCTACCTGCTCGGCCCACTTC	0.527													C|||	699	0.139577	0.2526	0.1628	5008	,	,		21318	0.005		0.2038	False		,,,				2504	0.0429				p.S241L		Atlas-SNP	.											OR4E2,NS,carcinoma,-1,1	OR4E2	44	1	0			c.C722T						PASS	.	C	LEU/SER	921,2999		109,703,1148	96.0	93.0	94.0		722	4.8	1.0	14	dbSNP_129	94	1719,6581		190,1339,2621	yes	missense	OR4E2	NM_001001912.1	145	299,2042,3769	TT,TC,CC		20.7108,23.4949,21.6039	benign	241/314	22134018	2640,9580	1960	4150	6110	SO:0001583	missense	26686	exon1			CCTGCTCGGCCCA		CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"""GPCR / Class A : Olfactory receptors"""	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.722C>T	14.37:g.22134018C>T	ENSP00000386195:p.Ser241Leu	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	236	235	0.995763	NM_001001912	Q6IET6|Q96R62	Missense_Mutation	SNP	ENST00000408935.1	37	CCDS41916.1	311	0.1423992673992674	106	0.21544715447154472	59	0.16298342541436464	2	0.0034965034965034965	144	0.18997361477572558	C	12.41	1.928415	0.34002	0.234949	0.207108	ENSG00000221977	ENST00000408935	T	0.35789	1.29	5.68	4.79	0.61399	GPCR, rhodopsin-like superfamily (1);	0.255127	0.19259	U	0.118721	T	0.00012	0.0000	L	0.59967	1.855	0.39721	P	0.02852600000000005	P	0.35363	0.497	B	0.33254	0.16	T	0.10474	-1.0628	9	0.54805	T	0.06	.	13.0304	0.58839	0.0:0.9212:0.0:0.0788	rs61732411	241	Q8NGC2	OR4E2_HUMAN	L	241	ENSP00000386195:S241L	ENSP00000386195:S241L	S	+	2	0	OR4E2	21203858	0.000000	0.05858	0.997000	0.53966	0.487000	0.33371	0.099000	0.15210	1.534000	0.49203	0.655000	0.94253	TCG	C|0.830;T|0.170	0.170	strong		0.527	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1		
PPP2R2B	5521	hgsc.bcm.edu	37	5	145972610	145972610	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:145972610G>A	ENST00000394413.3	-	8	1546	c.976C>T	c.(976-978)Cgc>Tgc	p.R326C	PPP2R2B_ENST00000394409.3_Missense_Mutation_p.R384C|PPP2R2B_ENST00000336640.6_Missense_Mutation_p.R329C|PPP2R2B_ENST00000356826.3_Missense_Mutation_p.R326C|PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000394411.4_Missense_Mutation_p.R326C|PPP2R2B_ENST00000453001.1_Missense_Mutation_p.R326C|PPP2R2B_ENST00000394410.2_Missense_Mutation_p.R315C|PPP2R2B_ENST00000504198.1_Missense_Mutation_p.R332C|PPP2R2B_ENST00000508545.2_Missense_Mutation_p.R315C|PPP2R2B_ENST00000394414.1_Missense_Mutation_p.R392C|CTB-99A3.1_ENST00000512730.1_RNA			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta	326					apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGCTTGCTGCGGAGGTAGTCA	0.418																																					p.R432C		Atlas-SNP	.											PPP2R2B_ENST00000508545,NS,carcinoma,0,4	PPP2R2B	271	4	0			c.C1294T						scavenged	.						144.0	154.0	151.0					5																	145972610		2203	4300	6503	SO:0001583	missense	5521	exon9			TGCTGCGGAGGTA	M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9305	protein-coding gene	gene with protein product	"""PP2A subunit B isoform beta"""	604325	"""spinocerebellar ataxia 12"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"""	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000394413.3:c.976C>T	5.37:g.145972610G>A	ENSP00000377935:p.Arg326Cys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	148	3	0.0202703	NM_181675	A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	Missense_Mutation	SNP	ENST00000394413.3	37	CCDS4284.1	.	.	.	.	.	.	.	.	.	.	G	18.86	3.714039	0.68730	.	.	ENSG00000156475	ENST00000394413;ENST00000508545;ENST00000394414;ENST00000394411;ENST00000356826;ENST00000453001;ENST00000394410;ENST00000336640;ENST00000504198;ENST00000394409	T;T;T;T;T;T;T;T;T;T	0.77358	-1.08;-1.08;1.18;-1.08;-1.08;-1.08;-1.08;-1.08;-1.09;1.18	5.39	5.39	0.77823	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.90584	0.7048	M	0.93550	3.43	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.74023	0.967;0.967;0.951;0.967;0.982;0.973	D	0.92388	0.5919	10	0.87932	D	0	-13.6789	15.0059	0.71513	0.0:0.0:0.8572:0.1428	.	384;332;315;392;329;326	Q00005-4;Q00005-3;G3V149;Q00005-5;Q00005-2;Q00005	.;.;.;.;.;2ABB_HUMAN	C	326;315;392;326;326;326;315;329;332;384	ENSP00000377935:R326C;ENSP00000431320:R315C;ENSP00000377936:R392C;ENSP00000377933:R326C;ENSP00000349283:R326C;ENSP00000398779:R326C;ENSP00000377932:R315C;ENSP00000336591:R329C;ENSP00000421396:R332C;ENSP00000377931:R384C	ENSP00000336591:R329C	R	-	1	0	AC011357.1	145952803	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	1.492000	0.35594	2.808000	0.96608	0.655000	0.94253	CGC	.	.	none		0.418	PPP2R2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251893.2	NM_181678	
FCN2	2220	hgsc.bcm.edu	37	9	137779091	137779091	+	Missense_Mutation	SNP	G	G	T	rs7851696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:137779091G>T	ENST00000291744.6	+	8	782	c.772G>T	c.(772-774)Gct>Tct	p.A258S	FCN2_ENST00000350339.2_Missense_Mutation_p.A220S	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	258	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		A -> S (in dbSNP:rs7851696).		complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		CGGAAATTGTGCTGTGATGTT	0.493													G|||	780	0.155751	0.2095	0.121	5008	,	,		22332	0.1895		0.1044	False		,,,				2504	0.1258				p.A258S		Atlas-SNP	.											.	FCN2	55	.	0			c.G772T	GRCh37	CM051923	FCN2	M	rs7851696	PASS	.	G	SER/ALA,SER/ALA	850,3556	335.7+/-304.0	86,678,1439	168.0	148.0	155.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	772,658	4.1	0.1	9	dbSNP_116	155	919,7681	204.1+/-246.9	48,823,3429	yes	missense,missense	FCN2	NM_004108.2,NM_015837.2	99,99	134,1501,4868	TT,TG,GG		10.686,19.2919,13.6014	probably-damaging,probably-damaging	258/314,220/276	137779091	1769,11237	2203	4300	6503	SO:0001583	missense	2220	exon8			AATTGTGCTGTGA	D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"""Fibrinogen C domain containing"""	3624	protein-coding gene	gene with protein product	"""hucolin"", ""collagen/fibrinogen domain-containing protein 2"", ""ficolin B"", ""serum lectin p35"", ""L-ficolin"""	601624	"""ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"""			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.772G>T	9.37:g.137779091G>T	ENSP00000291744:p.Ala258Ser	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	209	96	0.45933	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	326	0.14926739926739926	94	0.1910569105691057	50	0.13812154696132597	102	0.17832167832167833	80	0.10554089709762533	G	21.6	4.173027	0.78452	0.192919	0.10686	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.79352	-1.26;-1.26	4.05	4.05	0.47172	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.000000	0.41938	D	0.000783	T	0.00695	0.0023	M	0.87328	2.875	0.09310	P	0.999999198096	P;P	0.51537	0.946;0.865	P;P	0.59889	0.865;0.839	T	0.18967	-1.0320	9	0.87932	D	0	.	13.7007	0.62606	0.0:0.0:1.0:0.0	rs7851696;rs17549200;rs57217091;rs7851696	220;258	Q15485-2;Q15485	.;FCN2_HUMAN	S	220;258	ENSP00000291741:A220S;ENSP00000291744:A258S	ENSP00000291744:A258S	A	+	1	0	FCN2	136918912	1.000000	0.71417	0.077000	0.20336	0.008000	0.06430	6.062000	0.71155	1.791000	0.52520	0.563000	0.77884	GCT	G|0.858;T|0.142	0.142	strong		0.493	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	
CDCA7L	55536	hgsc.bcm.edu	37	7	21956405	21956405	+	Silent	SNP	G	G	A	rs1128250	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:21956405G>A	ENST00000406877.3	-	2	411	c.132C>T	c.(130-132)tgC>tgT	p.C44C	CDCA7L_ENST00000465490.1_5'UTR|CDCA7L_ENST00000356195.5_Silent_p.C10C|CDCA7L_ENST00000373934.4_Silent_p.C44C	NM_018719.4	NP_061189.2	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like	44					positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	29						CAAAACTATCGCAGCTCTCCT	0.468													G|||	1548	0.309105	0.1074	0.4179	5008	,	,		17366	0.5784		0.1779	False		,,,				2504	0.362				p.C44C		Atlas-SNP	.											CDCA7L,caecum,carcinoma,0,1	CDCA7L	56	1	0			c.C132T						PASS	.	G	,,	581,3825	258.6+/-262.5	35,511,1657	173.0	164.0	167.0		30,132,132	-9.0	0.5	7	dbSNP_86	167	1598,7002	297.5+/-303.5	156,1286,2858	no	coding-synonymous,coding-synonymous,coding-synonymous	CDCA7L	NM_001127370.2,NM_001127371.2,NM_018719.4	,,	191,1797,4515	AA,AG,GG		18.5814,13.1866,16.7538	,,	10/421,44/409,44/455	21956405	2179,10827	2203	4300	6503	SO:0001819	synonymous_variant	55536	exon2			ACTATCGCAGCTC		CCDS5374.1, CCDS47558.1, CCDS47559.1	7p15.3	2007-04-27			ENSG00000164649	ENSG00000164649			30777	protein-coding gene	gene with protein product		609685				16829576	Standard	NM_018719		Approved	RAM2, R1, JPO2	uc010kuk.3	Q96GN5	OTTHUMG00000128429	ENST00000406877.3:c.132C>T	7.37:g.21956405G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	140	69	0.492857	NM_018719	A4D141|A6NF50|B3KTR5|B4DUT3|C9K0Y1|Q6PIL4|Q86YT0|Q8IXN5|Q96C70|Q9H9A2|Q9NPV2	Silent	SNP	ENST00000406877.3	37	CCDS5374.1																																																																																			G|0.773;A|0.227	0.227	strong		0.468	CDCA7L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250218.4	NM_018719	
NOX3	50508	hgsc.bcm.edu	37	6	155775980	155775980	+	Silent	SNP	G	G	T	rs12195525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:155775980G>T	ENST00000159060.2	-	3	322	c.220C>A	c.(220-222)Cga>Aga	p.R74R		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	74	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		ATAAGGTTTCGACTGACAGGT	0.368													G|||	644	0.128594	0.1067	0.2291	5008	,	,		17917	0.1171		0.1044	False		,,,				2504	0.1237				p.R74R		Atlas-SNP	.											NOX3,rectum,carcinoma,+1,1	NOX3	93	1	0			c.C220A						PASS	.	G		472,3934	216.1+/-234.9	30,412,1761	65.0	65.0	65.0		220	5.9	1.0	6	dbSNP_120	65	965,7635	208.9+/-250.2	57,851,3392	no	coding-synonymous	NOX3	NM_015718.2		87,1263,5153	TT,TG,GG		11.2209,10.7127,11.0487		74/569	155775980	1437,11569	2203	4300	6503	SO:0001819	synonymous_variant	50508	exon3			GGTTTCGACTGAC	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.220C>A	6.37:g.155775980G>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	37	CCDS5250.1																																																																																			G|0.886;T|0.114	0.114	strong		0.368	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
ZNF414	84330	hgsc.bcm.edu	37	19	8578000	8578000	+	Missense_Mutation	SNP	G	G	A	rs1064010	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8578000G>A	ENST00000255616.8	-	2	330	c.229C>T	c.(229-231)Cct>Tct	p.P77S	ZNF414_ENST00000393927.4_Missense_Mutation_p.P77S	NM_032370.2	NP_115746.2	Q96IQ9	ZN414_HUMAN	zinc finger protein 414	77			P -> S (in dbSNP:rs1064010). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(2)	2						CCGGGGCCAGGCTGGCAGCTG	0.701													G|||	1028	0.205272	0.3041	0.1686	5008	,	,		15338	0.1746		0.1978	False		,,,				2504	0.137				p.P77S		Atlas-SNP	.											.	ZNF414	25	.	0			c.C229T						PASS	.	G	SER/PRO,SER/PRO	926,3244		105,716,1264	7.0	6.0	6.0		229,229	-1.0	0.1	19	dbSNP_86	6	1228,7006		91,1046,2980	no	missense,missense	ZNF414	NM_001146175.1,NM_032370.2	74,74	196,1762,4244	AA,AG,GG		14.9138,22.2062,17.3654	benign,benign	77/391,77/313	8578000	2154,10250	2085	4117	6202	SO:0001583	missense	84330	exon2			GGCCAGGCTGGCA	AK074191	CCDS12205.1, CCDS54211.1	19p13.2	2008-02-05				ENSG00000133250		"""Zinc fingers, C2H2-type"""	20630	protein-coding gene	gene with protein product							Standard	NM_032370		Approved	MGC15716, Zfp414	uc002mke.4	Q96IQ9		ENST00000255616.8:c.229C>T	19.37:g.8578000G>A	ENSP00000255616:p.Pro77Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_032370	A8MY94	Missense_Mutation	SNP	ENST00000255616.8	37	CCDS12205.1	462	0.21153846153846154	164	0.3333333333333333	58	0.16022099447513813	95	0.1660839160839161	145	0.19129287598944592	G	9.250	1.040485	0.19669	0.222062	0.149138	ENSG00000133250	ENST00000393927;ENST00000255616	T;T	0.06528	3.29;3.29	4.45	-0.996	0.10218	.	0.615749	0.14178	N	0.336251	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.47522	-0.9111	9	0.20519	T	0.43	0.0073	1.1561	0.01796	0.1978:0.1465:0.4299:0.2257	rs1064010;rs3205029	77;77	Q96IQ9;A8MY94	ZN414_HUMAN;.	S	77	ENSP00000377504:P77S;ENSP00000255616:P77S	ENSP00000255616:P77S	P	-	1	0	ZNF414	8484000	0.001000	0.12720	0.125000	0.21846	0.934000	0.57294	0.029000	0.13666	-0.294000	0.08973	0.655000	0.94253	CCT	G|0.788;A|0.212	0.212	strong		0.701	ZNF414-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460199.2	NM_032370	
OR10A6	390093	hgsc.bcm.edu	37	11	7950024	7950024	+	Silent	SNP	A	A	G	rs12272735	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7950024A>G	ENST00000309838.2	-	1	185	c.186T>C	c.(184-186)ttT>ttC	p.F62F		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGTTCAGGAGAAACAGGTACA	0.443													A|||	1669	0.333267	0.2617	0.4568	5008	,	,		17833	0.2698		0.3718	False		,,,				2504	0.3681				p.F62F		Atlas-SNP	.											.	OR10A6	49	.	0			c.T186C						PASS	.	A		1257,3145	430.8+/-342.7	187,883,1131	119.0	114.0	116.0		186	-3.1	0.9	11	dbSNP_120	116	3233,5359	486.1+/-371.8	643,1947,1706	no	coding-synonymous	OR10A6	NM_001004461.1		830,2830,2837	GG,GA,AA		37.628,28.5552,34.5544		62/315	7950024	4490,8504	2201	4296	6497	SO:0001819	synonymous_variant	390093	exon1			CAGGAGAAACAGG	AB065515	CCDS31420.1	11p15.4	2012-08-09			ENSG00000175393	ENSG00000175393		"""GPCR / Class A : Olfactory receptors"""	15132	protein-coding gene	gene with protein product							Standard	NM_001004461		Approved		uc010rbh.2	Q8NH74	OTTHUMG00000165671	ENST00000309838.2:c.186T>C	11.37:g.7950024A>G		Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	260	111	0.426923	NM_001004461	Q6IF59	Silent	SNP	ENST00000309838.2	37	CCDS31420.1																																																																																			A|0.658;G|0.342	0.342	strong		0.443	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461	
CASS4	57091	hgsc.bcm.edu	37	20	55033635	55033635	+	Silent	SNP	C	C	T	rs3746624	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:55033635C>T	ENST00000360314.3	+	7	2418	c.2193C>T	c.(2191-2193)aaC>aaT	p.N731N	CASS4_ENST00000371336.3_Silent_p.N731N|AL121914.1_ENST00000390795.2_RNA|CASS4_ENST00000434344.1_Silent_p.N294N	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	731					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						ACGTGCGCAACGAGATCCTCC	0.627													C|||	1846	0.36861	0.0711	0.4784	5008	,	,		19357	0.6786		0.335	False		,,,				2504	0.408				p.N731N		Atlas-SNP	.											.	CASS4	121	.	0			c.C2193T						PASS	.	C	,,,	494,3912	230.4+/-244.6	36,422,1745	74.0	59.0	64.0		2031,882,2193,2193	-8.1	0.1	20	dbSNP_107	64	2890,5710	451.8+/-362.8	463,1964,1873	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	,,,	499,2386,3618	TT,TC,CC		33.6047,11.212,26.0188	,,,	677/733,294/350,731/787,731/787	55033635	3384,9622	2203	4300	6503	SO:0001819	synonymous_variant	57091	exon6			GCGCAACGAGATC	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.2193C>T	20.37:g.55033635C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Silent	SNP	ENST00000360314.3	37	CCDS33492.1																																																																																			C|0.699;T|0.301	0.301	strong		0.627	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
NBPF4	148545	hgsc.bcm.edu	37	1	108771721	108771721	+	Missense_Mutation	SNP	T	T	C	rs79996376	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:108771721T>C	ENST00000415641.3	-	13	1684	c.1481A>G	c.(1480-1482)cAg>cGg	p.Q494R		NM_001143989.2	NP_001137461.1	Q96M43	NBPF4_HUMAN	neuroblastoma breakpoint family, member 4	494	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				endometrium(2)|lung(1)|skin(1)	4						CACCTCTGACTGGTGGTGGCT	0.582																																					p.Q494R		Atlas-SNP	.											.	NBPF4	4	.	0			c.A1481G						PASS	.						75.0	77.0	76.0					1																	108771721		692	1591	2283	SO:0001583	missense	148545	exon13			TCTGACTGGTGGT	AK057395	CCDS44182.1	1p13.3	2013-01-17			ENSG00000196427	ENSG00000196427		"""neuroblastoma breakpoint family"""	26550	protein-coding gene	gene with protein product		613994				16079250	Standard	NM_001143989		Approved	FLJ32833	uc009weo.2	Q96M43	OTTHUMG00000011318	ENST00000415641.3:c.1481A>G	1.37:g.108771721T>C	ENSP00000389237:p.Gln494Arg	Somatic	309	2	0.00647249		WXS	Illumina HiSeq	Phase_I	710	513	0.722535	NM_001143989	Q5T483	Missense_Mutation	SNP	ENST00000415641.3	37	CCDS44182.1	.	.	.	.	.	.	.	.	.	.	C	1.000	-0.691135	0.03303	.	.	ENSG00000196427	ENST00000415641;ENST00000428601;ENST00000370038	T	0.02158	4.42	1.55	-0.859	0.10685	.	.	.	.	.	T	0.00241	0.0007	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36212	-0.9757	9	0.06236	T	0.91	.	3.8615	0.08998	0.2811:0.5354:0.0:0.1835	.	494	Q5T483	.	R	494;523;494	ENSP00000389237:Q494R	ENSP00000359055:Q494R	Q	-	2	0	NBPF4	108573244	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.262000	0.08682	-0.739000	0.04809	-2.186000	0.00314	CAG	T|0.838;C|0.162	0.162	strong		0.582	NBPF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031255.5	NM_152488	
TMA16	55319	hgsc.bcm.edu	37	4	164435265	164435265	+	Missense_Mutation	SNP	A	A	C	rs2304802	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:164435265A>C	ENST00000358572.5	+	4	535	c.194A>C	c.(193-195)cAa>cCa	p.Q65P	TMA16_ENST00000513134.1_Missense_Mutation_p.Q65P|TMA16_ENST00000511562.1_3'UTR|TMA16_ENST00000508268.1_Missense_Mutation_p.Q65P|TMA16_ENST00000513272.1_Missense_Mutation_p.Q65P	NM_018352.2	NP_060822.2	Q96EY4	TMA16_HUMAN	translation machinery associated 16 homolog (S. cerevisiae)	65			Q -> P (in dbSNP:rs2304802). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)		p.Q65P(2)									CTTGATCCCCAAAAAAAGAGA	0.358													A|||	1903	0.379992	0.2504	0.6009	5008	,	,		19903	0.3423		0.4682	False		,,,				2504	0.3466				p.Q65P		Atlas-SNP	.											C4orf43,NS,carcinoma,0,2	.	.	2	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.A194C						PASS	.	A	PRO/GLN	977,2675		145,687,994	95.0	86.0	89.0		194	3.0	0.1	4	dbSNP_100	89	3823,4325		962,1899,1213	yes	missense	C4orf43	NM_018352.2	76	1107,2586,2207	CC,CA,AA		46.9195,26.7525,40.678	benign	65/204	164435265	4800,7000	1826	4074	5900	SO:0001583	missense	55319	exon4			ATCCCCAAAAAAA		CCDS43278.1	4q32.3	2012-03-02	2012-03-02	2012-03-02	ENSG00000198498	ENSG00000198498			25638	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 43"""	C4orf43		12477932	Standard	NM_018352		Approved	FLJ11184	uc003iqq.4	Q96EY4	OTTHUMG00000161528	ENST00000358572.5:c.194A>C	4.37:g.164435265A>C	ENSP00000351380:p.Gln65Pro	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_018352	Q0P6E4|Q0P6J1|Q9NUR7	Missense_Mutation	SNP	ENST00000358572.5	37	CCDS43278.1	901	0.4125457875457875	124	0.25203252032520324	216	0.5966850828729282	197	0.34440559440559443	364	0.48021108179419525	A	6.442	0.449727	0.12223	0.267525	0.469195	ENSG00000198498	ENST00000358572;ENST00000513272;ENST00000513134;ENST00000508268	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.39	2.96	0.34315	.	0.787793	0.12848	N	0.434179	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40608	-0.9554	9	0.37606	T	0.19	-0.3681	8.7145	0.34403	0.8405:0.0:0.1595:0.0	rs2304802;rs3207214;rs17576322;rs17850804;rs52811362;rs2304802	65	Q96EY4	CD043_HUMAN	P	65	ENSP00000351380:Q65P;ENSP00000426933:Q65P;ENSP00000423901:Q65P;ENSP00000423375:Q65P	ENSP00000351380:Q65P	Q	+	2	0	C4orf43	164654715	0.002000	0.14202	0.068000	0.19968	0.570000	0.35934	1.401000	0.34589	0.978000	0.38470	0.528000	0.53228	CAA	C|0.418;N|0.000	0.418	strong		0.358	TMA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365208.1	NM_018352	
KHDRBS2	202559	hgsc.bcm.edu	37	6	62887099	62887099	+	Silent	SNP	C	C	T	rs6921170	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:62887099C>T	ENST00000281156.4	-	2	488	c.210G>A	c.(208-210)caG>caA	p.Q70Q		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	70	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		CCTTTGGATACTGCTTGACAG	0.294													T|||	2967	0.592452	0.6256	0.4798	5008	,	,		15390	0.5923		0.6571	False		,,,				2504	0.5613				p.Q70Q		Atlas-SNP	.											.	KHDRBS2	103	.	0			c.G210A						PASS	.	T		2748,1656	503.5+/-365.6	854,1040,308	110.0	103.0	105.0		210	-7.1	0.6	6	dbSNP_116	105	5294,3302	490.0+/-372.7	1622,2050,626	no	coding-synonymous	KHDRBS2	NM_152688.2		2476,3090,934	TT,TC,CC		38.4132,37.6022,38.1385		70/350	62887099	8042,4958	2202	4298	6500	SO:0001819	synonymous_variant	202559	exon2			TGGATACTGCTTG	BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"""Sam68-like mammalian protein 1"""	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.210G>A	6.37:g.62887099C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Silent	SNP	ENST00000281156.4	37	CCDS4963.1																																																																																			C|0.396;T|0.604	0.604	strong		0.294	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688	
NID2	22795	hgsc.bcm.edu	37	14	52495455	52495455	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:52495455G>A	ENST00000216286.5	-	11	2514	c.2515C>T	c.(2515-2517)Cgg>Tgg	p.R839W	NID2_ENST00000541773.1_Missense_Mutation_p.R786W	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	839	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)	p.R839W(2)		NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					CAAGTATGCCGGTCATCTGCA	0.458																																					p.R839W		Atlas-SNP	.											NID2,colon,carcinoma,0,3	NID2	201	3	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C2515T						scavenged	.						95.0	88.0	90.0					14																	52495455		2203	4300	6503	SO:0001583	missense	22795	exon11			TATGCCGGTCATC	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.2515C>T	14.37:g.52495455G>A	ENSP00000216286:p.Arg839Trp	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	201	3	0.0149254	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.53|16.53	3.149046|3.149046	0.57151|0.57151	.|.	.|.	ENSG00000087303|ENSG00000087303	ENST00000556572|ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	.|D;D	.|0.92446	.|-2.27;-3.04	5.94|5.94	0.526|0.526	0.17078|0.17078	.|EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|1.160920	.|0.06054	.|N	.|0.657132	D|D	0.91690|0.91690	0.7373|0.7373	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	0.999993|0.999993	.|D;D;D;D	.|0.76494	.|0.994;0.997;0.999;0.995	.|P;P;D;P	.|0.63033	.|0.892;0.648;0.91;0.586	T|T	0.81291|0.81291	-0.0999|-0.0999	5|10	.|0.72032	.|D	.|0.01	.|.	4.5713|4.5713	0.12210|0.12210	0.0733:0.2894:0.4078:0.2295|0.0733:0.2894:0.4078:0.2295	.|.	.|433;786;841;839	.|E7EPP3;Q14112-2;Q5CZI2;Q14112	.|.;.;.;NID2_HUMAN	L|W	155|839;433;786;841	.|ENSP00000216286:R839W;ENSP00000443730:R786W	.|ENSP00000216286:R839W	P|R	-|-	2|1	0|2	NID2|NID2	51565205|51565205	0.004000|0.004000	0.15560|0.15560	0.328000|0.328000	0.25416|0.25416	0.795000|0.795000	0.44927|0.44927	-0.030000|-0.030000	0.12308|0.12308	0.382000|0.382000	0.24878|0.24878	0.563000|0.563000	0.77884|0.77884	CCG|CGG	.	.	none		0.458	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
TDGF1	6997	hgsc.bcm.edu	37	3	46620614	46620614	+	Missense_Mutation	SNP	T	T	C	rs11130097	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:46620614T>C	ENST00000296145.5	+	2	798	c.65T>C	c.(64-66)gTc>gCc	p.V22A	LRRC2_ENST00000296144.3_Intron|TDGF1_ENST00000542931.1_Missense_Mutation_p.V6A	NM_003212.3	NP_003203.1	P13385	TDGF1_HUMAN	teratocarcinoma-derived growth factor 1	22			V -> A (in dbSNP:rs11130097). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		activation of MAPK activity (GO:0000187)|anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle cell differentiation (GO:0055007)|cell differentiation (GO:0030154)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-6 (GO:0071354)|cellular response to tumor necrosis factor (GO:0071356)|embryo development (GO:0009790)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of signal transduction (GO:0009966)|vasculogenesis (GO:0001570)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	growth factor activity (GO:0008083)|receptor binding (GO:0005102)			cervix(2)|endometrium(1)|kidney(1)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0173)|Kidney(197;0.0204)		ATTTCTAAAGTCTTTGAACTG	0.383													C|||	2539	0.506989	0.4887	0.4942	5008	,	,		18591	0.4157		0.5497	False		,,,				2504	0.591				p.V22A		Atlas-SNP	.											TDGF1,NS,carcinoma,-1,1	TDGF1	17	1	0			c.T65C						PASS	.	C	ALA/VAL,ALA/VAL	2150,2256	595.8+/-388.5	529,1092,582	196.0	181.0	186.0		17,65	1.4	0.0	3	dbSNP_120	186	4576,4024	556.1+/-386.8	1203,2170,927	yes	missense,missense	TDGF1	NM_001174136.1,NM_003212.3	64,64	1732,3262,1509	CC,CT,TT		46.7907,48.7971,48.2854	benign,benign	6/173,22/189	46620614	6726,6280	2203	4300	6503	SO:0001583	missense	6997	exon2			CTAAAGTCTTTGA	M96955	CCDS2742.1, CCDS54575.1	3p21.31	2012-10-03			ENSG00000241186	ENSG00000241186			11701	protein-coding gene	gene with protein product		187395				1882841, 10393436	Standard	NM_003212		Approved	CRIPTO, CR, Cripto-1	uc021wxd.1	P13385	OTTHUMG00000133482	ENST00000296145.5:c.65T>C	3.37:g.46620614T>C	ENSP00000296145:p.Val22Ala	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	213	212	0.995305	NM_003212	Q8TCC1	Missense_Mutation	SNP	ENST00000296145.5	37	CCDS2742.1	1020	0.46703296703296704	205	0.4166666666666667	182	0.5027624309392266	227	0.3968531468531469	406	0.5356200527704486	C	0.005	-2.153231	0.00325	0.487971	0.532093	ENSG00000241186	ENST00000542931;ENST00000296145	T;T	0.60171	0.21;0.23	4.17	1.43	0.22495	.	0.643479	0.15159	N	0.277248	T	0.00012	0.0000	N	0.00823	-1.155	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45585	-0.9251	9	0.02654	T	1	.	6.6908	0.23169	0.0:0.6052:0.0:0.3948	rs11130097;rs17855497;rs11130097	22	P13385	TDGF1_HUMAN	A	6;22	ENSP00000446375:V6A;ENSP00000296145:V22A	ENSP00000296145:V22A	V	+	2	0	AC104304.1	46595618	0.000000	0.05858	0.003000	0.11579	0.197000	0.23852	-0.226000	0.09139	0.064000	0.16427	-0.735000	0.03563	GTC	T|0.504;C|0.496	0.496	strong		0.383	TDGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257378.2	NM_003212	
MUC16	94025	hgsc.bcm.edu	37	19	9048035	9048035	+	Missense_Mutation	SNP	G	G	C	rs10417358	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9048035G>C	ENST00000397910.4	-	5	33799	c.33596C>G	c.(33595-33597)gCt>gGt	p.A11199G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11201	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGGGGAGACAGCTAAAGTTGG	0.453													G|||	949	0.189497	0.1982	0.1988	5008	,	,		24115	0.0258		0.2823	False		,,,				2504	0.2444				p.A11199G		Atlas-SNP	.											.	MUC16	4315	.	0			c.C33596G						PASS	.		GLY/ALA	753,3155		71,611,1272	60.0	53.0	55.0		33596	1.4	0.0	19	dbSNP_119	55	2512,5794		398,1716,2039	yes	missense	MUC16	NM_024690.2	60	469,2327,3311	CC,CG,GG		30.2432,19.2682,26.7316	possibly-damaging	11199/14508	9048035	3265,8949	1954	4153	6107	SO:0001583	missense	94025	exon5			GAGACAGCTAAAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33596C>G	19.37:g.9048035G>C	ENSP00000381008:p.Ala11199Gly	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	408	0.18681318681318682	103	0.20934959349593496	76	0.20994475138121546	11	0.019230769230769232	218	0.287598944591029	g	9.969	1.225012	0.22457	0.192682	0.302432	ENSG00000181143	ENST00000397910	T	0.02763	4.17	2.54	1.44	0.22558	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	.	.	.	P	0.34977	0.478	B	0.41236	0.351	T	0.51529	-0.8694	8	0.87932	D	0	.	5.6913	0.17831	0.1608:0.0:0.8392:0.0	rs10417358;rs52819888;rs10417358	11199	B5ME49	.	G	11199	ENSP00000381008:A11199G	ENSP00000381008:A11199G	A	-	2	0	MUC16	8909035	0.002000	0.14202	0.001000	0.08648	0.590000	0.36582	0.657000	0.24963	0.586000	0.29626	0.306000	0.20318	GCT	G|0.780;C|0.220	0.220	strong		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
OR52E4	390081	hgsc.bcm.edu	37	11	5906291	5906291	+	Missense_Mutation	SNP	T	T	C	rs11823842	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5906291T>C	ENST00000316987.2	+	1	791	c.769T>C	c.(769-771)Ttt>Ctt	p.F257L		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	257			F -> L (in dbSNP:rs11823842).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACACCAGCATTTTTTTCTTT	0.433													T|||	1790	0.357428	0.3207	0.402	5008	,	,		21006	0.3641		0.4085	False		,,,				2504	0.316				p.F257L		Atlas-SNP	.											.	OR52E4	65	.	0			c.T769C						PASS	.	T	LEU/PHE	1495,2907	473.5+/-356.7	259,977,965	217.0	197.0	204.0		769	3.9	1.0	11	dbSNP_120	204	3624,4968	522.1+/-380.0	780,2064,1452	yes	missense	OR52E4	NM_001005165.1	22	1039,3041,2417	CC,CT,TT		42.1788,33.9618,39.3951	benign	257/313	5906291	5119,7875	2201	4296	6497	SO:0001583	missense	390081	exon1			CCAGCATTTTTTT	AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"""GPCR / Class A : Olfactory receptors"""	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.769T>C	11.37:g.5906291T>C	ENSP00000321426:p.Phe257Leu	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	238	121	0.508403	NM_001005165	Q6IFG0	Missense_Mutation	SNP	ENST00000316987.2	37	CCDS31401.1	828	0.3791208791208791	154	0.3130081300813008	153	0.42265193370165743	204	0.35664335664335667	317	0.4182058047493404	T	6.783	0.513407	0.12944	0.339618	0.421788	ENSG00000180974	ENST00000316987	T	0.00025	8.95	5.1	3.94	0.45596	GPCR, rhodopsin-like superfamily (1);	0.128823	0.35466	N	0.003198	T	0.00012	0.0000	N	0.04275	-0.24	0.42048	P	0.008894999999999986	B	0.02656	0.0	B	0.12837	0.008	T	0.00024	-1.2322	9	0.15499	T	0.54	.	6.8055	0.23774	0.0:0.1821:0.0:0.8179	rs11823842;rs17807520;rs52828559;rs57975452;rs11823842	257	Q8NGH9	O52E4_HUMAN	L	257	ENSP00000321426:F257L	ENSP00000321426:F257L	F	+	1	0	OR52E4	5862867	0.000000	0.05858	0.980000	0.43619	0.990000	0.78478	-0.489000	0.06490	0.923000	0.37045	0.523000	0.50628	TTT	T|0.627;C|0.373	0.373	strong		0.433	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165	
SYTL2	54843	hgsc.bcm.edu	37	11	85436352	85436352	+	Intron	SNP	G	G	A	rs641393	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:85436352G>A	ENST00000528231.1	-	7	1737				SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000359152.5_Missense_Mutation_p.T907M|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000525423.1_Missense_Mutation_p.T383M|SYTL2_ENST00000354566.3_Missense_Mutation_p.T383M	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CGAAATTTCCGTTTGAGAAGG	0.473													G|||	2611	0.521366	0.4062	0.4957	5008	,	,		20487	0.5972		0.6282	False		,,,				2504	0.5072				p.T383M		Atlas-SNP	.											SYTL2,NS,carcinoma,+1,1	SYTL2	231	1	0			c.C1148T						PASS	.	G	,,,MET/THR,MET/THR	1923,2483	530.0+/-372.8	436,1051,716	53.0	54.0	54.0		,,,1148,1148	-0.9	0.8	11	dbSNP_83	54	5429,3167	629.7+/-398.3	1730,1969,599	yes	intron,intron,intron,missense,missense	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,81,81	2166,3020,1315	AA,AG,GG		36.8427,43.645,43.4549	,,,possibly-damaging,possibly-damaging	,,,383/1273,383/1257	85436352	7352,5650	2203	4298	6501	SO:0001627	intron_variant	54843	exon1			ATTTCCGTTTGAG	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2586C>T	11.37:g.85436352G>A		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	1200	0.5494505494505495	204	0.4146341463414634	196	0.5414364640883977	323	0.5646853146853147	477	0.6292875989445911	G	0.463	-0.888140	0.02511	0.43645	0.631573	ENSG00000137501	ENST00000359152;ENST00000354566;ENST00000525423	T;T;T	0.25579	1.79;1.79;1.79	6.16	-0.906	0.10524	.	0.743599	0.12813	N	0.437013	T	0.00012	0.0000	N	0.04508	-0.205	0.43857	P	0.0035410000000000164	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.06405	0.002;0.002;0.002	T	0.37641	-0.9697	8	.	.	.	-6.2622	2.8743	0.05626	0.2165:0.4856:0.0993:0.1986	rs641393;rs17208805;rs52804408;rs58119009;rs641393	383;383;383	Q9HCH5-11;Q9HCH5-7;Q9HCH5-8	.;.;.	M	907;383;383	ENSP00000352065:T907M;ENSP00000346576:T383M;ENSP00000432694:T383M	.	T	-	2	0	SYTL2	85114000	0.000000	0.05858	0.819000	0.32651	0.225000	0.24961	-0.488000	0.06497	-0.026000	0.13895	-0.839000	0.03059	ACG	G|0.451;A|0.549	0.549	strong		0.473	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
HSD17B4	3295	hgsc.bcm.edu	37	5	118861713	118861713	+	Missense_Mutation	SNP	A	A	G	rs11205	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:118861713A>G	ENST00000256216.6	+	19	1808	c.1675A>G	c.(1675-1677)Att>Gtt	p.I559V	HSD17B4_ENST00000414835.2_Missense_Mutation_p.I419V|HSD17B4_ENST00000504811.1_Missense_Mutation_p.I584V|HSD17B4_ENST00000509514.1_Missense_Mutation_p.I297V|HSD17B4_ENST00000515320.1_Missense_Mutation_p.I541V|HSD17B4_ENST00000522415.1_3'UTR|HSD17B4_ENST00000513628.1_Missense_Mutation_p.I422V|HSD17B4_ENST00000510025.1_Missense_Mutation_p.I535V	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	559	Enoyl-CoA hydratase 2.|MaoC-like.		I -> V (in dbSNP:rs11205). {ECO:0000269|PubMed:14702039}.		alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.I559V(1)		breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		ATTCAAGGCAATTAAGGTAAA	0.313													A|||	2004	0.40016	0.4092	0.4683	5008	,	,		15465	0.4177		0.4125	False		,,,				2504	0.3088				p.I584V	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											HSD17B4,NS,carcinoma,0,1	HSD17B4	63	1	1	Substitution - Missense(1)	prostate(1)	c.A1750G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	1741,2663	519.1+/-369.9	341,1059,802	148.0	142.0	144.0		1675,1750,1621	5.4	1.0	5	dbSNP_52	144	3518,5082	512.7+/-378.0	717,2084,1499	yes	missense,missense,missense	HSD17B4	NM_000414.3,NM_001199291.1,NM_001199292.1	29,29,29	1058,3143,2301	GG,GA,AA		40.907,39.5322,40.4414	benign,benign,benign	559/737,584/762,541/719	118861713	5259,7745	2202	4300	6502	SO:0001583	missense	3295	exon20			AAGGCAATTAAGG		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.1675A>G	5.37:g.118861713A>G	ENSP00000256216:p.Ile559Val	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	210	93	0.442857	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Missense_Mutation	SNP	ENST00000256216.6	37	CCDS4126.1	888	0.4065934065934066	181	0.3678861788617886	164	0.4530386740331492	213	0.3723776223776224	330	0.43535620052770446	A	14.61	2.587740	0.46110	0.395322	0.40907	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628;ENST00000509514	T;T;T;T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4;-1.4;-1.4;-1.4	5.39	5.39	0.77823	MaoC-like dehydratase (1);	0.046452	0.85682	D	0.000000	T	0.00012	0.0000	L	0.28740	0.885	0.09310	P	0.9999982734	P;B;B;B;B	0.42827	0.791;0.223;0.418;0.094;0.118	B;B;B;B;B	0.40534	0.332;0.204;0.088;0.264;0.17	T	0.34527	-0.9825	9	0.39692	T	0.17	-21.7798	14.3833	0.66926	1.0:0.0:0.0:0.0	rs11205;rs1130646;rs3189732;rs11539470;rs11740179;rs16918307;rs17342666;rs60097041;rs11205	584;541;535;297;559	F5HE57;E9PB82;E7EWE5;E7EPL9;P51659	.;.;.;.;DHB4_HUMAN	V	559;541;535;584;419;422;297	ENSP00000256216:I559V;ENSP00000424613:I541V;ENSP00000424940:I535V;ENSP00000420914:I584V;ENSP00000411960:I419V;ENSP00000425993:I422V;ENSP00000426272:I297V	ENSP00000256216:I559V	I	+	1	0	HSD17B4	118889612	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	3.836000	0.55813	2.050000	0.60909	0.482000	0.46254	ATT	A|0.591;G|0.409	0.409	strong		0.313	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	
FAM71F2	346653	hgsc.bcm.edu	37	7	128315889	128315889	+	Missense_Mutation	SNP	A	A	T	rs6971819	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:128315889A>T	ENST00000480462.1	+	2	447	c.341A>T	c.(340-342)gAc>gTc	p.D114V	FAM71F2_ENST00000460349.1_3'UTR|FAM71F2_ENST00000477515.1_Missense_Mutation_p.D114V|FAM71F2_ENST00000378704.3_Missense_Mutation_p.D105V			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	114			D -> V (in dbSNP:rs6971819). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:15489334}.							NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						ACACCTGGTGACGCCCCAGTC	0.562													.|||	567	0.113219	0.2186	0.0677	5008	,	,		15377	0.0278		0.1203	False		,,,				2504	0.0838				p.D114V		Atlas-SNP	.											.	FAM71F2	19	.	0			c.A341T						PASS	.	A	VAL/ASP,VAL/ASP	755,3051		85,585,1233	43.0	41.0	41.0		341,314	0.5	0.0	7	dbSNP_116	41	957,7289		62,833,3228	yes	missense,missense	FAM71F2	NM_001012454.3,NM_001128926.1	152,152	147,1418,4461	TT,TA,AA		11.6056,19.8371,14.2051	benign,benign	114/310,105/301	128315889	1712,10340	1903	4123	6026	SO:0001583	missense	346653	exon2			CTGGTGACGCCCC	BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member B"""	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.341A>T	7.37:g.128315889A>T	ENSP00000420140:p.Asp114Val	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	33	19	0.575758	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	235	0.10760073260073261	90	0.18292682926829268	28	0.07734806629834254	18	0.03146853146853147	99	0.13060686015831136	A	2.983	-0.209937	0.06140	0.198371	0.116056	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001;ENST00000477515	T;T;T;T;T	0.30714	2.2;2.2;2.2;2.2;1.52	4.16	0.475	0.16774	.	2.399370	0.01787	N	0.032075	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.25152	-1.0140	9	0.33940	T	0.23	-6.2876	0.5566	0.00672	0.2287:0.3575:0.2032:0.2107	rs6971819;rs6971819	105;114	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	V	105;114;105;105;114	ENSP00000418907:D105V;ENSP00000420140:D114V;ENSP00000367976:D105V;ENSP00000401654:D105V;ENSP00000419649:D114V	ENSP00000367976:D105V	D	+	2	0	FAM71F2	128103125	0.005000	0.15991	0.025000	0.17156	0.320000	0.28249	-0.094000	0.11094	-0.021000	0.14009	0.455000	0.32223	GAC	A|0.892;T|0.108	0.108	strong		0.562	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1		
IGF2BP2	10644	hgsc.bcm.edu	37	3	185375100	185375100	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:185375100C>T	ENST00000382199.2	-	12	1455	c.1360G>A	c.(1360-1362)Gcg>Acg	p.A454T	IGF2BP2_ENST00000457616.2_Missense_Mutation_p.A460T|IGF2BP2_ENST00000346192.3_Missense_Mutation_p.A411T|IGF2BP2_ENST00000494906.1_5'UTR|IGF2BP2_ENST00000421047.2_Missense_Mutation_p.A397T	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	454	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			GCGAATCTCGCCAGCTGTTTG	0.597																																					p.A454T		Atlas-SNP	.											IGF2BP2,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	IGF2BP2	69	1	0			c.G1360A						scavenged	.						65.0	60.0	62.0					3																	185375100		2203	4300	6503	SO:0001583	missense	10644	exon12			ATCTCGCCAGCTG	BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792		"""RNA binding motif (RRM) containing"""	28867	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 2"""	608289				10190901, 9891060	Standard	NM_001007225		Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.1360G>A	3.37:g.185375100C>T	ENSP00000371634:p.Ala454Thr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	107	3	0.0280374	NM_006548	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Missense_Mutation	SNP	ENST00000382199.2	37	CCDS3273.2	.	.	.	.	.	.	.	.	.	.	C	12.01	1.808370	0.31961	.	.	ENSG00000073792	ENST00000382199;ENST00000421047;ENST00000457616;ENST00000346192	T;T;T;T	0.28069	1.63;1.63;1.63;1.63	5.22	5.22	0.72569	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.32133	0.0819	N	0.17674	0.51	0.58432	D	0.999994	P;P;P;P;B;P	0.52316	0.881;0.94;0.94;0.753;0.109;0.952	P;P;P;P;B;P	0.56127	0.511;0.688;0.688;0.591;0.037;0.792	T	0.02098	-1.1214	10	0.28530	T	0.3	-9.0754	12.9605	0.58455	0.1621:0.8379:0.0:0.0	.	348;391;397;460;411;454	Q9Y6M1-5;Q9Y6M1-3;Q9Y6M1-4;F8W930;Q9Y6M1-1;Q9Y6M1	.;.;.;.;.;IF2B2_HUMAN	T	454;397;460;411	ENSP00000371634:A454T;ENSP00000413787:A397T;ENSP00000410242:A460T;ENSP00000320204:A411T	ENSP00000320204:A411T	A	-	1	0	IGF2BP2	186857794	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	2.392000	0.44433	2.586000	0.87340	0.655000	0.94253	GCG	.	.	none		0.597	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548	
CNGA3	1261	hgsc.bcm.edu	37	2	98986510	98986510	+	Silent	SNP	T	T	C	rs6727412	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:98986510T>C	ENST00000272602.2	+	1	111	c.72T>C	c.(70-72)gaT>gaC	p.D24D	CNGA3_ENST00000436404.2_Silent_p.D24D|CNGA3_ENST00000393504.1_Silent_p.D24D			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	24					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						CAGACCGAGATCTCAATCGCG	0.507													T|||	450	0.0898562	0.084	0.1282	5008	,	,		18669	0.0099		0.166	False		,,,				2504	0.0746				p.D24D		Atlas-SNP	.											.	CNGA3	118	.	0			c.T72C						PASS	.	T	,	478,3928	225.2+/-241.2	23,432,1748	138.0	113.0	121.0		72,72	-6.6	0.0	2	dbSNP_116	121	1522,7078	288.1+/-298.6	130,1262,2908	no	coding-synonymous,coding-synonymous	CNGA3	NM_001079878.1,NM_001298.2	,	153,1694,4656	CC,CT,TT		17.6977,10.8488,15.3775	,	24/677,24/695	98986510	2000,11006	2203	4300	6503	SO:0001819	synonymous_variant	1261	exon2			CCGAGATCTCAAT	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.72T>C	2.37:g.98986510T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Silent	SNP	ENST00000272602.2	37	CCDS2034.1																																																																																			T|0.869;C|0.131	0.131	strong		0.507	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298	
PSMB8	5696	hgsc.bcm.edu	37	6	32809947	32809947	+	Silent	SNP	G	G	A	rs11540143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32809947G>A	ENST00000374882.3	-	4	551	c.501C>T	c.(499-501)ctC>ctT	p.L167L	PSMB8_ENST00000395339.3_Silent_p.L143L|PSMB9_ENST00000395330.1_5'Flank|PSMB8_ENST00000374881.2_Silent_p.L163L|TAPSAR1_ENST00000453426.1_lincRNA	NM_148919.3	NP_683720.2	P28062	PSB8_HUMAN	proteasome (prosome, macropain) subunit, beta type, 8	167					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	11					Carfilzomib(DB08889)	TGCCCATAGAGAGGCCCATGC	0.532													G|||	6	0.00119808	0.0	0.0029	5008	,	,		20162	0.001		0.003	False		,,,				2504	0.0				p.L167L	NSCLC(48;53 1172 10859 13624 22883)	Atlas-SNP	.											.	PSMB8	42	.	0			c.C501T						PASS	.	G	,	0,3022		0,0,1511	133.0	117.0	122.0		489,501	4.2	1.0	6	dbSNP_120	122	35,5383		0,35,2674	no	coding-synonymous,coding-synonymous	PSMB8	NM_004159.4,NM_148919.3	,	0,35,4185	AA,AG,GG		0.646,0.0,0.4147	,	163/273,167/277	32809947	35,8405	1511	2709	4220	SO:0001819	synonymous_variant	5696	exon4			CATAGAGAGGCCC		CCDS4756.1, CCDS4757.1	6p21.3	2013-03-27	2013-03-27		ENSG00000204264	ENSG00000204264		"""Proteasome (prosome, macropain) subunits"""	9545	protein-coding gene	gene with protein product		177046	"""proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)"", ""large multifunctional peptidase 7"""	LMP7		1529427, 10329130	Standard	XM_005275000		Approved	RING10, D6S216E, PSMB5i, beta5i	uc003oce.3	P28062	OTTHUMG00000031285	ENST00000374882.3:c.501C>T	6.37:g.32809947G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_148919	B0UZC0|Q29824|Q5JNW6|Q5QNR8|Q96J48	Silent	SNP	ENST00000374882.3	37	CCDS4757.1																																																																																			G|0.996;A|0.004	0.004	strong		0.532	PSMB8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076617.3	NM_148919	
CCDC88B	283234	hgsc.bcm.edu	37	11	64110668	64110668	+	Silent	SNP	G	G	A	rs574835	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64110668G>A	ENST00000356786.5	+	11	1124	c.1080G>A	c.(1078-1080)tcG>tcA	p.S360S	CCDC88B_ENST00000301897.4_5'Flank|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	360						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GGGTGCTCTCGGGGGTGCTGG	0.697													A|||	1126	0.22484	0.0855	0.3703	5008	,	,		10601	0.1657		0.3658	False		,,,				2504	0.226				p.S360S		Atlas-SNP	.											.	CCDC88B	89	.	0			c.G1080A						PASS	.	A		471,3691		29,413,1639	9.0	8.0	8.0		1080	-8.7	0.0	11	dbSNP_83	8	2492,5608		402,1688,1960	no	coding-synonymous	CCDC88B	NM_032251.5		431,2101,3599	AA,AG,GG		30.7654,11.3167,24.1641		360/1477	64110668	2963,9299	2081	4050	6131	SO:0001819	synonymous_variant	283234	exon11			GCTCTCGGGGGTG	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.1080G>A	11.37:g.64110668G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	19	8	0.421053	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			G|0.738;A|0.262	0.262	strong		0.697	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
SPTBN2	6712	hgsc.bcm.edu	37	11	66457681	66457681	+	Missense_Mutation	SNP	C	C	T	rs35532855	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:66457681C>T	ENST00000533211.1	-	28	5970	c.5639G>A	c.(5638-5640)cGc>cAc	p.R1880H	SPTBN2_ENST00000529997.1_Missense_Mutation_p.R1880H|SPTBN2_ENST00000309996.2_Missense_Mutation_p.R1880H			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1880					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CTGCATGTGGCGGCCGATCTC	0.687													C|||	49	0.00978435	0.0	0.0159	5008	,	,		14353	0.0		0.0338	False		,,,				2504	0.0041				p.R1880H		Atlas-SNP	.											.	SPTBN2	188	.	0			c.G5639A						PASS	.	C	HIS/ARG	21,4375	28.1+/-56.4	0,21,2177	35.0	37.0	37.0		5639	3.8	1.0	11	dbSNP_126	37	219,8365	90.4+/-152.6	1,217,4074	yes	missense	SPTBN2	NM_006946.2	29	1,238,6251	TT,TC,CC		2.5513,0.4777,1.849	possibly-damaging	1880/2391	66457681	240,12740	2198	4292	6490	SO:0001583	missense	6712	exon27			ATGTGGCGGCCGA	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.5639G>A	11.37:g.66457681C>T	ENSP00000432568:p.Arg1880His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	66	0.717391	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	27	0.012362637362637362	0	0.0	4	0.011049723756906077	0	0.0	23	0.030343007915567283	C	25.2	4.614794	0.87359	0.004777	0.025513	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.35236	1.32;1.32;1.32	4.75	3.83	0.44106	.	0.065617	0.64402	D	0.000013	T	0.28599	0.0708	M	0.66939	2.045	0.54753	D	0.999983	D	0.69078	0.997	D	0.64144	0.922	T	0.35351	-0.9792	10	0.44086	T	0.13	.	11.9673	0.53042	0.0:0.9143:0.0:0.0857	rs35532855	1880	O15020	SPTN2_HUMAN	H	1880	ENSP00000432568:R1880H;ENSP00000311489:R1880H;ENSP00000433593:R1880H	ENSP00000311489:R1880H	R	-	2	0	SPTBN2	66214257	0.947000	0.32204	1.000000	0.80357	0.990000	0.78478	1.870000	0.39529	1.232000	0.43678	0.563000	0.77884	CGC	C|0.982;T|0.018	0.018	strong		0.687	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
NBPF3	84224	hgsc.bcm.edu	37	1	21806667	21806667	+	Missense_Mutation	SNP	C	C	G	rs12043777	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:21806667C>G	ENST00000318249.5	+	11	1682	c.1332C>G	c.(1330-1332)gaC>gaG	p.D444E	NBPF3_ENST00000342104.5_Missense_Mutation_p.D432E|NBPF3_ENST00000318220.6_Missense_Mutation_p.D388E|NBPF3_ENST00000454000.2_Missense_Mutation_p.D374E	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	444	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.		D -> E (in dbSNP:rs12043777). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)		p.D444E(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ACAGAAGTGACTTTTACTCAT	0.453																																					p.S444S		Atlas-SNP	.											NBPF3,NS,carcinoma,0,2	NBPF3	55	2	1	Substitution - Missense(1)	prostate(1)	c.T1332G						scavenged	.	C	GLU/ASP	128,4248		35,58,2095	87.0	47.0	61.0		1332	-1.3	0.0	1	dbSNP_120	61	1540,6608		435,670,2969	no	missense	NBPF3	NM_032264.2	45	470,728,5064	GG,GC,CC		18.9003,2.925,13.3184	benign	444/634	21806667	1668,10856	2188	4074	6262	SO:0001583	missense	84224	exon11			AAGTGACTTTTAC	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.1332C>G	1.37:g.21806667C>G	ENSP00000316782:p.Asp444Glu	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	113	12	0.106195	NM_032264	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Silent	SNP	ENST00000318249.5	37	CCDS216.1	705	0.3228021978021978	55	0.11178861788617886	140	0.3867403314917127	235	0.41083916083916083	275	0.3627968337730871	.	1.891	-0.455414	0.04540	0.02925	0.189003	ENSG00000142794	ENST00000454000;ENST00000318220;ENST00000318249;ENST00000342104;ENST00000434838	T;T;T;T;T	0.06294	3.32;3.32;3.32;3.32;3.32	0.658	-1.32	0.09201	DUF1220 (2);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.24823	0.0;0.112	B;B	0.25140	0.001;0.058	T	0.45279	-0.9272	7	0.52906	T	0.07	.	.	.	.	rs56119644	432;444	Q9H094-3;Q9H094	.;NBPF3_HUMAN	E	374;388;444;432;388	ENSP00000415711:D374E;ENSP00000316739:D388E;ENSP00000316782:D444E;ENSP00000340336:D432E;ENSP00000391865:D388E	ENSP00000316739:D388E	D	+	3	2	NBPF3	21679254	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	0.088000	0.14979	-0.800000	0.04433	0.121000	0.15741	GAC	C|0.874;G|0.126	0.126	strong		0.453	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
MUC2	4583	hgsc.bcm.edu	37	11	1093769	1093769	+	Missense_Mutation	SNP	G	G	A	rs41361144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1093769G>A	ENST00000441003.2	+	30	5615	c.5588G>A	c.(5587-5589)cGg>cAg	p.R1863Q	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Missense_Mutation_p.R151Q	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4225					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.R1863L(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CAGACCTCTCGGTCCACCTCT	0.617													G|||	325	0.0648962	0.0681	0.0418	5008	,	,		18686	0.0585		0.0825	False		,,,				2504	0.0654				p.R1859Q		Atlas-SNP	.											.	MUC2	614	.	1	Substitution - Missense(1)	lung(1)	c.G5576A						PASS	.	G	GLN/ARG	241,4075		7,227,1924	246.0	294.0	278.0		5573	-3.4	0.0	11	dbSNP_127	278	662,7836		18,626,3605	yes	missense	MUC2	NM_002457.2	43	25,853,5529	AA,AG,GG		7.7901,5.5839,7.047	benign	1858/2813	1093769	903,11911	2158	4249	6407	SO:0001583	missense	4583	exon31			CCTCTCGGTCCAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5588G>A	11.37:g.1093769G>A	ENSP00000415183:p.Arg1863Gln	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		128	0.05860805860805861	23	0.046747967479674794	16	0.04419889502762431	29	0.050699300699300696	60	0.079155672823219	G	0.371	-0.934206	0.02340	0.055839	0.077901	ENSG00000198788	ENST00000441003;ENST00000333592	T;T	0.12255	2.7;3.1	1.7	-3.39	0.04868	.	.	.	.	.	T	0.00328	0.0010	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43376	-0.9395	8	0.13108	T	0.6	.	4.124	0.10118	0.4559:0.3763:0.1678:0.0	rs41361144	1863	E7EUV1	.	Q	1863;151	ENSP00000415183:R1863Q;ENSP00000331373:R151Q	ENSP00000331373:R151Q	R	+	2	0	MUC2	1083769	0.000000	0.05858	0.001000	0.08648	0.040000	0.13550	-4.255000	0.00265	-1.321000	0.02281	-0.727000	0.03589	CGG	G|0.937;A|0.063	0.063	strong		0.617	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
USP15	9958	hgsc.bcm.edu	37	12	62783462	62783462	+	Silent	SNP	A	A	G	rs61760205	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:62783462A>G	ENST00000280377.5	+	13	1693	c.1635A>G	c.(1633-1635)gaA>gaG	p.E545E	USP15_ENST00000353364.3_Silent_p.E516E|USP15_ENST00000393654.3_Silent_p.E520E	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	545	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		GTATTATGGAACGGGATGATA	0.264													A|||	10	0.00199681	0.0	0.0029	5008	,	,		17126	0.0		0.008	False		,,,				2504	0.0				p.E545E	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.A1635G						PASS	.	A		6,4398	11.4+/-27.6	0,6,2196	81.0	93.0	89.0		1548	-0.6	1.0	12	dbSNP_129	89	58,8534	36.4+/-91.3	1,56,4239	no	coding-synonymous	USP15	NM_006313.1		1,62,6435	GG,GA,AA		0.675,0.1362,0.4925		516/953	62783462	64,12932	2202	4296	6498	SO:0001819	synonymous_variant	9958	exon13			TATGGAACGGGAT	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.1635A>G	12.37:g.62783462A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	37	CCDS58251.1																																																																																			A|0.996;G|0.004	0.004	strong		0.264	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
PRSS58	136541	hgsc.bcm.edu	37	7	141952110	141952110	+	Silent	SNP	G	G	A	rs1052406	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:141952110G>A	ENST00000552471.1	-	5	976	c.657C>T	c.(655-657)gcC>gcT	p.A219A	PRSS58_ENST00000547058.2_Silent_p.A219A			Q8IYP2	PRS58_HUMAN	protease, serine, 58	219	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	19						TGCCAACATCGGCTCTCAAAA	0.428													G|||	1030	0.205671	0.2088	0.2277	5008	,	,		17409	0.0089		0.3469	False		,,,				2504	0.2434				p.A219A		Atlas-SNP	.											.	PRSS58	41	.	0			c.C657T						PASS	.	G		1072,3334	390.7+/-327.8	121,830,1252	61.0	66.0	64.0		657	-4.1	1.0	7	dbSNP_86	64	3212,5388	484.6+/-371.4	603,2006,1691	no	coding-synonymous	PRSS58	NM_001001317.3		724,2836,2943	AA,AG,GG		37.3488,24.3305,32.9386		219/242	141952110	4284,8722	2203	4300	6503	SO:0001819	synonymous_variant	136541	exon6			AACATCGGCTCTC		CCDS5871.1	7q34	2012-10-03			ENSG00000258223	ENSG00000258223	3.4.21.4	"""Serine peptidases / Serine peptidases"""	39125	protein-coding gene	gene with protein product	"""trypsin X3"""						Standard	NM_001001317		Approved	TRYX3	uc003vxc.4	Q8IYP2	OTTHUMG00000158565	ENST00000552471.1:c.657C>T	7.37:g.141952110G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001001317	B3KVJ6|D3DXD2	Silent	SNP	ENST00000552471.1	37	CCDS5871.1																																																																																			G|0.709;A|0.291	0.291	strong		0.428	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317	
PRPF8	10594	hgsc.bcm.edu	37	17	1578939	1578939	+	Silent	SNP	C	C	T	rs33965342	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1578939C>T	ENST00000572621.1	-	18	3112	c.2847G>A	c.(2845-2847)ccG>ccA	p.P949P	PRPF8_ENST00000304992.6_Silent_p.P949P			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	949	Reverse transcriptase homology domain.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		AAACAAGCAGCGGAGGTGGTT	0.502													c|||	1310	0.261581	0.5893	0.1441	5008	,	,		21620	0.0893		0.1948	False		,,,				2504	0.1483				p.P949P		Atlas-SNP	.											.	PRPF8	169	.	0			c.G2847A						PASS	.	C		2229,2177	593.0+/-387.9	559,1111,533	175.0	193.0	187.0		2847	1.1	1.0	17	dbSNP_126	187	1820,6780	326.3+/-317.3	188,1444,2668	no	coding-synonymous	PRPF8	NM_006445.3		747,2555,3201	TT,TC,CC		21.1628,49.4099,31.1318		949/2336	1578939	4049,8957	2203	4300	6503	SO:0001819	synonymous_variant	10594	exon19			AAGCAGCGGAGGT	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.2847G>A	17.37:g.1578939C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	NM_006445	O14547|O75965	Silent	SNP	ENST00000572621.1	37	CCDS11010.1																																																																																			C|0.711;T|0.289	0.289	strong		0.502	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
CARS2	79587	hgsc.bcm.edu	37	13	111340342	111340342	+	Silent	SNP	G	G	A	rs2304767	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:111340342G>A	ENST00000257347.4	-	4	480	c.417C>T	c.(415-417)ctC>ctT	p.L139L	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	139					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	AAAGACTGGCGAGGGAAGCGG	0.527													G|||	741	0.147963	0.0151	0.2176	5008	,	,		18287	0.12		0.325	False		,,,				2504	0.1247				p.L139L		Atlas-SNP	.											.	CARS2	37	.	0			c.C417T						PASS	.	G		301,4105	164.4+/-196.0	13,275,1915	68.0	61.0	63.0		417	-9.4	0.0	13	dbSNP_100	63	2879,5721	449.7+/-362.2	494,1891,1915	no	coding-synonymous	CARS2	NM_024537.2		507,2166,3830	AA,AG,GG		33.4767,6.8316,24.4503		139/565	111340342	3180,9826	2203	4300	6503	SO:0001819	synonymous_variant	79587	exon4			ACTGGCGAGGGAA	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.417C>T	13.37:g.111340342G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_024537	Q8NI84|Q96IV4	Silent	SNP	ENST00000257347.4	37	CCDS9514.1																																																																																			G|0.791;A|0.209	0.209	strong		0.527	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537	
PTPRG	5793	hgsc.bcm.edu	37	3	62189437	62189437	+	Silent	SNP	G	G	C	rs17634074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:62189437G>C	ENST00000474889.1	+	12	2345	c.1968G>C	c.(1966-1968)acG>acC	p.T656T	PTPRG_ENST00000295874.10_Silent_p.T656T	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	656					brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		CAGACCAGACGGGCGGAAGGA	0.652													G|||	532	0.10623	0.087	0.0764	5008	,	,		15683	0.0139		0.1471	False		,,,				2504	0.2065				p.T656T		Atlas-SNP	.											.	PTPRG	153	.	0			c.G1968C						PASS	.	G		430,3976	190.9+/-216.7	24,382,1797	31.0	36.0	34.0		1968	-7.8	0.0	3	dbSNP_123	34	1343,7257	236.1+/-268.4	99,1145,3056	no	coding-synonymous	PTPRG	NM_002841.3		123,1527,4853	CC,CG,GG		15.6163,9.7594,13.6322		656/1446	62189437	1773,11233	2203	4300	6503	SO:0001819	synonymous_variant	5793	exon12			CCAGACGGGCGGA	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.1968G>C	3.37:g.62189437G>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	124	54	0.435484	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Silent	SNP	ENST00000474889.1	37	CCDS2895.1																																																																																			G|0.887;C|0.113	0.113	strong		0.652	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
C3	718	hgsc.bcm.edu	37	19	6677989	6677989	+	Silent	SNP	G	G	A	rs17030	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:6677989G>A	ENST00000245907.6	-	41	4988	c.4896C>T	c.(4894-4896)ccC>ccT	p.P1632P	C3_ENST00000599668.1_5'UTR	NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1632	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CGTCCTCCTCGGGCCAGTGCT	0.612													G|||	2669	0.532947	0.497	0.5043	5008	,	,		17315	0.5476		0.5109	False		,,,				2504	0.6094				p.P1632P		Atlas-SNP	.											.	C3	192	.	0			c.C4896T						PASS	.			2193,2213	587.0+/-386.6	542,1109,552	150.0	118.0	129.0		4896	-9.9	0.0	19	dbSNP_60	129	4445,4155	588.6+/-392.4	1147,2151,1002	no	coding-synonymous	C3	NM_000064.2		1689,3260,1554	AA,AG,GG		48.314,49.773,48.962		1632/1664	6677989	6638,6368	2203	4300	6503	SO:0001819	synonymous_variant	718	exon41			CTCCTCGGGCCAG	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.4896C>T	19.37:g.6677989G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	37	CCDS32883.1																																																																																			G|0.494;A|0.506	0.506	strong		0.612	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
GPR110	266977	hgsc.bcm.edu	37	6	46977475	46977475	+	Silent	SNP	A	A	G	rs73480725	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46977475A>G	ENST00000371253.2	-	11	1911	c.1696T>C	c.(1696-1698)Ttg>Ctg	p.L566L	GPR110_ENST00000283297.5_Silent_p.L369L|GPR110_ENST00000449332.2_5'UTR	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	566	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						AAGGAGGTCAAGTGAGTACAT	0.458													A|||	106	0.0211661	0.0151	0.0389	5008	,	,		20922	0.0		0.0537	False		,,,				2504	0.0051				p.L566L		Atlas-SNP	.											.	GPR110	102	.	0			c.T1696C						PASS	.	A		88,4318	73.6+/-111.7	1,86,2116	147.0	127.0	134.0		1696	1.9	1.0	6	dbSNP_130	134	444,8156	134.4+/-191.8	12,420,3868	no	coding-synonymous	GPR110	NM_153840.2		13,506,5984	GG,GA,AA		5.1628,1.9973,4.0904		566/911	46977475	532,12474	2203	4300	6503	SO:0001819	synonymous_variant	266977	exon11			AGGTCAAGTGAGT	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"""-"", ""GPCR / Class B : Orphans"""	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.1696T>C	6.37:g.46977475A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	37	CCDS34471.1																																																																																			A|0.958;G|0.042	0.042	strong		0.458	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
ZNF705A	440077	hgsc.bcm.edu	37	12	8329652	8329652	+	Missense_Mutation	SNP	A	A	G	rs10743251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:8329652A>G	ENST00000359286.4	+	5	465	c.376A>G	c.(376-378)Act>Gct	p.T126A		NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	126			T -> A (in dbSNP:rs10743251).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T126A(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		AGAAGATTGCACTCACAGTTC	0.403																																					p.T126A		Atlas-SNP	.											ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	1	Substitution - Missense(1)	stomach(1)	c.A376G						PASS	.						99.0	99.0	99.0					12																	8329652		2202	4291	6493	SO:0001583	missense	440077	exon5			GATTGCACTCACA	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"""Zinc fingers, C2H2-type"", ""-"""	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.376A>G	12.37:g.8329652A>G	ENSP00000352233:p.Thr126Ala	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	238	107	0.44958	NM_001004328		Missense_Mutation	SNP	ENST00000359286.4	37	CCDS31737.1	1046	0.47893772893772896	208	0.42276422764227645	167	0.4613259668508287	276	0.4825174825174825	395	0.521108179419525	.	7.485	0.649440	0.14516	.	.	ENSG00000196946	ENST00000396570;ENST00000359286	T;T	0.07216	3.21;3.21	1.35	1.35	0.21983	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.20807	0.61	0.80722	P	0.0	B	0.28850	0.225	B	0.17979	0.02	T	0.39121	-0.9629	8	0.28530	T	0.3	.	4.2628	0.10749	0.6373:0.3627:0.0:0.0	rs10743251;rs57777260	126	Q6ZN79	Z705A_HUMAN	A	126	ENSP00000379816:T126A;ENSP00000352233:T126A	ENSP00000352233:T126A	T	+	1	0	ZNF705A	8220919	0.067000	0.21026	0.047000	0.18901	0.094000	0.18550	2.005000	0.40864	0.891000	0.36235	0.329000	0.21502	ACT	A|0.527;G|0.473	0.473	strong		0.403	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328	
SEMA3G	56920	hgsc.bcm.edu	37	3	52469628	52469628	+	Silent	SNP	C	C	T	rs61729091	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52469628C>T	ENST00000231721.2	-	16	2339	c.2340G>A	c.(2338-2340)gaG>gaA	p.E780E		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	780					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		TCTACGTGGCCTCCACCTCCC	0.682													C|||	69	0.013778	0.003	0.0144	5008	,	,		14557	0.0		0.0497	False		,,,				2504	0.0051				p.E780E		Atlas-SNP	.											.	SEMA3G	58	.	0			c.G2340A						PASS	.	C		46,4352		0,46,2153	48.0	57.0	54.0		2340	3.2	1.0	3	dbSNP_129	54	409,8149		7,395,3877	no	coding-synonymous	SEMA3G	NM_020163.1		7,441,6030	TT,TC,CC		4.7792,1.0459,3.5119		780/783	52469628	455,12501	2199	4279	6478	SO:0001819	synonymous_variant	56920	exon16			CGTGGCCTCCACC		CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.2340G>A	3.37:g.52469628C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	214	101	0.471963	NM_020163	Q7L9D9|Q9H7Q3	Silent	SNP	ENST00000231721.2	37	CCDS2856.1																																																																																			C|0.968;T|0.032	0.032	strong		0.682	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163	
XRCC4	7518	hgsc.bcm.edu	37	5	82648943	82648943	+	Splice_Site	SNP	G	G	A	rs1805377	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:82648943G>A	ENST00000511817.1	+	8	973		c.e8-1		XRCC4_ENST00000282268.3_Intron|XRCC4_ENST00000338635.6_Splice_Site|XRCC4_ENST00000396027.4_Intron			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4						cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		TTTCTTTTCAGTTCTAGGCCT	0.343								Non-homologous end-joining					A|||	1879	0.3752	0.4758	0.3329	5008	,	,		16220	0.7044		0.1402	False		,,,				2504	0.1718				.		Atlas-SNP	.											.	XRCC4	37	.	0			c.894-1G>A	GRCh37	CS075240	XRCC4	S	rs1805377	PASS	.	A	,,	1933,2469	591.6+/-387.6	422,1089,690	76.0	86.0	82.0		,,	-0.1	0.7	5	dbSNP_92	82	1052,7548	764.1+/-407.6	64,924,3312	yes	intron,splice-3,intron	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	,,	486,2013,4002	AA,AG,GG		12.2326,43.9119,22.958	,,	,,	82648943	2985,10017	2201	4300	6501	SO:0001630	splice_region_variant	7518	exon8			TTTTCAGTTCTAG	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.894-1G>A	5.37:g.82648943G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	223	100	0.44843	NM_022406	A8K3X4|Q9BS72|Q9UP94	Splice_Site	SNP	ENST00000511817.1	37	CCDS4059.1	858	0.39285714285714285	239	0.48577235772357724	115	0.31767955801104975	394	0.6888111888111889	110	0.14511873350923482	A	0.718	-0.784496	0.02907	0.439119	0.122326	ENSG00000152422	ENST00000338635;ENST00000511817;ENST00000514538	.	.	.	5.51	-0.0652	0.13769	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.3151	0.07030	0.3839:0.0:0.2655:0.3506	rs1805377;rs3777014;rs61086000;rs1805377	.	.	.	.	-1	.	.	.	+	.	.	XRCC4	82684699	0.003000	0.15002	0.723000	0.30687	0.002000	0.02628	-0.958000	0.03857	-0.153000	0.11137	-2.023000	0.00429	.	G|0.679;A|0.321	0.321	strong		0.343	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	Intron
ZKSCAN8	7745	hgsc.bcm.edu	37	6	28117331	28117331	+	Missense_Mutation	SNP	C	C	T	rs62620225	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28117331C>T	ENST00000330236.6	+	3	672	c.488C>T	c.(487-489)cCt>cTt	p.P163L	ZKSCAN8_ENST00000457389.2_Missense_Mutation_p.P163L	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	163			P -> L (in dbSNP:rs62620225). {ECO:0000269|PubMed:9244436}.		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)										GCACCAGAGCCTCCAAATACT	0.478													C|||	126	0.0251597	0.0068	0.0202	5008	,	,		16583	0.0109		0.0249	False		,,,				2504	0.0685				p.P163L		Atlas-SNP	.											.	.	.	.	0			c.C488T						PASS	.	C	LEU/PRO	45,4361	47.5+/-82.1	0,45,2158	142.0	127.0	132.0		488	3.4	0.5	6	dbSNP_129	132	354,8246	119.4+/-178.7	3,348,3949	yes	missense	ZNF192	NM_006298.2	98	3,393,6107	TT,TC,CC		4.1163,1.0213,3.0678	benign	163/579	28117331	399,12607	2203	4300	6503	SO:0001583	missense	7745	exon3			CAGAGCCTCCAAA		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12983	protein-coding gene	gene with protein product		602240	"""zinc finger protein 192"""	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	ENST00000330236.6:c.488C>T	6.37:g.28117331C>T	ENSP00000332750:p.Pro163Leu	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	162	73	0.450617	NM_006298	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	Missense_Mutation	SNP	ENST00000330236.6	37	CCDS4645.1	38	0.0173992673992674	4	0.008130081300813009	6	0.016574585635359115	7	0.012237762237762238	21	0.027704485488126648	C	9.204	1.029323	0.19512	0.010213	0.041163	ENSG00000198315	ENST00000330236;ENST00000457389	T;T	0.06768	3.26;3.26	4.27	3.36	0.38483	.	0.455201	0.18661	N	0.134724	T	0.01661	0.0053	N	0.14661	0.345	0.37768	D	0.926562	B	0.02656	0.0	B	0.01281	0.0	T	0.41431	-0.9509	10	0.30078	T	0.28	.	7.9946	0.30261	0.0:0.8733:0.0:0.1267	rs62620225	163	Q15776	ZN192_HUMAN	L	163	ENSP00000332750:P163L;ENSP00000402948:P163L	ENSP00000332750:P163L	P	+	2	0	ZNF192	28225310	0.108000	0.22018	0.489000	0.27452	0.934000	0.57294	0.928000	0.28831	1.037000	0.40024	0.563000	0.77884	CCT	C|0.971;T|0.029	0.029	strong		0.478	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2		
RSRP1	57035	hgsc.bcm.edu	37	1	25570081	25570081	+	Missense_Mutation	SNP	T	T	C	rs1043879	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:25570081T>C	ENST00000243189.7	-	4	992	c.716A>G	c.(715-717)gAa>gGa	p.E239G	C1orf63_ENST00000417642.2_Missense_Mutation_p.E240G	NM_020317.3	NP_064713.3	Q9BUV0	RSRP1_HUMAN		239			E -> G (in dbSNP:rs1043879). {ECO:0000269|PubMed:15489334}.							breast(1)|large_intestine(1)|lung(4)|pancreas(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGTAGGTTTTTCATTGGGATT	0.353													T|||	540	0.107827	0.0129	0.2089	5008	,	,		17228	0.0327		0.2724	False		,,,				2504	0.0726				p.E239G		Atlas-SNP	.											.	C1orf63	17	.	0			c.A716G						PASS	.	T	GLY/GLU	237,4169	138.8+/-174.5	11,215,1977	228.0	204.0	212.0	http://www.ncbi.nlm.nih.gov/pubmed?term	716	4.0	0.2	1	dbSNP_86	212	2306,6294	388.1+/-342.4	314,1678,2308	yes	missense	C1orf63	NM_020317.3	98	325,1893,4285	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	26.814,5.379,19.5525	probably-damaging	239/291	25570081	2543,10463	2203	4300	6503	SO:0001583	missense	57035	exon4			GGTTTTTCATTGG																												ENST00000243189.7:c.716A>G	1.37:g.25570081T>C	ENSP00000243189:p.Glu239Gly	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	290	147	0.506897	NM_020317	A8K917|Q49AA4|Q5TH71|Q9GZP6	Missense_Mutation	SNP	ENST00000243189.7	37	CCDS260.1	316	0.1446886446886447	10	0.02032520325203252	76	0.20994475138121546	13	0.022727272727272728	217	0.2862796833773087	T	8.815	0.936144	0.18206	0.05379	0.26814	ENSG00000117616	ENST00000243189;ENST00000417642	T;T	0.34472	1.36;1.41	5.1	3.97	0.46021	.	0.551981	0.14928	N	0.290259	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.999999853191	B	0.23540	0.087	B	0.25759	0.063	T	0.17653	-1.0362	9	0.59425	D	0.04	-3.633	8.5213	0.33277	0.0:0.0886:0.0:0.9114	rs1043879;rs17844932;rs17857662;rs17859787;rs57469912;rs1043879	239	Q9BUV0	CA063_HUMAN	G	239;240	ENSP00000243189:E239G;ENSP00000411631:E240G	ENSP00000243189:E239G	E	-	2	0	C1orf63	25442668	1.000000	0.71417	0.182000	0.23118	0.052000	0.14988	1.995000	0.40767	0.969000	0.38237	0.477000	0.44152	GAA	T|0.831;C|0.169	0.169	strong		0.353	C1orf63-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101966.2		
NRDE2	55051	hgsc.bcm.edu	37	14	90745442	90745442	+	Silent	SNP	T	T	C	rs141933992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:90745442T>C	ENST00000354366.3	-	13	3565	c.3333A>G	c.(3331-3333)gtA>gtG	p.V1111V	NRDE2_ENST00000357904.3_Silent_p.V880V	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	1111																	CTTTGTAGAATACACCTTTGC	0.458													T|||	8	0.00159744	0.0	0.0	5008	,	,		23470	0.0		0.006	False		,,,				2504	0.002				p.V1111V		Atlas-SNP	.											.	.	.	.	0			c.A3333G						PASS	.	T	,	1,4405	2.1+/-5.4	0,1,2202	230.0	214.0	220.0		3333,2640	-0.1	1.0	14	dbSNP_134	220	35,8565	22.8+/-68.1	0,35,4265	no	coding-synonymous,coding-synonymous	C14orf102	NM_017970.3,NM_199043.1	,	0,36,6467	CC,CT,TT		0.407,0.0227,0.2768	,	1111/1165,880/934	90745442	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	55051	exon13			GTAGAATACACCT	AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 102"""	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.3333A>G	14.37:g.90745442T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	46	0.429907	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Silent	SNP	ENST00000354366.3	37	CCDS9890.1																																																																																			T|0.998;C|0.002	0.002	strong		0.458	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970	
PEX10	5192	hgsc.bcm.edu	37	1	2340212	2340212	+	Silent	SNP	G	G	A	rs1143016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:2340212G>A	ENST00000447513.2	-	3	347	c.279C>T	c.(277-279)ggC>ggT	p.G93G	PEX10_ENST00000507596.1_Silent_p.G93G|PEX10_ENST00000515760.1_5'UTR|PEX10_ENST00000288774.3_Silent_p.G93G	NM_002617.3	NP_002608.1	O60683	PEX10_HUMAN	peroxisomal biogenesis factor 10	93					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)	integral component of peroxisomal membrane (GO:0005779)|intracellular (GO:0005622)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)	p.G93G(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	7	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00102)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0169)|Lung(427;0.199)		TCACCAGCACGCCACGGCGCA	0.662													G|||	100	0.0199681	0.0053	0.0115	5008	,	,		18508	0.001		0.0596	False		,,,				2504	0.0245				p.G93G	GBM(12;9 508 1649 13619)	Atlas-SNP	.											.	PEX10	18	.	1	Substitution - coding silent(1)	lung(1)	c.C279T						PASS	.	G	,	65,4341	61.1+/-98.1	1,63,2139	97.0	96.0	97.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	279,279	-9.2	0.0	1	dbSNP_86	97	539,8061	148.8+/-204.0	20,499,3781	no	coding-synonymous,coding-synonymous	PEX10	NM_002617.3,NM_153818.1	,	21,562,5920	AA,AG,GG		6.2674,1.4753,4.644	,	93/327,93/347	2340212	604,12402	2203	4300	6503	SO:0001819	synonymous_variant	5192	exon3			CAGCACGCCACGG	AF060502	CCDS41.1, CCDS44045.1	1p36.32	2013-01-09	2008-08-26		ENSG00000157911	ENSG00000157911		"""RING-type (C3HC4) zinc fingers"""	8851	protein-coding gene	gene with protein product		602859	"""peroxisome biogenesis factor 10"""			9683594	Standard	NM_002617		Approved	RNF69	uc001ajg.3	O60683	OTTHUMG00000001637	ENST00000447513.2:c.279C>T	1.37:g.2340212G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	160	92	0.575	NM_002617	B3KWD8|Q5T095|Q9BW90	Silent	SNP	ENST00000447513.2	37	CCDS44045.1																																																																																			G|0.960;A|0.040	0.040	strong		0.662	PEX10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367454.1	NM_153818	
IGFN1	91156	hgsc.bcm.edu	37	1	201181920	201181920	+	Silent	SNP	G	G	T	rs12060924	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:201181920G>T	ENST00000335211.4	+	12	8029	c.7899G>T	c.(7897-7899)ggG>ggT	p.G2633G	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Intron	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	0						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						AAAACCAGGGGTTTAGCCAAG	0.577													g|||	1537	0.306909	0.1853	0.3141	5008	,	,		18307	0.3105		0.3499	False		,,,				2504	0.4182				p.G2633G		Atlas-SNP	.											.	IGFN1	220	.	0			c.G7899T						PASS	.			272,1112		28,216,448	26.0	30.0	29.0		7899	1.0	0.0	1	dbSNP_120	29	1062,2120		180,702,709	no	coding-synonymous	IGFN1	NM_001164586.1		208,918,1157	TT,TG,GG		33.3752,19.6532,29.2159		2633/3709	201181920	1334,3232	692	1591	2283	SO:0001819	synonymous_variant	91156	exon12			CCAGGGGTTTAGC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.7899G>T	1.37:g.201181920G>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	672	0.3076923076923077	104	0.21138211382113822	113	0.31215469613259667	191	0.3339160839160839	264	0.3482849604221636	g	3.553	-0.091204	0.07053	0.196532	0.333752	ENSG00000163395	ENST00000412892	.	.	.	3.15	1.04	0.20106	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53688	P	2.1000000000048757E-5	.	.	.	.	.	.	T	0.40117	-0.9580	3	.	.	.	.	4.9669	0.14094	0.1306:0.2162:0.6532:0.0	rs12060924	.	.	.	F	51	.	.	V	+	1	0	IGFN1	199448543	0.000000	0.05858	0.001000	0.08648	0.091000	0.18340	0.052000	0.14163	-0.135000	0.11495	0.306000	0.20318	GTT	G|0.691;T|0.309	0.309	strong		0.577	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
NPAP1	23742	hgsc.bcm.edu	37	15	24921649	24921649	+	Missense_Mutation	SNP	T	T	C	rs3784246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:24921649T>C	ENST00000329468.2	+	1	1109	c.635T>C	c.(634-636)gTc>gCc	p.V212A		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	212			V -> A (in dbSNP:rs3784246).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											GAGGGAAATGTCTACCACAAG	0.612													T|||	536	0.107029	0.0703	0.1542	5008	,	,		16374	0.1478		0.0746	False		,,,				2504	0.1145				p.V212A		Atlas-SNP	.											C15orf2,caecum,carcinoma,0,1	.	.	1	0			c.T635C						PASS	.	T	ALA/VAL	294,4112		13,268,1922	38.0	37.0	37.0		635	0.5	0.0	15	dbSNP_107	37	682,7918		23,636,3641	yes	missense	C15orf2	NM_018958.2	64	36,904,5563	CC,CT,TT		7.9302,6.6727,7.5042	possibly-damaging	212/1157	24921649	976,12030	2203	4300	6503	SO:0001583	missense	23742	exon1			GAAATGTCTACCA	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.635T>C	15.37:g.24921649T>C	ENSP00000333735:p.Val212Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	209	0.09569597069597069	22	0.044715447154471545	48	0.13259668508287292	77	0.1346153846153846	62	0.08179419525065963	.	12.25	1.880335	0.33162	0.066727	0.079302	ENSG00000185823	ENST00000329468	T	0.12039	2.72	1.74	0.509	0.16977	.	.	.	.	.	T	0.00144	0.0004	L	0.39898	1.24	0.80722	P	0.0	D	0.57257	0.979	P	0.53401	0.725	T	0.21415	-1.0246	8	0.34782	T	0.22	.	4.53	0.12001	0.0:0.0:0.345:0.655	rs3784246;rs57747131;rs3784246	212	Q9NZP6	CO002_HUMAN	A	212	ENSP00000333735:V212A	ENSP00000333735:V212A	V	+	2	0	C15orf2	22472742	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.414000	0.07114	0.118000	0.18165	0.358000	0.22013	GTC	T|0.914;C|0.086	0.086	strong		0.612	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
TRERF1	55809	hgsc.bcm.edu	37	6	42236589	42236589	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:42236589C>G	ENST00000372922.4	-	5	1302	c.740G>C	c.(739-741)gGa>gCa	p.G247A	TRERF1_ENST00000354325.2_Missense_Mutation_p.G247A|TRERF1_ENST00000340840.2_Missense_Mutation_p.G247A|TRERF1_ENST00000372917.4_Missense_Mutation_p.G247A|TRERF1_ENST00000541110.1_Missense_Mutation_p.G247A	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	247	Gln-rich.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGGCTGTCCTCCCTGCACTGG	0.602																																					p.G247A		Atlas-SNP	.											.	TRERF1	124	.	0			c.G740C						PASS	.						48.0	47.0	47.0					6																	42236589		2202	4299	6501	SO:0001583	missense	55809	exon5			TGTCCTCCCTGCA	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.740G>C	6.37:g.42236589C>G	ENSP00000362013:p.Gly247Ala	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648503	0.47258	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.12465	2.84;2.68;2.84;2.68;2.68	5.54	3.63	0.41609	.	0.268702	0.25566	N	0.029784	T	0.07593	0.0191	N	0.24115	0.695	0.25742	N	0.985152	D;D;D;B;B	0.71674	0.998;0.997;0.997;0.008;0.008	D;D;D;B;B	0.70935	0.971;0.936;0.936;0.015;0.015	T	0.15206	-1.0445	10	0.25106	T	0.35	-6.3785	4.8502	0.13533	0.0:0.4353:0.3986:0.1661	.	247;247;247;86;86	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	A	247	ENSP00000439689:G247A;ENSP00000362008:G247A;ENSP00000362013:G247A;ENSP00000339438:G247A;ENSP00000346285:G247A	ENSP00000339438:G247A	G	-	2	0	TRERF1	42344567	0.891000	0.30450	0.993000	0.49108	0.992000	0.81027	0.852000	0.27764	1.319000	0.45190	0.462000	0.41574	GGA	.	.	none		0.602	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
OR5I1	10798	hgsc.bcm.edu	37	11	55703010	55703010	+	Silent	SNP	C	C	A	rs9665863	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55703010C>A	ENST00000301532.3	-	1	866	c.867G>T	c.(865-867)ccG>ccT	p.P289P		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	289					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						TATAAATCAACGGATTCAGCA	0.363													C|||	160	0.0319489	0.003	0.0331	5008	,	,		19027	0.001		0.0905	False		,,,				2504	0.0419				p.P289P		Atlas-SNP	.											OR5I1,NS,carcinoma,0,1	OR5I1	110	1	0			c.G867T						PASS	.	C		58,4342	54.2+/-90.2	1,56,2143	66.0	65.0	65.0		867	-9.6	0.0	11	dbSNP_119	65	676,7912	166.1+/-218.1	33,610,3651	no	coding-synonymous	OR5I1	NM_006637.1		34,666,5794	AA,AC,CC		7.8714,1.3182,5.6514		289/315	55703010	734,12254	2200	4294	6494	SO:0001819	synonymous_variant	10798	exon1			AATCAACGGATTC	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.867G>T	11.37:g.55703010C>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_006637	Q6IEU4	Silent	SNP	ENST00000301532.3	37	CCDS7949.1																																																																																			C|0.955;A|0.045	0.045	strong		0.363	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
C2orf42	54980	hgsc.bcm.edu	37	2	70387826	70387826	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:70387826C>A	ENST00000264434.2	-	9	1826	c.1447G>T	c.(1447-1449)Gaa>Taa	p.E483*	C2orf42_ENST00000420306.1_Nonsense_Mutation_p.E483*	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	483										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						CCGTAGGTTTCTGCTATGCTT	0.418																																					p.E483X		Atlas-SNP	.											.	C2orf42	30	.	0			c.G1447T						PASS	.						156.0	154.0	154.0					2																	70387826		2203	4300	6503	SO:0001587	stop_gained	54980	exon9			AGGTTTCTGCTAT	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.1447G>T	2.37:g.70387826C>A	ENSP00000264434:p.Glu483*	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	370	247	0.667568	NM_017880	D6W5G3|Q9H629	Nonsense_Mutation	SNP	ENST00000264434.2	37	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	C	37	6.198271	0.97367	.	.	ENSG00000115998	ENST00000264434;ENST00000420306	.	.	.	5.24	5.24	0.73138	.	0.212745	0.47852	D	0.000210	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-25.1419	17.5771	0.87953	0.0:1.0:0.0:0.0	.	.	.	.	X	483	.	ENSP00000264434:E483X	E	-	1	0	C2orf42	70241330	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.278000	0.65592	2.726000	0.93360	0.650000	0.86243	GAA	.	.	none		0.418	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18649057	18649057	+	Missense_Mutation	SNP	C	C	T	rs12312266	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:18649057C>T	ENST00000266497.5	+	19	2770	c.2732C>T	c.(2731-2733)cCg>cTg	p.P911L	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.P952L|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.P911L			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	911			P -> L (in dbSNP:rs12312266). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9878262, ECO:0000269|Ref.3}.		chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				AATGCTAATCCGATGGGCAAA	0.323													C|||	1875	0.374401	0.5008	0.366	5008	,	,		18017	0.3046		0.2425	False		,,,				2504	0.4172				p.P911L		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.C2732T						PASS	.	C	LEU/PRO	1621,2027		369,883,572	103.0	89.0	94.0		2732	4.4	1.0	12	dbSNP_120	94	1837,6305		236,1365,2470	yes	missense	PIK3C2G	NM_004570.4	98	605,2248,3042	TT,TC,CC		22.562,44.4353,29.3299	probably-damaging	911/1446	18649057	3458,8332	1824	4071	5895	SO:0001583	missense	5288	exon20			CTAATCCGATGGG	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2732C>T	12.37:g.18649057C>T	ENSP00000266497:p.Pro911Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	98	40	0.408163	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	703	0.3218864468864469	218	0.44308943089430897	129	0.356353591160221	178	0.3111888111888112	178	0.23482849604221637	C	24.1	4.498890	0.85069	0.444353	0.22562	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	D;D;D	0.81908	-1.55;-1.55;-1.55	4.37	4.37	0.52481	Protein kinase-like domain (1);	0.071120	0.56097	D	0.000035	T	0.00012	0.0000	M	0.78456	2.415	0.09310	P	0.99999999684936	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.94	T	0.00768	-1.1574	9	0.59425	D	0.04	-16.2062	16.7234	0.85416	0.0:1.0:0.0:0.0	rs12312266;rs17847799;rs52825188;rs58825824;rs12312266	952;911	F5H369;O75747	.;P3C2G_HUMAN	L	911;911;952	ENSP00000404845:P911L;ENSP00000266497:P911L;ENSP00000445381:P952L	ENSP00000266497:P911L	P	+	2	0	PIK3C2G	18540324	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.384000	0.66225	2.724000	0.93272	0.650000	0.86243	CCG	C|0.665;N|0.000	.	strong		0.323	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
OR51G1	79324	hgsc.bcm.edu	37	11	4945236	4945236	+	Missense_Mutation	SNP	T	T	C	rs35666095	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:4945236T>C	ENST00000321961.2	-	1	401	c.334A>G	c.(334-336)Atg>Gtg	p.M112V	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGACTCCATTGAAGACAAG	0.507													C|||	385	0.076877	0.0613	0.1527	5008	,	,		22605	0.0089		0.1083	False		,,,				2504	0.0818				p.M112V		Atlas-SNP	.											.	OR51G1	74	.	0			c.A334G						PASS	.	C	VAL/MET	276,4126	801.0+/-415.6	3,270,1928	100.0	93.0	95.0		334	-0.0	0.1	11	dbSNP_126	95	930,7666	776.4+/-407.7	61,808,3429	yes	missense	OR51G1	NM_001005237.1	21	64,1078,5357	CC,CT,TT		10.819,6.2699,9.2784	benign	112/322	4945236	1206,11792	2201	4298	6499	SO:0001583	missense	79324	exon1			ACTCCATTGAAGA	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.334A>G	11.37:g.4945236T>C	ENSP00000322546:p.Met112Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	171	0.0782967032967033	34	0.06910569105691057	30	0.08287292817679558	5	0.008741258741258742	102	0.1345646437994723	C	0.005	-2.188683	0.00305	0.062699	0.10819	ENSG00000176879	ENST00000321961	T	0.02812	4.15	4.2	-0.00795	0.14007	GPCR, rhodopsin-like superfamily (1);	0.206562	0.23916	N	0.043292	T	0.00039	0.0001	L	0.47190	1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43621	-0.9380	9	0.30078	T	0.28	.	1.644	0.02758	0.1365:0.3161:0.1337:0.4136	rs35666095	112	Q8NGK1	O51G1_HUMAN	V	112	ENSP00000322546:M112V	ENSP00000322546:M112V	M	-	1	0	OR51G1	4901812	0.000000	0.05858	0.095000	0.20976	0.034000	0.12701	-1.074000	0.03427	-0.143000	0.11334	-0.996000	0.02517	ATG	T|0.912;C|0.088	0.088	strong		0.507	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
FRMD1	79981	hgsc.bcm.edu	37	6	168461516	168461516	+	Missense_Mutation	SNP	C	C	T	rs148097635	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168461516C>T	ENST00000283309.6	-	9	1331	c.1267G>A	c.(1267-1269)Ggg>Agg	p.G423R	FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000537786.1_Missense_Mutation_p.G194R|FRMD1_ENST00000440994.2_Missense_Mutation_p.G355R	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	423						cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		TCATGGAGCCCGTGGACCTCC	0.657													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17850	0.002		0.0	False		,,,				2504	0.0				p.G423R	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.G1267A						PASS	.	C	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	47.0	42.0	44.0		1063,1267	-2.6	0.0	6	dbSNP_134	44	17,8583	11.2+/-40.8	0,17,4283	yes	missense,missense	FRMD1	NM_001122841.1,NM_024919.3	125,125	0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384	benign,benign	355/482,423/550	168461516	18,12988	2203	4300	6503	SO:0001583	missense	79981	exon9			GGAGCCCGTGGAC		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.1267G>A	6.37:g.168461516C>T	ENSP00000283309:p.Gly423Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	148	78	0.527027	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	37	CCDS5306.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	2.675	-0.276625	0.05679	2.27E-4	0.001977	ENSG00000153303	ENST00000283309;ENST00000440994;ENST00000537786	T;T;T	0.50277	0.75;0.75;0.75	2.48	-2.6	0.06190	.	2.404160	0.02924	U	0.138326	T	0.09642	0.0237	L	0.36672	1.1	0.09310	N	1	B;P;B;B	0.36733	0.076;0.567;0.207;0.262	B;B;B;B	0.22152	0.012;0.038;0.027;0.021	T	0.04053	-1.0981	10	0.10636	T	0.68	.	4.8184	0.13378	0.1237:0.1851:0.5734:0.1178	.	358;423;355;318	B7Z8G9;Q8N878;Q8N878-2;Q5SZU5	.;FRMD1_HUMAN;.;.	R	423;355;194	ENSP00000283309:G423R;ENSP00000414115:G355R;ENSP00000440078:G194R	ENSP00000283309:G423R	G	-	1	0	FRMD1	168204365	0.001000	0.12720	0.000000	0.03702	0.053000	0.15095	0.872000	0.28037	-0.378000	0.07918	0.313000	0.20887	GGG	C|0.999;T|0.001	0.001	strong		0.657	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919	
OR11H6	122748	hgsc.bcm.edu	37	14	20691962	20691962	+	Missense_Mutation	SNP	C	C	G	rs9323693	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20691962C>G	ENST00000315519.2	+	1	172	c.94C>G	c.(94-96)Ctc>Gtc	p.L32V		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	32			L -> V (in dbSNP:rs9323693).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		TGAGTTTGTCCTCCTGGGTTT	0.428													c|||	498	0.0994409	0.121	0.049	5008	,	,		20383	0.0903		0.0815	False		,,,				2504	0.1339				p.L32V		Atlas-SNP	.											.	OR11H6	60	.	0			c.C94G						PASS	.	C	VAL/LEU	429,3977	209.8+/-230.5	18,393,1792	133.0	130.0	131.0		94	4.6	1.0	14	dbSNP_119	131	633,7967	164.2+/-216.6	34,565,3701	yes	missense	OR11H6	NM_001004480.1	32	52,958,5493	GG,GC,CC		7.3605,9.7367,8.1655	benign	32/331	20691962	1062,11944	2203	4300	6503	SO:0001583	missense	122748	exon1			TTTGTCCTCCTGG		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"""GPCR / Class A : Olfactory receptors"""	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.94C>G	14.37:g.20691962C>G	ENSP00000319071:p.Leu32Val	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	319	168	0.526646	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	204	0.09340659340659341	72	0.14634146341463414	17	0.04696132596685083	53	0.09265734265734266	62	0.08179419525065963	C	13.14	2.149408	0.37923	0.097367	0.073605	ENSG00000176219	ENST00000315519	T	0.00563	6.58	4.57	4.57	0.56435	.	0.000000	0.44483	D	0.000445	T	0.00012	0.0000	H	0.95611	3.695	0.35325	P	0.21487999999999996	P	0.45672	0.864	B	0.42214	0.38	T	0.18555	-1.0333	9	0.87932	D	0	.	15.2129	0.73241	0.0:1.0:0.0:0.0	rs9323693;rs17211271;rs52805624;rs9323693	32	Q8NGC7	O11H6_HUMAN	V	32	ENSP00000319071:L32V	ENSP00000319071:L32V	L	+	1	0	OR11H6	19761802	0.297000	0.24408	1.000000	0.80357	0.759000	0.43091	0.917000	0.28665	2.521000	0.84997	0.442000	0.29010	CTC	C|0.918;G|0.082	0.082	strong		0.428	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
RSBN1	54665	hgsc.bcm.edu	37	1	114354654	114354654	+	Silent	SNP	T	T	C	rs3195954	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:114354654T>C	ENST00000261441.5	-	1	444	c.381A>G	c.(379-381)ccA>ccG	p.P127P	RP5-1073O3.2_ENST00000418238.1_RNA|RP5-1073O3.2_ENST00000429398.1_RNA	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	127	Pro-rich.					nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTGCATTCGTTGGCGGCAGCG	0.746													T|||	610	0.121805	0.0045	0.1311	5008	,	,		11529	0.2282		0.1869	False		,,,				2504	0.0971				p.P127P		Atlas-SNP	.											RSBN1,colon,carcinoma,0,2	RSBN1	71	2	0			c.A381G						PASS	.	T		149,4053		2,145,1954	13.0	24.0	21.0		381	-4.9	0.5	1	dbSNP_105	21	1412,6854		115,1182,2836	no	coding-synonymous	RSBN1	NM_018364.3		117,1327,4790	CC,CT,TT		17.082,3.5459,12.5201		127/803	114354654	1561,10907	2101	4133	6234	SO:0001819	synonymous_variant	54665	exon1			ATTCGTTGGCGGC	AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.381A>G	1.37:g.114354654T>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	18	11	0.611111	NM_018364	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Silent	SNP	ENST00000261441.5	37	CCDS862.1																																																																																			T|0.861;C|0.139	0.139	strong		0.746	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364	
OR5AK2	390181	hgsc.bcm.edu	37	11	56756399	56756399	+	Missense_Mutation	SNP	G	G	T	rs10896563	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56756399G>T	ENST00000326855.2	+	1	53	c.11G>T	c.(10-12)gGa>gTa	p.G4V		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	4			G -> V (in dbSNP:rs10896563).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						ATGACACTAGGAAACAGCACT	0.398													G|||	684	0.136581	0.025	0.0778	5008	,	,		18225	0.3879		0.0746	False		,,,				2504	0.1339				p.G4V		Atlas-SNP	.											.	OR5AK2	45	.	0			c.G11T						PASS	.	G	VAL/GLY	112,4290	85.8+/-124.5	1,110,2090	124.0	121.0	122.0		11	-4.2	0.0	11	dbSNP_120	122	608,7984	158.2+/-211.7	27,554,3715	yes	missense	OR5AK2	NM_001005323.1	109	28,664,5805	TT,TG,GG		7.0764,2.5443,5.541	benign	4/310	56756399	720,12274	2201	4296	6497	SO:0001583	missense	390181	exon1			CACTAGGAAACAG	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.11G>T	11.37:g.56756399G>T	ENSP00000322784:p.Gly4Val	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	240	115	0.479167	NM_001005323	B2RNZ9	Missense_Mutation	SNP	ENST00000326855.2	37	CCDS31538.1	295	0.13507326007326007	15	0.03048780487804878	18	0.049723756906077346	211	0.3688811188811189	51	0.06728232189973615	G	3.646	-0.072519	0.07228	0.025443	0.070764	ENSG00000181273	ENST00000326855	T	0.00484	7.08	3.85	-4.16	0.03869	.	1.353690	0.05313	N	0.525229	T	0.00012	0.0000	L	0.37897	1.145	0.58432	P	1.999999999946489E-6	B	0.29936	0.262	B	0.35039	0.194	T	0.04165	-1.0972	9	0.39692	T	0.17	2.4039	6.529	0.22316	0.6307:0.0:0.2311:0.1382	rs10896563;rs52794870	4	Q8NH90	O5AK2_HUMAN	V	4	ENSP00000322784:G4V	ENSP00000322784:G4V	G	+	2	0	OR5AK2	56512975	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.403000	0.01046	-1.062000	0.03181	0.194000	0.17425	GGA	G|0.918;T|0.082	0.082	strong		0.398	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323	
EHD2	30846	hgsc.bcm.edu	37	19	48219929	48219929	+	Silent	SNP	G	G	A	rs61746407	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48219929G>A	ENST00000263277.3	+	2	311	c.60G>A	c.(58-60)acG>acA	p.T20T	EHD2_ENST00000538399.1_Intron|CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	20					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		CCATCCGCACGGTGACCTCGG	0.697													G|||	79	0.0157748	0.0015	0.0274	5008	,	,		16061	0.002		0.0427	False		,,,				2504	0.0133				p.T20T		Atlas-SNP	.											EHD2,NS,carcinoma,0,1	EHD2	59	1	0			c.G60A						PASS	.	G		38,4362		0,38,2162	20.0	17.0	18.0		60	-2.9	1.0	19	dbSNP_129	18	341,8253		8,325,3964	no	coding-synonymous	EHD2	NM_014601.3		8,363,6126	AA,AG,GG		3.9679,0.8636,2.9167		20/544	48219929	379,12615	2200	4297	6497	SO:0001819	synonymous_variant	30846	exon2			CCGCACGGTGACC	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.60G>A	19.37:g.48219929G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	70	46	0.657143	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	37	CCDS12704.1																																																																																			G|0.975;A|0.025	0.025	strong		0.697	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
FAT2	2196	hgsc.bcm.edu	37	5	150945483	150945483	+	Missense_Mutation	SNP	C	C	T	rs3734055	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150945483C>T	ENST00000261800.5	-	1	3022	c.3010G>A	c.(3010-3012)Ggt>Agt	p.G1004S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1004	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.		G -> S (in dbSNP:rs3734055).		epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGCCTCCCACCATCACTGGCC	0.597													T|||	2016	0.402556	0.3767	0.4524	5008	,	,		17724	0.3571		0.4901	False		,,,				2504	0.3589				p.G1004S		Atlas-SNP	.											.	FAT2	465	.	0			c.G3010A						PASS	.	T	SER/GLY	1713,2693	641.3+/-397.4	335,1043,825	44.0	37.0	39.0		3010	3.2	1.0	5	dbSNP_107	39	4496,4104	554.9+/-386.6	1181,2134,985	yes	missense	FAT2	NM_001447.2	56	1516,3177,1810	TT,TC,CC		47.7209,38.8788,47.7395	benign	1004/4350	150945483	6209,6797	2203	4300	6503	SO:0001583	missense	2196	exon1			TCCCACCATCACT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3010G>A	5.37:g.150945483C>T	ENSP00000261800:p.Gly1004Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	935	0.4281135531135531	204	0.4146341463414634	161	0.4447513812154696	202	0.3531468531468531	368	0.48548812664907653	T	9.338	1.062294	0.19987	0.388788	0.522791	ENSG00000086570	ENST00000261800	T	0.50001	0.76	5.53	3.19	0.36642	Cadherin (4);Cadherin-like (1);	0.327956	0.30464	N	0.009564	T	0.00012	0.0000	L	0.39397	1.21	0.49798	P	1.7800000000001148E-4	B	0.06786	0.001	B	0.12156	0.007	T	0.47535	-0.9110	9	0.06236	T	0.91	.	4.9317	0.13921	0.0:0.3749:0.1616:0.4635	rs3734055;rs52828169;rs3734055	1004	Q9NYQ8	FAT2_HUMAN	S	1004	ENSP00000261800:G1004S	ENSP00000261800:G1004S	G	-	1	0	FAT2	150925676	0.146000	0.22672	0.999000	0.59377	0.963000	0.63663	0.364000	0.20325	0.402000	0.25451	-0.254000	0.11334	GGT	C|0.544;T|0.456	0.456	strong		0.597	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
NCLN	56926	hgsc.bcm.edu	37	19	3207646	3207646	+	Missense_Mutation	SNP	A	A	G	rs2288949	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:3207646A>G	ENST00000246117.4	+	15	2083	c.1652A>G	c.(1651-1653)aAg>aGg	p.K551R	NCLN_ENST00000590671.1_Missense_Mutation_p.K477R|NCLN_ENST00000591062.1_3'UTR	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	551			K -> R (in dbSNP:rs2288949). {ECO:0000269|PubMed:11230166, ECO:0000269|Ref.6}.		regulation of signal transduction (GO:0009966)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				kidney(1)|lung(3)|skin(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.83e-113)|Epithelial(107;1.65e-111)|all cancers(105;1.53e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00139)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCCTCTACAAGACCGTCCAG	0.672													A|||	1029	0.205471	0.1301	0.1614	5008	,	,		13460	0.4087		0.0646	False		,,,				2504	0.274				p.K551R		Atlas-SNP	.											.	NCLN	27	.	0			c.A1652G						PASS	.	A	ARG/LYS	591,3815	251.2+/-258.0	38,515,1650	44.0	38.0	40.0		1652	2.6	1.0	19	dbSNP_100	40	398,8202	123.8+/-182.6	10,378,3912	yes	missense	NCLN	NM_020170.3	26	48,893,5562	GG,GA,AA		4.6279,13.4135,7.6042	benign	551/564	3207646	989,12017	2203	4300	6503	SO:0001583	missense	56926	exon15			TCTACAAGACCGT	BC025926	CCDS32869.1	19p13.3	2010-08-13	2010-08-13			ENSG00000125912			26923	protein-coding gene	gene with protein product	"""nicastrin-like protein"""	609156	"""nicalin homolog (zebrafish)"""			11230166	Standard	NM_020170		Approved	NICALIN, NET59	uc002lxi.3	Q969V3		ENST00000246117.4:c.1652A>G	19.37:g.3207646A>G	ENSP00000246117:p.Lys551Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	167	88	0.526946	NM_020170	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Missense_Mutation	SNP	ENST00000246117.4	37	CCDS32869.1	418	0.19139194139194138	66	0.13414634146341464	57	0.1574585635359116	244	0.42657342657342656	51	0.06728232189973615	A	12.46	1.945716	0.34377	0.134135	0.046279	ENSG00000125912	ENST00000246117	T	0.30448	1.53	3.61	2.58	0.30949	.	0.862061	0.10469	N	0.670979	T	0.00012	0.0000	N	0.12182	0.205	0.38347	P	0.05578000000000005	B;B	0.15930	0.015;0.009	B;B	0.16289	0.015;0.006	T	0.49072	-0.8977	9	0.20046	T	0.44	-8.9712	6.4848	0.22083	0.8827:0.0:0.1173:0.0	rs2288949;rs11551091;rs17696536;rs57678984;rs2288949	550;551	Q969V3-2;Q969V3	.;NCLN_HUMAN	R	551	ENSP00000246117:K551R	ENSP00000246117:K551R	K	+	2	0	NCLN	3158646	0.972000	0.33761	0.972000	0.41901	0.843000	0.47879	1.070000	0.30653	0.461000	0.27071	0.459000	0.35465	AAG	A|0.876;G|0.124	0.124	strong		0.672	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1	NM_020170	
KIF27	55582	hgsc.bcm.edu	37	9	86474262	86474262	+	Missense_Mutation	SNP	T	T	C	rs79324787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:86474262T>C	ENST00000297814.2	-	14	3102	c.2959A>G	c.(2959-2961)Ata>Gta	p.I987V	RP11-575L7.4_ENST00000590417.1_RNA|RP11-575L7.4_ENST00000586206.1_RNA|RP11-575L7.4_ENST00000591217.1_RNA|RP11-575L7.4_ENST00000608866.1_RNA|RP11-575L7.4_ENST00000586211.1_RNA|KIF27_ENST00000334204.2_Missense_Mutation_p.I890V|RP11-575L7.4_ENST00000589817.1_RNA|RP11-575L7.4_ENST00000590368.1_RNA|RP11-575L7.4_ENST00000590813.1_RNA|RP11-575L7.4_ENST00000589233.1_RNA|RP11-575L7.4_ENST00000421734.3_RNA|RP11-575L7.4_ENST00000592283.1_RNA|KIF27_ENST00000413982.1_Missense_Mutation_p.I921V	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	987					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						CGAGTTGATATTTTCAAACTA	0.378													T|||	54	0.0107827	0.0333	0.0043	5008	,	,		16078	0.001		0.003	False		,,,				2504	0.0031				p.I987V		Atlas-SNP	.											.	KIF27	103	.	0			c.A2959G						PASS	.	T	VAL/ILE	16,4390	9.9+/-24.2	0,16,2187	94.0	81.0	85.0		2959	4.5	1.0	9	dbSNP_131	85	1,8599		0,1,4299	yes	missense	KIF27	NM_017576.1	29	0,17,6486	CC,CT,TT		0.0116,0.3631,0.1307	benign	987/1402	86474262	17,12989	2203	4300	6503	SO:0001583	missense	55582	exon14			TTGATATTTTCAA	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.2959A>G	9.37:g.86474262T>C	ENSP00000297814:p.Ile987Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	136	11	0.0808824	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	T	1.953	-0.440642	0.04636	0.003631	1.16E-4	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.55930	0.49;0.49;0.49	4.49	4.49	0.54785	.	0.125199	0.34067	N	0.004296	T	0.28466	0.0704	N	0.20685	0.6	0.09310	N	0.999999	B;P;P	0.35656	0.049;0.514;0.506	B;B;B	0.36989	0.05;0.238;0.12	T	0.35599	-0.9782	10	0.02654	T	1	.	4.0383	0.09740	0.2382:0.0971:0.0:0.6647	.	890;921;987	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	V	987;921;890	ENSP00000297814:I987V;ENSP00000401688:I921V;ENSP00000333928:I890V	ENSP00000297814:I987V	I	-	1	0	KIF27	85664082	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.394000	0.44450	1.880000	0.54463	0.397000	0.26171	ATA	T|0.994;C|0.006	0.006	strong		0.378	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
MED10	84246	hgsc.bcm.edu	37	5	6377293	6377293	+	Silent	SNP	C	C	T	rs17831958	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:6377293C>T	ENST00000255764.3	-	2	302	c.192G>A	c.(190-192)ccG>ccA	p.P64P		NM_032286.2	NP_115662.2	Q9BTT4	MED10_HUMAN	mediator complex subunit 10	64					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						AAACTTCTAACGGTACAGTAA	0.398													C|||	175	0.0349441	0.0106	0.0461	5008	,	,		19371	0.0		0.1074	False		,,,				2504	0.0215				p.P64P		Atlas-SNP	.											.	MED10	7	.	0			c.G192A						PASS	.	C		92,4314	76.8+/-115.0	1,90,2112	108.0	105.0	106.0		192	-3.3	0.7	5	dbSNP_123	106	779,7821	183.7+/-231.9	45,689,3566	no	coding-synonymous	MED10	NM_032286.2		46,779,5678	TT,TC,CC		9.0581,2.0881,6.6969		64/136	6377293	871,12135	2203	4300	6503	SO:0001819	synonymous_variant	84246	exon2			TTCTAACGGTACA		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.192G>A	5.37:g.6377293C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_032286	C6G491	Silent	SNP	ENST00000255764.3	37	CCDS34134.1																																																																																			C|0.942;T|0.058	0.058	strong		0.398	MED10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365714.1	NM_032286	
HLA-B	3106	hgsc.bcm.edu	37	6	31324562	31324562	+	Silent	SNP	C	C	T	rs1050564	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324562C>T	ENST00000412585.2	-	2	274	c.246G>A	c.(244-246)gaG>gaA	p.E82E		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	82	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GGTCCCAATACTCCGGCCCCT	0.652									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	273	0.0545128	0.0166	0.1254	5008	,	,		7647	0.0694		0.0746	False		,,,				2504	0.0194				p.E82E		Atlas-SNP	.											.	HLA-B	54	.	0			c.G246A						PASS	.	C		180,4116		28,124,1996	60.0	59.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	246	1.4	0.2	6	dbSNP_86	59	745,7603		139,467,3568	no	coding-synonymous	HLA-B	NM_005514.6		167,591,5564	TT,TC,CC		8.9243,4.1899,7.3157		82/363	31324562	925,11719	2148	4174	6322	SO:0001819	synonymous_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CCAATACTCCGGC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.246G>A	6.37:g.31324562C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	144	70	0.486111	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			T|0.074;C|0.926	0.074	strong		0.652	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
LOXL3	84695	hgsc.bcm.edu	37	2	74761539	74761539	+	Missense_Mutation	SNP	T	T	A	rs17010021	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:74761539T>A	ENST00000264094.3	-	11	1914	c.1843A>T	c.(1843-1845)Atc>Ttc	p.I615F	LOXL3_ENST00000409986.1_Missense_Mutation_p.I470F|LOXL3_ENST00000409549.1_Missense_Mutation_p.I559F|LOXL3_ENST00000393937.2_Missense_Mutation_p.I470F|LOXL3_ENST00000409249.1_Intron	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	615	Lysyl-oxidase like.		I -> F (in dbSNP:rs17010021).		epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						TGAGTGAAGATGTCCATGCTG	0.532													T|||	651	0.129992	0.0257	0.0965	5008	,	,		24452	0.3313		0.0427	False		,,,				2504	0.1769				p.I615F		Atlas-SNP	.											.	LOXL3	73	.	0			c.A1843T						PASS	.	T	PHE/ILE	126,4280	93.0+/-131.7	1,124,2078	214.0	206.0	209.0		1843	3.7	1.0	2	dbSNP_123	209	309,8291	110.2+/-170.6	5,299,3996	yes	missense	LOXL3	NM_032603.2	21	6,423,6074	AA,AT,TT		3.593,2.8597,3.3446	benign	615/754	74761539	435,12571	2203	4300	6503	SO:0001583	missense	84695	exon11			TGAAGATGTCCAT	AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.1843A>T	2.37:g.74761539T>A	ENSP00000264094:p.Ile615Phe	Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	314	205	0.652866	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Missense_Mutation	SNP	ENST00000264094.3	37	CCDS1953.1	266	0.12179487179487179	10	0.02032520325203252	33	0.09116022099447514	194	0.33916083916083917	29	0.03825857519788918	T	16.07	3.018957	0.54576	0.028597	0.03593	ENSG00000115318	ENST00000264094;ENST00000393937;ENST00000409549;ENST00000409986	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	4.87	3.7	0.42460	.	0.110173	0.64402	D	0.000010	T	0.00012	0.0000	L	0.44542	1.39	0.20489	P	0.999895742	D;D;D;P	0.67145	0.996;0.983;0.984;0.922	D;D;D;P	0.65443	0.935;0.932;0.917;0.697	T	0.32903	-0.9889	9	0.59425	D	0.04	.	6.3422	0.21328	0.0:0.192:0.0:0.808	rs17010021;rs52799143;rs17010021	470;559;470;615	B9A025;E7END4;Q6IPL7;P58215	.;.;.;LOXL3_HUMAN	F	615;470;559;470	ENSP00000264094:I615F;ENSP00000377512:I470F;ENSP00000386696:I559F;ENSP00000386545:I470F	ENSP00000264094:I615F	I	-	1	0	LOXL3	74615047	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.738000	0.38207	0.983000	0.38602	0.460000	0.39030	ATC	T|0.937;A|0.063	0.063	strong		0.532	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603	
SUV39H2	79723	hgsc.bcm.edu	37	10	14941654	14941654	+	Silent	SNP	C	C	T	rs17353856	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:14941654C>T	ENST00000354919.6	+	4	966	c.966C>T	c.(964-966)taC>taT	p.Y322Y	DCLRE1C_ENST00000378289.4_Intron|SUV39H2_ENST00000313519.5_Silent_p.Y262Y|SUV39H2_ENST00000378325.3_Silent_p.Y142Y	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	322	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell differentiation (GO:0030154)|chromatin assembly or disassembly (GO:0006333)|chromatin remodeling (GO:0006338)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|male meiosis (GO:0007140)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nuclear heterochromatin (GO:0005720)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						CGGCTCGATACGGCAATGTGT	0.403													C|||	277	0.0553115	0.0204	0.1153	5008	,	,		18355	0.002		0.1163	False		,,,				2504	0.0521				p.Y322Y		Atlas-SNP	.											.	SUV39H2	72	.	0			c.C966T						PASS	.	C	,,,,	146,4260	101.2+/-139.8	4,138,2061	165.0	143.0	151.0		966,786,426,246,786	1.7	1.0	10	dbSNP_123	151	1124,7476	233.3+/-266.6	77,970,3253	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SUV39H2	NM_001193424.1,NM_001193425.1,NM_001193426.1,NM_001193427.1,NM_024670.3	,,,,	81,1108,5314	TT,TC,CC		13.0698,3.3137,9.7647	,,,,	322/411,262/351,142/231,82/171,262/351	14941654	1270,11736	2203	4300	6503	SO:0001819	synonymous_variant	79723	exon4			TCGATACGGCAAT	AK027067	CCDS7104.1, CCDS53493.1, CCDS53494.1	10p13	2011-07-01			ENSG00000152455	ENSG00000152455		"""Chromatin-modifying enzymes / K-methyltransferases"""	17287	protein-coding gene	gene with protein product		606503				11094092	Standard	NM_001193424		Approved	FLJ23414, KMT1B	uc021png.1	Q9H5I1	OTTHUMG00000017718	ENST00000354919.6:c.966C>T	10.37:g.14941654C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	179	96	0.536313	NM_001193424	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Silent	SNP	ENST00000354919.6	37	CCDS53494.1	143	0.06547619047619048	14	0.028455284552845527	39	0.10773480662983426	3	0.005244755244755245	87	0.11477572559366754	C	8.874	0.950101	0.18431	0.033137	0.130698	ENSG00000152455	ENST00000358298	.	.	.	5.62	1.72	0.24424	.	.	.	.	.	T	0.00496	0.0016	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.10428	-1.0630	3	.	.	.	.	8.2438	0.31675	0.0:0.2756:0.0:0.7244	rs17353856;rs17353856	.	.	.	M	88	.	.	T	+	2	0	SUV39H2	14981660	0.991000	0.36638	1.000000	0.80357	0.971000	0.66376	0.265000	0.18515	0.087000	0.17167	-0.484000	0.04775	ACG	C|0.912;T|0.088	0.088	strong		0.403	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670	
IHH	3549	hgsc.bcm.edu	37	2	219920412	219920412	+	Silent	SNP	A	A	G	rs3731881	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:219920412A>G	ENST00000295731.6	-	3	752	c.753T>C	c.(751-753)ccT>ccC	p.P251P	MIR3131_ENST00000583592.1_RNA	NM_002181.3	NP_002172.2	Q14623	IHH_HUMAN	indian hedgehog	251					bone resorption (GO:0045453)|camera-type eye photoreceptor cell fate commitment (GO:0060220)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|chondrocyte proliferation (GO:0035988)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint development (GO:0072498)|epithelial cell morphogenesis (GO:0003382)|epithelial cell-cell adhesion (GO:0090136)|head morphogenesis (GO:0060323)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intein-mediated protein splicing (GO:0016539)|maternal process involved in female pregnancy (GO:0060135)|multicellular organism growth (GO:0035264)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of eye pigmentation (GO:0048074)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell differentiation in thymus (GO:0033085)|neuron development (GO:0048666)|osteoblast differentiation (GO:0001649)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of growth (GO:0040008)|response to estradiol (GO:0032355)|retinal pigment epithelium development (GO:0003406)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|somite development (GO:0061053)|vitelline membrane formation (GO:0030704)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|patched binding (GO:0005113)|peptidase activity (GO:0008233)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000188)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCAGCCTGTGAGGCTCGCGGT	0.642													G|||	2428	0.484824	0.4395	0.5331	5008	,	,		15926	0.2788		0.672	False		,,,				2504	0.5317				p.P251P		Atlas-SNP	.											.	IHH	33	.	0			c.T753C						PASS	.	G		1999,2407	613.7+/-392.2	456,1087,660	56.0	58.0	58.0		753	-5.8	0.0	2	dbSNP_107	58	5732,2868	449.0+/-362.0	1881,1970,449	yes	coding-synonymous	IHH	NM_002181.3		2337,3057,1109	GG,GA,AA		33.3488,45.37,40.5582		251/412	219920412	7731,5275	2203	4300	6503	SO:0001819	synonymous_variant	3549	exon3			CCTGTGAGGCTCG	L38517	CCDS33380.1	2q33-q35	2013-02-15	2013-02-15		ENSG00000163501	ENSG00000163501			5956	protein-coding gene	gene with protein product		600726	"""Indian hedgehog (Drosophila) homolog"", ""Indian hedgehog homolog (Drosophila)"""			7590746, 14770182	Standard	NM_002181		Approved	HHG2, BDA1	uc002vjo.2	Q14623	OTTHUMG00000154631	ENST00000295731.6:c.753T>C	2.37:g.219920412A>G		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	103	101	0.980583	NM_002181	B9EGM5|O43322|Q8N4B9	Silent	SNP	ENST00000295731.6	37	CCDS33380.1																																																																																			A|0.454;G|0.546	0.546	strong		0.642	IHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336408.2	NM_002181	
TEK	7010	hgsc.bcm.edu	37	9	27205021	27205021	+	Silent	SNP	G	G	A	rs542913	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:27205021G>A	ENST00000380036.4	+	14	2764	c.2322G>A	c.(2320-2322)agG>agA	p.R774R	TEK_ENST00000406359.4_Silent_p.R731R|TEK_ENST00000519097.1_Silent_p.R627R	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	774					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	AATTGAAGAGGGCAAATGTGC	0.493													G|||	756	0.150958	0.0764	0.1599	5008	,	,		19378	0.122		0.2525	False		,,,				2504	0.1708				p.R774R		Atlas-SNP	.											.	TEK	250	.	0			c.G2322A						PASS	.	G		525,3881	239.6+/-250.7	33,459,1711	141.0	110.0	120.0		2322	2.2	1.0	9	dbSNP_83	120	2223,6377	378.3+/-338.9	283,1657,2360	no	coding-synonymous	TEK	NM_000459.3		316,2116,4071	AA,AG,GG		25.8488,11.9156,21.1287		774/1125	27205021	2748,10258	2203	4300	6503	SO:0001819	synonymous_variant	7010	exon14			GAAGAGGGCAAAT	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2322G>A	9.37:g.27205021G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	234	107	0.457265	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																			G|0.808;A|0.192	0.192	strong		0.493	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
DYX1C1	161582	hgsc.bcm.edu	37	15	55722956	55722956	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55722956G>A	ENST00000321149.3	-	10	1542	c.1175C>T	c.(1174-1176)gCa>gTa	p.A392V	DYX1C1_ENST00000448430.2_Intron|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000380679.1_Intron|DYX1C1_ENST00000348518.3_Missense_Mutation_p.H357Y|DYX1C1_ENST00000457155.2_Missense_Mutation_p.H357Y	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	392					cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		AATCTTAAGTGCCGCTTCATA	0.294																																					p.A392V		Atlas-SNP	.											DYX1C1,NS,carcinoma,-1,1	DYX1C1	54	1	0			c.C1175T						PASS	.						126.0	123.0	124.0					15																	55722956		2192	4290	6482	SO:0001583	missense	161582	exon10			TTAAGTGCCGCTT		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.1175C>T	15.37:g.55722956G>A	ENSP00000323275:p.Ala392Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_130810	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.120950|5.120950	0.94385|0.94385	.|.	.|.	ENSG00000256061|ENSG00000256061	ENST00000321149|ENST00000457155;ENST00000348518	D|T;T	0.82803|0.27557	-1.65|1.66;1.66	5.6|5.6	5.6|5.6	0.85130|0.85130	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.19846|0.19846	0.0477|0.0477	.|.	.|.	.|.	0.34596|0.34596	D|D	0.715963|0.715963	D|B	0.89917|0.29766	1.0|0.256	D|B	0.91635|0.34138	0.999|0.176	T|T	0.05632|0.05632	-1.0873|-1.0873	9|8	0.66056|0.02654	D|T	0.02|1	.|.	18.6754|18.6754	0.91526|0.91526	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	392|357	Q8WXU2|Q8WXU2-3	DYXC1_HUMAN|.	V|Y	392|357	ENSP00000323275:A392V|ENSP00000402640:H357Y;ENSP00000299561:H357Y	ENSP00000323275:A392V|ENSP00000299561:H357Y	A|H	-|-	2|1	0|0	DYX1C1|DYX1C1	53510248|53510248	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.977000|7.977000	0.88081|0.88081	2.650000|2.650000	0.89964|0.89964	0.558000|0.558000	0.71614|0.71614	GCA|CAC	.	.	none		0.294	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499274	59499274	+	Silent	SNP	C	C	A	rs3809528	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:59499274C>A	ENST00000307144.4	+	1	233	c.135C>A	c.(133-135)acC>acA	p.T45T	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	45					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						GGCTCTTCACCCCCGTGAGCA	0.562													C|||	2509	0.500998	0.5113	0.4409	5008	,	,		20835	0.6131		0.34	False		,,,				2504	0.5798				p.T45T		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.C135A						PASS	.	C	,	2053,2329	567.5+/-382.2	502,1049,640	78.0	70.0	72.0		,135	-0.3	0.0	15	dbSNP_107	72	2754,5826	439.4+/-359.2	437,1880,1973	no	intron,coding-synonymous	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,	939,2929,2613	AA,AC,CC		32.0979,46.8508,37.0853	,	,45/382	59499274	4807,8155	2191	4290	6481	SO:0001819	synonymous_variant	92483	exon1			CTTCACCCCCGTG	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.135C>A	15.37:g.59499274C>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	NM_033195	Q6DUY4|Q96LI2	Silent	SNP	ENST00000307144.4	37	CCDS10171.1																																																																																			C|0.586;A|0.414	0.414	strong		0.562	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
SYNE3	161176	hgsc.bcm.edu	37	14	95910933	95910933	+	Silent	SNP	T	T	C	rs9919918	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:95910933T>C	ENST00000334258.5	-	9	1679	c.1665A>G	c.(1663-1665)gcA>gcG	p.A555A	SYNE3_ENST00000557275.1_Silent_p.A555A|SYNE3_ENST00000554873.1_Silent_p.A312A|SYNE3_ENST00000553340.1_Silent_p.A555A	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	555					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)	p.A555A(1)		breast(1)|endometrium(2)|lung(25)	28						GCTCAAAAGCTGCTCCAAAGT	0.577													C|||	1410	0.28155	0.3427	0.4035	5008	,	,		19740	0.3155		0.2078	False		,,,				2504	0.1534				p.A555A		Atlas-SNP	.											C14orf49,NS,carcinoma,0,1	SYNE3	130	1	1	Substitution - coding silent(1)	stomach(1)	c.A1665G						scavenged	.	C		1436,2970	682.6+/-404.1	244,948,1011	52.0	51.0	51.0		1665	-10.8	0.0	14	dbSNP_119	51	1620,6980	742.8+/-407.2	171,1278,2851	no	coding-synonymous	C14orf49	NM_152592.3		415,2226,3862	CC,CT,TT		18.8372,32.5919,23.4968		555/976	95910933	3056,9950	2203	4300	6503	SO:0001819	synonymous_variant	161176	exon9			AAAAGCTGCTCCA	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.1665A>G	14.37:g.95910933T>C		Somatic	76	2	0.0263158		WXS	Illumina HiSeq	Phase_I	75	43	0.573333	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	37	CCDS9935.1																																																																																			C|0.242;N|0.000	0.242	strong		0.577	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
FMN1	342184	hgsc.bcm.edu	37	15	33260973	33260973	+	Missense_Mutation	SNP	C	C	T	rs150962800	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:33260973C>T	ENST00000559047.1	-	5	2928	c.2929G>A	c.(2929-2931)Gag>Aag	p.E977K	SNORD77_ENST00000391113.1_RNA|FMN1_ENST00000334528.9_Missense_Mutation_p.E754K|FMN1_ENST00000561249.1_Missense_Mutation_p.E879K			Q68DA7	FMN1_HUMAN	formin 1	977	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.|Pro-rich.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		CAACTGGGCTCGATGGCTGGT	0.507													C|||	39	0.00778754	0.0008	0.0173	5008	,	,		10701	0.001		0.0189	False		,,,				2504	0.0061				p.E754K		Atlas-SNP	.											.	FMN1	174	.	0			c.G2260A						PASS	.	C	LYS/GLU	14,3668		0,14,1827	125.0	121.0	122.0		2260	4.4	0.9	15	dbSNP_134	122	184,7998		3,178,3910	yes	missense	FMN1	NM_001103184.2	56	3,192,5737	TT,TC,CC		2.2488,0.3802,1.6689	probably-damaging	754/1197	33260973	198,11666	1841	4091	5932	SO:0001583	missense	342184	exon4			TGGGCTCGATGGC	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2929G>A	15.37:g.33260973C>T	ENSP00000454047:p.Glu977Lys	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	321	154	0.479751	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		27	0.012362637362637362	1	0.0020325203252032522	9	0.024861878453038673	1	0.0017482517482517483	16	0.021108179419525065	C	13.16	2.153144	0.38021	0.003802	0.022488	ENSG00000248905	ENST00000334528	T	0.15718	2.4	4.42	4.42	0.53409	.	0.052449	0.85682	D	0.000000	T	0.19725	0.0474	L	0.47190	1.495	.	.	.	D	0.69078	0.997	D	0.69142	0.962	T	0.08659	-1.0711	9	0.45353	T	0.12	.	17.2139	0.86937	0.0:1.0:0.0:0.0	.	754	Q68DA7-5	.	K	754	ENSP00000333950:E754K	ENSP00000333950:E754K	E	-	1	0	FMN1	31048265	1.000000	0.71417	0.943000	0.38184	0.517000	0.34286	5.800000	0.69108	2.279000	0.76181	0.650000	0.86243	GAG	C|0.987;T|0.013	0.013	strong		0.507	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
ABCC8	6833	hgsc.bcm.edu	37	11	17419279	17419279	+	Silent	SNP	C	C	T	rs1799859	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:17419279C>T	ENST00000389817.3	-	31	3887	c.3819G>A	c.(3817-3819)agG>agA	p.R1273R	ABCC8_ENST00000302539.4_Silent_p.R1274R			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1273	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	CAGAGAGCTCCCTGTGCAGGG	0.652													C|||	1958	0.390974	0.77	0.4236	5008	,	,		18243	0.0873		0.2704	False		,,,				2504	0.2924				p.R1273R		Atlas-SNP	.											.	ABCC8	170	.	0			c.G3819A	GRCh37	CM981881	ABCC8	M	rs1799859	PASS	.	C		3006,1394	686.5+/-404.7	1022,962,216	90.0	84.0	86.0		3819	-0.4	1.0	11	dbSNP_89	86	2314,6272	389.5+/-342.9	307,1700,2286	no	coding-synonymous	ABCC8	NM_000352.3		1329,2662,2502	TT,TC,CC		26.9509,31.6818,40.9672		1273/1582	17419279	5320,7666	2200	4293	6493	SO:0001819	synonymous_variant	6833	exon31			GAGCTCCCTGTGC	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"""ATP binding cassette transporters / subfamily C"""	59	protein-coding gene	gene with protein product	"""sulfonylurea receptor (hyperinsulinemia)"""	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.3819G>A	11.37:g.17419279C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Silent	SNP	ENST00000389817.3	37	CCDS31437.1	723	0.33104395604395603	322	0.6544715447154471	144	0.39779005524861877	56	0.0979020979020979	201	0.26517150395778366	C	9.687	1.150834	0.21371	0.683182	0.269509	ENSG00000006071	ENST00000528374	.	.	.	5.12	-0.368	0.12537	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27281	P	0.9580932	.	.	.	.	.	.	T	0.35549	-0.9784	3	.	.	.	.	0.9041	0.01281	0.1595:0.2632:0.1952:0.3822	rs1799859;rs2229689;rs4148643;rs12787564;rs17846763;rs57092202;rs1799859	.	.	.	R	97	.	.	G	-	1	0	ABCC8	17375855	0.983000	0.35010	0.977000	0.42913	0.974000	0.67602	0.311000	0.19380	0.034000	0.15491	0.555000	0.69702	GGA	C|0.611;T|0.389	0.389	strong		0.652	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
RHBG	57127	hgsc.bcm.edu	37	1	156351699	156351699	+	Missense_Mutation	SNP	G	G	A	rs3748569	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156351699G>A	ENST00000368249.1	+	6	981	c.943G>A	c.(943-945)Ggg>Agg	p.G315R	RHBG_ENST00000255013.3_Missense_Mutation_p.G246R|RHBG_ENST00000400992.2_Missense_Mutation_p.G283R|RHBG_ENST00000368246.2_Missense_Mutation_p.G315R|RHBG_ENST00000451864.2_Intron|RHBG_ENST00000537040.1_Missense_Mutation_p.G153R	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	315			G -> R (in dbSNP:rs3748569). {ECO:0000269|PubMed:15489334}.		ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					CTTCTTGGCTGGGACTGTCTC	0.572													G|||	2728	0.544728	0.5719	0.6037	5008	,	,		18935	0.7014		0.4095	False		,,,				2504	0.4438				p.G315R		Atlas-SNP	.											.	RHBG	133	.	0			c.G943A						PASS	.	G	ARG/GLY	2175,1959		576,1023,468	95.0	106.0	103.0		943	4.4	1.0	1	dbSNP_107	103	3575,4831		782,2011,1410	yes	missense	RHBG	NM_020407.3	125	1358,3034,1878	AA,AG,GG		42.5291,47.3875,45.8533	probably-damaging	315/459	156351699	5750,6790	2067	4203	6270	SO:0001583	missense	57127	exon6			TTGGCTGGGACTG	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.943G>A	1.37:g.156351699G>A	ENSP00000357232:p.Gly315Arg	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	292	147	0.503425	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		1209	0.5535714285714286	287	0.5833333333333334	208	0.574585635359116	403	0.7045454545454546	311	0.4102902374670185	G	26.5	4.744673	0.89663	0.526125	0.425291	ENSG00000132677	ENST00000368249;ENST00000368246;ENST00000537040;ENST00000400992;ENST00000255013	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	4.44	4.44	0.53790	Ammonium transporter AmtB-like (3);	0.049574	0.85682	D	0.000000	T	0.67325	0.2881	M	0.93763	3.455	0.09310	P	1.0	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.986;0.998;1.0;0.999	T	0.77643	-0.2511	9	0.72032	D	0.01	-1.7511	14.5902	0.68359	0.0:0.0:1.0:0.0	rs3748569;rs17855953;rs52807244;rs58877861;rs3748569	315;153;283;352	Q9H310;F5GWZ4;Q9H310-3;Q5SZW5	RHBG_HUMAN;.;.;.	R	315;315;153;283;246	ENSP00000357232:G315R;ENSP00000357229:G315R;ENSP00000441197:G153R;ENSP00000383777:G283R;ENSP00000255013:G246R	ENSP00000255013:G246R	G	+	1	0	RHBG	154618323	1.000000	0.71417	0.957000	0.39632	0.996000	0.88848	7.438000	0.80431	2.286000	0.76751	0.561000	0.74099	GGG	G|0.472;A|0.528	0.528	strong		0.572	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
SDK2	54549	hgsc.bcm.edu	37	17	71410891	71410891	+	Silent	SNP	C	C	T	rs12386051	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:71410891C>T	ENST00000392650.3	-	18	2376	c.2376G>A	c.(2374-2376)acG>acA	p.T792T	SDK2_ENST00000388726.3_Silent_p.T792T	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	792					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CCGGAGGGACCGTGGGAACTA	0.612													C|||	1251	0.2498	0.0552	0.2205	5008	,	,		13989	0.4831		0.2495	False		,,,				2504	0.2935				p.T792T		Atlas-SNP	.											SDK2,NS,carcinoma,0,1	SDK2	219	1	0			c.G2376A						PASS	.	C		454,3952	212.5+/-232.4	38,378,1787	65.0	58.0	60.0		2376	-6.6	0.9	17	dbSNP_120	60	1958,6642	344.0+/-325.1	245,1468,2587	yes	coding-synonymous	SDK2	NM_001144952.1		283,1846,4374	TT,TC,CC		22.7674,10.3041,18.5453		792/2173	71410891	2412,10594	2203	4300	6503	SO:0001819	synonymous_variant	54549	exon18			AGGGACCGTGGGA	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.2376G>A	17.37:g.71410891C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1																																																																																			C|0.787;T|0.213	0.213	strong		0.612	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
CEP89	84902	hgsc.bcm.edu	37	19	33370161	33370161	+	Silent	SNP	A	A	C	rs745959	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:33370161A>C	ENST00000305768.5	-	19	2347	c.2259T>G	c.(2257-2259)gtT>gtG	p.V753V	CTD-2085J24.4_ENST00000586628.2_lincRNA	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	753					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						GGCTGGGGGCAACCAGAGCTC	0.562													C|||	825	0.164736	0.0703	0.1527	5008	,	,		14878	0.1091		0.334	False		,,,				2504	0.184				p.V753V		Atlas-SNP	.											.	CEP89	82	.	0			c.T2259G						PASS	.	C		481,3925	781.9+/-414.5	25,431,1747	137.0	130.0	132.0		2259	-2.6	0.0	19	dbSNP_86	132	3052,5548	661.5+/-401.9	565,1922,1813	no	coding-synonymous	CEP89	NM_032816.3		590,2353,3560	CC,CA,AA		35.4884,10.9169,27.1644		753/784	33370161	3533,9473	2203	4300	6503	SO:0001819	synonymous_variant	84902	exon19			GGGGGCAACCAGA	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.2259T>G	19.37:g.33370161A>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_032816	B9EGA6|Q8N5J8	Silent	SNP	ENST00000305768.5	37	CCDS32987.1																																																																																			A|0.759;C|0.241	0.241	strong		0.562	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
SAMD9L	219285	hgsc.bcm.edu	37	7	92760738	92760738	+	Missense_Mutation	SNP	T	T	G	rs10282508	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:92760738T>G	ENST00000318238.4	-	5	5763	c.4547A>C	c.(4546-4548)aAt>aCt	p.N1516T	SAMD9L_ENST00000411955.1_Missense_Mutation_p.N1516T|SAMD9L_ENST00000437805.1_Missense_Mutation_p.N1516T	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1516			N -> T (in dbSNP:rs10282508).		common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TTTGACTTCATTTTTTTTCCA	0.393													T|||	534	0.106629	0.2247	0.0461	5008	,	,		19427	0.1369		0.0467	False		,,,				2504	0.0204				p.N1516T		Atlas-SNP	.											.	SAMD9L	227	.	0			c.A4547C						PASS	.	T	THR/ASN	859,3547	337.6+/-304.9	86,687,1430	128.0	127.0	127.0		4547	-1.9	0.1	7	dbSNP_119	127	438,8162	132.6+/-190.3	22,394,3884	yes	missense	SAMD9L	NM_152703.2	65	108,1081,5314	GG,GT,TT		5.093,19.4961,9.9723	benign	1516/1585	92760738	1297,11709	2203	4300	6503	SO:0001583	missense	219285	exon5			ACTTCATTTTTTT	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"""Sterile alpha motif (SAM) domain containing"""	1349	protein-coding gene	gene with protein product		611170	"""chromosome 7 open reading frame 6"""	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.4547A>C	7.37:g.92760738T>G	ENSP00000326247:p.Asn1516Thr	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	283	115	0.40636	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	267	0.12225274725274725	122	0.24796747967479674	16	0.04419889502762431	95	0.1660839160839161	34	0.044854881266490766	T	2.359	-0.347034	0.05208	0.194961	0.05093	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472	T;T;T	0.21543	2.0;2.0;2.0	4.77	-1.89	0.07689	.	0.928117	0.09002	N	0.862767	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.43294	-0.9400	9	0.48119	T	0.1	0.0887	5.8963	0.18941	0.0:0.3078:0.1296:0.5625	rs10282508;rs10282508	1516	Q8IVG5	SAM9L_HUMAN	T	1516;1516;1516;338	ENSP00000326247:N1516T;ENSP00000405760:N1516T;ENSP00000408796:N1516T	ENSP00000326247:N1516T	N	-	2	0	SAMD9L	92598674	0.000000	0.05858	0.098000	0.21074	0.437000	0.31866	0.047000	0.14056	-0.193000	0.10415	0.383000	0.25322	AAT	T|0.887;G|0.113	0.113	strong		0.393	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703	
BOD1L1	259282	hgsc.bcm.edu	37	4	13604182	13604182	+	Missense_Mutation	SNP	T	T	C	rs17745676	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:13604182T>C	ENST00000040738.5	-	10	4477	c.4342A>G	c.(4342-4344)Aca>Gca	p.T1448A		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1448			T -> A (in dbSNP:rs17745676).			nucleus (GO:0005634)	DNA binding (GO:0003677)										TATTTTTCTGTATTCAGGCCT	0.358													T|||	665	0.132788	0.1415	0.2089	5008	,	,		24405	0.003		0.1501	False		,,,				2504	0.183				p.T1448A		Atlas-SNP	.											.	.	.	.	0			c.A4342G						PASS	.	T	ALA/THR	655,3751	279.0+/-274.6	40,575,1588	97.0	89.0	92.0		4342	2.9	0.0	4	dbSNP_123	92	1295,7305	255.5+/-280.4	86,1123,3091	yes	missense	BOD1L	NM_148894.2	58	126,1698,4679	CC,CT,TT		15.0581,14.8661,14.9931	probably-damaging	1448/3052	13604182	1950,11056	2203	4300	6503	SO:0001583	missense	259282	exon10			TTTCTGTATTCAG	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.4342A>G	4.37:g.13604182T>C	ENSP00000040738:p.Thr1448Ala	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	317	148	0.466877	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	261	0.11950549450549451	80	0.16260162601626016	70	0.19337016574585636	0	0.0	111	0.14643799472295516	T	9.995	1.231917	0.22626	0.148661	0.150581	ENSG00000038219	ENST00000040738	T	0.07444	3.19	5.37	2.86	0.33363	.	0.235838	0.29335	N	0.012456	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.14012	0.009	B	0.12156	0.007	T	0.40627	-0.9553	9	0.39692	T	0.17	-2.3293	7.9535	0.30029	0.0:0.2567:0.0:0.7433	rs17745676;rs52821402;rs17745676	1448	Q8NFC6	BOD1L_HUMAN	A	1448	ENSP00000040738:T1448A	ENSP00000040738:T1448A	T	-	1	0	BOD1L	13213280	0.000000	0.05858	0.023000	0.16930	0.006000	0.05464	-0.055000	0.11807	0.327000	0.23409	-0.263000	0.10527	ACA	T|0.855;C|0.145	0.145	strong		0.358	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
MAGEB18	286514	hgsc.bcm.edu	37	X	26157220	26157220	+	Missense_Mutation	SNP	C	C	T	rs5944317	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:26157220C>T	ENST00000325250.1	+	2	305	c.118C>T	c.(118-120)Cct>Tct	p.P40S		NM_173699.3	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	40			P -> S (in dbSNP:rs5944317). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(17)|skin(2)|stomach(1)|urinary_tract(2)	33						GTCACCCTCCCCTGCCTATCT	0.582													T|||	2793	0.739868	0.6339	0.5504	3775	,	,		13555	0.6935		0.3141	False		,,,				2504	0.5706				p.P40S		Atlas-SNP	.											.	MAGEB18	67	.	0			c.C118T						PASS	.	T	SER/PRO	3042,791		1013,547,469,71,102	50.0	44.0	46.0		118	-6.6	0.0	X	dbSNP_114	46	2836,3892		443,1164,786,821,1086	yes	missense	MAGEB18	NM_173699.3	74	1456,1711,1255,892,1188	TT,TC,T,CC,C		42.1522,20.6366,44.3424	benign	40/344	26157220	5878,4683	2202	4300	6502	SO:0001583	missense	286514	exon2			CCCTCCCCTGCCT	AK057361	CCDS14216.1	Xp21.3	2008-02-05			ENSG00000176774	ENSG00000176774			28515	protein-coding gene	gene with protein product							Standard	NM_173699		Approved	MGC33889	uc004dbq.2	Q96M61	OTTHUMG00000021282	ENST00000325250.1:c.118C>T	X.37:g.26157220C>T	ENSP00000314543:p.Pro40Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_173699		Missense_Mutation	SNP	ENST00000325250.1	37	CCDS14216.1	1129	0.6805304400241109	216	0.7105263157894737	117	0.5176991150442478	258	0.8376623376623377	161	0.27288135593220336	T	0.019	-1.457964	0.01071	0.793634	0.421522	ENSG00000176774	ENST00000325250	T	0.02280	4.36	4.17	-6.57	0.01842	Melanoma associated antigen, MAGE, N-terminal (1);	2.302700	0.02191	N	0.061355	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.46303	-0.9201	9	0.02654	T	1	.	12.8095	0.57631	0.1225:0.715:0.0:0.1625	rs5944317;rs6526550;rs17845895;rs17858870;rs58835272;rs5944317	40	Q96M61	MAGBI_HUMAN	S	40	ENSP00000314543:P40S	ENSP00000314543:P40S	P	+	1	0	MAGEB18	26067141	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.829000	0.00356	-2.305000	0.00654	-1.286000	0.01371	CCT	C|0.372;T|0.628	0.628	strong		0.582	MAGEB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056120.1	NM_173699	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807620	18807620	+	Missense_Mutation	SNP	G	G	C	rs34109355	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18807620G>C	ENST00000400664.1	+	1	197	c.145G>C	c.(145-147)Ggt>Cgt	p.G49R		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	49						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CCAGCGGTGGGGTGGGAATGG	0.667													G|||	473	0.0944489	0.1233	0.1239	5008	,	,		16342	0.0377		0.1233	False		,,,				2504	0.0634				p.G49R		Atlas-SNP	.											KLHDC7A,NS,carcinoma,0,1	KLHDC7A	60	1	0			c.G145C						PASS	.	G	ARG/GLY	389,3633		18,353,1640	24.0	28.0	27.0		145	3.9	0.0	1	dbSNP_126	27	1022,7330		60,902,3214	yes	missense	KLHDC7A	NM_152375.2	125	78,1255,4854	CC,CG,GG		12.2366,9.6718,11.4029	probably-damaging	49/778	18807620	1411,10963	2011	4176	6187	SO:0001583	missense	127707	exon1			CGGTGGGGTGGGA	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.145G>C	1.37:g.18807620G>C	ENSP00000383505:p.Gly49Arg	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	193	98	0.507772	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	213	0.09752747252747253	45	0.09146341463414634	50	0.13812154696132597	29	0.050699300699300696	89	0.11741424802110818	G	17.46	3.396154	0.62177	0.096718	0.122366	ENSG00000179023	ENST00000400664	D	0.86694	-2.16	5.82	3.89	0.44902	.	.	.	.	.	T	0.04048	0.0113	N	0.19112	0.55	0.80722	P	0.0	D	0.69078	0.997	D	0.64410	0.925	T	0.61168	-0.7117	8	0.87932	D	0	.	8.2772	0.31879	0.2557:0.0:0.7443:0.0	rs34109355	49	Q5VTJ3	KLD7A_HUMAN	R	49	ENSP00000383505:G49R	ENSP00000383505:G49R	G	+	1	0	KLHDC7A	18680207	0.017000	0.18338	0.003000	0.11579	0.076000	0.17211	0.662000	0.25038	0.742000	0.32697	0.591000	0.81541	GGT	G|0.899;C|0.101	0.101	strong		0.667	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
SWT1	54823	hgsc.bcm.edu	37	1	185240474	185240474	+	Missense_Mutation	SNP	A	A	G	rs12041704	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:185240474A>G	ENST00000367500.4	+	17	2626	c.2461A>G	c.(2461-2463)Aat>Gat	p.N821D	SWT1_ENST00000367501.3_Missense_Mutation_p.N821D	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	821			N -> D (in dbSNP:rs12041704). {ECO:0000269|PubMed:15489334}.							breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						CCCAAACAGTAATTATCAAGA	0.284													A|||	1743	0.348043	0.2428	0.3963	5008	,	,		13198	0.245		0.4433	False		,,,				2504	0.4642				p.N821D		Atlas-SNP	.											SWT1,NS,carcinoma,0,1	SWT1	88	1	0			c.A2461G						PASS	.	A	ASP/ASN,ASP/ASN	1203,3175	380.2+/-323.6	164,875,1150	38.0	39.0	39.0		2461,2461	4.8	1.0	1	dbSNP_120	39	3641,4921	504.5+/-376.2	786,2069,1426	yes	missense,missense	SWT1	NM_001105518.1,NM_017673.6	23,23	950,2944,2576	GG,GA,AA		42.5251,27.4783,37.4343	benign,benign	821/901,821/901	185240474	4844,8096	2189	4281	6470	SO:0001583	missense	54823	exon17			AACAGTAATTATC	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.2461A>G	1.37:g.185240474A>G	ENSP00000356470:p.Asn821Asp	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	249	247	0.991968	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	763	0.34935897435897434	132	0.2682926829268293	134	0.3701657458563536	170	0.2972027972027972	327	0.4313984168865435	A	16.44	3.123324	0.56613	0.274783	0.425251	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.20200	2.09;2.09	6.02	4.8	0.61643	.	0.263012	0.43747	D	0.000535	T	0.00012	0.0000	N	0.24115	0.695	0.41524	P	0.011584000000000039	P	0.49090	0.919	B	0.42692	0.395	T	0.42068	-0.9473	9	0.11794	T	0.64	.	9.9289	0.41510	0.838:0.0:0.0:0.162	rs12041704;rs12756341;rs17578728;rs17852826;rs52806916;rs60303559;rs12041704	821	Q5T5J6	SWT1_HUMAN	D	821	ENSP00000356471:N821D;ENSP00000356470:N821D	ENSP00000356470:N821D	N	+	1	0	SWT1	183507097	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.076000	0.50081	2.299000	0.77371	0.528000	0.53228	AAT	A|0.637;G|0.363	0.363	strong		0.284	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
CLEC16A	23274	hgsc.bcm.edu	37	16	11154770	11154770	+	Silent	SNP	G	G	A	rs2286973	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:11154770G>A	ENST00000409790.1	+	19	2237	c.2007G>A	c.(2005-2007)gtG>gtA	p.V669V	CLEC16A_ENST00000409552.3_Silent_p.V651V|CLEC16A_ENST00000465491.1_3'UTR	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.V669V(1)|p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CCATCCGGGTGTTCTTCATGC	0.542													A|||	2486	0.496406	0.7421	0.3458	5008	,	,		18000	0.3363		0.4135	False		,,,				2504	0.5215				p.V669V		Atlas-SNP	.											CLEC16A,NS,carcinoma,0,1	CLEC16A	101	1	2	Whole gene deletion(1)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)|stomach(1)	c.G2007A						PASS	.	A		3061,1315	391.0+/-327.9	1083,895,210	196.0	213.0	207.0		2007	-0.5	1.0	16	dbSNP_100	207	3700,4888	602.3+/-394.5	820,2060,1414	no	coding-synonymous	CLEC16A	NM_015226.2		1903,2955,1624	AA,AG,GG		43.0834,30.0503,47.8479		669/1054	11154770	6761,6203	2188	4294	6482	SO:0001819	synonymous_variant	23274	exon18			CCGGGTGTTCTTC	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2007G>A	16.37:g.11154770G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	36	0.467532	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			G|0.516;A|0.484	0.484	strong		0.542	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
ZNF354B	117608	hgsc.bcm.edu	37	5	178294059	178294059	+	Silent	SNP	T	T	C	rs113633676|rs11952817|rs386695542	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:178294059T>C	ENST00000322434.3	+	4	469	c.243T>C	c.(241-243)ggT>ggC	p.G81G		NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	81	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G81G(1)		breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACAGTTCTGGTGTCTCCTCTC	0.507													C|||	1517	0.302915	0.379	0.3055	5008	,	,		17700	0.1538		0.4254	False		,,,				2504	0.226				p.G81G		Atlas-SNP	.											ZNF354B,NS,carcinoma,0,1	ZNF354B	67	1	1	Substitution - coding silent(1)	stomach(1)	c.T243C						PASS	.	C		1588,2818		329,930,944	148.0	139.0	142.0		243	-2.0	0.0	5	dbSNP_120	142	3351,5249		699,1953,1648	no	coding-synonymous	ZNF354B	NM_058230.2		1028,2883,2592	CC,CT,TT		38.9651,36.0418,37.9748		81/613	178294059	4939,8067	2203	4300	6503	SO:0001819	synonymous_variant	117608	exon4			TTCTGGTGTCTCC	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"""Zinc fingers, C2H2-type"", ""-"""	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.243T>C	5.37:g.178294059T>C		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	231	123	0.532468	NM_058230	A8K0V2|Q5U5Z4	Silent	SNP	ENST00000322434.3	37	CCDS4439.1																																																																																			T|0.635;C|0.365	0.365	strong		0.507	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230	
ASCL3	56676	hgsc.bcm.edu	37	11	8959370	8959370	+	Silent	SNP	G	G	A	rs2742505	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:8959370G>A	ENST00000531618.1	-	1	388	c.339C>T	c.(337-339)taC>taT	p.Y113Y	ASCL3_ENST00000325884.1_Silent_p.Y113Y			Q9NQ33	ASCL3_HUMAN	achaete-scute family bHLH transcription factor 3	112	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)	p.Y113Y(1)		breast(1)|large_intestine(2)|lung(5)|stomach(1)	9				Epithelial(150;1.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0228)		GGAGCTGGGCGTAGCCTTCAT	0.527													G|||	1343	0.268171	0.1051	0.2478	5008	,	,		18734	0.2212		0.3549	False		,,,				2504	0.4622				p.Y113Y		Atlas-SNP	.											ASCL3,NS,carcinoma,-1,2	ASCL3	19	2	1	Substitution - coding silent(1)	stomach(1)	c.C339T						PASS	.	G		583,3819	258.6+/-262.5	41,501,1659	82.0	82.0	82.0		339	-4.9	1.0	11	dbSNP_100	82	3030,5560	466.8+/-366.9	545,1940,1810	no	coding-synonymous	ASCL3	NM_020646.1		586,2441,3469	AA,AG,GG		35.2736,13.244,27.8094		113/182	8959370	3613,9379	2201	4295	6496	SO:0001819	synonymous_variant	56676	exon2			CTGGGCGTAGCCT	AJ400877	CCDS7795.1	11p15.3	2013-10-17	2013-10-17			ENSG00000176009		"""Basic helix-loop-helix proteins"""	740	protein-coding gene	gene with protein product		609154	"""achaete-scute complex (Drosophila) homolog-like 3"", ""achaete-scute complex homolog 3 (Drosophila)"""			11528127	Standard	NM_020646		Approved	bHLHa42, HASH3, Sgn1	uc001mhd.1	Q9NQ33	OTTHUMG00000165679	ENST00000531618.1:c.339C>T	11.37:g.8959370G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_020646	Q8WYQ6	Silent	SNP	ENST00000531618.1	37	CCDS7795.1																																																																																			G|0.718;A|0.282	0.282	strong		0.527	ASCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385773.1		
AGR2	10551	hgsc.bcm.edu	37	7	16834597	16834597	+	Silent	SNP	A	A	G	rs6842	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:16834597A>G	ENST00000419304.2	-	7	593	c.441T>C	c.(439-441)aaT>aaC	p.N147N	AGR2_ENST00000401412.1_Silent_p.N147N|AGR2_ENST00000419572.2_Silent_p.N167N	NM_006408.3	NP_006399.1	O95994	AGR2_HUMAN	anterior gradient 2	147					lung goblet cell differentiation (GO:0060480)|mucus secretion (GO:0070254)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	dystroglycan binding (GO:0002162)			endometrium(2)|lung(1)|prostate(1)|skin(2)	6	Lung NSC(10;0.0376)|all_lung(11;0.0855)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		CATAGAGACGATTTGAATATC	0.418													A|||	1680	0.335463	0.1051	0.4957	5008	,	,		22739	0.2976		0.4672	False		,,,				2504	0.4366				p.N147N		Atlas-SNP	.											.	AGR2	14	.	0			c.T441C						PASS	.	A		733,3673	303.0+/-287.7	62,609,1532	150.0	120.0	130.0		441	-7.1	0.9	7	dbSNP_52	130	4273,4327	574.8+/-390.1	1044,2185,1071	no	coding-synonymous	AGR2	NM_006408.3		1106,2794,2603	GG,GA,AA		49.686,16.6364,38.4899		147/176	16834597	5006,8000	2203	4300	6503	SO:0001819	synonymous_variant	10551	exon7			GAGACGATTTGAA	AF038451	CCDS5364.1	7p21.3	2013-07-31	2013-07-31		ENSG00000106541	ENSG00000106541		"""Protein disulfide isomerases"""	328	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 17"""	606358	"""anterior gradient 2 homolog (Xenopus laevis)"""			9790916	Standard	NM_006408		Approved	XAG-2, HAG-2, AG2, PDIA17	uc003str.3	O95994	OTTHUMG00000023446	ENST00000419304.2:c.441T>C	7.37:g.16834597A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	145	144	0.993103	NM_006408		Silent	SNP	ENST00000419304.2	37	CCDS5364.1																																																																																			T|0.132;G|0.313;C|0.057;A|0.498	0.313	strong		0.418	AGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207594.2	NM_006408	
HLA-B	3106	hgsc.bcm.edu	37	6	31324705	31324705	+	Missense_Mutation	SNP	A	A	C	rs1131170	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324705A>C	ENST00000412585.2	-	2	131	c.103T>G	c.(103-105)Tcc>Gcc	p.S35A		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	35	Alpha-1.		S -> A (in dbSNP:rs1131170).		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CGGGACACGGAGGTGTAGAAA	0.706									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	3531	0.705072	0.7201	0.6643	5008	,	,		10505	0.7312		0.675	False		,,,				2504	0.7178				p.S35A		Atlas-SNP	.											.	HLA-B	54	.	0			c.T103G						PASS	.	C	ALA/SER	2362,1724		805,752,486	13.0	11.0	12.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	103	0.1	0.0	6	dbSNP_86	12	4261,3735		1497,1267,1234	no	missense	HLA-B	NM_005514.6	99	2302,2019,1720	CC,CA,AA		46.7109,42.1929,45.1829		35/363	31324705	6623,5459	2043	3998	6041	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	ACACGGAGGTGTA	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.103T>G	6.37:g.31324705A>C	ENSP00000399168:p.Ser35Ala	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	1412	0.6465201465201466	299	0.6077235772357723	227	0.6270718232044199	393	0.6870629370629371	493	0.6503957783641161	N	0.048	-1.259216	0.01445	0.578071	0.532891	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00622	6.16;6.16	3.2	0.113	0.14631	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	2.346170	0.03598	N	0.232900	T	0.00210	0.0006	.	.	.	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.003;0.002;0.005	T	0.47923	-0.9079	8	0.18276	T	0.48	.	12.8503	0.57855	0.4978:0.5022:0.0:0.0	rs1131170;rs3177894;rs3177911;rs9266187;rs17416905	35;35;10	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	A	35;46	ENSP00000399168:S35A;ENSP00000405931:S46A	ENSP00000399168:S35A	S	-	1	0	HLA-B	31432684	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.692000	0.05127	-0.833000	0.04245	-4.197000	0.00009	TCC	C|0.646;A|0.354	0.646	strong		0.706	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
TSHZ2	128553	hgsc.bcm.edu	37	20	51872869	51872869	+	Missense_Mutation	SNP	C	C	A	rs61760185	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:51872869C>A	ENST00000371497.5	+	2	3759	c.2872C>A	c.(2872-2874)Cgc>Agc	p.R958S	TSHZ2_ENST00000603338.2_Missense_Mutation_p.R955S|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R955S|RP4-678D15.1_ENST00000606932.1_RNA	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	958					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			GGACATGACCCGCTTGTCAGT	0.507													C|||	2	0.000399361	0.0	0.0	5008	,	,		19232	0.0		0.002	False		,,,				2504	0.0				p.R958S		Atlas-SNP	.											.	TSHZ2	209	.	0			c.C2872A						PASS	.	C	SER/ARG,SER/ARG	2,4404	4.2+/-10.8	0,2,2201	77.0	77.0	77.0		2863,2872	4.7	1.0	20	dbSNP_129	77	25,8575	16.0+/-53.3	0,25,4275	yes	missense,missense	TSHZ2	NM_001193421.1,NM_173485.5	110,110	0,27,6476	AA,AC,CC		0.2907,0.0454,0.2076	probably-damaging,probably-damaging	955/1032,958/1035	51872869	27,12979	2203	4300	6503	SO:0001583	missense	128553	exon2			ATGACCCGCTTGT	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2872C>A	20.37:g.51872869C>A	ENSP00000360552:p.Arg958Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	121	75	0.619835	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.55	3.417888	0.62622	4.54E-4	0.002907	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.15603	2.42;2.41	5.7	4.7	0.59300	.	0.047245	0.85682	D	0.000000	T	0.14700	0.0355	N	0.22421	0.69	0.52501	D	0.999954	P	0.52842	0.956	P	0.45681	0.49	T	0.00844	-1.1543	10	0.62326	D	0.03	-11.6406	11.9946	0.53194	0.3361:0.6639:0.0:0.0	rs61760185	958	Q9NRE2	TSH2_HUMAN	S	958;955;484	ENSP00000360552:R958S;ENSP00000333114:R955S	ENSP00000333114:R955S	R	+	1	0	TSHZ2	51306276	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	6.371000	0.73119	2.685000	0.91497	0.643000	0.83706	CGC	C|0.999;A|0.001	0.001	strong		0.507	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
OR2T12	127064	hgsc.bcm.edu	37	1	248458736	248458736	+	Missense_Mutation	SNP	A	A	G	rs28409263	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248458736A>G	ENST00000317996.1	-	1	144	c.145T>C	c.(145-147)Tgg>Cgg	p.W49R		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	49						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			CGGTGGTCCCAGTGAATCAGG	0.537													-|||	1138	0.227236	0.0567	0.2522	5008	,	,		14030	0.3601		0.1769	False		,,,				2504	0.3548				p.W49R		Atlas-SNP	.											.	OR2T12	113	.	0			c.T145C						PASS	.	G	ARG/TRP	279,4127	793.8+/-415.2	21,237,1945	96.0	80.0	85.0		145	-3.1	0.0	1	dbSNP_125	85	1221,7379	745.6+/-407.3	124,973,3203	no	missense	OR2T12	NM_001004692.1	101	145,1210,5148	GG,GA,AA		14.1977,6.3323,11.5331	benign	49/321	248458736	1500,11506	2203	4300	6503	SO:0001583	missense	127064	exon1			GGTCCCAGTGAAT	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.145T>C	1.37:g.248458736A>G	ENSP00000324583:p.Trp49Arg	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	264	112	0.424242	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	395	0.18086080586080586	37	0.07520325203252033	63	0.17403314917127072	179	0.3129370629370629	116	0.15303430079155672	g	1.445	-0.566654	0.03910	0.063323	0.141977	ENSG00000177201	ENST00000317996	T	0.02890	4.12	1.55	-3.09	0.05331	GPCR, rhodopsin-like superfamily (1);	3.014640	0.01683	N	0.026254	T	0.00012	0.0000	N	0.03177	-0.4	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48222	-0.9054	9	0.37606	T	0.19	.	0.2054	0.00150	0.3304:0.2518:0.1575:0.2603	rs28409263	49	Q8NG77	O2T12_HUMAN	R	49	ENSP00000324583:W49R	ENSP00000324583:W49R	W	-	1	0	OR2T12	246525359	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-3.039000	0.00633	-1.597000	0.01609	-1.352000	0.01234	TGG	A|0.868;G|0.132	0.132	strong		0.537	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
MRPS9	64965	hgsc.bcm.edu	37	2	105713697	105713697	+	Silent	SNP	A	A	G	rs15567	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:105713697A>G	ENST00000258455.3	+	10	1124	c.1014A>G	c.(1012-1014)tcA>tcG	p.S338S	AC104655.2_ENST00000449177.1_RNA|AC104655.2_ENST00000432211.1_RNA	NM_182640.2	NP_872578.1	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9	338					DNA damage response, detection of DNA damage (GO:0042769)|peptide biosynthetic process (GO:0043043)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						GCGGGAGGTCAGCGCAGGCTG	0.552													G|||	836	0.166933	0.1339	0.2781	5008	,	,		17379	0.1091		0.2247	False		,,,				2504	0.1329				p.S338S		Atlas-SNP	.											.	MRPS9	32	.	0			c.A1014G						PASS	.	G		645,3761	766.3+/-413.4	33,579,1591	107.0	94.0	98.0		1014	-4.8	0.1	2	dbSNP_52	98	2071,6529	717.9+/-406.2	230,1611,2459	no	coding-synonymous	MRPS9	NM_182640.2		263,2190,4050	GG,GA,AA		24.0814,14.6391,20.8827		338/397	105713697	2716,10290	2203	4300	6503	SO:0001819	synonymous_variant	64965	exon10			GAGGTCAGCGCAG		CCDS2065.1	2q12.1	2012-09-13			ENSG00000135972	ENSG00000135972		"""Mitochondrial ribosomal proteins / small subunits"""	14501	protein-coding gene	gene with protein product	"""28S ribosomal protein S9, mitochondrial"""	611975				11279123	Standard	NM_182640		Approved	RPMS9, MRP-S9, S9mt	uc002tcn.4	P82933	OTTHUMG00000130807	ENST00000258455.3:c.1014A>G	2.37:g.105713697A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_182640	Q6PG40	Silent	SNP	ENST00000258455.3	37	CCDS2065.1																																																																																			T|0.000;G|0.203;C|0.000;A|0.797	0.203	strong		0.552	MRPS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253352.1	NM_182640	
VN1R2	317701	hgsc.bcm.edu	37	19	53762675	53762675	+	Silent	SNP	G	G	A	rs61734062	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53762675G>A	ENST00000341702.3	+	1	1131	c.1047G>A	c.(1045-1047)gtG>gtA	p.V349V	VN1R2_ENST00000598458.1_Intron	NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	349					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		GGTGGCTAGTGAACACTGCTG	0.468													G|||	82	0.0163738	0.0023	0.0288	5008	,	,		21790	0.0		0.0467	False		,,,				2504	0.0123				p.V349V		Atlas-SNP	.											.	VN1R2	71	.	0			c.G1047A						PASS	.	G		40,4366	43.8+/-77.6	0,40,2163	248.0	224.0	232.0		1047	1.7	0.0	19	dbSNP_129	232	328,8272	114.8+/-174.7	9,310,3981	no	coding-synonymous	VN1R2	NM_173856.2		9,350,6144	AA,AG,GG		3.814,0.9079,2.8295		349/396	53762675	368,12638	2203	4300	6503	SO:0001819	synonymous_variant	317701	exon1			GCTAGTGAACACT	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.1047G>A	19.37:g.53762675G>A		Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	331	180	0.543807	NM_173856	A1L411|Q8TDU4	Silent	SNP	ENST00000341702.3	37	CCDS12862.1																																																																																			G|0.974;A|0.026	0.026	strong		0.468	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856	
ENO3	2027	hgsc.bcm.edu	37	17	4856376	4856376	+	Missense_Mutation	SNP	A	A	G	rs238238	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4856376A>G	ENST00000323997.6	+	4	344	c.212A>G	c.(211-213)aAt>aGt	p.N71S	ENO3_ENST00000518175.1_Missense_Mutation_p.N71S|ENO3_ENST00000519584.1_Intron	NM_001976.4|NM_053013.3	NP_001967.3|NP_443739.3	P13929	ENOB_HUMAN	enolase 3 (beta, muscle)	71			N -> S (in dbSNP:rs238238). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8513787}.		aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to drug (GO:0042493)|skeletal muscle tissue regeneration (GO:0043403)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|phosphopyruvate hydratase complex (GO:0000015)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			cervix(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)	15						AACATCAACAATACTCTGGGC	0.602													A|||	2825	0.564097	0.5499	0.7795	5008	,	,		17474	0.3988		0.6809	False		,,,				2504	0.4806				p.N71S		Atlas-SNP	.											ENO3,NS,carcinoma,0,1	ENO3	36	1	0			c.A212G						PASS	.	A	,SER/ASN,SER/ASN	2639,1767	644.5+/-398.0	780,1079,344	79.0	75.0	76.0		,212,212	5.4	1.0	17	dbSNP_79	76	6063,2537	692.7+/-404.6	2127,1809,364	yes	intron,missense,missense	ENO3	NM_001193503.1,NM_001976.4,NM_053013.3	,46,46	2907,2888,708	GG,GA,AA		29.5,40.1044,33.0924	,benign,benign	,71/435,71/435	4856376	8702,4304	2203	4300	6503	SO:0001583	missense	2027	exon4			TCAACAATACTCT	X16504	CCDS11062.1, CCDS54070.1	17p13.2	2013-09-19	2004-11-22		ENSG00000108515	ENSG00000108515	4.2.1.11		3354	protein-coding gene	gene with protein product		131370	"""enolase 3, (beta, muscle)"""				Standard	NM_001976		Approved		uc002gab.4	P13929	OTTHUMG00000099394	ENST00000323997.6:c.212A>G	17.37:g.4856376A>G	ENSP00000324105:p.Asn71Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	139	137	0.985611	NM_001976	B4DUI6|B4DUM6|D3DTL2|E7ENK8|Q96AE2	Missense_Mutation	SNP	ENST00000323997.6	37	CCDS11062.1	1308	0.5989010989010989	292	0.5934959349593496	279	0.7707182320441989	221	0.38636363636363635	516	0.6807387862796834	A	13.59	2.282795	0.40394	0.598956	0.705	ENSG00000108515	ENST00000522798;ENST00000519602;ENST00000323997;ENST00000522249;ENST00000518175	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	5.4	5.4	0.78164	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.40295	P	0.02145600000000003	B	0.02656	0.0	B	0.04013	0.001	T	0.22312	-1.0220	7	0.33141	T	0.24	-15.9177	13.6512	0.62312	1.0:0.0:0.0:0.0	rs238238;rs2230256;rs3180329;rs3209189;rs11537779;rs58818159;rs238238	71	D3DTL2	.	S	71	ENSP00000428502:N71S;ENSP00000430055:N71S;ENSP00000324105:N71S;ENSP00000428811:N71S;ENSP00000431087:N71S	ENSP00000324105:N71S	N	+	2	0	ENO3	4797122	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.651000	0.54431	2.176000	0.68965	0.533000	0.62120	AAT	A|0.376;G|0.624	0.624	strong		0.602	ENO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216851.2		
CCT5	22948	hgsc.bcm.edu	37	5	10261764	10261764	+	Missense_Mutation	SNP	C	C	G	rs141675330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:10261764C>G	ENST00000280326.4	+	8	1506	c.1086C>G	c.(1084-1086)atC>atG	p.I362M	CTD-2256P15.4_ENST00000606194.1_RNA|CCT5_ENST00000506600.1_Missense_Mutation_p.I269M|CCT5_ENST00000515390.1_Missense_Mutation_p.I307M|CCT5_ENST00000515676.1_Missense_Mutation_p.I324M|CCT5_ENST00000503026.1_Missense_Mutation_p.I341M	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	362					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						TACAGGAGATCTCATTTGGGA	0.478													C|||	15	0.00299521	0.0008	0.0144	5008	,	,		19303	0.0		0.004	False		,,,				2504	0.0				p.I362M		Atlas-SNP	.											.	CCT5	49	.	0			c.C1086G						PASS	.	C	MET/ILE	8,4398	14.3+/-33.2	0,8,2195	146.0	154.0	151.0		1086	3.6	1.0	5	dbSNP_134	151	57,8543	36.4+/-91.3	0,57,4243	yes	missense	CCT5	NM_012073.3	10	0,65,6438	GG,GC,CC		0.6628,0.1816,0.4998	benign	362/542	10261764	65,12941	2203	4300	6503	SO:0001583	missense	22948	exon8			GGAGATCTCATTT	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"""Heat Shock Proteins / Chaperonins"""	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.1086C>G	5.37:g.10261764C>G	ENSP00000280326:p.Ile362Met	Somatic	374	1	0.0026738		WXS	Illumina HiSeq	Phase_I	376	196	0.521277	NM_012073	A8JZY8|A8K2X8|B4DYD8	Missense_Mutation	SNP	ENST00000280326.4	37	CCDS3877.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	13.57	2.278030	0.40294	0.001816	0.006628	ENSG00000150753	ENST00000280326;ENST00000503026;ENST00000515390;ENST00000440011;ENST00000515676;ENST00000506600	T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18	5.39	3.59	0.41128	.	0.045544	0.85682	D	0.000000	T	0.59959	0.2232	L	0.28014	0.82	0.58432	D	0.999999	B;B;B;B;B;B	0.25772	0.113;0.012;0.134;0.006;0.006;0.006	B;B;B;B;B;B	0.34722	0.188;0.079;0.049;0.049;0.049;0.049	T	0.62286	-0.6886	10	0.45353	T	0.12	-30.4305	9.1905	0.37195	0.0:0.7727:0.0:0.2273	.	269;307;211;360;362;362	B4DYD8;E7ENZ3;B4DZY9;Q9BU08;A8K2X8;P48643	.;.;.;.;.;TCPE_HUMAN	M	362;341;307;335;324;269	ENSP00000280326:I362M;ENSP00000423318:I341M;ENSP00000426923:I307M;ENSP00000427297:I324M;ENSP00000423052:I269M	ENSP00000280326:I362M	I	+	3	3	CCT5	10314764	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	1.786000	0.38694	1.266000	0.44231	0.558000	0.71614	ATC	C|0.996;G|0.004	0.004	strong		0.478	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2		
CEACAM18	729767	hgsc.bcm.edu	37	19	51986547	51986547	+	Missense_Mutation	SNP	A	A	G	rs10426247	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51986547A>G	ENST00000396477.4	+	4	971	c.950A>G	c.(949-951)cAt>cGt	p.H317R	CEACAM18_ENST00000451626.1_Missense_Mutation_p.H378R	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	317										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CAGGCCCCCCATGAGTGCAGC	0.612													a|||	888	0.177316	0.1278	0.1686	5008	,	,		20149	0.1429		0.2445	False		,,,				2504	0.2168				p.H378R		Atlas-SNP	.											CEACAM18_ENST00000451626,colon,carcinoma,0,1	CEACAM18	96	1	0			c.A1133G						PASS	.	A	ARG/HIS	556,3676		35,486,1595	56.0	58.0	57.0		1133	1.5	0.0	19	dbSNP_119	57	2006,6466		222,1562,2452	no	missense	CEACAM18	NM_001080405.1	29	257,2048,4047	GG,GA,AA		23.678,13.138,20.1669	benign	378/399	51986547	2562,10142	2116	4236	6352	SO:0001583	missense	729767	exon5			CCCCCCATGAGTG			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.950A>G	19.37:g.51986547A>G	ENSP00000379738:p.His317Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		368	0.1684981684981685	55	0.11178861788617886	69	0.19060773480662985	74	0.12937062937062938	170	0.22427440633245382	.	0.006	-2.020692	0.00418	0.13138	0.23678	ENSG00000213822	ENST00000451626;ENST00000451086	T	0.04706	3.57	2.53	1.48	0.22813	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46898	-0.9158	7	.	.	.	.	5.6185	0.17444	0.1594:0.0:0.8406:0.0	rs10426247	378	A8MTB9	CEA18_HUMAN	R	378;317	ENSP00000402203:H378R	.	H	+	2	0	CEACAM18	56678359	0.032000	0.19561	0.036000	0.18154	0.008000	0.06430	0.395000	0.20850	0.670000	0.31165	-0.413000	0.06143	CAT	A|0.816;G|0.184	0.184	strong		0.612	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
SPANXD	64648	hgsc.bcm.edu	37	X	140785739	140785739	+	Missense_Mutation	SNP	A	A	C	rs149295712		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:140785739A>C	ENST00000370515.3	-	2	510	c.177T>G	c.(175-177)ttT>ttG	p.F59L		NM_032417.2|NM_145665.1	NP_115793.1|NP_663698.1	Q9BXN6	SPNXD_HUMAN	SPANX family, member D	59						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	Acute lymphoblastic leukemia(192;7.65e-05)					ATGTTCTTTTAAAGTTCCTCC	0.483																																					p.F59L		Atlas-SNP	.											.	.	.	.	0			c.T177G						PASS	.						232.0	182.0	199.0					X																	140785739		2202	4287	6489	SO:0001583	missense	171489	exon2			TCTTTTAAAGTTC	AJ457791	CCDS14675.1	Xq27.2	2014-06-19			ENSG00000196406	ENSG00000196406			14332	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 4"""	300670, 300671	"""SPANX family, member E"""	SPANXE			Standard	NM_032417		Approved	CT11.4		Q9BXN6	OTTHUMG00000022563	ENST00000370515.3:c.177T>G	X.37:g.140785739A>C	ENSP00000359546:p.Phe59Leu	Somatic	405	1	0.00246914		WXS	Illumina HiSeq	Phase_I	522	325	0.622605	NM_145665	Q5JWI1	Missense_Mutation	SNP	ENST00000370515.3	37	CCDS14675.1	.	.	.	.	.	.	.	.	.	.	N	6.679	0.493851	0.12702	.	.	ENSG00000196406	ENST00000370515	T	0.05925	3.37	.	.	.	.	.	.	.	.	T	0.03915	0.0110	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.44682	-0.9312	6	0.26408	T	0.33	.	.	.	.	rs1059179;rs2933669;rs3176112;rs17845058;rs17857837;rs17859694	59	Q9BXN6	SPNXD_HUMAN	L	59	ENSP00000359546:F59L	ENSP00000359546:F59L	F	-	3	2	SPANXD	140613405	0.008000	0.16893	0.009000	0.14445	0.008000	0.06430	0.072000	0.14617	0.358000	0.24211	0.058000	0.15282	TTT	.	.	weak		0.483	SPANXD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058598.1		
DNHD1	144132	hgsc.bcm.edu	37	11	6579106	6579106	+	Missense_Mutation	SNP	C	C	A	rs11040920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6579106C>A	ENST00000527990.2	+	23	8581	c.8581C>A	c.(8581-8583)Cac>Aac	p.H2861N	DNHD1_ENST00000254579.6_Missense_Mutation_p.H2861N			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2861					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GTTGAGCCCCCACCTGGCCCG	0.662													C|||	1195	0.238618	0.0582	0.304	5008	,	,		17730	0.2242		0.3897	False		,,,				2504	0.2955				p.H2861N		Atlas-SNP	.											.	DNHD1	198	.	0			c.C8581A						PASS	.						18.0	17.0	17.0					11																	6579106		692	1591	2283	SO:0001583	missense	144132	exon25			AGCCCCCACCTGG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.8581C>A	11.37:g.6579106C>A	ENSP00000436180:p.His2861Asn	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	613	0.2806776556776557	34	0.06910569105691057	121	0.3342541436464088	160	0.27972027972027974	298	0.39313984168865435	C	0.873	-0.731308	0.03135	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210	T;T	0.24538	1.85;1.85	5.07	0.889	0.19212	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.48927	-0.8991	8	0.16896	T	0.51	.	4.0421	0.09756	0.2519:0.4131:0.2597:0.0753	rs11040920;rs60122228	2861;608	Q96M86;E9PHZ7	DNHD1_HUMAN;.	N	2861;2861;608	ENSP00000254579:H2861N;ENSP00000436180:H2861N	ENSP00000254579:H2861N	H	+	1	0	DNHD1	6535682	0.661000	0.27430	0.013000	0.15412	0.840000	0.47671	0.350000	0.20079	0.008000	0.14787	-0.175000	0.13238	CAC	A|0.281;C|0.718;T|0.001	0.281	strong		0.662	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
DOCK8	81704	hgsc.bcm.edu	37	9	334337	334337	+	Missense_Mutation	SNP	A	A	G	rs10970979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:334337A>G	ENST00000453981.1	+	11	1350	c.1238A>G	c.(1237-1239)aAt>aGt	p.N413S	DOCK8_ENST00000469391.1_Missense_Mutation_p.N345S|DOCK8_ENST00000432829.2_Missense_Mutation_p.N345S			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	413			N -> S (in dbSNP:rs10970979). {ECO:0000269|PubMed:15489334}.		blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		AGCTTCTTCAATGTCTCCACC	0.512													A|||	1000	0.199681	0.2073	0.2061	5008	,	,		18913	0.0377		0.2724	False		,,,				2504	0.2771				p.N413S		Atlas-SNP	.											.	DOCK8	401	.	0			c.A1238G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	1009,3397	375.4+/-321.6	121,767,1315	106.0	102.0	103.0		1034,1034,1238	2.3	0.9	9	dbSNP_120	103	2659,5941	428.2+/-355.8	395,1869,2036	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	46,46,46	516,2636,3351	GG,GA,AA		30.9186,22.9006,28.2024	benign,benign,benign	345/2000,345/2032,413/2100	334337	3668,9338	2203	4300	6503	SO:0001583	missense	81704	exon11			TCTTCAATGTCTC	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.1238A>G	9.37:g.334337A>G	ENSP00000408464:p.Asn413Ser	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	204	97	0.47549	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	414	0.18956043956043955	99	0.20121951219512196	87	0.24033149171270718	18	0.03146853146853147	210	0.2770448548812665	A	8.178	0.793247	0.16327	0.229006	0.309186	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391	T;T;T	0.30981	1.51;1.51;1.51	5.87	2.28	0.28536	.	0.351259	0.33772	N	0.004578	T	0.00012	0.0000	N	0.02775	-0.495	0.26695	P	0.9712807999999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43475	-0.9389	9	0.02654	T	1	.	8.7127	0.34393	0.654:0.0:0.346:0.0	rs10970979;rs17846376;rs17859413;rs60522712;rs10970979	345;413	E9PH09;Q8NF50	.;DOCK8_HUMAN	S	413;413;345;345	ENSP00000408464:N413S;ENSP00000394888:N345S;ENSP00000419438:N345S	ENSP00000287364:N413S	N	+	2	0	DOCK8	324337	0.005000	0.15991	0.918000	0.36340	0.928000	0.56348	0.417000	0.21214	0.559000	0.29153	0.533000	0.62120	AAT	A|0.758;G|0.242	0.242	strong		0.512	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
OR2T12	127064	hgsc.bcm.edu	37	1	248457993	248457993	+	Missense_Mutation	SNP	C	C	G	rs11204625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248457993C>G	ENST00000317996.1	-	1	887	c.888G>C	c.(886-888)aaG>aaC	p.K296N		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	296			K -> N (in dbSNP:rs11204625).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			TCAGGGCTTCCTTGACCTCAC	0.473													N|||	1067	0.213059	0.0091	0.2464	5008	,	,		18443	0.3591		0.174	False		,,,				2504	0.3548				p.K296N		Atlas-SNP	.											.	OR2T12	113	.	0			c.G888C						PASS	.	C	ASN/LYS	194,4212		4,186,2013	165.0	160.0	161.0		888	-3.4	0.0	1	dbSNP_120	161	1474,7126		128,1218,2954	no	missense	OR2T12	NM_001004692.1	94	132,1404,4967	GG,GC,CC		17.1395,4.4031,12.8249	probably-damaging	296/321	248457993	1668,11338	2203	4300	6503	SO:0001583	missense	127064	exon1			GGCTTCCTTGACC	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.888G>C	1.37:g.248457993C>G	ENSP00000324583:p.Lys296Asn	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	293	160	0.546075	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	424	0.19413919413919414	8	0.016260162601626018	74	0.20441988950276244	198	0.34615384615384615	144	0.18997361477572558	-	11.27	1.588879	0.28357	0.044031	0.171395	ENSG00000177201	ENST00000317996	T	0.40756	1.02	1.71	-3.42	0.04825	.	0.258640	0.19945	U	0.102541	T	0.00012	0.0000	M	0.69248	2.105	0.80722	P	0.0	P	0.52316	0.952	P	0.52598	0.703	T	0.11108	-1.0601	9	0.34782	T	0.22	.	4.0137	0.09634	0.1652:0.4839:0.0:0.351	rs11204625;rs11204625	296	Q8NG77	O2T12_HUMAN	N	296	ENSP00000324583:K296N	ENSP00000324583:K296N	K	-	3	2	OR2T12	246524616	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-0.317000	0.08060	-0.825000	0.04290	0.418000	0.28097	AAG	.	.	weak		0.473	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
AMZ1	155185	hgsc.bcm.edu	37	7	2752487	2752487	+	Missense_Mutation	SNP	G	G	A	rs7776970	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:2752487G>A	ENST00000312371.4	+	7	1840	c.1472G>A	c.(1471-1473)cGt>cAt	p.R491H	AMZ1_ENST00000407112.1_3'UTR|AMZ1_ENST00000489665.1_Intron	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	491			R -> H (in dbSNP:rs7776970).				metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		TCGGCCCCCCGTCCCTGGGAT	0.627													G|||	1610	0.321486	0.5552	0.2695	5008	,	,		18006	0.0933		0.341	False		,,,				2504	0.2577				p.R491H		Atlas-SNP	.											.	AMZ1	41	.	0			c.G1472A						PASS	.	G	HIS/ARG	2154,2178		582,990,594	25.0	28.0	27.0		1472	2.6	0.0	7	dbSNP_116	27	2606,5858		446,1714,2072	yes	missense	AMZ1	NM_133463.1	29	1028,2704,2666	AA,AG,GG		30.7892,49.723,37.1991	benign	491/499	2752487	4760,8036	2166	4232	6398	SO:0001583	missense	155185	exon7			CCCCCCGTCCCTG	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.1472G>A	7.37:g.2752487G>A	ENSP00000308149:p.Arg491His	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_133463	B3KRS0|Q8TF51	Missense_Mutation	SNP	ENST00000312371.4	37	CCDS34589.1	664	0.304029304029304	268	0.5447154471544715	91	0.2513812154696133	51	0.08916083916083917	254	0.33509234828496043	G	9.366	1.069149	0.20147	0.49723	0.307892	ENSG00000174945	ENST00000312371	T	0.22539	1.95	4.49	2.57	0.30868	.	1.324050	0.04846	N	0.441400	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45745	-0.9240	9	0.37606	T	0.19	-1.1562	5.7029	0.17893	0.1654:0.1793:0.6552:0.0	rs7776970;rs10375652;rs61189668;rs7776970	491	Q400G9	AMZ1_HUMAN	H	491	ENSP00000308149:R491H	ENSP00000308149:R491H	R	+	2	0	AMZ1	2719013	0.003000	0.15002	0.001000	0.08648	0.001000	0.01503	1.428000	0.34892	0.962000	0.38057	0.561000	0.74099	CGT	G|0.664;A|0.336	0.336	strong		0.627	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
CHPF2	54480	hgsc.bcm.edu	37	7	150934975	150934975	+	Silent	SNP	C	C	G	rs2487154	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:150934975C>G	ENST00000035307.2	+	4	3040	c.1527C>G	c.(1525-1527)gcC>gcG	p.A509A	MIR671_ENST00000390183.1_RNA|RP4-548D19.3_ENST00000607902.1_RNA|CHPF2_ENST00000495645.1_Silent_p.A501A	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	509					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						TCCTCGAGGCCTTTGCAGCCA	0.602													C|||	2171	0.433506	0.2685	0.4164	5008	,	,		17374	0.7153		0.4503	False		,,,				2504	0.3609				p.A509A		Atlas-SNP	.											.	CHPF2	52	.	0			c.C1527G						PASS	.	C		1305,3099		204,897,1101	34.0	33.0	33.0		1527	5.0	1.0	7	dbSNP_100	33	3510,5088		712,2086,1501	no	coding-synonymous	CHPF2	NM_019015.1		916,2983,2602	GG,GC,CC		40.8234,29.6322,37.0328		509/773	150934975	4815,8187	2202	4299	6501	SO:0001819	synonymous_variant	54480	exon4			CGAGGCCTTTGCA	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.1527C>G	7.37:g.150934975C>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Silent	SNP	ENST00000035307.2	37	CCDS34779.1																																																																																			C|0.595;G|0.405	0.405	strong		0.602	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
HLA-C	3107	hgsc.bcm.edu	37	6	31238138	31238138	+	Silent	SNP	C	C	T	rs1050320	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238138C>T	ENST00000376228.5	-	4	758	c.744G>A	c.(742-744)caG>caA	p.Q248Q	HLA-C_ENST00000383329.3_Silent_p.Q248Q	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	248	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TGTCCTGGGTCTGGTCCTCCC	0.622													T|||	3889	0.776558	0.8056	0.8112	5008	,	,		14233	0.8046		0.7197	False		,,,				2504	0.7423				p.Q248Q		Atlas-SNP	.											.	HLA-C	92	.	0			c.G744A						PASS	.						42.0	37.0	39.0					6																	31238138		2197	4291	6488	SO:0001819	synonymous_variant	3107	exon4			CTGGGTCTGGTCC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.744G>A	6.37:g.31238138C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1																																																																																			C|0.320;T|0.680	0.680	strong		0.622	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
CSRNP1	64651	hgsc.bcm.edu	37	3	39185525	39185525	+	Missense_Mutation	SNP	G	G	A	rs375810664		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:39185525G>A	ENST00000273153.5	-	5	968	c.791C>T	c.(790-792)aCa>aTa	p.T264I	CSRNP1_ENST00000514182.1_Missense_Mutation_p.T264I	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	264	Cys-rich.				apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						GGGGAATGCTGTGTGGTCCAT	0.552																																					p.T264I		Atlas-SNP	.											.	CSRNP1	59	.	0			c.C791T						PASS	.	G	ILE/THR	0,4406		0,0,2203	39.0	39.0	39.0		791	4.5	0.9	3		39	1,8599	1.2+/-3.3	0,1,4299	no	missense	CSRNP1	NM_033027.3	89	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	264/590	39185525	1,13005	2203	4300	6503	SO:0001583	missense	64651	exon5			AATGCTGTGTGGT	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"""AXIN1 up-regulated 1"""	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.791C>T	3.37:g.39185525G>A	ENSP00000273153:p.Thr264Ile	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_033027	Q69YY5	Missense_Mutation	SNP	ENST00000273153.5	37	CCDS2682.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.087702	0.55968	0.0	1.16E-4	ENSG00000144655	ENST00000273153;ENST00000514182	T;T	0.14516	2.5;2.5	4.48	4.48	0.54585	.	0.061123	0.64402	D	0.000003	T	0.28599	0.0708	L	0.51422	1.61	0.36804	D	0.885495	D	0.67145	0.996	P	0.59889	0.865	T	0.10042	-1.0647	10	0.46703	T	0.11	-16.1823	17.7133	0.88328	0.0:0.0:1.0:0.0	.	264	Q96S65	CSRN1_HUMAN	I	264	ENSP00000273153:T264I;ENSP00000422532:T264I	ENSP00000273153:T264I	T	-	2	0	CSRNP1	39160529	0.997000	0.39634	0.946000	0.38457	0.905000	0.53344	2.532000	0.45659	2.475000	0.83589	0.561000	0.74099	ACA	.	.	weak		0.552	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027	
PCED1B	91523	hgsc.bcm.edu	37	12	47629368	47629368	+	Silent	SNP	G	G	T	rs2244818	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:47629368G>T	ENST00000546455.1	+	4	1253	c.522G>T	c.(520-522)ggG>ggT	p.G174G	PCED1B_ENST00000432328.1_Silent_p.G174G|RP11-493L12.3_ENST00000547748.1_RNA			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	174							hydrolase activity (GO:0016787)										AAGTCACCGGGGGTTTTCTTC	0.602													G|||	742	0.148163	0.1846	0.1081	5008	,	,		15708	0.12		0.1759	False		,,,				2504	0.1278				p.G174G		Atlas-SNP	.											.	.	.	.	0			c.G522T						PASS	.	G		776,3630		59,658,1486	36.0	35.0	35.0		522	-4.3	0.0	12	dbSNP_100	35	1392,7208		106,1180,3014	no	coding-synonymous	FAM113B	NM_138371.1		165,1838,4500	TT,TG,GG		16.186,17.6123,16.6692		174/433	47629368	2168,10838	2203	4300	6503	SO:0001819	synonymous_variant	91523	exon2			CACCGGGGGTTTT	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.522G>T	12.37:g.47629368G>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_138371	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																			G|0.835;T|0.165	0.165	strong		0.602	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
DCLK3	85443	hgsc.bcm.edu	37	3	36779707	36779707	+	Silent	SNP	G	G	A	rs3796187	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:36779707G>A	ENST00000416516.2	-	2	934	c.444C>T	c.(442-444)ctC>ctT	p.L148L		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	148						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.L148L(1)		breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						GGCTCTGCTGGAGCTCCCTCT	0.542													G|||	1232	0.246006	0.0681	0.3847	5008	,	,		18934	0.1687		0.4076	False		,,,				2504	0.3016				p.L148L		Atlas-SNP	.											DCLK3,NS,carcinoma,0,1	DCLK3	95	1	1	Substitution - coding silent(1)	stomach(1)	c.C444T						scavenged	.	G		519,3321		35,449,1436	126.0	130.0	129.0		444	-4.7	0.7	3	dbSNP_107	129	3569,4701		764,2041,1330	no	coding-synonymous	DCLK3	NM_033403.1		799,2490,2766	AA,AG,GG		43.156,13.5156,33.7572		148/649	36779707	4088,8022	1920	4135	6055	SO:0001819	synonymous_variant	85443	exon2			CTGCTGGAGCTCC	AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"""doublecortin and CaM kinase-like 3"""	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.444C>T	3.37:g.36779707G>A		Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	223	110	0.493274	NM_033403		Silent	SNP	ENST00000416516.2	37	CCDS43064.1																																																																																			G|0.709;A|0.291	0.291	strong		0.542	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355	
NFKBIL1	4795	hgsc.bcm.edu	37	6	31525448	31525448	+	Silent	SNP	C	C	T	rs2230365	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31525448C>T	ENST00000376148.4	+	3	492	c.378C>T	c.(376-378)tcC>tcT	p.S126S	NFKBIL1_ENST00000376145.4_Silent_p.S126S	NM_005007.3	NP_004998.3	Q9UBC1	IKBL1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1	126					cellular response to lipopolysaccharide (GO:0071222)|cytoplasmic sequestering of transcription factor (GO:0042994)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)	cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7						GCTGTCCCTCCGCCATGGGAA	0.577													C|||	710	0.141773	0.0477	0.1225	5008	,	,		15650	0.2103		0.1372	False		,,,				2504	0.2168				p.S126S		Atlas-SNP	.											.	NFKBIL1	17	.	0			c.C378T						PASS	.	C	,,,	280,4126	153.7+/-187.2	6,268,1929	47.0	48.0	47.0		378,309,309,378	-0.7	1.0	6	dbSNP_98	47	1322,7278	255.2+/-280.2	102,1118,3080	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFKBIL1	NM_001144961.1,NM_001144962.1,NM_001144963.1,NM_005007.3	,,,	108,1386,5009	TT,TC,CC		15.3721,6.355,12.3174	,,,	126/367,103/359,103/344,126/382	31525448	1602,11404	2203	4300	6503	SO:0001819	synonymous_variant	4795	exon3			TCCCTCCGCCATG	X77909	CCDS4700.1, CCDS47399.1, CCDS47400.1	6p21.3	2010-02-17			ENSG00000204498	ENSG00000204498			7800	protein-coding gene	gene with protein product		601022		NFKBIL		8081366	Standard	NM_005007		Approved	IKBL	uc003nub.3	Q9UBC1	OTTHUMG00000031038	ENST00000376148.4:c.378C>T	6.37:g.31525448C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_005007	A6NL91|B4DUW1|Q14625|Q5HYU4|Q5RJ72|Q5ST96|Q5STV4|Q5STV5|Q9UBX4	Silent	SNP	ENST00000376148.4	37	CCDS4700.1																																																																																			C|0.865;T|0.135	0.135	strong		0.577	NFKBIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076036.3	NM_005007	
TTYH2	94015	hgsc.bcm.edu	37	17	72246101	72246101	+	Silent	SNP	T	T	C	rs3897753	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72246101T>C	ENST00000269346.4	+	9	1031	c.957T>C	c.(955-957)ctT>ctC	p.L319L	TTYH2_ENST00000529107.1_Silent_p.L298L|TTYH2_ENST00000534346.1_3'UTR|TTYH2_ENST00000441391.2_5'UTR	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	319						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						AGCGCGCACTTACCACCATGC	0.642													C|||	2057	0.410743	0.7443	0.3141	5008	,	,		13697	0.1101		0.3638	False		,,,				2504	0.3865				p.L319L		Atlas-SNP	.											.	TTYH2	63	.	0			c.T957C						PASS	.	C	,	3011,1395	460.0+/-352.4	1026,959,218	100.0	96.0	97.0		957,	3.1	1.0	17	dbSNP_108	97	3484,5116	633.4+/-398.7	709,2066,1525	no	coding-synonymous,utr-5	TTYH2	NM_032646.5,NM_052869.1	,	1735,3025,1743	CC,CT,TT		40.5116,31.6614,49.9385	,	319/535,	72246101	6495,6511	2203	4300	6503	SO:0001819	synonymous_variant	94015	exon9			CGCACTTACCACC		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.957T>C	17.37:g.72246101T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	214	87	0.406542	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Silent	SNP	ENST00000269346.4	37	CCDS32717.1																																																																																			T|0.549;C|0.451	0.451	strong		0.642	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
ZNF485	220992	hgsc.bcm.edu	37	10	44112214	44112214	+	Silent	SNP	C	C	T	rs7478426	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:44112214C>T	ENST00000361807.3	+	5	917	c.723C>T	c.(721-723)ccC>ccT	p.P241P	ZNF485_ENST00000374437.2_Silent_p.P150P|ZNF485_ENST00000374435.3_Silent_p.P241P	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	241					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GCCAGAAACCCTACAAATGTA	0.388													C|||	425	0.0848642	0.1717	0.0591	5008	,	,		21213	0.002		0.0716	False		,,,				2504	0.0849				p.P241P		Atlas-SNP	.											.	ZNF485	102	.	0			c.C723T						PASS	.	C		741,3665	302.1+/-287.2	58,625,1520	59.0	64.0	62.0		723	2.2	0.6	10	dbSNP_116	62	663,7937	167.8+/-219.5	32,599,3669	no	coding-synonymous	ZNF485	NM_145312.3		90,1224,5189	TT,TC,CC		7.7093,16.818,10.795		241/442	44112214	1404,11602	2203	4300	6503	SO:0001819	synonymous_variant	220992	exon5			GAAACCCTACAAA	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.723C>T	10.37:g.44112214C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_145312	B4DSE6|Q96CL0	Silent	SNP	ENST00000361807.3	37	CCDS7205.2																																																																																			C|0.904;T|0.096	0.096	strong		0.388	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
MYH9	4627	hgsc.bcm.edu	37	22	36685329	36685329	+	Silent	SNP	C	C	T	rs202127454		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:36685329C>T	ENST00000216181.5	-	32	4589	c.4359G>A	c.(4357-4359)gaG>gaA	p.E1453E		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1453					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						AGATGGTCTTCTCCTCCGCCA	0.677			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				C|||	1	0.000199681	0.0	0.0	5008	,	,		19418	0.0		0.001	False		,,,				2504	0.0				p.E1453E		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.G4359A						PASS	.	C		0,4406		0,0,2203	22.0	20.0	21.0		4359	4.0	1.0	22		21	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	MYH9	NM_002473.4		0,5,6498	TT,TC,CC		0.0581,0.0,0.0384		1453/1961	36685329	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	4627	exon32	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GGTCTTCTCCTCC		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.4359G>A	22.37:g.36685329C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	22	0.385965	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	9.292	1.050864	0.19827	0.0	5.81E-4	ENSG00000100345	ENST00000397231	.	.	.	5.02	4.01	0.46588	.	.	.	.	.	T	0.31136	0.0787	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.12993	-1.0526	5	0.02654	T	1	.	9.9391	0.41570	0.0:0.8436:0.0:0.1564	.	.	.	.	K	56	.	ENSP00000380408:R56K	R	-	2	0	MYH9	35015275	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.320000	0.51991	1.253000	0.44018	0.491000	0.48974	AGA	C|1.000;T|0.000	0.000	strong		0.677	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
OR5I1	10798	hgsc.bcm.edu	37	11	55703650	55703650	+	Missense_Mutation	SNP	A	A	G	rs9666086	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55703650A>G	ENST00000301532.3	-	1	226	c.227T>C	c.(226-228)tTc>tCc	p.F76S		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	76			F -> S (in dbSNP:rs9666086).		signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						AATGTCTGAGAAATAGCAAAG	0.388													G|||	175	0.0349441	0.0136	0.0346	5008	,	,		18614	0.001		0.0905	False		,,,				2504	0.0419				p.F76S		Atlas-SNP	.											OR5I1,NS,carcinoma,+1,1	OR5I1	110	1	0			c.T227C						PASS	.	G	SER/PHE	105,4291	806.1+/-415.8	3,99,2096	50.0	51.0	50.0		227	5.1	0.2	11	dbSNP_119	50	681,7911	781.4+/-407.6	34,613,3649	yes	missense	OR5I1	NM_006637.1	155	37,712,5745	GG,GA,AA		7.926,2.3885,6.0517	benign	76/315	55703650	786,12202	2198	4296	6494	SO:0001583	missense	10798	exon1			TCTGAGAAATAGC	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.227T>C	11.37:g.55703650A>G	ENSP00000301532:p.Phe76Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	37	CCDS7949.1	81	0.03708791208791209	4	0.008130081300813009	10	0.027624309392265192	0	0.0	67	0.08839050131926121	G	0.039	-1.292521	0.01375	0.023885	0.07926	ENSG00000167825	ENST00000301532	T	0.00013	9.24	5.05	5.05	0.67936	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	N	0.000289	T	0.00012	0.0000	N	0.00002	-3.625	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46679	-0.9174	10	0.02654	T	1	.	11.9859	0.53147	0.0857:0.0:0.9143:0.0	rs9666086;rs17512794;rs60806737;rs9666086	76	Q13606	OR5I1_HUMAN	S	76	ENSP00000301532:F76S	ENSP00000301532:F76S	F	-	2	0	OR5I1	55460226	0.000000	0.05858	0.193000	0.23327	0.514000	0.34195	0.192000	0.17096	1.255000	0.44051	-0.154000	0.13518	TTC	A|0.953;G|0.047	0.047	strong		0.388	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
POLQ	10721	hgsc.bcm.edu	37	3	121151784	121151784	+	Missense_Mutation	SNP	G	G	A	rs2306211	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121151784G>A	ENST00000264233.5	-	29	7768	c.7640C>T	c.(7639-7641)gCa>gTa	p.A2547V		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2547				A -> V (in Ref. 1; AAC33565). {ECO:0000305}.	ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		ATCTTCTTCTGCCACTTCATA	0.438								DNA polymerases (catalytic subunits)					G|||	169	0.033746	0.003	0.0159	5008	,	,		19728	0.0685		0.0139	False		,,,				2504	0.0726				p.A2547V	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C7640T						PASS	.	G	VAL/ALA	13,4393	19.1+/-41.9	0,13,2190	120.0	111.0	114.0		7640	6.1	1.0	3	dbSNP_100	114	151,8449	72.3+/-134.9	2,147,4151	yes	missense	POLQ	NM_199420.3	64	2,160,6341	AA,AG,GG		1.7558,0.2951,1.261	probably-damaging	2547/2591	121151784	164,12842	2203	4300	6503	SO:0001583	missense	10721	exon29			TCTTCTGCCACTT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.7640C>T	3.37:g.121151784G>A	ENSP00000264233:p.Ala2547Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	132	74	0.560606	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	54	0.024725274725274724	6	0.012195121951219513	4	0.011049723756906077	32	0.055944055944055944	12	0.0158311345646438	G	27.8	4.862466	0.91511	0.002951	0.017558	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	D	0.96745	-4.11	6.07	6.07	0.98685	DNA-directed DNA polymerase, family A, palm domain (2);	0.105878	0.64402	D	0.000003	D	0.84772	0.5546	L	0.39633	1.23	0.43355	D	0.995428	D;D	0.89917	1.0;0.996	D;D	0.76071	0.987;0.945	D	0.86776	0.1976	10	0.59425	D	0.04	.	19.4308	0.94765	0.0:0.0:1.0:0.0	rs2306211;rs52826415;rs2306211	2547;1719	O75417;O75417-2	DPOLQ_HUMAN;.	V	2170;2547;2683	ENSP00000264233:A2547V	ENSP00000264233:A2547V	A	-	2	0	POLQ	122634474	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	5.418000	0.66429	2.885000	0.99019	0.655000	0.94253	GCA	G|0.977;A|0.023	0.023	strong		0.438	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
PTX4	390667	hgsc.bcm.edu	37	16	1538464	1538464	+	Intron	SNP	C	C	T	rs2745103	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1538464C>T	ENST00000447419.2	-	1	167				PTX4_ENST00000440447.2_Intron|PTX4_ENST00000293922.1_Missense_Mutation_p.G2E			Q96A99	PTX4_HUMAN	pentraxin 4, long							extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GTTTCCACTCCCCATGACACT	0.652													C|||	1291	0.257788	0.1316	0.1945	5008	,	,		15785	0.497		0.2416	False		,,,				2504	0.2434				p.G2E		Atlas-SNP	.											.	PTX4	46	.	0			c.G5A						PASS	.	C	GLU/GLY	591,3807	258.6+/-262.5	37,517,1645	64.0	54.0	57.0		5	0.9	0.0	16	dbSNP_100	57	2187,6413	367.0+/-334.5	254,1679,2367	yes	missense	PTX4	NM_001013658.1	98	291,2196,4012	TT,TC,CC		25.4302,13.4379,21.3725	benign	2/474	1538464	2778,10220	2199	4300	6499	SO:0001627	intron_variant	390667	exon1			CCACTCCCCATGA		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.141+305G>A	16.37:g.1538464C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	222	89	0.400901	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		632	0.2893772893772894	57	0.11585365853658537	67	0.1850828729281768	309	0.5402097902097902	199	0.262532981530343	C	5.219	0.226002	0.09916	0.134379	0.254302	ENSG00000251692	ENST00000293922	T	0.07444	3.19	2.87	0.856	0.19019	.	1820.570000	0.00166	N	0.000000	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.27498	0.18	B	0.26310	0.068	T	0.46992	-0.9151	8	0.87932	D	0	.	4.118	0.10092	0.0:0.6175:0.2436:0.1389	rs2745103;rs58765039;rs2745103	2	Q96A99-2	.	E	2	ENSP00000293922:G2E	ENSP00000293922:G2E	G	-	2	0	PTX4	1478465	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	0.239000	0.18023	0.260000	0.21731	0.563000	0.77884	GGG	C|0.758;T|0.242	0.242	strong		0.652	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
AKAP9	10142	hgsc.bcm.edu	37	7	91712698	91712698	+	Missense_Mutation	SNP	A	A	G	rs6960867	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:91712698A>G	ENST00000359028.2	+	34	8636	c.8411A>G	c.(8410-8412)aAt>aGt	p.N2804S	AKAP9_ENST00000356239.3_Missense_Mutation_p.N2792S|AKAP9_ENST00000358100.2_Missense_Mutation_p.N2804S			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2804			N -> S (in dbSNP:rs6960867).		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGTAGCAGCAATCAGACTCCA	0.378			T	BRAF	papillary thyroid								A|||	1482	0.295927	0.2209	0.3458	5008	,	,		19775	0.1617		0.3837	False		,,,				2504	0.41				p.N2792S		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.A8375G						PASS	.	A	SER/ASN,SER/ASN	1180,3226	413.3+/-336.4	165,850,1188	76.0	74.0	75.0		8375,8351	-2.1	0.2	7	dbSNP_116	75	3451,5149	508.1+/-377.0	670,2111,1519	yes	missense,missense	AKAP9	NM_005751.4,NM_147185.2	46,46	835,2961,2707	GG,GA,AA		40.1279,26.7817,35.6066	benign,benign	2792/3908,2784/3900	91712698	4631,8375	2203	4300	6503	SO:0001583	missense	10142	exon33			GCAGCAATCAGAC	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.8411A>G	7.37:g.91712698A>G	ENSP00000351922:p.Asn2804Ser	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		647	0.29624542124542125	121	0.2459349593495935	132	0.36464088397790057	100	0.17482517482517482	294	0.38786279683377306	A	7.078	0.569650	0.13560	0.267817	0.401279	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	4.8	-2.13	0.07144	.	0.961519	0.08519	N	0.933795	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B;B;B;B;B	0.17667	0.023;0.0;0.0;0.0;0.0	B;B;B;B;B	0.12156	0.007;0.002;0.001;0.002;0.002	T	0.45818	-0.9235	9	0.18276	T	0.48	.	1.523	0.02520	0.3963:0.2606:0.2292:0.114	rs6960867;rs6960867	2796;2796;2804;2792;2784	F5H3X5;Q99996-6;Q99996;Q99996-2;Q99996-3	.;.;AKAP9_HUMAN;.;.	S	2792;2804;2804;2796;638	ENSP00000348573:N2792S;ENSP00000351922:N2804S;ENSP00000350813:N2804S;ENSP00000378042:N638S	ENSP00000348573:N2792S	N	+	2	0	AKAP9	91550634	0.002000	0.14202	0.157000	0.22605	0.795000	0.44927	0.398000	0.20899	-0.542000	0.06249	0.482000	0.46254	AAT	A|0.667;G|0.333	0.333	strong		0.378	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
RPS6KA4	8986	hgsc.bcm.edu	37	11	64138805	64138805	+	Silent	SNP	T	T	C	rs11542299	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64138805T>C	ENST00000334205.4	+	17	2237	c.2172T>C	c.(2170-2172)aaT>aaC	p.N724N	RPS6KA4_ENST00000528057.1_Silent_p.N717N|RPS6KA4_ENST00000294261.4_Silent_p.N476N|MIR1237_ENST00000408346.1_RNA	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	724					axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						GCGTGGAGAATGCACCCCTGG	0.706													C|||	1267	0.252995	0.0514	0.3833	5008	,	,		9149	0.2113		0.3708	False		,,,				2504	0.3548				p.N724N		Atlas-SNP	.											RPS6KA4_ENST00000334205,NS,carcinoma,+1,2	RPS6KA4	85	2	0			c.T2172C						PASS	.	C	,	433,3879		36,361,1759	38.0	43.0	42.0		2154,2172	1.6	1.0	11	dbSNP_120	42	2938,5552		502,1934,1809	no	coding-synonymous,coding-synonymous	RPS6KA4	NM_001006944.1,NM_003942.2	,	538,2295,3568	CC,CT,TT		34.6054,10.0417,26.3318	,	718/767,724/773	64138805	3371,9431	2156	4245	6401	SO:0001819	synonymous_variant	8986	exon17			GGAGAATGCACCC	AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"""ribosomal protein S6 kinase, 90kD, polypeptide 4"""			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.2172T>C	11.37:g.64138805T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_003942	A8K7Z8|O75585|Q53ES8	Silent	SNP	ENST00000334205.4	37	CCDS8073.1																																																																																			T|0.729;C|0.271	0.271	strong		0.706	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942	
DECR2	26063	hgsc.bcm.edu	37	16	461554	461554	+	Missense_Mutation	SNP	C	C	G	rs370013477		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:461554C>G	ENST00000219481.5	+	8	993	c.855C>G	c.(853-855)ttC>ttG	p.F285L	DECR2_ENST00000461947.1_Intron|DECR2_ENST00000424398.2_Missense_Mutation_p.F273L	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	285					unsaturated fatty acid biosynthetic process (GO:0006636)	peroxisomal membrane (GO:0005778)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)	9		Hepatocellular(16;0.00015)				TGCCGGATTTCGCATCCTTCT	0.622																																					p.F285L		Atlas-SNP	.											.	DECR2	47	.	0			c.C855G						PASS	.	C	LEU/PHE	0,4404		0,0,2202	149.0	121.0	131.0		855	-10.7	0.0	16		131	1,8599	1.2+/-3.3	0,1,4299	no	missense	DECR2	NM_020664.3	22	0,1,6501	GG,GC,CC		0.0116,0.0,0.0077	benign	285/293	461554	1,13003	2202	4300	6502	SO:0001583	missense	26063	exon8			GGATTTCGCATCC	AJ293009	CCDS10409.1	16p13.3	2011-09-14			ENSG00000242612	ENSG00000242612	1.3.1.34	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	2754	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 17C, member 1"""	615839				11514237, 19027726	Standard	NM_020664		Approved	PDCR, SDR17C1	uc002chb.3	Q9NUI1	OTTHUMG00000047846	ENST00000219481.5:c.855C>G	16.37:g.461554C>G	ENSP00000219481:p.Phe285Leu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_020664	Q6ZRS7|Q96ET0	Missense_Mutation	SNP	ENST00000219481.5	37	CCDS10409.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995624	0.35226	0.0	1.16E-4	ENSG00000242612	ENST00000219481;ENST00000424398	T;T	0.80909	-1.43;-1.06	5.34	-10.7	0.00240	.	1.461700	0.03592	N	0.232010	T	0.59004	0.2162	N	0.04297	-0.235	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.55134	-0.8188	10	0.21014	T	0.42	.	15.9692	0.79998	0.0:0.6665:0.1013:0.2322	.	285	Q9NUI1	DECR2_HUMAN	L	285;273	ENSP00000219481:F285L;ENSP00000400374:F273L	ENSP00000219481:F285L	F	+	3	2	DECR2	401555	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.158000	0.03153	-2.920000	0.00305	-1.036000	0.02392	TTC	.	.	weak		0.622	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664	
FGA	2243	hgsc.bcm.edu	37	4	155507590	155507590	+	Missense_Mutation	SNP	T	T	C	rs6050	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:155507590T>C	ENST00000302053.3	-	5	1069	c.991A>G	c.(991-993)Act>Gct	p.T331A	FGA_ENST00000403106.3_Missense_Mutation_p.T331A	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	331			T -> A (in dbSNP:rs6050). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)	p.T331A(1)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	CAGCTTCCAGTACTTCCAGGT	0.572													T|||	1638	0.327077	0.4334	0.2176	5008	,	,		16658	0.4315		0.2356	False		,,,				2504	0.2474				p.T331A	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											FGA,NS,carcinoma,0,1	FGA	179	1	1	Substitution - Missense(1)	prostate(1)	c.A991G	GRCh37	CM994632	FGA	M	rs6050	PASS	.	T	ALA/THR,ALA/THR	1603,2803	496.9+/-363.7	292,1019,892	91.0	98.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	991,991	-6.7	0.0	4	dbSNP_52	96	2168,6432	371.1+/-336.1	293,1582,2425	yes	missense,missense	FGA	NM_000508.3,NM_021871.2	58,58	585,2601,3317	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	25.2093,36.3822,28.9943	benign,benign	331/867,331/645	155507590	3771,9235	2203	4300	6503	SO:0001583	missense	2243	exon5			TTCCAGTACTTCC		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3661	protein-coding gene	gene with protein product		134820	"""fibrinogen, A alpha polypeptide"""				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.991A>G	4.37:g.155507590T>C	ENSP00000306361:p.Thr331Ala	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	37	CCDS3787.1	720	0.32967032967032966	181	0.3678861788617886	80	0.22099447513812154	280	0.48951048951048953	179	0.23614775725593667	T	5.196	0.221707	0.09863	0.363822	0.252093	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.70986	-0.53;-0.53	4.95	-6.65	0.01795	.	3.217810	0.01539	N	0.019120	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B	0.18013	0.001;0.025	B;B	0.12837	0.003;0.008	T	0.22800	-1.0206	9	0.07325	T	0.83	.	1.1703	0.01824	0.4201:0.2848:0.1048:0.1903	rs6050;rs2070019;rs2236789;rs56492214;rs6050	331;331	P02671-2;P02671	.;FIBA_HUMAN	A	331	ENSP00000306361:T331A;ENSP00000385981:T331A	ENSP00000306361:T331A	T	-	1	0	FGA	155727040	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-6.952000	0.00048	-0.905000	0.03871	0.528000	0.53228	ACT	T|0.700;C|0.300	0.300	strong		0.572	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508	
KCNA10	3744	hgsc.bcm.edu	37	1	111061011	111061011	+	Silent	SNP	C	C	A	rs3748731	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111061011C>A	ENST00000369771.2	-	1	786	c.399G>T	c.(397-399)cgG>cgT	p.R133R		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	133					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	TGGGCCGGTTCCGATCAAAGA	0.448													C|||	911	0.181909	0.1868	0.2478	5008	,	,		19162	0.1736		0.1978	False		,,,				2504	0.1207				p.R133R		Atlas-SNP	.											.	KCNA10	92	.	0			c.G399T						PASS	.	C		834,3572	329.3+/-301.0	88,658,1457	59.0	64.0	62.0		399	1.1	1.0	1	dbSNP_107	62	1924,6676	337.8+/-322.5	225,1474,2601	no	coding-synonymous	KCNA10	NM_005549.2		313,2132,4058	AA,AC,CC		22.3721,18.9287,21.2056		133/512	111061011	2758,10248	2203	4300	6503	SO:0001819	synonymous_variant	3744	exon1			CCGGTTCCGATCA	U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.399G>T	1.37:g.111061011C>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_005549		Silent	SNP	ENST00000369771.2	37	CCDS826.1																																																																																			C|0.792;A|0.208	0.208	strong		0.448	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549	
SPTA1	6708	hgsc.bcm.edu	37	1	158607935	158607935	+	Missense_Mutation	SNP	T	T	G	rs857725	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:158607935T>G	ENST00000368147.4	-	36	5257	c.5077A>C	c.(5077-5079)Aag>Cag	p.K1693Q		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1693			K -> Q (in dbSNP:rs857725).		actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGGAAACGCTTGTTGACATTA	0.438													T|||	1230	0.245607	0.1036	0.3026	5008	,	,		19957	0.4365		0.2763	False		,,,				2504	0.1687				p.K1693Q		Atlas-SNP	.											.	SPTA1	720	.	0			c.A5077C						PASS	.	T	GLN/LYS	467,3331		24,419,1456	111.0	102.0	105.0		5077	-5.4	0.1	1	dbSNP_86	105	2159,6069		302,1555,2257	yes	missense	SPTA1	NM_003126.2	53	326,1974,3713	GG,GT,TT		26.2397,12.2959,21.836	benign	1693/2420	158607935	2626,9400	1899	4114	6013	SO:0001583	missense	6708	exon36			AACGCTTGTTGAC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5077A>C	1.37:g.158607935T>G	ENSP00000357129:p.Lys1693Gln	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	121	69	0.570248	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	603	0.2760989010989011	63	0.12804878048780488	103	0.2845303867403315	227	0.3968531468531469	210	0.2770448548812665	T	3.448	-0.112719	0.06881	0.122959	0.262397	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.49720	0.77;1.41	5.36	-5.37	0.02681	.	0.853565	0.09526	N	0.790277	T	0.06142	0.0159	N	0.11560	0.145	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.27938	-1.0059	9	0.13470	T	0.59	.	3.7514	0.08568	0.0939:0.3839:0.1154:0.4068	rs857725;rs16840421;rs52824360;rs58989186;rs857725	1693	P02549	SPTA1_HUMAN	Q	1693	ENSP00000357130:K1693Q;ENSP00000357129:K1693Q	ENSP00000357129:K1693Q	K	-	1	0	SPTA1	156874559	0.000000	0.05858	0.077000	0.20336	0.027000	0.11550	-0.128000	0.10531	-0.844000	0.04184	-0.376000	0.06991	AAG	G|0.277;N|0.000	0.277	strong		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
C3orf20	84077	hgsc.bcm.edu	37	3	14724413	14724413	+	Missense_Mutation	SNP	G	G	A	rs9821143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:14724413G>A	ENST00000253697.3	+	3	645	c.193G>A	c.(193-195)Gac>Aac	p.D65N	C3orf20_ENST00000412910.1_Intron|C3orf20_ENST00000435614.1_Intron	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	65			D -> N (in dbSNP:rs9821143).			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						TACCCCGTCCGACATCTTGGG	0.552													G|||	1491	0.297724	0.2806	0.4438	5008	,	,		19624	0.2252		0.3658	False		,,,				2504	0.2219				p.D65N		Atlas-SNP	.											.	C3orf20	109	.	0			c.G193A						PASS	.	G	,,ASN/ASP	1359,3047	451.6+/-349.7	215,929,1059	111.0	110.0	110.0		,,193	0.6	0.0	3	dbSNP_119	110	2990,5610	463.5+/-366.0	486,2018,1796	yes	intron,intron,missense	C3orf20	NM_001184957.1,NM_001184958.1,NM_032137.4	,,23	701,2947,2855	AA,AG,GG		34.7674,30.8443,33.4384	,,benign	,,65/905	14724413	4349,8657	2203	4300	6503	SO:0001583	missense	84077	exon3			CCGTCCGACATCT	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.193G>A	3.37:g.14724413G>A	ENSP00000253697:p.Asp65Asn	Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	732	0.33516483516483514	159	0.3231707317073171	154	0.425414364640884	139	0.243006993006993	280	0.36939313984168864	G	9.562	1.118756	0.20877	0.308443	0.347674	ENSG00000131379	ENST00000253697	T	0.06449	3.3	5.28	0.576	0.17380	.	0.883554	0.09670	N	0.771197	T	0.00012	0.0000	L	0.29908	0.895	0.48901	P	2.7800000000000047E-4	B	0.32800	0.385	B	0.21360	0.034	T	0.45056	-0.9287	9	0.37606	T	0.19	-8.4977	1.4841	0.02443	0.3045:0.1444:0.4042:0.1469	rs9821143;rs52827165;rs57810074;rs9821143	65	Q8ND61	CC020_HUMAN	N	65	ENSP00000253697:D65N	ENSP00000253697:D65N	D	+	1	0	C3orf20	14699417	0.000000	0.05858	0.003000	0.11579	0.024000	0.10985	-0.301000	0.08232	0.166000	0.19597	0.591000	0.81541	GAC	G|0.672;A|0.328	0.328	strong		0.552	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919267	51919267	+	Silent	SNP	A	A	G	rs7258638	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51919267A>G	ENST00000339313.5	-	5	1025	c.909T>C	c.(907-909)ccT>ccC	p.P303P	SIGLEC10_ENST00000432469.2_Silent_p.P220P|SIGLEC10_ENST00000439889.2_Silent_p.P245P|SIGLEC10_ENST00000353836.5_Silent_p.P303P|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Silent_p.P245P|SIGLEC10_ENST00000436984.2_Silent_p.P255P|SIGLEC10_ENST00000356298.5_Silent_p.P303P|SIGLEC10_ENST00000525998.1_Intron|CTD-2616J11.2_ENST00000526996.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	303	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CCAGGGGTCTAGGGCCCCAGG	0.677																																					p.P303P		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.T909C						PASS	.						26.0	30.0	29.0					19																	51919267		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			GGGTCTAGGGCCC	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.909T>C	19.37:g.51919267A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	169	26	0.153846	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			A|0.996;G|0.004	0.004	strong		0.677	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
CRTC3	64784	hgsc.bcm.edu	37	15	91161163	91161163	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91161163C>T	ENST00000268184.6	+	8	666	c.662C>T	c.(661-663)cCg>cTg	p.P221L	RP11-387D10.2_ENST00000559531.1_RNA|CRTC3_ENST00000420329.2_Missense_Mutation_p.P221L			Q6UUV7	CRTC3_HUMAN	CREB regulated transcription coactivator 3	221					energy homeostasis (GO:0097009)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of lipid catabolic process (GO:0050995)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)		CRTC3/MAML2(26)	breast(1)|endometrium(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			TTAAATGTTCCGAAGCCACTG	0.433			T	MAML2	salivary gland mucoepidermoid																																p.P221L		Atlas-SNP	.		Dom	yes		15	15q26.1	64784	CREB regulated transcription coactivator 3		E	CRTC3,NS,carcinoma,0,1	CRTC3	47	1	0			c.C662T						scavenged	.						86.0	78.0	80.0					15																	91161163		2198	4298	6496	SO:0001583	missense	64784	exon8			ATGTTCCGAAGCC		CCDS32331.1, CCDS45348.1	15q26.1	2005-11-24				ENSG00000140577			26148	protein-coding gene	gene with protein product		608986				14536081, 14506290	Standard	NM_022769		Approved	FLJ21868	uc002bpp.4	Q6UUV7		ENST00000268184.6:c.662C>T	15.37:g.91161163C>T	ENSP00000268184:p.Pro221Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	112	2	0.0178571	NM_022769	Q6DK61|Q6DK62|Q8NF38|Q9H6U2	Missense_Mutation	SNP	ENST00000268184.6	37	CCDS32331.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.520475	0.44866	.	.	ENSG00000140577	ENST00000437186;ENST00000268184;ENST00000420329	T;T	0.42513	0.97;0.97	4.98	4.98	0.66077	Transducer of regulated CREB activity, middle domain (1);	0.455157	0.24126	N	0.041308	T	0.49847	0.1581	L	0.29908	0.895	0.47698	D	0.999497	D;D	0.71674	0.998;0.998	D;P	0.65233	0.933;0.89	T	0.37596	-0.9699	10	0.32370	T	0.25	-24.9924	15.8047	0.78483	0.0:1.0:0.0:0.0	.	221;221	Q6UUV7;Q6UUV7-3	CRTC3_HUMAN;.	L	185;221;221	ENSP00000268184:P221L;ENSP00000416573:P221L	ENSP00000268184:P221L	P	+	2	0	CRTC3	88962167	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	3.241000	0.51376	2.573000	0.86826	0.467000	0.42956	CCG	.	.	none		0.433	CRTC3-001	KNOWN	NAGNAG_splice_site|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417716.2	NM_022769	
TMEM125	128218	hgsc.bcm.edu	37	1	43738760	43738760	+	Missense_Mutation	SNP	G	G	A	rs143350378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43738760G>A	ENST00000432792.2	+	4	937	c.367G>A	c.(367-369)Gtg>Atg	p.V123M	TMEM125_ENST00000439858.1_Missense_Mutation_p.V123M			Q96AQ2	TM125_HUMAN	transmembrane protein 125	123						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(1)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CAGTGGCCTCGTGCTGCTGGT	0.721													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		15058	0.0		0.003	False		,,,				2504	0.0				p.V123M		Atlas-SNP	.											.	TMEM125	18	.	0			c.G367A						PASS	.	G	MET/VAL	5,4391		0,5,2193	22.0	24.0	23.0		367	5.2	0.9	1	dbSNP_134	23	33,8553		1,31,4261	no	missense	TMEM125	NM_144626.2	21	1,36,6454	AA,AG,GG		0.3843,0.1137,0.2927	possibly-damaging	123/220	43738760	38,12944	2198	4293	6491	SO:0001583	missense	128218	exon4			GGCCTCGTGCTGC	BC016858	CCDS480.1	1p34.2	2006-02-16			ENSG00000179178	ENSG00000179178			28275	protein-coding gene	gene with protein product							Standard	NM_144626		Approved	MGC17299	uc021oml.1	Q96AQ2	OTTHUMG00000007288	ENST00000432792.2:c.367G>A	1.37:g.43738760G>A	ENSP00000429275:p.Val123Met	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	24	13	0.541667	NM_144626	D3DPX1	Missense_Mutation	SNP	ENST00000432792.2	37	CCDS480.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397316	0.62177	0.001137	0.003843	ENSG00000179178	ENST00000439858;ENST00000432792	T;T	0.47177	0.85;0.85	5.24	5.24	0.73138	.	0.350030	0.29059	N	0.013275	T	0.46268	0.1384	L	0.27053	0.805	0.30773	N	0.742775	D	0.69078	0.997	P	0.53360	0.724	T	0.52946	-0.8507	10	0.62326	D	0.03	.	12.2066	0.54355	0.0783:0.0:0.9217:0.0	.	123	Q96AQ2	TM125_HUMAN	M	123	ENSP00000429775:V123M;ENSP00000429275:V123M	ENSP00000429275:V123M	V	+	1	0	TMEM125	43511347	0.980000	0.34600	0.929000	0.37066	0.676000	0.39594	2.566000	0.45948	2.446000	0.82766	0.455000	0.32223	GTG	G|0.997;A|0.003	0.003	strong		0.721	TMEM125-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019032.2	NM_144626	
OAS3	4940	hgsc.bcm.edu	37	12	113379390	113379390	+	Missense_Mutation	SNP	C	C	T	rs12819767	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:113379390C>T	ENST00000228928.7	+	2	372	c.193C>T	c.(193-195)Cgg>Tgg	p.R65W	RP1-71H24.1_ENST00000552784.1_RNA|OAS3_ENST00000551007.1_Missense_Mutation_p.R65W|OAS3_ENST00000548514.1_Missense_Mutation_p.R65W|OAS3_ENST00000546638.1_Intron	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	65	OAS domain 1.		R -> W (in dbSNP:rs12819767).		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						CTCCTCGGGCCGGGGCACAGC	0.537													C|||	34	0.00678914	0.0008	0.0043	5008	,	,		18839	0.001		0.0268	False		,,,				2504	0.002				p.R65W		Atlas-SNP	.											.	OAS3	63	.	0			c.C193T						PASS	.	C	TRP/ARG	10,3790		0,10,1890	73.0	76.0	75.0		193	0.6	0.9	12	dbSNP_121	75	175,8047		1,173,3937	yes	missense	OAS3	NM_006187.2	101	1,183,5827	TT,TC,CC		2.1284,0.2632,1.5388	probably-damaging	65/1088	113379390	185,11837	1900	4111	6011	SO:0001583	missense	4940	exon2			TCGGGCCGGGGCA	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.193C>T	12.37:g.113379390C>T	ENSP00000228928:p.Arg65Trp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	24	0.01098901098901099	0	0.0	2	0.0055248618784530384	0	0.0	22	0.029023746701846966	C	15.61	2.883585	0.51908	0.002632	0.021284	ENSG00000111331	ENST00000228928;ENST00000551007;ENST00000548514;ENST00000323881	T;T;T	0.14516	2.5;2.5;2.5	3.69	0.621	0.17643	2-5-oligoadenylate synthetase, N-terminal (1);2-5-oligoadenylate synthetase, conserved site (1);	.	.	.	.	T	0.12987	0.0315	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.958;1.0;1.0	T	0.00706	-1.1601	9	0.87932	D	0	.	9.4628	0.38796	0.5553:0.4447:0.0:0.0	rs12819767;rs12819767	65;65;65	Q9Y6K5;F8VS35;F8VWK9	OAS3_HUMAN;.;.	W	65	ENSP00000228928:R65W;ENSP00000449299:R65W;ENSP00000448388:R65W	ENSP00000228928:R65W	R	+	1	2	OAS3	111863773	0.970000	0.33590	0.921000	0.36526	0.840000	0.47671	0.104000	0.15313	0.009000	0.14813	-0.268000	0.10319	CGG	C|0.988;T|0.012	0.012	strong		0.537	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
FAM166A	401565	hgsc.bcm.edu	37	9	140139106	140139106	+	Silent	SNP	G	G	A	rs62584882	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140139106G>A	ENST00000344774.4	-	5	789	c.735C>T	c.(733-735)ttC>ttT	p.F245F		NM_001001710.1	NP_001001710.1	Q6J272	F166A_HUMAN	family with sequence similarity 166, member A	245						nucleus (GO:0005634)				kidney(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(2)	15						GGCTCTTGTCGAATTCGTCCA	0.582													G|||	11	0.00219649	0.0008	0.0	5008	,	,		19622	0.0		0.0089	False		,,,				2504	0.001				p.F245F		Atlas-SNP	.											.	FAM166A	44	.	0			c.C735T						PASS	.	G		6,4392	12.9+/-30.5	0,6,2193	139.0	119.0	126.0		735	-3.4	0.8	9	dbSNP_129	126	94,8504	51.9+/-112.3	1,92,4206	no	coding-synonymous	FAM166A	NM_001001710.1		1,98,6399	AA,AG,GG		1.0933,0.1364,0.7695		245/318	140139106	100,12896	2199	4299	6498	SO:0001819	synonymous_variant	401565	exon5			CTTGTCGAATTCG	BC132916	CCDS35186.1	9q34.3	2008-08-08			ENSG00000188163	ENSG00000188163			33818	protein-coding gene	gene with protein product							Standard	XR_245332		Approved		uc004cmi.1	Q6J272	OTTHUMG00000159545	ENST00000344774.4:c.735C>T	9.37:g.140139106G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	223	98	0.439462	NM_001001710	A6NND9|Q8N830	Silent	SNP	ENST00000344774.4	37	CCDS35186.1																																																																																			G|0.994;A|0.006	0.006	strong		0.582	FAM166A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356125.1	NM_001001710	
SH3BP4	23677	hgsc.bcm.edu	37	2	235950391	235950391	+	Silent	SNP	C	C	T	rs35039245	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:235950391C>T	ENST00000409212.1	+	4	1485	c.978C>T	c.(976-978)tcC>tcT	p.S326S	SH3BP4_ENST00000392011.2_Silent_p.S326S|SH3BP4_ENST00000344528.4_Silent_p.S326S			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	326					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		TGGATAGCTCCGGGGGTGCTG	0.637													C|||	61	0.0121805	0.0	0.0144	5008	,	,		17472	0.001		0.0278	False		,,,				2504	0.0225				p.S326S		Atlas-SNP	.											.	SH3BP4	109	.	0			c.C978T						PASS	.	C		35,4371		1,33,2169	31.0	37.0	35.0		978	-11.6	0.0	2	dbSNP_126	35	292,8304		6,280,4012	no	coding-synonymous	SH3BP4	NM_014521.2		7,313,6181	TT,TC,CC		3.3969,0.7944,2.515		326/964	235950391	327,12675	2203	4298	6501	SO:0001819	synonymous_variant	23677	exon4			TAGCTCCGGGGGT	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.978C>T	2.37:g.235950391C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	CCDS2513.1																																																																																			C|0.976;T|0.024	0.024	strong		0.637	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
DUSP16	80824	hgsc.bcm.edu	37	12	12630346	12630346	+	Silent	SNP	G	G	A	rs12815760	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:12630346G>A	ENST00000228862.2	-	7	2050	c.1419C>T	c.(1417-1419)acC>acT	p.T473T	DUSP16_ENST00000298573.4_3'UTR|DUSP16_ENST00000545864.1_5'Flank	NM_030640.2	NP_085143.1	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	473					dephosphorylation (GO:0016311)|inactivation of MAPK activity (GO:0000188)|MAPK export from nucleus (GO:0045204)|MAPK phosphatase export from nucleus, leptomycin B sensitive (GO:0045209)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(7)|kidney(2)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(3)	26		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		AAGGCCTGGCGGTCTGCAGCT	0.562													G|||	152	0.0303514	0.0053	0.0389	5008	,	,		19818	0.0		0.0974	False		,,,				2504	0.0204				p.T473T	Ovarian(158;443 1896 15437 36069 46477)	Atlas-SNP	.											.	DUSP16	64	.	0			c.C1419T						PASS	.	G		64,4342	60.5+/-97.4	1,62,2140	113.0	111.0	111.0		1419	-10.1	0.0	12	dbSNP_121	111	805,7795	187.2+/-234.5	33,739,3528	no	coding-synonymous	DUSP16	NM_030640.2		34,801,5668	AA,AG,GG		9.3605,1.4526,6.6815		473/666	12630346	869,12137	2203	4300	6503	SO:0001819	synonymous_variant	80824	exon7			CCTGGCGGTCTGC	AB052156	CCDS8650.1	12p13	2011-06-09				ENSG00000111266		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	17909	protein-coding gene	gene with protein product	"""MAPK phosphatase-7"""	607175				11359773, 11489891, 15888437	Standard	NM_030640		Approved	MKP-7, KIAA1700, MKP7	uc001rao.2	Q9BY84		ENST00000228862.2:c.1419C>T	12.37:g.12630346G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	171	83	0.48538	NM_030640	Q547C7|Q96QS2|Q9C0G3	Silent	SNP	ENST00000228862.2	37	CCDS8650.1																																																																																			G|0.940;A|0.060	0.060	strong		0.562	DUSP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400311.1	NM_030640	
PDHX	8050	hgsc.bcm.edu	37	11	34937813	34937813	+	5'Flank	SNP	G	G	A	rs2956114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:34937813G>A	ENST00000227868.4	+	0	0				APIP_ENST00000395787.3_Missense_Mutation_p.R7W|APIP_ENST00000278359.5_5'UTR|PDHX_ENST00000448838.3_5'UTR|PDHX_ENST00000430469.2_5'Flank|APIP_ENST00000527830.1_5'UTR			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X						cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			TCTCCCTCCCGAGCATCACAG	0.716													G|||	2177	0.434704	0.2239	0.3977	5008	,	,		10339	0.7371		0.3539	False		,,,				2504	0.5174				p.R7W		Atlas-SNP	.											.	APIP	21	.	0			c.C19T						PASS	.	G	,,,TRP/ARG	1067,3329		142,783,1273	17.0	19.0	18.0		,,,19	2.5	0.0	11	dbSNP_101	18	3045,5543		555,1935,1804	yes	utr-5,utr-5,utr-5,missense	PDHX,APIP	NM_001135024.1,NM_001166158.1,NM_003477.2,NM_015957.2	,,,101	697,2718,3077	AA,AG,GG		35.4565,24.2721,31.6697	,,,benign	,,,7/243	34937813	4112,8872	2198	4294	6492	SO:0001631	upstream_gene_variant	51074	exon1			CCTCCCGAGCATC	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491		11.37:g.34937813G>A	Exception_encountered	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_015957	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	37	CCDS7896.1	947	0.4336080586080586	128	0.2601626016260163	142	0.39226519337016574	406	0.7097902097902098	271	0.3575197889182058	G	14.24	2.476444	0.44044	0.242721	0.354565	ENSG00000149089	ENST00000395787	T	0.18810	2.19	4.48	2.5	0.30297	.	1.377040	0.04518	N	0.384034	T	0.00012	0.0000	N	0.08118	0	0.47441	P	5.789999999999962E-4	P	0.41159	0.74	B	0.26969	0.075	T	0.42565	-0.9444	9	0.56958	D	0.05	.	10.8523	0.46777	0.0:0.3704:0.6296:0.0	rs2956114;rs17348273;rs17851547;rs52829807;rs57274539;rs2956114	7	Q96GX9	MTNB_HUMAN	W	7	ENSP00000379133:R7W	ENSP00000379133:R7W	R	-	1	2	APIP	34894389	0.138000	0.22547	0.032000	0.17829	0.005000	0.04900	0.295000	0.19065	0.561000	0.29186	0.491000	0.48974	CGG	G|0.630;A|0.370	0.370	strong		0.716	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
MYH9	4627	hgsc.bcm.edu	37	22	36708244	36708244	+	Silent	SNP	G	G	C	rs201827299		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:36708244G>C	ENST00000216181.5	-	14	1808	c.1578C>G	c.(1576-1578)gcC>gcG	p.A526A		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	526	Myosin motor.				actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						CGTCCAGCAGGGCCAGAATGC	0.647			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				G|||	1	0.000199681	0.0	0.0	5008	,	,		16777	0.0		0.001	False		,,,				2504	0.0				p.A526A		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.C1578G						PASS	.						67.0	60.0	62.0					22																	36708244		2203	4300	6503	SO:0001819	synonymous_variant	4627	exon14	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CAGCAGGGCCAGA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.1578C>G	22.37:g.36708244G>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			G|1.000;C|0.000	0.000	strong		0.647	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
OSGEPL1	64172	hgsc.bcm.edu	37	2	190617700	190617700	+	Silent	SNP	T	T	C	rs16831960	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:190617700T>C	ENST00000264151.5	-	6	1071	c.969A>G	c.(967-969)gcA>gcG	p.A323A	OSGEPL1_ENST00000522700.1_Silent_p.A323A|Y_RNA_ENST00000411317.1_RNA|OSGEPL1_ENST00000519810.1_Silent_p.A323A	NM_022353.2	NP_071748.2			O-sialoglycoprotein endopeptidase-like 1											large_intestine(2)|upper_aerodigestive_tract(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0293)|all cancers(119;0.0831)			CACCACCAGATGCAACCTGAA	0.378													T|||	387	0.0772764	0.0908	0.0317	5008	,	,		17221	0.0486		0.0726	False		,,,				2504	0.1258				p.A323A		Atlas-SNP	.											.	OSGEPL1	19	.	0			c.A969G						PASS	.	T		304,3410		10,284,1563	61.0	55.0	57.0		969	-5.2	0.5	2	dbSNP_123	57	535,7667		11,513,3577	no	coding-synonymous	OSGEPL1	NM_022353.2		21,797,5140	CC,CT,TT		6.5228,8.1852,7.041		323/415	190617700	839,11077	1857	4101	5958	SO:0001819	synonymous_variant	64172	exon6			ACCAGATGCAACC	AJ295148	CCDS46472.1	2q32	2011-08-12			ENSG00000128694	ENSG00000128694			23075	protein-coding gene	gene with protein product						19578062	Standard	NM_022353		Approved	Qri7	uc002uqz.1	Q9H4B0	OTTHUMG00000164096	ENST00000264151.5:c.969A>G	2.37:g.190617700T>C		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	274	131	0.478102	NM_022353		Silent	SNP	ENST00000264151.5	37	CCDS46472.1																																																																																			T|0.939;C|0.061	0.061	strong		0.378	OSGEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377257.1	NM_022353	
SVIL	6840	hgsc.bcm.edu	37	10	29812602	29812602	+	Silent	SNP	G	G	T	rs7070678	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:29812602G>T	ENST00000355867.4	-	15	3693	c.2941C>A	c.(2941-2943)Cga>Aga	p.R981R	SVIL_ENST00000535393.1_5'Flank|SVIL_ENST00000375400.3_Silent_p.R555R|SVIL_ENST00000375398.2_Silent_p.R981R	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	981					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				TCCCTGGCTCGGTTCAGGATG	0.537													T|||	1915	0.382388	0.562	0.438	5008	,	,		18611	0.0804		0.4284	False		,,,				2504	0.364				p.R981R		Atlas-SNP	.											SVIL,colon,carcinoma,0,1	SVIL	226	1	0			c.C2941A						scavenged	.	T	,	2409,1997	560.6+/-380.5	663,1083,457	155.0	136.0	143.0		1663,2941	-1.8	0.0	10	dbSNP_116	143	3521,5079	632.1+/-398.6	738,2045,1517	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	1401,3128,1974	TT,TG,GG		40.9419,45.3246,45.5943	,	555/1789,981/2215	29812602	5930,7076	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon15			TGGCTCGGTTCAG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.2941C>A	10.37:g.29812602G>T		Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	158	82	0.518987	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			G|0.584;T|0.416	0.416	strong		0.537	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
CASZ1	54897	hgsc.bcm.edu	37	1	10725498	10725498	+	Silent	SNP	G	G	A	rs284322	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:10725498G>A	ENST00000377022.3	-	5	464	c.147C>T	c.(145-147)gaC>gaT	p.D49D	CASZ1_ENST00000478728.2_5'UTR|CASZ1_ENST00000344008.5_Silent_p.D49D	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	49					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GGGAGCCGGCGTCAGCTCGCT	0.706													G|||	899	0.179513	0.2216	0.1412	5008	,	,		14988	0.1498		0.169	False		,,,				2504	0.1912				p.D49D		Atlas-SNP	.											.	CASZ1	150	.	0			c.C147T						PASS	.	G	,	700,3600		59,582,1509	23.0	28.0	27.0		147,147	2.5	0.9	1	dbSNP_79	27	1293,7179		89,1115,3032	no	coding-synonymous,coding-synonymous	CASZ1	NM_001079843.1,NM_017766.3	,	148,1697,4541	AA,AG,GG		15.262,16.2791,15.6044	,	49/1760,49/1167	10725498	1993,10779	2150	4236	6386	SO:0001819	synonymous_variant	54897	exon5			GCCGGCGTCAGCT	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.147C>T	1.37:g.10725498G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	12	7	0.583333	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																			G|0.817;A|0.183	0.183	strong		0.706	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
TTN	7273	hgsc.bcm.edu	37	2	179579822	179579822	+	Silent	SNP	T	T	A	rs2562836	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179579822T>A	ENST00000591111.1	-	88	25364	c.25140A>T	c.(25138-25140)ctA>ctT	p.L8380L	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.L7453L|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Silent_p.L8697L|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12554	Ig-like 66.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGATACTGGTTAGGAAGTTCT	0.463													A|||	2226	0.444489	0.4644	0.379	5008	,	,		20441	0.6577		0.2237	False		,,,				2504	0.4714				p.L8697L		Atlas-SNP	.											.	TTN	18412	.	0			c.A26091T						PASS	.	A	,,,	1560,2344		323,914,715	314.0	300.0	305.0		,22359,,	-4.7	0.0	2	dbSNP_100	305	1660,6618		160,1340,2639	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	483,2254,3354	AA,AT,TT		20.0532,39.959,26.4324	,,,	,7453/33424,,	179579822	3220,8962	1952	4139	6091	SO:0001819	synonymous_variant	7273	exon90			ACTGGTTAGGAAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25140A>T	2.37:g.179579822T>A		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	276	139	0.503623	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.630;N|0.001	.	strong		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FHAD1	114827	hgsc.bcm.edu	37	1	15708540	15708540	+	Missense_Mutation	SNP	A	A	G	rs1010294	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:15708540A>G	ENST00000375998.4	+	29	3973	c.3973A>G	c.(3973-3975)Att>Gtt	p.I1325V	FHAD1_ENST00000417793.1_Missense_Mutation_p.I1289V|FHAD1_ENST00000375999.3_Missense_Mutation_p.I1325V|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000314740.8_Missense_Mutation_p.I578V|FHAD1_ENST00000358897.4_Missense_Mutation_p.I1325V			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1325										skin(1)|stomach(1)	2						CAAAGTGTCCATTGAGATGTA	0.532													G|||	2114	0.422125	0.77	0.3055	5008	,	,		22117	0.2589		0.2624	False		,,,				2504	0.3671				p.I1325V		Atlas-SNP	.											.	FHAD1	78	.	0			c.A3973G						PASS	.	G	VAL/ILE	961,423		341,279,72	65.0	67.0	66.0		3973	-4.3	0.0	1	dbSNP_86	66	836,2346		102,632,857	yes	missense	FHAD1	NM_052929.1	29	443,911,929	GG,GA,AA		26.2728,30.5636,39.3561	benign	1325/1413	15708540	1797,2769	692	1591	2283	SO:0001583	missense	114827	exon30			GTGTCCATTGAGA	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.3973A>G	1.37:g.15708540A>G	ENSP00000365166:p.Ile1325Val	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	288	155	0.538194	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		834	0.38186813186813184	369	0.75	125	0.3453038674033149	141	0.2465034965034965	199	0.262532981530343	G	0.006	-2.038631	0.00402	0.694364	0.262728	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998;ENST00000529606;ENST00000314740;ENST00000314668	T;T;T;T;T;T;T	0.39406	1.17;1.17;1.08;1.17;1.08;1.09;1.14	5.95	-4.31	0.03698	.	.	.	.	.	T	0.00012	0.0000	N	0.00116	-2.08	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38908	-0.9639	8	0.15952	T	0.53	-6.224	7.5924	0.28029	0.5737:0.2316:0.1946:0.0	rs1010294;rs3765368;rs52824203;rs61149895;rs1010294	578;1325	B7WPP2;B1AJZ9	.;FHAD1_HUMAN	V	1325;1289;1325;1325;596;578;560	ENSP00000351770:I1325V;ENSP00000407615:I1289V;ENSP00000365167:I1325V;ENSP00000365166:I1325V;ENSP00000434909:I596V;ENSP00000322979:I578V;ENSP00000318812:I560V	ENSP00000318812:I560V	I	+	1	0	FHAD1	15581127	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-1.470000	0.02346	-0.699000	0.05077	-0.716000	0.03619	ATT	T|0.004;G|0.400	0.400	strong		0.532	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
PAQR9	344838	hgsc.bcm.edu	37	3	142681249	142681249	+	Silent	SNP	G	G	A	rs62276870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:142681249G>A	ENST00000340634.3	-	1	929	c.930C>T	c.(928-930)agC>agT	p.S310S	RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA|RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	310						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						AGAGCTGGTGGCTGTGGCCGA	0.607													G|||	144	0.028754	0.0053	0.0389	5008	,	,		17580	0.0		0.0895	False		,,,				2504	0.0204				p.S310S		Atlas-SNP	.											.	PAQR9	57	.	0			c.C930T						PASS	.	G		60,4346	56.8+/-93.2	1,58,2144	69.0	73.0	71.0		930	2.9	1.0	3	dbSNP_129	71	679,7921	170.4+/-221.6	29,621,3650	no	coding-synonymous	PAQR9	NM_198504.2		30,679,5794	AA,AG,GG		7.8953,1.3618,5.682		310/378	142681249	739,12267	2203	4300	6503	SO:0001819	synonymous_variant	344838	exon1			CTGGTGGCTGTGG	AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.930C>T	3.37:g.142681249G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_198504	Q147T6	Silent	SNP	ENST00000340634.3	37	CCDS3128.1	93	0.042582417582417584	4	0.008130081300813009	17	0.04696132596685083	0	0.0	72	0.09498680738786279	G	7.505	0.653518	0.14580	0.013618	0.078953	ENSG00000188582	ENST00000492509	.	.	.	5.62	2.88	0.33553	.	.	.	.	.	T	0.05502	0.0145	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.42682	-0.9437	3	.	.	.	-29.595	13.4878	0.61377	0.1896:0.0:0.8104:0.0	rs62276870	.	.	.	S	51	.	.	P	-	1	0	PAQR9	144163939	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	2.840000	0.48215	0.075000	0.16796	-0.813000	0.03139	CCA	G|0.946;A|0.054	0.054	strong		0.607	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504	
SHB	6461	hgsc.bcm.edu	37	9	38068330	38068330	+	Missense_Mutation	SNP	T	T	C	rs147813967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:38068330T>C	ENST00000377707.3	-	1	878	c.313A>G	c.(313-315)Aaa>Gaa	p.K105E	RP11-613M10.9_ENST00000540557.1_Missense_Mutation_p.K105E|SHB_ENST00000377700.4_Missense_Mutation_p.K105E	NM_003028.2	NP_003019.2	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein B	105	Mediates interaction with LAT, PTK2/FAK1, JAK1 and JAK3.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(4)|lung(1)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)	11		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)		GCGCGCAGTTTGCGCAGCGAC	0.736													T|||	14	0.00279553	0.0	0.0043	5008	,	,		9271	0.0		0.007	False		,,,				2504	0.0041				p.K105E		Atlas-SNP	.											.	SHB	31	.	0			c.A313G						PASS	.	T	GLU/LYS	12,3704		0,12,1846	8.0	10.0	10.0		313	4.1	1.0	9	dbSNP_134	10	80,8056		0,80,3988	yes	missense	SHB	NM_003028.2	56	0,92,5834	CC,CT,TT		0.9833,0.3229,0.7762	possibly-damaging	105/510	38068330	92,11760	1858	4068	5926	SO:0001583	missense	6461	exon1			GCAGTTTGCGCAG		CCDS43806.1	9p13.2	2013-09-23	2005-05-24		ENSG00000107338	ENSG00000107338		"""SH2 domain containing"""	10838	protein-coding gene	gene with protein product		600314	"""SHB adaptor protein (a Src homology 2 protein)"", ""SHB (Src homology 2 domain containing) adaptor protein B"""			7713524	Standard	NM_003028		Approved		uc004aax.3	Q15464	OTTHUMG00000019936	ENST00000377707.3:c.313A>G	9.37:g.38068330T>C	ENSP00000366936:p.Lys105Glu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	30	11	0.366667	NM_003028	B9EGM0|D3DRQ5|Q504U5|Q5VUM8	Missense_Mutation	SNP	ENST00000377707.3	37	CCDS43806.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	T	24.5	4.541216	0.85917	0.003229	0.009833	ENSG00000107338	ENST00000377707;ENST00000377700	T	0.55588	0.51	4.07	4.07	0.47477	.	1.081180	0.07327	N	0.878683	T	0.37785	0.1016	L	0.29908	0.895	0.35952	D	0.834008	B	0.32409	0.37	B	0.35413	0.202	T	0.42616	-0.9441	10	0.51188	T	0.08	-7.5117	11.3282	0.49460	0.0:0.0:0.0:1.0	.	105	Q15464	SHB_HUMAN	E	105	ENSP00000366936:K105E	ENSP00000366929:K105E	K	-	1	0	SHB	38058330	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.797000	0.47877	1.607000	0.50170	0.358000	0.22013	AAA	T|0.996;C|0.004	0.004	strong		0.736	SHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052490.1		
TIMMDC1	51300	hgsc.bcm.edu	37	3	119222456	119222456	+	Silent	SNP	G	G	C	rs1131265	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:119222456G>C	ENST00000494664.1	+	3	640	c.438G>C	c.(436-438)gtG>gtC	p.V146V	TIMMDC1_ENST00000493694.1_Intron	NM_016589.3	NP_057673.2	Q9NPL8	TIDC1_HUMAN	translocase of inner mitochondrial membrane domain containing 1	146						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.V146V(1)		autonomic_ganglia(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	15						CAGTGTTTGTGACTATATTCA	0.408													G|||	1038	0.207268	0.1747	0.0994	5008	,	,		17210	0.3562		0.164	False		,,,				2504	0.2188				p.V146V		Atlas-SNP	.											TIMMDC1,NS,carcinoma,0,1	TIMMDC1	29	1	1	Substitution - coding silent(1)	stomach(1)	c.G438C						PASS	.	G		914,3492	343.1+/-307.5	100,714,1389	79.0	77.0	77.0		438	3.7	1.0	3	dbSNP_86	77	1590,7010	285.9+/-297.4	156,1278,2866	no	coding-synonymous	TIMMDC1	NM_016589.3		256,1992,4255	CC,CG,GG		18.4884,20.7444,19.2527		146/286	119222456	2504,10502	2203	4300	6503	SO:0001819	synonymous_variant	51300	exon3			GTTTGTGACTATA	AF210057	CCDS33831.1	3q13.33	2013-12-05	2011-07-05	2011-07-05	ENSG00000113845	ENSG00000113845			1321	protein-coding gene	gene with protein product		615534	"""chromosome 3 open reading frame 1"""	C3orf1		11092749	Standard	NM_016589		Approved	FLJ22597	uc003ecn.3	Q9NPL8	OTTHUMG00000159388	ENST00000494664.1:c.438G>C	3.37:g.119222456G>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	108	0.981818	NM_016589	D3DN81|Q6IAJ7|Q6UWU6|Q9NPR3|Q9NPS5|Q9P0Y6	Silent	SNP	ENST00000494664.1	37	CCDS33831.1																																																																																			G|0.795;C|0.205	0.205	strong		0.408	TIMMDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355077.3	NM_016589	
MEP1A	4224	hgsc.bcm.edu	37	6	46801071	46801071	+	Missense_Mutation	SNP	G	G	T	rs2274658	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46801071G>T	ENST00000230588.4	+	11	1414	c.1405G>T	c.(1405-1407)Gta>Tta	p.V469L		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	469	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.		V -> L (in dbSNP:rs2274658). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			TGGTTTTGGGGTAACTTTATA	0.488													T|||	1991	0.397564	0.5272	0.428	5008	,	,		20322	0.2133		0.3777	False		,,,				2504	0.411				p.V469L		Atlas-SNP	.											.	MEP1A	93	.	0			c.G1405T						PASS	.	T	LEU/VAL	2227,2179	585.8+/-386.3	553,1121,529	81.0	84.0	83.0		1405	1.2	0.8	6	dbSNP_100	83	3416,5184	637.7+/-399.3	687,2042,1571	yes	missense	MEP1A	NM_005588.2	32	1240,3163,2100	TT,TG,GG		39.7209,49.4553,43.3877	benign	469/747	46801071	5643,7363	2203	4300	6503	SO:0001583	missense	4224	exon11			TTTGGGGTAACTT		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.1405G>T	6.37:g.46801071G>T	ENSP00000230588:p.Val469Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	109	54	0.495413	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	37	CCDS4918.1	716	0.32783882783882784	217	0.4410569105691057	133	0.3674033149171271	89	0.1555944055944056	277	0.3654353562005277	T	4.104	0.017364	0.07959	0.505447	0.397209	ENSG00000112818	ENST00000230588	T	0.19669	2.13	5.72	1.18	0.20946	TRAF-type (1);TRAF-like (1);MATH (3);	0.247838	0.38111	N	0.001820	T	0.02533	0.0077	N	0.12853	0.265	0.50632	P	1.1399999999994748E-4	B;B	0.11235	0.001;0.004	B;B	0.13407	0.005;0.009	T	0.43605	-0.9381	9	0.28530	T	0.3	-2.8526	2.3762	0.04343	0.1811:0.1767:0.4488:0.1934	rs2274658;rs17467855;rs52817116;rs2274658	497;469	B7ZL91;Q16819	.;MEP1A_HUMAN	L	469	ENSP00000230588:V469L	ENSP00000230588:V469L	V	+	1	0	MEP1A	46909030	0.023000	0.18921	0.803000	0.32268	0.002000	0.02628	0.342000	0.19926	-0.031000	0.13781	-1.006000	0.02489	GTA	G|0.604;T|0.396	0.396	strong		0.488	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588	
CSAG1	158511	hgsc.bcm.edu	37	X	151908845	151908845	+	Nonsense_Mutation	SNP	C	C	G	rs1894360	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:151908845C>G	ENST00000370287.3	+	4	412	c.84C>G	c.(82-84)taC>taG	p.Y28*	CSAG1_ENST00000452779.2_Nonsense_Mutation_p.Y28*|CSAG1_ENST00000370291.2_Nonsense_Mutation_p.Y28*	NM_153478.1	NP_705611.1	Q6PB30	CSAG1_HUMAN	chondrosarcoma associated gene 1	28			Y -> F (in dbSNP:rs1894359).	Y -> C (in Ref. 1; AF195880). {ECO:0000305}.						central_nervous_system(1)|kidney(1)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)					GTAGACTGTACAGAGACACTG	0.537													.|||	377	0.0998675	0.0802	0.0533	3775	,	,		11961	0.0238		0.1531	False		,,,				2504	0.0573				p.Y28X		Atlas-SNP	.											.	CSAG1	27	.	0			c.C84G						PASS	.	G	stop/TYR,stop/TYR	322,3513		19,231,53,1382,518	231.0	209.0	217.0		84,84	0.8	0.0	X	dbSNP_92	217	1058,5670		80,555,343,1793,1529	no	stop-gained,stop-gained	CSAG1	NM_001102576.1,NM_153478.1	,	99,786,396,3175,2047	GG,GC,G,CC,C		15.7253,8.3963,13.0645	,	28/79,28/79	151908845	1380,9183	2203	4300	6503	SO:0001587	stop_gained	158511	exon4			ACTGTACAGAGAC	AF268419	CCDS76047.1	Xq28	2009-08-07			ENSG00000198930	ENSG00000198930			24294	protein-coding gene	gene with protein product	"""cancer/testis antigen family 24, member 1"""					12039054	Standard	XM_006724810		Approved	CSAGE, CT24.1	uc004fgf.3	Q6PB30	OTTHUMG00000022648	ENST00000370287.3:c.84C>G	X.37:g.151908845C>G	ENSP00000359310:p.Tyr28*	Somatic	386	1	0.00259067		WXS	Illumina HiSeq	Phase_I	847	490	0.578512	NM_153478	A6NE22	Nonsense_Mutation	SNP	ENST00000370287.3	37	CCDS14711.1	146	0.08800482218203737	18	0.0375	16	0.04519774011299435	5	0.008896797153024912	67	0.09544159544159544	G	14.71	2.618155	0.46736	0.083963	0.157253	ENSG00000198930	ENST00000370287;ENST00000452779;ENST00000370291	.	.	.	0.837	0.837	0.18896	.	.	.	.	.	.	.	.	.	.	.	0.22666	P	0.99887022	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	.	.	.	.	rs1894360;rs52835846;rs60699427;rs1894360	.	.	.	X	28	.	ENSP00000359310:Y28X	Y	+	3	2	CSAG1	151659501	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	-0.060000	0.11712	-0.097000	0.12307	-1.113000	0.02065	TAC	C|0.870;0|0.002	.	strong		0.537	CSAG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058760.2	NM_153479	
PEMT	10400	hgsc.bcm.edu	37	17	17425631	17425631	+	Missense_Mutation	SNP	C	C	T	rs897453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17425631C>T	ENST00000395783.1	-	3	351	c.172G>A	c.(172-174)Gtc>Atc	p.V58I	PEMT_ENST00000435340.2_Missense_Mutation_p.V73I|PEMT_ENST00000395781.2_Missense_Mutation_p.V95I|PEMT_ENST00000395782.1_Missense_Mutation_p.V58I|PEMT_ENST00000255389.5_Missense_Mutation_p.V95I	NM_007169.2	NP_009100.2	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase	58			V -> I (in dbSNP:rs897453). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.|V -> L (in dbSNP:rs897453).		cell proliferation (GO:0008283)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	phosphatidyl-N-dimethylethanolamine N-methyltransferase activity (GO:0080101)|phosphatidyl-N-methylethanolamine N-methyltransferase activity (GO:0000773)|phosphatidylethanolamine N-methyltransferase activity (GO:0004608)			endometrium(1)|kidney(1)|large_intestine(2)|prostate(3)	7				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)		AGGATGGTGACGCTTAGAGAG	0.602													C|||	996	0.198882	0.0635	0.2767	5008	,	,		18536	0.0952		0.4513	False		,,,				2504	0.1738				p.V95I		Atlas-SNP	.											.	PEMT	12	.	0			c.G283A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	574,3832	253.4+/-259.3	51,472,1680	127.0	92.0	104.0		172,283,172	-5.1	0.0	17	dbSNP_86	104	3877,4723	542.3+/-384.2	852,2173,1275	yes	missense,missense,missense	PEMT	NM_007169.2,NM_148172.1,NM_148173.1	29,29,29	903,2645,2955	TT,TC,CC		45.0814,13.0277,34.2227	benign,benign,benign	58/200,95/237,58/200	17425631	4451,8555	2203	4300	6503	SO:0001583	missense	10400	exon3			TGGTGACGCTTAG	AF176806	CCDS11186.1, CCDS11187.1, CCDS58520.1	17p11.2	2008-02-05			ENSG00000133027	ENSG00000133027	2.1.1.17		8830	protein-coding gene	gene with protein product		602391				9989271, 17881348	Standard	NM_148173		Approved	PEMPT, PEMT2	uc002grl.4	Q9UBM1	OTTHUMG00000059290	ENST00000395783.1:c.172G>A	17.37:g.17425631C>T	ENSP00000379129:p.Val58Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	48	0.436364	NM_001267552	A8MZ66|B4DY41|D3DXC3|Q6IAQ5|Q86VL3|Q9BW86|Q9UHY6|Q9Y6V9	Missense_Mutation	SNP	ENST00000395783.1	37	CCDS11187.1	539	0.2467948717948718	30	0.06097560975609756	115	0.31767955801104975	51	0.08916083916083917	343	0.4525065963060686	C	1.927	-0.446896	0.04572	0.130277	0.450814	ENSG00000133027	ENST00000255389;ENST00000395783;ENST00000395782;ENST00000435340;ENST00000395781;ENST00000421096	T;T;T;T;T	0.25579	2.43;2.42;2.42;1.79;1.8	4.87	-5.06	0.02946	.	1.493750	0.04051	N	0.304729	T	0.00012	0.0000	N	0.11284	0.12	0.80722	P	0.0	B;B;B	0.10296	0.002;0.003;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.45381	-0.9265	9	0.13853	T	0.58	-40.4928	4.3382	0.11097	0.2841:0.1905:0.0:0.5254	rs897453;rs1044987;rs3184799;rs3744119;rs17796661;rs17849340;rs56524175;rs897453	95;95;58	A8MZ66;Q9UBM1-2;Q9UBM1	.;.;PEMT_HUMAN	I	95;58;58;73;95;95	ENSP00000255389:V95I;ENSP00000379129:V58I;ENSP00000379128:V58I;ENSP00000391288:V73I;ENSP00000379127:V95I	ENSP00000255389:V95I	V	-	1	0	PEMT	17366356	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	-0.039000	0.12124	-0.796000	0.04456	-0.254000	0.11334	GTC	T|0.286;G|0.001;C|0.713;N|0.000	0.286	strong		0.602	PEMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131657.1	NM_007169	
MAP3K5	4217	hgsc.bcm.edu	37	6	136977568	136977568	+	Silent	SNP	T	T	C	rs2076260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:136977568T>C	ENST00000359015.4	-	10	1917	c.1557A>G	c.(1555-1557)ttA>ttG	p.L519L	MAP3K5_ENST00000355845.4_5'UTR	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	519					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GCTTATATATTAAAATTGTCT	0.403													C|||	2199	0.439097	0.7254	0.2997	5008	,	,		16911	0.5565		0.171	False		,,,				2504	0.3057				p.L519L		Atlas-SNP	.											MAP3K5,NS,carcinoma,0,1	MAP3K5	136	1	0			c.A1557G						PASS	.	C		2853,1553	487.8+/-361.0	929,995,279	115.0	109.0	111.0		1557	5.7	1.0	6	dbSNP_96	111	1499,7101	748.6+/-407.3	122,1255,2923	no	coding-synonymous	MAP3K5	NM_005923.3		1051,2250,3202	CC,CT,TT		17.4302,35.2474,33.4615		519/1375	136977568	4352,8654	2203	4300	6503	SO:0001819	synonymous_variant	4217	exon10			ATATATTAAAATT	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.1557A>G	6.37:g.136977568T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	37	CCDS5179.1																																																																																			T|0.613;C|0.387	0.387	strong		0.403	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
KANSL1	284058	hgsc.bcm.edu	37	17	44248837	44248837	+	Missense_Mutation	SNP	T	T	C	rs553586616	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44248837T>C	ENST00000262419.6	-	2	1143	c.673A>G	c.(673-675)Aat>Gat	p.N225D	KANSL1_ENST00000574590.1_Missense_Mutation_p.N225D|KANSL1_ENST00000575318.1_Missense_Mutation_p.N225D|KANSL1_ENST00000572904.1_Missense_Mutation_p.N225D|KANSL1_ENST00000432791.1_Missense_Mutation_p.N225D|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000393476.3_5'UTR	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	225			N -> D (in dbSNP:rs35643216).		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GTGCTATTATTGCTATACAAA	0.443													T|||	364	0.0726837	0.0113	0.1398	5008	,	,		24410	0.001		0.1998	False		,,,				2504	0.0511				p.N225D		Atlas-SNP	.											.	.	.	.	0			c.A673G						PASS	.	T	ASP/ASN,ASP/ASN,ASP/ASN	167,4239		0,167,2036	132.0	164.0	154.0		673,673,673	5.0	1.0	17	dbSNP_126	154	1565,7035		0,1565,2735	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	23,23,23	0,1732,4771	CC,CT,TT		18.1977,3.7903,13.3169	benign,benign,benign	225/1105,225/1106,225/1106	44248837	1732,11274	2203	4300	6503	SO:0001583	missense	284058	exon2			TATTATTGCTATA	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.673A>G	17.37:g.44248837T>C	ENSP00000262419:p.Asn225Asp	Somatic	368	0	0		WXS	Illumina HiSeq	Phase_I	456	96	0.210526	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	215	0.09844322344322344	10	0.02032520325203252	58	0.16022099447513813	1	0.0017482517482517483	146	0.19261213720316622	T	12.33	1.907105	0.33628	0.037903	0.181977	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.10668	2.85;2.85	6.04	4.97	0.65823	.	0.224065	0.47455	D	0.000233	T	0.00012	0.0000	N	0.12182	0.205	0.80722	D	1	B;B	0.33637	0.011;0.42	B;B	0.31337	0.007;0.128	T	0.61222	-0.7106	10	0.44086	T	0.13	-16.177	9.254	0.37573	0.0:0.0809:0.0:0.9191	rs35643216	225;225	C9JHY2;Q7Z3B3	.;K1267_HUMAN	D	225	ENSP00000262419:N225D;ENSP00000387393:N225D	ENSP00000262419:N225D	N	-	1	0	KIAA1267	41604614	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.265000	0.51561	2.317000	0.78254	0.459000	0.35465	AAT	T|0.857;C|0.143	0.143	strong		0.443	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
SLC4A8	9498	hgsc.bcm.edu	37	12	51856159	51856159	+	Silent	SNP	C	C	T	rs71449805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:51856159C>T	ENST00000453097.2	+	10	1384	c.1167C>T	c.(1165-1167)ttC>ttT	p.F389F	SLC4A8_ENST00000514353.3_Silent_p.F336F|SLC4A8_ENST00000394856.1_Silent_p.F336F|SLC4A8_ENST00000358657.3_Silent_p.F416F|SLC4A8_ENST00000535225.2_Silent_p.F336F	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		TTGATGAGTTCCTAGACCAGG	0.473													C|||	48	0.00958466	0.0015	0.0187	5008	,	,		18122	0.0		0.0278	False		,,,				2504	0.0051				p.F389F		Atlas-SNP	.											.	SLC4A8	292	.	0			c.C1167T						PASS	.	C	,	36,4370	41.6+/-74.8	0,36,2167	123.0	118.0	120.0		1167,1167	4.3	1.0	12	dbSNP_130	120	351,8249	118.5+/-177.9	5,341,3954	no	coding-synonymous,coding-synonymous	SLC4A8	NM_001039960.1,NM_004858.2	,	5,377,6121	TT,TC,CC		4.0814,0.8171,2.9755	,	389/1094,389/1045	51856159	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	9498	exon10			TGAGTTCCTAGAC	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"""Solute carriers"""	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1167C>T	12.37:g.51856159C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	109	58	0.53211	NM_001039960		Silent	SNP	ENST00000453097.2	37	CCDS44890.1																																																																																			C|0.974;T|0.026	0.026	strong		0.473	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858	
SP100	6672	hgsc.bcm.edu	37	2	231307660	231307660	+	Missense_Mutation	SNP	C	C	T	rs373614701		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:231307660C>T	ENST00000264052.5	+	3	471	c.116C>T	c.(115-117)aCg>aTg	p.T39M	SP100_ENST00000409897.1_Missense_Mutation_p.T4M|SP100_ENST00000409824.1_Missense_Mutation_p.T14M|SP100_ENST00000341950.4_Missense_Mutation_p.T39M|SP100_ENST00000427101.2_Missense_Mutation_p.T14M|SP100_ENST00000409341.1_Missense_Mutation_p.T39M|SP100_ENST00000340126.4_Missense_Mutation_p.T39M|SP100_ENST00000409112.1_Missense_Mutation_p.T39M	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	39	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.				cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		AGGATGTTCACGGAAGACCAG	0.383																																					p.T39M		Atlas-SNP	.											SP100_ENST00000340126,NS,carcinoma,0,2	SP100	167	2	0			c.C116T						scavenged	.	C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	120.0	117.0	118.0		116,116,116,41,11,116	-7.2	0.0	2		118	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	SP100	NM_001080391.1,NM_001206701.1,NM_001206702.1,NM_001206703.1,NM_001206704.1,NM_003113.3	81,81,81,81,81,81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	39/886,39/689,39/481,14/453,4/446,39/880	231307660	1,13005	2203	4300	6503	SO:0001583	missense	6672	exon3			TGTTCACGGAAGA	AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"""Zinc fingers, PHD-type"""	11206	protein-coding gene	gene with protein product		604585	"""nuclear antigen Sp100"""			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.116C>T	2.37:g.231307660C>T	ENSP00000264052:p.Thr39Met	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	309	4	0.012945	NM_001206702	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	ENST00000264052.5	37	CCDS2477.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.369010	0.42003	0.0	1.16E-4	ENSG00000067066	ENST00000264052;ENST00000427101;ENST00000432979;ENST00000409824;ENST00000409341;ENST00000409112;ENST00000340126;ENST00000341950;ENST00000409897	T;T;T;T;T;D;T;T;T	0.81499	2.14;2.07;0.75;2.07;2.03;-1.5;0.06;2.01;2.09	4.08	-7.16	0.01516	Sp100 (1);	.	.	.	.	T	0.81331	0.4800	M	0.65975	2.015	0.09310	N	1	D;D;D;D;D;P;P;D	0.71674	0.995;0.987;0.99;0.997;0.998;0.928;0.943;0.997	P;P;P;P;P;B;B;P	0.58013	0.769;0.499;0.587;0.821;0.773;0.373;0.226;0.831	T	0.75602	-0.3261	9	0.54805	T	0.06	.	6.5378	0.22363	0.0:0.2089:0.3446:0.4465	.	14;39;4;39;39;39;14;39	F8WFE2;B4E2B9;B8ZZD8;P23497-4;P23497;E7EUA7;E9PHV6;P23497-2	.;.;.;.;SP100_HUMAN;.;.;.	M	39;14;14;14;39;39;39;39;4	ENSP00000264052:T39M;ENSP00000399389:T14M;ENSP00000391616:T14M;ENSP00000387311:T14M;ENSP00000386404:T39M;ENSP00000386427:T39M;ENSP00000343023:T39M;ENSP00000342729:T39M;ENSP00000386998:T4M	ENSP00000264052:T39M	T	+	2	0	SP100	231015904	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.762000	0.01803	-1.697000	0.01420	-0.244000	0.11960	ACG	.	.	weak		0.383	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
HDAC4	9759	hgsc.bcm.edu	37	2	240011717	240011717	+	Silent	SNP	T	T	C	rs61752234	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:240011717T>C	ENST00000345617.3	-	18	3152	c.2361A>G	c.(2359-2361)acA>acG	p.T787T	HDAC4_ENST00000543185.1_Silent_p.T371T	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	787	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		TCAGCTCCCCTGTGGCCACCT	0.667													C|||	169	0.033746	0.0015	0.1066	5008	,	,		15025	0.0367		0.0427	False		,,,				2504	0.0133				p.T787T		Atlas-SNP	.											.	HDAC4	127	.	0			c.A2361G						PASS	.	C		46,4360	820.8+/-416.4	1,44,2158	74.0	73.0	73.0		2361	-8.0	0.3	2	dbSNP_129	73	379,8221	801.6+/-407.4	10,359,3931	no	coding-synonymous	HDAC4	NM_006037.3		11,403,6089	CC,CT,TT		4.407,1.044,3.2677		787/1085	240011717	425,12581	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon18			CTCCCCTGTGGCC	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.2361A>G	2.37:g.240011717T>C		Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	292	136	0.465753	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			T|0.965;C|0.035	0.035	strong		0.667	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
VN1R1	57191	hgsc.bcm.edu	37	19	57967133	57967133	+	Missense_Mutation	SNP	G	G	A	rs28649880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57967133G>A	ENST00000321039.3	-	1	721	c.722C>T	c.(721-723)tCc>tTc	p.S241F	AC004076.9_ENST00000596831.1_Intron|AC004076.9_ENST00000415705.3_Intron	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	241			S -> F (in allele VN1R1*3; dbSNP:rs28649880). {ECO:0000269|PubMed:10973240, ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		GAAGACCATGGAGCCACTGGC	0.468													G|||	2073	0.413938	0.3124	0.451	5008	,	,		19142	0.5913		0.2793	False		,,,				2504	0.4806				p.S241F		Atlas-SNP	.											VN1R1,NS,adenoma,0,1	VN1R1	48	1	0			c.C722T						PASS	.	G	PHE/SER	1344,3062	450.6+/-349.4	189,966,1048	112.0	87.0	95.0		722	0.4	0.0	19	dbSNP_125	95	2453,6147	403.9+/-348.0	330,1793,2177	yes	missense	VN1R1	NM_020633.3	155	519,2759,3225	AA,AG,GG		28.5233,30.5039,29.1942	probably-damaging	241/354	57967133	3797,9209	2203	4300	6503	SO:0001583	missense	57191	exon1			ACCATGGAGCCAC	AF255342	CCDS12951.1	19q13.4	2012-08-22	2003-01-15		ENSG00000178201	ENSG00000178201		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	13548	protein-coding gene	gene with protein product		605234	"""vomeronasal olfactory receptor, (chromosome 19) subtype I, member 1"""	VNR19I1		10973240	Standard	NM_020633		Approved	V1RL1, ZVNR1, ZVNH1	uc002qos.2	Q9GZP7		ENST00000321039.3:c.722C>T	19.37:g.57967133G>A	ENSP00000322339:p.Ser241Phe	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	265	127	0.479245	NM_020633	B3KSV5|Q7Z5H8|Q7Z5H9	Missense_Mutation	SNP	ENST00000321039.3	37	CCDS12951.1	878	0.40201465201465203	149	0.30284552845528456	135	0.3729281767955801	368	0.6433566433566433	226	0.29815303430079154	G	11.87	1.766615	0.31228	0.305039	0.285233	ENSG00000178201	ENST00000321039	T	0.08370	3.1	4.11	0.384	0.16244	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	L	0.48877	1.53	0.80722	P	0.0	P	0.45283	0.855	P	0.47573	0.55	T	0.30179	-0.9987	8	0.08599	T	0.76	.	2.0499	0.03568	0.1073:0.1653:0.4256:0.3017	rs28649880	241	Q9GZP7	VN1R1_HUMAN	F	241	ENSP00000322339:S241F	ENSP00000322339:S241F	S	-	2	0	VN1R1	62658945	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	-0.546000	0.06062	0.461000	0.27071	0.603000	0.83216	TCC	G|0.674;A|0.326	0.326	strong		0.468	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466464.1	NM_020633	
DLGAP2	9228	hgsc.bcm.edu	37	8	1514009	1514009	+	Missense_Mutation	SNP	C	C	A	rs2301963	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:1514009C>A	ENST00000421627.2	+	3	1285	c.1151C>A	c.(1150-1152)cCa>cAa	p.P384Q	RP11-666I19.2_ENST00000518063.1_RNA	NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	463					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GCAATCCTACCAGAGCCGCTG	0.562													C|||	2307	0.460663	0.3434	0.5749	5008	,	,		16949	0.4484		0.4503	False		,,,				2504	0.5613				p.P384Q		Atlas-SNP	.											.	DLGAP2	292	.	0			c.C1151A						PASS	.	C	GLN/PRO	1604,2696		288,1028,834	35.0	40.0	39.0		1151	4.6	0.0	8	dbSNP_100	39	3828,4728		872,2084,1322	yes	missense	DLGAP2	NM_004745.3	76	1160,3112,2156	AA,AC,CC		44.7405,37.3023,42.2526	possibly-damaging	384/976	1514009	5432,7424	2150	4278	6428	SO:0001583	missense	9228	exon3			TCCTACCAGAGCC	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.1151C>A	8.37:g.1514009C>A	ENSP00000400258:p.Pro384Gln	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	959|959	0.4391025641025641|0.4391025641025641	172|172	0.34959349593495936|0.34959349593495936	200|200	0.5524861878453039|0.5524861878453039	260|260	0.45454545454545453|0.45454545454545453	327|327	0.4313984168865435|0.4313984168865435	C|C	14.97|14.97	2.695380|2.695380	0.48202|0.48202	0.373023|0.373023	0.447405|0.447405	ENSG00000198010|ENSG00000198010	ENST00000356067;ENST00000421627|ENST00000520901	T|.	0.21932|.	1.98|.	4.55|4.55	4.55|4.55	0.56014|0.56014	.|.	0.333684|.	0.36409|.	N|.	0.002603|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.72479|0.72479	2.2|2.2	0.33270|0.33270	P|P	0.43908899999999995|0.43908899999999995	D;P|.	0.56521|.	0.976;0.918|.	P;B|.	0.50270|.	0.636;0.372|.	T|T	0.49707|0.49707	-0.8911|-0.8911	9|4	0.62326|.	D|.	0.03|.	-2.2526|-2.2526	17.7159|17.7159	0.88336|0.88336	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs2301963;rs17748827;rs58660533;rs2301963|rs2301963;rs17748827;rs58660533;rs2301963	463;463|.	Q9P1A6-2;Q9P1A6|.	.;DLGP2_HUMAN|.	Q|K	429;384|401	ENSP00000400258:P384Q|.	ENSP00000348366:P429Q|.	P|Q	+|+	2|1	0|0	DLGAP2|DLGAP2	1501416|1501416	0.559000|0.559000	0.26562|0.26562	0.049000|0.049000	0.19019|0.19019	0.107000|0.107000	0.19398|0.19398	3.412000|3.412000	0.52679|0.52679	2.238000|2.238000	0.73509|0.73509	0.585000|0.585000	0.79938|0.79938	CCA|CAG	C|0.556;A|0.444	0.444	strong		0.562	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
GP2	2813	hgsc.bcm.edu	37	16	20328685	20328685	+	Silent	SNP	T	T	C	rs1129818	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20328685T>C	ENST00000381362.4	-	9	1351	c.1275A>G	c.(1273-1275)caA>caG	p.Q425Q	GP2_ENST00000573897.1_5'Flank|GP2_ENST00000302555.5_Silent_p.Q422Q|GP2_ENST00000341642.5_Silent_p.Q275Q|GP2_ENST00000381360.5_Silent_p.Q278Q	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	425	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				antigen transcytosis by M cells in mucosal-associated lymphoid tissue (GO:0002412)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						TGGAATCACGTTGATTTGAGC	0.483													T|||	1194	0.238419	0.0522	0.3012	5008	,	,		16717	0.1071		0.4364	False		,,,				2504	0.3773				p.Q425Q		Atlas-SNP	.											.	GP2	122	.	0			c.A1275G						PASS	.	T	,,,	557,3849	248.4+/-256.2	29,499,1675	86.0	69.0	75.0		1275,834,825,1266	-1.7	0.0	16	dbSNP_86	75	3778,4822	535.9+/-382.9	830,2118,1352	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GP2	NM_001007240.1,NM_001007241.1,NM_001007242.1,NM_001502.2	,,,	859,2617,3027	CC,CT,TT		43.9302,12.6419,33.3308	,,,	425/538,278/391,275/388,422/535	20328685	4335,8671	2203	4300	6503	SO:0001819	synonymous_variant	2813	exon9			ATCACGTTGATTT	U36221	CCDS10582.2, CCDS42128.1, CCDS45432.1, CCDS45433.1	16p12.3	2008-02-05			ENSG00000169347	ENSG00000169347			4441	protein-coding gene	gene with protein product		602977				9605860	Standard	XM_005255259		Approved		uc002dgw.3	P55259	OTTHUMG00000131489	ENST00000381362.4:c.1275A>G	16.37:g.20328685T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	87	31	0.356322	NM_001007240	A6NFM9|A6NJA8|Q13338|Q9UIF1	Silent	SNP	ENST00000381362.4	37	CCDS42128.1																																																																																			T|0.687;C|0.313	0.313	strong		0.483	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295	
CNTNAP2	26047	hgsc.bcm.edu	37	7	147092861	147092861	+	Silent	SNP	G	G	A	rs34592169	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:147092861G>A	ENST00000361727.3	+	10	2175	c.1659G>A	c.(1657-1659)gcG>gcA	p.A553A		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	553					adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			ACATGTGTGCGATCATAGACA	0.428										HNSCC(39;0.1)			G|||	469	0.0936502	0.0197	0.1599	5008	,	,		16618	0.006		0.2207	False		,,,				2504	0.1063				p.A553A		Atlas-SNP	.											CNTNAP2,colon,carcinoma,0,1	CNTNAP2	392	1	0			c.G1659A						PASS	.	G		246,4160	145.0+/-179.8	6,234,1963	139.0	123.0	128.0		1659	3.5	1.0	7	dbSNP_126	128	2020,6578	353.4+/-329.1	238,1544,2517	no	coding-synonymous	CNTNAP2	NM_014141.5		244,1778,4480	AA,AG,GG		23.4938,5.5833,17.4254		553/1332	147092861	2266,10738	2203	4299	6502	SO:0001819	synonymous_variant	26047	exon10			GTGTGCGATCATA	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1659G>A	7.37:g.147092861G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	148	72	0.486486	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	37	CCDS5889.1																																																																																			G|0.845;A|0.155	0.155	strong		0.428	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1		
LAMA3	3909	hgsc.bcm.edu	37	18	21511034	21511034	+	Missense_Mutation	SNP	C	C	A	rs1154232	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:21511034C>A	ENST00000313654.9	+	65	8686	c.8445C>A	c.(8443-8445)aaC>aaA	p.N2815K	LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000587184.1_Missense_Mutation_p.N1150K|LAMA3_ENST00000269217.6_Missense_Mutation_p.N1206K|LAMA3_ENST00000399516.3_Missense_Mutation_p.N2759K	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2815	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		N -> K (in dbSNP:rs1154232).		cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					AGACAAGGAACCTGCAGGTCA	0.388													C|||	785	0.156749	0.0393	0.1657	5008	,	,		16460	0.1815		0.2097	False		,,,				2504	0.229				p.N2815K		Atlas-SNP	.											.	LAMA3	397	.	0			c.C8445A						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN	274,4132	152.9+/-186.6	8,258,1937	128.0	128.0	128.0		3618,8277,3450,8445	2.6	0.2	18	dbSNP_87	128	1711,6889	312.3+/-310.8	161,1389,2750	yes	missense,missense,missense,missense	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	94,94,94,94	169,1647,4687	AA,AC,CC		19.8953,6.2188,15.2622	benign,benign,benign,benign	1206/1725,2759/3278,1150/1669,2815/3334	21511034	1985,11021	2203	4300	6503	SO:0001583	missense	3909	exon65			AAGGAACCTGCAG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.8445C>A	18.37:g.21511034C>A	ENSP00000324532:p.Asn2815Lys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	344	0.1575091575091575	20	0.04065040650406504	62	0.1712707182320442	98	0.17132867132867133	164	0.21635883905013192	C	3.542	-0.093580	0.07053	0.062188	0.198953	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.77489	-1.1;-1.1;-1.1	5.46	2.56	0.30785	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.00073	0.0002	L	0.46157	1.445	0.09310	P	0.9999999999999983	B;B;B;B	0.09022	0.0;0.0;0.001;0.002	B;B;B;B	0.11329	0.006;0.005;0.004;0.004	T	0.04128	-1.0975	8	0.29301	T	0.29	.	5.0531	0.14518	0.0:0.6432:0.1722:0.1846	rs1154232;rs1786308;rs52789840;rs61436488;rs1154232	1150;1206;2759;2815	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	K	2815;2759;1206	ENSP00000324532:N2815K;ENSP00000382432:N2759K;ENSP00000269217:N1206K	ENSP00000269217:N1206K	N	+	3	2	LAMA3	19765032	0.038000	0.19896	0.212000	0.23672	0.415000	0.31203	-0.007000	0.12810	0.677000	0.31305	0.655000	0.94253	AAC	C|0.849;A|0.151	0.151	strong		0.388	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
RARS	5917	hgsc.bcm.edu	37	5	167933158	167933158	+	Missense_Mutation	SNP	T	T	A	rs2305734	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:167933158T>A	ENST00000231572.3	+	10	1244	c.1190T>A	c.(1189-1191)tTt>tAt	p.F397Y	RARS_ENST00000538719.1_Missense_Mutation_p.F191Y	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	397			F -> Y (in dbSNP:rs2305734).		arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		CAAAGACTATTTGAGGAAAAA	0.353													T|||	220	0.0439297	0.0038	0.0418	5008	,	,		19735	0.0635		0.0785	False		,,,				2504	0.044				p.F397Y		Atlas-SNP	.											.	RARS	58	.	0			c.T1190A						PASS	.	T	TYR/PHE	157,4249		2,153,2048	149.0	145.0	146.0		1190	3.1	0.1	5	dbSNP_100	146	1483,7117		162,1159,2979	yes	missense	RARS	NM_002887.3	22	164,1312,5027	AA,AT,TT		17.2442,3.5633,12.6096	benign	397/661	167933158	1640,11366	2203	4300	6503	SO:0001583	missense	5917	exon10			GACTATTTGAGGA	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1190T>A	5.37:g.167933158T>A	ENSP00000231572:p.Phe397Tyr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Missense_Mutation	SNP	ENST00000231572.3	37	CCDS4367.1	228	0.1043956043956044	10	0.02032520325203252	41	0.1132596685082873	43	0.07517482517482517	134	0.17678100263852242	T	0.270	-0.993336	0.02145	0.035633	0.172442	ENSG00000113643	ENST00000231572;ENST00000538719	T;T	0.63913	-0.07;-0.07	5.58	3.13	0.36017	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.478529	0.26995	N	0.021457	T	0.00144	0.0004	L	0.41824	1.3	0.80722	P	0.0	B	0.06786	0.001	B	0.19148	0.024	T	0.05699	-1.0869	9	0.59425	D	0.04	-1.9146	4.3967	0.11367	0.206:0.0619:0.1064:0.6257	rs2305734;rs17633764;rs2305734	397	P54136	SYRC_HUMAN	Y	397;191	ENSP00000231572:F397Y;ENSP00000439108:F191Y	ENSP00000231572:F397Y	F	+	2	0	RARS	167865736	0.996000	0.38824	0.121000	0.21740	0.944000	0.59088	2.391000	0.44424	0.120000	0.18254	-2.514000	0.00186	TTT	T|0.869;A|0.131	0.131	strong		0.353	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249152	71249152	+	Silent	SNP	C	C	T	rs112809261	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:71249152C>T	ENST00000398534.3	+	1	82	c.51C>T	c.(49-51)tgC>tgT	p.C17C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	17						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						GTGGGGGCTGCGGCTCTGGCT	0.652																																					p.C17C		Atlas-SNP	.											KRTAP5-8,NS,carcinoma,+1,1	KRTAP5-8	28	1	0			c.C51T						scavenged	.						55.0	75.0	68.0					11																	71249152		2195	4284	6479	SO:0001819	synonymous_variant	57830	exon1			GGGCTGCGGCTCT	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.51C>T	11.37:g.71249152C>T		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	104	16	0.153846	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																			C|0.896;T|0.104	0.104	strong		0.652	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
HLA-C	3107	hgsc.bcm.edu	37	6	31238984	31238984	+	Missense_Mutation	SNP	G	G	T	rs2308584	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238984G>T	ENST00000376228.5	-	3	499	c.485C>A	c.(484-486)aCc>aAc	p.T162N	HLA-C_ENST00000383329.3_Missense_Mutation_p.T162N	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	162	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CTGAGCCGCGGTGTCCGCGGC	0.692																																					p.T162N		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,+1,2	HLA-C	92	2	0			c.C485A						scavenged	.						30.0	22.0	25.0					6																	31238984		2148	4183	6331	SO:0001583	missense	3107	exon3			GCCGCGGTGTCCG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.485C>A	6.37:g.31238984G>T	ENSP00000365402:p.Thr162Asn	Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	161	36	0.223602	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	161|161	0.07371794871794872|0.07371794871794872	35|35	0.07113821138211382|0.07113821138211382	50|50	0.13812154696132597|0.13812154696132597	3|3	0.005244755244755245|0.005244755244755245	73|73	0.09630606860158311|0.09630606860158311	.|.	6.067|6.067	0.380613|0.380613	0.11466|0.11466	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.00010	.|9.44;9.44	2.81|2.81	-2.67|-2.67	0.06059|0.06059	.|MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|771.080000	.|0.01279	.|U	.|0.009683	T|T	0.00073|0.00073	0.0002|0.0002	M|M	0.92970|0.92970	3.365|3.365	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.20459	.|0.022;0.022;0.022;0.045	.|B;B;B;B	.|0.33254	.|0.061;0.061;0.098;0.16	T|T	0.41484|0.41484	-0.9506|-0.9506	5|10	.|0.87932	.|D	.|0	.|.	8.222|8.222	0.31547|0.31547	0.4359:0.0:0.5641:0.0|0.4359:0.0:0.5641:0.0	rs2308584;rs9264658;rs17849597;rs17850338|rs2308584;rs9264658;rs17849597;rs17850338	.|162;162;162;162	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	Q|N	161|162;162;162;199	.|ENSP00000365402:T162N;ENSP00000372819:T162N	.|ENSP00000365402:T162N	H|T	-|-	3|2	2|0	HLA-C|HLA-C	31346963|31346963	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-4.377000|-4.377000	0.00244|0.00244	-0.721000|-0.721000	0.04929|0.04929	-0.786000|-0.786000	0.03341|0.03341	CAC|ACC	T|0.057;G|0.944	0.057	strong		0.692	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
CCDC33	80125	hgsc.bcm.edu	37	15	74622533	74622533	+	Missense_Mutation	SNP	A	A	G	rs2277603	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:74622533A>G	ENST00000398814.3	+	12	1725	c.1294A>G	c.(1294-1296)Atg>Gtg	p.M432V	CCDC33_ENST00000558821.1_Missense_Mutation_p.M25V|CCDC33_ENST00000321288.5_Missense_Mutation_p.M635V|CCDC33_ENST00000268082.4_Missense_Mutation_p.M25V	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	635										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						TCCACAGGAGATGAACAACTA	0.582													A|||	602	0.120208	0.0121	0.0692	5008	,	,		18218	0.2222		0.0875	False		,,,				2504	0.2311				p.M432V		Atlas-SNP	.											.	CCDC33	160	.	0			c.A1294G						PASS	.	A	VAL/MET,VAL/MET	99,3977		2,95,1941	40.0	44.0	42.0		1294,73	-2.5	0.6	15	dbSNP_100	42	791,7553		36,719,3417	yes	missense,missense	CCDC33	NM_025055.3,NM_182791.2	21,21	38,814,5358	GG,GA,AA		9.4799,2.4289,7.1659	benign,benign	432/756,25/368	74622533	890,11530	2038	4172	6210	SO:0001583	missense	80125	exon12			CAGGAGATGAACA	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.1294A>G	15.37:g.74622533A>G	ENSP00000381795:p.Met432Val	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	191	92	0.481675	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	CCDS42058.1	218	0.09981684981684982	9	0.018292682926829267	37	0.10220994475138122	111	0.19405594405594406	61	0.08047493403693931	A	3.593	-0.083181	0.07141	0.024289	0.094799	ENSG00000140481	ENST00000321288;ENST00000398814;ENST00000321374;ENST00000268082	T;T;T;T	0.34667	1.35;2.33;1.97;1.95	4.3	-2.45	0.06481	.	0.524699	0.20717	N	0.086996	T	0.00039	0.0001	M	0.70595	2.14	0.58432	P	5.000000000032756E-6	B;B;B;B	0.27351	0.065;0.081;0.176;0.038	B;B;B;B	0.20577	0.022;0.03;0.025;0.015	T	0.10800	-1.0614	9	0.62326	D	0.03	.	0.5572	0.00673	0.249:0.1459:0.1791:0.4261	rs2277603;rs56484983;rs56997916;rs2277603	25;25;635;432	Q8N5R6-4;Q8N5R6-5;C9JFX2;Q8N5R6-6	.;.;.;.	V	635;432;25;25	ENSP00000325012:M635V;ENSP00000381795:M432V;ENSP00000325661:M25V;ENSP00000268082:M25V	ENSP00000268082:M25V	M	+	1	0	CCDC33	72409586	0.003000	0.15002	0.612000	0.29024	0.021000	0.10359	-0.893000	0.04127	-0.324000	0.08589	-0.353000	0.07706	ATG	A|0.887;G|0.113;T|0.000	0.113	strong		0.582	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
PXDNL	137902	hgsc.bcm.edu	37	8	52321728	52321728	+	Missense_Mutation	SNP	G	G	C	rs201184283		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:52321728G>C	ENST00000356297.4	-	17	2556	c.2456C>G	c.(2455-2457)cCt>cGt	p.P819R	PXDNL_ENST00000543296.1_Missense_Mutation_p.P819R	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	819					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GCTCAGCGCAGGCACTGTGTG	0.677																																					p.P819R		Atlas-SNP	.											PXDNL_ENST00000356297,uveal_tract,malignant_melanoma,0,2	PXDNL	414	2	0			c.C2456G						PASS	.	G	ARG/PRO	0,4240		0,0,2120	15.0	19.0	18.0		2456	2.5	0.0	8		18	14,8462		0,14,4224	yes	missense	PXDNL	NM_144651.4	103	0,14,6344	CC,CG,GG		0.1652,0.0,0.1101	possibly-damaging	819/1464	52321728	14,12702	2120	4238	6358	SO:0001583	missense	137902	exon17			AGCGCAGGCACTG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2456C>G	8.37:g.52321728G>C	ENSP00000348645:p.Pro819Arg	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	28	15	0.535714	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	7.942	0.742913	0.15642	0.0	0.001652	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.67698	-0.28;-0.28	3.4	2.49	0.30216	.	0.143845	0.31989	N	0.006753	T	0.75803	0.3899	M	0.80746	2.51	0.27711	N	0.945471	D	0.58620	0.983	D	0.63703	0.917	T	0.66705	-0.5856	10	0.62326	D	0.03	.	4.3235	0.11029	0.1247:0.0:0.6474:0.2279	.	819	A1KZ92	PXDNL_HUMAN	R	819	ENSP00000348645:P819R;ENSP00000444865:P819R	ENSP00000348645:P819R	P	-	2	0	PXDNL	52484281	0.809000	0.29036	0.007000	0.13788	0.001000	0.01503	2.425000	0.44723	0.516000	0.28340	-0.188000	0.12872	CCT	.	.	weak		0.677	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
RIMBP2	23504	hgsc.bcm.edu	37	12	130884347	130884347	+	Silent	SNP	A	A	G	rs756186	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:130884347A>G	ENST00000261655.4	-	18	3172	c.3009T>C	c.(3007-3009)aaT>aaC	p.N1003N		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	1003	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CTTTCTGCCCATTCAGCTCCC	0.458													A|||	1115	0.222644	0.2632	0.1916	5008	,	,		17559	0.1538		0.328	False		,,,				2504	0.1524				p.N1003N		Atlas-SNP	.											.	RIMBP2	220	.	0			c.T3009C						PASS	.	A		1250,3156	429.1+/-342.1	178,894,1131	91.0	84.0	87.0		3009	-1.1	0.9	12	dbSNP_86	87	3075,5525	471.7+/-368.2	557,1961,1782	no	coding-synonymous	RIMBP2	NM_015347.4		735,2855,2913	GG,GA,AA		35.7558,28.3704,33.2539		1003/1053	130884347	4325,8681	2203	4300	6503	SO:0001819	synonymous_variant	23504	exon18			CTGCCCATTCAGC	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.3009T>C	12.37:g.130884347A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_015347	Q96ID2	Silent	SNP	ENST00000261655.4	37	CCDS31925.1																																																																																			A|0.703;G|0.297	0.297	strong		0.458	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
SGOL2	151246	hgsc.bcm.edu	37	2	201437048	201437048	+	Missense_Mutation	SNP	A	A	G	rs17532665	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:201437048A>G	ENST00000357799.4	+	7	2077	c.1979A>G	c.(1978-1980)aAc>aGc	p.N660S		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	660			N -> S (in dbSNP:rs17532665). {ECO:0000269|Ref.1}.		meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						ATCTCTGAAAACATAGAAGTT	0.353													A|||	343	0.0684904	0.0454	0.0677	5008	,	,		17373	0.002		0.1501	False		,,,				2504	0.0849				p.N660S		Atlas-SNP	.											.	SGOL2	126	.	0			c.A1979G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	205,3409		4,197,1606	55.0	55.0	55.0		1979,1979,1979	4.1	0.0	2	dbSNP_123	55	1245,6869		95,1055,2907	yes	missense,missense,missense	SGOL2	NM_001160033.1,NM_001160046.1,NM_152524.5	46,46,46	99,1252,4513	GG,GA,AA		15.3439,5.6724,12.3636	probably-damaging,probably-damaging,probably-damaging	660/1261,660/1262,660/1266	201437048	1450,10278	1807	4057	5864	SO:0001583	missense	151246	exon7			CTGAAAACATAGA	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.1979A>G	2.37:g.201437048A>G	ENSP00000350447:p.Asn660Ser	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	217	107	0.493088	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	37	CCDS42796.1	164	0.07509157509157509	26	0.052845528455284556	26	0.0718232044198895	1	0.0017482517482517483	111	0.14643799472295516	A	8.418	0.845831	0.16963	0.056724	0.153439	ENSG00000163535	ENST00000357799	T	0.14640	2.49	5.25	4.09	0.47781	.	0.000000	0.56097	D	0.000027	T	0.00073	0.0002	L	0.60455	1.87	0.48087	P	4.1800000000002946E-4	P;P;P	0.46277	0.875;0.875;0.875	B;B;B	0.40825	0.341;0.341;0.341	T	0.23119	-1.0197	9	0.37606	T	0.19	-6.109	7.7712	0.29010	0.9071:0.0:0.0929:0.0	rs17532665;rs17532665	660;660;660	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	S	660	ENSP00000350447:N660S	ENSP00000350447:N660S	N	+	2	0	SGOL2	201145293	0.436000	0.25586	0.010000	0.14722	0.022000	0.10575	2.484000	0.45242	1.126000	0.42016	0.477000	0.44152	AAC	A|0.914;G|0.086	0.086	strong		0.353	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
ADCY6	112	hgsc.bcm.edu	37	12	49176872	49176872	+	Silent	SNP	G	G	T	rs3730308	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:49176872G>T	ENST00000307885.4	-	1	1040	c.346C>A	c.(346-348)Cga>Aga	p.R116R	ADCY6_ENST00000357869.3_Silent_p.R116R|ADCY6_ENST00000550422.1_Silent_p.R116R	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	116					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)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|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)|negative regulation of neuron projection development (GO:0010977)|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)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						CAGCAGGATCGCCCACTCCTG	0.672													G|||	753	0.150359	0.2557	0.1066	5008	,	,		16341	0.001		0.1461	False		,,,				2504	0.1973				p.R116R		Atlas-SNP	.											.	ADCY6	81	.	0			c.C346A						PASS	.	G	,	1018,3388	344.4+/-308.1	116,786,1301	37.0	41.0	40.0		346,346	0.4	0.0	12	dbSNP_107	40	1331,7269	248.7+/-276.3	101,1129,3070	no	coding-synonymous,coding-synonymous	ADCY6	NM_015270.3,NM_020983.2	,	217,1915,4371	TT,TG,GG		15.4767,23.1049,18.0609	,	116/1169,116/1116	49176872	2349,10657	2203	4300	6503	SO:0001819	synonymous_variant	112	exon2			AGGATCGCCCACT		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"""Adenylate cyclases"""	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.346C>A	12.37:g.49176872G>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	74	44	0.594595	NM_020983	Q9NR75|Q9UDB0	Silent	SNP	ENST00000307885.4	37	CCDS8767.1																																																																																			G|0.834;T|0.166	0.166	strong		0.672	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983	
SUGP1	57794	hgsc.bcm.edu	37	19	19413092	19413092	+	Missense_Mutation	SNP	C	C	T	rs17751061	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19413092C>T	ENST00000247001.5	-	7	1216	c.869G>A	c.(868-870)cGt>cAt	p.R290H	SUGP1_ENST00000585763.1_Intron	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	290			R -> H (in dbSNP:rs17751061).		gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						CTGGTTCTCACGGTTGTTCTG	0.612													C|||	345	0.0688898	0.0061	0.1037	5008	,	,		16253	0.0		0.164	False		,,,				2504	0.1022				p.R290H		Atlas-SNP	.											.	SUGP1	63	.	0			c.G869A						PASS	.	C	HIS/ARG	134,4272	96.7+/-135.4	0,134,2069	183.0	151.0	162.0		869	5.0	1.0	19	dbSNP_123	162	1359,7241	266.0+/-286.5	104,1151,3045	yes	missense	SUGP1	NM_172231.3	29	104,1285,5114	TT,TC,CC		15.8023,3.0413,11.4793	probably-damaging	290/646	19413092	1493,11513	2203	4300	6503	SO:0001583	missense	57794	exon7			TTCTCACGGTTGT	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"""G patch domain containing"""	18643	protein-coding gene	gene with protein product		607992	"""splicing factor 4"""	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.869G>A	19.37:g.19413092C>T	ENSP00000247001:p.Arg290His	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	130	62	0.476923	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Missense_Mutation	SNP	ENST00000247001.5	37	CCDS12399.1	162	0.07417582417582418	7	0.014227642276422764	44	0.12154696132596685	0	0.0	111	0.14643799472295516	C	29.1	4.973750	0.92919	0.030413	0.158023	ENSG00000105705	ENST00000247001	T	0.44083	0.93	5.03	5.03	0.67393	SWAP/Surp (3);	0.000000	0.85682	D	0.000000	T	0.00468	0.0015	M	0.74881	2.28	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.00857	-1.1538	9	0.54805	T	0.06	.	16.9243	0.86172	0.0:1.0:0.0:0.0	rs17751061;rs17751061	290	Q8IWZ8	SUGP1_HUMAN	H	290	ENSP00000247001:R290H	ENSP00000247001:R290H	R	-	2	0	SUGP1	19274092	1.000000	0.71417	0.964000	0.40570	0.985000	0.73830	5.788000	0.69020	2.350000	0.79820	0.563000	0.77884	CGT	C|0.891;T|0.109	0.109	strong		0.612	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164	
TAP2	6891	hgsc.bcm.edu	37	6	32798548	32798548	+	Silent	SNP	G	G	A	rs1042116	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32798548G>A	ENST00000452392.2	-	8	1481	c.1308C>T	c.(1306-1308)aaC>aaT	p.N436N	TAP2_ENST00000485701.1_5'Flank|TAP2_ENST00000374899.4_Silent_p.N436N|TAP2_ENST00000374897.2_Silent_p.N436N			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)									Vitamin E(DB00163)	CAGCTCCCACGTTGCTGAGCA	0.522													G|||	214	0.0427316	0.0068	0.0634	5008	,	,		18305	0.0188		0.1183	False		,,,				2504	0.0235				p.N436N		Atlas-SNP	.											.	TAP2	98	.	0			c.C1308T						PASS	.	G	,	90,2932		0,90,1421	54.0	44.0	48.0		1308,1308	-2.4	1.0	6	dbSNP_86	48	586,4832		28,530,2151	no	coding-synonymous,coding-synonymous	TAP2	NM_000544.3,NM_018833.2	,	28,620,3572	AA,AG,GG		10.8158,2.9782,8.0095	,	436/704,436/654	32798548	676,7764	1511	2709	4220	SO:0001819	synonymous_variant	6891	exon8			TCCCACGTTGCTG	M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1308C>T	6.37:g.32798548G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Silent	SNP	ENST00000452392.2	37																																																																																				.	.	weak		0.522	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
TDRD6	221400	hgsc.bcm.edu	37	6	46658915	46658915	+	Missense_Mutation	SNP	G	G	A	rs140575009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46658915G>A	ENST00000316081.6	+	1	3050	c.3050G>A	c.(3049-3051)tGt>tAt	p.C1017Y	TDRD6_ENST00000544460.1_Missense_Mutation_p.C1017Y	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1017					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			CAGTTGTCATGTAGTATTACA	0.348																																					p.C1017Y		Atlas-SNP	.											.	TDRD6	205	.	0			c.G3050A						PASS	.	G	TYR/CYS,TYR/CYS	1,4405	2.1+/-5.4	0,1,2202	50.0	54.0	53.0		3050,3050	-1.1	0.0	6	dbSNP_134	53	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	TDRD6	NM_001010870.2,NM_001168359.1	194,194	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	benign,benign	1017/2097,1017/2067	46658915	6,13000	2203	4300	6503	SO:0001583	missense	221400	exon1			TGTCATGTAGTAT	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.3050G>A	6.37:g.46658915G>A	ENSP00000346065:p.Cys1017Tyr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.250495	0.00268	2.27E-4	5.81E-4	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.09073	3.02;3.02	5.36	-1.1	0.09872	Maternal tudor protein (1);	1.918670	0.01499	N	0.017422	T	0.02012	0.0063	N	0.20986	0.625	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.45731	-0.9241	10	0.51188	T	0.08	1.382	8.6227	0.33870	0.6481:0.1225:0.2294:0.0	.	1017;1017	F5H5M3;O60522	.;TDRD6_HUMAN	Y	1017	ENSP00000443299:C1017Y;ENSP00000346065:C1017Y	ENSP00000346065:C1017Y	C	+	2	0	TDRD6	46766874	0.000000	0.05858	0.000000	0.03702	0.985000	0.73830	0.088000	0.14979	-0.617000	0.05664	-0.136000	0.14681	TGT	G|0.999;A|0.001	0.001	strong		0.348	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443	
SLC6A12	6539	hgsc.bcm.edu	37	12	319111	319111	+	Silent	SNP	T	T	C	rs526690	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:319111T>C	ENST00000428720.1	-	3	785	c.42A>G	c.(40-42)gcA>gcG	p.A14A	SLC6A12_ENST00000397296.2_Silent_p.A14A|SLC6A12_ENST00000359674.4_Silent_p.A14A|SLC6A12_ENST00000536824.1_Silent_p.A14A|SLC6A12_ENST00000424061.2_Silent_p.A14A	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	14					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			CCCAGGAGACTGCAGGAGGCC	0.617													C|||	2650	0.529153	0.7284	0.4366	5008	,	,		17247	0.3075		0.5268	False		,,,				2504	0.5562				p.A14A		Atlas-SNP	.											.	SLC6A12	60	.	0			c.A42G						PASS	.	C	,,,	3130,1276	435.9+/-344.5	1113,904,186	96.0	84.0	88.0		42,42,42,42	1.2	0.2	12	dbSNP_83	88	4598,4002	554.1+/-386.4	1219,2160,921	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC6A12	NM_001122847.2,NM_001122848.2,NM_001206931.1,NM_003044.4	,,,	2332,3064,1107	CC,CT,TT		46.5349,28.9605,40.5813	,,,	14/615,14/615,14/615,14/615	319111	7728,5278	2203	4300	6503	SO:0001819	synonymous_variant	6539	exon3			GGAGACTGCAGGA	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"""Solute carriers"""	11045	protein-coding gene	gene with protein product	"""betaine/GABA transporter-1"""	603080	"""solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"""			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.42A>G	12.37:g.319111T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	154	76	0.493506	NM_001122848	A0AV52|B2R992|D3DUN8	Silent	SNP	ENST00000428720.1	37	CCDS8501.1																																																																																			T|0.434;C|0.566	0.566	strong		0.617	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044	
KLK14	43847	hgsc.bcm.edu	37	19	51584951	51584951	+	Missense_Mutation	SNP	T	T	C	rs35287116	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51584951T>C	ENST00000156499.2	-	4	316	c.98A>G	c.(97-99)cAg>cGg	p.Q33R	KLK14_ENST00000391802.1_Missense_Mutation_p.Q33R			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	33			Q -> R (in dbSNP:rs35287116). {ECO:0000269|PubMed:15489334}.		epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		CTCTTGGCTCTGTGTCATGGC	0.567													N|||	2074	0.414137	0.6717	0.2781	5008	,	,		17406	0.0952		0.3966	False		,,,				2504	0.5092				p.Q33R	GBM(117;2161 2172 2448 22911)	Atlas-SNP	.											.	KLK14	49	.	0			c.A98G						PASS	.		ARG/GLN	2268,1724		697,874,425	32.0	33.0	33.0		98	3.5	0.8	19	dbSNP_126	33	3132,5144		653,1826,1659	yes	missense	KLK14	NM_022046.4	43	1350,2700,2084	CC,CT,TT		37.8444,43.1864,44.017	benign	33/268	51584951	5400,6868	1996	4138	6134	SO:0001583	missense	43847	exon4			TGGCTCTGTGTCA	AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"""Kallikreins"""	6362	protein-coding gene	gene with protein product		606135	"""kallikrein 14"""			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.98A>G	19.37:g.51584951T>C	ENSP00000156499:p.Gln33Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_022046	A7UNK5|Q1RMZ2|Q6B089	Missense_Mutation	SNP	ENST00000156499.2	37	CCDS12823.2	747	0.34203296703296704	302	0.6138211382113821	111	0.30662983425414364	43	0.07517482517482517	291	0.3839050131926121	.	10.13	1.264708	0.23136	0.568136	0.378444	ENSG00000129437	ENST00000156499;ENST00000391802	D;D	0.92752	-3.1;-3.1	4.57	3.55	0.40652	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.48830	P	2.8600000000000847E-4	B	0.13145	0.007	B	0.09377	0.004	T	0.47923	-0.9079	8	0.23891	T	0.37	.	8.7263	0.34471	0.0:0.1015:0.0:0.8985	rs35287116;rs61747483	33	Q9P0G3	KLK14_HUMAN	R	33	ENSP00000156499:Q33R;ENSP00000375678:Q33R	ENSP00000156499:Q33R	Q	-	2	0	KLK14	56276763	0.590000	0.26815	0.771000	0.31576	0.682000	0.39822	0.745000	0.26259	0.373000	0.24621	-1.351000	0.01236	CAG	T|0.653;C|0.347	0.347	strong		0.567	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046	
OR10J5	127385	hgsc.bcm.edu	37	1	159505101	159505101	+	Missense_Mutation	SNP	G	G	A	rs35393723	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:159505101G>A	ENST00000334857.2	-	1	741	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	233			R -> W (in dbSNP:rs35393723).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					GTCTTCTTCCGGCCCTCAGCT	0.483													G|||	493	0.0984425	0.0257	0.1556	5008	,	,		21197	0.0248		0.1869	False		,,,				2504	0.1411				p.R233W		Atlas-SNP	.											.	OR10J5	68	.	0			c.C697T						PASS	.	G	TRP/ARG	223,4183	134.1+/-170.4	3,217,1983	79.0	78.0	79.0		697	-7.3	0.0	1	dbSNP_126	79	1596,7004	297.8+/-303.6	151,1294,2855	yes	missense	OR10J5	NM_001004469.1	101	154,1511,4838	AA,AG,GG		18.5581,5.0613,13.9859	benign	233/310	159505101	1819,11187	2203	4300	6503	SO:0001583	missense	127385	exon1			TCTTCCGGCCCTC		CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"""GPCR / Class A : Olfactory receptors"""	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.697C>T	1.37:g.159505101G>A	ENSP00000334441:p.Arg233Trp	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_001004469	B9EH35|Q6IFH2	Missense_Mutation	SNP	ENST00000334857.2	37	CCDS30910.1	220	0.10073260073260074	7	0.014227642276422764	52	0.143646408839779	8	0.013986013986013986	153	0.20184696569920843	G	1.851	-0.465148	0.04476	0.050613	0.185581	ENSG00000184155	ENST00000334857	T	0.00335	8.06	4.13	-7.29	0.01451	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	M	0.70595	2.14	0.80722	P	0.0	B	0.26258	0.145	B	0.23275	0.045	T	0.20472	-1.0274	8	0.72032	D	0.01	.	5.1421	0.14965	0.3364:0.0:0.3769:0.2866	rs35393723;rs61823683	233	Q8NHC4	O10J5_HUMAN	W	233	ENSP00000334441:R233W	ENSP00000334441:R233W	R	-	1	2	OR10J5	157771725	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.216000	0.02982	-2.366000	0.00606	-2.313000	0.00255	CGG	G|0.871;A|0.129	0.129	strong		0.483	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469	
FERMT1	55612	hgsc.bcm.edu	37	20	6096632	6096632	+	Silent	SNP	G	G	A	rs1056141	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:6096632G>A	ENST00000217289.4	-	3	999	c.211C>T	c.(211-213)Ctg>Ttg	p.L71L	FERMT1_ENST00000536936.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	71					cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						TGGGTTTTCAGAAGCCAGCAA	0.468													G|||	442	0.0882588	0.1339	0.0576	5008	,	,		20955	0.0794		0.0905	False		,,,				2504	0.0552				p.L71L		Atlas-SNP	.											.	FERMT1	106	.	0			c.C211T						PASS	.	G		594,3812	260.1+/-263.5	47,500,1656	50.0	51.0	51.0		211	5.5	1.0	20	dbSNP_86	51	816,7784	188.9+/-235.7	33,750,3517	no	coding-synonymous	FERMT1	NM_017671.4		80,1250,5173	AA,AG,GG		9.4884,13.4816,10.8412		71/678	6096632	1410,11596	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon3			TTTTCAGAAGCCA	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.211C>T	20.37:g.6096632G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	155	79	0.509677	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			G|0.894;A|0.106	0.106	strong		0.468	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
HLA-C	3107	hgsc.bcm.edu	37	6	31239577	31239577	+	Missense_Mutation	SNP	A	A	C	rs707911	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239577A>C	ENST00000376228.5	-	2	156	c.142T>G	c.(142-144)Tca>Gca	p.S48A	HLA-C_ENST00000383329.3_Missense_Mutation_p.S48A	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	48	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TAGCCCACTGAGATGAAGCGG	0.721													N|||	3173	0.633586	0.705	0.6671	5008	,	,		12339	0.6161		0.5934	False		,,,				2504	0.5726				p.S48A		Atlas-SNP	.											.	HLA-C	92	.	0			c.T142G						PASS	.						31.0	30.0	30.0					6																	31239577		1510	2704	4214	SO:0001583	missense	3107	exon2			CCACTGAGATGAA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.142T>G	6.37:g.31239577A>C	ENSP00000365402:p.Ser48Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	79	77	0.974684	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1346|1346	0.6163003663003663|0.6163003663003663	334|334	0.6788617886178862|0.6788617886178862	245|245	0.6767955801104972|0.6767955801104972	334|334	0.583916083916084|0.583916083916084	433|433	0.5712401055408971|0.5712401055408971	N|N	4.403|4.403	0.074476|0.074476	0.08485|0.08485	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.00007	.|9.65;9.65	2.81|2.81	-5.62|-5.62	0.02481|0.02481	.|MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|2.443560	.|0.02916	.|N	.|0.137302	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.10450	.|0.005;0.005;0.003;0.003	T|T	0.30031|0.30031	-0.9992|-0.9992	3|8	.|0.02654	.|T	.|1	.|.	1.0385|1.0385	0.01554|0.01554	0.4374:0.1213:0.2186:0.2227|0.4374:0.1213:0.2186:0.2227	rs707911;rs1050433;rs1050511;rs2308547;rs3175990;rs3179176;rs3190746;rs3200117;rs11547357;rs12721928;rs16893469|rs707911;rs1050433;rs1050511;rs2308547;rs3175990;rs3179176;rs3190746;rs3200117;rs11547357;rs12721928;rs16893469	.|48;48;48;48	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	R|A	47|48;48;48;85	.|ENSP00000365402:S48A;ENSP00000372819:S48A	.|ENSP00000365402:S48A	L|S	-|-	2|1	0|0	HLA-C|HLA-C	31347556|31347556	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-10.610000|-10.610000	0.00006|0.00006	-3.265000|-3.265000	0.00201|0.00201	-4.734000|-4.734000	0.00003|0.00003	CTC|TCA	C|0.594;A|0.406	0.594	strong		0.721	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
MST1L	11223	hgsc.bcm.edu	37	1	17086941	17086941	+	RNA	SNP	C	C	T	rs28462251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17086941C>T	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.R128H(1)|p.R133H(1)									ATCAGGGTTACGGCAGAAGTT	0.627													.|||	911	0.181909	0.1241	0.1945	5008	,	,		35567	0.2073		0.2038	False		,,,				2504	0.2025				p.R128H		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,2	.	.	2	2	Substitution - Missense(2)	endometrium(2)	c.G383A						scavenged	.																																					11223	exon4			GGGTTACGGCAGA	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17086941C>T		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	168	25	0.14881	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	15.86	2.958957	0.53400	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	0.000000	0.41938	D	0.000799	T	0.66147	0.2760	.	.	.	.	.	.	D	0.89917	1.0	D	0.97110	1.0	T	0.71925	-0.4445	6	0.72032	D	0.01	.	6.7402	0.23431	0.0:0.9998:0.0:2.0E-4	rs28462251	128	Q2TV78-2	.	H	133;128;128	.	ENSP00000439273:R128H	R	-	2	0	MST1P9	16959528	1.000000	0.71417	0.831000	0.32960	0.000000	0.00434	5.217000	0.65252	0.502000	0.28037	0.000000	0.15137	CGT	C|0.946;T|0.054	0.054	strong		0.627	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
TTC3	7267	hgsc.bcm.edu	37	21	38525356	38525356	+	Missense_Mutation	SNP	T	T	C	rs1053808	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:38525356T>C	ENST00000399017.2	+	27	5266	c.2519T>C	c.(2518-2520)aTg>aCg	p.M840T	TTC3_ENST00000355666.1_Missense_Mutation_p.M840T|TTC3_ENST00000354749.2_Missense_Mutation_p.M840T|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000540756.1_Missense_Mutation_p.M530T	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	840			M -> T (in dbSNP:rs1053808). {ECO:0000269|PubMed:9254009}.		negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AATACAGCCATGCTTCTCAAA	0.373													C|||	3145	0.627995	0.7103	0.6628	5008	,	,		14405	0.621		0.505	False		,,,				2504	0.6258				p.M840T	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.T2519C						PASS	.	C	THR/MET,THR/MET	3029,1377	451.8+/-349.8	1050,929,224	59.0	63.0	62.0		2519,2519	-0.1	0.9	21	dbSNP_86	62	4181,4419	584.6+/-391.7	1044,2093,1163	no	missense,missense	TTC3	NM_001001894.1,NM_003316.3	81,81	2094,3022,1387	CC,CT,TT		48.6163,31.2528,44.564	benign,benign	840/2026,840/2026	38525356	7210,5796	2203	4300	6503	SO:0001583	missense	7267	exon27			CAGCCATGCTTCT	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.2519T>C	21.37:g.38525356T>C	ENSP00000381981:p.Met840Thr	Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	187	185	0.989305	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	1332|1332	0.6098901098901099|0.6098901098901099	349|349	0.709349593495935|0.709349593495935	232|232	0.6408839779005525|0.6408839779005525	371|371	0.6486013986013986|0.6486013986013986	380|380	0.5013192612137203|0.5013192612137203	C|C	0.005|0.005	-2.135049|-2.135049	0.00335|0.00335	0.687472|0.687472	0.486163|0.486163	ENSG00000182670|ENSG00000182670	ENST00000414818|ENST00000418766;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	.|T;T;T;T;T;T	.|0.39056	.|2.91;2.9;3.28;1.1;3.28;3.28	5.31|5.31	-0.107|-0.107	0.13592|0.13592	.|.	.|0.373403	.|0.25307	.|N	.|0.031607	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02011|0.02011	-0.69|-0.69	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.45131|0.45131	-0.9282|-0.9282	4|9	.|0.02654	.|T	.|1	-3.43|-3.43	12.196|12.196	0.54298|0.54298	0.2818:0.6132:0.0:0.105|0.2818:0.6132:0.0:0.105	rs1053808;rs3194399;rs17229136;rs52815049;rs57260467;rs1053808|rs1053808;rs3194399;rs17229136;rs52815049;rs57260467;rs1053808	.|530;840	.|B4DSZ9;P53804	.|.;TTC3_HUMAN	R|T	204|840;822;840;530;840;840	.|ENSP00000403943:M840T;ENSP00000391891:M822T;ENSP00000347889:M840T;ENSP00000442875:M530T;ENSP00000381981:M840T;ENSP00000346791:M840T	.|ENSP00000346791:M840T	C|M	+|+	1|2	0|0	TTC3|TTC3	37447226|37447226	0.009000|0.009000	0.17119|0.17119	0.888000|0.888000	0.34837|0.34837	0.231000|0.231000	0.25187|0.25187	0.014000|0.014000	0.13333|0.13333	-0.472000|-0.472000	0.06881|0.06881	-1.123000|-1.123000	0.02005|0.02005	TGC|ATG	T|0.427;C|0.573	0.573	strong		0.373	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
CEACAM1	634	hgsc.bcm.edu	37	19	43013363	43013363	+	Silent	SNP	A	A	G	rs11666350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:43013363A>G	ENST00000161559.6	-	9	1613	c.1479T>C	c.(1477-1479)taT>taC	p.Y493Y	CEACAM1_ENST00000488639.2_5'UTR|CEACAM1_ENST00000403444.3_3'UTR|CEACAM1_ENST00000351134.3_Silent_p.Y219Y|CEACAM1_ENST00000403461.1_3'UTR|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000599389.1_3'UTR|CEACAM1_ENST00000352591.5_Silent_p.Y397Y|LIPE-AS1_ENST00000457234.2_RNA|CEACAM1_ENST00000358394.3_Silent_p.Y428Y|CEACAM1_ENST00000308072.4_3'UTR	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	493					angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	TCAGGGTAGAATAAGTAACTT	0.443													a|||	789	0.157548	0.1256	0.255	5008	,	,		20205	0.2123		0.0964	False		,,,				2504	0.138				p.Y493Y		Atlas-SNP	.											.	CEACAM1	43	.	0			c.T1479C						PASS	.		,,,,,	468,3938	224.3+/-240.5	34,400,1769	170.0	156.0	161.0		,1191,1284,,,1479	-0.0	0.4	19	dbSNP_120	161	812,7788	189.6+/-236.3	31,750,3519	yes	utr-3,coding-synonymous,coding-synonymous,utr-3,utr-3,coding-synonymous	CEACAM1	NM_001024912.2,NM_001184813.1,NM_001184815.1,NM_001184816.1,NM_001205344.1,NM_001712.4	,,,,,	65,1150,5288	GG,GA,AA		9.4419,10.6219,9.8416	,,,,,	,397/431,428/462,,,493/527	43013363	1280,11726	2203	4300	6503	SO:0001819	synonymous_variant	634	exon9			GGTAGAATAAGTA	M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.1479T>C	19.37:g.43013363A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	175	70	0.4	NM_001712	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Silent	SNP	ENST00000161559.6	37	CCDS12609.1																																																																																			A|0.874;G|0.126	0.126	strong		0.443	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712	
OR5M9	390162	hgsc.bcm.edu	37	11	56230120	56230120	+	Missense_Mutation	SNP	G	G	A	rs61902868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56230120G>A	ENST00000279791.1	-	1	757	c.758C>T	c.(757-759)cCc>cTc	p.P253L		NM_001004743.1	NP_001004743.1	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M, member 9	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	36	Esophageal squamous(21;0.00448)					CATGAAGATGGGGGTCCCATA	0.517													a|||	326	0.0650958	0.112	0.0432	5008	,	,		17831	0.001		0.0934	False		,,,				2504	0.0542				p.P253L		Atlas-SNP	.											.	OR5M9	75	.	0			c.C758T						PASS	.	A	LEU/PRO	426,3976	786.5+/-414.8	19,388,1794	57.0	52.0	54.0		758	3.2	0.1	11	dbSNP_129	54	694,7898	787.5+/-407.6	35,624,3637	yes	missense	OR5M9	NM_001004743.1	98	54,1012,5431	AA,AG,GG		8.0773,9.6774,8.6194	benign	253/311	56230120	1120,11874	2201	4296	6497	SO:0001583	missense	390162	exon1			AAGATGGGGGTCC	AB065747	CCDS31531.1	11q11	2012-08-09			ENSG00000150269	ENSG00000150269		"""GPCR / Class A : Olfactory receptors"""	15294	protein-coding gene	gene with protein product							Standard	NM_001004743		Approved		uc010rjj.2	Q8NGP3	OTTHUMG00000166874	ENST00000279791.1:c.758C>T	11.37:g.56230120G>A	ENSP00000279791:p.Pro253Leu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_001004743	Q6IEW5|Q96RB9	Missense_Mutation	SNP	ENST00000279791.1	37	CCDS31531.1	155	0.07097069597069597	72	0.14634146341463414	13	0.03591160220994475	0	0.0	70	0.09234828496042216	A	0.004	-2.280342	0.00254	0.096774	0.080773	ENSG00000150269	ENST00000279791	T	0.00031	8.89	4.39	3.16	0.36331	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39083	N	0.001472	T	0.00012	0.0000	N	0.00009	-3.075	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28170	-1.0052	9	0.02654	T	1	-11.5265	5.6082	0.17391	0.7322:0.1708:0.097:0.0	rs61902868	253	Q8NGP3	OR5M9_HUMAN	L	253	ENSP00000279791:P253L	ENSP00000279791:P253L	P	-	2	0	OR5M9	55986696	0.000000	0.05858	0.101000	0.21167	0.014000	0.08584	-0.177000	0.09796	0.644000	0.30656	-0.442000	0.05670	CCC	G|0.922;A|0.078	0.078	strong		0.517	OR5M9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391638.1	NM_001004743	
ENPP2	5168	hgsc.bcm.edu	37	8	120575249	120575249	+	Missense_Mutation	SNP	C	C	T	rs61758149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:120575249C>T	ENST00000075322.6	-	24	2327	c.2269G>A	c.(2269-2271)Gtg>Atg	p.V757M	ENPP2_ENST00000259486.6_Missense_Mutation_p.V809M|ENPP2_ENST00000522167.1_Missense_Mutation_p.V392M|ENPP2_ENST00000427067.2_Missense_Mutation_p.V778M|ENPP2_ENST00000522826.1_Missense_Mutation_p.V782M	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	757					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CTGCCTTCCACGTACCTGAAA	0.443													C|||	7	0.00139776	0.0	0.0014	5008	,	,		20547	0.0		0.002	False		,,,				2504	0.0041				p.V809M	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.G2425A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	120.0	101.0	108.0		2269,2344,2425	5.7	1.0	8	dbSNP_129	108	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense,missense	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	21,21,21	0,14,6489	TT,TC,CC		0.1512,0.0227,0.1076	possibly-damaging,possibly-damaging,possibly-damaging	757/864,782/889,809/916	120575249	14,12992	2203	4300	6503	SO:0001583	missense	5168	exon25			CTTCCACGTACCT	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2269G>A	8.37:g.120575249C>T	ENSP00000075322:p.Val757Met	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	21.3	4.123821	0.77436	2.27E-4	0.001512	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522167;ENST00000522826;ENST00000075322	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	5.67	5.67	0.87782	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.000000	0.46442	D	0.000285	T	0.51517	0.1679	L	0.49778	1.585	0.80722	D	1	D;D;D;D;D	0.89917	0.997;0.993;0.999;0.998;1.0	D;P;D;P;D	0.67548	0.952;0.894;0.919;0.896;0.919	T	0.46261	-0.9204	10	0.56958	D	0.05	.	19.7743	0.96385	0.0:1.0:0.0:0.0	rs61758149	295;782;757;809;392	B4DJD3;E9PHP7;Q13822;Q13822-2;E5RIA2	.;.;ENPP2_HUMAN;.;.	M	809;778;392;782;757	ENSP00000259486:V809M;ENSP00000403315:V778M;ENSP00000429476:V392M;ENSP00000428291:V782M;ENSP00000075322:V757M	ENSP00000075322:V757M	V	-	1	0	ENPP2	120644430	1.000000	0.71417	0.993000	0.49108	0.949000	0.60115	5.281000	0.65609	2.663000	0.90544	0.557000	0.71058	GTG	C|0.998;T|0.002	0.002	strong		0.443	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
SIGLEC11	114132	hgsc.bcm.edu	37	19	50463670	50463670	+	Missense_Mutation	SNP	T	T	G	rs77553517	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50463670T>G	ENST00000447370.2	-	3	559	c.469A>C	c.(469-471)Aag>Cag	p.K157Q	CTC-326K19.6_ENST00000451973.1_5'Flank|SIGLEC11_ENST00000426971.2_Missense_Mutation_p.K157Q	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	157					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		TCAGGCTTCTTAGTCAGGGCT	0.607																																					p.K157Q		Atlas-SNP	.											.	SIGLEC11	70	.	0			c.A469C						PASS	.	G	GLN/LYS,GLN/LYS	840,2990		167,506,1242	35.0	54.0	48.0		469,469	-0.6	0.0	19	dbSNP_131	48	1503,7087		54,1395,2846	yes	missense,missense	SIGLEC11	NM_001135163.1,NM_052884.2	53,53	221,1901,4088	GG,GT,TT		17.4971,21.9321,18.8647	benign,benign	157/603,157/699	50463670	2343,10077	1915	4295	6210	SO:0001583	missense	114132	exon3			GCTTCTTAGTCAG	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.469A>C	19.37:g.50463670T>G	ENSP00000412361:p.Lys157Gln	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	172	53	0.30814	NM_052884		Missense_Mutation	SNP	ENST00000447370.2	37	CCDS12790.2	363	0.1662087912087912	102	0.2073170731707317	48	0.13259668508287292	112	0.1958041958041958	101	0.13324538258575197	G	0.021	-1.424972	0.01126	0.219321	0.174971	ENSG00000161640	ENST00000447370;ENST00000458019	T	0.03124	4.04	3.28	-0.577	0.11727	Immunoglobulin-like fold (1);	0.404011	0.21813	N	0.068733	T	0.00012	0.0000	N	0.00036	-2.54	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38950	-0.9637	9	0.16420	T	0.52	.	1.9279	0.03321	0.1102:0.1707:0.3701:0.349	.	157;157	Q96RL6-2;Q96RL6	.;SIG11_HUMAN	Q	157	ENSP00000412361:K157Q	ENSP00000412361:K157Q	K	-	1	0	SIGLEC11	55155482	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-0.174000	0.09839	-0.459000	0.07013	-0.217000	0.12591	AAG	T|0.840;G|0.160	0.160	strong		0.607	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884	
VN1R4	317703	hgsc.bcm.edu	37	19	53770746	53770746	+	Missense_Mutation	SNP	C	C	A	rs140031028	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53770746C>A	ENST00000311170.4	-	1	226	c.173G>T	c.(172-174)cGc>cTc	p.R58L	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	58			R -> L (in allele VN1R4*4). {ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)	p.R58L(1)		central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	22				GBM - Glioblastoma multiforme(134;0.00294)		TCCTTTACAGCGGAGAGCTAA	0.453										HNSCC(26;0.072)																											p.R58L		Atlas-SNP	.											VN1R4,mouth,carcinoma,0,1	VN1R4	65	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G173T						PASS	.						37.0	38.0	38.0					19																	53770746		2203	4297	6500	SO:0001583	missense	317703	exon1			TTACAGCGGAGAG	AY114733	CCDS33099.1	19q13.42	2012-08-22			ENSG00000228567	ENSG00000228567		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19871	protein-coding gene	gene with protein product						12123587	Standard	NM_173857		Approved	V1RL4	uc010ydu.2	Q7Z5H5		ENST00000311170.4:c.173G>T	19.37:g.53770746C>A	ENSP00000310856:p.Arg58Leu	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	258	28	0.108527	NM_173857	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Missense_Mutation	SNP	ENST00000311170.4	37	CCDS33099.1	172	0.07875457875457875	80	0.16260162601626016	30	0.08287292817679558	19	0.033216783216783216	43	0.05672823218997362	A	0.012	-1.657194	0.00779	.	.	ENSG00000228567	ENST00000311170	T	0.05447	3.44	2.27	1.24	0.21308	GPCR, rhodopsin-like superfamily (1);	0.307925	0.17948	N	0.156612	T	0.00012	0.0000	N	0.00003	-3.44	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40572	-0.9556	10	0.02654	T	1	.	3.7525	0.08572	0.6401:0.2234:0.1365:0.0	.	58	Q7Z5H5	VN1R4_HUMAN	L	58	ENSP00000310856:R58L	ENSP00000310856:R58L	R	-	2	0	VN1R4	58462558	0.028000	0.19301	0.000000	0.03702	0.001000	0.01503	3.077000	0.50089	-0.026000	0.13895	-0.397000	0.06425	CGC	A|0.055;C|0.945;G|0.001	0.055	strong		0.453	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857	
MUC20	200958	hgsc.bcm.edu	37	3	195456561	195456561	+	Missense_Mutation	SNP	C	C	G	rs3762739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:195456561C>G	ENST00000447234.2	+	3	2138	c.2012C>G	c.(2011-2013)tCc>tGc	p.S671C	MUC20_ENST00000445522.2_Missense_Mutation_p.S636C|MUC20_ENST00000436408.1_Missense_Mutation_p.S671C|MUC20_ENST00000320736.6_Missense_Mutation_p.S500C	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	671	Interaction with MET.		S -> C (in dbSNP:rs3762739).		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		AGTGTGGCTTCCCCGGAAGAC	0.587																																					p.S500C		Atlas-SNP	.											.	MUC20	84	.	0			c.C1499G						PASS	.						45.0	43.0	44.0					3																	195456561		1997	4174	6171	SO:0001583	missense	200958	exon4			TGGCTTCCCCGGA	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.2012C>G	3.37:g.195456561C>G	ENSP00000414350:p.Ser671Cys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	88	29	0.329545	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		532|532	0.24358974358974358|0.24358974358974358	101|101	0.20528455284552846|0.20528455284552846	98|98	0.27071823204419887|0.27071823204419887	229|229	0.40034965034965037|0.40034965034965037	104|104	0.13720316622691292|0.13720316622691292	c|c	15.24|15.24	2.775028|2.775028	0.49786|0.49786	.|.	.|.	ENSG00000176945|ENSG00000176945	ENST00000423938|ENST00000381954;ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	.|T;T;T;T	.|0.38401	.|1.66;1.98;2.23;1.14	4.63|4.63	4.63|4.63	0.57726|0.57726	.|.	.|0.187733	.|0.26528	.|N	.|0.023880	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.39245|0.39245	1.2|1.2	0.31261|0.31261	P|P	0.692931|0.692931	.|D	.|0.89917	.|1.0	.|D	.|0.79108	.|0.992	T|T	0.42582|0.42582	-0.9443|-0.9443	4|9	.|0.66056	.|D	.|0.02	-14.3302|-14.3302	12.8995|12.8995	0.58117|0.58117	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs3762739;rs59929965|rs3762739;rs59929965	.|500	.|E9PH32	.|.	L|C	82|482;671;500;671;636	.|ENSP00000414350:S671C;ENSP00000325431:S500C;ENSP00000396774:S671C;ENSP00000405629:S636C	.|ENSP00000325431:S500C	F|S	+|+	3|2	2|0	MUC20|MUC20	196942232|196942232	0.960000|0.960000	0.32886|0.32886	0.966000|0.966000	0.40874|0.40874	0.236000|0.236000	0.25371|0.25371	3.051000|3.051000	0.49885|0.49885	2.396000|2.396000	0.81511|0.81511	0.558000|0.558000	0.71614|0.71614	TTC|TCC	C|0.780;G|0.220	0.220	strong		0.587	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
MUC16	94025	hgsc.bcm.edu	37	19	9071916	9071916	+	Missense_Mutation	SNP	G	G	A	rs35346115	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9071916G>A	ENST00000397910.4	-	3	15733	c.15530C>T	c.(15529-15531)aCt>aTt	p.T5177I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5179	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AATGTTTGTAGTCTCAGAGGA	0.478													G|||	49	0.00978435	0.0008	0.0216	5008	,	,		20472	0.001		0.0268	False		,,,				2504	0.0051				p.T5177I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C15530T						PASS	.	G	ILE/THR	17,3971		0,17,1977	283.0	266.0	272.0		15530	0.6	0.0	19	dbSNP_126	272	253,8085		5,243,3921	yes	missense	MUC16	NM_024690.2	89	5,260,5898	AA,AG,GG		3.0343,0.4263,2.1905	probably-damaging	5177/14508	9071916	270,12056	1994	4169	6163	SO:0001583	missense	94025	exon3			TTTGTAGTCTCAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15530C>T	19.37:g.9071916G>A	ENSP00000381008:p.Thr5177Ile	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	207	92	0.444444	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	28	0.01282051282051282	0	0.0	6	0.016574585635359115	1	0.0017482517482517483	21	0.027704485488126648	g	2.171	-0.389853	0.04932	0.004263	0.030343	ENSG00000181143	ENST00000397910	T	0.23147	1.92	1.65	0.563	0.17296	.	.	.	.	.	T	0.11281	0.0275	L	0.55481	1.735	.	.	.	D	0.65815	0.995	P	0.51945	0.685	T	0.24621	-1.0155	8	0.87932	D	0	.	4.0586	0.09827	0.2293:0.0:0.7707:0.0	rs35346115	5177	B5ME49	.	I	5177	ENSP00000381008:T5177I	ENSP00000381008:T5177I	T	-	2	0	MUC16	8932916	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.111000	0.03303	0.269000	0.21961	0.121000	0.15741	ACT	G|0.980;A|0.020	0.020	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
WASL	8976	hgsc.bcm.edu	37	7	123388732	123388732	+	Silent	SNP	G	G	A	rs1054706	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:123388732G>A	ENST00000223023.4	-	1	389	c.57C>T	c.(55-57)tcC>tcT	p.S19S	RP11-390E23.6_ENST00000607957.1_RNA	NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	19					actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TGAGCAACAGGGACCCCACGT	0.667													G|||	2390	0.477236	0.2973	0.428	5008	,	,		12049	0.5565		0.4384	False		,,,				2504	0.7137				p.S19S		Atlas-SNP	.											.	WASL	70	.	0			c.C57T						PASS	.	G		1472,2934	460.5+/-352.6	265,942,996	43.0	40.0	41.0		57	2.8	1.0	7	dbSNP_129	41	4037,4563	543.2+/-384.4	943,2151,1206	no	coding-synonymous	WASL	NM_003941.2		1208,3093,2202	AA,AG,GG		46.9419,33.409,42.3574		19/506	123388732	5509,7497	2203	4300	6503	SO:0001819	synonymous_variant	8976	exon1			CAACAGGGACCCC	D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.57C>T	7.37:g.123388732G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	58	56	0.965517	NM_003941	A1JUI9|Q7Z746	Silent	SNP	ENST00000223023.4	37	CCDS34743.1																																																																																			G|0.567;A|0.433	0.433	strong		0.667	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941	
GGTLC2	91227	hgsc.bcm.edu	37	22	22989281	22989281	+	Silent	SNP	T	T	C	rs3966363	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:22989281T>C	ENST00000480559.1	+	2	234	c.234T>C	c.(232-234)gaT>gaC	p.D78D	POM121L1P_ENST00000402027.1_RNA|GGTLC2_ENST00000448514.1_Silent_p.D78D	NM_199127.2	NP_954578.2	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase light chain 2	78					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)	gamma-glutamyltransferase activity (GO:0003840)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)		ATGAAATGGATGACTTCAGCT	0.597													.|||	873	0.174321	0.0711	0.1095	5008	,	,		9629	0.2143		0.2296	False		,,,				2504	0.2618				p.D78D		Atlas-SNP	.											.	GGTLC2	20	.	0			c.T234C						PASS	.	T		307,4099		10,287,1906	111.0	111.0	111.0		234		0.0	22	dbSNP_108	111	1347,7251		175,997,3127	no	coding-synonymous	GGTLC2	NM_199127.2		185,1284,5033	CC,CT,TT		15.6664,6.9678,12.7192		78/219	22989281	1654,11350	2203	4299	6502	SO:0001819	synonymous_variant	91227	exon2			AATGGATGACTTC	X98922	CCDS13802.2	22q11.21	2008-03-25	2008-03-10	2008-03-10	ENSG00000100121	ENSG00000100121		"""Gamma-glutamyltransferases"""	18596	protein-coding gene	gene with protein product		612339	"""gamma-glutamyltransferase-like 4"""	GGTL4		9074928, 18357469	Standard	NM_199127		Approved		uc010gtt.2	Q14390	OTTHUMG00000151177	ENST00000480559.1:c.234T>C	22.37:g.22989281T>C		Somatic	370	1	0.0027027		WXS	Illumina HiSeq	Phase_I	31	11	0.354839	NM_199127	A1A516|A2VCM9|Q5NV76|Q6ISH0	Silent	SNP	ENST00000480559.1	37	CCDS13802.2																																																																																			T|0.877;C|0.123	0.123	strong		0.597	GGTLC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321662.1	NM_199127	
POLR1E	64425	hgsc.bcm.edu	37	9	37493588	37493588	+	Silent	SNP	C	C	T	rs10758434	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:37493588C>T	ENST00000377798.4	+	6	548	c.435C>T	c.(433-435)acC>acT	p.T145T	POLR1E_ENST00000442009.2_Silent_p.T75T|POLR1E_ENST00000377792.3_Silent_p.T207T	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	0					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		TTGGTACCACCAAACAGAAGC	0.468													C|||	1078	0.215256	0.1694	0.3112	5008	,	,		24276	0.244		0.2018	False		,,,				2504	0.1933				p.T145T	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.C435T						PASS	.	C		806,3600	321.0+/-296.9	71,664,1468	124.0	112.0	116.0		435	6.0	1.0	9	dbSNP_120	116	1872,6728	334.9+/-321.2	201,1470,2629	no	coding-synonymous	POLR1E	NM_022490.1		272,2134,4097	TT,TC,CC		21.7674,18.2932,20.5905		145/420	37493588	2678,10328	2203	4300	6503	SO:0001819	synonymous_variant	64425	exon6			TACCACCAAACAG	AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"""RNA polymerase subunits"""	17631	protein-coding gene	gene with protein product	"""RNA polymerase I associated factor 53"""		"""polymerase (RNA) I associated factor 1"""	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.435C>T	9.37:g.37493588C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	106	60	0.566038	NM_022490	O75395|Q5JTE3	Silent	SNP	ENST00000377798.4	37	CCDS6611.1																																																																																			C|0.796;T|0.204	0.204	strong		0.468	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490	
BTNL2	56244	hgsc.bcm.edu	37	6	32372863	32372863	+	Missense_Mutation	SNP	A	A	T	rs28362682	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32372863A>T	ENST00000374993.1	-	2	279	c.280T>A	c.(280-282)Tgg>Agg	p.W94R	BTNL2_ENST00000429232.2_Missense_Mutation_p.W94R|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000454136.3_Missense_Mutation_p.W94R|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000374995.3_Missense_Mutation_p.W94R	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	94	Ig-like V-type 1.		W -> R (in dbSNP:rs28362682).			integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CACTCTACCCAGCCTCTGTAC	0.532													G|||	672	0.134185	0.1369	0.1369	5008	,	,		20650	0.1984		0.0974	False		,,,				2504	0.1002				p.W94R		Atlas-SNP	.											.	BTNL2	50	.	0			c.T280A						PASS	.	G	ARG/TRP	340,2682		12,316,1183	314.0	286.0	296.0		280	3.0	0.9	6	dbSNP_125	296	428,4990		15,398,2296	yes	missense	BTNL2	NM_019602.1	101	27,714,3479	TT,TA,AA		7.8996,11.2508,9.0995	benign	94/456	32372863	768,7672	1511	2709	4220	SO:0001583	missense	56244	exon2			CTACCCAGCCTCT	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.280T>A	6.37:g.32372863A>T	ENSP00000364132:p.Trp94Arg	Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	318	166	0.522013	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		290	0.13278388278388278	55	0.11178861788617886	51	0.1408839779005525	107	0.18706293706293706	77	0.10158311345646438	G	0.009	-1.848563	0.00563	0.112508	0.078996	ENSG00000204290	ENST00000468270;ENST00000374995;ENST00000374993;ENST00000429232;ENST00000446536	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	4.91	2.97	0.34412	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.182486	0.27004	N	0.021409	T	0.01387	0.0045	N	0.00001	-3.66	0.44908	P	0.0020769999999999955	B	0.02656	0.0	B	0.01281	0.0	T	0.40515	-0.9559	9	0.02654	T	1	.	6.1886	0.20512	0.0879:0.0:0.4834:0.4287	rs28362682	94	Q9UIR0	BTNL2_HUMAN	R	94;94;94;94;93	ENSP00000364134:W94R;ENSP00000364132:W94R;ENSP00000411166:W94R;ENSP00000388434:W93R	ENSP00000364132:W94R	W	-	1	0	BTNL2	32480841	0.139000	0.22563	0.946000	0.38457	0.016000	0.09150	0.970000	0.29383	0.811000	0.34303	-0.143000	0.13931	TGG	A|0.894;T|0.106	0.106	strong		0.532	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
OR13C5	138799	hgsc.bcm.edu	37	9	107361002	107361002	+	Silent	SNP	C	C	G	rs78992791	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:107361002C>G	ENST00000374779.2	-	1	786	c.693G>C	c.(691-693)tcG>tcC	p.S231S		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	231						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						TTCTCCCCTCCGAAGAGCTAA	0.428													G|||	5	0.000998403	0.0	0.0014	5008	,	,		22312	0.0		0.001	False		,,,				2504	0.0031				p.S231S		Atlas-SNP	.											OR13C5,right_upper_lobe,carcinoma,0,2	OR13C5	60	2	0			c.G693C						PASS	.						123.0	114.0	117.0					9																	107361002		2203	4300	6503	SO:0001819	synonymous_variant	138799	exon1			CCCCTCCGAAGAG		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.693G>C	9.37:g.107361002C>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	218	109	0.5	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			C|0.999;G|0.001	0.001	strong		0.428	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
GAS8	2622	hgsc.bcm.edu	37	16	90103659	90103659	+	Missense_Mutation	SNP	G	G	A	rs17178299	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:90103659G>A	ENST00000268699.4	+	7	898	c.776G>A	c.(775-777)cGg>cAg	p.R259Q	GAS8_ENST00000536122.1_Missense_Mutation_p.R234Q|GAS8_ENST00000540721.1_3'UTR	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	259			R -> Q (in dbSNP:rs17178299).		cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		GAGGACATGCGGAAGAAGGAG	0.637													G|||	240	0.0479233	0.0038	0.013	5008	,	,		21050	0.1488		0.0507	False		,,,				2504	0.0256				p.R259Q		Atlas-SNP	.											.	GAS8	29	.	0			c.G776A						PASS	.	G	GLN/ARG	50,4346	50.2+/-85.5	0,50,2148	58.0	56.0	57.0		776	4.4	1.0	16	dbSNP_123	57	516,8084	144.7+/-200.5	15,486,3799	yes	missense	GAS8	NM_001481.2	43	15,536,5947	AA,AG,GG		6.0,1.1374,4.3552	possibly-damaging	259/479	90103659	566,12430	2198	4300	6498	SO:0001583	missense	2622	exon7			ACATGCGGAAGAA	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.776G>A	16.37:g.90103659G>A	ENSP00000268699:p.Arg259Gln	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	192	95	0.494792	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	100	0.045787545787545784	3	0.006097560975609756	7	0.019337016574585635	47	0.08216783216783216	43	0.05672823218997362	G	19.36	3.812005	0.70797	0.011374	0.06	ENSG00000141013	ENST00000536122;ENST00000268699;ENST00000540721	T;T	0.46451	0.87;0.87	5.49	4.44	0.53790	.	0.258952	0.37955	N	0.001866	T	0.01558	0.0050	L	0.45352	1.415	0.22918	P	0.99856096	P;P	0.46656	0.882;0.774	B;B	0.40228	0.323;0.126	T	0.15321	-1.0441	8	.	.	.	-37.1049	3.5798	0.07947	0.3568:0.0:0.6432:0.0	rs17178299;rs17178299	230;259	B7Z1X3;O95995	.;GAS8_HUMAN	Q	234;259;230	ENSP00000440977:R234Q;ENSP00000268699:R259Q	.	R	+	2	0	GAS8	88631160	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.732000	0.68563	2.578000	0.87016	0.563000	0.77884	CGG	G|0.958;A|0.042	0.042	strong		0.637	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
GSTM3	2947	hgsc.bcm.edu	37	1	110279701	110279701	+	Missense_Mutation	SNP	C	C	T	rs7483	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:110279701C>T	ENST00000540225.1	-	9	980	c.670G>A	c.(670-672)Gta>Ata	p.V224I	RP4-735C1.4_ENST00000431955.1_RNA|GSTM3_ENST00000488824.1_5'UTR|GSTM3_ENST00000361066.2_Missense_Mutation_p.V224I|GSTM3_ENST00000256594.3_Missense_Mutation_p.V224I			P21266	GSTM3_HUMAN	glutathione S-transferase mu 3 (brain)	224			V -> I (in dbSNP:rs7483). {ECO:0000269|PubMed:15489334}.		cellular detoxification of nitrogen compound (GO:0070458)|establishment of blood-nerve barrier (GO:0008065)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|skin(1)	9		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)|Vitamin E(DB00163)	GCTCAGCATACAGGCTTGTTG	0.478													C|||	1806	0.360623	0.0628	0.4035	5008	,	,		20552	0.7252		0.2962	False		,,,				2504	0.4233				p.V224I		Atlas-SNP	.											.	GSTM3	21	.	0			c.G670A						PASS	.	C	ILE/VAL	493,3913	228.8+/-243.5	29,435,1739	93.0	81.0	85.0		670	-5.2	0.0	1	dbSNP_52	85	2550,6050	416.3+/-352.1	377,1796,2127	yes	missense	GSTM3	NM_000849.4	29	406,2231,3866	TT,TC,CC		29.6512,11.1893,23.3969	benign	224/226	110279701	3043,9963	2203	4300	6503	SO:0001583	missense	2947	exon9			AGCATACAGGCTT	BC000088	CCDS812.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134202	ENSG00000134202	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4635	protein-coding gene	gene with protein product		138390	"""glutathione S-transferase M3 (brain)"""			2345169	Standard	NM_000849		Approved	GST5	uc001dyo.2	P21266	OTTHUMG00000011640	ENST00000540225.1:c.670G>A	1.37:g.110279701C>T	ENSP00000444978:p.Val224Ile	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	218	103	0.472477	NM_000849	O60550|Q96HA3	Missense_Mutation	SNP	ENST00000540225.1	37	CCDS812.1	829	0.37957875457875456	42	0.08536585365853659	132	0.36464088397790057	420	0.7342657342657343	235	0.3100263852242744	C	0.011	-1.711288	0.00712	0.111893	0.296512	ENSG00000134202	ENST00000540225;ENST00000256594;ENST00000361066	T;T;T	0.01397	4.94;4.94;4.94	5.29	-5.25	0.02781	.	1.179520	0.05914	N	0.632318	T	0.00144	0.0004	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45440	-0.9261	9	0.02654	T	1	-16.1483	1.767	0.03004	0.2593:0.3854:0.1323:0.223	rs7483;rs3167664;rs17845187;rs17857997;rs52802282;rs58618587;rs7483	230;224	Q59EJ5;P21266	.;GSTM3_HUMAN	I	224	ENSP00000444978:V224I;ENSP00000256594:V224I;ENSP00000354357:V224I	ENSP00000256594:V224I	V	-	1	0	GSTM3	110081224	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.859000	0.01657	-0.786000	0.04516	-0.982000	0.02568	GTA	C|0.700;T|0.300	0.300	strong		0.478	GSTM3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032182.1	NM_000849	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249183	71249183	+	Missense_Mutation	SNP	T	T	C	rs55921335	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:71249183T>C	ENST00000398534.3	+	1	113	c.82T>C	c.(82-84)Tgc>Cgc	p.C28R		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	28	9 X 4 AA repeats of C-C-X-P.		C -> R (in dbSNP:rs55921335).	SC -> GCGGCGSSR (in Ref. 1; CAA07188). {ECO:0000305}.		keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						TGGCTCTAGCTGCTGTGTGCC	0.677													t|||	1658	0.33107	0.27	0.4323	5008	,	,		12402	0.4772		0.3141	False		,,,				2504	0.2086				p.C28R		Atlas-SNP	.											KRTAP5-8,colon,carcinoma,0,1	KRTAP5-8	28	1	0			c.T82C						scavenged	.	T	ARG/CYS	1293,3107		205,883,1112	78.0	101.0	93.0		82	1.6	0.9	11	dbSNP_129	93	2482,6104		366,1750,2177	no	missense	KRTAP5-8	NM_021046.2	180	571,2633,3289	CC,CT,TT		28.9075,29.3864,29.0698	probably-damaging	28/188	71249183	3775,9211	2200	4293	6493	SO:0001583	missense	57830	exon1			TCTAGCTGCTGTG	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.82T>C	11.37:g.71249183T>C	ENSP00000420723:p.Cys28Arg	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	107	38	0.35514	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	37	CCDS41683.1	861	0.3942307692307692	142	0.2886178861788618	159	0.43922651933701656	307	0.5367132867132867	253	0.3337730870712401	t	0.655	-0.808097	0.02819	0.293864	0.289075	ENSG00000241233	ENST00000398534	T	0.03242	4.0	1.57	1.57	0.23409	.	.	.	.	.	T	0.00012	0.0000	M	0.90542	3.125	0.24078	P	0.9959551	D	0.76494	0.999	D	0.74023	0.982	T	0.45131	-0.9282	8	0.72032	D	0.01	.	3.3369	0.07105	0.0:0.225:0.0:0.775	rs55921335	28	O75690	KRA58_HUMAN	R	28	ENSP00000420723:C28R	ENSP00000420723:C28R	C	+	1	0	KRTAP5-8	70926831	0.997000	0.39634	0.853000	0.33588	0.060000	0.15804	2.213000	0.42844	0.974000	0.38366	0.421000	0.28195	TGC	T|0.650;C|0.350	0.350	strong		0.677	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
NUGGC	389643	hgsc.bcm.edu	37	8	27925204	27925204	+	Missense_Mutation	SNP	T	T	C	rs4732620	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27925204T>C	ENST00000413272.2	-	6	680	c.538A>G	c.(538-540)Agc>Ggc	p.S180G	NUGGC_ENST00000341513.6_Missense_Mutation_p.S180G	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	180			S -> G (in dbSNP:rs4732620).		cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										TCTTCTCTGCTCAGCTCCTCC	0.542													C|||	2927	0.584465	0.6089	0.6095	5008	,	,		19722	0.6101		0.5159	False		,,,				2504	0.5777				p.S180G		Atlas-SNP	.											.	.	.	.	0			c.A538G						PASS	.	C	GLY/SER	2457,1663		755,947,358	79.0	81.0	80.0		538	0.7	0.0	8	dbSNP_111	80	4583,3859		1257,2069,895	yes	missense	C8orf80	NM_001010906.1	56	2012,3016,1253	CC,CT,TT		45.7119,40.3641,43.958	benign	180/797	27925204	7040,5522	2060	4221	6281	SO:0001583	missense	389643	exon6			CTCTGCTCAGCTC	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"""speckled-like pattern in the germinal center"""		"""chromosome 8 open reading frame 80"""	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.538A>G	8.37:g.27925204T>C	ENSP00000408697:p.Ser180Gly	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	167	72	0.431138	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	37	CCDS47833.1	1250	0.5723443223443223	308	0.6260162601626016	204	0.56353591160221	352	0.6153846153846154	386	0.5092348284960422	C	0.333	-0.954775	0.02285	0.596359	0.542881	ENSG00000189233	ENST00000413272;ENST00000341513	D;D	0.96992	-4.2;-4.2	6.1	0.743	0.18347	Dynamin, GTPase domain (1);	0.667758	0.14497	N	0.315964	T	0.00012	0.0000	N	0.01454	-0.855	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46331	-0.9199	9	0.20519	T	0.43	-6.2663	1.2115	0.01905	0.1437:0.3801:0.14:0.3362	rs4732620;rs52834159;rs58100087;rs4732620	180	Q68CJ6	SLIP_HUMAN	G	180	ENSP00000408697:S180G;ENSP00000345031:S180G	ENSP00000345031:S180G	S	-	1	0	C8orf80	27981123	0.000000	0.05858	0.000000	0.03702	0.259000	0.26198	-0.491000	0.06474	-0.083000	0.12618	-0.176000	0.13171	AGC	T|0.419;C|0.581	0.581	strong		0.542	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
ITGA2	3673	hgsc.bcm.edu	37	5	52347369	52347369	+	Silent	SNP	C	C	T	rs1126643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:52347369C>T	ENST00000296585.5	+	7	902	c.759C>T	c.(757-759)ttC>ttT	p.F253F		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	253	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				CAAACACATTCGGAGCAATTC	0.328													C|||	1691	0.33766	0.2806	0.4424	5008	,	,		16165	0.2827		0.4026	False		,,,				2504	0.3303				p.F253F		Atlas-SNP	.											.	ITGA2	211	.	0			c.C759T	GRCh37	CM993453	ITGA2	M	rs1126643	PASS	.	C		1343,3063	448.1+/-348.6	209,925,1069	108.0	105.0	106.0		759	4.9	1.0	5	dbSNP_86	106	3414,5186	503.8+/-376.0	651,2112,1537	no	coding-synonymous	ITGA2	NM_002203.3		860,3037,2606	TT,TC,CC		39.6977,30.4812,36.5754		253/1182	52347369	4757,8249	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon7			CACATTCGGAGCA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.759C>T	5.37:g.52347369C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			C|0.629;T|0.371	0.371	strong		0.328	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
RPS6KA2	6196	hgsc.bcm.edu	37	6	166862233	166862233	+	Silent	SNP	T	T	C	rs2230730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:166862233T>C	ENST00000265678.4	-	14	1534	c.1311A>G	c.(1309-1311)acA>acG	p.T437T	RPS6KA2_ENST00000481261.2_Silent_p.T348T|RPS6KA2_ENST00000503859.1_Silent_p.T445T|RPS6KA2_ENST00000405189.3_Silent_p.T348T|RPS6KA2_ENST00000510118.1_Silent_p.T462T	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	437	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		ACTCGGTGTCTGTGGCTTTAT	0.582													C|||	996	0.198882	0.1876	0.2723	5008	,	,		24814	0.0764		0.3082	False		,,,				2504	0.1759				p.T445T		Atlas-SNP	.											RPS6KA2_ENST00000503859,NS,carcinoma,-1,2	RPS6KA2	212	2	0			c.A1335G						PASS	.	C	,	931,3475	736.1+/-410.7	99,733,1371	238.0	158.0	185.0		1335,1311	-8.8	0.6	6	dbSNP_120	185	2587,6013	688.1+/-404.3	387,1813,2100	no	coding-synonymous,coding-synonymous	RPS6KA2	NM_001006932.1,NM_021135.4	,	486,2546,3471	CC,CT,TT		30.0814,21.1303,27.0491	,	445/742,437/734	166862233	3518,9488	2203	4300	6503	SO:0001819	synonymous_variant	6196	exon15			GGTGTCTGTGGCT	L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"""ribosomal protein S6 kinase, 90kD, polypeptide 2"""			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.1311A>G	6.37:g.166862233T>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	203	88	0.433498	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Silent	SNP	ENST00000265678.4	37	CCDS5294.1																																																																																			T|0.764;C|0.236;A|0.000	0.236	strong		0.582	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	
SPPL2C	162540	hgsc.bcm.edu	37	17	43924219	43924219	+	Silent	SNP	T	T	C	rs12373124	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43924219T>C	ENST00000329196.5	+	1	1964	c.1947T>C	c.(1945-1947)caT>caC	p.H649H	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	649						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										AGCTGGGCCATGTCCATGCCC	0.637													t|||	431	0.0860623	0.0151	0.1571	5008	,	,		18869	0.001		0.2396	False		,,,				2504	0.0613				p.H649H		Atlas-SNP	.											.	.	.	.	0			c.T1947C						PASS	.	C		204,4202	124.9+/-162.1	5,194,2004	38.0	38.0	38.0		1947	-8.8	0.0	17	dbSNP_120	38	1927,6673	331.1+/-319.5	222,1483,2595	yes	coding-synonymous	IMP5	NM_175882.2		227,1677,4599	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	22.407,4.63,16.3847		649/685	43924219	2131,10875	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			GGGCCATGTCCAT		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1947T>C	17.37:g.43924219T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			A|0.854;G|0.146	.	strong		0.637	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
SLC16A7	9194	hgsc.bcm.edu	37	12	60173356	60173356	+	Missense_Mutation	SNP	A	A	T	rs3763980	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:60173356A>T	ENST00000261187.4	+	5	1497	c.1333A>T	c.(1333-1335)Acc>Tcc	p.T445S	SLC16A7_ENST00000547379.1_Missense_Mutation_p.T445S|SLC16A7_ENST00000552432.1_Missense_Mutation_p.T445S|SLC16A7_ENST00000543448.1_Missense_Mutation_p.T346S|SLC16A7_ENST00000552024.1_Missense_Mutation_p.T445S	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	445			T -> S (in dbSNP:rs3763980). {ECO:0000269|Ref.2}.		lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	AAGGCAGAAGACCAGAGAATC	0.423													A|||	1227	0.245008	0.2088	0.1801	5008	,	,		15272	0.3175		0.3002	False		,,,				2504	0.2086				p.T445S		Atlas-SNP	.											.	SLC16A7	82	.	0			c.A1333T						PASS	.	A	SER/THR	934,3472	351.1+/-311.1	92,750,1361	96.0	82.0	87.0		1333	-2.5	0.0	12	dbSNP_107	87	2055,6545	355.9+/-330.1	263,1529,2508	yes	missense	SLC16A7	NM_004731.3	58	355,2279,3869	TT,TA,AA		23.8953,21.1984,22.9817	benign	445/479	60173356	2989,10017	2203	4300	6503	SO:0001583	missense	9194	exon6			CAGAAGACCAGAG	AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"""Solute carriers"""	10928	protein-coding gene	gene with protein product		603654	"""solute carrier family 16 (monocarboxylic acid transporters), member 7"""			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000261187.4:c.1333A>T	12.37:g.60173356A>T	ENSP00000261187:p.Thr445Ser	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	108	60	0.555556	NM_001270622	Q8NEM3|Q9UPB3	Missense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	602	0.27564102564102566	105	0.21341463414634146	86	0.23756906077348067	191	0.3339160839160839	220	0.29023746701846964	A	0.008	-1.902371	0.00512	0.211984	0.238953	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000261187;ENST00000543448	T;T;T;T;T	0.16196	2.49;2.49;2.49;2.49;2.36	1.88	-2.51	0.06365	.	1.506430	0.03748	N	0.256134	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.44436	-0.9328	8	.	.	.	.	2.9296	0.05795	0.393:0.2573:0.3497:0.0	rs3763980;rs17571543;rs56973174;rs3763980	445	O60669	MOT2_HUMAN	S	445;445;445;445;346	ENSP00000449547:T445S;ENSP00000448071:T445S;ENSP00000448742:T445S;ENSP00000261187:T445S;ENSP00000443731:T346S	.	T	+	1	0	SLC16A7	58459623	0.503000	0.26115	0.000000	0.03702	0.010000	0.07245	1.138000	0.31491	-0.635000	0.05531	-0.456000	0.05471	ACC	T|0.245;N|0.000	0.245	strong		0.423	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731	
ZNF143	7702	hgsc.bcm.edu	37	11	9549142	9549142	+	Silent	SNP	G	G	A	rs11607631	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:9549142G>A	ENST00000396602.2	+	16	2018	c.1899G>A	c.(1897-1899)acG>acA	p.T633T	ZNF143_ENST00000299606.2_Silent_p.T605T|ZNF143_ENST00000530463.1_Silent_p.T632T|ZNF143_ENST00000396597.3_Silent_p.T602T|ZNF143_ENST00000396604.1_Silent_p.T632T	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	633					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		AAGGAGAAACGCCAGGGTTGG	0.463													G|||	146	0.0291534	0.0	0.0259	5008	,	,		17894	0.0		0.0716	False		,,,				2504	0.0573				p.T633T		Atlas-SNP	.											.	ZNF143	38	.	0			c.G1899A						PASS	.	G		66,4336	61.7+/-98.7	0,66,2135	96.0	92.0	94.0		1899	-11.4	0.5	11	dbSNP_120	94	643,7945	165.5+/-217.6	20,603,3671	no	coding-synonymous	ZNF143	NM_003442.5		20,669,5806	AA,AG,GG		7.4872,1.4993,5.458		633/639	9549142	709,12281	2201	4294	6495	SO:0001819	synonymous_variant	7702	exon16			AGAAACGCCAGGG	U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"""Zinc fingers, C2H2-type"""	12928	protein-coding gene	gene with protein product		603433	"""zinc finger protein 143 (clone pHZ-1)"""				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.1899G>A	11.37:g.9549142G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_003442	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Silent	SNP	ENST00000396602.2	37	CCDS7799.2																																																																																			G|0.953;A|0.047	0.047	strong		0.463	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442	
DXO	1797	hgsc.bcm.edu	37	6	31938412	31938412	+	Missense_Mutation	SNP	G	G	T	rs17207867	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31938412G>T	ENST00000375349.3	-	4	1194	c.783C>A	c.(781-783)caC>caA	p.H261Q	STK19_ENST00000375331.2_5'Flank|DXO_ENST00000337523.5_Missense_Mutation_p.H261Q|DXO_ENST00000478221.1_5'UTR|DXO_ENST00000375356.3_Missense_Mutation_p.H261Q|STK19_ENST00000375333.2_5'Flank			O77932	DXO_HUMAN	decapping exoribonuclease	261			H -> Q (in dbSNP:rs17207867). {ECO:0000269|PubMed:14574404}.		metabolic process (GO:0008152)|mRNA catabolic process (GO:0006402)|nuclear mRNA surveillance (GO:0071028)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA destabilization (GO:0050779)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|magnesium ion binding (GO:0000287)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA pyrophosphohydrolase activity (GO:0034353)										GGCCAGGGCTGTGCATCTCCT	0.602													G|||	594	0.11861	0.1694	0.0764	5008	,	,		17477	0.0347		0.0974	False		,,,				2504	0.1881				p.H261Q		Atlas-SNP	.											.	DOM3Z	20	.	0			c.C783A						PASS	.	G	GLN/HIS	444,2578		34,376,1101	72.0	75.0	74.0		783	3.6	1.0	6	dbSNP_123	74	496,4922		35,426,2248	yes	missense	DOM3Z	NM_005510.3	24	69,802,3349	TT,TG,GG		9.1547,14.6923,11.1374	benign	261/397	31938412	940,7500	1511	2709	4220	SO:0001583	missense	1797	exon4			AGGGCTGTGCATC	AF059252	CCDS4732.1	6p21.3	2013-09-11	2013-09-11	2013-09-11	ENSG00000204348	ENSG00000204348			2992	protein-coding gene	gene with protein product		605996	"""DOM-3 (C. elegans) homolog Z"", ""dom-3 homolog Z (C. elegans)"""	DOM3Z		9799600, 23523372	Standard	NM_005510		Approved		uc003nyp.1	O77932	OTTHUMG00000031272	ENST00000375349.3:c.783C>A	6.37:g.31938412G>T	ENSP00000364498:p.His261Gln	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	101	35	0.346535	NM_005510	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Missense_Mutation	SNP	ENST00000375349.3	37	CCDS4732.1	220|220	0.10073260073260074|0.10073260073260074	94|94	0.1910569105691057|0.1910569105691057	26|26	0.0718232044198895|0.0718232044198895	22|22	0.038461538461538464|0.038461538461538464	78|78	0.10290237467018469|0.10290237467018469	G|G	14.38|14.38	2.518585|2.518585	0.44763|0.44763	0.146923|0.146923	0.091547|0.091547	ENSG00000204348|ENSG00000204348	ENST00000337523;ENST00000375349;ENST00000375356|ENST00000495340	T;T;T|.	0.39787|.	1.06;1.06;1.06|.	4.46|4.46	3.59|3.59	0.41128|0.41128	RAI1-like (1);|.	0.109458|.	0.64402|.	D|.	0.000006|.	T|T	0.18383|0.18383	0.0441|0.0441	N|N	0.25426|0.25426	0.745|0.745	0.29311|0.29311	P|P	0.868011|0.868011	B|.	0.25272|.	0.122|.	B|.	0.18871|.	0.023|.	T|T	0.08994|0.08994	-1.0695|-1.0695	9|4	0.12430|.	T|.	0.62|.	-25.2902|-25.2902	6.6042|6.6042	0.22716|0.22716	0.0938:0.0:0.7283:0.1779|0.0938:0.0:0.7283:0.1779	rs17207867;rs59177784|rs17207867;rs59177784	261|.	O77932|.	DOM3Z_HUMAN|.	Q|K	261|68	ENSP00000337759:H261Q;ENSP00000364498:H261Q;ENSP00000364505:H261Q|.	ENSP00000337759:H261Q|.	H|T	-|-	3|2	2|0	DOM3Z|DOM3Z	32046391|32046391	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.570000|2.570000	0.45981|0.45981	1.088000|1.088000	0.41272|0.41272	0.561000|0.561000	0.74099|0.74099	CAC|ACA	A|0.000;C|0.000;G|0.895;T|0.105	0.105	strong		0.602	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3		
TNC	3371	hgsc.bcm.edu	37	9	117808785	117808785	+	Missense_Mutation	SNP	T	T	A	rs2104772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:117808785T>A	ENST00000350763.4	-	17	5440	c.5029A>T	c.(5029-5031)Ata>Tta	p.I1677L	TNC_ENST00000537320.1_Intron|TNC_ENST00000340094.3_Missense_Mutation_p.I1313L|TNC_ENST00000535648.1_Missense_Mutation_p.I1222L|TNC_ENST00000341037.4_Missense_Mutation_p.I1495L|TNC_ENST00000345230.3_Intron|TNC_ENST00000346706.3_Missense_Mutation_p.I1131L|TNC_ENST00000423613.2_Intron|TNC_ENST00000542877.1_Missense_Mutation_p.I1314L|TNC_ENST00000481475.1_5'Flank	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1677	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> L (in dbSNP:rs2104772). {ECO:0000269|PubMed:1704365, ECO:0000269|PubMed:1719530, ECO:0000269|PubMed:2466295, ECO:0000269|PubMed:7531707}.		bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						AGACCTGTTATGTCCCTGGTA	0.453													T|||	2409	0.48103	0.6006	0.4755	5008	,	,		21554	0.4514		0.4503	False		,,,				2504	0.3855				p.I1677L		Atlas-SNP	.											.	TNC	282	.	0			c.A5029T	GRCh37	CM053428	TNC	M	rs2104772	PASS	.	T	LEU/ILE	2482,1924	625.1+/-394.5	715,1052,436	189.0	182.0	184.0	http://www.ncbi.nlm.nih.gov/omim/608584,613207|http://omim.org/entry/613207|http://omim.org/entry/608584	5029	3.4	1.0	9	dbSNP_96	184	3705,4895	529.0+/-381.5	804,2097,1399	yes	missense	TNC	NM_002160.3	5	1519,3149,1835	AA,AT,TT		43.0814,43.6677,47.5704	benign	1677/2202	117808785	6187,6819	2203	4300	6503	SO:0001583	missense	3371	exon17			CTGTTATGTCCCT		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5029A>T	9.37:g.117808785T>A	ENSP00000265131:p.Ile1677Leu	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	287	287	1	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	1045|1045	0.4784798534798535|0.4784798534798535	291|291	0.5914634146341463|0.5914634146341463	161|161	0.4447513812154696|0.4447513812154696	258|258	0.45104895104895104|0.45104895104895104	335|335	0.4419525065963061|0.4419525065963061	T|T	5.997|5.997	0.367903|0.367903	0.11352|0.11352	0.563323|0.563323	0.430814|0.430814	ENSG00000041982|ENSG00000041982	ENST00000544972|ENST00000340094;ENST00000535648;ENST00000346706;ENST00000350763;ENST00000341037;ENST00000542877	.|T;T;T;T;T;T	.|0.52983	.|0.64;0.64;0.64;0.64;0.64;0.64	5.81|5.81	3.42|3.42	0.39159|0.39159	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.112647	.|0.64402	.|D	.|0.000014	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.52011|0.52011	1.625|1.625	0.09310|0.09310	P|P	1.0|1.0	.|B	.|0.11235	.|0.004	.|B	.|0.20955	.|0.032	T|T	0.45963|0.45963	-0.9225|-0.9225	4|9	.|0.02654	.|T	.|1	.|.	8.6288|8.6288	0.33906|0.33906	0.0:0.2099:0.0:0.7901|0.0:0.2099:0.0:0.7901	rs2104772;rs3207863;rs52807719;rs58058251;rs2104772|rs2104772;rs3207863;rs52807719;rs58058251;rs2104772	.|1677	.|P24821	.|TENA_HUMAN	L|L	239|1313;1222;1131;1677;1495;1314	.|ENSP00000344400:I1313L;ENSP00000438152:I1222L;ENSP00000344555:I1131L;ENSP00000265131:I1677L;ENSP00000339553:I1495L;ENSP00000442242:I1314L	.|ENSP00000344400:I1313L	H|I	-|-	2|1	0|0	TNC|TNC	116848606|116848606	0.631000|0.631000	0.27164|0.27164	0.997000|0.997000	0.53966|0.53966	0.998000|0.998000	0.95712|0.95712	0.633000|0.633000	0.24598|0.24598	0.435000|0.435000	0.26365|0.26365	0.460000|0.460000	0.39030|0.39030	CAT|ATA	T|0.519;A|0.481	0.481	strong		0.453	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
C17orf97	400566	hgsc.bcm.edu	37	17	263613	263613	+	Missense_Mutation	SNP	C	C	A	rs71369083|rs71145728|rs184547508	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:263613C>A	ENST00000360127.6	+	2	995	c.979C>A	c.(979-981)Ccc>Acc	p.P327T	C17orf97_ENST00000571106.1_Intron|AC108004.3_ENST00000466740.2_RNA	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	357	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.									breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						GGGCTTCCACCCCGACCCCAA	0.706																																					p.P327T		Atlas-SNP	.											C17orf97_ENST00000360127,NS,carcinoma,-2,1	C17orf97	76	1	0			c.C979A						scavenged	.						15.0	19.0	18.0					17																	263613		2187	4274	6461	SO:0001583	missense	400566	exon2			TTCCACCCCGACC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.979C>A	17.37:g.263613C>A	ENSP00000353245:p.Pro327Thr	Somatic	158	3	0.0189873		WXS	Illumina HiSeq	Phase_I	207	28	0.135266	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Missense_Mutation	SNP	ENST00000360127.6	37	CCDS32519.2	128	0.05860805860805861	32	0.06504065040650407	24	0.06629834254143646	27	0.0472027972027972	45	0.059366754617414245	C	0.001	-3.707992	0.00005	.	.	ENSG00000187624	ENST00000360127	T	0.32023	1.47	2.05	-4.1	0.03940	.	.	.	.	.	T	0.00666	0.0022	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04320	-1.0960	9	0.22109	T	0.4	.	2.459	0.04537	0.2976:0.4433:0.1475:0.1116	.	327	Q6ZQX7-4	.	T	327	ENSP00000353245:P327T	ENSP00000353245:P327T	P	+	1	0	C17orf97	263959	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.155000	0.00284	-4.249000	0.00062	-4.503000	0.00005	CCC	C|0.942;A|0.058	0.058	strong		0.706	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
BRSK2	9024	hgsc.bcm.edu	37	11	1411572	1411572	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1411572C>T	ENST00000528841.1	+	1	442	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W	BRSK2_ENST00000531197.1_Missense_Mutation_p.R20W|BRSK2_ENST00000308219.9_Missense_Mutation_p.R20W|BRSK2_ENST00000526678.1_Missense_Mutation_p.R20W|BRSK2_ENST00000308230.5_Missense_Mutation_p.R20W			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	20	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		TGGGCCCTACCGGCTGGAGAA	0.796																																					p.R20W		Atlas-SNP	.											.	BRSK2	97	.	0			c.C58T						PASS	.						4.0	6.0	6.0					11																	1411572		1915	4006	5921	SO:0001583	missense	9024	exon1			CCCTACCGGCTGG	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"""serine/threonine kinase 29"""	609236	"""chromsosome 11 open reading frame 7"""	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.58C>T	11.37:g.1411572C>T	ENSP00000432000:p.Arg20Trp	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	23	13	0.565217	NM_001256629	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	37	CCDS58107.1	.	.	.	.	.	.	.	.	.	.	c	17.64	3.440051	0.63067	.	.	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	1.54	1.54	0.23209	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.78868	0.4351	M	0.86573	2.825	0.80722	D	1	D;D;D;D	0.67145	0.996;0.994;0.988;0.985	P;P;P;P	0.61722	0.721;0.606;0.893;0.828	T	0.79960	-0.1583	9	0.87932	D	0	.	8.6612	0.34093	0.0:1.0:0.0:0.0	.	20;20;20;20	Q8IWQ3-4;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;BRSK2_HUMAN;.	W	20	ENSP00000310697:R20W;ENSP00000431152:R20W;ENSP00000310805:R20W;ENSP00000432000:R20W;ENSP00000433370:R20W	ENSP00000310697:R20W	R	+	1	2	BRSK2	1368148	0.920000	0.31207	1.000000	0.80357	0.993000	0.82548	0.856000	0.27818	0.855000	0.35359	0.409000	0.27619	CGG	.	.	none		0.796	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957	
OR8I2	120586	hgsc.bcm.edu	37	11	55861297	55861297	+	Missense_Mutation	SNP	A	A	G	rs117967749	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55861297A>G	ENST00000302124.2	+	1	545	c.514A>G	c.(514-516)Agc>Ggc	p.S172G		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	172						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					CTGTGATTCCAGCATCAATCA	0.443													A|||	182	0.0363419	0.003	0.0432	5008	,	,		21537	0.001		0.0944	False		,,,				2504	0.0532				p.S172G		Atlas-SNP	.											.	OR8I2	119	.	0			c.A514G						PASS	.	A	GLY/SER	58,4344	55.5+/-91.7	0,58,2143	161.0	151.0	155.0		514	0.2	0.0	11	dbSNP_132	155	690,7902	169.6+/-220.9	34,622,3640	yes	missense	OR8I2	NM_001003750.1	56	34,680,5783	GG,GA,AA		8.0307,1.3176,5.7565	benign	172/311	55861297	748,12246	2201	4296	6497	SO:0001583	missense	120586	exon1			GATTCCAGCATCA	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.514A>G	11.37:g.55861297A>G	ENSP00000303864:p.Ser172Gly	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	145	58	0.4	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	37	CCDS31517.1	82	0.037545787545787544	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	68	0.08970976253298153	A	6.840	0.524184	0.13066	0.013176	0.080307	ENSG00000172154	ENST00000302124	T	0.00054	8.8	4.33	0.175	0.15045	GPCR, rhodopsin-like superfamily (1);	2.086290	0.02733	U	0.115390	T	0.00012	0.0000	N	0.05441	-0.05	0.09310	N	1	B	0.14438	0.01	B	0.19666	0.026	T	0.30765	-0.9967	10	0.87932	D	0	0.0088	1.491	0.02456	0.4671:0.1462:0.0856:0.3012	.	172	Q8N0Y5	OR8I2_HUMAN	G	172	ENSP00000303864:S172G	ENSP00000303864:S172G	S	+	1	0	OR8I2	55617873	0.000000	0.05858	0.000000	0.03702	0.184000	0.23303	0.450000	0.21762	-0.177000	0.10690	0.362000	0.22060	AGC	A|0.950;G|0.050	0.050	strong		0.443	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
WDR81	124997	hgsc.bcm.edu	37	17	1630584	1630584	+	Silent	SNP	A	A	G	rs7221974	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1630584A>G	ENST00000409644.1	+	1	2331	c.2331A>G	c.(2329-2331)ctA>ctG	p.L777L	WDR81_ENST00000419248.1_Intron|WDR81_ENST00000446363.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000437219.2_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	777					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TGGGTGTCCTATTGGCAGAGA	0.667													G|||	1495	0.298522	0.2648	0.2219	5008	,	,		18563	0.4861		0.2614	False		,,,				2504	0.2434				p.L777L		Atlas-SNP	.											.	WDR81	180	.	0			c.A2331G						PASS	.	G	,,,	374,1010		49,276,367	23.0	25.0	25.0		,2331,,	-3.6	0.8	17	dbSNP_116	25	838,2340		105,628,856	no	intron,coding-synonymous,intron,intron	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	154,904,1223	GG,GA,AA		26.3688,27.0231,26.5673	,,,	,777/1942,,	1630584	1212,3350	692	1589	2281	SO:0001819	synonymous_variant	124997	exon1			TGTCCTATTGGCA	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.2331A>G	17.37:g.1630584A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	42	25	0.595238	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			A|0.680;G|0.320	0.320	strong		0.667	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
TCTN3	26123	hgsc.bcm.edu	37	10	97447373	97447373	+	Silent	SNP	A	A	T	rs10786229	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:97447373A>T	ENST00000371217.5	-	4	626	c.603T>A	c.(601-603)acT>acA	p.T201T	TCTN3_ENST00000430368.2_Intron|TCTN3_ENST00000265993.9_Silent_p.T219T|TCTN3_ENST00000371209.5_Silent_p.T201T			Q6NUS6	TECT3_HUMAN	tectonic family member 3	201					apoptotic process (GO:0006915)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(3)|endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		GTGGTGATTGAGTTTGGAATG	0.448													A|||	2127	0.42472	0.4236	0.255	5008	,	,		17807	0.7133		0.3469	False		,,,				2504	0.3292				p.T201T		Atlas-SNP	.											.	TCTN3	66	.	0			c.T603A						PASS	.	A	,	1829,2577	534.8+/-374.1	384,1061,758	100.0	96.0	97.0		,603	-2.4	0.0	10	dbSNP_120	97	2746,5854	438.1+/-358.8	449,1848,2003	no	intron,coding-synonymous	TCTN3	NM_001143973.1,NM_015631.5	,	833,2909,2761	TT,TA,AA		31.9302,41.5116,35.1761	,	,201/608	97447373	4575,8431	2203	4300	6503	SO:0001819	synonymous_variant	26123	exon4			TGATTGAGTTTGG	AK098295	CCDS31258.2, CCDS44461.1	10q24.1	2014-01-28	2007-08-20	2007-08-20	ENSG00000119977	ENSG00000119977		"""Tectonic proteins"""	24519	protein-coding gene	gene with protein product		613847	"""chromosome 10 open reading frame 61"""	C10orf61		12975309	Standard	NM_015631		Approved	DKFZP564D116, TECT3, JBTS18	uc001klb.4	Q6NUS6	OTTHUMG00000018814	ENST00000371217.5:c.603T>A	10.37:g.97447373A>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	59	44	0.745763	NM_015631	A6NIC8|B0QZ90|B4DR81|Q6P7P3|Q6UW27|Q6ZQQ0|Q8N7K1|Q8NBQ0|Q96GF7|Q9Y3U1	Silent	SNP	ENST00000371217.5	37	CCDS31258.2																																																																																			A|0.624;T|0.376	0.376	strong		0.448	TCTN3-009	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000471858.1	NM_015631	
AKAP13	11214	hgsc.bcm.edu	37	15	86123988	86123988	+	Missense_Mutation	SNP	G	G	A	rs4075254	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86123988G>A	ENST00000394518.2	+	7	2784	c.2689G>A	c.(2689-2691)Gtg>Atg	p.V897M	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.V897M	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	897			V -> M (in dbSNP:rs4075254). {ECO:0000269|PubMed:11546812, ECO:0000269|Ref.3}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CCTGCAAAGTGTGGGTAAGGC	0.488													G|||	2915	0.582069	0.5469	0.6182	5008	,	,		21370	0.5784		0.6153	False		,,,				2504	0.5736				p.V897M	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G2689A						PASS	.	G	MET/VAL,MET/VAL	2605,1799	634.4+/-396.2	778,1049,375	71.0	71.0	71.0		2689,2689	3.8	0.0	15	dbSNP_108	71	5540,3058	654.5+/-401.2	1798,1944,557	yes	missense,missense	AKAP13	NM_006738.4,NM_007200.3	21,21	2576,2993,932	AA,AG,GG		35.5664,40.8492,37.3558	possibly-damaging,possibly-damaging	897/2818,897/2814	86123988	8145,4857	2202	4299	6501	SO:0001583	missense	11214	exon7			CAAAGTGTGGGTA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.2689G>A	15.37:g.86123988G>A	ENSP00000378026:p.Val897Met	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	1277	0.5847069597069597	261	0.5304878048780488	221	0.6104972375690608	334	0.583916083916084	461	0.6081794195250659	G	11.23	1.577444	0.28180	0.591508	0.644336	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.18338	2.22;2.22	5.68	3.8	0.43715	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	8.000000000008E-6	B;B	0.19073	0.02;0.033	B;B	0.17979	0.009;0.02	T	0.30736	-0.9968	8	0.59425	D	0.04	.	7.9598	0.30064	0.1812:0.0:0.8188:0.0	rs4075254;rs60325649;rs4075254	897;897	Q12802;Q12802-2	AKP13_HUMAN;.	M	897;897;896;896	ENSP00000354718:V897M;ENSP00000378026:V897M	ENSP00000354718:V897M	V	+	1	0	AKAP13	83924992	0.001000	0.12720	0.004000	0.12327	0.016000	0.09150	0.662000	0.25038	1.397000	0.46682	0.655000	0.94253	GTG	G|0.388;N|0.001	.	strong		0.488	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
MBD3L3	653657	hgsc.bcm.edu	37	19	7056571	7056571	+	Missense_Mutation	SNP	G	G	T	rs111605618	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7056571G>T	ENST00000333843.4	-	2	423	c.389C>A	c.(388-390)gCt>gAt	p.A130D		NM_001164425.1	NP_001157897.1	A6NE82	MB3L3_HUMAN	methyl-CpG binding domain protein 3-like 3	130					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.A130D(1)		central_nervous_system(1)|lung(5)|stomach(1)	7						CTCAGCACCAGCCCTGTCCAG	0.637													-|||	838	0.167332	0.118	0.2522	5008	,	,		41704	0.0417		0.2962	False		,,,				2504	0.1708				p.A130D		Atlas-SNP	.											MBD3L3,NS,haematopoietic_neoplasm,0,3	MBD3L3	12	3	1	Substitution - Missense(1)	stomach(1)	c.C389A						scavenged	.						52.0	62.0	59.0					19																	7056571		692	1591	2283	SO:0001583	missense	653657	exon2			GCACCAGCCCTGT		CCDS45944.1	19p13.2	2014-04-01			ENSG00000182315	ENSG00000182315			37205	protein-coding gene	gene with protein product							Standard	NM_001164425		Approved		uc021uns.1	A6NE82	OTTHUMG00000181976	ENST00000333843.4:c.389C>A	19.37:g.7056571G>T	ENSP00000333183:p.Ala130Asp	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	177	116	0.655367	NM_001164425		Missense_Mutation	SNP	ENST00000333843.4	37	CCDS45944.1	.	.	.	.	.	.	.	.	.	.	.	3.926	-0.017102	0.07681	.	.	ENSG00000182315	ENST00000333843	.	.	.	0.742	-1.48	0.08745	.	.	.	.	.	T	0.32615	0.0835	L	0.43923	1.385	0.80722	P	0.0	.	.	.	.	.	.	T	0.33752	-0.9856	5	0.42905	T	0.14	-12.4801	2.5805	0.04817	0.2531:0.3037:0.4432:0.0	.	.	.	.	D	130	.	ENSP00000333183:A130D	A	-	2	0	MBD3L3	7007571	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.980000	0.03770	-1.270000	0.02433	-1.511000	0.00944	GCT	G|0.747;T|0.253	0.253	strong		0.637	MBD3L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458500.1	NM_001164425	
OR51Q1	390061	hgsc.bcm.edu	37	11	5443739	5443739	+	Silent	SNP	T	T	C	rs2736587	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5443739T>C	ENST00000300778.4	+	1	399	c.309T>C	c.(307-309)ttT>ttC	p.F103F	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGCTCAGTTTTTCTTCCTTC	0.517													C|||	2272	0.453674	0.2799	0.3991	5008	,	,		22512	0.7024		0.3986	False		,,,				2504	0.5276				p.F103F		Atlas-SNP	.											.	OR51Q1	79	.	0			c.T309C						PASS	.	C		1332,3070	694.1+/-405.8	203,926,1072	157.0	138.0	144.0		309	-10.0	0.0	11	dbSNP_100	144	3373,5221	641.9+/-399.7	676,2021,1600	no	coding-synonymous	OR51Q1	NM_001004757.2		879,2947,2672	CC,CT,TT		39.2483,30.259,36.2034		103/318	5443739	4705,8291	2201	4297	6498	SO:0001819	synonymous_variant	390061	exon1			TCAGTTTTTCTTC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.309T>C	11.37:g.5443739T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	197	101	0.51269	NM_001004757	B2RNN1	Silent	SNP	ENST00000300778.4	37	CCDS31381.1																																																																																			T|0.601;C|0.399	0.399	strong		0.517	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
STK17B	9262	hgsc.bcm.edu	37	2	197004439	197004439	+	Silent	SNP	A	A	G	rs1054537	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:197004439A>G	ENST00000263955.4	-	7	1027	c.741T>C	c.(739-741)atT>atC	p.I247I	STK17B_ENST00000409228.1_Silent_p.I247I	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	247	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(10)	15			OV - Ovarian serous cystadenocarcinoma(117;0.141)			TAACTTGAGAAATATTGAGGT	0.338													A|||	3521	0.703075	0.5794	0.7305	5008	,	,		13926	0.9028		0.6481	False		,,,				2504	0.7014				p.I247I		Atlas-SNP	.											.	STK17B	28	.	0			c.T741C						PASS	.	A		2569,1837	634.2+/-396.2	724,1121,358	106.0	108.0	107.0		741	4.0	1.0	2	dbSNP_86	107	5350,3242	647.5+/-400.4	1662,2026,608	no	coding-synonymous	STK17B	NM_004226.3		2386,3147,966	GG,GA,AA		37.7328,41.6931,39.0752		247/373	197004439	7919,5079	2203	4296	6499	SO:0001819	synonymous_variant	9262	exon7			TTGAGAAATATTG	AB011421	CCDS2315.1	2q33.1	2008-02-05	2007-02-12		ENSG00000081320	ENSG00000081320			11396	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 2"""	604727	"""serine/threonine kinase 17b (apoptosis-inducing)"""			9786912	Standard	NM_004226		Approved	DRAK2	uc002utk.3	O94768	OTTHUMG00000132735	ENST00000263955.4:c.741T>C	2.37:g.197004439A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	203	106	0.522168	NM_004226		Silent	SNP	ENST00000263955.4	37	CCDS2315.1																																																																																			A|0.349;G|0.651	0.651	strong		0.338	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2		
NOTCH4	4855	hgsc.bcm.edu	37	6	32188603	32188603	+	Silent	SNP	C	C	T	rs520803	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32188603C>T	ENST00000375023.3	-	5	990	c.852G>A	c.(850-852)caG>caA	p.Q284Q		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	284	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		Q -> H (in dbSNP:rs520803).		cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CATTCTGACACTGGTGGCTGA	0.557													T|||	1341	0.267772	0.208	0.2594	5008	,	,		18909	0.1935		0.3519	False		,,,				2504	0.3446				p.Q284Q		Atlas-SNP	.											NOTCH4,left_upper_lobe,carcinoma,-1,1	NOTCH4	201	1	0			c.G852A						PASS	.	T		942,3464	736.4+/-410.8	91,760,1352	114.0	104.0	107.0		852	-5.3	0.0	6	dbSNP_83	107	2753,5847	679.8+/-403.6	449,1855,1996	no	coding-synonymous	NOTCH4	NM_004557.3		540,2615,3348	TT,TC,CC		32.0116,21.3799,28.41		284/2004	32188603	3695,9311	2203	4300	6503	SO:0001819	synonymous_variant	4855	exon5			CTGACACTGGTGG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.852G>A	6.37:g.32188603C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	114	47	0.412281	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			T|0.292;C|0.708	0.292	strong		0.557	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
KMO	8564	hgsc.bcm.edu	37	1	241712134	241712134	+	Silent	SNP	C	C	T	rs11556464	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:241712134C>T	ENST00000366559.4	+	2	371	c.60C>T	c.(58-60)ggC>ggT	p.G20G	KMO_ENST00000366558.3_Silent_p.G20G|KMO_ENST00000484628.1_3'UTR|KMO_ENST00000366557.4_Silent_p.G20G	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)											NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			tCTAGGTTGGCTCATTACAAG	0.348													C|||	1869	0.373203	0.528	0.4236	5008	,	,		15923	0.2788		0.3042	False		,,,				2504	0.2965				p.G20G		Atlas-SNP	.											.	KMO	69	.	0			c.C60T						PASS	.	C		2194,2212	583.2+/-385.8	540,1114,549	66.0	68.0	68.0		60	3.0	1.0	1	dbSNP_120	68	2833,5767	443.9+/-360.5	465,1903,1932	no	coding-synonymous	KMO	NM_003679.3		1005,3017,2481	TT,TC,CC		32.9419,49.7957,38.6514		20/487	241712134	5027,7979	2203	4300	6503	SO:0001819	synonymous_variant	8564	exon2			GGTTGGCTCATTA	AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	1.14.13.9		6381	protein-coding gene	gene with protein product		603538				9237672	Standard	NM_003679		Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.60C>T	1.37:g.241712134C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	20	15	0.75	NM_003679		Silent	SNP	ENST00000366559.4	37	CCDS1618.1																																																																																			C|0.616;T|0.384	0.384	strong		0.348	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095612.1	NM_003679	
PTPRU	10076	hgsc.bcm.edu	37	1	29631909	29631909	+	Missense_Mutation	SNP	A	A	G	rs2235937	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:29631909A>G	ENST00000345512.3	+	19	2948	c.2819A>G	c.(2818-2820)aAt>aGt	p.N940S	PTPRU_ENST00000428026.2_Missense_Mutation_p.N930S|PTPRU_ENST00000356870.3_Missense_Mutation_p.N930S|PTPRU_ENST00000323874.8_Missense_Mutation_p.N930S|PTPRU_ENST00000373779.3_Missense_Mutation_p.N930S|PTPRU_ENST00000460170.2_Missense_Mutation_p.N930S|PTPRU_ENST00000415600.2_3'UTR	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	940	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.		N -> S (in dbSNP:rs2235937).		canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.N940S(1)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GGAGACCCCAATGCCGACTAC	0.577													A|||	1685	0.336462	0.2209	0.3775	5008	,	,		20588	0.4851		0.2425	False		,,,				2504	0.407				p.N940S		Atlas-SNP	.											PTPRU,NS,carcinoma,0,1	PTPRU	374	1	1	Substitution - Missense(1)	stomach(1)	c.A2819G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN,SER/ASN	993,3413	369.3+/-319.0	99,795,1309	152.0	128.0	136.0		2789,2819,2789,2789	1.8	0.5	1	dbSNP_98	136	2002,6598	350.3+/-327.8	235,1532,2533	yes	missense,missense,missense,missense	PTPRU	NM_001195001.1,NM_005704.4,NM_133177.3,NM_133178.3	46,46,46,46	334,2327,3842	GG,GA,AA		23.2791,22.5374,23.0278	benign,benign,benign,benign	930/1434,940/1447,930/1441,930/1437	29631909	2995,10011	2203	4300	6503	SO:0001583	missense	10076	exon19			ACCCCAATGCCGA	U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9683	protein-coding gene	gene with protein product	"""pi R-PTP-Psi"""	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.2819A>G	1.37:g.29631909A>G	ENSP00000334941:p.Asn940Ser	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_005704	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	672	0.3076923076923077	106	0.21544715447154472	114	0.3149171270718232	275	0.4807692307692308	177	0.23350923482849603	A	1.995	-0.430790	0.04669	0.225374	0.232791	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62	4.06	1.77	0.24775	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.185620	0.43747	D	0.000528	T	0.00012	0.0000	N	0.10645	0.015	0.37194	P	0.09595200000000004	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.001;0.001	T	0.48647	-0.9017	8	.	.	.	.	6.9338	0.24455	0.7275:0.0:0.2725:0.0	rs2235937;rs56473288;rs61086159;rs2235937	930;930;930;930;940	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	S	940;930;930;930;930;930	ENSP00000334941:N940S;ENSP00000362884:N930S;ENSP00000349333:N930S;ENSP00000314987:N930S;ENSP00000392332:N930S;ENSP00000432906:N930S	.	N	+	2	0	PTPRU	29504496	0.990000	0.36364	0.529000	0.27951	0.990000	0.78478	2.492000	0.45311	0.386000	0.24997	0.460000	0.39030	AAT	A|0.730;G|0.269	0.269	strong		0.577	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1		
OR2T34	127068	hgsc.bcm.edu	37	1	248737230	248737230	+	Missense_Mutation	SNP	T	T	C	rs199863869	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248737230T>C	ENST00000328782.2	-	1	850	c.829A>G	c.(829-831)Atg>Gtg	p.M277V		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M277V(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GACACCATCATGTCCTGCTCA	0.532													t|||	796	0.158946	0.3079	0.111	5008	,	,		8657	0.0942		0.1044	False		,,,				2504	0.1145				p.M277V		Atlas-SNP	.											OR2T34,NS,carcinoma,0,1	OR2T34	72	1	1	Substitution - Missense(1)	stomach(1)	c.A829G						scavenged	.						20.0	14.0	16.0					1																	248737230		2093	4220	6313	SO:0001583	missense	127068	exon1			CCATCATGTCCTG	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.829A>G	1.37:g.248737230T>C	ENSP00000330904:p.Met277Val	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	224	63	0.28125	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	292	0.1336996336996337	132	0.2682926829268293	37	0.10220994475138122	42	0.07342657342657342	81	0.10686015831134564	.	2.413	-0.334881	0.05278	.	.	ENSG00000183310	ENST00000328782	T	0.00054	8.8	2.37	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	L	0.39326	1.205	0.80722	P	0.0	B	0.19583	0.037	B	0.24006	0.05	T	0.11767	-1.0574	8	0.87932	D	0	.	6.6859	0.23144	0.0:0.0:0.2414:0.7586	.	277	Q8NGX1	O2T34_HUMAN	V	277	ENSP00000330904:M277V	ENSP00000330904:M277V	M	-	1	0	OR2T34	246803853	0.001000	0.12720	0.987000	0.45799	0.354000	0.29330	0.758000	0.26447	0.964000	0.38108	0.104000	0.15600	ATG	T|0.875;C|0.125	0.125	strong		0.532	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
PRRT3	285368	hgsc.bcm.edu	37	3	9991163	9991163	+	Missense_Mutation	SNP	A	A	G	rs55847610	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9991163A>G	ENST00000412055.1	-	2	766	c.637T>C	c.(637-639)Tcc>Ccc	p.S213P	PRRT3_ENST00000411976.2_Missense_Mutation_p.S213P|PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	213			S -> P (in dbSNP:rs55847610). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)		p.S213P(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						CCTGAGTGGGAAACAAGGGTG	0.587													G|||	1913	0.381989	0.8139	0.3271	5008	,	,		19533	0.1558		0.2147	False		,,,				2504	0.2423				p.S213P		Atlas-SNP	.											PRRT3,NS,carcinoma,0,1	PRRT3	35	1	1	Substitution - Missense(1)	stomach(1)	c.T637C						PASS	.	G	PRO/SER	2830,1382		992,846,268	53.0	63.0	60.0		637	0.5	0.0	3	dbSNP_129	60	2062,6408		264,1534,2437	yes	missense	PRRT3	NM_207351.3	74	1256,2380,2705	GG,GA,AA		24.3447,32.811,38.5744	benign	213/982	9991163	4892,7790	2106	4235	6341	SO:0001583	missense	285368	exon2			AGTGGGAAACAAG	AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"""Proline-rich transmembrane proteins"""	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.637T>C	3.37:g.9991163A>G	ENSP00000392511:p.Ser213Pro	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Missense_Mutation	SNP	ENST00000412055.1	37	CCDS43049.1	806	0.36904761904761907	398	0.8089430894308943	124	0.3425414364640884	118	0.2062937062937063	166	0.21899736147757257	G	0	-2.631277	0.00115	0.67189	0.243447	ENSG00000163704	ENST00000412055;ENST00000411976	T;T	0.14391	2.79;2.51	3.41	0.544	0.17185	.	0.464418	0.18502	N	0.139323	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08493	-1.0719	8	.	.	.	-5.5063	3.5365	0.07795	0.3453:0.1944:0.4603:0.0	rs55847610;rs59599102;rs62245484	213;213	Q5FWE3-3;Q5FWE3	.;PRRT3_HUMAN	P	213	ENSP00000392511:S213P;ENSP00000404512:S213P	.	S	-	1	0	PRRT3	9966163	0.001000	0.12720	0.000000	0.03702	0.139000	0.21198	0.079000	0.14782	-0.124000	0.11724	-0.748000	0.03510	TCC	A|0.673;G|0.327	0.327	strong		0.587	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351	
CR1L	1379	hgsc.bcm.edu	37	1	207890866	207890866	+	Missense_Mutation	SNP	T	T	C	rs2796257	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207890866T>C	ENST00000508064.2	+	11	1532	c.1472T>C	c.(1471-1473)cTt>cCt	p.L491P		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	491	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.		L -> P (in dbSNP:rs2796257).			cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GGAACTCCCCTTGGAGATATT	0.453													t|||	1347	0.26897	0.1362	0.5115	5008	,	,		18096	0.1171		0.4344	False		,,,				2504	0.2628				p.L491P		Atlas-SNP	.											.	CR1L	97	.	0			c.T1472C						PASS	.	T	PRO/LEU	640,3070		49,542,1264	116.0	106.0	109.0		1472	-0.9	0.0	1	dbSNP_100	109	3543,4643		742,2059,1292	no	missense	CR1L	NM_175710.1	98	791,2601,2556	CC,CT,TT		43.2812,17.2507,35.1631	possibly-damaging	491/570	207890866	4183,7713	1855	4093	5948	SO:0001583	missense	1379	exon11			CTCCCCTTGGAGA	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1472T>C	1.37:g.207890866T>C	ENSP00000421736:p.Leu491Pro	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	251	126	0.501992	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	664	0.304029304029304	75	0.1524390243902439	178	0.49171270718232046	80	0.13986013986013987	331	0.4366754617414248	.	9.255	1.041822	0.19748	0.172507	0.432812	ENSG00000197721	ENST00000508064	T	0.23754	1.89	3.01	-0.852	0.10713	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	L	0.58925	1.835	0.80722	P	0.0	P	0.48230	0.907	P	0.56865	0.808	T	0.43523	-0.9386	8	0.33141	T	0.24	.	2.8399	0.05526	0.0:0.3307:0.2605:0.4088	rs2796257;rs12735951	491	Q2VPA4	CR1L_HUMAN	P	491	ENSP00000421736:L491P	ENSP00000421736:L491P	L	+	2	0	CR1L	205957489	0.000000	0.05858	0.000000	0.03702	0.129000	0.20672	0.293000	0.19029	-0.041000	0.13558	0.254000	0.18369	CTT	T|0.675;C|0.325	0.325	strong		0.453	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
DNAH14	127602	hgsc.bcm.edu	37	1	225533684	225533684	+	Missense_Mutation	SNP	A	A	G	rs6667999	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225533684A>G	ENST00000445597.2	+	48	8011	c.8011A>G	c.(8011-8013)Aaa>Gaa	p.K2671E	DNAH14_ENST00000439375.2_Missense_Mutation_p.K3474E|DNAH14_ENST00000430092.1_Missense_Mutation_p.K3474E			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2671			K -> E (in dbSNP:rs6667999).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AGATGATGACAAAATTGTAGA	0.328													G|||	2649	0.528954	0.6399	0.4697	5008	,	,		18280	0.5089		0.4046	False		,,,				2504	0.5695				p.K3474E		Atlas-SNP	.											.	DNAH14	300	.	0			c.A10420G						PASS	.	G	GLU/LYS	842,542		268,306,118	62.0	46.0	51.0		10420	3.4	0.0	1	dbSNP_116	51	1406,1776		323,760,508	yes	missense	DNAH14	NM_001373.1	56	591,1066,626	GG,GA,AA		44.186,39.1618,49.2335	benign	3474/4516	225533684	2248,2318	692	1591	2283	SO:0001583	missense	127602	exon68			GATGACAAAATTG	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.8011A>G	1.37:g.225533684A>G	ENSP00000409472:p.Lys2671Glu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	129	52	0.403101	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	G	0.005	-2.137791	0.00335	0.608382	0.44186	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.54071	0.59;0.59;0.59	5.34	3.37	0.38596	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45862	-0.9232	7	0.02654	T	1	.	7.3982	0.26948	0.1499:0.0:0.7149:0.1352	rs6667999;rs52791604;rs60868380;rs6667999	3474	Q0VDD8-4	.	E	2671;3474;3474	ENSP00000409472:K2671E;ENSP00000414402:K3474E;ENSP00000392061:K3474E	ENSP00000414402:K3474E	K	+	1	0	DNAH14	223600307	0.836000	0.29430	0.026000	0.17262	0.022000	0.10575	1.958000	0.40402	0.621000	0.30232	-0.294000	0.09567	AAA	A|0.507;G|0.493	0.493	strong		0.328	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
PCDHA1	56147	hgsc.bcm.edu	37	5	140168070	140168070	+	Missense_Mutation	SNP	A	A	G	rs2240696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140168070A>G	ENST00000504120.2	+	1	2195	c.2195A>G	c.(2194-2196)tAt>tGt	p.Y732C	PCDHA1_ENST00000378133.3_Missense_Mutation_p.Y732C|PCDHA1_ENST00000394633.3_Intron	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	732			Y -> C (in dbSNP:rs2240696).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGGGTGCGTATGTGCCGGGC	0.662													.|||	2631	0.525359	0.4796	0.5879	5008	,	,		16765	0.5317		0.5368	False		,,,				2504	0.5245				p.Y732C		Atlas-SNP	.											PCDHA1_ENST00000504120,colon,carcinoma,0,2	PCDHA1	387	2	0			c.A2195G						PASS	.	G	CYS/TYR,CYS/TYR,	2186,2220		528,1130,545	51.0	45.0	47.0		2195,2195,	2.2	0.0	5	dbSNP_98	47	4539,4061		1192,2155,953	no	missense,missense,intron	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	194,194,	1720,3285,1498	GG,GA,AA		47.2209,49.6142,48.2931	,,	732/951,732/808,	140168070	6725,6281	2203	4300	6503	SO:0001583	missense	56147	exon1			GTGCGTATGTGCC	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.2195A>G	5.37:g.140168070A>G	ENSP00000420840:p.Tyr732Cys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	178	76	0.426966	NM_031410	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	1158	0.5302197802197802	251	0.5101626016260162	192	0.5303867403314917	311	0.5437062937062938	404	0.5329815303430079	N	0	-2.739289	0.00088	0.496142	0.527791	ENSG00000204970	ENST00000504120;ENST00000378133	T;T	0.08984	3.03;3.03	4.16	2.24	0.28232	.	0.365789	0.19576	N	0.110983	T	0.00012	0.0000	N	0.00025	-2.685	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.34477	-0.9827	9	0.07325	T	0.83	.	3.7944	0.08733	0.2812:0.0:0.5369:0.182	rs2240696;rs17208229;rs17844241;rs52830508;rs2240696	732;732	Q9Y5I3;Q9Y5I3-3	PCDA1_HUMAN;.	C	732	ENSP00000420840:Y732C;ENSP00000367373:Y732C	ENSP00000367373:Y732C	Y	+	2	0	PCDHA1	140148254	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.396000	0.20867	0.322000	0.23283	-0.133000	0.14855	TAT	A|0.482;G|0.518	0.518	strong		0.662	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
SCFD2	152579	hgsc.bcm.edu	37	4	54011603	54011603	+	Silent	SNP	C	C	T	rs17082453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:54011603C>T	ENST00000401642.3	-	5	1591	c.1458G>A	c.(1456-1458)acG>acA	p.T486T	SCFD2_ENST00000388940.4_Silent_p.T486T	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	486					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)					breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CTTTGTCTACCGTGAGCTCTC	0.438													c|||	637	0.127196	0.0144	0.1715	5008	,	,		18655	0.2321		0.0765	False		,,,				2504	0.1922				p.T486T		Atlas-SNP	.											.	SCFD2	78	.	0			c.G1458A						PASS	.	C		104,4302	81.4+/-119.9	1,102,2100	128.0	121.0	123.0		1458	-8.8	0.0	4	dbSNP_123	123	586,8014	156.4+/-210.3	23,540,3737	no	coding-synonymous	SCFD2	NM_152540.3		24,642,5837	TT,TC,CC		6.814,2.3604,5.3052		486/685	54011603	690,12316	2203	4300	6503	SO:0001819	synonymous_variant	152579	exon5			GTCTACCGTGAGC	AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.1458G>A	4.37:g.54011603C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	166	85	0.512048	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Silent	SNP	ENST00000401642.3	37	CCDS33984.1																																																																																			C|0.913;T|0.087	0.087	strong		0.438	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	
MAPT	4137	hgsc.bcm.edu	37	17	44061278	44061278	+	Missense_Mutation	SNP	C	C	T	rs17651549	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44061278C>T	ENST00000571987.1	+	5	1108	c.1108C>T	c.(1108-1110)Cgg>Tgg	p.R370W	MAPT_ENST00000576518.1_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.R370W|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.R370W|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.R370W|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	370			R -> W (in dbSNP:rs17651549).		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GCCCGTCAGCCGGGTCCCTCA	0.647													C|||	429	0.0856629	0.0129	0.1571	5008	,	,		15403	0.001		0.2406	False		,,,				2504	0.0613				p.R370W		Atlas-SNP	.											.	MAPT	135	.	0			c.C1108T						PASS	.	C	TRP/ARG,,,,,,TRP/ARG,	171,3947		5,161,1893	65.0	79.0	75.0		1108,,,,,,1108,	4.5	1.0	17	dbSNP_123	75	1750,6338		186,1378,2480	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	101,,,,,,101,	191,1539,4373	TT,TC,CC		21.637,4.1525,15.7382	probably-damaging,,,,,,probably-damaging,	370/777,,,,,,370/759,	44061278	1921,10285	2059	4044	6103	SO:0001583	missense	4137	exon6			GTCAGCCGGGTCC	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1108C>T	17.37:g.44061278C>T	ENSP00000458742:p.Arg370Trp	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	253	0.11584249084249085	9	0.018292682926829267	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	18.18	3.567727	0.65651	0.041525	0.21637	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.15139	2.54;2.45;2.54	5.51	4.51	0.55191	.	0.000000	0.37857	N	0.001904	T	0.00012	0.0000	L	0.58101	1.795	0.09310	P	0.9999999999999999	D;D	0.71674	0.998;0.998	P;P	0.62491	0.903;0.774	T	0.07616	-1.0763	9	0.66056	D	0.02	-12.7384	12.1085	0.53825	0.0:0.827:0.173:0.0	rs17651549;rs52812169;rs17651549	370;370	P10636-9;P10636	.;TAU_HUMAN	W	370	ENSP00000340820:R370W;ENSP00000262410:R370W;ENSP00000410838:R370W	ENSP00000262410:R370W	R	+	1	2	MAPT	41417115	1.000000	0.71417	1.000000	0.80357	0.552000	0.35366	2.545000	0.45769	1.277000	0.44412	0.511000	0.50034	CGG	C|0.867;T|0.133	0.133	strong		0.647	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
SGOL2	151246	hgsc.bcm.edu	37	2	201437932	201437932	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:201437932C>T	ENST00000357799.4	+	7	2961	c.2863C>T	c.(2863-2865)Caa>Taa	p.Q955*		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	955					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						ACTTGAATGCCAAGACATTAT	0.279																																					p.Q955X		Atlas-SNP	.											SGOL2,NS,carcinoma,-1,1	SGOL2	126	1	0			c.C2863T						scavenged	.						48.0	49.0	48.0					2																	201437932		1813	4051	5864	SO:0001587	stop_gained	151246	exon7			GAATGCCAAGACA	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.2863C>T	2.37:g.201437932C>T	ENSP00000350447:p.Gln955*	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	216	3	0.0138889	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Nonsense_Mutation	SNP	ENST00000357799.4	37	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.929544	0.73327	.	.	ENSG00000163535	ENST00000357799	.	.	.	5.02	2.15	0.27550	.	0.319207	0.22857	N	0.054783	.	.	.	.	.	.	0.24021	N	0.996145	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-0.9945	12.9522	0.58407	0.0:0.522:0.478:0.0	.	.	.	.	X	955	.	ENSP00000350447:Q955X	Q	+	1	0	SGOL2	201146177	0.388000	0.25197	0.019000	0.16419	0.025000	0.11179	0.766000	0.26560	0.262000	0.21774	-0.515000	0.04445	CAA	.	.	none		0.279	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
CDC27	996	hgsc.bcm.edu	37	17	45234411	45234411	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:45234411G>T	ENST00000066544.3	-	7	803	c.710C>A	c.(709-711)tCa>tAa	p.S237*	CDC27_ENST00000527547.1_Nonsense_Mutation_p.S237*|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000531206.1_Nonsense_Mutation_p.S237*|CDC27_ENST00000446365.2_Nonsense_Mutation_p.S176*	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	237					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						AATTACAGCTGAATCAATATA	0.338																																					p.S237X		Atlas-SNP	.											CDC27_ENST00000531206,caecum,carcinoma,0,2	CDC27	337	2	0			c.C710A						PASS	.						39.0	44.0	42.0					17																	45234411		2188	4290	6478	SO:0001587	stop_gained	996	exon7			ACAGCTGAATCAA	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.710C>A	17.37:g.45234411G>T	ENSP00000066544:p.Ser237*	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	7	0.127273	NM_001114091	G3V1C4|Q16349|Q96F35	Nonsense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028766	0.75504	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	.	.	.	5.44	5.44	0.79542	.	0.068298	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.6807	16.7505	0.85484	0.0:0.0:1.0:0.0	.	.	.	.	X	237;237;176;237;237	.	ENSP00000066544:S237X	S	-	2	0	CDC27	42589410	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.255000	0.95524	2.555000	0.86185	0.460000	0.39030	TCA	.	.	none		0.338	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
NIPBL	25836	hgsc.bcm.edu	37	5	37036492	37036492	+	Silent	SNP	C	C	T	rs61748200	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:37036492C>T	ENST00000282516.8	+	33	6373	c.5874C>T	c.(5872-5874)tcC>tcT	p.S1958S	NIPBL_ENST00000448238.2_Silent_p.S1958S	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1958					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TGTTGAAGTCCGAAGAGGATT	0.279													C|||	859	0.171526	0.0303	0.1167	5008	,	,		6564	0.3026		0.169	False		,,,				2504	0.2689				p.S1958S		Atlas-SNP	.											.	NIPBL	513	.	0			c.C5874T						PASS	.	C	,	203,4119		5,193,1963	15.0	15.0	15.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5874,5874	-7.7	1.0	5	dbSNP_129	15	1104,7266		60,984,3141	no	coding-synonymous,coding-synonymous	NIPBL	NM_015384.4,NM_133433.3	,	65,1177,5104	TT,TC,CC		13.19,4.6969,10.2978	,	1958/2698,1958/2805	37036492	1307,11385	2161	4185	6346	SO:0001819	synonymous_variant	25836	exon33			GAAGTCCGAAGAG	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.5874C>T	5.37:g.37036492C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																			C|0.844;T|0.156	0.156	strong		0.279	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
PEX11B	8799	hgsc.bcm.edu	37	1	145522887	145522887	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:145522887C>T	ENST00000369306.3	+	4	897	c.748C>T	c.(748-750)Cta>Tta	p.L250L	ITGA10_ENST00000538811.1_5'Flank|ITGA10_ENST00000369304.3_5'Flank|ITGA10_ENST00000539363.1_5'Flank|PEX11B_ENST00000537888.1_Silent_p.L236L	NM_003846.2	NP_003837.1	O96011	PX11B_HUMAN	peroxisomal biogenesis factor 11 beta	250	Interaction with PEX19 and peroxisome targeting.				peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|protein homooligomerization (GO:0051260)|regulation of peroxisome size (GO:0044375)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TATTCTCACCCTAATCTATCC	0.542																																					p.L250L		Atlas-SNP	.											PEX11B,NS,carcinoma,-2,1	PEX11B	26	1	0			c.C748T						scavenged	.						105.0	93.0	97.0					1																	145522887		2203	4300	6503	SO:0001819	synonymous_variant	8799	exon4			CTCACCCTAATCT	AF093670	CCDS72870.1, CCDS72871.1	1q21	2008-08-26	2008-08-26		ENSG00000131779	ENSG00000131779			8853	protein-coding gene	gene with protein product		603867	"""peroxisomal biogenesis factor 11B"""			9792670	Standard	NM_003846		Approved		uc001eny.2	O96011	OTTHUMG00000013756	ENST00000369306.3:c.748C>T	1.37:g.145522887C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	153	3	0.0196078	NM_003846	B3KN85|B4DXH9|Q96ET2	Silent	SNP	ENST00000369306.3	37	CCDS917.1																																																																																			.	.	none		0.542	PEX11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038549.1	NM_003846	
GPANK1	7918	hgsc.bcm.edu	37	6	31630241	31630241	+	Silent	SNP	C	C	T	rs7992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31630241C>T	ENST00000375906.1	-	4	1557	c.873G>A	c.(871-873)agG>agA	p.R291R	GPANK1_ENST00000375900.4_Silent_p.R291R|GPANK1_ENST00000375893.2_Silent_p.R291R|C6orf47-AS1_ENST00000422049.1_RNA|GPANK1_ENST00000375896.4_Silent_p.R291R|CSNK2B_ENST00000375885.4_5'Flank|Y_RNA_ENST00000364337.1_RNA|C6orf47_ENST00000375911.1_5'Flank|GPANK1_ENST00000375895.2_Silent_p.R291R	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	291	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.						nucleic acid binding (GO:0003676)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						CTTCCTGGTCCCTCTTGAGGA	0.652													C|||	2058	0.410942	0.6135	0.4078	5008	,	,		17114	0.369		0.2952	False		,,,				2504	0.3016				p.R291R		Atlas-SNP	.											.	GPANK1	19	.	0			c.G873A						PASS	.	C	,,,,	1649,1373		451,747,313	81.0	83.0	82.0		873,873,873,873,873	1.8	1.0	6	dbSNP_52	82	1446,3972		198,1050,1461	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPANK1	NM_001199237.1,NM_001199238.1,NM_001199239.1,NM_001199240.1,NM_033177.3	,,,,	649,1797,1774	TT,TC,CC		26.6888,45.4335,36.6706	,,,,	291/357,291/357,291/357,291/357,291/357	31630241	3095,5345	1511	2709	4220	SO:0001819	synonymous_variant	7918	exon4			CTGGTCCCTCTTG		CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"""Ankyrin repeat domain containing"", ""G patch domain containing"""	13920	protein-coding gene	gene with protein product	"""G patch domain containing 10"", ""ankyrin repeat domain 59"""	142610	"""HLA-B associated transcript 4"""	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.873G>A	6.37:g.31630241C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	174	80	0.45977	NM_001199238	A6NG25|B0UXA2|Q5SQ49	Silent	SNP	ENST00000375906.1	37	CCDS4711.1																																																																																			C|0.620;T|0.380	0.380	strong		0.652	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2	NM_033177	
ZNF721	170960	hgsc.bcm.edu	37	4	436991	436991	+	Missense_Mutation	SNP	C	C	T	rs376220761		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:436991C>T	ENST00000338977.5	-	2	1277	c.1229G>A	c.(1228-1230)cGt>cAt	p.R410H	ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000507078.1_Intron|ZNF721_ENST00000511833.2_Missense_Mutation_p.R422H			Q8TF20	ZN721_HUMAN	zinc finger protein 721	410				R -> C (in Ref. 1; CAH10687). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						GGCTCTGCCACGATCTTCACA	0.378																																					p.P422H		Atlas-SNP	.											ZNF721_ENST00000511833,NS,carcinoma,-1,2	ZNF721	205	2	0			c.C1265A						scavenged	.	C	HIS/ARG	0,4098		0,0,2049	75.0	78.0	77.0		1265	1.0	0.0	4		77	1,8439		0,1,4219	no	missense	ZNF721	NM_133474.2	29	0,1,6268	TT,TC,CC		0.0118,0.0,0.0080	possibly-damaging	422/924	436991	1,12537	2049	4220	6269	SO:0001583	missense	170960	exon3			CTGCCACGATCTT	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1229G>A	4.37:g.436991C>T	ENSP00000340524:p.Arg410His	Somatic	47	1	0.0212766		WXS	Illumina HiSeq	Phase_I	39	16	0.410256	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	C	12.31	1.900631	0.33535	0.0	1.18E-4	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.17854	2.25;2.25	1.03	1.03	0.20045	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13798	0.0334	N	0.25647	0.755	0.09310	N	1	D;D;D	0.62365	0.991;0.975;0.985	B;B;P	0.45881	0.208;0.301;0.496	T	0.17961	-1.0352	9	0.87932	D	0	.	7.9579	0.30053	0.0:1.0:0.0:0.0	.	410;422;422	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	H	410;422	ENSP00000340524:R410H;ENSP00000428878:R422H	ENSP00000340524:R410H	R	-	2	0	ZNF721	426991	0.888000	0.30383	0.003000	0.11579	0.003000	0.03518	2.751000	0.47508	0.890000	0.36211	0.194000	0.17425	CGT	.	.	weak		0.378	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474	
TTYH2	94015	hgsc.bcm.edu	37	17	72248483	72248483	+	Silent	SNP	A	A	G	rs4789640|rs386799126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72248483A>G	ENST00000269346.4	+	11	1301	c.1227A>G	c.(1225-1227)gcA>gcG	p.A409A	TTYH2_ENST00000529107.1_Silent_p.A388A|TTYH2_ENST00000441391.2_Silent_p.A88A	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	409			A -> E (in dbSNP:rs9892705).			chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.A409A(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						TGATCTGTGCAGGGCCAAGGG	0.637													G|||	1797	0.358826	0.5582	0.2983	5008	,	,		18175	0.1101		0.3608	False		,,,				2504	0.3865				p.A409A		Atlas-SNP	.											TTYH2,NS,carcinoma,0,1	TTYH2	63	1	1	Substitution - coding silent(1)	stomach(1)	c.A1227G						scavenged	.	G	,	2201,2205		634,933,636	66.0	55.0	59.0		1227,264	-7.2	0.0	17	dbSNP_111	59	3295,5305		699,1897,1704	no	coding-synonymous,coding-synonymous	TTYH2	NM_032646.5,NM_052869.1	,	1333,2830,2340	GG,GA,AA		38.314,49.9546,42.2574	,	409/535,88/214	72248483	5496,7510	2203	4300	6503	SO:0001819	synonymous_variant	94015	exon11			CTGTGCAGGGCCA		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.1227A>G	17.37:g.72248483A>G		Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Silent	SNP	ENST00000269346.4	37	CCDS32717.1																																																																																			A|0.567;G|0.433	0.433	strong		0.637	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
MRO	83876	hgsc.bcm.edu	37	18	48346024	48346024	+	5'UTR	SNP	G	G	T	rs3813089	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:48346024G>T	ENST00000428869.2	-	0	142				MRO_ENST00000256425.2_5'UTR|MRO_ENST00000587291.1_5'Flank|MRO_ENST00000436348.2_Missense_Mutation_p.T23N|MRO_ENST00000588444.1_Intron|MRO_ENST00000431965.2_Missense_Mutation_p.T23N|MRO_ENST00000398439.3_5'UTR			Q9BYG7	MSTRO_HUMAN	maestro							nucleolus (GO:0005730)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|skin(2)	10		Colorectal(6;0.0596)		Colorectal(21;0.082)		GCTTTCCCGGGTAGTAGCCAA	0.572											OREG0024982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	740	0.147764	0.1362	0.1369	5008	,	,		16608	0.0952		0.2157	False		,,,				2504	0.1554				p.T23N		Atlas-SNP	.											.	MRO	36	.	0			c.C68A						PASS	.	G	,ASN/THR,ASN/THR,	194,1190		12,170,510	37.0	39.0	38.0		,68,68,	-0.7	0.0	18	dbSNP_107	38	733,2449		79,575,937	yes	intron,missense,missense,utr-5	MRO	NM_001127174.1,NM_001127175.1,NM_001127176.1,NM_031939.3	,65,65,	91,745,1447	TT,TG,GG		23.0358,14.0173,20.3022	,possibly-damaging,possibly-damaging,	,23/211,23/263,	48346024	927,3639	692	1591	2283	SO:0001623	5_prime_UTR_variant	83876	exon2			TCCCGGGTAGTAG	AK054702	CCDS11947.1, CCDS45867.1, CCDS45868.1, CCDS45869.1	18q21	2012-12-19	2004-06-15		ENSG00000134042	ENSG00000134042		"""maestro heat-like repeat containing"""	24121	protein-coding gene	gene with protein product	"""B29 protein"", ""beside the Ma29 deletion"""	608080	"""chromosome 18 open reading frame 3"""	C18orf3		11401430	Standard	NM_031939		Approved	B29, FLJ30140	uc010dpa.3	Q9BYG7	OTTHUMG00000132692	ENST00000428869.2:c.-117C>A	18.37:g.48346024G>T		Somatic	83	0	0	953	WXS	Illumina HiSeq	Phase_I	111	58	0.522523	NM_001127175	B7Z2I5|B7Z3B2|E9PAT5|E9PBI3|K7EKJ8|Q8N6K5	Missense_Mutation	SNP	ENST00000428869.2	37	CCDS11947.1	357	0.16346153846153846	84	0.17073170731707318	58	0.16022099447513813	61	0.10664335664335664	154	0.20316622691292877	G	6.659	0.490034	0.12702	0.140173	0.230358	ENSG00000134042	ENST00000436348;ENST00000431965	T;T	0.19105	2.61;2.17	1.57	-0.692	0.11301	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.44825	P	0.0021640000000000548	B;B	0.15719	0.014;0.014	B;B	0.10450	0.005;0.003	T	0.42103	-0.9471	8	0.44086	T	0.13	.	3.2894	0.06944	0.0:0.3072:0.4187:0.2741	rs3813089;rs17663367;rs56429856;rs57952343;rs3813089	23;23	E9PBI3;E9PAT5	.;.	N	23	ENSP00000397900:T23N;ENSP00000392614:T23N	ENSP00000392614:T23N	T	-	2	0	MRO	46600022	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.404000	0.07205	-0.210000	0.10140	0.511000	0.50034	ACC	G|0.849;T|0.151	0.151	strong		0.572	MRO-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449478.2	NM_031939	
FRAS1	80144	hgsc.bcm.edu	37	4	79434685	79434685	+	Missense_Mutation	SNP	T	T	G	rs35933858	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:79434685T>G	ENST00000264895.6	+	65	10593	c.10153T>G	c.(10153-10155)Tat>Gat	p.Y3385D		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3381					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AGTTACCACCTATGACCTGAG	0.488													T|||	399	0.0796725	0.0688	0.1023	5008	,	,		23930	0.002		0.1819	False		,,,				2504	0.0532				p.Y3385D		Atlas-SNP	.											.	FRAS1	779	.	0			c.T10153G						PASS	.	T	ASP/TYR	308,3718		18,272,1723	161.0	153.0	156.0		10153	3.6	0.6	4	dbSNP_126	156	1636,6724		166,1304,2710	yes	missense	FRAS1	NM_025074.6	160	184,1576,4433	GG,GT,TT		19.5694,7.6503,15.6951	benign	3385/4013	79434685	1944,10442	2013	4180	6193	SO:0001583	missense	80144	exon65			ACCACCTATGACC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.10153T>G	4.37:g.79434685T>G	ENSP00000264895:p.Tyr3385Asp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	222|222	0.10164835164835165|0.10164835164835165	41|41	0.08333333333333333|0.08333333333333333	42|42	0.11602209944751381|0.11602209944751381	1|1	0.0017482517482517483|0.0017482517482517483	138|138	0.1820580474934037|0.1820580474934037	T|T	1.297|1.297	-0.605941|-0.605941	0.03717|0.03717	0.076503|0.076503	0.195694|0.195694	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.11385	.|2.78	5.44|5.44	3.58|3.58	0.41010|0.41010	.|.	.|0.533866	.|0.19050	.|N	.|0.124064	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01874|0.01874	-0.695|-0.695	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.19073	.|0.033	.|B	.|0.17979	.|0.02	T|T	0.43861|0.43861	-0.9365|-0.9365	4|9	.|0.22706	.|T	.|0.39	.|.	8.2084|8.2084	0.31469|0.31469	0.1171:0.69:0.115:0.0779|0.1171:0.69:0.115:0.0779	rs35933858|rs35933858	.|3385	.|E9PHH6	.|.	R|D	1613|3385	.|ENSP00000264895:Y3385D	.|ENSP00000264895:Y3385D	L|Y	+|+	2|1	0|0	FRAS1|FRAS1	79653709|79653709	0.504000|0.504000	0.26123|0.26123	0.635000|0.635000	0.29338|0.29338	0.902000|0.902000	0.53008|0.53008	1.768000|1.768000	0.38511|0.38511	1.257000|1.257000	0.44085|0.44085	-0.456000|-0.456000	0.05471|0.05471	CTA|TAT	T|0.882;G|0.118	0.118	strong		0.488	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
STKLD1	169436	hgsc.bcm.edu	37	9	136268084	136268084	+	Missense_Mutation	SNP	A	A	G	rs3124747	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:136268084A>G	ENST00000371957.3	+	14	1524	c.1417A>G	c.(1417-1419)Aaa>Gaa	p.K473E	C9orf96_ENST00000371955.1_Intron	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		473			K -> E (in dbSNP:rs3124747). {ECO:0000269|PubMed:15489334}.				ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CAGCTCCCTCAAAAGCAGGGA	0.667													G|||	2354	0.470048	0.3533	0.5648	5008	,	,		17050	0.2837		0.6889	False		,,,				2504	0.5276				p.K473E		Atlas-SNP	.											.	C9orf96	77	.	0			c.A1417G						PASS	.	G	GLU/LYS	1810,2574		388,1034,770	33.0	29.0	30.0		1417	-4.6	0.0	9	dbSNP_103	30	5614,2966		1877,1860,553	yes	missense	C9orf96	NM_153710.3	56	2265,2894,1323	GG,GA,AA		34.5688,41.2865,42.7337	benign	473/681	136268084	7424,5540	2192	4290	6482	SO:0001583	missense	169436	exon14			TCCCTCAAAAGCA																												ENST00000371957.3:c.1417A>G	9.37:g.136268084A>G	ENSP00000361025:p.Lys473Glu	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	163	72	0.441718	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	37	CCDS35169.1	1069	0.48946886446886445	178	0.3617886178861789	197	0.5441988950276243	157	0.2744755244755245	537	0.7084432717678101	G	0.426	-0.905737	0.02453	0.412865	0.654312	ENSG00000198870	ENST00000371957	T	0.46063	0.88	4.18	-4.6	0.03390	Armadillo-like helical (1);Armadillo-type fold (1);	1.456700	0.04337	N	0.353447	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37407	-0.9707	9	0.02654	T	1	-0.0051	6.4652	0.21977	0.4299:0.291:0.2791:0.0	rs3124747;rs9411511;rs17150551;rs3124747	473	Q8NE28	SGK71_HUMAN	E	473	ENSP00000361025:K473E	ENSP00000361025:K473E	K	+	1	0	C9orf96	135257905	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.236000	0.02925	-0.960000	0.03613	-1.608000	0.00805	AAA	A|0.479;G|0.521	0.521	strong		0.667	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
CDC6	990	hgsc.bcm.edu	37	17	38457151	38457151	+	Missense_Mutation	SNP	G	G	A	rs13706	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:38457151G>A	ENST00000209728.4	+	10	1792	c.1321G>A	c.(1321-1323)Gtt>Att	p.V441I	CTD-2267D19.6_ENST00000602403.1_lincRNA	NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	441			V -> I (in dbSNP:rs13706). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						CATCTCAGAAGTTGATGGTAA	0.428													G|||	1402	0.279952	0.5348	0.183	5008	,	,		21220	0.3482		0.1113	False		,,,				2504	0.1074				p.V441I		Atlas-SNP	.											.	CDC6	53	.	0			c.G1321A	GRCh37	CM065057	CDC6	M	rs13706	PASS	.	G	ILE/VAL	2014,2392	561.4+/-380.7	479,1056,668	217.0	194.0	202.0		1321	3.8	1.0	17	dbSNP_52	202	950,7650	208.7+/-250.1	57,836,3407	yes	missense	CDC6	NM_001254.3	29	536,1892,4075	AA,AG,GG		11.0465,45.7104,22.7895	possibly-damaging	441/561	38457151	2964,10042	2203	4300	6503	SO:0001583	missense	990	exon10			TCAGAAGTTGATG	U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"""CDC6 (cell division cycle 6, S. cerevisiae) homolog"", ""CDC6 cell division cycle 6 homolog (S. cerevisiae)"", ""cell division cycle 6 homolog (S. cerevisiae)"""	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.1321G>A	17.37:g.38457151G>A	ENSP00000209728:p.Val441Ile	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	231	108	0.467532	NM_001254	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	37	CCDS11365.1	608	0.2783882783882784	255	0.5182926829268293	62	0.1712707182320442	215	0.3758741258741259	76	0.10026385224274406	G	19.42	3.823558	0.71143	0.457104	0.110465	ENSG00000094804	ENST00000209728	T	0.52983	0.64	5.96	3.82	0.43975	.	0.185081	0.46442	N	0.000289	T	0.00012	0.0000	L	0.54908	1.71	0.24597	P	0.99379435	P	0.44578	0.838	B	0.44224	0.444	T	0.49670	-0.8915	9	0.17369	T	0.5	-11.9661	10.4299	0.44400	0.204:0.0:0.796:0.0	rs13706;rs1048815;rs2230629;rs3188865;rs17852245;rs57349852;rs13706	441	Q99741	CDC6_HUMAN	I	441	ENSP00000209728:V441I	ENSP00000209728:V441I	V	+	1	0	CDC6	35710677	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	4.003000	0.57061	1.539000	0.49286	0.655000	0.94253	GTT	G|0.734;A|0.266	0.266	strong		0.428	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1		
DCLK1	9201	hgsc.bcm.edu	37	13	36402426	36402426	+	Silent	SNP	A	A	G	rs2296645	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:36402426A>G	ENST00000360631.3	-	9	1459	c.1248T>C	c.(1246-1248)taT>taC	p.Y416Y	DCLK1_ENST00000379893.1_Silent_p.Y109Y|DCLK1_ENST00000255448.4_Silent_p.Y416Y			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	416	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.Y416Y(1)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		TTTTCAGAGCATACTCTCTAG	0.318													A|||	1664	0.332268	0.0968	0.3934	5008	,	,		18258	0.2867		0.504	False		,,,				2504	0.4775				p.Y416Y		Atlas-SNP	.											DCLK1_ENST00000255448,NS,carcinoma,0,1	DCLK1	350	1	1	Substitution - coding silent(1)	stomach(1)	c.T1248C						PASS	.	A	,,	600,3804	263.8+/-265.7	47,506,1649	94.0	88.0	90.0		327,327,1248	4.9	1.0	13	dbSNP_100	90	4095,4499	559.0+/-387.3	988,2119,1190	no	coding-synonymous,coding-synonymous,coding-synonymous	DCLK1	NM_001195415.1,NM_001195416.1,NM_004734.4	,,	1035,2625,2839	GG,GA,AA		47.6495,13.624,36.1209	,,	109/423,109/434,416/730	36402426	4695,8303	2202	4297	6499	SO:0001819	synonymous_variant	9201	exon9			CAGAGCATACTCT	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"""doublecortin and CaM kinase-like 1"""	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1248T>C	13.37:g.36402426A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	30	28	0.933333	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	37																																																																																				A|0.650;G|0.350	0.350	strong		0.318	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
ACKR1	2532	hgsc.bcm.edu	37	1	159175527	159175527	+	Missense_Mutation	SNP	G	G	A	rs13962	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:159175527G>A	ENST00000368122.2	+	2	977	c.298G>A	c.(298-300)Gca>Aca	p.A100T	DARC_ENST00000368121.2_Missense_Mutation_p.A102T|CTA-134P22.2_ENST00000609696.1_RNA|DARC_ENST00000537147.1_Missense_Mutation_p.A100T	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		100			A -> T (in dbSNP:rs13962). {ECO:0000269|PubMed:9731074, ECO:0000269|PubMed:9886340}.		chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					GCCTGTCCTGGCACAGCTGGC	0.617													G|||	345	0.0688898	0.0045	0.0937	5008	,	,		21381	0.0		0.1839	False		,,,				2504	0.091				p.A102T		Atlas-SNP	.											.	DARC	76	.	0			c.G304A	GRCh37	CM983824	DARC	M	rs13962	PASS	.	G	THR/ALA,THR/ALA	140,4266	100.3+/-138.9	5,130,2068	105.0	100.0	102.0	http://www.ncbi.nlm.nih.gov/pubmed?term	304,298	3.1	0.2	1	dbSNP_52	102	1467,7133	279.1+/-293.8	127,1213,2960	yes	missense,missense	DARC	NM_001122951.2,NM_002036.3	58,58	132,1343,5028	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	17.0581,3.1775,12.3558	probably-damaging,probably-damaging	102/339,100/337	159175527	1607,11399	2203	4300	6503	SO:0001583	missense	2532	exon1			GTCCTGGCACAGC																												ENST00000368122.2:c.298G>A	1.37:g.159175527G>A	ENSP00000357104:p.Ala100Thr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	176	94	0.534091	NM_001122951	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Missense_Mutation	SNP	ENST00000368122.2	37	CCDS1183.1	178	0.0815018315018315	1	0.0020325203252032522	38	0.10497237569060773	0	0.0	139	0.18337730870712401	G	14.11	2.438188	0.43326	0.031775	0.170581	ENSG00000213088	ENST00000368122;ENST00000537147;ENST00000359381;ENST00000435307;ENST00000368121	T;T;T;T	0.37915	1.17;1.17;1.66;1.17	5.09	3.07	0.35406	.	0.300710	0.17478	U	0.172829	T	0.22513	0.0543	L	0.38175	1.15	0.58432	P	1.0000000000287557E-6	D;D	0.54772	0.968;0.968	P;P	0.54889	0.763;0.763	T	0.06552	-1.0820	9	0.45353	T	0.12	-3.8727	5.8028	0.18424	0.0989:0.0:0.7105:0.1906	rs13962;rs13962	102;100	Q5Y7A1;Q16570	.;DUFFY_HUMAN	T	100;100;100;102;102	ENSP00000357104:A100T;ENSP00000441985:A100T;ENSP00000398406:A102T;ENSP00000357103:A102T	ENSP00000352341:A100T	A	+	1	0	DARC	157442151	0.098000	0.21812	0.224000	0.23877	0.170000	0.22686	0.380000	0.20602	1.259000	0.44117	0.561000	0.74099	GCA	.	.	none		0.617	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2		
RAB3IL1	5866	hgsc.bcm.edu	37	11	61672265	61672265	+	Silent	SNP	T	T	C	rs174474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61672265T>C	ENST00000394836.2	-	6	904	c.747A>G	c.(745-747)cgA>cgG	p.R249R	RAB3IL1_ENST00000301773.5_Silent_p.R223R	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	249					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						CCACGTCCTCTCGGTACACCC	0.667													C|||	1571	0.313698	0.27	0.2003	5008	,	,		15287	0.3353		0.2336	False		,,,				2504	0.5133				p.R249R		Atlas-SNP	.											RAB3IL1,NS,carcinoma,-2,1	RAB3IL1	39	1	0			c.A747G						PASS	.	C		1226,3178	670.8+/-402.4	167,892,1143	29.0	29.0	29.0		747	-2.0	1.0	11	dbSNP_79	29	1940,6658	699.3+/-405.1	222,1496,2581	no	coding-synonymous	RAB3IL1	NM_013401.2		389,2388,3724	CC,CT,TT		22.5634,27.8383,24.3501		249/383	61672265	3166,9836	2202	4299	6501	SO:0001819	synonymous_variant	5866	exon6			GTCCTCTCGGTAC	AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.747A>G	11.37:g.61672265T>C		Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	285	103	0.361403	NM_013401	Q86V32|Q9P1Q8	Silent	SNP	ENST00000394836.2	37	CCDS8014.1																																																																																			T|0.759;C|0.241	0.241	strong		0.667	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401	
PNPLA7	375775	hgsc.bcm.edu	37	9	140356422	140356422	+	Silent	SNP	G	G	C	rs28452008	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140356422G>C	ENST00000277531.4	-	31	3828	c.3642C>G	c.(3640-3642)ctC>ctG	p.L1214L	PNPLA7_ENST00000371457.1_Silent_p.L820L|NSMF_ENST00000371475.3_5'Flank|NSMF_ENST00000265663.7_5'Flank|NSMF_ENST00000371472.2_5'Flank|NSMF_ENST00000437259.1_5'Flank|PNPLA7_ENST00000492278.1_5'UTR|NSMF_ENST00000371474.3_5'Flank|PNPLA7_ENST00000406427.1_Silent_p.L1239L|NSMF_ENST00000371473.3_5'Flank|NSMF_ENST00000392812.4_5'Flank	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1214					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		GCTGGTCGCGGAGCATCTTCT	0.706													C|||	2452	0.489617	0.3177	0.3588	5008	,	,		14382	0.8204		0.3847	False		,,,				2504	0.5818				p.L1239L		Atlas-SNP	.											PNPLA7,NS,carcinoma,0,1	PNPLA7	124	1	0			c.C3717G						PASS	.	C	,	1420,2962		231,958,1002	11.0	13.0	13.0		3717,3642	1.1	1.0	9	dbSNP_125	13	3144,5428		623,1898,1765	no	coding-synonymous,coding-synonymous	PNPLA7	NM_001098537.1,NM_152286.3	,	854,2856,2767	CC,CG,GG		36.6776,32.4053,35.2324	,	1239/1343,1214/1318	140356422	4564,8390	2191	4286	6477	SO:0001819	synonymous_variant	375775	exon32			GTCGCGGAGCATC	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.3642C>G	9.37:g.140356422G>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	ENST00000277531.4	37	CCDS7045.1																																																																																			G|0.620;C|0.380	0.380	strong		0.706	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
KMT2C	58508	hgsc.bcm.edu	37	7	151970859	151970859	+	Missense_Mutation	SNP	C	C	A	rs149992209	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:151970859C>A	ENST00000262189.6	-	7	1161	c.943G>T	c.(943-945)Ggc>Tgc	p.G315C	KMT2C_ENST00000355193.2_Missense_Mutation_p.G315C	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	315					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TGAAAGGTGCCGGCTCCTGCA	0.428																																					p.G315C		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,14	MLL3	1564	14	0			c.G943T						PASS	.						263.0	245.0	251.0					7																	151970859		2203	4300	6503	SO:0001583	missense	58508	exon7			AGGTGCCGGCTCC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.943G>T	7.37:g.151970859C>A	ENSP00000262189:p.Gly315Cys	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	330	17	0.0515152	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.586790	0.66105	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.73575	-0.76;-0.76	4.87	4.87	0.63330	Zinc finger, PHD-type (1);	0.000000	0.45606	D	0.000359	D	0.88654	0.6495	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90967	0.4817	10	0.87932	D	0	.	18.3752	0.90433	0.0:1.0:0.0:0.0	.	315	Q8NEZ4	MLL3_HUMAN	C	315	ENSP00000262189:G315C;ENSP00000347325:G315C	ENSP00000262189:G315C	G	-	1	0	MLL3	151601792	1.000000	0.71417	0.992000	0.48379	0.975000	0.68041	7.752000	0.85141	2.423000	0.82170	0.650000	0.86243	GGC	C|0.994;T|0.006	.	strong		0.428	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
HCRTR1	3061	hgsc.bcm.edu	37	1	32084904	32084904	+	Silent	SNP	C	C	T	rs1056526	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32084904C>T	ENST00000373706.5	+	1	264	c.111C>T	c.(109-111)cgC>cgT	p.R37R	HCRTR1_ENST00000468521.1_3'UTR|HCRTR1_ENST00000373705.1_Silent_p.R37R|HCRTR1_ENST00000403528.2_Silent_p.R37R			O43613	OX1R_HUMAN	hypocretin (orexin) receptor 1	37					feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|orexin receptor activity (GO:0016499)|peptide hormone binding (GO:0017046)			breast(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	7		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)		ATCTGTGGCGCGATTATCTGT	0.612													C|||	1767	0.352835	0.0794	0.4654	5008	,	,		21465	0.2371		0.5636	False		,,,				2504	0.545				p.R37R		Atlas-SNP	.											.	HCRTR1	20	.	0			c.C111T						PASS	.	C		718,3688	297.8+/-285.0	70,578,1555	150.0	151.0	151.0		111	-6.0	1.0	1	dbSNP_86	151	4750,3850	610.1+/-395.6	1318,2114,868	no	coding-synonymous	HCRTR1	NM_001525.2		1388,2692,2423	TT,TC,CC		44.7674,16.296,42.0421		37/426	32084904	5468,7538	2203	4300	6503	SO:0001819	synonymous_variant	3061	exon3			GTGGCGCGATTAT	AF041243	CCDS344.1	1p33	2012-08-08			ENSG00000121764	ENSG00000121764		"""GPCR / Class A : Hypocretin (orexin) receptors"""	4848	protein-coding gene	gene with protein product		602392				9491897	Standard	NM_001525		Approved	OX1R	uc009vtx.2	O43613	OTTHUMG00000003876	ENST00000373706.5:c.111C>T	1.37:g.32084904C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_001525	A8K3A6|Q9HBV6	Silent	SNP	ENST00000373706.5	37	CCDS344.1																																																																																			C|0.612;T|0.388	0.388	strong		0.612	HCRTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011042.1	NM_001525	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249121	71249121	+	Missense_Mutation	SNP	C	C	G	rs200585722		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:71249121C>G	ENST00000398534.3	+	1	51	c.20C>G	c.(19-21)tCt>tGt	p.S7C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	7						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						TGTGGCTGCTCTGGAGGCTGT	0.657																																					p.S7C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.C20G						PASS	.						47.0	66.0	60.0					11																	71249121		2189	4282	6471	SO:0001583	missense	57830	exon1			GCTGCTCTGGAGG	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.20C>G	11.37:g.71249121C>G	ENSP00000420723:p.Ser7Cys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	102	7	0.0686275	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	37	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	c	3.358	-0.131059	0.06753	.	.	ENSG00000241233	ENST00000398534	T	0.01527	4.8	1.57	1.57	0.23409	.	.	.	.	.	T	0.03564	0.0102	M	0.74389	2.26	0.09310	N	1	P	0.39094	0.659	B	0.43225	0.412	T	0.34204	-0.9838	9	0.62326	D	0.03	.	3.9595	0.09404	0.0:0.775:0.0:0.225	.	7	O75690	KRA58_HUMAN	C	7	ENSP00000420723:S7C	ENSP00000420723:S7C	S	+	2	0	KRTAP5-8	70926769	0.030000	0.19436	0.804000	0.32291	0.223000	0.24884	-0.589000	0.05767	1.182000	0.42928	0.514000	0.50259	TCT	.	.	weak		0.657	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
TCERG1	10915	hgsc.bcm.edu	37	5	145838656	145838656	+	Silent	SNP	G	G	A	rs569890952		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:145838656G>A	ENST00000296702.5	+	4	686	c.648G>A	c.(646-648)caG>caA	p.Q216Q	TCERG1_ENST00000394421.2_Silent_p.Q216Q	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	216	Ala/Gln-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			cccaggcccaggcccaggccc	0.731																																					p.Q216Q		Atlas-SNP	.											TCERG1,NS,carcinoma,0,2	TCERG1	148	2	0			c.G648A						scavenged	.						10.0	14.0	13.0					5																	145838656		2190	4261	6451	SO:0001819	synonymous_variant	10915	exon4			GGCCCAGGCCCAG	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"""transcription factor CA150"", ""co-activator of 150 kDa"", ""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"", ""TATA box-binding protein-associated factor 2S"""	605409	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"""	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.648G>A	5.37:g.145838656G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	26	3	0.115385	NM_006706	Q2NKN2|Q59EA1	Silent	SNP	ENST00000296702.5	37	CCDS4282.1																																																																																			.	.	none		0.731	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006	
LCN8	138307	hgsc.bcm.edu	37	9	139649612	139649612	+	Splice_Site	SNP	C	C	A	rs2282258	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139649612C>A	ENST00000371688.3	-	6	717	c.422G>T	c.(421-423)gGg>gTg	p.G141V	LCN8_ENST00000482893.1_5'UTR	NM_178469.3	NP_848564.2	Q6JVE9	LCN8_HUMAN	lipocalin 8	164					response to hormone (GO:0009725)|transport (GO:0006810)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	10	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)		GGCACACCGCCCTGCAGGATA	0.716													C|||	776	0.154952	0.1467	0.2363	5008	,	,		14332	0.1518		0.1292	False		,,,				2504	0.138				p.G141V		Atlas-SNP	.											LCN8,colon,carcinoma,0,1	LCN8	14	1	0			c.G422T						PASS	.	C	VAL/GLY	616,3770		43,530,1620	23.0	25.0	24.0		422	2.7	1.0	9	dbSNP_100	24	1184,7410		84,1016,3197	yes	missense-near-splice	LCN8	NM_178469.3	109	127,1546,4817	AA,AC,CC		13.7771,14.0447,13.8675	probably-damaging	141/153	139649612	1800,11180	2193	4297	6490	SO:0001630	splice_region_variant	138307	exon6			CACCGCCCTGCAG	AK124003	CCDS35183.1	9q34.3	2011-10-24	2005-01-11		ENSG00000204001	ENSG00000204001		"""Lipocalins"""	27038	protein-coding gene	gene with protein product		612902	"""chromosome 9 open reading frame 137"", ""lipocalin 5"""	LCN5			Standard	XM_005266058		Approved		uc004cjb.1	Q6JVE9	OTTHUMG00000020942	ENST00000371688.3:c.422-1G>T	9.37:g.139649612C>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	149	76	0.510067	NM_178469	A1L4A8|A6NMN9|Q5T5R4	Missense_Mutation	SNP	ENST00000371688.3	37	CCDS35183.1	350	0.16025641025641027	98	0.1991869918699187	73	0.20165745856353592	83	0.1451048951048951	96	0.1266490765171504	C	10.47	1.358374	0.24598	0.140447	0.137771	ENSG00000204001	ENST00000371688	T	0.52295	0.67	2.74	2.74	0.32292	.	.	.	.	.	T	0.00073	0.0002	L	0.27053	0.805	0.19575	P	0.999969191	D	0.89917	1.0	D	0.91635	0.999	T	0.03829	-1.1000	8	0.28530	T	0.3	.	9.1522	0.36971	0.0:1.0:0.0:0.0	rs2282258	141	Q6JVE9-2	.	V	141	ENSP00000360753:G141V	ENSP00000360753:G141V	G	-	2	0	LCN8	138769433	0.896000	0.30565	0.962000	0.40283	0.010000	0.07245	1.807000	0.38902	1.850000	0.53721	0.561000	0.74099	GGG	C|0.851;A|0.149	0.149	strong		0.716	LCN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055109.1	NM_178469	Missense_Mutation
PDE1C	5137	hgsc.bcm.edu	37	7	31855625	31855625	+	Missense_Mutation	SNP	C	C	G	rs61736729	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:31855625C>G	ENST00000396191.1	-	15	2181	c.1726G>C	c.(1726-1728)Gtc>Ctc	p.V576L	PDE1C_ENST00000396193.1_Missense_Mutation_p.V636L|PDE1C_ENST00000479980.1_5'UTR|PDE1C_ENST00000396184.3_Missense_Mutation_p.V576L|PDE1C_ENST00000321453.7_Missense_Mutation_p.V576L|PDE1C_ENST00000396182.2_Missense_Mutation_p.V576L	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	576					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GTTCCATTGACTTGATTCTTA	0.473													C|||	13	0.00259585	0.0	0.0072	5008	,	,		20836	0.0		0.008	False		,,,				2504	0.0				p.V636L		Atlas-SNP	.											.	PDE1C	465	.	0			c.G1906C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	11,4395	17.9+/-39.9	0,11,2192	271.0	268.0	269.0		1726,1726,1906,1726,1726	5.3	1.0	7	dbSNP_129	269	108,8492	59.1+/-120.7	0,108,4192	yes	missense,missense,missense,missense,missense	PDE1C	NM_001191056.1,NM_001191057.1,NM_001191058.1,NM_001191059.1,NM_005020.2	32,32,32,32,32	0,119,6384	GG,GC,CC		1.2558,0.2497,0.915	benign,benign,benign,benign,benign	576/635,576/710,636/770,576/710,576/635	31855625	119,12887	2203	4300	6503	SO:0001583	missense	5137	exon16			CATTGACTTGATT	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1726G>C	7.37:g.31855625C>G	ENSP00000379494:p.Val576Leu	Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	333	168	0.504505	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	8.002	0.755676	0.15846	0.002497	0.012558	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.65;-0.65	5.34	5.34	0.76211	.	2.382430	0.01786	N	0.032006	T	0.53578	0.1805	N	0.19112	0.55	0.19775	N	0.999959	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.13407	0.009;0.004;0.004	T	0.40608	-0.9554	10	0.25751	T	0.34	.	12.0225	0.53352	0.0:0.9176:0.0:0.0824	rs61736729	576;636;576	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	L	636;576;576;576;576	ENSP00000379496:V636L;ENSP00000379494:V576L;ENSP00000318105:V576L;ENSP00000379487:V576L;ENSP00000379485:V576L	ENSP00000318105:V576L	V	-	1	0	PDE1C	31822150	0.060000	0.20803	0.993000	0.49108	0.186000	0.23388	1.274000	0.33132	2.779000	0.95612	0.655000	0.94253	GTC	C|0.983;G|0.017	0.017	strong		0.473	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31238259	31238259	+	Missense_Mutation	SNP	G	G	T	rs1131096	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238259G>T	ENST00000376228.5	-	4	637	c.623C>A	c.(622-624)cCc>cAc	p.P208H	HLA-C_ENST00000383329.3_Missense_Mutation_p.P208H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	208	Alpha-3.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TGTCTTTGGGGGTTCTGACGG	0.582													t|||	3807	0.760184	0.736	0.8026	5008	,	,		17620	0.8135		0.7167	False		,,,				2504	0.7526				p.P208H		Atlas-SNP	.											HLA-C_ENST00000383329,NS,neuroblastoma,0,2	HLA-C	92	2	0			c.C623A						PASS	.	T	HIS/PRO	3416,990		1375,666,162	44.0	48.0	47.0		623	1.8	0.0	6	dbSNP_86	47	5804,2794		2001,1802,496	yes	missense	HLA-C	NM_002117.5	77	3376,2468,658	TT,TG,GG		32.4959,22.4694,29.0987	benign	208/367	31238259	9220,3784	2203	4299	6502	SO:0001583	missense	3107	exon4			TTTGGGGGTTCTG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.623C>A	6.37:g.31238259G>T	ENSP00000365402:p.Pro208His	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	134	127	0.947761	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1692	0.7747252747252747	395	0.8028455284552846	291	0.8038674033149171	458	0.8006993006993007	548	0.7229551451187335	.	1.336	-0.595471	0.03771	0.775306	0.675041	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.15834	2.39;2.39	2.65	1.77	0.24775	MHC class I-like antigen recognition (1);	0.390141	0.18306	N	0.145260	T	0.03477	0.0100	.	.	.	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.38178	-0.9673	8	0.28530	T	0.3	.	6.9981	0.24795	0.0:0.0:0.7288:0.2712	rs1131096;rs2308607;rs3177873;rs3190644	208;208;208;208	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	H	208;208;208;245	ENSP00000365402:P208H;ENSP00000372819:P208H	ENSP00000365402:P208H	P	-	2	0	HLA-C	31346238	0.001000	0.12720	0.011000	0.14972	0.045000	0.14185	0.627000	0.24506	0.701000	0.31803	-0.797000	0.03246	CCC	T|0.722;G|0.275;C|0.003	0.722	strong		0.582	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
FOS	2353	hgsc.bcm.edu	37	14	75746690	75746690	+	Silent	SNP	C	C	T	rs1046117	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:75746690C>T	ENST00000303562.4	+	2	461	c.252C>T	c.(250-252)tcC>tcT	p.S84S	FOS_ENST00000555686.1_5'UTR|FOS_ENST00000535987.1_Silent_p.S84S|FOS_ENST00000555347.1_5'Flank|FOS_ENST00000555242.1_Silent_p.S84S|FOS_ENST00000554617.1_Silent_p.S84S	NM_005252.3	NP_005243.1	P01100	FOS_HUMAN	FBJ murine osteosarcoma viral oncogene homolog	84					aging (GO:0007568)|cellular response to calcium ion (GO:0071277)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hormone stimulus (GO:0032870)|cellular response to reactive oxygen species (GO:0034614)|conditioned taste aversion (GO:0001661)|DNA methylation (GO:0006306)|Fc-epsilon receptor signaling pathway (GO:0038095)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to cold (GO:0009409)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gravity (GO:0009629)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|skeletal muscle cell differentiation (GO:0035914)|sleep (GO:0030431)|SMAD protein signal transduction (GO:0060395)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	double-stranded DNA binding (GO:0003690)|R-SMAD binding (GO:0070412)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_lung(585;0.0138)|all_epithelial(191;0.0263)|all_neural(303;0.112)		BRCA - Breast invasive adenocarcinoma(234;0.0117)	Nadroparin(DB08813)|Pseudoephedrine(DB00852)	TCGTCTCCTCCGTGGCCCCAT	0.667													C|||	3518	0.702476	0.9191	0.647	5008	,	,		15086	0.5665		0.7237	False		,,,				2504	0.5675				p.S84S		Atlas-SNP	.											.	FOS	30	.	0			c.C252T						PASS	.	C		3894,512	778.4+/-414.3	1729,436,38	53.0	54.0	54.0		252	-1.1	1.0	14	dbSNP_86	54	6258,2342	702.5+/-405.3	2283,1692,325	no	coding-synonymous	FOS	NM_005252.3		4012,2128,363	TT,TC,CC		27.2326,11.6205,21.9437		84/381	75746690	10152,2854	2203	4300	6503	SO:0001819	synonymous_variant	2353	exon2			CTCCTCCGTGGCC	K00650	CCDS9841.1	14q24.3	2013-01-10	2009-07-23			ENSG00000170345		"""basic leucine zipper proteins"""	3796	protein-coding gene	gene with protein product		164810	"""v-fos FBJ murine osteosarcoma viral oncogene homolog"""			16123044, 16055710, 15926923	Standard	NM_005252		Approved	c-fos, AP-1	uc001xrn.3	P01100		ENST00000303562.4:c.252C>T	14.37:g.75746690C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	145	80	0.551724	NM_005252	A8K4E2|B4DQ65|P18849	Silent	SNP	ENST00000303562.4	37	CCDS9841.1	1559	0.7138278388278388	450	0.9146341463414634	234	0.6464088397790055	318	0.5559440559440559	557	0.7348284960422163	C	12.73	2.025885	0.35701	0.883795	0.727674	ENSG00000170345	ENST00000554212;ENST00000557139	T	0.80304	-1.36	5.95	-1.11	0.09840	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.27400	-1.0075	4	.	.	.	0.0319	4.1673	0.10313	0.0866:0.3418:0.3419:0.2297	rs1046117;rs3174644;rs17845024;rs17857793	.	.	.	C	75;4	ENSP00000451786:R4C	.	R	+	1	0	FOS	74816443	0.001000	0.12720	0.987000	0.45799	0.816000	0.46133	-1.756000	0.01813	-0.320000	0.08640	-1.119000	0.02030	CGT	C|0.238;T|0.762	0.762	strong		0.667	FOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415044.1	NM_005252	
CHPT1	56994	hgsc.bcm.edu	37	12	102108345	102108345	+	Missense_Mutation	SNP	T	T	C	rs3205421	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:102108345T>C	ENST00000229266.3	+	3	720	c.485T>C	c.(484-486)tTc>tCc	p.F162S	CHPT1_ENST00000549872.1_Missense_Mutation_p.F162S|CHPT1_ENST00000550385.1_3'UTR	NM_020244.2	NP_064629.2	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	162			F -> S (in dbSNP:rs3205421). {ECO:0000269|PubMed:10893425}.		CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	diacylglycerol binding (GO:0019992)|diacylglycerol cholinephosphotransferase activity (GO:0004142)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						TGGTTTTTTTTCTGCTCTTTT	0.353													T|||	1137	0.227037	0.0741	0.2738	5008	,	,		15511	0.3433		0.3022	False		,,,				2504	0.2035				p.F162S		Atlas-SNP	.											.	CHPT1	27	.	0			c.T485C						PASS	.	T	SER/PHE	495,3911	221.0+/-238.3	25,445,1733	160.0	148.0	152.0		485	6.1	1.0	12	dbSNP_105	152	2483,6117	393.6+/-344.4	351,1781,2168	yes	missense	CHPT1	NM_020244.2	155	376,2226,3901	CC,CT,TT		28.8721,11.2347,22.8971	possibly-damaging	162/407	102108345	2978,10028	2203	4300	6503	SO:0001583	missense	56994	exon3			TTTTTTTCTGCTC		CCDS9086.1	12q	2010-07-08				ENSG00000111666	2.7.8.2		17852	protein-coding gene	gene with protein product	"""phosphatidylcholine synthesizing enzyme"""					10893425	Standard	NM_020244		Approved	CPT1	uc001tin.3	Q8WUD6		ENST00000229266.3:c.485T>C	12.37:g.102108345T>C	ENSP00000229266:p.Phe162Ser	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	294	290	0.986395	NM_020244	B3KQM2|Q7Z7H0|Q7Z7H1|Q7Z7H2|Q8IWQ4|Q8IWQ5|Q8WYI4|Q9NRQ6|Q9NRQ7|Q9Y6M6	Missense_Mutation	SNP	ENST00000229266.3	37	CCDS9086.1	570	0.260989010989011	40	0.08130081300813008	104	0.287292817679558	201	0.3513986013986014	225	0.29683377308707126	T	22.8	4.339740	0.81911	0.112347	0.288721	ENSG00000111666	ENST00000229266;ENST00000549872	T;T	0.40225	1.04;1.04	6.06	6.06	0.98353	.	0.089068	0.85682	D	0.000000	T	0.00012	0.0000	M	0.80982	2.52	0.21802	P	0.999532065	D;D	0.76494	0.997;0.999	D;D	0.79784	0.962;0.993	T	0.33675	-0.9859	9	0.56958	D	0.05	-0.3375	11.3701	0.49694	0.1353:0.0:0.0:0.8647	rs3205421;rs52798048;rs59280515;rs3205421	162;162	F8W1B3;Q8WUD6	.;CHPT1_HUMAN	S	162	ENSP00000229266:F162S;ENSP00000448766:F162S	ENSP00000229266:F162S	F	+	2	0	CHPT1	100632476	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.808000	0.69165	2.324000	0.78689	0.533000	0.62120	TTC	T|0.760;C|0.240	0.240	strong		0.353	CHPT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409173.1	NM_020244	
EVPL	2125	hgsc.bcm.edu	37	17	74014619	74014619	+	Silent	SNP	G	G	A	rs140458042	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:74014619G>A	ENST00000301607.3	-	12	1600	c.1347C>T	c.(1345-1347)gtC>gtT	p.V449V	EVPL_ENST00000586740.1_Silent_p.V449V	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	449	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						GGCCCTGCACGACCCAGGCGT	0.662													G|||	23	0.00459265	0.0015	0.0101	5008	,	,		14833	0.001		0.006	False		,,,				2504	0.0072				p.V449V		Atlas-SNP	.											.	EVPL	155	.	0			c.C1347T						PASS	.	G		5,4401		0,5,2198	20.0	22.0	22.0		1347	-10.2	0.4	17	dbSNP_134	22	41,8559		0,41,4259	no	coding-synonymous	EVPL	NM_001988.2		0,46,6457	AA,AG,GG		0.4767,0.1135,0.3537		449/2034	74014619	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	2125	exon12			CTGCACGACCCAG	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.1347C>T	17.37:g.74014619G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	274	167	0.609489	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																			G|0.996;A|0.004	0.004	strong		0.662	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
BCAT1	586	hgsc.bcm.edu	37	12	24970966	24970966	+	Silent	SNP	G	G	A	rs117200620	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:24970966G>A	ENST00000261192.7	-	11	1663	c.1137C>T	c.(1135-1137)agC>agT	p.S379S	BCAT1_ENST00000342945.5_Silent_p.S318S|BCAT1_ENST00000539282.1_Silent_p.S391S|BCAT1_ENST00000538118.1_Silent_p.S378S|BCAT1_ENST00000539780.1_Silent_p.S342S	NM_001178091.1|NM_005504.6	NP_001171562.1|NP_005495.2	P54687	BCAT1_HUMAN	branched chain amino-acid transaminase 1, cytosolic	379					branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cell proliferation (GO:0008283)|cellular nitrogen compound metabolic process (GO:0034641)|G1/S transition of mitotic cell cycle (GO:0000082)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)			breast(1)|large_intestine(1)|lung(3)|prostate(2)	7	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)	TTGTCCAGTCGCTCTCTTCTC	0.398													G|||	71	0.0141773	0.003	0.0058	5008	,	,		21169	0.001		0.0099	False		,,,				2504	0.0532				p.S391S		Atlas-SNP	.											BCAT1,NS,carcinoma,0,1	BCAT1	44	1	0			c.C1173T						scavenged	.	G	,,,,	24,3794		0,24,1885	165.0	153.0	157.0		1026,954,1173,1134,1137	-5.2	0.8	12	dbSNP_132	157	101,8187		1,99,4044	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCAT1	NM_001178091.1,NM_001178092.1,NM_001178093.1,NM_001178094.1,NM_005504.6	,,,,	1,123,5929	AA,AG,GG		1.2186,0.6286,1.0325	,,,,	342/350,318/326,391/399,378/386,379/387	24970966	125,11981	1909	4144	6053	SO:0001819	synonymous_variant	586	exon11			CCAGTCGCTCTCT		CCDS44845.1, CCDS53760.1, CCDS53761.1, CCDS53762.1, CCDS53763.1	12p12.1	2012-10-02	2010-05-07		ENSG00000060982	ENSG00000060982	2.6.1.42		976	protein-coding gene	gene with protein product		113520	"""branched chain aminotransferase 1, cytosolic"""	BCT1		9165094	Standard	NM_005504		Approved		uc010six.2	P54687	OTTHUMG00000169053	ENST00000261192.7:c.1137C>T	12.37:g.24970966G>A		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	240	114	0.475	NM_001178093	B3KY27|B7Z2M5|B7Z5L0|F5H5E4|Q68DQ7|Q96MY9	Silent	SNP	ENST00000261192.7	37	CCDS44845.1																																																																																			G|0.992;A|0.008	0.008	strong		0.398	BCAT1-001	KNOWN	upstream_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402080.1	NM_005504	
CYP4A22	284541	hgsc.bcm.edu	37	1	47608983	47608983	+	Missense_Mutation	SNP	G	G	T	rs113777592	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:47608983G>T	ENST00000371891.3	+	5	584	c.553G>T	c.(553-555)Gtc>Ttc	p.V185F	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000294337.3_Missense_Mutation_p.V185F|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000371890.3_Missense_Mutation_p.V185F	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	185			V -> F (in allele CYP4A22*10, allele CYP4A22*11, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs113777592). {ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCCTCTGGAGGTCTTTCAGCA	0.542													G|||	1681	0.335663	0.2057	0.232	5008	,	,		19651	0.5536		0.1928	False		,,,				2504	0.5072				p.V185F	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											CYP4A22,colon,carcinoma,-2,1	CYP4A22	60	1	0			c.G553T						PASS	.	G	PHE/VAL	1006,3400	372.0+/-320.2	107,792,1304	70.0	64.0	66.0		553	-1.9	0.0	1	dbSNP_132	66	1731,6865	315.9+/-312.5	184,1363,2751	no	missense	CYP4A22	NM_001010969.2	50	291,2155,4055	TT,TG,GG		20.1373,22.8325,21.0506	possibly-damaging	185/520	47608983	2737,10265	2203	4298	6501	SO:0001583	missense	284541	exon5			CTGGAGGTCTTTC		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.553G>T	1.37:g.47608983G>T	ENSP00000360958:p.Val185Phe	Somatic	610	0	0		WXS	Illumina HiSeq	Phase_I	687	305	0.443959	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	613	0.2806776556776557	95	0.19308943089430894	83	0.2292817679558011	298	0.5209790209790209	137	0.18073878627968337	g	12.99	2.104200	0.37145	0.228325	0.201373	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.70516	-0.45;-0.49;-0.49	1.44	-1.89	0.07689	.	0.621999	0.16471	N	0.212985	T	0.00012	0.0000	M	0.63843	1.955	0.45567	P	0.0014880000000000448	P;P	0.46064	0.846;0.872	B;P	0.49597	0.264;0.616	T	0.37478	-0.9704	9	0.62326	D	0.03	.	5.0373	0.14441	0.5021:0.2748:0.2231:0.0	.	185;185	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	F	185	ENSP00000360957:V185F;ENSP00000360958:V185F;ENSP00000294337:V185F	ENSP00000294337:V185F	V	+	1	0	CYP4A22	47381570	0.001000	0.12720	0.002000	0.10522	0.478000	0.33099	-1.183000	0.03079	-0.551000	0.06175	0.194000	0.17425	GTC	G|0.849;T|0.151	0.151	strong		0.542	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
RNF13	11342	hgsc.bcm.edu	37	3	149678534	149678534	+	Silent	SNP	C	C	T	rs6768054	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:149678534C>T	ENST00000344229.3	+	11	1491	c.789C>T	c.(787-789)caC>caT	p.H263H	RNF13_ENST00000392894.3_Silent_p.H263H|RNF13_ENST00000361785.6_Silent_p.H144H	NM_007282.4	NP_009213.1	O43567	RNF13_HUMAN	ring finger protein 13	263					protein autoubiquitination (GO:0051865)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	11		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			CAGCTTATCACTGCAAGTGTG	0.373													C|||	3349	0.66873	0.4501	0.7176	5008	,	,		16979	0.8661		0.7068	False		,,,				2504	0.6871				p.H263H		Atlas-SNP	.											RNF13_ENST00000344229,NS,adenoma,0,1	RNF13	57	1	0			c.C789T						PASS	.	C	,	2057,2349	564.5+/-381.5	502,1053,648	55.0	54.0	54.0		789,789	1.1	1.0	3	dbSNP_116	54	5891,2709	680.7+/-403.7	2042,1807,451	no	coding-synonymous,coding-synonymous	RNF13	NM_007282.4,NM_183381.2	,	2544,2860,1099	TT,TC,CC		31.5,46.6863,38.8897	,	263/382,263/382	149678534	7948,5058	2203	4300	6503	SO:0001819	synonymous_variant	11342	exon11			TTATCACTGCAAG	AF037204	CCDS3146.1	3q25.1	2013-01-09			ENSG00000082996	ENSG00000082996		"""RING-type (C3HC4) zinc fingers"""	10057	protein-coding gene	gene with protein product		609247					Standard	NM_183381		Approved	RZF	uc003exp.4	O43567	OTTHUMG00000150338	ENST00000344229.3:c.789C>T	3.37:g.149678534C>T		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	269	130	0.483271	NM_007282	A6NC87|B3KR12|Q05D66|Q6IBJ9	Silent	SNP	ENST00000344229.3	37	CCDS3146.1																																																																																			C|0.360;T|0.640	0.640	strong		0.373	RNF13-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356876.1	NM_183384	
IPO7	10527	hgsc.bcm.edu	37	11	9455374	9455374	+	Silent	SNP	T	T	C	rs4910052	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:9455374T>C	ENST00000379719.3	+	18	2197	c.2055T>C	c.(2053-2055)gaT>gaC	p.D685D	CTD-2371O3.2_ENST00000531111.1_RNA	NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	685					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		TTCAGCAAGATGGCTTTGATT	0.398													T|||	142	0.0283546	0.0	0.0245	5008	,	,		19604	0.0		0.0646	False		,,,				2504	0.0613				p.D685D		Atlas-SNP	.											.	IPO7	72	.	0			c.T2055C						PASS	.	T		63,4339	59.3+/-96.0	0,63,2138	84.0	79.0	81.0		2055	1.5	1.0	11	dbSNP_111	81	620,7970	161.7+/-214.6	19,582,3694	no	coding-synonymous	IPO7	NM_006391.2		19,645,5832	CC,CT,TT		7.2177,1.4312,5.2571		685/1039	9455374	683,12309	2201	4295	6496	SO:0001819	synonymous_variant	10527	exon18			GCAAGATGGCTTT	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"""Importins"""	9852	protein-coding gene	gene with protein product		605586	"""RAN binding protein 7"""	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.2055T>C	11.37:g.9455374T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Silent	SNP	ENST00000379719.3	37	CCDS31425.1																																																																																			T|0.955;C|0.045	0.045	strong		0.398	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188356	140188356	+	Silent	SNP	A	A	G	rs144593807	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140188356A>G	ENST00000530339.1	+	1	1584	c.1584A>G	c.(1582-1584)ctA>ctG	p.L528L	PCDHA4_ENST00000356878.4_Silent_p.L528L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Silent_p.L528L	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGAGGAGCTAGAGCTGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17817	0.0		0.0755	False		,,,				2504	0.0082				p.L528L		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,+2,8	PCDHA4	419	8	0			c.A1584G						scavenged	.	A	,,,,,	11,4395		0,11,2192	70.0	75.0	73.0		,,,1584,,1584	1.3	1.0	5	dbSNP_134	73	57,8543		9,39,4252	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	9,50,6444	GG,GA,AA		0.6628,0.2497,0.5228	,,,,,	,,,528/948,,528/799	140188356	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			GGAGCTAGAGCTG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1584A>G	5.37:g.140188356A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	60	15	0.25	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			A|0.976;G|0.024	0.024	strong		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
C1orf210	149466	hgsc.bcm.edu	37	1	43748763	43748763	+	Missense_Mutation	SNP	G	G	A	rs35465732	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43748763G>A	ENST00000523677.1	-	3	268	c.35C>T	c.(34-36)tCg>tTg	p.S12L	C1orf210_ENST00000423420.1_Missense_Mutation_p.S12L	NM_001164829.1|NM_182517.2	NP_001158301.1|NP_872323.1	Q8IVY1	CA210_HUMAN	chromosome 1 open reading frame 210	12			S -> L (in dbSNP:rs35465732).			integral component of membrane (GO:0016021)				breast(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GGGGAGCTCCGAAGGCCCAAC	0.642													G|||	29	0.00579073	0.0008	0.0029	5008	,	,		15217	0.0		0.0189	False		,,,				2504	0.0072				p.S12L		Atlas-SNP	.											C1orf210,NS,carcinoma,+1,1	C1orf210	9	1	0			c.C35T						PASS	.	G	LEU/SER,LEU/SER	16,4390	24.3+/-50.5	0,16,2187	25.0	27.0	26.0		35,35	2.0	0.0	1	dbSNP_126	26	158,8442	71.6+/-134.2	0,158,4142	yes	missense,missense	C1orf210	NM_001164829.1,NM_182517.2	145,145	0,174,6329	AA,AG,GG		1.8372,0.3631,1.3378	possibly-damaging,possibly-damaging	12/114,12/114	43748763	174,12832	2203	4300	6503	SO:0001583	missense	149466	exon3			AGCTCCGAAGGCC	BC041633	CCDS481.1	1p34.2	2006-03-22			ENSG00000253313	ENSG00000253313			28755	protein-coding gene	gene with protein product						12477932	Standard	NM_182517		Approved	MGC52423	uc001cit.4	Q8IVY1	OTTHUMG00000007289	ENST00000523677.1:c.35C>T	1.37:g.43748763G>A	ENSP00000430918:p.Ser12Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_182517	D3DPX2	Missense_Mutation	SNP	ENST00000523677.1	37	CCDS481.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	G	17.71	3.457811	0.63401	0.003631	0.018372	ENSG00000253313	ENST00000523677;ENST00000423420	T;T	0.47869	0.83;0.83	4.96	2.04	0.26737	.	0.670270	0.13234	N	0.403431	T	0.18593	0.0446	L	0.36672	1.1	0.09310	N	1	B	0.17465	0.022	B	0.09377	0.004	T	0.23154	-1.0196	10	0.72032	D	0.01	.	3.4949	0.07651	0.2809:0.0:0.5414:0.1777	rs35465732	12	Q8IVY1	CA210_HUMAN	L	12	ENSP00000430918:S12L;ENSP00000429399:S12L	ENSP00000429399:S12L	S	-	2	0	C1orf210	43521350	0.129000	0.22400	0.008000	0.14137	0.346000	0.29079	0.752000	0.26362	0.277000	0.22141	0.561000	0.74099	TCG	G|0.989;A|0.011	0.011	strong		0.642	C1orf210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019035.2	NM_182517	
ACSM2A	123876	hgsc.bcm.edu	37	16	20471450	20471450	+	Missense_Mutation	SNP	G	G	A	rs59292608	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20471450G>A	ENST00000573854.1	+	2	128	c.14G>A	c.(13-15)cGa>cAa	p.R5Q	ACSM2A_ENST00000417235.2_Intron|ACSM2A_ENST00000424070.1_Missense_Mutation_p.R5Q|ACSM2A_ENST00000575690.1_Missense_Mutation_p.R5Q|ACSM2A_ENST00000396104.2_Missense_Mutation_p.R5Q|ACSM2A_ENST00000219054.6_Missense_Mutation_p.R5Q|ACSM2A_ENST00000536134.1_5'UTR|ACSM2A_ENST00000575558.1_Intron	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	5					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)	p.R5Q(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						CATTGGCTGCGAAAAGTTCAG	0.493													G|||	849	0.169529	0.0121	0.0706	5008	,	,		18579	0.4018		0.172	False		,,,				2504	0.2106				p.R5Q		Atlas-SNP	.											ACSM2A,colon,carcinoma,+1,2	ACSM2A	120	2	1	Substitution - Missense(1)	stomach(1)	c.G14A						scavenged	.	G	GLN/ARG	138,4268	97.6+/-136.3	0,138,2065	65.0	65.0	65.0		14	-4.7	0.0	16	dbSNP_129	65	1271,7329	251.1+/-277.7	100,1071,3129	yes	missense	ACSM2A	NM_001010845.2	43	100,1209,5194	AA,AG,GG		14.7791,3.1321,10.8335	benign	5/578	20471450	1409,11597	2203	4300	6503	SO:0001583	missense	123876	exon3			GGCTGCGAAAAGT	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"""Acyl-CoA synthetase family"""	32017	protein-coding gene	gene with protein product		614358	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.14G>A	16.37:g.20471450G>A	ENSP00000459451:p.Arg5Gln	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	406	0.1858974358974359	7	0.014227642276422764	30	0.08287292817679558	226	0.3951048951048951	143	0.18865435356200527	G	8.575	0.880844	0.17467	0.031321	0.147791	ENSG00000183747	ENST00000219054;ENST00000424070;ENST00000396104	T;T;T	0.42900	0.96;2.28;0.96	3.28	-4.66	0.03329	.	2.661960	0.01665	N	0.025335	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.41784	0.762	B	0.32149	0.141	T	0.31081	-0.9956	9	0.26408	T	0.33	1.0797	0.439	0.00483	0.2256:0.2934:0.228:0.253	rs59292608	5	Q08AH3	ACS2A_HUMAN	Q	5	ENSP00000219054:R5Q;ENSP00000394904:R5Q;ENSP00000379411:R5Q	ENSP00000219054:R5Q	R	+	2	0	ACSM2A	20378951	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-1.073000	0.03430	-0.830000	0.04262	0.454000	0.30748	CGA	G|0.870;A|0.130	0.130	strong		0.493	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845	
TTN	7273	hgsc.bcm.edu	37	2	179578730	179578730	+	Silent	SNP	G	G	A	rs2562839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179578730G>A	ENST00000591111.1	-	90	25928	c.25704C>T	c.(25702-25704)tcC>tcT	p.S8568S	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.S7641S|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Silent_p.S8885S|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12732	Ig-like 68.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTAAGGCCGGATACTTTGT	0.448													A|||	2227	0.444688	0.4644	0.379	5008	,	,		20000	0.6567		0.2237	False		,,,				2504	0.4734				p.S8885S		Atlas-SNP	.											.	TTN	18412	.	0			c.C26655T						PASS	.	A	,,,	1514,2252		311,892,680	177.0	165.0	168.0		,22923,,	1.8	1.0	2	dbSNP_100	168	1660,6590		158,1344,2623	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	469,2236,3303	AA,AG,GG		20.1212,40.2018,26.4148	,,,	,7641/33424,,	179578730	3174,8842	1883	4125	6008	SO:0001819	synonymous_variant	7273	exon92			AAGGCCGGATACT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25704C>T	2.37:g.179578730G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	203	102	0.502463	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.613;A|0.387	0.387	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
C8A	731	hgsc.bcm.edu	37	1	57383358	57383358	+	Missense_Mutation	SNP	C	C	T	rs17300936	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:57383358C>T	ENST00000361249.3	+	11	1820	c.1724C>T	c.(1723-1725)cCa>cTa	p.P575L		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	575	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.		P -> L (in dbSNP:rs17300936).	P -> S (in Ref. 3; AAA82124). {ECO:0000305}.	complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						GCCTCGTGTCCAGGGCGGAAA	0.567													C|||	307	0.0613019	0.0174	0.0432	5008	,	,		17737	0.0585		0.1233	False		,,,				2504	0.0726				p.P575L		Atlas-SNP	.											.	C8A	103	.	0			c.C1724T						PASS	.	C	LEU/PRO	151,4255	104.7+/-143.2	2,147,2054	57.0	57.0	57.0		1724	1.6	0.5	1	dbSNP_123	57	1084,7516	227.5+/-262.8	75,934,3291	yes	missense	C8A	NM_000562.2	98	77,1081,5345	TT,TC,CC		12.6047,3.4271,9.4956	benign	575/585	57383358	1235,11771	2203	4300	6503	SO:0001583	missense	731	exon11			CGTGTCCAGGGCG	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"""Complement system"""	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1724C>T	1.37:g.57383358C>T	ENSP00000354458:p.Pro575Leu	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	306	143	0.46732	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	159	0.07280219780219781	12	0.024390243902439025	19	0.052486187845303865	33	0.057692307692307696	95	0.12532981530343007	C	0.124	-1.122112	0.01785	0.034271	0.126047	ENSG00000157131	ENST00000361249	T	0.54071	0.59	4.82	1.63	0.23807	.	0.346426	0.30879	N	0.008683	T	0.00271	0.0008	N	0.12471	0.22	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.06643	-1.0815	9	0.21540	T	0.41	-1.0877	6.014	0.19592	0.1444:0.5988:0.0:0.2568	rs17300936;rs58858987;rs17300936	575	P07357	CO8A_HUMAN	L	575	ENSP00000354458:P575L	ENSP00000354458:P575L	P	+	2	0	C8A	57155946	0.150000	0.22732	0.470000	0.27216	0.009000	0.06853	0.722000	0.25925	0.611000	0.30052	-0.251000	0.11542	CCA	C|0.917;N|0.000	.	strong		0.567	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
BTNL8	79908	hgsc.bcm.edu	37	5	180374534	180374534	+	Silent	SNP	G	G	A	rs3733756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:180374534G>A	ENST00000340184.4	+	4	902	c.696G>A	c.(694-696)tcG>tcA	p.S232S	BTNL8_ENST00000508408.1_Silent_p.S232S|BTNL8_ENST00000231229.4_Silent_p.S232S|BTNL8_ENST00000505126.1_Silent_p.S25S|BTNL8_ENST00000400707.3_Silent_p.S107S|BTNL8_ENST00000511704.1_Silent_p.S116S|BTNL8_ENST00000533815.2_Silent_p.S48S	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	232					immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.S232S(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGCCTATATCGTGGCACCTGG	0.398													A|||	2208	0.440895	0.6641	0.4496	5008	,	,		19003	0.3462		0.4036	False		,,,				2504	0.2689				p.S232S		Atlas-SNP	.											BTNL8_ENST00000340184,NS,carcinoma,0,2	BTNL8	114	2	2	Substitution - coding silent(2)	prostate(2)	c.G696A						PASS	.	A	,,,,,	2840,1566	490.4+/-361.8	924,992,287	216.0	230.0	225.0		696,348,696,321,144,696	-1.3	0.0	5	dbSNP_107	225	3469,5123	636.0+/-399.0	705,2059,1532	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	,,,,,	1629,3051,1819	AA,AG,GG		40.3748,35.5424,48.5382	,,,,,	232/501,116/385,232/341,107/376,48/317,232/348	180374534	6309,6689	2203	4296	6499	SO:0001819	synonymous_variant	79908	exon4			TATATCGTGGCAC	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.696G>A	5.37:g.180374534G>A		Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	278	275	0.989209	NM_001159708	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Silent	SNP	ENST00000340184.4	37	CCDS43413.1																																																																																			G|0.508;A|0.492	0.492	strong		0.398	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
GBP4	115361	hgsc.bcm.edu	37	1	89652094	89652094	+	Silent	SNP	G	G	A	rs1142887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89652094G>A	ENST00000355754.6	-	10	1726	c.1629C>T	c.(1627-1629)gcC>gcT	p.A543A	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	543						cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		TCTCCATTTGGGCCATGTATT	0.483													G|||	1798	0.359026	0.1445	0.3141	5008	,	,		18373	0.3988		0.4881	False		,,,				2504	0.5072				p.A543A		Atlas-SNP	.											.	GBP4	89	.	0			c.C1629T						PASS	.	G		364,4038		116,132,1953	167.0	103.0	125.0		1629	-0.4	0.0	1	dbSNP_86	125	2588,5944		995,598,2673	no	coding-synonymous	GBP4	NM_052941.4		1111,730,4626	AA,AG,GG		30.3329,8.269,22.8236		543/641	89652094	2952,9982	2201	4266	6467	SO:0001819	synonymous_variant	115361	exon10			CATTTGGGCCATG	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1629C>T	1.37:g.89652094G>A		Somatic	357	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Silent	SNP	ENST00000355754.6	37	CCDS721.1																																																																																			G|0.527;A|0.473	0.473	strong		0.483	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
MXD1	4084	hgsc.bcm.edu	37	2	70162534	70162534	+	Silent	SNP	T	T	G	rs2228183	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:70162534T>G	ENST00000264444.2	+	4	515	c.255T>G	c.(253-255)ctT>ctG	p.L85L	MXD1_ENST00000540449.1_Silent_p.L75L	NM_001202513.1|NM_001202514.1|NM_002357.3	NP_001189442.1|NP_001189443.1|NP_002348.1	Q05195	MAD1_HUMAN	MAX dimerization protein 1	85	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	7						TGGTGCCACTTGGACCCGAAT	0.453													T|||	2924	0.583866	0.8502	0.4035	5008	,	,		20786	0.5407		0.4443	False		,,,				2504	0.5399				p.L85L		Atlas-SNP	.											.	MXD1	23	.	0			c.T255G						PASS	.	T	,,	3451,955	735.3+/-410.7	1350,751,102	115.0	100.0	105.0		255,225,255	-2.1	1.0	2	dbSNP_120	105	3669,4931	525.4+/-380.7	803,2063,1434	no	coding-synonymous,coding-synonymous,coding-synonymous	MXD1	NM_001202513.1,NM_001202514.1,NM_002357.3	,,	2153,2814,1536	GG,GT,TT		42.6628,21.675,45.256	,,	85/221,75/212,85/222	70162534	7120,5886	2203	4300	6503	SO:0001819	synonymous_variant	4084	exon4			GCCACTTGGACCC		CCDS1896.1, CCDS56123.1	2p13-p12	2010-07-07		2005-02-11	ENSG00000059728	ENSG00000059728		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	6761	protein-coding gene	gene with protein product		600021		MAD		7829091	Standard	NM_002357		Approved	MAD1, bHLHc58	uc002sfy.3	Q05195	OTTHUMG00000129646	ENST00000264444.2:c.255T>G	2.37:g.70162534T>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	263	79	0.30038	NM_001202513	B2R6V8|B7ZLI6|D6W5G2|Q6FI41	Silent	SNP	ENST00000264444.2	37	CCDS1896.1																																																																																			T|0.439;G|0.561	0.561	strong		0.453	MXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251845.3	NM_002357	
IDI2	91734	hgsc.bcm.edu	37	10	1068668	1068668	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:1068668G>A	ENST00000277517.1	-	3	254	c.190C>T	c.(190-192)Cga>Tga	p.R64*	IDI2-AS1_ENST00000434470.1_RNA|IDI2-AS1_ENST00000428780.2_RNA|IDI2-AS1_ENST00000420381.1_RNA|IDI2-AS1_ENST00000536039.1_RNA|IDI2-AS1_ENST00000437374.1_RNA	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	64	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isopentenyl diphosphate metabolic process (GO:0046490)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|metal ion binding (GO:0046872)	p.R64*(1)		kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.143)	Epithelial(11;0.067)|OV - Ovarian serous cystadenocarcinoma(14;0.169)|all cancers(11;0.192)		ATCAGGATTCGATTCTTGGTG	0.517																																					p.R64X		Atlas-SNP	.											IDI2,caecum,carcinoma,0,1	IDI2	20	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C190T						scavenged	.						132.0	106.0	115.0					10																	1068668		2203	4300	6503	SO:0001587	stop_gained	91734	exon3			GGATTCGATTCTT	AF271725	CCDS7055.1	10p15.3	2003-11-19			ENSG00000148377	ENSG00000148377			23487	protein-coding gene	gene with protein product		615389				12477932	Standard	NM_033261		Approved	IPPI2	uc001ifv.1	Q9BXS1	OTTHUMG00000017537	ENST00000277517.1:c.190C>T	10.37:g.1068668G>A	ENSP00000277517:p.Arg64*	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	2	0.0235294	NM_033261		Nonsense_Mutation	SNP	ENST00000277517.1	37	CCDS7055.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.059729	0.55325	.	.	ENSG00000148377	ENST00000277517	.	.	.	3.06	-6.12	0.02124	.	0.301126	0.33854	U	0.004487	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-6.8684	9.4123	0.38500	0.0:0.175:0.6093:0.2157	.	.	.	.	X	64	.	ENSP00000277517:R64X	R	-	1	2	IDI2	1058668	0.149000	0.22717	0.000000	0.03702	0.089000	0.18198	0.373000	0.20484	-2.751000	0.00374	0.134000	0.15878	CGA	.	.	none		0.517	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291454	1291454	+	Missense_Mutation	SNP	G	G	A	rs201351744		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1291454G>A	ENST00000338844.3	+	4	286	c.253G>A	c.(253-255)Gcc>Acc	p.A85T	TPSAB1_ENST00000461509.2_Missense_Mutation_p.A92T	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	85	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		A -> T (in dbSNP:rs1141968). {ECO:0000269|PubMed:10898108, ECO:0000269|PubMed:2677049, ECO:0000269|Ref.5}.		defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				GGATCTGGCCGCCCTCAGGGT	0.667																																					p.A85T		Atlas-SNP	.											TPSAB1,NS,carcinoma,0,2	TPSAB1	24	2	0			c.G253A						scavenged	.						6.0	7.0	7.0					16																	1291454		2030	4042	6072	SO:0001583	missense	7177	exon4			CTGGCCGCCCTCA	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.253G>A	16.37:g.1291454G>A	ENSP00000343577:p.Ala85Thr	Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	386	42	0.108808	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	37	CCDS10431.1	.	.	.	.	.	.	.	.	.	.	g	1.250	-0.618741	0.03663	.	.	ENSG00000172236	ENST00000338844;ENST00000461509	D;D	0.88975	-2.45;-2.45	2.93	-5.57	0.02521	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	2.192380	0.02106	N	0.054344	T	0.64204	0.2577	N	0.01146	-0.985	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.63475	-0.6629	10	0.12766	T	0.61	.	1.3572	0.02184	0.1257:0.3104:0.2064:0.3575	.	85	Q15661	TRYB1_HUMAN	T	85;92	ENSP00000343577:A85T;ENSP00000418247:A92T	ENSP00000343577:A85T	A	+	1	0	TPSAB1	1231455	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.166000	0.03129	-0.748000	0.04753	-0.346000	0.07831	GCC	.	.	weak		0.667	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
SIRPG	55423	hgsc.bcm.edu	37	20	1610939	1610939	+	Silent	SNP	G	G	A	rs3746722	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:1610939G>A	ENST00000303415.3	-	5	1159	c.1095C>T	c.(1093-1095)tcC>tcT	p.S365S	SIRPG_ENST00000344103.4_Silent_p.S148S|SIRPG_ENST00000381583.2_Silent_p.S254S|SIRPG_ENST00000216927.4_Silent_p.S254S|SIRPG_ENST00000478145.2_5'UTR|SIRPG_ENST00000381580.1_Silent_p.S332S	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	365					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						GCGCAGTAAGGGATGATGCCG	0.582													a|||	4144	0.827476	0.9372	0.7781	5008	,	,		18784	0.8631		0.6541	False		,,,				2504	0.8558				p.S365S		Atlas-SNP	.											SIRPG,NS,carcinoma,0,1	SIRPG	61	1	0			c.C1095T						PASS	.	A	,,	3894,504		1722,450,27	55.0	55.0	55.0		762,1095,444	-0.4	0.0	20	dbSNP_107	55	5591,3005		1832,1927,539	no	coding-synonymous,coding-synonymous,coding-synonymous	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	3554,2377,566	AA,AG,GG		34.9581,11.4598,27.0048	,,	254/277,365/388,148/171	1610939	9485,3509	2199	4298	6497	SO:0001819	synonymous_variant	55423	exon5			AGTAAGGGATGAT	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.1095C>T	20.37:g.1610939G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_018556	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			G|0.220;A|0.780	0.780	strong		0.582	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
CACNA1S	779	hgsc.bcm.edu	37	1	201060865	201060865	+	Silent	SNP	G	G	A	rs2296383	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:201060865G>A	ENST00000362061.3	-	5	823	c.597C>T	c.(595-597)atC>atT	p.I199I	CACNA1S_ENST00000367338.3_Silent_p.I199I	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	199					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCAGCAGGGCGATGTGAAAGA	0.552													G|||	1528	0.305112	0.0522	0.3963	5008	,	,		21186	0.3929		0.4105	False		,,,				2504	0.3834				p.I199I		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C597T						PASS	.	G		490,3916	228.1+/-243.1	27,436,1740	88.0	70.0	76.0		597	-1.6	1.0	1	dbSNP_100	76	3799,4801	537.8+/-383.3	844,2111,1345	no	coding-synonymous	CACNA1S	NM_000069.2		871,2547,3085	AA,AG,GG		44.1744,11.1212,32.9771		199/1874	201060865	4289,8717	2203	4300	6503	SO:0001819	synonymous_variant	779	exon5			CAGGGCGATGTGA	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.597C>T	1.37:g.201060865G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	177	85	0.480226	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			G|0.684;A|0.316	0.316	strong		0.552	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
KRT71	112802	hgsc.bcm.edu	37	12	52946543	52946543	+	Missense_Mutation	SNP	C	C	T	rs665522	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:52946543C>T	ENST00000267119.5	-	1	388	c.319G>A	c.(319-321)Gtc>Atc	p.V107I		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	107	Head.		V -> I (in dbSNP:rs665522).		hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		CTCTCATTGACGGTAACCTGG	0.617													C|||	1019	0.203474	0.3366	0.1556	5008	,	,		18020	0.0208		0.2286	False		,,,				2504	0.2198				p.V107I		Atlas-SNP	.											.	KRT71	70	.	0			c.G319A						PASS	.	C	ILE/VAL	1323,3083	445.7+/-347.8	196,931,1076	94.0	88.0	90.0		319	3.0	0.7	12	dbSNP_83	90	2037,6563	355.0+/-329.7	250,1537,2513	yes	missense	KRT71	NM_033448.2	29	446,2468,3589	TT,TC,CC		23.686,30.0272,25.8342	benign	107/524	52946543	3360,9646	2203	4300	6503	SO:0001583	missense	112802	exon1			CATTGACGGTAAC	AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.319G>A	12.37:g.52946543C>T	ENSP00000267119:p.Val107Ile	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	167	72	0.431138	NM_033448	B3KVC1|Q3SY85|Q96DU2	Missense_Mutation	SNP	ENST00000267119.5	37	CCDS8831.1	383	0.17536630036630035	143	0.29065040650406504	60	0.16574585635359115	10	0.017482517482517484	170	0.22427440633245382	C	8.203	0.798579	0.16397	0.300272	0.23686	ENSG00000139648	ENST00000267119	T	0.76839	-1.05	4.82	3.0	0.34707	.	0.000000	0.40728	N	0.001039	T	0.00012	0.0000	L	0.37697	1.125	0.36952	P	0.10709500000000005	B	0.26147	0.143	B	0.21360	0.034	T	0.07501	-1.0769	9	0.23891	T	0.37	.	8.1494	0.31132	0.0:0.6857:0.0:0.3143	rs665522;rs1621577;rs17730179;rs665522	107	Q3SY84	K2C71_HUMAN	I	107	ENSP00000267119:V107I	ENSP00000267119:V107I	V	-	1	0	KRT71	51232810	0.001000	0.12720	0.740000	0.30986	0.941000	0.58515	-0.112000	0.10791	0.579000	0.29504	-0.258000	0.10820	GTC	C|0.784;T|0.216	0.216	strong		0.617	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448	
COL12A1	1303	hgsc.bcm.edu	37	6	75848181	75848181	+	Missense_Mutation	SNP	A	A	G	rs240736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:75848181A>G	ENST00000322507.8	-	29	5522	c.5213T>C	c.(5212-5214)aTt>aCt	p.I1738T	COL12A1_ENST00000345356.6_Missense_Mutation_p.I574T|COL12A1_ENST00000416123.2_Missense_Mutation_p.I1738T|COL12A1_ENST00000483888.2_Missense_Mutation_p.I1738T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1738	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> T (in dbSNP:rs240736).		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CTCACTGCCAATCAGGTCATC	0.373													A|||	1327	0.264976	0.3487	0.2911	5008	,	,		19678	0.1548		0.2883	False		,,,				2504	0.2229				p.I1738T		Atlas-SNP	.											.	COL12A1	385	.	0			c.T5213C						PASS	.	A	THR/ILE,THR/ILE	1179,2649		179,821,914	95.0	88.0	90.0		5213,1721	-11.6	0.0	6	dbSNP_79	90	2364,5942		327,1710,2116	yes	missense,missense	COL12A1	NM_004370.5,NM_080645.2	89,89	506,2531,3030	GG,GA,AA		28.4614,30.7994,29.1989	benign,benign	1738/3064,574/1900	75848181	3543,8591	1914	4153	6067	SO:0001583	missense	1303	exon29			CTGCCAATCAGGT	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.5213T>C	6.37:g.75848181A>G	ENSP00000325146:p.Ile1738Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	148	80	0.540541	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	563	0.25778388278388276	169	0.3434959349593496	102	0.281767955801105	86	0.15034965034965034	206	0.2717678100263852	A	6.073	0.381789	0.11524	0.307994	0.284614	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	D;D;D;D	0.86769	-2.13;-2.17;-2.14;-2.11	5.79	-11.6	0.00059	Fibronectin, type III (2);	1.352220	0.04630	N	0.403531	T	0.44138	0.1279	N	0.05306	-0.075	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42103	-0.9471	9	0.12766	T	0.61	.	11.4509	0.50151	0.6276:0.2382:0.1342:0.0	rs240736;rs1758118;rs52807243;rs60846728;rs240736	574;1738	Q99715-2;Q99715	.;COCA1_HUMAN	T	1738;1738;574;1738;1738	ENSP00000325146:I1738T;ENSP00000305147:I574T;ENSP00000412864:I1738T;ENSP00000421216:I1738T	ENSP00000325146:I1738T	I	-	2	0	COL12A1	75904901	0.004000	0.15560	0.002000	0.10522	0.480000	0.33159	0.400000	0.20932	-2.627000	0.00436	-1.074000	0.02243	ATT	A|0.734;G|0.266	0.266	strong		0.373	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
CERKL	375298	hgsc.bcm.edu	37	2	182521578	182521578	+	Silent	SNP	G	G	A	rs1473295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:182521578G>A	ENST00000339098.5	-	1	155	c.156C>T	c.(154-156)ttC>ttT	p.F52F	CERKL_ENST00000374969.2_Silent_p.F52F|CERKL_ENST00000374970.2_Silent_p.F52F|CERKL_ENST00000479558.1_Intron|CERKL_ENST00000410087.3_Silent_p.F52F|CERKL_ENST00000409440.3_Silent_p.F52F			Q49MI3	CERKL_HUMAN	ceramide kinase-like	52					negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			TCCCGATCTCGAAGATGCCCC	0.716													G|||	2541	0.507388	0.1747	0.5216	5008	,	,		13568	0.7312		0.4433	False		,,,				2504	0.7822				p.F52F		Atlas-SNP	.											.	CERKL	138	.	0			c.C156T						PASS	.	G	,,,,	1077,3329		140,797,1266	28.0	34.0	32.0		156,156,156,156,156	1.5	1.0	2	dbSNP_88	32	4151,4447		1031,2089,1179	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CERKL	NM_001030311.2,NM_001030312.2,NM_001030313.2,NM_001160277.1,NM_201548.4	,,,,	1171,2886,2445	AA,AG,GG		48.2787,24.4439,40.203	,,,,	52/559,52/420,52/464,52/515,52/533	182521578	5228,7776	2203	4299	6502	SO:0001819	synonymous_variant	375298	exon1			GATCTCGAAGATG	BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"""retinitis pigmentosa 26 (autosomal recessive)"""	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.156C>T	2.37:g.182521578G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001160277	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Silent	SNP	ENST00000339098.5	37	CCDS42789.1																																																																																			G|0.565;A|0.435	0.435	strong		0.716	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1		
SVIL	6840	hgsc.bcm.edu	37	10	29821523	29821523	+	Silent	SNP	T	T	C	rs1328323	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:29821523T>C	ENST00000355867.4	-	8	2525	c.1773A>G	c.(1771-1773)aaA>aaG	p.K591K	SVIL_ENST00000375400.3_Intron|SVIL_ENST00000375398.2_Silent_p.K591K	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	591					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CGACAGAGACTTTTGTGTCCA	0.577													C|||	1489	0.297324	0.3351	0.3818	5008	,	,		20218	0.0764		0.4245	False		,,,				2504	0.2832				p.K591K		Atlas-SNP	.											.	SVIL	226	.	0			c.A1773G						PASS	.	C	,	1556,2850	669.8+/-402.2	283,990,930	71.0	65.0	67.0		,1773	4.5	1.0	10	dbSNP_88	67	3807,4793	611.6+/-395.8	843,2121,1336	no	intron,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	1126,3111,2266	CC,CT,TT		44.2674,35.3155,41.2348	,	,591/2215	29821523	5363,7643	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon8			AGAGACTTTTGTG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1773A>G	10.37:g.29821523T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	176	84	0.477273	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			C|0.381;G|0.000;T|0.619	0.381	strong		0.577	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
ALPK2	115701	hgsc.bcm.edu	37	18	56204932	56204932	+	Missense_Mutation	SNP	T	T	G	rs3809973	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56204932T>G	ENST00000361673.3	-	5	2700	c.2487A>C	c.(2485-2487)aaA>aaC	p.K829N	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	829			K -> N (in dbSNP:rs3809973).	K -> S (in Ref. 1; CAD89922). {ECO:0000305}.		nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GAGGCGAATATTTATCAACTG	0.418													T|||	2025	0.404353	0.4319	0.4294	5008	,	,		23287	0.2361		0.5726	False		,,,				2504	0.3497				p.K829N		Atlas-SNP	.											.	ALPK2	487	.	0			c.A2487C						PASS	.	T	ASN/LYS	1984,2422	555.8+/-379.4	446,1092,665	87.0	85.0	86.0		2487	4.4	0.4	18	dbSNP_107	86	4588,4012	597.0+/-393.7	1237,2114,949	yes	missense	ALPK2	NM_052947.3	94	1683,3206,1614	GG,GT,TT		46.6512,45.0295,49.4695	probably-damaging	829/2171	56204932	6572,6434	2203	4300	6503	SO:0001583	missense	115701	exon5			CGAATATTTATCA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2487A>C	18.37:g.56204932T>G	ENSP00000354991:p.Lys829Asn	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	230	113	0.491304	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	955	0.43727106227106227	189	0.38414634146341464	184	0.5082872928176796	137	0.2395104895104895	445	0.5870712401055409	T	13.19	2.163361	0.38217	0.450295	0.533488	ENSG00000198796	ENST00000361673	T	0.50813	0.73	5.57	4.36	0.52297	.	1.150850	0.06324	N	0.705000	T	0.00012	0.0000	L	0.54323	1.7	0.53688	P	2.199999999996649E-5	D;D	0.65815	0.995;0.976	P;P	0.61592	0.891;0.524	T	0.43343	-0.9397	9	0.54805	T	0.06	-8.4207	10.1922	0.43032	0.0:0.0:0.1787:0.8213	rs3809973;rs56693680;rs3809973	829;829	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	N	829	ENSP00000354991:K829N	ENSP00000354991:K829N	K	-	3	2	ALPK2	54355912	0.831000	0.29352	0.362000	0.25862	0.039000	0.13416	1.866000	0.39489	2.126000	0.65437	0.482000	0.46254	AAA	T|0.534;G|0.466	0.466	strong		0.418	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
RHOT2	89941	hgsc.bcm.edu	37	16	722548	722548	+	Silent	SNP	A	A	G	rs1128550	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:722548A>G	ENST00000315082.4	+	16	1500	c.1386A>G	c.(1384-1386)ggA>ggG	p.G462G		NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	462	Miro 2.				cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				AGGTCAATGGACAGGAGAAGT	0.667													G|||	3554	0.709665	0.9054	0.5908	5008	,	,		18572	0.997		0.3797	False		,,,				2504	0.5726				p.G462G		Atlas-SNP	.											RHOT2,NS,carcinoma,0,1	RHOT2	35	1	0			c.A1386G						scavenged	.	G		3543,853	321.3+/-297.0	1429,685,84	54.0	64.0	60.0		1386	-2.1	0.2	16	dbSNP_86	60	3063,5529	651.2+/-400.8	556,1951,1789	no	coding-synonymous	RHOT2	NM_138769.1		1985,2636,1873	GG,GA,AA		35.6494,19.404,49.1377		462/619	722548	6606,6382	2198	4296	6494	SO:0001819	synonymous_variant	89941	exon16			CAATGGACAGGAG	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"""EF-hand domain containing"""	21169	protein-coding gene	gene with protein product	"""mitochondrial Rho (MIRO) GTPase 2"""	613889	"""chromosome 16 open reading frame 39"", ""ras homolog gene family, member T2"""	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.1386A>G	16.37:g.722548A>G		Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Silent	SNP	ENST00000315082.4	37	CCDS10417.1																																																																																			A|0.452;G|0.548	0.548	strong		0.667	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769	
SEPT12	124404	hgsc.bcm.edu	37	16	4833970	4833970	+	Silent	SNP	C	C	T	rs759991	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:4833970C>T	ENST00000268231.8	-	5	737	c.474G>A	c.(472-474)gtG>gtA	p.V158V	SEPT12_ENST00000591861.1_5'Flank|SEPT12_ENST00000396693.5_Intron	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	158	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)	p.V158V(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						CGCAGCAGTGCACCCGGGTGT	0.642													C|||	1568	0.313099	0.1989	0.3559	5008	,	,		16641	0.2966		0.3131	False		,,,				2504	0.454				p.V158V		Atlas-SNP	.											SEPT12,NS,carcinoma,0,1	SEPT12	40	1	1	Substitution - coding silent(1)	stomach(1)	c.G474A						PASS	.	C	,	899,3495	346.9+/-309.2	95,709,1393	136.0	124.0	128.0		,474	1.4	1.0	16	dbSNP_86	128	2295,6305	385.5+/-341.5	307,1681,2312	no	intron,coding-synonymous	SEPT12	NM_001154458.2,NM_144605.4	,	402,2390,3705	TT,TC,CC		26.686,20.4597,24.5806	,	,158/359	4833970	3194,9800	2197	4300	6497	SO:0001819	synonymous_variant	124404	exon5			GCAGTGCACCCGG	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.474G>A	16.37:g.4833970C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Silent	SNP	ENST00000268231.8	37	CCDS10522.1																																																																																			C|0.728;T|0.272	0.272	strong		0.642	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605	
ABCC1	4363	hgsc.bcm.edu	37	16	16177275	16177275	+	Missense_Mutation	SNP	G	G	A	rs587779731|rs4148356	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:16177275G>A	ENST00000399410.3	+	17	2343	c.2168G>A	c.(2167-2169)cGa>cAa	p.R723Q	ABCC1_ENST00000349029.5_Intron|ABCC1_ENST00000346370.5_Missense_Mutation_p.R723Q|ABCC1_ENST00000351154.5_Intron|ABCC1_ENST00000399408.2_Missense_Mutation_p.R723Q|ABCC1_ENST00000345148.5_Missense_Mutation_p.R723Q	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	723	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> Q (in dbSNP:rs4148356). {ECO:0000269|PubMed:11266082, ECO:0000269|Ref.4}.		arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	GATTCTCTCCGAGAAAACATC	0.527													G|||	110	0.0219649	0.0008	0.0648	5008	,	,		21711	0.0476		0.0129	False		,,,				2504	0.0031				p.R723Q		Atlas-SNP	.											.	ABCC1	156	.	0			c.G2168A						PASS	.	G	GLN/ARG,,GLN/ARG,,GLN/ARG	14,4032		0,14,2009	74.0	77.0	76.0		2168,,2168,,2168	-2.9	0.1	16	dbSNP_110	76	101,8341		1,99,4121	yes	missense,intron,missense,intron,missense	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	43,,43,,43	1,113,6130	AA,AG,GG		1.1964,0.346,0.9209	benign,,benign,,benign	723/1532,,723/1476,,723/1467	16177275	115,12373	2023	4221	6244	SO:0001583	missense	4363	exon17			CTCTCCGAGAAAA	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.2168G>A	16.37:g.16177275G>A	ENSP00000382342:p.Arg723Gln	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	188	104	0.553191	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	60	0.027472527472527472	0	0.0	15	0.04143646408839779	30	0.05244755244755245	15	0.01978891820580475	G	0.483	-0.879154	0.02550	0.00346	0.011964	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000345148;ENST00000536381	D;D;D;D	0.94184	-3.37;-3.37;-3.37;-3.37	5.27	-2.86	0.05717	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.675642	0.14454	N	0.318598	T	0.66015	0.2747	M	0.68593	2.085	0.09310	N	1	B;B;B;B	0.17268	0.009;0.021;0.014;0.011	B;B;B;B	0.15484	0.002;0.007;0.013;0.007	T	0.65467	-0.6161	10	0.10377	T	0.69	1.3785	13.8447	0.63459	0.6074:0.0:0.3926:0.0	rs4148356;rs52805887;rs60989413;rs4148356	723;723;723;723	P33527-4;P33527-3;P33527;P33527-9	.;.;MRP1_HUMAN;.	Q	723;723;723;723;397	ENSP00000382342:R723Q;ENSP00000382340:R723Q;ENSP00000263019:R723Q;ENSP00000263014:R723Q	ENSP00000263014:R723Q	R	+	2	0	ABCC1	16084776	0.000000	0.05858	0.073000	0.20177	0.439000	0.31926	0.166000	0.16583	-1.263000	0.02455	-2.010000	0.00438	CGA	G|0.977;A|0.023	0.023	strong		0.527	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
RAB1B	81876	hgsc.bcm.edu	37	11	66043586	66043586	+	Silent	SNP	G	G	A	rs367843963		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:66043586G>A	ENST00000311481.6	+	6	630	c.483G>A	c.(481-483)gcG>gcA	p.A161A	CNIH2_ENST00000311445.6_5'Flank|RP11-867G23.4_ENST00000528650.1_RNA|RAB1B_ENST00000527397.1_Silent_p.A129A|RP11-867G23.4_ENST00000526951.1_RNA|RP11-867G23.3_ENST00000501708.1_lincRNA|CNIH2_ENST00000528852.1_5'Flank	NM_030981.2	NP_112243.1	Q9H0U4	RAB1B_HUMAN	RAB1B, member RAS oncogene family	161					ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of glycoprotein metabolic process (GO:1903020)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|virion assembly (GO:0019068)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)			large_intestine(2)|lung(1)|ovary(1)|prostate(1)	5						TCGAGCAGGCGTTCATGACCA	0.582																																					p.A161A		Atlas-SNP	.											.	RAB1B	14	.	0			c.G483A						PASS	.	G		0,4400		0,0,2200	46.0	44.0	45.0		483	-7.8	1.0	11		45	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	RAB1B	NM_030981.2		0,1,6494	AA,AG,GG		0.0116,0.0,0.0077		161/202	66043586	1,12989	2200	4295	6495	SO:0001819	synonymous_variant	81876	exon6			GCAGGCGTTCATG	AJ245875	CCDS31613.1	11q13.1	2008-02-05			ENSG00000174903	ENSG00000174903		"""RAB, member RAS oncogene"""	18370	protein-coding gene	gene with protein product		612565				9030196	Standard	NM_030981		Approved		uc001ohf.3	Q9H0U4	OTTHUMG00000166916	ENST00000311481.6:c.483G>A	11.37:g.66043586G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_030981	A8K7S1	Silent	SNP	ENST00000311481.6	37	CCDS31613.1	.	.	.	.	.	.	.	.	.	.	G	8.325	0.825167	0.16749	0.0	1.16E-4	ENSG00000174903	ENST00000314965	.	.	.	3.9	-7.77	0.01227	.	.	.	.	.	T	0.49712	0.1573	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61068	-0.7137	5	0.87932	D	0	.	2.2152	0.03958	0.3414:0.3799:0.1636:0.1151	.	.	.	.	H	161	.	ENSP00000313814:R161H	R	+	2	0	RAB1B	65800162	0.031000	0.19500	0.975000	0.42487	0.825000	0.46686	-0.719000	0.04974	-0.989000	0.03485	0.313000	0.20887	CGT	.	.	weak		0.582	RAB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391886.2	NM_030981	
LRTOMT	220074	hgsc.bcm.edu	37	11	71800166	71800166	+	Missense_Mutation	SNP	G	G	A	rs146942815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:71800166G>A	ENST00000289488.2	+	3	415	c.37G>A	c.(37-39)Gag>Aag	p.E13K	LRTOMT_ENST00000435085.1_5'UTR|LRTOMT_ENST00000539587.1_Intron|LRTOMT_ENST00000538478.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000324866.7_Missense_Mutation_p.E13K|LRTOMT_ENST00000536917.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000419228.1_5'UTR|LRTOMT_ENST00000541614.1_Missense_Mutation_p.E13K|LAMTOR1_ENST00000545249.1_Intron|LRTOMT_ENST00000447974.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000439209.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000539271.1_Intron|LRTOMT_ENST00000423494.2_Intron|LRTOMT_ENST00000307198.7_Intron	NM_001271471.2|NM_145309.5	NP_001258400.1|NP_660352.1	Q96E66	LRC51_HUMAN	leucine rich transmembrane and O-methyltransferase domain containing	13						cytoplasm (GO:0005737)				large_intestine(2)|lung(1)|ovary(1)	4						TTCGGTACAGGAGCCCCCTCT	0.547													G|||	8	0.00159744	0.0008	0.0029	5008	,	,		17430	0.0		0.004	False		,,,				2504	0.001				p.E13K		Atlas-SNP	.											.	LRTOMT	20	.	0			c.G37A						PASS	.	G	LYS/GLU,,,LYS/GLU	3,4397	6.2+/-15.9	0,3,2197	146.0	121.0	129.0		37,,,37	4.8	1.0	11	dbSNP_134	129	54,8532	34.8+/-89.0	1,52,4240	yes	missense,intron,intron,missense	LRTOMT	NM_001145307.2,NM_001145308.2,NM_001205138.1,NM_145309.3	56,,,56	1,55,6437	AA,AG,GG		0.6289,0.0682,0.4389	possibly-damaging,,,possibly-damaging	13/159,,,13/193	71800166	57,12929	2200	4293	6493	SO:0001583	missense	220074	exon3			GTACAGGAGCCCC		CCDS8208.1, CCDS44667.1, CCDS44668.1, CCDS55778.1, CCDS59227.1	11q13.4	2014-09-05	2013-08-19	2008-11-27	ENSG00000184154	ENSG00000184154			25033	protein-coding gene	gene with protein product		612414	"""leucine rich repeat containing 51"", ""deafness, autosomal recessive 63"""	LRRC51, DFNB63		18794526, 18953341	Standard	NM_145309		Approved	COMT2, CFAP111	uc010rqw.2	Q8WZ04	OTTHUMG00000154887	ENST00000289488.2:c.37G>A	11.37:g.71800166G>A	ENSP00000289488:p.Glu13Lys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_001271471	B2R7X1|B6CZ35|B6CZ36|B6CZ37|B6CZ38|B6CZ39|B7Z5I4	Missense_Mutation	SNP	ENST00000289488.2	37	CCDS8208.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	23.4	4.410355	0.83340	6.82E-4	0.006289	ENSG00000184154	ENST00000538413;ENST00000289488;ENST00000447974;ENST00000538478;ENST00000324866;ENST00000439209;ENST00000542846;ENST00000541614;ENST00000537483;ENST00000536917	T;T;T	0.30182	2.54;2.54;1.54	4.77	4.77	0.60923	.	0.057240	0.64402	D	0.000001	T	0.25306	0.0615	L	0.53249	1.67	0.80722	D	1	P;P	0.43352	0.628;0.804	B;B	0.40066	0.318;0.318	T	0.08889	-1.0700	10	0.46703	T	0.11	-25.2568	17.0634	0.86553	0.0:0.0:1.0:0.0	.	13;13	Q96E66-2;Q96E66	.;LRC51_HUMAN	K	13	ENSP00000289488:E13K;ENSP00000444583:E13K;ENSP00000395139:E13K	ENSP00000289488:E13K	E	+	1	0	LRTOMT	71477814	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.266000	0.65525	2.643000	0.89663	0.655000	0.94253	GAG	G|0.996;A|0.004	0.004	strong		0.547	LRTOMT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337504.1	NM_145309	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110036365	110036365	+	Missense_Mutation	SNP	A	A	C	rs61756697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:110036365A>C	ENST00000278590.3	+	6	2606	c.2555A>C	c.(2554-2556)gAc>gCc	p.D852A	ZC3H12C_ENST00000528673.1_Missense_Mutation_p.D853A|ZC3H12C_ENST00000453089.2_Missense_Mutation_p.D821A	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	852							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		TTCCCCCCTGACCTTGTGAGA	0.493													A|||	50	0.00998403	0.0015	0.0173	5008	,	,		20146	0.0		0.0308	False		,,,				2504	0.0051				p.D852A		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.A2555C						PASS	.	A	ALA/ASP	27,3773		0,27,1873	26.0	26.0	26.0		2555	5.9	1.0	11	dbSNP_129	26	223,8013		3,217,3898	yes	missense	ZC3H12C	NM_033390.1	126	3,244,5771	CC,CA,AA		2.7076,0.7105,2.0771	benign	852/884	110036365	250,11786	1900	4118	6018	SO:0001583	missense	85463	exon6			CCCCTGACCTTGT		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.2555A>C	11.37:g.110036365A>C	ENSP00000278590:p.Asp852Ala	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_033390	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	37	CCDS44727.1	24	0.01098901098901099	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	18	0.023746701846965697	A	13.46	2.244439	0.39697	0.007105	0.027076	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.32515	1.45;1.45;1.46	5.88	5.88	0.94601	.	0.111853	0.64402	D	0.000009	T	0.12390	0.0301	L	0.47716	1.5	0.44018	D	0.996735	P;P;P	0.46395	0.877;0.877;0.877	B;B;B	0.40636	0.335;0.335;0.335	T	0.01386	-1.1368	10	0.56958	D	0.05	-20.8081	16.3015	0.82820	1.0:0.0:0.0:0.0	rs61756697	853;852;852	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	A	852;853;821	ENSP00000278590:D852A;ENSP00000431821:D853A;ENSP00000413094:D821A	ENSP00000278590:D852A	D	+	2	0	ZC3H12C	109541575	1.000000	0.71417	0.998000	0.56505	0.238000	0.25445	7.306000	0.78905	2.239000	0.73571	0.533000	0.62120	GAC	A|0.987;C|0.013	0.013	strong		0.493	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
ALPL	249	hgsc.bcm.edu	37	1	21889635	21889635	+	Silent	SNP	T	T	C	rs1780316|rs200166222	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:21889635T>C	ENST00000374840.3	+	5	580	c.330T>C	c.(328-330)agT>agC	p.S110S	ALPL_ENST00000539907.1_Silent_p.S33S|ALPL_ENST00000540617.1_Silent_p.S55S|ALPL_ENST00000425315.2_Silent_p.S110S|ALPL_ENST00000468526.1_3'UTR|ALPL_ENST00000374832.1_Silent_p.S110S	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	110					cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	TCCCTGACAGTGCCGGCACCG	0.667													C|||	4655	0.929513	0.8495	0.9539	5008	,	,		16617	0.9821		0.9374	False		,,,				2504	0.9581				p.S110S		Atlas-SNP	.											.	ALPL	50	.	0			c.T330C						PASS	.	C	,,	3824,582	251.2+/-258.0	1671,482,50	72.0	64.0	67.0		330,165,99	-3.6	0.8	1	dbSNP_89	67	8164,436	132.5+/-190.1	3872,420,8	no	coding-synonymous,coding-synonymous,coding-synonymous	ALPL	NM_000478.4,NM_001127501.2,NM_001177520.1	,,	5543,902,58	CC,CT,TT		5.0698,13.2093,7.8272	,,	110/525,55/470,33/448	21889635	11988,1018	2203	4300	6503	SO:0001819	synonymous_variant	249	exon5			TGACAGTGCCGGC	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.330T>C	1.37:g.21889635T>C		Somatic	307	2	0.00651466		WXS	Illumina HiSeq	Phase_I	286	284	0.993007	NM_000478	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Silent	SNP	ENST00000374840.3	37	CCDS217.1																																																																																			T|0.072;C|0.928	0.928	strong		0.667	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478	
DLGAP2	9228	hgsc.bcm.edu	37	8	1626541	1626541	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:1626541C>T	ENST00000421627.2	+	9	2344	c.2210C>T	c.(2209-2211)gCg>gTg	p.A737V	DLGAP2_ENST00000524065.1_3'UTR	NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	816					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		CAGTACAGCGCGGTGAGAACT	0.632																																					p.A737V		Atlas-SNP	.											DLGAP2_ENST00000356067,NS,carcinoma,0,3	DLGAP2	292	3	0			c.C2210T						scavenged	.						46.0	54.0	51.0					8																	1626541		2014	4169	6183	SO:0001583	missense	9228	exon9			ACAGCGCGGTGAG	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.2210C>T	8.37:g.1626541C>T	ENSP00000400258:p.Ala737Val	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	82	3	0.0365854	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.22|13.22	2.172334|2.172334	0.38315|0.38315	.|.	.|.	ENSG00000198010|ENSG00000198010	ENST00000356067;ENST00000421627|ENST00000520901	T|.	0.19938|.	2.11|.	5.32|5.32	4.44|4.44	0.53790|0.53790	.|.	0.094982|.	0.64402|.	N|.	0.000001|.	T|T	0.60157|0.60157	0.2247|0.2247	L|L	0.46614|0.46614	1.455|1.455	0.48696|0.48696	D|D	0.999694|0.999694	P;P|.	0.50943|.	0.94;0.894|.	B;P|.	0.46237|.	0.374;0.508|.	T|T	0.57063|0.57063	-0.7875|-0.7875	10|5	0.02654|.	T|.	1|.	-8.3498|-8.3498	13.6933|13.6933	0.62562|0.62562	0.0:0.9256:0.0:0.0744|0.0:0.9256:0.0:0.0744	.|.	802;816|.	Q9P1A6-2;Q9P1A6|.	.;DLGP2_HUMAN|.	V|W	768;737|740	ENSP00000400258:A737V|.	ENSP00000348366:A768V|.	A|R	+|+	2|1	0|2	DLGAP2|DLGAP2	1613948|1613948	1.000000|1.000000	0.71417|0.71417	0.422000|0.422000	0.26621|0.26621	0.513000|0.513000	0.34164|0.34164	4.501000|4.501000	0.60393|0.60393	1.233000|1.233000	0.43693|0.43693	0.650000|0.650000	0.86243|0.86243	GCG|CGG	.	.	none		0.632	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
CACNA2D4	93589	hgsc.bcm.edu	37	12	1949939	1949939	+	Silent	SNP	C	C	T	rs33972365	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:1949939C>T	ENST00000382722.5	-	26	2879	c.2517G>A	c.(2515-2517)gcG>gcA	p.A839A	CACNA2D4_ENST00000587995.1_Silent_p.A814A|CACNA2D4_ENST00000588077.1_Silent_p.A775A|CACNA2D4_ENST00000585708.1_Silent_p.A775A|CACNA2D4_ENST00000586184.1_Silent_p.A839A|CACNA2D4_ENST00000585732.1_Silent_p.A700A	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	839					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		CCACGGTCACCGCCACAGCTG	0.582													C|||	637	0.127196	0.2602	0.0706	5008	,	,		15002	0.0238		0.1163	False		,,,				2504	0.1053				p.A839A	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.G2517A						PASS	.	C		990,3304		110,770,1267	77.0	84.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2517	-7.2	0.0	12	dbSNP_126	82	813,7681		42,729,3476	no	coding-synonymous	CACNA2D4	NM_172364.4		152,1499,4743	TT,TC,CC		9.5715,23.0554,14.0992		839/1138	1949939	1803,10985	2147	4247	6394	SO:0001819	synonymous_variant	93589	exon26			GGTCACCGCCACA	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.2517G>A	12.37:g.1949939C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Silent	SNP	ENST00000382722.5	37	CCDS44785.1																																																																																			C|0.890;T|0.110	0.110	strong		0.582	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
NAA25	80018	hgsc.bcm.edu	37	12	112471090	112471090	+	Missense_Mutation	SNP	G	G	T	rs12298022	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:112471090G>T	ENST00000261745.4	-	23	2991	c.2743C>A	c.(2743-2745)Cta>Ata	p.L915I		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	915			L -> I (in dbSNP:rs12298022).			cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						AGTGCAATTAGATGTGTTTCA	0.388													g|||	563	0.11242	0.298	0.098	5008	,	,		19040	0.0		0.0706	False		,,,				2504	0.0307				p.L915I		Atlas-SNP	.											.	NAA25	105	.	0			c.C2743A						PASS	.	G	ILE/LEU	1133,3273	404.6+/-333.2	148,837,1218	111.0	116.0	114.0		2743	5.0	1.0	12	dbSNP_120	114	629,7971	164.1+/-216.5	22,585,3693	yes	missense	NAA25	NM_024953.3	5	170,1422,4911	TT,TG,GG		7.314,25.7149,13.5476	benign	915/973	112471090	1762,11244	2203	4300	6503	SO:0001583	missense	80018	exon23			CAATTAGATGTGT	AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"""N(alpha)-acetyltransferase subunits"""	25783	protein-coding gene	gene with protein product		612755	"""chromosome 12 open reading frame 30"""	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.2743C>A	12.37:g.112471090G>T	ENSP00000261745:p.Leu915Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	145	67	0.462069	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	237	0.10851648351648352	147	0.29878048780487804	45	0.12430939226519337	0	0.0	45	0.059366754617414245	G	14.73	2.621707	0.46736	0.257149	0.07314	ENSG00000111300	ENST00000261745	T	0.35421	1.31	5.91	5.01	0.66863	.	0.257811	0.33916	N	0.004423	T	0.00012	0.0000	N	0.19112	0.55	0.26394	P	0.9765313	D	0.52996	0.957	P	0.44696	0.458	T	0.33929	-0.9849	9	0.40728	T	0.16	-2.1641	14.549	0.68052	0.0695:0.0:0.9305:0.0	rs12298022;rs52836486;rs57720948;rs12298022	915	Q14CX7	NAA25_HUMAN	I	915	ENSP00000261745:L915I	ENSP00000261745:L915I	L	-	1	2	NAA25	110955473	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.008000	0.49544	2.816000	0.96949	0.644000	0.83932	CTA	G|0.868;T|0.132	0.132	strong		0.388	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953	
WDR66	144406	hgsc.bcm.edu	37	12	122369762	122369762	+	Silent	SNP	C	C	T	rs7313748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:122369762C>T	ENST00000288912.4	+	4	1712	c.858C>T	c.(856-858)aaC>aaT	p.N286N	WDR66_ENST00000397454.2_Silent_p.N286N	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	286							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		TCATCTACAACGTGTTCAGGA	0.438													C|||	1400	0.279553	0.0204	0.3602	5008	,	,		21400	0.4821		0.3131	False		,,,				2504	0.3292				p.N286N	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C858T						PASS	.	C	,	228,3760		10,208,1776	162.0	148.0	152.0		858,858	-1.1	0.1	12	dbSNP_116	152	2499,5849		383,1733,2058	no	coding-synonymous,coding-synonymous	WDR66	NM_001178003.1,NM_144668.5	,	393,1941,3834	TT,TC,CC		29.9353,5.7172,22.106	,	286/942,286/1150	122369762	2727,9609	1994	4174	6168	SO:0001819	synonymous_variant	144406	exon4			CTACAACGTGTTC	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.858C>T	12.37:g.122369762C>T		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	238	110	0.462185	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Silent	SNP	ENST00000288912.4	37	CCDS41853.1																																																																																			C|0.713;T|0.287	0.287	strong		0.438	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
SNUPN	10073	hgsc.bcm.edu	37	15	75909803	75909803	+	Silent	SNP	A	A	G	rs11547316	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75909803A>G	ENST00000564644.1	-	4	827	c.249T>C	c.(247-249)gaT>gaC	p.D83D	SNUPN_ENST00000371091.5_Silent_p.D125D|SNUPN_ENST00000308588.5_Silent_p.D83D|SNUPN_ENST00000567134.1_Silent_p.D83D|SNUPN_ENST00000564675.1_Silent_p.D83D			O95149	SPN1_HUMAN	snurportin 1	83	Necessary for interaction with XPO1.				gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein import into nucleus (GO:0006606)|RNA metabolic process (GO:0016070)|snRNA import into nucleus (GO:0061015)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear pore (GO:0005643)	protein transporter activity (GO:0008565)|RNA cap binding (GO:0000339)			endometrium(2)|large_intestine(3)|lung(2)|pancreas(1)	8						CCATTTCTTCATCATCTTTCT	0.438													A|||	386	0.0770767	0.0219	0.0865	5008	,	,		21267	0.0		0.1044	False		,,,				2504	0.1963				p.D83D		Atlas-SNP	.											.	SNUPN	26	.	0			c.T249C						PASS	.	A	,,	156,4238	105.6+/-144.1	6,144,2047	406.0	317.0	347.0		249,249,249	-6.4	1.0	15	dbSNP_120	347	871,7717	197.3+/-242.0	37,797,3460	no	coding-synonymous,coding-synonymous,coding-synonymous	SNUPN	NM_001042581.1,NM_001042588.1,NM_005701.3	,,	43,941,5507	GG,GA,AA		10.1421,3.5503,7.911	,,	83/361,83/361,83/361	75909803	1027,11955	2197	4294	6491	SO:0001819	synonymous_variant	10073	exon3			TTCTTCATCATCT	AF039029	CCDS10281.1	15q24.2	2008-02-05	2006-07-14	2006-07-14	ENSG00000169371	ENSG00000169371			14245	protein-coding gene	gene with protein product		607902	"""RNA, U transporter 1"""	RNUT1		9670026	Standard	NM_005701		Approved	SNURPORTIN-1, Snurportin1	uc002bas.3	O95149	OTTHUMG00000142833	ENST00000564644.1:c.249T>C	15.37:g.75909803A>G		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	199	103	0.517588	NM_001042581	A6NE34|A8K0B0|D3DW76	Silent	SNP	ENST00000564644.1	37	CCDS10281.1																																																																																			A|0.923;G|0.077	0.077	strong		0.438	SNUPN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420332.1	NM_005701	
OPTN	10133	hgsc.bcm.edu	37	10	13151224	13151224	+	Silent	SNP	G	G	A	rs2234968	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:13151224G>A	ENST00000378748.3	+	4	464	c.102G>A	c.(100-102)acG>acA	p.T34T	OPTN_ENST00000378764.2_Silent_p.T34T|OPTN_ENST00000378752.3_Silent_p.T34T|OPTN_ENST00000378747.3_Silent_p.T34T|OPTN_ENST00000482140.1_3'UTR|OPTN_ENST00000378757.2_Silent_p.T34T|OPTN_ENST00000263036.5_Silent_p.T34T	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	34					cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)	p.T34T(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						ACCTGGACACGTTTACCCCGG	0.597													G|||	893	0.178315	0.0144	0.2262	5008	,	,		15083	0.1925		0.2654	False		,,,				2504	0.2618				p.T34T		Atlas-SNP	.											OPTN,NS,carcinoma,0,1	OPTN	57	1	1	Substitution - coding silent(1)	stomach(1)	c.G102A	GRCh37	CM066944	OPTN	M	rs2234968	PASS	.	G	,,,	258,4148	147.6+/-182.1	6,246,1951	82.0	82.0	82.0		102,102,102,102	-10.6	0.2	10	dbSNP_98	82	2360,6240	394.1+/-344.6	311,1738,2251	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OPTN	NM_001008211.1,NM_001008212.1,NM_001008213.1,NM_021980.4	,,,	317,1984,4202	AA,AG,GG		27.4419,5.8557,20.1292	,,,	34/578,34/578,34/578,34/578	13151224	2618,10388	2203	4300	6503	SO:0001819	synonymous_variant	10133	exon3			GGACACGTTTACC	AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"""glaucoma 1, open angle, E (adult-onset)"""	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.102G>A	10.37:g.13151224G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	78	45	0.576923	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Silent	SNP	ENST00000378748.3	37	CCDS7094.1																																																																																			G|0.815;A|0.185	0.185	strong		0.597	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980	
RAX2	84839	hgsc.bcm.edu	37	19	3771684	3771684	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:3771684G>A	ENST00000555633.1	-	2	397	c.57C>T	c.(55-57)ggC>ggT	p.G19G	RAX2_ENST00000555978.1_Silent_p.G19G			Q96IS3	RAX2_HUMAN	retina and anterior neural fold homeobox 2	19					regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGCCTCCTCGCCCGGCCCCA	0.701																																					p.G19G		Atlas-SNP	.											.	RAX2	4	.	0			c.C57T						PASS	.						45.0	40.0	42.0					19																	3771684		2200	4298	6498	SO:0001819	synonymous_variant	84839	exon2			CTCCTCGCCCGGC	AY211277	CCDS12112.1	19p13.3	2013-06-06	2007-08-28	2007-08-28				"""Homeoboxes / PRD class"""	18286	protein-coding gene	gene with protein product		610362	"""retina and anterior neural fold homeobox like 1"""	RAXL1			Standard	NM_032753		Approved	MGC15631, ARMD6, CORD11	uc002lys.3	Q96IS3		ENST00000555633.1:c.57C>T	19.37:g.3771684G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_032753		Silent	SNP	ENST00000555633.1	37	CCDS12112.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.466341	0.43839	.	.	ENSG00000173976	ENST00000555978	.	.	.	2.98	-5.96	0.02234	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.1764	0.06570	0.3839:0.0:0.3174:0.2987	.	.	.	.	X	39	.	.	R	-	1	2	RAX2	3722684	0.000000	0.05858	0.160000	0.22671	0.866000	0.49608	-2.379000	0.01067	-1.095000	0.03050	0.491000	0.48974	CGA	.	.	none		0.701	RAX2-001	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411919.2	NM_032753	
BPIFB6	128859	hgsc.bcm.edu	37	20	31622083	31622083	+	Missense_Mutation	SNP	G	G	A	rs2070317	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:31622083G>A	ENST00000349552.1	+	3	289	c.289G>A	c.(289-291)Gtc>Atc	p.V97I		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	97			V -> I (in dbSNP:rs2070317).			extracellular region (GO:0005576)	lipid binding (GO:0008289)										AGGCATGACCGTCACTGGCAA	0.547													A|||	2850	0.569089	0.4592	0.5303	5008	,	,		20988	0.7579		0.5179	False		,,,				2504	0.6033				p.V97I		Atlas-SNP	.											.	.	.	.	0			c.G289A						PASS	.	A	ILE/VAL	1962,2444	619.7+/-393.4	449,1064,690	125.0	98.0	107.0		289	4.7	1.0	20	dbSNP_96	107	4389,4211	571.1+/-389.5	1131,2127,1042	yes	missense	BPIFB6	NM_174897.2	29	1580,3191,1732	AA,AG,GG		48.9651,44.5302,48.8313	benign	97/454	31622083	6351,6655	2203	4300	6503	SO:0001583	missense	128859	exon3			ATGACCGTCACTG	AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"""BPI fold containing"""	16504	protein-coding gene	gene with protein product		614110	"""bactericidal/permeability-increasing protein-like 3"""	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.289G>A	20.37:g.31622083G>A	ENSP00000344929:p.Val97Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_174897		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	1246	0.5705128205128205	239	0.48577235772357724	181	0.5	429	0.75	397	0.5237467018469657	A	4.462	0.085670	0.08583	0.445302	0.510349	ENSG00000167104	ENST00000349552	T	0.04275	3.66	4.7	4.7	0.59300	.	0.109676	0.40385	N	0.001117	T	0.00012	0.0000	N	0.00188	-1.89	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.16867	-1.0388	9	0.07813	T	0.8	.	7.2204	0.25983	0.8961:0.0:0.1039:0.0	rs2070317;rs17373278;rs2070317	97	Q8NFQ5	BPIB6_HUMAN	I	97	ENSP00000344929:V97I	ENSP00000344929:V97I	V	+	1	0	BPIFB6	31085744	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.180000	0.42537	0.649000	0.30751	-0.361000	0.07541	GTC	G|0.480;A|0.520	0.520	strong		0.547	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897	
PLIN4	729359	hgsc.bcm.edu	37	19	4512669	4512669	+	Missense_Mutation	SNP	T	T	C	rs55901236	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:4512669T>C	ENST00000301286.3	-	3	1260	c.1261A>G	c.(1261-1263)Acc>Gcc	p.T421A		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	421	27 X 33 AA approximate tandem repeat.		T -> A (in dbSNP:rs55901236).			cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CTGCAGACGGTGTCCTTTGTA	0.557													T|||	2274	0.454073	0.118	0.4741	5008	,	,		19060	0.7153		0.5696	False		,,,				2504	0.5061				p.T421A		Atlas-SNP	.											.	PLIN4	191	.	0			c.A1261G						PASS	.	T	ALA/THR	828,3146		215,398,1374	90.0	130.0	117.0		1261	0.1	0.0	19	dbSNP_129	117	4493,3881		1426,1641,1120	yes	missense	PLIN4	NM_001080400.1	58	1641,2039,2494	CC,CT,TT		46.3458,20.8354,43.092	possibly-damaging	421/1358	4512669	5321,7027	1987	4187	6174	SO:0001583	missense	729359	exon3			AGACGGTGTCCTT	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1261A>G	19.37:g.4512669T>C	ENSP00000301286:p.Thr421Ala	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	194	87	0.448454	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	1099	0.5032051282051282	73	0.1483739837398374	186	0.5138121546961326	407	0.7115384615384616	433	0.5712401055408971	T	9.686	1.150525	0.21371	0.208354	0.536542	ENSG00000167676	ENST00000301286	T	0.15139	2.45	4.69	0.0866	0.14447	.	0.115125	0.38837	N	0.001559	T	0.00012	0.0000	L	0.45422	1.42	0.80722	P	0.0	B	0.14012	0.009	B	0.12837	0.008	T	0.20140	-1.0284	9	0.40728	T	0.16	-9.8017	8.6452	0.34000	0.0:0.3322:0.0:0.6678	rs55901236;rs61730736	421	Q96Q06	PLIN4_HUMAN	A	421	ENSP00000301286:T421A	ENSP00000301286:T421A	T	-	1	0	PLIN4	4463669	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.441000	0.06879	-0.085000	0.12573	0.369000	0.22263	ACC	T|0.494;C|0.506	0.506	strong		0.557	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
TANC1	85461	hgsc.bcm.edu	37	2	160035195	160035195	+	Silent	SNP	C	C	T	rs12988603	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160035195C>T	ENST00000263635.6	+	14	2268	c.2031C>T	c.(2029-2031)aaC>aaT	p.N677N	TANC1_ENST00000454300.1_Silent_p.N571N	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	677					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						TCCTCAGCAACATCTCCCTGA	0.567													C|||	800	0.159744	0.0703	0.2478	5008	,	,		18770	0.0635		0.3688	False		,,,				2504	0.1022				p.N677N		Atlas-SNP	.											.	TANC1	157	.	0			c.C2031T						PASS	.	C	,	549,3793		35,479,1657	55.0	58.0	57.0		2007,2031	5.0	1.0	2	dbSNP_121	57	3069,5431		549,1971,1730	no	coding-synonymous,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	584,2450,3387	TT,TC,CC		36.1059,12.6439,28.1732	,	669/1391,677/1862	160035195	3618,9224	2171	4250	6421	SO:0001819	synonymous_variant	85461	exon14			CAGCAACATCTCC	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.2031C>T	2.37:g.160035195C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	215	113	0.525581	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			C|0.763;T|0.237	0.237	strong		0.567	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
ECM1	1893	hgsc.bcm.edu	37	1	150483355	150483355	+	Missense_Mutation	SNP	C	C	T	rs3737240	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:150483355C>T	ENST00000369047.4	+	6	514	c.389C>T	c.(388-390)aCg>aTg	p.T130M	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Missense_Mutation_p.T157M|ECM1_ENST00000346569.6_Missense_Mutation_p.T130M	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	130			T -> M (in dbSNP:rs3737240). {ECO:0000269|PubMed:12603844, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			ATTCCAGGAACGCCAGCTCCA	0.597													C|||	1121	0.223842	0.0325	0.2493	5008	,	,		17844	0.2371		0.3757	False		,,,				2504	0.2945				p.T157M	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											ECM1_ENST00000369049,NS,carcinoma,0,2	ECM1	96	2	0			c.C470T						PASS	.	C	MET/THR,MET/THR,MET/THR	418,3954		29,360,1797	53.0	54.0	53.0		470,389,389	-5.2	0.0	1	dbSNP_107	53	3405,5143		706,1993,1575	yes	missense,missense,missense	ECM1	NM_001202858.1,NM_004425.3,NM_022664.2	81,81,81	735,2353,3372	TT,TC,CC		39.8339,9.5608,29.5898	benign,benign,benign	157/568,130/541,130/416	150483355	3823,9097	2186	4274	6460	SO:0001583	missense	1893	exon6			CAGGAACGCCAGC	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.389C>T	1.37:g.150483355C>T	ENSP00000358043:p.Thr130Met	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	157	77	0.490446	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Missense_Mutation	SNP	ENST00000369047.4	37	CCDS953.1	533	0.24404761904761904	15	0.03048780487804878	106	0.292817679558011	134	0.23426573426573427	278	0.36675461741424803	C	9.009	0.981920	0.18812	0.095608	0.398339	ENSG00000143369	ENST00000369049;ENST00000369047;ENST00000346569	T;T;T	0.75821	-0.97;-0.97;-0.97	4.86	-5.22	0.02806	.	0.733388	0.12158	N	0.494295	T	0.38506	0.1043	L	0.29908	0.895	0.80722	P	0.0	D;B;B;B;B	0.64830	0.994;0.02;0.11;0.0;0.136	P;B;B;B;B	0.47744	0.556;0.005;0.01;0.0;0.023	T	0.25710	-1.0124	9	0.35671	T	0.21	-2.6117	1.2462	0.01973	0.2141:0.1373:0.1627:0.4858	rs3737240;rs11541581;rs17852141;rs3737240	59;157;130;130;130	Q16610-3;Q16610-4;C8CHS3;Q16610-2;Q16610	.;.;.;.;ECM1_HUMAN	M	157;130;130	ENSP00000358045:T157M;ENSP00000358043:T130M;ENSP00000271630:T130M	ENSP00000271630:T130M	T	+	2	0	ECM1	148749979	0.189000	0.23263	0.001000	0.08648	0.001000	0.01503	-0.279000	0.08479	-0.716000	0.04962	-2.727000	0.00130	ACG	C|0.728;T|0.272	0.272	strong		0.597	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
KIAA1328	57536	hgsc.bcm.edu	37	18	34647323	34647323	+	Silent	SNP	T	T	A	rs3747896	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:34647323T>A	ENST00000280020.5	+	7	1069	c.1047T>A	c.(1045-1047)ggT>ggA	p.G349G	KIAA1328_ENST00000586135.1_Silent_p.G65G|KIAA1328_ENST00000543923.1_Silent_p.G241G|KIAA1328_ENST00000591619.1_Silent_p.G345G|KIAA1328_ENST00000435985.2_Silent_p.G65G|KIAA1328_ENST00000586501.1_Silent_p.G65G	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	349										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		TGCATGGTGGTGGGGCACTGC	0.448													A|||	1299	0.259385	0.6445	0.1311	5008	,	,		19160	0.1101		0.1292	False		,,,				2504	0.1176				p.G349G		Atlas-SNP	.											.	KIAA1328	39	.	0			c.T1047A						PASS	.	A		2353,1669		730,893,388	72.0	69.0	70.0		1047	-0.9	0.0	18	dbSNP_107	70	1345,7043		269,807,3118	no	coding-synonymous	KIAA1328	NM_020776.1		999,1700,3506	AA,AT,TT		16.0348,41.4968,29.7985		349/578	34647323	3698,8712	2011	4194	6205	SO:0001819	synonymous_variant	57536	exon7			TGGTGGTGGGGCA	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.1047T>A	18.37:g.34647323T>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	233	105	0.450644	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Silent	SNP	ENST00000280020.5	37	CCDS45855.1																																																																																			A|0.237;G|0.031;T|0.732	0.237	strong		0.448	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776	
PCNT	5116	hgsc.bcm.edu	37	21	47831621	47831621	+	Silent	SNP	C	C	T	rs61735811	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47831621C>T	ENST00000359568.5	+	28	5741	c.5634C>T	c.(5632-5634)gaC>gaT	p.D1878D	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1878					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TAGAAATCGACGCTCTGAACC	0.642													C|||	119	0.023762	0.0212	0.0303	5008	,	,		15874	0.001		0.0646	False		,,,				2504	0.0041				p.D1878D		Atlas-SNP	.											PCNT,colon,carcinoma,0,1	PCNT	283	1	0			c.C5634T						PASS	.	C		150,4246		2,146,2050	25.0	28.0	27.0		5634	-11.6	0.0	21	dbSNP_129	27	514,8068		9,496,3786	no	coding-synonymous	PCNT	NM_006031.5		11,642,5836	TT,TC,CC		5.9893,3.4122,5.1164		1878/3337	47831621	664,12314	2198	4291	6489	SO:0001819	synonymous_variant	5116	exon28			AATCGACGCTCTG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.5634C>T	21.37:g.47831621C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.953;T|0.047	0.047	strong		0.642	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
TMEM207	131920	hgsc.bcm.edu	37	3	190158168	190158168	+	Missense_Mutation	SNP	G	G	C	rs35161724	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:190158168G>C	ENST00000354905.2	-	4	235	c.169C>G	c.(169-171)Ctg>Gtg	p.L57V		NM_207316.1	NP_997199.1	Q6UWW9	TM207_HUMAN	transmembrane protein 207	57			L -> V (in dbSNP:rs35161724).			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(4)	7	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)		AAAACCAGCAGCAGGAGGATC	0.527													G|||	349	0.0696885	0.0681	0.111	5008	,	,		17689	0.0179		0.1441	False		,,,				2504	0.0194				p.L57V		Atlas-SNP	.											.	TMEM207	19	.	0			c.C169G						PASS	.	G	VAL/LEU	388,4018	194.3+/-219.2	27,334,1842	39.0	37.0	38.0		169	-0.8	0.0	3	dbSNP_126	38	1180,7420	236.9+/-269.0	90,1000,3210	yes	missense	TMEM207	NM_207316.1	32	117,1334,5052	CC,CG,GG		13.7209,8.8062,12.056	probably-damaging	57/147	190158168	1568,11438	2203	4300	6503	SO:0001583	missense	131920	exon4			CCAGCAGCAGGAG	BC071780	CCDS3297.1	3q28	2008-02-18			ENSG00000198398	ENSG00000198398			33705	protein-coding gene	gene with protein product		614786					Standard	NM_207316		Approved		uc003fsj.2	Q6UWW9	OTTHUMG00000156213	ENST00000354905.2:c.169C>G	3.37:g.190158168G>C	ENSP00000346981:p.Leu57Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_207316		Missense_Mutation	SNP	ENST00000354905.2	37	CCDS3297.1	202	0.0924908424908425	45	0.09146341463414634	39	0.10773480662983426	7	0.012237762237762238	111	0.14643799472295516	G	11.44	1.639457	0.29157	0.088062	0.137209	ENSG00000198398	ENST00000354905	T	0.17854	2.25	6.07	-0.803	0.10886	.	0.318696	0.22483	N	0.059478	T	0.00073	0.0002	N	0.20881	0.62	0.54753	P	1.3000000000040757E-5	D	0.55385	0.971	P	0.48270	0.572	T	0.24977	-1.0145	9	0.87932	D	0	-2.4688	5.0979	0.14742	0.3395:0.0:0.5073:0.1532	rs35161724	57	Q6UWW9	TM207_HUMAN	V	57	ENSP00000346981:L57V	ENSP00000346981:L57V	L	-	1	2	TMEM207	191640862	0.044000	0.20184	0.026000	0.17262	0.056000	0.15407	0.311000	0.19380	-0.059000	0.13154	0.650000	0.86243	CTG	G|0.893;C|0.107	0.107	strong		0.527	TMEM207-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343515.1	NM_207316	
NLRP4	147945	hgsc.bcm.edu	37	19	56392875	56392875	+	Silent	SNP	T	T	G	rs302456	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56392875T>G	ENST00000301295.6	+	10	3329	c.2907T>G	c.(2905-2907)ctT>ctG	p.L969L	NLRP4_ENST00000587891.1_Silent_p.L894L|NLRP4_ENST00000346986.5_Silent_p.L913L	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	969					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.L969L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CCCAGGCACTTCTGACGGCTG	0.428													T|||	1257	0.250998	0.3525	0.2839	5008	,	,		18541	0.2063		0.2326	False		,,,				2504	0.1554				p.L969L		Atlas-SNP	.											NLRP4_ENST00000301295,colon,carcinoma,+2,2	NLRP4	331	2	1	Substitution - coding silent(1)	stomach(1)	c.T2907G						PASS	.	T		1455,2951	470.5+/-355.8	231,993,979	72.0	60.0	64.0		2907	-4.7	0.0	19	dbSNP_79	64	2382,6218	396.3+/-345.4	311,1760,2229	no	coding-synonymous	NLRP4	NM_134444.4		542,2753,3208	GG,GT,TT		27.6977,33.0232,29.5018		969/995	56392875	3837,9169	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon10			GGCACTTCTGACG	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.2907T>G	19.37:g.56392875T>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	76	46	0.605263	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			T|0.716;G|0.284	0.284	strong		0.428	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
ZBTB21	49854	hgsc.bcm.edu	37	21	43413553	43413553	+	Missense_Mutation	SNP	T	T	G	rs871546	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:43413553T>G	ENST00000310826.5	-	3	835	c.652A>C	c.(652-654)Aag>Cag	p.K218Q	ZBTB21_ENST00000398505.3_Missense_Mutation_p.K218Q|ZBTB21_ENST00000398499.1_Missense_Mutation_p.K218Q|ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398511.3_Missense_Mutation_p.K218Q	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	218			K -> Q (in dbSNP:rs871546).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										TCAAGAGACTTTGCATATACC	0.393													T|||	878	0.175319	0.1415	0.1297	5008	,	,		21882	0.0764		0.2634	False		,,,				2504	0.2648				p.K218Q		Atlas-SNP	.											.	.	.	.	0			c.A652C						PASS	.	T	GLN/LYS,GLN/LYS,GLN/LYS	729,3677	303.2+/-287.8	66,597,1540	100.0	100.0	100.0		652,652,652	4.6	0.1	21	dbSNP_86	100	2222,6378	377.7+/-338.6	295,1632,2373	yes	missense,missense,missense	ZNF295	NM_001098402.1,NM_001098403.1,NM_020727.4	53,53,53	361,2229,3913	GG,GT,TT		25.8372,16.5456,22.6895	benign,benign,benign	218/1067,218/866,218/1067	43413553	2951,10055	2203	4300	6503	SO:0001583	missense	49854	exon3			GAGACTTTGCATA	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.652A>C	21.37:g.43413553T>G	ENSP00000308759:p.Lys218Gln	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	273	140	0.512821	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Missense_Mutation	SNP	ENST00000310826.5	37	CCDS13678.1	371	0.16987179487179488	60	0.12195121951219512	55	0.15193370165745856	41	0.07167832167832168	215	0.2836411609498681	T	20.5	4.006780	0.74932	0.165456	0.258372	ENSG00000173276	ENST00000398505;ENST00000310826;ENST00000398499;ENST00000398511	T;T;T;T	0.09911	3.08;2.93;2.93;2.93	5.8	4.64	0.57946	.	0.681137	0.14431	N	0.320024	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B;B	0.20052	0.041;0.008	B;B	0.20955	0.032;0.005	T	0.25813	-1.0121	9	0.62326	D	0.03	-20.2354	11.8973	0.52663	0.0:0.0:0.1457:0.8543	rs871546;rs17766787;rs59181259;rs871546	218;218	Q9ULJ3-2;Q9ULJ3	.;ZN295_HUMAN	Q	218	ENSP00000381517:K218Q;ENSP00000308759:K218Q;ENSP00000381512:K218Q;ENSP00000381523:K218Q	ENSP00000308759:K218Q	K	-	1	0	ZNF295	42286622	0.955000	0.32602	0.097000	0.21041	0.998000	0.95712	3.556000	0.53734	1.011000	0.39340	0.533000	0.62120	AAG	T|0.803;G|0.197	0.197	strong		0.393	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727	
CEACAM18	729767	hgsc.bcm.edu	37	19	51981753	51981753	+	5'Flank	SNP	G	G	C	rs11878388	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51981753G>C	ENST00000396477.4	+	0	0				CEACAM18_ENST00000451626.1_Missense_Mutation_p.A14P	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18											breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TGGTCAGAGTGCACCCTGGGG	0.562													c|||	925	0.184704	0.2383	0.1643	5008	,	,		14516	0.123		0.1958	False		,,,				2504	0.1789				p.A14P		Atlas-SNP	.											.	CEACAM18	96	.	0			c.G40C						PASS	.	C	PRO/ALA	791,3035		84,623,1206	11.0	13.0	12.0		40	1.8	0.6	19	dbSNP_120	12	1429,6789		139,1151,2819	yes	missense	CEACAM18	NM_001080405.1	27	223,1774,4025	CC,CG,GG		17.3887,20.6743,18.4324	possibly-damaging	14/399	51981753	2220,9824	1913	4109	6022	SO:0001631	upstream_gene_variant	729767	exon2			CAGAGTGCACCCT			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9			19.37:g.51981753G>C	Exception_encountered	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		366	0.16758241758241757	111	0.22560975609756098	63	0.17403314917127072	56	0.0979020979020979	136	0.17941952506596306	.	0.080	-1.184648	0.01620	0.206743	0.173887	ENSG00000213822	ENST00000451626	T	0.08102	3.13	2.82	1.78	0.24846	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45205	-0.9277	8	0.87932	D	0	.	4.3821	0.11299	0.0:0.6337:0.2327:0.1336	rs11878388;rs11878388	14	A8MTB9	CEA18_HUMAN	P	14	ENSP00000402203:A14P	ENSP00000402203:A14P	A	+	1	0	CEACAM18	56673565	0.111000	0.22076	0.573000	0.28510	0.014000	0.08584	-0.052000	0.11865	0.286000	0.22352	-0.704000	0.03662	GCA	G|0.834;C|0.166	0.166	strong		0.562	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
RP1L1	94137	hgsc.bcm.edu	37	8	10470068	10470068	+	Missense_Mutation	SNP	C	C	T	rs74990397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:10470068C>T	ENST00000382483.3	-	4	1763	c.1540G>A	c.(1540-1542)Ggc>Agc	p.G514S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	514				G -> S (in Ref. 2; CAD36957). {ECO:0000305}.	cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGCTCTGGGCCGCCCAGCCCT	0.682													C|||	1476	0.294728	0.348	0.3112	5008	,	,		14828	0.0208		0.5109	False		,,,				2504	0.271				p.G514S		Atlas-SNP	.											RP1L1,NS,haematopoietic_neoplasm,0,1	RP1L1	453	1	0			c.G1540A						PASS	.	C	SER/GLY	1311,2557		228,855,851	27.0	31.0	30.0		1540	-8.6	0.0	8	dbSNP_131	30	4110,4122		1087,1936,1093	yes	missense	RP1L1	NM_178857.5	56	1315,2791,1944	TT,TC,CC		49.9271,33.8935,44.8017	benign	514/2401	10470068	5421,6679	1934	4116	6050	SO:0001583	missense	94137	exon4			CTGGGCCGCCCAG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1540G>A	8.37:g.10470068C>T	ENSP00000371923:p.Gly514Ser	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	32	22	0.6875	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	687	0.31456043956043955	171	0.3475609756097561	123	0.3397790055248619	13	0.022727272727272728	380	0.5013192612137203	C	0.510	-0.866735	0.02590	0.338935	0.499271	ENSG00000183638	ENST00000382483	T	0.03663	3.85	4.29	-8.57	0.00900	.	1.462110	0.04952	N	0.460442	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.16166	0.016	B	0.06405	0.002	T	0.44559	-0.9320	9	0.25106	T	0.35	0.7598	4.828	0.13427	0.1825:0.5318:0.1832:0.1026	.	514	A6NKC6	.	S	514	ENSP00000371923:G514S	ENSP00000371923:G514S	G	-	1	0	RP1L1	10507478	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-3.501000	0.00450	-3.027000	0.00267	-1.632000	0.00781	GGC	C|0.632;T|0.368	0.368	strong		0.682	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
SETDB1	9869	hgsc.bcm.edu	37	1	150923099	150923099	+	Silent	SNP	T	T	C	rs17661357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:150923099T>C	ENST00000271640.5	+	13	1936	c.1746T>C	c.(1744-1746)tgT>tgC	p.C582C	SETDB1_ENST00000368969.4_Silent_p.C582C|SETDB1_ENST00000459773.1_Intron	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	582					bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			GCTATACCTGTCTGTCTCGAG	0.572													T|||	156	0.0311502	0.003	0.0476	5008	,	,		18897	0.001		0.0944	False		,,,				2504	0.0235				p.C582C		Atlas-SNP	.											.	SETDB1	204	.	0			c.T1746C						PASS	.	T	,	57,4349	55.5+/-91.7	1,55,2147	98.0	97.0	97.0		1746,1746	4.3	1.0	1	dbSNP_123	97	642,7958	164.1+/-216.5	26,590,3684	no	coding-synonymous,coding-synonymous	SETDB1	NM_001145415.1,NM_012432.3	,	27,645,5831	CC,CT,TT		7.4651,1.2937,5.3744	,	582/1292,582/1291	150923099	699,12307	2203	4300	6503	SO:0001819	synonymous_variant	9869	exon13			TACCTGTCTGTCT	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Tudor domain containing"""	10761	protein-coding gene	gene with protein product	"""tudor domain containing 21"""	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.1746T>C	1.37:g.150923099T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	103	57	0.553398	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Silent	SNP	ENST00000271640.5	37	CCDS44217.1																																																																																			T|0.949;C|0.051	0.051	strong		0.572	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2		
APEH	327	hgsc.bcm.edu	37	3	49723750	49723750	+	IGR	SNP	A	A	G	rs71324987	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49723750A>G	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000383728.3_Missense_Mutation_p.C263R|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Missense_Mutation_p.C338R|MST1_ENST00000545762.1_3'UTR	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCTCACTTGCACGCGTATTTT	0.652																																					p.C338R		Atlas-SNP	.											.	MST1	84	.	0			c.T1012C						PASS	.						7.0	8.0	8.0					3																	49723750		2118	4171	6289	SO:0001628	intergenic_variant	4485	exon8			ACTTGCACGCGTA	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723750A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	133	36	0.270677	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	73	0.033424908424908424	5	0.01016260162601626	14	0.03867403314917127	3	0.005244755244755245	51	0.06728232189973615	A	24.6	4.547378	0.86022	.	.	ENSG00000173531	ENST00000449682;ENST00000383728	T;T	0.64991	-0.13;-0.13	5.15	5.15	0.70609	Kringle (4);Kringle-like fold (1);	0.000000	0.46442	D	0.000289	T	0.20577	0.0495	L	0.49640	1.575	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.75020	0.981;0.985	T	0.58912	-0.7552	10	0.87932	D	0	.	15.1447	0.72641	1.0:0.0:0.0:0.0	.	324;338	P26927;G3XAK1	HGFL_HUMAN;.	R	338;263	ENSP00000414287:C338R;ENSP00000373234:C263R	ENSP00000373234:C263R	C	-	1	0	MST1	49698754	1.000000	0.71417	0.970000	0.41538	0.706000	0.40770	9.306000	0.96204	2.159000	0.67721	0.533000	0.62120	TGC	A|0.970;G|0.030	0.030	strong		0.652	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
PRDM8	56978	hgsc.bcm.edu	37	4	81124596	81124596	+	Silent	SNP	G	G	C	rs12780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:81124596G>C	ENST00000504452.1	+	8	2819	c.1980G>C	c.(1978-1980)cgG>cgC	p.R660R	PRDM8_ENST00000339711.4_Silent_p.R660R|PRDM8_ENST00000415738.2_Silent_p.R660R			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	660					corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						TGGTGAAGCGGCGGCGAGAGG	0.572													G|||	1745	0.348442	0.1672	0.3372	5008	,	,		12837	0.626		0.2724	False		,,,				2504	0.3937				p.R660R		Atlas-SNP	.											PRDM8,colon,carcinoma,0,1	PRDM8	44	1	0			c.G1980C						PASS	.	G	,	746,3544		70,606,1469	32.0	38.0	36.0		1980,1980	1.1	1.0	4	dbSNP_52	36	2160,6384		289,1582,2401	no	coding-synonymous,coding-synonymous	PRDM8	NM_001099403.1,NM_020226.3	,	359,2188,3870	CC,CG,GG		25.2809,17.3893,22.643	,	660/690,660/690	81124596	2906,9928	2145	4272	6417	SO:0001819	synonymous_variant	56978	exon4			GAAGCGGCGGCGA	AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.1980G>C	4.37:g.81124596G>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	147	65	0.442177	NM_001099403	A8K7X2|Q6IQ36	Silent	SNP	ENST00000504452.1	37	CCDS43243.1																																																																																			G|0.671;C|0.329	0.329	strong		0.572	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1		
NKX3-1	4824	hgsc.bcm.edu	37	8	23538908	23538908	+	Silent	SNP	A	A	G	rs35350906	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:23538908A>G	ENST00000380871.4	-	2	568	c.531T>C	c.(529-531)taT>taC	p.Y177Y	NKX3-1_ENST00000523261.1_Silent_p.Y102Y	NM_006167.3	NP_006158.2	Q99801	NKX31_HUMAN	NK3 homeobox 1	177					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|androgen receptor signaling pathway (GO:0030521)|branching involved in prostate gland morphogenesis (GO:0060442)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to steroid hormone stimulus (GO:0071383)|cellular response to tumor necrosis factor (GO:0071356)|dorsal aorta development (GO:0035907)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|heart development (GO:0007507)|male gonad development (GO:0008584)|metanephros development (GO:0001656)|mitotic cell cycle arrest (GO:0071850)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of transcription, DNA-templated (GO:0045892)|pharyngeal system development (GO:0060037)|positive regulation of androgen secretion (GO:2000836)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell death (GO:0010942)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein kinase B signaling (GO:0043491)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|salivary gland development (GO:0007431)|somitogenesis (GO:0001756)|steroid hormone mediated signaling pathway (GO:0043401)	intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|core promoter binding (GO:0001047)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|histone deacetylase binding (GO:0042826)|protein kinase activator activity (GO:0030295)|protein self-association (GO:0043621)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			large_intestine(3)|lung(4)|prostate(5)|skin(2)	14		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)		GCTTAGTCTTATAGCGTCTGT	0.587													A|||	104	0.0207668	0.0756	0.0058	5008	,	,		20558	0.0		0.0	False		,,,				2504	0.0				p.Y177Y		Atlas-SNP	.											NKX3-1,NS,carcinoma,-1,4	NKX3-1	25	4	0			c.T531C						scavenged	.	A		240,4166	140.8+/-176.2	7,226,1970	167.0	164.0	165.0		531	-0.9	1.0	8	dbSNP_126	165	1,8599		0,1,4299	no	coding-synonymous	NKX3-1	NM_006167.3		7,227,6269	GG,GA,AA		0.0116,5.4471,1.853		177/235	23538908	241,12765	2203	4300	6503	SO:0001819	synonymous_variant	4824	exon2			AGTCTTATAGCGT		CCDS6042.1, CCDS59095.1	8p21.2	2012-03-09	2007-07-09	2002-10-04	ENSG00000167034	ENSG00000167034		"""Homeoboxes / ANTP class : NKL subclass"""	7838	protein-coding gene	gene with protein product		602041	"""NK homeobox (Drosophila), family 3, A"", ""NK3 transcription factor related, locus 1 (Drosophila)"""	NKX3A		9226374	Standard	NM_006167		Approved	NKX3.1, BAPX2	uc011kzx.2	Q99801	OTTHUMG00000097851	ENST00000380871.4:c.531T>C	8.37:g.23538908A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	145	2	0.0137931	NM_006167	O15465|Q9H2P4|Q9H2P5|Q9H2P6|Q9H2P7|Q9HBG0	Silent	SNP	ENST00000380871.4	37	CCDS6042.1																																																																																			A|0.981;G|0.019	0.019	strong		0.587	NKX3-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215141.2		
SYCP1	6847	hgsc.bcm.edu	37	1	115399884	115399884	+	Silent	SNP	C	C	G	rs17544210	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:115399884C>G	ENST00000369522.3	+	4	465	c.225C>G	c.(223-225)ccC>ccG	p.P75P	SYCP1_ENST00000369518.1_Silent_p.P75P	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	75	Asp/Glu-rich (acidic).				chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATTTCTTGCCCGTGCTTGAGC	0.313													C|||	192	0.0383387	0.0121	0.0519	5008	,	,		15488	0.0159		0.0686	False		,,,				2504	0.0562				p.P75P		Atlas-SNP	.											SYCP1,caecum,carcinoma,+1,1	SYCP1	149	1	0			c.C225G						PASS	.	C		101,4305	74.7+/-112.8	5,91,2107	44.0	44.0	44.0		225	3.2	1.0	1	dbSNP_123	44	597,7995	155.1+/-209.2	18,561,3717	no	coding-synonymous	SYCP1	NM_003176.2		23,652,5824	GG,GC,CC		6.9483,2.2923,5.3701		75/977	115399884	698,12300	2203	4296	6499	SO:0001819	synonymous_variant	6847	exon4			CTTGCCCGTGCTT	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"""cancer/testis antigen 8"""	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.225C>G	1.37:g.115399884C>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_003176	O14963|Q5VXJ6	Silent	SNP	ENST00000369522.3	37	CCDS879.1																																																																																			C|0.950;G|0.048;T|0.002	0.048	strong		0.313	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176	
IGSF10	285313	hgsc.bcm.edu	37	3	151155758	151155758	+	Silent	SNP	A	A	C	rs9864533	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:151155758A>C	ENST00000282466.3	-	6	6590	c.6591T>G	c.(6589-6591)tcT>tcG	p.S2197S	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2197	Ig-like C2-type 8.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGATGGTCAAAGACCCATTGG	0.443													A|||	1035	0.206669	0.1868	0.2089	5008	,	,		22739	0.3819		0.0924	False		,,,				2504	0.1687				p.S2197S		Atlas-SNP	.											IGSF10,colon,carcinoma,-1,1	IGSF10	279	1	0			c.T6591G						PASS	.	A	,,	688,3718	289.2+/-280.3	53,582,1568	110.0	107.0	108.0		672,528,6591	3.3	0.9	3	dbSNP_119	108	655,7945	166.7+/-218.6	27,601,3672	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	80,1183,5240	CC,CA,AA		7.6163,15.6151,10.326	,,	224/651,176/603,2197/2624	151155758	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			GGTCAAAGACCCA	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.6591T>G	3.37:g.151155758A>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	164	76	0.463415	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			A|0.843;C|0.157	0.157	strong		0.443	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
MST1L	11223	hgsc.bcm.edu	37	1	17087593	17087593	+	RNA	SNP	C	C	T	rs12145944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17087593C>T	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										ATGGCGAGCGCTGCCCTGCAG	0.577																																					p.Q24Q		Atlas-SNP	.											Q13209_HUMAN,right_upper_lobe,carcinoma,0,2	.	.	2	0			c.G72A						PASS	.																																					11223	exon2			CGAGCGCTGCCCT	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17087593C>T		Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	447	49	0.10962	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				C|0.942;T|0.058	0.058	strong		0.577	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
KCTD18	130535	hgsc.bcm.edu	37	2	201355106	201355106	+	Missense_Mutation	SNP	G	G	A	rs13018579	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:201355106G>A	ENST00000359878.3	-	7	1508	c.998C>T	c.(997-999)gCc>gTc	p.A333V	KCTD18_ENST00000409157.1_Missense_Mutation_p.A333V|KCTD18_ENST00000468413.1_5'Flank	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	333			A -> V (in dbSNP:rs13018579). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		protein homooligomerization (GO:0051260)					endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						GCCCACCAGGGCCGTGGCTCT	0.642													G|||	497	0.0992412	0.0393	0.1427	5008	,	,		16517	0.002		0.2336	False		,,,				2504	0.1115				p.A333V		Atlas-SNP	.											.	KCTD18	44	.	0			c.C998T						PASS	.	G	VAL/ALA	299,4107	160.3+/-192.7	8,283,1912	44.0	48.0	47.0		998	2.4	0.0	2	dbSNP_121	47	1952,6648	341.4+/-324.0	238,1476,2586	yes	missense	KCTD18	NM_152387.2	64	246,1759,4498	AA,AG,GG		22.6977,6.7862,17.3074	benign	333/427	201355106	2251,10755	2203	4300	6503	SO:0001583	missense	130535	exon7			ACCAGGGCCGTGG	AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 18"""				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.998C>T	2.37:g.201355106G>A	ENSP00000352941:p.Ala333Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	96	56	0.583333	NM_152387	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Missense_Mutation	SNP	ENST00000359878.3	37	CCDS2330.1	266	0.12179487179487179	27	0.054878048780487805	65	0.17955801104972377	1	0.0017482517482517483	173	0.22823218997361477	G	11.88	1.770629	0.31320	0.067862	0.226977	ENSG00000155729	ENST00000359878;ENST00000409157	T;T	0.35236	1.32;1.32	4.22	2.38	0.29361	.	1.417830	0.04433	N	0.369665	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.17038	0.02	B	0.17433	0.018	T	0.20505	-1.0273	9	0.05959	T	0.93	0.2009	6.6967	0.23203	0.0926:0.0:0.7314:0.176	rs13018579;rs17532385;rs57796327;rs13018579	333	Q6PI47	KCD18_HUMAN	V	333	ENSP00000352941:A333V;ENSP00000386751:A333V	ENSP00000352941:A333V	A	-	2	0	KCTD18	201063351	0.072000	0.21174	0.000000	0.03702	0.004000	0.04260	2.880000	0.48530	0.404000	0.25506	0.655000	0.94253	GCC	G|0.849;A|0.151	0.151	strong		0.642	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387	
CCDC50	152137	hgsc.bcm.edu	37	3	191093053	191093053	+	Intron	SNP	T	T	C	rs2028572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:191093053T>C	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Silent_p.H217H	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		ACAATCCCCATATTAACAATG	0.502													T|||	2514	0.501997	0.7239	0.4697	5008	,	,		21524	0.4702		0.4105	False		,,,				2504	0.3517				p.H217H		Atlas-SNP	.											.	CCDC50	39	.	0			c.T651C						PASS	.	T	,	2955,1451	680.4+/-403.8	985,985,233	83.0	75.0	78.0		,651	-7.5	0.0	3	dbSNP_94	78	3404,5196	501.4+/-375.5	674,2056,1570	no	intron,coding-synonymous	CCDC50	NM_174908.3,NM_178335.2	,	1659,3041,1803	CC,CT,TT		39.5814,32.9324,48.8928	,	,217/483	191093053	6359,6647	2203	4300	6503	SO:0001627	intron_variant	152137	exon6			TCCCCATATTAAC	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-4895T>C	3.37:g.191093053T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	225	224	0.995556	NM_178335	Q86VH7	Silent	SNP	ENST00000392455.3	37	CCDS33913.1																																																																																			T|0.501;C|0.499	0.499	strong		0.502	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
PIGN	23556	hgsc.bcm.edu	37	18	59810563	59810563	+	Silent	SNP	A	A	G	rs34227891	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:59810563A>G	ENST00000357637.5	-	11	1354	c.939T>C	c.(937-939)aaT>aaC	p.N313N	PIGN_ENST00000400334.3_Silent_p.N313N	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	313					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				GCCTCTTCCAATTCTCCAATC	0.299													G|||	872	0.174121	0.1906	0.1671	5008	,	,		15670	0.0764		0.2972	False		,,,				2504	0.1309				p.N313N		Atlas-SNP	.											PIGN,NS,carcinoma,0,1	PIGN	62	1	0			c.T939C						PASS	.	G	,	759,2851		79,601,1125	55.0	47.0	50.0		939,939	-3.0	0.0	18	dbSNP_126	50	2141,5965		283,1575,2195	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	362,2176,3320	GG,GA,AA		26.4125,21.0249,24.7525	,	313/932,313/932	59810563	2900,8816	1805	4053	5858	SO:0001819	synonymous_variant	23556	exon11			CTTCCAATTCTCC	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.939T>C	18.37:g.59810563A>G		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	244	110	0.45082	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			A|0.789;G|0.211	0.211	strong		0.299	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
METTL21A	151194	hgsc.bcm.edu	37	2	208477956	208477956	+	Silent	SNP	C	C	T	rs2709416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:208477956C>T	ENST00000411432.1	-	4	687	c.471G>A	c.(469-471)caG>caA	p.Q157Q	METTL21A_ENST00000448007.2_Silent_p.Q157Q|METTL21A_ENST00000272839.3_Silent_p.Q175Q|METTL21A_ENST00000426075.1_Silent_p.Q157Q|METTL21A_ENST00000448823.2_3'UTR|METTL21A_ENST00000477919.1_5'Flank|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000406927.2_Silent_p.Q157Q|METTL21A_ENST00000432416.1_Intron|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000442521.1_Silent_p.Q157Q	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	157					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						GTTCCAGTGTCTGAAGAAGAT	0.403													T|||	4528	0.904153	0.8646	0.879	5008	,	,		21003	0.998		0.831	False		,,,				2504	0.954				p.Q157Q		Atlas-SNP	.											.	METTL21A	24	.	0			c.G471A						PASS	.	T	,	3826,580	258.0+/-262.2	1661,504,38	127.0	129.0	128.0		471,471	-9.3	0.3	2	dbSNP_100	128	7027,1573	295.4+/-302.4	2857,1313,130	no	coding-synonymous,coding-synonymous	METTL21A	NM_001127395.1,NM_145280.4	,	4518,1817,168	TT,TC,CC		18.2907,13.1639,16.5539	,	157/219,157/219	208477956	10853,2153	2203	4300	6503	SO:0001819	synonymous_variant	151194	exon4			CAGTGTCTGAAGA	AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 557b"", ""heat shock protein 70kDa lysine (K) methyltransferase"""	615257	"""family with sequence similarity 119, member A"""	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.471G>A	2.37:g.208477956C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_145280	Q53RV0|Q8N1Z9|Q96GH6	Silent	SNP	ENST00000411432.1	37	CCDS2376.1																																																																																			C|0.146;T|0.854	0.854	strong		0.403	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280	
TXK	7294	hgsc.bcm.edu	37	4	48115264	48115264	+	Missense_Mutation	SNP	C	C	T	rs7658300	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:48115264C>T	ENST00000264316.4	-	3	219	c.134G>A	c.(133-135)cGt>cAt	p.R45H	TXK_ENST00000510457.1_5'UTR	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	45			R -> H (in dbSNP:rs7658300). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7951233}.		activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						CGGCCTGCGACGCTGGGTGTA	0.403													c|||	865	0.172724	0.0257	0.3429	5008	,	,		18748	0.0685		0.3658	False		,,,				2504	0.1595				p.R45H		Atlas-SNP	.											.	TXK	58	.	0			c.G134A						PASS	.	T	HIS/ARG	354,4052	182.2+/-210.1	14,326,1863	146.0	148.0	147.0		134	-7.5	0.0	4	dbSNP_116	147	3146,5454	479.8+/-370.2	602,1942,1756	yes	missense	TXK	NM_003328.2	29	616,2268,3619	TT,TC,CC		36.5814,8.0345,26.9107	benign	45/528	48115264	3500,9506	2203	4300	6503	SO:0001583	missense	7294	exon3			CTGCGACGCTGGG	L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"""SH2 domain containing"""	12434	protein-coding gene	gene with protein product		600058	"""PTK4 protein tyrosine kinase 4"""	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.134G>A	4.37:g.48115264C>T	ENSP00000264316:p.Arg45His	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	230	119	0.517391	NM_003328	Q14220	Missense_Mutation	SNP	ENST00000264316.4	37	CCDS3480.1	454	0.2078754578754579	18	0.036585365853658534	118	0.3259668508287293	37	0.06468531468531469	281	0.370712401055409	c	9.127	1.010474	0.19277	0.080345	0.365814	ENSG00000074966	ENST00000264316;ENST00000506073	T;T	0.74526	-0.85;0.23	5.03	-7.49	0.01355	.	1.279830	0.05322	N	0.526822	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07462	-1.0771	9	0.36615	T	0.2	.	9.2889	0.37775	0.0:0.1692:0.2098:0.621	rs7658300;rs56561099;rs61166743;rs7658300	45;45	E7EQN8;P42681	.;TXK_HUMAN	H	45	ENSP00000264316:R45H;ENSP00000422798:R45H	ENSP00000264316:R45H	R	-	2	0	TXK	47810021	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.757000	0.00374	-2.472000	0.00529	-0.906000	0.02833	CGT	C|0.766;T|0.234	0.234	strong		0.403	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328	
SMC1B	27127	hgsc.bcm.edu	37	22	45749966	45749966	+	Missense_Mutation	SNP	G	G	C	rs61735519	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:45749966G>C	ENST00000357450.4	-	21	3164	c.3165C>G	c.(3163-3165)ttC>ttG	p.F1055L	SMC1B_ENST00000404354.3_Missense_Mutation_p.F1055L	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1055					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TCACTTGCTCGAACTCTTGCC	0.403													G|||	191	0.038139	0.0068	0.0879	5008	,	,		15728	0.0238		0.0557	False		,,,				2504	0.0419				p.F1055L		Atlas-SNP	.											.	SMC1B	215	.	0			c.C3165G						PASS	.	G	LEU/PHE	51,3681		0,51,1815	169.0	149.0	156.0		3165	2.2	1.0	22	dbSNP_129	156	475,7723		15,445,3639	yes	missense	SMC1B	NM_148674.3	22	15,496,5454	CC,CG,GG		5.7941,1.3666,4.4091	probably-damaging	1055/1236	45749966	526,11404	1866	4099	5965	SO:0001583	missense	27127	exon21			TTGCTCGAACTCT	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.3165C>G	22.37:g.45749966G>C	ENSP00000350036:p.Phe1055Leu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	99	0.04532967032967033	3	0.006097560975609756	38	0.10497237569060773	19	0.033216783216783216	39	0.051451187335092345	G	18.09	3.546664	0.65198	0.013666	0.057941	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.80304	-1.21;-1.36	5.58	2.25	0.28309	.	0.000000	0.64402	D	0.000014	T	0.26774	0.0655	M	0.91249	3.19	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.65697	-0.6105	10	0.42905	T	0.14	.	10.0391	0.42146	0.7364:0.0:0.2636:0.0	rs61735519	1055;1055	Q8NDV3-2;Q8NDV3-3	.;.	L	1055	ENSP00000350036:F1055L;ENSP00000385902:F1055L	ENSP00000350036:F1055L	F	-	3	2	SMC1B	44128630	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.069000	0.41481	0.078000	0.16900	-1.273000	0.01405	TTC	G|0.936;C|0.064	0.064	strong		0.403	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
HYDIN	54768	hgsc.bcm.edu	37	16	71015329	71015329	+	Missense_Mutation	SNP	G	G	T	rs78763837	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:71015329G>T	ENST00000393567.2	-	29	4625	c.4475C>A	c.(4474-4476)cCc>cAc	p.P1492H		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1492					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GCAGATTTGGGGAAAGATTCC	0.483													G|||	2340	0.467252	0.4455	0.5591	5008	,	,		18143	0.5645		0.328	False		,,,				2504	0.4744				p.P1492H		Atlas-SNP	.											LOC652153,NS,haematopoietic_neoplasm,0,2	HYDIN	788	2	0			c.C4475A						scavenged	.						66.0	66.0	66.0					16																	71015329		1844	4072	5916	SO:0001583	missense	54768	exon29			ATTTGGGGAAAGA	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.4475C>A	16.37:g.71015329G>T	ENSP00000377197:p.Pro1492His	Somatic	156	2	0.0128205		WXS	Illumina HiSeq	Phase_I	163	153	0.93865	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	964	0.4413919413919414	233	0.4735772357723577	184	0.5082872928176796	312	0.5454545454545454	235	0.3100263852242744	G	24.0	4.480970	0.84747	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01221	5.15	4.26	4.26	0.50523	.	0.000000	0.33023	U	0.005376	T	0.00012	0.0000	M	0.80183	2.485	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.45056	-0.9287	9	0.49607	T	0.09	.	16.6224	0.84934	0.0:0.0:1.0:0.0	.	1491	F8WD23	.	H	1492;1491	ENSP00000377197:P1492H	ENSP00000313052:P1491H	P	-	2	0	HYDIN	69572830	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.105000	0.94246	2.083000	0.62718	0.603000	0.83216	CCC	.	.	weak		0.483	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
CD101	9398	hgsc.bcm.edu	37	1	117560818	117560818	+	Silent	SNP	A	A	G	rs3736908	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:117560818A>G	ENST00000256652.4	+	6	1711	c.1653A>G	c.(1651-1653)caA>caG	p.Q551Q	CD101_ENST00000369470.1_Silent_p.Q551Q	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	551	Ig-like C2-type 5.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GTCAGCCGCAAGTGATGTTAA	0.438													A|||	1725	0.344449	0.0408	0.4438	5008	,	,		19499	0.6181		0.2813	False		,,,				2504	0.4673				p.Q551Q		Atlas-SNP	.											.	CD101	95	.	0			c.A1653G						PASS	.	A		367,4039	185.3+/-212.5	18,331,1854	106.0	82.0	90.0		1653	1.6	1.0	1	dbSNP_107	90	2365,6235	390.0+/-343.1	324,1717,2259	no	coding-synonymous	CD101	NM_004258.3		342,2048,4113	GG,GA,AA		27.5,8.3296,21.0057		551/1022	117560818	2732,10274	2203	4300	6503	SO:0001819	synonymous_variant	9398	exon6			GCCGCAAGTGATG	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.1653A>G	1.37:g.117560818A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_001256109	Q15856	Silent	SNP	ENST00000256652.4	37	CCDS891.1																																																																																			A|0.738;G|0.262	0.262	strong		0.438	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
CNTROB	116840	hgsc.bcm.edu	37	17	7849087	7849087	+	Silent	SNP	C	C	G	rs4462665	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7849087C>G	ENST00000563694.1	+	13	2701	c.1776C>G	c.(1774-1776)ccC>ccG	p.P592P	CNTROB_ENST00000565740.1_Silent_p.P592P|CNTROB_ENST00000380255.3_Missense_Mutation_p.P538R|CNTROB_ENST00000380262.3_Silent_p.P592P	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	592	Pro-rich.|Required for centrosome localization.				centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				CTCAGGAGCCCGAGAAGGAGG	0.602													G|||	3160	0.63099	0.5424	0.67	5008	,	,		16148	0.8016		0.4493	False		,,,				2504	0.7342				p.P592P		Atlas-SNP	.											CNTROB,colon,carcinoma,0,1	CNTROB	61	1	0			c.C1776G						PASS	.	G	,	2443,1963	552.7+/-378.6	670,1103,430	57.0	59.0	59.0		1776,1776	-5.3	0.0	17	dbSNP_111	59	3953,4647	599.3+/-394.1	915,2123,1262	no	coding-synonymous,coding-synonymous	CNTROB	NM_001037144.5,NM_053051.3	,	1585,3226,1692	GG,GC,CC		45.9651,44.5529,49.1773	,	592/926,592/904	7849087	6396,6610	2203	4300	6503	SO:0001819	synonymous_variant	116840	exon13			GGAGCCCGAGAAG	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.1776C>G	17.37:g.7849087C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	30	0.379747	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Silent	SNP	ENST00000563694.1	37	CCDS11126.1	1270	0.5815018315018315	277	0.5630081300813008	222	0.6132596685082873	424	0.7412587412587412	347	0.4577836411609499	G	0.238	-1.015843	0.02078	0.554471	0.459651	ENSG00000170037	ENST00000380255	T	0.46451	0.87	5.48	-5.31	0.02730	.	0.553031	0.16472	N	0.212908	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.13980	-1.0489	6	0.27082	T	0.32	0.0029	7.964	0.30087	0.3758:0.2132:0.411:0.0	rs4462665;rs59940402;rs4462665	.	.	.	R	538	ENSP00000369605:P538R	ENSP00000369605:P538R	P	+	2	0	CNTROB	7789812	0.000000	0.05858	0.002000	0.10522	0.109000	0.19521	-1.603000	0.02077	-1.742000	0.01342	-2.784000	0.00117	CCG	C|0.474;G|0.526	0.526	strong		0.602	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	
LZTR1	8216	hgsc.bcm.edu	37	22	21337325	21337325	+	Silent	SNP	G	G	A	rs13054014	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:21337325G>A	ENST00000215739.8	+	2	569	c.210G>A	c.(208-210)aaG>aaA	p.K70K	XXbac-B135H6.18_ENST00000610278.1_lincRNA|LZTR1_ENST00000389355.3_Silent_p.K70K|LZTR1_ENST00000479606.1_3'UTR	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	70					anatomical structure morphogenesis (GO:0009653)|regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)	42	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			GGCGCAGCAAGCACACAGTGG	0.542													G|||	1428	0.285144	0.2443	0.3444	5008	,	,		20810	0.2014		0.2594	False		,,,				2504	0.411				p.K70K		Atlas-SNP	.											.	LZTR1	99	.	0			c.G210A						PASS	.	G		1155,3251	410.2+/-335.3	163,829,1211	136.0	122.0	127.0		210	1.2	1.0	22	dbSNP_121	127	2257,6343	381.1+/-339.9	293,1671,2336	no	coding-synonymous	LZTR1	NM_006767.3		456,2500,3547	AA,AG,GG		26.2442,26.2143,26.234		70/841	21337325	3412,9594	2203	4300	6503	SO:0001819	synonymous_variant	8216	exon2			CAGCAAGCACACA	D38496	CCDS33606.1	22q11.21	2013-01-09	2004-12-10		ENSG00000099949	ENSG00000099949		"""BTB/POZ domain containing"""	6742	protein-coding gene	gene with protein product		600574	"""leucine-zipper-like transcriptional regulator 1"""			7633402, 16356934	Standard	NM_006767		Approved	LZTR-1, BTBD29	uc002zto.3	Q8N653	OTTHUMG00000150878	ENST00000215739.8:c.210G>A	22.37:g.21337325G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_006767	Q14776|Q20WK0	Silent	SNP	ENST00000215739.8	37	CCDS33606.1																																																																																			G|0.733;A|0.267	0.267	strong		0.542	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767	
C1GALT1C1	29071	hgsc.bcm.edu	37	X	119760629	119760629	+	Missense_Mutation	SNP	A	A	T	rs17261572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:119760629A>T	ENST00000304661.5	-	2	631	c.393T>A	c.(391-393)gaT>gaA	p.D131E	C1GALT1C1_ENST00000371313.2_Missense_Mutation_p.D131E	NM_001011551.2	NP_001011551.1	Q96EU7	C1GLC_HUMAN	C1GALT1-specific chaperone 1	131			D -> E (common polymorphism; retains capacity to promote Tn synthase activity; dbSNP:rs17261572). {ECO:0000269|PubMed:16251947, ECO:0000269|PubMed:18537974}.		cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	11						CTCTATACTTATCAAAGGCGT	0.343													A|||	557	0.14755	0.0068	0.1138	3775	,	,		16525	0.0853		0.1809	False		,,,				2504	0.2055				p.D131E		Atlas-SNP	.											.	C1GALT1C1	22	.	0			c.T393A						PASS	.	A	GLU/ASP,GLU/ASP	156,3679		6,127,17,1499,554	78.0	77.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	393,393	1.5	1.0	X	dbSNP_123	77	1532,5194		132,858,410,1438,1460	yes	missense,missense	C1GALT1C1	NM_001011551.2,NM_152692.4	45,45	138,985,427,2937,2014	TT,TA,T,AA,A		22.7773,4.0678,15.9833	benign,benign	131/319,131/319	119760629	1688,8873	2203	4298	6501	SO:0001583	missense	29071	exon3			ATACTTATCAAAG	AJ238398	CCDS14602.1	Xq24	2008-02-05			ENSG00000171155	ENSG00000171155			24338	protein-coding gene	gene with protein product		300611				11042152, 12361956	Standard	NM_152692		Approved	COSMC, C1GALT2	uc004esz.3	Q96EU7	OTTHUMG00000022305	ENST00000304661.5:c.393T>A	X.37:g.119760629A>T	ENSP00000304364:p.Asp131Glu	Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	242	173	0.714876	NM_152692	A8K246|Q8WWS3|Q9NZX1	Missense_Mutation	SNP	ENST00000304661.5	37	CCDS14602.1	219	0.13200723327305605	5	0.01020408163265306	22	0.06321839080459771	35	0.06340579710144928	95	0.1417910447761194	A	0.405	-0.916361	0.02415	0.040678	0.227773	ENSG00000171155	ENST00000304661;ENST00000371313	T;T	0.39787	1.06;1.06	5.14	1.52	0.23074	.	0.148977	0.64402	N	0.000018	T	0.00012	0.0000	N	0.04880	-0.145	0.32476	P	0.5421050000000001	B	0.06786	0.001	B	0.04013	0.001	T	0.28681	-1.0036	8	.	.	.	-17.4976	0.8454	0.01160	0.3838:0.1652:0.2885:0.1626	rs17261572;rs17261572	131	Q96EU7	C1GLC_HUMAN	E	131	ENSP00000304364:D131E;ENSP00000360363:D131E	.	D	-	3	2	C1GALT1C1	119644657	0.491000	0.26019	0.971000	0.41717	0.984000	0.73092	-0.134000	0.10436	0.243000	0.21327	0.441000	0.28932	GAT	A|0.847;0|0.015	.	strong		0.343	C1GALT1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058117.1	NM_152692	
DSC2	1824	hgsc.bcm.edu	37	18	28673565	28673565	+	Silent	SNP	T	T	C	rs12954874	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:28673565T>C	ENST00000280904.6	-	2	554	c.111A>G	c.(109-111)ttA>ttG	p.L37L	DSC2_ENST00000251081.6_Silent_p.L37L	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	37					bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			AGGGAACATGTAATGTCACAT	0.318													T|||	619	0.123602	0.084	0.1643	5008	,	,		13763	0.1399		0.1014	False		,,,				2504	0.1544				p.L37L		Atlas-SNP	.											.	DSC2	168	.	0			c.A111G						PASS	.	T	,	352,4054	183.6+/-211.2	14,324,1865	102.0	106.0	105.0		111,111	-10.6	0.0	18	dbSNP_121	105	1041,7559	222.2+/-259.3	52,937,3311	no	coding-synonymous,coding-synonymous	DSC2	NM_004949.3,NM_024422.3	,	66,1261,5176	CC,CT,TT		12.1047,7.9891,10.7104	,	37/848,37/902	28673565	1393,11613	2203	4300	6503	SO:0001819	synonymous_variant	1824	exon2			AACATGTAATGTC	X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"""Cadherins / Major cadherins"""	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.111A>G	18.37:g.28673565T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	88	32	0.363636	NM_024422		Silent	SNP	ENST00000280904.6	37	CCDS11892.1																																																																																			T|0.885;C|0.115	0.115	strong		0.318	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949	
PREX1	57580	hgsc.bcm.edu	37	20	47253043	47253043	+	Silent	SNP	G	G	A	rs11553083	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:47253043G>A	ENST00000371941.3	-	32	4147	c.4125C>T	c.(4123-4125)ggC>ggT	p.G1375G	PREX1_ENST00000396220.1_Silent_p.G1375G	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1375					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GCAGCAGGACGCCCGTGGCCG	0.716													.|||	506	0.101038	0.1407	0.0865	5008	,	,		13341	0.0615		0.1163	False		,,,				2504	0.0828				p.G1375G		Atlas-SNP	.											PREX1_ENST00000396220,colon,carcinoma,0,2	PREX1	441	2	0			c.C4125T						PASS	.	G		497,3711		32,433,1639	11.0	13.0	13.0		4125	-8.9	0.1	20	dbSNP_120	13	911,7385		52,807,3289	no	coding-synonymous	PREX1	NM_020820.3		84,1240,4928	AA,AG,GG		10.9812,11.8108,11.2604		1375/1660	47253043	1408,11096	2104	4148	6252	SO:0001819	synonymous_variant	57580	exon32			CAGGACGCCCGTG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.4125C>T	20.37:g.47253043G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			G|0.878;A|0.122	0.122	strong		0.716	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
ZNF3	7551	hgsc.bcm.edu	37	7	99669802	99669802	+	Missense_Mutation	SNP	A	A	G	rs11550034	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99669802A>G	ENST00000424697.1	-	6	611	c.305T>C	c.(304-306)aTt>aCt	p.I102T	ZNF3_ENST00000303915.6_Missense_Mutation_p.I102T|ZNF3_ENST00000413658.2_Intron|ZNF3_ENST00000299667.4_Missense_Mutation_p.I102T	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	102	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		I -> T (in dbSNP:rs11550034).		cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			GTCTTCAGAAATTTCTTGATC	0.393													A|||	529	0.105631	0.0371	0.147	5008	,	,		21325	0.1399		0.1223	False		,,,				2504	0.1166				p.I102T		Atlas-SNP	.											.	ZNF3	54	.	0			c.T305C						PASS	.	A	,THR/ILE	188,3516		6,176,1670	100.0	90.0	93.0		,305	5.0	1.0	7	dbSNP_120	93	1097,7093		80,937,3078	yes	intron,missense	ZNF3	NM_017715.2,NM_032924.3	,89	86,1113,4748	GG,GA,AA		13.3944,5.0756,10.8038	,benign	,102/447	99669802	1285,10609	1852	4095	5947	SO:0001583	missense	7551	exon6			TCAGAAATTTCTT	AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"""Zinc fingers, C2H2-type"", ""-"""	13089	protein-coding gene	gene with protein product		194510	"""zinc finger protein 3 (A8-51)"""				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.305T>C	7.37:g.99669802A>G	ENSP00000415358:p.Ile102Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_032924	D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Missense_Mutation	SNP	ENST00000424697.1	37	CCDS43619.1	240	0.10989010989010989	13	0.026422764227642278	55	0.15193370165745856	77	0.1346153846153846	95	0.12532981530343007	A	8.294	0.818412	0.16607	0.050756	0.133944	ENSG00000166526	ENST00000424697;ENST00000303915;ENST00000299667;ENST00000412947;ENST00000449785;ENST00000428683;ENST00000441298;ENST00000415068	T;T;T;T;T;T;T;T	0.07908	3.15;3.15;3.15;4.9;5.04;5.04;4.86;4.76	5.01	5.01	0.66863	Krueppel-associated box (3);	0.250008	0.28612	N	0.014733	T	0.00039	0.0001	L	0.38175	1.15	0.33188	P	0.449523	P;P	0.44627	0.839;0.455	B;B	0.41236	0.351;0.149	T	0.42682	-0.9437	9	0.18710	T	0.47	-13.4665	7.34	0.26632	0.9043:0.0:0.0957:0.0	rs11550034;rs11982602;rs17852252;rs60937757;rs11550034	85;102	B3KRP4;P17036	.;ZNF3_HUMAN	T	102;102;102;66;102;102;66;102	ENSP00000415358:I102T;ENSP00000306372:I102T;ENSP00000299667:I102T;ENSP00000416088:I66T;ENSP00000405970:I102T;ENSP00000388042:I102T;ENSP00000394113:I66T;ENSP00000416686:I102T	ENSP00000299667:I102T	I	-	2	0	ZNF3	99507738	0.000000	0.05858	0.960000	0.40013	0.824000	0.46624	0.352000	0.20113	2.114000	0.64651	0.402000	0.26972	ATT	A|0.890;G|0.110	0.110	strong		0.393	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	NM_017715	
LILRB3	11025	hgsc.bcm.edu	37	19	54721042	54721042	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54721042T>C	ENST00000391750.1	-	14	1952	c.1816A>G	c.(1816-1818)Aag>Gag	p.K606E	LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.K607E|LILRB3_ENST00000245620.9_Missense_Mutation_p.K607E|LILRB3_ENST00000407860.2_Missense_Mutation_p.K623E|LILRA6_ENST00000440558.2_Missense_Mutation_p.K606E|LILRA6_ENST00000270464.5_Missense_Mutation_p.K607E|LILRB3_ENST00000346401.6_Missense_Mutation_p.K618E|LILRB3_ENST00000424807.1_Missense_Mutation_p.K606E|LILRA6_ENST00000391735.3_3'UTR			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	606					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TCAGTTGCCTTCCGTCTAAGG	0.627																																					p.K607E		Atlas-SNP	.											LILRB3,NS,carcinoma,0,1	LILRB3	67	1	0			c.A1819G						scavenged	.						108.0	108.0	108.0					19																	54721042		2202	4300	6502	SO:0001583	missense	11025	exon13			TTGCCTTCCGTCT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1816A>G	19.37:g.54721042T>C	ENSP00000375630:p.Lys606Glu	Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	279	5	0.0179211	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.739940	0.00675	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00490	7.07;7.07;7.03;7.06;7.03;7.07;7.07;7.09	2.64	-4.43	0.03568	.	.	.	.	.	T	0.00109	0.0003	N	0.00746	-1.225	0.09310	N	1	B;B;B;B;B;B;B	0.16802	0.001;0.007;0.0;0.019;0.001;0.001;0.001	B;B;B;B;B;B;B	0.19391	0.003;0.007;0.001;0.025;0.006;0.003;0.005	T	0.33624	-0.9861	9	0.02654	T	1	.	4.0644	0.09854	0.0:0.3045:0.3422:0.3533	.	623;606;607;618;623;606;607	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	E	606;606;618;607;623;606;607;607	ENSP00000375630:K606E;ENSP00000412771:K606E;ENSP00000345184:K618E;ENSP00000245620:K607E;ENSP00000384274:K623E;ENSP00000390120:K606E;ENSP00000270464:K607E;ENSP00000411227:K607E	ENSP00000270464:K607E	K	-	1	0	LILRB3;LILRA6	59412854	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.125000	0.03257	-0.821000	0.04312	-1.525000	0.00928	AAG	.	.	none		0.627	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
PARP1	142	hgsc.bcm.edu	37	1	226573364	226573364	+	Silent	SNP	A	A	G	rs1805414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:226573364A>G	ENST00000366794.5	-	7	995	c.852T>C	c.(850-852)gcT>gcC	p.A284A		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	284					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CCATGCCATCAGCTACTCGGT	0.537								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					G|||	2587	0.516573	0.5582	0.5029	5008	,	,		19644	0.7946		0.329	False		,,,				2504	0.3763				p.A284A		Atlas-SNP	.											.	PARP1	100	.	0			c.T852C	GRCh37	CM071915	PARP1	M	rs1805414	PASS	.	G		2366,2040	564.7+/-381.5	626,1114,463	80.0	73.0	75.0		852	-4.1	1.0	1	dbSNP_92	75	2937,5663	668.7+/-402.6	501,1935,1864	no	coding-synonymous	PARP1	NM_001618.3		1127,3049,2327	GG,GA,AA		34.1512,46.3005,40.7735		284/1015	226573364	5303,7703	2203	4300	6503	SO:0001819	synonymous_variant	142	exon7			GCCATCAGCTACT	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.852T>C	1.37:g.226573364A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_001618	B1ANJ4|Q8IUZ9	Silent	SNP	ENST00000366794.5	37	CCDS1554.1																																																																																			A|0.543;G|0.457	0.457	strong		0.537	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
NLGN2	57555	hgsc.bcm.edu	37	17	7318061	7318061	+	Silent	SNP	T	T	C	rs78355381	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7318061T>C	ENST00000302926.2	+	4	811	c.738T>C	c.(736-738)agT>agC	p.S246S	NLGN2_ENST00000575301.1_Silent_p.S246S	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	246					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				GCTGGCTCAGTGAAAACATCG	0.597													T|||	394	0.0786741	0.0144	0.0793	5008	,	,		17985	0.001		0.1441	False		,,,				2504	0.1779				p.S246S		Atlas-SNP	.											.	NLGN2	61	.	0			c.T738C						PASS	.	T		184,4222	118.8+/-156.5	6,172,2025	65.0	72.0	70.0		738	2.4	1.0	17	dbSNP_132	70	1477,7123	281.6+/-295.1	158,1161,2981	no	coding-synonymous	NLGN2	NM_020795.2		164,1333,5006	CC,CT,TT		17.1744,4.1761,12.771		246/836	7318061	1661,11345	2203	4300	6503	SO:0001819	synonymous_variant	57555	exon4			GCTCAGTGAAAAC	AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.738T>C	17.37:g.7318061T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	139	79	0.568345	NM_020795	Q9P2I1	Silent	SNP	ENST00000302926.2	37	CCDS11103.1																																																																																			A|0.000;C|0.114;T|0.886	0.114	strong		0.597	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795	
TTC3	7267	hgsc.bcm.edu	37	21	38568009	38568009	+	Missense_Mutation	SNP	G	G	C	rs1053966	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:38568009G>C	ENST00000399017.2	+	42	7998	c.5251G>C	c.(5251-5253)Gac>Cac	p.D1751H	TTC3_ENST00000355666.1_Missense_Mutation_p.D1751H|TTC3_ENST00000354749.2_Missense_Mutation_p.D1751H|TTC3_ENST00000479930.1_3'UTR|TTC3-AS1_ENST00000424733.1_RNA	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1751			D -> H (in dbSNP:rs1053966). {ECO:0000269|PubMed:8724848, ECO:0000269|PubMed:8947847}.		negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GTCTTCAGGCGACGATGGCCA	0.547													C|||	3698	0.738419	0.9024	0.7334	5008	,	,		14341	0.8492		0.5129	False		,,,				2504	0.638				p.D1751H	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.G5251C						PASS	.	C	HIS/ASP,HIS/ASP	3715,691	284.9+/-277.9	1567,581,55	216.0	221.0	219.0		5251,5251	2.8	0.0	21	dbSNP_86	219	4255,4345	574.7+/-390.1	1083,2089,1128	yes	missense,missense	TTC3	NM_001001894.1,NM_003316.3	81,81	2650,2670,1183	CC,CG,GG		49.4767,15.6832,38.7206	benign,benign	1751/2026,1751/2026	38568009	7970,5036	2203	4300	6503	SO:0001583	missense	7267	exon42			TCAGGCGACGATG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5251G>C	21.37:g.38568009G>C	ENSP00000381981:p.Asp1751His	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	187	187	1	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	1577|1577	0.7220695970695971|0.7220695970695971	449|449	0.9126016260162602|0.9126016260162602	256|256	0.7071823204419889|0.7071823204419889	487|487	0.8513986013986014|0.8513986013986014	385|385	0.5079155672823219|0.5079155672823219	C|C	0.314|0.314	-0.966110|-0.966110	0.02232|0.02232	0.843168|0.843168	0.494767|0.494767	ENSG00000182670|ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749|ENST00000428693	T;T;T|.	0.08102|.	3.13;3.13;3.13|.	4.72|4.72	2.82|2.82	0.32997|0.32997	.|.	1.572250|.	0.04014|.	N|.	0.298665|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00368|0.00368	-1.59|-1.59	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.24261|0.24261	-1.0165|-1.0165	9|4	0.22706|.	T|.	0.39|.	2.2531|2.2531	7.6428|7.6428	0.28303|0.28303	0.3344:0.5039:0.1617:0.0|0.3344:0.5039:0.1617:0.0	rs1053966;rs3194526;rs16992061;rs52829718;rs56795266;rs1053966|rs1053966;rs3194526;rs16992061;rs52829718;rs56795266;rs1053966	1751|.	P53804|.	TTC3_HUMAN|.	H|P	1751|42	ENSP00000347889:D1751H;ENSP00000381981:D1751H;ENSP00000346791:D1751H|.	ENSP00000346791:D1751H|.	D|R	+|+	1|2	0|0	TTC3|TTC3	37489879|37489879	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.019000|0.019000	0.09904|0.09904	-2.243000|-2.243000	0.01194|0.01194	0.145000|0.145000	0.18977|0.18977	-0.215000|-0.215000	0.12644|0.12644	GAC|CGA	G|0.348;C|0.652	0.652	strong		0.547	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
DNAH3	55567	hgsc.bcm.edu	37	16	20975303	20975303	+	Silent	SNP	A	A	G	rs3743697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20975303A>G	ENST00000261383.3	-	53	9902	c.9903T>C	c.(9901-9903)tcT>tcC	p.S3301S	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3301					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		AGATGGTGGCAGAATGCACAG	0.483													G|||	698	0.139377	0.1725	0.0793	5008	,	,		20201	0.1726		0.0726	False		,,,				2504	0.1718				p.S3301S		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T9903C						PASS	.	G		682,3720	762.2+/-413.1	46,590,1565	108.0	108.0	108.0		9903	-6.2	0.0	16	dbSNP_107	108	670,7930	788.8+/-407.6	23,624,3653	no	coding-synonymous	DNAH3	NM_017539.1		69,1214,5218	GG,GA,AA		7.7907,15.493,10.3984		3301/4117	20975303	1352,11650	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon53			GGTGGCAGAATGC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.9903T>C	16.37:g.20975303A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	180	178	0.988889	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			A|0.889;G|0.111	0.111	strong		0.483	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
OR8B2	26595	hgsc.bcm.edu	37	11	124252892	124252892	+	Silent	SNP	A	A	G	rs644147	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124252892A>G	ENST00000375013.2	-	1	366	c.348T>C	c.(346-348)acT>acC	p.T116T		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		ATGCCATTGAAGTCAACATGT	0.398																																					p.T116T		Atlas-SNP	.											.	OR8B2	42	.	0			c.T348C						PASS	.	G		1314,3088		362,590,1249	73.0	74.0	74.0		348	-5.0	0.6	11	dbSNP_83	74	1962,6632		368,1226,2703	no	coding-synonymous	OR8B2	NM_001005468.1		730,1816,3952	GG,GA,AA		22.8299,29.8501,25.2078		116/314	124252892	3276,9720	2201	4297	6498	SO:0001819	synonymous_variant	26595	exon1			CATTGAAGTCAAC	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"""GPCR / Class A : Olfactory receptors"""	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.348T>C	11.37:g.124252892A>G		Somatic	320	1	0.003125		WXS	Illumina HiSeq	Phase_I	315	115	0.365079	NM_001005468	Q8NGH2	Silent	SNP	ENST00000375013.2	37	CCDS31708.1																																																																																			A|0.723;G|0.277	0.277	strong		0.398	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468	
WDR19	57728	hgsc.bcm.edu	37	4	39207318	39207318	+	Silent	SNP	A	A	G	rs17584431	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:39207318A>G	ENST00000399820.3	+	9	1006	c.852A>G	c.(850-852)tcA>tcG	p.S284S	WDR19_ENST00000288634.7_Silent_p.S124S|WDR19_ENST00000506503.1_Silent_p.S284S	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	284					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						TTGCAGTATCACAGACTCTTA	0.353													A|||	616	0.123003	0.0053	0.1484	5008	,	,		18494	0.1508		0.1551	False		,,,				2504	0.2025				p.S284S		Atlas-SNP	.											.	WDR19	96	.	0			c.A852G						PASS	.	A		92,3616		2,88,1764	82.0	71.0	74.0		852	3.0	1.0	4	dbSNP_123	74	1224,6966		90,1044,2961	no	coding-synonymous	WDR19	NM_025132.3		92,1132,4725	GG,GA,AA		14.9451,2.4811,11.0607		284/1343	39207318	1316,10582	1854	4095	5949	SO:0001819	synonymous_variant	57728	exon9			AGTATCACAGACT	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.852A>G	4.37:g.39207318A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	251	111	0.442231	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	37	CCDS47042.1																																																																																			A|0.881;G|0.119	0.119	strong		0.353	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		
DOCK1	1793	hgsc.bcm.edu	37	10	129245684	129245684	+	Missense_Mutation	SNP	G	G	A	rs869801	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:129245684G>A	ENST00000280333.6	+	51	5486	c.5377G>A	c.(5377-5379)Gcg>Acg	p.A1793T		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1793	Interaction with NCK2 second and third SH3 domain (minor).		A -> T (in dbSNP:rs869801).		apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.A1793T(1)		NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		CATGACGGGGGCGGACGTGGC	0.592													G|||	1025	0.204673	0.211	0.2233	5008	,	,		17616	0.12		0.2584	False		,,,				2504	0.2147				p.A1793T		Atlas-SNP	.											DOCK1,NS,carcinoma,0,1	DOCK1	188	1	1	Substitution - Missense(1)	stomach(1)	c.G5377A						PASS	.	G	THR/ALA	769,3209		69,631,1289	32.0	36.0	35.0		5332	-10.4	0.0	10	dbSNP_86	35	2153,6171		278,1597,2287	yes	missense	DOCK1	NM_001380.3	58	347,2228,3576	AA,AG,GG		25.865,19.3313,23.7522	benign	1778/1851	129245684	2922,9380	1989	4162	6151	SO:0001583	missense	1793	exon51			ACGGGGGCGGACG	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.5377G>A	10.37:g.129245684G>A	ENSP00000280333:p.Ala1793Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	111	44	0.396396	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		458	0.2097069597069597	99	0.20121951219512196	91	0.2513812154696133	69	0.12062937062937062	199	0.262532981530343	G	6.324	0.427794	0.11987	0.193313	0.25865	ENSG00000150760	ENST00000280333	T	0.03663	3.85	5.22	-10.4	0.00318	.	1.639210	0.04650	U	0.407008	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48536	-0.9027	9	0.21014	T	0.42	.	0.4032	0.00429	0.3463:0.1465:0.2334:0.2738	rs869801;rs2229602;rs17777746;rs869801	1793;1793	B2RUU3;Q14185	.;DOCK1_HUMAN	T	1793	ENSP00000280333:A1793T	ENSP00000280333:A1793T	A	+	1	0	DOCK1	129135674	0.000000	0.05858	0.000000	0.03702	0.340000	0.28889	-0.958000	0.03857	-1.651000	0.01504	0.655000	0.94253	GCG	G|0.786;A|0.214	0.214	strong		0.592	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
TAF4	6874	hgsc.bcm.edu	37	20	60585139	60585139	+	Missense_Mutation	SNP	G	G	A	rs141880507		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60585139G>A	ENST00000252996.4	-	4	1723	c.1724C>T	c.(1723-1725)aCg>aTg	p.T575M	TAF4_ENST00000609045.1_5'UTR	NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	575					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			CCCTGGTACCGTGCGCTGAGG	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		16776	0.001		0.0	False		,,,				2504	0.0				p.T575M		Atlas-SNP	.											.	TAF4	84	.	0			c.C1724T						PASS	.						98.0	79.0	85.0					20																	60585139		2203	4300	6503	SO:0001583	missense	6874	exon4			GGTACCGTGCGCT	Y11354	CCDS33500.1	20q13.33	2010-02-26	2002-08-29	2002-01-18	ENSG00000130699	ENSG00000130699			11537	protein-coding gene	gene with protein product		601796	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1, 130kD"""	TAF4A, TAF2C1, TAF2C		8942982, 9192867	Standard	NM_003185		Approved	TAFII130, TAFII135	uc002ybs.3	O00268	OTTHUMG00000032893	ENST00000252996.4:c.1724C>T	20.37:g.60585139G>A	ENSP00000252996:p.Thr575Met	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_003185	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Missense_Mutation	SNP	ENST00000252996.4	37	CCDS33500.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	14.17	2.456706	0.43634	.	.	ENSG00000130699	ENST00000252996;ENST00000436129	T;T	0.26660	1.72;1.73	4.8	4.8	0.61643	.	0.550327	0.19671	N	0.108752	T	0.30479	0.0766	L	0.34521	1.04	0.22541	N	0.999006	D	0.69078	0.997	P	0.49332	0.607	T	0.13098	-1.0522	10	0.62326	D	0.03	-4.0056	17.8435	0.88722	0.0:0.0:1.0:0.0	.	575	O00268	TAF4_HUMAN	M	575;439	ENSP00000252996:T575M;ENSP00000399091:T439M	ENSP00000252996:T575M	T	-	2	0	TAF4	60018534	0.969000	0.33509	0.095000	0.20976	0.149000	0.21700	6.757000	0.74924	2.226000	0.72624	0.313000	0.20887	ACG	G|1.000;A|0.000	0.000	strong		0.612	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185	
AKAP3	10566	hgsc.bcm.edu	37	12	4735770	4735770	+	Silent	SNP	G	G	A	rs34392018	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:4735770G>A	ENST00000545990.2	-	5	2822	c.2298C>T	c.(2296-2298)gaC>gaT	p.D766D	AKAP3_ENST00000228850.1_Silent_p.D766D|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	766					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						TCTGAACTGTGTCCGTTAGGT	0.493													A|||	83	0.0165735	0.0272	0.0101	5008	,	,		20182	0.0		0.0328	False		,,,				2504	0.0072				p.D766D		Atlas-SNP	.											.	AKAP3	212	.	0			c.C2298T						PASS	.	A		109,4297	816.6+/-416.3	0,109,2094	181.0	163.0	169.0		2298	-3.0	0.1	12	dbSNP_126	169	280,8320	807.0+/-407.2	6,268,4026	no	coding-synonymous	AKAP3	NM_006422.2		6,377,6120	AA,AG,GG		3.2558,2.4739,2.9909		766/854	4735770	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	10566	exon4			AACTGTGTCCGTT	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.2298C>T	12.37:g.4735770G>A		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	318	153	0.481132	NM_006422	O75945|Q86X01|Q9UM61	Silent	SNP	ENST00000545990.2	37	CCDS8531.1																																																																																			G|0.974;A|0.026	0.026	strong		0.493	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
SVEP1	79987	hgsc.bcm.edu	37	9	113220820	113220820	+	Silent	SNP	C	C	T	rs10980398	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:113220820C>T	ENST00000401783.2	-	20	3843	c.3507G>A	c.(3505-3507)gcG>gcA	p.A1169A	SVEP1_ENST00000374469.1_Silent_p.A1146A|SVEP1_ENST00000302728.8_Silent_p.A1169A|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1169					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.A1169A(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TTTCCTCTGCCGCTGAGAAAG	0.398													C|||	923	0.184305	0.0129	0.2406	5008	,	,		17487	0.4067		0.1819	False		,,,				2504	0.1493				p.A1169A		Atlas-SNP	.											SVEP1,NS,carcinoma,-1,2	SVEP1	326	2	1	Substitution - coding silent(1)	stomach(1)	c.G3507A						PASS	.	C		137,3557		3,131,1713	42.0	42.0	42.0		3507	-4.0	1.0	9	dbSNP_120	42	1401,6795		118,1165,2815	no	coding-synonymous	SVEP1	NM_153366.3		121,1296,4528	TT,TC,CC		17.0937,3.7087,12.9352		1169/3572	113220820	1538,10352	1847	4098	5945	SO:0001819	synonymous_variant	79987	exon20			CTCTGCCGCTGAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.3507G>A	9.37:g.113220820C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			C|0.795;T|0.205	0.205	strong		0.398	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CDC42BPB	9578	hgsc.bcm.edu	37	14	103440473	103440473	+	Silent	SNP	G	G	C	rs8009219	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:103440473G>C	ENST00000361246.2	-	12	1809	c.1521C>G	c.(1519-1521)ctC>ctG	p.L507L		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		GCTGTCGCTCGAGCCTGTTTG	0.517													G|||	2959	0.590855	0.4138	0.6758	5008	,	,		19823	0.5764		0.659	False		,,,				2504	0.7147				p.L507L		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.C1521G						PASS	.	G		2049,2357	567.3+/-382.1	495,1059,649	46.0	47.0	47.0		1521	-10.8	0.0	14	dbSNP_116	47	5602,2998	665.3+/-402.3	1855,1892,553	no	coding-synonymous	CDC42BPB	NM_006035.3		2350,2951,1202	CC,CG,GG		34.8605,46.5048,41.1733		507/1712	103440473	7651,5355	2203	4300	6503	SO:0001819	synonymous_variant	9578	exon12			TCGCTCGAGCCTG	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.1521C>G	14.37:g.103440473G>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_006035		Silent	SNP	ENST00000361246.2	37	CCDS9978.1																																																																																			G|0.410;C|0.589	0.589	strong		0.517	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035	
THAP4	51078	hgsc.bcm.edu	37	2	242573211	242573211	+	Missense_Mutation	SNP	T	T	C	rs7424328	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242573211T>C	ENST00000407315.1	-	2	792	c.361A>G	c.(361-363)Agc>Ggc	p.S121G		NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	121			S -> G (in dbSNP:rs7424328). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15498874}.				DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		GCTCCTCTGCTGGTGGCGGCA	0.637													C|||	3055	0.610024	0.5257	0.5908	5008	,	,		18238	0.8889		0.4592	False		,,,				2504	0.6053				p.S121G		Atlas-SNP	.											.	THAP4	27	.	0			c.A361G						PASS	.	C	GLY/SER	2226,2180	580.5+/-385.1	555,1116,532	74.0	75.0	74.0		361	-1.9	0.0	2	dbSNP_116	74	3893,4699	602.4+/-394.5	893,2107,1296	yes	missense	THAP4	NM_015963.5	56	1448,3223,1828	CC,CT,TT		45.3096,49.478,47.0765	benign	121/578	242573211	6119,6879	2203	4296	6499	SO:0001583	missense	51078	exon2			CTCTGCTGGTGGC	AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946		"""THAP (C2CH-type zinc finger) domain containing"""	23187	protein-coding gene	gene with protein product		612533				12575992, 10810093	Standard	NM_015963		Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000407315.1:c.361A>G	2.37:g.242573211T>C	ENSP00000385006:p.Ser121Gly	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_015963	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Missense_Mutation	SNP	ENST00000407315.1	37	CCDS2551.1	1302	0.5961538461538461	258	0.524390243902439	198	0.5469613259668509	499	0.8723776223776224	347	0.4577836411609499	C	0.108	-1.141827	0.01728	0.50522	0.453096	ENSG00000176946	ENST00000407315	D	0.95690	-3.78	4.69	-1.86	0.07760	.	1.710450	0.03691	N	0.247116	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.32134	-0.9918	9	0.10636	T	0.68	-7.9501	5.9451	0.19213	0.1647:0.3858:0.0:0.4495	rs7424328	121	Q8WY91	THAP4_HUMAN	G	121	ENSP00000385006:S121G	ENSP00000385006:S121G	S	-	1	0	THAP4	242221884	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.450000	0.06803	-0.591000	0.05859	-1.557000	0.00889	AGC	T|0.492;C|0.508	0.508	strong		0.637	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963	
OR1S2	219958	hgsc.bcm.edu	37	11	57971190	57971190	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57971190G>A	ENST00000302592.6	-	1	463	c.464C>T	c.(463-465)aCt>aTt	p.T155I		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T155I(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				TGTGAGCAAAGTGCCGAACCT	0.488																																					p.T155I		Atlas-SNP	.											OR1S2,trunk,malignant_melanoma,0,1	OR1S2	119	1	1	Substitution - Missense(1)	skin(1)	c.C464T						PASS	.						183.0	172.0	176.0					11																	57971190		2201	4296	6497	SO:0001583	missense	219958	exon1			AGCAAAGTGCCGA	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.464C>T	11.37:g.57971190G>A	ENSP00000305469:p.Thr155Ile	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	269	17	0.063197	NM_001004459	Q6IFG5|Q96R85	Missense_Mutation	SNP	ENST00000302592.6	37	CCDS31545.1	.	.	.	.	.	.	.	.	.	.	g	0.008	-1.862128	0.00552	.	.	ENSG00000197887	ENST00000302592	T	0.35421	1.31	4.47	0.804	0.18697	GPCR, rhodopsin-like superfamily (1);	1.024400	0.07804	N	0.956995	T	0.11367	0.0277	N	0.00525	-1.395	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.24440	-1.0160	10	0.34782	T	0.22	.	7.5141	0.27590	0.6178:0.0:0.3822:0.0	.	155	Q8NGQ3	OR1S2_HUMAN	I	155	ENSP00000305469:T155I	ENSP00000305469:T155I	T	-	2	0	OR1S2	57727766	0.000000	0.05858	0.013000	0.15412	0.026000	0.11368	-0.153000	0.10144	0.277000	0.22141	-0.285000	0.09966	ACT	.	.	none		0.488	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
ANKRD44	91526	hgsc.bcm.edu	37	2	197990741	197990741	+	Missense_Mutation	SNP	A	A	C	rs35338671	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:197990741A>C	ENST00000328737.2	-	5	283	c.207T>G	c.(205-207)atT>atG	p.I69M	ANKRD44_ENST00000337207.5_Missense_Mutation_p.I69M|ANKRD44_ENST00000539527.1_Missense_Mutation_p.I22M|ANKRD44_ENST00000450567.1_Missense_Mutation_p.I69M|ANKRD44_ENST00000409153.1_Missense_Mutation_p.I94M|ANKRD44_ENST00000282272.8_Missense_Mutation_p.I86M|ANKRD44_ENST00000409919.1_Missense_Mutation_p.I94M			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	94										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CTGAGTGCTTAATCAAAACCT	0.458													A|||	125	0.0249601	0.0197	0.0274	5008	,	,		20453	0.0		0.0557	False		,,,				2504	0.0245				p.I94M		Atlas-SNP	.											.	ANKRD44	281	.	0			c.T282G						PASS	.	A	MET/ILE,MET/ILE	78,4328	68.1+/-105.8	0,78,2125	136.0	128.0	131.0		282,282	0.4	1.0	2	dbSNP_126	131	466,8134	138.4+/-195.2	9,448,3843	yes	missense,missense	ANKRD44	NM_001195144.1,NM_153697.2	10,10	9,526,5968	CC,CA,AA		5.4186,1.7703,4.1827	benign,benign	94/994,94/368	197990741	544,12462	2203	4300	6503	SO:0001583	missense	91526	exon5			GTGCTTAATCAAA	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.207T>G	2.37:g.197990741A>C	ENSP00000331516:p.Ile69Met	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	187	96	0.513369	NM_153697	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	37		63	0.028846153846153848	19	0.03861788617886179	9	0.024861878453038673	0	0.0	35	0.04617414248021108	A	14.37	2.515912	0.44763	0.017703	0.054186	ENSG00000065413	ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000409153;ENST00000539527;ENST00000409919;ENST00000443014	T;T;T;T;T;T;T;T	0.67171	-0.25;1.9;1.9;1.89;1.89;1.41;1.9;-0.25	5.46	0.431	0.16523	.	0.000000	0.85682	D	0.000000	T	0.38506	0.1043	M	0.78916	2.43	0.40933	D	0.984406	B;D	0.65815	0.09;0.995	B;D	0.74674	0.193;0.984	T	0.63143	-0.6703	10	0.87932	D	0	.	5.6615	0.17672	0.3819:0.0:0.4678:0.1502	rs35338671;rs61752175	22;94	F5H682;Q8N8A2-3	.;.	M	86;69;69;69;94;22;94;69	ENSP00000282272:I86M;ENSP00000331516:I69M;ENSP00000402420:I69M;ENSP00000338794:I69M;ENSP00000387141:I94M;ENSP00000437825:I22M;ENSP00000387233:I94M;ENSP00000399895:I69M	ENSP00000282272:I86M	I	-	3	3	ANKRD44	197698986	0.001000	0.12720	1.000000	0.80357	0.862000	0.49288	-1.148000	0.03185	0.170000	0.19704	-0.250000	0.11733	ATT	A|0.959;C|0.041	0.041	strong		0.458	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	
HLA-C	3107	hgsc.bcm.edu	37	6	31239108	31239108	+	Missense_Mutation	SNP	T	T	A	rs1131118	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239108T>A	ENST00000376228.5	-	3	375	c.361A>T	c.(361-363)Agg>Tgg	p.R121W	HLA-C_ENST00000383329.3_Missense_Mutation_p.R121W	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	121	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CCAGACATCCTCTGGAGGGTG	0.701													N|||	1342	0.267971	0.2179	0.2839	5008	,	,		10532	0.3026		0.2664	False		,,,				2504	0.2904				p.R121W		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	0			c.A361T						scavenged	.	A	TRP/ARG	967,3349		93,781,1284	20.0	19.0	19.0		361	-5.6	0.0	6	dbSNP_86	19	1933,6525		189,1555,2485	no	missense	HLA-C	NM_002117.5	101	282,2336,3769	AA,AT,TT		22.8541,22.405,22.7024	benign	121/367	31239108	2900,9874	2158	4229	6387	SO:0001583	missense	3107	exon3			ACATCCTCTGGAG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.361A>T	6.37:g.31239108T>A	ENSP00000365402:p.Arg121Trp	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	76	19	0.25	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	3.319|3.319	-0.139116|-0.139116	0.06669|0.06669	0.22405|0.22405	0.228541|0.228541	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.00010	.|9.41;9.41	2.81|2.81	-5.62|-5.62	0.02481|0.02481	.|MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|1.047180	.|0.07713	.|N	.|0.942312	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.11255|0.11255	0.115|0.115	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.24368	.|0.102;0.062;0.03;0.03;0.03	.|B;B;B;B;B	.|0.36335	.|0.222;0.027;0.027;0.014;0.027	T|T	0.16808|0.16808	-1.0390|-1.0390	5|9	0.62326|0.42905	D|T	0.03|0.14	.|.	4.3487|4.3487	0.11144|0.11144	0.3799:0.2718:0.0:0.3483|0.3799:0.2718:0.0:0.3483	rs1131118;rs2308566;rs3177883;rs3190686;rs11547358;rs17366166;rs17413520;rs28367579|rs1131118;rs2308566;rs3177883;rs3190686;rs11547358;rs17366166;rs17413520;rs28367579	.|121;96;121;121;121	.|A2AEA4;Q92671;A6H578;A2AEA2;P10321	.|.;.;.;.;1C07_HUMAN	V|W	120|121;121;121;158	.|ENSP00000365402:R121W;ENSP00000372819:R121W	ENSP00000365412:E115V|ENSP00000365402:R121W	E|R	-|-	2|1	0|2	HLA-C|HLA-C	31347087|31347087	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-6.442000|-6.442000	0.00066|0.00066	-2.961000|-2.961000	0.00290|0.00290	-2.002000|-2.002000	0.00443|0.00443	GAG|AGG	T|0.768;A|0.232	0.232	strong		0.701	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377012	168377012	+	lincRNA	SNP	G	G	T	rs78475769		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168377012G>T	ENST00000538528.1	-	0	607																											CAGTGTGTGGGGAGGAGAAGA	0.637																																					p.S107S		Atlas-SNP	.											.	.	.	.	0			c.C321A						PASS	.						13.0	11.0	12.0					6																	168377012		691	1589	2280			0	exon1			GTGTGGGGAGGAG																													6.37:g.168377012G>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	179	49	0.273743	NM_001129895		Silent	SNP	ENST00000538528.1	37																																																																																				T|1.000;|0.000	1.000	weak		0.637	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
HTR3C	170572	hgsc.bcm.edu	37	3	183778010	183778010	+	Missense_Mutation	SNP	G	G	C	rs6807362	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:183778010G>C	ENST00000318351.1	+	9	1248	c.1214G>C	c.(1213-1215)gGa>gCa	p.G405A		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	405			G -> A (in dbSNP:rs6807362). {ECO:0000269|PubMed:12801637}.		ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.G405A(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	GGGGGCTCAGGATGGACAAAG	0.607													G|||	2786	0.55631	0.4418	0.6715	5008	,	,		19887	0.746		0.5676	False		,,,				2504	0.4223				p.G405A		Atlas-SNP	.											HTR3C,NS,carcinoma,0,1	HTR3C	65	1	1	Substitution - Missense(1)	stomach(1)	c.G1214C						PASS	.	G	ALA/GLY	2079,2327	570.5+/-382.9	477,1125,601	124.0	113.0	117.0		1214	-6.8	0.0	3	dbSNP_116	117	4568,4032	597.4+/-393.8	1247,2074,979	yes	missense	HTR3C	NM_130770.2	60	1724,3199,1580	CC,CG,GG		46.8837,47.1857,48.8928	benign	405/448	183778010	6647,6359	2203	4300	6503	SO:0001583	missense	170572	exon9			GCTCAGGATGGAC	AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24003	protein-coding gene	gene with protein product		610121	"""5-hydroxytryptamine (serotonin) receptor 3, family member C"""			12801637, 15157181	Standard	NM_130770		Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	ENST00000318351.1:c.1214G>C	3.37:g.183778010G>C	ENSP00000322617:p.Gly405Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	138	74	0.536232	NM_130770	A2RRR5	Missense_Mutation	SNP	ENST00000318351.1	37	CCDS3250.1	1298	0.5943223443223443	211	0.42886178861788615	232	0.6408839779005525	428	0.7482517482517482	427	0.5633245382585752	G	1.740	-0.491959	0.04322	0.471857	0.531163	ENSG00000178084	ENST00000318351	D	0.82081	-1.57	3.66	-6.84	0.01687	Neurotransmitter-gated ion-channel transmembrane domain (1);	1.216240	0.06253	N	0.692431	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	P	0.38788	0.647	B	0.32980	0.156	T	0.32295	-0.9912	9	0.15952	T	0.53	.	6.4174	0.21723	0.2833:0.1682:0.5484:0.0	rs6807362;rs52825356;rs6807362	405	Q8WXA8	5HT3C_HUMAN	A	405	ENSP00000322617:G405A	ENSP00000322617:G405A	G	+	2	0	HTR3C	185260704	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.507000	0.06352	-0.832000	0.04251	0.563000	0.77884	GGA	G|0.457;C|0.543	0.543	strong		0.607	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770	
HLA-C	3107	hgsc.bcm.edu	37	6	31238234	31238234	+	Silent	SNP	G	G	A	rs1050344	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238234G>A	ENST00000376228.5	-	4	662	c.648C>T	c.(646-648)caC>caT	p.H216H	HLA-C_ENST00000383329.3_Silent_p.H216H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	216	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CAGAGAGGGGGTGGTGGGTCA	0.607													a|||	3932	0.785144	0.8124	0.8184	5008	,	,		17539	0.8135		0.7276	False		,,,				2504	0.7546				p.H216H		Atlas-SNP	.											.	HLA-C	92	.	0			c.C648T						PASS	.	A		3459,947		1363,733,107	47.0	53.0	51.0		648	1.8	0.2	6	dbSNP_86	51	5816,2782		1988,1840,471	no	coding-synonymous	HLA-C	NM_002117.5		3351,2573,578	AA,AG,GG		32.3564,21.4934,28.6758		216/367	31238234	9275,3729	2203	4299	6502	SO:0001819	synonymous_variant	3107	exon4			GAGGGGGTGGTGG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.648C>T	6.37:g.31238234G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	1692	0.7747252747252747	396	0.8048780487804879	290	0.8011049723756906	458	0.8006993006993007	548	0.7229551451187335	.	2.093	-0.407972	0.04832	0.785066	0.676436	ENSG00000204525	ENST00000415537	.	.	.	2.65	1.77	0.24775	.	.	.	.	.	T	0.21022	0.0506	.	.	.	0.45747	P	0.001350999999999991	.	.	.	.	.	.	T	0.08932	-1.0698	3	.	.	.	.	5.8828	0.18864	0.1532:0.0:0.8468:0.0	rs1050344;rs2308609;rs3177871;rs3190639;rs9264635;rs17413485;rs17849593;rs17850333	.	.	.	S	216	.	.	P	-	1	0	HLA-C	31346213	0.006000	0.16342	0.227000	0.23927	0.014000	0.08584	-0.000000	0.12993	0.697000	0.31718	-0.849000	0.03036	CCC	G|0.275;A|0.725	0.725	strong		0.607	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
PIGR	5284	hgsc.bcm.edu	37	1	207104881	207104881	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207104881C>T	ENST00000356495.4	-	10	2343	c.2160G>A	c.(2158-2160)gaG>gaA	p.E720E	PIGR_ENST00000487208.1_5'UTR	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	720					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CTGTGGTGCTCTCAGTGGTGG	0.498																																					p.E720E		Atlas-SNP	.											PIGR,NS,carcinoma,-1,1	PIGR	98	1	0			c.G2160A						scavenged	.						213.0	190.0	198.0					1																	207104881		2203	4300	6503	SO:0001819	synonymous_variant	5284	exon10			GGTGCTCTCAGTG		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"""Immunoglobulin superfamily / V-set domain containing"""	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.2160G>A	1.37:g.207104881C>T		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	264	4	0.0151515	NM_002644	Q68D81|Q8IZY7	Silent	SNP	ENST00000356495.4	37	CCDS1474.1																																																																																			.	.	none		0.498	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644	
AMTN	401138	hgsc.bcm.edu	37	4	71396989	71396989	+	Silent	SNP	C	C	T	rs17676820	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:71396989C>T	ENST00000339336.4	+	8	721	c.591C>T	c.(589-591)atC>atT	p.I197I	AMTN_ENST00000504451.1_Silent_p.I196I	NM_212557.2	NP_997722.1	Q6UX39	AMTN_HUMAN	amelotin	197					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|odontogenesis of dentin-containing tooth (GO:0042475)	basal lamina (GO:0005605)|cell-cell junction (GO:0005911)|proteinaceous extracellular matrix (GO:0005578)		p.I197I(1)		NS(3)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)|skin(1)	19			Lung(101;0.235)			CACATGCCATCGAGGAAGCCA	0.522													C|||	1371	0.273762	0.1157	0.4568	5008	,	,		19732	0.1994		0.4453	False		,,,				2504	0.2577				p.I197I		Atlas-SNP	.											AMTN,NS,carcinoma,0,1	AMTN	28	1	1	Substitution - coding silent(1)	prostate(1)	c.C591T						PASS	.	C		801,3605	314.1+/-293.5	65,671,1467	70.0	55.0	60.0		591	-12.3	0.0	4	dbSNP_123	60	3794,4806	526.2+/-380.9	853,2088,1359	no	coding-synonymous	AMTN	NM_212557.2		918,2759,2826	TT,TC,CC		44.1163,18.1798,35.3298		197/210	71396989	4595,8411	2203	4300	6503	SO:0001819	synonymous_variant	401138	exon8			TGCCATCGAGGAA	AY358528	CCDS3542.1, CCDS68716.1	4q13.3	2006-12-12			ENSG00000187689	ENSG00000187689			33188	protein-coding gene	gene with protein product		610912				16304441	Standard	NM_001286731		Approved	UNQ689, RSTI689	uc003hfk.1	Q6UX39	OTTHUMG00000129906	ENST00000339336.4:c.591C>T	4.37:g.71396989C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	237	102	0.43038	NM_212557	Q0P503|Q0P506	Silent	SNP	ENST00000339336.4	37	CCDS3542.1																																																																																			C|0.684;T|0.316	0.316	strong		0.522	AMTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252157.1	NM_212557	
IFIT2	3433	hgsc.bcm.edu	37	10	91066460	91066460	+	Silent	SNP	T	T	A	rs954439	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:91066460T>A	ENST00000371826.3	+	2	916	c.747T>A	c.(745-747)gtT>gtA	p.V249V	LIPA_ENST00000371837.1_Intron|LIPA_ENST00000487618.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	249					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				TAACAGATGTTCTTCGCAGTG	0.433													A|||	3412	0.68131	0.879	0.4957	5008	,	,		22062	0.8571		0.5089	False		,,,				2504	0.5419				p.V249V		Atlas-SNP	.											.	IFIT2	39	.	0			c.T747A						PASS	.	A		3279,687		1358,563,62	83.0	82.0	83.0		747	-1.7	0.0	10	dbSNP_86	83	4062,4308		979,2104,1102	no	coding-synonymous	IFIT2	NM_001547.4		2337,2667,1164	AA,AT,TT		48.5305,17.3222,40.4912		249/473	91066460	7341,4995	1983	4185	6168	SO:0001819	synonymous_variant	3433	exon2			AGATGTTCTTCGC	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"""Tetratricopeptide (TTC) repeat domain containing"""	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.747T>A	10.37:g.91066460T>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	62	54	0.870968	NM_001547	Q5T767	Silent	SNP	ENST00000371826.3	37	CCDS41548.1																																																																																			T|0.339;A|0.661	0.661	strong		0.433	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547	
LAPTM5	7805	hgsc.bcm.edu	37	1	31208042	31208042	+	Missense_Mutation	SNP	C	C	T	rs35351292	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:31208042C>T	ENST00000294507.3	-	7	751	c.677G>A	c.(676-678)aGa>aAa	p.R226K		NM_006762.2	NP_006753.1	Q13571	LAPM5_HUMAN	lysosomal protein transmembrane 5	226			R -> K (in dbSNP:rs35351292). {ECO:0000269|PubMed:15489334}.		transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)				large_intestine(2)|lung(7)|skin(1)	10		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)		CTTGGAGTTTCTCTTCTCCTC	0.537													C|||	578	0.115415	0.0408	0.1124	5008	,	,		20260	0.0764		0.2664	False		,,,				2504	0.1033				p.R226K		Atlas-SNP	.											.	LAPTM5	30	.	0			c.G677A						PASS	.	C	LYS/ARG	363,4043	186.0+/-213.0	12,339,1852	307.0	269.0	282.0		677	-3.4	0.0	1	dbSNP_126	282	2178,6422	370.8+/-336.0	283,1612,2405	yes	missense	LAPTM5	NM_006762.2	26	295,1951,4257	TT,TC,CC		25.3256,8.2388,19.5371	benign	226/263	31208042	2541,10465	2203	4300	6503	SO:0001583	missense	7805	exon7			GAGTTTCTCTTCT	U51240	CCDS337.1	1p34	2009-07-20	2009-07-20		ENSG00000162511	ENSG00000162511			29612	protein-coding gene	gene with protein product		601476	"""lysosomal multispanning membrane protein 5"""			8661146, 12527926	Standard	NM_006762		Approved		uc001bsc.2	Q13571	OTTHUMG00000003707	ENST00000294507.3:c.677G>A	1.37:g.31208042C>T	ENSP00000294507:p.Arg226Lys	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_006762	Q13240|Q14698|Q3KP54	Missense_Mutation	SNP	ENST00000294507.3	37	CCDS337.1	299	0.13690476190476192	23	0.046747967479674794	45	0.12430939226519337	37	0.06468531468531469	194	0.2559366754617414	C	3.338	-0.135257	0.06711	0.082388	0.253256	ENSG00000162511	ENST00000294507;ENST00000424259	T	0.42900	0.96	5.5	-3.43	0.04810	.	1.182330	0.05835	N	0.618151	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.18263	0.021	T	0.22312	-1.0220	9	0.06099	T	0.92	-0.9238	1.3828	0.02233	0.1734:0.2608:0.3426:0.2231	rs35351292;rs61750962	226	Q13571	LAPM5_HUMAN	K	226	ENSP00000294507:R226K	ENSP00000294507:R226K	R	-	2	0	LAPTM5	30980629	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.033000	0.03571	-0.202000	0.10268	-0.175000	0.13238	AGA	T|0.179;G|0.000;C|0.821	0.179	strong		0.537	LAPTM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010463.1	NM_006762	
GABBR2	9568	hgsc.bcm.edu	37	9	101151192	101151192	+	Silent	SNP	G	G	A	rs144313756		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:101151192G>A	ENST00000259455.2	-	10	1932	c.1473C>T	c.(1471-1473)ctC>ctT	p.L491L		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	491					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	TGATCATCCCGAGGATGGTGA	0.498													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21052	0.0		0.0	False		,,,				2504	0.0				p.L491L		Atlas-SNP	.											.	GABBR2	126	.	0			c.C1473T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	263.0	212.0	229.0		1473	-6.8	0.7	9	dbSNP_134	229	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	GABBR2	NM_005458.7		0,15,6488	AA,AG,GG		0.1512,0.0454,0.1153		491/942	101151192	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	9568	exon10			CATCCCGAGGATG	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.1473C>T	9.37:g.101151192G>A		Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	393	203	0.516539	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Silent	SNP	ENST00000259455.2	37	CCDS6736.1																																																																																			G|0.999;A|0.001	0.001	strong		0.498	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
FAM47B	170062	hgsc.bcm.edu	37	X	34961479	34961479	+	Silent	SNP	C	C	T	rs149160457		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:34961479C>T	ENST00000329357.5	+	1	567	c.531C>T	c.(529-531)acC>acT	p.T177T		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	177										breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						AGGTACCCACCGAGTCTGGTA	0.612																																					p.T177T		Atlas-SNP	.											.	FAM47B	209	.	0			c.C531T						PASS	.	C		1,3832		0,1,1630,571	31.0	31.0	31.0		531	-1.7	0.0	X	dbSNP_134	31	0,6728		0,0,2428,1872	no	coding-synonymous	FAM47B	NM_152631.2		0,1,4058,2443	TT,TC,CC,C		0.0,0.0261,0.0095		177/646	34961479	1,10560	2202	4300	6502	SO:0001819	synonymous_variant	170062	exon1			ACCCACCGAGTCT	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.531C>T	X.37:g.34961479C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	124	107	0.862903	NM_152631	Q5JQN5|Q6PIG3	Silent	SNP	ENST00000329357.5	37	CCDS14236.1																																																																																			C|1.000;T|0.000	0.000	weak		0.612	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631	
SZT2	23334	hgsc.bcm.edu	37	1	43890811	43890811	+	Missense_Mutation	SNP	G	G	A	rs143992266	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43890811G>A	ENST00000562955.1	+	18	2578	c.2578G>A	c.(2578-2580)Gaa>Aaa	p.E860K	SZT2_ENST00000372442.1_Missense_Mutation_p.E18K	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	860					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						GGCTGCAGCTGAAGAGAAGCA	0.582													G|||	58	0.0115815	0.0	0.0634	5008	,	,		21675	0.0		0.0109	False		,,,				2504	0.0031				p.E860K		Atlas-SNP	.											.	SZT2	383	.	0			c.G2578A						PASS	.	G	LYS/GLU	15,4391	21.2+/-45.6	0,15,2188	134.0	109.0	118.0		2578	1.2	0.7	1	dbSNP_134	118	65,8535	39.3+/-95.6	1,63,4236	yes	missense	SZT2	NM_015284.3	56	1,78,6424	AA,AG,GG		0.7558,0.3404,0.6151	benign	860/3376	43890811	80,12926	2203	4300	6503	SO:0001583	missense	23334	exon18			GCAGCTGAAGAGA	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.2578G>A	1.37:g.43890811G>A	ENSP00000457168:p.Glu860Lys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	24	0.01098901098901099	0	0.0	14	0.03867403314917127	0	0.0	10	0.013192612137203167	G	13.67	2.307631	0.40795	0.003404	0.007558	ENSG00000198198	ENST00000372442	.	.	.	5.56	1.24	0.21308	.	0.499535	0.20729	N	0.086746	T	0.02888	0.0086	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16394	-1.0404	9	0.30078	T	0.28	.	6.1351	0.20227	0.3205:0.1314:0.5481:0.0	.	860;860	Q5T011-4;Q5T011-5	.;.	K	18	.	ENSP00000361519:E18K	E	+	1	0	SZT2	43663398	0.027000	0.19231	0.672000	0.29872	0.829000	0.46940	2.512000	0.45485	0.655000	0.30866	0.561000	0.74099	GAA	G|0.992;A|0.008	0.008	strong		0.582	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
DACT2	168002	hgsc.bcm.edu	37	6	168708793	168708793	+	Silent	SNP	C	C	G	rs10945500	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168708793C>G	ENST00000366795.3	-	4	1732	c.1644G>C	c.(1642-1644)cgG>cgC	p.R548R	DACT2_ENST00000610183.1_Silent_p.R378R|DACT2_ENST00000607983.1_Silent_p.R140R|DACT2_ENST00000366796.3_Intron	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	548					epithelial cell morphogenesis (GO:0003382)|hematopoietic progenitor cell differentiation (GO:0002244)|inner medullary collecting duct development (GO:0072061)|negative regulation of cell adhesion (GO:0007162)|negative regulation of nodal signaling pathway (GO:1900108)|skin development (GO:0043588)	mitochondrion (GO:0005739)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)|transcription factor binding (GO:0008134)			endometrium(1)	1		Breast(66;1.46e-05)|Ovarian(120;0.0728)		OV - Ovarian serous cystadenocarcinoma(33;5.33e-21)|BRCA - Breast invasive adenocarcinoma(81;1.18e-06)|GBM - Glioblastoma multiforme(31;0.000957)		GGGCTGGCCTCCGCTGGAGCC	0.706													C|||	1287	0.256989	0.4251	0.1902	5008	,	,		10832	0.122		0.2475	False		,,,				2504	0.226				p.R548R		Atlas-SNP	.											.	DACT2	46	.	0			c.G1644C						PASS	.						14.0	20.0	18.0					6																	168708793		692	1588	2280	SO:0001819	synonymous_variant	168002	exon4			TGGCCTCCGCTGG	AF318336	CCDS47519.1, CCDS69241.1, CCDS75554.1	6q27	2013-05-15	2013-05-15	2003-09-17	ENSG00000164488	ENSG00000164488			21231	protein-coding gene	gene with protein product		608966	"""chromosome 6 open reading frame 116"", ""dapper homolog 2, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 2 (Xenopus laevis)"""	C6orf116			Standard	NM_001286351		Approved	bA503C24.7, DAPPER2	uc003qwq.3	Q5SW24	OTTHUMG00000016046	ENST00000366795.3:c.1644G>C	6.37:g.168708793C>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	28	8	0.285714	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Silent	SNP	ENST00000366795.3	37	CCDS47519.1																																																																																			C|0.753;G|0.247	0.247	strong		0.706	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
MUC20	200958	hgsc.bcm.edu	37	3	195452987	195452987	+	Missense_Mutation	SNP	G	G	A	rs9866681	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:195452987G>A	ENST00000447234.2	+	2	1639	c.1513G>A	c.(1513-1515)Gcc>Acc	p.A505T	MUC20_ENST00000445522.2_Missense_Mutation_p.A470T|MUC20_ENST00000436408.1_Missense_Mutation_p.A505T|MUC20_ENST00000320736.6_Missense_Mutation_p.A334T	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	505	Involved in oligomerization.		Missing. {ECO:0000269|PubMed:14702039}.	AT -> TI (in Ref. 5; AAH29267). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CACTAACAGCGCCACAGAAAG	0.607																																					p.A334T		Atlas-SNP	.											.	MUC20	84	.	0			c.G1000A						PASS	.						58.0	50.0	53.0					3																	195452987		2168	4263	6431	SO:0001583	missense	200958	exon3			AACAGCGCCACAG	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1513G>A	3.37:g.195452987G>A	ENSP00000414350:p.Ala505Thr	Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	387	93	0.24031	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	G	1.115	-0.657053	0.03480	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.12039	3.12;3.06;3.29;2.72	3.86	-7.73	0.01245	.	1.341070	0.05085	N	0.484323	T	0.03220	0.0094	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30387	-0.9980	10	0.02654	T	1	0.679	2.3761	0.04342	0.5083:0.2221:0.1604:0.1091	rs9866681	334	E9PH32	.	T	505;334;505;470	ENSP00000414350:A505T;ENSP00000325431:A334T;ENSP00000396774:A505T;ENSP00000405629:A470T	ENSP00000325431:A334T	A	+	1	0	MUC20	196938658	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.229000	0.02945	-2.048000	0.00907	-2.708000	0.00134	GCC	G|0.891;A|0.109	0.109	strong		0.607	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
ARHGAP24	83478	hgsc.bcm.edu	37	4	86844835	86844835	+	Silent	SNP	A	A	G	rs6824722	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:86844835A>G	ENST00000395184.1	+	4	769	c.303A>G	c.(301-303)gaA>gaG	p.E101E	ARHGAP24_ENST00000503995.1_Silent_p.E101E|ARHGAP24_ENST00000395183.2_Silent_p.E6E	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	101	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		CAAATCATGAAAGCTACCTCC	0.493													G|||	1985	0.396366	0.4304	0.3689	5008	,	,		17440	0.3601		0.2744	False		,,,				2504	0.5327				p.E101E		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.A303G						PASS	.	G	,	1765,2641	644.4+/-398.0	365,1035,803	101.0	92.0	95.0		303,18	3.4	1.0	4	dbSNP_116	95	2352,6248	703.2+/-405.3	329,1694,2277	no	coding-synonymous,coding-synonymous	ARHGAP24	NM_001025616.2,NM_001042669.1	,	694,2729,3080	GG,GA,AA		27.3488,40.059,31.6546	,	101/749,6/654	86844835	4117,8889	2203	4300	6503	SO:0001819	synonymous_variant	83478	exon4			TCATGAAAGCTAC	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.303A>G	4.37:g.86844835A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	156	79	0.50641	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Silent	SNP	ENST00000395184.1	37	CCDS34025.1																																																																																			A|0.669;G|0.331	0.331	strong		0.493	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
ATRN	8455	hgsc.bcm.edu	37	20	3515924	3515924	+	Silent	SNP	G	G	A	rs151518	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3515924G>A	ENST00000262919.5	+	2	503	c.435G>A	c.(433-435)gtG>gtA	p.V145V	ATRN_ENST00000446916.2_Silent_p.V145V	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	145	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						CTGGGTTTGTGACAGATGGAC	0.284													A|||	960	0.191693	0.3306	0.1945	5008	,	,		10612	0.0169		0.2873	False		,,,				2504	0.0838				p.V145V		Atlas-SNP	.											.	ATRN	118	.	0			c.G435A						PASS	.	A	,,	1419,2987	673.2+/-402.8	222,975,1006	68.0	72.0	70.0		87,435,435	3.1	1.0	20	dbSNP_79	70	2364,6236	697.4+/-404.9	320,1724,2256	no	coding-synonymous,coding-synonymous,coding-synonymous	ATRN	NM_001207047.1,NM_139321.2,NM_139322.2	,,	542,2699,3262	AA,AG,GG		27.4884,32.2061,29.0866	,,	29/1157,145/1430,145/1273	3515924	3783,9223	2203	4300	6503	SO:0001819	synonymous_variant	8455	exon2			GTTTGTGACAGAT	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"""mahogany protein"""	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.435G>A	20.37:g.3515924G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Silent	SNP	ENST00000262919.5	37	CCDS13053.1																																																																																			G|0.754;A|0.246	0.246	strong		0.284	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321	
BDP1	55814	hgsc.bcm.edu	37	5	70806457	70806457	+	Missense_Mutation	SNP	G	G	A	rs715748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:70806457G>A	ENST00000358731.4	+	17	3801	c.3538G>A	c.(3538-3540)Ggt>Agt	p.G1180S	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	1180	9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.		G -> S (in dbSNP:rs715748).		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TGGAAGAGAGGGTTCCTCAAG	0.448													A|||	2202	0.439696	0.4107	0.3444	5008	,	,		19273	0.379		0.492	False		,,,				2504	0.5552				p.G1180S		Atlas-SNP	.											.	BDP1	204	.	0			c.G3538A						PASS	.	A	SER/GLY	1447,2343		288,871,736	105.0	103.0	104.0		3538	-4.5	0.0	5	dbSNP_86	104	3967,4273		984,1999,1137	yes	missense	BDP1	NM_018429.2	56	1272,2870,1873	AA,AG,GG		48.1432,38.1794,45.0042	benign	1180/2625	70806457	5414,6616	1895	4120	6015	SO:0001583	missense	55814	exon17			AGAGAGGGTTCCT	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.3538G>A	5.37:g.70806457G>A	ENSP00000351575:p.Gly1180Ser	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	145	80	0.551724	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	921	0.4217032967032967	195	0.39634146341463417	126	0.34806629834254144	223	0.38986013986013984	377	0.4973614775725594	A	9.024	0.985723	0.18889	0.381794	0.481432	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.05513	3.43	3.11	-4.52	0.03472	.	1.492680	0.04313	N	0.349377	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44817	-0.9303	9	0.40728	T	0.16	.	6.2203	0.20677	0.304:0.0:0.5335:0.1625	rs715748;rs41404848;rs52825079;rs61636267;rs715748	1180;1180;1180	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	S	1180;760	ENSP00000351575:G1180S	ENSP00000351575:G1180S	G	+	1	0	BDP1	70842213	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-2.097000	0.01348	-1.480000	0.01865	-1.140000	0.01884	GGT	A|0.426;C|0.014	0.426	strong		0.448	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
ELF2	1998	hgsc.bcm.edu	37	4	140046466	140046466	+	Silent	SNP	A	A	C	rs115767880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:140046466A>C	ENST00000394235.2	-	4	592	c.90T>G	c.(88-90)tcT>tcG	p.S30S	ELF2_ENST00000265495.4_Silent_p.S30S|ELF2_ENST00000379550.1_Silent_p.S30S	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)											endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					CTGGATATTCAGAAACCTTTT	0.373													a|||	6	0.00119808	0.0	0.0	5008	,	,		17185	0.0		0.006	False		,,,				2504	0.0				p.E30E		Atlas-SNP	.											.	ELF2	43	.	0			c.G90G						PASS	.	A		3,4403	8.1+/-20.4	0,3,2200	102.0	100.0	100.0		90	3.0	1.0	4	dbSNP_132	100	51,8549	32.8+/-85.7	0,51,4249	no	coding-synonymous	ELF2	NM_201999.1		0,54,6449	CC,CA,AA		0.593,0.0681,0.4152		30/582	140046466	54,12952	2203	4300	6503	SO:0001819	synonymous_variant	1998	exon3			ATATTCAGAAACC	AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.90T>G	4.37:g.140046466A>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	134	59	0.440298	NM_201999		Silent	SNP	ENST00000394235.2	37	CCDS3744.1																																																																																			A|0.997;C|0.003	0.003	strong		0.373	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874	
SCD	6319	hgsc.bcm.edu	37	10	102116311	102116311	+	Missense_Mutation	SNP	A	A	C	rs2234970	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:102116311A>C	ENST00000370355.2	+	5	1051	c.670A>C	c.(670-672)Atg>Ctg	p.M224L		NM_005063.4	NP_005054.3	O00767	ACOD_HUMAN	stearoyl-CoA desaturase (delta-9-desaturase)	224			M -> L (in dbSNP:rs2234970). {ECO:0000269|PubMed:10229681, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.7}.		fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|large_intestine(3)|lung(5)	9		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)		TGGCTTGCTGATGATGTGCTT	0.498													C|||	1948	0.388978	0.3631	0.5461	5008	,	,		20017	0.4028		0.4245	False		,,,				2504	0.2618				p.M224L	Colon(67;260 1459 9574 11663)	Atlas-SNP	.											.	SCD	25	.	0			c.A670C						PASS	.	C	LEU/MET	1570,2836	667.9+/-401.9	275,1020,908	183.0	144.0	158.0		670	-8.8	0.0	10	dbSNP_98	158	3627,4973	624.8+/-397.6	737,2153,1410	yes	missense	SCD	NM_005063.4	15	1012,3173,2318	CC,CA,AA		42.1744,35.6332,39.9585	benign	224/360	102116311	5197,7809	2203	4300	6503	SO:0001583	missense	6319	exon5			TTGCTGATGATGT	AF097514	CCDS7493.1	10q23-q24	2013-01-25			ENSG00000099194	ENSG00000099194	1.14.19.1	"""Fatty acid desaturases"""	10571	protein-coding gene	gene with protein product	"""acyl-CoA desaturase"", ""fatty acid desaturase"", ""delta-9-desaturase"""	604031	"""stearoyl-CoA desaturase opposite strand"""	SCDOS		7909540, 10229681	Standard	NM_005063		Approved	FADS5	uc001kqy.3	O00767	OTTHUMG00000018906	ENST00000370355.2:c.670A>C	10.37:g.102116311A>C	ENSP00000359380:p.Met224Leu	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	110	9	0.0818182	NM_005063	B2R5U0|D3DR68|Q16150|Q53GR9|Q5W037|Q5W038|Q6GSS4|Q96KF6|Q9BS07|Q9Y695	Missense_Mutation	SNP	ENST00000370355.2	37	CCDS7493.1	925	0.42353479853479853	182	0.3699186991869919	185	0.511049723756906	230	0.4020979020979021	328	0.43271767810026385	C	0.009	-1.827876	0.00584	0.356332	0.421744	ENSG00000099194	ENST00000423840;ENST00000370355	T	0.15372	2.43	5.53	-8.81	0.00813	Fatty acid desaturase, type 1 (1);	0.506214	0.17853	N	0.159772	T	0.00012	0.0000	N	0.00010	-3.025	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34428	-0.9829	9	0.02654	T	1	-5.4107	4.4685	0.11701	0.1465:0.1341:0.1456:0.5738	rs2234970;rs11598233;rs17855743;rs52813351;rs59706801;rs2234970	224	O00767	ACOD_HUMAN	L	224	ENSP00000359380:M224L	ENSP00000359380:M224L	M	+	1	0	SCD	102106301	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-3.819000	0.00358	-2.211000	0.00737	-1.169000	0.01745	ATG	A|0.604;C|0.396	0.396	strong		0.498	SCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049857.2	NM_005063	
C7orf55	154791	hgsc.bcm.edu	37	7	139026152	139026152	+	Missense_Mutation	SNP	T	T	G	rs10265	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:139026152T>G	ENST00000297534.6	+	1	275	c.22T>G	c.(22-24)Tcg>Gcg	p.S8A	LUC7L2_ENST00000541515.3_Missense_Mutation_p.S8A|C7orf55-LUC7L2_ENST00000541170.3_Intron|C7orf55_ENST00000481123.1_Intron	NM_197964.4	NP_932068.2	Q96HJ9	CG055_HUMAN	chromosome 7 open reading frame 55	8			S -> A (in dbSNP:rs10265). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)				breast(1)|lung(2)	3						AGGGTCCCCGTCGCACACTTT	0.652											OREG0018357	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2089	0.417133	0.879	0.2709	5008	,	,		15366	0.2024		0.2763	False		,,,				2504	0.2628				p.S8A		Atlas-SNP	.											C7orf55,brain,glioma,0,1	.	.	1	0			c.T22G						PASS	.	G	ALA/SER	3444,962	361.4+/-315.7	1347,750,106	55.0	64.0	61.0		22	2.6	1.0	7	dbSNP_52	61	2112,6488	716.4+/-406.1	259,1594,2447	yes	missense	C7orf55	NM_197964.3	99	1606,2344,2553	GG,GT,TT		24.5581,21.8339,42.7187		8/114	139026152	5556,7450	2203	4300	6503	SO:0001583	missense	100996928	exon1			TCCCCGTCGCACA	AF161386	CCDS5853.1	7q34	2009-01-22	2009-01-22	2009-01-22	ENSG00000164898	ENSG00000164898			26946	protein-coding gene	gene with protein product	"""formation of mitochondrial complexes 1 homolog (S. cerevisiae)"""					12477932	Standard	NM_197964		Approved	HSPC268, FMC1		Q96HJ9	OTTHUMG00000151719	ENST00000297534.6:c.22T>G	7.37:g.139026152T>G	ENSP00000297534:p.Ser8Ala	Somatic	30	0	0	1645	WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_001244584	B7Z4Q3|Q75M90|Q9P0B3	Missense_Mutation	SNP	ENST00000297534.6	37	CCDS5853.1	864	0.3956043956043956	426	0.8658536585365854	110	0.30386740331491713	125	0.21853146853146854	203	0.2678100263852243	G	9.961	1.222766	0.22457	0.781661	0.245581	ENSG00000164898;ENSG00000146963	ENST00000297534;ENST00000541515	T;T	0.39997	1.05;1.63	5.46	2.58	0.30949	.	0.803958	0.11207	N	0.588099	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29971	-0.9994	9	0.12103	T	0.63	-0.0075	9.3002	0.37840	0.0:0.4049:0.2811:0.314	rs10265;rs1129736;rs3187976;rs10330642;rs11556588;rs17716206;rs17845169;rs17857976;rs60395458;rs10265	8;8	B7Z4Q3;Q96HJ9	.;CG055_HUMAN	A	8	ENSP00000297534:S8A;ENSP00000440222:S8A	ENSP00000297534:S8A	S	+	1	0	LUC7L2;C7orf55	138676692	1.000000	0.71417	0.997000	0.53966	0.796000	0.44982	1.201000	0.32259	0.103000	0.17682	-0.187000	0.12897	TCG	T|0.587;G|0.413	0.413	strong		0.652	C7orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323626.1	NM_197964	
FAM181B	220382	hgsc.bcm.edu	37	11	82443754	82443754	+	Missense_Mutation	SNP	G	G	A	rs147683846	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:82443754G>A	ENST00000329203.3	-	1	1152	c.1018C>T	c.(1018-1020)Ccc>Tcc	p.P340S		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	340	Pro-rich.									large_intestine(1)|lung(2)|prostate(1)	4						CCGCCGCGGGGGGCAGTCAGG	0.697													G|||	39	0.00778754	0.0015	0.0043	5008	,	,		11170	0.0238		0.007	False		,,,				2504	0.0031				p.P340S		Atlas-SNP	.											.	FAM181B	14	.	0			c.C1018T						PASS	.	G	SER/PRO	1,1743		0,1,871	1.0	1.0	1.0		1018	-4.4	0.0	11	dbSNP_134	1	38,4482		0,38,2222	yes	missense	FAM181B	NM_175885.3	74	0,39,3093	AA,AG,GG		0.8407,0.0573,0.6226	possibly-damaging	340/427	82443754	39,6225	872	2260	3132	SO:0001583	missense	220382	exon1			CGCGGGGGGCAGT	AK095054, BC039262	CCDS31648.1	11q14.1	2011-11-30			ENSG00000182103	ENSG00000182103			28512	protein-coding gene	gene with protein product						12477932	Standard	NM_175885		Approved	LOC220382, MGC33846	uc001ozp.3	A6NEQ2	OTTHUMG00000166869	ENST00000329203.3:c.1018C>T	11.37:g.82443754G>A	ENSP00000365295:p.Pro340Ser	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_175885	B2RWP1	Missense_Mutation	SNP	ENST00000329203.3	37	CCDS31648.1	39	0.017857142857142856	12	0.024390243902439025	3	0.008287292817679558	17	0.02972027972027972	7	0.009234828496042216	G	4.247	0.044790	0.08196	5.73E-4	0.008407	ENSG00000182103	ENST00000329203	T	0.29397	1.57	5.27	-4.36	0.03645	.	0.754197	0.11109	N	0.598752	T	0.04318	0.0119	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.13407	0.009	T	0.25187	-1.0139	9	.	.	.	.	2.0392	0.03546	0.1466:0.2205:0.3614:0.2715	.	340	A6NEQ2	F181B_HUMAN	S	340	ENSP00000365295:P340S	.	P	-	1	0	FAM181B	82121402	0.000000	0.05858	0.000000	0.03702	0.530000	0.34684	-0.239000	0.08965	-0.564000	0.06070	0.561000	0.74099	CCC	G|0.982;A|0.018	0.018	strong		0.697	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885	
APOL3	80833	hgsc.bcm.edu	37	22	36537725	36537725	+	Silent	SNP	G	G	A	rs61731692	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:36537725G>A	ENST00000349314.2	-	3	769	c.732C>T	c.(730-732)taC>taT	p.Y244Y	APOL3_ENST00000397287.2_Silent_p.Y44Y|APOL3_ENST00000397293.2_Silent_p.Y173Y|APOL3_ENST00000487423.1_5'Flank|APOL3_ENST00000424878.2_Silent_p.Y44Y|APOL3_ENST00000361710.2_Silent_p.Y44Y	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	244					inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|signal transducer activity (GO:0004871)			endometrium(2)|large_intestine(1)|lung(1)|stomach(1)	5						CTGATGATGTGTATGAGTGCT	0.537													G|||	472	0.0942492	0.0983	0.0735	5008	,	,		21525	0.0198		0.16	False		,,,				2504	0.1125				p.Y244Y		Atlas-SNP	.											.	APOL3	60	.	0			c.C732T						PASS	.	G	,,	385,4021	192.6+/-218.0	14,357,1832	65.0	55.0	59.0		732,132,132	-6.8	0.0	22	dbSNP_129	59	1324,7276	260.3+/-283.2	106,1112,3082	yes	coding-synonymous,coding-synonymous,coding-synonymous	APOL3	NM_145640.2,NM_145641.2,NM_145642.2	,,	120,1469,4914	AA,AG,GG		15.3953,8.7381,13.1401	,,	244/403,44/203,44/203	36537725	1709,11297	2203	4300	6503	SO:0001819	synonymous_variant	80833	exon3			TGATGTGTATGAG	AF305227	CCDS13922.1, CCDS13924.1	22q13.1	2013-01-24			ENSG00000128284	ENSG00000128284		"""Apolipoproteins"""	14868	protein-coding gene	gene with protein product		607253				11374903	Standard	NM_145640		Approved	CG12-1, APOLIII	uc003aot.3	O95236	OTTHUMG00000150632	ENST00000349314.2:c.732C>T	22.37:g.36537725G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	43	17	0.395349	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Silent	SNP	ENST00000349314.2	37	CCDS13922.1																																																																																			G|0.888;A|0.112	0.112	strong		0.537	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641	
JAKMIP2	9832	hgsc.bcm.edu	37	5	147012291	147012291	+	Silent	SNP	G	G	A	rs3763094	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:147012291G>A	ENST00000265272.5	-	13	2195	c.1728C>T	c.(1726-1728)gaC>gaT	p.D576D	JAKMIP2_ENST00000507386.1_Silent_p.D555D|JAKMIP2_ENST00000333010.6_Silent_p.D534D	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	576						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTCTCTGGCGTCCTGTAGTT	0.368													G|||	787	0.157149	0.0212	0.2233	5008	,	,		18120	0.2073		0.1551	False		,,,				2504	0.2444				p.D576D		Atlas-SNP	.											.	JAKMIP2	154	.	0			c.C1728T						PASS	.	G		170,4236	111.2+/-149.4	3,164,2036	226.0	223.0	224.0		1728	3.4	1.0	5	dbSNP_107	224	1133,7467	234.2+/-267.2	69,995,3236	no	coding-synonymous	JAKMIP2	NM_014790.3		72,1159,5272	AA,AG,GG		13.1744,3.8584,10.0185		576/811	147012291	1303,11703	2203	4300	6503	SO:0001819	synonymous_variant	9832	exon13			TCTGGCGTCCTGT	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.1728C>T	5.37:g.147012291G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	173	78	0.450867	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Silent	SNP	ENST00000265272.5	37	CCDS4285.1																																																																																			G|0.876;A|0.124	0.124	strong		0.368	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
TAS2R30	259293	hgsc.bcm.edu	37	12	11286088	11286088	+	Missense_Mutation	SNP	A	A	C	rs2599404	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11286088A>C	ENST00000539585.1	-	1	1155	c.756T>G	c.(754-756)ttT>ttG	p.F252L	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	252			F -> L (in dbSNP:rs2599404). {ECO:0000269|PubMed:15496549}.		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						CCAGCCTCCCAAAATTACAAA	0.418													t|||	1759	0.351238	0.357	0.4697	5008	,	,		19770	0.1944		0.5109	False		,,,				2504	0.2566				p.F252L		Atlas-SNP	.											.	TAS2R30	28	.	0			c.T756G						PASS	.	T	LEU/PHE	1662,2742		322,1018,862	132.0	141.0	138.0		756	-3.5	0.0	12	dbSNP_100	138	4332,4266		1117,2098,1084	yes	missense	TAS2R30	NM_001097643.1	22	1439,3116,1946	CC,CA,AA		49.6162,37.7384,46.1006	benign	252/320	11286088	5994,7008	2202	4299	6501	SO:0001583	missense	259293	exon1			CCTCCCAAAATTA	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19112	protein-coding gene	gene with protein product		613963	"""taste receptor, type 2, member 47"""	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.756T>G	12.37:g.11286088A>C	ENSP00000444736:p.Phe252Leu	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	236	126	0.533898	NM_001097643	Q645X7	Missense_Mutation	SNP	ENST00000539585.1	37	CCDS53750.1	868	0.3974358974358974	180	0.36585365853658536	160	0.4419889502762431	126	0.2202797202797203	402	0.5303430079155673	-	0	-2.760374	0.00084	0.377384	0.503838	ENSG00000256188	ENST00000539585	T	0.35973	1.28	2.6	-3.51	0.04696	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.48375	-0.9041	5	0.10111	T	0.7	.	0.3526	0.00351	0.285:0.1967:0.1327:0.3856	rs2599404	.	.	.	L	252	ENSP00000444736:F252L	ENSP00000444736:F252L	F	-	3	2	TAS2R30	11177355	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.060000	0.03475	-0.589000	0.05874	-2.910000	0.00091	TTT	A|0.579;C|0.421	0.421	strong		0.418	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643	
TPSB2	64499	hgsc.bcm.edu	37	16	1279704	1279704	+	RNA	SNP	A	A	G	rs202107419	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1279704A>G	ENST00000339687.6	-	0	118				TPSB2_ENST00000445910.1_RNA|TPSB2_ENST00000430512.2_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				CCTGACCCCCAACGATGCCCA	0.697																																					p.V32V		Atlas-SNP	.											.	TPSB2	8	.	0			c.T96C						PASS	.						30.0	38.0	35.0					16																	1279704		2182	4298	6480			64499	exon3			ACCCCCAACGATG	AF099143		16p13.3	2009-11-20	2009-11-18		ENSG00000197253	ENSG00000197253			14120	protein-coding gene	gene with protein product	"""tryptase beta II"", ""tryptase beta III"""	191081	"""tryptase beta 2"""			19748655	Standard	NM_024164		Approved		uc002cky.3	P20231	OTTHUMG00000155926		16.37:g.1279704A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	81	27	0.333333	NM_024164	D2E6S0|D2E6S2|O95827|Q15664|Q9UQI6|Q9UQI7	Silent	SNP	ENST00000339687.6	37																																																																																				.	.	weak		0.697	TPSB2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000342364.1	NM_024164	
ST6GALNAC2	10610	hgsc.bcm.edu	37	17	74562308	74562308	+	Missense_Mutation	SNP	C	C	T	rs373585653		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:74562308C>T	ENST00000225276.5	-	9	1322	c.1003G>A	c.(1003-1005)Gac>Aac	p.D335N		NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	335					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						AAATAGTGGTCGGAAAATTTC	0.473																																					p.D335N		Atlas-SNP	.											.	ST6GALNAC2	29	.	0			c.G1003A						PASS	.	C	ASN/ASP	0,4406		0,0,2203	171.0	154.0	160.0		1003	3.5	0.7	17		160	1,8599	1.2+/-3.3	0,1,4299	no	missense	ST6GALNAC2	NM_006456.2	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	335/375	74562308	1,13005	2203	4300	6503	SO:0001583	missense	10610	exon9			AGTGGTCGGAAAA	U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"""Sialyltransferases"""	10867	protein-coding gene	gene with protein product		610137	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)"", ""sialyltransferase-like 1"""	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.1003G>A	17.37:g.74562308C>T	ENSP00000225276:p.Asp335Asn	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_006456	Q12971	Missense_Mutation	SNP	ENST00000225276.5	37	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646027	0.67358	0.0	1.16E-4	ENSG00000070731	ENST00000225276	T	0.29397	1.57	5.45	3.47	0.39725	.	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	L	0.54323	1.7	0.50171	D	0.999853	D	0.76494	0.999	P	0.62435	0.902	T	0.13629	-1.0502	10	0.31617	T	0.26	-26.2793	10.7107	0.45982	0.0:0.8435:0.0:0.1565	.	335	Q9UJ37	SIA7B_HUMAN	N	335	ENSP00000225276:D335N	ENSP00000225276:D335N	D	-	1	0	ST6GALNAC2	72073903	1.000000	0.71417	0.683000	0.30040	0.636000	0.38137	5.182000	0.65059	0.681000	0.31386	0.655000	0.94253	GAC	.	.	weak		0.473	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456	
OR52B6	340980	hgsc.bcm.edu	37	11	5602929	5602929	+	Missense_Mutation	SNP	C	C	A	rs74053516	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5602929C>A	ENST00000345043.2	+	1	823	c.823C>A	c.(823-825)Ctt>Att	p.L275I	HBG2_ENST00000380259.2_Intron|AC015691.13_ENST00000394793.2_RNA	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTCCCTGCGCTTTTTTCTGT	0.517													C|||	144	0.028754	0.0257	0.0504	5008	,	,		21880	0.0089		0.0557	False		,,,				2504	0.0102				p.L275I		Atlas-SNP	.											.	OR52B6	37	.	0			c.C823A						PASS	.	C	ILE/LEU	112,3820		1,110,1855	264.0	271.0	269.0		823	1.2	0.6	11	dbSNP_130	269	441,7883		11,419,3732	yes	missense	OR52B6	NM_001005162.2	5	12,529,5587	AA,AC,CC		5.2979,2.8484,4.5121	probably-damaging	275/336	5602929	553,11703	1966	4162	6128	SO:0001583	missense	340980	exon1			CCTGCGCTTTTTT	AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"""GPCR / Class A : Olfactory receptors"""	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.823C>A	11.37:g.5602929C>A	ENSP00000341581:p.Leu275Ile	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	261	134	0.51341	NM_001005162	Q6IFI7	Missense_Mutation	SNP	ENST00000345043.2	37	CCDS41611.1	79	0.036172161172161175	17	0.034552845528455285	20	0.055248618784530384	7	0.012237762237762238	35	0.04617414248021108	C	1.806	-0.475855	0.04414	0.028484	0.052979	ENSG00000187747	ENST00000345043	T	0.00158	8.65	4.67	1.21	0.21127	GPCR, rhodopsin-like superfamily (1);	0.221905	0.22526	U	0.058903	T	0.00012	0.0000	N	0.01576	-0.805	0.09310	N	1	B	0.15930	0.015	B	0.22601	0.04	T	0.27365	-1.0076	10	0.51188	T	0.08	.	2.8762	0.05631	0.1704:0.5381:0.1656:0.1258	.	275	Q8NGF0	O52B6_HUMAN	I	275	ENSP00000341581:L275I	ENSP00000341581:L275I	L	+	1	0	OR52B6	5559505	0.000000	0.05858	0.648000	0.29521	0.157000	0.22087	-1.422000	0.02453	0.057000	0.16193	0.591000	0.81541	CTT	C|0.961;A|0.039	0.039	strong		0.517	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
DNAH5	1767	hgsc.bcm.edu	37	5	13719089	13719089	+	Missense_Mutation	SNP	G	G	A	rs30168	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13719089G>A	ENST00000265104.4	-	72	12505	c.12401C>T	c.(12400-12402)gCt>gTt	p.A4134V		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4134	AAA 6. {ECO:0000250}.		A -> V (in dbSNP:rs30168). {ECO:0000269|PubMed:10997877}.		cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTGCTTATGAGCCTCGGTGGT	0.463									Kartagener syndrome				A|||	2331	0.465455	0.5514	0.4265	5008	,	,		15643	0.4415		0.3976	False		,,,				2504	0.4714				p.A4134V		Atlas-SNP	.											DNAH5,colon,carcinoma,-1,1	DNAH5	868	1	0			c.C12401T						scavenged	.	A	VAL/ALA	2357,2049	566.7+/-382.0	646,1065,492	147.0	144.0	145.0		12401	1.7	0.7	5	dbSNP_76	145	3654,4946	623.1+/-397.4	758,2138,1404	yes	missense	DNAH5	NM_001369.2	64	1404,3203,1896	AA,AG,GG		42.4884,46.5048,46.2171	benign	4134/4625	13719089	6011,6995	2203	4300	6503	SO:0001583	missense	1767	exon72	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TTATGAGCCTCGG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12401C>T	5.37:g.13719089G>A	ENSP00000265104:p.Ala4134Val	Somatic	187	2	0.0106952		WXS	Illumina HiSeq	Phase_I	234	231	0.987179	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	965	0.44184981684981683	265	0.5386178861788617	152	0.4198895027624309	233	0.40734265734265734	315	0.4155672823218997	A	0.031	-1.335950	0.01287	0.534952	0.424884	ENSG00000039139	ENST00000265104	T	0.07800	3.16	5.59	1.72	0.24424	Dynein heavy chain (1);	0.198108	0.41823	N	0.000814	T	0.00012	0.0000	N	0.00405	-1.535	0.49798	P	1.7800000000001148E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.37753	-0.9692	9	0.02654	T	1	.	3.0235	0.06083	0.6362:0.1205:0.128:0.1153	rs30168;rs3756670;rs17262811;rs52829614;rs58199971;rs30168	4134	Q8TE73	DYH5_HUMAN	V	4134	ENSP00000265104:A4134V	ENSP00000265104:A4134V	A	-	2	0	DNAH5	13772089	0.769000	0.28531	0.664000	0.29753	0.024000	0.10985	1.691000	0.37721	-0.174000	0.10743	-1.228000	0.01579	GCT	G|0.549;A|0.451	0.451	strong		0.463	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
MMD2	221938	hgsc.bcm.edu	37	7	4959807	4959807	+	Silent	SNP	G	G	A	rs932061	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:4959807G>A	ENST00000404774.3	-	3	479	c.285C>T	c.(283-285)caC>caT	p.H95H	MMD2_ENST00000406755.1_Silent_p.H95H|MMD2_ENST00000401401.3_Silent_p.H95H	NM_001100600.1	NP_001094070.1	Q8IY49	PAQRA_HUMAN	monocyte to macrophage differentiation-associated 2	95						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(11)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		GGCACCTGAGGTGGCTCTTCT	0.657													G|||	2212	0.441693	0.618	0.5951	5008	,	,		16463	0.2996		0.4085	False		,,,				2504	0.2751				p.H95H		Atlas-SNP	.											.	MMD2	63	.	0			c.C285T						PASS	.	G	,	2135,1691		630,875,408	19.0	21.0	20.0		285,285	1.5	1.0	7	dbSNP_86	20	3359,4821		740,1879,1471	yes	coding-synonymous,coding-synonymous	MMD2	NM_001100600.1,NM_198403.3	,	1370,2754,1879	AA,AG,GG		41.0636,44.1976,45.7605	,	95/271,95/247	4959807	5494,6512	1913	4090	6003	SO:0001819	synonymous_variant	221938	exon3			CCTGAGGTGGCTC	BC037881	CCDS47529.1, CCDS47530.1, CCDS59047.1	7p22	2004-06-23			ENSG00000136297	ENSG00000136297			30133	protein-coding gene	gene with protein product		614581				12477932	Standard	NM_198403		Approved	PAQR10	uc003sno.4	Q8IY49	OTTHUMG00000151844	ENST00000404774.3:c.285C>T	7.37:g.4959807G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_198403	B5MBW4|Q6NVU5|Q6TCH0	Silent	SNP	ENST00000404774.3	37	CCDS47529.1																																																																																			G|0.545;A|0.455	0.455	strong		0.657	MMD2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324136.1	NM_198403	
NPSR1	387129	hgsc.bcm.edu	37	7	34851393	34851393	+	Silent	SNP	C	C	G	rs9655357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:34851393C>G	ENST00000360581.1	+	4	524	c.396C>G	c.(394-396)ctC>ctG	p.L132L	NPSR1_ENST00000359791.1_Silent_p.L132L|NPSR1_ENST00000531252.1_Silent_p.L121L|NPSR1_ENST00000381539.3_Silent_p.L132L|NPSR1_ENST00000381542.1_Intron	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	132						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	TTGTGCTGCTCTACGCCTCTA	0.473													C|||	744	0.148562	0.0113	0.1556	5008	,	,		20300	0.3165		0.2068	False		,,,				2504	0.0961				p.L132L		Atlas-SNP	.											NPSR1_ENST00000359791,NS,carcinoma,+2,2	NPSR1	134	2	0			c.C396G						PASS	.	C	,	201,4205	125.3+/-162.5	6,189,2008	250.0	187.0	208.0		396,396	1.1	1.0	7	dbSNP_119	208	1589,7011	296.7+/-303.1	140,1309,2851	no	coding-synonymous,coding-synonymous	NPSR1	NM_207172.1,NM_207173.1	,	146,1498,4859	GG,GC,CC		18.4767,4.562,13.7629	,	132/372,132/378	34851393	1790,11216	2203	4300	6503	SO:0001819	synonymous_variant	387129	exon4			GCTGCTCTACGCC	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.396C>G	7.37:g.34851393C>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Silent	SNP	ENST00000360581.1	37	CCDS5444.1																																																																																			C|0.847;G|0.153	0.153	strong		0.473	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173	
REST	5978	hgsc.bcm.edu	37	4	57798189	57798189	+	Silent	SNP	G	G	A	rs2227901	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:57798189G>A	ENST00000309042.7	+	4	3479	c.3165G>A	c.(3163-3165)gcG>gcA	p.A1055A		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	1055	Interaction with RCOR1.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CAGTCAAAGCGGCTAAGGGAG	0.433													G|||	1270	0.253594	0.2595	0.2161	5008	,	,		20278	0.3661		0.1849	False		,,,				2504	0.227				p.A1055A		Atlas-SNP	.											.	REST	104	.	0			c.G3165A						PASS	.	G	,	1041,3365	384.9+/-325.5	111,819,1273	80.0	77.0	78.0		3165,3165	1.1	0.0	4	dbSNP_98	78	1641,6959	303.6+/-306.5	143,1355,2802	no	coding-synonymous,coding-synonymous	REST	NM_001193508.1,NM_005612.4	,	254,2174,4075	AA,AG,GG		19.0814,23.6269,20.6213	,	1055/1098,1055/1098	57798189	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	5978	exon4			CAAAGCGGCTAAG	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.3165G>A	4.37:g.57798189G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	157	64	0.407643	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Silent	SNP	ENST00000309042.7	37	CCDS3509.1																																																																																			G|0.791;A|0.209	0.209	strong		0.433	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
ABHD16A	7920	hgsc.bcm.edu	37	6	31660848	31660848	+	Silent	SNP	G	G	A	rs11552114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31660848G>A	ENST00000395952.3	-	7	744	c.582C>T	c.(580-582)gaC>gaT	p.D194D	ABHD16A_ENST00000440843.2_Silent_p.D161D|XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|ABHD16A_ENST00000471644.1_5'Flank|ABHD16A_ENST00000538874.1_Missense_Mutation_p.T96I|ABHD16A_ENST00000375842.4_5'UTR	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	194						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						TGAGGAGGGTGTCTGCTGTCC	0.647													G|||	49	0.00978435	0.0068	0.0389	5008	,	,		12997	0.0		0.0129	False		,,,				2504	0.0				p.D194D		Atlas-SNP	.											.	ABHD16A	34	.	0			c.C582T						PASS	.	G	,	27,4379	31.7+/-61.6	1,25,2177	57.0	54.0	55.0		483,582	3.5	1.0	6	dbSNP_120	55	163,8437	77.2+/-139.8	3,157,4140	no	coding-synonymous,coding-synonymous	ABHD16A	NM_001177515.1,NM_021160.2	,	4,182,6317	AA,AG,GG		1.8953,0.6128,1.4609	,	161/526,194/559	31660848	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	7920	exon7			GAGGGTGTCTGCT	AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"""Abhydrolase domain containing"""	13921	protein-coding gene	gene with protein product		142620	"""HLA-B associated transcript 5"""	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.582C>T	6.37:g.31660848G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_021160	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Silent	SNP	ENST00000395952.3	37	CCDS4713.1	30	0.013736263736263736	5	0.01016260162601626	15	0.04143646408839779	0	0.0	10	0.013192612137203167	G	16.60	3.168241	0.57476	0.006128	0.018953	ENSG00000204427	ENST00000538874	.	.	.	5.63	3.53	0.40419	.	.	.	.	.	T	0.18718	0.0449	.	.	.	0.25057	N	0.991098	B	0.27997	0.197	B	0.27887	0.084	T	0.22661	-1.0210	7	0.87932	D	0	-27.769	10.989	0.47539	0.1792:0.0:0.8208:0.0	rs11552114;rs11552114	96	B7Z8I9	.	I	96	.	ENSP00000442151:T96I	T	-	2	0	ABHD16A	31768827	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	2.372000	0.44257	1.379000	0.46325	0.561000	0.74099	ACA	G|0.983;A|0.017	0.017	strong		0.647	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4		
ZNF362	149076	hgsc.bcm.edu	37	1	33764617	33764617	+	Silent	SNP	C	C	T	rs55887741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:33764617C>T	ENST00000539719.1	+	9	1403	c.1233C>T	c.(1231-1233)ccC>ccT	p.P411P	ZNF362_ENST00000373428.5_Silent_p.P411P	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	411					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CGGAGTCCCCCGGCATCCCGG	0.657											OREG0013343	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	7	0.00139776	0.0	0.0014	5008	,	,		16576	0.0		0.006	False		,,,				2504	0.0				p.P411P	Pancreas(162;1431 2676 35353 38425)	Atlas-SNP	.											.	ZNF362	31	.	0			c.C1233T						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	70.0	68.0	69.0		1233	3.3	1.0	1	dbSNP_129	69	75,8525	43.1+/-100.9	0,75,4225	no	coding-synonymous	ZNF362	NM_152493.2		0,83,6420	TT,TC,CC		0.8721,0.1816,0.6382		411/421	33764617	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	149076	exon9			GTCCCCCGGCATC		CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"""Zinc fingers, C2H2-type"""	18079	protein-coding gene	gene with protein product	"""rotund homolog (Drosophila)"""						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.1233C>T	1.37:g.33764617C>T		Somatic	58	0	0	842	WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_152493	Q8WYU4	Silent	SNP	ENST00000539719.1	37	CCDS377.1																																																																																			C|0.997;T|0.003	0.003	strong		0.657	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011857.2	NM_152493	
TTLL2	83887	hgsc.bcm.edu	37	6	167754702	167754702	+	Silent	SNP	C	C	T	rs909546	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:167754702C>T	ENST00000239587.5	+	3	1402	c.1314C>T	c.(1312-1314)gaC>gaT	p.D438D		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	438					cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CCAACATCGACGCTGCAAAAA	0.428													C|||	2571	0.513379	0.6437	0.4265	5008	,	,		23083	0.6181		0.3966	False		,,,				2504	0.411				p.D438D		Atlas-SNP	.											TTLL2,NS,carcinoma,0,1	TTLL2	82	1	0			c.C1314T						PASS	.	C		2691,1715	650.3+/-399.0	823,1045,335	102.0	95.0	98.0		1314	-0.3	0.0	6	dbSNP_86	98	3605,4995	521.5+/-379.9	736,2133,1431	no	coding-synonymous	TTLL2	NM_031949.4		1559,3178,1766	TT,TC,CC		41.9186,38.9242,48.4084		438/593	167754702	6296,6710	2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			CATCGACGCTGCA	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1314C>T	6.37:g.167754702C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	37	CCDS5301.1																																																																																			C|0.503;A|0.003	.	strong		0.428	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
TP53TG5	27296	hgsc.bcm.edu	37	20	44005936	44005936	+	Missense_Mutation	SNP	C	C	T	rs2231616	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:44005936C>T	ENST00000372726.3	-	3	326	c.170G>A	c.(169-171)cGc>cAc	p.R57H	SYS1-DBNDD2_ENST00000475242.1_Intron|TP53TG5_ENST00000494455.1_5'UTR|TP53TG5_ENST00000537995.1_Missense_Mutation_p.R41H|SYS1-DBNDD2_ENST00000452133.1_Intron	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	57			R -> H (in dbSNP:rs2231616).		intracellular signal transduction (GO:0035556)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	12						TTGGATCCGGCGGTTTGAGCT	0.502													C|||	1008	0.201278	0.0696	0.2579	5008	,	,		18364	0.2897		0.1123	False		,,,				2504	0.3395				p.R57H		Atlas-SNP	.											.	TP53TG5	36	.	0			c.G170A						PASS	.	C	HIS/ARG	429,3977	208.8+/-229.8	25,379,1799	175.0	168.0	170.0		170	-2.1	0.0	20	dbSNP_98	170	1122,7478	233.2+/-266.6	69,984,3247	yes	missense	TP53TG5	NM_014477.2	29	94,1363,5046	TT,TC,CC		13.0465,9.7367,11.9253	possibly-damaging	57/291	44005936	1551,11455	2203	4300	6503	SO:0001583	missense	27296	exon3			ATCCGGCGGTTTG	AB017802	CCDS13352.1	20q13.12	2008-09-18	2008-09-18	2008-09-18	ENSG00000124251	ENSG00000124251			15856	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 10"""	C20orf10			Standard	NM_014477		Approved	CLG01, dJ453C12.5	uc002xny.3	Q9Y2B4	OTTHUMG00000032582	ENST00000372726.3:c.170G>A	20.37:g.44005936C>T	ENSP00000361811:p.Arg57His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	110	41	0.372727	NM_014477		Missense_Mutation	SNP	ENST00000372726.3	37	CCDS13352.1	338	0.15476190476190477	32	0.06504065040650407	73	0.20165745856353592	144	0.2517482517482518	89	0.11741424802110818	C	10.75	1.438782	0.25900	0.097367	0.130465	ENSG00000124251	ENST00000372726;ENST00000537995	T;T	0.14022	2.54;2.54	5.52	-2.06	0.07298	.	0.660669	0.14744	N	0.301018	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.22276	0.067	B	0.12837	0.008	T	0.42565	-0.9444	9	0.36615	T	0.2	-0.0354	9.6207	0.39719	0.0:0.4882:0.317:0.1948	rs2231616;rs3746590;rs57771799;rs2231616	57	Q9Y2B4	T53G5_HUMAN	H	57;41	ENSP00000361811:R57H;ENSP00000438374:R41H	ENSP00000361811:R57H	R	-	2	0	TP53TG5	43439350	0.015000	0.18098	0.007000	0.13788	0.771000	0.43674	-1.108000	0.03313	-0.161000	0.10983	-0.176000	0.13171	CGC	C|0.863;T|0.137	0.137	strong		0.502	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477	
SPINK5	11005	hgsc.bcm.edu	37	5	147480080	147480080	+	Missense_Mutation	SNP	G	G	A	rs2303064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:147480080G>A	ENST00000256084.7	+	13	1198	c.1156G>A	c.(1156-1158)Gat>Aat	p.D386N	SPINK5_ENST00000359874.3_Missense_Mutation_p.D386N|SPINK5_ENST00000398454.1_Missense_Mutation_p.D386N|SPINK5_ENST00000476608.1_3'UTR	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	386	Kazal-like 6. {ECO:0000255|PROSITE- ProRule:PRU00798}.		D -> N (in dbSNP:rs2303064).		anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAGAGAACGATCCTATCCA	0.493													G|||	1744	0.348243	0.559	0.1614	5008	,	,		17510	0.4246		0.1213	False		,,,				2504	0.3507				p.D386N		Atlas-SNP	.											.	SPINK5	245	.	0			c.G1156A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP	1800,2126		404,992,567	159.0	155.0	156.0		1156,1156,1156	3.8	0.2	5	dbSNP_100	156	1044,7304		52,940,3182	yes	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	23,23,23	456,1932,3749	AA,AG,GG		12.506,45.8482,23.1709	benign,benign,benign	386/1095,386/917,386/1065	147480080	2844,9430	1963	4174	6137	SO:0001583	missense	11005	exon13			GAGAACGATCCTA	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1156G>A	5.37:g.147480080G>A	ENSP00000256084:p.Asp386Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	660	0.3021978021978022	247	0.5020325203252033	59	0.16298342541436464	257	0.4493006993006993	97	0.1279683377308707	G	10.88	1.476580	0.26511	0.458482	0.12506	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.04654	3.58;3.58;3.58;3.58	4.69	3.82	0.43975	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.189270	0.25349	N	0.031317	T	0.00012	0.0000	L	0.61387	1.9	0.51482	P	7.100000000004325E-5	P;P;P;B	0.40970	0.455;0.689;0.734;0.4	B;B;B;B	0.37780	0.125;0.167;0.258;0.12	T	0.38308	-0.9667	9	0.28530	T	0.3	-8.6523	9.1943	0.37217	0.0998:0.0:0.9002:0.0	rs2303064;rs17860503;rs52823786;rs59833491;rs2303064	367;386;386;386	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	N	386;386;367;386	ENSP00000381472:D386N;ENSP00000352936:D386N;ENSP00000421519:D367N;ENSP00000256084:D386N	ENSP00000256084:D386N	D	+	1	0	SPINK5	147460273	0.377000	0.25106	0.164000	0.22755	0.362000	0.29581	1.896000	0.39789	1.349000	0.45751	0.591000	0.81541	GAT	G|0.688;A|0.312	0.312	strong		0.493	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
EPG5	57724	hgsc.bcm.edu	37	18	43490602	43490602	+	Silent	SNP	G	G	A	rs3744996	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:43490602G>A	ENST00000282041.5	-	23	4123	c.4089C>T	c.(4087-4089)caC>caT	p.H1363H	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1363					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TTGCAGCATGGTGGAAGTCAG	0.507											OREG0024952	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1334	0.266374	0.2632	0.3055	5008	,	,		20007	0.3095		0.166	False		,,,				2504	0.3016				p.H1363H		Atlas-SNP	.											.	EPG5	199	.	0			c.C4089T						PASS	.	G		947,2861		112,723,1069	86.0	86.0	86.0		4089	3.2	1.0	18	dbSNP_107	86	1170,7092		82,1006,3043	no	coding-synonymous	EPG5	NM_020964.2		194,1729,4112	AA,AG,GG		14.1612,24.8687,17.5394		1363/2580	43490602	2117,9953	1904	4131	6035	SO:0001819	synonymous_variant	57724	exon23			AGCATGGTGGAAG	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.4089C>T	18.37:g.43490602G>A		Somatic	68	0	0	916	WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	37	CCDS11926.2																																																																																			G|0.786;A|0.214	0.214	strong		0.507	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
KRT1	3848	hgsc.bcm.edu	37	12	53069014	53069014	+	Missense_Mutation	SNP	T	T	C	rs14024	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53069014T>C	ENST00000252244.3	-	9	1956	c.1898A>G	c.(1897-1899)aAg>aGg	p.K633R		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	633	Gly/Ser-rich.|Tail.		K -> R (in dbSNP:rs14024). {ECO:0000269|PubMed:10903910, ECO:0000269|PubMed:11286630, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2580302, ECO:0000269|PubMed:2581964}.		complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						AGAAACAAACTTCACGCTGGA	0.562													T|||	1380	0.275559	0.0219	0.2478	5008	,	,		13965	0.5784		0.331	False		,,,				2504	0.2689				p.K633R		Atlas-SNP	.											.	KRT1	110	.	0			c.A1898G						PASS	.	T	ARG/LYS	300,4106	162.9+/-194.8	8,284,1911	97.0	107.0	103.0		1898	2.3	1.0	12	dbSNP_52	103	2605,5995	419.6+/-353.1	396,1813,2091	yes	missense	KRT1	NM_006121.3	26	404,2097,4002	CC,CT,TT		30.2907,6.8089,22.3358	benign	633/645	53069014	2905,10101	2203	4300	6503	SO:0001583	missense	3848	exon9			ACAAACTTCACGC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1898A>G	12.37:g.53069014T>C	ENSP00000252244:p.Lys633Arg	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	37	CCDS8836.1	717	0.3282967032967033	16	0.032520325203252036	101	0.27900552486187846	343	0.5996503496503497	257	0.3390501319261214	T	6.961	0.547217	0.13312	0.068089	0.302907	ENSG00000167768	ENST00000252244	D	0.83914	-1.78	3.52	2.33	0.28932	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.40850	P	0.01625399999999999	B	0.31611	0.331	B	0.27262	0.078	T	0.42649	-0.9439	8	0.02654	T	1	.	4.7427	0.13022	0.0:0.1057:0.1945:0.6998	rs14024;rs1050879;rs3191224;rs3825223;rs17855875;rs52799434;rs14024	633	P04264	K2C1_HUMAN	R	633	ENSP00000252244:K633R	ENSP00000252244:K633R	K	-	2	0	KRT1	51355281	0.629000	0.27146	0.999000	0.59377	0.469000	0.32828	1.269000	0.33074	0.533000	0.28675	0.260000	0.18958	AAG	T|0.726;C|0.274	0.274	strong		0.562	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
VPS13D	55187	hgsc.bcm.edu	37	1	12339619	12339619	+	Missense_Mutation	SNP	A	A	T	rs4845898	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:12339619A>T	ENST00000358136.3	+	20	4644	c.4514A>T	c.(4513-4515)gAa>gTa	p.E1505V	VPS13D_ENST00000356315.4_Missense_Mutation_p.E1505V	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		ATAGAGAGAGAATCTGAATTG	0.378													A|||	807	0.161142	0.0151	0.2118	5008	,	,		16353	0.1964		0.2356	False		,,,				2504	0.2096				p.E1505V		Atlas-SNP	.											.	VPS13D	316	.	0			c.A4514T						PASS	.	A	VAL/GLU,VAL/GLU	190,4216	121.3+/-158.8	6,178,2019	103.0	104.0	104.0		4514,4514	6.0	1.0	1	dbSNP_111	104	1970,6630	346.9+/-326.4	213,1544,2543	yes	missense,missense	VPS13D	NM_015378.2,NM_018156.2	121,121	219,1722,4562	TT,TA,AA		22.907,4.3123,16.6077	benign,benign	1505/4389,1505/4364	12339619	2160,10846	2203	4300	6503	SO:0001583	missense	55187	exon20			AGAGAGAATCTGA	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.4514A>T	1.37:g.12339619A>T	ENSP00000350854:p.Glu1505Val	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	244	238	0.97541	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	374|374	0.17124542124542125|0.17124542124542125	13|13	0.026422764227642278|0.026422764227642278	75|75	0.20718232044198895|0.20718232044198895	114|114	0.1993006993006993|0.1993006993006993	172|172	0.22691292875989447|0.22691292875989447	A|A	17.77|17.77	3.471713|3.471713	0.63737|0.63737	0.043123|0.043123	0.22907|0.22907	ENSG00000048707|ENSG00000048707	ENST00000356315;ENST00000358136|ENST00000011700	T;T|.	0.54279|.	0.58;0.59|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.213969|.	0.47852|.	D|.	0.000216|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	P|P	1.0|1.0	P;B|.	0.49559|.	0.925;0.09|.	P;B|.	0.45712|.	0.491;0.046|.	T|T	0.04140|0.04140	-1.0974|-1.0974	9|4	0.38643|.	T|.	0.18|.	.|.	16.542|16.542	0.84395|0.84395	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs4845898;rs17350565;rs4845898|rs4845898;rs17350565;rs4845898	1505;1505|.	Q5THJ4-2;Q5THJ4|.	.;VP13D_HUMAN|.	V|Y	1505|328	ENSP00000348666:E1505V;ENSP00000350854:E1505V|.	ENSP00000348666:E1505V|.	E|N	+|+	2|1	0|0	VPS13D|VPS13D	12262206|12262206	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.771000|4.771000	0.62318|0.62318	2.304000|2.304000	0.77564|0.77564	0.528000|0.528000	0.53228|0.53228	GAA|AAT	A|0.831;T|0.169	0.169	strong		0.378	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
TGOLN2	10618	hgsc.bcm.edu	37	2	85554080	85554080	+	Missense_Mutation	SNP	G	G	A	rs4247303	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:85554080G>A	ENST00000409232.3	-	2	836	c.775C>T	c.(775-777)Cgg>Tgg	p.R259W	TGOLN2_ENST00000398263.2_Intron|TGOLN2_ENST00000377386.3_Missense_Mutation_p.R259W|TGOLN2_ENST00000444342.2_Missense_Mutation_p.R259W|TGOLN2_ENST00000409015.1_Missense_Mutation_p.R259W|TGOLN2_ENST00000282120.2_Intron			O43493	TGON2_HUMAN	trans-golgi network protein 2	259			R -> W (in dbSNP:rs4247303). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8907712, ECO:0000269|Ref.4, ECO:0000269|Ref.7}.			Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											TGGTCTTTCCGGGAAGGCTGC	0.562													G|||	2903	0.579673	0.3419	0.6787	5008	,	,		18921	0.8671		0.4881	False		,,,				2504	0.6288				p.R259W		Atlas-SNP	.											TGOLN2_ENST00000377386,colon,carcinoma,0,1	TGOLN2	32	1	0			c.C775T						PASS	.	G	TRP/ARG,TRP/ARG,,TRP/ARG	1390,2502		244,902,800	82.0	81.0	81.0		775,775,,775	-3.7	0.0	2	dbSNP_111	81	4087,4191		1011,2065,1063	yes	missense,missense,intron,missense	TGOLN2	NM_001206840.1,NM_001206841.1,NM_001206844.1,NM_006464.3	101,101,,101	1255,2967,1863	AA,AG,GG		49.3718,35.7143,45.0041	probably-damaging,probably-damaging,,probably-damaging	259/481,259/454,,259/438	85554080	5477,6693	1946	4139	6085	SO:0001583	missense	10618	exon2			CTTTCCGGGAAGG	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"""trans-Golgi network protein (46, 48, 51kD isoforms)"""	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.775C>T	2.37:g.85554080G>A	ENSP00000386443:p.Arg259Trp	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Missense_Mutation	SNP	ENST00000409232.3	37	CCDS56126.1	1255	0.5746336996336996	174	0.35365853658536583	228	0.6298342541436464	485	0.8479020979020979	368	0.48548812664907653	G	10.02	1.236273	0.22626	0.357143	0.493718	ENSG00000152291	ENST00000377386;ENST00000409232;ENST00000409015;ENST00000444342	T;T;T;T	0.10860	2.83;2.84;2.83;2.83	1.87	-3.74	0.04385	.	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	1.0000000000287557E-6	D;D;D	0.76494	0.999;0.999;0.997	P;P;P	0.58721	0.844;0.844;0.844	T	0.55903	-0.8067	8	0.72032	D	0.01	0.4595	0.9419	0.01357	0.4213:0.1167:0.2684:0.1936	rs4247303;rs17359940;rs59582594;rs4247303	259;259;259	O43493;O43493-5;O43493-2	TGON2_HUMAN;.;.	W	259	ENSP00000366603:R259W;ENSP00000386443:R259W;ENSP00000387035:R259W;ENSP00000391190:R259W	ENSP00000366603:R259W	R	-	1	2	TGOLN2	85407591	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.303000	0.01135	-3.248000	0.00205	-1.488000	0.00978	CGG	G|0.432;A|0.567	0.567	strong		0.562	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464	
HDAC9	9734	hgsc.bcm.edu	37	7	18993870	18993870	+	Silent	SNP	C	C	T	rs2389998	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:18993870C>T	ENST00000432645.2	+	23	3030	c.3030C>T	c.(3028-3030)ttC>ttT	p.F1010F	HDAC9_ENST00000401921.1_Intron|HDAC9_ENST00000406451.4_Intron|HDAC9_ENST00000441542.2_Intron	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	1010					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	CTTTAAAGTTCTCTTAAAAAT	0.294													T|||	3874	0.773562	0.7927	0.8184	5008	,	,		15936	0.7302		0.7714	False		,,,				2504	0.7628				p.F1010F		Atlas-SNP	.											.	HDAC9	560	.	0			c.C3030T						PASS	.	T	,,	2867,685		1159,549,68	17.0	16.0	17.0		3030,,	1.5	0.0	7	dbSNP_100	17	6052,1998		2286,1480,259	no	coding-synonymous,intron,intron	HDAC9	NM_058176.2,NM_178423.1,NM_178425.2	,,	3445,2029,327	TT,TC,CC		24.8199,19.2849,23.1253	,,	1010/1012,,	18993870	8919,2683	1776	4025	5801	SO:0001819	synonymous_variant	9734	exon23			AAAGTTCTCTTAA	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.3030C>T	7.37:g.18993870C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_058176	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			C|0.237;T|0.763	0.763	strong		0.294	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
EPN3	55040	hgsc.bcm.edu	37	17	48616271	48616271	+	Silent	SNP	C	C	T	rs72835715	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48616271C>T	ENST00000268933.3	+	4	1287	c.708C>T	c.(706-708)gaC>gaT	p.D236D	RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000541226.1_Intron|EPN3_ENST00000537145.1_Intron	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	236						clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			CCCACAGGGACGAGGACCTGC	0.677													C|||	64	0.0127796	0.0008	0.0144	5008	,	,		17972	0.0		0.0437	False		,,,				2504	0.0092				p.D236D		Atlas-SNP	.											.	EPN3	32	.	0			c.C708T						PASS	.	C		46,4360	46.0+/-80.4	1,44,2158	33.0	30.0	31.0		708	-5.9	0.8	17	dbSNP_130	31	395,8205	121.0+/-180.1	12,371,3917	no	coding-synonymous	EPN3	NM_017957.2		13,415,6075	TT,TC,CC		4.593,1.044,3.3907		236/633	48616271	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	55040	exon4			CAGGGACGAGGAC	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.708C>T	17.37:g.48616271C>T		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	291	152	0.522337	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Silent	SNP	ENST00000268933.3	37	CCDS11570.1																																																																																			C|0.973;T|0.027	0.027	strong		0.677	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
COPS7A	50813	hgsc.bcm.edu	37	12	6839913	6839913	+	Silent	SNP	C	C	T	rs2286730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6839913C>T	ENST00000543155.1	+	7	1197	c.715C>T	c.(715-717)Ctg>Ttg	p.L239L	COPS7A_ENST00000229251.3_Silent_p.L239L|COPS7A_ENST00000538410.1_Intron|COPS7A_ENST00000542150.1_3'UTR|COPS7A_ENST00000534877.1_Silent_p.L239L|COPS7A_ENST00000534947.1_Silent_p.L239L|COPS7A_ENST00000539735.1_Silent_p.L239L	NM_001164094.1	NP_001157566.1	Q9UBW8	CSN7A_HUMAN	COP9 signalosome subunit 7A	239					cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	10						TGAGCAACACCTGACTGAGCT	0.562													C|||	550	0.109824	0.2632	0.0591	5008	,	,		19356	0.0694		0.0656	False		,,,				2504	0.0256				p.L239L		Atlas-SNP	.											.	COPS7A	26	.	0			c.C715T						PASS	.	C	,,,	1026,3380	373.9+/-321.0	109,808,1286	43.0	45.0	44.0		715,715,715,715	3.7	1.0	12	dbSNP_100	44	783,7817	184.3+/-232.3	37,709,3554	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COPS7A	NM_001164093.1,NM_001164094.1,NM_001164095.1,NM_016319.2	,,,	146,1517,4840	TT,TC,CC		9.1047,23.2864,13.909	,,,	239/276,239/276,239/276,239/276	6839913	1809,11197	2203	4300	6503	SO:0001819	synonymous_variant	50813	exon7			CAACACCTGACTG	AF193844	CCDS8558.1	12p13.31	2013-03-14	2013-03-14		ENSG00000111652	ENSG00000111652			16758	protein-coding gene	gene with protein product			"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7A"", ""COP9 constitutive photomorphogenic homolog subunit 7A (Arabidopsis)"""				Standard	NM_001164093		Approved	CSN7A	uc001qqh.3	Q9UBW8	OTTHUMG00000169182	ENST00000543155.1:c.715C>T	12.37:g.6839913C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_001164094	A8K9A6|Q9NVX3|Q9UJW4	Silent	SNP	ENST00000543155.1	37	CCDS8558.1																																																																																			C|0.879;T|0.121	0.121	strong		0.562	COPS7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402740.1		
TBC1D1	23216	hgsc.bcm.edu	37	4	37904082	37904082	+	Silent	SNP	T	T	C	rs2279026	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:37904082T>C	ENST00000261439.4	+	2	721	c.366T>C	c.(364-366)gcT>gcC	p.A122A	TBC1D1_ENST00000402522.1_Silent_p.A122A|TBC1D1_ENST00000508802.1_Silent_p.A122A	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	122					membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						AGGAAGACGCTGTCCACCGGC	0.443													C|||	2025	0.404353	0.6377	0.3444	5008	,	,		19716	0.373		0.2038	False		,,,				2504	0.3701				p.A122A		Atlas-SNP	.											.	TBC1D1	94	.	0			c.T366C						PASS	.	C		2488,1918	546.7+/-377.1	693,1102,408	86.0	85.0	85.0		366	-5.8	0.0	4	dbSNP_100	85	1858,6742	730.2+/-406.8	221,1416,2663	no	coding-synonymous	TBC1D1	NM_015173.2		914,2518,3071	CC,CT,TT		21.6047,43.5315,33.4153		122/1169	37904082	4346,8660	2203	4300	6503	SO:0001819	synonymous_variant	23216	exon2			AGACGCTGTCCAC	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.366T>C	4.37:g.37904082T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Silent	SNP	ENST00000261439.4	37	CCDS33972.1																																																																																			T|0.642;C|0.358	0.358	strong		0.443	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052736	33052736	+	Missense_Mutation	SNP	G	G	A	rs1126537	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33052736G>A	ENST00000418931.2	+	3	490	c.374G>A	c.(373-375)aGg>aAg	p.R125K		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	125	Beta-2.|Ig-like C1-type.		R -> K (in allele DPB1*01:01, allele DPB1*03:01, allele DPB1*05:01, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*09:01, allele DPB1*09:02, allele DPB1*13:01, allele DPB1*14:01, allele DPB1*15:01, allele DPB1*18:01, allele DPB1*19:01, allele DPB1*20:01, allele DPB1*26:01, allele DPB1*45:01 and allele DPB1*85:01; dbSNP:rs1126537). {ECO:0000269|PubMed:6330724}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GTCCAGCCTAGGGTGAATGTT	0.498																																					p.R125K		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.G374A						PASS	.						51.0	74.0	66.0					6																	33052736		1508	2708	4216	SO:0001583	missense	3115	exon3			AGCCTAGGGTGAA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.374G>A	6.37:g.33052736G>A	ENSP00000408146:p.Arg125Lys	Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	280	78	0.278571	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	0.043|0.043	-1.274971|-1.274971	0.01410|0.01410	.|.	.|.	ENSG00000223865|ENSG00000223865	ENST00000416804|ENST00000418931;ENST00000428835	.|T;T	.|0.00590	.|6.36;6.36	3.85|3.85	-4.33|-4.33	0.03677|0.03677	.|Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.882556	.|0.09685	.|N	.|0.769161	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.01686|0.01686	-0.76|-0.76	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.32561|0.32561	-0.9902|-0.9902	4|9	.|0.02654	.|T	.|1	.|.	2.476|2.476	0.04575|0.04575	0.5431:0.1169:0.2255:0.1145|0.5431:0.1169:0.2255:0.1145	rs1126537;rs3176950;rs3181631;rs17434218|rs1126537;rs3176950;rs3181631;rs17434218	.|91;135;125	.|A2ALJ6;Q59GY1;P04440	.|.;.;DPB1_HUMAN	R|K	92|125;102	.|ENSP00000408146:R125K;ENSP00000412654:R102K	.|ENSP00000408146:R125K	G|R	+|+	1|2	0|0	HLA-DPB1|HLA-DPB1	33160714|33160714	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.016000|-0.016000	0.12613|0.12613	-1.442000|-1.442000	0.01955|0.01955	-2.167000|-2.167000	0.00324|0.00324	GGG|AGG	G|0.710;A|0.290	0.290	strong		0.498	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
MS4A5	64232	hgsc.bcm.edu	37	11	60197299	60197299	+	Splice_Site	SNP	G	G	A	rs34169848	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:60197299G>A	ENST00000300190.2	+	1	238	c.152G>A	c.(151-153)gGg>gAg	p.G51E	MS4A5_ENST00000534071.1_3'UTR	NM_023945.2	NP_076434.2	Q9H3V2	MS4A5_HUMAN	membrane-spanning 4-domains, subfamily A, member 5	51						integral component of membrane (GO:0016021)				large_intestine(7)|lung(7)|ovary(1)|skin(1)	16						AAAATCTTAGGGGTAAGTAAG	0.403													G|||	80	0.0159744	0.0008	0.0259	5008	,	,		19383	0.0		0.0507	False		,,,				2504	0.0102				p.G51E		Atlas-SNP	.											.	MS4A5	35	.	0			c.G152A						PASS	.	G	GLU/GLY	58,4348	53.6+/-89.4	0,58,2145	48.0	53.0	51.0		152	4.7	1.0	11	dbSNP_126	51	508,8092	142.2+/-198.4	10,488,3802	yes	missense-near-splice	MS4A5	NM_023945.2	98	10,546,5947	AA,AG,GG		5.907,1.3164,4.3518	probably-damaging	51/201	60197299	566,12440	2203	4300	6503	SO:0001630	splice_region_variant	64232	exon1			TCTTAGGGGTAAG	AB013103	CCDS7987.1	11q12	2008-03-25			ENSG00000166930	ENSG00000166930			13374	protein-coding gene	gene with protein product		606499				11245982, 11401424	Standard	NM_023945		Approved	CD20L2	uc001npo.3	Q9H3V2	OTTHUMG00000167613	ENST00000300190.2:c.153+1G>A	11.37:g.60197299G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_023945	Q9BZH1	Missense_Mutation	SNP	ENST00000300190.2	37	CCDS7987.1	41	0.018772893772893772	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	14.87	2.665848	0.47677	0.013164	0.05907	ENSG00000166930	ENST00000300190	T	0.10192	2.9	4.66	4.66	0.58398	.	0.118079	0.64402	D	0.000018	T	0.05456	0.0144	M	0.88105	2.93	0.39099	D	0.961245	D	0.89917	1.0	D	0.97110	1.0	T	0.03969	-1.0988	10	0.87932	D	0	-5.9109	13.2445	0.60016	0.0:0.0:1.0:0.0	rs34169848;rs34169848	51	Q9H3V2	MS4A5_HUMAN	E	51	ENSP00000300190:G51E	ENSP00000300190:G51E	G	+	2	0	MS4A5	59953875	1.000000	0.71417	1.000000	0.80357	0.152000	0.21847	3.950000	0.56676	2.578000	0.87016	0.467000	0.42956	GGG	G|0.965;A|0.035	0.035	strong		0.403	MS4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395392.1		Missense_Mutation
SYCE1	93426	hgsc.bcm.edu	37	10	135368590	135368590	+	Missense_Mutation	SNP	T	T	C	rs3737031	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135368590T>C	ENST00000343131.5	-	13	1066	c.962A>G	c.(961-963)cAc>cGc	p.H321R	SYCE1_ENST00000432597.2_Intron|SPRN_ENST00000541506.1_Intron|SYCE1_ENST00000368517.3_Intron	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	321				H -> R (in Ref. 5; AAH34821). {ECO:0000305}.	synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.H321R(1)		breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		CCCTGCTTGGTGTGCAGCTCC	0.552													t|||	775	0.154752	0.0454	0.1715	5008	,	,		20610	0.2698		0.1093	False		,,,				2504	0.2188				p.H321R		Atlas-SNP	.											SYCE1_ENST00000343131,NS,carcinoma,0,1	SYCE1	81	1	1	Substitution - Missense(1)	stomach(1)	c.A962G						PASS	.	A	,ARG/HIS,	76,1308		3,70,619	167.0	139.0	147.0		,962,	-0.0	0.0	10	dbSNP_107	147	282,2900		10,262,1319	yes	intron,missense,intron	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	,29,	13,332,1938	CC,CT,TT		8.8624,5.4913,7.8406	,benign,	,321/352,	135368590	358,4208	692	1591	2283	SO:0001583	missense	93426	exon13			GCTTGGTGTGCAG	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.962A>G	10.37:g.135368590T>C	ENSP00000341282:p.His321Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	273	68	0.249084	NM_001143764	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	37	CCDS44501.1	329	0.15064102564102563	24	0.04878048780487805	62	0.1712707182320442	153	0.2674825174825175	90	0.11873350923482849	t	5.594	0.294345	0.10567	0.054913	0.088624	ENSG00000171772	ENST00000343131	T	0.08634	3.07	3.84	-0.0272	0.13927	.	2.080430	0.01972	N	0.044198	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.11235	0.004	B	0.10450	0.005	T	0.46373	-0.9196	9	0.46703	T	0.11	4.5253	1.2555	0.01990	0.1808:0.104:0.1877:0.5274	rs3737031;rs17846112;rs17859115;rs52813729;rs3737031	321	Q8N0S2	SYCE1_HUMAN	R	321	ENSP00000341282:H321R	ENSP00000341282:H321R	H	-	2	0	SYCE1	135218580	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.269000	0.18589	-0.003000	0.14444	-0.364000	0.07487	CAC	T|0.856;C|0.144	0.144	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
KIAA1683	80726	hgsc.bcm.edu	37	19	18376517	18376517	+	Silent	SNP	C	C	T	rs61740752	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18376517C>T	ENST00000600328.3	-	3	2026	c.1833G>A	c.(1831-1833)caG>caA	p.Q611Q	KIAA1683_ENST00000392413.4_Silent_p.Q611Q|KIAA1683_ENST00000600359.3_Silent_p.Q565Q			Q9H0B3	K1683_HUMAN	KIAA1683	611						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TCGCCTGTTTCTGGGTGCCAG	0.557													C|||	761	0.151957	0.0257	0.1196	5008	,	,		20306	0.3036		0.1292	False		,,,				2504	0.2127				p.Q611Q		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G1833A						PASS	.	C	,,	177,4229	115.4+/-153.4	1,175,2027	53.0	59.0	57.0		1833,1695,1833	0.8	0.0	19	dbSNP_129	57	1171,7429	236.1+/-268.4	79,1013,3208	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	80,1188,5235	TT,TC,CC		13.6163,4.0172,10.3644	,,	611/1368,565/1135,611/1181	18376517	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	80726	exon3			CTGTTTCTGGGTG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1833G>A	19.37:g.18376517C>T		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	200	101	0.505	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			C|0.886;T|0.114	0.114	strong		0.557	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
SKIV2L	6499	hgsc.bcm.edu	37	6	31930351	31930351	+	Silent	SNP	A	A	G	rs2734331	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31930351A>G	ENST00000375394.2	+	11	1313	c.1200A>G	c.(1198-1200)acA>acG	p.T400T	SKIV2L_ENST00000544581.1_Silent_p.T207T	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	400	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						TCATGACCACAGAGATCCTTC	0.577													A|||	259	0.0517173	0.0068	0.0562	5008	,	,		19732	0.127		0.0318	False		,,,				2504	0.0521				p.T400T		Atlas-SNP	.											.	SKIV2L	97	.	0			c.A1200G						PASS	.	A		87,4319	73.1+/-111.1	2,83,2118	57.0	53.0	54.0		1200	-3.3	0.9	6	dbSNP_100	54	340,8260	117.6+/-177.1	7,326,3967	yes	coding-synonymous	SKIV2L	NM_006929.4		9,409,6085	GG,GA,AA		3.9535,1.9746,3.2831		400/1247	31930351	427,12579	2203	4300	6503	SO:0001819	synonymous_variant	6499	exon11			GACCACAGAGATC		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"""superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"""	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.1200A>G	6.37:g.31930351A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	123	53	0.430894	NM_006929	O15005|Q12902|Q15476|Q5ST66	Silent	SNP	ENST00000375394.2	37	CCDS4731.1																																																																																			T|0.005;G|0.039	0.039	strong		0.577	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3		
LMOD2	442721	hgsc.bcm.edu	37	7	123301940	123301940	+	Silent	SNP	A	A	G	rs7809453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:123301940A>G	ENST00000458573.2	+	2	457	c.300A>G	c.(298-300)gaA>gaG	p.E100E	LMOD2_ENST00000456238.2_Intron	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	100	Glu-rich.					cytoskeleton (GO:0005856)											AGGAAAGTGAAGAAGAGCTTA	0.373													G|||	2531	0.505391	0.3979	0.4337	5008	,	,		18096	0.5575		0.4414	False		,,,				2504	0.7137				p.E100E		Atlas-SNP	.											.	LMOD2	62	.	0			c.A300G						PASS	.	G		1354,2234		283,788,723	45.0	43.0	44.0		300	2.2	1.0	7	dbSNP_116	44	3444,4302		838,1768,1267	yes	coding-synonymous	LMOD2	NM_207163.1		1121,2556,1990	GG,GA,AA		44.4617,37.7369,42.3328		100/548	123301940	4798,6536	1794	3873	5667	SO:0001819	synonymous_variant	442721	exon2			AAGTGAAGAAGAG	AC006333	CCDS47693.1	7q31.32	2008-08-08			ENSG00000170807	ENSG00000170807			6648	protein-coding gene	gene with protein product		608006					Standard	NM_207163		Approved		uc003vky.2	Q6P5Q4	OTTHUMG00000157149	ENST00000458573.2:c.300A>G	7.37:g.123301940A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_207163	A4D0W9|A4D0Y2|Q8WVJ8	Silent	SNP	ENST00000458573.2	37	CCDS47693.1	1025	0.4693223443223443	182	0.3699186991869919	178	0.49171270718232046	334	0.583916083916084	331	0.4366754617414248	G	9.145	1.014926	0.19355	0.377369	0.444617	ENSG00000170807	ENST00000332074	.	.	.	4.99	2.15	0.27550	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999999871515	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.7792	0.13194	0.4603:0.0:0.3965:0.1432	rs7809453;rs17621877;rs7809453	.	.	.	.	-1	.	.	.	+	.	.	LMOD2	123089176	0.987000	0.35691	0.996000	0.52242	0.992000	0.81027	0.254000	0.18314	-0.073000	0.12842	-0.186000	0.12905	.	A|0.535;G|0.465	0.465	strong		0.373	LMOD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348525.1		
IGFALS	3483	hgsc.bcm.edu	37	16	1841033	1841033	+	Silent	SNP	G	G	A	rs17559	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1841033G>A	ENST00000215539.3	-	2	1496	c.1386C>T	c.(1384-1386)taC>taT	p.Y462Y	IGFALS_ENST00000415638.3_Silent_p.Y500Y			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit	462					cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						AGAGCAGCAGGTACTCCAGCT	0.716													G|||	1283	0.25619	0.4818	0.0922	5008	,	,		15016	0.1548		0.0934	False		,,,				2504	0.3395				p.Y500Y		Atlas-SNP	.											IGFALS,NS,carcinoma,0,1	IGFALS	29	1	0			c.C1500T						scavenged	.	G	,	1637,2645		297,1043,801	16.0	18.0	17.0		1500,1386	2.7	1.0	16	dbSNP_63	17	755,7657		34,687,3485	no	coding-synonymous,coding-synonymous	IGFALS	NM_001146006.1,NM_004970.2	,	331,1730,4286	AA,AG,GG		8.9753,38.2298,18.8435	,	500/644,462/606	1841033	2392,10302	2141	4206	6347	SO:0001819	synonymous_variant	3483	exon2			CAGCAGGTACTCC	M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638	ENST00000215539.3:c.1386C>T	16.37:g.1841033G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_001146006	B4DZY8|E9PGU3	Silent	SNP	ENST00000215539.3	37	CCDS10446.1																																																																																			G|0.790;A|0.210	0.210	strong		0.716	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
COL5A2	1290	hgsc.bcm.edu	37	2	189932764	189932764	+	Missense_Mutation	SNP	G	G	A	rs35830636	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:189932764G>A	ENST00000374866.3	-	21	1652	c.1378C>T	c.(1378-1380)Cct>Tct	p.P460S		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	460			P -> S (in dbSNP:rs35830636).		axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			ATTCCCTGAGGACCAGTGCTA	0.502													G|||	58	0.0115815	0.0015	0.0245	5008	,	,		17254	0.001		0.0308	False		,,,				2504	0.0072				p.P460S		Atlas-SNP	.											.	COL5A2	230	.	0			c.C1378T						PASS	.	G	SER/PRO	50,4356	50.9+/-86.3	0,50,2153	77.0	76.0	76.0		1378	5.7	1.0	2	dbSNP_126	76	467,8133	139.0+/-195.8	15,437,3848	yes	missense	COL5A2	NM_000393.3	74	15,487,6001	AA,AG,GG		5.4302,1.1348,3.9751	probably-damaging	460/1500	189932764	517,12489	2203	4300	6503	SO:0001583	missense	1290	exon21			CCTGAGGACCAGT	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.1378C>T	2.37:g.189932764G>A	ENSP00000364000:p.Pro460Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	152	59	0.388158	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	34	0.015567765567765568	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	19	0.025065963060686015	G	16.31	3.086016	0.55861	0.011348	0.054302	ENSG00000204262	ENST00000374866	D	0.97665	-4.48	5.74	5.74	0.90152	.	0.252743	0.27640	N	0.018475	T	0.80042	0.4551	L	0.43701	1.375	0.41778	D	0.989808	B	0.16802	0.019	B	0.14023	0.01	D	0.84390	0.0554	9	.	.	.	.	15.4173	0.74980	0.0:0.1384:0.8616:0.0	rs35830636	460	P05997	CO5A2_HUMAN	S	460	ENSP00000364000:P460S	.	P	-	1	0	COL5A2	189641009	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.297000	0.72757	2.716000	0.92895	0.591000	0.81541	CCT	G|0.965;A|0.035	0.035	strong		0.502	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	
BBS12	166379	hgsc.bcm.edu	37	4	123664427	123664427	+	Silent	SNP	G	G	C	rs13135766	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:123664427G>C	ENST00000314218.3	+	2	1573	c.1380G>C	c.(1378-1380)gtG>gtC	p.V460V	BBS12_ENST00000542236.1_Silent_p.V460V	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	460					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TTACACAAGTGAATGAAGATT	0.478									Bardet-Biedl syndrome				G|||	474	0.0946486	0.0484	0.1081	5008	,	,		19718	0.0		0.2177	False		,,,				2504	0.1186				p.V460V		Atlas-SNP	.											.	BBS12	63	.	0			c.G1380C						PASS	.	G	,	294,4112	161.4+/-193.6	15,264,1924	79.0	79.0	79.0		1380,1380	3.0	0.2	4	dbSNP_121	79	1981,6619	347.3+/-326.5	241,1499,2560	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	256,1763,4484	CC,CG,GG		23.0349,6.6727,17.4919	,	460/711,460/711	123664427	2275,10731	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	ACAAGTGAATGAA	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1380G>C	4.37:g.123664427G>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	167	66	0.39521	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			G|0.853;C|0.147	0.147	strong		0.478	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
OR4A5	81318	hgsc.bcm.edu	37	11	51412066	51412066	+	Silent	SNP	G	G	C	rs5002409	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:51412066G>C	ENST00000319760.6	-	1	382	c.330C>G	c.(328-330)gtC>gtG	p.V110V		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				CCAGAAGGAAGACCTCAGCCC	0.453													.|||	5	0.000998403	0.0	0.0029	5008	,	,		21048	0.0		0.003	False		,,,				2504	0.0				p.V110V		Atlas-SNP	.											.	OR4A5	116	.	0			c.C330G						PASS	.	A		2,4400		0,2,2199	72.0	71.0	71.0		330	-2.0	0.8	11	dbSNP_113	71	22,8570		0,22,4274	no	coding-synonymous	OR4A5	NM_001005272.3		0,24,6473	CC,CG,GG		0.2561,0.0454,0.1847		110/316	51412066	24,12970	2201	4296	6497	SO:0001819	synonymous_variant	81318	exon1			AAGGAAGACCTCA	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.330C>G	11.37:g.51412066G>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	37	CCDS31497.1																																																																																			C|0.001;G|0.999	0.001	strong		0.453	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
RALGAPA2	57186	hgsc.bcm.edu	37	20	20493550	20493550	+	Missense_Mutation	SNP	T	T	C	rs45484900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:20493550T>C	ENST00000202677.7	-	32	4470	c.4463A>G	c.(4462-4464)aAt>aGt	p.N1488S		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1488				N -> S (in Ref. 1; ABC33805 and 3; BAA86586). {ECO:0000305}.	activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						ATTTCTTCCATTGGGTGCTAA	0.448													T|||	132	0.0263578	0.0008	0.0476	5008	,	,		20719	0.0		0.0567	False		,,,				2504	0.0419				p.N1488S		Atlas-SNP	.											.	RALGAPA2	274	.	0			c.A4463G						PASS	.	T	SER/ASN	58,3758		2,54,1852	68.0	66.0	67.0		4463	-9.3	0.0	20	dbSNP_127	67	524,7724		15,494,3615	yes	missense	RALGAPA2	NM_020343.3	46	17,548,5467	CC,CT,TT		6.3531,1.5199,4.8243	benign	1488/1874	20493550	582,11482	1908	4124	6032	SO:0001583	missense	57186	exon32			CTTCCATTGGGTG	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 74"""	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.4463A>G	20.37:g.20493550T>C	ENSP00000202677:p.Asn1488Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Missense_Mutation	SNP	ENST00000202677.7	37	CCDS46584.1	64|64	0.029304029304029304|0.029304029304029304	0|0	0.0|0.0	21|21	0.058011049723756904|0.058011049723756904	0|0	0.0|0.0	43|43	0.05672823218997362|0.05672823218997362	T|T	0.019|0.019	-1.450862|-1.450862	0.01080|0.01080	0.015199|0.015199	0.063531|0.063531	ENSG00000188559|ENSG00000188559	ENST00000430436|ENST00000202677	.|D	.|0.94576	.|-3.46	6.11|6.11	-9.32|-9.32	0.00643|0.00643	.|.	.|1.760750	.|0.02365	.|N	.|0.077303	T|T	0.45955|0.45955	0.1368|0.1368	N|N	0.03948|0.03948	-0.315|-0.315	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.001;0.001;0.0	T|T	0.68292|0.68292	-0.5447|-0.5447	5|9	.|.	.|.	.|.	.|.	16.8866|16.8866	0.86077|0.86077	0.0:0.3098:0.0:0.6902|0.0:0.3098:0.0:0.6902	rs45484900;rs61747151|rs45484900;rs61747151	.|1326;1488;1488	.|A8MSM5;Q2PPJ7-2;Q2PPJ7	.|.;.;RGPA2_HUMAN	V|S	1305|1488	.|ENSP00000202677:N1488S	.|.	M|N	-|-	1|2	0|0	RALGAPA2|RALGAPA2	20441550|20441550	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.397000|0.397000	0.30659|0.30659	-0.058000|-0.058000	0.11750|0.11750	-1.242000|-1.242000	0.02523|0.02523	-1.064000|-1.064000	0.02280|0.02280	ATG|AAT	T|0.964;C|0.036	0.036	strong		0.448	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343	
NLRP3	114548	hgsc.bcm.edu	37	1	247588140	247588140	+	Silent	SNP	C	C	T	rs111400208	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:247588140C>T	ENST00000336119.3	+	3	2141	c.1395C>T	c.(1393-1395)caC>caT	p.H465H	NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000366497.2_Silent_p.H465H|NLRP3_ENST00000391827.2_Silent_p.H465H|NLRP3_ENST00000348069.2_Silent_p.H465H|NLRP3_ENST00000366496.2_Silent_p.H465H|NLRP3_ENST00000391828.3_Silent_p.H465H	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	465	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			TCTGCGCCCACCTCTGGGGGC	0.592													C|||	7	0.00139776	0.0	0.0014	5008	,	,		19340	0.0		0.006	False		,,,				2504	0.0				p.H465H		Atlas-SNP	.											.	NLRP3	286	.	0			c.C1395T						PASS	.	C	,,,,	4,4402	8.1+/-20.4	0,4,2199	28.0	28.0	28.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1395,1395,1395,1395,1395	3.2	0.0	1	dbSNP_132	28	47,8553	29.6+/-80.5	0,47,4253	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP3	NM_001079821.2,NM_001127461.2,NM_001127462.2,NM_004895.4,NM_183395.2	,,,,	0,51,6452	TT,TC,CC		0.5465,0.0908,0.3921	,,,,	465/1037,465/980,465/980,465/1037,465/923	247588140	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	114548	exon3			CGCCCACCTCTGG	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1395C>T	1.37:g.247588140C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Silent	SNP	ENST00000336119.3	37	CCDS1632.1																																																																																			C|0.997;T|0.003	0.003	strong		0.592	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
TREML4	285852	hgsc.bcm.edu	37	6	41196733	41196733	+	Silent	SNP	C	C	T	rs147088240	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41196733C>T	ENST00000341495.2	+	2	449	c.345C>T	c.(343-345)tcC>tcT	p.S115S	TREML4_ENST00000448827.2_Silent_p.S115S	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	115	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					ACAACGCTTCCGAAAACATCA	0.488													C|||	12	0.00239617	0.0	0.0086	5008	,	,		19933	0.0		0.006	False		,,,				2504	0.0				p.S115S		Atlas-SNP	.											.	TREML4	25	.	0			c.C345T						PASS	.	C		6,4400		0,6,2197	83.0	80.0	81.0		345	-1.0	0.0	6	dbSNP_134	81	41,8559		0,41,4259	no	coding-synonymous	TREML4	NM_198153.2		0,47,6456	TT,TC,CC		0.4767,0.1362,0.3614		115/201	41196733	47,12959	2203	4300	6503	SO:0001819	synonymous_variant	285852	exon2			CGCTTCCGAAAAC	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"""Immunoglobulin superfamily / V-set domain containing"""	30807	protein-coding gene	gene with protein product	"""TREM like transcript 4"""	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.345C>T	6.37:g.41196733C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	168	88	0.52381	NM_198153	B7ZL92	Silent	SNP	ENST00000341495.2	37	CCDS34446.1																																																																																			C|0.996;T|0.004	0.004	strong		0.488	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2		
LAMB4	22798	hgsc.bcm.edu	37	7	107696130	107696130	+	Silent	SNP	A	A	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:107696130A>T	ENST00000388781.3	-	25	3785	c.3702T>A	c.(3700-3702)ccT>ccA	p.P1234P	LAMB4_ENST00000205386.4_Silent_p.P1234P|LAMB4_ENST00000388780.3_Silent_p.P1234P	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1234	Domain II.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						ATGGGAAAACAGGATGTTTCA	0.403																																					p.P1234P		Atlas-SNP	.											LAMB4,mucosal,malignant_melanoma,-2,1	LAMB4	253	1	0			c.T3702A						scavenged	.						94.0	101.0	99.0					7																	107696130		2203	4300	6503	SO:0001819	synonymous_variant	22798	exon25			GAAAACAGGATGT	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.3702T>A	7.37:g.107696130A>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	2	0.0243902	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			.	.	none		0.403	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
TATDN2	9797	hgsc.bcm.edu	37	3	10312633	10312633	+	Silent	SNP	G	G	A	rs115984909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:10312633G>A	ENST00000287652.4	+	4	2818	c.1767G>A	c.(1765-1767)gtG>gtA	p.V589V	TATDN2_ENST00000448281.2_Silent_p.V589V|RP11-438J1.1_ENST00000450534.1_3'UTR	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	589					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						CTAAGGCTGTGGCATTTGGAG	0.473													G|||	5	0.000998403	0.0	0.0	5008	,	,		20193	0.0		0.004	False		,,,				2504	0.001				p.V589V		Atlas-SNP	.											.	TATDN2	59	.	0			c.G1767A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	107.0	114.0	112.0		1767	0.4	1.0	3	dbSNP_132	112	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous	TATDN2	NM_014760.3		0,20,6483	AA,AG,GG		0.2209,0.0227,0.1538		589/762	10312633	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	9797	exon4			GGCTGTGGCATTT	D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.1767G>A	3.37:g.10312633G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	30	18	0.6	NM_014760	Q3MIL9|Q5BKU0	Silent	SNP	ENST00000287652.4	37	CCDS33698.1																																																																																			G|0.998;A|0.002	0.002	strong		0.473	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
EFCAB7	84455	hgsc.bcm.edu	37	1	63997633	63997633	+	Silent	SNP	A	A	T	rs9804078	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:63997633A>T	ENST00000371088.4	+	3	576	c.330A>T	c.(328-330)tcA>tcT	p.S110S	RN7SL488P_ENST00000585186.1_RNA	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	110	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						TACTAAAATCATTTAAGCAAT	0.294													A|||	983	0.196286	0.2738	0.1715	5008	,	,		17546	0.1855		0.1441	False		,,,				2504	0.1738				p.S110S		Atlas-SNP	.											EFCAB7,colon,carcinoma,+1,1	EFCAB7	45	1	0			c.A330T						PASS	.	A		997,3409	346.2+/-308.9	114,769,1320	47.0	50.0	49.0		330	4.1	1.0	1	dbSNP_119	49	1324,7266	252.8+/-278.7	92,1140,3063	no	coding-synonymous	EFCAB7	NM_032437.2		206,1909,4383	TT,TA,AA		15.4133,22.6282,17.8593		110/630	63997633	2321,10675	2203	4295	6498	SO:0001819	synonymous_variant	84455	exon3			AAAATCATTTAAG	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.330A>T	1.37:g.63997633A>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	172	82	0.476744	NM_032437	Q658P0|Q96B95|Q96JM6	Silent	SNP	ENST00000371088.4	37	CCDS30737.1																																																																																			A|0.815;T|0.185	0.185	strong		0.294	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
IL4R	3566	hgsc.bcm.edu	37	16	27373872	27373872	+	Missense_Mutation	SNP	A	A	C	rs1805011	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:27373872A>C	ENST00000395762.2	+	11	1458	c.1199A>C	c.(1198-1200)gAg>gCg	p.E400A	IL4R_ENST00000380922.3_Missense_Mutation_p.E385A|IL4R_ENST00000543915.2_Missense_Mutation_p.E400A|IL4R_ENST00000170630.2_Missense_Mutation_p.E400A	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	400			E -> A (associated with cedar pollen sensitization; dbSNP:rs1805011). {ECO:0000269|PubMed:11285129, ECO:0000269|PubMed:14657871, ECO:0000269|PubMed:9070874, ECO:0000269|Ref.5}.		defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)	p.E400A(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						GAGGGAAGGGAGGGCATTGTG	0.597													A|||	1184	0.236422	0.6218	0.1599	5008	,	,		20414	0.0833		0.1064	False		,,,				2504	0.0613				p.E400A		Atlas-SNP	.											IL4R,NS,carcinoma,0,1	IL4R	70	1	1	Substitution - Missense(1)	stomach(1)	c.A1199C	GRCh37	CM993665	IL4R	M	rs1805011	PASS	.	A	ALA/GLU	2307,2087	602.3+/-389.9	600,1107,490	69.0	71.0	70.0		1199	0.2	0.1	16	dbSNP_89	70	961,7639	208.6+/-250.0	61,839,3400	yes	missense	IL4R	NM_000418.2	107	661,1946,3890	CC,CA,AA		11.1744,47.4966,25.1501	possibly-damaging	400/826	27373872	3268,9726	2197	4300	6497	SO:0001583	missense	3566	exon11			GAAGGGAGGGCAT	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1199A>C	16.37:g.27373872A>C	ENSP00000379111:p.Glu400Ala	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	98	56	0.571429	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	488	0.22344322344322345	298	0.6056910569105691	63	0.17403314917127072	42	0.07342657342657342	85	0.11213720316622691	A	4.095	0.015726	0.07959	0.525034	0.111744	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	5.42	0.212	0.15240	.	24.689100	0.00589	N	0.000344	T	0.00012	0.0000	L	0.43923	1.385	0.80722	P	0.0	B;B;B	0.33857	0.429;0.429;0.429	B;B;B	0.24006	0.05;0.05;0.05	T	0.46512	-0.9186	9	0.22706	T	0.39	-15.7238	7.3209	0.26528	0.3929:0.4658:0.0:0.1414	rs1805011;rs17548775;rs58115555;rs1805011	385;400;400	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	A	400;400;385;400	ENSP00000379111:E400A;ENSP00000441667:E400A;ENSP00000370309:E385A;ENSP00000170630:E400A	ENSP00000170630:E400A	E	+	2	0	IL4R	27281373	0.993000	0.37304	0.092000	0.20876	0.093000	0.18481	0.330000	0.19715	-0.253000	0.09514	-0.336000	0.08194	GAG	A|0.756;C|0.244	0.244	strong		0.597	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
THEMIS2	9473	hgsc.bcm.edu	37	1	28203156	28203156	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:28203156A>G	ENST00000373921.3	+	2	156	c.152A>G	c.(151-153)aAg>aGg	p.K51R	THEMIS2_ENST00000373925.1_Missense_Mutation_p.K51R|THEMIS2_ENST00000373927.3_Missense_Mutation_p.K51R|THEMIS2_ENST00000328928.7_Missense_Mutation_p.K51R	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	51	CABIT 1.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GACCTGATCAAGGTCACCCAG	0.592																																					p.K51R		Atlas-SNP	.											.	.	.	.	0			c.A152G						PASS	.						88.0	86.0	87.0					1																	28203156		2203	4300	6503	SO:0001583	missense	9473	exon2			TGATCAAGGTCAC	AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"""induced by contact to basement membrane 1"""		"""chromosome 1 open reading frame 38"""	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.152A>G	1.37:g.28203156A>G	ENSP00000363031:p.Lys51Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	39	0.619048	NM_001039477	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Missense_Mutation	SNP	ENST00000373921.3	37	CCDS41290.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.829475	0.71258	.	.	ENSG00000130775	ENST00000373925;ENST00000328928;ENST00000373927;ENST00000442118;ENST00000373921	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.45054	0.1323	M	0.81802	2.56	0.46564	D	0.999102	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;1.0;0.991;0.989	T	0.47623	-0.9103	10	0.72032	D	0.01	-42.0968	14.6767	0.68986	1.0:0.0:0.0:0.0	.	51;51;51;51;51	Q5TEJ8-5;Q5TEJ8-6;Q5TEJ8;Q5TEJ8-4;Q5TEJ8-2	.;.;THMS2_HUMAN;.;.	R	51	ENSP00000363035:K51R;ENSP00000329862:K51R;ENSP00000363037:K51R;ENSP00000413725:K51R;ENSP00000363031:K51R	ENSP00000329862:K51R	K	+	2	0	C1orf38	28075743	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.414000	0.73318	2.146000	0.66826	0.528000	0.53228	AAG	.	.	none		0.592	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848	
CD207	50489	hgsc.bcm.edu	37	2	71061108	71061108	+	Silent	SNP	G	G	A	rs17662453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:71061108G>A	ENST00000410009.3	-	3	279	c.234C>T	c.(232-234)gtC>gtT	p.V78V		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	78					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						TCAGCAACTGGACATTGGTCT	0.517													G|||	712	0.142173	0.1059	0.219	5008	,	,		19065	0.0972		0.1839	False		,,,				2504	0.1401				p.V78V		Atlas-SNP	.											.	CD207	47	.	0			c.C234T						PASS	.	T		473,3465		30,413,1526	46.0	41.0	42.0		234	-2.0	0.0	2	dbSNP_123	42	1789,6511		190,1409,2551	no	coding-synonymous	CD207	NM_015717.3		220,1822,4077	AA,AG,GG		21.5542,12.0112,18.4834		78/329	71061108	2262,9976	1969	4150	6119	SO:0001819	synonymous_variant	50489	exon3			CAACTGGACATTG	AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"""C-type lectin domain containing"", ""CD molecules"""	17935	protein-coding gene	gene with protein product		604862	"""CD207 antigen, langerin"""			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.234C>T	2.37:g.71061108G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	179	113	0.631285	NM_015717		Silent	SNP	ENST00000410009.3	37																																																																																				G|0.858;A|0.142	0.142	strong		0.517	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
ARRDC5	645432	hgsc.bcm.edu	37	19	4902754	4902754	+	Silent	SNP	G	G	A	rs2779168	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:4902754G>A	ENST00000381781.2	-	1	125	c.126C>T	c.(124-126)atC>atT	p.I42I	UHRF1_ENST00000592666.1_RNA	NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	42										endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		TCAGGGTTAAGATCACCTGCC	0.557													G|||	648	0.129393	0.059	0.17	5008	,	,		18274	0.0		0.3181	False		,,,				2504	0.135				p.I42I		Atlas-SNP	.											.	ARRDC5	19	.	0			c.C126T						PASS	.	G		388,3418		24,340,1539	134.0	123.0	127.0		126	-5.8	0.1	19	dbSNP_100	127	2801,5437		475,1851,1793	no	coding-synonymous	ARRDC5	NM_001080523.1		499,2191,3332	AA,AG,GG		34.001,10.1944,26.4779		42/343	4902754	3189,8855	1903	4119	6022	SO:0001819	synonymous_variant	645432	exon1			GGTTAAGATCACC		CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.126C>T	19.37:g.4902754G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	242	106	0.438017	NM_001080523		Silent	SNP	ENST00000381781.2	37	CCDS45929.1																																																																																			G|0.806;A|0.194	0.194	strong		0.557	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1	XM_292803	
LIMCH1	22998	hgsc.bcm.edu	37	4	41687843	41687843	+	Missense_Mutation	SNP	C	C	T	rs76461603	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:41687843C>T	ENST00000313860.7	+	23	2986	c.2932C>T	c.(2932-2934)Cgg>Tgg	p.R978W	LIMCH1_ENST00000513024.1_Missense_Mutation_p.R831W|LIMCH1_ENST00000509277.1_Missense_Mutation_p.R811W|LIMCH1_ENST00000512820.1_Missense_Mutation_p.R990W|LIMCH1_ENST00000514096.1_Missense_Mutation_p.R818W|LIMCH1_ENST00000508501.1_Missense_Mutation_p.R977W|LIMCH1_ENST00000511496.1_Missense_Mutation_p.R818W|LIMCH1_ENST00000503057.1_Missense_Mutation_p.R1362W|LIMCH1_ENST00000512946.1_Missense_Mutation_p.R978W|LIMCH1_ENST00000381753.4_Missense_Mutation_p.R811W|LIMCH1_ENST00000512632.1_Missense_Mutation_p.R901W|LIMCH1_ENST00000396595.3_Missense_Mutation_p.R823W	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	978					actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						CAGTGAAAGGCGGAAGTGAGT	0.433													C|||	11	0.00219649	0.0	0.0043	5008	,	,		20909	0.0069		0.001	False		,,,				2504	0.0				p.R978W		Atlas-SNP	.											.	LIMCH1	233	.	0			c.C2932T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83.0	71.0	75.0		2932,2929,2467,2431,2932	4.6	1.0	4	dbSNP_131	75	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,missense	LIMCH1	NM_001112717.1,NM_001112718.1,NM_001112719.1,NM_001112720.1,NM_014988.2	101,101,101,101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	978/1058,977/1057,823/903,811/891,978/1084	41687843	1,13005	2203	4300	6503	SO:0001583	missense	22998	exon23			GAAAGGCGGAAGT	AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.2932C>T	4.37:g.41687843C>T	ENSP00000316891:p.Arg978Trp	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	127	16	0.125984	NM_014988	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Missense_Mutation	SNP	ENST00000313860.7	37	CCDS33977.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	5	0.008741258741258742	1	0.0013192612137203166	C	14.03	2.414116	0.42817	0.0	1.16E-4	ENSG00000064042	ENST00000513024;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000396595;ENST00000381753;ENST00000537405	T;T;T;T;T;T;T;T;T;T;T;T	0.49720	0.82;1.38;1.39;1.38;0.8;1.39;0.79;0.79;0.79;0.77;0.8;0.79	5.51	4.61	0.57282	.	0.066428	0.64402	D	0.000014	T	0.53642	0.1809	L	0.60455	1.87	0.34467	D	0.702395	D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.998;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0	P;P;P;D;D;D;D;D;D;D;D;D	0.79108	0.642;0.88;0.719;0.99;0.949;0.949;0.992;0.947;0.981;0.958;0.981;0.958	T	0.68969	-0.5269	10	0.87932	D	0	-20.9146	10.6354	0.45563	0.2036:0.7964:0.0:0.0	.	818;728;811;901;811;823;1362;831;990;977;978;978	E7EPK0;B7Z3G0;E9PDJ9;D6RD46;Q9UPQ0-9;Q9UPQ0-6;G5EA03;Q9UPQ0-5;Q9UPQ0-4;E9PHM7;Q9UPQ0-2;Q9UPQ0	.;.;.;.;.;.;.;.;.;.;.;LIMC1_HUMAN	W	831;977;978;978;901;990;1362;818;1361;818;811;823;811;330	ENSP00000425222:R831W;ENSP00000424825:R977W;ENSP00000424645:R978W;ENSP00000316891:R978W;ENSP00000427045:R901W;ENSP00000424437:R990W;ENSP00000425631:R1362W;ENSP00000421242:R818W;ENSP00000426334:R818W;ENSP00000422864:R811W;ENSP00000379840:R823W;ENSP00000371172:R811W	ENSP00000316891:R978W	R	+	1	2	LIMCH1	41382600	1.000000	0.71417	1.000000	0.80357	0.660000	0.38997	1.469000	0.35343	2.873000	0.98535	0.561000	0.74099	CGG	C|0.999;T|0.001	0.001	strong		0.433	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988	
TAF2	6873	hgsc.bcm.edu	37	8	120814172	120814172	+	Silent	SNP	G	G	A	rs61753749	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:120814172G>A	ENST00000378164.2	-	6	952	c.654C>T	c.(652-654)ggC>ggT	p.G218G		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	218					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CCACCAAATCGCCATTAGAAA	0.378													G|||	22	0.00439297	0.0023	0.0072	5008	,	,		18509	0.0		0.0119	False		,,,				2504	0.002				p.G218G		Atlas-SNP	.											.	TAF2	204	.	0			c.C654T						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	117.0	103.0	108.0		654	-2.3	1.0	8	dbSNP_129	108	117,8483	61.0+/-122.8	2,113,4185	no	coding-synonymous	TAF2	NM_003184.3		2,125,6376	AA,AG,GG		1.3605,0.2724,0.9918		218/1200	120814172	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	6873	exon6			CAAATCGCCATTA	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.654C>T	8.37:g.120814172G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Silent	SNP	ENST00000378164.2	37	CCDS34937.1																																																																																			G|0.992;A|0.008	0.008	strong		0.378	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
ACSM5	54988	hgsc.bcm.edu	37	16	20442562	20442562	+	Silent	SNP	C	C	T	rs78006992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20442562C>T	ENST00000331849.4	+	10	1374	c.1227C>T	c.(1225-1227)aaC>aaT	p.N409N		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	409					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.N409N(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						ATGAGGGCAACGTCCTGCCTC	0.557																																					p.N409N		Atlas-SNP	.											ACSM5,NS,carcinoma,0,1	ACSM5	101	1	1	Substitution - coding silent(1)	kidney(1)	c.C1227T						PASS	.						157.0	135.0	142.0					16																	20442562		2203	4300	6503	SO:0001819	synonymous_variant	54988	exon10			GGGCAACGTCCTG		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1227C>T	16.37:g.20442562C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	130	19	0.146154	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Silent	SNP	ENST00000331849.4	37	CCDS10585.1																																																																																			C|0.500;T|0.500	0.500	strong		0.557	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
PLSCR4	57088	hgsc.bcm.edu	37	3	145938619	145938619	+	Missense_Mutation	SNP	T	T	C	rs3762685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:145938619T>C	ENST00000354952.2	-	3	341	c.101A>G	c.(100-102)aAt>aGt	p.N34S	PLSCR4_ENST00000446574.2_Missense_Mutation_p.N34S|PLSCR4_ENST00000433593.2_Missense_Mutation_p.N19S|PLSCR4_ENST00000493382.1_Missense_Mutation_p.N34S|PLSCR4_ENST00000383083.2_Missense_Mutation_p.N34S	NM_020353.2	NP_065086.2	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4	34	Proline-rich domain (PRD). {ECO:0000250}.		N -> S (in dbSNP:rs3762685). {ECO:0000269|PubMed:10930526, ECO:0000269|Ref.2}.		cellular response to lipopolysaccharide (GO:0071222)|phospholipid scrambling (GO:0017121)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|enzyme binding (GO:0019899)|phospholipid scramblase activity (GO:0017128)			kidney(1)|large_intestine(6)|lung(9)|urinary_tract(1)	17						AAAATGAGAATTGTATTCAGG	0.383													T|||	1547	0.308906	0.3457	0.415	5008	,	,		15089	0.1915		0.341	False		,,,				2504	0.272				p.N34S		Atlas-SNP	.											.	PLSCR4	44	.	0			c.A101G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	1544,2862	484.9+/-360.2	282,980,941	103.0	96.0	98.0		101,56,101	-8.5	0.1	3	dbSNP_107	98	3021,5579	464.5+/-366.3	547,1927,1826	yes	missense,missense,missense	PLSCR4	NM_001128306.1,NM_001177304.1,NM_020353.2	46,46,46	829,2907,2767	CC,CT,TT		35.1279,35.0431,35.0992	benign,benign,benign	34/240,19/225,34/330	145938619	4565,8441	2203	4300	6503	SO:0001583	missense	57088	exon3			TGAGAATTGTATT	AF199023	CCDS3133.1, CCDS54651.1	3q24	2008-07-18			ENSG00000114698	ENSG00000114698			16497	protein-coding gene	gene with protein product		607612				10930526	Standard	NM_020353		Approved		uc003evt.4	Q9NRQ2	OTTHUMG00000159415	ENST00000354952.2:c.101A>G	3.37:g.145938619T>C	ENSP00000347038:p.Asn34Ser	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_020353	A8K2E9|Q2TTR3|Q658L3|Q6ZR73|Q7Z505	Missense_Mutation	SNP	ENST00000354952.2	37	CCDS3133.1	683	0.31272893772893773	164	0.3333333333333333	134	0.3701657458563536	117	0.20454545454545456	268	0.35356200527704484	T	4.895	0.166350	0.09339	0.350431	0.351279	ENSG00000114698	ENST00000354952;ENST00000383083;ENST00000433593;ENST00000446574;ENST00000493382;ENST00000460350;ENST00000460885;ENST00000476202;ENST00000481701;ENST00000498625	T;T;T;T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04	4.73	-8.49	0.00931	.	0.999489	0.08099	N	0.998132	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.40590	-0.9555	9	0.08837	T	0.75	.	0.8042	0.01081	0.2348:0.308:0.2393:0.2179	rs3762685;rs52810966;rs58731158;rs3762685	34;34	E9PHR9;Q9NRQ2	.;PLS4_HUMAN	S	34;34;19;34;34;34;34;34;34;34	ENSP00000347038:N34S;ENSP00000372561:N34S;ENSP00000415605:N19S;ENSP00000399315:N34S;ENSP00000419040:N34S;ENSP00000417896:N34S;ENSP00000420385:N34S;ENSP00000418173:N34S;ENSP00000418419:N34S;ENSP00000417248:N34S	ENSP00000347038:N34S	N	-	2	0	PLSCR4	147421309	0.008000	0.16893	0.075000	0.20258	0.432000	0.31715	-2.202000	0.01235	-1.326000	0.02266	-0.295000	0.09555	AAT	T|0.671;C|0.329	0.329	strong		0.383	PLSCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355172.1	NM_020353	
DDX49	54555	hgsc.bcm.edu	37	19	19037176	19037176	+	Silent	SNP	G	G	A	rs115860110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19037176G>A	ENST00000247003.4	+	10	1159	c.1092G>A	c.(1090-1092)gaG>gaA	p.E364E	DDX49_ENST00000438170.2_3'UTR|AC002985.3_ENST00000596918.1_Intron|DDX49_ENST00000599156.1_3'UTR	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	364	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	18			Epithelial(12;0.0289)			ACGCCATCGAGGAGCAGATCA	0.627													G|||	22	0.00439297	0.0015	0.0101	5008	,	,		11044	0.0		0.0129	False		,,,				2504	0.0				p.E364E		Atlas-SNP	.											.	DDX49	37	.	0			c.G1092A						PASS	.	G		6,4368		0,6,2181	60.0	40.0	47.0		1092	4.7	1.0	19	dbSNP_132	47	88,8458		0,88,4185	no	coding-synonymous	DDX49	NM_019070.4		0,94,6366	AA,AG,GG		1.0297,0.1372,0.7276		364/484	19037176	94,12826	2187	4273	6460	SO:0001819	synonymous_variant	54555	exon10			CATCGAGGAGCAG		CCDS12390.1	19p12	2008-02-05				ENSG00000105671		"""DEAD-boxes"""	18684	protein-coding gene	gene with protein product							Standard	NM_019070		Approved	FLJ10432	uc002nkq.2	Q9Y6V7		ENST00000247003.4:c.1092G>A	19.37:g.19037176G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	224	90	0.401786	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Silent	SNP	ENST00000247003.4	37	CCDS12390.1																																																																																			G|0.993;A|0.007	0.007	strong		0.627	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070	
TAS2R46	259292	hgsc.bcm.edu	37	12	11214212	11214212	+	Missense_Mutation	SNP	A	A	T	rs2708380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11214212A>T	ENST00000533467.1	-	1	681	c.682T>A	c.(682-684)Ttg>Atg	p.L228M	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	228			L -> M (in dbSNP:rs2708380). {ECO:0000269|PubMed:15496549}.		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		ACAGTTTGCAAAGCTTTTATG	0.403													.|||	1682	0.335863	0.3404	0.4625	5008	,	,		21856	0.1925		0.4841	False		,,,				2504	0.2352				p.L228M		Atlas-SNP	.											.	TAS2R46	43	.	0			c.T682A						PASS	.	A	MET/LEU	1615,2791	493.6+/-362.7	303,1009,891	191.0	197.0	195.0		682	-3.1	0.0	12	dbSNP_100	195	4198,4400	569.4+/-389.2	1055,2088,1156	no	missense	TAS2R46	NM_176887.2	15	1358,3097,2047	TT,TA,AA		48.8253,36.6546,44.7016	benign	228/310	11214212	5813,7191	2203	4299	6502	SO:0001583	missense	259292	exon1			TTTGCAAAGCTTT	AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18877	protein-coding gene	gene with protein product		612774				12379855	Standard	NM_176887		Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.682T>A	12.37:g.11214212A>T	ENSP00000436450:p.Leu228Met	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	229	85	0.371179	NM_176887	P59548|Q645X6	Missense_Mutation	SNP	ENST00000533467.1	37	CCDS53748.1	744	0.34065934065934067	158	0.32113821138211385	135	0.3729281767955801	118	0.2062937062937063	333	0.4393139841688654	A	10.08	1.252660	0.22965	0.366546	0.488253	ENSG00000226761	ENST00000533467	T	0.01133	5.29	2.54	-3.08	0.05347	.	.	.	.	.	T	0.00012	0.0000	L	0.48877	1.53	0.80722	P	0.0	P	0.46706	0.883	P	0.46585	0.521	T	0.28267	-1.0049	8	0.33940	T	0.23	.	4.1272	0.10133	0.5503:0.0:0.1781:0.2716	rs2708380;rs2923228	228	P59540	T2R46_HUMAN	M	228	ENSP00000436450:L228M	ENSP00000436450:L228M	L	-	1	2	TAS2R46	11105479	0.022000	0.18835	0.000000	0.03702	0.100000	0.18952	-0.066000	0.11598	-0.745000	0.04772	0.163000	0.16589	TTG	A|0.642;T|0.358	0.358	strong		0.403	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887	
CDH4	1002	hgsc.bcm.edu	37	20	60419750	60419750	+	Silent	SNP	C	C	T	rs34912551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60419750C>T	ENST00000360469.5	+	5	691	c.603C>T	c.(601-603)atC>atT	p.I201I	CDH4_ENST00000543233.1_Silent_p.I127I	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	201	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			ACAATGACATCCCCATCCGGT	0.592													C|||	75	0.014976	0.0015	0.013	5008	,	,		19118	0.0		0.0417	False		,,,				2504	0.0225				p.I201I		Atlas-SNP	.											.	CDH4	172	.	0			c.C603T						PASS	.	C		53,4353	54.2+/-90.2	0,53,2150	96.0	83.0	88.0		603	1.6	1.0	20	dbSNP_126	88	402,8198	127.0+/-185.4	12,378,3910	no	coding-synonymous	CDH4	NM_001794.2		12,431,6060	TT,TC,CC		4.6744,1.2029,3.4984		201/917	60419750	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	1002	exon5			TGACATCCCCATC	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.603C>T	20.37:g.60419750C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Silent	SNP	ENST00000360469.5	37	CCDS13488.1																																																																																			C|0.970;T|0.030	0.030	strong		0.592	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
HEATR5B	54497	hgsc.bcm.edu	37	2	37241050	37241050	+	Silent	SNP	G	G	A	rs17020125	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:37241050G>A	ENST00000233099.5	-	27	4313	c.4218C>T	c.(4216-4218)tcC>tcT	p.S1406S	HEATR5B_ENST00000354531.2_Silent_p.S1406S	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1406						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				ACAGCTGGCTGGAAGATCCTT	0.463													G|||	1304	0.260383	0.0484	0.2651	5008	,	,		14467	0.5288		0.1948	False		,,,				2504	0.3344				p.S1406S		Atlas-SNP	.											.	HEATR5B	185	.	0			c.C4218T						PASS	.	G		336,4070	176.2+/-205.4	11,314,1878	131.0	125.0	127.0		4218	-0.9	1.0	2	dbSNP_123	127	1590,7010	297.9+/-303.7	164,1262,2874	no	coding-synonymous	HEATR5B	NM_019024.1		175,1576,4752	AA,AG,GG		18.4884,7.626,14.8085		1406/2072	37241050	1926,11080	2203	4300	6503	SO:0001819	synonymous_variant	54497	exon27			CTGGCTGGAAGAT	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.4218C>T	2.37:g.37241050G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																			G|0.798;A|0.202	0.202	strong		0.463	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
SLC13A2	9058	hgsc.bcm.edu	37	17	26817537	26817537	+	Silent	SNP	G	G	A	rs11568466	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:26817537G>A	ENST00000314669.5	+	3	717	c.297G>A	c.(295-297)gcG>gcA	p.A99A	SLC13A2_ENST00000444914.3_Silent_p.A148A|SLC13A2_ENST00000545060.1_Silent_p.A56A|SLC13A2_ENST00000537681.1_Silent_p.A28A	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	99					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	TGGCCATCGCGGTGGAACACT	0.622													G|||	770	0.153754	0.1679	0.1628	5008	,	,		18210	0.0446		0.2137	False		,,,				2504	0.1789				p.A148A		Atlas-SNP	.											.	SLC13A2	125	.	0			c.G444A						PASS	.	G	,,	702,3704	292.4+/-282.0	71,560,1572	137.0	110.0	119.0		444,168,297	-11.2	0.0	17	dbSNP_126	119	1809,6791	325.6+/-317.0	177,1455,2668	yes	coding-synonymous,coding-synonymous,coding-synonymous	SLC13A2	NM_001145975.1,NM_001145976.1,NM_003984.3	,,	248,2015,4240	AA,AG,GG		21.0349,15.9328,19.3065	,,	148/642,56/550,99/593	26817537	2511,10495	2203	4300	6503	SO:0001819	synonymous_variant	9058	exon3			CATCGCGGTGGAA	U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"""Solute carriers"""	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.297G>A	17.37:g.26817537G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_001145975	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Silent	SNP	ENST00000314669.5	37	CCDS11231.1																																																																																			G|0.830;C|0.000;A|0.170	0.170	strong		0.622	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984	
CPAMD8	27151	hgsc.bcm.edu	37	19	17108052	17108052	+	Missense_Mutation	SNP	C	C	T	rs62622858	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17108052C>T	ENST00000443236.1	-	11	1136	c.1105G>A	c.(1105-1107)Gtg>Atg	p.V369M	CPAMD8_ENST00000388925.4_Missense_Mutation_p.V322M	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	322						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						ACACTGGTCACCATGGCCCAG	0.642													c|||	122	0.024361	0.0023	0.036	5008	,	,		18753	0.0		0.0487	False		,,,				2504	0.046				p.V369M		Atlas-SNP	.											.	CPAMD8	192	.	0			c.G1105A						PASS	.	C	MET/VAL	27,3781		0,27,1877	22.0	24.0	23.0		1105	3.0	0.0	19	dbSNP_129	23	342,7810		8,326,3742	no	missense	CPAMD8	NM_015692.2	21	8,353,5619	TT,TC,CC		4.1953,0.709,3.0853	probably-damaging	369/1933	17108052	369,11591	1904	4076	5980	SO:0001583	missense	27151	exon11			TGGTCACCATGGC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1105G>A	19.37:g.17108052C>T	ENSP00000402505:p.Val369Met	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	227	106	0.46696	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	52|52	0.023809523809523808|0.023809523809523808	2|2	0.0040650406504065045|0.0040650406504065045	10|10	0.027624309392265192|0.027624309392265192	0|0	0.0|0.0	40|40	0.052770448548812667|0.052770448548812667	c|c	14.83|14.83	2.653663|2.653663	0.47362|0.47362	0.00709|0.00709	0.041953|0.041953	ENSG00000160111|ENSG00000160111	ENST00000291440;ENST00000388925|ENST00000443236	T;T|.	0.61627|.	0.09;0.12|.	3.0|3.0	3.0|3.0	0.34707|0.34707	.|.	1.833260|.	0.03821|.	N|.	0.267544|.	T|.	0.37046|.	0.0989|.	M|M	0.80982|0.80982	2.52|2.52	0.48632|0.48632	D|D	0.999687|0.999687	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|.	0.65319|.	-0.6197|.	10|.	0.87932|.	D|.	0|.	.|.	14.3086|14.3086	0.66400|0.66400	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs62622858|rs62622858	322|.	Q8IZJ3|.	CPMD8_HUMAN|.	M|X	369;322|379	ENSP00000291440:V369M;ENSP00000373577:V322M|.	ENSP00000291440:V369M|.	V|W	-|-	1|3	0|0	CPAMD8|CPAMD8	16969052|16969052	1.000000|1.000000	0.71417|0.71417	0.011000|0.011000	0.14972|0.14972	0.142000|0.142000	0.21351|0.21351	6.398000|6.398000	0.73244|0.73244	1.423000|1.423000	0.47198|0.47198	0.555000|0.555000	0.69702|0.69702	GTG|TGG	C|0.964;T|0.036	0.036	strong		0.642	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
PRSS54	221191	hgsc.bcm.edu	37	16	58318604	58318604	+	Missense_Mutation	SNP	T	T	C	rs3815803	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:58318604T>C	ENST00000219301.4	-	6	938	c.544A>G	c.(544-546)Agt>Ggt	p.S182G	PRSS54_ENST00000567164.1_Missense_Mutation_p.S182G|PRSS54_ENST00000543437.1_Missense_Mutation_p.S83G|PRSS54_ENST00000563336.1_5'UTR	NM_001080492.1	NP_001073961.1	Q6PEW0	PRS54_HUMAN	protease, serine, 54	182	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		S -> G (in dbSNP:rs3815803). {ECO:0000269|PubMed:14702039}.			cytoplasm (GO:0005737)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.S182G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CTCAGGACACTCATCGTCATG	0.473													T|||	2689	0.536941	0.767	0.3718	5008	,	,		20351	0.3929		0.5537	False		,,,				2504	0.4744				p.S182G		Atlas-SNP	.											PRSS54,NS,carcinoma,0,1	PRSS54	48	1	1	Substitution - Missense(1)	stomach(1)	c.A544G						PASS	.	T	GLY/SER	3265,1131	716.2+/-408.6	1199,867,132	130.0	117.0	121.0		544	3.3	1.0	16	dbSNP_107	121	4801,3799	612.9+/-396.0	1382,2037,881	yes	missense	PRSS54	NM_001080492.1	56	2581,2904,1013	CC,CT,TT		44.1744,25.7279,37.9347	probably-damaging	182/396	58318604	8066,4930	2198	4300	6498	SO:0001583	missense	221191	exon6			GGACACTCATCGT	AK058068	CCDS32463.1	16q21	2010-05-07			ENSG00000103023	ENSG00000103023		"""Serine peptidases / Serine peptidases"""	26336	protein-coding gene	gene with protein product	"""cancer/testis antigen 67"""					17521433	Standard	NM_001080492		Approved	FLJ25339, KLKBL4, CT67	uc002enf.3	Q6PEW0		ENST00000219301.4:c.544A>G	16.37:g.58318604T>C	ENSP00000219301:p.Ser182Gly	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	NM_001080492	Q96LN9|Q9NT77	Missense_Mutation	SNP	ENST00000219301.4	37	CCDS32463.1	1149	0.5260989010989011	359	0.7296747967479674	150	0.4143646408839779	213	0.3723776223776224	427	0.5633245382585752	T	9.832	1.188593	0.21954	0.742721	0.558256	ENSG00000103023	ENST00000219301;ENST00000543437	T;T	0.59083	0.29;0.29	5.83	3.28	0.37604	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.072852	0.64402	D	0.000016	T	0.00012	0.0000	M	0.62154	1.92	0.32894	P	0.48773999999999995	P	0.41978	0.767	B	0.37989	0.262	T	0.41963	-0.9479	9	0.19147	T	0.46	-15.3263	7.4576	0.27276	0.0:0.1924:0.0:0.8076	rs3815803;rs17241105;rs52819921;rs56905288;rs3815803	182	Q6PEW0	PRS54_HUMAN	G	182;83	ENSP00000219301:S182G;ENSP00000437705:S83G	ENSP00000219301:S182G	S	-	1	0	PRSS54	56876105	1.000000	0.71417	1.000000	0.80357	0.109000	0.19521	1.893000	0.39758	1.046000	0.40249	-0.371000	0.07208	AGT	T|0.421;C|0.579	0.579	strong		0.473	PRSS54-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422556.1	NM_001080492	
TANC1	85461	hgsc.bcm.edu	37	2	159954175	159954175	+	Missense_Mutation	SNP	C	C	T	rs34588551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:159954175C>T	ENST00000263635.6	+	4	325	c.88C>T	c.(88-90)Cca>Tca	p.P30S	TANC1_ENST00000454300.1_Missense_Mutation_p.P30S	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	30			P -> S (in dbSNP:rs34588551).		dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						AGAGACTTCTCCAGTCCTGCA	0.458													C|||	683	0.136382	0.0295	0.2493	5008	,	,		18486	0.003		0.3469	False		,,,				2504	0.1217				p.P30S		Atlas-SNP	.											.	TANC1	157	.	0			c.C88T						PASS	.	C	SER/PRO,SER/PRO	309,3621		8,293,1664	119.0	113.0	115.0		88,88	0.7	0.0	2	dbSNP_126	115	2993,5307		533,1927,1690	yes	missense,missense	TANC1	NM_001145909.1,NM_033394.2	74,74	541,2220,3354	TT,TC,CC		36.0602,7.8626,26.9992	benign,benign	30/1391,30/1862	159954175	3302,8928	1965	4150	6115	SO:0001583	missense	85461	exon4			ACTTCTCCAGTCC	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.88C>T	2.37:g.159954175C>T	ENSP00000263635:p.Pro30Ser	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	130	60	0.461538	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	386	0.17673992673992675	20	0.04065040650406504	112	0.30939226519337015	1	0.0017482517482517483	253	0.3337730870712401	C	7.078	0.569622	0.13560	0.078626	0.360602	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.68624	-0.34;-0.32	5.76	0.726	0.18248	.	0.550760	0.16234	N	0.223445	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.11235	0.004;0.0	B;B	0.16289	0.015;0.0	T	0.33007	-0.9885	9	0.27082	T	0.32	.	2.2854	0.04124	0.124:0.4056:0.2705:0.2	rs34588551	30;30	Q9C0D5-2;Q9C0D5	.;TANC1_HUMAN	S	30	ENSP00000396339:P30S;ENSP00000263635:P30S	ENSP00000263635:P30S	P	+	1	0	TANC1	159662421	0.001000	0.12720	0.003000	0.11579	0.987000	0.75469	0.420000	0.21263	0.127000	0.18452	0.655000	0.94253	CCA	C|0.753;T|0.247	0.247	strong		0.458	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
KIAA0753	9851	hgsc.bcm.edu	37	17	6524298	6524298	+	Missense_Mutation	SNP	T	T	A	rs9889363	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:6524298T>A	ENST00000361413.3	-	7	1483	c.1125A>T	c.(1123-1125)gaA>gaT	p.E375D	KIAA0753_ENST00000572370.1_Missense_Mutation_p.E76D|KIAA0753_ENST00000542606.1_Missense_Mutation_p.E76D|KIAA0753_ENST00000589033.1_5'Flank	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	375			E -> D (in dbSNP:rs9889363).|E -> G (in dbSNP:rs17794522).			centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		ACAGTTTCTTTTCCAGGAGAG	0.373													T|||	1542	0.307907	0.1581	0.4006	5008	,	,		15891	0.3562		0.3489	False		,,,				2504	0.3528				p.E375D		Atlas-SNP	.											.	KIAA0753	63	.	0			c.A1125T						PASS	.	T	ASP/GLU	734,2898		74,586,1156	62.0	60.0	60.0		1125	3.8	1.0	17	dbSNP_119	60	3078,5082		548,1982,1550	yes	missense	KIAA0753	NM_014804.2	45	622,2568,2706	AA,AT,TT		37.7206,20.2093,32.327	probably-damaging	375/968	6524298	3812,7980	1816	4080	5896	SO:0001583	missense	9851	exon7			TTTCTTTTCCAGG		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.1125A>T	17.37:g.6524298T>A	ENSP00000355250:p.Glu375Asp	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	669	0.30631868131868134	83	0.16869918699186992	154	0.425414364640884	178	0.3111888111888112	254	0.33509234828496043	T	24.0	4.484199	0.84854	0.202093	0.377206	ENSG00000198920	ENST00000361413;ENST00000542606	D;D	0.86956	-2.19;-2.19	4.92	3.84	0.44239	.	0.429523	0.27901	N	0.017391	T	0.00012	0.0000	M	0.76574	2.34	0.09310	P	0.9999999999992082	D	0.76494	0.999	D	0.80764	0.994	T	0.01074	-1.1460	9	0.62326	D	0.03	-12.5411	7.6264	0.28214	0.0:0.099:0.0:0.901	rs9889363;rs17804307;rs9889363	375	Q2KHM9	K0753_HUMAN	D	375;76	ENSP00000355250:E375D;ENSP00000444634:E76D	ENSP00000355250:E375D	E	-	3	2	KIAA0753	6465022	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.810000	0.27183	0.991000	0.38814	0.377000	0.23210	GAA	T|0.697;A|0.303	0.303	strong		0.373	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
SCRN2	90507	hgsc.bcm.edu	37	17	45917703	45917703	+	Silent	SNP	C	C	T	rs11652952	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:45917703C>T	ENST00000290216.9	-	3	335	c.210G>A	c.(208-210)acG>acA	p.T70T	SCRN2_ENST00000584123.1_Silent_p.T78T|SCRN2_ENST00000407215.3_Silent_p.T70T	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	70						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						TCACAGCGTGCGTCTTCGACA	0.592													C|||	147	0.029353	0.0658	0.0231	5008	,	,		20332	0.0		0.0358	False		,,,				2504	0.0082				p.T70T		Atlas-SNP	.											.	SCRN2	35	.	0			c.G210A						PASS	.	C	,	237,4169	139.2+/-174.8	7,223,1973	103.0	77.0	86.0		210,210	-10.2	0.3	17	dbSNP_120	86	295,8305	108.8+/-169.4	6,283,4011	no	coding-synonymous,coding-synonymous	SCRN2	NM_001145023.1,NM_138355.3	,	13,506,5984	TT,TC,CC		3.4302,5.379,4.0904	,	70/379,70/426	45917703	532,12474	2203	4300	6503	SO:0001819	synonymous_variant	90507	exon3			AGCGTGCGTCTTC	BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.210G>A	17.37:g.45917703C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	185	89	0.481081	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	37	CCDS11519.1																																																																																			C|0.963;T|0.037	0.037	strong		0.592	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355	
BCL2	596	hgsc.bcm.edu	37	18	60985879	60985879	+	Silent	SNP	T	T	C	rs1801018	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:60985879T>C	ENST00000398117.1	-	1	1482	c.21A>G	c.(19-21)acA>acG	p.T7T	BCL2_ENST00000589955.1_Silent_p.T7T|BCL2_ENST00000333681.4_Silent_p.T7T|BCL2_ENST00000444484.1_Silent_p.T7T	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	7			T -> S. {ECO:0000269|PubMed:2834197, ECO:0000269|PubMed:3285301}.		actin filament organization (GO:0007015)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|axonogenesis (GO:0007409)|B cell homeostasis (GO:0001782)|B cell lineage commitment (GO:0002326)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|behavioral fear response (GO:0001662)|branching involved in ureteric bud morphogenesis (GO:0001658)|CD8-positive, alpha-beta T cell lineage commitment (GO:0043375)|cell aging (GO:0007569)|cell growth (GO:0016049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to organic substance (GO:0071310)|cochlear nucleus development (GO:0021747)|defense response to virus (GO:0051607)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|ear development (GO:0043583)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|female pregnancy (GO:0007565)|focal adhesion assembly (GO:0048041)|gland morphogenesis (GO:0022612)|glomerulus development (GO:0032835)|hair follicle morphogenesis (GO:0031069)|homeostasis of number of cells within a tissue (GO:0048873)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|melanin metabolic process (GO:0006582)|melanocyte differentiation (GO:0030318)|mesenchymal cell development (GO:0014031)|metanephros development (GO:0001656)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of autophagy (GO:0010507)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cellular pH reduction (GO:0032848)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of retinal cell programmed cell death (GO:0046671)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|oocyte development (GO:0048599)|organ growth (GO:0035265)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pigment granule organization (GO:0048753)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell growth (GO:0030307)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron maturation (GO:0014042)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smooth muscle cell migration (GO:0014911)|post-embryonic development (GO:0009791)|protein dephosphorylation (GO:0006470)|protein polyubiquitination (GO:0000209)|reactive oxygen species metabolic process (GO:0072593)|regulation of calcium ion transport (GO:0051924)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glycoprotein biosynthetic process (GO:0010559)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|regulation of protein stability (GO:0031647)|regulation of transmembrane transporter activity (GO:0022898)|regulation of viral genome replication (GO:0045069)|release of cytochrome c from mitochondria (GO:0001836)|renal system process (GO:0003014)|response to acid chemical (GO:0001101)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to iron ion (GO:0010039)|response to ischemia (GO:0002931)|response to nicotine (GO:0035094)|response to radiation (GO:0009314)|response to toxic substance (GO:0009636)|response to UV-B (GO:0010224)|single organismal cell-cell adhesion (GO:0016337)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|channel inhibitor activity (GO:0016248)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(106)|kidney(1)|large_intestine(1)|lung(3)	113		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Ibuprofen(DB01050)|Paclitaxel(DB01229)|Rasagiline(DB01367)	TATCGTACCCTGTTCTCCCAG	0.627			T	IGH@	"""NHL, CLL"""								T|||	1218	0.243211	0.0318	0.389	5008	,	,		14585	0.0923		0.4751	False		,,,				2504	0.3425				p.T7T		Atlas-SNP	.		Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	BCL2_ENST00000444484,brain,glioma,0,15	BCL2	272	15	0			c.A21G						PASS	.	T	,	337,3577		16,305,1636	67.0	74.0	71.0		21,21	0.5	0.9	18	dbSNP_89	71	3402,4728		707,1988,1370	no	coding-synonymous,coding-synonymous	BCL2	NM_000633.2,NM_000657.2	,	723,2293,3006	CC,CT,TT		41.845,8.6101,31.0445	,	7/240,7/206	60985879	3739,8305	1957	4065	6022	SO:0001819	synonymous_variant	596	exon2			GTACCCTGTTCTC	M14745	CCDS11981.1, CCDS45882.1	18q21.3	2014-03-07			ENSG00000171791	ENSG00000171791		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	990	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 50"""	151430					Standard	XM_006722523		Approved	Bcl-2, PPP1R50	uc002lit.1	P10415	OTTHUMG00000132791	ENST00000398117.1:c.21A>G	18.37:g.60985879T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	119	47	0.394958	NM_000633	C9JHD5|P10416|Q13842|Q16197	Silent	SNP	ENST00000398117.1	37	CCDS11981.1																																																																																			T|0.720;C|0.280	0.280	strong		0.627	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657	
MADCAM1	8174	hgsc.bcm.edu	37	19	501762	501762	+	Missense_Mutation	SNP	A	A	C	rs200007467		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:501762A>C	ENST00000215637.3	+	4	807	c.761A>C	c.(760-762)cAg>cCg	p.Q254P	MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.Q35P	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	254	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.			Q -> P (in Ref. 1; AAC13661). {ECO:0000305}.	aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)	p.Q254P(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCACCTCCCAGGAGCCTCCC	0.721																																					p.Q254P		Atlas-SNP	.											MADCAM1,NS,carcinoma,0,1	MADCAM1	29	1	1	Substitution - Missense(1)	kidney(1)	c.A761C						scavenged	.						31.0	36.0	34.0					19																	501762		2194	4290	6484	SO:0001583	missense	8174	exon4			CCTCCCAGGAGCC	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.761A>C	19.37:g.501762A>C	ENSP00000215637:p.Gln254Pro	Somatic	90	3	0.0333333		WXS	Illumina HiSeq	Phase_I	93	28	0.301075	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	N	5.739	0.320845	0.10845	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.09073	3.02	2.86	-5.72	0.02406	.	.	.	.	.	T	0.01940	0.0061	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40869	-0.9540	9	0.02654	T	1	.	3.6031	0.08032	0.3032:0.5048:0.0:0.192	.	254	Q13477	MADCA_HUMAN	P	278;270;262;254	ENSP00000215637:Q254P	ENSP00000215637:Q254P	Q	+	2	0	MADCAM1	452762	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.356000	0.00247	-1.159000	0.02807	-1.988000	0.00451	CAG	.	.	weak		0.721	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
CLC	1178	hgsc.bcm.edu	37	19	40225646	40225646	+	Missense_Mutation	SNP	G	G	A	rs17608	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40225646G>A	ENST00000221804.4	-	2	158	c.83C>T	c.(82-84)gCc>gTc	p.A28V		NM_001828.5	NP_001819.2	Q05315	LEG10_HUMAN	Charcot-Leyden crystal galectin	28	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.		A -> V (in dbSNP:rs17608). {ECO:0000269|PubMed:15057824, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1577491, ECO:0000269|PubMed:19497882, ECO:0000269|PubMed:8419478, ECO:0000269|PubMed:9119387}.		multicellular organismal development (GO:0007275)|regulation of activated T cell proliferation (GO:0046006)|regulation of T cell anergy (GO:0002667)|regulation of T cell cytokine production (GO:0002724)|T cell apoptotic process (GO:0070231)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)	p.A28V(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(2)|stomach(1)	12	all_cancers(60;2.99e-06)|all_lung(34;4.7e-08)|Lung NSC(34;5.46e-08)|Ovarian(47;0.06)	Renal(1328;0.000147)|Hepatocellular(1079;0.0202)|Myeloproliferative disorder(2;0.0255)	Epithelial(26;6.43e-25)|OV - Ovarian serous cystadenocarcinoma(5;1.07e-24)|all cancers(26;8.38e-23)	GBM - Glioblastoma multiforme(1328;4.97e-06)|STAD - Stomach adenocarcinoma(1328;0.00655)		CAAGAAACAGGCAAGTGGTCG	0.498													N|||	3073	0.613618	0.7617	0.5187	5008	,	,		20640	0.3373		0.6988	False		,,,				2504	0.6779				p.A28V		Atlas-SNP	.											CLC,NS,carcinoma,0,1	CLC	20	1	1	Substitution - Missense(1)	stomach(1)	c.C83T						PASS	.		VAL/ALA	3398,1008		1308,782,113	92.0	86.0	88.0		83	0.7	0.0	19	dbSNP_63	88	5735,2865		1884,1967,449	yes	missense	CLC	NM_001828.4	64	3192,2749,562	AA,AG,GG		33.314,22.8779,29.7786	benign	28/143	40225646	9133,3873	2203	4300	6503	SO:0001583	missense	1178	exon2			AAACAGGCAAGTG	L01664	CCDS33025.1	19q13.1	2013-06-12	2013-06-12		ENSG00000105205	ENSG00000105205		"""Lectins, galactoside-binding"""	2014	protein-coding gene	gene with protein product	"""eosinophil lysophospholipase"", ""lysolecithin acylhydrolase"", ""galectin 10"", ""lectin, galactoside-binding, soluble, 10"""	153310	"""Charcot-Leyden crystal protein"""			1577491, 11834744	Standard	NM_001828		Approved	LGALS10, MGC149659, Gal-10	uc002omh.3	Q05315		ENST00000221804.4:c.83C>T	19.37:g.40225646G>A	ENSP00000221804:p.Ala28Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	143	63	0.440559	NM_001828	C5HZ13|C5HZ14|Q0VDE3	Missense_Mutation	SNP	ENST00000221804.4	37	CCDS33025.1	1297	0.5938644688644689	382	0.7764227642276422	193	0.5331491712707183	203	0.3548951048951049	519	0.6846965699208444	.	0.078	-1.189921	0.01607	0.771221	0.66686	ENSG00000105205	ENST00000221804	T	0.17370	2.28	0.725	0.725	0.18242	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.00012	0.0000	N	0.04018	-0.295	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18618	-1.0331	7	0.10111	T	0.7	.	.	.	.	rs17608;rs374185;rs1126595;rs3181719;rs17709441;rs52813820;rs60928794;rs17608	28	Q05315	LPPL_HUMAN	V	28	ENSP00000221804:A28V	ENSP00000221804:A28V	A	-	2	0	CLC	44917486	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.110000	0.10824	-0.271000	0.09272	-0.965000	0.02619	GCC	G|0.343;A|0.657	0.657	strong		0.498	CLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465225.1	NM_001828	
SLC25A6	293	hgsc.bcm.edu	37	X	1508583	1508583	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:1508583T>C	ENST00000381401.5	-	2	863	c.149A>G	c.(148-150)cAg>cGg	p.Q50R	SLC25A6_ENST00000475167.1_5'UTR	NM_001636.3	NP_001627.2	P12236	ADT3_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6	50					active induction of host immune response by virus (GO:0046732)|ADP transport (GO:0015866)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|modulation by virus of host morphology or physiology (GO:0019048)|protein targeting to mitochondrion (GO:0006626)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP:ADP antiporter activity (GO:0005471)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(8)|upper_aerodigestive_tract(1)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Clodronate(DB00720)	GCCCTTGTACTGCTTGTCGGC	0.617													t|||	519	0.103634	0.0038	0.1138	5008	,	,		17301	0.0506		0.1958	False		,,,				2504	0.1912				p.Q50R		Atlas-SNP	.											.	SLC25A6	27	.	0			c.A149G						PASS	.	T	ARG/GLN	132,4274		2,128,2073	141.0	126.0	131.0		149	1.7	1.0	X	dbSNP_134	131	1352,7240		109,1134,3053	no	missense	SLC25A6	NM_001636.3	43	111,1262,5126	CC,CT,TT		15.7356,2.9959,11.4171	benign	50/299	1508583	1484,11514	2203	4296	6499	SO:0001583	missense	293	exon2			TTGTACTGCTTGT	AY007135	CCDS14114.1	Xp22.32 and Yp11.3	2013-05-22			ENSG00000169100	ENSG00000169100		"""Pseudoautosomal regions / PAR1"", ""Solute carriers"""	10992	protein-coding gene	gene with protein product		300151, 403000		ANT3			Standard	NM_001636		Approved	ANT3Y, MGC17525	uc004cpt.3	P12236	OTTHUMG00000021058	ENST00000381401.5:c.149A>G	X.37:g.1508583T>C	ENSP00000370808:p.Gln50Arg	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	101	95	0.940594	NM_001636	Q96C49	Missense_Mutation	SNP	ENST00000381401.5	37	CCDS14114.1	217	0.09935897435897435	3	0.006097560975609756	45	0.12430939226519337	31	0.05419580419580419	138	0.1820580474934037	.	0.448	-0.895217	0.02491	0.029959	0.157356	ENSG00000169100	ENST00000381401;ENST00000447786	T	0.78707	-1.2	1.69	1.69	0.24217	Mitochondrial carrier domain (2);	0.000000	0.48767	U	0.000167	T	0.00109	0.0003	N	0.03324	-0.35	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.01405	-1.1363	10	0.02654	T	1	.	9.2302	0.37432	0.0:0.0:0.0:1.0	.	50	P12236	ADT3_HUMAN	R	50	ENSP00000370808:Q50R	ENSP00000370808:Q50R	Q	-	2	0	SLC25A6	1468583	1.000000	0.71417	0.978000	0.43139	0.450000	0.32258	6.090000	0.71397	0.731000	0.32448	0.138000	0.15974	CAG	T|0.888;C|0.112	0.112	strong		0.617	SLC25A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055596.1	NM_001636	
SORBS1	10580	hgsc.bcm.edu	37	10	97174537	97174537	+	Missense_Mutation	SNP	C	C	A	rs7081076	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:97174537C>A	ENST00000361941.3	-	7	550	c.524G>T	c.(523-525)gGc>gTc	p.G175V	SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000371249.2_Missense_Mutation_p.G143V|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000393949.1_Missense_Mutation_p.G166V|SORBS1_ENST00000354106.3_Missense_Mutation_p.G166V|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000371227.4_Missense_Mutation_p.G175V|SORBS1_ENST00000277982.5_Missense_Mutation_p.G175V|SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000371247.2_Missense_Mutation_p.G175V|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000371246.2_Missense_Mutation_p.G175V	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TCTGGCAGTGCCTTCTTGCCC	0.582													C|||	315	0.0628994	0.059	0.0317	5008	,	,		18292	0.0923		0.0308	False		,,,				2504	0.093				p.G175V		Atlas-SNP	.											.	SORBS1	185	.	0			c.G524T						PASS	.	C	VAL/GLY,VAL/GLY,,,,VAL/GLY,	232,4174	138.0+/-173.8	5,222,1976	61.0	65.0	63.0		524,524,,,,428,	4.8	1.0	10	dbSNP_116	63	252,8348	99.3+/-160.8	4,244,4052	yes	missense,missense,intron,intron,intron,missense,intron	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	109,109,,,,109,	9,466,6028	AA,AC,CC		2.9302,5.2655,3.7214	probably-damaging,probably-damaging,,,,probably-damaging,	175/1293,175/1152,,,,143/817,	97174537	484,12522	2203	4300	6503	SO:0001583	missense	10580	exon7			GCAGTGCCTTCTT	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.524G>T	10.37:g.97174537C>A	ENSP00000355136:p.Gly175Val	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	86	80	0.930233	NM_001034955		Missense_Mutation	SNP	ENST00000361941.3	37	CCDS31255.1	126	0.057692307692307696	34	0.06910569105691057	13	0.03591160220994475	55	0.09615384615384616	24	0.0316622691292876	C	18.18	3.567283	0.65651	0.052655	0.029302	ENSG00000095637	ENST00000371249;ENST00000371247;ENST00000371227;ENST00000371246;ENST00000393949;ENST00000361941;ENST00000277982;ENST00000354106	T;T;T;T;T;T;T;T	0.23552	1.95;2.23;1.9;2.51;2.03;2.23;2.51;2.03	5.68	4.77	0.60923	.	0.169985	0.28448	N	0.015314	T	0.01156	0.0038	N	0.24115	0.695	0.80722	D	1	D;D;D;B;D;P	0.89917	0.999;1.0;0.993;0.161;0.986;0.952	D;D;D;B;P;P	0.97110	0.96;1.0;0.945;0.049;0.796;0.52	T	0.01549	-1.1327	10	0.66056	D	0.02	-7.2734	16.5515	0.84473	0.0:0.8693:0.1307:0.0	rs7081076;rs17849164;rs7081076	373;143;175;143;175;175	B7Z9B7;F2Z2S3;Q9BX66-11;Q9BX66-10;Q9BX66;Q9BX66-2	.;.;.;.;SRBS1_HUMAN;.	V	143;175;175;175;166;175;175;166	ENSP00000360295:G143V;ENSP00000360293:G175V;ENSP00000360271:G175V;ENSP00000360292:G175V;ENSP00000377521:G166V;ENSP00000355136:G175V;ENSP00000277982:G175V;ENSP00000277984:G166V	ENSP00000277982:G175V	G	-	2	0	SORBS1	97164527	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.078000	0.50096	1.383000	0.46405	0.555000	0.69702	GGC	C|0.952;A|0.048	0.048	strong		0.582	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
APOBR	55911	hgsc.bcm.edu	37	16	28506872	28506872	+	Silent	SNP	A	A	G	rs149271	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:28506872A>G	ENST00000431282.1	+	2	520	c.510A>G	c.(508-510)gaA>gaG	p.E170E	CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000328423.5_Silent_p.E170E|APOBR_ENST00000564831.1_Silent_p.E170E|CLN3_ENST00000569430.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	170	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						TGAACAGAGAAGAGAGGCTGA	0.607													G|||	1476	0.294728	0.3888	0.4294	5008	,	,		16994	0.1042		0.3479	False		,,,				2504	0.2137				p.E170E		Atlas-SNP	.											.	APOBR	89	.	0			c.A510G						PASS	.	G		1634,2640		361,912,864	11.0	13.0	12.0		510	2.1	0.9	16	dbSNP_79	12	3311,5217		694,1923,1647	no	coding-synonymous	APOBR	NM_018690.3		1055,2835,2511	GG,GA,AA		38.825,38.2312,38.6268		170/1089	28506872	4945,7857	2137	4264	6401	SO:0001819	synonymous_variant	55911	exon2			CAGAGAAGAGAGG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.510A>G	16.37:g.28506872A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	41	0.41	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	37																																																																																				A|0.711;G|0.289	0.289	strong		0.607	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
FAM186A	121006	hgsc.bcm.edu	37	12	50749554	50749554	+	Missense_Mutation	SNP	G	G	T	rs74090114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:50749554G>T	ENST00000327337.5	-	4	1060	c.1061C>A	c.(1060-1062)cCt>cAt	p.P354H	FAM186A_ENST00000543111.1_Missense_Mutation_p.P354H	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	354																	AGAAGGTCCAGGTAACACTTT	0.353													G|||	919	0.183506	0.2201	0.1945	5008	,	,		21664	0.3591		0.0159	False		,,,				2504	0.1176				p.P354H	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.C1061A						PASS	.	G	HIS/PRO	262,1122		20,222,450	195.0	152.0	165.0		1061	3.0	0.0	12	dbSNP_130	165	48,3134		1,46,1544	yes	missense	FAM186A	NM_001145475.1	77	21,268,1994	TT,TG,GG		1.5085,18.9306,6.7893	probably-damaging	354/2352	50749554	310,4256	692	1591	2283	SO:0001583	missense	121006	exon4			GGTCCAGGTAACA		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.1061C>A	12.37:g.50749554G>T	ENSP00000329995:p.Pro354His	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	186	76	0.408602	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	394	0.1804029304029304	102	0.2073170731707317	64	0.17679558011049723	215	0.3758741258741259	13	0.017150395778364115	G	12.94	2.089080	0.36855	0.189306	0.015085	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.10860	2.83;2.83	3.94	3.03	0.35002	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	1.999999999946489E-6	D;D	0.69078	0.997;0.997	D;D	0.63192	0.912;0.912	T	0.49263	-0.8958	8	0.87932	D	0	.	8.9865	0.35997	0.0:0.0:0.7794:0.2206	.	354;354	F5GYN0;A6NE01	.;F186A_HUMAN	H	354	ENSP00000441337:P354H;ENSP00000329995:P354H	ENSP00000329995:P354H	P	-	2	0	FAM186A	49035821	0.002000	0.14202	0.001000	0.08648	0.006000	0.05464	0.704000	0.25661	1.232000	0.43678	0.591000	0.81541	CCT	G|0.820;T|0.180	0.180	strong		0.353	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
PIGR	5284	hgsc.bcm.edu	37	1	207106478	207106478	+	Missense_Mutation	SNP	G	G	A	rs291102	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207106478G>A	ENST00000356495.4	-	7	1922	c.1739C>T	c.(1738-1740)gCt>gTt	p.A580V	PIGR_ENST00000487208.1_5'Flank	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	580			A -> V (in dbSNP:rs291102).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)	p.A580V(1)		central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ATCAGGAGCAGCGTCTGCCTT	0.537													G|||	1336	0.266773	0.7632	0.1931	5008	,	,		20941	0.121		0.0258	False		,,,				2504	0.046				p.A580V		Atlas-SNP	.											PIGR,rectum,carcinoma,-1,3	PIGR	98	3	1	Substitution - Missense(1)	stomach(1)	c.C1739T	GRCh37	CM035762	PIGR	M	rs291102	PASS	.	G	VAL/ALA	2890,1516	674.5+/-402.9	975,940,288	66.0	65.0	66.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1739	1.1	0.0	1	dbSNP_79	66	252,8348	98.4+/-159.9	7,238,4055	yes	missense	PIGR	NM_002644.3	64	982,1178,4343	AA,AG,GG		2.9302,34.4076,24.1581	benign	580/765	207106478	3142,9864	2203	4300	6503	SO:0001583	missense	5284	exon7			GGAGCAGCGTCTG		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"""Immunoglobulin superfamily / V-set domain containing"""	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1739C>T	1.37:g.207106478G>A	ENSP00000348888:p.Ala580Val	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	54	0.580645	NM_002644	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	37	CCDS1474.1	504	0.23076923076923078	360	0.7317073170731707	73	0.20165745856353592	59	0.10314685314685315	12	0.0158311345646438	G	6.784	0.513547	0.12944	0.655924	0.029302	ENSG00000162896	ENST00000356495	T	0.16324	2.35	2.02	1.08	0.20341	.	1.246790	0.05490	N	0.556394	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.13594	0.008	B	0.09377	0.004	T	0.32613	-0.9900	9	0.31617	T	0.26	-32.5565	4.7313	0.12966	0.1905:0.0:0.8095:0.0	rs291102;rs508707;rs1150259;rs52792010;rs57447753;rs291102	580	P01833	PIGR_HUMAN	V	580	ENSP00000348888:A580V	ENSP00000348888:A580V	A	-	2	0	PIGR	205173101	0.001000	0.12720	0.008000	0.14137	0.004000	0.04260	0.523000	0.22925	0.422000	0.26005	-0.300000	0.09419	GCT	G|0.748;T|0.004	.	strong		0.537	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644	
ZNF438	220929	hgsc.bcm.edu	37	10	31146615	31146615	+	Intron	SNP	T	T	C	rs16932010	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:31146615T>C	ENST00000361310.3	-	6	367				ZNF438_ENST00000436087.2_Intron|ZNF438_ENST00000331737.6_Start_Codon_SNP_p.M1V|ZNF438_ENST00000442986.1_Intron|ZNF438_ENST00000375311.1_Intron|ZNF438_ENST00000413025.1_Intron|ZNF438_ENST00000538351.2_Intron|ZNF438_ENST00000444692.2_Start_Codon_SNP_p.M1V|ZNF438_ENST00000452305.1_Start_Codon_SNP_p.M1V			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438						negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(15)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(175;0.0587)				TTACTATCCATAGGACTCTGA	0.378													T|||	827	0.165136	0.3079	0.1369	5008	,	,		19151	0.0655		0.1819	False		,,,				2504	0.0777				p.M1V		Atlas-SNP	.											.	ZNF438	90	.	0			c.A1G						PASS	.	T	,,,,VAL/MET,VAL/MET,	419,965		61,297,334	89.0	83.0	85.0		,,,,1,1,	-3.7	0.0	10	dbSNP_123	85	597,2585		59,479,1053	yes	intron,intron,intron,intron,missense,missense,intron	ZNF438	NM_001143766.1,NM_001143767.1,NM_001143768.1,NM_001143769.1,NM_001143770.1,NM_001143771.1,NM_182755.2	,,,,21,21,	120,776,1387	CC,CT,TT		18.7618,30.2746,22.2514	,,,,,,	,,,,1/819,1/819,	31146615	1016,3550	692	1591	2283	SO:0001627	intron_variant	220929	exon7			TATCCATAGGACT	AK057323	CCDS7168.1, CCDS44369.1, CCDS53504.1	10p11.23	2006-02-15			ENSG00000183621	ENSG00000183621		"""Zinc fingers, C2H2-type"""	21029	protein-coding gene	gene with protein product							Standard	NM_182755		Approved	bA330O11.1	uc010qeb.2	Q7Z4V0	OTTHUMG00000017904	ENST00000361310.3:c.38-7319A>G	10.37:g.31146615T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_001143770	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Missense_Mutation	SNP	ENST00000361310.3	37	CCDS7168.1	381	0.17445054945054944	159	0.3231707317073171	48	0.13259668508287292	42	0.07342657342657342	132	0.1741424802110818	T	13.08	2.130121	0.37630	0.302746	0.187618	ENSG00000183621	ENST00000331737;ENST00000452305;ENST00000444692	T;T;T	0.08546	3.08;3.08;3.08	3.45	-3.72	0.04411	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47995	-0.9073	7	0.52906	T	0.07	.	5.5315	0.16987	0.0:0.4605:0.176:0.3635	rs16932010;rs56491826;rs60292100;rs16932010	1	Q7Z4V0-2	.	V	1	ENSP00000333571:M1V;ENSP00000413060:M1V;ENSP00000410898:M1V	ENSP00000333571:M1V	M	-	1	0	ZNF438	31186621	0.000000	0.05858	0.001000	0.08648	0.963000	0.63663	-2.174000	0.01264	-0.762000	0.04664	-0.254000	0.11334	ATG	T|0.811;C|0.189	0.189	strong		0.378	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755	
DNAH3	55567	hgsc.bcm.edu	37	16	21151913	21151913	+	Missense_Mutation	SNP	G	G	T	rs72780891	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:21151913G>T	ENST00000261383.3	-	5	639	c.640C>A	c.(640-642)Cag>Aag	p.Q214K	DNAH3_ENST00000415178.1_Missense_Mutation_p.Q214K|DNAH3_ENST00000575491.1_5'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	214	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		ATCTCCTGCTGTAACATGACA	0.488													G|||	856	0.170927	0.0968	0.2954	5008	,	,		22605	0.129		0.1869	False		,,,				2504	0.2096				p.Q214K		Atlas-SNP	.											DNAH3_ENST00000261383,colon,carcinoma,0,2	DNAH3	1142	2	0			c.C640A						scavenged	.	G	LYS/GLN	531,3871	240.6+/-251.3	33,465,1703	275.0	222.0	240.0		640	4.1	1.0	16	dbSNP_130	240	1751,6849	319.2+/-314.1	183,1385,2732	yes	missense	DNAH3	NM_017539.1	53	216,1850,4435	TT,TG,GG		20.3605,12.0627,17.5511	benign	214/4117	21151913	2282,10720	2201	4300	6501	SO:0001583	missense	55567	exon5			CCTGCTGTAACAT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.640C>A	16.37:g.21151913G>T	ENSP00000261383:p.Gln214Lys	Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	210	84	0.4	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	355	0.16254578754578755	45	0.09146341463414634	90	0.24861878453038674	65	0.11363636363636363	155	0.20448548812664907	G	8.534	0.871685	0.17322	0.120627	0.203605	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.20881	2.04;2.21	5.07	4.1	0.47936	.	0.771253	0.12304	N	0.480826	T	0.00012	0.0000	L	0.42245	1.32	0.40662	P	0.017862000000000045	B;B	0.26363	0.001;0.147	B;B	0.25506	0.001;0.061	T	0.35574	-0.9783	9	0.05525	T	0.97	.	3.8791	0.09071	0.0866:0.1655:0.5763:0.1716	.	214;185	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	K	214;214;185	ENSP00000261383:Q214K;ENSP00000394245:Q214K	ENSP00000261383:Q214K	Q	-	1	0	DNAH3	21059414	0.540000	0.26410	1.000000	0.80357	0.906000	0.53458	0.697000	0.25556	1.318000	0.45170	0.655000	0.94253	CAG	G|0.825;T|0.175	0.175	strong		0.488	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
FRAS1	80144	hgsc.bcm.edu	37	4	79343111	79343111	+	Silent	SNP	G	G	A	rs78575519	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:79343111G>A	ENST00000325942.6	+	34	5075	c.4635G>A	c.(4633-4635)ccG>ccA	p.P1545P	FRAS1_ENST00000264895.6_Silent_p.P1545P	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1545					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GCCCTCCCCCGGCAGCACCCC	0.572													G|||	496	0.0990415	0.0567	0.1599	5008	,	,		19452	0.001		0.2276	False		,,,				2504	0.0818				p.P1545P		Atlas-SNP	.											.	FRAS1	779	.	0			c.G4635A						PASS	.	G	,	396,3690		18,360,1665	127.0	140.0	136.0		4635,4635	-11.4	0.0	4	dbSNP_132	136	1945,6407		238,1469,2469	no	coding-synonymous,coding-synonymous	FRAS1	NM_001166133.1,NM_025074.6	,	256,1829,4134	AA,AG,GG		23.2878,9.6916,18.8214	,	1545/1977,1545/4013	79343111	2341,10097	2043	4176	6219	SO:0001819	synonymous_variant	80144	exon34			TCCCCCGGCAGCA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.4635G>A	4.37:g.79343111G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	48	29	0.604167	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	37	CCDS54772.1																																																																																			G|0.863;A|0.137	0.137	strong		0.572	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
NDUFA13	51079	hgsc.bcm.edu	37	19	19625547	19625547	+	5'Flank	SNP	A	A	G	rs7250893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19625547A>G	ENST00000507754.4	+	0	0				NDUFA13_ENST00000252576.5_5'Flank|NDUFA13_ENST00000428459.2_5'Flank|CTC-260F20.3_ENST00000555938.1_5'Flank|NDUFA13_ENST00000512771.3_5'Flank|TSSK6_ENST00000360913.3_Silent_p.Y230Y|TSSK6_ENST00000585580.3_Silent_p.Y230Y|YJEFN3_ENST00000608404.1_5'Flank|NDUFA13_ENST00000503283.1_5'Flank			Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13						apoptotic signaling pathway (GO:0097190)|cellular metabolic process (GO:0044237)|cellular response to interferon-beta (GO:0035458)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of peptidase activity (GO:0010952)|positive regulation of protein catabolic process (GO:0045732)|protein import into mitochondrial inner membrane (GO:0045039)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	12						GGCCTTCGGGATAGAGCACGC	0.701													G|||	2374	0.474042	0.6573	0.4798	5008	,	,		15799	0.3194		0.325	False		,,,				2504	0.5348				p.Y230Y		Atlas-SNP	.											TSSK6,NS,carcinoma,0,1	TSSK6	32	1	0			c.T690C						PASS	.	G		2723,1675		841,1041,317	32.0	34.0	33.0		690	4.0	1.0	19	dbSNP_116	33	3001,5585		545,1911,1837	no	coding-synonymous	TSSK6	NM_032037.2		1386,2952,2154	GG,GA,AA		34.9522,38.0855,44.085		230/274	19625547	5724,7260	2199	4293	6492	SO:0001631	upstream_gene_variant	83983	exon1			TTCGGGATAGAGC	AF261134	CCDS12404.1, CCDS12404.2	19p13.11	2011-07-04			ENSG00000186010	ENSG00000186010		"""Mitochondrial respiratory chain complex / Complex I"""	17194	protein-coding gene	gene with protein product	"""complex I B16.6 subunit"""	609435				12837546, 10924506, 15367666	Standard	NM_015965		Approved	CGI-39, CDA016, GRIM-19, GRIM19, B16.6		Q9P0J0	OTTHUMG00000162211		19.37:g.19625547A>G	Exception_encountered	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	15	6	0.4	NM_032037	B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327	Silent	SNP	ENST00000507754.4	37	CCDS12404.2																																																																																			A|0.563;G|0.437	0.437	strong		0.701	NDUFA13-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367916.6	NM_015965	
FRAS1	80144	hgsc.bcm.edu	37	4	79238649	79238649	+	Silent	SNP	T	T	C	rs345514	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:79238649T>C	ENST00000325942.6	+	17	2387	c.1947T>C	c.(1945-1947)caT>caC	p.H649H	FRAS1_ENST00000264895.6_Silent_p.H649H|FRAS1_ENST00000264899.6_Silent_p.H649H	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	649					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ACTCTGACCATGGAGTCTGCA	0.507																																					p.H649H		Atlas-SNP	.											.	FRAS1	779	.	0			c.T1947C						PASS	.	C	,	3500,548		1514,472,38	67.0	70.0	69.0		1947,1947	-4.8	0.0	4	dbSNP_79	69	6434,1970		2458,1518,226	no	coding-synonymous,coding-synonymous	FRAS1	NM_001166133.1,NM_025074.6	,	3972,1990,264	CC,CT,TT		23.4412,13.5375,20.2217	,	649/1977,649/4013	79238649	9934,2518	2024	4202	6226	SO:0001819	synonymous_variant	80144	exon17			TGACCATGGAGTC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1947T>C	4.37:g.79238649T>C		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	139	137	0.985611	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	37	CCDS54772.1	1657|1657	0.7586996336996337|0.7586996336996337	425|425	0.8638211382113821|0.8638211382113821	264|264	0.7292817679558011|0.7292817679558011	392|392	0.6853146853146853|0.6853146853146853	576|576	0.7598944591029023|0.7598944591029023	C|C	0.017|0.017	-1.505937|-1.505937	0.00992|0.00992	0.864625|0.864625	0.765588|0.765588	ENSG00000138759|ENSG00000138759	ENST00000502446|ENST00000508900	.|.	.|.	.|.	5.71|5.71	-4.78|-4.78	0.03209|0.03209	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.10730|0.10730	-1.0617|-1.0617	3|3	.|.	.|.	.|.	.|.	10.4255|10.4255	0.44375|0.44375	0.0898:0.296:0.0:0.6143|0.0898:0.296:0.0:0.6143	rs345514;rs3921856;rs17423214;rs57642403;rs345514|rs345514;rs3921856;rs17423214;rs57642403;rs345514	.|.	.|.	.|.	T|R	578|492	.|.	.|.	M|W	+|+	2|1	0|0	FRAS1|FRAS1	79457673|79457673	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-2.489000|-2.489000	0.00976|0.00976	-1.424000|-1.424000	0.01999|0.01999	-0.215000|-0.215000	0.12644|0.12644	ATG|TGG	T|0.234;G|0.013	.	strong		0.507	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
CILP2	148113	hgsc.bcm.edu	37	19	19654117	19654117	+	Silent	SNP	G	G	C	rs7252453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19654117G>C	ENST00000291495.5	+	7	1123	c.1038G>C	c.(1036-1038)ctG>ctC	p.L346L	CILP2_ENST00000586018.1_Silent_p.L352L	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	346	Ig-like C2-type.					extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						ACCTGGAGCTGCGGGGACTGC	0.652													C|||	1277	0.254992	0.4947	0.2248	5008	,	,		16755	0.0308		0.173	False		,,,				2504	0.2679				p.L346L		Atlas-SNP	.											.	CILP2	84	.	0			c.G1038C						PASS	.	C		1950,2456	604.8+/-390.4	430,1090,683	44.0	49.0	47.0		1038	-9.6	0.0	19	dbSNP_116	47	1516,7084	738.0+/-407.0	125,1266,2909	no	coding-synonymous	CILP2	NM_153221.2		555,2356,3592	CC,CG,GG		17.6279,44.2578,26.6492		346/1157	19654117	3466,9540	2203	4300	6503	SO:0001819	synonymous_variant	148113	exon7			GGAGCTGCGGGGA	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1038G>C	19.37:g.19654117G>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	207	111	0.536232	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			G|0.754;C|0.246	0.246	strong		0.652	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
AGRN	375790	hgsc.bcm.edu	37	1	985377	985377	+	Silent	SNP	C	C	T	rs113020870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:985377C>T	ENST00000379370.2	+	27	4889	c.4839C>T	c.(4837-4839)tgC>tgT	p.C1613C		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1613	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		GTGCTCAGTGCGAGTGCCCCC	0.716													C|||	6	0.00119808	0.0	0.0043	5008	,	,		7759	0.0		0.002	False		,,,				2504	0.001				p.C1613C		Atlas-SNP	.											.	AGRN	110	.	0			c.C4839T						PASS	.	C		6,4366		0,6,2180	16.0	17.0	16.0		4839	0.6	0.7	1	dbSNP_132	16	26,8532		0,26,4253	no	coding-synonymous	AGRN	NM_198576.3		0,32,6433	TT,TC,CC		0.3038,0.1372,0.2475		1613/2046	985377	32,12898	2186	4279	6465	SO:0001819	synonymous_variant	375790	exon27			TCAGTGCGAGTGC	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.4839C>T	1.37:g.985377C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	65	41	0.630769	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			C|0.998;T|0.002	0.002	strong		0.716	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
SRRM4	84530	hgsc.bcm.edu	37	12	119568596	119568596	+	Missense_Mutation	SNP	G	G	A	rs7297606	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:119568596G>A	ENST00000267260.4	+	8	1116	c.728G>A	c.(727-729)aGt>aAt	p.S243N	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	243	Ser-rich.		S -> N (in dbSNP:rs7297606).		cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						CGCCCGCCCAGTCAACCCCTC	0.627													G|||	500	0.0998403	0.2042	0.1124	5008	,	,		15715	0.0268		0.0547	False		,,,				2504	0.0716				p.S243N		Atlas-SNP	.											.	SRRM4	131	.	0			c.G728A						PASS	.	G	ASN/SER	638,3266		55,528,1369	25.0	31.0	29.0		728	3.3	1.0	12	dbSNP_116	29	626,7648		17,592,3528	yes	missense	SRRM4	NM_194286.3	46	72,1120,4897	AA,AG,GG		7.5659,16.3422,10.3794	benign	243/612	119568596	1264,10914	1952	4137	6089	SO:0001583	missense	84530	exon8			CGCCCAGTCAACC	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.728G>A	12.37:g.119568596G>A	ENSP00000267260:p.Ser243Asn	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	30	17	0.566667	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	191	0.08745421245421245	94	0.1910569105691057	36	0.09944751381215469	20	0.03496503496503497	41	0.05408970976253298	G	7.164	0.586356	0.13749	0.163422	0.075659	ENSG00000139767	ENST00000267260	T	0.24538	1.85	5.21	3.34	0.38264	.	0.747332	0.13340	N	0.395235	T	0.00039	0.0001	L	0.44542	1.39	0.41880	P	0.009688999999999948	B	0.30281	0.275	B	0.29942	0.109	T	0.23440	-1.0188	9	0.12430	T	0.62	-8.2941	11.354	0.49605	0.0752:0.1274:0.7974:0.0	rs7297606;rs52809663;rs58175205;rs7297606	243	A7MD48	SRRM4_HUMAN	N	243	ENSP00000267260:S243N	ENSP00000267260:S243N	S	+	2	0	SRRM4	118052979	1.000000	0.71417	0.992000	0.48379	0.053000	0.15095	1.326000	0.33735	0.207000	0.20607	-1.688000	0.00730	AGT	G|0.908;A|0.092	0.092	strong		0.627	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
MINK1	50488	hgsc.bcm.edu	37	17	4787720	4787720	+	Silent	SNP	C	C	T	rs6502827	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4787720C>T	ENST00000355280.6	+	5	565	c.369C>T	c.(367-369)aaC>aaT	p.N123N	MINK1_ENST00000347992.7_Silent_p.N123N|RN7SL784P_ENST00000577319.1_RNA|MINK1_ENST00000453408.3_Silent_p.N123N	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						CAAAAGGCAACGCCCTGAAGG	0.542													C|||	52	0.0103834	0.0015	0.0173	5008	,	,		18206	0.0		0.0368	False		,,,				2504	0.001				p.N123N		Atlas-SNP	.											.	MINK1	110	.	0			c.C369T						PASS	.	C	,,,	25,4143		0,25,2059	154.0	158.0	156.0		369,369,369,369	-0.2	1.0	17	dbSNP_116	156	265,8163		3,259,3952	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MINK1	NM_001024937.3,NM_015716.4,NM_153827.4,NM_170663.4	,,,	3,284,6011	TT,TC,CC		3.1443,0.5998,2.3023	,,,	123/1313,123/1296,123/1333,123/1304	4787720	290,12306	2084	4214	6298	SO:0001819	synonymous_variant	50488	exon5			AGGCAACGCCCTG	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.369C>T	17.37:g.4787720C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	225	108	0.48	NM_170663		Silent	SNP	ENST00000355280.6	37	CCDS45588.1																																																																																			C|0.985;T|0.015	0.015	strong		0.542	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	
SP4	6671	hgsc.bcm.edu	37	7	21468934	21468934	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:21468934C>T	ENST00000222584.3	+	3	369	c.151C>T	c.(151-153)Ctg>Ttg	p.L51L		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	51					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						TCTGGCTTTACTGGCAGCTAC	0.478																																					p.L51L		Atlas-SNP	.											.	SP4	91	.	0			c.C151T						PASS	.						39.0	42.0	41.0					7																	21468934		2203	4300	6503	SO:0001819	synonymous_variant	6671	exon3			GCTTTACTGGCAG		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.151C>T	7.37:g.21468934C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_003112	O60402|Q32M52	Silent	SNP	ENST00000222584.3	37	CCDS5373.1																																																																																			.	.	none		0.478	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112	
OR2M7	391196	hgsc.bcm.edu	37	1	248487016	248487016	+	Silent	SNP	C	C	T	rs4451579	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248487016C>T	ENST00000317965.2	-	1	883	c.855G>A	c.(853-855)ctG>ctA	p.L285L		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	285						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGAGAGGATTCAGCATGGGAG	0.433													.|||	1070	0.213658	0.0091	0.245	5008	,	,		19077	0.3641		0.172	False		,,,				2504	0.3558				p.L285L		Atlas-SNP	.											.	OR2M7	84	.	0			c.G855A						PASS	.	C		194,4212	120.8+/-158.4	4,186,2013	100.0	93.0	96.0		855	-1.1	0.7	1	dbSNP_111	96	1451,7149	277.8+/-293.0	125,1201,2974	no	coding-synonymous	OR2M7	NM_001004691.1		129,1387,4987	TT,TC,CC		16.8721,4.4031,12.648		285/313	248487016	1645,11361	2203	4300	6503	SO:0001819	synonymous_variant	391196	exon1			AGGATTCAGCATG	BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"""GPCR / Class A : Olfactory receptors"""	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.855G>A	1.37:g.248487016C>T		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	261	130	0.498084	NM_001004691	B2RNL0|Q6IEX6	Silent	SNP	ENST00000317965.2	37	CCDS31111.1																																																																																			C|0.847;T|0.153	0.153	strong		0.433	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691	
SLC3A2	6520	hgsc.bcm.edu	37	11	62652779	62652779	+	Silent	SNP	C	C	T	rs4726	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62652779C>T	ENST00000377890.2	+	9	1420	c.1252C>T	c.(1252-1254)Cta>Tta	p.L418L	SLC3A2_ENST00000538682.1_3'UTR|SLC3A2_ENST00000535296.1_Silent_p.L387L|SLC3A2_ENST00000377892.1_Silent_p.L449L|SLC3A2_ENST00000338663.7_Silent_p.L317L|SLC3A2_ENST00000377891.2_Silent_p.L419L|SLC3A2_ENST00000377889.2_Silent_p.L356L|SLC3A2_ENST00000536981.1_5'UTR	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	418					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						TACAAAATCCCTAGTCACACA	0.502													C|||	632	0.126198	0.0151	0.134	5008	,	,		21584	0.2014		0.2475	False		,,,				2504	0.0685				p.L419L		Atlas-SNP	.											.	SLC3A2	55	.	0			c.C1255T						PASS	.	C	,,,	238,4164	138.0+/-173.8	11,216,1974	97.0	96.0	97.0		1255,1066,949,1252	2.2	0.1	11	dbSNP_52	97	2008,6588	350.6+/-327.9	231,1546,2521	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC3A2	NM_001012662.2,NM_001012664.2,NM_001013251.2,NM_002394.5	,,,	242,1762,4495	TT,TC,CC		23.3597,5.4066,17.2796	,,,	419/632,356/569,317/530,418/631	62652779	2246,10752	2201	4298	6499	SO:0001819	synonymous_variant	6520	exon9			AAATCCCTAGTCA		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"""Solute carriers"""	11026	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43"", ""antigen defined by monoclonal antibody 4F2"", ""heavy chain"", ""4F2 heavy chain"", ""CD98 heavy chain"", ""monoclonal antibody 44D7"", ""4F2 cell-surface antigen heavy chain"", ""lymphocyte activation antigen 4F2 large subunit"""	158070	"""solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"""	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.1252C>T	11.37:g.62652779C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	182	99	0.543956	NM_001012662	Q13543	Silent	SNP	ENST00000377890.2	37	CCDS8039.2	358	0.16391941391941392	15	0.03048780487804878	54	0.14917127071823205	102	0.17832167832167833	187	0.24670184696569922	C	11.49	1.654527	0.29425	0.054066	0.233597	ENSG00000168003	ENST00000539507	.	.	.	4.31	2.25	0.28309	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53688	P	2.199999999996649E-5	.	.	.	.	.	.	T	0.21143	-1.0254	3	.	.	.	-4.2211	5.4395	0.16500	0.0:0.7379:0.0:0.2621	rs4726;rs1050652;rs3168079;rs17543270;rs4726	.	.	.	L	44	.	.	P	+	2	0	SLC3A2	62409355	0.000000	0.05858	0.062000	0.19696	0.883000	0.51084	-0.513000	0.06305	1.026000	0.39733	0.313000	0.20887	CCT	C|0.834;A|0.001	.	strong		0.502	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661	
FBXO34	55030	hgsc.bcm.edu	37	14	55818706	55818706	+	Missense_Mutation	SNP	T	T	C	rs3742569	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:55818706T>C	ENST00000313833.4	+	2	1843	c.1598T>C	c.(1597-1599)cTg>cCg	p.L533P	FBXO34_ENST00000440021.1_Missense_Mutation_p.L533P	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	533			L -> P (in dbSNP:rs3742569). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.					p.L533P(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						CCATTTGTACTGCCAGCCTCT	0.502													t|||	1992	0.397764	0.4713	0.3314	5008	,	,		19439	0.3185		0.4245	False		,,,				2504	0.3998				p.L533P		Atlas-SNP	.											FBXO34,NS,carcinoma,0,1	FBXO34	61	1	1	Substitution - Missense(1)	stomach(1)	c.T1598C						PASS	.	C	PRO/LEU,PRO/LEU	1984,2422	617.4+/-393.0	424,1136,643	130.0	126.0	127.0		1598,1598	-1.4	0.0	14	dbSNP_107	127	3629,4971	625.6+/-397.7	784,2061,1455	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	98,98	1208,3197,2098	CC,CT,TT		42.1977,45.0295,43.157	benign,benign	533/712,533/712	55818706	5613,7393	2203	4300	6503	SO:0001583	missense	55030	exon2			TTGTACTGCCAGC	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1598T>C	14.37:g.55818706T>C	ENSP00000313159:p.Leu533Pro	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	215	103	0.47907	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	857	0.3923992673992674	224	0.45528455284552843	119	0.3287292817679558	191	0.3339160839160839	323	0.4261213720316623	C	0.442	-0.898108	0.02472	0.450295	0.421977	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.20069	2.1;2.1	5.49	-1.35	0.09114	.	0.711289	0.12725	N	0.444330	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45512	-0.9256	9	0.42905	T	0.14	-15.7575	11.6878	0.51497	0.0:0.3231:0.0:0.6769	rs3742569;rs17674206;rs52807065;rs61280222;rs3742569	533	Q9NWN3	FBX34_HUMAN	P	533	ENSP00000313159:L533P;ENSP00000394117:L533P	ENSP00000313159:L533P	L	+	2	0	FBXO34	54888459	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.774000	0.04684	-0.553000	0.06158	-0.716000	0.03619	CTG	T|0.582;C|0.418	0.418	strong		0.502	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
DNM1L	10059	hgsc.bcm.edu	37	12	32854366	32854366	+	Silent	SNP	A	A	C	rs10844308	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:32854366A>C	ENST00000549701.1	+	2	194	c.120A>C	c.(118-120)tcA>tcC	p.S40S	DNM1L_ENST00000548671.1_3'UTR|DNM1L_ENST00000452533.2_Silent_p.S40S|DNM1L_ENST00000547312.1_Silent_p.S40S|DNM1L_ENST00000414834.2_5'UTR|DNM1L_ENST00000553257.1_Silent_p.S40S|DNM1L_ENST00000381000.4_Silent_p.S40S|DNM1L_ENST00000266481.6_Silent_p.S40S|DNM1L_ENST00000358214.5_Silent_p.S40S			O00429	DNM1L_HUMAN	dynamin 1-like	40	Dynamin-type G.|GTPase domain.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GAAAGAGCTCAGTGCTAGAAA	0.423													a|||	634	0.126597	0.177	0.0937	5008	,	,		14408	0.0813		0.161	False		,,,				2504	0.093				p.S40S		Atlas-SNP	.											.	DNM1L	52	.	0			c.A120C						PASS	.		,,	721,3685	297.3+/-284.7	57,607,1539	66.0	72.0	70.0		120,120,120	0.2	1.0	12	dbSNP_120	70	1248,7352	250.1+/-277.1	105,1038,3157	no	coding-synonymous,coding-synonymous,coding-synonymous	DNM1L	NM_005690.3,NM_012062.3,NM_012063.2	,,	162,1645,4696	CC,CA,AA		14.5116,16.364,15.1392	,,	40/700,40/737,40/711	32854366	1969,11037	2203	4300	6503	SO:0001819	synonymous_variant	10059	exon2			GAGCTCAGTGCTA	AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.120A>C	12.37:g.32854366A>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	85	49	0.576471	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Silent	SNP	ENST00000549701.1	37	CCDS8729.1																																																																																			A|0.858;C|0.142	0.142	strong		0.423	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062	
GALNS	2588	hgsc.bcm.edu	37	16	88891240	88891240	+	Missense_Mutation	SNP	C	C	A	rs2303269	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:88891240C>A	ENST00000268695.5	-	11	1265	c.1177G>T	c.(1177-1179)Gcc>Tcc	p.A393S	GALNS_ENST00000542788.1_Missense_Mutation_p.A318S	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	393			A -> S (in dbSNP:rs2303269). {ECO:0000269|PubMed:16287098, ECO:0000269|PubMed:9452036}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		CCGAGGGTGGCCGCCATCAGC	0.632													C|||	293	0.0585064	0.034	0.0807	5008	,	,		14790	0.0506		0.0527	False		,,,				2504	0.09				p.A393S	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											.	GALNS	37	.	0			c.G1177T						PASS	.	C	SER/ALA	191,4205	121.3+/-158.8	1,189,2008	107.0	86.0	93.0		1177	1.6	0.0	16	dbSNP_100	93	424,8176	131.0+/-188.9	7,410,3883	yes	missense	GALNS	NM_000512.4	99	8,599,5891	AA,AC,CC		4.9302,4.3449,4.7322	possibly-damaging	393/523	88891240	615,12381	2198	4300	6498	SO:0001583	missense	2588	exon11			GGGTGGCCGCCAT	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"""Arylsulfatase family"""	4122	protein-coding gene	gene with protein product	"""Morquio syndrome"", ""mucopolysaccharidosis type IVA"""	612222	"""galactosamine (N-acetyl)-6-sulfate sulfatase"""			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.1177G>T	16.37:g.88891240C>A	ENSP00000268695:p.Ala393Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_000512	Q86VK3	Missense_Mutation	SNP	ENST00000268695.5	37	CCDS10970.1	115	0.052655677655677656	24	0.04878048780487805	33	0.09116022099447514	17	0.02972027972027972	41	0.05408970976253298	C	8.597	0.886018	0.17540	0.043449	0.049302	ENSG00000141012	ENST00000268695;ENST00000542788	D;D	0.90261	-2.64;-2.64	4.68	1.61	0.23674	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.517005	0.19715	N	0.107728	T	0.27419	0.0673	L	0.56769	1.78	0.19775	N	0.999959	B;B	0.17038	0.011;0.02	B;B	0.17979	0.02;0.02	T	0.63010	-0.6732	10	0.72032	D	0.01	.	10.1583	0.42836	0.0:0.7714:0.0:0.2286	rs2303269	393;393	B2R6P1;P34059	.;GALNS_HUMAN	S	393;318	ENSP00000268695:A393S;ENSP00000438197:A318S	ENSP00000268695:A393S	A	-	1	0	GALNS	87418741	0.984000	0.35163	0.016000	0.15963	0.036000	0.12997	2.679000	0.46909	0.137000	0.18759	-0.355000	0.07637	GCC	C|0.952;A|0.048	0.048	strong		0.632	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1		
LGI4	163175	hgsc.bcm.edu	37	19	35617639	35617639	+	Silent	SNP	C	C	G	rs1687998	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:35617639C>G	ENST00000310123.3	-	8	1353	c.834G>C	c.(832-834)ccG>ccC	p.P278P	LGI4_ENST00000392225.3_Missense_Mutation_p.R304P|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	278					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CGAAGAGGCTCGGGCCCAGCA	0.741													C|||	1718	0.343051	0.2965	0.2493	5008	,	,		12239	0.254		0.3708	False		,,,				2504	0.5358				p.P278P		Atlas-SNP	.											.	LGI4	32	.	0			c.G834C						PASS	.	C		730,2116		146,438,839	2.0	3.0	3.0		834	-8.7	0.4	19	dbSNP_89	3	1965,4439		401,1163,1638	no	coding-synonymous	LGI4	NM_139284.2		547,1601,2477	GG,GC,CC		30.6839,25.65,29.1351		278/538	35617639	2695,6555	1423	3202	4625	SO:0001819	synonymous_variant	163175	exon8			GAGGCTCGGGCCC	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.834G>C	19.37:g.35617639C>G		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	10	5	0.5	NM_139284	B2RN53|B9EGS7|Q5M8T1	Silent	SNP	ENST00000310123.3	37	CCDS12444.1	663	0.30357142857142855	157	0.31910569105691056	85	0.23480662983425415	131	0.229020979020979	290	0.38258575197889183	C	8.226	0.803486	0.16397	0.2565	0.306839	ENSG00000153902	ENST00000392225	T	0.63417	-0.04	4.35	-8.69	0.00855	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.39978	P	0.025124000000000035	.	.	.	.	.	.	T	0.14172	-1.0482	4	.	.	.	.	7.4446	0.27203	0.0993:0.1544:0.588:0.1583	rs1687998;rs17712562;rs59273846	.	.	.	P	304	ENSP00000376059:R304P	.	R	-	2	0	LGI4	40309479	0.000000	0.05858	0.378000	0.26068	0.633000	0.38033	-0.796000	0.04575	-1.234000	0.02548	-0.802000	0.03209	CGA	C|0.694;G|0.306	0.306	strong		0.741	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1		
NFKBIE	4794	hgsc.bcm.edu	37	6	44232977	44232977	+	Missense_Mutation	SNP	G	G	A	rs2233433	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:44232977G>A	ENST00000275015.5	-	1	523	c.524C>T	c.(523-525)cCa>cTa	p.P175L		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	175					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCCGGAGGCTGGAGCCGAGGT	0.697													G|||	265	0.0529153	0.0	0.0375	5008	,	,		12905	0.1667		0.0497	False		,,,				2504	0.0215				p.P175L		Atlas-SNP	.											.	NFKBIE	31	.	0			c.C524T						PASS	.	G	LEU/PRO	38,4158		0,38,2060	12.0	16.0	15.0		524	1.3	0.0	6	dbSNP_98	15	290,7986		7,276,3855	yes	missense	NFKBIE	NM_004556.2	98	7,314,5915	AA,AG,GG		3.5041,0.9056,2.6299	benign	175/501	44232977	328,12144	2098	4138	6236	SO:0001583	missense	4794	exon1			GAGGCTGGAGCCG	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"""Ankyrin repeat domain containing"""	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.524C>T	6.37:g.44232977G>A	ENSP00000275015:p.Pro175Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_004556	Q5T9V9	Missense_Mutation	SNP	ENST00000275015.5	37	CCDS34463.1	136	0.06227106227106227	0	0.0	8	0.022099447513812154	94	0.16433566433566432	34	0.044854881266490766	G	12.07	1.828098	0.32329	0.009056	0.035041	ENSG00000146232	ENST00000275015	T	0.22945	1.93	4.78	1.34	0.21922	.	1.063800	0.07345	N	0.881411	T	0.05456	0.0144	N	0.20986	0.625	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.06405	0.002	T	0.39057	-0.9632	9	0.25106	T	0.35	-20.0442	6.411	0.21690	0.2011:0.1582:0.6408:0.0	rs2233433;rs2233433	175	O00221	IKBE_HUMAN	L	175	ENSP00000275015:P175L	ENSP00000275015:P175L	P	-	2	0	NFKBIE	44340955	0.001000	0.12720	0.000000	0.03702	0.056000	0.15407	0.729000	0.26028	0.404000	0.25506	0.561000	0.74099	CCA	G|0.930;A|0.070	0.070	strong		0.697	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2		
HS1BP3	64342	hgsc.bcm.edu	37	2	20838318	20838318	+	Silent	SNP	G	G	A	rs3796064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:20838318G>A	ENST00000304031.3	-	4	526	c.501C>T	c.(499-501)ttC>ttT	p.F167F	HS1BP3_ENST00000402541.1_Silent_p.F167F	NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	167							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAAAAAGTCGAAAGCCTCTT	0.587													G|||	1798	0.359026	0.2292	0.3055	5008	,	,		19367	0.5565		0.2763	False		,,,				2504	0.454				p.F167F		Atlas-SNP	.											.	HS1BP3	33	.	0			c.C501T						PASS	.	G		985,3421	367.3+/-318.2	117,751,1335	155.0	141.0	146.0		501	-8.4	0.8	2	dbSNP_107	146	2254,6346	381.0+/-339.9	298,1658,2344	no	coding-synonymous	HS1BP3	NM_022460.3		415,2409,3679	AA,AG,GG		26.2093,22.3559,24.9039		167/393	20838318	3239,9767	2203	4300	6503	SO:0001819	synonymous_variant	64342	exon4			AAAGTCGAAAGCC		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.501C>T	2.37:g.20838318G>A		Somatic	279	1	0.00358423		WXS	Illumina HiSeq	Phase_I	324	132	0.407407	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	37	CCDS1700.1																																																																																			G|0.702;A|0.298	0.298	strong		0.587	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
THAP4	51078	hgsc.bcm.edu	37	2	242572846	242572846	+	Silent	SNP	A	A	G	rs3208142	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242572846A>G	ENST00000407315.1	-	2	1157	c.726T>C	c.(724-726)tcT>tcC	p.S242S		NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	242							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		GGGTGTGCTTAGAGGAGAAAC	0.537													G|||	2144	0.428115	0.41	0.3429	5008	,	,		19156	0.5665		0.3181	False		,,,				2504	0.4836				p.S242S		Atlas-SNP	.											.	THAP4	27	.	0			c.T726C						PASS	.	G		1638,2768	657.4+/-400.2	300,1038,865	70.0	80.0	76.0		726	2.1	1.0	2	dbSNP_105	76	2586,6006	687.2+/-404.2	410,1766,2120	no	coding-synonymous	THAP4	NM_015963.5		710,2804,2985	GG,GA,AA		30.0978,37.1766,32.4973		242/578	242572846	4224,8774	2203	4296	6499	SO:0001819	synonymous_variant	51078	exon2			GTGCTTAGAGGAG	AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946		"""THAP (C2CH-type zinc finger) domain containing"""	23187	protein-coding gene	gene with protein product		612533				12575992, 10810093	Standard	NM_015963		Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000407315.1:c.726T>C	2.37:g.242572846A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_015963	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Silent	SNP	ENST00000407315.1	37	CCDS2551.1																																																																																			A|0.650;G|0.350	0.350	strong		0.537	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963	
CCDC13	152206	hgsc.bcm.edu	37	3	42787467	42787467	+	Missense_Mutation	SNP	G	G	A	rs141737119	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:42787467G>A	ENST00000310232.6	-	7	856	c.773C>T	c.(772-774)tCg>tTg	p.S258L	CCDC13-AS1_ENST00000418161.1_RNA|CCDC13-AS1_ENST00000446950.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	258										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						GGTCCCTGGCGAAGATAGGAG	0.512																																					p.S258L		Atlas-SNP	.											CCDC13,colon,carcinoma,+1,1	CCDC13	71	1	0			c.C773T						PASS	.	G	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	92.0	89.0	90.0		773	3.3	0.4	3	dbSNP_134	90	2,8598	2.2+/-6.3	0,2,4298	no	missense	CCDC13	NM_144719.3	145	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	benign	258/716	42787467	3,13003	2203	4300	6503	SO:0001583	missense	152206	exon7			CCTGGCGAAGATA	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.773C>T	3.37:g.42787467G>A	ENSP00000309836:p.Ser258Leu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	37	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	G	8.690	0.907306	0.17833	2.27E-4	2.33E-4	ENSG00000244607	ENST00000310232	T	0.25085	1.82	5.08	3.27	0.37495	.	0.461691	0.22580	N	0.058238	T	0.22399	0.0540	L	0.52905	1.665	0.18873	N	0.999983	B	0.16396	0.017	B	0.12156	0.007	T	0.18777	-1.0326	10	0.26408	T	0.33	.	9.0645	0.36455	0.0787:0.0:0.7746:0.1466	.	258	Q8IYE1	CCD13_HUMAN	L	258	ENSP00000309836:S258L	ENSP00000309836:S258L	S	-	2	0	CCDC13	42762471	0.405000	0.25336	0.434000	0.26772	0.186000	0.23388	0.648000	0.24828	0.539000	0.28788	-0.137000	0.14449	TCG	G|1.000;A|0.000	0.000	strong		0.512	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
HHLA2	11148	hgsc.bcm.edu	37	3	108095365	108095365	+	Silent	SNP	G	G	A	rs2124736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:108095365G>A	ENST00000357759.5	+	9	1599	c.1185G>A	c.(1183-1185)gaG>gaA	p.E395E	HHLA2_ENST00000467761.1_Silent_p.E395E|HHLA2_ENST00000491820.1_Silent_p.E378E|HHLA2_ENST00000467562.1_Silent_p.E331E|HHLA2_ENST00000489514.2_Silent_p.E395E	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	395					positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						CTCCTGGTGAGCGCTGTCCCA	0.363													G|||	449	0.0896565	0.0136	0.1527	5008	,	,		19715	0.001		0.2326	False		,,,				2504	0.092				p.E395E		Atlas-SNP	.											.	HHLA2	95	.	0			c.G1185A						PASS	.	G		212,3540		5,202,1669	82.0	84.0	83.0		1185	-2.5	0.0	3	dbSNP_96	83	1901,6307		236,1429,2439	no	coding-synonymous	HHLA2	NM_007072.2		241,1631,4108	AA,AG,GG		23.1603,5.6503,17.6672		395/415	108095365	2113,9847	1876	4104	5980	SO:0001819	synonymous_variant	11148	exon9			TGGTGAGCGCTGT	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.1185G>A	3.37:g.108095365G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Silent	SNP	ENST00000357759.5	37	CCDS46883.1	256	0.11721611721611722	7	0.014227642276422764	64	0.17679558011049723	0	0.0	185	0.24406332453825857	G	1.601	-0.526518	0.04141	0.056503	0.231603	ENSG00000114455	ENST00000482099	.	.	.	3.44	-2.48	0.06423	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.34601	-0.9822	3	.	.	.	-15.1402	1.081	0.01643	0.2254:0.3121:0.3019:0.1606	rs2124736;rs17373363;rs2124736	.	.	.	T	298	.	.	A	+	1	0	HHLA2	109578055	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.141000	0.10327	-0.545000	0.06224	0.561000	0.74099	GCG	G|0.881;A|0.119	0.119	strong		0.363	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072	
C14orf159	80017	hgsc.bcm.edu	37	14	91681888	91681888	+	Silent	SNP	G	G	A	rs34424078	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:91681888G>A	ENST00000523771.1	+	13	2292	c.1689G>A	c.(1687-1689)ccG>ccA	p.P563P	C14orf159_ENST00000523816.1_Silent_p.P563P|C14orf159_ENST00000520328.1_Silent_p.P511P|C14orf159_ENST00000525393.2_Silent_p.P439P|C14orf159_ENST00000256324.10_Silent_p.P568P|C14orf159_ENST00000522322.1_Silent_p.P563P|C14orf159_ENST00000428926.2_Silent_p.P563P|C14orf159_ENST00000412671.2_Silent_p.P568P|C14orf159_ENST00000518868.1_Silent_p.P568P|C14orf159_ENST00000521077.2_Silent_p.P528P			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	563						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		AGGCCCTCCCGTCGGTCATTA	0.597													G|||	413	0.0824681	0.0121	0.1254	5008	,	,		16399	0.0516		0.0895	False		,,,				2504	0.1718				p.P568P		Atlas-SNP	.											.	C14orf159	57	.	0			c.G1704A						PASS	.	G	,,,,	129,4277	93.4+/-132.2	2,125,2076	56.0	55.0	55.0		1689,1689,1704,1533,1689	-10.5	0.0	14	dbSNP_126	55	722,7878	176.5+/-226.3	35,652,3613	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	37,777,5689	AA,AG,GG		8.3953,2.9278,6.5431	,,,,	563/617,563/617,568/622,511/565,563/617	91681888	851,12155	2203	4300	6503	SO:0001819	synonymous_variant	80017	exon13			CCTCCCGTCGGTC	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1689G>A	14.37:g.91681888G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	33	20	0.606061	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	143	0.06547619047619048	8	0.016260162601626018	35	0.09668508287292818	32	0.055944055944055944	68	0.08970976253298153	G	5.806	0.333064	0.11013	0.029278	0.083953	ENSG00000133943	ENST00000522816	.	.	.	5.45	-10.5	0.00291	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.27654	N	0.947302	.	.	.	.	.	.	T	0.11036	-1.0604	4	.	.	.	.	1.9974	0.03459	0.2148:0.2977:0.3285:0.1591	rs34424078	.	.	.	H	164	.	.	R	+	2	0	C14orf159	90751641	0.003000	0.15002	0.021000	0.16686	0.007000	0.05969	-1.710000	0.01888	-1.122000	0.02945	-0.345000	0.07892	CGT	G|0.936;A|0.064	0.064	strong		0.597	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
STARD13	90627	hgsc.bcm.edu	37	13	33703656	33703656	+	Silent	SNP	T	T	C	rs495680	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:33703656T>C	ENST00000336934.5	-	5	1274	c.1158A>G	c.(1156-1158)gaA>gaG	p.E386E	STARD13_ENST00000399365.3_Silent_p.E268E|STARD13_ENST00000255486.4_Silent_p.E378E	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	386					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GGGAGTGAAATTCATGCATAC	0.537													C|||	2582	0.515575	0.3275	0.621	5008	,	,		18928	0.5407		0.6103	False		,,,				2504	0.5716				p.E386E		Atlas-SNP	.											.	STARD13	100	.	0			c.A1158G						PASS	.	C	,,	1688,2718	651.8+/-399.3	303,1082,818	71.0	72.0	72.0		804,1158,1134	0.6	0.1	13	dbSNP_83	72	5395,3205	481.4+/-370.6	1717,1961,622	yes	coding-synonymous,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	2020,3043,1440	CC,CT,TT		37.2674,38.3114,45.5405	,,	268/996,386/1114,378/1106	33703656	7083,5923	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon5			GTGAAATTCATGC	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.1158A>G	13.37:g.33703656T>C		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			T|0.463;C|0.537	0.537	strong		0.537	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
CXCR5	643	hgsc.bcm.edu	37	11	118765108	118765108	+	Silent	SNP	G	G	A	rs113967672	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:118765108G>A	ENST00000292174.4	+	2	1031	c.855G>A	c.(853-855)gcG>gcA	p.A285A	BCL9L_ENST00000334801.3_3'UTR	NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	285					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		ACACCCTGGCGAGGCTGAAGG	0.602													G|||	5	0.000998403	0.0	0.0014	5008	,	,		22112	0.0		0.004	False		,,,				2504	0.0				p.A285A		Atlas-SNP	.											CXCR5,NS,carcinoma,+1,1	CXCR5	34	1	0			c.G855A						PASS	.	G	,	3,4397	8.1+/-20.4	0,3,2197	142.0	108.0	119.0		855,720	-2.9	0.0	11	dbSNP_132	119	36,8554	24.0+/-70.4	0,36,4259	no	coding-synonymous,coding-synonymous	CXCR5	NM_001716.4,NM_032966.2	,	0,39,6456	AA,AG,GG		0.4191,0.0682,0.3002	,	285/373,240/328	118765108	39,12951	2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			CCTGGCGAGGCTG	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	1060	protein-coding gene	gene with protein product		601613	"""Burkitt lymphoma receptor 1, GTP-binding protein"", ""Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"""	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.855G>A	11.37:g.118765108G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	135	62	0.459259	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			G|0.997;A|0.003	0.003	strong		0.602	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716	
DHX34	9704	hgsc.bcm.edu	37	19	47858489	47858489	+	Missense_Mutation	SNP	C	C	G	rs34802163	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:47858489C>G	ENST00000328771.4	+	3	1248	c.899C>G	c.(898-900)cCc>cGc	p.P300R		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	300	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		CGCCTGTTGCCCACGCGGCCT	0.587													C|||	66	0.0131789	0.0008	0.0115	5008	,	,		16986	0.001		0.0318	False		,,,				2504	0.0245				p.P300R		Atlas-SNP	.											DHX34,lower_third,carcinoma,-1,1	DHX34	98	1	0			c.C899G						PASS	.	C	ARG/PRO	21,4385	29.9+/-59.1	1,19,2183	133.0	115.0	121.0		899	4.4	1.0	19	dbSNP_126	121	258,8342	101.4+/-162.7	3,252,4045	yes	missense	DHX34	NM_014681.5	103	4,271,6228	GG,GC,CC		3.0,0.4766,2.1452	benign	300/1144	47858489	279,12727	2203	4300	6503	SO:0001583	missense	9704	exon3			TGTTGCCCACGCG	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"""DEAH-boxes"""	16719	protein-coding gene	gene with protein product		615475	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"""	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.899C>G	19.37:g.47858489C>G	ENSP00000331907:p.Pro300Arg	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_014681	B4DMY8	Missense_Mutation	SNP	ENST00000328771.4	37	CCDS12700.1	35	0.016025641025641024	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	27	0.03562005277044855	C	10.91	1.484804	0.26598	0.004766	0.03	ENSG00000134815	ENST00000328771;ENST00000257252	T	0.26373	1.74	4.41	4.41	0.53225	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.359689	0.23656	N	0.045867	T	0.04861	0.0131	N	0.02697	-0.525	0.36709	D	0.880551	B;D	0.62365	0.238;0.991	B;P	0.61658	0.126;0.892	T	0.18398	-1.0338	10	0.35671	T	0.21	0.6401	9.6656	0.39983	0.0:0.9004:0.0:0.0996	rs34802163;rs61750959	300;300	Q14147;B4E3G3	DHX34_HUMAN;.	R	300	ENSP00000331907:P300R	ENSP00000257252:P300R	P	+	2	0	DHX34	52550329	0.920000	0.31207	0.984000	0.44739	0.859000	0.49053	2.414000	0.44627	2.010000	0.58986	0.456000	0.33151	CCC	C|0.979;G|0.021	0.021	strong		0.587	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
CAGE1	285782	hgsc.bcm.edu	37	6	7387236	7387236	+	Silent	SNP	G	G	A	rs9406026	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:7387236G>A	ENST00000512086.1	-	2	373	c.171C>T	c.(169-171)acC>acT	p.T57T	CAGE1_ENST00000338150.4_Silent_p.T57T|CAGE1_ENST00000296742.7_Intron|RIOK1_ENST00000379834.2_5'Flank|CAGE1_ENST00000379918.4_Silent_p.T57T|CAGE1_ENST00000509324.1_5'UTR|CAGE1_ENST00000502583.1_Silent_p.T57T			Q8TC20	CAGE1_HUMAN	cancer antigen 1	57										breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					AAGTGGTGCCGGTGGTTTCCA	0.403													G|||	1871	0.373602	0.3079	0.4337	5008	,	,		19276	0.4504		0.3638	False		,,,				2504	0.3507				p.T57T		Atlas-SNP	.											.	CAGE1	165	.	0			c.C171T						PASS	.						197.0	178.0	184.0					6																	7387236		692	1591	2283	SO:0001819	synonymous_variant	285782	exon2			GGTGCCGGTGGTT	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"""cancer/testis antigen 95"""	608304	"""cancer/testis antigen 3"""	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.171C>T	6.37:g.7387236G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Silent	SNP	ENST00000512086.1	37																																																																																				G|0.618;A|0.382	0.382	strong		0.403	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745	
CRELD1	78987	hgsc.bcm.edu	37	3	9985656	9985656	+	Intron	SNP	C	C	T	rs3774207	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9985656C>T	ENST00000383811.3	+	10	1647				CRELD1_ENST00000452070.1_Intron|CRELD1_ENST00000489674.1_Intron|CRELD1_ENST00000326434.5_Silent_p.H373H|CRELD1_ENST00000397170.3_Intron	NM_015513.4	NP_056328	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1						cardiac septum development (GO:0003279)|endocardial cushion development (GO:0003197)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.H373H(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|urinary_tract(1)	14						ctcatccccactctacatatg	0.468													T|||	1903	0.379992	0.8132	0.3256	5008	,	,		21784	0.1558		0.2107	False		,,,				2504	0.2382				p.H373H		Atlas-SNP	.											CRELD1,NS,carcinoma,0,1	CRELD1	48	1	1	Substitution - coding silent(1)	stomach(1)	c.C1119T						PASS	.	T	,,	3129,1277	435.9+/-344.5	1114,901,188	103.0	101.0	102.0		1119,,	-1.3	0.0	3	dbSNP_107	102	2145,6455	714.7+/-406.0	277,1591,2432	no	coding-synonymous,intron,intron	CRELD1	NM_001031717.3,NM_001077415.2,NM_015513.4	,,	1391,2492,2620	TT,TC,CC		24.9419,28.9832,40.5505	,,	373/423,,	9985656	5274,7732	2203	4300	6503	SO:0001627	intron_variant	78987	exon11			TCCCCACTCTACA	AF452623	CCDS2593.1, CCDS33693.1	3p25.3	2005-12-08	2004-02-13		ENSG00000163703	ENSG00000163703			14630	protein-coding gene	gene with protein product		607170	"""atrioventricular septal defect 2"""	AVSD2		10922384, 12137942	Standard	NM_015513		Approved		uc003buf.3	Q96HD1	OTTHUMG00000128653	ENST00000383811.3:c.1049-393C>T	3.37:g.9985656C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	124	52	0.419355	NM_001031717	A8MX90|B2RAA9|Q6I9X5|Q8NFT4|Q9Y409	Silent	SNP	ENST00000383811.3	37	CCDS2593.1																																																																																			C|0.600;T|0.400	0.400	strong		0.468	CRELD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250533.1	NM_015513	
PGR	5241	hgsc.bcm.edu	37	11	100999245	100999245	+	Missense_Mutation	SNP	G	G	A	rs11571145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:100999245G>A	ENST00000325455.5	-	1	2010	c.557C>T	c.(556-558)cCc>cTc	p.P186L	PGR_ENST00000263463.5_Missense_Mutation_p.P186L|PGR_ENST00000534013.1_Intron	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	186	Modulating, Pro-Rich.		P -> L (in dbSNP:rs11571145). {ECO:0000269|Ref.8}.		cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	CAGGCCCCGGGGCAGCACTTT	0.721													G|||	24	0.00479233	0.0008	0.0086	5008	,	,		13887	0.0		0.0119	False		,,,				2504	0.0051				p.P186L	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											PGR,NS,carcinoma,0,1	PGR	115	1	0			c.C557T						PASS	.	G	LEU/PRO,LEU/PRO	6,4072		0,6,2033	5.0	7.0	6.0		557,65	2.7	0.8	11	dbSNP_120	6	97,8103		0,97,4003	yes	missense,missense	PGR	NM_000926.4,NM_001202474.1	98,98	0,103,6036	AA,AG,GG		1.1829,0.1471,0.8389	possibly-damaging,possibly-damaging	186/934,22/770	100999245	103,12175	2039	4100	6139	SO:0001583	missense	5241	exon1			CCCCGGGGCAGCA	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.557C>T	11.37:g.100999245G>A	ENSP00000325120:p.Pro186Leu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	14	6	0.428571	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	14.65	2.598041	0.46318	0.001471	0.011829	ENSG00000082175	ENST00000325455;ENST00000263463;ENST00000537623	T;T	0.18657	2.2;2.2	3.62	2.65	0.31530	.	1.295630	0.05245	N	0.512963	T	0.25680	0.0625	M	0.70275	2.135	0.46078	D	0.998855	B;B	0.31413	0.322;0.322	B;B	0.39876	0.312;0.312	T	0.11542	-1.0583	10	0.87932	D	0	.	8.4855	0.33069	0.0:0.0:0.5311:0.4689	rs11571145;rs11571145	186;186	Q8TDS3;P06401	.;PRGR_HUMAN	L	186	ENSP00000325120:P186L;ENSP00000263463:P186L	ENSP00000263463:P186L	P	-	2	0	PGR	100504455	1.000000	0.71417	0.840000	0.33206	0.780000	0.44128	3.317000	0.51968	0.788000	0.33755	0.561000	0.74099	CCC	G|0.994;A|0.006	0.006	strong		0.721	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
OR8A1	390275	hgsc.bcm.edu	37	11	124440362	124440362	+	Missense_Mutation	SNP	C	C	G	rs55861866	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124440362C>G	ENST00000284287.3	+	1	470	c.398C>G	c.(397-399)aCa>aGa	p.T133R		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	133			T -> R (in dbSNP:rs55861866).		axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		TACATGCTGACAGTGATGGCC	0.478													C|||	1363	0.272165	0.0726	0.3847	5008	,	,		24437	0.2659		0.3598	False		,,,				2504	0.3783				p.T133R		Atlas-SNP	.											OR8A1,colon,carcinoma,+1,1	OR8A1	61	1	0			c.C398G						PASS	.	C	ARG/THR	578,3824	257.7+/-262.0	42,494,1665	174.0	146.0	156.0		398	3.2	0.6	11	dbSNP_129	156	2985,5613	463.4+/-366.0	530,1925,1844	yes	missense	OR8A1	NM_001005194.1	71	572,2419,3509	GG,GC,CC		34.7174,13.1304,27.4077	probably-damaging	133/327	124440362	3563,9437	2201	4299	6500	SO:0001583	missense	390275	exon1			TGCTGACAGTGAT	BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"""GPCR / Class A : Olfactory receptors"""	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.398C>G	11.37:g.124440362C>G	ENSP00000284287:p.Thr133Arg	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	159	76	0.477987	NM_001005194	Q6IEW7|Q96RC6	Missense_Mutation	SNP	ENST00000284287.3	37	CCDS31712.1	609	0.27884615384615385	43	0.08739837398373984	136	0.3756906077348066	163	0.28496503496503495	267	0.35224274406332456	C	18.12	3.552723	0.65425	0.131304	0.347174	ENSG00000196119	ENST00000284287	T	0.01359	4.98	5.03	3.17	0.36434	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000211	T	0.00012	0.0000	H	0.95187	3.635	0.27424	P	0.9542106	P	0.52842	0.956	P	0.58266	0.836	T	0.33059	-0.9883	9	0.87932	D	0	.	7.485	0.27427	0.0:0.7083:0.1377:0.154	rs55861866;rs56775161;rs61748725	133	Q8NGG7	OR8A1_HUMAN	R	133	ENSP00000284287:T133R	ENSP00000284287:T133R	T	+	2	0	OR8A1	123945572	0.734000	0.28142	0.646000	0.29493	0.982000	0.71751	3.401000	0.52601	0.707000	0.31934	0.650000	0.86243	ACA	C|0.718;G|0.282	0.282	strong		0.478	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194	
PDZD2	23037	hgsc.bcm.edu	37	5	32087808	32087808	+	Silent	SNP	G	G	C	rs3733720	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:32087808G>C	ENST00000438447.1	+	20	4642	c.4254G>C	c.(4252-4254)ggG>ggC	p.G1418G	PDZD2_ENST00000282493.3_Silent_p.G1418G			O15018	PDZD2_HUMAN	PDZ domain containing 2	1418					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GCCCAGGGGGGAGTAGAGAGA	0.602													G|||	589	0.117612	0.0439	0.1441	5008	,	,		19185	0.2371		0.0755	False		,,,				2504	0.1186				p.G1418G		Atlas-SNP	.											.	PDZD2	306	.	0			c.G4254C						PASS	.																																			SO:0001819	synonymous_variant	23037	exon19			AGGGGGGAGTAGA	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.4254G>C	5.37:g.32087808G>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			G|0.891;C|0.109	0.109	strong		0.602	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
PCSK5	5125	hgsc.bcm.edu	37	9	78506187	78506187	+	Silent	SNP	T	T	C	rs7040769	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:78506187T>C	ENST00000545128.1	+	1	628	c.90T>C	c.(88-90)tgT>tgC	p.C30C	PCSK5_ENST00000376752.4_Silent_p.C30C|PCSK5_ENST00000376767.3_Silent_p.C30C	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	30					anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						TCCCCGTGTGTCGGACGCGCG	0.672													C|||	962	0.192093	0.525	0.1124	5008	,	,		12372	0.0		0.1441	False		,,,				2504	0.046				p.C30C		Atlas-SNP	.											.	PCSK5	329	.	0			c.T90C						PASS	.	C	,	2039,2365	580.3+/-385.1	491,1057,654	43.0	52.0	49.0		90,90	3.9	1.0	9	dbSNP_116	49	1231,7369	738.2+/-407.0	86,1059,3155	no	coding-synonymous,coding-synonymous	PCSK5	NM_001190482.1,NM_006200.3	,	577,2116,3809	CC,CT,TT		14.314,46.2988,25.1461	,	30/1861,30/914	78506187	3270,9734	2202	4300	6502	SO:0001819	synonymous_variant	5125	exon1			CGTGTGTCGGACG		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.90T>C	9.37:g.78506187T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			T|0.760;C|0.240	0.240	strong		0.672	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SNCG	6623	hgsc.bcm.edu	37	10	88722398	88722398	+	Missense_Mutation	SNP	A	A	T	rs9864	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:88722398A>T	ENST00000372017.3	+	4	371	c.329A>T	c.(328-330)gAg>gTg	p.E110V	SNCG_ENST00000483064.1_3'UTR|SNCG_ENST00000348795.4_Nonstop_Mutation_p.*127C	NM_003087.2	NP_003078.2	O76070	SYUG_HUMAN	synuclein, gamma (breast cancer-specific protein 1)	110			E -> V (in dbSNP:rs9864). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9737786}.		adult locomotory behavior (GO:0008344)|aggressive behavior (GO:0002118)|cellular response to hydrostatic pressure (GO:0071464)|protein secretion (GO:0009306)|regulation of dopamine secretion (GO:0014059)|regulation of neurotransmitter secretion (GO:0046928)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				endometrium(1)|skin(1)	2						CAGGAGGGTGAGGCATCCAAA	0.612													a|||	1020	0.203674	0.1679	0.2233	5008	,	,		18772	0.0635		0.2336	False		,,,				2504	0.3517				p.E110V		Atlas-SNP	.											.	SNCG	8	.	0			c.A329T						PASS	.	A	VAL/GLU	824,3582	319.3+/-296.1	86,652,1465	87.0	103.0	98.0		329	2.6	0.0	10	dbSNP_52	98	2144,6456	358.5+/-331.2	247,1650,2403	yes	missense	SNCG	NM_003087.2	121	333,2302,3868	TT,TA,AA		24.9302,18.7018,22.8202	benign	110/128	88722398	2968,10038	2203	4300	6503	SO:0001583	missense	6623	exon4			AGGGTGAGGCATC	AF044311	CCDS7380.1	10q23.2-q23.3	2006-06-28			ENSG00000173267	ENSG00000173267			11141	protein-coding gene	gene with protein product	"""synoretin"""	602998				9044857, 9700196	Standard	NM_003087		Approved	BCSG1, SR, persyn	uc001keb.2	O76070	OTTHUMG00000018656	ENST00000372017.3:c.329A>T	10.37:g.88722398A>T	ENSP00000361087:p.Glu110Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	86	84	0.976744	NM_003087	O15104|Q96P61	Missense_Mutation	SNP	ENST00000372017.3	37	CCDS7380.1	398|398	0.18223443223443223|0.18223443223443223	82|82	0.16666666666666666|0.16666666666666666	94|94	0.2596685082872928|0.2596685082872928	38|38	0.06643356643356643|0.06643356643356643	184|184	0.24274406332453827|0.24274406332453827	A|A	5.966|5.966	0.362125|0.362125	0.11296|0.11296	0.187018|0.187018	0.249302|0.249302	ENSG00000173267|ENSG00000173267	ENST00000372017|ENST00000348795	D|.	0.84589|.	-1.87|.	3.81|3.81	2.63|2.63	0.31362|0.31362	.|.	1.114660|.	0.06941|.	N|.	0.812842|.	T|.	0.00012|.	0.0000|.	N|N	0.25647|0.25647	0.755|0.755	0.80722|0.80722	P|P	0.0|0.0	B|.	0.27286|.	0.174|.	B|.	0.30316|.	0.114|.	T|.	0.28073|.	-1.0055|.	9|.	0.36615|.	T|.	0.2|.	-0.49|-0.49	7.1573|7.1573	0.25645|0.25645	0.7705:0.2295:0.0:0.0|0.7705:0.2295:0.0:0.0	rs9864;rs1130096;rs3188626;rs9325593;rs11550196;rs17354005;rs17469989;rs60364371;rs9864|rs9864;rs1130096;rs3188626;rs9325593;rs11550196;rs17354005;rs17469989;rs60364371;rs9864	110|.	O76070|.	SYUG_HUMAN|.	V|C	110|127	ENSP00000361087:E110V|.	ENSP00000361087:E110V|.	E|X	+|+	2|3	0|0	SNCG|SNCG	88712378|88712378	0.082000|0.082000	0.21442|0.21442	0.003000|0.003000	0.11579|0.11579	0.453000|0.453000	0.32348|0.32348	1.097000|1.097000	0.30988|0.30988	0.791000|0.791000	0.33826|0.33826	0.482000|0.482000	0.46254|0.46254	GAG|TGA	A|0.789;T|0.211	0.211	strong		0.612	SNCG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049167.1		
PATE1	160065	hgsc.bcm.edu	37	11	125617610	125617610	+	Missense_Mutation	SNP	A	A	G	rs2114084	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:125617610A>G	ENST00000305738.5	+	4	152	c.140A>G	c.(139-141)cAg>cGg	p.Q47R	PATE1_ENST00000437148.2_Missense_Mutation_p.Q35R	NM_138294.2	NP_612151.1	Q8WXA2	PATE1_HUMAN	prostate and testis expressed 1	47			Q -> R (in dbSNP:rs2114084). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				large_intestine(1)|lung(5)	6						GAAATTGTTCAGTGTAGGATG	0.493													A|||	1690	0.33746	0.3797	0.2219	5008	,	,		20322	0.4375		0.2893	False		,,,				2504	0.3088				p.Q47R		Atlas-SNP	.											.	PATE1	21	.	0			c.A140G						PASS	.	A	ARG/GLN	1661,2741	505.2+/-366.1	329,1003,869	90.0	86.0	87.0		140	4.2	0.7	11	dbSNP_96	87	2480,6118	407.8+/-349.3	358,1764,2177	yes	missense	PATE1	NM_138294.2	43	687,2767,3046	GG,GA,AA		28.8439,37.7328,31.8538	possibly-damaging	47/127	125617610	4141,8859	2201	4299	6500	SO:0001583	missense	160065	exon4			TTGTTCAGTGTAG	AF462605	CCDS8464.1	11q24.2	2008-12-17				ENSG00000171053		"""PATE family"""	24664	protein-coding gene	gene with protein product	"""expressed in prostate and testis"""	606861				11880645, 15798027	Standard	NM_138294		Approved	PATE	uc001qct.3	Q8WXA2		ENST00000305738.5:c.140A>G	11.37:g.125617610A>G	ENSP00000307164:p.Gln47Arg	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_138294	Q3KNX2	Missense_Mutation	SNP	ENST00000305738.5	37	CCDS8464.1	724	0.3315018315018315	191	0.3882113821138211	96	0.26519337016574585	221	0.38636363636363635	216	0.2849604221635884	A	9.678	1.148572	0.21288	0.377328	0.288439	ENSG00000171053	ENST00000305738;ENST00000437148	T;T	0.34275	1.37;1.37	4.19	4.19	0.49359	.	0.229282	0.22480	N	0.059503	T	0.00012	0.0000	L	0.40543	1.245	0.38885	P	0.04301100000000002	D;D	0.71674	0.992;0.998	P;D	0.64776	0.876;0.929	T	0.44174	-0.9345	9	0.32370	T	0.25	0.6542	9.9222	0.41470	1.0:0.0:0.0:0.0	rs2114084;rs57813227;rs2114084	35;47	Q8WXA2-2;Q8WXA2	.;PATE1_HUMAN	R	47;35	ENSP00000307164:Q47R;ENSP00000396056:Q35R	ENSP00000307164:Q47R	Q	+	2	0	PATE1	125122820	0.341000	0.24801	0.664000	0.29753	0.188000	0.23474	1.778000	0.38614	2.115000	0.64714	0.533000	0.62120	CAG	A|0.675;G|0.325	0.325	strong		0.493	PATE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386726.2	NM_138294	
MRPL9	65005	hgsc.bcm.edu	37	1	151735604	151735604	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:151735604G>A	ENST00000368830.3	-	2	256	c.172C>T	c.(172-174)Cgc>Tgc	p.R58C	MRPL9_ENST00000368829.3_Missense_Mutation_p.R58C|OAZ3_ENST00000453029.2_5'Flank|MRPL9_ENST00000467306.1_5'UTR|OAZ3_ENST00000479764.1_5'Flank|RP11-98D18.3_ENST00000512280.1_RNA|RP11-98D18.2_ENST00000420382.1_RNA|OAZ3_ENST00000315067.8_5'UTR|OAZ3_ENST00000321531.5_5'UTR	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	58					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			TTCCACCAGCGCTCCACGATG	0.667																																					p.R58C		Atlas-SNP	.											MRPL9,colon,carcinoma,+1,1	MRPL9	21	1	0			c.C172T						scavenged	.						28.0	30.0	29.0					1																	151735604		2203	4299	6502	SO:0001583	missense	65005	exon2			ACCAGCGCTCCAC	AK026363	CCDS1003.1, CCDS72916.1	1q21	2012-09-13			ENSG00000143436	ENSG00000143436		"""Mitochondrial ribosomal proteins / large subunits"""	14277	protein-coding gene	gene with protein product		611824					Standard	XM_005245455		Approved		uc001eyv.3	Q9BYD2	OTTHUMG00000013063	ENST00000368830.3:c.172C>T	1.37:g.151735604G>A	ENSP00000357823:p.Arg58Cys	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	130	2	0.0153846	NM_031420	B2RD99|Q5SZR2|Q9BSW8	Missense_Mutation	SNP	ENST00000368830.3	37	CCDS1003.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.853832	0.91355	.	.	ENSG00000143436	ENST00000368830;ENST00000368829	T;T	0.54279	0.58;0.75	4.84	3.93	0.45458	.	0.000000	0.85682	D	0.000000	T	0.58409	0.2120	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.64037	-0.6501	10	0.87932	D	0	-6.5342	8.9501	0.35783	0.0997:0.0:0.9003:0.0	.	58;58;58	B4DDZ7;B4DUJ1;Q9BYD2	.;.;RM09_HUMAN	C	58	ENSP00000357823:R58C;ENSP00000357822:R58C	ENSP00000357822:R58C	R	-	1	0	MRPL9	150002228	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.582000	0.60957	1.273000	0.44346	-0.140000	0.14226	CGC	.	.	none		0.667	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2	NM_031420	
PBRM1	55193	hgsc.bcm.edu	37	3	52668638	52668638	+	Silent	SNP	G	G	A	rs17052357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52668638G>A	ENST00000296302.7	-	11	1282	c.1281C>T	c.(1279-1281)ccC>ccT	p.P427P	PBRM1_ENST00000356770.4_Silent_p.P395P|PBRM1_ENST00000337303.4_Silent_p.P427P|PBRM1_ENST00000409767.1_Silent_p.P427P|PBRM1_ENST00000409114.3_Silent_p.P427P|PBRM1_ENST00000410007.1_Silent_p.P427P|PBRM1_ENST00000394830.3_Silent_p.P427P|PBRM1_ENST00000409057.1_Silent_p.P427P			Q86U86	PB1_HUMAN	polybromo 1	427	Bromo 3. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GTAGTGATATGGGCATTTTAA	0.353			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								G|||	628	0.125399	0.4092	0.0533	5008	,	,		16031	0.0		0.0099	False		,,,				2504	0.0409				p.P427P		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	PBRM1_ENST00000356770,NS,carcinoma,-2,3	PBRM1	1252	3	0			c.C1281T						scavenged	.	G	,,	1511,2895	472.0+/-356.2	261,989,953	162.0	182.0	175.0		1185,1281,1281	4.7	1.0	3	dbSNP_123	175	192,8408	84.8+/-147.2	2,188,4110	no	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	263,1177,5063	AA,AG,GG		2.2326,34.2941,13.094	,,	395/1603,427/1583,427/1583	52668638	1703,11303	2203	4300	6503	SO:0001819	synonymous_variant	55193	exon12			TGATATGGGCATT	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1281C>T	3.37:g.52668638G>A		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	121	56	0.46281	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				G|0.876;A|0.124	0.124	strong		0.353	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
ZNF470	388566	hgsc.bcm.edu	37	19	57088850	57088850	+	Silent	SNP	T	T	C	rs3752180	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57088850T>C	ENST00000330619.8	+	6	1739	c.1053T>C	c.(1051-1053)gaT>gaC	p.D351D	ZNF470_ENST00000391709.3_Silent_p.D351D|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		CTTTTAGTGATTGCTCATCCC	0.438													T|||	1455	0.290535	0.1362	0.3401	5008	,	,		21092	0.379		0.3867	False		,,,				2504	0.274				p.D351D		Atlas-SNP	.											.	ZNF470	103	.	0			c.T1053C						PASS	.	T		801,3605	320.4+/-296.6	64,673,1466	86.0	82.0	84.0		1053	-2.2	0.7	19	dbSNP_107	84	3198,5402	482.3+/-370.9	598,2002,1700	no	coding-synonymous	ZNF470	NM_001001668.3		662,2675,3166	CC,CT,TT		37.186,18.1798,30.7473		351/718	57088850	3999,9007	2203	4300	6503	SO:0001819	synonymous_variant	388566	exon6			TAGTGATTGCTCA	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"""Zinc fingers, C2H2-type"", ""-"""	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.1053T>C	19.37:g.57088850T>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Silent	SNP	ENST00000330619.8	37	CCDS33122.1																																																																																			T|0.693;C|0.307	0.307	strong		0.438	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668	
VEGFA	7422	hgsc.bcm.edu	37	6	43738977	43738977	+	5'UTR	SNP	C	C	T	rs25648	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:43738977C>T	ENST00000523873.1	+	0	32				VEGFA_ENST00000457104.2_5'Flank|VEGFA_ENST00000518824.1_5'Flank|RP1-261G23.7_ENST00000607600.1_RNA|VEGFA_ENST00000523125.1_5'Flank|VEGFA_ENST00000425836.2_Silent_p.S178S|VEGFA_ENST00000372055.4_Silent_p.S178S|VEGFA_ENST00000372064.4_Silent_p.S178S|VEGFA_ENST00000372077.4_5'UTR|VEGFA_ENST00000523950.1_5'UTR|VEGFA_ENST00000417285.2_Silent_p.S178S|VEGFA_ENST00000518689.1_5'Flank|VEGFA_ENST00000372067.3_Silent_p.S178S|VEGFA_ENST00000520948.1_5'UTR|VEGFA_ENST00000230480.6_5'Flank|VEGFA_ENST00000324450.6_Silent_p.S178S|VEGFA_ENST00000413642.3_Silent_p.S178S|VEGFA_ENST00000482630.2_Silent_p.S178S			P15692	VEGFA_HUMAN	vascular endothelial growth factor A						activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|artery morphogenesis (GO:0048844)|basophil chemotaxis (GO:0002575)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|camera-type eye morphogenesis (GO:0048593)|cardiac muscle fiber development (GO:0048739)|cardiac vascular smooth muscle cell development (GO:0060948)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to hypoxia (GO:0071456)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|dopaminergic neuron differentiation (GO:0071542)|endothelial cell chemotaxis (GO:0035767)|epithelial cell differentiation (GO:0030855)|eye photoreceptor cell development (GO:0042462)|growth (GO:0040007)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|induction of positive chemotaxis (GO:0050930)|kidney development (GO:0001822)|lactation (GO:0007595)|lung development (GO:0030324)|lymph vessel morphogenesis (GO:0036303)|macrophage differentiation (GO:0030225)|mammary gland alveolus development (GO:0060749)|mesoderm development (GO:0007498)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|outflow tract morphogenesis (GO:0003151)|ovarian follicle development (GO:0001541)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cellular component movement (GO:0051272)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine autophosphorylation (GO:1900086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein localization to early endosome (GO:1902966)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor internalization (GO:0002092)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular permeability (GO:0043117)|post-embryonic camera-type eye development (GO:0031077)|primitive erythrocyte differentiation (GO:0060319)|regulation of cell shape (GO:0008360)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)|surfactant homeostasis (GO:0043129)|tube formation (GO:0035148)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|VEGF-activated neuropilin signaling pathway (GO:0038190)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|neuropilin binding (GO:0038191)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor agonist activity (GO:0048018)|vascular endothelial growth factor receptor 1 binding (GO:0043183)|vascular endothelial growth factor receptor 2 binding (GO:0043184)|vascular endothelial growth factor receptor binding (GO:0005172)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9	all_cancers(18;5.46e-07)|all_epithelial(2;5.96e-08)|Lung NSC(15;0.000157)|all_lung(25;0.000486)|Hepatocellular(11;0.00309)		all cancers(41;0.000413)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0742)|OV - Ovarian serous cystadenocarcinoma(102;0.196)		Aflibercept(DB08885)|Bevacizumab(DB00112)|Carvedilol(DB01136)|Dalteparin(DB06779)|Gliclazide(DB01120)|Minocycline(DB01017)|Ranibizumab(DB01270)|Vandetanib(DB05294)	GTCGGGCCTCCGAAACCATGA	0.697													c|||	607	0.121206	0.0711	0.1412	5008	,	,		12416	0.1002		0.173	False		,,,				2504	0.1431				p.S178S		Atlas-SNP	.											.	VEGFA	21	.	0			c.C534T						PASS	.		,,,,,,,,,,,,,,,,,	212,2616		4,204,1206	20.0	21.0	21.0		534,534,534,534,534,534,534,,,,,,,,,,534,534	2.6	1.0	6	dbSNP_72	21	881,5503		52,777,2363	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-5,utr-5,utr-5,utr-5,utr-5,utr-5,utr-5,utr-5,utr-5,coding-synonymous,coding-synonymous	VEGFA	NM_001025366.2,NM_001025367.2,NM_001025368.2,NM_001025369.2,NM_001025370.2,NM_001033756.2,NM_001171622.1,NM_001171623.1,NM_001171624.1,NM_001171625.1,NM_001171626.1,NM_001171627.1,NM_001171628.1,NM_001171629.1,NM_001171630.1,NM_001204384.1,NM_001204385.1,NM_003376.5	,,,,,,,,,,,,,,,,,	56,981,3569	TT,TC,CC		13.8001,7.4965,11.865	,,,,,,,,,,,,,,,,,	178/413,178/390,178/372,178/355,178/328,178/372,178/318,,,,,,,,,,178/352,178/396	43738977	1093,8119	1414	3192	4606	SO:0001623	5_prime_UTR_variant	7422	exon1			GGCCTCCGAAACC	AB021221	CCDS34457.1, CCDS4907.2, CCDS34458.1, CCDS47432.1, CCDS47433.1, CCDS47434.1, CCDS47435.1, CCDS55007.1, CCDS55008.1, CCDS55009.1, CCDS55010.1, CCDS55011.1, CCDS55012.1, CCDS55013.1, CCDS55014.1, CCDS55015.1, CCDS69125.1	6p12	2008-02-05	2006-10-31	2006-10-31	ENSG00000112715	ENSG00000112715			12680	protein-coding gene	gene with protein product		192240	"""vascular endothelial growth factor"""	VEGF		8786112	Standard	NM_001025366		Approved	VEGF-A, VPF	uc003owh.3	P15692	OTTHUMG00000014745	ENST00000523873.1:c.-7C>T	6.37:g.43738977C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_001171622	B5BU86|H0Y2S8|H0Y407|H0Y414|H0Y462|H0Y8N2|H3BLW7|O60720|O75875|Q074Z4|Q16889|Q5UB46|Q6P0P5|Q96KJ0|Q96L82|Q96NW5|Q9H1W8|Q9H1W9|Q9UH58|Q9UL23	Silent	SNP	ENST00000523873.1	37	CCDS55010.1	281	0.12866300366300365	31	0.06300813008130081	51	0.1408839779005525	68	0.11888111888111888	131	0.17282321899736147	c	9.893	1.204780	0.22205	0.074965	0.138001	ENSG00000112715	ENST00000519767	.	.	.	3.52	2.62	0.31277	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999999891876	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.8125	7.0029	0.24820	0.0:0.8686:0.0:0.1314	rs25648;rs25648	.	.	.	X	150	.	.	R	+	1	2	VEGFA	43846955	0.999000	0.42202	1.000000	0.80357	0.988000	0.76386	0.235000	0.17948	0.666000	0.31087	0.457000	0.33378	CGA	C|0.876;T|0.124	0.124	strong		0.697	VEGFA-021	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374460.1	NM_001025366	
OR2AG1	144125	hgsc.bcm.edu	37	11	6806827	6806827	+	Missense_Mutation	SNP	G	G	T	rs2659880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6806827G>T	ENST00000307401.4	+	1	580	c.559G>T	c.(559-561)Gtg>Ttg	p.V187L		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	187			V -> L (in dbSNP:rs2659880). {ECO:0000269|PubMed:11416212}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTTGCTGAAGGTGGCCTGTGC	0.498													T|||	966	0.192891	0.1059	0.2032	5008	,	,		23859	0.1815		0.328	False		,,,				2504	0.1759				p.V187L		Atlas-SNP	.											.	OR2AG1	57	.	0			c.G559T						PASS	.	T	LEU/VAL	574,3828	772.6+/-413.9	35,504,1662	186.0	157.0	167.0		559	-3.2	0.8	11	dbSNP_100	167	2886,5706	671.2+/-402.8	504,1878,1914	yes	missense	OR2AG1	NM_001004489.2	32	539,2382,3576	TT,TG,GG		33.5894,13.0395,26.6277	benign	187/317	6806827	3460,9534	2201	4296	6497	SO:0001583	missense	144125	exon1			CTGAAGGTGGCCT	AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"""GPCR / Class A : Olfactory receptors"""	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.559G>T	11.37:g.6806827G>T	ENSP00000307447:p.Val187Leu	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	206	84	0.407767	NM_001004489	B9EKV7|Q6IFG7|Q96R26	Missense_Mutation	SNP	ENST00000307401.4	37	CCDS31414.1	521	0.23855311355311357	47	0.09552845528455285	92	0.2541436464088398	134	0.23426573426573427	248	0.32717678100263853	T	0.003	-2.493496	0.00159	0.130395	0.335894	ENSG00000170803	ENST00000307401	T	0.00002	9.87	4.23	-3.24	0.05094	GPCR, rhodopsin-like superfamily (1);	0.182212	0.26373	N	0.024742	T	0.00012	0.0000	N	0.00106	-2.12	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44003	-0.9356	9	0.02654	T	1	.	8.5763	0.33601	0.0:0.5121:0.1292:0.3588	rs2659880;rs52819882;rs2659880	187	Q9H205	O2AG1_HUMAN	L	187	ENSP00000307447:V187L	ENSP00000307447:V187L	V	+	1	0	OR2AG1	6763403	0.000000	0.05858	0.788000	0.31933	0.014000	0.08584	-0.260000	0.08708	-0.893000	0.03930	-1.182000	0.01712	GTG	G|0.741;T|0.259	0.259	strong		0.498	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385980.1	NM_001004489	
SLC17A6	57084	hgsc.bcm.edu	37	11	22360167	22360167	+	Splice_Site	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:22360167T>C	ENST00000263160.3	+	1	523		c.e1+2		CTD-2140G10.2_ENST00000530569.1_RNA|CTD-2140G10.2_ENST00000531304.1_RNA|CTD-2140G10.2_ENST00000528009.1_RNA	NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6						ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						GATCTACAGGTAAGACAAAGC	0.453																																					.		Atlas-SNP	.											SLC17A6,caecum,carcinoma,0,1	SLC17A6	135	1	0			c.86+2T>C						scavenged	.						51.0	54.0	53.0					11																	22360167		2203	4299	6502	SO:0001630	splice_region_variant	57084	exon1			TACAGGTAAGACA	AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"""Solute carriers"""	16703	protein-coding gene	gene with protein product	"""vesicular glutamate transporter 2"", ""differentiation-associated Na-dependent inorganic phosphate cotransporter"""	607563	"""solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"""			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.86+2T>C	11.37:g.22360167T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	124	2	0.016129	NM_020346	A6NKS2	Splice_Site	SNP	ENST00000263160.3	37	CCDS7856.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.298467	0.60195	.	.	ENSG00000091664	ENST00000263160	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2186	0.73292	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC17A6	22316743	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	7.673000	0.83973	1.997000	0.58415	0.533000	0.62120	.	.	.	none		0.453	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346	Intron
DYRK4	8798	hgsc.bcm.edu	37	12	4700352	4700352	+	Silent	SNP	G	G	A	rs35827006	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:4700352G>A	ENST00000540757.2	+	3	166	c.6G>A	c.(4-6)ccG>ccA	p.P2P	DYRK4_ENST00000543431.1_Silent_p.P2P|DYRK4_ENST00000010132.5_Silent_p.P2P	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	2						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			ATCAGATGCCGGCCTCAGAGC	0.458													G|||	167	0.0333466	0.0832	0.0202	5008	,	,		20680	0.0		0.0358	False		,,,				2504	0.0072				p.P2P		Atlas-SNP	.											.	DYRK4	75	.	0			c.G6A						PASS	.	G		326,4080	173.0+/-202.9	12,302,1889	80.0	74.0	76.0		6	-4.3	0.0	12	dbSNP_126	76	301,8299	109.2+/-169.8	7,287,4006	no	coding-synonymous	DYRK4	NM_003845.1		19,589,5895	AA,AG,GG		3.5,7.399,4.8209		2/521	4700352	627,12379	2203	4300	6503	SO:0001819	synonymous_variant	8798	exon3			GATGCCGGCCTCA	Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.6G>A	12.37:g.4700352G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_003845	A8K8F7|Q8NEF2|Q92631	Silent	SNP	ENST00000540757.2	37	CCDS8530.1																																																																																			G|0.957;A|0.043	0.043	strong		0.458	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398780.2		
EML5	161436	hgsc.bcm.edu	37	14	89205265	89205265	+	Missense_Mutation	SNP	T	T	C	rs17188228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:89205265T>C	ENST00000380664.5	-	6	804	c.805A>G	c.(805-807)Att>Gtt	p.I269V	EML5_ENST00000554922.1_Missense_Mutation_p.I269V|EML5_ENST00000352093.5_Missense_Mutation_p.I269V			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	269			I -> V (in dbSNP:rs17188228).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						ATCACAGTAATTGGTTTAAAA	0.373													T|||	1232	0.246006	0.1619	0.2291	5008	,	,		15501	0.3909		0.2256	False		,,,				2504	0.2434				p.I269V		Atlas-SNP	.											.	EML5	141	.	0			c.A805G						PASS	.	T	VAL/ILE	651,3069		60,531,1269	73.0	65.0	68.0		805	5.5	1.0	14	dbSNP_123	68	2066,6144		259,1548,2298	yes	missense	EML5	NM_183387.2	29	319,2079,3567	CC,CT,TT		25.1644,17.5,22.7745	benign	269/1978	89205265	2717,9213	1860	4105	5965	SO:0001583	missense	161436	exon6			CAGTAATTGGTTT	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.805A>G	14.37:g.89205265T>C	ENSP00000370039:p.Ile269Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	593	0.2715201465201465	101	0.20528455284552846	86	0.23756906077348067	230	0.4020979020979021	176	0.23218997361477572	T	14.85	2.659503	0.47467	0.175	0.251644	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.01287	5.05;5.05;5.05	5.5	5.5	0.81552	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.52266	1.64	0.09310	P	0.99999262538	D	0.61080	0.989	P	0.58577	0.841	T	0.64681	-0.6350	9	0.14252	T	0.57	-17.9194	15.5946	0.76569	0.0:0.0:0.0:1.0	rs17188228;rs52811369;rs17188228	269	Q05BV3	EMAL5_HUMAN	V	269	ENSP00000451998:I269V;ENSP00000298315:I269V;ENSP00000370039:I269V	ENSP00000298315:I269V	I	-	1	0	EML5	88275018	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.091000	0.63221	0.454000	0.30748	ATT	T|0.733;C|0.267	0.267	strong		0.373	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
SMC6	79677	hgsc.bcm.edu	37	2	17897488	17897488	+	Missense_Mutation	SNP	T	T	C	rs35195207	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:17897488T>C	ENST00000448223.2	-	15	1659	c.1390A>G	c.(1390-1392)Agg>Ggg	p.R464G	SMC6_ENST00000351948.4_Missense_Mutation_p.R464G|SMC6_ENST00000402989.1_Missense_Mutation_p.R464G|SMC6_ENST00000381272.4_Missense_Mutation_p.R490G	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	464	Flexible hinge.		R -> G (in dbSNP:rs35195207). {ECO:0000269|PubMed:11408570, ECO:0000269|PubMed:15489334}.		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTCAGTTGCCTCTGATTGTAG	0.348													T|||	507	0.101238	0.0567	0.1671	5008	,	,		16462	0.0139		0.2416	False		,,,				2504	0.0603				p.R464G		Atlas-SNP	.											.	SMC6	102	.	0			c.A1390G						PASS	.	T	GLY/ARG,GLY/ARG	362,4044	182.9+/-210.6	14,334,1855	152.0	153.0	152.0		1390,1390	4.4	1.0	2	dbSNP_126	152	2272,6328	385.1+/-341.3	310,1652,2338	yes	missense,missense	SMC6	NM_001142286.1,NM_024624.5	125,125	324,1986,4193	CC,CT,TT		26.4186,8.2161,20.2522	benign,benign	464/1092,464/1092	17897488	2634,10372	2203	4300	6503	SO:0001583	missense	79677	exon15			GTTGCCTCTGATT	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"""Structural maintenance of chromosomes proteins"""	20466	protein-coding gene	gene with protein product		609387	"""SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"""	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.1390A>G	2.37:g.17897488T>C	ENSP00000404092:p.Arg464Gly	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	232	117	0.50431	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	37	CCDS1690.1	286	0.13095238095238096	32	0.06504065040650407	69	0.19060773480662985	13	0.022727272727272728	172	0.22691292875989447	T	12.70	2.016854	0.35606	0.082161	0.264186	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.34275	1.56;1.56;1.56;1.56;1.37	5.62	4.42	0.53409	RecF/RecN/SMC (1);	0.184484	0.53938	D	0.000043	T	0.00012	0.0000	L	0.43923	1.385	0.51233	P	8.900000000000574E-5	B;B;B	0.29508	0.246;0.001;0.083	B;B;B	0.33254	0.134;0.006;0.16	T	0.30822	-0.9965	9	0.21540	T	0.41	.	12.249	0.54587	0.0:0.0:0.2626:0.7374	rs35195207;rs61754181	490;490;464	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	G	464;464;490;464;490	ENSP00000404092:R464G;ENSP00000323439:R464G;ENSP00000370672:R490G;ENSP00000384539:R464G;ENSP00000408644:R490G	ENSP00000323439:R464G	R	-	1	2	SMC6	17760969	1.000000	0.71417	0.996000	0.52242	0.612000	0.37316	3.853000	0.55941	2.141000	0.66446	0.454000	0.30748	AGG	T|0.825;C|0.175	0.175	strong		0.348	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624	
C2orf71	388939	hgsc.bcm.edu	37	2	29297068	29297068	+	Silent	SNP	C	C	T	rs35929540	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29297068C>T	ENST00000331664.5	-	1	59	c.60G>A	c.(58-60)caG>caA	p.Q20Q		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	20					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TTTTCAAGAACTGAATGCCAC	0.473													C|||	584	0.116613	0.0303	0.1585	5008	,	,		21773	0.123		0.2137	False		,,,				2504	0.0971				p.Q20Q		Atlas-SNP	.											.	C2orf71	146	.	0			c.G60A						PASS	.	C		274,3694		9,256,1719	93.0	87.0	89.0		60	5.0	1.0	2	dbSNP_126	89	1859,6489		189,1481,2504	no	coding-synonymous	C2orf71	NM_001029883.1		198,1737,4223	TT,TC,CC		22.2688,6.9052,17.3189		20/1289	29297068	2133,10183	1984	4174	6158	SO:0001819	synonymous_variant	388939	exon1			CAAGAACTGAATG		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.60G>A	2.37:g.29297068C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_001029883		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																			C|0.822;T|0.178	0.178	strong		0.473	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
PRAMEF11	440560	hgsc.bcm.edu	37	1	12888397	12888397	+	Missense_Mutation	SNP	C	C	T	rs202156326	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:12888397C>T	ENST00000535591.1	-	2	322	c.127G>A	c.(127-129)Gat>Aat	p.D43N		NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	43					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.D43N(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						TCAAGCCCATCGAGCACAGCT	0.627													.|||	63	0.0125799	0.0454	0.0043	5008	,	,		16628	0.0		0.0	False		,,,				2504	0.0				p.D43N		Atlas-SNP	.											PRAMEF11,NS,other,0,1	PRAMEF11	72	1	1	Substitution - Missense(1)	pancreas(1)	c.G127A						scavenged	.																																			SO:0001583	missense	440560	exon2			GCCCATCGAGCAC	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.127G>A	1.37:g.12888397C>T	ENSP00000439551:p.Asp43Asn	Somatic	225	26	0.115556		WXS	Illumina HiSeq	Phase_I	376	74	0.196809	NM_001146344		Missense_Mutation	SNP	ENST00000535591.1	37	CCDS53268.1	.	.	.	.	.	.	.	.	.	.	.	13.12	2.143414	0.37825	.	.	ENSG00000204513	ENST00000535591;ENST00000331684;ENST00000437584	T;T	0.05996	3.36;3.36	1.45	1.45	0.22620	.	0.744226	0.12606	N	0.454302	T	0.10766	0.0263	M	0.77712	2.385	0.09310	N	1	D	0.53745	0.962	P	0.44921	0.464	T	0.18366	-1.0339	10	0.87932	D	0	.	6.4008	0.21638	0.0:1.0:0.0:0.0	.	43	O60813	PRA11_HUMAN	N	43;84;43	ENSP00000439551:D43N;ENSP00000391839:D43N	ENSP00000328783:D84N	D	-	1	0	PRAMEF11	12810984	0.004000	0.15560	0.007000	0.13788	0.013000	0.08279	0.287000	0.18920	1.122000	0.41944	0.380000	0.24917	GAT	C|0.250;T|0.750	0.750	weak		0.627	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
SYTL1	84958	hgsc.bcm.edu	37	1	27679954	27679954	+	Silent	SNP	G	G	A	rs1128918	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:27679954G>A	ENST00000543823.1	+	13	1986	c.1524G>A	c.(1522-1524)ggG>ggA	p.G508G	SYTL1_ENST00000318074.5_Silent_p.G496G|SYTL1_ENST00000490170.1_3'UTR			Q8IYJ3	SYTL1_HUMAN	synaptotagmin-like 1	508	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|melanosome (GO:0042470)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)			NS(1)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	12		Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0908)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.0013)|KIRC - Kidney renal clear cell carcinoma(1967;0.00158)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GCCAGCTGGGGGGCACACGCC	0.677													G|||	1207	0.241014	0.1233	0.2176	5008	,	,		16953	0.1756		0.3678	False		,,,				2504	0.3538				p.G508G		Atlas-SNP	.											.	SYTL1	57	.	0			c.G1524A						PASS	.	G	,	709,3695		58,593,1551	21.0	23.0	22.0		1524,1488	3.6	1.0	1	dbSNP_86	22	3122,5476		579,1964,1756	no	coding-synonymous,coding-synonymous	SYTL1	NM_001193308.1,NM_032872.2	,	637,2557,3307	AA,AG,GG		36.3108,16.099,29.4647	,	508/563,496/551	27679954	3831,9171	2202	4299	6501	SO:0001819	synonymous_variant	84958	exon14			GCTGGGGGGCACA	AK027902	CCDS298.1, CCDS53286.1	1p35.3	2008-02-05			ENSG00000142765	ENSG00000142765			15584	protein-coding gene	gene with protein product		608042				12137562	Standard	NM_032872		Approved	SLP1, JFC1, FLJ14996, exophilin-7	uc001bnw.2	Q8IYJ3	OTTHUMG00000005770	ENST00000543823.1:c.1524G>A	1.37:g.27679954G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_001193308	Q5SSC9|Q96BB6|Q96GU6|Q96S89|Q96SI0	Silent	SNP	ENST00000543823.1	37	CCDS53286.1																																																																																			G|0.746;A|0.254	0.254	strong		0.677	SYTL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032872	
WDR90	197335	hgsc.bcm.edu	37	16	701656	701656	+	Missense_Mutation	SNP	C	C	T	rs11642546	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:701656C>T	ENST00000293879.4	+	8	749	c.749C>T	c.(748-750)cCg>cTg	p.P250L	WDR90_ENST00000549091.1_Missense_Mutation_p.P250L|AL022341.3_ENST00000455294.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	250			P -> L (in dbSNP:rs11642546). {ECO:0000269|PubMed:15489334}.							endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CTCCTGGGGCCGGGGCCACAG	0.657													c|||	2000	0.399361	0.2776	0.4006	5008	,	,		16039	0.6796		0.2594	False		,,,				2504	0.4182				p.P250L		Atlas-SNP	.											WDR90,NS,carcinoma,0,1	WDR90	107	1	0			c.C749T						PASS	.		LEU/PRO	962,2982		117,728,1127	93.0	108.0	103.0		749	-7.5	0.0	16	dbSNP_120	103	1878,6428		203,1472,2478	yes	missense	WDR90	NM_145294.4	98	320,2200,3605	TT,TC,CC		22.6102,24.3915,23.1837	benign	250/1749	701656	2840,9410	1972	4153	6125	SO:0001583	missense	197335	exon8			TGGGGCCGGGGCC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.749C>T	16.37:g.701656C>T	ENSP00000293879:p.Pro250Leu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	51	14	0.27451	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	852	0.3901098901098901	125	0.2540650406504065	142	0.39226519337016574	375	0.6555944055944056	210	0.2770448548812665	c	2.059	-0.415961	0.04766	0.243915	0.226102	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.28255	1.65;1.62	3.75	-7.51	0.01346	.	4.180590	0.01442	U	0.015155	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;B;B	0.35959	0.53;0.273;0.299	B;B;B	0.21708	0.036;0.013;0.035	T	0.42865	-0.9426	9	0.19590	T	0.45	.	2.8762	0.05631	0.3583:0.2309:0.3229:0.0879	rs11642546;rs11642546	250;250;250	Q96KV7;C9JMK1;Q96KV7-3	WDR90_HUMAN;.;.	L	250	ENSP00000448122:P250L;ENSP00000293879:P250L	ENSP00000293879:P250L	P	+	2	0	WDR90	641657	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.804000	0.01738	-1.506000	0.01805	0.506000	0.49869	CCG	C|0.651;T|0.349	0.349	strong		0.657	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
FCGBP	8857	hgsc.bcm.edu	37	19	40392496	40392496	+	Missense_Mutation	SNP	C	C	T	rs143680639	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40392496C>T	ENST00000221347.6	-	16	8015	c.8008G>A	c.(8008-8010)Ggg>Agg	p.G2670R		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2670	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.G2670R(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GACAGTGGCCCTGTGGGGCTG	0.597																																					p.G2670R		Atlas-SNP	.											FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	large_intestine(1)	c.G8008A						PASS	.						36.0	38.0	37.0					19																	40392496		2171	4287	6458	SO:0001583	missense	8857	exon16			GTGGCCCTGTGGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8008G>A	19.37:g.40392496C>T	ENSP00000221347:p.Gly2670Arg	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	272	88	0.323529	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.401441	0.42613	.	.	ENSG00000090920	ENST00000221347	T	0.24908	1.83	2.66	2.66	0.31614	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	0.000000	0.85682	D	0.000000	T	0.57533	0.2060	M	0.92784	3.345	0.42617	D	0.993336	D	0.89917	1.0	D	0.97110	1.0	T	0.70223	-0.4931	10	0.87932	D	0	.	12.5273	0.56093	0.0:1.0:0.0:0.0	.	2670	Q9Y6R7	FCGBP_HUMAN	R	2670	ENSP00000221347:G2670R	ENSP00000221347:G2670R	G	-	1	0	FCGBP	45084336	1.000000	0.71417	0.382000	0.26119	0.147000	0.21601	5.593000	0.67550	1.495000	0.48549	0.298000	0.19748	GGG	C|0.970;T|0.030	0.030	strong		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CCL16	6360	hgsc.bcm.edu	37	17	34304644	34304644	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:34304644A>G	ENST00000293275.3	-	3	396	c.321T>C	c.(319-321)atT>atC	p.I107I		NM_004590.2	NP_004581.1	O15467	CCL16_HUMAN	chemokine (C-C motif) ligand 16	107					cell chemotaxis (GO:0060326)|cell communication (GO:0007154)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive chemotaxis (GO:0050918)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)			endometrium(1)|lung(2)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCTTTGCTGTAATAATTTTAA	0.478																																					p.I107I		Atlas-SNP	.											CCL16,colon,carcinoma,-1,1	CCL16	7	1	0			c.T321C						scavenged	.						176.0	156.0	163.0					17																	34304644		2203	4300	6503	SO:0001819	synonymous_variant	6360	exon3			TGCTGTAATAATT	AB007454	CCDS11303.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000161573	ENSG00000275152		"""Chemokine ligands"", ""Endogenous ligands"""	10614	protein-coding gene	gene with protein product		601394	"""small inducible cytokine subfamily A (Cys-Cys), member 16"""	SCYA16		8661057	Standard	NM_004590		Approved	NCC-4, SCYL4, LEC, HCC-4, LMC, LCC-1, CKb12, Mtn-1	uc002hkl.3	O15467	OTTHUMG00000188402	ENST00000293275.3:c.321T>C	17.37:g.34304644A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	212	3	0.0141509	NM_004590	Q4KKU0	Silent	SNP	ENST00000293275.3	37	CCDS11303.1																																																																																			.	.	none		0.478	CCL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256579.1	NM_004590	
IFRD2	7866	hgsc.bcm.edu	37	3	50326883	50326883	+	Silent	SNP	A	A	G	rs78165652	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:50326883A>G	ENST00000429673.2	-	7	965	c.966T>C	c.(964-966)ctT>ctC	p.L322L	IFRD2_ENST00000336089.4_Silent_p.L424L|IFRD2_ENST00000484043.1_5'Flank|IFRD2_ENST00000436390.1_Silent_p.L258L|IFRD2_ENST00000417626.2_Silent_p.L258L			Q12894	IFRD2_HUMAN	interferon-related developmental regulator 2	322						nucleus (GO:0005634)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CCTACCTGTCAAGGATGTGGC	0.632													A|||	30	0.00599042	0.0008	0.0101	5008	,	,		17527	0.0		0.0179	False		,,,				2504	0.0041				p.L322L		Atlas-SNP	.											.	IFRD2	34	.	0			c.T966C						PASS	.	A		9,3949		0,9,1970	13.0	16.0	15.0		966	-4.9	0.9	3	dbSNP_132	15	149,8185		2,145,4020	no	coding-synonymous	IFRD2	NM_006764.4		2,154,5990	GG,GA,AA		1.7879,0.2274,1.2854		322/507	50326883	158,12134	1979	4167	6146	SO:0001819	synonymous_variant	7866	exon7			CCTGTCAAGGATG	U09585		3p21.3	2008-07-18			ENSG00000214706	ENSG00000214706			5457	protein-coding gene	gene with protein product	"""interferon-related protein"""	602725				9050919	Standard	NM_006764		Approved	SKMc15, SM15, IFNRP	uc011bdp.2	Q12894	OTTHUMG00000156935	ENST00000429673.2:c.966T>C	3.37:g.50326883A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	133	76	0.571429	NM_006764	Q9BVB4|Q9UJ88	Silent	SNP	ENST00000429673.2	37	CCDS46831.1																																																																																			A|0.992;G|0.008	0.008	strong		0.632	IFRD2-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006764	
AKR7A2	8574	hgsc.bcm.edu	37	1	19635011	19635011	+	Missense_Mutation	SNP	C	C	T	rs1043657	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:19635011C>T	ENST00000235835.3	-	2	445	c.424G>A	c.(424-426)Gca>Aca	p.A142T		NM_003689.3	NP_003680.2	O43488	ARK72_HUMAN	aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)	142			A -> T (in dbSNP:rs1043657). {ECO:0000269|PubMed:18752886, ECO:0000269|PubMed:9576847}.		carbohydrate metabolic process (GO:0005975)|cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|phenanthrene-9,10-epoxide hydrolase activity (GO:0019119)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGGTCAGGTGCGTGTAGGTAG	0.617													C|||	188	0.0375399	0.0257	0.0605	5008	,	,		18086	0.003		0.0974	False		,,,				2504	0.0112				p.A142T		Atlas-SNP	.											.	AKR7A2	19	.	0			c.G424A						PASS	.	C	THR/ALA	136,4270	97.6+/-136.3	4,128,2071	78.0	77.0	77.0		424	0.9	0.0	1	dbSNP_86	77	806,7794	188.3+/-235.3	41,724,3535	yes	missense	AKR7A2	NM_003689.2	58	45,852,5606	TT,TC,CC		9.3721,3.0867,7.2428	possibly-damaging	142/360	19635011	942,12064	2203	4300	6503	SO:0001583	missense	8574	exon2			CAGGTGCGTGTAG	AF026947	CCDS194.1	1p36.13	2010-09-30			ENSG00000053371	ENSG00000053371		"""Aldo-keto reductases"""	389	protein-coding gene	gene with protein product		603418				9576847	Standard	NM_003689		Approved	AFAR	uc001bbw.3	O43488	OTTHUMG00000002522	ENST00000235835.3:c.424G>A	1.37:g.19635011C>T	ENSP00000235835:p.Ala142Thr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	160	77	0.48125	NM_003689	O75749|Q5TG63	Missense_Mutation	SNP	ENST00000235835.3	37	CCDS194.1	108	0.04945054945054945	9	0.018292682926829267	26	0.0718232044198895	0	0.0	73	0.09630606860158311	C	10.15	1.272395	0.23221	0.030867	0.093721	ENSG00000053371	ENST00000235835;ENST00000330072	T;T	0.04275	3.66;3.66	4.09	0.911	0.19343	NADP-dependent oxidoreductase domain (3);	0.220555	0.46442	D	0.000292	T	0.00356	0.0011	M	0.66297	2.02	0.58432	P	5.000000000032756E-6	D;D;D	0.76494	0.998;0.999;0.998	D;D;P	0.67548	0.936;0.952;0.907	T	0.04115	-1.0976	9	0.66056	D	0.02	.	5.664	0.17684	0.1571:0.6414:0.0:0.2014	rs1043657;rs1043657	113;113;142	C9JSL3;B4DZX4;O43488	.;.;ARK72_HUMAN	T	142;132	ENSP00000235835:A142T;ENSP00000339084:A132T	ENSP00000235835:A142T	A	-	1	0	AKR7A2	19507598	0.850000	0.29656	0.001000	0.08648	0.040000	0.13550	2.267000	0.43329	0.384000	0.24942	-0.367000	0.07326	GCA	C|0.938;T|0.062	0.062	strong		0.617	AKR7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007165.2	NM_003689	
NOTCH3	4854	hgsc.bcm.edu	37	19	15299112	15299112	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:15299112T>C	ENST00000263388.2	-	9	1501	c.1426A>G	c.(1426-1428)Agc>Ggc	p.S476G		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	476	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			ACACAGGGGCTACTCTGACAC	0.592																																					p.S476G		Atlas-SNP	.											.	NOTCH3	340	.	0			c.A1426G						PASS	.						55.0	46.0	49.0					19																	15299112		2203	4300	6503	SO:0001583	missense	4854	exon9			AGGGGCTACTCTG	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1426A>G	19.37:g.15299112T>C	ENSP00000263388:p.Ser476Gly	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	96	4	0.0416667	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	t	16.92	3.255393	0.59321	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.91686	-2.89	5.04	5.04	0.67666	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.38058	N	0.001835	D	0.90823	0.7118	L	0.58101	1.795	0.36208	D	0.851202	P;B	0.35401	0.499;0.256	B;B	0.39617	0.168;0.305	D	0.92578	0.6072	10	0.41790	T	0.15	.	13.7877	0.63119	0.0:0.0:0.0:1.0	.	479;476	Q59FL3;Q9UM47	.;NOTC3_HUMAN	G	476;478	ENSP00000263388:S476G	ENSP00000263388:S476G	S	-	1	0	NOTCH3	15160112	1.000000	0.71417	0.999000	0.59377	0.848000	0.48234	5.718000	0.68455	1.903000	0.55091	0.454000	0.30748	AGC	.	.	none		0.592	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
TBX6	6911	hgsc.bcm.edu	37	16	30097630	30097630	+	Silent	SNP	C	C	T	rs2289292	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30097630C>T	ENST00000395224.2	-	9	1286	c.1227G>A	c.(1225-1227)ccG>ccA	p.P409P	TBX6_ENST00000279386.2_Silent_p.P409P	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	409					anatomical structure morphogenesis (GO:0009653)|cell fate specification (GO:0001708)|mesoderm development (GO:0007498)|mesoderm formation (GO:0001707)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P409P(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	9						GGAGAAAGTGCGGGGCAAAGG	0.677													C|||	1256	0.250799	0.0219	0.3112	5008	,	,		10946	0.4633		0.339	False		,,,				2504	0.2076				p.P409P		Atlas-SNP	.											TBX6,NS,lymphoid_neoplasm,0,2	TBX6	29	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.G1227A						PASS	.	C		356,4038		16,324,1857	26.0	30.0	28.0		1227	-9.5	0.3	16	dbSNP_100	28	2909,5687		502,1905,1891	no	coding-synonymous	TBX6	NM_004608.3		518,2229,3748	TT,TC,CC		33.8413,8.102,25.1347		409/437	30097630	3265,9725	2197	4298	6495	SO:0001819	synonymous_variant	6911	exon9			AAAGTGCGGGGCA	AJ007989	CCDS10670.1	16p11.2	2008-02-05			ENSG00000149922	ENSG00000149922		"""T-boxes"""	11605	protein-coding gene	gene with protein product		602427				9888994, 9933572	Standard	NM_004608		Approved		uc010veh.2	O95947	OTTHUMG00000132115	ENST00000395224.2:c.1227G>A	16.37:g.30097630C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_004608	Q8TAS4|Q9HA44	Silent	SNP	ENST00000395224.2	37	CCDS10670.1																																																																																			C|0.749;T|0.251	0.251	strong		0.677	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758	
IDH3B	3420	hgsc.bcm.edu	37	20	2641471	2641471	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2641471T>C	ENST00000380843.4	-	6	433	c.403A>G	c.(403-405)Aag>Gag	p.K135E	IDH3B_ENST00000488299.1_5'UTR|IDH3B_ENST00000380851.5_Missense_Mutation_p.K135E	NM_006899.3	NP_008830.2	O43837	IDH3B_HUMAN	isocitrate dehydrogenase 3 (NAD+) beta	135					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|isocitrate metabolic process (GO:0006102)|NADH metabolic process (GO:0006734)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			breast(1)|endometrium(3)|kidney(2)|lung(7)|prostate(1)	14						AAGTCCAACTTACGCCTGAGG	0.537																																					p.K135E		Atlas-SNP	.											.	IDH3B	25	.	0			c.A403G						PASS	.						118.0	110.0	113.0					20																	2641471		2203	4300	6503	SO:0001583	missense	3420	exon6			CCAACTTACGCCT		CCDS13031.1, CCDS13032.1, CCDS74696.1	20p13	2013-02-14			ENSG00000101365	ENSG00000101365	1.1.1.41		5385	protein-coding gene	gene with protein product		604526				10575215	Standard	NM_006899		Approved	RP46	uc002wgp.4	O43837	OTTHUMG00000031699	ENST00000380843.4:c.403A>G	20.37:g.2641471T>C	ENSP00000370223:p.Lys135Glu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_006899	B2RDR1|D3DVX2|D3DVX3|O95106|Q5JXS8|Q9NQ06|Q9NQ07|Q9NUZ0|Q9UEX0|Q9UG99	Missense_Mutation	SNP	ENST00000380843.4	37	CCDS13032.1	.	.	.	.	.	.	.	.	.	.	T	8.127	0.782172	0.16189	.	.	ENSG00000101365	ENST00000380851;ENST00000380843;ENST00000341825	T;T	0.66638	-0.22;-0.22	5.28	5.28	0.74379	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	T	0.35799	0.0944	N	0.01809	-0.71	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.15052	0.009;0.012	T	0.42050	-0.9474	10	0.02654	T	1	-21.4299	13.2215	0.59890	0.0:0.0:0.0:1.0	.	135;135	O43837-2;O43837	.;IDH3B_HUMAN	E	135	ENSP00000370232:K135E;ENSP00000370223:K135E	ENSP00000343215:K135E	K	-	1	0	IDH3B	2589471	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.457000	0.80775	2.217000	0.71921	0.533000	0.62120	AAG	.	.	none		0.537	IDH3B-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077613.1		
LAMA1	284217	hgsc.bcm.edu	37	18	7008591	7008591	+	Missense_Mutation	SNP	T	T	C	rs662471	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:7008591T>C	ENST00000389658.3	-	28	4111	c.4018A>G	c.(4018-4020)Atg>Gtg	p.M1340V		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1340	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.		M -> V (in dbSNP:rs662471). {ECO:0000269|PubMed:1714537}.		axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CCAACCTCCATTGAAATGTCT	0.428													T|||	937	0.187101	0.2292	0.1945	5008	,	,		18687	0.0099		0.3012	False		,,,				2504	0.1902				p.M1340V		Atlas-SNP	.											.	LAMA1	458	.	0			c.A4018G						PASS	.	T	VAL/MET	1072,3334	387.9+/-326.7	136,800,1267	119.0	111.0	113.0		4018	-7.8	0.0	18	dbSNP_83	113	2578,6022	419.2+/-353.0	368,1842,2090	yes	missense	LAMA1	NM_005559.3	21	504,2642,3357	CC,CT,TT		29.9767,24.3305,28.064	possibly-damaging	1340/3076	7008591	3650,9356	2203	4300	6503	SO:0001583	missense	284217	exon28			CCTCCATTGAAAT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.4018A>G	18.37:g.7008591T>C	ENSP00000374309:p.Met1340Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	31	0.364706	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	426	0.19505494505494506	109	0.22154471544715448	84	0.23204419889502761	3	0.005244755244755245	230	0.3034300791556728	T	16.41	3.115673	0.56505	0.243305	0.299767	ENSG00000101680	ENST00000389658	T	0.36520	1.25	5.47	-7.83	0.01201	Laminin B type IV (2);Laminin B, subgroup (1);	0.264036	0.40908	N	0.000983	T	0.00012	0.0000	M	0.88450	2.955	0.43160	P	0.005055999999999949	P	0.36354	0.549	B	0.42625	0.393	T	0.04153	-1.0973	9	0.62326	D	0.03	.	5.1126	0.14817	0.094:0.122:0.4681:0.3159	rs662471;rs59106429;rs662471	1340	P25391	LAMA1_HUMAN	V	1340	ENSP00000374309:M1340V	ENSP00000374309:M1340V	M	-	1	0	LAMA1	6998591	0.009000	0.17119	0.006000	0.13384	0.427000	0.31564	-0.035000	0.12205	-0.925000	0.03775	-0.304000	0.09214	ATG	T|0.753;C|0.247	0.247	strong		0.428	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
KRT27	342574	hgsc.bcm.edu	37	17	38936659	38936659	+	Missense_Mutation	SNP	C	C	T	rs17558560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:38936659C>T	ENST00000301656.3	-	3	617	c.577G>A	c.(577-579)Ggt>Agt	p.G193S	KRT27_ENST00000540723.1_5'Flank	NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				CTTCGCAAACCATTGATGTCC	0.478													C|||	1747	0.348842	0.121	0.2939	5008	,	,		15522	0.6617		0.4076	False		,,,				2504	0.3129				p.G193S		Atlas-SNP	.											.	KRT27	41	.	0			c.G577A						PASS	.	C	SER/GLY	694,3712	291.5+/-281.6	54,586,1563	83.0	72.0	75.0		577	3.4	0.0	17	dbSNP_123	75	3747,4853	531.4+/-382.0	830,2087,1383	yes	missense	KRT27	NM_181537.3	56	884,2673,2946	TT,TC,CC		43.5698,15.7512,34.1458	benign	193/460	38936659	4441,8565	2203	4300	6503	SO:0001583	missense	342574	exon3			GCAAACCATTGAT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.577G>A	17.37:g.38936659C>T	ENSP00000301656:p.Gly193Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	37	CCDS11375.1	864	0.3956043956043956	59	0.11991869918699187	111	0.30662983425414364	372	0.6503496503496503	322	0.42480211081794195	C	14.69	2.609788	0.46527	0.157512	0.435698	ENSG00000171446	ENST00000301656	D	0.82619	-1.63	5.5	3.41	0.39046	Filament (1);	0.185812	0.37955	N	0.001863	T	0.00012	0.0000	L	0.56396	1.775	0.25741	P	0.9851618	B	0.26547	0.152	B	0.39935	0.314	T	0.49978	-0.8881	9	0.49607	T	0.09	.	11.131	0.48347	0.0:0.8023:0.0:0.1977	rs17558560;rs61120769;rs17558560	193	Q7Z3Y8	K1C27_HUMAN	S	193	ENSP00000301656:G193S	ENSP00000301656:G193S	G	-	1	0	KRT27	36190185	0.002000	0.14202	0.032000	0.17829	0.435000	0.31806	0.735000	0.26115	0.639000	0.30564	0.655000	0.94253	GGT	C|0.642;T|0.358	0.358	strong		0.478	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
ICAM5	7087	hgsc.bcm.edu	37	19	10407169	10407169	+	Silent	SNP	G	G	C	rs710845	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10407169G>C	ENST00000221980.4	+	11	2715	c.2652G>C	c.(2650-2652)ctG>ctC	p.L884L		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	884					phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CCGTGTGTCTGAACGGAgcgg	0.771													C|||	2557	0.510583	0.5681	0.6455	5008	,	,		6247	0.3313		0.5895	False		,,,				2504	0.4407				p.L884L		Atlas-SNP	.											.	ICAM5	53	.	0			c.G2652C						PASS	.	C		1682,962		566,550,206	4.0	3.0	3.0		2652	0.5	1.0	19	dbSNP_86	3	2905,1749		979,947,401	no	coding-synonymous	ICAM5	NM_003259.3		1545,1497,607	CC,CG,GG		37.5806,36.3843,37.1472		884/925	10407169	4587,2711	1322	2327	3649	SO:0001819	synonymous_variant	7087	exon11			GTGTCTGAACGGA	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.2652G>C	19.37:g.10407169G>C		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_003259	Q9Y6F3	Silent	SNP	ENST00000221980.4	37	CCDS12233.1																																																																																			G|0.499;C|0.501	0.501	strong		0.771	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
F5	2153	hgsc.bcm.edu	37	1	169529826	169529826	+	Silent	SNP	C	C	A	rs6022	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:169529826C>A	ENST00000367797.3	-	4	753	c.552G>T	c.(550-552)tcG>tcT	p.S184S	F5_ENST00000367796.3_Silent_p.S184S|F5_ENST00000546081.1_Silent_p.S47S	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	184	F5/8 type A 1.|Plastocyanin-like 1.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	CAATCAGCCCCGAGTTGAAAT	0.468													A|||	2092	0.417732	0.6543	0.2911	5008	,	,		17222	0.6647		0.1819	False		,,,				2504	0.1759				p.S184S		Atlas-SNP	.											.	F5	301	.	0			c.G552T						PASS	.	A		2531,1875	539.3+/-375.2	737,1057,409	125.0	122.0	123.0		552	-1.7	1.0	1	dbSNP_52	123	1517,7083	748.0+/-407.3	132,1253,2915	no	coding-synonymous	F5	NM_000130.4		869,2310,3324	AA,AC,CC		17.6395,42.5556,31.1241		184/2225	169529826	4048,8958	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon4			CAGCCCCGAGTTG	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.552G>T	1.37:g.169529826C>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	173	98	0.566474	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			C|0.638;A|0.362	0.362	strong		0.468	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
USP40	55230	hgsc.bcm.edu	37	2	234449358	234449358	+	Missense_Mutation	SNP	C	C	G	rs202235068		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:234449358C>G	ENST00000427112.2	-	9	1152	c.1117G>C	c.(1117-1119)Gga>Cga	p.G373R	USP40_ENST00000251722.6_Missense_Mutation_p.G373R|USP40_ENST00000450966.1_Missense_Mutation_p.G385R			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	373	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CAAGATATTCCTATCTTTTTC	0.388																																					p.G385R		Atlas-SNP	.											.	USP40	174	.	0			c.G1153C						PASS	.	C	ARG/GLY	1,3697		0,1,1848	180.0	168.0	172.0		1153	5.1	1.0	2		172	2,8216		0,2,4107	yes	missense	USP40	NM_018218.2	125	0,3,5955	GG,GC,CC		0.0243,0.027,0.0252	probably-damaging	385/1248	234449358	3,11913	1849	4109	5958	SO:0001583	missense	55230	exon9			ATATTCCTATCTT	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1117G>C	2.37:g.234449358C>G	ENSP00000387898:p.Gly373Arg	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	221	109	0.493213	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026869	0.75390	2.7E-4	2.43E-4	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.07021	3.23;3.24;3.24	5.09	5.09	0.68999	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	13.261800	0.00166	N	0.000000	T	0.31796	0.0808	M	0.66939	2.045	0.53005	D	0.999963	D;D	0.69078	0.997;0.996	D;D	0.77557	0.99;0.982	T	0.00540	-1.1681	10	0.87932	D	0	.	10.533	0.44988	0.0:0.8747:0.0:0.1253	.	373;385	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	R	385;373;373	ENSP00000415434:G385R;ENSP00000251722:G373R;ENSP00000387898:G373R	ENSP00000251722:G373R	G	-	1	0	USP40	234114097	1.000000	0.71417	0.993000	0.49108	0.877000	0.50540	4.295000	0.59049	2.526000	0.85167	0.561000	0.74099	GGA	.	.	weak		0.388	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
LLGL2	3993	hgsc.bcm.edu	37	17	73567801	73567801	+	Missense_Mutation	SNP	G	G	A	rs148020757	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73567801G>A	ENST00000392550.3	+	18	2347	c.2230G>A	c.(2230-2232)Gcc>Acc	p.A744T	LLGL2_ENST00000167462.5_Missense_Mutation_p.A744T|LLGL2_ENST00000577200.1_Missense_Mutation_p.A744T	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	744					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CACCATCTATGCCTTCTCCCT	0.667													G|||	13	0.00259585	0.0	0.0043	5008	,	,		17173	0.0		0.0099	False		,,,				2504	0.0				p.A744T		Atlas-SNP	.											.	LLGL2	155	.	0			c.G2230A						PASS	.	G	THR/ALA,THR/ALA	7,4399	12.9+/-30.5	0,7,2196	36.0	35.0	35.0		2230,2230	5.4	1.0	17	dbSNP_134	35	88,8512	48.9+/-108.6	2,84,4214	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	58,58	2,91,6410	AA,AG,GG		1.0233,0.1589,0.7304	probably-damaging,probably-damaging	744/1021,744/1016	73567801	95,12911	2203	4300	6503	SO:0001583	missense	3993	exon18			ATCTATGCCTTCT	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2230G>A	17.37:g.73567801G>A	ENSP00000376333:p.Ala744Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	20.2	3.951271	0.73787	0.001589	0.010233	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.05447	3.44;3.56	5.4	5.4	0.78164	.	0.048273	0.85682	N	0.000000	T	0.19366	0.0465	M	0.69823	2.125	0.80722	D	1	D;D;D;P;D	0.89917	0.998;1.0;1.0;0.866;0.998	D;D;D;P;D	0.91635	0.962;0.997;0.999;0.517;0.917	T	0.00138	-1.2002	10	0.49607	T	0.09	-0.0651	19.1611	0.93533	0.0:0.0:1.0:0.0	.	371;733;733;744;744	B4DVR9;B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;.;L2GL2_HUMAN	T	744;744;733	ENSP00000167462:A744T;ENSP00000376333:A744T	ENSP00000167462:A744T	A	+	1	0	LLGL2	71079396	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	9.552000	0.98115	2.544000	0.85801	0.549000	0.68633	GCC	G|0.994;A|0.006	0.006	strong		0.667	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
BSN	8927	hgsc.bcm.edu	37	3	49698115	49698115	+	Missense_Mutation	SNP	G	G	A	rs116113662	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49698115G>A	ENST00000296452.4	+	6	8951	c.8837G>A	c.(8836-8838)cGg>cAg	p.R2946Q		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2946					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GAGCTGGACCGGGACCTGCGG	0.642													G|||	24	0.00479233	0.0	0.0029	5008	,	,		18137	0.0		0.0139	False		,,,				2504	0.0082				p.R2946Q		Atlas-SNP	.											BSN,NS,carcinoma,-1,1	BSN	272	1	0			c.G8837A						PASS	.	G	GLN/ARG	16,4376		0,16,2180	23.0	24.0	24.0		8837	4.5	1.0	3	dbSNP_132	24	113,8475		0,113,4181	yes	missense	BSN	NM_003458.3	43	0,129,6361	AA,AG,GG		1.3158,0.3643,0.9938	probably-damaging	2946/3927	49698115	129,12851	2196	4294	6490	SO:0001583	missense	8927	exon6			TGGACCGGGACCT	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.8837G>A	3.37:g.49698115G>A	ENSP00000296452:p.Arg2946Gln	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	120	54	0.45	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	G	14.70	2.614137	0.46631	0.003643	0.013158	ENSG00000164061	ENST00000296452	T	0.24151	1.87	4.5	4.5	0.54988	.	0.080992	0.49305	D	0.000146	T	0.38026	0.1025	M	0.64404	1.975	0.43338	D	0.995383	D	0.76494	0.999	P	0.61275	0.886	T	0.46317	-0.9200	10	0.66056	D	0.02	-17.5126	17.2151	0.86941	0.0:0.0:1.0:0.0	.	2946	Q9UPA5	BSN_HUMAN	Q	2946	ENSP00000296452:R2946Q	ENSP00000296452:R2946Q	R	+	2	0	BSN	49673119	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.338000	0.59316	2.043000	0.60533	0.561000	0.74099	CGG	G|0.990;A|0.010	0.010	strong		0.642	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
CD300C	10871	hgsc.bcm.edu	37	17	72541052	72541052	+	Silent	SNP	C	C	T	rs2292107	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72541052C>T	ENST00000330793.1	-	2	456	c.96G>A	c.(94-96)gcG>gcA	p.A32A		NM_006678.3	NP_006669.1	Q08708	CLM6_HUMAN	CD300c molecule	32	Ig-like V-type.				cellular defense response (GO:0006968)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|skin(2)|upper_aerodigestive_tract(1)	21						CCACGGGGCCCGCCACGGTCA	0.567													C|||	297	0.0593051	0.0219	0.0951	5008	,	,		19241	0.005		0.1163	False		,,,				2504	0.0818				p.A32A	Esophageal Squamous(66;421 1121 20537 25337 27468)	Atlas-SNP	.											CD300C,NS,carcinoma,-2,1	CD300C	41	1	0			c.G96A						PASS	.	C		145,4261	93.4+/-132.2	2,141,2060	42.0	47.0	45.0		96	-8.7	0.0	17	dbSNP_100	45	1132,7468	218.8+/-257.1	73,986,3241	no	coding-synonymous	CD300C	NM_006678.3		75,1127,5301	TT,TC,CC		13.1628,3.291,9.8185		32/225	72541052	1277,11729	2203	4300	6503	SO:0001819	synonymous_variant	10871	exon2			GGGGCCCGCCACG	BC022279	CCDS11701.1	17q25.2	2014-05-15	2006-03-28		ENSG00000167850	ENSG00000167850		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19320	protein-coding gene	gene with protein product		606786	"""CD300c antigen"""			1349532, 10746781	Standard	NM_006678		Approved	CMRF35, LIR, CMRF-35A, CMRF35A, IGSF16	uc002jky.2	Q08708	OTTHUMG00000067608	ENST00000330793.1:c.96G>A	17.37:g.72541052C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_006678		Silent	SNP	ENST00000330793.1	37	CCDS11701.1																																																																																			C|0.911;T|0.089	0.089	strong		0.567	CD300C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145084.1	NM_006678	
LRRN2	10446	hgsc.bcm.edu	37	1	204589101	204589101	+	Missense_Mutation	SNP	G	G	A	rs3789044	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:204589101G>A	ENST00000367175.1	-	1	2232	c.20C>T	c.(19-21)cCa>cTa	p.P7L	LRRN2_ENST00000367176.3_Missense_Mutation_p.P7L|LRRN2_ENST00000496057.1_5'UTR|LRRN2_ENST00000367177.3_Missense_Mutation_p.P7L			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	7			P -> L (in dbSNP:rs3789044).		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			TAGCAAGAGTGGGGCCACGAG	0.622													G|||	895	0.178714	0.0446	0.0908	5008	,	,		17566	0.3085		0.2247	False		,,,				2504	0.2413				p.P7L		Atlas-SNP	.											LRRN2,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,2	LRRN2	81	2	0			c.C20T						PASS	.	G	LEU/PRO,LEU/PRO	306,4064		13,280,1892	14.0	16.0	16.0		20,20	3.8	1.0	1	dbSNP_107	16	1859,6727		196,1467,2630	yes	missense,missense	LRRN2	NM_201630.1,NM_006338.2	98,98	209,1747,4522	AA,AG,GG		21.6515,7.0023,16.7104	benign,benign	7/714,7/714	204589101	2165,10791	2185	4293	6478	SO:0001583	missense	10446	exon3			AAGAGTGGGGCCA	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.20C>T	1.37:g.204589101G>A	ENSP00000356143:p.Pro7Leu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	135	56	0.414815	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	415	0.190018315018315	33	0.06707317073170732	38	0.10497237569060773	174	0.3041958041958042	170	0.22427440633245382	G	0.632	-0.816888	0.02776	0.070023	0.216515	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.20881	2.04;2.04;2.04	5.79	3.8	0.43715	.	0.360808	0.20218	N	0.096750	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.43376	-0.9395	9	0.15952	T	0.53	.	10.3029	0.43663	0.0:0.1355:0.7092:0.1552	rs3789044;rs59340562;rs3789044	7	O75325	LRRN2_HUMAN	L	7	ENSP00000356144:P7L;ENSP00000356145:P7L;ENSP00000356143:P7L	ENSP00000356143:P7L	P	-	2	0	LRRN2	202855724	0.519000	0.26242	0.968000	0.41197	0.317000	0.28152	0.541000	0.23207	2.746000	0.94184	0.650000	0.86243	CCA	G|0.822;A|0.178	0.178	strong		0.622	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
AKAP13	11214	hgsc.bcm.edu	37	15	86123170	86123170	+	Missense_Mutation	SNP	G	G	T	rs745191	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86123170G>T	ENST00000394518.2	+	7	1966	c.1871G>T	c.(1870-1872)gGg>gTg	p.G624V	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.G624V	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	624			G -> V (in dbSNP:rs745191). {ECO:0000269|PubMed:11546812}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						GCCCTTCTTGGGCTGGAAGAA	0.443													G|||	674	0.134585	0.0106	0.2233	5008	,	,		23115	0.0169		0.3032	False		,,,				2504	0.1871				p.G624V	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G1871T						PASS	.	G	VAL/GLY,VAL/GLY	212,4192	129.8+/-166.5	8,196,1998	102.0	94.0	97.0		1871,1871	0.4	0.0	15	dbSNP_86	97	2442,6156	403.9+/-348.0	377,1688,2234	yes	missense,missense	AKAP13	NM_006738.4,NM_007200.3	109,109	385,1884,4232	TT,TG,GG		28.402,4.8138,20.4122	probably-damaging,probably-damaging	624/2818,624/2814	86123170	2654,10348	2202	4299	6501	SO:0001583	missense	11214	exon7			TTCTTGGGCTGGA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.1871G>T	15.37:g.86123170G>T	ENSP00000378026:p.Gly624Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	341	0.15613553113553114	6	0.012195121951219513	89	0.24585635359116023	13	0.022727272727272728	233	0.3073878627968338	G	12.56	1.976134	0.34848	0.048138	0.28402	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.09630	2.98;2.96	5.76	0.36	0.16097	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.09377	0.002;0.004	T	0.47129	-0.9141	8	0.51188	T	0.08	.	3.1963	0.06634	0.2565:0.0:0.4238:0.3197	rs745191;rs52806275;rs58434555;rs745191	624;624	Q12802;Q12802-2	AKP13_HUMAN;.	V	624;624;623;623	ENSP00000354718:G624V;ENSP00000378026:G624V	ENSP00000354718:G624V	G	+	2	0	AKAP13	83924174	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.120000	0.15647	0.437000	0.26423	-0.140000	0.14226	GGG	G|0.813;T|0.187	0.187	strong		0.443	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
TTC23	64927	hgsc.bcm.edu	37	15	99762041	99762041	+	Missense_Mutation	SNP	C	C	T	rs78534478	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:99762041C>T	ENST00000394132.2	-	6	1026	c.209G>A	c.(208-210)cGt>cAt	p.R70H	TTC23_ENST00000394129.2_Missense_Mutation_p.R70H|TTC23_ENST00000558613.1_Missense_Mutation_p.R70H|TTC23_ENST00000394135.3_Missense_Mutation_p.R70H|TTC23_ENST00000262074.4_Missense_Mutation_p.R70H|TTC23_ENST00000558663.1_Missense_Mutation_p.R70H|TTC23_ENST00000394130.1_Missense_Mutation_p.R70H|TTC23_ENST00000394136.1_Missense_Mutation_p.R70H			Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23	70										endometrium(2)|large_intestine(3)|lung(9)|urinary_tract(2)	16	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)			TGCTACGCAACGCACAAGCTC	0.438													C|||	77	0.0153754	0.0121	0.0303	5008	,	,		19292	0.0		0.0358	False		,,,				2504	0.0041				p.R70H		Atlas-SNP	.											TTC23,colon,carcinoma,-1,1	TTC23	33	1	0			c.G209A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	57,4337	55.5+/-91.7	0,57,2140	119.0	96.0	104.0		209,209,209,209,209,209,209	3.5	0.6	15	dbSNP_131	104	438,8156	133.5+/-191.0	20,398,3879	yes	missense,missense,missense,missense,missense,missense,missense	TTC23	NM_001040655.1,NM_001040656.1,NM_001040657.1,NM_001040658.1,NM_001040659.1,NM_001040660.1,NM_022905.4	29,29,29,29,29,29,29	20,455,6019	TT,TC,CC		5.0966,1.2972,3.8112	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	70/448,70/448,70/448,70/448,70/448,70/448,70/448	99762041	495,12493	2197	4297	6494	SO:0001583	missense	64927	exon4			ACGCAACGCACAA		CCDS10379.2	15q26.3	2013-01-11			ENSG00000103852	ENSG00000103852		"""Tetratricopeptide (TTC) repeat domain containing"""	25730	protein-coding gene	gene with protein product						12477932	Standard	NM_001288615		Approved	FLJ12572, HCC-8	uc002bux.3	Q5W5X9	OTTHUMG00000147344	ENST00000394132.2:c.209G>A	15.37:g.99762041C>T	ENSP00000377690:p.Arg70His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_001040657	A8K6M5|Q53HK0|Q96BC9|Q9H8W9|Q9H9S7	Missense_Mutation	SNP	ENST00000394132.2	37	CCDS10379.2	42	0.019230769230769232	6	0.012195121951219513	8	0.022099447513812154	0	0.0	28	0.036939313984168866	C	15.07	2.723432	0.48728	0.012972	0.050966	ENSG00000103852	ENST00000394132;ENST00000394136;ENST00000262074;ENST00000394135;ENST00000394130;ENST00000394129	T;T;T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95;-0.95;0.92	5.39	3.53	0.40419	Tetratricopeptide-like helical (1);	0.068746	0.64402	N	0.000016	T	0.24890	0.0604	M	0.62088	1.915	0.38571	D	0.949938	P;P	0.41710	0.76;0.647	B;B	0.32533	0.147;0.093	T	0.52983	-0.8502	10	0.52906	T	0.07	-7.6336	8.457	0.32906	0.0:0.8204:0.0:0.1796	.	70;70	Q5W5X9-2;Q5W5X9	.;TTC23_HUMAN	H	70	ENSP00000377690:R70H;ENSP00000377693:R70H;ENSP00000262074:R70H;ENSP00000377692:R70H;ENSP00000377688:R70H;ENSP00000457901:R70H	ENSP00000262074:R70H	R	-	2	0	TTC23	97579564	0.989000	0.36119	0.555000	0.28281	0.991000	0.79684	2.931000	0.48932	0.765000	0.33221	0.655000	0.94253	CGT	C|0.970;T|0.030	0.030	strong		0.438	TTC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303953.2	NM_022905	
DDX50	79009	hgsc.bcm.edu	37	10	70700944	70700944	+	Silent	SNP	A	A	G	rs5030900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70700944A>G	ENST00000373585.3	+	13	1991	c.1884A>G	c.(1882-1884)ggA>ggG	p.G628G	DDX50_ENST00000466265.1_3'UTR	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	628						membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						TCCTGAAAGGAAATATGGTAG	0.368													A|||	3285	0.65595	0.528	0.6326	5008	,	,		17918	0.9038		0.6412	False		,,,				2504	0.6053				p.G628G		Atlas-SNP	.											.	DDX50	65	.	0			c.A1884G						PASS	.	A		2412,1994	611.9+/-391.9	661,1090,452	66.0	69.0	68.0		1884	4.6	1.0	10	dbSNP_113	68	5553,3047	657.3+/-401.5	1795,1963,542	no	coding-synonymous	DDX50	NM_024045.1		2456,3053,994	GG,GA,AA		35.4302,45.2565,38.759		628/738	70700944	7965,5041	2203	4300	6503	SO:0001819	synonymous_variant	79009	exon13			GAAAGGAAATATG	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"""DEAD-boxes"""	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.1884A>G	10.37:g.70700944A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Silent	SNP	ENST00000373585.3	37	CCDS7283.1																																																																																			A|0.368;G|0.632	0.632	strong		0.368	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045	
MDN1	23195	hgsc.bcm.edu	37	6	90384216	90384216	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:90384216T>G	ENST00000369393.3	-	79	12969	c.12854A>C	c.(12853-12855)cAg>cCg	p.Q4285P	MDN1_ENST00000428876.1_Missense_Mutation_p.Q4285P|RP1-122O8.7_ENST00000438877.1_RNA|MDN1_ENST00000468568.1_5'Flank			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4285					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTCTGTCCACTGCTGCACGCC	0.642																																					p.Q4285P		Atlas-SNP	.											.	MDN1	478	.	0			c.A12854C						PASS	.						22.0	23.0	23.0					6																	90384216		2203	4299	6502	SO:0001583	missense	23195	exon79			GTCCACTGCTGCA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.12854A>C	6.37:g.90384216T>G	ENSP00000358400:p.Gln4285Pro	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.129345	0.37630	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03301	3.98;3.98	5.87	5.87	0.94306	.	0.308307	0.33691	N	0.004644	T	0.03263	0.0095	M	0.63428	1.95	0.34397	D	0.694857	P	0.51653	0.947	P	0.44597	0.454	T	0.41179	-0.9523	10	0.48119	T	0.1	.	12.0858	0.53695	0.0:0.0685:0.0:0.9315	.	4285	Q9NU22	MDN1_HUMAN	P	4285	ENSP00000358400:Q4285P;ENSP00000413970:Q4285P	ENSP00000358400:Q4285P	Q	-	2	0	MDN1	90440937	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.651000	0.37302	2.248000	0.74166	0.533000	0.62120	CAG	.	.	none		0.642	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
OR52B4	143496	hgsc.bcm.edu	37	11	4388905	4388905	+	Silent	SNP	C	C	T	rs11031960	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:4388905C>T	ENST00000408920.2	-	1	711	c.621G>A	c.(619-621)tcG>tcA	p.S207S		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	207					cognition (GO:0050890)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGACCACCGTCGACATTAGAA	0.388													C|||	1228	0.245208	0.2436	0.2709	5008	,	,		22618	0.1706		0.3618	False		,,,				2504	0.1861				p.S207S		Atlas-SNP	.											.	OR52B4	56	.	0			c.G621A						PASS	.	C		984,2842		117,750,1046	83.0	81.0	82.0		621	-8.6	0.0	11	dbSNP_120	82	2871,5385		500,1871,1757	no	coding-synonymous	OR52B4	NM_001005161.3		617,2621,2803	TT,TC,CC		34.7747,25.7188,31.907		207/315	4388905	3855,8227	1913	4128	6041	SO:0001819	synonymous_variant	143496	exon1			CACCGTCGACATT	AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"""GPCR / Class A : Olfactory receptors"""	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.621G>A	11.37:g.4388905C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_001005161	A6NP68|Q6IFK6	Silent	SNP	ENST00000408920.2	37	CCDS41609.1																																																																																			C|0.718;T|0.282	0.282	strong		0.388	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3	NM_001005161	
STKLD1	169436	hgsc.bcm.edu	37	9	136270538	136270538	+	Missense_Mutation	SNP	T	T	G	rs41302673	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:136270538T>G	ENST00000371957.3	+	18	2143	c.2036T>G	c.(2035-2037)cTg>cGg	p.L679R	C9orf96_ENST00000371955.1_Missense_Mutation_p.L212R	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		679							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TCTGGGGGACTGGAATAGATG	0.557													T|||	187	0.0373403	0.0023	0.0677	5008	,	,		18018	0.0		0.1014	False		,,,				2504	0.0358				p.L679R		Atlas-SNP	.											C9orf96_ENST00000371957,NS,carcinoma,0,1	C9orf96	77	1	0			c.T2036G						PASS	.	T	ARG/LEU	68,4338	61.1+/-98.1	0,68,2135	35.0	37.0	36.0		2036	-5.6	0.0	9	dbSNP_127	36	851,7749	191.4+/-237.6	51,749,3500	yes	missense	C9orf96	NM_153710.3	102	51,817,5635	GG,GT,TT		9.8953,1.5433,7.066	possibly-damaging	679/681	136270538	919,12087	2203	4300	6503	SO:0001583	missense	169436	exon18			GGGGACTGGAATA																												ENST00000371957.3:c.2036T>G	9.37:g.136270538T>G	ENSP00000361025:p.Leu679Arg	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	30	24	0.8	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	37	CCDS35169.1	105	0.04807692307692308	3	0.006097560975609756	24	0.06629834254143646	0	0.0	78	0.10290237467018469	T	10.74	1.435227	0.25813	0.015433	0.098953	ENSG00000198870	ENST00000371957;ENST00000371955	T;T	0.71222	-0.55;0.56	3.37	-5.58	0.02512	.	6.515760	0.00960	U	0.003081	T	0.01454	0.0047	N	0.08118	0	0.09310	N	1	P	0.40476	0.718	B	0.32864	0.154	T	0.26360	-1.0105	10	0.87932	D	0	12.8738	5.8566	0.18722	0.0:0.529:0.1608:0.3103	rs41302673	679	Q8NE28	SGK71_HUMAN	R	679;212	ENSP00000361025:L679R;ENSP00000361023:L212R	ENSP00000361023:L212R	L	+	2	0	C9orf96	135260359	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-1.438000	0.02416	-0.816000	0.04340	0.379000	0.24179	CTG	T|0.932;G|0.068	0.068	strong		0.557	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
MAP9	79884	hgsc.bcm.edu	37	4	156289900	156289900	+	Silent	SNP	C	C	T	rs3733390	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:156289900C>T	ENST00000311277.4	-	5	809	c.546G>A	c.(544-546)ttG>ttA	p.L182L	AC097467.2_ENST00000596165.1_RNA|MAP9_ENST00000515654.1_Silent_p.L182L|AC097467.2_ENST00000600928.1_RNA|AC097467.2_ENST00000598890.1_RNA|MAP9_ENST00000379248.2_Silent_p.L109L|AC097467.2_ENST00000597831.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	182					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		TTTTCTTTTTCAACATACTCC	0.388													C|||	1848	0.36901	0.1649	0.3963	5008	,	,		18797	0.6419		0.3549	False		,,,				2504	0.3589				p.L182L		Atlas-SNP	.											.	MAP9	79	.	0			c.G546A						PASS	.	C		805,3601	320.4+/-296.6	58,689,1456	157.0	144.0	148.0		546	-1.9	0.1	4	dbSNP_107	148	2785,5815	439.7+/-359.3	457,1871,1972	no	coding-synonymous	MAP9	NM_001039580.1		515,2560,3428	TT,TC,CC		32.3837,18.2705,27.6026		182/648	156289900	3590,9416	2203	4300	6503	SO:0001819	synonymous_variant	79884	exon5			CTTTTTCAACATA	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"""aster-associated protein"""	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.546G>A	4.37:g.156289900C>T		Somatic	551	1	0.00181488		WXS	Illumina HiSeq	Phase_I	546	252	0.461538	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Silent	SNP	ENST00000311277.4	37	CCDS35493.1																																																																																			C|0.687;T|0.313	0.313	strong		0.388	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	
CA5A	763	hgsc.bcm.edu	37	16	87938398	87938398	+	Silent	SNP	G	G	A	rs7186698	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:87938398G>A	ENST00000309893.2	-	3	518	c.453C>T	c.(451-453)ccC>ccT	p.P151P		NM_001739.1	NP_001730.1	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial	151					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(80;0.0513)	Brinzolamide(DB01194)|Zonisamide(DB00909)	AAACCTCTGCGGGGTACGCGT	0.577													G|||	837	0.167133	0.0772	0.1354	5008	,	,		19267	0.1677		0.1958	False		,,,				2504	0.2812				p.P151P		Atlas-SNP	.											.	CA5A	32	.	0			c.C453T						PASS	.	G		420,3976	202.8+/-225.5	21,378,1799	100.0	90.0	93.0		453	-8.4	0.1	16	dbSNP_116	93	1751,6849	317.6+/-313.3	191,1369,2740	no	coding-synonymous	CA5A	NM_001739.1		212,1747,4539	AA,AG,GG		20.3605,9.5541,16.7051		151/306	87938398	2171,10825	2198	4300	6498	SO:0001819	synonymous_variant	763	exon3			CTCTGCGGGGTAC	L19297	CCDS10965.1	16q24.2	2012-08-21			ENSG00000174990	ENSG00000174990	4.2.1.1	"""Carbonic anhydrases"""	1377	protein-coding gene	gene with protein product		114761		CA5		8356065, 7490083	Standard	NM_001739		Approved	CAV, CAVA	uc002fkn.1	P35218	OTTHUMG00000137677	ENST00000309893.2:c.453C>T	16.37:g.87938398G>A		Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	278	156	0.561151	NM_001739	B2RPF2	Silent	SNP	ENST00000309893.2	37	CCDS10965.1																																																																																			G|0.840;A|0.160	0.160	strong		0.577	CA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269164.1	NM_001739	
CYFIP1	23191	hgsc.bcm.edu	37	15	22969232	22969232	+	Missense_Mutation	SNP	G	G	A	rs7170637	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:22969232G>A	ENST00000313077.7	+	22	2583	c.2458G>A	c.(2458-2460)Ggc>Agc	p.G820S	CYFIP1_ENST00000560848.1_Missense_Mutation_p.G820S|CYFIP1_ENST00000435939.2_Missense_Mutation_p.G389S	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		GACGCTGGACGGCTTCGACGC	0.607													A|||	1331	0.265775	0.6906	0.1484	5008	,	,		20818	0.004		0.1769	False		,,,				2504	0.136				p.G820S		Atlas-SNP	.											CYFIP1_ENST00000435939,colon,carcinoma,0,2	CYFIP1	159	2	0			c.G2458A						PASS	.	A	SER/GLY,SER/GLY	2625,1781	527.9+/-372.3	787,1051,365	137.0	101.0	113.0		1165,2458	5.4	1.0	15	dbSNP_116	113	1407,7193	753.6+/-407.5	124,1159,3017	yes	missense,missense	CYFIP1	NM_001033028.1,NM_014608.2	56,56	911,2210,3382	AA,AG,GG		16.3605,40.4222,31.0011	benign,benign	389/823,820/1254	22969232	4032,8974	2203	4300	6503	SO:0001583	missense	23191	exon22			CTGGACGGCTTCG	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.2458G>A	15.37:g.22969232G>A	ENSP00000324549:p.Gly820Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_014608		Missense_Mutation	SNP	ENST00000313077.7	37	CCDS10009.1	532	0.24358974358974358	340	0.6910569105691057	51	0.1408839779005525	3	0.005244755244755245	138	0.1820580474934037	A	9.988	1.229904	0.22542	0.595778	0.163605	ENSG00000068793	ENST00000313077;ENST00000412127;ENST00000435939	T;T	0.20332	2.08;2.08	5.41	5.41	0.78517	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00210	-1.845	0.41978	P	0.009217999999999948	B;B;B	0.13145	0.002;0.007;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.33701	-0.9858	9	0.08381	T	0.77	-23.3927	11.3522	0.49594	0.9287:0.0:0.0713:0.0	rs7170637;rs17844900;rs17857620;rs7170637	848;389;820	E7EQ04;Q7L576-2;Q7L576	.;.;CYFP1_HUMAN	S	820;848;389	ENSP00000324549:G820S;ENSP00000405956:G389S	ENSP00000324549:G820S	G	+	1	0	CYFIP1	20520673	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	6.190000	0.72057	0.901000	0.36495	-0.361000	0.07541	GGC	G|0.704;A|0.296	0.296	strong		0.607	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
VWA5B2	90113	hgsc.bcm.edu	37	3	183955109	183955109	+	Silent	SNP	C	C	T	rs843334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:183955109C>T	ENST00000426955.2	+	11	1729	c.1629C>T	c.(1627-1629)ccC>ccT	p.P543P	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Silent_p.P324P	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	554										breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						TGCTGACCCCCCGGGAGATCC	0.622													C|||	996	0.198882	0.1377	0.1844	5008	,	,		16035	0.2351		0.2256	False		,,,				2504	0.227				p.P543P		Atlas-SNP	.											.	VWA5B2	47	.	0			c.C1629T						PASS	.	C		207,1177		17,173,502	42.0	43.0	43.0		1629	1.4	1.0	3	dbSNP_86	43	660,2522		69,522,1000	no	coding-synonymous	VWA5B2	NM_138345.1		86,695,1502	TT,TC,CC		20.7417,14.9566,18.9882		543/1243	183955109	867,3699	692	1591	2283	SO:0001819	synonymous_variant	90113	exon11			GACCCCCCGGGAG		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.1629C>T	3.37:g.183955109C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	125	123	0.984	NM_138345	B9EGN7	Silent	SNP	ENST00000426955.2	37	CCDS54686.1																																																																																			C|0.817;T|0.183	0.183	strong		0.622	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G	rs142480630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140188354C>G	ENST00000530339.1	+	1	1582	c.1582C>G	c.(1582-1584)Cta>Gta	p.L528V	PCDHA4_ENST00000356878.4_Missense_Mutation_p.L528V|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.L528V	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACGAGGAGCTAGAGCTGCT	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17618	0.0		0.0755	False		,,,				2504	0.0082				p.L528V		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,8	PCDHA4	419	8	0			c.C1582G						scavenged	.						70.0	75.0	74.0					5																	140188354		2203	4300	6503	SO:0001583	missense	56144	exon1			GAGGAGCTAGAGC	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1582C>G	5.37:g.140188354C>G	ENSP00000435300:p.Leu528Val	Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	56	13	0.232143	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	c	11.23	1.577307	0.28092	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.51325	0.71;0.71;0.71	4.18	2.19	0.27852	Cadherin (5);Cadherin-like (1);	0.000000	0.28952	U	0.013601	T	0.34948	0.0915	N	0.25332	0.735	0.20764	N	0.999854	P;B;B	0.43662	0.814;0.101;0.207	B;B;B	0.43508	0.422;0.421;0.214	T	0.15150	-1.0447	10	0.51188	T	0.08	.	8.8809	0.35374	0.2588:0.4914:0.2498:0.0	.	528;528;528	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	V	528	ENSP00000423470:L528V;ENSP00000349344:L528V;ENSP00000435300:L528V	ENSP00000349344:L528V	L	+	1	2	PCDHA4	140168538	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-1.847000	0.01675	0.874000	0.35823	0.580000	0.79431	CTA	C|0.999;G|0.001	0.001	weak		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
NEIL3	55247	hgsc.bcm.edu	37	4	178262784	178262784	+	Missense_Mutation	SNP	A	A	G	rs34193982	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:178262784A>G	ENST00000264596.3	+	6	975	c.857A>G	c.(856-858)cAt>cGt	p.H286R	RP11-376O6.2_ENST00000506895.1_RNA	NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	286			H -> R (in dbSNP:rs34193982). {ECO:0000269|Ref.3}.		base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		AATCCTCAACATGTTGACATA	0.363								Base excision repair (BER), DNA glycosylases					A|||	457	0.091254	0.0053	0.0533	5008	,	,		18278	0.1012		0.161	False		,,,				2504	0.1524				p.H286R		Atlas-SNP	.											.	NEIL3	89	.	0			c.A857G						PASS	.	A	ARG/HIS	118,4288	88.7+/-127.4	2,114,2087	85.0	76.0	79.0		857	-4.6	0.0	4	dbSNP_126	79	1324,7276	260.6+/-283.4	97,1130,3073	yes	missense	NEIL3	NM_018248.2	29	99,1244,5160	GG,GA,AA		15.3953,2.6782,11.0872	benign	286/606	178262784	1442,11564	2203	4300	6503	SO:0001583	missense	55247	exon6			CTCAACATGTTGA	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.857A>G	4.37:g.178262784A>G	ENSP00000264596:p.His286Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	54	17	0.314815	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	223	0.1021062271062271	4	0.008130081300813009	33	0.09116022099447514	63	0.11013986013986014	123	0.16226912928759896	A	6.487	0.458106	0.12342	0.026782	0.153953	ENSG00000109674	ENST00000264596	T	0.03717	3.83	5.24	-4.55	0.03441	.	0.860608	0.10787	N	0.634143	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48875	-0.8996	9	0.13853	T	0.58	-1.6377	0.0153	0.00002	0.3143:0.1952:0.2021:0.2884	rs34193982	286	Q8TAT5	NEIL3_HUMAN	R	286	ENSP00000264596:H286R	ENSP00000264596:H286R	H	+	2	0	NEIL3	178499778	0.011000	0.17503	0.007000	0.13788	0.997000	0.91878	0.245000	0.18142	-0.480000	0.06803	0.533000	0.62120	CAT	A|0.894;G|0.106	0.106	strong		0.363	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
MYO5B	4645	hgsc.bcm.edu	37	18	47566678	47566678	+	Missense_Mutation	SNP	C	C	G	rs141998504	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:47566678C>G	ENST00000285039.7	-	3	444	c.145G>C	c.(145-147)Gaa>Caa	p.E49Q		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	49					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		ATTGGGTATTCCAGAATCTAA	0.423													C|||	37	0.00738818	0.0	0.0072	5008	,	,		21143	0.0		0.0119	False		,,,				2504	0.0204				p.E49Q		Atlas-SNP	.											.	MYO5B	178	.	0			c.G145C						PASS	.	C	GLN/GLU	9,3901		0,9,1946	236.0	229.0	231.0		145	5.1	0.5	18	dbSNP_134	231	109,8203		2,105,4049	yes	missense	MYO5B	NM_001080467.2	29	2,114,5995	GG,GC,CC		1.3114,0.2302,0.9655	benign	49/1849	47566678	118,12104	1955	4156	6111	SO:0001583	missense	4645	exon3			GGTATTCCAGAAT	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.145G>C	18.37:g.47566678C>G	ENSP00000285039:p.Glu49Gln	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	285	141	0.494737	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	11.82	1.752493	0.31046	0.002302	0.013114	ENSG00000167306	ENST00000285039;ENST00000356732	D	0.95342	-3.68	5.95	5.07	0.68467	.	0.286641	0.37304	N	0.002144	D	0.88055	0.6334	L	0.41824	1.3	0.80722	D	1	B;B	0.10296	0.003;0.0	B;B	0.14023	0.01;0.003	D	0.85261	0.1050	10	0.19590	T	0.45	.	14.4235	0.67200	0.0:0.7192:0.2808:0.0	.	48;49	Q7Z7A5;Q9ULV0	.;MYO5B_HUMAN	Q	49;48	ENSP00000285039:E49Q	ENSP00000285039:E49Q	E	-	1	0	MYO5B	45820676	0.998000	0.40836	0.542000	0.28115	0.279000	0.26890	3.687000	0.54692	1.508000	0.48769	0.563000	0.77884	GAA	C|0.992;G|0.008	0.008	strong		0.423	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
KIAA2018	205717	hgsc.bcm.edu	37	3	113376119	113376119	+	Silent	SNP	C	C	T	rs62265538|rs112313093|rs59601191		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:113376119C>T	ENST00000478658.1	-	5	4427	c.4410G>A	c.(4408-4410)caG>caA	p.Q1470Q	KIAA2018_ENST00000316407.4_Silent_p.Q1470Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1470	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgctgctgctgctgctgct	0.493																																					p.Q1470Q		Atlas-SNP	.											KIAA2018,rectum,carcinoma,0,1	KIAA2018	180	1	0			c.G4410A						PASS	.						58.0	65.0	63.0					3																	113376119		2185	4279	6464	SO:0001819	synonymous_variant	205717	exon7			CTGCTGCTGCTGC	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4410G>A	3.37:g.113376119C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	141	24	0.170213	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			C|0.500;T|0.500	0.500	weak		0.493	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
PCDHGB2	56103	hgsc.bcm.edu	37	5	140741761	140741761	+	Missense_Mutation	SNP	A	A	G	rs57735633	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140741761A>G	ENST00000522605.1	+	1	2059	c.2059A>G	c.(2059-2061)Aaa>Gaa	p.K687E	PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	687			K -> E (in dbSNP:rs57735633).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K687E(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCCCAGGCAAAACTGCAGTT	0.592													.|||	650	0.129792	0.3124	0.0692	5008	,	,		18834	0.0407		0.0875	False		,,,				2504	0.0613				p.K687E		Atlas-SNP	.											PCDHGB2_ENST00000522605,NS,carcinoma,0,1	PCDHGB2	196	1	1	Substitution - Missense(1)	stomach(1)	c.A2059G						PASS	.	G	,,,,,GLU/LYS,GLU/LYS	1085,2951		131,823,1064	75.0	77.0	77.0		,,,,,2059,2059	4.1	0.8	5	dbSNP_129	77	752,7590		30,692,3449	no	intron,intron,intron,intron,intron,missense,missense	PCDHGB2,PCDHGB1,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018922.2,NM_018923.2,NM_032096.1	,,,,,56,56	161,1515,4513	GG,GA,AA		9.0146,26.8831,14.8408	,,,,,,	,,,,,687/932,687/812	140741761	1837,10541	2018	4171	6189	SO:0001583	missense	56103	exon1			CAGGCAAAACTGC	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"""Cadherins / Protocadherins : Clustered"""	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.2059A>G	5.37:g.140741761A>G	ENSP00000429018:p.Lys687Glu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	170	82	0.482353	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	37	CCDS54924.1	284	0.13003663003663005	154	0.3130081300813008	29	0.08011049723756906	24	0.04195804195804196	77	0.10158311345646438	.	5.134	0.210329	0.09757	0.268831	0.090146	ENSG00000253910	ENST00000522605	T	0.47869	0.83	4.95	4.06	0.47325	.	.	.	.	.	T	0.00012	0.0000	N	0.00055	-2.37	0.48040	P	4.250000000000087E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30446	-0.9978	8	0.11182	T	0.66	.	9.6584	0.39941	0.2318:0.0:0.7682:0.0	rs57735633;rs62378418	687;687	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	E	687	ENSP00000429018:K687E	ENSP00000429018:K687E	K	+	1	0	PCDHGB2	140721945	0.608000	0.26966	0.828000	0.32881	0.054000	0.15201	0.831000	0.27476	1.235000	0.43724	-0.380000	0.06706	AAA	A|0.877;G|0.123	0.123	strong		0.592	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923	
TBC1D32	221322	hgsc.bcm.edu	37	6	121629167	121629167	+	Silent	SNP	G	G	A	rs9398629	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:121629167G>A	ENST00000398212.2	-	5	694	c.645C>T	c.(643-645)tgC>tgT	p.C215C	TBC1D32_ENST00000275159.6_Silent_p.C215C	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	215					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TCAGTTTTTCGCAGAGAGTAG	0.358													G|||	1581	0.315695	0.0885	0.2118	5008	,	,		15123	0.5863		0.2644	False		,,,				2504	0.4703				p.C215C		Atlas-SNP	.											.	C6orf170	146	.	0			c.C645T						PASS	.	G		468,3224		31,406,1409	107.0	100.0	102.0		645	0.8	1.0	6	dbSNP_119	102	2136,6054		270,1596,2229	no	coding-synonymous	C6orf170	NM_152730.4		301,2002,3638	AA,AG,GG		26.0806,12.6761,21.9155		215/1258	121629167	2604,9278	1846	4095	5941	SO:0001819	synonymous_variant	221322	exon5			TTTTTCGCAGAGA	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.645C>T	6.37:g.121629167G>A		Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	262	129	0.492366	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																			G|0.704;A|0.296	0.296	strong		0.358	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
PCDHGA3	56112	hgsc.bcm.edu	37	5	140724060	140724060	+	Missense_Mutation	SNP	A	A	C	rs11575948	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140724060A>C	ENST00000253812.6	+	1	460	c.460A>C	c.(460-462)Att>Ctt	p.I154L	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	154	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> L (in dbSNP:rs11575948).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGATTTCCAATTAAAACTGC	0.388													N|||	644	0.128594	0.3079	0.0692	5008	,	,		18568	0.0407		0.0885	False		,,,				2504	0.0603				p.I154L		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.A460C						PASS	.	C	,,LEU/ILE,LEU/ILE	991,2731		121,749,991	65.0	62.0	63.0		,,460,460	5.7	1.0	5	dbSNP_120	63	743,7473		29,685,3394	yes	intron,intron,missense,missense	PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_032011.1	,,5,5	150,1434,4385	CC,CA,AA		9.0433,26.6255,14.525	,,,	,,154/933,154/830	140724060	1734,10204	1861	4108	5969	SO:0001583	missense	56112	exon1			TTTCCAATTAAAA	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.460A>C	5.37:g.140724060A>C	ENSP00000253812:p.Ile154Leu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	95	60	0.631579	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	269	0.12316849816849818	149	0.30284552845528456	28	0.07734806629834254	20	0.03496503496503497	72	0.09498680738786279	.	1.161	-0.643718	0.03531	0.266255	0.090433	ENSG00000254245	ENST00000253812	T	0.18338	2.22	5.65	5.65	0.86999	Cadherin (2);Cadherin-like (1);	0.000000	0.30118	N	0.010365	T	0.00012	0.0000	N	0.00020	-2.76	0.48040	P	4.269999999999552E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35871	-0.9771	9	0.02654	T	1	.	6.9223	0.24395	0.1475:0.7133:0.0:0.1393	rs11575948;rs52796144;rs57987613;rs11575948	154;154	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	L	154	ENSP00000253812:I154L	ENSP00000253812:I154L	I	+	1	0	PCDHGA3	140704244	0.002000	0.14202	0.996000	0.52242	0.917000	0.54804	0.068000	0.14531	1.543000	0.49345	-0.121000	0.15023	ATT	A|0.881;C|0.119	0.119	strong		0.388	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
ZNF717	100131827	hgsc.bcm.edu	37	3	75790797	75790797	+	De_novo_Start_InFrame	SNP	C	C	T	rs147946451	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:75790797C>T	ENST00000478296.1	-	0	274				ZNF717_ENST00000491507.1_5'UTR|ZNF717_ENST00000477374.1_Missense_Mutation_p.V50M|ZNF717_ENST00000400845.3_Missense_Mutation_p.V43M|ZNF717_ENST00000422325.1_Missense_Mutation_p.V50M			Q9BY31	ZN717_HUMAN	zinc finger protein 717						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)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TCCAGCATCACGTCCCTGTAC	0.502																																					p.V50M		Atlas-SNP	.											ZNF717,NS,malignant_melanoma,0,1	ZNF717	160	1	0			c.G148A						scavenged	.						16.0	13.0	14.0					3																	75790797		444	1237	1681			100131827	exon3			GCATCACGTCCCT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965		3.37:g.75790797C>T		Somatic	4	1	0.25		WXS	Illumina HiSeq	Phase_I	14	6	0.428571	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		562	0.2573260073260073	83	0.16869918699186992	111	0.30662983425414364	134	0.23426573426573427	234	0.3087071240105541	.	14.80	2.645039	0.47258	.	.	ENSG00000227124	ENST00000477374;ENST00000422325;ENST00000400845;ENST00000468296	T;T;T;T	0.04015	3.73;3.73;3.73;3.73	1.97	1.97	0.26223	.	.	.	.	.	T	0.00012	0.0000	M	0.92833	3.35	0.36926	P	0.10836100000000004	D	0.89917	1.0	D	0.64776	0.929	T	0.22417	-1.0217	8	0.72032	D	0.01	.	9.6897	0.40120	0.0:1.0:0.0:0.0	.	50	C9JSV9	.	M	50;50;43;50	ENSP00000417902:V50M;ENSP00000409514:V50M;ENSP00000383643:V43M;ENSP00000418187:V50M	ENSP00000383643:V43M	V	-	1	0	ZNF717	75873487	0.243000	0.23878	0.981000	0.43875	0.552000	0.35366	1.184000	0.32053	1.127000	0.42034	0.545000	0.68477	GTG	C|0.753;T|0.247	0.247	strong		0.502	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
FREM2	341640	hgsc.bcm.edu	37	13	39430314	39430314	+	Missense_Mutation	SNP	C	C	T	rs9548509	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:39430314C>T	ENST00000280481.7	+	12	7193	c.6977C>T	c.(6976-6978)aCc>aTc	p.T2326I		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2326	Calx-beta 5.		T -> I (in dbSNP:rs9548509). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		ATCGAAGTTACCTTTGACGGG	0.383													T|||	3866	0.771965	0.7254	0.7911	5008	,	,		16647	0.9712		0.6889	False		,,,				2504	0.7014				p.T2326I		Atlas-SNP	.											FREM2,NS,carcinoma,0,1	FREM2	385	1	0			c.C6977T						PASS	.	T	ILE/THR	3365,1041	381.6+/-324.1	1289,787,127	93.0	93.0	93.0		6977	5.7	0.0	13	dbSNP_119	93	6024,2576	418.7+/-352.8	2118,1788,394	yes	missense	FREM2	NM_207361.4	89	3407,2575,521	TT,TC,CC		29.9535,23.6269,27.8102	benign	2326/3170	39430314	9389,3617	2203	4300	6503	SO:0001583	missense	341640	exon12			AAGTTACCTTTGA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.6977C>T	13.37:g.39430314C>T	ENSP00000280481:p.Thr2326Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	1692	0.7747252747252747	359	0.7296747967479674	269	0.7430939226519337	558	0.9755244755244755	506	0.6675461741424802	T	10.12	1.263681	0.23136	0.763731	0.700465	ENSG00000150893	ENST00000280481	T	0.25749	1.78	5.66	5.66	0.87406	Na-Ca exchanger/integrin-beta4 (2);	0.208390	0.41001	N	0.000976	T	0.00012	0.0000	N	0.00608	-1.33	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38757	-0.9646	9	0.22706	T	0.39	.	11.7377	0.51775	0.0:0.069:0.0:0.931	rs9548509;rs52835266;rs61503873;rs9548509	2326;2326	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	I	2326	ENSP00000280481:T2326I	ENSP00000280481:T2326I	T	+	2	0	FREM2	38328314	0.969000	0.33509	0.003000	0.11579	0.198000	0.23893	6.137000	0.71710	0.979000	0.38497	-0.361000	0.07541	ACC	C|0.256;T|0.744	0.744	strong		0.383	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
NT5DC2	64943	hgsc.bcm.edu	37	3	52563199	52563199	+	Missense_Mutation	SNP	A	A	T	rs35920544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52563199A>T	ENST00000307076.4	-	2	673	c.273T>A	c.(271-273)agT>agA	p.S91R	NT5DC2_ENST00000459839.1_Missense_Mutation_p.S128R|NT5DC2_ENST00000490681.1_5'UTR|NT5DC2_ENST00000422318.2_Missense_Mutation_p.S128R|NT5DC2_ENST00000307092.4_Missense_Mutation_p.S57R	NM_022908.2	NP_075059.1	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2	91			S -> R (in dbSNP:rs35920544).				hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(1)|lung(3)|prostate(1)|stomach(1)	6				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)		CACGGGCGGTACTGAAGATCT	0.592													A|||	374	0.0746805	0.2247	0.0403	5008	,	,		19872	0.0		0.0089	False		,,,				2504	0.0409				p.S128R		Atlas-SNP	.											.	NT5DC2	35	.	0			c.T384A						PASS	.	A	ARG/SER,ARG/SER	942,3464	358.4+/-314.3	104,734,1365	231.0	183.0	200.0		384,273	0.3	0.0	3	dbSNP_126	200	187,8413	82.9+/-145.4	1,185,4114	yes	missense,missense	NT5DC2	NM_001134231.1,NM_022908.2	110,110	105,919,5479	TT,TA,AA		2.1744,21.3799,8.6806	benign,benign	128/558,91/521	52563199	1129,11877	2203	4300	6503	SO:0001583	missense	64943	exon2			GGCGGTACTGAAG	AF131781	CCDS2858.1, CCDS46843.1	3p21.1	2006-02-03			ENSG00000168268	ENSG00000168268			25717	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_022908		Approved	FLJ12442	uc003den.3	Q9H857	OTTHUMG00000158626	ENST00000307076.4:c.273T>A	3.37:g.52563199A>T	ENSP00000302468:p.Ser91Arg	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	165	71	0.430303	NM_001134231	C9JTZ6|E9PAL9|O95888|Q96C80|Q9H9Z8	Missense_Mutation	SNP	ENST00000307076.4	37	CCDS2858.1	138|138	0.06318681318681318|0.06318681318681318	118|118	0.23983739837398374|0.23983739837398374	13|13	0.03591160220994475|0.03591160220994475	0|0	0.0|0.0	7|7	0.009234828496042216|0.009234828496042216	A|A	13.39|13.39	2.223778|2.223778	0.39300|0.39300	0.213799|0.213799	0.021744|0.021744	ENSG00000168268|ENSG00000168268	ENST00000307092;ENST00000307076;ENST00000422318;ENST00000459839|ENST00000489316	T;T;T;T|.	0.22336|.	1.96;1.96;1.96;1.96|.	5.41|5.41	0.323|0.323	0.15893|0.15893	HAD-like domain (1);|.	0.479285|.	0.24433|.	N|.	0.038576|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.33485|0.33485	1.01|1.01	0.30519|0.30519	P|P	0.768655|0.768655	B;B;B|.	0.31705|.	0.336;0.034;0.044|.	B;B;B|.	0.39027|.	0.288;0.071;0.103|.	T|T	0.24870|0.24870	-1.0148|-1.0148	9|4	0.66056|.	D|.	0.02|.	-0.4759|-0.4759	7.7153|7.7153	0.28700|0.28700	0.4676:0.0:0.5324:0.0|0.4676:0.0:0.5324:0.0	rs35920544;rs59661193|rs35920544;rs59661193	128;91;128|.	C9JTZ6;Q9H857;E9PAL9|.	.;NT5D2_HUMAN;.|.	R|N	57;91;128;128|60	ENSP00000306017:S57R;ENSP00000302468:S91R;ENSP00000406933:S128R;ENSP00000419547:S128R|.	ENSP00000302468:S91R|.	S|Y	-|-	3|1	2|0	NT5DC2|NT5DC2	52538239|52538239	0.565000|0.565000	0.26610|0.26610	0.042000|0.042000	0.18584|0.18584	0.352000|0.352000	0.29268|0.29268	1.035000|1.035000	0.30216|0.30216	0.056000|0.056000	0.16144|0.16144	-1.280000|-1.280000	0.01385|0.01385	AGT|TAC	A|0.925;T|0.075	0.075	strong		0.592	NT5DC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000351509.1	NM_022908	
OVGP1	5016	hgsc.bcm.edu	37	1	111957592	111957592	+	Missense_Mutation	SNP	A	A	G	rs56294468|rs376377993	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111957592A>G	ENST00000369732.3	-	11	1586	c.1531T>C	c.(1531-1533)Tct>Cct	p.S511P		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	511				S -> P (in Ref. 2; AAB04126). {ECO:0000305}.	binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		TAACCCACAGAGGTCAGGGTC	0.572													a|||	1118	0.223243	0.1989	0.1715	5008	,	,		18021	0.1587		0.2763	False		,,,				2504	0.3047				p.S511P		Atlas-SNP	.											OVGP1_ENST00000369728,NS,malignant_melanoma,+1,2	OVGP1	177	2	0			c.T1531C						PASS	.	A	PRO/SER	774,3610	297.3+/-284.7	91,592,1509	64.0	61.0	62.0		1531	-5.5	0.0	1	dbSNP_129	62	2579,6021	404.8+/-348.3	388,1803,2109	yes	missense	OVGP1	NM_002557.3	74	479,2395,3618	GG,GA,AA		29.9884,17.6551,25.8241	benign	511/679	111957592	3353,9631	2192	4300	6492	SO:0001583	missense	5016	exon11			CCACAGAGGTCAG	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1531T>C	1.37:g.111957592A>G	ENSP00000358747:p.Ser511Pro	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	185	67	0.362162	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	440	0.20146520146520147	91	0.18495934959349594	70	0.19337016574585636	77	0.1346153846153846	202	0.26649076517150394	a	3.357	-0.131299	0.06753	0.176551	0.299884	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.03386	3.95	2.76	-5.52	0.02560	.	.	.	.	.	T	0.00356	0.0011	N	0.01576	-0.805	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46359	-0.9197	8	0.25751	T	0.34	.	4.3367	0.11090	0.4549:0.0:0.3888:0.1564	rs56294468;rs61742540	511;575	Q12889;Q59HH5	OVGP1_HUMAN;.	P	511;575;319	ENSP00000358747:S511P	ENSP00000358743:S575P	S	-	1	0	OVGP1	111759115	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.421000	0.07053	-1.460000	0.01911	-0.621000	0.04028	TCT	A|0.767;G|0.233	0.233	strong		0.572	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49379167	49379167	+	Silent	SNP	C	C	T	rs386810065|rs524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49379167C>T	ENST00000200453.5	+	3	2231	c.1962C>T	c.(1960-1962)gcC>gcT	p.A654A		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	654					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		AAGCTGTGGCCACACCTTCCC	0.587													C|||	1786	0.356629	0.5764	0.2896	5008	,	,		15979	0.1984		0.2803	False		,,,				2504	0.3487				p.A654A		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.C1962T						PASS	.	C		2270,2136	590.6+/-387.4	567,1136,500	85.0	83.0	83.0		1962	2.1	0.0	19	dbSNP_36	83	2469,6131	402.4+/-347.5	352,1765,2183	no	coding-synonymous	PPP1R15A	NM_014330.3		919,2901,2683	TT,TC,CC		28.7093,48.4793,36.437		654/675	49379167	4739,8267	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon3			TGTGGCCACACCT	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1962C>T	19.37:g.49379167C>T		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			C|0.647;T|0.353	0.353	strong		0.587	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
TNIP1	10318	hgsc.bcm.edu	37	5	150441711	150441711	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150441711G>C	ENST00000389378.2	-	4	922	c.334C>G	c.(334-336)Cca>Gca	p.P112A	TNIP1_ENST00000523338.1_Missense_Mutation_p.P112A|TNIP1_ENST00000315050.7_Missense_Mutation_p.P112A|TNIP1_ENST00000518977.1_Missense_Mutation_p.P112A|TNIP1_ENST00000523200.1_Missense_Mutation_p.P112A|TNIP1_ENST00000522226.1_Missense_Mutation_p.P112A|TNIP1_ENST00000520931.1_Missense_Mutation_p.P59A|TNIP1_ENST00000521591.1_Missense_Mutation_p.P112A|TNIP1_ENST00000524280.1_Missense_Mutation_p.P112A	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	112	Interacts with Nef.				defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCTGGACTGGTGCTGGCTTG	0.498																																					p.P112A		Atlas-SNP	.											.	TNIP1	51	.	0			c.C334G						PASS	.						115.0	102.0	106.0					5																	150441711		2203	4300	6503	SO:0001583	missense	10318	exon4			GGACTGGTGCTGG	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.334C>G	5.37:g.150441711G>C	ENSP00000374029:p.Pro112Ala	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Missense_Mutation	SNP	ENST00000389378.2	37	CCDS34280.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.971545	0.34754	.	.	ENSG00000145901	ENST00000520931;ENST00000389378;ENST00000315050;ENST00000523338;ENST00000544828;ENST00000417127;ENST00000539213;ENST00000522226;ENST00000521591;ENST00000518977;ENST00000524280;ENST00000523200;ENST00000545840;ENST00000522100;ENST00000520695;ENST00000521001	T;T;T;T;T;T;T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36	4.96	-1.53	0.08611	.	0.304128	0.34484	N	0.003934	T	0.23649	0.0572	L	0.56769	1.78	0.09310	N	1	B;B;B;B;B;B;B	0.23377	0.081;0.052;0.084;0.052;0.052;0.028;0.015	B;B;B;B;B;B;B	0.20184	0.028;0.011;0.022;0.017;0.024;0.015;0.015	T	0.09143	-1.0688	10	0.30078	T	0.28	-0.1324	1.0768	0.01634	0.2623:0.2792:0.3156:0.1429	.	112;66;66;112;112;112;112	B7Z8K2;A4F1X9;A4F1X7;E7EPY1;E7ET96;A4F1W9;Q15025	.;.;.;.;.;.;TNIP1_HUMAN	A	59;112;112;112;69;69;74;112;112;112;112;112;69;59;112;112	ENSP00000429891:P59A;ENSP00000374029:P112A;ENSP00000317891:P112A;ENSP00000428243:P112A;ENSP00000428187:P112A;ENSP00000430760:P112A;ENSP00000430971:P112A;ENSP00000429912:P112A;ENSP00000431105:P112A;ENSP00000428487:P59A;ENSP00000430279:P112A;ENSP00000428404:P112A	ENSP00000317891:P112A	P	-	1	0	TNIP1	150421904	0.527000	0.26306	0.003000	0.11579	0.632000	0.37999	1.069000	0.30641	0.009000	0.14813	-0.142000	0.14014	CCA	.	.	none		0.498	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
PGR	5241	hgsc.bcm.edu	37	11	100922202	100922202	+	Silent	SNP	G	G	A	rs1042839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:100922202G>A	ENST00000325455.5	-	5	3763	c.2310C>T	c.(2308-2310)caC>caT	p.H770H	PGR_ENST00000263463.5_Silent_p.H668H|PGR_ENST00000534013.1_Silent_p.H176H	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	770	Steroid-binding.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	GCCCACTGACGTGTTTGTAGG	0.348													G|||	352	0.0702875	0.0061	0.1354	5008	,	,		16564	0.0099		0.1789	False		,,,				2504	0.0613				p.H770H	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.C2310T						PASS	.	G	,	131,4275	94.8+/-133.5	1,129,2073	127.0	123.0	124.0		2310,1818	-0.9	1.0	11	dbSNP_86	124	1407,7193	271.7+/-289.7	106,1195,2999	no	coding-synonymous,coding-synonymous	PGR	NM_000926.4,NM_001202474.1	,	107,1324,5072	AA,AG,GG		16.3605,2.9732,11.8253	,	770/934,606/770	100922202	1538,11468	2203	4300	6503	SO:0001819	synonymous_variant	5241	exon5			ACTGACGTGTTTG	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.2310C>T	11.37:g.100922202G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	210	97	0.461905	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Silent	SNP	ENST00000325455.5	37	CCDS8310.1																																																																																			G|0.892;A|0.108	0.108	strong		0.348	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
CACNA2D4	93589	hgsc.bcm.edu	37	12	1988167	1988167	+	Silent	SNP	T	T	C	rs7966806	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:1988167T>C	ENST00000382722.5	-	15	1961	c.1599A>G	c.(1597-1599)tcA>tcG	p.S533S	CACNA2D4_ENST00000586184.1_Silent_p.S533S|CACNA2D4_ENST00000587995.1_Silent_p.S533S|CACNA2D4_ENST00000588077.1_Silent_p.S469S|CACNA2D4_ENST00000585732.1_Silent_p.S418S|CACNA2D4_ENST00000585708.1_Silent_p.S469S	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	533	Cache.				calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.S533S(1)		endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GGGCCACATCTGAGCCCACCA	0.602													T|||	763	0.152356	0.3396	0.0663	5008	,	,		16899	0.0357		0.1083	False		,,,				2504	0.1258				p.S533S	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											CACNA2D4_ENST00000382722,NS,carcinoma,0,1	CACNA2D4	220	1	1	Substitution - coding silent(1)	stomach(1)	c.A1599G						PASS	.	T		1179,2869		171,837,1016	42.0	48.0	46.0		1599	-10.2	0.5	12	dbSNP_116	46	802,7566		40,722,3422	no	coding-synonymous	CACNA2D4	NM_172364.4		211,1559,4438	CC,CT,TT		9.5841,29.1255,15.9552		533/1138	1988167	1981,10435	2024	4184	6208	SO:0001819	synonymous_variant	93589	exon15			CACATCTGAGCCC	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.1599A>G	12.37:g.1988167T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	70	25	0.357143	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Silent	SNP	ENST00000382722.5	37	CCDS44785.1																																																																																			T|0.874;C|0.126	0.126	strong		0.602	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
SWT1	54823	hgsc.bcm.edu	37	1	185143721	185143721	+	Missense_Mutation	SNP	A	A	G	rs10489579	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:185143721A>G	ENST00000367500.4	+	5	607	c.442A>G	c.(442-444)Att>Gtt	p.I148V	SWT1_ENST00000367501.3_Missense_Mutation_p.I148V	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	148			I -> V (in dbSNP:rs10489579). {ECO:0000269|PubMed:15489334}.							breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						TGACCATGGAATTAAAAGCCT	0.368													A|||	2177	0.434704	0.6982	0.3487	5008	,	,		19153	0.2718		0.3439	False		,,,				2504	0.4008				p.I148V		Atlas-SNP	.											.	SWT1	88	.	0			c.A442G						PASS	.	A	VAL/ILE,VAL/ILE	2802,1604	659.4+/-400.6	907,988,308	53.0	53.0	53.0		442,442	0.9	0.0	1	dbSNP_119	53	3071,5529	467.9+/-367.2	556,1959,1785	yes	missense,missense	SWT1	NM_001105518.1,NM_017673.6	29,29	1463,2947,2093	GG,GA,AA		35.7093,36.4049,45.1561	benign,benign	148/901,148/901	185143721	5873,7133	2203	4300	6503	SO:0001583	missense	54823	exon5			CATGGAATTAAAA	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.442A>G	1.37:g.185143721A>G	ENSP00000356470:p.Ile148Val	Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	221	220	0.995475	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	914	0.4184981684981685	350	0.7113821138211383	119	0.3287292817679558	187	0.3269230769230769	258	0.3403693931398417	A	0.583	-0.836082	0.02713	0.635951	0.357093	ENSG00000116668	ENST00000367501;ENST00000367500;ENST00000450350	T;T;T	0.37915	1.17;1.17;1.17	5.35	0.918	0.19386	.	1.040850	0.07571	N	0.918619	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.45687	-0.9244	9	0.11794	T	0.64	.	1.757	0.02984	0.2943:0.2806:0.308:0.1171	rs10489579;rs17845931;rs17858910;rs58368482;rs10489579	148	Q5T5J6	SWT1_HUMAN	V	148	ENSP00000356471:I148V;ENSP00000356470:I148V;ENSP00000401413:I148V	ENSP00000356470:I148V	I	+	1	0	SWT1	183410344	0.955000	0.32602	0.002000	0.10522	0.559000	0.35586	0.566000	0.23593	-0.149000	0.11215	0.455000	0.32223	ATT	G|0.396;N|0.000	0.396	strong		0.368	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
PELP1	27043	hgsc.bcm.edu	37	17	4574751	4574751	+	Missense_Mutation	SNP	T	T	A	rs9436	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4574751T>A	ENST00000574876.1	-	17	3393	c.3376A>T	c.(3376-3378)Aca>Tca	p.T1126S	PELP1_ENST00000269230.7_Missense_Mutation_p.T1036S|PELP1_ENST00000436683.2_Missense_Mutation_p.T902S|PELP1_ENST00000572293.1_Missense_Mutation_p.T1176S|PELP1_ENST00000301396.4_Missense_Mutation_p.T1270S			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	1126			T -> S (in dbSNP:rs9436).		cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						TCAGGCTCTGTGGGAGGTGGT	0.502													T|||	383	0.0764776	0.0098	0.1297	5008	,	,		18659	0.003		0.2187	False		,,,				2504	0.0583				p.T1126S		Atlas-SNP	.											.	PELP1	102	.	0			c.A3376T						PASS	.	T	SER/THR	176,4116		6,164,1976	88.0	92.0	91.0		3376	-6.8	0.0	17	dbSNP_52	91	1984,6510		221,1542,2484	yes	missense	PELP1	NM_014389.2	58	227,1706,4460	AA,AT,TT		23.3577,4.1007,16.8935	benign	1126/1131	4574751	2160,10626	2146	4247	6393	SO:0001583	missense	27043	exon17			GCTCTGTGGGAGG		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.3376A>T	17.37:g.4574751T>A	ENSP00000461625:p.Thr1126Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	94	36	0.382979	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	37	CCDS58503.1	212	0.09706959706959707	3	0.006097560975609756	50	0.13812154696132597	1	0.0017482517482517483	158	0.20844327176781002	T	11.08	1.532834	0.27387	0.041007	0.233577	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.47528	0.84;0.86;1.47	4.85	-6.82	0.01698	.	0.524293	0.18951	N	0.126683	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.14062	-1.0486	9	0.87932	D	0	-0.2289	5.3463	0.16010	0.1984:0.0767:0.5556:0.1692	rs9436;rs1061099;rs3202093;rs9436	902;1126	E7EV54;Q8IZL8	.;PELP1_HUMAN	S	1270;1036;902	ENSP00000301396:T1270S;ENSP00000269230:T1036S;ENSP00000416231:T902S	ENSP00000269230:T1036S	T	-	1	0	AC091153.1	4521500	0.000000	0.05858	0.007000	0.13788	0.822000	0.46500	-0.622000	0.05553	-1.060000	0.03189	0.459000	0.35465	ACA	T|0.893;A|0.107	0.107	strong		0.502	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
WNK1	65125	hgsc.bcm.edu	37	12	998365	998365	+	Missense_Mutation	SNP	G	G	T	rs12828016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:998365G>T	ENST00000315939.6	+	21	6067	c.5424G>T	c.(5422-5424)atG>atT	p.M1808I	WNK1_ENST00000340908.4_Missense_Mutation_p.M1401I|WNK1_ENST00000535572.1_Missense_Mutation_p.M1561I|WNK1_ENST00000537687.1_Missense_Mutation_p.M2068I|WNK1_ENST00000530271.2_Missense_Mutation_p.M2306I	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1808			M -> I (in dbSNP:rs12828016). {ECO:0000269|PubMed:11571656, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.3}.		intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GTCCAGAGATGATCACAGTGA	0.398													T|||	2091	0.417532	0.5522	0.3213	5008	,	,		19593	0.2808		0.3877	False		,,,				2504	0.4755				p.M2068I	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G6204T						PASS	.	T	ILE/MET,ILE/MET,ILE/MET,ILE/MET	2248,2158	581.2+/-385.3	569,1110,524	177.0	171.0	173.0		6180,5424,4683,6204	2.2	0.2	12	dbSNP_121	173	3363,5237	642.5+/-399.8	675,2013,1612	yes	missense,missense,missense,missense	WNK1	NM_213655.4,NM_018979.3,NM_014823.2,NM_001184985.1	10,10,10,10	1244,3123,2136	TT,TG,GG		39.1047,48.9787,43.1416	benign,benign,benign,benign	2060/2635,1808/2383,1561/2135,2068/2643	998365	5611,7395	2203	4300	6503	SO:0001583	missense	65125	exon21			AGAGATGATCACA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.5424G>T	12.37:g.998365G>T	ENSP00000313059:p.Met1808Ile	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	155	68	0.43871	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	843	0.385989010989011	261	0.5304878048780488	127	0.35082872928176795	165	0.28846153846153844	290	0.38258575197889183	T	10.15	1.272499	0.23221	0.510213	0.391047	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	5.77	2.16	0.27623	.	0.262166	0.33346	N	0.005003	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45629	-0.9248	9	0.20046	T	0.44	-1.5706	2.5504	0.04747	0.1087:0.2441:0.1125:0.5346	rs12828016;rs60054820;rs12828016	1561;1561;1808	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	I	1561;1808;2068;981;2306;1401	ENSP00000441972:M1561I;ENSP00000313059:M1808I;ENSP00000444465:M2068I;ENSP00000433548:M2306I;ENSP00000341292:M1401I	ENSP00000252477:M981I	M	+	3	0	WNK1	868626	0.822000	0.29219	0.163000	0.22734	0.446000	0.32137	-0.071000	0.11505	0.183000	0.20059	-0.256000	0.11100	ATG	G|0.585;T|0.415	0.415	strong		0.398	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
PPAT	5471	hgsc.bcm.edu	37	4	57273840	57273840	+	Silent	SNP	C	C	G	rs11538098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:57273840C>G	ENST00000264220.2	-	2	308	c.171G>C	c.(169-171)tcG>tcC	p.S57S	PPAT_ENST00000507648.1_5'UTR|AC068620.1_ENST00000598320.1_5'Flank	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	57	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)	p.S57S(1)		cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	ATGTTGGCACCGAACTCCCAT	0.408													T|||	1303	0.260184	0.239	0.2795	5008	,	,		20452	0.0704		0.4016	False		,,,				2504	0.3252				p.S57S		Atlas-SNP	.											PPAT,NS,carcinoma,0,2	PPAT	41	2	1	Substitution - coding silent(1)	prostate(1)	c.G171C						PASS	.	T		1117,3289		127,863,1213	154.0	130.0	138.0		171	1.8	0.4	4	dbSNP_120	138	3585,5015		724,2137,1439	no	coding-synonymous	PPAT	NM_002703.4		851,3000,2652	GG,GC,CC		41.686,25.3518,36.1525		57/518	57273840	4702,8304	2203	4300	6503	SO:0001819	synonymous_variant	5471	exon2			TGGCACCGAACTC		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.171G>C	4.37:g.57273840C>G		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_002703		Silent	SNP	ENST00000264220.2	37	CCDS3505.1																																																																																			C|0.671;G|0.329	0.329	strong		0.408	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703	
OR4A5	81318	hgsc.bcm.edu	37	11	51412327	51412327	+	Missense_Mutation	SNP	T	T	A	rs56302591	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:51412327T>A	ENST00000319760.6	-	1	121	c.69A>T	c.(67-69)aaA>aaT	p.K23N		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	23			K -> N (in dbSNP:rs56302591).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				CAAATAATGCTTTTTGCACAC	0.423													.|||	381	0.0760783	0.0401	0.0591	5008	,	,		19387	0.0853		0.1223	False		,,,				2504	0.0798				p.K23N		Atlas-SNP	.											.	OR4A5	116	.	0			c.A69T						PASS	.	T	ASN/LYS	213,4187		6,201,1993	45.0	43.0	44.0		69	0.8	0.0	11	dbSNP_129	44	1026,7566		58,910,3328	no	missense	OR4A5	NM_001005272.3	94	64,1111,5321	AA,AT,TT		11.9413,4.8409,9.5366	benign	23/316	51412327	1239,11753	2200	4296	6496	SO:0001583	missense	81318	exon1			TAATGCTTTTTGC	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.69A>T	11.37:g.51412327T>A	ENSP00000367664:p.Lys23Asn	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	169	0.07738095238095238	16	0.032520325203252036	28	0.07734806629834254	34	0.05944055944055944	91	0.12005277044854881	.	3.543	-0.093218	0.07053	0.048409	0.119413	ENSG00000221840	ENST00000319760	T	0.00433	7.43	2.01	0.836	0.18891	.	0.291535	0.24630	N	0.036893	T	0.00012	0.0000	L	0.49699	1.58	0.80722	P	0.0	B	0.10296	0.003	B	0.17979	0.02	T	0.41215	-0.9521	9	0.54805	T	0.06	.	4.2576	0.10724	0.0:0.3576:0.0:0.6424	rs56302591	23	Q8NH83	OR4A5_HUMAN	N	23	ENSP00000367664:K23N	ENSP00000367664:K23N	K	-	3	2	OR4A5	51268903	0.000000	0.05858	0.019000	0.16419	0.216000	0.24613	-3.197000	0.00562	0.225000	0.20959	0.136000	0.15936	AAA	T|0.908;A|0.092	0.092	strong		0.423	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
ALG12	79087	hgsc.bcm.edu	37	22	50301430	50301430	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50301430G>A	ENST00000330817.6	-	7	1204	c.931C>T	c.(931-933)Cgc>Tgc	p.R311C		NM_024105.3	NP_077010.1	Q9BV10	ALG12_HUMAN	ALG12, alpha-1,6-mannosyltransferase	311					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-1,6-mannosyltransferase activity (GO:0000009)|dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity (GO:0052917)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(3)	12		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		BRCA - Breast invasive adenocarcinoma(115;0.199)|LUAD - Lung adenocarcinoma(64;0.247)		ATGATGAAGCGTAGCTCCTTG	0.547																																					p.R311C		Atlas-SNP	.											.	ALG12	35	.	0			c.C931T	GRCh37	CM050360	ALG12	M		PASS	.						125.0	109.0	115.0					22																	50301430		2203	4300	6503	SO:0001583	missense	79087	exon7			TGAAGCGTAGCTC	AJ303120	CCDS14081.1	22q13.33	2013-02-26	2013-02-26		ENSG00000182858	ENSG00000182858	2.4.1.260	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	19358	protein-coding gene	gene with protein product	"""dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichol alpha-1,6-mannosyltransferase"", ""dol-P-Man dependent alpha-1,6-mannosyltransferase"""	607144	"""asparagine-linked glycosylation 12 homolog (yeast, alpha-1,6-mannosyltransferase)"", ""asparagine-linked glycosylation 12, alpha-1,6-mannosyltransferase homolog (S. cerevisiae)"""			11983712	Standard	NM_024105		Approved	ECM39	uc003biy.3	Q9BV10	OTTHUMG00000150289	ENST00000330817.6:c.931C>T	22.37:g.50301430G>A	ENSP00000333813:p.Arg311Cys	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	167	85	0.508982	NM_024105	A6PWM1|Q4KMH4|Q8NG10|Q96AA4	Missense_Mutation	SNP	ENST00000330817.6	37	CCDS14081.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.35|17.35	3.368561|3.368561	0.61624|0.61624	.|.	.|.	ENSG00000182858|ENSG00000182858	ENST00000330817|ENST00000486602	D|.	0.91351|.	-2.83|.	4.28|4.28	4.28|4.28	0.50868|0.50868	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87111|0.87111	0.6096|0.6096	H|H	0.95470|0.95470	3.675|3.675	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.91436|0.91436	0.5170|0.5170	10|5	0.87932|.	D|.	0|.	-9.9379|-9.9379	17.2733|17.2733	0.87109|0.87109	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	311|.	Q9BV10|.	ALG12_HUMAN|.	C|M	311|46	ENSP00000333813:R311C|.	ENSP00000333813:R311C|.	R|T	-|-	1|2	0|0	ALG12|ALG12	48687434|48687434	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.041000|0.041000	0.13682|0.13682	9.334000|9.334000	0.96470|0.96470	2.378000|2.378000	0.81104|0.81104	0.655000|0.655000	0.94253|0.94253	CGC|ACG	.	.	none		0.547	ALG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317405.2	NM_024105	
LMF2	91289	hgsc.bcm.edu	37	22	50942121	50942121	+	Missense_Mutation	SNP	C	C	T	rs112797830|rs13056405	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50942121C>T	ENST00000474879.2	-	14	1838	c.1823G>A	c.(1822-1824)aGc>aAc	p.S608N	LMF2_ENST00000216080.5_Missense_Mutation_p.S583N|LMF2_ENST00000505981.1_5'Flank|LMF2_ENST00000380796.3_Missense_Mutation_p.S495N	NM_033200.2	NP_149977.2	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	608						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|cervix(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GCGAGGTGGGCTTTTCTCCTG	0.701													c|||	694	0.138578	0.1619	0.1369	5008	,	,		10131	0.0417		0.2227	False		,,,				2504	0.1217				p.S608N		Atlas-SNP	.											.	LMF2	40	.	0			c.G1823A						PASS	.	C	ASN/SER	673,3729		51,571,1579	19.0	24.0	22.0		1823	0.5	0.9	22	dbSNP_121	22	1869,6715		198,1473,2621	no	missense	LMF2	NM_033200.2	46	249,2044,4200	TT,TC,CC		21.7731,15.2885,19.5749	benign	608/708	50942121	2542,10444	2201	4292	6493	SO:0001583	missense	91289	exon14			GGTGGGCTTTTCT	BC002942	CCDS14093.1, CCDS14093.2	22q13.33	2008-02-04	2007-11-29	2007-11-29	ENSG00000100258	ENSG00000100258			25096	protein-coding gene	gene with protein product			"""transmembrane protein 153"", ""transmembrane protein 112B"""	TMEM153, TMEM112B		12477932	Standard	NM_033200		Approved		uc003blp.2	Q9BU23	OTTHUMG00000150206	ENST00000474879.2:c.1823G>A	22.37:g.50942121C>T	ENSP00000424381:p.Ser608Asn	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	21	10	0.47619	NM_033200	A6NEZ0|Q13392|Q6ZNR2|Q8WU74|Q96C62	Missense_Mutation	SNP	ENST00000474879.2	37	CCDS14093.2	335	0.1533882783882784	87	0.17682926829268292	58	0.16022099447513813	18	0.03146853146853147	172	0.22691292875989447	C	6.610	0.480878	0.12581	0.152885	0.217731	ENSG00000100258	ENST00000380796;ENST00000474879;ENST00000216080	T;T;T	0.33654	1.4;1.87;1.86	5.33	0.458	0.16670	.	0.608600	0.17404	N	0.175437	T	0.00012	0.0000	M	0.65975	2.015	0.51482	P	7.100000000004325E-5	B;B	0.06786	0.0;0.001	B;B	0.09377	0.004;0.004	T	0.19418	-1.0306	9	0.19590	T	0.45	-6.0E-4	5.4231	0.16411	0.0:0.509:0.3144:0.1766	rs13056405	608;583	Q9BU23;Q9BU23-2	LMF2_HUMAN;.	N	495;608;583	ENSP00000370173:S495N;ENSP00000424381:S608N;ENSP00000216080:S583N	ENSP00000216080:S583N	S	-	2	0	LMF2	49288987	0.117000	0.22190	0.943000	0.38184	0.073000	0.16967	0.491000	0.22419	0.311000	0.23014	-0.143000	0.13931	AGC	C|0.841;T|0.159	0.159	strong		0.701	LMF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316833.2	NM_033200	
KMT2D	8085	hgsc.bcm.edu	37	12	49434074	49434074	+	Silent	SNP	C	C	A	rs10747559	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:49434074C>A	ENST00000301067.7	-	31	7478	c.7479G>T	c.(7477-7479)ggG>ggT	p.G2493G	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2493	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CTGCTGGGAACCCCCCAGCCC	0.657													A|||	2181	0.435503	0.4796	0.3271	5008	,	,		14453	0.4514		0.3966	False		,,,				2504	0.4765				p.G2493G		Atlas-SNP	.											.	MLL2	1173	.	0			c.G7479T						PASS	.	A		1699,1993		413,873,560	18.0	22.0	21.0		7479	0.8	1.0	12	dbSNP_120	21	3214,4890		692,1830,1530	no	coding-synonymous	MLL2	NM_003482.3		1105,2703,2090	AA,AC,CC		39.6594,46.0184,41.6497		2493/5538	49434074	4913,6883	1846	4052	5898	SO:0001819	synonymous_variant	8085	exon31			TGGGAACCCCCCA	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.7479G>T	12.37:g.49434074C>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			C|0.614;A|0.386	0.386	strong		0.657	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
NECAB2	54550	hgsc.bcm.edu	37	16	84028014	84028014	+	Missense_Mutation	SNP	C	C	G	rs2292324	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84028014C>G	ENST00000305202.4	+	7	721	c.704C>G	c.(703-705)aCc>aGc	p.T235S	NECAB2_ENST00000565691.1_Missense_Mutation_p.T152S|NECAB2_ENST00000567703.1_3'UTR	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	235			T -> S (in dbSNP:rs2292324).			cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)	p.T235S(1)		endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						CAAGGCAAGACCCTTCCATCT	0.627													G|||	1122	0.224042	0.4781	0.2017	5008	,	,		16529	0.125		0.1103	False		,,,				2504	0.1155				p.T235S		Atlas-SNP	.											NECAB2,NS,carcinoma,0,1	NECAB2	36	1	1	Substitution - Missense(1)	stomach(1)	c.C704G						PASS	.	G	SER/THR	1921,2479	616.2+/-392.7	427,1067,706	53.0	53.0	53.0		704	3.6	0.0	16	dbSNP_100	53	835,7765	780.3+/-407.7	42,751,3507	yes	missense	NECAB2	NM_019065.2	58	469,1818,4213	GG,GC,CC		9.7093,43.6591,21.2	benign	235/387	84028014	2756,10244	2200	4300	6500	SO:0001583	missense	54550	exon7			GCAAGACCCTTCC	AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	23746	protein-coding gene	gene with protein product			"""EF-hand calcium binding protein 2"""	EFCBP2		12044471	Standard	NM_019065		Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.704C>G	16.37:g.84028014C>G	ENSP00000307449:p.Thr235Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_019065	A2RRG3|O75547|Q6ZSK0	Missense_Mutation	SNP	ENST00000305202.4	37	CCDS10940.1	436	0.19963369963369965	217	0.4410569105691057	73	0.20165745856353592	70	0.12237762237762238	76	0.10026385224274406	G	1.174	-0.640164	0.03557	0.436591	0.097093	ENSG00000103154	ENST00000305202	T	0.16324	2.35	4.58	3.6	0.41247	.	0.546226	0.20389	N	0.093299	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46020	-0.9221	9	0.02654	T	1	-12.9837	4.4669	0.11694	0.0864:0.1455:0.6008:0.1674	rs2292324;rs52822327;rs2292324	235	Q7Z6G3	NECA2_HUMAN	S	235	ENSP00000307449:T235S	ENSP00000307449:T235S	T	+	2	0	NECAB2	82585515	0.299000	0.24426	0.007000	0.13788	0.005000	0.04900	0.389000	0.20751	0.437000	0.26423	-0.120000	0.15030	ACC	C|0.800;G|0.200	0.200	strong		0.627	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269077.2	NM_019065	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188353	140188353	+	Silent	SNP	G	G	A	rs561061447	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140188353G>A	ENST00000530339.1	+	1	1581	c.1581G>A	c.(1579-1581)gaG>gaA	p.E527E	PCDHA4_ENST00000356878.4_Silent_p.E527E|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Silent_p.E527E	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	527	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCACGAGGAGCTAGAGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17480	0.0		0.0755	False		,,,				2504	0.0082				p.E527E		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G1581A						PASS	.						71.0	76.0	74.0					5																	140188353		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CGAGGAGCTAGAG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1581G>A	5.37:g.140188353G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	58	15	0.258621	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
CACNA2D4	93589	hgsc.bcm.edu	37	12	1983782	1983782	+	Silent	SNP	C	C	T	rs758160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:1983782C>T	ENST00000382722.5	-	18	2228	c.1866G>A	c.(1864-1866)ccG>ccA	p.P622P	CACNA2D4_ENST00000586184.1_Silent_p.P622P|CACNA2D4_ENST00000587995.1_Silent_p.P597P|CACNA2D4_ENST00000539048.2_5'UTR|CACNA2D4_ENST00000588077.1_Silent_p.P558P|CACNA2D4_ENST00000585732.1_Intron|CACNA2D4_ENST00000585708.1_Silent_p.P558P	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	622					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.P622P(1)		endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		CTTTATCCATCGGAACCTTCA	0.488													C|||	476	0.0950479	0.1377	0.0461	5008	,	,		25448	0.0357		0.1034	False		,,,				2504	0.1247				p.P622P	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											CACNA2D4_ENST00000382722,NS,carcinoma,0,1	CACNA2D4	220	1	1	Substitution - coding silent(1)	stomach(1)	c.G1866A						PASS	.	C		516,3456		35,446,1505	199.0	177.0	184.0		1866	-8.8	0.7	12	dbSNP_86	184	779,7533		38,703,3415	no	coding-synonymous	CACNA2D4	NM_172364.4		73,1149,4920	TT,TC,CC		9.372,12.9909,10.5422		622/1138	1983782	1295,10989	1986	4156	6142	SO:0001819	synonymous_variant	93589	exon18			ATCCATCGGAACC	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.1866G>A	12.37:g.1983782C>T		Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	406	187	0.460591	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Silent	SNP	ENST00000382722.5	37	CCDS44785.1																																																																																			C|0.904;T|0.096	0.096	strong		0.488	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
GPLD1	2822	hgsc.bcm.edu	37	6	24463020	24463020	+	Missense_Mutation	SNP	G	G	C	rs17300770	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:24463020G>C	ENST00000230036.1	-	11	935	c.825C>G	c.(823-825)gaC>gaG	p.D275E		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	275			D -> E (in dbSNP:rs17300770).		cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						GCAGGTTGCAGTCACTGAGGA	0.443													G|||	484	0.0966454	0.0212	0.0965	5008	,	,		21551	0.1022		0.169	False		,,,				2504	0.1186				p.D275E		Atlas-SNP	.											.	GPLD1	91	.	0			c.C825G						PASS	.	G	GLU/ASP	166,4240	108.6+/-147.0	3,160,2040	127.0	124.0	125.0		825	4.1	0.9	6	dbSNP_123	125	1104,7496	229.1+/-263.9	65,974,3261	yes	missense	GPLD1	NM_001503.2	45	68,1134,5301	CC,CG,GG		12.8372,3.7676,9.7647	benign	275/841	24463020	1270,11736	2203	4300	6503	SO:0001583	missense	2822	exon11			GTTGCAGTCACTG	L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.825C>G	6.37:g.24463020G>C	ENSP00000230036:p.Asp275Glu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	37	CCDS4553.1	236	0.10805860805860806	10	0.02032520325203252	37	0.10220994475138122	57	0.09965034965034965	132	0.1741424802110818	G	3.182	-0.167636	0.06461	0.037676	0.128372	ENSG00000112293	ENST00000230036	T	0.64260	-0.09	5.92	4.14	0.48551	.	0.649497	0.15089	N	0.281206	T	0.28896	0.0717	L	0.59436	1.845	0.09310	P	0.9999999999714789	B	0.33583	0.418	B	0.32864	0.154	T	0.17107	-1.0380	9	0.06757	T	0.87	-9.359	5.0959	0.14733	0.1666:0.0:0.6665:0.1669	rs17300770;rs52799916;rs58678836;rs17300770	275	P80108	PHLD_HUMAN	E	275	ENSP00000230036:D275E	ENSP00000230036:D275E	D	-	3	2	GPLD1	24570999	0.999000	0.42202	0.875000	0.34327	0.053000	0.15095	1.284000	0.33249	1.506000	0.48736	-0.140000	0.14226	GAC	G|0.900;C|0.100	0.100	strong		0.443	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503	
CEBPB	1051	hgsc.bcm.edu	37	20	48808011	48808011	+	Silent	SNP	C	C	T	rs4253439	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:48808011C>T	ENST00000303004.3	+	1	636	c.441C>T	c.(439-441)gcC>gcT	p.A147A		NM_005194.3	NP_005185.2	P17676	CEBPB_HUMAN	CCAAT/enhancer binding protein (C/EBP), beta	147					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cellular response to amino acid stimulus (GO:0071230)|embryonic placenta development (GO:0001892)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mammary gland epithelial cell differentiation (GO:0060644)|mammary gland epithelial cell proliferation (GO:0033598)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|response to lipopolysaccharide (GO:0032496)|transcription from RNA polymerase II promoter (GO:0006366)	condensed chromosome, centromeric region (GO:0000779)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|lung(1)	2			BRCA - Breast invasive adenocarcinoma(9;5.72e-08)|STAD - Stomach adenocarcinoma(23;0.19)			GCCTGGGGGCCGCCAAGGGCG	0.741													C|||	1852	0.369808	0.1944	0.3977	5008	,	,		3841	0.4752		0.4344	False		,,,				2504	0.4121				p.A147A		Atlas-SNP	.											.	CEBPB	5	.	0			c.C441T						PASS	.	C		875,3041		180,515,1263	3.0	3.0	3.0		441	2.0	1.0	20	dbSNP_111	3	3024,4628		751,1522,1553	no	coding-synonymous	CEBPB	NM_005194.2		931,2037,2816	TT,TC,CC		39.5191,22.3442,33.705		147/346	48808011	3899,7669	1958	3826	5784	SO:0001819	synonymous_variant	1051	exon1			GGGGGCCGCCAAG	AY193834	CCDS13429.1	20q13.1	2013-01-10			ENSG00000172216	ENSG00000172216		"""basic leucine zipper proteins"""	1834	protein-coding gene	gene with protein product	"""liver-enriched transcriptional activator protein"", ""nuclear factor of interleukin 6"", ""interleukin 6-dependent DNA-binding protein"""	189965		TCF5		1535333, 1840554	Standard	NM_005194		Approved	LAP, CRP2, NFIL6, IL6DBP, C/EBP-beta	uc002xvi.2	P17676	OTTHUMG00000032715	ENST00000303004.3:c.441C>T	20.37:g.48808011C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_005194	A8K671|Q96IH2|Q9H4Z5	Silent	SNP	ENST00000303004.3	37	CCDS13429.1																																																																																			C|0.638;T|0.362	0.362	strong		0.741	CEBPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079672.1	NM_005194	
DNAJC24	120526	hgsc.bcm.edu	37	11	31447864	31447864	+	Missense_Mutation	SNP	A	A	G	rs144649932	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:31447864A>G	ENST00000465995.1	+	4	387	c.281A>G	c.(280-282)gAt>gGt	p.D94G	DNAJC24_ENST00000536040.1_3'UTR	NM_181706.4	NP_859057.4	Q6P3W2	DJC24_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 24	93					chaperone-mediated protein folding (GO:0061077)|oxidation-reduction process (GO:0055114)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|positive regulation of ATPase activity (GO:0032781)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATPase activator activity (GO:0001671)|ferrous iron binding (GO:0008198)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|skin(1)|upper_aerodigestive_tract(2)	11						GGACCAGTAGATGCTCAAGTA	0.269													A|||	7	0.00139776	0.0	0.0014	5008	,	,		16417	0.0		0.005	False		,,,				2504	0.001				p.D94G		Atlas-SNP	.											.	DNAJC24	23	.	0			c.A281G						PASS	.	A	GLY/ASP	5,3647		0,5,1821	115.0	111.0	112.0		281	4.4	1.0	11	dbSNP_134	112	28,8128		0,28,4050	yes	missense	DNAJC24	NM_181706.4	94	0,33,5871	GG,GA,AA		0.3433,0.1369,0.2795	benign	94/150	31447864	33,11775	1826	4078	5904	SO:0001583	missense	120526	exon4			CAGTAGATGCTCA	AL833128	CCDS7873.2	11p14.1	2011-09-02	2008-07-03	2008-07-03	ENSG00000170946	ENSG00000170946		"""Heat shock proteins / DNAJ (HSP40)"""	26979	protein-coding gene	gene with protein product		611072	"""zinc finger, CSL-type containing 3"", ""DPH4 homolog (JJJ3, S. cerevisiae)"", ""DPH4, JJJ3 homolog (S. cerevisiae)"""	ZCSL3, DPH4		15485916	Standard	NM_181706		Approved	JJJ3	uc001msx.3	Q6P3W2	OTTHUMG00000133712	ENST00000465995.1:c.281A>G	11.37:g.31447864A>G	ENSP00000417548:p.Asp94Gly	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_181706	A8K0V0|B1ALC1|I6L9B4	Missense_Mutation	SNP	ENST00000465995.1	37	CCDS7873.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	15.76	2.927163	0.52759	0.001369	0.003433	ENSG00000170946	ENST00000465995	T	0.31769	1.48	5.52	4.4	0.53042	Zinc finger, DPH-type (1);	0.143219	0.64402	N	0.000012	T	0.21881	0.0527	L	0.59436	1.845	0.80722	D	1	B	0.14438	0.01	B	0.20577	0.03	T	0.04307	-1.0961	10	0.27785	T	0.31	.	10.0993	0.42495	0.924:0.0:0.076:0.0	.	93	Q6P3W2	DJC24_HUMAN	G	94	ENSP00000417548:D94G	ENSP00000417548:D94G	D	+	2	0	DNAJC24	31404440	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	5.131000	0.64751	1.037000	0.40024	0.528000	0.53228	GAT	A|0.998;G|0.002	0.002	strong		0.269	DNAJC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258011.3	NM_181706	
LRRC16B	90668	hgsc.bcm.edu	37	14	24526206	24526206	+	Silent	SNP	T	T	C	rs45484702	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24526206T>C	ENST00000342740.5	+	13	1189	c.1035T>C	c.(1033-1035)ccT>ccC	p.P345P	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	345						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		GCAAGAATCCTGGGCTCCTCG	0.612													T|||	1077	0.215056	0.0673	0.1614	5008	,	,		21456	0.38		0.1859	False		,,,				2504	0.3129				p.P345P		Atlas-SNP	.											.	LRRC16B	120	.	0			c.T1035C						PASS	.	T		409,3997	199.1+/-222.7	23,363,1817	38.0	40.0	39.0		1035	-6.3	1.0	14	dbSNP_127	39	1811,6789	319.3+/-314.1	181,1449,2670	no	coding-synonymous	LRRC16B	NM_138360.3		204,1812,4487	CC,CT,TT		21.0581,9.2828,17.069		345/1373	24526206	2220,10786	2203	4300	6503	SO:0001819	synonymous_variant	90668	exon13			GAATCCTGGGCTC	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.1035T>C	14.37:g.24526206T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	131	129	0.984733	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																			T|0.820;C|0.180	0.180	strong		0.612	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
RASAL3	64926	hgsc.bcm.edu	37	19	15565046	15565046	+	Silent	SNP	G	G	A	rs9646651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:15565046G>A	ENST00000343625.7	-	14	2278	c.2193C>T	c.(2191-2193)acC>acT	p.T731T		NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	731					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						CTCGCAGGATGGTGGGCAGTG	0.607											OREG0025322	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	643	0.128395	0.2156	0.111	5008	,	,		17847	0.1141		0.0805	False		,,,				2504	0.0869				p.T731T		Atlas-SNP	.											.	RASAL3	49	.	0			c.C2193T						PASS	.	G		698,3578		48,602,1488	28.0	36.0	33.0		2193	-0.2	1.0	19	dbSNP_119	33	608,7862		20,568,3647	no	coding-synonymous	RASAL3	NM_022904.1		68,1170,5135	AA,AG,GG		7.1783,16.3237,10.2464		731/1012	15565046	1306,11440	2138	4235	6373	SO:0001819	synonymous_variant	64926	exon14			CAGGATGGTGGGC		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.2193C>T	19.37:g.15565046G>A		Somatic	124	0	0	703	WXS	Illumina HiSeq	Phase_I	141	63	0.446809	NM_022904	Q8N2T9|Q9H735	Silent	SNP	ENST00000343625.7	37	CCDS46006.1																																																																																			G|0.871;A|0.129	0.129	strong		0.607	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904	
HLA-B	3106	hgsc.bcm.edu	37	6	31323203	31323203	+	Silent	SNP	A	A	G	rs1050823	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323203A>G	ENST00000412585.2	-	4	814	c.786T>C	c.(784-786)gaT>gaC	p.D262D		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	262	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GGAAGGTTCTATCTCCTGCTG	0.587									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				A|||	269	0.0537141	0.0257	0.1167	5008	,	,		21731	0.0694		0.0656	False		,,,				2504	0.0184				p.D262D		Atlas-SNP	.											.	HLA-B	54	.	0			c.T786C						PASS	.	A		202,4204		3,196,2004	94.0	80.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	786	-3.0	0.3	6	dbSNP_86	84	681,7919		27,627,3646	no	coding-synonymous	HLA-B	NM_005514.6		30,823,5650	GG,GA,AA		7.9186,4.5847,6.7892		262/363	31323203	883,12123	2203	4300	6503	SO:0001819	synonymous_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	GGTTCTATCTCCT	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.786T>C	6.37:g.31323203A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	180	68	0.377778	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			A|0.927;G|0.073	0.073	strong		0.587	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
COQ10A	93058	hgsc.bcm.edu	37	12	56664041	56664041	+	Silent	SNP	G	G	A	rs11543260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56664041G>A	ENST00000308197.5	+	5	945	c.684G>A	c.(682-684)aaG>aaA	p.K228K	COQ10A_ENST00000433805.2_Silent_p.K196K|COQ10A_ENST00000546544.1_Silent_p.K211K|RP11-977G19.14_ENST00000546464.1_RNA	NM_144576.3	NP_653177.3	Q96MF6	CQ10A_HUMAN	coenzyme Q10 homolog A (S. cerevisiae)	228						mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	8						CAGCCACCAAGTTTGGTCCAG	0.527													G|||	43	0.00858626	0.0038	0.0115	5008	,	,		20738	0.0		0.0278	False		,,,				2504	0.002				p.K228K		Atlas-SNP	.											.	COQ10A	20	.	0			c.G684A						PASS	.	G	,	36,3956		0,36,1960	127.0	126.0	126.0		588,684	4.8	1.0	12	dbSNP_120	126	172,8168		3,166,4001	no	coding-synonymous,coding-synonymous	COQ10A	NM_001099337.1,NM_144576.3	,	3,202,5961	AA,AG,GG		2.0624,0.9018,1.6867	,	196/216,228/248	56664041	208,12124	1996	4170	6166	SO:0001819	synonymous_variant	93058	exon5			CACCAAGTTTGGT	AK057003	CCDS41796.1, CCDS44921.1	12q13.3	2011-09-16	2006-04-04		ENSG00000135469	ENSG00000135469			26515	protein-coding gene	gene with protein product			"""coenzyme Q10 homolog A (yeast)"""				Standard	NM_144576		Approved	FLJ32452	uc001sko.4	Q96MF6	OTTHUMG00000170283	ENST00000308197.5:c.684G>A	12.37:g.56664041G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_144576	Q6GMR6|Q6UWB9|Q86X16|Q8TAL2|Q96MF1|Q9BUP4	Silent	SNP	ENST00000308197.5	37	CCDS41796.1	23	0.010531135531135532	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	19	0.025065963060686015	G	1.929	-0.446438	0.04604	0.009018	0.020624	ENSG00000135469	ENST00000553234;ENST00000551814	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	T	0.41190	0.1148	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53158	-0.8478	4	.	.	.	.	13.5848	0.61924	0.0:0.1571:0.8428:0.0	rs11543260;rs11543260	.	.	.	N	134;45	.	.	S	+	2	0	COQ10A	54950308	1.000000	0.71417	1.000000	0.80357	0.278000	0.26855	0.701000	0.25616	2.675000	0.91044	0.655000	0.94253	AGT	G|0.986;A|0.014	0.014	strong		0.527	COQ10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408332.1	NM_144576	
MUS81	80198	hgsc.bcm.edu	37	11	65631361	65631361	+	Missense_Mutation	SNP	C	C	T	rs34891773	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65631361C>T	ENST00000308110.4	+	10	1397	c.1048C>T	c.(1048-1050)Cgg>Tgg	p.R350W	MUS81_ENST00000533035.1_Missense_Mutation_p.R275W|EFEMP2_ENST00000532648.1_5'Flank|CFL1_ENST00000534769.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	350	ERCC4.		R -> W (in dbSNP:rs34891773).		DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		CGGCCGCTTCCGGGAGCAGAA	0.587								Homologous recombination					C|||	62	0.0123802	0.0197	0.0159	5008	,	,		18549	0.0		0.0239	False		,,,				2504	0.001				p.R350W		Atlas-SNP	.											.	MUS81	68	.	0			c.C1048T						PASS	.	C	TRP/ARG	59,4343	58.1+/-94.6	1,57,2143	62.0	69.0	67.0		1048	4.9	1.0	11	dbSNP_126	67	245,8347	97.7+/-159.3	3,239,4054	yes	missense	MUS81	NM_025128.4	101	4,296,6197	TT,TC,CC		2.8515,1.3403,2.3395	probably-damaging	350/552	65631361	304,12690	2201	4296	6497	SO:0001583	missense	80198	exon10			CGCTTCCGGGAGC		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"""SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	606591	"""MUS81 endonuclease homolog (yeast)"", ""MUS81 endonuclease homolog (S. cerevisiae)"""			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.1048C>T	11.37:g.65631361C>T	ENSP00000307853:p.Arg350Trp	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_025128	Q9H7D9	Missense_Mutation	SNP	ENST00000308110.4	37	CCDS8115.1	32|32	0.014652014652014652|0.014652014652014652	13|13	0.026422764227642278|0.026422764227642278	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	14|14	0.018469656992084433|0.018469656992084433	C|C	24.3|24.3	4.513249|4.513249	0.85389|0.85389	0.013403|0.013403	0.028515|0.028515	ENSG00000172732|ENSG00000172732	ENST00000529374|ENST00000533035;ENST00000308110;ENST00000437855	.|T;T	.|0.23754	.|1.89;1.89	5.8|5.8	4.89|4.89	0.63831|0.63831	.|DNA repair nuclease, XPF-type/Helicase (1);Restriction endonuclease, type II-like (1);ERCC4 domain (2);	.|0.177713	.|0.45126	.|D	.|0.000400	T|T	0.17066|0.17066	0.0410|0.0410	L|L	0.45228|0.45228	1.405|1.405	0.52501|0.52501	D|D	0.999959|0.999959	.|D	.|0.89917	.|1.0	.|D	.|0.64877	.|0.93	T|T	0.01298|0.01298	-1.1392|-1.1392	5|10	.|0.37606	.|T	.|0.19	-12.1179|-12.1179	12.8651|12.8651	0.57936|0.57936	0.0:0.9207:0.0:0.0793|0.0:0.9207:0.0:0.0793	rs34891773;rs61893866|rs34891773;rs61893866	.|350	.|Q96NY9	.|MUS81_HUMAN	L|W	275|275;350;350	.|ENSP00000432287:R275W;ENSP00000307853:R350W	.|ENSP00000307853:R350W	P|R	+|+	2|1	0|2	MUS81|MUS81	65387937|65387937	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.971000|0.971000	0.66376|0.66376	2.194000|2.194000	0.42668|0.42668	1.453000|1.453000	0.47775|0.47775	0.655000|0.655000	0.94253|0.94253	CCG|CGG	C|0.979;T|0.021	0.021	strong		0.587	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	
DNAH9	1770	hgsc.bcm.edu	37	17	11502188	11502188	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:11502188C>T	ENST00000262442.4	+	1	441	c.373C>T	c.(373-375)Ctg>Ttg	p.L125L	DNAH9_ENST00000579828.1_Silent_p.L125L|DNAH9_ENST00000454412.2_Silent_p.L125L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	125	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CTGCGGGGACCTGCCCGCGGC	0.701																																					p.L125L		Atlas-SNP	.											.	DNAH9	695	.	0			c.C373T						PASS	.						3.0	4.0	4.0					17																	11502188		1807	3723	5530	SO:0001819	synonymous_variant	1770	exon1			GGGGACCTGCCCG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.373C>T	17.37:g.11502188C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			.	.	none		0.701	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
CEP112	201134	hgsc.bcm.edu	37	17	63822357	63822357	+	Intron	SNP	T	T	C	rs62065084	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:63822357T>C	ENST00000392769.2	-	21	2613				CEP112_ENST00000580482.1_Intron|CEP112_ENST00000537949.1_Intron|CEP112_ENST00000541355.1_Intron|CEP112_ENST00000535342.2_Intron|CEP112_ENST00000317442.8_Missense_Mutation_p.I21V	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa						receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						CTCATCTCTATCAGTCTCAGG	0.463													T|||	1074	0.214457	0.2368	0.2262	5008	,	,		21080	0.125		0.2207	False		,,,				2504	0.2618				p.I21V		Atlas-SNP	.											.	CEP112	192	.	0			c.A61G						PASS	.	T	VAL/ILE,,	1069,3337	390.7+/-327.8	141,787,1275	259.0	258.0	258.0		61,,	-0.8	0.0	17	dbSNP_129	258	2066,6534	359.0+/-331.4	238,1590,2472	yes	missense,intron,intron	CEP112	NM_001037325.2,NM_001199165.1,NM_145036.3	29,,	379,2377,3747	CC,CT,TT		24.0233,24.2624,24.1043	,,	21/212,,	63822357	3135,9871	2203	4300	6503	SO:0001627	intron_variant	201134	exon1			TCTCTATCAGTCT	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"""coiled-coil domain containing 46"""	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.2394+25564A>G	17.37:g.63822357T>C		Somatic	327	1	0.0030581		WXS	Illumina HiSeq	Phase_I	188	178	0.946809	NM_001037325	Q6PIB5|Q8NCR4|Q8NFR4	Missense_Mutation	SNP	ENST00000392769.2	37	CCDS32710.1	440	0.20146520146520147	115	0.23373983739837398	86	0.23756906077348067	77	0.1346153846153846	162	0.21372031662269128	T	8.616	0.890231	0.17613	0.242624	0.240233	ENSG00000154240	ENST00000317442	.	.	.	3.01	-0.831	0.10789	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.32981	-0.9886	6	0.24483	T	0.36	.	4.3253	0.11038	0.0:0.1211:0.4057:0.4732	rs62065084	21	Q8N8E3-2	.	V	21	.	ENSP00000320592:I21V	I	-	1	0	CEP112	61252819	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.252000	0.08806	-0.210000	0.10140	0.454000	0.30748	ATA	T|0.765;C|0.235	0.235	strong		0.463	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	
PCLO	27445	hgsc.bcm.edu	37	7	82785097	82785097	+	Missense_Mutation	SNP	T	T	C	rs61741659	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:82785097T>C	ENST00000333891.9	-	2	1197	c.860A>G	c.(859-861)gAc>gGc	p.D287G	PCLO_ENST00000423517.2_Missense_Mutation_p.D287G	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CCTTACTATGTCTGCCTGTTT	0.507													T|||	768	0.153355	0.1225	0.147	5008	,	,		18860	0.0675		0.2664	False		,,,				2504	0.1718				p.D287G		Atlas-SNP	.											.	PCLO	1506	.	0			c.A860G						PASS	.	T	GLY/ASP,GLY/ASP	525,3621		39,447,1587	121.0	110.0	114.0		860,860	4.1	0.7	7	dbSNP_129	114	1914,6508		223,1468,2520	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	94,94	262,1915,4107	CC,CT,TT		22.7262,12.6628,19.4064	benign,benign	287/5143,287/4936	82785097	2439,10129	2073	4211	6284	SO:0001583	missense	27445	exon2			ACTATGTCTGCCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.860A>G	7.37:g.82785097T>C	ENSP00000334319:p.Asp287Gly	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	312	145	0.464744	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	368	0.1684981684981685	69	0.1402439024390244	57	0.1574585635359116	47	0.08216783216783216	195	0.25725593667546176	T	8.676	0.903995	0.17760	0.126628	0.227262	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.20463	2.07;2.08	5.26	4.08	0.47627	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	B;B	0.17268	0.021;0.021	B;B	0.15484	0.013;0.013	T	0.26849	-1.0091	8	0.87932	D	0	.	9.6854	0.40096	0.0:0.081:0.0:0.919	.	287;287	Q9Y6V0-5;Q9Y6V0-6	.;.	G	287	ENSP00000334319:D287G;ENSP00000388393:D287G	ENSP00000334319:D287G	D	-	2	0	PCLO	82623033	0.990000	0.36364	0.696000	0.30242	0.886000	0.51366	2.445000	0.44899	0.819000	0.34492	0.533000	0.62120	GAC	T|0.813;C|0.187	0.187	strong		0.507	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
CSPG4	1464	hgsc.bcm.edu	37	15	75979782	75979782	+	Silent	SNP	G	G	T	rs8030131	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:75979782G>T	ENST00000308508.5	-	3	3716	c.3624C>A	c.(3622-3624)cgC>cgA	p.R1208R		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1208	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.			R -> E (in Ref. 1; CAA65529). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCATGGTGTCGCGGGGGCTGA	0.642													G|||	1925	0.384385	0.2716	0.5245	5008	,	,		20048	0.2292		0.5189	False		,,,				2504	0.4591				p.R1208R		Atlas-SNP	.											.	CSPG4	175	.	0			c.C3624A						PASS	.	G		1317,3075		195,927,1074	52.0	53.0	53.0		3624	-10.1	0.0	15	dbSNP_116	53	4650,3936		1272,2106,915	no	coding-synonymous	CSPG4	NM_001897.4		1467,3033,1989	TT,TG,GG		45.8421,29.9863,45.9778		1208/2323	75979782	5967,7011	2196	4293	6489	SO:0001819	synonymous_variant	1464	exon3			GGTGTCGCGGGGG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.3624C>A	15.37:g.75979782G>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	162	161	0.993827	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			G|0.567;T|0.433	0.433	strong		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
KIF26A	26153	hgsc.bcm.edu	37	14	104641792	104641792	+	Silent	SNP	C	C	T	rs2487305	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:104641792C>T	ENST00000423312.2	+	12	2667	c.2667C>T	c.(2665-2667)gcC>gcT	p.A889A	KIF26A_ENST00000315264.7_Silent_p.A750A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	889					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		CCAGGAAGGCCGTGGGCACCC	0.706													C|||	2243	0.447883	0.6747	0.3228	5008	,	,		14769	0.3869		0.3439	False		,,,				2504	0.3998				p.A889A		Atlas-SNP	.											KIF26A,NS,carcinoma,0,1	KIF26A	84	1	0			c.C2667T						PASS	.	C		2328,1614		714,900,357	10.0	15.0	14.0		2667	-3.1	0.0	14	dbSNP_100	14	2781,5447		504,1773,1837	no	coding-synonymous	KIF26A	NM_015656.1		1218,2673,2194	TT,TC,CC		33.7992,40.9437,41.9803		889/1883	104641792	5109,7061	1971	4114	6085	SO:0001819	synonymous_variant	26153	exon12			GAAGGCCGTGGGC	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.2667C>T	14.37:g.104641792C>T		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	12	7	0.583333	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			C|0.573;T|0.427	0.427	strong		0.706	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
CFAP61	26074	hgsc.bcm.edu	37	20	20055848	20055848	+	Silent	SNP	A	A	G	rs367870948		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:20055848A>G	ENST00000245957.5	+	5	463	c.387A>G	c.(385-387)gcA>gcG	p.A129A	C20orf26_ENST00000451767.2_Silent_p.A129A|C20orf26_ENST00000377306.1_Silent_p.A129A|C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000377309.2_5'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		129										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		TGTATAAGGCAGTGCCAGAGC	0.502																																					p.A129A		Atlas-SNP	.											.	C20orf26	188	.	0			c.A387G						PASS	.	A	,	0,4406		0,0,2203	173.0	147.0	156.0		387,387	-11.4	0.4	20		156	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	C20orf26	NM_001167816.1,NM_015585.3	,	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,	129/471,129/1238	20055848	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	26074	exon5			TAAGGCAGTGCCA																												ENST00000245957.5:c.387A>G	20.37:g.20055848A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	157	78	0.496815	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Silent	SNP	ENST00000245957.5	37	CCDS33447.1																																																																																			.	.	weak		0.502	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
C12orf4	57102	hgsc.bcm.edu	37	12	4627414	4627414	+	Silent	SNP	C	C	T	rs35924298	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:4627414C>T	ENST00000261250.3	-	8	930	c.843G>A	c.(841-843)caG>caA	p.Q281Q	C12orf4_ENST00000545746.1_Silent_p.Q281Q	NM_020374.2	NP_065107.1	Q9NQ89	CL004_HUMAN	chromosome 12 open reading frame 4	281										NS(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)		TGGTCTTCAACTGGGCTCCTG	0.428													C|||	238	0.047524	0.0023	0.0735	5008	,	,		16358	0.003		0.1282	False		,,,				2504	0.0532				p.Q281Q		Atlas-SNP	.											.	C12orf4	58	.	0			c.G843A						PASS	.	C		87,4319	73.6+/-111.7	0,87,2116	105.0	108.0	107.0		843	4.3	1.0	12	dbSNP_126	107	1016,7584	217.4+/-256.1	63,890,3347	no	coding-synonymous	C12orf4	NM_020374.2		63,977,5463	TT,TC,CC		11.814,1.9746,8.4807		281/553	4627414	1103,11903	2203	4300	6503	SO:0001819	synonymous_variant	57102	exon8			CTTCAACTGGGCT	AJ272205	CCDS8528.1	12p13.3	2012-08-10			ENSG00000047621	ENSG00000047621			1184	protein-coding gene	gene with protein product							Standard	NM_020374		Approved		uc001qms.3	Q9NQ89	OTTHUMG00000168258	ENST00000261250.3:c.843G>A	12.37:g.4627414C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	31	0.352273	NM_020374	D3DUQ8|Q6MZH5	Silent	SNP	ENST00000261250.3	37	CCDS8528.1																																																																																			C|0.922;T|0.078	0.078	strong		0.428	C12orf4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398992.1	NM_020374	
ADAMTS8	11095	hgsc.bcm.edu	37	11	130275749	130275749	+	Missense_Mutation	SNP	T	T	C	rs11222085	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130275749T>C	ENST00000257359.6	-	9	3080	c.2374A>G	c.(2374-2376)Aca>Gca	p.T792A		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	792	Spacer.				negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		CCAGGGACTGTCAGGAGCTGC	0.572													T|||	420	0.0838658	0.0129	0.2464	5008	,	,		19597	0.0		0.175	False		,,,				2504	0.0573				p.T792A		Atlas-SNP	.											.	ADAMTS8	172	.	0			c.A2374G						PASS	.	T	ALA/THR	130,3920		3,124,1898	146.0	153.0	151.0		2374	5.3	0.9	11	dbSNP_120	151	1518,6844		127,1264,2790	yes	missense	ADAMTS8	NM_007037.4	58	130,1388,4688	CC,CT,TT		18.1536,3.2099,13.2775	benign	792/890	130275749	1648,10764	2025	4181	6206	SO:0001583	missense	11095	exon9			GGACTGTCAGGAG	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	224	protein-coding gene	gene with protein product		605175	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"""			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.2374A>G	11.37:g.130275749T>C	ENSP00000257359:p.Thr792Ala	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	117	67	0.57265	NM_007037	Q9NZS0	Missense_Mutation	SNP	ENST00000257359.6	37	CCDS41732.1	225	0.10302197802197802	7	0.014227642276422764	75	0.20718232044198895	0	0.0	143	0.18865435356200527	T	8.604	0.887485	0.17540	0.032099	0.181536	ENSG00000134917	ENST00000531752;ENST00000257359;ENST00000414575	T	0.50277	0.75	5.34	5.34	0.76211	ADAM-TS Spacer 1 (1);	0.282192	0.41823	D	0.000807	T	0.00039	0.0001	L	0.37561	1.115	0.29572	P	0.849801	B;B	0.20368	0.009;0.044	B;B	0.24269	0.01;0.052	T	0.14476	-1.0471	9	0.15952	T	0.53	.	9.4078	0.38473	0.2749:0.0:0.0:0.7251	rs11222085;rs52823834;rs11222085	792;273	Q9UP79;B3KVX9	ATS8_HUMAN;.	A	190;792;821	ENSP00000257359:T792A	ENSP00000257359:T792A	T	-	1	0	ADAMTS8	129780959	0.999000	0.42202	0.948000	0.38648	0.204000	0.24138	0.973000	0.29422	2.018000	0.59344	0.377000	0.23210	ACA	T|0.886;C|0.114	0.114	strong		0.572	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037	
OR5AU1	390445	hgsc.bcm.edu	37	14	21623648	21623648	+	Silent	SNP	G	G	A	rs7161544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21623648G>A	ENST00000304418.3	-	1	574	c.537C>T	c.(535-537)aaC>aaT	p.N179N		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(12)|pancreas(1)	21	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		AGAGCAGGGGGTTACAAATAG	0.517													G|||	1742	0.347843	0.3162	0.3501	5008	,	,		22270	0.1389		0.5755	False		,,,				2504	0.3701				p.N179N		Atlas-SNP	.											.	OR5AU1	46	.	0			c.C537T						PASS	.	G		1590,2816	493.9+/-362.8	281,1028,894	63.0	61.0	62.0		537	-2.3	0.0	14	dbSNP_116	62	5015,3585	627.4+/-398.0	1453,2109,738	no	coding-synonymous	OR5AU1	NM_001004731.1		1734,3137,1632	AA,AG,GG		41.686,36.0872,49.2157		179/363	21623648	6605,6401	2203	4300	6503	SO:0001819	synonymous_variant	390445	exon1			CAGGGGGTTACAA	AL157687	CCDS32042.1	14q11.2	2013-09-23			ENSG00000169327	ENSG00000169327		"""GPCR / Class A : Olfactory receptors"""	15362	protein-coding gene	gene with protein product							Standard	NM_001004731		Approved		uc010tlp.2	Q8NGC0	OTTHUMG00000170753	ENST00000304418.3:c.537C>T	14.37:g.21623648G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_001004731	B2RP78|Q6IEU2|Q96R10	Silent	SNP	ENST00000304418.3	37	CCDS32042.1																																																																																			G|0.567;A|0.433	0.433	strong		0.517	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1		
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693003	187693003	+	Missense_Mutation	SNP	A	A	T	rs10195632	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:187693003A>T	ENST00000295131.2	-	9	1649	c.1610T>A	c.(1609-1611)tTt>tAt	p.F537Y		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	537				F -> Y (in Ref. 4; AAH31094). {ECO:0000305}.	apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			ACTAGTGTGAAATTTTCCACT	0.398													T|||	872	0.174121	0.4213	0.1066	5008	,	,		15598	0.0208		0.1103	False		,,,				2504	0.1115				p.F537Y		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.T1610A						PASS	.	T	TYR/PHE	1755,2651	643.9+/-397.9	345,1065,793	87.0	82.0	84.0		1610	-0.8	0.0	2	dbSNP_119	84	980,7620	773.6+/-407.7	44,892,3364	yes	missense	ZSWIM2	NM_182521.2	22	389,1957,4157	TT,TA,AA		11.3953,39.832,21.0288	benign	537/634	187693003	2735,10271	2203	4300	6503	SO:0001583	missense	151112	exon9			GTGTGAAATTTTC	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1610T>A	2.37:g.187693003A>T	ENSP00000295131:p.Phe537Tyr	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	198	86	0.434343	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	326	0.14926739926739926	193	0.39227642276422764	41	0.1132596685082873	10	0.017482517482517484	82	0.10817941952506596	T	0.003	-2.476034	0.00165	0.39832	0.113953	ENSG00000163012	ENST00000295131	T	0.21031	2.03	4.48	-0.832	0.10785	.	1.451510	0.04341	N	0.354113	T	0.00012	0.0000	N	0.00841	-1.15	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41574	-0.9501	9	0.02654	T	1	2.3903	0.1252	0.00068	0.306:0.1875:0.1577:0.3489	rs10195632;rs17856917;rs52835959;rs10195632	537	Q8NEG5	ZSWM2_HUMAN	Y	537	ENSP00000295131:F537Y	ENSP00000295131:F537Y	F	-	2	0	ZSWIM2	187401248	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.020000	0.03618	-0.653000	0.05401	-0.496000	0.04628	TTT	A|0.813;T|0.187	0.187	strong		0.398	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
DGKQ	1609	hgsc.bcm.edu	37	4	960542	960542	+	Silent	SNP	T	T	G	rs35117553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:960542T>G	ENST00000273814.3	-	11	1433	c.1360A>C	c.(1360-1362)Agg>Cgg	p.R454R	DGKQ_ENST00000502309.1_5'UTR	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	454	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to ATP (GO:0033198)|thrombin receptor signaling pathway (GO:0070493)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|phospholipase binding (GO:0043274)	p.R454R(1)		breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TCACCGTGCCTGCAGCCCATC	0.667													T|||	59	0.0117812	0.0023	0.0159	5008	,	,		16345	0.0		0.0398	False		,,,				2504	0.0051				p.R454R	Esophageal Squamous(17;537 645 4447 26373)	Atlas-SNP	.											DGKQ,NS,carcinoma,0,1	DGKQ	29	1	1	Substitution - coding silent(1)	breast(1)	c.A1360C						scavenged	.	T		42,4348		0,42,2153	45.0	38.0	40.0		1360	-1.9	0.9	4	dbSNP_126	40	336,8260		11,314,3973	no	coding-synonymous	DGKQ	NM_001347.2		11,356,6126	GG,GT,TT		3.9088,0.9567,2.9108		454/943	960542	378,12608	2195	4298	6493	SO:0001819	synonymous_variant	1609	exon11			CGTGCCTGCAGCC	L38707	CCDS3342.1	4p16.3	2008-08-29	2002-08-29		ENSG00000145214	ENSG00000145214			2856	protein-coding gene	gene with protein product		601207	"""diacylglycerol kinase, theta (110kD)"""	DAGK4		8617502, 9099683	Standard	NM_001347		Approved	DAGK, DAGK7	uc003gbw.4	P52824	OTTHUMG00000088629	ENST00000273814.3:c.1360A>C	4.37:g.960542T>G		Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	155	77	0.496774	NM_001347	Q6P3W4	Silent	SNP	ENST00000273814.3	37	CCDS3342.1																																																																																			T|0.975;G|0.025	0.025	strong		0.667	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1		
PTX4	390667	hgsc.bcm.edu	37	16	1537451	1537451	+	Missense_Mutation	SNP	C	C	G	rs28473314	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1537451C>G	ENST00000447419.2	-	2	687	c.662G>C	c.(661-663)gGc>gCc	p.G221A	PTX4_ENST00000440447.2_Intron|PTX4_ENST00000293922.1_Missense_Mutation_p.G216A			Q96A99	PTX4_HUMAN	pentraxin 4, long	221						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CTGTGGGGGGCCCCTGTGCTC	0.687													C|||	868	0.173323	0.0681	0.0922	5008	,	,		13846	0.4405		0.0964	False		,,,				2504	0.1769				p.G216A		Atlas-SNP	.											.	PTX4	46	.	0			c.G647C						PASS	.						16.0	20.0	19.0					16																	1537451		2187	4287	6474	SO:0001583	missense	390667	exon2			GGGGGGCCCCTGT		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.662G>C	16.37:g.1537451C>G	ENSP00000445277:p.Gly221Ala	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		401	0.18360805860805862	39	0.07926829268292683	27	0.07458563535911603	262	0.458041958041958	73	0.09630606860158311	C	8.192	0.796120	0.16327	.	.	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.04809	3.69;3.55	5.04	-0.381	0.12485	.	2.921420	0.01079	N	0.004955	T	0.00012	0.0000	N	0.22421	0.69	0.09310	N	1	B	0.24426	0.103	B	0.21708	0.036	T	0.46638	-0.9177	10	0.08179	T	0.78	.	9.7711	0.40589	0.0:0.147:0.0:0.853	rs28473314;rs57671569	216	Q96A99-2	.	A	221;216	ENSP00000445277:G221A;ENSP00000293922:G216A	ENSP00000293922:G216A	G	-	2	0	PTX4	1477452	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.287000	0.08388	-0.274000	0.09232	0.609000	0.83330	GGC	C|0.810;G|0.190	0.190	strong		0.687	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
ULK4	54986	hgsc.bcm.edu	37	3	41756965	41756965	+	Missense_Mutation	SNP	C	C	T	rs61744388	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:41756965C>T	ENST00000301831.4	-	24	3013	c.2551G>A	c.(2551-2553)Gta>Ata	p.V851I		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	851					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TGAAGCACTACAGGCATCAGG	0.428													T|||	1330	0.265575	0.5348	0.1628	5008	,	,		17563	0.1478		0.1839	False		,,,				2504	0.18				p.V851I		Atlas-SNP	.											.	ULK4	150	.	0			c.G2551A						PASS	.	T	ILE/VAL	1816,2052		436,944,554	103.0	104.0	104.0		2551	-10.1	0.0	3	dbSNP_129	104	1420,6868		128,1164,2852	yes	missense	ULK4	NM_017886.2	29	564,2108,3406	TT,TC,CC		17.1332,46.9493,26.6206	benign	851/1276	41756965	3236,8920	1934	4144	6078	SO:0001583	missense	54986	exon24			GCACTACAGGCAT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2551G>A	3.37:g.41756965C>T	ENSP00000301831:p.Val851Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	550	0.2518315018315018	262	0.532520325203252	57	0.1574585635359116	86	0.15034965034965034	145	0.19129287598944592	T	8.060	0.767962	0.15983	0.469493	0.171332	ENSG00000168038	ENST00000301831	T	0.62941	-0.01	5.72	-10.1	0.00402	Armadillo-type fold (1);	0.423778	0.22435	N	0.060092	T	0.00012	0.0000	N	0.24115	0.695	0.49915	P	1.6599999999999948E-4	B	0.09022	0.002	B	0.10450	0.005	T	0.36768	-0.9734	9	0.25106	T	0.35	.	25.2475	0.99993	0.0:0.8218:0.0:0.1782	.	851	Q96C45	ULK4_HUMAN	I	851	ENSP00000301831:V851I	ENSP00000301831:V851I	V	-	1	0	ULK4	41731969	0.000000	0.05858	0.000000	0.03702	0.404000	0.30871	-0.947000	0.03901	-2.451000	0.00543	-1.977000	0.00459	GTA	C|0.772;T|0.228	0.228	strong		0.428	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
ROR1	4919	hgsc.bcm.edu	37	1	64643277	64643277	+	Missense_Mutation	SNP	C	C	T	rs7527017	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:64643277C>T	ENST00000371079.1	+	9	1928	c.1553C>T	c.(1552-1554)aCg>aTg	p.T518M	ROR1_ENST00000545203.1_5'UTR	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	518	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		T -> M (in dbSNP:rs7527017). {ECO:0000269|PubMed:1334494, ECO:0000269|PubMed:17344846}.		peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						CAGCAATGGACGGAATTTCAA	0.483													C|||	1218	0.243211	0.0416	0.2968	5008	,	,		18991	0.3115		0.3549	False		,,,				2504	0.2924				p.T518M		Atlas-SNP	.											.	ROR1	113	.	0			c.C1553T						PASS	.	C	MET/THR	346,4060	180.1+/-208.5	20,306,1877	247.0	244.0	245.0		1553	5.0	1.0	1	dbSNP_116	245	2857,5743	449.8+/-362.2	483,1891,1926	yes	missense	ROR1	NM_005012.2	81	503,2197,3803	TT,TC,CC		33.2209,7.8529,24.6271	benign	518/938	64643277	3203,9803	2203	4300	6503	SO:0001583	missense	4919	exon9			AATGGACGGAATT	M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"""Immunoglobulin superfamily / I-set domain containing"""	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.1553C>T	1.37:g.64643277C>T	ENSP00000360120:p.Thr518Met	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	163	163	1	NM_005012	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	37	CCDS626.1	622	0.2847985347985348	18	0.036585365853658534	123	0.3397790055248619	193	0.3374125874125874	288	0.37994722955145116	C	14.02	2.410795	0.42817	0.078529	0.332209	ENSG00000185483	ENST00000371079;ENST00000544776	D	0.83075	-1.68	5.97	5.04	0.67666	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.175205	0.27460	N	0.019273	T	0.70491	0.3230	N	0.17379	0.485	0.09310	P	0.9999999999999218	P	0.42735	0.788	P	0.46940	0.532	T	0.76745	-0.2846	9	0.52906	T	0.07	.	17.0082	0.86399	0.0:0.8726:0.1273:0.0	rs7527017;rs17357178;rs56598333;rs60936730;rs7527017	518	Q01973	ROR1_HUMAN	M	518;521	ENSP00000360120:T518M	ENSP00000360120:T518M	T	+	2	0	ROR1	64415865	0.953000	0.32496	0.999000	0.59377	0.970000	0.65996	1.785000	0.38684	1.475000	0.48197	0.655000	0.94253	ACG	C|0.748;T|0.252	0.252	strong		0.483	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012	
TPPP	11076	hgsc.bcm.edu	37	5	665295	665295	+	Silent	SNP	A	A	G	rs61731455	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:665295A>G	ENST00000360578.5	-	4	703	c.582T>C	c.(580-582)gaT>gaC	p.D194D	CEP72_ENST00000514507.1_3'UTR|AC026740.1_ENST00000594226.1_5'Flank	NM_007030.2	NP_008961.1	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	194					microtubule bundle formation (GO:0001578)|microtubule polymerization (GO:0046785)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein polymerization (GO:0032273)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		CGTCCACCAGATCCACGCGGC	0.652													G|||	481	0.0960463	0.0061	0.1599	5008	,	,		18022	0.0208		0.1909	False		,,,				2504	0.1524				p.D194D		Atlas-SNP	.											TPPP,caecum,carcinoma,0,1	TPPP	24	1	0			c.T582C						PASS	.	G		169,4237	809.7+/-416.0	0,169,2034	86.0	75.0	79.0		582	4.2	1.0	5	dbSNP_129	79	1686,6914	738.4+/-407.1	171,1344,2785	no	coding-synonymous	TPPP	NM_007030.2		171,1513,4819	GG,GA,AA		19.6047,3.8357,14.2626		194/220	665295	1855,11151	2203	4300	6503	SO:0001819	synonymous_variant	11076	exon4			CACCAGATCCACG	AB017016	CCDS3856.1	5p15.33	2008-02-05			ENSG00000171368	ENSG00000171368			24164	protein-coding gene	gene with protein product	"""brain specific protein p25 alpha"""	608773				10083737, 12093283, 15590652, 17105200	Standard	NM_007030		Approved	p25alpha, TPPP1, p25, TPPP/p25	uc003jbh.4	O94811	OTTHUMG00000131011	ENST00000360578.5:c.582T>C	5.37:g.665295A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_007030		Silent	SNP	ENST00000360578.5	37	CCDS3856.1																																																																																			A|0.870;G|0.130	0.130	strong		0.652	TPPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253645.3	NM_007030	
PSMF1	9491	hgsc.bcm.edu	37	20	1108122	1108122	+	Silent	SNP	C	C	T	rs6514113	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:1108122C>T	ENST00000335877.6	+	3	512	c.336C>T	c.(334-336)atC>atT	p.I112I	PSMF1_ENST00000438768.2_Silent_p.I112I|PSMF1_ENST00000381898.4_Silent_p.I24I|PSMF1_ENST00000246015.4_Silent_p.I112I|PSMF1_ENST00000333082.3_Silent_p.I112I	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	112	Important for homodimerization and interaction with FBXO7.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						ATGATTATATCGATGCAGAAC	0.433													C|||	470	0.0938498	0.1657	0.0793	5008	,	,		18898	0.0546		0.1243	False		,,,				2504	0.0164				p.I112I		Atlas-SNP	.											.	PSMF1	27	.	0			c.C336T						PASS	.	C	,	740,3666	304.4+/-288.4	65,610,1528	125.0	125.0	125.0		336,336	-1.8	1.0	20	dbSNP_116	125	913,7687	202.5+/-245.8	52,809,3439	no	coding-synonymous,coding-synonymous	PSMF1	NM_006814.3,NM_178578.2	,	117,1419,4967	TT,TC,CC		10.6163,16.7953,12.7095	,	112/272,112/272	1108122	1653,11353	2203	4300	6503	SO:0001819	synonymous_variant	9491	exon3			TTATATCGATGCA	D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"""Proteasome (prosome, macropain) subunits"""	9571	protein-coding gene	gene with protein product	"""proteasome inhibitor hP131 subunit"""					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.336C>T	20.37:g.1108122C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_006814	A0AVQ9|D3DVW3|Q9H4I1	Silent	SNP	ENST00000335877.6	37	CCDS13010.1																																																																																			C|0.885;T|0.115	0.115	strong		0.433	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578	
WWTR1	25937	hgsc.bcm.edu	37	3	149374873	149374873	+	Missense_Mutation	SNP	G	G	T	rs1055153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:149374873G>T	ENST00000465804.1	-	3	477	c.221C>A	c.(220-222)cCg>cAg	p.P74Q	WWTR1-AS1_ENST00000479752.1_RNA|WWTR1_ENST00000360632.3_Missense_Mutation_p.P74Q|WWTR1-AS1_ENST00000466836.1_RNA|WWTR1_ENST00000467467.1_Missense_Mutation_p.P74Q|WWTR1-AS1_ENST00000495094.1_RNA	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	74					cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TCGAGGCCCCGGGTGGCCGCC	0.711			T	CAMTA1	epitheliod hemangioendothelioma								G|||	370	0.0738818	0.0582	0.0418	5008	,	,		12401	0.1478		0.0666	False		,,,				2504	0.0491				p.P74Q		Atlas-SNP	.		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	.	WWTR1	42	.	0			c.C221A						PASS	.	G	GLN/PRO,GLN/PRO,GLN/PRO	230,4124		5,220,1952	7.0	8.0	8.0		221,221,221	5.1	1.0	3	dbSNP_86	8	553,7949		28,497,3726	no	missense,missense,missense	WWTR1	NM_001168278.1,NM_001168280.1,NM_015472.4	76,76,76	33,717,5678	TT,TG,GG		6.5044,5.2825,6.0905	probably-damaging,probably-damaging,probably-damaging	74/401,74/401,74/401	149374873	783,12073	2177	4251	6428	SO:0001583	missense	25937	exon3			GGCCCCGGGTGGC	AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.221C>A	3.37:g.149374873G>T	ENSP00000419465:p.Pro74Gln	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	12	7	0.583333	NM_001168278	D3DNH7|Q8N3P2|Q9Y3W6	Missense_Mutation	SNP	ENST00000465804.1	37	CCDS3144.1	159	0.07280219780219781	30	0.06097560975609756	14	0.03867403314917127	58	0.10139860139860139	57	0.07519788918205805	G	25.8	4.671276	0.88348	0.052825	0.065044	ENSG00000018408	ENST00000465804;ENST00000360632;ENST00000467467;ENST00000479238;ENST00000485352;ENST00000475579	T;T;T;T	0.45276	0.9;0.9;0.9;0.91	5.09	5.09	0.68999	.	0.076177	0.52532	D	0.000076	T	0.02380	0.0073	L	0.43152	1.355	0.09310	P	0.99999795331	D	0.76494	0.999	D	0.72625	0.978	T	0.02339	-1.1174	9	0.12103	T	0.63	-17.8884	18.1077	0.89525	0.0:0.0:1.0:0.0	rs1055153;rs3195644;rs1055153	74	Q9GZV5	WWTR1_HUMAN	Q	74	ENSP00000419465:P74Q;ENSP00000353847:P74Q;ENSP00000419234:P74Q;ENSP00000418580:P74Q	ENSP00000353847:P74Q	P	-	2	0	WWTR1	150857563	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	5.329000	0.65892	2.360000	0.80028	0.462000	0.41574	CCG	G|0.923;T|0.077	0.077	strong		0.711	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472	
OR52K1	390036	hgsc.bcm.edu	37	11	4510587	4510587	+	Missense_Mutation	SNP	C	C	T	rs331510	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:4510587C>T	ENST00000307632.3	+	1	479	c.457C>T	c.(457-459)Cgg>Tgg	p.R153W		NM_001005171.2	NP_001005171.2	Q8NGK4	O52K1_HUMAN	olfactory receptor, family 52, subfamily K, member 1	153			R -> W (in dbSNP:rs331510). {ECO:0000269|PubMed:14983052, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(18)|skin(2)|stomach(1)	32		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.76e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0836)|LUSC - Lung squamous cell carcinoma(625;0.192)		TGCTGTGGCCCGGGCTGTGAC	0.572													C|||	1105	0.220647	0.115	0.1441	5008	,	,		19921	0.2282		0.2416	False		,,,				2504	0.3885				p.R153W		Atlas-SNP	.											OR52K1,NS,carcinoma,-1,1	OR52K1	70	1	0			c.C457T						PASS	.	C	TRP/ARG	575,3827	255.5+/-260.7	32,511,1658	98.0	84.0	89.0		457	2.2	0.1	11	dbSNP_79	89	1976,6620	346.3+/-326.1	234,1508,2556	no	missense	OR52K1	NM_001005171.2	101	266,2019,4214	TT,TC,CC		22.9874,13.0622,19.6261	benign	153/315	4510587	2551,10447	2201	4298	6499	SO:0001583	missense	390036	exon1			GTGGCCCGGGCTG	AB065790	CCDS31352.1	11p15.4	2012-08-09			ENSG00000196778	ENSG00000196778		"""GPCR / Class A : Olfactory receptors"""	15222	protein-coding gene	gene with protein product							Standard	NM_001005171		Approved		uc001lza.2	Q8NGK4	OTTHUMG00000165705	ENST00000307632.3:c.457C>T	11.37:g.4510587C>T	ENSP00000302422:p.Arg153Trp	Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	219	111	0.506849	NM_001005171	B9EH54|Q6IFK5	Missense_Mutation	SNP	ENST00000307632.3	37	CCDS31352.1	434	0.1987179487179487	55	0.11178861788617886	69	0.19060773480662985	144	0.2517482517482518	166	0.21899736147757257	C	5.539	0.284441	0.10513	0.130622	0.229874	ENSG00000196778	ENST00000307632	T	0.00030	8.9	4.07	2.18	0.27775	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41097	D	0.000957	T	0.00012	0.0000	M	0.82056	2.57	0.80722	P	0.0	B	0.22276	0.067	B	0.21360	0.034	T	0.32561	-0.9902	9	0.72032	D	0.01	.	7.9006	0.29731	0.1611:0.7509:0.0:0.0881	rs331510;rs12420202;rs331510	153	Q8NGK4	O52K1_HUMAN	W	153	ENSP00000302422:R153W	ENSP00000302422:R153W	R	+	1	2	OR52K1	4467163	0.000000	0.05858	0.052000	0.19188	0.132000	0.20833	-2.560000	0.00921	0.661000	0.30985	-0.426000	0.05927	CGG	C|0.809;T|0.191	0.191	strong		0.572	OR52K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385846.1	NM_001005171	
OR4K17	390436	hgsc.bcm.edu	37	14	20586432	20586432	+	Silent	SNP	C	C	T	rs9323534	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20586432C>T	ENST00000315543.4	+	1	867	c.867C>T	c.(865-867)taC>taT	p.Y289Y		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		TCTTTATCTACATTTGGCCCT	0.423													T|||	2369	0.473043	0.3873	0.4424	5008	,	,		18583	0.5823		0.4433	False		,,,				2504	0.5286				p.Y289Y		Atlas-SNP	.											.	OR4K17	58	.	0			c.C867T						PASS	.	T		1829,2577		385,1059,759	107.0	97.0	100.0		867	-5.7	0.0	14	dbSNP_119	100	3778,4822		830,2118,1352	no	coding-synonymous	OR4K17	NM_001004715.1		1215,3177,2111	TT,TC,CC		43.9302,41.5116,43.1109		289/344	20586432	5607,7399	2203	4300	6503	SO:0001819	synonymous_variant	390436	exon1			TATCTACATTTGG		CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"""GPCR / Class A : Olfactory receptors"""	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.867C>T	14.37:g.20586432C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	185	91	0.491892	NM_001004715	Q6IF12	Silent	SNP	ENST00000315543.4	37	CCDS32030.1																																																																																			C|0.566;T|0.434	0.434	strong		0.423	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1		
ASTL	431705	hgsc.bcm.edu	37	2	96789787	96789787	+	Silent	SNP	T	T	C	rs893173	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:96789787T>C	ENST00000342380.2	-	9	1097	c.1098A>G	c.(1096-1098)ctA>ctG	p.L366L		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						GGGAGGAAGCTAGGGTCTGAG	0.647													C|||	1650	0.329473	0.2829	0.3775	5008	,	,		17091	0.4256		0.3549	False		,,,				2504	0.2331				p.L366L		Atlas-SNP	.											ASTL,NS,carcinoma,0,1	ASTL	59	1	0			c.A1098G						PASS	.	C		1315,3091	690.9+/-405.3	188,939,1076	71.0	75.0	74.0		1098	-7.1	0.0	2	dbSNP_86	74	3118,5482	651.1+/-400.8	551,2016,1733	no	coding-synonymous	ASTL	NM_001002036.3		739,2955,2809	CC,CT,TT		36.2558,29.8457,34.0843		366/432	96789787	4433,8573	2203	4300	6503	SO:0001819	synonymous_variant	431705	exon9			GGAAGCTAGGGTC	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"""sperm acrosomal SLLP1 binding"""	608860	"""astacin-like metalloendopeptidase (M12 family)"""			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.1098A>G	2.37:g.96789787T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001002036		Silent	SNP	ENST00000342380.2	37	CCDS33249.1																																																																																			T|0.657;C|0.343	0.343	strong		0.647	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1		
TTYH2	94015	hgsc.bcm.edu	37	17	72246466	72246466	+	Silent	SNP	C	C	T	rs7224615	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:72246466C>T	ENST00000269346.4	+	10	1160	c.1086C>T	c.(1084-1086)acC>acT	p.T362T	TTYH2_ENST00000529107.1_Silent_p.T341T|TTYH2_ENST00000441391.2_Silent_p.T41T	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	362						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.T362T(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						ACCAGCTGACCGCCATGGTGG	0.622													C|||	1781	0.355631	0.5499	0.2954	5008	,	,		17653	0.1101		0.3588	False		,,,				2504	0.3855				p.T362T		Atlas-SNP	.											TTYH2,NS,carcinoma,0,1	TTYH2	63	1	1	Substitution - coding silent(1)	stomach(1)	c.C1086T						PASS	.	C	,	2337,2069	596.7+/-388.7	617,1103,483	42.0	39.0	40.0		1086,123	-10.5	0.3	17	dbSNP_116	40	3459,5141	499.6+/-375.0	699,2061,1540	no	coding-synonymous,coding-synonymous	TTYH2	NM_032646.5,NM_052869.1	,	1316,3164,2023	TT,TC,CC		40.2209,46.9587,44.564	,	362/535,41/214	72246466	5796,7210	2203	4300	6503	SO:0001819	synonymous_variant	94015	exon10			GCTGACCGCCATG		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.1086C>T	17.37:g.72246466C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	177	80	0.451977	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Silent	SNP	ENST00000269346.4	37	CCDS32717.1																																																																																			C|0.592;T|0.408	0.408	strong		0.622	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
STK39	27347	hgsc.bcm.edu	37	2	168931636	168931636	+	Missense_Mutation	SNP	C	C	T	rs56031549	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:168931636C>T	ENST00000355999.4	-	11	1900	c.1195G>A	c.(1195-1197)Gct>Act	p.A399T	STK39_ENST00000487143.1_5'UTR	NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	399					cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						TGAGAAAAAGCTGCTTTCCCT	0.413													C|||	32	0.00638978	0.0	0.0159	5008	,	,		19516	0.0		0.0169	False		,,,				2504	0.0041				p.A399T		Atlas-SNP	.											.	STK39	95	.	0			c.G1195A						PASS	.	C	THR/ALA	8,3970		0,8,1981	223.0	224.0	223.0		1195	5.6	1.0	2	dbSNP_129	223	120,8202		2,116,4043	yes	missense	STK39	NM_013233.2	58	2,124,6024	TT,TC,CC		1.442,0.2011,1.0407	benign	399/546	168931636	128,12172	1989	4161	6150	SO:0001583	missense	27347	exon11			AAAAAGCTGCTTT	AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648			17717	protein-coding gene	gene with protein product	"""STE20/SPS1 homolog (yeast)"""	607648				10980603	Standard	NM_013233		Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.1195G>A	2.37:g.168931636C>T	ENSP00000348278:p.Ala399Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	146	63	0.431507	NM_013233	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	Missense_Mutation	SNP	ENST00000355999.4	37	CCDS42770.1	21	0.009615384615384616	0	0.0	10	0.027624309392265192	0	0.0	11	0.014511873350923483	C	27.9	4.874365	0.91664	0.002011	0.01442	ENSG00000198648	ENST00000355999	T	0.73363	-0.74	5.58	5.58	0.84498	.	0.054749	0.64402	D	0.000001	T	0.47764	0.1463	L	0.54323	1.7	0.80722	D	1	P	0.37548	0.599	B	0.38156	0.266	T	0.61589	-0.7032	10	0.32370	T	0.25	-0.3125	14.4169	0.67155	0.1475:0.8525:0.0:0.0	rs56031549;rs61731484	399	Q9UEW8	STK39_HUMAN	T	399	ENSP00000348278:A399T	ENSP00000348278:A399T	A	-	1	0	STK39	168639882	1.000000	0.71417	0.981000	0.43875	0.991000	0.79684	5.930000	0.70104	2.638000	0.89438	0.563000	0.77884	GCT	C|0.987;T|0.013	0.013	strong		0.413	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258112.2	NM_013233	
FANCA	2175	hgsc.bcm.edu	37	16	89839766	89839766	+	Missense_Mutation	SNP	G	G	C	rs17232910	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89839766G>C	ENST00000389301.3	-	22	1957	c.1927C>G	c.(1927-1929)Ccc>Gcc	p.P643A	FANCA_ENST00000568369.1_Missense_Mutation_p.P643A|FANCA_ENST00000567284.2_5'UTR	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	643			P -> A (in dbSNP:rs17232910).		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GCAGAGTTGGGTTCTGCCCTC	0.542			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	371	0.0740815	0.0038	0.0202	5008	,	,		17511	0.2698		0.0626	False		,,,				2504	0.0174				p.P643A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.C1927G						PASS	.	G	ALA/PRO	51,4029		0,51,1989	31.0	26.0	28.0		1927	-2.4	0.0	16	dbSNP_123	28	519,7361		11,497,3432	yes	missense	FANCA	NM_000135.2	27	11,548,5421	CC,CG,GG		6.5863,1.25,4.7659	benign	643/1456	89839766	570,11390	2040	3940	5980	SO:0001583	missense	2175	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGTTGGGTTCTGC	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1927C>G	16.37:g.89839766G>C	ENSP00000373952:p.Pro643Ala	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	60	17	0.283333	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	190	0.08699633699633699	3	0.006097560975609756	10	0.027624309392265192	127	0.22202797202797203	50	0.06596306068601583	G	6.741	0.505585	0.12822	0.0125	0.065863	ENSG00000187741	ENST00000389301	D	0.83591	-1.74	3.82	-2.44	0.06502	.	0.752143	0.11984	N	0.510486	T	0.00039	0.0001	N	0.08118	0	0.53688	P	2.6999999999999247E-5	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.03706	-1.1011	9	0.07030	T	0.85	-10.2216	2.1006	0.03679	0.1027:0.3278:0.2668:0.3028	rs17232910	643;643	B4DRI7;O15360	.;FANCA_HUMAN	A	643	ENSP00000373952:P643A	ENSP00000373952:P643A	P	-	1	0	FANCA	88367267	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	-0.040000	0.12104	-0.163000	0.10946	-0.131000	0.14894	CCC	G|0.936;C|0.064	0.064	strong		0.542	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197248	39197248	+	Silent	SNP	G	G	A	rs570985299	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39197248G>A	ENST00000306271.4	-	1	465	c.402C>T	c.(400-402)tgC>tgT	p.C134C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	134						keratin filament (GO:0045095)		p.C134C(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCTCACCACGCAGCAGGGGG	0.672													a|||	3	0.000599042	0.0008	0.0	5008	,	,		16961	0.0		0.0	False		,,,				2504	0.002				p.C134C		Atlas-SNP	.											KRTAP1-1,NS,carcinoma,0,1	KRTAP1-1	23	1	1	Substitution - coding silent(1)	endometrium(1)	c.C402T						scavenged	.						24.0	29.0	27.0					17																	39197248		2078	4173	6251	SO:0001819	synonymous_variant	81851	exon1			CACCACGCAGCAG	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.402C>T	17.37:g.39197248G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	127	4	0.0314961	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			.	.	none		0.672	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84606647	84606647	+	Missense_Mutation	SNP	A	A	G	rs112107496	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:84606647A>G	ENST00000344803.2	+	4	1309	c.1262A>G	c.(1261-1263)aAa>aGa	p.K421R		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	421					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CAAGTCAAAAAAAGGGGTGAT	0.443													A|||	59	0.0117812	0.0045	0.0173	5008	,	,		19879	0.0		0.0318	False		,,,				2504	0.0092				p.K421R		Atlas-SNP	.											.	.	.	.	0			c.A1262G						PASS	.	A	ARG/LYS	21,3659		0,21,1819	78.0	68.0	71.0		1262	2.2	0.0	9	dbSNP_132	71	230,7954		8,214,3870	no	missense	FAM75D1	NM_001001670.2	26	8,235,5689	GG,GA,AA		2.8104,0.5707,2.1156	benign	421/1577	84606647	251,11613	1840	4092	5932	SO:0001583	missense	389763	exon4			TCAAAAAAAGGGG		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.1262A>G	9.37:g.84606647A>G	ENSP00000341988:p.Lys421Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	181	91	0.502762	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	40	0.018315018315018316	3	0.006097560975609756	9	0.024861878453038673	0	0.0	28	0.036939313984168866	A	7.757	0.704540	0.15172	0.005707	0.028104	ENSG00000214929	ENST00000344803	T	0.06933	3.24	3.41	2.24	0.28232	.	0.842492	0.10369	N	0.683060	T	0.02688	0.0081	M	0.75615	2.305	0.09310	N	1	B	0.30563	0.285	B	0.35510	0.204	T	0.25537	-1.0129	10	0.51188	T	0.08	-12.5151	5.6204	0.17453	0.8694:0.0:0.1306:0.0	.	421	Q6ZQQ2	F75D1_HUMAN	R	421	ENSP00000341988:K421R	ENSP00000341988:K421R	K	+	2	0	FAM75D1	83796467	0.269000	0.24143	0.010000	0.14722	0.036000	0.12997	1.298000	0.33412	0.522000	0.28464	-0.260000	0.10688	AAA	A|0.982;G|0.018	0.018	strong		0.443	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
C15orf40	123207	hgsc.bcm.edu	37	15	83680329	83680329	+	Missense_Mutation	SNP	G	G	A	rs17361375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:83680329G>A	ENST00000513601.2	-	1	38	c.31C>T	c.(31-33)Ctt>Ttt	p.L11F	RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000304177.5_5'UTR|C15orf40_ENST00000451195.3_Missense_Mutation_p.L11F|RP11-382A20.7_ENST00000570202.1_RNA|C15orf40_ENST00000538348.2_Missense_Mutation_p.L11F|C15orf40_ENST00000565712.1_Missense_Mutation_p.L11F			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40	11										large_intestine(3)|lung(2)|skin(1)	6						GTTGCCCGAAGGTGCCTCAGC	0.697											OREG0023391	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	651	0.129992	0.1566	0.2291	5008	,	,		13813	0.003		0.1918	False		,,,				2504	0.091				p.L11F		Atlas-SNP	.											.	C15orf40	18	.	0			c.C31T						PASS	.	G	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	726,3678		46,634,1522	18.0	20.0	19.0		31,31,31,31,31	-1.2	0.0	15	dbSNP_123	19	1780,6820		176,1428,2696	yes	missense,missense,missense,missense,missense	C15orf40	NM_144597.2,NM_001160116.1,NM_001160115.1,NM_001160114.1,NM_001160113.1	22,22,22,22,22	222,2062,4218	AA,AG,GG		20.6977,16.485,19.271	benign,benign,benign,benign,benign	11/154,11/150,11/168,11/154,11/168	83680329	2506,10498	2202	4300	6502	SO:0001583	missense	123207	exon1			CCCGAAGGTGCCT	BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.31C>T	15.37:g.83680329G>A	ENSP00000424666:p.Leu11Phe	Somatic	31	0	0	1223	WXS	Illumina HiSeq	Phase_I	30	16	0.533333	NM_001160116	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Missense_Mutation	SNP	ENST00000513601.2	37	CCDS32312.2	290	0.13278388278388278	71	0.1443089430894309	73	0.20165745856353592	1	0.0017482517482517483	145	0.19129287598944592	G	10.89	1.479786	0.26511	0.16485	0.206977	ENSG00000169609	ENST00000538348;ENST00000451195;ENST00000513601	.	.	.	3.61	-1.25	0.09405	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.51482	P	7.900000000005125E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.36939	-0.9727	7	0.11182	T	0.66	.	3.9244	0.09257	0.2978:0.3667:0.3354:0.0	rs17361375;rs17361375	11;11;11	F8WD31;F5GX92;G5EA00	.;.;.	F	11	.	ENSP00000403987:L11F	L	-	1	0	C15orf40	81471333	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.601000	0.05687	-0.228000	0.09869	-1.717000	0.00709	CTT	G|0.855;A|0.145	0.145	strong		0.697	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597	
TAP1	6890	hgsc.bcm.edu	37	6	32816772	32816772	+	Missense_Mutation	SNP	C	C	A	rs41550019	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32816772C>A	ENST00000354258.4	-	6	1713	c.1552G>T	c.(1552-1554)Gtg>Ttg	p.V518L	TAP1_ENST00000425148.2_Missense_Mutation_p.V257L|PSMB9_ENST00000395330.1_Intron|TAPSAR1_ENST00000453426.1_lincRNA	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	518	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.|Involved in peptide-binding site.		V -> L (in allele TAP1*04:01; dbSNP:rs41550019). {ECO:0000269|PubMed:11250043, ECO:0000269|PubMed:12878362, ECO:0000269|PubMed:8248212}.		antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	CTCACCTCCACAGCCTGGGTG	0.542													C|||	296	0.0591054	0.171	0.049	5008	,	,		20359	0.001		0.0338	False		,,,				2504	0.001				p.V518L		Atlas-SNP	.											.	TAP1	39	.	0			c.G1552T						PASS	.	C	LEU/VAL	376,2646		22,332,1157	78.0	52.0	61.0		1552	4.1	1.0	6	dbSNP_127	61	158,5260		2,154,2553	yes	missense	TAP1	NM_000593.5	32	24,486,3710	AA,AC,CC		2.9162,12.4421,6.327	possibly-damaging	518/809	32816772	534,7906	1511	2709	4220	SO:0001583	missense	6890	exon6			CCTCCACAGCCTG		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"""ATP binding cassette transporters / subfamily B"""	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.1552G>T	6.37:g.32816772C>A	ENSP00000346206:p.Val518Leu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	105	40	0.380952	NM_000593	Q16149|Q96CP4	Missense_Mutation	SNP	ENST00000354258.4	37	CCDS4758.1	132	0.06043956043956044	95	0.19308943089430894	16	0.04419889502762431	1	0.0017482517482517483	20	0.026385224274406333	C	15.34	2.804766	0.50315	0.124421	0.029162	ENSG00000168394	ENST00000354258;ENST00000425148	D;D	0.86769	-2.17;-2.17	5.02	4.05	0.47172	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	2.649620	0.01818	N	0.033862	T	0.78578	0.4305	L	0.42245	1.32	0.19300	P	0.9999799193	B	0.33135	0.399	B	0.39531	0.302	T	0.62163	-0.6912	9	0.34782	T	0.22	-15.3442	10.8749	0.46904	0.0:0.9001:0.0:0.0999	rs41550019;rs60844934;rs62621091	518	Q03518	TAP1_HUMAN	L	518;257	ENSP00000346206:V518L;ENSP00000401919:V257L	ENSP00000346206:V518L	V	-	1	0	TAP1	32924750	0.344000	0.24827	0.994000	0.49952	0.339000	0.28857	0.669000	0.25142	1.178000	0.42870	0.643000	0.83706	GTG	G|0.000;C|0.939;A|0.061	0.061	strong		0.542	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593	
CCDC88B	283234	hgsc.bcm.edu	37	11	64120703	64120703	+	Silent	SNP	G	G	A	rs61744422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64120703G>A	ENST00000356786.5	+	21	3722	c.3678G>A	c.(3676-3678)acG>acA	p.T1226T	CCDC88B_ENST00000359902.2_Silent_p.T378T|CCDC88B_ENST00000301897.4_5'UTR|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	1226						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GGCTGACCACGCAGTGTGAGG	0.692													G|||	28	0.00559105	0.0008	0.0101	5008	,	,		13374	0.0		0.0149	False		,,,				2504	0.0051				p.T1226T		Atlas-SNP	.											.	CCDC88B	89	.	0			c.G3678A						PASS	.	G		20,4252		0,20,2116	5.0	7.0	6.0		3678	-8.1	0.9	11	dbSNP_129	6	104,8316		1,102,4107	no	coding-synonymous	CCDC88B	NM_032251.5		1,122,6223	AA,AG,GG		1.2352,0.4682,0.977		1226/1477	64120703	124,12568	2136	4210	6346	SO:0001819	synonymous_variant	283234	exon21			GACCACGCAGTGT	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.3678G>A	11.37:g.64120703G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			G|0.990;A|0.010	0.010	strong		0.692	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
GUCA1C	9626	hgsc.bcm.edu	37	3	108634973	108634973	+	Splice_Site	SNP	C	C	A	rs10933973	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:108634973C>A	ENST00000261047.3	-	3	575		c.e3+1		GUCA1C_ENST00000393963.3_Missense_Mutation_p.G148V|GUCA1C_ENST00000471108.1_Missense_Mutation_p.G148V	NM_005459.3	NP_005450.3	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C						phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(2)|large_intestine(1)|liver(1)|lung(8)|pancreas(1)|skin(1)	14						AGCTCCATTACCATCATTGTT	0.428													C|||	1250	0.249601	0.2519	0.3084	5008	,	,		18757	0.1806		0.3042	False		,,,				2504	0.2198				.	NSCLC(157;1360 1999 30631 40189 44208)	Atlas-SNP	.											.	GUCA1C	39	.	0			c.442+1G>T						PASS	.	C		1193,3213	417.0+/-337.8	156,881,1166	164.0	156.0	159.0			-0.3	0.0	3	dbSNP_120	159	2696,5904	433.1+/-357.3	416,1864,2020	yes	splice-5	GUCA1C	NM_005459.3		572,2745,3186	AA,AC,CC		31.3488,27.0767,29.9016			108634973	3889,9117	2203	4300	6503	SO:0001630	splice_region_variant	9626	exon4			CCATTACCATCAT	AF110002	CCDS2954.1	3q13.1	2013-01-10			ENSG00000138472	ENSG00000138472		"""EF-hand domain containing"""	4680	protein-coding gene	gene with protein product	"""guanylyl cyclase-activating protein 3"""	605128				10037746, 11860507	Standard	NM_005459		Approved	GCAP3	uc003dxj.2	O95843	OTTHUMG00000159204	ENST00000261047.3:c.442+1G>T	3.37:g.108634973C>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	192	91	0.473958	NM_005459	O95844|Q9UNM0	Splice_Site	SNP	ENST00000261047.3	37	CCDS2954.1	562|562	0.2573260073260073|0.2573260073260073	97|97	0.19715447154471544|0.19715447154471544	108|108	0.2983425414364641|0.2983425414364641	127|127	0.22202797202797203|0.22202797202797203	230|230	0.3034300791556728|0.3034300791556728	c|c	14.10|14.10	2.433951|2.433951	0.43224|0.43224	0.270767|0.270767	0.313488|0.313488	ENSG00000138472|ENSG00000138472	ENST00000261047|ENST00000393963;ENST00000471108	.|D;D	.|0.84070	.|-1.8;-1.8	4.2|4.2	-0.274|-0.274	0.12910|0.12910	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999866305|0.9999999866305	.|D	.|0.89917	.|1.0	.|D	.|0.81914	.|0.995	.|T	.|0.07083	.|-1.0791	.|7	.|0.87932	.|D	.|0	.|.	7.7152|7.7152	0.28700|0.28700	0.2868:0.4257:0.2875:0.0|0.2868:0.4257:0.2875:0.0	rs10933973;rs52825108;rs61623352;rs10933973|rs10933973;rs52825108;rs61623352;rs10933973	.|148	.|C9JNI2	.|.	.|V	-1|148	.|ENSP00000377535:G148V;ENSP00000417761:G148V	.|ENSP00000377535:G148V	.|G	-|-	.|2	.|0	GUCA1C|GUCA1C	110117663|110117663	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.970000|0.970000	0.65996|0.65996	1.417000|1.417000	0.34770|0.34770	-0.323000|-0.323000	0.08602|0.08602	0.651000|0.651000	0.88453|0.88453	.|GGT	C|0.727;A|0.273	0.273	strong		0.428	GUCA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353819.1	NM_005459	Intron
PRKRIR	5612	hgsc.bcm.edu	37	11	76072085	76072085	+	Missense_Mutation	SNP	C	C	T	rs76214254	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:76072085C>T	ENST00000260045.3	-	3	338	c.233G>A	c.(232-234)cGa>cAa	p.R78Q	PRKRIR_ENST00000531878.1_5'UTR	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	78					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						TGCATTATCTCGAAGAACTGT	0.308																																					p.R78Q		Atlas-SNP	.											PRKRIR,caecum,adenoma,0,1	PRKRIR	65	1	0			c.G233A						scavenged	.						114.0	110.0	112.0					11																	76072085		2200	4292	6492	SO:0001583	missense	5612	exon3			TTATCTCGAAGAA	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"""THAP (C2CH-type zinc finger) domain containing"""	9440	protein-coding gene	gene with protein product	"""THAP domain containing 12"""	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.233G>A	11.37:g.76072085C>T	ENSP00000260045:p.Arg78Gln	Somatic	107	3	0.0280374		WXS	Illumina HiSeq	Phase_I	110	5	0.0454545	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	ENST00000260045.3	37	CCDS8243.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552130	0.65311	.	.	ENSG00000137492	ENST00000260045	D	0.96459	-4.02	5.44	5.44	0.79542	Zinc finger, C2CH-type (4);	0.052263	0.85682	D	0.000000	D	0.93035	0.7783	L	0.31526	0.94	0.44899	D	0.997917	B	0.28470	0.213	B	0.20184	0.028	D	0.90113	0.4193	10	0.36615	T	0.2	.	19.6212	0.95656	0.0:1.0:0.0:0.0	.	78	O43422	P52K_HUMAN	Q	78	ENSP00000260045:R78Q	ENSP00000260045:R78Q	R	-	2	0	PRKRIR	75749733	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.216000	0.58540	2.723000	0.93209	0.655000	0.94253	CGA	C|0.999;T|0.001	0.001	strong		0.308	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705	
ZBBX	79740	hgsc.bcm.edu	37	3	167068256	167068256	+	Missense_Mutation	SNP	T	T	A	rs4619784	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:167068256T>A	ENST00000392766.2	-	9	820	c.480A>T	c.(478-480)aaA>aaT	p.K160N	ZBBX_ENST00000392767.2_Missense_Mutation_p.K160N|ZBBX_ENST00000307529.5_Missense_Mutation_p.K160N|ZBBX_ENST00000455345.2_Missense_Mutation_p.K160N|ZBBX_ENST00000392764.1_Missense_Mutation_p.K131N|ZBBX_ENST00000469220.1_Intron	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	160			K -> N (in dbSNP:rs4619784).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						TCTGGTGAACTTTAGCAAAGC	0.308													T|||	1278	0.255192	0.0756	0.3343	5008	,	,		13253	0.1756		0.4076	False		,,,				2504	0.3671				p.K160N		Atlas-SNP	.											.	ZBBX	299	.	0			c.A480T						PASS	.	T	ASN/LYS,ASN/LYS,ASN/LYS	474,3148		29,416,1366	190.0	182.0	184.0		480,393,480	5.5	1.0	3	dbSNP_111	184	3474,4674		723,2028,1323	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	94,94,94	752,2444,2689	AA,AT,TT		42.6362,13.0867,33.5429	probably-damaging,probably-damaging,probably-damaging	160/840,131/772,160/801	167068256	3948,7822	1811	4074	5885	SO:0001583	missense	79740	exon9			GTGAACTTTAGCA	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.480A>T	3.37:g.167068256T>A	ENSP00000376519:p.Lys160Asn	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	221	102	0.461538	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	591	0.2706043956043956	58	0.11788617886178862	128	0.35359116022099446	101	0.17657342657342656	304	0.40105540897097625	T	20.9	4.065775	0.76187	0.130867	0.426362	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764;ENST00000474464	T;T;T;T;T;T	0.33865	1.54;1.54;1.54;1.54;1.54;1.39	5.54	5.54	0.83059	Zinc finger, B-box (1);	0.235594	0.20612	U	0.088941	T	0.00012	0.0000	L	0.36672	1.1	0.26900	P	0.9671236	D;D	0.69078	0.996;0.997	D;D	0.71184	0.953;0.972	T	0.46261	-0.9204	9	0.72032	D	0.01	-11.1017	13.6397	0.62243	0.0:0.0:0.0:1.0	rs4619784;rs17857007;rs52831775;rs4619784	160;160	A8MT70-2;A8MT70	.;ZBBX_HUMAN	N	160;160;160;160;131;160	ENSP00000376519:K160N;ENSP00000376520:K160N;ENSP00000390232:K160N;ENSP00000305065:K160N;ENSP00000376517:K131N;ENSP00000419307:K160N	ENSP00000305065:K160N	K	-	3	2	ZBBX	168550950	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	2.674000	0.46867	2.101000	0.63845	0.377000	0.23210	AAA	T|0.693;A|0.307	0.307	strong		0.308	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
C1S	716	hgsc.bcm.edu	37	12	7175047	7175047	+	Silent	SNP	A	A	G	rs1143664	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7175047A>G	ENST00000406697.1	+	13	1795	c.1167A>G	c.(1165-1167)ccA>ccG	p.P389P	C1S_ENST00000402681.3_Silent_p.P222P|C1S_ENST00000328916.3_Silent_p.P389P|C1S_ENST00000495061.1_3'UTR|C1S_ENST00000360817.5_Silent_p.P389P			P09871	C1S_HUMAN	complement component 1, s subcomponent	389	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GTGAGGAGCCATATTACTACA	0.463													G|||	481	0.0960463	0.1914	0.0677	5008	,	,		-128	0.004		0.0845	False		,,,				2504	0.0941				p.P389P	GBM(156;750 1943 12971 24779 31015)	Atlas-SNP	.											.	C1S	93	.	0			c.A1167G						PASS	.	G	,	720,3686	759.1+/-412.9	57,606,1540	134.0	135.0	135.0		1167,1167	-10.4	0.4	12	dbSNP_86	135	665,7935	789.4+/-407.6	32,601,3667	no	coding-synonymous,coding-synonymous	C1S	NM_001734.3,NM_201442.2	,	89,1207,5207	GG,GA,AA		7.7326,16.3414,10.6489	,	389/689,389/689	7175047	1385,11621	2203	4300	6503	SO:0001819	synonymous_variant	716	exon10			GGAGCCATATTAC		CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"""Complement system"""	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.1167A>G	12.37:g.7175047A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Silent	SNP	ENST00000406697.1	37	CCDS31735.1																																																																																			A|0.900;G|0.100	0.100	strong		0.463	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734	
KRT32	3882	hgsc.bcm.edu	37	17	39616429	39616429	+	Missense_Mutation	SNP	G	G	A	rs117083040	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39616429G>A	ENST00000225899.3	-	7	1383	c.1280C>T	c.(1279-1281)cCc>cTc	p.P427L		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	427	Tail.		P -> T (in dbSNP:rs2604953). {ECO:0000269|PubMed:7556444, ECO:0000269|PubMed:8823373}.		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				GACGGTGCGGGGCACGCATGG	0.607													G|||	25	0.00499201	0.0	0.0058	5008	,	,		19971	0.0		0.0199	False		,,,				2504	0.001				p.P427L		Atlas-SNP	.											.	KRT32	57	.	0			c.C1280T						PASS	.	G	LEU/PRO	18,4386	17.9+/-39.9	1,16,2185	78.0	56.0	63.0		1280	3.9	0.0	17	dbSNP_132	63	160,8438	48.9+/-108.6	5,150,4144	no	missense	KRT32	NM_002278.3	98	6,166,6329	AA,AG,GG		1.8609,0.4087,1.369	benign	427/449	39616429	178,12824	2202	4299	6501	SO:0001583	missense	3882	exon7			GTGCGGGGCACGC	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.1280C>T	17.37:g.39616429G>A	ENSP00000225899:p.Pro427Leu	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	221	106	0.479638	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	16	0.007326007326007326	0	0.0	1	0.0027624309392265192	0	0.0	15	0.01978891820580475	G	12.51	1.958842	0.34565	0.004087	0.018609	ENSG00000108759	ENST00000225899	D	0.87571	-2.27	3.89	3.89	0.44902	.	0.677027	0.12165	N	0.493574	T	0.77751	0.4177	M	0.79926	2.475	0.09310	N	0.999999	B	0.30793	0.295	B	0.21151	0.033	T	0.76764	-0.2839	10	0.59425	D	0.04	.	11.5515	0.50723	0.0:0.0:1.0:0.0	.	427	Q14532	K1H2_HUMAN	L	427	ENSP00000225899:P427L	ENSP00000225899:P427L	P	-	2	0	KRT32	36869955	0.025000	0.19082	0.015000	0.15790	0.002000	0.02628	1.659000	0.37387	2.161000	0.67846	0.511000	0.50034	CCC	G|0.987;A|0.013	0.013	strong		0.607	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
DDX20	11218	hgsc.bcm.edu	37	1	112309123	112309123	+	Missense_Mutation	SNP	C	C	A	rs197414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:112309123C>A	ENST00000369702.4	+	11	2697	c.2077C>A	c.(2077-2079)Cgt>Agt	p.R693S	DDX20_ENST00000475700.1_Missense_Mutation_p.R301S	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	693			R -> S (in dbSNP:rs197414).		ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGTGGATGATCGTATTTCTTT	0.433													C|||	831	0.165935	0.4274	0.0965	5008	,	,		20348	0.003		0.1252	False		,,,				2504	0.0716				p.R693S		Atlas-SNP	.											.	DDX20	50	.	0			c.C2077A	GRCh37	CM086198	DDX20	M	rs197414	PASS	.	C	SER/ARG	1627,2779	487.6+/-361.0	296,1035,872	79.0	82.0	81.0		2077	4.1	0.5	1	dbSNP_79	81	1099,7499	228.6+/-263.6	69,961,3269	yes	missense	DDX20	NM_007204.4	110	365,1996,4141	AA,AC,CC		12.782,36.9269,20.9628	benign	693/825	112309123	2726,10278	2203	4299	6502	SO:0001583	missense	11218	exon11			GATGATCGTATTT	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2077C>A	1.37:g.112309123C>A	ENSP00000358716:p.Arg693Ser	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	116	61	0.525862	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	338	0.15476190476190477	213	0.4329268292682927	30	0.08287292817679558	0	0.0	95	0.12532981530343007	C	4.758	0.140947	0.09083	0.369269	0.12782	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.31247	1.5;2.06	5.0	4.09	0.47781	.	2.687950	0.00649	N	0.000558	T	0.09247	0.0228	N	0.22421	0.69	0.09310	P	0.9999999999930954	B;B	0.12630	0.006;0.002	B;B	0.12837	0.008;0.005	T	0.11891	-1.0569	8	.	.	.	-0.8902	8.3507	0.32301	0.1541:0.7669:0.0:0.079	rs197414;rs665164;rs742792;rs52835282;rs57983595;rs197414	301;693	E9PJ60;Q9UHI6	.;DDX20_HUMAN	S	693;301	ENSP00000358716:R693S;ENSP00000435660:R301S	.	R	+	1	0	DDX20	112110646	0.005000	0.15991	0.498000	0.27564	0.024000	0.10985	1.194000	0.32174	1.476000	0.48215	0.655000	0.94253	CGT	C|0.846;A|0.154	0.154	strong		0.433	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
NUP107	57122	hgsc.bcm.edu	37	12	69090624	69090624	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:69090624C>T	ENST00000229179.4	+	6	806	c.474C>T	c.(472-474)ttC>ttT	p.F158F	NUP107_ENST00000378905.2_Silent_p.F7F|NUP107_ENST00000539906.1_Silent_p.F129F	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	158					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			TTTCTGATTTCCTGCAGTCTT	0.363																																					p.F158F		Atlas-SNP	.											.	NUP107	88	.	0			c.C474T						PASS	.						129.0	113.0	118.0					12																	69090624		2203	4300	6503	SO:0001819	synonymous_variant	57122	exon6			TGATTTCCTGCAG	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.474C>T	12.37:g.69090624C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	56	4	0.0714286	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			.	.	none		0.363	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
GDF9	2661	hgsc.bcm.edu	37	5	132198100	132198100	+	Silent	SNP	C	C	T	rs10491279	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:132198100C>T	ENST00000378673.2	-	3	1412	c.546G>A	c.(544-546)gaG>gaA	p.E182E	GDF9_ENST00000296875.2_Silent_p.E182E|GDF9_ENST00000464378.1_5'UTR			O60383	GDF9_HUMAN	growth differentiation factor 9	182					female gamete generation (GO:0007292)|negative regulation of cell growth (GO:0030308)|oocyte growth (GO:0001555)|positive regulation of cell proliferation (GO:0008284)|regulation of progesterone secretion (GO:2000870)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(1)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	22		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AAGACTTTGGCTCCTTTATCA	0.393													C|||	675	0.134784	0.1952	0.1138	5008	,	,		21253	0.1498		0.1561	False		,,,				2504	0.0307				p.E182E		Atlas-SNP	.											.	GDF9	50	.	0			c.G546A						PASS	.	C		925,3481	350.3+/-310.7	93,739,1371	122.0	124.0	123.0		546	-1.6	0.0	5	dbSNP_119	123	1488,7112	283.7+/-296.3	128,1232,2940	no	coding-synonymous	GDF9	NM_005260.3		221,1971,4311	TT,TC,CC		17.3023,20.9941,18.553		182/455	132198100	2413,10593	2203	4300	6503	SO:0001819	synonymous_variant	2661	exon2			CTTTGGCTCCTTT		CCDS4162.1, CCDS75299.1	5q31.1	2014-01-30			ENSG00000164404	ENSG00000164404		"""Endogenous ligands"""	4224	protein-coding gene	gene with protein product		601918				7760846	Standard	NM_005260		Approved		uc003kxz.1	O60383	OTTHUMG00000059842	ENST00000378673.2:c.546G>A	5.37:g.132198100C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	113	110	0.973451	NM_005260	Q4VAW5	Silent	SNP	ENST00000378673.2	37	CCDS4162.1																																																																																			C|0.826;T|0.174	0.174	strong		0.393	GDF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133060.2	NM_005260	
IL17F	112744	hgsc.bcm.edu	37	6	52101844	52101844	+	Missense_Mutation	SNP	T	T	C	rs2397084	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:52101844T>C	ENST00000336123.4	-	3	484	c.377A>G	c.(376-378)gAg>gGg	p.E126G		NM_052872.3	NP_443104.1	Q96PD4	IL17F_HUMAN	interleukin 17F	126			E -> G (in dbSNP:rs2397084).		cartilage development (GO:0051216)|cytokine biosynthetic process (GO:0042089)|inflammatory response (GO:0006954)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045423)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of interleukin-8 biosynthetic process (GO:0045414)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine binding (GO:0019955)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)	14	Lung NSC(77;0.116)					GACCAGGGTCTCTTGCTGGAT	0.547													T|||	166	0.033147	0.003	0.0476	5008	,	,		21490	0.004		0.0785	False		,,,				2504	0.047				p.E126G		Atlas-SNP	.											IL17F,NS,carcinoma,+1,2	IL17F	28	2	0			c.A377G						PASS	.	T	GLY/GLU	95,4311	75.7+/-113.9	0,95,2108	95.0	87.0	90.0		377	5.7	1.0	6	dbSNP_100	90	772,7828	183.5+/-231.7	29,714,3557	yes	missense	IL17F	NM_052872.3	98	29,809,5665	CC,CT,TT		8.9767,2.1562,6.6662	probably-damaging	126/164	52101844	867,12139	2203	4300	6503	SO:0001583	missense	112744	exon3			AGGGTCTCTTGCT	AF384857	CCDS4938.1	6p12	2014-09-17			ENSG00000112116	ENSG00000112116		"""Interleukins and interleukin receptors"""	16404	protein-coding gene	gene with protein product		606496				11591732, 11591768	Standard	NM_052872		Approved	IL-17F, ML-1, ML1	uc003pam.1	Q96PD4	OTTHUMG00000014845	ENST00000336123.4:c.377A>G	6.37:g.52101844T>C	ENSP00000337432:p.Glu126Gly	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_052872	Q6NSI0|Q7Z6P4|Q96PI8|Q9NUE6	Missense_Mutation	SNP	ENST00000336123.4	37	CCDS4938.1	89	0.04075091575091575	4	0.008130081300813009	22	0.06077348066298342	1	0.0017482517482517483	62	0.08179419525065963	T	21.9	4.216069	0.79352	0.021562	0.089767	ENSG00000112116	ENST00000336123	T	0.57107	0.42	5.72	5.72	0.89469	.	0.056430	0.64402	D	0.000001	T	0.69324	0.3098	M	0.84846	2.72	0.46749	D	0.999186	D	0.89917	1.0	D	0.77557	0.99	T	0.75473	-0.3305	10	0.66056	D	0.02	-37.3585	13.9726	0.64250	0.0:0.0:0.0:1.0	rs2397084;rs2397084	126	Q96PD4	IL17F_HUMAN	G	126	ENSP00000337432:E126G	ENSP00000337432:E126G	E	-	2	0	IL17F	52209803	1.000000	0.71417	0.973000	0.42090	0.860000	0.49131	4.643000	0.61390	2.194000	0.70268	0.533000	0.62120	GAG	T|0.948;C|0.052	0.052	strong		0.547	IL17F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040901.3	NM_052872	
BFAR	51283	hgsc.bcm.edu	37	16	14742400	14742400	+	Missense_Mutation	SNP	T	T	G	rs11546303	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:14742400T>G	ENST00000261658.2	+	3	696	c.419T>G	c.(418-420)aTg>aGg	p.M140R	BFAR_ENST00000563971.1_Intron|BFAR_ENST00000426842.2_Intron	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	140			M -> R (in dbSNP:rs11546303).		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	11						AATCAGCAGATGGGAGGGGGA	0.507													G|||	1262	0.251997	0.1172	0.4049	5008	,	,		17221	0.1558		0.3917	False		,,,				2504	0.2812				p.M140R		Atlas-SNP	.											BFAR,colon,carcinoma,0,1	BFAR	38	1	0			c.T419G						PASS	.	G	ARG/MET	775,3619	752.4+/-412.3	65,645,1487	207.0	204.0	205.0		419	6.1	1.0	16	dbSNP_120	205	3346,5254	643.3+/-399.9	658,2030,1612	yes	missense	BFAR	NM_016561.2	91	723,2675,3099	GG,GT,TT		38.907,17.6377,31.7146	benign	140/451	14742400	4121,8873	2197	4300	6497	SO:0001583	missense	51283	exon3			AGCAGATGGGAGG	AF173003	CCDS10554.1	16p13.2	2013-01-10			ENSG00000103429	ENSG00000103429		"""RING-type (C3HC4) zinc fingers"", ""Sterile alpha motif (SAM) domain containing"""	17613	protein-coding gene	gene with protein product						10716992	Standard	NM_016561		Approved	BAR, RNF47	uc002dco.3	Q9NZS9	OTTHUMG00000129848	ENST00000261658.2:c.419T>G	16.37:g.14742400T>G	ENSP00000261658:p.Met140Arg	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	176	175	0.994318	NM_016561	A8K4Z9|B4DUT0|D3DUG8	Missense_Mutation	SNP	ENST00000261658.2	37	CCDS10554.1	592	0.27106227106227104	64	0.13008130081300814	136	0.3756906077348066	90	0.15734265734265734	302	0.39841688654353563	G	2.593	-0.294767	0.05568	0.176377	0.38907	ENSG00000103429	ENST00000261658	T	0.05855	3.38	6.08	6.08	0.98989	.	0.094567	0.64402	N	0.000001	T	0.00012	0.0000	N	0.01048	-1.04	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45877	-0.9231	9	0.02654	T	1	.	16.121	0.81357	0.0:0.0:0.8652:0.1348	rs11546303;rs52806449;rs11546303	140	Q9NZS9	BFAR_HUMAN	R	140	ENSP00000261658:M140R	ENSP00000261658:M140R	M	+	2	0	BFAR	14649901	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	3.507000	0.53371	1.599000	0.50093	-0.121000	0.15023	ATG	T|0.708;G|0.292	0.292	strong		0.507	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561	
TRPV4	59341	hgsc.bcm.edu	37	12	110222182	110222182	+	Silent	SNP	C	C	T	rs141301107		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:110222182C>T	ENST00000418703.2	-	14	2491	c.2397G>A	c.(2395-2397)ccG>ccA	p.P799P	TRPV4_ENST00000392719.2_Silent_p.P752P|TRPV4_ENST00000537083.1_Silent_p.P739P|TRPV4_ENST00000346520.2_Silent_p.P739P|TRPV4_ENST00000536838.1_Silent_p.P765P|TRPV4_ENST00000541794.1_Silent_p.P752P|TRPV4_ENST00000544971.1_Silent_p.P692P|TRPV4_ENST00000261740.2_Silent_p.P799P	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	799			P -> A (in MTD). {ECO:0000269|PubMed:20577006}.|P -> L (in MTD; also found in a patient with spondyloepiphyseal dysplasia Maroteaux type). {ECO:0000269|PubMed:19232556, ECO:0000269|PubMed:20425821, ECO:0000269|PubMed:20503319, ECO:0000269|PubMed:20577006}.|P -> R (in MTD). {ECO:0000269|PubMed:20577006}.|P -> S (in MTD). {ECO:0000269|PubMed:20577006}.		actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						CATTCTTGCCCGGGTCCTCGT	0.627																																					p.P799P		Atlas-SNP	.											TRPV4,right_lower_lobe,carcinoma,0,1	TRPV4	88	1	0			c.G2397A						scavenged	.	C	,,,,	0,4406		0,0,2203	165.0	141.0	149.0		2256,2295,2076,2397,2217	-9.6	0.1	12	dbSNP_134	149	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV4	NM_001177428.1,NM_001177431.1,NM_001177433.1,NM_021625.4,NM_147204.2	,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,	752/825,765/838,692/765,799/872,739/812	110222182	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	59341	exon15			CTTGCCCGGGTCC	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18083	protein-coding gene	gene with protein product	"""osmosensitive transient receptor potential channel 4"""	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.2397G>A	12.37:g.110222182C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	231	3	0.012987	NM_021625	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Silent	SNP	ENST00000418703.2	37	CCDS9134.1																																																																																			C|1.000;T|0.000	0.000	weak		0.627	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625	
TECPR1	25851	hgsc.bcm.edu	37	7	97873994	97873994	+	Silent	SNP	G	G	A	rs1874344	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:97873994G>A	ENST00000447648.2	-	5	719	c.420C>T	c.(418-420)taC>taT	p.Y140Y	TECPR1_ENST00000379795.3_Silent_p.Y140Y|TECPR1_ENST00000542604.1_Silent_p.Y61Y			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	140					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						AGTCGATGGCGTACGTCCACC	0.587													g|||	1513	0.302117	0.2126	0.3285	5008	,	,		18002	0.4534		0.2744	False		,,,				2504	0.2771				p.Y140Y		Atlas-SNP	.											TECPR1,NS,carcinoma,0,2	TECPR1	77	2	0			c.C420T						PASS	.	A		774,3230		69,636,1297	91.0	96.0	94.0		420	-3.8	0.4	7	dbSNP_92	94	1969,6335		244,1481,2427	no	coding-synonymous	TECPR1	NM_015395.1		313,2117,3724	AA,AG,GG		23.7115,19.3307,22.2863		140/1166	97873994	2743,9565	2002	4152	6154	SO:0001819	synonymous_variant	25851	exon5			GATGGCGTACGTC		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.420C>T	7.37:g.97873994G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	37	CCDS47648.1																																																																																			G|0.696;A|0.304	0.304	strong		0.587	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
SDHA	6389	hgsc.bcm.edu	37	5	256508	256508	+	Silent	SNP	C	C	T	rs3211499		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:256508C>T	ENST00000264932.6	+	15	2083	c.1968C>T	c.(1966-1968)acC>acT	p.T656T	SDHA_ENST00000504309.1_Silent_p.T575T|SDHA_ENST00000507522.1_3'UTR|SDHA_ENST00000510361.1_Silent_p.T608T	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	656					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	ACTGTGCCACCGTCCCGCCAG	0.438									Familial Paragangliomas																												p.T656T		Atlas-SNP	.											SDHA,NS,carcinoma,+2,1	SDHA	80	1	0			c.C1968T						scavenged	.						70.0	78.0	75.0					5																	256508		2203	4300	6503	SO:0001819	synonymous_variant	6389	exon15	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	TGCCACCGTCCCG	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"""Mitochondrial respiratory chain complex / Complex II"""	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1968C>T	5.37:g.256508C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	144	6	0.0416667	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			.	.	weak		0.438	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
HPGD	3248	hgsc.bcm.edu	37	4	175443156	175443156	+	Silent	SNP	C	C	T	rs1050145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:175443156C>T	ENST00000296522.6	-	2	602	c.156G>A	c.(154-156)caG>caA	p.Q52Q	HPGD_ENST00000541923.1_5'UTR|HPGD_ENST00000542498.1_Silent_p.Q52Q|HPGD_ENST00000422112.2_Silent_p.Q52Q|RP11-440I14.2_ENST00000515178.1_lincRNA|HPGD_ENST00000296521.7_Silent_p.Q52Q|HPGD_ENST00000504433.1_Silent_p.Q52Q|HPGD_ENST00000510901.1_5'UTR	NM_000860.5|NM_001145816.2|NM_001256301.1|NM_001256307.1	NP_000851.2|NP_001139288.1|NP_001243230.1|NP_001243236.1	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)	52					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|ductus arteriosus closure (GO:0097070)|female pregnancy (GO:0007565)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|ovulation (GO:0030728)|parturition (GO:0007567)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|thrombin receptor signaling pathway (GO:0070493)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|catalytic activity (GO:0003824)|NAD binding (GO:0051287)|NAD+ binding (GO:0070403)|prostaglandin E receptor activity (GO:0004957)|protein homodimerization activity (GO:0042803)	p.Q52Q(1)		kidney(1)|lung(3)|prostate(3)	7		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)		GAGGTTCAAACTGCTCATCCA	0.522													T|||	1699	0.339257	0.261	0.3213	5008	,	,		18302	0.4554		0.4066	False		,,,				2504	0.2689				p.Q52Q		Atlas-SNP	.											HPGD,NS,carcinoma,0,1	HPGD	19	1	1	Substitution - coding silent(1)	prostate(1)	c.G156A						PASS	.	T	,	1196,3210	710.0+/-407.8	166,864,1173	171.0	165.0	167.0		156,156	1.4	1.0	4	dbSNP_86	167	3690,4910	620.8+/-397.1	793,2104,1403	no	coding-synonymous,coding-synonymous	HPGD	NM_000860.4,NM_001145816.1	,	959,2968,2576	TT,TC,CC		42.907,27.1448,37.5673	,	52/267,52/179	175443156	4886,8120	2203	4300	6503	SO:0001819	synonymous_variant	3248	exon2			TTCAAACTGCTCA		CCDS3821.1, CCDS54821.1, CCDS58933.1, CCDS58934.1, CCDS58935.1	4q34-q35	2011-09-14			ENSG00000164120	ENSG00000164120	1.1.1.141	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	5154	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 36C, member 1"""	601688				19027726	Standard	NM_000860		Approved	SDR36C1	uc003itu.3	P15428	OTTHUMG00000160772	ENST00000296522.6:c.156G>A	4.37:g.175443156C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_000860	B4DTA4|B4DU74|B4DV57|D3DP43|E7EV11|O00749|Q06F08|Q12998	Silent	SNP	ENST00000296522.6	37	CCDS3821.1																																																																																			C|0.628;T|0.372	0.372	strong		0.522	HPGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362228.3		
ESPNL	339768	hgsc.bcm.edu	37	2	239040343	239040343	+	Silent	SNP	G	G	A	rs73102311	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:239040343G>A	ENST00000343063.3	+	9	3251	c.2988G>A	c.(2986-2988)aaG>aaA	p.K996K	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Silent_p.K628K|ESPNL_ENST00000409169.1_Silent_p.K952K	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	996										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGAAGGAGAAGGAAGCTGAGA	0.547													G|||	429	0.0856629	0.0923	0.062	5008	,	,		19468	0.0546		0.0915	False		,,,				2504	0.1196				p.K996K		Atlas-SNP	.											.	ESPNL	63	.	0			c.G2988A						PASS	.	G		379,4025	183.3+/-210.9	17,345,1840	70.0	75.0	74.0		2988	-4.2	0.9	2	dbSNP_130	74	763,7837	181.0+/-229.8	35,693,3572	no	coding-synonymous	ESPNL	NM_194312.2		52,1038,5412	AA,AG,GG		8.8721,8.6058,8.7819		996/1006	239040343	1142,11862	2202	4300	6502	SO:0001819	synonymous_variant	339768	exon9			GGAGAAGGAAGCT	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2988G>A	2.37:g.239040343G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			G|0.914;A|0.086	0.086	strong		0.547	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291308	1291308	+	Silent	SNP	A	A	G	rs201568970	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1291308A>G	ENST00000338844.3	+	3	249	c.216A>G	c.(214-216)gcA>gcG	p.A72A	TPSAB1_ENST00000461509.2_Silent_p.A79A	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	72	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				TGCTGACCGCAGCGCACTGCG	0.706																																					p.A72A		Atlas-SNP	.											TPSAB1,NS,carcinoma,+2,1	TPSAB1	24	1	0			c.A216G						scavenged	.						43.0	43.0	43.0					16																	1291308		2198	4298	6496	SO:0001819	synonymous_variant	7177	exon3			GACCGCAGCGCAC	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.216A>G	16.37:g.1291308A>G		Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	215	21	0.0976744	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Silent	SNP	ENST00000338844.3	37	CCDS10431.1																																																																																			G|1.000;|0.000	1.000	weak		0.706	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
OR2T4	127074	hgsc.bcm.edu	37	1	248525780	248525780	+	Missense_Mutation	SNP	C	C	T	rs28698997	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248525780C>T	ENST00000366475.1	+	1	898	c.898C>T	c.(898-900)Cct>Tct	p.P300S		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	300						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTACCACACCCCTGAGAAGGA	0.507													c|||	1474	0.294329	0.2405	0.2709	5008	,	,		20748	0.4276		0.1799	False		,,,				2504	0.364				p.P300S		Atlas-SNP	.											OR2T4,NS,carcinoma,-1,1	OR2T4	126	1	0			c.C898T						PASS	.	C	SER/PRO	1063,3343	386.5+/-326.1	140,783,1280	143.0	142.0	142.0		898	0.7	1.0	1	dbSNP_125	142	1400,7200	271.1+/-289.3	113,1174,3013	no	missense	OR2T4	NM_001004696.1	74	253,1957,4293	TT,TC,CC		16.2791,24.1262,18.9374	benign	300/349	248525780	2463,10543	2203	4300	6503	SO:0001583	missense	127074	exon1			CACACCCCTGAGA	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.898C>T	1.37:g.248525780C>T	ENSP00000355431:p.Pro300Ser	Somatic	749	0	0		WXS	Illumina HiSeq	Phase_I	837	412	0.492234	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	605	0.27701465201465203	136	0.2764227642276423	84	0.23204419889502761	238	0.4160839160839161	147	0.19393139841688653	C	10.26	1.299887	0.23650	0.241262	0.162791	ENSG00000196944	ENST00000366475	T	0.00183	8.6	3.0	0.732	0.18283	GPCR, rhodopsin-like superfamily (1);	0.309688	0.23494	N	0.047579	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.31790	0.34	B	0.38683	0.279	T	0.03193	-1.1062	9	0.54805	T	0.06	.	4.7106	0.12870	0.0:0.4376:0.3575:0.2049	rs28698997	300	Q8NH00	OR2T4_HUMAN	S	300	ENSP00000355431:P300S	ENSP00000355431:P300S	P	+	1	0	OR2T4	246592403	0.000000	0.05858	0.953000	0.39169	0.941000	0.58515	-0.266000	0.08631	0.407000	0.25591	0.585000	0.79938	CCT	.	.	weak		0.507	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
PIGN	23556	hgsc.bcm.edu	37	18	59780424	59780424	+	Silent	SNP	A	A	G	rs17714875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:59780424A>G	ENST00000357637.5	-	16	1792	c.1377T>C	c.(1375-1377)tcT>tcC	p.S459S	PIGN_ENST00000400334.3_Silent_p.S459S	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	459					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				TGATCAACAAAGAGGCATAAG	0.348													A|||	468	0.0934505	0.0061	0.1239	5008	,	,		16939	0.0069		0.2694	False		,,,				2504	0.0982				p.S459S		Atlas-SNP	.											.	PIGN	62	.	0			c.T1377C						PASS	.	A	,	194,3520		5,184,1668	115.0	104.0	108.0		1377,1377	2.7	1.0	18	dbSNP_123	108	2043,6155		245,1553,2301	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	250,1737,3969	GG,GA,AA		24.9207,5.2235,18.7794	,	459/932,459/932	59780424	2237,9675	1857	4099	5956	SO:0001819	synonymous_variant	23556	exon16			CAACAAAGAGGCA	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.1377T>C	18.37:g.59780424A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			A|0.877;G|0.123	0.123	strong		0.348	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
NRAP	4892	hgsc.bcm.edu	37	10	115381747	115381747	+	Missense_Mutation	SNP	G	G	A	rs868738	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:115381747G>A	ENST00000359988.3	-	24	2894	c.2650C>T	c.(2650-2652)Cgc>Tgc	p.R884C	NRAP_ENST00000369360.3_Missense_Mutation_p.R857C|NRAP_ENST00000369358.4_Missense_Mutation_p.R892C|NRAP_ENST00000360478.3_Missense_Mutation_p.R849C	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.R884C(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TGAGCTTTGCGGGCATGCACG	0.537													G|||	1049	0.209465	0.0446	0.4409	5008	,	,		23149	0.1786		0.3211	False		,,,				2504	0.1851				p.R884C		Atlas-SNP	.											NRAP,colon,carcinoma,0,2	NRAP	208	2	1	Substitution - Missense(1)	stomach(1)	c.C2650T						PASS	.	G	CYS/ARG,CYS/ARG	455,3951	215.5+/-234.4	24,407,1772	265.0	199.0	221.0		2545,2650	5.1	1.0	10	dbSNP_86	221	2904,5696	455.2+/-363.7	500,1904,1896	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	180,180	524,2311,3668	AA,AG,GG		33.7674,10.3268,25.8265	probably-damaging,probably-damaging	849/1696,884/1731	115381747	3359,9647	2203	4300	6503	SO:0001583	missense	4892	exon24			CTTTGCGGGCATG		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.2650C>T	10.37:g.115381747G>A	ENSP00000353078:p.Arg884Cys	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	269	135	0.501859	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	519	0.23763736263736263	30	0.06097560975609756	144	0.39779005524861877	98	0.17132867132867133	247	0.3258575197889182	G	21.7	4.187415	0.78789	0.103268	0.337674	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.38240	1.15;1.15;1.15;1.15	5.99	5.08	0.68730	.	0.176401	0.50627	D	0.000110	T	0.00012	0.0000	L	0.27053	0.805	0.21740	P	0.99956126	D;D;D	0.59767	0.975;0.985;0.986	P;P;P	0.54815	0.582;0.761;0.582	T	0.44267	-0.9339	9	0.72032	D	0.01	.	8.3557	0.32329	0.0765:0.0:0.6729:0.2506	rs868738;rs17772691;rs52791341;rs59077407;rs868738	884;849;884	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	C	892;857;884;849	ENSP00000358365:R892C;ENSP00000358367:R857C;ENSP00000353078:R884C;ENSP00000353666:R849C	ENSP00000353078:R884C	R	-	1	0	NRAP	115371737	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	4.833000	0.62766	1.529000	0.49120	0.655000	0.94253	CGC	G|0.758;N|0.000	.	strong		0.537	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43891639	43891639	+	Silent	SNP	G	G	A	rs200586830	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:43891639G>A	ENST00000377564.3	+	17	3075	c.2682G>A	c.(2680-2682)caG>caA	p.Q894Q		NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	894	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						AAGTTGATCAGCTTCCTCAGA	0.507													G|||	1197	0.239018	0.0885	0.3703	5008	,	,		15500	0.1508		0.338	False		,,,				2504	0.3384				p.Q894Q		Atlas-SNP	.											CNTNAP3B,NS,carcinoma,0,1	CNTNAP3B	37	1	0			c.G2682A						scavenged	.																																			SO:0001819	synonymous_variant	728577	exon17			TGATCAGCTTCCT	BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.2682G>A	9.37:g.43891639G>A		Somatic	585	0	0		WXS	Illumina HiSeq	Phase_I	868	149	0.171659	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Silent	SNP	ENST00000377564.3	37	CCDS55312.1	.	.	.	.	.	.	.	.	.	.	G	3.543	-0.093219	0.07053	.	.	ENSG00000154529	ENST00000377561	.	.	.	2.67	0.632	0.17705	.	.	.	.	.	T	0.39572	0.1083	.	.	.	0.09310	P	0.999999999870063	.	.	.	.	.	.	T	0.45977	-0.9224	3	.	.	.	.	6.8519	0.24020	0.3621:0.0:0.6379:0.0	.	.	.	.	N	943	.	.	S	+	2	0	CNTNAP3B	43831635	0.966000	0.33281	0.086000	0.20670	0.722000	0.41435	1.539000	0.36104	0.030000	0.15379	0.121000	0.15741	AGC	.	.	weak		0.507	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
CRYBA1	1411	hgsc.bcm.edu	37	17	27580756	27580756	+	Silent	SNP	C	C	T	rs1047790	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:27580756C>T	ENST00000225387.3	+	5	457	c.456C>T	c.(454-456)ggC>ggT	p.G152G		NM_005208.4	NP_005199.2	P05813	CRBA1_HUMAN	crystallin, beta A1	152	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|large_intestine(2)|lung(1)|prostate(1)	5			BRCA - Breast invasive adenocarcinoma(11;3.3e-05)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			AAGCCATGGGCTGGTTCAACA	0.453													T|||	1456	0.290735	0.3578	0.1916	5008	,	,		17909	0.3244		0.173	False		,,,				2504	0.3569				p.G152G		Atlas-SNP	.											.	CRYBA1	15	.	0			c.C456T						PASS	.	T		1462,2944	680.2+/-403.8	236,990,977	83.0	82.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	456	-4.9	0.8	17	dbSNP_86	82	1403,7197	753.3+/-407.4	104,1195,3001	no	coding-synonymous	CRYBA1	NM_005208.4		340,2185,3978	TT,TC,CC		16.314,33.182,22.0283		152/216	27580756	2865,10141	2203	4300	6503	SO:0001819	synonymous_variant	1411	exon5			CATGGGCTGGTTC		CCDS11249.1	17q11.2-q12	2008-07-18			ENSG00000108255	ENSG00000108255			2394	protein-coding gene	gene with protein product	"""eye lens structural protein"""	123610		CRYB1		3745196, 3770741	Standard	NM_005208		Approved		uc002hdw.3	P05813	OTTHUMG00000132729	ENST00000225387.3:c.456C>T	17.37:g.27580756C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_005208	Q13633|Q14CM9	Silent	SNP	ENST00000225387.3	37	CCDS11249.1																																																																																			C|0.756;T|0.244	0.244	strong		0.453	CRYBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256071.2	NM_005208	
PALM	5064	hgsc.bcm.edu	37	19	746712	746712	+	Silent	SNP	C	C	T	rs10421265	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:746712C>T	ENST00000338448.5	+	9	1108	c.1062C>T	c.(1060-1062)gcC>gcT	p.A354A	PALM_ENST00000264560.7_Silent_p.A310A|PALM_ENST00000593172.1_3'UTR	NM_002579.2	NP_002570.2	O75781	PALM_HUMAN	paralemmin	354					cellular component movement (GO:0006928)|cellular response to electrical stimulus (GO:0071257)|cytoskeleton organization (GO:0007010)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of filopodium assembly (GO:0051491)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)|synapse maturation (GO:0060074)	apicolateral plasma membrane (GO:0016327)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasmic membrane-bounded vesicle (GO:0016023)|dendrite membrane (GO:0032590)|dendritic spine membrane (GO:0032591)|filopodium membrane (GO:0031527)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)		CCACGGAGGCCGCCTCCAGGG	0.637													C|||	1000	0.199681	0.2958	0.2392	5008	,	,		11057	0.0655		0.2227	False		,,,				2504	0.1564				p.A354A		Atlas-SNP	.											.	PALM	26	.	0			c.C1062T						PASS	.	C	,	1213,3171		182,849,1161	13.0	15.0	14.0		930,1062	-2.5	0.0	19	dbSNP_119	14	1938,6646		230,1478,2584	no	coding-synonymous,coding-synonymous	PALM	NM_001040134.1,NM_002579.2	,	412,2327,3745	TT,TC,CC		22.5769,27.6688,24.2983	,	310/344,354/388	746712	3151,9817	2192	4292	6484	SO:0001819	synonymous_variant	5064	exon9			GGAGGCCGCCTCC	Y16270	CCDS32857.1, CCDS32858.1	19p13.3	2008-07-17				ENSG00000099864			8594	protein-coding gene	gene with protein product		608134				9615234, 9813098	Standard	XM_005259565		Approved	KIAA0270	uc002lpm.1	O75781		ENST00000338448.5:c.1062C>T	19.37:g.746712C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_002579	O43359|O95673|Q92559|Q9UPJ4|Q9UQS2|Q9UQS3	Silent	SNP	ENST00000338448.5	37	CCDS32857.1																																																																																			C|0.778;T|0.222	0.222	strong		0.637	PALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457592.1	NM_002579	
MMRN2	79812	hgsc.bcm.edu	37	10	88702390	88702390	+	Silent	SNP	G	G	A	rs10887673	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:88702390G>A	ENST00000372027.5	-	6	2472	c.2151C>T	c.(2149-2151)gcC>gcT	p.A717A	MMRN2_ENST00000488950.1_5'Flank	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	717					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						CCCCGGCCTCGGCCTCGCAGC	0.731													G|||	1013	0.202276	0.1142	0.2248	5008	,	,		10659	0.0645		0.3002	False		,,,				2504	0.3466				p.A717A		Atlas-SNP	.											.	MMRN2	49	.	0			c.C2151T						PASS	.	G		638,3764		58,522,1621	18.0	17.0	17.0		2151	2.0	0.2	10	dbSNP_120	17	2588,6006		384,1820,2093	no	coding-synonymous	MMRN2	NM_024756.2		442,2342,3714	AA,AG,GG		30.114,14.4934,24.823		717/950	88702390	3226,9770	2201	4297	6498	SO:0001819	synonymous_variant	79812	exon6			GGCCTCGGCCTCG	AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"""EMI domain containing"""	19888	protein-coding gene	gene with protein product		608925	"""elastin microfibril interfacer 3"""	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.2151C>T	10.37:g.88702390G>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	8	7	0.875	NM_024756	Q504V7|Q6P2N2	Silent	SNP	ENST00000372027.5	37	CCDS7379.1																																																																																			A|0.213;C|0.000;G|0.787	0.213	strong		0.731	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756	
GLRA4	441509	hgsc.bcm.edu	37	X	102978806	102978806	+	Silent	SNP	G	G	C	rs5945807	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:102978806G>C	ENST00000372617.4	-	5	975	c.555C>G	c.(553-555)acC>acG	p.T185T	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	185						cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			cervix(1)|endometrium(2)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GCATCGTGCAGGTCTGGATGT	0.493													G|||	602	0.15947	0.0287	0.1412	3775	,	,		15940	0.0079		0.2594	False		,,,				2504	0.2014				p.T185T		Atlas-SNP	.											.	GLRA4	86	.	0			c.C555G						PASS	.	G	,	255,3201		12,191,40,1240,530	114.0	104.0	107.0		555,555	-2.6	1.0	X	dbSNP_114	107	2449,4069		338,1067,706,952,1098	no	coding-synonymous,coding-synonymous	GLRA4	NM_001024452.2,NM_001172285.1	,	350,1258,746,2192,1628	CC,CG,C,GG,G		37.5729,7.3785,27.1105	,	185/418,185/343	102978806	2704,7270	2013	4161	6174	SO:0001819	synonymous_variant	441509	exon5			CGTGCAGGTCTGG	Z93848	CCDS43980.2	Xq22.2	2012-01-16			ENSG00000188828	ENSG00000188828		"""Ligand-gated ion channels / Glycine receptors"""	31715	protein-coding gene	gene with protein product							Standard	NM_001024452		Approved		uc011mse.2	Q5JXX5	OTTHUMG00000022110	ENST00000372617.4:c.555C>G	X.37:g.102978806G>C		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	394	25	0.0634518	NM_001024452		Silent	SNP	ENST00000372617.4	37	CCDS43980.2																																																																																			0|0.009;C|0.169	0.169	strong		0.493	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452	
OR8K5	219453	hgsc.bcm.edu	37	11	55927442	55927442	+	Missense_Mutation	SNP	T	T	C	rs61746523	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55927442T>C	ENST00000313447.1	-	1	351	c.352A>G	c.(352-354)Atg>Gtg	p.M118V		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				TCATAGGCCATGGCTGACAGG	0.408													T|||	198	0.0395367	0.0121	0.0447	5008	,	,		21193	0.001		0.0944	False		,,,				2504	0.0562				p.M118V		Atlas-SNP	.											.	OR8K5	82	.	0			c.A352G						PASS	.	T	VAL/MET	99,4303	78.3+/-116.7	0,99,2102	85.0	85.0	85.0		352	2.7	1.0	11	dbSNP_129	85	691,7899	171.0+/-222.0	34,623,3638	yes	missense	OR8K5	NM_001004058.2	21	34,722,5740	CC,CT,TT		8.0442,2.249,6.0807	probably-damaging	118/308	55927442	790,12202	2201	4295	6496	SO:0001583	missense	219453	exon1			AGGCCATGGCTGA	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"""GPCR / Class A : Olfactory receptors"""	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.352A>G	11.37:g.55927442T>C	ENSP00000323853:p.Met118Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_001004058	Q6IFB5	Missense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	87	0.03983516483516483	4	0.008130081300813009	14	0.03867403314917127	0	0.0	69	0.09102902374670185	T	14.03	2.412614	0.42817	0.02249	0.080442	ENSG00000181752	ENST00000313447	T	0.00995	5.46	3.88	2.74	0.32292	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.00271	0.0008	M	0.93550	3.43	0.31567	N	0.656836	D	0.64830	0.994	D	0.72338	0.977	T	0.00981	-1.1492	10	0.87932	D	0	.	8.6825	0.34218	0.0:0.0962:0.0:0.9038	.	118	Q8NH50	OR8K5_HUMAN	V	118	ENSP00000323853:M118V	ENSP00000323853:M118V	M	-	1	0	OR8K5	55684018	1.000000	0.71417	0.974000	0.42286	0.372000	0.29890	5.264000	0.65513	0.659000	0.30945	0.462000	0.41574	ATG	T|0.948;C|0.052	0.052	strong		0.408	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058	
ZFHX3	463	hgsc.bcm.edu	37	16	72992626	72992626	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992626C>T	ENST00000268489.5	-	2	2091	c.1419G>A	c.(1417-1419)gaG>gaA	p.E473E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	473	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cctcctcctcctccgcctctt	0.577																																					p.E473E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G1419A						PASS	.						41.0	44.0	43.0					16																	72992626		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCCTCCTCCGCC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1419G>A	16.37:g.72992626C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	57	9	0.157895	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	none		0.577	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
FBXW10	10517	hgsc.bcm.edu	37	17	18653070	18653070	+	Missense_Mutation	SNP	G	G	A	rs9895749	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18653070G>A	ENST00000395665.4	+	3	927	c.706G>A	c.(706-708)Gaa>Aaa	p.E236K	FBXW10_ENST00000308799.4_Missense_Mutation_p.E236K|FBXW10_ENST00000301938.4_Missense_Mutation_p.E236K|FBXW10_ENST00000395667.1_Missense_Mutation_p.E236K			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	236				E -> K (in Ref. 2; CAB66756). {ECO:0000305}.						NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GTGTATATCCGAAATGAATAG	0.473																																					p.E236K		Atlas-SNP	.											.	FBXW10	82	.	0			c.G706A						PASS	.	G	LYS/GLU	1325,3081		44,1237,922	144.0	118.0	127.0		706	1.5	0.1	17	dbSNP_119	127	3457,5143		498,2461,1341	no	missense	FBXW10	NM_031456.3	56	542,3698,2263	AA,AG,GG		40.1977,30.0726,36.7676	probably-damaging	236/1052	18653070	4782,8224	2203	4300	6503	SO:0001583	missense	10517	exon3			ATATCCGAAATGA	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.706G>A	17.37:g.18653070G>A	ENSP00000379025:p.Glu236Lys	Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	433	282	0.65127	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	768	0.3516483516483517	151	0.30691056910569103	136	0.3756906077348066	155	0.270979020979021	326	0.43007915567282323	G	13.41	2.228790	0.39399	0.300726	0.401977	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	2.49	1.48	0.22813	.	0.437341	0.16220	N	0.224080	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B;B;B;B	0.27416	0.178;0.178;0.111;0.108	B;B;B;B	0.23018	0.043;0.043;0.019;0.024	T	0.40346	-0.9568	9	0.62326	D	0.03	.	5.1562	0.15036	0.1795:0.0:0.8205:0.0	rs9895749	236;236;236;236	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	K	236	ENSP00000379026:E236K;ENSP00000310382:E236K;ENSP00000306937:E236K;ENSP00000379025:E236K	ENSP00000306937:E236K	E	+	1	0	FBXW10	18593795	0.661000	0.27430	0.129000	0.21949	0.040000	0.13550	0.490000	0.22403	0.368000	0.24481	0.405000	0.27470	GAA	G|0.630;A|0.370	0.370	strong		0.473	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
DOPEY2	9980	hgsc.bcm.edu	37	21	37609571	37609571	+	Silent	SNP	T	T	C	rs2835322	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:37609571T>C	ENST00000399151.3	+	16	2719	c.2634T>C	c.(2632-2634)cgT>cgC	p.R878R		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	878					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GGGTGGCTCGTGTGCTTTGGA	0.592													T|||	2203	0.439896	0.2882	0.5072	5008	,	,		18081	0.4276		0.5447	False		,,,				2504	0.502				p.R878R		Atlas-SNP	.											DOPEY2,right_upper_lobe,carcinoma,+1,1	DOPEY2	184	1	0			c.T2634C						PASS	.	T		1585,2821	495.8+/-363.4	271,1043,889	94.0	80.0	85.0		2634	-4.1	1.0	21	dbSNP_100	85	4583,4017	596.7+/-393.6	1253,2077,970	no	coding-synonymous	DOPEY2	NM_005128.2		1524,3120,1859	CC,CT,TT		46.7093,35.9737,47.4243		878/2299	37609571	6168,6838	2203	4300	6503	SO:0001819	synonymous_variant	9980	exon16			GGCTCGTGTGCTT	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.2634T>C	21.37:g.37609571T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	37	CCDS13643.1																																																																																			C|0.464;N|0.001	0.464	strong		0.592	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
C3orf58	205428	hgsc.bcm.edu	37	3	143708645	143708645	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:143708645C>A	ENST00000315691.3	+	3	1790	c.1255C>A	c.(1255-1257)Cgt>Agt	p.R419S	C3orf58_ENST00000493396.1_Intron|C3orf58_ENST00000495414.1_Missense_Mutation_p.R210S|C3orf58_ENST00000441925.2_Missense_Mutation_p.R181S	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	419					cardiac muscle cell proliferation (GO:0060038)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	COPI vesicle coat (GO:0030126)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AAAAGAACTGCGTGAATACCT	0.448																																					p.R419S		Atlas-SNP	.											.	C3orf58	36	.	0			c.C1255A						PASS	.						69.0	73.0	72.0					3																	143708645		2203	4300	6503	SO:0001583	missense	205428	exon3			GAACTGCGTGAAT	AK095161	CCDS3130.1, CCDS46929.1	3q24	2013-12-06			ENSG00000181744	ENSG00000181744			28490	protein-coding gene	gene with protein product	"""deleted in autism 1"", ""hypoxia and Akt induced stem cell factor"""	612200				21283809, 23784961, 24269490	Standard	NM_173552		Approved	MGC33365, DIA1, HASF	uc003evo.3	Q8NDZ4	OTTHUMG00000159380	ENST00000315691.3:c.1255C>A	3.37:g.143708645C>A	ENSP00000320081:p.Arg419Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	90	48	0.533333	NM_173552	B2RCF2|B7Z1W3	Missense_Mutation	SNP	ENST00000315691.3	37	CCDS3130.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387226	0.61956	.	.	ENSG00000181744	ENST00000315691;ENST00000495414;ENST00000441925	T	0.32272	1.46	6.17	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.46718	0.1407	L	0.45581	1.43	0.58432	D	0.999997	B;D	0.63046	0.168;0.992	B;D	0.72982	0.077;0.979	T	0.22730	-1.0208	10	0.21540	T	0.41	.	15.7877	0.78319	0.2489:0.7511:0.0:0.0	.	210;419	B7Z1W3;Q8NDZ4	.;CC058_HUMAN	S	419;210;181	ENSP00000320081:R419S	ENSP00000320081:R419S	R	+	1	0	C3orf58	145191335	1.000000	0.71417	0.991000	0.47740	0.998000	0.95712	4.658000	0.61497	0.900000	0.36469	0.655000	0.94253	CGT	.	.	none		0.448	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552	
VNN1	8876	hgsc.bcm.edu	37	6	133015271	133015271	+	Missense_Mutation	SNP	T	T	C	rs2272996	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:133015271T>C	ENST00000367928.4	-	3	405	c.392A>G	c.(391-393)aAc>aGc	p.N131S		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	131	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		N -> S (in dbSNP:rs2272996). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		ATAGATAGAGTTGTTCTTGGC	0.433													T|||	1332	0.265974	0.1725	0.1916	5008	,	,		17060	0.3621		0.2972	False		,,,				2504	0.3139				p.N131S		Atlas-SNP	.											.	VNN1	69	.	0			c.A392G						PASS	.	T	SER/ASN	840,3566	331.8+/-302.1	84,672,1447	141.0	128.0	132.0		392	6.1	0.4	6	dbSNP_100	132	2320,6280	388.5+/-342.6	309,1702,2289	yes	missense	VNN1	NM_004666.2	46	393,2374,3736	CC,CT,TT		26.9767,19.0649,24.2965	probably-damaging	131/514	133015271	3160,9846	2203	4300	6503	SO:0001583	missense	8876	exon3			ATAGAGTTGTTCT	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.392A>G	6.37:g.133015271T>C	ENSP00000356905:p.Asn131Ser	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	209	91	0.435407	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	597	0.2733516483516483	91	0.18495934959349594	62	0.1712707182320442	216	0.3776223776223776	228	0.3007915567282322	T	19.74	3.883832	0.72410	0.190649	0.269767	ENSG00000112299	ENST00000367928	D	0.85861	-2.04	6.07	6.07	0.98685	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.064498	0.64402	D	0.000007	D	0.89646	0.6775	M	0.68728	2.09	0.26675	P	0.9716475	D	0.67145	0.996	D	0.72075	0.976	D	0.89228	0.3575	9	0.44086	T	0.13	-24.5999	16.6277	0.84984	0.0:0.0:0.0:1.0	rs2272996;rs60821439;rs2272996	131	O95497	VNN1_HUMAN	S	131	ENSP00000356905:N131S	ENSP00000356905:N131S	N	-	2	0	VNN1	133056964	1.000000	0.71417	0.443000	0.26883	0.833000	0.47200	3.909000	0.56363	2.330000	0.79161	0.528000	0.53228	AAC	T|0.736;C|0.264	0.264	strong		0.433	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
HK2	3099	hgsc.bcm.edu	37	2	75099477	75099477	+	Missense_Mutation	SNP	A	A	T	rs2229621	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:75099477A>T	ENST00000290573.2	+	4	1026	c.426A>T	c.(424-426)caA>caT	p.Q142H	HK2_ENST00000409174.1_Missense_Mutation_p.Q114H	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	142	Hexokinase type-1 1.|Regulatory.		Q -> H (does not affect activity; dbSNP:rs2229621). {ECO:0000269|PubMed:7883122, ECO:0000269|PubMed:7883123, ECO:0000269|PubMed:8786021, ECO:0000269|Ref.4}.		apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						ATAAGCTACAAATCAAAGACA	0.483													A|||	899	0.179513	0.2148	0.1657	5008	,	,		20281	0.1587		0.1769	False		,,,				2504	0.1656				p.Q142H		Atlas-SNP	.											.	HK2	85	.	0			c.A426T						PASS	.	A	HIS/GLN	891,3515	345.9+/-308.8	88,715,1400	149.0	139.0	143.0		426	-8.1	0.7	2	dbSNP_98	143	1590,7010	296.5+/-302.9	147,1296,2857	yes	missense	HK2	NM_000189.4	24	235,2011,4257	TT,TA,AA		18.4884,20.2224,19.0758	benign	142/918	75099477	2481,10525	2203	4300	6503	SO:0001583	missense	3099	exon4			GCTACAAATCAAA		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.426A>T	2.37:g.75099477A>T	ENSP00000290573:p.Gln142His	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	355	226	0.63662	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	37	CCDS1956.1	412	0.18864468864468864	109	0.22154471544715448	64	0.17679558011049723	108	0.1888111888111888	131	0.17282321899736147	A	11.85	1.760905	0.31137	0.202224	0.184884	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	T;T	0.53423	0.62;0.62	5.35	-8.09	0.01090	Hexokinase, N-terminal (1);	0.215706	0.49916	D	0.000128	T	0.00012	0.0000	N	0.04880	-0.145	0.44337	P	0.0027730000000000254	P	0.39535	0.677	B	0.37451	0.25	T	0.23368	-1.0190	9	0.30078	T	0.28	-8.0647	10.9078	0.47090	0.1794:0.3176:0.503:0.0	rs2229621;rs3732299;rs17847155;rs3732299	142	P52789	HXK2_HUMAN	H	142;142;114	ENSP00000290573:Q142H;ENSP00000387140:Q114H	ENSP00000290573:Q142H	Q	+	3	2	HK2	74952985	0.000000	0.05858	0.727000	0.30756	0.825000	0.46686	-1.973000	0.01500	-1.419000	0.02012	-1.220000	0.01600	CAA	A|0.784;0|0.001	.	strong		0.483	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
WDR90	197335	hgsc.bcm.edu	37	16	715990	715990	+	Missense_Mutation	SNP	G	G	A	rs7190775	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:715990G>A	ENST00000293879.4	+	36	4475	c.4475G>A	c.(4474-4476)cGc>cAc	p.R1492H	RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000547944.1_Missense_Mutation_p.R91H|WDR90_ENST00000549091.1_Missense_Mutation_p.R1494H|WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000315764.4_Missense_Mutation_p.R91H			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1492			R -> H (in dbSNP:rs7190775).							endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				TGCTGTGGCCGCCCTGAGCAG	0.682													G|||	3511	0.701078	0.8865	0.5965	5008	,	,		13104	0.9841		0.3738	False		,,,				2504	0.5695				p.R1492H		Atlas-SNP	.											.	WDR90	107	.	0			c.G4475A						PASS	.	G	HIS/ARG	3019,1047		1139,741,153	27.0	32.0	31.0		4475	-4.8	0.0	16	dbSNP_116	31	2845,5425		542,1761,1832	no	missense	WDR90	NM_145294.4	29	1681,2502,1985	AA,AG,GG		34.4015,25.7501,47.5357	possibly-damaging	1492/1749	715990	5864,6472	2033	4135	6168	SO:0001583	missense	197335	exon36			GTGGCCGCCCTGA	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.4475G>A	16.37:g.715990G>A	ENSP00000293879:p.Arg1492His	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	48	47	0.979167	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	1460	0.6684981684981685	417	0.8475609756097561	198	0.5469613259668509	562	0.9825174825174825	283	0.3733509234828496	G	6.778	0.512413	0.12944	0.742499	0.344015	ENSG00000161996	ENST00000549091;ENST00000293879;ENST00000547944;ENST00000315764	T;T;T;T	0.32515	1.66;1.45;3.66;4.04	4.45	-4.83	0.03161	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.961470	0.02062	N	0.050883	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B;B;B;B	0.27140	0.051;0.042;0.025;0.169	B;B;B;B	0.19391	0.019;0.01;0.007;0.025	T	0.41413	-0.9510	9	0.40728	T	0.16	.	1.9117	0.03288	0.3742:0.119:0.3787:0.1281	rs7190775;rs60747281	91;91;91;1492	Q96KV7-10;Q96KV7-7;G3V201;Q96KV7	.;.;.;WDR90_HUMAN	H	1494;1492;91;91	ENSP00000448122:R1494H;ENSP00000293879:R1492H;ENSP00000449576:R91H;ENSP00000322808:R91H	ENSP00000293879:R1492H	R	+	2	0	WDR90	655991	0.000000	0.05858	0.000000	0.03702	0.150000	0.21749	-1.108000	0.03313	-1.499000	0.01821	-0.218000	0.12543	CGC	G|0.423;A|0.577	0.577	strong		0.682	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
UBA6	55236	hgsc.bcm.edu	37	4	68534392	68534392	+	Splice_Site	SNP	C	C	T	rs10010188	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:68534392C>T	ENST00000322244.5	-	9	729	c.670G>A	c.(670-672)Gca>Aca	p.A224T	UBA6_ENST00000420827.2_Splice_Site_p.A224T	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	224			A -> T (in dbSNP:rs10010188). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17597759, ECO:0000269|PubMed:17974005}.		protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						CCAGGATTTGCCTAAAAATAA	0.299													C|||	776	0.154952	0.1536	0.1167	5008	,	,		17296	0.1052		0.165	False		,,,				2504	0.2249				p.A224T		Atlas-SNP	.											UBA6,colon,carcinoma,+1,1	UBA6	98	1	0			c.G670A						PASS	.	C	THR/ALA	736,3670	296.7+/-284.4	70,596,1537	80.0	77.0	78.0		670	4.7	1.0	4	dbSNP_119	78	1203,7395	240.4+/-271.1	79,1045,3175	yes	missense-near-splice	UBA6	NM_018227.5	58	149,1641,4712	TT,TC,CC		13.9916,16.7045,14.9108	benign	224/1053	68534392	1939,11065	2203	4299	6502	SO:0001630	splice_region_variant	55236	exon9			GATTTGCCTAAAA	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"""Ubiquitin-like modifier activating enzymes"""	25581	protein-coding gene	gene with protein product	"""UBA6, ubiquitin-activating enzyme E1"""	611361	"""ubiquitin-activating enzyme E1-like 2"""	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.670-1G>A	4.37:g.68534392C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Missense_Mutation	SNP	ENST00000322244.5	37	CCDS3516.1	341	0.15613553113553114	83	0.16869918699186992	49	0.13535911602209943	76	0.13286713286713286	133	0.17546174142480211	C	14.72	2.619904	0.46736	0.167045	0.139916	ENSG00000033178	ENST00000322244;ENST00000420827	T;T	0.29397	1.57;1.57	5.54	4.69	0.59074	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.408988	0.27298	N	0.020013	T	0.00073	0.0002	L	0.46614	1.455	0.29936	P	0.821452	P;P;P	0.40602	0.723;0.723;0.536	B;B;B	0.37144	0.242;0.16;0.079	T	0.09487	-1.0672	9	0.54805	T	0.06	-9.4738	12.6904	0.56972	0.443:0.557:0.0:0.0	rs10010188;rs17571482;rs61257058;rs10010188	224;224;224	A0AVT1-4;A0AVT1-3;A0AVT1	.;.;UBA6_HUMAN	T	224	ENSP00000313454:A224T;ENSP00000399234:A224T	ENSP00000313454:A224T	A	-	1	0	UBA6	68216987	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	2.201000	0.42734	1.328000	0.45358	0.655000	0.94253	GCA	C|0.849;T|0.151	0.151	strong		0.299	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	Missense_Mutation
ARL5C	390790	hgsc.bcm.edu	37	17	37319029	37319029	+	Missense_Mutation	SNP	T	T	G	rs544198	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:37319029T>G	ENST00000269586.7	-	3	189	c.190A>C	c.(190-192)Atg>Ctg	p.M64L	ARL5C_ENST00000444555.1_Missense_Mutation_p.M64L|ARL5C_ENST00000583123.1_5'Flank	NM_001143968.1	NP_001137440.1	A6NH57	ARL5C_HUMAN	ADP-ribosylation factor-like 5C	64					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)										ATGTCCCACATGAAGAAGTGG	0.542													T|||	1178	0.235224	0.3154	0.1801	5008	,	,		19789	0.256		0.2386	False		,,,				2504	0.1411				p.M64L		Atlas-SNP	.											.	ARL5C	3	.	0			c.A190C						PASS	.	T	LEU/MET	436,948		68,300,324	114.0	89.0	97.0		190	0.9	1.0	17	dbSNP_83	97	609,2573		54,501,1036	yes	missense	ARL5C	NM_001143968.1	15	122,801,1360	GG,GT,TT		19.1389,31.5029,22.8866	possibly-damaging	64/180	37319029	1045,3521	692	1591	2283	SO:0001583	missense	390790	exon3			CCCACATGAAGAA		CCDS45664.1	17q12	2014-05-09	2005-11-08	2005-11-08	ENSG00000141748	ENSG00000141748		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	31111	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 12"""	ARL12			Standard	NM_001143968		Approved		uc010wea.2	A6NH57		ENST00000269586.7:c.190A>C	17.37:g.37319029T>G	ENSP00000269586:p.Met64Leu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	159	80	0.503145	NM_001143968		Missense_Mutation	SNP	ENST00000269586.7	37	CCDS45664.1	547	0.25045787545787546	160	0.3252032520325203	74	0.20441988950276244	137	0.2395104895104895	176	0.23218997361477572	T	12.05	1.820876	0.32237	0.315029	0.191389	ENSG00000141748	ENST00000444555;ENST00000269586	T;T	0.79940	-1.32;-1.32	4.28	0.877	0.19145	Small GTP-binding protein domain (1);	0.186935	0.45361	D	0.000368	T	0.00012	0.0000	L	0.29908	0.895	0.29742	P	0.837041	B	0.23990	0.095	B	0.37650	0.255	T	0.19063	-1.0317	9	0.87932	D	0	-24.2929	7.0499	0.25067	0.0:0.2888:0.0:0.7112	rs544198;rs52817936;rs59543438;rs544198	64	A6NH57	ARL5C_HUMAN	L	64	ENSP00000387615:M64L;ENSP00000269586:M64L	ENSP00000269586:M64L	M	-	1	0	ARL5C	34572555	0.336000	0.24757	0.999000	0.59377	0.013000	0.08279	0.606000	0.24194	0.022000	0.15160	-0.250000	0.11733	ATG	T|0.752;G|0.248	0.248	strong		0.542	ARL5C-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444566.1	NM_001143968	
TMEM144	55314	hgsc.bcm.edu	37	4	159161483	159161483	+	Missense_Mutation	SNP	A	A	T	rs62335898	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:159161483A>T	ENST00000296529.6	+	10	1235	c.715A>T	c.(715-717)Atc>Ttc	p.I239F	TMEM144_ENST00000503404.1_3'UTR	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	239						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		CTTCAGTGGCATCTTTCTTAC	0.343													A|||	11	0.00219649	0.0	0.0	5008	,	,		19029	0.0		0.0109	False		,,,				2504	0.0				p.I239F		Atlas-SNP	.											.	TMEM144	34	.	0			c.A715T						PASS	.	A	PHE/ILE	9,4397	15.5+/-35.6	0,9,2194	132.0	118.0	122.0		715	5.3	1.0	4	dbSNP_129	122	81,8519	47.6+/-106.9	0,81,4219	yes	missense	TMEM144	NM_018342.4	21	0,90,6413	TT,TA,AA		0.9419,0.2043,0.692	probably-damaging	239/346	159161483	90,12916	2203	4300	6503	SO:0001583	missense	55314	exon10			AGTGGCATCTTTC	AK002017	CCDS3799.1	4q32.1	2008-02-05			ENSG00000164124	ENSG00000164124			25633	protein-coding gene	gene with protein product						12477932	Standard	NM_018342		Approved	FLJ11155	uc003ipx.3	Q7Z5S9	OTTHUMG00000162013	ENST00000296529.6:c.715A>T	4.37:g.159161483A>T	ENSP00000296529:p.Ile239Phe	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	169	79	0.467456	NM_018342	D3DP24|Q49A05|Q9NUT3	Missense_Mutation	SNP	ENST00000296529.6	37	CCDS3799.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	A	23.0	4.361799	0.82353	0.002043	0.009419	ENSG00000164124	ENST00000296529	T	0.53640	0.61	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.66386	0.2784	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.75988	-0.3123	10	0.56958	D	0.05	-63.7644	14.3292	0.66541	1.0:0.0:0.0:0.0	rs62335898	239	Q7Z5S9	TM144_HUMAN	F	239	ENSP00000296529:I239F	ENSP00000296529:I239F	I	+	1	0	TMEM144	159380933	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	7.272000	0.78516	2.027000	0.59764	0.383000	0.25322	ATC	A|0.994;T|0.006	0.006	strong		0.343	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342	
MED9	55090	hgsc.bcm.edu	37	17	17394611	17394611	+	Silent	SNP	G	G	A	rs1242489	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17394611G>A	ENST00000268711.3	+	2	299	c.243G>A	c.(241-243)ccG>ccA	p.P81P		NM_018019.2	NP_060489.1	Q9NWA0	MED9_HUMAN	mediator complex subunit 9	81						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			cervix(1)|endometrium(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						AGGACAGCCCGGAGGTCCACC	0.597													G|||	801	0.159944	0.025	0.2925	5008	,	,		19957	0.1409		0.3211	False		,,,				2504	0.1022				p.P81P		Atlas-SNP	.											.	MED9	11	.	0			c.G243A						PASS	.	G		320,4086	169.8+/-200.3	10,300,1893	91.0	74.0	80.0		243	-9.5	0.0	17	dbSNP_87	80	2619,5981	424.1+/-354.6	400,1819,2081	no	coding-synonymous	MED9	NM_018019.2		410,2119,3974	AA,AG,GG		30.4535,7.2628,22.5973		81/147	17394611	2939,10067	2203	4300	6503	SO:0001819	synonymous_variant	55090	exon2			CAGCCCGGAGGTC	BC000647	CCDS11184.1	17p11.2	2007-07-30	2007-07-30		ENSG00000141026	ENSG00000141026			25487	protein-coding gene	gene with protein product		609878	"""mediator of RNA polymerase II transcription, subunit 9 homolog (S. cerevisiae)"""			11997338	Standard	NM_018019		Approved	FLJ10193, MED25	uc002grh.1	Q9NWA0	OTTHUMG00000059293	ENST00000268711.3:c.243G>A	17.37:g.17394611G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_018019		Silent	SNP	ENST00000268711.3	37	CCDS11184.1																																																																																			G|0.779;A|0.221	0.221	strong		0.597	MED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131669.2	NM_018019	
NCKIPSD	51517	hgsc.bcm.edu	37	3	48716536	48716536	+	Missense_Mutation	SNP	G	G	A	rs75577765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:48716536G>A	ENST00000294129.2	-	10	1770	c.1651C>T	c.(1651-1653)Ccg>Tcg	p.P551S	NCKIPSD_ENST00000341520.4_Missense_Mutation_p.P551S|NCKIPSD_ENST00000416649.2_Missense_Mutation_p.P544S	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	551	Leu-rich.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CAGAGGTCCGGCAGCTGCTCT	0.652													G|||	26	0.00519169	0.0	0.0029	5008	,	,		16917	0.0		0.0139	False		,,,				2504	0.0102				p.P551S		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.C1651T						PASS	.	G	SER/PRO,SER/PRO	16,4390	22.3+/-47.3	0,16,2187	53.0	54.0	54.0		1651,1630	5.4	1.0	3	dbSNP_131	54	112,8488	52.3+/-112.8	0,112,4188	yes	missense,missense	NCKIPSD	NM_016453.2,NM_184231.1	74,74	0,128,6375	AA,AG,GG		1.3023,0.3631,0.9842	probably-damaging,probably-damaging	551/723,544/716	48716536	128,12878	2203	4300	6503	SO:0001583	missense	51517	exon10			GGTCCGGCAGCTG	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"""dia interacting protein"", ""diaphanous protein interacting protein"", ""SH3 protein interacting with Nck, 90 kDa"""	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.1651C>T	3.37:g.48716536G>A	ENSP00000294129:p.Pro551Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Missense_Mutation	SNP	ENST00000294129.2	37	CCDS2776.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	G|G	26.1|26.1	4.700036|4.700036	0.88924|0.88924	0.003631|0.003631	0.013023|0.013023	ENSG00000213672|ENSG00000213672	ENST00000415281|ENST00000341520;ENST00000416649;ENST00000294129;ENST00000413374	.|T;T;T;T	.|0.64260	.|1.02;-0.09;-0.09;1.02	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Domain of unknown function DUF2013 (1);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.71813|0.71813	0.3384|0.3384	M|M	0.76328|0.76328	2.33|2.33	0.80722|0.80722	D|D	1|1	.|D;D	.|0.62365	.|0.991;0.989	.|D;P	.|0.66497	.|0.944;0.906	T|T	0.72067|0.72067	-0.4402|-0.4402	5|10	.|0.25106	.|T	.|0.35	.|.	19.105|19.105	0.93291|0.93291	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|551;544	.|Q9NZQ3;Q9NZQ3-3	.|SPN90_HUMAN;.	V|S	259|551;544;551;7	.|ENSP00000342621:P551S;ENSP00000389059:P544S;ENSP00000294129:P551S;ENSP00000396683:P7S	.|ENSP00000294129:P551S	A|P	-|-	2|1	0|0	NCKIPSD|NCKIPSD	48691540|48691540	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.839000|0.839000	0.47603|0.47603	9.307000|9.307000	0.96226|0.96226	2.498000|2.498000	0.84270|0.84270	0.650000|0.650000	0.86243|0.86243	GCC|CCG	G|0.990;A|0.010	0.010	strong		0.652	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453	
TTN	7273	hgsc.bcm.edu	37	2	179631323	179631323	+	Missense_Mutation	SNP	C	C	T	rs149755500	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179631323C>T	ENST00000591111.1	-	41	9712	c.9488G>A	c.(9487-9489)cGt>cAt	p.R3163H	TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R3117H|TTN_ENST00000342992.6_Missense_Mutation_p.R3163H|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R3163H|TTN_ENST00000359218.5_Missense_Mutation_p.R3117H|TTN_ENST00000342175.6_Missense_Mutation_p.R3117H|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.R3163H			Q8WZ42	TITIN_HUMAN	titin	13495					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AACAACAGCACGCTGTTTCTC	0.358																																					p.R3163H		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,-1,6	TTN	18412	6	0			c.G9488A						scavenged	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	101.0	89.0	93.0		9350,9488,9488,9350,9350	5.7	1.0	2	dbSNP_134	93	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	29,29,29,29,29	0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	3117/26927,3163/33424,3163/5605,3117/27052,3117/27119	179631323	5,13001	2203	4300	6503	SO:0001583	missense	7273	exon41			ACAGCACGCTGTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.9488G>A	2.37:g.179631323C>T	ENSP00000465570:p.Arg3163His	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	121	2	0.0165289	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	17.36	3.371256	0.61624	2.27E-4	4.65E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.7	5.7	0.88788	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.83778	0.5328	M	0.80183	2.485	0.34605	D	0.71696	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	D	0.88353	0.2982	9	0.87932	D	0	.	19.8277	0.96624	0.0:1.0:0.0:0.0	.	3117;3117;3117;3163;3163	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	H	3163;3117;3117;3117;3117;3163	ENSP00000343764:R3163H;ENSP00000434586:R3117H;ENSP00000340554:R3117H;ENSP00000352154:R3117H;ENSP00000354117:R3163H	ENSP00000340554:R3117H	R	-	2	0	TTN	179339568	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.485000	0.81204	2.695000	0.91970	0.591000	0.81541	CGT	C|0.999;T|0.001	0.001	strong		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PLG	5340	hgsc.bcm.edu	37	6	161132146	161132146	+	Silent	SNP	C	C	T	rs4757	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:161132146C>T	ENST00000308192.9	+	4	393	c.330C>T	c.(328-330)aaC>aaT	p.N110N	PLG_ENST00000462918.1_3'UTR|PLG_ENST00000366924.2_Silent_p.N110N	NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	110	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	ATGGAAAGAACTACAGAGGGA	0.453													C|||	1249	0.249401	0.5083	0.2248	5008	,	,		21058	0.001		0.3012	False		,,,				2504	0.1196				p.N110N		Atlas-SNP	.											.	PLG	150	.	0			c.C330T						PASS	.	C	,	2084,2322	573.3+/-383.5	478,1128,597	111.0	98.0	103.0		330,330	1.2	0.9	6	dbSNP_52	103	2713,5883	434.7+/-357.8	407,1899,1992	no	coding-synonymous,coding-synonymous	PLG	NM_000301.3,NM_001168338.1	,	885,3027,2589	TT,TC,CC		31.5612,47.2991,36.8943	,	110/811,110/137	161132146	4797,8205	2203	4298	6501	SO:0001819	synonymous_variant	5340	exon4			AAAGAACTACAGA	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.330C>T	6.37:g.161132146C>T		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	286	140	0.48951	NM_001168338	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			C|0.671;T|0.329	0.329	strong		0.453	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
SEMA5B	54437	hgsc.bcm.edu	37	3	122646828	122646828	+	Missense_Mutation	SNP	A	A	G	rs2276774	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:122646828A>G	ENST00000357599.3	-	8	1045	c.659T>C	c.(658-660)aTt>aCt	p.I220T	SEMA5B_ENST00000195173.4_Missense_Mutation_p.I220T|SEMA5B_ENST00000451055.2_Missense_Mutation_p.I274T|AC078794.1_ENST00000408284.1_RNA	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	220	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		I -> T (in dbSNP:rs2276774). {ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GATCTTCTCAATAGTCCGGCT	0.582													a|||	682	0.136182	0.1846	0.1744	5008	,	,		18987	0.0595		0.1392	False		,,,				2504	0.1196				p.I274T		Atlas-SNP	.											.	SEMA5B	303	.	0			c.T821C						PASS	.		THR/ILE	684,3722	289.2+/-280.3	57,570,1576	76.0	75.0	75.0		659	5.6	0.1	3	dbSNP_100	75	1301,7299	257.2+/-281.3	89,1123,3088	yes	missense	SEMA5B	NM_001031702.2	89	146,1693,4664	GG,GA,AA		15.1279,15.5243,15.2622	possibly-damaging	220/1152	122646828	1985,11021	2203	4300	6503	SO:0001583	missense	54437	exon8			TTCTCAATAGTCC	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.659T>C	3.37:g.122646828A>G	ENSP00000350215:p.Ile220Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	282	0.12912087912087913	90	0.18292682926829268	60	0.16574585635359115	32	0.055944055944055944	100	0.13192612137203166	a	11.03	1.520285	0.27211	0.155243	0.151279	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.10382	2.88;2.88;2.88;2.88	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.347111	0.32687	N	0.005776	T	0.00012	0.0000	N	0.12502	0.225	0.36606	P	0.12503699999999995	B;B;B	0.22851	0.062;0.076;0.076	B;B;B	0.32022	0.085;0.139;0.139	T	0.51687	-0.8674	9	0.21014	T	0.42	.	13.7366	0.62821	1.0:0.0:0.0:0.0	rs2276774;rs52822678;rs59346924;rs2276774	162;220;220	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	T	220;220;162;274;220	ENSP00000350215:I220T;ENSP00000195173:I220T;ENSP00000389588:I274T;ENSP00000377208:I220T	ENSP00000195173:I220T	I	-	2	0	SEMA5B	124129518	0.992000	0.36948	0.056000	0.19401	0.862000	0.49288	6.819000	0.75262	2.368000	0.80403	0.529000	0.55759	ATT	A|0.858;G|0.142	0.142	strong		0.582	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
PPP1R36	145376	hgsc.bcm.edu	37	14	65031534	65031534	+	Missense_Mutation	SNP	C	C	T	rs6573560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:65031534C>T	ENST00000298705.1	+	4	344	c.248C>T	c.(247-249)aCt>aTt	p.T83I	RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	83			T -> I (in dbSNP:rs6573560). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TTTGCAGAAACTGATGGTCCA	0.418													T|||	3094	0.617812	0.7209	0.6095	5008	,	,		20958	0.6597		0.493	False		,,,				2504	0.5695				p.T83I		Atlas-SNP	.											.	.	.	.	0			c.C248T						PASS	.	T	ILE/THR	3041,1365	452.2+/-349.9	1043,955,205	226.0	227.0	227.0		248	-4.0	0.0	14	dbSNP_116	227	4394,4206	571.7+/-389.6	1102,2190,1008	yes	missense	C14orf50	NM_172365.1	89	2145,3145,1213	TT,TC,CC		48.907,30.9805,42.8341	benign	83/423	65031534	7435,5571	2203	4300	6503	SO:0001583	missense	145376	exon4			CAGAAACTGATGG		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20097	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 50"""	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.248C>T	14.37:g.65031534C>T	ENSP00000298705:p.Thr83Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	1335	0.6112637362637363	356	0.7235772357723578	217	0.5994475138121547	380	0.6643356643356644	382	0.503957783641161	T	0.016	-1.511987	0.00984	0.690195	0.51093	ENSG00000165807	ENST00000298705	T	0.35973	1.28	5.9	-4.04	0.04010	.	0.942352	0.08875	N	0.880906	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40515	-0.9559	9	0.12103	T	0.63	-0.0323	1.7676	0.03005	0.1165:0.2952:0.2159:0.3725	rs6573560;rs17824809;rs60418610;rs6573560	83	Q96LQ0	PPR36_HUMAN	I	83	ENSP00000298705:T83I	ENSP00000298705:T83I	T	+	2	0	C14orf50	64101287	0.006000	0.16342	0.043000	0.18650	0.199000	0.23934	-1.585000	0.02112	-0.715000	0.04968	-0.360000	0.07572	ACT	C|0.407;N|0.000	.	strong		0.418	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365	
RPTOR	57521	hgsc.bcm.edu	37	17	78599562	78599562	+	Silent	SNP	C	C	G	rs17848685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78599562C>G	ENST00000306801.3	+	2	596	c.234C>G	c.(232-234)acC>acG	p.T78T	RPTOR_ENST00000570891.1_Silent_p.T78T|RPTOR_ENST00000544334.2_Silent_p.T78T|RPTOR_ENST00000537330.1_5'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	78					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						TGGTGAAGACCACGCCCTGTG	0.552													C|||	579	0.115615	0.0431	0.1239	5008	,	,		13519	0.0565		0.2137	False		,,,				2504	0.1677				p.T78T		Atlas-SNP	.											RPTOR,right_lower_lobe,carcinoma,+1,1	RPTOR	122	1	0			c.C234G						PASS	.	C	,	304,4102	165.1+/-196.6	10,284,1909	212.0	162.0	178.0		234,234	1.7	1.0	17	dbSNP_123	178	1895,6705	336.0+/-321.7	209,1477,2614	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	219,1761,4523	GG,GC,CC		22.0349,6.8997,16.9076	,	78/1178,78/1336	78599562	2199,10807	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon2			GAAGACCACGCCC		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.234C>G	17.37:g.78599562C>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			C|0.836;G|0.164	0.164	strong		0.552	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
GNG13	51764	hgsc.bcm.edu	37	16	848755	848755	+	Silent	SNP	G	G	A	rs36073541	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:848755G>A	ENST00000248150.4	-	3	269	c.168C>T	c.(166-168)aaC>aaT	p.N56N		NM_016541.2	NP_057625.1	Q9P2W3	GBG13_HUMAN	guanine nucleotide binding protein (G protein), gamma 13	56					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|sensory perception of taste (GO:0050909)|small molecule metabolic process (GO:0044281)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|signal transducer activity (GO:0004871)			ovary(1)	1		Hepatocellular(780;0.00335)				CCACCCATGGGTTGTTCTTCA	0.642													G|||	454	0.090655	0.0787	0.0403	5008	,	,		15514	0.1012		0.0119	False		,,,				2504	0.2127				p.N56N		Atlas-SNP	.											.	GNG13	8	.	0			c.C168T						PASS	.	G		299,4101	163.3+/-195.1	12,275,1913	156.0	160.0	159.0		168	4.1	1.0	16	dbSNP_126	159	107,8493	58.3+/-119.8	1,105,4194	no	coding-synonymous	GNG13	NM_016541.2		13,380,6107	AA,AG,GG		1.2442,6.7955,3.1231		56/68	848755	406,12594	2200	4300	6500	SO:0001819	synonymous_variant	51764	exon3			CCATGGGTTGTTC	AB030207	CCDS10427.1	16p13.3	2008-08-01			ENSG00000127588	ENSG00000127588			14131	protein-coding gene	gene with protein product	"""G gamma subunit, clone:h2-35"""	607298				10570481	Standard	NM_016541		Approved	h2-35, G(gamma)13	uc002ckh.4	Q9P2W3	OTTHUMG00000047839	ENST00000248150.4:c.168C>T	16.37:g.848755G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_016541	B2R5C8|Q52LX0|Q9UJJ3	Silent	SNP	ENST00000248150.4	37	CCDS10427.1																																																																																			G|0.950;A|0.050	0.050	strong		0.642	GNG13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109062.3	NM_016541	
COLEC12	81035	hgsc.bcm.edu	37	18	334742	334742	+	Splice_Site	SNP	C	C	T	rs17857498|rs2305027	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:334742C>T	ENST00000400256.3	-	6	2023	c.1816G>A	c.(1816-1818)Ggc>Agc	p.G606S		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	606			G -> S (in dbSNP:rs2305027). {ECO:0000269|PubMed:11162630, ECO:0000269|PubMed:12601552, ECO:0000269|PubMed:15489334}.		carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				TTGGACTTACCATTGTCCTCC	0.647													C|||	1841	0.367612	0.2572	0.3473	5008	,	,		15417	0.4563		0.493	False		,,,				2504	0.3108				p.G606S		Atlas-SNP	.											.	COLEC12	121	.	0			c.G1816A						PASS	.	C	SER/GLY	1275,3131	425.1+/-340.7	182,911,1110	45.0	41.0	42.0		1816	4.5	1.0	18	dbSNP_100	42	4264,4336	563.0+/-388.1	1037,2190,1073	yes	missense-near-splice	COLEC12	NM_130386.2	56	1219,3101,2183	TT,TC,CC		49.5814,28.9378,42.588	probably-damaging	606/743	334742	5539,7467	2203	4300	6503	SO:0001630	splice_region_variant	81035	exon6			ACTTACCATTGTC	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"""Collectins"""	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.1816+1G>A	18.37:g.334742C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	115	45	0.391304	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000400256.3	37	CCDS32782.1	888	0.4065934065934066	161	0.32723577235772355	121	0.3342541436464088	237	0.4143356643356643	369	0.4868073878627968	C	16.56	3.156627	0.57259	0.289378	0.495814	ENSG00000158270	ENST00000400256	T	0.16324	2.35	5.39	4.5	0.54988	C-type lectin-like (1);	0.178977	0.50627	D	0.000107	T	0.00012	0.0000	M	0.61703	1.905	0.09310	P	0.999999706947	D	0.89917	1.0	D	0.87578	0.998	T	0.49000	-0.8984	8	.	.	.	-14.835	14.4479	0.67364	0.1484:0.8516:0.0:0.0	rs2305027;rs17450950;rs52830862;rs56583438;rs59614806;rs2305027	606	Q5KU26	COL12_HUMAN	S	606	ENSP00000383115:G606S	.	G	-	1	0	COLEC12	324742	1.000000	0.71417	0.967000	0.41034	0.058000	0.15608	5.137000	0.64789	1.232000	0.43678	0.561000	0.74099	GGC	C|0.591;T|0.409	0.409	strong		0.647	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1		Missense_Mutation
GFRA4	64096	hgsc.bcm.edu	37	20	3640823	3640823	+	Silent	SNP	C	C	T	rs2853208	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3640823C>T	ENST00000319242.3	-	4	800	c.801G>A	c.(799-801)ccG>ccA	p.P267P	GFRA4_ENST00000290417.2_Silent_p.P237P			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	267					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			large_intestine(1)|lung(2)	3						GGCTGTGCTCCGGGTCTCCCT	0.677													C|||	1900	0.379393	0.0499	0.5303	5008	,	,		14648	0.4117		0.5258	False		,,,				2504	0.5337				p.P267P		Atlas-SNP	.											GFRA4,NS,carcinoma,0,1	GFRA4	10	1	0			c.G801A						PASS	.	C	,	611,3773		62,487,1643	12.0	13.0	13.0		711,801	-6.0	0.0	20	dbSNP_100	13	4376,4176		1164,2048,1064	no	coding-synonymous,coding-synonymous	GFRA4	NM_022139.3,NM_145762.2	,	1226,2535,2707	TT,TC,CC		48.8307,13.937,38.5513	,	237/270,267/300	3640823	4987,7949	2192	4276	6468	SO:0001819	synonymous_variant	64096	exon4			GTGCTCCGGGTCT	AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"""persephin receptor"""					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.801G>A	20.37:g.3640823C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	106	60	0.566038	NM_145762	Q5JT74|Q9H191|Q9H192	Silent	SNP	ENST00000319242.3	37	CCDS13056.1																																																																																			C|0.641;T|0.359	0.359	strong		0.677	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762	
PDIA5	10954	hgsc.bcm.edu	37	3	122880191	122880191	+	Silent	SNP	T	T	C	rs8935	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:122880191T>C	ENST00000316218.7	+	16	1463	c.1368T>C	c.(1366-1368)tgT>tgC	p.C456C	PDIA5_ENST00000467157.1_3'UTR	NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	456	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		CTGTTGACTGTGTCAAAGACA	0.537													T|||	1412	0.281949	0.1195	0.281	5008	,	,		19701	0.4613		0.328	False		,,,				2504	0.2699				p.C456C		Atlas-SNP	.											.	PDIA5	66	.	0			c.T1368C						PASS	.	T		748,3658	306.3+/-289.4	72,604,1527	101.0	89.0	93.0		1368	-3.0	0.9	3	dbSNP_52	93	2632,5968	425.7+/-355.0	412,1808,2080	no	coding-synonymous	PDIA5	NM_006810.3		484,2412,3607	CC,CT,TT		30.6047,16.9768,25.988		456/520	122880191	3380,9626	2203	4300	6503	SO:0001819	synonymous_variant	10954	exon16			TGACTGTGTCAAA	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"""Protein disulfide isomerases"""	24811	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 5"""			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.1368T>C	3.37:g.122880191T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	115	44	0.382609	NM_006810	D3DN95|Q9BV43	Silent	SNP	ENST00000316218.7	37	CCDS3020.1																																																																																			C|0.276;T|0.724	0.276	strong		0.537	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810	
SLC7A13	157724	hgsc.bcm.edu	37	8	87241847	87241847	+	Silent	SNP	G	G	A	rs7814198	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:87241847G>A	ENST00000297524.3	-	1	763	c.660C>T	c.(658-660)ggC>ggT	p.G220G	SLC7A13_ENST00000419776.2_Splice_Site|SLC7A13_ENST00000520624.1_Intron	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	220						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						AGCATGCCCCGCCTGAATATG	0.353													G|||	2232	0.445687	0.4932	0.4481	5008	,	,		21344	0.502		0.2296	False		,,,				2504	0.544				p.G220G		Atlas-SNP	.											.	SLC7A13	97	.	0			c.C660T						PASS	.	G		1947,2459	552.0+/-378.4	443,1061,699	140.0	134.0	136.0		660	-9.4	0.0	8	dbSNP_116	136	2012,6588	352.7+/-328.8	237,1538,2525	no	coding-synonymous	SLC7A13	NM_138817.2		680,2599,3224	AA,AG,GG		23.3953,44.1897,30.4398		220/471	87241847	3959,9047	2203	4300	6503	SO:0001819	synonymous_variant	157724	exon1			TGCCCCGCCTGAA	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.660C>T	8.37:g.87241847G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	82	50	0.609756	NM_138817	Q05C37|Q08AH9|Q96N84	Silent	SNP	ENST00000297524.3	37	CCDS34917.1	803	0.3676739926739927	211	0.42886178861788615	142	0.39226519337016574	271	0.4737762237762238	179	0.23614775725593667	G	2.670	-0.277869	0.05679	0.441897	0.233953	ENSG00000164893	ENST00000419776	.	.	.	4.68	-9.36	0.00629	.	.	.	.	.	.	.	.	.	.	.	0.38146	P	0.061417000000000055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.1558	0.20335	0.5134:0.0:0.1228:0.3638	rs7814198;rs59432753;rs7814198	.	.	.	.	-1	.	.	.	-	.	.	SLC7A13	87310963	0.001000	0.12720	0.000000	0.03702	0.452000	0.32318	-1.919000	0.01572	-2.658000	0.00420	-1.263000	0.01449	.	G|0.644;A|0.356	0.356	strong		0.353	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
OR6C2	341416	hgsc.bcm.edu	37	12	55846623	55846623	+	Missense_Mutation	SNP	T	T	C	rs11171467	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:55846623T>C	ENST00000322678.1	+	1	626	c.626T>C	c.(625-627)cTa>cCa	p.L209P	RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_054105.1	NP_473446.1	Q9NZP2	OR6C2_HUMAN	olfactory receptor, family 6, subfamily C, member 2	209			L -> P (in dbSNP:rs11171467). {ECO:0000269|PubMed:10706615}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(5)|lung(8)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	23						ATTATCACCCTAGTTTGTGTG	0.413													T|||	457	0.091254	0.1346	0.0937	5008	,	,		23872	0.0		0.1571	False		,,,				2504	0.0573				p.L209P		Atlas-SNP	.											.	OR6C2	39	.	0			c.T626C						PASS	.	T	PRO/LEU	582,3824	257.4+/-261.8	35,512,1656	173.0	164.0	167.0		626	5.4	0.0	12	dbSNP_120	167	1415,7185	273.9+/-290.9	122,1171,3007	yes	missense	OR6C2	NM_054105.1	98	157,1683,4663	CC,CT,TT		16.4535,13.2093,15.3545	probably-damaging	209/313	55846623	1997,11009	2203	4300	6503	SO:0001583	missense	341416	exon1			TCACCCTAGTTTG	AF179766	CCDS31824.1	12q13.2	2012-08-09				ENSG00000179695		"""GPCR / Class A : Olfactory receptors"""	15436	protein-coding gene	gene with protein product							Standard	NM_054105		Approved	OR6C67	uc001sgz.1	Q9NZP2	OTTHUMG00000169957	ENST00000322678.1:c.626T>C	12.37:g.55846623T>C	ENSP00000323606:p.Leu209Pro	Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	285	136	0.477193	NM_054105		Missense_Mutation	SNP	ENST00000322678.1	37	CCDS31824.1	224	0.10256410256410256	69	0.1402439024390244	37	0.10220994475138122	0	0.0	118	0.15567282321899736	T	13.95	2.389734	0.42410	0.132093	0.164535	ENSG00000179695	ENST00000322678	T	0.49432	0.78	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	D	0.000319	T	0.00637	0.0021	M	0.91300	3.195	0.52501	P	4.4000000000044004E-5	D	0.63046	0.992	D	0.64776	0.929	T	0.49707	-0.8911	9	0.87932	D	0	.	11.0786	0.48047	0.0:0.0:0.155:0.845	rs11171467;rs52792749;rs56775732;rs11171467	209	Q9NZP2	OR6C2_HUMAN	P	209	ENSP00000323606:L209P	ENSP00000323606:L209P	L	+	2	0	OR6C2	54132890	0.042000	0.20092	0.007000	0.13788	0.006000	0.05464	2.168000	0.42424	2.275000	0.75901	0.496000	0.49642	CTA	T|0.865;C|0.135	0.135	strong		0.413	OR6C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406676.1	NM_054105	
PARP10	84875	hgsc.bcm.edu	37	8	145059425	145059425	+	Missense_Mutation	SNP	T	T	C	rs11136344	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:145059425T>C	ENST00000313028.7	-	5	839	c.745A>G	c.(745-747)Atc>Gtc	p.I249V	PARP10_ENST00000525773.1_Missense_Mutation_p.I261V|PARP10_ENST00000533665.1_5'UTR|PARP10_ENST00000524918.1_Missense_Mutation_p.I249V	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	249			I -> V (in dbSNP:rs11136344).		negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGCTCCAGgatgtcgtagtgg	0.627													C|||	1959	0.391174	0.6165	0.2795	5008	,	,		18107	0.1458		0.4314	False		,,,				2504	0.3773				p.I249V		Atlas-SNP	.											.	PARP10	57	.	0			c.A745G						PASS	.		VAL/ILE	2628,1778	516.2+/-369.1	781,1066,356	40.0	42.0	41.0		745	-0.6	0.0	8	dbSNP_120	41	3640,4960	614.2+/-396.2	796,2048,1456	yes	missense	PARP10	NM_032789.3	29	1577,3114,1812	CC,CT,TT		42.3256,40.3541,48.1931	benign	249/1026	145059425	6268,6738	2203	4300	6503	SO:0001583	missense	84875	exon5			CCAGGATGTCGTA	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"""Poly (ADP-ribose) polymerases"""	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.745A>G	8.37:g.145059425T>C	ENSP00000325618:p.Ile249Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	69	37	0.536232	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Missense_Mutation	SNP	ENST00000313028.7	37	CCDS34960.1	832	0.38095238095238093	308	0.6260162601626016	116	0.32044198895027626	88	0.15384615384615385	320	0.42216358839050133	C	0.003	-2.464539	0.00171	0.596459	0.423256	ENSG00000178685	ENST00000524918;ENST00000313028;ENST00000525773;ENST00000313059	T;T;T;T	0.24908	3.14;3.15;3.15;1.83	3.8	-0.575	0.11734	.	0.572735	0.14302	N	0.328229	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.36407	-0.9749	9	0.02654	T	1	.	3.4917	0.07639	0.179:0.3745:0.0:0.4465	rs11136344;rs57845841;rs11136344	261;249;249	E9PNI7;E9PK67;Q53GL7	.;.;PAR10_HUMAN	V	249;249;261;164	ENSP00000431620:I249V;ENSP00000325618:I249V;ENSP00000434776:I261V;ENSP00000314320:I164V	ENSP00000325618:I249V	I	-	1	0	PARP10	145131413	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.973000	0.01500	-0.436000	0.07254	-1.016000	0.02456	ATC	T|0.554;C|0.446	0.446	strong		0.627	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789	
CFAP57	149465	hgsc.bcm.edu	37	1	43647424	43647424	+	Missense_Mutation	SNP	C	C	T	rs138300205	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43647424C>T	ENST00000372492.4	+	3	701	c.377C>T	c.(376-378)aCg>aTg	p.T126M	WDR65_ENST00000528956.1_Missense_Mutation_p.T126M	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		126										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTGGCTCAGACGTCACCTCCA	0.423													C|||	28	0.00559105	0.0015	0.0	5008	,	,		17818	0.0		0.0159	False		,,,				2504	0.0102				p.T126M		Atlas-SNP	.											.	WDR65	76	.	0			c.C377T						PASS	.	C	MET/THR,MET/THR,MET/THR	12,4394	20.2+/-43.8	0,12,2191	81.0	86.0	84.0		377,377,377	5.6	1.0	1	dbSNP_134	84	150,8450	72.6+/-135.2	0,150,4150	yes	missense,missense,missense	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	81,81,81	0,162,6341	TT,TC,CC		1.7442,0.2724,1.2456	probably-damaging,probably-damaging,probably-damaging	126/699,126/699,126/699	43647424	162,12844	2203	4300	6503	SO:0001583	missense	149465	exon3			CTCAGACGTCACC																												ENST00000372492.4:c.377C>T	1.37:g.43647424C>T	ENSP00000361570:p.Thr126Met	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	163	75	0.460123	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	37		13	0.005952380952380952	1	0.0020325203252032522	0	0.0	0	0.0	12	0.0158311345646438	C	20.1	3.937291	0.73557	0.002724	0.017442	ENSG00000243710	ENST00000372492;ENST00000528956;ENST00000529956	T;T;T	0.38401	4.93;1.14;4.93	5.57	5.57	0.84162	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.153918	0.64402	D	0.000017	T	0.43100	0.1232	M	0.66939	2.045	0.47862	D	0.999536	D;D	0.76494	0.999;0.998	P;D	0.67900	0.899;0.954	T	0.50931	-0.8769	10	0.48119	T	0.1	.	19.1541	0.93503	0.0:1.0:0.0:0.0	.	126;126	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	M	126	ENSP00000361570:T126M;ENSP00000435310:T126M;ENSP00000434133:T126M	ENSP00000361570:T126M	T	+	2	0	WDR65	43420011	1.000000	0.71417	0.999000	0.59377	0.588000	0.36517	5.291000	0.65667	2.626000	0.88956	0.557000	0.71058	ACG	C|0.990;T|0.010	0.010	strong		0.423	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
EFCAB12	90288	hgsc.bcm.edu	37	3	129130197	129130197	+	Splice_Site	SNP	T	T	C	rs9836111	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129130197T>C	ENST00000505956.1	-	5	1001	c.839A>G	c.(838-840)cAt>cGt	p.H280R	EFCAB12_ENST00000326085.3_Splice_Site_p.H280R	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	280			H -> R (in dbSNP:rs9836111).				calcium ion binding (GO:0005509)										CAAGATATAATCTGGAGTCAG	0.562													C|||	757	0.151158	0.1309	0.1225	5008	,	,		19359	0.4603		0.002	False		,,,				2504	0.0337				p.H280R		Atlas-SNP	.											.	.	.	.	0			c.A839G						PASS	.	C	ARG/HIS	418,3676		22,374,1651	50.0	51.0	51.0		839	-5.3	0.0	3	dbSNP_119	51	33,8351		1,31,4160	yes	missense-near-splice	C3orf25	NM_207307.1	29	23,405,5811	CC,CT,TT		0.3936,10.2101,3.6144	benign	280/573	129130197	451,12027	2047	4192	6239	SO:0001630	splice_region_variant	90288	exon5			ATATAATCTGGAG	AK096099	CCDS54638.1	3q21.3	2013-01-10	2012-07-20	2012-07-20	ENSG00000172771	ENSG00000172771		"""EF-hand domain containing"""	28061	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 25"""	C3orf25			Standard	NM_207307		Approved		uc003emg.3	Q6NXP0	OTTHUMG00000159464	ENST00000505956.1:c.839-1A>G	3.37:g.129130197T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_207307	Q69YX4	Missense_Mutation	SNP	ENST00000505956.1	37	CCDS54638.1	359	0.16437728937728938	64	0.13008130081300814	40	0.11049723756906077	253	0.4423076923076923	2	0.002638522427440633	C	4.368	0.067849	0.08436	0.102101	0.003936	ENSG00000172771	ENST00000505956;ENST00000326085;ENST00000503957	T;T;T	0.28895	2.57;2.57;1.59	3.8	-5.34	0.02705	.	4.594920	0.00166	N	0.000011	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38090	-0.9677	9	0.25106	T	0.35	.	6.6196	0.22796	0.1252:0.4418:0.0:0.433	rs9836111;rs52817258;rs9836111	280	Q6NXP0	CC025_HUMAN	R	280;280;130	ENSP00000420854:H280R;ENSP00000324241:H280R;ENSP00000421462:H130R	ENSP00000324241:H280R	H	-	2	0	C3orf25	130612887	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.836000	0.04382	-1.864000	0.01148	-1.212000	0.01626	CAT	T|0.847;C|0.153	0.153	strong		0.562	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	Missense_Mutation
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557449	32557449	+	Missense_Mutation	SNP	G	G	A	rs187619904		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32557449G>A	ENST00000360004.5	-	1	176	c.71C>T	c.(70-72)tCc>tTc	p.S24F		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	24					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)		p.S24F(1)		large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						AGCCAGTGGGGAGCTCAGCAC	0.572										Multiple Myeloma(14;0.17)																											p.S24F		Atlas-SNP	.											HLA-DRB1,extremity,malignant_melanoma,0,1	HLA-DRB1	41	1	1	Substitution - Missense(1)	skin(1)	c.C71T						scavenged	.						75.0	91.0	85.0					6																	32557449		1511	2709	4220	SO:0001583	missense	3123	exon1			AGTGGGGAGCTCA	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.71C>T	6.37:g.32557449G>A	ENSP00000353099:p.Ser24Phe	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	238	21	0.0882353	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	27	0.012362637362637362	7	0.014227642276422764	7	0.019337016574585635	6	0.01048951048951049	7	0.009234828496042216	.	5.206	0.223607	0.09863	.	.	ENSG00000196126	ENST00000360004	T	0.00267	8.38	4.4	1.53	0.23141	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00144	0.0004	L	0.58810	1.83	0.09310	N	1	D	0.63880	0.993	P	0.60541	0.876	T	0.28839	-1.0031	9	0.62326	D	0.03	.	3.8678	0.09024	0.2075:0.0:0.6026:0.1899	.	24	P01911	2B1F_HUMAN	F	24	ENSP00000353099:S24F	ENSP00000353099:S24F	S	-	2	0	HLA-DRB1	32665427	0.014000	0.17966	0.085000	0.20634	0.032000	0.12392	2.097000	0.41748	0.479000	0.27511	0.462000	0.41574	TCC	G|0.988;A|0.012	0.012	strong		0.572	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
RARS2	57038	hgsc.bcm.edu	37	6	88239266	88239266	+	Missense_Mutation	SNP	T	T	C	rs17850652	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:88239266T>C	ENST00000369536.5	-	10	917	c.872A>G	c.(871-873)aAa>aGa	p.K291R		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	291			K -> R (in dbSNP:rs17850652). {ECO:0000269|PubMed:15489334}.		arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		ATACATTGTTTTCAGTAGGAG	0.333													T|||	493	0.0984425	0.1165	0.0605	5008	,	,		17657	0.1081		0.0895	False		,,,				2504	0.1002				p.K291R		Atlas-SNP	.											.	RARS2	61	.	0			c.A872G						PASS	.	T	ARG/LYS	529,3873	239.0+/-250.2	28,473,1700	71.0	74.0	73.0		872	4.1	1.0	6	dbSNP_123	73	683,7913	169.7+/-221.0	26,631,3641	yes	missense	RARS2	NM_020320.3	26	54,1104,5341	CC,CT,TT		7.9456,12.0173,9.3245	benign	291/579	88239266	1212,11786	2201	4298	6499	SO:0001583	missense	57038	exon10			ATTGTTTTCAGTA	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	21406	protein-coding gene	gene with protein product	"""arginine tRNA ligase 2, mitochondrial (putative)"""	611524	"""arginyl-tRNA synthetase-like"""	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.872A>G	6.37:g.88239266T>C	ENSP00000358549:p.Lys291Arg	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	236	106	0.449153	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	193	0.08836996336996338	53	0.10772357723577236	25	0.06906077348066299	50	0.08741258741258741	65	0.08575197889182058	T	13.98	2.399445	0.42512	0.120173	0.079456	ENSG00000146282	ENST00000369536	T	0.64085	-0.08	5.5	4.13	0.48395	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.093597	0.64402	D	0.000001	T	0.28632	0.0709	N	0.13371	0.34	0.25122	P	0.99063097	B	0.02656	0.0	B	0.09377	0.004	T	0.30736	-0.9968	9	0.72032	D	0.01	.	11.6962	0.51544	0.0:0.0822:0.0:0.9178	rs17850652;rs17850652	291	Q5T160	SYRM_HUMAN	R	291	ENSP00000358549:K291R	ENSP00000358549:K291R	K	-	2	0	RARS2	88295985	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.508000	0.35769	2.084000	0.62774	0.528000	0.53228	AAA	T|0.911;C|0.089	0.089	strong		0.333	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21329738	21329738	+	Missense_Mutation	SNP	A	A	G	rs2306283	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:21329738A>G	ENST00000256958.2	+	5	484	c.388A>G	c.(388-390)Aat>Gat	p.N130D		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	130			N -> D (in dbSNP:rs2306283). {ECO:0000269|PubMed:10601278, ECO:0000269|PubMed:11477075, ECO:0000269|PubMed:12130747, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	AACTAATATCAATTCATCAGA	0.299													G|||	3117	0.622404	0.8177	0.4726	5008	,	,		17062	0.7619		0.4026	False		,,,				2504	0.547				p.N130D		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.A388G	GRCh37	CM043776	SLCO1B1	M	rs2306283	PASS	.	G	ASP/ASN	3365,1033	373.7+/-320.9	1296,773,130	77.0	78.0	77.0		388	-2.6	0.0	12	dbSNP_100	77	3460,5110	626.2+/-397.8	717,2026,1542	yes	missense	SLCO1B1	NM_006446.4	23	2013,2799,1672	GG,GA,AA		40.3734,23.4879,47.3705	benign	130/692	21329738	6825,6143	2199	4285	6484	SO:0001583	missense	10599	exon5			AATATCAATTCAT		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.388A>G	12.37:g.21329738A>G	ENSP00000256958:p.Asn130Asp	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	270	119	0.440741	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	1298	0.5943223443223443	395	0.8028455284552846	171	0.4723756906077348	431	0.7534965034965035	301	0.3970976253298153	G	1.400	-0.578401	0.03854	0.765121	0.403734	ENSG00000134538	ENST00000256958	T	0.38722	1.12	3.52	-2.63	0.06133	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.665010	0.03303	N	0.189390	T	0.00012	0.0000	N	0.17564	0.495	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.34354	-0.9832	9	0.10902	T	0.67	.	9.285	0.37751	0.6625:0.0:0.3375:0.0	rs2306283;rs17389242;rs52832430;rs60767041;rs2306283	130	Q9Y6L6	SO1B1_HUMAN	D	130	ENSP00000256958:N130D	ENSP00000256958:N130D	N	+	1	0	SLCO1B1	21221005	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.302000	0.08221	-0.797000	0.04450	-1.840000	0.00586	AAT	A|0.422;G|0.578	0.578	strong		0.299	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
UGGT2	55757	hgsc.bcm.edu	37	13	96540172	96540172	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:96540172G>A	ENST00000376747.3	-	26	3082	c.3012C>T	c.(3010-3012)ggC>ggT	p.G1004G		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1004					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						CTGAAAGCCTGCCCCTACAGT	0.308																																					p.G1004G		Atlas-SNP	.											UGGT2,NS,malignant_melanoma,-2,1	UGGT2	127	1	0			c.C3012T						scavenged	.						45.0	50.0	48.0					13																	96540172		2203	4299	6502	SO:0001819	synonymous_variant	55757	exon26			AAGCCTGCCCCTA	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.3012C>T	13.37:g.96540172G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	237	3	0.0126582	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Silent	SNP	ENST00000376747.3	37	CCDS9480.1																																																																																			.	.	none		0.308	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
SLC1A6	6511	hgsc.bcm.edu	37	19	15063757	15063757	+	Silent	SNP	A	A	G	rs2229896	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:15063757A>G	ENST00000221742.3	-	8	1489	c.1482T>C	c.(1480-1482)atT>atC	p.I494I	SLC1A6_ENST00000600144.1_Silent_p.I416I|SLC1A6_ENST00000430939.2_Silent_p.I430I	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	494					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						AGTCCACGGCAATGATGAGCG	0.597													N|||	1265	0.252596	0.4236	0.2118	5008	,	,		14440	0.3244		0.1421	False		,,,				2504	0.09				p.I494I		Atlas-SNP	.											.	SLC1A6	111	.	0			c.T1482C						PASS	.	G		1658,2748		331,996,876	196.0	148.0	164.0		1482	-2.1	1.0	19	dbSNP_98	164	1024,7576		66,892,3342	no	coding-synonymous	SLC1A6	NM_005071.1		397,1888,4218	GG,GA,AA		11.907,37.6305,20.6213		494/565	15063757	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	6511	exon8			CACGGCAATGATG		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1482T>C	19.37:g.15063757A>G		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	183	80	0.437158	NM_005071	Q8N753	Silent	SNP	ENST00000221742.3	37	CCDS12321.1																																																																																			T|0.131;G|0.183;C|0.054;A|0.632	0.183	strong		0.597	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
TRPC3	7222	hgsc.bcm.edu	37	4	122824052	122824052	+	Silent	SNP	C	C	T	rs11732666	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:122824052C>T	ENST00000379645.3	-	9	2491	c.2418G>A	c.(2416-2418)agG>agA	p.R806R	TRPC3_ENST00000513531.1_Silent_p.R678R|TRPC3_ENST00000264811.5_Silent_p.R733R	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	721					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CCTTCTGAAGCCTTCTCCTTC	0.358													C|||	1399	0.279353	0.0961	0.4049	5008	,	,		17706	0.4137		0.3121	False		,,,				2504	0.2658				p.R806R		Atlas-SNP	.											.	TRPC3	201	.	0			c.G2418A						PASS	.	C	,	586,3820	257.7+/-262.0	40,506,1657	123.0	114.0	117.0		2418,2199	2.7	1.0	4	dbSNP_120	117	2851,5749	448.1+/-361.7	499,1853,1948	no	coding-synonymous,coding-synonymous	TRPC3	NM_001130698.1,NM_003305.2	,	539,2359,3605	TT,TC,CC		33.1512,13.3,26.4263	,	806/922,733/849	122824052	3437,9569	2203	4300	6503	SO:0001819	synonymous_variant	7222	exon9			CTGAAGCCTTCTC	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.2418G>A	4.37:g.122824052C>T		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	231	100	0.4329	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	ENST00000379645.3	37	CCDS47130.1																																																																																			C|0.721;T|0.279	0.279	strong		0.358	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305	
COL28A1	340267	hgsc.bcm.edu	37	7	7495735	7495735	+	Missense_Mutation	SNP	T	T	C	rs55745506	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:7495735T>C	ENST00000399429.3	-	16	1451	c.1311A>G	c.(1309-1311)atA>atG	p.I437M		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	437			I -> M (in dbSNP:rs55745506).		cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCACAGGTCCTATATCCCCCT	0.408													C|||	1584	0.316294	0.5726	0.2522	5008	,	,		15221	0.2103		0.2107	False		,,,				2504	0.2331				p.I437M		Atlas-SNP	.											.	COL28A1	113	.	0			c.A1311G						PASS	.	C	MET/ILE	1760,1876		433,894,491	73.0	72.0	72.0		1311	1.4	1.0	7	dbSNP_129	72	1664,6492		155,1354,2569	yes	missense	COL28A1	NM_001037763.2	10	588,2248,3060	CC,CT,TT		20.4022,48.4048,29.0366	benign	437/1126	7495735	3424,8368	1818	4078	5896	SO:0001583	missense	340267	exon16			AGGTCCTATATCC	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.1311A>G	7.37:g.7495735T>C	ENSP00000382356:p.Ile437Met	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	658	0.30128205128205127	292	0.5934959349593496	96	0.26519337016574585	115	0.20104895104895104	155	0.20448548812664907	C	8.864	0.947737	0.18356	0.484048	0.204022	ENSG00000215018	ENST00000399429;ENST00000399419	D	0.94280	-3.39	4.53	1.44	0.22558	.	2.249830	0.03373	N	0.199275	T	0.00012	0.0000	N	0.12611	0.24	0.48830	P	2.870000000000372E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37337	-0.9710	9	0.44086	T	0.13	0.4197	6.775	0.23615	0.0:0.5303:0.0:0.4697	rs55745506;rs59850353	437;437	Q2UY09-2;Q2UY09	.;COSA1_HUMAN	M	437	ENSP00000382356:I437M	ENSP00000382347:I437M	I	-	3	3	COL28A1	7462260	0.993000	0.37304	0.996000	0.52242	0.906000	0.53458	0.148000	0.16224	-0.044000	0.13491	-1.082000	0.02213	ATA	T|0.729;C|0.271	0.271	strong		0.408	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
ZBTB12	221527	hgsc.bcm.edu	37	6	31868075	31868075	+	Silent	SNP	G	G	C	rs9267664	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31868075G>C	ENST00000375527.2	-	2	1183	c.1008C>G	c.(1006-1008)acC>acG	p.T336T	EHMT2_ENST00000375537.4_5'Flank|C2_ENST00000469372.1_Intron|C2_ENST00000452323.2_5'Flank|EHMT2_ENST00000375530.4_5'Flank	NM_181842.2	NP_862825.1	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	336					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(5)|prostate(1)|skin(1)	10						CCGGGCACTTGGTGCACTTGA	0.657													G|||	473	0.0944489	0.1815	0.085	5008	,	,		11878	0.0397		0.0417	False		,,,				2504	0.0941				p.T336T		Atlas-SNP	.											.	ZBTB12	25	.	0			c.C1008G						PASS	.	G		624,3782	249.6+/-257.0	45,534,1624	39.0	40.0	40.0		1008	2.9	1.0	6	dbSNP_118	40	354,8244	111.8+/-172.0	15,324,3960	no	coding-synonymous	ZBTB12	NM_181842.2		60,858,5584	CC,CG,GG		4.1172,14.1625,7.5208		336/460	31868075	978,12026	2203	4299	6502	SO:0001819	synonymous_variant	221527	exon2			GCACTTGGTGCAC	BC043609	CCDS4727.1	6p21.31	2013-01-08	2004-04-15	2004-04-16	ENSG00000204366	ENSG00000204366		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	19066	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 46"""	C6orf46		9545376	Standard	NM_181842		Approved	G10, NG35, D6S59E	uc003nyd.1	Q9Y330	OTTHUMG00000031169	ENST00000375527.2:c.1008C>G	6.37:g.31868075G>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_181842	B0UY00|Q5JQ98	Silent	SNP	ENST00000375527.2	37	CCDS4727.1																																																																																			G|0.924;C|0.076	0.076	strong		0.657	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842	
FGD2	221472	hgsc.bcm.edu	37	6	36976637	36976637	+	Missense_Mutation	SNP	G	G	C	rs831510	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:36976637G>C	ENST00000274963.8	+	2	267	c.96G>C	c.(94-96)caG>caC	p.Q32H		NM_173558.3	NP_775829.2	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	32			Q -> H (in dbSNP:rs831510). {ECO:0000269|PubMed:15489334}.		actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.Q32H(1)		central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	25						CCAGAGGCCAGAGGCTAGAGG	0.637													C|||	1632	0.325879	0.264	0.3761	5008	,	,		18864	0.5417		0.2575	False		,,,				2504	0.2219				p.Q32H		Atlas-SNP	.											FGD2,NS,carcinoma,0,1	FGD2	65	1	1	Substitution - Missense(1)	prostate(1)	c.G96C						PASS	.	C	HIS/GLN	1276,3130	680.9+/-403.9	197,882,1124	50.0	57.0	55.0		96	2.2	0.0	6	dbSNP_86	55	2137,6463	696.1+/-404.9	281,1575,2444	yes	missense	FGD2	NM_173558.3	24	478,2457,3568	CC,CG,GG		24.8488,28.9605,26.2417	benign	32/656	36976637	3413,9593	2203	4300	6503	SO:0001583	missense	221472	exon2			AGGCCAGAGGCTA	AK097230	CCDS4829.1	6p21.2	2013-01-10	2004-08-24		ENSG00000146192	ENSG00000146192		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	3664	protein-coding gene	gene with protein product		605091	"""FGD1 family, member 2"""			10458911	Standard	NM_173558		Approved	ZFYVE4	uc010jwp.1	Q7Z6J4	OTTHUMG00000014616	ENST00000274963.8:c.96G>C	6.37:g.36976637G>C	ENSP00000274963:p.Gln32His	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	188	90	0.478723	NM_173558	Q5T8I1|Q6P6A8|Q6ZNL5|Q8IZ32|Q8N868|Q9H7M2	Missense_Mutation	SNP	ENST00000274963.8	37	CCDS4829.1	777	0.3557692307692308	142	0.2886178861788618	122	0.3370165745856354	311	0.5437062937062938	202	0.26649076517150394	C	0.024	-1.385287	0.01194	0.289605	0.248488	ENSG00000146192	ENST00000274963	T	0.58210	0.35	5.0	2.16	0.27623	.	0.767167	0.11414	N	0.566460	T	0.06142	0.0159	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33954	-0.9848	9	0.12766	T	0.61	.	4.6034	0.12364	0.0:0.5542:0.1599:0.2858	rs831510;rs17855748;rs17856702;rs52822242;rs57642495;rs831510	32;32	Q7Z6J4;F8WEZ2	FGD2_HUMAN;.	H	32	ENSP00000274963:Q32H	ENSP00000274963:Q32H	Q	+	3	2	FGD2	37084615	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.243000	0.18106	0.157000	0.19338	-0.647000	0.03941	CAG	G|0.699;C|0.301	0.301	strong		0.637	FGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040398.2	NM_173558	
IBSP	3381	hgsc.bcm.edu	37	4	88732763	88732763	+	Missense_Mutation	SNP	A	A	G	rs17013181	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:88732763A>G	ENST00000226284.5	+	7	722	c.655A>G	c.(655-657)Agg>Ggg	p.R219G		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	219			R -> G (in dbSNP:rs17013181). {ECO:0000269|PubMed:2404984, ECO:0000269|PubMed:8406493}.		biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		AGAGACCGGAAGGCAGGGCAA	0.537													G|||	1302	0.259984	0.3979	0.2651	5008	,	,		18038	0.2302		0.1928	False		,,,				2504	0.1697				p.R219G		Atlas-SNP	.											.	IBSP	53	.	0			c.A655G						PASS	.	G	GLY/ARG	1590,2816	662.4+/-401.0	293,1004,906	135.0	134.0	134.0		655	3.3	0.0	4	dbSNP_123	134	1890,6710	726.8+/-406.6	208,1474,2618	yes	missense	IBSP	NM_004967.3	125	501,2478,3524	GG,GA,AA		21.9767,36.0872,26.7569	benign	219/318	88732763	3480,9526	2203	4300	6503	SO:0001583	missense	3381	exon7			ACCGGAAGGCAGG		CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"""bone sialoprotein"", ""bone sialoprotein II"""	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.655A>G	4.37:g.88732763A>G	ENSP00000226284:p.Arg219Gly	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_004967		Missense_Mutation	SNP	ENST00000226284.5	37	CCDS3624.1	579	0.2651098901098901	210	0.4268292682926829	97	0.26795580110497236	127	0.22202797202797203	145	0.19129287598944592	G	7.604	0.673451	0.14776	0.360872	0.219767	ENSG00000029559	ENST00000226284	T	0.11930	2.73	4.15	3.27	0.37495	.	1.270430	0.05318	N	0.526129	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48490	-0.9031	9	0.24483	T	0.36	.	7.4088	0.27006	0.2177:0.0:0.7823:0.0	rs17013181;rs52811255;rs57322105;rs17013181	219	P21815	SIAL_HUMAN	G	219	ENSP00000226284:R219G	ENSP00000226284:R219G	R	+	1	2	IBSP	88951787	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	0.404000	0.20999	0.478000	0.27488	-0.186000	0.12905	AGG	A|0.733;G|0.267	0.267	strong		0.537	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2		
XRCC1	7515	hgsc.bcm.edu	37	19	44047550	44047550	+	Silent	SNP	T	T	C	rs3547	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:44047550T>C	ENST00000262887.5	-	17	2443	c.1896A>G	c.(1894-1896)caA>caG	p.Q632Q	XRCC1_ENST00000543982.1_Silent_p.Q601Q			P18887	XRCC1_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 1	632					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|hippocampus development (GO:0021766)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to organic substance (GO:0010033)|single strand break repair (GO:0000012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Prostate(69;0.0153)				TACTTCAGGCTTGCGGCACCA	0.493								Other BER factors					C|||	3559	0.710663	0.674	0.7853	5008	,	,		15005	0.8849		0.5934	False		,,,				2504	0.6483				p.Q632Q		Atlas-SNP	.											.	XRCC1	47	.	0			c.A1896G						PASS	.	C		2878,1528	483.9+/-359.9	933,1012,258	96.0	83.0	87.0		1896	2.7	1.0	19	dbSNP_36	87	5023,3577	518.4+/-379.2	1466,2091,743	no	coding-synonymous	XRCC1	NM_006297.2		2399,3103,1001	CC,CT,TT		41.593,34.68,39.2511		632/634	44047550	7901,5105	2203	4300	6503	SO:0001819	synonymous_variant	7515	exon17			TCAGGCTTGCGGC	M36089	CCDS12624.1	19q13.2	2014-09-17				ENSG00000073050			12828	protein-coding gene	gene with protein product		194360		RCC		2247054	Standard	NM_006297		Approved		uc002owt.2	P18887		ENST00000262887.5:c.1896A>G	19.37:g.44047550T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_006297	Q6IBS4|Q9HCB1	Silent	SNP	ENST00000262887.5	37	CCDS12624.1																																																																																			T|0.344;C|0.656	0.656	strong		0.493	XRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463194.1	NM_006297	
MUC21	394263	hgsc.bcm.edu	37	6	30954729	30954729	+	Missense_Mutation	SNP	G	G	C	rs111834205	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954729G>C	ENST00000376296.3	+	2	1018	c.777G>C	c.(775-777)gaG>gaC	p.E259D	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	259	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAACTCTGAGTCCAGCACGA	0.622																																					p.E259D		Atlas-SNP	.											MUC21,bladder,carcinoma,0,1	MUC21	98	1	0			c.G777C						scavenged	.						143.0	144.0	144.0					6																	30954729		2203	4300	6503	SO:0001583	missense	394263	exon2			CTCTGAGTCCAGC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.777G>C	6.37:g.30954729G>C	ENSP00000365473:p.Glu259Asp	Somatic	120	2	0.0166667		WXS	Illumina HiSeq	Phase_I	115	28	0.243478	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	128	0.05860805860805861	26	0.052845528455284556	42	0.11602209944751381	34	0.05944055944055944	26	0.03430079155672823	G	11.64	1.699361	0.30142	.	.	ENSG00000204544	ENST00000376296	T	0.01787	4.64	4.28	-5.78	0.02362	.	.	.	.	.	T	0.00412	0.0013	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.44726	-0.9309	8	.	.	.	.	6.5913	0.22647	0.2903:0.3922:0.3175:0.0	.	259	Q5SSG8	MUC21_HUMAN	D	259	ENSP00000365473:E259D	.	E	+	3	2	MUC21	31062708	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-2.711000	0.00817	-0.718000	0.04949	-0.348000	0.07805	GAG	G|0.938;C|0.062	0.062	strong		0.622	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
ZCCHC16	340595	hgsc.bcm.edu	37	X	111698440	111698440	+	Missense_Mutation	SNP	G	G	T	rs7474140	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:111698440G>T	ENST00000340433.2	+	1	714	c.484G>T	c.(484-486)Gac>Tac	p.D162Y		NM_001004308.2	NP_001004308.2	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	162			D -> Y (in dbSNP:rs7474140).				nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27						CTCTCAGCAGGACCCTGCTAC	0.443													G|||	314	0.0831788	0.0272	0.0735	3775	,	,		15500	0.001		0.1551	False		,,,				2504	0.0716				p.D162Y		Atlas-SNP	.											.	ZCCHC16	66	.	0			c.G484T						PASS	.	G	TYR/ASP	259,3576		10,211,28,1411,543	75.0	73.0	73.0		484	-0.3	0.0	X	dbSNP_116	73	1474,5254		119,831,405,1478,1467	yes	missense	ZCCHC16	NM_001004308.2	160	129,1042,433,2889,2010	TT,TG,T,GG,G		21.9084,6.7536,16.4063	probably-damaging	162/311	111698440	1733,8830	2203	4300	6503	SO:0001583	missense	340595	exon3			CAGCAGGACCCTG	AK128465	CCDS35369.1	Xq23	2008-05-02			ENSG00000187823	ENSG00000187823		"""Zinc fingers, CCHC domain containing"""	25214	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_001004308		Approved	Mart4, Mar4, FLJ46608	uc004epo.1	Q6ZR62	OTTHUMG00000159706	ENST00000340433.2:c.484G>T	X.37:g.111698440G>T	ENSP00000340590:p.Asp162Tyr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	174	7	0.0402299	NM_001004308	B2RPG1	Missense_Mutation	SNP	ENST00000340433.2	37	CCDS35369.1	162	0.09764918625678119	10	0.02109704641350211	25	0.07183908045977011	0	0.0	73	0.10703812316715543	G	0.013	-1.643386	0.00792	0.067536	0.219084	ENSG00000187823	ENST00000340433	T	0.15952	2.38	3.73	-0.266	0.12942	.	0.533187	0.14888	N	0.292551	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.16802	0.019	B	0.15052	0.012	T	0.40175	-0.9577	9	0.02654	T	1	-2.1091	2.7787	0.05355	0.3851:0.0:0.3731:0.2419	rs7474140;rs52792855;rs56925057;rs7474140	162	Q6ZR62	ZCH16_HUMAN	Y	162	ENSP00000340590:D162Y	ENSP00000340590:D162Y	D	+	1	0	ZCCHC16	111585096	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-0.719000	0.04974	-0.205000	0.10219	0.529000	0.55759	GAC	G|0.866;T|0.134	0.134	strong		0.443	ZCCHC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356964.1	NM_001004308	
GXYLT1	283464	hgsc.bcm.edu	37	12	42481732	42481732	+	Silent	SNP	G	G	A	rs7972986	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:42481732G>A	ENST00000398675.3	-	8	1411	c.1179C>T	c.(1177-1179)gaC>gaT	p.D393D	GXYLT1_ENST00000280876.6_Silent_p.D362D	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	393					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						AACGGATGTTGTCATCTTCAA	0.264													G|||	932	0.186102	0.1498	0.2435	5008	,	,		15660	0.1597		0.1879	False		,,,				2504	0.2198				p.D393D		Atlas-SNP	.											.	GXYLT1	47	.	0			c.C1179T						PASS	.	G	,	561,3005		45,471,1267	52.0	46.0	48.0		1086,1179	0.9	0.3	12	dbSNP_116	48	1433,6685		116,1201,2742	yes	coding-synonymous,coding-synonymous	GXYLT1	NM_001099650.1,NM_173601.1	,	161,1672,4009	AA,AG,GG		17.6521,15.7319,17.0661	,	362/410,393/441	42481732	1994,9690	1783	4059	5842	SO:0001819	synonymous_variant	283464	exon8			GATGTTGTCATCT	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"""Glycosyltransferase family 8 domain containing"""	27482	protein-coding gene	gene with protein product		613321	"""glycosyltransferase 8 domain containing 3"""	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.1179C>T	12.37:g.42481732G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Silent	SNP	ENST00000398675.3	37	CCDS41772.1																																																																																			G|0.820;A|0.180	0.180	strong		0.264	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597	
MTCH2	23788	hgsc.bcm.edu	37	11	47640429	47640429	+	Missense_Mutation	SNP	G	G	C	rs1064608	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:47640429G>C	ENST00000302503.3	-	13	1025	c.868C>G	c.(868-870)Ccc>Gcc	p.P290A	MTCH2_ENST00000534074.1_5'UTR|MTCH2_ENST00000542981.1_Missense_Mutation_p.P142A	NM_014342.3	NP_055157.1	Q9Y6C9	MTCH2_HUMAN	mitochondrial carrier 2	290			P -> A (in dbSNP:rs1064608).		protein localization to mitochondrion (GO:0070585)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)		p.P290A(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11						TTCCCAAAGGGGACCTTCCGG	0.408													G|||	1289	0.257388	0.0454	0.4035	5008	,	,		19522	0.2768		0.3539	False		,,,				2504	0.3211				p.P290A		Atlas-SNP	.											MTCH2,NS,carcinoma,0,1	MTCH2	25	1	1	Substitution - Missense(1)	stomach(1)	c.C868G						PASS	.	G	ALA/PRO	427,3975	207.2+/-228.6	28,371,1802	97.0	104.0	101.0		868	5.1	1.0	11	dbSNP_86	101	3023,5573	466.3+/-366.7	527,1969,1802	yes	missense	MTCH2	NM_014342.3	27	555,2340,3604	CC,CG,GG		35.1675,9.7001,26.5425	probably-damaging	290/304	47640429	3450,9548	2201	4298	6499	SO:0001583	missense	23788	exon13			CAAAGGGGACCTT	AF085361	CCDS7943.1	11p11.2	2013-05-22	2011-05-19		ENSG00000109919	ENSG00000109919		"""Solute carriers"""	17587	protein-coding gene	gene with protein product	"""solute carrier family 25, member 50"""	613221	"""mitochondrial carrier homolog 2 (C. elegans)"""				Standard	NM_014342		Approved	SLC25A50	uc010rho.2	Q9Y6C9	OTTHUMG00000166926	ENST00000302503.3:c.868C>G	11.37:g.47640429G>C	ENSP00000303222:p.Pro290Ala	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_014342	B2R7L8	Missense_Mutation	SNP	ENST00000302503.3	37	CCDS7943.1	618	0.28296703296703296	28	0.056910569105691054	131	0.36187845303867405	189	0.3304195804195804	270	0.3562005277044855	G	21.2	4.119413	0.77323	0.097001	0.351675	ENSG00000109919	ENST00000302503;ENST00000542981	D;T	0.81908	-1.55;-0.55	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.64567	1.98	0.21604	P	0.999620262	D	0.57571	0.98	P	0.60949	0.881	T	0.00003	-1.2590	9	0.66056	D	0.02	.	15.5263	0.75910	0.0:0.0:1.0:0.0	rs1064608;rs1064608	290	Q9Y6C9	MTCH2_HUMAN	A	290;142	ENSP00000303222:P290A;ENSP00000439013:P142A	ENSP00000303222:P290A	P	-	1	0	MTCH2	47597005	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.708000	0.74660	2.387000	0.81309	0.555000	0.69702	CCC	G|0.727;C|0.273	0.273	strong		0.408	MTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391921.2	NM_014342	
CDH2	1000	hgsc.bcm.edu	37	18	25543387	25543387	+	Silent	SNP	G	G	A	rs1041985	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:25543387G>A	ENST00000269141.3	-	15	2871	c.2448C>T	c.(2446-2448)gcC>gcT	p.A816A	CDH2_ENST00000399380.3_Silent_p.A785A|AC015933.2_ENST00000423367.1_RNA	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	816					adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.A816A(1)		NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ACTGGGGCTCGGCGTGGATGG	0.537													G|||	1640	0.327476	0.1498	0.464	5008	,	,		15977	0.4216		0.3419	False		,,,				2504	0.3589				p.A816A		Atlas-SNP	.											CDH2,colon,carcinoma,-2,2	CDH2	194	2	1	Substitution - coding silent(1)	stomach(1)	c.C2448T						PASS	.	G		785,3621	316.9+/-294.8	80,625,1498	90.0	71.0	78.0		2448	-11.7	0.1	18	dbSNP_86	78	2690,5910	432.0+/-357.0	405,1880,2015	no	coding-synonymous	CDH2	NM_001792.3		485,2505,3513	AA,AG,GG		31.2791,17.8166,26.7184		816/907	25543387	3475,9531	2203	4300	6503	SO:0001819	synonymous_variant	1000	exon15			GGGCTCGGCGTGG	S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"""CD molecules"", ""Cadherins / Major cadherins"""	1759	protein-coding gene	gene with protein product	"""N-cadherin"""	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.2448C>T	18.37:g.25543387G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	144	144	1	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Silent	SNP	ENST00000269141.3	37	CCDS11891.1																																																																																			G|0.706;A|0.294	0.294	strong		0.537	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792	
LRPPRC	10128	hgsc.bcm.edu	37	2	44209477	44209477	+	Silent	SNP	C	C	T	rs6741066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:44209477C>T	ENST00000260665.7	-	2	303	c.246G>A	c.(244-246)caG>caA	p.Q82Q	LRPPRC_ENST00000409946.1_Silent_p.Q82Q|LRPPRC_ENST00000409659.1_Silent_p.Q82Q	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	82					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CCCAATCAAACTGATTGGAAA	0.423													T|||	2524	0.503994	0.68	0.5548	5008	,	,		16473	0.0367		0.7416	False		,,,				2504	0.4673				p.Q82Q		Atlas-SNP	.											LRPPRC,colon,carcinoma,0,1	LRPPRC	105	1	0			c.G246A						PASS	.	T		3088,1318	423.4+/-340.1	1083,922,198	59.0	64.0	63.0		246	-11.3	0.0	2	dbSNP_116	63	6331,2267	380.4+/-339.6	2352,1627,320	no	coding-synonymous	LRPPRC	NM_133259.3		3435,2549,518	TT,TC,CC		26.3666,29.9138,27.5684		82/1395	44209477	9419,3585	2203	4299	6502	SO:0001819	synonymous_variant	10128	exon2			ATCAAACTGATTG	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.246G>A	2.37:g.44209477C>T		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	225	225	1	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			C|0.367;T|0.633	0.633	strong		0.423	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
GLI4	2738	hgsc.bcm.edu	37	8	144358381	144358381	+	Missense_Mutation	SNP	G	G	A	rs1056148	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144358381G>A	ENST00000523522.1	+	3	577	c.538G>A	c.(538-540)Gcc>Acc	p.A180T	ZFP41_ENST00000522452.1_3'UTR|GLI4_ENST00000340042.1_Missense_Mutation_p.A180T|GLI4_ENST00000523812.1_3'UTR			P10075	GLI4_HUMAN	GLI family zinc finger 4	180			A -> T (in dbSNP:rs1056148). {ECO:0000269|PubMed:2850480}.		regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(1)|lung(5)	9	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CGCGCGGGGGGCCAAGCCGCA	0.701													G|||	2352	0.469649	0.0749	0.6628	5008	,	,		11535	0.6577		0.4841	False		,,,				2504	0.6575				p.A180T		Atlas-SNP	.											GLI4,NS,carcinoma,0,1	GLI4	28	1	0			c.G538A						PASS	.	G	THR/ALA	549,3695		70,409,1643	6.0	7.0	7.0		538	1.4	0.0	8	dbSNP_86	7	3701,4669		906,1889,1390	yes	missense	GLI4	NM_138465.3	58	976,2298,3033	AA,AG,GG		44.2174,12.9359,33.6927	benign	180/377	144358381	4250,8364	2122	4185	6307	SO:0001583	missense	2738	exon4			CGGGGGGCCAAGC		CCDS6398.1	8q24.3	2013-01-08	2009-03-05		ENSG00000250571	ENSG00000250571		"""Zinc fingers, C2H2-type"""	4320	protein-coding gene	gene with protein product		165280	"""GLI-Kruppel family member GLI4"", ""glioma-associated oncogene family zinc finger 4"""			2850480	Standard	NM_138465		Approved	HKR4, ZNF928	uc003yxx.3	P10075	OTTHUMG00000164952	ENST00000523522.1:c.538G>A	8.37:g.144358381G>A	ENSP00000430987:p.Ala180Thr	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_138465	Q96CK9	Missense_Mutation	SNP	ENST00000523522.1	37	CCDS6398.1	1032	0.4725274725274725	47	0.09552845528455285	226	0.6243093922651933	388	0.6783216783216783	371	0.4894459102902375	G	12.90	2.077678	0.36662	0.129359	0.442174	ENSG00000250571	ENST00000340042;ENST00000523522	T;T	0.07567	3.18;3.18	3.26	1.38	0.22167	.	.	.	.	.	T	0.00012	0.0000	N	0.21097	0.63	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13282	-1.0515	8	0.52906	T	0.07	.	7.0503	0.25069	0.2184:0.0:0.7816:0.0	rs1056148;rs3196763;rs1056148	180	P10075	GLI4_HUMAN	T	180	ENSP00000345024:A180T;ENSP00000430987:A180T	ENSP00000345024:A180T	A	+	1	0	GLI4	144429756	0.000000	0.05858	0.004000	0.12327	0.544000	0.35116	0.141000	0.16076	0.201000	0.20466	0.462000	0.41574	GCC	G|0.531;A|0.469	0.469	strong		0.701	GLI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381128.2		
CILP2	148113	hgsc.bcm.edu	37	19	19656615	19656615	+	Silent	SNP	C	C	T	rs61744761	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19656615C>T	ENST00000291495.5	+	8	3346	c.3261C>T	c.(3259-3261)ggC>ggT	p.G1087G	CILP2_ENST00000586018.1_Silent_p.G1093G	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	1087						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCTCTGACGGCTTCTCCAGAG	0.622													C|||	582	0.116214	0.174	0.1167	5008	,	,		14302	0.0		0.166	False		,,,				2504	0.1063				p.G1087G		Atlas-SNP	.											.	CILP2	84	.	0			c.C3261T						PASS	.	C		761,3643	284.3+/-277.5	57,647,1498	31.0	24.0	26.0		3261	3.5	1.0	19	dbSNP_129	26	1411,7189	252.2+/-278.4	111,1189,3000	no	coding-synonymous	CILP2	NM_153221.2		168,1836,4498	TT,TC,CC		16.407,17.2797,16.7026		1087/1157	19656615	2172,10832	2202	4300	6502	SO:0001819	synonymous_variant	148113	exon8			TGACGGCTTCTCC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.3261C>T	19.37:g.19656615C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	252	118	0.468254	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			C|0.845;T|0.155	0.155	strong		0.622	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
ADAMTS17	170691	hgsc.bcm.edu	37	15	100636586	100636586	+	Silent	SNP	G	G	A	rs4965583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:100636586G>A	ENST00000268070.4	-	15	2217	c.2112C>T	c.(2110-2112)ggC>ggT	p.G704G		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	704	Spacer.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		GGCTGAAGTCGCCCTTCACCA	0.577													g|||	1321	0.263778	0.2504	0.2925	5008	,	,		17908	0.5		0.1262	False		,,,				2504	0.1595				p.G704G		Atlas-SNP	.											.	ADAMTS17	127	.	0			c.C2112T						PASS	.	G		1028,3378	376.8+/-322.2	113,802,1288	110.0	118.0	115.0		2112	-9.5	0.9	15	dbSNP_111	115	1127,7473	231.2+/-265.3	82,963,3255	no	coding-synonymous	ADAMTS17	NM_139057.2		195,1765,4543	AA,AG,GG		13.1047,23.3318,16.5693		704/1096	100636586	2155,10851	2203	4300	6503	SO:0001819	synonymous_variant	170691	exon15			GAAGTCGCCCTTC	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.2112C>T	15.37:g.100636586G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	61	24	0.393443	NM_139057	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	37	CCDS10383.1																																																																																			G|0.801;A|0.199	0.199	strong		0.577	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
MSLN	10232	hgsc.bcm.edu	37	16	816414	816414	+	Missense_Mutation	SNP	G	G	A	rs150147307		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:816414G>A	ENST00000382862.3	+	12	1249	c.1154G>A	c.(1153-1155)cGc>cAc	p.R385H	MSLN_ENST00000545450.2_Missense_Mutation_p.R385H|MSLN_ENST00000563941.1_Missense_Mutation_p.R385H|MSLN_ENST00000566549.1_Missense_Mutation_p.R385H	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	385					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				GAGGACATTCGCAAGTGGAAT	0.567																																					p.R385H		Atlas-SNP	.											.	MSLN	109	.	0			c.G1154A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4380		0,0,2190	88.0	78.0	81.0		1154,1154,1154	-3.5	0.0	16	dbSNP_134	81	1,8573	1.2+/-3.3	0,1,4286	no	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	29,29,29	0,1,6476	AA,AG,GG		0.0117,0.0,0.0077	benign,benign,benign	385/623,385/623,385/631	816414	1,12953	2190	4287	6477	SO:0001583	missense	10232	exon13			ACATTCGCAAGTG	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.1154G>A	16.37:g.816414G>A	ENSP00000372313:p.Arg385His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	153	65	0.424837	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	.	.	.	.	.	.	.	.	.	.	G	0.244	-1.011226	0.02095	0.0	1.17E-4	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.13420	2.59;2.59	4.97	-3.46	0.04767	.	1.820510	0.02850	N	0.129024	T	0.07279	0.0184	N	0.12569	0.235	0.09310	N	1	B;B;B;B	0.28350	0.029;0.037;0.208;0.029	B;B;B;B	0.16289	0.005;0.014;0.015;0.005	T	0.30679	-0.9970	10	0.13470	T	0.59	-0.7879	11.3272	0.49456	0.3512:0.0:0.6488:0.0	.	384;385;385;385	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	H	385	ENSP00000442965:R385H;ENSP00000372313:R385H	ENSP00000372313:R385H	R	+	2	0	MSLN	756415	0.000000	0.05858	0.043000	0.18650	0.104000	0.19210	-1.290000	0.02777	-0.567000	0.06046	0.297000	0.19635	CGC	G|1.000;A|0.000	0.000	weak		0.567	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
ZGLP1	100125288	hgsc.bcm.edu	37	19	10415781	10415781	+	Missense_Mutation	SNP	T	T	C	rs2291473	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:10415781T>C	ENST00000403903.3	-	4	2000	c.802A>G	c.(802-804)Att>Gtt	p.I268V	ZGLP1_ENST00000403352.1_Missense_Mutation_p.I184V	NM_001103167.1	NP_001096637.1	P0C6A0	ZGLP1_HUMAN	zinc finger, GATA-like protein 1	268					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oocyte development (GO:0048599)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|ovary(1)	6						CCTTCCTGAATGGGGTCCAGG	0.567													T|||	560	0.111821	0.0038	0.0591	5008	,	,		18673	0.1151		0.1332	False		,,,				2504	0.2699				p.I268V		Atlas-SNP	.											.	ZGLP1	18	.	0			c.A802G						PASS	.	T	VAL/ILE	107,3981		3,101,1940	66.0	70.0	68.0		802	-9.2	0.0	19	dbSNP_100	68	1038,7378		63,912,3233	yes	missense	ZGLP1	NM_001103167.1	29	66,1013,5173	CC,CT,TT		12.3337,2.6174,9.1571	benign	268/272	10415781	1145,11359	2044	4208	6252	SO:0001583	missense	100125288	exon4			CCTGAATGGGGTC	AK096830	CCDS45959.1	19p13.2	2013-01-25			ENSG00000220201	ENSG00000220201		"""GATA zinc finger domain containing"""	37245	protein-coding gene	gene with protein product	"""GATA like protein 1"", ""GATA zinc finger domain containing 3"""	611639				16982049	Standard	NM_001103167		Approved	GLP1, GLP-1, GATAD3	uc002mnw.4	P0C6A0	OTTHUMG00000152114	ENST00000403903.3:c.802A>G	19.37:g.10415781T>C	ENSP00000384434:p.Ile268Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	165	164	0.993939	NM_001103167		Missense_Mutation	SNP	ENST00000403903.3	37	CCDS45959.1	204	0.09340659340659341	3	0.006097560975609756	25	0.06906077348066299	68	0.11888111888111888	108	0.1424802110817942	T	0.197	-1.047724	0.01981	0.026174	0.123337	ENSG00000220201	ENST00000403903;ENST00000403352	D;D	0.97924	-4.61;-4.58	4.62	-9.24	0.00669	.	.	.	.	.	T	0.05273	0.0140	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.69049	-0.5248	8	0.02654	T	1	-0.0021	5.6537	0.17631	0.2028:0.5166:0.103:0.1776	rs2291473;rs61421282;rs2291473	268	P0C6A0	ZGLP1_HUMAN	V	268;184	ENSP00000384434:I268V;ENSP00000385403:I184V	ENSP00000385403:I184V	I	-	1	0	ZGLP1	10276781	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-4.119000	0.00291	-2.727000	0.00386	-0.337000	0.08149	ATT	T|0.890;C|0.110	0.110	strong		0.567	ZGLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325278.1	NM_001103167	
PAX9	5083	hgsc.bcm.edu	37	14	37135752	37135752	+	Silent	SNP	C	C	T	rs12881240	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:37135752C>T	ENST00000361487.6	+	3	942	c.717C>T	c.(715-717)caC>caT	p.H239H	PAX9_ENST00000557107.1_3'UTR|PAX9_ENST00000402703.2_Silent_p.H239H|PAX9_ENST00000554201.1_Silent_p.H52H			P55771	PAX9_HUMAN	paired box 9	239					cellular response to growth factor stimulus (GO:0071363)|endoderm development (GO:0007492)|face morphogenesis (GO:0060325)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|regulation of odontogenesis (GO:0042481)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(3)	12	Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.218)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.00998)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0181)		CCGCCCCGCACGCGGTGAACG	0.687													C|||	802	0.160144	0.0129	0.1196	5008	,	,		13934	0.3155		0.2167	False		,,,				2504	0.1697				p.H239H		Atlas-SNP	.											PAX9,NS,carcinoma,0,1	PAX9	34	1	0			c.C717T						PASS	.	C		209,4153		6,197,1978	20.0	14.0	16.0		717	3.5	1.0	14	dbSNP_121	16	1756,6802		203,1350,2726	no	coding-synonymous	PAX9	NM_006194.3		209,1547,4704	TT,TC,CC		20.5188,4.7914,15.209		239/342	37135752	1965,10955	2181	4279	6460	SO:0001819	synonymous_variant	5083	exon4			CCCGCACGCGGTG	AJ238381	CCDS9662.1	14q13.3	2007-07-12	2007-07-12		ENSG00000198807	ENSG00000198807		"""Paired boxes"""	8623	protein-coding gene	gene with protein product		167416	"""paired box gene 9"""			7981748	Standard	NM_006194		Approved		uc001wty.4	P55771	OTTHUMG00000140251	ENST00000361487.6:c.717C>T	14.37:g.37135752C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_006194	Q99582|Q9UQR4	Silent	SNP	ENST00000361487.6	37	CCDS9662.1																																																																																			C|0.841;T|0.159	0.159	strong		0.687	PAX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276733.2		
SDK1	221935	hgsc.bcm.edu	37	7	4189075	4189075	+	Silent	SNP	G	G	C	rs659182	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:4189075G>C	ENST00000404826.2	+	30	4744	c.4605G>C	c.(4603-4605)gcG>gcC	p.A1535A	SDK1_ENST00000389531.3_Silent_p.A1535A	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1535	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GCCATGAGGCGACAGCATGCG	0.662													C|||	3939	0.786542	0.9592	0.7738	5008	,	,		17088	0.7817		0.6918	False		,,,				2504	0.6646				p.A1535A		Atlas-SNP	.											.	SDK1	361	.	0			c.G4605C						PASS	.	C		4086,320		1894,298,11	40.0	33.0	35.0		4605	4.2	1.0	7	dbSNP_83	35	5967,2633		2058,1851,391	no	coding-synonymous	SDK1	NM_152744.3		3952,2149,402	CC,CG,GG		30.6163,7.2628,22.7049		1535/2214	4189075	10053,2953	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon30			TGAGGCGACAGCA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4605G>C	7.37:g.4189075G>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	92	90	0.978261	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			G|0.219;C|0.781	0.781	strong		0.662	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
SLC5A9	200010	hgsc.bcm.edu	37	1	48697751	48697751	+	Silent	SNP	C	C	T	rs61997212	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:48697751C>T	ENST00000438567.2	+	7	877	c.825C>T	c.(823-825)agC>agT	p.S275S	RP5-1024N4.4_ENST00000606809.1_RNA|SLC5A9_ENST00000420136.2_Intron|SLC5A9_ENST00000533824.1_Silent_p.S296S|SLC5A9_ENST00000236495.5_Silent_p.S300S	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	275					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						ACCCTGTGAGCGGGGACATCC	0.612													C|||	330	0.0658946	0.0174	0.0879	5008	,	,		20909	0.0		0.17	False		,,,				2504	0.0767				p.S300S		Atlas-SNP	.											.	SLC5A9	82	.	0			c.C900T						PASS	.	C	,	163,4243	109.1+/-147.4	2,159,2042	99.0	89.0	92.0		825,900	-3.0	0.7	1	dbSNP_129	92	1679,6921	307.4+/-308.4	149,1381,2770	no	coding-synonymous,coding-synonymous	SLC5A9	NM_001011547.2,NM_001135181.1	,	151,1540,4812	TT,TC,CC		19.5233,3.6995,14.1627	,	275/682,300/707	48697751	1842,11164	2203	4300	6503	SO:0001819	synonymous_variant	200010	exon8			TGTGAGCGGGGAC	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.825C>T	1.37:g.48697751C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	191	75	0.39267	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Silent	SNP	ENST00000438567.2	37	CCDS30709.2																																																																																			C|0.877;T|0.123	0.123	strong		0.612	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
TRIM58	25893	hgsc.bcm.edu	37	1	248028219	248028219	+	Silent	SNP	G	G	A	rs946696	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248028219G>A	ENST00000366481.3	+	3	777	c.729G>A	c.(727-729)ccG>ccA	p.P243P		NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	243						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GCCAGCGCCCGGCCCTGGGTC	0.617													G|||	2082	0.415735	0.0499	0.4409	5008	,	,		15781	0.5744		0.5716	False		,,,				2504	0.5685				p.P243P		Atlas-SNP	.											TRIM58,NS,carcinoma,+1,1	TRIM58	143	1	0			c.G729A						PASS	.	G		577,3779		65,447,1666	7.0	12.0	10.0		729	-3.4	0.0	1	dbSNP_86	10	4781,3771		1387,2007,882	no	coding-synonymous	TRIM58	NM_015431.3		1452,2454,2548	AA,AG,GG		44.0949,13.2461,41.5091		243/487	248028219	5358,7550	2178	4276	6454	SO:0001819	synonymous_variant	25893	exon3			GCGCCCGGCCCTG	AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	24150	protein-coding gene	gene with protein product			"""tripartite motif-containing 58"""				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.729G>A	1.37:g.248028219G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	59	56	0.949153	NM_015431	Q6B0H9	Silent	SNP	ENST00000366481.3	37	CCDS1636.1																																																																																			G|0.573;A|0.427	0.427	strong		0.617	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431	
C6orf165	154313	hgsc.bcm.edu	37	6	88125542	88125542	+	Missense_Mutation	SNP	G	G	A	rs61731441	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:88125542G>A	ENST00000507897.1	+	5	505	c.422G>A	c.(421-423)cGc>cAc	p.R141H	C6ORF165_ENST00000369562.4_Missense_Mutation_p.R141H			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	141										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		GTGTTACTCCGCTCTGGCCTT	0.398													G|||	534	0.106629	0.1051	0.0706	5008	,	,		15940	0.1042		0.1203	False		,,,				2504	0.1227				p.R141H		Atlas-SNP	.											.	C6orf165	116	.	0			c.G422A						PASS	.	G	HIS/ARG	512,3894	235.2+/-247.8	25,462,1716	103.0	105.0	104.0		422	5.6	1.0	6	dbSNP_129	104	943,7657	208.2+/-249.7	47,849,3404	yes	missense	C6orf165	NM_001031743.2	29	72,1311,5120	AA,AG,GG		10.9651,11.6205,11.1871	probably-damaging	141/623	88125542	1455,11551	2203	4300	6503	SO:0001583	missense	154313	exon5			TACTCCGCTCTGG	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.422G>A	6.37:g.88125542G>A	ENSP00000426769:p.Arg141His	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	117	65	0.555556	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	223	0.1021062271062271	48	0.0975609756097561	29	0.08011049723756906	56	0.0979020979020979	90	0.11873350923482849	G	15.83	2.949349	0.53186	0.116205	0.109651	ENSG00000213204	ENST00000369562;ENST00000480123	T;T	0.29917	1.55;1.55	5.6	5.6	0.85130	.	0.181219	0.49305	D	0.000155	T	0.37461	0.1004	L	0.52126	1.63	0.33467	P	0.414242	D;D	0.89917	1.0;1.0	D;D	0.66497	0.912;0.944	T	0.02512	-1.1148	9	0.15952	T	0.53	.	19.2026	0.93717	0.0:0.0:1.0:0.0	rs61731441	141;141	Q8IYR0;E1P509	CF165_HUMAN;.	H	141	ENSP00000358575:R141H;ENSP00000422494:R141H	ENSP00000358575:R141H	R	+	2	0	C6orf165	88182261	0.951000	0.32395	0.998000	0.56505	0.083000	0.17756	3.124000	0.50461	2.640000	0.89533	0.585000	0.79938	CGC	G|0.892;A|0.108	0.108	strong		0.398	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823	
AGL	178	hgsc.bcm.edu	37	1	100358103	100358103	+	Missense_Mutation	SNP	C	C	T	rs3753494	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:100358103C>T	ENST00000294724.4	+	24	3677	c.3199C>T	c.(3199-3201)Cct>Tct	p.P1067S	AGL_ENST00000361302.3_Missense_Mutation_p.P1051S|AGL_ENST00000361915.3_Missense_Mutation_p.P1067S|AGL_ENST00000370163.3_Missense_Mutation_p.P1067S|AGL_ENST00000370161.2_Missense_Mutation_p.P1051S|AGL_ENST00000370165.3_Missense_Mutation_p.P1067S|AGL_ENST00000361522.4_Missense_Mutation_p.P1050S	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	1067			P -> S (in dbSNP:rs3753494).		carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		AATGGATGTACCTTATAGGTT	0.378													C|||	554	0.110623	0.1203	0.0951	5008	,	,		15854	0.0278		0.1551	False		,,,				2504	0.1483				p.P1067S		Atlas-SNP	.											.	AGL	137	.	0			c.C3199T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO	557,3849	249.0+/-256.6	36,485,1682	99.0	94.0	96.0		3199,3199,3199,3199,3148,3151	5.2	0.4	1	dbSNP_107	96	1257,7343	251.5+/-278.0	96,1065,3139	yes	missense,missense,missense,missense,missense,missense	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000645.2,NM_000646.2	74,74,74,74,74,74	132,1550,4821	TT,TC,CC		14.6163,12.6419,13.9474	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1067/1533,1067/1533,1067/1533,1067/1533,1050/1516,1051/1517	100358103	1814,11192	2203	4300	6503	SO:0001583	missense	178	exon24			GATGTACCTTATA	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.3199C>T	1.37:g.100358103C>T	ENSP00000294724:p.Pro1067Ser	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	237	0.10851648351648352	69	0.1402439024390244	43	0.11878453038674033	13	0.022727272727272728	112	0.14775725593667546	C	13.10	2.137783	0.37728	0.126419	0.146163	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	T;T;T;T;T;T;T	0.74947	-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.89	5.2	5.2	0.72013	.	0.111526	0.64402	D	0.000006	T	0.66703	0.2816	M	0.67953	2.075	0.09310	P	0.999999999670201	B;B;B	0.26318	0.12;0.12;0.146	B;B;B	0.29353	0.047;0.047;0.101	T	0.66460	-0.5918	9	0.37606	T	0.19	.	19.1022	0.93277	0.0:1.0:0.0:0.0	rs3753494;rs17449932;rs52793848;rs56862711;rs3753494	1050;1051;1067	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	S	1067;1067;1067;1067;1051;1051;1050	ENSP00000355106:P1067S;ENSP00000359184:P1067S;ENSP00000359182:P1067S;ENSP00000294724:P1067S;ENSP00000354971:P1051S;ENSP00000359180:P1051S;ENSP00000354635:P1050S	ENSP00000294724:P1067S	P	+	1	0	AGL	100130691	1.000000	0.71417	0.412000	0.26496	0.008000	0.06430	7.230000	0.78097	2.553000	0.86117	0.573000	0.79308	CCT	C|0.869;T|0.131	0.131	strong		0.378	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
OR2G3	81469	hgsc.bcm.edu	37	1	247769592	247769592	+	Silent	SNP	C	C	T	rs1151683	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:247769592C>T	ENST00000320002.2	+	1	737	c.705C>T	c.(703-705)caC>caT	p.H235H	RP11-978I15.10_ENST00000435333.1_RNA|RNU6-691P_ENST00000516585.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(31)|skin(5)	50	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			AGGCAAGGCACAAAGCCTTCA	0.473													C|||	1552	0.309904	0.3048	0.3689	5008	,	,		21641	0.3413		0.2217	False		,,,				2504	0.3333				p.H235H		Atlas-SNP	.											.	OR2G3	108	.	0			c.C705T						PASS	.	C		1342,3064	450.0+/-349.2	219,904,1080	174.0	152.0	160.0		705	-0.7	0.2	1	dbSNP_87	160	1998,6602	350.2+/-327.8	231,1536,2533	no	coding-synonymous	OR2G3	NM_001001914.1		450,2440,3613	TT,TC,CC		23.2326,30.4585,25.6805		235/310	247769592	3340,9666	2203	4300	6503	SO:0001819	synonymous_variant	81469	exon1			AAGGCACAAAGCC	BK004417	CCDS31093.1	1q44	2012-08-09			ENSG00000177476	ENSG00000177476		"""GPCR / Class A : Olfactory receptors"""	15008	protein-coding gene	gene with protein product							Standard	NM_001001914		Approved		uc010pyz.2	Q8NGZ4	OTTHUMG00000040576	ENST00000320002.2:c.705C>T	1.37:g.247769592C>T		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	339	180	0.530973	NM_001001914	B2RN64|Q5JQT1|Q6IF45	Silent	SNP	ENST00000320002.2	37	CCDS31093.1																																																																																			C|0.736;T|0.264	0.264	strong		0.473	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1		
MLLT4	4301	hgsc.bcm.edu	37	6	168315978	168315978	+	Silent	SNP	G	G	C	rs3213590	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168315978G>C	ENST00000447894.2	+	18	2409	c.2409G>C	c.(2407-2409)gtG>gtC	p.V803V	MLLT4_ENST00000366806.2_Silent_p.V803V|MLLT4_ENST00000400822.3_Silent_p.V802V|MLLT4_ENST00000392108.3_Silent_p.V803V|MLLT4_ENST00000392112.1_Silent_p.V787V|MLLT4_ENST00000351017.4_Silent_p.V810V|MLLT4_ENST00000344191.4_Silent_p.V803V			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	803	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		ATAGATTGGTGACCGACCCAG	0.547			T	MLL	AL								G|||	946	0.188898	0.2103	0.2104	5008	,	,		19363	0.1954		0.0775	False		,,,				2504	0.2526				p.V803V		Atlas-SNP	.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	.	MLLT4	351	.	0			c.G2409C						PASS	.	G	,	723,3683	300.1+/-286.2	51,621,1531	122.0	96.0	105.0		2409,2361	-1.4	0.7	6	dbSNP_106	105	678,7922	170.7+/-221.8	26,626,3648	no	coding-synonymous,coding-synonymous	MLLT4	NM_001040000.2,NM_001207008.1	,	77,1247,5179	CC,CG,GG		7.8837,16.4094,10.772	,	803/1652,787/1744	168315978	1401,11605	2203	4300	6503	SO:0001819	synonymous_variant	4301	exon18			ATTGGTGACCGAC	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.2409G>C	6.37:g.168315978G>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	183	83	0.453552	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				G|0.880;C|0.120	0.120	strong		0.547	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
MFHAS1	9258	hgsc.bcm.edu	37	8	8748058	8748058	+	Silent	SNP	C	C	T	rs146502253	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:8748058C>T	ENST00000276282.6	-	1	3097	c.2511G>A	c.(2509-2511)aaG>aaA	p.K837K		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	837										endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		AAGGCTTGCCCTTGGGTTTAT	0.537													C|||	3	0.000599042	0.0	0.0	5008	,	,		18898	0.0		0.002	False		,,,				2504	0.001				p.K837K	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.G2511A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	73.0	72.0	72.0		2511	4.1	1.0	8	dbSNP_134	72	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	MFHAS1	NM_004225.2		0,16,6487	TT,TC,CC		0.1628,0.0454,0.123		837/1053	8748058	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			CTTGCCCTTGGGT	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.2511G>A	8.37:g.8748058C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			C|0.998;T|0.002	0.002	strong		0.537	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
COL25A1	84570	hgsc.bcm.edu	37	4	109863370	109863370	+	Missense_Mutation	SNP	C	C	T	rs17531474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:109863370C>T	ENST00000399127.1	-	8	894	c.547G>A	c.(547-549)Gtc>Atc	p.V183I	COL25A1_ENST00000399132.1_Intron|COL25A1_ENST00000399126.1_Intron	NM_001256074.1	NP_001243003.1			collagen, type XXV, alpha 1											NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		CAAACCTTGACGGTGAGGATC	0.517													C|||	240	0.0479233	0.0144	0.1153	5008	,	,		19844	0.002		0.1113	False		,,,				2504	0.0276				p.V183I		Atlas-SNP	.											.	COL25A1	178	.	0			c.G547A						PASS	.																																			SO:0001583	missense	84570	exon7			CCTTGACGGTGAG	AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"""Collagens"""	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399127.1:c.547G>A	4.37:g.109863370C>T	ENSP00000382078:p.Val183Ile	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	162	93	0.574074	NM_001256074		Missense_Mutation	SNP	ENST00000399127.1	37	CCDS58922.1	132	0.06043956043956044	4	0.008130081300813009	45	0.12430939226519337	1	0.0017482517482517483	82	0.10817941952506596	C	16.50	3.140536	0.56936	.	.	ENSG00000188517	ENST00000399127	D	0.90444	-2.67	5.54	5.54	0.83059	.	.	.	.	.	T	0.29190	0.0726	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.64952	-0.6286	4	.	.	.	.	19.9261	0.97102	0.0:1.0:0.0:0.0	rs17531474;rs61271252;rs17531474	.	.	.	I	183	ENSP00000382078:V183I	.	V	-	1	0	COL25A1	110082819	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.442000	0.80503	2.778000	0.95560	0.650000	0.86243	GTC	C|0.939;T|0.061	0.061	strong		0.517	COL25A1-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000315940.1	NM_032518	
PCSK4	54760	hgsc.bcm.edu	37	19	1487195	1487195	+	Missense_Mutation	SNP	G	G	A	rs36123574	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1487195G>A	ENST00000300954.5	-	7	861	c.800C>T	c.(799-801)aCg>aTg	p.T267M	CTB-25B13.6_ENST00000585643.1_RNA|PCSK4_ENST00000587784.1_5'Flank	NM_017573.3	NP_060043.2			proprotein convertase subtilisin/kexin type 4											cervix(2)|endometrium(2)|kidney(1)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCGTCCACCGTGCGGCCGTC	0.697													G|||	89	0.0177716	0.0159	0.0144	5008	,	,		14129	0.0		0.0477	False		,,,				2504	0.0102				p.T267M		Atlas-SNP	.											.	PCSK4	44	.	0			c.C800T						PASS	.	G	MET/THR	87,4313		1,85,2114	20.0	21.0	21.0		800	2.5	1.0	19	dbSNP_126	21	416,8178		9,398,3890	yes	missense	PCSK4	NM_017573.3	81	10,483,6004	AA,AG,GG		4.8406,1.9773,3.871	probably-damaging	267/756	1487195	503,12491	2200	4297	6497	SO:0001583	missense	54760	exon7			TCCACCGTGCGGC	AK057235	CCDS12069.2	19p13.3	2008-02-05			ENSG00000115257	ENSG00000115257			8746	protein-coding gene	gene with protein product		600487				7782070	Standard	XM_005259586		Approved	PC4, SPC5, DKFZp434B217, MGC34749	uc002ltb.1	Q6UW60	OTTHUMG00000128541	ENST00000300954.5:c.800C>T	19.37:g.1487195G>A	ENSP00000300954:p.Thr267Met	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	39	29	0.74359	NM_017573		Missense_Mutation	SNP	ENST00000300954.5	37	CCDS12069.2	47	0.02152014652014652	6	0.012195121951219513	3	0.008287292817679558	0	0.0	38	0.05013192612137203	G	16.77	3.213691	0.58452	0.019773	0.048406	ENSG00000115257	ENST00000300954;ENST00000441747	D	0.81821	-1.54	3.63	2.55	0.30701	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.151480	0.30201	U	0.010164	T	0.50188	0.1601	M	0.84773	2.715	0.45676	D	0.998594	D;D	0.59357	0.985;0.977	P;P	0.47915	0.561;0.448	T	0.74383	-0.3683	10	0.87932	D	0	.	9.4115	0.38494	0.1123:0.0:0.8877:0.0	rs36123574	267;79	Q6UW60;B3KQ28	PCSK4_HUMAN;.	M	267;79	ENSP00000300954:T267M	ENSP00000300954:T267M	T	-	2	0	PCSK4	1438195	1.000000	0.71417	0.996000	0.52242	0.946000	0.59487	5.179000	0.65043	1.742000	0.51746	0.491000	0.48974	ACG	G|0.968;A|0.032	0.032	strong		0.697	PCSK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449703.1	NM_017573	
EXOC4	60412	hgsc.bcm.edu	37	7	133692514	133692514	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:133692514T>G	ENST00000253861.4	+	17	2642	c.2613T>G	c.(2611-2613)tgT>tgG	p.C871W	EXOC4_ENST00000541309.1_Missense_Mutation_p.C159W|EXOC4_ENST00000545148.1_Missense_Mutation_p.C481W|EXOC4_ENST00000539845.1_Missense_Mutation_p.C770W	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	871					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				AGAAAATGTGTAGGAACATTT	0.502																																					p.C871W		Atlas-SNP	.											.	EXOC4	118	.	0			c.T2613G						PASS	.						86.0	72.0	77.0					7																	133692514		2203	4300	6503	SO:0001583	missense	60412	exon17			AATGTGTAGGAAC	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2613T>G	7.37:g.133692514T>G	ENSP00000253861:p.Cys871Trp	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	T	18.38	3.610461	0.66558	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.45	-4.48	0.03515	.	0.000000	0.85682	D	0.000000	T	0.79782	0.4505	M	0.82716	2.605	0.80722	D	1	D;D;D	0.89917	0.996;1.0;1.0	P;D;D	0.80764	0.855;0.994;0.987	T	0.81232	-0.1026	9	0.48119	T	0.1	.	17.5564	0.87890	0.0:0.6695:0.0:0.3305	.	403;481;871	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	W	871;490;770;481;159	.	ENSP00000253861:C871W	C	+	3	2	EXOC4	133343054	0.920000	0.31207	0.962000	0.40283	0.983000	0.72400	0.028000	0.13644	-0.786000	0.04516	-0.353000	0.07706	TGT	.	.	none		0.502	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
SSFA2	6744	hgsc.bcm.edu	37	2	182780307	182780307	+	Missense_Mutation	SNP	G	G	A	rs75716247	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:182780307G>A	ENST00000431877.2	+	11	2119	c.1940G>A	c.(1939-1941)gGt>gAt	p.G647D	SSFA2_ENST00000409001.1_Missense_Mutation_p.G647D|SSFA2_ENST00000428267.2_Missense_Mutation_p.G494D|SSFA2_ENST00000409136.1_Missense_Mutation_p.G156D|SSFA2_ENST00000320370.7_Missense_Mutation_p.G647D	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	647						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			AGTGATGTGGGTAAAAGCAGT	0.398													A|||	423	0.0844649	0.1241	0.0403	5008	,	,		23194	0.0843		0.0348	False		,,,				2504	0.1135				p.G647D		Atlas-SNP	.											.	SSFA2	130	.	0			c.G1940A						PASS	.	A	ASP/GLY,ASP/GLY	527,3879	775.2+/-414.1	31,465,1707	95.0	87.0	90.0		1940,1940	5.6	1.0	2	dbSNP_131	90	204,8396	809.3+/-407.2	3,198,4099	yes	missense,missense	SSFA2	NM_001130445.1,NM_006751.5	94,94	34,663,5806	AA,AG,GG		2.3721,11.961,5.6205	benign,benign	647/1260,647/1257	182780307	731,12275	2203	4300	6503	SO:0001583	missense	6744	exon11			ATGTGGGTAAAAG	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"""cleavage signal-1 protein"", ""KRAS-induced actin-interacting protein"", ""sperm associated antigen 13"""	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.1940G>A	2.37:g.182780307G>A	ENSP00000388731:p.Gly647Asp	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	171	77	0.450292	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	160	0.07326007326007326	60	0.12195121951219512	15	0.04143646408839779	61	0.10664335664335664	24	0.0316622691292876	A	3.925	-0.017296	0.07681	0.11961	0.023721	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136	T;T;T;T;T	0.11063	3.04;2.81;3.05;3.03;2.88	5.56	5.56	0.83823	.	0.311692	0.34879	N	0.003611	T	0.00039	0.0001	N	0.00104	-2.125	0.51012	P	9.999999999998899E-5	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.31752	-0.9932	9	0.02654	T	1	-8.6969	11.3486	0.49575	0.9281:0.0:0.0719:0.0	.	494;156;647;647;647	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	D	647;647;647;494;156	ENSP00000388731:G647D;ENSP00000314669:G647D;ENSP00000387319:G647D;ENSP00000409867:G494D;ENSP00000386916:G156D	ENSP00000314669:G647D	G	+	2	0	SSFA2	182488552	0.998000	0.40836	0.987000	0.45799	0.908000	0.53690	3.857000	0.55972	0.948000	0.37687	-0.381000	0.06696	GGT	G|0.938;A|0.062	0.062	strong		0.398	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751	
C10orf62	414157	hgsc.bcm.edu	37	10	99350128	99350128	+	Silent	SNP	A	A	G	rs7093643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:99350128A>G	ENST00000370640.3	+	1	679	c.474A>G	c.(472-474)ctA>ctG	p.L158L	PI4K2A_ENST00000370649.3_Intron|PI4K2A_ENST00000555577.1_Intron|HOGA1_ENST00000370646.4_Intron|HOGA1_ENST00000370647.4_Intron	NM_001009997.2	NP_001009997.2	Q5T681	CJ062_HUMAN	chromosome 10 open reading frame 62	158										endometrium(2)|kidney(1)|lung(1)	4		Colorectal(252;0.162)		Epithelial(162;9.58e-11)|all cancers(201;8.62e-09)		CAGGTCACCTAGAGTCCAAGG	0.587													G|||	1392	0.277955	0.3548	0.2968	5008	,	,		20226	0.1369		0.3091	False		,,,				2504	0.274				p.L158L		Atlas-SNP	.											C10orf62,colon,carcinoma,0,1	C10orf62	14	1	0			c.A474G						PASS	.	G	,,	1611,2795	663.3+/-401.2	295,1021,887	75.0	74.0	75.0		474,,	2.0	0.9	10	dbSNP_116	75	2716,5884	681.7+/-403.7	422,1872,2006	no	coding-synonymous,intron,intron	HOGA1,C10orf62	NM_001009997.2,NM_001134670.1,NM_138413.3	,,	717,2893,2893	GG,GA,AA		31.5814,36.5638,33.2693	,,	158/224,,	99350128	4327,8679	2203	4300	6503	SO:0001819	synonymous_variant	414157	exon1			TCACCTAGAGTCC		CCDS31261.1	10q24.2	2012-05-31			ENSG00000203942	ENSG00000203942			23294	protein-coding gene	gene with protein product							Standard	NM_001009997		Approved	bA548K23.1	uc001koa.3	Q5T681	OTTHUMG00000018858	ENST00000370640.3:c.474A>G	10.37:g.99350128A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	27	23	0.851852	NM_001009997	Q49A70|Q8N3Y6	Silent	SNP	ENST00000370640.3	37	CCDS31261.1																																																																																			A|0.704;G|0.296	0.296	strong		0.587	C10orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049723.1	NM_001009997	
PRDM2	7799	hgsc.bcm.edu	37	1	14105639	14105639	+	Missense_Mutation	SNP	G	G	A	rs17350795	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14105639G>A	ENST00000235372.7	+	8	2205	c.1349G>A	c.(1348-1350)aGt>aAt	p.S450N	PRDM2_ENST00000343137.4_Missense_Mutation_p.S249N|PRDM2_ENST00000311066.5_Missense_Mutation_p.S450N|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.S249N	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	450			S -> N (in dbSNP:rs17350795).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		AGTCCTCCCAGTCTTGGGCCA	0.458													A|||	198	0.0395367	0.0083	0.0	5008	,	,		19234	0.0218		0.0169	False		,,,				2504	0.1513				p.S450N		Atlas-SNP	.											.	PRDM2	147	.	0			c.G1349A						PASS	.	A	ASN/SER,,ASN/SER,ASN/SER	19,4387	814.6+/-416.2	0,19,2184	41.0	40.0	41.0		746,,1349,1349	-10.7	0.0	1	dbSNP_123	41	175,8425	801.1+/-407.4	2,171,4127	yes	missense,intron,missense,missense	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	46,,46,46	2,190,6311	AA,AG,GG		2.0349,0.4312,1.4916	benign,,benign,benign	249/1482,,450/1719,450/1683	14105639	194,12812	2203	4300	6503	SO:0001583	missense	7799	exon8			CTCCCAGTCTTGG	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.1349G>A	1.37:g.14105639G>A	ENSP00000235372:p.Ser450Asn	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	136	68	0.5	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	25	0.011446886446886446	3	0.006097560975609756	1	0.0027624309392265192	9	0.015734265734265736	12	0.0158311345646438	A	0.517	-0.864002	0.02590	0.004312	0.020349	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.01613	4.86;4.73;4.74;4.74	5.48	-10.7	0.00240	.	1.292300	0.04843	N	0.440781	T	0.00440	0.0014	N	0.08118	0	0.09310	N	1	B;B;B;B	0.20459	0.026;0.0;0.026;0.045	B;B;B;B	0.18871	0.01;0.0;0.01;0.023	T	0.45308	-0.9270	10	0.13470	T	0.59	.	5.3858	0.16218	0.2912:0.2222:0.4128:0.0738	rs17350795;rs52805087;rs17350795	450;308;450;450	A8MW16;Q5THJ0;Q13029;Q13029-2	.;.;PRDM2_HUMAN;.	N	450;450;450;249;249	ENSP00000235372:S450N;ENSP00000312352:S450N;ENSP00000411103:S249N;ENSP00000341621:S249N	ENSP00000235372:S450N	S	+	2	0	PRDM2	13978226	0.000000	0.05858	0.000000	0.03702	0.346000	0.29079	-1.064000	0.03461	-2.744000	0.00378	-2.680000	0.00142	AGT	G|0.981;A|0.019	0.019	strong		0.458	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
TYRP1	7306	hgsc.bcm.edu	37	9	12698471	12698471	+	Silent	SNP	T	T	C	rs35866166	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:12698471T>C	ENST00000388918.5	+	4	858	c.729T>C	c.(727-729)tcT>tcC	p.S243S	TYRP1_ENST00000381136.2_Intron|TYRP1_ENST00000381137.2_Intron|RP11-3L8.3_ENST00000417638.1_RNA	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	243					acetoacetic acid metabolic process (GO:0043438)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen (GO:0016716)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|stomach(1)	22		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		AAGAGCCTTCTTTCTCCCTTC	0.403									Oculocutaneous Albinism				T|||	84	0.0167732	0.003	0.0202	5008	,	,		17979	0.0		0.0567	False		,,,				2504	0.0092				p.S243S		Atlas-SNP	.											.	TYRP1	60	.	0			c.T729C						PASS	.	T		72,4334	64.7+/-102.0	0,72,2131	116.0	110.0	112.0		729	2.4	1.0	9	dbSNP_126	112	527,8073	148.0+/-203.3	20,487,3793	no	coding-synonymous	TYRP1	NM_000550.2		20,559,5924	CC,CT,TT		6.1279,1.6341,4.6056		243/538	12698471	599,12407	2203	4300	6503	SO:0001819	synonymous_variant	7306	exon4	Familial Cancer Database		GCCTTCTTTCTCC	L33830	CCDS34990.1	9p23	2013-01-08			ENSG00000107165	ENSG00000107165			12450	protein-coding gene	gene with protein product		115501		TYRP, CAS2		9434945	Standard	NM_000550		Approved	GP75, CATB, TRP, b-PROTEIN, OCA3	uc003zkv.4	P17643	OTTHUMG00000021034	ENST00000388918.5:c.729T>C	9.37:g.12698471T>C		Somatic	309	1	0.00323625		WXS	Illumina HiSeq	Phase_I	341	169	0.495601	NM_000550	P78468|P78469|Q13721|Q15679	Silent	SNP	ENST00000388918.5	37	CCDS34990.1																																																																																			T|0.958;C|0.042	0.042	strong		0.403	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550	
MTHFD1	4522	hgsc.bcm.edu	37	14	64908845	64908845	+	Missense_Mutation	SNP	G	G	A	rs2236225	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:64908845G>A	ENST00000545908.1	+	20	2355	c.2126G>A	c.(2125-2127)cGg>cAg	p.R709Q	MTHFD1_ENST00000216605.8_Missense_Mutation_p.R653Q|CTD-2555O16.2_ENST00000556640.1_RNA|CTD-2555O16.4_ENST00000609125.1_RNA			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	653	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	ATTGCAGACCGGATCGCACTC	0.488													G|||	1712	0.341853	0.1581	0.5447	5008	,	,		20044	0.1984		0.4294	False		,,,				2504	0.5041				p.R653Q	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.G1958A	GRCh37	CM022820	MTHFD1	M	rs2236225	PASS	.	G	GLN/ARG	943,3463	358.4+/-314.3	103,737,1363	124.0	109.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1958	5.0	1.0	14	dbSNP_98	114	3934,4666	546.9+/-385.1	892,2150,1258	yes	missense	MTHFD1	NM_005956.3	43	995,2887,2621	AA,AG,GG		45.7442,21.4026,37.4981	benign	653/936	64908845	4877,8129	2203	4300	6503	SO:0001583	missense	4522	exon20			CAGACCGGATCGC	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2126G>A	14.37:g.64908845G>A	ENSP00000438588:p.Arg709Gln	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	37		757	0.3466117216117216	105	0.21341463414634146	193	0.5331491712707183	134	0.23426573426573427	325	0.4287598944591029	G	14.88	2.667518	0.47677	0.214026	0.457442	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605	T;T;T	0.21932	1.98;1.98;1.98	5.87	4.97	0.65823	.	0.052299	0.85682	D	0.000000	T	0.00012	0.0000	L	0.33668	1.02	0.26730	P	0.970606	B;B	0.31599	0.33;0.009	B;B	0.19666	0.026;0.016	T	0.47736	-0.9094	9	0.41790	T	0.15	-5.0748	5.9329	0.19148	0.2468:0.0:0.7532:0.0	rs2236225;rs17751608;rs17850560;rs52810262;rs56503831;rs58065500;rs2236225	709;653	F5H2F4;G3V2B8	.;.	Q	709;653;709	ENSP00000438588:R709Q;ENSP00000450560:R653Q;ENSP00000216605:R709Q	ENSP00000216605:R653Q	R	+	2	0	MTHFD1	63978598	1.000000	0.71417	1.000000	0.80357	0.197000	0.23852	5.247000	0.65416	2.941000	0.99782	0.655000	0.94253	CGG	G|0.641;N|0.000	.	strong		0.488	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1		
HLA-B	3106	hgsc.bcm.edu	37	6	31324152	31324152	+	Silent	SNP	A	A	G	rs1050628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324152A>G	ENST00000412585.2	-	3	439	c.411T>C	c.(409-411)caT>caC	p.H137H		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	137	Alpha-2.		H -> Y (in dbSNP:rs1050379).		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CGTACTGGTCATGCCCGCGGA	0.706									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				A|||	133	0.0265575	0.0159	0.0245	5008	,	,		8325	0.0159		0.0547	False		,,,				2504	0.0245				p.H137H		Atlas-SNP	.											.	HLA-B	54	.	0			c.T411C						PASS	.																																			SO:0001819	synonymous_variant	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	CTGGTCATGCCCG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.411T>C	6.37:g.31324152A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			A|0.973;G|0.027	0.027	strong		0.706	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
CNGB3	54714	hgsc.bcm.edu	37	8	87660100	87660100	+	Missense_Mutation	SNP	T	T	C	rs13265557	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:87660100T>C	ENST00000320005.5	-	8	966	c.919A>G	c.(919-921)Ata>Gta	p.I307V		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	307			I -> V (in dbSNP:rs13265557). {ECO:0000269|PubMed:14757870, ECO:0000269|PubMed:15712225}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						AATGGTATTATTGATGCGACA	0.328													T|||	351	0.0700879	0.0408	0.0605	5008	,	,		18072	0.0794		0.0706	False		,,,				2504	0.1063				p.I307V		Atlas-SNP	.											.	CNGB3	176	.	0			c.A919G						PASS	.	T	VAL/ILE	229,4177	136.1+/-172.1	4,221,1978	116.0	109.0	112.0		919	-6.9	0.2	8	dbSNP_121	112	515,8081	145.6+/-201.3	19,477,3802	yes	missense	CNGB3	NM_019098.4	29	23,698,5780	CC,CT,TT		5.9912,5.1975,5.7222	benign	307/810	87660100	744,12258	2203	4298	6501	SO:0001583	missense	54714	exon8			GTATTATTGATGC	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2153	protein-coding gene	gene with protein product		605080	"""achromatopsia (rod monochromacy) 3"", ""achromatopsia (rod monochromacy) 1"""	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.919A>G	8.37:g.87660100T>C	ENSP00000316605:p.Ile307Val	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	189	79	0.417989	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	125	0.05723443223443223	26	0.052845528455284556	16	0.04419889502762431	34	0.05944055944055944	49	0.06464379947229551	T	8.357	0.832259	0.16820	0.051975	0.059912	ENSG00000170289	ENST00000320005	D	0.97209	-4.29	5.93	-6.88	0.01665	.	0.546233	0.18589	N	0.136797	T	0.60235	0.2253	N	0.12920	0.275	0.28884	N	0.894244	B;B	0.06786	0.001;0.001	B;B	0.15484	0.008;0.013	T	0.67063	-0.5765	10	0.25751	T	0.34	.	14.6236	0.68605	0.0:0.7012:0.1171:0.1817	rs13265557;rs17684456;rs56523294;rs13265557	307;307	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	V	307	ENSP00000316605:I307V	ENSP00000316605:I307V	I	-	1	0	CNGB3	87729216	0.184000	0.23200	0.232000	0.24009	0.397000	0.30659	-0.538000	0.06120	-1.257000	0.02475	0.482000	0.46254	ATA	T|0.940;C|0.060	0.060	strong		0.328	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098	
TACC2	10579	hgsc.bcm.edu	37	10	123845211	123845211	+	Missense_Mutation	SNP	G	G	A	rs11200387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:123845211G>A	ENST00000369005.1	+	4	3536	c.3196G>A	c.(3196-3198)Gcc>Acc	p.A1066T	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.A1066T|TACC2_ENST00000515603.1_Missense_Mutation_p.A1066T|TACC2_ENST00000515273.1_Missense_Mutation_p.A1066T|TACC2_ENST00000334433.3_Missense_Mutation_p.A1066T|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1066					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CCTGGCGCCCGCCAGCCCCGG	0.647													G|||	694	0.138578	0.1929	0.1499	5008	,	,		15541	0.0913		0.17	False		,,,				2504	0.0736				p.A1066T		Atlas-SNP	.											.	TACC2	271	.	0			c.G3196A						PASS	.	G	,THR/ALA	992,3414	350.3+/-310.7	115,762,1326	37.0	43.0	41.0		,3196	2.5	0.0	10	dbSNP_120	41	1441,7157	262.0+/-284.2	117,1207,2975	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,58	232,1969,4301	AA,AG,GG		16.7597,22.5148,18.7096	,benign	,1066/2949	123845211	2433,10571	2203	4299	6502	SO:0001583	missense	10579	exon4			GCGCCCGCCAGCC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.3196G>A	10.37:g.123845211G>A	ENSP00000358001:p.Ala1066Thr	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	349	0.15979853479853479	92	0.18699186991869918	63	0.17403314917127072	66	0.11538461538461539	128	0.16886543535620052	G	11.06	1.528723	0.27387	0.225148	0.167597	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.03242	4.06;4.01;4.0;4.06;4.01	5.37	2.46	0.29980	.	0.496053	0.15164	N	0.276983	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	P;P;P	0.35872	0.525;0.525;0.525	B;B;B	0.28638	0.092;0.092;0.092	T	0.46359	-0.9197	9	0.12430	T	0.62	-0.0562	5.8983	0.18951	0.1754:0.1576:0.667:0.0	rs11200387;rs58225650	1066;1066;1066	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	T	1066;1066;1066;1066;1066;1056	ENSP00000358001:A1066T;ENSP00000424467:A1066T;ENSP00000427618:A1066T;ENSP00000334280:A1066T;ENSP00000395048:A1066T	ENSP00000334280:A1066T	A	+	1	0	TACC2	123835201	0.001000	0.12720	0.005000	0.12908	0.048000	0.14542	0.705000	0.25675	0.240000	0.21263	0.478000	0.44815	GCC	G|0.826;A|0.174	0.174	strong		0.647	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197538	39197538	+	Missense_Mutation	SNP	G	G	T	rs146863522		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39197538G>T	ENST00000306271.4	-	1	175	c.112C>A	c.(112-114)Cgc>Agc	p.R38S		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	38			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)		p.R38S(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TCACAGCAGCGTGGCTGGCAG	0.607																																					p.R38S		Atlas-SNP	.											KRTAP1-1,NS,NS,0,1	KRTAP1-1	23	1	1	Substitution - Missense(1)	NS(1)	c.C112A						scavenged	.						54.0	68.0	63.0					17																	39197538		2019	4207	6226	SO:0001583	missense	81851	exon1			AGCAGCGTGGCTG	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.112C>A	17.37:g.39197538G>T	ENSP00000305975:p.Arg38Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	177	48	0.271186	NM_030967	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	93	0.042582417582417584	46	0.09349593495934959	8	0.022099447513812154	30	0.05244755244755245	9	0.011873350923482849	g	0.001	-3.345547	0.00016	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.24723	1.84	2.68	-1.04	0.10068	.	.	.	.	.	T	0.00144	0.0004	N	0.00031	-2.6	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.27226	-1.0080	8	0.02654	T	1	.	0.9532	0.01380	0.2199:0.1031:0.2626:0.4145	.	38	Q07627	KRA11_HUMAN	S	38;28	ENSP00000305975:R38S	ENSP00000305975:R38S	R	-	1	0	KRTAP1-1	36451064	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.060000	0.14342	-0.640000	0.05495	-3.131000	0.00060	CGC	G|0.957;T|0.043	0.043	strong		0.607	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
EPN3	55040	hgsc.bcm.edu	37	17	48608717	48608717	+	5'Flank	SNP	T	T	C	rs1064055	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48608717T>C	ENST00000268933.3	+	0	0				EPN3_ENST00000541226.1_5'Flank|MYCBPAP_ENST00000323776.5_Silent_p.T961T|MYCBPAP_ENST00000436259.2_3'UTR|EPN3_ENST00000537145.1_5'Flank	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3							clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			CCCTGGTGACTGACCTGATGG	0.547													C|||	4081	0.814896	0.9289	0.7003	5008	,	,		17445	0.8859		0.7356	False		,,,				2504	0.7505				p.T961T		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.T2883C						PASS	.	C		3964,442	210.8+/-231.2	1789,386,28	74.0	61.0	66.0		2883	-10.8	0.0	17	dbSNP_86	66	6266,2334	391.1+/-343.5	2295,1676,329	no	coding-synonymous	MYCBPAP	NM_032133.4		4084,2062,357	CC,CT,TT		27.1395,10.0318,21.344		961/985	48608717	10230,2776	2203	4300	6503	SO:0001631	upstream_gene_variant	84073	exon19			GGTGACTGACCTG	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201			17.37:g.48608717T>C	Exception_encountered	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	142	64	0.450704	NM_032133	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Silent	SNP	ENST00000268933.3	37	CCDS11570.1																																																																																			T|0.195;C|0.805	0.805	strong		0.547	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188575	140188575	+	Silent	SNP	G	G	C	rs2879087	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140188575G>C	ENST00000530339.1	+	1	1803	c.1803G>C	c.(1801-1803)tcG>tcC	p.S601S	PCDHA4_ENST00000356878.4_Silent_p.S601S|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Silent_p.S601S	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	601	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGCTGACTCGGGCTACAACG	0.687													.|||	2962	0.591454	0.7194	0.6066	5008	,	,		17183	0.5317		0.5388	False		,,,				2504	0.5235				p.S601S		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G1803C						PASS	.	G	,,,,,	3110,1296		1107,896,200	127.0	114.0	118.0		,,,1803,,1803	-8.2	0.5	5	dbSNP_101	118	4548,4050		1198,2152,949	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	2305,3048,1149	CC,CG,GG		47.104,29.4144,41.1104	,,,,,	,,,601/948,,601/799	140188575	7658,5346	2203	4299	6502	SO:0001819	synonymous_variant	56144	exon1			TGACTCGGGCTAC	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1803G>C	5.37:g.140188575G>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			G|0.413;C|0.587	0.587	strong		0.687	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
ZNF326	284695	hgsc.bcm.edu	37	1	90486412	90486412	+	Silent	SNP	T	T	G	rs2816881	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:90486412T>G	ENST00000340281.4	+	10	1379	c.1236T>G	c.(1234-1236)gtT>gtG	p.V412V	ZNF326_ENST00000370447.3_Silent_p.V323V|ZNF326_ENST00000455342.2_Silent_p.V206V	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	412					mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		CTTGCAGTGTTTATATCCCTG	0.348													G|||	3471	0.693091	0.6626	0.7205	5008	,	,		18601	0.8909		0.5736	False		,,,				2504	0.6339				p.V412V		Atlas-SNP	.											.	ZNF326	60	.	0			c.T1236G						PASS	.	G		2887,1519	480.8+/-358.9	946,995,262	142.0	140.0	141.0		1236	-1.4	1.0	1	dbSNP_100	141	4828,3772	534.7+/-382.7	1338,2152,810	no	coding-synonymous	ZNF326	NM_182976.2		2284,3147,1072	GG,GT,TT		43.8605,34.4757,40.6812		412/583	90486412	7715,5291	2203	4300	6503	SO:0001819	synonymous_variant	284695	exon10			CAGTGTTTATATC	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"""Zinc fingers, C2H2-type"""	14104	protein-coding gene	gene with protein product	"""ZNF-protein interacting with nuclear mRNPs and DBC1"""	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1236T>G	1.37:g.90486412T>G		Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	310	140	0.451613	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Silent	SNP	ENST00000340281.4	37	CCDS727.1																																																																																			T|0.355;G|0.645	0.645	strong		0.348	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781	
RBL2	5934	hgsc.bcm.edu	37	16	53503943	53503943	+	Silent	SNP	C	C	G	rs11540358	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:53503943C>G	ENST00000262133.6	+	15	2228	c.2091C>G	c.(2089-2091)cgC>cgG	p.R697R	RBL2_ENST00000544545.1_Intron|RBL2_ENST00000379935.4_3'UTR	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	697	Pocket; binds E1A.|Spacer.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CGCCTGGGCGCATGCCCCCAC	0.552													C|||	1274	0.254393	0.3835	0.2406	5008	,	,		17307	0.0496		0.2992	False		,,,				2504	0.2546				p.R697R		Atlas-SNP	.											.	RBL2	115	.	0			c.C2091G						PASS	.	C		1532,2864	483.2+/-359.6	260,1012,926	73.0	70.0	71.0		2091	2.9	1.0	16	dbSNP_120	71	2726,5874	433.9+/-357.6	437,1852,2011	no	coding-synonymous	RBL2	NM_005611.3		697,2864,2937	GG,GC,CC		31.6977,34.8499,32.7639		697/1140	53503943	4258,8738	2198	4300	6498	SO:0001819	synonymous_variant	5934	exon15			TGGGCGCATGCCC	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2091C>G	16.37:g.53503943C>G		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	148	146	0.986486	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Silent	SNP	ENST00000262133.6	37	CCDS10748.1																																																																																			C|0.706;G|0.294	0.294	strong		0.552	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
CCDC144A	9720	hgsc.bcm.edu	37	17	16635980	16635980	+	Splice_Site	SNP	G	G	A	rs61179727	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:16635980G>A	ENST00000360524.8	+	11	2494	c.2418G>A	c.(2416-2418)gaG>gaA	p.E806E	CCDC144A_ENST00000443444.2_Splice_Site_p.E806E|CCDC144A_ENST00000456009.1_Splice_Site_p.E526E|RP11-219A15.1_ENST00000448331.3_Splice_Site_p.E806E|CCDC144A_ENST00000399273.1_Splice_Site_p.E806E	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	806																	TGAATTCTGAGGTATTTTCTT	0.303													G|||	610	0.121805	0.0129	0.1455	5008	,	,		16761	0.3075		0.0865	False		,,,				2504	0.0971				p.E806E		Atlas-SNP	.											.	CCDC144A	53	.	0			c.G2418A						PASS	.	G		110,3510		3,104,1703	30.0	29.0	30.0		2418	2.1	1.0	17	dbSNP_129	30	768,7416		31,706,3355	no	coding-synonymous-near-splice	CCDC144A	NM_014695.1		34,810,5058	AA,AG,GG		9.3842,3.0387,7.4382		806/1428	16635980	878,10926	1810	4092	5902	SO:0001630	splice_region_variant	9720	exon11			TTCTGAGGTATTT	BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.2418+1G>A	17.37:g.16635980G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	215	106	0.493023	NM_014695	O60311|Q6ZU57	Silent	SNP	ENST00000360524.8	37	CCDS45621.1	287	0.13141025641025642	6	0.012195121951219513	32	0.08839779005524862	186	0.32517482517482516	63	0.08311345646437995	.	1.298	-0.605686	0.03717	0.030387	0.093842	ENSG00000170160	ENST00000328495	.	.	.	2.08	2.08	0.27032	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.38156	-0.9674	3	.	.	.	.	7.6329	0.28249	0.0:0.0:1.0:0.0	rs61179727	.	.	.	K	290	.	.	R	+	2	0	CCDC144A	16576705	1.000000	0.71417	0.985000	0.45067	0.217000	0.24651	3.618000	0.54188	1.153000	0.42468	0.393000	0.25936	AGA	G|0.875;A|0.125	0.125	strong		0.303	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1		Silent
RBMXL3	139804	hgsc.bcm.edu	37	X	114424148	114424148	+	Silent	SNP	G	G	A	rs62601525		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:114424148G>A	ENST00000424776.3	+	1	186	c.144G>A	c.(142-144)tcG>tcA	p.S48S	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	48	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						CCAACAAGTCGAGGGGCTTCG	0.532													G|||	221	0.058543	0.0038	0.0533	3775	,	,		13320	0.002		0.1133	False		,,,				2504	0.0644				p.S48S		Atlas-SNP	.											.	RBMXL3	83	.	0			c.G144A						PASS	.	G	,	34,1175		1,25,7,491,168	84.0	77.0	79.0		144,	-0.4	0.0	X	dbSNP_129	79	391,2000		18,215,140,567,651	no	coding-synonymous,intron	LRCH2,RBMXL3	NM_001145346.1,NM_020871.3	,	19,240,147,1058,819	AA,AG,A,GG,G		16.353,2.8122,11.8056	,	48/1068,	114424148	425,3175	692	1591	2283	SO:0001819	synonymous_variant	139804	exon1			CAAGTCGAGGGGC	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.144G>A	X.37:g.114424148G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	136	126	0.926471	NM_001145346	B4DXC0	Silent	SNP	ENST00000424776.3	37	CCDS55478.1																																																																																			G|0.929;A|0.071	0.071	strong		0.532	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
OSER1	51526	hgsc.bcm.edu	37	20	42826350	42826350	+	Missense_Mutation	SNP	A	A	C	rs9346	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:42826350A>C	ENST00000372970.2	-	6	401	c.221T>G	c.(220-222)gTg>gGg	p.V74G	OSER1_ENST00000255174.2_Missense_Mutation_p.V74G			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	74			V -> G (in dbSNP:rs9346).		cellular response to hydrogen peroxide (GO:0070301)												CTGAGTTCTCACTGCTCCTCG	0.423													A|||	1771	0.353634	0.5862	0.1354	5008	,	,		22691	0.4196		0.1531	False		,,,				2504	0.3323				p.V74G		Atlas-SNP	.											.	C20orf111	28	.	0			c.T221G						PASS	.	A	GLY/VAL	2235,2171	589.5+/-387.1	574,1087,542	59.0	57.0	58.0		221	1.0	1.0	20	dbSNP_52	58	1215,7385	243.9+/-273.3	80,1055,3165	yes	missense	C20orf111	NM_016470.7	109	654,2142,3707	CC,CA,AA		14.1279,49.2737,26.5262	benign	74/293	42826350	3450,9556	2203	4300	6503	SO:0001583	missense	51526	exon4			GTTCTCACTGCTC	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"""peroxide-inducible transcript 1"", ""oxidative stress-responsive 1"""		"""chromosome 20 open reading frame 111"""	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.221T>G	20.37:g.42826350A>C	ENSP00000362061:p.Val74Gly	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Missense_Mutation	SNP	ENST00000372970.2	37	CCDS13327.1	718	0.32875457875457875	294	0.5975609756097561	58	0.16022099447513813	242	0.4230769230769231	124	0.16358839050131926	A	12.62	1.992149	0.35131	0.507263	0.141279	ENSG00000132823	ENST00000255174;ENST00000372970	T;T	0.54479	0.57;0.57	5.72	1.03	0.20045	.	0.636671	0.16840	N	0.197362	T	0.00012	0.0000	L	0.53249	1.67	0.09310	P	0.9999999260926	B	0.21905	0.062	B	0.30716	0.119	T	0.43845	-0.9366	9	0.66056	D	0.02	-0.5225	9.1613	0.37023	0.7244:0.0:0.2756:0.0	rs9346;rs1049822;rs3171228;rs52815417;rs58950417;rs9346	74	Q9NX31	CT111_HUMAN	G	74	ENSP00000255174:V74G;ENSP00000362061:V74G	ENSP00000255174:V74G	V	-	2	0	C20orf111	42259764	0.533000	0.26354	0.992000	0.48379	0.919000	0.55068	1.618000	0.36954	0.116000	0.18110	0.383000	0.25322	GTG	T|0.004;G|0.002	.	strong		0.423	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470	
CAPN3	825	hgsc.bcm.edu	37	15	42679977	42679977	+	Silent	SNP	C	C	T	rs144383442		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:42679977C>T	ENST00000397163.3	+	4	744	c.525C>T	c.(523-525)gaC>gaT	p.D175D	CAPN3_ENST00000349748.3_Silent_p.D175D|CAPN3_ENST00000318023.7_Silent_p.D175D|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000357568.3_Silent_p.D175D|CAPN3_ENST00000356316.3_Silent_p.D88D	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	175	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AGTGGGTGGACGTGGTTATAG	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		21839	0.0		0.0	False		,,,				2504	0.001				p.D175D		Atlas-SNP	.											CAPN3_ENST00000356316,NS,carcinoma,0,2	CAPN3	172	2	0			c.C525T						PASS	.	C	,,	3,4403	6.2+/-15.9	0,3,2200	310.0	251.0	271.0		525,525,525	-5.8	0.9	15	dbSNP_134	271	15,8583	9.8+/-36.6	0,15,4284	yes	coding-synonymous,coding-synonymous,coding-synonymous	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1	,,	0,18,6484	TT,TC,CC		0.1745,0.0681,0.1384	,,	175/822,175/816,175/730	42679977	18,12986	2203	4299	6502	SO:0001819	synonymous_variant	825	exon4			GGTGGACGTGGTT	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"""EF-hand domain containing"""	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.525C>T	15.37:g.42679977C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	137	129	0.941606	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																			C|0.999;T|0.001	0.001	strong		0.493	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		
COLEC11	78989	hgsc.bcm.edu	37	2	3685163	3685163	+	Silent	SNP	T	T	C	rs34347618	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:3685163T>C	ENST00000349077.4	+	4	346	c.243T>C	c.(241-243)cgT>cgC	p.R81R	COLEC11_ENST00000403096.3_Silent_p.R55R|COLEC11_ENST00000404205.1_Intron|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000418971.2_Silent_p.R95R|COLEC11_ENST00000236693.7_Silent_p.R78R|COLEC11_ENST00000382062.2_Intron|COLEC11_ENST00000402922.1_Intron|COLEC11_ENST00000402794.1_Silent_p.R31R	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	81	Collagen-like.				developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		GTGTGGGTCGTCATGGAAAAA	0.512													C|||	277	0.0553115	0.0605	0.0418	5008	,	,		21109	0.0228		0.0249	False		,,,				2504	0.1227				p.R95R		Atlas-SNP	.											COLEC11_ENST00000418971,colon,carcinoma,+1,4	COLEC11	93	4	0			c.T285C						scavenged	.	C	,	257,4149	803.1+/-415.7	8,241,1954	293.0	228.0	250.0		243,234	2.0	1.0	2	dbSNP_126	250	277,8323	807.2+/-407.2	6,265,4029	no	coding-synonymous,coding-synonymous	COLEC11	NM_024027.3,NM_199235.1	,	14,506,5983	CC,CT,TT		3.2209,5.833,4.1058	,	81/272,78/269	3685163	534,12472	2203	4300	6503	SO:0001819	synonymous_variant	78989	exon5			GGGTCGTCATGGA	BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"""Collectins"""	17213	protein-coding gene	gene with protein product	"""Collectin K1"""	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.243T>C	2.37:g.3685163T>C		Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	191	102	0.534031	NM_001255985	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Silent	SNP	ENST00000349077.4	37	CCDS1649.1																																																																																			T|0.961;C|0.039	0.039	strong		0.512	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027	
PON1	5444	hgsc.bcm.edu	37	7	94946084	94946084	+	Missense_Mutation	SNP	A	A	T	rs854560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:94946084A>T	ENST00000222381.3	-	3	394	c.163T>A	c.(163-165)Ttg>Atg	p.L55M	PON1_ENST00000542556.1_Missense_Mutation_p.L55M	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	55			L -> M (in dbSNP:rs854560). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1657140, ECO:0000269|PubMed:7916578, ECO:0000269|PubMed:8393742, ECO:0000269|PubMed:8393745, ECO:0000269|PubMed:8812495}.		aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	AGTATCTCCAAGTCTTCAGAG	0.403													A|||	915	0.182708	0.1498	0.2061	5008	,	,		17849	0.0337		0.3579	False		,,,				2504	0.184				p.L55M	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											.	PON1	55	.	0			c.T163A	GRCh37	CM971236	PON1	M	rs854560	PASS	.	A	MET/LEU	762,3644	308.8+/-290.8	64,634,1505	168.0	161.0	163.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	163	-1.8	1.0	7	dbSNP_86	163	3208,5392	485.5+/-371.6	618,1972,1710	yes	missense	PON1	NM_000446.5	15	682,2606,3215	TT,TA,AA		37.3023,17.2946,30.5244	benign	55/356	94946084	3970,9036	2203	4300	6503	SO:0001583	missense	5444	exon3			TCTCCAAGTCTTC	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.163T>A	7.37:g.94946084A>T	ENSP00000222381:p.Leu55Met	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	134	72	0.537313	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	447	0.20467032967032966	75	0.1524390243902439	88	0.2430939226519337	18	0.03146853146853147	266	0.35092348284960423	A	18.84	3.709500	0.68730	0.172946	0.373023	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.49139	0.79;0.79	5.05	-1.76	0.08006	Six-bladed beta-propeller, TolB-like (1);	0.199502	0.43416	D	0.000561	T	0.00012	0.0000	L	0.59436	1.845	0.32800	P	0.500057	D;B	0.58620	0.983;0.004	D;B	0.64410	0.925;0.04	T	0.19063	-1.0317	9	0.66056	D	0.02	-10.6907	4.2104	0.10509	0.3107:0.0:0.2524:0.4369	rs854560;rs1138340;rs1801051;rs2228157;rs3179555;rs3202100;rs11567862;rs17434839;rs57937067	55;55	F5H4W9;P27169	.;PON1_HUMAN	M	55	ENSP00000222381:L55M;ENSP00000444854:L55M	ENSP00000222381:L55M	L	-	1	2	PON1	94784020	0.991000	0.36638	0.995000	0.50966	0.975000	0.68041	0.196000	0.17176	-0.066000	0.12998	0.528000	0.53228	TTG	A|0.717;T|0.283	0.283	strong		0.403	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
MAPT	4137	hgsc.bcm.edu	37	17	44073889	44073889	+	Silent	SNP	A	A	G	rs1052553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44073889A>G	ENST00000571987.1	+	9	1632	c.1632A>G	c.(1630-1632)gcA>gcG	p.A544A	STH_ENST00000537309.1_5'Flank|MAPT_ENST00000576518.1_Silent_p.A158A|MAPT_ENST00000574436.1_Silent_p.A227A|MAPT_ENST00000431008.3_Silent_p.A227A|MAPT_ENST00000344290.5_Silent_p.A562A|MAPT_ENST00000570299.1_3'UTR|MAPT_ENST00000340799.5_Silent_p.A198A|MAPT_ENST00000415613.2_Silent_p.A562A|MAPT_ENST00000446361.3_Silent_p.A169A|MAPT_ENST00000262410.5_Silent_p.A544A|MAPT_ENST00000535772.1_Silent_p.A227A|MAPT_ENST00000420682.2_Silent_p.A198A|MAPT_ENST00000347967.5_Silent_p.A133A|MAPT_ENST00000334239.8_Silent_p.A169A|MAPT_ENST00000351559.5_Silent_p.A227A			P10636	TAU_HUMAN	microtubule-associated protein tau	544					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	AGAAGGTGGCAGTGGTCCGTA	0.682													G|||	442	0.0882588	0.0219	0.1571	5008	,	,		11254	0.001		0.2416	False		,,,				2504	0.0613				p.A562A		Atlas-SNP	.											MAPT_ENST00000344290,NS,carcinoma,0,2	MAPT	135	2	0			c.A1686G						scavenged	.	G	,,,,,,,	231,4175	776.6+/-414.2	6,219,1978	24.0	25.0	24.0		1686,594,594,681,681,507,1632,507	-11.2	0.4	17	dbSNP_86	24	1901,6699	699.3+/-405.1	215,1471,2614	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	,,,,,,,	221,1690,4592	GG,GA,AA		22.1047,5.2429,16.3924	,,,,,,,	562/777,198/413,198/382,227/411,227/442,169/384,544/759,169/353	44073889	2132,10874	2203	4300	6503	SO:0001819	synonymous_variant	4137	exon11			GGTGGCAGTGGTC	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1632A>G	17.37:g.44073889A>G		Somatic	154	2	0.012987		WXS	Illumina HiSeq	Phase_I	115	36	0.313043	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																			A|0.865;G|0.135	0.135	strong		0.682	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
GCDH	2639	hgsc.bcm.edu	37	19	13008607	13008607	+	Silent	SNP	G	G	T	rs1060218	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:13008607G>T	ENST00000222214.5	+	11	1384	c.1173G>T	c.(1171-1173)ggG>ggT	p.G391G	GCDH_ENST00000422947.2_Silent_p.G347G|GCDH_ENST00000457854.1_Silent_p.G391G|GCDH_ENST00000591470.1_Silent_p.G391G			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase	391					cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	TGCTGGGGGGGAATGGGATTT	0.602													G|||	1254	0.250399	0.171	0.4308	5008	,	,		19457	0.1438		0.325	False		,,,				2504	0.2628				p.S391S	GBM(123;875 1636 7726 16444 26754)	Atlas-SNP	.											GCDH_ENST00000457854,NS,carcinoma,+2,2	GCDH	76	2	0			c.C1173T	GRCh37	CD962014	GCDH	D	rs1060218	PASS	.	G	,	913,3493	345.7+/-308.6	82,749,1372	64.0	69.0	67.0		1173,1173	-11.2	0.2	19	dbSNP_86	67	3081,5519	465.6+/-366.6	539,2003,1758	no	coding-synonymous,coding-synonymous	GCDH	NM_000159.2,NM_013976.2	,	621,2752,3130	TT,TG,GG		35.8256,20.7217,30.7089	,	391/439,391/429	13008607	3994,9012	2203	4300	6503	SO:0001819	synonymous_variant	2639	exon11			GGGGGGGAATGGG	AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"""glutaryl-Coenzyme A dehydrogenase"""			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.1173G>T	19.37:g.13008607G>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_013976	A8K2Z2|O14719	Silent	SNP	ENST00000222214.5	37	CCDS12286.1																																																																																			G|0.732;T|0.268	0.268	strong		0.602	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1		
LRRC43	254050	hgsc.bcm.edu	37	12	122676013	122676013	+	Silent	SNP	A	A	C	rs11060167	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:122676013A>C	ENST00000339777.4	+	6	1016	c.988A>C	c.(988-990)Agg>Cgg	p.R330R	LRRC43_ENST00000425921.1_Silent_p.R145R	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	330										NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		CCCGGAACCCAGGCCCGAAGG	0.527											OREG0022219	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1475	0.294529	0.0696	0.1772	5008	,	,		17106	0.7123		0.2316	False		,,,				2504	0.316				p.R330R		Atlas-SNP	.											.	LRRC43	105	.	0			c.A988C						PASS	.	G	,	360,3464		20,320,1572	63.0	63.0	63.0		988,433	4.3	0.4	12	dbSNP_120	63	2137,6083		293,1551,2266	no	coding-synonymous,coding-synonymous	LRRC43	NM_001098519.1,NM_152759.4	,	313,1871,3838	CC,CA,AA		25.9976,9.4142,20.7323	,	330/657,145/472	122676013	2497,9547	1912	4110	6022	SO:0001819	synonymous_variant	254050	exon6			GAACCCAGGCCCG	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.988A>C	12.37:g.122676013A>C		Somatic	139	0	0	1520	WXS	Illumina HiSeq	Phase_I	125	69	0.552	NM_001098519	Q6ZVT9	Silent	SNP	ENST00000339777.4	37	CCDS45001.1																																																																																			A|0.675;C|0.325	0.325	strong		0.527	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
CDR2L	30850	hgsc.bcm.edu	37	17	73000061	73000061	+	Silent	SNP	A	A	G	rs3744203	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73000061A>G	ENST00000337231.5	+	5	1702	c.1290A>G	c.(1288-1290)gaA>gaG	p.E430E		NM_014603.2	NP_055418.2	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like	430												all_lung(278;0.226)					AGCGGCTGGAACAGAGCCAGC	0.612													G|||	2336	0.466454	0.7504	0.513	5008	,	,		15723	0.1935		0.4225	False		,,,				2504	0.3763				p.E430E		Atlas-SNP	.											HUMPPA,NS,carcinoma,0,1	.	.	1	0			c.A1290G						scavenged	.	G		3061,1345		1067,927,209	27.0	24.0	25.0		1290	3.0	1.0	17	dbSNP_107	25	3324,5272		636,2052,1610	no	coding-synonymous	CDR2L	NM_014603.2		1703,2979,1819	GG,GA,AA		38.6691,30.5266,49.1078		430/466	73000061	6385,6617	2203	4298	6501	SO:0001819	synonymous_variant	30850	exon5			GCTGGAACAGAGC		CCDS11710.2	17q25.1	2006-03-28			ENSG00000109089	ENSG00000109089			29999	protein-coding gene	gene with protein product	"""paraneoplastic antigen"""						Standard	NM_014603		Approved	HUMPPA	uc002jml.4	Q86X02	OTTHUMG00000150435	ENST00000337231.5:c.1290A>G	17.37:g.73000061A>G		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	NM_014603	B4DFA7|Q15175	Silent	SNP	ENST00000337231.5	37	CCDS11710.2																																																																																			A|0.528;G|0.472	0.472	strong		0.612	CDR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318080.1	NM_014603	
NAA40	79829	hgsc.bcm.edu	37	11	63713317	63713317	+	Silent	SNP	G	G	A	rs3740637	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:63713317G>A	ENST00000377793.4	+	2	113	c.12G>A	c.(10-12)aaG>aaA	p.K4K	NAA40_ENST00000536939.1_3'UTR|NAA40_ENST00000539656.1_Silent_p.K4K|NAA40_ENST00000456907.2_5'UTR|NAA40_ENST00000542163.1_5'UTR	NM_024771.2	NP_079047.2	Q86UY6	NAA40_HUMAN	N(alpha)-acetyltransferase 40, NatD catalytic subunit	4					lipid metabolic process (GO:0006629)		N-acetyltransferase activity (GO:0008080)			NS(1)|endometrium(1)|lung(2)|prostate(1)	5						TGCAGAGAAAGTCAAGCAAAG	0.537											OREG0021041	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	852	0.170128	0.0189	0.1499	5008	,	,		21146	0.0565		0.3946	False		,,,				2504	0.2751				p.K4K		Atlas-SNP	.											.	NAA40	13	.	0			c.G12A						PASS	.	G		359,4043	183.6+/-211.2	23,313,1865	184.0	149.0	161.0		12	5.0	1.0	11	dbSNP_107	161	3425,5169	504.9+/-376.3	658,2109,1530	no	coding-synonymous	NAA40	NM_024771.2		681,2422,3395	AA,AG,GG		39.8534,8.1554,29.1167		4/238	63713317	3784,9212	2201	4297	6498	SO:0001819	synonymous_variant	79829	exon2			GAGAAAGTCAAGC	AK023910	CCDS8053.1, CCDS73311.1	11q13.1	2013-10-11	2013-08-28	2010-01-14	ENSG00000110583	ENSG00000110583		"""N(alpha)-acetyltransferase subunits"""	25845	protein-coding gene	gene with protein product			"""N-acetyltransferase 11"", ""N-acetyltransferase 11 (GCN5-related, putative)"", ""N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)"""	NAT11		19660095	Standard	XM_005274296		Approved	FLJ13848	uc009yoz.3	Q86UY6	OTTHUMG00000167784	ENST00000377793.4:c.12G>A	11.37:g.63713317G>A		Somatic	104	0	0	1071	WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_024771	B4DR03|B4DU10|Q5HYL5|Q9H897	Silent	SNP	ENST00000377793.4	37	CCDS8053.1																																																																																			G|0.756;A|0.244	0.244	strong		0.537	NAA40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396266.1	NM_024771	
MOB3A	126308	hgsc.bcm.edu	37	19	2078409	2078409	+	Silent	SNP	A	A	G	rs2074893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:2078409A>G	ENST00000357066.3	-	3	530	c.151T>C	c.(151-153)Ttg>Ctg	p.L51L	MOB3A_ENST00000592143.1_Intron|MOB3A_ENST00000592280.1_Silent_p.L51L	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	51						intracellular (GO:0005622)	metal ion binding (GO:0046872)										CCCGGGGGCAACTGCACGGCC	0.652													G|||	2042	0.407748	0.6702	0.2579	5008	,	,		14489	0.1964		0.3618	False		,,,				2504	0.4243				p.L51L		Atlas-SNP	.											.	.	.	.	0			c.T151C						PASS	.	G		2808,1598	493.4+/-362.7	898,1012,293	53.0	56.0	55.0		151	2.0	1.0	19	dbSNP_96	55	2976,5624	664.4+/-402.2	523,1930,1847	no	coding-synonymous	MOB3A	NM_130807.2		1421,2942,2140	GG,GA,AA		34.6047,36.2687,44.4718		51/218	2078409	5784,7222	2203	4300	6503	SO:0001819	synonymous_variant	126308	exon3			GGGGCAACTGCAC	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.151T>C	19.37:g.2078409A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			A|0.578;G|0.422	0.422	strong		0.652	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
PTPRS	5802	hgsc.bcm.edu	37	19	5225802	5225802	+	Silent	SNP	G	G	A	rs10415592	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:5225802G>A	ENST00000587303.1	-	16	2529	c.2430C>T	c.(2428-2430)gcC>gcT	p.A810A	PTPRS_ENST00000588552.1_Intron|PTPRS_ENST00000262963.6_Silent_p.A806A|PTPRS_ENST00000372412.4_Silent_p.A811A|PTPRS_ENST00000357368.4_Silent_p.A810A|PTPRS_ENST00000588012.1_Silent_p.A788A|PTPRS_ENST00000592099.1_Intron|PTPRS_ENST00000348075.2_Silent_p.A788A|PTPRS_ENST00000353284.2_Intron			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	810	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A810A(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	TGGTGTAGGCGGCTACCGTGA	0.637													G|||	611	0.122005	0.2935	0.072	5008	,	,		15334	0.0407		0.0716	False		,,,				2504	0.0613				p.A810A		Atlas-SNP	.											PTPRS,NS,lymphoid_neoplasm,0,1	PTPRS	169	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2430T						PASS	.	G	,,,	1146,3260	406.2+/-333.8	159,828,1216	125.0	90.0	102.0		2430,,2364,	-0.6	1.0	19	dbSNP_119	102	683,7917	170.7+/-221.8	34,615,3651	no	coding-synonymous,intron,coding-synonymous,intron	PTPRS	NM_002850.3,NM_130853.2,NM_130854.2,NM_130855.2	,,,	193,1443,4867	AA,AG,GG		7.9419,26.01,14.0627	,,,	810/1949,,788/1911,	5225802	1829,11177	2203	4300	6503	SO:0001819	synonymous_variant	5802	exon17			GTAGGCGGCTACC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.2430C>T	19.37:g.5225802G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																			G|0.867;A|0.133	0.133	strong		0.637	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
CCDC168	643677	hgsc.bcm.edu	37	13	103383417	103383417	+	Missense_Mutation	SNP	T	T	C	rs9554897	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:103383417T>C	ENST00000322527.2	-	1	5742	c.5743A>G	c.(5743-5745)Aaa>Gaa	p.K1915E		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1915			K -> E (in dbSNP:rs9554897). {ECO:0000269|PubMed:14702039}.														CCTTTTTCTTTTACTGAGTGG	0.388													T|||	1690	0.33746	0.3608	0.3545	5008	,	,		21052	0.1587		0.3877	False		,,,				2504	0.4264				p.K6544E		Atlas-SNP	.											.	.	.	.	0			c.A19630G						PASS	.	T	GLU/LYS	493,891		94,305,293	133.0	115.0	120.0		19630	-6.2	0.0	13	dbSNP_119	120	1269,1913		256,757,578	yes	missense	CCDC168	NM_001146197.1	56	350,1062,871	CC,CT,TT		39.8806,35.6214,38.5896	benign	6544/7082	103383417	1762,2804	692	1591	2283	SO:0001583	missense	643677	exon4			TTTCTTTTACTGA		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.5743A>G	13.37:g.103383417T>C	ENSP00000320232:p.Lys1915Glu	Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	315	314	0.996825	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		699	0.32005494505494503	170	0.34552845528455284	141	0.38950276243093923	99	0.17307692307692307	289	0.3812664907651715	T	0.724	-0.782461	0.02907	0.356214	0.398806	ENSG00000175820	ENST00000322527	T	0.03242	4.0	5.53	-6.17	0.02091	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.15473	0.013	B	0.16722	0.016	T	0.43909	-0.9362	8	0.06365	T	0.9	.	9.4401	0.38664	0.0:0.271:0.1014:0.6276	rs9554897;rs17592424;rs52805221;rs58718993;rs9554897	1915	Q8NDH2	CC168_HUMAN	E	1915	ENSP00000320232:K1915E	ENSP00000320232:K1915E	K	-	1	0	CCDC168	102181418	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.003000	0.03682	-1.216000	0.02607	-0.250000	0.11733	AAA	C|0.312;N|0.000	0.312	strong		0.388	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
ADAMTS10	81794	hgsc.bcm.edu	37	19	8651562	8651562	+	Silent	SNP	A	A	G	rs4476282	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8651562A>G	ENST00000597188.1	-	20	2553	c.2283T>C	c.(2281-2283)ccT>ccC	p.P761P	ADAMTS10_ENST00000595838.1_Silent_p.P248P|ADAMTS10_ENST00000270328.4_Silent_p.P761P	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	761	Spacer.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						GGGGGGTCCCAGGCAGCCCCT	0.642											OREG0025221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	925	0.184704	0.2322	0.2061	5008	,	,		14798	0.125		0.2097	False		,,,				2504	0.1411				p.P761P		Atlas-SNP	.											ADAMTS10,NS,carcinoma,0,2	ADAMTS10	132	2	0			c.T2283C						scavenged	.	G		962,3444	699.5+/-406.5	101,760,1342	45.0	53.0	51.0		2283	-9.9	0.5	19	dbSNP_111	51	1864,6736	706.5+/-405.5	201,1462,2637	no	coding-synonymous	ADAMTS10	NM_030957.2		302,2222,3979	GG,GA,AA		21.6744,21.8339,21.7284		761/1104	8651562	2826,10180	2203	4300	6503	SO:0001819	synonymous_variant	81794	exon20			GGTCCCAGGCAGC	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13201	protein-coding gene	gene with protein product		608990	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"""				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.2283T>C	19.37:g.8651562A>G		Somatic	89	1	0.011236	81	WXS	Illumina HiSeq	Phase_I	94	94	1	NM_030957	M0QZE4	Silent	SNP	ENST00000597188.1	37	CCDS12206.1																																																																																			A|0.790;G|0.210	0.210	strong		0.642	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957	
EYA1	2138	hgsc.bcm.edu	37	8	72111599	72111599	+	Silent	SNP	A	A	G	rs10103397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:72111599A>G	ENST00000340726.3	-	18	2394	c.1755T>C	c.(1753-1755)caT>caC	p.H585H	EYA1_ENST00000388743.2_Silent_p.H584H|EYA1_ENST00000388740.3_Silent_p.H552H|RP11-326E22.1_ENST00000521685.1_RNA|EYA1_ENST00000303824.7_Silent_p.H579H|EYA1_ENST00000388741.2_Silent_p.H551H|EYA1_ENST00000419131.1_Silent_p.H550H|EYA1_ENST00000388742.4_Silent_p.H585H	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	585					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			GTTCCAAGGCATGGTGCAGGG	0.607													G|||	2387	0.476637	0.3623	0.464	5008	,	,		18146	0.7688		0.3101	False		,,,				2504	0.5102				p.H585H		Atlas-SNP	.											.	EYA1	108	.	0			c.T1755C						PASS	.	G	,,,	1532,2874	668.8+/-402.1	262,1008,933	88.0	65.0	73.0		1755,1755,1650,1656	-12.3	0.0	8	dbSNP_119	73	2625,5975	684.3+/-404.0	385,1855,2060	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EYA1	NM_000503.4,NM_172058.2,NM_172059.2,NM_172060.2	,,,	647,2863,2993	GG,GA,AA		30.5233,34.7708,31.9622	,,,	585/593,585/593,550/558,552/560	72111599	4157,8849	2203	4300	6503	SO:0001819	synonymous_variant	2138	exon18			CAAGGCATGGTGC	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3519	protein-coding gene	gene with protein product		601653	"""eyes absent (Drosophila) homolog 1"", ""eyes absent homolog 1 (Drosophila)"""	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.1755T>C	8.37:g.72111599A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_000503	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Silent	SNP	ENST00000340726.3	37	CCDS34906.1																																																																																			A|0.620;G|0.380	0.380	strong		0.607	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060	
WSCD2	9671	hgsc.bcm.edu	37	12	108641799	108641799	+	Silent	SNP	G	G	A	rs144706841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:108641799G>A	ENST00000332082.4	+	10	2195	c.1377G>A	c.(1375-1377)ccG>ccA	p.P459P	WSCD2_ENST00000261400.3_Silent_p.P479P|WSCD2_ENST00000547525.1_Silent_p.P459P|WSCD2_ENST00000549903.1_Silent_p.P479P			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	459						integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						ACTATGCCCCGTGGTGGGCCA	0.567													G|||	4	0.000798722	0.0008	0.0	5008	,	,		19841	0.0		0.003	False		,,,				2504	0.0				p.P459P		Atlas-SNP	.											.	WSCD2	125	.	0			c.G1377A						PASS	.	G		2,4082		0,2,2040	62.0	65.0	64.0		1377	-3.8	1.0	12	dbSNP_134	64	20,8424		0,20,4202	no	coding-synonymous	WSCD2	NM_014653.2		0,22,6242	AA,AG,GG		0.2369,0.049,0.1756		459/566	108641799	22,12506	2042	4222	6264	SO:0001819	synonymous_variant	9671	exon9			TGCCCCGTGGTGG		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.1377G>A	12.37:g.108641799G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Silent	SNP	ENST00000332082.4	37	CCDS41828.1																																																																																			G|0.998;A|0.002	0.002	strong		0.567	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653	
HEATR2	54919	hgsc.bcm.edu	37	7	796430	796430	+	Silent	SNP	C	C	T	rs73036225	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:796430C>T	ENST00000297440.6	+	6	1289	c.1269C>T	c.(1267-1269)tcC>tcT	p.S423S	HEATR2_ENST00000313147.5_Silent_p.S423S	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	423						cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		GTACCAGATCCGCAGAGCTCG	0.597													c|||	473	0.0944489	0.0129	0.1066	5008	,	,		18605	0.0		0.2127	False		,,,				2504	0.1718				p.S423S		Atlas-SNP	.											.	HEATR2	62	.	0			c.C1269T						PASS	.			224,4182	134.1+/-170.4	5,214,1984	87.0	88.0	87.0		1269	-11.0	0.0	7	dbSNP_130	87	1948,6652	339.0+/-323.0	232,1484,2584	no	coding-synonymous	HEATR2	NM_017802.3		237,1698,4568	TT,TC,CC		22.6512,5.084,16.7		423/856	796430	2172,10834	2203	4300	6503	SO:0001819	synonymous_variant	54919	exon6			CAGATCCGCAGAG	AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.1269C>T	7.37:g.796430C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_017802	Q69YL1|Q96FI9|Q9NX75	Silent	SNP	ENST00000297440.6	37	CCDS34580.1	206	0.09432234432234432	7	0.014227642276422764	33	0.09116022099447514	0	0.0	166	0.21899736147757257	C	4.574	0.106613	0.08780	0.05084	0.226512	ENSG00000164818	ENST00000440747	.	.	.	5.49	-11.0	0.00169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999992945	.	.	.	.	.	.	T	0.07635	-1.0762	3	.	.	.	-15.5902	10.2483	0.43354	0.1267:0.621:0.065:0.1874	.	.	.	.	C	225	.	.	R	+	1	0	HEATR2	762956	0.003000	0.15002	0.000000	0.03702	0.005000	0.04900	-1.344000	0.02639	-3.807000	0.00104	-2.136000	0.00340	CGC	C|0.850;T|0.150	0.150	strong		0.597	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802	
PTPRK	5796	hgsc.bcm.edu	37	6	128388799	128388799	+	Silent	SNP	G	G	T	rs35030557	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:128388799G>T	ENST00000368215.3	-	12	2021	c.2022C>A	c.(2020-2022)ctC>ctA	p.L674L	PTPRK_ENST00000368226.4_Silent_p.L674L|PTPRK_ENST00000368210.3_Silent_p.L674L|PTPRK_ENST00000368227.3_Silent_p.L674L|PTPRK_ENST00000368207.3_Silent_p.L674L|PTPRK_ENST00000532331.1_Silent_p.L674L|PTPRK_ENST00000368213.5_Silent_p.L674L|PTPRK_ENST00000524481.1_5'UTR|RP11-103C16.2_ENST00000417390.1_RNA			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	674	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.			AEL -> CRT (in Ref. 2; AAC37599). {ECO:0000305}.	cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		TTCCCGGGGGGAGTTCTGCAG	0.552													G|||	1228	0.245208	0.0408	0.4092	5008	,	,		15066	0.2411		0.4334	False		,,,				2504	0.2157				p.L674L		Atlas-SNP	.											.	PTPRK	330	.	0			c.C2022A						PASS	.	G	,	422,3984	206.8+/-228.3	22,378,1803	114.0	111.0	112.0		2022,2022	-11.9	0.0	6	dbSNP_126	112	3675,4925	527.0+/-381.1	772,2131,1397	no	coding-synonymous,coding-synonymous	PTPRK	NM_001135648.1,NM_002844.3	,	794,2509,3200	TT,TG,GG		42.7326,9.5778,31.5008	,	674/1447,674/1441	128388799	4097,8909	2203	4300	6503	SO:0001819	synonymous_variant	5796	exon12			CGGGGGGAGTTCT	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2022C>A	6.37:g.128388799G>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Silent	SNP	ENST00000368215.3	37																																																																																				T|0.314;G|0.686;C|0.000	0.314	strong		0.552	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1		
PLA2R1	22925	hgsc.bcm.edu	37	2	160885432	160885432	+	Missense_Mutation	SNP	T	T	C	rs139957604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160885432T>C	ENST00000283243.7	-	5	1090	c.884A>G	c.(883-885)aAt>aGt	p.N295S	PLA2R1_ENST00000392771.1_Missense_Mutation_p.N295S	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	295	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						ATCCAGCTGATTGAGGCCCAT	0.468																																					p.N295S		Atlas-SNP	.											.	PLA2R1	153	.	0			c.A884G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	119.0	94.0	103.0		884,884,884	5.8	1.0	2	dbSNP_134	103	11,8589	7.7+/-29.5	0,11,4289	yes	missense,missense,missense	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	46,46,46	0,11,6492	CC,CT,TT		0.1279,0.0,0.0846	probably-damaging,probably-damaging,probably-damaging	295/1325,295/1462,295/1464	160885432	11,12995	2203	4300	6503	SO:0001583	missense	22925	exon5			AGCTGATTGAGGC	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.884A>G	2.37:g.160885432T>C	ENSP00000283243:p.Asn295Ser	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	298	155	0.520134	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.932188	0.52866	0.0	0.001279	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.15718	2.4;2.4	5.83	5.83	0.93111	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.85682	D	0.000000	T	0.35711	0.0941	L	0.48935	1.535	0.58432	D	0.999993	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.995;0.998;0.999	T	0.02498	-1.1150	10	0.48119	T	0.1	.	15.1831	0.72975	0.0:0.0:0.0:1.0	.	295;295;295	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	S	295	ENSP00000283243:N295S;ENSP00000376524:N295S	ENSP00000283243:N295S	N	-	2	0	PLA2R1	160593678	1.000000	0.71417	0.998000	0.56505	0.093000	0.18481	4.310000	0.59141	2.227000	0.72691	0.528000	0.53228	AAT	T|0.999;C|0.001	0.001	strong		0.468	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
TTN	7273	hgsc.bcm.edu	37	2	179454394	179454394	+	Silent	SNP	A	A	G	rs1560221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179454394A>G	ENST00000591111.1	-	254	57359	c.57135T>C	c.(57133-57135)taT>taC	p.Y19045Y	TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000460472.2_Silent_p.Y11621Y|TTN_ENST00000342992.6_Silent_p.Y18118Y|TTN_ENST00000589042.1_Silent_p.Y20686Y|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Silent_p.Y11746Y|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.Y11813Y|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19045	Fibronectin type-III 38. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCACTTTAGATAGACAAATG	0.448													G|||	2566	0.51238	0.5681	0.4092	5008	,	,		22023	0.7232		0.2545	False		,,,				2504	0.5583				p.Y20686Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T62058C						PASS	.	G	,,,	2027,1825		546,935,445	194.0	187.0	189.0		34863,54354,35238,35439	3.9	1.0	2	dbSNP_88	189	1858,6404		196,1466,2469	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	742,2401,2914	GG,GA,AA		22.4885,47.378,32.0703	,,,	11621/26927,18118/33424,11746/27052,11813/27119	179454394	3885,8229	1926	4131	6057	SO:0001819	synonymous_variant	7273	exon304			CTTTAGATAGACA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.57135T>C	2.37:g.179454394A>G		Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	219	118	0.538813	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.558;G|0.442	0.442	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SYT10	341359	hgsc.bcm.edu	37	12	33579297	33579297	+	Silent	SNP	C	C	G	rs11052695	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:33579297C>G	ENST00000228567.3	-	2	581	c.285G>C	c.(283-285)acG>acC	p.T95T	SYT10_ENST00000535526.1_5'UTR|SYT10_ENST00000567656.1_5'Flank	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	95					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					TCTGTGGAAGCGTAGTGATGT	0.428													G|||	700	0.139776	0.2065	0.2219	5008	,	,		14833	0.0635		0.1054	False		,,,				2504	0.1053				p.T95T		Atlas-SNP	.											.	SYT10	109	.	0			c.G285C						PASS	.	G		782,3624	751.9+/-412.2	77,628,1498	91.0	90.0	90.0		285	-1.7	0.0	12	dbSNP_120	90	925,7675	776.6+/-407.7	51,823,3426	no	coding-synonymous	SYT10	NM_198992.3		128,1451,4924	GG,GC,CC		10.7558,17.7485,13.1247		95/524	33579297	1707,11299	2203	4300	6503	SO:0001819	synonymous_variant	341359	exon2			TGGAAGCGTAGTG	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"""Synaptotagmins"""	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.285G>C	12.37:g.33579297C>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_198992	Q495U2	Silent	SNP	ENST00000228567.3	37	CCDS8732.1																																																																																			C|0.867;G|0.133;T|0.000	0.133	strong		0.428	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992	
FBLIM1	54751	hgsc.bcm.edu	37	1	16101217	16101217	+	Silent	SNP	C	C	T	rs41268337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:16101217C>T	ENST00000375766.3	+	7	1456	c.816C>T	c.(814-816)tgC>tgT	p.C272C	FBLIM1_ENST00000441801.2_Silent_p.C272C|FBLIM1_ENST00000332305.5_Silent_p.C175C|FBLIM1_ENST00000400773.1_Silent_p.C175C|FBLIM1_ENST00000375771.1_Silent_p.C272C	NM_017556.2	NP_060026.2	Q8WUP2	FBLI1_HUMAN	filamin binding LIM protein 1	272	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell junction assembly (GO:0034329)|regulation of cell shape (GO:0008360)|regulation of integrin activation (GO:0033623)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|stress fiber (GO:0001725)	filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	16		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|READ - Rectum adenocarcinoma(331;0.0649)|STAD - Stomach adenocarcinoma(313;0.138)		GTGTGACCTGCGCCCGGTGCA	0.627													C|||	277	0.0553115	0.0446	0.085	5008	,	,		17349	0.0		0.1243	False		,,,				2504	0.0348				p.C272C		Atlas-SNP	.											.	FBLIM1	46	.	0			c.C816T						PASS	.	C	,,	226,4180	135.3+/-171.4	6,214,1983	123.0	112.0	116.0		816,525,816	-6.8	0.4	1	dbSNP_127	116	791,7809	187.2+/-234.5	36,719,3545	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLIM1	NM_001024215.1,NM_001024216.1,NM_017556.2	,,	42,933,5528	TT,TC,CC		9.1977,5.1294,7.8195	,,	272/375,175/277,272/374	16101217	1017,11989	2203	4300	6503	SO:0001819	synonymous_variant	54751	exon6			GACCTGCGCCCGG		CCDS163.1, CCDS30609.1, CCDS44064.1	1p36.13	2014-04-07			ENSG00000162458	ENSG00000162458			24686	protein-coding gene	gene with protein product		607747				12679033, 12496242	Standard	XM_005245900		Approved	FBLP-1, CAL, migfilin	uc001axe.1	Q8WUP2	OTTHUMG00000003079	ENST00000375766.3:c.816C>T	1.37:g.16101217C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_001024215	B3KNY0|Q5VVE0|Q5VVE1|Q8IX23|Q96T00|Q9UFD6	Silent	SNP	ENST00000375766.3	37	CCDS163.1																																																																																			C|0.920;T|0.080	0.080	strong		0.627	FBLIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008511.3	NM_001024215	
OR2L8	391190	hgsc.bcm.edu	37	1	248112915	248112915	+	Silent	SNP	A	A	G	rs10888280	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248112915A>G	ENST00000357191.3	+	1	756	c.756A>G	c.(754-756)gcA>gcG	p.A252A	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	252						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TCTACTATGCACCTTTTGTCT	0.478													A|||	1552	0.309904	0.1354	0.3458	5008	,	,		21316	0.4216		0.2952	False		,,,				2504	0.4202				p.A252A		Atlas-SNP	.											OR2L8,right_upper_lobe,carcinoma,+1,1	OR2L8	92	1	0			c.A756G						PASS	.	A	,	673,3733		48,577,1578	142.0	102.0	115.0		756,	0.6	0.2	1	dbSNP_120	115	2622,5974		396,1830,2072	no	coding-synonymous,intron	OR2L13,OR2L8	NM_001001963.1,NM_175911.2	,	444,2407,3650	GG,GA,AA		30.5026,15.2746,25.3423	,	252/313,	248112915	3295,9707	2203	4298	6501	SO:0001819	synonymous_variant	391190	exon1			CTATGCACCTTTT	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"""GPCR / Class A : Olfactory receptors"""	15014	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily L, member 8"""				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.756A>G	1.37:g.248112915A>G		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	205	97	0.473171	NM_001001963	Q6IF03	Silent	SNP	ENST00000357191.3	37	CCDS31101.1																																																																																			.	.	weak		0.478	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2		
PDCL3	79031	hgsc.bcm.edu	37	2	101192883	101192883	+	Silent	SNP	G	G	A	rs4618078	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:101192883G>A	ENST00000264254.6	+	6	1023	c.645G>A	c.(643-645)ccG>ccA	p.P215P	snoU13_ENST00000458824.1_RNA	NM_024065.4	NP_076970.1	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	215	Thioredoxin fold. {ECO:0000250}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|protein folding (GO:0006457)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|viral process (GO:0016032)	cytoplasm (GO:0005737)	protein binding involved in protein folding (GO:0044183)			endometrium(3)|large_intestine(2)|liver(1)|lung(6)	12						CTAAGAAGCCGATTGAAGACG	0.483																																					p.P215P		Atlas-SNP	.											.	PDCL3	27	.	0			c.G645A						PASS	.	G		40,4366		0,40,2163	92.0	84.0	87.0		645	-3.2	0.0	2	dbSNP_111	87	265,8335		0,265,4035	no	coding-synonymous	PDCL3	NM_024065.4		0,305,6198	AA,AG,GG		3.0814,0.9079,2.3451		215/240	101192883	305,12701	2203	4300	6503	SO:0001819	synonymous_variant	79031	exon6			GAAGCCGATTGAA	AF267853	CCDS33261.1	2q12	2008-02-05			ENSG00000115539	ENSG00000115539			28860	protein-coding gene	gene with protein product		611678					Standard	NM_024065		Approved	VIAF1	uc002tao.2	Q9H2J4	OTTHUMG00000153141	ENST00000264254.6:c.645G>A	2.37:g.101192883G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	65	21	0.323077	NM_024065	B2RA00|Q53S68	Silent	SNP	ENST00000264254.6	37	CCDS33261.1																																																																																			G|0.975;A|0.025	0.025	strong		0.483	PDCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329734.1	NM_024065	
SON	6651	hgsc.bcm.edu	37	21	34922804	34922804	+	Missense_Mutation	SNP	C	C	T	rs201446136	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:34922804C>T	ENST00000356577.4	+	3	1742	c.1267C>T	c.(1267-1269)Cca>Tca	p.P423S	SON_ENST00000300278.4_Missense_Mutation_p.P423S|SON_ENST00000290239.6_Missense_Mutation_p.P423S|SON_ENST00000381679.4_Missense_Mutation_p.P423S|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	423					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						CCTTTCTACCCCAGTGCCTGA	0.652													C|||	2	0.000399361	0.0	0.0	5008	,	,		18430	0.0		0.002	False		,,,				2504	0.0				p.P423S		Atlas-SNP	.											SON_ENST00000300278,right_lower_lobe,carcinoma,0,2	SON	343	2	0			c.C1267T						PASS	.	C	SER/PRO,SER/PRO	0,4406		0,0,2203	40.0	44.0	43.0		1267,1267	3.6	1.0	21		43	3,8593		0,3,4295	yes	missense,missense	SON	NM_032195.1,NM_138927.1	74,74	0,3,6498	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	423/2304,423/2427	34922804	3,12999	2203	4298	6501	SO:0001583	missense	6651	exon3			TCTACCCCAGTGC	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.1267C>T	21.37:g.34922804C>T	ENSP00000348984:p.Pro423Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.68	2.010597	0.35511	0.0	3.49E-4	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.12147	2.87;2.95;2.94;2.71	5.44	3.6	0.41247	.	0.239020	0.30219	N	0.010126	T	0.11024	0.0269	L	0.29908	0.895	0.27339	N	0.956563	B;P;B	0.34615	0.33;0.459;0.157	B;B;B	0.34824	0.093;0.19;0.069	T	0.13710	-1.0499	10	0.72032	D	0.01	.	10.8006	0.46487	0.0:0.8335:0.0:0.1665	.	423;423;423	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	S	423	ENSP00000348984:P423S;ENSP00000290239:P423S;ENSP00000300278:P423S;ENSP00000371095:P423S	ENSP00000290239:P423S	P	+	1	0	SON	33844674	0.779000	0.28652	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	1.438000	0.47492	0.491000	0.48974	CCA	C|1.000;T|0.000	0.000	strong		0.652	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
PRCC	5546	hgsc.bcm.edu	37	1	156761540	156761540	+	Missense_Mutation	SNP	C	C	A	rs17850664	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156761540C>A	ENST00000271526.4	+	4	1407	c.1135C>A	c.(1135-1137)Ccc>Acc	p.P379T	PRCC_ENST00000491853.1_3'UTR|PRCC_ENST00000353233.3_Intron	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	379					mitotic cell cycle checkpoint (GO:0007093)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)			PRCC/TFE3(25)	breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(5)|upper_aerodigestive_tract(1)	15	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCTGGTCCCCCCCCAGGAAAT	0.512			T	TFE3	papillary renal								C|||	21	0.00419329	0.0008	0.0043	5008	,	,		16912	0.0		0.0099	False		,,,				2504	0.0072				p.P379T		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.C1135A						PASS	.	C	THR/PRO	12,4394	19.1+/-41.9	0,12,2191	74.0	74.0	74.0		1135	-1.0	0.2	1	dbSNP_123	74	84,8516	48.1+/-107.5	0,84,4216	yes	missense	PRCC	NM_005973.4	38	0,96,6407	AA,AC,CC		0.9767,0.2724,0.7381	benign	379/492	156761540	96,12910	2203	4300	6503	SO:0001583	missense	5546	exon4			GTCCCCCCCCAGG	X99720	CCDS1157.1	1q21.1	2008-02-05			ENSG00000143294	ENSG00000143294			9343	protein-coding gene	gene with protein product		179755				8872474	Standard	NM_005973		Approved	RCCP1	uc001fqa.3	Q92733	OTTHUMG00000041294	ENST00000271526.4:c.1135C>A	1.37:g.156761540C>A	ENSP00000271526:p.Pro379Thr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	163	86	0.527607	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Missense_Mutation	SNP	ENST00000271526.4	37	CCDS1157.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	7.049	0.564048	0.13498	0.002724	0.009767	ENSG00000143294	ENST00000271526;ENST00000368201	T	0.44482	0.92	5.39	-1.04	0.10068	.	0.674960	0.15238	N	0.273053	T	0.07458	0.0188	N	0.14661	0.345	0.32356	N	0.557795	B	0.11235	0.004	B	0.08055	0.003	T	0.30090	-0.9990	10	0.20519	T	0.43	-0.1729	6.3416	0.21327	0.1139:0.5723:0.0:0.3138	rs17850664	379	Q92733	PRCC_HUMAN	T	379;355	ENSP00000271526:P379T	ENSP00000271526:P379T	P	+	1	0	PRCC	155028164	0.001000	0.12720	0.160000	0.22671	0.907000	0.53573	-0.090000	0.11163	-0.094000	0.12374	0.655000	0.94253	CCC	C|0.993;A|0.007	0.007	strong		0.512	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973	
PRKAR2B	5577	hgsc.bcm.edu	37	7	106685448	106685448	+	Silent	SNP	G	G	T	rs75385144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:106685448G>T	ENST00000265717.4	+	1	355	c.96G>T	c.(94-96)gcG>gcT	p.A32A		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	32	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TGGAGTTCGCGCTGCAGCACT	0.701													G|||	1434	0.286342	0.0197	0.4164	5008	,	,		6544	0.3433		0.3579	False		,,,				2504	0.4223				p.A32A		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.G96T						PASS	.	G		271,3937		14,243,1847	6.0	8.0	7.0		96	2.0	1.0	7	dbSNP_131	7	2493,5831		437,1619,2106	no	coding-synonymous	PRKAR2B	NM_002736.2		451,1862,3953	TT,TG,GG		29.9495,6.4401,22.0555		32/419	106685448	2764,9768	2104	4162	6266	SO:0001819	synonymous_variant	5577	exon1			GTTCGCGCTGCAG		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.96G>T	7.37:g.106685448G>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_002736	A4D0R9	Silent	SNP	ENST00000265717.4	37	CCDS5740.1																																																																																			G|0.707;T|0.293	0.293	strong		0.701	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
NUFIP1	26747	hgsc.bcm.edu	37	13	45563215	45563215	+	Silent	SNP	A	A	G	rs116755008	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:45563215A>G	ENST00000379161.4	-	1	403	c.357T>C	c.(355-357)taT>taC	p.Y119Y	GPALPP1_ENST00000379151.4_5'Flank|GPALPP1_ENST00000361121.2_5'Flank|RP11-321C24.1_ENST00000437748.2_lincRNA	NM_012345.2	NP_036477.2	Q9UHK0	NUFP1_HUMAN	nuclear fragile X mental retardation protein interacting protein 1	119					box C/D snoRNP assembly (GO:0000492)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA processing (GO:0006396)	cytosolic ribosome (GO:0022626)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|pre-snoRNP complex (GO:0070761)|presynaptic active zone (GO:0048786)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(4)|skin(3)	18		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)		ACTGTCTCCAATACCACGATG	0.552													A|||	13	0.00259585	0.0008	0.0043	5008	,	,		19062	0.0		0.0089	False		,,,				2504	0.0				p.Y119Y		Atlas-SNP	.											.	NUFIP1	41	.	0			c.T357C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	47.0	45.0	46.0		357	2.2	1.0	13	dbSNP_132	46	45,8549	28.5+/-78.6	0,45,4252	yes	coding-synonymous	NUFIP1	NM_012345.2		0,48,6452	GG,GA,AA		0.5236,0.0681,0.3692		119/496	45563215	48,12952	2203	4297	6500	SO:0001819	synonymous_variant	26747	exon1			TCTCCAATACCAC	AF159548	CCDS9393.1	13q14	2008-02-05			ENSG00000083635	ENSG00000083635			8057	protein-coding gene	gene with protein product		604354				10556305, 10894927	Standard	NM_012345		Approved	NUFIP	uc001uzp.2	Q9UHK0	OTTHUMG00000016842	ENST00000379161.4:c.357T>C	13.37:g.45563215A>G		Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	166	145	0.873494	NM_012345	Q8WVM5|Q96SG1	Silent	SNP	ENST00000379161.4	37	CCDS9393.1																																																																																			A|0.997;G|0.003	0.003	strong		0.552	NUFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044755.2	NM_012345	
WWP1	11059	hgsc.bcm.edu	37	8	87473473	87473473	+	Silent	SNP	T	T	C	rs201436587		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:87473473T>C	ENST00000517970.1	+	23	2827	c.2520T>C	c.(2518-2520)aaT>aaC	p.N840N	WWP1_ENST00000349423.2_Silent_p.N622N|WWP1_ENST00000341922.2_Silent_p.N710N|WWP1_ENST00000265428.4_Silent_p.N840N	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	840	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						AGACAGACAATGAAGTAAGAA	0.343													T|||	1	0.000199681	0.0	0.0014	5008	,	,		19862	0.0		0.0	False		,,,				2504	0.0				p.N840N		Atlas-SNP	.											.	WWP1	97	.	0			c.T2520C						PASS	.	T		0,4406		0,0,2203	148.0	139.0	142.0		2520	2.9	1.0	8		142	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WWP1	NM_007013.3		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		840/923	87473473	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	11059	exon23			AGACAATGAAGTA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.2520T>C	8.37:g.87473473T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_007013	O00307|Q5YLC1|Q96BP4	Silent	SNP	ENST00000517970.1	37	CCDS6242.1																																																																																			T|1.000;C|0.000	0.000	strong		0.343	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013	
ZNF214	7761	hgsc.bcm.edu	37	11	7022531	7022531	+	Missense_Mutation	SNP	A	A	T	rs1156525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7022531A>T	ENST00000278314.4	-	3	698	c.383T>A	c.(382-384)cTc>cAc	p.L128H	ZNF214_ENST00000536068.1_Missense_Mutation_p.L128H|ZNF214_ENST00000531083.1_5'Flank	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	128			L -> H (in dbSNP:rs1156525).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		TAAGTTCCTGAGACTTTTGCT	0.393													C|||	2883	0.575679	0.357	0.6268	5008	,	,		17911	0.7073		0.6223	False		,,,				2504	0.6513				p.L128H	Ovarian(22;251 657 736 21522 46864)	Atlas-SNP	.											.	ZNF214	65	.	0			c.T383A						PASS	.	C	HIS/LEU	1763,2639		320,1123,758	142.0	153.0	149.0		383	-3.3	0.0	11	dbSNP_87	149	5443,3147		1691,2061,543	yes	missense	ZNF214	NM_013249.2	99	2011,3184,1301	TT,TA,AA		36.6356,40.05,44.5351	benign	128/607	7022531	7206,5786	2201	4295	6496	SO:0001583	missense	7761	exon3			TTCCTGAGACTTT	AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"""Zinc fingers, C2H2-type"", ""-"""	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.383T>A	11.37:g.7022531A>T	ENSP00000278314:p.Leu128His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_013249	B2R8Q1	Missense_Mutation	SNP	ENST00000278314.4	37	CCDS31418.1	1341	0.614010989010989	184	0.37398373983739835	226	0.6243093922651933	448	0.7832167832167832	483	0.637203166226913	C	0.001	-3.896005	0.00003	0.4005	0.633644	ENSG00000149050	ENST00000278314;ENST00000536068	T;T	0.06608	3.28;3.28	4.03	-3.27	0.05048	.	1.352770	0.05114	N	0.489396	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18777	-1.0326	9	0.13108	T	0.6	.	2.2653	0.04077	0.1542:0.1174:0.2632:0.4652	rs1156525;rs16921100;rs17278413;rs52789561;rs59931558;rs1156525	128	Q9UL59	ZN214_HUMAN	H	128	ENSP00000278314:L128H;ENSP00000445373:L128H	ENSP00000278314:L128H	L	-	2	0	ZNF214	6979107	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.814000	0.01723	-1.265000	0.02449	-1.856000	0.00563	CTC	A|0.424;C|0.004;T|0.572	0.572	strong		0.393	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1		
REG3A	5068	hgsc.bcm.edu	37	2	79385823	79385823	+	Missense_Mutation	SNP	T	T	G	rs201139260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:79385823T>G	ENST00000409839.3	-	3	185	c.149A>C	c.(148-150)cAc>cCc	p.H50P	REG3A_ENST00000393878.1_Missense_Mutation_p.H50P|AC011754.1_ENST00000415201.1_RNA|REG3A_ENST00000305165.2_Missense_Mutation_p.H50P	NM_002580.2|NM_138937.2	NP_002571.1|NP_620354.1	Q06141	REG3A_HUMAN	regenerating islet-derived 3 alpha	50	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|cell proliferation (GO:0008283)|heterophilic cell-cell adhesion (GO:0007157)|multicellular organismal development (GO:0007275)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)			breast(2)|large_intestine(4)|lung(41)|prostate(2)|skin(1)	50						GGCATAGCAGTGGGAGCCATA	0.567																																					p.H50P		Atlas-SNP	.											REG3A,colon,carcinoma,-1,3	REG3A	76	3	0			c.A149C						scavenged	.						110.0	98.0	102.0					2																	79385823		2203	4300	6503	SO:0001583	missense	5068	exon2			TAGCAGTGGGAGC	S51768	CCDS1965.1	2p12	2008-02-05	2005-02-11	2005-02-11	ENSG00000172016	ENSG00000172016			8601	protein-coding gene	gene with protein product		167805	"""pancreatitis-associated protein"""	PAP		8188210	Standard	NM_002580		Approved	HIP, REG-III, REG3, PBCGF, PAP1	uc002sof.2	Q06141	OTTHUMG00000130017	ENST00000409839.3:c.149A>C	2.37:g.79385823T>G	ENSP00000386630:p.His50Pro	Somatic	132	5	0.0378788		WXS	Illumina HiSeq	Phase_I	189	20	0.10582	NM_138938		Missense_Mutation	SNP	ENST00000409839.3	37	CCDS1965.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.573344	0.45902	.	.	ENSG00000172016	ENST00000409839;ENST00000393878;ENST00000305165	T;T;T	0.15372	2.43;2.43;2.43	3.87	2.69	0.31865	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.576639	0.15737	N	0.247095	T	0.31167	0.0788	M	0.79805	2.47	0.23896	N	0.996538	P	0.38992	0.653	P	0.49085	0.6	T	0.10567	-1.0624	10	0.59425	D	0.04	.	7.406	0.26991	0.0:0.0:0.2224:0.7776	.	50	Q06141	REG3A_HUMAN	P	50	ENSP00000386630:H50P;ENSP00000377456:H50P;ENSP00000304311:H50P	ENSP00000304311:H50P	H	-	2	0	REG3A	79239331	0.876000	0.30132	0.610000	0.28997	0.032000	0.12392	0.627000	0.24506	0.813000	0.34350	0.491000	0.48974	CAC	T|0.972;G|0.028	0.028	strong		0.567	REG3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252290.2	NM_002580	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318760	21318760	+	Missense_Mutation	SNP	G	G	T	rs74880280	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:21318760G>T	ENST00000583088.1	+	3	1001	c.106G>T	c.(106-108)Gtg>Ttg	p.V36L	KCNJ12_ENST00000331718.5_Missense_Mutation_p.V36L	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	36					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CAACGGCAAGGTGCACACGCG	0.642										Prostate(3;0.18)																											p.V36L		Atlas-SNP	.											.	.	.	.	0			c.G106T						PASS	.						105.0	83.0	90.0					17																	21318760		2203	4300	6503	SO:0001583	missense	100134444	exon3			GGCAAGGTGCACA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.106G>T	17.37:g.21318760G>T	ENSP00000463778:p.Val36Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	139	25	0.179856	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	300	0.13736263736263737	124	0.25203252032520324	51	0.1408839779005525	0	0.0	125	0.16490765171503957	G	13.78	2.339733	0.41398	.	.	ENSG00000184185	ENST00000331718	T	0.47177	0.85	5.33	4.28	0.50868	Potassium channel, inwardly rectifying, Kir, N-terminal (1);	1.347560	0.05111	N	0.488898	T	0.00012	0.0000	N	0.08118	0	0.35222	D	0.776081	B	0.02656	0.0	B	0.06405	0.002	T	0.50857	-0.8778	10	0.19590	T	0.45	.	3.4799	0.07598	0.3718:0.0:0.6282:0.0	.	36	Q14500	IRK12_HUMAN	L	36	ENSP00000328150:V36L	ENSP00000328150:V36L	V	+	1	0	KCNJ12	21259353	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.295000	0.65692	2.506000	0.84524	0.591000	0.81541	GTG	G|0.887;T|0.113	0.113	strong		0.642	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
CCDC28A	25901	hgsc.bcm.edu	37	6	139097232	139097232	+	Missense_Mutation	SNP	C	C	T	rs2273510	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:139097232C>T	ENST00000332797.6	+	2	400	c.245C>T	c.(244-246)cCg>cTg	p.P82L		NM_015439.2	NP_056254.1	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A	82			P -> L (in dbSNP:rs2273510).							autonomic_ganglia(1)|large_intestine(3)|lung(8)|ovary(1)	13				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		AGAAGCTGGCCGTGGTGCAAT	0.388													C|||	360	0.071885	0.143	0.0317	5008	,	,		19158	0.0923		0.0278	False		,,,				2504	0.0286				p.P82L		Atlas-SNP	.											.	CCDC28A	34	.	0			c.C245T						PASS	.	C	LEU/PRO	591,3815	260.4+/-263.7	43,505,1655	84.0	83.0	84.0		245	0.6	0.1	6	dbSNP_100	84	176,8424	79.8+/-142.4	1,174,4125	yes	missense	CCDC28A	NM_015439.2	98	44,679,5780	TT,TC,CC		2.0465,13.4135,5.8973	possibly-damaging	82/275	139097232	767,12239	2203	4300	6503	SO:0001583	missense	25901	exon2			GCTGGCCGTGGTG	AY167571	CCDS5192.1	6q23.1-q24.1	2008-02-05	2005-09-12	2005-09-12	ENSG00000024862	ENSG00000024862			21098	protein-coding gene	gene with protein product		615353	"""chromosome 6 open reading frame 80"""	C6orf80			Standard	NM_015439		Approved	CCRL1AP, DKFZp586D0623	uc003qie.3	Q8IWP9	OTTHUMG00000015683	ENST00000332797.6:c.245C>T	6.37:g.139097232C>T	ENSP00000332716:p.Pro82Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_015439	E1P591|Q32NC7|Q66K67|Q96E23|Q9Y430	Missense_Mutation	SNP	ENST00000332797.6	37	CCDS5192.1	140	0.0641025641025641	69	0.1402439024390244	12	0.03314917127071823	41	0.07167832167832168	18	0.023746701846965697	C	13.20	2.165822	0.38217	0.134135	0.020465	ENSG00000024862	ENST00000332797	T	0.22945	1.93	5.79	0.619	0.17630	.	0.353145	0.20890	N	0.083855	T	0.05868	0.0153	L	0.36672	1.1	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.18967	-1.0320	9	0.72032	D	0.01	-4.3418	2.1887	0.03893	0.3388:0.3124:0.2202:0.1286	rs2273510;rs52791761;rs2273510	82	Q8IWP9	CC28A_HUMAN	L	82	ENSP00000332716:P82L	ENSP00000332716:P82L	P	+	2	0	CCDC28A	139138925	0.000000	0.05858	0.060000	0.19600	0.955000	0.61496	0.001000	0.13038	0.081000	0.16988	-0.258000	0.10820	CCG	C|0.936;T|0.064	0.064	strong		0.388	CCDC28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042444.1	NM_015439	
OAS2	4939	hgsc.bcm.edu	37	12	113424893	113424893	+	Silent	SNP	C	C	G	rs2072138	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:113424893C>G	ENST00000342315.4	+	2	442	c.228C>G	c.(226-228)acC>acG	p.T76T	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000449768.2_Silent_p.T76T|OAS2_ENST00000392583.2_Silent_p.T76T	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	76	OAS domain 1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CCGATGGTACCCTTGTCCTCT	0.463													C|||	1097	0.21905	0.2141	0.3401	5008	,	,		19158	0.0863		0.2753	False		,,,				2504	0.2188				p.T76T	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											OAS2_ENST00000449768,NS,carcinoma,+1,1	OAS2	86	1	0			c.C228G						PASS	.	C	,,	1037,3369	379.7+/-323.4	117,803,1283	111.0	104.0	106.0		228,228,228	1.2	0.0	12	dbSNP_96	106	2475,6125	406.4+/-348.8	353,1769,2178	no	coding-synonymous,coding-synonymous,coding-synonymous	OAS2	NM_001032731.1,NM_002535.2,NM_016817.2	,,	470,2572,3461	GG,GC,CC		28.7791,23.5361,27.0029	,,	76/173,76/688,76/720	113424893	3512,9494	2203	4300	6503	SO:0001819	synonymous_variant	4939	exon2			TGGTACCCTTGTC	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.228C>G	12.37:g.113424893C>G		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	201	196	0.975124	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Silent	SNP	ENST00000342315.4	37	CCDS31906.1																																																																																			C|0.753;G|0.247	0.247	strong		0.463	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1		
SLC12A1	6557	hgsc.bcm.edu	37	15	48539587	48539587	+	Silent	SNP	T	T	C	rs6493311	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:48539587T>C	ENST00000558405.1	+	12	1628	c.1614T>C	c.(1612-1614)taT>taC	p.Y538Y	SLC12A1_ENST00000396577.3_Silent_p.Y538Y|SLC12A1_ENST00000380993.3_Silent_p.Y538Y			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	538					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CAAAGGGATATGGGAAAAACA	0.348													C|||	2482	0.495607	0.8366	0.2968	5008	,	,		18177	0.5883		0.2097	False		,,,				2504	0.3742				p.Y538Y		Atlas-SNP	.											.	SLC12A1	243	.	0			c.T1614C						PASS	.	C	,	3133,1263	429.1+/-342.1	1128,877,193	76.0	78.0	77.0		1614,1614	-4.5	0.8	15	dbSNP_116	77	1618,6976	741.7+/-407.2	156,1306,2835	no	coding-synonymous,coding-synonymous	SLC12A1	NM_000338.2,NM_001184832.1	,	1284,2183,3028	CC,CT,TT		18.8271,28.7307,36.5743	,	538/1100,538/1100	48539587	4751,8239	2198	4297	6495	SO:0001819	synonymous_variant	6557	exon13			GGGATATGGGAAA		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1614T>C	15.37:g.48539587T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_001184832	A8JYA2|E9PDW4	Silent	SNP	ENST00000558405.1	37	CCDS10129.2																																																																																			T|0.563;C|0.437	0.437	strong		0.348	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		
HSPG2	3339	hgsc.bcm.edu	37	1	22163390	22163390	+	Silent	SNP	G	G	A	rs35444472	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22163390G>A	ENST00000374695.3	-	75	10339	c.10260C>T	c.(10258-10260)caC>caT	p.H3420H		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3420	Ig-like C2-type 20.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCACAGCACAGTGGAACTCAA	0.657													G|||	431	0.0860623	0.1664	0.0519	5008	,	,		16913	0.001		0.0676	False		,,,				2504	0.1084				p.H3420H		Atlas-SNP	.											.	HSPG2	311	.	0			c.C10260T						PASS	.	G		729,3651		59,611,1520	51.0	42.0	45.0		10260	2.6	1.0	1	dbSNP_126	45	633,7953		25,583,3685	no	coding-synonymous	HSPG2	NM_005529.5		84,1194,5205	AA,AG,GG		7.3725,16.6438,10.5044		3420/4392	22163390	1362,11604	2190	4293	6483	SO:0001819	synonymous_variant	3339	exon75			AGCACAGTGGAAC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.10260C>T	1.37:g.22163390G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			A|0.098;C|0.000;G|0.902;T|0.000	0.098	strong		0.657	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
WDR88	126248	hgsc.bcm.edu	37	19	33647379	33647379	+	Missense_Mutation	SNP	T	T	C	rs11881580	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:33647379T>C	ENST00000355868.3	+	7	1004	c.928T>C	c.(928-930)Tgt>Cgt	p.C310R	WDR88_ENST00000361680.2_Missense_Mutation_p.C310R	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	310			C -> R (in dbSNP:rs11881580). {ECO:0000269|PubMed:14702039}.							breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					GTTTCGAAACTGTGGAGCCTG	0.463													C|||	1279	0.255391	0.5295	0.3184	5008	,	,		20658	0.1855		0.0835	False		,,,				2504	0.089				p.C310R		Atlas-SNP	.											.	WDR88	50	.	0			c.T928C						PASS	.	C	ARG/CYS	2019,2387	613.3+/-392.2	471,1077,655	108.0	103.0	105.0		928	-1.4	0.0	19	dbSNP_120	105	687,7913	788.3+/-407.6	32,623,3645	yes	missense	WDR88	NM_173479.3	180	503,1700,4300	CC,CT,TT		7.9884,45.8239,20.8058	benign	310/473	33647379	2706,10300	2203	4300	6503	SO:0001583	missense	126248	exon7			CGAAACTGTGGAG	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"""WD repeat domain containing"""	26999	protein-coding gene	gene with protein product			"""PQQ repeat and WD repeat domain containing"""	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.928T>C	19.37:g.33647379T>C	ENSP00000348129:p.Cys310Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_173479	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	37	CCDS12429.1	488	0.22344322344322345	247	0.5020325203252033	88	0.2430939226519337	99	0.17307692307692307	54	0.0712401055408971	C	0.005	-2.213718	0.00289	0.458239	0.079884	ENSG00000166359	ENST00000355868;ENST00000361680	T;T	0.60920	0.45;0.15	5.59	-1.36	0.09085	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	7739.210000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.01096	-1.015	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35724	-0.9777	9	0.11182	T	0.66	.	3.4696	0.07562	0.1074:0.496:0.106:0.2906	rs11881580;rs60048014;rs11881580	310	Q6ZMY6	WDR88_HUMAN	R	310	ENSP00000348129:C310R;ENSP00000355148:C310R	ENSP00000348129:C310R	C	+	1	0	WDR88	38339219	0.000000	0.05858	0.038000	0.18304	0.184000	0.23303	-0.233000	0.09041	-0.207000	0.10187	-0.222000	0.12452	TGT	T|0.773;C|0.227	0.227	strong		0.463	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
DNHD1	144132	hgsc.bcm.edu	37	11	6530297	6530297	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6530297C>T	ENST00000527990.2	+	3	1108	c.1108C>T	c.(1108-1110)Cgc>Tgc	p.R370C	DNHD1_ENST00000354685.3_Missense_Mutation_p.R370C|DNHD1_ENST00000254579.6_Missense_Mutation_p.R370C			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	370					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TTGCCTCTTACGCAAGTCCTT	0.453																																					p.R370C		Atlas-SNP	.											DNHD1,rectum,carcinoma,0,6	DNHD1	198	6	0			c.C1108T						scavenged	.						190.0	175.0	180.0					11																	6530297		2201	4296	6497	SO:0001583	missense	144132	exon4			CTCTTACGCAAGT	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.1108C>T	11.37:g.6530297C>T	ENSP00000436180:p.Arg370Cys	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	274	3	0.0109489	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.680339	0.68042	.	.	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.17691	2.26;2.26;2.26	5.47	3.33	0.38152	.	0.523957	0.16861	N	0.196527	T	0.36853	0.0982	M	0.78801	2.425	0.38032	D	0.935202	D;D	0.89917	1.0;1.0	P;D	0.63597	0.877;0.916	T	0.31833	-0.9929	10	0.56958	D	0.05	.	8.7968	0.34885	0.1575:0.7492:0.0:0.0933	.	370;370	Q96M86;Q96M86-4	DNHD1_HUMAN;.	C	370	ENSP00000254579:R370C;ENSP00000346716:R370C;ENSP00000436180:R370C	ENSP00000254579:R370C	R	+	1	0	DNHD1	6486873	0.994000	0.37717	1.000000	0.80357	0.993000	0.82548	0.780000	0.26760	1.242000	0.43836	0.650000	0.86243	CGC	.	.	none		0.453	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
BEST1	7439	hgsc.bcm.edu	37	11	61730183	61730183	+	Silent	SNP	C	C	T	rs1800008	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61730183C>T	ENST00000378043.4	+	10	2200	c.1557C>T	c.(1555-1557)agC>agT	p.S519S	FTH1_ENST00000529631.1_Intron|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000449131.2_Silent_p.S459S|BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000301774.9_Silent_p.S147S|BEST1_ENST00000378042.3_Silent_p.S432S	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	519					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						TCTCAGAGAGCGATGGGGCCT	0.473													C|||	508	0.101438	0.0166	0.1239	5008	,	,		21604	0.003		0.2167	False		,,,				2504	0.183				p.S519S		Atlas-SNP	.											BEST1_ENST00000449131,NS,carcinoma,+1,2	BEST1	85	2	0			c.C1557T						PASS	.	C	,	219,4185	132.9+/-169.3	6,207,1989	78.0	74.0	76.0		1377,1557	-6.9	0.0	11	dbSNP_89	76	1998,6600	351.3+/-328.2	229,1540,2530	no	coding-synonymous,coding-synonymous	BEST1	NM_001139443.1,NM_004183.3	,	235,1747,4519	TT,TC,CC		23.238,4.9728,17.0512	,	459/605,519/586	61730183	2217,10785	2202	4299	6501	SO:0001819	synonymous_variant	7439	exon10			AGAGAGCGATGGG	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1557C>T	11.37:g.61730183C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			C|0.846;T|0.154	0.154	strong		0.473	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
PHAX	51808	hgsc.bcm.edu	37	5	125939409	125939409	+	Missense_Mutation	SNP	C	C	T	rs3734173	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:125939409C>T	ENST00000297540.4	+	2	939	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C	PHAX_ENST00000514725.1_3'UTR	NM_032177.3	NP_115553.2	Q9H814	PHAX_HUMAN	phosphorylated adaptor for RNA export	82	Necessary for interaction with CBP80. {ECO:0000250}.		R -> C (in dbSNP:rs3734173).		gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein transport (GO:0015031)|RNA metabolic process (GO:0016070)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA binding (GO:0003723)|toxic substance binding (GO:0015643)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	8						TCTTTGGAAACGCAAACGACA	0.423													C|||	436	0.0870607	0.0023	0.062	5008	,	,		19161	0.2698		0.0437	False		,,,				2504	0.0757				p.R82C		Atlas-SNP	.											.	PHAX	20	.	0			c.C244T						PASS	.	C	CYS/ARG	44,4362	45.3+/-79.5	0,44,2159	130.0	131.0	131.0		244	5.7	1.0	5	dbSNP_107	131	358,8242	119.0+/-178.4	7,344,3949	yes	missense	PHAX	NM_032177.3	180	7,388,6108	TT,TC,CC		4.1628,0.9986,3.0909	probably-damaging	82/395	125939409	402,12604	2203	4300	6503	SO:0001583	missense	51808	exon2			TGGAAACGCAAAC	AK023255	CCDS4138.1	5q23.2	2011-05-24	2008-10-01	2008-10-01	ENSG00000164902	ENSG00000164902			10241	protein-coding gene	gene with protein product		604924	"""RNA U, small nuclear RNA export adaptor (phosphorylation regulated)"""	RNUXA		10786834	Standard	NM_032177		Approved	FLJ13193	uc003kua.2	Q9H814	OTTHUMG00000163273	ENST00000297540.4:c.244C>T	5.37:g.125939409C>T	ENSP00000297540:p.Arg82Cys	Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	283	139	0.491166	NM_032177	Q9H8W1	Missense_Mutation	SNP	ENST00000297540.4	37	CCDS4138.1	220	0.10073260073260074	3	0.006097560975609756	17	0.04696132596685083	166	0.2902097902097902	34	0.044854881266490766	C	23.6	4.431419	0.83776	0.009986	0.041628	ENSG00000164902	ENST00000297540;ENST00000456348	T	0.23950	1.88	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.70275	2.135	0.09310	P	0.999999999354703	D	0.71674	0.998	P	0.57283	0.817	T	0.00597	-1.1652	9	0.87932	D	0	-24.2835	19.9279	0.97110	0.0:1.0:0.0:0.0	rs3734173;rs52819871;rs59043674;rs3734173	82	Q9H814	PHAX_HUMAN	C	82	ENSP00000297540:R82C	ENSP00000297540:R82C	R	+	1	0	PHAX	125967308	0.989000	0.36119	1.000000	0.80357	0.998000	0.95712	1.004000	0.29822	2.715000	0.92844	0.655000	0.94253	CGC	C|0.935;T|0.065	0.065	strong		0.423	PHAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250924.1	NM_032177	
MCM8	84515	hgsc.bcm.edu	37	20	5953815	5953815	+	Silent	SNP	A	A	G	rs34464794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:5953815A>G	ENST00000378896.3	+	12	1745	c.1368A>G	c.(1366-1368)ccA>ccG	p.P456P	MCM8_ENST00000265187.4_Silent_p.P440P|MCM8_ENST00000378883.1_Intron|MCM8_ENST00000378886.2_Silent_p.P496P	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	456	MCM.				cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						TTGGAGATCCAGGCCTAGGAA	0.403													A|||	98	0.0195687	0.003	0.013	5008	,	,		19499	0.0		0.0646	False		,,,				2504	0.0204				p.P456P		Atlas-SNP	.											MCM8_ENST00000378896,NS,carcinoma,+2,2	MCM8	125	2	0			c.A1368G						PASS	.	A	,	58,4348	54.9+/-90.9	0,58,2145	131.0	123.0	126.0		1368,1320	3.9	1.0	20	dbSNP_126	126	552,8048	152.7+/-207.2	16,520,3764	no	coding-synonymous,coding-synonymous	MCM8	NM_032485.4,NM_182802.1	,	16,578,5909	GG,GA,AA		6.4186,1.3164,4.6901	,	456/841,440/825	5953815	610,12396	2203	4300	6503	SO:0001819	synonymous_variant	84515	exon12			AGATCCAGGCCTA	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.1368A>G	20.37:g.5953815A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	140	65	0.464286	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Silent	SNP	ENST00000378896.3	37	CCDS13094.1																																																																																			A|0.960;G|0.040	0.040	strong		0.403	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
SNTA1	6640	hgsc.bcm.edu	37	20	32026766	32026766	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32026766G>A	ENST00000217381.2	-	2	648	c.377C>T	c.(376-378)aCa>aTa	p.T126I		NM_003098.2	NP_003089.1	Q13424	SNTA1_HUMAN	syntrophin, alpha 1	126	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|neuromuscular junction development (GO:0007528)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of vasoconstriction by circulating norepinephrine (GO:0003117)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular (GO:0005622)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	ATPase binding (GO:0051117)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)			breast(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(1)	13						AAGGGCCTCTGTCTGGTCAGC	0.542																																					p.T126I		Atlas-SNP	.											.	SNTA1	35	.	0			c.C377T						PASS	.						127.0	124.0	125.0					20																	32026766		2203	4300	6503	SO:0001583	missense	6640	exon2			GCCTCTGTCTGGT	U40571	CCDS13220.1	20q11.2	2014-09-17	2012-06-15		ENSG00000101400	ENSG00000101400			11167	protein-coding gene	gene with protein product	"""pro-TGF-alpha cytoplasmic domain-interacting protein 1"", ""dystrophin-associated protein A1, 59kDa, acidic component"""	601017	"""syntrophin, alpha 1 (dystrophin-associated protein A1, 59kD, acidic component)"""	SNT1		8576247, 8612778	Standard	NM_003098		Approved	TACIP1, LQT12	uc002wzd.1	Q13424	OTTHUMG00000032259	ENST00000217381.2:c.377C>T	20.37:g.32026766G>A	ENSP00000217381:p.Thr126Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_003098	A8K7H9|B4DX40|E1P5N1|Q16438	Missense_Mutation	SNP	ENST00000217381.2	37	CCDS13220.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.967218	0.74131	.	.	ENSG00000101400	ENST00000217381	T	0.27256	1.68	5.03	5.03	0.67393	PDZ/DHR/GLGF (4);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.55114	0.1900	M	0.80028	2.48	0.58432	D	0.999999	D;P	0.89917	1.0;0.918	D;D	0.81914	0.995;0.961	T	0.60757	-0.7200	10	0.87932	D	0	-14.1481	18.1836	0.89786	0.0:0.0:1.0:0.0	.	126;126	B4DX40;Q13424	.;SNTA1_HUMAN	I	126	ENSP00000217381:T126I	ENSP00000217381:T126I	T	-	2	0	SNTA1	31490427	1.000000	0.71417	0.987000	0.45799	0.833000	0.47200	6.092000	0.71414	2.614000	0.88457	0.561000	0.74099	ACA	.	.	none		0.542	SNTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078704.2	NM_003098	
SPTB	6710	hgsc.bcm.edu	37	14	65263347	65263347	+	Silent	SNP	C	C	T	rs229586	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:65263347C>T	ENST00000389721.5	-	10	1301	c.1269G>A	c.(1267-1269)ctG>ctA	p.L423L	SPTB_ENST00000542895.1_Silent_p.L423L|SPTB_ENST00000389722.3_Silent_p.L423L|SPTB_ENST00000389720.3_Silent_p.L423L|SPTB_ENST00000556626.1_Silent_p.L423L	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	423					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		AGCGCCGGGCCAGTTGCTCTA	0.592													C|||	1409	0.28135	0.267	0.232	5008	,	,		16522	0.2907		0.2266	False		,,,				2504	0.3824				p.L423L		Atlas-SNP	.											.	SPTB	378	.	0			c.G1269A						PASS	.	C	,	1191,3215	417.4+/-337.9	165,861,1177	64.0	66.0	65.0		1269,1269	4.0	1.0	14	dbSNP_79	65	2094,6506	362.5+/-332.8	257,1580,2463	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	422,2441,3640	TT,TC,CC		24.3488,27.0313,25.2576	,	423/2138,423/2329	65263347	3285,9721	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon10			CCGGGCCAGTTGC		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.1269G>A	14.37:g.65263347C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			C|0.746;T|0.254	0.254	strong		0.592	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
BRINP1	1620	hgsc.bcm.edu	37	9	122001000	122001000	+	Silent	SNP	G	G	A	rs2274157	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:122001000G>A	ENST00000265922.3	-	5	1079	c.618C>T	c.(616-618)agC>agT	p.S206S	BRINP1_ENST00000373964.2_Silent_p.S206S	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	206	MACPF.				cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)		p.S206S(1)									GATTGTCATAGCTGTTACAGC	0.502													G|||	2214	0.442093	0.1664	0.4726	5008	,	,		19411	0.6736		0.4523	False		,,,				2504	0.544				p.S206S		Atlas-SNP	.											DBC1,NS,carcinoma,0,1	DBC1	194	1	1	Substitution - coding silent(1)	stomach(1)	c.C618T						PASS	.	G		900,3506	349.3+/-310.3	95,710,1398	129.0	93.0	105.0		618	5.9	1.0	9	dbSNP_100	105	3669,4931	526.4+/-380.9	780,2109,1411	no	coding-synonymous	DBC1	NM_014618.2		875,2819,2809	AA,AG,GG		42.6628,20.4267,35.1299		206/762	122001000	4569,8437	2203	4300	6503	SO:0001819	synonymous_variant	1620	exon5			GTCATAGCTGTTA	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"""deleted in bladder cancer chromosome region candidate 1"", ""deleted in bladder cancer 1"""	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.618C>T	9.37:g.122001000G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	169	97	0.573964	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																			A|0.392;C|0.004	0.392	strong		0.502	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
DNAH14	127602	hgsc.bcm.edu	37	1	225373072	225373072	+	Missense_Mutation	SNP	C	C	T	rs61851487	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225373072C>T	ENST00000445597.2	+	24	4334	c.4334C>T	c.(4333-4335)aCg>aTg	p.T1445M	DNAH14_ENST00000439375.2_Missense_Mutation_p.T1850M|DNAH14_ENST00000430092.1_Missense_Mutation_p.T1850M			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1445					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AAAGCATTAACGCTATTACCA	0.338													C|||	877	0.17512	0.1331	0.1902	5008	,	,		14696	0.3125		0.1133	False		,,,				2504	0.1431				p.T1850M		Atlas-SNP	.											.	DNAH14	300	.	0			c.C5549T						PASS	.	C	MET/THR	179,1205		11,157,524	132.0	121.0	124.0		5549	-0.1	0.0	1	dbSNP_129	124	381,2801		16,349,1226	yes	missense	DNAH14	NM_001373.1	81	27,506,1750	TT,TC,CC		11.9736,12.9335,12.2646	possibly-damaging	1850/4516	225373072	560,4006	692	1591	2283	SO:0001583	missense	127602	exon36			CATTAACGCTATT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.4334C>T	1.37:g.225373072C>T	ENSP00000409472:p.Thr1445Met	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	182	85	0.467033	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		360	0.16483516483516483	57	0.11585365853658537	55	0.15193370165745856	171	0.29895104895104896	77	0.10158311345646438	C	8.763	0.923986	0.18056	0.129335	0.119736	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375;ENST00000328556	T;T;T;T	0.35048	3.24;1.33;1.33;1.57	4.91	-0.12	0.13539	.	.	.	.	.	T	0.00012	0.0000	M	0.74647	2.275	0.80722	P	0.0	B	0.22276	0.067	B	0.16722	0.016	T	0.16041	-1.0416	8	0.52906	T	0.07	.	8.5999	0.33738	0.0:0.3252:0.0:0.6748	rs61851487	1850	Q0VDD8-4	.	M	1445;1850;1850;944	ENSP00000409472:T1445M;ENSP00000414402:T1850M;ENSP00000392061:T1850M;ENSP00000332424:T944M	ENSP00000332424:T944M	T	+	2	0	DNAH14	223439695	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.204000	0.17335	-0.306000	0.08818	-0.438000	0.05819	ACG	C|0.848;T|0.152	0.152	strong		0.338	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
PTGES2	80142	hgsc.bcm.edu	37	9	130886050	130886050	+	Missense_Mutation	SNP	C	C	G	rs149102151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:130886050C>G	ENST00000338961.6	-	4	1361	c.617G>C	c.(616-618)gGc>gCc	p.G206A	PTGES2_ENST00000277462.5_Missense_Mutation_p.G15A|PTGES2_ENST00000483625.1_5'UTR	NM_001256335.1|NM_025072.6	NP_001243264.1|NP_079348.1	Q9H7Z7	PGES2_HUMAN	prostaglandin E synthase 2	206					cell redox homeostasis (GO:0045454)|positive regulation of transcription, DNA-templated (GO:0045893)|prostaglandin biosynthetic process (GO:0001516)|secretion (GO:0046903)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|glutathione binding (GO:0043295)|heme binding (GO:0020037)|lyase activity (GO:0016829)|prostaglandin-E synthase activity (GO:0050220)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(2)	4						GTACTTATTGCCGAACTCGGT	0.592													C|||	14	0.00279553	0.0008	0.0029	5008	,	,		14684	0.0		0.007	False		,,,				2504	0.0041				p.G206A		Atlas-SNP	.											.	PTGES2	14	.	0			c.G617C						PASS	.	C	ALA/GLY	4,4402	6.2+/-15.9	0,4,2199	175.0	125.0	142.0		617	4.9	0.9	9	dbSNP_134	142	62,8538	38.8+/-94.9	0,62,4238	yes	missense	PTGES2	NM_025072.5	60	0,66,6437	GG,GC,CC		0.7209,0.0908,0.5075	benign	206/378	130886050	66,12940	2203	4300	6503	SO:0001583	missense	80142	exon4			TTATTGCCGAACT	AK024100	CCDS6891.1	9q34.12	2008-05-06	2002-06-13	2002-06-14	ENSG00000148334	ENSG00000148334			17822	protein-coding gene	gene with protein product		608152	"""chromosome 9 open reading frame 15"""	C9orf15		11866447	Standard	NM_025072		Approved	FLJ14038	uc004bti.4	Q9H7Z7	OTTHUMG00000020730	ENST00000338961.6:c.617G>C	9.37:g.130886050C>G	ENSP00000345341:p.Gly206Ala	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	155	83	0.535484	NM_025072	Q53EW9|Q5SYV6|Q96GI0|Q96GL2	Missense_Mutation	SNP	ENST00000338961.6	37	CCDS6891.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	8.598	0.886079	0.17540	9.08E-4	0.007209	ENSG00000148334	ENST00000338961;ENST00000277462;ENST00000449878	T;T;T	0.39787	2.7;1.06;2.7	5.84	4.94	0.65067	Thioredoxin-like fold (1);	0.329789	0.40640	N	0.001045	T	0.19087	0.0458	L	0.28274	0.84	0.30778	N	0.742268	B	0.16603	0.018	B	0.10450	0.005	T	0.19321	-1.0309	10	0.09843	T	0.71	-0.0806	9.3167	0.37939	0.0:0.779:0.0:0.221	.	206	Q9H7Z7	PGES2_HUMAN	A	206;15;171	ENSP00000345341:G206A;ENSP00000277462:G15A;ENSP00000411378:G171A	ENSP00000277462:G15A	G	-	2	0	PTGES2	129925871	1.000000	0.71417	0.937000	0.37676	0.664000	0.39144	1.134000	0.31442	1.485000	0.48380	0.561000	0.74099	GGC	C|0.995;G|0.005	0.005	strong		0.592	PTGES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054339.1		
CEP72	55722	hgsc.bcm.edu	37	5	639231	639231	+	Missense_Mutation	SNP	C	C	A	rs12522955	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:639231C>A	ENST00000264935.5	+	8	1324	c.1234C>A	c.(1234-1236)Ccc>Acc	p.P412T	CEP72_ENST00000444221.1_3'UTR	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	centrosomal protein 72kDa	412			P -> T (in dbSNP:rs12522955).		G2/M transition of mitotic cell cycle (GO:0000086)|gamma-tubulin complex localization (GO:0033566)|mitotic cell cycle (GO:0000278)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)				autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	20			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			CTCGGCTCTACCCGGGAAGAA	0.647													C|||	453	0.0904553	0.0045	0.1138	5008	,	,		17828	0.0099		0.1928	False		,,,				2504	0.1677				p.P412T		Atlas-SNP	.											.	CEP72	53	.	0			c.C1234A						PASS	.	C	THR/PRO	169,4237	106.5+/-144.9	0,169,2034	37.0	42.0	40.0		1234	3.6	0.0	5	dbSNP_120	40	1709,6891	299.8+/-304.6	175,1359,2766	yes	missense	CEP72	NM_018140.3	38	175,1528,4800	AA,AC,CC		19.8721,3.8357,14.4395	probably-damaging	412/648	639231	1878,11128	2203	4300	6503	SO:0001583	missense	55722	exon8			GCTCTACCCGGGA	BC000132	CCDS34126.1	5p15.33	2014-02-20			ENSG00000112877	ENSG00000112877			25547	protein-coding gene	gene with protein product						10819331	Standard	NM_018140		Approved	KIAA1519, FLJ10565	uc003jbf.3	Q9P209	OTTHUMG00000161745	ENST00000264935.5:c.1234C>A	5.37:g.639231C>A	ENSP00000264935:p.Pro412Thr	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	263	140	0.532319	NM_018140	B4DR26|Q9BV03|Q9BWM3|Q9NVR4	Missense_Mutation	SNP	ENST00000264935.5	37	CCDS34126.1	210	0.09615384615384616	2	0.0040650406504065045	50	0.13812154696132597	5	0.008741258741258742	153	0.20184696569920843	C	10.31	1.314332	0.23908	0.038357	0.198721	ENSG00000112877	ENST00000264935	T	0.32753	1.44	4.45	3.58	0.41010	.	0.286634	0.29266	N	0.012641	T	0.00039	0.0001	M	0.65975	2.015	0.44694	P	0.0023140000000000382	D	0.60160	0.987	P	0.54544	0.755	T	0.16129	-1.0413	9	0.08599	T	0.76	-10.98	8.9781	0.35948	0.0:0.8928:0.0:0.1072	rs12522955;rs12522955	412	Q9P209	CEP72_HUMAN	T	412	ENSP00000264935:P412T	ENSP00000264935:P412T	P	+	1	0	CEP72	692231	0.003000	0.15002	0.007000	0.13788	0.003000	0.03518	1.019000	0.30014	1.171000	0.42768	0.462000	0.41574	CCC	C|0.877;A|0.123	0.123	strong		0.647	CEP72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365967.3	NM_018140	
OR7C1	26664	hgsc.bcm.edu	37	19	14910210	14910210	+	Missense_Mutation	SNP	C	C	G	rs73004304	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14910210C>G	ENST00000248073.2	-	1	813	c.739G>C	c.(739-741)Gtg>Ctg	p.V247L	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	247				V -> L (in Ref. 3; CAA61823). {ECO:0000305}.	spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(2)|ovary(2)|prostate(1)	18						AAGGTGACCACTGAGAGGTGG	0.458													C|||	866	0.172923	0.2337	0.2089	5008	,	,		19085	0.0486		0.2137	False		,,,				2504	0.1513				p.V247L		Atlas-SNP	.											.	OR7C1	58	.	0			c.G739C						PASS	.	C	LEU/VAL	1067,3339	390.7+/-327.8	135,797,1271	79.0	74.0	76.0		739	1.4	0.0	19	dbSNP_130	76	1733,6867	314.9+/-312.0	174,1385,2741	yes	missense	OR7C1	NM_198944.1	32	309,2182,4012	GG,GC,CC		20.1512,24.217,21.5285	possibly-damaging	247/321	14910210	2800,10206	2203	4300	6503	SO:0001583	missense	26664	exon1			TGACCACTGAGAG	X89676	CCDS12317.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8373	protein-coding gene	gene with protein product				OR7C4			Standard	NM_198944		Approved	OR19-5	uc010xnz.2	O76099		ENST00000248073.2:c.739G>C	19.37:g.14910210C>G	ENSP00000248073:p.Val247Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	113	60	0.530973	NM_198944	Q15621|Q6IFP2|Q96R94	Missense_Mutation	SNP	ENST00000248073.2	37	CCDS12317.1	370	0.16941391941391942	107	0.21747967479674796	75	0.20718232044198895	18	0.03146853146853147	170	0.22427440633245382	c	15.09	2.731310	0.48939	0.24217	0.201512	ENSG00000127530	ENST00000248073	T	0.00216	8.53	3.64	1.43	0.22495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31709	U	0.007199	T	0.00012	0.0000	H	0.97158	3.95	0.80722	P	0.0	D	0.55385	0.971	P	0.55508	0.777	T	0.36187	-0.9758	9	0.87932	D	0	.	7.0136	0.24875	0.0:0.7223:0.1746:0.103	.	247	O76099	OR7C1_HUMAN	L	247	ENSP00000248073:V247L	ENSP00000248073:V247L	V	-	1	0	OR7C1	14771210	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	1.003000	0.29809	0.335000	0.23614	-0.253000	0.11424	GTG	C|0.801;G|0.199	0.199	strong		0.458	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1		
UGT2B11	10720	hgsc.bcm.edu	37	4	70066376	70066376	+	Missense_Mutation	SNP	C	C	G	rs144149579	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:70066376C>G	ENST00000446444.1	-	6	1380	c.1372G>C	c.(1372-1374)Gat>Cat	p.D458H	RP11-704M14.1_ENST00000505646.1_RNA|RP11-704M14.1_ENST00000504301.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	458					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.D458H(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						ACTGCTCGATCCAGGGGCTTT	0.408																																					p.D458H		Atlas-SNP	.											UGT2B11,trunk,malignant_melanoma,0,1	UGT2B11	92	1	1	Substitution - Missense(1)	skin(1)	c.G1372C						scavenged	.						104.0	107.0	106.0					4																	70066376		2203	4298	6501	SO:0001583	missense	10720	exon6			CTCGATCCAGGGG	AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.1372G>C	4.37:g.70066376C>G	ENSP00000387683:p.Asp458His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	118	14	0.118644	NM_001073	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	.	.	.	.	.	.	.	.	.	.	-	11.29	1.595749	0.28445	.	.	ENSG00000213759	ENST00000446444	T	0.73469	-0.75	1.27	1.27	0.21489	.	0.000000	0.64402	U	0.000002	D	0.88738	0.6518	H	0.97415	4	0.31420	N	0.674431	D	0.89917	1.0	D	0.81914	0.995	D	0.86564	0.1843	10	0.87932	D	0	.	8.4963	0.33130	0.0:1.0:0.0:0.0	.	458	O75310	UDB11_HUMAN	H	458	ENSP00000387683:D458H	ENSP00000387683:D458H	D	-	1	0	UGT2B11	70100965	0.997000	0.39634	0.937000	0.37676	0.142000	0.21351	3.075000	0.50073	1.023000	0.39654	0.184000	0.17185	GAT	C|0.959;G|0.041	0.041	strong		0.408	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
TMC2	117532	hgsc.bcm.edu	37	20	2618140	2618140	+	Silent	SNP	T	T	C	rs6083915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2618140T>C	ENST00000358864.1	+	19	2421	c.2406T>C	c.(2404-2406)agT>agC	p.S802S		NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	802					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TTGAGAAGAGTCACAAATCTG	0.468													C|||	3901	0.778954	0.6823	0.7983	5008	,	,		19424	0.8581		0.7515	False		,,,				2504	0.8425				p.S802S		Atlas-SNP	.											.	TMC2	121	.	0			c.T2406C						PASS	.	C		3086,1320	441.6+/-346.4	1095,896,212	103.0	99.0	100.0		2406	4.1	1.0	20	dbSNP_114	100	6459,2141	367.6+/-334.8	2422,1615,263	no	coding-synonymous	TMC2	NM_080751.2		3517,2511,475	CC,CT,TT		24.8953,29.9591,26.6108		802/907	2618140	9545,3461	2203	4300	6503	SO:0001819	synonymous_variant	117532	exon19			GAAGAGTCACAAA	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"""transmembrane, cochlear expressed, 2"""	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.2406T>C	20.37:g.2618140T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Silent	SNP	ENST00000358864.1	37	CCDS13029.2																																																																																			T|0.247;C|0.753	0.753	strong		0.468	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
DSPP	1834	hgsc.bcm.edu	37	4	88536520	88536520	+	Silent	SNP	T	T	C	rs62651554	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:88536520T>C	ENST00000282478.7	+	4	2739	c.2706T>C	c.(2704-2706)gaT>gaC	p.D902D	DSPP_ENST00000399271.1_Silent_p.D902D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	902	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgatagtgacagca	0.478													t|||	1630	0.325479	0.2352	0.4179	5008	,	,		33602	0.2867		0.3519	False		,,,				2504	0.3947				p.D902D		Atlas-SNP	.											.	DSPP	174	.	0			c.T2706C						PASS	.			883,2419		145,593,913	82.0	96.0	91.0		2706	-0.5	0.0	4	dbSNP_132	91	2213,3715		456,1301,1207	no	coding-synonymous	DSPP	NM_014208.3		601,1894,2120	CC,CT,TT		37.3313,26.7414,33.5428		902/1302	88536520	3096,6134	1651	2964	4615	SO:0001819	synonymous_variant	1834	exon5			CAGTGATAGTGAC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2706T>C	4.37:g.88536520T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	144	75	0.520833	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			T|0.673;C|0.327	0.327	strong		0.478	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ABHD16A	7920	hgsc.bcm.edu	37	6	31656517	31656517	+	Silent	SNP	G	G	A	rs147830631		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31656517G>A	ENST00000395952.3	-	14	1395	c.1233C>T	c.(1231-1233)aaC>aaT	p.N411N	ABHD16A_ENST00000440843.2_Silent_p.N378N|XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|ABHD16A_ENST00000471644.1_5'UTR|ABHD16A_ENST00000375842.4_Silent_p.N192N	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	411						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						GCTGCTCCGCGTTGTTTAGAT	0.577																																					p.N411N		Atlas-SNP	.											.	ABHD16A	34	.	0			c.C1233T						PASS	.	G	,	0,3016		0,0,1508	36.0	35.0	35.0		1134,1233	-10.4	0.0	6	dbSNP_134	35	1,5417		0,1,2708	yes	coding-synonymous,coding-synonymous	ABHD16A	NM_001177515.1,NM_021160.2	,	0,1,4216	AA,AG,GG		0.0185,0.0,0.0119	,	378/526,411/559	31656517	1,8433	1508	2709	4217	SO:0001819	synonymous_variant	7920	exon14			CTCCGCGTTGTTT	AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"""Abhydrolase domain containing"""	13921	protein-coding gene	gene with protein product		142620	"""HLA-B associated transcript 5"""	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.1233C>T	6.37:g.31656517G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_021160	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Silent	SNP	ENST00000395952.3	37	CCDS4713.1																																																																																			G|1.000;A|0.000	0.000	weak		0.577	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4		
SNAP47	116841	hgsc.bcm.edu	37	1	227954677	227954677	+	Missense_Mutation	SNP	C	C	T	rs17851681	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:227954677C>T	ENST00000366759.4	+	4	1555	c.1141C>T	c.(1141-1143)Cgt>Tgt	p.R381C	SNAP47_ENST00000366760.1_Missense_Mutation_p.R139C|SNAP47_ENST00000315781.5_Missense_Mutation_p.R381C	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	381			R -> C (in dbSNP:rs17851681). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		long-term synaptic potentiation (GO:0060291)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17						GCTGATGGGCCGTACCCTGCA	0.607													C|||	313	0.0625	0.0068	0.0634	5008	,	,		20219	0.0486		0.1064	False		,,,				2504	0.1063				p.R381C		Atlas-SNP	.											.	SNAP47	42	.	0			c.C1141T						PASS	.	C	CYS/ARG	130,4276	94.8+/-133.5	1,128,2074	69.0	60.0	63.0		1141	-3.0	0.0	1	dbSNP_123	63	925,7675	204.1+/-246.9	56,813,3431	yes	missense	SNAP47	NM_053052.3	180	57,941,5505	TT,TC,CC		10.7558,2.9505,8.1116	benign	381/465	227954677	1055,11951	2203	4300	6503	SO:0001583	missense	116841	exon4			ATGGGCCGTACCC	AY090635	CCDS1562.1	1q42.13	2013-10-11	2008-10-27	2008-10-27	ENSG00000143740	ENSG00000143740			30669	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 142"""	C1orf142		16621800	Standard	NM_053052		Approved	SVAP1, SNAP-47	uc001hrf.2	Q5SQN1	OTTHUMG00000037697	ENST00000366759.4:c.1141C>T	1.37:g.227954677C>T	ENSP00000355721:p.Arg381Cys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	97	40	0.412371	NM_053052	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	37	CCDS1562.1	147|147	0.0673076923076923|0.0673076923076923	8|8	0.016260162601626018|0.016260162601626018	30|30	0.08287292817679558|0.08287292817679558	30|30	0.05244755244755245|0.05244755244755245	79|79	0.10422163588390501|0.10422163588390501	C|C	10.82|10.82	1.458522|1.458522	0.26248|0.26248	0.029505|0.029505	0.107558|0.107558	ENSG00000143740|ENSG00000143740	ENST00000418653;ENST00000426344|ENST00000366760;ENST00000366759;ENST00000315781	.|T;T;T	.|0.41758	.|0.99;2.28;2.27	4.52|4.52	-2.95|-2.95	0.05564|0.05564	.|.	.|0.803739	.|0.11903	.|N	.|0.518417	T|T	0.00356|0.00356	0.0011|0.0011	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B	.|0.14438	.|0.001;0.002;0.001;0.01	.|B;B;B;B	.|0.06405	.|0.001;0.001;0.001;0.002	T|T	0.10359|0.10359	-1.0633|-1.0633	4|9	.|0.49607	.|T	.|0.09	-19.1569|-19.1569	4.5638|4.5638	0.12173|0.12173	0.1769:0.2335:0.0:0.5896|0.1769:0.2335:0.0:0.5896	rs17851681;rs17851681|rs17851681;rs17851681	.|381;193;381;139	.|Q5SQN1;Q5TBZ4;Q5SQN1-2;Q5SQN1-4	.|SNP47_HUMAN;.;.;.	L|C	193;372|139;381;381	.|ENSP00000355722:R139C;ENSP00000355721:R381C;ENSP00000314157:R381C	.|ENSP00000314157:R381C	P|R	+|+	2|1	0|0	SNAP47|SNAP47	226021300|226021300	0.012000|0.012000	0.17670|0.17670	0.013000|0.013000	0.15412|0.15412	0.076000|0.076000	0.17211|0.17211	-0.378000|-0.378000	0.07446|0.07446	-0.262000|-0.262000	0.09392|0.09392	-0.300000|-0.300000	0.09419|0.09419	CCG|CGT	C|0.925;T|0.075	0.075	strong		0.607	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052	
CNTNAP3	79937	hgsc.bcm.edu	37	9	39103775	39103775	+	Silent	SNP	C	C	G	rs72721583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:39103775C>G	ENST00000297668.6	-	16	2575	c.2502G>C	c.(2500-2502)ctG>ctC	p.L834L	CNTNAP3_ENST00000358144.2_Silent_p.L746L|CNTNAP3_ENST00000377656.2_Silent_p.L833L	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	834	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		CTGTGATCCCCAGGTTCTCCA	0.463													C|||	121	0.0241613	0.0038	0.1066	5008	,	,		15740	0.0		0.0358	False		,,,				2504	0.0061				p.L834L		Atlas-SNP	.											.	CNTNAP3	82	.	0			c.G2502C						PASS	.	C		46,4360	47.5+/-82.1	0,46,2157	45.0	50.0	49.0		2502	3.5	1.0	9	dbSNP_131	49	312,8288	110.4+/-170.8	3,306,3991	no	coding-synonymous	CNTNAP3	NM_033655.3		3,352,6148	GG,GC,CC		3.6279,1.044,2.7526		834/1289	39103775	358,12648	2203	4300	6503	SO:0001819	synonymous_variant	79937	exon16			GATCCCCAGGTTC	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"""cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"""	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.2502G>C	9.37:g.39103775C>G		Somatic	448	0	0		WXS	Illumina HiSeq	Phase_I	515	258	0.500971	NM_033655	B1AMA0|Q9C0E9	Silent	SNP	ENST00000297668.6	37	CCDS6616.1																																																																																			C|0.971;G|0.029	0.029	strong		0.463	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655	
FASTKD3	79072	hgsc.bcm.edu	37	5	7867027	7867027	+	Silent	SNP	A	A	G	rs77130393	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7867027A>G	ENST00000264669.5	-	2	1306	c.1170T>C	c.(1168-1170)aaT>aaC	p.N390N	FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000341013.6_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	390					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CTGCCACTGCATTGAGGATGG	0.438													A|||	32	0.00638978	0.0	0.0173	5008	,	,		18240	0.0		0.0189	False		,,,				2504	0.001				p.N390N		Atlas-SNP	.											.	FASTKD3	88	.	0			c.T1170C						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	63.0	64.0	63.0		1170	-5.6	0.0	5	dbSNP_134	63	199,8401	87.1+/-149.5	1,197,4102	no	coding-synonymous	FASTKD3	NM_024091.3		1,221,6281	GG,GA,AA		2.314,0.5447,1.7146		390/663	7867027	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			CACTGCATTGAGG	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.1170T>C	5.37:g.7867027A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	176	81	0.460227	NM_024091	Q9BVD3	Silent	SNP	ENST00000264669.5	37	CCDS3873.1																																																																																			A|0.984;G|0.016	0.016	strong		0.438	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091	
TULP2	7288	hgsc.bcm.edu	37	19	49400634	49400634	+	Missense_Mutation	SNP	C	C	T	rs7260579	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49400634C>T	ENST00000221399.3	-	3	196	c.52G>A	c.(52-54)Gct>Act	p.A18T	NUCB1_ENST00000407032.1_5'Flank|NUCB1_ENST00000405315.4_5'Flank	NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	18			A -> T (in dbSNP:rs7260579).		visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		CTCATAGCAGCGAGCTCATGC	0.607													C|||	1024	0.204473	0.3676	0.1974	5008	,	,		18145	0.0704		0.1292	False		,,,				2504	0.2045				p.A18T		Atlas-SNP	.											.	TULP2	60	.	0			c.G52A						PASS	.	C	THR/ALA	1386,3020	453.6+/-350.4	211,964,1028	141.0	99.0	113.0		52	-0.4	0.0	19	dbSNP_116	113	1029,7571	218.1+/-256.6	62,905,3333	yes	missense	TULP2	NM_003323.2	58	273,1869,4361	TT,TC,CC		11.9651,31.4571,18.5684	benign	18/521	49400634	2415,10591	2203	4300	6503	SO:0001583	missense	7288	exon3			TAGCAGCGAGCTC	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"""cancer/testis antigen 65"""	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.52G>A	19.37:g.49400634C>T	ENSP00000221399:p.Ala18Thr	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	37	CCDS12739.1	402	0.18406593406593408	184	0.37398373983739835	72	0.19889502762430938	41	0.07167832167832168	105	0.13852242744063326	C	7.542	0.660812	0.14645	0.314571	0.119651	ENSG00000104804	ENST00000221399;ENST00000518572;ENST00000522945	D;T;T	0.83335	-1.71;2.21;1.31	4.35	-0.411	0.12370	.	0.455494	0.19372	N	0.115897	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.21905	0.062	B	0.14578	0.011	T	0.09818	-1.0657	9	0.08381	T	0.77	-3.4787	3.3478	0.07141	0.1879:0.5029:0.0:0.3092	rs7260579;rs17847561;rs60155229;rs7260579	18	O00295	TULP2_HUMAN	T	18	ENSP00000221399:A18T;ENSP00000428420:A18T;ENSP00000430040:A18T	ENSP00000221399:A18T	A	-	1	0	TULP2	54092446	0.000000	0.05858	0.000000	0.03702	0.171000	0.22731	-0.133000	0.10451	-0.050000	0.13356	0.498000	0.49722	GCT	C|0.804;T|0.196	0.196	strong		0.607	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	
JAKMIP2	9832	hgsc.bcm.edu	37	5	147051261	147051261	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:147051261G>A	ENST00000265272.5	-	2	576	c.109C>T	c.(109-111)Ctg>Ttg	p.L37L	JAKMIP2_ENST00000507386.1_Silent_p.L37L|JAKMIP2_ENST00000333010.6_Intron	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	37						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTGATGCAGCTCTATCTGA	0.552																																					p.L37L		Atlas-SNP	.											JAKMIP2,caecum,carcinoma,0,1	JAKMIP2	154	1	0			c.C109T						scavenged	.						169.0	137.0	148.0					5																	147051261		2203	4300	6503	SO:0001819	synonymous_variant	9832	exon2			GATGCAGCTCTAT	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.109C>T	5.37:g.147051261G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	201	3	0.0149254	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Silent	SNP	ENST00000265272.5	37	CCDS4285.1																																																																																			.	.	none		0.552	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
OR2T4	127074	hgsc.bcm.edu	37	1	248525650	248525650	+	Silent	SNP	C	C	T	rs28602650	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248525650C>T	ENST00000366475.1	+	1	768	c.768C>T	c.(766-768)acC>acT	p.T256T		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	256						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCTCCTCACCATCCACGGGA	0.512													t|||	1473	0.294129	0.2398	0.2709	5008	,	,		21451	0.4276		0.1799	False		,,,				2504	0.364				p.T256T		Atlas-SNP	.											.	OR2T4	126	.	0			c.C768T						PASS	.	T		1061,3345	723.4+/-409.4	140,781,1282	130.0	127.0	128.0		768	-0.3	0.2	1	dbSNP_125	128	1394,7206	753.1+/-407.4	112,1170,3018	no	coding-synonymous	OR2T4	NM_001004696.1		252,1951,4300	TT,TC,CC		16.2093,24.0808,18.8759		256/349	248525650	2455,10551	2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			CCTCACCATCCAC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.768C>T	1.37:g.248525650C>T		Somatic	663	1	0.0015083		WXS	Illumina HiSeq	Phase_I	705	335	0.475177	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			C|0.791;T|0.209	0.209	strong		0.512	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
NUP107	57122	hgsc.bcm.edu	37	12	69115698	69115698	+	Silent	SNP	G	G	A	rs17851475	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:69115698G>A	ENST00000229179.4	+	16	1721	c.1389G>A	c.(1387-1389)caG>caA	p.Q463Q	NUP107_ENST00000378905.2_Silent_p.Q312Q|NUP107_ENST00000539906.1_Silent_p.Q434Q	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	463					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			TGGTAGAACAGGAGATCCAGA	0.468													G|||	1101	0.219848	0.059	0.2968	5008	,	,		16799	0.2996		0.2922	False		,,,				2504	0.226				p.Q463Q		Atlas-SNP	.											.	NUP107	88	.	0			c.G1389A						PASS	.	G		404,4002	200.8+/-224.0	20,364,1819	115.0	114.0	115.0		1389	2.1	1.0	12	dbSNP_123	115	2348,6252	393.9+/-344.5	319,1710,2271	no	coding-synonymous	NUP107	NM_020401.2		339,2074,4090	AA,AG,GG		27.3023,9.1693,21.1595		463/926	69115698	2752,10254	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon16			AGAACAGGAGATC	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.1389G>A	12.37:g.69115698G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			G|0.782;A|0.218	0.218	strong		0.468	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
CLCN1	1180	hgsc.bcm.edu	37	7	143016928	143016928	+	Silent	SNP	C	C	T	rs6962852	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143016928C>T	ENST00000343257.2	+	2	348	c.261C>T	c.(259-261)acC>acT	p.T87T		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	87					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					CCAGTTCTACCGTGGACAGCA	0.453													C|||	1617	0.322883	0.5961	0.2378	5008	,	,		20869	0.0427		0.328	False		,,,				2504	0.2975				p.T87T		Atlas-SNP	.											.	CLCN1	141	.	0			c.C261T						PASS	.	C		2504,1902		705,1094,404	201.0	165.0	177.0		261	-2.3	0.0	7	dbSNP_116	177	2802,5798		465,1872,1963	no	coding-synonymous	CLCN1	NM_000083.2		1170,2966,2367	TT,TC,CC		32.5814,43.1684,40.7966		87/989	143016928	5306,7700	2203	4300	6503	SO:0001819	synonymous_variant	1180	exon2			TTCTACCGTGGAC	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"""Ion channels / Chloride channels : Voltage-sensitive"""	2019	protein-coding gene	gene with protein product	"""Thomsen disease, autosomal dominant"""	118425	"""chloride channel 1, skeletal muscle"""			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.261C>T	7.37:g.143016928C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_000083	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	37	CCDS5881.1																																																																																			C|0.646;T|0.354	0.354	strong		0.453	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083	
OR4C11	219429	hgsc.bcm.edu	37	11	55371807	55371807	+	Missense_Mutation	SNP	A	A	T	rs11230346	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55371807A>T	ENST00000302231.4	-	1	67	c.43T>A	c.(43-45)Tta>Ata	p.L15I		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	15			L -> I (in dbSNP:rs11230346). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						TCCTGTGTTAATCCTAACAGT	0.353													a|||	1161	0.231829	0.1354	0.3401	5008	,	,		11921	0.2173		0.2922	False		,,,				2504	0.2382				p.L15I		Atlas-SNP	.											OR4C11,colon,carcinoma,0,1	OR4C11	73	1	0			c.T43A						PASS	.	A	ILE/LEU	666,3680		123,420,1630	66.0	61.0	63.0		43	-3.7	0.0	11	dbSNP_120	63	2382,5626		698,986,2320	yes	missense	OR4C11	NM_001004700.2	5	821,1406,3950	TT,TA,AA		29.7453,15.3244,24.6722	probably-damaging	15/311	55371807	3048,9306	2173	4004	6177	SO:0001583	missense	219429	exon1			GTGTTAATCCTAA	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"""GPCR / Class A : Olfactory receptors"""	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.43T>A	11.37:g.55371807A>T	ENSP00000306651:p.Leu15Ile	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_001004700	B9EIL4|Q8NGL8	Missense_Mutation	SNP	ENST00000302231.4	37	CCDS31503.1	546	0.25	46	0.09349593495934959	126	0.34806629834254144	139	0.243006993006993	235	0.3100263852242744	A	9.510	1.105539	0.20632	0.153244	0.297453	ENSG00000172188	ENST00000302231	T	0.00335	8.06	4.43	-3.74	0.04385	.	0.000000	0.38272	U	0.001741	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	P	0.44241	0.829	B	0.33254	0.16	T	0.48581	-0.9023	9	0.62326	D	0.03	.	5.2332	0.15434	0.277:0.0:0.4447:0.2784	rs11230346	15	Q6IEV9	OR4CB_HUMAN	I	15	ENSP00000306651:L15I	ENSP00000306651:L15I	L	-	1	2	OR4C11	55128383	0.000000	0.05858	0.019000	0.16419	0.041000	0.13682	-0.968000	0.03817	-0.563000	0.06078	0.448000	0.29417	TTA	A|0.734;T|0.266	0.266	strong		0.353	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700	
RAB39A	54734	hgsc.bcm.edu	37	11	107799426	107799426	+	Silent	SNP	C	C	A	rs77818165	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:107799426C>A	ENST00000320578.2	+	1	198	c.132C>A	c.(130-132)acC>acA	p.T44T	SLC35F2_ENST00000525071.1_5'Flank|SLC35F2_ENST00000429869.1_5'Flank	NM_017516.1	NP_059986.1	Q14964	RB39A_HUMAN	RAB39A, member RAS oncogene family	44					phagosome acidification (GO:0090383)|phagosome-lysosome fusion (GO:0090385)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)										GCGACCCCACCGTCGGCGTGG	0.682													C|||	207	0.0413339	0.003	0.0216	5008	,	,		10481	0.1012		0.0408	False		,,,				2504	0.046				p.T44T		Atlas-SNP	.											.	.	.	.	0			c.C132A						PASS	.	C		46,4352	43.8+/-77.6	0,46,2153	29.0	30.0	29.0		132	-9.2	0.7	11	dbSNP_131	29	439,8157	128.3+/-186.6	12,415,3871	no	coding-synonymous	RAB39	NM_017516.1		12,461,6024	AA,AC,CC		5.107,1.0459,3.7325		44/218	107799426	485,12509	2199	4298	6497	SO:0001819	synonymous_variant	54734	exon1			CCCCACCGTCGGC	X99962	CCDS8338.1	11q22.3	2011-11-22	2011-11-22	2011-11-22	ENSG00000179331	ENSG00000179331		"""RAB, member RAS oncogene"""	16521	protein-coding gene	gene with protein product	"""rab-related GTP-binding protein"""		"""RAB39, member RAS oncogene family"""	RAB39		9119394	Standard	NM_017516		Approved		uc001pjt.3	Q14964	OTTHUMG00000166367	ENST00000320578.2:c.132C>A	11.37:g.107799426C>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	62	36	0.580645	NM_017516	A8KAA4|Q8N6W2	Silent	SNP	ENST00000320578.2	37	CCDS8338.1																																																																																			C|0.961;A|0.039	0.039	strong		0.682	RAB39A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389423.1	NM_017516	
MAST3	23031	hgsc.bcm.edu	37	19	18255359	18255359	+	Missense_Mutation	SNP	G	G	A	rs8108738	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18255359G>A	ENST00000262811.6	+	22	2581	c.2581G>A	c.(2581-2583)Ggc>Agc	p.G861S	AC007192.6_ENST00000600364.2_RNA	NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	861			G -> S (in dbSNP:rs8108738).				ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						TCTGGATGCCGGCCGGGGCCG	0.711													G|||	2665	0.532149	0.3215	0.5245	5008	,	,		13469	0.6806		0.502	False		,,,				2504	0.7004				p.G861S		Atlas-SNP	.											.	MAST3	83	.	0			c.G2581A						PASS	.	G	SER/GLY	1317,2539		251,815,862	17.0	22.0	21.0		2581	2.3	0.3	19	dbSNP_116	21	4297,3945		1159,1979,983	yes	missense	MAST3	NM_015016.1	56	1410,2794,1845	AA,AG,GG		47.8646,34.1546,46.4044	benign	861/1310	18255359	5614,6484	1928	4121	6049	SO:0001583	missense	23031	exon22			GATGCCGGCCGGG	AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.2581G>A	19.37:g.18255359G>A	ENSP00000262811:p.Gly861Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	88	48	0.545455	NM_015016	Q7LDZ8|Q9UPI0	Missense_Mutation	SNP	ENST00000262811.6	37	CCDS46014.1	1111	0.5086996336996337	154	0.3130081300813008	186	0.5138121546961326	397	0.6940559440559441	374	0.49340369393139843	G	6.292	0.421969	0.11928	0.341546	0.521354	ENSG00000099308	ENST00000262811	T	0.65364	-0.15	4.57	2.28	0.28536	.	0.514144	0.18802	N	0.130767	T	0.00012	0.0000	L	0.60455	1.87	0.58432	P	1.0000000000287557E-6	B	0.09022	0.002	B	0.06405	0.002	T	0.47071	-0.9145	9	0.05620	T	0.96	-15.9265	8.3821	0.32477	0.2922:0.0:0.7078:0.0	rs8108738;rs58325632;rs8108738	861	O60307	MAST3_HUMAN	S	861	ENSP00000262811:G861S	ENSP00000262811:G861S	G	+	1	0	MAST3	18116359	0.943000	0.32029	0.303000	0.25071	0.664000	0.39144	2.388000	0.44398	0.283000	0.22279	0.491000	0.48974	GGC	G|0.504;A|0.496	0.496	strong		0.711	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150	
CD207	50489	hgsc.bcm.edu	37	2	71058226	71058226	+	Silent	SNP	C	C	T	rs2080390	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:71058226C>T	ENST00000410009.3	-	6	987	c.942G>A	c.(940-942)acG>acA	p.T314T		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	314	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						TGAAAAGAAACGTTTTGTCAC	0.488													C|||	689	0.13758	0.0386	0.2406	5008	,	,		18402	0.0794		0.2197	False		,,,				2504	0.1738				p.T314T		Atlas-SNP	.											.	CD207	47	.	0			c.G942A						PASS	.	C		251,3645		6,239,1703	120.0	113.0	115.0		942	-4.1	0.0	2	dbSNP_96	115	2068,6206		255,1558,2324	no	coding-synonymous	CD207	NM_015717.3		261,1797,4027	TT,TC,CC		24.994,6.4425,19.0551		314/329	71058226	2319,9851	1948	4137	6085	SO:0001819	synonymous_variant	50489	exon6			AAGAAACGTTTTG	AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"""C-type lectin domain containing"", ""CD molecules"""	17935	protein-coding gene	gene with protein product		604862	"""CD207 antigen, langerin"""			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.942G>A	2.37:g.71058226C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	243	154	0.633745	NM_015717		Silent	SNP	ENST00000410009.3	37																																																																																				C|0.863;T|0.137	0.137	strong		0.488	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
TLE3	7090	hgsc.bcm.edu	37	15	70345626	70345626	+	Silent	SNP	C	C	T	rs1057865	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:70345626C>T	ENST00000558939.1	-	17	3300	c.1923G>A	c.(1921-1923)acG>acA	p.T641T	TLE3_ENST00000558201.1_Silent_p.T647T|TLE3_ENST00000539550.1_Silent_p.T568T|TLE3_ENST00000442299.2_Silent_p.T633T|TLE3_ENST00000440567.3_Silent_p.T631T|TLE3_ENST00000559048.1_Silent_p.T641T|TLE3_ENST00000557907.1_Silent_p.T633T|TLE3_ENST00000317509.8_Silent_p.T629T|TLE3_ENST00000557997.1_Silent_p.T633T|TLE3_ENST00000560589.1_Silent_p.T585T|TLE3_ENST00000559191.1_Silent_p.T222T|TLE3_ENST00000560939.1_Silent_p.T643T|TLE3_ENST00000559929.1_Silent_p.T651T|TLE3_ENST00000558379.1_Silent_p.T636T|TLE3_ENST00000451782.2_Silent_p.T638T	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	641					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						AGGAGCGCACCGTGTTGTCCA	0.607													C|||	1818	0.363019	0.2284	0.4726	5008	,	,		18331	0.256		0.4791	False		,,,				2504	0.4581				p.T641T		Atlas-SNP	.											.	TLE3	104	.	0			c.G1923A						PASS	.	C	,,	1175,3125		187,801,1162	61.0	66.0	65.0		1914,1923,1887	-10.1	0.0	15	dbSNP_86	65	4018,4520		965,2088,1216	no	coding-synonymous,coding-synonymous,coding-synonymous	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	,,	1152,2889,2378	TT,TC,CC		47.0602,27.3256,40.4502	,,	638/770,641/773,629/761	70345626	5193,7645	2150	4269	6419	SO:0001819	synonymous_variant	7090	exon17			GCGCACCGTGTTG	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.1923G>A	15.37:g.70345626C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	203	115	0.566502	NM_005078	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Silent	SNP	ENST00000558939.1	37	CCDS45293.1																																																																																			C|0.639;T|0.361	0.361	strong		0.607	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
ECH1	1891	hgsc.bcm.edu	37	19	39322087	39322087	+	Missense_Mutation	SNP	T	T	G	rs9419	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:39322087T>G	ENST00000221418.4	-	2	354	c.122A>C	c.(121-123)gAg>gCg	p.E41A	AC104534.3_ENST00000594769.1_Silent_p.R211R|ECH1_ENST00000597805.1_Intron	NM_001398.2	NP_001389.2	Q13011	ECH1_HUMAN	enoyl CoA hydratase 1, peroxisomal	41			E -> A (in dbSNP:rs9419). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		fatty acid beta-oxidation (GO:0006635)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	isomerase activity (GO:0016853)|receptor binding (GO:0005102)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	6	all_cancers(60;9.36e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			TCCGGAAGCCTCCTCTTGTGC	0.577													T|||	1828	0.365016	0.2035	0.4207	5008	,	,		17584	0.244		0.5915	False		,,,				2504	0.4356				p.E41A		Atlas-SNP	.											.	ECH1	14	.	0			c.A122C						PASS	.	T	ALA/GLU	1120,3286	400.1+/-331.5	141,838,1224	60.0	60.0	60.0		122	2.9	0.1	19	dbSNP_52	60	4745,3855	609.1+/-395.5	1313,2119,868	yes	missense	ECH1	NM_001398.2	107	1454,2957,2092	GG,GT,TT		44.8256,25.4199,45.0946		41/329	39322087	5865,7141	2203	4300	6503	SO:0001583	missense	1891	exon2			GAAGCCTCCTCTT	U16660	CCDS33014.1	19q13.1	2010-04-30	2010-04-30			ENSG00000104823			3149	protein-coding gene	gene with protein product		600696	"""enoyl Coenzyme A hydratase 1, peroxisomal"""			7558027	Standard	XM_005258610		Approved	HPXEL		Q13011		ENST00000221418.4:c.122A>C	19.37:g.39322087T>G	ENSP00000221418:p.Glu41Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	67	38	0.567164	NM_001398	A8K745|Q8WVX0|Q96EZ9	Missense_Mutation	SNP	ENST00000221418.4	37	CCDS33014.1	878	0.40201465201465203	95	0.19308943089430894	156	0.430939226519337	173	0.30244755244755245	454	0.5989445910290238	T	11.56	1.675316	0.29783	0.254199	0.551744	ENSG00000104823	ENST00000221418	T	0.63255	-0.03	5.13	2.94	0.34122	.	1.246300	0.07145	U	0.848028	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.18610	0.029	B	0.12837	0.008	T	0.45205	-0.9277	9	0.10902	T	0.67	.	5.3291	0.15922	0.0:0.0943:0.1767:0.729	rs9419;rs1061152;rs2228165;rs3202165;rs11083480;rs17349837;rs17590312;rs17851525;rs9419	41	Q13011	ECH1_HUMAN	A	41	ENSP00000221418:E41A	ENSP00000221418:E41A	E	-	2	0	ECH1	44013927	0.001000	0.12720	0.057000	0.19452	0.016000	0.09150	0.652000	0.24888	0.799000	0.34018	0.533000	0.62120	GAG	T|0.581;G|0.419	0.419	strong		0.577	ECH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462650.1		
OR6A2	8590	hgsc.bcm.edu	37	11	6816792	6816792	+	Missense_Mutation	SNP	T	T	C	rs61741824	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6816792T>C	ENST00000332601.3	-	1	336	c.148A>G	c.(148-150)Att>Gtt	p.I50V		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	50					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGGTTCCTAATTGCCATAATG	0.463													t|||	83	0.0165735	0.0008	0.0101	5008	,	,		23756	0.0		0.0288	False		,,,				2504	0.047				p.I50V		Atlas-SNP	.											.	OR6A2	68	.	0			c.A148G						PASS	.	T	VAL/ILE	35,4367	40.0+/-72.8	0,35,2166	163.0	139.0	148.0		148	-6.0	0.0	11	dbSNP_129	148	291,8301	108.0+/-168.7	8,275,4013	yes	missense	OR6A2	NM_003696.2	29	8,310,6179	CC,CT,TT		3.3869,0.7951,2.5089	benign	50/328	6816792	326,12668	2201	4296	6497	SO:0001583	missense	8590	exon1			TCCTAATTGCCAT	AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"""GPCR / Class A : Olfactory receptors"""	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.148A>G	11.37:g.6816792T>C	ENSP00000330384:p.Ile50Val	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	250	115	0.46	NM_003696	Q3MJC7|Q6IF35|Q9H206	Missense_Mutation	SNP	ENST00000332601.3	37	CCDS7772.1	24	0.01098901098901099	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	18	0.023746701846965697	t	0.031	-1.337374	0.01287	0.007951	0.033869	ENSG00000184933	ENST00000332601	T	0.06687	3.27	4.95	-6.02	0.02192	GPCR, rhodopsin-like superfamily (1);	0.397790	0.20442	N	0.092272	T	0.00967	0.0032	N	0.12663	0.25	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39482	-0.9612	10	0.02654	T	1	.	12.8703	0.57960	0.0:0.4366:0.0:0.5634	rs61741824	50	O95222	OR6A2_HUMAN	V	50	ENSP00000330384:I50V	ENSP00000330384:I50V	I	-	1	0	OR6A2	6773368	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.270000	0.02831	-0.806000	0.04398	-3.168000	0.00057	ATT	T|0.981;C|0.019	0.019	strong		0.463	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696	
MB21D2	151963	hgsc.bcm.edu	37	3	192516430	192516430	+	Silent	SNP	C	C	T	rs3732388	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:192516430C>T	ENST00000392452.2	-	2	1541	c.1221G>A	c.(1219-1221)ccG>ccA	p.P407P		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	407							protein complex binding (GO:0032403)			endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						AGTGCTCTGCCGGGTCTGAGC	0.592													C|||	338	0.067492	0.0038	0.0937	5008	,	,		18930	0.1647		0.0189	False		,,,				2504	0.0849				p.P407P		Atlas-SNP	.											.	MB21D2	75	.	0			c.G1221A						PASS	.	C		60,4346	58.1+/-94.6	1,58,2144	49.0	45.0	46.0		1221	-10.5	0.0	3	dbSNP_107	46	184,8416	82.3+/-144.9	1,182,4117	no	coding-synonymous	MB21D2	NM_178496.3		2,240,6261	TT,TC,CC		2.1395,1.3618,1.8761		407/492	192516430	244,12762	2203	4300	6503	SO:0001819	synonymous_variant	151963	exon2			CTCTGCCGGGTCT	AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 59"""	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.1221G>A	3.37:g.192516430C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_178496	Q86VD8	Silent	SNP	ENST00000392452.2	37	CCDS3302.2																																																																																			C|0.969;T|0.031	0.031	strong		0.592	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496	
NPAP1	23742	hgsc.bcm.edu	37	15	24923799	24923799	+	Missense_Mutation	SNP	A	A	C	rs34413216	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:24923799A>C	ENST00000329468.2	+	1	3259	c.2785A>C	c.(2785-2787)Aca>Cca	p.T929P		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	929			T -> P (in dbSNP:rs34413216).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											TATAGGCTTAACATCTCCTTC	0.483													C|||	74	0.0147764	0.0045	0.0259	5008	,	,		20138	0.0		0.0318	False		,,,				2504	0.0184				p.T929P		Atlas-SNP	.											.	.	.	.	0			c.A2785C						PASS	.	C	PRO/THR	55,4351		0,55,2148	88.0	91.0	90.0		2785	-2.3	0.0	15	dbSNP_126	90	328,8272		8,312,3980	yes	missense	C15orf2	NM_018958.2	38	8,367,6128	CC,CA,AA		3.814,1.2483,2.9448	benign	929/1157	24923799	383,12623	2203	4300	6503	SO:0001583	missense	23742	exon1			GGCTTAACATCTC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2785A>C	15.37:g.24923799A>C	ENSP00000333735:p.Thr929Pro	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	41	0.018772893772893772	3	0.006097560975609756	9	0.024861878453038673	0	0.0	29	0.03825857519788918	.	0.012	-1.677019	0.00751	0.012483	0.03814	ENSG00000185823	ENST00000329468	T	0.10099	2.91	2.04	-2.28	0.06826	.	1.446920	0.04526	N	0.385475	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.38887	-0.9640	10	0.22706	T	0.39	.	4.6396	0.12541	0.5249:0.3313:0.1438:0.0	rs34413216	929	Q9NZP6	CO002_HUMAN	P	929	ENSP00000333735:T929P	ENSP00000333735:T929P	T	+	1	0	C15orf2	22474892	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.643000	0.05421	-1.124000	0.02936	-0.648000	0.03929	ACA	A|0.973;C|0.027	0.027	strong		0.483	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
KSR2	283455	hgsc.bcm.edu	37	12	118020115	118020115	+	Silent	SNP	G	G	A	rs11068551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:118020115G>A	ENST00000339824.5	-	6	1948	c.1221C>T	c.(1219-1221)ctC>ctT	p.L407L	KSR2_ENST00000302438.5_Silent_p.L104L|KSR2_ENST00000545002.1_5'UTR|KSR2_ENST00000425217.1_Silent_p.L378L			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	407					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGGAGTTGCCGAGATCTCTGC	0.602													G|||	1999	0.399161	0.115	0.4611	5008	,	,		20466	0.5486		0.4742	False		,,,				2504	0.5082				p.L378L		Atlas-SNP	.											.	KSR2	208	.	0			c.C1134T						PASS	.	G		673,3549		61,551,1499	117.0	119.0	118.0		1134	-8.2	0.9	12	dbSNP_120	118	4051,4417		977,2097,1160	no	coding-synonymous	KSR2	NM_173598.4		1038,2648,2659	AA,AG,GG		47.8389,15.9403,37.2262		378/922	118020115	4724,7966	2111	4234	6345	SO:0001819	synonymous_variant	283455	exon6			GTTGCCGAGATCT	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.1221C>T	12.37:g.118020115G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_173598	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	37																																																																																				G|0.596;A|0.404	0.404	strong		0.602	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598	
TMEM177	80775	hgsc.bcm.edu	37	2	120438515	120438515	+	Missense_Mutation	SNP	G	G	C	rs11684353	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:120438515G>C	ENST00000424086.1	+	2	559	c.86G>C	c.(85-87)gGa>gCa	p.G29A	TMEM177_ENST00000496203.1_Intron|TMEM177_ENST00000409951.1_Missense_Mutation_p.G29A|TMEM177_ENST00000401466.1_Missense_Mutation_p.G29A|TMEM177_ENST00000272521.6_Missense_Mutation_p.G29A	NM_001105198.1	NP_001098668.1	Q53S58	TM177_HUMAN	transmembrane protein 177	29			G -> A (in dbSNP:rs11684353).			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	13	Colorectal(110;0.196)					GGCCTGTTTGGAGTTCCAATC	0.612													G|||	701	0.139976	0.1589	0.134	5008	,	,		18151	0.119		0.1511	False		,,,				2504	0.1288				p.G29A		Atlas-SNP	.											.	TMEM177	26	.	0			c.G86C						PASS	.	G	ALA/GLY,ALA/GLY,ALA/GLY	758,3648	308.0+/-290.3	58,642,1503	70.0	69.0	70.0		86,86,86	4.0	1.0	2	dbSNP_120	70	1278,7322	253.9+/-279.4	100,1078,3122	yes	missense,missense,missense	TMEM177	NM_001105198.1,NM_001105199.1,NM_030577.2	60,60,60	158,1720,4625	CC,CG,GG		14.8605,17.2038,15.6543	possibly-damaging,possibly-damaging,possibly-damaging	29/312,29/312,29/312	120438515	2036,10970	2203	4300	6503	SO:0001583	missense	80775	exon2			TGTTTGGAGTTCC	BC004404	CCDS2128.1	2q14.2	2008-02-05			ENSG00000144120	ENSG00000144120			28143	protein-coding gene	gene with protein product						12477932	Standard	NM_001105198		Approved	MGC10993	uc002tmc.1	Q53S58	OTTHUMG00000153312	ENST00000424086.1:c.86G>C	2.37:g.120438515G>C	ENSP00000402661:p.Gly29Ala	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	231	118	0.510823	NM_030577	Q9BT20	Missense_Mutation	SNP	ENST00000424086.1	37	CCDS2128.1	335	0.1533882783882784	82	0.16666666666666666	57	0.1574585635359116	79	0.1381118881118881	117	0.15435356200527706	G	2.536	-0.307404	0.05458	0.172038	0.148605	ENSG00000144120	ENST00000401466;ENST00000424086;ENST00000272521;ENST00000445518;ENST00000409951;ENST00000415646	T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11	3.95	3.95	0.45737	.	0.117634	0.56097	D	0.000034	T	0.00039	0.0001	L	0.27053	0.805	0.26645	P	0.972203	B;P	0.35745	0.202;0.518	B;B	0.32533	0.104;0.147	T	0.16748	-1.0392	9	0.07644	T	0.81	-1.8004	9.9146	0.41425	0.0:0.2076:0.7924:0.0	rs11684353;rs17609082	29;29	B8ZZT5;Q53S58	.;TM177_HUMAN	A	29	ENSP00000385966:G29A;ENSP00000402661:G29A;ENSP00000272521:G29A;ENSP00000405898:G29A;ENSP00000386430:G29A	ENSP00000272521:G29A	G	+	2	0	TMEM177	120154985	0.999000	0.42202	0.993000	0.49108	0.174000	0.22865	3.461000	0.53035	2.509000	0.84616	0.549000	0.68633	GGA	C|0.155;G|0.845;T|0.000	0.155	strong		0.612	TMEM177-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330673.1	NM_030577	
CASD1	64921	hgsc.bcm.edu	37	7	94180691	94180691	+	Silent	SNP	T	T	C	rs10280457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:94180691T>C	ENST00000297273.4	+	15	2144	c.1857T>C	c.(1855-1857)gcT>gcC	p.A619A		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	619						integral component of membrane (GO:0016021)				NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			TTTATCTGGCTTTGCAGAAGC	0.308													T|||	596	0.11901	0.1657	0.1124	5008	,	,		14738	0.1478		0.1093	False		,,,				2504	0.0409				p.A619A		Atlas-SNP	.											.	CASD1	70	.	0			c.T1857C						PASS	.	T		664,3740	266.2+/-267.1	54,556,1592	72.0	73.0	73.0		1857	1.8	1.0	7	dbSNP_119	73	913,7681	198.7+/-243.0	46,821,3430	no	coding-synonymous	CASD1	NM_022900.4		100,1377,5022	CC,CT,TT		10.6237,15.0772,12.1326		619/798	94180691	1577,11421	2202	4297	6499	SO:0001819	synonymous_variant	64921	exon15			TCTGGCTTTGCAG	AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 12"""	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1857T>C	7.37:g.94180691T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	NM_022900	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Silent	SNP	ENST00000297273.4	37	CCDS5636.1																																																																																			T|0.879;C|0.121	0.121	strong		0.308	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900	
PODXL2	50512	hgsc.bcm.edu	37	3	127379270	127379270	+	Silent	SNP	C	C	T	rs920232	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:127379270C>T	ENST00000342480.6	+	3	438	c.399C>T	c.(397-399)acC>acT	p.T133T		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	133	O-glycosylated at one site.				leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						TTGAAGACACCAGCCAGGCTC	0.473													C|||	846	0.16893	0.1755	0.1744	5008	,	,		20261	0.1766		0.1392	False		,,,				2504	0.1789				p.T133T		Atlas-SNP	.											.	PODXL2	53	.	0			c.C399T						PASS	.	C		690,3716	290.1+/-280.8	62,566,1575	83.0	77.0	79.0		399	-1.6	0.0	3	dbSNP_86	79	1384,7216	268.3+/-287.8	108,1168,3024	no	coding-synonymous	PODXL2	NM_015720.2		170,1734,4599	TT,TC,CC		16.093,15.6605,15.9465		133/606	127379270	2074,10932	2203	4300	6503	SO:0001819	synonymous_variant	50512	exon3			AGACACCAGCCAG	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"""endoglycan"""					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.399C>T	3.37:g.127379270C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	145	65	0.448276	NM_015720	Q6UVY4|Q8WUV6	Silent	SNP	ENST00000342480.6	37	CCDS3044.1																																																																																			C|0.837;T|0.163	0.163	strong		0.473	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720	
TNFSF13	8741	hgsc.bcm.edu	37	17	7462555	7462555	+	Missense_Mutation	SNP	G	G	A	rs11552708	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7462555G>A	ENST00000338784.4	+	1	642	c.199G>A	c.(199-201)Ggg>Agg	p.G67R	TNFSF12-TNFSF13_ENST00000293826.4_Intron|TNFSF13_ENST00000396542.1_Missense_Mutation_p.G50R|TNFSF13_ENST00000349228.4_Missense_Mutation_p.G67R|TNFSF13_ENST00000396545.4_Missense_Mutation_p.G67R|TNFSF12_ENST00000557233.1_Intron|SENP3_ENST00000429205.2_5'Flank|SENP3_ENST00000321337.7_5'Flank|TNFSF13_ENST00000380535.4_Missense_Mutation_p.G67R|TNFSF13_ENST00000483039.1_Intron	NM_003808.3	NP_003799.1	O75888	TNF13_HUMAN	tumor necrosis factor (ligand) superfamily, member 13	67			G -> R (in dbSNP:rs11552708). {ECO:0000269|Ref.9}.		gene expression (GO:0010467)|immunoglobulin production in mucosal tissue (GO:0002426)|mRNA metabolic process (GO:0016071)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	receptor binding (GO:0005102)			large_intestine(2)|lung(2)|skin(1)	5		Prostate(122;0.157)				CCGGCTGCAGGGGACAGGAGG	0.647													A|||	690	0.13778	0.084	0.1499	5008	,	,		15359	0.3026		0.1004	False		,,,				2504	0.0706				p.G67R		Atlas-SNP	.											.	TNFSF13	12	.	0			c.G199A						PASS	.	A	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,	356,3942		14,328,1807	11.0	11.0	11.0		199,199,148,199,199,199,	2.2	1.0	17	dbSNP_120	11	932,7508		61,810,3349	yes	missense,missense,missense,missense,missense,missense,intron	TNFSF13,TNFSF12-TNFSF13	NM_001198622.1,NM_001198623.1,NM_001198624.1,NM_003808.3,NM_172087.2,NM_172088.2,NM_172089.3	125,125,125,125,125,125,	75,1138,5156	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	11.0427,8.2829,10.1115	,,,,,,	67/224,67/223,50/206,67/251,67/235,67/248,	7462555	1288,11450	2149	4220	6369	SO:0001583	missense	8741	exon1			CTGCAGGGGACAG	AF046888	CCDS11111.1, CCDS11112.1, CCDS42256.1, CCDS56019.1, CCDS73957.1	17p13.1	2007-07-23			ENSG00000161955	ENSG00000161955		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11928	protein-coding gene	gene with protein product		604472				9743536	Standard	NM_172088		Approved	APRIL, CD256		O75888	OTTHUMG00000108145	ENST00000338784.4:c.199G>A	17.37:g.7462555G>A	ENSP00000343505:p.Gly67Arg	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	NM_001198623	A8MYD5|B4DVT2|Q541E1|Q5U0G8|Q96HV6|Q9P1M8|Q9P1M9	Missense_Mutation	SNP	ENST00000338784.4	37	CCDS11111.1	378	0.17307692307692307	34	0.06910569105691057	55	0.15193370165745856	209	0.36538461538461536	80	0.10554089709762533	A	0.101	-1.151752	0.01700	0.082829	0.110427	ENSG00000161955	ENST00000396542;ENST00000438470;ENST00000436057;ENST00000349228;ENST00000338784;ENST00000380535;ENST00000396545	D;T;T;D;D;D;D	0.97016	-4.2;1.66;1.65;-3.64;-3.7;-4.21;-3.7	4.88	2.21	0.28008	.	.	.	.	.	T	0.00012	0.0000	N	0.00419	-1.52	0.53688	P	2.2999999999995246E-5	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.06405	0.0;0.0;0.002;0.001;0.001	T	0.37220	-0.9715	8	0.13853	T	0.58	-2.4838	3.3198	0.07047	0.5011:0.2259:0.273:0.0	rs11552708;rs58340751;rs11552708	67;67;67;67;67	B4DVT2;Q2QBA2;O75888-2;O75888;O75888-3	.;.;.;TNF13_HUMAN;.	R	50;50;50;67;67;67;67	ENSP00000379792:G50R;ENSP00000390771:G50R;ENSP00000410094:G50R;ENSP00000314455:G67R;ENSP00000343505:G67R;ENSP00000369908:G67R;ENSP00000379794:G67R	ENSP00000343505:G67R	G	+	1	0	TNFSF13	7403279	1.000000	0.71417	0.998000	0.56505	0.674000	0.39518	1.442000	0.35046	0.285000	0.22329	-0.361000	0.07541	GGG	G|0.857;A|0.143	0.143	strong		0.647	TNFSF13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226948.2	NM_003808	
KLHL31	401265	hgsc.bcm.edu	37	6	53517035	53517035	+	Silent	SNP	G	G	A	rs3823111	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:53517035G>A	ENST00000407079.1	-	2	1265	c.1266C>T	c.(1264-1266)taC>taT	p.Y422Y	KLHL31_ENST00000370905.3_Silent_p.Y422Y			Q9H511	KLH31_HUMAN	kelch-like family member 31	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(3)	20	Lung NSC(77;0.0158)					CGCCCGCGGCGTACACGAGCC	0.637													G|||	663	0.132388	0.121	0.0937	5008	,	,		16333	0.2163		0.0596	False		,,,				2504	0.1636				p.Y422Y		Atlas-SNP	.											KLHL31,NS,carcinoma,-2,1	KLHL31	48	1	0			c.C1266T						PASS	.	G		475,3931	222.0+/-238.9	26,423,1754	56.0	58.0	57.0		1266	4.6	1.0	6	dbSNP_107	57	558,8042	151.6+/-206.3	17,524,3759	no	coding-synonymous	KLHL31	NM_001003760.4		43,947,5513	AA,AG,GG		6.4884,10.7808,7.9425		422/635	53517035	1033,11973	2203	4300	6503	SO:0001819	synonymous_variant	401265	exon3			CGCGGCGTACACG		CCDS34478.1	6p12.1	2013-09-27	2013-02-22	2007-01-09	ENSG00000124743	ENSG00000124743		"""Kelch-like"", ""BTB/POZ domain containing"""	21353	protein-coding gene	gene with protein product		610749	"""kelch repeat and BTB (POZ) domain containing 1"", ""kelch-like 31 (Drosophila)"""	KBTBD1			Standard	NM_001003760		Approved	bA345L23.2, BKLHD6	uc003pcb.4	Q9H511	OTTHUMG00000014882	ENST00000407079.1:c.1266C>T	6.37:g.53517035G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_001003760	A6N9J2|B2RP49	Silent	SNP	ENST00000407079.1	37	CCDS34478.1																																																																																			G|0.903;A|0.097	0.097	strong		0.637	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040965.1	NM_001003760	
TMEM132C	92293	hgsc.bcm.edu	37	12	129028586	129028586	+	Silent	SNP	C	C	T	rs73426420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:129028586C>T	ENST00000435159.2	+	3	1059	c.1059C>T	c.(1057-1059)agC>agT	p.S353S	TMEM132C_ENST00000315208.8_5'UTR	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	353						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(2)|prostate(2)|skin(1)	13						AGGTGGGCAGCGGCGGAAAGC	0.662													C|||	681	0.135982	0.056	0.0821	5008	,	,		15052	0.2431		0.1302	False		,,,				2504	0.1779				p.S353S		Atlas-SNP	.											.	TMEM132C	142	.	0			c.C1059T						PASS	.	C		74,1310		1,72,619	29.0	41.0	37.0		1059	-4.6	0.0	12	dbSNP_130	37	439,2743		30,379,1182	no	coding-synonymous	TMEM132C	NM_001136103.2		31,451,1801	TT,TC,CC		13.7964,5.3468,11.2352		353/1109	129028586	513,4053	692	1591	2283	SO:0001819	synonymous_variant	92293	exon3			GGGCAGCGGCGGA	AK126715		12q24.32	2014-06-13				ENSG00000181234			25436	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 152"""						Standard	NM_001136103		Approved	DKFZp761O2018, PPP1R152	uc021rgn.1	Q8N3T6		ENST00000435159.2:c.1059C>T	12.37:g.129028586C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	95	60	0.631579	NM_001136103	Q69YX8	Silent	SNP	ENST00000435159.2	37																																																																																				C|0.848;T|0.152	0.152	strong		0.662	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
CROCC	9696	hgsc.bcm.edu	37	1	17275337	17275337	+	Missense_Mutation	SNP	C	C	T	rs143866013	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17275337C>T	ENST00000375541.5	+	19	2821	c.2752C>T	c.(2752-2754)Cgg>Tgg	p.R918W	CROCC_ENST00000467938.1_Intron	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin									p.R918W(2)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		TGAGGTGCAACGGCAGCTGGC	0.677																																					p.R918W		Atlas-SNP	.											CROCC,NS,haematopoietic_neoplasm,0,6	CROCC	185	6	2	Substitution - Missense(2)	skin(2)	c.C2752T						PASS	.						38.0	43.0	41.0					1																	17275337		2203	4298	6501	SO:0001583	missense	9696	exon19			GTGCAACGGCAGC	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2752C>T	1.37:g.17275337C>T	ENSP00000364691:p.Arg918Trp	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	276	33	0.119565	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.216169	0.58452	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.23552	1.9	4.38	2.36	0.29203	.	.	.	.	.	T	0.39886	0.1095	L	0.50333	1.59	0.34311	D	0.68543	D;D	0.76494	0.999;0.999	D;D	0.63488	0.915;0.915	T	0.53143	-0.8480	9	0.72032	D	0.01	.	10.9364	0.47247	0.41:0.59:0.0:0.0	.	221;918	Q5TZA2-2;Q5TZA2	.;CROCC_HUMAN	W	918;799	ENSP00000364691:R918W	ENSP00000364691:R918W	R	+	1	2	CROCC	17147924	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	1.205000	0.32308	0.452000	0.26830	0.557000	0.71058	CGG	C|0.900;T|0.100	0.100	strong		0.677	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
KIAA2018	205717	hgsc.bcm.edu	37	3	113376107	113376107	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:113376107C>T	ENST00000478658.1	-	5	4439	c.4422G>A	c.(4420-4422)caG>caA	p.Q1474Q	KIAA2018_ENST00000316407.4_Silent_p.Q1474Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1474	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgttgttgctgttgctgct	0.493																																					p.Q1474Q		Atlas-SNP	.											KIAA2018,colon,carcinoma,0,1	KIAA2018	180	1	0			c.G4422A						scavenged	.						88.0	96.0	93.0					3																	113376107		2193	4279	6472	SO:0001819	synonymous_variant	205717	exon7			TTGTTGCTGTTGC	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4422G>A	3.37:g.113376107C>T		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	158	13	0.0822785	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.	.	none		0.493	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
SPTBN5	51332	hgsc.bcm.edu	37	15	42149506	42149506	+	Missense_Mutation	SNP	G	G	C	rs12442525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:42149506G>C	ENST00000320955.6	-	51	8778	c.8551C>G	c.(8551-8553)Cag>Gag	p.Q2851E		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2851					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		ACAAAGGCCTGGGCCTGGCCC	0.662													G|||	2358	0.470847	0.0598	0.5951	5008	,	,		17472	0.9454		0.4712	False		,,,				2504	0.4489				p.Q2816E		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C8446G						PASS	.	G	GLU/GLN	544,3628		65,414,1607	12.0	14.0	13.0		8446	3.5	0.2	15	dbSNP_120	13	3960,4476		982,1996,1240	yes	missense	SPTBN5	NM_016642.2	29	1047,2410,2847	CC,CG,GG		46.9417,13.0393,35.7234	benign	2816/3640	42149506	4504,8104	2086	4218	6304	SO:0001583	missense	51332	exon51			AGGCCTGGGCCTG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8551C>G	15.37:g.42149506G>C	ENSP00000317790:p.Gln2851Glu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		1164	0.532967032967033	35	0.07113821138211382	214	0.5911602209944752	542	0.9475524475524476	373	0.4920844327176781	.	8.517	0.867948	0.17250	0.130393	0.469417	ENSG00000137877	ENST00000320955	T	0.33216	1.42	4.53	3.54	0.40534	.	0.549056	0.16416	N	0.215395	T	0.00012	0.0000	L	0.50919	1.6	0.80722	P	0.0	B	0.33777	0.425	B	0.31290	0.127	T	0.21724	-1.0237	9	0.59425	D	0.04	.	13.9202	0.63926	0.0:0.1531:0.8469:0.0	rs12442525;rs60096193	2851	Q9NRC6	SPTN5_HUMAN	E	2851	ENSP00000317790:Q2851E	ENSP00000317790:Q2851E	Q	-	1	0	SPTBN5	39936798	0.997000	0.39634	0.208000	0.23602	0.897000	0.52465	2.774000	0.47694	2.063000	0.61619	0.467000	0.42956	CAG	G|0.462;C|0.538	0.538	strong		0.662	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
HLA-G	3135	hgsc.bcm.edu	37	6	29797406	29797406	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29797406G>A	ENST00000360323.6	+	4	855	c.831G>A	c.(829-831)gaG>gaA	p.E277E	HLA-G_ENST00000376828.2_Silent_p.E282E|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000428701.1_Silent_p.E277E|HLA-G_ENST00000376818.3_Silent_p.E185E			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	277	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.E277E(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CTTCTGGAGAGGAGCAGAGAT	0.607																																					p.E277E		Atlas-SNP	.											HLA-G,NS,carcinoma,0,1	HLA-G	90	1	1	Substitution - coding silent(1)	prostate(1)	c.G831A						scavenged	.						62.0	58.0	59.0					6																	29797406		2203	4298	6501	SO:0001819	synonymous_variant	3135	exon5			TGGAGAGGAGCAG		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.831G>A	6.37:g.29797406G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	145	8	0.0551724	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			.	.	weak		0.607	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
LILRA4	23547	hgsc.bcm.edu	37	19	54848684	54848684	+	Silent	SNP	G	G	A	rs8105624	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54848684G>A	ENST00000291759.4	-	5	995	c.939C>T	c.(937-939)gaC>gaT	p.D313D	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	313	Ig-like C2-type 3.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		CGATCAGGATGTCCAGGGGGT	0.677													G|||	986	0.196885	0.1611	0.2075	5008	,	,		13174	0.2609		0.2008	False		,,,				2504	0.1677				p.D313D		Atlas-SNP	.											.	LILRA4	91	.	0			c.C939T						PASS	.	G		715,3681		62,591,1545	24.0	26.0	25.0		939	0.4	0.5	19	dbSNP_116	25	1651,6921		173,1305,2808	no	coding-synonymous	LILRA4	NM_012276.3		235,1896,4353	AA,AG,GG		19.2604,16.2648,18.2449		313/500	54848684	2366,10602	2198	4286	6484	SO:0001819	synonymous_variant	23547	exon5			CAGGATGTCCAGG	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.939C>T	19.37:g.54848684G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																			G|0.821;A|0.179	0.179	strong		0.677	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
SLC5A4	6527	hgsc.bcm.edu	37	22	32651306	32651306	+	Missense_Mutation	SNP	G	G	A	rs16990065	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:32651306G>A	ENST00000266086.4	-	1	22	c.11C>T	c.(10-12)aCg>aTg	p.T4M	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	4			T -> M (in dbSNP:rs16990065).		carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GGGGCTAACCGTACTGGCCAT	0.517											OREG0003502	type=REGULATORY REGION|Gene=SLC5A4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	g|||	164	0.0327476	0.0552	0.0144	5008	,	,		19777	0.0218		0.0229	False		,,,				2504	0.0368				p.T4M		Atlas-SNP	.											.	SLC5A4	82	.	0			c.C11T						PASS	.	G	MET/THR	204,4202	127.4+/-164.3	4,196,2003	276.0	231.0	246.0		11	3.7	0.7	22	dbSNP_123	246	180,8420	82.0+/-144.6	1,178,4121	yes	missense	SLC5A4	NM_014227.2	81	5,374,6124	AA,AG,GG		2.093,4.63,2.9525	probably-damaging	4/660	32651306	384,12622	2203	4300	6503	SO:0001583	missense	6527	exon1			CTAACCGTACTGG	U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"""Solute carriers"""	11039	protein-coding gene	gene with protein product			"""solute carrier family 5 (low affinity glucose cotransporter), member 4"""			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.11C>T	22.37:g.32651306G>A	ENSP00000266086:p.Thr4Met	Somatic	132	0	0	834	WXS	Illumina HiSeq	Phase_I	154	78	0.506494	NM_014227	O15279	Missense_Mutation	SNP	ENST00000266086.4	37	CCDS13903.1	72	0.03296703296703297	29	0.05894308943089431	6	0.016574585635359115	20	0.03496503496503497	17	0.022427440633245383	G	11.61	1.689665	0.29962	0.0463	0.02093	ENSG00000100191	ENST00000266086	D	0.86497	-2.13	4.73	3.7	0.42460	.	1.001670	0.08050	N	0.996523	T	0.69079	0.3071	M	0.78801	2.425	0.31202	N	0.699624	D	0.89917	1.0	D	0.75020	0.985	T	0.74487	-0.3649	10	0.87932	D	0	.	10.1034	0.42519	0.0:0.0:0.8:0.2	rs16990065;rs52836933;rs16990065	4	Q9NY91	SC5A4_HUMAN	M	4	ENSP00000266086:T4M	ENSP00000266086:T4M	T	-	2	0	SLC5A4	30981306	0.933000	0.31639	0.684000	0.30055	0.055000	0.15305	1.970000	0.40520	1.198000	0.43158	-0.188000	0.12872	ACG	G|0.968;A|0.032	0.032	strong		0.517	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227	
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1017974C>G	ENST00000421673.2	-	31	4877	c.4827G>C	c.(4825-4827)caG>caC	p.Q1609H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1609	Approximate repeats.|Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.Q1609H(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAAGTGTGGTCTGAGGGTGTG	0.547																																					p.Q1609H		Atlas-SNP	.											MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	2	Substitution - Missense(2)	large_intestine(2)	c.G4827C						scavenged	.						473.0	441.0	452.0					11																	1017974		2186	4282	6468	SO:0001583	missense	4588	exon31			TGTGGTCTGAGGG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4827G>C	11.37:g.1017974C>G	ENSP00000406861:p.Gln1609His	Somatic	336	6	0.0178571		WXS	Illumina HiSeq	Phase_I	397	14	0.0352645	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	5.277	0.236564	0.10023	.	.	ENSG00000184956	ENST00000421673	T	0.35421	1.31	2.39	0.333	0.15943	.	.	.	.	.	T	0.26702	0.0653	L	0.52011	1.625	0.09310	N	1	B	0.25486	0.127	B	0.27715	0.082	T	0.28681	-1.0036	9	0.22109	T	0.4	.	3.4702	0.07565	0.0:0.5042:0.2173:0.2785	.	1609	Q6W4X9	MUC6_HUMAN	H	1609	ENSP00000406861:Q1609H	ENSP00000406861:Q1609H	Q	-	3	2	MUC6	1007974	0.000000	0.05858	0.003000	0.11579	0.027000	0.11550	-2.394000	0.01054	-0.057000	0.13199	-0.710000	0.03640	CAG	.	.	weak		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
KIAA1683	80726	hgsc.bcm.edu	37	19	18376518	18376518	+	Missense_Mutation	SNP	T	T	A	rs61740751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18376518T>A	ENST00000600328.3	-	3	2025	c.1832A>T	c.(1831-1833)cAg>cTg	p.Q611L	KIAA1683_ENST00000392413.4_Missense_Mutation_p.Q611L|KIAA1683_ENST00000600359.3_Missense_Mutation_p.Q565L			Q9H0B3	K1683_HUMAN	KIAA1683	611						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						CGCCTGTTTCTGGGTGCCAGT	0.557													T|||	79	0.0157748	0.0045	0.0173	5008	,	,		20077	0.001		0.0427	False		,,,				2504	0.0174				p.Q611L		Atlas-SNP	.											.	KIAA1683	190	.	0			c.A1832T						PASS	.	T	LEU/GLN,LEU/GLN,LEU/GLN	49,4357	50.2+/-85.5	0,49,2154	52.0	59.0	57.0		1832,1694,1832	1.9	0.0	19	dbSNP_129	57	463,8137	137.8+/-194.7	13,437,3850	no	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	113,113,113	13,486,6004	AA,AT,TT		5.3837,1.1121,3.9366	possibly-damaging,possibly-damaging,possibly-damaging	611/1368,565/1135,611/1181	18376518	512,12494	2203	4300	6503	SO:0001583	missense	80726	exon3			TGTTTCTGGGTGC	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1832A>T	19.37:g.18376518T>A	ENSP00000470780:p.Gln611Leu	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	202	98	0.485149	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	44	0.020146520146520148	0	0.0	9	0.024861878453038673	0	0.0	35	0.04617414248021108	T	11.97	1.798598	0.31777	0.011121	0.053837	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634	T;T;T	0.03860	3.85;3.85;3.78	4.34	1.91	0.25777	.	0.551463	0.13716	N	0.367735	T	0.00695	0.0023	L	0.48642	1.525	0.09310	N	1	B;B	0.34290	0.447;0.447	B;B	0.34180	0.177;0.177	T	0.43491	-0.9388	10	0.30078	T	0.28	-5.896	4.8953	0.13748	0.1669:0.0:0.2712:0.5618	rs61740751	611;611	E9PDE0;Q9H0B3	.;K1683_HUMAN	L	611;611;565	ENSP00000376213:Q611L;ENSP00000352774:Q611L;ENSP00000404501:Q565L	ENSP00000352774:Q611L	Q	-	2	0	KIAA1683	18237518	0.028000	0.19301	0.003000	0.11579	0.001000	0.01503	0.515000	0.22801	0.082000	0.17018	-0.333000	0.08304	CAG	A|0.041;G|0.000;T|0.959	0.041	strong		0.557	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
ACPT	93650	hgsc.bcm.edu	37	19	51297825	51297825	+	Missense_Mutation	SNP	G	G	A	rs55716643|rs386810263	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51297825G>A	ENST00000270593.1	+	9	973	c.973G>A	c.(973-975)Gcc>Acc	p.A325T	ACPT_ENST00000270594.3_Missense_Mutation_p.A232T|CTD-2568A17.8_ENST00000594114.1_RNA	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	325						integral component of membrane (GO:0016021)	acid phosphatase activity (GO:0003993)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(3)	11		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GGGGAATCCCGCCAAAGATGG	0.617													g|||	1652	0.329872	0.1309	0.2161	5008	,	,		17338	0.6538		0.3012	False		,,,				2504	0.3753				p.A325T		Atlas-SNP	.											.	ACPT	43	.	0			c.G973A						PASS	.	G	THR/ALA	673,3733	271.6+/-270.3	44,585,1574	40.0	39.0	39.0		973	1.7	0.0	19	dbSNP_129	39	2385,6215	365.6+/-334.0	349,1687,2264	yes	missense	ACPT	NM_033068.2	58	393,2272,3838	AA,AG,GG		27.7326,15.2746,23.5122	benign	325/427	51297825	3058,9948	2203	4300	6503	SO:0001583	missense	93650	exon9			AATCCCGCCAAAG	AF321918	CCDS12802.1	19q13.33	2012-10-02			ENSG00000142513	ENSG00000142513			14376	protein-coding gene	gene with protein product		606362				11414767	Standard	NM_033068		Approved		uc002pta.1	Q9BZG2		ENST00000270593.1:c.973G>A	19.37:g.51297825G>A	ENSP00000270593:p.Ala325Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Missense_Mutation	SNP	ENST00000270593.1	37	CCDS12802.1	641	0.2934981684981685	50	0.1016260162601626	71	0.19613259668508287	330	0.5769230769230769	190	0.25065963060686014	g	6.161	0.397948	0.11696	0.152746	0.277326	ENSG00000142513	ENST00000270593;ENST00000270594	T;T	0.76448	2.98;-1.02	3.9	1.74	0.24563	.	0.642945	0.14811	N	0.297051	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.14805	0.011	B	0.04013	0.001	T	0.45512	-0.9256	9	0.28530	T	0.3	-10.0341	4.3799	0.11288	0.2057:0.1884:0.6059:0.0	rs55716643;rs60842760	325	Q9BZG2	PPAT_HUMAN	T	325;232	ENSP00000270593:A325T;ENSP00000270594:A232T	ENSP00000270593:A325T	A	+	1	0	ACPT	55989637	0.001000	0.12720	0.009000	0.14445	0.000000	0.00434	0.419000	0.21247	0.468000	0.27243	-0.931000	0.02705	GCC	G|0.751;A|0.249	0.249	strong		0.617	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068	
SIGLEC9	27180	hgsc.bcm.edu	37	19	51630485	51630485	+	Missense_Mutation	SNP	C	C	A	rs273688	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51630485C>A	ENST00000250360.3	+	4	1014	c.947C>A	c.(946-948)gCt>gAt	p.A316D	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.A316D	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	316	Ig-like C2-type 2.		A -> D (in dbSNP:rs273688).		cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		AGGGATGCAGCTGAATTCACC	0.637													.|||	529	0.105631	0.3805	0.0331	5008	,	,		20814	0.0		0.0	False		,,,				2504	0.0031				p.A316D		Atlas-SNP	.											SIGLEC9,NS,carcinoma,+1,1	SIGLEC9	85	1	0			c.C947A						scavenged	.	A	ASP/ALA,ASP/ALA	1473,2933		252,969,982	41.0	40.0	40.0		947,947	-0.0	0.0	19	dbSNP_79	40	11,8589		0,11,4289	no	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	126,126	252,980,5271	AA,AC,CC		0.1279,33.4317,11.4101	benign,benign	316/480,316/464	51630485	1484,11522	2203	4300	6503	SO:0001583	missense	27180	exon4			ATGCAGCTGAATT	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.947C>A	19.37:g.51630485C>A	ENSP00000250360:p.Ala316Asp	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	110	2	0.0181818	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	196	0.08974358974358974	183	0.3719512195121951	13	0.03591160220994475	0	0.0	0	0.0	.	6.207	0.406368	0.11754	0.334317	0.001279	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.12255	2.7;2.7	2.3	-0.0215	0.13951	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.635768	0.12920	N	0.428257	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.16166	0.016	B	0.12156	0.007	T	0.46665	-0.9175	9	0.72032	D	0.01	.	5.4292	0.16444	0.1485:0.2067:0.6448:0.0	rs273688;rs60086561;rs273688	316	Q9Y336	SIGL9_HUMAN	D	316	ENSP00000413861:A316D;ENSP00000250360:A316D	ENSP00000250360:A316D	A	+	2	0	SIGLEC9	56322297	0.018000	0.18449	0.000000	0.03702	0.001000	0.01503	0.516000	0.22817	-0.622000	0.05626	-3.343000	0.00043	GCT	C|0.895;A|0.105	0.105	strong		0.637	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441	
RYR2	6262	hgsc.bcm.edu	37	1	237617757	237617757	+	Silent	SNP	C	C	T	rs3765097	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:237617757C>T	ENST00000366574.2	+	15	1676	c.1359C>T	c.(1357-1359)agC>agT	p.S453S	RYR2_ENST00000542537.1_Silent_p.S437S|RYR2_ENST00000360064.6_Silent_p.S451S	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	453					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGTCCGTAAGCCTAAGTCTGC	0.458													T|||	2683	0.535743	0.2769	0.5447	5008	,	,		17132	0.7391		0.5994	False		,,,				2504	0.6043				p.S453S		Atlas-SNP	.											RYR2,lower_third,carcinoma,+1,1	RYR2	1273	1	0			c.C1359T						PASS	.	T		1231,2599		190,851,874	90.0	86.0	87.0		1359	-1.8	0.8	1	dbSNP_107	87	4947,3291		1477,1993,649	no	coding-synonymous	RYR2	NM_001035.2		1667,2844,1523	TT,TC,CC		39.949,32.141,48.8068		453/4968	237617757	6178,5890	1915	4119	6034	SO:0001819	synonymous_variant	6262	exon15			CGTAAGCCTAAGT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.1359C>T	1.37:g.237617757C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	55	0.470085	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			C|0.454;T|0.546	0.546	strong		0.458	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
LAMA5	3911	hgsc.bcm.edu	37	20	60892545	60892545	+	Missense_Mutation	SNP	C	C	T	rs2427282	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60892545C>T	ENST00000252999.3	-	55	7433	c.7367G>A	c.(7366-7368)cGc>cAc	p.R2456H		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2456	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGCGGCGAGGCGCTCCAGCTC	0.662													.|||	37	0.00738818	0.0008	0.0115	5008	,	,		15961	0.0		0.0268	False		,,,				2504	0.001				p.R2456H		Atlas-SNP	.											.	LAMA5	268	.	0			c.G7367A						PASS	.		HIS/ARG	30,4310		0,30,2140	20.0	23.0	22.0		7367	-4.2	0.8	20	dbSNP_100	22	232,8314		3,226,4044	yes	missense	LAMA5	NM_005560.3	29	3,256,6184	TT,TC,CC		2.7147,0.6912,2.0332	benign	2456/3696	60892545	262,12624	2170	4273	6443	SO:0001583	missense	3911	exon55			GCGAGGCGCTCCA	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7367G>A	20.37:g.60892545C>T	ENSP00000252999:p.Arg2456His	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	26	0.011904761904761904	0	0.0	5	0.013812154696132596	0	0.0	21	0.027704485488126648	c	7.206	0.594372	0.13875	0.006912	0.027147	ENSG00000130702	ENST00000252999	T	0.18960	2.18	3.54	-4.23	0.03789	.	0.473582	0.22319	N	0.061639	T	0.01592	0.0051	N	0.01048	-1.04	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39820	-0.9595	10	0.25106	T	0.35	.	10.7393	0.46143	0.0:0.3638:0.0:0.6362	rs2427282	2456	O15230	LAMA5_HUMAN	H	2456	ENSP00000252999:R2456H	ENSP00000252999:R2456H	R	-	2	0	LAMA5	60325940	0.672000	0.27530	0.804000	0.32291	0.108000	0.19459	-0.278000	0.08490	-0.734000	0.04843	0.436000	0.28706	CGC	C|0.984;T|0.016	0.016	strong		0.662	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
MAGEE1	57692	hgsc.bcm.edu	37	X	75649430	75649430	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:75649430G>A	ENST00000361470.2	+	1	1385	c.1107G>A	c.(1105-1107)ccG>ccA	p.P369P		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	369	Pro-rich.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						CCTCTGTGCCGCCCACCGCCT	0.672																																					p.P369P		Atlas-SNP	.											.	MAGEE1	236	.	0			c.G1107A						PASS	.						33.0	26.0	28.0					X																	75649430		2203	4297	6500	SO:0001819	synonymous_variant	57692	exon1			TGTGCCGCCCACC	AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.1107G>A	X.37:g.75649430G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	70	64	0.914286	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	CCDS14433.1																																																																																			.	.	none		0.672	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932	
OR5H6	79295	hgsc.bcm.edu	37	3	97983981	97983981	+	Missense_Mutation	SNP	G	G	A	rs9871143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:97983981G>A	ENST00000383696.2	+	1	894	c.853G>A	c.(853-855)Gac>Aac	p.D285N	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	285			D -> N (in dbSNP:rs9871143).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D285N(1)		cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GCAAGCAGATGACCAAGATAT	0.423													G|||	1593	0.318091	0.2179	0.3372	5008	,	,		16723	0.1319		0.5616	False		,,,				2504	0.3814				p.D285N		Atlas-SNP	.											OR5H6,NS,adenoma,0,2	OR5H6	89	2	1	Substitution - Missense(1)	stomach(1)	c.G853A						scavenged	.	G	ASN/ASP	1100,3306		133,834,1236	66.0	63.0	64.0		853	2.2	0.1	3	dbSNP_119	64	4776,3822		1337,2102,860	yes	missense	OR5H6	NM_001005479.1	23	1470,2936,2096	AA,AG,GG		44.4522,24.966,45.1861	benign	285/326	97983981	5876,7128	2203	4299	6502	SO:0001583	missense	79295	exon1			GCAGATGACCAAG	BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"""GPCR / Class A : Olfactory receptors"""	14767	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily H, member 6"""				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.853G>A	3.37:g.97983981G>A	ENSP00000373196:p.Asp285Asn	Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	176	85	0.482955	NM_001005479	Q6IF88	Missense_Mutation	SNP	ENST00000383696.2	37	CCDS33800.1	725	0.33195970695970695	116	0.23577235772357724	132	0.36464088397790057	63	0.11013986013986014	414	0.5461741424802111	-	8.509	0.866164	0.17250	0.24966	0.555478	ENSG00000230301	ENST00000383696	T	0.00145	8.67	2.19	2.19	0.27852	GPCR, rhodopsin-like superfamily (1);	0.416536	0.20370	N	0.093671	T	0.00012	0.0000	L	0.42632	1.34	0.80722	P	0.0	B	0.24092	0.097	B	0.33254	0.16	T	0.03641	-1.1017	9	0.56958	D	0.05	.	6.8129	0.23814	0.0:0.295:0.7049:0.0	rs9871143;rs9871143	285	Q8NGV6	OR5H6_HUMAN	N	285	ENSP00000373196:D285N	ENSP00000373196:D285N	D	+	1	0	OR5H6	99466671	0.000000	0.05858	0.102000	0.21198	0.166000	0.22503	0.591000	0.23969	1.220000	0.43490	0.194000	0.17425	GAC	G|0.610;A|0.390	0.390	strong		0.423	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2		
KLHDC7B	113730	hgsc.bcm.edu	37	22	50987175	50987175	+	Missense_Mutation	SNP	G	G	T	rs116500907	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50987175G>T	ENST00000395676.2	+	1	714	c.580G>T	c.(580-582)Gtg>Ttg	p.V194L	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	194										central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	14		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGGTTGGGGGGTGGTGGAGGG	0.756													G|||	268	0.0535144	0.1014	0.0159	5008	,	,		9731	0.0119		0.0328	False		,,,				2504	0.0798				p.V194L		Atlas-SNP	.											.	KLHDC7B	39	.	0			c.G580T						PASS	.	G	LEU/VAL	134,2544		3,128,1208	2.0	3.0	3.0		580	2.9	0.9	22	dbSNP_132	3	127,6159		2,123,3018	no	missense	KLHDC7B	NM_138433.3	32	5,251,4226	TT,TG,GG		2.0204,5.0037,2.9116	benign	194/595	50987175	261,8703	1339	3143	4482	SO:0001583	missense	113730	exon1			TGGGGGGTGGTGG	BC009980	CCDS14097.2	22q13.33	2006-11-29		2005-12-13	ENSG00000130487	ENSG00000130487			25145	protein-coding gene	gene with protein product							Standard	NM_138433		Approved	MGC16635	uc003bmi.3	Q96G42	OTTHUMG00000150250	ENST00000395676.2:c.580G>T	22.37:g.50987175G>T	ENSP00000379034:p.Val194Leu	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	12	10	0.833333	NM_138433		Missense_Mutation	SNP	ENST00000395676.2	37	CCDS14097.2	83	0.038003663003663	45	0.09146341463414634	8	0.022099447513812154	4	0.006993006993006993	26	0.03430079155672823	g	10.23	1.291785	0.23564	0.050037	0.020204	ENSG00000130487	ENST00000395676	D	0.82619	-1.63	3.97	2.88	0.33553	.	.	.	.	.	T	0.07188	0.0182	L	0.27053	0.805	0.23168	N	0.998184	P	0.40970	0.734	B	0.32090	0.14	T	0.05289	-1.0894	9	0.31617	T	0.26	.	8.4306	0.32755	0.13:0.0:0.87:0.0	.	194	Q96G42	KLD7B_HUMAN	L	194	ENSP00000379034:V194L	ENSP00000379034:V194L	V	+	1	0	KLHDC7B	49334041	0.231000	0.23751	0.915000	0.36163	0.135000	0.20990	1.505000	0.35736	2.067000	0.61834	0.306000	0.20318	GTG	G|0.958;T|0.042	0.042	strong		0.756	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433	
KHDC1L	100129128	hgsc.bcm.edu	37	6	73934037	73934037	+	Silent	SNP	C	C	A	rs190736560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:73934037C>A	ENST00000370388.3	-	2	190	c.147G>T	c.(145-147)ctG>ctT	p.L49L	KHDC1L_ENST00000471312.1_5'UTR|RP11-257K9.8_ENST00000423730.3_Missense_Mutation_p.C152F	NM_001126063.2	NP_001119535.1	Q5JSQ8	KHDCL_HUMAN	KH homology domain containing 1-like	49										breast(1)|endometrium(1)|kidney(1)|lung(3)|skin(1)	7						TGTGGCTGTGCAGCTCAATGC	0.547													C|||	11	0.00219649	0.0	0.0086	5008	,	,		21209	0.0		0.005	False		,,,				2504	0.0				p.L49L		Atlas-SNP	.											.	KHDC1L	22	.	0			c.G147T						PASS	.						146.0	125.0	131.0					6																	73934037		692	1591	2283	SO:0001819	synonymous_variant	100129128	exon2			GCTGTGCAGCTCA	BC004267	CCDS47450.1	6q13	2014-05-15			ENSG00000256980	ENSG00000256980			37274	protein-coding gene	gene with protein product							Standard	NM_001126063		Approved	RP11-257K9.7	uc003pgm.4	Q5JSQ8	OTTHUMG00000132474	ENST00000370388.3:c.147G>T	6.37:g.73934037C>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_001126063	E1P535	Silent	SNP	ENST00000370388.3	37	CCDS47450.1	6	0.0027472527472527475	0	0.0	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	13.63	2.294460	0.40594	.	.	ENSG00000256980	ENST00000370385	.	.	.	1.91	-0.00495	0.14019	.	.	.	.	.	T	0.18087	0.0434	.	.	.	0.25487	N	0.98769	.	.	.	.	.	.	T	0.28933	-1.0028	5	0.59425	D	0.04	.	4.0495	0.09788	0.0:0.5876:0.0:0.4124	.	.	.	.	F	152	.	ENSP00000359412:C152F	C	-	2	0	RP11-257K9.7	73990758	0.039000	0.19947	0.188000	0.23233	0.487000	0.33371	-0.022000	0.12480	-0.026000	0.13895	0.205000	0.17691	TGC	C|0.997;A|0.003	0.003	strong		0.547	KHDC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255640.1	NM_001126063	
PVR	5817	hgsc.bcm.edu	37	19	45150614	45150614	+	Missense_Mutation	SNP	G	G	A	rs1058402	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:45150614G>A	ENST00000425690.3	+	2	498	c.199G>A	c.(199-201)Gcg>Acg	p.A67T	PVR_ENST00000344956.4_Missense_Mutation_p.A67T|PVR_ENST00000406449.4_Missense_Mutation_p.A67T|PVR_ENST00000403059.4_Missense_Mutation_p.A67T|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	67	Ig-like V-type.		A -> T (in dbSNP:rs1058402).		adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		GCTGACTTGGGCGCGGCATGG	0.632													G|||	512	0.102236	0.0696	0.1023	5008	,	,		11873	0.126		0.0427	False		,,,				2504	0.183				p.A67T		Atlas-SNP	.											.	PVR	23	.	0			c.G199A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	273,4133	151.8+/-185.6	12,249,1942	41.0	33.0	36.0		199,199,199,199	-9.6	0.0	19	dbSNP_86	36	418,8182	126.5+/-185.0	17,384,3899	yes	missense,missense,missense,missense	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	58,58,58,58	29,633,5841	AA,AG,GG		4.8605,6.1961,5.3129	benign,benign,benign,benign	67/373,67/365,67/393,67/418	45150614	691,12315	2203	4300	6503	SO:0001583	missense	5817	exon2			ACTTGGGCGCGGC	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9705	protein-coding gene	gene with protein product	"""nectin-like 5"""	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.199G>A	19.37:g.45150614G>A	ENSP00000402060:p.Ala67Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	37	CCDS12640.1	182	0.08333333333333333	27	0.054878048780487805	38	0.10497237569060773	88	0.15384615384615385	29	0.03825857519788918	G	2.285	-0.363833	0.05103	0.061961	0.048605	ENSG00000073008	ENST00000344956;ENST00000425690;ENST00000406449;ENST00000403059	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	4.79	-9.59	0.00556	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	3.044690	0.01062	N	0.004675	T	0.00109	0.0003	N	0.00317	-1.655	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.12837	0.001;0.003;0.005;0.008	T	0.04165	-1.0972	9	0.02654	T	1	.	4.5535	0.12126	0.1515:0.4059:0.3454:0.0972	rs1058402;rs3199019;rs52822493;rs57254218;rs1058402	67;67;67;67	P15151-2;P15151-3;P15151-4;P15151	.;.;.;PVR_HUMAN	T	67	ENSP00000340870:A67T;ENSP00000402060:A67T;ENSP00000383907:A67T;ENSP00000385344:A67T	ENSP00000340870:A67T	A	+	1	0	PVR	49842454	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.252000	0.02880	-1.950000	0.01030	-3.289000	0.00047	GCG	G|0.931;A|0.069	0.069	strong		0.632	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505	
GSTT2	2953	hgsc.bcm.edu	37	22	24323227	24323227	+	Splice_Site	SNP	G	G	A	rs76498342	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:24323227G>A	ENST00000215780.5	+	2	250		c.e2+1		DDT_ENST00000404092.1_5'Flank|DDT_ENST00000350608.3_5'Flank|GSTT2_ENST00000402588.3_Splice_Site	NM_000854.3	NP_000845.1	P0CG29	GST2_HUMAN	glutathione S-transferase theta 2							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			lung(1)	1						TGACCGAAAGGTGCCCTCCTT	0.617																																					.		Atlas-SNP	.											.	GSTT2	3	.	0			c.200+1G>A						PASS	.	G		349,4057		1,347,1855	439.0	350.0	380.0			3.1	1.0	22	dbSNP_131	380	1220,7376		7,1206,3085	no	splice-5	GSTT2	NM_000854.3		8,1553,4940	AA,AG,GG		14.1926,7.921,12.0674			24323227	1569,11433	2203	4298	6501	SO:0001630	splice_region_variant	2953	exon2			CGAAAGGTGCCCT	L38503		22q11.23	2012-06-21			ENSG00000099984	ENSG00000099984	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4642	protein-coding gene	gene with protein product		600437				7789971, 9729470	Standard	NM_000854		Approved		uc002zyw.4	P0CG29	OTTHUMG00000150786	ENST00000215780.5:c.200+1G>A	22.37:g.24323227G>A		Somatic	457	0	0		WXS	Illumina HiSeq	Phase_I	925	269	0.290811	NM_000854	O60665|P30712|Q6IPV7|Q9HD76	Splice_Site	SNP	ENST00000215780.5	37	CCDS13821.1	367	0.16804029304029305	37	0.07520325203252033	50	0.13812154696132597	170	0.2972027972027972	110	0.14511873350923482	.	13.58	2.279780	0.40294	0.07921	0.141926	ENSG00000099984	ENST00000215780;ENST00000402588	.	.	.	3.11	3.11	0.35812	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.9816	0.41817	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GSTT2	22653227	1.000000	0.71417	0.966000	0.40874	0.223000	0.24884	3.348000	0.52209	1.807000	0.52817	0.591000	0.81541	.	G|0.873;A|0.127	0.127	strong		0.617	GSTT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320080.1	NM_000854	Intron
DRC1	92749	hgsc.bcm.edu	37	2	26676395	26676395	+	Missense_Mutation	SNP	G	G	T	rs12623642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:26676395G>T	ENST00000288710.2	+	14	1971	c.1897G>T	c.(1897-1899)Gtc>Ttc	p.V633F		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	633			V -> F (in dbSNP:rs12623642).		axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											GGAGGCCTTCGTCATGGGTCT	0.617													G|||	971	0.19389	0.0257	0.2651	5008	,	,		17792	0.5873		0.0716	False		,,,				2504	0.091				p.V633F		Atlas-SNP	.											.	CCDC164	84	.	0			c.G1897T						PASS	.	G	PHE/VAL	143,4263	99.4+/-138.0	1,141,2061	52.0	54.0	54.0		1897	5.0	1.0	2	dbSNP_120	54	584,8016	155.4+/-209.4	22,540,3738	yes	missense	CCDC164	NM_145038.2	50	23,681,5799	TT,TG,GG		6.7907,3.2456,5.5897	probably-damaging	633/741	26676395	727,12279	2203	4300	6503	SO:0001583	missense	92749	exon14			GCCTTCGTCATGG	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"""chromosome 2 open reading frame 39"", ""coiled-coil domain containing 164"", ""dynein regulatory complex subunit 1 homolog (Chlamydomonas)"""	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.1897G>T	2.37:g.26676395G>T	ENSP00000288710:p.Val633Phe	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	37	CCDS1723.1	508	0.2326007326007326	11	0.022357723577235773	76	0.20994475138121546	367	0.6416083916083916	54	0.0712401055408971	G	23.3	4.396076	0.83011	0.032456	0.067907	ENSG00000157856	ENST00000288710	T	0.20598	2.06	5.03	5.03	0.67393	.	0.302633	0.31747	N	0.007127	T	0.00012	0.0000	M	0.83012	2.62	0.25125	P	0.99061866	D	0.57257	0.979	P	0.61132	0.884	T	0.46289	-0.9202	9	0.87932	D	0	-28.8909	17.4982	0.87724	0.0:0.0:1.0:0.0	rs12623642;rs52797399;rs57231544;rs12623642	633	Q96MC2	CC164_HUMAN	F	633	ENSP00000288710:V633F	ENSP00000288710:V633F	V	+	1	0	CCDC164	26529899	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.667000	0.54547	2.506000	0.84524	0.609000	0.83330	GTC	G|0.875;T|0.125	0.125	strong		0.617	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038	
PDGFRA	5156	hgsc.bcm.edu	37	4	55130078	55130078	+	Silent	SNP	T	T	C	rs2229307	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55130078T>C	ENST00000257290.5	+	4	943	c.612T>C	c.(610-612)aaT>aaC	p.N204N	FIP1L1_ENST00000507166.1_Intron|PDGFRA_ENST00000508170.1_Silent_p.N204N	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	204	Ig-like C2-type 3.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	TCCCATTTAATGTTTATGCTT	0.393			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)			C|||	1183	0.236222	0.2776	0.3487	5008	,	,		19351	0.2034		0.1233	False		,,,				2504	0.2505				p.N204N	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	.	PDGFRA	1583	.	0			c.T612C						PASS	.	C		1102,3304	719.5+/-408.9	128,846,1229	73.0	73.0	73.0		612	-3.1	0.0	4	dbSNP_98	73	1044,7556	771.5+/-407.7	67,910,3323	no	coding-synonymous	PDGFRA	NM_006206.4		195,1756,4552	CC,CT,TT		12.1395,25.0113,16.5001		204/1090	55130078	2146,10860	2203	4300	6503	SO:0001819	synonymous_variant	5156	exon4	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	ATTTAATGTTTAT	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.612T>C	4.37:g.55130078T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	48	27	0.5625	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																			T|0.828;C|0.172	0.172	strong		0.393	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
PLA2R1	22925	hgsc.bcm.edu	37	2	160808075	160808075	+	Missense_Mutation	SNP	C	C	T	rs3828323	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160808075C>T	ENST00000283243.7	-	24	3522	c.3316G>A	c.(3316-3318)Ggt>Agt	p.G1106S	PLA2R1_ENST00000392771.1_Missense_Mutation_p.G1106S	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	1106			G -> S (in dbSNP:rs3828323).		cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						GTATTTACACCGTGTCCAGAA	0.363													C|||	1249	0.249401	0.0401	0.2824	5008	,	,		22780	0.2917		0.5169	False		,,,				2504	0.1902				p.G1106S		Atlas-SNP	.											.	PLA2R1	153	.	0			c.G3316A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	468,3938	221.3+/-238.5	20,428,1755	116.0	104.0	108.0		3316,3316,3316	-3.0	0.0	2	dbSNP_107	108	4216,4384	570.1+/-389.3	1035,2146,1119	yes	missense,missense,missense	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	56,56,56	1055,2574,2874	TT,TC,CC		49.0233,10.6219,36.0141	benign,benign,benign	1106/1325,1106/1462,1106/1464	160808075	4684,8322	2203	4300	6503	SO:0001583	missense	22925	exon24			TTACACCGTGTCC	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.3316G>A	2.37:g.160808075C>T	ENSP00000283243:p.Gly1106Ser	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	186	185	0.994624	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	686	0.3141025641025641	27	0.054878048780487805	107	0.2955801104972376	165	0.28846153846153844	387	0.5105540897097626	C	0.031	-1.336677	0.01287	0.106219	0.490233	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.06294	3.39;3.32	5.92	-3.0	0.05480	C-type lectin-like (1);	1.622470	0.03024	N	0.151168	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.44019	-0.9355	9	0.07482	T	0.82	.	4.5914	0.12307	0.0934:0.1082:0.2383:0.5601	rs3828323;rs17232626;rs56981515;rs3828323	1106;1106;1106	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	S	1106	ENSP00000283243:G1106S;ENSP00000376524:G1106S	ENSP00000283243:G1106S	G	-	1	0	PLA2R1	160516321	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.698000	0.05092	-0.402000	0.07633	-1.283000	0.01379	GGT	C|0.679;T|0.321	0.321	strong		0.363	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
CA11	770	hgsc.bcm.edu	37	19	49143533	49143533	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49143533C>T	ENST00000084798.4	-	4	969	c.290G>A	c.(289-291)cGg>cAg	p.R97Q	SEC1P_ENST00000430145.2_RNA|DBP_ENST00000222122.5_5'Flank|DBP_ENST00000601104.1_5'Flank	NM_001217.3	NP_001208.2	O75493	CAH11_HUMAN	carbonic anhydrase XI	97						basolateral plasma membrane (GO:0016323)|extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	14		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000103)|all cancers(93;0.000119)|GBM - Glioblastoma multiforme(486;0.00634)|Epithelial(262;0.016)	Zonisamide(DB00909)	CAAGGTTCCCCGGAGCTGTGG	0.552																																					p.R97Q		Atlas-SNP	.											.	CA11	29	.	0			c.G290A						PASS	.						47.0	47.0	47.0					19																	49143533		2203	4300	6503	SO:0001583	missense	770	exon4			GTTCCCCGGAGCT	AF067662	CCDS12729.1	19q13.3	2012-07-02			ENSG00000063180	ENSG00000063180		"""Carbonic anhydrases"""	1370	protein-coding gene	gene with protein product	"""CA-RP XI"", ""carbonic anhydrase-related protein XI"", ""carbonic anhydrase-related protein 2"""	604644				9878252	Standard	XR_243956		Approved	CARP2, CARPX1	uc002pjz.1	O75493		ENST00000084798.4:c.290G>A	19.37:g.49143533C>T	ENSP00000084798:p.Arg97Gln	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_001217	O60596|Q6FHI1|Q9UEC4	Missense_Mutation	SNP	ENST00000084798.4	37	CCDS12729.1	.	.	.	.	.	.	.	.	.	.	C	19.68	3.872278	0.72180	.	.	ENSG00000063180	ENST00000084798	T	0.67698	-0.28	3.46	3.46	0.39613	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.218732	0.39544	N	0.001325	T	0.48750	0.1517	N	0.10916	0.065	0.36952	D	0.892938	D	0.55385	0.971	P	0.45310	0.476	T	0.60910	-0.7169	10	0.54805	T	0.06	.	10.6521	0.45655	0.0:1.0:0.0:0.0	.	97	O75493	CAH11_HUMAN	Q	97	ENSP00000084798:R97Q	ENSP00000084798:R97Q	R	-	2	0	CA11	53835345	0.995000	0.38212	1.000000	0.80357	0.988000	0.76386	2.667000	0.46808	1.970000	0.57323	0.462000	0.41574	CGG	.	.	none		0.552	CA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466172.1	NM_001217	
TBP	6908	hgsc.bcm.edu	37	6	170871058	170871058	+	Silent	SNP	G	G	A	rs113440919		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:170871058G>A	ENST00000392092.2	+	3	513	c.234G>A	c.(232-234)caG>caA	p.Q78Q	TBP_ENST00000540980.1_Silent_p.Q58Q|TBP_ENST00000230354.6_Silent_p.Q78Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	78	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.577																																					p.Q78Q		Atlas-SNP	.											TBP,caecum,carcinoma,0,1	TBP	58	1	0			c.G234A						scavenged	.						13.0	18.0	16.0					6																	170871058		1927	3786	5713	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAGCAG	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.234G>A	6.37:g.170871058G>A		Somatic	67	2	0.0298507		WXS	Illumina HiSeq	Phase_I	70	7	0.1	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			G|0.500;A|0.500	0.500	weak		0.577	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
UCHL1	7345	hgsc.bcm.edu	37	4	41259633	41259633	+	Missense_Mutation	SNP	C	C	A	rs5030732	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:41259633C>A	ENST00000284440.4	+	3	197	c.53C>A	c.(52-54)tCc>tAc	p.S18Y	UCHL1_ENST00000512788.1_Missense_Mutation_p.S18Y|UCHL1-AS1_ENST00000510073.1_RNA|UCHL1_ENST00000508768.1_Missense_Mutation_p.S18Y|UCHL1_ENST00000504818.1_3'UTR|UCHL1-AS1_ENST00000507190.1_RNA|UCHL1_ENST00000503431.1_Missense_Mutation_p.S18Y	NM_004181.4	NP_004172.2	P09936	UCHL1_HUMAN	ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)	18			S -> Y (found in patients with cataract; unknown pathological significance; loss of dimerization ability; impaired ligase activity; confers an antioxidant protective function when expressed at physiological levels in neuroblastoma cells and primary cortical neurons; dbSNP:rs5030732). {ECO:0000269|PubMed:10203348, ECO:0000269|PubMed:11027850, ECO:0000269|PubMed:15048890, ECO:0000269|PubMed:16450370, ECO:0000269|PubMed:21268678}.		adult walking behavior (GO:0007628)|axon target recognition (GO:0007412)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|cell proliferation (GO:0008283)|eating behavior (GO:0042755)|muscle fiber development (GO:0048747)|negative regulation of MAP kinase activity (GO:0043407)|neuromuscular process (GO:0050905)|protein deubiquitination (GO:0016579)|response to ischemia (GO:0002931)|sensory perception of pain (GO:0019233)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	alpha-2A adrenergic receptor binding (GO:0031694)|cysteine-type endopeptidase activity (GO:0004197)|ligase activity (GO:0016874)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(2)	8						CAGGTGCTGTCCCGGCTGGGG	0.766													C|||	1272	0.253994	0.0121	0.2939	5008	,	,		10899	0.5437		0.1809	False		,,,				2504	0.3292				p.S18Y		Atlas-SNP	.											.	UCHL1	19	.	0			c.C53A	GRCh37	CM994452	UCHL1	M	rs5030732	PASS	.	C	TYR/SER	114,4064		2,110,1977	6.0	8.0	7.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	53	2.8	0.9	4	dbSNP_113	7	1114,7164		61,992,3086	no	missense	UCHL1	NM_004181.4	144	63,1102,5063	AA,AC,CC		13.4574,2.7286,9.8587	benign	18/224	41259633	1228,11228	2089	4139	6228	SO:0001583	missense	7345	exon3			TGCTGTCCCGGCT	BC000332	CCDS3462.1	4p13	2011-07-21			ENSG00000154277	ENSG00000154277	3.4.19.12	"""Parkinson disease"""	12513	protein-coding gene	gene with protein product		191342		PARK5		1840236	Standard	NM_004181		Approved	PGP9.5, Uch-L1	uc003gvo.3	P09936	OTTHUMG00000099377	ENST00000284440.4:c.53C>A	4.37:g.41259633C>A	ENSP00000284440:p.Ser18Tyr	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	18	13	0.722222	NM_004181	Q4W5K6|Q71UM0	Missense_Mutation	SNP	ENST00000284440.4	37	CCDS3462.1	528	0.24175824175824176	16	0.032520325203252036	97	0.26795580110497236	282	0.493006993006993	133	0.17546174142480211	C	8.406	0.842968	0.16963	0.027286	0.134574	ENSG00000154277	ENST00000514924;ENST00000503431;ENST00000284440;ENST00000508768;ENST00000512788	T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47	3.7	2.84	0.33178	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (4);	1.003210	0.08035	N	0.994193	T	0.00012	0.0000	L	0.37697	1.125	0.28202	P	0.9273172	P	0.38300	0.626	B	0.36567	0.228	T	0.44406	-0.9330	9	0.23891	T	0.37	-1.0546	13.1671	0.59577	0.0:0.8388:0.1611:0.0	rs5030732	18	P09936	UCHL1_HUMAN	Y	18	ENSP00000426634:S18Y;ENSP00000422542:S18Y;ENSP00000284440:S18Y;ENSP00000426895:S18Y;ENSP00000423623:S18Y	ENSP00000284440:S18Y	S	+	2	0	UCHL1	40954390	0.422000	0.25473	0.940000	0.37924	0.849000	0.48306	1.040000	0.30278	0.724000	0.32296	0.462000	0.41574	TCC	C|0.758;A|0.242	0.242	strong		0.766	UCHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216827.1	NM_004181	
ZNF17	7565	hgsc.bcm.edu	37	19	57932027	57932027	+	Silent	SNP	C	C	T	rs2158009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57932027C>T	ENST00000601808.1	+	3	1380	c.1167C>T	c.(1165-1167)aaC>aaT	p.N389N	ZNF17_ENST00000307658.7_Silent_p.N391N|AC004076.7_ENST00000597410.1_Intron	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	389					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		ATGAATGCAACGAATGTGGGA	0.398													C|||	792	0.158147	0.0144	0.2061	5008	,	,		22756	0.253		0.174	False		,,,				2504	0.2045				p.N389N	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.C1167T						PASS	.	C		184,4200	103.8+/-142.4	6,172,2014	85.0	88.0	87.0		1167	-3.6	0.0	19	dbSNP_96	87	1703,6891	300.2+/-304.8	177,1349,2771	no	coding-synonymous	ZNF17	NM_006959.2		183,1521,4785	TT,TC,CC		19.8162,4.1971,14.54		389/663	57932027	1887,11091	2192	4297	6489	SO:0001819	synonymous_variant	7565	exon3			ATGCAACGAATGT	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"""Zinc fingers, C2H2-type"", ""-"""	12958	protein-coding gene	gene with protein product			"""zinc finger protein 17 (HPF3, KOX 10)"""			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.1167C>T	19.37:g.57932027C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Silent	SNP	ENST00000601808.1	37	CCDS42636.1																																																																																			C|0.820;T|0.180	0.180	strong		0.398	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959	
GPC1	2817	hgsc.bcm.edu	37	2	241405608	241405608	+	Silent	SNP	A	A	G	rs1042841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241405608A>G	ENST00000264039.2	+	9	1826	c.1578A>G	c.(1576-1578)ggA>ggG	p.G526G	GPC1_ENST00000466624.1_3'UTR	NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	526					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		AGCAGGAAGGACAGAAGACCT	0.667													g|||	440	0.0878594	0.1362	0.0793	5008	,	,		14005	0.0238		0.1093	False		,,,				2504	0.0726				p.G526G		Atlas-SNP	.											.	GPC1	32	.	0			c.A1578G						PASS	.			506,3900	775.8+/-414.1	28,450,1725	64.0	78.0	73.0		1578	-4.1	0.0	2	dbSNP_86	73	948,7652	773.9+/-407.7	39,870,3391	no	coding-synonymous	GPC1	NM_002081.2		67,1320,5116	GG,GA,AA		11.0233,11.4843,11.1795		526/559	241405608	1454,11552	2203	4300	6503	SO:0001819	synonymous_variant	2817	exon9			GGAAGGACAGAAG	AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"""Proteoglycans / Cell Surface : Glypicans"""	4449	protein-coding gene	gene with protein product	"""glypican proteoglycan 1"""	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.1578A>G	2.37:g.241405608A>G		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	258	112	0.434109	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	179	0.08195970695970696	53	0.10772357723577236	34	0.09392265193370165	4	0.006993006993006993	88	0.11609498680738786	g	0.018	-1.470472	0.01044	0.114843	0.110233	ENSG00000063660	ENST00000420138;ENST00000455111	.	.	.	3.29	-4.13	0.03904	.	.	.	.	.	T	0.00271	0.0008	.	.	.	0.23886	P	0.99656389	.	.	.	.	.	.	T	0.21075	-1.0256	3	.	.	.	-28.5777	2.8007	0.05414	0.4758:0.1486:0.2756:0.1	rs1042841;rs3172189;rs17442443;rs57479708;rs1042841	.	.	.	A	566;278	.	.	T	+	1	0	GPC1	241054281	0.200000	0.23398	0.010000	0.14722	0.008000	0.06430	0.185000	0.16958	-1.096000	0.03046	-1.177000	0.01723	ACA	A|0.901;G|0.099	0.099	strong		0.667	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
BTNL8	79908	hgsc.bcm.edu	37	5	180338368	180338368	+	Missense_Mutation	SNP	A	A	G	rs386695827|rs2276995	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:180338368A>G	ENST00000340184.4	+	3	633	c.427A>G	c.(427-429)Acg>Gcg	p.T143A	BTNL8_ENST00000533815.2_5'UTR|BTNL8_ENST00000505126.1_5'UTR|BTNL8_ENST00000511704.1_Missense_Mutation_p.T27A|BTNL8_ENST00000508408.1_Missense_Mutation_p.T143A|BTNL8_ENST00000400707.3_Missense_Mutation_p.T18A|BTNL8_ENST00000231229.4_Missense_Mutation_p.T143A|Y_RNA_ENST00000410920.1_RNA	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	143	Ig-like V-type 2.		T -> A (in dbSNP:rs2276995). {ECO:0000269|PubMed:15489334}.		immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CATTTCCATCACGGGATATGT	0.527													G|||	2166	0.432508	0.6702	0.4236	5008	,	,		20380	0.3462		0.3757	False		,,,				2504	0.2648				p.T143A		Atlas-SNP	.											BTNL8,colon,carcinoma,-2,1	BTNL8	114	1	0			c.A427G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR,ALA/THR,,ALA/THR	2834,1572	658.7+/-400.4	925,984,294	248.0	272.0	264.0		427,79,427,52,,427	-5.4	0.0	5	dbSNP_100	264	3247,5345	485.0+/-371.5	625,1997,1674	yes	missense,missense,missense,missense,utr-5,missense	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	58,58,58,58,,58	1550,2981,1968	GG,GA,AA		37.791,35.6786,46.7841	benign,benign,benign,benign,,benign	143/501,27/385,143/341,18/376,,143/348	180338368	6081,6917	2203	4296	6499	SO:0001583	missense	79908	exon3			TCCATCACGGGAT	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.427A>G	5.37:g.180338368A>G	ENSP00000342197:p.Thr143Ala	Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	207	206	0.995169	NM_001159708	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	ENST00000340184.4	37	CCDS43413.1	983	0.4500915750915751	338	0.6869918699186992	143	0.39502762430939226	204	0.35664335664335667	298	0.39313984168865435	a	7.914	0.737065	0.15574	0.643214	0.37791	ENSG00000113303	ENST00000231229;ENST00000340184;ENST00000400707;ENST00000508408;ENST00000511704	T;T;T;T;T	0.06371	3.31;3.31;3.31;3.31;3.31	3.86	-5.37	0.02681	.	.	.	.	.	T	0.00012	0.0000	N	0.25485	0.75	0.54753	P	1.4999999999987246E-5	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.26326	-1.0106	8	0.25751	T	0.34	.	6.8869	0.24208	0.5006:0.1261:0.3733:0.0	rs2276995;rs17704309;rs62406680;rs2276995	18;27;143;143;143	E9PG07;E9PEF6;F2Z2B2;A6NEX6;Q6UX41	.;.;.;.;BTNL8_HUMAN	A	143;143;18;143;27	ENSP00000231229:T143A;ENSP00000342197:T143A;ENSP00000383543:T18A;ENSP00000424585:T143A;ENSP00000425207:T27A	ENSP00000231229:T143A	T	+	1	0	BTNL8	180270974	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.743000	0.01834	-1.000000	0.03438	-2.568000	0.00172	ACG	A|0.529;G|0.471	0.471	strong		0.527	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74203789	74203789	+	Missense_Mutation	SNP	G	G	A	rs17782124	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:74203789G>A	ENST00000286523.5	-	3	2443	c.1661C>T	c.(1660-1662)cCt>cTt	p.P554L	ELMSAN1_ENST00000394071.2_Missense_Mutation_p.P554L|ELMSAN1_ENST00000486739.1_5'Flank	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	554			P -> L (in dbSNP:rs17782124). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										GTTCTGTTCAGGACCCTTCCC	0.607													G|||	766	0.152955	0.0507	0.1182	5008	,	,		17647	0.1409		0.1839	False		,,,				2504	0.2965				p.P554L		Atlas-SNP	.											.	.	.	.	0			c.C1661T						PASS	.	G	LEU/PRO,LEU/PRO	284,4122	157.0+/-190.0	12,260,1931	98.0	82.0	88.0		1661,1661	-0.3	0.0	14	dbSNP_123	88	1667,6933	307.6+/-308.5	164,1339,2797	yes	missense,missense	C14orf43	NM_001043318.1,NM_194278.3	98,98	176,1599,4728	AA,AG,GG		19.3837,6.4458,15.0008	benign,benign	554/1046,554/1046	74203789	1951,11055	2203	4300	6503	SO:0001583	missense	91748	exon3			TGTTCAGGACCCT	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.1661C>T	14.37:g.74203789G>A	ENSP00000286523:p.Pro554Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Missense_Mutation	SNP	ENST00000286523.5	37	CCDS9819.1	301	0.13782051282051283	32	0.06504065040650407	48	0.13259668508287292	82	0.14335664335664336	139	0.18337730870712401	G	9.069	0.996364	0.19043	0.064458	0.193837	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371	T;T;T;T	0.15372	2.43;2.43;2.43;2.44	5.24	-0.259	0.12971	.	1.035740	0.07600	N	0.923432	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43212	-0.9405	9	0.35671	T	0.21	0.7439	3.6785	0.08301	0.3888:0.0:0.2685:0.3428	rs17782124;rs52804069;rs17782124	554;554	A0PJD3;Q6PJG2	.;CN043_HUMAN	L	554	ENSP00000377634:P554L;ENSP00000286523:P554L;ENSP00000407767:P554L;ENSP00000402380:P554L	ENSP00000286523:P554L	P	-	2	0	C14orf43	73273542	0.997000	0.39634	0.000000	0.03702	0.822000	0.46500	0.506000	0.22658	-0.216000	0.10048	-0.182000	0.12963	CCT	G|0.856;A|0.144	0.144	strong		0.607	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278	
KRT40	125115	hgsc.bcm.edu	37	17	39135084	39135084	+	Missense_Mutation	SNP	A	A	G	rs8064733	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39135084A>G	ENST00000398486.2	-	8	1328	c.1168T>C	c.(1168-1170)Tgg>Cgg	p.W390R	AC004231.2_ENST00000418393.1_RNA|KRT40_ENST00000377755.4_Missense_Mutation_p.W390R	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	390	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				AGCAGGCCCCAGTACGTGTTG	0.582													G|||	1841	0.367612	0.7231	0.2435	5008	,	,		16119	0.1736		0.2704	False		,,,				2504	0.2751				p.W390R		Atlas-SNP	.											.	KRT40	27	.	0			c.T1168C						PASS	.	G	ARG/TRP	2834,1572	469.6+/-355.5	924,986,293	66.0	74.0	71.0		1168	3.5	0.1	17	dbSNP_116	71	2366,6224	683.3+/-403.9	318,1730,2247	yes	missense	KRT40	NM_182497.3	101	1242,2716,2540	GG,GA,AA		27.5437,35.6786,40.0123	benign	390/432	39135084	5200,7796	2203	4295	6498	SO:0001583	missense	125115	exon8			GGCCCCAGTACGT	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.1168T>C	17.37:g.39135084A>G	ENSP00000381500:p.Trp390Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	752	0.3443223443223443	351	0.7134146341463414	94	0.2596685082872928	99	0.17307692307692307	208	0.27440633245382584	G	0.003	-2.418205	0.00188	0.643214	0.275437	ENSG00000204889	ENST00000377755;ENST00000398486	T;T	0.79352	-1.26;-1.26	5.56	3.53	0.40419	Filament (1);	1.239200	0.06295	N	0.699907	T	0.00012	0.0000	N	0.00000	-4.295	0.58432	P	8.000000000008E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.52997	-0.8500	9	0.02654	T	1	.	6.0995	0.20039	0.134:0.0:0.5974:0.2685	rs8064733	390	Q6A162	K1C40_HUMAN	R	390	ENSP00000366984:W390R;ENSP00000381500:W390R	ENSP00000366984:W390R	W	-	1	0	KRT40	36388610	0.933000	0.31639	0.077000	0.20336	0.009000	0.06853	1.367000	0.34204	0.378000	0.24764	-0.716000	0.03619	TGG	A|0.654;G|0.346	0.346	strong		0.582	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
MANBA	4126	hgsc.bcm.edu	37	4	103553372	103553372	+	Missense_Mutation	SNP	C	C	T	rs75826658	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:103553372C>T	ENST00000226578.4	-	17	2581	c.2482G>A	c.(2482-2484)Gtt>Att	p.V828I	MANBA_ENST00000505239.1_Missense_Mutation_p.V771I	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	828					cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)			cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		TCCAACCAAACAAAGGGAGCG	0.423													C|||	32	0.00638978	0.0008	0.0101	5008	,	,		20461	0.0		0.0239	False		,,,				2504	0.0				p.V828I		Atlas-SNP	.											.	MANBA	78	.	0			c.G2482A						PASS	.	C	ILE/VAL	17,4389	24.3+/-50.5	0,17,2186	102.0	106.0	105.0		2482	5.2	1.0	4	dbSNP_131	105	151,8449	74.5+/-137.1	1,149,4150	yes	missense	MANBA	NM_005908.3	29	1,166,6336	TT,TC,CC		1.7558,0.3858,1.2917	probably-damaging	828/880	103553372	168,12838	2203	4300	6503	SO:0001583	missense	4126	exon17			ACCAAACAAAGGG		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.2482G>A	4.37:g.103553372C>T	ENSP00000226578:p.Val828Ile	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	238	101	0.42437	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	26	0.011904761904761904	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	20	0.026385224274406333	C	25.5	4.645483	0.87859	0.003858	0.017558	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.77098	-1.06;-1.07	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.77644	0.4161	M	0.86740	2.835	0.58432	D	0.999992	D;D	0.76494	0.997;0.999	P;D	0.70016	0.907;0.967	D	0.85752	0.1344	10	0.72032	D	0.01	-22.6841	16.8489	0.85988	0.0:1.0:0.0:0.0	.	771;828	E9PFW2;O00462	.;MANBA_HUMAN	I	828;771	ENSP00000226578:V828I;ENSP00000427322:V771I	ENSP00000226578:V828I	V	-	1	0	MANBA	103772420	1.000000	0.71417	0.997000	0.53966	0.852000	0.48524	5.317000	0.65822	2.404000	0.81709	0.460000	0.39030	GTT	C|0.986;T|0.014	0.014	strong		0.423	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
CPZ	8532	hgsc.bcm.edu	37	4	8605818	8605818	+	Silent	SNP	C	C	T	rs6852001	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:8605818C>T	ENST00000360986.4	+	4	786	c.612C>T	c.(610-612)tgC>tgT	p.C204C	CPZ_ENST00000315782.6_Silent_p.C193C|CPZ_ENST00000429646.2_5'UTR|CPZ_ENST00000382480.2_Silent_p.C67C	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	204					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CCTCCCGCTGCGCCCACGTGG	0.692													C|||	807	0.161142	0.0204	0.1988	5008	,	,		16720	0.2976		0.2465	False		,,,				2504	0.0961				p.C204C		Atlas-SNP	.											CPZ,NS,carcinoma,0,1	CPZ	95	1	0			c.C612T						PASS	.	C	,,	237,4125		10,217,1954	19.0	16.0	17.0		612,201,579	1.0	1.0	4	dbSNP_116	17	2178,6368		284,1610,2379	no	coding-synonymous,coding-synonymous,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	294,1827,4333	TT,TC,CC		25.4856,5.4333,18.7093	,,	204/653,67/516,193/642	8605818	2415,10493	2181	4273	6454	SO:0001819	synonymous_variant	8532	exon4			CCGCTGCGCCCAC	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"""metallocarboxypeptidase Z"""	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.612C>T	4.37:g.8605818C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	75	54	0.72	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			C|0.812;T|0.188	0.188	strong		0.692	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
BBS12	166379	hgsc.bcm.edu	37	4	123664204	123664204	+	Missense_Mutation	SNP	G	G	A	rs309370	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:123664204G>A	ENST00000314218.3	+	2	1350	c.1157G>A	c.(1156-1158)cGg>cAg	p.R386Q	BBS12_ENST00000542236.1_Missense_Mutation_p.R386Q	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	386			R -> Q (in dbSNP:rs309370). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.4}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						GATAGCATGCGGCTTCAAGAA	0.438									Bardet-Biedl syndrome				A|||	2536	0.50639	0.584	0.4726	5008	,	,		21101	0.6597		0.3191	False		,,,				2504	0.4601				p.R386Q		Atlas-SNP	.											.	BBS12	63	.	0			c.G1157A						PASS	.	A	GLN/ARG,GLN/ARG	2479,1927	548.5+/-377.6	698,1083,422	58.0	61.0	60.0		1157,1157	0.3	0.0	4	dbSNP_79	60	2903,5697	670.7+/-402.8	493,1917,1890	yes	missense,missense	BBS12	NM_001178007.1,NM_152618.2	43,43	1191,3000,2312	AA,AG,GG		33.7558,43.7358,41.3809	benign,benign	386/711,386/711	123664204	5382,7624	2203	4300	6503	SO:0001583	missense	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GCATGCGGCTTCA	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1157G>A	4.37:g.123664204G>A	ENSP00000319062:p.Arg386Gln	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	162	85	0.524691	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	37	CCDS3728.1	1045	0.4784798534798535	272	0.5528455284552846	168	0.46408839779005523	362	0.6328671328671329	243	0.32058047493403696	A	3.101	-0.184690	0.06340	0.562642	0.337558	ENSG00000181004	ENST00000314218;ENST00000542236	T;T	0.78924	-1.22;-1.22	5.68	0.337	0.15966	.	1.224000	0.05487	N	0.555912	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.41179	-0.9523	9	0.13470	T	0.59	-14.8675	2.2036	0.03930	0.3363:0.2377:0.3201:0.106	rs309370;rs17857449;rs52791731;rs56506272;rs59462913;rs309370	386	Q6ZW61	BBS12_HUMAN	Q	386	ENSP00000319062:R386Q;ENSP00000438273:R386Q	ENSP00000319062:R386Q	R	+	2	0	BBS12	123883654	0.000000	0.05858	0.000000	0.03702	0.390000	0.30446	-0.101000	0.10973	0.085000	0.17107	-0.269000	0.10298	CGG	G|0.542;A|0.458	0.458	strong		0.438	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
FOXP4	116113	hgsc.bcm.edu	37	6	41533579	41533579	+	Silent	SNP	C	C	A	rs2104506	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41533579C>A	ENST00000307972.4	+	1	93	c.81C>A	c.(79-81)gcC>gcA	p.A27A	FOXP4_ENST00000373057.3_Silent_p.A27A|FOXP4_ENST00000373063.3_Silent_p.A27A|FOXP4_ENST00000373060.1_Silent_p.A27A|FOXP4_ENST00000409208.1_Silent_p.A27A			Q8IVH2	FOXP4_HUMAN	forkhead box P4	27					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					CTGGGCAAGCCGATGGCAGCA	0.627													C|||	1939	0.387181	0.5106	0.4049	5008	,	,		20199	0.3393		0.3022	False		,,,				2504	0.3446				p.A27A		Atlas-SNP	.											FOXP4_ENST00000373060,NS,carcinoma,0,2	FOXP4	83	2	0			c.C81A						PASS	.	C	,,	2010,2390		461,1088,651	85.0	87.0	86.0		81,81,81	-7.3	0.1	6	dbSNP_96	86	2306,6278		327,1652,2313	no	coding-synonymous,coding-synonymous,coding-synonymous	FOXP4	NM_001012426.1,NM_001012427.1,NM_138457.2	,,	788,2740,2964	AA,AC,CC		26.8639,45.6818,33.2409	,,	27/681,27/679,27/668	41533579	4316,8668	2200	4292	6492	SO:0001819	synonymous_variant	116113	exon2			GCAAGCCGATGGC	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.81C>A	6.37:g.41533579C>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	240	128	0.533333	NM_001012427	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Silent	SNP	ENST00000307972.4	37	CCDS34447.1																																																																																			C|0.647;A|0.353	0.353	strong		0.627	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457	
FNDC1	84624	hgsc.bcm.edu	37	6	159654829	159654829	+	Silent	SNP	G	G	A	rs638551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:159654829G>A	ENST00000297267.9	+	11	3485	c.3285G>A	c.(3283-3285)gcG>gcA	p.A1095A	FNDC1_ENST00000340366.6_Silent_p.A1032A	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1095					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		gggcccccgcgcacgccgcgc	0.706													G|||	1071	0.213858	0.1422	0.1729	5008	,	,		14056	0.3492		0.1352	False		,,,				2504	0.2812				p.A1095A		Atlas-SNP	.											.	FNDC1	250	.	0			c.G3285A						PASS	.	G		347,3035		17,313,1361	8.0	12.0	11.0		3285	-7.2	0.0	6	dbSNP_83	11	631,5853		24,583,2635	no	coding-synonymous	FNDC1	NM_032532.2		41,896,3996	AA,AG,GG		9.7316,10.2602,9.9128		1095/1895	159654829	978,8888	1691	3242	4933	SO:0001819	synonymous_variant	84624	exon11			CCCCGCGCACGCC	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3285G>A	6.37:g.159654829G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	25	17	0.68	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	459	0.21016483516483517	89	0.18089430894308944	58	0.16022099447513813	211	0.3688811188811189	101	0.13324538258575197	G	7.390	0.630505	0.14322	0.102602	0.097316	ENSG00000164694	ENST00000329629	T	0.03035	4.07	4.15	-7.18	0.01505	.	1.506840	0.04171	N	0.324754	T	0.00440	0.0014	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.48175	-0.9058	6	0.17832	T	0.49	0.0702	1.1768	0.01837	0.3648:0.2452:0.2595:0.1305	rs638551	.	.	.	T	991	ENSP00000333297:A991T	ENSP00000333297:A991T	A	+	1	0	FNDC1	159574819	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	-2.264000	0.01173	-1.016000	0.03371	0.313000	0.20887	GCA	G|0.789;A|0.211	0.211	strong		0.706	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
CD33	945	hgsc.bcm.edu	37	19	51738917	51738917	+	Missense_Mutation	SNP	G	G	A	rs35112940	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51738917G>A	ENST00000262262.4	+	6	931	c.910G>A	c.(910-912)Ggg>Agg	p.G304R	CD33_ENST00000391796.3_Missense_Mutation_p.G304R|CD33_ENST00000421133.2_Missense_Mutation_p.G177R|CD33_ENST00000436584.2_Missense_Mutation_p.G177R	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	304			G -> R (in dbSNP:rs35112940). {ECO:0000269|PubMed:14702039}.		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	CCCTACCACAGGGTCAGCCTC	0.597													g|||	357	0.0712859	0.025	0.1095	5008	,	,		16413	0.0		0.2117	False		,,,				2504	0.0358				p.G304R		Atlas-SNP	.											.	CD33	55	.	0			c.G910A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY	239,4167	138.0+/-173.8	4,231,1968	78.0	68.0	71.0		529,910,910	0.3	0.0	19	dbSNP_126	71	1704,6896	302.6+/-306.0	173,1358,2769	yes	missense,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	125,125,125	177,1589,4737	AA,AG,GG		19.814,5.4244,14.9393	probably-damaging,probably-damaging,probably-damaging	177/238,304/311,304/365	51738917	1943,11063	2203	4300	6503	SO:0001583	missense	945	exon6			ACCACAGGGTCAG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.910G>A	19.37:g.51738917G>A	ENSP00000262262:p.Gly304Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	227	0.10393772893772894	14	0.028455284552845527	46	0.1270718232044199	0	0.0	167	0.22031662269129287	G	8.653	0.898675	0.17686	0.054244	0.19814	ENSG00000105383	ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796	T;T;T;T	0.40756	1.02;2.28;1.23;2.07	3.7	0.282	0.15692	.	.	.	.	.	T	0.00012	0.0000	L	0.53729	1.69	0.80722	P	0.0	B;B;B	0.26120	0.015;0.129;0.142	B;B;B	0.23419	0.009;0.046;0.02	T	0.22382	-1.0218	8	0.11794	T	0.64	.	3.4582	0.07523	0.2525:0.2174:0.5301:0.0	rs35112940	177;304;304	C9JEN7;F8WAL2;P20138	.;.;CD33_HUMAN	R	177;304;177;304	ENSP00000403331:G177R;ENSP00000262262:G304R;ENSP00000410126:G177R;ENSP00000375673:G304R	ENSP00000262262:G304R	G	+	1	0	CD33	56430729	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.610000	0.02064	0.154000	0.19237	0.563000	0.77884	GGG	G|0.866;A|0.134	0.134	strong		0.597	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
SLCO1B7	338821	hgsc.bcm.edu	37	12	21200089	21200089	+	Missense_Mutation	SNP	A	A	G	rs11045681	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:21200089A>G	ENST00000421593.2	+	7	932	c.932A>G	c.(931-933)tAt>tGt	p.Y311C	LST3_ENST00000540229.1_Intron|SLCO1B3_ENST00000553473.1_Intron|LST3_ENST00000381541.3_Missense_Mutation_p.Y358C|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.Y358C	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TCTCTTACTTATATCATTAAA	0.333													A|||	379	0.0756789	0.0083	0.1354	5008	,	,		15229	0.003		0.1869	False		,,,				2504	0.0849				p.Y311C		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.A932G						PASS	.	A	CYS/TYR	170,4136		5,160,1988	112.0	113.0	112.0		932	3.4	0.7	12	dbSNP_120	112	1683,6879		164,1355,2762	yes	missense	SLCO1B7	NM_001009562.4	194	169,1515,4750	GG,GA,AA		19.6566,3.948,14.4001		311/641	21200089	1853,11015	2153	4281	6434	SO:0001583	missense	338821	exon7			TTACTTATATCAT	AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.932A>G	12.37:g.21200089A>G	ENSP00000394168:p.Tyr311Cys	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	201	102	0.507463	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	188	0.08608058608058608	6	0.012195121951219513	47	0.1298342541436464	1	0.0017482517482517483	134	0.17678100263852242	.	14.21	2.467159	0.43839	0.03948	0.196566	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.48522	0.81;0.81;0.81	3.36	3.36	0.38483	.	0.262265	0.38720	N	0.001594	T	0.00178	0.0005	M	0.88570	2.965	0.24286	P	0.9951805	D;D	0.76494	0.996;0.999	D;D	0.70016	0.967;0.967	T	0.19712	-1.0297	9	0.87932	D	0	.	9.6342	0.39798	1.0:0.0:0.0:0.0	rs11045681;rs11045681	311;358	G3V0H7;F5H094	.;.	C	358;358;311	ENSP00000370952:Y358C;ENSP00000452013:Y358C;ENSP00000394168:Y311C	ENSP00000370952:Y358C	Y	+	2	0	SLCO1B7;RP11-545J16.1	21091356	0.777000	0.28628	0.652000	0.29579	0.010000	0.07245	1.339000	0.33885	1.510000	0.48803	0.377000	0.23210	TAT	A|0.896;G|0.104	0.104	strong		0.333	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
PRDM2	7799	hgsc.bcm.edu	37	1	14107135	14107135	+	Missense_Mutation	SNP	C	C	G	rs116238585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14107135C>G	ENST00000235372.7	+	8	3701	c.2845C>G	c.(2845-2847)Cct>Gct	p.P949A	PRDM2_ENST00000343137.4_Missense_Mutation_p.P748A|PRDM2_ENST00000311066.5_Missense_Mutation_p.P949A|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.P748A	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	949	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TCCTTCATCACCTGCCCTGCA	0.567													C|||	160	0.0319489	0.0015	0.0	5008	,	,		16785	0.0218		0.0169	False		,,,				2504	0.1217				p.P949A		Atlas-SNP	.											.	PRDM2	147	.	0			c.C2845G						PASS	.	C	ALA/PRO,,ALA/PRO,ALA/PRO	12,4394	19.1+/-41.9	0,12,2191	176.0	158.0	164.0		2242,,2845,2845	5.0	0.1	1	dbSNP_132	164	175,8425	79.5+/-142.1	2,171,4127	yes	missense,intron,missense,missense	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	27,,27,27	2,183,6318	GG,GC,CC		2.0349,0.2724,1.4378	probably-damaging,,probably-damaging,probably-damaging	748/1482,,949/1719,949/1683	14107135	187,12819	2203	4300	6503	SO:0001583	missense	7799	exon8			TCATCACCTGCCC	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.2845C>G	1.37:g.14107135C>G	ENSP00000235372:p.Pro949Ala	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	23	0.010531135531135532	1	0.0020325203252032522	1	0.0027624309392265192	9	0.015734265734265736	12	0.0158311345646438	C	14.61	2.586372	0.46110	0.002724	0.020349	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.01584	4.89;4.75;4.77;4.77	5.97	5.04	0.67666	.	0.249699	0.41294	D	0.000905	T	0.01287	0.0042	L	0.56769	1.78	0.37134	D	0.9014	P;P;P	0.42692	0.546;0.682;0.787	B;B;B	0.37601	0.09;0.197;0.254	T	0.62091	-0.6927	10	0.21014	T	0.42	.	15.052	0.71881	0.1431:0.8569:0.0:0.0	.	807;949;949	Q5THJ0;Q13029;Q13029-2	.;PRDM2_HUMAN;.	A	949;949;949;748;748	ENSP00000235372:P949A;ENSP00000312352:P949A;ENSP00000411103:P748A;ENSP00000341621:P748A	ENSP00000235372:P949A	P	+	1	0	PRDM2	13979722	0.016000	0.18221	0.143000	0.22291	0.216000	0.24613	0.490000	0.22403	1.472000	0.48140	0.655000	0.94253	CCT	C|0.984;G|0.016	0.016	strong		0.567	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
CUBN	8029	hgsc.bcm.edu	37	10	16932490	16932490	+	Missense_Mutation	SNP	G	G	T	rs1801238	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:16932490G>T	ENST00000377833.4	-	55	8700	c.8635C>A	c.(8635-8637)Cta>Ata	p.L2879I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2879	CUB 21. {ECO:0000255|PROSITE- ProRule:PRU00059}.		L -> I (in dbSNP:rs45474496). {ECO:0000269|PubMed:10080186}.		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)	CCAGTGGCTAGCAGGGCTTTG	0.522													G|||	70	0.0139776	0.0023	0.0144	5008	,	,		14824	0.0		0.0398	False		,,,				2504	0.0174				p.L2879I		Atlas-SNP	.											.	CUBN	515	.	0			c.C8635A						PASS	.	G	ILE/LEU	23,4383	29.9+/-59.1	0,23,2180	112.0	102.0	106.0		8635	-0.4	0.9	10	dbSNP_127	106	322,8278	113.9+/-173.9	7,308,3985	yes	missense	CUBN	NM_001081.3	5	7,331,6165	TT,TG,GG		3.7442,0.522,2.6526	probably-damaging	2879/3624	16932490	345,12661	2203	4300	6503	SO:0001583	missense	8029	exon55			TGGCTAGCAGGGC	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.8635C>A	10.37:g.16932490G>T	ENSP00000367064:p.Leu2879Ile	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	30	0.013736263736263736	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	24	0.0316622691292876	G	14.23	2.473839	0.43942	0.00522	0.037442	ENSG00000107611	ENST00000377833	T	0.19250	2.16	5.78	-0.444	0.12245	CUB (5);	0.000000	0.36703	N	0.002460	T	0.09555	0.0235	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00891	-1.1525	10	0.72032	D	0.01	.	6.8581	0.24052	0.4405:0.0:0.4375:0.1221	rs45474496;rs52835348	2879	O60494	CUBN_HUMAN	I	2879	ENSP00000367064:L2879I	ENSP00000367064:L2879I	L	-	1	2	CUBN	16972496	0.986000	0.35501	0.875000	0.34327	0.192000	0.23643	0.421000	0.21280	-0.028000	0.13850	0.655000	0.94253	CTA	G|0.977;T|0.023	0.023	strong		0.522	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
C12orf45	121053	hgsc.bcm.edu	37	12	105380152	105380152	+	Missense_Mutation	SNP	A	A	C	rs1129593|rs11554637	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:105380152A>C	ENST00000552951.1	+	1	65	c.22A>C	c.(22-24)Aag>Cag	p.K8Q	C12orf45_ENST00000280749.5_Missense_Mutation_p.K8Q	NM_152318.2	NP_689531.2	Q8N5I9	CL045_HUMAN	chromosome 12 open reading frame 45	8			K -> Q (in dbSNP:rs1129593).							large_intestine(1)|lung(2)	3						TGGCAAGCCCAAGGCTAGCCC	0.662													C|||	2021	0.403554	0.6641	0.2767	5008	,	,		14115	0.502		0.2485	False		,,,				2504	0.1994				p.K8Q		Atlas-SNP	.											.	C12orf45	14	.	0			c.A22C						PASS	.	C	GLN/LYS	2236,1686		644,948,369	21.0	27.0	25.0		22	-0.5	0.0	12	dbSNP_86	25	1851,6455		204,1443,2506	yes	missense	C12orf45	NM_152318.2	53	848,2391,2875	CC,CA,AA		22.2851,42.9883,33.4233	benign	8/186	105380152	4087,8141	1961	4153	6114	SO:0001583	missense	121053	exon1			AAGCCCAAGGCTA	BC032326	CCDS41825.1	12q23.3	2012-05-30			ENSG00000151131	ENSG00000151131			28628	protein-coding gene	gene with protein product						12477932	Standard	NM_152318		Approved	MGC40397	uc001tlb.3	Q8N5I9	OTTHUMG00000169822	ENST00000552951.1:c.22A>C	12.37:g.105380152A>C	ENSP00000447057:p.Lys8Gln	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_152318		Missense_Mutation	SNP	ENST00000552951.1	37	CCDS41825.1	917	0.4198717948717949	320	0.6504065040650406	107	0.2955801104972376	307	0.5367132867132867	183	0.24142480211081793	C	1.394	-0.580017	0.03854	0.570117	0.222851	ENSG00000151131	ENST00000552951;ENST00000280749	T;T	0.30182	1.54;1.57	3.7	-0.504	0.11997	.	2.072210	0.02429	N	0.083336	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40608	-0.9554	9	0.09084	T	0.74	-7.9944	4.5687	0.12200	0.136:0.2394:0.524:0.1006	rs1129593;rs17845994;rs17858978;rs59115175;rs1129593	8	Q8N5I9	CL045_HUMAN	Q	8	ENSP00000447057:K8Q;ENSP00000280749:K8Q	ENSP00000280749:K8Q	K	+	1	0	C12orf45	103904282	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.538000	0.06120	-0.363000	0.08101	-0.225000	0.12378	AAG	A|0.606;C|0.394	0.394	strong		0.662	C12orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406076.1	NM_152318	
OR5T2	219464	hgsc.bcm.edu	37	11	55999737	55999737	+	Missense_Mutation	SNP	G	G	C	rs7121880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55999737G>C	ENST00000313264.4	-	1	1000	c.925C>G	c.(925-927)Cat>Gat	p.H309D		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	309			H -> D (in dbSNP:rs7121880).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					ATCATGTCATGGTCCGAAGCA	0.403													g|||	293	0.0585064	0.0787	0.0548	5008	,	,		19141	0.001		0.0944	False		,,,				2504	0.0562				p.H309D		Atlas-SNP	.											.	OR5T2	107	.	0			c.C925G						PASS	.	G	ASP/HIS	343,4059	179.4+/-207.9	14,315,1872	191.0	169.0	176.0		925	4.1	0.9	11	dbSNP_116	176	696,7896	171.4+/-222.4	34,628,3634	no	missense	OR5T2	NM_001004746.1	81	48,943,5506	CC,CG,GG		8.1006,7.7919,7.996	possibly-damaging	309/360	55999737	1039,11955	2201	4296	6497	SO:0001583	missense	219464	exon1			TGTCATGGTCCGA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.925C>G	11.37:g.55999737G>C	ENSP00000323688:p.His309Asp	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	169	87	0.514793	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	126	0.057692307692307696	38	0.07723577235772358	19	0.052486187845303865	0	0.0	69	0.09102902374670185	G	12.10	1.835695	0.32421	0.077919	0.081006	ENSG00000181718	ENST00000313264	T	0.00084	8.75	5.07	4.08	0.47627	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43416	U	0.000572	T	0.00012	0.0000	L	0.32530	0.975	0.39486	P	0.03203299999999998	B	0.22800	0.075	B	0.39339	0.297	T	0.31530	-0.9940	9	0.38643	T	0.18	.	7.1718	0.25722	0.0878:0.0:0.7407:0.1714	rs7121880;rs52812723;rs7121880	309	Q8NGG2	OR5T2_HUMAN	D	309	ENSP00000323688:H309D	ENSP00000323688:H309D	H	-	1	0	OR5T2	55756313	0.000000	0.05858	0.950000	0.38849	0.086000	0.17979	-0.334000	0.07883	2.520000	0.84964	0.471000	0.43371	CAT	G|0.930;C|0.070	0.070	strong		0.403	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
NFU1	27247	hgsc.bcm.edu	37	2	69659126	69659126	+	Missense_Mutation	SNP	A	A	T	rs4453725	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:69659126A>T	ENST00000410022.2	-	2	279	c.74T>A	c.(73-75)aTg>aAg	p.M25K	NFU1_ENST00000394305.1_5'UTR|NFU1_ENST00000471185.1_5'UTR|NFU1_ENST00000303698.3_Start_Codon_SNP_p.M1K	NM_001002755.2	NP_001002755.1	Q9UMS0	NFU1_HUMAN	NFU1 iron-sulfur cluster scaffold	25			M -> K (in dbSNP:rs4453725). {ECO:0000269|PubMed:12915448, ECO:0000269|PubMed:14702039}.		iron-sulfur cluster assembly (GO:0016226)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron ion binding (GO:0005506)	p.M25K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	7						ATTCTTCAACATATGACAGAA	0.348													a|||	1588	0.317093	0.2526	0.3818	5008	,	,		16119	0.2103		0.4185	False		,,,				2504	0.364				p.M25K		Atlas-SNP	.											NFU1,NS,carcinoma,0,1	NFU1	19	1	1	Substitution - Missense(1)	prostate(1)	c.T74A						PASS	.	A	LYS/MET,,,LYS/MET	1235,3171	425.5+/-340.8	158,919,1126	113.0	107.0	109.0		74,,,2	3.9	0.1	2	dbSNP_111	109	3671,4929	526.5+/-381.0	815,2041,1444	yes	missense,utr-5,utr-5,missense	NFU1	NM_001002755.1,NM_001002756.1,NM_001002757.1,NM_015700.2	95,,,95	973,2960,2570	TT,TA,AA		42.686,28.03,37.7211	benign,,,benign	25/255,,,1/231	69659126	4906,8100	2203	4300	6503	SO:0001583	missense	27247	exon2			TTCAACATATGAC	AJ132584	CCDS33217.1, CCDS42694.1, CCDS46315.1	2p15-p13	2014-07-03	2014-07-03	2006-10-24	ENSG00000169599	ENSG00000169599			16287	protein-coding gene	gene with protein product		608100	"""HIRA interacting protein 5"", ""NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae)"""	HIRIP5		11342215, 12886008	Standard	NR_045631		Approved	CGI-33, NifU, NIFUC	uc002sfk.3	Q9UMS0	OTTHUMG00000152668	ENST00000410022.2:c.74T>A	2.37:g.69659126A>T	ENSP00000387219:p.Met25Lys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	106	67	0.632075	NM_001002755	B4DUL9|Q53QE5|Q6VNZ8|Q7Z5B1|Q7Z5B2|Q9Y322	Missense_Mutation	SNP	ENST00000410022.2	37	CCDS33217.1	676	0.30952380952380953	113	0.22967479674796748	138	0.3812154696132597	107	0.18706293706293706	318	0.41952506596306066	A	3.853	-0.031371	0.07543	0.2803	0.42686	ENSG00000169599	ENST00000410022;ENST00000303698	T;T	0.63096	-0.02;0.01	5.1	3.94	0.45596	.	1.058880	0.07247	N	0.865204	T	0.00012	0.0000	N	0.14661	0.345	0.53688	P	2.999999999997449E-5	B;B	0.19817	0.039;0.007	B;B	0.17722	0.019;0.008	T	0.33394	-0.9870	9	0.72032	D	0.01	-1.1234	6.8836	0.24187	0.8227:0.0:0.1773:0.0	rs4453725;rs4453725	1;25	Q9UMS0-3;Q9UMS0	.;NFU1_HUMAN	K	25;1	ENSP00000387219:M25K;ENSP00000306965:M1K	ENSP00000306965:M1K	M	-	2	0	NFU1	69512630	0.001000	0.12720	0.121000	0.21740	0.006000	0.05464	0.978000	0.29488	1.066000	0.40716	-0.261000	0.10672	ATG	A|0.636;T|0.364	0.364	strong		0.348	NFU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327279.3	NM_015700	
MTOR	2475	hgsc.bcm.edu	37	1	11182093	11182093	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:11182093C>T	ENST00000361445.4	-	48	6829	c.6753G>A	c.(6751-6753)cgG>cgA	p.R2251R	MTOR_ENST00000376838.1_Silent_p.R456R	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2251	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CCCTGTAGTCCCGGATGAGGG	0.577																																					p.R2251R		Atlas-SNP	.											MTOR,right_lower_lobe,carcinoma,-1,1	MTOR	327	1	0			c.G6753A						scavenged	.						141.0	124.0	130.0					1																	11182093		2203	4300	6503	SO:0001819	synonymous_variant	2475	exon48			GTAGTCCCGGATG	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6753G>A	1.37:g.11182093C>T		Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	278	3	0.0107914	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			.	.	none		0.577	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
MRPS9	64965	hgsc.bcm.edu	37	2	105665808	105665808	+	Splice_Site	SNP	C	C	T	rs11538197	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:105665808C>T	ENST00000258455.3	+	2	425	c.315C>T	c.(313-315)gaC>gaT	p.D105D		NM_182640.2	NP_872578.1	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9	105					DNA damage response, detection of DNA damage (GO:0042769)|peptide biosynthetic process (GO:0043043)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						AAGATATTGACGTAAGTACAG	0.338													T|||	963	0.192292	0.2239	0.2882	5008	,	,		18484	0.1101		0.2247	False		,,,				2504	0.1329				p.D105D		Atlas-SNP	.											.	MRPS9	32	.	0			c.C315T						PASS	.	T		973,3429	675.7+/-403.1	102,769,1330	59.0	60.0	60.0		315	1.6	1.0	2	dbSNP_123	60	2069,6527	701.9+/-405.2	232,1605,2461	yes	coding-synonymous-near-splice	MRPS9	NM_182640.2		334,2374,3791	TT,TC,CC		24.0693,22.1036,23.4036		105/397	105665808	3042,9956	2201	4298	6499	SO:0001630	splice_region_variant	64965	exon2			TATTGACGTAAGT		CCDS2065.1	2q12.1	2012-09-13			ENSG00000135972	ENSG00000135972		"""Mitochondrial ribosomal proteins / small subunits"""	14501	protein-coding gene	gene with protein product	"""28S ribosomal protein S9, mitochondrial"""	611975				11279123	Standard	NM_182640		Approved	RPMS9, MRP-S9, S9mt	uc002tcn.4	P82933	OTTHUMG00000130807	ENST00000258455.3:c.315+1C>T	2.37:g.105665808C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_182640	Q6PG40	Silent	SNP	ENST00000258455.3	37	CCDS2065.1																																																																																			C|0.797;T|0.203	0.203	strong		0.338	MRPS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253352.1	NM_182640	Silent
IKBKAP	8518	hgsc.bcm.edu	37	9	111659483	111659483	+	Missense_Mutation	SNP	T	T	G	rs2230793	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:111659483T>G	ENST00000374647.5	-	23	2753	c.2446A>C	c.(2446-2448)Ata>Cta	p.I816L	IKBKAP_ENST00000537196.1_Missense_Mutation_p.I467L	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	816			I -> L (in dbSNP:rs2230793).		chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						ACAAGGTCTATTTTATTCCCG	0.463													G|||	1491	0.297724	0.4803	0.2507	5008	,	,		20905	0.2599		0.1998	False		,,,				2504	0.2239				p.I816L		Atlas-SNP	.											IKBKAP,NS,carcinoma,+2,1	IKBKAP	122	1	0			c.A2446C						PASS	.	G	LEU/ILE	1945,2461	622.6+/-394.0	436,1073,694	202.0	170.0	181.0		2446	3.4	0.2	9	dbSNP_98	181	1575,7025	744.7+/-407.2	146,1283,2871	yes	missense	IKBKAP	NM_003640.3	5	582,2356,3565	GG,GT,TT		18.314,44.1443,27.0644	benign	816/1333	111659483	3520,9486	2203	4300	6503	SO:0001583	missense	8518	exon23			GGTCTATTTTATT	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.2446A>C	9.37:g.111659483T>G	ENSP00000363779:p.Ile816Leu	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	196	85	0.433673	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	37	CCDS6773.1	624	0.2857142857142857	225	0.4573170731707317	98	0.27071823204419887	158	0.2762237762237762	143	0.18865435356200527	G	11.24	1.581764	0.28180	0.441443	0.18314	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.27402	1.67;1.67	5.24	3.39	0.38822	.	0.128507	0.52532	N	0.000080	T	0.00012	0.0000	N	0.24115	0.695	0.52501	P	4.700000000001925E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.46512	-0.9186	9	0.41790	T	0.15	-3.3164	10.2342	0.43273	0.0:0.6919:0.2107:0.0974	rs2230793;rs10759326;rs57174619;rs2230793	816	O95163	ELP1_HUMAN	L	816;467	ENSP00000363779:I816L;ENSP00000439367:I467L	ENSP00000363779:I816L	I	-	1	0	IKBKAP	110699304	0.999000	0.42202	0.203000	0.23512	0.394000	0.30568	1.614000	0.36911	0.304000	0.22809	-0.352000	0.07741	ATA	T|0.728;G|0.272	0.272	strong		0.463	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
TREML2	79865	hgsc.bcm.edu	37	6	41166025	41166025	+	Silent	SNP	G	G	A	rs113267424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41166025G>A	ENST00000483722.1	-	2	383	c.198C>T	c.(196-198)ggC>ggT	p.G66G		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	66	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					CTCGGGCAAAGCCAGGCTCAC	0.567																																					p.G66G		Atlas-SNP	.											TREML2,caecum,carcinoma,0,1	TREML2	41	1	0			c.C198T						scavenged	.						139.0	139.0	139.0					6																	41166025		2203	4300	6503	SO:0001819	synonymous_variant	79865	exon2			GGCAAAGCCAGGC	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.198C>T	6.37:g.41166025G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	6	0.06	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Silent	SNP	ENST00000483722.1	37	CCDS4853.2																																																																																			G|0.996;A|0.004	0.004	strong		0.567	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
PEG3	5178	hgsc.bcm.edu	37	19	57335022	57335022	+	Silent	SNP	G	G	A	rs1860565	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57335022G>A	ENST00000326441.9	-	5	783	c.420C>T	c.(418-420)agC>agT	p.S140S	ZIM2_ENST00000593711.1_Silent_p.S14S|PEG3_ENST00000598410.1_Silent_p.S14S|PEG3_ENST00000423103.2_Silent_p.S140S|ZIM2_ENST00000221722.5_Silent_p.S14S|PEG3_ENST00000593695.1_Silent_p.S14S|PEG3_ENST00000594706.1_5'Flank|ZIM2_ENST00000601070.1_Silent_p.S14S|ZIM2_ENST00000593931.1_Silent_p.S14S|ZIM2_ENST00000391708.3_Silent_p.S14S|ZIM2_ENST00000599935.1_Silent_p.S14S	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	140					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TGTCGTCGTCGCTGGTCACGT	0.557													G|||	1020	0.203674	0.0424	0.3285	5008	,	,		18634	0.1677		0.2773	False		,,,				2504	0.2945				p.S140S		Atlas-SNP	.											.	PEG3	414	.	0			c.C420T						PASS	.	G	,,,,,,,	340,4066	177.3+/-206.3	16,308,1879	287.0	210.0	236.0		420,42,420,42,42,42,420,42	-7.9	0.0	19	dbSNP_92	236	2462,6138	405.2+/-348.4	366,1730,2204	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PEG3,ZIM2	NM_001146184.1,NM_001146185.1,NM_001146186.1,NM_001146187.1,NM_001146326.1,NM_001146327.1,NM_006210.2,NM_015363.4	,,,,,,,	382,2038,4083	AA,AG,GG		28.6279,7.7167,21.5439	,,,,,,,	140/1589,14/1463,140/1589,14/1465,14/528,14/528,140/1589,14/528	57335022	2802,10204	2203	4300	6503	SO:0001819	synonymous_variant	5178	exon4			GTCGTCGCTGGTC	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.420C>T	19.37:g.57335022G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	ENST00000326441.9	37	CCDS12948.1																																																																																			G|0.798;A|0.202	0.202	strong		0.557	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
TSEN54	283989	hgsc.bcm.edu	37	17	73519758	73519758	+	Missense_Mutation	SNP	C	C	G	rs150169668	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73519758C>G	ENST00000333213.6	+	10	1364	c.1328C>G	c.(1327-1329)tCt>tGt	p.S443C	LLGL2_ENST00000167462.5_5'Flank|LLGL2_ENST00000392550.3_5'Flank|LLGL2_ENST00000578363.1_5'Flank|LLGL2_ENST00000375227.4_5'Flank	NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	443					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)	13	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TTGGAGAAGTCTGGGGGCTTG	0.488													C|||	39	0.00778754	0.0	0.0043	5008	,	,		21840	0.0		0.0199	False		,,,				2504	0.0164				p.S443C		Atlas-SNP	.											.	TSEN54	27	.	0			c.C1328G						PASS	.	C	CYS/SER	10,4396	16.8+/-37.8	1,8,2194	94.0	92.0	93.0		1328	6.1	0.1	17	dbSNP_134	93	94,8506	53.6+/-114.3	0,94,4206	yes	missense	TSEN54	NM_207346.2	112	1,102,6400	GG,GC,CC		1.093,0.227,0.7996	benign	443/527	73519758	104,12902	2203	4300	6503	SO:0001583	missense	283989	exon10			AGAAGTCTGGGGG	AK097583	CCDS11724.1	17q25.1	2013-08-06	2013-08-06		ENSG00000182173	ENSG00000182173		"""tRNA splicing endonuclease subunits"""	27561	protein-coding gene	gene with protein product		608755	"""tRNA splicing endonuclease 54 homolog (SEN54, S. cerevisiae)"", ""tRNA splicing endonuclease 54 homolog (S. cerevisiae)"""			15109492	Standard	NM_207346		Approved	SEN54, SEN54L	uc002jof.1	Q7Z6J9		ENST00000333213.6:c.1328C>G	17.37:g.73519758C>G	ENSP00000327487:p.Ser443Cys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_207346	Q86WV3|Q86XE4|Q8N9H2	Missense_Mutation	SNP	ENST00000333213.6	37	CCDS11724.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	C	6.870	0.529970	0.13127	0.00227	0.01093	ENSG00000182173	ENST00000333213	T	0.66099	-0.19	6.06	6.06	0.98353	.	0.541549	0.22695	N	0.056765	T	0.50326	0.1609	L	0.61218	1.895	0.09310	N	1	D	0.55605	0.972	P	0.50490	0.642	T	0.60419	-0.7267	10	0.49607	T	0.09	-1.1234	10.5014	0.44808	0.1331:0.7989:0.0:0.068	.	443	Q7Z6J9	SEN54_HUMAN	C	443	ENSP00000327487:S443C	ENSP00000327487:S443C	S	+	2	0	TSEN54	71031353	0.006000	0.16342	0.098000	0.21074	0.321000	0.28281	2.242000	0.43106	2.879000	0.98667	0.650000	0.86243	TCT	C|0.991;G|0.009	0.009	strong		0.488	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447618.1	NM_207346	
CASS4	57091	hgsc.bcm.edu	37	20	55028167	55028167	+	Silent	SNP	G	G	A	rs2870738	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:55028167G>A	ENST00000360314.3	+	6	2160	c.1935G>A	c.(1933-1935)agG>agA	p.R645R	CASS4_ENST00000371336.3_Silent_p.R645R|CASS4_ENST00000434344.1_Intron	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	645					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						AGAAAAATAGGGCAAATATCT	0.428													A|||	1890	0.377396	0.0938	0.4813	5008	,	,		17745	0.6885		0.338	False		,,,				2504	0.407				p.R645R		Atlas-SNP	.											.	CASS4	121	.	0			c.G1935A						PASS	.	A	,,,	594,3810		57,480,1665	29.0	28.0	29.0		1773,,1935,1935	3.2	0.0	20	dbSNP_101	29	2862,5738		458,1946,1896	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	,,,	515,2426,3561	AA,AG,GG		33.2791,13.4877,26.5764	,,,	591/733,,645/787,645/787	55028167	3456,9548	2202	4300	6502	SO:0001819	synonymous_variant	57091	exon5			AAATAGGGCAAAT	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.1935G>A	20.37:g.55028167G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Silent	SNP	ENST00000360314.3	37	CCDS33492.1																																																																																			G|0.681;A|0.319	0.319	strong		0.428	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
PCDHB7	56129	hgsc.bcm.edu	37	5	140554562	140554562	+	Missense_Mutation	SNP	A	A	T	rs2910314	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140554562A>T	ENST00000231137.3	+	1	2320	c.2146A>T	c.(2146-2148)Agg>Tgg	p.R716W	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	716			R -> W (in dbSNP:rs2910314).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGGAGGAGCAGGGCGGCCCC	0.667													A|||	486	0.0970447	0.0166	0.0879	5008	,	,		21367	0.0913		0.1461	False		,,,				2504	0.1677				p.R716W		Atlas-SNP	.											.	PCDHB7	231	.	0			c.A2146T						PASS	.	A	TRP/ARG	207,4199		5,197,2001	71.0	121.0	104.0		2146	-7.1	0.0	5	dbSNP_101	104	1311,7281		126,1059,3111	no	missense	PCDHB7	NM_018940.2	101	131,1256,5112	TT,TA,AA		15.2584,4.6981,11.6787	probably-damaging	716/794	140554562	1518,11480	2203	4296	6499	SO:0001583	missense	56129	exon1			AGGAGCAGGGCGG	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.2146A>T	5.37:g.140554562A>T	ENSP00000231137:p.Arg716Trp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	110	35	0.318182	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	219	0.10027472527472528	12	0.024390243902439025	40	0.11049723756906077	51	0.08916083916083917	116	0.15303430079155672	A	18.61	3.661912	0.67700	0.046981	0.152584	ENSG00000113212	ENST00000231137	T	0.14144	2.53	3.55	-7.1	0.01547	.	.	.	.	.	T	0.00241	0.0007	H	0.97131	3.945	0.54753	P	2.0000000000020002E-5	D	0.67145	0.996	D	0.64687	0.928	T	0.04153	-1.0973	8	0.87932	D	0	.	7.6427	0.28303	0.3131:0.4147:0.2722:0.0	rs2910314;rs17844477	716	Q9Y5E2	PCDB7_HUMAN	W	716	ENSP00000231137:R716W	ENSP00000231137:R716W	R	+	1	2	PCDHB7	140534746	0.000000	0.05858	0.000000	0.03702	0.310000	0.27922	0.554000	0.23407	-2.362000	0.00609	-0.685000	0.03747	AGG	A|0.899;T|0.101	0.101	strong		0.667	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
ZNF773	374928	hgsc.bcm.edu	37	19	58017758	58017758	+	Missense_Mutation	SNP	G	G	C	rs55823456	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58017758G>C	ENST00000282292.4	+	4	435	c.295G>C	c.(295-297)Gct>Cct	p.A99P	ZNF773_ENST00000598770.1_Missense_Mutation_p.A98P|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	99					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)		TGAGGCAGCTGCTGAGCAGAG	0.488													C|||	859	0.171526	0.2716	0.1484	5008	,	,		22607	0.1002		0.2018	False		,,,				2504	0.0951				p.A99P		Atlas-SNP	.											.	ZNF773	62	.	0			c.G295C						PASS	.	C	PRO/ALA	1157,3249	711.0+/-407.9	167,823,1213	85.0	88.0	87.0		295	0.2	0.0	19	dbSNP_129	87	1699,6901	736.3+/-407.0	152,1395,2753	yes	missense	ZNF773	NM_198542.1	27	319,2218,3966	CC,CG,GG		19.7558,26.2596,21.9591	benign	99/443	58017758	2856,10150	2203	4300	6503	SO:0001583	missense	374928	exon4			GCAGCTGCTGAGC	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"""Zinc fingers, C2H2-type"", ""-"""	30487	protein-coding gene	gene with protein product			"""zinc finger protein 419B"""	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.295G>C	19.37:g.58017758G>C	ENSP00000282292:p.Ala99Pro	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_198542	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	37	CCDS33134.1	409	0.18727106227106227	147	0.29878048780487804	56	0.15469613259668508	61	0.10664335664335664	145	0.19129287598944592	C	0.004	-2.325317	0.00229	0.262596	0.197558	ENSG00000152439	ENST00000282292	T	0.06068	3.35	1.25	0.189	0.15119	.	.	.	.	.	T	0.00012	0.0000	N	0.04090	-0.28	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47686	-0.9098	8	0.31617	T	0.26	.	3.0571	0.06188	0.0:0.4158:0.2725:0.3116	rs55823456;rs61731280	98;99	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	P	99	ENSP00000282292:A99P	ENSP00000282292:A99P	A	+	1	0	ZNF773	62709570	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.360000	0.07622	-0.421000	0.07416	-0.647000	0.03941	GCT	G|0.790;C|0.210	0.210	strong		0.488	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542	
ELF5	2001	hgsc.bcm.edu	37	11	34502345	34502345	+	Silent	SNP	T	T	C	rs2231828	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:34502345T>C	ENST00000312319.2	-	6	904	c.675A>G	c.(673-675)acA>acG	p.T225T	ELF5_ENST00000429939.2_Silent_p.T120T|ELF5_ENST00000528709.1_5'Flank|ELF5_ENST00000257832.2_Silent_p.T215T	NM_001243081.1|NM_198381.1	NP_001230010.1|NP_938195.1	Q9UKW6	ELF5_HUMAN	E74-like factor 5 (ets domain transcription factor)	225					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|ectoderm development (GO:0007398)|mammary gland epithelial cell differentiation (GO:0060644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			large_intestine(4)|skin(1)	5		Acute lymphoblastic leukemia(5;0.0087)|all_hematologic(20;0.0384)				ACTTTTCATATGTCATTCTGT	0.398													C|||	961	0.191893	0.0333	0.2334	5008	,	,		15592	0.0288		0.4076	False		,,,				2504	0.3231				p.T225T	Melanoma(61;202 1660 4348 21594)	Atlas-SNP	.											.	ELF5	21	.	0			c.A675G						PASS	.	C	,	381,4023	791.1+/-415.1	26,329,1847	174.0	169.0	170.0		645,675	-11.4	0.0	11	dbSNP_98	170	3489,5107	633.6+/-398.7	718,2053,1527	no	coding-synonymous,coding-synonymous	ELF5	NM_001422.3,NM_198381.1	,	744,2382,3374	CC,CT,TT		40.5886,8.6512,29.7692	,	215/256,225/266	34502345	3870,9130	2202	4298	6500	SO:0001819	synonymous_variant	2001	exon6			TTCATATGTCATT	AF049703	CCDS7892.1, CCDS7893.1, CCDS58129.1, CCDS73273.1	11p13-p12	2008-05-14			ENSG00000135374	ENSG00000135374			3320	protein-coding gene	gene with protein product		605169				9840936	Standard	NM_001422		Approved		uc001mvp.2	Q9UKW6	OTTHUMG00000166451	ENST00000312319.2:c.675A>G	11.37:g.34502345T>C		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	194	194	1	NM_198381	A6XAE6|A8K452|O95175|Q8N2K9|Q96QY3|Q9UKW5	Silent	SNP	ENST00000312319.2	37	CCDS7892.1																																																																																			T|0.745;C|0.255	0.255	strong		0.398	ELF5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389845.1	NM_198381	
GPR133	283383	hgsc.bcm.edu	37	12	131590404	131590404	+	Silent	SNP	G	G	A	rs4759544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:131590404G>A	ENST00000261654.5	+	17	2440	c.1881G>A	c.(1879-1881)ccG>ccA	p.P627P	GPR133_ENST00000535015.1_Silent_p.P659P|GPR133_ENST00000543617.1_Silent_p.P146P|GPR133_ENST00000376682.4_Silent_p.P313P	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	627					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GCCTCGAGCCGGGCACGGTGA	0.617													G|||	1030	0.205671	0.028	0.1859	5008	,	,		20228	0.1935		0.2922	False		,,,				2504	0.3834				p.P627P		Atlas-SNP	.											.	GPR133	136	.	0			c.G1881A						PASS	.	G		328,4078	165.8+/-197.2	15,298,1890	113.0	75.0	88.0		1881	-2.0	1.0	12	dbSNP_111	88	2488,6112	393.7+/-344.5	382,1724,2194	no	coding-synonymous	GPR133	NM_198827.3		397,2022,4084	AA,AG,GG		28.9302,7.4444,21.6515		627/875	131590404	2816,10190	2203	4300	6503	SO:0001819	synonymous_variant	283383	exon17			CGAGCCGGGCACG	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.1881G>A	12.37:g.131590404G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Silent	SNP	ENST00000261654.5	37	CCDS9272.1																																																																																			G|0.798;A|0.202	0.202	strong		0.617	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
NPHP4	261734	hgsc.bcm.edu	37	1	5935096	5935096	+	Missense_Mutation	SNP	C	C	T	rs183885357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:5935096C>T	ENST00000378156.4	-	21	3147	c.2882G>A	c.(2881-2883)cGc>cAc	p.R961H	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	961			R -> H (in NPHP4; dbSNP:rs183885357). {ECO:0000269|PubMed:15776426}.		actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GGCCTTCGTGCGTTCCCGGTA	0.652													c|||	6	0.00119808	0.0	0.0029	5008	,	,		17500	0.0		0.004	False		,,,				2504	0.0				p.R961H		Atlas-SNP	.											.	NPHP4	119	.	0			c.G2882A	GRCh37	CM051580	NPHP4	M	rs183885357	PASS	.		HIS/ARG	6,4380	11.4+/-27.6	0,6,2187	63.0	78.0	73.0		2882	4.9	0.9	1		73	35,8527	23.4+/-69.3	0,35,4246	yes	missense	NPHP4	NM_015102.3	29	0,41,6433	TT,TC,CC		0.4088,0.1368,0.3167	possibly-damaging	961/1427	5935096	41,12907	2193	4281	6474	SO:0001583	missense	261734	exon21			TTCGTGCGTTCCC	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.2882G>A	1.37:g.5935096C>T	ENSP00000367398:p.Arg961His	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	2	0.0034965034965034965	3	0.00395778364116095	c	12.12	1.841986	0.32513	0.001368	0.004088	ENSG00000131697	ENST00000378156	D	0.88431	-2.38	4.88	4.88	0.63580	.	0.074186	0.53938	D	0.000041	D	0.90188	0.6933	M	0.75264	2.295	0.48511	D	0.999666	D	0.56746	0.977	P	0.48840	0.592	D	0.90860	0.4738	10	0.56958	D	0.05	.	12.536	0.56142	0.0:0.9169:0.0:0.0831	.	961	O75161	NPHP4_HUMAN	H	961	ENSP00000367398:R961H	ENSP00000367398:R961H	R	-	2	0	NPHP4	5857683	1.000000	0.71417	0.923000	0.36655	0.015000	0.08874	3.579000	0.53900	2.272000	0.75746	0.550000	0.68814	CGC	C|0.996;T|0.004	0.004	strong		0.652	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
HSPG2	3339	hgsc.bcm.edu	37	1	22169926	22169926	+	Silent	SNP	G	G	A	rs62642513	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22169926G>A	ENST00000374695.3	-	66	8701	c.8622C>T	c.(8620-8622)caC>caT	p.H2874H		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2874	Ig-like C2-type 14.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCAGTGGGCCGTGGACCTGGC	0.652													G|||	251	0.0501198	0.1589	0.0274	5008	,	,		16760	0.0		0.0189	False		,,,				2504	0.0031				p.H2874H		Atlas-SNP	.											.	HSPG2	311	.	0			c.C8622T						PASS	.	G		716,3690	288.1+/-279.7	60,596,1547	33.0	35.0	34.0		8622	-3.0	0.7	1	dbSNP_129	34	170,8430	75.4+/-138.0	2,166,4132	no	coding-synonymous	HSPG2	NM_005529.5		62,762,5679	AA,AG,GG		1.9767,16.2506,6.8122		2874/4392	22169926	886,12120	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon66			TGGGCCGTGGACC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.8622C>T	1.37:g.22169926G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	138	62	0.449275	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			G|0.935;A|0.065	0.065	strong		0.652	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
POTEM	641455	hgsc.bcm.edu	37	14	19990641	19990641	+	Silent	SNP	C	C	T	rs138327719		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:19990641C>T	ENST00000551509.1	-	10	1485	c.1434G>A	c.(1432-1434)aaG>aaA	p.K478K		NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN	POTE ankyrin domain family, member M	478										endometrium(4)|kidney(1)|lung(4)	9						CAGAAAGTTGCTTCTGAGTAT	0.358																																					p.K478K		Atlas-SNP	.											POTEM_ENST00000551509,NS,carcinoma,0,2	POTEM	51	2	0			c.G1434A						scavenged	.																																			SO:0001819	synonymous_variant	641455	exon10			AAGTTGCTTCTGA		CCDS73609.1	14q11.2	2013-01-10			ENSG00000187537	ENSG00000187537		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	37096	protein-coding gene	gene with protein product	"""prostate-specific P704P"""					16364570	Standard	NM_001145442		Approved	POTE14beta, P704P, ACT	uc001vwc.3	A6NI47		ENST00000551509.1:c.1434G>A	14.37:g.19990641C>T		Somatic	809	0	0		WXS	Illumina HiSeq	Phase_I	690	153	0.221739	NM_001145442		Silent	SNP	ENST00000551509.1	37	CCDS45076.1																																																																																			C|1.000;|0.000	.	weak		0.358	POTEM-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409490.3	NM_001145442	
ADAMTS17	170691	hgsc.bcm.edu	37	15	100794363	100794363	+	Silent	SNP	C	C	T	rs4369638	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:100794363C>T	ENST00000268070.4	-	7	1158	c.1053G>A	c.(1051-1053)aaG>aaA	p.K351K	ADAMTS17_ENST00000559976.1_5'UTR	NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	351	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		ACGGTTCATCCTTGTGTACAC	0.408													T|||	4114	0.821486	0.8555	0.7637	5008	,	,		20149	0.8829		0.7276	False		,,,				2504	0.8497				p.K351K		Atlas-SNP	.											.	ADAMTS17	127	.	0			c.G1053A						PASS	.	T		3630,776	313.8+/-293.3	1499,632,72	113.0	106.0	108.0		1053	4.4	1.0	15	dbSNP_111	108	6064,2536	412.7+/-350.9	2132,1800,368	no	coding-synonymous	ADAMTS17	NM_139057.2		3631,2432,440	TT,TC,CC		29.4884,17.6123,25.4652		351/1096	100794363	9694,3312	2203	4300	6503	SO:0001819	synonymous_variant	170691	exon7			TTCATCCTTGTGT	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.1053G>A	15.37:g.100794363C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_139057	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	37	CCDS10383.1																																																																																			C|0.238;T|0.762	0.762	strong		0.408	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
RBM19	9904	hgsc.bcm.edu	37	12	114377835	114377835	+	Missense_Mutation	SNP	A	A	G	rs2290788	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:114377835A>G	ENST00000545145.2	-	15	1946	c.1868T>C	c.(1867-1869)aTc>aCc	p.I623T	RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.I623T|RBM19_ENST00000392561.3_Missense_Mutation_p.I623T	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	623	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.		I -> T (in dbSNP:rs2290788). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GATGGCAGTGATTCCGCCCTC	0.642													A|||	965	0.192692	0.3245	0.0735	5008	,	,		16454	0.1885		0.1133	False		,,,				2504	0.1851				p.I623T		Atlas-SNP	.											.	RBM19	117	.	0			c.T1868C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE	1342,3064	436.1+/-344.5	224,894,1085	54.0	60.0	58.0		1868,1868,1868	3.1	0.7	12	dbSNP_100	58	888,7712	196.3+/-241.3	39,810,3451	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	89,89,89	263,1704,4536	GG,GA,AA		10.3256,30.4585,17.1459	benign,benign,benign	623/961,623/961,623/961	114377835	2230,10776	2203	4300	6503	SO:0001583	missense	9904	exon15			GCAGTGATTCCGC	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1868T>C	12.37:g.114377835A>G	ENSP00000442053:p.Ile623Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	351	0.16071428571428573	137	0.2784552845528455	26	0.0718232044198895	102	0.17832167832167833	86	0.11345646437994723	A	12.45	1.941992	0.34283	0.304585	0.103256	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.06608	3.28;3.28;3.28	4.3	3.08	0.35506	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.262265	0.37219	N	0.002186	T	0.00012	0.0000	N	0.10645	0.015	0.21915	P	0.999477564	B	0.20261	0.043	B	0.36808	0.233	T	0.44390	-0.9331	9	0.02654	T	1	-12.7717	10.0478	0.42197	0.8499:0.0:0.0:0.1501	rs2290788;rs17849835;rs17857860;rs2290788	623	Q9Y4C8	RBM19_HUMAN	T	623	ENSP00000442053:I623T;ENSP00000376344:I623T;ENSP00000261741:I623T	ENSP00000261741:I623T	I	-	2	0	RBM19	112862218	1.000000	0.71417	0.693000	0.30195	0.561000	0.35649	8.500000	0.90498	1.600000	0.50102	0.459000	0.35465	ATC	A|0.832;G|0.168	0.168	strong		0.642	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
KLHL36	79786	hgsc.bcm.edu	37	16	84695490	84695490	+	Silent	SNP	C	C	T	rs12928590	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84695490C>T	ENST00000564996.1	+	5	1743	c.1602C>T	c.(1600-1602)caC>caT	p.H534H	KLHL36_ENST00000258157.5_Silent_p.H471H	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	534					protein ubiquitination (GO:0016567)					endometrium(3)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CGCTGCTGCACGCCAACAGCG	0.657													C|||	718	0.143371	0.2526	0.098	5008	,	,		16086	0.0327		0.2068	False		,,,				2504	0.0767				p.H534H		Atlas-SNP	.											.	KLHL36	51	.	0			c.C1602T						PASS	.	C		1100,3296	369.3+/-319.0	142,816,1240	32.0	29.0	30.0		1602	-1.2	1.0	16	dbSNP_121	30	1948,6650	318.0+/-313.5	232,1484,2583	no	coding-synonymous	KLHL36	NM_024731.2		374,2300,3823	TT,TC,CC		22.6564,25.0227,23.457		534/617	84695490	3048,9946	2198	4299	6497	SO:0001819	synonymous_variant	79786	exon5			GCTGCACGCCAAC	AK022605	CCDS10948.1	16q24.1	2013-02-22	2013-02-22	2008-07-07	ENSG00000135686	ENSG00000135686		"""Kelch-like"", ""BTB/POZ domain containing"""	17844	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 44"", ""kelch-like 36 (Drosophila)"""	C16orf44			Standard	NM_024731		Approved	FLJ12543	uc002fig.3	Q8N4N3	OTTHUMG00000137642	ENST00000564996.1:c.1602C>T	16.37:g.84695490C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	52	32	0.615385	NM_024731	Q8N5G6|Q9H9U6	Silent	SNP	ENST00000564996.1	37	CCDS10948.1																																																																																			C|0.807;T|0.193	0.193	strong		0.657	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2		
FRG2B	441581	hgsc.bcm.edu	37	10	135438951	135438951	+	Silent	SNP	G	G	A	rs200483318		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135438951G>A	ENST00000425520.1	-	4	541	c.489C>T	c.(487-489)gcC>gcT	p.A163A	FRG2B_ENST00000443774.1_Silent_p.A164A	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	163						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		GGACTCCTAGGGCCCGAGACC	0.567																																					p.A163A		Atlas-SNP	.											.	FRG2B	47	.	0			c.C489T						PASS	.						119.0	144.0	136.0					10																	135438951		2193	4293	6486	SO:0001819	synonymous_variant	441581	exon4			TCCTAGGGCCCGA	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.489C>T	10.37:g.135438951G>A		Somatic	369	1	0.00271003		WXS	Illumina HiSeq	Phase_I	354	138	0.38983	NM_001080998	Q5VSQ1	Silent	SNP	ENST00000425520.1	37	CCDS44502.1																																																																																			.	.	weak		0.567	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
ZNF682	91120	hgsc.bcm.edu	37	19	20133846	20133846	+	Missense_Mutation	SNP	C	C	T	rs7255165	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:20133846C>T	ENST00000397165.2	-	3	353	c.193G>A	c.(193-195)Gtg>Atg	p.V65M	ZNF682_ENST00000358523.5_Missense_Mutation_p.V33M|ZNF682_ENST00000397162.1_Missense_Mutation_p.V33M|ZNF682_ENST00000596019.1_Missense_Mutation_p.V65M|ZNF682_ENST00000595736.1_Intron|ZNF682_ENST00000597972.1_Missense_Mutation_p.V71M|ZNF682_ENST00000593468.1_Missense_Mutation_p.V65M	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	65	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> M (in dbSNP:rs7255165).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						TGTCTCTTCACATTCCAGGGC	0.453													N|||	1041	0.207867	0.3578	0.2003	5008	,	,		18567	0.0744		0.1759	False		,,,				2504	0.181				p.V65M		Atlas-SNP	.											.	ZNF682	51	.	0			c.G193A						PASS	.	C	MET/VAL,MET/VAL	1446,2768		257,932,918	152.0	159.0	156.0		97,193	0.9	0.3	19	dbSNP_116	156	1421,7093		132,1157,2968	yes	missense,missense	ZNF682	NM_001077349.1,NM_033196.2	21,21	389,2089,3886	TT,TC,CC		16.6902,34.3142,22.5251	benign,benign	33/467,65/499	20133846	2867,9861	2107	4257	6364	SO:0001583	missense	91120	exon3			TCTTCACATTCCA	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.193G>A	19.37:g.20133846C>T	ENSP00000380351:p.Val65Met	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	142	57	0.401408	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	37	CCDS42533.1	430	0.19688644688644688	168	0.34146341463414637	80	0.22099447513812154	39	0.06818181818181818	143	0.18865435356200527	c	0.634	-0.816113	0.02776	0.343142	0.166902	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000358523	T;T;T	0.06371	3.43;3.31;3.31	0.898	0.898	0.19264	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	L	0.43646	1.37	0.80722	P	0.0	B	0.12013	0.005	B	0.08055	0.003	T	0.46830	-0.9163	8	0.02654	T	1	.	4.929	0.13907	0.0:1.0:0.0:0.0	rs7255165;rs52797555;rs7255165	65	O95780	ZN682_HUMAN	M	65;33;33	ENSP00000380351:V65M;ENSP00000380348:V33M;ENSP00000351324:V33M	ENSP00000351324:V33M	V	-	1	0	ZNF682	19994846	0.051000	0.20477	0.300000	0.25030	0.305000	0.27757	0.727000	0.25999	0.284000	0.22305	0.289000	0.19496	GTG	C|0.801;T|0.199	0.199	strong		0.453	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196	
XPNPEP2	7512	hgsc.bcm.edu	37	X	128880614	128880614	+	Silent	SNP	T	T	C	rs3747343	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:128880614T>C	ENST00000371106.3	+	6	639	c.447T>C	c.(445-447)ccT>ccC	p.P149P	XPNPEP2_ENST00000371105.3_Silent_p.P149P	NM_003399.5	NP_003390.4	O43895	XPP2_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	149						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(3)|kidney(3)|large_intestine(5)|liver(1)|lung(20)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	37						CCGAGATTCCTGCTGGAGGGC	0.537													C|||	2230	0.590728	0.6619	0.2622	3775	,	,		13709	0.5923		0.2306	False		,,,				2504	0.3517				p.P149P		Atlas-SNP	.											.	XPNPEP2	84	.	0			c.T447C						PASS	.	C		3023,812		1023,530,447,79,124	252.0	233.0	239.0		447	-2.8	0.2	X	dbSNP_107	239	1805,4922		206,905,488,1317,1383	no	coding-synonymous	XPNPEP2	NM_003399.5		1229,1435,935,1396,1507	CC,CT,C,TT,T		26.8322,21.1734,45.711		149/675	128880614	4828,5734	2203	4299	6502	SO:0001819	synonymous_variant	7512	exon6			GATTCCTGCTGGA	U90724	CCDS14613.1	Xq25	2008-02-05			ENSG00000122121	ENSG00000122121	3.4.11.9		12823	protein-coding gene	gene with protein product		300145				9375790, 9628831	Standard	NM_003399		Approved		uc004eut.1	O43895	OTTHUMG00000022373	ENST00000371106.3:c.447T>C	X.37:g.128880614T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	203	191	0.940887	NM_003399	A0AV16|O75994	Silent	SNP	ENST00000371106.3	37	CCDS14613.1																																																																																			T|0.456;C|0.544	0.544	strong		0.537	XPNPEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058210.1	NM_003399	
SLC47A1	55244	hgsc.bcm.edu	37	17	19474875	19474875	+	Missense_Mutation	SNP	C	C	T	rs111653425	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:19474875C>T	ENST00000270570.4	+	15	1480	c.1394C>T	c.(1393-1395)gCc>gTc	p.A465V	SLC47A1_ENST00000575023.1_Intron|RP11-1113L8.1_ENST00000574267.1_RNA|SLC47A1_ENST00000571335.1_Intron|SLC47A1_ENST00000457293.1_Missense_Mutation_p.A465V|SLC47A1_ENST00000436810.2_Intron|SLC47A1_ENST00000395585.1_Missense_Mutation_p.A465V	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	465					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	TGGAAAAAAGCCTGTCAGCAG	0.393													C|||	11	0.00219649	0.0	0.0043	5008	,	,		18046	0.0		0.007	False		,,,				2504	0.001				p.A465V		Atlas-SNP	.											.	SLC47A1	55	.	0			c.C1394T						PASS	.	C	VAL/ALA	17,4389	24.3+/-50.5	0,17,2186	117.0	110.0	112.0		1394	5.4	1.0	17	dbSNP_132	112	68,8532	41.2+/-98.3	0,68,4232	yes	missense	SLC47A1	NM_018242.2	64	0,85,6418	TT,TC,CC		0.7907,0.3858,0.6535	benign	465/571	19474875	85,12921	2203	4300	6503	SO:0001583	missense	55244	exon15			AAAAAGCCTGTCA		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"""Solute carriers"""	25588	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 1"""	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.1394C>T	17.37:g.19474875C>T	ENSP00000270570:p.Ala465Val	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	174	92	0.528736	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	37	CCDS11209.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	C	14.34	2.506541	0.44558	0.003858	0.007907	ENSG00000142494	ENST00000270570;ENST00000457293;ENST00000395585;ENST00000424755	T;T;T	0.32023	1.48;1.47;1.47	5.4	5.4	0.78164	.	0.273024	0.41001	D	0.000979	T	0.20170	0.0485	L	0.42581	1.335	0.80722	D	1	B;P	0.40794	0.1;0.729	B;B	0.43251	0.109;0.413	T	0.01972	-1.1237	10	0.14656	T	0.56	-19.0703	10.1604	0.42849	0.0:0.9096:0.0:0.0904	.	465;465	Q96FL8;Q96FL8-3	S47A1_HUMAN;.	V	465;465;465;177	ENSP00000270570:A465V;ENSP00000415586:A465V;ENSP00000378951:A465V	ENSP00000270570:A465V	A	+	2	0	SLC47A1	19415467	1.000000	0.71417	0.964000	0.40570	0.629000	0.37895	2.731000	0.47343	2.539000	0.85634	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.393	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242	
FRAS1	80144	hgsc.bcm.edu	37	4	79421011	79421011	+	Silent	SNP	G	G	T	rs11933630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:79421011G>T	ENST00000264895.6	+	61	9692	c.9252G>T	c.(9250-9252)cgG>cgT	p.R3084R		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3080	Calx-beta 5.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GCAGCACGCGGGATGGCTCTG	0.542													G|||	404	0.0806709	0.0696	0.1052	5008	,	,		17039	0.002		0.1839	False		,,,				2504	0.0532				p.R3084R		Atlas-SNP	.											.	FRAS1	779	.	0			c.G9252T						PASS	.	G		311,3659		18,275,1692	123.0	123.0	123.0		9252	-0.8	0.7	4	dbSNP_120	123	1705,6657		178,1349,2654	no	coding-synonymous	FRAS1	NM_025074.6		196,1624,4346	TT,TG,GG		20.3899,7.8338,16.3477		3084/4013	79421011	2016,10316	1985	4181	6166	SO:0001819	synonymous_variant	80144	exon61			CACGCGGGATGGC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.9252G>T	4.37:g.79421011G>T		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	243	127	0.522634	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	251	0.11492673992673992	57	0.11585365853658537	45	0.12430939226519337	4	0.006993006993006993	145	0.19129287598944592	G	8.107	0.777851	0.16120	0.078338	0.203899	ENSG00000138759	ENST00000512123	.	.	.	5.91	-0.818	0.10833	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.9956	0.01466	0.2183:0.1709:0.1652:0.4455	rs11933630;rs17428935;rs11933630	.	.	.	X	1313	.	.	G	+	1	0	FRAS1	79640035	0.646000	0.27295	0.733000	0.30861	0.737000	0.42083	-0.189000	0.09629	0.084000	0.17077	0.655000	0.94253	GGA	G|0.885;T|0.115	0.115	strong		0.542	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
RSU1	6251	hgsc.bcm.edu	37	10	16796919	16796919	+	Silent	SNP	C	C	A	rs1049632	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:16796919C>A	ENST00000377921.3	-	4	652	c.351G>T	c.(349-351)acG>acT	p.T117T	RSU1_ENST00000602389.1_Silent_p.T64T|RSU1_ENST00000345264.5_Silent_p.T117T|RSU1_ENST00000464074.2_5'UTR			Q15404	RSU1_HUMAN	Ras suppressor protein 1	117					cell junction assembly (GO:0034329)|positive regulation of neural precursor cell proliferation (GO:2000179)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(1;7.54e-08)		AGTTGTTGTACGTCAAGTCCA	0.448													A|||	2090	0.417332	0.736	0.2911	5008	,	,		15063	0.4028		0.2624	False		,,,				2504	0.2505				p.T117T		Atlas-SNP	.											.	RSU1	31	.	0			c.G351T						PASS	.	A	,	2881,1525	481.9+/-359.3	945,991,267	84.0	93.0	90.0		351,192	2.8	1.0	10	dbSNP_86	90	2149,6451	714.3+/-406.0	268,1613,2419	no	coding-synonymous,coding-synonymous	RSU1	NM_012425.3,NM_152724.2	,	1213,2604,2686	AA,AC,CC		24.9884,34.6119,38.6745	,	117/278,64/225	16796919	5030,7976	2203	4300	6503	SO:0001819	synonymous_variant	6251	exon5			GTTGTACGTCAAG	AK055596	CCDS7112.1, CCDS31157.1	10p13	2012-09-20			ENSG00000148484	ENSG00000148484			10464	protein-coding gene	gene with protein product		179555				8288261	Standard	NM_152724		Approved	RSP-1, FLJ31034	uc001iol.3	Q15404	OTTHUMG00000017740	ENST00000377921.3:c.351G>T	10.37:g.16796919C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_012425	A8KA46|D3DRU3|Q6FI17	Silent	SNP	ENST00000377921.3	37	CCDS7112.1																																																																																			C|0.598;A|0.402	0.402	strong		0.448	RSU1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047006.1	NM_012425, NM_152724	
CYP39A1	51302	hgsc.bcm.edu	37	6	46563779	46563779	+	Missense_Mutation	SNP	C	C	T	rs147961800	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46563779C>T	ENST00000275016.2	-	8	1213	c.1010G>A	c.(1009-1011)cGt>cAt	p.R337H		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	337					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						AGCTTTTAAACGAATGGTTTC	0.338													C|||	7	0.00139776	0.0	0.0029	5008	,	,		15087	0.0		0.004	False		,,,				2504	0.001				p.R337H		Atlas-SNP	.											CYP39A1,caecum,carcinoma,-1,1	CYP39A1	41	1	0			c.G1010A						PASS	.	C	HIS/ARG	0,4406		0,0,2203	92.0	98.0	96.0		1010	3.9	0.7	6	dbSNP_134	96	14,8586	10.5+/-38.8	0,14,4286	yes	missense	CYP39A1	NM_016593.3	29	0,14,6489	TT,TC,CC		0.1628,0.0,0.1076	probably-damaging	337/470	46563779	14,12992	2203	4300	6503	SO:0001583	missense	51302	exon8			TTTAAACGAATGG	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.1010G>A	6.37:g.46563779C>T	ENSP00000275016:p.Arg337His	Somatic	324	1	0.00308642		WXS	Illumina HiSeq	Phase_I	316	143	0.452532	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	21.3	4.127159	0.77549	0.0	0.001628	ENSG00000146233	ENST00000275016	D	0.97505	-4.41	5.7	3.91	0.45181	.	0.141963	0.47455	D	0.000237	D	0.98099	0.9373	M	0.89601	3.045	0.51012	D	0.9999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98321	1.0528	10	0.87932	D	0	-13.1901	9.8571	0.41092	0.0:0.7875:0.1394:0.0731	.	317;337	B7Z786;Q9NYL5	.;CP39A_HUMAN	H	337	ENSP00000275016:R337H	ENSP00000275016:R337H	R	-	2	0	CYP39A1	46671738	0.999000	0.42202	0.739000	0.30968	0.954000	0.61252	4.208000	0.58486	0.746000	0.32786	0.557000	0.71058	CGT	C|0.999;T|0.001	0.001	strong		0.338	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
ANO1	55107	hgsc.bcm.edu	37	11	69934085	69934085	+	Silent	SNP	G	G	A	rs10898112	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:69934085G>A	ENST00000355303.5	+	2	641	c.336G>A	c.(334-336)tcG>tcA	p.S112S	ANO1_ENST00000316296.5_Silent_p.S84S|ANO1_ENST00000530676.1_5'UTR|ANO1_ENST00000538023.1_Silent_p.S112S|ANO1_ENST00000398543.2_5'UTR	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	112					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	ATGCAGGCTCGGGGGAGCCCC	0.701													G|||	999	0.199481	0.2943	0.2911	5008	,	,		10523	0.0268		0.2654	False		,,,				2504	0.1166				p.S112S		Atlas-SNP	.											.	ANO1	156	.	0			c.G336A						PASS	.	G		944,2910		127,690,1110	12.0	16.0	15.0		336	-3.2	0.0	11	dbSNP_120	15	2037,6217		273,1491,2363	no	coding-synonymous	ANO1	NM_018043.5		400,2181,3473	AA,AG,GG		24.6789,24.494,24.6201		112/987	69934085	2981,9127	1927	4127	6054	SO:0001819	synonymous_variant	55107	exon2			AGGCTCGGGGGAG	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.336G>A	11.37:g.69934085G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Silent	SNP	ENST00000355303.5	37	CCDS44663.1																																																																																			G|0.801;A|0.199	0.199	strong		0.701	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043	
ETAA1	54465	hgsc.bcm.edu	37	2	67632125	67632125	+	Missense_Mutation	SNP	C	C	T	rs3770655	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:67632125C>T	ENST00000272342.5	+	5	2441	c.2311C>T	c.(2311-2313)Cca>Tca	p.P771S	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	771			P -> S (in dbSNP:rs3770655). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)		p.P771S(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						ATTGGTTCTTCCAGGAAGTTC	0.318													T|||	3735	0.745807	0.916	0.7233	5008	,	,		20216	0.5685		0.7316	False		,,,				2504	0.729				p.P771S		Atlas-SNP	.											ETAA1,NS,carcinoma,-1,2	ETAA1	88	2	1	Substitution - Missense(1)	stomach(1)	c.C2311T						scavenged	.	T	SER/PRO	3929,475	214.1+/-233.5	1752,425,25	45.0	47.0	46.0		2311	-8.3	0.0	2	dbSNP_107	46	6160,2438	398.3+/-346.1	2220,1720,359	yes	missense	ETAA1	NM_019002.3	74	3972,2145,384	TT,TC,CC		28.3554,10.7856,22.4042	benign	771/927	67632125	10089,2913	2202	4299	6501	SO:0001583	missense	54465	exon5			GTTCTTCCAGGAA	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.2311C>T	2.37:g.67632125C>T	ENSP00000272342:p.Pro771Ser	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	200	62	0.31	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	1596	0.7307692307692307	451	0.9166666666666666	267	0.7375690607734806	325	0.5681818181818182	553	0.7295514511873351	T	0.330	-0.956856	0.02267	0.892144	0.716446	ENSG00000143971	ENST00000272342	T	0.15834	2.39	5.83	-8.29	0.01009	.	1.402030	0.04371	N	0.359154	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37220	-0.9715	9	0.05833	T	0.94	5.3941	0.9202	0.01313	0.4421:0.1547:0.1612:0.2421	rs3770655;rs52826099;rs60544664;rs3770655	771	Q9NY74	ETAA1_HUMAN	S	771	ENSP00000272342:P771S	ENSP00000272342:P771S	P	+	1	0	ETAA1	67485629	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.232000	0.09055	-1.968000	0.01006	-2.541000	0.00179	CCA	C|0.244;T|0.756	0.756	strong		0.318	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002	
POTEF	728378	hgsc.bcm.edu	37	2	130832545	130832545	+	Missense_Mutation	SNP	C	C	T	rs199777567	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:130832545C>T	ENST00000409914.2	-	17	2899	c.2500G>A	c.(2500-2502)Gtg>Atg	p.V834M	POTEF_ENST00000357462.5_Missense_Mutation_p.V834M	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	834	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						TGGATGGCCACGTACATGGCT	0.592													.|||	6	0.00119808	0.0	0.0014	5008	,	,		20796	0.0		0.005	False		,,,				2504	0.0				p.V834M		Atlas-SNP	.											.	POTEF	140	.	0			c.G2500A						PASS	.	C	MET/VAL	2,4392		0,2,2195	104.0	125.0	118.0		2500		0.3	2		118	26,8544		0,26,4259	no	missense	POTEF	NM_001099771.2	21	0,28,6454	TT,TC,CC		0.3034,0.0455,0.216	probably-damaging	834/1076	130832545	28,12936	2197	4285	6482	SO:0001583	missense	728378	exon17			TGGCCACGTACAT	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2500G>A	2.37:g.130832545C>T	ENSP00000386786:p.Val834Met	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	145	73	0.503448	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	15.44	2.834922	0.50951	4.55E-4	0.003034	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.94723	-3.5;-3.5	.	.	.	.	.	.	.	.	D	0.95695	0.8600	M	0.88570	2.965	0.80722	D	1	D	0.57257	0.979	P	0.55055	0.767	D	0.93384	0.6746	8	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	.	834	A5A3E0	POTEF_HUMAN	M	834	ENSP00000350052:V834M;ENSP00000386786:V834M	ENSP00000350052:V834M	V	-	1	0	POTEF	130549015	1.000000	0.71417	0.299000	0.25016	0.302000	0.27658	3.653000	0.54446	0.119000	0.18210	0.121000	0.15741	GTG	C|0.993;T|0.007	0.007	strong		0.592	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
UCP2	7351	hgsc.bcm.edu	37	11	73689104	73689104	+	Missense_Mutation	SNP	G	G	A	rs660339	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:73689104G>A	ENST00000310473.3	-	4	1006	c.164C>T	c.(163-165)gCc>gTc	p.A55V	UCP2_ENST00000542615.1_5'Flank|UCP2_ENST00000536983.1_Missense_Mutation_p.A55V	NM_003355.2	NP_003346.2	P55851	UCP2_HUMAN	uncoupling protein 2 (mitochondrial, proton carrier)	55			A -> V (in dbSNP:rs660339). {ECO:0000269|PubMed:9133562, ECO:0000269|Ref.4, ECO:0000269|Ref.7, ECO:0000269|Ref.8}.		aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to amino acid starvation (GO:0034198)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|female pregnancy (GO:0007565)|liver regeneration (GO:0097421)|mitochondrial transport (GO:0006839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|positive regulation of cell death (GO:0010942)|proton transport (GO:0015992)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				large_intestine(1)|lung(3)|prostate(1)	5	Breast(11;0.000112)					CTGGGCGCTGGCTGTAGCGCG	0.617													g|||	2084	0.416134	0.447	0.4409	5008	,	,		18773	0.4177		0.4046	False		,,,				2504	0.3671				p.A55V	Colon(191;388 2040 43557 45622 48925)	Atlas-SNP	.											.	UCP2	24	.	0			c.C164T	GRCh37	CM994639	UCP2	M	rs660339	PASS	.	G	VAL/ALA	1923,2477	547.2+/-377.2	391,1141,668	38.0	42.0	41.0		164	5.1	1.0	11	dbSNP_83	41	3503,5083	510.0+/-377.4	717,2069,1507	yes	missense	UCP2	NM_003355.2	64	1108,3210,2175	AA,AG,GG		40.799,43.7045,41.7835	benign	55/310	73689104	5426,7560	2200	4293	6493	SO:0001583	missense	7351	exon4			GCGCTGGCTGTAG	U76367	CCDS8228.1	11q13	2014-02-12						"""Solute carriers"""	12518	protein-coding gene	gene with protein product		601693	"""body mass index QTL 4"", ""body mass index quantitative trait 4"""	BMIQ4		9196039, 11381268	Standard	NM_003355		Approved	SLC25A8	uc001oup.1	P55851		ENST00000310473.3:c.164C>T	11.37:g.73689104G>A	ENSP00000312029:p.Ala55Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_003355	Q4PJH8|Q53HM3	Missense_Mutation	SNP	ENST00000310473.3	37	CCDS8228.1	943	0.4317765567765568	208	0.42276422764227645	160	0.4419889502762431	258	0.45104895104895104	317	0.4182058047493404	G	9.072	0.997031	0.19043	0.437045	0.40799	ENSG00000175567	ENST00000310473;ENST00000536983;ENST00000544615	T;T;T	0.80393	-1.37;-1.37;-1.37	6.07	5.14	0.70334	Mitochondrial carrier domain (2);	0.170469	0.49916	D	0.000126	T	0.00012	0.0000	N	0.13043	0.29	0.42283	P	0.007897000000000043	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.29397	-1.0013	9	0.39692	T	0.17	-31.8322	9.5193	0.39124	0.0:0.1378:0.5773:0.2849	rs660339;rs1050841;rs2228495;rs17848359;rs59652865;rs660339	55;55	F5GX45;P55851	.;UCP2_HUMAN	V	55;55;28	ENSP00000312029:A55V;ENSP00000441147:A55V;ENSP00000439951:A28V	ENSP00000312029:A55V	A	-	2	0	UCP2	73366752	0.146000	0.22672	0.974000	0.42286	0.013000	0.08279	1.934000	0.40163	1.533000	0.49186	0.655000	0.94253	GCC	G|0.573;T|0.004	.	strong		0.617	UCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398108.1	NM_003355	
TTN	7273	hgsc.bcm.edu	37	2	179451420	179451420	+	Missense_Mutation	SNP	G	G	A	rs2042996	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179451420G>A	ENST00000591111.1	-	258	59509	c.59285C>T	c.(59284-59286)aCt>aTt	p.T19762I	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T12338I|TTN_ENST00000342992.6_Missense_Mutation_p.T18835I|TTN_ENST00000589042.1_Missense_Mutation_p.T21403I|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T12463I|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T12530I|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19762	Fibronectin type-III 43. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> I. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTGTAACTAGTGATGTAGCC	0.468													A|||	2542	0.507588	0.5582	0.4078	5008	,	,		19158	0.7212		0.2485	False		,,,				2504	0.5562				p.T21403I		Atlas-SNP	.											.	TTN	18412	.	0			c.C64208T						PASS	.	A	ILE/THR,ILE/THR,ILE/THR,ILE/THR	2009,1945		527,955,495	184.0	180.0	181.0		37589,37388,56504,37013	6.1	0.9	2	dbSNP_94	181	1837,6525		187,1463,2531	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	714,2418,3026	AA,AG,GG		21.9684,49.1907,31.2277	benign,benign,benign,benign	12530/27119,12463/27052,18835/33424,12338/26927	179451420	3846,8470	1977	4181	6158	SO:0001583	missense	7273	exon308			TAACTAGTGATGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.59285C>T	2.37:g.179451420G>A	ENSP00000465570:p.Thr19762Ile	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	250	127	0.508	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		977	0.44734432234432236	274	0.556910569105691	130	0.35911602209944754	390	0.6818181818181818	183	0.24142480211081793	A	15.37	2.813873	0.50527	0.508093	0.219684	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.07	6.07	0.98685	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00004	-3.385	0.50039	P	1.5100000000001224E-4	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.48031	-0.9070	8	0.87932	D	0	.	12.3663	0.55230	0.9347:0.0:0.0653:0.0	rs2042996;rs52829581;rs2042996	12338;12463;12530;19762	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	18835;12338;12530;12463;12336	ENSP00000343764:T18835I;ENSP00000434586:T12338I;ENSP00000340554:T12530I;ENSP00000352154:T12463I	ENSP00000340554:T12530I	T	-	2	0	TTN	179159666	1.000000	0.71417	0.901000	0.35422	0.836000	0.47400	7.476000	0.81055	1.120000	0.41904	-0.254000	0.11334	ACT	G|0.553;N|0.000	.	strong		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
HLA-B	3106	hgsc.bcm.edu	37	6	31323128	31323128	+	Silent	SNP	A	A	G	rs41551014		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323128A>G	ENST00000412585.2	-	4	889	c.861T>C	c.(859-861)caT>caC	p.H287H		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	287	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GCAGCCCCTCATGCTGTACAT	0.572									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.H287H		Atlas-SNP	.											.	HLA-B	54	.	0			c.T861C						PASS	.						67.0	61.0	63.0					6																	31323128		2203	4300	6503	SO:0001819	synonymous_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	CCCCTCATGCTGT	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.861T>C	6.37:g.31323128A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	177	47	0.265537	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	weak		0.572	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
BAI2	576	hgsc.bcm.edu	37	1	32221913	32221913	+	Silent	SNP	G	G	A	rs4949223	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32221913G>A	ENST00000373658.3	-	4	866	c.525C>T	c.(523-525)ccC>ccT	p.P175P	BAI2_ENST00000527361.1_Silent_p.P175P|MIR4254_ENST00000581063.1_RNA|BAI2_ENST00000398547.1_Silent_p.P163P|BAI2_ENST00000398538.1_Silent_p.P163P|BAI2_ENST00000257070.4_Silent_p.P175P|BAI2_ENST00000398556.3_Silent_p.P178P|BAI2_ENST00000398542.1_Silent_p.P163P|BAI2_ENST00000373655.2_Silent_p.P175P	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	175					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		CTAGGGCAGCGGGCGCCAGCA	0.617													G|||	683	0.136382	0.0333	0.1715	5008	,	,		15990	0.1121		0.1133	False		,,,				2504	0.2996				p.P175P		Atlas-SNP	.											.	BAI2	128	.	0			c.C525T						PASS	.	G		202,4204		2,198,2003	28.0	35.0	33.0		525	-3.1	0.0	1	dbSNP_111	33	1104,7492		73,958,3267	no	coding-synonymous	BAI2	NM_001703.2		75,1156,5270	AA,AG,GG		12.8432,4.5847,10.0446		175/1586	32221913	1306,11696	2203	4298	6501	SO:0001819	synonymous_variant	576	exon4			GGCAGCGGGCGCC	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.525C>T	1.37:g.32221913G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	126	69	0.547619	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	37	CCDS346.2																																																																																			G|0.896;A|0.104	0.104	strong		0.617	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
WDPCP	51057	hgsc.bcm.edu	37	2	63660902	63660902	+	Missense_Mutation	SNP	C	C	T	rs17617459	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:63660902C>T	ENST00000272321.7	-	9	1329	c.802G>A	c.(802-804)Ggt>Agt	p.G268S	WDPCP_ENST00000409562.3_Missense_Mutation_p.G268S|WDPCP_ENST00000409835.1_5'UTR|WDPCP_ENST00000409199.1_Missense_Mutation_p.G76S|WDPCP_ENST00000398544.3_Missense_Mutation_p.G109S|WDPCP_ENST00000409120.1_Missense_Mutation_p.G76S	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	268			G -> S (in dbSNP:rs17617459).		auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						TGAGCATAACCCAGGAGGAGT	0.373													C|||	86	0.0171725	0.0045	0.0231	5008	,	,		15439	0.0		0.0557	False		,,,				2504	0.0082				p.G268S		Atlas-SNP	.											.	WDPCP	79	.	0			c.G802A						PASS	.	C	SER/GLY	41,3665		1,39,1813	60.0	57.0	58.0		802	4.6	1.0	2	dbSNP_123	58	490,7702		13,464,3619	yes	missense	WDPCP	NM_015910.5	56	14,503,5432	TT,TC,CC		5.9814,1.1063,4.4629	benign	268/747	63660902	531,11367	1853	4096	5949	SO:0001583	missense	51057	exon9			CATAACCCAGGAG		CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"""chromosome 2 open reading frame 86"""	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.802G>A	2.37:g.63660902C>T	ENSP00000272321:p.Gly268Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	114	73	0.640351	NM_015910	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	37	CCDS42688.1	50	0.022893772893772892	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	44	0.05804749340369393	C	9.131	1.011327	0.19277	0.011063	0.059814	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544;ENST00000409562	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06	5.43	4.56	0.56223	.	0.194738	0.45126	N	0.000394	T	0.02571	0.0078	N	0.14661	0.345	0.29805	N	0.832089	B;B;B;B	0.17465	0.022;0.002;0.01;0.003	B;B;B;B	0.17433	0.018;0.012;0.012;0.005	T	0.05767	-1.0865	10	0.20519	T	0.43	-6.9153	9.621	0.39721	0.0:0.8411:0.0:0.1589	rs17617459;rs52811496;rs17617459	76;268;268;109	E9PFG9;O95876-2;O95876;O95876-3	.;.;FRITZ_HUMAN;.	S	268;76;76;109;268	ENSP00000272321:G268S;ENSP00000386592:G76S;ENSP00000386769:G76S;ENSP00000381552:G109S;ENSP00000387222:G268S	ENSP00000272321:G268S	G	-	1	0	WDPCP	63514406	0.992000	0.36948	0.996000	0.52242	0.992000	0.81027	0.541000	0.23207	1.297000	0.44761	0.563000	0.77884	GGT	C|0.970;T|0.030	0.030	strong		0.373	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910	
WRN	7486	hgsc.bcm.edu	37	8	30924557	30924557	+	Silent	SNP	C	C	T	rs1800389	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:30924557C>T	ENST00000298139.5	+	6	762	c.513C>T	c.(511-513)tgC>tgT	p.C171C		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	171	3'-5' exonuclease.|Interaction with WRNIP1. {ECO:0000250}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		AGCTGAAATGCACAGAGACCT	0.368			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				T|||	3442	0.6873	0.4902	0.7939	5008	,	,		16385	0.87		0.7087	False		,,,				2504	0.6677				p.C171C	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.C513T						PASS	.	T		2360,2046	567.3+/-382.1	649,1062,492	103.0	93.0	96.0		513	2.1	0.0	8	dbSNP_89	96	6142,2458	404.8+/-348.3	2182,1778,340	no	coding-synonymous	WRN	NM_000553.4		2831,2840,832	TT,TC,CC		28.5814,46.4367,34.6302		171/1433	30924557	8502,4504	2203	4300	6503	SO:0001819	synonymous_variant	7486	exon6	Familial Cancer Database	WS, Adult Progeria	GAAATGCACAGAG		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.513C>T	8.37:g.30924557C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_000553	A1KYY9	Silent	SNP	ENST00000298139.5	37	CCDS6082.1																																																																																			C|0.321;T|0.679	0.679	strong		0.368	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
OR2T4	127074	hgsc.bcm.edu	37	1	248525193	248525193	+	Missense_Mutation	SNP	C	C	T	rs28655275	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248525193C>T	ENST00000366475.1	+	1	311	c.311C>T	c.(310-312)gCg>gTg	p.A104V		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATGGACATGGCGTACATTTCT	0.498																																					p.A104V		Atlas-SNP	.											OR2T4,NS,carcinoma,-1,2	OR2T4	126	2	0			c.C311T						scavenged	.	T	VAL/ALA	130,4276	811.1+/-416.0	3,124,2076	316.0	232.0	260.0		311	-3.2	0.2	1	dbSNP_125	260	1067,7529	759.6+/-407.6	51,965,3282	no	missense	OR2T4	NM_001004696.1	64	54,1089,5358	TT,TC,CC		12.4128,2.9505,9.2063	benign	104/349	248525193	1197,11805	2203	4298	6501	SO:0001583	missense	127074	exon1			ACATGGCGTACAT	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.311C>T	1.37:g.248525193C>T	ENSP00000355431:p.Ala104Val	Somatic	797	2	0.00250941		WXS	Illumina HiSeq	Phase_I	876	225	0.256849	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	440	0.20146520146520147	7	0.014227642276422764	74	0.20441988950276244	221	0.38636363636363635	138	0.1820580474934037	T	9.915	1.210607	0.22289	0.029505	0.124128	ENSG00000196944	ENST00000366475	T	0.78924	-1.22	3.48	-3.16	0.05217	GPCR, rhodopsin-like superfamily (1);	0.368836	0.23365	N	0.048969	T	0.00012	0.0000	N	0.10972	0.075	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28586	-1.0039	9	0.42905	T	0.14	.	6.5165	0.22250	0.0:0.3:0.2192:0.4808	rs28655275	104	Q8NH00	OR2T4_HUMAN	V	104	ENSP00000355431:A104V	ENSP00000355431:A104V	A	+	2	0	OR2T4	246591816	0.147000	0.22687	0.163000	0.22734	0.796000	0.44982	1.283000	0.33237	-0.481000	0.06792	-1.330000	0.01273	GCG	.	.	weak		0.498	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
TRHDE	29953	hgsc.bcm.edu	37	12	73014917	73014917	+	Silent	SNP	A	A	G	rs7139238	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:73014917A>G	ENST00000261180.4	+	14	2460	c.2364A>G	c.(2362-2364)acA>acG	p.T788T		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	788					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						TTGCAACAACATATATCAAGC	0.308													G|||	918	0.183307	0.5772	0.1009	5008	,	,		15804	0.0		0.0736	False		,,,				2504	0.0112				p.T788T		Atlas-SNP	.											.	TRHDE	194	.	0			c.A2364G						PASS	.	G		2225,2181	586.0+/-386.4	566,1093,544	94.0	89.0	91.0		2364	-10.2	0.1	12	dbSNP_116	91	667,7933	788.1+/-407.6	24,619,3657	no	coding-synonymous	TRHDE	NM_013381.2		590,1712,4201	GG,GA,AA		7.7558,49.5007,22.2359		788/1025	73014917	2892,10114	2203	4300	6503	SO:0001819	synonymous_variant	29953	exon14			AACAACATATATC	AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"""pyroglutamyl-peptidase II"", ""pyroglutamyl aminopeptidase II"", ""TRH-specific aminopeptidase"""	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.2364A>G	12.37:g.73014917A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_013381	A5PL19|Q6UWJ4	Silent	SNP	ENST00000261180.4	37	CCDS9004.1																																																																																			A|0.784;G|0.216	0.216	strong		0.308	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381	
MOGAT2	80168	hgsc.bcm.edu	37	11	75428958	75428958	+	Missense_Mutation	SNP	A	A	G	rs554202	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:75428958A>G	ENST00000198801.5	+	1	95	c.25A>G	c.(25-27)Atg>Gtg	p.M9V	MOGAT2_ENST00000526712.1_5'Flank	NM_025098.2	NP_079374.2	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	9			M -> V (in dbSNP:rs554202). {ECO:0000269|PubMed:15489334}.		diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|intestinal absorption (GO:0050892)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|acetyltransferase activity (GO:0016407)			NS(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	20	Ovarian(111;0.103)					GCCCTTGTTTATGCCGTGGGA	0.582													G|||	1740	0.347444	0.4319	0.2968	5008	,	,		19475	0.1587		0.4573	False		,,,				2504	0.3507				p.M9V		Atlas-SNP	.											.	MOGAT2	49	.	0			c.A25G						PASS	.	G	VAL/MET	1908,2492	626.3+/-394.7	432,1044,724	119.0	83.0	95.0		25	2.8	0.5	11	dbSNP_83	95	4047,4539	596.1+/-393.6	949,2149,1195	yes	missense	MOGAT2	NM_025098.2	21	1381,3193,1919	GG,GA,AA		47.1349,43.3636,45.8571	benign	9/335	75428958	5955,7031	2200	4293	6493	SO:0001583	missense	80168	exon1			TTGTTTATGCCGT	AY157608	CCDS8240.1	11q13.5	2008-02-05			ENSG00000166391	ENSG00000166391			23248	protein-coding gene	gene with protein product		610270				14970677	Standard	NM_025098		Approved	MGAT2, DGAT2L5, FLJ22644	uc010rru.2	Q3SYC2	OTTHUMG00000165341	ENST00000198801.5:c.25A>G	11.37:g.75428958A>G	ENSP00000198801:p.Met9Val	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	220	109	0.495455	NM_025098	A8K7I3|Q3SYC1|Q6ZQZ2|Q86UH6|Q9H630	Missense_Mutation	SNP	ENST00000198801.5	37	CCDS8240.1	779	0.3566849816849817	209	0.4247967479674797	121	0.3342541436464088	105	0.18356643356643357	344	0.45382585751978893	G	0.013	-1.638189	0.00799	0.433636	0.471349	ENSG00000166391	ENST00000198801	T	0.18960	2.18	4.87	2.81	0.32909	.	0.144299	0.46145	N	0.000307	T	0.00012	0.0000	N	0.00041	-2.485	0.09310	P	0.9999999515061	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44682	-0.9312	9	0.02654	T	1	4.5669	1.7744	0.03019	0.1808:0.1625:0.4891:0.1677	rs554202;rs3740848;rs60954562;rs554202	9;9	Q3SYC2;Q3SYC2-3	MOGT2_HUMAN;.	V	9	ENSP00000198801:M9V	ENSP00000198801:M9V	M	+	1	0	MOGAT2	75106606	0.013000	0.17824	0.461000	0.27105	0.446000	0.32137	-0.003000	0.12901	0.560000	0.29169	-0.226000	0.12346	ATG	A|0.591;G|0.408	0.408	strong		0.582	MOGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383520.1	NM_025098	
HLA-C	3107	hgsc.bcm.edu	37	6	31239601	31239601	+	Missense_Mutation	SNP	C	C	T	rs281860337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239601C>T	ENST00000376228.5	-	2	132	c.118G>A	c.(118-120)Ggc>Agc	p.G40S	HLA-C_ENST00000383329.3_Missense_Mutation_p.G40S	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	40	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TCTCCGCGGCCGGGCCGGGAC	0.726													c|||	209	0.0417332	0.0794	0.0274	5008	,	,		11918	0.0198		0.0447	False		,,,				2504	0.0204				p.G40S		Atlas-SNP	.											.	HLA-C	92	.	0			c.G118A						PASS	.	C	SER/GLY	218,2784		6,206,1289	21.0	21.0	21.0		118	-0.5	0.0	6	dbSNP_86	21	220,5174		5,210,2482	no	missense	HLA-C	NM_002117.5	56	11,416,3771	TT,TC,CC		4.0786,7.2618,5.2168	possibly-damaging	40/367	31239601	438,7958	1501	2697	4198	SO:0001583	missense	3107	exon2			CGCGGCCGGGCCG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.118G>A	6.37:g.31239601C>T	ENSP00000365402:p.Gly40Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	73|73	0.033424908424908424|0.033424908424908424	35|35	0.07113821138211382|0.07113821138211382	7|7	0.019337016574585635|0.019337016574585635	3|3	0.005244755244755245|0.005244755244755245	28|28	0.036939313984168866|0.036939313984168866	c|c	9.427|9.427	1.084516|1.084516	0.20309|0.20309	0.072618|0.072618	0.040786|0.040786	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00882|.	5.58;5.58|.	2.49|2.49	-0.509|-0.509	0.11977|0.11977	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	0.283264|.	0.18054|.	U|.	0.153199|.	T|T	0.54271|0.54271	0.1848|0.1848	H|H	0.97291|0.97291	3.975|3.975	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.29432|.	0.244;0.002;0.009;0.02|.	B;B;B;B|.	0.30646|.	0.118;0.018;0.031;0.037|.	T|T	0.53592|0.53592	-0.8417|-0.8417	10|5	0.72032|.	D|.	0.01|.	.|.	2.2892|2.2892	0.04134|0.04134	0.2427:0.4573:0.0:0.2999|0.2427:0.4573:0.0:0.2999	rs41551915|rs41551915	40;40;40;40|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	S|Q	40;40;40;77|39	ENSP00000365402:G40S;ENSP00000372819:G40S|.	ENSP00000365402:G40S|.	G|R	-|-	1|2	0|0	HLA-C|HLA-C	31347580|31347580	0.020000|0.020000	0.18652|0.18652	0.035000|0.035000	0.18076|0.18076	0.020000|0.020000	0.10135|0.10135	0.078000|0.078000	0.14761|0.14761	-0.149000|-0.149000	0.11215|0.11215	0.305000|0.305000	0.20034|0.20034	GGC|CGG	T|0.034;C|0.966	0.034	weak		0.726	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
MUC16	94025	hgsc.bcm.edu	37	19	9057896	9057896	+	Missense_Mutation	SNP	G	G	C	rs12984471	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9057896G>C	ENST00000397910.4	-	3	29753	c.29550C>G	c.(29548-29550)gaC>gaG	p.D9850E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9852	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGTGGTATCGTCCACAGCGG	0.473													C|||	1046	0.208866	0.2352	0.219	5008	,	,		21466	0.0258		0.3121	False		,,,				2504	0.2485				p.D9850E		Atlas-SNP	.											.	MUC16	4315	.	0			c.C29550G						PASS	.	C	GLU/ASP	931,3103		102,727,1188	156.0	149.0	151.0		29550	-1.6	0.0	19	dbSNP_121	151	2825,5553		499,1827,1863	yes	missense	MUC16	NM_024690.2	45	601,2554,3051	CC,CG,GG		33.7193,23.0788,30.261	benign	9850/14508	9057896	3756,8656	2017	4189	6206	SO:0001583	missense	94025	exon3			GGTATCGTCCACA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29550C>G	19.37:g.9057896G>C	ENSP00000381008:p.Asp9850Glu	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	205	205	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	455	0.20833333333333334	123	0.25	82	0.2265193370165746	11	0.019230769230769232	239	0.3153034300791557	c	5.757	0.324052	0.10900	0.230788	0.337193	ENSG00000181143	ENST00000397910	T	0.19806	2.12	2.43	-1.59	0.08453	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.45687	-0.9244	8	0.87932	D	0	.	4.2005	0.10464	0.0:0.4824:0.185:0.3325	rs12984471;rs52797430;rs57305113;rs12984471	9850	B5ME49	.	E	9850	ENSP00000381008:D9850E	ENSP00000381008:D9850E	D	-	3	2	MUC16	8918896	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.110000	0.00293	-0.660000	0.05352	-0.224000	0.12420	GAC	G|0.760;C|0.240	0.240	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MSH3	4437	hgsc.bcm.edu	37	5	80109479	80109479	+	Missense_Mutation	SNP	T	T	G	rs41545019	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:80109479T>G	ENST00000265081.6	+	20	2812	c.2732T>G	c.(2731-2733)tTg>tGg	p.L911W		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	911					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CAAGTTGCATTGATTACCATC	0.413								Mismatch excision repair (MMR)					T|||	5	0.000998403	0.0	0.0014	5008	,	,		18784	0.0		0.004	False		,,,				2504	0.0				p.L911W	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.T2732G						PASS	.	T	TRP/LEU	2,4404	4.2+/-10.8	0,2,2201	192.0	187.0	188.0		2732	5.6	0.2	5	dbSNP_127	188	41,8559	27.4+/-76.7	0,41,4259	yes	missense	MSH3	NM_002439.3	61	0,43,6460	GG,GT,TT		0.4767,0.0454,0.3306	probably-damaging	911/1138	80109479	43,12963	2203	4300	6503	SO:0001583	missense	4437	exon20			TTGCATTGATTAC	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.2732T>G	5.37:g.80109479T>G	ENSP00000265081:p.Leu911Trp	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	229	120	0.524017	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	17.41	3.383061	0.61845	4.54E-4	0.004767	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.88896	-2.44	5.57	5.57	0.84162	DNA mismatch repair protein MutS, C-terminal (2);	0.000000	0.64402	D	0.000001	D	0.95968	0.8687	H	0.94698	3.57	0.47245	D	0.999368	D	0.89917	1.0	D	0.72625	0.978	D	0.97127	0.9815	9	.	.	.	-4.0755	15.7269	0.77766	0.0:0.0:0.0:1.0	rs41545019;rs61749610	911	P20585	MSH3_HUMAN	W	911;902	ENSP00000265081:L911W	.	L	+	2	0	MSH3	80145235	1.000000	0.71417	0.203000	0.23512	0.261000	0.26267	8.032000	0.88838	2.123000	0.65237	0.482000	0.46254	TTG	T|0.997;G|0.003	0.003	strong		0.413	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
GBP3	2635	hgsc.bcm.edu	37	1	89479074	89479074	+	Missense_Mutation	SNP	C	C	T	rs4656078	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89479074C>T	ENST00000370481.4	-	6	882	c.662G>A	c.(661-663)cGa>cAa	p.R221Q	GBP3_ENST00000475853.2_5'Flank	NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	254	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		GATACAGAGTCGGGGCAGATT	0.373													.|||	1672	0.333866	0.1793	0.2925	5008	,	,		18462	0.3075		0.4404	False		,,,				2504	0.4898				p.R221Q		Atlas-SNP	.											.	GBP3	53	.	0			c.G662A						PASS	.	C	GLN/ARG	1146,3258	371.7+/-320.1	142,862,1198	93.0	99.0	97.0		662	-0.5	0.5	1	dbSNP_111	97	3897,4703	528.3+/-381.3	871,2155,1274	yes	missense	GBP3	NM_018284.2	43	1013,3017,2472	TT,TC,CC		45.314,26.0218,38.7804	probably-damaging	221/596	89479074	5043,7961	2202	4300	6502	SO:0001583	missense	2635	exon6			CAGAGTCGGGGCA	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.662G>A	1.37:g.89479074C>T	ENSP00000359512:p.Arg221Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	705	0.3228021978021978	81	0.16463414634146342	124	0.3425414364640884	161	0.28146853146853146	339	0.4472295514511873	C	18.04	3.535117	0.64972	0.260218	0.45314	ENSG00000117226	ENST00000370481;ENST00000235878	D	0.84589	-1.87	3.85	-0.523	0.11924	Guanylate-binding protein, N-terminal (1);	0.391146	0.20230	N	0.096482	D	0.84808	0.5554	M	0.93375	3.41	0.51482	P	7.80000000000225E-5	D;D	0.69078	0.997;0.961	P;P	0.52217	0.693;0.498	T	0.80106	-0.1521	8	.	.	.	.	4.6468	0.12575	0.1512:0.5724:0.0:0.2764	rs4656078;rs4656078	87;221	F6X827;Q9H0R5	.;GBP3_HUMAN	Q	221	ENSP00000359512:R221Q	.	R	-	2	0	GBP3	89251662	0.307000	0.24500	0.490000	0.27465	0.898000	0.52572	2.143000	0.42187	-0.185000	0.10550	-0.290000	0.09829	CGA	C|0.661;T|0.339	0.339	strong		0.373	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	
HLA-C	3107	hgsc.bcm.edu	37	6	31239378	31239378	+	Missense_Mutation	SNP	T	T	G	rs1131123	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239378T>G	ENST00000376228.5	-	2	355	c.341A>C	c.(340-342)gAc>gCc	p.D114A	HLA-C_ENST00000383329.3_Missense_Mutation_p.D114A	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	114	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TCACTCACCGTCCTCGCTCTG	0.682													t|||	2745	0.548123	0.4705	0.5778	5008	,	,		9395	0.7212		0.4911	False		,,,				2504	0.5123				p.D114A		Atlas-SNP	.											.	HLA-C	92	.	0			c.A341C						PASS	.						32.0	34.0	33.0					6																	31239378		1511	2709	4220	SO:0001583	missense	3107	exon2			TCACCGTCCTCGC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.341A>C	6.37:g.31239378T>G	ENSP00000365402:p.Asp114Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	119	117	0.983193	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1043	0.4775641025641026	193	0.39227642276422764	183	0.505524861878453	352	0.6153846153846154	315	0.4155672823218997	.	10.21	1.288411	0.23478	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00009	9.47;9.47	2.81	-1.89	0.07689	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.0	T	0.47623	-0.9103	7	0.02654	T	1	.	5.3186	0.15870	0.0:0.2489:0.2609:0.4902	rs1131123;rs3190694;rs11547356;rs17366173;rs41555916	114;114;114;114	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	A	114;114;114;151	ENSP00000365402:D114A;ENSP00000372819:D114A	ENSP00000365402:D114A	D	-	2	0	HLA-C	31347357	0.000000	0.05858	0.165000	0.22776	0.503000	0.33858	-1.689000	0.01923	-0.470000	0.06901	-0.780000	0.03373	GAC	T|0.538;G|0.462	0.462	strong		0.682	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
RAD54B	25788	hgsc.bcm.edu	37	8	95399331	95399331	+	Silent	SNP	G	G	A	rs28605692	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:95399331G>A	ENST00000336148.5	-	11	1990	c.1866C>T	c.(1864-1866)ggC>ggT	p.G622G		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	622					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			CACTTAGCAAGCCTTTGTATA	0.388								Direct reversal of damage;Homologous recombination					G|||	78	0.0155751	0.0068	0.0346	5008	,	,		16975	0.0		0.0249	False		,,,				2504	0.0204				p.G622G		Atlas-SNP	.											.	RAD54B	88	.	0			c.C1866T						PASS	.	G	,	59,4347	58.1+/-94.6	0,59,2144	146.0	132.0	137.0		1314,1866	2.6	0.2	8	dbSNP_125	137	342,8258	117.6+/-177.1	12,318,3970	no	coding-synonymous,coding-synonymous	RAD54B	NM_001205263.1,NM_012415.3	,	12,377,6114	AA,AG,GG		3.9767,1.3391,3.0832	,	438/727,622/911	95399331	401,12605	2203	4300	6503	SO:0001819	synonymous_variant	25788	exon11			TAGCAAGCCTTTG	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.1866C>T	8.37:g.95399331G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	226	96	0.424779	NM_012415	F6WBS8	Silent	SNP	ENST00000336148.5	37	CCDS6262.1																																																																																			G|0.975;A|0.025	0.025	strong		0.388	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
DMGDH	29958	hgsc.bcm.edu	37	5	78338202	78338202	+	Missense_Mutation	SNP	T	T	C	rs77116243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:78338202T>C	ENST00000255189.3	-	7	1125	c.1097A>G	c.(1096-1098)aAt>aGt	p.N366S	DMGDH_ENST00000540686.1_Intron|DMGDH_ENST00000380311.4_Missense_Mutation_p.N165S	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	366					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		ATTGACAACATTGATGATGTC	0.458													T|||	38	0.00758786	0.0	0.0072	5008	,	,		18599	0.0		0.0179	False		,,,				2504	0.0153				p.N366S		Atlas-SNP	.											.	DMGDH	88	.	0			c.A1097G						PASS	.	T	SER/ASN	8,4398	12.9+/-30.5	0,8,2195	128.0	117.0	120.0		1097	3.0	0.5	5	dbSNP_131	120	112,8488	61.0+/-122.8	1,110,4189	yes	missense	DMGDH	NM_013391.2	46	1,118,6384	CC,CT,TT		1.3023,0.1816,0.9227	benign	366/867	78338202	120,12886	2203	4300	6503	SO:0001583	missense	29958	exon7			ACAACATTGATGA	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.1097A>G	5.37:g.78338202T>C	ENSP00000255189:p.Asn366Ser	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	204	96	0.470588	NM_013391	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	T	11.11	1.541978	0.27563	0.001816	0.013023	ENSG00000132837	ENST00000255189;ENST00000523732;ENST00000380311;ENST00000539598	T;T;T	0.80824	-1.42;-1.42;-1.42	5.44	3.01	0.34805	FAD dependent oxidoreductase (1);	0.194937	0.52532	D	0.000068	T	0.33644	0.0870	N	0.01649	-0.78	0.80722	D	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.09377	0.004;0.002;0.002	T	0.15235	-1.0444	10	0.10377	T	0.69	.	8.0518	0.30583	0.0:0.0714:0.1365:0.7921	.	165;216;366	F8W6P8;F5H1C7;Q9UI17	.;.;M2GD_HUMAN	S	366;205;165;216	ENSP00000255189:N366S;ENSP00000430972:N205S;ENSP00000369667:N165S	ENSP00000255189:N366S	N	-	2	0	DMGDH	78373958	1.000000	0.71417	0.481000	0.27354	0.903000	0.53119	3.289000	0.51747	0.366000	0.24427	0.529000	0.55759	AAT	T|0.990;C|0.010	0.010	strong		0.458	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
EFCAB6	64800	hgsc.bcm.edu	37	22	44178103	44178103	+	Silent	SNP	T	T	C	rs74957153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:44178103T>C	ENST00000262726.7	-	3	349	c.96A>G	c.(94-96)gtA>gtG	p.V32V	EFCAB6_ENST00000356087.4_5'UTR|EFCAB6_ENST00000358439.4_5'UTR|EFCAB6_ENST00000396231.2_Intron	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	32					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				TCCTTGAATATACTCTACACG	0.358													T|||	573	0.114417	0.0121	0.0375	5008	,	,		19553	0.2212		0.0924	False		,,,				2504	0.2198				p.V32V		Atlas-SNP	.											.	EFCAB6	177	.	0			c.A96G						PASS	.	T	,	118,4288	89.2+/-127.9	0,118,2085	206.0	191.0	196.0		96,	-8.0	0.0	22	dbSNP_131	196	894,7706	200.2+/-244.0	48,798,3454	yes	coding-synonymous,intron	EFCAB6	NM_022785.3,NM_198856.2	,	48,916,5539	CC,CT,TT		10.3953,2.6782,7.781	,	32/1502,	44178103	1012,11994	2203	4300	6503	SO:0001819	synonymous_variant	64800	exon3			TGAATATACTCTA	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.96A>G	22.37:g.44178103T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Silent	SNP	ENST00000262726.7	37	CCDS14049.1																																																																																			T|0.921;C|0.079	0.079	strong		0.358	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
C9orf139	401563	hgsc.bcm.edu	37	9	139929435	139929435	+	Missense_Mutation	SNP	A	A	G	rs12337910	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139929435A>G	ENST00000314330.2	+	3	2016	c.502A>G	c.(502-504)Aaa>Gaa	p.K168E	RP11-229P13.20_ENST00000457302.2_lincRNA|FUT7_ENST00000314412.6_5'Flank	NM_207511.1	NP_997394.1	Q6ZV77	CI139_HUMAN	chromosome 9 open reading frame 139	168			K -> E (in dbSNP:rs12337910). {ECO:0000269|PubMed:15489334}.							cervix(1)|lung(2)	3	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.99e-05)|Epithelial(140;0.000493)		AGAGGAAAGAAAAGGGCATGA	0.622													a|||	443	0.0884585	0.1604	0.0937	5008	,	,		18289	0.0337		0.1004	False		,,,				2504	0.0317				p.K168E		Atlas-SNP	.											.	C9orf139	12	.	0			c.A502G						PASS	.		GLU/LYS	788,3608		86,616,1496	47.0	61.0	56.0		502	0.2	0.0	9	dbSNP_120	56	737,7853		31,675,3589	yes	missense	C9orf139	NM_207511.1	56	117,1291,5085	GG,GA,AA		8.5797,17.9254,11.7434	possibly-damaging	168/191	139929435	1525,11461	2198	4295	6493	SO:0001583	missense	401563	exon3			GAAAGAAAAGGGC		CCDS7023.1	9q34.3	2008-02-05			ENSG00000180539	ENSG00000180539			31426	protein-coding gene	gene with protein product							Standard	NM_207511		Approved	FLJ36268, FLJ42909	uc004ckp.1	Q6ZV77	OTTHUMG00000020959	ENST00000314330.2:c.502A>G	9.37:g.139929435A>G	ENSP00000318119:p.Lys168Glu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_207511	A2RUA3|B9EGW2|Q5SPY0|Q8N224	Missense_Mutation	SNP	ENST00000314330.2	37	CCDS7023.1	181	0.08287545787545787	71	0.1443089430894309	30	0.08287292817679558	20	0.03496503496503497	60	0.079155672823219	a	7.360	0.624706	0.14193	0.179254	0.085797	ENSG00000180539	ENST00000314330	T	0.54675	0.56	2.81	0.229	0.15368	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	P	0.37955	0.612	B	0.34385	0.181	T	0.05451	-1.0884	8	0.06757	T	0.87	.	2.3462	0.04272	0.6173:0.0:0.1427:0.24	rs12337910;rs56576329;rs60912531;rs12337910	168	Q6ZV77	CI139_HUMAN	E	168	ENSP00000318119:K168E	ENSP00000318119:K168E	K	+	1	0	C9orf139	139049256	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-2.228000	0.01209	0.021000	0.15133	-1.064000	0.02280	AAA	A|0.906;G|0.094	0.094	strong		0.622	C9orf139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055213.2	NM_207511	
HLA-C	3107	hgsc.bcm.edu	37	6	31237786	31237786	+	Silent	SNP	A	A	T	rs41556617	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31237786A>T	ENST00000376228.5	-	5	986	c.972T>A	c.(970-972)ctT>ctA	p.L324L	HLA-C_ENST00000383329.3_Silent_p.L324L	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	330					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CCACAGCTCCAAGGACAGCTA	0.577																																					p.L324L		Atlas-SNP	.											.	HLA-C	92	.	0			c.T972A						PASS	.	T		3008,1352		1348,312,520	42.0	46.0	45.0		972	-4.9	0.0	6	dbSNP_127	45	4845,3673		1931,983,1345	no	coding-synonymous	HLA-C	NM_002117.5		3279,1295,1865	TT,TA,AA		43.1205,31.0092,39.02		324/367	31237786	7853,5025	2180	4259	6439	SO:0001819	synonymous_variant	3107	exon5			AGCTCCAAGGACA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.972T>A	6.37:g.31237786A>T		Somatic	297	1	0.003367		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1																																																																																			A|0.263;T|0.737	0.737	strong		0.577	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
NIN	51199	hgsc.bcm.edu	37	14	51204996	51204996	+	Silent	SNP	C	C	T	rs11376	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:51204996C>T	ENST00000382041.3	-	27	5827	c.5637G>A	c.(5635-5637)caG>caA	p.Q1879Q	NIN_ENST00000453196.1_Silent_p.Q1879Q|NIN_ENST00000245441.5_Silent_p.Q1879Q|NIN_ENST00000389868.3_Silent_p.Q1166Q|NIN_ENST00000382043.4_Silent_p.Q1166Q|NIN_ENST00000324330.9_Silent_p.Q1879Q|NIN_ENST00000530997.2_Silent_p.Q1879Q	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1879					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					TGGATTCCAACTGACGGACCT	0.388			T	PDGFRB	MPD								T|||	2548	0.508786	0.7375	0.4092	5008	,	,		20711	0.3155		0.4851	False		,,,				2504	0.4939				p.Q1879Q		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.G5637A						PASS	.	T	,,,	3067,1339	447.1+/-348.2	1080,907,216	160.0	140.0	147.0		3498,5637,5637,5637	-11.4	0.0	14	dbSNP_52	147	4449,4151	566.0+/-388.6	1141,2167,992	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	,,,	2221,3074,1208	TT,TC,CC		48.2674,30.3904,42.2113	,,,	1166/1378,1879/2134,1879/2047,1879/2091	51204996	7516,5490	2203	4300	6503	SO:0001819	synonymous_variant	51199	exon27			TTCCAACTGACGG	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"""EF-hand domain containing"""	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.5637G>A	14.37:g.51204996C>T		Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	294	128	0.435374	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	37	CCDS32079.1	1100	0.5036630036630036	382	0.7764227642276422	155	0.4281767955801105	188	0.32867132867132864	375	0.4947229551451187	T	2.392	-0.339670	0.05243	0.696096	0.517326	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	5.72	-11.4	0.00090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27919	P	0.9383365	.	.	.	.	.	.	T	0.03587	-1.1022	3	.	.	.	-7.271	15.2542	0.73571	0.0776:0.6719:0.0784:0.172	rs11376;rs1134126;rs3015463;rs11554814;rs17295972;rs17350344;rs17792348;rs17846102;rs17859105;rs52836159;rs61295335;rs11376	.	.	.	I	1370	.	.	V	-	1	0	NIN	50274746	0.024000	0.19004	0.001000	0.08648	0.541000	0.35023	-0.727000	0.04931	-3.046000	0.00261	-0.360000	0.07572	GTT	C|0.452;T|0.548	0.548	strong		0.388	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
OSBPL10	114884	hgsc.bcm.edu	37	3	31725316	31725316	+	Silent	SNP	G	G	A	rs2278959	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:31725316G>A	ENST00000396556.2	-	8	1658	c.1536C>T	c.(1534-1536)caC>caT	p.H512H	OSBPL10_ENST00000438237.2_Silent_p.H448H	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	512					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		TTGGGTGTTCGTGACAGCTGG	0.537													G|||	1175	0.234625	0.0983	0.2853	5008	,	,		19004	0.3234		0.3141	False		,,,				2504	0.2096				p.H512H		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C1536T						PASS	.	G	,	576,3830	256.4+/-261.2	41,494,1668	142.0	126.0	132.0		1344,1536	-11.4	0.0	3	dbSNP_100	132	2420,6180	401.6+/-347.2	332,1756,2212	no	coding-synonymous,coding-synonymous	OSBPL10	NM_001174060.1,NM_017784.4	,	373,2250,3880	AA,AG,GG		28.1395,13.0731,23.0355	,	448/701,512/765	31725316	2996,10010	2203	4300	6503	SO:0001819	synonymous_variant	114884	exon8			GTGTTCGTGACAG	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.1536C>T	3.37:g.31725316G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	157	74	0.471338	NM_017784	B4E212|Q9BTU5	Silent	SNP	ENST00000396556.2	37	CCDS2651.1	585	0.26785714285714285	48	0.0975609756097561	115	0.31767955801104975	197	0.34440559440559443	225	0.29683377308707126	G	0.013	-1.643961	0.00792	0.130731	0.281395	ENSG00000144645	ENST00000429492	.	.	.	5.68	-11.4	0.00090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.08432	-1.0722	3	.	.	.	-2.2597	11.7127	0.51635	0.0745:0.0716:0.711:0.1428	rs2278959;rs17383217;rs60439437;rs2278959	.	.	.	M	281	.	.	T	-	2	0	OSBPL10	31700320	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.905000	0.00171	-3.447000	0.00161	-1.076000	0.02234	ACG	G|0.754;A|0.246	0.246	strong		0.537	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
MUC21	394263	hgsc.bcm.edu	37	6	30954978	30954978	+	Silent	SNP	C	C	T	rs149178110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954978C>T	ENST00000376296.3	+	2	1267	c.1026C>T	c.(1024-1026)gcC>gcT	p.A342A	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	342	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAGTGGGGCCAGCACAGCCA	0.637																																					p.A342A		Atlas-SNP	.											MUC21,NS,carcinoma,+1,1	MUC21	98	1	0			c.C1026T						scavenged	.						134.0	135.0	134.0					6																	30954978		2203	4298	6501	SO:0001819	synonymous_variant	394263	exon2			TGGGGCCAGCACA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1026C>T	6.37:g.30954978C>T		Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	134	29	0.216418	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			C|0.924;T|0.076	0.076	strong		0.637	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
SYT10	341359	hgsc.bcm.edu	37	12	33579408	33579408	+	Silent	SNP	A	A	T	rs10844596	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:33579408A>T	ENST00000228567.3	-	2	470	c.174T>A	c.(172-174)gcT>gcA	p.A58A	SYT10_ENST00000535526.1_5'UTR|SYT10_ENST00000567656.1_5'Flank	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	58					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					TGACAACGACAGCTAACAGGC	0.363													T|||	700	0.139776	0.2065	0.2219	5008	,	,		16193	0.0635		0.1054	False		,,,				2504	0.1053				p.A58A		Atlas-SNP	.											.	SYT10	109	.	0			c.T174A						PASS	.	T		780,3626	749.2+/-412.0	77,626,1500	51.0	48.0	49.0		174	-7.7	0.2	12	dbSNP_120	49	925,7675	774.1+/-407.7	51,823,3426	no	coding-synonymous	SYT10	NM_198992.3		128,1449,4926	TT,TA,AA		10.7558,17.7031,13.1093		58/524	33579408	1705,11301	2203	4300	6503	SO:0001819	synonymous_variant	341359	exon2			AACGACAGCTAAC	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"""Synaptotagmins"""	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.174T>A	12.37:g.33579408A>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_198992	Q495U2	Silent	SNP	ENST00000228567.3	37	CCDS8732.1																																																																																			A|0.868;T|0.132	0.132	strong		0.363	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992	
SIRT5	23408	hgsc.bcm.edu	37	6	13599303	13599303	+	Silent	SNP	C	C	T	rs3757261	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:13599303C>T	ENST00000606117.1	+	8	953	c.657C>T	c.(655-657)caC>caT	p.H219H	SIRT5_ENST00000359782.3_Silent_p.H201H|SIRT5_ENST00000379262.4_Silent_p.H219H|SIRT5_ENST00000397350.2_Silent_p.H111H	NM_012241.4	NP_036373.1			sirtuin 5											breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	11	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)			TGCGACCTCACGTCGTGTGGT	0.577													C|||	860	0.171725	0.0461	0.1787	5008	,	,		15440	0.2054		0.2425	False		,,,				2504	0.229				p.H219H		Atlas-SNP	.											SIRT5_ENST00000379262,caecum,carcinoma,0,2	SIRT5	45	2	0			c.C657T						PASS	.	C	,,,	307,4099	166.2+/-197.5	13,281,1909	124.0	111.0	116.0		603,333,657,657	-2.3	0.8	6	dbSNP_107	116	2002,6598	349.7+/-327.5	216,1570,2514	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SIRT5	NM_001193267.2,NM_001242827.1,NM_012241.4,NM_031244.3	,,,	229,1851,4423	TT,TC,CC		23.2791,6.9678,17.7533	,,,	201/293,111/203,219/311,219/300	13599303	2309,10697	2203	4300	6503	SO:0001819	synonymous_variant	23408	exon8			ACCTCACGTCGTG	AF083110	CCDS4526.1, CCDS4527.1, CCDS54966.1, CCDS56398.1	6p23	2010-08-05	2010-06-25		ENSG00000124523	ENSG00000124523			14933	protein-coding gene	gene with protein product		604483	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 5"", ""sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae)"""			10381378	Standard	NM_012241		Approved		uc003nay.3	Q9NXA8	OTTHUMG00000014278	ENST00000606117.1:c.657C>T	6.37:g.13599303C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_012241		Silent	SNP	ENST00000606117.1	37	CCDS4526.1																																																																																			C|0.829;T|0.171	0.171	strong		0.577	SIRT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039908.2		
TMEM123	114908	hgsc.bcm.edu	37	11	102272839	102272839	+	Missense_Mutation	SNP	C	C	A	rs11547915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:102272839C>A	ENST00000398136.2	-	3	676	c.256G>T	c.(256-258)Gtc>Ttc	p.V86F	TMEM123_ENST00000532161.1_5'UTR|TMEM123_ENST00000361236.3_Missense_Mutation_p.V67F|TMEM123_ENST00000525577.1_5'UTR	NM_052932.2	NP_443164.2	Q8N131	PORIM_HUMAN	transmembrane protein 123	86	Thr-rich.		V -> F (in dbSNP:rs11547915).		oncosis (GO:0070267)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(3)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		ATGGTGGTGACCGTTGTATTA	0.438													C|||	98	0.0195687	0.0015	0.0274	5008	,	,		15296	0.004		0.0616	False		,,,				2504	0.0112				p.V86F		Atlas-SNP	.											.	TMEM123	16	.	0			c.G256T						PASS	.	C	PHE/VAL	48,4004		0,48,1978	367.0	343.0	351.0		256	-4.2	0.0	11	dbSNP_120	351	591,7785		24,543,3621	yes	missense	TMEM123	NM_052932.2	50	24,591,5599	AA,AC,CC		7.0559,1.1846,5.1416	possibly-damaging	86/209	102272839	639,11789	2026	4188	6214	SO:0001583	missense	114908	exon3			TGGTGACCGTTGT	AL050161	CCDS41702.1	11q22.1	2014-01-02			ENSG00000152558	ENSG00000152558			30138	protein-coding gene	gene with protein product	"""pro oncosis receptor inducing membrane injury gene"""	606356				11481458, 24318988	Standard	NM_052932		Approved	PORIMIN, KCT3	uc001pha.3	Q8N131	OTTHUMG00000167326	ENST00000398136.2:c.256G>T	11.37:g.102272839C>A	ENSP00000381204:p.Val86Phe	Somatic	426	1	0.00234742		WXS	Illumina HiSeq	Phase_I	428	172	0.401869	NM_052932	Q8IWS2|Q96QV2	Missense_Mutation	SNP	ENST00000398136.2	37	CCDS41702.1	61	0.027930402930402932	2	0.0040650406504065045	7	0.019337016574585635	2	0.0034965034965034965	50	0.06596306068601583	C	16.42	3.117415	0.56505	0.011846	0.070559	ENSG00000152558	ENST00000361236;ENST00000398136;ENST00000526676	T;T;T	0.53857	1.82;1.78;0.6	5.44	-4.21	0.03812	.	4.895910	0.00166	N	0.000010	T	0.03434	0.0099	N	0.22421	0.69	0.09310	N	0.999999	P;P	0.45011	0.662;0.848	B;B	0.43536	0.295;0.423	T	0.10382	-1.0632	10	0.62326	D	0.03	18.6864	1.6371	0.02744	0.1142:0.3345:0.202:0.3493	rs11547915;rs52827131;rs60824292;rs11547915	67;86	Q8N131-2;Q8N131	.;PORIM_HUMAN	F	67;86;44	ENSP00000355285:V67F;ENSP00000381204:V86F;ENSP00000435842:V44F	ENSP00000355285:V67F	V	-	1	0	TMEM123	101778049	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.354000	0.01089	-1.099000	0.03034	0.563000	0.77884	GTC	C|0.963;A|0.037	0.037	strong		0.438	TMEM123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394178.1	NM_052932	
NOTCH4	4855	hgsc.bcm.edu	37	6	32189032	32189032	+	Silent	SNP	T	T	C	rs415929	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32189032T>C	ENST00000375023.3	-	4	660	c.522A>G	c.(520-522)acA>acG	p.T174T		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	174	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TCTGGGGGTATGTGGCCAGAC	0.602													C|||	1402	0.279952	0.2088	0.2594	5008	,	,		18784	0.2421		0.3519	False		,,,				2504	0.3558				p.T174T		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A522G						PASS	.	C		659,2361		67,525,918	75.0	69.0	71.0		522	-8.9	0.1	6	dbSNP_80	71	1733,3685		282,1169,1258	yes	coding-synonymous	NOTCH4	NM_004557.3		349,1694,2176	CC,CT,TT		31.986,21.8212,28.3479		174/2004	32189032	2392,6046	1510	2709	4219	SO:0001819	synonymous_variant	4855	exon4			GGGGTATGTGGCC		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.522A>G	6.37:g.32189032T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			T|0.703;C|0.297	0.297	strong		0.602	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
ANKRD26	22852	hgsc.bcm.edu	37	10	27381349	27381349	+	Silent	SNP	T	T	C	rs2297145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:27381349T>C	ENST00000376087.4	-	4	789	c.624A>G	c.(622-624)gtA>gtG	p.V208V	ANKRD26_ENST00000436985.2_Silent_p.V208V	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	208					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CCAACTTATCTACTGCATTTA	0.313													C|||	1736	0.346645	0.3207	0.1873	5008	,	,		17605	0.5427		0.2137	False		,,,				2504	0.4294				p.V208V		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A624G						PASS	.	C		1119,2493		165,789,852	97.0	95.0	96.0		624	-8.6	0.0	10	dbSNP_100	96	1351,6793		102,1147,2823	no	coding-synonymous	ANKRD26	NM_014915.2		267,1936,3675	CC,CT,TT		16.5889,30.9801,21.0105		208/1711	27381349	2470,9286	1806	4072	5878	SO:0001819	synonymous_variant	22852	exon4			CTTATCTACTGCA	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.624A>G	10.37:g.27381349T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	24	0.369231	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Silent	SNP	ENST00000376087.4	37	CCDS41499.1																																																																																			T|0.691;C|0.309	0.309	strong		0.313	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
SMC6	79677	hgsc.bcm.edu	37	2	17884495	17884495	+	Missense_Mutation	SNP	C	C	T	rs1065381	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:17884495C>T	ENST00000448223.2	-	19	2340	c.2071G>A	c.(2071-2073)Gcc>Acc	p.A691T	SMC6_ENST00000351948.4_Missense_Mutation_p.A691T|SMC6_ENST00000402989.1_Missense_Mutation_p.A691T|SMC6_ENST00000381272.4_Missense_Mutation_p.A717T	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	691			A -> T (in dbSNP:rs1065381). {ECO:0000269|PubMed:11408570, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTTTCAAGGGCAGATAAATGT	0.299													C|||	1034	0.20647	0.3548	0.2161	5008	,	,		14389	0.0119		0.3241	False		,,,				2504	0.0787				p.A691T		Atlas-SNP	.											.	SMC6	102	.	0			c.G2071A						PASS	.	C	THR/ALA,THR/ALA	1395,3009	438.0+/-345.2	215,965,1022	78.0	82.0	81.0		2071,2071	1.5	1.0	2	dbSNP_86	81	2866,5730	447.2+/-361.5	471,1924,1903	yes	missense,missense	SMC6	NM_001142286.1,NM_024624.5	58,58	686,2889,2925	TT,TC,CC		33.3411,31.6757,32.7769	benign,benign	691/1092,691/1092	17884495	4261,8739	2202	4298	6500	SO:0001583	missense	79677	exon19			CAAGGGCAGATAA	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"""Structural maintenance of chromosomes proteins"""	20466	protein-coding gene	gene with protein product		609387	"""SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"""	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.2071G>A	2.37:g.17884495C>T	ENSP00000404092:p.Ala691Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	37	CCDS1690.1	492	0.22527472527472528	153	0.31097560975609756	89	0.24585635359116023	12	0.02097902097902098	238	0.31398416886543534	C	9.006	0.981245	0.18812	0.316757	0.333411	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.31769	1.57;1.57;1.57;1.57;1.48	5.75	1.55	0.23275	RecF/RecN/SMC (1);	0.528124	0.23204	N	0.050752	T	0.00012	0.0000	N	0.08118	0	0.39475	P	0.032214999999999994	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.002;0.003;0.002	T	0.46830	-0.9163	9	0.16420	T	0.52	.	4.2671	0.10768	0.2883:0.4449:0.0:0.2668	rs1065381;rs52791607;rs57702280;rs1065381	717;717;691	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	T	691;691;717;691;717	ENSP00000404092:A691T;ENSP00000323439:A691T;ENSP00000370672:A717T;ENSP00000384539:A691T;ENSP00000408644:A717T	ENSP00000323439:A691T	A	-	1	0	SMC6	17747976	1.000000	0.71417	0.990000	0.47175	0.186000	0.23388	0.736000	0.26130	0.371000	0.24564	0.579000	0.79373	GCC	C|0.738;T|0.262	0.262	strong		0.299	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624	
FMN1	342184	hgsc.bcm.edu	37	15	33357262	33357262	+	Missense_Mutation	SNP	A	A	G	rs2306277	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:33357262A>G	ENST00000559047.1	-	3	2056	c.2057T>C	c.(2056-2058)cTg>cCg	p.L686P	FMN1_ENST00000559150.1_5'UTR|FMN1_ENST00000558197.1_Missense_Mutation_p.L463P|FMN1_ENST00000334528.9_Missense_Mutation_p.L463P|FMN1_ENST00000561249.1_Intron			Q68DA7	FMN1_HUMAN	formin 1	686	Mediates interaction with alpha-catenin. {ECO:0000250}.		L -> P (in dbSNP:rs2306277). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L463P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		CTGCTCAGTCAGGCTGTGGTC	0.458													G|||	2253	0.44988	0.4342	0.5634	5008	,	,		16299	0.2054		0.5646	False		,,,				2504	0.5245				p.L463P		Atlas-SNP	.											FMN1_ENST00000334528,NS,carcinoma,0,1	FMN1	174	1	1	Substitution - Missense(1)	stomach(1)	c.T1388C						PASS	.	G	PRO/LEU	1766,2068		396,974,547	147.0	142.0	143.0		1388	5.1	1.0	15	dbSNP_100	143	4721,3531		1352,2017,757	yes	missense	FMN1	NM_001103184.2	98	1748,2991,1304	GG,GA,AA		42.7896,46.0616,46.3263	benign	463/1197	33357262	6487,5599	1917	4126	6043	SO:0001583	missense	342184	exon2			TCAGTCAGGCTGT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2057T>C	15.37:g.33357262A>G	ENSP00000454047:p.Leu686Pro	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	185	91	0.491892	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		960	0.43956043956043955	194	0.3943089430894309	212	0.585635359116022	127	0.22202797202797203	427	0.5633245382585752	G	2.387	-0.340750	0.05243	0.460616	0.572104	ENSG00000248905	ENST00000334528	T	0.31510	1.49	6.04	5.13	0.70059	.	0.052415	0.85682	N	0.000000	T	0.00012	0.0000	N	0.01009	-1.055	.	.	.	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41610	-0.9499	9	0.06494	T	0.89	.	13.1464	0.59463	0.1287:0.0:0.8713:0.0	rs2306277;rs17235540;rs56901218;rs2306277	463;463	Q68DA7-3;Q68DA7-5	.;.	P	463	ENSP00000333950:L463P	ENSP00000333950:L463P	L	-	2	0	FMN1	31144554	1.000000	0.71417	0.999000	0.59377	0.474000	0.32979	6.540000	0.73861	0.916000	0.36871	-0.215000	0.12644	CTG	G|0.444;N|0.000	0.444	strong		0.458	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
SLX4	84464	hgsc.bcm.edu	37	16	3639827	3639827	+	Missense_Mutation	SNP	G	G	A	rs3810813	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:3639827G>A	ENST00000294008.3	-	12	4452	c.3812C>T	c.(3811-3813)tCc>tTc	p.S1271F		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1271	Interaction with PLK1 and TERF2-TERF2IP.		S -> F (in dbSNP:rs3810813). {ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TTGGGTCTGGGAAGAACAGTC	0.652								Direct reversal of damage					G|||	315	0.0628994	0.0	0.0663	5008	,	,		15111	0.1429		0.0537	False		,,,				2504	0.0726				p.S1271F		Atlas-SNP	.											SLX4,colon,carcinoma,0,1	SLX4	173	1	0			c.C3812T						PASS	.	G	PHE/SER	58,4336	46.7+/-81.2	0,58,2139	75.0	75.0	75.0		3812	5.1	0.9	16	dbSNP_107	75	469,8131	129.2+/-187.3	12,445,3843	yes	missense	SLX4	NM_032444.2	155	12,503,5982	AA,AG,GG		5.4535,1.32,4.0557	probably-damaging	1271/1835	3639827	527,12467	2197	4300	6497	SO:0001583	missense	84464	exon12			GTCTGGGAAGAAC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.3812C>T	16.37:g.3639827G>A	ENSP00000294008:p.Ser1271Phe	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	163	0.07463369963369963	0	0.0	27	0.07458563535911603	90	0.15734265734265734	46	0.06068601583113457	G	19.87	3.907943	0.72868	0.0132	0.054535	ENSG00000188827	ENST00000294008	T	0.36340	1.26	6.07	5.11	0.69529	.	0.284216	0.30649	N	0.009179	T	0.00300	0.0009	L	0.59436	1.845	0.34090	P	0.33942399999999995	D	0.76494	0.999	D	0.68765	0.96	T	0.02975	-1.1087	9	0.87932	D	0	.	12.1585	0.54091	0.0775:0.0:0.9225:0.0	rs3810813;rs17183645;rs52833846;rs3810813	1271	Q8IY92	SLX4_HUMAN	F	1271	ENSP00000294008:S1271F	ENSP00000294008:S1271F	S	-	2	0	SLX4	3579828	0.909000	0.30893	0.866000	0.34008	0.792000	0.44763	3.057000	0.49931	2.884000	0.98904	0.655000	0.94253	TCC	G|0.943;A|0.057	0.057	strong		0.652	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
PTCH1	5727	hgsc.bcm.edu	37	9	98238379	98238379	+	Silent	SNP	A	A	G	rs1805155	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:98238379A>G	ENST00000331920.6	-	12	1964	c.1665T>C	c.(1663-1665)aaT>aaC	p.N555N	PTCH1_ENST00000437951.1_Silent_p.N489N|PTCH1_ENST00000375274.2_Silent_p.N554N|PTCH1_ENST00000418258.1_Silent_p.N404N|PTCH1_ENST00000430669.2_Silent_p.N489N|PTCH1_ENST00000421141.1_Silent_p.N404N|PTCH1_ENST00000429896.2_Silent_p.N404N	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	555	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				AGGCTGTGACATTGCTGATGG	0.582													A|||	559	0.111621	0.1687	0.0764	5008	,	,		18339	0.1131		0.1093	False		,,,				2504	0.0603				p.N555N		Atlas-SNP	.											.	PTCH1	1850	.	0			c.T1665C						PASS	.	A	,,,,,,	813,3593	323.7+/-298.2	78,657,1468	86.0	63.0	71.0		1665,1467,1662,1212,1212,1212,1212	-4.1	1.0	9	dbSNP_89	71	890,7710	199.0+/-243.2	48,794,3458	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	,,,,,,	126,1451,4926	GG,GA,AA		10.3488,18.4521,13.094	,,,,,,	555/1448,489/1382,554/1447,404/1297,404/1297,404/1297,404/1297	98238379	1703,11303	2203	4300	6503	SO:0001819	synonymous_variant	5727	exon12			TGTGACATTGCTG	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1665T>C	9.37:g.98238379A>G		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	43	17	0.395349	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																			A|0.874;G|0.126	0.126	strong		0.582	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
BRCA1	672	hgsc.bcm.edu	37	17	41244435	41244435	+	Missense_Mutation	SNP	T	T	C	rs80357920|rs16941	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:41244435T>C	ENST00000357654.3	-	10	3231	c.3113A>G	c.(3112-3114)gAa>gGa	p.E1038G	BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.E1038G|BRCA1_ENST00000471181.2_Missense_Mutation_p.E1038G|BRCA1_ENST00000309486.4_Missense_Mutation_p.E742G|BRCA1_ENST00000354071.3_Missense_Mutation_p.E1038G|BRCA1_ENST00000493795.1_Missense_Mutation_p.E991G|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1038			E -> G (common polymorphism; dbSNP:rs16941). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:15365993, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7894493, ECO:0000269|Ref.6}.		androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TGAGCTGGCTTCTTTAAAAAC	0.358			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			T|||	1681	0.335663	0.1573	0.3646	5008	,	,		20076	0.371		0.3569	False		,,,				2504	0.498				p.E1038G		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.A3113G	GRCh37	CM032861	BRCA1	M	rs16941	PASS	.	T	GLY/GLU,GLY/GLU,,,GLY/GLU	830,3576	326.4+/-299.6	76,678,1449	128.0	122.0	124.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3113,2972,,,3113	-1.0	0.5	17	dbSNP_60	124	2799,5801	440.8+/-359.6	444,1911,1945	yes	missense,missense,intron,intron,missense	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	98,98,,,98	520,2589,3394	CC,CT,TT		32.5465,18.8379,27.9025	benign,benign,,,benign	1038/1864,991/1817,,,1038/1885	41244435	3629,9377	2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		CTGGCTTCTTTAA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.3113A>G	17.37:g.41244435T>C	ENSP00000350283:p.Glu1038Gly	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	241	110	0.456432	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	662	0.3031135531135531	63	0.12804878048780488	139	0.3839779005524862	189	0.3304195804195804	271	0.3575197889182058	T	11.99	1.803390	0.31869	0.188379	0.325465	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24;-1.24	5.23	-0.974	0.10293	.	0.514353	0.17997	N	0.155009	T	0.00012	0.0000	M	0.81341	2.54	0.80722	P	0.0	B;B;B;B;P;B	0.50528	0.012;0.034;0.112;0.237;0.936;0.058	B;B;B;B;P;B	0.49301	0.006;0.006;0.118;0.177;0.606;0.065	T	0.04593	-1.0940	9	0.59425	D	0.04	-1.0083	6.1615	0.20366	0.1188:0.3513:0.0:0.5299	rs16941;rs16941	1038;997;1038;1038;1038;1038	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	G	1038;1038;1038;1038;742;1038;991	ENSP00000350283:E1038G;ENSP00000326002:E1038G;ENSP00000246907:E1038G;ENSP00000310938:E742G;ENSP00000418960:E1038G;ENSP00000418775:E991G	ENSP00000310938:E742G	E	-	2	0	BRCA1	38497961	0.000000	0.05858	0.509000	0.27700	0.856000	0.48823	-0.480000	0.06559	0.112000	0.17975	0.455000	0.32223	GAA	T|0.716;C|0.284	0.284	strong		0.358	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
HSPG2	3339	hgsc.bcm.edu	37	1	22159774	22159774	+	Silent	SNP	G	G	A	rs2229486	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22159774G>A	ENST00000374695.3	-	80	11161	c.11082C>T	c.(11080-11082)ccC>ccT	p.P3694P	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3694	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CGGCTGAGTCGGGCCGGAAGG	0.607													G|||	430	0.0858626	0.1672	0.0519	5008	,	,		20816	0.0		0.0676	False		,,,				2504	0.1074				p.P3694P		Atlas-SNP	.											.	HSPG2	311	.	0			c.C11082T						PASS	.	G		762,3644	310.2+/-291.5	67,628,1508	67.0	59.0	62.0		11082	-9.6	0.8	1	dbSNP_98	62	660,7940	165.9+/-218.0	26,608,3666	no	coding-synonymous	HSPG2	NM_005529.5		93,1236,5174	AA,AG,GG		7.6744,17.2946,10.9334		3694/4392	22159774	1422,11584	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon80			TGAGTCGGGCCGG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.11082C>T	1.37:g.22159774G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			T|0.000;G|0.907;C|0.000;A|0.093	0.093	strong		0.607	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
CAV2	858	hgsc.bcm.edu	37	7	116146074	116146074	+	Missense_Mutation	SNP	C	C	G	rs8940	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116146074C>G	ENST00000222693.4	+	3	780	c.388C>G	c.(388-390)Cag>Gag	p.Q130E	CAV2_ENST00000462876.1_3'UTR|CAV2_ENST00000343213.2_Missense_Mutation_p.A67G	NM_001206747.1|NM_001206748.1|NM_001233.4	NP_001193676.1|NP_001193677.1|NP_001224.1	P51636	CAV2_HUMAN	caveolin 2	130			Q -> E (in dbSNP:rs8940).		caveola assembly (GO:0070836)|endoplasmic reticulum organization (GO:0007029)|mitochondrion organization (GO:0007005)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of endothelial cell proliferation (GO:0001938)|protein oligomerization (GO:0051259)|regulation of mitosis (GO:0007088)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)|vesicle docking (GO:0048278)|vesicle fusion (GO:0006906)|vesicle organization (GO:0016050)	acrosomal membrane (GO:0002080)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	D1 dopamine receptor binding (GO:0031748)|protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(1)|skin(1)	3	all_epithelial(6;1.53e-06)|Lung NSC(10;0.00592)|all_lung(10;0.00642)		STAD - Stomach adenocarcinoma(10;0.00878)			GCCTTCAGTGCAGACAATATG	0.448													C|||	706	0.140974	0.1921	0.1499	5008	,	,		19664	0.0089		0.164	False		,,,				2504	0.1779				p.Q130E		Atlas-SNP	.											.	CAV2	10	.	0			c.C388G						PASS	.	C	GLU/GLN,GLU/GLN,GLU/GLN,GLY/ALA	845,3561	334.1+/-303.3	74,697,1432	163.0	142.0	149.0		349,139,388,200	5.9	1.0	7	dbSNP_52	149	1670,6930	307.8+/-308.6	186,1298,2816	yes	missense,missense,missense,missense	CAV2	NM_001206747.1,NM_001206748.1,NM_001233.4,NM_198212.2	29,29,29,60	260,1995,4248	GG,GC,CC		19.4186,19.1784,19.3372	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	117/150,47/80,130/163,67/113	116146074	2515,10491	2203	4300	6503	SO:0001583	missense	858	exon3			TCAGTGCAGACAA	AF035752	CCDS5765.1, CCDS5766.1	7q31	2006-02-09			ENSG00000105971	ENSG00000105971			1528	protein-coding gene	gene with protein product		601048				8552590, 10087206	Standard	NM_001233		Approved	CAV	uc003vid.3	P51636	OTTHUMG00000023414	ENST00000222693.4:c.388C>G	7.37:g.116146074C>G	ENSP00000222693:p.Gln130Glu	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	261	120	0.45977	NM_001233	A4D0U2|Q9UGM7	Missense_Mutation	SNP	ENST00000222693.4	37	CCDS5766.1	264|264	0.12087912087912088|0.12087912087912088	90|90	0.18292682926829268|0.18292682926829268	55|55	0.15193370165745856|0.15193370165745856	4|4	0.006993006993006993|0.006993006993006993	115|115	0.1517150395778364|0.1517150395778364	C|C	25.5|25.5	4.645540|4.645540	0.87859|0.87859	0.191784|0.191784	0.194186|0.194186	ENSG00000105971|ENSG00000105971	ENST00000343213|ENST00000222693	.|D	.|0.92545	.|-3.06	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	.|0.163752	.|0.56097	.|D	.|0.000024	T|T	0.01320|0.01320	0.0043|0.0043	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	D|B	0.69078|0.34241	0.997|0.444	P|B	0.61940|0.41135	0.896|0.348	T|T	0.35201|0.35201	-0.9798|-0.9798	6|8	0.87932|0.33141	D|T	0|0.24	-8.8607|-8.8607	20.5827|20.5827	0.99408|0.99408	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs8940;rs1055892;rs3173921;rs11539795;rs17515863;rs52790866;rs8940|rs8940;rs1055892;rs3173921;rs11539795;rs17515863;rs52790866;rs8940	67|130	P51636-3|P51636	.|CAV2_HUMAN	G|E	67|130	.|ENSP00000222693:Q130E	ENSP00000345679:A67G|ENSP00000222693:Q130E	A|Q	+|+	2|1	0|0	CAV2|CAV2	115933310|115933310	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.355000|4.355000	0.59424|0.59424	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCA|CAG	C|0.830;G|0.170	0.170	strong		0.448	CAV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059735.4	NM_001233	
MYOM1	8736	hgsc.bcm.edu	37	18	3215156	3215156	+	Silent	SNP	C	C	G	rs386800438|rs1662316	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:3215156C>G	ENST00000356443.4	-	2	399	c.66G>C	c.(64-66)gtG>gtC	p.V22V	MYOM1_ENST00000400569.3_Silent_p.V22V|MYOM1_ENST00000261606.7_Silent_p.V22V|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	22			V -> L (in dbSNP:rs1791085).		muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGGTGCTGCGCACGTCCTTGT	0.622													G|||	646	0.128994	0.1346	0.0879	5008	,	,		16440	0.1865		0.0934	False		,,,				2504	0.1278				p.V22V		Atlas-SNP	.											.	MYOM1	192	.	0			c.G66C						PASS	.	G	,	504,3708		30,444,1632	56.0	60.0	59.0		66,66	-11.3	0.0	18	dbSNP_89	59	728,7756		30,668,3544	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	60,1112,5176	GG,GC,CC		8.5809,11.9658,9.7038	,	22/1686,22/1590	3215156	1232,11464	2106	4242	6348	SO:0001819	synonymous_variant	8736	exon2			GCTGCGCACGTCC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.66G>C	18.37:g.3215156C>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			C|0.891;G|0.109	0.109	strong		0.622	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
ACTN2	88	hgsc.bcm.edu	37	1	236925844	236925844	+	Silent	SNP	G	G	A	rs12063382	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:236925844G>A	ENST00000366578.4	+	21	2776	c.2610G>A	c.(2608-2610)tcG>tcA	p.S870S	ACTN2_ENST00000542672.1_Silent_p.S870S|ACTN2_ENST00000546208.1_Silent_p.S364S	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	870					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			CCGCCTACTCGGGCCCAGGCA	0.587													G|||	982	0.196086	0.2057	0.1729	5008	,	,		16949	0.2183		0.171	False		,,,				2504	0.2025				p.S870S		Atlas-SNP	.											.	ACTN2	191	.	0			c.G2610A						PASS	.	G		828,3578	327.7+/-300.2	87,654,1462	55.0	51.0	52.0		2610	-10.9	0.1	1	dbSNP_120	52	1197,7403	242.9+/-272.7	72,1053,3175	yes	coding-synonymous	ACTN2	NM_001103.2		159,1707,4637	AA,AG,GG		13.9186,18.7926,15.5697		870/895	236925844	2025,10981	2203	4300	6503	SO:0001819	synonymous_variant	88	exon21			CTACTCGGGCCCA	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"""EF-hand domain containing"""	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.2610G>A	1.37:g.236925844G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Silent	SNP	ENST00000366578.4	37	CCDS1613.1																																																																																			G|0.832;A|0.168	0.168	strong		0.587	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103	
MTRR	4552	hgsc.bcm.edu	37	5	7897061	7897061	+	Silent	SNP	T	T	C	rs6874544	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7897061T>C	ENST00000264668.2	+	13	1872	c.1842T>C	c.(1840-1842)taT>taC	p.Y614Y	MTRR_ENST00000440940.2_Silent_p.Y587Y	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	614					cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	ATAGGGATTATCTATTCAGGT	0.368													T|||	40	0.00798722	0.0015	0.0245	5008	,	,		18320	0.0		0.0189	False		,,,				2504	0.002				p.Y614Y		Atlas-SNP	.											.	MTRR	74	.	0			c.T1842C						PASS	.	T	,	46,4360	48.2+/-83.0	0,46,2157	56.0	59.0	58.0		1761,1842	-3.0	0.0	5	dbSNP_116	58	207,8393	88.1+/-150.5	2,203,4095	yes	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,249,6252	CC,CT,TT		2.407,1.044,1.9453	,	587/699,614/726	7897061	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon13			GGATTATCTATTC	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1842T>C	5.37:g.7897061T>C		Somatic	370	1	0.0027027		WXS	Illumina HiSeq	Phase_I	379	189	0.498681	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			T|0.981;C|0.019	0.019	strong		0.368	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
DGCR6	8214	hgsc.bcm.edu	37	22	18898468	18898468	+	Missense_Mutation	SNP	G	G	A	rs139729355		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:18898468G>A	ENST00000331444.6	+	4	592	c.440G>A	c.(439-441)cGg>cAg	p.R147Q	DGCR6_ENST00000436645.1_3'UTR|DGCR6_ENST00000413981.1_Missense_Mutation_p.R11Q	NM_005675.4	NP_005666.2	Q14129	DGCR6_HUMAN	DiGeorge syndrome critical region gene 6	147					cell adhesion (GO:0007155)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|upper_aerodigestive_tract(1)	3						GAGCTGGACCGGAAGGTGGCT	0.682													.|||	1	0.000199681	0.0	0.0	5008	,	,		14833	0.0		0.001	False		,,,				2504	0.0				p.R147Q		Atlas-SNP	.											.	DGCR6	12	.	0			c.G440A						PASS	.	G	GLN/ARG	1,4405	4.2+/-10.8	0,1,2202	96.0	79.0	84.0		440	3.3	1.0	22	dbSNP_134	84	40,8558	26.3+/-74.7	0,40,4259	no	missense	DGCR6	NM_005675.4	43	0,41,6461	AA,AG,GG		0.4652,0.0227,0.3153	benign	147/221	18898468	41,12963	2203	4299	6502	SO:0001583	missense	8214	exon4			TGGACCGGAAGGT	X96484	CCDS13753.1	22q11.21	2008-06-12			ENSG00000183628	ENSG00000183628			2846	protein-coding gene	gene with protein product		601279				8733130	Standard	NM_005675		Approved		uc002zoh.4	Q14129	OTTHUMG00000150162	ENST00000331444.6:c.440G>A	22.37:g.18898468G>A	ENSP00000331681:p.Arg147Gln	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_005675	B2RCH5|D3DX15|G5E9J8|Q9BY28	Missense_Mutation	SNP	ENST00000331444.6	37	CCDS13753.1	.	.	.	.	.	.	.	.	.	.	g	10.25	1.299748	0.23650	2.27E-4	0.004652	ENSG00000183628	ENST00000331444;ENST00000436645	T	0.24151	1.87	4.31	3.3	0.37823	.	0.058938	0.64402	D	0.000001	T	0.05044	0.0135	N	0.00569	-1.365	0.41386	D	0.987582	B	0.18741	0.03	B	0.12837	0.008	T	0.39035	-0.9633	10	0.02654	T	1	-40.3259	5.9322	0.19144	0.2095:0.0:0.7905:0.0	.	147	Q14129	DGCR6_HUMAN	Q	147;67	ENSP00000331681:R147Q	ENSP00000331681:R147Q	R	+	2	0	DGCR6	17278468	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.351000	0.59398	2.421000	0.82119	0.430000	0.28490	CGG	G|0.997;A|0.003	0.003	strong		0.682	DGCR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316631.2	NM_005675	
SBNO2	22904	hgsc.bcm.edu	37	19	1122201	1122201	+	Silent	SNP	G	G	A	rs62131221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1122201G>A	ENST00000361757.3	-	11	1323	c.1086C>T	c.(1084-1086)ggC>ggT	p.G362G	SBNO2_ENST00000587024.1_Silent_p.G362G|SBNO2_ENST00000438103.2_Silent_p.G305G	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	362					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTGCTGGCCGCCGGCCTGGC	0.662													g|||	357	0.0712859	0.0121	0.1542	5008	,	,		13941	0.002		0.17	False		,,,				2504	0.0624				p.G362G		Atlas-SNP	.											.	SBNO2	112	.	0			c.C1086T						PASS	.	A	,	151,4199		3,145,2027	21.0	25.0	24.0		915,1086	-4.9	0.7	19	dbSNP_129	24	1379,7139		119,1141,2999	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	122,1286,5026	AA,AG,GG		16.1892,3.4713,11.89	,	305/1310,362/1367	1122201	1530,11338	2175	4259	6434	SO:0001819	synonymous_variant	22904	exon11			CTGGCCGCCGGCC	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.1086C>T	19.37:g.1122201G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			G|0.909;A|0.091	0.091	strong		0.662	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
C10orf62	414157	hgsc.bcm.edu	37	10	99350017	99350017	+	Missense_Mutation	SNP	G	G	C	rs7093840	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:99350017G>C	ENST00000370640.3	+	1	568	c.363G>C	c.(361-363)gaG>gaC	p.E121D	PI4K2A_ENST00000370649.3_Intron|PI4K2A_ENST00000555577.1_Intron|HOGA1_ENST00000370646.4_Intron|HOGA1_ENST00000370647.4_Intron	NM_001009997.2	NP_001009997.2	Q5T681	CJ062_HUMAN	chromosome 10 open reading frame 62	121			E -> D (in dbSNP:rs7093840). {ECO:0000269|PubMed:15489334}.							endometrium(2)|kidney(1)|lung(1)	4		Colorectal(252;0.162)		Epithelial(162;9.58e-11)|all cancers(201;8.62e-09)		CCACTGATGAGGCCACGTGGG	0.612													G|||	1327	0.264976	0.3124	0.2896	5008	,	,		17502	0.1369		0.3082	False		,,,				2504	0.271				p.E121D		Atlas-SNP	.											.	C10orf62	14	.	0			c.G363C						PASS	.	G	ASP/GLU,,	1472,2934	464.7+/-354.0	252,968,983	42.0	45.0	44.0		363,,	-0.3	0.4	10	dbSNP_116	44	2699,5901	425.6+/-355.0	414,1871,2015	yes	missense,intron,intron	HOGA1,C10orf62	NM_001009997.2,NM_001134670.1,NM_138413.3	45,,	666,2839,2998	CC,CG,GG		31.3837,33.409,32.0698	benign,,	121/224,,	99350017	4171,8835	2203	4300	6503	SO:0001583	missense	414157	exon1			TGATGAGGCCACG		CCDS31261.1	10q24.2	2012-05-31			ENSG00000203942	ENSG00000203942			23294	protein-coding gene	gene with protein product							Standard	NM_001009997		Approved	bA548K23.1	uc001koa.3	Q5T681	OTTHUMG00000018858	ENST00000370640.3:c.363G>C	10.37:g.99350017G>C	ENSP00000359674:p.Glu121Asp	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	20	18	0.9	NM_001009997	Q49A70|Q8N3Y6	Missense_Mutation	SNP	ENST00000370640.3	37	CCDS31261.1	555	0.2541208791208791	168	0.34146341463414637	91	0.2513812154696133	71	0.12412587412587413	225	0.29683377308707126	G	7.559	0.664348	0.14710	0.33409	0.313837	ENSG00000203942	ENST00000370640	T	0.51325	0.71	5.27	-0.32	0.12721	.	0.532357	0.15253	N	0.272205	T	0.00012	0.0000	N	0.12182	0.205	0.43214	P	0.0049120000000000275	B	0.20052	0.041	B	0.20184	0.028	T	0.43065	-0.9414	9	0.20519	T	0.43	-6.3121	4.6706	0.12687	0.1697:0.0:0.3888:0.4415	rs7093840;rs17853720;rs7093840	121	Q5T681	CJ062_HUMAN	D	121	ENSP00000359674:E121D	ENSP00000359674:E121D	E	+	3	2	C10orf62	99340007	0.000000	0.05858	0.396000	0.26296	0.743000	0.42351	-0.377000	0.07456	-0.074000	0.12820	0.643000	0.83706	GAG	G|0.706;C|0.294	0.294	strong		0.612	C10orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049723.1	NM_001009997	
GALNT14	79623	hgsc.bcm.edu	37	2	31348076	31348076	+	Intron	SNP	G	G	A	rs41280621	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:31348076G>A	ENST00000349752.5	-	1	769				GALNT14_ENST00000406653.1_5'UTR|GALNT14_ENST00000324589.5_Missense_Mutation_p.A58V|GALNT14_ENST00000356174.3_Intron|GALNT14_ENST00000420311.2_Intron	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14						cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					CACCTGAGGCGCCCAAGGGCT	0.512													G|||	13	0.00259585	0.0008	0.0043	5008	,	,		20381	0.0		0.004	False		,,,				2504	0.0051				p.A58V		Atlas-SNP	.											.	GALNT14	103	.	0			c.C173T						PASS	.																																			SO:0001627	intron_variant	79623	exon2			TGAGGCGCCCAAG	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	22946	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 14"""	608225	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"""			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.129+12747C>T	2.37:g.31348076G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001253826	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	37	CCDS1773.2	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	8.995	0.978610	0.18812	.	.	ENSG00000158089	ENST00000324589	T	0.58060	0.36	3.94	-7.88	0.01178	.	16.563700	0.00166	N	0.000002	T	0.23289	0.0563	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08493	-1.0719	9	0.30078	T	0.28	.	3.8926	0.09125	0.3307:0.1169:0.4366:0.1157	rs41280621	58	Q96FL9-3	.	V	58	ENSP00000314500:A58V	ENSP00000314500:A58V	A	-	2	0	GALNT14	31201580	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.055000	0.01397	-1.937000	0.01047	-4.460000	0.00005	GCG	G|0.994;A|0.006	0.006	strong		0.512	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572	
SIM2	6493	hgsc.bcm.edu	37	21	38117308	38117308	+	Missense_Mutation	SNP	C	C	A	rs2073601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:38117308C>A	ENST00000290399.6	+	10	2060	c.1447C>A	c.(1447-1449)Ctg>Atg	p.L483M	SIM2_ENST00000430056.3_Missense_Mutation_p.L483M	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	483	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.		L -> M (in dbSNP:rs2073601). {ECO:0000269|PubMed:9503011}.		cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						CCTGAGCACACTGCCAGCCAG	0.582													C|||	861	0.171925	0.0514	0.1729	5008	,	,		20231	0.0427		0.326	False		,,,				2504	0.3088				p.L483M		Atlas-SNP	.											.	SIM2	55	.	0			c.C1447A						PASS	.	C	MET/LEU,MET/LEU	419,3987	206.2+/-227.9	21,377,1805	80.0	69.0	73.0		1447,1447	3.5	1.0	21	dbSNP_96	73	3062,5538	471.1+/-368.0	540,1982,1778	yes	missense,missense	SIM2	NM_005069.3,NM_009586.2	15,15	561,2359,3583	AA,AC,CC		35.6047,9.5098,26.7646	possibly-damaging,possibly-damaging	483/668,483/571	38117308	3481,9525	2203	4300	6503	SO:0001583	missense	6493	exon10			AGCACACTGCCAG		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"""Basic helix-loop-helix proteins"""	10883	protein-coding gene	gene with protein product	"""transcription factor SIM2"""	600892	"""single-minded (Drosophila) homolog 2"", ""single-minded homolog 2 (Drosophila)"""	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.1447C>A	21.37:g.38117308C>A	ENSP00000290399:p.Leu483Met	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	137	81	0.591241	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Missense_Mutation	SNP	ENST00000290399.6	37	CCDS13646.1	378|378	0.17307692307692307|0.17307692307692307	33|33	0.06707317073170732|0.06707317073170732	71|71	0.19613259668508287|0.19613259668508287	25|25	0.043706293706293704|0.043706293706293704	249|249	0.32849604221635886|0.32849604221635886	C|C	17.56|17.56	3.420969|3.420969	0.62622|0.62622	0.095098|0.095098	0.356047|0.356047	ENSG00000159263|ENSG00000159263	ENST00000290399;ENST00000430056|ENST00000431229;ENST00000481730	T;T|T	0.37235|0.54866	1.21;1.21|0.55	4.46|4.46	3.55|3.55	0.40652|0.40652	Single-minded, C-terminal (2);|.	6.537880|.	0.00166|.	N|.	0.000004|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.59436|0.59436	1.845|1.845	0.34763|0.34763	P|P	0.267038|0.267038	D;D|.	0.71674|.	0.966;0.998|.	P;D|.	0.74348|.	0.908;0.983|.	T|T	0.30880|0.30880	-0.9963|-0.9963	9|6	0.34782|0.87932	T|D	0.22|0	.|.	11.0463|11.0463	0.47861|0.47861	0.0:0.8471:0.0:0.1529|0.0:0.8471:0.0:0.1529	rs2073601;rs52828939;rs58314380;rs2073601|rs2073601;rs52828939;rs58314380;rs2073601	483;483|.	Q14190;Q14190-2|.	SIM2_HUMAN;.|.	M|N	483|420;79	ENSP00000290399:L483M;ENSP00000404176:L483M|ENSP00000392003:T420N	ENSP00000290399:L483M|ENSP00000392003:T420N	L|T	+|+	1|2	2|0	SIM2|SIM2	37039178|37039178	0.123000|0.123000	0.22298|0.22298	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	0.413000|0.413000	0.21148|0.21148	2.194000|2.194000	0.70268|0.70268	0.558000|0.558000	0.71614|0.71614	CTG|ACT	C|0.777;A|0.223	0.223	strong		0.582	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586	
IFI44L	10964	hgsc.bcm.edu	37	1	79095581	79095581	+	Missense_Mutation	SNP	T	T	C	rs987495	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:79095581T>C	ENST00000370751.5	+	4	883	c.704T>C	c.(703-705)aTc>aCc	p.I235T	IFI44L_ENST00000342282.3_5'UTR|IFI44L_ENST00000476521.1_3'UTR	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	235			I -> T (in dbSNP:rs987495). {ECO:0000269|Ref.1}.		defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)				endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						GGGTCTGATATCACCAGCATA	0.408													T|||	1074	0.214457	0.1195	0.2709	5008	,	,		15403	0.245		0.2505	False		,,,				2504	0.2342				p.I235T		Atlas-SNP	.											IFI44L,NS,carcinoma,-1,1	IFI44L	93	1	0			c.T704C						PASS	.	T	THR/ILE	638,3768	274.9+/-272.2	44,550,1609	81.0	82.0	81.0		704	-5.6	0.0	1	dbSNP_86	81	2111,6489	364.0+/-333.3	259,1593,2448	yes	missense	IFI44L	NM_006820.2	89	303,2143,4057	CC,CT,TT		24.5465,14.4803,21.1364	benign	235/453	79095581	2749,10257	2203	4300	6503	SO:0001583	missense	10964	exon4			CTGATATCACCAG	AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"""chromosome 1 open reading frame 29"""	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.704T>C	1.37:g.79095581T>C	ENSP00000359787:p.Ile235Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_006820	Q86TE1|Q96B64|Q99984	Missense_Mutation	SNP	ENST00000370751.5	37	CCDS687.2	468	0.21428571428571427	45	0.09146341463414634	84	0.23204419889502761	141	0.2465034965034965	198	0.2612137203166227	T	0.144	-1.098806	0.01843	0.144803	0.245465	ENSG00000137959	ENST00000370751;ENST00000450498	T;T	0.13196	2.82;2.61	2.82	-5.64	0.02466	.	1.995390	0.02289	N	0.070148	T	0.00936	0.0031	N	0.02539	-0.55	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35699	-0.9778	9	0.12430	T	0.62	3.8519	4.0787	0.09916	0.406:0.1735:0.0:0.4204	rs987495;rs3766326;rs52810523;rs58826484;rs987495	235	Q53G44	IF44L_HUMAN	T	235;212	ENSP00000359787:I235T;ENSP00000400784:I212T	ENSP00000359787:I235T	I	+	2	0	IFI44L	78868169	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.687000	0.01927	-2.136000	0.00810	-2.622000	0.00156	ATC	T|0.785;G|0.001	.	strong		0.408	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820	
HNF4G	3174	hgsc.bcm.edu	37	8	76468282	76468282	+	Missense_Mutation	SNP	G	G	A	rs1805098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:76468282G>A	ENST00000354370.1	+	7	840	c.570G>A	c.(568-570)atG>atA	p.M190I	HNF4G_ENST00000396423.2_Missense_Mutation_p.M227I			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	190			M -> I (in dbSNP:rs1805098). {ECO:0000269|PubMed:10512380}.		endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			GATCCATGATGTATAAAGATA	0.313													G|||	3079	0.614816	0.9508	0.4914	5008	,	,		14265	0.3919		0.5895	False		,,,				2504	0.5041				p.M227I		Atlas-SNP	.											.	HNF4G	111	.	0			c.G681A						PASS	.	G	ILE/MET	3919,487	777.4+/-414.2	1744,431,28	63.0	73.0	69.0		681	2.5	1.0	8	dbSNP_89	69	4968,3632	623.6+/-397.5	1424,2120,756	yes	missense	HNF4G	NM_004133.4	10	3168,2551,784	AA,AG,GG		42.2326,11.0531,31.67	benign	227/446	76468282	8887,4119	2203	4300	6503	SO:0001583	missense	3174	exon6			CATGATGTATAAA		CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749		"""Nuclear hormone receptors"""	5026	protein-coding gene	gene with protein product		605966				8622695, 12220494	Standard	NM_004133		Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.570G>A	8.37:g.76468282G>A	ENSP00000346339:p.Met190Ile	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	37		1359	0.6222527472527473	472	0.959349593495935	182	0.5027624309392266	253	0.4423076923076923	452	0.5963060686015831	G	11.04	1.523031	0.27211	0.889469	0.577674	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.96232	-3.95;-3.95	5.38	2.52	0.30459	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.648819	0.18023	N	0.154173	T	0.00012	0.0000	L	0.32530	0.975	0.32593	P	0.526937	B;B	0.06786	0.001;0.0	B;B	0.17098	0.017;0.004	T	0.35992	-0.9766	9	0.37606	T	0.19	.	4.2586	0.10730	0.2305:0.0:0.3463:0.4233	rs1805098;rs52795844;rs60560135;rs1805098	227;190	F1D8Q4;Q14541	.;HNF4G_HUMAN	I	190;227	ENSP00000346339:M190I;ENSP00000379701:M227I	ENSP00000346339:M190I	M	+	3	0	HNF4G	76630837	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-1.558000	0.02164	0.295000	0.22570	0.655000	0.94253	ATG	G|0.338;A|0.662	0.662	strong		0.313	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133	
PPARG	5468	hgsc.bcm.edu	37	3	12393125	12393125	+	Missense_Mutation	SNP	C	C	G	rs1801282	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:12393125C>G	ENST00000287820.6	+	1	155	c.34C>G	c.(34-36)Cca>Gca	p.P12A	PPARG_ENST00000397026.2_Intron|PPARG_ENST00000397000.1_Intron|PPARG_ENST00000397015.2_Intron|PPARG_ENST00000539812.1_Intron|PPARG_ENST00000309576.6_Intron|PPARG_ENST00000397010.2_Intron|PPARG_ENST00000397012.2_Intron	NM_015869.4	NP_056953.2	P37231	PPARG_HUMAN	peroxisome proliferator-activated receptor gamma	12			P -> A (significant independent determinant of CIMT; may protect from early atherosclerosis in subject at risk for diabetes; associated with BMI; dbSNP:rs1801282). {ECO:0000269|PubMed:10394368, ECO:0000269|PubMed:10407229, ECO:0000269|PubMed:15562396, ECO:0000269|PubMed:9425261, ECO:0000269|Ref.12}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|brown fat cell differentiation (GO:0050873)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|cellular response to lithium ion (GO:0071285)|epithelial cell differentiation (GO:0030855)|fatty acid oxidation (GO:0019395)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|innate immune response (GO:0045087)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|lipoprotein transport (GO:0042953)|long-chain fatty acid transport (GO:0015909)|low-density lipoprotein particle receptor biosynthetic process (GO:0045713)|monocyte differentiation (GO:0030224)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of cell growth (GO:0030308)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ regeneration (GO:0031100)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|placenta development (GO:0001890)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fatty acid oxidation (GO:0046321)|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)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood pressure (GO:0008217)|regulation of cholesterol transporter activity (GO:0060694)|regulation of transcription involved in cell fate commitment (GO:0060850)|response to caffeine (GO:0031000)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to lipid (GO:0033993)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|arachidonic acid binding (GO:0050544)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|prostaglandin receptor activity (GO:0004955)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)		PAX8/PPARG(117)	breast(2)|endometrium(4)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20					Balsalazide(DB01014)|Bezafibrate(DB01393)|Glipizide(DB01067)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Mesalazine(DB00244)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Pioglitazone(DB01132)|Repaglinide(DB00912)|Rosiglitazone(DB00412)|Sulfasalazine(DB00795)|Telmisartan(DB00966)	TCCTATTGACCCAGAAAGCGA	0.423			T	PAX8	follicular thyroid		"""Insulin resistance ; lipodystrophy, familial partial L;diabetes mellitus, insulin-resistantI, with acanthosis nigricans and hypertension"""						C|||	352	0.0702875	0.0053	0.1167	5008	,	,		20205	0.0258		0.1203	False		,,,				2504	0.1196				p.P12A		Atlas-SNP	.		Dom	yes		3	3p25	5468	"""peroxisome proliferative activated receptor, gamma"""	yes	E	.	PPARG	49	.	0			c.C34G	GRCh37	CM981614	PPARG	M	rs1801282	PASS	.	C	,ALA/PRO,,	115,4291	89.7+/-128.4	0,115,2088	145.0	132.0	136.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,34,,	2.9	1.0	3	dbSNP_89	136	1063,7537	224.3+/-260.7	60,943,3297	yes	intron,missense,intron,intron	PPARG	NM_005037.5,NM_015869.4,NM_138711.3,NM_138712.3	,27,,	60,1058,5385	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	12.3605,2.6101,9.0574	,probably-damaging,,	,12/506,,	12393125	1178,11828	2203	4300	6503	SO:0001583	missense	5468	exon1			ATTGACCCAGAAA	X90563	CCDS2609.1, CCDS2610.2	3p25	2013-01-16	2006-10-17		ENSG00000132170	ENSG00000132170		"""Nuclear hormone receptors"""	9236	protein-coding gene	gene with protein product		601487	"""peroxisome proliferative activated receptor, gamma"""			7862171, 9750197	Standard	NM_005037		Approved	PPARG1, PPARG2, NR1C3, PPARgamma	uc003bwx.3	P37231	OTTHUMG00000129764	ENST00000287820.6:c.34C>G	3.37:g.12393125C>G	ENSP00000287820:p.Pro12Ala	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_015869	A8K3G6|B5BUA1|O00684|O00710|O14515|Q0QJH8|Q15178|Q15179|Q15180|Q15832|Q86U60|Q96J12	Missense_Mutation	SNP	ENST00000287820.6	37	CCDS2609.1	144	0.06593406593406594	5	0.01016260162601626	27	0.07458563535911603	23	0.04020979020979021	89	0.11741424802110818	C	13.25	2.181534	0.38511	0.026101	0.123605	ENSG00000132170	ENST00000287820	D	0.92199	-2.99	6.02	2.93	0.34026	.	0.743990	0.11673	N	0.540689	T	0.07638	0.0192	N	0.24115	0.695	0.09310	P	0.9999999999929415	B	0.02656	0.0	B	0.01281	0.0	T	0.60449	-0.7261	9	0.66056	D	0.02	.	5.3409	0.15982	0.1543:0.6281:0.1343:0.0832	rs1801282;rs17241090;rs17749580;rs36206375;rs56460253;rs1801282	12	P37231	PPARG_HUMAN	A	12	ENSP00000287820:P12A	ENSP00000287820:P12A	P	+	1	0	PPARG	12368125	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	0.376000	0.20535	0.859000	0.35456	0.655000	0.94253	CCA	C|0.921;G|0.079	0.079	strong		0.423	PPARG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251979.2	NM_005037	
OPA1	4976	hgsc.bcm.edu	37	3	193364872	193364872	+	Silent	SNP	A	A	C	rs78767626	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:193364872A>C	ENST00000392438.3	+	17	1842	c.1608A>C	c.(1606-1608)gcA>gcC	p.A536A	OPA1_ENST00000361510.2_Silent_p.A591A|OPA1_ENST00000361908.3_Silent_p.A573A|OPA1_ENST00000361715.2_Silent_p.A555A|OPA1_ENST00000361828.2_Silent_p.A554A|OPA1_ENST00000361150.2_Silent_p.A537A	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	536	Dynamin-type G.				apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		TGCTAAAGGCACACCAAGTGA	0.363													A|||	137	0.0273562	0.0318	0.0259	5008	,	,		16138	0.0367		0.0229	False		,,,				2504	0.0174				p.A591A		Atlas-SNP	.											.	OPA1	79	.	0			c.A1773C						PASS	.	A	,,,,,,,	165,4241	109.5+/-147.8	5,155,2043	79.0	78.0	79.0		1608,1500,1554,1611,1662,1665,1719,1773	3.1	1.0	3	dbSNP_132	79	250,8350	98.8+/-160.4	0,250,4050	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OPA1	NM_015560.2,NM_130831.2,NM_130832.2,NM_130833.2,NM_130834.2,NM_130835.2,NM_130836.2,NM_130837.2	,,,,,,,	5,405,6093	CC,CA,AA		2.907,3.7449,3.1908	,,,,,,,	536/961,500/925,518/943,537/962,554/979,555/980,573/998,591/1016	193364872	415,12591	2203	4300	6503	SO:0001819	synonymous_variant	4976	exon19			AAAGGCACACCAA	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"""mitochondrial dynamin-like GTPase"", ""dynamin-like guanosine triphosphatase"", ""Dynamin-like 120 kDa protein, mitochondrial"""	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.1608A>C	3.37:g.193364872A>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	31	19	0.612903	NM_130837	D3DNW4	Silent	SNP	ENST00000392438.3	37	CCDS43186.1																																																																																			A|0.971;C|0.029	0.029	strong		0.363	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837	
SIK3	23387	hgsc.bcm.edu	37	11	116728630	116728630	+	Missense_Mutation	SNP	G	G	C	rs12225230	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:116728630G>C	ENST00000292055.4	-	20	3268	c.3233C>G	c.(3232-3234)cCt>cGt	p.P1078R	SIK3_ENST00000446921.2_Missense_Mutation_p.P1076R|SIK3_ENST00000434315.2_Missense_Mutation_p.P917R|SIK3_ENST00000375288.1_Missense_Mutation_p.P413R|SIK3_ENST00000375300.1_Missense_Mutation_p.P1136R|SIK3_ENST00000488337.1_5'UTR|SIK3_ENST00000542607.1_Missense_Mutation_p.P1018R|AP006216.12_ENST00000444200.1_RNA	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	1078			P -> R (in dbSNP:rs12225230). {ECO:0000269|Ref.6}.		protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						CAAAGATTCAGGGTCCCCAGG	0.507													G|||	855	0.170727	0.1513	0.1902	5008	,	,		19995	0.0972		0.1511	False		,,,				2504	0.2791				p.P1078R		Atlas-SNP	.											.	SIK3	112	.	0			c.C3233G						PASS	.	G	ARG/PRO	603,3799	264.4+/-266.0	49,505,1647	92.0	88.0	89.0		3233	5.5	1.0	11	dbSNP_120	89	1488,7104	283.1+/-295.9	139,1210,2947	yes	missense	SIK3	NM_025164.3	103	188,1715,4594	CC,CG,GG		17.3184,13.6983,16.092	possibly-damaging	1078/1264	116728630	2091,10903	2201	4296	6497	SO:0001583	missense	23387	exon20			GATTCAGGGTCCC	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.3233C>G	11.37:g.116728630G>C	ENSP00000292055:p.Pro1078Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	181	74	0.40884	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	37	CCDS8379.1	328	0.15018315018315018	90	0.18292682926829268	70	0.19337016574585636	61	0.10664335664335664	107	0.14116094986807387	G	11.49	1.653340	0.29425	0.136983	0.173184	ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000375288;ENST00000542607;ENST00000434315	T;T;T;T;T	0.72942	-0.65;-0.7;1.37;-0.69;-0.29	5.54	5.54	0.83059	.	0.000000	0.41294	U	0.000917	T	0.00210	0.0006	L	0.27053	0.805	0.22541	P	0.999004559	D;P;P;P;D	0.54601	0.967;0.824;0.824;0.824;0.958	P;B;B;B;P	0.51229	0.587;0.26;0.26;0.26;0.663	T	0.12477	-1.0546	9	0.87932	D	0	.	13.7446	0.62868	0.0736:0.0:0.9263:0.0	rs12225230;rs52835371;rs12225230	1078;1018;917;1078;413	Q9Y2K2-3;A1A5A8;A1A5A9;Q9Y2K2;Q9Y2K2-2	.;.;.;SIK3_HUMAN;.	R	1136;1078;413;1018;917	ENSP00000364449:P1136R;ENSP00000292055:P1078R;ENSP00000364437:P413R;ENSP00000438108:P1018R;ENSP00000415873:P917R	ENSP00000292055:P1078R	P	-	2	0	SIK3	116233840	1.000000	0.71417	1.000000	0.80357	0.370000	0.29829	5.065000	0.64344	2.585000	0.87301	0.563000	0.77884	CCT	G|0.841;C|0.159	0.159	strong		0.507	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164	
FBXO34	55030	hgsc.bcm.edu	37	14	55818403	55818403	+	Missense_Mutation	SNP	T	T	C	rs35070799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:55818403T>C	ENST00000313833.4	+	2	1540	c.1295T>C	c.(1294-1296)gTt>gCt	p.V432A	FBXO34_ENST00000440021.1_Missense_Mutation_p.V432A	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	432			V -> A (in dbSNP:rs35070799).							breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						ACAGATGCTGTTGATTGTATG	0.418													T|||	230	0.0459265	0.0008	0.0807	5008	,	,		21205	0.006		0.0805	False		,,,				2504	0.0879				p.V432A		Atlas-SNP	.											.	FBXO34	61	.	0			c.T1295C						PASS	.	T	ALA/VAL,ALA/VAL	65,4341	60.5+/-97.4	0,65,2138	138.0	129.0	132.0		1295,1295	0.4	0.0	14	dbSNP_126	132	690,7910	171.2+/-222.1	24,642,3634	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	64,64	24,707,5772	CC,CT,TT		8.0233,1.4753,5.805	benign,benign	432/712,432/712	55818403	755,12251	2203	4300	6503	SO:0001583	missense	55030	exon2			ATGCTGTTGATTG	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1295T>C	14.37:g.55818403T>C	ENSP00000313159:p.Val432Ala	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	220	110	0.5	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	96	0.04395604395604396	1	0.0020325203252032522	38	0.10497237569060773	2	0.0034965034965034965	55	0.07255936675461741	T	2.813	-0.246439	0.05867	0.014753	0.080233	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.24908	1.83;1.83	5.48	0.452	0.16634	.	0.665108	0.13820	N	0.360485	T	0.00468	0.0015	L	0.56769	1.78	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.33803	-0.9854	10	0.06236	T	0.91	0.0061	6.0301	0.19675	0.0:0.1949:0.2462:0.559	rs35070799;rs61755585	432	Q9NWN3	FBX34_HUMAN	A	432	ENSP00000313159:V432A;ENSP00000394117:V432A	ENSP00000313159:V432A	V	+	2	0	FBXO34	54888156	0.001000	0.12720	0.000000	0.03702	0.376000	0.30014	0.337000	0.19841	-0.058000	0.13177	0.528000	0.53228	GTT	T|0.945;C|0.055	0.055	strong		0.418	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
NEUROD1	4760	hgsc.bcm.edu	37	2	182543455	182543455	+	Missense_Mutation	SNP	T	T	C	rs1801262	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:182543455T>C	ENST00000295108.3	-	2	590	c.133A>G	c.(133-135)Acc>Gcc	p.T45A	CERKL_ENST00000479558.1_Intron|NEUROD1_ENST00000496876.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	45			T -> A (in dbSNP:rs1801262). {ECO:0000269|PubMed:10366743, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21697133, ECO:0000269|PubMed:8786144, ECO:0000269|PubMed:8915591, ECO:0000269|Ref.11, ECO:0000269|Ref.3, ECO:0000269|Ref.5, ECO:0000269|Ref.6}.		amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			GCGTTCATGGTTTCGAGGTCG	0.587													C|||	3860	0.770767	0.7307	0.745	5008	,	,		19530	0.9196		0.6123	False		,,,				2504	0.8528				p.T45A		Atlas-SNP	.											NEUROD1,NS,adenoma,0,1	NEUROD1	67	1	0			c.A133G	GRCh37	CM032967	NEUROD1	M	rs1801262	scavenged	.	C	ALA/THR	3275,1131	403.3+/-332.7	1214,847,142	126.0	98.0	107.0		133	4.4	1.0	2	dbSNP_89	107	5431,3169	477.6+/-369.7	1715,2001,584	yes	missense	NEUROD1	NM_002500.3	58	2929,2848,726	CC,CT,TT		36.8488,25.6695,33.0617	benign	45/357	182543455	8706,4300	2203	4300	6503	SO:0001583	missense	4760	exon2			TCATGGTTTCGAG	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"""Basic helix-loop-helix proteins"""	7762	protein-coding gene	gene with protein product	"""beta-cell E-box transactivator 2"", ""neurogenic helix-loop-helix protein NEUROD"""	601724	"""neurogenic differentiation 1"""	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.133A>G	2.37:g.182543455T>C	ENSP00000295108:p.Thr45Ala	Somatic	104	2	0.0192308		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Missense_Mutation	SNP	ENST00000295108.3	37	CCDS2283.1	1603	0.7339743589743589	364	0.7398373983739838	253	0.6988950276243094	529	0.9248251748251748	457	0.6029023746701847	C	4.444	0.082289	0.08533	0.743305	0.631512	ENSG00000162992	ENST00000295108	D	0.94966	-3.57	5.37	4.43	0.53597	.	0.638419	0.14950	N	0.288948	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41124	-0.9526	9	0.08599	T	0.76	-6.9429	9.2816	0.37731	0.0:0.8135:0.0:0.1865	rs1801262;rs17847280;rs17856286;rs57194596;rs1801262	45	Q13562	NDF1_HUMAN	A	45	ENSP00000295108:T45A	ENSP00000295108:T45A	T	-	1	0	NEUROD1	182251700	0.920000	0.31207	0.999000	0.59377	0.911000	0.54048	1.164000	0.31810	0.741000	0.32674	-0.128000	0.14901	ACC	T|0.295;C|0.705	0.705	strong		0.587	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500	
PGAM2	5224	hgsc.bcm.edu	37	7	44104896	44104896	+	Nonsense_Mutation	SNP	C	C	T	rs10250779	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:44104896C>T	ENST00000297283.3	-	1	290	c.233G>A	c.(232-234)tGg>tAg	p.W78*	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	78					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						CACAGGCAGCCACATCTGGTC	0.622													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		16885	0.0		0.0	False		,,,				2504	0.0				p.W78X		Atlas-SNP	.											.	PGAM2	20	.	0			c.G233A	GRCh37	CM930584	PGAM2	M	rs10250779	PASS	.	C	stop/TRP	40,4366	43.8+/-77.6	1,38,2164	85.0	74.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	233	5.9	1.0	7	dbSNP_119	78	0,8600		0,0,4300	yes	stop-gained	PGAM2	NM_000290.3		1,38,6464	TT,TC,CC		0.0,0.9079,0.3076		78/254	44104896	40,12966	2203	4300	6503	SO:0001587	stop_gained	5224	exon1			GGCAGCCACATCT		CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.233G>A	7.37:g.44104896C>T	ENSP00000297283:p.Trp78*	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_000290		Nonsense_Mutation	SNP	ENST00000297283.3	37	CCDS34624.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	36	5.972079	0.97162	0.009079	0.0	ENSG00000164708	ENST00000297283	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-32.2844	17.8825	0.88844	0.0:1.0:0.0:0.0	rs10250779;rs10250779	.	.	.	X	78	.	ENSP00000297283:W78X	W	-	2	0	PGAM2	44071421	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.674000	0.83992	2.828000	0.97474	0.644000	0.83932	TGG	C|0.997;T|0.003	0.003	strong		0.622	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1		
DLC1	10395	hgsc.bcm.edu	37	8	12958025	12958025	+	Silent	SNP	C	C	A	rs3739298	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:12958025C>A	ENST00000276297.4	-	9	2230	c.1821G>T	c.(1819-1821)gcG>gcT	p.A607A	DLC1_ENST00000512044.2_Silent_p.A204A|DLC1_ENST00000358919.2_Silent_p.A170A|DLC1_ENST00000520226.1_Silent_p.A96A	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	607					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						CGCTGGGGGGCGCGTGGCTGG	0.677													C|||	1753	0.35004	0.1059	0.4957	5008	,	,		16123	0.6161		0.3241	False		,,,				2504	0.3292				p.A607A		Atlas-SNP	.											.	DLC1	411	.	0			c.G1821T						PASS	.	C	,,	722,3672		59,604,1534	36.0	43.0	41.0		288,510,1821	-0.5	0.0	8	dbSNP_107	41	2817,5767		473,1871,1948	no	coding-synonymous,coding-synonymous,coding-synonymous	DLC1	NM_001164271.1,NM_006094.4,NM_182643.2	,,	532,2475,3482	AA,AC,CC		32.8169,16.4315,27.2692	,,	96/1018,170/1092,607/1529	12958025	3539,9439	2197	4292	6489	SO:0001819	synonymous_variant	10395	exon9			GGGGGGCGCGTGG	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1821G>T	8.37:g.12958025C>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																			C|0.703;A|0.297	0.297	strong		0.677	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
PDE6C	5146	hgsc.bcm.edu	37	10	95381773	95381773	+	Missense_Mutation	SNP	T	T	A	rs701865	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:95381773T>A	ENST00000371447.3	+	4	946	c.808T>A	c.(808-810)Tca>Aca	p.S270T		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	270	GAF 2.		S -> T (in dbSNP:rs701865). {ECO:0000269|PubMed:8641425}.		phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	CACGGTTAGATCATATCTGAA	0.408													A|||	2075	0.414337	0.4803	0.4222	5008	,	,		19059	0.4861		0.3628	False		,,,				2504	0.2986				p.S270T		Atlas-SNP	.											.	PDE6C	97	.	0			c.T808A						PASS	.	A	THR/SER	2039,2367	610.8+/-391.6	494,1051,658	176.0	155.0	162.0		808	4.8	0.1	10	dbSNP_86	162	3050,5550	662.2+/-402.0	531,1988,1781	yes	missense	PDE6C	NM_006204.3	58	1025,3039,2439	AA,AT,TT		35.4651,46.2778,39.1281	benign	270/859	95381773	5089,7917	2203	4300	6503	SO:0001583	missense	5146	exon4			GTTAGATCATATC	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.808T>A	10.37:g.95381773T>A	ENSP00000360502:p.Ser270Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	48	6	0.125	NM_006204	A6NCR6|Q5VY29	Missense_Mutation	SNP	ENST00000371447.3	37	CCDS7429.1	935	0.4281135531135531	219	0.4451219512195122	156	0.430939226519337	290	0.506993006993007	270	0.3562005277044855	A	9.751	1.167381	0.21621	0.462778	0.354651	ENSG00000095464	ENST00000371447	T	0.67523	-0.27	4.85	4.85	0.62838	GAF (2);	0.269919	0.42294	N	0.000726	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44711	-0.9310	9	0.13108	T	0.6	.	6.0523	0.19792	0.7789:0.0:0.0759:0.1453	rs701865;rs52820372;rs58236055;rs701865	270	P51160	PDE6C_HUMAN	T	270	ENSP00000360502:S270T	ENSP00000360502:S270T	S	+	1	0	PDE6C	95371763	0.413000	0.25400	0.101000	0.21167	0.873000	0.50193	2.619000	0.46401	0.987000	0.38709	-0.364000	0.07487	TCA	A|0.403;N|0.000	0.403	strong		0.408	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
TBC1D1	23216	hgsc.bcm.edu	37	4	38054737	38054737	+	Intron	SNP	C	C	T	rs58983546	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:38054737C>T	ENST00000261439.4	+	12	2265				TBC1D1_ENST00000508802.1_Missense_Mutation_p.R695C	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1						membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						CATCTCCTACCGTAATGCCCT	0.308													C|||	298	0.0595048	0.0514	0.0937	5008	,	,		16574	0.001		0.1501	False		,,,				2504	0.0133				p.R695C		Atlas-SNP	.											.	TBC1D1	94	.	0			c.C2083T						PASS	.																																			SO:0001627	intron_variant	23216	exon13			TCCTACCGTAATG	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.1911-1083C>T	4.37:g.38054737C>T		Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	340	164	0.482353	NM_001253912	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	37	CCDS33972.1	189|189	0.08653846153846154|0.08653846153846154	27|27	0.054878048780487805|0.054878048780487805	43|43	0.11878453038674033|0.11878453038674033	0|0	0.0|0.0	119|119	0.15699208443271767|0.15699208443271767	C|C	22.2|22.2	4.264086|4.264086	0.80358|0.80358	.|.	.|.	ENSG00000065882|ENSG00000065882	ENST00000510573|ENST00000508802	.|T	.|0.05081	.|3.5	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|.	.|.	.|.	.|.	T|T	0.00109|0.00109	0.0003|0.0003	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|D	.|0.89917	.|1.0	.|D	.|0.83275	.|0.996	T|T	0.00010|0.00010	-1.2454|-1.2454	3|7	.|0.66056	.|D	.|0.02	.|.	19.4699|19.4699	0.94959|0.94959	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs58983546|rs58983546	.|695	.|E9PGH8	.|.	L|C	288|695	.|ENSP00000423651:R695C	.|ENSP00000423651:R695C	P|R	+|+	2|1	0|0	TBC1D1|TBC1D1	37731132|37731132	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.677000|5.677000	0.68142|0.68142	2.591000|2.591000	0.87537|0.87537	0.650000|0.650000	0.86243|0.86243	CCG|CGT	C|0.910;T|0.090	0.090	strong		0.308	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
AJUBA	84962	hgsc.bcm.edu	37	14	23444084	23444084	+	Silent	SNP	C	C	T	rs61737805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23444084C>T	ENST00000262713.2	-	6	1761	c.1386G>A	c.(1384-1386)aaG>aaA	p.K462K	AJUBA_ENST00000361265.4_Silent_p.K462K|AJUBA_ENST00000397388.3_Silent_p.K45K|RP11-298I3.5_ENST00000555074.1_Intron	NM_032876.4	NP_116265.1	Q96IF1	AJUBA_HUMAN	ajuba LIM protein	462	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				calcium-dependent cell-cell adhesion (GO:0016339)|cellular protein localization (GO:0034613)|focal adhesion assembly (GO:0048041)|G2/M transition of mitotic cell cycle (GO:0000086)|gene silencing by miRNA (GO:0035195)|glycerophospholipid biosynthetic process (GO:0046474)|lamellipodium assembly (GO:0030032)|mitotic cell cycle (GO:0000278)|negative regulation of hippo signaling (GO:0035331)|negative regulation of kinase activity (GO:0033673)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular biosynthetic process (GO:0031328)|positive regulation of gene silencing by miRNA (GO:2000637)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein complex assembly (GO:0031334)|regulation of cell migration (GO:0030334)|regulation of cellular response to hypoxia (GO:1900037)|regulation of GTPase activity (GO:0043087)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|wound healing, spreading of epidermal cells (GO:0035313)	cell-cell junction (GO:0005911)|cytoplasmic mRNA processing body (GO:0000932)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcription factor complex (GO:0005667)	alpha-catenin binding (GO:0045294)|chromatin binding (GO:0003682)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)										AGGCTGCACACTTAGGAGCAT	0.567													C|||	100	0.0199681	0.0053	0.0303	5008	,	,		21369	0.001		0.0646	False		,,,				2504	0.0061				p.K462K		Atlas-SNP	.											.	.	.	.	0			c.G1386A						PASS	.	C	,	59,4347	56.8+/-93.2	0,59,2144	108.0	98.0	101.0		1386,135	2.5	1.0	14	dbSNP_129	101	574,8026	155.5+/-209.5	21,532,3747	no	coding-synonymous,coding-synonymous	JUB	NM_032876.4,NM_198086.1	,	21,591,5891	TT,TC,CC		6.6744,1.3391,4.867	,	462/539,45/122	23444084	633,12373	2203	4300	6503	SO:0001819	synonymous_variant	84962	exon6			TGCACACTTAGGA	AK025567	CCDS9581.1, CCDS9582.1	14q11.2	2011-11-10	2011-11-10	2011-11-10	ENSG00000129474	ENSG00000129474			20250	protein-coding gene	gene with protein product		609066	"""jub, ajuba homolog (Xenopus laevis)"""	JUB		10330178	Standard	NM_032876		Approved	MGC15563	uc001whz.3	Q96IF1	OTTHUMG00000028711	ENST00000262713.2:c.1386G>A	14.37:g.23444084C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	121	51	0.421488	NM_032876	A8MX18|D3DS37	Silent	SNP	ENST00000262713.2	37	CCDS9581.1																																																																																			C|0.953;T|0.047	0.047	strong		0.567	AJUBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071685.2		
POM121L12	285877	hgsc.bcm.edu	37	7	53103673	53103673	+	Silent	SNP	C	C	A	rs1184320	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:53103673C>A	ENST00000408890.4	+	1	325	c.309C>A	c.(307-309)ccC>ccA	p.P103P		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	103										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CTGCCCTTCCCGGGGAGACCG	0.726													C|||	2433	0.485823	0.4682	0.3444	5008	,	,		13024	0.5992		0.3688	False		,,,				2504	0.6135				p.P103P		Atlas-SNP	.											.	POM121L12	146	.	0			c.C309A						PASS	.	C		1694,2198		379,936,631	20.0	24.0	22.0		309	-1.2	0.0	7	dbSNP_87	22	2863,5365		484,1895,1735	no	coding-synonymous	POM121L12	NM_182595.3		863,2831,2366	AA,AC,CC		34.7958,43.5252,37.599		103/297	53103673	4557,7563	1946	4114	6060	SO:0001819	synonymous_variant	285877	exon1			CCTTCCCGGGGAG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.309C>A	7.37:g.53103673C>A		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	12	6	0.5	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			C|0.563;A|0.437	0.437	strong		0.726	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
MICA	100507436	hgsc.bcm.edu	37	6	31379043	31379043	+	Missense_Mutation	SNP	A	A	G	rs41560824	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31379043A>G	ENST00000449934.2	+	3	574	c.520A>G	c.(520-522)Atg>Gtg	p.M174V	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				GGAAGATGCCATGAAGACCAA	0.527													a|||	69	0.013778	0.0106	0.0533	5008	,	,		22153	0.003		0.0149	False		,,,				2504	0.0				p.M174V		Atlas-SNP	.											.	MICA	21	.	0			c.A520G						PASS	.	A	VAL/MET	26,1358		1,24,667	126.0	108.0	113.0		520	-2.2	0.0	6	dbSNP_127	113	98,3084		4,90,1497	yes	missense	MICA	NM_001177519.1	21	5,114,2164	GG,GA,AA		3.0798,1.8786,2.7157	possibly-damaging	174/333	31379043	124,4442	692	1591	2283	SO:0001583	missense	100507436	exon3			GATGCCATGAAGA	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.520A>G	6.37:g.31379043A>G	ENSP00000413079:p.Met174Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	155	79	0.509677	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	42	0.019230769230769232	5	0.01016260162601626	24	0.06629834254143646	1	0.0017482517482517483	12	0.0158311345646438	N	3.083	-0.188672	0.06299	0.018786	0.030798	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934	T	0.00666	5.91	1.12	-2.24	0.06909	.	3.726100	0.01566	U	0.020352	T	0.00300	0.0009	L	0.45137	1.4	0.09310	N	1	B;B	0.16166	0.016;0.006	B;B	0.11329	0.006;0.004	T	0.46638	-0.9177	10	0.41790	T	0.15	.	2.3643	0.04315	0.4356:0.0:0.3038:0.2606	rs41560824;rs61733185	36;174	Q5SS58;Q96QC4	.;.	V	36;174;131;174	ENSP00000413079:M174V	ENSP00000365394:M174V	M	+	1	0	MICA	31487022	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.164000	0.09983	-0.778000	0.04566	0.254000	0.18369	ATG	A|0.977;G|0.023	0.023	strong		0.527	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
KIF24	347240	hgsc.bcm.edu	37	9	34306410	34306410	+	Missense_Mutation	SNP	C	C	A	rs17350674	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:34306410C>A	ENST00000402558.2	-	2	677	c.653G>T	c.(652-654)tGg>tTg	p.W218L	KIF24_ENST00000379166.2_Missense_Mutation_p.W218L|KIF24_ENST00000379174.3_Missense_Mutation_p.W218L|KIF24_ENST00000345050.2_Missense_Mutation_p.W218L			Q5T7B8	KIF24_HUMAN	kinesin family member 24	218			W -> L (in dbSNP:rs17350674).		ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			CATCTCAGTCCAAGGATTCTG	0.363													C|||	452	0.0902556	0.0098	0.147	5008	,	,		18714	0.0069		0.2177	False		,,,				2504	0.1135				p.W218L		Atlas-SNP	.											.	KIF24	64	.	0			c.G653T						PASS	.	C	LEU/TRP	120,3498		1,118,1690	166.0	156.0	159.0		653	5.6	1.0	9	dbSNP_123	159	1565,6597		146,1273,2662	yes	missense	KIF24	NM_194313.2	61	147,1391,4352	AA,AC,CC		19.1742,3.3167,14.3039	possibly-damaging	218/1369	34306410	1685,10095	1809	4081	5890	SO:0001583	missense	347240	exon3			TCAGTCCAAGGAT	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"""Kinesins"", ""Sterile alpha motif (SAM) domain containing"""	19916	protein-coding gene	gene with protein product		613747	"""chromosome 9 open reading frame 48"""	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.653G>T	9.37:g.34306410C>A	ENSP00000384433:p.Trp218Leu	Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	238	93	0.390756	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Missense_Mutation	SNP	ENST00000402558.2	37	CCDS6551.2	212	0.09706959706959707	5	0.01016260162601626	52	0.143646408839779	3	0.005244755244755245	152	0.20052770448548812	C	24.2	4.510651	0.85389	0.033167	0.191742	ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188	T;T;T;T	0.14893	2.47;2.47;2.47;2.47	5.6	5.6	0.85130	.	0.000000	0.40818	N	0.001017	T	0.00039	0.0001	M	0.66939	2.045	0.26078	P	0.9811238	D;D	0.57257	0.975;0.979	P;P	0.56788	0.806;0.644	T	0.10590	-1.0623	9	0.10111	T	0.7	.	19.6051	0.95577	0.0:1.0:0.0:0.0	rs17350674;rs17350674	218;218	Q5T7B8-4;Q5T7B8	.;KIF24_HUMAN	L	218	ENSP00000384433:W218L;ENSP00000368472:W218L;ENSP00000368464:W218L;ENSP00000340179:W218L	ENSP00000340179:W218L	W	-	2	0	KIF24	34296410	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.581000	0.67471	2.636000	0.89361	0.655000	0.94253	TGG	C|0.891;A|0.109	0.109	strong		0.363	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
ZNF618	114991	hgsc.bcm.edu	37	9	116770785	116770785	+	Silent	SNP	G	G	A	rs3748182	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:116770785G>A	ENST00000374126.5	+	9	804	c.705G>A	c.(703-705)acG>acA	p.T235T	ZNF618_ENST00000288466.7_Silent_p.T203T			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	235					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						TCGTGGCCACGGACGAGGTGA	0.672													G|||	1522	0.303914	0.062	0.2565	5008	,	,		17362	0.5962		0.3439	False		,,,				2504	0.3221				p.T203T		Atlas-SNP	.											.	ZNF618	184	.	0			c.G609A						PASS	.	G		422,3470		25,372,1549	47.0	55.0	53.0		609	-4.4	1.0	9	dbSNP_107	53	2692,5546		451,1790,1878	no	coding-synonymous	ZNF618	NM_133374.2		476,2162,3427	AA,AG,GG		32.6778,10.8428,25.6719		203/862	116770785	3114,9016	1946	4119	6065	SO:0001819	synonymous_variant	114991	exon8			GGCCACGGACGAG	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.705G>A	9.37:g.116770785G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				G|0.655;A|0.345	0.345	strong		0.672	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
SP110	3431	hgsc.bcm.edu	37	2	231077112	231077112	+	Missense_Mutation	SNP	G	G	A	rs28930679	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:231077112G>A	ENST00000358662.4	-	5	695	c.617C>T	c.(616-618)gCg>gTg	p.A206V	SP110_ENST00000338556.3_5'UTR|SP110_ENST00000258381.6_Missense_Mutation_p.A206V|SP110_ENST00000392048.3_Missense_Mutation_p.A206V|SP110_ENST00000486146.2_5'UTR|SP110_ENST00000258382.5_Missense_Mutation_p.A206V|SP110_ENST00000540870.1_Missense_Mutation_p.A212V	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	206			A -> V (in dbSNP:rs28930679). {ECO:0000269|PubMed:16816019}.		regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		GTCTTCTTCCGCATTCATTTT	0.468													G|||	797	0.159145	0.1165	0.2133	5008	,	,		21939	0.0873		0.2724	False		,,,				2504	0.136				p.A212V		Atlas-SNP	.											.	SP110	105	.	0			c.C635T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	623,3783	268.9+/-268.7	42,539,1622	220.0	172.0	188.0		635,617,617,617	-0.2	0.0	2	dbSNP_125	188	2177,6423	371.6+/-336.3	284,1609,2407	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	64,64,64,64	326,2148,4029	AA,AG,GG		25.314,14.1398,21.5285	benign,benign,benign,benign	212/556,206/690,206/550,206/714	231077112	2800,10206	2203	4300	6503	SO:0001583	missense	3431	exon6			TCTTCCGCATTCA	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"""interferon-induced protein 41, 30kD"""	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.617C>T	2.37:g.231077112G>A	ENSP00000351488:p.Ala206Val	Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	241	104	0.431535	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	371	0.16987179487179488	52	0.10569105691056911	71	0.19613259668508287	44	0.07692307692307693	204	0.2691292875989446	G	9.635	1.137510	0.21123	0.141398	0.25314	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000409815;ENST00000455674	T;T;T;T;T;T;T	0.09163	3.01;3.01;3.01;3.01;3.01;3.01;3.01	3.63	-0.151	0.13411	.	2.041240	0.02374	N	0.078122	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.27700	0.083;0.186;0.117;0.001	B;B;B;B	0.18263	0.021;0.021;0.009;0.0	T	0.42515	-0.9447	9	0.31617	T	0.26	.	4.5859	0.12282	0.0:0.1096:0.3972:0.4932	rs28930679	206;212;206;206	G5E9C0;F5H1M1;Q9HB58;Q9HB58-6	.;.;SP110_HUMAN;.	V	206;206;206;206;212;206;160	ENSP00000258381:A206V;ENSP00000351488:A206V;ENSP00000375902:A206V;ENSP00000258382:A206V;ENSP00000439558:A212V;ENSP00000387172:A206V;ENSP00000393992:A160V	ENSP00000258381:A206V	A	-	2	0	SP110	230785356	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.085000	0.11250	-0.031000	0.13781	-0.386000	0.06593	GCG	G|0.797;A|0.203	0.203	strong		0.468	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
DRC7	84229	hgsc.bcm.edu	37	16	57756643	57756643	+	Missense_Mutation	SNP	C	C	T	rs3809611	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:57756643C>T	ENST00000360716.3	+	11	1519	c.1298C>T	c.(1297-1299)cCg>cTg	p.P433L	CCDC135_ENST00000394337.4_Missense_Mutation_p.P433L|CCDC135_ENST00000336825.8_Missense_Mutation_p.P368L			Q8IY82	CC135_HUMAN		433			P -> L (in dbSNP:rs3809611). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						ACCCGCTGCCCGAACGGGAAG	0.577													.|||	1055	0.210663	0.2322	0.1441	5008	,	,		18750	0.1548		0.2465	False		,,,				2504	0.2495				p.P433L		Atlas-SNP	.											CCDC135,NS,carcinoma,-1,1	CCDC135	97	1	0			c.C1298T						PASS	.	C	LEU/PRO	970,3426		104,762,1332	80.0	78.0	79.0		1298	5.1	0.9	16	dbSNP_107	79	2022,6578		232,1558,2510	yes	missense	CCDC135	NM_032269.5	98	336,2320,3842	TT,TC,CC		23.5116,22.0655,23.0225	probably-damaging	433/875	57756643	2992,10004	2198	4300	6498	SO:0001583	missense	84229	exon10			GCTGCCCGAACGG																												ENST00000360716.3:c.1298C>T	16.37:g.57756643C>T	ENSP00000353942:p.Pro433Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	429	0.19642857142857142	100	0.2032520325203252	58	0.16022099447513813	85	0.1486013986013986	186	0.24538258575197888	.	16.58	3.162039	0.57368	0.220655	0.235116	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.07114	3.22;3.22;3.22	5.12	5.12	0.69794	.	0.054186	0.85682	D	0.000000	T	0.00012	0.0000	M	0.87971	2.92	0.09310	P	0.99999999748828	B;P	0.44090	0.07;0.826	B;B	0.35353	0.024;0.201	T	0.36625	-0.9740	9	0.49607	T	0.09	-27.9479	17.1416	0.86755	0.0:1.0:0.0:0.0	rs3809611;rs17857125;rs58281850;rs3809611	368;433	Q8IY82-2;Q8IY82	.;CC135_HUMAN	L	433;368;433	ENSP00000377869:P433L;ENSP00000338938:P368L;ENSP00000353942:P433L	ENSP00000338938:P368L	P	+	2	0	CCDC135	56314144	0.997000	0.39634	0.940000	0.37924	0.685000	0.39939	3.831000	0.55776	2.384000	0.81235	0.650000	0.86243	CCG	C|0.781;T|0.218	0.218	strong		0.577	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
PGM2	55276	hgsc.bcm.edu	37	4	37836302	37836302	+	Silent	SNP	T	T	C	rs3752683	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:37836302T>C	ENST00000381967.4	+	3	412	c.312T>C	c.(310-312)agT>agC	p.S104S	PGM2_ENST00000544359.1_5'UTR|PGM2_ENST00000537241.1_Intron	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	104					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						TCGTGATCAGTTTTGACGCCC	0.338													C|||	1722	0.34385	0.6755	0.2781	5008	,	,		14222	0.2748		0.2167	False		,,,				2504	0.1442				p.S104S		Atlas-SNP	.											.	PGM2	45	.	0			c.T312C						PASS	.	C		2711,1695	651.8+/-399.3	835,1041,327	91.0	102.0	99.0		312	2.3	1.0	4	dbSNP_107	99	1856,6744	331.4+/-319.6	196,1464,2640	no	coding-synonymous	PGM2	NM_018290.3		1031,2505,2967	CC,CT,TT		21.5814,38.4703,35.1146		104/613	37836302	4567,8439	2203	4300	6503	SO:0001819	synonymous_variant	55276	exon3			GATCAGTTTTGAC	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"""phosphopentomutase"""	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.312T>C	4.37:g.37836302T>C		Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	306	157	0.513072	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Silent	SNP	ENST00000381967.4	37	CCDS3443.1																																																																																			T|0.651;C|0.349	0.349	strong		0.338	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290	
WDR90	197335	hgsc.bcm.edu	37	16	716273	716273	+	Missense_Mutation	SNP	T	T	C	rs11866949	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:716273T>C	ENST00000293879.4	+	37	4663	c.4663T>C	c.(4663-4665)Tgc>Cgc	p.C1555R	RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000547944.1_Missense_Mutation_p.C154R|WDR90_ENST00000549091.1_Missense_Mutation_p.C1557R|WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000315764.4_Missense_Mutation_p.C154R			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1555			C -> R (in dbSNP:rs11866949).							endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GAGCCACCCCTGCACAGGGAC	0.622													C|||	1806	0.360623	0.7927	0.2133	5008	,	,		18164	0.3224		0.1163	False		,,,				2504	0.1718				p.C1555R		Atlas-SNP	.											.	WDR90	107	.	0			c.T4663C						PASS	.	C	ARG/CYS	2575,1497		813,949,274	43.0	52.0	49.0		4663	-3.8	0.0	16	dbSNP_120	49	1045,7297		58,929,3184	yes	missense	WDR90	NM_145294.4	180	871,1878,3458	CC,CT,TT		12.527,36.7633,29.1606	benign	1555/1749	716273	3620,8794	2036	4171	6207	SO:0001583	missense	197335	exon37			CACCCCTGCACAG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.4663T>C	16.37:g.716273T>C	ENSP00000293879:p.Cys1555Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	696	0.31868131868131866	373	0.758130081300813	63	0.17403314917127072	184	0.32167832167832167	76	0.10026385224274406	C	2.766	-0.256870	0.05829	0.632367	0.12527	ENSG00000161996	ENST00000549091;ENST00000293879;ENST00000547944;ENST00000315764	T;T;T;T	0.61980	3.57;1.81;0.06;1.84	4.48	-3.8	0.04307	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.579510	0.03030	N	0.151901	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.31943	-0.9925	9	0.12430	T	0.62	.	6.6725	0.23076	0.1253:0.3526:0.0:0.5221	rs11866949;rs61157244;rs11866949	154;154;154;1555	Q96KV7-10;Q96KV7-7;G3V201;Q96KV7	.;.;.;WDR90_HUMAN	R	1557;1555;154;154	ENSP00000448122:C1557R;ENSP00000293879:C1555R;ENSP00000449576:C154R;ENSP00000322808:C154R	ENSP00000293879:C1555R	C	+	1	0	WDR90	656274	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-1.058000	0.03482	-0.600000	0.05790	-1.381000	0.01174	TGC	T|0.694;C|0.306	0.306	strong		0.622	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
WDR11	55717	hgsc.bcm.edu	37	10	122665459	122665459	+	Silent	SNP	C	C	G	rs3740307	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122665459C>G	ENST00000263461.6	+	27	3609	c.3363C>G	c.(3361-3363)gtC>gtG	p.V1121V	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0	Mediates interaction with IRS1. {ECO:0000250}.				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)	p.V1121V(1)		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						CTCCACAAGTCAATCAGAAAT	0.498													C|||	777	0.155152	0.0129	0.2305	5008	,	,		16030	0.3373		0.1093	False		,,,				2504	0.1534				p.V1121V		Atlas-SNP	.											WDR11,NS,carcinoma,0,1	WDR11	95	1	1	Substitution - coding silent(1)	stomach(1)	c.C3363G						PASS	.	C		144,4262	102.1+/-140.7	1,142,2060	131.0	119.0	123.0		3363	1.7	1.0	10	dbSNP_107	123	1110,7490	230.4+/-264.8	70,970,3260	no	coding-synonymous	WDR11	NM_018117.11		71,1112,5320	GG,GC,CC		12.907,3.2683,9.6417		1121/1225	122665459	1254,11752	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon27			ACAAGTCAATCAG	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.3363C>G	10.37:g.122665459C>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	130	53	0.407692	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			C|0.885;G|0.115	0.115	strong		0.498	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
MYH6	4624	hgsc.bcm.edu	37	14	23874507	23874507	+	Silent	SNP	G	G	T	rs2277473	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23874507G>T	ENST00000356287.3	-	4	456	c.427C>A	c.(427-429)Cgg>Agg	p.R143R	MYH6_ENST00000405093.3_Silent_p.R143R			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	143	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TTCTTGCCCCGGTAGGCGGCC	0.612													G|||	389	0.0776757	0.0129	0.085	5008	,	,		18374	0.0675		0.1044	False		,,,				2504	0.1431				p.R143R		Atlas-SNP	.											.	MYH6	274	.	0			c.C427A						PASS	.	G		110,4296		1,108,2094	108.0	110.0	110.0		427	1.2	1.0	14	dbSNP_100	110	942,7658		54,834,3412	no	coding-synonymous	MYH6	NM_002471.3		55,942,5506	TT,TG,GG		10.9535,2.4966,8.0886		143/1940	23874507	1052,11954	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon5			TGCCCCGGTAGGC	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.427C>A	14.37:g.23874507G>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			A|0.000;C|0.007	.	strong		0.612	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
MOCOS	55034	hgsc.bcm.edu	37	18	33831189	33831189	+	Missense_Mutation	SNP	C	C	A	rs594445	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:33831189C>A	ENST00000261326.5	+	11	2128	c.2107C>A	c.(2107-2109)Cat>Aat	p.H703N		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CCGTCCTTGTCATTTGATCAA	0.373													C|||	1116	0.222843	0.0477	0.3487	5008	,	,		18745	0.244		0.2932	False		,,,				2504	0.2761				p.H703N		Atlas-SNP	.											.	MOCOS	84	.	0			c.C2107A						PASS	.	C	ASN/HIS	405,4001	200.4+/-223.7	12,381,1810	111.0	102.0	105.0		2107	5.5	1.0	18	dbSNP_83	105	2442,6158	403.2+/-347.7	341,1760,2199	yes	missense	MOCOS	NM_017947.2	68	353,2141,4009	AA,AC,CC		28.3953,9.192,21.8899	possibly-damaging	703/889	33831189	2847,10159	2203	4300	6503	SO:0001583	missense	55034	exon11			CCTTGTCATTTGA	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.2107C>A	18.37:g.33831189C>A	ENSP00000261326:p.His703Asn	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_017947		Missense_Mutation	SNP	ENST00000261326.5	37	CCDS11919.1	537	0.24587912087912087	24	0.04878048780487805	136	0.3756906077348066	155	0.270979020979021	222	0.2928759894459103	C	11.73	1.726291	0.30593	0.09192	0.283953	ENSG00000075643	ENST00000261326	T	0.16597	2.33	5.52	5.52	0.82312	Pyruvate kinase-like, insert domain (1);	0.100513	0.64402	D	0.000001	T	0.00012	0.0000	L	0.59436	1.845	0.37661	P	0.07721199999999995	B	0.23377	0.084	B	0.23716	0.048	T	0.45644	-0.9247	9	0.40728	T	0.16	-15.774	14.9506	0.71071	0.0:1.0:0.0:0.0	rs594445;rs3737372;rs17790830;rs56434535;rs57829177;rs594445	703	Q96EN8	MOCOS_HUMAN	N	703	ENSP00000261326:H703N	ENSP00000261326:H703N	H	+	1	0	MOCOS	32085187	1.000000	0.71417	0.968000	0.41197	0.333000	0.28666	3.537000	0.53590	2.597000	0.87782	0.655000	0.94253	CAT	C|0.776;A|0.224	0.224	strong		0.373	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1		
VEPH1	79674	hgsc.bcm.edu	37	3	156983375	156983375	+	Silent	SNP	C	C	T	rs75175345	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:156983375C>T	ENST00000362010.2	-	13	2512	c.2205G>A	c.(2203-2205)agG>agA	p.R735R	VEPH1_ENST00000543418.1_Silent_p.R690R|RP11-550I24.2_ENST00000488040.1_RNA|VEPH1_ENST00000392833.2_Silent_p.R690R|RP11-550I24.2_ENST00000475102.1_RNA|VEPH1_ENST00000392832.2_Silent_p.R735R|RP11-550I24.2_ENST00000487238.1_RNA	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	735	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			GTGTTTTCCACCTTTTGATGA	0.373													C|||	28	0.00559105	0.0	0.0058	5008	,	,		21125	0.0		0.0129	False		,,,				2504	0.0112				p.R735R		Atlas-SNP	.											.	VEPH1	129	.	0			c.G2205A						PASS	.	C	,,	18,4388	23.3+/-48.9	0,18,2185	175.0	162.0	166.0		2070,2205,2205	1.8	1.0	3	dbSNP_132	166	166,8434	78.4+/-141.0	2,162,4136	no	coding-synonymous,coding-synonymous,coding-synonymous	VEPH1	NM_001167911.1,NM_001167912.1,NM_024621.2	,,	2,180,6321	TT,TC,CC		1.9302,0.4085,1.4147	,,	690/789,735/834,735/834	156983375	184,12822	2203	4300	6503	SO:0001819	synonymous_variant	79674	exon13			TTTCCACCTTTTG	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"""Pleckstrin homology (PH) domain containing"""	25735	protein-coding gene	gene with protein product		609594	"""ventricular zone expressed PH domain homolog 1 (zebrafish)"""			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.2205G>A	3.37:g.156983375C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	155	60	0.387097	NM_001167912	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Silent	SNP	ENST00000362010.2	37	CCDS3179.1																																																																																			C|0.989;T|0.011	0.011	strong		0.373	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621	
IQCE	23288	hgsc.bcm.edu	37	7	2649777	2649777	+	Missense_Mutation	SNP	C	C	T	rs1061566	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:2649777C>T	ENST00000402050.2	+	22	2253	c.2069C>T	c.(2068-2070)aCg>aTg	p.T690M	IQCE_ENST00000325979.7_Missense_Mutation_p.T625M|IQCE_ENST00000438376.2_Missense_Mutation_p.T674M|IQCE_ENST00000404984.1_Missense_Mutation_p.T639M	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	690			T -> M (in dbSNP:rs1061566). {ECO:0000269|PubMed:10470851}.			mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		TCTCTGCCCACGAAGAACTTT	0.557													C|||	310	0.061901	0.0053	0.0865	5008	,	,		21817	0.003		0.1342	False		,,,				2504	0.1074				p.T690M		Atlas-SNP	.											.	IQCE	66	.	0			c.C2069T						PASS	.	C	MET/THR,MET/THR	141,4079		4,133,1973	101.0	102.0	101.0		2021,2069	-3.2	0.0	7	dbSNP_86	101	1311,7151		107,1097,3027	yes	missense,missense	IQCE	NM_001100390.1,NM_152558.3	81,81	111,1230,5000	TT,TC,CC		15.4928,3.3412,11.4493	probably-damaging,probably-damaging	674/680,690/696	2649777	1452,11230	2110	4231	6341	SO:0001583	missense	23288	exon22			TGCCCACGAAGAA	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.2069C>T	7.37:g.2649777C>T	ENSP00000385597:p.Thr690Met	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	237	97	0.409283	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	141	0.06456043956043957	6	0.012195121951219513	29	0.08011049723756906	0	0.0	106	0.13984168865435356	C	12.12	1.842166	0.32513	0.033412	0.154928	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979	T;T;T;T	0.11604	2.77;2.76;2.77;2.77	4.63	-3.23	0.05109	.	1.412350	0.04877	N	0.447051	T	0.00039	0.0001	L	0.28274	0.84	0.80722	P	0.0	B;B	0.20887	0.029;0.049	B;B	0.11329	0.003;0.006	T	0.43393	-0.9394	9	0.48119	T	0.1	.	5.2101	0.15312	0.0:0.1865:0.4057:0.4078	rs1061566;rs1061566	690;674	Q6IPM2;Q6IPM2-4	IQCE_HUMAN;.	M	690;639;674;625	ENSP00000385597:T690M;ENSP00000385945:T639M;ENSP00000396178:T674M;ENSP00000313772:T625M	ENSP00000313772:T625M	T	+	2	0	IQCE	2616303	0.003000	0.15002	0.000000	0.03702	0.005000	0.04900	-0.450000	0.06803	-0.358000	0.08162	-0.367000	0.07326	ACG	C|0.919;T|0.081	0.081	strong		0.557	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5146377	5146377	+	Missense_Mutation	SNP	T	T	C	rs1019747	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:5146377T>C	ENST00000274181.7	+	3	448	c.310T>C	c.(310-312)Tcc>Ccc	p.S104P	CTD-2297D10.1_ENST00000514848.1_RNA|ADAMTS16_ENST00000511368.1_Missense_Mutation_p.S104P	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	104				S -> P (in Ref. 1; CAC86015). {ECO:0000305}.	branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						GCTGAAAGGCTCCAGGCACGA	0.557													T|||	2476	0.494409	0.6248	0.5951	5008	,	,		17615	0.5		0.3857	False		,,,				2504	0.3528				p.S104P		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.T310C						PASS	.	T	PRO/SER	2288,1732		655,978,377	72.0	74.0	73.0		310	0.1	0.1	5	dbSNP_86	73	3183,5163		615,1953,1605	yes	missense	ADAMTS16	NM_139056.2	74	1270,2931,1982	CC,CT,TT		38.138,43.0846,44.2423	benign	104/1225	5146377	5471,6895	2010	4173	6183	SO:0001583	missense	170690	exon3			AAAGGCTCCAGGC	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17108	protein-coding gene	gene with protein product		607510	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"""			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.310T>C	5.37:g.5146377T>C	ENSP00000274181:p.Ser104Pro	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	1112	0.5091575091575091	309	0.6280487804878049	197	0.5441988950276243	302	0.527972027972028	304	0.40105540897097625	T	12.24	1.878622	0.33162	0.569154	0.38138	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	T;T	0.05447	3.44;3.44	5.55	0.125	0.14718	Peptidase M12B, propeptide (1);	0.312327	0.30383	N	0.009754	T	0.00012	0.0000	N	0.02539	-0.55	0.47153	P	6.690000000000307E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.001;0.002;0.004	T	0.21518	-1.0243	9	0.41790	T	0.15	.	2.4851	0.04596	0.2552:0.073:0.1329:0.5388	rs1019747;rs16874854;rs52824859;rs61222875;rs1019747	104;104;104	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	P	104	ENSP00000274181:S104P;ENSP00000421631:S104P	ENSP00000274181:S104P	S	+	1	0	ADAMTS16	5199377	0.982000	0.34865	0.106000	0.21319	0.801000	0.45260	0.309000	0.19332	-0.120000	0.11809	0.460000	0.39030	TCC	T|0.532;C|0.468	0.468	strong		0.557	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135721781	135721781	+	Missense_Mutation	SNP	C	C	G	rs34901937	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:135721781C>G	ENST00000264977.3	+	2	2058	c.1441C>G	c.(1441-1443)Cct>Gct	p.P481A	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	481			P -> A (in dbSNP:rs34901937).		eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TGTTAATCTACCTAAGGAAGA	0.333													C|||	155	0.0309505	0.0144	0.036	5008	,	,		18108	0.005		0.0646	False		,,,				2504	0.0419				p.P481A		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.C1441G						PASS	.	C	,ALA/PRO	98,4248		0,98,2075	55.0	60.0	58.0		,1441	-0.7	0.0	3	dbSNP_126	58	643,7935		23,597,3669	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,27	23,695,5744	GG,GC,CC		7.4959,2.2549,5.7335	,benign	,481/1151	135721781	741,12183	2173	4289	6462	SO:0001583	missense	5523	exon2			AATCTACCTAAGG	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.1441C>G	3.37:g.135721781C>G	ENSP00000264977:p.Pro481Ala	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	68	0.031135531135531136	8	0.016260162601626018	12	0.03314917127071823	0	0.0	48	0.0633245382585752	C	0.905	-0.720893	0.03182	0.022549	0.074959	ENSG00000073711	ENST00000264977	T	0.05786	3.39	5.42	-0.668	0.11392	.	0.807223	0.11400	N	0.567898	T	0.00412	0.0013	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39143	-0.9628	10	0.42905	T	0.14	.	5.0497	0.14501	0.0:0.267:0.3102:0.4229	rs34901937;rs61748113	481	Q06190	P2R3A_HUMAN	A	481	ENSP00000264977:P481A	ENSP00000264977:P481A	P	+	1	0	PPP2R3A	137204471	0.000000	0.05858	0.002000	0.10522	0.829000	0.46940	-0.238000	0.08977	0.010000	0.14839	-0.345000	0.07892	CCT	C|0.945;G|0.055	0.055	strong		0.333	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
CAP2	10486	hgsc.bcm.edu	37	6	17514088	17514088	+	Missense_Mutation	SNP	G	G	A	rs576260321		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:17514088G>A	ENST00000229922.2	+	7	1071	c.539G>A	c.(538-540)cGt>cAt	p.R180H	CAP2_ENST00000378990.2_Missense_Mutation_p.R154H|CAP2_ENST00000465994.1_Intron|CAP2_ENST00000493172.1_Intron|CAP2_ENST00000489374.1_Intron	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	180					activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			AGTGATTTGCGTCATGTGGAT	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		19343	0.0		0.0	False		,,,				2504	0.001				p.R180H		Atlas-SNP	.											CAP2,NS,carcinoma,0,1	CAP2	61	1	0			c.G539A						scavenged	.						105.0	89.0	94.0					6																	17514088		2203	4300	6503	SO:0001583	missense	10486	exon7			ATTTGCGTCATGT	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.539G>A	6.37:g.17514088G>A	ENSP00000229922:p.Arg180His	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	120	2	0.0166667	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Missense_Mutation	SNP	ENST00000229922.2	37	CCDS4539.1	.	.	.	.	.	.	.	.	.	.	G	17.13	3.311756	0.60414	.	.	ENSG00000112186	ENST00000229922;ENST00000378990	T;T	0.12039	2.72;2.72	5.84	4.97	0.65823	Adenylate cyclase-associated CAP, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.08714	0.0216	L	0.56396	1.775	0.80722	D	1	B;B	0.29766	0.048;0.256	B;B	0.29524	0.031;0.103	T	0.02728	-1.1118	10	0.54805	T	0.06	-10.4719	14.7994	0.69903	0.0699:0.0:0.9301:0.0	.	154;180	E9PDI2;P40123	.;CAP2_HUMAN	H	180;154	ENSP00000229922:R180H;ENSP00000368275:R154H	ENSP00000229922:R180H	R	+	2	0	CAP2	17622067	1.000000	0.71417	0.994000	0.49952	0.964000	0.63967	6.752000	0.74898	1.484000	0.48361	0.655000	0.94253	CGT	.	.	none		0.398	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
CDC5L	988	hgsc.bcm.edu	37	6	44413463	44413463	+	Silent	SNP	T	T	A	rs2273666	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:44413463T>A	ENST00000371477.3	+	15	2462	c.2163T>A	c.(2161-2163)ctT>ctA	p.L721L		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	721	Interaction with PLRG1.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AAATTTTGCTTGGGGGTTACC	0.463													T|||	1146	0.228834	0.0484	0.1441	5008	,	,		17504	0.5546		0.0785	False		,,,				2504	0.3517				p.L721L		Atlas-SNP	.											.	CDC5L	86	.	0			c.T2163A						PASS	.	T		245,4161	143.1+/-178.2	6,233,1964	89.0	87.0	87.0		2163	3.1	1.0	6	dbSNP_100	87	604,7996	159.2+/-212.6	19,566,3715	no	coding-synonymous	CDC5L	NM_001253.2		25,799,5679	AA,AT,TT		7.0233,5.5606,6.5278		721/803	44413463	849,12157	2203	4300	6503	SO:0001819	synonymous_variant	988	exon15			TTTGCTTGGGGGT	D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"""CDC5 (cell division cycle 5, S. pombe, homolog)-like"", ""CDC5 cell division cycle 5-like (S. pombe)"""			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.2163T>A	6.37:g.44413463T>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	179	88	0.49162	NM_001253	Q76N46|Q99974	Silent	SNP	ENST00000371477.3	37	CCDS4912.1																																																																																			T|0.878;A|0.122	0.122	strong		0.463	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1		
LPCAT3	10162	hgsc.bcm.edu	37	12	7092665	7092665	+	Missense_Mutation	SNP	A	A	G	rs34196984	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:7092665A>G	ENST00000261407.4	-	2	272	c.187T>C	c.(187-189)Ttc>Ctc	p.F63L	LPCAT3_ENST00000535021.1_5'Flank	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	63			F -> L (in dbSNP:rs34196984).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						TCCTTGTAGAAAAGGTAATGC	0.418													A|||	133	0.0265575	0.0272	0.0144	5008	,	,		-128	0.0188		0.0249	False		,,,				2504	0.044				p.F63L		Atlas-SNP	.											LPCAT3,right_upper_lobe,carcinoma,+2,1	LPCAT3	33	1	0			c.T187C						scavenged	.	A	LEU/PHE	101,4305	80.4+/-118.8	1,99,2103	160.0	162.0	162.0		187	5.4	1.0	12	dbSNP_126	162	166,8434	77.2+/-139.8	0,166,4134	yes	missense	LPCAT3	NM_005768.5	22	1,265,6237	GG,GA,AA		1.9302,2.2923,2.0529	benign	63/488	7092665	267,12739	2203	4300	6503	SO:0001583	missense	10162	exon2			TGTAGAAAAGGTA	U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"""O-acyltransferase (membrane bound) domain containing 5"", ""membrane bound O-acyltransferase domain containing 5"""	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970	ENST00000261407.4:c.187T>C	12.37:g.7092665A>G	ENSP00000261407:p.Phe63Leu	Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_005768	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Missense_Mutation	SNP	ENST00000261407.4	37	CCDS8572.1	44	0.020146520146520148	11	0.022357723577235773	5	0.013812154696132596	7	0.012237762237762238	21	0.027704485488126648	A	16.43	3.121966	0.56613	0.022923	0.019302	ENSG00000111684	ENST00000261407	T	0.71817	-0.6	5.39	5.39	0.77823	.	0.606837	0.17415	N	0.175051	T	0.23451	0.0567	N	0.02697	-0.525	0.58432	D	0.999995	P	0.48294	0.908	B	0.41860	0.368	T	0.43572	-0.9383	10	0.11485	T	0.65	-11.0296	15.7069	0.77592	1.0:0.0:0.0:0.0	rs34196984	63	Q6P1A2	MBOA5_HUMAN	L	63	ENSP00000261407:F63L	ENSP00000261407:F63L	F	-	1	0	LPCAT3	6962926	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.279000	0.89901	2.159000	0.67721	0.533000	0.62120	TTC	A|0.979;G|0.021	0.021	strong		0.418	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768	
CEP104	9731	hgsc.bcm.edu	37	1	3745924	3745924	+	Missense_Mutation	SNP	G	G	A	rs2275831	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:3745924G>A	ENST00000378230.3	-	15	2381	c.2057C>T	c.(2056-2058)gCg>gTg	p.A686V	CEP104_ENST00000460038.1_5'Flank	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	686			A -> V (in dbSNP:rs2275831).			centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						TTCTGTAGCCGCTTTTCTCCG	0.378													G|||	1054	0.210463	0.0802	0.1311	5008	,	,		17124	0.5208		0.0557	False		,,,				2504	0.2822				p.A686V		Atlas-SNP	.											.	CEP104	79	.	0			c.C2057T						PASS	.	G	VAL/ALA	389,4017	191.9+/-217.4	24,341,1838	51.0	54.0	53.0		2057	4.4	0.8	1	dbSNP_100	53	397,8203	126.2+/-184.7	9,379,3912	yes	missense	CEP104	NM_014704.3	64	33,720,5750	AA,AG,GG		4.6163,8.8289,6.0434	benign	686/926	3745924	786,12220	2203	4300	6503	SO:0001583	missense	9731	exon15			GTAGCCGCTTTTC	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"""glycine, glutamate, thienylcyclohexylpiperidine binding protein"""		"""KIAA0562"""	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.2057C>T	1.37:g.3745924G>A	ENSP00000367476:p.Ala686Val	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	37	CCDS30571.1	431	0.19734432234432234	43	0.08739837398373984	55	0.15193370165745856	289	0.5052447552447552	44	0.05804749340369393	G	7.460	0.644553	0.14451	0.088289	0.046163	ENSG00000116198	ENST00000378230	T	0.39997	1.05	5.32	4.39	0.52855	.	0.370796	0.27595	N	0.018662	T	0.00012	0.0000	L	0.38531	1.155	0.09310	P	0.9999999999980493	B	0.21821	0.061	B	0.17722	0.019	T	0.46884	-0.9159	9	0.28530	T	0.3	.	7.1488	0.25597	0.0889:0.0:0.7414:0.1696	rs2275831;rs52804137;rs56515208;rs56685513;rs2275831	686	O60308	CE104_HUMAN	V	686	ENSP00000367476:A686V	ENSP00000367476:A686V	A	-	2	0	CEP104	3735784	1.000000	0.71417	0.824000	0.32777	0.607000	0.37147	2.063000	0.41423	1.208000	0.43306	0.591000	0.81541	GCG	G|0.873;A|0.127	0.127	strong		0.378	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704	
UBR2	23304	hgsc.bcm.edu	37	6	42532102	42532102	+	Silent	SNP	C	C	T	rs3749897	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:42532102C>T	ENST00000372899.1	+	1	303	c.45C>T	c.(43-45)agC>agT	p.S15S	UBR2_ENST00000372903.2_Silent_p.S15S|UBR2_ENST00000372901.1_Silent_p.S15S	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	15					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TCGACCGGAGCTTGCTGGAAT	0.692													T|||	2341	0.467452	0.5325	0.4179	5008	,	,		15673	0.4464		0.4046	False		,,,				2504	0.501				p.S15S		Atlas-SNP	.											.	UBR2	134	.	0			c.C45T						PASS	.	T	,	2221,2183	566.8+/-382.0	551,1119,532	68.0	65.0	66.0		45,45	4.9	1.0	6	dbSNP_107	66	3544,5056	613.3+/-396.1	745,2054,1501	no	coding-synonymous,coding-synonymous	UBR2	NM_001184801.1,NM_015255.2	,	1296,3173,2033	TT,TC,CC		41.2093,49.5686,44.3325	,	15/440,15/1756	42532102	5765,7239	2202	4300	6502	SO:0001819	synonymous_variant	23304	exon1			CCGGAGCTTGCTG	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.45C>T	6.37:g.42532102C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	154	70	0.454545	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			C|0.559;G|0.000;T|0.440	0.440	strong		0.692	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
SORBS1	10580	hgsc.bcm.edu	37	10	97141487	97141487	+	Silent	SNP	G	G	A	rs61739184	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:97141487G>A	ENST00000361941.3	-	16	1634	c.1608C>T	c.(1606-1608)taC>taT	p.Y536Y	SORBS1_ENST00000306402.6_Silent_p.Y367Y|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000607232.1_Silent_p.Y325Y|SORBS1_ENST00000371249.2_Silent_p.Y458Y|SORBS1_ENST00000371239.1_Silent_p.Y335Y|SORBS1_ENST00000393949.1_Silent_p.Y506Y|SORBS1_ENST00000354106.3_Silent_p.Y506Y|SORBS1_ENST00000371241.1_Silent_p.Y326Y|SORBS1_ENST00000371227.4_Silent_p.Y490Y|SORBS1_ENST00000277982.5_Silent_p.Y558Y|SORBS1_ENST00000371245.3_Silent_p.Y421Y|SORBS1_ENST00000347291.4_Silent_p.Y404Y|SORBS1_ENST00000371247.2_Silent_p.Y536Y|SORBS1_ENST00000353505.5_Silent_p.Y421Y|SORBS1_ENST00000371246.2_Silent_p.Y558Y	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1									p.Y421Y(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		GCTGATATTCGTAAATGCTCT	0.393													G|||	228	0.0455272	0.0023	0.0245	5008	,	,		18852	0.0724		0.0298	False		,,,				2504	0.1074				p.Y558Y		Atlas-SNP	.											SORBS1,NS,carcinoma,0,1	SORBS1	185	1	1	Substitution - coding silent(1)	stomach(1)	c.C1674T						PASS	.	G	,,,,,,	41,4365	43.8+/-77.6	0,41,2162	219.0	210.0	213.0		1608,1674,1263,978,978,1374,1101	-0.2	1.0	10	dbSNP_129	213	261,8339	101.4+/-162.7	5,251,4044	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	,,,,,,	5,292,6206	AA,AG,GG		3.0349,0.9305,2.322	,,,,,,	536/1293,558/1152,421/906,326/741,326/685,458/817,367/782	97141487	302,12704	2203	4300	6503	SO:0001819	synonymous_variant	10580	exon16			ATATTCGTAAATG	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.1608C>T	10.37:g.97141487G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	79	72	0.911392	NM_001034955		Silent	SNP	ENST00000361941.3	37	CCDS31255.1																																																																																			G|0.974;A|0.026	0.026	strong		0.393	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
MKI67	4288	hgsc.bcm.edu	37	10	129905429	129905429	+	Missense_Mutation	SNP	C	C	T	rs7918199	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:129905429C>T	ENST00000368654.3	-	13	5050	c.4675G>A	c.(4675-4677)Gtg>Atg	p.V1559M	MKI67_ENST00000368653.3_Missense_Mutation_p.V1199M	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1559	16 X 122 AA approximate repeats.		V -> M (in dbSNP:rs7918199).		cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.V1559M(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				AGTTTCTGCACTGGAGTTCCC	0.498													C|||	515	0.102835	0.0666	0.1556	5008	,	,		20762	0.1359		0.0785	False		,,,				2504	0.1053				p.V1559M		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - Missense(1)	stomach(1)	c.G4675A						PASS	.	C	MET/VAL,MET/VAL	296,4110	162.5+/-194.5	11,274,1918	278.0	249.0	259.0		3595,4675	-2.0	0.0	10	dbSNP_116	259	771,7829	183.7+/-231.9	39,693,3568	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	21,21	50,967,5486	TT,TC,CC		8.9651,6.7181,8.2039	possibly-damaging,possibly-damaging	1199/2897,1559/3257	129905429	1067,11939	2203	4300	6503	SO:0001583	missense	4288	exon13			TCTGCACTGGAGT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.4675G>A	10.37:g.129905429C>T	ENSP00000357643:p.Val1559Met	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	352	158	0.448864	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	209	0.09569597069597069	33	0.06707317073170732	39	0.10773480662983426	79	0.1381118881118881	58	0.07651715039577836	C	10.76	1.440781	0.25900	0.067181	0.089651	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02258	4.37;4.37	4.21	-1.95	0.07548	.	1.347280	0.05153	N	0.496442	T	0.00039	0.0001	L	0.44542	1.39	0.80722	P	0.0	B;P;P	0.48503	0.128;0.911;0.56	B;P;B	0.49953	0.033;0.627;0.446	T	0.42464	-0.9450	9	0.46703	T	0.11	.	9.7412	0.40420	0.0:0.5379:0.0:0.4621	rs7918199;rs52813597;rs60630618;rs7918199	1558;1199;1559	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	M	1559;1199;1558	ENSP00000357643:V1559M;ENSP00000357642:V1199M	ENSP00000357642:V1199M	V	-	1	0	MKI67	129795419	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.562000	0.00920	-0.576000	0.05974	0.462000	0.41574	GTG	C|0.914;T|0.086	0.086	strong		0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
ATP13A2	23400	hgsc.bcm.edu	37	1	17313343	17313343	+	Silent	SNP	G	G	A	rs9435659	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17313343G>A	ENST00000326735.8	-	27	3225	c.3192C>T	c.(3190-3192)gcC>gcT	p.A1064A	ATP13A2_ENST00000452699.1_Silent_p.A1059A|ATP13A2_ENST00000341676.5_Silent_p.A1020A|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2	1064					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CCTTGGACACGGCTGCAGCCA	0.662													G|||	1695	0.338458	0.1369	0.4568	5008	,	,		13447	0.2599		0.5089	False		,,,				2504	0.4325				p.A1064A		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C3192T						PASS	.	G	,,	915,3491	346.2+/-308.9	101,713,1389	64.0	54.0	57.0		3177,3060,3192	-4.5	0.0	1	dbSNP_119	57	4501,4099	586.8+/-392.1	1158,2185,957	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	1259,2898,2346	AA,AG,GG		47.6628,20.7671,41.6423	,,	1059/1176,1020/1159,1064/1181	17313343	5416,7590	2203	4300	6503	SO:0001819	synonymous_variant	23400	exon27			GGACACGGCTGCA	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.3192C>T	1.37:g.17313343G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			G|0.606;A|0.394	0.394	strong		0.662	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
H2AFY	9555	hgsc.bcm.edu	37	5	134670741	134670741	+	Silent	SNP	C	C	T	rs3733728	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:134670741C>T	ENST00000511689.1	-	9	1637	c.1044G>A	c.(1042-1044)acG>acA	p.T348T	H2AFY_ENST00000512507.1_5'UTR|CTC-349C3.1_ENST00000432382.3_Intron|H2AFY_ENST00000510038.1_Silent_p.T348T|H2AFY_ENST00000423969.2_Silent_p.T176T|H2AFY_ENST00000312469.4_Silent_p.T345T|H2AFY_ENST00000304332.4_Silent_p.T347T	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	348	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CGAAGTACACCGTTTTGATGG	0.493													C|||	182	0.0363419	0.0068	0.0187	5008	,	,		22264	0.0516		0.0457	False		,,,				2504	0.0634				p.T348T		Atlas-SNP	.											.	H2AFY	61	.	0			c.G1044A						PASS	.	C	,,,	60,4346	56.8+/-93.2	1,58,2144	149.0	133.0	139.0		1041,1041,1035,1044	-1.9	1.0	5	dbSNP_107	139	473,8127	139.2+/-195.9	13,447,3840	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	H2AFY	NM_001040158.1,NM_004893.2,NM_138609.2,NM_138610.2	,,,	14,505,5984	TT,TC,CC		5.5,1.3618,4.0981	,,,	347/372,347/372,345/370,348/373	134670741	533,12473	2203	4300	6503	SO:0001819	synonymous_variant	9555	exon9			GTACACCGTTTTG	AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"""Histones / Replication-independent"""	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.1044G>A	5.37:g.134670741C>T		Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	342	163	0.476608	NM_138610	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Silent	SNP	ENST00000511689.1	37	CCDS4185.1																																																																																			C|0.963;T|0.037	0.037	strong		0.493	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893	
NFIA	4774	hgsc.bcm.edu	37	1	61869783	61869783	+	Silent	SNP	G	G	A	rs2236059	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:61869783G>A	ENST00000403491.3	+	8	1567	c.1083G>A	c.(1081-1083)ccG>ccA	p.P361P	NFIA_ENST00000479364.1_3'UTR|NFIA_ENST00000371189.4_Silent_p.P406P|NFIA_ENST00000371185.2_Silent_p.P339P|NFIA_ENST00000371187.3_Silent_p.P361P|NFIA_ENST00000371191.1_Silent_p.P384P|NFIA_ENST00000485903.2_Silent_p.P318P|NFIA_ENST00000407417.3_Silent_p.P353P|NFIA_ENST00000357977.5_Silent_p.P9P|NFIA_ENST00000371184.2_Silent_p.P232P	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	361					DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						CAGCAAGTCCGCATGCAACAC	0.483													G|||	1772	0.353834	0.289	0.3761	5008	,	,		19329	0.5625		0.2853	False		,,,				2504	0.2812				p.P406P		Atlas-SNP	.											.	NFIA	76	.	0			c.G1218A						PASS	.	G	,,,	1259,3147	433.3+/-343.5	179,901,1123	175.0	160.0	165.0		1083,1059,1218,1083	-10.5	0.6	1	dbSNP_98	165	2299,6301	387.1+/-342.1	331,1637,2332	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFIA	NM_001134673.3,NM_001145511.1,NM_001145512.1,NM_005595.4	,,,	510,2538,3455	AA,AG,GG		26.7326,28.5747,27.3566	,,,	361/510,353/502,406/555,361/499	61869783	3558,9448	2203	4300	6503	SO:0001819	synonymous_variant	4774	exon9			AAGTCCGCATGCA	U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599			7784	protein-coding gene	gene with protein product		600727				7590749	Standard	NM_001134673		Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.1083G>A	1.37:g.61869783G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	212	209	0.985849	NM_001145512	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	Silent	SNP	ENST00000403491.3	37	CCDS44156.1																																																																																			G|0.699;A|0.301	0.301	strong		0.483	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023799.3	NM_005595	
PIK3AP1	118788	hgsc.bcm.edu	37	10	98469507	98469507	+	Missense_Mutation	SNP	C	C	A	rs3748229	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:98469507C>A	ENST00000339364.5	-	2	366	c.247G>T	c.(247-249)Gcc>Tcc	p.A83S		NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	83	Necessary and sufficent to mediate inhibition of NF-kappa-B downstream of activated TLRs; may mediate interaction with MYD88 and TIRAP. {ECO:0000250}.		A -> S (in dbSNP:rs3748229). {ECO:0000269|PubMed:17974005}.		negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		GGCAGCAAGGCGGGCTTGTGG	0.642													C|||	2116	0.422524	0.5439	0.4092	5008	,	,		19812	0.3095		0.3191	False		,,,				2504	0.4908				p.A83S		Atlas-SNP	.											PIK3AP1,caecum,carcinoma,+2,1	PIK3AP1	111	1	0			c.G247T						PASS	.	C	SER/ALA	2222,2184	585.1+/-386.2	566,1090,547	53.0	54.0	53.0		247	2.0	0.0	10	dbSNP_107	53	2710,5890	430.9+/-356.6	463,1784,2053	yes	missense	PIK3AP1	NM_152309.2	99	1029,2874,2600	AA,AC,CC		31.5116,49.5688,37.921	benign	83/806	98469507	4932,8074	2203	4300	6503	SO:0001583	missense	118788	exon2			GCAAGGCGGGCTT	AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.247G>T	10.37:g.98469507C>A	ENSP00000339826:p.Ala83Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	54	52	0.962963	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Missense_Mutation	SNP	ENST00000339364.5	37	CCDS31259.1	795	0.364010989010989	264	0.5365853658536586	139	0.3839779005524862	146	0.25524475524475526	246	0.3245382585751979	C	4.397	0.073314	0.08485	0.504312	0.315116	ENSG00000155629	ENST00000339364	T	0.09255	3.0	5.01	2.01	0.26516	.	0.850864	0.10569	N	0.659363	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.43278	-0.9401	9	0.07325	T	0.83	-2.6884	2.6317	0.04946	0.143:0.5239:0.1577:0.1754	rs3748229;rs52814694;rs60576678;rs3748229	83	Q6ZUJ8	BCAP_HUMAN	S	83	ENSP00000339826:A83S	ENSP00000339826:A83S	A	-	1	0	PIK3AP1	98459497	0.000000	0.05858	0.002000	0.10522	0.864000	0.49448	0.168000	0.16622	0.588000	0.29660	0.655000	0.94253	GCC	C|0.621;A|0.379	0.379	strong		0.642	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309	
PNPLA5	150379	hgsc.bcm.edu	37	22	44282276	44282276	+	Missense_Mutation	SNP	A	A	G	rs739231	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:44282276A>G	ENST00000597664.1	-	6	985	c.856T>C	c.(856-858)Tgg>Cgg	p.W286R	PNPLA5_ENST00000593866.1_Missense_Mutation_p.W172R|PNPLA5_ENST00000216177.4_Missense_Mutation_p.W286R|PNPLA5_ENST00000381198.2_Missense_Mutation_p.W172R			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	286			W -> R (in dbSNP:rs739231). {ECO:0000269|PubMed:14702039}.		lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				CCCCCCTTCCAGCGTTGGTCA	0.587													G|||	2516	0.502396	0.2436	0.4597	5008	,	,		18495	0.9048		0.3748	False		,,,				2504	0.5992				p.W286R		Atlas-SNP	.											.	PNPLA5	46	.	0			c.T856C						PASS	.	G	ARG/TRP,ARG/TRP	1175,3231	711.3+/-408.0	165,845,1193	96.0	82.0	87.0		514,856	-2.7	0.0	22	dbSNP_86	87	3209,5391	652.7+/-401.0	585,2039,1676	yes	missense,missense	PNPLA5	NM_001177675.1,NM_138814.3	101,101	750,2884,2869	GG,GA,AA		37.314,26.6682,33.7075	benign,benign	172/316,286/430	44282276	4384,8622	2203	4300	6503	SO:0001583	missense	150379	exon6			CCTTCCAGCGTTG	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.856T>C	22.37:g.44282276A>G	ENSP00000471069:p.Trp286Arg	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	37		1066	0.4880952380952381	113	0.22967479674796748	157	0.43370165745856354	508	0.8881118881118881	288	0.37994722955145116	G	2.853	-0.237927	0.05944	0.266682	0.37314	ENSG00000100341	ENST00000216177;ENST00000381198;ENST00000438734	T;T;T	0.39406	1.56;1.08;1.8	4.2	-2.74	0.05932	.	1.460160	0.04604	N	0.399060	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.25537	-1.0129	9	0.15499	T	0.54	-1.3098	1.9577	0.03379	0.183:0.4234:0.2208:0.1728	rs739231;rs5764378;rs17493115;rs52834315;rs60718837;rs739231	194;172;286	E9PGS4;Q7Z6Z6-2;Q7Z6Z6	.;.;PLPL5_HUMAN	R	286;172;194	ENSP00000216177:W286R;ENSP00000370595:W172R;ENSP00000405732:W194R	ENSP00000216177:W286R	W	-	1	0	PNPLA5	42613609	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.878000	0.04192	-0.705000	0.05035	-1.288000	0.01363	TGG	A|0.572;G|0.428	0.428	strong		0.587	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
POLQ	10721	hgsc.bcm.edu	37	3	121228960	121228960	+	Missense_Mutation	SNP	G	G	A	rs487848	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121228960G>A	ENST00000264233.5	-	11	1870	c.1742C>T	c.(1741-1743)gCg>gTg	p.A581V		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	581					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		GGCCTCAATCGCTCCAAGCTG	0.428								DNA polymerases (catalytic subunits)					G|||	415	0.0828674	0.2179	0.0548	5008	,	,		18290	0.0		0.0825	False		,,,				2504	0.0061				p.A581V	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C1742T						PASS	.	G	VAL/ALA	888,3518	344.6+/-308.2	90,708,1405	205.0	175.0	185.0		1742	4.0	1.0	3	dbSNP_83	185	548,8052	151.0+/-205.8	15,518,3767	yes	missense	POLQ	NM_199420.3	64	105,1226,5172	AA,AG,GG		6.3721,20.1543,11.0411	possibly-damaging	581/2591	121228960	1436,11570	2203	4300	6503	SO:0001583	missense	10721	exon11			TCAATCGCTCCAA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.1742C>T	3.37:g.121228960G>A	ENSP00000264233:p.Ala581Val	Somatic	269	1	0.00371747		WXS	Illumina HiSeq	Phase_I	255	117	0.458824	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	205	0.09386446886446886	124	0.25203252032520324	19	0.052486187845303865	0	0.0	62	0.08179419525065963	G	16.10	3.028705	0.54790	0.201543	0.063721	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.40476	1.03	4.86	3.97	0.46021	.	0.132156	0.49916	D	0.000128	T	0.00012	0.0000	M	0.79926	2.475	0.24081	P	0.99594174	P	0.34815	0.47	B	0.28232	0.087	T	0.17684	-1.0361	9	0.18276	T	0.48	.	9.9512	0.41640	0.0:0.1439:0.6905:0.1656	rs487848;rs1677555;rs52797302;rs487848	581	O75417	DPOLQ_HUMAN	V	204;581;717	ENSP00000264233:A581V	ENSP00000264233:A581V	A	-	2	0	POLQ	122711650	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	7.472000	0.80996	0.988000	0.38734	0.460000	0.39030	GCG	G|0.889;A|0.111	0.111	strong		0.428	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
MAOA	4128	hgsc.bcm.edu	37	X	43571197	43571197	+	Silent	SNP	A	A	C	rs1800464	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:43571197A>C	ENST00000338702.3	+	4	508	c.385A>C	c.(385-387)Agg>Cgg	p.R129R	MAOA_ENST00000542639.1_5'UTR|MAOA_ENST00000497485.1_3'UTR	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	129					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	TAATCTGTGGAGGACAATAGA	0.393													C|||	593	0.157086	0.3843	0.0504	3775	,	,		14211	0.0		0.0308	False		,,,				2504	0.0194				p.R129R		Atlas-SNP	.											.	MAOA	48	.	0			c.A385C						PASS	.	C		1915,1920		426,785,278,421,293	132.0	123.0	126.0		385	0.9	1.0	X	dbSNP_89	126	276,6452		4,177,91,2247,1781	no	coding-synonymous	MAOA	NM_000240.2		430,962,369,2668,2074	CC,CA,C,AA,A		4.1023,49.9348,20.7422		129/528	43571197	2191,8372	2203	4300	6503	SO:0001819	synonymous_variant	4128	exon4			CTGTGGAGGACAA		CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.385A>C	X.37:g.43571197A>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	96	79	0.822917	NM_000240	B4DF46|Q16426	Silent	SNP	ENST00000338702.3	37	CCDS14260.1																																																																																			A|0.740;0|0.061	.	strong		0.393	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240	
FLYWCH1	84256	hgsc.bcm.edu	37	16	2983138	2983138	+	Silent	SNP	C	C	T	rs2074363	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2983138C>T	ENST00000253928.9	+	5	1209	c.804C>T	c.(802-804)gcC>gcT	p.A268A	FLYWCH1_ENST00000399667.2_Silent_p.A268A|FLYWCH1_ENST00000416288.2_Silent_p.A267A			Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1	268						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|lung(3)	4						TAGGACAGGCCCGGCCCCTCG	0.627													.|||	532	0.10623	0.1725	0.1009	5008	,	,		16167	0.0625		0.1143	False		,,,				2504	0.0573				p.A267A		Atlas-SNP	.											.	FLYWCH1	27	.	0			c.C801T						PASS	.	C	,	495,3431		39,417,1507	24.0	27.0	26.0		801,801	0.9	0.0	16	dbSNP_96	26	837,7425		44,749,3338	no	coding-synonymous,coding-synonymous	FLYWCH1	NM_020912.1,NM_032296.2	,	83,1166,4845	TT,TC,CC		10.1307,12.6083,10.9288	,	267/704,267/716	2983138	1332,10856	1963	4131	6094	SO:0001819	synonymous_variant	84256	exon5			ACAGGCCCGGCCC	AL136585	CCDS45390.1	16p13.3	2013-01-10	2007-06-21	2007-06-21	ENSG00000059122	ENSG00000059122		"""Zinc fingers"""	25404	protein-coding gene	gene with protein product						11230166, 10997877	Standard	XM_006720959		Approved	DKFZp761A132	uc002csc.3	Q4VC44		ENST00000253928.9:c.804C>T	16.37:g.2983138C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	45	44	0.977778	NM_020912	D3DUA1|Q6ZSQ1|Q8WV62|Q9BQG6|Q9BUS5|Q9HCM0	Silent	SNP	ENST00000253928.9	37																																																																																				C|0.877;T|0.123	0.123	strong		0.627	FLYWCH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000436479.1	NM_032296	
GEMIN5	25929	hgsc.bcm.edu	37	5	154307070	154307070	+	Missense_Mutation	SNP	G	G	C	rs35522740	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:154307070G>C	ENST00000285873.7	-	7	1030	c.955C>G	c.(955-957)Cgg>Ggg	p.R319G		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	319					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GTGTATTTCCGTCTCCAAGAT	0.378													G|||	55	0.0109824	0.003	0.0115	5008	,	,		21838	0.0		0.0328	False		,,,				2504	0.0102				p.R319G		Atlas-SNP	.											.	GEMIN5	120	.	0			c.C955G						PASS	.	G	GLY/ARG	16,4390	22.3+/-47.3	0,16,2187	134.0	124.0	127.0		955	5.6	1.0	5	dbSNP_126	127	228,8372	94.0+/-155.9	6,216,4078	yes	missense	GEMIN5	NM_015465.3	125	6,232,6265	CC,CG,GG		2.6512,0.3631,1.8761	probably-damaging	319/1509	154307070	244,12762	2203	4300	6503	SO:0001583	missense	25929	exon7			ATTTCCGTCTCCA	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"""WD repeat domain containing"""	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.955C>G	5.37:g.154307070G>C	ENSP00000285873:p.Arg319Gly	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	161	79	0.490683	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	37	CCDS4330.1	32	0.014652014652014652	3	0.006097560975609756	5	0.013812154696132596	0	0.0	24	0.0316622691292876	G	28.4	4.916127	0.92178	0.003631	0.026512	ENSG00000082516	ENST00000285873	T	0.04758	3.56	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.070336	0.64402	D	0.000010	T	0.04543	0.0124	L	0.41824	1.3	0.54753	D	0.999987	D;D	0.67145	0.996;0.996	D;D	0.63877	0.919;0.919	T	0.11665	-1.0578	10	0.26408	T	0.33	-20.5766	19.7174	0.96129	0.0:0.0:1.0:0.0	rs35522740	318;319	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	G	319	ENSP00000285873:R319G	ENSP00000285873:R319G	R	-	1	2	GEMIN5	154287263	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.678000	0.61641	2.653000	0.90120	0.655000	0.94253	CGG	G|0.979;C|0.021	0.021	strong		0.378	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1		
TTC3	7267	hgsc.bcm.edu	37	21	38563725	38563725	+	Splice_Site	SNP	G	G	A	rs2835655	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:38563725G>A	ENST00000399017.2	+	40	7862	c.5115G>A	c.(5113-5115)aaG>aaA	p.K1705K	TTC3_ENST00000355666.1_Splice_Site_p.K1705K|TTC3_ENST00000354749.2_Splice_Site_p.K1705K|TTC3_ENST00000479930.1_3'UTR|TTC3-AS1_ENST00000424733.1_RNA	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1705					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AGAAAGCAAAGGTAAGTTGTA	0.318													G|||	2007	0.400759	0.3033	0.268	5008	,	,		14083	0.5238		0.3439	False		,,,				2504	0.5583				p.K1705K	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.G5115A						PASS	.	G	,	1406,2998		233,940,1029	34.0	34.0	34.0		5115,5115	2.3	0.4	21	dbSNP_100	34	2626,5944		431,1764,2090	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	TTC3	NM_001001894.1,NM_003316.3	,	664,2704,3119	AA,AG,GG		30.6418,31.9255,31.0775	,	1705/2026,1705/2026	38563725	4032,8942	2202	4285	6487	SO:0001630	splice_region_variant	7267	exon40			AGCAAAGGTAAGT	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5115+1G>A	21.37:g.38563725G>A		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	216	102	0.472222	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1	807	0.3695054945054945	154	0.3130081300813008	98	0.27071823204419887	302	0.527972027972028	253	0.3337730870712401	G	10.31	1.314981	0.23908	0.319255	0.306418	ENSG00000182670	ENST00000428693	.	.	.	5.31	2.28	0.28536	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999886898	.	.	.	.	.	.	T	0.47114	-0.9142	3	.	.	.	-1.6023	4.3185	0.11005	0.2078:0.0:0.5966:0.1956	rs2835655;rs17284336;rs60772137;rs2835655	.	.	.	S	31	.	.	G	+	1	0	TTC3	37485595	1.000000	0.71417	0.353000	0.25747	0.753000	0.42808	1.881000	0.39638	0.223000	0.20920	-0.355000	0.07637	GGT	G|0.653;A|0.347	0.347	strong		0.318	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		Silent
PRTG	283659	hgsc.bcm.edu	37	15	55964778	55964778	+	Missense_Mutation	SNP	C	C	G	rs149494002	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55964778C>G	ENST00000389286.4	-	11	1953	c.1906G>C	c.(1906-1908)Gtg>Ctg	p.V636L		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		TGCCACCTCACAGAAATGGTG	0.458													C|||	12	0.00239617	0.0008	0.0029	5008	,	,		16822	0.0		0.008	False		,,,				2504	0.001				p.V636L		Atlas-SNP	.											.	PRTG	110	.	0			c.G1906C						PASS	.	C	LEU/VAL	8,3802		0,8,1897	78.0	74.0	75.0		1906	5.6	1.0	15	dbSNP_134	75	82,8162		0,82,4040	yes	missense	PRTG	NM_173814.4	32	0,90,5937	GG,GC,CC		0.9947,0.21,0.7466	benign	636/1151	55964778	90,11964	1905	4122	6027	SO:0001583	missense	283659	exon11			ACCTCACAGAAAT	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.1906G>C	15.37:g.55964778C>G	ENSP00000373937:p.Val636Leu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	152	66	0.434211	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	15.36	2.810509	0.50421	0.0021	0.009947	ENSG00000166450	ENST00000389286	T	0.22336	1.96	5.62	5.62	0.85841	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.232951	0.37483	N	0.002061	T	0.16685	0.0401	L	0.43701	1.375	0.80722	D	1	B	0.22541	0.071	B	0.22152	0.038	T	0.01537	-1.1330	10	0.40728	T	0.16	-15.7028	18.6782	0.91537	0.0:1.0:0.0:0.0	.	636	Q2VWP7	PRTG_HUMAN	L	636	ENSP00000373937:V636L	ENSP00000373937:V636L	V	-	1	0	PRTG	53752070	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	4.585000	0.60977	2.648000	0.89879	0.650000	0.86243	GTG	C|0.994;G|0.006	0.006	strong		0.458	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
HLA-B	3106	hgsc.bcm.edu	37	6	31322910	31322910	+	Missense_Mutation	SNP	G	G	A	rs74189305		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31322910G>A	ENST00000412585.2	-	5	1014	c.986C>T	c.(985-987)gCt>gTt	p.A329V		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	329			A -> T (in dbSNP:rs1051488).		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)	p.A329V(4)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						ACACATCACAGCAGCGACCAC	0.587									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.A329V		Atlas-SNP	.											HLA-B,NS,carcinoma,-1,7	HLA-B	54	7	4	Substitution - Missense(4)	kidney(4)	c.C986T						scavenged	.						102.0	101.0	101.0					6																	31322910		1511	2709	4220	SO:0001583	missense	3106	exon5	Familial Cancer Database	;Lichen Sclerosis, Familial	ATCACAGCAGCGA	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.986C>T	6.37:g.31322910G>A	ENSP00000399168:p.Ala329Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	134	8	0.0597015	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	9.051	0.992087	0.18966	.	.	ENSG00000234745	ENST00000412585;ENST00000428231	T	0.00622	6.16	3.73	-3.02	0.05446	.	.	.	.	.	T	0.00109	0.0003	N	0.00729	-1.24	0.09310	N	1	B	0.20052	0.041	B	0.29077	0.098	T	0.22906	-1.0203	9	0.49607	T	0.09	.	5.2273	0.15401	0.4363:0.3516:0.2121:0.0	.	329	P01889	1B07_HUMAN	V	329;208	ENSP00000399168:A329V	ENSP00000399168:A329V	A	-	2	0	HLA-B	31430889	0.000000	0.05858	0.128000	0.21923	0.021000	0.10359	0.033000	0.13754	-0.241000	0.09681	0.448000	0.29417	GCT	.	.	weak		0.587	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ATRN	8455	hgsc.bcm.edu	37	20	3624848	3624848	+	Silent	SNP	C	C	T	rs34398666	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3624848C>T	ENST00000262919.5	+	28	4166	c.4098C>T	c.(4096-4098)gcC>gcT	p.A1366A		NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	1366					cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						GCAACAAAGCCGCTGTCCTCT	0.512													C|||	279	0.0557109	0.0136	0.1037	5008	,	,		20291	0.0		0.169	False		,,,				2504	0.0194				p.A1366A		Atlas-SNP	.											.	ATRN	118	.	0			c.C4098T						PASS	.	C		159,4247	107.8+/-146.2	5,149,2049	132.0	113.0	120.0		4098	-6.8	1.0	20	dbSNP_126	120	1251,7349	250.0+/-277.0	80,1091,3129	no	coding-synonymous	ATRN	NM_139321.2		85,1240,5178	TT,TC,CC		14.5465,3.6087,10.8412		1366/1430	3624848	1410,11596	2203	4300	6503	SO:0001819	synonymous_variant	8455	exon28			CAAAGCCGCTGTC	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"""mahogany protein"""	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.4098C>T	20.37:g.3624848C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	167	80	0.479042	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Silent	SNP	ENST00000262919.5	37	CCDS13053.1																																																																																			C|0.897;T|0.103	0.103	strong		0.512	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321	
GTF2E1	2960	hgsc.bcm.edu	37	3	120500065	120500065	+	Silent	SNP	C	C	T	rs17243695	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:120500065C>T	ENST00000283875.5	+	5	1161	c.1068C>T	c.(1066-1068)agC>agT	p.S356S		NM_005513.2	NP_005504.2	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1, alpha 56kDa	356					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)	22				GBM - Glioblastoma multiforme(114;0.159)		ACTCAGAAAGCGAGACCAGTG	0.537													c|||	26	0.00519169	0.0045	0.0072	5008	,	,		18210	0.0		0.0119	False		,,,				2504	0.0031				p.S356S		Atlas-SNP	.											.	GTF2E1	52	.	0			c.C1068T						PASS	.	T		20,4386	26.2+/-53.5	0,20,2183	107.0	107.0	107.0		1068	-1.2	1.0	3	dbSNP_123	107	127,8473	65.3+/-127.6	0,127,4173	no	coding-synonymous	GTF2E1	NM_005513.2		0,147,6356	TT,TC,CC		1.4767,0.4539,1.1302		356/440	120500065	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	2960	exon5			AGAAAGCGAGACC	S67859	CCDS3002.1	3q21-q24	2010-03-23	2002-08-29		ENSG00000153767	ENSG00000153767		"""General transcription factors"""	4650	protein-coding gene	gene with protein product		189962	"""general transcription factor IIE, polypeptide 1 (alpha subunit, 56kD)"""			1454543, 8162052	Standard	NM_005513		Approved	TFIIE-A, FE	uc003edz.4	P29083	OTTHUMG00000159667	ENST00000283875.5:c.1068C>T	3.37:g.120500065C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	146	63	0.431507	NM_005513	Q16103	Silent	SNP	ENST00000283875.5	37	CCDS3002.1																																																																																			C|0.990;T|0.010	0.010	strong		0.537	GTF2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356770.1	NM_005513	
FLVCR2	55640	hgsc.bcm.edu	37	14	76045963	76045963	+	Silent	SNP	C	C	G	rs2287017	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:76045963C>G	ENST00000238667.4	+	1	1004	c.648C>G	c.(646-648)tcC>tcG	p.S216S	AC007182.6_ENST00000455232.1_RNA	NM_017791.2	NP_060261.2	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular receptor family, member 2	216					heme transport (GO:0015886)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	heme binding (GO:0020037)|heme transporter activity (GO:0015232)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15				BRCA - Breast invasive adenocarcinoma(234;0.029)		CAGCCTGCTCCGTGGCTGTCT	0.532													C|||	2373	0.473842	0.7194	0.3501	5008	,	,		21716	0.5694		0.2137	False		,,,				2504	0.3988				p.S216S		Atlas-SNP	.											.	FLVCR2	39	.	0			c.C648G						PASS	.	C		2908,1498	640.5+/-397.3	971,966,266	40.0	41.0	41.0		648	-1.1	0.0	14	dbSNP_100	41	1929,6671	323.7+/-316.1	216,1497,2587	no	coding-synonymous	FLVCR2	NM_017791.2		1187,2463,2853	GG,GC,CC		22.4302,33.9991,37.1905		216/527	76045963	4837,8169	2203	4300	6503	SO:0001819	synonymous_variant	55640	exon1			CTGCTCCGTGGCT	AK000378	CCDS9844.1, CCDS55933.1	14q24.3	2013-05-22	2007-05-01	2007-05-01	ENSG00000119686	ENSG00000119686		"""Solute carriers"""	20105	protein-coding gene	gene with protein product		610865	"""chromosome 14 open reading frame 58"", ""feline leukemia virus subgroup C cellular receptor 2"""	C14orf58		16439531, 20206334	Standard	NM_017791		Approved	FLJ20371, MFSD7C	uc001xrs.2	Q9UPI3	OTTHUMG00000171487	ENST00000238667.4:c.648C>G	14.37:g.76045963C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	NM_017791	B7Z485|Q53ZT9|Q96JY3|Q9NX90	Silent	SNP	ENST00000238667.4	37	CCDS9844.1																																																																																			C|0.621;G|0.379	0.379	strong		0.532	FLVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413672.1	NM_017791	
FBXO30	84085	hgsc.bcm.edu	37	6	146125793	146125793	+	Missense_Mutation	SNP	A	A	T	rs3811102	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:146125793A>T	ENST00000237281.4	-	2	1915	c.1749T>A	c.(1747-1749)caT>caA	p.H583Q		NM_032145.4	NP_115521.3	Q8TB52	FBX30_HUMAN	F-box protein 30	583			H -> Q (in dbSNP:rs3811102). {ECO:0000269|Ref.3}.				ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		ATGACCTCAAATGGCGGTCAT	0.418																																					p.H583Q		Atlas-SNP	.											.	FBXO30	56	.	0			c.T1749A						PASS	.	A	GLN/HIS	960,3446	362.6+/-316.2	110,740,1353	99.0	86.0	91.0		1749	0.4	0.9	6	dbSNP_107	91	3546,5052	515.7+/-378.7	724,2098,1477	yes	missense	FBXO30	NM_032145.4	24	834,2838,2830	TT,TA,AA		41.2421,21.7885,34.6509	probably-damaging	583/746	146125793	4506,8498	2203	4299	6502	SO:0001583	missense	84085	exon2			CCTCAAATGGCGG	AF248640	CCDS5208.1	6q24	2008-02-05	2004-06-15		ENSG00000118496	ENSG00000118496		"""F-boxes /  ""other"""""	15600	protein-coding gene	gene with protein product		609101	"""F-box only protein, helicase, 18"""				Standard	XM_005267159		Approved	MGC21674, Fbx30	uc003qla.3	Q8TB52	OTTHUMG00000015749	ENST00000237281.4:c.1749T>A	6.37:g.146125793A>T	ENSP00000237281:p.His583Gln	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	178	94	0.52809	NM_032145	Q9BXZ7	Missense_Mutation	SNP	ENST00000237281.4	37	CCDS5208.1	654	0.29945054945054944	106	0.21544715447154472	89	0.24585635359116023	149	0.26048951048951047	310	0.40897097625329815	A	9.123	1.009522	0.19277	0.217885	0.412421	ENSG00000118496	ENST00000237281	T	0.17213	2.29	5.73	0.452	0.16634	.	0.135004	0.64402	N	0.000002	T	0.03520	0.0101	L	0.29908	0.895	0.23030	P	0.99840109	B	0.06786	0.001	B	0.12156	0.007	T	0.35375	-0.9791	9	0.46703	T	0.11	-7.8808	5.4721	0.16676	0.5341:0.2505:0.2154:0.0	rs3811102;rs17822232;rs3811102	583	Q8TB52	FBX30_HUMAN	Q	583	ENSP00000237281:H583Q	ENSP00000237281:H583Q	H	-	3	2	FBXO30	146167486	0.953000	0.32496	0.912000	0.35992	0.957000	0.61999	0.282000	0.18829	-0.138000	0.11434	0.533000	0.62120	CAT	A|0.672;T|0.328	0.328	strong		0.418	FBXO30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042570.2		
CUBN	8029	hgsc.bcm.edu	37	10	16918972	16918972	+	Silent	SNP	A	A	G	rs1801241	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:16918972A>G	ENST00000377833.4	-	57	9095	c.9030T>C	c.(9028-9030)gcT>gcC	p.A3010A		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3010	CUB 22. {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)	p.A3010A(1)		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)	GAACCGGCCCAGCGATGGTGA	0.488													G|||	1239	0.247404	0.354	0.2882	5008	,	,		17623	0.3065		0.0855	False		,,,				2504	0.18				p.A3010A		Atlas-SNP	.											CUBN,NS,carcinoma,0,1	CUBN	515	1	1	Substitution - coding silent(1)	stomach(1)	c.T9030C						PASS	.	G		1441,2965	682.7+/-404.2	242,957,1004	121.0	105.0	111.0		9030	-6.2	0.0	10	dbSNP_89	111	494,8106	797.5+/-407.4	16,462,3822	no	coding-synonymous	CUBN	NM_001081.3		258,1419,4826	GG,GA,AA		5.7442,32.7054,14.8777		3010/3624	16918972	1935,11071	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon57			CGGCCCAGCGATG	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.9030T>C	10.37:g.16918972A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			A|0.814;G|0.186	0.186	strong		0.488	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
MERTK	10461	hgsc.bcm.edu	37	2	112765973	112765973	+	Silent	SNP	A	A	G	rs1131244	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:112765973A>G	ENST00000295408.4	+	14	2138	c.1881A>G	c.(1879-1881)tcA>tcG	p.S627S	MERTK_ENST00000409780.1_Silent_p.S451S|MERTK_ENST00000421804.2_Silent_p.S627S			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	627	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						ACAACTCTTCACAGCGGGAGA	0.448													G|||	2580	0.515176	0.4992	0.5951	5008	,	,		19421	0.2738		0.6243	False		,,,				2504	0.6166				p.S627S		Atlas-SNP	.											.	MERTK	112	.	0			c.A1881G						PASS	.	G		2277,2129	579.1+/-384.8	581,1115,507	95.0	88.0	90.0		1881	-11.9	0.0	2	dbSNP_86	90	5368,3232	486.5+/-371.9	1694,1980,626	no	coding-synonymous	MERTK	NM_006343.2		2275,3095,1133	GG,GA,AA		37.5814,48.3205,41.2194		627/1000	112765973	7645,5361	2203	4300	6503	SO:0001819	synonymous_variant	10461	exon14			CTCTTCACAGCGG	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1881A>G	2.37:g.112765973A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	37	CCDS2094.1																																																																																			A|0.458;G|0.542	0.542	strong		0.448	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651169	1651169	+	Silent	SNP	T	T	C	rs71454095	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1651169T>C	ENST00000399676.2	+	1	137	c.99T>C	c.(97-99)tcT>tcC	p.S33S		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	33						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		gctgtggctctggctgtgggg	0.721													N|||	2639	0.526957	0.643	0.4827	5008	,	,		7432	0.4018		0.5527	False		,,,				2504	0.5041				p.S33S		Atlas-SNP	.											KRTAP5-5,rectum,carcinoma,0,2	KRTAP5-5	86	2	0			c.T99C						scavenged	.	C		2322,1648		759,804,422	20.0	30.0	27.0		99	-1.5	0.0	11	dbSNP_130	27	4372,3646		1321,1730,958	no	coding-synonymous	KRTAP5-5	NM_001001480.2		2080,2534,1380	CC,CT,TT		45.4727,41.5113,44.1608		33/238	1651169	6694,5294	1985	4009	5994	SO:0001819	synonymous_variant	439915	exon1			TGGCTCTGGCTGT	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.99T>C	11.37:g.1651169T>C		Somatic	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			T|0.509;C|0.491	0.491	strong		0.721	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
MKX	283078	hgsc.bcm.edu	37	10	27964470	27964470	+	Silent	SNP	G	G	A	rs2253230	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:27964470G>A	ENST00000375790.5	-	6	1284	c.852C>T	c.(850-852)aaC>aaT	p.N284N	MKX_ENST00000419761.1_Silent_p.N284N			Q8IYA7	MKX_HUMAN	mohawk homeobox	284					collagen fibril organization (GO:0030199)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|positive regulation of collagen biosynthetic process (GO:0032967)|tendon cell differentiation (GO:0035990)|tendon sheath development (GO:0002932)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16						TATTGGATCCGTTTTCCAGAG	0.378													G|||	1428	0.285144	0.295	0.353	5008	,	,		19342	0.121		0.338	False		,,,				2504	0.3384				p.N284N		Atlas-SNP	.											.	MKX	43	.	0			c.C852T						PASS	.	G	,	1379,3027	457.5+/-351.6	235,909,1059	79.0	67.0	71.0		852,852	-2.1	1.0	10	dbSNP_100	71	2853,5747	447.7+/-361.6	469,1915,1916	no	coding-synonymous,coding-synonymous	MKX	NM_001242702.1,NM_173576.2	,	704,2824,2975	AA,AG,GG		33.1744,31.2982,32.5388	,	284/353,284/353	27964470	4232,8774	2203	4300	6503	SO:0001819	synonymous_variant	283078	exon6			GGATCCGTTTTCC	BC036207	CCDS7156.1	10p12.1	2011-06-20	2006-03-31	2006-03-31	ENSG00000150051	ENSG00000150051		"""Homeoboxes / TALE class"""	23729	protein-coding gene	gene with protein product		601332	"""chromosome 10 open reading frame 48"", ""iroquois homeobox protein-like 1"""	C10orf48, IRXL1		16408284	Standard	NM_173576		Approved	MGC39616	uc001itx.4	Q8IYA7	OTTHUMG00000017862	ENST00000375790.5:c.852C>T	10.37:g.27964470G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	195	88	0.451282	NM_001242702	B3KWM5	Silent	SNP	ENST00000375790.5	37	CCDS7156.1																																																																																			G|0.693;A|0.307	0.307	strong		0.378	MKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047332.3	NM_173576	
TTC17	55761	hgsc.bcm.edu	37	11	43472746	43472746	+	Silent	SNP	C	C	T	rs11551137	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:43472746C>T	ENST00000039989.4	+	21	2975	c.2961C>T	c.(2959-2961)ctC>ctT	p.L987L		NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	987					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						TACAAAATCTCGGCAAAGACC	0.423													C|||	416	0.0830671	0.0023	0.2579	5008	,	,		19439	0.0317		0.0954	False		,,,				2504	0.1084				p.L987L		Atlas-SNP	.											.	TTC17	112	.	0			c.C2961T						PASS	.	C		96,4310	77.8+/-116.1	0,96,2107	99.0	91.0	94.0		2961	0.3	1.0	11	dbSNP_120	94	764,7836	182.2+/-230.7	33,698,3569	no	coding-synonymous	TTC17	NM_018259.5		33,794,5676	TT,TC,CC		8.8837,2.1788,6.6123		987/1142	43472746	860,12146	2203	4300	6503	SO:0001819	synonymous_variant	55761	exon21			AAATCTCGGCAAA	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"""Tetratricopeptide (TTC) repeat domain containing"""	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.2961C>T	11.37:g.43472746C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_018259	G3XAB3|Q8NEC0	Silent	SNP	ENST00000039989.4	37	CCDS31466.1	179	0.08195970695970696	2	0.0040650406504065045	85	0.23480662983425415	18	0.03146853146853147	74	0.09762532981530343	C	9.492	1.100985	0.20552	0.021788	0.088837	ENSG00000052841	ENST00000418561	.	.	.	5.84	0.274	0.15654	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.20240	-1.0281	3	.	.	.	-11.7732	6.2318	0.20738	0.0:0.1449:0.3789:0.4762	rs11551137;rs12420769;rs17594421;rs11551137	.	.	.	L	6	.	.	S	+	2	0	TTC17	43429322	0.906000	0.30813	1.000000	0.80357	0.985000	0.73830	-0.334000	0.07883	0.109000	0.17891	-0.300000	0.09419	TCG	C|0.929;T|0.071	0.071	strong		0.423	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259	
OR8J3	81168	hgsc.bcm.edu	37	11	55904751	55904751	+	Silent	SNP	T	T	C	rs1947923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55904751T>C	ENST00000301529.1	-	1	443	c.444A>G	c.(442-444)acA>acG	p.T148T		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	148						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					CATAGAGGTATGTGAGGGACA	0.453													C|||	310	0.061901	0.0938	0.0548	5008	,	,		17372	0.001		0.0944	False		,,,				2504	0.0532				p.T148T		Atlas-SNP	.											.	OR8J3	112	.	0			c.A444G						PASS	.	C		401,4001	789.2+/-415.0	19,363,1819	101.0	97.0	98.0		444	-5.5	0.0	11	dbSNP_92	98	700,7892	787.6+/-407.6	34,632,3630	no	coding-synonymous	OR8J3	NM_001004064.1		53,995,5449	CC,CT,TT		8.1471,9.1095,8.4731		148/316	55904751	1101,11893	2201	4296	6497	SO:0001819	synonymous_variant	81168	exon1			GAGGTATGTGAGG		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.444A>G	11.37:g.55904751T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	163	70	0.429448	NM_001004064	Q6IFB6|Q96RC2	Silent	SNP	ENST00000301529.1	37	CCDS31520.1																																																																																			T|0.925;C|0.075	0.075	strong		0.453	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
SBNO2	22904	hgsc.bcm.edu	37	19	1110829	1110829	+	Silent	SNP	G	G	A	rs2302109	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1110829G>A	ENST00000361757.3	-	26	3180	c.2943C>T	c.(2941-2943)aaC>aaT	p.N981N	SBNO2_ENST00000587024.1_Silent_p.N971N|SBNO2_ENST00000438103.2_Silent_p.N924N	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	981					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAACAGGGCGTTCTGCTTGT	0.592													G|||	2796	0.558307	0.6604	0.6383	5008	,	,		16879	0.4405		0.505	False		,,,				2504	0.5399				p.N981N		Atlas-SNP	.											.	SBNO2	112	.	0			c.C2943T						PASS	.	G	,	2801,1399		942,917,241	135.0	141.0	139.0		2772,2943	1.7	1.0	19	dbSNP_100	139	4229,4221		1041,2147,1037	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	1983,3064,1278	AA,AG,GG		49.9527,33.3095,44.4269	,	924/1310,981/1367	1110829	7030,5620	2100	4225	6325	SO:0001819	synonymous_variant	22904	exon26			CAGGGCGTTCTGC	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.2943C>T	19.37:g.1110829G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	235	113	0.480851	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			G|0.461;A|0.539	0.539	strong		0.592	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
KIAA1683	80726	hgsc.bcm.edu	37	19	18375846	18375846	+	Missense_Mutation	SNP	G	G	A	rs2277921	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:18375846G>A	ENST00000600328.3	-	3	2697	c.2504C>T	c.(2503-2505)cCg>cTg	p.P835L	KIAA1683_ENST00000392413.4_Missense_Mutation_p.P835L|KIAA1683_ENST00000600359.3_Missense_Mutation_p.P789L			Q9H0B3	K1683_HUMAN	KIAA1683	835			P -> L (in dbSNP:rs2277921). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GGGTGCCATCGGCGGCACCAG	0.677													A|||	1503	0.30012	0.4554	0.2478	5008	,	,		18101	0.3165		0.1581	False		,,,				2504	0.2566				p.P835L		Atlas-SNP	.											KIAA1683_ENST00000392413,right_lower_lobe,carcinoma,+1,2	KIAA1683	190	2	0			c.C2504T						PASS	.	A	LEU/PRO,LEU/PRO,LEU/PRO	1854,2552	614.4+/-392.4	397,1060,746	60.0	58.0	59.0		2504,2366,2504	4.3	0.0	19	dbSNP_100	59	1408,7192	730.2+/-406.8	110,1188,3002	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	98,98,98	507,2248,3748	AA,AG,GG		16.3721,42.079,25.0807	benign,benign,benign	835/1368,789/1135,835/1181	18375846	3262,9744	2203	4300	6503	SO:0001583	missense	80726	exon3			GCCATCGGCGGCA	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2504C>T	19.37:g.18375846G>A	ENSP00000470780:p.Pro835Leu	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	589	0.2696886446886447	228	0.4634146341463415	83	0.2292817679558011	168	0.2937062937062937	110	0.14511873350923482	A	0.927	-0.713913	0.03206	0.42079	0.163721	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000411671	T;T;T	0.02301	4.4;4.42;4.35	4.29	4.29	0.51040	.	0.000000	0.29466	N	0.012075	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25710	-1.0124	9	0.23891	T	0.37	-13.7477	6.905	0.24303	0.8914:0.0:0.1086:0.0	rs2277921;rs59632950;rs2277921	835;835	E9PDE0;Q9H0B3	.;K1683_HUMAN	L	835;835;789;449	ENSP00000376213:P835L;ENSP00000352774:P835L;ENSP00000404501:P789L	ENSP00000352774:P835L	P	-	2	0	KIAA1683	18236846	0.008000	0.16893	0.032000	0.17829	0.004000	0.04260	1.552000	0.36244	0.625000	0.30304	-0.516000	0.04426	CCG	G|0.734;A|0.266	0.266	strong		0.677	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
ITGAD	3681	hgsc.bcm.edu	37	16	31418869	31418869	+	Silent	SNP	A	A	G	rs62001041	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31418869A>G	ENST00000389202.2	+	8	787	c.738A>G	c.(736-738)cgA>cgG	p.R246R	RP11-120K18.2_ENST00000567545.1_RNA	NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	246	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						ATGGGGCCCGAAAAAGTGCCA	0.478													a|||	229	0.0457268	0.0053	0.0317	5008	,	,		19588	0.0298		0.0467	False		,,,				2504	0.1258				p.R246R		Atlas-SNP	.											.	ITGAD	154	.	0			c.A738G						PASS	.	A		61,4333	53.6+/-89.4	0,61,2136	91.0	84.0	86.0		738	-10.6	0.0	16	dbSNP_129	86	519,8081	143.0+/-199.1	16,487,3797	no	coding-synonymous	ITGAD	NM_005353.2		16,548,5933	GG,GA,AA		6.0349,1.3883,4.4636		246/1162	31418869	580,12414	2197	4300	6497	SO:0001819	synonymous_variant	3681	exon8			GGCCCGAAAAAGT	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.738A>G	16.37:g.31418869A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	NM_005353	Q15575|Q15576	Silent	SNP	ENST00000389202.2	37	CCDS32438.1																																																																																			A|0.961;G|0.039	0.039	strong		0.478	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
ZNF248	57209	hgsc.bcm.edu	37	10	38120720	38120720	+	Silent	SNP	C	C	T	rs1779132	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:38120720C>T	ENST00000395867.3	-	6	2113	c.1563G>A	c.(1561-1563)aaG>aaA	p.K521K	ZNF248_ENST00000494133.1_Intron|AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000357328.4_Silent_p.K521K	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	521					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						ATTCATTACACTTATATGGTT	0.413													C|||	158	0.0315495	0.0015	0.0648	5008	,	,		20360	0.0		0.1024	False		,,,				2504	0.0082				p.K521K		Atlas-SNP	.											.	ZNF248	61	.	0			c.G1563A						PASS	.	C		79,4327	69.2+/-107.0	1,77,2125	115.0	107.0	110.0		1563	-0.5	1.0	10	dbSNP_89	110	756,7842	181.0+/-229.8	32,692,3575	no	coding-synonymous	ZNF248	NM_021045.1		33,769,5700	TT,TC,CC		8.7927,1.793,6.4211		521/580	38120720	835,12169	2203	4299	6502	SO:0001819	synonymous_variant	57209	exon6			ATTACACTTATAT	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"""Zinc fingers, C2H2-type"", ""-"""	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.1563G>A	10.37:g.38120720C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_001267597	Q8NDV8|Q9UMP3	Silent	SNP	ENST00000395867.3	37	CCDS7194.1																																																																																			C|0.937;T|0.063	0.063	strong		0.413	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045	
UPK3B	80761	hgsc.bcm.edu	37	7	76144483	76144483	+	Missense_Mutation	SNP	A	A	G	rs1636632	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:76144483A>G	ENST00000257632.5	+	4	1006	c.878A>G	c.(877-879)cAa>cGa	p.Q293R	UPK3B_ENST00000394849.1_Missense_Mutation_p.Q238R|UPK3B_ENST00000443097.2_Missense_Mutation_p.K265E|UPK3B_ENST00000448265.3_Missense_Mutation_p.Q293R|UPK3B_ENST00000334348.3_Missense_Mutation_p.K265E|UPK3B_ENST00000419923.2_Missense_Mutation_p.Q293R			Q9BT76	UPK3B_HUMAN	uroplakin 3B	293			Q -> R (in dbSNP:rs1636632).		negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				GGTGGGCTGCAAGCCTGGCCT	0.682													.|||	1707	0.340855	0.211	0.3847	5008	,	,		13677	0.4425		0.4036	False		,,,				2504	0.316				p.Q293R		Atlas-SNP	.											.	UPK3B	15	.	0			c.A878G						PASS	.	G	ARG/GLN,GLU/LYS	958,3436		107,744,1346	18.0	18.0	18.0		878,793	3.8	0.9	7	dbSNP_89	18	3321,5265		691,1939,1663	no	missense,missense	UPK3B	NM_030570.2,NM_182684.1	43,56	798,2683,3009	GG,GA,AA		38.6792,21.8025,32.9661	benign,benign	293/321,265/277	76144483	4279,8701	2197	4293	6490	SO:0001583	missense	80761	exon4			GGCTGCAAGCCTG	BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566			21444	protein-coding gene	gene with protein product	"""uroplakin IIIb"""	611887				12446744	Standard	XM_005250612		Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000257632.5:c.878A>G	7.37:g.76144483A>G	ENSP00000257632:p.Gln293Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	96	35	0.364583	NM_030570	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Missense_Mutation	SNP	ENST00000257632.5	37	CCDS5588.1	803|803	0.3676739926739927|0.3676739926739927	98|98	0.1991869918699187|0.1991869918699187	145|145	0.4005524861878453|0.4005524861878453	255|255	0.4458041958041958|0.4458041958041958	305|305	0.4023746701846966|0.4023746701846966	.|.	0.193|0.193	-1.051771|-1.051771	0.01981|0.01981	0.218025|0.218025	0.386792|0.386792	ENSG00000243566|ENSG00000243566	ENST00000334348;ENST00000443097|ENST00000419923;ENST00000448265;ENST00000257632;ENST00000394849	T;T|T;T;T;T	0.52983|0.32753	0.64;0.64|1.44;1.44;1.44;1.47	3.76|3.76	3.76|3.76	0.43208|0.43208	.|.	.|2.830080	.|0.01498	.|N	.|0.017366	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|B;B	0.02656|0.02656	0.0|0.0;0.0	B|B;B	0.01281|0.01281	0.0|0.0;0.0	T|T	0.38156|0.38156	-0.9674|-0.9674	8|9	0.02654|0.02654	T|T	1|1	-4.3506|-4.3506	9.2025|9.2025	0.37268|0.37268	0.1028:0.0:0.8972:0.0|0.1028:0.0:0.8972:0.0	rs1636632|rs1636632	265|238;293	A6NHH5|Q9BT76-2;Q9BT76	.|.;UPK3B_HUMAN	E|R	265|293;293;293;238	ENSP00000334938:K265E;ENSP00000444585:K265E|ENSP00000441602:Q293R;ENSP00000441284:Q293R;ENSP00000257632:Q293R;ENSP00000378319:Q238R	ENSP00000334938:K265E|ENSP00000257632:Q293R	K|Q	+|+	1|2	0|0	UPK3B|UPK3B	75982419|75982419	0.014000|0.014000	0.17966|0.17966	0.928000|0.928000	0.36995|0.36995	0.349000|0.349000	0.29174|0.29174	0.888000|0.888000	0.28268|0.28268	0.952000|0.952000	0.37798|0.37798	-0.224000|-0.224000	0.12420|0.12420	AAG|CAA	A|0.673;G|0.327	0.327	strong		0.682	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570	
KIDINS220	57498	hgsc.bcm.edu	37	2	8871342	8871342	+	Missense_Mutation	SNP	C	C	A	rs1044280	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:8871342C>A	ENST00000256707.3	-	30	5005	c.4824G>T	c.(4822-4824)caG>caT	p.Q1608H	KIDINS220_ENST00000473731.1_Missense_Mutation_p.Q1589H|KIDINS220_ENST00000427284.1_Missense_Mutation_p.Q1589H|KIDINS220_ENST00000418530.1_Missense_Mutation_p.Q1509H	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1608			Q -> H (in dbSNP:rs1044280). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CCTTTTCAAGCTGGGAGTCAT	0.488													C|||	1177	0.235024	0.2368	0.2435	5008	,	,		19898	0.1637		0.2893	False		,,,				2504	0.2444				p.Q1608H		Atlas-SNP	.											.	KIDINS220	136	.	0			c.G4824T						PASS	.	C	HIS/GLN	883,3163		93,697,1233	72.0	68.0	69.0		4824	2.9	1.0	2	dbSNP_86	69	2209,6181		288,1633,2274	yes	missense	KIDINS220	NM_020738.2	24	381,2330,3507	AA,AC,CC		26.329,21.824,24.8633	benign	1608/1772	8871342	3092,9344	2023	4195	6218	SO:0001583	missense	57498	exon30			TTCAAGCTGGGAG	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"""Ankyrin repeat domain containing"""	29508	protein-coding gene	gene with protein product	"""ankyrin repeat-rich membrane-spanning protein"""	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4824G>T	2.37:g.8871342C>A	ENSP00000256707:p.Gln1608His	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	142	68	0.478873	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	37	CCDS42650.1	511	0.23397435897435898	108	0.21951219512195122	85	0.23480662983425415	94	0.16433566433566432	224	0.2955145118733509	C	11.69	1.714197	0.30413	0.21824	0.26329	ENSG00000134313	ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731	T;T;T;T	0.68479	-0.33;-0.31;-0.29;-0.31	5.92	2.88	0.33553	.	0.327612	0.32736	N	0.005718	T	0.00012	0.0000	L	0.29908	0.895	0.36986	P	0.10544699999999996	B;B;B	0.09022	0.001;0.0;0.002	B;B;B	0.13407	0.006;0.003;0.009	T	0.12604	-1.0541	9	0.52906	T	0.07	.	9.7658	0.40559	0.125:0.7398:0.0:0.1352	rs1044280;rs3183986;rs3749009;rs52797127;rs58740115;rs1044280	1509;1608;462	Q9ULH0-2;Q9ULH0;B4DG84	.;KDIS_HUMAN;.	H	1608;1589;1509;1589	ENSP00000256707:Q1608H;ENSP00000411849:Q1589H;ENSP00000414923:Q1509H;ENSP00000418974:Q1589H	ENSP00000256707:Q1608H	Q	-	3	2	KIDINS220	8788793	0.067000	0.21026	0.993000	0.49108	0.615000	0.37417	-0.047000	0.11963	1.481000	0.48307	0.655000	0.94253	CAG	C|0.762;A|0.238	0.238	strong		0.488	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738	
GGT1	2678	hgsc.bcm.edu	37	22	25023419	25023419	+	Silent	SNP	C	C	T	rs202087650	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25023419C>T	ENST00000400382.1	+	12	1796	c.1041C>T	c.(1039-1041)tcC>tcT	p.S347S	GGT1_ENST00000403838.1_Silent_p.S3S|GGT1_ENST00000401885.1_Silent_p.S3S|GGT1_ENST00000406383.2_Silent_p.S347S|GGT1_ENST00000404532.1_Silent_p.S3S|GGT1_ENST00000400380.1_Silent_p.S347S|GGT1_ENST00000404223.1_Silent_p.S3S|GGT1_ENST00000248923.4_Silent_p.S347S|GGT1_ENST00000404920.1_Silent_p.S3S|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400383.1_Silent_p.S347S			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	347					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	ACATGACCTCCGAGTTCTTCG	0.647																																					p.S347S		Atlas-SNP	.											GGT1,NS,carcinoma,0,2	GGT1	68	2	0			c.C1041T						scavenged	.						53.0	54.0	54.0					22																	25023419		2201	4297	6498	SO:0001819	synonymous_variant	2678	exon12			GACCTCCGAGTTC	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1041C>T	22.37:g.25023419C>T		Somatic	231	8	0.034632		WXS	Illumina HiSeq	Phase_I	303	10	0.0330033	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Silent	SNP	ENST00000400382.1	37	CCDS42992.1																																																																																			C|0.989;T|0.011	0.011	strong		0.647	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
STK32B	55351	hgsc.bcm.edu	37	4	5448429	5448429	+	Missense_Mutation	SNP	A	A	G	rs3733182	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:5448429A>G	ENST00000282908.5	+	7	1014	c.592A>G	c.(592-594)Aga>Gga	p.R198G	STK32B_ENST00000508728.1_3'UTR|STK32B_ENST00000512636.1_Missense_Mutation_p.R121G|STK32B_ENST00000510398.1_Missense_Mutation_p.R151G	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						GTACATGGACAGAGGCCCCGG	0.572													G|||	1282	0.25599	0.1445	0.1671	5008	,	,		16642	0.5437		0.1093	False		,,,				2504	0.3241				p.R198G		Atlas-SNP	.											STK32B,right_upper_lobe,carcinoma,-1,2	STK32B	87	2	0			c.A592G						PASS	.	G	GLY/ARG	748,3658	755.8+/-412.6	55,638,1510	89.0	82.0	84.0		592	5.4	1.0	4	dbSNP_107	84	972,7628	774.6+/-407.7	47,878,3375	yes	missense	STK32B	NM_018401.1	125	102,1516,4885	GG,GA,AA		11.3023,16.9768,13.2247	benign	198/415	5448429	1720,11286	2203	4300	6503	SO:0001583	missense	55351	exon7			ATGGACAGAGGCC	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.592A>G	4.37:g.5448429A>G	ENSP00000282908:p.Arg198Gly	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_018401		Missense_Mutation	SNP	ENST00000282908.5	37	CCDS3380.1	513	0.2348901098901099	68	0.13821138211382114	66	0.18232044198895028	296	0.5174825174825175	83	0.10949868073878628	G	11.49	1.653571	0.29425	0.169768	0.113023	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.64085	-0.08;-0.08;-0.08	5.39	5.39	0.77823	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.41938	N	0.000785	T	0.00012	0.0000	N	0.13327	0.33	0.53688	P	2.8000000000028002E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.44742	-0.9308	9	0.21540	T	0.41	.	12.1606	0.54101	0.0833:0.0:0.9167:0.0	rs3733182;rs17846223;rs17859240;rs52834044;rs59173302;rs3733182	198	Q9NY57	ST32B_HUMAN	G	198;121;151	ENSP00000282908:R198G;ENSP00000423209:R121G;ENSP00000420984:R151G	ENSP00000282908:R198G	R	+	1	2	STK32B	5499330	1.000000	0.71417	0.998000	0.56505	0.628000	0.37860	4.292000	0.59031	1.288000	0.44600	-0.215000	0.12644	AGA	A|0.824;G|0.176	0.176	strong		0.572	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401	
OR12D2	26529	hgsc.bcm.edu	37	6	29364643	29364643	+	Missense_Mutation	SNP	T	T	C	rs4987411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29364643T>C	ENST00000383555.2	+	1	228	c.167T>C	c.(166-168)cTt>cCt	p.L56P	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	56			L -> P (in dbSNP:rs4987411).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CTCCATTCCCTTATGTATTTC	0.453													C|||	1597	0.31889	0.1921	0.3458	5008	,	,		21557	0.3641		0.4523	False		,,,				2504	0.2873				p.L56P		Atlas-SNP	.											.	OR12D2	42	.	0			c.T167C						PASS	.	C	PRO/LEU	663,2357		75,513,922	113.0	115.0	114.0		167	3.2	0.1	6	dbSNP_113	114	2407,3011		535,1337,837	yes	missense	OR12D2	NM_013936.3	98	610,1850,1759	CC,CT,TT		44.426,21.9536,36.383	benign	56/308	29364643	3070,5368	1510	2709	4219	SO:0001583	missense	26529	exon1			ATTCCCTTATGTA		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.167T>C	6.37:g.29364643T>C	ENSP00000373047:p.Leu56Pro	Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	290	129	0.444828	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	787	0.36034798534798534	101	0.20528455284552846	123	0.3397790055248619	208	0.36363636363636365	355	0.4683377308707124	C	0.008	-1.929605	0.00488	0.219536	0.44426	ENSG00000168787	ENST00000383555	T	0.00000	10.38	4.07	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000019	T	0.00012	0.0000	N	0.00002	-3.6	0.20307	P	0.9999180459	B	0.02656	0.0	B	0.01281	0.0	T	0.48885	-0.8995	9	0.02654	T	1	.	9.8586	0.41101	0.0:0.8292:0.0:0.1708	rs4987411;rs56924123;rs4987411	56	P58182	O12D2_HUMAN	P	56	ENSP00000373047:L56P	ENSP00000373047:L56P	L	+	2	0	OR12D2	29472622	1.000000	0.71417	0.108000	0.21378	0.018000	0.09664	5.299000	0.65716	0.387000	0.25024	-0.473000	0.04963	CTT	T|0.630;C|0.370	0.370	strong		0.453	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
SYT8	90019	hgsc.bcm.edu	37	11	1858262	1858262	+	Missense_Mutation	SNP	C	C	T	rs484955	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1858262C>T	ENST00000381968.3	+	8	1036	c.908C>T	c.(907-909)aCg>aTg	p.T303M	TNNI2_ENST00000381911.1_5'Flank|TNNI2_ENST00000252898.7_5'Flank|SYT8_ENST00000341958.3_Missense_Mutation_p.T289M|TNNI2_ENST00000381906.1_5'Flank|SYT8_ENST00000535046.1_3'UTR	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	303	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosome reaction (GO:0007340)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AAAAAGGGCACGGCGGCCCCC	0.622													C|||	929	0.185503	0.0507	0.2262	5008	,	,		18566	0.4137		0.1282	False		,,,				2504	0.1626				p.T303M		Atlas-SNP	.											SYT8,colon,carcinoma,0,1	SYT8	29	1	0			c.C908T						PASS	.	C	MET/THR	270,4134	151.0+/-185.0	12,246,1944	97.0	112.0	107.0		908	2.3	0.1	11	dbSNP_83	107	1035,7563	219.7+/-257.6	60,915,3324	yes	missense	SYT8	NM_138567.3	81	72,1161,5268	TT,TC,CC		12.0377,6.1308,10.0369	probably-damaging	303/402	1858262	1305,11697	2202	4299	6501	SO:0001583	missense	90019	exon8			AGGGCACGGCGGC	AL137708	CCDS7726.2	11p15.5	2013-01-21			ENSG00000149043	ENSG00000149043		"""Synaptotagmins"""	19264	protein-coding gene	gene with protein product		607719				7791877	Standard	XM_005253216		Approved	DKFZp434K0322	uc001lue.1	Q8NBV8	OTTHUMG00000009026	ENST00000381968.3:c.908C>T	11.37:g.1858262C>T	ENSP00000371394:p.Thr303Met	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	417	0.19093406593406592	22	0.044715447154471545	80	0.22099447513812154	220	0.38461538461538464	95	0.12532981530343007	c	13.83	2.354034	0.41700	0.061308	0.120377	ENSG00000149043	ENST00000381968;ENST00000341958	T;T	0.12039	2.72;2.72	3.28	2.34	0.29019	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.00012	0.0000	H	0.94620	3.56	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	T	0.29274	-1.0017	8	0.87932	D	0	.	10.6724	0.45766	0.0:0.9005:0.0:0.0995	rs484955;rs484955	303;289	Q8NBV8;A6NCR4	SYT8_HUMAN;.	M	303;289	ENSP00000371394:T303M;ENSP00000343691:T289M	ENSP00000343691:T289M	T	+	2	0	SYT8	1814838	0.689000	0.27690	0.051000	0.19133	0.176000	0.22953	2.807000	0.47955	0.720000	0.32209	0.436000	0.28706	ACG	C|0.863;T|0.137	0.137	strong		0.622	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4		
DLEC1	9940	hgsc.bcm.edu	37	3	38151731	38151731	+	Silent	SNP	T	T	C	rs12630114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:38151731T>C	ENST00000308059.6	+	23	3423	c.3402T>C	c.(3400-3402)taT>taC	p.Y1134Y	DLEC1_ENST00000346219.3_Silent_p.Y1134Y|DLEC1_ENST00000452631.2_Silent_p.Y1137Y					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		AGTTTGAGTATTTCGGGAGCC	0.542													C|||	2292	0.457668	0.5673	0.451	5008	,	,		18060	0.6131		0.3628	False		,,,				2504	0.2515				p.Y1134Y		Atlas-SNP	.											.	DLEC1	278	.	0			c.T3402C						PASS	.	C	,	2082,1840		556,970,435	99.0	108.0	105.0		3402,3402	4.2	0.7	3	dbSNP_120	105	3052,5276		592,1868,1704	no	coding-synonymous,coding-synonymous	DLEC1	NM_007335.2,NM_007337.2	,	1148,2838,2139	CC,CT,TT		36.6475,46.9148,41.9102	,	1134/1756,1134/1779	38151731	5134,7116	1961	4164	6125	SO:0001819	synonymous_variant	9940	exon23			TGAGTATTTCGGG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.3402T>C	3.37:g.38151731T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_007337		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																			C|0.467;N|0.000	0.467	strong		0.542	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
GJA9	81025	hgsc.bcm.edu	37	1	39340862	39340862	+	Silent	SNP	A	A	G	rs874243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:39340862A>G	ENST00000360786.3	-	1	1161	c.909T>C	c.(907-909)tcT>tcC	p.S303S	GJA9_ENST00000454994.2_Silent_p.S303S|RP5-864K19.4_ENST00000456813.1_RNA|MYCBP_ENST00000489803.1_5'UTR|GJA9_ENST00000357771.3_Silent_p.S303S|MYCBP_ENST00000397572.2_5'Flank|RP5-864K19.4_ENST00000433671.2_RNA|RP5-864K19.4_ENST00000443161.1_RNA			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	303					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			GGAATACAGAAGATGAATTTA	0.383													A|||	519	0.103634	0.0061	0.1167	5008	,	,		19276	0.1319		0.2177	False		,,,				2504	0.0798				p.S303S		Atlas-SNP	.											.	GJA9	55	.	0			c.T909C						PASS	.	A		189,4217	119.6+/-157.3	8,173,2022	97.0	95.0	96.0		909	3.8	0.1	1	dbSNP_86	96	1824,6776	326.6+/-317.4	199,1426,2675	no	coding-synonymous	GJA9	NM_030772.4		207,1599,4697	GG,GA,AA		21.2093,4.2896,15.4775		303/516	39340862	2013,10993	2203	4300	6503	SO:0001819	synonymous_variant	81025	exon2			TACAGAAGATGAA	AF179597	CCDS432.1	1p34	2008-02-05	2007-11-06	2007-11-06	ENSG00000131233	ENSG00000131233		"""Ion channels / Gap junction proteins (connexins)"""	19155	protein-coding gene	gene with protein product	"""connexin 59"""	611923	"""gap junction protein, alpha 10, 59kDa"""	GJA10			Standard	NM_030772		Approved	CX59, CX58	uc021olr.1	P57773	OTTHUMG00000000482	ENST00000360786.3:c.909T>C	1.37:g.39340862A>G		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	290	287	0.989655	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Silent	SNP	ENST00000360786.3	37	CCDS432.1																																																																																			G|0.140;N|0.000	0.140	strong		0.383	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772	
L3MBTL4	91133	hgsc.bcm.edu	37	18	5956238	5956238	+	Missense_Mutation	SNP	C	C	T	rs3737353	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:5956238C>T	ENST00000284898.6	-	20	2053	c.1853G>A	c.(1852-1854)gGc>gAc	p.G618D	RP11-793A3.1_ENST00000577704.1_RNA|L3MBTL4_ENST00000400105.2_Missense_Mutation_p.G618D|L3MBTL4_ENST00000535782.1_Missense_Mutation_p.G422D|L3MBTL4_ENST00000317931.7_Missense_Mutation_p.G609D	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	618			G -> D (in dbSNP:rs3737353). {ECO:0000269|PubMed:14702039}.		chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				GACTTCTTGGCCTGAGGCAAT	0.463													C|||	1927	0.384784	0.2927	0.2723	5008	,	,		20537	0.4742		0.3976	False		,,,				2504	0.4836				p.G618D	Esophageal Squamous(41;748 902 17366 28959 43175)	Atlas-SNP	.											L3MBTL4,colon,carcinoma,0,1	L3MBTL4	87	1	0			c.G1853A						PASS	.	C	ASP/GLY	1114,2710		168,778,966	154.0	150.0	151.0		1853	2.8	0.0	18	dbSNP_107	151	3192,5078		658,1876,1601	yes	missense	L3MBTL4	NM_173464.3	94	826,2654,2567	TT,TC,CC		38.5973,29.1318,35.6044	possibly-damaging	618/624	5956238	4306,7788	1912	4135	6047	SO:0001583	missense	91133	exon20			TCTTGGCCTGAGG	BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"""Sterile alpha motif (SAM) domain containing"""	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.1853G>A	18.37:g.5956238C>T	ENSP00000284898:p.Gly618Asp	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	200	196	0.98	NM_173464	A8MTL8|Q8IXS3	Missense_Mutation	SNP	ENST00000284898.6	37	CCDS11839.2	831	0.3804945054945055	147	0.29878048780487804	103	0.2845303867403315	268	0.46853146853146854	313	0.4129287598944591	C	10.73	1.432921	0.25813	0.291318	0.385973	ENSG00000154655	ENST00000400105;ENST00000317931;ENST00000284898;ENST00000535782	T;T;T;T	0.16457	2.34;2.36;2.34;2.36	5.49	2.78	0.32641	.	0.425518	0.20187	N	0.097387	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.21225	0.053;0.049	B;B	0.23018	0.019;0.043	T	0.46062	-0.9218	9	0.39692	T	0.17	.	7.854	0.29472	0.0:0.741:0.0:0.259	rs3737353;rs58882188;rs3737353	618;609	Q8NA19;F8W9S8	LMBL4_HUMAN;.	D	618;609;618;422	ENSP00000382976:G618D;ENSP00000318543:G609D;ENSP00000284898:G618D;ENSP00000444774:G422D	ENSP00000284898:G618D	G	-	2	0	L3MBTL4	5946238	0.015000	0.18098	0.010000	0.14722	0.006000	0.05464	0.125000	0.15749	0.310000	0.22990	-0.880000	0.02959	GGC	C|0.627;T|0.373	0.373	strong		0.463	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464	
FAM86B1	85002	hgsc.bcm.edu	37	8	12044264	12044264	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:12044264C>T	ENST00000448228.2	-	4	368	c.319G>A	c.(319-321)Gcc>Acc	p.A107T	FAM86B1_ENST00000534520.1_Missense_Mutation_p.A107T|FAM86B1_ENST00000321602.8_Start_Codon_SNP_p.M1I|FAM86B1_ENST00000533513.1_Missense_Mutation_p.A141T|FAM86B1_ENST00000533852.2_Missense_Mutation_p.A141T	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	107										kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		TAGAGGGCGGCATCCCATGTG	0.612																																					p.A107T		Atlas-SNP	.											FAM86B1,NS,carcinoma,+2,1	FAM86B1	7	1	0			c.G319A						scavenged	.						1.0	1.0	1.0					8																	12044264		461	1070	1531	SO:0001583	missense	85002	exon4			GGGCGGCATCCCA	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.319G>A	8.37:g.12044264C>T	ENSP00000407067:p.Ala107Thr	Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	320	27	0.084375	NM_001083537		Missense_Mutation	SNP	ENST00000448228.2	37	CCDS59512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	11.97|11.97	1.796969|1.796969	0.31777|0.31777	.|.	.|.	ENSG00000186523|ENSG00000186523	ENST00000431227;ENST00000340537;ENST00000448228;ENST00000534520;ENST00000526708;ENST00000524571;ENST00000533513|ENST00000321602;ENST00000526802	T;T;T;T;T|T	0.36340|0.24350	1.26;2.52;1.26;1.56;4.06|1.86	1.17|1.17	1.17|1.17	0.20885|0.20885	.|.	10.022600|.	0.01570|.	U|.	0.020538|.	T|T	0.33731|0.33731	0.0873|0.0873	M|M	0.90309|0.90309	3.105|3.105	0.80722|0.80722	D|D	1|1	P;P|B;B	0.46457|0.15719	0.878;0.749|0.014;0.003	D;P|B;B	0.64144|0.08055	0.922;0.624|0.003;0.002	T|T	0.42050|0.42050	-0.9474|-0.9474	10|9	0.72032|0.87932	D|D	0.01|0	.|.	8.2654|8.2654	0.31810|0.31810	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	107;141|1;38	Q8N7N1;E9PN63|F6QN85;Q4KMP3	F86B1_HUMAN;.|.;.	T|I	141;107;107;107;141;79;141|1;102	ENSP00000342610:A107T;ENSP00000407067:A107T;ENSP00000431362:A107T;ENSP00000432790:A79T;ENSP00000435201:A141T|ENSP00000439686:M1I	ENSP00000342610:A107T|ENSP00000439686:M1I	A|M	-|-	1|3	0|0	FAM86B1|FAM86B1	12081673|12081673	1.000000|1.000000	0.71417|0.71417	0.088000|0.088000	0.20740|0.20740	0.049000|0.049000	0.14656|0.14656	6.283000|6.283000	0.72646|0.72646	0.950000|0.950000	0.37743|0.37743	0.173000|0.173000	0.16961|0.16961	GCC|ATG	.	.	none		0.612	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916	
VAT1	10493	hgsc.bcm.edu	37	17	41174025	41174025	+	Silent	SNP	A	A	C	rs2070835	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:41174025A>C	ENST00000355653.3	-	1	410	c.315T>G	c.(313-315)ccT>ccG	p.P105P	VAT1_ENST00000587173.1_Intron|VAT1_ENST00000420567.3_5'Flank	NM_006373.3	NP_006364.2	P54219	VMAT1_HUMAN	vesicle amine transport 1	0					monoamine transport (GO:0015844)|neurotransmitter transport (GO:0006836)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	drug transmembrane transporter activity (GO:0015238)|monoamine transmembrane transporter activity (GO:0008504)			endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	9		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Ephedra(DB01363)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Reserpine(DB00206)	TGACAGGCAGAGGCGGGAGAC	0.706													C|||	1716	0.342652	0.2224	0.2939	5008	,	,		10101	0.374		0.3559	False		,,,				2504	0.4939				p.P105P		Atlas-SNP	.											VAT1,NS,carcinoma,0,1	VAT1	19	1	0			c.T315G						PASS	.	C		930,3384		103,724,1330	13.0	13.0	13.0		315	-0.9	1.0	17	dbSNP_96	13	2522,5898		395,1732,2083	no	coding-synonymous	VAT1	NM_006373.3		498,2456,3413	CC,CA,AA		29.9525,21.5577,27.1085		105/394	41174025	3452,9282	2157	4210	6367	SO:0001819	synonymous_variant	10493	exon1			AGGCAGAGGCGGG	U18009	CCDS11451.1	17q21	2013-08-23	2013-08-23			ENSG00000108828			16919	protein-coding gene	gene with protein product		604631	"""vesicle amine transport protein 1 homolog (T. californica)"""			7774926, 8938427	Standard	NM_006373		Approved	VATI, FLJ20230	uc002icm.1	Q99536		ENST00000355653.3:c.315T>G	17.37:g.41174025A>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_006373	E9PDJ5|Q9BRE4	Silent	SNP	ENST00000355653.3	37	CCDS11451.1																																																																																			A|0.711;C|0.289	0.289	strong		0.706	VAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453101.1	NM_006373	
FAT2	2196	hgsc.bcm.edu	37	5	150945699	150945699	+	Silent	SNP	G	G	A	rs10085060	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150945699G>A	ENST00000261800.5	-	1	2806	c.2794C>T	c.(2794-2796)Ctg>Ttg	p.L932L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	932	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGAACCTTCAGCCTGTTGTGT	0.547													G|||	2102	0.419728	0.441	0.4539	5008	,	,		20695	0.3571		0.4901	False		,,,				2504	0.3589				p.L932L		Atlas-SNP	.											.	FAT2	465	.	0			c.C2794T						PASS	.	G		1959,2447	553.0+/-378.7	422,1115,666	60.0	52.0	55.0		2794	3.6	1.0	5	dbSNP_119	55	4499,4101	591.6+/-392.9	1184,2131,985	no	coding-synonymous	FAT2	NM_001447.2		1606,3246,1651	AA,AG,GG		47.686,44.4621,49.654		932/4350	150945699	6458,6548	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			CCTTCAGCCTGTT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2794C>T	5.37:g.150945699G>A		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	217	217	1	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.529;A|0.471	0.471	strong		0.547	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
FRAS1	80144	hgsc.bcm.edu	37	4	79205699	79205699	+	Missense_Mutation	SNP	T	T	A	rs12504081	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:79205699T>A	ENST00000325942.6	+	13	1836	c.1396T>A	c.(1396-1398)Tta>Ata	p.L466I	FRAS1_ENST00000264895.6_Missense_Mutation_p.L466I|FRAS1_ENST00000264899.6_Missense_Mutation_p.L466I	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	466			L -> I (in dbSNP:rs12504081).		cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CAGTCTCTGTTTAGGTATGGC	0.488													T|||	1608	0.321086	0.1725	0.4179	5008	,	,		17983	0.377		0.3728	False		,,,				2504	0.3425				p.L466I		Atlas-SNP	.											.	FRAS1	779	.	0			c.T1396A						PASS	.	T	ILE/LEU,ILE/LEU	762,3334		69,624,1355	165.0	161.0	162.0		1396,1396	4.3	1.0	4	dbSNP_120	162	2921,5461		506,1909,1776	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	5,5	575,2533,3131	AA,AT,TT		34.8485,18.6035,29.5159	possibly-damaging,possibly-damaging	466/1977,466/4013	79205699	3683,8795	2048	4191	6239	SO:0001583	missense	80144	exon13			CTCTGTTTAGGTA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1396T>A	4.37:g.79205699T>A	ENSP00000326330:p.Leu466Ile	Somatic	446	1	0.00224215		WXS	Illumina HiSeq	Phase_I	438	434	0.990868	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	743|743	0.3402014652014652|0.3402014652014652	95|95	0.19308943089430894|0.19308943089430894	144|144	0.39779005524861877|0.39779005524861877	216|216	0.3776223776223776|0.3776223776223776	288|288	0.37994722955145116|0.37994722955145116	T|T	13.62|13.62	2.290707|2.290707	0.40494|0.40494	0.186035|0.186035	0.348485|0.348485	ENSG00000138759|ENSG00000138759	ENST00000508900|ENST00000325942;ENST00000264895;ENST00000264899;ENST00000534913	.|T;T;T	.|0.53423	.|0.62;0.62;0.62	5.52|5.52	4.33|4.33	0.51752|0.51752	.|Growth factor, receptor (1);	.|0.185532	.|0.36034	.|N	.|0.002837	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.39898|0.39898	1.24|1.24	0.34651|0.34651	P|P	0.278292|0.278292	.|P;P;D;D	.|0.76494	.|0.945;0.945;0.999;0.993	.|P;P;D;D	.|0.66196	.|0.573;0.549;0.942;0.926	T|T	0.40850|0.40850	-0.9541|-0.9541	4|9	.|0.49607	.|T	.|0.09	.|.	7.3395|7.3395	0.26630|0.26630	0.0:0.072:0.1461:0.782|0.0:0.072:0.1461:0.782	rs12504081;rs52833533;rs12504081|rs12504081;rs52833533;rs12504081	.|466;466;466;466	.|E9PHH6;Q86XX4;E7EWM9;A2RRR8	.|.;FRAS1_HUMAN;.;.	Y|I	308|466;466;466;206	.|ENSP00000326330:L466I;ENSP00000264895:L466I;ENSP00000264899:L466I	.|ENSP00000264895:L466I	F|L	+|+	2|1	0|2	FRAS1|FRAS1	79424723|79424723	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.187000|0.187000	0.23431|0.23431	0.955000|0.955000	0.29188|0.29188	0.907000|0.907000	0.36646|0.36646	-0.313000|-0.313000	0.08912|0.08912	TTT|TTA	T|0.661;A|0.339	0.339	strong		0.488	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
FMN2	56776	hgsc.bcm.edu	37	1	240371075	240371075	+	Missense_Mutation	SNP	C	C	T	rs71646825		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:240371075C>T	ENST00000319653.9	+	5	3193	c.2963C>T	c.(2962-2964)cCt>cTt	p.P988L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	988	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGCATACCCCCTCCTCCCCCA	0.711																																					p.P988L		Atlas-SNP	.											.	FMN2	451	.	0			c.C2963T						PASS	.						13.0	15.0	15.0					1																	240371075		2181	4262	6443	SO:0001583	missense	56776	exon5			TACCCCCTCCTCC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2963C>T	1.37:g.240371075C>T	ENSP00000318884:p.Pro988Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	75	12	0.16	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	391	0.17902930402930403	114	0.23170731707317074	55	0.15193370165745856	93	0.16258741258741258	129	0.17018469656992086	C	8.181	0.793768	0.16327	.	.	ENSG00000155816	ENST00000319653	T	0.65549	-0.16	2.73	0.76	0.18442	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.00039	0.0001	M	0.90542	3.125	0.24734	P	0.99307642	B	0.12630	0.006	B	0.12156	0.007	T	0.08700	-1.0709	7	.	.	.	.	5.5141	0.16896	0.0:0.5739:0.1599:0.2661	.	988	Q9NZ56	FMN2_HUMAN	L	988	ENSP00000318884:P988L	.	P	+	2	0	FMN2	238437698	0.082000	0.21442	0.001000	0.08648	0.076000	0.17211	1.602000	0.36783	0.229000	0.21039	0.472000	0.43445	CCT	C|0.820;T|0.180	0.180	strong		0.711	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
TULP4	56995	hgsc.bcm.edu	37	6	158910743	158910743	+	Missense_Mutation	SNP	G	G	A	rs61742077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:158910743G>A	ENST00000367097.3	+	9	2967	c.1610G>A	c.(1609-1611)aGc>aAc	p.S537N	TULP4_ENST00000367094.2_Missense_Mutation_p.S537N	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	537					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		TCCAGAGCTAGCAAATCACCC	0.473													G|||	9	0.00179712	0.0	0.0058	5008	,	,		19135	0.0		0.004	False		,,,				2504	0.001				p.S537N		Atlas-SNP	.											.	TULP4	137	.	0			c.G1610A						PASS	.	G	ASN/SER,ASN/SER	1,4405	2.1+/-5.4	0,1,2202	131.0	118.0	123.0		1610,1610	4.7	1.0	6	dbSNP_129	123	66,8534	40.3+/-97.0	0,66,4234	yes	missense,missense	TULP4	NM_001007466.1,NM_020245.3	46,46	0,67,6436	AA,AG,GG		0.7674,0.0227,0.5151	benign,benign	537/679,537/1544	158910743	67,12939	2203	4300	6503	SO:0001583	missense	56995	exon9			GAGCTAGCAAATC		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.1610G>A	6.37:g.158910743G>A	ENSP00000356064:p.Ser537Asn	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	152	74	0.486842	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	7	0.003205128205128205	0	0.0	4	0.011049723756906077	0	0.0	3	0.00395778364116095	G	17.26	3.344506	0.61073	2.27E-4	0.007674	ENSG00000130338	ENST00000367097;ENST00000367094	T;T	0.61627	0.09;0.89	5.57	4.68	0.58851	Tubby, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.22513	0.0543	N	0.10874	0.06	0.58432	D	0.999991	B;B	0.16166	0.002;0.016	B;B	0.14023	0.009;0.01	T	0.04678	-1.0934	10	0.24483	T	0.36	-30.6907	16.3085	0.82859	0.0:0.1325:0.8675:0.0	rs61742077	537;537	Q9NRJ4-2;Q9NRJ4	.;TULP4_HUMAN	N	537	ENSP00000356064:S537N;ENSP00000356061:S537N	ENSP00000356061:S537N	S	+	2	0	TULP4	158830731	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.437000	0.80417	1.299000	0.44798	0.655000	0.94253	AGC	G|0.996;A|0.004	0.004	strong		0.473	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
TMC3	342125	hgsc.bcm.edu	37	15	81665021	81665021	+	Missense_Mutation	SNP	T	T	A	rs76902501	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:81665021T>A	ENST00000359440.5	-	2	282	c.147A>T	c.(145-147)caA>caT	p.Q49H	TMC3_ENST00000558726.1_Missense_Mutation_p.Q49H	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						TCTGGAAGATTTGTTCCGGAT	0.458													T|||	289	0.0577077	0.0923	0.0231	5008	,	,		19275	0.0694		0.0278	False		,,,				2504	0.0542				p.Q49H		Atlas-SNP	.											.	TMC3	112	.	0			c.A147T						PASS	.	T	HIS/GLN	253,3541		6,241,1650	166.0	150.0	155.0		147	1.5	1.0	15	dbSNP_131	155	341,7877		4,333,3772	yes	missense	TMC3	NM_001080532.1	24	10,574,5422	AA,AT,TT		4.1494,6.6684,4.9451	possibly-damaging	49/1101	81665021	594,11418	1897	4109	6006	SO:0001583	missense	342125	exon2			GAAGATTTGTTCC	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.147A>T	15.37:g.81665021T>A	ENSP00000352413:p.Gln49His	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	215	117	0.544186	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	115	0.052655677655677656	39	0.07926829268292683	10	0.027624309392265192	47	0.08216783216783216	19	0.025065963060686015	T	17.23	3.337639	0.60963	0.066684	0.041494	ENSG00000188869	ENST00000359440	T	0.66280	-0.2	5.14	1.45	0.22620	.	0.175895	0.37437	N	0.002083	T	0.05502	0.0145	L	0.55990	1.75	0.28100	P	0.931437	P;P	0.47604	0.771;0.898	B;P	0.47645	0.404;0.553	T	0.43750	-0.9372	9	0.72032	D	0.01	-12.2791	1.0495	0.01577	0.1441:0.244:0.1494:0.4625	.	49;49	Q7Z5M5-2;Q7Z5M5	.;TMC3_HUMAN	H	49	ENSP00000352413:Q49H	ENSP00000352413:Q49H	Q	-	3	2	TMC3	79452076	0.999000	0.42202	0.997000	0.53966	0.992000	0.81027	0.464000	0.21988	0.046000	0.15833	0.383000	0.25322	CAA	T|0.950;A|0.050	0.050	strong		0.458	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841	
SLC35A3	23443	hgsc.bcm.edu	37	1	100472604	100472604	+	Silent	SNP	A	A	G	rs534252	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:100472604A>G	ENST00000370155.3	+	4	749	c.357A>G	c.(355-357)ttA>ttG	p.L119L	SLC35A3_ENST00000427993.2_Silent_p.L119L|SLC35A3_ENST00000465289.1_Silent_p.L119L|SLC35A3_ENST00000370156.3_3'UTR|SLC35A3_ENST00000370153.1_Silent_p.L161L	NM_012243.1	NP_036375.1	Q9Y2D2	S35A3_HUMAN	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3	119					transmembrane transport (GO:0055085)|UDP-N-acetylglucosamine metabolic process (GO:0006047)|UDP-N-acetylglucosamine transport (GO:0015788)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)|UDP-N-acetylglucosamine transmembrane transporter activity (GO:0005462)			biliary_tract(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	11		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.124)|all cancers(265;0.198)|Lung(183;0.199)		CGTATCAGTTAAAAATTCTTA	0.308													G|||	1013	0.202276	0.466	0.1124	5008	,	,		17395	0.0724		0.1471	False		,,,				2504	0.1002				p.L161L	Ovarian(7;298 356 944 2149 6911)	Atlas-SNP	.											.	SLC35A3	25	.	0			c.A483G						PASS	.	G		1897,2509		413,1071,719	66.0	66.0	66.0		357	3.9	1.0	1	dbSNP_83	66	1329,7267		97,1135,3066	no	coding-synonymous	SLC35A3	NM_012243.1		510,2206,3785	GG,GA,AA		15.4607,43.0549,24.8116		119/326	100472604	3226,9776	2203	4298	6501	SO:0001819	synonymous_variant	23443	exon4			TCAGTTAAAAATT	AB021981	CCDS762.1, CCDS60204.1, CCDS60205.1	1p21	2013-05-22			ENSG00000117620	ENSG00000117620		"""Solute carriers"""	11023	protein-coding gene	gene with protein product		605632	"""solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3"""			10393322	Standard	NM_001271685		Approved		uc001dsr.2	Q9Y2D2	OTTHUMG00000010805	ENST00000370155.3:c.357A>G	1.37:g.100472604A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	NM_001271685	A8K3F8|D3DT54|Q68CR2|Q9BSB7	Silent	SNP	ENST00000370155.3	37	CCDS762.1																																																																																			A|0.755;G|0.245	0.245	strong		0.308	SLC35A3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000029783.1	NM_012243	
PPP2R2C	5522	hgsc.bcm.edu	37	4	6325086	6325086	+	Silent	SNP	G	G	A	rs3796403	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:6325086G>A	ENST00000382599.4	-	9	1503	c.1287C>T	c.(1285-1287)atC>atT	p.I429I	PPP2R2C_ENST00000515571.1_Silent_p.I412I|PPP2R2C_ENST00000335585.5_Silent_p.I429I|PPP2R2C_ENST00000506140.1_Silent_p.I422I|PPP2R2C_ENST00000507294.1_Silent_p.I422I			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	429					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						TGGTGGCGGCGATGGCAATGA	0.577													G|||	3274	0.653754	0.4266	0.6614	5008	,	,		18326	0.9385		0.5795	False		,,,				2504	0.7382				p.I429I		Atlas-SNP	.											.	PPP2R2C	63	.	0			c.C1287T						PASS	.	G	,,,	2013,2393	560.8+/-380.6	460,1093,650	197.0	144.0	162.0		1266,1266,1236,1287	-0.2	0.7	4	dbSNP_107	162	5064,3536	631.1+/-398.4	1488,2088,724	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP2R2C	NM_001206994.1,NM_001206995.1,NM_001206996.1,NM_181876.2	,,,	1948,3181,1374	AA,AG,GG		41.1163,45.6877,45.5867	,,,	422/441,422/441,412/431,429/448	6325086	7077,5929	2203	4300	6503	SO:0001819	synonymous_variant	5522	exon9			GGCGGCGATGGCA	AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9306	protein-coding gene	gene with protein product	"""PP2A subunit B isoform gamma"""	605997	"""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform"""			10574460, 10945473	Standard	NM_020416		Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.1287C>T	4.37:g.6325086G>A		Somatic	373	1	0.00268097		WXS	Illumina HiSeq	Phase_I	372	369	0.991935	NM_181876	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Silent	SNP	ENST00000382599.4	37																																																																																				G|0.407;A|0.593	0.593	strong		0.577	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876	
PNPLA5	150379	hgsc.bcm.edu	37	22	44282307	44282307	+	Silent	SNP	G	G	A	rs739232	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:44282307G>A	ENST00000597664.1	-	6	954	c.825C>T	c.(823-825)gaC>gaT	p.D275D	PNPLA5_ENST00000593866.1_Silent_p.D161D|PNPLA5_ENST00000216177.4_Silent_p.D275D|PNPLA5_ENST00000381198.2_Silent_p.D161D			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	275					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				CCCAGTTTCCGTCAGCCGGGG	0.572													A|||	2486	0.496406	0.2224	0.4568	5008	,	,		18935	0.9048		0.3748	False		,,,				2504	0.5992				p.D275D		Atlas-SNP	.											.	PNPLA5	46	.	0			c.C825T						PASS	.	A	,	1099,3307	720.0+/-409.0	142,815,1246	85.0	77.0	80.0		483,825	-4.8	0.0	22	dbSNP_86	80	3208,5392	652.5+/-400.9	585,2038,1677	no	coding-synonymous,coding-synonymous	PNPLA5	NM_001177675.1,NM_138814.3	,	727,2853,2923	AA,AG,GG		37.3023,24.9433,33.1155	,	161/316,275/430	44282307	4307,8699	2203	4300	6503	SO:0001819	synonymous_variant	150379	exon6			GTTTCCGTCAGCC	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.825C>T	22.37:g.44282307G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Silent	SNP	ENST00000597664.1	37																																																																																				G|0.598;A|0.402	0.402	strong		0.572	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
ACADM	34	hgsc.bcm.edu	37	1	76227022	76227022	+	Silent	SNP	A	A	G	rs1061337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:76227022A>G	ENST00000370841.4	+	11	1598	c.1161A>G	c.(1159-1161)gtA>gtG	p.V387V	ACADM_ENST00000420607.2_Silent_p.V391V|ACADM_ENST00000370834.5_Silent_p.V420V|ACADM_ENST00000543667.1_Silent_p.V198V|ACADM_ENST00000541113.1_Silent_p.V351V|ACADM_ENST00000481374.1_3'UTR	NM_000016.4|NM_001127328.1	NP_000007.1|NP_001120800.1	P11310	ACADM_HUMAN	acyl-CoA dehydrogenase, C-4 to C-12 straight chain	387					cardiac muscle cell differentiation (GO:0055007)|carnitine biosynthetic process (GO:0045329)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|glycogen biosynthetic process (GO:0005978)|liver development (GO:0001889)|medium-chain fatty acid catabolic process (GO:0051793)|medium-chain fatty acid metabolic process (GO:0051791)|oxidation-reduction process (GO:0055114)|post-embryonic development (GO:0009791)|regulation of gluconeogenesis (GO:0006111)|response to cold (GO:0009409)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|identical protein binding (GO:0042802)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)			breast(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	18					Flavin adenine dinucleotide(DB03147)	AATATCCTGTAGAAAAACTAA	0.358													A|||	873	0.174321	0.1362	0.2522	5008	,	,		16861	0.0228		0.3002	False		,,,				2504	0.1973				p.V391V		Atlas-SNP	.											.	ACADM	50	.	0			c.A1173G						PASS	.	A	,	700,3706	293.6+/-282.7	59,582,1562	116.0	110.0	112.0		1161,1173	-0.3	1.0	1	dbSNP_86	112	2551,6049	416.2+/-352.0	393,1765,2142	no	coding-synonymous,coding-synonymous	ACADM	NM_000016.4,NM_001127328.1	,	452,2347,3704	GG,GA,AA		29.6628,15.8874,24.9962	,	387/422,391/426	76227022	3251,9755	2203	4300	6503	SO:0001819	synonymous_variant	34	exon11			TCCTGTAGAAAAA	M16827	CCDS668.1, CCDS44165.1, CCDS65562.1, CCDS72807.1	1p31	2014-09-17	2010-04-30		ENSG00000117054	ENSG00000117054	1.3.99.3		89	protein-coding gene	gene with protein product		607008	"""acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain"""			3035565	Standard	NM_000016		Approved	MCAD, MCADH, ACAD1	uc009wbp.3	P11310	OTTHUMG00000009784	ENST00000370841.4:c.1161A>G	1.37:g.76227022A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_001127328	Q5T4U4|Q9NYF1	Silent	SNP	ENST00000370841.4	37	CCDS668.1																																																																																			A|0.777;G|0.223	0.223	strong		0.358	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1		
MUC16	94025	hgsc.bcm.edu	37	19	9056941	9056941	+	Missense_Mutation	SNP	A	A	G	rs10410136	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9056941A>G	ENST00000397910.4	-	3	30708	c.30505T>C	c.(30505-30507)Ttt>Ctt	p.F10169L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10171	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCTTCCTAAATCCAGAAGTC	0.453													A|||	970	0.19369	0.1762	0.2666	5008	,	,		22681	0.0258		0.2823	False		,,,				2504	0.2474				p.F10169L		Atlas-SNP	.											.	MUC16	4315	.	0			c.T30505C						PASS	.	A	LEU/PHE	711,3201		59,593,1304	112.0	109.0	110.0		30505	-0.5	0.0	19	dbSNP_119	110	2507,5789		400,1707,2041	yes	missense	MUC16	NM_024690.2	22	459,2300,3345	GG,GA,AA		30.2194,18.1748,26.3598	benign	10169/14508	9056941	3218,8990	1956	4148	6104	SO:0001583	missense	94025	exon3			TCCTAAATCCAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30505T>C	19.37:g.9056941A>G	ENSP00000381008:p.Phe10169Leu	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	413	0.1891025641025641	91	0.18495934959349594	93	0.2569060773480663	11	0.019230769230769232	218	0.287598944591029	a	8.852	0.944925	0.18356	0.181748	0.302194	ENSG00000181143	ENST00000397910	T	0.02446	4.29	3.07	-0.497	0.12023	.	.	.	.	.	T	0.00012	0.0000	N	0.01168	-0.975	.	.	.	B	0.12630	0.006	B	0.06405	0.002	T	0.44877	-0.9299	8	0.87932	D	0	.	5.5872	0.17281	0.6046:0.0:0.3954:0.0	rs10410136;rs56575663;rs60219599;rs10410136	10169	B5ME49	.	L	10169	ENSP00000381008:F10169L	ENSP00000381008:F10169L	F	-	1	0	MUC16	8917941	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.150000	0.16263	-0.091000	0.12440	0.383000	0.25322	TTT	A|0.797;G|0.203	0.203	strong		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
FRS3	10817	hgsc.bcm.edu	37	6	41739173	41739173	+	Silent	SNP	C	C	T	rs35310379	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41739173C>T	ENST00000373018.3	-	7	914	c.663G>A	c.(661-663)ccG>ccA	p.P221P	FRS3_ENST00000259748.2_Silent_p.P221P	NM_006653.3	NP_006644.1	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3	221			P -> L (in dbSNP:rs3747747).		fibroblast growth factor receptor signaling pathway (GO:0008543)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CCCGGGCCTGCGGGAGGAAGG	0.662													C|||	222	0.0443291	0.0023	0.0908	5008	,	,		16194	0.001		0.1213	False		,,,				2504	0.0337				p.P221P		Atlas-SNP	.											.	FRS3	53	.	0			c.G663A						PASS	.	C		108,4298	82.4+/-120.9	2,104,2097	44.0	50.0	48.0		663	-10.2	0.0	6	dbSNP_126	48	938,7662	202.3+/-245.6	67,804,3429	no	coding-synonymous	FRS3	NM_006653.3		69,908,5526	TT,TC,CC		10.907,2.4512,8.0424		221/493	41739173	1046,11960	2203	4300	6503	SO:0001819	synonymous_variant	10817	exon7			GGCCTGCGGGAGG	AF036718	CCDS4860.1	6p21.1	2010-08-05			ENSG00000137218	ENSG00000137218			16970	protein-coding gene	gene with protein product		607744				8761293, 9660748	Standard	NM_006653		Approved	SNT-2, FRS2beta, FRS2B	uc003orc.1	O43559	OTTHUMG00000014686	ENST00000373018.3:c.663G>A	6.37:g.41739173C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_006653	Q5T3D5	Silent	SNP	ENST00000373018.3	37	CCDS4860.1																																																																																			C|0.931;T|0.069	0.069	strong		0.662	FRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040532.2	NM_006653	
PLA2G15	23659	hgsc.bcm.edu	37	16	68289739	68289739	+	Silent	SNP	C	C	T	rs76404867	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:68289739C>T	ENST00000219345.5	+	5	656	c.573C>T	c.(571-573)ccC>ccT	p.P191P	RP11-96D1.7_ENST00000569843.1_RNA|PLA2G15_ENST00000566188.1_Intron|PLA2G15_ENST00000413021.2_Intron|RP11-96D1.7_ENST00000563175.1_RNA|PLA2G15_ENST00000444212.2_Intron	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	191					ceramide metabolic process (GO:0006672)|fatty acid catabolic process (GO:0009062)|phosphatidylcholine metabolic process (GO:0046470)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)|O-acyltransferase activity (GO:0008374)|phospholipid binding (GO:0005543)			kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						ATGGGGGCCCCGTGGTGCTGG	0.607													C|||	22	0.00439297	0.0015	0.0043	5008	,	,		18228	0.0		0.0169	False		,,,				2504	0.0				p.P191P		Atlas-SNP	.											.	PLA2G15	30	.	0			c.C573T						PASS	.	C		18,4378	24.3+/-50.5	0,18,2180	49.0	53.0	52.0		573	-8.0	0.6	16	dbSNP_132	52	173,8427	79.8+/-142.4	2,169,4129	yes	coding-synonymous	PLA2G15	NM_012320.3		2,187,6309	TT,TC,CC		2.0116,0.4095,1.4697		191/413	68289739	191,12805	2198	4300	6498	SO:0001819	synonymous_variant	23659	exon5			GGGCCCCGTGGTG	AB017494	CCDS10864.1	16q22.1	2008-09-19	2008-09-19	2008-09-19	ENSG00000103066	ENSG00000103066			17163	protein-coding gene	gene with protein product		609362	"""lysophospholipase 3 (lysosomal phospholipase A2)"""	LYPLA3		10092508, 16973413	Standard	XM_005255886		Approved	LLPL, GXVPLA2	uc002evr.3	Q8NCC3	OTTHUMG00000137554	ENST00000219345.5:c.573C>T	16.37:g.68289739C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	168	85	0.505952	NM_012320	B3KMF3|B4DUD1|Q53GZ1|Q9NPQ6|Q9UG04|Q9Y2B3	Silent	SNP	ENST00000219345.5	37	CCDS10864.1																																																																																			C|0.987;T|0.013	0.013	strong		0.607	PLA2G15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268888.2	NM_012320	
GPR75-ASB3	100302652	hgsc.bcm.edu	37	2	53941579	53941579	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:53941579C>T	ENST00000263634.3	-	7	1056	c.922G>A	c.(922-924)Gcc>Acc	p.A308T	GPR75-ASB3_ENST00000352846.3_Missense_Mutation_p.A346T|ASB3_ENST00000498475.2_5'UTR|GPR75-ASB3_ENST00000406687.1_Missense_Mutation_p.A235T|GPR75-ASB3_ENST00000394717.2_Missense_Mutation_p.A235T|GPR75-ASB3_ENST00000482829.1_5'UTR|ASB3_ENST00000406625.2_Missense_Mutation_p.A343T	NM_016115.4	NP_057199.1			GPR75-ASB3 readthrough									p.A308S(1)									CACGCCTGGGCGTCTGGGCTG	0.423																																					p.A346T		Atlas-SNP	.											ASB3,colon,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1036A						scavenged	.						105.0	105.0	105.0					2																	53941579		2203	4300	6503	SO:0001583	missense	100302652	exon7			CCTGGGCGTCTGG		CCDS54361.1	2p16	2013-01-23			ENSG00000115239	ENSG00000115239			40043	other	readthrough							Standard	NM_001164165		Approved				OTTHUMG00000129279	ENST00000263634.3:c.922G>A	2.37:g.53941579C>T	ENSP00000263634:p.Ala308Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	110	2	0.0181818	NM_001164165		Missense_Mutation	SNP	ENST00000263634.3	37	CCDS1846.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.802329|5.802329	0.96960|0.96960	.|.	.|.	ENSG00000115239|ENSG00000115239	ENST00000263634;ENST00000406625;ENST00000406687;ENST00000394717;ENST00000352846;ENST00000446049|ENST00000406053	T;T;T;T;T|.	0.69435|.	-0.15;-0.15;-0.4;-0.4;-0.15|.	6.02|6.02	6.02|6.02	0.97574|0.97574	Ankyrin repeat-containing domain (4);|.	0.047372|.	0.85682|.	D|.	0.000000|.	T|T	0.79381|0.79381	0.4436|0.4436	M|M	0.66560|0.66560	2.04|2.04	0.38261|.	D|.	0.941892|.	D;D;D|.	0.89917|.	1.0;0.997;0.997|.	D;P;P|.	0.91635|.	0.999;0.81;0.725|.	T|T	0.75539|0.75539	-0.3282|-0.3282	9|4	0.34782|.	T|.	0.22|.	.|.	20.5407|20.5407	0.99260|0.99260	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	225;343;308|.	B4DZX6;Q2TAI4;Q9Y575|.	.;.;ASB3_HUMAN|.	T|H	308;343;235;235;346;225|300	ENSP00000263634:A308T;ENSP00000385085:A343T;ENSP00000384728:A235T;ENSP00000378206:A235T;ENSP00000313756:A346T|.	ENSP00000263634:A308T|.	A|R	-|-	1|2	0|0	ASB3|ASB3	53795083|53795083	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.910000|0.910000	0.53928|0.53928	7.294000|7.294000	0.78760|0.78760	2.865000|2.865000	0.98341|0.98341	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.	none		0.423	GPR75-ASB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251402.3		
UTRN	7402	hgsc.bcm.edu	37	6	145093052	145093052	+	Silent	SNP	A	A	G	rs80110270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:145093052A>G	ENST00000367545.3	+	58	8505	c.8505A>G	c.(8503-8505)acA>acG	p.T2835T	UTRN_ENST00000367526.4_Silent_p.T390T	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2835	Interaction with SYNM.|WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GCCATCAAACACAGACCACCT	0.318													A|||	171	0.0341454	0.0015	0.0259	5008	,	,		12716	0.0486		0.0487	False		,,,				2504	0.0542				p.T2835T		Atlas-SNP	.											UTRN,NS,carcinoma,+1,1	UTRN	327	1	0			c.A8505G						PASS	.	A		32,4374	36.8+/-68.6	0,32,2171	63.0	68.0	66.0		8505	-1.8	1.0	6	dbSNP_131	66	373,8227	123.1+/-182.0	12,349,3939	no	coding-synonymous	UTRN	NM_007124.2		12,381,6110	GG,GA,AA		4.3372,0.7263,3.1139		2835/3434	145093052	405,12601	2203	4300	6503	SO:0001819	synonymous_variant	7402	exon58			TCAAACACAGACC	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.8505A>G	6.37:g.145093052A>G		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	19	11	0.578947	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	37	CCDS34547.1																																																																																			A|0.969;G|0.031	0.031	strong		0.318	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
RICTOR	253260	hgsc.bcm.edu	37	5	38955796	38955796	+	Missense_Mutation	SNP	G	G	A	rs2043112	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:38955796G>A	ENST00000357387.3	-	26	2540	c.2510C>T	c.(2509-2511)tCc>tTc	p.S837F	RICTOR_ENST00000503698.1_5'UTR|RICTOR_ENST00000296782.5_Missense_Mutation_p.S837F	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					AACATATTTGGAGTTGTATTC	0.358													G|||	1822	0.363818	0.2648	0.3631	5008	,	,		19314	0.4494		0.4284	False		,,,				2504	0.3436				p.S837F		Atlas-SNP	.											.	RICTOR	182	.	0			c.C2510T						PASS	.	G	PHE/SER	1257,3149	432.4+/-343.3	185,887,1131	141.0	132.0	135.0		2510	4.8	1.0	5	dbSNP_94	135	3449,5151	506.0+/-376.5	693,2063,1544	yes	missense	RICTOR	NM_152756.3	155	878,2950,2675	AA,AG,GG		40.1047,28.5293,36.1833	benign	837/1709	38955796	4706,8300	2203	4300	6503	SO:0001583	missense	253260	exon26			TATTTGGAGTTGT		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.2510C>T	5.37:g.38955796G>A	ENSP00000349959:p.Ser837Phe	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	149	70	0.469799	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	856	0.39194139194139194	121	0.2459349593495935	130	0.35911602209944754	282	0.493006993006993	323	0.4261213720316623	G	6.873	0.530458	0.13127	0.285293	0.401047	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.69561	-0.41;0.93	5.73	4.77	0.60923	Armadillo-type fold (1);	0.136957	0.44902	D	0.000403	T	0.00012	0.0000	N	0.08118	0	0.33719	P	0.38330299999999995	B;B	0.28324	0.002;0.207	B;B	0.26864	0.004;0.074	T	0.41342	-0.9514	9	0.87932	D	0	-4.1193	7.1014	0.25340	0.3154:0.0:0.6846:0.0	rs2043112;rs17460877;rs17846482;rs17859541;rs52813560;rs57589026;rs2043112	837;837	Q6R327;Q6R327-3	RICTR_HUMAN;.	F	837	ENSP00000349959:S837F;ENSP00000296782:S837F	ENSP00000296782:S837F	S	-	2	0	RICTOR	38991553	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	4.186000	0.58337	1.258000	0.44101	0.650000	0.86243	TCC	G|0.620;N|0.000	.	strong		0.358	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
RFC5	5985	hgsc.bcm.edu	37	12	118465820	118465820	+	Silent	SNP	T	T	C	rs5745873	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:118465820T>C	ENST00000454402.2	+	9	974	c.856T>C	c.(856-858)Ttg>Ctg	p.L286L	RFC5_ENST00000543153.1_3'UTR|RFC5_ENST00000229043.3_Silent_p.L201L|RFC5_ENST00000392542.2_Silent_p.L265L	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	286					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGAGATACACTTGTTTGTGCA	0.458													T|||	474	0.0946486	0.2489	0.0461	5008	,	,		17914	0.0		0.0964	False		,,,				2504	0.0164				p.L286L		Atlas-SNP	.											.	RFC5	35	.	0			c.T856C						PASS	.	T	,,,	993,3413	370.8+/-319.7	114,765,1324	122.0	112.0	115.0		601,847,856,793	-1.5	1.0	12	dbSNP_114	115	696,7904	172.2+/-222.9	21,654,3625	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RFC5	NM_001130112.2,NM_001206801.1,NM_007370.5,NM_181578.3	,,,	135,1419,4949	CC,CT,TT		8.093,22.5374,12.9863	,,,	201/256,283/338,286/341,265/320	118465820	1689,11317	2203	4300	6503	SO:0001819	synonymous_variant	5985	exon9			ATACACTTGTTTG		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"""ATPases / AAA-type"""	9973	protein-coding gene	gene with protein product		600407	"""replication factor C (activator 1) 5 (36.5kD)"""			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.856T>C	12.37:g.118465820T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_007370	A8MZ62|B3KSX8	Silent	SNP	ENST00000454402.2	37	CCDS9185.1																																																																																			T|0.884;C|0.116	0.116	strong		0.458	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370	
MBD1	4152	hgsc.bcm.edu	37	18	47800179	47800179	+	Missense_Mutation	SNP	G	G	C	rs125555	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:47800179G>C	ENST00000591416.1	-	12	1632	c.1201C>G	c.(1201-1203)Cca>Gca	p.P401A	MBD1_ENST00000382948.5_Missense_Mutation_p.P401A|MBD1_ENST00000349085.2_Missense_Mutation_p.P345A|MBD1_ENST00000587605.1_Missense_Mutation_p.P345A|MBD1_ENST00000353909.3_Missense_Mutation_p.P352A|MBD1_ENST00000269468.5_Missense_Mutation_p.P401A|MBD1_ENST00000585672.1_Missense_Mutation_p.P351A|MBD1_ENST00000457839.2_Missense_Mutation_p.P426A|MBD1_ENST00000339998.6_Missense_Mutation_p.P401A|MBD1_ENST00000398493.1_Missense_Mutation_p.P345A|MBD1_ENST00000269471.5_Missense_Mutation_p.P378A|MBD1_ENST00000588937.1_Missense_Mutation_p.P378A|MBD1_ENST00000590208.1_Missense_Mutation_p.P401A|MBD1_ENST00000347968.3_Missense_Mutation_p.P345A|MBD1_ENST00000591535.1_Missense_Mutation_p.P378A|MBD1_ENST00000398488.1_Missense_Mutation_p.P345A|MBD1_ENST00000398495.2_Missense_Mutation_p.P370A|MBD1_ENST00000424334.2_Missense_Mutation_p.P452A|MBD1_ENST00000436910.1_Missense_Mutation_p.P378A|MBD1_ENST00000585595.1_Missense_Mutation_p.P426A			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	401			P -> A (in dbSNP:rs125555). {ECO:0000269|PubMed:10441743}.		negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						CGGTAAGGTGGGGGCGATCCT	0.607													G|||	890	0.177716	0.1407	0.17	5008	,	,		16641	0.1806		0.1829	False		,,,				2504	0.2249				p.P426A		Atlas-SNP	.											.	MBD1	228	.	0			c.C1276G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	604,3802	261.3+/-264.2	49,506,1648	89.0	86.0	87.0		1201,1276,1273,1201,1108,1051,1201,1033,1132,1033,1033,1132,1201,1054	1.9	0.1	18	dbSNP_78	87	1692,6908	309.3+/-309.3	171,1350,2779	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	MBD1	NM_001204136.1,NM_001204137.1,NM_001204138.1,NM_001204139.1,NM_001204140.1,NM_001204141.1,NM_001204142.1,NM_001204143.1,NM_001204151.1,NM_002384.2,NM_015844.2,NM_015845.3,NM_015846.3,NM_015847.3	27,27,27,27,27,27,27,27,27,27,27,27,27,27	220,1856,4427	CC,CG,GG		19.6744,13.7086,17.6534	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	401/656,426/631,425/630,401/606,370/575,351/568,401/551,345/536,378/537,345/504,345/550,378/587,401/606,352/557	47800179	2296,10710	2203	4300	6503	SO:0001583	missense	4152	exon13			AAGGTGGGGGCGA	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.1201C>G	18.37:g.47800179G>C	ENSP00000467017:p.Pro401Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Missense_Mutation	SNP	ENST00000591416.1	37	CCDS11943.1	385	0.1762820512820513	74	0.15040650406504066	66	0.18232044198895028	102	0.17832167832167833	143	0.18865435356200527	G	10.33	1.319949	0.23994	0.137086	0.196744	ENSG00000141644	ENST00000382948;ENST00000353909;ENST00000349085;ENST00000269468;ENST00000347968;ENST00000436910;ENST00000269471;ENST00000424334;ENST00000339998;ENST00000398495;ENST00000457839;ENST00000398493;ENST00000398488	D;D;D;D;D;D;D;D;D;D;D;D;D	0.98633	-3.89;-3.93;-4.78;-3.89;-5.04;-3.82;-3.82;-3.9;-3.84;-3.88;-3.88;-5.04;-4.78	4.98	1.89	0.25635	.	0.218980	0.32081	N	0.006607	T	0.02156	0.0067	L	0.32530	0.975	0.53688	P	2.599999999997049E-5	P;B;B;B;P;P;B;B;B;P;B;P	0.43314	0.803;0.409;0.081;0.245;0.51;0.644;0.359;0.433;0.154;0.681;0.245;0.681	B;B;B;B;B;B;B;B;B;B;B;B	0.44133	0.338;0.188;0.073;0.118;0.167;0.335;0.234;0.164;0.118;0.442;0.08;0.442	T	0.48514	-0.9029	9	0.44086	T	0.13	-0.1939	5.6276	0.17490	0.1987:0.1579:0.6434:0.0	rs125555;rs760283;rs52805720;rs60253010;rs125555	345;452;378;401;401;378;352;345;401;345;426;345	B4DUR3;B4DI41;Q9UIS9-8;A8K654;Q9UIS9-6;Q9UIS9-2;Q9UIS9-5;Q9UIS9-4;Q9UIS9;Q9UIS9-7;B4DXJ5;Q9UIS9-3	.;.;.;.;.;.;.;.;MBD1_HUMAN;.;.;.	A	401;352;345;401;345;378;378;452;401;401;426;345;345	ENSP00000372407:P401A;ENSP00000269469:P352A;ENSP00000342531:P345A;ENSP00000269468:P401A;ENSP00000285102:P345A;ENSP00000409561:P378A;ENSP00000269471:P378A;ENSP00000408846:P452A;ENSP00000339546:P401A;ENSP00000381508:P401A;ENSP00000405268:P426A;ENSP00000381506:P345A;ENSP00000381502:P345A	ENSP00000269468:P401A	P	-	1	0	MBD1	46054177	0.343000	0.24818	0.126000	0.21872	0.987000	0.75469	0.249000	0.18216	0.254000	0.21573	0.555000	0.69702	CCA	G|0.819;C|0.181	0.181	strong		0.607	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
GBP4	115361	hgsc.bcm.edu	37	1	89652071	89652071	+	Missense_Mutation	SNP	T	T	C	rs386633303|rs561042	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89652071T>C	ENST00000355754.6	-	10	1749	c.1652A>G	c.(1651-1653)gAg>gGg	p.E551G	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	551			E -> G (in dbSNP:rs561042).|E -> K (in dbSNP:rs561037).	LEE -> MER (in Ref. 1; AAL02054 and 3; BAC85144). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		TTCCCTTTCCTCCTCCAACTT	0.493													T|||	1790	0.357428	0.143	0.3141	5008	,	,		18881	0.3978		0.4881	False		,,,				2504	0.502				p.E551G		Atlas-SNP	.											GBP4,NS,carcinoma,+1,1	GBP4	89	1	0			c.A1652G						PASS	.	T	GLY/GLU	34,4372		5,24,2174	194.0	136.0	156.0		1652	-6.3	0.0	1	dbSNP_83	156	186,8414		23,140,4137	yes	missense	GBP4	NM_052941.4	98	28,164,6311	CC,CT,TT		2.1628,0.7717,1.6915	benign	551/641	89652071	220,12786	2203	4300	6503	SO:0001583	missense	115361	exon10			CTTTCCTCCTCCA	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1652A>G	1.37:g.89652071T>C	ENSP00000359490:p.Glu551Gly	Somatic	325	2	0.00615385		WXS	Illumina HiSeq	Phase_I	144	142	0.986111	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.484517	0.26598	0.007717	0.021628	ENSG00000162654	ENST00000355754	T	0.02216	4.39	4.14	-6.34	0.01982	Guanylate-binding protein, C-terminal (3);	1.061500	0.07205	N	0.858069	T	0.01156	0.0038	M	0.73962	2.25	0.80722	P	0.0	B	0.23990	0.095	B	0.33121	0.158	T	0.44697	-0.9311	9	0.52906	T	0.07	.	4.4945	0.11830	0.1154:0.1531:0.1208:0.6107	rs561042;rs34567676;rs52816340;rs561042	551	Q96PP9	GBP4_HUMAN	G	551	ENSP00000359490:E551G	ENSP00000359490:E551G	E	-	2	0	GBP4	89424659	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.078000	0.01370	-1.292000	0.02366	-0.232000	0.12228	GAG	T|0.620;C|0.380	0.380	strong		0.493	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
DSP	1832	hgsc.bcm.edu	37	6	7581032	7581032	+	Missense_Mutation	SNP	C	C	T	rs28763967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:7581032C>T	ENST00000379802.3	+	23	4950	c.4609C>T	c.(4609-4611)Cgc>Tgc	p.R1537C	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1537	Central fibrous rod domain.		R -> C (in dbSNP:rs28763967). {ECO:0000269|PubMed:19863551, ECO:0000269|PubMed:20031617}.		adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AGAACTGACACGCCTGAGGAT	0.493													C|||	18	0.00359425	0.0008	0.0014	5008	,	,		21149	0.0		0.0159	False		,,,				2504	0.0				p.R1537C		Atlas-SNP	.											.	DSP	306	.	0			c.C4609T						PASS	.	C	,CYS/ARG	13,4393	20.2+/-43.8	0,13,2190	120.0	121.0	120.0		,4609	5.8	1.0	6	dbSNP_125	120	123,8477	62.8+/-124.8	3,117,4180	yes	intron,missense	DSP	NM_001008844.1,NM_004415.2	,180	3,130,6370	TT,TC,CC		1.4302,0.2951,1.0457	,probably-damaging	,1537/2872	7581032	136,12870	2203	4300	6503	SO:0001583	missense	1832	exon23			CTGACACGCCTGA	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.4609C>T	6.37:g.7581032C>T	ENSP00000369129:p.Arg1537Cys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	28	0.345679	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	12	0.005494505494505495	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	16.80	3.224244	0.58668	0.002951	0.014302	ENSG00000096696	ENST00000379802	T	0.74737	-0.87	5.85	5.85	0.93711	.	0.000000	0.64402	D	0.000009	T	0.76047	0.3933	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	T	0.77800	-0.2452	10	0.59425	D	0.04	.	15.812	0.78571	0.1441:0.8559:0.0:0.0	rs28763967	1537	P15924	DESP_HUMAN	C	1537	ENSP00000369129:R1537C	ENSP00000369129:R1537C	R	+	1	0	DSP	7526031	0.859000	0.29813	0.966000	0.40874	0.971000	0.66376	2.051000	0.41307	2.772000	0.95346	0.655000	0.94253	CGC	C|0.992;T|0.008	0.008	strong		0.493	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
TSPYL4	23270	hgsc.bcm.edu	37	6	116574455	116574455	+	Silent	SNP	G	G	A	rs2232472	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:116574455G>A	ENST00000420283.1	-	1	806	c.717C>T	c.(715-717)caC>caT	p.H239H	RP3-486I3.7_ENST00000448740.2_lincRNA|DSE_ENST00000540275.1_5'Flank	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	239					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(2)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.045)|OV - Ovarian serous cystadenocarcinoma(136;0.0666)|GBM - Glioblastoma multiforme(226;0.095)|Epithelial(106;0.125)		TGCGCTGCATGTGGAGCCTTC	0.527													G|||	1945	0.388379	0.0923	0.3804	5008	,	,		19788	0.6359		0.3648	False		,,,				2504	0.5634				p.H239H		Atlas-SNP	.											.	TSPYL4	18	.	0			c.C717T						PASS	.	G		453,3545		37,379,1583	34.0	35.0	35.0		717	-3.5	1.0	6	dbSNP_98	35	2966,5398		529,1908,1745	no	coding-synonymous	TSPYL4	NM_021648.4		566,2287,3328	AA,AG,GG		35.4615,11.3307,27.6573		239/415	116574455	3419,8943	1999	4182	6181	SO:0001819	synonymous_variant	23270	exon1			CTGCATGTGGAGC		CCDS5106.1	6q22.1	2010-05-12			ENSG00000187189	ENSG00000187189			21559	protein-coding gene	gene with protein product							Standard	NM_021648		Approved	dJ486I3.2, KIAA0721	uc003pwn.3	Q9UJ04	OTTHUMG00000015429	ENST00000420283.1:c.717C>T	6.37:g.116574455G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_021648	B4DYQ2|O94828|Q96GW8	Silent	SNP	ENST00000420283.1	37	CCDS5106.1																																																																																			G|0.630;A|0.370	0.370	strong		0.527	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2		
TUSC1	286319	hgsc.bcm.edu	37	9	25677698	25677698	+	Missense_Mutation	SNP	A	A	C	rs72631815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:25677698A>C	ENST00000358022.3	-	1	1158	c.622T>G	c.(622-624)Tct>Gct	p.S208A		NM_001004125.2	NP_001004125.1	Q2TAM9	TUSC1_HUMAN	tumor suppressor candidate 1	208										kidney(1)	1	all_hematologic(1;0.197)	all_neural(3;5.42e-18)|Glioma(3;5.54e-17)		GBM - Glioblastoma multiforme(1;1.51e-108)|Lung(42;2.88e-14)|LUSC - Lung squamous cell carcinoma(38;3.16e-11)		CAGGGCCCAGAGGGCTCCGAG	0.736													A|||	833	0.166334	0.034	0.1744	5008	,	,		11360	0.1577		0.326	False		,,,				2504	0.184				p.S208A	Pancreas(19;648 672 25630 30820 31331)	Atlas-SNP	.											.	TUSC1	7	.	0			c.T622G						PASS	.	A	ALA/SER	228,3728		13,202,1763	6.0	6.0	6.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	622	-1.1	0.0	9	dbSNP_130	6	2027,5715		281,1465,2125	no	missense	TUSC1	NM_001004125.2	99	294,1667,3888	CC,CA,AA		26.1819,5.7634,19.2768	benign	208/213	25677698	2255,9443	1978	3871	5849	SO:0001583	missense	286319	exon1			GCCCAGAGGGCTC	AY168647	CCDS34999.1	9p21.2	2014-05-22			ENSG00000198680	ENSG00000198680			31010	protein-coding gene	gene with protein product		610529				15208665	Standard	NM_001004125		Approved	TSG-9	uc003zpx.3	Q2TAM9	OTTHUMG00000159591	ENST00000358022.3:c.622T>G	9.37:g.25677698A>C	ENSP00000350716:p.Ser208Ala	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_001004125	A0PJ78|Q67GI3|Q86SS1|Q8TAH8	Missense_Mutation	SNP	ENST00000358022.3	37	CCDS34999.1	446	0.2042124542124542	35	0.07113821138211382	74	0.20441988950276244	96	0.16783216783216784	241	0.3179419525065963	A	3.000	-0.206320	0.06180	0.057634	0.261819	ENSG00000198680	ENST00000358022	T	0.48201	0.82	3.71	-1.1	0.09872	.	0.850927	0.09559	U	0.785795	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.14012	0.009	B	0.08055	0.003	T	0.34279	-0.9835	9	0.06757	T	0.87	0.0163	4.2113	0.10512	0.3572:0.3245:0.3183:0.0	.	208	Q2TAM9	TUSC1_HUMAN	A	208	ENSP00000350716:S208A	ENSP00000350716:S208A	S	-	1	0	TUSC1	25667698	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.236000	0.09003	-0.521000	0.06426	0.379000	0.24179	TCT	A|0.795;C|0.205	0.205	strong		0.736	TUSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356351.1	NM_001004125	
BCAM	4059	hgsc.bcm.edu	37	19	45322744	45322744	+	Missense_Mutation	SNP	A	A	G	rs1135062	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:45322744A>G	ENST00000270233.6	+	12	1637	c.1615A>G	c.(1615-1617)Acc>Gcc	p.T539A	BCAM_ENST00000589651.1_Missense_Mutation_p.T539A	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	539	Ig-like C2-type 3.		T -> A (in dbSNP:rs1135062). {ECO:0000269|PubMed:7777537, ECO:0000269|PubMed:7954395, ECO:0000269|Ref.7}.		cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CCACTTCGGCACCGGTGAGTG	0.642													a|||	1354	0.270367	0.4349	0.2305	5008	,	,		15269	0.1131		0.3002	False		,,,				2504	0.2076				p.T539A		Atlas-SNP	.											BCAM,NS,adenoma,0,1	BCAM	53	1	0			c.A1615G	GRCh37	CM973377	BCAM	M	rs1135062	PASS	.		ALA/THR,ALA/THR	1803,2603		376,1051,776	55.0	61.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1615,1615	-8.3	0.0	19	dbSNP_86	59	2588,6012		384,1820,2096	yes	missense,missense	BCAM	NM_001013257.1,NM_005581.3	58,58	760,2871,2872	GG,GA,AA		30.093,40.9215,33.7613	benign,benign	539/589,539/629	45322744	4391,8615	2203	4300	6503	SO:0001583	missense	4059	exon12			TTCGGCACCGGTG	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6722	protein-coding gene	gene with protein product		612773	"""Lutheran blood group (Auberger b antigen included)"", ""basal cell adhesion molecule (Lu and Au blood groups)"""	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1615A>G	19.37:g.45322744A>G	ENSP00000270233:p.Thr539Ala	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	145	68	0.468966	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	579	0.2651098901098901	205	0.4166666666666667	88	0.2430939226519337	55	0.09615384615384616	231	0.30474934036939316	.	5.337	0.247523	0.10130	0.409215	0.30093	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.59364	0.27;0.29	4.24	-8.33	0.00992	Immunoglobulin subtype (1);Immunoglobulin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29731	-1.0002	8	0.05620	T	0.96	0.1002	1.2179	0.01918	0.1523:0.2382:0.3376:0.2719	rs1135062;rs11548861;rs11880954;rs16979448;rs58063257;rs1135062	539	P50895	BCAM_HUMAN	A	539	ENSP00000270233:T539A;ENSP00000375817:T539A	ENSP00000270233:T539A	T	+	1	0	BCAM	50014584	0.000000	0.05858	0.001000	0.08648	0.187000	0.23431	-0.967000	0.03821	-1.683000	0.01444	0.434000	0.28630	ACC	A|0.703;G|0.297	0.297	strong		0.642	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	
FPGT	8790	hgsc.bcm.edu	37	1	74670172	74670172	+	Silent	SNP	A	A	G	rs12046751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:74670172A>G	ENST00000609362.1	+	4	478	c.441A>G	c.(439-441)aaA>aaG	p.K147K	FPGT_ENST00000534056.1_Intron|FPGT_ENST00000370894.5_Intron|FPGT_ENST00000482102.2_3'UTR|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000370898.3_Silent_p.K160K|FPGT_ENST00000467578.2_3'UTR|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT_ENST00000524915.1_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|TNNI3K_ENST00000370891.2_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	147					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)			breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						TAGAATTAAAACTAGCCATGT	0.368													A|||	1186	0.236821	0.1362	0.428	5008	,	,		15853	0.1171		0.4085	False		,,,				2504	0.184				p.K147K		Atlas-SNP	.											.	FPGT	77	.	0			c.A441G						PASS	.	A	,,,,	854,3552	333.9+/-303.2	80,694,1429	106.0	113.0	111.0		,,,,441	3.3	1.0	1	dbSNP_120	111	3451,5149	505.6+/-376.4	704,2043,1553	no	intron,intron,intron,intron,coding-synonymous	FPGT,FPGT-TNNI3K	NM_001112808.2,NM_001199327.1,NM_001199328.1,NM_001199329.1,NM_003838.3	,,,,	784,2737,2982	GG,GA,AA		40.1279,19.3827,33.1001	,,,,	,,,,147/595	74670172	4305,8701	2203	4300	6503	SO:0001819	synonymous_variant	8790	exon4			ATTAAAACTAGCC	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.441A>G	1.37:g.74670172A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	134	72	0.537313	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Silent	SNP	ENST00000609362.1	37	CCDS663.1																																																																																			A|0.697;G|0.303	0.303	strong		0.368	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PACSIN2	11252	hgsc.bcm.edu	37	22	43289473	43289473	+	Silent	SNP	G	G	A	rs5759013	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:43289473G>A	ENST00000263246.3	-	3	408	c.207C>T	c.(205-207)ctC>ctT	p.L69L	PACSIN2_ENST00000337959.4_Silent_p.L69L|PACSIN2_ENST00000402229.1_Silent_p.L69L|PACSIN2_ENST00000407585.1_Silent_p.L69L|PACSIN2_ENST00000403744.3_Silent_p.L69L	NM_001184970.1	NP_001171899.1	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in neurons 2	69	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin cytoskeleton organization (GO:0030036)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cell projection morphogenesis (GO:0048858)|membrane tubulation (GO:0097320)|negative regulation of endocytosis (GO:0045806)|protein localization to endosome (GO:0036010)	caveola (GO:0005901)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	19		Glioma(61;0.222)				CTTTCTCCACGAGCTGCCTCC	0.667													G|||	1374	0.274361	0.1581	0.3573	5008	,	,		16356	0.0933		0.4304	False		,,,				2504	0.3988				p.L69L		Atlas-SNP	.											PACSIN2,NS,carcinoma,-2,1	PACSIN2	48	1	0			c.C207T						PASS	.	G	,,	867,3281		110,647,1317	27.0	31.0	29.0		207,207,207	-9.0	0.1	22	dbSNP_114	29	3811,4661		904,2003,1329	no	coding-synonymous,coding-synonymous,coding-synonymous	PACSIN2	NM_001184970.1,NM_001184971.1,NM_007229.3	,,	1014,2650,2646	AA,AG,GG		44.9835,20.9016,37.0681	,,	69/487,69/446,69/487	43289473	4678,7942	2074	4236	6310	SO:0001819	synonymous_variant	11252	exon3			CTCCACGAGCTGC	AF128536	CCDS43023.1, CCDS54536.1	22q13.2-q13.33	2009-05-08			ENSG00000100266	ENSG00000100266			8571	protein-coding gene	gene with protein product	"""syndapin II"""	604960				10431838, 11082044	Standard	NM_007229		Approved	SDPII	uc003bdg.4	Q9UNF0	OTTHUMG00000150701	ENST00000263246.3:c.207C>T	22.37:g.43289473G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_007229	O95921|Q96HV9|Q9H0D3|Q9NPN1|Q9Y4V2	Silent	SNP	ENST00000263246.3	37	CCDS43023.1																																																																																			G|0.724;A|0.276	0.276	strong		0.667	PACSIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319665.1	NM_007229	
CCHCR1	54535	hgsc.bcm.edu	37	6	31116210	31116210	+	Silent	SNP	G	G	A	rs130071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31116210G>A	ENST00000376266.5	-	10	1407	c.1285C>T	c.(1285-1287)Ctg>Ttg	p.L429L	CCHCR1_ENST00000396263.2_Silent_p.L429L|CCHCR1_ENST00000396268.3_Silent_p.L518L|CCHCR1_ENST00000480060.1_5'Flank|CCHCR1_ENST00000451521.2_Silent_p.L482L	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	429					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						ACAAGCCTCAGCTGCTCCTCG	0.622													G|||	979	0.195487	0.1815	0.2608	5008	,	,		17553	0.0575		0.2793	False		,,,				2504	0.2239				p.L518L		Atlas-SNP	.											.	CCHCR1	68	.	0			c.C1552T						PASS	.		,,	649,2367		69,511,928	114.0	112.0	113.0		1444,1552,1285	3.3	1.0	6	dbSNP_78	113	1572,3844		242,1088,1378	yes	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	311,1599,2306	AA,AG,GG		29.0251,21.5186,26.3401	,,	482/836,518/872,429/783	31116210	2221,6211	1508	2708	4216	SO:0001819	synonymous_variant	54535	exon10			GCCTCAGCTGCTC	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1285C>T	6.37:g.31116210G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	204	102	0.5	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			G|0.746;A|0.254	0.254	strong		0.622	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
SNX19	399979	hgsc.bcm.edu	37	11	130784694	130784694	+	Missense_Mutation	SNP	C	C	T	rs61736758	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130784694C>T	ENST00000265909.4	-	1	1710	c.1141G>A	c.(1141-1143)Ggc>Agc	p.G381S	SNX19_ENST00000533318.1_Intron|SNX19_ENST00000533214.1_Missense_Mutation_p.G381S|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000530356.1_Intron|SNX19_ENST00000539184.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	381					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GTTTCTTTGCCCAGTTCAGAC	0.498													C|||	639	0.127596	0.0492	0.0893	5008	,	,		19824	0.1538		0.1988	False		,,,				2504	0.1605				p.G381S		Atlas-SNP	.											.	SNX19	84	.	0			c.G1141A						PASS	.	C	SER/GLY	314,4088	167.6+/-198.6	14,286,1901	68.0	67.0	67.0		1141	-2.5	0.8	11	dbSNP_129	67	1787,6807	322.6+/-315.6	173,1441,2683	yes	missense	SNX19	NM_014758.2	56	187,1727,4584	TT,TC,CC		20.7936,7.1331,16.1665	benign	381/993	130784694	2101,10895	2201	4297	6498	SO:0001583	missense	399979	exon1			CTTTGCCCAGTTC	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1141G>A	11.37:g.130784694C>T	ENSP00000265909:p.Gly381Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	37	CCDS31721.1	315	0.14423076923076922	25	0.0508130081300813	35	0.09668508287292818	99	0.17307692307692307	156	0.20580474934036938	C	12.06	1.824359	0.32237	0.071331	0.207936	ENSG00000120451	ENST00000265909;ENST00000533214	T;T	0.17054	2.3;2.3	5.59	-2.47	0.06442	.	1.059020	0.07195	N	0.856444	T	0.00012	0.0000	N	0.04880	-0.145	0.09310	P	0.9999999628354	B;B	0.18461	0.028;0.006	B;B	0.12156	0.007;0.005	T	0.48210	-0.9055	9	0.11182	T	0.66	-1.5606	11.3915	0.49817	0.0:0.5718:0.0:0.4282	.	381;381	E9PKB9;Q92543	.;SNX19_HUMAN	S	381	ENSP00000265909:G381S;ENSP00000435390:G381S	ENSP00000265909:G381S	G	-	1	0	SNX19	130289904	0.077000	0.21312	0.810000	0.32431	0.993000	0.82548	-0.006000	0.12833	-0.858000	0.04110	0.644000	0.83932	GGC	C|0.845;T|0.155	0.155	strong		0.498	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
TTN	7273	hgsc.bcm.edu	37	2	179579212	179579212	+	Silent	SNP	T	T	C	rs2562838	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179579212T>C	ENST00000591111.1	-	89	25562	c.25338A>G	c.(25336-25338)gaA>gaG	p.E8446E	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.E7519E|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Silent_p.E8763E|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12617	Ig-like 67.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGAAATGGGTTCAGCGCCTT	0.398													C|||	2421	0.483427	0.6021	0.3934	5008	,	,		19704	0.6587		0.2237	False		,,,				2504	0.4734				p.E8763E		Atlas-SNP	.											.	TTN	18412	.	0			c.A26289G						PASS	.	C	,,,	1989,1739		543,903,418	67.0	62.0	63.0		,22557,,	4.2	1.0	2	dbSNP_100	63	1654,6538		157,1340,2599	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	700,2243,3017	CC,CT,TT		20.1904,46.647,30.5621	,,,	,7519/33424,,	179579212	3643,8277	1864	4096	5960	SO:0001819	synonymous_variant	7273	exon91			AATGGGTTCAGCG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25338A>G	2.37:g.179579212T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	145	80	0.551724	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.582;C|0.418	0.418	strong		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ARID3A	1820	hgsc.bcm.edu	37	19	966693	966693	+	Silent	SNP	C	C	T	rs6510986	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:966693C>T	ENST00000263620.3	+	7	1647	c.1320C>T	c.(1318-1320)gcC>gcT	p.A440A		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	440	Ala-rich.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCTGTGGCCGCACAGGCAG	0.677													.|||	3580	0.714856	0.6702	0.6066	5008	,	,		6401	0.5724		0.8698	False		,,,				2504	0.8395				p.A440A	Pancreas(29;54 1022 32760 50921)	Atlas-SNP	.											.	ARID3A	35	.	0			c.C1320T						PASS	.	C		3062,1236		1106,850,193	12.0	15.0	14.0		1320	-10.0	0.7	19	dbSNP_116	14	7254,1074		3161,932,71	no	coding-synonymous	ARID3A	NM_005224.2		4267,1782,264	TT,TC,CC		12.8963,28.7576,18.2956		440/594	966693	10316,2310	2149	4164	6313	SO:0001819	synonymous_variant	1820	exon7			TGTGGCCGCACAG	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"""-"""	3031	protein-coding gene	gene with protein product		603265	"""dead ringer-like 1 (Drosophila)"", ""AT rich interactive domain 3A (BRIGHT- like)"""	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.1320C>T	19.37:g.966693C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Silent	SNP	ENST00000263620.3	37	CCDS12050.1																																																																																			C|0.233;T|0.767	0.767	strong		0.677	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224	
CHRM3	1131	hgsc.bcm.edu	37	1	240071447	240071447	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:240071447T>C	ENST00000255380.4	+	5	1475	c.696T>C	c.(694-696)acT>acC	p.T232T		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	232					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CCACCATTACTTTTGGCACAG	0.448																																					p.T232T		Atlas-SNP	.											CHRM3,NS,carcinoma,+2,1	CHRM3	118	1	0			c.T696C						scavenged	.						106.0	111.0	109.0					1																	240071447		2203	4300	6503	SO:0001819	synonymous_variant	1131	exon5			CATTACTTTTGGC	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1952	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 3"""	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.696T>C	1.37:g.240071447T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	151	3	0.0198676	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Silent	SNP	ENST00000255380.4	37	CCDS1616.1																																																																																			.	.	none		0.448	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
OR8H3	390152	hgsc.bcm.edu	37	11	55890609	55890609	+	Missense_Mutation	SNP	C	C	T	rs61743026	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55890609C>T	ENST00000313472.3	+	1	761	c.761C>T	c.(760-762)aCt>aTt	p.T254I		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	254						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TTCTATGGAACTATGATTTTT	0.388													C|||	191	0.038139	0.0091	0.0447	5008	,	,		19849	0.001		0.0944	False		,,,				2504	0.0532				p.T254I		Atlas-SNP	.											.	OR8H3	92	.	0			c.C761T						PASS	.	C	ILE/THR	85,4317	70.9+/-108.8	0,85,2116	109.0	106.0	107.0		761	2.7	0.3	11	dbSNP_129	107	692,7900	170.6+/-221.7	34,624,3638	yes	missense	OR8H3	NM_001005201.1	89	34,709,5754	TT,TC,CC		8.054,1.9309,5.9797	probably-damaging	254/313	55890609	777,12217	2201	4296	6497	SO:0001583	missense	390152	exon1			ATGGAACTATGAT	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.761C>T	11.37:g.55890609C>T	ENSP00000323928:p.Thr254Ile	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	248	101	0.407258	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	85	0.03891941391941392	3	0.006097560975609756	14	0.03867403314917127	0	0.0	68	0.08970976253298153	C	9.638	1.138095	0.21123	0.019309	0.08054	ENSG00000181761	ENST00000313472	T	0.00289	8.28	3.62	2.68	0.31781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000041	T	0.00039	0.0001	M	0.77103	2.36	0.09310	N	1	D	0.60575	0.988	D	0.65323	0.934	T	0.46428	-0.9192	10	0.87932	D	0	.	7.3412	0.26637	0.1679:0.7398:0.0:0.0923	rs61743026	254	Q8N146	OR8H3_HUMAN	I	254	ENSP00000323928:T254I	ENSP00000323928:T254I	T	+	2	0	OR8H3	55647185	0.035000	0.19736	0.335000	0.25508	0.103000	0.19146	3.281000	0.51685	0.612000	0.30071	0.173000	0.16961	ACT	C|0.950;T|0.050	0.050	strong		0.388	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
SWT1	54823	hgsc.bcm.edu	37	1	185171869	185171869	+	Missense_Mutation	SNP	A	A	G	rs6698109	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:185171869A>G	ENST00000367500.4	+	11	1772	c.1607A>G	c.(1606-1608)cAc>cGc	p.H536R	SWT1_ENST00000367501.3_Missense_Mutation_p.H536R	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	536			H -> R (in dbSNP:rs6698109). {ECO:0000269|PubMed:15489334}.							breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						GAGTTATTACACTTATCTCTG	0.353													A|||	1380	0.275559	0.2179	0.2464	5008	,	,		12733	0.1964		0.341	False		,,,				2504	0.3885				p.H536R		Atlas-SNP	.											.	SWT1	88	.	0			c.A1607G						PASS	.	A	ARG/HIS,ARG/HIS	1090,3316	393.3+/-328.8	138,814,1251	88.0	89.0	89.0		1607,1607	-0.0	0.0	1	dbSNP_116	89	3038,5562	466.1+/-366.7	551,1936,1813	yes	missense,missense	SWT1	NM_001105518.1,NM_017673.6	29,29	689,2750,3064	GG,GA,AA		35.3256,24.739,31.7392	benign,benign	536/901,536/901	185171869	4128,8878	2203	4300	6503	SO:0001583	missense	54823	exon11			TATTACACTTATC	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.1607A>G	1.37:g.185171869A>G	ENSP00000356470:p.His536Arg	Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	615	0.2815934065934066	130	0.26422764227642276	87	0.24033149171270718	140	0.24475524475524477	258	0.3403693931398417	A	7.659	0.684572	0.14973	0.24739	0.353256	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.16457	2.34;2.34	5.49	-0.0357	0.13891	.	0.525254	0.22752	N	0.056064	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.49194	-0.8965	9	0.23302	T	0.38	.	4.8888	0.13717	0.5657:0.1491:0.2852:0.0	rs6698109;rs17856891;rs52826833;rs61051695;rs6698109	536	Q5T5J6	SWT1_HUMAN	R	536	ENSP00000356471:H536R;ENSP00000356470:H536R	ENSP00000356470:H536R	H	+	2	0	SWT1	183438492	0.844000	0.29557	0.003000	0.11579	0.720000	0.41350	0.715000	0.25822	-0.187000	0.10516	-0.274000	0.10170	CAC	A|0.699;G|0.301	0.301	strong		0.353	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
TMEM230	29058	hgsc.bcm.edu	37	20	5086939	5086939	+	Silent	SNP	A	A	T	rs6116651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:5086939A>T	ENST00000379286.2	-	4	537	c.117T>A	c.(115-117)ccT>ccA	p.P39P	TMEM230_ENST00000492419.1_5'UTR|TMEM230_ENST00000379277.2_Silent_p.P39P|TMEM230_ENST00000342308.5_Silent_p.P102P|TMEM230_ENST00000379279.2_Silent_p.P39P|TMEM230_ENST00000202834.7_Silent_p.P39P|TMEM230_ENST00000379283.2_Silent_p.P39P	NM_001009924.1	NP_001009924.1	Q96A57	TM230_HUMAN	transmembrane protein 230	39						integral component of membrane (GO:0016021)											AAGGGATCTTAGGAGGGGTTT	0.393													A|||	621	0.124002	0.3154	0.1167	5008	,	,		16410	0.0		0.0905	False		,,,				2504	0.0327				p.P102P		Atlas-SNP	.											.	.	.	.	0			c.T306A						PASS	.	A	,,,	1283,3123	432.2+/-343.2	195,893,1115	53.0	54.0	53.0		306,117,117,117	-1.4	1.0	20	dbSNP_114	53	940,7660	206.3+/-248.5	49,842,3409	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C20orf30	NM_001009923.1,NM_001009924.1,NM_001009925.1,NM_014145.4	,,,	244,1735,4524	TT,TA,AA		10.9302,29.1194,17.0921	,,,	102/184,39/121,39/121,39/121	5086939	2223,10783	2203	4300	6503	SO:0001819	synonymous_variant	29058	exon4			GATCTTAGGAGGG	AF161392	CCDS13086.1, CCDS33438.1	20p13	2012-03-16	2012-03-16	2012-03-16	ENSG00000089063	ENSG00000089063			15876	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 30"""	C20orf30			Standard	XM_005260713		Approved	HSPC274	uc002wlk.3	Q96A57	OTTHUMG00000031796	ENST00000379286.2:c.117T>A	20.37:g.5086939A>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_001009923	B2RDM8|D3DVZ9|Q0VGC8|Q5TDS5|Q96ES2|Q9P0A7	Silent	SNP	ENST00000379286.2	37	CCDS13086.1																																																																																			A|0.852;T|0.148	0.148	strong		0.393	TMEM230-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077846.1		
SIK1	150094	hgsc.bcm.edu	37	21	44846016	44846016	+	Missense_Mutation	SNP	C	C	T	rs3746951	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:44846016C>T	ENST00000270162.6	-	2	175	c.43G>A	c.(43-45)Ggt>Agt	p.G15S		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	15			G -> S (in dbSNP:rs3746951). {ECO:0000269|PubMed:17344846}.		cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	TGGCCCTGACCCTGGCCCGCG	0.692													C|||	834	0.166534	0.0129	0.2925	5008	,	,		11980	0.2153		0.2684	False		,,,				2504	0.1299				p.G15S		Atlas-SNP	.											.	SIK1	65	.	0			c.G43A						PASS	.	C	SER/GLY	212,4172		8,196,1988	15.0	17.0	16.0		43	2.4	0.5	21	dbSNP_107	16	2211,6371		269,1673,2349	yes	missense	SIK1	NM_173354.3	56	277,1869,4337	TT,TC,CC		25.7632,4.8358,18.6873	benign	15/784	44846016	2423,10543	2192	4291	6483	SO:0001583	missense	150094	exon2			CCTGACCCTGGCC	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.43G>A	21.37:g.44846016C>T	ENSP00000270162:p.Gly15Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	43	27	0.627907	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	435	0.19917582417582416	11	0.022357723577235773	95	0.26243093922651933	122	0.21328671328671328	207	0.27308707124010556	C	9.340	1.062697	0.19987	0.048358	0.257632	ENSG00000142178	ENST00000270162	T	0.70869	-0.52	3.5	2.39	0.29439	Protein kinase-like domain (1);	0.506824	0.20703	N	0.087231	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.06607	-1.0817	9	0.09084	T	0.74	.	5.0217	0.14365	0.0:0.6186:0.0:0.3814	rs3746951;rs3746951	15	P57059	SIK1_HUMAN	S	15	ENSP00000270162:G15S	ENSP00000270162:G15S	G	-	1	0	SIK1	43670444	0.800000	0.28916	0.467000	0.27180	0.405000	0.30901	1.484000	0.35508	1.506000	0.48736	0.405000	0.27470	GGT	C|0.827;T|0.173	0.173	strong		0.692	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
NCOR2	9612	hgsc.bcm.edu	37	12	124957627	124957627	+	Silent	SNP	C	C	T	rs10846679	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:124957627C>T	ENST00000405201.1	-	4	462	c.462G>A	c.(460-462)ccG>ccA	p.P154P	NCOR2_ENST00000356219.3_Silent_p.P154P|NCOR2_ENST00000404621.1_Silent_p.P154P|NCOR2_ENST00000429285.2_Silent_p.P154P|NCOR2_ENST00000397355.1_Silent_p.P154P|NCOR2_ENST00000404121.2_5'UTR			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	154					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GGTCAGTGTGCGGGGGGCTGG	0.642													C|||	594	0.11861	0.0061	0.1772	5008	,	,		17742	0.1409		0.1173	False		,,,				2504	0.2076				p.P154P		Atlas-SNP	.											.	NCOR2	475	.	0			c.G462A						PASS	.	C	,,	111,3865		0,111,1877	54.0	59.0	58.0		462,462,462	-11.1	0.0	12	dbSNP_120	58	1092,7242		66,960,3141	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	66,1071,5018	TT,TC,CC		13.103,2.7918,9.7725	,,	154/2459,154/2505,154/2515	124957627	1203,11107	1988	4167	6155	SO:0001819	synonymous_variant	9612	exon6			AGTGTGCGGGGGG	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.462G>A	12.37:g.124957627C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2	222	0.10164835164835165	7	0.014227642276422764	55	0.15193370165745856	71	0.12412587412587413	89	0.11741424802110818	C	0.791	-0.759004	0.03019	0.027918	0.13103	ENSG00000196498	ENST00000542927	.	.	.	5.53	-11.1	0.00147	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.22171	P	0.999313185	.	.	.	.	.	.	T	0.10753	-1.0616	3	.	.	.	-31.4287	1.0572	0.01592	0.1864:0.2098:0.2707:0.3331	rs10846679	.	.	.	H	77	.	.	R	-	2	0	NCOR2	123523580	0.000000	0.05858	0.005000	0.12908	0.027000	0.11550	-5.520000	0.00116	-1.820000	0.01215	-1.288000	0.01363	CGC	C|0.889;T|0.111	0.111	strong		0.642	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558212	140558212	+	Missense_Mutation	SNP	A	A	C	rs2950845	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140558212A>C	ENST00000239444.2	+	1	842	c.597A>C	c.(595-597)aaA>aaC	p.K199N	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	199	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		K -> N (in dbSNP:rs2950845). {ECO:0000269|PubMed:10380929}.		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGCTGGACAAAGCGCTGGACC	0.522													A|||	484	0.0966454	0.0166	0.0893	5008	,	,		25623	0.0913		0.1441	False		,,,				2504	0.1667				p.K199N		Atlas-SNP	.											.	PCDHB8	199	.	0			c.A597C						PASS	.	A	ASN/LYS	219,4185		6,207,1989	48.0	69.0	62.0		597	4.2	0.8	5	dbSNP_101	62	1285,7267		136,1013,3127	no	missense	PCDHB8	NM_019120.3	94	142,1220,5116	CC,CA,AA		15.0257,4.9728,11.6085	possibly-damaging	199/802	140558212	1504,11452	2202	4276	6478	SO:0001583	missense	56128	exon1			GGACAAAGCGCTG	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.597A>C	5.37:g.140558212A>C	ENSP00000239444:p.Lys199Asn	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	471	141	0.299363	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	218	0.09981684981684982	12	0.024390243902439025	40	0.11049723756906077	51	0.08916083916083917	115	0.1517150395778364	a	14.88	2.668435	0.47677	0.049728	0.150257	ENSG00000120322	ENST00000239444	T	0.57107	0.42	4.25	4.25	0.50352	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00815	0.0027	M	0.88241	2.94	0.50632	P	1.1799999999995148E-4	D	0.60575	0.988	D	0.64877	0.93	T	0.51694	-0.8673	8	0.72032	D	0.01	.	4.6337	0.12514	0.7353:0.0:0.0943:0.1704	rs2950845;rs3822338;rs17844485;rs2950845	199	Q9UN66	PCDB8_HUMAN	N	199	ENSP00000239444:K199N	ENSP00000239444:K199N	K	+	3	2	PCDHB8	140538396	0.019000	0.18553	0.833000	0.33012	0.943000	0.58893	0.506000	0.22658	1.558000	0.49541	0.477000	0.44152	AAA	C|1.000;|0.000	1.000	weak		0.522	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
WDR19	57728	hgsc.bcm.edu	37	4	39216221	39216221	+	Splice_Site	SNP	C	C	T	rs2167494	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:39216221C>T	ENST00000399820.3	+	10	1045	c.891C>T	c.(889-891)tgC>tgT	p.C297C	WDR19_ENST00000288634.7_Splice_Site_p.C137C|WDR19_ENST00000506503.1_Splice_Site_p.C297C	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	297					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						TGTTTTTCAGCATTAAAATCC	0.269													C|||	1301	0.259784	0.2973	0.2406	5008	,	,		14844	0.1597		0.3231	False		,,,				2504	0.2607				p.C297C		Atlas-SNP	.											.	WDR19	96	.	0			c.C891T						PASS	.	C		1034,2546		162,710,918	42.0	40.0	41.0		891	2.9	1.0	4	dbSNP_96	41	2522,5596		376,1770,1913	yes	coding-synonymous-near-splice	WDR19	NM_025132.3		538,2480,2831	TT,TC,CC		31.0668,28.8827,30.3984		297/1343	39216221	3556,8142	1790	4059	5849	SO:0001630	splice_region_variant	57728	exon10			TTTCAGCATTAAA	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.891-1C>T	4.37:g.39216221C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	124	52	0.419355	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	37	CCDS47042.1																																																																																			C|0.721;T|0.279	0.279	strong		0.269	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		Silent
MCCC1	56922	hgsc.bcm.edu	37	3	182759360	182759360	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:182759360C>T	ENST00000265594.4	-	11	1408	c.1262G>A	c.(1261-1263)cGg>cAg	p.R421Q	MCCC1_ENST00000492597.1_Missense_Mutation_p.R312Q|MCCC1_ENST00000539926.1_Missense_Mutation_p.R286Q	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	421	Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	TTTACCTTGCCGTACTCCAGT	0.423																																					p.R421Q		Atlas-SNP	.											MCCC1,NS,carcinoma,+1,1	MCCC1	87	1	0			c.G1262A						scavenged	.						86.0	87.0	86.0					3																	182759360		2203	4300	6503	SO:0001583	missense	56922	exon11			CCTTGCCGTACTC	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"""methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"""			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1262G>A	3.37:g.182759360C>T	ENSP00000265594:p.Arg421Gln	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	186	2	0.0107527	NM_020166	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	37	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	C	16.40	3.112976	0.56398	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176;ENST00000448585	T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47	5.45	5.45	0.79879	Rudiment single hybrid motif (1);ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);Biotin carboxylase, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.76666	0.4019	L	0.48935	1.535	0.80722	D	1	B;P;P	0.41366	0.204;0.576;0.747	B;B;B	0.37387	0.069;0.2;0.248	T	0.76934	-0.2775	10	0.38643	T	0.18	.	19.2699	0.94004	0.0:1.0:0.0:0.0	.	374;312;421	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	Q	421;312;271;286;374;374	ENSP00000265594:R421Q;ENSP00000419898:R312Q;ENSP00000441253:R286Q;ENSP00000420433:R374Q	ENSP00000265594:R421Q	R	-	2	0	MCCC1	184242054	1.000000	0.71417	0.980000	0.43619	0.447000	0.32167	3.063000	0.49978	2.554000	0.86153	0.557000	0.71058	CGG	.	.	none		0.423	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735579	55735579	+	Silent	SNP	A	A	G	rs61896166	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55735579A>G	ENST00000312345.2	-	1	411	c.361T>C	c.(361-363)Ttg>Ctg	p.L121L		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					GGATACTGCAAAGGCTTACAA	0.438													A|||	194	0.038738	0.0129	0.0389	5008	,	,		18818	0.001		0.0934	False		,,,				2504	0.0562				p.L121L		Atlas-SNP	.											.	OR10AG1	100	.	0			c.T361C						PASS	.	A		108,4294	82.9+/-121.4	3,102,2096	78.0	77.0	77.0		361	4.6	0.8	11	dbSNP_129	77	691,7901	170.6+/-221.7	34,623,3639	no	coding-synonymous	OR10AG1	NM_001005491.1		37,725,5735	GG,GA,AA		8.0424,2.4534,6.149		121/302	55735579	799,12195	2201	4296	6497	SO:0001819	synonymous_variant	282770	exon1			ACTGCAAAGGCTT	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.361T>C	11.37:g.55735579A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_001005491	B2RNH4|Q6IEU3	Silent	SNP	ENST00000312345.2	37	CCDS31514.1																																																																																			A|0.947;G|0.053	0.053	strong		0.438	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
BARD1	580	hgsc.bcm.edu	37	2	215674224	215674224	+	Missense_Mutation	SNP	G	G	A	rs1048108	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:215674224G>A	ENST00000260947.4	-	1	204	c.70C>T	c.(70-72)Ccc>Tcc	p.P24S	BARD1_ENST00000449967.2_5'UTR|AC072062.1_ENST00000607412.1_RNA|BARD1_ENST00000471787.1_5'UTR	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	24			P -> S (common polymorphism in Caucasians; less frequent in Africans; dbSNP:rs1048108). {ECO:0000269|PubMed:9425226}.		cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCCATGGCGGGCGCGGAACGA	0.687									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				G|||	1659	0.33127	0.1929	0.4006	5008	,	,		10138	0.3313		0.3946	False		,,,				2504	0.4039				p.P24S		Atlas-SNP	.											BARD1_ENST00000260947,NS,carcinoma,0,4	BARD1	138	4	0			c.C70T	GRCh37	CM076015	BARD1	M	rs1048108	scavenged	.	G	SER/PRO	892,3252		114,664,1294	9.0	10.0	10.0		70	3.1	1.0	2	dbSNP_86	10	2859,5371		518,1823,1774	no	missense	BARD1	NM_000465.2	74	632,2487,3068	AA,AG,GG		34.7388,21.5251,30.3136	benign	24/778	215674224	3751,8623	2072	4115	6187	SO:0001583	missense	580	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TGGCGGGCGCGGA		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.70C>T	2.37:g.215674224G>A	ENSP00000260947:p.Pro24Ser	Somatic	60	1	0.0166667		WXS	Illumina HiSeq	Phase_I	49	35	0.714286	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	757	0.3466117216117216	95	0.19308943089430894	152	0.4198895027624309	203	0.3548951048951049	307	0.4050131926121372	G	14.84	2.656841	0.47467	0.215251	0.347388	ENSG00000138376	ENST00000260947;ENST00000421162	T;D	0.85088	-0.72;-1.94	3.99	3.1	0.35709	.	0.095711	0.44902	D	0.000412	T	0.00012	0.0000	N	0.16478	0.41	0.09310	P	0.9999999999951874	B	0.09022	0.002	B	0.10450	0.005	T	0.15723	-1.0427	9	0.34782	T	0.22	-12.5199	5.3151	0.15850	0.1147:0.2331:0.6522:0.0	rs1048108;rs2070095;rs3188086;rs1048108	24	Q99728	BARD1_HUMAN	S	24	ENSP00000260947:P24S;ENSP00000392245:P24S	ENSP00000260947:P24S	P	-	1	0	BARD1	215382469	0.675000	0.27558	0.990000	0.47175	0.038000	0.13279	0.968000	0.29357	2.221000	0.72209	0.561000	0.74099	CCC	G|0.674;A|0.326	0.326	strong		0.687	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133954011	133954011	+	Silent	SNP	C	C	T	rs2818387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:133954011C>T	ENST00000298622.4	+	9	1539	c.1401C>T	c.(1399-1401)gaC>gaT	p.D467D		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	467						Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TGGAATCCGACGGCTCCTCCG	0.592													C|||	2574	0.513978	0.4584	0.5793	5008	,	,		13772	0.5883		0.4841	False		,,,				2504	0.4969				p.D467D		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.C1401T						PASS	.	C		1813,2195		417,979,608	57.0	66.0	63.0		1401	-5.4	0.0	10	dbSNP_100	63	4080,4234		995,2090,1072	yes	coding-synonymous	JAKMIP3	NM_001105521.2		1412,3069,1680	TT,TC,CC		49.0739,45.2345,47.825		467/845	133954011	5893,6429	2004	4157	6161	SO:0001819	synonymous_variant	282973	exon9			ATCCGACGGCTCC	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.1401C>T	10.37:g.133954011C>T		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	182	181	0.994505	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																			C|0.497;T|0.503	0.503	strong		0.592	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
SETD1B	23067	hgsc.bcm.edu	37	12	122255284	122255284	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:122255284C>T	ENST00000604567.1	+	9	3054	c.2986C>T	c.(2986-2988)Cga>Tga	p.R996*	SETD1B_ENST00000267197.5_Nonsense_Mutation_p.R996*|SETD1B_ENST00000542440.1_Nonsense_Mutation_p.R996*			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	996	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						AGAGTCCGAGCGAGAGCGAGA	0.682																																					p.R996X		Atlas-SNP	.											SETD1B_ENST00000267197,colon,carcinoma,-1,1	SETD1B	105	1	0			c.C2986T						scavenged	.						35.0	49.0	45.0					12																	122255284		692	1591	2283	SO:0001587	stop_gained	23067	exon8			TCCGAGCGAGAGC	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.2986C>T	12.37:g.122255284C>T	ENSP00000474253:p.Arg996*	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	67	2	0.0298507	NM_015048	F6MFW1	Nonsense_Mutation	SNP	ENST00000604567.1	37		.	.	.	.	.	.	.	.	.	.	C	37	6.456763	0.97581	.	.	ENSG00000139718	ENST00000542440;ENST00000267197	.	.	.	3.05	3.05	0.35203	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.6121	0.28137	0.2535:0.7465:0.0:0.0	.	.	.	.	X	996	.	ENSP00000267197:R996X	R	+	1	2	SETD1B	120739667	0.995000	0.38212	0.997000	0.53966	0.223000	0.24884	0.921000	0.28718	2.030000	0.59900	0.591000	0.81541	CGA	.	.	none		0.682	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
MOK	5891	hgsc.bcm.edu	37	14	102695693	102695693	+	Missense_Mutation	SNP	T	T	C	rs2236493	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102695693T>C	ENST00000361847.2	-	12	1424	c.1193A>G	c.(1192-1194)cAg>cGg	p.Q398R	MOK_ENST00000524370.1_Silent_p.A92A|MOK_ENST00000524214.1_Missense_Mutation_p.Q368R|MOK_ENST00000519058.1_Silent_p.A122A|MOK_ENST00000522874.1_Missense_Mutation_p.Q397R|MOK_ENST00000522534.1_Silent_p.A122A|MOK_ENST00000193029.6_Intron|MOK_ENST00000523231.1_Silent_p.A92A|MOK_ENST00000520266.1_5'UTR|MOK_ENST00000517966.1_Silent_p.A92A|MOK_ENST00000522867.1_Silent_p.A92A|MOK_ENST00000561150.1_Intron	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	398			Q -> R (in dbSNP:rs2236493). {ECO:0000269|PubMed:17344846}.		protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.Q398R(1)									AAGGTCCTTCTGCGGATCTGT	0.577													C|||	1499	0.299321	0.5817	0.1729	5008	,	,		16698	0.1429		0.1958	False		,,,				2504	0.2751				p.Q398R		Atlas-SNP	.											RAGE,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A1193G						PASS	.	C	ARG/GLN	2218,2188	587.6+/-386.7	582,1054,567	59.0	59.0	59.0		1193	1.7	0.0	14	dbSNP_98	59	1705,6895	738.0+/-407.0	154,1397,2749	yes	missense	MOK	NM_014226.1	43	736,2451,3316	CC,CT,TT		19.8256,49.6596,30.163	benign	398/420	102695693	3923,9083	2203	4300	6503	SO:0001583	missense	5891	exon12			TCCTTCTGCGGAT	AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"""renal tumor antigen"""	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.1193A>G	14.37:g.102695693T>C	ENSP00000355304:p.Gln398Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Missense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	569	0.26053113553113555	278	0.5650406504065041	76	0.20994475138121546	82	0.14335664335664336	133	0.17546174142480211	C	0.030	-1.343368	0.01277	0.503404	0.198256	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	T;T;T	0.76186	-0.45;-0.51;-1.0	5.37	1.66	0.24008	.	0.461500	0.21486	N	0.073744	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.99999611406	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44128	-0.9348	9	0.06365	T	0.9	-22.8097	9.4719	0.38847	0.0:0.2379:0.0:0.7621	rs2236493;rs52809368;rs58401053;rs2236493	368;398	E7ERR8;Q9UQ07	.;MOK_HUMAN	R	397;398;368	ENSP00000429469:Q397R;ENSP00000355304:Q398R;ENSP00000428942:Q368R	ENSP00000355304:Q398R	Q	-	2	0	RAGE	101765446	1.000000	0.71417	0.027000	0.17364	0.002000	0.02628	0.935000	0.28924	-0.193000	0.10415	-1.163000	0.01768	CAG	T|0.713;C|0.287	0.287	strong		0.577	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		
HS6ST3	266722	hgsc.bcm.edu	37	13	97484830	97484830	+	Missense_Mutation	SNP	A	A	G	rs9516771	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:97484830A>G	ENST00000376705.2	+	2	818	c.794A>G	c.(793-795)aAa>aGa	p.K265R		NM_153456.3	NP_703157.2	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	265			K -> R (in dbSNP:rs9516771).		heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)	integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					GCCACTTGGAAAACCTCTCTT	0.502													A|||	189	0.0377396	0.0038	0.0375	5008	,	,		5790	0.0208		0.0487	False		,,,				2504	0.09				p.K265R		Atlas-SNP	.											HS6ST3,NS,carcinoma,0,1	HS6ST3	54	1	0			c.A794G						PASS	.	A	ARG/LYS	62,4344	57.4+/-93.9	0,62,2141	61.0	61.0	61.0		794	5.7	1.0	13	dbSNP_119	61	498,8102	142.5+/-198.7	14,470,3816	yes	missense	HS6ST3	NM_153456.2	26	14,532,5957	GG,GA,AA		5.7907,1.4072,4.3057	probably-damaging	265/472	97484830	560,12446	2203	4300	6503	SO:0001583	missense	266722	exon2			CTTGGAAAACCTC	AF539426	CCDS9481.1	13q32.2	2007-12-04			ENSG00000185352	ENSG00000185352		"""Sulfotransferases, membrane-bound"""	19134	protein-coding gene	gene with protein product		609401					Standard	NM_153456		Approved		uc001vmw.4	Q8IZP7	OTTHUMG00000017232	ENST00000376705.2:c.794A>G	13.37:g.97484830A>G	ENSP00000365895:p.Lys265Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	NM_153456	Q5W0L0|Q68CW6	Missense_Mutation	SNP	ENST00000376705.2	37	CCDS9481.1	64	0.029304029304029304	5	0.01016260162601626	15	0.04143646408839779	8	0.013986013986013986	36	0.047493403693931395	A	22.9	4.345489	0.82022	0.014072	0.057907	ENSG00000185352	ENST00000376705	T	0.75050	-0.9	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.26521	0.0648	M	0.72576	2.205	0.58432	D	0.999996	B	0.33940	0.433	B	0.29524	0.103	T	0.59402	-0.7461	10	0.48119	T	0.1	-11.9424	15.9622	0.79939	1.0:0.0:0.0:0.0	rs9516771;rs9516771	265	Q8IZP7	H6ST3_HUMAN	R	265	ENSP00000365895:K265R	ENSP00000365895:K265R	K	+	2	0	HS6ST3	96282831	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.335000	0.96500	2.157000	0.67596	0.533000	0.62120	AAA	A|0.962;G|0.038	0.038	strong		0.502	HS6ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045517.2	NM_153456	
FCGBP	8857	hgsc.bcm.edu	37	19	40367862	40367862	+	Silent	SNP	T	T	C	rs6508920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40367862T>C	ENST00000221347.6	-	29	13105	c.13098A>G	c.(13096-13098)ccA>ccG	p.P4366P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4366	TIL 10.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GACAGCTGGCTGGGCAGGGTG	0.612													C|||	3623	0.723442	0.8986	0.6628	5008	,	,		7088	0.7659		0.5467	False		,,,				2504	0.6677				p.P4366P		Atlas-SNP	.											.	FCGBP	416	.	0			c.A13098G						PASS	.						24.0	44.0	37.0					19																	40367862		2160	4047	6207	SO:0001819	synonymous_variant	8857	exon29			GCTGGCTGGGCAG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.13098A>G	19.37:g.40367862T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	135	37	0.274074	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			T|0.333;C|0.667	0.667	strong		0.612	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
NCKAP5	344148	hgsc.bcm.edu	37	2	133542585	133542585	+	Missense_Mutation	SNP	C	C	G	rs17325719	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:133542585C>G	ENST00000409261.1	-	14	2172	c.1799G>C	c.(1798-1800)aGt>aCt	p.S600T	NCKAP5_ENST00000317721.6_Missense_Mutation_p.S600T|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	600			S -> T (in dbSNP:rs17325719).							NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						GTCTGAAGGACTTTTCTCATC	0.512													c|||	410	0.081869	0.0582	0.1052	5008	,	,		20870	0.0526		0.1412	False		,,,				2504	0.0665				p.S600T		Atlas-SNP	.											.	NCKAP5	322	.	0			c.G1799C						PASS	.	C	THR/SER,	300,3646		13,274,1686	71.0	72.0	72.0		1799,	5.6	1.0	2	dbSNP_123	72	1314,7004		114,1086,2959	yes	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	58,	127,1360,4645	GG,GC,CC		15.7971,7.6026,13.1605	benign,	600/1910,	133542585	1614,10650	1973	4159	6132	SO:0001583	missense	344148	exon14			GAAGGACTTTTCT	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.1799G>C	2.37:g.133542585C>G	ENSP00000387128:p.Ser600Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	196	0.08974358974358974	29	0.05894308943089431	44	0.12154696132596685	25	0.043706293706293704	98	0.12928759894459102	c	20.2	3.953142	0.73902	0.076026	0.157971	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.42513	0.97;0.97	5.64	5.64	0.86602	.	0.172048	0.26099	U	0.026347	T	0.00178	0.0005	L	0.29908	0.895	0.09310	P	1.0	P	0.46656	0.882	B	0.41813	0.367	T	0.01697	-1.1293	9	0.72032	D	0.01	.	18.0683	0.89398	0.0:1.0:0.0:0.0	rs17325719;rs56459376;rs17325719	600	O14513	NCKP5_HUMAN	T	600	ENSP00000387128:S600T;ENSP00000380603:S600T	ENSP00000380603:S600T	S	-	2	0	NCKAP5	133259055	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.761000	0.68801	2.937000	0.99478	0.651000	0.88453	AGT	C|0.892;G|0.108	0.108	strong		0.512	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
NEDD4L	23327	hgsc.bcm.edu	37	18	55816791	55816791	+	Intron	SNP	G	G	A	rs4149601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:55816791G>A	ENST00000400345.3	+	2	331				NEDD4L_ENST00000588516.1_Intron|NEDD4L_ENST00000356462.6_Intron|NEDD4L_ENST00000586263.1_Splice_Site_p.Q8Q|NEDD4L_ENST00000382850.4_Intron|NEDD4L_ENST00000357895.5_Splice_Site_p.Q8Q|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000456986.1_Intron|NEDD4L_ENST00000256830.9_Intron|NEDD4L_ENST00000256832.7_Intron|NEDD4L_ENST00000435432.2_5'UTR	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase						cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						CATTTGAGCAGGTAACACTCG	0.433													A|||	1383	0.276158	0.3608	0.2089	5008	,	,		21751	0.2113		0.3539	False		,,,				2504	0.1963				p.Q8Q		Atlas-SNP	.											.	NEDD4L	126	.	0			c.G24A	GRCh37	CS024266	NEDD4L	S	rs4149601	PASS	.	A	,,,,,,	453,931		66,321,305	189.0	166.0	173.0		,,,24,24,,	2.8	0.0	18	dbSNP_110	173	1101,2081		196,709,686	yes	intron,utr-5,intron,coding-synonymous-near-splice,coding-synonymous-near-splice,utr-5,intron	NEDD4L	NM_001144964.1,NM_001144965.1,NM_001144967.2,NM_001144968.1,NM_001144969.1,NM_001144971.1,NM_015277.5	,,,,,,	262,1030,991	AA,AG,GG		34.6009,32.7312,34.0342	,,,,,,	,,,8/968,8/948,,	55816791	1554,3012	692	1591	2283	SO:0001627	intron_variant	23327	exon1			TGAGCAGGTAACA	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"""neural precursor cell expressed, developmentally down-regulated 4-like"""			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.49-16229G>A	18.37:g.55816791G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_001144968	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	37	CCDS45872.1																																																																																			G|0.696;A|0.304	0.304	strong		0.433	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1		
CCHCR1	54535	hgsc.bcm.edu	37	6	31110391	31110391	+	Missense_Mutation	SNP	G	G	C	rs1576	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31110391G>C	ENST00000376266.5	-	18	2449	c.2327C>G	c.(2326-2328)tCc>tGc	p.S776C	CCHCR1_ENST00000396263.2_Missense_Mutation_p.S723C|CCHCR1_ENST00000396268.3_Missense_Mutation_p.S865C|CCHCR1_ENST00000451521.2_Missense_Mutation_p.S829C	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	776			S -> C (in allele HCR*WWCC; associated with psoriasis; dbSNP:rs1576). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:10888604, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CTGGGGATTGGAGCTGGAGCA	0.567													G|||	1117	0.223043	0.2315	0.2767	5008	,	,		20640	0.0724		0.3141	False		,,,				2504	0.2352				p.S865C		Atlas-SNP	.											.	CCHCR1	68	.	0			c.C2594G						PASS	.	G	CYS/SER,CYS/SER,CYS/SER	1094,3312	396.3+/-330.0	134,826,1243	92.0	79.0	84.0		2486,2594,2327	-5.4	0.0	6	dbSNP_36	84	2776,5824	439.7+/-359.3	464,1848,1988	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	112,112,112	598,2674,3231	CC,CG,GG		32.2791,24.8298,29.7555	benign,benign,benign	829/836,865/872,776/783	31110391	3870,9136	2203	4300	6503	SO:0001583	missense	54535	exon18			GGATTGGAGCTGG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.2327C>G	6.37:g.31110391G>C	ENSP00000365442:p.Ser776Cys	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	525	0.2403846153846154	121	0.2459349593495935	105	0.2900552486187845	49	0.08566433566433566	250	0.32981530343007914	G	8.219	0.802047	0.16397	0.248298	0.322791	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521	T;T;T;T	0.03717	3.83;3.83;3.83;3.83	4.04	-5.36	0.02689	.	4.983430	0.00644	N	0.000536	T	0.01287	0.0042	L	0.51422	1.61	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.46707	-0.9172	9	0.38643	T	0.18	.	7.4966	0.27492	0.2789:0.5368:0.1843:0.0	rs1576;rs130081;rs3173366;rs17456616;rs1576	762;776;829;865	B4DIA2;Q8TD31;E9PE84;Q8TD31-2	.;CCHCR_HUMAN;.;.	C	865;776;723;762;829	ENSP00000379566:S865C;ENSP00000365442:S776C;ENSP00000379561:S723C;ENSP00000401039:S829C	ENSP00000365442:S776C	S	-	2	0	CCHCR1	31218370	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.312000	0.08113	-0.977000	0.03537	-0.326000	0.08463	TCC	G|0.722;C|0.278	0.278	strong		0.567	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798761	55798761	+	Silent	SNP	T	T	C	rs61889974	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55798761T>C	ENST00000313555.1	+	1	867	c.867T>C	c.(865-867)atT>atC	p.I289I		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	289						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					ATCCAATAATTTATAGTTTCA	0.323													C|||	192	0.0383387	0.0129	0.0403	5008	,	,		19026	0.001		0.0934	False		,,,				2504	0.0532				p.I289I		Atlas-SNP	.											OR5AS1,NS,carcinoma,0,1	OR5AS1	121	1	0			c.T867C						PASS	.	C		110,4292	814.7+/-416.2	3,104,2094	49.0	51.0	50.0		867	-2.2	0.0	11	dbSNP_129	50	690,7902	782.8+/-407.6	34,622,3640	no	coding-synonymous	OR5AS1	NM_001001921.1		37,726,5734	CC,CT,TT		8.0307,2.4989,6.1567		289/325	55798761	800,12194	2201	4296	6497	SO:0001819	synonymous_variant	219447	exon1			AATAATTTATAGT	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.867T>C	11.37:g.55798761T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_001001921	Q6IFB8	Silent	SNP	ENST00000313555.1	37	CCDS31516.1																																																																																			T|0.948;C|0.052	0.052	strong		0.323	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
PRDM2	7799	hgsc.bcm.edu	37	1	14107164	14107164	+	Silent	SNP	C	C	T	rs115572434	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14107164C>T	ENST00000235372.7	+	8	3730	c.2874C>T	c.(2872-2874)tcC>tcT	p.S958S	PRDM2_ENST00000343137.4_Silent_p.S757S|PRDM2_ENST00000311066.5_Silent_p.S958S|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Silent_p.S757S	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	958	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		CCCTTTCATCCGGTCAGCTGC	0.602													C|||	160	0.0319489	0.0015	0.0	5008	,	,		16552	0.0218		0.0169	False		,,,				2504	0.1217				p.S958S		Atlas-SNP	.											.	PRDM2	147	.	0			c.C2874T						PASS	.	C	,,,	12,4394	19.1+/-41.9	0,12,2191	175.0	158.0	164.0		2271,,2874,2874	-11.9	0.0	1	dbSNP_132	164	175,8425	79.5+/-142.1	2,171,4127	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	,,,	2,183,6318	TT,TC,CC		2.0349,0.2724,1.4378	,,,	757/1482,,958/1719,958/1683	14107164	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	7799	exon8			TTCATCCGGTCAG	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.2874C>T	1.37:g.14107164C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	159	68	0.427673	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Silent	SNP	ENST00000235372.7	37	CCDS150.1																																																																																			C|0.984;T|0.016	0.016	strong		0.602	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
OR2T2	401992	hgsc.bcm.edu	37	1	248616401	248616401	+	Silent	SNP	G	G	A	rs77680148	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248616401G>A	ENST00000342927.3	+	1	325	c.303G>A	c.(301-303)caG>caA	p.Q101Q		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	101						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTGCAGTTCAGATCTTCCTCT	0.532																																					p.Q101Q		Atlas-SNP	.											.	OR2T2	73	.	0			c.G303A						PASS	.						303.0	339.0	327.0					1																	248616401		2203	4300	6503	SO:0001819	synonymous_variant	401992	exon1			AGTTCAGATCTTC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.303G>A	1.37:g.248616401G>A		Somatic	913	1	0.00109529		WXS	Illumina HiSeq	Phase_I	980	693	0.707143	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			G|0.913;A|0.087	0.087	strong		0.532	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
MUC21	394263	hgsc.bcm.edu	37	6	30954999	30954999	+	Missense_Mutation	SNP	G	G	C	rs141934200	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954999G>C	ENST00000376296.3	+	2	1288	c.1047G>C	c.(1045-1047)gaG>gaC	p.E349D	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	349	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAACTCTGAGTCCAGCACAA	0.627																																					p.E349D		Atlas-SNP	.											MUC21,NS,carcinoma,0,1	MUC21	98	1	0			c.G1047C						PASS	.						136.0	136.0	136.0					6																	30954999		2203	4298	6501	SO:0001583	missense	394263	exon2			CTCTGAGTCCAGC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1047G>C	6.37:g.30954999G>C	ENSP00000365473:p.Glu349Asp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	115	29	0.252174	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	g	3.448	-0.112665	0.06881	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.01787	4.64	4.18	-8.37	0.00976	.	.	.	.	.	T	0.00328	0.0010	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.47058	-0.9146	9	0.13470	T	0.59	1.1568	6.8368	0.23941	0.115:0.4568:0.3375:0.0907	.	349	Q5SSG8	MUC21_HUMAN	D	199;349	ENSP00000365473:E349D	ENSP00000365473:E349D	E	+	3	2	MUC21	31062978	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.743000	0.00378	-3.056000	0.00258	-0.437000	0.05841	GAG	G|0.975;C|0.026	0.026	strong		0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
PALM	5064	hgsc.bcm.edu	37	19	731144	731144	+	Missense_Mutation	SNP	A	A	G	rs1050457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:731144A>G	ENST00000338448.5	+	5	365	c.319A>G	c.(319-321)Act>Gct	p.T107A	PALM_ENST00000264560.7_Missense_Mutation_p.T107A|PALM_ENST00000593172.1_3'UTR	NM_002579.2	NP_002570.2	O75781	PALM_HUMAN	paralemmin	107			T -> A (in dbSNP:rs1050457). {ECO:0000269|PubMed:9615234}.		cellular component movement (GO:0006928)|cellular response to electrical stimulus (GO:0071257)|cytoskeleton organization (GO:0007010)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of filopodium assembly (GO:0051491)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)|synapse maturation (GO:0060074)	apicolateral plasma membrane (GO:0016327)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasmic membrane-bounded vesicle (GO:0016023)|dendrite membrane (GO:0032590)|dendritic spine membrane (GO:0032591)|filopodium membrane (GO:0031527)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)		CGCCCCAGCCACTGCCAAGGA	0.657													G|||	2736	0.546326	0.7315	0.4942	5008	,	,		13926	0.5446		0.4394	False		,,,				2504	0.4448				p.T107A		Atlas-SNP	.											.	PALM	26	.	0			c.A319G						PASS	.	G	ALA/THR,ALA/THR	2971,1427		1013,945,241	24.0	26.0	25.0		319,319	-0.3	0.0	19	dbSNP_86	25	3856,4724		869,2118,1303	yes	missense,missense	PALM	NM_001040134.1,NM_002579.2	58,58	1882,3063,1544	GG,GA,AA		44.9417,32.4466,47.3956	benign,benign	107/344,107/388	731144	6827,6151	2199	4290	6489	SO:0001583	missense	5064	exon5			CCAGCCACTGCCA	Y16270	CCDS32857.1, CCDS32858.1	19p13.3	2008-07-17				ENSG00000099864			8594	protein-coding gene	gene with protein product		608134				9615234, 9813098	Standard	XM_005259565		Approved	KIAA0270	uc002lpm.1	O75781		ENST00000338448.5:c.319A>G	19.37:g.731144A>G	ENSP00000341911:p.Thr107Ala	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	113	41	0.362832	NM_002579	O43359|O95673|Q92559|Q9UPJ4|Q9UQS2|Q9UQS3	Missense_Mutation	SNP	ENST00000338448.5	37	CCDS32857.1	1144	0.5238095238095238	325	0.6605691056910569	186	0.5138121546961326	305	0.5332167832167832	328	0.43271767810026385	G	0.174	-1.068560	0.01934	0.675534	0.449417	ENSG00000099864	ENST00000338448;ENST00000264560	T;T	0.15256	2.44;2.44	4.06	-0.33	0.12683	.	1.296050	0.05908	N	0.631180	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.13407	0.001;0.001;0.009	T	0.40327	-0.9569	9	0.02654	T	1	-0.7764	4.8321	0.13445	0.6145:0.1804:0.2051:0.0	rs1050457;rs3190775;rs1050457	107;107;107	B7Z649;O75781-2;O75781	.;.;PALM_HUMAN	A	107	ENSP00000341911:T107A;ENSP00000264560:T107A	ENSP00000264560:T107A	T	+	1	0	PALM	682144	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.358000	0.01085	-0.100000	0.12241	-0.282000	0.10007	ACT	A|0.468;G|0.532	0.532	strong		0.657	PALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457592.1	NM_002579	
PTX4	390667	hgsc.bcm.edu	37	16	1537839	1537839	+	Missense_Mutation	SNP	G	G	A	rs2745101	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1537839G>A	ENST00000447419.2	-	2	299	c.274C>T	c.(274-276)Cgg>Tgg	p.R92W	PTX4_ENST00000440447.2_Missense_Mutation_p.R92W|PTX4_ENST00000293922.1_Missense_Mutation_p.R87W			Q96A99	PTX4_HUMAN	pentraxin 4, long	92			R -> W (in dbSNP:rs2745101).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GCCTGTGACCGGTTGACTGCC	0.652													G|||	1333	0.266174	0.1679	0.1945	5008	,	,		16731	0.5079		0.2316	False		,,,				2504	0.2362				p.R87W		Atlas-SNP	.											.	PTX4	46	.	0			c.C259T						PASS	.	G	TRP/ARG	697,3701		57,583,1559	76.0	79.0	78.0		259	-0.6	0.0	16	dbSNP_100	78	2102,6492		238,1626,2433	yes	missense	PTX4	NM_001013658.1	101	295,2209,3992	AA,AG,GG		24.4589,15.8481,21.544	probably-damaging	87/474	1537839	2799,10193	2199	4297	6496	SO:0001583	missense	390667	exon2			GTGACCGGTTGAC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.274C>T	16.37:g.1537839G>A	ENSP00000445277:p.Arg92Trp	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		645	0.29532967032967034	74	0.15040650406504066	67	0.1850828729281768	315	0.5506993006993007	189	0.24934036939313983	G	10.43	1.346709	0.24426	0.158481	0.244589	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.05382	3.6;3.45	5.78	-0.593	0.11667	.	2.089320	0.01936	N	0.041576	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.13145	0.007	B	0.08055	0.003	T	0.47497	-0.9113	9	0.72032	D	0.01	.	2.2422	0.04023	0.179:0.1478:0.523:0.1502	rs2745101;rs2745101	87	Q96A99-2	.	W	92;87	ENSP00000445277:R92W;ENSP00000293922:R87W	ENSP00000293922:R87W	R	-	1	2	PTX4	1477840	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	0.282000	0.18829	-0.015000	0.14150	-0.251000	0.11542	CGG	G|0.753;A|0.247	0.247	strong		0.652	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
SPDYE1	285955	hgsc.bcm.edu	37	7	44047066	44047066	+	Missense_Mutation	SNP	T	T	C	rs78424385	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:44047066T>C	ENST00000258704.3	+	5	969	c.832T>C	c.(832-834)Tgc>Cgc	p.C278R	POLR2J4_ENST00000427076.1_RNA|RP5-1165K10.2_ENST00000454572.1_RNA|AC004951.6_ENST00000447643.1_lincRNA	NM_001099435.2|NM_175064.2	NP_001092905.2|NP_778234.2	Q8NFV5	SPDE1_HUMAN	speedy/RINGO cell cycle regulator family member E1	278	Arg-rich.									endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	11						GTTACGCCGTTGCATGAACCC	0.552													t|||	2127	0.42472	0.4531	0.3818	5008	,	,		18930	0.4474		0.329	False		,,,				2504	0.4918				p.C278R		Atlas-SNP	.											.	SPDYE1	29	.	0			c.T832C						PASS	.	T	ARG/CYS	1870,2536		396,1078,729	130.0	139.0	136.0		832		0.1	7	dbSNP_131	136	3026,5572		546,1934,1819	no	missense	SPDYE1	NM_175064.2	180	942,3012,2548	CC,CT,TT		35.1942,42.4421,37.65	possibly-damaging	278/337	44047066	4896,8108	2203	4299	6502	SO:0001583	missense	285955	exon5			CGCCGTTGCATGA	AF412027	CCDS5475.1	7q11.23	2013-05-08	2013-05-08	2009-02-17	ENSG00000136206	ENSG00000136206		"""Speedy homologs"""	16408	protein-coding gene	gene with protein product	"""Speedy E"""		"""Williams Beuren syndrome chromosome region 19"", ""speedy homolog E1 (Xenopus laevis)"""	WBSCR19		12073013	Standard	NM_175064		Approved	Ringo1, SPDYE	uc003tjf.3	Q8NFV5	OTTHUMG00000128985	ENST00000258704.3:c.832T>C	7.37:g.44047066T>C	ENSP00000258704:p.Cys278Arg	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	218	121	0.555046	NM_175064	Q9NTH5	Missense_Mutation	SNP	ENST00000258704.3	37	CCDS5475.1	846	0.3873626373626374	211	0.42886178861788615	141	0.38950276243093923	237	0.4143356643356643	257	0.3390501319261214	.	4.489	0.090703	0.08632	0.424421	0.351942	ENSG00000136206	ENST00000258704	.	.	.	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.48670	-0.9015	5	0.24483	T	0.36	.	.	.	.	.	278	Q8NFV5	SPDE1_HUMAN	R	278	.	ENSP00000258704:C278R	C	+	1	0	SPDYE1	44013591	0.169000	0.23002	0.117000	0.21633	0.117000	0.20001	0.077000	0.14738	0.077000	0.16863	0.076000	0.15429	TGC	.	.	weak		0.552	SPDYE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250974.1	NM_175064	
OR2A2	442361	hgsc.bcm.edu	37	7	143807515	143807515	+	Missense_Mutation	SNP	T	T	G	rs2961149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:143807515T>G	ENST00000408979.2	+	1	909	c.840T>G	c.(838-840)ttT>ttG	p.F280L		NM_001005480.2	NP_001005480.2	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A, member 2	280			F -> L (in dbSNP:rs2961149). {ECO:0000269|PubMed:12853948}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)|skin(4)	22	Melanoma(164;0.0783)					ACAGTGTCTTTAATCCAATGC	0.502													-|||	2503	0.4998	0.3525	0.6095	5008	,	,		17324	0.7391		0.3191	False		,,,				2504	0.5603				p.F280L		Atlas-SNP	.											.	OR2A2	48	.	0			c.T840G						PASS	.	T	LEU/PHE	1322,2612		228,866,873	157.0	150.0	152.0		840	-1.9	0.0	7	dbSNP_101	152	2682,5678		449,1784,1947	no	missense	OR2A2	NM_001005480.2	22	677,2650,2820	GG,GT,TT		32.0813,33.6045,32.5687	benign	280/319	143807515	4004,8290	1967	4180	6147	SO:0001583	missense	442361	exon1			TGTCTTTAATCCA		CCDS43671.1	7q35	2013-09-20		2004-03-10	ENSG00000221989	ENSG00000221989		"""GPCR / Class A : Olfactory receptors"""	8230	protein-coding gene	gene with protein product				OR2A2P, OR2A17P			Standard	NM_001005480		Approved	OST008	uc011ktz.2	Q6IF42	OTTHUMG00000158001	ENST00000408979.2:c.840T>G	7.37:g.143807515T>G	ENSP00000386209:p.Phe280Leu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	131	56	0.427481	NM_001005480	B2RN85|Q8NGT6	Missense_Mutation	SNP	ENST00000408979.2	37	CCDS43671.1	977	0.44734432234432236	148	0.3008130081300813	201	0.5552486187845304	417	0.7290209790209791	211	0.2783641160949868	T	4.540	0.100309	0.08731	0.336045	0.320813	ENSG00000221989	ENST00000408979	T	0.00027	8.93	3.47	-1.85	0.07784	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34338	U	0.004056	T	0.00012	0.0000	N	0.03891	-0.335	0.80722	P	0.0	B	0.20550	0.046	B	0.30716	0.119	T	0.48043	-0.9069	9	0.30854	T	0.27	-24.1065	5.2051	0.15287	0.0:0.276:0.1665:0.5574	rs2961149	280	Q6IF42	OR2A2_HUMAN	L	280	ENSP00000386209:F280L	ENSP00000386209:F280L	F	+	3	2	OR2A2	143438448	0.000000	0.05858	0.012000	0.15200	0.015000	0.08874	-4.661000	0.00202	-0.278000	0.09180	-0.385000	0.06624	TTT	T|0.584;G|0.416	0.416	strong		0.502	OR2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349978.1		
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22974325	22974325	+	Silent	SNP	G	G	A	rs11780493	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22974325G>A	ENST00000356864.3	+	5	1093	c.561G>A	c.(559-561)ccG>ccA	p.P187P	TNFRSF10C_ENST00000540813.1_Silent_p.P85P	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	187					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		ACACCAGCCCGGGGACTCCTG	0.622																																					p.P187P		Atlas-SNP	.											.	TNFRSF10C	30	.	0			c.G561A						PASS	.						53.0	65.0	61.0					8																	22974325		2203	4297	6500	SO:0001819	synonymous_variant	8794	exon5			CAGCCCGGGGACT	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.561G>A	8.37:g.22974325G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	149	130	0.872483	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Silent	SNP	ENST00000356864.3	37	CCDS6037.1																																																																																			G|0.382;A|0.618	0.618	strong		0.622	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461185	141461185	+	Silent	SNP	A	A	G	rs3735802	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:141461185A>G	ENST00000438773.2	-	2	421	c.288T>C	c.(286-288)ttT>ttC	p.F96F	TRAPPC9_ENST00000389328.4_Silent_p.F194F|TRAPPC9_ENST00000389327.3_Silent_p.F96F	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	96					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						GGAACTTCTCAAAGGTCTGTG	0.592													G|||	2699	0.538938	0.5635	0.4121	5008	,	,		20640	0.5347		0.5586	False		,,,				2504	0.5798				p.F194F		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.T582C						PASS	.	G	,	2452,1954	555.8+/-379.4	674,1104,425	88.0	80.0	83.0		288,582	-1.8	0.9	8	dbSNP_107	83	4907,3693	528.5+/-381.4	1419,2069,812	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	2093,3173,1237	GG,GA,AA		42.9419,44.3486,43.4184	,	96/1149,194/1247	141461185	7359,5647	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon2			CTTCTCAAAGGTC	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.288T>C	8.37:g.141461185A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1																																																																																			A|0.436;G|0.564	0.564	strong		0.592	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
ZBBX	79740	hgsc.bcm.edu	37	3	167034814	167034814	+	Silent	SNP	T	T	C	rs13068132	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:167034814T>C	ENST00000392766.2	-	14	1513	c.1173A>G	c.(1171-1173)ctA>ctG	p.L391L	ZBBX_ENST00000392767.2_Silent_p.L391L|ZBBX_ENST00000307529.5_Silent_p.L391L|ZBBX_ENST00000455345.2_Silent_p.L391L|ZBBX_ENST00000392764.1_Silent_p.L362L|ZBBX_ENST00000469220.1_5'UTR	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	391						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.L391L(2)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						CGACTATCTTTAGAGATGGTT	0.343													T|||	1475	0.294529	0.2103	0.3444	5008	,	,		16345	0.1865		0.4105	False		,,,				2504	0.365				p.L391L		Atlas-SNP	.											ZBBX_ENST00000455345,NS,carcinoma,0,2	ZBBX	299	2	2	Substitution - coding silent(2)	stomach(2)	c.A1173G						PASS	.	T	,,	973,2759		136,701,1029	158.0	145.0	149.0		1173,1086,1173	1.0	0.9	3	dbSNP_121	149	3468,4720		721,2026,1347	no	coding-synonymous,coding-synonymous,coding-synonymous	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	,,	857,2727,2376	CC,CT,TT		42.3547,26.0718,37.2567	,,	391/840,362/772,391/801	167034814	4441,7479	1866	4094	5960	SO:0001819	synonymous_variant	79740	exon14			TATCTTTAGAGAT	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1173A>G	3.37:g.167034814T>C		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	277	123	0.444043	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	37	CCDS3199.2																																																																																			T|0.678;C|0.322	0.322	strong		0.343	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
DGKB	1607	hgsc.bcm.edu	37	7	14620536	14620536	+	Silent	SNP	C	C	A	rs61753128		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:14620536C>A	ENST00000403951.2	-	19	1982	c.1563G>T	c.(1561-1563)ctG>ctT	p.L521L	DGKB_ENST00000444700.2_Silent_p.L502L|DGKB_ENST00000406247.3_Silent_p.L521L|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000258767.5_Silent_p.L521L|DGKB_ENST00000399322.3_Silent_p.L521L|DGKB_ENST00000407950.1_Silent_p.L513L|DGKB_ENST00000402815.1_Silent_p.L520L			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	521	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						TCCCAAGAGGCAGAATCGCAA	0.423																																					p.L521L		Atlas-SNP	.											.	DGKB	166	.	0			c.G1563T						PASS	.	C	,	1,3881		0,1,1940	94.0	84.0	87.0		1563,1563	3.9	1.0	7	dbSNP_129	87	9,8297		0,9,4144	no	coding-synonymous,coding-synonymous	DGKB	NM_004080.2,NM_145695.2	,	0,10,6084	AA,AC,CC		0.1084,0.0258,0.082	,	521/805,521/774	14620536	10,12178	1941	4153	6094	SO:0001819	synonymous_variant	1607	exon18			AAGAGGCAGAATC	AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"""EF-hand domain containing"""	2850	protein-coding gene	gene with protein product		604070	"""diacylglycerol kinase, beta (90kD)"""	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.1563G>T	7.37:g.14620536C>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	140	60	0.428571	NM_145695	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Silent	SNP	ENST00000403951.2	37	CCDS47547.1																																																																																			.	.	weak		0.423	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080	
TTN	7273	hgsc.bcm.edu	37	2	179430997	179430997	+	Missense_Mutation	SNP	G	G	A	rs3731746	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179430997G>A	ENST00000591111.1	-	276	75163	c.74939C>T	c.(74938-74940)aCg>aTg	p.T24980M	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T17556M|TTN_ENST00000342992.6_Missense_Mutation_p.T24053M|TTN_ENST00000589042.1_Missense_Mutation_p.T26621M|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T17681M|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T17748M|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24980	Ig-like 123.		T -> M. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GATCTCAGGCGTTGGACGACC	0.418													G|||	1714	0.342252	0.3442	0.2061	5008	,	,		22404	0.629		0.171	False		,,,				2504	0.317				p.T26621M		Atlas-SNP	.											.	TTN	18412	.	0			c.C79862T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	1257,2583		208,841,871	161.0	155.0	157.0		52667,72158,53042,53243	5.0	1.0	2	dbSNP_107	157	1385,6915		116,1153,2881	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	81,81,81,81	324,1994,3752	AA,AG,GG		16.6867,32.7344,21.7628	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	17556/26927,24053/33424,17681/27052,17748/27119	179430997	2642,9498	1920	4150	6070	SO:0001583	missense	7273	exon326			TCAGGCGTTGGAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.74939C>T	2.37:g.179430997G>A	ENSP00000465570:p.Thr24980Met	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	203	97	0.477833	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		693	0.3173076923076923	157	0.31910569105691056	68	0.1878453038674033	341	0.5961538461538461	127	0.16754617414248021	G	9.152	1.016420	0.19355	0.327344	0.166867	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.91	5.03	0.67393	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.80183	2.485	0.25672	P	0.9858806	P;P;P;P	0.48694	0.914;0.914;0.914;0.914	P;P;P;P	0.50270	0.636;0.636;0.636;0.636	T	0.50338	-0.8840	8	0.87932	D	0	.	11.7884	0.52055	0.1854:0.0:0.8146:0.0	rs3731746;rs52794037;rs56683294;rs3731746	17556;17681;17748;24980	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	24053;17556;17748;17681;17554	ENSP00000343764:T24053M;ENSP00000434586:T17556M;ENSP00000340554:T17748M;ENSP00000352154:T17681M	ENSP00000340554:T17748M	T	-	2	0	TTN	179139243	1.000000	0.71417	0.980000	0.43619	0.991000	0.79684	2.938000	0.48987	1.485000	0.48380	0.555000	0.69702	ACG	T|0.000;G|0.681;N|0.000;A|0.318	0.318	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PCDHA1	56147	hgsc.bcm.edu	37	5	140166734	140166734	+	Missense_Mutation	SNP	C	C	T	rs144952734		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140166734C>T	ENST00000504120.2	+	1	859	c.859C>T	c.(859-861)Cgt>Tgt	p.R287C	PCDHA1_ENST00000378133.3_Missense_Mutation_p.R287C|PCDHA1_ENST00000394633.3_Missense_Mutation_p.R287C	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	287	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGTATTTCTCGTGACATTCA	0.363																																					p.R287C		Atlas-SNP	.											PCDHA1_ENST00000504120,colon,carcinoma,-1,2	PCDHA1	387	2	0			c.C859T						scavenged	.	C	CYS/ARG,CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	116.0	117.0	117.0		859,859,859	-0.3	0.0	5	dbSNP_134	117	0,8600		0,0,4300	no	missense,missense,missense	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	180,180,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	287/951,287/808,287/687	140166734	1,13005	2203	4300	6503	SO:0001583	missense	56147	exon1			ATTTCTCGTGACA	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.859C>T	5.37:g.140166734C>T	ENSP00000420840:p.Arg287Cys	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	207	4	0.0193237	NM_031411	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	.	.	.	.	.	.	.	.	.	.	c	11.69	1.714305	0.30413	2.27E-4	0.0	ENSG00000204970	ENST00000504120;ENST00000394633;ENST00000378133	T;T;T	0.61274	0.12;0.12;0.12	3.93	-0.326	0.12698	Cadherin (4);Cadherin-like (1);	1.298300	0.05853	U	0.621586	T	0.59810	0.2221	L	0.42245	1.32	0.09310	N	1	D;D;D	0.59767	0.979;0.986;0.974	B;P;B	0.57776	0.231;0.827;0.148	T	0.48445	-0.9035	10	0.72032	D	0.01	.	2.9784	0.05945	0.1305:0.5276:0.1282:0.2137	.	287;287;287	Q9Y5I3;Q9Y5I3-2;Q9Y5I3-3	PCDA1_HUMAN;.;.	C	287	ENSP00000420840:R287C;ENSP00000378129:R287C;ENSP00000367373:R287C	ENSP00000367373:R287C	R	+	1	0	PCDHA1	140146918	0.000000	0.05858	0.002000	0.10522	0.580000	0.36256	-1.541000	0.02198	-0.046000	0.13446	0.555000	0.69702	CGT	C|1.000;T|0.000	0.000	weak		0.363	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45258457	45258457	+	Silent	SNP	A	A	G	rs8881	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:45258457A>G	ENST00000389774.2	+	13	1518	c.1377A>G	c.(1375-1377)gcA>gcG	p.A459A	ARHGAP8_ENST00000389773.5_Silent_p.A550A|ARHGAP8_ENST00000336963.4_3'UTR|PRR5-ARHGAP8_ENST00000361473.5_Silent_p.A559A|PRR5-ARHGAP8_ENST00000352766.7_Silent_p.A638A|ARHGAP8_ENST00000517296.3_Silent_p.A638A|ARHGAP8_ENST00000356099.6_Silent_p.A428A	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	459					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|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)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CCCTGATGGCAGCCAGAAGAC	0.557													A|||	242	0.0483227	0.0204	0.0893	5008	,	,		17995	0.001		0.1153	False		,,,				2504	0.0368				p.A550A		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.A1650G						PASS	.	A	,,,	177,4229	115.0+/-153.0	6,165,2032	71.0	60.0	63.0		1377,,1650,1284	-5.6	0.0	22	dbSNP_52	63	1145,7455	235.0+/-267.7	85,975,3240	no	coding-synonymous,utr-3,coding-synonymous,coding-synonymous	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	,,,	91,1140,5272	GG,GA,AA		13.314,4.0172,10.1645	,,,	459/465,,550/556,428/434	45258457	1322,11684	2203	4300	6503	SO:0001819	synonymous_variant	553158	exon15			GATGGCAGCCAGA	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.1377A>G	22.37:g.45258457A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000389774.2	37	CCDS33664.1	135	0.061813186813186816	11	0.022357723577235773	34	0.09392265193370165	1	0.0017482517482517483	89	0.11741424802110818	A	3.285	-0.146116	0.06627	0.040172	0.13314	ENSG00000248405	ENST00000515632	.	.	.	2.78	-5.57	0.02521	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.10474	-1.0628	3	.	.	.	.	1.4089	0.02287	0.3695:0.2427:0.2669:0.121	rs8881;rs3171769;rs56598445;rs60182129;rs8881	.	.	.	R	499	.	.	Q	+	2	0	PRR5-ARHGAP8	43637121	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.357000	0.02607	-2.807000	0.00349	-2.545000	0.00179	CAG	A|0.917;G|0.083	0.083	strong		0.557	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
EGFL8	80864	hgsc.bcm.edu	37	6	32134510	32134510	+	Missense_Mutation	SNP	G	G	A	rs3096697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32134510G>A	ENST00000395512.1	+	4	362	c.257G>A	c.(256-258)aGg>aAg	p.R86K	PPT2-EGFL8_ENST00000422437.1_3'UTR|EGFL8_ENST00000333845.6_Missense_Mutation_p.R86K|AGPAT1_ENST00000490711.1_5'Flank			Q99944	EGFL8_HUMAN	EGF-like-domain, multiple 8	86	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.		R -> K (in dbSNP:rs3096697). {ECO:0000269|PubMed:14574404}.			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	10						CGGGAGGTGAGGCGGGAGGTT	0.652													G|||	777	0.155152	0.2095	0.1023	5008	,	,		15949	0.0367		0.2008	False		,,,				2504	0.1943				p.R86K		Atlas-SNP	.											.	EGFL8	15	.	0			c.G257A						PASS	.	G	LYS/ARG	825,3581	316.1+/-294.4	77,671,1455	45.0	54.0	51.0		257	3.4	1.0	6	dbSNP_103	51	1861,6739	322.8+/-315.7	197,1467,2636	yes	missense	EGFL8	NM_030652.3	26	274,2138,4091	AA,AG,GG		21.6395,18.7245,20.652	benign	86/294	32134510	2686,10320	2203	4300	6503	SO:0001583	missense	80864	exon4			AGGTGAGGCGGGA	U89336	CCDS4743.1	6p21	2010-06-25	2003-05-21	2003-05-23	ENSG00000241404	ENSG00000241404			13944	protein-coding gene	gene with protein product		609897	"""chromosome 6 open reading frame 8"""	C6orf8			Standard	NM_030652		Approved	NG3		Q99944	OTTHUMG00000031222	ENST00000395512.1:c.257G>A	6.37:g.32134510G>A	ENSP00000378888:p.Arg86Lys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_030652	B0S884|G5E9Q0|Q5JP23|Q5SSX3|Q8IV30	Missense_Mutation	SNP	ENST00000395512.1	37	CCDS4743.1	311	0.1423992673992674	105	0.21341463414634146	33	0.09116022099447514	23	0.04020979020979021	150	0.19788918205804748	G	9.290	1.050493	0.19827	0.187245	0.216395	ENSG00000241404	ENST00000333845;ENST00000395512;ENST00000432129	T;T;T	0.40225	1.04;1.04;1.04	6.08	3.38	0.38709	EMI domain (2);	.	.	.	.	T	0.08268	0.0206	N	0.11560	0.145	0.43421	P	0.004430000000000045	B	0.09022	0.002	B	0.08055	0.003	T	0.26780	-1.0093	8	0.19590	T	0.45	-9.8585	8.4318	0.32761	0.2396:0.0:0.7604:0.0	rs3096697;rs17421868;rs58410180;rs3096697	86	Q99944	EGFL8_HUMAN	K	86	ENSP00000333380:R86K;ENSP00000378888:R86K;ENSP00000401694:R86K	ENSP00000333380:R86K	R	+	2	0	EGFL8	32242488	0.002000	0.14202	0.990000	0.47175	0.990000	0.78478	0.683000	0.25349	0.474000	0.27392	-0.136000	0.14681	AGG	G|0.830;A|0.170	0.170	strong		0.652	EGFL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076463.3	NM_030652	
NOP56	10528	hgsc.bcm.edu	37	20	2635212	2635212	+	Missense_Mutation	SNP	A	A	G	rs2273137	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2635212A>G	ENST00000329276.5	+	4	877	c.361A>G	c.(361-363)Atc>Gtc	p.I121V	SNORD57_ENST00000448188.1_RNA|SNORD56_ENST00000413522.1_RNA|SNORD86_ENST00000391196.1_RNA|SNORA51_ENST00000606420.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORD110_ENST00000408189.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	121			I -> V (in dbSNP:rs2273137).		cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						CATAGCTGAGATCCTGCGAGG	0.478													A|||	593	0.118411	0.0416	0.1196	5008	,	,		22903	0.2232		0.0716	False		,,,				2504	0.1616				p.I121V		Atlas-SNP	.											.	NOP56	73	.	0			c.A361G						PASS	.	A	VAL/ILE	241,4165	140.8+/-176.2	5,231,1967	130.0	124.0	126.0		361	4.7	1.0	20	dbSNP_100	126	670,7930	168.7+/-220.2	35,600,3665	yes	missense	NOP56	NM_006392.3	29	40,831,5632	GG,GA,AA		7.7907,5.4698,7.0045	benign	121/595	2635212	911,12095	2203	4300	6503	SO:0001583	missense	10528	exon4			GCTGAGATCCTGC	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.361A>G	20.37:g.2635212A>G	ENSP00000370589:p.Ile121Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	102	43	0.421569	NM_006392	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	250	0.11446886446886446	23	0.046747967479674794	46	0.1270718232044199	122	0.21328671328671328	59	0.07783641160949868	A	13.68	2.308106	0.40895	0.054698	0.077907	ENSG00000101361	ENST00000329276;ENST00000445139	T;T	0.58797	0.31;0.92	5.79	4.69	0.59074	.	0.041485	0.85682	N	0.000000	T	0.00039	0.0001	N	0.20401	0.57	0.09310	P	0.999999538822	B	0.23650	0.089	B	0.21360	0.034	T	0.07986	-1.0744	9	0.29301	T	0.29	-10.1813	10.1163	0.42593	0.9207:0.0:0.0793:0.0	rs2273137;rs56986304;rs2273137	121	O00567	NOP56_HUMAN	V	121	ENSP00000370589:I121V;ENSP00000388497:I121V	ENSP00000370589:I121V	I	+	1	0	NOP56	2583212	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.567000	0.53813	1.005000	0.39183	-0.451000	0.05528	ATC	A|0.909;G|0.091	0.091	strong		0.478	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
PHYHIP	9796	hgsc.bcm.edu	37	8	22084503	22084503	+	Silent	SNP	C	C	T	rs11547656	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22084503C>T	ENST00000321613.3	-	4	657	c.201G>A	c.(199-201)ccG>ccA	p.P67P	PHYHIP_ENST00000454243.2_Silent_p.P67P	NM_001099335.1	NP_001092805.1	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein	67	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.									endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	10				Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)		TCATGGGCAGCGGCACTGCCT	0.622													C|||	1615	0.322484	0.2398	0.3401	5008	,	,		20345	0.2044		0.4304	False		,,,				2504	0.4325				p.P67P		Atlas-SNP	.											.	PHYHIP	24	.	0			c.G201A						PASS	.	C	,	1098,3244		154,790,1227	51.0	60.0	57.0		201,201	-11.4	0.4	8	dbSNP_120	57	3514,5002		728,2058,1472	no	coding-synonymous,coding-synonymous	PHYHIP	NM_001099335.1,NM_014759.3	,	882,2848,2699	TT,TC,CC		41.2635,25.2879,35.8687	,	67/331,67/331	22084503	4612,8246	2171	4258	6429	SO:0001819	synonymous_variant	9796	exon3			GGGCAGCGGCACT	D87463	CCDS43723.1	8p21.2	2010-02-17	2006-01-09		ENSG00000168490	ENSG00000168490			16865	protein-coding gene	gene with protein product		608511	"""phytanoyl-CoA hydroxylase interacting protein"", ""DYRK1A interacting protein 3"""	DYRK1AP3		9039502, 10686344	Standard	NM_014759		Approved	KIAA0273, PAHX-AP	uc003xbj.4	Q92561	OTTHUMG00000163776	ENST00000321613.3:c.201G>A	8.37:g.22084503C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_014759	D3DSR1|Q8N4I9	Silent	SNP	ENST00000321613.3	37	CCDS43723.1																																																																																			T|0.357;G|0.000;C|0.642	0.357	strong		0.622	PHYHIP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375388.1	NM_014759	
C17orf97	400566	hgsc.bcm.edu	37	17	263417	263417	+	Silent	SNP	C	C	T	rs202025012	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:263417C>T	ENST00000360127.6	+	2	799	c.783C>T	c.(781-783)gcC>gcT	p.A261A	C17orf97_ENST00000571106.1_Intron|AC108004.3_ENST00000466740.2_RNA	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	291	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.									breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						ACCCCGAGGCCCTCAAGGGCT	0.687																																					p.A261A		Atlas-SNP	.											.	C17orf97	76	.	0			c.C783T						PASS	.						12.0	15.0	14.0					17																	263417		2135	4193	6328	SO:0001819	synonymous_variant	400566	exon2			CGAGGCCCTCAAG	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.783C>T	17.37:g.263417C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	214	45	0.21028	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Silent	SNP	ENST00000360127.6	37	CCDS32519.2																																																																																			C|0.915;T|0.085	0.085	strong		0.687	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
DVL2	1856	hgsc.bcm.edu	37	17	7132556	7132556	+	Silent	SNP	C	C	T	rs222837	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7132556C>T	ENST00000005340.5	-	8	1137	c.855G>A	c.(853-855)caG>caA	p.Q285Q	DVL2_ENST00000575458.1_Silent_p.Q279Q|DVL2_ENST00000574642.1_5'UTR	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	285	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						GCTCATTGCTCTGGCCAACAA	0.592													T|||	3281	0.655152	0.8487	0.5591	5008	,	,		17964	0.6359		0.5229	False		,,,				2504	0.6176				p.Q285Q		Atlas-SNP	.											.	DVL2	49	.	0			c.G855A						PASS	.	T		3543,863	337.8+/-305.0	1427,689,87	82.0	84.0	84.0		855	-2.1	1.0	17	dbSNP_79	84	4379,4221	570.8+/-389.4	1131,2117,1052	no	coding-synonymous	DVL2	NM_004422.2		2558,2806,1139	TT,TC,CC		49.0814,19.5869,39.0897		285/737	7132556	7922,5084	2203	4300	6503	SO:0001819	synonymous_variant	1856	exon8			ATTGCTCTGGCCA	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.855G>A	17.37:g.7132556C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	138	136	0.985507	NM_004422	D3DTN3|Q53XM0	Silent	SNP	ENST00000005340.5	37	CCDS11091.1																																																																																			C|0.365;T|0.635	0.635	strong		0.592	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
ABCB6	10058	hgsc.bcm.edu	37	2	220081416	220081416	+	Missense_Mutation	SNP	G	G	A	rs57467915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:220081416G>A	ENST00000265316.3	-	3	1142	c.826C>T	c.(826-828)Cgg>Tgg	p.R276W	ABCB6_ENST00000439002.2_Missense_Mutation_p.R230W	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	276	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTGAGTGCCCGTTCCAAACCC	0.587													g|||	19	0.00379393	0.0008	0.0029	5008	,	,		18760	0.0		0.0149	False		,,,				2504	0.001				p.R276W		Atlas-SNP	.											.	ABCB6	76	.	0			c.C826T						PASS	.	G	TRP/ARG	17,4387		0,17,2185	30.0	27.0	28.0		826	3.0	1.0	2	dbSNP_129	28	114,8480		0,114,4183	yes	missense	ABCB6	NM_005689.2	101	0,131,6368	AA,AG,GG		1.3265,0.386,1.0078	probably-damaging	276/843	220081416	131,12867	2202	4297	6499	SO:0001583	missense	10058	exon3			GTGCCCGTTCCAA	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"""ATP binding cassette transporters / subfamily B"""	47	protein-coding gene	gene with protein product	"""ATP-binding cassette half-transporter"""	605452	"""ATP-binding cassette, sub-family B (MDR/TAP), member 6"""			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.826C>T	2.37:g.220081416G>A	ENSP00000265316:p.Arg276Trp	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	178	84	0.47191	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	SNP	ENST00000265316.3	37	CCDS2436.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	G	18.91	3.722642	0.68959	0.00386	0.013265	ENSG00000115657	ENST00000265316;ENST00000439002	D;D	0.89746	-2.56;-2.56	4.82	2.97	0.34412	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.94142	0.8121	M	0.94142	3.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94502	0.7710	10	0.87932	D	0	-27.738	13.9801	0.64299	0.0:0.0:0.7233:0.2767	rs57467915;rs61733625	230;276	Q9NP58-4;Q9NP58	.;ABCB6_HUMAN	W	276;230	ENSP00000265316:R276W;ENSP00000394333:R230W	ENSP00000265316:R276W	R	-	1	2	ABCB6	219789660	1.000000	0.71417	0.982000	0.44146	0.883000	0.51084	2.553000	0.45837	0.719000	0.32188	-0.122000	0.15005	CGG	G|0.992;A|0.008	0.008	strong		0.587	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689	
FCN2	2220	hgsc.bcm.edu	37	9	137778402	137778402	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:137778402G>A	ENST00000291744.6	+	7	696	c.686G>A	c.(685-687)gGc>gAc	p.G229D	FCN2_ENST00000350339.2_Missense_Mutation_p.G191D	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	229	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		TTCGTGGAGGGCAGTGCGGGT	0.582																																					p.G229D		Atlas-SNP	.											FCN2,NS,carcinoma,0,1	FCN2	55	1	0			c.G686A						scavenged	.						135.0	126.0	129.0					9																	137778402		2203	4300	6503	SO:0001583	missense	2220	exon7			TGGAGGGCAGTGC	D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"""Fibrinogen C domain containing"""	3624	protein-coding gene	gene with protein product	"""hucolin"", ""collagen/fibrinogen domain-containing protein 2"", ""ficolin B"", ""serum lectin p35"", ""L-ficolin"""	601624	"""ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"""			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.686G>A	9.37:g.137778402G>A	ENSP00000291744:p.Gly229Asp	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	186	2	0.0107527	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.323974	0.81580	.	.	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.28454	1.61;1.61	4.12	4.12	0.48240	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.40818	U	0.001016	T	0.73497	0.3594	H	0.99626	4.665	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.85789	0.1366	10	0.87932	D	0	.	13.8582	0.63542	0.0:0.0:1.0:0.0	.	191;229	Q15485-2;Q15485	.;FCN2_HUMAN	D	191;229	ENSP00000291741:G191D;ENSP00000291744:G229D	ENSP00000291744:G229D	G	+	2	0	FCN2	136918223	1.000000	0.71417	0.147000	0.22382	0.385000	0.30292	7.540000	0.82074	1.822000	0.53115	0.563000	0.77884	GGC	.	.	none		0.582	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	
OR5R1	219479	hgsc.bcm.edu	37	11	56185347	56185347	+	Missense_Mutation	SNP	T	T	C	rs7111634	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56185347T>C	ENST00000312253.1	-	1	361	c.362A>G	c.(361-363)gAt>gGt	p.D121G		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	121			D -> G (in dbSNP:rs7111634).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					GACATAGCAATCGTAGGCCAT	0.463													T|||	186	0.0371406	0.003	0.0432	5008	,	,		21605	0.001		0.0944	False		,,,				2504	0.0573				p.D121G		Atlas-SNP	.											OR5R1,right_upper_lobe,carcinoma,-1,3	OR5R1	83	3	0			c.A362G						PASS	.	T	GLY/ASP	56,4346	54.2+/-90.2	0,56,2145	108.0	103.0	105.0		362	5.8	1.0	11	dbSNP_116	105	694,7898	171.6+/-222.5	33,628,3635	yes	missense	OR5R1	NM_001004744.1	94	33,684,5780	CC,CT,TT		8.0773,1.2721,5.7719	probably-damaging	121/325	56185347	750,12244	2201	4296	6497	SO:0001583	missense	219479	exon1			TAGCAATCGTAGG	AB065504	CCDS31530.1	11q11	2012-08-09		2004-03-10	ENSG00000174942	ENSG00000174942		"""GPCR / Class A : Olfactory receptors"""	14841	protein-coding gene	gene with protein product				OR5R1P			Standard	NM_001004744		Approved		uc010rji.2	Q8NH85	OTTHUMG00000154219	ENST00000312253.1:c.362A>G	11.37:g.56185347T>C	ENSP00000308595:p.Asp121Gly	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	37	CCDS31530.1	85	0.03891941391941392	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	71	0.09366754617414248	T	24.0	4.480206	0.84747	0.012721	0.080773	ENSG00000174942	ENST00000312253	T	0.02177	4.41	5.78	5.78	0.91487	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33670	U	0.004674	T	0.00845	0.0028	H	0.98577	4.27	0.43199	D	0.995046	D	0.69078	0.997	D	0.65987	0.94	T	0.04128	-1.0975	10	0.87932	D	0	-12.8088	15.7602	0.78073	0.0:0.0:0.0:1.0	rs7111634;rs7111634	121	Q8NH85	OR5R1_HUMAN	G	121	ENSP00000308595:D121G	ENSP00000308595:D121G	D	-	2	0	OR5R1	55941923	1.000000	0.71417	0.984000	0.44739	0.844000	0.47949	7.811000	0.86092	2.211000	0.71520	0.391000	0.25812	GAT	T|0.952;C|0.048	0.048	strong		0.463	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744	
STAG3	10734	hgsc.bcm.edu	37	7	99799845	99799845	+	Silent	SNP	T	T	A	rs1043915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99799845T>A	ENST00000426455.1	+	24	2852	c.2445T>A	c.(2443-2445)atT>atA	p.I815I	GATS_ENST00000436886.2_3'UTR|STAG3_ENST00000394018.2_Silent_p.I757I|STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000543273.1_RNA|STAG3_ENST00000317296.5_Silent_p.I815I	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	815					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTCAGATGATTGTTGGGGGCC	0.458													T|||	1969	0.393171	0.3343	0.5173	5008	,	,		19641	0.621		0.2664	False		,,,				2504	0.2802				p.I815I		Atlas-SNP	.											.	STAG3	121	.	0			c.T2445A						PASS	.	T	,	1502,2904		245,1012,946	144.0	153.0	150.0		2445,	-0.2	0.1	7	dbSNP_86	150	2263,6337		305,1653,2342	no	coding-synonymous,utr-3	STAG3,GATS	NM_012447.2,NM_178831.6	,	550,2665,3288	AA,AT,TT		26.314,34.0899,28.9482	,	815/1226,	99799845	3765,9241	2203	4300	6503	SO:0001819	synonymous_variant	10734	exon24			GATGATTGTTGGG	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2445T>A	7.37:g.99799845T>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Silent	SNP	ENST00000426455.1	37	CCDS34703.1																																																																																			T|0.679;A|0.321	0.321	strong		0.458	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
PRF1	5551	hgsc.bcm.edu	37	10	72358655	72358655	+	Silent	SNP	G	G	A	rs885821	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:72358655G>A	ENST00000441259.1	-	3	982	c.822C>T	c.(820-822)gcC>gcT	p.A274A	PRF1_ENST00000373209.2_Silent_p.A274A	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	274	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CCTTGGCTTCGGCAGAGATGC	0.617			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				G|||	564	0.11262	0.0537	0.1513	5008	,	,		18354	0.1101		0.1988	False		,,,				2504	0.0787				p.A274A		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.C822T						PASS	.	G	,	368,4038	188.8+/-215.1	21,326,1856	202.0	127.0	152.0		822,822	-11.7	0.0	10	dbSNP_86	152	1555,7045	292.3+/-300.8	161,1233,2906	no	coding-synonymous,coding-synonymous	PRF1	NM_001083116.1,NM_005041.4	,	182,1559,4762	AA,AG,GG		18.0814,8.3522,14.7855	,	274/556,274/556	72358655	1923,11083	2203	4300	6503	SO:0001819	synonymous_variant	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GGCTTCGGCAGAG	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.822C>T	10.37:g.72358655G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	222	108	0.486486	NM_001083116	B2R6X4|Q59F57|Q86WX7	Silent	SNP	ENST00000441259.1	37	CCDS7305.1																																																																																			G|0.861;A|0.139	0.139	strong		0.617	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
PDLIM1	9124	hgsc.bcm.edu	37	10	96997820	96997820	+	Silent	SNP	A	A	G	rs1049814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:96997820A>G	ENST00000329399.6	-	7	960	c.852T>C	c.(850-852)taT>taC	p.Y284Y	PDLIM1_ENST00000477757.1_5'UTR	NM_020992.2	NP_066272.1	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	284	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|skin(2)	10		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		CAGTGCACACATAACACTCAG	0.547													A|||	867	0.173123	0.2073	0.2594	5008	,	,		21924	0.0724		0.1769	False		,,,				2504	0.1656				p.Y284Y		Atlas-SNP	.											.	PDLIM1	33	.	0			c.T852C						PASS	.	A		822,3584	330.4+/-301.5	73,676,1454	93.0	74.0	80.0		852	-3.3	0.8	10	dbSNP_86	80	1745,6855	318.3+/-313.6	151,1443,2706	no	coding-synonymous	PDLIM1	NM_020992.2		224,2119,4160	GG,GA,AA		20.2907,18.6564,19.737		284/330	96997820	2567,10439	2203	4300	6503	SO:0001819	synonymous_variant	9124	exon7			GCACACATAACAC	U90878	CCDS7441.1	10q23.1	2008-07-29	2008-07-29		ENSG00000107438	ENSG00000107438			2067	protein-coding gene	gene with protein product	"""carboxyl terminal LIM domain protein 1"", ""elfin"""	605900	"""PDZ and LIM domain 1 (elfin)"""	CLIM1		10861853	Standard	NM_020992		Approved	CLP-36, hCLIM1, CLP36	uc001kkh.4	O00151	OTTHUMG00000018810	ENST00000329399.6:c.852T>C	10.37:g.96997820A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	82	79	0.963415	NM_020992	B2RBS6|Q5VZH5|Q9BPZ9	Silent	SNP	ENST00000329399.6	37	CCDS7441.1																																																																																			A|0.818;G|0.182	0.182	strong		0.547	PDLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049508.1		
VPREB1	7441	hgsc.bcm.edu	37	22	22599674	22599674	+	Silent	SNP	C	C	T	rs5995719	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:22599674C>T	ENST00000403807.3	+	2	502	c.363C>T	c.(361-363)agC>agT	p.S121S	VPREB1_ENST00000302273.2_Silent_p.S120S			P12018	VPREB_HUMAN	pre-B lymphocyte 1	121	Ig-like V-type.									large_intestine(1)|liver(1)|lung(6)|skin(1)	9	all_hematologic(9;0.0312)|Acute lymphoblastic leukemia(84;0.155)	all_cancers(3;3.14e-14)|Acute lymphoblastic leukemia(3;2.97e-57)|all_hematologic(3;5.9e-52)		READ - Rectum adenocarcinoma(21;0.145)		GGGCCCGCAGCTCggagaagg	0.572													c|||	798	0.159345	0.3094	0.1009	5008	,	,		16238	0.003		0.1759	False		,,,				2504	0.1421				p.S121S		Atlas-SNP	.											VPREB1,NS,carcinoma,+1,1	VPREB1	20	1	0			c.C363T						scavenged	.	C		1327,3059		210,907,1076	15.0	17.0	16.0		363	3.3	0.0	22	dbSNP_114	16	1647,6935		157,1333,2801	yes	coding-synonymous	VPREB1	NM_007128.2		367,2240,3877	TT,TC,CC		19.1913,30.2554,22.9334		121/146	22599674	2974,9994	2193	4291	6484	SO:0001819	synonymous_variant	7441	exon2			CCGCAGCTCGGAG	M34927	CCDS13798.1	22q11.2	2014-05-16	2008-09-12		ENSG00000169575	ENSG00000169575		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	12709	protein-coding gene	gene with protein product		605141				3139558	Standard	NM_007128		Approved	VpreB, CD179A	uc002zvx.1	P12018	OTTHUMG00000151042	ENST00000403807.3:c.363C>T	22.37:g.22599674C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	20	7	0.35	NM_007128	B5MCG2	Silent	SNP	ENST00000403807.3	37	CCDS13798.1																																																																																			C|0.808;T|0.192	0.192	strong		0.572	VPREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321101.1		
KIF26B	55083	hgsc.bcm.edu	37	1	245704130	245704130	+	Missense_Mutation	SNP	G	G	C	rs61754898	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:245704130G>C	ENST00000407071.2	+	5	1668	c.1228G>C	c.(1228-1230)Gct>Cct	p.A410P	KIF26B_ENST00000366518.4_Missense_Mutation_p.A29P	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	410					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.A410P(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			CACTTCTTCCGCTGCCGAACC	0.517													G|||	636	0.126997	0.0091	0.1744	5008	,	,		15020	0.2262		0.1292	False		,,,				2504	0.1483				p.A410P		Atlas-SNP	.											KIF26B_ENST00000407071,NS,carcinoma,0,1	KIF26B	343	1	1	Substitution - Missense(1)	stomach(1)	c.G1228C						PASS	.	G	PRO/ALA	89,3661		3,83,1789	88.0	90.0	89.0		1228	3.5	0.0	1	dbSNP_129	89	874,7324		45,784,3270	yes	missense	KIF26B	NM_018012.3	27	48,867,5059	CC,CG,GG		10.6611,2.3733,8.0599	benign	410/2109	245704130	963,10985	1875	4099	5974	SO:0001583	missense	55083	exon5			TCTTCCGCTGCCG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.1228G>C	1.37:g.245704130G>C	ENSP00000385545:p.Ala410Pro	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	295	135	0.457627	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	37	CCDS44342.1	304	0.1391941391941392	4	0.008130081300813009	58	0.16022099447513813	139	0.243006993006993	103	0.1358839050131926	G	2.974	-0.211870	0.06140	0.023733	0.106611	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.77750	-1.12;-1.09	5.44	3.53	0.40419	.	.	.	.	.	T	0.00039	0.0001	N	0.11927	0.2	0.80722	P	0.0	B;B	0.14438	0.01;0.002	B;B	0.11329	0.004;0.006	T	0.02860	-1.1101	8	0.13853	T	0.58	.	11.0293	0.47763	0.0701:0.1295:0.8004:0.0	rs61754898	29;410	B7WPD9;Q2KJY2	.;KI26B_HUMAN	P	410;29;26	ENSP00000385545:A410P;ENSP00000355475:A29P	ENSP00000355475:A29P	A	+	1	0	KIF26B	243770753	0.768000	0.28519	0.000000	0.03702	0.002000	0.02628	3.501000	0.53325	0.632000	0.30432	-0.140000	0.14226	GCT	G|0.865;C|0.135	0.135	strong		0.517	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
PLCG1	5335	hgsc.bcm.edu	37	20	39792063	39792063	+	Missense_Mutation	SNP	A	A	G	rs2228246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:39792063A>G	ENST00000373271.1	+	9	1240	c.835A>G	c.(835-837)Agc>Ggc	p.S279G	PLCG1_ENST00000373272.2_Missense_Mutation_p.S279G|PLCG1_ENST00000244007.3_Missense_Mutation_p.S279G	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	279			S -> G (in dbSNP:rs2228246). {ECO:0000269|Ref.2}.		activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				GTTCATGCTCAGCTTCCTCCG	0.557													A|||	395	0.0788738	0.0802	0.1167	5008	,	,		18612	0.002		0.162	False		,,,				2504	0.044				p.S279G		Atlas-SNP	.											.	PLCG1	111	.	0			c.A835G						PASS	.	A	GLY/SER,GLY/SER	447,3959	216.1+/-234.9	21,405,1777	72.0	66.0	68.0		835,835	4.6	1.0	20	dbSNP_98	68	1346,7254	263.4+/-285.0	116,1114,3070	yes	missense,missense	PLCG1	NM_002660.2,NM_182811.1	56,56	137,1519,4847	GG,GA,AA		15.6512,10.1453,13.7859	benign,benign	279/1292,279/1291	39792063	1793,11213	2203	4300	6503	SO:0001583	missense	5335	exon9			ATGCTCAGCTTCC	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"", ""SH2 domain containing"""	9065	protein-coding gene	gene with protein product		172420	"""phospholipase C, gamma 1 (formerly subtype 148)"""	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.835A>G	20.37:g.39792063A>G	ENSP00000362368:p.Ser279Gly	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	37	CCDS13314.1	208	0.09523809523809523	36	0.07317073170731707	34	0.09392265193370165	1	0.0017482517482517483	137	0.18073878627968337	A	12.03	1.816252	0.32145	0.101453	0.156512	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.42513	0.97;0.97;0.97	5.69	4.6	0.57074	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);	0.439299	0.31450	N	0.007636	T	0.00039	0.0001	N	0.24115	0.695	0.30622	P	0.75836	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.09840	-1.0656	9	0.33940	T	0.23	.	7.5861	0.27993	0.7877:0.1412:0.071:0.0	rs2228246;rs8192707;rs52803627;rs57350391;rs2228246	279;279	P19174;A2A284	PLCG1_HUMAN;.	G	279	ENSP00000244007:S279G;ENSP00000362368:S279G;ENSP00000362369:S279G	ENSP00000244007:S279G	S	+	1	0	PLCG1	39225477	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.993000	0.40747	0.998000	0.38996	0.459000	0.35465	AGC	A|0.883;G|0.117	0.117	strong		0.557	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811	
IL3	3562	hgsc.bcm.edu	37	5	131396478	131396478	+	Missense_Mutation	SNP	C	C	T	rs40401	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:131396478C>T	ENST00000296870.2	+	1	257	c.79C>T	c.(79-81)Ccc>Tcc	p.P27S		NM_000588.3	NP_000579.2	P08700	IL3_HUMAN	interleukin 3	27			P -> S (in dbSNP:rs40401). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2544122, ECO:0000269|Ref.4}.		cell-cell signaling (GO:0007267)|embryonic hemopoiesis (GO:0035162)|immune response (GO:0006955)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-3 receptor binding (GO:0005135)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)	10		all_cancers(142;7.42e-12)|Lung NSC(810;4.25e-07)|all_lung(232;1.93e-06)|Prostate(281;0.00741)|Breast(839;0.0544)|Lung SC(612;0.122)|Ovarian(839;0.223)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	GBM - Glioblastoma multiforme(465;0.0161)|Lung(113;0.105)	Amlexanox(DB01025)	CCAGACAACGCCCTTGAAGAC	0.537													T|||	2101	0.419529	0.5703	0.3156	5008	,	,		21475	0.5714		0.2515	False		,,,				2504	0.3057				p.P27S		Atlas-SNP	.											IL3,NS,carcinoma,0,1	IL3	28	1	0			c.C79T						PASS	.	T	SER/PRO	2268,2138	578.4+/-384.7	588,1092,523	100.0	97.0	98.0		79	1.2	0.0	5	dbSNP_76	98	1951,6649	725.2+/-406.5	226,1499,2575	yes	missense	IL3	NM_000588.3	74	814,2591,3098	TT,TC,CC		22.686,48.5247,32.4389	benign	27/153	131396478	4219,8787	2203	4300	6503	SO:0001583	missense	3562	exon1			ACAACGCCCTTGA	M14743	CCDS4149.1	5q23-q31	2014-04-04	2014-04-04		ENSG00000164399	ENSG00000164399		"""Interleukins and interleukin receptors"""	6011	protein-coding gene	gene with protein product	"""multilineage-colony-stimulating factor"", ""hematopoietic growth factor"", ""P-cell stimulating factor"", ""mast-cell growth factor"", ""colony-stimulating factor, multiple"""	147740	"""interleukin 3 (colony-stimulating factor, multiple)"""			3489530	Standard	NM_000588		Approved	IL-3, MULTI-CSF, MCGF, MGC79398, MGC79399	uc003kwe.1	P08700	OTTHUMG00000059640	ENST00000296870.2:c.79C>T	5.37:g.131396478C>T	ENSP00000296870:p.Pro27Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	126	68	0.539683	NM_000588	Q6GS87	Missense_Mutation	SNP	ENST00000296870.2	37	CCDS4149.1	911	0.41712454212454214	291	0.5914634146341463	100	0.27624309392265195	319	0.5576923076923077	201	0.26517150395778366	T	0.343	-0.949559	0.02304	0.514753	0.22686	ENSG00000164399	ENST00000296870	T	0.26373	1.74	3.24	1.18	0.20946	.	1.255760	0.05782	N	0.608778	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.18968	0.032	B	0.20577	0.03	T	0.43766	-0.9371	9	0.07644	T	0.81	-2.5392	6.6006	0.22699	0.0:0.6449:0.2355:0.1196	rs40401;rs657709;rs3181636;rs52803049;rs59548569;rs40401	27	P08700	IL3_HUMAN	S	27	ENSP00000296870:P27S	ENSP00000296870:P27S	P	+	1	0	IL3	131424377	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.640000	0.00108	0.009000	0.14813	-0.834000	0.03071	CCC	C|0.616;N|0.000	.	strong		0.537	IL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132639.1	NM_000588	
KCNB2	9312	hgsc.bcm.edu	37	8	73850203	73850203	+	Silent	SNP	G	G	A	rs11782118	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:73850203G>A	ENST00000523207.1	+	3	3201	c.2613G>A	c.(2611-2613)gtG>gtA	p.V871V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	871					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	ACCATGCTGTGAGTGAAGTCA	0.483													G|||	1183	0.236222	0.1989	0.2767	5008	,	,		19028	0.0942		0.4314	False		,,,				2504	0.2035				p.V871V		Atlas-SNP	.											.	KCNB2	228	.	0			c.G2613A						PASS	.	G		1013,3393	376.3+/-322.0	111,791,1301	93.0	89.0	90.0		2613	2.7	0.6	8	dbSNP_120	90	3543,5057	516.7+/-378.9	723,2097,1480	no	coding-synonymous	KCNB2	NM_004770.2		834,2888,2781	AA,AG,GG		41.1977,22.9914,35.03		871/912	73850203	4556,8450	2203	4300	6503	SO:0001819	synonymous_variant	9312	exon3			TGCTGTGAGTGAA	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.2613G>A	8.37:g.73850203G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_004770	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																			G|0.686;A|0.314	0.314	strong		0.483	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
AKAP9	10142	hgsc.bcm.edu	37	7	91726927	91726927	+	Silent	SNP	A	A	C	rs1063243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:91726927A>C	ENST00000359028.2	+	42	10663	c.10438A>C	c.(10438-10440)Aga>Cga	p.R3480R	AKAP9_ENST00000356239.3_Silent_p.R3476R|AKAP9_ENST00000358100.2_Silent_p.R3426R			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3480					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AACCAGTGATAGAACTAGAAA	0.368			T	BRAF	papillary thyroid								C|||	1890	0.377396	0.5212	0.3573	5008	,	,		18085	0.1617		0.3867	False		,,,				2504	0.41				p.R3476R		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	AKAP9_ENST00000356239,NS,carcinoma,-1,2	AKAP9	788	2	0			c.A10426C						PASS	.	C	,	2333,2073	560.3+/-380.4	619,1095,489	68.0	69.0	69.0		10426,10402	1.1	0.9	7	dbSNP_86	69	3471,5129	632.1+/-398.6	681,2109,1510	yes	coding-synonymous,coding-synonymous	AKAP9	NM_005751.4,NM_147185.2	,	1300,3204,1999	CC,CA,AA		40.3605,47.0495,44.6256	,	3476/3908,3468/3900	91726927	5804,7202	2203	4300	6503	SO:0001819	synonymous_variant	10142	exon42			AGTGATAGAACTA	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.10438A>C	7.37:g.91726927A>C		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	185	78	0.421622	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				A|0.588;C|0.412	0.412	strong		0.368	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
CCHCR1	54535	hgsc.bcm.edu	37	6	31110789	31110789	+	Silent	SNP	T	T	C	rs1265084	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31110789T>C	ENST00000376266.5	-	17	2297	c.2175A>G	c.(2173-2175)tcA>tcG	p.S725S	CCHCR1_ENST00000396263.2_Silent_p.S672S|CCHCR1_ENST00000396268.3_Silent_p.S814S|CCHCR1_ENST00000451521.2_Silent_p.S778S	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	725					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						GTGCAGATGCTGAACACTCTG	0.542													T|||	92	0.0183706	0.0348	0.049	5008	,	,		20596	0.0		0.0119	False		,,,				2504	0.0				p.S814S		Atlas-SNP	.											.	CCHCR1	68	.	0			c.A2442G						PASS	.	T	,,	105,2913		0,105,1404	288.0	334.0	318.0		2334,2442,2175	0.9	0.0	6	dbSNP_87	318	114,5304		3,108,2598	no	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	3,213,4002	CC,CT,TT		2.1041,3.4791,2.596	,,	778/836,814/872,725/783	31110789	219,8217	1509	2709	4218	SO:0001819	synonymous_variant	54535	exon17			AGATGCTGAACAC	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.2175A>G	6.37:g.31110789T>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	229	95	0.414847	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			T|0.973;C|0.027	0.027	strong		0.542	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
ITGA2B	3674	hgsc.bcm.edu	37	17	42463054	42463054	+	Missense_Mutation	SNP	G	G	C	rs76066357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:42463054G>C	ENST00000262407.5	-	4	470	c.439C>G	c.(439-441)Cta>Gta	p.L147V	ITGA2B_ENST00000377068.3_5'Flank|ITGA2B_ENST00000353281.4_Missense_Mutation_p.L147V	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	147					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	GTCTTTTCTAGGACGTTCCAG	0.667													G|||	23	0.00459265	0.0008	0.0101	5008	,	,		11686	0.0		0.0139	False		,,,				2504	0.001				p.L147V		Atlas-SNP	.											.	ITGA2B	88	.	0			c.C439G	GRCh37	CM073147	ITGA2B	M	rs76066357	PASS	.	G	VAL/LEU	14,4386	19.1+/-41.9	0,14,2186	29.0	36.0	34.0		439	3.5	0.0	17	dbSNP_134	34	113,8485	59.1+/-120.7	1,111,4187	yes	missense	ITGA2B	NM_000419.3	32	1,125,6373	CC,CG,GG		1.3143,0.3182,0.9771	benign	147/1040	42463054	127,12871	2200	4299	6499	SO:0001583	missense	3674	exon4			TTTCTAGGACGTT		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.439C>G	17.37:g.42463054G>C	ENSP00000262407:p.Leu147Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Missense_Mutation	SNP	ENST00000262407.5	37	CCDS32665.1	11	0.005036630036630037	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	11.09	1.537077	0.27475	0.003182	0.013143	ENSG00000005961	ENST00000262407;ENST00000353281	T;T	0.71698	-0.59;-0.59	5.55	3.52	0.40303	.	0.000000	0.28515	N	0.015074	T	0.51126	0.1656	L	0.52573	1.65	0.24187	N	0.995568	B	0.26363	0.147	B	0.20184	0.028	T	0.46884	-0.9159	10	0.37606	T	0.19	.	6.7565	0.23516	0.0824:0.0:0.6063:0.3113	.	147	P08514	ITA2B_HUMAN	V	147	ENSP00000262407:L147V;ENSP00000340536:L147V	ENSP00000262407:L147V	L	-	1	2	ITGA2B	39818580	0.018000	0.18449	0.011000	0.14972	0.617000	0.37484	0.063000	0.14410	0.666000	0.31087	-0.254000	0.11334	CTA	G|0.991;C|0.009	0.009	strong		0.667	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		
SELP	6403	hgsc.bcm.edu	37	1	169562904	169562904	+	Silent	SNP	C	C	T	rs6128	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:169562904C>T	ENST00000263686.6	-	14	2383	c.2346G>A	c.(2344-2346)acG>acA	p.T782T	SELP_ENST00000367792.2_Silent_p.T598T|SELP_ENST00000367786.2_Silent_p.T720T|SELP_ENST00000458599.2_Silent_p.T598T|SELP_ENST00000367793.2_Silent_p.T720T|SELP_ENST00000367794.2_Silent_p.T720T|SELP_ENST00000367788.2_Silent_p.T720T|SELP_ENST00000367791.2_Silent_p.T596T	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	782					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|defense response to Gram-negative bacterium (GO:0050829)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of platelet activation (GO:0010572)|regulation of integrin activation (GO:0033623)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|platelet dense granule membrane (GO:0031088)	fucose binding (GO:0042806)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|lipopolysaccharide binding (GO:0001530)|oligosaccharide binding (GO:0070492)|sialic acid binding (GO:0033691)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(32)|ovary(4)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(923;0.208)				Dalteparin(DB06779)|Heparin(DB01109)|Nadroparin(DB08813)	TCAGACCTATCGTAGAAGCCA	0.443													C|||	1897	0.378794	0.5325	0.2767	5008	,	,		17543	0.6647		0.166	False		,,,				2504	0.1677				p.T782T		Atlas-SNP	.											SELP,NS,carcinoma,-1,2	SELP	132	2	0			c.G2346A						scavenged	.	C		2092,2314	574.3+/-383.7	505,1082,616	72.0	68.0	70.0		2346	-4.4	0.0	1	dbSNP_52	70	1375,7225	266.5+/-286.8	103,1169,3028	no	coding-synonymous	SELP	NM_003005.3		608,2251,3644	TT,TC,CC		15.9884,47.4807,26.6569		782/831	169562904	3467,9539	2203	4300	6503	SO:0001819	synonymous_variant	6403	exon14			ACCTATCGTAGAA	BC068533	CCDS1282.1	1q22-q25	2008-02-05	2002-08-29		ENSG00000174175	ENSG00000174175		"""CD molecules"""	10721	protein-coding gene	gene with protein product		173610	"""selectin P (granule membrane protein 140kD, antigen CD62)"""	GRMP		1375831	Standard	NM_003005		Approved	CD62, PSEL, PADGEM, GMP140, CD62P	uc001ggi.4	P16109	OTTHUMG00000034685	ENST00000263686.6:c.2346G>A	1.37:g.169562904C>T		Somatic	60	1	0.0166667		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_003005	Q5R344|Q8IVD1	Silent	SNP	ENST00000263686.6	37	CCDS1282.1	836	0.38278388278388276	252	0.5121951219512195	100	0.27624309392265195	367	0.6416083916083916	117	0.15435356200527706	C	0.040	-1.290092	0.01387	0.474807	0.159884	ENSG00000174175	ENST00000446728	.	.	.	5.62	-4.44	0.03557	.	.	.	.	.	T	0.06005	0.0156	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.33266	-0.9875	3	.	.	.	1.149	1.6588	0.02787	0.131:0.3144:0.2699:0.2847	rs6128;rs59265639;rs6128	.	.	.	N	598	.	.	D	-	1	0	SELP	167829528	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.164000	0.03135	-0.849000	0.04158	-1.111000	0.02071	GAT	C|0.687;T|0.313	0.313	strong		0.443	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005	
STK31	56164	hgsc.bcm.edu	37	7	23757162	23757162	+	Missense_Mutation	SNP	G	G	C	rs6945306	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:23757162G>C	ENST00000355870.3	+	4	332	c.213G>C	c.(211-213)caG>caC	p.Q71H	STK31_ENST00000354639.3_Missense_Mutation_p.Q48H|STK31_ENST00000433467.2_Missense_Mutation_p.Q71H|STK31_ENST00000428484.1_Missense_Mutation_p.Q48H	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	71			Q -> H (in dbSNP:rs6945306). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.			acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TTTGCCCCCAGGCCAGTTCAG	0.358																																					p.Q71H		Atlas-SNP	.											.	STK31	175	.	0			c.G213C						PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN	731,3675	299.8+/-286.0	72,587,1544	65.0	66.0	66.0		144,213,144	3.0	0.9	7	dbSNP_116	66	2492,6108	404.5+/-348.2	368,1756,2176	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	24,24,24	440,2343,3720	CC,CG,GG		28.9767,16.591,24.7809	benign,benign,benign	48/997,71/1020,48/997	23757162	3223,9783	2203	4300	6503	SO:0001583	missense	56164	exon4			CCCCCAGGCCAGT	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.213G>C	7.37:g.23757162G>C	ENSP00000348132:p.Gln71His	Somatic	262	2	0.00763359		WXS	Illumina HiSeq	Phase_I	267	266	0.996255	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	552|552	0.25274725274725274|0.25274725274725274	66|66	0.13414634146341464|0.13414634146341464	66|66	0.18232044198895028|0.18232044198895028	203|203	0.3548951048951049|0.3548951048951049	217|217	0.2862796833773087|0.2862796833773087	G|G	5.213|5.213	0.224817|0.224817	0.09916|0.09916	0.16591|0.16591	0.289767|0.289767	ENSG00000196335|ENSG00000196335	ENST00000422637|ENST00000355870;ENST00000456014;ENST00000433467;ENST00000354639;ENST00000444333;ENST00000428484	.|T;T;T;T;T;T	.|0.09817	.|2.94;2.94;2.94;2.94;2.94;2.94	5.23|5.23	2.95|2.95	0.34219|0.34219	.|Maternal tudor protein (1);	.|0.983616	.|0.08296	.|N	.|0.967629	.|T	.|0.00012	.|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.48087|0.48087	P|P	4.1400000000002546E-4|4.1400000000002546E-4	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.10450	.|0.001;0.005	.|T	.|0.48514	.|-0.9029	.|9	.|0.27785	.|T	.|0.31	.|-0.6565	6.0676|6.0676	0.19871|0.19871	0.1394:0.0:0.4391:0.4215|0.1394:0.0:0.4391:0.4215	rs6945306;rs11558824;rs17854998;rs52815535;rs6945306|rs6945306;rs11558824;rs17854998;rs52815535;rs6945306	.|71;71	.|B4DZ06;Q9BXU1	.|.;STK31_HUMAN	.|H	-1|71;48;71;48;48;48	.|ENSP00000348132:Q71H;ENSP00000389340:Q48H;ENSP00000411852:Q71H;ENSP00000346660:Q48H;ENSP00000398413:Q48H;ENSP00000406146:Q48H	.|ENSP00000346660:Q48H	.|Q	+|+	.|3	.|2	STK31|STK31	23723687|23723687	0.998000|0.998000	0.40836|0.40836	0.888000|0.888000	0.34837|0.34837	0.163000|0.163000	0.22366|0.22366	1.356000|1.356000	0.34079|0.34079	0.838000|0.838000	0.34948|0.34948	-0.518000|-0.518000	0.04402|0.04402	.|CAG	G|0.742;C|0.258	0.258	strong		0.358	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651540	1651540	+	Missense_Mutation	SNP	C	C	G	rs61867581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1651540C>G	ENST00000399676.2	+	1	508	c.470C>G	c.(469-471)tCc>tGc	p.S157C		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	157	8 X 4 AA repeats of C-C-X-P.			S -> C (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		TGCTCCCAGTCCAGCTGCTGC	0.652													g|||	2644	0.527955	0.643	0.4841	5008	,	,		8310	0.4067		0.5527	False		,,,				2504	0.5031				p.S157C		Atlas-SNP	.											KRTAP5-5,NS,carcinoma,-1,1	KRTAP5-5	86	1	0			c.C470G						PASS	.	G	CYS/SER	2763,1633		903,957,338	42.0	59.0	53.0		470	-0.4	0.0	11	dbSNP_129	53	4890,3664		1454,1982,841	no	missense	KRTAP5-5	NM_001001480.2	112	2357,2939,1179	GG,GC,CC		42.8338,37.1474,40.9035	benign	157/238	1651540	7653,5297	2198	4277	6475	SO:0001583	missense	439915	exon1			CCCAGTCCAGCTG	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.470C>G	11.37:g.1651540C>G	ENSP00000382584:p.Ser157Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_001001480	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	1043	0.4775641025641026	274	0.556910569105691	178	0.49171270718232046	224	0.3916083916083916	367	0.4841688654353562	N	0.656	-0.807636	0.02819	0.628526	0.571662	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01159	5.25	3.67	-0.425	0.12317	.	.	.	.	.	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	B	0.12013	0.005	B	0.12837	0.008	T	0.18840	-1.0324	8	0.87932	D	0	.	3.0339	0.06116	0.1324:0.435:0.2945:0.138	rs61867581	157	Q701N2	KRA55_HUMAN	C	157;128	ENSP00000382584:S157C	ENSP00000382584:S157C	S	+	2	0	KRTAP5-5	1608116	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.393000	0.20817	-0.968000	0.03578	-3.669000	0.00025	TCC	C|0.492;G|0.508	0.508	strong		0.652	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
SYNE3	161176	hgsc.bcm.edu	37	14	95906321	95906321	+	Missense_Mutation	SNP	G	G	A	rs9671369	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:95906321G>A	ENST00000334258.5	-	11	2017	c.2003C>T	c.(2002-2004)aCg>aTg	p.T668M	SYNE3_ENST00000557275.1_Missense_Mutation_p.T668M|SYNE3_ENST00000554873.1_Missense_Mutation_p.T425M	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	668			T -> M (in dbSNP:rs9671369). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						CAGCTTTTGCGTGGTCACAAC	0.647													G|||	2066	0.41254	0.1914	0.5562	5008	,	,		16914	0.6399		0.3807	False		,,,				2504	0.408				p.T668M		Atlas-SNP	.											SYNE3_ENST00000334258,NS,carcinoma,0,3	SYNE3	130	3	0			c.C2003T						PASS	.	G	MET/THR	973,3433	363.6+/-316.6	119,735,1349	81.0	84.0	83.0		2003	3.9	0.0	14	dbSNP_119	83	3220,5380	479.3+/-370.1	585,2050,1665	yes	missense	C14orf49	NM_152592.3	81	704,2785,3014	AA,AG,GG		37.4419,22.0835,32.239	probably-damaging	668/976	95906321	4193,8813	2203	4300	6503	SO:0001583	missense	161176	exon11			TTTTGCGTGGTCA	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.2003C>T	14.37:g.95906321G>A	ENSP00000334308:p.Thr668Met	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	944	0.43223443223443225	106	0.21544715447154472	184	0.5082872928176796	364	0.6363636363636364	290	0.38258575197889183	G	15.33	2.802166	0.50315	0.220835	0.374419	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.34072	1.38;1.38;1.38	4.93	3.9	0.45041	.	0.348520	0.20892	N	0.083808	T	0.00012	0.0000	M	0.70595	2.14	0.42751	P	0.006221000000000032	D;D	0.76494	0.999;0.999	P;D	0.65874	0.899;0.939	T	0.47459	-0.9116	9	0.45353	T	0.12	-9.251	10.0543	0.42235	0.0:0.0:0.6125:0.3874	rs9671369;rs56526633;rs59880763;rs9671369	668;668	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	M	668;425;668	ENSP00000334308:T668M;ENSP00000452154:T425M;ENSP00000450562:T668M	ENSP00000334308:T668M	T	-	2	0	C14orf49	94976074	0.040000	0.19996	0.025000	0.17156	0.005000	0.04900	0.891000	0.28309	2.435000	0.82474	0.561000	0.74099	ACG	G|0.638;A|0.362	0.362	strong		0.647	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
C15orf41	84529	hgsc.bcm.edu	37	15	36946303	36946303	+	Missense_Mutation	SNP	C	C	G	rs3784678	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:36946303C>G	ENST00000566621.1	+	4	467	c.217C>G	c.(217-219)Ctg>Gtg	p.L73V	C15orf41_ENST00000569302.1_Missense_Mutation_p.L73V|C15orf41_ENST00000562877.1_5'UTR|RP11-16L14.2_ENST00000565366.1_RNA|C15orf41_ENST00000567389.1_5'UTR|C15orf41_ENST00000437989.2_Missense_Mutation_p.L73V|C15orf41_ENST00000338183.4_5'UTR	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	73			L -> V (in dbSNP:rs3784678).							kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		GTCTAGGTACCTGAATGGAGT	0.448													C|||	2489	0.497005	0.3782	0.3818	5008	,	,		18193	0.6815		0.4423	False		,,,				2504	0.6053				p.L73V		Atlas-SNP	.											.	C15orf41	24	.	0			c.C217G						PASS	.	C	VAL/LEU,	1239,1893		241,757,568	96.0	85.0	89.0		217,	5.5	1.0	15	dbSNP_107	89	3286,3870		758,1770,1050	yes	missense,utr-5	C15orf41	NM_001130010.1,NM_032499.4	32,	999,2527,1618	GG,GC,CC		45.9195,39.5594,43.9833	possibly-damaging,	73/282,	36946303	4525,5763	1566	3578	5144	SO:0001583	missense	84529	exon4			AGGTACCTGAATG	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.217C>G	15.37:g.36946303C>G	ENSP00000455397:p.Leu73Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	163	163	1	NM_001130010	B2RD87	Missense_Mutation	SNP	ENST00000566621.1	37	CCDS45215.1	1078	0.4935897435897436	206	0.4186991869918699	137	0.3784530386740331	380	0.6643356643356644	355	0.4683377308707124	C	15.37	2.813509	0.50527	0.395594	0.459195	ENSG00000186073	ENST00000437989	T	0.47177	0.85	5.5	5.5	0.81552	.	.	.	.	.	T	0.00012	0.0000	L	0.46741	1.465	0.09310	P	1.0	P	0.46512	0.879	P	0.46076	0.503	T	0.47289	-0.9129	8	0.40728	T	0.16	-2.9736	12.8542	0.57876	0.0:0.9263:0.0:0.0737	rs3784678;rs17657081;rs60628223;rs3784678	73	Q9Y2V0	CO041_HUMAN	V	73	ENSP00000401362:L73V	ENSP00000401362:L73V	L	+	1	2	C15orf41	34733595	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.645000	0.54389	2.854000	0.98071	0.655000	0.94253	CTG	C|0.492;G|0.508	0.508	strong		0.448	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499	
HR	55806	hgsc.bcm.edu	37	8	21978469	21978469	+	Silent	SNP	A	A	G	rs57903149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21978469A>G	ENST00000381418.4	-	11	3850	c.2370T>C	c.(2368-2370)gaT>gaC	p.D790D	HR_ENST00000312841.8_Silent_p.D790D	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	790					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		TGATGCGGTCATCCTGCAGAG	0.672													G|||	570	0.113818	0.3533	0.0562	5008	,	,		16476	0.0149		0.0229	False		,,,				2504	0.0266				p.D790D		Atlas-SNP	.											.	HR	71	.	0			c.T2370C						PASS	.	G	,	1359,3003		216,927,1038	14.0	17.0	16.0		2370,2370	-7.3	0.2	8	dbSNP_129	16	165,8349		2,161,4094	no	coding-synonymous,coding-synonymous	HR	NM_005144.4,NM_018411.4	,	218,1088,5132	GG,GA,AA		1.938,31.1554,11.836	,	790/1190,790/1135	21978469	1524,11352	2181	4257	6438	SO:0001819	synonymous_variant	55806	exon11			GCGGTCATCCTGC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.2370T>C	8.37:g.21978469A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	143	65	0.454545	NM_018411	Q6GS30|Q96H33|Q9NPE1	Silent	SNP	ENST00000381418.4	37	CCDS6022.1																																																																																			A|0.895;G|0.105	0.105	strong		0.672	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
DAD1	1603	hgsc.bcm.edu	37	14	23044004	23044004	+	Silent	SNP	C	C	T	rs386775535|rs1051154	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:23044004C>T	ENST00000250498.4	-	2	452	c.341G>A	c.(340-342)tGa>tAa	p.*114*	DAD1_ENST00000489532.2_5'Flank|DAD1_ENST00000543337.1_Silent_p.*86*|DAD1_ENST00000538631.1_Intron	NM_001344.2	NP_001335.1	P61803	DAD1_HUMAN	defender against cell death 1	0					apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			large_intestine(2)|ovary(2)|prostate(1)	5	all_cancers(95;5.49e-05)			GBM - Glioblastoma multiforme(265;0.0156)		GAGAATGAGTCAGCCAACAAA	0.408													C|||	460	0.091853	0.2731	0.036	5008	,	,		19696	0.001		0.0537	False		,,,				2504	0.0194				p.X114X		Atlas-SNP	.											.	DAD1	8	.	0			c.G341A						PASS	.	C		1007,3399	374.2+/-321.1	101,805,1297	133.0	130.0	131.0		341	5.7	1.0	14	dbSNP_86	131	390,8210	125.0+/-183.6	8,374,3918	no	coding-synonymous	DAD1	NM_001344.2		109,1179,5215	TT,TC,CC		4.5349,22.8552,10.7412		114/114	23044004	1397,11609	2203	4300	6503	SO:0001819	synonymous_variant	1603	exon2			ATGAGTCAGCCAA	AK223129	CCDS9571.1	14q11.2	2013-03-06			ENSG00000129562	ENSG00000129562			2664	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 2 homolog (S. cerevisiae)"", ""oligosaccharyltransferase subunit 2 (non-catalytic)"""	600243					Standard	NM_001344		Approved	OST2	uc001wgl.2	P61803	OTTHUMG00000028685	ENST00000250498.4:c.341G>A	14.37:g.23044004C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	NM_001344	D3DS25|O08552|O70364|P46966|P46968|Q6FGA3|Q96GB7	Silent	SNP	ENST00000250498.4	37	CCDS9571.1																																																																																			C|0.901;T|0.099	0.099	strong		0.408	DAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071617.2	NM_001344	
FERMT1	55612	hgsc.bcm.edu	37	20	6064731	6064731	+	Silent	SNP	C	C	T	rs2232079	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:6064731C>T	ENST00000217289.4	-	13	2462	c.1674G>A	c.(1672-1674)gcG>gcA	p.A558A	FERMT1_ENST00000478194.1_5'UTR|FERMT1_ENST00000536936.1_Silent_p.A301A	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	558	FERM.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)		p.A558A(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						GTGACTGCCACGCCTGGATGA	0.527													C|||	583	0.116414	0.2284	0.072	5008	,	,		17985	0.0704		0.1123	False		,,,				2504	0.0481				p.A558A		Atlas-SNP	.											FERMT1,NS,carcinoma,0,2	FERMT1	106	2	1	Substitution - coding silent(1)	prostate(1)	c.G1674A						PASS	.	C		1085,3321	392.6+/-328.5	148,789,1266	72.0	55.0	61.0		1674	-9.6	0.3	20	dbSNP_98	61	907,7693	203.1+/-246.2	43,821,3436	no	coding-synonymous	FERMT1	NM_017671.4		191,1610,4702	TT,TC,CC		10.5465,24.6255,15.316		558/678	6064731	1992,11014	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon13			CTGCCACGCCTGG	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1674G>A	20.37:g.6064731C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			C|0.861;T|0.139	0.139	strong		0.527	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
GPANK1	7918	hgsc.bcm.edu	37	6	31631907	31631907	+	Silent	SNP	G	G	A	rs928814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31631907G>A	ENST00000375906.1	-	3	1033	c.349C>T	c.(349-351)Ctg>Ttg	p.L117L	GPANK1_ENST00000375900.4_Silent_p.L117L|GPANK1_ENST00000375893.2_Silent_p.L117L|CSNK2B_ENST00000375882.2_5'Flank|GPANK1_ENST00000375896.4_Silent_p.L117L|CSNK2B_ENST00000375866.2_5'Flank|CSNK2B-LY6G5B-1181_ENST00000375880.2_5'Flank|CSNK2B_ENST00000375885.4_5'Flank|Y_RNA_ENST00000364337.1_RNA|GPANK1_ENST00000375895.2_Silent_p.L117L|CSNK2B_ENST00000375865.2_5'Flank	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	117							nucleic acid binding (GO:0003676)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						AGTTCTGGCAGGTCCCCCTCC	0.587													G|||	273	0.0545128	0.1263	0.0692	5008	,	,		16734	0.0179		0.0249	False		,,,				2504	0.0153				p.L117L		Atlas-SNP	.											.	GPANK1	19	.	0			c.C349T						PASS	.	G	,,,,	482,3924	227.8+/-242.9	25,432,1746	89.0	83.0	85.0		349,349,349,349,349	-4.9	0.1	6	dbSNP_86	85	232,8368	95.0+/-156.8	3,226,4071	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPANK1	NM_001199237.1,NM_001199238.1,NM_001199239.1,NM_001199240.1,NM_033177.3	,,,,	28,658,5817	AA,AG,GG		2.6977,10.9396,5.4898	,,,,	117/357,117/357,117/357,117/357,117/357	31631907	714,12292	2203	4300	6503	SO:0001819	synonymous_variant	7918	exon3			CTGGCAGGTCCCC		CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"""Ankyrin repeat domain containing"", ""G patch domain containing"""	13920	protein-coding gene	gene with protein product	"""G patch domain containing 10"", ""ankyrin repeat domain 59"""	142610	"""HLA-B associated transcript 4"""	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.349C>T	6.37:g.31631907G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	149	71	0.47651	NM_001199238	A6NG25|B0UXA2|Q5SQ49	Silent	SNP	ENST00000375906.1	37	CCDS4711.1																																																																																			G|0.935;A|0.065	0.065	strong		0.587	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2	NM_033177	
MICAL2	9645	hgsc.bcm.edu	37	11	12229655	12229655	+	Silent	SNP	T	T	G	rs2279390	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:12229655T>G	ENST00000256194.4	+	5	846	c.558T>G	c.(556-558)gtT>gtG	p.V186V	MICAL2_ENST00000527546.1_Silent_p.V186V|MICAL2_ENST00000342902.5_Silent_p.V186V|MICAL2_ENST00000537344.1_Silent_p.V186V|MICAL2_ENST00000379612.3_Silent_p.V186V|MICAL2_ENST00000527195.1_3'UTR	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	186	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		TCGTGAAGGTTCTAGAGCCTC	0.423													T|||	2012	0.401757	0.4856	0.245	5008	,	,		20845	0.501		0.2584	False		,,,				2504	0.4448				p.V186V		Atlas-SNP	.											.	MICAL2	114	.	0			c.T558G						PASS	.	T		2029,2373	564.5+/-381.5	461,1107,633	185.0	169.0	174.0		558	-0.9	0.7	11	dbSNP_100	174	2028,6560	354.2+/-329.4	230,1568,2496	no	coding-synonymous	MICAL2	NM_014632.2		691,2675,3129	GG,GT,TT		23.6143,46.0927,31.2317		186/1125	12229655	4057,8933	2201	4294	6495	SO:0001819	synonymous_variant	9645	exon5			GAAGGTTCTAGAG	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.558T>G	11.37:g.12229655T>G		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	223	223	1	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																			G|0.341;N|0.000	0.341	strong		0.423	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
SDPR	8436	hgsc.bcm.edu	37	2	192701393	192701393	+	Silent	SNP	A	A	G	rs10167187	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:192701393A>G	ENST00000304141.4	-	2	863	c.534T>C	c.(532-534)ggT>ggC	p.G178G		NM_004657.5	NP_004648.1			serum deprivation response											NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			CTTCCACGGCACCGGAAACGG	0.488													G|||	3174	0.633786	0.5121	0.6686	5008	,	,		17761	0.7609		0.5795	False		,,,				2504	0.6984				p.G178G		Atlas-SNP	.											.	SDPR	67	.	0			c.T534C						PASS	.	G		2229,2177	527.3+/-372.1	578,1073,552	42.0	48.0	46.0		534	2.3	0.0	2	dbSNP_119	46	4996,3602	502.7+/-375.8	1481,2034,784	no	coding-synonymous	SDPR	NM_004657.5		2059,3107,1336	GG,GA,AA		41.8935,49.4099,44.4402		178/426	192701393	7225,5779	2203	4299	6502	SO:0001819	synonymous_variant	8436	exon2			CACGGCACCGGAA	AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"""phosphatidylserine binding protein"""	606728	"""serum deprivation response (phosphatidylserine-binding protein)"", ""serum deprivation response (phosphatidylserine binding protein)"""			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.534T>C	2.37:g.192701393A>G		Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_004657		Silent	SNP	ENST00000304141.4	37	CCDS2313.1																																																																																			A|0.407;G|0.593	0.593	strong		0.488	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657	
CENPJ	55835	hgsc.bcm.edu	37	13	25466955	25466955	+	Silent	SNP	T	T	C	rs3742165	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:25466955T>C	ENST00000381884.4	-	10	3227	c.3042A>G	c.(3040-3042)gaA>gaG	p.E1014E	CENPJ_ENST00000545981.1_Silent_p.E1014E	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	1014					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		ACCATTTGGTTTCCTTTCTTT	0.353													T|||	2424	0.484026	0.2436	0.5836	5008	,	,		17231	0.7024		0.507	False		,,,				2504	0.4898				p.E1014E		Atlas-SNP	.											.	CENPJ	116	.	0			c.A3042G						PASS	.	T		1257,3149	431.8+/-343.0	179,899,1125	166.0	164.0	165.0		3042	4.0	1.0	13	dbSNP_107	165	4620,3980	600.5+/-394.2	1222,2176,902	no	coding-synonymous	CENPJ	NM_018451.3		1401,3075,2027	CC,CT,TT		46.2791,28.5293,45.1868		1014/1339	25466955	5877,7129	2203	4300	6503	SO:0001819	synonymous_variant	55835	exon10			TTTGGTTTCCTTT	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"""centrosomal P4.1-associated protein"""	609279	"""microcephaly, primary autosomal recessive 6"""	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.3042A>G	13.37:g.25466955T>C		Somatic	357	0	0		WXS	Illumina HiSeq	Phase_I	341	335	0.982405	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Silent	SNP	ENST00000381884.4	37	CCDS9310.1	1109	0.5077838827838828	111	0.22560975609756098	200	0.5524861878453039	397	0.6940559440559441	401	0.5290237467018469	T	8.641	0.896043	0.17686	0.285293	0.537209	ENSG00000151849	ENST00000418179	.	.	.	5.22	4.02	0.46733	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.42258	-0.9462	3	.	.	.	.	8.1855	0.31337	0.0:0.1613:0.0:0.8387	rs3742165;rs17480938;rs17845747;rs17858700;rs60581405;rs3742165	.	.	.	D	96	.	.	N	-	1	0	CENPJ	24364955	0.993000	0.37304	1.000000	0.80357	0.928000	0.56348	0.181000	0.16880	2.106000	0.64143	0.454000	0.30748	AAC	T|0.531;C|0.469	0.469	strong		0.353	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451	
IRAK1	3654	hgsc.bcm.edu	37	X	153284483	153284483	+	Silent	SNP	G	G	A	rs1059701	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153284483G>A	ENST00000369980.3	-	4	650	c.483C>T	c.(481-483)gtC>gtT	p.V161V	IRAK1_ENST00000393682.1_Silent_p.V187V|IRAK1_ENST00000477274.1_5'Flank|IRAK1_ENST00000393687.2_Silent_p.V161V|MIR718_ENST00000390190.2_RNA|IRAK1_ENST00000429936.2_Silent_p.V187V|IRAK1_ENST00000369974.2_Silent_p.V161V	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	161	ProST region.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)	p.V161V(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGGCTTGGGACCAGGCCGA	0.612													G|||	1537	0.407152	0.1808	0.366	3775	,	,		12467	0.1548		0.6213	False		,,,				2504	0.2689				p.V161V		Atlas-SNP	.											.	IRAK1	107	.	1	Substitution - coding silent(1)	stomach(1)	c.C483T						PASS	.	G	,,	1147,2686		161,679,146,792,423	49.0	52.0	51.0		483,483,483	1.1	0.0	X	dbSNP_86	51	5408,1319		1581,754,1492,93,379	no	coding-synonymous,coding-synonymous,coding-synonymous	IRAK1	NM_001025242.1,NM_001025243.1,NM_001569.3	,,	1742,1433,1638,885,802	AA,AG,A,GG,G		19.6076,29.9243,37.9261	,,	161/683,161/634,161/713	153284483	6555,4005	2201	4299	6500	SO:0001819	synonymous_variant	3654	exon4			GCTTGGGACCAGG	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.483C>T	X.37:g.153284483G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	137	86	0.627737	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Silent	SNP	ENST00000369980.3	37	CCDS14740.1																																																																																			0|0.004;T|0.000;G|0.457;A|0.540	0.540	strong		0.612	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3		
PTPRE	5791	hgsc.bcm.edu	37	10	129866449	129866449	+	Silent	SNP	C	C	G	rs7100666	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:129866449C>G	ENST00000254667.3	+	12	1185	c.906C>G	c.(904-906)ccC>ccG	p.P302P	PTPRE_ENST00000430713.2_3'UTR|PTPRE_ENST00000419012.2_Silent_p.P302P|PTPRE_ENST00000306042.5_Silent_p.P244P	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	302	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	CCAGCTGGCCCGACTTCGGAG	0.607													C|||	876	0.17492	0.1528	0.1585	5008	,	,		17460	0.2609		0.0835	False		,,,				2504	0.2219				p.P302P	Colon(52;977 1184 20575 41685)	Atlas-SNP	.											PTPRE_ENST00000306042,NS,carcinoma,0,4	PTPRE	132	4	0			c.C906G						PASS	.	C	,	697,3709	291.5+/-281.6	60,577,1566	56.0	54.0	55.0		906,732	-5.1	1.0	10	dbSNP_116	55	720,7880	174.8+/-225.0	34,652,3614	no	coding-synonymous,coding-synonymous	PTPRE	NM_006504.4,NM_130435.3	,	94,1229,5180	GG,GC,CC		8.3721,15.8193,10.895	,	302/701,244/643	129866449	1417,11589	2203	4300	6503	SO:0001819	synonymous_variant	5791	exon12			CTGGCCCGACTTC	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.906C>G	10.37:g.129866449C>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	114	68	0.596491	NM_006504	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Silent	SNP	ENST00000254667.3	37	CCDS7657.1																																																																																			C|0.880;G|0.120	0.120	strong		0.607	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1		
GPRC5B	51704	hgsc.bcm.edu	37	16	19883991	19883991	+	Silent	SNP	C	C	T	rs146958511	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:19883991C>T	ENST00000300571.2	-	2	368	c.177G>A	c.(175-177)gtG>gtA	p.V59V	GPRC5B_ENST00000537135.1_Silent_p.V85V|GPRC5B_ENST00000569479.1_Silent_p.V59V|GPRC5B_ENST00000535671.1_Silent_p.V59V|GPRC5B_ENST00000569847.1_Silent_p.V59V	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	59					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						CCACCGCCTCCACCACAATGC	0.642													C|||	5	0.000998403	0.0	0.0014	5008	,	,		17723	0.0		0.003	False		,,,				2504	0.001				p.V59V		Atlas-SNP	.											.	GPRC5B	54	.	0			c.G177A						PASS	.	C		7,4387	12.9+/-30.5	0,7,2190	39.0	43.0	42.0		177	5.8	1.0	16	dbSNP_134	42	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous	GPRC5B	NM_016235.1		0,41,6456	TT,TC,CC		0.3953,0.1593,0.3155		59/404	19883991	41,12953	2197	4300	6497	SO:0001819	synonymous_variant	51704	exon2			CGCCTCCACCACA	AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"""GPCR / Class C : Orphans"""	13308	protein-coding gene	gene with protein product		605948	"""G protein-coupled receptor, family C, group 1, member B"", ""G protein-coupled receptor, family C, group 5, member B"""			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.177G>A	16.37:g.19883991C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_016235	D2DFB0|O75205|Q8NBZ8	Silent	SNP	ENST00000300571.2	37	CCDS10581.1																																																																																			C|0.998;T|0.002	0.002	strong		0.642	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1		
DOK6	220164	hgsc.bcm.edu	37	18	67365668	67365668	+	Silent	SNP	A	A	G	rs4426448	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:67365668A>G	ENST00000382713.5	+	5	628	c.438A>G	c.(436-438)acA>acG	p.T146T	DOK6_ENST00000584435.1_3'UTR	NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	146	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.									central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	20		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				TTATGCCTACACCAAACCTGG	0.408													G|||	2429	0.485024	0.4213	0.3501	5008	,	,		20482	0.7331		0.4692	False		,,,				2504	0.4274				p.T146T		Atlas-SNP	.											.	DOK6	56	.	0			c.A438G						PASS	.	G		1966,2440	620.0+/-393.5	426,1114,663	124.0	109.0	114.0		438	-5.9	0.7	18	dbSNP_111	114	4006,4594	598.3+/-393.9	916,2174,1210	no	coding-synonymous	DOK6	NM_152721.5		1342,3288,1873	GG,GA,AA		46.5814,44.621,45.9173		146/332	67365668	5972,7034	2203	4300	6503	SO:0001819	synonymous_variant	220164	exon5			GCCTACACCAAAC	AK057795	CCDS32841.1	18q22.2	2013-01-10	2005-01-18	2005-01-18		ENSG00000206052		"""Pleckstrin homology (PH) domain containing"""	28301	protein-coding gene	gene with protein product		611402	"""docking protein 5-like"""	DOK5L		15286081	Standard	NM_152721		Approved	MGC20785, HsT3226	uc002lkl.3	Q6PKX4		ENST00000382713.5:c.438A>G	18.37:g.67365668A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	139	61	0.438849	NM_152721	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Silent	SNP	ENST00000382713.5	37	CCDS32841.1																																																																																			A|0.522;G|0.478	0.478	strong		0.408	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721	
C17orf97	400566	hgsc.bcm.edu	37	17	263615	263615	+	Silent	SNP	C	C	T	rs71369083|rs71145728|rs75457484	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:263615C>T	ENST00000360127.6	+	2	997	c.981C>T	c.(979-981)ccC>ccT	p.P327P	C17orf97_ENST00000571106.1_Intron|AC108004.3_ENST00000466740.2_RNA	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	357	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.							p.P327P(1)		breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						GCTTCCACCCCGACCCCAAGG	0.706																																					p.P327P		Atlas-SNP	.											C17orf97_ENST00000360127,NS,carcinoma,0,1	C17orf97	76	1	1	Substitution - coding silent(1)	prostate(1)	c.C981T						scavenged	.						15.0	19.0	18.0					17																	263615		2177	4262	6439	SO:0001819	synonymous_variant	400566	exon2			CCACCCCGACCCC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.981C>T	17.37:g.263615C>T		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	206	26	0.126214	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Silent	SNP	ENST00000360127.6	37	CCDS32519.2																																																																																			C|0.960;T|0.040	0.040	strong		0.706	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
MED24	9862	hgsc.bcm.edu	37	17	38179492	38179492	+	Silent	SNP	A	A	G	rs2302777	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:38179492A>G	ENST00000394128.2	-	20	2223	c.2142T>C	c.(2140-2142)atT>atC	p.I714I	MED24_ENST00000394126.1_Silent_p.I739I|MED24_ENST00000394127.2_Silent_p.I701I|MED24_ENST00000501516.3_Silent_p.I733I|MED24_ENST00000356271.3_Silent_p.I701I	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	714					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CCTTGGCAAAAATGTCCGTCA	0.597													G|||	1575	0.314497	0.0537	0.4135	5008	,	,		18077	0.4226		0.3668	False		,,,				2504	0.4315				p.I714I		Atlas-SNP	.											.	MED24	89	.	0			c.T2142C						PASS	.	G	,	462,3944	783.4+/-414.6	20,422,1761	67.0	62.0	64.0		2103,2142	1.1	1.0	17	dbSNP_100	64	3225,5375	649.3+/-400.6	590,2045,1665	no	coding-synonymous,coding-synonymous	MED24	NM_001079518.1,NM_014815.3	,	610,2467,3426	GG,GA,AA		37.5,10.4857,28.3485	,	701/977,714/990	38179492	3687,9319	2203	4300	6503	SO:0001819	synonymous_variant	9862	exon20			GGCAAAAATGTCC	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2142T>C	17.37:g.38179492A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	148	56	0.378378	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1																																																																																			A|0.706;G|0.294	0.294	strong		0.597	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
PARP2	10038	hgsc.bcm.edu	37	14	20824181	20824181	+	Silent	SNP	T	T	C	rs3093930	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20824181T>C	ENST00000250416.5	+	11	1158	c.1131T>C	c.(1129-1131)taT>taC	p.Y377Y	PARP2_ENST00000429687.3_Silent_p.Y364Y|PARP2_ENST00000527915.1_Silent_p.Y377Y	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	377	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		ATGAAAGTTATGAGTTCAAAG	0.418								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					T|||	2557	0.510583	0.2867	0.6225	5008	,	,		20925	0.6002		0.675	False		,,,				2504	0.4724				p.Y377Y		Atlas-SNP	.											.	PARP2	92	.	0			c.T1131C						PASS	.	T	,	1332,2462		232,868,797	150.0	137.0	141.0		1092,1131	2.3	0.4	14	dbSNP_103	141	5527,2693		1864,1799,447	no	coding-synonymous,coding-synonymous	PARP2	NM_001042618.1,NM_005484.3	,	2096,2667,1244	CC,CT,TT		32.7616,35.1081,42.9083	,	364/571,377/584	20824181	6859,5155	1897	4110	6007	SO:0001819	synonymous_variant	10038	exon11			AAGTTATGAGTTC	AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484		"""Poly (ADP-ribose) polymerases"""	272	protein-coding gene	gene with protein product		607725	"""ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2"", ""poly (ADP-ribose) polymerase family, member 2"""	ADPRTL2		10329013, 18353725	Standard	NM_005484		Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000250416.5:c.1131T>C	14.37:g.20824181T>C		Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	172	97	0.563953	NM_005484	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Silent	SNP	ENST00000250416.5	37	CCDS41910.1	1261	0.5773809523809523	145	0.29471544715447157	232	0.6408839779005525	370	0.6468531468531469	514	0.6781002638522428	T	3.016	-0.202879	0.06219	0.351081	0.672384	ENSG00000129484	ENST00000539930	.	.	.	6.03	2.32	0.28847	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999773513	.	.	.	.	.	.	.	.	.	.	.	.	.	0.2828	5.6326	0.17518	0.0:0.1499:0.1438:0.7062	rs3093930;rs17308338;rs57586296;rs3093930	.	.	.	R	54	.	.	X	+	1	0	PARP2	19894021	0.080000	0.21391	0.422000	0.26621	0.835000	0.47333	-0.093000	0.11111	0.150000	0.19136	0.533000	0.62120	TGA	T|0.445;C|0.555	0.555	strong		0.418	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2		
SPEG	10290	hgsc.bcm.edu	37	2	220354108	220354108	+	Missense_Mutation	SNP	A	A	G	rs55760516	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:220354108A>G	ENST00000312358.7	+	36	8500	c.8368A>G	c.(8368-8370)Agg>Ggg	p.R2790G	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2790	Pro-rich.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TGTCACCTCAAGGCCAGCCAG	0.627													G|||	2045	0.408347	0.5333	0.4092	5008	,	,		11102	0.2321		0.334	False		,,,				2504	0.4969				p.R2790G		Atlas-SNP	.											.	SPEG	272	.	0			c.A8368G						PASS	.	G	GLY/ARG	1850,1998		457,936,531	41.0	41.0	41.0		8368	4.3	1.0	2	dbSNP_129	41	2676,5588		426,1824,1882	yes	missense	SPEG	NM_005876.4	125	883,2760,2413	GG,GA,AA		32.3814,48.0769,37.3679	benign	2790/3268	220354108	4526,7586	1924	4132	6056	SO:0001583	missense	10290	exon36			ACCTCAAGGCCAG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.8368A>G	2.37:g.220354108A>G	ENSP00000311684:p.Arg2790Gly	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	798	0.36538461538461536	254	0.516260162601626	155	0.4281767955801105	141	0.2465034965034965	248	0.32717678100263853	G	8.848	0.943804	0.18281	0.480769	0.323814	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.63255	-0.03	4.33	4.33	0.51752	.	0.000000	0.37393	N	0.002120	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999956163	B	0.02656	0.0	B	0.01281	0.0	T	0.42120	-0.9470	9	0.02654	T	1	.	6.8063	0.23779	0.2075:0.0:0.7925:0.0	rs55760516;rs61733895	2790	Q15772	SPEG_HUMAN	G	2790	ENSP00000311684:R2790G	ENSP00000265327:R2790G	R	+	1	2	SPEG	220062352	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.890000	0.39728	1.063000	0.40649	-0.366000	0.07423	AGG	A|0.648;G|0.352	0.352	strong		0.627	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
ZNF860	344787	hgsc.bcm.edu	37	3	32031622	32031622	+	Missense_Mutation	SNP	T	T	C	rs13087612	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:32031622T>C	ENST00000360311.4	+	2	1600	c.1051T>C	c.(1051-1053)Ttc>Ctc	p.F351L		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						TGAAAAGGCTTTCAGGCGTGA	0.398													T|||	2329	0.465056	0.7799	0.3573	5008	,	,		21477	0.4524		0.1968	False		,,,				2504	0.4049				p.F351L		Atlas-SNP	.											ZNF860_ENST00000360311,NS,carcinoma,0,2	ZNF860	96	2	0			c.T1051C						PASS	.	T	LEU/PHE	897,487		298,301,93	48.0	49.0	49.0		1051	0.3	0.0	3	dbSNP_121	49	608,2574		57,494,1040	yes	missense	ZNF860	NM_001137674.2	22	355,795,1133	CC,CT,TT		19.1075,35.1879,32.961	probably-damaging	351/633	32031622	1505,3061	692	1591	2283	SO:0001583	missense	344787	exon2			AAGGCTTTCAGGC	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1051T>C	3.37:g.32031622T>C	ENSP00000373274:p.Phe351Leu	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	262	87	0.332061	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	899	0.4116300366300366	373	0.758130081300813	125	0.3453038674033149	248	0.43356643356643354	153	0.20184696569920843	T	14.79	2.640073	0.47153	0.648121	0.191075	ENSG00000197385	ENST00000360311	T	0.46063	0.88	0.345	0.345	0.16011	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.90977	3.165	0.58432	P	5.999999999950489E-6	D	0.63880	0.993	D	0.68192	0.956	T	0.39683	-0.9602	7	.	.	.	.	4.9959	0.14240	0.0:2.0E-4:0.0:0.9998	rs13087612;rs59979195;rs13087612	351	A6NHJ4	ZN860_HUMAN	L	351	ENSP00000373274:F351L	.	F	+	1	0	ZNF860	32006626	0.979000	0.34478	0.003000	0.11579	0.003000	0.03518	5.394000	0.66285	0.332000	0.23536	0.323000	0.21402	TTC	T|0.621;C|0.379	0.379	strong		0.398	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
EFCAB12	90288	hgsc.bcm.edu	37	3	129140499	129140499	+	Missense_Mutation	SNP	T	T	C	rs3774787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:129140499T>C	ENST00000505956.1	-	2	359	c.197A>G	c.(196-198)gAg>gGg	p.E66G	EFCAB12_ENST00000326085.3_Missense_Mutation_p.E66G	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	66			E -> G (in dbSNP:rs3774787).				calcium ion binding (GO:0005509)										TGTCTGATCCTCCTTGCGAGG	0.567													T|||	758	0.151358	0.1309	0.1239	5008	,	,		19241	0.4603		0.002	False		,,,				2504	0.0337				p.E66G		Atlas-SNP	.											.	.	.	.	0			c.A197G						PASS	.	T	GLY/GLU	397,3507		22,353,1577	60.0	61.0	60.0		197	2.8	0.0	3	dbSNP_107	60	33,8261		1,31,4115	yes	missense	C3orf25	NM_207307.1	98	23,384,5692	CC,CT,TT		0.3979,10.1691,3.5252	probably-damaging	66/573	129140499	430,11768	1952	4147	6099	SO:0001583	missense	90288	exon2			TGATCCTCCTTGC	AK096099	CCDS54638.1	3q21.3	2013-01-10	2012-07-20	2012-07-20	ENSG00000172771	ENSG00000172771		"""EF-hand domain containing"""	28061	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 25"""	C3orf25			Standard	NM_207307		Approved		uc003emg.3	Q6NXP0	OTTHUMG00000159464	ENST00000505956.1:c.197A>G	3.37:g.129140499T>C	ENSP00000420854:p.Glu66Gly	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	111	43	0.387387	NM_207307	Q69YX4	Missense_Mutation	SNP	ENST00000505956.1	37	CCDS54638.1	359	0.16437728937728938	64	0.13008130081300814	40	0.11049723756906077	253	0.4423076923076923	2	0.002638522427440633	T	14.63	2.591628	0.46214	0.101691	0.003979	ENSG00000172771	ENST00000505956;ENST00000326085	T;T	0.16073	2.37;2.37	3.97	2.81	0.32909	.	0.441304	0.19102	N	0.122662	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P	0.40731	0.728	P	0.44359	0.447	T	0.48055	-0.9068	9	0.66056	D	0.02	-12.898	6.0984	0.20033	0.0:0.1156:0.0:0.8844	rs3774787;rs52820508;rs60466249;rs3774787	66	Q6NXP0	CC025_HUMAN	G	66	ENSP00000420854:E66G;ENSP00000324241:E66G	ENSP00000324241:E66G	E	-	2	0	C3orf25	130623189	0.006000	0.16342	0.010000	0.14722	0.005000	0.04900	0.979000	0.29500	0.862000	0.35528	0.533000	0.62120	GAG	T|0.857;C|0.143	0.143	strong		0.567	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	
FRY	10129	hgsc.bcm.edu	37	13	32776603	32776603	+	Silent	SNP	T	T	C	rs2428249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:32776603T>C	ENST00000380250.3	+	31	4453	c.3957T>C	c.(3955-3957)ctT>ctC	p.L1319L		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1319						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GCGTGTCACTTGCCCTCTTGT	0.493													C|||	1732	0.345847	0.4191	0.4409	5008	,	,		15251	0.1657		0.4404	False		,,,				2504	0.2679				p.L1319L		Atlas-SNP	.											.	FRY	312	.	0			c.T3957C						PASS	.	C		1652,2342		357,938,702	82.0	82.0	82.0		3957	-10.8	0.0	13	dbSNP_100	82	3426,4904		698,2030,1437	no	coding-synonymous	FRY	NM_023037.2		1055,2968,2139	CC,CT,TT		41.1285,41.362,41.2042		1319/3014	32776603	5078,7246	1997	4165	6162	SO:0001819	synonymous_variant	10129	exon31			GTCACTTGCCCTC	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3957T>C	13.37:g.32776603T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	66	62	0.939394	NM_023037	Q9Y3N6	Silent	SNP	ENST00000380250.3	37	CCDS41875.1																																																																																			T|0.634;C|0.366	0.366	strong		0.493	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
XIAP	331	hgsc.bcm.edu	37	X	123034511	123034511	+	Missense_Mutation	SNP	A	A	C	rs5956583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:123034511A>C	ENST00000371199.3	+	6	1567	c.1268A>C	c.(1267-1269)cAa>cCa	p.Q423P	XIAP_ENST00000355640.3_Missense_Mutation_p.Q423P|XIAP_ENST00000468691.1_3'UTR|XIAP_ENST00000434753.3_Missense_Mutation_p.Q423P	NM_001167.3	NP_001158.2	P98170	XIAP_HUMAN	X-linked inhibitor of apoptosis	423			Q -> P (in dbSNP:rs5956583). {ECO:0000269|PubMed:8654366, ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|copper ion homeostasis (GO:0055070)|inhibition of cysteine-type endopeptidase activity involved in apoptotic process (GO:1990001)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of protein ubiquitination (GO:0031398)|protein ubiquitination (GO:0016567)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)	25						GACAGTATGCAAGATGAGTCA	0.393									X-linked Lymphoproliferative syndrome				A|||	1146	0.303576	0.3722	0.2954	3775	,	,		14242	0.0655		0.2893	False		,,,				2504	0.0941				p.Q423P		Atlas-SNP	.											.	XIAP	56	.	0			c.A1268C						PASS	.	A	PRO/GLN,PRO/GLN	1810,2025		382,778,268,472,303	85.0	79.0	81.0		1268,1268	4.6	0.3	X	dbSNP_114	81	2379,4349		317,1104,641,1007,1231	yes	missense,missense	XIAP	NM_001167.3,NM_001204401.1	76,76	699,1882,909,1479,1534	CC,CA,C,AA,A		35.3597,47.1969,39.6573	benign,benign	423/498,423/498	123034511	4189,6374	2203	4300	6503	SO:0001583	missense	331	exon6	Familial Cancer Database	XLP, Duncan syndrome, Familial Fatal Epstein-Barr Infection, incl. XLP2	GTATGCAAGATGA	U45880	CCDS14606.1	Xq25	2014-09-17	2008-03-04	2008-03-04	ENSG00000101966	ENSG00000101966		"""Baculoviral IAP repeat containing"""	592	protein-coding gene	gene with protein product		300079	"""baculoviral IAP repeat-containing 4"""	API3, BIRC4		8552191, 8654366	Standard	NM_001167		Approved	hILP	uc010nqu.3	P98170	OTTHUMG00000022336	ENST00000371199.3:c.1268A>C	X.37:g.123034511A>C	ENSP00000360242:p.Gln423Pro	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	451	310	0.687361	NM_001204401	D3DTF2|Q9NQ14	Missense_Mutation	SNP	ENST00000371199.3	37	CCDS14606.1	540	0.325497287522604	125	0.32216494845360827	83	0.27483443708609273	24	0.043795620437956206	156	0.24299065420560748	a	6.132	0.392630	0.11638	0.471969	0.353597	ENSG00000101966	ENST00000434753;ENST00000371199;ENST00000355640	T;T;T	0.30448	1.53;1.53;1.53	4.61	4.61	0.57282	.	0.660669	0.14278	N	0.329725	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.42015	-0.9476	9	0.66056	D	0.02	-2.7599	7.8327	0.29353	0.8127:0.0:0.0:0.1873	rs5956583;rs17259511;rs52834392;rs5956583	423	P98170	XIAP_HUMAN	P	423	ENSP00000395230:Q423P;ENSP00000360242:Q423P;ENSP00000347858:Q423P	ENSP00000347858:Q423P	Q	+	2	0	XIAP	122862192	0.367000	0.25023	0.288000	0.24862	0.259000	0.26198	2.079000	0.41577	1.709000	0.51313	0.350000	0.21858	CAA	A|0.624;0|0.022	.	strong		0.393	XIAP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058165.5	NM_001167	
HPCAL4	51440	hgsc.bcm.edu	37	1	40150156	40150156	+	Silent	SNP	G	G	A	rs9662128	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:40150156G>A	ENST00000372844.3	-	2	511	c.120C>T	c.(118-120)agC>agT	p.S40S		NM_001282396.1|NM_001282397.1|NM_016257.2	NP_001269325.1|NP_001269326.1|NP_057341.1	Q9UM19	HPCL4_HUMAN	hippocalcin like 4	40	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				central nervous system development (GO:0007417)|signal transduction (GO:0007165)	intracellular (GO:0005622)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)	p.S40S(1)		breast(1)|central_nervous_system(1)|lung(5)|stomach(1)	8	all_cancers(7;4.65e-13)|Lung NSC(20;2.88e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TGAGGATGCCGCTGGGGCAGT	0.622													G|||	1782	0.355831	0.4811	0.2406	5008	,	,		14737	0.2698		0.3519	False		,,,				2504	0.3609				p.S40S		Atlas-SNP	.											HPCAL4,NS,carcinoma,0,1	HPCAL4	20	1	1	Substitution - coding silent(1)	stomach(1)	c.C120T						PASS	.	G		2018,2388	561.9+/-380.8	482,1054,667	64.0	53.0	57.0		120	1.1	1.0	1	dbSNP_119	57	2855,5745	447.0+/-361.4	460,1935,1905	no	coding-synonymous	HPCAL4	NM_016257.2		942,2989,2572	AA,AG,GG		33.1977,45.8012,37.4673		40/192	40150156	4873,8133	2203	4300	6503	SO:0001819	synonymous_variant	51440	exon2			GATGCCGCTGGGG	AB001105	CCDS441.1, CCDS72761.1	1p34.2	2013-01-10			ENSG00000116983	ENSG00000116983		"""EF-hand domain containing"""	18212	protein-coding gene	gene with protein product						10520747	Standard	NM_016257		Approved	HLP4, DKFZp761G122	uc001cdr.3	Q9UM19	OTTHUMG00000009246	ENST00000372844.3:c.120C>T	1.37:g.40150156G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	118	45	0.381356	NM_016257	B2R5U2|D3DPU1|Q5TG97|Q8N611	Silent	SNP	ENST00000372844.3	37	CCDS441.1																																																																																			G|0.645;A|0.355	0.355	strong		0.622	HPCAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025640.1	NM_016257	
KRT40	125115	hgsc.bcm.edu	37	17	39138712	39138712	+	Silent	SNP	G	G	A	rs4243257	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39138712G>A	ENST00000398486.2	-	5	694	c.534C>T	c.(532-534)taC>taT	p.Y178Y	KRT40_ENST00000377755.4_Silent_p.Y178Y	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	178	Coil 1B.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				GTTCACTCTCGTACCTTTCAC	0.527													G|||	1808	0.361022	0.6861	0.2378	5008	,	,		16176	0.1716		0.2684	False		,,,				2504	0.2996				p.Y178Y		Atlas-SNP	.											.	KRT40	27	.	0			c.C534T						PASS	.	G		2368,1634		717,934,350	75.0	74.0	74.0		534	-3.0	1.0	17	dbSNP_111	74	2305,6065		312,1681,2192	no	coding-synonymous	KRT40	NM_182497.3		1029,2615,2542	AA,AG,GG		27.5388,40.8296,37.7708		178/432	39138712	4673,7699	2001	4185	6186	SO:0001819	synonymous_variant	125115	exon5			ACTCTCGTACCTT	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.534C>T	17.37:g.39138712G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	56	28	0.5	NM_182497	Q6IFU5	Silent	SNP	ENST00000398486.2	37	CCDS42320.1																																																																																			G|0.652;A|0.348	0.348	strong		0.527	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
UBASH3A	53347	hgsc.bcm.edu	37	21	43824123	43824123	+	Silent	SNP	G	G	C	rs2277799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:43824123G>C	ENST00000319294.6	+	1	100	c.69G>C	c.(67-69)tcG>tcC	p.S23S	UBASH3A_ENST00000291535.6_Silent_p.S23S|UBASH3A_ENST00000398367.1_Silent_p.S23S|UBASH3A_ENST00000450356.1_Silent_p.S23S	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	23	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						GCAGCCCCTCGCTCCTGGAGC	0.667													G|||	2002	0.39976	0.4228	0.3415	5008	,	,		14549	0.4593		0.3688	False		,,,				2504	0.3804				p.S23S		Atlas-SNP	.											.	UBASH3A	72	.	0			c.G69C						PASS	.	G	,	1640,2638		357,926,856	19.0	17.0	18.0		69,69	-5.3	0.3	21	dbSNP_100	18	3233,5075		710,1813,1631	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	1067,2739,2487	CC,CG,GG		38.9143,38.3357,38.7176	,	23/624,23/662	43824123	4873,7713	2139	4154	6293	SO:0001819	synonymous_variant	53347	exon1			CCCCTCGCTCCTG	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.69G>C	21.37:g.43824123G>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																			G|0.601;C|0.399	0.399	strong		0.667	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
MAP3K19	80122	hgsc.bcm.edu	37	2	135745129	135745129	+	Missense_Mutation	SNP	G	G	A	rs16831235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:135745129G>A	ENST00000375845.3	-	7	1343	c.1313C>T	c.(1312-1314)aCt>aTt	p.T438I	MAP3K19_ENST00000358371.4_Missense_Mutation_p.T325I|MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.T455I|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000315513.3_5'UTR	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	438			T -> I (in dbSNP:rs16831235).				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										TTTAAGTACAGTACACTCTTC	0.343													G|||	663	0.132388	0.0424	0.2262	5008	,	,		20720	0.122		0.2028	False		,,,				2504	0.1258				p.T438I		Atlas-SNP	.											.	.	.	.	0			c.C1313T						PASS	.	G	,ILE/THR	283,4123	156.3+/-189.4	10,263,1930	100.0	102.0	102.0		,1313	2.1	0.0	2	dbSNP_123	102	1408,7192	270.2+/-288.9	141,1126,3033	yes	intron,missense	YSK4	NM_001018046.1,NM_025052.3	,89	151,1389,4963	AA,AG,GG		16.3721,6.4231,13.0017	,probably-damaging	,438/1329	135745129	1691,11315	2203	4300	6503	SO:0001583	missense	80122	exon7			AGTACAGTACACT	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	26249	protein-coding gene	gene with protein product			"""Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"""	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.1313C>T	2.37:g.135745129G>A	ENSP00000365005:p.Thr438Ile	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	230	114	0.495652	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	330	0.1510989010989011	21	0.042682926829268296	77	0.212707182320442	80	0.13986013986013987	152	0.20052770448548812	G	18.74	3.689257	0.68271	0.064231	0.163721	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915	T;T;T	0.70986	-0.53;-0.52;1.84	5.03	2.11	0.27256	.	0.321510	0.22554	N	0.058555	T	0.00073	0.0002	L	0.42245	1.32	0.39130	P	0.03816200000000003	P;P;P	0.51147	0.85;0.942;0.766	B;P;B	0.46110	0.325;0.504;0.174	T	0.04635	-1.0937	9	0.87932	D	0	.	8.4706	0.32982	0.0818:0.3007:0.6175:0.0	rs16831235;rs56486351;rs58384630;rs16831235	325;455;438	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	I	438;325;455	ENSP00000365005:T438I;ENSP00000351140:T325I;ENSP00000376647:T455I	ENSP00000351140:T325I	T	-	2	0	YSK4	135461599	0.671000	0.27521	0.024000	0.17045	0.798000	0.45092	2.295000	0.43576	0.663000	0.31027	0.585000	0.79938	ACT	G|0.865;A|0.135	0.135	strong		0.343	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058968	79058968	+	Silent	SNP	T	T	C	rs112827102	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:79058968T>C	ENST00000388820.4	-	19	3495	c.3285A>G	c.(3283-3285)acA>acG	p.T1095T	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1095					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GTGGTGGGGGTGTCCGGTCCC	0.622													t|||	553	0.110423	0.0477	0.0562	5008	,	,		13778	0.2063		0.0855	False		,,,				2504	0.1605				p.T1095T		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.A3285G						PASS	.	C		153,4213		5,143,2035	16.0	23.0	21.0		3285	-7.3	0.0	15	dbSNP_132	21	545,8023		18,509,3757	no	coding-synonymous	ADAMTS7	NM_014272.3		23,652,5792	CC,CT,TT		6.3609,3.5044,5.3966		1095/1687	79058968	698,12236	2183	4284	6467	SO:0001819	synonymous_variant	11173	exon19			TGGGGGTGTCCGG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3285A>G	15.37:g.79058968T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	106	41	0.386792	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			T|0.935;C|0.065	0.065	strong		0.622	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
TAS2R16	50833	hgsc.bcm.edu	37	7	122634843	122634843	+	Silent	SNP	C	C	T	rs1204014	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:122634843C>T	ENST00000249284.2	-	1	911	c.846G>A	c.(844-846)acG>acA	p.T282T		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	282					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	bitter taste receptor activity (GO:0033038)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TCCTTTTCAACGTAGGGCTGC	0.423													T|||	501	0.10004	0.323	0.0432	5008	,	,		21099	0.0		0.0378	False		,,,				2504	0.0061				p.T282T		Atlas-SNP	.											TAS2R16,right_lower_lobe,carcinoma,-1,2	TAS2R16	57	2	0			c.G846A						scavenged	.	T		1246,3160	700.8+/-406.7	171,904,1128	110.0	113.0	112.0		846	0.5	0.0	7	dbSNP_87	112	367,8233	800.7+/-407.4	11,345,3944	no	coding-synonymous	TAS2R16	NM_016945.2		182,1249,5072	TT,TC,CC		4.2674,28.2796,12.402		282/292	122634843	1613,11393	2203	4300	6503	SO:0001819	synonymous_variant	50833	exon1			TTTCAACGTAGGG	AF227139	CCDS5785.1	7q31.1-q31.3	2012-08-22			ENSG00000128519	ENSG00000128519		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14921	protein-coding gene	gene with protein product		604867				10761934	Standard	NM_016945		Approved	T2R16	uc003vkl.1	Q9NYV7	OTTHUMG00000157090	ENST00000249284.2:c.846G>A	7.37:g.122634843C>T		Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_016945	A4D0X2|Q502V3|Q549U8|Q645W1	Silent	SNP	ENST00000249284.2	37	CCDS5785.1																																																																																			C|0.884;T|0.116	0.116	strong		0.423	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3682242	3682242	+	Silent	SNP	C	C	T	rs45472900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:3682242C>T	ENST00000344754.4	-	6	1274	c.1275G>A	c.(1273-1275)gcG>gcA	p.A425A	SIGLEC1_ENST00000202578.4_Silent_p.A425A	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	425	Ig-like C2-type 4.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CCACAAGTCCCGCCTGGGTCT	0.627													c|||	204	0.0407348	0.0015	0.0288	5008	,	,		19293	0.1012		0.0636	False		,,,				2504	0.0164				p.A425A		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.G1275A						PASS	.	T		62,4344	59.3+/-96.0	1,60,2142	51.0	46.0	48.0		1275	-11.1	0.0	20	dbSNP_127	48	611,7989	159.2+/-212.6	25,561,3714	no	coding-synonymous	SIGLEC1	NM_023068.3		26,621,5856	TT,TC,CC		7.1047,1.4072,5.1745		425/1710	3682242	673,12333	2203	4300	6503	SO:0001819	synonymous_variant	6614	exon6			AAGTCCCGCCTGG	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.1275G>A	20.37:g.3682242C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	140	74	0.528571	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1																																																																																			C|0.947;T|0.053	0.053	strong		0.627	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
OR1S2	219958	hgsc.bcm.edu	37	11	57971201	57971201	+	Silent	SNP	G	G	A	rs11229280	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57971201G>A	ENST00000302592.6	-	1	452	c.453C>T	c.(451-453)gcC>gcT	p.A151A		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	151						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A151A(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				TGCCGAACCTGGCCCGCATGA	0.478													G|||	2575	0.514177	0.2806	0.4971	5008	,	,		22031	0.7927		0.4245	False		,,,				2504	0.6472				p.A151A		Atlas-SNP	.											OR1S2,NS,carcinoma,-2,3	OR1S2	119	3	1	Substitution - coding silent(1)	stomach(1)	c.C453T						scavenged	.	G		1327,3075	446.5+/-348.0	200,927,1074	165.0	156.0	159.0		453	-1.2	0.0	11	dbSNP_120	159	3639,4953	524.0+/-380.4	784,2071,1441	no	coding-synonymous	OR1S2	NM_001004459.1		984,2998,2515	AA,AG,GG		42.3534,30.1454,38.2176		151/326	57971201	4966,8028	2201	4296	6497	SO:0001819	synonymous_variant	219958	exon1			GAACCTGGCCCGC	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.453C>T	11.37:g.57971201G>A		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	254	102	0.401575	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	37	CCDS31545.1																																																																																			G|0.585;A|0.415	0.415	strong		0.478	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
TACSTD2	4070	hgsc.bcm.edu	37	1	59042181	59042181	+	Missense_Mutation	SNP	G	G	T	rs14008	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:59042181G>T	ENST00000371225.2	-	1	985	c.648C>A	c.(646-648)gaC>gaA	p.D216E		NM_002353.2	NP_002344.2	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	216			D -> E (in dbSNP:rs14008). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8382772}.		cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell motility (GO:2000146)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of stem cell differentiation (GO:2000738)|regulation of epithelial cell proliferation (GO:0050678)|ureteric bud morphogenesis (GO:0060675)|visual perception (GO:0007601)	basal plasma membrane (GO:0009925)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)					all_cancers(7;6.54e-05)					CGATATCCACGTCACCGGCGG	0.647													G|||	787	0.157149	0.3449	0.0533	5008	,	,		14915	0.1379		0.0497	False		,,,				2504	0.1074				p.D216E		Atlas-SNP	.											.	TACSTD2	6	.	0			c.C648A						PASS	.	G	GLU/ASP	1358,3034		216,926,1054	14.0	17.0	16.0		648	0.2	1.0	1	dbSNP_52	16	579,8011		27,525,3743	yes	missense	TACSTD2	NM_002353.2	45	243,1451,4797	TT,TG,GG		6.7404,30.9199,14.9207	benign	216/324	59042181	1937,11045	2196	4295	6491	SO:0001583	missense	4070	exon1			ATCCACGTCACCG	X77753	CCDS609.1	1p32	2008-02-05			ENSG00000184292	ENSG00000184292			11530	protein-coding gene	gene with protein product		137290		M1S1		8382772, 11306819	Standard	NM_002353		Approved	TROP2, GA733-1, EGP-1	uc001cyz.4	P09758	OTTHUMG00000010067	ENST00000371225.2:c.648C>A	1.37:g.59042181G>T	ENSP00000360269:p.Asp216Glu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_002353	Q15658|Q6FG48|Q7Z7Q4|Q96QD2	Missense_Mutation	SNP	ENST00000371225.2	37	CCDS609.1	273	0.125	135	0.27439024390243905	19	0.052486187845303865	82	0.14335664335664336	37	0.048812664907651716	G	8.456	0.854221	0.17106	0.309199	0.067404	ENSG00000184292	ENST00000371225	T	0.77489	-1.1	4.64	0.165	0.14995	.	0.406641	0.24611	N	0.037056	T	0.00012	0.0000	N	0.16098	0.37	0.35294	P	0.21758299999999997	B	0.21520	0.057	B	0.17979	0.02	T	0.10086	-1.0645	9	0.31617	T	0.26	-12.9943	5.1262	0.14886	0.3106:0.2655:0.4239:0.0	rs14008;rs232837;rs481082;rs59139961;rs14008	216	P09758	TACD2_HUMAN	E	216	ENSP00000360269:D216E	ENSP00000360269:D216E	D	-	3	2	TACSTD2	58814769	0.969000	0.33509	1.000000	0.80357	0.193000	0.23685	-0.111000	0.10807	0.146000	0.19002	0.561000	0.74099	GAC	G|0.865;T|0.135	0.135	strong		0.647	TACSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027818.1	NM_002353	
PLD2	5338	hgsc.bcm.edu	37	17	4720469	4720469	+	Missense_Mutation	SNP	C	C	T	rs1052748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4720469C>T	ENST00000263088.6	+	17	1861	c.1730C>T	c.(1729-1731)aCa>aTa	p.T577I	PLD2_ENST00000572940.1_Missense_Mutation_p.T577I	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	577	Catalytic.		T -> I (in dbSNP:rs1052748). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9582313}.		cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	AAGACTCCCACATACCCCTAC	0.617													C|||	1251	0.2498	0.1051	0.415	5008	,	,		17674	0.1062		0.4443	False		,,,				2504	0.2761				p.T577I		Atlas-SNP	.											.	PLD2	138	.	0			c.C1730T	GRCh37	CM030489	PLD2	M	rs1052748	PASS	.	C	ILE/THR	735,3671	302.4+/-287.4	67,601,1535	292.0	242.0	259.0		1730	-9.0	0.0	17	dbSNP_86	259	4136,4464	565.5+/-388.5	1006,2124,1170	yes	missense	PLD2	NM_002663.4	89	1073,2725,2705	TT,TC,CC		48.093,16.6818,37.4519	benign	577/934	4720469	4871,8135	2203	4300	6503	SO:0001583	missense	5338	exon17			CTCCCACATACCC	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"""choline phosphatase 2"""	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1730C>T	17.37:g.4720469C>T	ENSP00000263088:p.Thr577Ile	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	164	62	0.378049	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	637	0.2916666666666667	67	0.13617886178861788	158	0.43646408839779005	52	0.09090909090909091	360	0.47493403693931396	C	0.323	-0.960831	0.02249	0.166818	0.48093	ENSG00000129219	ENST00000263088	T	0.21361	2.01	4.48	-8.96	0.00761	.	1.318270	0.04748	N	0.423943	T	0.00012	0.0000	N	0.12961	0.28	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.38993	-0.9635	9	0.22109	T	0.4	3.9285	5.7643	0.18217	0.0887:0.4622:0.0898:0.3593	rs1052748;rs17856479;rs59776031;rs1052748	434;577;577	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	I	577	ENSP00000263088:T577I	ENSP00000263088:T577I	T	+	2	0	PLD2	4667435	0.000000	0.05858	0.000000	0.03702	0.149000	0.21700	-1.345000	0.02637	-2.558000	0.00475	-1.223000	0.01593	ACA	C|0.670;T|0.330	0.330	strong		0.617	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
PFAS	5198	hgsc.bcm.edu	37	17	8166498	8166498	+	Silent	SNP	G	G	A	rs34778863	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:8166498G>A	ENST00000314666.6	+	13	1615	c.1482G>A	c.(1480-1482)aaG>aaA	p.K494K	PFAS_ENST00000545834.1_Silent_p.K70K|PFAS_ENST00000585319.1_3'UTR	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	494					'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	TGGAACAGAAGATGAACCGTG	0.572													G|||	76	0.0151757	0.0076	0.0317	5008	,	,		18258	0.0		0.0398	False		,,,				2504	0.0041				p.K494K		Atlas-SNP	.											.	PFAS	91	.	0			c.G1482A						PASS	.	G		55,4351	54.2+/-90.2	1,53,2149	138.0	137.0	138.0		1482	2.9	1.0	17	dbSNP_126	138	326,8274	114.4+/-174.4	6,314,3980	no	coding-synonymous	PFAS	NM_012393.2		7,367,6129	AA,AG,GG		3.7907,1.2483,2.9294		494/1339	8166498	381,12625	2203	4300	6503	SO:0001819	synonymous_variant	5198	exon13			ACAGAAGATGAAC	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"""FGAR amidotransferase"""	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.1482G>A	17.37:g.8166498G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_012393	A6H8V8	Silent	SNP	ENST00000314666.6	37	CCDS11136.1																																																																																			G|0.973;A|0.027	0.027	strong		0.572	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
ENDOV	284131	hgsc.bcm.edu	37	17	78389478	78389478	+	Missense_Mutation	SNP	G	G	A	rs35549084	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78389478G>A	ENST00000518137.1	+	2	113	c.85G>A	c.(85-87)Gta>Ata	p.V29I	ENDOV_ENST00000518907.1_Intron|ENDOV_ENST00000518901.1_Intron|ENDOV_ENST00000517795.1_Intron|ENDOV_ENST00000520367.1_Missense_Mutation_p.V29I|ENDOV_ENST00000521847.1_3'UTR|CTD-2047H16.4_ENST00000575034.1_RNA|ENDOV_ENST00000517295.2_5'UTR|ENDOV_ENST00000522751.1_5'UTR|ENDOV_ENST00000518644.1_5'UTR|ENDOV_ENST00000323854.5_Missense_Mutation_p.V29I|CTD-2047H16.4_ENST00000573394.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|ENDOV_ENST00000523999.1_Missense_Mutation_p.V29I|ENDOV_ENST00000520284.1_5'UTR	NM_173627.3	NP_775898.2	Q8N8Q3	ENDOV_HUMAN	endonuclease V	29			V -> I (in dbSNP:rs35549084). {ECO:0000269|Ref.2}.		DNA repair (GO:0006281)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|magnesium ion binding (GO:0000287)|single-stranded RNA binding (GO:0003727)|structure-specific DNA binding (GO:0043566)			endometrium(1)|lung(1)|pancreas(1)|prostate(1)	4						GGCCCACGTCGTAGACCGGGA	0.662								Direct reversal of damage					G|||	124	0.0247604	0.0023	0.0216	5008	,	,		15959	0.0		0.0527	False		,,,				2504	0.0542				p.V29I		Atlas-SNP	.											.	ENDOV	26	.	0			c.G85A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	42,4036		0,42,1997	34.0	40.0	38.0		85,85,85	-0.3	0.0	17	dbSNP_126	38	455,7875		7,441,3717	yes	missense,missense,missense	ENDOV	NM_001164637.1,NM_001164638.1,NM_173627.3	29,29,29	7,483,5714	AA,AG,GG		5.4622,1.0299,4.0055	benign,benign,benign	29/238,29/265,29/283	78389478	497,11911	2039	4165	6204	SO:0001583	missense	284131	exon2			CACGTCGTAGACC		CCDS54172.1, CCDS54173.1, CCDS54174.1	17q25.3	2011-05-05			ENSG00000173818	ENSG00000173818			26640	protein-coding gene	gene with protein product						12853604	Standard	NM_001164638		Approved	FLJ35220	uc021ueo.1	Q8N8Q3	OTTHUMG00000164638	ENST00000518137.1:c.85G>A	17.37:g.78389478G>A	ENSP00000429190:p.Val29Ile	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	162	77	0.475309	NM_173627	I3L3S4|Q6P2G2|Q86X99|Q8NAK0	Missense_Mutation	SNP	ENST00000518137.1	37	CCDS54172.1	48	0.02197802197802198	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	37	0.048812664907651716	G	5.336	0.247325	0.10130	0.010299	0.054622	ENSG00000173818	ENST00000518137;ENST00000520367;ENST00000523999;ENST00000323854;ENST00000517295	T;T;T;T	0.41065	2.59;2.09;1.01;2.08	4.62	-0.278	0.12894	.	0.476317	0.19507	U	0.112599	T	0.01905	0.0060	N	0.13098	0.295	0.46131	D	0.99888	B;B;B;P	0.45986	0.163;0.134;0.134;0.87	B;B;B;B	0.35470	0.042;0.025;0.025;0.203	T	0.33033	-0.9884	10	0.07175	T	0.84	0.4039	1.5967	0.02666	0.3765:0.1345:0.3529:0.1362	rs35549084	29;29;29;29	Q8N8Q3;Q8N8Q3-2;Q8N8Q3-3;E5RFW0	ENDOV_HUMAN;.;.;.	I	29;29;29;29;4	ENSP00000429190:V29I;ENSP00000431036:V29I;ENSP00000427921:V29I;ENSP00000317810:V29I	ENSP00000317810:V29I	V	+	1	0	ENDOV	76004073	0.988000	0.35896	0.008000	0.14137	0.132000	0.20833	1.046000	0.30354	0.375000	0.24679	0.585000	0.79938	GTA	G|0.972;A|0.028	0.028	strong		0.662	ENDOV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379487.1	NM_173627	
ABCA2	20	hgsc.bcm.edu	37	9	139916879	139916879	+	Missense_Mutation	SNP	C	C	T	rs34039859	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139916879C>T	ENST00000371605.3	-	5	635	c.488G>A	c.(487-489)cGt>cAt	p.R163H	ABCA2_ENST00000341511.6_Missense_Mutation_p.R164H|ABCA2_ENST00000492260.1_5'UTR|ABCA2_ENST00000265662.5_Missense_Mutation_p.R164H			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	163					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CGTCAGGAAACGCCAGAGCTC	0.642													c|||	160	0.0319489	0.0113	0.062	5008	,	,		15427	0.0		0.0795	False		,,,				2504	0.0225				p.R194H		Atlas-SNP	.											.	ABCA2	113	.	0			c.G581A						PASS	.	C	HIS/ARG,HIS/ARG	92,3976		1,90,1943	33.0	41.0	38.0		491,581	-1.0	0.5	9	dbSNP_126	38	629,7709		21,587,3561	yes	missense,missense	ABCA2	NM_001606.4,NM_212533.2	29,29	22,677,5504	TT,TC,CC		7.5438,2.2616,5.8117	benign,benign	164/2437,194/2467	139916879	721,11685	2034	4169	6203	SO:0001583	missense	20	exon6			AGGAAACGCCAGA	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.488G>A	9.37:g.139916879C>T	ENSP00000360666:p.Arg163His	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	181	93	0.513812	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Missense_Mutation	SNP	ENST00000371605.3	37		74	0.03388278388278388	3	0.006097560975609756	21	0.058011049723756904	0	0.0	50	0.06596306068601583	c	11.15	1.555328	0.27739	0.022616	0.075438	ENSG00000107331	ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	D;D;D	0.86562	-2.14;-2.14;-2.14	4.39	-1.01	0.10169	.	259.577000	0.00424	U	0.000075	T	0.10035	0.0246	N	0.00926	-1.1	0.09310	N	1	B;B;B	0.10296	0.002;0.003;0.001	B;B;B	0.04013	0.0;0.001;0.0	T	0.52411	-0.8579	10	0.45353	T	0.12	.	4.5612	0.12161	0.151:0.4932:0.0:0.3558	rs34039859	163;193;194	Q9BZC7;E7EU84;E7ETC3	ABCA2_HUMAN;.;.	H	164;163;194;164	ENSP00000265662:R164H;ENSP00000360666:R163H;ENSP00000344155:R164H	ENSP00000265662:R164H	R	-	2	0	ABCA2	139036700	0.000000	0.05858	0.528000	0.27938	0.504000	0.33889	-0.347000	0.07750	-0.015000	0.14150	0.486000	0.48141	CGT	C|0.958;T|0.042	0.042	strong		0.642	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	
RGS1	5996	hgsc.bcm.edu	37	1	192544940	192544940	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:192544940C>T	ENST00000367459.3	+	1	84	c.18C>T	c.(16-18)atC>atT	p.I6I	RGS1_ENST00000469578.2_Silent_p.I6I	NM_002922.3	NP_002913.3	Q08116	RGS1_HUMAN	regulator of G-protein signaling 1	6					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|immune response (GO:0006955)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			kidney(8)|large_intestine(1)|lung(13)	22		Breast(1374;0.188)				CAGCAGCCATCTCCACTCCAA	0.438																																					p.I6I		Atlas-SNP	.											RGS1_ENST00000367459,NS,carcinoma,+2,1	RGS1	75	1	0			c.C18T						scavenged	.						86.0	86.0	86.0					1																	192544940		2203	4300	6503	SO:0001819	synonymous_variant	5996	exon1			AGCCATCTCCACT	AF493925	CCDS1375.2	1q31	2008-02-05	2007-08-14		ENSG00000090104	ENSG00000090104		"""Regulators of G-protein signaling"""	9991	protein-coding gene	gene with protein product		600323	"""regulator of G-protein signalling 1"""	IER1		8241276, 8602223	Standard	NM_002922		Approved	1R20, IR20, BL34	uc001gsi.1	Q08116	OTTHUMG00000035598	ENST00000367459.3:c.18C>T	1.37:g.192544940C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	115	3	0.026087	NM_002922	B2RDM9|B4DZY0|Q07918|Q9H1W2	Silent	SNP	ENST00000367459.3	37	CCDS1375.2																																																																																			.	.	none		0.438	RGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086391.1	NM_002922	
USP4	7375	hgsc.bcm.edu	37	3	49343175	49343175	+	Silent	SNP	G	G	A	rs2230929	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49343175G>A	ENST00000265560.4	-	9	1147	c.1101C>T	c.(1099-1101)gaC>gaT	p.D367D	USP4_ENST00000488520.1_5'UTR|USP4_ENST00000351842.4_Silent_p.D320D	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	367	USP.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.D367D(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		CCACATGGGCGTCCCTTCCAG	0.468													G|||	459	0.0916534	0.0651	0.098	5008	,	,		19901	0.0546		0.1968	False		,,,				2504	0.0532				p.D367D		Atlas-SNP	.											USP4,NS,carcinoma,0,1	USP4	72	1	1	Substitution - coding silent(1)	stomach(1)	c.C1101T						PASS	.	G	,	426,3980	207.5+/-228.8	17,392,1794	113.0	99.0	104.0		1101,960	-11.4	0.0	3	dbSNP_98	104	1491,7109	283.7+/-296.3	132,1227,2941	no	coding-synonymous,coding-synonymous	USP4	NM_003363.3,NM_199443.2	,	149,1619,4735	AA,AG,GG		17.3372,9.6686,14.7394	,	367/964,320/917	49343175	1917,11089	2203	4300	6503	SO:0001819	synonymous_variant	7375	exon9			ATGGGCGTCCCTT	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"""Ubiquitin-specific peptidases"""	12627	protein-coding gene	gene with protein product		603486	"""ubiquitin specific protease 4 (proto-oncogene)"""	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.1101C>T	3.37:g.49343175G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	227	119	0.524229	NM_003363	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	37	CCDS2793.1	279	0.12774725274725274	36	0.07317073170731707	50	0.13812154696132597	41	0.07167832167832168	152	0.20052770448548812	G	4.516	0.095814	0.08681	0.096686	0.173372	ENSG00000114316	ENST00000431357	.	.	.	5.92	-11.4	0.00090	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.19775	P	0.9999511744	.	.	.	.	.	.	T	0.30937	-0.9961	3	.	.	.	-12.157	16.2274	0.82306	0.18:0.1428:0.6772:0.0	rs2230929;rs11130188;rs11130188	.	.	.	C	124	.	.	R	-	1	0	USP4	49318179	0.000000	0.05858	0.000000	0.03702	0.717000	0.41224	-0.668000	0.05268	-2.469000	0.00531	-2.040000	0.00418	CGC	G|0.864;C|0.000;A|0.136	0.136	strong		0.468	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443	
CCDC66	285331	hgsc.bcm.edu	37	3	56653427	56653427	+	Missense_Mutation	SNP	T	T	C	rs61747994	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:56653427T>C	ENST00000394672.3	+	16	2577	c.2507T>C	c.(2506-2508)tTa>tCa	p.L836S	CCDC66_ENST00000436465.2_Missense_Mutation_p.L836S|CCDC66_ENST00000326595.7_Missense_Mutation_p.L802S	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	836					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		CAAACAGAATTATCATCTGGG	0.363													T|||	283	0.0565096	0.0726	0.0331	5008	,	,		14972	0.0833		0.0437	False		,,,				2504	0.0368				p.L836S		Atlas-SNP	.											.	CCDC66	145	.	0			c.T2507C						PASS	.	T	SER/LEU,SER/LEU	221,4185	133.7+/-170.0	1,219,1983	95.0	105.0	101.0		2405,2507	-5.0	0.0	3	dbSNP_129	101	425,8175	131.3+/-189.1	15,395,3890	yes	missense,missense	CCDC66	NM_001012506.4,NM_001141947.1	145,145	16,614,5873	CC,CT,TT		4.9419,5.0159,4.9669	benign,benign	802/915,836/949	56653427	646,12360	2203	4300	6503	SO:0001583	missense	285331	exon16			CAGAATTATCATC	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.2507T>C	3.37:g.56653427T>C	ENSP00000378167:p.Leu836Ser	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	233	123	0.527897	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	114	0.0521978021978022	23	0.046747967479674794	11	0.03038674033149171	53	0.09265734265734266	27	0.03562005277044855	T	6.559	0.471492	0.12461	0.050159	0.049419	ENSG00000180376	ENST00000394672;ENST00000326595;ENST00000436465	T;T;T	0.23552	1.9;1.92;1.9	5.23	-5.02	0.02982	.	2.084970	0.02479	N	0.088266	T	0.00695	0.0023	L	0.34521	1.04	0.80722	P	0.0	B	0.11235	0.004	B	0.10450	0.005	T	0.32534	-0.9903	9	0.10111	T	0.7	9.6206	15.0086	0.71533	0.0:0.6819:0.0:0.3181	rs61747994	836	A2RUB6	CCD66_HUMAN	S	836;802;836	ENSP00000378167:L836S;ENSP00000326050:L802S;ENSP00000404320:L836S	ENSP00000326050:L802S	L	+	2	0	CCDC66	56628467	0.000000	0.05858	0.000000	0.03702	0.200000	0.23975	-1.425000	0.02446	-0.659000	0.05359	-0.326000	0.08463	TTA	T|0.952;C|0.048	0.048	strong		0.363	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
DOCK6	57572	hgsc.bcm.edu	37	19	11326125	11326125	+	Silent	SNP	C	C	T	rs2304154	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:11326125C>T	ENST00000294618.7	-	32	4055	c.4044G>A	c.(4042-4044)ccG>ccA	p.P1348P	DOCK6_ENST00000319867.7_Silent_p.P687P|CTC-510F12.2_ENST00000588634.1_RNA	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1348					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GCACATTCTCCGGATTCCCAA	0.562													C|||	2267	0.452676	0.2405	0.4899	5008	,	,		18382	0.5109		0.6272	False		,,,				2504	0.4734				p.P1348P		Atlas-SNP	.											.	DOCK6	104	.	0			c.G4044A						PASS	.	C		1325,2701		216,893,904	50.0	49.0	49.0		4044	3.5	1.0	19	dbSNP_100	49	5203,3141		1612,1979,581	no	coding-synonymous	DOCK6	NM_020812.2		1828,2872,1485	TT,TC,CC		37.6438,32.9111,47.2272		1348/2048	11326125	6528,5842	2013	4172	6185	SO:0001819	synonymous_variant	57572	exon32			ATTCTCCGGATTC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.4044G>A	19.37:g.11326125C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			C|0.497;T|0.503	0.503	strong		0.562	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
STOML2	30968	hgsc.bcm.edu	37	9	35101776	35101776	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35101776G>A	ENST00000356493.5	-	5	437	c.375C>T	c.(373-375)gcC>gcT	p.A125A	STOML2_ENST00000452248.2_Silent_p.A125A|STOML2_ENST00000487490.1_5'Flank	NM_013442.1	NP_038470.1	Q9UJZ1	STML2_HUMAN	stomatin (EPB72)-like 2	125					CD4-positive, alpha-beta T cell activation (GO:0035710)|cellular calcium ion homeostasis (GO:0006874)|interleukin-2 production (GO:0032623)|lipid localization (GO:0010876)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|mitochondrial calcium ion transport (GO:0006851)|mitochondrial protein processing (GO:0034982)|mitochondrion organization (GO:0007005)|positive regulation of cardiolipin metabolic process (GO:1900210)|positive regulation of mitochondrial DNA replication (GO:0090297)|positive regulation of mitochondrial membrane potential (GO:0010918)|protein oligomerization (GO:0051259)|stress-induced mitochondrial fusion (GO:1990046)|T cell receptor signaling pathway (GO:0050852)	cytoskeleton (GO:0005856)|extrinsic component of plasma membrane (GO:0019897)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	cardiolipin binding (GO:1901612)|receptor binding (GO:0005102)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	16			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GCTGGGTGACGGCATACTCAG	0.507																																					p.A125A		Atlas-SNP	.											STOML2,NS,carcinoma,-1,1	STOML2	27	1	0			c.C375T						scavenged	.						149.0	148.0	148.0					9																	35101776		2203	4300	6503	SO:0001819	synonymous_variant	30968	exon5			GGTGACGGCATAC	AF190167	CCDS6577.1, CCDS69588.1, CCDS75830.1	9p13.1	2008-02-05			ENSG00000165283	ENSG00000165283			14559	protein-coding gene	gene with protein product		608292				10713127, 17121834	Standard	NM_001287031		Approved	SLP-2, HSPC108	uc003zwi.3	Q9UJZ1	OTTHUMG00000019851	ENST00000356493.5:c.375C>T	9.37:g.35101776G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	183	2	0.010929	NM_013442	B4E1K7|D3DRN3|O60376|Q53G29|Q96FY2|Q9P042	Silent	SNP	ENST00000356493.5	37	CCDS6577.1																																																																																			.	.	none		0.507	STOML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052273.1	NM_013442	
AKAP13	11214	hgsc.bcm.edu	37	15	86122654	86122654	+	Missense_Mutation	SNP	T	T	C	rs2061821	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:86122654T>C	ENST00000394518.2	+	7	1450	c.1355T>C	c.(1354-1356)aTg>aCg	p.M452T	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.M452T	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	452			M -> T (in dbSNP:rs2061821). {ECO:0000269|Ref.3}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						GACTTGGTCATGGAGCCAGGC	0.507													T|||	2920	0.583067	0.5507	0.6182	5008	,	,		19093	0.5784		0.6153	False		,,,				2504	0.5736				p.M452T	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.T1355C						PASS	.	T	THR/MET,THR/MET	2614,1790	641.9+/-397.6	784,1046,372	63.0	67.0	65.0		1355,1355	-8.7	0.0	15	dbSNP_94	65	5540,3058	661.7+/-401.9	1798,1944,557	yes	missense,missense	AKAP13	NM_006738.4,NM_007200.3	81,81	2582,2990,929	CC,CT,TT		35.5664,40.6449,37.2866	benign,benign	452/2818,452/2814	86122654	8154,4848	2202	4299	6501	SO:0001583	missense	11214	exon7			TGGTCATGGAGCC	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.1355T>C	15.37:g.86122654T>C	ENSP00000378026:p.Met452Thr	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	190	190	1	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	1279	0.5856227106227107	263	0.5345528455284553	221	0.6104972375690608	334	0.583916083916084	461	0.6081794195250659	T	8.395	0.840732	0.16891	0.593551	0.644336	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.07688	3.17;3.19	5.18	-8.74	0.00838	.	.	.	.	.	T	0.00012	0.0000	N	0.17082	0.46	0.58432	P	1.0000000000287557E-6	B;B	0.10296	0.002;0.003	B;B	0.04013	0.001;0.001	T	0.47812	-0.9088	8	0.02654	T	1	.	14.316	0.66452	0.0:0.7177:0.113:0.1693	rs2061821;rs56675185;rs2061821	452;452	Q12802;Q12802-2	AKP13_HUMAN;.	T	452;452;451;451	ENSP00000354718:M452T;ENSP00000378026:M452T	ENSP00000354718:M452T	M	+	2	0	AKAP13	83923658	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.755000	0.04782	-1.276000	0.02414	-0.371000	0.07208	ATG	T|0.388;C|0.612	0.612	strong		0.507	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
SACS	26278	hgsc.bcm.edu	37	13	23929095	23929095	+	Silent	SNP	T	T	C	rs1536365	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:23929095T>C	ENST00000382292.3	-	7	1929	c.1656A>G	c.(1654-1656)ctA>ctG	p.L552L	SACS_ENST00000476776.1_5'Flank|SACS_ENST00000402364.1_5'UTR|SACS_ENST00000382298.3_Silent_p.L552L			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	552					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GCTCGCTGAATAGAGGCTCTA	0.448													T|||	434	0.0866613	0.0068	0.0922	5008	,	,		20446	0.121		0.1302	False		,,,				2504	0.1104				p.L552L		Atlas-SNP	.											.	SACS	871	.	0			c.A1656G						PASS	.	T		103,4303	79.9+/-118.3	2,99,2102	92.0	90.0	91.0		1656	3.0	0.8	13	dbSNP_88	91	1000,7600	214.9+/-254.4	49,902,3349	no	coding-synonymous	SACS	NM_014363.4		51,1001,5451	CC,CT,TT		11.6279,2.3377,8.4807		552/4580	23929095	1103,11903	2203	4300	6503	SO:0001819	synonymous_variant	26278	exon8			GCTGAATAGAGGC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.1656A>G	13.37:g.23929095T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	141	84	0.595745	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2	209	0.09569597069597069	2	0.0040650406504065045	32	0.08839779005524862	74	0.12937062937062938	101	0.13324538258575197	T	6.072	0.381670	0.11524	0.023377	0.116279	ENSG00000151835	ENST00000455470	.	.	.	5.74	2.98	0.34508	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.12243	-1.0555	3	.	.	.	.	1.3758	0.02220	0.237:0.4256:0.1283:0.2092	rs1536365;rs17378673;rs1536365	.	.	.	V	452	.	.	I	-	1	0	SACS	22827095	0.449000	0.25689	0.846000	0.33378	0.721000	0.41392	-0.234000	0.09028	0.451000	0.26802	-1.239000	0.01543	ATT	T|0.909;C|0.091	0.091	strong		0.448	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
TYR	7299	hgsc.bcm.edu	37	11	89017961	89017961	+	Missense_Mutation	SNP	G	G	A	rs1126809	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:89017961G>A	ENST00000263321.5	+	4	1707	c.1205G>A	c.(1204-1206)cGa>cAa	p.R402Q		NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	402			R -> G (in OCA1B).|R -> L (in OCA1A). {ECO:0000269|PubMed:15146472}.|R -> Q (in dbSNP:rs1126809). {ECO:0000269|PubMed:10987646, ECO:0000269|PubMed:15146472, ECO:0000269|PubMed:2342539, ECO:0000269|PubMed:7955413, ECO:0000269|PubMed:9158138}.		cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	CAGTGGCTCCGAAGGCACCGT	0.368													G|||	407	0.08127	0.0091	0.1254	5008	,	,		15773	0.001		0.2525	False		,,,				2504	0.0542				p.R402Q		Atlas-SNP	.											TYR,NS,carcinoma,+1,1	TYR	130	1	0			c.G1205A	GRCh37	CM041478|CM971555	TYR	M	rs1126809	PASS	.	G	GLN/ARG	223,4179	130.2+/-166.9	8,207,1986	60.0	61.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1205	4.7	1.0	11	dbSNP_86	61	2418,6180	399.1+/-346.3	322,1774,2203	yes	missense	TYR	NM_000372.4	43	330,1981,4189	AA,AG,GG		28.1228,5.0659,20.3154	probably-damaging	402/530	89017961	2641,10359	2201	4299	6500	SO:0001583	missense	7299	exon4			GGCTCCGAAGGCA	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.1205G>A	11.37:g.89017961G>A	ENSP00000263321:p.Arg402Gln	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	263	261	0.992395	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	244	0.11172161172161173	5	0.01016260162601626	53	0.1464088397790055	0	0.0	186	0.24538258575197888	G	29.5	5.013726	0.93404	0.050659	0.281228	ENSG00000077498	ENST00000263321	D	0.98234	-4.81	4.68	4.68	0.58851	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.000000	0.85682	D	0.000000	T	0.00440	0.0014	M	0.66378	2.025	0.09310	P	0.999999826736	D	0.76494	0.999	D	0.80764	0.994	T	0.00000	-1.7609	8	.	.	.	.	17.6247	0.88091	0.0:0.0:1.0:0.0	rs62645918	402	P14679	TYRO_HUMAN	Q	402	ENSP00000263321:R402Q	.	R	+	2	0	TYR	88657609	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.499000	0.81566	2.166000	0.68216	0.555000	0.69702	CGA	G|0.831;A|0.169	0.169	strong		0.368	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
KIAA1462	57608	hgsc.bcm.edu	37	10	30317838	30317838	+	Silent	SNP	A	A	G	rs7920686	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:30317838A>G	ENST00000375377.1	-	3	1340	c.1239T>C	c.(1237-1239)ccT>ccC	p.P413P		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	413	Pro-rich.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						AGGCAGTGACAGGTCGGGGAT	0.572													G|||	2621	0.523363	0.8676	0.3833	5008	,	,		18115	0.3413		0.4841	False		,,,				2504	0.3855				p.P413P		Atlas-SNP	.											.	KIAA1462	162	.	0			c.T1239C						PASS	.	G		3211,685		1325,561,62	68.0	73.0	72.0		1239	-5.7	0.0	10	dbSNP_116	72	3924,4336		923,2078,1129	no	coding-synonymous	KIAA1462	NM_020848.2		2248,2639,1191	GG,GA,AA		47.5061,17.5821,41.3047		413/1360	30317838	7135,5021	1948	4130	6078	SO:0001819	synonymous_variant	57608	exon3			AGTGACAGGTCGG	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.1239T>C	10.37:g.30317838A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																			A|0.470;G|0.530	0.530	strong		0.572	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
STON1	11037	hgsc.bcm.edu	37	2	48822381	48822381	+	Silent	SNP	G	G	A	rs2140551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:48822381G>A	ENST00000406226.1	+	5	2343	c.2148G>A	c.(2146-2148)aaG>aaA	p.K716K	STON1_ENST00000309835.3_Silent_p.K716K|STON1-GTF2A1L_ENST00000309827.2_Intron|STON1-GTF2A1L_ENST00000394754.1_Intron|STON1-GTF2A1L_ENST00000405008.1_Intron|STON1-GTF2A1L_ENST00000394751.3_Intron|STON1-GTF2A1L_ENST00000402114.2_Intron|STON1_ENST00000404752.1_Silent_p.K716K	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	716					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AAATAGAAAAGAAGTGGATTA	0.388													G|||	2432	0.485623	0.2814	0.5749	5008	,	,		20052	0.5575		0.5577	False		,,,				2504	0.5501				p.K716K		Atlas-SNP	.											.	STON1	100	.	0			c.G2148A						PASS	.	G	,,,,	1405,3001	457.5+/-351.6	213,979,1011	109.0	101.0	103.0		,,2148,2148,	3.0	1.0	2	dbSNP_96	103	4744,3856	606.3+/-395.1	1316,2112,872	yes	intron,intron,coding-synonymous,coding-synonymous,intron	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	,,,,	1529,3091,1883	AA,AG,GG		44.8372,31.8883,47.2782	,,,,	,,716/736,716/736,	48822381	6149,6857	2203	4300	6503	SO:0001819	synonymous_variant	11037	exon5			AGAAAAGAAGTGG	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.2148G>A	2.37:g.48822381G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																			G|0.518;A|0.482	0.482	strong		0.388	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
TMCO4	255104	hgsc.bcm.edu	37	1	20009737	20009737	+	Silent	SNP	G	G	A	rs10917514	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:20009737G>A	ENST00000294543.6	-	16	1942	c.1701C>T	c.(1699-1701)tcC>tcT	p.S567S	TMCO4_ENST00000489814.1_5'UTR|TMCO4_ENST00000375122.2_Silent_p.S527S|TMCO4_ENST00000375127.1_Intron	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	567						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		AGGTGTCTCCGGATATGGGAC	0.667													G|||	627	0.1252	0.0537	0.111	5008	,	,		16666	0.2113		0.1133	False		,,,				2504	0.1554				p.S567S		Atlas-SNP	.											.	TMCO4	46	.	0			c.C1701T						PASS	.	G		249,4157	145.4+/-180.2	7,235,1961	65.0	69.0	67.0		1701	-6.1	0.0	1	dbSNP_120	67	1129,7471	233.5+/-266.7	79,971,3250	no	coding-synonymous	TMCO4	NM_181719.4		86,1206,5211	AA,AG,GG		13.1279,5.6514,10.5951		567/635	20009737	1378,11628	2203	4300	6503	SO:0001819	synonymous_variant	255104	exon16			GTCTCCGGATATG		CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.1701C>T	1.37:g.20009737G>A		Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	223	105	0.470852	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Silent	SNP	ENST00000294543.6	37	CCDS198.1																																																																																			G|0.888;A|0.112	0.112	strong		0.667	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719	
MUC16	94025	hgsc.bcm.edu	37	19	9070402	9070402	+	Missense_Mutation	SNP	G	G	T	rs12150888	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9070402G>T	ENST00000397910.4	-	3	17247	c.17044C>A	c.(17044-17046)Ccc>Acc	p.P5682T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5684	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTCGTTACGGGCTCTGGGCTT	0.512													g|||	819	0.163538	0.1142	0.2536	5008	,	,		20669	0.0089		0.2634	False		,,,				2504	0.2229				p.P5682T		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+2,3	MUC16	4315	3	0			c.C17044A						PASS	.	A	THR/PRO	518,3486		33,452,1517	145.0	139.0	141.0		17044	-2.5	0.0	19	dbSNP_120	141	2434,5912		372,1690,2111	yes	missense	MUC16	NM_024690.2	38	405,2142,3628	TT,TG,GG		29.1637,12.9371,23.9028	probably-damaging	5682/14508	9070402	2952,9398	2002	4173	6175	SO:0001583	missense	94025	exon3			TTACGGGCTCTGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.17044C>A	19.37:g.9070402G>T	ENSP00000381008:p.Pro5682Thr	Somatic	287	2	0.00696864		WXS	Illumina HiSeq	Phase_I	332	330	0.993976	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	353	0.16163003663003664	53	0.10772357723577236	92	0.2541436464088398	5	0.008741258741258742	203	0.2678100263852243	g	1.261	-0.615735	0.03663	0.129371	0.291637	ENSG00000181143	ENST00000397910	T	0.35048	1.33	1.87	-2.48	0.06423	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	D	0.71674	0.998	P	0.58454	0.839	T	0.08126	-1.0737	7	0.87932	D	0	.	0.9034	0.01279	0.1587:0.2289:0.3795:0.2329	rs12150888;rs52815216;rs12150888	5682	B5ME49	.	T	5682	ENSP00000381008:P5682T	ENSP00000381008:P5682T	P	-	1	0	MUC16	8931402	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.309000	0.01130	-0.422000	0.07405	-1.549000	0.00901	CCC	G|0.815;T|0.185	0.185	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZSWIM4	65249	hgsc.bcm.edu	37	19	13941255	13941255	+	Silent	SNP	G	G	A	rs138305620	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:13941255G>A	ENST00000254323.2	+	13	2550	c.2361G>A	c.(2359-2361)gcG>gcA	p.A787A	ZSWIM4_ENST00000440752.2_Silent_p.A621A	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	787							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			CCTTCGAGGCGGCCTACCAGA	0.706													G|||	2	0.000399361	0.0	0.0	5008	,	,		15823	0.0		0.002	False		,,,				2504	0.0				p.A787A		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.G2361A						PASS	.	G		0,4406		0,0,2203	68.0	70.0	69.0		2361	-8.3	1.0	19	dbSNP_134	69	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	ZSWIM4	NM_023072.2		0,14,6489	AA,AG,GG		0.1628,0.0,0.1076		787/990	13941255	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	65249	exon13			CGAGGCGGCCTAC	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"""Zinc fingers, SWIM-type"""	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.2361G>A	19.37:g.13941255G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	41	25	0.609756	NM_023072		Silent	SNP	ENST00000254323.2	37	CCDS32924.1																																																																																			G|0.999;A|0.001	0.001	strong		0.706	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342	
ZNF418	147686	hgsc.bcm.edu	37	19	58437623	58437623	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58437623A>G	ENST00000396147.1	-	4	2217	c.1926T>C	c.(1924-1926)acT>acC	p.T642T	ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000595830.1_Silent_p.T642T|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599852.1_Silent_p.T557T|ZNF418_ENST00000425570.3_Silent_p.T663T	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	642					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		GCCTTTCTCCAGTGTGTACTC	0.443																																					p.T642T		Atlas-SNP	.											.	ZNF418	76	.	0			c.T1926C						PASS	.						119.0	121.0	120.0					19																	58437623		2202	4300	6502	SO:0001819	synonymous_variant	147686	exon4			TTCTCCAGTGTGT	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1926T>C	19.37:g.58437623A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	89	16	0.179775	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			.	.	none		0.443	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
CELSR1	9620	hgsc.bcm.edu	37	22	46787694	46787694	+	Missense_Mutation	SNP	A	A	G	rs6008794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:46787694A>G	ENST00000262738.3	-	15	5983	c.5984T>C	c.(5983-5985)cTa>cCa	p.L1995P		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1995	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		L -> P (in dbSNP:rs6008794).		anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GTCCTGGGCTAGGAGCTTGTA	0.637													G|||	1377	0.27496	0.7413	0.1398	5008	,	,		16398	0.0129		0.159	False		,,,				2504	0.1299				p.L1995P		Atlas-SNP	.											.	CELSR1	242	.	0			c.T5984C						PASS	.	G	PRO/LEU	2860,1544		955,950,297	26.0	35.0	32.0		5984	3.4	0.7	22	dbSNP_114	32	1210,7390		77,1056,3167	yes	missense	CELSR1	NM_014246.1	98	1032,2006,3464	GG,GA,AA		14.0698,35.059,31.2981	benign	1995/3015	46787694	4070,8934	2202	4300	6502	SO:0001583	missense	9620	exon15			TGGGCTAGGAGCT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5984T>C	22.37:g.46787694A>G	ENSP00000262738:p.Leu1995Pro	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	537	0.24587912087912087	359	0.7296747967479674	53	0.1464088397790055	7	0.012237762237762238	118	0.15567282321899736	G	0.013	-1.617194	0.00828	0.64941	0.140698	ENSG00000075275	ENST00000262738	T	0.68479	-0.33	4.52	3.4	0.38934	.	0.295595	0.27486	N	0.019156	T	0.00012	0.0000	N	0.01454	-0.855	0.24745	P	0.99301956	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.41716	-0.9493	9	0.14656	T	0.56	.	7.2011	0.25881	0.1006:0.0:0.6132:0.2863	rs6008794;rs7290897;rs57574545;rs6008794	316;1995	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	P	1995	ENSP00000262738:L1995P	ENSP00000262738:L1995P	L	-	2	0	CELSR1	45166358	0.995000	0.38212	0.720000	0.30636	0.016000	0.09150	2.771000	0.47670	0.924000	0.37069	-0.355000	0.07637	CTA	A|0.696;G|0.304	0.304	strong		0.637	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
PRSS55	203074	hgsc.bcm.edu	37	8	10390452	10390452	+	Missense_Mutation	SNP	C	C	T	rs4406360	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:10390452C>T	ENST00000328655.3	+	4	675	c.635C>T	c.(634-636)gCg>gTg	p.A212V	PRSS55_ENST00000522210.1_Missense_Mutation_p.A212V|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	212	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		A -> V (in dbSNP:rs4406360). {ECO:0000269|PubMed:12975309}.			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						CTGATGAAAGCGCCAATGGTC	0.478													C|||	1709	0.341254	0.2224	0.3329	5008	,	,		20467	0.4266		0.334	False		,,,				2504	0.4274				p.A212V		Atlas-SNP	.											.	PRSS55	67	.	0			c.C635T						PASS	.	C	VAL/ALA,VAL/ALA	1085,3321	393.3+/-328.8	113,859,1231	115.0	107.0	110.0		635,635	-4.1	0.6	8	dbSNP_111	110	2962,5638	460.7+/-365.2	476,2010,1814	yes	missense,missense	PRSS55	NM_001197020.1,NM_198464.3	64,64	589,2869,3045	TT,TC,CC		34.4419,24.6255,31.1164	benign,benign	212/277,212/353	10390452	4047,8959	2203	4300	6503	SO:0001583	missense	203074	exon4			TGAAAGCGCCAAT	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"""Serine peptidases / Serine peptidases"""	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.635C>T	8.37:g.10390452C>T	ENSP00000333003:p.Ala212Val	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	87	32	0.367816	NM_001197020	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	749	0.34294871794871795	126	0.25609756097560976	128	0.35359116022099446	232	0.40559440559440557	263	0.3469656992084433	C	7.360	0.624582	0.14193	0.246255	0.344419	ENSG00000184647	ENST00000328655;ENST00000522210	D;D	0.92446	-3.04;-3.04	5.27	-4.08	0.03963	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.552989	0.13570	N	0.378158	T	0.00012	0.0000	N	0.05280	-0.08	0.80722	P	0.0	B	0.24651	0.108	B	0.16289	0.015	T	0.14200	-1.0481	9	0.20519	T	0.43	.	7.1514	0.25612	0.0:0.4539:0.1334:0.4127	rs4406360;rs61420274;rs4406360	212	Q6UWB4	PRS55_HUMAN	V	212	ENSP00000333003:A212V;ENSP00000430459:A212V	ENSP00000333003:A212V	A	+	2	0	PRSS55	10427862	0.002000	0.14202	0.642000	0.29436	0.005000	0.04900	-0.579000	0.05834	-0.461000	0.06993	-0.218000	0.12543	GCG	C|0.668;T|0.332	0.332	strong		0.478	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464	
RLN3	117579	hgsc.bcm.edu	37	19	14141666	14141666	+	Missense_Mutation	SNP	G	G	T	rs78161395	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14141666G>T	ENST00000431365.2	+	2	392	c.335G>T	c.(334-336)gGg>gTg	p.G112V	RLN3_ENST00000585987.1_3'UTR|CTB-55O6.4_ENST00000590528.1_RNA|IL27RA_ENST00000263379.2_5'Flank	NM_080864.2	NP_543140.1	Q8WXF3	REL3_HUMAN	relaxin 3	112						extracellular region (GO:0005576)				endometrium(1)|lung(4)	5						GGAACCCCTGGGGTTCTTCGG	0.612													G|||	951	0.189896	0.0469	0.17	5008	,	,		17645	0.2946		0.1511	False		,,,				2504	0.3292				p.G112V		Atlas-SNP	.											.	RLN3	10	.	0			c.G335T						PASS	.	G	VAL/GLY	355,4051	171.2+/-201.5	9,337,1857	44.0	49.0	47.0		335	1.2	0.0	19	dbSNP_131	47	1282,7318	241.0+/-271.5	88,1106,3106	yes	missense	RLN3	NM_080864.2	109	97,1443,4963	TT,TG,GG		14.907,8.0572,12.5865	possibly-damaging	112/143	14141666	1637,11369	2203	4300	6503	SO:0001583	missense	117579	exon2			CCCCTGGGGTTCT	AF447451	CCDS12302.1	19p13.2	2013-02-26	2004-11-15					"""Endogenous ligands"""	17135	protein-coding gene	gene with protein product	"""prorelaxin H3"""	606855	"""relaxin 3 (H3)"""				Standard	NM_080864		Approved	ZINS4, RXN3, H3	uc002mxw.1	Q8WXF3		ENST00000431365.2:c.335G>T	19.37:g.14141666G>T	ENSP00000397415:p.Gly112Val	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_080864	Q6UXW5	Missense_Mutation	SNP	ENST00000431365.2	37	CCDS12302.1	368	0.1684981684981685	23	0.046747967479674794	48	0.13259668508287292	174	0.3041958041958042	123	0.16226912928759896	G	11.28	1.591005	0.28357	0.080572	0.14907	ENSG00000171136	ENST00000431365	T	0.39056	1.1	4.62	1.21	0.21127	Insulin-like (3);	0.908383	0.09740	N	0.761990	T	0.00012	0.0000	L	0.46947	1.48	0.54753	P	1.3000000000040757E-5	B	0.13145	0.007	B	0.16289	0.015	T	0.25467	-1.0131	9	0.45353	T	0.12	-7.3272	6.2509	0.20845	0.1664:0.0:0.6851:0.1485	.	112	Q8WXF3	REL3_HUMAN	V	112	ENSP00000397415:G112V	ENSP00000397415:G112V	G	+	2	0	RLN3	14002666	0.009000	0.17119	0.004000	0.12327	0.003000	0.03518	0.842000	0.27627	0.059000	0.16252	-1.531000	0.00922	GGG	G|0.865;T|0.135	0.135	strong		0.612	RLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458529.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13830749	13830749	+	Silent	SNP	A	A	G	rs368456533		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13830749A>G	ENST00000265104.4	-	36	6122	c.6018T>C	c.(6016-6018)tgT>tgC	p.C2006C		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2006	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCTGGTCTGAACAATTGAAAA	0.473									Kartagener syndrome																												p.C2006C		Atlas-SNP	.											.	DNAH5	868	.	0			c.T6018C						PASS	.	A		0,4406		0,0,2203	129.0	126.0	127.0		6018	1.7	1.0	5		127	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DNAH5	NM_001369.2		0,2,6501	GG,GA,AA		0.0233,0.0,0.0154		2006/4625	13830749	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon36	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GTCTGAACAATTG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.6018T>C	5.37:g.13830749A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	110	59	0.536364	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			.	.	weak		0.473	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
DMTN	2039	hgsc.bcm.edu	37	8	21929924	21929924	+	Missense_Mutation	SNP	A	A	G	rs113027572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21929924A>G	ENST00000523266.1	+	9	1154	c.692A>G	c.(691-693)aAg>aGg	p.K231R	DMTN_ENST00000519907.1_Missense_Mutation_p.K231R|DMTN_ENST00000265800.5_Missense_Mutation_p.K231R|DMTN_ENST00000517600.1_Missense_Mutation_p.K191R|DMTN_ENST00000443491.2_Missense_Mutation_p.K206R|DMTN_ENST00000432128.1_Missense_Mutation_p.K231R|DMTN_ENST00000415253.1_Missense_Mutation_p.K231R|DMTN_ENST00000523782.2_Missense_Mutation_p.K206R|DMTN_ENST00000358242.3_Missense_Mutation_p.K231R|DMTN_ENST00000381470.3_Missense_Mutation_p.K231R	NM_001978.2	NP_001969.2	Q08495	DEMA_HUMAN	dematin actin binding protein	231	Interaction with RASGRF2.				actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|actin filament capping (GO:0051693)|actin filament reorganization (GO:0090527)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cellular response to calcium ion (GO:0071277)|cellular response to cAMP (GO:0071320)|cytoskeleton organization (GO:0007010)|erythrocyte development (GO:0048821)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of platelet aggregation (GO:1901731)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of wound healing (GO:0090303)|protein complex assembly (GO:0006461)|protein secretion by platelet (GO:0070560)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)|regulation of lamellipodium assembly (GO:0010591)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection membrane (GO:0031253)|cortical cytoskeleton (GO:0030863)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|protein self-association (GO:0043621)|receptor binding (GO:0005102)|spectrin binding (GO:0030507)										GAGGAGATGAAGGCTCTCAGG	0.587													A|||	110	0.0219649	0.059	0.0072	5008	,	,		15183	0.004		0.0159	False		,,,				2504	0.0072				p.K231R		Atlas-SNP	.											.	EPB49	35	.	0			c.A692G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	212,4192		2,208,1992	116.0	88.0	98.0		692,692,692,692,617,692	5.2	1.0	8	dbSNP_132	98	111,8485		0,111,4187	yes	missense,missense,missense,missense,missense,missense	EPB49	NM_001114135.2,NM_001114136.1,NM_001114137.1,NM_001114138.1,NM_001114139.1,NM_001978.2	26,26,26,26,26,26	2,319,6179	GG,GA,AA		1.2913,4.8138,2.4846	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	231/406,231/406,231/384,231/384,206/359,231/406	21929924	323,12677	2202	4298	6500	SO:0001583	missense	2039	exon9			AGATGAAGGCTCT	U28389	CCDS6020.1, CCDS47820.1, CCDS47821.1	8p21.1	2013-05-03	2013-05-03	2013-05-03	ENSG00000158856	ENSG00000158856			3382	protein-coding gene	gene with protein product		125305	"""erythrocyte membrane protein band 4.9 (dematin)"""	EPB49		8341682, 12011427	Standard	NM_001978		Approved	DMT		Q08495	OTTHUMG00000097087	ENST00000523266.1:c.692A>G	8.37:g.21929924A>G	ENSP00000427866:p.Lys231Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_001978	A8K0T5|B3KP70|B3KRH3|E9PEJ0|Q13215|Q9BRE3	Missense_Mutation	SNP	ENST00000523266.1	37	CCDS6020.1	28	0.01282051282051282	15	0.03048780487804878	1	0.0027624309392265192	3	0.005244755244755245	9	0.011873350923482849	A	15.94	2.981859	0.53827	0.048138	0.012913	ENSG00000158856	ENST00000381470;ENST00000432128;ENST00000443491;ENST00000517600;ENST00000541895;ENST00000265800;ENST00000381455;ENST00000358242;ENST00000415253;ENST00000523266;ENST00000519907	T;T;T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47	5.15	5.15	0.70609	.	0.449219	0.23865	N	0.043806	T	0.06826	0.0174	N	0.22421	0.69	0.46131	D	0.998882	D;P;D;P;P;P	0.63880	0.982;0.953;0.993;0.919;0.915;0.936	D;P;D;P;P;P	0.70935	0.952;0.551;0.971;0.45;0.468;0.553	T	0.02339	-1.1174	10	0.07325	T	0.83	.	11.6538	0.51306	1.0:0.0:0.0:0.0	.	170;191;231;206;206;231	E9PD40;B4DI75;Q08495;B3KRH3;E9PEJ0;Q08495-2	.;.;DEMA_HUMAN;.;.;.	R	231;231;206;191;191;231;170;231;231;231;231	ENSP00000370879:K231R;ENSP00000416111:K231R;ENSP00000397904:K206R;ENSP00000430618:K191R;ENSP00000265800:K231R;ENSP00000350977:K231R;ENSP00000401291:K231R;ENSP00000427866:K231R;ENSP00000429377:K231R	ENSP00000265800:K231R	K	+	2	0	EPB49	21985870	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.752000	0.47516	2.068000	0.61886	0.460000	0.39030	AAG	A|0.976;C|0.000;G|0.024;T|0.000	0.024	strong		0.587	DMTN-009	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375178.1	NM_001978	
GALNT9	50614	hgsc.bcm.edu	37	12	132862976	132862976	+	Silent	SNP	G	G	A	rs28503969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:132862976G>A	ENST00000328957.8	-	2	278	c.279C>T	c.(277-279)ggC>ggT	p.G93G		NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	93					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		CCTGGCCCAGGCCTCCTGGCC	0.677													G|||	1715	0.342452	0.3411	0.2277	5008	,	,		10324	0.4415		0.3072	False		,,,				2504	0.3599				p.G93G	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.C279T						PASS	.						30.0	31.0	31.0					12																	132862976		692	1591	2283	SO:0001819	synonymous_variant	50614	exon2			GCCCAGGCCTCCT	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.279C>T	12.37:g.132862976G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	37																																																																																				G|0.670;A|0.330	0.330	strong		0.677	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	
HLA-C	3107	hgsc.bcm.edu	37	6	31238909	31238909	+	Missense_Mutation	SNP	G	G	T	rs281860524|rs1050686	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31238909G>T	ENST00000376228.5	-	3	574	c.560C>A	c.(559-561)aCg>aAg	p.T187K	HLA-C_ENST00000383329.3_Missense_Mutation_p.T187K	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	187	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CTCCACGCACGTGCCCTCCAG	0.677													a|||	165	0.0329473	0.0635	0.0288	5008	,	,		13654	0.0109		0.0427	False		,,,				2504	0.0072				p.T187K		Atlas-SNP	.											.	HLA-C	92	.	0			c.C560A						PASS	.																																			SO:0001583	missense	3107	exon3			ACGCACGTGCCCT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.560C>A	6.37:g.31238909G>T	ENSP00000365402:p.Thr187Lys	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	206	52	0.252427	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	1.055|1.055	-0.674656|-0.674656	0.03378|0.03378	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.00730	.|5.77;5.77	2.71|2.71	-5.41|-5.41	0.02648|0.02648	.|MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|792.755000	.|0.00166	.|U	.|0.000007	T|T	0.00241|0.00241	0.0007|0.0007	M|M	0.68728|0.68728	2.09|2.09	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.09022	.|0.002;0.0;0.0;0.0	.|B;B;B;B	.|0.15052	.|0.012;0.01;0.002;0.006	T|T	0.55392|0.55392	-0.8148|-0.8148	5|10	.|0.02654	.|T	.|1	.|.	7.0124|7.0124	0.24869|0.24869	0.2059:0.0819:0.5899:0.1223|0.2059:0.0819:0.5899:0.1223	rs1050686;rs2308596;rs3173175;rs3191026;rs12721962|rs1050686;rs2308596;rs3173175;rs3191026;rs12721962	.|187;187;187;187	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	Q|K	186|187;187;187;224	.|ENSP00000365402:T187K;ENSP00000372819:T187K	.|ENSP00000365402:T187K	H|T	-|-	3|2	2|0	HLA-C|HLA-C	31346888|31346888	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-9.317000|-9.317000	0.00012|0.00012	-5.533000|-5.533000	0.00013|0.00013	-4.896000|-4.896000	0.00002|0.00002	CAC|ACG	T|0.500;G|0.500	0.500	weak		0.677	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
PIEZO2	63895	hgsc.bcm.edu	37	18	10696227	10696227	+	Silent	SNP	C	C	T	rs2277860	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:10696227C>T	ENST00000503781.3	-	43	6695	c.6696G>A	c.(6694-6696)ccG>ccA	p.P2232P	PIEZO2_ENST00000580640.1_Silent_p.P2257P|PIEZO2_ENST00000302079.6_Silent_p.P2232P|PIEZO2_ENST00000285141.4_Silent_p.P87P|PIEZO2_ENST00000538948.1_Silent_p.P189P	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2232					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										TCACCAAAAACGGCCCCGGGA	0.522													C|||	1098	0.219249	0.1967	0.2133	5008	,	,		20401	0.1111		0.3569	False		,,,				2504	0.2239				p.P2232P		Atlas-SNP	.											.	.	.	.	0			c.G6696A						PASS	.	C		1040,3366	381.6+/-324.1	129,782,1292	65.0	65.0	65.0		6696	-11.1	0.0	18	dbSNP_100	65	3132,5468	477.0+/-369.5	602,1928,1770	no	coding-synonymous	PIEZO2	NM_022068.2		731,2710,3062	TT,TC,CC		36.4186,23.6042,32.0775		2232/2753	10696227	4172,8834	2203	4300	6503	SO:0001819	synonymous_variant	63895	exon43			CAAAAACGGCCCC	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"""chromosome 18 open reading frame 30"", ""chromosome 18 open reading frame 58"", ""family with sequence similarity 38, member B"""	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.6696G>A	18.37:g.10696227C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Silent	SNP	ENST00000503781.3	37																																																																																				C|0.712;T|0.288	0.288	strong		0.522	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068	
HLA-C	3107	hgsc.bcm.edu	37	6	31239543	31239543	+	Missense_Mutation	SNP	C	C	T	rs1050428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239543C>T	ENST00000376228.5	-	2	190	c.176G>A	c.(175-177)cGg>cAg	p.R59Q	HLA-C_ENST00000383329.3_Missense_Mutation_p.R59Q	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	59	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GCTGTCGAACCGCACGAACTG	0.677													c|||	452	0.0902556	0.0628	0.1441	5008	,	,		12142	0.1022		0.1133	False		,,,				2504	0.0532				p.R59Q		Atlas-SNP	.											HLA-C_ENST00000383329,colon,carcinoma,-1,2	HLA-C	92	2	0			c.G176A						PASS	.	C	GLN/ARG	236,2786		11,214,1286	41.0	39.0	40.0		176	2.8	1.0	6	dbSNP_131	40	686,4728		49,588,2070	no	missense	HLA-C	NM_002117.5	43	60,802,3356	TT,TC,CC		12.6709,7.8094,10.9294	benign	59/367	31239543	922,7514	1511	2707	4218	SO:0001583	missense	3107	exon2			TCGAACCGCACGA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.176G>A	6.37:g.31239543C>T	ENSP00000365402:p.Arg59Gln	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	250	0.11446886446886446	41	0.08333333333333333	64	0.17679558011049723	56	0.0979020979020979	89	0.11741424802110818	-	11.31	1.602012	0.28534	0.078094	0.126709	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00882	5.58;5.58	2.81	2.81	0.32909	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.899723	0.08941	U	0.871602	T	0.00440	0.0014	.	.	.	0.40544	P	0.018950000000000022	B;B;B;B	0.23128	0.039;0.011;0.039;0.08	B;B;B;B	0.22753	0.025;0.015;0.041;0.034	T	0.40646	-0.9552	8	0.54805	T	0.06	.	9.2778	0.37709	0.0:1.0:0.0:0.0	rs1050428;rs2308550;rs3173346;rs3179179;rs11547345;rs16895965;rs16895968;rs16896547;rs16896549	59;59;59;59	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	Q	59;59;59;96	ENSP00000365402:R59Q;ENSP00000372819:R59Q	ENSP00000365402:R59Q	R	-	2	0	HLA-C	31347522	0.000000	0.05858	1.000000	0.80357	0.326000	0.28443	-0.272000	0.08560	1.886000	0.54624	0.305000	0.20034	CGG	T|0.107;C|0.893	0.107	strong		0.677	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
MUC16	94025	hgsc.bcm.edu	37	19	9090531	9090531	+	Silent	SNP	T	T	C	rs12976721	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9090531T>C	ENST00000397910.4	-	1	1487	c.1284A>G	c.(1282-1284)gaA>gaG	p.E428E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	428	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.E428E(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCCTTCTGTTTCCTTTCCAC	0.502													T|||	1082	0.216054	0.27	0.2248	5008	,	,		21630	0.0228		0.3091	False		,,,				2504	0.2403				p.E428E		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - coding silent(2)	prostate(2)	c.A1284G						PASS	.	T		1019,2945		145,729,1108	152.0	141.0	145.0		1284	-2.8	0.0	19	dbSNP_121	145	2733,5603		459,1815,1894	no	coding-synonymous	MUC16	NM_024690.2		604,2544,3002	CC,CT,TT		32.7855,25.7064,30.5041		428/14508	9090531	3752,8548	1982	4168	6150	SO:0001819	synonymous_variant	94025	exon1			TTCTGTTTCCTTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.1284A>G	19.37:g.9090531T>C		Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	337	334	0.991098	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.772;C|0.228	0.228	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TRPM1	4308	hgsc.bcm.edu	37	15	31330313	31330313	+	Silent	SNP	A	A	G	rs12913672	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:31330313A>G	ENST00000256552.6	-	19	2520	c.2373T>C	c.(2371-2373)taT>taC	p.Y791Y	TRPM1_ENST00000397795.2_Silent_p.Y769Y|RP11-348B17.1_ENST00000561299.1_RNA|RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000542188.1_Silent_p.Y808Y	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		AGAAATCATCATATGTGCGAA	0.388													A|||	914	0.182508	0.2678	0.2219	5008	,	,		18787	0.0079		0.2913	False		,,,				2504	0.1074				p.Y808Y		Atlas-SNP	.											.	TRPM1	183	.	0			c.T2424C						PASS	.	A		919,2787		113,693,1047	97.0	88.0	91.0		2307	-2.7	0.1	15	dbSNP_121	91	2128,6046		278,1572,2237	no	coding-synonymous	TRPM1	NM_002420.4		391,2265,3284	GG,GA,AA		26.0338,24.7976,25.6481		769/1604	31330313	3047,8833	1853	4087	5940	SO:0001819	synonymous_variant	4308	exon18			ATCATCATATGTG	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2373T>C	15.37:g.31330313A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			A|0.799;G|0.201	0.201	strong		0.388	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
KRT81	3887	hgsc.bcm.edu	37	12	52681437	52681437	+	Silent	SNP	A	A	G	rs3187034	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:52681437A>G	ENST00000327741.5	-	6	1037	c.969T>C	c.(967-969)aaT>aaC	p.N323N	KRT86_ENST00000423955.2_Intron|KRT86_ENST00000544024.1_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	323	Coil 2.|Rod.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.N323N(1)		breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		GGTTCAGCTCATTGATCTCCT	0.592													.|||	2106	0.420527	0.5688	0.3761	5008	,	,		19637	0.1577		0.5169	False		,,,				2504	0.4233				p.N323N		Atlas-SNP	.											KRT81,NS,carcinoma,0,1	KRT81	46	1	1	Substitution - coding silent(1)	stomach(1)	c.T969C						PASS	.	G		2534,1872	627.3+/-394.9	771,992,440	101.0	86.0	91.0		969	-2.5	1.0	12	dbSNP_105	91	4375,4221	578.0+/-390.6	1117,2141,1040	no	coding-synonymous	KRT81	NM_002281.3		1888,3133,1480	GG,GA,AA		49.1042,42.4875,46.862		323/506	52681437	6909,6093	2203	4298	6501	SO:0001819	synonymous_variant	3887	exon6			CAGCTCATTGATC	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6458	protein-coding gene	gene with protein product	"""hard keratin type II 1"""	602153	"""keratin, hair, basic, 1"""	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.969T>C	12.37:g.52681437A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	114	42	0.368421	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Silent	SNP	ENST00000327741.5	37	CCDS31805.1																																																																																			A|0.668;G|0.332	0.332	strong		0.592	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281	
REG3A	5068	hgsc.bcm.edu	37	2	79385787	79385787	+	Missense_Mutation	SNP	G	G	A	rs77686105	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:79385787G>A	ENST00000409839.3	-	3	221	c.185C>T	c.(184-186)aCa>aTa	p.T62I	REG3A_ENST00000393878.1_Missense_Mutation_p.T62I|AC011754.1_ENST00000415201.1_RNA|REG3A_ENST00000305165.2_Missense_Mutation_p.T62I	NM_002580.2|NM_138937.2	NP_002571.1|NP_620354.1	Q06141	REG3A_HUMAN	regenerating islet-derived 3 alpha	62	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|cell proliferation (GO:0008283)|heterophilic cell-cell adhesion (GO:0007157)|multicellular organismal development (GO:0007275)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)			breast(2)|large_intestine(4)|lung(41)|prostate(2)|skin(1)	50						ATCTGCATCTGTCCAGGATTT	0.552																																					p.T62I		Atlas-SNP	.											.	REG3A	76	.	0			c.C185T						PASS	.						130.0	118.0	122.0					2																	79385787		2203	4300	6503	SO:0001583	missense	5068	exon2			GCATCTGTCCAGG	S51768	CCDS1965.1	2p12	2008-02-05	2005-02-11	2005-02-11	ENSG00000172016	ENSG00000172016			8601	protein-coding gene	gene with protein product		167805	"""pancreatitis-associated protein"""	PAP		8188210	Standard	NM_002580		Approved	HIP, REG-III, REG3, PBCGF, PAP1	uc002sof.2	Q06141	OTTHUMG00000130017	ENST00000409839.3:c.185C>T	2.37:g.79385787G>A	ENSP00000386630:p.Thr62Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	215	35	0.162791	NM_138938		Missense_Mutation	SNP	ENST00000409839.3	37	CCDS1965.1	.	.	.	.	.	.	.	.	.	.	G	3.884	-0.025360	0.07589	.	.	ENSG00000172016	ENST00000409839;ENST00000393878;ENST00000305165	T;T;T	0.19806	2.12;2.12;2.12	4.02	-4.6	0.03390	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.733660	0.02668	N	0.108266	T	0.11239	0.0274	N	0.17764	0.52	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.16778	-1.0391	10	0.22706	T	0.39	.	3.4681	0.07557	0.425:0.0:0.2967:0.2784	.	62	Q06141	REG3A_HUMAN	I	62	ENSP00000386630:T62I;ENSP00000377456:T62I;ENSP00000304311:T62I	ENSP00000304311:T62I	T	-	2	0	REG3A	79239295	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.065000	0.03458	-0.910000	0.03847	-1.155000	0.01812	ACA	G|0.894;A|0.106	0.106	strong		0.552	REG3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252290.2	NM_002580	
ZNF768	79724	hgsc.bcm.edu	37	16	30536918	30536918	+	Missense_Mutation	SNP	C	C	G	rs10871453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30536918C>G	ENST00000380412.5	-	2	718	c.543G>C	c.(541-543)gaG>gaC	p.E181D	ZNF768_ENST00000562803.1_Missense_Mutation_p.E150D	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	181			E -> D (in dbSNP:rs10871453). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	DNA-directed RNA polymerase II, core complex (GO:0005665)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						GACTCTTTTCCTCGGGGTTCA	0.527													C|||	1342	0.267971	0.4856	0.2695	5008	,	,		16355	0.005		0.3827	False		,,,				2504	0.1258				p.E181D		Atlas-SNP	.											.	ZNF768	28	.	0			c.G543C						PASS	.	C	ASP/GLU	2024,2370	564.0+/-381.3	463,1098,636	108.0	115.0	112.0		543	0.6	0.9	16	dbSNP_120	112	3348,5252	497.9+/-374.6	642,2064,1594	yes	missense	ZNF768	NM_024671.3	45	1105,3162,2230	GG,GC,CC		38.9302,46.0628,41.3422	possibly-damaging	181/541	30536918	5372,7622	2197	4300	6497	SO:0001583	missense	79724	exon2			CTTTTCCTCGGGG	BC013760	CCDS10681.2	16p11.2	2013-01-08			ENSG00000169957	ENSG00000169957		"""Zinc fingers, C2H2-type"""	26273	protein-coding gene	gene with protein product						12477932	Standard	NM_024671		Approved	FLJ23436	uc002dyk.4	Q9H5H4	OTTHUMG00000132392	ENST00000380412.5:c.543G>C	16.37:g.30536918C>G	ENSP00000369777:p.Glu181Asp	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	201	100	0.497512	NM_024671	Q569L7|Q96CX4	Missense_Mutation	SNP	ENST00000380412.5	37	CCDS10681.2	629	0.288003663003663	240	0.4878048780487805	111	0.30662983425414364	1	0.0017482517482517483	277	0.3654353562005277	C	15.47	2.842609	0.51057	0.460628	0.389302	ENSG00000169957	ENST00000380412;ENST00000538507	T	0.07216	3.21	5.06	0.635	0.17723	.	0.000000	0.45867	D	0.000332	T	0.00012	0.0000	N	0.08118	0	0.36384	P	0.13787899999999997	D	0.53885	0.963	P	0.47299	0.543	T	0.36407	-0.9749	9	0.25751	T	0.34	-12.5986	3.7619	0.08607	0.1637:0.4368:0.0:0.3994	rs10871453;rs17845396;rs17858253;rs60711858;rs10871453	181	Q9H5H4	ZN768_HUMAN	D	181;150	ENSP00000369777:E181D	ENSP00000369777:E181D	E	-	3	2	ZNF768	30444419	0.998000	0.40836	0.914000	0.36105	0.628000	0.37860	0.396000	0.20867	-0.007000	0.14345	0.561000	0.74099	GAG	C|0.640;G|0.360	0.360	strong		0.527	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671	
KIAA1468	57614	hgsc.bcm.edu	37	18	59936142	59936142	+	Silent	SNP	C	C	T	rs17645999	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:59936142C>T	ENST00000398130.2	+	20	2953	c.2721C>T	c.(2719-2721)gtC>gtT	p.V907V	KIAA1468_ENST00000256858.6_Silent_p.V907V	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	907										autonomic_ganglia(1)|breast(4)|endometrium(4)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47		Colorectal(73;0.186)				AAGCTACAGTCCCCATTTATG	0.303													C|||	458	0.0914537	0.0061	0.1167	5008	,	,		13536	0.002		0.2674	False		,,,				2504	0.1002				p.V907V		Atlas-SNP	.											.	KIAA1468	93	.	0			c.C2721T						PASS	.	C		213,4193	115.4+/-153.4	3,207,1993	49.0	49.0	49.0		2721	3.0	1.0	18	dbSNP_123	49	2049,6549	329.2+/-318.6	236,1577,2486	no	coding-synonymous	KIAA1468	NM_020854.3		239,1784,4479	TT,TC,CC		23.8311,4.8343,17.3946		907/1217	59936142	2262,10742	2203	4299	6502	SO:0001819	synonymous_variant	57614	exon20			TACAGTCCCCATT	BC011992	CCDS11979.2	18q21.33	2005-11-03			ENSG00000134444	ENSG00000134444			29289	protein-coding gene	gene with protein product						11973628	Standard	NM_020854		Approved	HsT885, HsT3308, FLJ33841	uc002lil.3	Q9P260	OTTHUMG00000132780	ENST00000398130.2:c.2721C>T	18.37:g.59936142C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	173	91	0.526012	NM_020854		Silent	SNP	ENST00000398130.2	37	CCDS11979.2																																																																																			C|0.849;T|0.151	0.151	strong		0.303	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854	
CD109	135228	hgsc.bcm.edu	37	6	74497152	74497152	+	Missense_Mutation	SNP	G	G	A	rs5023688	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:74497152G>A	ENST00000287097.5	+	21	2645	c.2533G>A	c.(2533-2535)Gtc>Atc	p.V845I	CD109_ENST00000437994.2_Missense_Mutation_p.V845I|CD109_ENST00000422508.2_Missense_Mutation_p.V768I			Q6YHK3	CD109_HUMAN	CD109 molecule	845			V -> I (in dbSNP:rs5023688). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14980714, ECO:0000269|PubMed:16754747, ECO:0000269|PubMed:17974005}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTCTGATGCTGTCACCCAGAT	0.403													A|||	1861	0.371605	0.4644	0.4049	5008	,	,		18074	0.4087		0.339	False		,,,				2504	0.2178				p.V845I		Atlas-SNP	.											.	CD109	170	.	0			c.G2533A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	2043,2363	610.5+/-391.6	492,1059,652	94.0	92.0	93.0		2533,2302,2533	-9.1	0.0	6	dbSNP_113	93	3057,5543	660.7+/-401.8	552,1953,1795	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	29,29,29	1044,3012,2447	AA,AG,GG		35.5465,46.3686,39.2127	benign,benign,benign	845/1429,768/1369,845/1446	74497152	5100,7906	2203	4300	6503	SO:0001583	missense	135228	exon21			GATGCTGTCACCC	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2533G>A	6.37:g.74497152G>A	ENSP00000287097:p.Val845Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	878	0.40201465201465203	249	0.5060975609756098	143	0.39502762430939226	239	0.4178321678321678	247	0.3258575197889182	A	0.009	-1.810761	0.00600	0.463686	0.355465	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.30981	1.51;1.78;1.56	5.45	-9.1	0.00714	.	0.845913	0.10991	N	0.611562	T	0.04907	0.0132	N	0.25060	0.705	0.80722	P	0.0	B;B;B	0.15930	0.002;0.015;0.0	B;B;B	0.24269	0.008;0.052;0.007	T	0.28554	-1.0040	9	0.13108	T	0.6	.	11.6482	0.51273	0.525:0.1959:0.2791:0.0	rs5023688;rs52793634;rs58164751;rs5023688	768;845;845	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	I	845;768;845	ENSP00000388062:V845I;ENSP00000404475:V768I;ENSP00000287097:V845I	ENSP00000287097:V845I	V	+	1	0	CD109	74553873	0.000000	0.05858	0.001000	0.08648	0.106000	0.19336	-1.860000	0.01656	-2.465000	0.00533	-2.361000	0.00239	GTC	G|0.598;A|0.402	0.402	strong		0.403	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
C16orf96	342346	hgsc.bcm.edu	37	16	4625938	4625938	+	Missense_Mutation	SNP	A	A	T	rs2450386	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:4625938A>T	ENST00000444310.4	+	5	1457	c.1457A>T	c.(1456-1458)gAt>gTt	p.D486V		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96									p.D486V(1)		NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						ACTCGCAAGGATGGGGTCCCC	0.577													A|||	777	0.155152	0.1301	0.0965	5008	,	,		16929	0.13		0.162	False		,,,				2504	0.2495				p.D486V		Atlas-SNP	.											C16orf96,NS,carcinoma,0,1	C16orf96	28	1	1	Substitution - Missense(1)	endometrium(1)	c.A1457T						PASS	.	A	VAL/ASP	208,1176		14,180,498	80.0	75.0	77.0		1457	-3.3	0.0	16	dbSNP_100	77	515,2667		44,427,1120	yes	missense	C16orf96	NM_001145011.1	152	58,607,1618	TT,TA,AA		16.1848,15.0289,15.8344	benign	486/1142	4625938	723,3843	692	1591	2283	SO:0001583	missense	342346	exon5			GCAAGGATGGGGT		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.1457A>T	16.37:g.4625938A>T	ENSP00000415027:p.Asp486Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	76	29	0.381579	NM_001145011		Missense_Mutation	SNP	ENST00000444310.4	37	CCDS53986.1	292	0.1336996336996337	74	0.15040650406504066	41	0.1132596685082873	60	0.1048951048951049	117	0.15435356200527706	A	5.567	0.289366	0.10513	0.150289	0.161848	ENSG00000205832	ENST00000444310	.	.	.	1.78	-3.3	0.05003	.	.	.	.	.	T	0.00073	0.0002	L	0.27053	0.805	0.31961	P	0.608405	B	0.23540	0.087	B	0.20184	0.028	T	0.25012	-1.0144	7	0.30854	T	0.27	.	0.5877	0.00722	0.4543:0.2008:0.1473:0.1976	rs2450386;rs52832531;rs2450386	486	A6NNT2	CP096_HUMAN	V	486	.	ENSP00000415027:D486V	D	+	2	0	C16orf96	4565939	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	0.330000	0.19715	-0.880000	0.03997	-0.991000	0.02546	GAT	A|0.865;T|0.135	0.135	strong		0.577	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432384.1	NM_001145011	
SLC44A5	204962	hgsc.bcm.edu	37	1	75672376	75672376	+	Silent	SNP	A	A	G	rs1948874	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:75672376A>G	ENST00000370855.5	-	24	2189	c.2076T>C	c.(2074-2076)tcT>tcC	p.S692S	SLC44A5_ENST00000370859.3_Intron|SLC44A5_ENST00000535611.1_Silent_p.S562S	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	692					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						GTTTTTCTGTAGATCCATCAT	0.403													A|||	2207	0.440695	0.177	0.4669	5008	,	,		18568	0.8323		0.3966	False		,,,				2504	0.4202				p.S692S		Atlas-SNP	.											.	SLC44A5	231	.	0			c.T2076C						PASS	.	A	,	913,3493	352.1+/-311.5	97,719,1387	174.0	166.0	168.0		,2076	-0.5	1.0	1	dbSNP_92	168	3247,5353	486.3+/-371.9	619,2009,1672	no	intron,coding-synonymous	SLC44A5	NM_001130058.1,NM_152697.4	,	716,2728,3059	GG,GA,AA		37.7558,20.7217,31.9852	,	,692/720	75672376	4160,8846	2203	4300	6503	SO:0001819	synonymous_variant	204962	exon24			TTCTGTAGATCCA	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"""Solute carriers"""	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.2076T>C	1.37:g.75672376A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	147	82	0.557823	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Silent	SNP	ENST00000370855.5	37	CCDS667.1																																																																																			A|0.619;G|0.381	0.381	strong		0.403	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697	
USP53	54532	hgsc.bcm.edu	37	4	120181724	120181724	+	Silent	SNP	A	A	G	rs35372126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:120181724A>G	ENST00000274030.6	+	11	1917	c.738A>G	c.(736-738)acA>acG	p.T246T	USP53_ENST00000450251.1_Silent_p.T246T	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						AGATTGTTACAATTGGTTTAG	0.353													A|||	1190	0.23762	0.0666	0.3372	5008	,	,		15472	0.2629		0.2724	False		,,,				2504	0.3364				p.T246T		Atlas-SNP	.											.	USP53	69	.	0			c.A738G						PASS	.	A		347,3325		17,313,1506	144.0	132.0	136.0		738	-0.9	1.0	4	dbSNP_126	136	2141,6027		293,1555,2236	no	coding-synonymous	USP53	NM_019050.2		310,1868,3742	GG,GA,AA		26.212,9.4499,21.0135		246/1074	120181724	2488,9352	1836	4084	5920	SO:0001819	synonymous_variant	54532	exon10			TGTTACAATTGGT	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"""Ubiquitin-specific peptidases"""	29255	protein-coding gene	gene with protein product			"""ubiquitin specific protease 53"""			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.738A>G	4.37:g.120181724A>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	180	96	0.533333	NM_019050		Silent	SNP	ENST00000274030.6	37	CCDS43265.1																																																																																			A|0.753;G|0.247	0.247	strong		0.353	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597	
CCDC88C	440193	hgsc.bcm.edu	37	14	91883129	91883129	+	Silent	SNP	G	G	A	rs45437097	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:91883129G>A	ENST00000389857.6	-	2	200	c.114C>T	c.(112-114)taC>taT	p.Y38Y	CCDC88C_ENST00000389856.5_Silent_p.Y30Y|RP11-895M11.3_ENST00000557524.1_lincRNA|CCDC88C_ENST00000553403.1_Silent_p.Y38Y|CCDC88C_ENST00000554165.1_5'UTR	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	38					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				CTAAATCCATGTACATAGTCA	0.488													G|||	540	0.107827	0.056	0.1297	5008	,	,		19364	0.0228		0.2177	False		,,,				2504	0.137				p.Y38Y		Atlas-SNP	.											.	CCDC88C	192	.	0			c.C114T						PASS	.	G		329,3583		13,303,1640	52.0	51.0	51.0		114	-0.0	1.0	14	dbSNP_127	51	1930,6364		240,1450,2457	no	coding-synonymous	CCDC88C	NM_001080414.3		253,1753,4097	AA,AG,GG		23.2698,8.41,18.5073		38/2029	91883129	2259,9947	1956	4147	6103	SO:0001819	synonymous_variant	440193	exon2			ATCCATGTACATA		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.114C>T	14.37:g.91883129G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			G|0.855;A|0.145	0.145	strong		0.488	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
JAG2	3714	hgsc.bcm.edu	37	14	105617042	105617042	+	Missense_Mutation	SNP	C	C	T	rs1057744	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105617042C>T	ENST00000331782.3	-	12	1904	c.1501G>A	c.(1501-1503)Gag>Aag	p.E501K	RP11-44N21.4_ENST00000548203.1_RNA|JAG2_ENST00000347004.2_Missense_Mutation_p.E463K	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	501	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.		E -> K (in dbSNP:rs1057744). {ECO:0000269|PubMed:10079256, ECO:0000269|PubMed:10662552, ECO:0000269|PubMed:9315665}.		auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		CTGGCACACTCGTCTCGTTCC	0.701													C|||	2605	0.520168	0.8238	0.4107	5008	,	,		14114	0.3185		0.5417	False		,,,				2504	0.3732				p.E501K		Atlas-SNP	.											JAG2,NS,carcinoma,0,1	JAG2	69	1	0			c.G1501A						PASS	.	C	LYS/GLU,LYS/GLU	3254,1012		1278,698,157	17.0	15.0	16.0		1501,1387	1.4	0.1	14	dbSNP_86	16	4465,3887		1284,1897,995	yes	missense,missense	JAG2	NM_002226.3,NM_145159.1	56,56	2562,2595,1152	TT,TC,CC		46.5398,23.7225,38.8255	benign,benign	501/1239,463/1201	105617042	7719,4899	2133	4176	6309	SO:0001583	missense	3714	exon12			CACACTCGTCTCG	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.1501G>A	14.37:g.105617042C>T	ENSP00000328169:p.Glu501Lys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	37	CCDS9998.1	1182	0.5412087912087912	397	0.806910569105691	168	0.46408839779005523	196	0.34265734265734266	421	0.5554089709762533	C	10.53	1.376496	0.24857	0.762775	0.534602	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.87412	-2.25;-2.25	3.37	1.36	0.22044	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.823265	0.10860	N	0.626157	T	0.00012	0.0000	M	0.68728	2.09	0.58432	P	9.99999999995449E-6	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.41161	-0.9524	9	0.39692	T	0.17	.	2.7873	0.05377	0.24:0.4941:0.0:0.2659	rs1057744;rs61261226;rs1057744	463;501	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	K	501;463	ENSP00000328169:E501K;ENSP00000328566:E463K	ENSP00000328169:E501K	E	-	1	0	JAG2	104688087	0.000000	0.05858	0.068000	0.19968	0.763000	0.43281	0.056000	0.14256	0.035000	0.15519	0.297000	0.19635	GAG	C|0.423;T|0.577	0.577	strong		0.701	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
HLA-B	3106	hgsc.bcm.edu	37	6	31324549	31324549	+	Missense_Mutation	SNP	T	T	C	rs1050570|rs281864604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31324549T>C	ENST00000412585.2	-	2	287	c.259A>G	c.(259-261)Aac>Gac	p.N87D		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	87	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)	p.N87D(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						ATCTGTGTGTTCCGGTCCCAA	0.662									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	2278	0.454872	0.3676	0.4179	5008	,	,		7135	0.5853		0.3936	False		,,,				2504	0.5276				p.N87D		Atlas-SNP	.											HLA-B,NS,lymphoid_neoplasm,0,2	HLA-B	54	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A259G						PASS	.	C	ASP/ASN	753,3491		200,353,1569	66.0	64.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	259	-6.4	0.0	6	dbSNP_86	65	1610,6680		502,606,3037	no	missense	HLA-B	NM_005514.6	23	702,959,4606	CC,CT,TT		19.421,17.7427,18.8527		87/363	31324549	2363,10171	2122	4145	6267	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	GTGTGTTCCGGTC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.259A>G	6.37:g.31324549T>C	ENSP00000399168:p.Asn87Asp	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	763	0.34935897435897434	121	0.2459349593495935	98	0.27071823204419887	304	0.5314685314685315	240	0.316622691292876	N	4.450	0.083394	0.08533	0.177427	0.19421	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00682	5.86;5.86	3.2	-6.41	0.01938	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.715036	0.10428	U	0.675817	T	0.00754	0.0025	M	0.87758	2.905	0.80722	P	0.0	B;B;B	0.22276	0.014;0.039;0.067	B;B;B	0.40741	0.035;0.083;0.339	T	0.13150	-1.0520	9	0.54805	T	0.06	.	10.2106	0.43138	0.0:0.2081:0.4878:0.3041	rs9266174	87;87;62	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	D	87;98	ENSP00000399168:N87D;ENSP00000405931:N98D	ENSP00000399168:N87D	N	-	1	0	HLA-B	31432528	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.522000	0.00116	-3.541000	0.00144	-3.744000	0.00022	AAC	T|0.668;C|0.332	0.332	strong		0.662	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
YTHDC2	64848	hgsc.bcm.edu	37	5	112929013	112929013	+	Missense_Mutation	SNP	T	T	A	rs1132528	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:112929013T>A	ENST00000161863.4	+	29	4439	c.4226T>A	c.(4225-4227)cTg>cAg	p.L1409Q		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1409	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.		L -> Q (in dbSNP:rs1132528). {ECO:0000269|PubMed:14702039}.		ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		CTAGAACCTCTGGTTGGTGAA	0.353													A|||	2859	0.570887	0.9667	0.5922	5008	,	,		17274	0.3175		0.496	False		,,,				2504	0.3589				p.L1409Q		Atlas-SNP	.											.	YTHDC2	118	.	0			c.T4226A						PASS	.	A	GLN/LEU	3972,432	207.8+/-229.1	1796,380,26	92.0	87.0	89.0		4226	6.0	1.0	5	dbSNP_86	89	4354,4246	573.4+/-389.9	1089,2176,1035	yes	missense	YTHDC2	NM_022828.3	113	2885,2556,1061	AA,AT,TT		49.3721,9.8093,35.9735	benign	1409/1431	112929013	8326,4678	2202	4300	6502	SO:0001583	missense	64848	exon29			AACCTCTGGTTGG	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.4226T>A	5.37:g.112929013T>A	ENSP00000161863:p.Leu1409Gln	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	37	CCDS4113.1	1249	0.5718864468864469	471	0.9573170731707317	201	0.5552486187845304	186	0.32517482517482516	391	0.5158311345646438	A	3.972	-0.008205	0.07773	0.901907	0.506279	ENSG00000047188	ENST00000161863;ENST00000511372	T	0.27720	1.65	5.98	5.98	0.97165	YTH domain (2);	0.131568	0.53938	N	0.000055	T	0.00012	0.0000	N	0.01277	-0.915	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41858	-0.9485	9	0.02654	T	1	.	10.6689	0.45747	0.7445:0.0:0.0:0.2555	rs1132528;rs3178175;rs3193360;rs3763137;rs17332600;rs17417907;rs52803189;rs1132528	1409	Q9H6S0	YTDC2_HUMAN	Q	1409;1319	ENSP00000161863:L1409Q	ENSP00000161863:L1409Q	L	+	2	0	YTHDC2	112956912	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.386000	0.44380	1.087000	0.41251	-0.265000	0.10407	CTG	T|0.393;A|0.607	0.607	strong		0.353	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651550	1651550	+	Silent	SNP	C	C	T	rs61867582	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1651550C>T	ENST00000399676.2	+	1	518	c.480C>T	c.(478-480)tgC>tgT	p.C160C		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	160	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCAGCTGCTGCAAGCCCTGCT	0.647													t|||	2644	0.527955	0.643	0.4841	5008	,	,		9002	0.4067		0.5527	False		,,,				2504	0.5031				p.C160C		Atlas-SNP	.											.	KRTAP5-5	86	.	0			c.C480T						PASS	.	T		2787,1615		901,985,315	51.0	67.0	61.0		480	-3.1	0.0	11	dbSNP_129	61	4935,3653		1454,2027,813	no	coding-synonymous	KRTAP5-5	NM_001001480.2		2355,3012,1128	TT,TC,CC		42.5361,36.6879,40.5543		160/238	1651550	7722,5268	2201	4294	6495	SO:0001819	synonymous_variant	439915	exon1			CTGCTGCAAGCCC	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.480C>T	11.37:g.1651550C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			C|0.478;T|0.522	0.522	strong		0.647	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
MOXD1	26002	hgsc.bcm.edu	37	6	132722527	132722527	+	Silent	SNP	G	G	A	rs77906164	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:132722527G>A	ENST00000367963.3	-	1	157	c.39C>T	c.(37-39)ctC>ctT	p.L13L	MOXD1_ENST00000392401.3_Silent_p.L13L	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	13						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		CCGTCCCGGGGAGCAGCCCCC	0.746													G|||	486	0.0970447	0.034	0.1037	5008	,	,		7906	0.002		0.2097	False		,,,				2504	0.1595				p.L13L		Atlas-SNP	.											.	MOXD1	136	.	0			c.C39T						PASS	.	G		227,3493		9,209,1642	3.0	4.0	4.0		39	1.3	1.0	6	dbSNP_131	4	1403,6167		112,1179,2494	no	coding-synonymous	MOXD1	NM_015529.2		121,1388,4136	AA,AG,GG		18.5337,6.1022,14.4376		13/614	132722527	1630,9660	1860	3785	5645	SO:0001819	synonymous_variant	26002	exon1			CCCGGGGAGCAGC	AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.39C>T	6.37:g.132722527G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_015529	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Silent	SNP	ENST00000367963.3	37	CCDS5152.2																																																																																			G|0.888;A|0.112	0.112	strong		0.746	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529	
CHIA	27159	hgsc.bcm.edu	37	1	111854895	111854895	+	Missense_Mutation	SNP	G	G	A	rs41282494	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111854895G>A	ENST00000369740.1	+	4	242	c.139G>A	c.(139-141)Gac>Aac	p.D47N	CHIA_ENST00000430615.1_Intron|CHIA_ENST00000343320.6_Missense_Mutation_p.D47N|CHIA_ENST00000483391.1_Intron|CHIA_ENST00000451398.2_Intron|CHIA_ENST00000353665.6_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	47			D -> N (increased chitinase activity; when associated with N-47 and M-61; dbSNP:rs41282494). {ECO:0000269|PubMed:19435888}.		apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TGACAACATCGACCCCTGCCT	0.562													G|||	540	0.107827	0.2103	0.0821	5008	,	,		18353	0.0		0.1093	False		,,,				2504	0.0971				p.D47N		Atlas-SNP	.											.	CHIA	115	.	0			c.G139A						PASS	.	G	,ASN/ASP	759,3377		64,631,1373	101.0	101.0	101.0		,139	3.2	0.9	1	dbSNP_127	101	981,7445		50,881,3282	yes	intron,missense	CHIA	NM_021797.2,NM_201653.2	,23	114,1512,4655	AA,AG,GG		11.6425,18.3511,13.8513	,benign	,47/477	111854895	1740,10822	2068	4213	6281	SO:0001583	missense	27159	exon4			AACATCGACCCCT	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.139G>A	1.37:g.111854895G>A	ENSP00000358755:p.Asp47Asn	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	141	60	0.425532	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	226	0.10347985347985347	103	0.20934959349593496	35	0.09668508287292818	0	0.0	88	0.11609498680738786	G	18.14	3.556625	0.65425	0.183511	0.116425	ENSG00000134216	ENST00000369740;ENST00000343320	T;T	0.06528	3.29;3.29	5.08	3.22	0.36961	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.093706	0.39341	N	0.001392	T	0.04407	0.0121	M	0.64630	1.985	0.09310	P	1.0	P	0.51351	0.944	P	0.46110	0.504	T	0.31223	-0.9951	9	0.44086	T	0.13	-19.9434	9.9902	0.41865	0.1669:0.0:0.8331:0.0	rs41282494;rs61752487	47	Q9BZP6	CHIA_HUMAN	N	47	ENSP00000358755:D47N;ENSP00000341828:D47N	ENSP00000341828:D47N	D	+	1	0	CHIA	111656418	1.000000	0.71417	0.910000	0.35882	0.571000	0.35966	4.098000	0.57748	0.662000	0.31006	-0.122000	0.15005	GAC	G|0.881;A|0.119	0.119	strong		0.562	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
COLEC12	81035	hgsc.bcm.edu	37	18	334994	334994	+	Missense_Mutation	SNP	A	A	G	rs2305025	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:334994A>G	ENST00000400256.3	-	6	1771	c.1564T>C	c.(1564-1566)Tcc>Ccc	p.S522P		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	522	Collagen-like 2.		S -> P (in dbSNP:rs2305025). {ECO:0000269|PubMed:11162630, ECO:0000269|PubMed:11564734, ECO:0000269|PubMed:12601552, ECO:0000269|PubMed:12761161, ECO:0000269|PubMed:15489334}.		carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				TCCCCACTGGAGCCCTGAGGG	0.711													G|||	3131	0.6252	0.615	0.572	5008	,	,		13662	0.7907		0.6103	False		,,,				2504	0.5215				p.S522P		Atlas-SNP	.											COLEC12,NS,carcinoma,0,1	COLEC12	121	1	0			c.T1564C						PASS	.	G	PRO/SER	2658,1608		875,908,350	11.0	14.0	13.0		1564	2.8	0.9	18	dbSNP_100	13	5211,3233		1660,1891,671	no	missense	COLEC12	NM_130386.2	74	2535,2799,1021	GG,GA,AA		38.2875,37.6934,38.0881	benign	522/743	334994	7869,4841	2133	4222	6355	SO:0001583	missense	81035	exon6			CACTGGAGCCCTG	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"""Collectins"""	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.1564T>C	18.37:g.334994A>G	ENSP00000383115:p.Ser522Pro	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000400256.3	37	CCDS32782.1	1408	0.6446886446886447	319	0.6483739837398373	195	0.5386740331491713	430	0.7517482517482518	464	0.6121372031662269	G	0.023	-1.404266	0.01165	0.623066	0.617125	ENSG00000158270	ENST00000400256	D	0.86230	-2.09	5.67	2.81	0.32909	.	0.348368	0.34484	N	0.003939	T	0.00012	0.0000	N	0.00078	-2.235	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48258	-0.9051	9	0.18276	T	0.48	-3.8418	7.4255	0.27096	0.1387:0.2564:0.6049:0.0	rs2305025;rs17857497;rs58564592;rs2305025	522	Q5KU26	COL12_HUMAN	P	522	ENSP00000383115:S522P	ENSP00000383115:S522P	S	-	1	0	COLEC12	324994	0.068000	0.21057	0.897000	0.35233	0.548000	0.35241	0.108000	0.15396	0.041000	0.15688	-0.733000	0.03571	TCC	A|0.363;G|0.637	0.637	strong		0.711	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1		
OSGIN1	29948	hgsc.bcm.edu	37	16	83999033	83999033	+	Silent	SNP	A	A	G	rs173776	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:83999033A>G	ENST00000343939.2	+	7	1487	c.1104A>G	c.(1102-1104)tcA>tcG	p.S368S	OSGIN1_ENST00000393306.1_Silent_p.S285S|OSGIN1_ENST00000361711.3_Silent_p.S285S			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	368					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						CCCCGGCCTCAGACCCTGTCC	0.711													G|||	1647	0.328874	0.7421	0.1715	5008	,	,		13678	0.1052		0.1978	False		,,,				2504	0.2474				p.S285S		Atlas-SNP	.											.	OSGIN1	33	.	0			c.A855G						PASS	.	G	,,	2804,1566		932,940,313	21.0	26.0	24.0		1104,855,855	-6.6	0.4	16	dbSNP_79	24	1482,7028		147,1188,2920	no	coding-synonymous,coding-synonymous,coding-synonymous	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	,,	1079,2128,3233	GG,GA,AA		17.4148,35.8352,33.2764	,,	368/561,285/478,285/478	83999033	4286,8594	2185	4255	6440	SO:0001819	synonymous_variant	29948	exon6			GGCCTCAGACCCT	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"""bone marrow stromal cell-derived growth inhibitor"", ""pregnancy induced growth inhibitor"""	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.1104A>G	16.37:g.83999033A>G		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Silent	SNP	ENST00000343939.2	37																																																																																				A|0.701;G|0.299	0.299	strong		0.711	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
NAALADL2	254827	hgsc.bcm.edu	37	3	174814920	174814920	+	Missense_Mutation	SNP	A	A	G	rs9836841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:174814920A>G	ENST00000454872.1	+	2	512	c.384A>G	c.(382-384)atA>atG	p.I128M	NAALADL2-AS3_ENST00000453180.1_RNA|NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	128			I -> M (in dbSNP:rs9836841). {ECO:0000269|PubMed:15168106, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TCTTAAAAATACTTTGCACAG	0.383													A|||	1985	0.396366	0.2912	0.4524	5008	,	,		19667	0.4375		0.4433	False		,,,				2504	0.408				p.I128M		Atlas-SNP	.											.	NAALADL2	86	.	0			c.A384G						PASS	.	A	MET/ILE	1037,2635		157,723,956	102.0	104.0	104.0		384	-1.5	0.1	3	dbSNP_119	104	3684,4500		838,2008,1246	yes	missense	NAALADL2	NM_207015.2	10	995,2731,2202	GG,GA,AA		45.0147,28.2407,39.8195	benign	128/796	174814920	4721,7135	1836	4092	5928	SO:0001583	missense	254827	exon2			AAAAATACTTTGC		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.384A>G	3.37:g.174814920A>G	ENSP00000404705:p.Ile128Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	138	70	0.507246	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	37	CCDS46960.1	883	0.4043040293040293	148	0.3008130081300813	172	0.47513812154696133	236	0.4125874125874126	327	0.4313984168865435	A	1.481	-0.557312	0.03967	0.282407	0.450147	ENSG00000177694	ENST00000434257;ENST00000454872	T;T	0.34472	1.42;1.36	5.63	-1.48	0.08745	.	0.315558	0.27008	N	0.021400	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.23316	0.083;0.017	B;B	0.17098	0.017;0.009	T	0.48151	-0.9060	9	0.44086	T	0.13	-1.755	6.1917	0.20528	0.5894:0.2263:0.1843:0.0	rs9836841;rs52822748;rs61284953;rs9836841	111;128	Q58DX5-2;Q58DX5	.;NADL2_HUMAN	M	111;128	ENSP00000409858:I111M;ENSP00000404705:I128M	ENSP00000409858:I111M	I	+	3	3	NAALADL2	176297614	0.012000	0.17670	0.085000	0.20634	0.151000	0.21798	-0.003000	0.12901	-0.076000	0.12775	0.477000	0.44152	ATA	A|0.617;G|0.383	0.383	strong		0.383	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015	
HLA-C	3107	hgsc.bcm.edu	37	6	31239016	31239016	+	Silent	SNP	G	G	A	rs1050373	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31239016G>A	ENST00000376228.5	-	3	467	c.453C>T	c.(451-453)aaC>aaT	p.N151N	HLA-C_ENST00000383329.3_Silent_p.N151N	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	151	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GCAGGTCCTCGTTCAGGGCGA	0.697																																					p.N151N		Atlas-SNP	.											.	HLA-C	92	.	0			c.C453T						PASS	.						38.0	29.0	32.0					6																	31239016		2189	4260	6449	SO:0001819	synonymous_variant	3107	exon3			GTCCTCGTTCAGG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.453C>T	6.37:g.31239016G>A		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	192	58	0.302083	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	229	0.10485347985347986	35	0.07113821138211382	60	0.16574585635359115	53	0.09265734265734266	81	0.10686015831134564	.	9.651	1.141557	0.21205	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	0.984	0.19773	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999999857543	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.6398	0.22903	0.258:0.0:0.742:0.0	rs1050373;rs2308580;rs3175102	.	.	.	X	151	.	.	R	-	1	2	HLA-C	31346995	0.000000	0.05858	0.984000	0.44739	0.096000	0.18686	-0.255000	0.08769	0.250000	0.21479	0.305000	0.20034	CGA	G|0.918;A|0.083	0.083	strong		0.697	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
SVEP1	79987	hgsc.bcm.edu	37	9	113192655	113192655	+	Missense_Mutation	SNP	T	T	G	rs2986671	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:113192655T>G	ENST00000401783.2	-	33	5765	c.5429A>C	c.(5428-5430)gAa>gCa	p.E1810A	SVEP1_ENST00000374469.1_Missense_Mutation_p.E1787A|SVEP1_ENST00000297826.5_5'Flank	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1810	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.		E -> A (in dbSNP:rs2986671).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.E1813A(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						AAATGTGACTTCGGCACCTAC	0.408													T|||	930	0.185703	0.0129	0.2406	5008	,	,		17798	0.4087		0.1829	False		,,,				2504	0.1534				p.E1810A		Atlas-SNP	.											SVEP1,NS,carcinoma,-1,3	SVEP1	326	3	1	Substitution - Missense(1)	stomach(1)	c.A5429C						PASS	.	T	ALA/GLU	137,3617		3,131,1743	68.0	61.0	63.0		5429	2.8	0.0	9	dbSNP_101	63	1400,6836		119,1162,2837	yes	missense	SVEP1	NM_153366.3	107	122,1293,4580	GG,GT,TT		16.9985,3.6494,12.819	benign	1810/3572	113192655	1537,10453	1877	4118	5995	SO:0001583	missense	79987	exon33			GTGACTTCGGCAC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.5429A>C	9.37:g.113192655T>G	ENSP00000384917:p.Glu1810Ala	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	201	107	0.532338	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	495	0.22664835164835165	10	0.02032520325203252	84	0.23204419889502761	249	0.4353146853146853	152	0.20052770448548812	T	6.654	0.489110	0.12641	0.036494	0.169985	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.64991	-0.13;-0.13	5.27	2.82	0.32997	Complement control module (2);Sushi/SCR/CCP (3);	0.403453	0.29021	N	0.013385	T	0.00012	0.0000	L	0.37897	1.145	0.21915	P	0.99947619	B	0.11235	0.004	B	0.12156	0.007	T	0.41538	-0.9503	9	0.10636	T	0.68	.	8.6135	0.33817	0.1283:0.0:0.1345:0.7371	rs2986671;rs3739449;rs11567627;rs17807596;rs2986671	1810	Q4LDE5	SVEP1_HUMAN	A	1810;1787	ENSP00000384917:E1810A;ENSP00000363593:E1787A	ENSP00000363593:E1787A	E	-	2	0	SVEP1	112232476	0.493000	0.26035	0.022000	0.16811	0.798000	0.45092	2.345000	0.44018	0.397000	0.25310	0.533000	0.62120	GAA	T|0.723;G|0.277	0.277	strong		0.408	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MB21D1	115004	hgsc.bcm.edu	37	6	74150048	74150048	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:74150048C>T	ENST00000370315.3	-	3	1092	c.998G>A	c.(997-999)aGc>aAc	p.S333N	MB21D1_ENST00000370318.1_Missense_Mutation_p.S333N	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	333					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						TTCTTGGGTGCTAGCAGGCCA	0.438																																					p.S333N		Atlas-SNP	.											MB21D1,NS,carcinoma,0,1	MB21D1	33	1	0			c.G998A						scavenged	.						123.0	119.0	120.0					6																	74150048		2203	4300	6503	SO:0001583	missense	115004	exon3			TGGGTGCTAGCAG	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"""chromosome 6 open reading frame 150"""	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.998G>A	6.37:g.74150048C>T	ENSP00000359339:p.Ser333Asn	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	200	4	0.02	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Missense_Mutation	SNP	ENST00000370315.3	37	CCDS4978.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.724343	0.30593	.	.	ENSG00000164430	ENST00000370318;ENST00000370315;ENST00000296913	T;T	0.08807	3.05;3.05	5.28	3.14	0.36123	.	0.308306	0.33199	N	0.005170	T	0.13798	0.0334	M	0.80028	2.48	0.25252	N	0.989665	D	0.62365	0.991	D	0.63192	0.912	T	0.05162	-1.0902	10	0.66056	D	0.02	-6.6337	10.9866	0.47526	0.0:0.8915:0.0:0.1085	.	333	Q8N884	M21D1_HUMAN	N	333	ENSP00000359342:S333N;ENSP00000359339:S333N	ENSP00000296913:S333N	S	-	2	0	MB21D1	74206769	0.962000	0.33011	0.284000	0.24805	0.069000	0.16628	1.958000	0.40402	0.411000	0.25702	0.455000	0.32223	AGC	.	.	none		0.438	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441	
PCDHGA11	56105	hgsc.bcm.edu	37	5	140802456	140802456	+	Silent	SNP	G	G	A	rs62378455	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140802456G>A	ENST00000398587.2	+	1	1695	c.1662G>A	c.(1660-1662)ctG>ctA	p.L554L	PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA11_ENST00000518882.1_Silent_p.L554L|PCDHGB4_ENST00000519479.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA9_ENST00000573521.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	554	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTTCGTGCTGGACCAGAACG	0.627													g|||	190	0.0379393	0.0756	0.036	5008	,	,		18899	0.001		0.0328	False		,,,				2504	0.0317				p.L554L		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.G1662A						PASS	.	G	,,,,,,,,,,,,,,,,,,,	303,4103	162.9+/-194.8	11,281,1911	159.0	179.0	172.0		,,,1662,,,,,,,,,,,,,,,1662,1662	3.0	0.9	5	dbSNP_129	172	317,8283	111.8+/-172.0	6,305,3989	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032091.1,NM_032092.1	,,,,,,,,,,,,,,,,,,,	17,586,5900	AA,AG,GG		3.686,6.877,4.767	,,,,,,,,,,,,,,,,,,,	,,,554/936,,,,,,,,,,,,,,,554/838,554/751	140802456	620,12386	2203	4300	6503	SO:0001819	synonymous_variant	56105	exon1			CGTGCTGGACCAG	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"""Cadherins / Protocadherins : Clustered"""	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.1662G>A	5.37:g.140802456G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	172	80	0.465116	NM_032091	B7ZVY8|Q9Y5D8|Q9Y5D9	Silent	SNP	ENST00000398587.2	37	CCDS47294.1																																																																																			G|0.963;A|0.037	0.037	strong		0.627	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914	
SCAP	22937	hgsc.bcm.edu	37	3	47459679	47459679	+	Missense_Mutation	SNP	C	C	T	rs12487736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:47459679C>T	ENST00000265565.5	-	16	2804	c.2392G>A	c.(2392-2394)Gtc>Atc	p.V798I	SCAP_ENST00000441517.2_Missense_Mutation_p.V543I|SCAP_ENST00000465628.1_5'Flank|SCAP_ENST00000545718.1_Missense_Mutation_p.V406I	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	798	Interaction with SREBF2. {ECO:0000250}.		V -> I (in dbSNP:rs12487736). {ECO:0000269|PubMed:10570919}.		aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		CACACGCAGACGTGGCCTGCC	0.687													c|||	2265	0.452276	0.233	0.5245	5008	,	,		9125	0.4583		0.5905	False		,,,				2504	0.5491				p.V798I	Pancreas(149;978 1908 29304 37806 46700)	Atlas-SNP	.											.	SCAP	88	.	0			c.G2392A						PASS	.		ILE/VAL	1178,3170		206,766,1202	19.0	21.0	20.0		2392	3.6	0.9	3	dbSNP_120	20	4846,3680		1440,1966,857	no	missense	SCAP	NM_012235.2	29	1646,2732,2059	TT,TC,CC		43.1621,27.0929,46.792	benign	798/1280	47459679	6024,6850	2174	4263	6437	SO:0001583	missense	22937	exon16			CGCAGACGTGGCC	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"""WD repeat domain containing"""	30634	protein-coding gene	gene with protein product	"""SREBP cleavage activating protein"""	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.2392G>A	3.37:g.47459679C>T	ENSP00000265565:p.Val798Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	75	44	0.586667	NM_012235	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	37	CCDS2755.2	1039|1039	0.4757326007326007|0.4757326007326007	137|137	0.2784552845528455|0.2784552845528455	191|191	0.5276243093922652|0.5276243093922652	265|265	0.4632867132867133|0.4632867132867133	446|446	0.5883905013192612|0.5883905013192612	c|c	3.908|3.908	-0.020663|-0.020663	0.07634|0.07634	0.270929|0.270929	0.568379|0.568379	ENSG00000114650|ENSG00000114650	ENST00000383739|ENST00000360832;ENST00000265565;ENST00000441517;ENST00000545718	.|T;T;T	.|0.41758	.|1.61;2.2;0.99	4.59|4.59	3.62|3.62	0.41486|0.41486	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.|0.054283	.|0.64402	.|D	.|0.000001	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01705|0.01705	-0.755|-0.755	0.26338|0.26338	P|P	0.9774169|0.9774169	.|B;B	.|0.13594	.|0.005;0.008	.|B;B	.|0.12156	.|0.003;0.007	T|T	0.48525|0.48525	-0.9028|-0.9028	5|9	0.87932|0.02654	D|T	0|1	-31.7751|-31.7751	3.9583|3.9583	0.09399|0.09399	0.0:0.6739:0.0:0.3261|0.0:0.6739:0.0:0.3261	rs12487736;rs17845631;rs17849135;rs17858562|rs12487736;rs17845631;rs17849135;rs17858562	.|543;798	.|F8W921;Q12770	.|.;SCAP_HUMAN	H|I	322|425;798;543;406	.|ENSP00000265565:V798I;ENSP00000416847:V543I;ENSP00000438956:V406I	ENSP00000373245:R322H|ENSP00000265565:V798I	R|V	-|-	2|1	0|0	SCAP|SCAP	47434683|47434683	1.000000|1.000000	0.71417|0.71417	0.905000|0.905000	0.35620|0.35620	0.192000|0.192000	0.23643|0.23643	3.194000|3.194000	0.51005|0.51005	2.393000|2.393000	0.81446|0.81446	0.556000|0.556000	0.70494|0.70494	CGT|GTC	C|0.531;T|0.469	0.469	strong		0.687	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235	
RARRES1	5918	hgsc.bcm.edu	37	3	158428642	158428642	+	Silent	SNP	G	G	A	rs2307064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:158428642G>A	ENST00000237696.5	-	3	700	c.420C>T	c.(418-420)acC>acT	p.T140T	RARRES1_ENST00000498640.1_Intron|RARRES1_ENST00000479756.1_Silent_p.T140T	NM_206963.1	NP_996846.1	P49788	TIG1_HUMAN	retinoic acid receptor responder (tazarotene induced) 1	140					negative regulation of cell proliferation (GO:0008285)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)	TTACATTGATGGTTGGTCTGG	0.413													G|||	806	0.160942	0.1225	0.1412	5008	,	,		20560	0.1498		0.2356	False		,,,				2504	0.1616				p.T140T		Atlas-SNP	.											.	RARRES1	22	.	0			c.C420T						PASS	.	G	,	604,3802	265.0+/-266.4	48,508,1647	201.0	184.0	190.0		420,420	1.8	0.0	3	dbSNP_100	190	2047,6553	356.6+/-330.4	253,1541,2506	no	coding-synonymous,coding-synonymous	RARRES1	NM_002888.2,NM_206963.1	,	301,2049,4153	AA,AG,GG		23.8023,13.7086,20.3829	,	140/229,140/295	158428642	2651,10355	2203	4300	6503	SO:0001819	synonymous_variant	5918	exon3			ATTGATGGTTGGT	U27185	CCDS3184.1, CCDS54665.1	3q25.32	2013-07-29			ENSG00000118849	ENSG00000118849			9867	protein-coding gene	gene with protein product	"""latexin-like"""	605090				8601727, 9270552	Standard	NM_002888		Approved	TIG1, LXNL	uc003fci.3	P49788	OTTHUMG00000158834	ENST00000237696.5:c.420C>T	3.37:g.158428642G>A		Somatic	411	1	0.00243309		WXS	Illumina HiSeq	Phase_I	433	207	0.47806	NM_206963	Q8N1D7	Silent	SNP	ENST00000237696.5	37	CCDS3184.1																																																																																			G|0.814;A|0.186	0.186	strong		0.413	RARRES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352358.1		
CROCC	9696	hgsc.bcm.edu	37	1	17282573	17282573	+	Silent	SNP	G	G	A	rs2273114	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17282573G>A	ENST00000375541.5	+	25	3855	c.3786G>A	c.(3784-3786)ggG>ggA	p.G1262G		NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		AGGAGGCCGGGGAGCTGCGAA	0.662													G|||	803	0.160343	0.1861	0.1628	5008	,	,		17329	0.1101		0.1014	False		,,,				2504	0.2362				p.G1262G		Atlas-SNP	.											.	CROCC	185	.	0			c.G3786A						PASS	.	G		569,3525		35,499,1513	22.0	23.0	22.0		3786	0.2	0.9	1	dbSNP_100	22	887,7115		45,797,3159	no	coding-synonymous	CROCC	NM_014675.3		80,1296,4672	AA,AG,GG		11.0847,13.8984,12.037		1262/2018	17282573	1456,10640	2047	4001	6048	SO:0001819	synonymous_variant	9696	exon25			GGCCGGGGAGCTG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.3786G>A	1.37:g.17282573G>A		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	179	94	0.52514	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			G|0.854;A|0.146	0.146	strong		0.662	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
ALPK2	115701	hgsc.bcm.edu	37	18	56204991	56204991	+	Missense_Mutation	SNP	C	C	T	rs3809970	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56204991C>T	ENST00000361673.3	-	5	2641	c.2428G>A	c.(2428-2430)Ggt>Agt	p.G810S	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	810			G -> S (in dbSNP:rs3809970). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCTTGGTCACCAGCCTCAAAA	0.473													C|||	2021	0.403554	0.4312	0.4265	5008	,	,		22527	0.2361		0.5716	False		,,,				2504	0.3497				p.G810S		Atlas-SNP	.											.	ALPK2	487	.	0			c.G2428A						PASS	.	C	SER/GLY	1983,2423	557.1+/-379.7	445,1093,665	134.0	122.0	126.0		2428	1.6	0.0	18	dbSNP_107	126	4590,4010	598.1+/-393.9	1236,2118,946	yes	missense	ALPK2	NM_052947.3	56	1681,3211,1611	TT,TC,CC		46.6279,45.0068,49.4618	probably-damaging	810/2171	56204991	6573,6433	2203	4300	6503	SO:0001583	missense	115701	exon5			GGTCACCAGCCTC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2428G>A	18.37:g.56204991C>T	ENSP00000354991:p.Gly810Ser	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	287	135	0.470383	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	955	0.43727106227106227	189	0.38414634146341464	184	0.5082872928176796	137	0.2395104895104895	445	0.5870712401055409	C	12.69	2.012911	0.35511	0.450068	0.533721	ENSG00000198796	ENST00000361673	T	0.52983	0.64	5.39	1.65	0.23941	.	1.545420	0.03173	N	0.171067	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P;B	0.50943	0.94;0.197	P;B	0.47015	0.534;0.092	T	0.41787	-0.9489	9	0.41790	T	0.15	-2.7978	2.4506	0.04517	0.1531:0.5408:0.1483:0.1578	rs3809970;rs17309830;rs52812207;rs57583190;rs3809970	810;810	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	S	810	ENSP00000354991:G810S	ENSP00000354991:G810S	G	-	1	0	ALPK2	54355971	0.000000	0.05858	0.040000	0.18447	0.017000	0.09413	0.230000	0.17852	0.021000	0.15133	0.591000	0.81541	GGT	C|0.532;T|0.468	0.468	strong		0.473	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
ATP13A2	23400	hgsc.bcm.edu	37	1	17319011	17319011	+	Silent	SNP	G	G	A	rs2076603	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:17319011G>A	ENST00000326735.8	-	17	1848	c.1815C>T	c.(1813-1815)ccC>ccT	p.P605P	ATP13A2_ENST00000452699.1_Silent_p.P600P|ATP13A2_ENST00000341676.5_Silent_p.P600P|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2	605					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CCCAAAGTGGGGGTCTCATCA	0.657													G|||	2246	0.448482	0.4145	0.5216	5008	,	,		16691	0.2589		0.6153	False		,,,				2504	0.4663				p.P605P		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C1815T						PASS	.	G	,,	1966,2440	553.5+/-378.8	426,1114,663	87.0	90.0	89.0		1800,1800,1815	1.4	1.0	1	dbSNP_96	89	5438,3162	649.6+/-400.6	1714,2010,576	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	2140,3124,1239	AA,AG,GG		36.7674,44.621,43.0724	,,	600/1176,600/1159,605/1181	17319011	7404,5602	2203	4300	6503	SO:0001819	synonymous_variant	23400	exon17			AAGTGGGGGTCTC	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.1815C>T	1.37:g.17319011G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	213	211	0.99061	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			G|0.467;C|0.000;A|0.533	0.533	strong		0.657	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
MKI67	4288	hgsc.bcm.edu	37	10	129906364	129906364	+	Missense_Mutation	SNP	G	G	A	rs4750685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:129906364G>A	ENST00000368654.3	-	13	4115	c.3740C>T	c.(3739-3741)aCt>aTt	p.T1247I	MKI67_ENST00000368653.3_Missense_Mutation_p.T887I	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1247	16 X 122 AA approximate repeats.		T -> I (in dbSNP:rs4750685).		cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.T1247I(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGGTATTTTAGTGGTTTTACC	0.512													G|||	515	0.102835	0.0666	0.1556	5008	,	,		18082	0.1359		0.0785	False		,,,				2504	0.1053				p.T1247I		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - Missense(1)	stomach(1)	c.C3740T						PASS	.	G	ILE/THR,ILE/THR	295,4111	161.4+/-193.6	11,273,1919	105.0	108.0	107.0		2660,3740	1.0	0.0	10	dbSNP_111	107	771,7829	183.5+/-231.7	39,693,3568	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	89,89	50,966,5487	AA,AG,GG		8.9651,6.6954,8.1962	possibly-damaging,possibly-damaging	887/2897,1247/3257	129906364	1066,11940	2203	4300	6503	SO:0001583	missense	4288	exon13			ATTTTAGTGGTTT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.3740C>T	10.37:g.129906364G>A	ENSP00000357643:p.Thr1247Ile	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	221	112	0.506787	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	209	0.09569597069597069	33	0.06707317073170732	39	0.10773480662983426	79	0.1381118881118881	58	0.07651715039577836	G	12.96	2.093039	0.36952	0.066954	0.089651	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.03242	4.0;4.0	3.0	1.05	0.20165	.	0.914623	0.08986	N	0.865071	T	0.00073	0.0002	M	0.65975	2.015	0.80722	P	0.0	P;D;D	0.89917	0.936;1.0;0.997	P;D;D	0.79108	0.559;0.992;0.939	T	0.31280	-0.9949	9	0.32370	T	0.25	.	4.5988	0.12343	0.4006:0.0:0.5994:0.0	rs4750685;rs52820823;rs57830646;rs4750685	1246;887;1247	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	I	1247;887;1246	ENSP00000357643:T1247I;ENSP00000357642:T887I	ENSP00000357642:T887I	T	-	2	0	MKI67	129796354	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	0.535000	0.23114	0.583000	0.29574	0.456000	0.33151	ACT	G|0.915;A|0.085	0.085	strong		0.512	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
TPMT	7172	hgsc.bcm.edu	37	6	18139228	18139228	+	Missense_Mutation	SNP	C	C	T	rs1800460	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:18139228C>T	ENST00000309983.4	-	6	545	c.460G>A	c.(460-462)Gca>Aca	p.A154T		NM_000367.2	NP_000358.1	P51580	TPMT_HUMAN	thiopurine S-methyltransferase	154			A -> T (in TPMT deficiency; allele TPMT*3A and allele TPMT*3B; very low activity; protein shows enhanced degradation leading to strongly reduced protein levels; TPMT*3A is most common mutant in American Caucasians; TPMT*3A allele frequencies are 4.5% in the Caucasian; 0.8% in the African Americans and 3.2% in the Caucasian Americans population; dbSNP:rs1800460). {ECO:0000269|PubMed:10208641, ECO:0000269|PubMed:10751626, ECO:0000269|PubMed:15819814, ECO:0000269|PubMed:16220112, ECO:0000269|PubMed:16476125, ECO:0000269|PubMed:16789994, ECO:0000269|PubMed:8561894, ECO:0000269|PubMed:8644731, ECO:0000269|PubMed:9246020, ECO:0000269|PubMed:9336428, ECO:0000269|PubMed:9931345}.		methylation (GO:0032259)|nucleobase-containing compound metabolic process (GO:0006139)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	thiopurine S-methyltransferase activity (GO:0008119)			large_intestine(2)|lung(1)	3	Ovarian(93;0.016)|Breast(50;0.0245)	all_hematologic(90;0.146)	all cancers(50;0.06)|Epithelial(50;0.0654)		Azathioprine(DB00993)|Bendroflumethiazide(DB00436)|Cefazolin(DB01327)|Mercaptopurine(DB01033)|Olsalazine(DB01250)|Trichlormethiazide(DB01021)	GCAACTAATGCTCCTCTATCC	0.313													C|||	64	0.0127796	0.003	0.0403	5008	,	,		19715	0.0		0.0278	False		,,,				2504	0.0041				p.A154T	Colon(190;1381 2791 16728 32493)	Atlas-SNP	.											.	TPMT	17	.	0			c.G460A	GRCh37	CM961382	TPMT	M	rs1800460	PASS	.	C	THR/ALA	44,4360	44.6+/-78.6	1,42,2159	85.0	87.0	86.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	460	-0.5	0.9	6	dbSNP_89	86	323,8277	113.1+/-173.2	11,301,3988	yes	missense	TPMT	NM_000367.2	58	12,343,6147	TT,TC,CC		3.7558,0.9991,2.8222	probably-damaging	154/246	18139228	367,12637	2202	4300	6502	SO:0001583	missense	7172	exon6			CTAATGCTCCTCT		CCDS4543.1	6p22.3	2014-09-17			ENSG00000137364	ENSG00000137364	2.1.1.67		12014	protein-coding gene	gene with protein product		187680				8316220	Standard	NM_000367		Approved		uc003ncm.3	P51580	OTTHUMG00000014317	ENST00000309983.4:c.460G>A	6.37:g.18139228C>T	ENSP00000312304:p.Ala154Thr	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	186	65	0.349462	NM_000367	O14806|O15423|O15424|O15425|O15426|O15515|O15548|O43213|Q5VUK6|Q9UBE6|Q9UBT8|Q9UE62	Missense_Mutation	SNP	ENST00000309983.4	37	CCDS4543.1	38	0.0173992673992674	3	0.006097560975609756	16	0.04419889502762431	0	0.0	19	0.025065963060686015	C	21.7	4.194798	0.78902	0.009991	0.037558	ENSG00000137364	ENST00000309983	T	0.75477	-0.94	6.07	-0.479	0.12089	.	0.199420	0.52532	D	0.000073	D	0.83257	0.5215	M	0.94063	3.49	0.46222	A	0.998933	D;D	0.63880	0.993;0.977	D;P	0.66847	0.947;0.846	D	0.85565	0.1230	9	0.66056	D	0.02	-11.2715	11.7517	0.51852	0.5802:0.3588:0.0:0.061	rs1800460;rs11568060;rs16880273;rs57650974	154;154	Q9BS45;P51580	.;TPMT_HUMAN	T	154	ENSP00000312304:A154T	ENSP00000312304:A154T	A	-	1	0	TPMT	18247207	0.882000	0.30256	0.899000	0.35326	0.989000	0.77384	-0.257000	0.08745	0.102000	0.17638	0.655000	0.94253	GCA	C|0.974;T|0.026	0.026	strong		0.313	TPMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039960.1		
TRIM45	80263	hgsc.bcm.edu	37	1	117656088	117656088	+	Missense_Mutation	SNP	A	A	G	rs1289658	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:117656088A>G	ENST00000256649.4	-	5	2013	c.1487T>C	c.(1486-1488)aTg>aCg	p.M496T	TRIM45_ENST00000369461.3_Missense_Mutation_p.M439T|TRIM45_ENST00000369464.3_Missense_Mutation_p.M478T	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	496			M -> T (in dbSNP:rs1289658). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15351693, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		bone development (GO:0060348)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|prostate(1)	23	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		TCTCCTCACCATCACAGTGAA	0.557													G|||	2229	0.445088	0.6793	0.4755	5008	,	,		22011	0.1865		0.4364	False		,,,				2504	0.3824				p.M496T		Atlas-SNP	.											.	TRIM45	55	.	0			c.T1487C						PASS	.	G	THR/MET,THR/MET	2732,1674	508.8+/-367.0	873,986,344	66.0	61.0	62.0		1433,1487	4.0	0.6	1	dbSNP_87	62	3455,5145	636.3+/-399.1	680,2095,1525	yes	missense,missense	TRIM45	NM_001145635.1,NM_025188.3	81,81	1553,3081,1869	GG,GA,AA		40.1744,37.9936,47.5704	benign,benign	478/563,496/581	117656088	6187,6819	2203	4300	6503	SO:0001583	missense	80263	exon5			CTCACCATCACAG		CCDS893.1, CCDS44200.1	1p13.1	2011-04-20	2011-01-25		ENSG00000134253	ENSG00000134253		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19018	protein-coding gene	gene with protein product		609318	"""tripartite motif-containing 45"""			15351693	Standard	NM_025188		Approved	FLJ13181, RNF99	uc001egz.2	Q9H8W5	OTTHUMG00000012119	ENST00000256649.4:c.1487T>C	1.37:g.117656088A>G	ENSP00000256649:p.Met496Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_025188	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	909	0.41620879120879123	317	0.6443089430894309	169	0.46685082872928174	93	0.16258741258741258	330	0.43535620052770446	G	0.005	-2.228181	0.00280	0.620064	0.401744	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	T;T;T	0.39406	2.08;1.08;2.08	4.96	3.99	0.46301	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.522971	0.20258	N	0.095923	T	0.02929	0.0087	N	0.00823	-1.155	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39663	-0.9603	9	0.07030	T	0.85	-10.0408	3.8833	0.09088	0.1845:0.0:0.4103:0.4052	rs1289658;rs17524007;rs52814348;rs60516003;rs1289658	478;496	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	T	496;478;439	ENSP00000256649:M496T;ENSP00000358476:M478T;ENSP00000358473:M439T	ENSP00000256649:M496T	M	-	2	0	TRIM45	117457611	0.023000	0.18921	0.629000	0.29254	0.342000	0.28953	0.149000	0.16243	0.562000	0.29204	-0.213000	0.12676	ATG	A|0.549;G|0.451	0.451	strong		0.557	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188	
PCDHA4	56144	hgsc.bcm.edu	37	5	140187048	140187048	+	Silent	SNP	G	G	C	rs3822349	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140187048G>C	ENST00000530339.1	+	1	276	c.276G>C	c.(274-276)cgG>cgC	p.R92R	PCDHA4_ENST00000356878.4_Silent_p.R92R|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Silent_p.R92R	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	92	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R92R(2)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGATCGACCGGGAGGAGCTGT	0.617																																					p.R92R		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,4	PCDHA4	419	4	2	Substitution - coding silent(2)	stomach(2)	c.G276C						scavenged	.						71.0	82.0	78.0					5																	140187048		2201	4284	6485	SO:0001819	synonymous_variant	56144	exon1			CGACCGGGAGGAG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.276G>C	5.37:g.140187048G>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	73	22	0.30137	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			G|0.926;C|0.074	0.074	strong		0.617	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
TMEM70	54968	hgsc.bcm.edu	37	8	74893653	74893653	+	Missense_Mutation	SNP	G	G	A	rs77410280	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:74893653G>A	ENST00000312184.5	+	3	653	c.580G>A	c.(580-582)Gtg>Atg	p.V194M	Y_RNA_ENST00000365350.1_RNA	NM_001040613.2|NM_017866.5	NP_001035703.1|NP_060336.3	Q9BUB7	TMM70_HUMAN	transmembrane protein 70	194					mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)				breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	8	Breast(64;0.0311)		Epithelial(68;0.0186)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0564)			AACGAGTACAGTGTTTCACCA	0.368													G|||	36	0.0071885	0.0008	0.0058	5008	,	,		20433	0.0		0.0268	False		,,,				2504	0.0041				p.V194M		Atlas-SNP	.											.	TMEM70	12	.	0			c.G580A						PASS	.	G	,MET/VAL	9,4397	17.9+/-39.9	0,9,2194	153.0	139.0	144.0		,580	3.6	1.0	8	dbSNP_131	144	134,8466	68.0+/-130.5	2,130,4168	yes	utr-3,missense	TMEM70	NM_001040613.2,NM_017866.5	,21	2,139,6362	AA,AG,GG		1.5581,0.2043,1.0995	,possibly-damaging	,194/261	74893653	143,12863	2203	4300	6503	SO:0001583	missense	54968	exon3			AGTACAGTGTTTC	BC002748	CCDS6215.1, CCDS47876.1	8q21.11	2013-05-23				ENSG00000175606			26050	protein-coding gene	gene with protein product		612418				21945727, 22986587	Standard	NM_017866		Approved	FLJ20533	uc003yab.3	Q9BUB7		ENST00000312184.5:c.580G>A	8.37:g.74893653G>A	ENSP00000312599:p.Val194Met	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	202	98	0.485149	NM_017866	E9PDY9|Q9NWY5	Missense_Mutation	SNP	ENST00000312184.5	37	CCDS6215.1	25	0.011446886446886446	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	22	0.029023746701846966	G	12.94	2.089658	0.36855	0.002043	0.015581	ENSG00000175606	ENST00000312184	T	0.64991	-0.13	5.38	3.56	0.40772	.	0.424990	0.22692	N	0.056804	T	0.49457	0.1558	M	0.68952	2.095	0.38412	D	0.945952	P	0.49307	0.922	P	0.54706	0.759	T	0.67405	-0.5679	10	0.54805	T	0.06	-4.7047	14.8932	0.70625	0.0:0.1113:0.7721:0.1166	.	194	Q9BUB7	TMM70_HUMAN	M	194	ENSP00000312599:V194M	ENSP00000312599:V194M	V	+	1	0	TMEM70	75056207	1.000000	0.71417	0.994000	0.49952	0.227000	0.25037	2.895000	0.48648	0.390000	0.25115	-0.808000	0.03180	GTG	G|0.989;A|0.011	0.011	strong		0.368	TMEM70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379028.1	NM_017866	
EIF2B4	8890	hgsc.bcm.edu	37	2	27590415	27590415	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:27590415T>C	ENST00000347454.4	-	9	965	c.794A>G	c.(793-795)cAg>cGg	p.Q265R	EIF2B4_ENST00000451130.2_Missense_Mutation_p.Q285R|SNX17_ENST00000233575.2_5'Flank|AC074117.10_ENST00000412749.1_RNA|EIF2B4_ENST00000445933.2_Missense_Mutation_p.Q264R|EIF2B4_ENST00000493344.2_Missense_Mutation_p.Q286R	NM_001034116.1|NM_015636.3	NP_001029288.1|NP_056451.3	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B, subunit 4 delta, 67kDa	265					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation (GO:0045947)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translation (GO:0006417)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(5)|skin(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGACGGCACTGAGTCAGGAA	0.433																																					p.Q285R		Atlas-SNP	.											.	EIF2B4	48	.	0			c.A854G						PASS	.						108.0	104.0	105.0					2																	27590415		2203	4300	6503	SO:0001583	missense	8890	exon8			CGGCACTGAGTCA	AJ011306	CCDS33164.1, CCDS46244.1, CCDS46245.1	2p23.3	2008-02-05	2002-08-29		ENSG00000115211	ENSG00000115211			3260	protein-coding gene	gene with protein product		606687	"""eukaryotic translation initiation factor 2B, subunit 4 (delta, 67kD)"""			8929216, 7982969	Standard	NM_172195		Approved	EIF2Bdelta, EIF-2B, DKFZP586J0119, EIF2B	uc002rjz.3	Q9UI10	OTTHUMG00000151927	ENST00000347454.4:c.794A>G	2.37:g.27590415T>C	ENSP00000233552:p.Gln265Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_172195	Q53RY7|Q5BJF4|Q9BUV9|Q9UBG4|Q9UIQ9|Q9UJ95	Missense_Mutation	SNP	ENST00000347454.4	37	CCDS33164.1	.	.	.	.	.	.	.	.	.	.	T	15.84	2.953247	0.53293	.	.	ENSG00000115211	ENST00000347454;ENST00000414437;ENST00000445933;ENST00000451130;ENST00000493344	D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.90793	0.7109	L	0.60455	1.87	0.80722	D	1	B;B;B;B	0.31790	0.34;0.34;0.071;0.057	B;B;B;B	0.36922	0.108;0.236;0.055;0.032	D	0.88128	0.2836	10	0.21014	T	0.42	-20.7409	15.2744	0.73732	0.0:0.0:0.0:1.0	.	262;264;265;285	F5H6W1;Q9UI10-3;Q9UI10;Q9UI10-2	.;.;EI2BD_HUMAN;.	R	265;262;264;285;286	ENSP00000233552:Q265R;ENSP00000394397:Q264R;ENSP00000394869:Q285R;ENSP00000429323:Q286R	ENSP00000233552:Q265R	Q	-	2	0	EIF2B4	27443919	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.460000	0.80816	2.288000	0.76882	0.533000	0.62120	CAG	.	.	none		0.433	EIF2B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324448.1		
HAS1	3036	hgsc.bcm.edu	37	19	52217128	52217128	+	Missense_Mutation	SNP	G	G	A	rs34682338	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52217128G>A	ENST00000222115.1	-	5	1323	c.1289C>T	c.(1288-1290)gCg>gTg	p.A430V	HAS1_ENST00000601714.1_Missense_Mutation_p.A437V|HAS1_ENST00000540069.2_Missense_Mutation_p.A429V	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	430					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		CCACAGCAGCGCCCAAGGGCG	0.697													g|||	10	0.00199681	0.0008	0.0014	5008	,	,		15365	0.0		0.005	False		,,,				2504	0.0031				p.A430V	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											HAS1,lower_third,carcinoma,0,1	HAS1	61	1	0			c.C1289T						scavenged	.		VAL/ALA	12,4360		0,12,2174	24.0	25.0	25.0		1289	3.2	1.0	19	dbSNP_126	25	93,8495		0,93,4201	yes	missense	HAS1	NM_001523.2	64	0,105,6375	AA,AG,GG		1.0829,0.2745,0.8102	possibly-damaging	430/579	52217128	105,12855	2186	4294	6480	SO:0001583	missense	3036	exon5			AGCAGCGCCCAAG	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.1289C>T	19.37:g.52217128G>A	ENSP00000222115:p.Ala430Val	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	5	3	0.6	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	37	CCDS12838.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	g	13.44	2.236984	0.39498	0.002745	0.010829	ENSG00000105509	ENST00000540069;ENST00000222115	T;T	0.59083	0.29;0.29	3.19	3.19	0.36642	.	0.146701	0.44483	U	0.000446	T	0.27278	0.0669	N	0.22421	0.69	0.33217	D	0.554145	B;P;P	0.42757	0.334;0.789;0.789	B;B;B	0.32928	0.04;0.155;0.155	T	0.53085	-0.8488	10	0.66056	D	0.02	-18.9542	7.85	0.29448	0.0:0.0:0.7525:0.2475	rs34682338	429;430;429	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	V	429;430	ENSP00000445021:A429V;ENSP00000222115:A430V	ENSP00000222115:A430V	A	-	2	0	HAS1	56908940	1.000000	0.71417	1.000000	0.80357	0.270000	0.26580	5.291000	0.65667	1.812000	0.52913	0.165000	0.16767	GCG	G|0.995;A|0.005	0.005	strong		0.697	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
LURAP1L	286343	hgsc.bcm.edu	37	9	12821695	12821695	+	Missense_Mutation	SNP	T	T	C	rs61755264	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:12821695T>C	ENST00000319264.3	+	2	1318	c.623T>C	c.(622-624)aTa>aCa	p.I208T		NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	211																	AGCTCCCTCATAGAGGACTCA	0.493													T|||	33	0.00658946	0.0008	0.0144	5008	,	,		18761	0.0		0.0129	False		,,,				2504	0.0092				p.I208T		Atlas-SNP	.											.	.	.	.	0			c.T623C						PASS	.	T	THR/ILE	7,4399	12.9+/-30.5	0,7,2196	182.0	164.0	170.0		623	4.4	0.4	9	dbSNP_129	170	78,8522	45.8+/-104.6	0,78,4222	yes	missense	C9orf150	NM_203403.1	89	0,85,6418	CC,CT,TT		0.907,0.1589,0.6535	benign	208/229	12821695	85,12921	2203	4300	6503	SO:0001583	missense	286343	exon2			CCCTCATAGAGGA	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"""similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"""		"""chromosome 9 open reading frame 150"""	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.623T>C	9.37:g.12821695T>C	ENSP00000321026:p.Ile208Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Missense_Mutation	SNP	ENST00000319264.3	37	CCDS6473.1	17	0.007783882783882784	0	0.0	7	0.019337016574585635	0	0.0	10	0.013192612137203167	T	8.760	0.923302	0.18056	0.001589	0.00907	ENSG00000153714	ENST00000319264	T	0.47528	0.84	5.59	4.45	0.53987	.	1.264020	0.05579	N	0.572551	T	0.20659	0.0497	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.17899	-1.0354	10	0.44086	T	0.13	.	6.1872	0.20503	0.0:0.1423:0.1354:0.7223	rs61755264	211	Q8IV03	CI150_HUMAN	T	208	ENSP00000321026:I208T	ENSP00000321026:I208T	I	+	2	0	C9orf150	12811695	0.131000	0.22433	0.357000	0.25798	0.813000	0.45954	1.783000	0.38664	0.956000	0.37904	0.460000	0.39030	ATA	T|0.992;C|0.008	0.008	strong		0.493	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403	
FLG	2312	hgsc.bcm.edu	37	1	152283267	152283267	+	Silent	SNP	T	T	A	rs11581451	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152283267T>A	ENST00000368799.1	-	3	4130	c.4095A>T	c.(4093-4095)gcA>gcT	p.A1365A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1365	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGAGCTGTCTGCTGACTGCT	0.537									Ichthyosis				T|||	37	0.00738818	0.0	0.0072	5008	,	,		21371	0.001		0.0119	False		,,,				2504	0.0194				p.A1365A		Atlas-SNP	.											FLG,NS,carcinoma,-2,1	FLG	900	1	0			c.A4095T						scavenged	.	T		14,4392	21.2+/-45.6	0,14,2189	392.0	369.0	377.0		4095	-8.4	0.0	1	dbSNP_120	377	98,8498	55.2+/-116.2	1,96,4201	no	coding-synonymous	FLG	NM_002016.1		1,110,6390	AA,AT,TT		1.1401,0.3177,0.8614		1365/4062	152283267	112,12890	2203	4298	6501	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTGTCTGCTGAC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4095A>T	1.37:g.152283267T>A		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	176	91	0.517045	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			T|0.993;A|0.007	0.007	strong		0.537	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150167	39150167	+	Silent	SNP	G	G	A	rs12452295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39150167G>A	ENST00000391586.1	-	1	218	c.183C>T	c.(181-183)tgC>tgT	p.C61C		NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	61						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.C61C(1)		lung(2)|prostate(2)	4		Breast(137;0.00043)				AGGTGGGCACGCAGGGCTGAG	0.632													G|||	1210	0.241613	0.0567	0.3141	5008	,	,		18403	0.3234		0.2823	False		,,,				2504	0.3139				p.C61C		Atlas-SNP	.											KRTAP3-3,NS,carcinoma,0,1	KRTAP3-3	11	1	1	Substitution - coding silent(1)	prostate(1)	c.C183T						PASS	.	G		407,3999	201.8+/-224.7	22,363,1818	106.0	77.0	87.0		183	3.5	1.0	17	dbSNP_120	87	2540,6048	415.2+/-351.7	370,1800,2124	no	coding-synonymous	KRTAP3-3	NM_033185.2		392,2163,3942	AA,AG,GG		29.5762,9.2374,22.6797		61/99	39150167	2947,10047	2203	4294	6497	SO:0001819	synonymous_variant	85293	exon1			GGGCACGCAGGGC	AJ406933	CCDS32643.1	17q21.2	2013-06-25			ENSG00000212899	ENSG00000212899		"""Keratin associated proteins"""	18890	protein-coding gene	gene with protein product						11279113	Standard	NM_033185		Approved	KAP3.3	uc002hvr.1	Q9BYR6	OTTHUMG00000133591	ENST00000391586.1:c.183C>T	17.37:g.39150167G>A		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	236	115	0.487288	NM_033185	Q52LP0|Q6NTD4	Silent	SNP	ENST00000391586.1	37	CCDS32643.1																																																																																			G|0.777;A|0.223	0.223	strong		0.632	KRTAP3-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257695.1		
RHOT2	89941	hgsc.bcm.edu	37	16	722331	722331	+	Missense_Mutation	SNP	C	C	T	rs3177338	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:722331C>T	ENST00000315082.4	+	15	1387	c.1273C>T	c.(1273-1275)Cgt>Tgt	p.R425C		NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	425	Miro 2.		R -> C (in dbSNP:rs3177338). {ECO:0000269|PubMed:12482879}.		cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				GGTAGGGGCCCGTGGAGTGGG	0.657													C|||	3348	0.66853	0.7821	0.5706	5008	,	,		18089	0.9891		0.3787	False		,,,				2504	0.5521				p.R425C		Atlas-SNP	.											.	RHOT2	35	.	0			c.C1273T						PASS	.	C	CYS/ARG	3138,1256	683.9+/-404.3	1132,874,191	51.0	53.0	53.0		1273	4.1	0.3	16	dbSNP_105	53	3058,5532	459.9+/-365.0	556,1946,1793	yes	missense	RHOT2	NM_138769.1	180	1688,2820,1984	TT,TC,CC		35.5995,28.5844,47.7203	probably-damaging	425/619	722331	6196,6788	2197	4295	6492	SO:0001583	missense	89941	exon15			GGGGCCCGTGGAG	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"""EF-hand domain containing"""	21169	protein-coding gene	gene with protein product	"""mitochondrial Rho (MIRO) GTPase 2"""	613889	"""chromosome 16 open reading frame 39"", ""ras homolog gene family, member T2"""	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.1273C>T	16.37:g.722331C>T	ENSP00000321971:p.Arg425Cys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Missense_Mutation	SNP	ENST00000315082.4	37	CCDS10417.1	1421	0.6506410256410257	377	0.766260162601626	189	0.5220994475138122	567	0.9912587412587412	288	0.37994722955145116	C	15.75	2.924253	0.52653	0.714156	0.355995	ENSG00000140983	ENST00000315082	T	0.66815	-0.23	5.1	4.12	0.48240	Mitochondrial Rho-like (1);MIRO (1);	0.308380	0.35151	N	0.003413	T	0.00012	0.0000	M	0.87180	2.865	0.09310	P	0.9999999901694	D	0.69078	0.997	P	0.61722	0.893	T	0.05989	-1.0852	9	0.87932	D	0	-12.9004	9.9376	0.41561	0.156:0.6931:0.1509:0.0	rs3177338;rs3830143;rs59724834	425	Q8IXI1	MIRO2_HUMAN	C	425	ENSP00000321971:R425C	ENSP00000321971:R425C	R	+	1	0	RHOT2	662332	0.003000	0.15002	0.328000	0.25416	0.075000	0.17131	1.309000	0.33539	1.103000	0.41568	0.462000	0.41574	CGT	C|0.469;T|0.531	0.531	strong		0.657	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769	
LOXL1	4016	hgsc.bcm.edu	37	15	74219582	74219582	+	Missense_Mutation	SNP	G	G	A	rs3825942	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:74219582G>A	ENST00000261921.7	+	1	784	c.458G>A	c.(457-459)gGc>gAc	p.G153D	LOXL1-AS1_ENST00000562739.1_RNA|LOXL1-AS1_ENST00000562130.1_RNA|LOXL1-AS1_ENST00000568087.1_RNA|LOXL1-AS1_ENST00000564963.1_RNA|LOXL1-AS1_ENST00000564194.1_RNA|LOXL1-AS1_ENST00000565756.1_RNA|LOXL1-AS1_ENST00000567644.1_RNA|LOXL1-AS1_ENST00000562965.1_RNA|LOXL1-AS1_ENST00000566675.1_RNA|LOXL1-AS1_ENST00000565416.1_RNA|LOXL1-AS1_ENST00000568229.1_RNA|LOXL1-AS1_ENST00000567257.1_RNA	NM_005576.2	NP_005567.2	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1	153			G -> D (associated with exfoliation syndrome in the presence of L-141; dbSNP:rs3825942). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17690259}.		extracellular matrix organization (GO:0030198)|oxidation-reduction process (GO:0055114)|protein deamination (GO:0018277)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor (GO:0016641)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						CGGCACGGGGGCTCCGCCTCC	0.731													G|||	1240	0.247604	0.41	0.1686	5008	,	,		5995	0.1399		0.1769	False		,,,				2504	0.2679				p.G153D		Atlas-SNP	.											.	LOXL1	25	.	0			c.G458A	GRCh37	CM074330	LOXL1	M	rs3825942	PASS	.	G	ASP/GLY	1563,2767		299,965,901	20.0	25.0	24.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	458	3.2	1.0	15	dbSNP_107	24	1231,7241		106,1019,3111	no	missense	LOXL1	NM_005576.2	94	405,1984,4012	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.5302,36.097,21.8247	possibly-damaging	153/575	74219582	2794,10008	2165	4236	6401	SO:0001583	missense	4016	exon1			ACGGGGGCTCCGC	L21186	CCDS10253.1	15q24-q25	2008-07-18			ENSG00000129038	ENSG00000129038			6665	protein-coding gene	gene with protein product		153456				7689553	Standard	NM_005576		Approved	LOXL, LOL	uc002awc.1	Q08397	OTTHUMG00000137595	ENST00000261921.7:c.458G>A	15.37:g.74219582G>A	ENSP00000261921:p.Gly153Asp	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	10	7	0.7	NM_005576	Q6NUL3|Q96BW7	Missense_Mutation	SNP	ENST00000261921.7	37	CCDS10253.1	491	0.22481684981684982	203	0.41260162601626016	71	0.19613259668508287	78	0.13636363636363635	139	0.18337730870712401	G	18.67	3.673592	0.67928	0.36097	0.145302	ENSG00000129038	ENST00000261921;ENST00000395162	T	0.32988	1.43	4.1	3.17	0.36434	.	0.201537	0.31936	N	0.006833	T	0.00012	0.0000	L	0.40543	1.245	0.25425	P	0.9882311	B	0.06786	0.001	B	0.06405	0.002	T	0.44003	-0.9356	9	0.36615	T	0.2	.	5.5084	0.16866	0.2367:0.0:0.7633:0.0	rs3825942;rs3825942	153	Q08397	LOXL1_HUMAN	D	153;15	ENSP00000261921:G153D	ENSP00000261921:G153D	G	+	2	0	LOXL1	72006635	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.700000	0.47085	1.818000	0.53035	0.448000	0.29417	GGC	G|0.767;A|0.233	0.233	strong		0.731	LOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268995.2	NM_005576	
AATK	9625	hgsc.bcm.edu	37	17	79093211	79093211	+	Silent	SNP	G	G	A	rs201255728	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79093211G>A	ENST00000326724.4	-	13	4077	c.4053C>T	c.(4051-4053)caC>caT	p.H1351H	AATK_ENST00000417379.1_Silent_p.H1248H	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1351					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			AGTCAGACACGTGCGTGATGG	0.746													G|||	4	0.000798722	0.0	0.0	5008	,	,		12763	0.0		0.003	False		,,,				2504	0.001				p.H1351H		Atlas-SNP	.											.	AATK	102	.	0			c.C4053T						PASS	.	G	,	2,4040		0,2,2019	15.0	19.0	18.0		4053,3744	-2.3	0.7	17		18	15,8273		0,15,4129	no	coding-synonymous,coding-synonymous	AATK	NM_001080395.2,NM_004920.2	,	0,17,6148	AA,AG,GG		0.181,0.0495,0.1379	,	1351/1375,1248/1272	79093211	17,12313	2021	4144	6165	SO:0001819	synonymous_variant	9625	exon13			AGACACGTGCGTG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.4053C>T	17.37:g.79093211G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	37	CCDS45807.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	5.059	0.196531	0.09599	4.95E-4	0.00181	ENSG00000181409	ENST00000417379	.	.	.	3.52	-2.34	0.06704	.	.	.	.	.	T	0.52289	0.1725	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48547	-0.9026	4	.	.	.	.	8.3273	0.32165	0.0794:0.0:0.3373:0.5832	.	.	.	.	M	1304	.	.	T	-	2	0	AATK	76707806	0.871000	0.30034	0.747000	0.31113	0.083000	0.17756	-0.123000	0.10611	-0.245000	0.09625	0.297000	0.19635	ACG	G|0.999;A|0.001	0.001	strong		0.746	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
SON	6651	hgsc.bcm.edu	37	21	34925697	34925697	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:34925697C>T	ENST00000356577.4	+	3	4635	c.4160C>T	c.(4159-4161)tCg>tTg	p.S1387L	SON_ENST00000300278.4_Missense_Mutation_p.S1387L|SON_ENST00000290239.6_Missense_Mutation_p.S1387L|SON_ENST00000381679.4_Missense_Mutation_p.S1387L|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1387	4 X 8 AA tandem repeats of V-L-E-SS- [AVT]-VT.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.S1387L(2)		breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						CTGGAGCCTTCGGTTGTGACT	0.557																																					p.S1387L		Atlas-SNP	.											SON_ENST00000300278,NS,carcinoma,0,2	SON	343	2	2	Substitution - Missense(2)	cervix(2)	c.C4160T						scavenged	.						80.0	73.0	75.0					21																	34925697		2203	4300	6503	SO:0001583	missense	6651	exon3			AGCCTTCGGTTGT	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.4160C>T	21.37:g.34925697C>T	ENSP00000348984:p.Ser1387Leu	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	214	4	0.0186916	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.08|12.08	1.829863|1.829863	0.32329|0.32329	.|.	.|.	ENSG00000159140|ENSG00000159140	ENST00000436227|ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	.|T;T;T;T	.|0.11821	.|2.95;2.94;2.93;2.74	5.68|5.68	1.53|1.53	0.23141|0.23141	.|.	.|1.520600	.|0.03714	.|N	.|0.250755	T|T	0.06554|0.06554	0.0168|0.0168	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B	.|0.01281	.|0.0;0.0;0.0;0.0;0.0	T|T	0.32640|0.32640	-0.9899|-0.9899	5|10	.|0.66056	.|D	.|0.02	.|.	2.2075|2.2075	0.03939|0.03939	0.1274:0.4798:0.1909:0.202|0.1274:0.4798:0.1909:0.202	.|.	.|1387;1387;1068;1387;1387	.|P18583-10;P18583;P18583-2;P18583-3;P18583-6	.|.;SON_HUMAN;.;.;.	W|L	382|1387	.|ENSP00000348984:S1387L;ENSP00000290239:S1387L;ENSP00000300278:S1387L;ENSP00000371095:S1387L	.|ENSP00000290239:S1387L	R|S	+|+	1|2	2|0	SON|SON	33847567|33847567	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-0.010000|-0.010000	0.12743|0.12743	0.282000|0.282000	0.22254|0.22254	-0.192000|-0.192000	0.12808|0.12808	CGG|TCG	.	.	none		0.557	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
ALOX15B	247	hgsc.bcm.edu	37	17	7950952	7950952	+	Silent	SNP	C	C	A	rs9898751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7950952C>A	ENST00000380183.4	+	12	1789	c.1650C>A	c.(1648-1650)tcC>tcA	p.S550S	ALOX15B_ENST00000380173.2_Silent_p.S521S|ALOX15B_ENST00000572022.1_Silent_p.S538S|ALOX15B_ENST00000573359.1_Silent_p.S476S	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	550	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)	p.S550S(2)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						TCACCTGCTCCGCCAAGCATG	0.627													A|||	2241	0.447484	0.5855	0.5043	5008	,	,		18084	0.3423		0.4105	False		,,,				2504	0.3671				p.S550S		Atlas-SNP	.											ALOX15B,NS,carcinoma,0,2	ALOX15B	66	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(1)|stomach(1)	c.C1650A						PASS	.	A	,,	2378,2028	556.3+/-379.5	642,1094,467	47.0	41.0	43.0		1563,1428,1650	-1.7	0.9	17	dbSNP_119	43	3429,5171	627.2+/-397.9	699,2031,1570	no	coding-synonymous,coding-synonymous,coding-synonymous	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	,,	1341,3125,2037	AA,AC,CC		39.8721,46.0281,44.6486	,,	521/648,476/603,550/677	7950952	5807,7199	2203	4300	6503	SO:0001819	synonymous_variant	247	exon12			CTGCTCCGCCAAG	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1650C>A	17.37:g.7950952C>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Silent	SNP	ENST00000380183.4	37	CCDS11128.1																																																																																			C|0.565;A|0.435	0.435	strong		0.627	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
IL3RA	3563	hgsc.bcm.edu	37	X	1471062	1471062	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:1471062G>C	ENST00000331035.4	+	5	717	c.368G>C	c.(367-369)aGc>aCc	p.S123T	IL3RA_ENST00000381469.2_Missense_Mutation_p.S45T	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha (low affinity)	123			S -> T (in dbSNP:rs17883572). {ECO:0000269|Ref.5}.		cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-3 receptor activity (GO:0004912)			lung(1)|skin(2)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	TTGAGCTGCAGCTGGGCGGTA	0.607													g|||	10	0.00199681	0.0008	0.0043	5008	,	,		15306	0.0		0.006	False		,,,				2504	0.0				p.S123T		Atlas-SNP	.											.	IL3RA	49	.	0			c.G368C						PASS	.	G	THR/SER	3,4399		0,3,2198	120.0	137.0	131.0		368	-1.7	0.0	X	dbSNP_134	131	34,8558		0,34,4262	no	missense	IL3RA	NM_002183.2	58	0,37,6460	CC,CG,GG		0.3957,0.0682,0.2847	benign	123/379	1471062	37,12957	2201	4296	6497	SO:0001583	missense	3563	exon5			GCTGCAGCTGGGC	M74782	CCDS14113.1, CCDS59158.1	Xp22.3 and Yp13.3	2008-07-21			ENSG00000185291	ENSG00000185291		"""Pseudoautosomal regions / PAR1"", ""Interleukins and interleukin receptors"", ""CD molecules"""	6012	protein-coding gene	gene with protein product		308385, 430000				1833064	Standard	NM_002183		Approved	CD123	uc004cps.3	P26951	OTTHUMG00000021059	ENST00000331035.4:c.368G>C	X.37:g.1471062G>C	ENSP00000327890:p.Ser123Thr	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	115	107	0.930435	NM_002183	A8K3F3|B9VI81|Q5HYQ7|Q5HYQ8|Q9UEH7	Missense_Mutation	SNP	ENST00000331035.4	37	CCDS14113.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	.	3.020	-0.202042	0.06219	6.82E-4	0.003957	ENSG00000185291	ENST00000331035;ENST00000432757;ENST00000381469	D;D;D	0.82803	-1.65;-1.65;-1.65	1.88	-1.72	0.08107	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Short hematopoietin receptor, family 2, conserved site (1);Immunoglobulin-like fold (1);	12.972700	0.00397	U	0.000044	T	0.64853	0.2636	N	0.10707	0.03	0.09310	N	1	D;P	0.55172	0.97;0.62	P;B	0.53146	0.719;0.388	T	0.61739	-0.7001	10	0.11485	T	0.65	0.013	2.6035	0.04872	0.4136:0.2668:0.3195:0.0	.	44;123	P26951-2;P26951	.;IL3RA_HUMAN	T	123;45;45	ENSP00000327890:S123T;ENSP00000414867:S45T;ENSP00000370878:S45T	ENSP00000327890:S123T	S	+	2	0	IL3RA	1431062	0.115000	0.22152	0.001000	0.08648	0.020000	0.10135	-0.706000	0.05047	-0.389000	0.07786	0.365000	0.22127	AGC	.	.	weak		0.607	IL3RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055600.3		
ABCA13	154664	hgsc.bcm.edu	37	7	48313510	48313510	+	Missense_Mutation	SNP	A	A	G	rs17547830	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:48313510A>G	ENST00000435803.1	+	17	4271	c.4247A>G	c.(4246-4248)cAt>cGt	p.H1416R		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1416				H -> R (in Ref. 1; AAP13576). {ECO:0000305}.	transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TCACAAGGTCATCTTCAAAAT	0.303													A|||	938	0.1873	0.1566	0.2032	5008	,	,		17417	0.0129		0.3917	False		,,,				2504	0.1871				p.H1416R		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A4247G						PASS	.	A	ARG/HIS	671,2947		69,533,1207	39.0	36.0	37.0		4247	-7.5	0.0	7	dbSNP_123	37	2865,5253		499,1867,1693	yes	missense	ABCA13	NM_152701.3	29	568,2400,2900	GG,GA,AA		35.2919,18.5462,30.1295	benign	1416/5059	48313510	3536,8200	1809	4059	5868	SO:0001583	missense	154664	exon17			AAGGTCATCTTCA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4247A>G	7.37:g.48313510A>G	ENSP00000411096:p.His1416Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	154	84	0.545455	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	477	0.2184065934065934	85	0.17276422764227642	80	0.22099447513812154	5	0.008741258741258742	307	0.4050131926121372	A	3.082	-0.188874	0.06299	0.185462	0.352919	ENSG00000179869	ENST00000435803	D	0.85088	-1.94	5.04	-7.5	0.01351	.	0.720289	0.12327	N	0.478767	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.19192	-1.0313	8	.	.	.	.	2.3723	0.04333	0.2845:0.3312:0.2764:0.1079	rs17547830;rs52821200;rs58931054;rs17547830	1416	Q86UQ4	ABCAD_HUMAN	R	1416	ENSP00000411096:H1416R	.	H	+	2	0	ABCA13	48284056	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.100000	0.10990	-1.571000	0.01663	-0.464000	0.05259	CAT	A|0.781;G|0.219	0.219	strong		0.303	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
NPEPL1	79716	hgsc.bcm.edu	37	20	57282190	57282190	+	Silent	SNP	G	G	A	rs41310841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:57282190G>A	ENST00000356091.6	+	7	1122	c.834G>A	c.(832-834)ccG>ccA	p.P278P	STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525817.1_Silent_p.P230P|NPEPL1_ENST00000525967.1_Silent_p.P250P	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	278						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			CTACCATGCCGGGGATGAAGC	0.692													G|||	179	0.0357428	0.0038	0.0389	5008	,	,		12769	0.1042		0.0358	False		,,,				2504	0.0061				p.P278P		Atlas-SNP	.											NPEPL1,NS,carcinoma,0,1	NPEPL1	36	1	0			c.G834A						PASS	.	G	,,	27,3877		0,27,1925	11.0	15.0	13.0		750,690,834	-8.9	0.1	20	dbSNP_127	13	240,7886		2,236,3825	no	coding-synonymous,coding-synonymous,coding-synonymous	NPEPL1	NM_001204872.1,NM_001204873.1,NM_024663.3	,,	2,263,5750	AA,AG,GG		2.9535,0.6916,2.2195	,,	250/496,230/476,278/524	57282190	267,11763	1952	4063	6015	SO:0001819	synonymous_variant	79716	exon7			CATGCCGGGGATG	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.834G>A	20.37:g.57282190G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	161	68	0.42236	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	37	CCDS46621.1																																																																																			G|0.947;A|0.053	0.053	strong		0.692	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240804	39240804	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240804C>A	ENST00000391417.4	+	1	346	c.346C>A	c.(346-348)Cgc>Agc	p.R116S		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	141	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)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						cagctgctgccgcccctgctg	0.672																																					p.R116S		Atlas-SNP	.											KRTAP4-7,caecum,carcinoma,0,1	KRTAP4-7	49	1	0			c.C346A						scavenged	.						15.0	16.0	16.0					17																	39240804		692	1588	2280	SO:0001583	missense	100132476	exon1			TGCTGCCGCCCCT	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.346C>A	17.37:g.39240804C>A	ENSP00000375236:p.Arg116Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	64	9	0.140625	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.016	-1.524493	0.00959	.	.	ENSG00000240871	ENST00000391417	T	0.00596	6.32	3.15	-6.29	0.02013	.	0.163808	0.19966	U	0.102091	T	0.00241	0.0007	.	.	.	0.09310	N	0.999997	B	0.33748	0.423	B	0.29524	0.103	T	0.47661	-0.9100	9	0.11794	T	0.64	.	1.8893	0.03244	0.1228:0.1811:0.2435:0.4526	.	171	Q9BYR0	KRA47_HUMAN	S	116	ENSP00000375236:R116S	ENSP00000375236:R116S	R	+	1	0	KRTAP4-7	36494330	0.000000	0.05858	0.002000	0.10522	0.468000	0.32798	-3.208000	0.00557	-2.496000	0.00513	-0.734000	0.03567	CGC	.	.	none		0.672	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
TMPO	7112	hgsc.bcm.edu	37	12	98927830	98927830	+	Intron	SNP	C	C	G	rs17459334	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:98927830C>G	ENST00000556029.1	+	3	921				TMPO_ENST00000266732.4_Missense_Mutation_p.Q599E|TMPO_ENST00000261210.5_Intron|TMPO_ENST00000393053.2_Intron|TMPO_ENST00000343315.5_Intron	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						AGACATTAGTCAAGCTGCACA	0.468													C|||	295	0.0589058	0.003	0.0403	5008	,	,		22302	0.001		0.1093	False		,,,				2504	0.1554				p.Q599E		Atlas-SNP	.											TMPO_ENST00000266732,rectum,carcinoma,0,1	TMPO	111	1	0			c.C1795G						PASS	.	C	,,GLU/GLN	95,4311	77.3+/-115.6	2,91,2110	99.0	79.0	86.0		,,1795	6.0	1.0	12	dbSNP_123	86	830,7770	192.0+/-238.1	32,766,3502	yes	intron,intron,missense	TMPO	NM_001032283.2,NM_001032284.2,NM_003276.2	,,29	34,857,5612	GG,GC,CC		9.6512,2.1562,7.1121	,,possibly-damaging	,,599/695	98927830	925,12081	2203	4300	6503	SO:0001627	intron_variant	7112	exon4			ATTAGTCAAGCTG		CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"""LEM domain containing 4"""	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.565+2214C>G	12.37:g.98927830C>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_003276	A2T926|Q14861	Missense_Mutation	SNP	ENST00000556029.1	37	CCDS31879.1	101	0.04624542124542125	1	0.0020325203252032522	19	0.052486187845303865	0	0.0	81	0.10686015831134564	C	14.20	2.463925	0.43736	0.021562	0.096512	ENSG00000120802	ENST00000266732	T	0.59772	0.24	5.96	5.96	0.96718	.	0.461649	0.22945	N	0.053734	T	0.01254	0.0041	N	0.24115	0.695	0.09310	P	1.0	P	0.49090	0.919	P	0.44447	0.45	T	0.10428	-1.0630	9	0.42905	T	0.14	.	15.9221	0.79583	0.0:1.0:0.0:0.0	rs17459334;rs52831524;rs17459334	599	P42166	LAP2A_HUMAN	E	599	ENSP00000266732:Q599E	ENSP00000266732:Q599E	Q	+	1	0	TMPO	97451961	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.147000	0.42226	2.832000	0.97577	0.655000	0.94253	CAA	C|0.934;G|0.066	0.066	strong		0.468	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276	
OR14C36	127066	hgsc.bcm.edu	37	1	248512498	248512498	+	Missense_Mutation	SNP	A	A	G	rs28448343	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248512498A>G	ENST00000317861.1	+	1	422	c.422A>G	c.(421-423)cAg>cGg	p.Q141R		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	141			Q -> R (in dbSNP:rs28448343).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						ATCTGCATCCAGATGACACTG	0.522													a|||	1274	0.254393	0.0923	0.2594	5008	,	,		22483	0.4276		0.1938	False		,,,				2504	0.3538				p.Q141R		Atlas-SNP	.											OR14C36,rectum,carcinoma,+1,1	OR14C36	113	1	0			c.A422G						PASS	.	A	ARG/GLN	484,3922	225.2+/-241.2	28,428,1747	108.0	94.0	99.0		422	-1.4	0.0	1	dbSNP_125	99	1637,6963	303.4+/-306.4	154,1329,2817	yes	missense	OR14C36	NM_001001918.1	43	182,1757,4564	GG,GA,AA		19.0349,10.985,16.3079	probably-damaging	141/313	248512498	2121,10885	2203	4300	6503	SO:0001583	missense	127066	exon1			GCATCCAGATGAC	BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"""GPCR / Class A : Olfactory receptors"""	15026	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BF, member 1"""	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.422A>G	1.37:g.248512498A>G	ENSP00000324534:p.Gln141Arg	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	178	94	0.52809	NM_001001918	Q6IEZ6	Missense_Mutation	SNP	ENST00000317861.1	37	CCDS31112.1	530	0.24267399267399267	61	0.12398373983739837	80	0.22099447513812154	232	0.40559440559440557	157	0.20712401055408972	A	10.28	1.305831	0.23736	0.10985	0.190349	ENSG00000177174	ENST00000317861	T	0.00091	8.74	4.05	-1.39	0.08997	GPCR, rhodopsin-like superfamily (1);	0.581781	0.14757	N	0.300211	T	0.00012	0.0000	L	0.42686	1.345	0.80722	P	0.0	D	0.60575	0.988	D	0.64877	0.93	T	0.11227	-1.0596	9	0.17832	T	0.49	.	1.3952	0.02259	0.4131:0.2239:0.2448:0.1182	rs28448343	141	Q8NHC7	O14CZ_HUMAN	R	141	ENSP00000324534:Q141R	ENSP00000324534:Q141R	Q	+	2	0	OR14C36	246579121	0.000000	0.05858	0.000000	0.03702	0.388000	0.30384	-1.082000	0.03400	-0.119000	0.11830	-0.560000	0.04181	CAG	A|0.811;G|0.189	0.189	strong		0.522	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918	
OR1N2	138882	hgsc.bcm.edu	37	9	125316033	125316033	+	Silent	SNP	T	T	C	rs1341042	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:125316033T>C	ENST00000373688.2	+	1	643	c.585T>C	c.(583-585)taT>taC	p.Y195Y		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						CTCATTTCTATTGTGATCCTA	0.537													C|||	2799	0.558906	0.5961	0.5908	5008	,	,		18406	0.6637		0.4791	False		,,,				2504	0.4601				p.Y195Y		Atlas-SNP	.											.	OR1N2	51	.	0			c.T585C						PASS	.	C		2530,1876	541.1+/-375.7	715,1100,388	168.0	154.0	159.0		585	2.5	1.0	9	dbSNP_88	159	4211,4389	583.4+/-391.5	1011,2189,1100	no	coding-synonymous	OR1N2	NM_001004457.1		1726,3289,1488	CC,CT,TT		48.9651,42.5783,48.1701		195/331	125316033	6741,6265	2203	4300	6503	SO:0001819	synonymous_variant	138882	exon1			TTTCTATTGTGAT		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.585T>C	9.37:g.125316033T>C		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	246	105	0.426829	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Silent	SNP	ENST00000373688.2	37	CCDS35123.1																																																																																			T|0.470;C|0.530	0.530	strong		0.537	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
OR8D4	338662	hgsc.bcm.edu	37	11	123777302	123777302	+	Missense_Mutation	SNP	T	T	G	rs17127947	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:123777302T>G	ENST00000321355.2	+	1	194	c.164T>G	c.(163-165)cTt>cGt	p.L55R		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	55			L -> R (in dbSNP:rs17127947).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L55R(1)		large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		AATCGTCAACTTCATACCCCC	0.408													T|||	934	0.186502	0.2844	0.1455	5008	,	,		20366	0.0933		0.1829	False		,,,				2504	0.183				p.L55R		Atlas-SNP	.											OR8D4,NS,carcinoma,0,1	OR8D4	62	1	1	Substitution - Missense(1)	stomach(1)	c.T164G						PASS	.	T	ARG/LEU	1081,3323	392.4+/-328.5	140,801,1261	243.0	230.0	235.0		164	5.7	0.8	11	dbSNP_123	235	1636,6962	303.2+/-306.3	164,1308,2827	yes	missense	OR8D4	NM_001005197.1	102	304,2109,4088	GG,GT,TT		19.0277,24.5459,20.8968	probably-damaging	55/315	123777302	2717,10285	2202	4299	6501	SO:0001583	missense	338662	exon1			GTCAACTTCATAC	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"""GPCR / Class A : Olfactory receptors"""	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.164T>G	11.37:g.123777302T>G	ENSP00000325381:p.Leu55Arg	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	261	134	0.51341	NM_001005197	Q6IFE9	Missense_Mutation	SNP	ENST00000321355.2	37	CCDS31698.1	406	0.1858974358974359	133	0.2703252032520325	57	0.1574585635359116	75	0.13111888111888112	141	0.18601583113456466	T	15.75	2.926498	0.52759	0.245459	0.190277	ENSG00000181518	ENST00000321355	T	0.14766	2.48	5.67	5.67	0.87782	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42821	D	0.000647	T	0.00012	0.0000	H	0.98802	4.335	0.20873	P	0.999832108	D	0.89917	1.0	D	0.79108	0.992	T	0.23511	-1.0186	9	0.87932	D	0	.	14.8892	0.70594	0.0:0.0:0.0:1.0	rs17127947;rs17127947	55	Q8NGM9	OR8D4_HUMAN	R	55	ENSP00000325381:L55R	ENSP00000325381:L55R	L	+	2	0	OR8D4	123282512	1.000000	0.71417	0.780000	0.31762	0.121000	0.20230	7.872000	0.87187	2.143000	0.66587	0.533000	0.62120	CTT	G|0.199;N|0.000	0.199	strong		0.408	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197	
KIAA0556	23247	hgsc.bcm.edu	37	16	27752099	27752099	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:27752099G>T	ENST00000261588.4	+	15	2500	c.2481G>T	c.(2479-2481)caG>caT	p.Q827H		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	827						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						AGAGACCCCAGAGGGCAACCA	0.607																																					p.Q827H		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G2481T						PASS	.						47.0	49.0	48.0					16																	27752099		2197	4300	6497	SO:0001583	missense	23247	exon15			ACCCCAGAGGGCA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.2481G>T	16.37:g.27752099G>T	ENSP00000261588:p.Gln827His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.817035	0.32145	.	.	ENSG00000047578	ENST00000261588	T	0.10960	2.82	5.15	-1.1	0.09872	.	0.718739	0.13839	N	0.359178	T	0.12092	0.0294	L	0.50333	1.59	0.09310	N	1	P	0.42649	0.786	P	0.47251	0.542	T	0.15350	-1.0440	10	0.41790	T	0.15	-18.0325	5.0513	0.14511	0.3084:0.4201:0.2715:0.0	.	827	O60303	K0556_HUMAN	H	827	ENSP00000261588:Q827H	ENSP00000261588:Q827H	Q	+	3	2	KIAA0556	27659600	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.385000	0.20685	-0.176000	0.10707	-0.305000	0.09177	CAG	.	.	none		0.607	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558345	140558345	+	Missense_Mutation	SNP	G	G	C	rs2950844	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140558345G>C	ENST00000239444.2	+	1	975	c.730G>C	c.(730-732)Gag>Cag	p.E244Q	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	244			E -> Q (in dbSNP:rs2950844). {ECO:0000269|PubMed:10380929}.		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTGAATTTGAGCAGCCTTT	0.502													G|||	485	0.096845	0.0166	0.0879	5008	,	,		3441	0.0913		0.1451	False		,,,				2504	0.1677				p.E244Q		Atlas-SNP	.											.	PCDHB8	199	.	0			c.G730C						PASS	.	G	GLN/GLU	214,4192	131.0+/-167.6	5,204,1994	205.0	266.0	246.0		730	2.3	1.0	5	dbSNP_101	246	1403,7197	268.9+/-288.1	136,1131,3033	yes	missense	PCDHB8	NM_019120.3	29	141,1335,5027	CC,CG,GG		16.314,4.857,12.4327	benign	244/802	140558345	1617,11389	2203	4300	6503	SO:0001583	missense	56128	exon1			GAATTTGAGCAGC	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.730G>C	5.37:g.140558345G>C	ENSP00000239444:p.Glu244Gln	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	467	156	0.334047	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	219	0.10027472527472528	12	0.024390243902439025	40	0.11049723756906077	51	0.08916083916083917	116	0.15303430079155672	g	8.522	0.868938	0.17322	0.04857	0.16314	ENSG00000120322	ENST00000239444	T	0.60920	0.15	4.25	2.31	0.28768	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.00144	0.0004	N	0.21448	0.665	0.39918	P	0.02588900000000005	B	0.12013	0.005	B	0.11329	0.006	T	0.04115	-1.0976	8	0.39692	T	0.17	.	2.2067	0.03937	0.3016:0.0:0.4496:0.2488	rs2950844;rs17844491	244	Q9UN66	PCDB8_HUMAN	Q	244	ENSP00000239444:E244Q	ENSP00000239444:E244Q	E	+	1	0	PCDHB8	140538529	0.009000	0.17119	0.993000	0.49108	0.993000	0.82548	0.192000	0.17096	1.911000	0.55334	0.585000	0.79938	GAG	G|0.884;C|0.116	0.116	strong		0.502	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
ZNF326	284695	hgsc.bcm.edu	37	1	90493026	90493026	+	Silent	SNP	G	G	A	rs10922744	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:90493026G>A	ENST00000340281.4	+	12	1658	c.1515G>A	c.(1513-1515)gaG>gaA	p.E505E	ZNF326_ENST00000370447.3_Silent_p.E416E|ZNF326_ENST00000455342.2_Silent_p.E299E	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	505	Glu-rich.				mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		atgaagatgaggaagaagaag	0.443													G|||	3165	0.631989	0.4667	0.7032	5008	,	,		16829	0.8899		0.5706	False		,,,				2504	0.6022				p.E505E		Atlas-SNP	.											.	ZNF326	60	.	0			c.G1515A						PASS	.	G		2181,2225	583.5+/-385.8	537,1107,559	87.0	86.0	87.0		1515	-9.7	0.0	1	dbSNP_120	87	4786,3814	610.0+/-395.6	1320,2146,834	no	coding-synonymous	ZNF326	NM_182976.2		1857,3253,1393	AA,AG,GG		44.3488,49.5007,46.4324		505/583	90493026	6967,6039	2203	4300	6503	SO:0001819	synonymous_variant	284695	exon12			AGATGAGGAAGAA	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"""Zinc fingers, C2H2-type"""	14104	protein-coding gene	gene with protein product	"""ZNF-protein interacting with nuclear mRNPs and DBC1"""	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1515G>A	1.37:g.90493026G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	141	67	0.475177	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Silent	SNP	ENST00000340281.4	37	CCDS727.1																																																																																			A|0.588;G|0.412	0.588	strong		0.443	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781	
Unknown	0	hgsc.bcm.edu	37	X	71379881	71379881	+	IGR	SNP	G	G	A	rs6624600	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:71379881G>A								BX119917.1 (7617 upstream) : PIN4 (21644 downstream)																							CAAAGGTACCGAAAGCACAGT	0.453													G|||	1652	0.437616	0.1747	0.3112	3775	,	,		16157	0.7143		0.1769	False		,,,				2504	0.3139				p.E68K		Atlas-SNP	.											.	FLJ44635	13	.	0			c.G202A						PASS	.	G	LYS/GLU	926,2909		93,592,148,947,423	102.0	87.0	92.0		202	0.5	0.5	X	dbSNP_116	92	1509,5219		122,838,427,1468,1445	no	missense	FLJ44635	NM_207422.2	56	215,1430,575,2415,1868	AA,AG,A,GG,G		22.4287,24.146,23.0522	benign	68/141	71379881	2435,8128	2203	4300	6503	SO:0001628	intergenic_variant	0	exon2			GGTACCGAAAGCA																													X.37:g.71379881G>A		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	128	125	0.976562	NM_207422		Missense_Mutation	SNP		37																																																																																				G|0.566;A|0.434	0.434	strong	0	0.453								
HIVEP1	3096	hgsc.bcm.edu	37	6	12122174	12122174	+	Missense_Mutation	SNP	A	A	G	rs34746669|rs2228210	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:12122174A>G	ENST00000379388.2	+	4	2478	c.2146A>G	c.(2146-2148)Acg>Gcg	p.T716A		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	716			T -> A (in dbSNP:rs2228210).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TCTTGTCACCACGTCAACACC	0.527													A|||	1043	0.208267	0.0204	0.245	5008	,	,		21328	0.2232		0.34	False		,,,				2504	0.2853				p.T716A		Atlas-SNP	.											.	HIVEP1	242	.	0			c.A2146G						PASS	.	A	ALA/THR	274,3896		10,254,1821	65.0	65.0	65.0		2146	-7.6	0.0	6	dbSNP_98	65	2940,5464		518,1904,1780	yes	missense	HIVEP1	NM_002114.2	58	528,2158,3601	GG,GA,AA		34.9833,6.5707,25.5607	benign	716/2719	12122174	3214,9360	2085	4202	6287	SO:0001583	missense	3096	exon4			GTCACCACGTCAA	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.2146A>G	6.37:g.12122174A>G	ENSP00000368698:p.Thr716Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	490	0.22435897435897437	15	0.03048780487804878	88	0.2430939226519337	134	0.23426573426573427	253	0.3337730870712401	A	8.900	0.956058	0.18507	0.065707	0.349833	ENSG00000095951	ENST00000379388	T	0.06849	3.25	5.81	-7.64	0.01286	.	0.486110	0.15530	N	0.257524	T	0.01029	0.0034	N	0.16368	0.405	0.38073	P	0.06356600000000001	B	0.10296	0.003	B	0.04013	0.001	T	0.47799	-0.9089	8	.	.	.	-2.3451	8.1908	0.31368	0.3201:0.3697:0.3102:0.0	rs2228210;rs3800501;rs17609169;rs60098115;rs2228210	716	P15822	ZEP1_HUMAN	A	716	ENSP00000368698:T716A	.	T	+	1	0	HIVEP1	12230160	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.339000	0.07832	-1.190000	0.02698	-1.077000	0.02231	ACG	A|0.754;C|0.002	.	strong		0.527	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
TRIM5	85363	hgsc.bcm.edu	37	11	5688940	5688940	+	Splice_Site	SNP	C	C	T	rs11038628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5688940C>T	ENST00000380034.3	-	5	1002	c.746G>A	c.(745-747)gGt>gAt	p.G249D	TRIM5_ENST00000396853.4_Intron|TRIM5_ENST00000483835.1_5'UTR|TRIM5_ENST00000380027.1_Splice_Site_p.G249D|TRIM5_ENST00000305836.5_Intron|TRIM5_ENST00000396855.3_Splice_Site_p.G249D|TRIM5_ENST00000396847.3_Splice_Site_p.G249D	NM_033034.2|NM_033092.2	NP_149023.2|NP_149083.2	Q9C035	TRIM5_HUMAN	tripartite motif containing 5	249			G -> D (in dbSNP:rs11038628). {ECO:0000269|PubMed:16401428, ECO:0000269|Ref.9}.		activation of innate immune response (GO:0002218)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|signaling pattern recognition receptor activity (GO:0008329)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		GCCATCCACACCCTAGGAAGA	0.418													C|||	1228	0.245208	0.3124	0.2291	5008	,	,		16810	0.4256		0.0586	False		,,,				2504	0.1718				p.G249D		Atlas-SNP	.											.	TRIM5	111	.	0			c.G746A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY	1122,3280	401.5+/-332.0	146,830,1225	131.0	119.0	123.0		746,746,746	1.3	1.0	11	dbSNP_120	123	502,8092	144.3+/-200.2	20,462,3815	yes	missense-near-splice,missense-near-splice,missense-near-splice	TRIM5	NM_033034.2,NM_033092.2,NM_033093.2	94,94,94	166,1292,5040	TT,TC,CC		5.8413,25.4884,12.4962	possibly-damaging,possibly-damaging,possibly-damaging	249/494,249/348,249/327	5688940	1624,11372	2201	4297	6498	SO:0001630	splice_region_variant	85363	exon5			TCCACACCCTAGG	AF220025	CCDS31392.1, CCDS31393.1, CCDS31394.1	11p15	2014-06-03	2011-01-25		ENSG00000132256	ENSG00000132256		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16276	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM5"", ""tripartite motif protein TRIM"""	608487	"""tripartite motif-containing 5"""			11331580	Standard	NM_033034		Approved	RNF88, TRIM5alpha	uc001mbm.2	Q9C035	OTTHUMG00000066893	ENST00000380034.3:c.745-1G>A	11.37:g.5688940C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	104	61	0.586538	NM_033093	A6NGQ1|A8WFA8|D3DQS8|D3DQS9|G3GJY1|Q2MLV4|Q2MLV8|Q2MLV9|Q2MLW1|Q2MLW3|Q2MLW4|Q2MLW6|Q2MLW7|Q2MLX1|Q2MLX2|Q2MLX3|Q2MLX5|Q2MLY3|Q2MLY4|Q2V6Q6|Q6GX26|Q8WU46|Q96SR5|Q9C031|Q9C032|Q9C033|Q9C034	Missense_Mutation	SNP	ENST00000380034.3	37	CCDS31393.1	519|519	0.23763736263736263|0.23763736263736263	160|160	0.3252032520325203|0.3252032520325203	73|73	0.20165745856353592|0.20165745856353592	243|243	0.42482517482517484|0.42482517482517484	43|43	0.05672823218997362|0.05672823218997362	C|C	0.074|0.074	-1.197052|-1.197052	0.01594|0.01594	0.254884|0.254884	0.058413|0.058413	ENSG00000132256|ENSG00000132256	ENST00000396855;ENST00000380034;ENST00000380027;ENST00000396847|ENST00000438025	T;T;T;T|.	0.03920|.	3.76;3.76;3.76;3.76|.	3.6|3.6	1.31|1.31	0.21738|0.21738	.|.	118.454000|.	0.00166|.	N|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02842|0.02842	-0.48|-0.48	0.09310|0.09310	P|P	0.99999999276468|0.99999999276468	B;B;B|.	0.06786|.	0.001;0.0;0.0|.	B;B;B|.	0.08055|.	0.003;0.002;0.001|.	T|T	0.47761|0.47761	-0.9092|-0.9092	9|4	0.02654|.	T|.	1|.	.|.	4.6583|4.6583	0.12630|0.12630	0.0:0.3059:0.0:0.6941|0.0:0.3059:0.0:0.6941	rs11038628;rs52820439;rs61161783;rs11038628|rs11038628;rs52820439;rs61161783;rs11038628	249;249;249|.	Q9C035-3;Q9C035-4;Q9C035|.	.;.;TRIM5_HUMAN|.	D|M	249|126	ENSP00000380064:G249D;ENSP00000369373:G249D;ENSP00000369366:G249D;ENSP00000380058:G249D|.	ENSP00000369366:G249D|.	G|V	-|-	2|1	0|0	TRIM5|TRIM5	5645516|5645516	0.411000|0.411000	0.25384|0.25384	0.971000|0.971000	0.41717|0.41717	0.026000|0.026000	0.11368|0.11368	-0.094000|-0.094000	0.11094|0.11094	0.279000|0.279000	0.22186|0.22186	-0.378000|-0.378000	0.06908|0.06908	GGT|GTG	C|0.821;T|0.179	0.179	strong		0.418	TRIM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143360.3	NM_033034	Missense_Mutation
ERAP2	64167	hgsc.bcm.edu	37	5	96232142	96232142	+	Silent	SNP	T	T	A	rs2548538	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96232142T>A	ENST00000437043.3	+	8	2016	c.1305T>A	c.(1303-1305)ccT>ccA	p.P435P	CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000515095.1_3'UTR|ERAP2_ENST00000379904.4_Silent_p.P390P	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	435					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		CATCCCGCCCTATCTCCAAAC	0.368													T|||	2768	0.552716	0.6014	0.5793	5008	,	,		18506	0.5278		0.5199	False		,,,				2504	0.5276				p.P435P		Atlas-SNP	.											.	ERAP2	77	.	0			c.T1305A						PASS	.	T	,	2553,1853	627.4+/-394.9	724,1105,374	78.0	81.0	80.0		1305,1305	-0.0	0.0	5	dbSNP_100	80	4482,4118	588.4+/-392.4	1154,2174,972	no	coding-synonymous,coding-synonymous	ERAP2	NM_001130140.1,NM_022350.3	,	1878,3279,1346	AA,AT,TT		47.8837,42.0563,45.9096	,	435/961,435/961	96232142	7035,5971	2203	4300	6503	SO:0001819	synonymous_variant	64167	exon8			CCGCCCTATCTCC	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1305T>A	5.37:g.96232142T>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	247	111	0.449393	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Silent	SNP	ENST00000437043.3	37	CCDS4086.1																																																																																			T|0.450;A|0.550	0.550	strong		0.368	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
OR1S1	219959	hgsc.bcm.edu	37	11	57982229	57982229	+	Missense_Mutation	SNP	A	A	G	rs1966836	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57982229A>G	ENST00000309433.6	+	1	13	c.13A>G	c.(13-15)Agt>Ggt	p.S5G		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	5			S -> G (in dbSNP:rs1966836).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				GAAGACTTTTAGTTCCTTTCT	0.378													G|||	3330	0.664936	0.3759	0.7622	5008	,	,		21265	0.8681		0.662	False		,,,				2504	0.7802				p.S5G		Atlas-SNP	.											.	OR1S1	139	.	0			c.A13G						PASS	.	G	GLY/SER	1840,2562	633.2+/-396.0	383,1074,744	114.0	104.0	107.0		13	-0.8	0.0	11	dbSNP_92	107	5871,2721	435.2+/-358.0	2036,1799,461	yes	missense	OR1S1	NM_001004458.1	56	2419,2873,1205	GG,GA,AA		31.669,41.7992,40.6572	benign	5/326	57982229	7711,5283	2201	4296	6497	SO:0001583	missense	219959	exon1			ACTTTTAGTTCCT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.13A>G	11.37:g.57982229A>G	ENSP00000311688:p.Ser5Gly	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	174	74	0.425287	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1421	0.6506410256410257	182	0.3699186991869919	262	0.7237569060773481	480	0.8391608391608392	497	0.6556728232189973	G	3.465	-0.109212	0.06924	0.417992	0.68331	ENSG00000172774	ENST00000309433	T	0.51817	0.69	3.1	-0.787	0.10943	.	1.086920	0.07475	N	0.902836	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.16166	0.016	B	0.12837	0.008	T	0.31779	-0.9931	9	0.26408	T	0.33	.	0.5763	0.00704	0.1698:0.2047:0.1803:0.4453	rs1966836;rs17152497;rs60905495;rs1966836	5	Q8NH92	OR1S1_HUMAN	G	5	ENSP00000311688:S5G	ENSP00000311688:S5G	S	+	1	0	OR1S1	57738805	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-1.762000	0.01803	-0.695000	0.05105	-2.467000	0.00204	AGT	G|0.613;N|0.000	0.613	strong		0.378	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
ITGB1	3688	hgsc.bcm.edu	37	10	33217110	33217110	+	Silent	SNP	G	G	A	rs2230394	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:33217110G>A	ENST00000396033.2	-	5	594	c.459C>T	c.(457-459)taC>taT	p.Y153Y	ITGB1_ENST00000423113.1_Silent_p.Y153Y|ITGB1_ENST00000302278.3_Silent_p.Y153Y|ITGB1_ENST00000484088.1_Intron|ITGB1_ENST00000374956.4_Silent_p.Y153Y	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	153	VWFA.				axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	CTTTCATTGAGTAAGACAGGT	0.383													G|||	1001	0.19988	0.2852	0.0951	5008	,	,		18832	0.3125		0.1233	False		,,,				2504	0.1217				p.Y153Y		Atlas-SNP	.											.	ITGB1	156	.	0			c.C459T						PASS	.	G	,,	1170,3236	411.5+/-335.8	165,840,1198	152.0	151.0	151.0		459,459,459	4.2	1.0	10	dbSNP_98	151	869,7731	197.8+/-242.3	40,789,3471	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB1	NM_002211.3,NM_033668.2,NM_133376.2	,,	205,1629,4669	AA,AG,GG		10.1047,26.5547,15.6774	,,	153/799,153/802,153/799	33217110	2039,10967	2203	4300	6503	SO:0001819	synonymous_variant	3688	exon5			CATTGAGTAAGAC	BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"""CD molecules"", ""Integrins"""	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.459C>T	10.37:g.33217110G>A		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	267	112	0.419476	NM_002211	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Silent	SNP	ENST00000396033.2	37	CCDS7174.1																																																																																			T|0.047;G|0.667;C|0.138;A|0.148	0.148	strong		0.383	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211	
SPTB	6710	hgsc.bcm.edu	37	14	65249052	65249052	+	Missense_Mutation	SNP	C	C	G	rs17245552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:65249052C>G	ENST00000389721.5	-	19	4254	c.4222G>C	c.(4222-4224)Ggc>Cgc	p.G1408R	SPTB_ENST00000542895.1_Missense_Mutation_p.G1408R|SPTB_ENST00000389722.3_Missense_Mutation_p.G1408R|SPTB_ENST00000389720.3_Missense_Mutation_p.G1408R|SPTB_ENST00000556626.1_Missense_Mutation_p.G1408R	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1408			G -> R (in dbSNP:rs17245552).		actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		AGGTCCTTGCCCGGGTCGTCT	0.582													C|||	509	0.101637	0.0938	0.0187	5008	,	,		20009	0.2262		0.0427	False		,,,				2504	0.1033				p.G1408R		Atlas-SNP	.											.	SPTB	378	.	0			c.G4222C						PASS	.	C	ARG/GLY,ARG/GLY	316,4090	169.8+/-200.3	11,294,1898	109.0	98.0	101.0		4222,4222	5.4	1.0	14	dbSNP_123	101	489,8111	140.5+/-197.0	12,465,3823	yes	missense,missense	SPTB	NM_000347.5,NM_001024858.2	125,125	23,759,5721	GG,GC,CC		5.686,7.172,6.1895	probably-damaging,probably-damaging	1408/2138,1408/2329	65249052	805,12201	2203	4300	6503	SO:0001583	missense	6710	exon19			CCTTGCCCGGGTC		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4222G>C	14.37:g.65249052C>G	ENSP00000374371:p.Gly1408Arg	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	179	103	0.575419	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	212	0.09706959706959707	53	0.10772357723577236	8	0.022099447513812154	117	0.20454545454545456	34	0.044854881266490766	C	29.1	4.980937	0.92982	0.07172	0.05686	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000553938;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T;T	0.56941	0.43;0.99;0.43;0.99;0.99;0.43	5.36	5.36	0.76844	.	0.166644	0.53938	D	0.000059	T	0.00241	0.0007	M	0.84219	2.685	0.09310	P	0.99999815977	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.85130	0.995;0.997;0.989	T	0.00926	-1.1512	9	0.72032	D	0.01	.	18.2137	0.89878	0.0:1.0:0.0:0.0	rs17245552;rs52835393;rs17245552	192;1408;1412	E7EV95;P11277;Q59FP5	.;SPTB1_HUMAN;.	R	1412;1408;192;73;1408;1408;1408;1408	ENSP00000374372:G1408R;ENSP00000451324:G73R;ENSP00000451752:G1408R;ENSP00000374371:G1408R;ENSP00000443882:G1408R;ENSP00000374370:G1408R	ENSP00000334218:G192R	G	-	1	0	SPTB	64318805	0.994000	0.37717	1.000000	0.80357	0.985000	0.73830	6.066000	0.71185	2.681000	0.91329	0.462000	0.41574	GGC	C|0.925;G|0.075	0.075	strong		0.582	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
MICAL1	64780	hgsc.bcm.edu	37	6	109768295	109768295	+	Silent	SNP	G	G	A	rs910730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:109768295G>A	ENST00000358807.3	-	17	2519	c.2208C>T	c.(2206-2208)taC>taT	p.Y736Y	MICAL1_ENST00000358577.3_Silent_p.Y650Y|MICAL1_ENST00000368952.4_Silent_p.Y755Y	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	736	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		GGTGCTGCTCGTAGCCACCTG	0.617													A|||	2762	0.551518	0.7557	0.4928	5008	,	,		18102	0.4504		0.4284	False		,,,				2504	0.5481				p.Y736Y		Atlas-SNP	.											.	MICAL1	79	.	0			c.C2208T						PASS	.	A	,	3070,1336	439.4+/-345.7	1071,928,204	65.0	65.0	65.0		1950,2208	-6.0	0.0	6	dbSNP_86	65	3613,4987	619.4+/-396.9	753,2107,1440	no	coding-synonymous,coding-synonymous	MICAL1	NM_001159291.1,NM_022765.3	,	1824,3035,1644	AA,AG,GG		42.0116,30.3223,48.616	,	650/982,736/1068	109768295	6683,6323	2203	4300	6503	SO:0001819	synonymous_variant	64780	exon17			CTGCTCGTAGCCA	AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"""NEDD9 interacting protein with calponin homology and LIM domains"""	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.2208C>T	6.37:g.109768295G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_022765	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Silent	SNP	ENST00000358807.3	37	CCDS5076.1																																																																																			G|0.464;A|0.536	0.536	strong		0.617	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765	
C21orf91	54149	hgsc.bcm.edu	37	21	19169218	19169218	+	Missense_Mutation	SNP	G	G	C	rs2824495	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:19169218G>C	ENST00000400558.3	-	3	435	c.345C>G	c.(343-345)aaC>aaG	p.N115K	C21orf91_ENST00000400559.3_Missense_Mutation_p.N115K|C21orf91_ENST00000284881.4_Missense_Mutation_p.N115K|C21orf91_ENST00000493464.1_5'UTR|AL109761.5_ENST00000428689.1_RNA	NM_001100421.1	NP_001093891.1			chromosome 21 open reading frame 91											endometrium(2)|large_intestine(2)|lung(4)|ovary(1)	9				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)		GATGCTGGGGGTTTTTAGAAC	0.353													G|||	1225	0.244609	0.2027	0.2435	5008	,	,		18011	0.3978		0.1918	False		,,,				2504	0.1984				p.N115K		Atlas-SNP	.											.	C21orf91	21	.	0			c.C345G						PASS	.	G	LYS/ASN,LYS/ASN,LYS/ASN	777,2847		70,637,1105	104.0	95.0	98.0		345,345,345	0.9	0.2	21	dbSNP_100	98	1655,6523		164,1327,2598	yes	missense,missense,missense	C21orf91	NM_001100420.1,NM_001100421.1,NM_017447.3	94,94,94	234,1964,3703	CC,CG,GG		20.2372,21.4404,20.6067	benign,benign,benign	115/298,115/222,115/297	19169218	2432,9370	1812	4089	5901	SO:0001583	missense	54149	exon3			CTGGGGGTTTTTA	AF239726	CCDS42907.1, CCDS42908.1, CCDS42909.1	21q21.1	2011-12-12	2003-07-22		ENSG00000154642	ENSG00000154642			16459	protein-coding gene	gene with protein product	"""cold sore susceptibility gene 1"", ""early undifferentiated retina and lens"""		"""chromosome 21 open reading frame 38"""	C21orf38, C21orf14		22039568	Standard	NM_001100421		Approved	YG81, EURL, CSSG1	uc002yko.4	Q9NYK6	OTTHUMG00000074509	ENST00000400558.3:c.345C>G	21.37:g.19169218G>C	ENSP00000383403:p.Asn115Lys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_017447		Missense_Mutation	SNP	ENST00000400558.3	37	CCDS42909.1	552	0.25274725274725274	103	0.20934959349593496	81	0.22375690607734808	216	0.3776223776223776	152	0.20052770448548812	G	1.977	-0.435132	0.04669	0.214404	0.202372	ENSG00000154642	ENST00000284881;ENST00000400559;ENST00000400558;ENST00000405964	T;T;T;T	0.13196	2.61;2.61;2.61;2.61	5.42	0.945	0.19543	.	0.742572	0.13586	N	0.376982	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.47142	-0.9140	8	.	.	.	-3.4099	4.9795	0.14157	0.6044:0.0:0.2421:0.1535	rs2824495;rs52814372;rs58817251;rs2824495	115;115	Q9NYK6-3;Q9NYK6	.;EURL_HUMAN	K	115	ENSP00000284881:N115K;ENSP00000383404:N115K;ENSP00000383403:N115K;ENSP00000385566:N115K	.	N	-	3	2	C21orf91	18091089	0.000000	0.05858	0.155000	0.22561	0.076000	0.17211	0.565000	0.23578	0.020000	0.15106	0.650000	0.86243	AAC	G|0.749;C|0.251	0.251	strong		0.353	C21orf91-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000158214.1	NM_017447	
GPR146	115330	hgsc.bcm.edu	37	7	1097394	1097394	+	Silent	SNP	T	T	C	rs11767527	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1097394T>C	ENST00000397095.1	+	2	466	c.243T>C	c.(241-243)ccT>ccC	p.P81P	C7orf50_ENST00000397100.2_Intron|GPR146_ENST00000297468.3_Silent_p.P81P|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000357429.6_Intron			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	81						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P81P(2)		autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		CCCTGGCCCCTGTGCACCTGC	0.652													t|||	345	0.0688898	0.0204	0.0821	5008	,	,		18317	0.0		0.1262	False		,,,				2504	0.137				p.P81P		Atlas-SNP	.											GPR146,NS,carcinoma,0,3	GPR146	20	3	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.T243C						PASS	.		,,,	200,4200	116.3+/-154.2	3,194,2003	34.0	31.0	32.0		,,,243	-7.6	0.0	7	dbSNP_120	32	1339,7259	240.0+/-270.9	102,1135,3062	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	105,1329,5065	CC,CT,TT		15.5734,4.5455,11.8403	,,,	,,,81/334	1097394	1539,11459	2200	4299	6499	SO:0001819	synonymous_variant	115330	exon1			GGCCCCTGTGCAC	BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"""GPCR / Class A : Orphans"""	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.243T>C	7.37:g.1097394T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_138445	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																			T|0.898;C|0.102	0.102	strong		0.652	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
SLC2A13	114134	hgsc.bcm.edu	37	12	40499347	40499347	+	Silent	SNP	G	G	A	rs7305377	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:40499347G>A	ENST00000280871.4	-	1	314	c.264C>T	c.(262-264)tcC>tcT	p.S88S	SLC2A13_ENST00000380858.1_Silent_p.S88S	NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	88					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				CGCCCAGCGCGGAGAAGACGG	0.721										HNSCC(50;0.14)			G|||	331	0.0660942	0.0212	0.0908	5008	,	,		11287	0.0308		0.1581	False		,,,				2504	0.0511				p.S88S		Atlas-SNP	.											.	SLC2A13	91	.	0			c.C264T						PASS	.	G		167,4153		5,157,1998	10.0	11.0	11.0		264	-3.8	1.0	12	dbSNP_116	11	1118,7344		58,1002,3171	no	coding-synonymous	SLC2A13	NM_052885.3		63,1159,5169	AA,AG,GG		13.212,3.8657,10.0532		88/649	40499347	1285,11497	2160	4231	6391	SO:0001819	synonymous_variant	114134	exon1			CAGCGCGGAGAAG	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"""Solute carriers"""	15956	protein-coding gene	gene with protein product	"""H(+)-myo-inositol symporter"""	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.264C>T	12.37:g.40499347G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_052885	Q17S07	Silent	SNP	ENST00000280871.4	37	CCDS8736.2																																																																																			G|0.909;A|0.091	0.091	strong		0.721	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2		
UBQLNL	143630	hgsc.bcm.edu	37	11	5536309	5536309	+	Missense_Mutation	SNP	G	G	C	rs12223282	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5536309G>C	ENST00000380184.1	-	1	1626	c.1363C>G	c.(1363-1365)Cag>Gag	p.Q455E	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	455			Q -> E (in dbSNP:rs12223282). {ECO:0000269|PubMed:15489334}.							endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		TGCCTCCACTGTTCACTCAGC	0.493													g|||	129	0.0257588	0.0038	0.049	5008	,	,		20936	0.0258		0.0477	False		,,,				2504	0.0164				p.Q455E		Atlas-SNP	.											.	UBQLNL	74	.	0			c.C1363G						PASS	.	C	GLU/GLN	39,4363	43.1+/-76.7	0,39,2162	112.0	109.0	110.0		1363	4.9	0.8	11	dbSNP_120	110	418,8176	130.8+/-188.7	6,406,3885	yes	missense	UBQLNL	NM_145053.4	29	6,445,6047	CC,CG,GG		4.8639,0.886,3.5165	benign	455/476	5536309	457,12539	2201	4297	6498	SO:0001583	missense	143630	exon1			TCCACTGTTCACT	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.1363C>G	11.37:g.5536309G>C	ENSP00000369531:p.Gln455Glu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	151	84	0.556291	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Missense_Mutation	SNP	ENST00000380184.1	37	CCDS31385.1	76	0.0347985347985348	3	0.006097560975609756	21	0.058011049723756904	21	0.03671328671328671	31	0.040897097625329816	g	4.784	0.145847	0.09134	0.00886	0.048639	ENSG00000175518	ENST00000380184;ENST00000538889	T	0.70164	-0.46	5.82	4.92	0.64577	.	0.455157	0.18573	N	0.137300	T	0.13927	0.0337	L	0.46819	1.47	0.18873	N	0.999983	P	0.46395	0.877	B	0.38106	0.265	T	0.21449	-1.0245	10	0.56958	D	0.05	.	13.1534	0.59503	0.0:0.1602:0.8398:0.0	rs12223282;rs17856392;rs52808354;rs12223282	455	Q8IYU4	UBQLN_HUMAN	E	455;240	ENSP00000369531:Q455E	ENSP00000369531:Q455E	Q	-	1	0	UBQLNL	5492885	0.558000	0.26554	0.791000	0.31998	0.006000	0.05464	1.818000	0.39012	1.461000	0.47929	-0.121000	0.15023	CAG	G|0.966;C|0.034	0.034	strong		0.493	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
ARHGEF40	55701	hgsc.bcm.edu	37	14	21553057	21553057	+	Missense_Mutation	SNP	T	T	C	rs943992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21553057T>C	ENST00000298694.4	+	18	4062	c.3935T>C	c.(3934-3936)aTg>aCg	p.M1312T	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.M1312T			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	1312	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		M -> T (in dbSNP:rs943992).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						GGGTCAGAGATGTTTGTTTAC	0.498													C|||	408	0.0814696	0.1604	0.0375	5008	,	,		20044	0.0337		0.0497	False		,,,				2504	0.0879				p.M1312T		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.T3935C						PASS	.	C	THR/MET	722,3684	758.4+/-412.8	61,600,1542	123.0	126.0	125.0		3935	2.3	0.9	14	dbSNP_86	125	427,8173	800.4+/-407.4	14,399,3887	yes	missense	ARHGEF40	NM_018071.3	81	75,999,5429	CC,CT,TT		4.9651,16.3867,8.8344	benign	1312/1520	21553057	1149,11857	2203	4300	6503	SO:0001583	missense	55701	exon18			CAGAGATGTTTGT		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.3935T>C	14.37:g.21553057T>C	ENSP00000298694:p.Met1312Thr	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	191	89	0.465969	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	37	CCDS32041.1	129	0.059065934065934064	63	0.12804878048780488	16	0.04419889502762431	13	0.022727272727272728	37	0.048812664907651716	C	0	-2.632363	0.00115	0.163867	0.049651	ENSG00000165801	ENST00000298694;ENST00000298693	T;T	0.10382	2.88;2.88	5.65	2.35	0.29111	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.502303	0.18658	N	0.134806	T	0.00012	0.0000	N	0.00075	-2.25	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38045	-0.9679	9	0.19147	T	0.46	.	8.5724	0.33578	0.122:0.6943:0.0:0.1836	rs943992;rs52791310;rs60297979;rs943992	1312;1312;598	Q8TER5-4;Q8TER5;Q8TER5-2	.;ARH40_HUMAN;.	T	1312	ENSP00000298694:M1312T;ENSP00000298693:M1312T	ENSP00000298693:M1312T	M	+	2	0	ARHGEF40	20622897	0.003000	0.15002	0.931000	0.37212	0.033000	0.12548	0.119000	0.15626	0.328000	0.23435	-2.068000	0.00393	ATG	T|0.922;C|0.078	0.078	strong		0.498	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
ZNF443	10224	hgsc.bcm.edu	37	19	12540971	12540971	+	Nonstop_Mutation	SNP	T	T	A	rs28559848	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12540971T>A	ENST00000301547.5	-	4	2212	c.2015A>T	c.(2014-2016)tAg>tTg	p.*672L	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						GAGAGAATGCTAGTGAGTCTT	0.358													.|||	1386	0.276757	0.3941	0.2378	5008	,	,		21465	0.13		0.1938	False		,,,				2504	0.3824				p.X672L		Atlas-SNP	.											.	ZNF443	63	.	0			c.A2015T						PASS	.						57.0	60.0	59.0					19																	12540971		2198	4293	6491	SO:0001578	stop_lost	10224	exon4			GAATGCTAGTGAG	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.2015A>T	19.37:g.12540971T>A		Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	248	206	0.830645	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	451	0.2065018315018315	175	0.3556910569105691	80	0.22099447513812154	61	0.10664335664335664	135	0.17810026385224276	T	0.181	-1.062509	0.01950	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	.	.	.	1.23	-1.27	0.09347	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.2666	0.20930	0.0:0.4958:0.0:0.5042	rs28559848;rs59804898;rs28559848	.	.	.	L	672;644	.	.	X	-	2	0	ZNF443	12401971	0.000000	0.05858	0.001000	0.08648	0.043000	0.13939	-1.865000	0.01649	-0.448000	0.07128	0.163000	0.16589	TAG	T|0.500;A|0.500	0.500	strong		0.358	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
SPTBN1	6711	hgsc.bcm.edu	37	2	54858435	54858435	+	Missense_Mutation	SNP	C	C	T	rs377200533		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:54858435C>T	ENST00000356805.4	+	16	3532	c.3251C>T	c.(3250-3252)gCg>gTg	p.A1084V	SPTBN1_ENST00000333896.5_Missense_Mutation_p.A1071V	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1084					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			ACCCAGACAGCGATCGCCTCG	0.587																																					p.A1084V		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C3251T						PASS	.	C	VAL/ALA,VAL/ALA	0,4406		0,0,2203	91.0	87.0	88.0		3212,3251	5.6	1.0	2		88	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SPTBN1	NM_178313.2,NM_003128.2	64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	1071/2156,1084/2365	54858435	1,13005	2203	4300	6503	SO:0001583	missense	6711	exon16			AGACAGCGATCGC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3251C>T	2.37:g.54858435C>T	ENSP00000349259:p.Ala1084Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	37	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.699502	0.68501	0.0	1.16E-4	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.49432	0.78;0.78	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.49609	0.1567	L	0.49640	1.575	0.80722	D	1	B;B	0.22800	0.029;0.075	B;B	0.29598	0.046;0.104	T	0.45425	-0.9262	10	0.54805	T	0.06	.	19.5376	0.95260	0.0:1.0:0.0:0.0	.	1071;1084	Q01082-3;Q01082	.;SPTB2_HUMAN	V	1084;1071	ENSP00000349259:A1084V;ENSP00000334156:A1071V	ENSP00000334156:A1071V	A	+	2	0	SPTBN1	54711939	1.000000	0.71417	0.997000	0.53966	0.709000	0.40893	4.910000	0.63321	2.620000	0.88729	0.655000	0.94253	GCG	.	.	weak		0.587	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
OR5H1	26341	hgsc.bcm.edu	37	3	97851661	97851661	+	Missense_Mutation	SNP	G	G	T	rs200721525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:97851661G>T	ENST00000354565.2	+	1	120	c.120G>T	c.(118-120)atG>atT	p.M40I	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M40I(4)		breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						TCACCATCATGGGGAATCTTG	0.413																																					p.M40I		Atlas-SNP	.											OR5H1,NS,carcinoma,0,7	OR5H1	71	7	4	Substitution - Missense(4)	endometrium(2)|kidney(2)	c.G120T						scavenged	.						46.0	50.0	48.0					3																	97851661		2173	4250	6423	SO:0001583	missense	26341	exon1			CATCATGGGGAAT	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"""GPCR / Class A : Olfactory receptors"""	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.120G>T	3.37:g.97851661G>T	ENSP00000346575:p.Met40Ile	Somatic	522	4	0.00766284		WXS	Illumina HiSeq	Phase_I	682	11	0.016129	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	37	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	G	3.467	-0.108676	0.06924	.	.	ENSG00000231192	ENST00000354565	T	0.00433	7.43	3.63	2.75	0.32379	.	0.578292	0.14348	N	0.325303	T	0.00178	0.0005	N	0.02842	-0.48	0.20764	N	0.999858	B	0.06786	0.001	B	0.04013	0.001	T	0.29882	-0.9997	10	0.33940	T	0.23	.	8.5896	0.33679	0.1182:0.0:0.8818:0.0	.	40	A6NKK0	OR5H1_HUMAN	I	40	ENSP00000346575:M40I	ENSP00000346575:M40I	M	+	3	0	OR5H1	99334351	0.002000	0.14202	0.678000	0.29963	0.118000	0.20060	-0.111000	0.10807	0.729000	0.32403	0.195000	0.17529	ATG	G|0.982;T|0.018	0.018	strong		0.413	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338	
CCDC88B	283234	hgsc.bcm.edu	37	11	64120835	64120835	+	Silent	SNP	C	C	T	rs61746624	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64120835C>T	ENST00000356786.5	+	22	3744	c.3700C>T	c.(3700-3702)Ctg>Ttg	p.L1234L	CCDC88B_ENST00000359902.2_Silent_p.L386L|CCDC88B_ENST00000301897.4_5'UTR|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	1234						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						ATTGACACAGCTGCGAAGTGC	0.652													C|||	6	0.00119808	0.0008	0.0	5008	,	,		16046	0.0		0.005	False		,,,				2504	0.0				p.L1234L		Atlas-SNP	.											.	CCDC88B	89	.	0			c.C3700T						PASS	.	C		4,4398		0,4,2197	20.0	26.0	24.0		3700	3.5	1.0	11	dbSNP_129	24	105,8487		2,101,4193	no	coding-synonymous	CCDC88B	NM_032251.5		2,105,6390	TT,TC,CC		1.2221,0.0909,0.8388		1234/1477	64120835	109,12885	2201	4296	6497	SO:0001819	synonymous_variant	283234	exon22			ACACAGCTGCGAA	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.3700C>T	11.37:g.64120835C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			C|0.993;T|0.007	0.007	strong		0.652	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
SLC9A1	6548	hgsc.bcm.edu	37	1	27480757	27480757	+	Silent	SNP	A	A	G	rs34306208	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:27480757A>G	ENST00000263980.3	-	1	644	c.69T>C	c.(67-69)gtT>gtC	p.V23V	SLC9A1_ENST00000374086.3_Silent_p.V23V|SLC9A1_ENST00000545949.1_5'UTR	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	23					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	CCACCAAAGCAACCACCACGA	0.597													G|||	1251	0.2498	0.2534	0.1902	5008	,	,		17269	0.1161		0.332	False		,,,				2504	0.3405				p.V23V		Atlas-SNP	.											.	SLC9A1	68	.	0			c.T69C						PASS	.	G		1195,3211	707.3+/-407.5	166,863,1174	86.0	74.0	78.0		69	-9.2	0.0	1	dbSNP_126	78	3056,5544	661.1+/-401.8	546,1964,1790	no	coding-synonymous	SLC9A1	NM_003047.3		712,2827,2964	GG,GA,AA		35.5349,27.1221,32.6849		23/816	27480757	4251,8755	2203	4300	6503	SO:0001819	synonymous_variant	6548	exon1			CAAAGCAACCACC	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"""Solute carriers"""	11071	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 143"""	107310	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 1"""	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.69T>C	1.37:g.27480757A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_003047	B1ALD6|D3DPL4|Q96EM2	Silent	SNP	ENST00000263980.3	37	CCDS295.1																																																																																			A|0.711;G|0.289	0.289	strong		0.597	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047	
FHAD1	114827	hgsc.bcm.edu	37	1	15668319	15668319	+	Missense_Mutation	SNP	G	G	A	rs12126178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:15668319G>A	ENST00000375998.4	+	14	1994	c.1994G>A	c.(1993-1995)cGa>cAa	p.R665Q	FHAD1_ENST00000417793.1_Missense_Mutation_p.R665Q|FHAD1_ENST00000375999.3_Missense_Mutation_p.R665Q|RP3-467K16.2_ENST00000428747.1_RNA|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000358897.4_Missense_Mutation_p.R665Q			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	665								p.R665Q(1)|p.E380K(1)		skin(1)|stomach(1)	2						GAAGCTGAACGAGGAGAGGCT	0.493													G|||	250	0.0499201	0.1036	0.0447	5008	,	,		19553	0.0		0.0477	False		,,,				2504	0.0348				p.R665Q		Atlas-SNP	.											FHAD1_ENST00000375999,NS,carcinoma,0,2	FHAD1	78	2	2	Substitution - Missense(2)	stomach(2)	c.G1994A						PASS	.	G	GLN/ARG	146,1238		10,126,556	115.0	105.0	108.0		1994	-3.3	0.0	1	dbSNP_120	108	220,2962		4,212,1375	yes	missense	FHAD1	NM_052929.1	43	14,338,1931	AA,AG,GG		6.9139,10.5491,8.0158	benign	665/1413	15668319	366,4200	692	1591	2283	SO:0001583	missense	114827	exon15			CTGAACGAGGAGA	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.1994G>A	1.37:g.15668319G>A	ENSP00000365166:p.Arg665Gln	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	201	97	0.482587	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		112	0.05128205128205128	57	0.11585365853658537	19	0.052486187845303865	0	0.0	36	0.047493403693931395	G	3.210	-0.161861	0.06502	0.105491	0.069139	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998	D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94	4.49	-3.3	0.05003	.	3.151500	0.01328	N	0.011174	T	0.01695	0.0054	N	0.03608	-0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.36407	-0.9749	9	0.14252	T	0.57	8.5824	2.6167	0.04906	0.1772:0.4109:0.2724:0.1395	rs12126178;rs52808140;rs59045252;rs12126178	665	B1AJZ9	FHAD1_HUMAN	Q	665	ENSP00000351770:R665Q;ENSP00000407615:R665Q;ENSP00000365167:R665Q;ENSP00000365166:R665Q	ENSP00000351770:R665Q	R	+	2	0	FHAD1	15540906	0.000000	0.05858	0.007000	0.13788	0.100000	0.18952	-2.620000	0.00879	-0.479000	0.06813	-1.355000	0.01225	CGA	G|0.930;A|0.070	0.070	strong		0.493	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
HHAT	55733	hgsc.bcm.edu	37	1	210577884	210577884	+	Missense_Mutation	SNP	G	G	A	rs2294851	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:210577884G>A	ENST00000367010.1	+	6	772	c.545G>A	c.(544-546)aGc>aAc	p.S182N	HHAT_ENST00000308852.6_Missense_Mutation_p.S137N|HHAT_ENST00000537898.1_Missense_Mutation_p.S117N|HHAT_ENST00000545781.1_Missense_Mutation_p.S119N|HHAT_ENST00000391905.3_Missense_Mutation_p.S182N|HHAT_ENST00000545154.1_Missense_Mutation_p.S183N|HHAT_ENST00000261458.3_Missense_Mutation_p.S182N|HHAT_ENST00000413764.2_Missense_Mutation_p.S182N|HHAT_ENST00000541565.1_Intron	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	182			S -> N (in dbSNP:rs2294851). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)	p.S182N(1)		breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		TACTACACCAGCTTCAGCCTG	0.507													G|||	618	0.123403	0.0083	0.1671	5008	,	,		20382	0.253		0.1292	False		,,,				2504	0.1084				p.S183N		Atlas-SNP	.											HHAT,NS,carcinoma,0,1	HHAT	66	1	1	Substitution - Missense(1)	stomach(1)	c.G548A						PASS	.	G	ASN/SER,,ASN/SER,ASN/SER,ASN/SER,ASN/SER	130,4276	93.9+/-132.6	3,124,2076	102.0	87.0	92.0		545,,545,548,350,545	5.5	1.0	1	dbSNP_100	92	1231,7369	248.1+/-275.9	95,1041,3164	yes	missense,intron,missense,missense,missense,missense	HHAT	NM_001122834.2,NM_001170564.1,NM_001170580.1,NM_001170587.1,NM_001170588.1,NM_018194.4	46,,46,46,46,46	98,1165,5240	AA,AG,GG		14.314,2.9505,10.4644	probably-damaging,,probably-damaging,probably-damaging,probably-damaging,probably-damaging	182/494,,182/494,183/495,117/429,182/494	210577884	1361,11645	2203	4300	6503	SO:0001583	missense	55733	exon5			ACACCAGCTTCAG	AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.545G>A	1.37:g.210577884G>A	ENSP00000355977:p.Ser182Asn	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	114	112	0.982456	NM_001170587	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Missense_Mutation	SNP	ENST00000367010.1	37	CCDS1495.1	337	0.1543040293040293	7	0.014227642276422764	71	0.19613259668508287	157	0.2744755244755245	102	0.1345646437994723	G	33	5.248353	0.95305	0.029505	0.14314	ENSG00000054392	ENST00000413764;ENST00000545154;ENST00000537898;ENST00000391905;ENST00000545781;ENST00000261458;ENST00000308852;ENST00000367010;ENST00000426968	T;T;T;T;T;T;T;T;T	0.28666	1.81;1.81;1.95;1.81;1.85;1.81;1.85;1.81;1.6	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.81341	2.54	0.09310	P	0.999999890035	D;D;B;D	0.89917	1.0;1.0;0.06;1.0	D;D;B;D	0.97110	0.999;0.999;0.168;1.0	T	0.00183	-1.1945	9	0.59425	D	0.04	-24.9362	19.1127	0.93323	0.0:0.0:1.0:0.0	rs2294851;rs2294851	137;183;117;182	B7Z2U8;F5H444;B7Z5I1;Q5VTY9	.;.;.;HHAT_HUMAN	N	182;183;117;182;119;182;137;182;54	ENSP00000416845:S182N;ENSP00000438468:S183N;ENSP00000442625:S117N;ENSP00000375773:S182N;ENSP00000439229:S119N;ENSP00000261458:S182N;ENSP00000308628:S137N;ENSP00000355977:S182N;ENSP00000413399:S54N	ENSP00000261458:S182N	S	+	2	0	HHAT	208644507	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.717000	0.91425	2.605000	0.88082	0.591000	0.81541	AGC	G|0.875;A|0.125	0.125	strong		0.507	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194	
ARHGAP32	9743	hgsc.bcm.edu	37	11	128839550	128839550	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:128839550G>T	ENST00000310343.9	-	22	5515	c.5516C>A	c.(5515-5517)gCc>gAc	p.A1839D	ARHGAP32_ENST00000392657.3_Missense_Mutation_p.A1490D|ARHGAP32_ENST00000527272.1_Missense_Mutation_p.A1490D|ARHGAP32_ENST00000524655.1_3'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1839	Interaction with FYN.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						GTGATGGTGGGCTCTGTCCAT	0.622																																					p.A1839D		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.C5516A						PASS	.						72.0	65.0	67.0					11																	128839550		2201	4297	6498	SO:0001583	missense	9743	exon22			TGGTGGGCTCTGT	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"""Rho GTPase activating proteins"""	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.5516C>A	11.37:g.128839550G>T	ENSP00000310561:p.Ala1839Asp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	37	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	G	9.632	1.136685	0.21123	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.10099	2.93;2.91;2.91	5.95	4.11	0.48088	.	0.273133	0.35525	N	0.003151	T	0.14270	0.0345	M	0.62723	1.935	0.34234	D	0.676855	B	0.13594	0.008	B	0.10450	0.005	T	0.05989	-1.0852	10	0.87932	D	0	.	12.7738	0.57436	0.1319:0.0:0.8681:0.0	.	1839	A7KAX9	RHG32_HUMAN	D	1839;1490;1490	ENSP00000310561:A1839D;ENSP00000376425:A1490D;ENSP00000432862:A1490D	ENSP00000310561:A1839D	A	-	2	0	ARHGAP32	128344760	0.998000	0.40836	0.111000	0.21465	0.020000	0.10135	2.664000	0.46783	0.875000	0.35847	-0.126000	0.14955	GCC	.	.	none		0.622	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150525425	150525425	+	Missense_Mutation	SNP	G	G	A	rs41317513	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:150525425G>A	ENST00000369038.2	+	3	331	c.130G>A	c.(130-132)Gaa>Aaa	p.E44K	ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.E44K|MIR4257_ENST00000581735.1_RNA|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.E44K|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.E44K|RP11-54A4.2_ENST00000442435.2_RNA			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	44					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CCAGGGCCCCGAAGGTGTCTG	0.592													G|||	56	0.0111821	0.0008	0.0245	5008	,	,		15197	0.0		0.0338	False		,,,				2504	0.0041				p.E44K		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.G130A						PASS	.	G	LYS/GLU,LYS/GLU	33,4343		0,33,2155	35.0	44.0	41.0		130,130	4.6	0.8	1	dbSNP_127	41	336,8238		10,316,3961	yes	missense,missense	ADAMTSL4	NM_019032.4,NM_025008.3	56,56	10,349,6116	AA,AG,GG		3.9188,0.7541,2.8494	benign,benign	44/1075,44/878	150525425	369,12581	2188	4287	6475	SO:0001583	missense	54507	exon5			GGCCCCGAAGGTG	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.130G>A	1.37:g.150525425G>A	ENSP00000358034:p.Glu44Lys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	140	69	0.492857	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	37	CCDS955.1	34	0.015567765567765568	5	0.01016260162601626	6	0.016574585635359115	0	0.0	23	0.030343007915567283	G	17.55	3.416539	0.62511	0.007541	0.039188	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000369039;ENST00000369038	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	4.63	4.63	0.57726	.	.	.	.	.	T	0.11110	0.0271	L	0.27053	0.805	0.35656	D	0.812154	P;D;D;P	0.59767	0.466;0.986;0.957;0.729	B;P;B;B	0.47705	0.019;0.555;0.165;0.123	T	0.04607	-1.0939	9	0.42905	T	0.14	.	12.9585	0.58444	0.0:0.0:1.0:0.0	rs41317513	44;44;44;44	B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2	.;.;ATL4_HUMAN;.	K	44	ENSP00000358037:E44K;ENSP00000271643:E44K;ENSP00000358035:E44K;ENSP00000358034:E44K	ENSP00000271643:E44K	E	+	1	0	ADAMTSL4	148792049	1.000000	0.71417	0.825000	0.32803	0.695000	0.40330	4.741000	0.62095	2.115000	0.64714	0.561000	0.74099	GAA	G|0.974;A|0.026	0.026	strong		0.592	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
DIEXF	27042	hgsc.bcm.edu	37	1	210004332	210004332	+	Missense_Mutation	SNP	G	G	A	rs61747285	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:210004332G>A	ENST00000491415.2	+	3	389	c.332G>A	c.(331-333)gGt>gAt	p.G111D		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	111	Glu-rich.			G -> D (in Ref. 1; CAH18684/CAH56170). {ECO:0000305}.	multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						GAAGATGGTGGTAGCGATGTC	0.418													G|||	585	0.116813	0.0847	0.085	5008	,	,		20872	0.0784		0.1312	False		,,,				2504	0.2076				p.G111D		Atlas-SNP	.											DIEXF,NS,carcinoma,+1,1	DIEXF	97	1	0			c.G332A						PASS	.	G	ASP/GLY	389,4017	195.7+/-220.2	16,357,1830	180.0	165.0	170.0		332	-2.7	0.0	1	dbSNP_129	170	1322,7278	260.1+/-283.0	118,1086,3096	yes	missense	DIEXF	NM_014388.6	94	134,1443,4926	AA,AG,GG		15.3721,8.8289,13.1555	benign	111/757	210004332	1711,11295	2203	4300	6503	SO:0001583	missense	27042	exon3			ATGGTGGTAGCGA	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 107"""	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.332G>A	1.37:g.210004332G>A	ENSP00000419005:p.Gly111Asp	Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	162	162	1	NM_014388	O75992|Q4VY00|Q63HL9	Missense_Mutation	SNP	ENST00000491415.2	37	CCDS1493.1	217	0.09935897435897435	33	0.06707317073170732	36	0.09944751381215469	45	0.07867132867132867	103	0.1358839050131926	G	9.097	1.003091	0.19121	0.088289	0.153721	ENSG00000117597	ENST00000491415	T	0.40756	1.02	5.34	-2.7	0.06004	.	2.042040	0.01787	N	0.032091	T	0.00109	0.0003	N	0.02960	-0.455	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09378	-1.0677	9	0.13853	T	0.58	-0.0263	8.0098	0.30347	0.5552:0.1057:0.3391:0.0	rs61747285	111	Q68CQ4	DIEXF_HUMAN	D	111	ENSP00000419005:G111D	ENSP00000419005:G111D	G	+	2	0	DIEXF	208070955	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.400000	0.07241	-0.658000	0.05366	-0.345000	0.07892	GGT	G|0.875;A|0.125	0.125	strong		0.418	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388	
VPS41	27072	hgsc.bcm.edu	37	7	38796570	38796570	+	Silent	SNP	G	G	A	rs2240350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:38796570G>A	ENST00000310301.4	-	19	1617	c.1563C>T	c.(1561-1563)gaC>gaT	p.D521D	VPS41_ENST00000395969.2_Silent_p.D496D	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	521					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						CATAGTTCTTGTCATAGGTGT	0.299													G|||	1794	0.358227	0.2549	0.5965	5008	,	,		16905	0.4206		0.3469	False		,,,				2504	0.2761				p.D521D		Atlas-SNP	.											.	VPS41	102	.	0			c.C1563T						PASS	.	G	,	1278,3126	433.5+/-343.6	186,906,1110	103.0	106.0	105.0		1563,1488	4.1	1.0	7	dbSNP_98	105	3076,5516	469.7+/-367.6	510,2056,1730	no	coding-synonymous,coding-synonymous	VPS41	NM_014396.3,NM_080631.3	,	696,2962,2840	AA,AG,GG		35.8007,29.0191,33.5026	,	521/855,496/830	38796570	4354,8642	2202	4296	6498	SO:0001819	synonymous_variant	27072	exon19			GTTCTTGTCATAG	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1563C>T	7.37:g.38796570G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	37	CCDS5457.1																																																																																			G|0.643;A|0.357	0.357	strong		0.299	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
GSAP	54103	hgsc.bcm.edu	37	7	76991935	76991935	+	Missense_Mutation	SNP	C	C	T	rs1527263	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:76991935C>T	ENST00000257626.7	-	13	992	c.914G>A	c.(913-915)gGa>gAa	p.G305E		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	305			G -> E (in dbSNP:rs1527263).		positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										TGTGATTTGTCCCCAAGAGGC	0.303													T|||	1512	0.301917	0.5454	0.219	5008	,	,		21657	0.0883		0.2326	False		,,,				2504	0.3231				p.G305E		Atlas-SNP	.											PION,colon,carcinoma,+1,4	PION	74	4	0			c.G914A						PASS	.	T	GLU/GLY	2189,2217	589.8+/-387.2	548,1093,562	98.0	100.0	100.0		914	4.5	0.9	7	dbSNP_88	100	2170,6430	712.4+/-405.9	260,1650,2390	yes	missense	PION	NM_017439.3	98	808,2743,2952	TT,TC,CC		25.2326,49.6823,33.5153	benign	305/855	76991935	4359,8647	2203	4300	6503	SO:0001583	missense	54103	exon13			ATTTGTCCCCAAG		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"""pigeon homolog (Drosophila)"""	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.914G>A	7.37:g.76991935C>T	ENSP00000257626:p.Gly305Glu	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	159	73	0.459119	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Missense_Mutation	SNP	ENST00000257626.7	37	CCDS34672.2	615	0.2815934065934066	288	0.5853658536585366	92	0.2541436464088398	52	0.09090909090909091	183	0.24142480211081793	T	0.009	-1.815517	0.00600	0.496823	0.252326	ENSG00000186088	ENST00000257626	T	0.15372	2.43	5.72	4.5	0.54988	.	0.533626	0.16507	N	0.211404	T	0.00012	0.0000	N	0.00926	-1.1	0.53688	P	2.5000000000052758E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43540	-0.9385	9	0.02654	T	1	.	5.7871	0.18338	0.1477:0.0807:0.0:0.7717	rs1527263;rs57606158;rs1527263	305;305	A4D1B5-3;A4D1B5	.;GSAP_HUMAN	E	305	ENSP00000257626:G305E	ENSP00000257626:G305E	G	-	2	0	PION	76829871	0.005000	0.15991	0.947000	0.38551	0.060000	0.15804	1.184000	0.32053	0.999000	0.39023	-0.524000	0.04348	GGA	C|0.675;N|0.000	.	strong		0.303	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
POPDC3	64208	hgsc.bcm.edu	37	6	105609468	105609468	+	Missense_Mutation	SNP	C	C	T	rs11961225	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:105609468C>T	ENST00000254765.3	-	2	595	c.317G>A	c.(316-318)cGa>cAa	p.R106Q	BVES-AS1_ENST00000369120.2_RNA|BVES-AS1_ENST00000580854.1_RNA|BVES-AS1_ENST00000580511.1_RNA|POPDC3_ENST00000474760.1_Intron|BVES-AS1_ENST00000369122.3_RNA	NM_022361.4	NP_071756.2	Q9HBV1	POPD3_HUMAN	popeye domain containing 3	106			R -> Q (in dbSNP:rs11961225).		regulation of membrane potential (GO:0042391)	integral component of membrane (GO:0016021)				NS(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(3)|urinary_tract(1)	26		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)				TTGGAATTCTCGGGCAAAGGT	0.433													C|||	160	0.0319489	0.0651	0.0245	5008	,	,		19999	0.001		0.0447	False		,,,				2504	0.0112				p.R106Q		Atlas-SNP	.											POPDC3,right_lower_lobe,carcinoma,-1,1	POPDC3	47	1	0			c.G317A						PASS	.	C	GLN/ARG	231,4175	137.3+/-173.1	5,221,1977	162.0	173.0	169.0		317	4.7	1.0	6	dbSNP_120	169	257,8343	100.8+/-162.1	3,251,4046	yes	missense	POPDC3	NM_022361.4	43	8,472,6023	TT,TC,CC		2.9884,5.2429,3.7521	benign	106/292	105609468	488,12518	2203	4300	6503	SO:0001583	missense	64208	exon2			AATTCTCGGGCAA	BC022323	CCDS5052.1	6q21	2003-06-12			ENSG00000132429	ENSG00000132429			17649	protein-coding gene	gene with protein product		605824				10882522	Standard	NM_022361		Approved	POP3, MGC22671, bA355M14.1	uc003prb.3	Q9HBV1	OTTHUMG00000015293	ENST00000254765.3:c.317G>A	6.37:g.105609468C>T	ENSP00000254765:p.Arg106Gln	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	208	101	0.485577	NM_022361	B2RA98|Q5T3Y8|Q8TBW6	Missense_Mutation	SNP	ENST00000254765.3	37	CCDS5052.1	84	0.038461538461538464	31	0.06300813008130081	10	0.027624309392265192	0	0.0	43	0.05672823218997362	C	14.69	2.611671	0.46631	0.052429	0.029884	ENSG00000132429	ENST00000254765	T	0.43688	0.94	5.72	4.67	0.58626	.	0.309977	0.32785	N	0.005656	T	0.12220	0.0297	N	0.19112	0.55	0.32385	N	0.554067	B	0.13145	0.007	B	0.06405	0.002	T	0.07462	-1.0771	10	0.25751	T	0.34	-7.4986	9.4445	0.38688	0.0:0.7725:0.0:0.2275	rs11961225;rs52836944;rs11961225	106	Q9HBV1	POPD3_HUMAN	Q	106	ENSP00000254765:R106Q	ENSP00000254765:R106Q	R	-	2	0	POPDC3	105716161	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.563000	0.36364	2.704000	0.92352	0.655000	0.94253	CGA	C|0.962;T|0.038	0.038	strong		0.433	POPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041651.1	NM_022361	
ZNF556	80032	hgsc.bcm.edu	37	19	2877365	2877365	+	Missense_Mutation	SNP	C	C	T	rs10421121	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:2877365C>T	ENST00000307635.2	+	4	496	c.409C>T	c.(409-411)Cgc>Tgc	p.R137C	ZNF556_ENST00000586426.1_Missense_Mutation_p.R136C	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	137			R -> C (in dbSNP:rs10421121).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGTCATCTGCGCAAGAATTG	0.423													C|||	492	0.0982428	0.2663	0.0692	5008	,	,		21015	0.001		0.0656	False		,,,				2504	0.0256				p.R137C		Atlas-SNP	.											.	ZNF556	73	.	0			c.C409T						PASS	.	C	CYS/ARG	1125,3281	402.2+/-332.3	141,843,1219	130.0	112.0	118.0		409	-1.8	0.0	19	dbSNP_119	118	497,8103	143.6+/-199.6	15,467,3818	yes	missense	ZNF556	NM_024967.1	180	156,1310,5037	TT,TC,CC		5.7791,25.5334,12.4712	benign	137/457	2877365	1622,11384	2203	4300	6503	SO:0001583	missense	80032	exon4			CATCTGCGCAAGA	BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"""Zinc fingers, C2H2-type"", ""-"""	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.409C>T	19.37:g.2877365C>T	ENSP00000302603:p.Arg137Cys	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_024967	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	37	CCDS12097.1	186	0.08516483516483517	115	0.23373983739837398	27	0.07458563535911603	1	0.0017482517482517483	43	0.05672823218997362	C	11.41	1.631765	0.29068	0.255334	0.057791	ENSG00000172000	ENST00000307635	T	0.06142	3.34	1.95	-1.8	0.07907	.	.	.	.	.	T	0.00012	0.0000	L	0.39245	1.2	0.80722	P	0.0	P	0.46952	0.887	B	0.23419	0.046	T	0.48559	-0.9025	8	0.87932	D	0	.	6.0856	0.19964	0.0:0.6044:0.0:0.3956	rs10421121;rs10421121	137	Q9HAH1	ZN556_HUMAN	C	137	ENSP00000302603:R137C	ENSP00000302603:R137C	R	+	1	0	ZNF556	2828365	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.315000	0.08081	-0.540000	0.06265	-0.501000	0.04562	CGC	C|0.889;T|0.111	0.111	strong		0.423	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967	
ZNF333	84449	hgsc.bcm.edu	37	19	14817548	14817548	+	Silent	SNP	T	T	A	rs6511961	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14817548T>A	ENST00000292530.6	+	7	565	c.474T>A	c.(472-474)acT>acA	p.T158T	ZNF333_ENST00000536363.1_Silent_p.T49T|ZNF333_ENST00000540689.2_Silent_p.T158T|ZNF333_ENST00000601134.1_Missense_Mutation_p.S99T	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						CAGTGCCTACTCTGGGCCACC	0.597													A|||	4154	0.829473	0.9675	0.7046	5008	,	,		18133	0.8889		0.6223	False		,,,				2504	0.8834				p.T158T	NSCLC(60;75 1281 16985 25154 29885)	Atlas-SNP	.											.	ZNF333	76	.	0			c.T474A						PASS	.	A		4003,403	201.1+/-224.2	1824,355,24	91.0	85.0	87.0		474	-2.8	0.0	19	dbSNP_116	87	5183,3417	504.0+/-376.0	1605,1973,722	no	coding-synonymous	ZNF333	NM_032433.2		3429,2328,746	AA,AT,TT		39.7326,9.1466,29.3711		158/666	14817548	9186,3820	2203	4300	6503	SO:0001819	synonymous_variant	84449	exon7			GCCTACTCTGGGC		CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"""Zinc fingers, C2H2-type"", ""-"""	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.474T>A	19.37:g.14817548T>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_032433	Q6P2E6|Q86WS6|Q8TDL0	Silent	SNP	ENST00000292530.6	37	CCDS12316.1																																																																																			T|0.274;A|0.726	0.726	strong		0.597	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433	
ATF7IP	55729	hgsc.bcm.edu	37	12	14649196	14649196	+	Silent	SNP	A	A	G	rs61754409	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:14649196A>G	ENST00000540793.1	+	13	3467	c.3312A>G	c.(3310-3312)acA>acG	p.T1104T	ATF7IP_ENST00000544627.1_Silent_p.T1112T|ATF7IP_ENST00000536444.1_Silent_p.T1103T|ATF7IP_ENST00000261168.4_Silent_p.T1104T			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	1104					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						AAACAACCACATATGTTGTAA	0.388													A|||	299	0.0597045	0.0045	0.2983	5008	,	,		18214	0.0		0.0557	False		,,,				2504	0.0307				p.T1104T		Atlas-SNP	.											.	ATF7IP	136	.	0			c.A3312G						PASS	.	A		69,4337	62.3+/-99.4	0,69,2134	118.0	91.0	100.0		3312	-10.2	0.4	12	dbSNP_129	100	577,8023	155.8+/-209.8	21,535,3744	no	coding-synonymous	ATF7IP	NM_018179.3		21,604,5878	GG,GA,AA		6.7093,1.566,4.9669		1104/1271	14649196	646,12360	2203	4300	6503	SO:0001819	synonymous_variant	55729	exon14			AACCACATATGTT	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.3312A>G	12.37:g.14649196A>G		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Silent	SNP	ENST00000540793.1	37	CCDS8663.1																																																																																			A|0.946;G|0.054	0.054	strong		0.388	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
TIMELESS	8914	hgsc.bcm.edu	37	12	56822378	56822378	+	Missense_Mutation	SNP	T	T	A	rs774027	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56822378T>A	ENST00000553532.1	-	12	1513	c.1363A>T	c.(1363-1365)Ata>Tta	p.I455L	TIMELESS_ENST00000229201.4_Missense_Mutation_p.I454L|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						TCTGGAGATATGTCCATCTCA	0.557													T|||	2537	0.506589	0.2534	0.683	5008	,	,		18483	0.746		0.4513	False		,,,				2504	0.5337				p.I455L		Atlas-SNP	.											.	TIMELESS	107	.	0			c.A1363T						PASS	.	T	LEU/ILE	1188,3218	413.7+/-336.6	150,888,1165	80.0	66.0	71.0		1363	-2.3	0.3	12	dbSNP_86	71	3907,4693	546.8+/-385.0	872,2163,1265	yes	missense	TIMELESS	NM_003920.3	5	1022,3051,2430	AA,AT,TT		45.4302,26.9632,39.1742	benign	455/1209	56822378	5095,7911	2203	4300	6503	SO:0001583	missense	8914	exon12			GAGATATGTCCAT	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.1363A>T	12.37:g.56822378T>A	ENSP00000450607:p.Ile455Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	1081	0.49496336996337	115	0.23373983739837398	221	0.6104972375690608	402	0.7027972027972028	343	0.4525065963060686	T	3.196	-0.164811	0.06502	0.269632	0.454302	ENSG00000111602	ENST00000229201;ENST00000553532	T;T	0.06068	3.35;3.35	5.13	-2.3	0.06785	.	0.643166	0.16789	N	0.199479	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.99999894515	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.11108	-1.0601	9	0.28530	T	0.3	-0.0721	2.3831	0.04359	0.0947:0.1834:0.1921:0.5298	rs774027;rs1063961;rs3204991;rs17441804;rs52789933;rs774027	454;455	Q9UNS1-2;Q9UNS1	.;TIM_HUMAN	L	454;455	ENSP00000229201:I454L;ENSP00000450607:I455L	ENSP00000229201:I455L	I	-	1	0	TIMELESS	55108645	0.098000	0.21812	0.273000	0.24645	0.427000	0.31564	0.322000	0.19576	-0.517000	0.06461	-2.479000	0.00199	ATA	T|0.566;A|0.434	0.434	strong		0.557	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
PLP1	5354	hgsc.bcm.edu	37	X	103042882	103042882	+	Silent	SNP	T	T	C	rs1126707	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:103042882T>C	ENST00000303958.2	+	4	755	c.609T>C	c.(607-609)gaT>gaC	p.D203D	PLP1_ENST00000466486.1_3'UTR|PLP1_ENST00000361621.2_Silent_p.D168D|PLP1_ENST00000418604.1_Silent_p.D203D	NM_000533.3	NP_000524.3	P60201	MYPR_HUMAN	proteolipid protein 1	203			D -> E (in HLD1). {ECO:0000269|PubMed:10417279, ECO:0000269|PubMed:11093273}.|D -> G (in HLD1). {ECO:0000269|PubMed:10417279}.|D -> H (in HLD1). {ECO:0000269|PubMed:1376966}.|D -> N (in HLD1). {ECO:0000269|PubMed:10417279}.|D -> V (in HLD1). {ECO:0000269|PubMed:9747038}.		astrocyte development (GO:0014002)|axon development (GO:0061564)|axon ensheathment (GO:0008366)|cell death (GO:0008219)|cell maturation (GO:0048469)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|long-chain fatty acid biosynthetic process (GO:0042759)|positive regulation of gene expression (GO:0010628)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	structural constituent of myelin sheath (GO:0019911)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	17						TCTGTGCTGATGCCAGAATGT	0.488													T|||	780	0.206623	0.0628	0.2738	3775	,	,		15438	0.1736		0.2107	False		,,,				2504	0.1227				p.D203D		Atlas-SNP	.											.	PLP1	37	.	0			c.T609C	GRCh37	CM002830	PLP1	M	rs1126707	PASS	.	T	,,	489,3346		41,348,59,1243,512	159.0	116.0	130.0		609,609,504	4.4	1.0	X	dbSNP_86	130	2100,4628		212,1073,603,1143,1269	no	coding-synonymous,coding-synonymous,coding-synonymous	PLP1	NM_000533.3,NM_001128834.1,NM_199478.1	,,	253,1421,662,2386,1781	CC,CT,C,TT,T		31.2128,12.751,24.5101	,,	203/278,203/278,168/243	103042882	2589,7974	2203	4300	6503	SO:0001819	synonymous_variant	5354	exon5			TGCTGATGCCAGA	M27110	CCDS14513.1, CCDS14514.1	Xq22	2013-05-14	2008-07-28		ENSG00000123560	ENSG00000123560			9086	protein-coding gene	gene with protein product	"""Pelizaeus-Merzbacher disease"""	300401	"""spastic paraplegia 2, uncomplicated"""	SPG2, PLP			Standard	NM_001128834		Approved	GPM6C	uc004elk.3	P60201	OTTHUMG00000022111	ENST00000303958.2:c.609T>C	X.37:g.103042882T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	120	115	0.958333	NM_001128834	P04400|P06905|Q502Y1|Q6FHZ6	Silent	SNP	ENST00000303958.2	37	CCDS14513.1																																																																																			T|0.774;C|0.226	0.226	strong		0.488	PLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057743.2		
CENPF	1063	hgsc.bcm.edu	37	1	214826196	214826196	+	Missense_Mutation	SNP	G	G	A	rs335524	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:214826196G>A	ENST00000366955.3	+	16	8354	c.8186G>A	c.(8185-8187)cGa>cAa	p.R2729Q	CENPF_ENST00000467765.1_3'UTR	NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2825	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CAGACATACCGAGAGAAATTG	0.338													G|||	2810	0.561102	0.2874	0.5893	5008	,	,		18335	0.8849		0.4443	False		,,,				2504	0.6973				p.R2729Q	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.G8186A						PASS	.	G	GLN/ARG	1400,3006	453.2+/-350.3	212,976,1015	71.0	72.0	71.0		8186	-6.4	0.0	1	dbSNP_79	71	3691,4909	526.1+/-380.9	762,2167,1371	yes	missense	CENPF	NM_016343.3	43	974,3143,2386	AA,AG,GG		42.9186,31.7749,39.1435	benign	2729/3115	214826196	5091,7915	2203	4300	6503	SO:0001583	missense	1063	exon16			CATACCGAGAGAA	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8186G>A	1.37:g.214826196G>A	ENSP00000355922:p.Arg2729Gln	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	142	61	0.429577	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	1225	0.5608974358974359	148	0.3008130081300813	197	0.5441988950276243	524	0.916083916083916	356	0.46965699208443273	G	0.014	-1.590593	0.00864	0.317749	0.429186	ENSG00000117724	ENST00000366955;ENST00000391896	T	0.02916	4.11	3.65	-6.44	0.01920	.	.	.	.	.	T	0.00012	0.0000	N	0.01874	-0.695	0.58432	P	1.999999999946489E-6	B	0.10296	0.003	B	0.04013	0.001	T	0.22173	-1.0224	8	0.11485	T	0.65	.	14.1733	0.65525	0.8841:0.0:0.1159:0.0	rs335524;rs17799735;rs52817986;rs58389012;rs335524	2825	P49454	CENPF_HUMAN	Q	2729;128	ENSP00000355922:R2729Q	ENSP00000355922:R2729Q	R	+	2	0	CENPF	212892819	0.376000	0.25098	0.001000	0.08648	0.049000	0.14656	-0.136000	0.10405	-1.534000	0.01743	-0.350000	0.07774	CGA	G|0.532;T|0.002	.	strong		0.338	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
IL17RC	84818	hgsc.bcm.edu	37	3	9974809	9974809	+	Silent	SNP	G	G	A	rs76999397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9974809G>A	ENST00000295981.3	+	19	2126	c.1908G>A	c.(1906-1908)gcG>gcA	p.A636A	CRELD1_ENST00000452070.1_5'Flank|RP11-1020A11.1_ENST00000602411.1_RNA|IL17RC_ENST00000413608.1_Silent_p.A552A|IL17RC_ENST00000403601.3_Silent_p.A565A|CRELD1_ENST00000383811.3_5'Flank|IL17RC_ENST00000498214.1_3'UTR|CRELD1_ENST00000326434.5_5'Flank|IL17RC_ENST00000416074.2_Silent_p.A391A|CRELD1_ENST00000397170.3_5'Flank|IL17RC_ENST00000383812.4_Silent_p.A550A|IL17RC_ENST00000455057.1_Silent_p.A533A	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	636	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGTTTCACGCGCAGCGGCGCC	0.711											OREG0015383	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	154	0.0307508	0.0	0.0216	5008	,	,		12731	0.0417		0.0378	False		,,,				2504	0.0603				p.A636A		Atlas-SNP	.											IL17RC,NS,carcinoma,0,1	IL17RC	55	1	0			c.G1908A						PASS	.	G	,,,,,	51,4341		1,49,2146	17.0	17.0	17.0		1656,1605,1599,1650,1695,1908	-7.9	0.8	3	dbSNP_132	17	417,8165		9,399,3883	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	,,,,,	10,448,6029	AA,AG,GG		4.859,1.1612,3.6072	,,,,,	552/708,535/691,533/689,550/706,565/721,636/792	9974809	468,12506	2196	4291	6487	SO:0001819	synonymous_variant	84818	exon19			TCACGCGCAGCGG	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.1908G>A	3.37:g.9974809G>A		Somatic	68	0	0	661	WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			G|0.968;A|0.032	0.032	strong		0.711	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
LILRB3	11025	hgsc.bcm.edu	37	19	54725019	54725019	+	Silent	SNP	G	G	A	rs78279726	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54725019G>A	ENST00000391750.1	-	6	1027	c.891C>T	c.(889-891)taC>taT	p.Y297Y	LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Silent_p.Y297Y|LILRB3_ENST00000407860.2_Silent_p.Y297Y|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Silent_p.Y297Y|LILRB3_ENST00000346401.6_Silent_p.Y297Y|LILRB3_ENST00000424807.1_Silent_p.Y297Y|LILRA6_ENST00000391735.3_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	297	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGTGTGCACCGTAGCACCTGT	0.682													.|||	1595	0.31849	0.2345	0.3069	5008	,	,		6728	0.5506		0.3211	False		,,,				2504	0.1984				p.Y297Y		Atlas-SNP	.											.	LILRB3	67	.	0			c.C891T						PASS	.	G	,	679,2939		111,457,1241	24.0	22.0	23.0		891,891	-3.6	0.1	19	dbSNP_131	23	369,3609		134,101,1754	no	coding-synonymous,coding-synonymous	LILRB3	NM_001081450.1,NM_006864.2	,	245,558,2995	AA,AG,GG		9.276,18.7673,13.7967	,	297/633,297/632	54725019	1048,6548	1809	1989	3798	SO:0001819	synonymous_variant	11025	exon5			TGCACCGTAGCAC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.891C>T	19.37:g.54725019G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			G|0.702;A|0.298	0.298	strong		0.682	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
SPATA2	9825	hgsc.bcm.edu	37	20	48524827	48524827	+	Silent	SNP	A	A	G	rs2769982	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:48524827A>G	ENST00000422556.1	-	2	550	c.201T>C	c.(199-201)taT>taC	p.Y67Y	SPATA2_ENST00000543716.1_Intron|SPATA2_ENST00000289431.5_Silent_p.Y67Y	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	67					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	20	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			CCACCACCTCATAGAACTGGA	0.622													G|||	2458	0.490815	0.1316	0.585	5008	,	,		19272	0.7738		0.4503	False		,,,				2504	0.6595				p.Y67Y		Atlas-SNP	.											.	SPATA2	36	.	0			c.T201C						PASS	.	G	,	844,3562	745.8+/-411.7	78,688,1437	79.0	67.0	71.0		201,201	-6.8	0.7	20	dbSNP_100	71	3968,4632	600.7+/-394.3	911,2146,1243	no	coding-synonymous,coding-synonymous	SPATA2	NM_001135773.1,NM_006038.3	,	989,2834,2680	GG,GA,AA		46.1395,19.1557,36.9983	,	67/521,67/521	48524827	4812,8194	2203	4300	6503	SO:0001819	synonymous_variant	9825	exon2			CACCTCATAGAAC	AB018300	CCDS13422.1	20q13.13	2014-06-13			ENSG00000158480	ENSG00000158480			14681	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 145"""	607662					Standard	NM_001135773		Approved	KIAA0757, PD1, tamo, PPP1R145	uc002xuw.3	Q9UM82	OTTHUMG00000032704	ENST00000422556.1:c.201T>C	20.37:g.48524827A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_006038	E1P626|O94857	Silent	SNP	ENST00000422556.1	37	CCDS13422.1																																																																																			A|0.584;G|0.416	0.416	strong		0.622	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038	
MLXIP	22877	hgsc.bcm.edu	37	12	122623000	122623000	+	Silent	SNP	T	T	C	rs4758686	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:122623000T>C	ENST00000319080.7	+	14	2418	c.2286T>C	c.(2284-2286)acT>acC	p.T762T	MLXIP_ENST00000538698.1_Silent_p.T369T					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		TGCAGAAGACTGTGGAGTACA	0.627													C|||	2734	0.545927	0.5454	0.6081	5008	,	,		20432	0.4931		0.5596	False		,,,				2504	0.5429				p.T762T	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.T2286C						PASS	.	C		2371,1989		662,1047,471	47.0	52.0	50.0		1876	-9.1	0.7	12	dbSNP_111	50	4397,4161		1138,2121,1020	no	coding-synonymous	MLXIP	NM_014938.3		1800,3168,1491	CC,CT,TT		48.6212,45.6193,47.608		762/920	122623000	6768,6150	2180	4279	6459	SO:0001819	synonymous_variant	22877	exon14			GAAGACTGTGGAG	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"""Basic helix-loop-helix proteins"""	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.2286T>C	12.37:g.122623000T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	102	58	0.568627	NM_014938		Silent	SNP	ENST00000319080.7	37		1178	0.5393772893772893	256	0.5203252032520326	208	0.574585635359116	290	0.506993006993007	424	0.5593667546174143	C	9.339	1.062615	0.19987	0.543807	0.513788	ENSG00000175727	ENST00000542417	.	.	.	5.03	-9.09	0.00717	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999966	.	.	.	.	.	.	T	0.38779	-0.9645	3	.	.	.	-27.2568	4.0873	0.09953	0.5082:0.0964:0.2638:0.1316	rs4758686;rs17563695;rs57585600	.	.	.	P	98	.	.	L	+	2	0	MLXIP	121188953	0.000000	0.05858	0.659000	0.29680	0.920000	0.55202	-2.579000	0.00907	-1.934000	0.01051	-2.078000	0.00380	CTG	T|0.472;C|0.528	0.528	strong		0.627	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938	
PALD1	27143	hgsc.bcm.edu	37	10	72289778	72289778	+	Missense_Mutation	SNP	C	C	T	rs2275060	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:72289778C>T	ENST00000263563.6	+	4	690	c.422C>T	c.(421-423)tCa>tTa	p.S141L		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	141			S -> L (in dbSNP:rs2275060). {ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:15489334}.			cytosol (GO:0005829)											CCCAGCCTCTCAGGGTTCAGG	0.627													C|||	641	0.127995	0.0113	0.1816	5008	,	,		17426	0.2173		0.2147	False		,,,				2504	0.0665				p.S141L		Atlas-SNP	.											.	.	.	.	0			c.C422T						PASS	.	C	LEU/SER	190,4216	120.0+/-157.7	5,180,2018	45.0	45.0	45.0		422	-4.2	0.0	10	dbSNP_100	45	1720,6880	312.5+/-310.9	177,1366,2757	yes	missense	KIAA1274	NM_014431.2	145	182,1546,4775	TT,TC,CC		20.0,4.3123,14.6855	benign	141/857	72289778	1910,11096	2203	4300	6503	SO:0001583	missense	27143	exon4			GCCTCTCAGGGTT	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.422C>T	10.37:g.72289778C>T	ENSP00000263563:p.Ser141Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	369	0.16895604395604397	7	0.014227642276422764	57	0.1574585635359116	131	0.229020979020979	174	0.22955145118733508	C	10.13	1.266029	0.23136	0.043123	0.2	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.37411	1.2	5.34	-4.24	0.03777	.	0.800301	0.11499	N	0.557882	T	0.00012	0.0000	L	0.28192	0.835	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.34825	-0.9813	9	0.22706	T	0.39	0.3488	2.882	0.05650	0.1589:0.5736:0.1337:0.1338	rs2275060;rs17598395;rs52838028;rs59062283;rs2275060	141	Q9ULE6	PALD_HUMAN	L	141	ENSP00000263563:S141L	ENSP00000263563:S141L	S	+	2	0	KIAA1274	71959784	0.000000	0.05858	0.001000	0.08648	0.814000	0.46013	-0.330000	0.07925	-0.596000	0.05821	-0.484000	0.04775	TCA	C|0.843;N|0.001	.	strong		0.627	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
MYZAP	100820829	hgsc.bcm.edu	37	15	57918069	57918069	+	Silent	SNP	A	A	G	rs2069133	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:57918069A>G	ENST00000267853.5	+	5	598	c.504A>G	c.(502-504)gcA>gcG	p.A168A	POLR2M_ENST00000380563.2_5'UTR|MYZAP_ENST00000380565.4_Silent_p.A168A|GCOM1_ENST00000572390.1_Silent_p.A168A|GCOM1_ENST00000380569.2_Silent_p.A168A|GCOM1_ENST00000380560.2_Intron|GCOM1_ENST00000587652.1_Silent_p.A168A|GCOM1_ENST00000380561.2_Silent_p.A137A|GCOM1_ENST00000396180.1_Silent_p.A137A|GCOM1_ENST00000574161.1_Silent_p.A168A|GCOM1_ENST00000380568.3_Silent_p.A168A			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	168					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											CAGCCTTGGCATCAGATTCCA	0.488													G|||	2677	0.534545	0.5825	0.5821	5008	,	,		20643	0.5536		0.4026	False		,,,				2504	0.5521				p.A168A		Atlas-SNP	.											.	GCOM1	66	.	0			c.A504G						PASS	.	G	,,,	2428,1956	554.0+/-378.9	679,1070,443	132.0	112.0	119.0		504,504,504,504	-8.3	0.0	15	dbSNP_96	119	3477,5107	634.0+/-398.8	686,2105,1501	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GCOM1	NM_001018090.3,NM_001018091.3,NM_001018100.3,NM_152451.6	,,,	1365,3175,1944	GG,GA,AA		40.5056,44.6168,45.5352	,,,	168/551,168/446,168/467,168/439	57918069	5905,7063	2192	4292	6484	SO:0001819	synonymous_variant	145781	exon5			CTTGGCATCAGAT	FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"""myocardium-enriched zonula adherens protein"""	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.504A>G	15.37:g.57918069A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	126	54	0.428571	NM_001018090	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Silent	SNP	ENST00000267853.5	37	CCDS10162.1																																																																																			A|0.516;G|0.484	0.484	strong		0.488	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100	
HSPG2	3339	hgsc.bcm.edu	37	1	22182115	22182115	+	Missense_Mutation	SNP	G	G	A	rs2229474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22182115G>A	ENST00000374695.3	-	46	5834	c.5755C>T	c.(5755-5757)Cgc>Tgc	p.R1919C	HSPG2_ENST00000430507.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1919	Ig-like C2-type 4.		R -> C (in dbSNP:rs2229474).		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCTGGCAGGCGCAGGATGCCG	0.687													G|||	10	0.00199681	0.0	0.0014	5008	,	,		13927	0.001		0.008	False		,,,				2504	0.0				p.R1919C		Atlas-SNP	.											.	HSPG2	311	.	0			c.C5755T						PASS	.	G	CYS/ARG	9,4359		0,9,2175	13.0	13.0	13.0		5755	5.1	1.0	1	dbSNP_98	13	74,8476		0,74,4201	no	missense	HSPG2	NM_005529.5	180	0,83,6376	AA,AG,GG		0.8655,0.206,0.6425	probably-damaging	1919/4392	22182115	83,12835	2184	4275	6459	SO:0001583	missense	3339	exon46			GCAGGCGCAGGAT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.5755C>T	1.37:g.22182115G>A	ENSP00000363827:p.Arg1919Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	9	0.004120879120879121	2	0.0040650406504065045	1	0.0027624309392265192	1	0.0017482517482517483	5	0.006596306068601583	G	14.28	2.487173	0.44249	0.00206	0.008655	ENSG00000142798	ENST00000374695	T	0.69435	-0.4	5.12	5.12	0.69794	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.181406	0.26939	N	0.021731	T	0.80385	0.4613	M	0.89353	3.025	0.41354	D	0.987383	D	0.89917	1.0	D	0.91635	0.999	D	0.85946	0.1461	10	0.72032	D	0.01	.	16.0425	0.80695	0.0:0.0:1.0:0.0	rs2229474	1919	P98160	PGBM_HUMAN	C	1919	ENSP00000363827:R1919C	ENSP00000363827:R1919C	R	-	1	0	HSPG2	22054702	1.000000	0.71417	1.000000	0.80357	0.027000	0.11550	2.974000	0.49272	2.399000	0.81585	0.462000	0.41574	CGC	G|0.994;A|0.006	0.006	strong		0.687	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
ZBTB7B	51043	hgsc.bcm.edu	37	1	154987526	154987526	+	Silent	SNP	C	C	T	rs11264295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:154987526C>T	ENST00000368426.3	+	3	527	c.390C>T	c.(388-390)atC>atT	p.I130I	ZBTB7B_ENST00000292176.2_Silent_p.I130I|ZBTB7B_ENST00000535420.1_Silent_p.I130I|ZBTB7B_ENST00000417934.2_Silent_p.I164I|ZBTB7B_ENST00000487542.1_3'UTR	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	130					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TGCTGGAGATCCCGTGTGTCA	0.617													C|||	3094	0.617812	0.4592	0.6671	5008	,	,		16567	0.9058		0.4513	False		,,,				2504	0.6718				p.I164I		Atlas-SNP	.											ZBTB7B,NS,carcinoma,0,1	ZBTB7B	69	1	0			c.C492T						PASS	.	C		2075,2331		472,1131,600	41.0	45.0	43.0		390	0.6	0.9	1	dbSNP_120	43	3651,4949		771,2109,1420	no	coding-synonymous	ZBTB7B	NM_015872.2		1243,3240,2020	TT,TC,CC		42.4535,47.0949,44.0258		130/540	154987526	5726,7280	2203	4300	6503	SO:0001819	synonymous_variant	51043	exon4			GGAGATCCCGTGT	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	18668	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 15"""	607646	"""zinc finger protein 67 homolog (mouse)"""	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.390C>T	1.37:g.154987526C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Silent	SNP	ENST00000368426.3	37	CCDS1081.1																																																																																			C|0.487;T|0.513	0.513	strong		0.617	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872	
ACSM5	54988	hgsc.bcm.edu	37	16	20442608	20442608	+	Missense_Mutation	SNP	C	C	A	rs79364355		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20442608C>A	ENST00000331849.4	+	10	1420	c.1273C>A	c.(1273-1275)Ccc>Acc	p.P425T		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	425					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						CCGTATCAGACCCACTCGGCC	0.507																																					p.P425T		Atlas-SNP	.											ACSM5,NS,NS,0,1	ACSM5	101	1	0			c.C1273A						PASS	.						181.0	152.0	162.0					16																	20442608		2203	4300	6503	SO:0001583	missense	54988	exon10			ATCAGACCCACTC		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1273C>A	16.37:g.20442608C>A	ENSP00000327916:p.Pro425Thr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	168	42	0.25	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.211007	0.58343	.	.	ENSG00000183549	ENST00000331849	T	0.46063	0.88	4.37	4.37	0.52481	AMP-dependent synthetase/ligase (1);	0.000000	0.52532	D	0.000068	T	0.42899	0.1223	L	0.41573	1.285	0.51482	D	0.999926	B	0.27700	0.186	B	0.37346	0.247	T	0.49679	-0.8914	10	0.87932	D	0	-15.5986	16.0686	0.80907	0.0:1.0:0.0:0.0	.	425	Q6NUN0	ACSM5_HUMAN	T	425	ENSP00000327916:P425T	ENSP00000327916:P425T	P	+	1	0	ACSM5	20350109	0.980000	0.34600	0.744000	0.31058	0.954000	0.61252	3.276000	0.51646	2.119000	0.64992	0.650000	0.86243	CCC	C|0.500;A|0.500	0.500	weak		0.507	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
MKI67	4288	hgsc.bcm.edu	37	10	129917560	129917560	+	Missense_Mutation	SNP	T	T	C	rs2071498	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:129917560T>C	ENST00000368654.3	-	5	686	c.311A>G	c.(310-312)aAt>aGt	p.N104S	MKI67_ENST00000368653.3_Missense_Mutation_p.N104S	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	104			N -> S (in dbSNP:rs2071498).		cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTTCCTTCCATTCTGAAGACT	0.353													T|||	3175	0.633986	0.5802	0.719	5008	,	,		17944	0.6389		0.665	False		,,,				2504	0.6094				p.N104S		Atlas-SNP	.											.	MKI67	363	.	0			c.A311G						PASS	.	T	SER/ASN,SER/ASN	2483,1919	619.8+/-393.4	694,1095,412	152.0	131.0	138.0		311,311	3.6	0.0	10	dbSNP_96	138	5515,3085	658.5+/-401.6	1767,1981,552	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	46,46	2461,3076,964	CC,CT,TT		35.8721,43.5938,38.4864	benign,benign	104/2897,104/3257	129917560	7998,5004	2201	4300	6501	SO:0001583	missense	4288	exon5			CTTCCATTCTGAA	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.311A>G	10.37:g.129917560T>C	ENSP00000357643:p.Asn104Ser	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	192	191	0.994792	NM_001145966	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	1413	0.646978021978022	303	0.6158536585365854	250	0.6906077348066298	359	0.6276223776223776	501	0.6609498680738787	T	15.63	2.889073	0.52014	0.564062	0.641279	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.21191	2.02;5.13	3.64	3.64	0.41730	.	0.625127	0.15550	N	0.256459	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	D;B	0.58268	0.982;0.242	P;B	0.52554	0.702;0.05	T	0.04621	-1.0938	8	.	.	.	.	8.955	0.35812	0.0:0.0:0.0:1.0	rs2071498;rs11549254;rs17348759;rs60971682;rs2071498	104;104	P46013-2;P46013	.;KI67_HUMAN	S	104;104;104;39	ENSP00000357643:N104S;ENSP00000357642:N104S	.	N	-	2	0	MKI67	129807550	0.003000	0.15002	0.003000	0.11579	0.344000	0.29017	1.414000	0.34736	1.890000	0.54733	0.528000	0.53228	AAT	T|0.378;C|0.622	0.622	strong		0.353	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
TRPV2	51393	hgsc.bcm.edu	37	17	16336992	16336992	+	Silent	SNP	C	C	G	rs14039	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:16336992C>G	ENST00000338560.7	+	13	2493	c.2094C>G	c.(2092-2094)ccC>ccG	p.P698P	TRPV2_ENST00000577397.1_Silent_p.P268P	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	698					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.P698P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		ATGGCAGCCCCGATGAGCGCT	0.627													C|||	1443	0.288139	0.3124	0.3401	5008	,	,		20447	0.2232		0.3579	False		,,,				2504	0.2137				p.P698P		Atlas-SNP	.											TRPV2,NS,carcinoma,0,1	TRPV2	74	1	1	Substitution - coding silent(1)	stomach(1)	c.C2094G						PASS	.	C		1464,2942	469.4+/-355.4	260,944,999	111.0	97.0	102.0		2094	-5.2	0.1	17	dbSNP_52	102	3244,5356	485.9+/-371.7	609,2026,1665	no	coding-synonymous	TRPV2	NM_016113.4		869,2970,2664	GG,GC,CC		37.7209,33.2274,36.1987		698/765	16336992	4708,8298	2203	4300	6503	SO:0001819	synonymous_variant	51393	exon13			CAGCCCCGATGAG	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.2094C>G	17.37:g.16336992C>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_016113	A6NML2|A8K0Z0|Q9Y670	Silent	SNP	ENST00000338560.7	37	CCDS32576.1																																																																																			T|0.000;G|0.355;C|0.645	0.355	strong		0.627	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
MYEOV2	150678	hgsc.bcm.edu	37	2	241066325	241066325	+	Silent	SNP	A	A	C	rs12614632	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241066325A>C	ENST00000307266.3	-	5	413	c.414T>G	c.(412-414)gcT>gcG	p.A138A		NM_138336.1	NP_612209.1	Q8WXC6	MYOV2_HUMAN	myeloma overexpressed 2	0										breast(1)|lung(5)|pancreas(1)	7		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)		CTCTGTCCAAAGCTGCCACTT	0.552													A|||	1081	0.215855	0.0817	0.196	5008	,	,		17504	0.4563		0.2058	False		,,,				2504	0.1738				p.A138A		Atlas-SNP	.											.	MYEOV2	20	.	0			c.T414G						PASS	.	A		396,4010	190.9+/-216.7	17,362,1824	74.0	84.0	81.0		414	0.8	0.0	2	dbSNP_120	81	1563,7035	285.4+/-297.1	134,1295,2870	no	coding-synonymous	MYEOV2	NM_138336.1		151,1657,4694	CC,CA,AA		18.1786,8.9877,15.0646		138/253	241066325	1959,11045	2203	4299	6502	SO:0001819	synonymous_variant	150678	exon5			GTCCAAAGCTGCC	AF453951	CCDS2532.1, CCDS63183.1	2q37.3	2008-02-05			ENSG00000172428	ENSG00000172428			21314	protein-coding gene	gene with protein product							Standard	NM_138336		Approved		uc002vyu.1	Q8WXC6	OTTHUMG00000133352	ENST00000307266.3:c.414T>G	2.37:g.241066325A>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_138336	Q8N110	Silent	SNP	ENST00000307266.3	37	CCDS2532.1																																																																																			A|0.814;C|0.186	0.186	strong		0.552	MYEOV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257182.2	NM_138336	
YARS2	51067	hgsc.bcm.edu	37	12	32908237	32908237	+	Missense_Mutation	SNP	C	C	A	rs11539445	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:32908237C>A	ENST00000324868.8	-	1	599	c.572G>T	c.(571-573)gGt>gTt	p.G191V		NM_001040436.2	NP_001035526.1	Q9Y2Z4	SYYM_HUMAN	tyrosyl-tRNA synthetase 2, mitochondrial	191			G -> V (in dbSNP:rs11539445). {ECO:0000269|PubMed:10810093}.		gene expression (GO:0010467)|mitochondrial tyrosyl-tRNA aminoacylation (GO:0070184)|translation (GO:0006412)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)|tyrosine binding (GO:0072545)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	16	Lung NSC(5;2.43e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)				L-Tyrosine(DB00135)	GCGGAAGTGACCCCCCACTGC	0.637											OREG0021729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	634	0.126597	0.177	0.0937	5008	,	,		16266	0.0833		0.162	False		,,,				2504	0.09				p.G191V		Atlas-SNP	.											.	YARS2	33	.	0			c.G572T						PASS	.	C	VAL/GLY	714,3692	279.9+/-275.1	54,606,1543	51.0	56.0	55.0		572	4.2	1.0	12	dbSNP_120	55	1231,7369	238.8+/-270.1	104,1023,3173	yes	missense	YARS2	NM_001040436.2	109	158,1629,4716	AA,AC,CC		14.314,16.2052,14.9546	probably-damaging	191/478	32908237	1945,11061	2203	4300	6503	SO:0001583	missense	51067	exon1			AAGTGACCCCCCA	AF132939	CCDS31770.1	12p11.21	2014-03-19	2007-02-23		ENSG00000139131	ENSG00000139131	6.1.1.1	"""Aminoacyl tRNA synthetases / Class I"""	24249	protein-coding gene	gene with protein product	"""tyrosine tRNA ligase 2, mitochondrial"""	610957				15779907, 15840810	Standard	NM_001040436		Approved	FLJ13995, CGI-04, mt-TyrRS	uc001rli.3	Q9Y2Z4	OTTHUMG00000169454	ENST00000324868.8:c.572G>T	12.37:g.32908237C>A	ENSP00000320658:p.Gly191Val	Somatic	81	0	0	836	WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_001040436	D3DUW8|Q9H817	Missense_Mutation	SNP	ENST00000324868.8	37	CCDS31770.1	279	0.12774725274725274	86	0.17479674796747968	33	0.09116022099447514	41	0.07167832167832168	119	0.15699208443271767	C	15.93	2.978490	0.53720	0.162052	0.14314	ENSG00000139131	ENST00000324868	T	0.51071	0.72	5.09	4.2	0.49525	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.058780	0.64402	D	0.000001	T	0.00073	0.0002	N	0.04203	-0.255	0.09310	P	0.9999999854493	P	0.38078	0.617	B	0.34722	0.188	T	0.09422	-1.0675	9	0.72032	D	0.01	-16.2261	11.5881	0.50931	0.1398:0.7255:0.1347:0.0	rs11539445;rs60431927	191	Q9Y2Z4	SYYM_HUMAN	V	191	ENSP00000320658:G191V	ENSP00000320658:G191V	G	-	2	0	YARS2	32799504	0.221000	0.23642	0.999000	0.59377	0.947000	0.59692	4.211000	0.58507	1.384000	0.46424	0.644000	0.83932	GGT	C|0.856;A|0.144	0.144	strong		0.637	YARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404153.1	NM_015936	
CSMD1	64478	hgsc.bcm.edu	37	8	3072107	3072107	+	Silent	SNP	G	G	C	rs73183587	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:3072107G>C	ENST00000520002.1	-	31	5337	c.4782C>G	c.(4780-4782)ggC>ggG	p.G1594G	CSMD1_ENST00000602723.1_Silent_p.G1594G|CSMD1_ENST00000537824.1_Silent_p.G1593G|CSMD1_ENST00000602557.1_Silent_p.G1594G|CSMD1_ENST00000400186.3_Silent_p.G1594G|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000542608.1_Silent_p.G1593G|CSMD1_ENST00000539096.1_Silent_p.G1593G			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1594	Sushi 9. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GAATCTTATAGCCAGAGTCAC	0.517													G|||	342	0.0682907	0.0076	0.085	5008	,	,		16384	0.0317		0.1551	False		,,,				2504	0.0869				p.G1593G		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C4779G						PASS	.	G		95,3973		0,95,1939	88.0	87.0	87.0		4779	-2.4	1.0	8	dbSNP_130	87	1086,7288		70,946,3171	no	coding-synonymous	CSMD1	NM_033225.5		70,1041,5110	CC,CG,GG		12.9687,2.3353,9.492		1593/3565	3072107	1181,11261	2034	4187	6221	SO:0001819	synonymous_variant	64478	exon30			CTTATAGCCAGAG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4782C>G	8.37:g.3072107G>C		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	230	118	0.513043	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		176	0.08058608058608059	1	0.0020325203252032522	37	0.10220994475138122	22	0.038461538461538464	116	0.15303430079155672	G	7.377	0.628068	0.14257	0.023353	0.129687	ENSG00000183117	ENST00000335551	.	.	.	5.39	-2.39	0.06602	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.26503	-1.0101	3	.	.	.	.	2.2472	0.04034	0.1512:0.2441:0.3767:0.2281	.	.	.	.	V	1074	.	.	L	-	1	2	CSMD1	3059514	1.000000	0.71417	0.997000	0.53966	0.754000	0.42855	0.594000	0.24014	-0.047000	0.13423	0.591000	0.81541	CTA	G|0.909;C|0.091	0.091	strong		0.517	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
MYO1G	64005	hgsc.bcm.edu	37	7	45005249	45005249	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:45005249C>T	ENST00000258787.7	-	17	2504	c.2368G>A	c.(2368-2370)Gca>Aca	p.A790T		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	790						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						CAGAAGAGTGCGTGGCAGGTG	0.617																																					p.A790T		Atlas-SNP	.											.	MYO1G	86	.	0			c.G2368A						PASS	.						75.0	72.0	73.0					7																	45005249		2203	4300	6503	SO:0001583	missense	64005	exon17			AGAGTGCGTGGCA	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"""Myosins / Myosin superfamily : Class I"""	13880	protein-coding gene	gene with protein product	"""minor histocompatibility antigen HA-2"""	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.2368G>A	7.37:g.45005249C>T	ENSP00000258787:p.Ala790Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	97	40	0.412371	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	37	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	C	0.298	-0.975870	0.02215	.	.	ENSG00000136286	ENST00000258787	D	0.86956	-2.19	4.37	1.42	0.22433	.	0.867457	0.09344	U	0.815042	T	0.73156	0.3551	N	0.20986	0.625	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.54397	-0.8300	10	0.13470	T	0.59	.	2.1804	0.03873	0.1374:0.4415:0.2463:0.1748	.	790	B0I1T2	MYO1G_HUMAN	T	790	ENSP00000258787:A790T	ENSP00000258787:A790T	A	-	1	0	MYO1G	44971774	0.000000	0.05858	0.000000	0.03702	0.383000	0.30230	-0.095000	0.11077	0.042000	0.15717	0.462000	0.41574	GCA	.	.	none		0.617	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		
SIGLEC11	114132	hgsc.bcm.edu	37	19	50453317	50453317	+	Silent	SNP	C	C	T	rs9304690	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50453317C>T	ENST00000447370.2	-	11	2097	c.2007G>A	c.(2005-2007)tcG>tcA	p.S669S	CTC-326K19.6_ENST00000451973.1_Intron|U3_ENST00000408198.1_RNA|SIGLEC11_ENST00000426971.2_Silent_p.S573S	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	669					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		TCTTGATCTCCGAGTACTCGG	0.617													C|||	1027	0.205072	0.0779	0.1643	5008	,	,		16936	0.2619		0.2396	False		,,,				2504	0.3119				p.S669S		Atlas-SNP	.											SIGLEC11,colon,carcinoma,0,1	SIGLEC11	70	1	0			c.G2007A						PASS	.	C	,	455,3949	215.5+/-234.4	30,395,1777	42.0	40.0	41.0		1719,2007	-7.3	0.0	19	dbSNP_119	41	2058,6542	355.9+/-330.1	238,1582,2480	no	coding-synonymous,coding-synonymous	SIGLEC11	NM_001135163.1,NM_052884.2	,	268,1977,4257	TT,TC,CC		23.9302,10.3315,19.3248	,	573/603,669/699	50453317	2513,10491	2202	4300	6502	SO:0001819	synonymous_variant	114132	exon11			GATCTCCGAGTAC	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.2007G>A	19.37:g.50453317C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	132	71	0.537879	NM_052884		Silent	SNP	ENST00000447370.2	37	CCDS12790.2	473	0.21657509157509158	48	0.0975609756097561	75	0.20718232044198895	154	0.2692307692307692	196	0.25857519788918204	C	3.560	-0.089762	0.07053	0.103315	0.239302	ENSG00000161640	ENST00000426971	.	.	.	3.64	-7.29	0.01451	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27274	P	0.9582925	.	.	.	.	.	.	T	0.38178	-0.9673	3	.	.	.	.	1.0129	0.01501	0.2576:0.3395:0.1309:0.272	rs9304690;rs56579996;rs9304690	.	.	.	Q	563	.	.	R	-	2	0	SIGLEC11	55145129	0.000000	0.05858	0.005000	0.12908	0.026000	0.11368	-3.084000	0.00612	-1.620000	0.01564	-1.192000	0.01694	CGG	C|0.803;T|0.197	0.197	strong		0.617	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884	
PLEC	5339	hgsc.bcm.edu	37	8	144997656	144997656	+	Silent	SNP	C	C	T	rs7016416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144997656C>T	ENST00000322810.4	-	31	7021	c.6852G>A	c.(6850-6852)gcG>gcA	p.A2284A	PLEC_ENST00000398774.2_Silent_p.A2115A|PLEC_ENST00000345136.3_Silent_p.A2147A|PLEC_ENST00000354589.3_Silent_p.A2147A|PLEC_ENST00000354958.2_Silent_p.A2125A|PLEC_ENST00000436759.2_Silent_p.A2174A|PLEC_ENST00000527096.1_Silent_p.A2170A|PLEC_ENST00000356346.3_Silent_p.A2133A|PLEC_ENST00000357649.2_Silent_p.A2151A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2284	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GTGCCCGCCGCGCCGCCTCTT	0.692													C|||	1153	0.230232	0.028	0.2954	5008	,	,		12031	0.1429		0.4245	False		,,,				2504	0.3476				p.A2284A		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	0			c.G6852A						scavenged	.	C	,,,,,,,	329,3527		26,277,1625	8.0	11.0	10.0		6522,6399,6375,6852,6345,6441,6453,6441	-7.4	0.0	8	dbSNP_116	10	3097,4915		616,1865,1525	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	642,2142,3150	TT,TC,CC		38.6545,8.5322,28.8675	,,,,,,,	2174/4575,2133/4534,2125/4526,2284/4685,2115/4516,2147/4548,2151/4552,2147/4548	144997656	3426,8442	1928	4006	5934	SO:0001819	synonymous_variant	5339	exon31			CCGCCGCGCCGCC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.6852G>A	8.37:g.144997656C>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	23	11	0.478261	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			C|0.718;T|0.282	0.282	strong		0.692	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
ALX4	60529	hgsc.bcm.edu	37	11	44286566	44286566	+	Silent	SNP	G	G	A	rs3802805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:44286566G>A	ENST00000329255.3	-	4	1177	c.1074C>T	c.(1072-1074)caC>caT	p.H358H		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	358					anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						TCTGGCCCACGTGACTGCCAG	0.677													G|||	1795	0.358427	0.1248	0.5202	5008	,	,		16259	0.5258		0.334	False		,,,				2504	0.4121				p.H358H		Atlas-SNP	.											ALX4,NS,adenoma,0,1	ALX4	58	1	0			c.C1074T						PASS	.	G		733,3673	291.0+/-281.2	66,601,1536	47.0	43.0	45.0		1074	3.0	1.0	11	dbSNP_107	45	2838,5760	430.8+/-356.6	470,1898,1931	no	coding-synonymous	ALX4	NM_021926.3		536,2499,3467	AA,AG,GG		33.0077,16.6364,27.4608		358/412	44286566	3571,9433	2203	4299	6502	SO:0001819	synonymous_variant	60529	exon4			GCCCACGTGACTG	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"""Homeoboxes / PRD class"""	450	protein-coding gene	gene with protein product		605420	"""parietal foramina 2"", ""aristaless-like homeobox 4"""	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.1074C>T	11.37:g.44286566G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_021926	Q96JN7|Q9H198|Q9HAY9	Silent	SNP	ENST00000329255.3	37	CCDS31468.1																																																																																			G|0.699;A|0.301	0.301	strong		0.677	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1		
CPA5	93979	hgsc.bcm.edu	37	7	130007388	130007388	+	Missense_Mutation	SNP	G	G	T	rs17854248	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:130007388G>T	ENST00000485477.1	+	10	2143	c.1014G>T	c.(1012-1014)gaG>gaT	p.E338D	CPA5_ENST00000466363.2_Missense_Mutation_p.E338D|CPA5_ENST00000393213.3_Missense_Mutation_p.E338D|CPA5_ENST00000355388.3_Missense_Mutation_p.E338D|CPA5_ENST00000431780.2_Missense_Mutation_p.E338D|CPA5_ENST00000474905.1_Missense_Mutation_p.E338D|CPA5_ENST00000461828.1_Missense_Mutation_p.E338D			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	338			E -> D (in dbSNP:rs17854248). {ECO:0000269|PubMed:11920156, ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					GATTGCTGGAGCCCGTTTCAA	0.517													G|||	670	0.133786	0.208	0.0908	5008	,	,		18238	0.003		0.1958	False		,,,				2504	0.135				p.E338D		Atlas-SNP	.											.	CPA5	61	.	0			c.G1014T						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU	929,3477	356.1+/-313.4	105,719,1379	116.0	112.0	114.0		1014,1014,1014	3.8	1.0	7	dbSNP_123	114	1797,6803	324.6+/-316.5	188,1421,2691	yes	missense,missense,missense	CPA5	NM_001127441.1,NM_001127442.1,NM_080385.4	45,45,45	293,2140,4070	TT,TG,GG		20.8953,21.0849,20.9596	benign,benign,benign	338/437,338/404,338/437	130007388	2726,10280	2203	4300	6503	SO:0001583	missense	93979	exon11			GCTGGAGCCCGTT	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.1014G>T	7.37:g.130007388G>T	ENSP00000420237:p.Glu338Asp	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	360	176	0.488889	NM_080385	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	37	CCDS5819.1	306	0.1401098901098901	111	0.22560975609756098	38	0.10497237569060773	1	0.0017482517482517483	156	0.20580474934036938	G	8.114	0.779385	0.16120	0.210849	0.208953	ENSG00000158525	ENST00000355388;ENST00000461828;ENST00000466363;ENST00000485477;ENST00000431780;ENST00000474905;ENST00000393213	T;T;T;T;T;T;T	0.11063	2.81;2.81;2.81;2.81;2.81;2.81;2.81	5.61	3.81	0.43845	Peptidase M14, carboxypeptidase A (2);	0.096048	0.45606	D	0.000349	T	0.00012	0.0000	L	0.32530	0.975	0.45733	P	0.0013640000000000319	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.45086	-0.9285	8	.	.	.	.	8.5473	0.33429	0.3033:0.0:0.6967:0.0	rs17854248;rs60477216	338;338	G3V0G8;Q8WXQ8	.;CBPA5_HUMAN	D	338	ENSP00000347549:E338D;ENSP00000418183:E338D;ENSP00000419025:E338D;ENSP00000420237:E338D;ENSP00000393045:E338D;ENSP00000417314:E338D;ENSP00000376907:E338D	.	E	+	3	2	CPA5	129794624	0.000000	0.05858	0.995000	0.50966	0.168000	0.22595	-0.706000	0.05047	0.732000	0.32470	0.462000	0.41574	GAG	G|0.810;T|0.190	0.190	strong		0.517	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441	
ZNF571	51276	hgsc.bcm.edu	37	19	38056574	38056574	+	Missense_Mutation	SNP	T	T	A	rs28512414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:38056574T>A	ENST00000328550.2	-	4	855	c.756A>T	c.(754-756)gaA>gaT	p.E252D	ZNF571-AS1_ENST00000587121.1_RNA|ZNF571-AS1_ENST00000592392.1_RNA|ZNF571-AS1_ENST00000590838.1_RNA|ZNF571_ENST00000590751.1_Intron|ZNF571_ENST00000358744.3_Missense_Mutation_p.E252D|ZNF571-AS1_ENST00000591430.1_RNA|ZNF571-AS1_ENST00000589802.1_RNA|ZNF540_ENST00000592533.1_Intron|ZNF571-AS1_ENST00000586139.1_RNA|ZNF571-AS1_ENST00000585578.1_RNA|ZNF571_ENST00000593133.1_Missense_Mutation_p.E252D|ZNF571-AS1_ENST00000586013.1_RNA|ZNF571_ENST00000451802.2_Missense_Mutation_p.E252D|ZNF571-AS1_ENST00000589750.1_RNA			Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	252			E -> D (in dbSNP:rs28512414). {ECO:0000269|PubMed:11042152}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	25			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATTTCTTACATTCATATGGTT	0.368													T|||	1844	0.368211	0.3555	0.2637	5008	,	,		21413	0.6528		0.168	False		,,,				2504	0.3722				p.E252D		Atlas-SNP	.											.	ZNF571	54	.	0			c.A756T						PASS	.	T	ASP/GLU	1389,3017	455.1+/-350.9	215,959,1029	60.0	59.0	59.0		756	3.9	1.0	19	dbSNP_125	59	1594,7000	295.4+/-302.4	146,1302,2849	no	missense	ZNF571	NM_016536.3	45	361,2261,3878	AA,AT,TT		18.5478,31.5252,22.9462	benign	252/610	38056574	2983,10017	2203	4297	6500	SO:0001583	missense	51276	exon4			CTTACATTCATAT	AF161544	CCDS12505.1	19q13.12	2013-09-20			ENSG00000180479	ENSG00000180479		"""Zinc fingers, C2H2-type"", ""-"""	25000	protein-coding gene	gene with protein product						11042152	Standard	XM_005258977		Approved	HSPC059	uc002ogt.3	Q7Z3V5	OTTHUMG00000182016	ENST00000328550.2:c.756A>T	19.37:g.38056574T>A	ENSP00000333660:p.Glu252Asp	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	52	17	0.326923	NM_016536	Q2HIY0|Q3ZCU3|Q9NZX7	Missense_Mutation	SNP	ENST00000328550.2	37	CCDS12505.1	791	0.36217948717948717	202	0.4105691056910569	91	0.2513812154696133	372	0.6503496503496503	126	0.1662269129287599	T	13.36	2.213757	0.39102	0.315252	0.185478	ENSG00000180479	ENST00000328550;ENST00000451802;ENST00000358744	T;T;T	0.22134	1.97;1.97;1.97	3.87	3.87	0.44632	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.53671	1.685	0.44085	P	0.0031520000000000437	B	0.10296	0.003	B	0.20767	0.031	T	0.35943	-0.9768	8	0.52906	T	0.07	.	7.5644	0.27870	0.1911:0.0:0.0:0.8089	rs28512414;rs57192031	252	Q7Z3V5	ZN571_HUMAN	D	252	ENSP00000333660:E252D;ENSP00000392638:E252D;ENSP00000351594:E252D	ENSP00000333660:E252D	E	-	3	2	ZNF571	42748414	0.000000	0.05858	0.994000	0.49952	0.921000	0.55340	-1.471000	0.02344	1.604000	0.50143	0.260000	0.18958	GAA	T|0.733;A|0.267	0.267	strong		0.368	ZNF571-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458669.1	NM_016536	
ECI2	10455	hgsc.bcm.edu	37	6	4133855	4133855	+	Missense_Mutation	SNP	C	C	T	rs3177253	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:4133855C>T	ENST00000380118.3	-	2	177	c.141G>A	c.(139-141)atG>atA	p.M47I	ECI2_ENST00000413766.2_5'UTR|RP3-400B16.4_ENST00000527831.1_RNA|ECI2_ENST00000465828.1_Missense_Mutation_p.M17I|ECI2_ENST00000380125.2_Missense_Mutation_p.M17I|ECI2_ENST00000361538.2_Missense_Mutation_p.M17I|RP3-400B16.1_ENST00000427049.2_lincRNA			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	47	ACB. {ECO:0000255|PROSITE- ProRule:PRU00573}.		M -> I (in dbSNP:rs3177253).		fatty acid catabolic process (GO:0009062)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|fatty-acyl-CoA binding (GO:0000062)|receptor binding (GO:0005102)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	11						TCACTTGATTCATTGAATTTT	0.408													C|||	672	0.134185	0.1067	0.1715	5008	,	,		20243	0.0218		0.2744	False		,,,				2504	0.1166				p.M47I		Atlas-SNP	.											.	ECI2	59	.	0			c.G141A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET	544,3862	245.9+/-254.7	33,478,1692	202.0	184.0	190.0		51,51,141	4.4	0.0	6	dbSNP_105	190	2144,6456	368.3+/-335.0	274,1596,2430	yes	missense,missense,missense	ECI2	NM_001166010.1,NM_006117.2,NM_206836.2	10,10,10	307,2074,4122	TT,TC,CC		24.9302,12.3468,20.6674	benign,benign,benign	17/365,17/365,47/395	4133855	2688,10318	2203	4300	6503	SO:0001583	missense	10455	exon2			TTGATTCATTGAA	AF069301	CCDS4490.1, CCDS43420.1, CCDS43420.2	6p24.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000198721	ENSG00000198721			14601	protein-coding gene	gene with protein product	"""acyl-Coenzyme A binding domain containing 2"", "" Hepatocellular carcinoma-associated antigen 88"""	608024	"""peroxisomal D3,D2-enoyl-CoA isomerase"""	PECI		10419495	Standard	NM_206836		Approved	ACBD2, DRS1, HCA88	uc003mwf.3	O75521	OTTHUMG00000014158	ENST00000380118.3:c.141G>A	6.37:g.4133855C>T	ENSP00000369461:p.Met47Ile	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	235	115	0.489362	NM_206836	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Missense_Mutation	SNP	ENST00000380118.3	37	CCDS43420.2	353	0.16163003663003664	50	0.1016260162601626	74	0.20441988950276244	15	0.026223776223776224	214	0.28232189973614774	C	13.93	2.384038	0.42308	0.123468	0.249302	ENSG00000198721	ENST00000380118;ENST00000380125;ENST00000361538;ENST00000465828;ENST00000495548	T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1	6.17	4.4	0.53042	FERM/acyl-CoA-binding protein, 3-helical bundle (1);Acyl-CoA-binding protein, ACBP (4);	4.707450	0.00166	N	0.000018	T	0.03608	0.0103	N	0.05306	-0.075	0.45035	P	0.0019460000000000033	B	0.02656	0.0	B	0.08055	0.003	T	0.31052	-0.9957	9	0.18276	T	0.48	.	7.5576	0.27833	0.0:0.7611:0.0:0.2389	rs3177253;rs52807695;rs59694716;rs3177253	47	O75521	ECI2_HUMAN	I	47;17;17;17;94	ENSP00000369461:M47I;ENSP00000369468:M17I;ENSP00000354737:M17I;ENSP00000420309:M17I;ENSP00000417459:M94I	ENSP00000354737:M17I	M	-	3	0	ECI2	4078854	0.217000	0.23597	0.033000	0.17914	0.886000	0.51366	1.505000	0.35736	1.630000	0.50440	0.655000	0.94253	ATG	C|0.821;T|0.179	0.179	strong		0.408	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117	
PRRT3	285368	hgsc.bcm.edu	37	3	9990800	9990800	+	Missense_Mutation	SNP	G	G	C	rs59465469	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9990800G>C	ENST00000412055.1	-	2	1129	c.1000C>G	c.(1000-1002)Cgg>Ggg	p.R334G	PRRT3_ENST00000411976.2_Missense_Mutation_p.R334G|PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	334	Pro-rich.		R -> G (in dbSNP:rs59465469). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)		p.R334G(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						TTAGACGGCCGATCAGGAGCC	0.612													C|||	1910	0.38139	0.8132	0.3256	5008	,	,		17430	0.1558		0.2137	False		,,,				2504	0.2423				p.R334G		Atlas-SNP	.											PRRT3,NS,carcinoma,0,1	PRRT3	35	1	1	Substitution - Missense(1)	stomach(1)	c.C1000G						PASS	.	C	GLY/ARG	2648,1206		933,782,212	51.0	61.0	58.0		1000	2.2	0.0	3	dbSNP_129	58	2056,6232		268,1520,2356	yes	missense	PRRT3	NM_207351.3	125	1201,2302,2568	CC,CG,GG		24.8069,31.2922,38.7416	benign	334/982	9990800	4704,7438	1927	4144	6071	SO:0001583	missense	285368	exon2			ACGGCCGATCAGG	AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"""Proline-rich transmembrane proteins"""	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.1000C>G	3.37:g.9990800G>C	ENSP00000392511:p.Arg334Gly	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Missense_Mutation	SNP	ENST00000412055.1	37	CCDS43049.1	803	0.3676739926739927	397	0.806910569105691	123	0.3397790055248619	118	0.2062937062937063	165	0.21767810026385223	C	0.009	-1.814685	0.00600	0.687078	0.248069	ENSG00000163704	ENST00000412055;ENST00000411976	T;T	0.16324	2.6;2.35	4.03	2.22	0.28083	.	0.272597	0.26967	N	0.021588	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.13872	-1.0493	8	.	.	.	-2.0801	6.3107	0.21163	0.0:0.5378:0.3618:0.1004	rs59465469;rs62245482	334;334	Q5FWE3-3;Q5FWE3	.;PRRT3_HUMAN	G	334	ENSP00000392511:R334G;ENSP00000404512:R334G	.	R	-	1	2	PRRT3	9965800	0.000000	0.05858	0.005000	0.12908	0.001000	0.01503	0.038000	0.13862	0.272000	0.22027	-0.978000	0.02582	CGG	G|0.675;C|0.325	0.325	strong		0.612	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351	
SLC25A46	91137	hgsc.bcm.edu	37	5	110079450	110079450	+	Silent	SNP	T	T	C	rs17446534	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:110079450T>C	ENST00000355943.3	+	3	472	c.346T>C	c.(346-348)Ttg>Ctg	p.L116L	SLC25A46_ENST00000509442.2_Silent_p.L25L|SLC25A46_ENST00000447245.2_Silent_p.L116L|SLC25A46_ENST00000513807.1_5'UTR|SLC25A46_ENST00000504098.1_5'UTR	NM_138773.1	NP_620128.1	Q96AG3	S2546_HUMAN	solute carrier family 25, member 46	116					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10		all_cancers(142;0.00203)|all_epithelial(76;4.52e-05)|Prostate(80;0.0115)|Colorectal(57;0.0676)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;2.58e-09)|Epithelial(69;7.29e-08)|all cancers(49;9.35e-06)|COAD - Colon adenocarcinoma(37;0.211)		AGAAAATGTATTGGCACATCC	0.313													T|||	202	0.0403355	0.0234	0.0519	5008	,	,		14586	0.0188		0.0905	False		,,,				2504	0.0256				p.L116L		Atlas-SNP	.											.	SLC25A46	33	.	0			c.T346C						PASS	.	T		163,4241	107.3+/-145.7	2,159,2041	81.0	70.0	74.0		346	1.3	1.0	5	dbSNP_123	74	786,7810	183.6+/-231.8	36,714,3548	no	coding-synonymous	SLC25A46	NM_138773.1		38,873,5589	CC,CT,TT		9.1438,3.7012,7.3		116/419	110079450	949,12051	2202	4298	6500	SO:0001819	synonymous_variant	91137	exon3			AATGTATTGGCAC	BC017169	CCDS4100.1	5q22.1	2013-05-22			ENSG00000164209	ENSG00000164209		"""Solute carriers"""	25198	protein-coding gene	gene with protein product		610826				1651562, 1651563, 16949250	Standard	NM_138773		Approved		uc003koz.3	Q96AG3	OTTHUMG00000128794	ENST00000355943.3:c.346T>C	5.37:g.110079450T>C		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	298	138	0.463087	NM_138773	A8K2F2|B3KRE6|B4DTA3|D3DSZ6|D6R9W7|Q04197	Silent	SNP	ENST00000355943.3	37	CCDS4100.1																																																																																			T|0.938;C|0.062	0.062	strong		0.313	SLC25A46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250721.5	NM_138773	
NINL	22981	hgsc.bcm.edu	37	20	25484623	25484623	+	Missense_Mutation	SNP	G	G	A	rs13044759	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:25484623G>A	ENST00000278886.6	-	7	899	c.826C>T	c.(826-828)Cgg>Tgg	p.R276W	NINL_ENST00000422516.1_Missense_Mutation_p.R276W	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	276			R -> W (in dbSNP:rs13044759).		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						GGTTTAACCCGAGTGGAAGAC	0.483													G|||	102	0.0203674	0.0015	0.0187	5008	,	,		18621	0.0		0.0288	False		,,,				2504	0.0593				p.R276W		Atlas-SNP	.											.	NINL	148	.	0			c.C826T						PASS	.	G	TRP/ARG	39,4367	43.1+/-76.7	0,39,2164	213.0	194.0	201.0		826	1.9	0.0	20	dbSNP_121	201	363,8237	120.6+/-179.8	5,353,3942	yes	missense	NINL	NM_025176.4	101	5,392,6106	AA,AG,GG		4.2209,0.8852,3.0909	benign	276/1383	25484623	402,12604	2203	4300	6503	SO:0001583	missense	22981	exon7			TAACCCGAGTGGA		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.826C>T	20.37:g.25484623G>A	ENSP00000278886:p.Arg276Trp	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	274	140	0.510949	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	28	0.01282051282051282	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	20	0.026385224274406333	G	13.18	2.161435	0.38119	0.008852	0.042209	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.32753	1.71;1.44	5.0	1.93	0.25924	.	2.258590	0.01562	N	0.020177	T	0.03263	0.0095	N	0.08118	0	0.09310	N	1	P;P	0.51537	0.946;0.561	B;B	0.29942	0.075;0.109	T	0.32348	-0.9910	10	0.66056	D	0.02	0.0046	9.2065	0.37293	0.0773:0.2769:0.6457:0.0	rs13044759;rs52821831;rs13044759	276;276	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	W	276	ENSP00000278886:R276W;ENSP00000410431:R276W	ENSP00000278886:R276W	R	-	1	2	NINL	25432623	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	0.974000	0.29436	0.268000	0.21939	0.655000	0.94253	CGG	G|0.973;A|0.027	0.027	strong		0.483	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176	
STPG2	285555	hgsc.bcm.edu	37	4	99027184	99027184	+	Missense_Mutation	SNP	T	T	C	rs2903150	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:99027184T>C	ENST00000295268.3	-	5	621	c.532A>G	c.(532-534)Atc>Gtc	p.I178V		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	178			I -> V (in dbSNP:rs2903150).														TCTCTCTTGATGTTAACATTT	0.254													t|||	1879	0.3752	0.4425	0.2882	5008	,	,		15525	0.2748		0.4026	False		,,,				2504	0.4213				p.I178V		Atlas-SNP	.											.	.	.	.	0			c.A532G						PASS	.	C	VAL/ILE	1967,2429	529.8+/-372.8	454,1059,685	81.0	83.0	82.0		532	2.6	1.0	4	dbSNP_101	82	3400,5194	487.8+/-372.2	692,2016,1589	yes	missense	C4orf37	NM_174952.2	29	1146,3075,2274	CC,CT,TT		39.5625,44.7452,41.3164	benign	178/460	99027184	5367,7623	2198	4297	6495	SO:0001583	missense	285555	exon5			TCTTGATGTTAAC	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.532A>G	4.37:g.99027184T>C	ENSP00000295268:p.Ile178Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	760	0.34798534798534797	193	0.39227642276422764	106	0.292817679558011	161	0.28146853146853146	300	0.39577836411609496	t	0.674	-0.800947	0.02841	0.447452	0.395625	ENSG00000163116	ENST00000295268	T	0.11385	2.78	5.04	2.61	0.31194	.	0.361157	0.28712	N	0.014387	T	0.00012	0.0000	L	0.52011	1.625	0.58432	P	8.000000000008E-6	B	0.22746	0.074	B	0.31614	0.133	T	0.46233	-0.9206	9	0.22109	T	0.4	-32.5742	6.054	0.19800	0.1206:0.1463:0.0:0.7331	rs2903150;rs52793168;rs61326598;rs2903150	178	Q8N412	CD037_HUMAN	V	178	ENSP00000295268:I178V	ENSP00000295268:I178V	I	-	1	0	C4orf37	99246207	1.000000	0.71417	0.997000	0.53966	0.048000	0.14542	0.706000	0.25690	0.089000	0.17243	-1.245000	0.01525	ATC	T|0.617;C|0.383	0.383	strong		0.254	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
WDR81	124997	hgsc.bcm.edu	37	17	1630208	1630208	+	Missense_Mutation	SNP	C	C	T	rs57207396|rs587780500	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1630208C>T	ENST00000409644.1	+	1	1955	c.1955C>T	c.(1954-1956)cCg>cTg	p.P652L	WDR81_ENST00000419248.1_Intron|WDR81_ENST00000446363.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000437219.2_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	652					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGAGACAGGCCGGTGGCAGGA	0.597													C|||	1168	0.233227	0.0303	0.1988	5008	,	,		18247	0.4821		0.2604	False		,,,				2504	0.2474				p.P652L		Atlas-SNP	.											.	WDR81	180	.	0			c.C1955T						PASS	.						7.0	8.0	7.0					17																	1630208		689	1575	2264	SO:0001583	missense	124997	exon1			ACAGGCCGGTGGC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.1955C>T	17.37:g.1630208C>T	ENSP00000386609:p.Pro652Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	592	0.27106227106227104	20	0.04065040650406504	79	0.21823204419889503	287	0.5017482517482518	206	0.2717678100263852	C	8.876	0.950427	0.18431	.	.	ENSG00000167716	ENST00000409644	T	0.51574	0.7	5.07	3.02	0.34903	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.44677	P	0.002334999999999976	.	.	.	.	.	.	T	0.45614	-0.9249	5	0.02654	T	1	.	5.6639	0.17684	0.1582:0.6808:0.0:0.1611	rs57207396;rs62090044	.	.	.	L	652	ENSP00000386609:P652L	ENSP00000386609:P652L	P	+	2	0	WDR81	1576958	0.001000	0.12720	0.143000	0.22291	0.832000	0.47134	1.499000	0.35671	0.670000	0.31165	0.462000	0.41574	CCG	C|0.727;G|0.000;T|0.272	0.272	strong		0.597	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
LILRB4	11006	hgsc.bcm.edu	37	19	55179377	55179377	+	Missense_Mutation	SNP	T	T	G	rs149600113		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55179377T>G	ENST00000391736.1	+	14	1569	c.1254T>G	c.(1252-1254)ttT>ttG	p.F418L	LILRB4_ENST00000430952.2_Missense_Mutation_p.F417L|LILRB4_ENST00000391734.3_Missense_Mutation_p.F365L|LILRB4_ENST00000391733.3_Missense_Mutation_p.F419L|LILRB4_ENST00000270452.2_Missense_Mutation_p.F418L	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	418					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		TGCACAGCTTTACCCTCAGAC	0.627													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16015	0.0		0.0	False		,,,				2504	0.0				p.F418L		Atlas-SNP	.											LILRB4,NS,carcinoma,0,1	LILRB4	86	1	0			c.T1254G						scavenged	.						93.0	97.0	95.0					19																	55179377		2203	4300	6503	SO:0001583	missense	11006	exon12			CAGCTTTACCCTC	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1254T>G	19.37:g.55179377T>G	ENSP00000375616:p.Phe418Leu	Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	257	5	0.0194553	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	G	0.039	-1.292496	0.01375	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733	T;T;T;T;T	0.00460	7.32;7.32;7.31;7.27;7.33	2.07	-0.638	0.11500	.	.	.	.	.	T	0.00073	0.0002	N	0.00251	-1.775	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.06405	0.0;0.0;0.002;0.0	T	0.42849	-0.9427	9	0.02654	T	1	.	0.6834	0.00878	0.1703:0.2396:0.3472:0.2428	.	365;419;417;418	A8MUE1;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	L	418;418;417;365;419	ENSP00000375616:F418L;ENSP00000270452:F418L;ENSP00000408995:F417L;ENSP00000375614:F365L;ENSP00000375613:F419L	ENSP00000270452:F418L	F	+	3	2	LILRB4	59871189	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	0.085000	0.14912	-0.134000	0.11516	-0.484000	0.04775	TTT	.	.	weak		0.627	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
COL6A3	1293	hgsc.bcm.edu	37	2	238267717	238267717	+	Silent	SNP	C	C	T	rs2646254	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:238267717C>T	ENST00000295550.4	-	20	6821	c.6369G>A	c.(6367-6369)ttG>ttA	p.L2123L	COL6A3_ENST00000409809.1_Silent_p.L1917L|COL6A3_ENST00000472056.1_Silent_p.L1516L|COL6A3_ENST00000353578.4_Silent_p.L1917L|COL6A3_ENST00000346358.4_Silent_p.L1923L|COL6A3_ENST00000347401.3_Silent_p.L1922L	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2123	Collagen-like 2.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AAGAACCAGGCAATCCTTTGT	0.418													C|||	1657	0.330871	0.5416	0.2507	5008	,	,		19812	0.3522		0.1511	False		,,,				2504	0.2658				p.L2123L		Atlas-SNP	.											.	COL6A3	608	.	0			c.G6369A						PASS	.	C	,,	2073,2333	570.8+/-382.9	485,1103,615	208.0	226.0	220.0		6369,4548,5751	4.3	0.2	2	dbSNP_100	220	1168,7432	239.0+/-270.3	77,1014,3209	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	562,2117,3824	TT,TC,CC		13.5814,47.0495,24.9193	,,	2123/3178,1516/2571,1917/2972	238267717	3241,9765	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon20			ACCAGGCAATCCT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.6369G>A	2.37:g.238267717C>T		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	271	114	0.420664	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.720;T|0.280	0.280	strong		0.418	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
TBC1D32	221322	hgsc.bcm.edu	37	6	121638682	121638682	+	Missense_Mutation	SNP	G	G	A	rs75540618	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:121638682G>A	ENST00000398212.2	-	3	503	c.454C>T	c.(454-456)Cgc>Tgc	p.R152C	TBC1D32_ENST00000275159.6_Missense_Mutation_p.R152C	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	152					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.R152C(1)									TTGTCTGTGCGGTAACTATGG	0.353													A|||	274	0.0547125	0.034	0.1196	5008	,	,		14978	0.124		0.0119	False		,,,				2504	0.0092				p.R152C		Atlas-SNP	.											C6orf170,rectum,carcinoma,+1,6	C6orf170	146	6	1	Substitution - Missense(1)	central_nervous_system(1)	c.C454T						PASS	.	A	CYS/ARG	110,3622		3,104,1759	316.0	286.0	295.0		454	3.9	1.0	6	dbSNP_131	295	100,8090		0,100,3995	yes	missense	C6orf170	NM_152730.4	180	3,204,5754	AA,AG,GG		1.221,2.9475,1.7614	benign	152/1258	121638682	210,11712	1866	4095	5961	SO:0001583	missense	221322	exon3			CTGTGCGGTAACT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.454C>T	6.37:g.121638682G>A	ENSP00000381270:p.Arg152Cys	Somatic	512	1	0.00195312		WXS	Illumina HiSeq	Phase_I	532	225	0.422932	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	143	0.06547619047619048	24	0.04878048780487805	34	0.09392265193370165	75	0.13111888111888112	10	0.013192612137203167	A	8.618	0.890616	0.17613	0.029475	0.01221	ENSG00000146350	ENST00000275159;ENST00000398212;ENST00000422369	T;T;T	0.15603	2.41;2.41;2.41	5.02	3.86	0.44501	.	0.166640	0.45606	N	0.000354	T	0.01287	0.0042	N	0.00368	-1.59	0.42130	P	0.008537000000000017	B	0.02656	0.0	B	0.01281	0.0	T	0.44651	-0.9314	9	0.31617	T	0.26	-3.4063	9.7544	0.40494	0.8589:0.0:0.1411:0.0	.	152	Q96NH3	BROMI_HUMAN	C	152	ENSP00000275159:R152C;ENSP00000381270:R152C;ENSP00000397993:R152C	ENSP00000275159:R152C	R	-	1	0	C6orf170	121680381	1.000000	0.71417	0.954000	0.39281	0.314000	0.28054	5.184000	0.65070	0.344000	0.23847	-1.036000	0.02392	CGC	G|0.954;A|0.046	0.046	strong		0.353	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
WNT9B	7484	hgsc.bcm.edu	37	17	44949945	44949945	+	Missense_Mutation	SNP	A	A	G	rs118185468	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44949945A>G	ENST00000290015.2	+	2	193	c.140A>G	c.(139-141)cAg>cGg	p.Q47R	WNT9B_ENST00000393461.2_Missense_Mutation_p.Q47R	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	47					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to starvation (GO:0009267)|collecting duct development (GO:0072044)|cornea development in camera-type eye (GO:0061303)|embryonic cranial skeleton morphogenesis (GO:0048701)|establishment of planar polarity involved in nephron morphogenesis (GO:0072046)|in utero embryonic development (GO:0001701)|kidney rudiment formation (GO:0072003)|male genitalia development (GO:0030539)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesonephric duct formation (GO:0072181)|metanephric tubule formation (GO:0072174)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|positive regulation of catalytic activity (GO:0043085)|regulation of asymmetric cell division (GO:0009786)|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003339)|regulation of protein phosphorylation (GO:0001932)|regulation of tube size (GO:0035150)|response to retinoic acid (GO:0032526)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			large_intestine(2)|lung(8)	10			BRCA - Breast invasive adenocarcinoma(9;0.0257)			GCCCCGGCACAGGGCGGGGCC	0.687													A|||	17	0.00339457	0.0	0.0	5008	,	,		13354	0.0		0.006	False		,,,				2504	0.0112				p.Q47R		Atlas-SNP	.											.	WNT9B	37	.	0			c.A140G						PASS	.	A	ARG/GLN	5,4395		0,5,2195	37.0	43.0	41.0		140	4.5	0.1	17	dbSNP_133	41	52,8536		1,50,4243	no	missense	WNT9B	NM_003396.1	43	1,55,6438	GG,GA,AA		0.6055,0.1136,0.4389	benign	47/358	44949945	57,12931	2200	4294	6494	SO:0001583	missense	7484	exon2			CGGCACAGGGCGG	AF028703	CCDS11506.1	17q21	2008-01-07	2003-03-11	2003-03-14		ENSG00000158955		"""Wingless-type MMTV integration sites"""	12779	protein-coding gene	gene with protein product		602864	"""wingless-type MMTV integration site family, member 15"""	WNT15		9441749, 11713592	Standard	NM_003396		Approved	WNT14B	uc002ikw.1	O14905		ENST00000290015.2:c.140A>G	17.37:g.44949945A>G	ENSP00000290015:p.Gln47Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_003396	Q6UXT4|Q96Q09	Missense_Mutation	SNP	ENST00000290015.2	37	CCDS11506.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	7.343	0.621314	0.14193	0.001136	0.006055	ENSG00000158955	ENST00000376843;ENST00000393461;ENST00000290015	T;T	0.78364	-1.17;-0.95	4.48	4.48	0.54585	.	0.507715	0.20964	N	0.082512	T	0.62974	0.2472	L	0.54323	1.7	0.29457	N	0.858057	B;B	0.22604	0.039;0.072	B;B	0.18871	0.011;0.023	T	0.58020	-0.7710	10	0.15952	T	0.53	.	11.5157	0.50520	0.8506:0.1494:0.0:0.0	.	47;47	E7EPC3;O14905	.;WNT9B_HUMAN	R	53;47;47	ENSP00000377105:Q47R;ENSP00000290015:Q47R	ENSP00000290015:Q47R	Q	+	2	0	WNT9B	42304944	.	.	0.080000	0.20451	0.128000	0.20619	.	.	2.013000	0.59113	0.374000	0.22700	CAG	A|0.997;G|0.003	0.003	strong		0.687	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396	
C2orf71	388939	hgsc.bcm.edu	37	2	29295016	29295016	+	Silent	SNP	A	A	G	rs10200693	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29295016A>G	ENST00000331664.5	-	1	2111	c.2112T>C	c.(2110-2112)aaT>aaC	p.N704N		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	704					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						ATGGGATGGCATTTGGAAGCT	0.498													A|||	1672	0.333866	0.4228	0.2579	5008	,	,		21897	0.4444		0.2604	False		,,,				2504	0.229				p.N704N		Atlas-SNP	.											.	C2orf71	146	.	0			c.T2112C						PASS	.	A		1536,2582		305,926,828	116.0	112.0	113.0		2112	-11.5	0.0	2	dbSNP_119	113	2295,6161		309,1677,2242	no	coding-synonymous	C2orf71	NM_001029883.1		614,2603,3070	GG,GA,AA		27.1405,37.2997,30.4676		704/1289	29295016	3831,8743	2059	4228	6287	SO:0001819	synonymous_variant	388939	exon1			GATGGCATTTGGA		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.2112T>C	2.37:g.29295016A>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	186	86	0.462366	NM_001029883		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																			A|0.660;G|0.340	0.340	strong		0.498	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
C4B	721	hgsc.bcm.edu	37	6	31996966	31996966	+	Missense_Mutation	SNP	G	G	A	rs2746414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31996966G>A	ENST00000435363.2	+	28	3611	c.3527G>A	c.(3526-3528)aGc>aAc	p.S1176N	C4B_ENST00000425700.2_Missense_Mutation_p.S1176N	NM_001002029.3	NP_001002029.3	P0C0L5	CO4B_HUMAN	complement component 4B (Chido blood group)	1176			S -> N (in allotype C4B1a; dbSNP:rs2746414). {ECO:0000269|PubMed:14989716}.		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|detection of molecule of bacterial origin (GO:0032490)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|complement binding (GO:0001848)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	TCAAAGGCAAGCTCATTTTTG	0.617																																					p.S1176N		Atlas-SNP	.											.	C4A	15	.	0			c.G3527A						PASS	.						107.0	90.0	95.0					6																	31996966		1559	3552	5111	SO:0001583	missense	720	exon28			AGGCAAGCTCATT	AF019413	CCDS47405.1	6p21.3	2014-09-17	2009-01-06		ENSG00000224389	ENSG00000224389		"""Blood group antigens"", ""Complement system"""	1324	protein-coding gene	gene with protein product		120820	"""complement component 4B"""				Standard	NM_001002029		Approved	CPAMD3, C4F, CO4, C4B1, C4B3, CH	uc011jpm.2	P0C0L5	OTTHUMG00000031187	ENST00000435363.2:c.3527G>A	6.37:g.31996966G>A	ENSP00000415941:p.Ser1176Asn	Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	272	43	0.158088	NM_007293	A2BHY4|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q6U2E9|Q6U2G1|Q6U2I5|Q6U2L1|Q6U2L7|Q6U2L9|Q6U2M5|Q6VCV8|Q96SA7|Q9NPK5|Q9UIP5	Missense_Mutation	SNP	ENST00000435363.2	37	CCDS47405.1	183	0.08379120879120878	58	0.11788617886178862	21	0.058011049723756904	37	0.06468531468531469	67	0.08839050131926121	A	0.004	-2.280506	0.00254	.	.	ENSG00000224389	ENST00000435363;ENST00000425700	T;T	0.13657	2.57;2.57	4.66	0.91	0.19337	.	.	.	.	.	T	0.01765	0.0056	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.48822	-0.9001	7	0.16420	T	0.52	.	3.9585	0.09401	0.5167:0.1842:0.2991:0.0	rs17874654;rs60964411	1176;1176	F5GXS0;Q6U2E9	.;.	N	1176	ENSP00000415941:S1176N;ENSP00000391933:S1176N	ENSP00000391933:S1176N	S	+	2	0	C4B	32104944	0.000000	0.05858	0.052000	0.19188	0.150000	0.21749	0.251000	0.18257	-0.086000	0.12550	-1.236000	0.01555	AGC	G|0.716;A|0.284	0.284	strong		0.617	C4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076368.5	NM_001002029	
ADCY8	114	hgsc.bcm.edu	37	8	131922027	131922027	+	Silent	SNP	T	T	G	rs12545028	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:131922027T>G	ENST00000286355.5	-	6	3659	c.1567A>C	c.(1567-1569)Agg>Cgg	p.R523R	ADCY8_ENST00000377928.3_Silent_p.R523R	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	523					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)			TGCCACTTCCTTAGTCCCAAA	0.473										HNSCC(32;0.087)			T|||	525	0.104832	0.0666	0.1311	5008	,	,		20298	0.0605		0.16	False		,,,				2504	0.1268				p.R523R		Atlas-SNP	.											.	ADCY8	291	.	0			c.A1567C						PASS	.	T		431,3975	207.5+/-228.8	17,397,1789	261.0	211.0	228.0		1567	4.0	0.8	8	dbSNP_120	228	1571,7029	294.2+/-301.7	139,1293,2868	no	coding-synonymous	ADCY8	NM_001115.2		156,1690,4657	GG,GT,TT		18.2674,9.7821,15.3929		523/1252	131922027	2002,11004	2203	4300	6503	SO:0001819	synonymous_variant	114	exon6			ACTTCCTTAGTCC	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.1567A>C	8.37:g.131922027T>G		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	245	124	0.506122	NM_001115		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																			T|0.866;G|0.134	0.134	strong		0.473	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
NCOA6	23054	hgsc.bcm.edu	37	20	33342629	33342629	+	Missense_Mutation	SNP	G	G	C	rs148359628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:33342629G>C	ENST00000374796.2	-	9	4141	c.1571C>G	c.(1570-1572)gCc>gGc	p.A524G	NCOA6_ENST00000359003.2_Missense_Mutation_p.A524G			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	524	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						GTTCGGATTGGCCTGTCCTGC	0.478																																					p.A524G		Atlas-SNP	.											.	NCOA6	219	.	0			c.C1571G						PASS	.	G	GLY/ALA,GLY/ALA	0,4406		0,0,2203	115.0	106.0	109.0		1571,1571	6.0	1.0	20	dbSNP_134	109	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	NCOA6	NM_001242539.1,NM_014071.3	60,60	0,6,6497	CC,CG,GG		0.0698,0.0,0.0461	benign,benign	524/1071,524/2064	33342629	6,13000	2203	4300	6503	SO:0001583	missense	23054	exon8			GGATTGGCCTGTC	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.1571C>G	20.37:g.33342629G>C	ENSP00000363929:p.Ala524Gly	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	144	76	0.527778	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.626084	0.46840	0.0	6.98E-4	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.25414	1.8;1.8	5.97	5.97	0.96955	.	0.081814	0.51477	D	0.000086	T	0.16685	0.0401	N	0.12182	0.205	0.48901	D	0.999723	B	0.09022	0.002	B	0.10450	0.005	T	0.08249	-1.0731	10	0.27082	T	0.32	-7.7298	15.8466	0.78899	0.0:0.1349:0.865:0.0	.	524	Q14686	NCOA6_HUMAN	G	524	ENSP00000363929:A524G;ENSP00000351894:A524G	ENSP00000351894:A524G	A	-	2	0	NCOA6	32806290	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.652000	0.54439	2.835000	0.97688	0.591000	0.81541	GCC	G|0.999;C|0.001	0.001	strong		0.478	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
CHTF18	63922	hgsc.bcm.edu	37	16	839269	839269	+	Missense_Mutation	SNP	G	G	A	rs77682584	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:839269G>A	ENST00000262315.9	+	3	409	c.346G>A	c.(346-348)Gag>Aag	p.E116K	CHTF18_ENST00000455171.2_Missense_Mutation_p.E144K|RPUSD1_ENST00000007264.2_5'Flank|CHTF18_ENST00000317063.6_Missense_Mutation_p.E313K|RPUSD1_ENST00000565809.1_5'Flank|RPUSD1_ENST00000561734.1_5'Flank|RPUSD1_ENST00000567114.1_5'Flank|CHTF18_ENST00000491530.1_3'UTR	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	116					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				CAGATCGGAGGAGATGGAGGA	0.672													G|||	806	0.160942	0.2065	0.0735	5008	,	,		14498	0.1161		0.0239	False		,,,				2504	0.3487				p.E116K		Atlas-SNP	.											.	CHTF18	52	.	0			c.G346A						PASS	.	G	LYS/GLU	640,3250		49,542,1354	15.0	18.0	17.0		346	-1.8	0.0	16	dbSNP_131	17	230,7948		1,228,3860	yes	missense	CHTF18	NM_022092.2	56	50,770,5214	AA,AG,GG		2.8124,16.4524,7.2091	benign	116/976	839269	870,11198	1945	4089	6034	SO:0001583	missense	63922	exon3			TCGGAGGAGATGG	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"""ATPases / AAA-type"""	18435	protein-coding gene	gene with protein product		613201	"""chromosome 16 open reading frame 41"""	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.346G>A	16.37:g.839269G>A	ENSP00000262315:p.Glu116Lys	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	204	97	0.47549	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	216	0.0989010989010989	107	0.21747967479674796	30	0.08287292817679558	61	0.10664335664335664	18	0.023746701846965697	G	10.85	1.466590	0.26335	0.164524	0.028124	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.10573	2.86;2.93;2.92	2.81	-1.81	0.07882	.	4.667180	0.00582	U	0.000320	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P;P;P	0.46512	0.879;0.634;0.455	B;B;B	0.42916	0.402;0.298;0.094	T	0.33599	-0.9862	9	0.06891	T	0.86	-1.1971	5.1501	0.15005	0.2095:0.3179:0.4726:0.0	.	116;144;116	B4DEY3;Q8WVB6-2;Q8WVB6	.;.;CTF18_HUMAN	K	313;144;116	ENSP00000313029:E313K;ENSP00000406252:E144K;ENSP00000262315:E116K	ENSP00000262315:E116K	E	+	1	0	CHTF18	779270	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.624000	0.24462	-0.341000	0.08376	-1.264000	0.01445	GAG	G|0.900;A|0.100	0.100	strong		0.672	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
GHRL	51738	hgsc.bcm.edu	37	3	10328453	10328453	+	Missense_Mutation	SNP	T	T	A	rs4684677	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:10328453T>A	ENST00000335542.8	-	5	1139	c.269A>T	c.(268-270)cAg>cTg	p.Q90L	GHRL_ENST00000430179.1_Missense_Mutation_p.Q89L|GHRL_ENST00000429122.1_Missense_Mutation_p.Q90L|LINC00852_ENST00000538717.1_RNA|GHRL_ENST00000476283.1_5'UTR|GHRL_ENST00000457360.1_Missense_Mutation_p.Q90L|GHRLOS_ENST00000603771.1_RNA|LINC00852_ENST00000475197.1_RNA|GHRL_ENST00000446937.2_Intron|GHRL_ENST00000437422.2_Missense_Mutation_p.Q78L|GHRL_ENST00000439975.2_Missense_Mutation_p.Q39L|GHRL_ENST00000422159.1_Intron|GHRL_ENST00000450603.1_Missense_Mutation_p.Q90L|GHRLOS_ENST00000605105.1_RNA|GHRLOS_ENST00000605014.1_RNA|GHRL_ENST00000449554.2_Missense_Mutation_p.Q89L|GHRLOS_ENST00000439539.3_RNA|GHRL_ENST00000449238.2_Missense_Mutation_p.Q77L|GHRL_ENST00000287656.7_Missense_Mutation_p.Q89L			Q9UBU3	GHRL_HUMAN	ghrelin/obestatin prepropeptide	90			Q -> L (in dbSNP:rs4684677).		actin polymerization or depolymerization (GO:0008154)|activation of MAPK activity (GO:0000187)|adult feeding behavior (GO:0008343)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|cortisol secretion (GO:0043400)|decidualization (GO:0046697)|dendrite development (GO:0016358)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|glucose metabolic process (GO:0006006)|growth hormone secretion (GO:0030252)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of circadian sleep/wake cycle, REM sleep (GO:0042322)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin secretion (GO:0046676)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of locomotion (GO:0040013)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of appetite (GO:0032100)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of corticotropin secretion (GO:0051461)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of synapse assembly (GO:0051965)|regulation of cell proliferation (GO:0042127)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to estrogen (GO:0043627)|response to hormone (GO:0009725)	axon (GO:0030424)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|ghrelin receptor binding (GO:0031768)|growth hormone-releasing hormone activity (GO:0016608)|protein tyrosine kinase activator activity (GO:0030296)			breast(2)|large_intestine(1)|lung(1)|ovary(1)	5						CTGCTGGTACTGAACCCCTGA	0.582											OREG0015386	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	307	0.0613019	0.0053	0.2392	5008	,	,		19509	0.006		0.0746	False		,,,				2504	0.0542				p.Q90L		Atlas-SNP	.											.	GHRL	8	.	0			c.A269T	GRCh37	CM024761	GHRL	M	rs4684677	PASS	.	T	LEU/GLN,LEU/GLN,LEU/GLN,LEU/GLN,LEU/GLN	63,4343	60.5+/-97.4	0,63,2140	72.0	59.0	63.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	266,233,230,116,269	4.8	1.0	3	dbSNP_111	63	507,8093	143.6+/-199.6	14,479,3807	yes	missense,missense,missense,missense,missense	GHRL	NM_001134941.1,NM_001134944.1,NM_001134945.1,NM_001134946.1,NM_016362.3	113,113,113,113,113	14,542,5947	AA,AT,TT		5.8953,1.4299,4.3826	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	89/117,78/106,77/105,39/67,90/118	10328453	570,12436	2203	4300	6503	SO:0001583	missense	51738	exon4			TGGTACTGAACCC	AF296558	CCDS33700.1, CCDS46747.1, CCDS46748.1, CCDS46749.1, CCDS46750.1	3p26-p25	2013-02-26	2008-07-02		ENSG00000157017	ENSG00000157017		"""Endogenous ligands"""	18129	protein-coding gene	gene with protein product	"""prepro-appetite regulatory hormone"""	605353	"""ghrelin, growth hormone secretagogue receptor ligand"""			10930375, 10604470, 16284174	Standard	NR_024133		Approved	MTLRP, ghrelin, obestatin	uc010hdj.2	Q9UBU3	OTTHUMG00000155360	ENST00000335542.8:c.269A>T	3.37:g.10328453T>A	ENSP00000335074:p.Gln90Leu	Somatic	89	0	0	663	WXS	Illumina HiSeq	Phase_I	118	65	0.550847	NM_016362	A8CF34|A8CF38|A8CF42|A8DN29|A8DN30|Q86YP8|Q8TAT9|Q9H3R3	Missense_Mutation	SNP	ENST00000335542.8	37	CCDS33700.1	143	0.06547619047619048	4	0.008130081300813009	73	0.20165745856353592	5	0.008741258741258742	61	0.08047493403693931	T	18.90	3.720946	0.68959	0.014299	0.058953	ENSG00000157017	ENST00000335542;ENST00000430179;ENST00000450603;ENST00000449554;ENST00000449238;ENST00000437422;ENST00000287656;ENST00000457360;ENST00000439975;ENST00000429122	T;T;T;T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36	4.76	4.76	0.60689	Motilin/ghrelin-associated peptide (1);	0.115879	0.39210	N	0.001439	T	0.00144	0.0004	M	0.67953	2.075	0.30139	P	0.80414	D;D;D;D;D	0.76494	0.989;0.996;0.997;0.996;0.999	D;D;D;D;D	0.80764	0.985;0.99;0.994;0.99;0.994	T	0.09930	-1.0652	9	0.51188	T	0.08	-19.1235	10.5811	0.45257	0.0:0.0:0.0:1.0	rs4684677;rs17847133;rs52799511;rs4684677	77;78;90;89;39	Q9UBU3-4;Q9UBU3-3;Q9UBU3;Q9UBU3-2;Q9UBU3-5	.;.;GHRL_HUMAN;.;.	L	90;89;90;89;77;78;89;90;39;90	ENSP00000335074:Q90L;ENSP00000399922:Q89L;ENSP00000389192:Q90L;ENSP00000415521:Q89L;ENSP00000388145:Q77L;ENSP00000416768:Q78L;ENSP00000287656:Q89L;ENSP00000391406:Q90L;ENSP00000403725:Q39L;ENSP00000414819:Q90L	ENSP00000287656:Q89L	Q	-	2	0	GHRL	10303453	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.169000	0.58223	1.992000	0.58205	0.533000	0.62120	CAG	T|0.950;A|0.050	0.050	strong		0.582	GHRL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000339625.1	NM_016362	
IP6K3	117283	hgsc.bcm.edu	37	6	33694659	33694659	+	Silent	SNP	G	G	A	rs34252064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33694659G>A	ENST00000293756.4	-	4	764	c.438C>T	c.(436-438)tcC>tcT	p.S146S	IP6K3_ENST00000451316.1_Silent_p.S146S	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	146					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						GGTGGGGCTCGGACCTCAGAA	0.647													G|||	453	0.0904553	0.2912	0.0317	5008	,	,		17666	0.001		0.0398	False		,,,				2504	0.0051				p.S146S		Atlas-SNP	.											.	IP6K3	52	.	0			c.C438T						PASS	.	G	,	1010,3396	376.1+/-321.9	114,782,1307	73.0	73.0	73.0		438,438	1.1	1.0	6	dbSNP_126	73	384,8216	125.0+/-183.6	12,360,3928	no	coding-synonymous,coding-synonymous	IP6K3	NM_001142883.1,NM_054111.4	,	126,1142,5235	AA,AG,GG		4.4651,22.9233,10.7181	,	146/411,146/411	33694659	1394,11612	2203	4300	6503	SO:0001819	synonymous_variant	117283	exon5			GGGCTCGGACCTC	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"""inositol hexaphosphate kinase 3"""	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.438C>T	6.37:g.33694659G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	159	86	0.540881	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	37	CCDS34435.1																																																																																			G|0.901;A|0.099	0.099	strong		0.647	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111	
ZNF76	7629	hgsc.bcm.edu	37	6	35259397	35259397	+	Missense_Mutation	SNP	C	C	T	rs33959228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:35259397C>T	ENST00000373953.3	+	9	1080	c.814C>T	c.(814-816)Cgc>Tgc	p.R272C	ZNF76_ENST00000440666.2_Missense_Mutation_p.R246C|ZNF76_ENST00000339411.5_Missense_Mutation_p.R272C	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	272			R -> C (in dbSNP:rs33959228).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						ATCTAACATCCGCAAGGTACA	0.597													C|||	32	0.00638978	0.0008	0.0072	5008	,	,		19156	0.001		0.0169	False		,,,				2504	0.0082				p.R272C	Esophageal Squamous(52;92 1039 20612 23956 34676)	Atlas-SNP	.											.	ZNF76	37	.	0			c.C814T						PASS	.	C	CYS/ARG	14,4392	21.2+/-45.6	0,14,2189	87.0	76.0	80.0		814	5.1	1.0	6	dbSNP_126	80	148,8452	72.6+/-135.2	1,146,4153	yes	missense	ZNF76	NM_003427.3	180	1,160,6342	TT,TC,CC		1.7209,0.3177,1.2456	possibly-damaging	272/571	35259397	162,12844	2203	4300	6503	SO:0001583	missense	7629	exon9			AACATCCGCAAGG	M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"""Zinc fingers, C2H2-type"""	13149	protein-coding gene	gene with protein product		194549	"""zinc finger protein 76 (expressed in testis)"""	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.814C>T	6.37:g.35259397C>T	ENSP00000363064:p.Arg272Cys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	145	85	0.586207	NM_003427	Q9BQB2	Missense_Mutation	SNP	ENST00000373953.3	37	CCDS4801.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	1	0.0017482517482517483	12	0.0158311345646438	C	21.7	4.190522	0.78789	0.003177	0.017209	ENSG00000065029	ENST00000469195;ENST00000448999;ENST00000373953;ENST00000417184;ENST00000440666;ENST00000339411	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	5.1	5.1	0.69264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44902	D	0.000403	T	0.33469	0.0864	N	0.12746	0.255	0.58432	D	0.999999	B;B;D	0.89917	0.169;0.059;1.0	B;B;D	0.69307	0.032;0.013;0.963	T	0.42481	-0.9449	10	0.66056	D	0.02	.	17.7212	0.88351	0.0:1.0:0.0:0.0	rs33959228	272;272;272	B7Z851;P36508-2;P36508	.;.;ZNF76_HUMAN	C	272;272;272;272;246;272	ENSP00000419106:R272C;ENSP00000363064:R272C;ENSP00000392243:R246C;ENSP00000344097:R272C	ENSP00000344097:R272C	R	+	1	0	ZNF76	35367375	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	3.737000	0.55060	2.652000	0.90054	0.655000	0.94253	CGC	C|0.989;T|0.011	0.011	strong		0.597	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427	
ERICH6	131831	hgsc.bcm.edu	37	3	150421419	150421419	+	Silent	SNP	G	G	A	rs17281287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:150421419G>A	ENST00000295910.6	-	1	319	c.267C>T	c.(265-267)gaC>gaT	p.D89D	FAM194A_ENST00000491361.1_Intron|RP11-103G8.2_ENST00000471093.1_RNA|RP11-103G8.2_ENST00000475393.1_RNA	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CTGGGAAGTCGTCGTCGTAGT	0.622													G|||	1618	0.323083	0.2179	0.4597	5008	,	,		13460	0.3591		0.4632	False		,,,				2504	0.1871				p.D89D		Atlas-SNP	.											FAM194A,NS,adenoma,0,1	FAM194A	91	1	0			c.C267T						PASS	.	G		1162,3244	409.5+/-335.0	152,858,1193	197.0	162.0	174.0		267	-4.4	0.0	3	dbSNP_123	174	4105,4495	562.1+/-387.9	985,2135,1180	no	coding-synonymous	FAM194A	NM_152394.3		1137,2993,2373	AA,AG,GG		47.7326,26.3731,40.4967		89/664	150421419	5267,7739	2203	4300	6503	SO:0001819	synonymous_variant	131831	exon1			GAAGTCGTCGTCG																												ENST00000295910.6:c.267C>T	3.37:g.150421419G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_152394		Silent	SNP	ENST00000295910.6	37	CCDS3151.2																																																																																			G|0.601;A|0.399	0.399	strong		0.622	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
LVRN	206338	hgsc.bcm.edu	37	5	115338958	115338958	+	Missense_Mutation	SNP	G	G	T	rs17138632	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:115338958G>T	ENST00000357872.4	+	12	2042	c.1918G>T	c.(1918-1920)Gtt>Ttt	p.V640F	AQPEP_ENST00000395528.2_Missense_Mutation_p.V157F	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		640			V -> F (in dbSNP:rs17138632).			integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AGAAATGCAAGTTTCAGATTC	0.289													G|||	130	0.0259585	0.0015	0.0836	5008	,	,		14198	0.001		0.0298	False		,,,				2504	0.0399				p.V640F		Atlas-SNP	.											FLJ90650,NS,carcinoma,0,1	.	.	1	0			c.G1918T						PASS	.	G	PHE/VAL	25,4377	31.7+/-61.6	0,25,2176	51.0	56.0	55.0		1918	-0.9	1.0	5	dbSNP_123	55	272,8304	100.1+/-161.6	4,264,4020	yes	missense	AQPEP	NM_173800.4	50	4,289,6196	TT,TG,GG		3.1716,0.5679,2.2885	benign	640/991	115338958	297,12681	2201	4288	6489	SO:0001583	missense	0	exon12			ATGCAAGTTTCAG																												ENST00000357872.4:c.1918G>T	5.37:g.115338958G>T	ENSP00000350541:p.Val640Phe	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	130	62	0.476923	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	59	0.027014652014652016	3	0.006097560975609756	31	0.0856353591160221	1	0.0017482517482517483	24	0.0316622691292876	G	11.64	1.698549	0.30142	0.005679	0.031716	ENSG00000172901	ENST00000395528;ENST00000357872;ENST00000379578	T;T	0.23552	1.9;1.9	5.03	-0.942	0.10398	.	0.861260	0.10039	N	0.723709	T	0.00580	0.0019	L	0.57536	1.79	0.24475	N	0.994371	P	0.39282	0.666	B	0.33521	0.165	T	0.14144	-1.0483	10	0.09843	T	0.71	.	4.9292	0.13909	0.4644:0.3211:0.2146:0.0	rs17138632;rs52805082;rs17138632	640	Q6Q4G3	AMPQ_HUMAN	F	157;640;629	ENSP00000378899:V157F;ENSP00000350541:V640F	ENSP00000350541:V640F	V	+	1	0	AC010282.1	115366857	0.986000	0.35501	0.999000	0.59377	0.995000	0.86356	0.095000	0.15127	0.102000	0.17638	0.460000	0.39030	GTT	G|0.972;T|0.028	0.028	strong		0.289	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
CES5A	221223	hgsc.bcm.edu	37	16	55880480	55880480	+	Missense_Mutation	SNP	A	A	C	rs11860456	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:55880480A>C	ENST00000290567.9	-	13	1732	c.1611T>G	c.(1609-1611)gaT>gaG	p.D537E	CES5A_ENST00000520435.1_Missense_Mutation_p.D507E|CES5A_ENST00000518005.1_Missense_Mutation_p.D431E|CES5A_ENST00000319165.9_Missense_Mutation_p.D487E|CES5A_ENST00000521992.1_Missense_Mutation_p.D566E|CES5A_ENST00000541580.1_5'UTR	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	537			D -> E (in dbSNP:rs11860456). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						TGGTCCAAAAATCCACCCGCG	0.522													C|||	1624	0.324281	0.4977	0.1988	5008	,	,		16733	0.2817		0.2793	False		,,,				2504	0.2689				p.D566E		Atlas-SNP	.											.	CES5A	206	.	0			c.T1698G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP	2089,2307		490,1109,599	211.0	208.0	209.0		1611,1698,1461	2.6	0.2	16	dbSNP_120	209	2086,6514		265,1556,2479	yes	missense,missense,missense	CES5A	NM_001143685.1,NM_001190158.1,NM_145024.2	45,45,45	755,2665,3078	CC,CA,AA		24.2558,47.5205,32.1253	benign,benign,benign	537/576,566/605,487/526	55880480	4175,8821	2198	4300	6498	SO:0001583	missense	221223	exon14			CCAAAAATCCACC	AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"""Carboxylesterases"""	26459	protein-coding gene	gene with protein product			"""carboxylesterase 7"""	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1611T>G	16.37:g.55880480A>C	ENSP00000290567:p.Asp537Glu	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	189	88	0.465608	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	695	0.3182234432234432	241	0.4898373983739837	84	0.23204419889502761	162	0.28321678321678323	208	0.27440633245382584	.	0.020	-1.432466	0.01108	0.475205	0.242558	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.61	2.58	0.30949	Carboxylesterase, type B (1);	1.217400	0.05929	N	0.634854	T	0.00012	0.0000	N	0.01809	-0.71	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.40979	-0.9534	9	0.19147	T	0.46	.	6.1655	0.20388	0.1316:0.6521:0.0:0.2163	rs11860456;rs12924366;rs16955806;rs52805099;rs58244961;rs11860456	537;487	Q6NT32;Q6NT32-2	EST5A_HUMAN;.	E	566;487;431;537;507;317	ENSP00000428864:D566E;ENSP00000324271:D487E;ENSP00000428571:D431E;ENSP00000290567:D537E;ENSP00000428887:D507E	ENSP00000290567:D537E	D	-	3	2	CES5A	54437981	0.000000	0.05858	0.183000	0.23137	0.011000	0.07611	-1.208000	0.03005	0.123000	0.18342	-0.121000	0.15023	GAT	A|0.672;C|0.328	0.328	strong		0.522	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	
ANK3	288	hgsc.bcm.edu	37	10	61965625	61965625	+	Silent	SNP	A	A	G	rs2297979	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:61965625A>G	ENST00000280772.2	-	11	1409	c.1218T>C	c.(1216-1218)atT>atC	p.I406I	ANK3_ENST00000503366.1_Silent_p.I389I|ANK3_ENST00000373827.2_Silent_p.I400I	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	406					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.I406I(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TCTTGCAGGCAATATGAAGAG	0.408													A|||	759	0.151558	0.1785	0.1398	5008	,	,		21317	0.0655		0.1879	False		,,,				2504	0.1748				p.I406I		Atlas-SNP	.											ANK3,NS,carcinoma,0,1	ANK3	703	1	1	Substitution - coding silent(1)	stomach(1)	c.T1218C						PASS	.	A	,,	851,3555	335.2+/-303.8	86,679,1438	113.0	97.0	103.0		1200,1167,1218	-6.8	1.0	10	dbSNP_100	103	1513,7087	286.5+/-297.7	131,1251,2918	no	coding-synonymous,coding-synonymous,coding-synonymous	ANK3	NM_001204403.1,NM_001204404.1,NM_020987.3	,,	217,1930,4356	GG,GA,AA		17.593,19.3146,18.1762	,,	400/1862,389/1869,406/4378	61965625	2364,10642	2203	4300	6503	SO:0001819	synonymous_variant	288	exon11			GCAGGCAATATGA	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.1218T>C	10.37:g.61965625A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	153	75	0.490196	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			A|0.830;G|0.170	0.170	strong		0.408	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
RNLS	55328	hgsc.bcm.edu	37	10	90342837	90342837	+	Missense_Mutation	SNP	C	C	G	rs2296545	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:90342837C>G	ENST00000331772.4	-	1	133	c.111G>C	c.(109-111)gaG>gaC	p.E37D	RNLS_ENST00000466945.1_5'UTR|RNLS_ENST00000437752.1_Missense_Mutation_p.E37D|Y_RNA_ENST00000364678.1_RNA|RNLS_ENST00000371947.3_Missense_Mutation_p.E37D	NM_001031709.2	NP_001026879.2	Q5VYX0	RNLS_HUMAN	renalase, FAD-dependent amine oxidase	37			E -> D (in dbSNP:rs2296545). {ECO:0000269|PubMed:15489334}.		cardiac left ventricle morphogenesis (GO:0003214)|dopamine metabolic process (GO:0042417)|epinephrine metabolic process (GO:0042414)|heart contraction (GO:0060047)|norepinephrine metabolic process (GO:0042415)|phosphate ion homeostasis (GO:0055062)|regulation of systemic arterial blood pressure (GO:0003073)|response to epinephrine (GO:0071871)|response to ischemia (GO:0002931)|response to norepinephrine (GO:0071873)|response to salt (GO:1902074)	extracellular space (GO:0005615)	oxidoreductase activity (GO:0016491)			breast(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	7						CACCTGAGTCCTCAGCCTTGT	0.607											OREG0020353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2395	0.478235	0.5408	0.3948	5008	,	,		14264	0.4484		0.4771	False		,,,				2504	0.4847				p.E37D		Atlas-SNP	.											RNLS_ENST00000331772,NS,carcinoma,0,2	RNLS	45	2	0			c.G111C	GRCh37	CM074076	RNLS	M	rs2296545	PASS	.	C	ASP/GLU,ASP/GLU	2367,2039	610.8+/-391.6	654,1059,490	66.0	65.0	66.0		111,111	-0.8	0.8	10	dbSNP_100	66	3735,4865	531.6+/-382.0	834,2067,1399	yes	missense,missense	RNLS	NM_001031709.2,NM_018363.3	45,45	1488,3126,1889	GG,GC,CC		43.4302,46.2778,46.9168	benign,benign	37/343,37/316	90342837	6102,6904	2203	4300	6503	SO:0001583	missense	55328	exon1			TGAGTCCTCAGCC	BC005364	CCDS7388.1, CCDS31239.1	10q23.31	2009-04-22	2009-04-22	2009-04-22	ENSG00000184719	ENSG00000184719			25641	protein-coding gene	gene with protein product		609360	"""chromosome 10 open reading frame 59"""	C10orf59		15841207, 17565281	Standard	NM_001031709		Approved	FLJ11218, renalase	uc001kfe.3	Q5VYX0	OTTHUMG00000018692	ENST00000331772.4:c.111G>C	10.37:g.90342837C>G	ENSP00000332530:p.Glu37Asp	Somatic	151	0	0	1274	WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_001031709	Q9BS33|Q9NUP8	Missense_Mutation	SNP	ENST00000331772.4	37	CCDS31239.1	1027	0.47023809523809523	276	0.5609756097560976	156	0.430939226519337	234	0.4090909090909091	361	0.4762532981530343	C	13.55	2.271614	0.40194	0.537222	0.434302	ENSG00000184719	ENST00000371947;ENST00000437752;ENST00000331772	T;T;D	0.95238	3.44;-1.32;-3.65	4.99	-0.832	0.10785	.	0.218916	0.35207	N	0.003372	T	0.00012	0.0000	N	0.04355	-0.22	0.49687	P	1.8099999999998673E-4	B;B;B	0.33777	0.425;0.072;0.192	B;B;B	0.30855	0.121;0.097;0.093	T	0.46679	-0.9174	9	0.52906	T	0.07	.	6.914	0.24349	0.1119:0.488:0.3289:0.0711	rs2296545;rs11544725;rs2296545	37;37;37	B4DJW3;Q5VYX0;Q5VYX0-2	.;RNLS_HUMAN;.	D	37	ENSP00000361015:E37D;ENSP00000387577:E37D;ENSP00000332530:E37D	ENSP00000332530:E37D	E	-	3	2	RNLS	90332817	0.000000	0.05858	0.775000	0.31657	0.017000	0.09413	-0.518000	0.06267	0.119000	0.18210	-0.362000	0.07510	GAG	C|0.532;G|0.468	0.468	strong		0.607	RNLS-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049250.1	NM_018363	
ZNF710	374655	hgsc.bcm.edu	37	15	90623052	90623052	+	Silent	SNP	T	T	C	rs2970357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:90623052T>C	ENST00000268154.4	+	5	2237	c.1986T>C	c.(1984-1986)aaT>aaC	p.N662N	RP11-617F23.1_ENST00000558334.1_RNA	NM_198526.2	NP_940928.2	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	662					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(1)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	19	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			CCTACTACAATGTGCTATAGC	0.627													C|||	3367	0.672324	0.7284	0.5778	5008	,	,		18418	0.8244		0.4751	False		,,,				2504	0.7096				p.N662N		Atlas-SNP	.											.	ZNF710	50	.	0			c.T1986C						PASS	.	C		3187,1213	418.5+/-338.3	1148,891,161	56.0	49.0	52.0		1986	-5.1	0.9	15	dbSNP_101	52	3825,4771	608.2+/-395.4	871,2083,1344	no	coding-synonymous	ZNF710	NM_198526.2		2019,2974,1505	CC,CT,TT		44.4974,27.5682,46.0449		662/665	90623052	7012,5984	2200	4298	6498	SO:0001819	synonymous_variant	374655	exon5			CTACAATGTGCTA	AK094712	CCDS10358.1	15q26.1	2013-01-08			ENSG00000140548	ENSG00000140548		"""Zinc fingers, C2H2-type"""	25352	protein-coding gene	gene with protein product							Standard	XM_005254905		Approved	DKFZp547K1113, FLJ37393, FLJ00306	uc002bov.2	Q8N1W2	OTTHUMG00000149812	ENST00000268154.4:c.1986T>C	15.37:g.90623052T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_198526	A0AVS3|Q6ZMK9|Q8NDU0	Silent	SNP	ENST00000268154.4	37	CCDS10358.1																																																																																			T|0.409;C|0.591	0.591	strong		0.627	ZNF710-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313423.1	NM_198526	
COL16A1	1307	hgsc.bcm.edu	37	1	32164206	32164206	+	Splice_Site	SNP	T	T	G	rs2228550	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:32164206T>G	ENST00000373672.3	-	5	784	c.268A>C	c.(268-270)Aga>Cga	p.R90R	COL16A1_ENST00000271069.6_Splice_Site_p.R90R|COL16A1_ENST00000373668.3_Splice_Site_p.R90R	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	90	Laminin G-like.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		GGGAATACTCTTCTGGAGATG	0.572													G|||	3134	0.625799	0.82	0.6599	5008	,	,		17431	0.3472		0.6541	False		,,,				2504	0.5971				p.R90R	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.A268C						PASS	.	G		3112,820		1245,622,99	54.0	57.0	56.0		268	4.7	0.9	1	dbSNP_98	56	5386,2900		1767,1852,524	yes	coding-synonymous-near-splice	COL16A1	NM_001856.3		3012,2474,623	GG,GT,TT		34.9988,20.8545,30.4469		90/1605	32164206	8498,3720	1966	4143	6109	SO:0001630	splice_region_variant	1307	exon5			ATACTCTTCTGGA	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.267-1A>C	1.37:g.32164206T>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	37	CCDS41297.1																																																																																			T|0.396;G|0.604	0.604	strong		0.572	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	Silent
ARHGEF3	50650	hgsc.bcm.edu	37	3	56835761	56835761	+	Silent	SNP	G	G	A	rs3732508	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:56835761G>A	ENST00000296315.3	-	1	234	c.66C>T	c.(64-66)ccC>ccT	p.P22P	ARHGEF3_ENST00000496106.1_Intron|ARHGEF3_ENST00000498517.1_Intron|ARHGEF3_ENST00000338458.4_Intron|ARHGEF3_ENST00000495373.1_Silent_p.P22P	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	22					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		CGCTGGCCGGGGGTAGCTCCA	0.652													G|||	1609	0.321286	0.0227	0.487	5008	,	,		16762	0.1944		0.5716	False		,,,				2504	0.4806				p.P22P		Atlas-SNP	.											ARHGEF3_ENST00000296315,NS,carcinoma,0,2	ARHGEF3	128	2	0			c.C66T						PASS	.	G	,	492,3902		44,404,1749	35.0	31.0	33.0		,66	4.0	1.0	3	dbSNP_107	33	4617,3949		1292,2033,958	no	intron,coding-synonymous	ARHGEF3	NM_001128615.1,NM_019555.2	,	1336,2437,2707	AA,AG,GG		46.1009,11.1971,39.4213	,	,22/527	56835761	5109,7851	2197	4283	6480	SO:0001819	synonymous_variant	50650	exon1			GGCCGGGGGTAGC	AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"""Rho guanine nucleotide exchange factors"""	683	protein-coding gene	gene with protein product	"""exchange factor found in platelets and leukemic and neuronal tissues, XPLN"", ""RhoGEF protein"""	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.66C>T	3.37:g.56835761G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	148	67	0.452703	NM_019555	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Silent	SNP	ENST00000296315.3	37	CCDS2878.1																																																																																			G|0.677;A|0.323	0.323	strong		0.652	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555	
DDX11	1663	hgsc.bcm.edu	37	12	31249861	31249861	+	Missense_Mutation	SNP	C	C	G	rs2075322	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:31249861C>G	ENST00000407793.2	+	17	1950	c.1699C>G	c.(1699-1701)Caa>Gaa	p.Q567E	DDX11_ENST00000545668.1_Missense_Mutation_p.Q567E|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000228264.6_Missense_Mutation_p.Q541E|DDX11_ENST00000542838.1_Missense_Mutation_p.Q567E|DDX11_ENST00000539673.1_3'UTR|DDX11_ENST00000350437.4_Missense_Mutation_p.Q567E	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	567			Q -> E (in dbSNP:rs2075322). {ECO:0000269|PubMed:9013641, ECO:0000269|Ref.3}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GATGCACATCCAAGGCTTCCT	0.622										Multiple Myeloma(12;0.14)			G|||	3211	0.641174	0.708	0.6066	5008	,	,		19076	0.8294		0.4284	False		,,,				2504	0.6002				p.Q567E		Atlas-SNP	.											.	DDX11	188	.	0			c.C1699G						PASS	.	G	GLU/GLN,GLU/GLN,GLU/GLN	3015,1391	454.4+/-350.6	1029,957,217	45.0	47.0	46.0		1699,1699,1699	2.6	0.4	12	dbSNP_96	46	3876,4724	606.1+/-395.1	890,2096,1314	yes	missense,missense,missense	DDX11	NM_004399.2,NM_030653.3,NM_152438.1	29,29,29	1919,3053,1531	GG,GC,CC		45.0698,31.5706,47.0168	benign,benign,benign	567/857,567/907,567/971	31249861	6891,6115	2203	4300	6503	SO:0001583	missense	1663	exon17			CACATCCAAGGCT	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1699C>G	12.37:g.31249861C>G	ENSP00000384703:p.Gln567Glu	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	151	64	0.423841	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	1393	0.6378205128205128	370	0.7520325203252033	213	0.5883977900552486	485	0.8479020979020979	325	0.4287598944591029	G	0.756	-0.770984	0.02974	0.684294	0.450698	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000404673;ENST00000228264;ENST00000545668;ENST00000350437	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	3.56	2.6	0.31112	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999919	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.40136	-0.9579	8	0.02654	T	1	.	10.8246	0.46625	0.0:0.3716:0.6284:0.0	rs2075322	541;567;567;567	Q96FC9-3;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	E	567;567;292;541;567;567	ENSP00000443426:Q567E;ENSP00000384703:Q567E;ENSP00000228264:Q541E;ENSP00000440402:Q567E;ENSP00000309965:Q567E	ENSP00000228264:Q541E	Q	+	1	0	DDX11	31141128	1.000000	0.71417	0.418000	0.26571	0.770000	0.43624	5.344000	0.65981	0.170000	0.19704	-0.293000	0.09583	CAA	C|0.436;G|0.564	0.564	strong		0.622	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
OR52E2	119678	hgsc.bcm.edu	37	11	5080844	5080844	+	Missense_Mutation	SNP	T	T	C	rs16909440	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5080844T>C	ENST00000321522.2	-	1	13	c.14A>G	c.(13-15)aAt>aGt	p.N5S		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	5			N -> S (in dbSNP:rs16909440).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(13)|ovary(2)|skin(3)	20		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.03e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.191)		CTGGGTGTCATTGGGAAGGAA	0.498													T|||	1548	0.309105	0.1853	0.353	5008	,	,		20137	0.3829		0.3241	False		,,,				2504	0.3538				p.N5S		Atlas-SNP	.											.	OR52E2	63	.	0			c.A14G						PASS	.	T	SER/ASN	969,3433	364.4+/-316.9	112,745,1344	86.0	78.0	81.0		14	3.6	0.1	11	dbSNP_123	81	3017,5579	465.4+/-366.5	536,1945,1817	yes	missense	OR52E2	NM_001005164.2	46	648,2690,3161	CC,CT,TT		35.0977,22.0127,30.6663	probably-damaging	5/326	5080844	3986,9012	2201	4298	6499	SO:0001583	missense	119678	exon1			GTGTCATTGGGAA	AB065800	CCDS31371.1	11p15.4	2012-08-09			ENSG00000176787	ENSG00000176787		"""GPCR / Class A : Olfactory receptors"""	14769	protein-coding gene	gene with protein product							Standard	NM_001005164		Approved		uc010qyw.2	Q8NGJ4	OTTHUMG00000066608	ENST00000321522.2:c.14A>G	11.37:g.5080844T>C	ENSP00000322088:p.Asn5Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	703	0.3218864468864469	102	0.2073170731707317	141	0.38950276243093923	219	0.38286713286713286	241	0.3179419525065963	T	14.76	2.632936	0.47049	0.220127	0.350977	ENSG00000176787	ENST00000321522	T	0.63913	-0.07	3.61	3.61	0.41365	.	0.000000	0.51477	D	0.000083	T	0.00012	0.0000	M	0.69823	2.125	0.38469	P	0.05258499999999999	D	0.53885	0.963	P	0.49140	0.601	T	0.34428	-0.9829	9	0.72032	D	0.01	.	7.0024	0.24817	0.0:0.1073:0.0:0.8927	rs16909440;rs52834501;rs16909440	5	Q8NGJ4	O52E2_HUMAN	S	5	ENSP00000322088:N5S	ENSP00000322088:N5S	N	-	2	0	OR52E2	5037420	0.130000	0.22417	0.051000	0.19133	0.011000	0.07611	0.736000	0.26130	1.885000	0.54596	0.533000	0.62120	AAT	C|0.306;N|0.000	0.306	strong		0.498	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
GAK	2580	hgsc.bcm.edu	37	4	843508	843508	+	Missense_Mutation	SNP	C	C	T	rs1134921	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:843508C>T	ENST00000314167.4	-	28	3999	c.3889G>A	c.(3889-3891)Gac>Aac	p.D1297N	GAK_ENST00000511163.1_Missense_Mutation_p.D1218N|GAK_ENST00000509566.1_5'UTR	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1297	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.		D -> N (in dbSNP:rs1134921). {ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		GACCAGGCGTCATTCAGCTCC	0.632													C|||	422	0.0842652	0.0053	0.1715	5008	,	,		14500	0.1319		0.1223	False		,,,				2504	0.0409				p.D1297N		Atlas-SNP	.											.	GAK	104	.	0			c.G3889A						PASS	.	C	ASN/ASP	111,4295	85.3+/-124.0	3,105,2095	59.0	56.0	57.0		3889	4.8	0.5	4	dbSNP_86	57	1112,7488	225.8+/-261.7	74,964,3262	yes	missense	GAK	NM_005255.2	23	77,1069,5357	TT,TC,CC		12.9302,2.5193,9.4034	probably-damaging	1297/1312	843508	1223,11783	2203	4300	6503	SO:0001583	missense	2580	exon28			AGGCGTCATTCAG	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3889G>A	4.37:g.843508C>T	ENSP00000314499:p.Asp1297Asn	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	211	102	0.483412	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	37	CCDS3340.1	250|250	0.11446886446886446|0.11446886446886446	6|6	0.012195121951219513|0.012195121951219513	64|64	0.17679558011049723|0.17679558011049723	90|90	0.15734265734265734|0.15734265734265734	90|90	0.11873350923482849|0.11873350923482849	C|C	18.45|18.45	3.627461|3.627461	0.66901|0.66901	0.025193|0.025193	0.129302|0.129302	ENSG00000178950|ENSG00000178950	ENST00000398567;ENST00000314167;ENST00000511163|ENST00000511980	T;T|.	0.29655|.	1.56;1.56|.	4.76|4.76	4.76|4.76	0.60689|0.60689	Heat shock protein DnaJ, N-terminal (5);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00178|0.00178	0.0005|0.0005	L|L	0.38953|0.38953	1.18|1.18	0.09310|0.09310	P|P	0.99999999819712|0.99999999819712	D;D;D;D|.	0.89917|.	0.999;1.0;0.999;0.999|.	D;D;D;D|.	0.97110|.	1.0;0.999;1.0;1.0|.	T|T	0.03221|0.03221	-1.1059|-1.1059	9|4	0.42905|.	T|.	0.14|.	-36.0573|-36.0573	15.2715|15.2715	0.73705|0.73705	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs1134921;rs3087764;rs3197299;rs56708161;rs1134921|rs1134921;rs3087764;rs3197299;rs56708161;rs1134921	1199;1218;1297;1182|.	B4DS37;E9PGR2;O14976;Q59HA5|.	.;.;GAK_HUMAN;.|.	N|I	573;1297;1218|452	ENSP00000314499:D1297N;ENSP00000421361:D1218N|.	ENSP00000314499:D1297N|.	D|M	-|-	1|3	0|0	GAK|GAK	833508|833508	1.000000|1.000000	0.71417|0.71417	0.492000|0.492000	0.27490|0.27490	0.390000|0.390000	0.30446|0.30446	7.295000|7.295000	0.78780|0.78780	2.167000|2.167000	0.68274|0.68274	0.643000|0.643000	0.83706|0.83706	GAC|ATG	C|0.900;T|0.100	0.100	strong		0.632	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
YEATS2	55689	hgsc.bcm.edu	37	3	183432983	183432983	+	Silent	SNP	C	C	T	rs3736535	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:183432983C>T	ENST00000305135.5	+	2	228	c.33C>T	c.(31-33)acC>acT	p.T11T		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	11					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TCAAAGAAACCGACCCTGATT	0.348													C|||	948	0.189297	0.1377	0.3256	5008	,	,		17209	0.2937		0.1382	False		,,,				2504	0.1074				p.T11T		Atlas-SNP	.											.	YEATS2	111	.	0			c.C33T						PASS	.	C		580,3174		46,488,1343	121.0	123.0	122.0		33	-11.3	0.4	3	dbSNP_107	122	1316,6900		119,1078,2911	no	coding-synonymous	YEATS2	NM_018023.4		165,1566,4254	TT,TC,CC		16.0175,15.4502,15.8396		11/1423	183432983	1896,10074	1877	4108	5985	SO:0001819	synonymous_variant	55689	exon2			AGAAACCGACCCT	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.33C>T	3.37:g.183432983C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	225	120	0.533333	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Silent	SNP	ENST00000305135.5	37	CCDS43175.1																																																																																			C|0.804;T|0.196	0.196	strong		0.348	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39190953	39190953	+	Missense_Mutation	SNP	G	G	C	rs78298475		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39190953G>C	ENST00000344363.5	-	1	154	c.121C>G	c.(121-123)Cag>Gag	p.Q41E		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	51			Missing (in allele KAP1.1). {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:12228244, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AAGCTGGTCTGGCAGCAGCTT	0.607																																					p.Q41E		Atlas-SNP	.											KRTAP1-3,NS,carcinoma,0,1	KRTAP1-3	18	1	0			c.C121G						PASS	.						44.0	52.0	50.0					17																	39190953		1972	4170	6142	SO:0001583	missense	81850	exon1			TGGTCTGGCAGCA	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"""Keratin associated proteins"""	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.121C>G	17.37:g.39190953G>C	ENSP00000344420:p.Gln41Glu	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	181	29	0.160221	NM_030966	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.657519	0.29425	.	.	ENSG00000221880	ENST00000344363	T	0.28255	1.62	4.04	3.06	0.35304	.	.	.	.	.	T	0.18676	0.0448	.	.	.	0.26867	N	0.967836	P	0.46784	0.884	P	0.48704	0.587	T	0.07121	-1.0789	8	0.02654	T	1	.	6.7054	0.23248	0.1272:0.0:0.8728:0.0	.	51	Q8IUG1	KRA13_HUMAN	E	41	ENSP00000344420:Q41E	ENSP00000344420:Q41E	Q	-	1	0	KRTAP1-3	36444479	0.722000	0.28017	0.656000	0.29637	0.648000	0.38561	1.257000	0.32932	2.206000	0.71126	0.563000	0.77884	CAG	C|1.000;|0.000	1.000	weak		0.607	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1		
EFCAB7	84455	hgsc.bcm.edu	37	1	63999868	63999868	+	Missense_Mutation	SNP	T	T	C	rs6657480	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:63999868T>C	ENST00000371088.4	+	6	1031	c.785T>C	c.(784-786)aTg>aCg	p.M262T	RNU7-123P_ENST00000515911.1_RNA	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	262			M -> T (in dbSNP:rs6657480). {ECO:0000269|PubMed:15489334}.				calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						TCAAAGTTAATGGAGCCAAAT	0.343													C|||	1440	0.28754	0.5825	0.196	5008	,	,		15429	0.1925		0.1491	False		,,,				2504	0.1943				p.M262T		Atlas-SNP	.											.	EFCAB7	45	.	0			c.T785C						PASS	.	C	THR/MET	2103,2303	597.0+/-388.8	514,1075,614	64.0	65.0	65.0		785	2.3	1.0	1	dbSNP_116	65	1344,7256	754.1+/-407.5	94,1156,3050	yes	missense	EFCAB7	NM_032437.2	81	608,2231,3664	CC,CT,TT		15.6279,47.7304,26.5032	benign	262/630	63999868	3447,9559	2203	4300	6503	SO:0001583	missense	84455	exon6			AGTTAATGGAGCC	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.785T>C	1.37:g.63999868T>C	ENSP00000360129:p.Met262Thr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	123	44	0.357724	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	561	0.25686813186813184	267	0.5426829268292683	74	0.20441988950276244	110	0.19230769230769232	110	0.14511873350923482	C	0.003	-2.489623	0.00161	0.477304	0.156279	ENSG00000203965	ENST00000371088	T	0.55588	0.51	5.65	2.32	0.28847	.	0.671131	0.16090	N	0.230086	T	0.04363	0.0120	N	0.00538	-1.39	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35276	-0.9795	9	0.08381	T	0.77	-6.203	4.47	0.11708	0.1582:0.5267:0.0:0.3151	rs6657480;rs17845480;rs17858360;rs52835496;rs60937630;rs6657480	262	A8K855	EFCB7_HUMAN	T	262	ENSP00000360129:M262T	ENSP00000360129:M262T	M	+	2	0	EFCAB7	63772456	0.083000	0.21467	0.980000	0.43619	0.037000	0.13140	0.268000	0.18571	0.346000	0.23899	-0.767000	0.03436	ATG	T|0.741;C|0.259	0.259	strong		0.343	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
TADA1	117143	hgsc.bcm.edu	37	1	166829522	166829522	+	Missense_Mutation	SNP	C	C	T	rs2272792	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:166829522C>T	ENST00000367874.4	-	6	686	c.593G>A	c.(592-594)cGg>cAg	p.R198Q	TADA1_ENST00000467021.1_5'UTR	NM_053053.3	NP_444281.1	Q96BN2	TADA1_HUMAN	transcriptional adaptor 1	198			R -> Q (in dbSNP:rs2272792).		chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	11						ATCTCGTAACCGATAAGCTTT	0.368													C|||	176	0.0351438	0.0	0.0187	5008	,	,		19844	0.1171		0.0099	False		,,,				2504	0.0358				p.R198Q		Atlas-SNP	.											.	TADA1	32	.	0			c.G593A						PASS	.	C	GLN/ARG	6,4400	11.4+/-27.6	0,6,2197	122.0	105.0	111.0		593	5.7	0.3	1	dbSNP_100	111	104,8496	57.2+/-118.5	0,104,4196	yes	missense	TADA1	NM_053053.3	43	0,110,6393	TT,TC,CC		1.2093,0.1362,0.8458	probably-damaging	198/336	166829522	110,12896	2203	4300	6503	SO:0001583	missense	117143	exon6			CGTAACCGATAAG	BC015401	CCDS1255.1	1q24.1	2009-10-02	2009-10-02	2009-10-02	ENSG00000152382	ENSG00000152382			30631	protein-coding gene	gene with protein product		612763	"""transcriptional adaptor 1 (HFI1 homolog, yeast)-like"", ""transcriptional adaptor 1 (HFI1 homolog, yeast)"""	TADA1L		11564863	Standard	NM_053053		Approved	STAF42, ADA1, hADA1, HFI1	uc001gdw.3	Q96BN2	OTTHUMG00000034321	ENST00000367874.4:c.593G>A	1.37:g.166829522C>T	ENSP00000356848:p.Arg198Gln	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	127	53	0.417323	NM_053053	A8K4J9	Missense_Mutation	SNP	ENST00000367874.4	37	CCDS1255.1	94	0.04304029304029304	0	0.0	8	0.022099447513812154	78	0.13636363636363635	8	0.010554089709762533	C	34	5.306289	0.95629	0.001362	0.012093	ENSG00000152382	ENST00000367874	T	0.50813	0.73	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.44350	0.1289	L	0.59436	1.845	0.45194	P	0.0018000000000000238	D	0.57571	0.98	P	0.47603	0.551	T	0.51364	-0.8715	9	0.66056	D	0.02	-4.1797	17.41	0.87482	0.0:1.0:0.0:0.0	rs2272792;rs2272792	198	Q96BN2	TADA1_HUMAN	Q	198	ENSP00000356848:R198Q	ENSP00000356848:R198Q	R	-	2	0	TADA1	165096146	1.000000	0.71417	0.281000	0.24762	0.962000	0.63368	5.472000	0.66768	2.710000	0.92621	0.650000	0.86243	CGG	C|0.971;T|0.029	0.029	strong		0.368	TADA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082881.1	NM_053053	
Unknown	0	hgsc.bcm.edu	37	13	103410912	103410912	+	IGR	SNP	G	G	A	rs548678555		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:103410912G>A								LINC00283 (13338 upstream) : TEX30 (7427 downstream)																							TGCTTTTGGGGCAACTGTCTT	0.279																																					p.C82C		Atlas-SNP	.											.	.	.	.	0			c.C246T						PASS	.																																			SO:0001628	intergenic_variant	643677	exon2			TTTGGGGCAACTG																													13.37:g.103410912G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_001146197		Silent	SNP		37																																																																																				.	.	none	0	0.279								
MADCAM1	8174	hgsc.bcm.edu	37	19	501725	501725	+	Missense_Mutation	SNP	G	G	A	rs62130833		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:501725G>A	ENST00000215637.3	+	4	770	c.724G>A	c.(724-726)Gac>Aac	p.D242N	MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.D23N	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	242	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.			D -> N (in Ref. 2; AAB02194 and 3; AAC51354). {ECO:0000305}.	aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAGTCTCCCGACACCACCTC	0.682																																					p.D242N		Atlas-SNP	.											.	MADCAM1	29	.	0			c.G724A						PASS	.						26.0	42.0	36.0					19																	501725		2201	4299	6500	SO:0001583	missense	8174	exon4			TCTCCCGACACCA	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.724G>A	19.37:g.501725G>A	ENSP00000215637:p.Asp242Asn	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	105	62	0.590476	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	618	0.28296703296703296	75	0.1524390243902439	133	0.3674033149171271	184	0.32167832167832167	226	0.29815303430079154	g	7.171	0.587634	0.13812	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.10288	2.89	3.55	-1.32	0.09201	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48670	-0.9015	8	0.22109	T	0.4	.	3.1363	0.06439	0.2817:0.0:0.3626:0.3557	rs62130833	242	Q13477	MADCA_HUMAN	N	266;258;250;242	ENSP00000215637:D242N	ENSP00000215637:D242N	D	+	1	0	MADCAM1	452725	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.632000	0.05489	-0.229000	0.09854	-0.378000	0.06908	GAC	G|0.717;A|0.283	0.283	strong		0.682	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
MRPL37	51253	hgsc.bcm.edu	37	1	54683856	54683856	+	Silent	SNP	C	C	G	rs15921	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:54683856C>G	ENST00000360840.5	+	7	1283	c.1206C>G	c.(1204-1206)ggC>ggG	p.G402G	MRPL37_ENST00000336230.6_Silent_p.G271G|MRPL37_ENST00000605337.1_Intron	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	402					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						AACCTGTTGGCCCAGTTGGTT	0.448													G|||	2031	0.405551	0.3502	0.3545	5008	,	,		20898	0.5942		0.2078	False		,,,				2504	0.5256				p.G402G		Atlas-SNP	.											MRPL37,NS,carcinoma,0,2	MRPL37	36	2	0			c.C1206G						scavenged	.	G		1355,3051	691.3+/-405.4	217,921,1065	199.0	208.0	205.0		1206	0.8	1.0	1	dbSNP_52	205	1862,6738	729.9+/-406.7	190,1482,2628	no	coding-synonymous	MRPL37	NM_016491.3		407,2403,3693	GG,GC,CC		21.6512,30.7535,24.7347		402/424	54683856	3217,9789	2203	4300	6503	SO:0001819	synonymous_variant	51253	exon7			TGTTGGCCCAGTT	AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221		"""Mitochondrial ribosomal proteins / large subunits"""	14034	protein-coding gene	gene with protein product		611843				10600119	Standard	NM_016491		Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.1206C>G	1.37:g.54683856C>G		Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	223	92	0.412556	NM_016491	Q96Q67|Q9BWR1|Q9P0P3	Silent	SNP	ENST00000360840.5	37	CCDS589.1																																																																																			C|0.704;G|0.296	0.296	strong		0.448	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022224.1	NM_016491	
CD276	80381	hgsc.bcm.edu	37	15	73996066	73996066	+	Missense_Mutation	SNP	G	G	A	rs11574483	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:73996066G>A	ENST00000318443.5	+	5	1102	c.800G>A	c.(799-801)cGc>cAc	p.R267H	CD276_ENST00000561213.1_Missense_Mutation_p.R267H|CD276_ENST00000537340.2_Missense_Mutation_p.R121H|CD276_ENST00000564751.1_Intron|CD276_ENST00000318424.5_Intron	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	267	Ig-like V-type 2.		R -> H (in dbSNP:rs11574483).		cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						GCCACCCTGCGCTGCTCCTTC	0.667													G|||	606	0.121006	0.1467	0.0793	5008	,	,		15361	0.127		0.0944	False		,,,				2504	0.137				p.R267H		Atlas-SNP	.											CD276,NS,carcinoma,0,1	CD276	29	1	0			c.G800A						scavenged	.	G	HIS/ARG,	643,3753	268.6+/-268.5	49,545,1604	32.0	31.0	31.0		800,	1.7	1.0	15	dbSNP_120	31	827,7767	187.3+/-234.6	34,759,3504	no	missense,intron	CD276	NM_001024736.1,NM_025240.2	29,	83,1304,5108	AA,AG,GG		9.623,14.6269,11.3164	benign,	267/535,	73996066	1470,11520	2198	4297	6495	SO:0001583	missense	80381	exon5			CCCTGCGCTGCTC	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.800G>A	15.37:g.73996066G>A	ENSP00000320084:p.Arg267His	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	139	2	0.0143885	NM_001024736	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	37	CCDS32288.1	232	0.10622710622710622	60	0.12195121951219512	33	0.09116022099447514	66	0.11538461538461539	73	0.09630606860158311	G	12.83	2.054435	0.36277	0.146269	0.09623	ENSG00000103855	ENST00000318443;ENST00000379823;ENST00000537340	T;T	0.65549	-0.16;-0.16	4.84	1.73	0.24493	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.373446	0.29579	N	0.011760	T	0.00210	0.0006	N	0.12637	0.245	0.09310	P	0.9999999999929695	B;B;B	0.17465	0.022;0.002;0.001	B;B;B	0.11329	0.004;0.006;0.001	T	0.03394	-1.1041	9	0.38643	T	0.18	-27.5137	6.0698	0.19883	0.2493:0.1388:0.6119:0.0	rs11574483	213;267;267	B4DK26;Q5ZPR3;Q5ZPR3-4	.;CD276_HUMAN;.	H	267;267;121	ENSP00000320084:R267H;ENSP00000441087:R121H	ENSP00000320084:R267H	R	+	2	0	CD276	71783119	0.307000	0.24500	0.976000	0.42696	0.970000	0.65996	0.403000	0.20982	0.574000	0.29417	0.561000	0.74099	CGC	G|0.889;A|0.111	0.111	strong		0.667	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
MOV10L1	54456	hgsc.bcm.edu	37	22	50584201	50584201	+	Silent	SNP	A	A	C	rs2272838	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50584201A>C	ENST00000262794.5	+	19	2672	c.2589A>C	c.(2587-2589)acA>acC	p.T863T	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Silent_p.T863T|MOV10L1_ENST00000540615.1_Silent_p.T843T|MOV10L1_ENST00000395852.1_5'Flank|MOV10L1_ENST00000545383.1_Silent_p.T863T	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	863					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.T863T(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TCATCACCACATGCAGCAGCT	0.582													a|||	1252	0.25	0.1233	0.3934	5008	,	,		17468	0.252		0.2376	False		,,,				2504	0.3303				p.T863T		Atlas-SNP	.											MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	1	Substitution - coding silent(1)	stomach(1)	c.A2589C						PASS	.		,,	676,3730	287.2+/-279.2	56,564,1583	123.0	120.0	121.0		2589,2529,2589	-11.4	0.0	22	dbSNP_100	121	2081,6519	362.5+/-332.8	254,1573,2473	no	coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	310,2137,4056	CC,CA,AA		24.1977,15.3427,21.1979	,,	863/1166,843/1166,863/1212	50584201	2757,10249	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon19			CACCACATGCAGC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2589A>C	22.37:g.50584201A>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			A|0.774;C|0.226	0.226	strong		0.582	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
MUC21	394263	hgsc.bcm.edu	37	6	30955024	30955024	+	Missense_Mutation	SNP	A	A	G	rs77433662		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30955024A>G	ENST00000376296.3	+	2	1313	c.1072A>G	c.(1072-1074)Agc>Ggc	p.S358G	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	358	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CAGTGGGGCCAGCACAGCCAC	0.642																																					p.S358G		Atlas-SNP	.											MUC21,NS,carcinoma,-1,5	MUC21	98	5	0			c.A1072G						PASS	.																																			SO:0001583	missense	394263	exon2			GGGGCCAGCACAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1072A>G	6.37:g.30955024A>G	ENSP00000365473:p.Ser358Gly	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	7	0.07	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	a	12.76	2.035191	0.35893	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02369	4.32	4.44	1.81	0.25067	.	.	.	.	.	T	0.00754	0.0025	L	0.27053	0.805	0.09310	N	1	B	0.27498	0.18	B	0.29176	0.099	T	0.48514	-0.9029	9	0.40728	T	0.16	-6.2264	3.5667	0.07903	0.6169:0.0:0.1031:0.2801	.	358	Q5SSG8	MUC21_HUMAN	G	208;358	ENSP00000365473:S358G	ENSP00000365473:S358G	S	+	1	0	MUC21	31063003	0.000000	0.05858	0.092000	0.20876	0.132000	0.20833	0.473000	0.22132	0.830000	0.34757	0.477000	0.44152	AGC	A|0.999;G|0.001	0.001	weak		0.642	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
SEPT4	5414	hgsc.bcm.edu	37	17	56598439	56598439	+	Silent	SNP	T	T	C	rs1057068	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:56598439T>C	ENST00000317268.3	-	10	1373	c.1197A>G	c.(1195-1197)acA>acG	p.T399T	SEPT4_ENST00000583114.1_Silent_p.T252T|SEPT4_ENST00000457347.2_Silent_p.T414T|SEPT4_ENST00000580844.1_Silent_p.T300T|SEPT4_ENST00000579371.1_Silent_p.T300T|SEPT4_ENST00000393086.1_Silent_p.T380T|SEPT4_ENST00000317256.6_Silent_p.T380T|SEPT4_ENST00000426861.1_3'UTR|SEPT4_ENST00000412945.3_Silent_p.T391T|RP11-112H10.4_ENST00000580589.1_RNA	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	399	Septin-type G.				apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GTGTCTCCCGTGTCACATCCT	0.547											OREG0024614	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2007	0.400759	0.2693	0.5778	5008	,	,		21447	0.5188		0.3708	False		,,,				2504	0.362				p.T414T		Atlas-SNP	.											.	SEPT4	48	.	0			c.A1242G						PASS	.	C	,,,	1323,3083	697.1+/-406.2	204,915,1084	182.0	158.0	166.0		1173,1197,,1140	-11.0	0.0	17	dbSNP_86	166	3292,5308	647.1+/-400.3	650,1992,1658	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous	SEPT4	NM_001198713.1,NM_004574.3,NM_080415.2,NM_080416.2	,,,	854,2907,2742	CC,CT,TT		38.2791,30.0272,35.4836	,,,	391/471,399/479,,380/460	56598439	4615,8391	2203	4300	6503	SO:0001819	synonymous_variant	5414	exon11			CTCCCGTGTCACA	AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"""Septins"""	9165	protein-coding gene	gene with protein product	"""bradeoin"", ""septin-M"""	603696	"""peanut-like 2 (Drosophila)"""	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.1197A>G	17.37:g.56598439T>C		Somatic	248	1	0.00403226	1016	WXS	Illumina HiSeq	Phase_I	237	236	0.995781	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Silent	SNP	ENST00000317268.3	37	CCDS11610.1																																																																																			T|0.629;C|0.371	0.371	strong		0.547	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417	
MT-CYB	4519	hgsc.bcm.edu	37	M	14798	14798	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:14798T>C	ENST00000361789.2	+	1	52	c.52T>C	c.(52-54)Ttc>Ctc	p.F18L	MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	18			F -> L (in dbSNP:rs28357681). {ECO:0000269|PubMed:10453733, ECO:0000269|PubMed:11130070, ECO:0000269|PubMed:11553319}.		cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						TTAACCACTCATTCATCGACC	0.448																																					p.F18L		Atlas-SNP	.											.	.	.	.	0			c.T52C						PASS	.																																			SO:0001583	missense	0	exon1			CACTCATTCATCG			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.52T>C	M.37:g.14798T>C	ENSP00000354554:p.Phe18Leu	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.448	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
ZNF318	24149	hgsc.bcm.edu	37	6	43323852	43323852	+	Missense_Mutation	SNP	C	C	A	rs34541323	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:43323852C>A	ENST00000361428.2	-	4	1297	c.1220G>T	c.(1219-1221)aGc>aTc	p.S407I	ZNF318_ENST00000318149.3_Missense_Mutation_p.S407I	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	407			S -> I (in dbSNP:rs34541323).		meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			GTGATCCTGGCTGGAGCTGGT	0.443													C|||	96	0.0191693	0.0121	0.013	5008	,	,		19111	0.002		0.0487	False		,,,				2504	0.0204				p.S407I		Atlas-SNP	.											.	ZNF318	175	.	0			c.G1220T						PASS	.	C	ILE/SER	56,4350	52.3+/-87.9	2,52,2149	52.0	56.0	55.0		1220	2.3	0.9	6	dbSNP_126	55	393,8207	124.8+/-183.5	9,375,3916	yes	missense	ZNF318	NM_014345.2	142	11,427,6065	AA,AC,CC		4.5698,1.271,3.4523	possibly-damaging	407/2280	43323852	449,12557	2203	4300	6503	SO:0001583	missense	24149	exon4			TCCTGGCTGGAGC	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"""Zinc fingers, C2H2-type"""	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.1220G>T	6.37:g.43323852C>A	ENSP00000354964:p.Ser407Ile	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	37	CCDS4895.2	56	0.02564102564102564	11	0.022357723577235773	4	0.011049723756906077	0	0.0	41	0.05408970976253298	C	15.67	2.902667	0.52227	0.01271	0.045698	ENSG00000171467	ENST00000318149;ENST00000361428	T;T	0.03920	3.76;3.76	5.97	2.3	0.28687	.	0.455403	0.26496	N	0.024052	T	0.01976	0.0062	N	0.24115	0.695	0.26354	N	0.977167	P	0.49090	0.919	P	0.48704	0.587	T	0.43750	-0.9372	10	0.62326	D	0.03	1.42	8.7609	0.34674	0.0:0.7146:0.0:0.2854	rs34541323	407	Q5VUA4	ZN318_HUMAN	I	407	ENSP00000323032:S407I;ENSP00000354964:S407I	ENSP00000323032:S407I	S	-	2	0	ZNF318	43431830	1.000000	0.71417	0.915000	0.36163	0.998000	0.95712	0.869000	0.27996	0.144000	0.18951	0.591000	0.81541	AGC	A|0.037;C|0.962;G|0.000	0.037	strong		0.443	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
SLC5A4	6527	hgsc.bcm.edu	37	22	32650200	32650200	+	Splice_Site	SNP	C	C	T	rs2235171	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:32650200C>T	ENST00000266086.4	-	2	147	c.136G>A	c.(136-138)Gcg>Acg	p.A46T	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	46			A -> T (in dbSNP:rs2235171).		carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TTCAGCATCGCCTGAGCAGAA	0.572													c|||	415	0.0828674	0.1914	0.036	5008	,	,		16970	0.0298		0.0368	False		,,,				2504	0.0716				p.A46T		Atlas-SNP	.											.	SLC5A4	82	.	0			c.G136A						PASS	.	C	THR/ALA	710,3696	295.6+/-283.7	66,578,1559	80.0	70.0	73.0		136	3.2	0.9	22	dbSNP_98	73	320,8280	113.5+/-173.5	10,300,3990	yes	missense-near-splice	SLC5A4	NM_014227.2	58	76,878,5549	TT,TC,CC		3.7209,16.1144,7.9194	possibly-damaging	46/660	32650200	1030,11976	2203	4300	6503	SO:0001630	splice_region_variant	6527	exon2			GCATCGCCTGAGC	U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"""Solute carriers"""	11039	protein-coding gene	gene with protein product			"""solute carrier family 5 (low affinity glucose cotransporter), member 4"""			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.136-1G>A	22.37:g.32650200C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_014227	O15279	Missense_Mutation	SNP	ENST00000266086.4	37	CCDS13903.1	159	0.07280219780219781	95	0.19308943089430894	15	0.04143646408839779	21	0.03671328671328671	28	0.036939313984168866	C	13.94	2.387342	0.42308	0.161144	0.037209	ENSG00000100191	ENST00000266086	D	0.88046	-2.33	5.4	3.19	0.36642	.	0.000000	0.85682	D	0.000000	T	0.00815	0.0027	M	0.82823	2.61	0.09310	P	0.99999723571	B	0.28933	0.228	B	0.35607	0.206	T	0.47749	-0.9093	9	0.72032	D	0.01	.	12.0818	0.53675	0.3135:0.6865:0.0:0.0	rs2235171;rs52837051;rs2235171	46	Q9NY91	SC5A4_HUMAN	T	46	ENSP00000266086:A46T	ENSP00000266086:A46T	A	-	1	0	SLC5A4	30980200	0.999000	0.42202	0.864000	0.33941	0.216000	0.24613	0.672000	0.25187	0.584000	0.29591	0.655000	0.94253	GCG	C|0.919;T|0.081	0.081	strong		0.572	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227	Missense_Mutation
ZZEF1	23140	hgsc.bcm.edu	37	17	3966064	3966064	+	Silent	SNP	A	A	G	rs781825	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:3966064A>G	ENST00000381638.2	-	30	4990	c.4866T>C	c.(4864-4866)tgT>tgC	p.C1622C		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1622							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						AATCTTTCTGACAGGTCAGAA	0.418													G|||	2377	0.474641	0.8132	0.4078	5008	,	,		20727	0.246		0.4076	False		,,,				2504	0.3691				p.C1622C		Atlas-SNP	.											.	ZZEF1	195	.	0			c.T4866C						PASS	.	G		3339,1067	376.1+/-321.9	1285,769,149	36.0	36.0	36.0		4866	4.7	1.0	17	dbSNP_86	36	3418,5182	622.0+/-397.3	661,2096,1543	no	coding-synonymous	ZZEF1	NM_015113.3		1946,2865,1692	GG,GA,AA		39.7442,24.217,48.0471		1622/2962	3966064	6757,6249	2203	4300	6503	SO:0001819	synonymous_variant	23140	exon30			TTTCTGACAGGTC	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.4866T>C	17.37:g.3966064A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																			A|0.487;G|0.513	0.513	strong		0.418	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
PDIK1L	149420	hgsc.bcm.edu	37	1	26448849	26448849	+	Silent	SNP	T	T	C	rs17356867	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26448849T>C	ENST00000374271.4	+	4	1094	c.807T>C	c.(805-807)taT>taC	p.Y269Y	PDIK1L_ENST00000374269.1_Silent_p.Y269Y	NM_001243532.1|NM_001243533.1|NM_152835.4	NP_001230461.1|NP_001230462.1|NP_690048.1	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like	269	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)		TGGGGAGTTATGTAAAACAAG	0.428													T|||	587	0.117212	0.1929	0.1052	5008	,	,		18706	0.0159		0.1789	False		,,,				2504	0.0644				p.Y269Y		Atlas-SNP	.											.	PDIK1L	19	.	0			c.T807C						PASS	.	T		895,3511	342.8+/-307.3	81,733,1389	96.0	100.0	98.0		807	-3.8	0.9	1	dbSNP_123	98	1535,7065	288.6+/-298.9	136,1263,2901	no	coding-synonymous	PDIK1L	NM_152835.4		217,1996,4290	CC,CT,TT		17.8488,20.3132,18.6837		269/342	26448849	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	149420	exon3			GAGTTATGTAAAA	AF411102	CCDS274.1	1p35.1	2008-02-05			ENSG00000175087	ENSG00000175087			18981	protein-coding gene	gene with protein product		610785				14631099	Standard	NM_152835		Approved	CLIK1L	uc009vsb.3	Q8N165	OTTHUMG00000007511	ENST00000374271.4:c.807T>C	1.37:g.26448849T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_001243532	B2R777|D3DPK2|Q5T2I0|Q8NDB3	Silent	SNP	ENST00000374271.4	37	CCDS274.1																																																																																			T|0.836;C|0.164	0.164	strong		0.428	PDIK1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019752.1	NM_152835	
SVIL	6840	hgsc.bcm.edu	37	10	29821089	29821089	+	Silent	SNP	C	C	T	rs17756919	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:29821089C>T	ENST00000355867.4	-	9	2603	c.1851G>A	c.(1849-1851)gtG>gtA	p.V617V	SVIL_ENST00000375400.3_Intron|SVIL_ENST00000375398.2_Silent_p.V617V	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	617					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CCGACCTCTCCACCCGTGATT	0.498													C|||	1436	0.286741	0.3313	0.3617	5008	,	,		20324	0.0764		0.3926	False		,,,				2504	0.2812				p.V617V		Atlas-SNP	.											.	SVIL	226	.	0			c.G1851A						PASS	.	C	,	1520,2886	480.4+/-358.8	273,974,956	56.0	54.0	55.0		,1851	0.4	0.8	10	dbSNP_123	55	3531,5069	514.6+/-378.4	732,2067,1501	no	intron,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	1005,3041,2457	TT,TC,CC		41.0581,34.4984,38.8359	,	,617/2215	29821089	5051,7955	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon9			CCTCTCCACCCGT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1851G>A	10.37:g.29821089C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	59	20	0.338983	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			C|0.659;T|0.341	0.341	strong		0.498	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
OR12D2	26529	hgsc.bcm.edu	37	6	29364815	29364815	+	Missense_Mutation	SNP	C	C	G	rs2073154	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29364815C>G	ENST00000383555.2	+	1	400	c.339C>G	c.(337-339)ttC>ttG	p.F113L	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	113			F -> L (in dbSNP:rs2073154).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CCATGTTGTTCGCCGTGATGG	0.493													G|||	1598	0.319089	0.1921	0.3458	5008	,	,		21376	0.3641		0.4533	False		,,,				2504	0.2873				p.F113L		Atlas-SNP	.											.	OR12D2	42	.	0			c.C339G						PASS	.	G	LEU/PHE	670,2350		75,520,915	85.0	86.0	86.0		339	1.0	0.0	6	dbSNP_96	86	2409,3007		534,1341,833	yes	missense	OR12D2	NM_013936.3	22	609,1861,1748	GG,GC,CC		44.4793,22.1854,36.4983	benign	113/308	29364815	3079,5357	1510	2708	4218	SO:0001583	missense	26529	exon1			GTTGTTCGCCGTG		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.339C>G	6.37:g.29364815C>G	ENSP00000373047:p.Phe113Leu	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	307	124	0.403909	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	787	0.36034798534798534	101	0.20528455284552846	123	0.3397790055248619	208	0.36363636363636365	355	0.4683377308707124	G	0	-2.845655	0.00067	0.221854	0.444793	ENSG00000168787	ENST00000383555	T	0.72394	-0.65	3.94	1.01	0.19927	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	N	0.000302	T	0.04048	0.0113	N	0.00014	-2.9	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29761	-1.0001	9	0.02654	T	1	.	3.1878	0.06607	0.1594:0.3698:0.3452:0.1256	rs2073154;rs52828851;rs59971655;rs2073154	113	P58182	O12D2_HUMAN	L	113	ENSP00000373047:F113L	ENSP00000373047:F113L	F	+	3	2	OR12D2	29472794	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.355000	0.07671	-0.258000	0.09446	-0.980000	0.02579	TTC	C|0.628;G|0.372	0.372	strong		0.493	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
PODN	127435	hgsc.bcm.edu	37	1	53544513	53544513	+	Missense_Mutation	SNP	C	C	T	rs12567021	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:53544513C>T	ENST00000312553.5	+	8	1482	c.1475C>T	c.(1474-1476)aCg>aTg	p.T492M	PODN_ENST00000371500.3_Missense_Mutation_p.T473M|RP11-334A14.5_ENST00000447867.1_RNA|PODN_ENST00000395871.2_Missense_Mutation_p.T350M	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	444					negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CGGCTGCACACGCTGCCACCT	0.667													C|||	245	0.0489217	0.0023	0.0086	5008	,	,		20573	0.1677		0.0179	False		,,,				2504	0.0501				p.T492M		Atlas-SNP	.											.	PODN	86	.	0			c.C1475T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR	24,4378	30.8+/-60.4	0,24,2177	52.0	42.0	45.0		1418,1418,1049,1475	2.9	1.0	1	dbSNP_120	45	194,8400	82.6+/-145.2	4,186,4107	yes	missense,missense,missense,missense	PODN	NM_001199080.1,NM_001199081.1,NM_001199082.1,NM_153703.4	81,81,81,81	4,210,6284	TT,TC,CC		2.2574,0.5452,1.6774	benign,benign,benign,benign	473/643,473/643,350/520,492/662	53544513	218,12778	2201	4297	6498	SO:0001583	missense	127435	exon8			TGCACACGCTGCC	AY313607	CCDS573.1, CCDS55601.1, CCDS55602.1	1p32.3	2008-02-05			ENSG00000174348	ENSG00000174348		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	23174	protein-coding gene	gene with protein product	"""podocan proteoglycan"""	608661					Standard	NM_153703		Approved	PCAN, PODOCAN, MGC24995, SLRR5A	uc010onr.2	Q7Z5L7	OTTHUMG00000008934	ENST00000312553.5:c.1475C>T	1.37:g.53544513C>T	ENSP00000308315:p.Thr492Met	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	93	66	0.709677	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Missense_Mutation	SNP	ENST00000312553.5	37	CCDS573.1	108	0.04945054945054945	2	0.0040650406504065045	2	0.0055248618784530384	88	0.15384615384615385	16	0.021108179419525065	C	11.23	1.577599	0.28180	0.005452	0.022574	ENSG00000174348	ENST00000371500;ENST00000395871;ENST00000312553	T;T;T	0.25749	3.53;1.78;2.19	4.81	2.89	0.33648	.	0.475465	0.23386	N	0.048750	T	0.00073	0.0002	L	0.38838	1.175	0.37959	P	0.06708199999999997	P;B;B	0.39624	0.681;0.075;0.09	B;B;B	0.28991	0.097;0.02;0.04	T	0.24225	-1.0166	9	0.32370	T	0.25	.	7.7088	0.28665	0.132:0.7219:0.0:0.1461	rs12567021;rs12567021	350;473;492	Q7Z5L7-4;Q7Z5L7-2;Q7Z5L7-3	.;.;.	M	473;350;492	ENSP00000360555:T473M;ENSP00000379212:T350M;ENSP00000308315:T492M	ENSP00000308315:T492M	T	+	2	0	PODN	53317101	0.033000	0.19621	0.996000	0.52242	0.967000	0.64934	1.633000	0.37113	0.594000	0.29761	0.555000	0.69702	ACG	C|0.972;T|0.028	0.028	strong		0.667	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703	
CRTAM	56253	hgsc.bcm.edu	37	11	122742050	122742050	+	Silent	SNP	T	T	C	rs34242434	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:122742050T>C	ENST00000227348.4	+	10	1172	c.1125T>C	c.(1123-1125)aaT>aaC	p.N375N	CRTAM_ENST00000533709.1_Silent_p.N176N	NM_019604.2	NP_062550.2			cytotoxic and regulatory T cell molecule											breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|prostate(1)	19		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		GGAAGGAAAATGTACAACATT	0.398													T|||	698	0.139377	0.1846	0.0692	5008	,	,		20815	0.1726		0.1004	False		,,,				2504	0.1339				p.N375N		Atlas-SNP	.											.	CRTAM	50	.	0			c.T1125C						PASS	.	T		711,3693	296.1+/-284.1	65,581,1556	106.0	98.0	101.0		1125	-9.3	0.0	11	dbSNP_126	101	877,7721	197.8+/-242.3	45,787,3467	no	coding-synonymous	CRTAM	NM_019604.2		110,1368,5023	CC,CT,TT		10.2,16.1444,12.2135		375/394	122742050	1588,11414	2202	4299	6501	SO:0001819	synonymous_variant	56253	exon10			GGAAAATGTACAA	AF001622	CCDS8437.1	11q24.1	2013-01-11			ENSG00000109943	ENSG00000109943		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	24313	protein-coding gene	gene with protein product	"""class I MHC restricted T cell associated molecule"""	612597				10811014, 16300832	Standard	NM_019604		Approved	CD355	uc001pyj.3	O95727	OTTHUMG00000166026	ENST00000227348.4:c.1125T>C	11.37:g.122742050T>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	166	166	1	NM_019604		Silent	SNP	ENST00000227348.4	37	CCDS8437.1																																																																																			T|0.878;C|0.122	0.122	strong		0.398	CRTAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387507.1	NM_019604	
KNTC1	9735	hgsc.bcm.edu	37	12	123105143	123105143	+	Silent	SNP	C	C	T	rs2270775	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:123105143C>T	ENST00000333479.7	+	60	6444	c.6267C>T	c.(6265-6267)caC>caT	p.H2089H	KNTC1_ENST00000534995.1_Silent_p.H10H|KNTC1_ENST00000436959.3_Silent_p.H10H|KNTC1_ENST00000450485.2_Silent_p.H1014H|HCAR1_ENST00000356987.2_3'UTR|KNTC1_ENST00000537348.1_3'UTR	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	2089					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		AGAAAAGACACCAGCAAATTA	0.458													C|||	1186	0.236821	0.0908	0.1744	5008	,	,		21635	0.4425		0.2376	False		,,,				2504	0.2658				p.H2089H		Atlas-SNP	.											.	KNTC1	182	.	0			c.C6267T						PASS	.	C		377,3643		16,345,1649	76.0	71.0	72.0		6267	2.6	1.0	12	dbSNP_100	72	1939,6435		242,1455,2490	no	coding-synonymous	KNTC1	NM_014708.4		258,1800,4139	TT,TC,CC		23.155,9.3781,18.6865		2089/2210	123105143	2316,10078	2010	4187	6197	SO:0001819	synonymous_variant	9735	exon60			AAGACACCAGCAA		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.6267C>T	12.37:g.123105143C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_014708	A7E2C4|B3KSG2	Silent	SNP	ENST00000333479.7	37	CCDS45002.1																																																																																			C|0.748;T|0.252	0.252	strong		0.458	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
ZNF646	9726	hgsc.bcm.edu	37	16	31088347	31088347	+	Silent	SNP	G	G	A	rs749671	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31088347G>A	ENST00000394979.2	+	1	1125	c.702G>A	c.(700-702)gaG>gaA	p.E234E	ZNF668_ENST00000300849.4_5'Flank|ZNF668_ENST00000564456.1_5'Flank|ZNF646_ENST00000300850.5_Silent_p.E234E			O15015	ZN646_HUMAN	zinc finger protein 646	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						CTCCTGCTGAGGAGGAGCGGC	0.597													G|||	1770	0.353435	0.0545	0.4035	5008	,	,		18624	0.8849		0.3817	False		,,,				2504	0.1452				p.E234E		Atlas-SNP	.											.	ZNF646	133	.	0			c.G702A						PASS	.	G		504,3890	230.1+/-244.4	33,438,1726	50.0	51.0	51.0		702	4.8	1.0	16	dbSNP_86	51	3413,5187	500.9+/-375.3	670,2073,1557	no	coding-synonymous	ZNF646	NM_014699.3		703,2511,3283	AA,AG,GG		39.686,11.4702,30.1447		234/1833	31088347	3917,9077	2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			TGCTGAGGAGGAG	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"""Zinc fingers, C2H2-type"""	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.702G>A	16.37:g.31088347G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	37																																																																																				G|0.646;A|0.354	0.354	strong		0.597	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
OR8I2	120586	hgsc.bcm.edu	37	11	55861484	55861484	+	Missense_Mutation	SNP	A	A	C	rs61887096	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55861484A>C	ENST00000302124.2	+	1	732	c.701A>C	c.(700-702)cAg>cCg	p.Q234P		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	234						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					GCAGGCAGGCAGAAGGCCTTC	0.468													A|||	195	0.0389377	0.0121	0.0447	5008	,	,		20623	0.001		0.0944	False		,,,				2504	0.0532				p.Q234P		Atlas-SNP	.											OR8I2,right_upper_lobe,carcinoma,-1,2	OR8I2	119	2	0			c.A701C						PASS	.	A	PRO/GLN	98,4304	78.3+/-116.7	0,98,2103	152.0	138.0	143.0		701	0.6	0.8	11	dbSNP_129	143	693,7899	171.3+/-222.3	34,625,3637	yes	missense	OR8I2	NM_001003750.1	76	34,723,5740	CC,CA,AA		8.0656,2.2263,6.0874	benign	234/311	55861484	791,12203	2201	4296	6497	SO:0001583	missense	120586	exon1			GCAGGCAGAAGGC	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.701A>C	11.37:g.55861484A>C	ENSP00000303864:p.Gln234Pro	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	135	71	0.525926	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	37	CCDS31517.1	86	0.039377289377289376	4	0.008130081300813009	14	0.03867403314917127	0	0.0	68	0.08970976253298153	A	13.42	2.232629	0.39498	0.022263	0.080656	ENSG00000172154	ENST00000302124	T	0.00130	8.69	4.33	0.564	0.17302	GPCR, rhodopsin-like superfamily (1);	1.321060	0.05579	U	0.572443	T	0.00012	0.0000	M	0.83483	2.645	0.09310	N	1	B	0.28082	0.2	B	0.32864	0.154	T	0.37865	-0.9687	10	0.37606	T	0.19	2.9586	8.255	0.31751	0.7351:0.0:0.2649:0.0	rs61887096	234	Q8N0Y5	OR8I2_HUMAN	P	234	ENSP00000303864:Q234P	ENSP00000303864:Q234P	Q	+	2	0	OR8I2	55618060	0.000000	0.05858	0.795000	0.32087	0.863000	0.49368	-0.420000	0.07062	0.170000	0.19704	0.362000	0.22060	CAG	A|0.948;C|0.052	0.052	strong		0.468	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
CCDC129	223075	hgsc.bcm.edu	37	7	31692409	31692409	+	Missense_Mutation	SNP	C	C	G	rs34177136	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:31692409C>G	ENST00000407970.3	+	14	3139	c.3101C>G	c.(3100-3102)cCt>cGt	p.P1034R	CCDC129_ENST00000409210.1_Missense_Mutation_p.P942R|CCDC129_ENST00000451887.2_Intron|CCDC129_ENST00000319386.3_Missense_Mutation_p.P886R	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	1034								p.P1034H(1)|p.P886H(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TCAAATTGTCCTGTTGGAGAA	0.453													C|||	6	0.00119808	0.0008	0.0029	5008	,	,		21006	0.0		0.003	False		,,,				2504	0.0				p.P1044R		Atlas-SNP	.											.	CCDC129	127	.	2	Substitution - Missense(2)	lung(2)	c.C3131G						PASS	.	C	ARG/PRO	1,4405	2.1+/-5.4	0,1,2202	107.0	98.0	101.0		3101	-0.3	0.0	7	dbSNP_126	101	41,8559	27.4+/-76.7	0,41,4259	yes	missense	CCDC129	NM_194300.2	103	0,42,6461	GG,GC,CC		0.4767,0.0227,0.3229	probably-damaging	1034/1045	31692409	42,12964	2203	4300	6503	SO:0001583	missense	223075	exon15			ATTGTCCTGTTGG	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.3101C>G	7.37:g.31692409C>G	ENSP00000384416:p.Pro1034Arg	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	275	140	0.509091	NM_001257967	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	9.917	1.211175	0.22289	2.27E-4	0.004767	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000538406;ENST00000409210	T;T;T	0.17691	2.26;2.53;2.27	3.96	-0.303	0.12792	.	1.098150	0.07119	N	0.843657	T	0.11836	0.0288	M	0.63428	1.95	0.09310	N	1	P;P;P	0.43701	0.815;0.815;0.815	B;B;B	0.39935	0.314;0.314;0.314	T	0.19549	-1.0302	10	0.42905	T	0.14	.	3.6334	0.08140	0.1791:0.504:0.0:0.3169	rs34177136	1044;1034;886	F5H2J8;Q6ZRS4;Q6ZRS4-2	.;CC129_HUMAN;.	R	886;1034;1044;942	ENSP00000313062:P886R;ENSP00000384416:P1034R;ENSP00000387214:P942R	ENSP00000313062:P886R	P	+	2	0	CCDC129	31658934	0.000000	0.05858	0.001000	0.08648	0.068000	0.16541	-0.005000	0.12855	-0.187000	0.10516	-0.793000	0.03317	CCT	C|0.997;G|0.003	0.003	strong		0.453	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
Unknown	0	hgsc.bcm.edu	37	7	63680098	63680098	+	IGR	SNP	C	C	T	rs35920205|rs4479992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:63680098C>T								GUSBP6 (68999 upstream) : ZNF679 (8753 downstream)																							AATCCTTTAACCACTCCTCAA	0.393													.|||	1119	0.223442	0.1551	0.2205	5008	,	,		19859	0.2679		0.2565	False		,,,				2504	0.2382				p.N223N		Atlas-SNP	.											.	.	.	.	0			c.C669T						PASS	.	C		216,1168		24,168,500	42.0	39.0	40.0		669	-0.5	0.0	7	dbSNP_111	40	780,2402		97,586,908	no	coding-synonymous	ZNF735	NM_001159524.1		121,754,1408	TT,TC,CC		24.5129,15.6069,21.8134		223/413	63680098	996,3570	692	1591	2283	SO:0001628	intergenic_variant	730291	exon4			CTTTAACCACTCC																													7.37:g.63680098C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_001159524		Silent	SNP		37																																																																																				C|0.803;T|0.197	0.197	strong	0	0.393								
GOLGA6A	342096	hgsc.bcm.edu	37	15	74365093	74365093	+	Silent	SNP	G	G	T	rs148069128	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:74365093G>T	ENST00000290438.3	-	13	1531	c.1491C>A	c.(1489-1491)ctC>ctA	p.L497L	RN7SL429P_ENST00000479090.2_RNA	NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	497						Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						CTTCTCCAGGGAGAGCCACGA	0.577																																					p.L497L		Atlas-SNP	.											GOLGA6A,colon,carcinoma,0,1	GOLGA6A	28	1	0			c.C1491A						PASS	.	G		15,4297		1,13,2142	37.0	47.0	44.0		1491	-2.0	0.8	15	dbSNP_134	44	145,8441		0,145,4148	no	coding-synonymous	GOLGA6A	NM_001038640.2		1,158,6290	TT,TG,GG		1.6888,0.3479,1.2405		497/694	74365093	160,12738	2156	4293	6449	SO:0001819	synonymous_variant	342096	exon13			TCCAGGGAGAGCC	AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289			13567	protein-coding gene	gene with protein product		610288	"""golgi autoantigen, golgin subfamily a, member 6"", ""golgi autoantigen, golgin subfamily a, 6"", ""golgi autoantigen, golgin subfamily a, 6A"""	GOLGA6		11161787	Standard	NM_001038640		Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1491C>A	15.37:g.74365093G>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	66	18	0.272727	NM_001038640	A8K959|Q9NYA7	Silent	SNP	ENST00000290438.3	37	CCDS32290.1																																																																																			G|0.992;T|0.008	0.008	strong		0.577	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421835.1	XM_292357	
ZNF385C	201181	hgsc.bcm.edu	37	17	40189830	40189830	+	Silent	SNP	C	C	T	rs60110245	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:40189830C>T	ENST00000436535.3	-	2	324	c.324G>A	c.(322-324)ccG>ccA	p.P108P	CTD-2132N18.2_ENST00000587304.1_RNA|CTD-2132N18.4_ENST00000602842.1_RNA			Q66K41	Z385C_HUMAN	zinc finger protein 385C	27						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	3		all_cancers(22;0.00127)|Breast(137;0.00104)|all_epithelial(22;0.0126)				TGAAGTCCAGCGGGGGCTGCA	0.706													C|||	459	0.0916534	0.2103	0.0562	5008	,	,		12615	0.0268		0.0934	False		,,,				2504	0.0215				p.P29P		Atlas-SNP	.											.	ZNF385C	7	.	0			c.G87A						PASS	.																																			SO:0001819	synonymous_variant	201181	exon2			GTCCAGCGGGGGC	BC067901	CCDS74065.1	17q21.2	2012-10-05			ENSG00000187595	ENSG00000187595			33722	protein-coding gene	gene with protein product							Standard	NM_001242704		Approved		uc021txr.1	Q66K41	OTTHUMG00000132073	ENST00000436535.3:c.324G>A	17.37:g.40189830C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_001242704	Q4G0J1	Silent	SNP	ENST00000436535.3	37																																																																																				C|0.898;T|0.102	0.102	strong		0.706	ZNF385C-001	NOVEL	not_organism_supported|mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000347740.3	NM_001013624	
ZNF419	79744	hgsc.bcm.edu	37	19	58002924	58002924	+	Missense_Mutation	SNP	G	G	A	rs145680611	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58002924G>A	ENST00000221735.7	+	3	344	c.158G>A	c.(157-159)cGc>cAc	p.R53H	ZNF419_ENST00000518999.1_Missense_Mutation_p.R54H|ZNF419_ENST00000354197.4_Missense_Mutation_p.R41H|ZNF419_ENST00000347466.6_Missense_Mutation_p.R54H|ZNF419_ENST00000442920.2_Missense_Mutation_p.R40H|ZNF419_ENST00000520540.1_Missense_Mutation_p.R41H|ZNF419_ENST00000426954.2_Missense_Mutation_p.R41H|AC003005.4_ENST00000601674.1_Missense_Mutation_p.R40H|ZNF419_ENST00000415379.2_Missense_Mutation_p.R40H|ZNF419_ENST00000424930.2_Missense_Mutation_p.R54H			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	53	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		CTCCTCTACCGCAATGTGATG	0.532													G|||	34	0.00678914	0.0	0.0101	5008	,	,		19458	0.0		0.0229	False		,,,				2504	0.0041				p.R54H		Atlas-SNP	.											ZNF419_ENST00000424930,colon,carcinoma,0,8	ZNF419	134	8	0			c.G161A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	19,4387	26.2+/-53.5	0,19,2184	109.0	106.0	107.0		161,122,119,161,122,119,158	-2.6	0.0	19	dbSNP_134	107	179,8415	81.5+/-144.1	0,179,4118	no	missense,missense,missense,missense,missense,missense,missense	ZNF419	NM_001098491.1,NM_001098492.1,NM_001098493.1,NM_001098494.1,NM_001098495.1,NM_001098496.1,NM_024691.3	29,29,29,29,29,29,29	0,198,6302	AA,AG,GG		2.0828,0.4312,1.5231	benign,benign,benign,benign,benign,benign,benign	54/512,41/499,40/498,54/479,41/466,40/465,53/511	58002924	198,12802	2203	4297	6500	SO:0001583	missense	79744	exon3			TCTACCGCAATGT	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.158G>A	19.37:g.58002924G>A	ENSP00000221735:p.Arg53His	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	264	95	0.359848	NM_001098494	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	37	CCDS54326.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	G	1.463	-0.561777	0.03939	0.004312	0.020828	ENSG00000105136	ENST00000284020;ENST00000524372;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000427558;ENST00000523882;ENST00000520540;ENST00000442920;ENST00000523312;ENST00000517598;ENST00000347466;ENST00000523138;ENST00000415379;ENST00000521754;ENST00000221735;ENST00000518999;ENST00000521137	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.02737	4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18	2.79	-2.61	0.06171	Krueppel-associated box (4);	.	.	.	.	T	0.01222	0.0040	L	0.43646	1.37	0.09310	N	1	B;B;B;B;B;B;P	0.41041	0.005;0.005;0.002;0.001;0.026;0.003;0.736	B;B;B;B;B;B;B	0.38655	0.002;0.002;0.002;0.002;0.009;0.002;0.278	T	0.34477	-0.9827	9	0.59425	D	0.04	.	3.4635	0.07541	0.3514:0.0:0.4706:0.1779	.	40;40;40;41;54;54;53	E9PFX9;B4DXU7;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;.;ZN419_HUMAN	H	33;41;54;41;41;53;54;41;40;40;54;54;53;40;41;53;54;53	ENSP00000388864:R54H;ENSP00000390916:R41H;ENSP00000346136:R41H;ENSP00000428181:R54H;ENSP00000429471:R41H;ENSP00000414709:R40H;ENSP00000428515:R40H;ENSP00000299860:R54H;ENSP00000429504:R53H;ENSP00000392129:R40H;ENSP00000428523:R41H;ENSP00000221735:R53H;ENSP00000427723:R54H;ENSP00000429628:R53H	ENSP00000221735:R53H	R	+	2	0	ZNF419	62694736	0.000000	0.05858	0.000000	0.03702	0.196000	0.23810	-1.838000	0.01687	-0.662000	0.05338	0.511000	0.50034	CGC	G|0.983;A|0.017	0.017	strong		0.532	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	
SNTN	132203	hgsc.bcm.edu	37	3	63645410	63645410	+	Missense_Mutation	SNP	A	A	G	rs73111385	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:63645410A>G	ENST00000343837.3	+	3	175	c.155A>G	c.(154-156)aAg>aGg	p.K52R	SNTN_ENST00000496807.1_Missense_Mutation_p.K48R	NM_001080537.1	NP_001074006.1	A6NMZ2	SNTAN_HUMAN	sentan, cilia apical structure protein	52						cilium (GO:0005929)	calcium ion binding (GO:0005509)			endometrium(2)|ovary(1)	3						GCTCTGAGGAAGTGCTCAGAT	0.428													A|||	61	0.0121805	0.0045	0.0202	5008	,	,		19708	0.0		0.0318	False		,,,				2504	0.0092				p.K52R		Atlas-SNP	.											.	SNTN	17	.	0			c.A155G						PASS	.	A	ARG/LYS	29,4377	35.2+/-66.4	1,27,2175	136.0	136.0	136.0		155	4.5	0.5	3	dbSNP_130	136	353,8247	118.8+/-178.2	9,335,3956	yes	missense	SNTN	NM_001080537.1	26	10,362,6131	GG,GA,AA		4.1047,0.6582,2.9371	benign	52/148	63645410	382,12624	2203	4300	6503	SO:0001583	missense	132203	exon3			TGAGGAAGTGCTC	AK126350	CCDS33779.1	3p14.2	2009-03-10	2009-03-10		ENSG00000188817	ENSG00000188817			33706	protein-coding gene	gene with protein product	"""S100A-like protein"""					18829862	Standard	NM_001080537		Approved	FLJ44379, S100AL	uc003dlr.3	A6NMZ2	OTTHUMG00000158766	ENST00000343837.3:c.155A>G	3.37:g.63645410A>G	ENSP00000341442:p.Lys52Arg	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	168	83	0.494048	NM_001080537	B7FF65	Missense_Mutation	SNP	ENST00000343837.3	37	CCDS33779.1	33	0.01510989010989011	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	23	0.030343007915567283	A	12.24	1.878359	0.33162	0.006582	0.041047	ENSG00000188817	ENST00000343837;ENST00000469440;ENST00000496807	T	0.51071	0.72	5.68	4.5	0.54988	.	0.080672	0.52532	N	0.000062	T	0.12178	0.0296	L	0.43701	1.375	0.31232	N	0.696253	B	0.32203	0.36	B	0.32022	0.139	T	0.29912	-0.9996	10	0.49607	T	0.09	-6.6993	10.3755	0.44079	0.921:0.0:0.079:0.0	.	52	A6NMZ2	SNTAN_HUMAN	R	52;52;48	ENSP00000341442:K52R	ENSP00000341442:K52R	K	+	2	0	SNTN	63620450	1.000000	0.71417	0.483000	0.27378	0.593000	0.36681	4.277000	0.58939	1.048000	0.40298	0.482000	0.46254	AAG	A|0.973;G|0.027	0.027	strong		0.428	SNTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352094.1	NM_001080537	
ALPK2	115701	hgsc.bcm.edu	37	18	56204977	56204977	+	Silent	SNP	C	C	T	rs3809971	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:56204977C>T	ENST00000361673.3	-	5	2655	c.2442G>A	c.(2440-2442)acG>acA	p.T814T	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	814						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TATCAAAACACGTTCCTTGGT	0.458													T|||	2024	0.404153	0.4312	0.4294	5008	,	,		22574	0.2361		0.5726	False		,,,				2504	0.3497				p.T814T		Atlas-SNP	.											.	ALPK2	487	.	0			c.G2442A						PASS	.	T		1983,2423	618.3+/-393.1	445,1093,665	121.0	112.0	115.0		2442	3.2	0.0	18	dbSNP_107	115	4589,4011	555.6+/-386.7	1236,2117,947	no	coding-synonymous	ALPK2	NM_052947.3		1681,3210,1612	TT,TC,CC		46.6395,45.0068,49.4695		814/2171	56204977	6572,6434	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			AAAACACGTTCCT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2442G>A	18.37:g.56204977C>T		Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	275	132	0.48	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			C|0.526;T|0.474	0.474	strong		0.458	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
PRICKLE4	29964	hgsc.bcm.edu	37	6	41754718	41754718	+	Missense_Mutation	SNP	G	G	A	rs149565703	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41754718G>A	ENST00000394260.1	+	5	886	c.886G>A	c.(886-888)Gac>Aac	p.D296N	TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000458694.1_Missense_Mutation_p.D336N|PRICKLE4_ENST00000394263.1_Missense_Mutation_p.D336N|TOMM6_ENST00000398884.3_5'Flank			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	296						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGATCCCAAGGACACCCCTTT	0.607											OREG0017435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3	0.000599042	0.0	0.0	5008	,	,		16181	0.0		0.002	False		,,,				2504	0.001				p.D336N		Atlas-SNP	.											.	PRICKLE4	29	.	0			c.G1006A						PASS	.	G	ASN/ASP	4,4402	8.1+/-20.4	0,4,2199	129.0	152.0	144.0		1006	2.0	0.1	6	dbSNP_134	144	19,8581	13.3+/-46.6	0,19,4281	yes	missense	PRICKLE4	NM_013397.5	23	0,23,6480	AA,AG,GG		0.2209,0.0908,0.1768	possibly-damaging	336/385	41754718	23,12983	2203	4300	6503	SO:0001583	missense	29964	exon8			CCCAAGGACACCC	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"""chromosome 6 open reading frame 49"""	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.886G>A	6.37:g.41754718G>A	ENSP00000377803:p.Asp296Asn	Somatic	78	0	0	903	WXS	Illumina HiSeq	Phase_I	97	40	0.412371	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Missense_Mutation	SNP	ENST00000394260.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	19.83	3.899836	0.72754	9.08E-4	0.002209	ENSG00000124593	ENST00000458694;ENST00000394263;ENST00000394260	D;D;D	0.86164	-2.08;-2.08;-2.08	3.87	1.98	0.26296	.	0.268702	0.26220	N	0.025637	T	0.77631	0.4159	L	0.56199	1.76	0.80722	D	1	P	0.47910	0.902	P	0.46659	0.523	T	0.75396	-0.3332	10	0.49607	T	0.09	-5.8117	6.5374	0.22361	0.0:0.202:0.5893:0.2088	.	336	Q2TBC4-3	.	N	336;336;296	ENSP00000404911:D336N;ENSP00000377806:D336N;ENSP00000377803:D296N	ENSP00000335185:D336N	D	+	1	0	PRICKLE4	41862696	0.830000	0.29337	0.117000	0.21633	0.009000	0.06853	1.326000	0.33735	0.545000	0.28902	0.561000	0.74099	GAC	G|0.998;A|0.002	0.002	strong		0.607	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397	
VPS41	27072	hgsc.bcm.edu	37	7	38807169	38807169	+	Silent	SNP	C	C	G	rs149665930	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:38807169C>G	ENST00000310301.4	-	15	1269	c.1215G>C	c.(1213-1215)ctG>ctC	p.L405L	VPS41_ENST00000395969.2_Silent_p.L380L	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	405					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						CTCTCTCCACCAGGTGATTTA	0.338													C|||	10	0.00199681	0.0008	0.0014	5008	,	,		13773	0.0		0.005	False		,,,				2504	0.0031				p.L405L		Atlas-SNP	.											.	VPS41	102	.	0			c.G1215C						PASS	.	C	,	18,4388	26.2+/-53.5	0,18,2185	92.0	86.0	88.0		1215,1140	1.5	1.0	7	dbSNP_134	88	103,8497	56.4+/-117.6	1,101,4198	no	coding-synonymous,coding-synonymous	VPS41	NM_014396.3,NM_080631.3	,	1,119,6383	GG,GC,CC		1.1977,0.4085,0.9303	,	405/855,380/830	38807169	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	27072	exon15			CTCCACCAGGTGA	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1215G>C	7.37:g.38807169C>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	56	38	0.678571	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	37	CCDS5457.1																																																																																			C|0.993;G|0.007	0.007	strong		0.338	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
GGT5	2687	hgsc.bcm.edu	37	22	24622648	24622648	+	Missense_Mutation	SNP	T	T	C	rs2275984	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:24622648T>C	ENST00000327365.4	-	7	1405	c.989A>G	c.(988-990)aAg>aGg	p.K330R	GGT5_ENST00000398292.3_Missense_Mutation_p.K330R|GGT5_ENST00000263112.7_Missense_Mutation_p.K298R|GGT5_ENST00000418439.2_Missense_Mutation_p.K253R	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	330			K -> R (in dbSNP:rs2275984). {ECO:0000269|PubMed:10591208, ECO:0000269|PubMed:1676842}.		arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						CCTCTGCCCCTTGGCAAACTT	0.607													C|||	1547	0.308906	0.3964	0.3689	5008	,	,		15944	0.2103		0.2982	False		,,,				2504	0.2607				p.K330R		Atlas-SNP	.											.	GGT5	61	.	0			c.A989G						PASS	.	C	ARG/LYS,ARG/LYS,ARG/LYS	1599,2807	662.7+/-401.1	313,973,917	107.0	98.0	101.0		989,893,989	0.8	0.1	22	dbSNP_100	101	2558,6042	689.0+/-404.3	385,1788,2127	yes	missense,missense,missense	GGT5	NM_001099781.1,NM_001099782.1,NM_004121.2	26,26,26	698,2761,3044	CC,CT,TT		29.7442,36.2914,31.9622	benign,benign,benign	330/588,298/555,330/587	24622648	4157,8849	2203	4300	6503	SO:0001583	missense	2687	exon7			TGCCCCTTGGCAA	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"""Gamma-glutamyltransferases"""	4260	protein-coding gene	gene with protein product		137168	"""gamma-glutamyltransferase-like activity 1"""	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.989A>G	22.37:g.24622648T>C	ENSP00000330080:p.Lys330Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Missense_Mutation	SNP	ENST00000327365.4	37	CCDS13825.1	691	0.3163919413919414	193	0.39227642276422764	127	0.35082872928176795	132	0.23076923076923078	239	0.3153034300791557	C	0.010	-1.758041	0.00657	0.362914	0.297442	ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000438024;ENST00000398292;ENST00000418439	T;T;T;T	0.06449	3.3;3.3;3.3;3.3	3.13	0.813	0.18749	.	0.534866	0.19492	N	0.112976	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.001;0.0;0.001	T	0.45338	-0.9268	9	0.25751	T	0.34	-0.267	2.7621	0.05310	0.2043:0.4328:0.0:0.363	rs2275984;rs58651718;rs2275984	253;298;330;330;330	E7EUG3;P36269-2;Q53XM9;Q6GMP0;P36269	.;.;.;.;GGT5_HUMAN	R	330;298;245;330;253	ENSP00000330080:K330R;ENSP00000263112:K298R;ENSP00000381340:K330R;ENSP00000392146:K253R	ENSP00000263112:K298R	K	-	2	0	GGT5	22952648	0.000000	0.05858	0.090000	0.20809	0.262000	0.26303	0.068000	0.14531	-0.122000	0.11766	-1.209000	0.01634	AAG	T|0.687;C|0.313	0.313	strong		0.607	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121	
MUC16	94025	hgsc.bcm.edu	37	19	9074265	9074265	+	Missense_Mutation	SNP	G	G	A	rs10406209	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9074265G>A	ENST00000397910.4	-	3	13384	c.13181C>T	c.(13180-13182)aCt>aTt	p.T4394I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4396	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGCAGCTCCAGTAGGACCTGT	0.468													G|||	768	0.153355	0.1142	0.183	5008	,	,		23652	0.0089		0.2634	False		,,,				2504	0.2209				p.T4394I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C13181T						PASS	.	G	ILE/THR	502,3590		32,438,1576	145.0	141.0	142.0		13181	0.5	0.0	19	dbSNP_119	142	2429,5961		370,1689,2136	yes	missense	MUC16	NM_024690.2	89	402,2127,3712	AA,AG,GG		28.9511,12.2678,23.4818	possibly-damaging	4394/14508	9074265	2931,9551	2046	4195	6241	SO:0001583	missense	94025	exon3			GCTCCAGTAGGAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.13181C>T	19.37:g.9074265G>A	ENSP00000381008:p.Thr4394Ile	Somatic	286	1	0.0034965		WXS	Illumina HiSeq	Phase_I	358	356	0.994413	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	334	0.15293040293040294	53	0.10772357723577236	73	0.20165745856353592	5	0.008741258741258742	203	0.2678100263852243	g	3.708	-0.060188	0.07317	0.122678	0.289511	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.67	0.509	0.16977	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	P	0.46020	0.871	B	0.34346	0.18	T	0.52170	-0.8611	8	0.87932	D	0	.	5.6254	0.17480	0.0:0.3493:0.6507:0.0	rs10406209;rs17515888;rs52837265;rs59614183;rs10406209	4394	B5ME49	.	I	4394	ENSP00000381008:T4394I	ENSP00000381008:T4394I	T	-	2	0	MUC16	8935265	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	0.366000	0.20365	0.231000	0.21079	0.305000	0.20034	ACT	G|0.826;A|0.174	0.174	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NDNF	79625	hgsc.bcm.edu	37	4	121958091	121958091	+	Silent	SNP	T	T	G	rs3733558	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:121958091T>G	ENST00000379692.4	-	4	1561	c.1035A>C	c.(1033-1035)ctA>ctC	p.L345L	NDNF_ENST00000506900.1_5'Flank	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	345					cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)	p.L345L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						TCCCATCTTTTAGCTCGACTG	0.418													T|||	2149	0.429113	0.09	0.4726	5008	,	,		22470	0.6458		0.6113	False		,,,				2504	0.4458				p.L345L		Atlas-SNP	.											NDNF,NS,carcinoma,0,1	NDNF	72	1	1	Substitution - coding silent(1)	prostate(1)	c.A1035C						PASS	.	T		783,3623	315.8+/-294.3	68,647,1488	154.0	127.0	136.0		1035	-11.8	0.0	4	dbSNP_107	136	5340,3260	649.4+/-400.6	1671,1998,631	no	coding-synonymous	NDNF	NM_024574.3		1739,2645,2119	GG,GT,TT		37.907,17.7712,47.0783		345/569	121958091	6123,6883	2203	4300	6503	SO:0001819	synonymous_variant	79625	exon4			ATCTTTTAGCTCG	BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 31"""	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.1035A>C	4.37:g.121958091T>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	157	85	0.541401	NM_024574	A8K0Q0|Q6UWE5|Q9H5P7	Silent	SNP	ENST00000379692.4	37	CCDS3717.2																																																																																			T|0.535;G|0.465	0.465	strong		0.418	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574	
EPDR1	54749	hgsc.bcm.edu	37	7	37988589	37988589	+	Silent	SNP	C	C	T	rs2044831	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:37988589C>T	ENST00000199448.4	+	2	796	c.417C>T	c.(415-417)atC>atT	p.I139I	EPDR1_ENST00000423717.1_Intron|EPDR1_ENST00000476620.1_Silent_p.I37I|EPDR1_ENST00000559325.1_Silent_p.I259I|EPDR1_ENST00000425345.1_Silent_p.I78I	NM_017549.4	NP_060019.2	Q9UM22	EPDR1_HUMAN	ependymin related 1	139					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	22						AGTACTCCATCGGGGGGCCTC	0.512													C|||	3300	0.658946	0.5098	0.7493	5008	,	,		16813	0.5933		0.7813	False		,,,				2504	0.7382				p.I139I		Atlas-SNP	.											EPDR1,caecum,carcinoma,0,1	EPDR1	48	1	0			c.C417T						PASS	.	C		2486,1920	625.9+/-394.6	710,1066,427	92.0	90.0	91.0		777	-4.3	1.0	7	dbSNP_94	91	6606,1994	722.8+/-406.4	2540,1526,234	no	coding-synonymous	EPDR1	NM_017549.4		3250,2592,661	TT,TC,CC		23.186,43.5769,30.0938		259/345	37988589	9092,3914	2203	4300	6503	SO:0001819	synonymous_variant	54749	exon2			CTCCATCGGGGGG	BC018299	CCDS5454.1, CCDS5454.2, CCDS59051.1, CCDS59052.1	7p14.1	2013-07-31	2013-07-31		ENSG00000086289	ENSG00000086289			17572	protein-coding gene	gene with protein product			"""ependymin related protein 1 (zebrafish)"""			11749721, 11248421	Standard	NM_001242946		Approved	MERP-1, MERP1, UCC1, EPDR	uc003tfp.4	Q9UM22	OTTHUMG00000102187	ENST00000199448.4:c.417C>T	7.37:g.37988589C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_017549	A8K4C0|C9JYS3|Q06BL0|Q99M77	Silent	SNP	ENST00000199448.4	37	CCDS5454.2																																																																																			C|0.322;T|0.678	0.678	strong		0.512	EPDR1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220037.3	NM_017549	
PRDM2	7799	hgsc.bcm.edu	37	1	14108988	14108988	+	Silent	SNP	A	A	G	rs61747665	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:14108988A>G	ENST00000235372.7	+	8	5554	c.4698A>G	c.(4696-4698)aaA>aaG	p.K1566K	PRDM2_ENST00000343137.4_Silent_p.K1365K|PRDM2_ENST00000311066.5_Silent_p.K1566K|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Silent_p.K1365K	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1566					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TGAAATCCAAAAAACCAAGCT	0.498													A|||	160	0.0319489	0.0015	0.0	5008	,	,		18389	0.0218		0.0169	False		,,,				2504	0.1217				p.K1566K		Atlas-SNP	.											.	PRDM2	147	.	0			c.A4698G						PASS	.	A	,,,	12,4394	17.9+/-39.9	0,12,2191	62.0	67.0	65.0		4095,,4698,4698	-0.9	0.9	1	dbSNP_129	65	174,8426	77.5+/-140.1	2,170,4128	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	,,,	2,182,6319	GG,GA,AA		2.0233,0.2724,1.4301	,,,	1365/1482,,1566/1719,1566/1683	14108988	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	7799	exon8			ATCCAAAAAACCA	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.4698A>G	1.37:g.14108988A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Silent	SNP	ENST00000235372.7	37	CCDS150.1																																																																																			A|0.983;G|0.017	0.017	strong		0.498	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
RNASE6	6039	hgsc.bcm.edu	37	14	21250124	21250124	+	Missense_Mutation	SNP	G	G	A	rs1045922	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:21250124G>A	ENST00000304677.2	+	2	559	c.266G>A	c.(265-267)cGg>cAg	p.R89Q	RP11-219E7.1_ENST00000556624.1_RNA	NM_005615.4	NP_005606.1	Q93091	RNAS6_HUMAN	ribonuclease, RNase A family, k6	89			R -> Q (in dbSNP:rs1045922).		defense response (GO:0006952)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			large_intestine(1)	1	all_cancers(95;0.00406)		Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)		AAAAATCGTCGGCACAACTGC	0.488													G|||	1527	0.304912	0.1089	0.2983	5008	,	,		19883	0.4286		0.2485	False		,,,				2504	0.5051				p.R89Q		Atlas-SNP	.											.	RNASE6	7	.	0			c.G266A						PASS	.	G	GLN/ARG	586,3820	260.4+/-263.7	36,514,1653	150.0	143.0	145.0		266	-9.9	0.0	14	dbSNP_86	145	2145,6455	367.9+/-334.9	266,1613,2421	yes	missense	RNASE6	NM_005615.4	43	302,2127,4074	AA,AG,GG		24.9419,13.3,20.998	benign	89/151	21250124	2731,10275	2203	4300	6503	SO:0001583	missense	6039	exon2			ATCGTCGGCACAA	U64998	CCDS9558.1	14q11	2008-07-09			ENSG00000169413	ENSG00000169413		"""Ribonucleases, RNase A"""	10048	protein-coding gene	gene with protein product	"""RNase k6"""	601981		RNS6		8836175, 9647635	Standard	NM_005615		Approved		uc001vye.4	Q93091	OTTHUMG00000029585	ENST00000304677.2:c.266G>A	14.37:g.21250124G>A	ENSP00000302046:p.Arg89Gln	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	270	138	0.511111	NM_005615		Missense_Mutation	SNP	ENST00000304677.2	37	CCDS9558.1	560	0.2564102564102564	52	0.10569105691056911	99	0.27348066298342544	228	0.3986013986013986	181	0.23878627968337732	G	2.735	-0.263495	0.05754	0.133	0.249419	ENSG00000169413	ENST00000304677	T	0.72505	-0.66	4.97	-9.94	0.00449	Ribonuclease A, domain (4);	1.849040	0.02663	N	0.107763	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.15141	0.012	B	0.08055	0.003	T	0.19582	-1.0301	9	0.12103	T	0.63	1.7176	14.2487	0.66004	0.1507:0.0:0.6666:0.1826	rs1045922;rs3168885;rs57753708;rs1045922	89	Q93091	RNAS6_HUMAN	Q	89	ENSP00000302046:R89Q	ENSP00000302046:R89Q	R	+	2	0	RNASE6	20319964	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.580000	0.00907	-3.814000	0.00103	-2.909000	0.00091	CGG	G|0.764;A|0.236	0.236	strong		0.488	RNASE6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073750.2		
HIST1H2AB	8335	hgsc.bcm.edu	37	6	26033506	26033506	+	Silent	SNP	G	G	A	rs2230655	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:26033506G>A	ENST00000259791.2	-	1	290	c.291C>T	c.(289-291)ctC>ctT	p.L97L	HIST1H3B_ENST00000244661.2_5'Flank	NM_003513.2	NP_003504.2	P04908	H2A1B_HUMAN	histone cluster 1, H2ab	97						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						CACGCCCCAAGAGTTTATTAA	0.567													A|||	3916	0.781949	0.9448	0.7219	5008	,	,		18656	0.8601		0.672	False		,,,				2504	0.637				p.L97L		Atlas-SNP	.											.	HIST1H2AB	18	.	0			c.C291T						PASS	.	A		3983,423	787.4+/-414.9	1805,373,25	74.0	77.0	76.0		291	1.5	1.0	6	dbSNP_98	76	5925,2675	684.6+/-404.0	2054,1817,429	no	coding-synonymous	HIST1H2AB	NM_003513.2		3859,2190,454	AA,AG,GG		31.1047,9.6005,23.8198		97/131	26033506	9908,3098	2203	4300	6503	SO:0001819	synonymous_variant	8335	exon1			CCCCAAGAGTTTA	X00089	CCDS4574.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000137259	ENSG00000278463		"""Histones / Replication-dependent"""	4734	protein-coding gene	gene with protein product		602795	"""H2A histone family, member M"", ""histone 1, H2ab"""	H2AFM		9439656, 9119399, 12408966	Standard	NM_003513		Approved	H2A/m	uc003nft.1	P04908	OTTHUMG00000014420	ENST00000259791.2:c.291C>T	6.37:g.26033506G>A		Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_003513	P28001|Q76P63	Silent	SNP	ENST00000259791.2	37	CCDS4574.1																																																																																			G|0.222;A|0.778	0.778	strong		0.567	HIST1H2AB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040082.1	NM_003513	
LBH	81606	hgsc.bcm.edu	37	2	30480466	30480466	+	Silent	SNP	G	G	A	rs372905950		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:30480466G>A	ENST00000395323.3	+	3	505	c.297G>A	c.(295-297)gcG>gcA	p.A99A	LBH_ENST00000404397.1_Intron|LBH_ENST00000401506.1_Silent_p.A105A|LBH_ENST00000467242.1_3'UTR|LBH_ENST00000407930.2_Silent_p.A82A|LBH_ENST00000406087.1_3'UTR	NM_030915.3	NP_112177.2	Q53QV2	LBH_HUMAN	limb bud and heart development	99					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(172;0.155)					AAGAGACAGCGAAAGAAAATA	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		16752	0.0		0.0	False		,,,				2504	0.001				p.A99A		Atlas-SNP	.											.	LBH	14	.	0			c.G297A						PASS	.	G		0,4406		0,0,2203	43.0	45.0	44.0		297	2.0	0.1	2		44	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LBH	NM_030915.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		99/106	30480466	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	81606	exon3			GACAGCGAAAGAA	AF110224	CCDS33173.1	2p23.1	2012-12-07	2012-12-07		ENSG00000213626	ENSG00000213626			29532	protein-coding gene	gene with protein product		611763	"""limb bud and heart development homolog (mouse)"""			11230166, 11336496	Standard	NM_030915		Approved		uc002rne.2	Q53QV2	OTTHUMG00000152051	ENST00000395323.3:c.297G>A	2.37:g.30480466G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_030915	B2RBC2|Q9H0Q1	Silent	SNP	ENST00000395323.3	37	CCDS33173.1																																																																																			.	.	weak		0.542	LBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325091.1	NM_030915	
IRS4	8471	hgsc.bcm.edu	37	X	107979437	107979437	+	Silent	SNP	G	G	A	rs73253702	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:107979437G>A	ENST00000372129.2	-	1	214	c.138C>T	c.(136-138)acC>acT	p.T46T	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	46					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						AAGACGACCCGGTCCCAATGA	0.657													g|||	188	0.0498013	0.0514	0.0576	3775	,	,		8094	0.002		0.0408	False		,,,				2504	0.0378				p.T46T		Atlas-SNP	.											.	IRS4	253	.	0			c.C138T						PASS	.			269,3555		10,211,38,1409,526	24.0	26.0	25.0		138	1.1	1.0	X	dbSNP_130	25	386,6312		9,251,117,2164,1733	no	coding-synonymous	IRS4	NM_003604.2		19,462,155,3573,2259	AA,AG,A,GG,G		5.7629,7.0345,6.2251		46/1258	107979437	655,9867	2194	4274	6468	SO:0001819	synonymous_variant	8471	exon1			CGACCCGGTCCCA	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.138C>T	X.37:g.107979437G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	100	92	0.92	NM_003604		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																			G|0.942;A|0.058	0.058	strong		0.657	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
INPP4B	8821	hgsc.bcm.edu	37	4	143033778	143033778	+	Silent	SNP	T	T	C	rs3822141	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:143033778T>C	ENST00000513000.1	-	23	2626	c.2193A>G	c.(2191-2193)ctA>ctG	p.L731L	INPP4B_ENST00000262992.4_Silent_p.L731L|INPP4B_ENST00000308502.4_Silent_p.L731L|INPP4B_ENST00000509777.1_Silent_p.L731L|INPP4B_ENST00000508116.1_Silent_p.L731L	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	731					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CTTTAATCTGTAGAGGTAGTG	0.398													T|||	375	0.0748802	0.003	0.0865	5008	,	,		17717	0.0764		0.0636	False		,,,				2504	0.1738				p.L731L		Atlas-SNP	.											.	INPP4B	132	.	0			c.A2193G						PASS	.	T	,	64,4342	60.5+/-97.4	0,64,2139	171.0	166.0	167.0		2193,2193	-11.4	0.0	4	dbSNP_107	167	643,7957	164.8+/-217.1	20,603,3677	no	coding-synonymous,coding-synonymous	INPP4B	NM_001101669.1,NM_003866.2	,	20,667,5816	CC,CT,TT		7.4767,1.4526,5.436	,	731/925,731/925	143033778	707,12299	2203	4300	6503	SO:0001819	synonymous_variant	8821	exon23			AATCTGTAGAGGT	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.2193A>G	4.37:g.143033778T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	157	82	0.522293	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			C|0.057;T|0.943	0.057	strong		0.398	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	
ESYT3	83850	hgsc.bcm.edu	37	3	138191232	138191232	+	Missense_Mutation	SNP	G	G	A	rs10935282	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:138191232G>A	ENST00000389567.4	+	18	1954	c.1768G>A	c.(1768-1770)Ggg>Agg	p.G590R		NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	590			G -> R (in dbSNP:rs10935282).		lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|organelle membrane contact site (GO:0044232)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	25						ACGAGAGCTGGGGAGCCCATA	0.542													G|||	1893	0.377995	0.0514	0.5447	5008	,	,		17433	0.5347		0.4374	False		,,,				2504	0.4785				p.G590R		Atlas-SNP	.											.	ESYT3	64	.	0			c.G1768A						PASS	.	G	ARG/GLY	430,3538		27,376,1581	103.0	107.0	106.0		1768	4.4	1.0	3	dbSNP_120	106	3713,4613		856,2001,1306	yes	missense	ESYT3	NM_031913.3	125	883,2377,2887	AA,AG,GG		44.5952,10.8367,33.6994	possibly-damaging	590/887	138191232	4143,8151	1984	4163	6147	SO:0001583	missense	83850	exon18			GAGCTGGGGAGCC	AJ303366	CCDS3101.2	3q22.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000158220	ENSG00000158220		"""Synaptotagmins"""	24295	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member C"""	FAM62C		11543631, 17672888	Standard	NM_031913		Approved	CHR3SYT	uc003esk.3	A0FGR9	OTTHUMG00000147354	ENST00000389567.4:c.1768G>A	3.37:g.138191232G>A	ENSP00000374218:p.Gly590Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Missense_Mutation	SNP	ENST00000389567.4	37	CCDS3101.2	851	0.38965201465201466	34	0.06910569105691057	160	0.4419889502762431	326	0.5699300699300699	331	0.4366754617414248	G	10.11	1.261640	0.23051	0.108367	0.445952	ENSG00000158220	ENST00000389567	T	0.70749	-0.51	4.45	4.45	0.53987	C2 calcium/lipid-binding domain, CaLB (1);	0.369897	0.21839	N	0.068343	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	1.0	B	0.28636	0.218	B	0.21546	0.035	T	0.42120	-0.9470	9	0.15499	T	0.54	-2.9836	14.6169	0.68556	0.0:0.0:1.0:0.0	rs10935282;rs58020269;rs10935282	590	A0FGR9	ESYT3_HUMAN	R	590	ENSP00000374218:G590R	ENSP00000374218:G590R	G	+	1	0	ESYT3	139673922	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.950000	0.40323	2.304000	0.77564	0.462000	0.41574	GGG	G|0.622;A|0.378	0.378	strong		0.542	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913	
TBC1D15	64786	hgsc.bcm.edu	37	12	72307637	72307637	+	Silent	SNP	C	C	G	rs11178983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:72307637C>G	ENST00000550746.1	+	13	1447	c.1383C>G	c.(1381-1383)tcC>tcG	p.S461S	TBC1D15_ENST00000393309.3_Silent_p.S215S|TBC1D15_ENST00000319106.8_Silent_p.S452S|TBC1D15_ENST00000485960.2_Silent_p.S444S|TBC1D15_ENST00000548679.1_3'UTR	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	461	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ATTTACTTTCCCCTCTTTTAT	0.353													C|||	315	0.0628994	0.003	0.0346	5008	,	,		16596	0.0734		0.0606	False		,,,				2504	0.1554				p.S461S		Atlas-SNP	.											.	TBC1D15	99	.	0			c.C1383G						PASS	.	C	,,	81,4325	67.6+/-105.2	0,81,2122	131.0	136.0	134.0		1332,1356,1383	-6.5	0.6	12	dbSNP_120	134	661,7939	166.5+/-218.5	26,609,3665	no	coding-synonymous,coding-synonymous,coding-synonymous	TBC1D15	NM_001146213.1,NM_001146214.1,NM_022771.4	,,	26,690,5787	GG,GC,CC		7.686,1.8384,5.7051	,,	444/675,452/683,461/692	72307637	742,12264	2203	4300	6503	SO:0001819	synonymous_variant	64786	exon13			ACTTTCCCCTCTT	AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.1383C>G	12.37:g.72307637C>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_022771	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Silent	SNP	ENST00000550746.1	37	CCDS31858.1																																																																																			C|0.947;G|0.053	0.053	strong		0.353	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771	
AHSP	51327	hgsc.bcm.edu	37	16	31539934	31539934	+	Silent	SNP	G	G	T	rs17677	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31539934G>T	ENST00000302312.4	+	3	334	c.231G>T	c.(229-231)ctG>ctT	p.L77L	AHSP_ENST00000569954.1_3'UTR	NM_016633.2	NP_057717.1	Q9NZD4	AHSP_HUMAN	alpha hemoglobin stabilizing protein	77					hemoglobin metabolic process (GO:0020027)|hemopoiesis (GO:0030097)|protein folding (GO:0006457)|protein stabilization (GO:0050821)	hemoglobin complex (GO:0005833)	hemoglobin binding (GO:0030492)|unfolded protein binding (GO:0051082)			lung(2)	2						TGAACACTCTGGCCAACCCTT	0.587													G|||	1590	0.317492	0.4667	0.1311	5008	,	,		18109	0.2222		0.1541	False		,,,				2504	0.5143				p.L77L		Atlas-SNP	.											.	AHSP	10	.	0			c.G231T						PASS	.	G		1786,2608	525.5+/-371.6	374,1038,785	63.0	57.0	59.0		231	1.0	0.0	16	dbSNP_63	59	1411,7189	270.7+/-289.1	121,1169,3010	no	coding-synonymous	AHSP	NM_016633.2		495,2207,3795	TT,TG,GG		16.407,40.6463,24.6037		77/103	31539934	3197,9797	2197	4300	6497	SO:0001819	synonymous_variant	51327	exon3			CACTCTGGCCAAC	AF208865	CCDS10716.1	16p11.1	2009-10-07	2009-10-07	2009-10-07	ENSG00000169877	ENSG00000169877			18075	protein-coding gene	gene with protein product	"""alpha hemoglobin stabilising protein"""	605821	"""erythroid associated factor"""	ERAF		11231637, 12066189	Standard	XM_005255352		Approved	EDRF	uc002ecj.3	Q9NZD4	OTTHUMG00000132461	ENST00000302312.4:c.231G>T	16.37:g.31539934G>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_016633	Q8TD01	Silent	SNP	ENST00000302312.4	37	CCDS10716.1																																																																																			G|0.755;T|0.245	0.245	strong		0.587	AHSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255624.1	NM_016633	
FAM118A	55007	hgsc.bcm.edu	37	22	45728370	45728370	+	Missense_Mutation	SNP	G	G	A	rs6007594	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:45728370G>A	ENST00000216214.3	+	7	1550	c.716G>A	c.(715-717)cGt>cAt	p.R239H	FAM118A_ENST00000441876.2_Missense_Mutation_p.R239H|FAM118A_ENST00000405548.3_Missense_Mutation_p.R57H	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	239			R -> H (in dbSNP:rs6007594). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)		p.R239H(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		GAGACCCTTCGTGATCAGATA	0.458													G|||	2632	0.525559	0.8411	0.3905	5008	,	,		20074	0.5218		0.2724	False		,,,				2504	0.4591				p.R239H		Atlas-SNP	.											FAM118A,NS,carcinoma,0,1	FAM118A	32	1	1	Substitution - Missense(1)	stomach(1)	c.G716A						PASS	.	G	HIS/ARG,HIS/ARG	3274,1132	714.4+/-408.4	1225,824,154	129.0	138.0	135.0		716,716	5.8	0.2	22	dbSNP_114	135	2331,6269	391.1+/-343.5	318,1695,2287	yes	missense,missense	FAM118A	NM_001104595.1,NM_017911.2	29,29	1543,2519,2441	AA,AG,GG		27.1047,25.6922,43.0955	probably-damaging,probably-damaging	239/358,239/358	45728370	5605,7401	2203	4300	6503	SO:0001583	missense	55007	exon6			CCCTTCGTGATCA	BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 8"""	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.716G>A	22.37:g.45728370G>A	ENSP00000216214:p.Arg239His	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	216	95	0.439815	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Missense_Mutation	SNP	ENST00000216214.3	37	CCDS14065.1	1048	0.47985347985347987	406	0.8252032520325203	149	0.4116022099447514	295	0.5157342657342657	198	0.2612137203166227	G	20.4	3.981425	0.74474	0.743078	0.271047	ENSG00000100376	ENST00000216214;ENST00000441876;ENST00000405548	T;T;T	0.29142	1.58;1.58;1.58	5.8	5.8	0.92144	.	0.132445	0.52532	D	0.000067	T	0.00012	0.0000	N	0.25647	0.755	0.24306	P	0.99510402	D	0.76494	0.999	D	0.65323	0.934	T	0.02852	-1.1102	9	0.46703	T	0.11	-4.8413	12.9483	0.58386	0.0748:0.0:0.9252:0.0	rs6007594;rs6519925;rs17845391;rs17858248;rs52828151;rs60885839;rs6007594	239	Q9NWS6	F118A_HUMAN	H	239;239;57	ENSP00000216214:R239H;ENSP00000395892:R239H;ENSP00000384836:R57H	ENSP00000216214:R239H	R	+	2	0	FAM118A	44107034	1.000000	0.71417	0.243000	0.24186	0.953000	0.61014	5.769000	0.68865	2.743000	0.94032	0.655000	0.94253	CGT	G|0.536;A|0.464	0.464	strong		0.458	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
POLE	5426	hgsc.bcm.edu	37	12	133212582	133212582	+	Silent	SNP	G	G	A	rs5744990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133212582G>A	ENST00000320574.5	-	42	5750	c.5707C>T	c.(5707-5709)Ctg>Ttg	p.L1903L	POLE_ENST00000434528.3_5'UTR|POLE_ENST00000535270.1_Silent_p.L1876L	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1903					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GAAATTGTCAGAGAATGGAAG	0.428								DNA polymerases (catalytic subunits)					A|||	671	0.133986	0.1301	0.2205	5008	,	,		23097	0.1141		0.1382	False		,,,				2504	0.0941				p.L1903L		Atlas-SNP	.											.	POLE	416	.	0			c.C5707T						PASS	.	A		641,3765	766.9+/-413.5	43,555,1605	99.0	91.0	94.0		5707	0.2	0.8	12	dbSNP_114	94	1377,7223	754.4+/-407.5	112,1153,3035	no	coding-synonymous	POLE	NM_006231.2		155,1708,4640	AA,AG,GG		16.0116,14.5483,15.5159		1903/2287	133212582	2018,10988	2203	4300	6503	SO:0001819	synonymous_variant	5426	exon42			TTGTCAGAGAATG		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.5707C>T	12.37:g.133212582G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			G|0.862;A|0.138	0.138	strong		0.428	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
COL4A6	1288	hgsc.bcm.edu	37	X	107417730	107417730	+	Silent	SNP	G	G	A	rs5973851	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:107417730G>A	ENST00000372216.4	-	31	3181	c.3081C>T	c.(3079-3081)ggC>ggT	p.G1027G	COL4A6_ENST00000334504.7_Silent_p.G1026G|COL4A6_ENST00000394872.2_Silent_p.G1027G|COL4A6_ENST00000545689.1_Silent_p.G1026G|COL4A6_ENST00000538570.1_Silent_p.G1026G	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	1027	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						GGCCAGGTAAGCCCCGGATTC	0.557									Alport syndrome with Diffuse Leiomyomatosis				G|||	1533	0.406093	0.2231	0.3934	3775	,	,		12961	0.4812		0.175	False		,,,				2504	0.3108				p.G1027G	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.C3081T						PASS	.	G	,	1065,2770		113,675,164,844,407	53.0	53.0	53.0		3081,3078	-2.2	0.6	X	dbSNP_114	53	1392,5336		114,772,392,1542,1480	no	coding-synonymous,coding-synonymous	COL4A6	NM_001847.2,NM_033641.2	,	227,1447,556,2386,1887	AA,AG,A,GG,G		20.6897,27.7705,23.2604	,	1027/1692,1026/1691	107417730	2457,8106	2203	4300	6503	SO:0001819	synonymous_variant	1288	exon31	Familial Cancer Database		AGGTAAGCCCCGG	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"""Collagens"""	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.3081C>T	X.37:g.107417730G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	77	72	0.935065	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Silent	SNP	ENST00000372216.4	37	CCDS14541.1																																																																																			G|0.712;A|0.288	0.288	strong		0.557	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2		
DYSF	8291	hgsc.bcm.edu	37	2	71747923	71747923	+	Silent	SNP	C	C	T	rs36122356	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:71747923C>T	ENST00000258104.3	+	11	1219	c.942C>T	c.(940-942)caC>caT	p.H314H	DYSF_ENST00000409582.3_Silent_p.H345H|DYSF_ENST00000429174.2_Silent_p.H314H|DYSF_ENST00000409762.1_Silent_p.H345H|DYSF_ENST00000409366.1_Silent_p.H315H|DYSF_ENST00000409651.1_Silent_p.H346H|DYSF_ENST00000410020.3_Silent_p.H346H|DYSF_ENST00000410041.1_Silent_p.H346H|DYSF_ENST00000394120.2_Silent_p.H315H|DYSF_ENST00000413539.2_Silent_p.H345H|DYSF_ENST00000409744.1_Silent_p.H315H	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	314					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TCTTAGGGCACGCCTATCTCA	0.582													C|||	421	0.0840655	0.1233	0.0274	5008	,	,		15660	0.0833		0.0547	False		,,,				2504	0.1022				p.H346H		Atlas-SNP	.											.	DYSF	536	.	0			c.C1038T						PASS	.	C	,,,,,,,,,,,,,	395,4011	197.1+/-221.3	16,363,1824	94.0	91.0	92.0		945,942,942,942,1035,1035,1035,1038,945,945,1038,945,1038,942	-10.5	0.2	2	dbSNP_126	92	477,8123	140.9+/-197.4	15,447,3838	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	31,810,5662	TT,TC,CC		5.5465,8.965,6.7046	,,,,,,,,,,,,,	315/2082,314/2067,314/2088,314/2102,345/2112,345/2098,345/2119,346/2113,315/2103,315/2089,346/2099,315/2068,346/2120,314/2081	71747923	872,12134	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon12			AGGGCACGCCTAT	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.942C>T	2.37:g.71747923C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	189	72	0.380952	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			C|0.930;T|0.070	0.070	strong		0.582	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
OR9Q2	219957	hgsc.bcm.edu	37	11	57958775	57958775	+	Silent	SNP	C	C	T	rs7120468	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57958775C>T	ENST00000311591.3	+	1	870	c.813C>T	c.(811-813)gaC>gaT	p.D271D		NM_001005283.2	NP_001005283.1	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q, member 2	271						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D271D(1)		breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(3)|lung(24)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41		Breast(21;0.0589)				CCGAGGGAGACCGAGTGGTGT	0.557													C|||	2123	0.423922	0.2209	0.3847	5008	,	,		19568	0.752		0.3082	False		,,,				2504	0.5072				p.D271D		Atlas-SNP	.											OR9Q2,NS,carcinoma,0,1	OR9Q2	78	1	1	Substitution - coding silent(1)	stomach(1)	c.C813T						PASS	.	C		1068,3334	390.0+/-327.5	126,816,1259	102.0	94.0	97.0		813	3.1	0.4	11	dbSNP_116	97	2749,5843	437.8+/-358.7	458,1833,2005	no	coding-synonymous	OR9Q2	NM_001005283.2		584,2649,3264	TT,TC,CC		31.9949,24.2617,29.3751		271/315	57958775	3817,9177	2201	4296	6497	SO:0001819	synonymous_variant	219957	exon1			GGGAGACCGAGTG	AB065859	CCDS31544.1	11q12.1	2012-08-09		2004-03-10	ENSG00000186513	ENSG00000186513		"""GPCR / Class A : Olfactory receptors"""	15328	protein-coding gene	gene with protein product				OR9Q2P			Standard	NM_001005283		Approved		uc010rka.2	Q8NGE9	OTTHUMG00000167414	ENST00000311591.3:c.813C>T	11.37:g.57958775C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	135	81	0.6	NM_001005283		Silent	SNP	ENST00000311591.3	37	CCDS31544.1																																																																																			C|0.651;T|0.349	0.349	strong		0.557	OR9Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394540.1	NM_001005283	
DDC	1644	hgsc.bcm.edu	37	7	50611751	50611751	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:50611751C>T	ENST00000444124.2	-	2	233	c.33G>A	c.(31-33)aaG>aaA	p.K11K	DDC_ENST00000380984.4_Silent_p.K11K|DDC_ENST00000357936.5_Silent_p.K11K|DDC_ENST00000431062.1_Silent_p.K11K|DDC_ENST00000426377.1_Silent_p.K11K|AC018705.5_ENST00000454521.1_RNA	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	11					catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021)	amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1)	40	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968)	CCACCATCTCCTTCCCTCTCC	0.537																																					p.K11K		Atlas-SNP	.											.	DDC	100	.	0			c.G33A						PASS	.						247.0	190.0	209.0					7																	50611751		2203	4300	6503	SO:0001819	synonymous_variant	1644	exon2			CATCTCCTTCCCT		CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1	7p12.1	2012-08-30			ENSG00000132437	ENSG00000132437	4.1.1.28		2719	protein-coding gene	gene with protein product		107930				1612608	Standard	NM_001082971		Approved	AADC	uc003tpf.4	P20711	OTTHUMG00000023353	ENST00000444124.2:c.33G>A	7.37:g.50611751C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	192	95	0.494792	NM_001082971	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Silent	SNP	ENST00000444124.2	37	CCDS5511.1																																																																																			.	.	none		0.537	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1		
ZNF667	63934	hgsc.bcm.edu	37	19	56954103	56954103	+	Silent	SNP	C	C	A	rs7253217	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56954103C>A	ENST00000504904.3	-	7	980	c.261G>T	c.(259-261)ggG>ggT	p.G87G	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Silent_p.G215G|ZNF667_ENST00000292069.6_Silent_p.G87G			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	87					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		CACATTTAGACCCCGAGTCTG	0.348													C|||	810	0.161741	0.1483	0.1873	5008	,	,		17863	0.0754		0.2406	False		,,,				2504	0.1697				p.G87G		Atlas-SNP	.											.	ZNF667	95	.	0			c.G261T						PASS	.	C		629,3655		54,521,1567	44.0	48.0	46.0		261	1.0	0.5	19	dbSNP_116	46	1560,6690		146,1268,2711	no	coding-synonymous	ZNF667	NM_022103.3		200,1789,4278	AA,AC,CC		18.9091,14.6825,17.4645		87/611	56954103	2189,10345	2142	4125	6267	SO:0001819	synonymous_variant	63934	exon5			TTTAGACCCCGAG		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.261G>T	19.37:g.56954103C>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	36	16	0.444444	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Silent	SNP	ENST00000504904.3	37	CCDS12944.1																																																																																			C|0.825;A|0.175	0.175	strong		0.348	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
OR4N2	390429	hgsc.bcm.edu	37	14	20295763	20295763	+	Silent	SNP	C	C	T	rs11621854	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20295763C>T	ENST00000315947.1	+	1	156	c.156C>T	c.(154-156)gaC>gaT	p.D52D	OR4N2_ENST00000568211.1_Silent_p.D52D	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TAAAGTCAGACCCTGGGCTCA	0.463																																					p.D52D		Atlas-SNP	.											.	OR4N2	125	.	0			c.C156T						PASS	.	C		1466,2940		210,1046,947	182.0	219.0	206.0		156	-0.9	0.9	14	dbSNP_120	206	1721,6879		148,1425,2727	no	coding-synonymous	OR4N2	NM_001004723.1		358,2471,3674	TT,TC,CC		20.0116,33.2728,24.5041		52/308	20295763	3187,9819	2203	4300	6503	SO:0001819	synonymous_variant	390429	exon1			GTCAGACCCTGGG		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.156C>T	14.37:g.20295763C>T		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	212	208	0.981132	NM_001004723	Q6IEY9|Q6IFA2	Silent	SNP	ENST00000315947.1	37	CCDS32022.1																																																																																			C|0.764;T|0.236	0.236	strong		0.463	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
UGCG	7357	hgsc.bcm.edu	37	9	114688677	114688677	+	Silent	SNP	G	G	A	rs17853855	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:114688677G>A	ENST00000374279.3	+	5	909	c.459G>A	c.(457-459)acG>acA	p.T153T	UGCG_ENST00000495085.1_3'UTR	NM_003358.1	NP_003349.1	Q16739	CEGT_HUMAN	UDP-glucose ceramide glucosyltransferase	153					epidermis development (GO:0008544)|glucosylceramide biosynthetic process (GO:0006679)|glycosphingolipid biosynthetic process (GO:0006688)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ceramide glucosyltransferase activity (GO:0008120)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	12				OV - Ovarian serous cystadenocarcinoma(323;0.0433)	Miglustat(DB00419)	TTCCAGATACGCTTACTGACA	0.388													G|||	67	0.0133786	0.0008	0.0144	5008	,	,		17303	0.001		0.0338	False		,,,				2504	0.0215				p.T153T		Atlas-SNP	.											.	UGCG	32	.	0			c.G459A						PASS	.	G		32,4374	37.6+/-69.7	0,32,2171	105.0	107.0	106.0		459	-3.5	1.0	9	dbSNP_123	106	240,8360	96.6+/-158.3	3,234,4063	no	coding-synonymous	UGCG	NM_003358.1		3,266,6234	AA,AG,GG		2.7907,0.7263,2.0913		153/395	114688677	272,12734	2203	4300	6503	SO:0001819	synonymous_variant	7357	exon5			AGATACGCTTACT	D50840	CCDS6782.1	9q31	2014-03-13			ENSG00000148154	ENSG00000148154	2.4.1.80	"""Glycosyltransferase family 2 domain containing"""	12524	protein-coding gene	gene with protein product	"""glucosylceramide synthase"", ""ceramide glucosyltransferase"""	602874				8643456, 9605861	Standard	NM_003358		Approved	GCS	uc004bft.3	Q16739	OTTHUMG00000020498	ENST00000374279.3:c.459G>A	9.37:g.114688677G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_003358	Q5T258	Silent	SNP	ENST00000374279.3	37	CCDS6782.1																																																																																			G|0.980;A|0.020	0.020	strong		0.388	UGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053661.1	NM_003358	
ZNF443	10224	hgsc.bcm.edu	37	19	12541543	12541543	+	Silent	SNP	A	A	G	rs74181783|rs79866505|rs386806904	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12541543A>G	ENST00000301547.5	-	4	1640	c.1443T>C	c.(1441-1443)ctT>ctC	p.L481L	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	481					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						AGGCTTTCCCAAGTTTGCATT	0.403													.|||	228	0.0455272	0.0431	0.0331	5008	,	,		20895	0.0		0.0497	False		,,,				2504	0.1002				p.L481L		Atlas-SNP	.											.	ZNF443	63	.	0			c.T1443C						PASS	.						64.0	69.0	67.0					19																	12541543		2201	4300	6501	SO:0001819	synonymous_variant	10224	exon4			TTTCCCAAGTTTG	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1443T>C	19.37:g.12541543A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_005815		Silent	SNP	ENST00000301547.5	37	CCDS32918.1																																																																																			A|0.948;G|0.052	0.052	strong		0.403	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
CASC5	57082	hgsc.bcm.edu	37	15	40913840	40913840	+	Missense_Mutation	SNP	G	G	T	rs2412541	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:40913840G>T	ENST00000346991.5	+	11	1846	c.1456G>T	c.(1456-1458)Gct>Tct	p.A486S	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Missense_Mutation_p.A460S			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	486	Interaction with BUB1 and BUB1B.		A -> S (in dbSNP:rs2412541). {ECO:0000269|PubMed:10980622, ECO:0000269|PubMed:12087463}.		acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		CAGTAATTATGCTAAAATGTA	0.363													T|||	3275	0.653954	0.7322	0.6124	5008	,	,		20367	0.3532		0.8559	False		,,,				2504	0.68				p.A486S		Atlas-SNP	.											CASC5_ENST00000346991,NS,carcinoma,-1,2	CASC5	269	2	0			c.G1456T						PASS	.	T	SER/ALA,SER/ALA	2830,832		1092,646,93	53.0	51.0	52.0		1378,1456	1.7	1.0	15	dbSNP_100	52	6881,1275		2909,1063,106	yes	missense,missense	CASC5	NM_144508.3,NM_170589.3	99,99	4001,1709,199	TT,TG,GG		15.6327,22.7198,17.8287	benign,benign	460/2317,486/2343	40913840	9711,2107	1831	4078	5909	SO:0001583	missense	57082	exon11			AATTATGCTAAAA	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1456G>T	15.37:g.40913840G>T	ENSP00000335463:p.Ala486Ser	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	1439	0.6588827838827839	364	0.7398373983739838	238	0.6574585635359116	183	0.31993006993006995	654	0.862796833773087	T	0.022	-1.417364	0.01136	0.772802	0.843673	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.04156	3.69;3.69	5.54	1.67	0.24075	.	0.264280	0.27554	N	0.018846	T	0.00012	0.0000	N	0.00142	-2.005	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.18840	-1.0324	9	0.02654	T	1	.	2.379	0.04349	0.1824:0.1456:0.4311:0.241	rs2412541;rs52823255;rs58521194;rs2412541	460;486;460	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	S	486;460;460	ENSP00000335463:A486S;ENSP00000382576:A460S	ENSP00000260369:A460S	A	+	1	0	CASC5	38701132	0.001000	0.12720	0.981000	0.43875	0.622000	0.37654	-0.054000	0.11826	0.373000	0.24621	-0.539000	0.04255	GCT	G|0.315;N|0.000	.	strong		0.363	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
PRTG	283659	hgsc.bcm.edu	37	15	55912875	55912875	+	Missense_Mutation	SNP	T	T	A	rs1438914	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55912875T>A	ENST00000389286.4	-	19	3231	c.3184A>T	c.(3184-3186)Ata>Tta	p.I1062L		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		TCAACTTGTATCTTCTTTGAG	0.313													T|||	183	0.0365415	0.0023	0.0519	5008	,	,		17191	0.0		0.1093	False		,,,				2504	0.0348				p.I1062L		Atlas-SNP	.											.	PRTG	110	.	0			c.A3184T						PASS	.	T	LEU/ILE	93,3503		0,93,1705	58.0	57.0	57.0		3184	0.3	0.2	15	dbSNP_88	57	845,7261		36,773,3244	yes	missense	PRTG	NM_173814.4	5	36,866,4949	AA,AT,TT		10.4244,2.5862,8.0157	benign	1062/1151	55912875	938,10764	1798	4053	5851	SO:0001583	missense	283659	exon19			CTTGTATCTTCTT	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.3184A>T	15.37:g.55912875T>A	ENSP00000373937:p.Ile1062Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	143	64	0.447552	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	102	0.046703296703296704	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	80	0.10554089709762533	T	10.27	1.305246	0.23736	0.025862	0.104244	ENSG00000166450	ENST00000389286	T	0.49139	0.79	5.9	0.324	0.15898	.	0.992602	0.08210	N	0.980882	T	0.00524	0.0017	N	0.22421	0.69	0.34187	D	0.671636	B	0.02656	0.0	B	0.01281	0.0	T	0.29912	-0.9996	10	0.32370	T	0.25	-0.7546	1.9025	0.03270	0.1262:0.2475:0.129:0.4974	rs1438914;rs52810544;rs1438914	1062	Q2VWP7	PRTG_HUMAN	L	1062	ENSP00000373937:I1062L	ENSP00000373937:I1062L	I	-	1	0	PRTG	53700167	0.148000	0.22702	0.241000	0.24154	0.879000	0.50718	0.326000	0.19646	0.114000	0.18032	0.528000	0.53228	ATA	T|0.504;A|0.496	0.496	strong		0.313	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
TAF1C	9013	hgsc.bcm.edu	37	16	84213254	84213254	+	Missense_Mutation	SNP	C	C	T	rs4150173	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84213254C>T	ENST00000567759.1	-	14	2085	c.1903G>A	c.(1903-1905)Ggc>Agc	p.G635S	TAF1C_ENST00000341690.6_Missense_Mutation_p.G541S|TAF1C_ENST00000566732.1_Missense_Mutation_p.G609S|TAF1C_ENST00000378541.4_Missense_Mutation_p.G635S|TAF1C_ENST00000570117.1_Missense_Mutation_p.G303S|TAF1C_ENST00000541676.1_Missense_Mutation_p.G542S	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	635			G -> S (in dbSNP:rs4150173). {ECO:0000269|Ref.4}.		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						TGGCTGCAGCCGGCAGTGTCC	0.657													C|||	14	0.00279553	0.0	0.0043	5008	,	,		15545	0.0		0.0099	False		,,,				2504	0.001				p.G635S		Atlas-SNP	.											.	TAF1C	60	.	0			c.G1903A						PASS	.	C	SER/GLY,SER/GLY	8,4372		0,8,2182	15.0	18.0	17.0		1903,1621	-0.7	0.8	16	dbSNP_110	17	74,8512		0,74,4219	yes	missense,missense	TAF1C	NM_005679.3,NM_139353.2	56,56	0,82,6401	TT,TC,CC		0.8619,0.1826,0.6324	benign,benign	635/870,541/776	84213254	82,12884	2190	4293	6483	SO:0001583	missense	9013	exon14			TGCAGCCGGCAGT	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.1903G>A	16.37:g.84213254C>T	ENSP00000455265:p.Gly635Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	37	CCDS32496.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	10.62	1.402300	0.25291	0.001826	0.008619	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000544090	T;T;T	0.03772	3.9;3.81;3.81	4.95	-0.686	0.11324	.	0.527046	0.17972	N	0.155821	T	0.01353	0.0044	N	0.22421	0.69	0.23515	N	0.997517	P;P;P;P	0.43701	0.564;0.815;0.769;0.564	B;B;B;B	0.30855	0.073;0.121;0.104;0.073	T	0.49925	-0.8887	10	0.13853	T	0.58	-1.2446	4.7794	0.13195	0.4519:0.1797:0.3684:0.0	rs4150173;rs4150173	609;158;635;541	Q15572-6;F5H0H4;Q15572;Q15572-2	.;.;TAF1C_HUMAN;.	S	635;542;541;158	ENSP00000367802:G635S;ENSP00000437900:G542S;ENSP00000345305:G541S	ENSP00000345305:G541S	G	-	1	0	TAF1C	82770755	0.000000	0.05858	0.783000	0.31826	0.784000	0.44337	-0.560000	0.05964	-0.432000	0.07297	-0.397000	0.06425	GGC	C|0.991;T|0.009	0.009	strong		0.657	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
ARFGAP3	26286	hgsc.bcm.edu	37	22	43195147	43195147	+	Silent	SNP	A	A	G	rs1128013	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:43195147A>G	ENST00000263245.5	-	15	1650	c.1431T>C	c.(1429-1431)agT>agC	p.S477S	ARFGAP3_ENST00000429508.2_Silent_p.S405S|ARFGAP3_ENST00000437119.2_Silent_p.S433S	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	477					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						TGGGCAGCACACTGGACAGGC	0.572													G|||	1890	0.377396	0.5053	0.3847	5008	,	,		17264	0.0813		0.4642	False		,,,				2504	0.4151				p.S477S	GBM(58;544 1030 21460 27159 48838)	Atlas-SNP	.											.	ARFGAP3	48	.	0			c.T1431C						PASS	.	G	,	2270,2136	578.4+/-384.7	588,1094,521	130.0	114.0	120.0		1299,1431	0.5	0.3	22	dbSNP_86	120	4152,4448	588.6+/-392.4	1038,2076,1186	no	coding-synonymous,coding-synonymous	ARFGAP3	NM_001142293.1,NM_014570.4	,	1626,3170,1707	GG,GA,AA		48.2791,48.4793,49.3772	,	433/473,477/517	43195147	6422,6584	2203	4300	6503	SO:0001819	synonymous_variant	26286	exon15			CAGCACACTGGAC	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"""ADP-ribosylation factor GTPase activating proteins"""	661	protein-coding gene	gene with protein product		612439	"""ADP-ribosylation factor GTPase activating protein 1"""	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.1431T>C	22.37:g.43195147A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_014570	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Silent	SNP	ENST00000263245.5	37	CCDS14042.1																																																																																			A|0.557;G|0.443	0.443	strong		0.572	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570	
ZNF445	353274	hgsc.bcm.edu	37	3	44489880	44489880	+	Missense_Mutation	SNP	T	T	C	rs11710965	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:44489880T>C	ENST00000396077.2	-	8	1630	c.1283A>G	c.(1282-1284)tAt>tGt	p.Y428C	ZNF445_ENST00000425708.2_Missense_Mutation_p.Y428C	NM_181489.5	NP_852466.1	P59923	ZN445_HUMAN	zinc finger protein 445	428			Y -> C (in dbSNP:rs11710965).		transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|skin(3)	31				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		CTTGTAGTCATAGTGGTGTGA	0.418													T|||	243	0.0485224	0.0121	0.0648	5008	,	,		22516	0.0		0.171	False		,,,				2504	0.0102				p.Y428C		Atlas-SNP	.											.	ZNF445	91	.	0			c.A1283G						PASS	.	T	CYS/TYR	165,4241	109.5+/-147.8	2,161,2040	123.0	124.0	124.0		1283	-3.7	0.0	3	dbSNP_120	124	1322,7278	260.6+/-283.4	98,1126,3076	yes	missense	ZNF445	NM_181489.5	194	100,1287,5116	CC,CT,TT		15.3721,3.7449,11.4332	benign	428/1032	44489880	1487,11519	2203	4300	6503	SO:0001583	missense	353274	exon8			TAGTCATAGTGGT	AY262260	CCDS2713.1	3p21.32	2013-01-09	2003-10-07		ENSG00000185219	ENSG00000185219		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	21018	protein-coding gene	gene with protein product			"""zinc finger protein 168"""	ZNF168		7814019	Standard	NM_181489		Approved	ZKSCAN15, ZSCAN47	uc003cnf.2	P59923	OTTHUMG00000133042	ENST00000396077.2:c.1283A>G	3.37:g.44489880T>C	ENSP00000379387:p.Tyr428Cys	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	267	125	0.468165	NM_181489	Q3MJD1	Missense_Mutation	SNP	ENST00000396077.2	37	CCDS2713.1	152	0.0695970695970696	5	0.01016260162601626	18	0.049723756906077346	0	0.0	129	0.17018469656992086	T	11.93	1.786117	0.31593	0.037449	0.153721	ENSG00000185219	ENST00000425708;ENST00000396077	T;T	0.05717	3.4;3.4	3.81	-3.72	0.04411	.	0.863253	0.09860	N	0.746305	T	0.00039	0.0001	M	0.81942	2.565	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.06405	0.002;0.002	T	0.32798	-0.9893	9	0.52906	T	0.07	.	5.022	0.14365	0.1326:0.329:0.0:0.5384	rs11710965;rs52799416;rs56621940;rs59518590;rs11710965	416;428	B7ZKX2;P59923	.;ZN445_HUMAN	C	428	ENSP00000413073:Y428C;ENSP00000379387:Y428C	ENSP00000379387:Y428C	Y	-	2	0	ZNF445	44464884	0.398000	0.25279	0.008000	0.14137	0.631000	0.37964	0.903000	0.28475	-0.657000	0.05373	-0.468000	0.05107	TAT	T|0.903;C|0.097	0.097	strong		0.418	ZNF445-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256647.2	NM_181489	
TTYH1	57348	hgsc.bcm.edu	37	19	54946784	54946784	+	Silent	SNP	A	A	G	rs3745420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54946784A>G	ENST00000376530.3	+	11	1291	c.1188A>G	c.(1186-1188)ctA>ctG	p.L396L	TTYH1_ENST00000391739.3_Missense_Mutation_p.T427A|TTYH1_ENST00000301194.4_Silent_p.L396L|CTD-2587H19.2_ENST00000596631.1_RNA|TTYH1_ENST00000489425.1_3'UTR|TTYH1_ENST00000376531.3_Silent_p.L396L|CTD-2587H19.3_ENST00000597355.1_lincRNA|AC008746.3_ENST00000457113.1_RNA	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1	396					cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)			endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		TCTTCCTGCTACTCTTCTCCC	0.687													G|||	2055	0.410343	0.7103	0.2939	5008	,	,		15108	0.2381		0.3052	False		,,,				2504	0.3732				p.L396L		Atlas-SNP	.											TTYH1_ENST00000376531,NS,carcinoma,0,2	TTYH1	78	2	0			c.A1188G						PASS	.	G	,,	2826,1580	469.4+/-355.4	905,1016,282	49.0	35.0	40.0		1188,1188,1188	1.8	1.0	19	dbSNP_107	40	2728,5868	655.5+/-401.3	450,1828,2020	no	coding-synonymous,coding-synonymous,coding-synonymous	TTYH1	NM_001005367.2,NM_001201461.1,NM_020659.3	,,	1355,2844,2302	GG,GA,AA		31.7357,35.8602,42.7165	,,	396/461,396/452,396/451	54946784	5554,7448	2203	4298	6501	SO:0001819	synonymous_variant	57348	exon11			CCTGCTACTCTTC	AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"""tweety (Drosophila) homolog 1"", ""tweety homolog 1 (Drosophila)"""			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.1188A>G	19.37:g.54946784A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	187	100	0.534759	NM_020659	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Silent	SNP	ENST00000376530.3	37	CCDS12893.1	826	0.3782051282051282	346	0.7032520325203252	129	0.356353591160221	128	0.22377622377622378	223	0.2941952506596306	G	3.095	-0.186131	0.06340	0.641398	0.317357	ENSG00000167614	ENST00000391739	T	0.15718	2.4	4.22	1.83	0.25207	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.50813	P	1.0900000000002574E-4	.	.	.	.	.	.	T	0.16541	-1.0399	5	0.66056	D	0.02	-3.7698	1.9179	0.03301	0.1923:0.1574:0.4891:0.1612	rs3745420;rs17845599;rs17858511;rs3745420	.	.	.	A	427	ENSP00000375619:T427A	ENSP00000375619:T427A	T	+	1	0	TTYH1	59638596	0.998000	0.40836	1.000000	0.80357	0.959000	0.62525	0.304000	0.19228	0.359000	0.24239	-0.215000	0.12644	ACT	A|0.569;G|0.431	0.431	strong		0.687	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1		
DOK2	9046	hgsc.bcm.edu	37	8	21766900	21766900	+	Silent	SNP	G	G	A	rs17853066	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21766900G>A	ENST00000276420.4	-	5	1419	c.1161C>T	c.(1159-1161)gcC>gcT	p.A387A	DOK2_ENST00000544659.1_Silent_p.A233A	NM_003974.2	NP_003965.2	O60496	DOK2_HUMAN	docking protein 2, 56kDa	387					blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|leukocyte migration (GO:0050900)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	receptor signaling protein activity (GO:0005057)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(3)|skin(1)	26				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		AATCCTGCCCGGCTGGCTGGA	0.602													G|||	719	0.14357	0.0991	0.0735	5008	,	,		17901	0.3274		0.1282	False		,,,				2504	0.0798				p.A387A		Atlas-SNP	.											.	DOK2	51	.	0			c.C1161T						PASS	.	G		421,3983	197.1+/-221.3	14,393,1795	49.0	52.0	51.0		1161	-8.2	0.0	8	dbSNP_123	51	976,7616	199.6+/-243.6	66,844,3386	no	coding-synonymous	DOK2	NM_003974.2		80,1237,5181	AA,AG,GG		11.3594,9.5595,10.7495		387/413	21766900	1397,11599	2202	4296	6498	SO:0001819	synonymous_variant	9046	exon5			CTGCCCGGCTGGC	AF034970	CCDS6016.1	8p21.3	2008-08-07	2002-08-29		ENSG00000147443	ENSG00000147443			2991	protein-coding gene	gene with protein product		604997	"""docking protein 2, 56kD"""			9478921, 14645010	Standard	NM_003974		Approved	p56dok-2, Dok-2	uc003wzy.1	O60496	OTTHUMG00000131075	ENST00000276420.4:c.1161C>T	8.37:g.21766900G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	110	66	0.6	NM_003974	Q8N5A4	Silent	SNP	ENST00000276420.4	37	CCDS6016.1																																																																																			G|0.869;A|0.131	0.131	strong		0.602	DOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253735.3	NM_003974	
LILRB3	11025	hgsc.bcm.edu	37	19	54721049	54721049	+	Silent	SNP	A	A	G	rs60566950	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54721049A>G	ENST00000391750.1	-	14	1945	c.1809T>C	c.(1807-1809)ctT>ctC	p.L603L	LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Silent_p.L604L|LILRB3_ENST00000245620.9_Silent_p.L604L|LILRB3_ENST00000407860.2_Silent_p.L620L|LILRA6_ENST00000440558.2_Silent_p.L603L|LILRA6_ENST00000270464.5_Silent_p.L604L|LILRB3_ENST00000346401.6_Silent_p.L615L|LILRB3_ENST00000424807.1_Silent_p.L603L|LILRA6_ENST00000391735.3_3'UTR			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	603					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCTTCCGTCTAAGGGTCAAGC	0.632													.|||	155	0.0309505	0.0998	0.0086	5008	,	,		17459	0.0		0.0	False		,,,				2504	0.0174				p.L604L		Atlas-SNP	.											LILRB3,NS,carcinoma,0,1	LILRB3	67	1	0			c.T1812C						scavenged	.	A	,	147,4257		24,99,2079	104.0	105.0	104.0		1812,1809	0.8	0.0	19	dbSNP_129	104	5,8595		0,5,4295	no	coding-synonymous,coding-synonymous	LILRB3	NM_001081450.1,NM_006864.2	,	24,104,6374	GG,GA,AA		0.0581,3.3379,1.1689	,	604/633,603/632	54721049	152,12852	2202	4300	6502	SO:0001819	synonymous_variant	11025	exon13			CCGTCTAAGGGTC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1809T>C	19.37:g.54721049A>G		Somatic	271	1	0.00369004		WXS	Illumina HiSeq	Phase_I	281	6	0.0213523	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			A|0.980;G|0.020	0.020	strong		0.632	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
GABRG2	2566	hgsc.bcm.edu	37	5	161522556	161522556	+	Silent	SNP	C	C	T	rs11135176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:161522556C>T	ENST00000361925.4	+	3	535	c.315C>T	c.(313-315)aaC>aaT	p.N105N	GABRG2_ENST00000356592.3_Silent_p.N105N|GABRG2_ENST00000414552.2_Silent_p.N105N|GABRG2_ENST00000393933.4_Silent_p.N10N			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	105					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GTCCAGTGAACGCTATCAATA	0.368													C|||	676	0.134984	0.0023	0.232	5008	,	,		15248	0.2242		0.0726	False		,,,				2504	0.2178				p.N105N		Atlas-SNP	.											.	GABRG2	142	.	0			c.C315T						PASS	.	C	,,	94,4312	76.2+/-114.5	1,92,2110	172.0	163.0	166.0		315,315,315	-2.0	1.0	5	dbSNP_120	166	704,7894	171.9+/-222.7	27,650,3622	no	coding-synonymous,coding-synonymous,coding-synonymous	GABRG2	NM_000816.3,NM_198903.2,NM_198904.2	,,	28,742,5732	TT,TC,CC		8.188,2.1335,6.1366	,,	105/468,105/516,105/476	161522556	798,12206	2203	4299	6502	SO:0001819	synonymous_variant	2566	exon3			AGTGAACGCTATC		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4087	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma 2"""	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.315C>T	5.37:g.161522556C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	157	63	0.401274	NM_198904	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Silent	SNP	ENST00000361925.4	37	CCDS4358.1																																																																																			C|0.912;T|0.088	0.088	strong		0.368	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1		
ARHGEF39	84904	hgsc.bcm.edu	37	9	35665153	35665153	+	Missense_Mutation	SNP	C	C	A	rs45567235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35665153C>A	ENST00000378387.3	-	1	131	c.14G>T	c.(13-15)tGc>tTc	p.C5F	ARHGEF39_ENST00000378395.2_Intron|ARHGEF39_ENST00000343259.3_Missense_Mutation_p.C5F|ARHGEF39_ENST00000490970.1_5'UTR	NM_032818.2	NP_116207.2	Q8N4T4	ARG39_HUMAN	Rho guanine nucleotide exchange factor (GEF) 39	5			C -> F (in dbSNP:rs45567235).		positive regulation of cell migration (GO:0030335)	plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)										CGAACCGGGGCAGGAGAGCTC	0.711													C|||	343	0.0684904	0.0991	0.0648	5008	,	,		14392	0.0278		0.0924	False		,,,				2504	0.047				p.C5F		Atlas-SNP	.											.	.	.	.	0			c.G14T						PASS	.	C	PHE/CYS	403,3887		8,387,1750	6.0	8.0	7.0		14	-1.6	0.0	9	dbSNP_127	7	802,7598		36,730,3434	yes	missense	C9orf100	NM_032818.2	205	44,1117,5184	AA,AC,CC		9.5476,9.3939,9.4957	benign	5/336	35665153	1205,11485	2145	4200	6345	SO:0001583	missense	84904	exon1			CCGGGGCAGGAGA	AK001187	CCDS6584.2	9p13.3	2012-08-08	2012-08-08	2012-08-08	ENSG00000137135	ENSG00000137135			25909	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 100"""	C9orf100		22327280	Standard	XR_242516		Approved	FLJ14642	uc003zxm.1	Q8N4T4	OTTHUMG00000019869	ENST00000378387.3:c.14G>T	9.37:g.35665153C>A	ENSP00000367638:p.Cys5Phe	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	39	25	0.641026	NM_032818	Q49AG0|Q6TPQ2|Q96ST6	Missense_Mutation	SNP	ENST00000378387.3	37	CCDS6584.2	159	0.07280219780219781	47	0.09552845528455285	21	0.058011049723756904	16	0.027972027972027972	75	0.09894459102902374	C	4.235	0.042612	0.08196	0.093939	0.095476	ENSG00000137135	ENST00000378387;ENST00000343259	T;T	0.72835	-0.69;1.93	5.34	-1.63	0.08345	Dbl homology (DH) domain (1);	0.709155	0.14661	N	0.305961	T	0.01454	0.0047	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.02121	-1.1210	10	0.46703	T	0.11	-19.2451	6.681	0.23119	0.0:0.4122:0.3454:0.2424	rs45567235;rs61752948	5;5	B4E0T1;Q8N4T4	.;CI100_HUMAN	F	5	ENSP00000367638:C5F;ENSP00000344922:C5F	ENSP00000344922:C5F	C	-	2	0	C9orf100	35655153	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.686000	0.05161	-0.641000	0.05487	-0.813000	0.03139	TGC	C|0.927;A|0.073	0.073	strong		0.711	ARHGEF39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052330.1	NM_032818	
LGALS3	3958	hgsc.bcm.edu	37	14	55611839	55611839	+	Missense_Mutation	SNP	A	A	T	rs11125	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:55611839A>T	ENST00000254301.9	+	6	864	c.603A>T	c.(601-603)caA>caT	p.Q201H		NM_002306.3	NP_002297.2	P17931	LEG3_HUMAN	lectin, galactoside-binding, soluble, 3	201	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				eosinophil chemotaxis (GO:0048245)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|mononuclear cell migration (GO:0071674)|mRNA processing (GO:0006397)|negative regulation of endocytosis (GO:0045806)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of immunological synapse formation (GO:2000521)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell receptor signaling pathway (GO:0050860)|neutrophil chemotaxis (GO:0030593)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of mononuclear cell migration (GO:0071677)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of T cell apoptotic process (GO:0070232)|regulation of T cell proliferation (GO:0042129)|RNA splicing (GO:0008380)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)	carbohydrate binding (GO:0030246)|chemoattractant activity (GO:0042056)|IgE binding (GO:0019863)|laminin binding (GO:0043236)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|prostate(1)	3						TTCAGATACAAGTACTGGTTG	0.373													A|||	231	0.0461262	0.0008	0.0793	5008	,	,		19985	0.006		0.0785	False		,,,				2504	0.092				p.Q201H		Atlas-SNP	.											.	LGALS3	10	.	0			c.A603T						PASS	.	A	,HIS/GLN	53,3809		0,53,1878	130.0	127.0	128.0		,603	2.4	1.0	14	dbSNP_52	128	636,7638		21,594,3522	yes	intron,missense	LGALS3	NM_001177388.1,NM_002306.3	,24	21,647,5400	TT,TA,AA		7.6867,1.3723,5.6773	,probably-damaging	,201/251	55611839	689,11447	1931	4137	6068	SO:0001583	missense	3958	exon6			GATACAAGTACTG	M64303	CCDS41956.1	14q22.3	2014-03-19	2007-02-01		ENSG00000131981	ENSG00000131981		"""Lectins, galactoside-binding"", ""Endogenous ligands"""	6563	protein-coding gene	gene with protein product	"""galectin 3"""	153619		LGALS2		2009535, 8063692	Standard	NR_003225		Approved	MAC-2, GALIG	uc001xbr.3	P17931	OTTHUMG00000171030	ENST00000254301.9:c.603A>T	14.37:g.55611839A>T	ENSP00000254301:p.Gln201His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_002306	B2RC38|Q16005|Q6IBA7|Q96J47	Missense_Mutation	SNP	ENST00000254301.9	37	CCDS41956.1	94	0.04304029304029304	1	0.0020325203252032522	37	0.10220994475138122	2	0.0034965034965034965	54	0.0712401055408971	A	13.59	2.282691	0.40394	0.013723	0.076867	ENSG00000131981	ENST00000254301	T	0.05786	3.39	6.02	2.37	0.29283	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.217575	0.48767	D	0.000171	T	0.00384	0.0012	L	0.58669	1.825	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.03750	-1.1007	10	0.34782	T	0.22	-8.9608	8.3987	0.32572	0.709:0.0:0.291:0.0	rs11125;rs1126860;rs3182151;rs11538650;rs17295916;rs17354346	201	P17931	LEG3_HUMAN	H	201	ENSP00000254301:Q201H	ENSP00000254301:Q201H	Q	+	3	2	LGALS3	54681592	0.963000	0.33076	0.971000	0.41717	0.019000	0.09904	0.091000	0.15046	0.491000	0.27793	0.533000	0.62120	CAA	A|0.943;T|0.057	0.057	strong		0.373	LGALS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411309.1	NM_002306	
MAGEB10	139422	hgsc.bcm.edu	37	X	27839981	27839981	+	Silent	SNP	A	A	C	rs139940961	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:27839981A>C	ENST00000356790.2	+	3	803	c.558A>C	c.(556-558)ctA>ctC	p.L186L		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	186	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.L186L(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						AACTAGATCTAGGCTGTGATG	0.483													A|||	60	0.015894	0.0008	0.0101	3775	,	,		15048	0.0		0.0159	False		,,,				2504	0.0368				p.L186L		Atlas-SNP	.											.	MAGEB10	107	.	1	Substitution - coding silent(1)	breast(1)	c.A558C						PASS	.	A		18,3815		0,17,1,1614,570	91.0	78.0	83.0		558	-1.9	0.0	X	dbSNP_134	83	162,6566		2,110,48,2316,1824	no	coding-synonymous	MAGEB10	NM_182506.3		2,127,49,3930,2394	CC,CA,C,AA,A		2.4078,0.4696,1.7044		186/348	27839981	180,10381	2202	4300	6502	SO:0001819	synonymous_variant	139422	exon3			AGATCTAGGCTGT		CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.558A>C	X.37:g.27839981A>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	88	84	0.954545	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Silent	SNP	ENST00000356790.2	37	CCDS35221.1																																																																																			A|0.986;C|0.014	0.014	strong		0.483	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506	
OSER1	51526	hgsc.bcm.edu	37	20	42825929	42825929	+	Silent	SNP	C	C	T	rs8268	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:42825929C>T	ENST00000372970.2	-	6	822	c.642G>A	c.(640-642)gtG>gtA	p.V214V	OSER1_ENST00000255174.2_Silent_p.V214V			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	214					cellular response to hydrogen peroxide (GO:0070301)												AAAAGGAATACACTTCCATAT	0.498													C|||	1496	0.298722	0.41	0.1124	5008	,	,		23065	0.4147		0.1471	False		,,,				2504	0.317				p.V214V		Atlas-SNP	.											.	C20orf111	28	.	0			c.G642A						PASS	.	C		1506,2900	480.4+/-358.8	237,1032,934	144.0	123.0	130.0		642	-3.3	0.9	20	dbSNP_52	130	1152,7448	237.6+/-269.4	73,1006,3221	no	coding-synonymous	C20orf111	NM_016470.7		310,2038,4155	TT,TC,CC		13.3953,34.1807,20.4367		214/293	42825929	2658,10348	2203	4300	6503	SO:0001819	synonymous_variant	51526	exon4			GGAATACACTTCC	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"""peroxide-inducible transcript 1"", ""oxidative stress-responsive 1"""		"""chromosome 20 open reading frame 111"""	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.642G>A	20.37:g.42825929C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	148	64	0.432432	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Silent	SNP	ENST00000372970.2	37	CCDS13327.1																																																																																			C|0.766;T|0.234	0.234	strong		0.498	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470	
NXPE2	120406	hgsc.bcm.edu	37	11	114576626	114576626	+	Missense_Mutation	SNP	A	A	T	rs1356428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:114576626A>T	ENST00000389586.4	+	5	1242	c.1052A>T	c.(1051-1053)aAt>aTt	p.N351I	NXPE2_ENST00000375475.5_Intron	NM_182495.5	NP_872301.2	Q96DL1	NXPE2_HUMAN	neurexophilin and PC-esterase domain family, member 2	351						integral component of membrane (GO:0016021)		p.N351I(1)									GAAACAAAAAATATAAATGAC	0.328													A|||	1527	0.304912	0.1067	0.3343	5008	,	,		11387	0.378		0.3956	False		,,,				2504	0.3834				p.N351I		Atlas-SNP	.											FAM55B_ENST00000389586,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A1052T						PASS	.	A	ILE/ASN	196,1188		18,160,514	60.0	57.0	58.0		1052	-4.2	0.0	11	dbSNP_88	58	1139,2037		219,701,668	yes	missense	FAM55B	NM_182495.5	149	237,861,1182	TT,TA,AA		35.8627,14.1618,29.2763	benign	351/560	114576626	1335,3225	692	1588	2280	SO:0001583	missense	120406	exon5			CAAAAAATATAAA	AK057953	CCDS44738.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000204361	ENSG00000204361			26331	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member B"""	FAM55B			Standard	NM_182495		Approved	FLJ25224	uc009yyy.2	Q96DL1	OTTHUMG00000168293	ENST00000389586.4:c.1052A>T	11.37:g.114576626A>T	ENSP00000374237:p.Asn351Ile	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	197	101	0.51269	NM_182495	Q2NKI8	Missense_Mutation	SNP	ENST00000389586.4	37	CCDS44738.1	663	0.30357142857142855	60	0.12195121951219512	118	0.3259668508287293	184	0.32167832167832167	301	0.3970976253298153	A	7.433	0.639102	0.14386	0.141618	0.358627	ENSG00000204361	ENST00000389586	T	0.12255	2.7	5.24	-4.15	0.03881	.	1.854680	0.02760	N	0.118463	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.13594	0.008	B	0.08055	0.003	T	0.48456	-0.9034	9	0.44086	T	0.13	.	0.8123	0.01096	0.3654:0.1138:0.1562:0.3647	rs1356428;rs17117289;rs58365752	351	Q96DL1	FA55B_HUMAN	I	351	ENSP00000374237:N351I	ENSP00000374237:N351I	N	+	2	0	FAM55B	114081836	0.000000	0.05858	0.000000	0.03702	0.481000	0.33189	-0.551000	0.06027	-0.279000	0.09167	0.460000	0.39030	AAT	A|0.682;T|0.318	0.318	strong		0.328	NXPE2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399181.1	NM_182495	
NYNRIN	57523	hgsc.bcm.edu	37	14	24878485	24878485	+	Silent	SNP	G	G	A	rs12897153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24878485G>A	ENST00000382554.3	+	4	1803	c.1485G>A	c.(1483-1485)ccG>ccA	p.P495P		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	495					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)	p.P495P(2)		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						GAGGTGAGCCGGGGGATCAAG	0.577													G|||	440	0.0878594	0.1415	0.1052	5008	,	,		18385	0.0		0.1362	False		,,,				2504	0.044				p.P495P		Atlas-SNP	.											.	NYNRIN	120	.	2	Substitution - coding silent(2)	lung(2)	c.G1485A						PASS	.	G		562,3228		37,488,1370	39.0	42.0	41.0		1485	-9.6	0.0	14	dbSNP_121	41	1133,7071		92,949,3061	no	coding-synonymous	NYNRIN	NM_025081.2		129,1437,4431	AA,AG,GG		13.8103,14.8285,14.1321		495/1899	24878485	1695,10299	1895	4102	5997	SO:0001819	synonymous_variant	57523	exon4			TGAGCCGGGGGAT	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.1485G>A	14.37:g.24878485G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	110	62	0.563636	NM_025081	Q6P153|Q86TR3|Q9HAC4	Silent	SNP	ENST00000382554.3	37	CCDS45090.1																																																																																			G|0.895;A|0.105	0.105	strong		0.577	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1		
CYP3A43	64816	hgsc.bcm.edu	37	7	99459256	99459256	+	Silent	SNP	C	C	T	rs17342647	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99459256C>T	ENST00000354829.2	+	11	1150	c.1047C>T	c.(1045-1047)gcC>gcT	p.A349A	CYP3A43_ENST00000417625.1_Silent_p.A239A|CYP3A43_ENST00000312017.5_Silent_p.A349A|CYP3A43_ENST00000415413.1_Silent_p.A138A|CYP3A43_ENST00000444905.1_Silent_p.A96A|CYP3A43_ENST00000342499.4_Silent_p.A209A|CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000222382.5_Silent_p.A349A	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	349			Missing (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	CCTACGATGCCCTGGTACAGA	0.408													C|||	154	0.0307508	0.003	0.0461	5008	,	,		20720	0.0		0.0934	False		,,,				2504	0.0245				p.A349A		Atlas-SNP	.											.	CYP3A43	52	.	0			c.C1047T						PASS	.	C	,,	108,4298	85.3+/-124.0	0,108,2095	81.0	75.0	77.0		1047,1047,1047	0.8	0.0	7	dbSNP_123	77	992,7608	216.2+/-255.3	62,868,3370	no	coding-synonymous,coding-synonymous,coding-synonymous	CYP3A43	NM_022820.3,NM_057095.1,NM_057096.2	,,	62,976,5465	TT,TC,CC		11.5349,2.4512,8.4576	,,	349/505,349/504,349/421	99459256	1100,11906	2203	4300	6503	SO:0001819	synonymous_variant	64816	exon11			CGATGCCCTGGTA	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"""Cytochrome P450s"""	17450	protein-coding gene	gene with protein product		606534	"""cytochrome P450, subfamily IIIA, polypeptide 43"""			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.1047C>T	7.37:g.99459256C>T		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	218	105	0.481651	NM_057096	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Silent	SNP	ENST00000354829.2	37	CCDS5676.1																																																																																			C|0.936;T|0.064	0.064	strong		0.408	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1		
CACNA1H	8912	hgsc.bcm.edu	37	16	1261219	1261219	+	Silent	SNP	A	A	G	rs2753326	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:1261219A>G	ENST00000348261.5	+	22	4523	c.4275A>G	c.(4273-4275)tcA>tcG	p.S1425S	CACNA1H_ENST00000358590.4_Silent_p.S1425S|CACNA1H_ENST00000565831.1_Silent_p.S1425S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1425					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CGCTGATATCATCACTCAGGC	0.597													G|||	3554	0.709665	0.7511	0.719	5008	,	,		16181	0.869		0.6372	False		,,,				2504	0.5573				p.S1425S		Atlas-SNP	.											.	CACNA1H	317	.	0			c.A4275G						PASS	.	G	,	3165,1165		1164,837,164	93.0	106.0	102.0		4275,4275	-8.1	0.1	16	dbSNP_100	102	5090,3414		1545,2000,707	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	2709,2837,871	GG,GA,AA		40.1458,26.9053,35.6787	,	1425/2348,1425/2354	1261219	8255,4579	2165	4252	6417	SO:0001819	synonymous_variant	8912	exon22			GATATCATCACTC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.4275A>G	16.37:g.1261219A>G		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	170	169	0.994118	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			A|0.288;G|0.712	0.712	strong		0.597	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
HIST1H2BA	255626	hgsc.bcm.edu	37	6	25727517	25727517	+	Silent	SNP	G	G	A	rs9358872	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:25727517G>A	ENST00000274764.2	+	1	381	c.381G>A	c.(379-381)aaG>aaA	p.K127K	HIST1H2AA_ENST00000297012.3_5'Flank	NM_170610.2	NP_733759.1	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	127					cellular response to acid chemical (GO:0071229)|chromatin organization (GO:0006325)|inflammatory response (GO:0006954)|mononuclear cell migration (GO:0071674)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|plasminogen activation (GO:0031639)|positive regulation of binding (GO:0051099)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	extrinsic component of plasma membrane (GO:0019897)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)	2						CCAGCTCCAAGTAAGCCTGCT	0.478													A|||	1738	0.347045	0.0976	0.4366	5008	,	,		19317	0.6825		0.2922	False		,,,				2504	0.3313				p.K127K		Atlas-SNP	.											.	HIST1H2BA	25	.	0			c.G381A						PASS	.	A		605,3801	769.6+/-413.7	47,511,1645	260.0	188.0	212.0		381	1.5	0.1	6	dbSNP_119	212	2390,6210	700.4+/-405.1	338,1714,2248	no	coding-synonymous	HIST1H2BA	NM_170610.2		385,2225,3893	AA,AG,GG		27.7907,13.7313,23.0278		127/128	25727517	2995,10011	2203	4300	6503	SO:0001819	synonymous_variant	255626	exon1			CTCCAAGTAAGCC	AF397301	CCDS4563.1	6p22.2	2011-01-27	2006-10-11		ENSG00000146047	ENSG00000146047		"""Histones / Replication-dependent"""	18730	protein-coding gene	gene with protein product		609904	"""H2B histone family, member U, (testis-specific)"", ""histone 1, H2ba"""			12408966, 12213818	Standard	NM_170610		Approved	bA317E16.3, STBP, TSH2B, H2BFU	uc003nfd.3	Q96A08	OTTHUMG00000014408	ENST00000274764.2:c.381G>A	6.37:g.25727517G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_170610	B2R544|Q6NZ98|Q6NZA0|Q6NZA1	Silent	SNP	ENST00000274764.2	37	CCDS4563.1																																																																																			G|0.713;A|0.287	0.287	strong		0.478	HIST1H2BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040066.1	NM_170610	
KIAA1614	57710	hgsc.bcm.edu	37	1	180905694	180905694	+	Silent	SNP	C	C	T	rs3795503	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:180905694C>T	ENST00000367588.4	+	5	2704	c.2649C>T	c.(2647-2649)aaC>aaT	p.N883N	KIAA1614_ENST00000367587.1_Silent_p.N504N	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	883										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						ACTGCAACAACAGCGCACCTC	0.697													C|||	1446	0.288738	0.1316	0.2738	5008	,	,		16039	0.495		0.3012	False		,,,				2504	0.2863				p.N883N		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C2649T						PASS	.	C		667,3347		63,541,1403	27.0	33.0	31.0		2649	2.4	0.0	1	dbSNP_107	31	2521,5791		392,1737,2027	no	coding-synonymous	KIAA1614	NM_020950.1		455,2278,3430	TT,TC,CC		30.3296,16.6168,25.864		883/1191	180905694	3188,9138	2007	4156	6163	SO:0001819	synonymous_variant	57710	exon5			CAACAACAGCGCA	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2649C>T	1.37:g.180905694C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_020950	Q5VZ45|Q9HCF8	Silent	SNP	ENST00000367588.4	37	CCDS41442.1																																																																																			C|0.696;T|0.304	0.304	strong		0.697	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
ADIPOR2	79602	hgsc.bcm.edu	37	12	1893077	1893077	+	Silent	SNP	C	C	A	rs35854772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:1893077C>A	ENST00000357103.4	+	7	1121	c.870C>A	c.(868-870)atC>atA	p.I290I		NM_024551.2	NP_078827.2	Q86V24	ADR2_HUMAN	adiponectin receptor 2	290					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|female pregnancy (GO:0007565)|heart development (GO:0007507)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of cell growth (GO:0030308)|positive regulation of glucose import (GO:0046326)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|receptor activity (GO:0004872)			endometrium(1)|large_intestine(3)|lung(7)|stomach(1)	12	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			TGAGTGGAATCATTCCTACCT	0.493													C|||	513	0.102436	0.1952	0.0663	5008	,	,		18446	0.0258		0.1252	False		,,,				2504	0.0583				p.I290I		Atlas-SNP	.											.	ADIPOR2	30	.	0			c.C870A						PASS	.	C		858,3548	335.5+/-303.9	88,682,1433	99.0	92.0	94.0		870	5.7	1.0	12	dbSNP_126	94	1047,7553	221.5+/-258.9	58,931,3311	no	coding-synonymous	ADIPOR2	NM_024551.2		146,1613,4744	AA,AC,CC		12.1744,19.4734,14.6471		290/387	1893077	1905,11101	2203	4300	6503	SO:0001819	synonymous_variant	79602	exon7			TGGAATCATTCCT	AY424280	CCDS8511.1	12p13	2012-08-22			ENSG00000006831	ENSG00000006831		"""GPCR / Unclassified : Adiponectin receptors"""	24041	protein-coding gene	gene with protein product		607946				12802337	Standard	NM_024551		Approved	PAQR2, ACDCR2	uc001qjm.3	Q86V24	OTTHUMG00000130139	ENST00000357103.4:c.870C>A	12.37:g.1893077C>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	162	59	0.364198	NM_024551	Q53YY5|Q9H737	Silent	SNP	ENST00000357103.4	37	CCDS8511.1																																																																																			C|0.873;A|0.127	0.127	strong		0.493	ADIPOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252447.2	NM_024551	
APPL2	55198	hgsc.bcm.edu	37	12	105583877	105583877	+	Missense_Mutation	SNP	G	G	A	rs2272495	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:105583877G>A	ENST00000258530.3	-	15	1523	c.1298C>T	c.(1297-1299)gCa>gTa	p.A433V	APPL2_ENST00000539978.2_Missense_Mutation_p.A390V|APPL2_ENST00000551662.1_Missense_Mutation_p.A439V	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						ACTGGCTGTTGCTTTGGGAAC	0.423													G|||	938	0.1873	0.1044	0.2464	5008	,	,		20710	0.2599		0.1869	False		,,,				2504	0.183				p.A439V		Atlas-SNP	.											.	APPL2	69	.	0			c.C1316T						PASS	.						118.0	109.0	112.0					12																	105583877		2203	4300	6503	SO:0001583	missense	55198	exon15			GCTGTTGCTTTGG	AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"""Pleckstrin homology (PH) domain containing"""	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.1298C>T	12.37:g.105583877G>A	ENSP00000258530:p.Ala433Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	114	50	0.438596	NM_001251904	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Missense_Mutation	SNP	ENST00000258530.3	37	CCDS9101.1	418	0.19139194139194138	50	0.1016260162601626	84	0.23204419889502761	150	0.26223776223776224	134	0.17678100263852242	G	12.58	1.981480	0.34942	.	.	ENSG00000136044	ENST00000258530;ENST00000539978;ENST00000551662	T;T;T	0.23348	2.71;1.91;2.49	5.46	4.51	0.55191	.	0.502179	0.22067	N	0.065091	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.20261	0.043;0.025;0.025	B;B;B	0.24541	0.054;0.015;0.022	T	0.28106	-1.0054	9	0.33141	T	0.24	-10.4262	8.5015	0.33161	0.0:0.1206:0.5073:0.3722	rs2272495;rs17853203;rs56646590;rs60975777;rs2272495	439;390;433	F8W1P5;B7Z1Q8;Q8NEU8	.;.;DP13B_HUMAN	V	433;390;439	ENSP00000258530:A433V;ENSP00000444472:A390V;ENSP00000446917:A439V	ENSP00000258530:A433V	A	-	2	0	APPL2	104108007	0.020000	0.18652	0.027000	0.17364	0.024000	0.10985	1.438000	0.35002	2.557000	0.86248	0.563000	0.77884	GCA	G|0.817;A|0.183	0.183	strong		0.423	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406238.3	NM_018171	
GBP3	2635	hgsc.bcm.edu	37	1	89479063	89479063	+	Missense_Mutation	SNP	G	G	A	rs4656077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:89479063G>A	ENST00000370481.4	-	6	893	c.673C>T	c.(673-675)Cgg>Tgg	p.R225W	GBP3_ENST00000475853.2_5'Flank	NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	258	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		AAGAACTTCCGGATACAGAGT	0.403													.|||	1671	0.333666	0.1793	0.2925	5008	,	,		18338	0.3075		0.4404	False		,,,				2504	0.4888				p.R225W		Atlas-SNP	.											.	GBP3	53	.	0			c.C673T						PASS	.	G	TRP/ARG	1150,3256	388.4+/-326.9	142,866,1195	100.0	107.0	104.0		673	2.9	0.9	1	dbSNP_111	104	3902,4698	534.8+/-382.7	871,2160,1269	yes	missense	GBP3	NM_018284.2	101	1013,3026,2464	AA,AG,GG		45.3721,26.1008,38.8436	probably-damaging	225/596	89479063	5052,7954	2203	4300	6503	SO:0001583	missense	2635	exon6			ACTTCCGGATACA	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.673C>T	1.37:g.89479063G>A	ENSP00000359512:p.Arg225Trp	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	705	0.3228021978021978	81	0.16463414634146342	124	0.3425414364640884	161	0.28146853146853146	339	0.4472295514511873	G	17.09	3.299634	0.60195	0.261008	0.453721	ENSG00000117226	ENST00000370481;ENST00000235878	T	0.77877	-1.13	3.85	2.92	0.33932	Guanylate-binding protein, N-terminal (1);	0.250311	0.32503	N	0.006009	D	0.87954	0.6308	H	0.95151	3.63	0.53005	P	3.100000000000325E-5	P;D	0.89917	0.928;1.0	B;D	0.77557	0.288;0.99	D	0.90092	0.4178	8	.	.	.	.	10.8342	0.46677	0.0:0.0:0.8105:0.1895	rs4656077;rs4656077	91;225	F6X827;Q9H0R5	.;GBP3_HUMAN	W	225	ENSP00000359512:R225W	.	R	-	1	2	GBP3	89251651	0.989000	0.36119	0.878000	0.34440	0.753000	0.42808	2.438000	0.44837	0.940000	0.37473	0.514000	0.50259	CGG	G|0.661;A|0.339	0.339	strong		0.403	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	
PKD1L1	168507	hgsc.bcm.edu	37	7	47851623	47851623	+	Missense_Mutation	SNP	C	C	T	rs73692834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:47851623C>T	ENST00000289672.2	-	50	7423	c.7373G>A	c.(7372-7374)cGa>cAa	p.R2458Q	PKD1L1_ENST00000462350.1_5'Flank|C7orf69_ENST00000258776.4_Intron|C7orf69_ENST00000418326.2_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2458					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GGCCCTGAGTCGGGACAGGGC	0.587													C|||	767	0.153155	0.0431	0.1974	5008	,	,		20821	0.2153		0.17	False		,,,				2504	0.1892				p.R2458Q		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G7373A						PASS	.	C	,GLN/ARG	301,4103		7,287,1908	55.0	45.0	48.0		,7373	-1.1	0.0	7	dbSNP_130	48	1291,7301		87,1117,3092	yes	intron,missense	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,43	94,1404,5000	TT,TC,CC		15.0256,6.8347,12.2499	,possibly-damaging	,2458/2850	47851623	1592,11404	2202	4296	6498	SO:0001583	missense	168507	exon50			CTGAGTCGGGACA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.7373G>A	7.37:g.47851623C>T	ENSP00000289672:p.Arg2458Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	64	0.598131	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	339	0.15521978021978022	20	0.04065040650406504	80	0.22099447513812154	111	0.19405594405594406	128	0.16886543535620052	C	8.932	0.963576	0.18583	0.068347	0.150256	ENSG00000158683	ENST00000289672	T	0.69561	-0.41	5.49	-1.15	0.09709	Polycystin cation channel, PKD1/PKD2 (1);	2.463310	0.01843	N	0.035450	T	0.00039	0.0001	N	0.25890	0.77	0.80722	P	0.0	D	0.55605	0.972	B	0.43623	0.425	T	0.02064	-1.1220	9	0.28530	T	0.3	1.3162	6.6941	0.23189	0.0:0.29:0.1582:0.5519	.	2458	Q8TDX9	PK1L1_HUMAN	Q	2458	ENSP00000289672:R2458Q	ENSP00000289672:R2458Q	R	-	2	0	PKD1L1	47818148	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.321000	0.08018	-0.120000	0.11809	0.453000	0.30009	CGA	C|0.871;T|0.129	0.129	strong		0.587	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
NFKBIA	4792	hgsc.bcm.edu	37	14	35873770	35873770	+	Silent	SNP	G	G	A	rs1957106	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:35873770G>A	ENST00000216797.5	-	1	182	c.81C>T	c.(79-81)gaC>gaT	p.D27D	NFKBIA_ENST00000557140.1_Silent_p.D27D|NFKBIA_ENST00000557389.1_5'Flank|NFKBIA_ENST00000557100.1_5'UTR	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	27					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	CGTGGCGGTCGTCCAGTAGCC	0.697													G|||	1224	0.244409	0.1354	0.1988	5008	,	,		7649	0.2649		0.2962	False		,,,				2504	0.3497				p.D27D		Atlas-SNP	.											.	NFKBIA	28	.	0			c.C81T						PASS	.	G		582,3696		63,456,1620	12.0	12.0	12.0		81	1.9	1.0	14	dbSNP_92	12	2316,6078		352,1612,2233	no	coding-synonymous	NFKBIA	NM_020529.2		415,2068,3853	AA,AG,GG		27.5911,13.6045,22.8693		27/318	35873770	2898,9774	2139	4197	6336	SO:0001819	synonymous_variant	4792	exon1			GCGGTCGTCCAGT		CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"""Ankyrin repeat domain containing"""	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.81C>T	14.37:g.35873770G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_020529	B2R8L6	Silent	SNP	ENST00000216797.5	37	CCDS9656.1																																																																																			G|0.770;A|0.230	0.230	strong		0.697	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529	
ABHD17A	81926	hgsc.bcm.edu	37	19	1880950	1880950	+	Intron	SNP	T	T	C	rs4807160	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1880950T>C	ENST00000292577.7	-	2	766				ABHD17A_ENST00000590661.1_Intron|ABHD17A_ENST00000250974.9_Missense_Mutation_p.K144E	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A							extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										CCCCAGCTCTTGCCCAGCAGG	0.657													N|||	3160	0.63099	0.6241	0.6686	5008	,	,		16727	0.5913		0.6243	False		,,,				2504	0.6616				p.K144E		Atlas-SNP	.											FAM108A1,NS,carcinoma,0,1	FAM108A1	29	1	0			c.A430G						scavenged	.	C	,GLU/LYS	2846,1556		908,1030,263	31.0	37.0	35.0		,430	-4.9	0.0	19	dbSNP_111	35	5388,3210		1692,2004,603	yes	intron,missense	FAM108A1	NM_001130111.1,NM_031213.3	,56	2600,3034,866	CC,CT,TT		37.3343,35.3476,36.6615	,	,144/362	1880950	8234,4766	2201	4299	6500	SO:0001627	intron_variant	81926	exon3			AGCTCTTGCCCAG	BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"""Abhydrolase domain containing"""	28756	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 27"", ""family with sequence similarity 108, member A1"""	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.332+283A>G	19.37:g.1880950T>C		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	NM_031213	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Missense_Mutation	SNP	ENST00000292577.7	37	CCDS45902.1	1370	0.6272893772893773	311	0.6321138211382114	246	0.6795580110497238	348	0.6083916083916084	465	0.6134564643799473	-	0.034	-1.315169	0.01331	0.646524	0.626657	ENSG00000129968	ENST00000250974	T	0.30448	1.53	2.47	-4.94	0.03057	.	9.963510	0.00357	N	0.000036	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35450	-0.9788	8	0.06236	T	0.91	.	6.6701	0.23064	0.0:0.2997:0.1519:0.5483	rs4807160;rs17856603;rs56812054	144	Q96GS6-2	.	E	144	ENSP00000250974:K144E	ENSP00000250974:K144E	K	-	1	0	FAM108A1	1831950	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	-0.878000	0.04192	-1.995000	0.00971	-0.231000	0.12243	AAG	T|0.372;C|0.628	0.628	strong		0.657	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213	
NLRP2	55655	hgsc.bcm.edu	37	19	55512137	55512137	+	Silent	SNP	C	C	A	rs12768	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:55512137C>A	ENST00000543010.1	+	13	3203	c.3060C>A	c.(3058-3060)atC>atA	p.I1020I	NLRP2_ENST00000538819.1_Silent_p.I996I|NLRP2_ENST00000391721.4_Silent_p.I996I|NLRP2_ENST00000537859.1_Silent_p.I998I|NLRP2_ENST00000448584.2_Silent_p.I1020I|NLRP2_ENST00000263437.6_Silent_p.I1017I|NLRP2_ENST00000427260.2_Silent_p.I997I|NLRP2_ENST00000339757.7_Silent_p.I998I	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	1020					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GGTTGAAAATCGATGACTTTA	0.388													A|||	2757	0.550519	0.4486	0.6686	5008	,	,		16582	0.6815		0.495	False		,,,				2504	0.5266				p.I1020I		Atlas-SNP	.											.	NLRP2	161	.	0			c.C3060A						PASS	.	A	,,,	2044,2362	610.0+/-391.5	478,1088,637	81.0	78.0	79.0		3060,2994,2991,3060	-6.3	0.0	19	dbSNP_52	79	4569,4031	556.8+/-386.9	1206,2157,937	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	1684,3245,1574	AA,AC,CC		46.8721,46.3913,49.1542	,,,	1020/1063,998/1041,997/1040,1020/1063	55512137	6613,6393	2203	4300	6503	SO:0001819	synonymous_variant	55655	exon13			GAAAATCGATGAC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.3060C>A	19.37:g.55512137C>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			T|0.004;G|0.004	.	strong		0.388	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
NCOA6	23054	hgsc.bcm.edu	37	20	33342623	33342623	+	Missense_Mutation	SNP	G	G	A	rs144477396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:33342623G>A	ENST00000374796.2	-	9	4147	c.1577C>T	c.(1576-1578)cCg>cTg	p.P526L	NCOA6_ENST00000359003.2_Missense_Mutation_p.P526L			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	526	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						CATAAAGTTCGGATTGGCCTG	0.493																																					p.P526L		Atlas-SNP	.											.	NCOA6	219	.	0			c.C1577T						PASS	.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	117.0	107.0	110.0		1577,1577	3.8	1.0	20	dbSNP_134	110	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	NCOA6	NM_001242539.1,NM_014071.3	98,98	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	possibly-damaging,possibly-damaging	526/1071,526/2064	33342623	6,13000	2203	4300	6503	SO:0001583	missense	23054	exon8			AAGTTCGGATTGG	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.1577C>T	20.37:g.33342623G>A	ENSP00000363929:p.Pro526Leu	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	152	80	0.526316	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.514740	0.44763	0.0	6.98E-4	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.23552	1.9;1.9	5.97	3.84	0.44239	.	0.486738	0.20890	N	0.083855	T	0.09598	0.0236	N	0.08118	0	0.46167	D	0.998908	P	0.45078	0.85	B	0.25614	0.062	T	0.20940	-1.0260	10	0.22706	T	0.39	-0.5866	13.5218	0.61572	0.0:0.0:0.6067:0.3933	.	526	Q14686	NCOA6_HUMAN	L	526	ENSP00000363929:P526L;ENSP00000351894:P526L	ENSP00000351894:P526L	P	-	2	0	NCOA6	32806284	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	1.538000	0.36094	1.470000	0.48102	0.591000	0.81541	CCG	G|0.999;A|0.001	0.001	strong		0.493	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
RPTOR	57521	hgsc.bcm.edu	37	17	78820374	78820374	+	Splice_Site	SNP	G	G	A	rs2589156	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78820374G>A	ENST00000306801.3	+	11	1676	c.1314G>A	c.(1312-1314)caG>caA	p.Q438Q	RPTOR_ENST00000537330.1_Splice_Site_p.Q253Q|RPTOR_ENST00000544334.2_Splice_Site_p.Q438Q|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	438					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.Q438Q(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						TCGTCCTGCAGGTGAGTTTCT	0.622													G|||	387	0.0772764	0.0825	0.0778	5008	,	,		17515	0.004		0.1074	False		,,,				2504	0.1145				p.Q438Q		Atlas-SNP	.											RPTOR,NS,carcinoma,0,1	RPTOR	122	1	1	Substitution - coding silent(1)	stomach(1)	c.G1314A						PASS	.	G	,	407,3999	200.8+/-224.0	23,361,1819	117.0	90.0	99.0		1314,1314	3.4	1.0	17	dbSNP_100	99	1160,7440	237.8+/-269.5	79,1002,3219	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	RPTOR	NM_001163034.1,NM_020761.2	,	102,1363,5038	AA,AG,GG		13.4884,9.2374,12.0483	,	438/1178,438/1336	78820374	1567,11439	2203	4300	6503	SO:0001630	splice_region_variant	57521	exon11			CCTGCAGGTGAGT		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.1314+1G>A	17.37:g.78820374G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	102	60	0.588235	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			G|0.895;A|0.105	0.105	strong		0.622	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	Silent
ZNF418	147686	hgsc.bcm.edu	37	19	58439306	58439306	+	Silent	SNP	G	G	A	rs7253514	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58439306G>A	ENST00000396147.1	-	4	534	c.243C>T	c.(241-243)gcC>gcT	p.A81A	ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000595830.1_Silent_p.A81A|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599852.1_5'UTR|ZNF418_ENST00000425570.3_Silent_p.A102A	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	81	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		CACAAGAGTGGGCCTTCTTGG	0.507													G|||	1448	0.289137	0.2595	0.3573	5008	,	,		18775	0.4048		0.2545	False		,,,				2504	0.1973				p.A81A		Atlas-SNP	.											.	ZNF418	76	.	0			c.C243T						PASS	.	G		1066,3340		131,804,1268	62.0	66.0	64.0		243	-1.5	0.0	19	dbSNP_116	64	2219,6381		293,1633,2374	no	coding-synonymous	ZNF418	NM_133460.1		424,2437,3642	AA,AG,GG		25.8023,24.1943,25.2576		81/677	58439306	3285,9721	2203	4300	6503	SO:0001819	synonymous_variant	147686	exon4			AGAGTGGGCCTTC	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.243C>T	19.37:g.58439306G>A		Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	356	162	0.455056	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			G|0.704;A|0.296	0.296	strong		0.507	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
PLXNC1	10154	hgsc.bcm.edu	37	12	94642023	94642023	+	Silent	SNP	C	C	T	rs2230756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:94642023C>T	ENST00000258526.4	+	14	2862	c.2613C>T	c.(2611-2613)aaC>aaT	p.N871N		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	871					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						ACAACTTCAACATTTCCAAAA	0.343													C|||	277	0.0553115	0.0348	0.0461	5008	,	,		19648	0.0		0.1243	False		,,,				2504	0.0757				p.N871N		Atlas-SNP	.											.	PLXNC1	135	.	0			c.C2613T						PASS	.	C		167,4239	105.2+/-143.6	7,153,2043	34.0	35.0	35.0		2613	5.0	1.0	12	dbSNP_98	35	948,7652	203.7+/-246.6	54,840,3406	no	coding-synonymous	PLXNC1	NM_005761.2		61,993,5449	TT,TC,CC		11.0233,3.7903,8.573		871/1569	94642023	1115,11891	2203	4300	6503	SO:0001819	synonymous_variant	10154	exon14			CTTCAACATTTCC	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.2613C>T	12.37:g.94642023C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	188	79	0.420213	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			C|0.932;T|0.068	0.068	strong		0.343	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
USP35	57558	hgsc.bcm.edu	37	11	77920563	77920563	+	Silent	SNP	G	G	T	rs2510045	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:77920563G>T	ENST00000529308.1	+	10	1923	c.1662G>T	c.(1660-1662)ccG>ccT	p.P554P	USP35_ENST00000530267.1_Silent_p.P122P|USP35_ENST00000530535.1_3'UTR|USP35_ENST00000441408.2_Silent_p.P140P|USP35_ENST00000526425.1_Silent_p.P285P	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	554	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			CGCCCTCTCCGCCCGAGGAGC	0.567													g|||	1316	0.26278	0.1952	0.3156	5008	,	,		18184	0.3968		0.1779	False		,,,				2504	0.2658				p.P554P		Atlas-SNP	.											.	USP35	179	.	0			c.G1662T						PASS	.			669,3251		55,559,1346	35.0	40.0	38.0		1662	-6.3	0.0	11	dbSNP_100	38	1291,6959		105,1081,2939	no	coding-synonymous	USP35	NM_020798.2		160,1640,4285	TT,TG,GG		15.6485,17.0663,16.1052		554/1019	77920563	1960,10210	1960	4125	6085	SO:0001819	synonymous_variant	57558	exon10			CTCTCCGCCCGAG	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.1662G>T	11.37:g.77920563G>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	156	76	0.487179	NM_020798		Silent	SNP	ENST00000529308.1	37	CCDS41693.1																																																																																			G|0.761;T|0.239	0.239	strong		0.567	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
DNAJC6	9829	hgsc.bcm.edu	37	1	65860687	65860687	+	Silent	SNP	A	A	C	rs4582839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:65860687A>C	ENST00000395325.3	+	13	1996	c.1839A>C	c.(1837-1839)ccA>ccC	p.P613P	DNAJC6_ENST00000371069.4_Silent_p.P670P|DNAJC6_ENST00000263441.7_Silent_p.P600P	NM_014787.3	NP_055602.1	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	613	Pro-rich.				cell death (GO:0008219)|clathrin coat disassembly (GO:0072318)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytosol (GO:0005829)|synapse (GO:0045202)	protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(22)|ovary(1)|prostate(2)|skin(1)	39						TTCTCCAGCCAACAAGAAGTC	0.423													C|||	3795	0.757788	0.9811	0.6282	5008	,	,		19335	0.7927		0.5924	False		,,,				2504	0.682				p.P670P		Atlas-SNP	.											.	DNAJC6	104	.	0			c.A2010C						PASS	.	C		4022,384	189.9+/-215.9	1846,330,27	151.0	157.0	155.0		1839	-4.8	0.8	1	dbSNP_111	155	5023,3577	517.8+/-379.1	1449,2125,726	no	coding-synonymous	DNAJC6	NM_014787.2		3295,2455,753	CC,CA,AA		41.593,8.7154,30.4552		613/914	65860687	9045,3961	2203	4300	6503	SO:0001819	synonymous_variant	9829	exon13			CCAGCCAACAAGA	AB007942	CCDS30739.1, CCDS58004.1, CCDS58005.1	1p31.3	2011-09-02			ENSG00000116675	ENSG00000116675		"""Heat shock proteins / DNAJ (HSP40)"""	15469	protein-coding gene	gene with protein product	"""auxilin"""	608375				9455484, 11147971	Standard	NM_001256864		Approved	KIAA0473	uc001dce.2	O75061	OTTHUMG00000009066	ENST00000395325.3:c.1839A>C	1.37:g.65860687A>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001256864	B7Z3V8|D3DQ65|D3DQ66|Q32M66|Q4G0K1|Q5T614|Q5T615	Silent	SNP	ENST00000395325.3	37	CCDS30739.1																																																																																			A|0.300;C|0.700	0.700	strong		0.423	DNAJC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025134.1		
CHIA	27159	hgsc.bcm.edu	37	1	111854938	111854938	+	Missense_Mutation	SNP	G	G	T	rs41282496	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111854938G>T	ENST00000369740.1	+	4	285	c.182G>T	c.(181-183)aGg>aTg	p.R61M	CHIA_ENST00000430615.1_Intron|CHIA_ENST00000343320.6_Missense_Mutation_p.R61M|CHIA_ENST00000483391.1_Intron|CHIA_ENST00000451398.2_Intron|CHIA_ENST00000353665.6_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	61			R -> M (increased chitinase activity; when associated with N-47 and M-61; dbSNP:rs41282496). {ECO:0000269|PubMed:19435888}.		apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TTTGCTGGGAGGCAGAACAAC	0.512													T|||	540	0.107827	0.2103	0.0821	5008	,	,		20169	0.0		0.1093	False		,,,				2504	0.0971				p.R61M		Atlas-SNP	.											.	CHIA	115	.	0			c.G182T						PASS	.	T	,MET/ARG	743,3303		62,619,1342	124.0	121.0	122.0		,182	4.9	0.9	1	dbSNP_127	122	974,7408		49,876,3266	yes	intron,missense	CHIA	NM_021797.2,NM_201653.2	,91	111,1495,4608	TT,TG,GG		11.6201,18.3638,13.8156	,benign	,61/477	111854938	1717,10711	2023	4191	6214	SO:0001583	missense	27159	exon4			CTGGGAGGCAGAA	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.182G>T	1.37:g.111854938G>T	ENSP00000358755:p.Arg61Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	226	0.10347985347985347	103	0.20934959349593496	35	0.09668508287292818	0	0.0	88	0.11609498680738786	T	0.290	-0.980904	0.02197	0.183638	0.116201	ENSG00000134216	ENST00000369740;ENST00000343320	T;T	0.05025	3.51;3.51	4.93	4.93	0.64822	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.063063	0.64402	N	0.000020	T	0.00241	0.0007	N	0.00004	-3.34	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39272	-0.9622	9	0.02654	T	1	-5.6312	10.4411	0.44466	0.0:0.0:0.1644:0.8356	rs41282496;rs61752531	61	Q9BZP6	CHIA_HUMAN	M	61	ENSP00000358755:R61M;ENSP00000341828:R61M	ENSP00000341828:R61M	R	+	2	0	CHIA	111656461	1.000000	0.71417	0.943000	0.38184	0.127000	0.20565	5.510000	0.67018	0.828000	0.34709	-0.256000	0.11100	AGG	G|0.882;T|0.118	0.118	strong		0.512	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048661	33048661	+	Missense_Mutation	SNP	A	A	G	rs386699871|rs1042151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33048661A>G	ENST00000418931.2	+	2	429	c.313A>G	c.(313-315)Atg>Gtg	p.M105V	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.M105V	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	105	Beta-1.		M -> I (in allele DPB1*08:02, allele DPB1*09:02, allele DPB1*13:01, allele DPB1*13:02 and allele DPB1*19:01; dbSNP:rs1042153).|M -> V (in allele DPB1*01:01, allele DPB1*03:01, allele DPB1*05:02, allele DPB1*08:01, allele DPB1*09:01, allele DPB1*10:01, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*17:02, allele DPB1*21:02, allele DPB1*22:02, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*29:01, allele DPB1*35:01, allele DPB1*37:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*50:01, allele DPB1*52:01, allele DPB1*54:01, allele DPB1*56:01, allele DPB1*57:01, allele DPB1*65:01, allele DPB1*67:01, allele DPB1*68:01, allele DPB1*70:01, allele DPB1*73:01, allele DPB1*75:01, allele DPB1*76:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*84:01, allele DPB1*88:01, allele DPB1*90:01 and allele DPB1*92:01; dbSNP:rs1042151). {ECO:0000269|PubMed:6330724}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)	p.M105V(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GCCGGACAGGATGTGCAGACA	0.706													.|||	1264	0.252396	0.416	0.2133	5008	,	,		12428	0.1171		0.2068	False		,,,				2504	0.2454				p.M105V		Atlas-SNP	.											HLA-DPB1,NS,lymphoid_neoplasm,0,1	HLA-DPB1	28	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A313G						scavenged	.						29.0	31.0	31.0					6																	33048661		1510	2709	4219	SO:0001583	missense	3115	exon2			GACAGGATGTGCA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.313A>G	6.37:g.33048661A>G	ENSP00000408146:p.Met105Val	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	505	0.23122710622710624	218	0.44308943089430897	66	0.18232044198895028	72	0.1258741258741259	149	0.19656992084432717	A	0.010	-1.789266	0.00623	.	.	ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835	T;T;T	0.00281	8.32;8.32;8.32	3.49	-6.98	0.01611	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	2.303120	0.02598	N	0.100781	T	0.00012	0.0000	N	0.00016	-2.855	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.40365	-0.9567	9	0.08837	T	0.75	.	3.2203	0.06713	0.5003:0.1109:0.2764:0.1123	rs1042151;rs3173291;rs11551417;rs17221143	71;115;105	A2ALJ6;Q59GY1;P04440	.;.;DPB1_HUMAN	V	105;105;105;82	ENSP00000408146:M105V;ENSP00000439674:M105V;ENSP00000412654:M82V	ENSP00000389210:M105V	M	+	1	0	HLA-DPB1	33156639	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.609000	0.00886	-1.748000	0.01332	-2.039000	0.00418	ATG	A|0.776;G|0.224	0.224	strong		0.706	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
DACT1	51339	hgsc.bcm.edu	37	14	59112475	59112475	+	Silent	SNP	C	C	T	rs863091	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:59112475C>T	ENST00000335867.4	+	4	1158	c.1134C>T	c.(1132-1134)gtC>gtT	p.V378V	DACT1_ENST00000556859.1_Silent_p.V97V|DACT1_ENST00000395153.3_Silent_p.V341V|DACT1_ENST00000541264.2_Silent_p.V97V			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	378					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						GCGTTTGTGTCAGAGCCCCGG	0.542													C|||	1357	0.270966	0.4342	0.3343	5008	,	,		19778	0.1498		0.1938	False		,,,				2504	0.2096				p.V378V		Atlas-SNP	.											.	DACT1	119	.	0			c.C1134T						PASS	.	C	,	1620,2786	491.5+/-362.1	300,1020,883	58.0	63.0	61.0		1023,1134	2.3	1.0	14	dbSNP_86	61	1659,6941	296.7+/-303.1	148,1363,2789	no	coding-synonymous,coding-synonymous	DACT1	NM_001079520.1,NM_016651.5	,	448,2383,3672	TT,TC,CC		19.2907,36.768,25.2114	,	341/800,378/837	59112475	3279,9727	2203	4300	6503	SO:0001819	synonymous_variant	51339	exon4			TTGTGTCAGAGCC	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.1134C>T	14.37:g.59112475C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_016651	A8MYJ2|Q86TY0	Silent	SNP	ENST00000335867.4	37	CCDS9736.1																																																																																			C|0.743;T|0.257	0.257	strong		0.542	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
STEAP1B	256227	hgsc.bcm.edu	37	7	22533235	22533235	+	Missense_Mutation	SNP	T	T	C	rs62619778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:22533235T>C	ENST00000406890.2	-	3	342	c.248A>G	c.(247-249)cAt>cGt	p.H83R	STEAP1B_ENST00000404369.4_Missense_Mutation_p.H102R	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	83						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						ATATTGTTGATGGGAAGTTGC	0.398													t|||	302	0.0603035	0.1309	0.0519	5008	,	,		19483	0.0		0.0666	False		,,,				2504	0.0266				p.H102R		Atlas-SNP	.											.	STEAP1B	22	.	0			c.A305G						PASS	.						56.0	52.0	53.0					7																	22533235		692	1590	2282	SO:0001583	missense	256227	exon3			TGTTGATGGGAAG		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.248A>G	7.37:g.22533235T>C	ENSP00000385239:p.His83Arg	Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	301	113	0.375415	NM_001164460	B5MCI2	Missense_Mutation	SNP	ENST00000406890.2	37	CCDS55094.1	125	0.05723443223443223	57	0.11585365853658537	17	0.04696132596685083	0	0.0	51	0.06728232189973615	t	0.015	-1.542851	0.00934	.	.	ENSG00000105889	ENST00000406890;ENST00000404369;ENST00000424363;ENST00000439708	T;T;T;T	0.10860	2.83;3.01;3.04;2.85	1.06	1.06	0.20224	.	0.461581	0.14785	U	0.298593	T	0.00109	0.0003	L	0.31065	0.9	0.50039	P	1.5399999999998748E-4	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.37798	-0.9690	9	0.15952	T	0.53	-9.4356	6.3811	0.21536	0.0:0.0:0.0:1.0	rs62619778	102;83	B5MCI2;Q6NZ63	.;STEAL_HUMAN	R	83;102;102;102	ENSP00000385239:H83R;ENSP00000384370:H102R;ENSP00000416608:H102R;ENSP00000408954:H102R	ENSP00000384370:H102R	H	-	2	0	STEAP1B	22499760	0.607000	0.26958	0.996000	0.52242	0.493000	0.33554	1.365000	0.34182	0.759000	0.33084	0.102000	0.15555	CAT	T|0.936;C|0.064	0.064	strong		0.398	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		
GGT1	2678	hgsc.bcm.edu	37	22	25016911	25016911	+	Missense_Mutation	SNP	C	C	T	rs199703506	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25016911C>T	ENST00000400382.1	+	9	1362	c.607C>T	c.(607-609)Cgg>Tgg	p.R203W	GGT1_ENST00000406383.2_Missense_Mutation_p.R203W|GGT1_ENST00000400380.1_Missense_Mutation_p.R203W|GGT1_ENST00000248923.4_Missense_Mutation_p.R203W|GGT1_ENST00000466310.1_Intron|GGT1_ENST00000400383.1_Missense_Mutation_p.R203W			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	203					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.R203W(1)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	AAAGGTGCTTCGGGAGGGGGA	0.652																																					p.R203W		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	breast(1)	c.C607T						scavenged	.						20.0	22.0	21.0					22																	25016911		1981	4142	6123	SO:0001583	missense	2678	exon9			GTGCTTCGGGAGG	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.607C>T	22.37:g.25016911C>T	ENSP00000383232:p.Arg203Trp	Somatic	361	6	0.0166205		WXS	Illumina HiSeq	Phase_I	408	12	0.0294118	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	16.88	3.244872	0.59103	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383	T;T;T;T;T;T	0.08193	3.12;3.12;3.12;3.12;3.12;3.12	3.94	1.51	0.23008	.	0.465560	0.21948	U	0.066770	T	0.18841	0.0452	M	0.62016	1.91	0.29917	N	0.823045	D	0.76494	0.999	P	0.58970	0.849	T	0.03121	-1.1070	10	0.87932	D	0	-23.2527	10.8877	0.46976	0.3395:0.6605:0.0:0.0	.	203	P19440	GGT1_HUMAN	W	203	ENSP00000248923:R203W;ENSP00000393537:R203W;ENSP00000383232:R203W;ENSP00000383233:R203W;ENSP00000383231:R203W;ENSP00000385975:R203W	ENSP00000248923:R203W	R	+	1	2	GGT1	23346911	0.047000	0.20315	0.042000	0.18584	0.549000	0.35272	1.263000	0.33004	0.735000	0.32537	0.555000	0.69702	CGG	C|0.996;T|0.004	0.004	strong		0.652	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
PGBD1	84547	hgsc.bcm.edu	37	6	28270047	28270047	+	Missense_Mutation	SNP	C	C	G	rs6456811	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:28270047C>G	ENST00000405948.2	+	7	2836	c.2416C>G	c.(2416-2418)Cat>Gat	p.H806D	PGBD1_ENST00000259883.3_Missense_Mutation_p.H806D	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	806			H -> D (in dbSNP:rs6456811).			membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						ACACAATGCTCATCTGTCAGA	0.388													G|||	1318	0.263179	0.472	0.1787	5008	,	,		19490	0.1448		0.1372	False		,,,				2504	0.2924				p.H806D		Atlas-SNP	.											.	PGBD1	106	.	0			c.C2416G						PASS	.	G	ASP/HIS,ASP/HIS	1670,2736	629.7+/-395.3	330,1010,863	45.0	48.0	47.0		2416,2416	-0.3	0.0	6	dbSNP_116	47	1099,7501	749.4+/-407.4	60,979,3261	yes	missense,missense	PGBD1	NM_001184743.1,NM_032507.3	81,81	390,1989,4124	GG,GC,CC		12.7791,37.9029,21.2902	benign,benign	806/810,806/810	28270047	2769,10237	2203	4300	6503	SO:0001583	missense	84547	exon7			AATGCTCATCTGT	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.2416C>G	6.37:g.28270047C>G	ENSP00000385213:p.His806Asp	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	150	61	0.406667	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	464	0.21245421245421245	231	0.4695121951219512	67	0.1850828729281768	73	0.12762237762237763	93	0.12269129287598944	G	0.001	-3.256800	0.00021	0.379029	0.127791	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.01185	5.21;5.21	3.94	-0.338	0.12651	.	0.687962	0.11302	N	0.578143	T	0.00178	0.0005	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28038	-1.0056	9	0.02654	T	1	-15.5109	5.7901	0.18355	0.347:0.5279:0.1251:0.0	rs6456811;rs52818940;rs60945396;rs6456811	806	Q96JS3	PGBD1_HUMAN	D	806	ENSP00000385213:H806D;ENSP00000259883:H806D	ENSP00000259883:H806D	H	+	1	0	PGBD1	28378026	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.497000	0.06428	-0.322000	0.08615	-1.758000	0.00672	CAT	C|0.779;G|0.221	0.221	strong		0.388	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
IQGAP2	10788	hgsc.bcm.edu	37	5	75906851	75906851	+	Missense_Mutation	SNP	T	T	C	rs7722711	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:75906851T>C	ENST00000274364.6	+	13	1661	c.1364T>C	c.(1363-1365)gTa>gCa	p.V455A	IQGAP2_ENST00000502745.1_Missense_Mutation_p.V8A|IQGAP2_ENST00000396234.3_Missense_Mutation_p.V8A|IQGAP2_ENST00000379730.3_Missense_Mutation_p.V14A|CTD-2236F14.1_ENST00000511327.1_RNA	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	455			V -> A (in dbSNP:rs7722711).		negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)	p.V455A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		CTAGGAGTTGTAGCTGTAGGG	0.373													T|||	417	0.0832668	0.0076	0.0749	5008	,	,		17132	0.2629		0.0537	False		,,,				2504	0.0368				p.V455A		Atlas-SNP	.											IQGAP2,NS,carcinoma,0,1	IQGAP2	186	1	1	Substitution - Missense(1)	stomach(1)	c.T1364C						PASS	.	T	ALA/VAL	94,4312	77.3+/-115.6	1,92,2110	103.0	95.0	98.0		1364	4.6	0.4	5	dbSNP_116	98	543,8057	150.0+/-205.0	19,505,3776	yes	missense	IQGAP2	NM_006633.2	64	20,597,5886	CC,CT,TT		6.314,2.1335,4.8977	benign	455/1576	75906851	637,12369	2203	4300	6503	SO:0001583	missense	10788	exon13			GAGTTGTAGCTGT	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.1364T>C	5.37:g.75906851T>C	ENSP00000274364:p.Val455Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	226	0.10347985347985347	3	0.006097560975609756	26	0.0718232044198895	153	0.2674825174825175	44	0.05804749340369393	T	28.7	4.939106	0.92526	0.021335	0.06314	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000514350;ENST00000505766;ENST00000514001;ENST00000396234;ENST00000545384;ENST00000509074;ENST00000502745	T;T;T;T;T;T;T;T	0.07216	3.21;3.21;3.21;3.21;3.21;3.21;3.21;3.21	5.8	4.63	0.57726	.	0.108661	0.64402	D	0.000013	T	0.00012	0.0000	N	0.20685	0.6	0.34586	P	0.285025	B;B;B;B	0.11235	0.0;0.004;0.001;0.002	B;B;B;B	0.10450	0.002;0.005;0.004;0.002	T	0.40776	-0.9545	9	0.06494	T	0.89	-18.543	12.0043	0.53251	0.0:0.0683:0.0:0.9317	rs7722711;rs52796825;rs7722711	14;405;8;455	F5H7S7;E7EWC2;Q13576-2;Q13576	.;.;.;IQGA2_HUMAN	A	455;14;428;405;8;8;8;8;8	ENSP00000274364:V455A;ENSP00000442313:V14A;ENSP00000423672:V428A;ENSP00000421097:V405A;ENSP00000422661:V8A;ENSP00000379535:V8A;ENSP00000425351:V8A;ENSP00000426027:V8A	ENSP00000274364:V455A	V	+	2	0	IQGAP2	75942607	1.000000	0.71417	0.363000	0.25875	0.885000	0.51271	5.544000	0.67231	2.213000	0.71641	0.477000	0.44152	GTA	T|0.924;C|0.076	0.076	strong		0.373	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
CA5A	763	hgsc.bcm.edu	37	16	87921846	87921846	+	Silent	SNP	T	T	A	rs72816311	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:87921846T>A	ENST00000309893.2	-	7	872	c.807A>T	c.(805-807)gcA>gcT	p.A269A		NM_001739.1	NP_001730.1	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial	269					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(80;0.0513)	Brinzolamide(DB01194)|Zonisamide(DB00909)	CTTCACCAAGTGCAGAAAACA	0.547													T|||	864	0.172524	0.1263	0.134	5008	,	,		20689	0.1567		0.1829	False		,,,				2504	0.2679				p.A269A		Atlas-SNP	.											.	CA5A	32	.	0			c.A807T						PASS	.	T		609,3787	262.8+/-265.1	39,531,1628	54.0	49.0	50.0		807	-9.5	0.0	16	dbSNP_131	50	1789,6811	322.8+/-315.7	197,1395,2708	no	coding-synonymous	CA5A	NM_001739.1		236,1926,4336	AA,AT,TT		20.8023,13.8535,18.4518		269/306	87921846	2398,10598	2198	4300	6498	SO:0001819	synonymous_variant	763	exon7			ACCAAGTGCAGAA	L19297	CCDS10965.1	16q24.2	2012-08-21			ENSG00000174990	ENSG00000174990	4.2.1.1	"""Carbonic anhydrases"""	1377	protein-coding gene	gene with protein product		114761		CA5		8356065, 7490083	Standard	NM_001739		Approved	CAV, CAVA	uc002fkn.1	P35218	OTTHUMG00000137677	ENST00000309893.2:c.807A>T	16.37:g.87921846T>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	184	82	0.445652	NM_001739	B2RPF2	Silent	SNP	ENST00000309893.2	37	CCDS10965.1																																																																																			T|0.825;A|0.175	0.175	strong		0.547	CA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269164.1	NM_001739	
LINS	55180	hgsc.bcm.edu	37	15	101113950	101113950	+	Silent	SNP	A	A	G	rs12592868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:101113950A>G	ENST00000314742.8	-	5	1350	c.1128T>C	c.(1126-1128)agT>agC	p.S376S	LINS_ENST00000559149.1_5'UTR|LINS_ENST00000561308.1_Silent_p.S376S|LINS_ENST00000560133.1_Silent_p.S257S	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	376								p.S376S(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						CATGATCTGGACTAGTGATAA	0.353													A|||	1640	0.327476	0.2973	0.2507	5008	,	,		20927	0.246		0.4513	False		,,,				2504	0.3793				p.S376S		Atlas-SNP	.											LINS,NS,carcinoma,0,1	LINS	62	1	1	Substitution - coding silent(1)	stomach(1)	c.T1128C						scavenged	.	A		1415,2991	461.3+/-352.9	206,1003,994	94.0	88.0	90.0		1128	-0.9	0.8	15	dbSNP_120	90	4040,4560	556.5+/-386.9	961,2118,1221	no	coding-synonymous	LINS	NM_001040616.2		1167,3121,2215	GG,GA,AA		46.9767,32.1153,41.9422		376/758	101113950	5455,7551	2203	4300	6503	SO:0001819	synonymous_variant	55180	exon5			ATCTGGACTAGTG	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"""lines homolog 1 (Drosophila)"""	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1128T>C	15.37:g.101113950A>G		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	196	85	0.433673	NM_001040616	Q96FW2|Q9NVQ3	Silent	SNP	ENST00000314742.8	37	CCDS10385.1																																																																																			A|0.609;G|0.391	0.391	strong		0.353	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148	
PIEZO2	63895	hgsc.bcm.edu	37	18	10691357	10691357	+	Silent	SNP	G	G	A	rs3748421	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:10691357G>A	ENST00000503781.3	-	44	6875	c.6876C>T	c.(6874-6876)gcC>gcT	p.A2292A	PIEZO2_ENST00000580640.1_Silent_p.A2317A|PIEZO2_ENST00000302079.6_Silent_p.A2292A|PIEZO2_ENST00000285141.4_Silent_p.A147A|PIEZO2_ENST00000538948.1_Silent_p.A249A	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2292					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										ACCAAAGCTGGGCAACCAGGT	0.428													G|||	1007	0.201078	0.1263	0.2046	5008	,	,		18269	0.1111		0.3559	False		,,,				2504	0.2331				p.A2292A		Atlas-SNP	.											.	.	.	.	0			c.C6876T						PASS	.	G		725,3681	301.0+/-286.6	64,597,1542	85.0	76.0	79.0		6876	-6.0	0.8	18	dbSNP_107	79	3116,5484	476.0+/-369.3	595,1926,1779	no	coding-synonymous	PIEZO2	NM_022068.2		659,2523,3321	AA,AG,GG		36.2326,16.4548,29.5325		2292/2753	10691357	3841,9165	2203	4300	6503	SO:0001819	synonymous_variant	63895	exon44			AAGCTGGGCAACC	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"""chromosome 18 open reading frame 30"", ""chromosome 18 open reading frame 58"", ""family with sequence similarity 38, member B"""	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.6876C>T	18.37:g.10691357G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Silent	SNP	ENST00000503781.3	37																																																																																				G|0.718;A|0.282	0.282	strong		0.428	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068	
STOM	2040	hgsc.bcm.edu	37	9	124103523	124103523	+	Missense_Mutation	SNP	A	A	G	rs41273438	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:124103523A>G	ENST00000286713.2	-	7	841	c.824T>C	c.(823-825)aTg>aCg	p.M275T	AL161784.1_ENST00000594963.1_5'Flank|STOM_ENST00000538954.1_Missense_Mutation_p.M224T|STOM_ENST00000347359.2_Missense_Mutation_p.M110T	NM_001270526.1|NM_004099.5	NP_001257455.1|NP_004090.4	P27105	STOM_HUMAN	stomatin	275	Interaction with LANCL1.				protein homooligomerization (GO:0051260)|regulation of acid-sensing ion channel activity (GO:1901585)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|vesicle (GO:0031982)				endometrium(1)|large_intestine(1)|lung(3)|urinary_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)		TCCTTGCAGCATATCTATGGG	0.488													A|||	97	0.019369	0.0045	0.0216	5008	,	,		19063	0.0		0.0368	False		,,,				2504	0.0399				p.M275T		Atlas-SNP	.											STOM,NS,carcinoma,-1,1	STOM	15	1	0			c.T824C						PASS	.	A	THR/MET,THR/MET	40,4366	43.8+/-77.6	1,38,2164	190.0	179.0	183.0		824,329	4.9	1.0	9	dbSNP_127	183	340,8260	116.6+/-176.3	10,320,3970	yes	missense,missense	STOM	NM_004099.4,NM_198194.1	81,81	11,358,6134	GG,GA,AA		3.9535,0.9079,2.9217	benign,benign	275/289,110/124	124103523	380,12626	2203	4300	6503	SO:0001583	missense	2040	exon7			TGCAGCATATCTA		CCDS6830.1, CCDS6831.1, CCDS75892.1	9q34.1	2008-07-21	2002-11-11	2002-11-15	ENSG00000148175	ENSG00000148175			3383	protein-coding gene	gene with protein product		133090	"""erythrocyte membrane protein band 7.2 (stomatin)"""	EPB7, EPB72		1883838	Standard	NM_198194		Approved	BND7	uc004blh.4	P27105	OTTHUMG00000020590	ENST00000286713.2:c.824T>C	9.37:g.124103523A>G	ENSP00000286713:p.Met275Thr	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	216	114	0.527778	NM_004099	B1AM77|Q14087|Q15609|Q5VX96|Q96FK4	Missense_Mutation	SNP	ENST00000286713.2	37	CCDS6830.1	41	0.018772893772893772	4	0.008130081300813009	8	0.022099447513812154	0	0.0	29	0.03825857519788918	A	16.46	3.130373	0.56721	0.009079	0.039535	ENSG00000148175	ENST00000286713;ENST00000538954;ENST00000347359	D;D;D	0.99571	-6.19;-6.19;-4.51	4.86	4.86	0.63082	.	0.088931	0.85682	D	0.000000	D	0.95999	0.8697	L	0.48877	1.53	0.54753	D	0.999989	B;B	0.24963	0.115;0.041	B;B	0.40199	0.322;0.03	D	0.91311	0.5074	10	0.66056	D	0.02	.	13.7961	0.63171	1.0:0.0:0.0:0.0	rs41273438;rs62640058	110;275	B1AM77;P27105	.;STOM_HUMAN	T	275;224;110	ENSP00000286713:M275T;ENSP00000445764:M224T;ENSP00000339607:M110T	ENSP00000286713:M275T	M	-	2	0	STOM	123143344	1.000000	0.71417	0.963000	0.40424	0.924000	0.55760	8.856000	0.92245	2.032000	0.59987	0.454000	0.30748	ATG	A|0.971;G|0.029	0.029	strong		0.488	STOM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053889.1	NM_004099	
FAM181B	220382	hgsc.bcm.edu	37	11	82443817	82443817	+	Silent	SNP	G	G	A	rs2291793	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:82443817G>A	ENST00000329203.3	-	1	1089	c.955C>T	c.(955-957)Ctg>Ttg	p.L319L		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	319	Pro-rich.									large_intestine(1)|lung(2)|prostate(1)	4						TCGGGGTACAGTAGGTTTCCC	0.711													G|||	1146	0.228834	0.0658	0.2262	5008	,	,		10575	0.497		0.172	False		,,,				2504	0.2331				p.L319L		Atlas-SNP	.											.	FAM181B	14	.	0			c.C955T						PASS	.	G		83,2091		1,81,1005	1.0	1.0	1.0		955	2.3	0.1	11	dbSNP_100	1	480,4156		6,468,1844	no	coding-synonymous	FAM181B	NM_175885.3		7,549,2849	AA,AG,GG		10.3538,3.8178,8.2673		319/427	82443817	563,6247	1087	2318	3405	SO:0001819	synonymous_variant	220382	exon1			GGTACAGTAGGTT	AK095054, BC039262	CCDS31648.1	11q14.1	2011-11-30			ENSG00000182103	ENSG00000182103			28512	protein-coding gene	gene with protein product						12477932	Standard	NM_175885		Approved	LOC220382, MGC33846	uc001ozp.3	A6NEQ2	OTTHUMG00000166869	ENST00000329203.3:c.955C>T	11.37:g.82443817G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	24	8	0.333333	NM_175885	B2RWP1	Silent	SNP	ENST00000329203.3	37	CCDS31648.1																																																																																			G|0.745;A|0.255	0.255	strong		0.711	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885	
PAPSS1	9061	hgsc.bcm.edu	37	4	108575955	108575955	+	Missense_Mutation	SNP	G	G	A	rs35176475	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:108575955G>A	ENST00000265174.4	-	8	1269	c.997C>T	c.(997-999)Cgc>Tgc	p.R333C	PAPSS1_ENST00000511304.1_5'UTR	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	333					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		GCCACACGGCGGCCCTCATAC	0.498													G|||	35	0.00698882	0.0023	0.0173	5008	,	,		16257	0.001		0.0159	False		,,,				2504	0.0031				p.R333C		Atlas-SNP	.											PAPSS1,colon,carcinoma,+1,1	PAPSS1	57	1	0			c.C997T						scavenged	.	G	CYS/ARG	23,4383	29.9+/-59.1	0,23,2180	124.0	129.0	127.0		997	2.1	1.0	4	dbSNP_126	127	220,8380	91.1+/-153.3	2,216,4082	yes	missense	PAPSS1	NM_005443.4	180	2,239,6262	AA,AG,GG		2.5581,0.522,1.8684	benign	333/625	108575955	243,12763	2203	4300	6503	SO:0001583	missense	9061	exon8			CACGGCGGCCCTC	Y10387	CCDS3676.1	4q24	2012-07-13			ENSG00000138801	ENSG00000138801	2.7.7.4, 2.7.1.25		8603	protein-coding gene	gene with protein product		603262				9576487, 9771708	Standard	NM_005443		Approved	ATPSK1, PAPSS	uc003hyk.3	O43252	OTTHUMG00000131210	ENST00000265174.4:c.997C>T	4.37:g.108575955G>A	ENSP00000265174:p.Arg333Cys	Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	254	115	0.452756	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Missense_Mutation	SNP	ENST00000265174.4	37	CCDS3676.1	21	0.009615384615384616	1	0.0020325203252032522	6	0.016574585635359115	1	0.0017482517482517483	13	0.017150395778364115	G	19.53	3.844286	0.71488	0.00522	0.025581	ENSG00000138801	ENST00000265174	T	0.23552	1.9	5.72	2.14	0.27477	Sulphate adenylyltransferase (2);PUA-like domain (1);	0.336525	0.35646	N	0.003079	T	0.07548	0.0190	L	0.54323	1.7	0.58432	D	0.999993	B	0.09022	0.002	B	0.04013	0.001	T	0.04522	-1.0945	10	0.66056	D	0.02	-0.2516	5.6069	0.17385	0.2661:0.0:0.6084:0.1254	rs35176475;rs45574832	333	O43252	PAPS1_HUMAN	C	333	ENSP00000265174:R333C	ENSP00000265174:R333C	R	-	1	0	PAPSS1	108795404	0.291000	0.24352	0.971000	0.41717	0.966000	0.64601	1.335000	0.33839	0.087000	0.17167	0.655000	0.94253	CGC	G|0.986;A|0.014	0.014	strong		0.498	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2		
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693155	187693155	+	Missense_Mutation	SNP	A	A	T	rs10195758	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:187693155A>T	ENST00000295131.2	-	9	1497	c.1458T>A	c.(1456-1458)gaT>gaA	p.D486E		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	486				D -> E (in Ref. 4; AAH31094). {ECO:0000305}.	apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			TAATTTTATAATCATAGGTTA	0.313													T|||	872	0.174121	0.4213	0.1066	5008	,	,		18538	0.0208		0.1103	False		,,,				2504	0.1115				p.D486E		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.T1458A						PASS	.	T	GLU/ASP	1744,2660	627.9+/-395.0	343,1058,801	40.0	45.0	43.0		1458	1.6	0.7	2	dbSNP_119	43	968,7632	763.8+/-407.6	44,880,3376	yes	missense	ZSWIM2	NM_182521.2	45	387,1938,4177	TT,TA,AA		11.2558,39.6004,20.8551	benign	486/634	187693155	2712,10292	2202	4300	6502	SO:0001583	missense	151112	exon9			TTTATAATCATAG	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1458T>A	2.37:g.187693155A>T	ENSP00000295131:p.Asp486Glu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	326	0.14926739926739926	193	0.39227642276422764	41	0.1132596685082873	10	0.017482517482517484	82	0.10817941952506596	T	0.006	-2.092970	0.00364	0.396004	0.112558	ENSG00000163012	ENST00000295131	T	0.21932	1.98	5.6	1.56	0.23342	.	0.342270	0.25377	N	0.031119	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45249	-0.9274	9	0.02654	T	1	-4.9417	3.3678	0.07210	0.3418:0.2581:0.0:0.4001	rs10195758;rs17856916;rs10195758	486	Q8NEG5	ZSWM2_HUMAN	E	486	ENSP00000295131:D486E	ENSP00000295131:D486E	D	-	3	2	ZSWIM2	187401400	0.001000	0.12720	0.711000	0.30485	0.001000	0.01503	-0.697000	0.05098	0.074000	0.16767	-0.336000	0.08194	GAT	A|0.819;T|0.181	0.181	strong		0.313	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
OR13H1	347468	hgsc.bcm.edu	37	X	130678467	130678467	+	Silent	SNP	A	A	G	rs499030	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:130678467A>G	ENST00000338616.3	+	1	518	c.420A>G	c.(418-420)gtA>gtG	p.V140V		NM_001004486.1	NP_001004486.1	Q8NG92	O13H1_HUMAN	olfactory receptor, family 13, subfamily H, member 1	140						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15	Acute lymphoblastic leukemia(192;0.000636)					ATGGCCCAGTATGTGTCTGCT	0.532													G|||	2626	0.695629	0.6346	0.4035	3775	,	,		15515	0.4841		0.4583	False		,,,				2504	0.5706				p.V140V		Atlas-SNP	.											.	OR13H1	41	.	0			c.A420G						PASS	.	G		3150,685		1095,485,475,52,96	240.0	199.0	213.0		420	-1.5	0.0	X	dbSNP_83	213	4237,2491		953,1145,1186,330,686	no	coding-synonymous	OR13H1	NM_001004486.1		2048,1630,1661,382,782	GG,GA,G,AA,A		37.0244,17.8618,30.0672		140/309	130678467	7387,3176	2203	4300	6503	SO:0001819	synonymous_variant	347468	exon1			CCCAGTATGTGTC		CCDS35396.1	Xq26.2	2012-08-23			ENSG00000171054	ENSG00000171054		"""GPCR / Class A : Olfactory receptors"""	14755	protein-coding gene	gene with protein product							Standard	NM_001004486		Approved		uc011muw.2	Q8NG92	OTTHUMG00000022411	ENST00000338616.3:c.420A>G	X.37:g.130678467A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	179	179	1	NM_001004486	B2RNQ3|Q6IET8|Q96R12	Silent	SNP	ENST00000338616.3	37	CCDS35396.1																																																																																			A|0.297;G|0.703	0.703	strong		0.532	OR13H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058297.1		
ALDH1B1	219	hgsc.bcm.edu	37	9	38396002	38396002	+	Missense_Mutation	SNP	C	C	T	rs2228093	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:38396002C>T	ENST00000377698.3	+	2	410	c.257C>T	c.(256-258)gCc>gTc	p.A86V		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	86			A -> V (in allele ALDHA1B1*2; dbSNP:rs2228093). {ECO:0000269|PubMed:8244338}.		carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)			NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		GCCCGGGAAGCCTTCCGCCTG	0.667													C|||	1154	0.230431	0.0809	0.2853	5008	,	,		17003	0.3929		0.1511	False		,,,				2504	0.3078				p.A86V		Atlas-SNP	.											ALDH1B1,NS,carcinoma,+1,1	ALDH1B1	50	1	0			c.C257T						PASS	.	C	VAL/ALA	472,3934	222.6+/-239.4	27,418,1758	64.0	68.0	67.0		257	5.5	1.0	9	dbSNP_98	67	1143,7457	235.1+/-267.8	82,979,3239	yes	missense	ALDH1B1	NM_000692.4	64	109,1397,4997	TT,TC,CC		13.2907,10.7127,12.4173	probably-damaging	86/518	38396002	1615,11391	2203	4300	6503	SO:0001583	missense	219	exon2			GGGAAGCCTTCCG	M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"""Aldehyde dehydrogenases"""	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.257C>T	9.37:g.38396002C>T	ENSP00000366927:p.Ala86Val	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_000692	B2R8F0|Q8WX76|Q9BV45	Missense_Mutation	SNP	ENST00000377698.3	37	CCDS6615.1	487	0.222985347985348	53	0.10772357723577236	92	0.2541436464088398	226	0.3951048951048951	116	0.15303430079155672	C	27.7	4.856835	0.91433	0.107127	0.132907	ENSG00000137124	ENST00000377698	T	0.26518	1.73	5.51	5.51	0.81932	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.64402	D	0.000010	T	0.00012	0.0000	M	0.89904	3.07	0.09310	P	0.999999663107	D	0.89917	1.0	D	0.83275	0.996	T	0.24764	-1.0151	9	0.87932	D	0	.	16.9009	0.86113	0.0:1.0:0.0:0.0	rs2228093;rs2228093	86	P30837	AL1B1_HUMAN	V	86	ENSP00000366927:A86V	ENSP00000366927:A86V	A	+	2	0	ALDH1B1	38386002	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.201000	0.77847	2.598000	0.87819	0.650000	0.86243	GCC	C|0.831;A|0.001	.	strong		0.667	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1		
PALD1	27143	hgsc.bcm.edu	37	10	72293713	72293713	+	Silent	SNP	C	C	T	rs12764399	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:72293713C>T	ENST00000263563.6	+	8	1174	c.906C>T	c.(904-906)caC>caT	p.H302H		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	302						cytosol (GO:0005829)		p.H302Q(1)									GTGATGCCCACGGGCCTCCCC	0.662													C|||	422	0.0842652	0.0371	0.0821	5008	,	,		18070	0.003		0.1392	False		,,,				2504	0.1769				p.H302H		Atlas-SNP	.											.	.	.	.	1	Substitution - Missense(1)	lung(1)	c.C906T						PASS	.	C		243,4163	136.9+/-172.8	6,231,1966	37.0	34.0	35.0		906	-8.8	0.0	10	dbSNP_121	35	1389,7211	258.8+/-282.3	121,1147,3032	no	coding-synonymous	KIAA1274	NM_014431.2		127,1378,4998	TT,TC,CC		16.1512,5.5152,12.5481		302/857	72293713	1632,11374	2203	4300	6503	SO:0001819	synonymous_variant	27143	exon8			TGCCCACGGGCCT	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.906C>T	10.37:g.72293713C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	176	79	0.448864	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Silent	SNP	ENST00000263563.6	37	CCDS31215.1																																																																																			C|0.893;T|0.107	0.107	strong		0.662	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
MYOM3	127294	hgsc.bcm.edu	37	1	24406535	24406535	+	Missense_Mutation	SNP	G	G	A	rs35446243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24406535G>A	ENST00000374434.3	-	20	2719	c.2557C>T	c.(2557-2559)Cca>Tca	p.P853S	RP11-293P20.4_ENST00000429191.1_RNA|RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000330966.7_Missense_Mutation_p.P854S|MYOM3_ENST00000475306.1_5'Flank|MYOM3_ENST00000329601.7_Missense_Mutation_p.P853S	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	853	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.		P -> S (in dbSNP:rs35446243). {ECO:0000269|PubMed:17974005}.			M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		ATGGGGCCTGGGGTGACCGGC	0.587													G|||	445	0.0888578	0.0091	0.2363	5008	,	,		19087	0.002		0.1859	False		,,,				2504	0.0818				p.P853S		Atlas-SNP	.											.	MYOM3	131	.	0			c.C2557T						PASS	.	G	SER/PRO	161,3759		6,149,1805	68.0	77.0	74.0		2557	1.2	0.4	1	dbSNP_126	74	1653,6647		172,1309,2669	yes	missense	MYOM3	NM_152372.3	74	178,1458,4474	AA,AG,GG		19.9157,4.1071,14.8445	possibly-damaging	853/1438	24406535	1814,10406	1960	4150	6110	SO:0001583	missense	127294	exon20			GGCCTGGGGTGAC	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.2557C>T	1.37:g.24406535G>A	ENSP00000363557:p.Pro853Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	240	0.10989010989010989	10	0.02032520325203252	88	0.2430939226519337	2	0.0034965034965034965	140	0.18469656992084432	G	7.875	0.729060	0.15507	0.041071	0.199157	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.52526	0.66;0.66;0.66	5.51	1.21	0.21127	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.543085	0.20338	N	0.094300	T	0.00012	0.0000	N	0.05534	-0.03	0.80722	P	0.0	B;B	0.17667	0.004;0.023	B;B	0.15052	0.012;0.012	T	0.25572	-1.0128	9	0.19590	T	0.45	.	1.5761	0.02624	0.1609:0.2173:0.4062:0.2155	rs35446243;rs61773553	853;853	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	S	853;854;853	ENSP00000363557:P853S;ENSP00000332670:P854S;ENSP00000328415:P853S	ENSP00000328415:P853S	P	-	1	0	MYOM3	24279122	0.164000	0.22935	0.357000	0.25798	0.376000	0.30014	0.246000	0.18160	0.691000	0.31592	-0.140000	0.14226	CCA	G|0.869;A|0.131	0.131	strong		0.587	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
C1orf141	400757	hgsc.bcm.edu	37	1	67561087	67561087	+	Missense_Mutation	SNP	A	A	C	rs145227724		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:67561087A>C	ENST00000371007.2	-	7	543	c.434T>G	c.(433-435)aTg>aGg	p.M145R	C1orf141_ENST00000371006.1_Missense_Mutation_p.M145R|C1orf141_ENST00000544837.1_Missense_Mutation_p.M145R	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	145										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						AAAATCGTTCATCTGTGGAGA	0.368													A|||	1	0.000199681	0.0	0.0	5008	,	,		19847	0.0		0.0	False		,,,				2504	0.001				p.M145R		Atlas-SNP	.											.	C1orf141	58	.	0			c.T434G						PASS	.	A	ARG/MET	0,4404		0,0,2202	47.0	44.0	45.0		434	-4.0	0.0	1	dbSNP_134	45	17,8579		0,17,4281	yes	missense	C1orf141	NM_001013674.1	91	0,17,6483	CC,CA,AA		0.1978,0.0,0.1308	possibly-damaging	145/401	67561087	17,12983	2202	4298	6500	SO:0001583	missense	400757	exon7			TCGTTCATCTGTG	BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963			32044	protein-coding gene	gene with protein product							Standard	NM_001276351		Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.434T>G	1.37:g.67561087A>C	ENSP00000360046:p.Met145Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_001276351	Q0P5P5|Q5JVX5	Missense_Mutation	SNP	ENST00000371007.2	37	CCDS30745.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.073770	0.36566	0.0	0.001978	ENSG00000203963	ENST00000371007;ENST00000371006;ENST00000544837;ENST00000371005;ENST00000448166	T;T;T	0.29397	1.57;1.57;1.57	5.76	-3.98	0.04082	.	0.801389	0.10895	N	0.622204	T	0.06962	0.0177	N	0.19112	0.55	0.09310	N	1	D	0.54601	0.967	P	0.52217	0.693	T	0.07829	-1.0752	10	0.10902	T	0.67	1.1288	2.2939	0.04145	0.3772:0.1336:0.3596:0.1296	.	145	Q5JVX7	CA141_HUMAN	R	145;145;145;216;216	ENSP00000360046:M145R;ENSP00000360045:M145R;ENSP00000444018:M145R	ENSP00000360044:M216R	M	-	2	0	C1orf141	67333675	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.277000	0.08502	-0.490000	0.06707	-0.263000	0.10527	ATG	A|0.999;C|0.001	0.001	strong		0.368	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674	
ZCCHC6	79670	hgsc.bcm.edu	37	9	88940359	88940359	+	Missense_Mutation	SNP	C	C	T	rs41310053	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:88940359C>T	ENST00000375963.3	-	12	1851	c.1679G>A	c.(1678-1680)cGg>cAg	p.R560Q	ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000469004.1_5'Flank|ZCCHC6_ENST00000375961.2_Missense_Mutation_p.R560Q|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.R437Q	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	560	PAP-associated 1.				RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						AGCATAGAACCGCAGCAATTC	0.398													C|||	10	0.00199681	0.0	0.0014	5008	,	,		17480	0.0		0.0089	False		,,,				2504	0.0				p.R560Q		Atlas-SNP	.											.	ZCCHC6	105	.	0			c.G1679A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	84.0	82.0	83.0		1679,1310,1679	5.2	1.0	9	dbSNP_127	83	48,8552	30.7+/-82.3	0,48,4252	yes	missense,missense,missense	ZCCHC6	NM_001185059.1,NM_001185074.1,NM_024617.3	43,43,43	0,50,6453	TT,TC,CC		0.5581,0.0454,0.3844	probably-damaging,probably-damaging,probably-damaging	560/1496,437/1260,560/1496	88940359	50,12956	2203	4300	6503	SO:0001583	missense	79670	exon12			TAGAACCGCAGCA	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"""Zinc fingers, CCHC domain containing"""	25817	protein-coding gene	gene with protein product	"""TUTase7"""					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.1679G>A	9.37:g.88940359C>T	ENSP00000365130:p.Arg560Gln	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	136	63	0.463235	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	37	CCDS35057.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	28.5	4.923726	0.92319	4.54E-4	0.005581	ENSG00000083223	ENST00000375960;ENST00000375961;ENST00000375963	T;T;T	0.76709	-1.04;-1.04;-1.04	5.24	5.24	0.73138	PAP/25A-associated (1);	0.000000	0.85682	D	0.000000	D	0.84889	0.5572	M	0.75615	2.305	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87244	0.2268	10	0.72032	D	0.01	-33.9822	19.0276	0.92939	0.0:1.0:0.0:0.0	rs41310053	437;560	Q5VYS8-4;Q5VYS8	.;TUT7_HUMAN	Q	437;560;560	ENSP00000365127:R437Q;ENSP00000365128:R560Q;ENSP00000365130:R560Q	ENSP00000365127:R437Q	R	-	2	0	ZCCHC6	88130179	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.420000	0.66441	2.745000	0.94114	0.650000	0.86243	CGG	C|0.997;T|0.003	0.003	strong		0.398	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617	
TOP1MT	116447	hgsc.bcm.edu	37	8	144392368	144392368	+	Missense_Mutation	SNP	G	G	A	rs2293925	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144392368G>A	ENST00000329245.4	-	13	1607	c.1573C>T	c.(1573-1575)Cgg>Tgg	p.R525W	TOP1MT_ENST00000521193.1_Missense_Mutation_p.R427W|TOP1MT_ENST00000519148.1_Missense_Mutation_p.R427W|TOP1MT_ENST00000523676.1_Missense_Mutation_p.R427W	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	525			R -> W (in dbSNP:rs2293925). {ECO:0000269|PubMed:14702039}.		DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	TCCAGGAGCCGCCTCTTCTTC	0.652													G|||	2288	0.456869	0.0393	0.6326	5008	,	,		17622	0.6716		0.4592	False		,,,				2504	0.6728				p.R525W		Atlas-SNP	.											.	TOP1MT	63	.	0			c.C1573T	GRCh37	CM066250	TOP1MT	M	rs2293925	PASS	.	G	TRP/ARG	434,3964		32,370,1797	28.0	29.0	29.0		1573	-3.1	0.0	8	dbSNP_100	29	3794,4806		845,2104,1351	yes	missense	TOP1MT	NM_052963.1	101	877,2474,3148	AA,AG,GG		44.1163,9.8681,32.5281	probably-damaging	525/602	144392368	4228,8770	2199	4300	6499	SO:0001583	missense	116447	exon13			GGAGCCGCCTCTT	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1573C>T	8.37:g.144392368G>A	ENSP00000328835:p.Arg525Trp	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Missense_Mutation	SNP	ENST00000329245.4	37	CCDS6400.1	990|990	0.4532967032967033|0.4532967032967033	27|27	0.054878048780487805|0.054878048780487805	211|211	0.5828729281767956|0.5828729281767956	397|397	0.6940559440559441|0.6940559440559441	355|355	0.4683377308707124|0.4683377308707124	G|G	23.0|23.0	4.365437|4.365437	0.82463|0.82463	0.098681|0.098681	0.441163|0.441163	ENSG00000184428|ENSG00000184428	ENST00000519977|ENST00000329245;ENST00000521193;ENST00000519148;ENST00000523676	.|T;T;T;T	.|0.50813	.|0.73;0.73;0.73;0.73	4.14|4.14	-3.14|-3.14	0.05250|0.05250	.|DNA breaking-rejoining enzyme, catalytic core (1);DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, catalytic core, alpha/beta subdomain, eukaryotic-type (1);DNA topoisomerases I, dispensable insert, eukaryotic-type (1);	.|0.179425	.|0.24889	.|U	.|0.034784	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.68952|0.68952	2.095|2.095	0.53688|0.53688	P|P	2.2999999999995246E-5|2.2999999999995246E-5	.|D;D	.|0.71674	.|0.998;0.991	.|P;P	.|0.57468	.|0.821;0.586	T|T	0.43750|0.43750	-0.9372|-0.9372	4|9	.|0.66056	.|D	.|0.02	.|.	6.8892|6.8892	0.24220|0.24220	0.0:0.1693:0.3022:0.5285|0.0:0.1693:0.3022:0.5285	rs2293925;rs11544481;rs2293925|rs2293925;rs11544481;rs2293925	.|320;525	.|E7ESI1;Q969P6	.|.;TOP1M_HUMAN	V|W	34|525;427;427;427	.|ENSP00000328835:R525W;ENSP00000428369:R427W;ENSP00000429169:R427W;ENSP00000429181:R427W	.|ENSP00000328835:R525W	A|R	-|-	2|1	0|2	TOP1MT|TOP1MT	144463743|144463743	0.634000|0.634000	0.27190|0.27190	0.000000|0.000000	0.03702|0.03702	0.865000|0.865000	0.49528|0.49528	0.360000|0.360000	0.20250|0.20250	-1.133000|-1.133000	0.02903|0.02903	0.508000|0.508000	0.49915|0.49915	GCG|CGG	G|0.617;A|0.383	0.383	strong		0.652	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963	
CHTF18	63922	hgsc.bcm.edu	37	16	840599	840599	+	Missense_Mutation	SNP	C	C	T	rs59706474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:840599C>T	ENST00000262315.9	+	7	890	c.827C>T	c.(826-828)gCc>gTc	p.A276V	CHTF18_ENST00000455171.2_Missense_Mutation_p.A304V|RPUSD1_ENST00000007264.2_5'Flank|CHTF18_ENST00000317063.6_Missense_Mutation_p.A471V|RPUSD1_ENST00000565809.1_5'Flank|RPUSD1_ENST00000561734.1_5'Flank|RPUSD1_ENST00000567114.1_5'Flank|CHTF18_ENST00000491530.1_3'UTR	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	276					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				GGTCAAGACGCCTCCAGTCAC	0.637													C|||	451	0.0900559	0.1467	0.0476	5008	,	,		13894	0.0288		0.0199	False		,,,				2504	0.1789				p.A276V		Atlas-SNP	.											.	CHTF18	52	.	0			c.C827T						PASS	.	C	VAL/ALA	506,3616		34,438,1589	33.0	39.0	37.0		827	-0.6	0.0	16	dbSNP_129	37	234,8132		4,226,3953	yes	missense	CHTF18	NM_022092.2	64	38,664,5542	TT,TC,CC		2.797,12.2756,5.9257	benign	276/976	840599	740,11748	2061	4183	6244	SO:0001583	missense	63922	exon7			AAGACGCCTCCAG	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"""ATPases / AAA-type"""	18435	protein-coding gene	gene with protein product		613201	"""chromosome 16 open reading frame 41"""	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.827C>T	16.37:g.840599C>T	ENSP00000262315:p.Ala276Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	128	0.05860805860805861	77	0.1565040650406504	21	0.058011049723756904	15	0.026223776223776224	15	0.01978891820580475	C	11.88	1.770471	0.31320	0.122756	0.02797	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.10573	2.86;2.88;2.88	5.2	-0.626	0.11544	.	1.151520	0.06027	N	0.652382	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B;B	0.29862	0.191;0.259	B;B	0.24701	0.046;0.055	T	0.42816	-0.9429	9	0.30854	T	0.27	-1.5086	10.2554	0.43394	0.5262:0.3562:0.1176:0.0	rs59706474;rs61753372	304;276	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	V	471;304;276	ENSP00000313029:A471V;ENSP00000406252:A304V;ENSP00000262315:A276V	ENSP00000262315:A276V	A	+	2	0	CHTF18	780600	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.076000	0.11412	-0.365000	0.08076	-0.534000	0.04291	GCC	C|0.947;T|0.053	0.053	strong		0.637	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
VDAC1	7416	hgsc.bcm.edu	37	5	133328003	133328003	+	Silent	SNP	A	A	G	rs142141751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:133328003A>G	ENST00000265333.3	-	3	355	c.111T>C	c.(109-111)aaT>aaC	p.N37N	VDAC1_ENST00000466080.1_5'UTR|VDAC1_ENST00000395044.3_Silent_p.N37N|VDAC1_ENST00000395047.2_Silent_p.N37N	NM_003374.2	NP_003365.1	P21796	VDAC1_HUMAN	voltage-dependent anion channel 1	37					anion transport (GO:0006820)|apoptotic process (GO:0006915)|behavioral fear response (GO:0001662)|epithelial cell differentiation (GO:0030855)|learning (GO:0007612)|neuron-neuron synaptic transmission (GO:0007270)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein kinase binding (GO:0019901)|voltage-gated anion channel activity (GO:0008308)			endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)	TTACCAATCCATTCTCAGATT	0.308													A|||	2	0.000399361	0.0	0.0	5008	,	,		16993	0.0		0.002	False		,,,				2504	0.0				p.N37N	NSCLC(127;1776 1806 35523 41489 48154)	Atlas-SNP	.											.	VDAC1	17	.	0			c.T111C						PASS	.	A		5,4399	8.1+/-20.4	0,5,2197	48.0	48.0	48.0		111	4.4	1.0	5	dbSNP_134	48	25,8575	18.5+/-59.3	0,25,4275	no	coding-synonymous	VDAC1	NM_003374.2		0,30,6472	GG,GA,AA		0.2907,0.1135,0.2307		37/284	133328003	30,12974	2202	4300	6502	SO:0001819	synonymous_variant	7416	exon3			CAATCCATTCTCA		CCDS4168.1	5q31	2011-11-15			ENSG00000213585	ENSG00000213585		"""Voltage-dependent anion channels"""	12669	protein-coding gene	gene with protein product		604492				7517385	Standard	NM_003374		Approved	MGC111064, PORIN	uc003kyr.2	P21796	OTTHUMG00000129118	ENST00000265333.3:c.111T>C	5.37:g.133328003A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	156	75	0.480769	NM_003374	B3KVK4|D3DQ93|Q5FVE7|Q9UIQ5|Q9UPL0	Silent	SNP	ENST00000265333.3	37	CCDS4168.1																																																																																			A|0.997;G|0.003	0.003	strong		0.308	VDAC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259208.1		
C16orf59	80178	hgsc.bcm.edu	37	16	2512523	2512523	+	Silent	SNP	G	G	A	rs3810794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2512523G>A	ENST00000361837.4	+	7	923	c.858G>A	c.(856-858)tcG>tcA	p.S286S	C16orf59_ENST00000569496.1_Silent_p.S286S|C16orf59_ENST00000483320.1_Silent_p.S119S|RP11-715J22.4_ENST00000566085.1_lincRNA|C16orf59_ENST00000563531.1_Silent_p.S286S|RP11-715J22.2_ENST00000563775.1_RNA	NM_025108.2	NP_079384.2	Q7L2K0	CP059_HUMAN	chromosome 16 open reading frame 59	286										lung(1)|skin(1)|urinary_tract(1)	3		Ovarian(90;0.17)				AGGAGCTCTCGGCAGGTCAGT	0.687													G|||	1418	0.283147	0.0182	0.3357	5008	,	,		16577	0.6111		0.3052	False		,,,				2504	0.2434				p.S286S		Atlas-SNP	.											.	C16orf59	13	.	0			c.G858A						PASS	.	G		240,3982		7,226,1878	14.0	19.0	18.0		858	-9.0	0.0	16	dbSNP_107	18	2306,6136		327,1652,2242	no	coding-synonymous	C16orf59	NM_025108.2		334,1878,4120	AA,AG,GG		27.3158,5.6845,20.1042		286/434	2512523	2546,10118	2111	4221	6332	SO:0001819	synonymous_variant	80178	exon7			GCTCTCGGCAGGT	AK023971	CCDS10468.2	16p13.3	2008-10-30			ENSG00000162062	ENSG00000162062			25849	protein-coding gene	gene with protein product						12477932	Standard	XM_006720955		Approved	FLJ13909	uc002cqh.3	Q7L2K0	OTTHUMG00000128859	ENST00000361837.4:c.858G>A	16.37:g.2512523G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_025108	B4DXD7|Q96H61|Q9H872	Silent	SNP	ENST00000361837.4	37	CCDS10468.2																																																																																			G|0.724;A|0.276	0.276	strong		0.687	C16orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250802.3	NM_025108	
PLXDC1	57125	hgsc.bcm.edu	37	17	37243927	37243927	+	Silent	SNP	A	A	G	rs12602945	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:37243927A>G	ENST00000315392.4	-	8	1051	c.840T>C	c.(838-840)taT>taC	p.Y280Y	PLXDC1_ENST00000444911.2_Silent_p.Y240Y|PLXDC1_ENST00000394316.2_Silent_p.Y280Y|PLXDC1_ENST00000493200.1_5'UTR|PLXDC1_ENST00000539608.1_Silent_p.Y207Y	NM_020405.4	NP_065138.2	Q8IUK5	PLDX1_HUMAN	plexin domain containing 1	280					angiogenesis (GO:0001525)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)	receptor activity (GO:0004872)			kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						CTATGCGGTGATATTCAAAGA	0.567													G|||	1459	0.291334	0.1067	0.4496	5008	,	,		21447	0.3492		0.3032	False		,,,				2504	0.3569				p.Y280Y		Atlas-SNP	.											PLXDC1,NS,carcinoma,0,1	PLXDC1	45	1	0			c.T840C						PASS	.	G		636,3770	767.7+/-413.5	53,530,1620	85.0	64.0	71.0		840	-0.4	1.0	17	dbSNP_120	71	2523,6077	693.3+/-404.6	374,1775,2151	no	coding-synonymous	PLXDC1	NM_020405.4		427,2305,3771	GG,GA,AA		29.3372,14.4349,24.2888		280/501	37243927	3159,9847	2203	4300	6503	SO:0001819	synonymous_variant	57125	exon8			GCGGTGATATTCA	AF279144	CCDS11333.1	17q21.1	2006-04-12			ENSG00000161381	ENSG00000161381			20945	protein-coding gene	gene with protein product	"""tumor endothelial marker 7 precursor"""	606826				10947988, 11559528	Standard	NM_020405		Approved	TEM3, TEM7	uc002hrg.2	Q8IUK5	OTTHUMG00000133183	ENST00000315392.4:c.840T>C	17.37:g.37243927A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_020405	B2R7I8|Q5QCZ7|Q5QCZ8|Q5QCZ9|Q9HCT9	Silent	SNP	ENST00000315392.4	37	CCDS11333.1																																																																																			A|0.747;G|0.253	0.253	strong		0.567	PLXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256892.2	NM_020405	
TAS2R19	259294	hgsc.bcm.edu	37	12	11175087	11175087	+	Silent	SNP	G	G	A	rs12313469	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11175087G>A	ENST00000390673.2	-	1	132	c.84C>T	c.(82-84)gcC>gcT	p.A28A	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176888.1	NP_795369.1	P59542	T2R19_HUMAN	taste receptor, type 2, member 19	28					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|stomach(1)	17						CATTTACTAGGGCTATGAAGC	0.403													.|||	1762	0.351837	0.3601	0.4669	5008	,	,		21367	0.1944		0.5109	False		,,,				2504	0.2577				p.A28A		Atlas-SNP	.											TAS2R19,NS,carcinoma,-2,1	TAS2R19	30	1	0			c.C84T						PASS	.	A		1670,2736		320,1030,853	85.0	79.0	81.0		84	-4.9	0.0	12	dbSNP_120	81	4346,4254		1121,2104,1075	no	coding-synonymous	TAS2R19	NM_176888.1		1441,3134,1928	AA,AG,GG		49.4651,37.9029,46.2556		28/300	11175087	6016,6990	2203	4300	6503	SO:0001819	synonymous_variant	259294	exon1			TACTAGGGCTATG	AX097730, AF494234	CCDS8640.1	12p13.2	2012-08-22			ENSG00000212124	ENSG00000212124		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19108	protein-coding gene	gene with protein product		613961	"""taste receptor, type 2, member 48"", ""taste receptor, type 2, member 23"""	TAS2R48, TAS2R23			Standard	NM_176888		Approved	T2R19, T2R23	uc010shj.2	P59542	OTTHUMG00000162687	ENST00000390673.2:c.84C>T	12.37:g.11175087G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_176888	Q3MIJ4|Q645X8	Silent	SNP	ENST00000390673.2	37	CCDS8640.1																																																																																			G|0.536;A|0.464	0.464	strong		0.403	TAS2R19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370080.1	NM_176888	
SMYD1	150572	hgsc.bcm.edu	37	2	88396123	88396123	+	Silent	SNP	C	C	G	rs2970912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:88396123C>G	ENST00000419482.2	+	6	793	c.708C>G	c.(706-708)ctC>ctG	p.L236L	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.L223L	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	236	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						GAATTGAGCTCCGGGCCCTAG	0.507													C|||	1572	0.313898	0.4244	0.2579	5008	,	,		20727	0.1627		0.3559	False		,,,				2504	0.317				p.L236L		Atlas-SNP	.											.	SMYD1	95	.	0			c.C708G						PASS	.	C		1785,2621	526.0+/-371.8	357,1071,775	97.0	96.0	96.0		708	1.3	1.0	2	dbSNP_101	96	3134,5466	473.7+/-368.7	570,1994,1736	no	coding-synonymous	SMYD1	NM_198274.3		927,3065,2511	GG,GC,CC		36.4419,40.5129,37.821		236/491	88396123	4919,8087	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon6			TGAGCTCCGGGCC	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.708C>G	2.37:g.88396123C>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	159	78	0.490566	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			C|0.650;G|0.350	0.350	strong		0.507	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
TLR8	51311	hgsc.bcm.edu	37	X	12939112	12939112	+	Silent	SNP	G	G	C	rs2407992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:12939112G>C	ENST00000218032.6	+	2	2040	c.1953G>C	c.(1951-1953)ctG>ctC	p.L651L	TLR8_ENST00000311912.5_Silent_p.L669L	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	651					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TTAATAGGCTGAAGCACATCC	0.368													C|||	2729	0.722914	0.7239	0.5231	3775	,	,		15448	0.6151		0.2893	False		,,,				2504	0.5092				p.L651L		Atlas-SNP	.											.	TLR8	134	.	0			c.G1953C						PASS	.	C		3387,448		1275,330,507,27,64	58.0	60.0	59.0		1953	-6.9	0.0	X	dbSNP_100	59	2654,4072		392,1133,737,903,1133	no	coding-synonymous	TLR8	NM_138636.4		1667,1463,1244,930,1197	CC,CG,C,GG,G		39.4588,11.6819,42.799		651/1042	12939112	6041,4520	2203	4298	6501	SO:0001819	synonymous_variant	51311	exon2			TAGGCTGAAGCAC	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1953G>C	X.37:g.12939112G>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	166	161	0.96988	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	37	CCDS14152.1																																																																																			0|0.007;C|0.613	0.613	strong		0.368	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
MATN2	4147	hgsc.bcm.edu	37	8	98943545	98943545	+	Silent	SNP	A	A	G	rs2290471	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:98943545A>G	ENST00000520016.1	+	2	631	c.507A>G	c.(505-507)acA>acG	p.T169T	MATN2_ENST00000254898.5_Silent_p.T169T|MATN2_ENST00000521689.1_Silent_p.T169T|MATN2_ENST00000524308.1_Silent_p.T169T|MATN2_ENST00000522025.2_Intron			O00339	MATN2_HUMAN	matrilin 2	169	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TGATCGTGACAGATGGGAGAC	0.592													G|||	1390	0.277556	0.5023	0.2565	5008	,	,		21133	0.0804		0.2883	False		,,,				2504	0.181				p.T169T		Atlas-SNP	.											MATN2_ENST00000520016,NS,carcinoma,+1,2	MATN2	165	2	0			c.A507G						PASS	.	G	,	1825,2387		422,981,703	38.0	44.0	42.0		507,507	-11.6	0.0	8	dbSNP_100	42	2405,6067		366,1673,2197	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	788,2654,2900	GG,GA,AA		28.3876,43.3286,33.3491	,	169/957,169/938	98943545	4230,8454	2106	4236	6342	SO:0001819	synonymous_variant	4147	exon3			CGTGACAGATGGG	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.507A>G	8.37:g.98943545A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1																																																																																			A|0.787;G|0.213	0.213	strong		0.592	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
OR52N2	390077	hgsc.bcm.edu	37	11	5842310	5842310	+	Missense_Mutation	SNP	T	T	G	rs8181529	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5842310T>G	ENST00000317037.2	+	1	767	c.745T>G	c.(745-747)Tcc>Gcc	p.S249A	TRIM5_ENST00000380027.1_Intron	NM_001005174.1	NP_001005174.1	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N, member 2	249			S -> A (in dbSNP:rs8181529).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|urinary_tract(1)	32		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.49e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCACATGTGTTCCATTGTGAT	0.428													G|||	2519	0.502995	0.447	0.5086	5008	,	,		24247	0.4702		0.5845	False		,,,				2504	0.5245				p.S249A		Atlas-SNP	.											OR52N2,NS,carcinoma,-1,1	OR52N2	58	1	0			c.T745G						PASS	.	G	ALA/SER	2081,2321	604.5+/-390.4	492,1097,612	234.0	183.0	200.0		745	6.1	1.0	11	dbSNP_117	200	5331,3261	489.2+/-372.6	1637,2057,602	yes	missense	OR52N2	NM_001005174.1	99	2129,3154,1214	GG,GT,TT		37.9539,47.274,42.9583	benign	249/322	5842310	7412,5582	2201	4296	6497	SO:0001583	missense	390077	exon1			ATGTGTTCCATTG	AB065816	CCDS31399.1	11p15.4	2012-08-09			ENSG00000180988	ENSG00000180988		"""GPCR / Class A : Olfactory receptors"""	15228	protein-coding gene	gene with protein product							Standard	NM_001005174		Approved		uc010qzp.2	Q8NGI0	OTTHUMG00000168801	ENST00000317037.2:c.745T>G	11.37:g.5842310T>G	ENSP00000322801:p.Ser249Ala	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	332	157	0.472892	NM_001005174	Q6IFF9	Missense_Mutation	SNP	ENST00000317037.2	37	CCDS31399.1	1133	0.5187728937728938	222	0.45121951219512196	192	0.5303867403314917	272	0.4755244755244755	447	0.5897097625329816	G	3.251	-0.153283	0.06585	0.47274	0.620461	ENSG00000180988	ENST00000317037	T	0.00036	8.86	6.09	6.09	0.99107	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	N	0.000057	T	0.00012	0.0000	N	0.00064	-2.315	0.53688	P	2.4000000000024002E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.09818	-1.0657	9	0.27082	T	0.32	.	15.7694	0.78152	0.0:0.0:0.8624:0.1376	rs8181529;rs52792772;rs60856863;rs8181529	249	Q8NGI0	O52N2_HUMAN	A	249	ENSP00000322801:S249A	ENSP00000322801:S249A	S	+	1	0	OR52N2	5798886	0.097000	0.21791	0.986000	0.45419	0.012000	0.07955	1.663000	0.37429	1.605000	0.50152	-0.132000	0.14878	TCC	T|0.455;G|0.545	0.545	strong		0.428	OR52N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401143.1	NM_001005174	
MMP10	4319	hgsc.bcm.edu	37	11	102651313	102651313	+	Missense_Mutation	SNP	G	G	C	rs17435959	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:102651313G>C	ENST00000279441.4	-	1	46	c.10C>G	c.(10-12)Ctt>Gtt	p.L4V		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	4			L -> V (in dbSNP:rs17435959). {ECO:0000269|Ref.5}.		collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	AGGAATGCAAGATGCATCATT	0.493													G|||	418	0.0834665	0.1982	0.0389	5008	,	,		19094	0.0486		0.0358	False		,,,				2504	0.045				p.L4V		Atlas-SNP	.											.	MMP10	44	.	0			c.C10G						PASS	.	G	VAL/LEU	678,3728	286.3+/-278.7	54,570,1579	249.0	188.0	209.0		10	1.6	0.0	11	dbSNP_123	209	262,8336	101.2+/-162.5	4,254,4041	yes	missense	MMP10	NM_002425.2	32	58,824,5620	CC,CG,GG		3.0472,15.3881,7.2285	benign	4/477	102651313	940,12064	2203	4299	6502	SO:0001583	missense	4319	exon1			ATGCAAGATGCAT	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"""matrix metalloproteinase 10 (stromelysin 2)"""	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.10C>G	11.37:g.102651313G>C	ENSP00000279441:p.Leu4Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_002425	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	37	CCDS8321.1	164	0.07509157509157509	100	0.2032520325203252	10	0.027624309392265192	26	0.045454545454545456	28	0.036939313984168866	g	9.913	1.209925	0.22289	0.153881	0.030472	ENSG00000166670	ENST00000279441;ENST00000539681	T;T	0.21932	2.58;1.98	3.46	1.59	0.23543	.	0.174050	0.27600	N	0.018657	T	0.00039	0.0001	M	0.86953	2.85	0.80722	P	0.0	P	0.48694	0.914	B	0.41236	0.351	T	0.07731	-1.0757	9	0.59425	D	0.04	.	8.088	0.30784	0.1944:0.0:0.8056:0.0	rs17435959;rs17860945;rs61641414	4	P09238	MMP10_HUMAN	V	4	ENSP00000279441:L4V;ENSP00000441485:L4V	ENSP00000279441:L4V	L	-	1	0	MMP10	102156523	0.121000	0.22262	0.009000	0.14445	0.018000	0.09664	1.532000	0.36029	0.478000	0.27488	0.549000	0.68633	CTT	G|0.926;C|0.074	0.074	strong		0.493	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		
PCDHAC2	56134	hgsc.bcm.edu	37	5	140347398	140347398	+	Silent	SNP	C	C	T	rs12153295	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140347398C>T	ENST00000289269.5	+	1	1579	c.1047C>T	c.(1045-1047)tgC>tgT	p.C349C	PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	349	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGGTCACTGCAAGGTGCTGG	0.572													C|||	381	0.0760783	0.0514	0.1254	5008	,	,		19977	0.0188		0.1451	False		,,,				2504	0.0624				p.C349C	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.C1047T						PASS	.	C	,,,,,,,,,,,,,,,,,,	338,4068	177.6+/-206.5	8,322,1873	64.0	56.0	58.0		,1047,,,,,,,,,,,,,,,,,1047	4.7	1.0	5	dbSNP_120	58	1350,7250	264.3+/-285.5	98,1154,3048	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	106,1476,4921	TT,TC,CC		15.6977,7.6714,12.9786	,,,,,,,,,,,,,,,,,,	,349/1008,,,,,,,,,,,,,,,,,349/885	140347398	1688,11318	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			TCACTGCAAGGTG	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1047C>T	5.37:g.140347398C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	82	47	0.573171	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			C|0.881;T|0.119	0.119	strong		0.572	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
DEPDC5	9681	hgsc.bcm.edu	37	22	32205632	32205632	+	Splice_Site	SNP	A	A	C	rs5998135	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:32205632A>C	ENST00000382112.3	+	18	1393	c.1323A>C	c.(1321-1323)acA>acC	p.T441T	DEPDC5_ENST00000400242.3_Splice_Site_p.T441T|DEPDC5_ENST00000382105.2_Splice_Site_p.T441T|DEPDC5_ENST00000400249.2_Splice_Site_p.T441T|DEPDC5_ENST00000536766.1_Splice_Site_p.T413T|DEPDC5_ENST00000535622.1_Splice_Site_p.T441T|DEPDC5_ENST00000400246.1_Splice_Site_p.T441T|DEPDC5_ENST00000400248.2_Splice_Site_p.T441T|DEPDC5_ENST00000382111.2_Splice_Site_p.T441T|DEPDC5_ENST00000266091.3_Splice_Site_p.T441T	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	441					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GCCGTGATACATGTGAGTATT	0.413													a|||	448	0.0894569	0.1097	0.1859	5008	,	,		18696	0.0347		0.0984	False		,,,				2504	0.0409				p.T441T		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A1323C						PASS	.	G	,,,,	469,3189		39,391,1399	90.0	86.0	87.0		1323,1323,1323,1323,1323	-10.8	0.6	22	dbSNP_114	87	814,7356		41,732,3312	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	DEPDC5	NM_001007188.2,NM_001136029.2,NM_001242896.1,NM_001242897.1,NM_014662.3	,,,,	80,1123,4711	CC,CA,AA		9.9633,12.8212,10.8471	,,,,	441/560,441/1595,441/1604,441/1504,441/1573	32205632	1283,10545	1829	4085	5914	SO:0001630	splice_region_variant	9681	exon19			TGATACATGTGAG	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.1324+1A>C	22.37:g.32205632A>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_001242897	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Silent	SNP	ENST00000382112.3	37	CCDS46692.1																																																																																			A|0.906;C|0.094	0.094	strong		0.413	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	Silent
ZNF839	55778	hgsc.bcm.edu	37	14	102805556	102805556	+	Silent	SNP	C	C	T	rs199523800		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102805556C>T	ENST00000558850.1	+	7	1925	c.1575C>T	c.(1573-1575)gcC>gcT	p.A525A	ZNF839_ENST00000442396.2_Silent_p.A641A|ZNF839_ENST00000559185.1_Silent_p.A525A|ZNF839_ENST00000262236.5_Silent_p.A525A|AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000420933.2_3'UTR	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	525							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						ATGCTTTGGCCGCTGGTGAGG	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		19149	0.0		0.001	False		,,,				2504	0.0				p.A641A		Atlas-SNP	.											.	ZNF839	41	.	0			c.C1923T						PASS	.	C		0,3844		0,0,1922	52.0	54.0	53.0		1923	-5.2	0.0	14		53	5,8281		0,5,4138	no	coding-synonymous	ZNF839	NM_018335.3		0,5,6060	TT,TC,CC		0.0603,0.0,0.0412		641/928	102805556	5,12125	1922	4143	6065	SO:0001819	synonymous_variant	55778	exon7			TTTGGCCGCTGGT	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.1575C>T	14.37:g.102805556C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	196	87	0.443878	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	37	CCDS58336.1																																																																																			C|0.998;T|0.002	0.002	weak		0.552	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
MUC21	394263	hgsc.bcm.edu	37	6	30954491	30954491	+	Missense_Mutation	SNP	C	C	T	rs34126344	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954491C>T	ENST00000376296.3	+	2	780	c.539C>T	c.(538-540)gCc>gTc	p.A180V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	180	28 X 15 AA approximate tandem repeats.|Ser-rich.			A -> V (in Ref. 4; CAQ07653). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GCCAGCACAGCCACCAACTCT	0.607													C|||	312	0.0623003	0.0166	0.0994	5008	,	,		27275	0.1319		0.0596	False		,,,				2504	0.0286				p.A180V		Atlas-SNP	.											MUC21,rectum,carcinoma,0,1	MUC21	98	1	0			c.C539T						scavenged	.	C	VAL/ALA	162,4244	108.6+/-147.0	1,160,2042	159.0	151.0	154.0		539	1.9	0.0	6	dbSNP_126	154	585,8015	155.4+/-209.4	23,539,3738	no	missense	MUC21	NM_001010909.2	64	24,699,5780	TT,TC,CC		6.8023,3.6768,5.7435	benign	180/567	30954491	747,12259	2203	4300	6503	SO:0001583	missense	394263	exon2			GCACAGCCACCAA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.539C>T	6.37:g.30954491C>T	ENSP00000365473:p.Ala180Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	145	9	0.062069	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	148	0.06776556776556776	10	0.02032520325203252	30	0.08287292817679558	62	0.10839160839160839	46	0.06068601583113457	C	9.071	0.996786	0.19043	0.036768	0.068023	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02787	4.16	3.72	1.89	0.25635	.	.	.	.	.	T	0.00695	0.0023	N	0.19112	0.55	0.80722	P	0.0	B	0.33044	0.395	B	0.36289	0.221	T	0.49725	-0.8909	7	.	.	.	-0.31	3.2061	0.06666	0.2079:0.5615:0.0:0.2305	rs34126344	180	Q5SSG8	MUC21_HUMAN	V	180	ENSP00000365473:A180V	.	A	+	2	0	MUC21	31062470	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	0.279000	0.18771	0.360000	0.24265	0.485000	0.47835	GCC	C|0.943;T|0.057	0.057	strong		0.607	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
FAM169B	283777	hgsc.bcm.edu	37	15	99023968	99023968	+	Silent	SNP	T	T	G	rs4528551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:99023968T>G	ENST00000558256.1	-	4	294	c.45A>C	c.(43-45)ctA>ctC	p.L15L	FAM169B_ENST00000332908.4_Silent_p.L15L	NM_182562.2	NP_872368.2	Q8N8A8	F169B_HUMAN	family with sequence similarity 169, member B	15										large_intestine(3)|lung(3)|urinary_tract(1)	7						TAATGGCGTTTAGAATGAAAA	0.373													T|||	1687	0.336861	0.2027	0.4957	5008	,	,		22923	0.3413		0.3519	False		,,,				2504	0.3855				p.L15L		Atlas-SNP	.											.	FAM169B	23	.	0			c.A45C						PASS	.	T		930,2798		117,696,1051	83.0	79.0	80.0		45	-10.5	0.0	15	dbSNP_111	80	2928,5264		514,1900,1682	no	coding-synonymous	FAM169B	NM_182562.2		631,2596,2733	GG,GT,TT		35.7422,24.9464,32.3658		15/193	99023968	3858,8062	1864	4096	5960	SO:0001819	synonymous_variant	283777	exon4			GGCGTTTAGAATG		CCDS45360.1	15q26.3	2008-08-08			ENSG00000185087	ENSG00000185087			26835	protein-coding gene	gene with protein product							Standard	NM_182562		Approved	FLJ39743, KIAA0888L	uc002buk.1	Q8N8A8		ENST00000558256.1:c.45A>C	15.37:g.99023968T>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_182562	B5MDL8	Silent	SNP	ENST00000558256.1	37	CCDS45360.1																																																																																			T|0.666;G|0.334	0.334	strong		0.373	FAM169B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415488.1	NM_182562	
LAMA3	3909	hgsc.bcm.edu	37	18	21481233	21481233	+	Silent	SNP	C	C	G	rs1154226	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:21481233C>G	ENST00000313654.9	+	48	6388	c.6147C>G	c.(6145-6147)gcC>gcG	p.A2049A	LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000587184.1_Silent_p.A384A|LAMA3_ENST00000269217.6_Silent_p.A440A|LAMA3_ENST00000399516.3_Silent_p.A1993A	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2049	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					CTGCCCAAGCCAAGCAGGCAA	0.478													C|||	843	0.168331	0.0151	0.1902	5008	,	,		19312	0.1885		0.2624	False		,,,				2504	0.2423				p.A2049A		Atlas-SNP	.											LAMA3_ENST00000269217,NS,adenoma,0,2	LAMA3	397	2	0			c.C6147G						PASS	.	C	,,,	254,4152	146.5+/-181.1	12,230,1961	59.0	56.0	57.0		1320,5979,1152,6147	-3.1	1.0	18	dbSNP_87	57	2332,6268	390.3+/-343.2	294,1744,2262	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	306,1974,4223	GG,GC,CC		27.1163,5.7649,19.8831	,,,	440/1725,1993/3278,384/1669,2049/3334	21481233	2586,10420	2203	4300	6503	SO:0001819	synonymous_variant	3909	exon48			CCAAGCCAAGCAG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.6147C>G	18.37:g.21481233C>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	83	81	0.975904	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.807;G|0.193	0.193	strong		0.478	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
TCP10	6953	hgsc.bcm.edu	37	6	167796319	167796319	+	Missense_Mutation	SNP	T	T	C	rs17855833	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:167796319T>C	ENST00000397829.4	-	2	210	c.43A>G	c.(43-45)Agc>Ggc	p.S15G	TCP10_ENST00000476779.2_Missense_Mutation_p.S15G|TCP10_ENST00000366827.2_Missense_Mutation_p.S15G	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	42						cytosol (GO:0005829)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(6)	18		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		CCGGCATTGCTGTCCTCCCTG	0.647													N|||	1184	0.236422	0.1747	0.2579	5008	,	,		17547	0.3839		0.1958	False		,,,				2504	0.1943				p.S15G		Atlas-SNP	.											.	TCP10	35	.	0			c.A43G						PASS	.	C	GLY/SER	933,3397		95,743,1327	26.0	36.0	32.0		43	-4.0	0.0	6	dbSNP_123	32	1806,6758		202,1402,2678	no	missense	TCP10	NM_004610.3	56	297,2145,4005	CC,CT,TT		21.0883,21.5473,21.2424	benign	15/327	167796319	2739,10155	2165	4282	6447	SO:0001583	missense	6953	exon2			CATTGCTGTCCTC	U03399	CCDS43527.1	6q27	2012-09-20	2012-09-20		ENSG00000203690	ENSG00000203690			11656	protein-coding gene	gene with protein product		187020	"""t-complex 10 (a murine tcp homolog)"", ""t-complex 10 (mouse)"", ""t-complex 10 homolog (mouse)"""			8111376	Standard	NM_004610		Approved		uc003qvv.1	Q12799	OTTHUMG00000016026	ENST00000397829.4:c.43A>G	6.37:g.167796319T>C	ENSP00000380929:p.Ser15Gly	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	167	80	0.479042	NM_004610	Q5JR60|Q6P4F4	Missense_Mutation	SNP	ENST00000397829.4	37	CCDS43527.1	547	0.25045787545787546	92	0.18699186991869918	83	0.2292817679558011	230	0.4020979020979021	142	0.18733509234828497	C	0.009	-1.838222	0.00573	0.215473	0.210883	ENSG00000203690	ENST00000366827;ENST00000397829;ENST00000476779;ENST00000485157	T;T;T;T	0.21191	2.02;2.02;2.02;2.02	2.02	-4.04	0.04010	.	.	.	.	.	T	0.01523	0.0049	N	0.04636	-0.2	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40590	-0.9555	8	0.11794	T	0.64	.	4.1844	0.10392	0.1649:0.3987:0.0:0.4364	rs17855833;rs57516253	42;42	Q12799;Q12799-2	TCP10_HUMAN;.	G	15	ENSP00000355792:S15G;ENSP00000380929:S15G;ENSP00000427675:S15G;ENSP00000423829:S15G	ENSP00000355792:S15G	S	-	1	0	TCP10	167716309	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.516000	0.00954	-2.017000	0.00944	-1.803000	0.00618	AGC	T|0.758;C|0.242	0.242	strong		0.647	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1	NM_004610	
KBTBD13	390594	hgsc.bcm.edu	37	15	65369242	65369242	+	Missense_Mutation	SNP	G	G	A	rs138484272	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:65369242G>A	ENST00000432196.2	+	1	89	c.89G>A	c.(88-90)gGc>gAc	p.G30D	RASL12_ENST00000434605.2_5'Flank	NM_001101362.2	NP_001094832.1	C9JR72	KBTBD_HUMAN	kelch repeat and BTB (POZ) domain containing 13	30	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(1)|prostate(1)|skin(1)	3						GAGCACTGTGGCTTCTTCCGA	0.711													G|||	17	0.00339457	0.0008	0.0072	5008	,	,		12608	0.001		0.008	False		,,,				2504	0.002				p.G30D		Atlas-SNP	.											.	KBTBD13	9	.	0			c.G89A						PASS	.	G	ASP/GLY	1,3913		0,1,1956	8.0	11.0	10.0		89	2.7	1.0	15	dbSNP_134	10	34,8164		1,32,4066	yes	missense	KBTBD13	NM_001101362.2	94	1,33,6022	AA,AG,GG		0.4147,0.0255,0.289	benign	30/459	65369242	35,12077	1957	4099	6056	SO:0001583	missense	390594	exon1			ACTGTGGCTTCTT		CCDS45281.1	15q22.31	2014-09-17			ENSG00000234438	ENSG00000234438		"""BTB/POZ domain containing"""	37227	protein-coding gene	gene with protein product	"""nemaline myopathy type 6"""	613727				21109227, 22542517	Standard	NM_001101362		Approved	hCG_1645727, NEM6	uc010uis.2	C9JR72		ENST00000432196.2:c.89G>A	15.37:g.65369242G>A	ENSP00000388723:p.Gly30Asp	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_001101362		Missense_Mutation	SNP	ENST00000432196.2	37	CCDS45281.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	0.322	-0.961406	0.02249	2.55E-4	0.004147	ENSG00000234438	ENST00000432196	T	0.70164	-0.46	4.58	2.65	0.31530	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	.	.	.	.	T	0.22589	0.0545	N	0.01668	-0.77	0.32502	N	0.538675	B	0.13145	0.007	B	0.13407	0.009	T	0.39333	-0.9619	9	0.02654	T	1	.	6.1145	0.20120	0.4083:0.0:0.5917:0.0	.	30	C9JR72	KBTBD_HUMAN	D	30	ENSP00000388723:G30D	ENSP00000388723:G30D	G	+	2	0	KBTBD13	63156295	0.983000	0.35010	1.000000	0.80357	0.682000	0.39822	2.317000	0.43770	1.142000	0.42291	0.650000	0.86243	GGC	G|0.996;A|0.004	0.004	strong		0.711	KBTBD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418468.2	NM_001101362	
EPHX2	2053	hgsc.bcm.edu	37	8	27401964	27401964	+	Silent	SNP	A	A	C	rs1126452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27401964A>C	ENST00000521400.1	+	19	2023	c.1593A>C	c.(1591-1593)ccA>ccC	p.P531P	EPHX2_ENST00000518379.1_Silent_p.P499P|EPHX2_ENST00000380476.3_Silent_p.P478P|EPHX2_ENST00000521780.1_Silent_p.P465P|EPHX2_ENST00000517536.1_Silent_p.P348P	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	531	Epoxide hydrolase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		CCCCCAGGCCAACCGAGGTGA	0.532													C|||	2158	0.430911	0.7655	0.255	5008	,	,		19379	0.4147		0.2366	False		,,,				2504	0.32				p.P531P		Atlas-SNP	.											EPHX2,NS,carcinoma,+2,1	EPHX2	57	1	0			c.A1593C						PASS	.	C		2862,1544	483.7+/-359.8	941,980,282	98.0	106.0	103.0		1593	-4.5	0.0	8	dbSNP_86	103	2310,6290	703.8+/-405.4	337,1636,2327	no	coding-synonymous	EPHX2	NM_001979.4		1278,2616,2609	CC,CA,AA		26.8605,35.0431,39.7663		531/556	27401964	5172,7834	2203	4300	6503	SO:0001819	synonymous_variant	2053	exon19			CAGGCCAACCGAG	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.1593A>C	8.37:g.27401964A>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	139	73	0.52518	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Silent	SNP	ENST00000521400.1	37	CCDS6060.1																																																																																			A|0.594;C|0.406	0.406	strong		0.532	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		
DQX1	165545	hgsc.bcm.edu	37	2	74746322	74746322	+	Silent	SNP	A	A	T	rs6546909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:74746322A>T	ENST00000404568.3	-	11	2061	c.1842T>A	c.(1840-1842)ctT>ctA	p.L614L	DQX1_ENST00000393951.2_Silent_p.L614L	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	614						nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						GGGTTAGGAGAAGGTAATTTC	0.493													T|||	2620	0.523163	0.8101	0.3213	5008	,	,		19600	0.8185		0.16	False		,,,				2504	0.3476				p.L614L		Atlas-SNP	.											.	DQX1	95	.	0			c.T1842A						PASS	.	T		3057,1349	447.7+/-348.4	1084,889,230	88.0	93.0	91.0		1842	2.6	0.9	2	dbSNP_116	91	1324,7276	758.0+/-407.5	109,1106,3085	no	coding-synonymous	DQX1	NM_133637.2		1193,1995,3315	TT,TA,AA		15.3953,30.6173,33.6845		614/718	74746322	4381,8625	2203	4300	6503	SO:0001819	synonymous_variant	165545	exon11			TAGGAGAAGGTAA	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"""DEAQ box polypeptide 1 (RNA-dependent ATPase)"""				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.1842T>A	2.37:g.74746322A>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	237	162	0.683544	NM_133637	Q6B017|Q8NAM8	Silent	SNP	ENST00000404568.3	37	CCDS1949.2																																																																																			A|0.580;T|0.420	0.420	strong		0.493	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637	
ERC2	26059	hgsc.bcm.edu	37	3	56330368	56330368	+	Silent	SNP	C	C	T	rs56227347	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:56330368C>T	ENST00000288221.6	-	3	1008	c.753G>A	c.(751-753)gcG>gcA	p.A251A		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	251						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		TGAAGTGCTCCGCTCCTCGGT	0.557													C|||	288	0.057508	0.1861	0.0303	5008	,	,		18109	0.001		0.0169	False		,,,				2504	0.0031				p.A251A		Atlas-SNP	.											.	ERC2	221	.	0			c.G753A						PASS	.	C		683,3399		51,581,1409	148.0	144.0	146.0		753	-11.7	0.0	3	dbSNP_129	146	148,8240		1,146,4047	no	coding-synonymous	ERC2	NM_015576.1		52,727,5456	TT,TC,CC		1.7644,16.732,6.664		251/958	56330368	831,11639	2041	4194	6235	SO:0001819	synonymous_variant	26059	exon3			GTGCTCCGCTCCT	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.753G>A	3.37:g.56330368C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	212	110	0.518868	NM_015576	Q2T9F6|Q86TK4	Silent	SNP	ENST00000288221.6	37	CCDS46851.1																																																																																			C|0.949;T|0.051	0.051	strong		0.557	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576	
MDM1	56890	hgsc.bcm.edu	37	12	68708979	68708979	+	Silent	SNP	G	G	A	rs139553308	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:68708979G>A	ENST00000303145.7	-	9	1334	c.1248C>T	c.(1246-1248)atC>atT	p.I416I	MDM1_ENST00000411698.2_Silent_p.I381I|MDM1_ENST00000540418.1_Silent_p.I136I	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	416					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		GTTCTTCCACGATATTTCCTT	0.423													G|||	12	0.00239617	0.0008	0.0029	5008	,	,		18479	0.0		0.008	False		,,,				2504	0.001				p.I416I		Atlas-SNP	.											.	MDM1	74	.	0			c.C1248T						PASS	.	G	,	9,4397	15.5+/-35.6	0,9,2194	83.0	86.0	85.0		1143,1248	-2.7	0.0	12	dbSNP_134	85	99,8501	54.8+/-115.7	0,99,4201	no	coding-synonymous,coding-synonymous	MDM1	NM_001205028.1,NM_017440.4	,	0,108,6395	AA,AG,GG		1.1512,0.2043,0.8304	,	381/680,416/715	68708979	108,12898	2203	4300	6503	SO:0001819	synonymous_variant	56890	exon9			TTCCACGATATTT	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"""Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"""			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.1248C>T	12.37:g.68708979G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	171	79	0.461988	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Silent	SNP	ENST00000303145.7	37	CCDS8983.1																																																																																			G|0.991;A|0.009	0.009	strong		0.423	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921136	12921136	+	Silent	SNP	C	C	T	rs368491327	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:12921136C>T	ENST00000240189.2	+	4	1014	c.927C>T	c.(925-927)gaC>gaT	p.D309D		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	309					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.D309D(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TAGAAGAGGACTTGAAGTGTC	0.498													.|||	12	0.00239617	0.0038	0.0058	5008	,	,		21997	0.001		0.001	False		,,,				2504	0.001				p.D309D		Atlas-SNP	.											PRAMEF2,pharynx,carcinoma,0,1	PRAMEF2	85	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C927T						scavenged	.						131.0	134.0	133.0					1																	12921136		2202	4297	6499	SO:0001819	synonymous_variant	65122	exon4			AGAGGACTTGAAG		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.927C>T	1.37:g.12921136C>T		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	159	2	0.0125786	NM_023014		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			.	.	none		0.498	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
KIAA1109	84162	hgsc.bcm.edu	37	4	123192383	123192383	+	Silent	SNP	T	T	C	rs45574236	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:123192383T>C	ENST00000264501.4	+	47	8077	c.7704T>C	c.(7702-7704)gaT>gaC	p.D2568D	KIAA1109_ENST00000455637.1_Silent_p.D2568D|KIAA1109_ENST00000388738.3_Silent_p.D2568D			Q2LD37	K1109_HUMAN	KIAA1109	2568					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.D2568D(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AGCATGTAGATATGGCTTTGG	0.393													T|||	1369	0.273363	0.0333	0.3026	5008	,	,		20839	0.3611		0.2913	False		,,,				2504	0.4683				p.D2568D		Atlas-SNP	.											KIAA1109,NS,carcinoma,0,1	KIAA1109	424	1	1	Substitution - coding silent(1)	prostate(1)	c.T7704C						PASS	.	T		307,3525		14,279,1623	193.0	184.0	187.0		7704	0.6	1.0	4	dbSNP_127	187	2507,5751		375,1757,1997	no	coding-synonymous	KIAA1109	NM_015312.3		389,2036,3620	CC,CT,TT		30.3584,8.0115,23.2754		2568/5006	123192383	2814,9276	1916	4129	6045	SO:0001819	synonymous_variant	84162	exon45			TGTAGATATGGCT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.7704T>C	4.37:g.123192383T>C		Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	271	121	0.446494	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	557|557	0.25503663003663|0.25503663003663	22|22	0.044715447154471545|0.044715447154471545	107|107	0.2955801104972376|0.2955801104972376	199|199	0.3479020979020979|0.3479020979020979	229|229	0.3021108179419525|0.3021108179419525	T|T	7.365|7.365	0.625574|0.625574	0.14257|0.14257	0.080115|0.080115	0.303584|0.303584	ENSG00000138688|ENSG00000138688	ENST00000446180|ENST00000419325	.|.	.|.	.|.	5.82|5.82	0.618|0.618	0.17624|0.17624	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.35992|0.35992	-0.9766|-0.9766	3|3	.|.	.|.	.|.	.|.	10.8498|10.8498	0.46763|0.46763	0.0:0.5064:0.0:0.4936|0.0:0.5064:0.0:0.4936	rs45574236|rs45574236	.|.	.|.	.|.	T|H	1141|526	.|.	.|.	I|Y	+|+	2|1	0|0	KIAA1109|KIAA1109	123411833|123411833	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.996000|0.996000	0.88848|0.88848	1.125000|1.125000	0.31332|0.31332	0.109000|0.109000	0.17891|0.17891	0.383000|0.383000	0.25322|0.25322	ATA|TAT	T|0.716;C|0.284	0.284	strong		0.393	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
IFNE	338376	hgsc.bcm.edu	37	9	21481556	21481556	+	Missense_Mutation	SNP	T	T	G	rs1125488	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:21481556T>G	ENST00000448696.3	-	1	756	c.138A>C	c.(136-138)caA>caC	p.Q46H	MIR31HG_ENST00000304425.3_RNA	NM_176891.4	NP_795372.1	Q86WN2	IFNE_HUMAN	interferon, epsilon	46			Q -> H (in dbSNP:rs1125488).		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(2)|lung(1)|skin(1)	4						TTGACAAGGTTTGCAACTTAT	0.408													T|||	249	0.0497204	0.0303	0.1009	5008	,	,		22045	0.0248		0.0547	False		,,,				2504	0.0603				p.Q46H		Atlas-SNP	.											.	IFNE	16	.	0			c.A138C						PASS	.	T	HIS/GLN	168,4238	110.8+/-149.0	2,164,2037	88.0	84.0	85.0		138	-8.9	0.0	9	dbSNP_86	85	605,7995	159.7+/-212.9	24,557,3719	yes	missense	IFNE	NM_176891.4	24	26,721,5756	GG,GT,TT		7.0349,3.813,5.9434	benign	46/209	21481556	773,12233	2203	4300	6503	SO:0001583	missense	338376	exon1			CAAGGTTTGCAAC	AY190045	CCDS34997.1	9p21.1	2008-12-12			ENSG00000184995	ENSG00000184995			18163	protein-coding gene	gene with protein product		615223				15546383, 17287131	Standard	NM_176891		Approved	IFNE1	uc003zpg.3	Q86WN2	OTTHUMG00000019672	ENST00000448696.3:c.138A>C	9.37:g.21481556T>G	ENSP00000418018:p.Gln46His	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	253	123	0.486166	NM_176891		Missense_Mutation	SNP	ENST00000448696.3	37	CCDS34997.1	101	0.04624542124542125	9	0.018292682926829267	35	0.09668508287292818	13	0.022727272727272728	44	0.05804749340369393	T	7.335	0.619629	0.14193	0.03813	0.070349	ENSG00000184995	ENST00000448696	T	0.03413	3.94	4.73	-8.88	0.00789	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.238330	0.06241	U	0.690404	T	0.00109	0.0003	L	0.45581	1.43	0.09310	N	1	B	0.22541	0.071	B	0.24006	0.05	T	0.45673	-0.9245	10	0.87932	D	0	.	5.6347	0.17530	0.1085:0.503:0.2199:0.1686	rs1125488;rs17729034;rs52826037;rs61637566;rs1125488	46	Q86WN2	IFNE_HUMAN	H	46	ENSP00000418018:Q46H	ENSP00000418018:Q46H	Q	-	3	2	IFNE	21471556	0.000000	0.05858	0.000000	0.03702	0.254000	0.26022	-2.452000	0.01005	-1.427000	0.01992	0.533000	0.62120	CAA	T|0.945;G|0.055	0.055	strong		0.408	IFNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051901.2	NM_176891	
KIAA0753	9851	hgsc.bcm.edu	37	17	6515387	6515387	+	Missense_Mutation	SNP	A	A	G	rs2289642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:6515387A>G	ENST00000361413.3	-	8	1755	c.1397T>C	c.(1396-1398)cTg>cCg	p.L466P	KIAA0753_ENST00000572370.1_Missense_Mutation_p.L167P|KIAA0753_ENST00000542606.1_Missense_Mutation_p.L167P|KIAA0753_ENST00000589033.1_Intron	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	466			L -> P (in dbSNP:rs2289642). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TCCTTCTTCCAGAACTATATC	0.443													G|||	3451	0.689097	0.8253	0.6801	5008	,	,		18156	0.7103		0.5467	False		,,,				2504	0.636				p.L466P		Atlas-SNP	.											.	KIAA0753	63	.	0			c.T1397C						PASS	.	G	PRO/LEU	2969,819		1169,631,94	154.0	155.0	155.0		1397	-3.8	0.0	17	dbSNP_100	155	4726,3512		1359,2008,752	yes	missense	KIAA0753	NM_014804.2	98	2528,2639,846	GG,GA,AA		42.6317,21.6209,36.0136	benign	466/968	6515387	7695,4331	1894	4119	6013	SO:0001583	missense	9851	exon8			TCTTCCAGAACTA		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.1397T>C	17.37:g.6515387A>G	ENSP00000355250:p.Leu466Pro	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	265	112	0.422642	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	1439	0.6588827838827839	404	0.8211382113821138	243	0.6712707182320442	391	0.6835664335664335	401	0.5290237467018469	G	0.702	-0.790487	0.02884	0.783791	0.573683	ENSG00000198920	ENST00000361413;ENST00000542606	T;T	0.10477	2.87;2.87	4.43	-3.82	0.04281	.	1.416230	0.03928	N	0.284834	T	0.00012	0.0000	N	0.00483	-1.445	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.23940	-1.0174	9	0.20519	T	0.43	2.309	5.0425	0.14465	0.5171:0.0:0.2025:0.2804	rs2289642;rs17804248;rs52813277;rs59469410;rs2289642	466	Q2KHM9	K0753_HUMAN	P	466;167	ENSP00000355250:L466P;ENSP00000444634:L167P	ENSP00000355250:L466P	L	-	2	0	KIAA0753	6456111	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.776000	0.04674	-1.047000	0.03242	-0.119000	0.15052	CTG	A|0.342;G|0.658	0.658	strong		0.443	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
ADA	100	hgsc.bcm.edu	37	20	43254298	43254298	+	Silent	SNP	C	C	T	rs61737144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:43254298C>T	ENST00000372874.4	-	5	524	c.390G>A	c.(388-390)gtG>gtA	p.V130V	ADA_ENST00000537820.1_Silent_p.V130V|ADA_ENST00000464097.1_5'UTR	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	130					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	CCACTAGGGCCACCACCTCGT	0.647									Adenosine Deaminase Deficiency				C|||	153	0.0305511	0.0643	0.0231	5008	,	,		18564	0.0		0.0378	False		,,,				2504	0.0143				p.V130V		Atlas-SNP	.											ADA,caecum,carcinoma,0,1	ADA	42	1	0			c.G390A						scavenged	.	C		251,4125		5,241,1942	25.0	20.0	22.0		390	3.7	0.7	20	dbSNP_129	22	297,8287		5,287,4000	no	coding-synonymous	ADA	NM_000022.2		10,528,5942	TT,TC,CC		3.4599,5.7358,4.2284		130/364	43254298	548,12412	2188	4292	6480	SO:0001819	synonymous_variant	100	exon5	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	TAGGGCCACCACC	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.390G>A	20.37:g.43254298C>T		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	193	98	0.507772	NM_000022	Q53F92|Q6LA59	Silent	SNP	ENST00000372874.4	37	CCDS13335.1																																																																																			C|0.960;T|0.040	0.040	strong		0.647	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	
ATAD3C	219293	hgsc.bcm.edu	37	1	1390866	1390866	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:1390866A>G	ENST00000378785.2	+	5	1400	c.405A>G	c.(403-405)cgA>cgG	p.R135R		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	135							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	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;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TCCTCAGTCGACCCCAGGACG	0.672																																					p.R135R		Atlas-SNP	.											ATAD3C,NS,carcinoma,+1,1	ATAD3C	23	1	0			c.A405G						scavenged	.						59.0	59.0	59.0					1																	1390866		692	1591	2283	SO:0001819	synonymous_variant	219293	exon5			CAGTCGACCCCAG	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"""ATPases / AAA-type"""	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.405A>G	1.37:g.1390866A>G		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	153	5	0.0326797	NM_001039211	Q8N1Z5	Silent	SNP	ENST00000378785.2	37	CCDS44039.1																																																																																			.	.	none		0.672	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
MUC21	394263	hgsc.bcm.edu	37	6	30954749	30954749	+	Missense_Mutation	SNP	G	G	A	rs146145256	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954749G>A	ENST00000376296.3	+	2	1038	c.797G>A	c.(796-798)gGg>gAg	p.G266E	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	266	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACCTCCAGTGGGGCCGGCACA	0.627																																					p.G266E		Atlas-SNP	.											.	MUC21	98	.	0			c.G797A						PASS	.						151.0	152.0	151.0					6																	30954749		2203	4300	6503	SO:0001583	missense	394263	exon2			CCAGTGGGGCCGG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.797G>A	6.37:g.30954749G>A	ENSP00000365473:p.Gly266Glu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	131	21	0.160305	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	0.449	-0.894490	0.02491	.	.	ENSG00000204544	ENST00000376296	T	0.01629	4.72	3.74	-2.92	0.05615	.	.	.	.	.	T	0.00440	0.0014	N	0.24115	0.695	0.09310	N	1	P	0.36412	0.552	B	0.34652	0.187	T	0.43147	-0.9409	8	.	.	.	2.9662	6.0873	0.19975	0.2518:0.3782:0.3699:0.0	.	266	Q5SSG8	MUC21_HUMAN	E	266	ENSP00000365473:G266E	.	G	+	2	0	MUC21	31062728	0.000000	0.05858	0.000000	0.03702	0.162000	0.22319	-2.615000	0.00882	-0.678000	0.05224	0.491000	0.48974	GGG	G|0.976;A|0.023	0.023	strong		0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
PTEN	5728	hgsc.bcm.edu	37	10	89690819	89690819	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:89690819T>G	ENST00000371953.3	+	4	1583	c.226T>G	c.(226-228)Tat>Gat	p.Y76D		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	76	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(6)|p.R55fs*1(5)|p.Y76fs*1(4)|p.L70fs*7(4)|p.C71fs*6(2)|p.Y76del(2)|p.Y27fs*1(2)|p.H75_T78del(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TGAAAGACATTATGACACCGC	0.303		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.Y76D		Atlas-SNP	.	yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	PTEN,NS,malignant_melanoma,-2,3	PTEN	3652	3	64	Whole gene deletion(37)|Deletion - Frameshift(18)|Unknown(6)|Deletion - In frame(3)	central_nervous_system(17)|prostate(17)|breast(6)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|endometrium(3)|ovary(3)|stomach(1)|soft_tissue(1)|urinary_tract(1)	c.T226G						PASS	.						80.0	75.0	77.0					10																	89690819		2202	4295	6497	SO:0001583	missense	5728	exon4	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	AGACATTATGACA	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.226T>G	10.37:g.89690819T>G	ENSP00000361021:p.Tyr76Asp	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	72	60	0.833333	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.697959	0.88830	.	.	ENSG00000171862	ENST00000371953	D	0.98585	-5.01	5.62	5.62	0.85841	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99102	0.9691	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99556	1.0967	9	.	.	.	-12.1246	16.1135	0.81278	0.0:0.0:0.0:1.0	.	76	P60484	PTEN_HUMAN	D	76	ENSP00000361021:Y76D	.	Y	+	1	0	PTEN	89680799	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.586000	0.82596	2.267000	0.75376	0.383000	0.25322	TAT	.	.	none		0.303	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
LGALS14	56891	hgsc.bcm.edu	37	19	40199914	40199914	+	Missense_Mutation	SNP	C	C	G	rs10755	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40199914C>G	ENST00000392052.3	+	4	604	c.381C>G	c.(379-381)ttC>ttG	p.F127L	LGALS14_ENST00000360675.3_Missense_Mutation_p.F156L	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14	127	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.		F -> L (in dbSNP:rs10755). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19497882, ECO:0000269|Ref.1, ECO:0000269|Ref.6}.		apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)	p.F156L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			TGCAAGTCTTCAGAGATATCT	0.468													G|||	3174	0.633786	0.7935	0.5216	5008	,	,		22823	0.376		0.7038	False		,,,				2504	0.6912				p.F156L		Atlas-SNP	.											LGALS14,NS,carcinoma,0,1	LGALS14	38	1	1	Substitution - Missense(1)	stomach(1)	c.C468G						PASS	.	G	LEU/PHE,LEU/PHE	3446,960		1342,762,99	99.0	92.0	94.0		381,468	-0.3	0.0	19	dbSNP_52	94	5792,2808		1927,1938,435	yes	missense,missense	LGALS14	NM_020129.2,NM_203471.1	22,22	3269,2700,534	GG,GC,CC		32.6512,21.7885,28.9712	benign,benign	127/140,156/169	40199914	9238,3768	2203	4300	6503	SO:0001583	missense	56891	exon5			AGTCTTCAGAGAT	AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"""Lectins, galactoside-binding"""	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.381C>G	19.37:g.40199914C>G	ENSP00000375905:p.Phe127Leu	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	110	65	0.590909	NM_203471	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Missense_Mutation	SNP	ENST00000392052.3	37	CCDS46073.1	1338	0.6126373626373627	403	0.8191056910569106	193	0.5331491712707183	219	0.38286713286713286	523	0.6899736147757256	.	0.052	-1.247059	0.01481	0.782115	0.673488	ENSG00000006659	ENST00000392052;ENST00000360675	T;T	0.05081	3.5;3.5	0.902	-0.278	0.12894	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.13594	0.0;0.008	B;B	0.04013	0.0;0.001	T	0.23154	-1.0196	8	0.07644	T	0.81	.	2.4839	0.04594	0.2471:0.3192:0.4337:0.0	rs10755;rs3170361;rs17709339;rs17845677;rs17858617;rs58137311;rs10755	127;156	Q8TCE9;A8MPV8	PPL13_HUMAN;.	L	127;156	ENSP00000375905:F127L;ENSP00000353893:F156L	ENSP00000353893:F156L	F	+	3	2	LGALS14	44891754	0.088000	0.21588	0.008000	0.14137	0.002000	0.02628	-0.276000	0.08514	-0.553000	0.06158	-0.647000	0.03941	TTC	C|0.331;G|0.668	0.668	strong		0.468	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129	
TMEM247	388946	hgsc.bcm.edu	37	2	46707884	46707884	+	Missense_Mutation	SNP	A	A	G	rs201742486		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:46707884A>G	ENST00000434431.1	+	2	458	c.458A>G	c.(457-459)cAa>cGa	p.Q153R		NM_001145051.2	NP_001138523.1	A6NEH6	TM247_HUMAN	transmembrane protein 247	153						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											CAGCTGCAGCAAGAGGCGGCG	0.677																																					p.Q153R		Atlas-SNP	.											ENSG00000187600_ENST00000434431,NS,carcinoma,0,2	.	.	2	0			c.A458G						PASS	.						16.0	21.0	19.0					2																	46707884		690	1589	2279	SO:0001583	missense	388946	exon2			TGCAGCAAGAGGC		CCDS56117.1	2p21	2012-04-11			ENSG00000187600	ENSG00000187600			42967	protein-coding gene	gene with protein product							Standard	NM_001145051		Approved		uc010yod.3	A6NEH6	OTTHUMG00000153137	ENST00000434431.1:c.458A>G	2.37:g.46707884A>G	ENSP00000388684:p.Gln153Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	121	14	0.115702	NM_001145051		Missense_Mutation	SNP	ENST00000434431.1	37	CCDS56117.1	.	.	.	.	.	.	.	.	.	.	A	0.156	-1.086034	0.01873	.	.	ENSG00000187600	ENST00000434431	.	.	.	2.03	0.734	0.18294	.	.	.	.	.	T	0.12987	0.0315	N	0.08118	0	.	.	.	B	0.10296	0.003	B	0.06405	0.002	T	0.33599	-0.9862	7	0.07175	T	0.84	.	2.5803	0.04816	0.5369:0.2887:0.1744:0.0	.	153	A6NEH6	YB028_HUMAN	R	153	.	ENSP00000388684:Q153R	Q	+	2	0	AC018682.6	46561388	0.002000	0.14202	0.158000	0.22627	0.001000	0.01503	-0.138000	0.10374	0.052000	0.16007	-0.609000	0.04063	CAA	.	.	weak		0.677	TMEM247-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329726.1	NM_001145051	
SH3TC2	79628	hgsc.bcm.edu	37	5	148408101	148408101	+	Silent	SNP	A	A	G	rs1432793	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:148408101A>G	ENST00000515425.1	-	11	1295	c.1194T>C	c.(1192-1194)ggT>ggC	p.G398G	SH3TC2_ENST00000538184.1_5'UTR|SH3TC2_ENST00000512049.1_Silent_p.G391G|SH3TC2_ENST00000513340.1_5'UTR|SH3TC2_ENST00000394358.2_Silent_p.G283G	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	398					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)		p.G283G(1)|p.G398G(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTCCTTGAAACCTTCAGGCT	0.607													G|||	2189	0.437101	0.6172	0.3516	5008	,	,		20639	0.2222		0.4652	False		,,,				2504	0.4468				p.G398G		Atlas-SNP	.											SH3TC2_ENST00000394358,NS,carcinoma,0,2	SH3TC2	178	2	2	Substitution - coding silent(2)	prostate(2)	c.T1194C						PASS	.	G		2469,1937	510.4+/-367.5	699,1071,433	33.0	34.0	34.0		1194	3.6	0.6	5	dbSNP_88	34	3835,4765	586.5+/-392.0	860,2115,1325	no	coding-synonymous	SH3TC2	NM_024577.3		1559,3186,1758	GG,GA,AA		44.593,43.9628,48.4699		398/1289	148408101	6304,6702	2203	4300	6503	SO:0001819	synonymous_variant	79628	exon11			CTTGAAACCTTCA	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"""Tetratricopeptide (TTC) repeat domain containing"""	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.1194T>C	5.37:g.148408101A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	71	42	0.591549	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Silent	SNP	ENST00000515425.1	37	CCDS4293.1																																																																																			A|0.535;G|0.465	0.465	strong		0.607	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577	
SLC5A5	6528	hgsc.bcm.edu	37	19	17999239	17999239	+	Silent	SNP	C	C	T	rs45602038	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17999239C>T	ENST00000222248.3	+	13	1973	c.1626C>T	c.(1624-1626)tgC>tgT	p.C542C		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	542					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						CTGTGCTGTGCGGAGCCCTCA	0.587													C|||	66	0.0131789	0.0	0.0274	5008	,	,		15316	0.001		0.0239	False		,,,				2504	0.0225				p.C542C	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.C1626T						PASS	.	C		23,4383	29.0+/-57.7	0,23,2180	117.0	102.0	107.0		1626	-4.6	0.7	19	dbSNP_127	107	252,8348	99.5+/-161.0	4,244,4052	no	coding-synonymous	SLC5A5	NM_000453.2		4,267,6232	TT,TC,CC		2.9302,0.522,2.1144		542/644	17999239	275,12731	2203	4300	6503	SO:0001819	synonymous_variant	6528	exon13			GCTGTGCGGAGCC		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"""Solute carriers"""	11040	protein-coding gene	gene with protein product		601843	"""solute carrier family 5 (sodium iodide symporter), member 5"""			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.1626C>T	19.37:g.17999239C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_000453	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	37	CCDS12368.1																																																																																			C|0.979;T|0.021	0.021	strong		0.587	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1		
POTEG	404785	hgsc.bcm.edu	37	14	19571357	19571357	+	Missense_Mutation	SNP	T	T	C	rs200944601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:19571357T>C	ENST00000409832.3	+	7	1188	c.1136T>C	c.(1135-1137)tTa>tCa	p.L379S		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	379				L -> S (in Ref. 3; AAI27624). {ECO:0000305}.						cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						GAACAAGACTTAAAGCTGACA	0.318																																					p.L379S		Atlas-SNP	.											POTEG,NS,carcinoma,0,3	POTEG	118	3	0			c.T1136C						scavenged	.						16.0	18.0	18.0					14																	19571357		1852	3837	5689	SO:0001583	missense	404785	exon7			AAGACTTAAAGCT		CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33896	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 4"""	608916	"""ANKRD26-like family C, member 2"""	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.1136T>C	14.37:g.19571357T>C	ENSP00000386971:p.Leu379Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	49	9	0.183673	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	37	CCDS32018.1	466	0.21336996336996336	89	0.18089430894308944	79	0.21823204419889503	119	0.20804195804195805	179	0.23614775725593667	t	11.66	1.704521	0.30232	.	.	ENSG00000222036	ENST00000409832	T	0.18174	2.23	1.18	1.18	0.20946	.	.	.	.	.	T	0.00012	0.0000	N	0.11560	0.145	0.09310	N	1	D	0.65815	0.995	P	0.56398	0.797	T	0.17410	-1.0370	9	0.06891	T	0.86	.	4.5755	0.12232	0.0:0.0:0.0:1.0	.	379	Q6S5H5	POTEG_HUMAN	S	379	ENSP00000386971:L379S	ENSP00000386971:L379S	L	+	2	0	POTEG	18641357	0.001000	0.12720	0.014000	0.15608	0.428000	0.31595	0.664000	0.25068	0.792000	0.33850	0.155000	0.16302	TTA	T|0.500;C|0.500	0.500	strong		0.318	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
MUC16	94025	hgsc.bcm.edu	37	19	9071878	9071878	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9071878G>A	ENST00000397910.4	-	3	15771	c.15568C>T	c.(15568-15570)Cct>Tct	p.P5190S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5192	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTCAGTCTAGGAGTCAAGAAA	0.483																																					p.P5190S		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+2,3	MUC16	4315	3	0			c.C15568T						scavenged	.						231.0	217.0	222.0					19																	9071878		1942	4152	6094	SO:0001583	missense	94025	exon3			GTCTAGGAGTCAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15568C>T	19.37:g.9071878G>A	ENSP00000381008:p.Pro5190Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	152	2	0.0131579	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.111	-0.182701	0.06340	.	.	ENSG00000181143	ENST00000397910	T	0.03124	4.04	1.81	0.0625	0.14345	.	.	.	.	.	T	0.02156	0.0067	N	0.14661	0.345	.	.	.	P	0.40282	0.711	B	0.35182	0.197	T	0.42498	-0.9448	8	0.87932	D	0	.	5.3735	0.16152	0.0:0.0:0.4818:0.5182	.	5190	B5ME49	.	S	5190	ENSP00000381008:P5190S	ENSP00000381008:P5190S	P	-	1	0	MUC16	8932878	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-1.282000	0.02799	0.009000	0.14813	0.305000	0.20034	CCT	.	.	none		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PZP	5858	hgsc.bcm.edu	37	12	9316773	9316773	+	Missense_Mutation	SNP	T	T	C	rs3213831	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:9316773T>C	ENST00000261336.2	-	20	2598	c.2570A>G	c.(2569-2571)aAt>aGt	p.N857S	PZP_ENST00000539983.1_5'UTR|PZP_ENST00000381997.2_Intron	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	857			N -> S (in dbSNP:rs3213831). {ECO:0000269|PubMed:1989698}.		female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						TTGTCTCTCATTTCCACAGAT	0.483													T|||	2021	0.403554	0.3858	0.3646	5008	,	,		-128	0.4187		0.3966	False		,,,				2504	0.4468				p.N857S	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A2570G						PASS	.	T	SER/ASN	1840,2566	537.5+/-374.7	392,1056,755	189.0	173.0	179.0		2570	1.4	0.0	12	dbSNP_106	179	3696,4904	529.3+/-381.6	802,2092,1406	yes	missense	PZP	NM_002864.2	46	1194,3148,2161	CC,CT,TT		42.9767,41.7612,42.565	possibly-damaging	857/1483	9316773	5536,7470	2203	4300	6503	SO:0001583	missense	5858	exon20			CTCTCATTTCCAC	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2570A>G	12.37:g.9316773T>C	ENSP00000261336:p.Asn857Ser	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	856	0.39194139194139194	183	0.3719512195121951	137	0.3784530386740331	243	0.42482517482517484	293	0.3865435356200528	T	11.65	1.701569	0.30142	0.417612	0.429767	ENSG00000126838	ENST00000261336	T	0.33438	1.41	3.85	1.37	0.22104	.	0.205916	0.31531	N	0.007482	T	0.00012	0.0000	M	0.70595	2.14	0.34545	P	0.28933	P	0.51933	0.949	P	0.49332	0.607	T	0.43507	-0.9387	9	0.54805	T	0.06	.	6.336	0.21296	0.0:0.0886:0.1598:0.7516	rs3213831;rs52795442;rs57015394;rs3213831	857	P20742	PZP_HUMAN	S	857	ENSP00000261336:N857S	ENSP00000261336:N857S	N	-	2	0	PZP	9208040	0.647000	0.27304	0.005000	0.12908	0.707000	0.40811	2.556000	0.45862	0.156000	0.19299	0.383000	0.25322	AAT	T|0.582;C|0.418	0.418	strong		0.483	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
SMYD4	114826	hgsc.bcm.edu	37	17	1704297	1704297	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1704297T>C	ENST00000305513.7	-	5	558	c.391A>G	c.(391-393)Aga>Gga	p.R131G		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	131			R -> I (in dbSNP:rs7224496). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.				metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						GTCTGTGCTCTGTTAATGTCT	0.428																																					p.R131G		Atlas-SNP	.											.	SMYD4	50	.	0			c.A391G						PASS	.						131.0	132.0	132.0					17																	1704297		2203	4300	6503	SO:0001583	missense	114826	exon5			GTGCTCTGTTAAT	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.391A>G	17.37:g.1704297T>C	ENSP00000304360:p.Arg131Gly	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	109	48	0.440367	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.887796	0.33348	.	.	ENSG00000186532	ENST00000305513	T	0.19532	2.14	5.98	4.88	0.63580	Tetratricopeptide-like helical (1);	0.518027	0.24193	N	0.040700	T	0.45935	0.1367	M	0.90705	3.14	0.35409	D	0.792262	D	0.63880	0.993	P	0.62184	0.899	T	0.59762	-0.7393	10	0.34782	T	0.22	-5.7323	7.6552	0.28371	0.0:0.0712:0.1398:0.7889	.	131	Q8IYR2	SMYD4_HUMAN	G	131	ENSP00000304360:R131G	ENSP00000304360:R131G	R	-	1	2	SMYD4	1651047	0.997000	0.39634	0.826000	0.32828	0.064000	0.16182	3.040000	0.49799	1.038000	0.40049	0.528000	0.53228	AGA	.	.	none		0.428	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194964	18194964	+	Missense_Mutation	SNP	A	A	G	rs1869788	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18194964A>G	ENST00000314254.3	+	1	581	c.161A>G	c.(160-162)tAc>tGc	p.Y54C	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	54			Y -> C (in dbSNP:rs1869788). {ECO:0000269|PubMed:11850634}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CTCCTGGGCTACCGCATGCGC	0.552													G|||	1845	0.368411	0.3873	0.3559	5008	,	,		21075	0.4415		0.3072	False		,,,				2504	0.3395				p.Y54C		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.A161G						PASS	.	G	CYS/TYR	1625,2773		297,1031,871	129.0	114.0	119.0		161	0.4	0.0	11	dbSNP_92	119	2463,6123		346,1771,2176	no	missense	MRGPRX4	NM_054032.3	194	643,2802,3047	GG,GA,AA		28.6862,36.9486,31.4849	benign	54/323	18194964	4088,8896	2199	4293	6492	SO:0001583	missense	117196	exon1			TGGGCTACCGCAT	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.161A>G	11.37:g.18194964A>G	ENSP00000314042:p.Tyr54Cys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	37	CCDS7831.1	823	0.3768315018315018	184	0.37398373983739835	122	0.3370165745856354	275	0.4807692307692308	242	0.31926121372031663	N	5.292	0.239257	0.10023	0.369486	0.286862	ENSG00000179817	ENST00000314254	T	0.09350	2.99	2.95	0.397	0.16314	GPCR, rhodopsin-like superfamily (1);	0.275863	0.31673	N	0.007243	T	0.00012	0.0000	N	0.02721	-0.515	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45131	-0.9282	9	0.56958	D	0.05	.	5.4252	0.16421	0.1592:0.0:0.3113:0.5295	rs1869788;rs56745486	54	Q96LA9	MRGX4_HUMAN	C	54	ENSP00000314042:Y54C	ENSP00000314042:Y54C	Y	+	2	0	MRGPRX4	18151540	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.336000	0.07863	-0.398000	0.07679	-4.918000	0.00002	TAC	A|0.673;G|0.327	0.327	strong		0.552	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
NEK10	152110	hgsc.bcm.edu	37	3	27332177	27332177	+	Silent	SNP	T	T	C	rs674303	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:27332177T>C	ENST00000429845.2	-	20	2036	c.1674A>G	c.(1672-1674)ggA>ggG	p.G558G	NEK10_ENST00000357467.2_Intron|NEK10_ENST00000341435.5_Silent_p.G558G			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	558	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCTTATCCTTTCCAAATGCTG	0.313													T|||	1952	0.389776	0.8502	0.2608	5008	,	,		20678	0.1776		0.2634	False		,,,				2504	0.2076				p.G558G		Atlas-SNP	.											.	NEK10	271	.	0			c.A1674G						PASS	.	T		2284,852		841,602,125	117.0	104.0	108.0		1674	1.6	1.0	3	dbSNP_83	108	1953,5211		256,1441,1885	no	coding-synonymous	NEK10	NM_199347.2		1097,2043,2010	CC,CT,TT		27.2613,27.1684,41.1359		558/713	27332177	4237,6063	1568	3582	5150	SO:0001819	synonymous_variant	152110	exon20			ATCCTTTCCAAAT	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1674A>G	3.37:g.27332177T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Silent	SNP	ENST00000429845.2	37		780	0.35714285714285715	409	0.8313008130081301	99	0.27348066298342544	80	0.13986013986013987	192	0.2532981530343008	T	9.910	1.209279	0.22205	0.728316	0.272613	ENSG00000163491	ENST00000435584	.	.	.	5.45	1.59	0.23543	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.15896	-1.0421	3	.	.	.	.	2.1593	0.03820	0.1263:0.1478:0.1314:0.5946	rs674303;rs17019631;rs60398725;rs674303	.	.	.	E	15	.	.	K	-	1	0	NEK10	27307181	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	0.201000	0.17276	0.090000	0.17273	0.533000	0.62120	AAA	T|0.619;C|0.381	0.381	strong		0.313	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534	
ROBO4	54538	hgsc.bcm.edu	37	11	124767067	124767067	+	Missense_Mutation	SNP	T	T	C	rs59648931	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124767067T>C	ENST00000306534.3	-	2	646	c.161A>G	c.(160-162)cAa>cGa	p.Q54R	ROBO4_ENST00000533054.1_Intron|ROBO4_ENST00000526899.1_5'UTR	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	54	Ig-like C2-type 1.		Q -> R (in dbSNP:rs59648931).		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GCCTGAGGCTTGGCAGCTCAT	0.677													C|||	1926	0.384585	0.646	0.2176	5008	,	,		16532	0.378		0.2555	False		,,,				2504	0.2894				p.Q54R		Atlas-SNP	.											.	ROBO4	130	.	0			c.A161G						PASS	.	C	ARG/GLN	2473,1929		709,1055,437	26.0	24.0	24.0		161	0.1	0.4	11	dbSNP_129	24	1992,6604		262,1468,2568	yes	missense	ROBO4	NM_019055.5	43	971,2523,3005	CC,CT,TT		23.1736,43.821,34.3514	benign	54/1008	124767067	4465,8533	2201	4298	6499	SO:0001583	missense	54538	exon2			GAGGCTTGGCAGC	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.161A>G	11.37:g.124767067T>C	ENSP00000304945:p.Gln54Arg	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	37	CCDS8455.1	787	0.36034798534798534	300	0.6097560975609756	70	0.19337016574585636	228	0.3986013986013986	189	0.24934036939313983	C	3.293	-0.144625	0.06627	0.56179	0.231736	ENSG00000154133	ENST00000306534	T	0.67171	-0.25	5.29	0.134	0.14771	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.502444	0.14893	N	0.292246	T	0.00012	0.0000	N	0.17901	0.54	0.44261	P	0.0028850000000000264	B	0.02656	0.0	B	0.01281	0.0	T	0.44436	-0.9328	9	0.07990	T	0.79	.	10.1259	0.42649	0.0:0.5542:0.0:0.4458	rs59648931	54	Q8WZ75	ROBO4_HUMAN	R	54	ENSP00000304945:Q54R	ENSP00000304945:Q54R	Q	-	2	0	ROBO4	124272277	0.000000	0.05858	0.436000	0.26797	0.934000	0.57294	-0.519000	0.06260	-0.125000	0.11703	-0.215000	0.12644	CAA	T|0.646;C|0.354	0.354	strong		0.677	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
CHRNA4	1137	hgsc.bcm.edu	37	20	61981104	61981104	+	Silent	SNP	C	C	T	rs1044397	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:61981104C>T	ENST00000370263.4	-	5	1880	c.1659G>A	c.(1657-1659)gcG>gcA	p.A553A	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	553					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GCGGGGGCGGCGCTTTGGTGC	0.672													C|||	1762	0.351837	0.0635	0.4899	5008	,	,		13346	0.4008		0.5288	False		,,,				2504	0.411				p.A553A		Atlas-SNP	.											.	CHRNA4	98	.	0			c.G1659A						PASS	.	C		665,3737	272.8+/-271.0	58,549,1594	34.0	40.0	38.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1659	-8.5	0.0	20	dbSNP_86	38	4656,3938	590.3+/-392.6	1279,2098,920	no	coding-synonymous	CHRNA4	NM_000744.5		1337,2647,2514	TT,TC,CC		45.8227,15.1068,40.9434		553/628	61981104	5321,7675	2201	4297	6498	SO:0001819	synonymous_variant	1137	exon5			GGGCGGCGCTTTG		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1958	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 4 (neuronal)"""	118504	"""cholinergic receptor, nicotinic, alpha polypeptide 4"""	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1659G>A	20.37:g.61981104C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	39	28	0.717949	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Silent	SNP	ENST00000370263.4	37	CCDS13517.1																																																																																			C|0.587;T|0.413	0.413	strong		0.672	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3		
ELL2	22936	hgsc.bcm.edu	37	5	95234377	95234377	+	Silent	SNP	C	C	T	rs3777203	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:95234377C>T	ENST00000237853.4	-	8	1441	c.1092G>A	c.(1090-1092)ccG>ccA	p.P364P	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	364					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		CAGGGGGCAGCGGGAGGCCTG	0.507													C|||	1826	0.364617	0.4531	0.245	5008	,	,		15044	0.4325		0.2803	False		,,,				2504	0.3466				p.P364P		Atlas-SNP	.											.	ELL2	63	.	0			c.G1092A						PASS	.	C		1841,2561		401,1039,761	67.0	84.0	78.0		1092	-6.1	0.8	5	dbSNP_107	78	2233,6367		291,1651,2358	no	coding-synonymous	ELL2	NM_012081.5		692,2690,3119	TT,TC,CC		25.9651,41.8219,31.3336		364/641	95234377	4074,8928	2201	4300	6501	SO:0001819	synonymous_variant	22936	exon8			GGGCAGCGGGAGG	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1092G>A	5.37:g.95234377C>T		Somatic	323	1	0.00309598		WXS	Illumina HiSeq	Phase_I	312	134	0.429487	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	37	CCDS4080.1																																																																																			C|0.691;T|0.309	0.309	strong		0.507	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
ATP1A1	476	hgsc.bcm.edu	37	1	116937809	116937809	+	Missense_Mutation	SNP	A	A	G	rs77217304	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:116937809A>G	ENST00000295598.5	+	13	1990	c.1738A>G	c.(1738-1740)Atc>Gtc	p.I580V	ATP1A1_ENST00000537345.1_Missense_Mutation_p.I580V|ATP1A1_ENST00000369496.4_Missense_Mutation_p.I549V	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	580					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	GAATTTCCCTATCGATAATCT	0.512													A|||	46	0.0091853	0.003	0.0202	5008	,	,		17691	0.0		0.0239	False		,,,				2504	0.0041				p.I580V		Atlas-SNP	.											.	ATP1A1	87	.	0			c.A1738G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	27,4379	33.5+/-64.1	0,27,2176	203.0	185.0	191.0		1738,1738,1645	-2.7	0.0	1	dbSNP_131	191	276,8324	105.0+/-166.0	6,264,4030	yes	missense,missense,missense	ATP1A1	NM_000701.7,NM_001160233.1,NM_001160234.1	29,29,29	6,291,6206	GG,GA,AA		3.2093,0.6128,2.3297	benign,benign,benign	580/1024,580/1024,549/993	116937809	303,12703	2203	4300	6503	SO:0001583	missense	476	exon13			TTCCCTATCGATA	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"""ATPases / P-type"""	799	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-1"", ""sodium pump subunit alpha-1"", ""sodium-potassium ATPase catalytic subunit alpha-1"""	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1738A>G	1.37:g.116937809A>G	ENSP00000295598:p.Ile580Val	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	208	102	0.490385	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	37	CCDS887.1	33	0.01510989010989011	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	21	0.027704485488126648	A	3.882	-0.025753	0.07589	0.006128	0.032093	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	T;T;T	0.75938	-0.98;-0.98;-0.98	4.54	-2.67	0.06059	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.461301	0.25178	N	0.032547	T	0.22742	0.0549	N	0.11927	0.2	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.34875	-0.9811	10	0.14252	T	0.57	.	5.1931	0.15220	0.3627:0.2485:0.3888:0.0	.	580;580	F5H3A1;P05023	.;AT1A1_HUMAN	V	580;580;579;549	ENSP00000295598:I580V;ENSP00000445306:I580V;ENSP00000358508:I549V	ENSP00000295598:I580V	I	+	1	0	ATP1A1	116739332	0.035000	0.19736	0.002000	0.10522	0.442000	0.32017	0.865000	0.27940	-0.556000	0.06134	-0.177000	0.13119	ATC	A|0.977;G|0.023	0.023	strong		0.512	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233	
PJA2	9867	hgsc.bcm.edu	37	5	108714681	108714681	+	Silent	SNP	A	A	G	rs35039318	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:108714681A>G	ENST00000361189.2	-	4	746	c.507T>C	c.(505-507)gaT>gaC	p.D169D	PJA2_ENST00000361557.3_Silent_p.D169D|PJA2_ENST00000511624.1_5'Flank	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	169					long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		TGCCATCTGGATCATAAGAGT	0.398													A|||	91	0.0181709	0.0068	0.0288	5008	,	,		21066	0.0		0.0417	False		,,,				2504	0.0204				p.D169D		Atlas-SNP	.											.	PJA2	53	.	0			c.T507C						PASS	.	A		47,4357	49.6+/-84.7	0,47,2155	144.0	134.0	137.0		507	2.6	0.5	5	dbSNP_126	137	440,8160	133.8+/-191.2	10,420,3870	no	coding-synonymous	PJA2	NM_014819.4		10,467,6025	GG,GA,AA		5.1163,1.0672,3.745		169/709	108714681	487,12517	2202	4300	6502	SO:0001819	synonymous_variant	9867	exon4			ATCTGGATCATAA	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"""RING-type (C3HC4) zinc fingers"""	17481	protein-coding gene	gene with protein product			"""ring finger protein 131"", ""praja ring finger 2"""	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.507T>C	5.37:g.108714681A>G		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	323	153	0.473684	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Silent	SNP	ENST00000361189.2	37	CCDS4099.1																																																																																			A|0.962;G|0.038	0.038	strong		0.398	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1605992	1605992	+	Missense_Mutation	SNP	G	G	C	rs60899198	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1605992G>C	ENST00000382171.2	-	1	521	c.488C>G	c.(487-489)tCc>tGc	p.S163C	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	163	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GGCCCCCTTGGAGCACCCACA	0.652													g|||	4	0.000798722	0.0	0.0014	5008	,	,		8301	0.002		0.0	False		,,,				2504	0.001				p.S163C		Atlas-SNP	.											KRTAP5-1,NS,carcinoma,0,1	KRTAP5-1	74	1	0			c.C488G						scavenged	.						69.0	84.0	79.0					11																	1605992		2202	4299	6501	SO:0001583	missense	387264	exon1			CCCTTGGAGCACC	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.488C>G	11.37:g.1605992G>C	ENSP00000371606:p.Ser163Cys	Somatic	115	2	0.0173913		WXS	Illumina HiSeq	Phase_I	114	13	0.114035	NM_001005922		Missense_Mutation	SNP	ENST00000382171.2	37	CCDS31330.1	.	.	.	.	.	.	.	.	.	.	-	2.030	-0.422638	0.04734	.	.	ENSG00000205869	ENST00000382171	T	0.04809	3.55	3.69	-5.66	0.02451	.	.	.	.	.	T	0.04588	0.0125	N	0.25992	0.78	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.30736	-0.9968	9	0.62326	D	0.03	.	17.1666	0.86818	0.0:0.7049:0.2951:0.0	rs60899198	163	Q6L8H4	KRA51_HUMAN	C	163	ENSP00000371606:S163C	ENSP00000371606:S163C	S	-	2	0	KRTAP5-1	1562568	0.000000	0.05858	0.150000	0.22450	0.017000	0.09413	-1.717000	0.01876	-1.045000	0.03250	-0.974000	0.02594	TCC	G|0.500;C|0.500	0.500	weak		0.652	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
DNAH8	1769	hgsc.bcm.edu	37	6	38800164	38800164	+	Missense_Mutation	SNP	G	G	A	rs9357283	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:38800164G>A	ENST00000359357.3	+	29	3858	c.3604G>A	c.(3604-3606)Gaa>Aaa	p.E1202K	DNAH8_ENST00000441566.1_Missense_Mutation_p.E1202K|DNAH8_ENST00000449981.2_Missense_Mutation_p.E1419K			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1202			E -> K (in dbSNP:rs9357283). {ECO:0000269|PubMed:12297094}.		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E1202K(1)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGAGTCTGTGGAAGTTTTTCG	0.343													G|||	913	0.182308	0.1415	0.1556	5008	,	,		20049	0.3423		0.1074	False		,,,				2504	0.1687				p.E1419K		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	1	Substitution - Missense(1)	stomach(1)	c.G4255A						PASS	.	G	LYS/GLU	638,3768	272.5+/-270.8	45,548,1610	130.0	122.0	125.0		4255	4.5	1.0	6	dbSNP_119	125	1188,7412	240.8+/-271.4	71,1046,3183	yes	missense	DNAH8	NM_001206927.1	56	116,1594,4793	AA,AG,GG		13.814,14.4803,14.0397	benign	1419/4708	38800164	1826,11180	2203	4300	6503	SO:0001583	missense	1769	exon31			TCTGTGGAAGTTT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.3604G>A	6.37:g.38800164G>A	ENSP00000352312:p.Glu1202Lys	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	145	72	0.496552	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		381	0.17445054945054944	63	0.12804878048780488	50	0.13812154696132597	195	0.3409090909090909	73	0.09630606860158311	G	8.047	0.765224	0.15914	0.144803	0.13814	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.25912	1.83;1.82;1.77	5.41	4.53	0.55603	.	0.264968	0.36066	N	0.002816	T	0.06096	0.0158	L	0.31157	0.91	0.30677	P	0.75271	B	0.02656	0.0	B	0.06405	0.002	T	0.23048	-1.0199	9	0.10377	T	0.69	.	10.1478	0.42774	0.073:0.1359:0.7911:0.0	rs9357283;rs59127177;rs9357283	1202	Q96JB1	DYH8_HUMAN	K	1407;1407;1202;1202	ENSP00000333363:E1407K;ENSP00000352312:E1202K;ENSP00000402294:E1202K	ENSP00000333363:E1407K	E	+	1	0	DNAH8	38908142	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	2.663000	0.46774	1.261000	0.44149	0.563000	0.77884	GAA	G|0.840;A|0.160	0.160	strong		0.343	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
TCP11L1	55346	hgsc.bcm.edu	37	11	33079580	33079580	+	Missense_Mutation	SNP	A	A	G	rs2273549	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:33079580A>G	ENST00000334274.4	+	5	933	c.533A>G	c.(532-534)aAg>aGg	p.K178R	TCP11L1_ENST00000432887.1_Missense_Mutation_p.K178R|TCP11L1_ENST00000530171.1_3'UTR|TCP11L1_ENST00000531632.2_Missense_Mutation_p.K178R|TCP11L1_ENST00000324357.9_5'Flank	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	178			K -> R (in dbSNP:rs2273549). {ECO:0000269|PubMed:15489334}.			microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						GACATTTCCAAGCTGGCAGAA	0.453													A|||	597	0.119209	0.0696	0.1297	5008	,	,		17057	0.122		0.1948	False		,,,				2504	0.0982				p.K178R		Atlas-SNP	.											.	TCP11L1	40	.	0			c.A533G						PASS	.	A	ARG/LYS,ARG/LYS	442,3962	212.2+/-232.1	27,388,1787	94.0	87.0	89.0		533,533	0.7	0.4	11	dbSNP_100	89	1535,7061	288.1+/-298.6	143,1249,2906	yes	missense,missense	TCP11L1	NM_001145541.1,NM_018393.3	26,26	170,1637,4693	GG,GA,AA		17.8571,10.0363,15.2077	benign,benign	178/510,178/510	33079580	1977,11023	2202	4298	6500	SO:0001583	missense	55346	exon5			TTTCCAAGCTGGC	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"""t-complex 11 (mouse) like 1"""				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.533A>G	11.37:g.33079580A>G	ENSP00000335595:p.Lys178Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_001145541	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	37	CCDS7882.1	315	0.14423076923076922	43	0.08739837398373984	59	0.16298342541436464	69	0.12062937062937062	144	0.18997361477572558	A	0.721	-0.783462	0.02907	0.100363	0.178571	ENSG00000176148	ENST00000334274;ENST00000531632;ENST00000432887	T;T;T	0.12361	2.69;2.69;2.69	5.53	0.691	0.18045	.	0.410144	0.28847	N	0.013949	T	0.00012	0.0000	N	0.12961	0.28	0.53688	P	2.6999999999999247E-5	B	0.10296	0.003	B	0.16289	0.015	T	0.45026	-0.9289	8	.	.	.	-23.1467	5.6678	0.17704	0.6024:0.1339:0.2637:0.0	rs2273549;rs17343833;rs17846314;rs17859344;rs59182277;rs2273549	178	Q9NUJ3	T11L1_HUMAN	R	178	ENSP00000335595:K178R;ENSP00000433067:K178R;ENSP00000395070:K178R	.	K	+	2	0	TCP11L1	33036156	0.893000	0.30496	0.442000	0.26870	0.199000	0.23934	1.417000	0.34770	0.383000	0.24910	-0.619000	0.04042	AAG	A|0.857;G|0.143	0.143	strong		0.453	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393	
PEAK1	79834	hgsc.bcm.edu	37	15	77450964	77450964	+	Missense_Mutation	SNP	C	C	T	rs12909704	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:77450964C>T	ENST00000560626.2	-	5	3687	c.3212G>A	c.(3211-3213)aGg>aAg	p.R1071K	PEAK1_ENST00000312493.4_Missense_Mutation_p.R1071K			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1071			R -> K (in dbSNP:rs12909704). {ECO:0000269|PubMed:17344846}.		cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										AGTGCAGCCCCTGCCATCTTG	0.468													C|||	992	0.198083	0.0794	0.2622	5008	,	,		21273	0.1121		0.3787	False		,,,				2504	0.2157				p.R1071K		Atlas-SNP	.											.	.	.	.	0			c.G3212A						PASS	.	C	LYS/ARG	415,3481		19,377,1552	130.0	123.0	125.0		3212	2.5	0.0	15	dbSNP_121	125	3003,5269		560,1883,1693	yes	missense	PEAK1	NM_024776.3	26	579,2260,3245	TT,TC,CC		36.3032,10.652,28.0901	benign	1071/1747	77450964	3418,8750	1948	4136	6084	SO:0001583	missense	0	exon6			CAGCCCCTGCCAT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3212G>A	15.37:g.77450964C>T	ENSP00000452796:p.Arg1071Lys	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	173	95	0.549133	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	499	0.22847985347985347	48	0.0975609756097561	100	0.27624309392265195	72	0.1258741258741259	279	0.36807387862796836	C	10.46	1.356279	0.24598	0.10652	0.363032	ENSG00000173517	ENST00000312493	T	0.67345	-0.26	4.5	2.54	0.30619	.	0.991955	0.08183	N	0.985190	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.25847	-1.0120	9	0.36615	T	0.2	1.4574	8.0609	0.30633	0.0:0.7527:0.1604:0.0868	rs12909704;rs52835769;rs61009837;rs12909704	1071	Q9H792	PEAK1_HUMAN	K	1071	ENSP00000309230:R1071K	ENSP00000309230:R1071K	R	-	2	0	AC087465.1	75238019	0.005000	0.15991	0.004000	0.12327	0.294000	0.27393	1.412000	0.34714	0.978000	0.38470	0.563000	0.77884	AGG	C|0.760;T|0.240	0.240	strong		0.468	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
STK10	6793	hgsc.bcm.edu	37	5	171523512	171523512	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:171523512G>A	ENST00000176763.5	-	8	1266	c.923C>T	c.(922-924)gCt>gTt	p.A308V	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	308					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTTGGCCTCAGCCACCAGCTC	0.622																																					p.A308V		Atlas-SNP	.											.	STK10	100	.	0			c.C923T						PASS	.						109.0	104.0	106.0					5																	171523512		2203	4300	6503	SO:0001583	missense	6793	exon8			GCCTCAGCCACCA	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.923C>T	5.37:g.171523512G>A	ENSP00000176763:p.Ala308Val	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	62	7	0.112903	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.433688	0.83776	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.69435	-0.4	4.96	4.96	0.65561	Protein kinase-like domain (1);	0.061568	0.64402	D	0.000005	T	0.73636	0.3612	M	0.74647	2.275	0.80722	D	1	D	0.56746	0.977	P	0.49922	0.626	T	0.76424	-0.2964	10	0.45353	T	0.12	.	15.7705	0.78164	0.0:0.0:1.0:0.0	.	308	O94804	STK10_HUMAN	V	308	ENSP00000176763:A308V	ENSP00000176763:A308V	A	-	2	0	STK10	171456117	1.000000	0.71417	0.947000	0.38551	0.941000	0.58515	9.834000	0.99428	2.320000	0.78422	0.485000	0.47835	GCT	.	.	none		0.622	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
DHX57	90957	hgsc.bcm.edu	37	2	39050141	39050141	+	Silent	SNP	A	A	C	rs3770681	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:39050141A>C	ENST00000295373.6	-	17	3411	c.3285T>G	c.(3283-3285)tcT>tcG	p.S1095S		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1095							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TTACAAACGGAGACTTAAAAG	0.473													A|||	3001	0.599241	0.3306	0.5836	5008	,	,		17536	0.8046		0.66	False		,,,				2504	0.6994				p.S1095S	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.T3285G						PASS	.	A		1652,2754	503.4+/-365.5	309,1034,860	70.0	59.0	63.0		3285	1.8	1.0	2	dbSNP_107	63	5586,3014	662.8+/-402.0	1824,1938,538	no	coding-synonymous	DHX57	NM_198963.1		2133,2972,1398	CC,CA,AA		35.0465,37.4943,44.3488		1095/1387	39050141	7238,5768	2203	4300	6503	SO:0001819	synonymous_variant	90957	exon17			AAACGGAGACTTA	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3285T>G	2.37:g.39050141A>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Silent	SNP	ENST00000295373.6	37	CCDS1800.1	1353	0.6195054945054945	164	0.3333333333333333	217	0.5994475138121547	464	0.8111888111888111	508	0.6701846965699209	A	9.500	1.102961	0.20632	0.374943	0.649535	ENSG00000163214	ENST00000452978	T	0.34472	1.36	5.51	1.79	0.24919	.	0.000000	0.51477	D	0.000095	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09707	-1.0662	6	0.66056	D	0.02	.	4.1767	0.10355	0.4934:0.0:0.3166:0.19	rs3770681;rs11557278;rs17494252;rs3770681	.	.	.	A	419	ENSP00000397841:S419A	ENSP00000397841:S419A	S	-	1	0	DHX57	38903645	0.975000	0.34042	1.000000	0.80357	0.987000	0.75469	0.123000	0.15708	0.381000	0.24851	0.528000	0.53228	TCC	A|0.422;C|0.578	0.578	strong		0.473	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
PNP	4860	hgsc.bcm.edu	37	14	20940606	20940606	+	Missense_Mutation	SNP	G	G	A	rs1049564	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20940606G>A	ENST00000361505.5	+	2	297	c.151G>A	c.(151-153)Ggt>Agt	p.G51S	RP11-203M5.8_ENST00000554678.1_lincRNA	NM_000270.3	NP_000261.2	P01298	PAHO_HUMAN	purine nucleoside phosphorylase	0					digestion (GO:0007586)|protein secretion (GO:0009306)	extracellular region (GO:0005576)	hormone activity (GO:0005179)|receptor binding (GO:0005102)	p.G51S(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|stomach(2)	10						CTTTGACTACGGTGAAATCCC	0.473													A|||	1025	0.204673	0.2474	0.2104	5008	,	,		20475	0.2063		0.1998	False		,,,				2504	0.1462				p.G51S		Atlas-SNP	.											PNP,NS,carcinoma,0,1	PNP	21	1	1	Substitution - Missense(1)	stomach(1)	c.G151A	GRCh37	CM073244	PNP	M	rs1049564	PASS	.	A	SER/GLY	1083,3323	720.9+/-409.1	121,841,1241	83.0	74.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	151	5.5	1.0	14	dbSNP_86	77	1522,7078	747.4+/-407.3	143,1236,2921	yes	missense	PNP	NM_000270.3	56	264,2077,4162	AA,AG,GG		17.6977,24.5801,20.0292	benign	51/290	20940606	2605,10401	2203	4300	6503	SO:0001583	missense	4860	exon2			GACTACGGTGAAA		CCDS9552.1	14q11.2	2014-09-17	2009-12-02	2009-12-02	ENSG00000198805	ENSG00000198805	2.4.2.1		7892	protein-coding gene	gene with protein product		164050	"""nucleoside phosphorylase"""	NP		6087295	Standard	NM_000270		Approved	PUNP	uc001vxo.4	P00491	OTTHUMG00000029546	ENST00000361505.5:c.151G>A	14.37:g.20940606G>A	ENSP00000354532:p.Gly51Ser	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	155	91	0.587097	NM_000270		Missense_Mutation	SNP	ENST00000361505.5	37	CCDS9552.1	484|484	0.2216117216117216|0.2216117216117216	139|139	0.28252032520325204|0.28252032520325204	84|84	0.23204419889502761|0.23204419889502761	120|120	0.2097902097902098|0.2097902097902098	141|141	0.18601583113456466|0.18601583113456466	A|A	2.844|2.844	-0.239923|-0.239923	0.05944|0.05944	0.245801|0.245801	0.176977|0.176977	ENSG00000198805|ENSG00000198805	ENST00000554469|ENST00000553418;ENST00000361505;ENST00000553591	.|T;D;D	.|0.94232	.|-0.88;-3.38;-3.38	5.54|5.54	5.54|5.54	0.83059|0.83059	.|Nucleoside phosphorylase domain (1);	0.389474|0.389474	0.33290|0.33290	N|N	0.005067|0.005067	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00683|0.00683	-1.26|-1.26	0.58432|0.58432	P|P	8.000000000008E-6|8.000000000008E-6	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.001;0.0;0.0	T|T	0.34428|0.34428	-0.9829|-0.9829	5|9	.|0.02654	.|T	.|1	-9.946|-9.946	6.5054|6.5054	0.22192|0.22192	0.7854:0.0:0.0759:0.1387|0.7854:0.0:0.0759:0.1387	rs1049564;rs1760937;rs2070219;rs17012367;rs17879175;rs17884346;rs58995400;rs1049564|rs1049564;rs1760937;rs2070219;rs17012367;rs17879175;rs17884346;rs58995400;rs1049564	.|51;51;51	.|Q8N7G1;G3V2H3;P00491	.|.;.;PNPH_HUMAN	R|S	51|51;51;90	.|ENSP00000450663:G51S;ENSP00000354532:G51S;ENSP00000452421:G90S	.|ENSP00000354532:G51S	G|G	+|+	1|1	0|0	PNP|PNP	20010446|20010446	0.331000|0.331000	0.24713|0.24713	0.998000|0.998000	0.56505|0.56505	0.741000|0.741000	0.42261|0.42261	1.210000|1.210000	0.32370|0.32370	1.120000|1.120000	0.41904|0.41904	-0.254000|-0.254000	0.11334|0.11334	GGG|GGT	G|0.786;A|0.214	0.214	strong		0.473	PNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073646.2	NM_000270.2	
KRT39	390792	hgsc.bcm.edu	37	17	39116728	39116728	+	Missense_Mutation	SNP	G	G	A	rs17843021	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39116728G>A	ENST00000355612.2	-	6	1057	c.1022C>T	c.(1021-1023)aCg>aTg	p.T341M	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	341	Coil 2.|Rod.		T -> M (in dbSNP:rs17843021).			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	17		Breast(137;0.00043)|Ovarian(249;0.15)				CTCTGTCTCCGTTAGGATGCA	0.493													G|||	585	0.116813	0.1452	0.0548	5008	,	,		18259	0.1399		0.1322	False		,,,				2504	0.0828				p.T341M		Atlas-SNP	.											.	KRT39	53	.	0			c.C1022T						PASS	.	G	MET/THR	630,3776	274.0+/-271.7	53,524,1626	137.0	135.0	135.0		1022	-1.1	0.0	17	dbSNP_123	135	1136,7456	235.1+/-267.8	71,994,3231	yes	missense	KRT39	NM_213656.3	81	124,1518,4857	AA,AG,GG		13.2216,14.2987,13.5867	possibly-damaging	341/492	39116728	1766,11232	2203	4296	6499	SO:0001583	missense	390792	exon6			GTCTCCGTTAGGA	AJ786657	CCDS11382.1	17q21.2	2013-01-16			ENSG00000196859	ENSG00000196859		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	32971	protein-coding gene	gene with protein product						16831889	Standard	NM_213656		Approved	KA35	uc002hvo.1	Q6A163	OTTHUMG00000133424	ENST00000355612.2:c.1022C>T	17.37:g.39116728G>A	ENSP00000347823:p.Thr341Met	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	147	78	0.530612	NM_213656	B2RXK6|Q6IFU6	Missense_Mutation	SNP	ENST00000355612.2	37	CCDS11382.1	273	0.125	69	0.1402439024390244	29	0.08011049723756906	75	0.13111888111888112	100	0.13192612137203166	G	6.273	0.418486	0.11870	0.142987	0.132216	ENSG00000196859	ENST00000355612	D	0.89050	-2.46	5.81	-1.12	0.09808	Filament (1);	1.437790	0.04585	N	0.395707	T	0.03651	0.0104	M	0.64170	1.965	0.80722	P	0.0	P	0.41947	0.766	B	0.37239	0.244	T	0.51655	-0.8678	9	0.62326	D	0.03	.	4.6774	0.12719	0.2521:0.0:0.3101:0.4378	rs17843021;rs17843021	341	Q6A163	K1C39_HUMAN	M	341	ENSP00000347823:T341M	ENSP00000347823:T341M	T	-	2	0	KRT39	36370254	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.117000	0.10708	-0.383000	0.07858	-0.218000	0.12543	ACG	G|0.868;A|0.132	0.132	strong		0.493	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656	
MUC6	4588	hgsc.bcm.edu	37	11	1029320	1029320	+	Missense_Mutation	SNP	C	C	T	rs11604757	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1029320C>T	ENST00000421673.2	-	10	1233	c.1183G>A	c.(1183-1185)Gga>Aga	p.G395R		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	395					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAGCAGTGTCCGGGGCACGGC	0.687													c|||	212	0.0423323	0.0129	0.0793	5008	,	,		13984	0.0		0.1203	False		,,,				2504	0.0194				p.G395R		Atlas-SNP	.											.	MUC6	408	.	0			c.G1183A						PASS	.	C	ARG/GLY	87,4123		0,87,2018	16.0	17.0	17.0		1183	2.7	0.0	11	dbSNP_120	17	985,7415		58,869,3273	yes	missense	MUC6	NM_005961.2	125	58,956,5291	TT,TC,CC		11.7262,2.0665,8.5012	possibly-damaging	395/2440	1029320	1072,11538	2105	4200	6305	SO:0001583	missense	4588	exon10			AGTGTCCGGGGCA	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.1183G>A	11.37:g.1029320C>T	ENSP00000406861:p.Gly395Arg	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	25	0.609756	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	130	0.05952380952380952	8	0.016260162601626018	32	0.08839779005524862	0	0.0	90	0.11873350923482849	C	16.24	3.067774	0.55539	0.020665	0.117262	ENSG00000184956	ENST00000421673	T	0.64085	-0.08	4.56	2.68	0.31781	von Willebrand factor, type D domain (1);	1.027660	0.07899	N	0.972423	T	0.01156	0.0038	M	0.69358	2.11	0.33001	P	0.47379499999999997	P	0.44659	0.84	B	0.30495	0.116	T	0.10683	-1.0619	9	0.54805	T	0.06	.	9.5498	0.39304	0.0:0.7562:0.1607:0.0831	rs11604757;rs59572872;rs11604757	395	Q6W4X9	MUC6_HUMAN	R	395	ENSP00000406861:G395R	ENSP00000406861:G395R	G	-	1	0	MUC6	1019320	0.091000	0.21658	0.004000	0.12327	0.162000	0.22319	1.681000	0.37618	0.489000	0.27749	0.313000	0.20887	GGA	C|0.945;T|0.055	0.055	strong		0.687	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702169	27702169	+	Silent	SNP	C	C	T	rs6482625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:27702169C>T	ENST00000438700.3	-	1	1128	c.1011G>A	c.(1009-1011)gtG>gtA	p.V337V		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	337					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						GCTTGCTCTGCACGTCGTACT	0.522													C|||	993	0.198283	0.3805	0.2839	5008	,	,		19255	0.0129		0.2137	False		,,,				2504	0.0665				p.V337V		Atlas-SNP	.											.	PTCHD3	140	.	0			c.G1011A						PASS	.	C		1589,2817	495.1+/-363.2	282,1025,896	132.0	135.0	134.0		1011	-0.2	0.0	10	dbSNP_116	134	1947,6653	341.6+/-324.1	234,1479,2587	no	coding-synonymous	PTCHD3	NM_001034842.3		516,2504,3483	TT,TC,CC		22.6395,36.0645,27.1875		337/768	27702169	3536,9470	2203	4300	6503	SO:0001819	synonymous_variant	374308	exon1			GCTCTGCACGTCG	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1011G>A	10.37:g.27702169C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	156	85	0.544872	NM_001034842	I3L499|Q6ZU28	Silent	SNP	ENST00000438700.3	37	CCDS31173.1																																																																																			C|0.765;T|0.235	0.235	strong		0.522	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
ITGA10	8515	hgsc.bcm.edu	37	1	145533175	145533175	+	Silent	SNP	T	T	C	rs11590105	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:145533175T>C	ENST00000369304.3	+	11	1445	c.1270T>C	c.(1270-1272)Ttg>Ctg	p.L424L	ITGA10_ENST00000538811.1_Silent_p.L293L|ITGA10_ENST00000539363.1_Silent_p.L281L	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	424					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCCCCCTGCATTGCAGAACCA	0.582													T|||	1001	0.19988	0.062	0.3458	5008	,	,		16859	0.1617		0.3559	False		,,,				2504	0.1616				p.L424L		Atlas-SNP	.											.	ITGA10	131	.	0			c.T1270C						PASS	.	T		500,3906	230.4+/-244.6	32,436,1735	48.0	43.0	45.0		1270	-5.7	0.0	1	dbSNP_120	45	3015,5585	463.6+/-366.0	549,1917,1834	no	coding-synonymous	ITGA10	NM_003637.3		581,2353,3569	CC,CT,TT		35.0581,11.3482,27.026		424/1168	145533175	3515,9491	2203	4300	6503	SO:0001819	synonymous_variant	8515	exon11			CCTGCATTGCAGA	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.1270T>C	1.37:g.145533175T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Silent	SNP	ENST00000369304.3	37	CCDS918.1																																																																																			T|0.762;C|0.238	0.238	strong		0.582	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518214	161518214	+	Missense_Mutation	SNP	T	T	C	rs148181339	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:161518214T>C	ENST00000436743.1	-	4	470	c.316A>G	c.(316-318)Atc>Gtc	p.I106V	RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000476031.1_5'UTR|FCGR3A_ENST00000443193.1_Missense_Mutation_p.I141V|FCGR3A_ENST00000367969.3_Missense_Mutation_p.I142V|FCGR3A_ENST00000540048.1_Missense_Mutation_p.I106V	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	106				I -> V (in Ref. 3; BAD96988/BAD97015). {ECO:0000305}.	Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AACTCACCGATATGGACTTCT	0.483																																					p.I142V		Atlas-SNP	.											FCGR3A,NS,carcinoma,+2,2	FCGR3A	38	2	0			c.A424G						scavenged	.						83.0	81.0	82.0					1																	161518214		2203	4296	6499	SO:0001583	missense	2214	exon3			CACCGATATGGAC	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000436743.1:c.316A>G	1.37:g.161518214T>C	ENSP00000416607:p.Ile106Val	Somatic	356	2	0.00561798		WXS	Illumina HiSeq	Phase_I	582	257	0.441581	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	522|522	0.23901098901098902|0.23901098901098902	75|75	0.1524390243902439|0.1524390243902439	115|115	0.31767955801104975|0.31767955801104975	185|185	0.32342657342657344|0.32342657342657344	147|147	0.19393139841688653|0.19393139841688653	T|T	6.273|6.273	0.418469|0.418469	0.11870|0.11870	.|.	.|.	ENSG00000203747|ENSG00000203747	ENST00000426740|ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048;ENST00000442336	.|T;T;T;T;T;T	.|0.03889	.|4.95;4.94;4.98;4.98;4.98;3.77	4.43|4.43	-8.86|-8.86	0.00795|0.00795	.|.	4.323350|4.323350	0.00674|0.00674	N|N	0.000659|0.000659	T|T	0.00468|0.00468	0.0015|0.0015	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.35699|0.35699	-0.9778|-0.9778	6|10	.|0.06236	.|T	.|0.91	.|.	8.7015|8.7015	0.34329|0.34329	0.0:0.1887:0.1973:0.614|0.0:0.1887:0.1973:0.614	.|.	.|106;141;106	.|P08637;E9PG94;Q9UPY7	.|FCG3A_HUMAN;.;.	M|V	122|142;141;106;106;106;105	.|ENSP00000356946:I142V;ENSP00000392047:I141V;ENSP00000416607:I106V;ENSP00000356944:I106V;ENSP00000444971:I106V;ENSP00000396567:I105V	.|ENSP00000356944:I106V	I|I	-|-	3|1	3|0	FCGR3A|FCGR3A	159784838|159784838	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-5.685000|-5.685000	0.00105|0.00105	-3.274000|-3.274000	0.00199|0.00199	-0.326000|-0.326000	0.08463|0.08463	ATA|ATC	.	.	weak		0.483	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
MUC16	94025	hgsc.bcm.edu	37	19	9049149	9049149	+	Missense_Mutation	SNP	G	G	A	rs12461007	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9049149G>A	ENST00000397910.4	-	5	32685	c.32482C>T	c.(32482-32484)Cct>Tct	p.P10828S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10830	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCTGTGCAGGATGCGTGACC	0.483													G|||	997	0.199081	0.1982	0.2695	5008	,	,		23097	0.0258		0.2813	False		,,,				2504	0.2444				p.P10828S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C32482T						PASS	.		SER/PRO	750,3182		72,606,1288	172.0	156.0	161.0		32482	-6.0	0.0	19	dbSNP_120	161	2519,5795		401,1717,2039	yes	missense	MUC16	NM_024690.2	74	473,2323,3327	AA,AG,GG		30.2983,19.0743,26.6944	benign	10828/14508	9049149	3269,8977	1966	4157	6123	SO:0001583	missense	94025	exon5			GTGCAGGATGCGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.32482C>T	19.37:g.9049149G>A	ENSP00000381008:p.Pro10828Ser	Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	232	230	0.991379	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	426	0.19505494505494506	103	0.20934959349593496	95	0.26243093922651933	11	0.019230769230769232	217	0.2862796833773087	g	5.293	0.239478	0.10023	0.190743	0.302983	ENSG00000181143	ENST00000397910	T	0.03124	4.04	3.0	-5.99	0.02213	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.20052	0.041	B	0.15870	0.014	T	0.50466	-0.8825	8	0.87932	D	0	.	6.055	0.19807	0.3575:0.1554:0.487:0.0	rs12461007;rs52811941;rs61073913;rs12461007	10828	B5ME49	.	S	10828	ENSP00000381008:P10828S	ENSP00000381008:P10828S	P	-	1	0	MUC16	8910149	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	-0.091000	0.11146	-1.512000	0.01791	-0.633000	0.03987	CCT	G|0.783;A|0.217	0.217	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
BOD1L1	259282	hgsc.bcm.edu	37	4	13604418	13604418	+	Missense_Mutation	SNP	G	G	C	rs17745712	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:13604418G>C	ENST00000040738.5	-	10	4241	c.4106C>G	c.(4105-4107)gCt>gGt	p.A1369G		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1369			A -> G (in dbSNP:rs17745712).			nucleus (GO:0005634)	DNA binding (GO:0003677)										AGCCTGGTGAGCTTCTGGAAT	0.413													C|||	695	0.138778	0.1619	0.2133	5008	,	,		22483	0.003		0.1501	False		,,,				2504	0.183				p.A1369G		Atlas-SNP	.											.	.	.	.	0			c.C4106G						PASS	.	C	GLY/ALA	715,3691	757.3+/-412.7	48,619,1536	152.0	151.0	151.0		4106	2.2	0.1	4	dbSNP_123	151	1296,7304	757.8+/-407.5	86,1124,3090	yes	missense	BOD1L	NM_148894.2	60	134,1743,4626	CC,CG,GG		15.0698,16.2279,15.4621	benign	1369/3052	13604418	2011,10995	2203	4300	6503	SO:0001583	missense	259282	exon10			TGGTGAGCTTCTG	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.4106C>G	4.37:g.13604418G>C	ENSP00000040738:p.Ala1369Gly	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	254	123	0.484252	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	269	0.12316849816849818	85	0.17276422764227642	73	0.20165745856353592	0	0.0	111	0.14643799472295516	C	0.007	-2.002897	0.00431	0.162279	0.150698	ENSG00000038219	ENST00000040738	T	0.07021	3.23	5.55	2.24	0.28232	.	0.628007	0.14931	N	0.290053	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46105	-0.9215	9	0.08381	T	0.77	-0.6927	5.4252	0.16421	0.0:0.4686:0.2543:0.2772	rs17745712;rs52797471;rs17745712	1369	Q8NFC6	BOD1L_HUMAN	G	1369	ENSP00000040738:A1369G	ENSP00000040738:A1369G	A	-	2	0	BOD1L	13213516	0.001000	0.12720	0.083000	0.20561	0.056000	0.15407	-0.124000	0.10595	-0.107000	0.12088	-0.120000	0.15030	GCT	G|0.848;C|0.152	0.152	strong		0.413	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
AADACL2	344752	hgsc.bcm.edu	37	3	151463421	151463421	+	Missense_Mutation	SNP	G	G	T	rs1972977	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:151463421G>T	ENST00000356517.3	+	4	665	c.556G>T	c.(556-558)Gcg>Tcg	p.A186S		NM_207365.3	NP_997248.2	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2	186			A -> S (in dbSNP:rs1972977). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(13)|skin(2)	24			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			AATCTGCATTGCGGGAGACAG	0.403													T|||	3539	0.706669	0.823	0.6455	5008	,	,		14886	0.624		0.668	False		,,,				2504	0.7178				p.A186S		Atlas-SNP	.											.	AADACL2	102	.	0			c.G556T						PASS	.	T	SER/ALA	3534,872	325.3+/-299.0	1412,710,81	70.0	78.0	75.0		556	-3.3	0.0	3	dbSNP_92	75	5545,3053	467.0+/-366.9	1798,1949,552	yes	missense	AADACL2	NM_207365.3	99	3210,2659,633	TT,TG,GG		35.5083,19.7912,30.183	benign	186/402	151463421	9079,3925	2203	4299	6502	SO:0001583	missense	344752	exon4			TGCATTGCGGGAG	BC065724	CCDS3161.2	3q25.1	2010-12-14			ENSG00000197953	ENSG00000197953			24427	protein-coding gene	gene with protein product							Standard	NM_207365		Approved	MGC72001	uc003ezc.3	Q6P093	OTTHUMG00000155914	ENST00000356517.3:c.556G>T	3.37:g.151463421G>T	ENSP00000348911:p.Ala186Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	111	109	0.981982	NM_207365	Q5HYJ4	Missense_Mutation	SNP	ENST00000356517.3	37	CCDS3161.2	1498	0.6858974358974359	400	0.8130081300813008	237	0.6546961325966851	352	0.6153846153846154	509	0.6715039577836411	T	0.004	-2.300516	0.00243	0.802088	0.644917	ENSG00000197953	ENST00000356517	T	0.59502	0.26	4.58	-3.34	0.04943	Alpha/beta hydrolase fold-3 (1);	0.421474	0.26481	N	0.024123	T	0.00012	0.0000	N	0.21142	0.635	0.80722	P	0.0	B	0.02656	0.0	B	0.11329	0.006	T	0.50145	-0.8862	9	0.02654	T	1	-10.789	18.9711	0.92715	0.0:0.0:0.7259:0.2741	rs1972977;rs17846703;rs17859806;rs52829017;rs1972977	186	Q6P093	ADCL2_HUMAN	S	186	ENSP00000348911:A186S	ENSP00000348911:A186S	A	+	1	0	AADACL2	152946111	0.235000	0.23794	0.022000	0.16811	0.000000	0.00434	0.113000	0.15499	-0.573000	0.05998	-1.487000	0.00979	GCG	G|0.306;T|0.694	0.694	strong		0.403	AADACL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342288.3	NM_207365	
STIL	6491	hgsc.bcm.edu	37	1	47717189	47717189	+	Silent	SNP	A	A	G	rs2758735	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:47717189A>G	ENST00000360380.3	-	18	3846	c.3483T>C	c.(3481-3483)ccT>ccC	p.P1161P	STIL_ENST00000337817.5_Silent_p.P1161P|STIL_ENST00000243182.6_Silent_p.P1161P|STIL_ENST00000396221.2_Silent_p.P1144P|STIL_ENST00000371877.3_Silent_p.P1162P	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	1161					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				CAAGCTGTTCAGGTATGGACC	0.413													A|||	1970	0.393371	0.1218	0.4078	5008	,	,		19950	0.4296		0.5427	False		,,,				2504	0.5593				p.P1162P		Atlas-SNP	.											.	STIL	91	.	0			c.T3486C						PASS	.	A	,	798,3608	318.8+/-295.8	74,650,1479	139.0	139.0	139.0		3486,3483	-3.0	0.0	1	dbSNP_100	139	4515,4085	592.6+/-393.0	1177,2161,962	no	coding-synonymous,coding-synonymous	STIL	NM_001048166.1,NM_003035.2	,	1251,2811,2441	GG,GA,AA		47.5,18.1117,40.8504	,	1162/1289,1161/1288	47717189	5313,7693	2203	4300	6503	SO:0001819	synonymous_variant	6491	exon17			CTGTTCAGGTATG	M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"""TAL1 (SCL) interrupting locus"""	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.3483T>C	1.37:g.47717189A>G		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	202	202	1	NM_001048166	Q5T0C5|Q68CN9	Silent	SNP	ENST00000360380.3	37	CCDS548.1																																																																																			G|0.406;A|0.594	0.406	strong		0.413	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035	
TECR	9524	hgsc.bcm.edu	37	19	14676578	14676578	+	Silent	SNP	C	C	T	rs61732092	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14676578C>T	ENST00000215567.5	+	13	959	c.822C>T	c.(820-822)ggC>ggT	p.G274G	TECR_ENST00000600083.1_Silent_p.G119G|TECR_ENST00000436007.2_Silent_p.G289G|TECR_ENST00000596073.1_Silent_p.G119G	NM_138501.5	NP_612510.1	Q9NZ01	TECR_HUMAN	trans-2,3-enoyl-CoA reductase	274					cellular lipid metabolic process (GO:0044255)|fatty acid elongation (GO:0030497)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|nucleus (GO:0005634)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|large_intestine(1)|ovary(1)	3						CCCTGGTGGGCTTCACCCAGA	0.697													C|||	493	0.0984425	0.208	0.0519	5008	,	,		15669	0.0149		0.0795	False		,,,				2504	0.089				p.G274G		Atlas-SNP	.											.	TECR	22	.	0			c.C822T						PASS	.	C		723,3677		72,579,1549	21.0	20.0	20.0		822	3.5	1.0	19	dbSNP_129	20	653,7947		27,599,3674	no	coding-synonymous	TECR	NM_138501.5		99,1178,5223	TT,TC,CC		7.593,16.4318,10.5846		274/309	14676578	1376,11624	2200	4300	6500	SO:0001819	synonymous_variant	9524	exon13			GGTGGGCTTCACC	AK001416	CCDS12313.1	19p13.12	2014-05-27	2009-07-21	2009-07-21	ENSG00000099797	ENSG00000099797			4551	protein-coding gene	gene with protein product		610057	"""glycoprotein, synaptic 2"""	SC2, GPSN2		9653160, 12482854	Standard	NM_138501		Approved	TER, MRT14	uc002mza.3	Q9NZ01		ENST00000215567.5:c.822C>T	19.37:g.14676578C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_138501	B2RD55|O75350|Q6IBB2|Q9BWK3|Q9Y6P0	Silent	SNP	ENST00000215567.5	37	CCDS12313.1																																																																																			C|0.904;T|0.096	0.096	strong		0.697	TECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466000.1	NM_138501	
MTR	4548	hgsc.bcm.edu	37	1	237048500	237048500	+	Missense_Mutation	SNP	A	A	G	rs1805087	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:237048500A>G	ENST00000366577.5	+	26	3150	c.2756A>G	c.(2755-2757)gAc>gGc	p.D919G	MTR_ENST00000535889.1_Missense_Mutation_p.D868G	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	919			D -> G (may be associated with susceptibility to FS-NTD; dbSNP:rs1805087). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9013615}.		cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	ATTAGACAGGACCATTATGAG	0.318													A|||	1093	0.218251	0.2844	0.1772	5008	,	,		20140	0.1052		0.173	False		,,,				2504	0.3211				p.D919G		Atlas-SNP	.											MTR,rectum,carcinoma,+1,1	MTR	127	1	0			c.A2756G	GRCh37	CM983303	MTR	M	rs1805087	PASS	.	A	GLY/ASP	1164,3242	407.1+/-334.1	154,856,1193	91.0	95.0	94.0		2756	6.0	1.0	1	dbSNP_89	94	1702,6898	309.6+/-309.4	177,1348,2775	yes	missense	MTR	NM_000254.2	94	331,2204,3968	GG,GA,AA		19.7907,26.4185,22.036	benign	919/1266	237048500	2866,10140	2203	4300	6503	SO:0001583	missense	4548	exon26			GACAGGACCATTA	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.2756A>G	1.37:g.237048500A>G	ENSP00000355536:p.Asp919Gly	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Missense_Mutation	SNP	ENST00000366577.5	37	CCDS1614.1	421	0.19276556776556777	154	0.3130081300813008	67	0.1850828729281768	74	0.12937062937062938	126	0.1662269129287599	A	14.35	2.510220	0.44660	0.264185	0.197907	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000535889;ENST00000366576	T;T;T	0.72051	-0.62;-0.62;-0.62	5.99	5.99	0.97316	Cobalamin (vitamin B12)-binding (2);	0.149441	0.64402	D	0.000017	T	0.00012	0.0000	L	0.28694	0.88	0.20196	P	0.9999212773	B;P;B	0.37176	0.159;0.586;0.159	B;B;B	0.35770	0.161;0.21;0.161	T	0.07046	-1.0793	9	0.59425	D	0.04	-19.2895	16.4943	0.84223	1.0:0.0:0.0:0.0	rs1805087;rs17658739;rs56618494;rs61036243;rs1805087	919;868;919	B7ZLW8;B7ZLW7;Q99707	.;.;METH_HUMAN	G	773;919;868;473	ENSP00000355536:D919G;ENSP00000441845:D868G;ENSP00000355535:D473G	ENSP00000355535:D473G	D	+	2	0	MTR	235115123	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.545000	0.90657	2.291000	0.77112	0.533000	0.62120	GAC	A|0.786;G|0.214	0.214	strong		0.318	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	
MSH5	4439	hgsc.bcm.edu	37	6	31709045	31709045	+	Missense_Mutation	SNP	C	C	T	rs28381349	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31709045C>T	ENST00000375755.3	+	3	539	c.253C>T	c.(253-255)Ctc>Ttc	p.L85F	MSH5_ENST00000375750.3_Missense_Mutation_p.L85F|CLIC1_ENST00000395892.1_5'Flank|MSH5_ENST00000534153.4_Missense_Mutation_p.L85F|MSH5-SAPCD1_ENST00000493662.2_Missense_Mutation_p.L85F|MSH5_ENST00000482280.1_3'UTR|MSH5_ENST00000375703.3_Missense_Mutation_p.L85F|MSH5_ENST00000375740.3_Missense_Mutation_p.L85F|MSH5_ENST00000375742.3_Missense_Mutation_p.L85F	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	85			L -> F (in dbSNP:rs28381349). {ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						CCACGAGAGCCTCAAGCTTCT	0.502								Direct reversal of damage;Mismatch excision repair (MMR)					C|||	163	0.0325479	0.0772	0.062	5008	,	,		17256	0.0		0.0169	False		,,,				2504	0.001				p.L85F		Atlas-SNP	.											.	MSH5	108	.	0			c.C253T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	207,2815		6,195,1310	237.0	213.0	222.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	253,253,253,253	5.0	1.0	6	dbSNP_125	222	115,5303		1,113,2595	yes	missense,missense,missense,missense	MSH5	NM_002441.4,NM_025259.5,NM_172165.3,NM_172166.3	22,22,22,22	7,308,3905	TT,TC,CC		2.1226,6.8498,3.8152	benign,benign,benign,benign	85/835,85/823,85/836,85/835	31709045	322,8118	1511	2709	4220	SO:0001583	missense	4439	exon3			GAGAGCCTCAAGC	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.253C>T	6.37:g.31709045C>T	ENSP00000364908:p.Leu85Phe	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	124	52	0.419355	NM_172165	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Missense_Mutation	SNP	ENST00000375755.3	37	CCDS4720.1	82	0.037545787545787544	46	0.09349593495934959	22	0.06077348066298342	0	0.0	14	0.018469656992084433	C	9.092	1.002008	0.19121	0.068498	0.021226	ENSG00000204410	ENST00000375755;ENST00000375742;ENST00000375750;ENST00000425703;ENST00000534153;ENST00000375703;ENST00000375740	T;T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53;0.53	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000004	T	0.20007	0.0481	L	0.31420	0.93	0.41340	P	0.012704999999999966	B;B;B;B	0.32717	0.127;0.013;0.007;0.381	B;B;B;B	0.32533	0.049;0.013;0.025;0.147	T	0.06991	-1.0796	9	0.14656	T	0.56	-22.2256	9.4858	0.38928	0.0:0.9033:0.0:0.0967	rs28381349;rs28381349	85;85;85;85	O43196-4;O43196;O43196-2;O43196-3	.;MSH5_HUMAN;.;.	F	85	ENSP00000364908:L85F;ENSP00000364894:L85F;ENSP00000364903:L85F;ENSP00000402842:L85F;ENSP00000431693:L85F;ENSP00000364855:L85F;ENSP00000364892:L85F	ENSP00000364855:L85F	L	+	1	0	MSH5	31817024	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.032000	0.57274	2.348000	0.79779	0.650000	0.86243	CTC	C|0.957;T|0.043	0.043	strong		0.502	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4		
TBC1D10B	26000	hgsc.bcm.edu	37	16	30380872	30380872	+	Missense_Mutation	SNP	C	C	G	rs71389465	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30380872C>G	ENST00000409939.3	-	1	713	c.633G>C	c.(631-633)gaG>gaC	p.E211D		NM_015527.3	NP_056342.3	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	211					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(1)|lung(2)|urinary_tract(1)	6			Colorectal(24;0.193)			CTGAGGGGTCCTCAGGAGCCT	0.627													C|||	567	0.113219	0.0113	0.0144	5008	,	,		16572	0.0873		0.0398	False		,,,				2504	0.4233				p.E211D		Atlas-SNP	.											.	TBC1D10B	32	.	0			c.G633C						PASS	.	C	ASP/GLU	24,1360		0,24,668	24.0	28.0	27.0		633	3.1	1.0	16	dbSNP_130	27	161,3021		7,147,1437	yes	missense	TBC1D10B	NM_015527.3	45	7,171,2105	GG,GC,CC		5.0597,1.7341,4.0517	possibly-damaging	211/809	30380872	185,4381	692	1591	2283	SO:0001583	missense	26000	exon1			GGGGTCCTCAGGA	BC063112	CCDS10676.2	16p11.2	2013-07-09			ENSG00000169221	ENSG00000169221			24510	protein-coding gene	gene with protein product		613620				20404108	Standard	NM_015527		Approved	DKFZP434P1750, Rab27A-GAPbeta, FLJ13130, EPI64B	uc002dxt.3	Q4KMP7	OTTHUMG00000132396	ENST00000409939.3:c.633G>C	16.37:g.30380872C>G	ENSP00000386538:p.Glu211Asp	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_015527	B9A6L0|Q6IN54|Q6P530|Q71RG7|Q86VC5|Q9H8Z2|Q9NUN6|Q9UFP2	Missense_Mutation	SNP	ENST00000409939.3	37	CCDS10676.2	88	0.040293040293040296	7	0.014227642276422764	6	0.016574585635359115	44	0.07692307692307693	31	0.040897097625329816	C	17.12	3.309354	0.60414	0.017341	0.050597	ENSG00000169221	ENST00000409939	T	0.05382	3.45	4.12	3.07	0.35406	.	.	.	.	.	T	0.00271	0.0008	N	0.22421	0.69	0.22675	N	0.998869	B	0.02656	0.0	B	0.04013	0.001	T	0.38950	-0.9637	9	0.42905	T	0.14	.	4.4105	0.11431	0.0:0.6308:0.2366:0.1326	.	211	Q4KMP7	TB10B_HUMAN	D	211	ENSP00000386538:E211D	ENSP00000386538:E211D	E	-	3	2	TBC1D10B	30288373	0.719000	0.27986	0.999000	0.59377	0.875000	0.50365	1.922000	0.40045	2.136000	0.66102	0.491000	0.48974	GAG	C|0.956;G|0.044	0.044	strong		0.627	TBC1D10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255527.3	NM_015527	
ST14	6768	hgsc.bcm.edu	37	11	130079574	130079574	+	Silent	SNP	C	C	T	rs116956726	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130079574C>T	ENST00000278742.5	+	19	2842	c.2424C>T	c.(2422-2424)ccC>ccT	p.P808P		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	808	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	CCGGGGGACCCCTGTCCAGCG	0.716													C|||	36	0.0071885	0.0	0.0101	5008	,	,		12333	0.0		0.0159	False		,,,				2504	0.0133				p.P808P		Atlas-SNP	.											.	ST14	82	.	0			c.C2424T						PASS	.	C		13,4389	17.9+/-39.9	0,13,2188	41.0	43.0	42.0		2424	-4.3	1.0	11	dbSNP_132	42	108,8486	56.4+/-117.6	0,108,4189	no	coding-synonymous	ST14	NM_021978.3		0,121,6377	TT,TC,CC		1.2567,0.2953,0.9311		808/856	130079574	121,12875	2201	4297	6498	SO:0001819	synonymous_variant	6768	exon19			GGGACCCCTGTCC	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.2424C>T	11.37:g.130079574C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Silent	SNP	ENST00000278742.5	37	CCDS8487.1																																																																																			C|0.993;T|0.007	0.007	strong		0.716	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
TENC1	23371	hgsc.bcm.edu	37	12	53454193	53454193	+	Silent	SNP	G	G	A	rs73099915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53454193G>A	ENST00000314250.6	+	19	2912	c.2622G>A	c.(2620-2622)tcG>tcA	p.S874S	TENC1_ENST00000552570.1_Silent_p.S874S|TENC1_ENST00000451358.1_Silent_p.S864S|TENC1_ENST00000314276.3_Silent_p.S884S|TENC1_ENST00000549700.1_Silent_p.S809S|TENC1_ENST00000546602.1_Silent_p.S777S|TENC1_ENST00000379902.3_Silent_p.S750S	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	874	Pro-rich.				cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						CTGCAGAGTCGCTGGAGCCGG	0.622													G|||	96	0.0191693	0.0325	0.0086	5008	,	,		18885	0.0		0.0348	False		,,,				2504	0.0123				p.S884S		Atlas-SNP	.											.	TENC1	148	.	0			c.G2652A						PASS	.	G	,,	238,4168	133.3+/-169.7	4,230,1969	37.0	34.0	35.0		2652,2622,2250	-9.6	0.0	12	dbSNP_130	35	327,8273	113.5+/-173.5	9,309,3982	no	coding-synonymous,coding-synonymous,coding-synonymous	TENC1	NM_015319.2,NM_170754.2,NM_198316.1	,,	13,539,5951	AA,AG,GG		3.8023,5.4017,4.3441	,,	884/1420,874/1410,750/1286	53454193	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	23371	exon19			AGAGTCGCTGGAG	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	19737	protein-coding gene	gene with protein product	"""tensin 2"""	607717	"""tensin like C1 domain-containing phosphatase"""				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.2622G>A	12.37:g.53454193G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Silent	SNP	ENST00000314250.6	37	CCDS8843.1																																																																																			G|0.965;A|0.035	0.035	strong		0.622	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754	
TRAK2	66008	hgsc.bcm.edu	37	2	202252539	202252539	+	Missense_Mutation	SNP	G	G	A	rs2244438	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:202252539G>A	ENST00000332624.3	-	13	2011	c.1583C>T	c.(1582-1584)aCa>aTa	p.T528I		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	528			T -> I (in dbSNP:rs2244438). {ECO:0000269|PubMed:11161814}.		protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						AAGGCTCTCTGTCGGGGTGAC	0.493													G|||	1197	0.239018	0.2095	0.3905	5008	,	,		17694	0.2431		0.3141	False		,,,				2504	0.09				p.T528I		Atlas-SNP	.											.	TRAK2	62	.	0			c.C1583T						PASS	.	G	ILE/THR	1027,3379	380.4+/-323.7	126,775,1302	105.0	100.0	102.0		1583	4.1	0.4	2	dbSNP_100	102	2617,5983	423.0+/-354.2	382,1853,2065	yes	missense	TRAK2	NM_015049.2	89	508,2628,3367	AA,AG,GG		30.4302,23.3091,28.0178	probably-damaging	528/915	202252539	3644,9362	2203	4300	6503	SO:0001583	missense	66008	exon13			CTCTCTGTCGGGG	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"""gamma-aminobutyric acid(A) receptor-interacting factor"", ""milton homolog 2 (Drosophila)"", ""O-linked N-acetylglucosamine transferase interacting protein 98"""	607334	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"""	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.1583C>T	2.37:g.202252539G>A	ENSP00000328875:p.Thr528Ile	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	205	104	0.507317	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	37	CCDS2347.1	633	0.28983516483516486	111	0.22560975609756098	145	0.4005524861878453	145	0.2534965034965035	232	0.30606860158311344	G	8.488	0.861341	0.17178	0.233091	0.304302	ENSG00000115993	ENST00000332624;ENST00000542292	T	0.45276	0.9	4.94	4.07	0.47477	Trafficking kinesin-binding protein domain (1);	0.566917	0.19621	N	0.109919	T	0.00012	0.0000	M	0.66939	2.045	0.32117	P	0.5885210000000001	B	0.23249	0.082	B	0.20577	0.03	T	0.32134	-0.9918	9	0.72032	D	0.01	.	10.4782	0.44678	0.1554:0.0:0.8446:0.0	rs2244438;rs52836839;rs60941354;rs2244438	528	O60296	TRAK2_HUMAN	I	528;434	ENSP00000328875:T528I	ENSP00000328875:T528I	T	-	2	0	TRAK2	201960784	0.036000	0.19791	0.398000	0.26321	0.143000	0.21401	1.979000	0.40608	1.334000	0.45468	0.655000	0.94253	ACA	G|0.722;A|0.278	0.278	strong		0.493	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049	
TET1	80312	hgsc.bcm.edu	37	10	70332672	70332672	+	Missense_Mutation	SNP	T	T	A	rs12773594	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70332672T>A	ENST00000373644.4	+	2	786	c.577T>A	c.(577-579)Tcc>Acc	p.S193T		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	193			S -> T (in dbSNP:rs12773594).		chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TCAGTTTTGGTCCCAAAGAGT	0.478													T|||	860	0.171725	0.0983	0.1513	5008	,	,		20171	0.1726		0.1849	False		,,,				2504	0.271				p.S193T		Atlas-SNP	.											.	TET1	255	.	0			c.T577A						PASS	.	T	THR/SER	494,3912	227.2+/-242.5	28,438,1737	61.0	61.0	61.0		577	2.5	0.7	10	dbSNP_121	61	1291,7309	252.3+/-278.5	105,1081,3114	yes	missense	TET1	NM_030625.2	58	133,1519,4851	AA,AT,TT		15.0116,11.212,13.7244	benign	193/2137	70332672	1785,11221	2203	4300	6503	SO:0001583	missense	80312	exon2			TTTTGGTCCCAAA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.577T>A	10.37:g.70332672T>A	ENSP00000362748:p.Ser193Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	87	35	0.402299	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	344	0.1575091575091575	29	0.05894308943089431	64	0.17679558011049723	111	0.19405594405594406	140	0.18469656992084432	T	11.91	1.780553	0.31502	0.11212	0.150116	ENSG00000138336	ENST00000373644	T	0.07688	3.17	5.0	2.55	0.30701	.	1.544370	0.04021	N	0.299769	T	0.00012	0.0000	N	0.24115	0.695	0.53005	P	3.6000000000036E-5	P	0.43477	0.808	B	0.29785	0.107	T	0.46062	-0.9218	9	0.27785	T	0.31	.	6.9496	0.24538	0.0:0.1915:0.0:0.8085	rs12773594;rs52825337;rs12773594	193	Q8NFU7	TET1_HUMAN	T	193	ENSP00000362748:S193T	ENSP00000362748:S193T	S	+	1	0	TET1	70002678	0.006000	0.16342	0.655000	0.29622	0.917000	0.54804	-0.025000	0.12413	0.301000	0.22738	0.460000	0.39030	TCC	T|0.854;A|0.146	0.146	strong		0.478	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
LTF	4057	hgsc.bcm.edu	37	3	46484964	46484964	+	Silent	SNP	G	G	A	rs1042073	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:46484964G>A	ENST00000231751.4	-	13	1918	c.1623C>T	c.(1621-1623)aaC>aaT	p.N541N	LTF_ENST00000493056.1_5'Flank|LTF_ENST00000417439.1_Silent_p.N539N|LTF_ENST00000426532.2_Silent_p.N497N	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	541	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		AGTATCTCTCGTTGCTGTTGG	0.542													A|||	2248	0.448882	0.4115	0.2997	5008	,	,		21020	0.6409		0.337	False		,,,				2504	0.5225				p.N541N		Atlas-SNP	.											.	LTF	98	.	0			c.C1623T						PASS	.	A	,	1763,2643	645.2+/-398.2	345,1073,785	239.0	222.0	227.0		1491,1623	-10.6	0.0	3	dbSNP_86	227	2588,6004	689.5+/-404.4	384,1820,2092	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	729,2893,2877	AA,AG,GG		30.121,40.0136,33.4744	,	497/667,541/711	46484964	4351,8647	2203	4296	6499	SO:0001819	synonymous_variant	4057	exon13			TCTCTCGTTGCTG		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.1623C>T	3.37:g.46484964G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	162	73	0.450617	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			G|0.597;A|0.403	0.403	strong		0.542	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
TBPL2	387332	hgsc.bcm.edu	37	14	55903716	55903716	+	Missense_Mutation	SNP	C	C	A	rs45612333	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:55903716C>A	ENST00000247219.5	-	2	241	c.171G>T	c.(169-171)agG>agT	p.R57S		NM_199047.2	NP_950248.1			TATA box binding protein like 2											endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8						ACAGGGGAGACCTGGGTGGGG	0.453													C|||	237	0.0473243	0.034	0.0677	5008	,	,		20723	0.005		0.0795	False		,,,				2504	0.0613				p.R57S		Atlas-SNP	.											.	TBPL2	27	.	0			c.G171T						PASS	.	C	SER/ARG	151,4231	94.4+/-133.1	2,147,2042	81.0	86.0	84.0		171	0.4	0.0	14	dbSNP_127	84	762,7824	176.2+/-226.1	37,688,3568	yes	missense	TBPL2	NM_199047.2	110	39,835,5610	AA,AC,CC		8.8749,3.4459,7.0404	benign	57/376	55903716	913,12055	2191	4293	6484	SO:0001583	missense	387332	exon2			GGGAGACCTGGGT	AY457923	CCDS9724.1	14q22.2	2004-06-03			ENSG00000182521	ENSG00000182521			19841	protein-coding gene	gene with protein product		608964				14634207	Standard	NM_199047		Approved	TRF3, TBP2	uc001xby.3	Q6SJ96	OTTHUMG00000140313	ENST00000247219.5:c.171G>T	14.37:g.55903716C>A	ENSP00000247219:p.Arg57Ser	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	173	85	0.491329	NM_199047		Missense_Mutation	SNP	ENST00000247219.5	37	CCDS9724.1	108	0.04945054945054945	21	0.042682926829268296	30	0.08287292817679558	1	0.0017482517482517483	56	0.07387862796833773	C	0.650	-0.809813	0.02798	0.034459	0.088749	ENSG00000182521	ENST00000247219	T	0.41758	0.99	4.99	0.384	0.16244	.	1.845360	0.02244	N	0.066064	T	0.00936	0.0031	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.04386	-1.0955	10	0.07325	T	0.83	11.7785	0.6339	0.00799	0.2488:0.372:0.1409:0.2383	rs45612333	57	Q6SJ96	TBPL2_HUMAN	S	57	ENSP00000247219:R57S	ENSP00000247219:R57S	R	-	3	2	TBPL2	54973469	0.002000	0.14202	0.037000	0.18230	0.480000	0.33159	-0.072000	0.11486	0.507000	0.28148	0.563000	0.77884	AGG	C|0.933;A|0.067	0.067	strong		0.453	TBPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276916.1	NM_199047	
REV1	51455	hgsc.bcm.edu	37	2	100019496	100019496	+	Silent	SNP	A	A	G	rs2305354	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:100019496A>G	ENST00000258428.3	-	20	3468	c.3240T>C	c.(3238-3240)atT>atC	p.I1080I	RP11-527J8.1_ENST00000608144.1_RNA|REV1_ENST00000393445.3_Silent_p.I1079I|REV1_ENST00000465835.1_5'Flank	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	1080					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TTGGTGAACCAATGGtttttt	0.408								Direct reversal of damage					G|||	2948	0.588658	0.7564	0.7017	5008	,	,		19090	0.3681		0.5696	False		,,,				2504	0.5286				p.I1080I		Atlas-SNP	.											.	REV1	100	.	0			c.T3240C						PASS	.	G	,	3240,1166	411.7+/-335.8	1195,850,158	80.0	76.0	77.0		3237,3240	3.1	0.0	2	dbSNP_100	77	4735,3865	542.5+/-384.2	1301,2133,866	no	coding-synonymous,coding-synonymous	REV1	NM_001037872.1,NM_016316.2	,	2496,2983,1024	GG,GA,AA		44.9419,26.4639,38.6821	,	1079/1251,1080/1252	100019496	7975,5031	2203	4300	6503	SO:0001819	synonymous_variant	51455	exon20			TGAACCAATGGTT	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"""DNA polymerases"""	14060	protein-coding gene	gene with protein product		606134	"""REV1 (yeast homolog)- like"", ""REV1-like (yeast)"", ""REV1 homolog (S. cerevisiae)"""	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.3240T>C	2.37:g.100019496A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_016316	O95941|Q53SI7|Q9C0J4|Q9NUP2	Silent	SNP	ENST00000258428.3	37	CCDS2045.1																																																																																			A|0.402;G|0.598	0.598	strong		0.408	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	
GLDN	342035	hgsc.bcm.edu	37	15	51689772	51689772	+	Missense_Mutation	SNP	G	G	A	rs17648128	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:51689772G>A	ENST00000335449.6	+	6	850	c.794G>A	c.(793-795)aGc>aAc	p.S265N	GLDN_ENST00000396399.2_Missense_Mutation_p.S141N	NM_181789.2	NP_861454.2	Q6ZMI3	GLDN_HUMAN	gliomedin	265			S -> N (in dbSNP:rs17648128). {ECO:0000269|PubMed:12975309}.		clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|microvillus organization (GO:0032528)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)		CGGCAGCCAAGCATGTTCAAC	0.637													A|||	1499	0.299321	0.2209	0.183	5008	,	,		13709	0.495		0.3181	False		,,,				2504	0.2669				p.S265N		Atlas-SNP	.											.	GLDN	54	.	0			c.G794A						PASS	.	A	ASN/SER	1023,3369	697.4+/-406.2	115,793,1288	34.0	43.0	40.0		794	4.1	1.0	15	dbSNP_123	40	2870,5716	655.6+/-401.3	481,1908,1904	yes	missense	GLDN	NM_181789.2	46	596,2701,3192	AA,AG,GG		33.4265,23.2923,29.9969	benign	265/552	51689772	3893,9085	2196	4293	6489	SO:0001583	missense	342035	exon6			AGCCAAGCATGTT	AY358144	CCDS10140.2	15q15.3	2008-02-05	2005-10-06	2005-10-06	ENSG00000186417	ENSG00000186417			29514	protein-coding gene	gene with protein product		608603	"""collomin"""	COLM		16039564, 12642876	Standard	XM_005254338		Approved	CRG-L2, CLOM, colmedin, UNC-112	uc002aba.3	Q6ZMI3	OTTHUMG00000131746	ENST00000335449.6:c.794G>A	15.37:g.51689772G>A	ENSP00000335196:p.Ser265Asn	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_181789	Q6UXZ7|Q7Z359	Missense_Mutation	SNP	ENST00000335449.6	37	CCDS10140.2	747	0.34203296703296704	104	0.21138211382113822	78	0.2154696132596685	308	0.5384615384615384	257	0.3390501319261214	A	4.124	0.021191	0.08006	0.232923	0.334265	ENSG00000186417	ENST00000335449;ENST00000396399;ENST00000537339	D;D	0.93488	-3.23;-3.23	5.17	4.05	0.47172	.	0.000000	0.44688	N	0.000433	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33599	-0.9862	9	0.07644	T	0.81	.	8.5264	0.33307	0.8425:0.0:0.1575:0.0	rs17648128;rs52807767;rs56468086;rs17648128	265	Q6ZMI3	GLDN_HUMAN	N	265;141;141	ENSP00000335196:S265N;ENSP00000379681:S141N	ENSP00000335196:S265N	S	+	2	0	GLDN	49477064	0.994000	0.37717	0.988000	0.46212	0.968000	0.65278	2.382000	0.44345	0.812000	0.34326	-0.269000	0.10298	AGC	G|0.690;A|0.310	0.310	strong		0.637	GLDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254667.2	NM_181789	
NLRC5	84166	hgsc.bcm.edu	37	16	57080528	57080528	+	Missense_Mutation	SNP	C	C	A	rs289723	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:57080528C>A	ENST00000262510.6	+	22	3538	c.3313C>A	c.(3313-3315)Cag>Aag	p.Q1105K	NLRC5_ENST00000308149.7_Missense_Mutation_p.Q1105K|NLRC5_ENST00000436936.1_Missense_Mutation_p.Q1105K|NLRC5_ENST00000539144.1_Missense_Mutation_p.Q1105K	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1105			Q -> K (in dbSNP:rs289723). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				AGGGTTCCGTCAGCGCTGCAT	0.557													C|||	843	0.168331	0.034	0.2911	5008	,	,		15508	0.1081		0.2455	False		,,,				2504	0.2454				p.Q1105K		Atlas-SNP	.											.	NLRC5	186	.	0			c.C3313A						PASS	.	C	LYS/GLN	355,4041	182.2+/-210.1	8,339,1851	93.0	83.0	86.0		3313	1.5	0.0	16	dbSNP_79	86	2499,6101	411.7+/-350.6	368,1763,2169	yes	missense	NLRC5	NM_032206.3	53	376,2102,4020	AA,AC,CC		29.0581,8.0755,21.9606	benign	1105/1867	57080528	2854,10142	2198	4300	6498	SO:0001583	missense	84166	exon21			TTCCGTCAGCGCT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.3313C>A	16.37:g.57080528C>A	ENSP00000262510:p.Gln1105Lys	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	173	80	0.462428	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	389|389	0.17811355311355312|0.17811355311355312	20|20	0.04065040650406504|0.04065040650406504	104|104	0.287292817679558|0.287292817679558	74|74	0.12937062937062938|0.12937062937062938	191|191	0.2519788918205805|0.2519788918205805	C|C	5.154|5.154	0.213957|0.213957	0.09810|0.09810	0.080755|0.080755	0.290581|0.290581	ENSG00000140853|ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144|ENST00000538805	T;T;T;T|.	0.72942|.	-0.51;-0.53;-0.7;-0.53|.	3.55|3.55	1.52|1.52	0.23074|0.23074	.|.	1.238210|.	0.06245|.	N|.	0.691069|.	T|.	0.00012|.	0.0000|.	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.18013|.	0.017;0.017;0.025|.	B;B;B|.	0.15484|.	0.004;0.009;0.013|.	T|.	0.15607|.	-1.0431|.	9|.	0.02654|.	T|.	1|.	.|.	5.0579|5.0579	0.14542|0.14542	0.0:0.6681:0.2131:0.1188|0.0:0.6681:0.2131:0.1188	rs289723;rs59401549;rs289723|rs289723;rs59401549;rs289723	790;1105;1105|.	Q9H6Y0;Q86WI3-6;Q86WI3|.	.;.;NLRC5_HUMAN|.	K|X	1105|857	ENSP00000262510:Q1105K;ENSP00000308886:Q1105K;ENSP00000389739:Q1105K;ENSP00000441727:Q1105K|.	ENSP00000262510:Q1105K|.	Q|S	+|+	1|2	0|0	NLRC5|NLRC5	55638029|55638029	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	0.665000|0.665000	0.25083|0.25083	0.475000|0.475000	0.27415|0.27415	-0.254000|-0.254000	0.11334|0.11334	CAG|TCA	T|0.002;G|0.001	.	strong		0.557	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
MUC2	4583	hgsc.bcm.edu	37	11	1080391	1080391	+	Missense_Mutation	SNP	G	G	A	rs41521547	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1080391G>A	ENST00000441003.2	+	8	1138	c.1111G>A	c.(1111-1113)Gag>Aag	p.E371K	MUC2_ENST00000359061.5_Missense_Mutation_p.E371K	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	371					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CAATGACTGCGAGCAGTGGTG	0.662													G|||	242	0.0483227	0.0333	0.0461	5008	,	,		16331	0.0496		0.0915	False		,,,				2504	0.0245				p.E371K		Atlas-SNP	.											.	MUC2	614	.	0			c.G1111A						PASS	.	G	LYS/GLU	155,4047		4,147,1950	21.0	25.0	24.0		1111	0.8	0.0	11	dbSNP_127	24	746,7658		36,674,3492	yes	missense	MUC2	NM_002457.2	56	40,821,5442	AA,AG,GG		8.8767,3.6887,7.1474	benign	371/2813	1080391	901,11705	2101	4202	6303	SO:0001583	missense	4583	exon8			GACTGCGAGCAGT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.1111G>A	11.37:g.1080391G>A	ENSP00000415183:p.Glu371Lys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		115	0.052655677655677656	14	0.028455284552845527	10	0.027624309392265192	25	0.043706293706293704	66	0.0870712401055409	G	13.29	2.193112	0.38707	0.036887	0.088767	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.64991	-0.13;-0.13	3.85	0.768	0.18487	.	0.340707	0.21166	U	0.079072	T	0.01627	0.0052	N	0.17800	0.525	0.80722	P	0.0	B	0.29646	0.253	B	0.27608	0.081	T	0.11084	-1.0602	9	0.13108	T	0.6	.	7.7094	0.28669	0.3541:0.0:0.6459:0.0	rs41521547;rs61732151	371	E7EUV1	.	K	371	ENSP00000415183:E371K;ENSP00000351956:E371K	ENSP00000351956:E371K	E	+	1	0	MUC2	1070391	0.207000	0.23482	0.040000	0.18447	0.145000	0.21501	2.397000	0.44477	0.296000	0.22592	0.491000	0.48974	GAG	G|0.947;A|0.053	0.053	strong		0.662	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR8K1	390157	hgsc.bcm.edu	37	11	56113764	56113764	+	Missense_Mutation	SNP	G	G	A	rs17614327	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56113764G>A	ENST00000279783.2	+	1	344	c.250G>A	c.(250-252)Gcc>Acc	p.A84T		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	84			A -> T (in dbSNP:rs17614327). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					CACTGTCATTGCCCCGAAGAT	0.398										HNSCC(65;0.19)			G|||	196	0.0391374	0.0121	0.0447	5008	,	,		20721	0.001		0.0915	False		,,,				2504	0.0573				p.A84T		Atlas-SNP	.											.	OR8K1	93	.	0			c.G250A						PASS	.	G	THR/ALA	94,4308	76.2+/-114.5	0,94,2107	171.0	162.0	165.0		250	4.0	0.0	11	dbSNP_123	165	696,7896	171.7+/-222.6	33,630,3633	yes	missense	OR8K1	NM_001002907.1	58	33,724,5740	AA,AG,GG		8.1006,2.1354,6.0797	benign	84/320	56113764	790,12204	2201	4296	6497	SO:0001583	missense	390157	exon1			GTCATTGCCCCGA	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.250G>A	11.37:g.56113764G>A	ENSP00000279783:p.Ala84Thr	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	185	99	0.535135	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	37	CCDS31528.1	87	0.03983516483516483	4	0.008130081300813009	14	0.03867403314917127	0	0.0	69	0.09102902374670185	G	2.597	-0.293825	0.05568	0.021354	0.081006	ENSG00000150261	ENST00000279783	T	0.03004	4.08	5.0	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.385688	0.22077	N	0.064954	T	0.00109	0.0003	N	0.13098	0.295	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.46428	-0.9192	10	0.02654	T	1	-3.592	14.8807	0.70531	0.0:0.2579:0.7421:0.0	rs17614327;rs17614327	84	Q8NGG5	OR8K1_HUMAN	T	84	ENSP00000279783:A84T	ENSP00000279783:A84T	A	+	1	0	OR8K1	55870340	0.000000	0.05858	0.035000	0.18076	0.114000	0.19823	-1.019000	0.03622	2.297000	0.77311	0.549000	0.68633	GCC	G|0.952;A|0.048	0.048	strong		0.398	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
FANCA	2175	hgsc.bcm.edu	37	16	89825065	89825065	+	Silent	SNP	G	G	A	rs17226980	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89825065G>A	ENST00000389301.3	-	30	2931	c.2901C>T	c.(2899-2901)tcC>tcT	p.S967S	FANCA_ENST00000568369.1_Silent_p.S967S	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	967					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CTGAAGCCGAGGACTCAGGGA	0.537			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	361	0.0720847	0.0038	0.0187	5008	,	,		22388	0.2599		0.0646	False		,,,				2504	0.0164				p.S967S		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.C2901T						PASS	.	G		76,4320	65.3+/-102.7	0,76,2122	121.0	110.0	114.0		2901	-4.4	0.0	16	dbSNP_123	114	696,7904	172.9+/-223.5	26,644,3630	no	coding-synonymous	FANCA	NM_000135.2		26,720,5752	AA,AG,GG		8.093,1.7288,5.9403		967/1456	89825065	772,12224	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon30	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGCCGAGGACTCA	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.2901C>T	16.37:g.89825065G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			G|0.933;A|0.067	0.067	strong		0.537	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
DYRK4	8798	hgsc.bcm.edu	37	12	4705317	4705317	+	Silent	SNP	C	C	T	rs3741925|rs17845948	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:4705317C>T	ENST00000540757.2	+	5	445	c.285C>T	c.(283-285)gtC>gtT	p.V95V	DYRK4_ENST00000543431.1_Silent_p.V95V|DYRK4_ENST00000010132.5_Silent_p.V95V	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	95			V -> I. {ECO:0000269|PubMed:11062477}.			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			TTCCACAGGTCCTGCATGATC	0.552													C|||	1183	0.236222	0.1044	0.2867	5008	,	,		19972	0.3135		0.2992	False		,,,				2504	0.2342				p.V95V		Atlas-SNP	.											.	DYRK4	75	.	0			c.C285T						PASS	.	C		518,3888	239.3+/-250.5	32,454,1717	120.0	125.0	123.0		285	1.7	1.0	12	dbSNP_107	123	2440,6160	404.9+/-348.3	366,1708,2226	no	coding-synonymous	DYRK4	NM_003845.1		398,2162,3943	TT,TC,CC		28.3721,11.7567,22.7433		95/521	4705317	2958,10048	2203	4300	6503	SO:0001819	synonymous_variant	8798	exon5			ACAGGTCCTGCAT	Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.285C>T	12.37:g.4705317C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_003845	A8K8F7|Q8NEF2|Q92631	Silent	SNP	ENST00000540757.2	37	CCDS8530.1																																																																																			C|0.758;T|0.242	0.242	strong		0.552	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398780.2		
DSG4	147409	hgsc.bcm.edu	37	18	28968959	28968959	+	Silent	SNP	C	C	T	rs9956865	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:28968959C>T	ENST00000308128.4	+	5	630	c.495C>T	c.(493-495)agC>agT	p.S165S	DSG4_ENST00000359747.4_Silent_p.S165S|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	165	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Missing (in HYPT6). {ECO:0000269|PubMed:12705872, ECO:0000269|PubMed:15191570}.		anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACACAGCCAGCATTGAAGAAA	0.408													T|||	4031	0.804912	0.7874	0.8847	5008	,	,		17727	0.9375		0.7654	False		,,,				2504	0.6759				p.S165S		Atlas-SNP	.											.	DSG4	343	.	0			c.C495T						PASS	.	T	,	3567,839	332.3+/-302.4	1452,663,88	100.0	95.0	97.0		495,495	2.9	1.0	18	dbSNP_119	97	6560,2038	355.0+/-329.7	2501,1558,240	no	coding-synonymous,coding-synonymous	DSG4	NM_001134453.1,NM_177986.3	,	3953,2221,328	TT,TC,CC		23.7032,19.0422,22.124	,	165/1060,165/1041	28968959	10127,2877	2203	4299	6502	SO:0001819	synonymous_variant	147409	exon5			AGCCAGCATTGAA	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.495C>T	18.37:g.28968959C>T		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Silent	SNP	ENST00000308128.4	37	CCDS11897.1																																																																																			C|0.195;T|0.805	0.805	strong		0.408	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
GPR101	83550	hgsc.bcm.edu	37	X	136113464	136113464	+	Missense_Mutation	SNP	C	C	A	rs1190736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:136113464C>A	ENST00000298110.1	-	1	369	c.370G>T	c.(370-372)Gtg>Ttg	p.V124L		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	124			V -> L (in dbSNP:rs1190736).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					ACTGACACCACGACAATGGTG	0.597													C|||	876	0.232053	0.0113	0.147	3775	,	,		16163	0.2619		0.3678	False		,,,				2504	0.1278				p.V124L		Atlas-SNP	.											.	GPR101	96	.	0			c.G370T						PASS	.	C	LEU/VAL	294,3541		13,221,47,1398,524	90.0	65.0	73.0		370	4.1	0.9	X	dbSNP_87	73	3427,3301		647,1209,924,572,948	yes	missense	GPR101	NM_054021.1	32	660,1430,971,1970,1472	AA,AC,A,CC,C		49.0636,7.6662,35.2267	possibly-damaging	124/509	136113464	3721,6842	2203	4300	6503	SO:0001583	missense	83550	exon1			ACACCACGACAAT	AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"""GPCR / Class A : Orphans"""	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.370G>T	X.37:g.136113464C>A	ENSP00000298110:p.Val124Leu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_054021	Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	37	CCDS14662.1	503	0.30319469559975887	7	0.014344262295081968	44	0.1375	91	0.1961206896551724	199	0.33843537414965985	C	12.46	1.945593	0.34377	0.076662	0.509364	ENSG00000165370	ENST00000298110	T	0.26810	1.71	5.04	4.14	0.48551	GPCR, rhodopsin-like superfamily (1);	0.000000	0.30920	N	0.008604	T	0.00012	0.0000	L	0.38531	1.155	0.23107	P	0.99828821	P	0.47604	0.898	P	0.51582	0.674	T	0.51052	-0.8754	9	0.32370	T	0.25	-14.0415	12.3336	0.55054	0.0:0.8342:0.1658:0.0	rs1190736;rs52826781;rs56790843;rs1190736	124	Q96P66	GP101_HUMAN	L	124	ENSP00000298110:V124L	ENSP00000298110:V124L	V	-	1	0	GPR101	135941130	0.981000	0.34729	0.862000	0.33874	0.179000	0.23085	2.797000	0.47877	2.081000	0.62600	0.600000	0.82982	GTG	C|0.690;A|0.310	0.310	strong		0.597	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1		
PPA2	27068	hgsc.bcm.edu	37	4	106317429	106317429	+	Missense_Mutation	SNP	C	C	G	rs13787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:106317429C>G	ENST00000341695.5	-	9	876	c.846G>C	c.(844-846)aaG>aaC	p.K282N	PPA2_ENST00000509426.1_5'Flank|PPA2_ENST00000348706.5_Missense_Mutation_p.K253N|PPA2_ENST00000380004.2_Missense_Mutation_p.K264N|PPA2_ENST00000432483.2_Missense_Mutation_p.K180N|PPA2_ENST00000354147.3_Missense_Mutation_p.K116N|PPA2_ENST00000357415.4_Missense_Mutation_p.K297N	NM_176869.2	NP_789845.1	Q9H2U2	IPYR2_HUMAN	pyrophosphatase (inorganic) 2	282			K -> N (in dbSNP:rs13787). {ECO:0000269|PubMed:11042152, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039}.		diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	11		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		CTCCATTACACTTCTTCATAA	0.294													C|||	2167	0.432708	0.0923	0.5086	5008	,	,		17915	0.6766		0.4592	False		,,,				2504	0.5603				p.K282N		Atlas-SNP	.											.	PPA2	23	.	0			c.G846C						PASS	.	C	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	585,3821	251.5+/-258.2	40,505,1658	96.0	91.0	93.0		759,540,348,846	0.1	0.7	4	dbSNP_52	93	3925,4669	539.8+/-383.7	890,2145,1262	yes	missense,missense,missense,missense	PPA2	NM_006903.4,NM_176866.2,NM_176867.3,NM_176869.2	94,94,94,94	930,2650,2920	GG,GC,CC		45.6714,13.2773,34.6923	benign,benign,benign,benign	253/306,180/233,116/169,282/335	106317429	4510,8490	2203	4297	6500	SO:0001583	missense	27068	exon9			ATTACACTTCTTC		CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1	4q25	2005-10-07			ENSG00000138777	ENSG00000138777			28883	protein-coding gene	gene with protein product		609988				11042152	Standard	NM_176869		Approved	FLJ20459	uc003hxl.3	Q9H2U2	OTTHUMG00000128781	ENST00000341695.5:c.846G>C	4.37:g.106317429C>G	ENSP00000343885:p.Lys282Asn	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	249	80	0.321285	NM_176869	B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0	Missense_Mutation	SNP	ENST00000341695.5	37	CCDS3667.1	973	0.44551282051282054	49	0.09959349593495935	163	0.45027624309392267	390	0.6818181818181818	371	0.4894459102902375	C	11.86	1.763782	0.31228	0.132773	0.456714	ENSG00000138777	ENST00000341695;ENST00000348706;ENST00000354147;ENST00000432483;ENST00000357415;ENST00000380004	T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81	5.93	0.105	0.14535	.	0.217385	0.45867	D	0.000321	T	0.00012	0.0000	M	0.73217	2.22	0.21386	P	0.999704449	P;B;B;B;B	0.36789	0.57;0.344;0.033;0.076;0.038	B;B;B;B;B	0.35240	0.198;0.05;0.049;0.011;0.011	T	0.38993	-0.9635	9	0.42905	T	0.14	-22.2528	6.7286	0.23371	0.1115:0.4337:0.0:0.4549	rs13787;rs1127137;rs3182696;rs11267057;rs11566570;rs17256954;rs17839004;rs13787	116;180;253;264;282	Q9H2U2-4;F8WDN9;Q9H2U2-3;E2QRM6;Q9H2U2	.;.;.;.;IPYR2_HUMAN	N	282;253;116;180;297;264	ENSP00000343885:K282N;ENSP00000313061:K253N;ENSP00000340352:K116N;ENSP00000389957:K180N;ENSP00000349996:K297N;ENSP00000369340:K264N	ENSP00000343885:K282N	K	-	3	2	PPA2	106536878	0.000000	0.05858	0.742000	0.31022	0.987000	0.75469	-0.843000	0.04350	-0.083000	0.12618	-0.181000	0.13052	AAG	C|0.611;G|0.389	0.389	strong		0.294	PPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250704.4	NM_176869	
FAM200A	221786	hgsc.bcm.edu	37	7	99145845	99145845	+	Silent	SNP	C	C	T	rs10238965	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:99145845C>T	ENST00000449309.1	-	2	565	c.186G>A	c.(184-186)ttG>ttA	p.L62L		NM_145111.3	NP_659802.1	Q8TCP9	F200A_HUMAN	family with sequence similarity 200, member A	62						integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			endometrium(1)|kidney(5)|large_intestine(2)|ovary(2)|skin(1)	11						aatacgatgacaataaggctc	0.403													T|||	2314	0.462061	0.9342	0.2853	5008	,	,		22164	0.3353		0.165	False		,,,				2504	0.3855				p.L62L		Atlas-SNP	.											.	FAM200A	27	.	0			c.G186A						PASS	.	T		3473,929		1369,735,97	117.0	111.0	113.0		186	-4.1	0.0	7	dbSNP_119	113	1235,7361		102,1031,3165	no	coding-synonymous	FAM200A	NM_145111.3		1471,1766,3262	TT,TC,CC		14.3671,21.104,36.221		62/574	99145845	4708,8290	2201	4298	6499	SO:0001819	synonymous_variant	221786	exon2			CGATGACAATAAG		CCDS5668.1	7q22.1	2010-02-22	2010-02-22	2010-02-22	ENSG00000221909	ENSG00000221909			25401	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 38"""	C7orf38		10607616	Standard	NM_145111		Approved	FLJ36794, DKFZp727G131	uc003ura.3	Q8TCP9	OTTHUMG00000156723	ENST00000449309.1:c.186G>A	7.37:g.99145845C>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	274	123	0.448905	NM_145111	A4D293|A8K3V9|B2RD92|C9J6A8|D6W5T2|Q8N9P3	Silent	SNP	ENST00000449309.1	37	CCDS5668.1																																																																																			C|0.566;T|0.434	0.434	strong		0.403	FAM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345467.1	NM_145111	
LRFN2	57497	hgsc.bcm.edu	37	6	40400288	40400288	+	Missense_Mutation	SNP	C	C	T	rs61731040	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:40400288C>T	ENST00000338305.6	-	2	1107	c.565G>A	c.(565-567)Gcc>Acc	p.A189T		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	189						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					GTGCCCTCGGCGATGTGATCC	0.622													C|||	371	0.0740815	0.1135	0.1196	5008	,	,		17438	0.001		0.1203	False		,,,				2504	0.0164				p.A189T		Atlas-SNP	.											.	LRFN2	133	.	0			c.G565A						PASS	.	C	THR/ALA	471,3935	223.6+/-240.1	18,435,1750	84.0	86.0	86.0		565	4.9	1.0	6	dbSNP_129	86	1166,7434	239.4+/-270.5	65,1036,3199	yes	missense	LRFN2	NM_020737.1	58	83,1471,4949	TT,TC,CC		13.5581,10.69,12.5865	benign	189/790	40400288	1637,11369	2203	4300	6503	SO:0001583	missense	57497	exon2			CCTCGGCGATGTG	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	21226	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 2"""	612808	"""KIAA1246"""	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.565G>A	6.37:g.40400288C>T	ENSP00000345985:p.Ala189Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_020737	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	37	CCDS34443.1	200	0.09157509157509157	54	0.10975609756097561	47	0.1298342541436464	1	0.0017482517482517483	98	0.12928759894459102	C	12.19	1.864037	0.32884	0.1069	0.135581	ENSG00000156564	ENST00000338305	T	0.57107	0.42	5.76	4.89	0.63831	.	0.199765	0.53938	D	0.000054	T	0.13884	0.0336	N	0.04705	-0.18	0.36592	P	0.125865	B	0.23937	0.094	B	0.21708	0.036	T	0.05632	-1.0873	9	0.40728	T	0.16	.	8.1605	0.31196	0.0:0.7667:0.0:0.2333	rs61731040	189	Q9ULH4	LRFN2_HUMAN	T	189	ENSP00000345985:A189T	ENSP00000345985:A189T	A	-	1	0	LRFN2	40508266	0.286000	0.24305	0.995000	0.50966	0.894000	0.52154	0.871000	0.28023	1.455000	0.47813	0.655000	0.94253	GCC	C|0.890;T|0.110	0.110	strong		0.622	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372	
EGFR	1956	hgsc.bcm.edu	37	7	55224507	55224507	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:55224507A>C	ENST00000275493.2	+	10	1366	c.1189A>C	c.(1189-1191)Acc>Ccc	p.T397P	EGFR_ENST00000344576.2_Missense_Mutation_p.T397P|EGFR_ENST00000455089.1_Missense_Mutation_p.T352P|EGFR_ENST00000442591.1_Missense_Mutation_p.T397P|EGFR_ENST00000454757.2_Missense_Mutation_p.T344P|EGFR_ENST00000342916.3_Missense_Mutation_p.T397P|EGFR_ENST00000420316.2_Missense_Mutation_p.T397P	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	397					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TATTCTGAAAACCGTAAAGGA	0.393		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.T397P		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	EGFR_ENST00000344576,NS,malignant_melanoma,0,2	EGFR	20426	2	0			c.A1189C						PASS	.						94.0	90.0	92.0					7																	55224507		2203	4300	6503	SO:0001583	missense	1956	exon10	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	CTGAAAACCGTAA		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1189A>C	7.37:g.55224507A>C	ENSP00000275493:p.Thr397Pro	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	177	78	0.440678	NM_201283	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	16.99	3.274643	0.59649	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000420316;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89	5.95	5.95	0.96441	EGF receptor, L domain (1);	0.045464	0.85682	D	0.000000	T	0.69611	0.3130	M	0.91300	3.195	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;0.998;1.0;0.997;0.999	D;D;D;D;D	0.87578	0.992;0.982;0.989;0.97;0.998	T	0.76263	-0.3023	10	0.87932	D	0	.	10.478	0.44676	0.855:0.0:0.0:0.145	.	352;397;397;397;397	Q504U8;P00533;P00533-3;P00533-4;P00533-2	.;EGFR_HUMAN;.;.;.	P	352;397;267;397;397;397;397;344;191	ENSP00000415559:T352P;ENSP00000342376:T397P;ENSP00000345973:T397P;ENSP00000413843:T397P;ENSP00000275493:T397P;ENSP00000410031:T397P;ENSP00000395243:T344P	ENSP00000275493:T397P	T	+	1	0	EGFR	55192001	1.000000	0.71417	0.591000	0.28745	0.427000	0.31564	6.996000	0.76263	2.279000	0.76181	0.533000	0.62120	ACC	.	.	none		0.393	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
OR2T2	401992	hgsc.bcm.edu	37	1	248616408	248616408	+	Missense_Mutation	SNP	C	C	T	rs67700848	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248616408C>T	ENST00000342927.3	+	1	332	c.310C>T	c.(310-312)Ctc>Ttc	p.L104F		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCAGATCTTCCTCTACCTGAC	0.532																																					p.L104F		Atlas-SNP	.											OR2T2,NS,carcinoma,-2,1	OR2T2	73	1	0			c.C310T						PASS	.						300.0	329.0	320.0					1																	248616408		2203	4300	6503	SO:0001583	missense	401992	exon1			ATCTTCCTCTACC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.310C>T	1.37:g.248616408C>T	ENSP00000343062:p.Leu104Phe	Somatic	901	1	0.00110988		WXS	Illumina HiSeq	Phase_I	993	701	0.705942	NM_001004136	B2RNM1|B9EH01	Missense_Mutation	SNP	ENST00000342927.3	37	CCDS31116.1	.	.	.	.	.	.	.	.	.	.	c	0.006	-2.038068	0.00402	.	.	ENSG00000196240	ENST00000342927	T	0.00495	6.99	3.59	-0.635	0.11512	GPCR, rhodopsin-like superfamily (1);	0.681714	0.12783	N	0.439555	T	0.00210	0.0006	N	0.04768	-0.165	0.80722	P	0.0	B	0.13594	0.008	B	0.14023	0.01	T	0.23904	-1.0175	9	0.02654	T	1	.	8.1475	0.31121	0.0:0.3677:0.0:0.6323	.	104	Q6IF00	OR2T2_HUMAN	F	104	ENSP00000343062:L104F	ENSP00000343062:L104F	L	+	1	0	OR2T2	246683031	0.000000	0.05858	0.036000	0.18154	0.224000	0.24922	-0.885000	0.04161	-0.046000	0.13446	0.298000	0.19748	CTC	C|0.875;T|0.125	0.125	strong		0.532	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
ASTN2	23245	hgsc.bcm.edu	37	9	119739015	119739015	+	Silent	SNP	G	G	A	rs10983437	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:119739015G>A	ENST00000313400.4	-	8	1741	c.1641C>T	c.(1639-1641)caC>caT	p.H547H	ASTN2_ENST00000361209.2_Silent_p.H496H|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Silent_p.H547H			O75129	ASTN2_HUMAN	astrotactin 2	547	EGF-like 1.				negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						GCACACACAGGTGTCTGTGAA	0.498													G|||	687	0.137181	0.2655	0.0793	5008	,	,		20485	0.0823		0.1123	False		,,,				2504	0.0869				p.H496H		Atlas-SNP	.											.	ASTN2	307	.	0			c.C1488T						PASS	.	G		1089,3317	392.4+/-328.5	143,803,1257	111.0	89.0	96.0		1488	4.0	1.0	9	dbSNP_120	96	917,7683	204.1+/-246.9	47,823,3430	no	coding-synonymous	ASTN2	NM_014010.4		190,1626,4687	AA,AG,GG		10.6628,24.7163,15.4237		496/1289	119739015	2006,11000	2203	4300	6503	SO:0001819	synonymous_variant	23245	exon7			ACACAGGTGTCTG	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1641C>T	9.37:g.119739015G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Silent	SNP	ENST00000313400.4	37																																																																																				G|0.856;A|0.144	0.144	strong		0.498	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
FAM83F	113828	hgsc.bcm.edu	37	22	40417820	40417820	+	Missense_Mutation	SNP	A	A	G	rs5995794	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:40417820A>G	ENST00000333407.6	+	4	1400	c.1306A>G	c.(1306-1308)Agg>Ggg	p.R436G	FAM83F_ENST00000473717.1_Missense_Mutation_p.R268G	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	436			R -> G (in dbSNP:rs5995794).							breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						CGCCCCCGCCAGGCGCTTCAG	0.657													A|||	1358	0.271166	0.3359	0.1585	5008	,	,		14624	0.0863		0.2863	False		,,,				2504	0.4387				p.R436G		Atlas-SNP	.											FAM83F,NS,carcinoma,0,1	FAM83F	29	1	0			c.A1306G						scavenged	.	A	GLY/ARG	1193,3207		184,825,1191	18.0	22.0	21.0		1306	2.7	0.9	22	dbSNP_114	21	2403,6191		332,1739,2226	yes	missense	FAM83F	NM_138435.2	125	516,2564,3417	GG,GA,AA		27.9614,27.1136,27.6743	possibly-damaging	436/501	40417820	3596,9398	2200	4297	6497	SO:0001583	missense	113828	exon4			CCCGCCAGGCGCT		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.1306A>G	22.37:g.40417820A>G	ENSP00000330432:p.Arg436Gly	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	42	14	0.333333	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	37	CCDS14000.2	500	0.22893772893772893	165	0.3353658536585366	62	0.1712707182320442	43	0.07517482517482517	230	0.3034300791556728	A	7.297	0.612217	0.14066	0.271136	0.279614	ENSG00000133477	ENST00000333407	T	0.10099	2.91	3.79	2.72	0.32119	.	0.560877	0.14341	N	0.325730	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.22276	0.067	B	0.19391	0.025	T	0.46091	-0.9216	9	0.42905	T	0.14	-11.3454	8.8472	0.35177	0.8099:0.1901:0.0:0.0	rs5995794;rs5995794	436	Q8NEG4	FA83F_HUMAN	G	436	ENSP00000330432:R436G	ENSP00000330432:R436G	R	+	1	2	FAM83F	38747766	0.996000	0.38824	0.875000	0.34327	0.027000	0.11550	3.639000	0.54339	0.478000	0.27488	0.374000	0.22700	AGG	A|0.766;G|0.234	0.234	strong		0.657	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
ARHGAP31	57514	hgsc.bcm.edu	37	3	119128398	119128398	+	Silent	SNP	G	G	A	rs2305249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:119128398G>A	ENST00000264245.4	+	11	2233	c.1701G>A	c.(1699-1701)ccG>ccA	p.P567P		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	567					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)	p.P567P(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						CTGAAGCACCGGGGACAGTGG	0.502													G|||	940	0.1877	0.09	0.0922	5008	,	,		19498	0.369		0.1551	False		,,,				2504	0.2342				p.P567P	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											ARHGAP31,colon,NS,+1,2	ARHGAP31	175	2	1	Substitution - coding silent(1)	stomach(1)	c.G1701A						PASS	.	G		461,3377		32,397,1490	43.0	44.0	44.0		1701	-2.4	0.0	3	dbSNP_100	44	1450,6818		138,1174,2822	no	coding-synonymous	ARHGAP31	NM_020754.2		170,1571,4312	AA,AG,GG		17.5375,12.0115,15.7856		567/1445	119128398	1911,10195	1919	4134	6053	SO:0001819	synonymous_variant	57514	exon11			AGCACCGGGGACA		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"""Rho GTPase activating proteins"""	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.1701G>A	3.37:g.119128398G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	216	215	0.99537	NM_020754	Q9ULL6	Silent	SNP	ENST00000264245.4	37	CCDS43135.1																																																																																			G|0.813;A|0.187	0.187	strong		0.502	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2		
BTBD10	84280	hgsc.bcm.edu	37	11	13441126	13441126	+	Silent	SNP	A	A	G	rs7114113	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:13441126A>G	ENST00000278174.5	-	4	710	c.465T>C	c.(463-465)aaT>aaC	p.N155N	BTBD10_ENST00000528120.1_Silent_p.N107N|BTBD10_ENST00000530907.1_Silent_p.N163N|BTBD10_ENST00000532261.1_5'UTR	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10	155	Interaction with AKT family members. {ECO:0000250|UniProtKB:Q80X66}.					nucleus (GO:0005634)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|prostate(1)	20				Epithelial(150;0.0214)		CTTCTTTTGCATTTTCATATA	0.428													A|||	742	0.148163	0.084	0.3012	5008	,	,		16577	0.1687		0.1481	False		,,,				2504	0.1053				p.N155N		Atlas-SNP	.											.	BTBD10	43	.	0			c.T465C						PASS	.	A		379,4021	191.6+/-217.2	19,341,1840	238.0	229.0	232.0		465	4.2	1.0	11	dbSNP_116	232	1493,7095	284.4+/-296.6	117,1259,2918	no	coding-synonymous	BTBD10	NM_032320.5		136,1600,4758	GG,GA,AA		17.3847,8.6136,14.4133		155/476	13441126	1872,11116	2200	4294	6494	SO:0001819	synonymous_variant	84280	exon4			TTTTGCATTTTCA	AY221959	CCDS7811.1, CCDS73261.1	11p15.2	2013-01-24			ENSG00000148925	ENSG00000148925		"""BTB/POZ domain containing"""	21445	protein-coding gene	gene with protein product		615933				15556295	Standard	XM_005253164		Approved	GMRP1, GMRP-1, MGC13007	uc001mkz.3	Q9BSF8	OTTHUMG00000165787	ENST00000278174.5:c.465T>C	11.37:g.13441126A>G		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	266	132	0.496241	NM_032320	B7Z228|Q86WG1	Silent	SNP	ENST00000278174.5	37	CCDS7811.1																																																																																			A|0.855;G|0.145	0.145	strong		0.428	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320	
TIRAP	114609	hgsc.bcm.edu	37	11	126162468	126162468	+	Missense_Mutation	SNP	G	G	A	rs3802813	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:126162468G>A	ENST00000392680.2	+	5	569	c.164G>A	c.(163-165)aGc>aAc	p.S55N	RP11-712L6.5_ENST00000528876.1_5'Flank|TIRAP_ENST00000392678.3_Missense_Mutation_p.S55N|TIRAP_ENST00000392679.1_Missense_Mutation_p.S55N|RP11-712L6.7_ENST00000533378.1_RNA	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	55			S -> N (does not affect NF-kappa-B activation and TNF-alpha production; dbSNP:rs3802813). {ECO:0000269|PubMed:11544529, ECO:0000269|PubMed:14702039}.		3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)			breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		TCACAGGACAGCCCACTACCC	0.587													G|||	479	0.095647	0.0613	0.1383	5008	,	,		17785	0.1756		0.0417	False		,,,				2504	0.0849				p.S55N		Atlas-SNP	.											.	TIRAP	37	.	0			c.G164A						PASS	.	G	ASN/SER,ASN/SER	272,4130	152.5+/-186.2	7,258,1936	116.0	99.0	105.0		164,164	-2.2	0.0	11	dbSNP_107	105	318,8278	112.3+/-172.5	7,304,3987	yes	missense,missense	TIRAP	NM_001039661.1,NM_148910.2	46,46	14,562,5923	AA,AG,GG		3.6994,6.179,4.5392	benign,benign	55/222,55/236	126162468	590,12408	2201	4298	6499	SO:0001583	missense	114609	exon5			AGGACAGCCCACT	AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"""MyD88 adapter-like"""	606252	"""Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"""			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.164G>A	11.37:g.126162468G>A	ENSP00000376447:p.Ser55Asn	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_148910	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Missense_Mutation	SNP	ENST00000392680.2	37	CCDS8472.1	206	0.09432234432234432	32	0.06504065040650407	50	0.13812154696132597	90	0.15734265734265734	34	0.044854881266490766	G	9.309	1.055139	0.19907	0.06179	0.036994	ENSG00000150455	ENST00000392679;ENST00000279992;ENST00000392678;ENST00000392680	T;T;T	0.10960	2.87;2.82;2.87	5.21	-2.15	0.07102	.	1.250100	0.05220	N	0.508327	T	0.00039	0.0001	L	0.35723	1.085	0.80722	P	0.0	B;B	0.12013	0.003;0.005	B;B	0.08055	0.002;0.003	T	0.43015	-0.9417	9	0.38643	T	0.18	-11.2992	4.6123	0.12408	0.2174:0.0:0.4219:0.3607	rs3802813;rs60787873;rs3802813	55;55	P58753;Q56UH9	TIRAP_HUMAN;.	N	55	ENSP00000376446:S55N;ENSP00000376445:S55N;ENSP00000376447:S55N	ENSP00000279992:S55N	S	+	2	0	TIRAP	125667678	.	.	0.000000	0.03702	0.009000	0.06853	.	.	-0.249000	0.09569	0.655000	0.94253	AGC	G|0.936;A|0.064	0.064	strong		0.587	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910	
RPL32	6161	hgsc.bcm.edu	37	3	12877704	12877704	+	Silent	SNP	G	G	A	rs6497	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:12877704G>A	ENST00000429711.2	-	4	396	c.297C>T	c.(295-297)atC>atT	p.I99I	RPL32_ENST00000396953.2_Silent_p.I99I|RPL32_ENST00000435983.1_Silent_p.I99I|RPL32_ENST00000396957.1_Silent_p.I99I|RPL32_ENST00000273223.6_Silent_p.I117I	NM_000994.3	NP_000985.1	P62910	RL32_HUMAN	ribosomal protein L32	99					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)	6						CATTGTGAGCGATCTCGGCAC	0.517													G|||	119	0.023762	0.0461	0.0072	5008	,	,		20645	0.0109		0.0249	False		,,,				2504	0.0174				p.I99I		Atlas-SNP	.											RPL32,NS,carcinoma,0,1	RPL32	11	1	0			c.C297T						scavenged	.	G	,,	183,4223	113.8+/-151.8	1,181,2021	67.0	58.0	61.0		297,297,297	-1.0	1.0	3	dbSNP_52	61	243,8357	93.8+/-155.7	5,233,4062	no	coding-synonymous,coding-synonymous,coding-synonymous	RPL32	NM_000994.3,NM_001007073.1,NM_001007074.1	,,	6,414,6083	AA,AG,GG		2.8256,4.1534,3.2754	,,	99/136,99/136,99/136	12877704	426,12580	2203	4300	6503	SO:0001819	synonymous_variant	6161	exon4			GTGAGCGATCTCG	CA436299, CF124158, CR608027	CCDS2614.1	3q13.3-q21	2011-04-06			ENSG00000144713	ENSG00000144713		"""L ribosomal proteins"""	10336	protein-coding gene	gene with protein product						9284913	Standard	NM_001007073		Approved	L32	uc003bxl.3	P62910	OTTHUMG00000129804	ENST00000429711.2:c.297C>T	3.37:g.12877704G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	12	3	0.25	NM_001007073	B2R4Q3|P02433	Silent	SNP	ENST00000429711.2	37	CCDS2614.1																																																																																			G|0.971;A|0.029	0.029	strong		0.517	RPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252032.2	NM_000994	
IL27RA	9466	hgsc.bcm.edu	37	19	14162740	14162740	+	Silent	SNP	A	A	G	rs148749814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14162740A>G	ENST00000263379.2	+	13	1796	c.1671A>G	c.(1669-1671)aaA>aaG	p.K557K		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	557					cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						TCTGGGAGAAAGTTCCTGATC	0.622													a|||	14	0.00279553	0.0	0.0	5008	,	,		13386	0.001		0.001	False		,,,				2504	0.0123				p.K557K	Colon(164;1849 1896 4443 37792 47834)	Atlas-SNP	.											.	IL27RA	56	.	0			c.A1671G						PASS	.	A		0,4402		0,0,2201	32.0	29.0	30.0		1671	-5.4	0.1	19	dbSNP_134	30	8,8582		0,8,4287	no	coding-synonymous	IL27RA	NM_004843.2		0,8,6488	GG,GA,AA		0.0931,0.0,0.0616		557/637	14162740	8,12984	2201	4295	6496	SO:0001819	synonymous_variant	9466	exon13			GGAGAAAGTTCCT	AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	17290	protein-coding gene	gene with protein product	"""T-cell cytokine receptor type 1"""	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.1671A>G	19.37:g.14162740A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	182	91	0.5	NM_004843	A0N0L1|O60624	Silent	SNP	ENST00000263379.2	37	CCDS12303.1																																																																																			A|0.999;G|0.001	0.001	strong		0.622	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843	
SEC14L3	266629	hgsc.bcm.edu	37	22	30856121	30856121	+	Missense_Mutation	SNP	G	G	A	rs35764129	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:30856121G>A	ENST00000215812.4	-	12	1180	c.1090C>T	c.(1090-1092)Cgc>Tgc	p.R364C	SEC14L3_ENST00000402286.1_Missense_Mutation_p.R287C|SEC14L3_ENST00000540910.1_Missense_Mutation_p.R287C|SEC14L3_ENST00000401751.1_Missense_Mutation_p.R305C|SEC14L3_ENST00000539629.1_Missense_Mutation_p.R305C|SEC14L3_ENST00000403066.1_Intron|SEC14L3_ENST00000415957.2_Intron	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	364	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.		R -> C (in dbSNP:rs35764129).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	TTGTCGAAGCGTAGGACATCT	0.537													G|||	211	0.0421326	0.0091	0.0533	5008	,	,		22775	0.0933		0.0318	False		,,,				2504	0.0368				p.R364C	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.C1090T						PASS	.	G	CYS/ARG	61,4345	60.5+/-97.4	0,61,2142	125.0	109.0	114.0		1090	4.9	1.0	22	dbSNP_126	114	319,8281	112.7+/-172.9	7,305,3988	yes	missense	SEC14L3	NM_174975.4	180	7,366,6130	AA,AG,GG		3.7093,1.3845,2.9217	possibly-damaging	364/401	30856121	380,12626	2203	4300	6503	SO:0001583	missense	266629	exon12			CGAAGCGTAGGAC	AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.1090C>T	22.37:g.30856121G>A	ENSP00000215812:p.Arg364Cys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	101	0.04624542124542125	6	0.012195121951219513	21	0.058011049723756904	51	0.08916083916083917	23	0.030343007915567283	G	15.63	2.889200	0.52014	0.013845	0.037093	ENSG00000100012	ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18	5.95	4.87	0.63330	GOLD (2);	0.000000	0.85682	D	0.000000	T	0.01222	0.0040	L	0.43598	1.365	0.80722	D	1	P;P	0.44260	0.83;0.701	B;B	0.35813	0.211;0.15	T	0.01360	-1.1375	10	0.66056	D	0.02	-20.3356	17.5625	0.87911	0.0:0.0:0.8681:0.1319	rs35764129	287;364	E9PE57;Q9UDX4	.;S14L3_HUMAN	C	364;287;305;305;287	ENSP00000215812:R364C;ENSP00000385004:R287C;ENSP00000383896:R305C;ENSP00000444691:R305C;ENSP00000439752:R287C	ENSP00000215812:R364C	R	-	1	0	SEC14L3	29186121	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.430000	0.34914	2.824000	0.97209	0.655000	0.94253	CGC	G|0.965;A|0.035	0.035	strong		0.537	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
DNAH3	55567	hgsc.bcm.edu	37	16	20966273	20966273	+	Missense_Mutation	SNP	G	G	A	rs12924551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20966273G>A	ENST00000261383.3	-	55	10932	c.10933C>T	c.(10933-10935)Cgc>Tgc	p.R3645C	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3645	AAA 6. {ECO:0000250}.		R -> C (in dbSNP:rs12924551).		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.R3645S(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		AGGTAGGAGCGCAACAGGTTG	0.493													G|||	439	0.0876597	0.0197	0.0706	5008	,	,		14793	0.1716		0.0746	False		,,,				2504	0.1186				p.R3645C		Atlas-SNP	.											DNAH3_ENST00000261383,NS,carcinoma,+1,4	DNAH3	1142	4	2	Substitution - Missense(2)	upper_aerodigestive_tract(2)	c.C10933T						PASS	.	G	CYS/ARG	122,4280	90.6+/-129.3	3,116,2082	123.0	120.0	121.0		10933	5.4	1.0	16	dbSNP_121	121	715,7885	175.6+/-225.6	28,659,3613	yes	missense	DNAH3	NM_017539.1	180	31,775,5695	AA,AG,GG		8.314,2.7715,6.4375	probably-damaging	3645/4117	20966273	837,12165	2201	4300	6501	SO:0001583	missense	55567	exon55			AGGAGCGCAACAG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.10933C>T	16.37:g.20966273G>A	ENSP00000261383:p.Arg3645Cys	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	159	157	0.987421	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	182	0.08333333333333333	15	0.03048780487804878	19	0.052486187845303865	83	0.1451048951048951	65	0.08575197889182058	G	24.4	4.531842	0.85706	0.027715	0.08314	ENSG00000158486	ENST00000261383	T	0.10960	2.82	5.43	5.43	0.79202	Dynein heavy chain (1);	0.064262	0.64402	D	0.000007	T	0.00356	0.0011	H	0.97315	3.98	0.09310	P	1.0	D	0.89917	1.0	D	0.68943	0.961	T	0.26643	-1.0097	9	0.87932	D	0	.	19.2436	0.93893	0.0:0.0:1.0:0.0	rs12924551;rs52819084;rs12924551	3645	Q8TD57	DYH3_HUMAN	C	3645	ENSP00000261383:R3645C	ENSP00000261383:R3645C	R	-	1	0	DNAH3	20873774	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.870000	0.87175	2.543000	0.85770	0.655000	0.94253	CGC	G|0.926;A|0.074	0.074	strong		0.493	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
MAGI3	260425	hgsc.bcm.edu	37	1	114196495	114196495	+	Silent	SNP	A	A	G	rs2359173	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:114196495A>G	ENST00000307546.9	+	15	2559	c.2484A>G	c.(2482-2484)acA>acG	p.T828T	MAGI3_ENST00000369615.1_Silent_p.T828T|MAGI3_ENST00000369617.4_Silent_p.T853T|MAGI3_ENST00000369611.4_Silent_p.T828T	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	853	Interaction with BAI1.|PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCATTTCAACACAGAATGGAT	0.473													A|||	973	0.194289	0.0098	0.2032	5008	,	,		2608	0.0933		0.327	False		,,,				2504	0.4049				p.T828T		Atlas-SNP	.											.	MAGI3	181	.	0			c.A2484G						PASS	.	A	,	299,4107	162.5+/-194.5	12,275,1916	137.0	151.0	146.0		2484,2484	-4.9	0.2	1	dbSNP_100	146	2612,5988	423.1+/-354.3	400,1812,2088	no	coding-synonymous,coding-synonymous	MAGI3	NM_001142782.1,NM_152900.2	,	412,2087,4004	GG,GA,AA		30.3721,6.7862,22.382	,	828/1482,828/1126	114196495	2911,10095	2203	4300	6503	SO:0001819	synonymous_variant	260425	exon15			TTCAACACAGAAT	AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.2484A>G	1.37:g.114196495A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Silent	SNP	ENST00000307546.9	37	CCDS44196.1																																																																																			A|0.804;G|0.196	0.196	strong		0.473	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900	
CLEC12A	160364	hgsc.bcm.edu	37	12	10137557	10137557	+	Missense_Mutation	SNP	A	A	C	rs479499	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:10137557A>C	ENST00000304361.4	+	6	912	c.730A>C	c.(730-732)Aaa>Caa	p.K244Q	CLEC12A_ENST00000350667.4_Missense_Mutation_p.K211Q|CLEC12A_ENST00000355690.4_Missense_Mutation_p.K254Q	NM_138337.5|NM_201623.3	NP_612210.4|NP_963917.2	Q5QGZ9	CL12A_HUMAN	C-type lectin domain family 12, member A	244	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		K -> Q (in dbSNP:rs479499). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14739280, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16239426, ECO:0000269|Ref.4, ECO:0000269|Ref.7}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	16						CACTTATAAAAAAAGAatgat	0.338													C|||	3693	0.73742	0.6687	0.6686	5008	,	,		18155	0.8998		0.5994	False		,,,				2504	0.8538				p.K254Q	Melanoma(197;1487 2125 16611 22221 34855)	Atlas-SNP	.											.	CLEC12A	65	.	0			c.A760C						PASS	.	C	GLN/LYS,GLN/LYS,GLN/LYS	2812,1550		923,966,292	43.0	40.0	41.0		760,730,631	-8.1	0.0	12	dbSNP_83	41	5442,3132		1769,1904,614	yes	missense,missense,missense	CLEC12A	NM_001207010.1,NM_138337.5,NM_201623.3	53,53,53	2692,2870,906	CC,CA,AA		36.529,35.5342,36.1936	benign,benign,benign	254/276,244/266,211/233	10137557	8254,4682	2181	4287	6468	SO:0001583	missense	160364	exon7			TATAAAAAAAGAA	AY498550	CCDS8608.1, CCDS8609.1, CCDS55803.1, CCDS73442.1	12p13.31	2010-08-17			ENSG00000172322	ENSG00000172322		"""C-type lectin domain containing"""	31713	protein-coding gene	gene with protein product		612088					Standard	NM_201623		Approved	CLL-1, MICL	uc001qwq.3	Q5QGZ9		ENST00000304361.4:c.730A>C	12.37:g.10137557A>C	ENSP00000302804:p.Lys244Gln	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001207010	B2RA16|Q6P4H1|Q6RH77|Q6RH78|Q8TDQ6	Missense_Mutation	SNP	ENST00000304361.4	37	CCDS8608.1	1549	0.7092490842490843	324	0.6585365853658537	242	0.6685082872928176	520	0.9090909090909091	463	0.6108179419525066	C	5.029	0.191087	0.09547	0.644658	0.63471	ENSG00000172322	ENST00000355690;ENST00000304361;ENST00000350667	T;T;T	0.18016	2.24;2.24;2.24	4.04	-8.09	0.01090	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B;B;B	0.24823	0.112;0.007;0.01	B;B;B	0.20955	0.032;0.021;0.012	T	0.08534	-1.0717	8	0.29301	T	0.29	.	8.0574	0.30612	0.1963:0.4933:0.0:0.3104	rs479499;rs58718325;rs479499	211;244;254	Q5QGZ9-4;Q5QGZ9;Q5QGZ9-1	.;CL12A_HUMAN;.	Q	254;244;211	ENSP00000347916:K254Q;ENSP00000302804:K244Q;ENSP00000345448:K211Q	ENSP00000302804:K244Q	K	+	1	0	CLEC12A	10028824	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.293000	0.08320	-2.272000	0.00682	-2.835000	0.00106	AAA	A|0.302;C|0.698	0.698	strong		0.338	CLEC12A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399545.1	NM_138337	
UBR4	23352	hgsc.bcm.edu	37	1	19499560	19499560	+	Missense_Mutation	SNP	T	T	C	rs16862578	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:19499560T>C	ENST00000375254.3	-	25	3346	c.3319A>G	c.(3319-3321)Acc>Gcc	p.T1107A	UBR4_ENST00000375267.2_Missense_Mutation_p.T1107A|UBR4_ENST00000375217.2_Missense_Mutation_p.T1107A|UBR4_ENST00000375226.2_Missense_Mutation_p.T1107A	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1107			T -> A (in dbSNP:rs16862578).		protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T1107A(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AAGATGGTGGTACAGTCGATA	0.418													T|||	694	0.138578	0.2814	0.1671	5008	,	,		21057	0.0109		0.164	False		,,,				2504	0.0307				p.T1107A		Atlas-SNP	.											UBR4,NS,carcinoma,0,1	UBR4	415	1	1	Substitution - Missense(1)	stomach(1)	c.A3319G						PASS	.	T	ALA/THR	1102,3304	397.4+/-330.4	127,848,1228	90.0	85.0	87.0		3319	4.8	1.0	1	dbSNP_123	87	1407,7193	272.4+/-290.1	116,1175,3009	yes	missense	UBR4	NM_020765.2	58	243,2023,4237	CC,CT,TT		16.3605,25.0113,19.2911	benign	1107/5184	19499560	2509,10497	2203	4300	6503	SO:0001583	missense	23352	exon25			TGGTGGTACAGTC	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.3319A>G	1.37:g.19499560T>C	ENSP00000364403:p.Thr1107Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	139	81	0.582734	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	330	0.1510989010989011	132	0.2682926829268293	70	0.19337016574585636	7	0.012237762237762238	121	0.15963060686015831	T	15.15	2.747935	0.49257	0.250113	0.163605	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.95	4.82	0.62117	.	0.165648	0.52532	N	0.000069	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.21280	-1.0250	9	0.45353	T	0.12	.	6.8415	0.23965	0.134:0.0711:0.0:0.7948	rs16862578;rs52813973;rs16862578	1107	Q5T4S7	UBR4_HUMAN	A	1107;1107;1107;1107;323	ENSP00000364403:T1107A;ENSP00000364416:T1107A;ENSP00000364365:T1107A;ENSP00000364374:T1107A	ENSP00000364365:T1107A	T	-	1	0	UBR4	19372147	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.726000	0.61986	1.075000	0.40932	0.533000	0.62120	ACC	T|0.826;C|0.174	0.174	strong		0.418	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
ASB5	140458	hgsc.bcm.edu	37	4	177137988	177137988	+	Silent	SNP	C	C	T	rs6827525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:177137988C>T	ENST00000296525.3	-	6	956	c.843G>A	c.(841-843)agG>agA	p.R281R	ASB5_ENST00000512254.1_Silent_p.R228R	NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	281	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		GAAGCAATATCCTTTCCACCA	0.348													T|||	2582	0.515575	0.5219	0.5533	5008	,	,		19224	0.5675		0.4751	False		,,,				2504	0.4683				p.R281R		Atlas-SNP	.											.	ASB5	88	.	0			c.G843A						PASS	.	T		2190,2216	591.1+/-387.5	534,1122,547	155.0	147.0	150.0		843	1.4	0.1	4	dbSNP_116	150	4095,4505	592.8+/-393.0	973,2149,1178	no	coding-synonymous	ASB5	NM_080874.3		1507,3271,1725	TT,TC,CC		47.6163,49.7049,48.3239		281/330	177137988	6285,6721	2203	4300	6503	SO:0001819	synonymous_variant	140458	exon6			CAATATCCTTTCC	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"""Ankyrin repeat domain containing"""	17180	protein-coding gene	gene with protein product		615050	"""ankyrin repeat and SOCS box-containing 5"""				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.843G>A	4.37:g.177137988C>T		Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	262	116	0.442748	NM_080874	Q8N7B5	Silent	SNP	ENST00000296525.3	37	CCDS3827.1																																																																																			C|0.504;T|0.496	0.496	strong		0.348	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1		
AUTS2	26053	hgsc.bcm.edu	37	7	70239034	70239034	+	Silent	SNP	C	C	T	rs139965676		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:70239034C>T	ENST00000342771.4	+	12	2172	c.1851C>T	c.(1849-1851)gtC>gtT	p.V617V	AUTS2_ENST00000406775.2_Intron	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	617										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CTATCGATGTCGCTGCTCGGC	0.488													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19785	0.0		0.0	False		,,,				2504	0.0				p.V617V		Atlas-SNP	.											AUTS2,NS,carcinoma,0,1	AUTS2	173	1	0			c.C1851T						PASS	.	C	,	0,4406		0,0,2203	132.0	104.0	113.0		,1851	-12.1	0.6	7	dbSNP_134	113	3,8597	3.0+/-9.4	0,3,4297	no	intron,coding-synonymous	AUTS2	NM_001127231.1,NM_015570.2	,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,	,617/1260	70239034	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	26053	exon12			CGATGTCGCTGCT	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.1851C>T	7.37:g.70239034C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	C	9.577	1.122506	0.20877	0.0	3.49E-4	ENSG00000158321	ENST00000443672	.	.	.	6.06	-12.1	0.00011	.	.	.	.	.	T	0.41166	0.1147	.	.	.	0.49915	D	0.999835	.	.	.	.	.	.	T	0.52268	-0.8598	4	.	.	.	-18.381	6.7154	0.23300	0.0845:0.4459:0.3111:0.1585	.	.	.	.	L	144	.	.	S	+	2	0	AUTS2	69876970	0.002000	0.14202	0.582000	0.28627	0.972000	0.66771	-1.549000	0.02182	-1.627000	0.01550	-0.768000	0.03414	TCG	C|1.000;T|0.000	0.000	weak		0.488	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
NFKBIA	4792	hgsc.bcm.edu	37	14	35871232	35871232	+	Missense_Mutation	SNP	C	C	T	rs142970414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:35871232C>T	ENST00000216797.5	-	6	1042	c.941G>A	c.(940-942)cGt>cAt	p.R314H	NFKBIA_ENST00000557140.1_Missense_Mutation_p.R271H|NFKBIA_ENST00000557389.1_Missense_Mutation_p.R224H|NFKBIA_ENST00000557100.1_5'Flank	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	314					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	TAACGTCAGACGCTGGCCTCC	0.413																																					p.R314H		Atlas-SNP	.											.	NFKBIA	28	.	0			c.G941A						PASS	.	C	HIS/ARG	1,4405		0,1,2202	90.0	96.0	94.0		941	5.9	1.0	14	dbSNP_134	94	0,8600		0,0,4300	no	missense	NFKBIA	NM_020529.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	314/318	35871232	1,13005	2203	4300	6503	SO:0001583	missense	4792	exon6			GTCAGACGCTGGC		CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"""Ankyrin repeat domain containing"""	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.941G>A	14.37:g.35871232C>T	ENSP00000216797:p.Arg314His	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	184	75	0.407609	NM_020529	B2R8L6	Missense_Mutation	SNP	ENST00000216797.5	37	CCDS9656.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.866682	0.51588	2.27E-4	0.0	ENSG00000100906	ENST00000216797;ENST00000557140;ENST00000557389	T;T;T	0.50001	0.76;0.82;0.97	5.91	5.91	0.95273	.	.	.	.	.	T	0.29749	0.0743	N	0.14661	0.345	0.42889	D	0.994191	B;B	0.17465	0.022;0.013	B;B	0.09377	0.004;0.002	T	0.10894	-1.0610	9	0.41790	T	0.15	-16.9643	9.1946	0.37220	0.0:0.8795:0.0:0.1205	.	271;314	G3V3I4;P25963	.;IKBA_HUMAN	H	314;271;224	ENSP00000216797:R314H;ENSP00000451257:R271H;ENSP00000450514:R224H	ENSP00000216797:R314H	R	-	2	0	NFKBIA	34940983	0.999000	0.42202	0.995000	0.50966	0.865000	0.49528	2.991000	0.49409	2.808000	0.96608	0.655000	0.94253	CGT	C|1.000;T|0.000	0.000	strong		0.413	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529	
GSAP	54103	hgsc.bcm.edu	37	7	76990178	76990178	+	Silent	SNP	C	C	G	rs4727366	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:76990178C>G	ENST00000257626.7	-	14	1068	c.990G>C	c.(988-990)ggG>ggC	p.G330G		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	330					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										TCATGTGTGACCCAACATTCT	0.458													G|||	1512	0.301917	0.5461	0.219	5008	,	,		22232	0.0873		0.2326	False		,,,				2504	0.3231				p.G330G		Atlas-SNP	.											PION,caecum,carcinoma,0,1	PION	74	1	0			c.G990C						scavenged	.	G		2185,2221	590.3+/-387.3	546,1093,564	227.0	187.0	200.0		990	2.1	0.1	7	dbSNP_111	200	2174,6426	712.8+/-405.9	261,1652,2387	no	coding-synonymous	PION	NM_017439.3		807,2745,2951	GG,GC,CC		25.2791,49.5915,33.5153		330/855	76990178	4359,8647	2203	4300	6503	SO:0001819	synonymous_variant	54103	exon14			GTGTGACCCAACA		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"""pigeon homolog (Drosophila)"""	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.990G>C	7.37:g.76990178C>G		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	163	85	0.521472	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Silent	SNP	ENST00000257626.7	37	CCDS34672.2																																																																																			C|0.688;G|0.312	0.312	strong		0.458	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
DAGLA	747	hgsc.bcm.edu	37	11	61511794	61511794	+	Missense_Mutation	SNP	C	C	G	rs117050893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61511794C>G	ENST00000257215.5	+	20	3078	c.2962C>G	c.(2962-2964)Ctc>Gtc	p.L988V	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	988					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		GGGCATCTCACTCTCGCCCTC	0.667													C|||	33	0.00658946	0.0	0.0331	5008	,	,		16155	0.002		0.006	False		,,,				2504	0.002				p.L988V		Atlas-SNP	.											.	DAGLA	109	.	0			c.C2962G						PASS	.	C	VAL/LEU	18,4386	24.3+/-50.5	0,18,2184	56.0	62.0	60.0		2962	2.0	0.0	11	dbSNP_132	60	38,8560	25.7+/-73.6	0,38,4261	yes	missense	DAGLA	NM_006133.2	32	0,56,6445	GG,GC,CC		0.442,0.4087,0.4307	benign	988/1043	61511794	56,12946	2202	4299	6501	SO:0001583	missense	747	exon20			ATCTCACTCTCGC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.2962C>G	11.37:g.61511794C>G	ENSP00000257215:p.Leu988Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	37	0.397849	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	37	CCDS31578.1	21	0.009615384615384616	0	0.0	15	0.04143646408839779	1	0.0017482517482517483	5	0.006596306068601583	C	5.197	0.221827	0.09863	0.004087	0.00442	ENSG00000134780	ENST00000257215	T	0.25085	1.82	4.03	1.95	0.26073	.	0.158981	0.41097	D	0.000955	T	0.01905	0.0060	N	0.03608	-0.345	0.18873	N	0.999989	B	0.02656	0.0	B	0.04013	0.001	T	0.32268	-0.9913	10	0.17369	T	0.5	-26.7772	8.6434	0.33991	0.0:0.5927:0.3026:0.1048	.	988	Q9Y4D2	DGLA_HUMAN	V	988	ENSP00000257215:L988V	ENSP00000257215:L988V	L	+	1	0	DAGLA	61268370	0.954000	0.32549	0.008000	0.14137	0.636000	0.38137	1.749000	0.38319	0.815000	0.34398	0.462000	0.41574	CTC	C|0.994;G|0.006	0.006	strong		0.667	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
GRIK3	2899	hgsc.bcm.edu	37	1	37356579	37356579	+	Silent	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:37356579G>T	ENST00000373091.3	-	2	250	c.234C>A	c.(232-234)acC>acA	p.T78T	GRIK3_ENST00000373093.4_Silent_p.T78T	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	78					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CATAGGTCAAGGTTGTGTTGG	0.547																																					p.T78T		Atlas-SNP	.											.	GRIK3	195	.	0			c.C234A						PASS	.						299.0	234.0	256.0					1																	37356579		2203	4300	6503	SO:0001819	synonymous_variant	2899	exon2			GGTCAAGGTTGTG	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.234C>A	1.37:g.37356579G>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	222	105	0.472973	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	37	CCDS416.1																																																																																			.	.	none		0.547	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831	
SLAMF1	6504	hgsc.bcm.edu	37	1	160616703	160616703	+	Missense_Mutation	SNP	G	G	T	rs2295612	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:160616703G>T	ENST00000302035.6	-	1	382	c.33C>A	c.(31-33)ttC>ttA	p.F11L	SLAMF1_ENST00000538290.1_Missense_Mutation_p.F11L|SLAMF1_ENST00000235739.5_Missense_Mutation_p.F11L|SLAMF1_ENST00000355199.3_Missense_Mutation_p.F11L	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	11			F -> L (in dbSNP:rs2295612).		lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.F11F(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GAAACAGCACGAAGGTCAAGG	0.567													G|||	493	0.0984425	0.0061	0.2075	5008	,	,		19271	0.0347		0.2167	False		,,,				2504	0.09				p.F11L		Atlas-SNP	.											SLAMF1,colon,carcinoma,0,1	SLAMF1	74	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C33A						PASS	.	G	LEU/PHE	158,4248	105.6+/-144.1	3,152,2048	68.0	62.0	64.0		33	0.8	0.0	1	dbSNP_100	64	1748,6852	308.2+/-308.8	190,1368,2742	yes	missense	SLAMF1	NM_003037.2	22	193,1520,4790	TT,TG,GG		20.3256,3.586,14.6548	benign	11/336	160616703	1906,11100	2203	4300	6503	SO:0001583	missense	6504	exon1			CAGCACGAAGGTC	U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10903	protein-coding gene	gene with protein product		603492	"""signaling lymphocytic activation molecule"""	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.33C>A	1.37:g.160616703G>T	ENSP00000306190:p.Phe11Leu	Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	182	180	0.989011	NM_003037	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	37	CCDS1207.1	267	0.12225274725274725	6	0.012195121951219513	77	0.212707182320442	18	0.03146853146853147	166	0.21899736147757257	G	0.031	-1.336977	0.01287	0.03586	0.203256	ENSG00000117090	ENST00000302035;ENST00000235739;ENST00000392208;ENST00000538290;ENST00000355199	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	3.84	0.793	0.18632	Signaling lymphocytic activation molecule, N-terminal (2);	1.960650	0.02772	N	0.119850	T	0.07548	0.0190	N	0.20685	0.6	0.80722	P	0.0	B;B	0.12630	0.006;0.002	B;B	0.14023	0.01;0.006	T	0.07539	-1.0767	9	0.05833	T	0.94	-13.3109	5.3222	0.15887	0.2009:0.0:0.632:0.1672	rs2295612;rs58261892;rs2295612	11;11	B4E2E4;Q13291	.;SLAF1_HUMAN	L	11	ENSP00000306190:F11L;ENSP00000235739:F11L;ENSP00000438406:F11L;ENSP00000347333:F11L	ENSP00000235739:F11L	F	-	3	2	SLAMF1	158883327	0.062000	0.20869	0.006000	0.13384	0.001000	0.01503	-0.151000	0.10175	-0.038000	0.13624	-1.119000	0.02030	TTC	G|0.877;T|0.123	0.123	strong		0.567	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1		
PI4KA	5297	hgsc.bcm.edu	37	22	21066789	21066789	+	Silent	SNP	A	A	G	rs5996654	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:21066789A>G	ENST00000572273.1	-	50	5843	c.5613T>C	c.(5611-5613)acT>acC	p.T1871T	PI4KA_ENST00000255882.6_Silent_p.T1929T|PI4KA_ENST00000414196.3_Silent_p.T681T			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1871	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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)	p.T1871T(1)		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)			GGAAGGCCAGAGTGGACTCAT	0.662																																					p.T1929T	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,0,1	PI4KA	313	1	1	Substitution - coding silent(1)	stomach(1)	c.T5787C						PASS	.						23.0	25.0	24.0					22																	21066789		2198	4284	6482	SO:0001819	synonymous_variant	5297	exon50			GGCCAGAGTGGAC	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.5613T>C	22.37:g.21066789A>G		Somatic	329	2	0.00607903		WXS	Illumina HiSeq	Phase_I	337	277	0.821958	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				A|0.618;G|0.382	0.382	strong		0.662	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
MGAT4C	25834	hgsc.bcm.edu	37	12	86373221	86373221	+	Missense_Mutation	SNP	G	G	C	rs17855890	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:86373221G>C	ENST00000604798.1	-	8	2487	c.1283C>G	c.(1282-1284)aCt>aGt	p.T428S	MGAT4C_ENST00000549405.2_Missense_Mutation_p.T428S|MGAT4C_ENST00000393205.2_Missense_Mutation_p.T457S|MGAT4C_ENST00000548651.1_Missense_Mutation_p.T428S|MGAT4C_ENST00000552808.2_Missense_Mutation_p.T428S|MGAT4C_ENST00000332156.1_Missense_Mutation_p.T428S			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	428			T -> S (in dbSNP:rs17855890). {ECO:0000269|PubMed:10570912, ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TCTTAAGTAAGTAGAACATTG	0.348													G|||	206	0.0411342	0.0061	0.0793	5008	,	,		17729	0.0		0.1143	False		,,,				2504	0.0286				p.T428S		Atlas-SNP	.											.	MGAT4C	110	.	0			c.C1283G						PASS	.	G	SER/THR	84,4322	73.1+/-111.1	2,80,2121	82.0	81.0	82.0		1283	4.8	0.2	12	dbSNP_123	82	910,7688	204.5+/-247.2	48,814,3437	yes	missense	MGAT4C	NM_013244.3	58	50,894,5558	CC,CG,GG		10.5839,1.9065,7.6438	benign	428/479	86373221	994,12010	2203	4299	6502	SO:0001583	missense	25834	exon7			AAGTAAGTAGAAC		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	30871	protein-coding gene	gene with protein product		607385	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"""			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.1283C>G	12.37:g.86373221G>C	ENSP00000474896:p.Thr428Ser	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	181	93	0.513812	NM_013244	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	37	CCDS9030.1	107	0.04899267399267399	5	0.01016260162601626	22	0.06077348066298342	0	0.0	80	0.10554089709762533	G	2.671	-0.277587	0.05679	0.019065	0.105839	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651	T;T;T;T;T	0.28895	1.6;1.59;1.6;1.6;1.6	5.76	4.85	0.62838	.	0.180320	0.48767	N	0.000168	T	0.00328	0.0010	N	0.16130	0.375	0.31148	N	0.705815	B;B	0.12630	0.006;0.006	B;B	0.10450	0.005;0.004	T	0.04870	-1.0921	10	0.06494	T	0.89	-19.8644	15.9183	0.79539	0.0:0.0:0.8637:0.1363	rs17855890	457;428	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	S	428;457;428;428;428;428	ENSP00000331664:T428S;ENSP00000376900:T457S;ENSP00000449022:T428S;ENSP00000446647:T428S;ENSP00000447253:T428S	ENSP00000331664:T428S	T	-	2	0	MGAT4C	84897352	1.000000	0.71417	0.163000	0.22734	0.837000	0.47467	4.624000	0.61254	1.366000	0.46076	0.585000	0.79938	ACT	G|0.927;C|0.073	0.073	strong		0.348	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244	
SYCE1	93426	hgsc.bcm.edu	37	10	135369532	135369532	+	Missense_Mutation	SNP	T	T	C	rs3747881	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135369532T>C	ENST00000343131.5	-	9	652	c.548A>G	c.(547-549)aAg>aGg	p.K183R	SYCE1_ENST00000432597.2_Missense_Mutation_p.K147R|SPRN_ENST00000541506.1_Intron|SYCE1_ENST00000368517.3_Missense_Mutation_p.K147R	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	183			K -> R (in dbSNP:rs3747881). {ECO:0000269|PubMed:15489334}.		synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		ACAAATCTCCTTTGCCAGCCG	0.552													C|||	988	0.197284	0.1997	0.1844	5008	,	,		21691	0.2698		0.1093	False		,,,				2504	0.2188				p.K183R		Atlas-SNP	.											.	SYCE1	81	.	0			c.A548G						PASS	.	C	ARG/LYS,ARG/LYS,ARG/LYS	722,3684	748.4+/-411.9	41,640,1522	99.0	87.0	91.0		548,548,440	-3.9	0.0	10	dbSNP_107	91	807,7793	779.6+/-407.7	45,717,3538	yes	missense,missense,missense	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	26,26,26	86,1357,5060	CC,CT,TT		9.3837,16.3867,11.7561	benign,benign,benign	183/319,183/352,147/283	135369532	1529,11477	2203	4300	6503	SO:0001583	missense	93426	exon9			ATCTCCTTTGCCA	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.548A>G	10.37:g.135369532T>C	ENSP00000341282:p.Lys183Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	94	30	0.319149	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	37	CCDS44501.1	404	0.184981684981685	93	0.18902439024390244	68	0.1878453038674033	153	0.2674825174825175	90	0.11873350923482849	C	0.855	-0.737129	0.03111	0.163867	0.093837	ENSG00000171772	ENST00000303903;ENST00000432597;ENST00000368517;ENST00000343131	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	4.38	-3.92	0.04155	.	0.864322	0.10196	N	0.704037	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.28996	-1.0026	9	0.05959	T	0.93	-9.816	7.6589	0.28392	0.133:0.1995:0.0:0.6675	rs3747881;rs17857025;rs52827544;rs60545805;rs3747881	55;183;147	Q8N0S2-3;Q8N0S2;Q8N0S2-2	.;SYCE1_HUMAN;.	R	183;147;147;183	ENSP00000303978:K183R;ENSP00000411779:K147R;ENSP00000357503:K147R;ENSP00000341282:K183R	ENSP00000303978:K183R	K	-	2	0	SYCE1	135219522	0.001000	0.12720	0.005000	0.12908	0.017000	0.09413	-1.544000	0.02192	-1.244000	0.02516	-0.119000	0.15052	AAG	T|0.851;C|0.149	0.149	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
TMEM200A	114801	hgsc.bcm.edu	37	6	130761957	130761957	+	Silent	SNP	A	A	G	rs3813359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:130761957A>G	ENST00000296978.3	+	3	1261	c.390A>G	c.(388-390)ccA>ccG	p.P130P	TMEM200A_ENST00000392429.1_Silent_p.P130P|TMEM200A_ENST00000545622.1_Silent_p.P130P	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	130						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TGCTTGGCCCATTCACCATGG	0.413													A|||	1396	0.278754	0.3699	0.2017	5008	,	,		20896	0.3413		0.1412	False		,,,				2504	0.2873				p.P130P		Atlas-SNP	.											.	TMEM200A	108	.	0			c.A390G						PASS	.	A		1590,2816	495.0+/-363.1	300,990,913	91.0	79.0	83.0		390	-5.3	0.9	6	dbSNP_107	83	1179,7421	240.4+/-271.1	74,1031,3195	no	coding-synonymous	TMEM200A	NM_052913.2		374,2021,4108	GG,GA,AA		13.7093,36.0872,21.2902		130/492	130761957	2769,10237	2203	4300	6503	SO:0001819	synonymous_variant	114801	exon3			TGGCCCATTCACC	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"""KIAA1913"""	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.390A>G	6.37:g.130761957A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_001258277	Q96PX5	Silent	SNP	ENST00000296978.3	37	CCDS5140.1																																																																																			A|0.770;G|0.230	0.230	strong		0.413	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913	
GDA	9615	hgsc.bcm.edu	37	9	74840668	74840668	+	Missense_Mutation	SNP	G	G	A	rs61752956	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:74840668G>A	ENST00000358399.3	+	8	883	c.790G>A	c.(790-792)Gtg>Atg	p.V264M	GDA_ENST00000376989.3_Missense_Mutation_p.V203M|GDA_ENST00000545168.1_Missense_Mutation_p.V190M|GDA_ENST00000477618.1_3'UTR|GDA_ENST00000376986.1_Missense_Mutation_p.V186M|GDA_ENST00000238018.4_Missense_Mutation_p.V264M	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase	264					guanine catabolic process (GO:0006147)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	guanine deaminase activity (GO:0008892)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(20)|ovary(2)|skin(2)|urinary_tract(1)	32		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		CTACACATCTGTGTATGATAA	0.269													G|||	39	0.00778754	0.0	0.0144	5008	,	,		13008	0.0		0.0268	False		,,,				2504	0.002				p.V264M		Atlas-SNP	.											.	GDA	113	.	0			c.G790A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL	22,4382	28.1+/-56.4	1,20,2181	71.0	81.0	77.0		790,568,568,790	4.0	1.0	9	dbSNP_129	77	161,8417	76.3+/-139.0	3,155,4131	yes	missense,missense,missense,missense	GDA	NM_001242505.1,NM_001242506.1,NM_001242507.1,NM_004293.3	21,21,21,21	4,175,6312	AA,AG,GG		1.8769,0.4995,1.4096	probably-damaging,probably-damaging,probably-damaging,probably-damaging	264/472,190/381,190/381,264/455	74840668	183,12799	2202	4289	6491	SO:0001583	missense	9615	exon8			ACATCTGTGTATG	AF095286	CCDS6641.1, CCDS56576.1, CCDS56577.1	9q21.13	2008-05-14			ENSG00000119125	ENSG00000119125			4212	protein-coding gene	gene with protein product		139260				10075721, 3966794	Standard	NM_001242507		Approved		uc004air.3	Q9Y2T3	OTTHUMG00000020005	ENST00000358399.3:c.790G>A	9.37:g.74840668G>A	ENSP00000351170:p.Val264Met	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	169	72	0.426035	NM_004293	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	Missense_Mutation	SNP	ENST00000358399.3	37	CCDS6641.1	24	0.01098901098901099	0	0.0	7	0.019337016574585635	0	0.0	17	0.022427440633245383	G	15.83	2.950242	0.53186	0.004995	0.018769	ENSG00000119125	ENST00000545168;ENST00000238018;ENST00000376989;ENST00000376986;ENST00000358399;ENST00000414671	D;D;D;D;D;D	0.90444	-2.67;-2.67;-2.67;-2.67;-2.67;-2.67	5.82	4.0	0.46444	Amidohydrolase 1 (1);	0.056978	0.64402	D	0.000002	D	0.90903	0.7141	M	0.88377	2.95	0.38360	D	0.944599	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.81914	0.983;0.981;0.995	D	0.91206	0.4995	10	0.87932	D	0	-8.0117	6.3115	0.21166	0.1619:0.1515:0.6866:0.0	rs61752956	186;264;264	Q5SZC6;Q9Y2T3-3;Q9Y2T3	.;.;GUAD_HUMAN	M	190;264;203;186;264;130	ENSP00000437972:V190M;ENSP00000238018:V264M;ENSP00000366188:V203M;ENSP00000366185:V186M;ENSP00000351170:V264M;ENSP00000403897:V130M	ENSP00000238018:V264M	V	+	1	0	GDA	74030488	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	2.835000	0.48175	0.819000	0.34492	-0.136000	0.14681	GTG	G|0.986;A|0.014	0.014	strong		0.269	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052633.1		
NUCB1	4924	hgsc.bcm.edu	37	19	49407660	49407660	+	Silent	SNP	G	G	A	rs1058483	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49407660G>A	ENST00000405315.4	+	3	526	c.192G>A	c.(190-192)acG>acA	p.T64T	NUCB1_ENST00000407032.1_Silent_p.T64T|NUCB1_ENST00000263273.5_Silent_p.T64T|NUCB1_ENST00000485798.1_Intron	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	64						endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		TACTGGAGACGGATGGGCATT	0.627													g|||	274	0.0547125	0.0076	0.062	5008	,	,		13827	0.001		0.1441	False		,,,				2504	0.0767				p.T64T		Atlas-SNP	.											NUCB1,NS,carcinoma,+1,1	NUCB1	44	1	0			c.G192A						PASS	.			135,4271	95.7+/-134.4	5,125,2073	90.0	67.0	75.0		192	-8.5	0.2	19	dbSNP_86	75	1442,7158	276.4+/-292.3	112,1218,2970	no	coding-synonymous	NUCB1	NM_006184.5		117,1343,5043	AA,AG,GG		16.7674,3.064,12.1252		64/462	49407660	1577,11429	2203	4300	6503	SO:0001819	synonymous_variant	4924	exon3			GGAGACGGATGGG	BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"""EF-hand domain containing"""	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.192G>A	19.37:g.49407660G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	101	36	0.356436	NM_006184	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Silent	SNP	ENST00000405315.4	37	CCDS12740.1	140	0.0641025641025641	7	0.014227642276422764	25	0.06906077348066299	1	0.0017482517482517483	107	0.14116094986807387	g	0.400	-0.918842	0.02396	0.03064	0.167674	ENSG00000104805	ENST00000424608	.	.	.	4.27	-8.54	0.00912	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.999999382115	.	.	.	.	.	.	T	0.11227	-1.0596	3	.	.	.	.	8.5909	0.33686	0.2339:0.0:0.5512:0.2149	rs1058483;rs3199107;rs17272721;rs1058483	.	.	.	Q	64	.	.	R	+	2	0	NUCB1	54099472	0.000000	0.05858	0.239000	0.24122	0.026000	0.11368	-6.299000	0.00071	-1.883000	0.01120	-0.849000	0.03036	CGG	G|0.903;A|0.097	0.097	strong		0.627	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184	
RCAN3	11123	hgsc.bcm.edu	37	1	24861704	24861704	+	Silent	SNP	G	G	A	rs196432	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24861704G>A	ENST00000374395.4	+	5	976	c.663G>A	c.(661-663)acG>acA	p.T221T	RCAN3_ENST00000412742.2_Missense_Mutation_p.R164Q|RCAN3_ENST00000436717.2_Silent_p.T211T|RCAN3_ENST00000374393.2_Missense_Mutation_p.R106Q|RCAN3_ENST00000538532.1_Silent_p.T163T	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3	221					anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		TTGCCCAGACGAGGCGCCCCG	0.582													G|||	2550	0.509185	0.4667	0.4006	5008	,	,		15419	0.7272		0.4573	False		,,,				2504	0.4724				p.R164Q		Atlas-SNP	.											RCAN3,colon,carcinoma,0,1	RCAN3	22	1	0			c.G491A						PASS	.	G		2045,2361	566.1+/-381.8	472,1101,630	53.0	55.0	54.0		663	-11.6	0.0	1	dbSNP_79	54	3966,4634	548.7+/-385.4	893,2180,1227	no	coding-synonymous	RCAN3	NM_013441.2		1365,3281,1857	AA,AG,GG		46.1163,46.414,46.2171		221/242	24861704	6011,6995	2203	4300	6503	SO:0001819	synonymous_variant	11123	exon3			CCAGACGAGGCGC		CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"""Down syndrome critical region gene 1-like 2"""	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.663G>A	1.37:g.24861704G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	190	93	0.489474	NM_001251982	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Missense_Mutation	SNP	ENST00000374395.4	37	CCDS254.1	1141	0.5224358974358975	218	0.44308943089430897	141	0.38950276243093923	416	0.7272727272727273	366	0.48284960422163586	G	0.029	-1.348475	0.01266	0.46414	0.461163	ENSG00000117602	ENST00000412742;ENST00000374393	.	.	.	5.78	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B;B	0.15719	0.014;0.0	B;B	0.10450	0.005;0.0	T	0.19844	-1.0293	6	0.06757	T	0.87	-5.9522	9.401	0.38433	0.4826:0.3354:0.1284:0.0537	rs196432;rs548092;rs3765891;rs17441326;rs17846158;rs17859166;rs60263682;rs196432	106;164	E7EWD8;E7ENV1	.;.	Q	164;106	.	ENSP00000363514:R106Q	R	+	2	0	RCAN3	24734291	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-3.588000	0.00422	-4.477000	0.00046	-1.753000	0.00675	CGA	G|0.515;A|0.485	0.485	strong		0.582	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2		
TBC1D4	9882	hgsc.bcm.edu	37	13	76055820	76055820	+	Silent	SNP	G	G	C	rs7327548	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:76055820G>C	ENST00000377636.3	-	1	430	c.84C>G	c.(82-84)ccC>ccG	p.P28P	TBC1D4_ENST00000431480.2_Silent_p.P28P|TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000377625.2_Silent_p.P28P	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	28					cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		TTGGCTTCCCGGGGCCGGGCT	0.677													G|||	1784	0.35623	0.5492	0.3573	5008	,	,		11294	0.2153		0.3976	False		,,,				2504	0.1973				p.P28P		Atlas-SNP	.											.	TBC1D4	142	.	0			c.C84G						PASS	.	G		1931,1805		532,867,469	10.0	13.0	12.0		84	-2.1	0.0	13	dbSNP_116	12	3195,4929		685,1825,1552	no	coding-synonymous	TBC1D4	NM_014832.2		1217,2692,2021	CC,CG,GG		39.3279,48.3137,43.2209		28/1299	76055820	5126,6734	1868	4062	5930	SO:0001819	synonymous_variant	9882	exon1			CTTCCCGGGGCCG	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.84C>G	13.37:g.76055820G>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	37	CCDS41901.1																																																																																			G|0.616;C|0.384	0.384	strong		0.677	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
KPRP	448834	hgsc.bcm.edu	37	1	152732106	152732106	+	Missense_Mutation	SNP	A	A	T	rs17612167	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152732106A>T	ENST00000606109.1	+	1	70	c.42A>T	c.(40-42)caA>caT	p.Q14H	KPRP_ENST00000368773.1_Missense_Mutation_p.Q14H			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	14	Gln-rich.		Q -> H (in dbSNP:rs17612167).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCCGCTCCAACAGTGCTGCG	0.582													A|||	887	0.177117	0.0106	0.1441	5008	,	,		20191	0.2262		0.2256	False		,,,				2504	0.3252				p.Q14H		Atlas-SNP	.											.	KPRP	152	.	0			c.A42T						PASS	.	A	HIS/GLN	191,4215	122.1+/-159.5	6,179,2018	78.0	77.0	77.0		42	-0.2	0.9	1	dbSNP_123	77	1997,6603	350.0+/-327.7	243,1511,2546	yes	missense	KPRP	NM_001025231.1	24	249,1690,4564	TT,TA,AA		23.2209,4.335,16.823	benign	14/580	152732106	2188,10818	2203	4300	6503	SO:0001583	missense	448834	exon2			GCTCCAACAGTGC	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.42A>T	1.37:g.152732106A>T	ENSP00000475216:p.Gln14His	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	217	111	0.511521	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	346	0.15842490842490842	8	0.016260162601626018	49	0.13535911602209943	109	0.19055944055944055	180	0.23746701846965698	A	13.87	2.367214	0.41902	0.04335	0.232209	ENSG00000203786	ENST00000368773	T	0.12147	2.71	5.54	-0.206	0.13193	.	0.316889	0.23211	N	0.050675	T	0.02230	0.0069	N	0.08118	0	0.50313	P	1.32000000000021E-4	P	0.39624	0.681	B	0.38056	0.264	T	0.45279	-0.9272	9	0.66056	D	0.02	.	8.3266	0.32160	0.4162:0.355:0.2288:0.0	rs17612167;rs17612167	14	Q5T749	KPRP_HUMAN	H	14	ENSP00000357762:Q14H	ENSP00000357762:Q14H	Q	+	3	2	KPRP	150998730	0.759000	0.28416	0.917000	0.36280	0.694000	0.40290	-0.281000	0.08456	0.066000	0.16515	-0.250000	0.11733	CAA	A|0.835;T|0.165	0.165	strong		0.582	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
CEACAM18	729767	hgsc.bcm.edu	37	19	51983673	51983673	+	Missense_Mutation	SNP	G	G	A	rs61743859	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51983673G>A	ENST00000396477.4	+	2	160	c.139G>A	c.(139-141)Gtg>Atg	p.V47M	CEACAM18_ENST00000451626.1_Missense_Mutation_p.V108M	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	47										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TCGGACTGTCGTGGCCCTGGA	0.552													c|||	926	0.184904	0.171	0.1628	5008	,	,		19388	0.1111		0.2594	False		,,,				2504	0.2188				p.V108M		Atlas-SNP	.											.	CEACAM18	96	.	0			c.G322A						PASS	.	C	MET/VAL	733,3265		78,577,1344	54.0	51.0	52.0		322	1.7	0.0	19	dbSNP_129	52	2069,6239		245,1579,2330	yes	missense	CEACAM18	NM_001080405.1	21	323,2156,3674	AA,AG,GG		24.9037,18.3342,22.7694	benign	108/399	51983673	2802,9504	1999	4154	6153	SO:0001583	missense	729767	exon3			ACTGTCGTGGCCC			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.139G>A	19.37:g.51983673G>A	ENSP00000379738:p.Val47Met	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		386	0.17673992673992675	82	0.16666666666666666	65	0.17955801104972377	57	0.09965034965034965	182	0.24010554089709762	.	14.64	2.595023	0.46318	0.183342	0.249037	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.05580	3.42	2.78	1.71	0.24356	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.34226	0.443	B	0.17722	0.019	T	0.50180	-0.8858	8	0.87932	D	0	-3.1057	5.3435	0.15996	0.2361:0.5348:0.2291:0.0	rs61743859	108	A8MTB9	CEA18_HUMAN	M	108;47;47	ENSP00000402203:V108M	ENSP00000379738:V47M	V	+	1	0	CEACAM18	56675485	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	-0.097000	0.11042	0.264000	0.21851	-0.857000	0.03018	GTG	G|0.806;A|0.194	0.194	strong		0.552	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
BNIPL	149428	hgsc.bcm.edu	37	1	151011325	151011325	+	Missense_Mutation	SNP	C	C	T	rs373344206|rs61751619	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:151011325C>T	ENST00000368931.3	+	4	412	c.256C>T	c.(256-258)Cgt>Tgt	p.R86C	BNIPL_ENST00000295294.7_Missense_Mutation_p.R4C	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	86					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CATGCGCAAGCGTCTTTCTGC	0.577													C|||	237	0.0473243	0.003	0.0648	5008	,	,		17748	0.0		0.1352	False		,,,				2504	0.0532				p.R86C		Atlas-SNP	.											BNIPL,colon,carcinoma,-1,1	BNIPL	45	1	0			c.C256T						PASS	.	C	CYS/ARG,CYS/ARG	135,4271	98.9+/-137.6	1,133,2069	67.0	66.0	66.0		10,256	5.2	1.0	1	dbSNP_129	66	1221,7379	246.1+/-274.7	99,1023,3178	yes	missense,missense	BNIPL	NM_001159642.1,NM_138278.3	180,180	100,1156,5247	TT,TC,CC		14.1977,3.064,10.426	probably-damaging,probably-damaging	4/276,86/358	151011325	1356,11650	2203	4300	6503	SO:0001583	missense	149428	exon4			CGCAAGCGTCTTT	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.256C>T	1.37:g.151011325C>T	ENSP00000357927:p.Arg86Cys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	118	65	0.550847	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Missense_Mutation	SNP	ENST00000368931.3	37	CCDS978.2	135	0.061813186813186816	0	0.0	27	0.07458563535911603	0	0.0	108	0.1424802110817942	C	20.5	3.994232	0.74703	0.03064	0.141977	ENSG00000163141	ENST00000368931;ENST00000361277;ENST00000295294;ENST00000392802	T;T;T	0.57595	1.1;1.13;0.39	5.15	5.15	0.70609	.	0.386996	0.26669	N	0.023114	T	0.66528	0.2798	M	0.79805	2.47	0.25649	P	0.9861115	D	0.89917	1.0	D	0.67231	0.95	T	0.72323	-0.4328	9	0.87932	D	0	.	14.0116	0.64500	0.0:1.0:0.0:0.0	rs61751619	86	Q7Z465	BNIPL_HUMAN	C	86;84;4;4	ENSP00000357927:R86C;ENSP00000355333:R84C;ENSP00000295294:R4C	ENSP00000295294:R4C	R	+	1	0	BNIPL	149277949	1.000000	0.71417	0.974000	0.42286	0.866000	0.49608	3.894000	0.56250	2.677000	0.91161	0.563000	0.77884	CGT	C|0.909;T|0.091	0.091	strong		0.577	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279	
EMILIN3	90187	hgsc.bcm.edu	37	20	39991144	39991144	+	Silent	SNP	A	A	G	rs41307177	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:39991144A>G	ENST00000332312.3	-	4	1257	c.1065T>C	c.(1063-1065)ctT>ctC	p.L355L		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	355						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				CCCGGCCATCAAGGCTCTGGT	0.682													A|||	406	0.0810703	0.0598	0.1225	5008	,	,		15115	0.003		0.1799	False		,,,				2504	0.0593				p.L355L		Atlas-SNP	.											EMILIN3,rectum,carcinoma,0,1	EMILIN3	63	1	0			c.T1065C						PASS	.	A		377,4021		11,355,1833	13.0	16.0	15.0		1065	-1.5	1.0	20	dbSNP_127	15	1411,7175		132,1147,3014	no	coding-synonymous	EMILIN3	NM_052846.1		143,1502,4847	GG,GA,AA		16.4337,8.5721,13.7708		355/767	39991144	1788,11196	2199	4293	6492	SO:0001819	synonymous_variant	90187	exon4			GCCATCAAGGCTC	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1065T>C	20.37:g.39991144A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	40	12	0.3	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																			A|0.888;G|0.112	0.112	strong		0.682	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
ALG2	85365	hgsc.bcm.edu	37	9	101980707	101980707	+	Silent	SNP	A	A	G	rs62562374	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:101980707A>G	ENST00000476832.1	-	2	821	c.760T>C	c.(760-762)Ttg>Ctg	p.L254L	ALG2_ENST00000319033.6_Silent_p.L161L	NM_033087.3	NP_149078.1	O75340	PDCD6_HUMAN	ALG2, alpha-1,3/1,6-mannosyltransferase	0					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|prostate(2)	22		Acute lymphoblastic leukemia(62;0.0559)				TGGGATGTCAATCTTCCACGC	0.463													A|||	8	0.00159744	0.0	0.0014	5008	,	,		22624	0.0		0.007	False		,,,				2504	0.0				p.L254L		Atlas-SNP	.											.	ALG2	37	.	0			c.T760C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	153.0	153.0	153.0		760	-2.3	0.0	9	dbSNP_129	153	48,8552	31.2+/-83.2	0,48,4252	no	coding-synonymous	ALG2	NM_033087.3		0,51,6452	GG,GA,AA		0.5581,0.0681,0.3921		254/417	101980707	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	85365	exon2			ATGTCAATCTTCC	AK027417	CCDS6739.1	9q31.1	2013-02-22	2013-02-22		ENSG00000119523	ENSG00000119523	2.4.1.132, 2.4.1.257	"""Glycosyltransferase group 1 domain containing"""	23159	protein-coding gene	gene with protein product		607905	"""asparagine-linked glycosylation 2 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 2, alpha-1,3-mannosyltransferase homolog (S. cerevisiae)"""			12684507	Standard	NR_024532		Approved	CDGIi, FLJ14511, hALPG2, NET38	uc004azf.3	Q9H553	OTTHUMG00000020355	ENST00000476832.1:c.760T>C	9.37:g.101980707A>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	NM_033087	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Silent	SNP	ENST00000476832.1	37	CCDS6739.1																																																																																			A|0.998;C|0.000;G|0.002	0.002	strong		0.463	ALG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215080.1	NM_033087	
SLC30A9	10463	hgsc.bcm.edu	37	4	42022464	42022464	+	Silent	SNP	C	C	A	rs15857	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:42022464C>A	ENST00000264451.7	+	4	546	c.366C>A	c.(364-366)ggC>ggA	p.G122G		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	122					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GGGAGTATGGCTCAAAGTACA	0.343													.|||	3341	0.667133	0.1884	0.804	5008	,	,		18317	0.9583		0.7763	False		,,,				2504	0.8047				p.G122G		Atlas-SNP	.											.	SLC30A9	58	.	0			c.C366A						PASS	.	A		1228,3178	706.3+/-407.4	173,882,1148	136.0	126.0	129.0		366	3.7	1.0	4	dbSNP_52	129	6672,1926	340.3+/-323.5	2575,1522,202	no	coding-synonymous	SLC30A9	NM_006345.3		2748,2404,1350	AA,AC,CC		22.4006,27.8711,39.2495		122/569	42022464	7900,5104	2203	4299	6502	SO:0001819	synonymous_variant	10463	exon4			GTATGGCTCAAAG	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"""Solute carriers"""	1329	protein-coding gene	gene with protein product	"""GRIP1-dependent nuclear receptor coactivator"""	604604	"""chromosome 4 open reading frame 1"""	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.366C>A	4.37:g.42022464C>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	124	121	0.975806	NM_006345	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Silent	SNP	ENST00000264451.7	37	CCDS3465.1																																																																																			C|0.359;A|0.641	0.641	strong		0.343	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3		
DNA2	1763	hgsc.bcm.edu	37	10	70225504	70225504	+	Silent	SNP	G	G	T	rs3758626	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:70225504G>T	ENST00000358410.3	-	4	557	c.507C>A	c.(505-507)gcC>gcA	p.A169A	DNA2_ENST00000399180.2_Silent_p.A255A|DNA2_ENST00000399179.2_Silent_p.A169A	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	169	Nuclease activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						TATTATTTATGGCTTTTTGAA	0.358													T|||	1835	0.366414	0.4554	0.3545	5008	,	,		15821	0.379		0.2087	False		,,,				2504	0.4039				p.A169A		Atlas-SNP	.											.	DNA2	76	.	0			c.C507A						PASS	.	T		1561,2093		339,883,605	67.0	63.0	64.0		507	0.6	0.9	10	dbSNP_107	64	1702,6474		188,1326,2574	no	coding-synonymous	DNA2	NM_001080449.2		527,2209,3179	TT,TG,GG		20.817,42.7203,27.5824		169/1061	70225504	3263,8567	1827	4088	5915	SO:0001819	synonymous_variant	1763	exon4			ATTTATGGCTTTT	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"""DNA2 DNA replication helicase 2-like (yeast)"", ""DNA replication helicase 2 homolog (yeast)"""	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.507C>A	10.37:g.70225504G>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				G|0.672;T|0.328	0.328	strong		0.358	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
PCDHA3	56145	hgsc.bcm.edu	37	5	140183058	140183058	+	Missense_Mutation	SNP	G	G	A	rs2240694	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140183058G>A	ENST00000522353.2	+	1	2276	c.2276G>A	c.(2275-2277)tGc>tAc	p.C759Y	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.C759Y|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	759	6 X 4 AA repeats of P-X-X-P.		C -> Y (in dbSNP:rs2240694).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAGGGTGTGCTCTGGAGAG	0.622													.|||	2631	0.525359	0.4788	0.5893	5008	,	,		15605	0.5317		0.5378	False		,,,				2504	0.5235				p.C759Y		Atlas-SNP	.											PCDHA3,NS,carcinoma,+1,1	PCDHA3	396	1	0			c.G2276A						scavenged	.	G	,,TYR/CYS,,TYR/CYS	2185,2221	585.8+/-386.3	533,1119,551	97.0	103.0	101.0		,,2276,,2276	3.3	1.0	5	dbSNP_98	101	4540,4060	594.5+/-393.3	1192,2156,952	yes	intron,intron,missense,intron,missense	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,194,,194	1725,3275,1503	AA,AG,GG		47.2093,49.5915,48.2931	,,,,	,,759/951,,759/825	140183058	6725,6281	2203	4300	6503	SO:0001583	missense	56145	exon1			GGGTGTGCTCTGG	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.2276G>A	5.37:g.140183058G>A	ENSP00000429808:p.Cys759Tyr	Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	230	92	0.4	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	1163	0.5325091575091575	252	0.5121951219512195	194	0.5359116022099447	311	0.5437062937062938	406	0.5356200527704486	g	12.10	1.836155	0.32421	0.495915	0.527907	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.14640	2.49;2.49	4.16	3.26	0.37387	.	0.338457	0.20695	U	0.087381	T	0.00012	0.0000	M	0.90019	3.08	0.39490	P	0.03197799999999995	B;B	0.19331	0.035;0.009	B;B	0.22880	0.042;0.013	T	0.35624	-0.9781	9	0.72032	D	0.01	.	13.8703	0.63615	0.0:0.1545:0.8455:0.0	rs2240694;rs17844263;rs52836725;rs2240694	759;759	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	Y	759	ENSP00000429808:C759Y;ENSP00000434086:C759Y	ENSP00000429808:C759Y	C	+	2	0	PCDHA3	140163242	.	.	0.987000	0.45799	0.619000	0.37552	.	.	0.828000	0.34709	0.467000	0.42956	TGC	G|0.476;A|0.524	0.524	strong		0.622	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
HELZ2	85441	hgsc.bcm.edu	37	20	62200576	62200576	+	Missense_Mutation	SNP	G	G	A	rs6090457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:62200576G>A	ENST00000467148.1	-	4	1082	c.1013C>T	c.(1012-1014)tCa>tTa	p.S338L	HELZ2_ENST00000479540.1_5'Flank|HELZ2_ENST00000427522.2_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	338					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GTTGGTTGGTGAGATGGGGCC	0.652													G|||	1096	0.21885	0.0091	0.0951	5008	,	,		15531	0.5298		0.1948	False		,,,				2504	0.2945				p.S338L		Atlas-SNP	.											.	.	.	.	0			c.C1013T						PASS	.	G	LEU/SER	203,4197		6,191,2003	34.0	34.0	34.0		1013	4.5	0.0	20	dbSNP_114	34	1626,6974		165,1296,2839	yes	missense	PRIC285	NM_001037335.2	145	171,1487,4842	AA,AG,GG		18.907,4.6136,14.0692	probably-damaging	338/2650	62200576	1829,11171	2200	4300	6500	SO:0001583	missense	85441	exon5			GTTGGTGAGATGG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.1013C>T	20.37:g.62200576G>A	ENSP00000417401:p.Ser338Leu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	449	0.20558608058608058	6	0.012195121951219513	38	0.10497237569060773	277	0.48426573426573427	128	0.16886543535620052	G	9.400	1.077747	0.20227	0.046136	0.18907	ENSG00000130589	ENST00000467148	T	0.24350	1.86	4.5	4.5	0.54988	.	0.264588	0.35466	N	0.003191	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B	0.30763	0.294	B	0.27887	0.084	T	0.47674	-0.9099	9	0.66056	D	0.02	-21.7885	17.1945	0.86888	0.0:0.0:1.0:0.0	rs6090457	338	Q9BYK8	PR285_HUMAN	L	338	ENSP00000417401:S338L	ENSP00000417401:S338L	S	-	2	0	RP4-697K14.7	61671020	0.992000	0.36948	0.005000	0.12908	0.002000	0.02628	3.690000	0.54713	2.068000	0.61886	0.563000	0.77884	TCA	G|0.840;A|0.160	0.160	strong		0.652	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
RECQL5	9400	hgsc.bcm.edu	37	17	73625286	73625286	+	Silent	SNP	G	G	A	rs820190	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:73625286G>A	ENST00000317905.5	-	16	2376	c.2217C>T	c.(2215-2217)agC>agT	p.S739S	RECQL5_ENST00000423245.2_Silent_p.S712S|RECQL5_ENST00000443199.2_5'UTR	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	739					chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)			breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			TGGCAAGGGAGCTGCCCCCAG	0.647								Other identified genes with known or suspected DNA repair function					G|||	1144	0.228435	0.2247	0.2118	5008	,	,		16511	0.1577		0.3439	False		,,,				2504	0.1994				p.S739S		Atlas-SNP	.											.	RECQL5	77	.	0			c.C2217T						PASS	.	G		843,3013		99,645,1184	31.0	34.0	33.0		2217	-7.5	0.0	17	dbSNP_86	33	2670,5558		429,1812,1873	no	coding-synonymous	RECQL5	NM_004259.6		528,2457,3057	AA,AG,GG		32.4502,21.862,29.0715		739/992	73625286	3513,8571	1928	4114	6042	SO:0001819	synonymous_variant	9400	exon16			AAGGGAGCTGCCC	AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"""RecQ protein 5"""	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.2217C>T	17.37:g.73625286G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	130	61	0.469231	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Silent	SNP	ENST00000317905.5	37	CCDS42380.1																																																																																			G|0.746;A|0.254	0.254	strong		0.647	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
TMEM200C	645369	hgsc.bcm.edu	37	18	5891637	5891637	+	Silent	SNP	C	C	A	rs28656885	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:5891637C>A	ENST00000581347.2	-	3	1071	c.426G>T	c.(424-426)ccG>ccT	p.P142P	RP11-945C19.4_ENST00000582939.1_RNA|RP11-945C19.4_ENST00000577694.1_RNA|RP11-945C19.4_ENST00000580845.1_RNA|TMEM200C_ENST00000383490.2_Silent_p.P142P			A6NKL6	T200C_HUMAN	transmembrane protein 200C	142						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)	12						AGGAGGAGGACGGGGAGGCGG	0.652													A|||	1704	0.340256	0.4319	0.3444	5008	,	,		13431	0.2986		0.3598	False		,,,				2504	0.2362				p.P142P		Atlas-SNP	.											.	TMEM200C	30	.	0			c.G426T						PASS	.	A		1809,2421		391,1027,697	58.0	71.0	67.0		426	-8.4	0.0	18	dbSNP_125	67	3219,5213		630,1959,1627	no	coding-synonymous	TMEM200C	NM_001080209.1		1021,2986,2324	AA,AC,CC		38.176,42.766,39.7094		142/622	5891637	5028,7634	2115	4216	6331	SO:0001819	synonymous_variant	645369	exon1			GGAGGACGGGGAG		CCDS45825.1	18p11.31	2009-09-08			ENSG00000206432	ENSG00000206432			37208	protein-coding gene	gene with protein product						15722956	Standard	NM_001080209		Approved	TTMA	uc002kmx.1	A6NKL6		ENST00000581347.2:c.426G>T	18.37:g.5891637C>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	26	0.371429	NM_001080209		Silent	SNP	ENST00000581347.2	37	CCDS45825.1																																																																																			C|0.642;A|0.358	0.358	strong		0.652	TMEM200C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441917.4	NM_001080209	
BCR	613	hgsc.bcm.edu	37	22	23631801	23631801	+	Silent	SNP	T	T	C	rs2227939	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:23631801T>C	ENST00000305877.8	+	13	3451	c.2700T>C	c.(2698-2700)aaT>aaC	p.N900N	BCR_ENST00000359540.3_Silent_p.N900N	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	900	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)		BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	TGACCATCAATAAGGAAGGTG	0.567			T	"""ABL1,  FGFR1, JAK2 """	"""CML, ALL, AML"""						OREG0026390	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1616	0.322684	0.5461	0.3242	5008	,	,		21488	0.0754		0.2982	False		,,,				2504	0.2996				p.N900N		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.T2700C						PASS	.	C	,	2258,2148	580.6+/-385.2	581,1096,526	92.0	75.0	81.0		2700,2700	2.7	1.0	22	dbSNP_98	81	2539,6061	692.1+/-404.6	379,1781,2140	no	coding-synonymous,coding-synonymous	BCR	NM_004327.3,NM_021574.2	,	960,2877,2666	CC,CT,TT		29.5233,48.7517,36.883	,	900/1272,900/1228	23631801	4797,8209	2203	4300	6503	SO:0001819	synonymous_variant	613	exon13			CATCAATAAGGAA		CCDS13806.1, CCDS13807.1	22q11	2013-01-10			ENSG00000186716	ENSG00000186716		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	1014	protein-coding gene	gene with protein product		151410		D22S11, BCR1		1657398, 18070886	Standard	NM_004327		Approved	D22S662, CML, PHL, ALL	uc002zww.3	P11274	OTTHUMG00000150655	ENST00000305877.8:c.2700T>C	22.37:g.23631801T>C		Somatic	146	0	0	765	WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Silent	SNP	ENST00000305877.8	37	CCDS13806.1	667	0.30540293040293043	278	0.5650406504065041	112	0.30939226519337015	48	0.08391608391608392	229	0.3021108179419525	C	8.196	0.797066	0.16327	0.512483	0.295233	ENSG00000186716	ENST00000290956	.	.	.	4.78	2.7	0.31948	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.5429	0.17047	0.0:0.5254:0.0:0.4746	rs2227939;rs9608099;rs11558698	.	.	.	Q	466	.	.	X	+	1	0	BCR	21961801	0.999000	0.42202	1.000000	0.80357	0.543000	0.35085	0.565000	0.23578	0.703000	0.31848	-0.213000	0.12676	TAA	T|0.659;C|0.341	0.341	strong		0.567	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327	
KDM6B	23135	hgsc.bcm.edu	37	17	7750010	7750010	+	Missense_Mutation	SNP	G	G	C	rs79548905	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7750010G>C	ENST00000448097.2	+	8	994	c.663G>C	c.(661-663)gaG>gaC	p.E221D	KDM6B_ENST00000254846.5_Missense_Mutation_p.E221D			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	221	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						CAGGGGAGGAGGGCCTCAGCC	0.647													G|||	34	0.00678914	0.0	0.0159	5008	,	,		10042	0.0		0.0199	False		,,,				2504	0.0031				p.E221D		Atlas-SNP	.											.	KDM6B	95	.	0			c.G663C						PASS	.	G	ASP/GLU	25,4381	29.9+/-59.1	0,25,2178	60.0	63.0	62.0		663	1.5	1.0	17	dbSNP_131	62	250,8350	96.6+/-158.3	3,244,4053	yes	missense	KDM6B	NM_001080424.1	45	3,269,6231	CC,CG,GG		2.907,0.5674,2.1144	benign	221/1683	7750010	275,12731	2203	4300	6503	SO:0001583	missense	23135	exon8			GGAGGAGGGCCTC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.663G>C	17.37:g.7750010G>C	ENSP00000412513:p.Glu221Asp	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	87	35	0.402299	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		23	0.010531135531135532	0	0.0	8	0.022099447513812154	0	0.0	15	0.01978891820580475	G	10.43	1.347466	0.24426	0.005674	0.02907	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.38077	1.27;1.16	4.62	1.48	0.22813	.	0.000000	0.53938	D	0.000046	T	0.09291	0.0229	N	0.08118	0	0.23293	N	0.997964	D	0.59767	0.986	P	0.57720	0.826	T	0.11665	-1.0578	10	0.14252	T	0.57	-17.4424	6.792	0.23705	0.3837:0.0:0.6162:0.0	.	221	O15054-1	.	D	221	ENSP00000254846:E221D;ENSP00000412513:E221D	ENSP00000254846:E221D	E	+	3	2	KDM6B	7690735	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.076000	0.41548	0.274000	0.22072	0.561000	0.74099	GAG	G|0.981;C|0.019	0.019	strong		0.647	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
RPRD1B	58490	hgsc.bcm.edu	37	20	36668874	36668874	+	Silent	SNP	G	G	A	rs2273353	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:36668874G>A	ENST00000373433.4	+	2	591	c.189G>A	c.(187-189)gcG>gcA	p.A63A		NM_021215.3	NP_067038.1	Q9NQG5	RPR1B_HUMAN	regulation of nuclear pre-mRNA domain containing 1B	63	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.				dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle process (GO:0010564)|transcription, DNA-templated (GO:0006351)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)	12						TGTATTTAGCGAATGATGTCA	0.323													G|||	1456	0.290735	0.4962	0.134	5008	,	,		18769	0.2163		0.164	False		,,,				2504	0.3313				p.A63A		Atlas-SNP	.											RPRD1B,NS,carcinoma,+1,2	RPRD1B	25	2	0			c.G189A						scavenged	.	G		1909,2495	546.1+/-377.0	425,1059,718	153.0	149.0	150.0		189	-10.3	0.4	20	dbSNP_100	150	1413,7187	269.8+/-288.6	113,1187,3000	no	coding-synonymous	RPRD1B	NM_021215.3		538,2246,3718	AA,AG,GG		16.4302,43.347,25.546		63/327	36668874	3322,9682	2202	4300	6502	SO:0001819	synonymous_variant	58490	exon2			TTTAGCGAATGAT	AL109823	CCDS13301.1	20q11.21-q12	2012-02-09	2008-08-15	2008-07-28	ENSG00000101413	ENSG00000101413			16209	protein-coding gene	gene with protein product		614694	"""chromosome 20 open reading frame 77"""	C20orf77		22231121	Standard	NM_021215		Approved	dJ1057B20.2, DKFZp434P0735, CREPT, FLJ44520, NET60	uc002xho.4	Q9NQG5	OTTHUMG00000032434	ENST00000373433.4:c.189G>A	20.37:g.36668874G>A		Somatic	159	2	0.0125786		WXS	Illumina HiSeq	Phase_I	159	80	0.503145	NM_021215	Q1WDE7|Q6PKF4	Silent	SNP	ENST00000373433.4	37	CCDS13301.1																																																																																			G|0.747;A|0.253	0.253	strong		0.323	RPRD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079142.2	NM_021215	
HLA-E	3133	hgsc.bcm.edu	37	6	30457732	30457732	+	Silent	SNP	T	T	C	rs1059510	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30457732T>C	ENST00000376630.4	+	2	359	c.294T>C	c.(292-294)aaT>aaC	p.N98N		NM_005516.5	NP_005507.3	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	98	Alpha-1.		N -> K (in dbSNP:rs1059510).		antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protection from natural killer cell mediated cytotoxicity (GO:0042270)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)|ovary(3)|skin(1)|urinary_tract(1)	18						TCCGAGTGAATCTGCGGACGC	0.682													C|||	3630	0.72484	0.7383	0.6383	5008	,	,		12158	0.7083		0.672	False		,,,				2504	0.8395				p.N98N		Atlas-SNP	.											.	HLA-E	35	.	0			c.T294C						PASS	.	C		2245,775		842,561,107	65.0	81.0	75.0		294	1.7	0.0	6	dbSNP_86	75	3616,1794		1222,1172,311	no	coding-synonymous	HLA-E	NM_005516.5		2064,1733,418	CC,CT,TT		33.1608,25.6623,30.4745		98/359	30457732	5861,2569	1510	2705	4215	SO:0001819	synonymous_variant	3133	exon2			AGTGAATCTGCGG	M20022	CCDS34379.1	6p21.3	2013-01-11			ENSG00000204592	ENSG00000204592		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4962	protein-coding gene	gene with protein product		143010				3131426	Standard	NM_005516		Approved		uc003nqg.3	P13747	OTTHUMG00000031155	ENST00000376630.4:c.294T>C	6.37:g.30457732T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	215	111	0.516279	NM_005516	Q30169|Q9BT83|Q9GIY7|Q9GIY8	Silent	SNP	ENST00000376630.4	37	CCDS34379.1																																																																																			T|0.287;C|0.713	0.713	strong		0.682	HLA-E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076282.2	NM_005516	
HLA-C	3107	hgsc.bcm.edu	37	6	31237833	31237833	+	Missense_Mutation	SNP	T	T	C	rs1050180|rs281860578	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31237833T>C	ENST00000376228.5	-	5	939	c.925A>G	c.(925-927)Atg>Gtg	p.M309V	HLA-C_ENST00000383329.3_Missense_Mutation_p.M309V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	309	Connecting peptide.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACGATGCCCATGATGGGGATG	0.617													C|||	3826	0.763978	0.7489	0.804	5008	,	,		16231	0.8125		0.7197	False		,,,				2504	0.7515				p.M309V		Atlas-SNP	.											.	HLA-C	92	.	0			c.A925G						PASS	.	C	VAL/MET	3289,1105		1369,551,277	44.0	44.0	44.0		925	-3.6	0.0	6	dbSNP_86	44	5494,3094		1984,1526,784	yes	missense	HLA-C	NM_002117.5	21	3353,2077,1061	CC,CT,TT		36.027,25.1479,32.3448	benign	309/367	31237833	8783,4199	2197	4294	6491	SO:0001583	missense	3107	exon5			TGCCCATGATGGG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.925A>G	6.37:g.31237833T>C	ENSP00000365402:p.Met309Val	Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1690	0.7738095238095238	396	0.8048780487804879	290	0.8011049723756906	457	0.798951048951049	547	0.7216358839050132	.	0.934	-0.711867	0.03206	0.748521	0.63973	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00686	5.85;5.85	2.67	-3.63	0.04529	Immunoglobulin-like fold (1);	.	.	.	.	T	0.00109	0.0003	.	.	.	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.23440	-1.0188	7	0.02654	T	1	.	10.5811	0.45257	0.0:0.2105:0.0:0.7895	rs1050180;rs1065602;rs3177849;rs3190480;rs3206612;rs9264620;rs16868052	309;309;309;309	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	V	309;309;309;346	ENSP00000365402:M309V;ENSP00000372819:M309V	ENSP00000365402:M309V	M	-	1	0	HLA-C	31345812	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.290000	0.01148	-1.536000	0.01738	-1.923000	0.00514	ATG	T|0.255;C|0.740;A|0.005	0.740	strong		0.617	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
ERAP1	51752	hgsc.bcm.edu	37	5	96122210	96122210	+	Missense_Mutation	SNP	C	C	T	rs10050860	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:96122210C>T	ENST00000443439.2	-	12	1789	c.1723G>A	c.(1723-1725)Gac>Aac	p.D575N	ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000512856.1_RNA|ERAP1_ENST00000296754.3_Missense_Mutation_p.D575N|CTD-2260A17.1_ENST00000602972.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	575			D -> G (in dbSNP:rs6863093).|D -> N (in dbSNP:rs10050860). {ECO:0000269|PubMed:11481040, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:9628581}.		angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TGGACCATGTCGGATTTGCTG	0.343													.|||	532	0.10623	0.0651	0.1311	5008	,	,		21138	0.0575		0.2286	False		,,,				2504	0.0685				p.D575N		Atlas-SNP	.											.	ERAP1	59	.	0			c.G1723A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	452,3954	216.1+/-234.9	21,410,1772	114.0	109.0	111.0		1723,1723,1723	5.3	0.9	5	dbSNP_119	111	1831,6769	328.2+/-318.2	202,1427,2671	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	23,23,23	223,1837,4443	TT,TC,CC		21.2907,10.2587,17.5534	benign,benign,benign	575/942,575/942,575/949	96122210	2283,10723	2203	4300	6503	SO:0001583	missense	51752	exon12			CCATGTCGGATTT	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.1723G>A	5.37:g.96122210C>T	ENSP00000406304:p.Asp575Asn	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	289	0.13232600732600733	26	0.052845528455284556	50	0.13812154696132597	40	0.06993006993006994	173	0.22823218997361477	C	3.756	-0.050536	0.07407	0.102587	0.212907	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.01422	4.91;4.91	5.33	5.33	0.75918	.	0.810719	0.11919	N	0.516871	T	0.00012	0.0000	N	0.21240	0.645	0.48830	P	2.8799999999995496E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.43956	-0.9359	9	0.05436	T	0.98	.	5.2857	0.15700	0.1717:0.6701:0.0:0.1582	rs10050860;rs17482411;rs52797642;rs59271093;rs10050860	575;575;575	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	N	575	ENSP00000296754:D575N;ENSP00000406304:D575N	ENSP00000296754:D575N	D	-	1	0	ERAP1	96147966	0.386000	0.25180	0.937000	0.37676	0.703000	0.40648	0.514000	0.22786	2.500000	0.84329	0.484000	0.47621	GAC	C|0.855;T|0.145	0.145	strong		0.343	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
C2orf54	79919	hgsc.bcm.edu	37	2	241831005	241831005	+	Silent	SNP	C	C	T	rs10195453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:241831005C>T	ENST00000388934.4	-	2	848	c.690G>A	c.(688-690)agG>agA	p.R230R	C2orf54_ENST00000307486.8_Silent_p.R81R|C2orf54_ENST00000402775.2_Silent_p.R62R	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	230										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		GGCTGAGGATCCTTCTCAAGC	0.667													C|||	2637	0.526558	0.7784	0.3473	5008	,	,		18639	0.4405		0.5179	False		,,,				2504	0.411				p.R230R		Atlas-SNP	.											.	C2orf54	14	.	0			c.G690A						PASS	.	C	,	2972,1046		1107,758,144	49.0	58.0	55.0		690,186	0.1	0.0	2	dbSNP_119	55	4121,4201		1036,2049,1076	no	coding-synonymous,coding-synonymous	C2orf54	NM_001085437.1,NM_024861.2	,	2143,2807,1220	TT,TC,CC		49.5193,26.0329,42.5203	,	230/448,62/280	241831005	7093,5247	2009	4161	6170	SO:0001819	synonymous_variant	79919	exon2			GAGGATCCTTCTC	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.690G>A	2.37:g.241831005C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	37	CCDS42839.1																																																																																			C|0.497;T|0.503	0.503	strong		0.667	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
PCDHGA5	56110	hgsc.bcm.edu	37	5	140744395	140744395	+	Silent	SNP	T	T	C	rs57308563	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140744395T>C	ENST00000518069.1	+	1	498	c.498T>C	c.(496-498)tcT>tcC	p.S166S	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	166	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S166S(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGTGAACTCTCTCCGGAGTT	0.522													.|||	650	0.129792	0.3124	0.0692	5008	,	,		17442	0.0407		0.0875	False		,,,				2504	0.0613				p.S166S		Atlas-SNP	.											PCDHGA5_ENST00000518069,NS,carcinoma,0,1	PCDHGA5	215	1	1	Substitution - coding silent(1)	stomach(1)	c.T498C						PASS	.	C	,,,,,,,	1074,2976		129,816,1080	53.0	56.0	55.0		,,,,498,,,498	-3.3	0.9	5	dbSNP_129	55	749,7615		29,691,3462	no	intron,intron,intron,intron,coding-synonymous,intron,intron,coding-synonymous	PCDHGB2,PCDHGB1,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018922.2,NM_018923.2,NM_032054.1	,,,,,,,	158,1507,4542	CC,CT,TT		8.955,26.5185,14.685	,,,,,,,	,,,,166/932,,,166/814	140744395	1823,10591	2025	4182	6207	SO:0001819	synonymous_variant	56110	exon1			GAACTCTCTCCGG	AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"""Cadherins / Protocadherins : Clustered"""	8703	other	protocadherin	"""cadherin ME3"""	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.498T>C	5.37:g.140744395T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	187	86	0.459893	NM_032054	Q2M3F5|Q9Y5D2	Silent	SNP	ENST00000518069.1	37	CCDS54925.1																																																																																			T|0.882;C|0.118	0.118	strong		0.522	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918	
XPC	7508	hgsc.bcm.edu	37	3	14190078	14190078	+	Missense_Mutation	SNP	C	C	T	rs200148127	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:14190078C>T	ENST00000285021.7	-	13	2618	c.2404G>A	c.(2404-2406)Ggc>Agc	p.G802S	AC093495.4_ENST00000428681.3_RNA|AC093495.4_ENST00000420253.1_RNA|XPC_ENST00000449060.2_Missense_Mutation_p.G765S	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	802	DNA-binding; preference for single stranded DNA; required for formation of stable nucleoprotein complex.				DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGGGAGTAGCCGCCATGGAAA	0.602			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	8	0.00159744	0.0	0.0	5008	,	,		18202	0.0		0.0	False		,,,				2504	0.0082				p.G802S		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	XPC,colon,carcinoma,0,1	XPC	60	1	0			c.G2404A						scavenged	.	C	SER/GLY,SER/GLY	0,3984		0,0,1992	61.0	62.0	61.0		2293,2404	5.8	1.0	3		61	5,8329		0,5,4162	yes	missense,missense	XPC	NM_001145769.1,NM_004628.4	56,56	0,5,6154	TT,TC,CC		0.06,0.0,0.0406	probably-damaging,probably-damaging	765/904,802/941	14190078	5,12313	1992	4167	6159	SO:0001583	missense	7508	exon13	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGTAGCCGCCATG		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group C protein"""	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.2404G>A	3.37:g.14190078C>T	ENSP00000285021:p.Gly802Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	207	3	0.0144928	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	.	.	.	.	.	.	.	.	.	.	C	35	5.529571	0.96446	0.0	6.0E-4	ENSG00000154767	ENST00000285021;ENST00000449060	T;T	0.41758	0.99;1.04	5.79	5.79	0.91817	DNA repair protein Rad4, DNA-binding domain 3 (1);	0.000000	0.85682	D	0.000000	T	0.69333	0.3099	M	0.86028	2.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.65861	-0.6065	10	0.26408	T	0.33	-26.3465	20.0207	0.97499	0.0:1.0:0.0:0.0	.	765;802	E9PH69;Q01831	.;XPC_HUMAN	S	802;765	ENSP00000285021:G802S;ENSP00000404002:G765S	ENSP00000285021:G802S	G	-	1	0	XPC	14165079	1.000000	0.71417	0.997000	0.53966	0.839000	0.47603	7.586000	0.82596	2.739000	0.93911	0.563000	0.77884	GGC	.	.	weak		0.602	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
ARHGEF25	115557	hgsc.bcm.edu	37	12	58009372	58009372	+	Silent	SNP	G	G	A	rs2277323	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:58009372G>A	ENST00000286494.4	+	12	1576	c.1116G>A	c.(1114-1116)ctG>ctA	p.L372L	AC025165.8_ENST00000593846.1_RNA|ARHGEF25_ENST00000333972.7_Silent_p.L411L|AC025165.8_ENST00000610219.1_RNA|AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000356672.3_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	372	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L372L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						GAGGGCTGCTGTCTTCCCGAG	0.572													G|||	844	0.16853	0.0779	0.2839	5008	,	,		19322	0.1468		0.2197	False		,,,				2504	0.1789				p.L411L		Atlas-SNP	.											ARHGEF25,NS,carcinoma,0,1	ARHGEF25	111	1	1	Substitution - coding silent(1)	stomach(1)	c.G1233A						PASS	.	G	,	431,3975	208.5+/-229.5	19,393,1791	68.0	63.0	65.0		1233,1116	-9.4	0.0	12	dbSNP_100	65	2004,6596	349.3+/-327.4	244,1516,2540	no	coding-synonymous,coding-synonymous	ARHGEF25	NM_001111270.1,NM_182947.2	,	263,1909,4331	AA,AG,GG		23.3023,9.7821,18.7221	,	411/620,372/581	58009372	2435,10571	2203	4300	6503	SO:0001819	synonymous_variant	115557	exon13			GCTGCTGTCTTCC		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"""Rho guanine nucleotide exchange factors"""	30275	protein-coding gene	gene with protein product	"""RAC/CDC42 exchange factor"""	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1116G>A	12.37:g.58009372G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_001111270	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Silent	SNP	ENST00000286494.4	37	CCDS8947.1																																																																																			G|0.818;A|0.182	0.182	strong		0.572	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084435	31084435	+	Intron	SNP	G	G	A	rs1062470	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31084435G>A	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Silent_p.Y319Y	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGCCCACAGGGTAGATTTTAC	0.532													G|||	2259	0.451078	0.6172	0.4035	5008	,	,		18839	0.506		0.3519	False		,,,				2504	0.3057				p.Y319Y		Atlas-SNP	.											.	CDSN	48	.	0			c.C957T						PASS	.	G	,	2042,1972		548,946,513	36.0	34.0	35.0		957,	3.2	1.0	6	dbSNP_86	35	2465,5563		451,1563,2000	no	coding-synonymous,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	,	999,2509,2513	AA,AG,GG		30.705,49.1281,37.4273	,	319/530,	31084435	4507,7535	2007	4014	6021	SO:0001627	intron_variant	1041	exon2			CACAGGGTAGATT	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1767G>A	6.37:g.31084435G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	32	31	0.96875	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	37	CCDS34390.1																																																																																			G|0.569;A|0.431	0.431	strong		0.532	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
LY6G6F	259215	hgsc.bcm.edu	37	6	31675501	31675501	+	Missense_Mutation	SNP	G	G	A	rs9267547	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31675501G>A	ENST00000375832.4	+	2	341	c.319G>A	c.(319-321)Gct>Act	p.A107T	LY6G6F_ENST00000556581.1_Missense_Mutation_p.A107T|MEGT1_ENST00000503322.1_Missense_Mutation_p.A107T|XXbac-BPG32J3.20_ENST00000461287.1_Intron	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	107	Ig-like V-type.		A -> T (in dbSNP:rs9267547). {ECO:0000269|PubMed:14574404}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A107T(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	12						GTACTGGTGCGCTGTGCTAGG	0.577													G|||	755	0.150759	0.2882	0.1182	5008	,	,		20295	0.0893		0.0875	False		,,,				2504	0.1166				p.A107T		Atlas-SNP	.											LY6G6F,NS,lymphoid_neoplasm,0,1	LY6G6F	23	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G319A						PASS	.	G	THR/ALA	1077,3329	391.7+/-328.2	126,825,1252	70.0	61.0	64.0		319	0.9	0.0	6	dbSNP_118	64	791,7809	185.0+/-232.9	41,709,3550	yes	missense	LY6G6F	NM_001003693.1	58	167,1534,4802	AA,AG,GG		9.1977,24.4439,14.3626	benign	107/298	31675501	1868,11138	2203	4300	6503	SO:0001583	missense	259215	exon2			TGGTGCGCTGTGC		CCDS34403.1	6p21	2013-01-11	2008-05-21	2008-05-21		ENSG00000204424		"""Immunoglobulin superfamily / V-set domain containing"""	13933	protein-coding gene	gene with protein product		611404	"""chromosome 6 open reading frame 21"""	LY6G6D, C6orf21		12852788	Standard	NM_001003693		Approved	G6f, NG32	uc003nwa.1	Q5SQ64	OTTHUMG00000031252	ENST00000375832.4:c.319G>A	6.37:g.31675501G>A	ENSP00000364992:p.Ala107Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	197	98	0.497462	NM_001003693	B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Missense_Mutation	SNP	ENST00000375832.4	37	CCDS34403.1	314	0.14377289377289376	150	0.3048780487804878	45	0.12430939226519337	50	0.08741258741258741	69	0.09102902374670185	G	11.78	1.740009	0.30865	0.244439	0.091977	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	T;T;T	0.67865	-0.29;-0.29;-0.29	5.51	0.936	0.19488	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.333539	0.25584	N	0.029665	T	0.29028	0.0721	L	0.42245	1.32	0.80722	P	0.0	B;B	0.24576	0.106;0.106	B;B	0.17979	0.02;0.02	T	0.02326	-1.1176	9	0.29301	T	0.29	-0.0497	3.1427	0.06461	0.2529:0.0:0.4535:0.2936	rs9267547;rs17207364;rs59072028;rs9267547	107;107	Q9NZJ1;Q5SQ64	.;LY66F_HUMAN	T	107	ENSP00000452432:A107T;ENSP00000364992:A107T;ENSP00000421232:A107T	ENSP00000364992:A107T	A	+	1	0	XXbac-BPG32J3.19;LY6G6F	31783480	0.000000	0.05858	0.030000	0.17652	0.983000	0.72400	0.004000	0.13106	0.585000	0.29608	0.591000	0.81541	GCT	G|0.854;A|0.146	0.146	strong		0.577	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693	
PTPRC	5788	hgsc.bcm.edu	37	1	198704294	198704294	+	Silent	SNP	C	C	T	rs7540378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:198704294C>T	ENST00000367376.2	+	23	2481	c.2310C>T	c.(2308-2310)ggC>ggT	p.G770G	PTPRC_ENST00000442510.2_Silent_p.G772G|PTPRC_ENST00000594404.1_Silent_p.G609G|PTPRC_ENST00000348564.6_Silent_p.G611G|PTPRC_ENST00000352140.3_Silent_p.G722G	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	770	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						TGGAAGAGGGCACTCGGGCTT	0.318													C|||	1133	0.226238	0.2738	0.2968	5008	,	,		13598	0.2361		0.1163	False		,,,				2504	0.2147				p.G772G		Atlas-SNP	.											.	PTPRC	229	.	0			c.C2316T						PASS	.	C	,	1083,3323	385.8+/-325.9	131,821,1251	83.0	80.0	81.0		2310,1827	0.7	0.5	1	dbSNP_116	81	1048,7550	220.2+/-258.0	59,930,3310	no	coding-synonymous,coding-synonymous	PTPRC	NM_002838.3,NM_080921.2	,	190,1751,4561	TT,TC,CC		12.1889,24.5801,16.3873	,	770/1305,609/1144	198704294	2131,10873	2203	4299	6502	SO:0001819	synonymous_variant	5788	exon23			AGAGGGCACTCGG	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.2310C>T	1.37:g.198704294C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	194	99	0.510309	NM_002838	A8K7W6|Q16614|Q9H0Y6	Silent	SNP	ENST00000367376.2	37																																																																																				C|0.817;T|0.183	0.183	strong		0.318	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
KRTAP10-5	386680	hgsc.bcm.edu	37	21	45999753	45999753	+	Missense_Mutation	SNP	C	C	G	rs464424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:45999753C>G	ENST00000400372.1	-	1	728	c.703G>C	c.(703-705)Gtg>Ctg	p.V235L	TSPEAR_ENST00000323084.4_Intron	NM_198694.2	NP_941967.2	P60370	KR105_HUMAN	keratin associated protein 10-5	235	22 X 5 AA repeats of C-C-X(3).		V -> L (in dbSNP:rs464424). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				endometrium(2)|kidney(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	14						GAGATGGGCACGCAGCAGGCG	0.711													.|||	589	0.117612	0.0923	0.0634	5008	,	,		18363	0.2024		0.0626	False		,,,				2504	0.1595				p.V235L		Atlas-SNP	.											.	KRTAP10-5	43	.	0			c.G703C						PASS	.	C	,LEU/VAL	417,3989	194.7+/-219.5	20,377,1806	51.0	61.0	58.0		,703	1.7	0.0	21	dbSNP_80	58	430,8168	129.5+/-187.6	15,400,3884	no	intron,missense	TSPEAR,KRTAP10-5	NM_144991.2,NM_198694.2	,32	35,777,5690	GG,GC,CC		5.0012,9.4644,6.5134	,probably-damaging	,235/272	45999753	847,12157	2203	4299	6502	SO:0001583	missense	386680	exon1			TGGGCACGCAGCA	AJ566384	CCDS42958.1	21q22.3	2007-10-05			ENSG00000241123	ENSG00000241123		"""Keratin associated proteins"""	22969	protein-coding gene	gene with protein product				KRTAP18-5			Standard	NM_198694		Approved	KAP10.5, KAP18.5	uc002zfl.1	P60370	OTTHUMG00000057638	ENST00000400372.1:c.703G>C	21.37:g.45999753C>G	ENSP00000383223:p.Val235Leu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	47	31	0.659574	NM_198694	Q0VAR7|Q0VAR8|Q70LJ3	Missense_Mutation	SNP	ENST00000400372.1	37	CCDS42958.1	226	0.10347985347985347	40	0.08130081300813008	24	0.06629834254143646	122	0.21328671328671328	40	0.052770448548812667	c	9.845	1.192015	0.21954	0.094644	0.050012	ENSG00000241123	ENST00000400372	T	0.00753	5.74	3.59	1.68	0.24146	.	.	.	.	.	T	0.00012	0.0000	M	0.80616	2.505	0.80722	P	0.0	D	0.56287	0.975	D	0.63597	0.916	T	0.44892	-0.9298	8	0.66056	D	0.02	.	6.6908	0.23169	0.0:0.7117:0.1807:0.1076	rs464424	235	P60370	KR105_HUMAN	L	235	ENSP00000383223:V235L	ENSP00000383223:V235L	V	-	1	0	KRTAP10-5	44824181	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	-0.031000	0.12287	0.290000	0.22444	-0.384000	0.06662	GTG	C|0.913;G|0.087	0.087	strong		0.711	KRTAP10-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128042.1		
TBX1	6899	hgsc.bcm.edu	37	22	19750773	19750773	+	Silent	SNP	T	T	C	rs41298814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:19750773T>C	ENST00000329705.7	+	4	549	c.420T>C	c.(418-420)ttT>ttC	p.F140F	TBX1_ENST00000332710.4_Silent_p.F140F|TBX1_ENST00000359500.3_Silent_p.F140F	NM_080646.1	NP_542377.1	O43435	TBX1_HUMAN	T-box 1	140					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|aorta morphogenesis (GO:0035909)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|blood vessel morphogenesis (GO:0048514)|blood vessel remodeling (GO:0001974)|cell fate specification (GO:0001708)|cell proliferation (GO:0008283)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|coronary artery morphogenesis (GO:0060982)|determination of left/right symmetry (GO:0007368)|ear morphogenesis (GO:0042471)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic viscerocranium morphogenesis (GO:0048703)|enamel mineralization (GO:0070166)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|lymph vessel development (GO:0001945)|mesenchymal cell apoptotic process (GO:0097152)|mesoderm development (GO:0007498)|middle ear morphogenesis (GO:0042474)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle organ morphogenesis (GO:0048644)|muscle tissue morphogenesis (GO:0060415)|negative regulation of cell differentiation (GO:0045596)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|parathyroid gland development (GO:0060017)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of tongue muscle cell differentiation (GO:2001037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of organ morphogenesis (GO:2000027)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retinoic acid receptor signaling pathway (GO:0048384)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|social behavior (GO:0035176)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tongue morphogenesis (GO:0043587)|transcription, DNA-templated (GO:0006351)|vagus nerve morphogenesis (GO:0021644)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|lung(3)|ovary(2)	8	Colorectal(54;0.0993)	all_lung(157;3.05e-06)				GGCGGATGTTTCCCACCTTCC	0.637													C|||	1143	0.228235	0.0227	0.2781	5008	,	,		18183	0.4583		0.2187	False		,,,				2504	0.2434				p.F140F		Atlas-SNP	.											.	TBX1	62	.	0			c.T420C						PASS	.	C	,,	196,4210	807.3+/-415.9	11,174,2018	132.0	101.0	112.0		420,420,420	5.1	1.0	22	dbSNP_127	112	1940,6660	721.7+/-406.4	249,1442,2609	no	coding-synonymous,coding-synonymous,coding-synonymous	TBX1	NM_005992.1,NM_080646.1,NM_080647.1	,,	260,1616,4627	CC,CT,TT		22.5581,4.4485,16.4232	,,	140/373,140/399,140/496	19750773	2136,10870	2203	4300	6503	SO:0001819	synonymous_variant	6899	exon4			GATGTTTCCCACC	AF012131	CCDS13765.1, CCDS13766.1, CCDS13767.1	22q11.21	2014-09-17			ENSG00000184058	ENSG00000184058		"""T-boxes"""	11592	protein-coding gene	gene with protein product		602054	"""velocardiofacial syndrome"""	VCF		9268629, 23000736	Standard	NM_080646		Approved	CATCH22	uc002zqa.1	O43435	OTTHUMG00000150421	ENST00000329705.7:c.420T>C	22.37:g.19750773T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	NM_080647	C6G493|C6G494|O43436|Q96RJ2	Silent	SNP	ENST00000329705.7	37	CCDS13766.1																																																																																			T|0.808;C|0.192	0.192	strong		0.637	TBX1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318033.1	NM_080647	
FAM196A	642938	hgsc.bcm.edu	37	10	128974220	128974220	+	Missense_Mutation	SNP	G	G	A	rs11594560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:128974220G>A	ENST00000522781.1	-	4	995	c.440C>T	c.(439-441)gCg>gTg	p.A147V	DOCK1_ENST00000280333.6_Intron|FAM196A_ENST00000424811.2_Missense_Mutation_p.A147V	NM_001039762.2	NP_001034851.1	Q6ZSG2	F196A_HUMAN	family with sequence similarity 196, member A	147			A -> V (in dbSNP:rs11594560).							breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CTTCTCTTTCGCATCTGTTAG	0.547													G|||	830	0.165735	0.0446	0.2133	5008	,	,		17929	0.0347		0.2793	False		,,,				2504	0.3139				p.A147V		Atlas-SNP	.											.	FAM196A	55	.	0			c.C440T						PASS	.	G	VAL/ALA,	341,4065	178.0+/-206.8	14,313,1876	90.0	85.0	87.0		440,	2.6	0.0	10	dbSNP_120	87	2355,6245	393.7+/-344.5	324,1707,2269	yes	missense,intron	DOCK1,FAM196A	NM_001039762.2,NM_001380.3	64,	338,2020,4145	AA,AG,GG		27.3837,7.7394,20.7289	benign,	147/480,	128974220	2696,10310	2203	4300	6503	SO:0001583	missense	642938	exon4			TCTTTCGCATCTG		CCDS31312.1	10q26.2	2009-09-11	2009-09-11	2009-09-11		ENSG00000188916			33859	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 141"""	C10orf141			Standard	NM_001039762		Approved	FLJ45557	uc001ljv.1	Q6ZSG2		ENST00000522781.1:c.440C>T	10.37:g.128974220G>A	ENSP00000429763:p.Ala147Val	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	188	92	0.489362	NM_001039762	B2RNT4|B7ZME7	Missense_Mutation	SNP	ENST00000522781.1	37	CCDS31312.1	346	0.15842490842490842	27	0.054878048780487805	92	0.2541436464088398	12	0.02097902097902098	215	0.2836411609498681	G	0.008	-1.931052	0.00488	0.077394	0.273837	ENSG00000188916	ENST00000522781;ENST00000424811	T;T	0.42513	0.97;0.97	4.46	2.58	0.30949	.	1.061370	0.07259	N	0.867102	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B	0.13145	0.007;0.003	B;B	0.09377	0.001;0.004	T	0.35375	-0.9791	9	0.02654	T	1	.	6.43	0.21790	0.3258:0.0:0.6742:0.0	rs11594560;rs56480626;rs60757760;rs11594560	147;147	B7ZME7;Q6ZSG2	.;F196A_HUMAN	V	147	ENSP00000429763:A147V;ENSP00000428730:A147V	ENSP00000428730:A147V	A	-	2	0	FAM196A	128864210	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	0.577000	0.23758	1.180000	0.42898	0.563000	0.77884	GCG	G|0.829;A|0.171	0.171	strong		0.547	FAM196A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050978.2	NM_001039762	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240692	39240692	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240692G>C	ENST00000391417.4	+	1	234	c.234G>C	c.(232-234)agG>agC	p.R78S		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	78	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						gccaccctaggtgctgcatct	0.667																																					p.R78S		Atlas-SNP	.											KRTAP4-9_ENST00000377734,colon,carcinoma,0,2	KRTAP4-7	49	2	0			c.G234C						scavenged	.																																			SO:0001583	missense	100132476	exon1			CCCTAGGTGCTGC	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.234G>C	17.37:g.39240692G>C	ENSP00000375236:p.Arg78Ser	Somatic	44	1	0.0227273		WXS	Illumina HiSeq	Phase_I	49	7	0.142857	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.666022	0.00105	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00547	6.66	2.45	-4.9	0.03094	.	1.381260	0.05066	N	0.480753	T	0.00210	0.0006	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41070	-0.9529	9	0.02654	T	1	.	3.5468	0.07831	0.1616:0.2372:0.4895:0.1118	.	78	Q9BYR0	KRA47_HUMAN	S	78;69	ENSP00000375236:R78S	ENSP00000375236:R78S	R	+	3	2	KRTAP4-9;KRTAP4-7	36494218	0.000000	0.05858	0.005000	0.12908	0.273000	0.26683	-0.900000	0.04097	-0.963000	0.03600	-2.430000	0.00215	AGG	.	.	none		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
OR5M9	390162	hgsc.bcm.edu	37	11	56230069	56230069	+	Missense_Mutation	SNP	T	T	C	rs1945237	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56230069T>C	ENST00000279791.1	-	1	808	c.809A>G	c.(808-810)aAa>aGa	p.K270R		NM_001004743.1	NP_001004743.1	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M, member 9	270			K -> R (in dbSNP:rs1945237).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	36	Esophageal squamous(21;0.00448)					AGCCACCATTTTGCCCTGCTC	0.453													t|||	182	0.0363419	0.003	0.0432	5008	,	,		19655	0.001		0.0934	False		,,,				2504	0.0542				p.K270R		Atlas-SNP	.											.	OR5M9	75	.	0			c.A809G						PASS	.	T	ARG/LYS	55,4347	53.6+/-89.4	0,55,2146	93.0	81.0	85.0		809	4.3	0.5	11	dbSNP_92	85	692,7900	171.3+/-222.3	35,622,3639	yes	missense	OR5M9	NM_001004743.1	26	35,677,5785	CC,CT,TT		8.054,1.2494,5.7488	probably-damaging	270/311	56230069	747,12247	2201	4296	6497	SO:0001583	missense	390162	exon1			ACCATTTTGCCCT	AB065747	CCDS31531.1	11q11	2012-08-09			ENSG00000150269	ENSG00000150269		"""GPCR / Class A : Olfactory receptors"""	15294	protein-coding gene	gene with protein product							Standard	NM_001004743		Approved		uc010rjj.2	Q8NGP3	OTTHUMG00000166874	ENST00000279791.1:c.809A>G	11.37:g.56230069T>C	ENSP00000279791:p.Lys270Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	138	74	0.536232	NM_001004743	Q6IEW5|Q96RB9	Missense_Mutation	SNP	ENST00000279791.1	37	CCDS31531.1	84	0.038461538461538464	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	70	0.09234828496042216	T	13.42	2.231716	0.39399	0.012494	0.08054	ENSG00000150269	ENST00000279791	T	0.00188	8.59	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45361	D	0.000362	T	0.00039	0.0001	L	0.58669	1.825	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51702	-0.8672	10	0.72032	D	0.01	-15.7678	11.6683	0.51387	0.0:0.0:0.0:1.0	rs1945237;rs52806456;rs59415383;rs1945237	270	Q8NGP3	OR5M9_HUMAN	R	270	ENSP00000279791:K270R	ENSP00000279791:K270R	K	-	2	0	OR5M9	55986645	0.028000	0.19301	0.466000	0.27168	0.275000	0.26752	1.180000	0.32005	1.707000	0.51288	0.443000	0.29094	AAA	T|0.951;C|0.049	0.049	strong		0.453	OR5M9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391638.1	NM_001004743	
GPR146	115330	hgsc.bcm.edu	37	7	1097895	1097895	+	Silent	SNP	A	A	G	rs61910751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1097895A>G	ENST00000397095.1	+	2	967	c.744A>G	c.(742-744)ccA>ccG	p.P248P	C7orf50_ENST00000397100.2_Intron|GPR146_ENST00000297468.3_Silent_p.P248P|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000357429.6_Intron			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		TCTGGACGCCACACTATCTGA	0.647													G|||	345	0.0688898	0.0204	0.0821	5008	,	,		17834	0.0		0.1262	False		,,,				2504	0.137				p.P248P		Atlas-SNP	.											.	GPR146	20	.	0			c.A744G						PASS	.		,,,	206,4198	800.2+/-415.6	2,202,1998	59.0	48.0	52.0		,,,744	-10.2	0.0	7	dbSNP_129	52	1354,7244	751.8+/-407.4	106,1142,3051	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	108,1344,5049	GG,GA,AA		15.7478,4.6776,11.9982	,,,	,,,248/334	1097895	1560,11442	2202	4299	6501	SO:0001819	synonymous_variant	115330	exon1			GACGCCACACTAT	BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"""GPCR / Class A : Orphans"""	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.744A>G	7.37:g.1097895A>G		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_138445	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																			A|0.893;G|0.106;T|0.000	0.106	strong		0.647	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
MARCH2	51257	hgsc.bcm.edu	37	19	8486884	8486884	+	Missense_Mutation	SNP	G	G	A	rs1133893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8486884G>A	ENST00000602117.1	+	2	615	c.160G>A	c.(160-162)Gcc>Acc	p.A54T	MARCH2_ENST00000215555.2_Missense_Mutation_p.A54T|RP11-886P16.6_ENST00000595706.1_RNA|MARCH2_ENST00000381035.4_Missense_Mutation_p.A54T|MARCH2_ENST00000601283.1_Intron|MARCH2_ENST00000393944.1_Missense_Mutation_p.A54T			Q9P0N8	MARH2_HUMAN	membrane-associated ring finger (C3HC4) 2, E3 ubiquitin protein ligase	54			A -> T (in dbSNP:rs1133893). {ECO:0000269|PubMed:15489334}.		endocytosis (GO:0006897)|protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|skin(1)|urinary_tract(1)	10						CGTCATCCGTGCCTTGGACAC	0.607													G|||	996	0.198882	0.0348	0.2723	5008	,	,		18467	0.2381		0.2922	False		,,,				2504	0.2321				p.A54T		Atlas-SNP	.											MARCH2,NS,carcinoma,0,1	MARCH2	17	1	0			c.G160A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	420,3986	204.1+/-226.4	23,374,1806	87.0	69.0	75.0		160,160,160	4.6	1.0	19	dbSNP_86	75	2872,5728	450.7+/-362.5	470,1932,1898	yes	missense,missense,missense	MARCH2	NM_001005415.1,NM_001005416.1,NM_016496.4	58,58,58	493,2306,3704	AA,AG,GG		33.3953,9.5325,25.3114	benign,benign,benign	54/247,54/177,54/247	8486884	3292,9714	2203	4300	6503	SO:0001583	missense	51257	exon2			ATCCGTGCCTTGG	AF151074	CCDS12202.1, CCDS32894.1	19p13.2	2013-01-09	2012-02-23			ENSG00000099785		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	28038	protein-coding gene	gene with protein product		613332	"""membrane-associated ring finger (C3HC4) 2"""			11042152, 14722266	Standard	NM_016496		Approved	HSPC240, MARCH-II, RNF172	uc002mjw.3	Q9P0N8		ENST00000602117.1:c.160G>A	19.37:g.8486884G>A	ENSP00000471536:p.Ala54Thr	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	52	22	0.423077	NM_001005415	A6NP10|Q5H785|Q8N5A3|Q96B78	Missense_Mutation	SNP	ENST00000602117.1	37	CCDS12202.1	476	0.21794871794871795	22	0.044715447154471545	109	0.3011049723756906	124	0.21678321678321677	221	0.29155672823219	G	14.98	2.696507	0.48202	0.095325	0.333953	ENSG00000099785	ENST00000393944;ENST00000215555;ENST00000381035	T;T;T	0.15017	2.46;2.46;2.46	5.65	4.6	0.57074	.	0.109437	0.64402	D	0.000010	T	0.00012	0.0000	L	0.52364	1.645	0.19775	P	0.999951435	B;B	0.30851	0.05;0.297	B;B	0.33890	0.073;0.172	T	0.46233	-0.9206	9	0.13853	T	0.58	-19.541	14.7238	0.69329	0.0:0.0:0.854:0.146	rs1133893;rs3196037;rs11540064;rs11882865;rs17352509;rs17846004;rs17858988;rs58815990;rs11882865	54;54	Q9P0N8-2;Q9P0N8	.;MARH2_HUMAN	T	54	ENSP00000377518:A54T;ENSP00000215555:A54T;ENSP00000370423:A54T	ENSP00000215555:A54T	A	+	1	0	MARCH2	8392884	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.156000	0.58138	1.362000	0.46000	0.555000	0.69702	GCC	T|0.034;G|0.603;C|0.163;A|0.200	0.200	strong		0.607	MARCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460361.2	NM_016496	
STAT2	6773	hgsc.bcm.edu	37	12	56740738	56740738	+	Splice_Site	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56740738G>A	ENST00000314128.4	-	20	1749	c.1726C>T	c.(1726-1728)Cgc>Tgc	p.R576C	STAT2_ENST00000556539.1_5'UTR|STAT2_ENST00000557235.1_Splice_Site_p.R572C			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	576	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						CCCATGATGCGTCTGGAGCAC	0.607																																					p.R576C		Atlas-SNP	.											.	STAT2	70	.	0			c.C1726T						PASS	.						63.0	56.0	58.0					12																	56740738		2203	4300	6503	SO:0001630	splice_region_variant	6773	exon20			TGATGCGTCTGGA	BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"""SH2 domain containing"""	11363	protein-coding gene	gene with protein product		600556	"""signal transducer and activator of transcription 2, 113kD"""			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1725-1C>T	12.37:g.56740738G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_005419	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Missense_Mutation	SNP	ENST00000314128.4	37	CCDS8917.1	.	.	.	.	.	.	.	.	.	.	G	10.90	1.480269	0.26598	.	.	ENSG00000170581	ENST00000314128;ENST00000557235	D;D	0.96459	-4.02;-4.02	5.76	1.27	0.21489	SH2 motif (2);EF-hand-like domain (1);	0.907952	0.09678	N	0.770112	D	0.89681	0.6785	N	0.08118	0	0.09310	N	0.999993	B;B	0.17465	0.0;0.022	B;B	0.15484	0.002;0.013	T	0.79610	-0.1732	10	0.36615	T	0.2	3.6003	9.3617	0.38199	0.3354:0.0:0.6646:0.0	.	572;576	G3V2M6;P52630	.;STAT2_HUMAN	C	576;572	ENSP00000315768:R576C;ENSP00000450751:R572C	ENSP00000315768:R576C	R	-	1	0	STAT2	55027005	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.091000	0.15046	0.031000	0.15407	-0.229000	0.12294	CGC	.	.	none		0.607	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419	Missense_Mutation
ANKRD35	148741	hgsc.bcm.edu	37	1	145561116	145561116	+	Silent	SNP	G	G	A	rs11578772	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:145561116G>A	ENST00000355594.4	+	10	891	c.804G>A	c.(802-804)caG>caA	p.Q268Q	ANKRD35_ENST00000544626.1_3'UTR	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	268										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTGAGCCCCAGGCAGGTTCTC	0.527													G|||	183	0.0365415	0.0023	0.0692	5008	,	,		19121	0.0		0.1133	False		,,,				2504	0.0184				p.Q268Q	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.G804A						PASS	.	G		115,4291	81.4+/-119.9	5,105,2093	35.0	41.0	39.0		804	0.8	0.9	1	dbSNP_120	39	1073,7527	221.5+/-258.9	75,923,3302	no	coding-synonymous	ANKRD35	NM_144698.3		80,1028,5395	AA,AG,GG		12.4767,2.6101,9.1342		268/1002	145561116	1188,11818	2203	4300	6503	SO:0001819	synonymous_variant	148741	exon10			GCCCCAGGCAGGT	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.804G>A	1.37:g.145561116G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	145	73	0.503448	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Silent	SNP	ENST00000355594.4	37	CCDS919.1																																																																																			G|0.922;A|0.078	0.078	strong		0.527	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
OR8G5	219865	hgsc.bcm.edu	37	11	124135619	124135619	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124135619T>C	ENST00000524943.2	+	1	897	c.897T>C	c.(895-897)tcT>tcC	p.S299S	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	299						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		AGCCATCATCTGTCAGCTCCA	0.507																																					p.S299S	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.T897C						PASS	.						106.0	104.0	105.0					11																	124135619		2109	4260	6369	SO:0001819	synonymous_variant	219865	exon1			ATCATCTGTCAGC	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.897T>C	11.37:g.124135619T>C		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	311	22	0.0707396	NM_001005198	B2RND3|Q6IEU6	Silent	SNP	ENST00000524943.2	37																																																																																				.	.	none		0.507	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
GPR98	84059	hgsc.bcm.edu	37	5	90012379	90012379	+	Missense_Mutation	SNP	G	G	A	rs13157270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:90012379G>A	ENST00000405460.2	+	43	9376	c.9280G>A	c.(9280-9282)Gtc>Atc	p.V3094I		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3094	Calx-beta 22. {ECO:0000255}.		V -> I (in dbSNP:rs13157270).		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGCTCTCTACGTCCAGGAGAG	0.443													G|||	233	0.0465256	0.0144	0.0331	5008	,	,		17257	0.004		0.1093	False		,,,				2504	0.0787				p.V3094I		Atlas-SNP	.											.	GPR98	605	.	0			c.G9280A						PASS	.	G	ILE/VAL	106,3604		2,102,1751	74.0	68.0	70.0		9280	-3.0	0.0	5	dbSNP_121	70	668,7524		25,618,3453	yes	missense	GPR98	NM_032119.3	29	27,720,5204	AA,AG,GG		8.1543,2.8571,6.5031	benign	3094/6307	90012379	774,11128	1855	4096	5951	SO:0001583	missense	84059	exon43			CTCTACGTCCAGG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.9280G>A	5.37:g.90012379G>A	ENSP00000384582:p.Val3094Ile	Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	189	88	0.465608	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	100	0.045787545787545784	3	0.006097560975609756	10	0.027624309392265192	0	0.0	87	0.11477572559366754	G	5.982	0.365041	0.11296	0.028571	0.081543	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.27557	1.66	6.01	-2.95	0.05564	Na-Ca exchanger/integrin-beta4 (1);	0.625852	0.17566	N	0.169654	T	0.00241	0.0007	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	B;B	0.14438	0.007;0.01	B;B	0.06405	0.002;0.001	T	0.20472	-1.0274	9	0.20046	T	0.44	.	4.0796	0.09921	0.4734:0.0798:0.3238:0.1229	rs13157270;rs52824610;rs60759220;rs13157270	3094;3094	E7ETI5;Q8WXG9	.;GPR98_HUMAN	I	3094	ENSP00000384582:V3094I	ENSP00000296619:V3094I	V	+	1	0	GPR98	90048135	0.000000	0.05858	0.001000	0.08648	0.158000	0.22134	-1.264000	0.02847	-0.291000	0.09012	-0.127000	0.14921	GTC	G|0.950;A|0.050	0.050	strong		0.443	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
FLNC	2318	hgsc.bcm.edu	37	7	128481578	128481578	+	Missense_Mutation	SNP	A	A	C	rs34972246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:128481578A>C	ENST00000325888.8	+	13	2339	c.2078A>C	c.(2077-2079)gAt>gCt	p.D693A	FLNC_ENST00000346177.6_Missense_Mutation_p.D693A	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	693					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TTCACCATTGATGCTCGTGCA	0.607													A|||	10	0.00199681	0.0008	0.0014	5008	,	,		20237	0.0		0.005	False		,,,				2504	0.0031				p.D693A		Atlas-SNP	.											.	FLNC	339	.	0			c.A2078C						PASS	.	A	ALA/ASP,ALA/ASP	5,4075		0,5,2035	139.0	144.0	142.0		2078,2078	5.6	1.0	7	dbSNP_126	142	45,8355		0,45,4155	yes	missense,missense	FLNC	NM_001127487.1,NM_001458.4	126,126	0,50,6190	CC,CA,AA		0.5357,0.1225,0.4006	benign,benign	693/2693,693/2726	128481578	50,12430	2040	4200	6240	SO:0001583	missense	2318	exon13			CCATTGATGCTCG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.2078A>C	7.37:g.128481578A>C	ENSP00000327145:p.Asp693Ala	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	167	72	0.431138	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	35	5.430186	0.96131	0.001225	0.005357	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.85411	-1.98;-1.98	5.57	5.57	0.84162	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93167	0.7824	H	0.95950	3.745	0.58432	D	0.999999	D;P	0.89917	1.0;0.923	D;P	0.91635	0.999;0.85	D	0.94673	0.7858	10	0.87932	D	0	.	15.7306	0.77800	1.0:0.0:0.0:0.0	rs34972246	693;693	Q14315-2;Q14315	.;FLNC_HUMAN	A	693	ENSP00000327145:D693A;ENSP00000344002:D693A	ENSP00000327145:D693A	D	+	2	0	FLNC	128268814	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	7.035000	0.76517	2.117000	0.64856	0.459000	0.35465	GAT	A|0.996;C|0.004	0.004	strong		0.607	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
C12orf54	121273	hgsc.bcm.edu	37	12	48884610	48884610	+	Missense_Mutation	SNP	C	C	T	rs61940778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48884610C>T	ENST00000548364.1	+	5	241	c.184C>T	c.(184-186)Cgg>Tgg	p.R62W	C12orf54_ENST00000314014.2_Missense_Mutation_p.R62W|RP11-722P11.4_ENST00000551847.1_RNA			Q6X4T0	CL054_HUMAN	chromosome 12 open reading frame 54	62										endometrium(1)|large_intestine(4)	5						GGAAGATGCTCGGATTCGAGG	0.433													C|||	122	0.024361	0.0023	0.049	5008	,	,		20210	0.001		0.0726	False		,,,				2504	0.0112				p.R62W		Atlas-SNP	.											.	C12orf54	11	.	0			c.C184T						PASS	.		TRP/ARG	61,4345	59.9+/-96.7	1,59,2143	149.0	148.0	149.0		184	4.2	1.0	12	dbSNP_129	149	651,7949	166.4+/-218.3	24,603,3673	yes	missense	C12orf54	NM_152319.3	101	25,662,5816	TT,TC,CC		7.5698,1.3845,5.4744	possibly-damaging	62/128	48884610	712,12294	2203	4300	6503	SO:0001583	missense	121273	exon6			GATGCTCGGATTC	BC031670	CCDS8764.1	12q13.11	2011-01-31			ENSG00000177627	ENSG00000177627			28553	protein-coding gene	gene with protein product						12477932	Standard	NM_152319		Approved	MGC35033	uc001rrr.3	Q6X4T0	OTTHUMG00000170019	ENST00000548364.1:c.184C>T	12.37:g.48884610C>T	ENSP00000447109:p.Arg62Trp	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_152319	Q6X4S9|Q8N5S2	Missense_Mutation	SNP	ENST00000548364.1	37	CCDS8764.1	69	0.03159340659340659	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	49	0.06464379947229551	C	12.50	1.956017	0.34471	0.013845	0.075698	ENSG00000177627	ENST00000314014;ENST00000548364	T;T	0.59906	0.23;0.23	5.06	4.15	0.48705	.	0.000000	0.41500	D	0.000878	T	0.06962	0.0177	N	0.24115	0.695	0.25024	N	0.991315	D	0.76494	0.999	D	0.64042	0.921	T	0.06180	-1.0841	10	0.87932	D	0	-12.3093	11.6184	0.51102	0.0:0.8208:0.1792:0.0	rs61940778	62	Q6X4T0	CL054_HUMAN	W	62	ENSP00000316898:R62W;ENSP00000447109:R62W	ENSP00000316898:R62W	R	+	1	2	C12orf54	47170877	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.842000	0.48230	1.477000	0.48234	0.645000	0.84053	CGG	C|0.954;T|0.046	0.046	strong		0.433	C12orf54-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406875.1	NM_152319	
SRRM1	10250	hgsc.bcm.edu	37	1	24993374	24993374	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:24993374C>A	ENST00000323848.9	+	13	2012	c.1697C>A	c.(1696-1698)cCt>cAt	p.P566H	SRRM1_ENST00000537199.1_3'UTR|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000374389.4_Missense_Mutation_p.P575H|SRRM1_ENST00000447431.2_Missense_Mutation_p.P578H|SRRM1_ENST00000479034.1_3'UTR	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	566	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.P566H(2)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CCCGCCCCTCCTCCTCGACGG	0.542																																					p.P566H	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											SRRM1,bladder,carcinoma,0,2	SRRM1	81	2	2	Substitution - Missense(2)	urinary_tract(1)|central_nervous_system(1)	c.C1697A						scavenged	.						53.0	45.0	48.0					1																	24993374		2203	4300	6503	SO:0001583	missense	10250	exon13			CCCCTCCTCCTCG	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1697C>A	1.37:g.24993374C>A	ENSP00000326261:p.Pro566His	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	140	4	0.0285714	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.173271	0.78452	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.56776	0.44;0.65;0.71	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000007	T	0.70613	0.3244	L	0.58101	1.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.68074	-0.5505	10	0.42905	T	0.14	-3.0627	19.3453	0.94361	0.0:1.0:0.0:0.0	.	578;566	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	H	566;578;575	ENSP00000326261:P566H;ENSP00000391430:P578H;ENSP00000363510:P575H	ENSP00000326261:P566H	P	+	2	0	SRRM1	24865961	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	4.865000	0.62998	2.654000	0.90174	0.650000	0.86243	CCT	.	.	none		0.542	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
ATG4B	23192	hgsc.bcm.edu	37	2	242610172	242610172	+	Missense_Mutation	SNP	A	A	G	rs138274580	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242610172A>G	ENST00000404914.3	+	11	1092	c.989A>G	c.(988-990)aAt>aGt	p.N330S	ATG4B_ENST00000405546.3_Missense_Mutation_p.N330S|ATG4B_ENST00000396411.3_Missense_Mutation_p.N256S|ATG4B_ENST00000402096.1_Missense_Mutation_p.N256S|ATG4B_ENST00000474739.2_Missense_Mutation_p.N316S	NM_013325.4|NM_178326.2	NP_037457.3|NP_847896.1	Q9Y4P1	ATG4B_HUMAN	autophagy related 4B, cysteine peptidase	330					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|positive regulation of autophagy (GO:0010508)|positive regulation of protein catabolic process (GO:0045732)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)			breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		GATGACTTCAATGATTGGTGC	0.557													a|||	391	0.0780751	0.1536	0.0259	5008	,	,		19379	0.0675		0.0099	False		,,,				2504	0.0941				p.N330S	Melanoma(78;458 1323 6342 12171 39523)	Atlas-SNP	.											.	ATG4B	35	.	0			c.A989G						PASS	.	G	SER/ASN,SER/ASN	525,3375		25,475,1450	74.0	74.0	74.0		989,989	3.3	0.0	2	dbSNP_134	74	112,8138		3,106,4016	yes	missense,missense	ATG4B	NM_013325.4,NM_178326.2	46,46	28,581,5466	GG,GA,AA		1.3576,13.4615,5.2428	benign,benign	330/394,330/381	242610172	637,11513	1950	4125	6075	SO:0001583	missense	23192	exon11			ACTTCAATGATTG	AB023160	CCDS46564.1, CCDS46565.1	2q37.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000168397	ENSG00000168397			20790	protein-coding gene	gene with protein product		611338	"""APG4 autophagy 4 homolog B (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog B (S. cerevisiae)"""	APG4B		12446702	Standard	NM_013325		Approved	Apg4B, KIAA0943, DKFZp586D1822, AUTL1	uc002wbv.3	Q9Y4P1	OTTHUMG00000151514	ENST00000404914.3:c.989A>G	2.37:g.242610172A>G	ENSP00000384259:p.Asn330Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	148	60	0.405405	NM_178326	B7WNK2|Q53NU4|Q6ZUV8|Q8WYM9|Q96K07|Q96K96|Q96SZ1|Q9Y2F2	Missense_Mutation	SNP	ENST00000404914.3	37	CCDS46564.1	120	0.054945054945054944	70	0.14227642276422764	9	0.024861878453038673	36	0.06293706293706294	5	0.006596306068601583	a	11.78	1.739671	0.30774	0.134615	0.013576	ENSG00000168397	ENST00000405546;ENST00000337606;ENST00000402096;ENST00000404914;ENST00000474739;ENST00000396411;ENST00000428861	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	5.66	3.29	0.37713	.	0.261099	0.44902	N	0.000402	T	0.00300	0.0009	L	0.56769	1.78	0.80722	P	0.0	B;B;B;B;B;B	0.32031	0.082;0.061;0.352;0.171;0.002;0.024	B;B;B;B;B;B	0.28916	0.043;0.063;0.061;0.096;0.027;0.026	T	0.05869	-1.0859	9	0.33940	T	0.23	-12.2164	10.7049	0.45950	0.882:0.0:0.118:0.0	.	316;447;83;418;330;256	F5H7P2;B4DZK0;B3KVU2;Q9Y4P1-2;Q9Y4P1;Q9Y4P1-4	.;.;.;.;ATG4B_HUMAN;.	S	330;447;256;330;316;256;167	ENSP00000383964:N330S;ENSP00000384661:N256S;ENSP00000384259:N330S;ENSP00000442378:N316S;ENSP00000379692:N256S;ENSP00000404783:N167S	ENSP00000336547:N447S	N	+	2	0	ATG4B	242258845	0.788000	0.28762	0.004000	0.12327	0.974000	0.67602	2.999000	0.49473	0.425000	0.26087	-1.050000	0.02344	AAT	A|0.945;G|0.055	0.055	strong		0.557	ATG4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322967.3	NM_013325	
EVC2	132884	hgsc.bcm.edu	37	4	5690902	5690902	+	Missense_Mutation	SNP	T	T	C	rs4689278	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:5690902T>C	ENST00000344408.5	-	5	741	c.688A>G	c.(688-690)Agc>Ggc	p.S230G	EVC2_ENST00000310917.2_Missense_Mutation_p.S150G|EVC2_ENST00000344938.1_Missense_Mutation_p.S230G	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	230			S -> G (in dbSNP:rs4689278).		smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S230G(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						AACTTCTTGCTAAAAGCCTGG	0.493													T|||	1328	0.265176	0.1914	0.2896	5008	,	,		20409	0.4028		0.2097	False		,,,				2504	0.2628				p.S230G		Atlas-SNP	.											EVC2,NS,carcinoma,0,1	EVC2	202	1	1	Substitution - Missense(1)	stomach(1)	c.A688G						PASS	.	T	GLY/SER,GLY/SER	887,3519	342.5+/-307.2	86,715,1402	88.0	84.0	85.0		448,688	1.9	0.5	4	dbSNP_111	85	1856,6744	332.4+/-320.1	202,1452,2646	yes	missense,missense	EVC2	NM_001166136.1,NM_147127.4	56,56	288,2167,4048	CC,CT,TT		21.5814,20.1316,21.0903	benign,benign	150/1229,230/1309	5690902	2743,10263	2203	4300	6503	SO:0001583	missense	132884	exon5			TCTTGCTAAAAGC	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.688A>G	4.37:g.5690902T>C	ENSP00000342144:p.Ser230Gly	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	517	0.2367216117216117	80	0.16260162601626016	91	0.2513812154696133	183	0.31993006993006995	163	0.21503957783641162	T	3.322	-0.138455	0.06669	0.201316	0.215814	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74315	-0.83;-0.81;-0.82	4.54	1.94	0.25998	.	0.628224	0.16647	N	0.205392	T	0.00012	0.0000	N	0.22421	0.69	0.47476	P	5.619999999999514E-4	B	0.23185	0.081	B	0.20184	0.028	T	0.14200	-1.0481	9	0.23891	T	0.37	-10.6293	9.0029	0.36092	0.0:0.0:0.3622:0.6378	rs4689278;rs58994043;rs4689278	230	Q86UK5	LBN_HUMAN	G	230;150;230	ENSP00000339954:S230G;ENSP00000311683:S150G;ENSP00000342144:S230G	ENSP00000311683:S150G	S	-	1	0	EVC2	5741803	0.926000	0.31397	0.461000	0.27105	0.160000	0.22226	0.997000	0.29731	0.190000	0.20209	-0.488000	0.04728	AGC	T|0.776;C|0.224	0.224	strong		0.493	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
KCNV2	169522	hgsc.bcm.edu	37	9	2718534	2718534	+	Silent	SNP	C	C	G	rs12237048	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:2718534C>G	ENST00000382082.3	+	1	1033	c.795C>G	c.(793-795)gcC>gcG	p.A265A		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	265					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		TCGGGGTGGCCTCCAGCACCT	0.692													C|||	2404	0.480032	0.3502	0.549	5008	,	,		16313	0.7173		0.4742	False		,,,				2504	0.3681				p.A265A		Atlas-SNP	.											KCNV2,NS,carcinoma,0,2	KCNV2	72	2	0			c.C795G						PASS	.	C		1661,2713		323,1015,849	22.0	18.0	19.0		795	4.9	1.0	9	dbSNP_120	19	3975,4589		956,2063,1263	no	coding-synonymous	KCNV2	NM_133497.3		1279,3078,2112	GG,GC,CC		46.4152,37.9744,43.5616		265/546	2718534	5636,7302	2187	4282	6469	SO:0001819	synonymous_variant	169522	exon1			GGTGGCCTCCAGC	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.795C>G	9.37:g.2718534C>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_133497	Q5T6X0	Silent	SNP	ENST00000382082.3	37	CCDS6447.1																																																																																			C|0.535;G|0.465	0.465	strong		0.692	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
ZNF490	57474	hgsc.bcm.edu	37	19	12692001	12692001	+	Silent	SNP	G	G	A	rs3745651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12692001G>A	ENST00000311437.6	-	5	1010	c.888C>T	c.(886-888)caC>caT	p.H296H	ZNF490_ENST00000465656.1_5'Flank|CTD-2192J16.20_ENST00000593682.1_5'Flank	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	296					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						GAGTCCTTTCGTGGGTTAGAA	0.428													G|||	1033	0.20627	0.0386	0.2983	5008	,	,		20580	0.0536		0.5099	False		,,,				2504	0.2127				p.H296H		Atlas-SNP	.											.	ZNF490	42	.	0			c.C888T						PASS	.	G		460,3946	216.8+/-235.3	28,404,1771	76.0	75.0	75.0		888	-2.0	0.1	19	dbSNP_107	75	4390,4210	581.3+/-391.2	1121,2148,1031	yes	coding-synonymous	ZNF490	NM_020714.2		1149,2552,2802	AA,AG,GG		48.9535,10.4403,37.2905		296/530	12692001	4850,8156	2203	4300	6503	SO:0001819	synonymous_variant	57474	exon5			CCTTTCGTGGGTT	AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"""Zinc fingers, C2H2-type"", ""-"""	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.888C>T	19.37:g.12692001G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	37	22	0.594595	NM_020714		Silent	SNP	ENST00000311437.6	37	CCDS12272.1																																																																																			G|0.688;A|0.312	0.312	strong		0.428	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714	
PLEKHH3	79990	hgsc.bcm.edu	37	17	40822678	40822678	+	Silent	SNP	C	C	T	rs2277618	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:40822678C>T	ENST00000591022.1	-	10	1854	c.1467G>A	c.(1465-1467)ggG>ggA	p.G489G	PLEKHH3_ENST00000293349.6_Silent_p.G486G|PLEKHH3_ENST00000412503.1_Silent_p.G486G|PLEKHH3_ENST00000456950.2_5'UTR	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	489	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		ATAGTCTCCACCCGGAGTCGG	0.647													C|||	1066	0.212859	0.0098	0.2378	5008	,	,		11351	0.5347		0.1421	False		,,,				2504	0.2106				p.G489G		Atlas-SNP	.											.	PLEKHH3	49	.	0			c.G1467A						PASS	.	C		140,4266	98.9+/-137.6	0,140,2063	48.0	47.0	47.0		1467	-1.6	0.9	17	dbSNP_100	47	1083,7517	224.1+/-260.6	59,965,3276	no	coding-synonymous	PLEKHH3	NM_024927.4		59,1105,5339	TT,TC,CC		12.593,3.1775,9.4034		489/794	40822678	1223,11783	2203	4300	6503	SO:0001819	synonymous_variant	79990	exon10			TCTCCACCCGGAG	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1467G>A	17.37:g.40822678C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Silent	SNP	ENST00000591022.1	37	CCDS11434.1																																																																																			C|0.843;T|0.157	0.157	strong		0.647	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	
CYP1B1	1545	hgsc.bcm.edu	37	2	38298139	38298139	+	Missense_Mutation	SNP	T	T	C	rs1800440	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:38298139T>C	ENST00000260630.3	-	3	1759	c.1358A>G	c.(1357-1359)aAc>aGc	p.N453S	CYP1B1_ENST00000494864.1_5'UTR|CYP1B1_ENST00000407341.1_Missense_Mutation_p.N453S	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	453			N -> S (in allele CYP1B1*4; dbSNP:rs1800440). {ECO:0000269|PubMed:10655546, ECO:0000269|PubMed:11854439, ECO:0000269|PubMed:12036985, ECO:0000269|PubMed:12525557, ECO:0000269|PubMed:14635112, ECO:0000269|PubMed:15342693, ECO:0000269|PubMed:15475877, ECO:0000269|PubMed:16688110, ECO:0000269|PubMed:9823305, ECO:0000269|Ref.4, ECO:0000269|Ref.5}.		angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	CAGGTCCTTGTTGATGAGGCC	0.473													T|||	499	0.0996406	0.0068	0.1311	5008	,	,		20848	0.005		0.1958	False		,,,				2504	0.2014				p.N453S		Atlas-SNP	.											CYP1B1,colon,carcinoma,0,3	CYP1B1	39	3	0			c.A1358G	GRCh37	CM994676	CYP1B1	M	rs1800440	PASS	.	T	SER/ASN	147,4259	103.4+/-141.9	4,139,2060	82.0	77.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1358	5.9	0.9	2	dbSNP_89	78	1608,6992	298.6+/-304.0	143,1322,2835	yes	missense	CYP1B1	NM_000104.3	46	147,1461,4895	CC,CT,TT		18.6977,3.3364,13.4938	possibly-damaging	453/544	38298139	1755,11251	2203	4300	6503	SO:0001583	missense	1545	exon3			TCCTTGTTGATGA	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"""Cytochrome P450s"""	2597	protein-coding gene	gene with protein product		601771	"""cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"""	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.1358A>G	2.37:g.38298139T>C	ENSP00000260630:p.Asn453Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	177	86	0.485876	NM_000104	Q5TZW8|Q93089|Q9H316	Missense_Mutation	SNP	ENST00000260630.3	37	CCDS1793.1	216	0.0989010989010989	3	0.006097560975609756	58	0.16022099447513813	4	0.006993006993006993	151	0.19920844327176782	T	18.56	3.651256	0.67472	0.033364	0.186977	ENSG00000138061	ENST00000260630;ENST00000407341	T;T	0.66638	-0.22;-0.22	5.95	5.95	0.96441	.	0.172254	0.64402	D	0.000008	T	0.00144	0.0004	L	0.55103	1.725	0.20403	P	0.9999085855	P	0.37466	0.596	B	0.39660	0.306	T	0.08411	-1.0723	9	0.59425	D	0.04	.	14.3758	0.66874	0.0:0.0:0.0:1.0	rs1800440;rs4134586;rs4986886;rs17405302;rs56879535;rs1800440	453	Q53TK1	.	S	453	ENSP00000260630:N453S;ENSP00000384972:N453S	ENSP00000260630:N453S	N	-	2	0	CYP1B1	38151643	1.000000	0.71417	0.934000	0.37439	0.897000	0.52465	6.035000	0.70940	2.279000	0.76181	0.533000	0.62120	AAC	T|0.882;C|0.118	0.118	strong		0.473	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104	
TCP10	6953	hgsc.bcm.edu	37	6	167796309	167796309	+	Missense_Mutation	SNP	C	C	T	rs17855834	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:167796309C>T	ENST00000397829.4	-	2	220	c.53G>A	c.(52-54)gGg>gAg	p.G18E	TCP10_ENST00000476779.2_Missense_Mutation_p.G18E|TCP10_ENST00000366827.2_Missense_Mutation_p.G18E	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	45						cytosol (GO:0005829)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(6)	18		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		CGGCATCTCCCCGGCATTGCT	0.642													c|||	1184	0.236422	0.1747	0.2579	5008	,	,		17823	0.3839		0.1958	False		,,,				2504	0.1943				p.G18E		Atlas-SNP	.											TCP10,NS,carcinoma,-1,1	TCP10	35	1	0			c.G53A						PASS	.	C	GLU/GLY	927,3395		96,735,1330	29.0	38.0	35.0		53	0.8	0.0	6	dbSNP_123	35	1798,6762		204,1390,2686	no	missense	TCP10	NM_004610.3	98	300,2125,4016	TT,TC,CC		21.0047,21.4484,21.1535	benign	18/327	167796309	2725,10157	2161	4280	6441	SO:0001583	missense	6953	exon2			ATCTCCCCGGCAT	U03399	CCDS43527.1	6q27	2012-09-20	2012-09-20		ENSG00000203690	ENSG00000203690			11656	protein-coding gene	gene with protein product		187020	"""t-complex 10 (a murine tcp homolog)"", ""t-complex 10 (mouse)"", ""t-complex 10 homolog (mouse)"""			8111376	Standard	NM_004610		Approved		uc003qvv.1	Q12799	OTTHUMG00000016026	ENST00000397829.4:c.53G>A	6.37:g.167796309C>T	ENSP00000380929:p.Gly18Glu	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	166	78	0.46988	NM_004610	Q5JR60|Q6P4F4	Missense_Mutation	SNP	ENST00000397829.4	37	CCDS43527.1	553	0.2532051282051282	93	0.18902439024390244	86	0.23756906077348067	230	0.4020979020979021	144	0.18997361477572558	C	0.009	-1.836301	0.00579	0.214484	0.210047	ENSG00000203690	ENST00000366827;ENST00000397829;ENST00000476779;ENST00000485157	T;T;T;T	0.30448	2.14;2.14;1.53;1.53	2.02	0.806	0.18708	.	.	.	.	.	T	0.04272	0.0118	L	0.27053	0.805	0.80722	P	0.0	B;B	0.34290	0.215;0.447	B;B	0.34038	0.174;0.118	T	0.32268	-0.9913	8	0.02654	T	1	.	3.5336	0.07786	0.0:0.2421:0.0:0.7579	rs17855834;rs60271163	45;45	Q12799;Q12799-2	TCP10_HUMAN;.	E	18	ENSP00000355792:G18E;ENSP00000380929:G18E;ENSP00000427675:G18E;ENSP00000423829:G18E	ENSP00000355792:G18E	G	-	2	0	TCP10	167716299	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	0.398000	0.20899	0.073000	0.16731	0.306000	0.20318	GGG	C|0.757;T|0.243	0.243	strong		0.642	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1	NM_004610	
FLYWCH1	84256	hgsc.bcm.edu	37	16	2983483	2983483	+	Silent	SNP	C	C	G	rs2074362	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2983483C>G	ENST00000253928.9	+	5	1554	c.1149C>G	c.(1147-1149)ctC>ctG	p.L383L	FLYWCH1_ENST00000399667.2_Silent_p.L383L|FLYWCH1_ENST00000416288.2_Silent_p.L382L			Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1	383						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|lung(3)	4						CCCTGACTCTCACCAGGCCTC	0.677													.|||	1699	0.339257	0.4206	0.281	5008	,	,		16161	0.4157		0.1491	False		,,,				2504	0.3875				p.L382L		Atlas-SNP	.											.	FLYWCH1	27	.	0			c.C1146G						PASS	.	C	,	1564,2578		312,940,819	12.0	18.0	16.0		1146,1146	0.5	0.0	16	dbSNP_96	16	1176,7176		84,1008,3084	no	coding-synonymous,coding-synonymous	FLYWCH1	NM_020912.1,NM_032296.2	,	396,1948,3903	GG,GC,CC		14.0805,37.7595,21.9305	,	382/704,382/716	2983483	2740,9754	2071	4176	6247	SO:0001819	synonymous_variant	84256	exon5			GACTCTCACCAGG	AL136585	CCDS45390.1	16p13.3	2013-01-10	2007-06-21	2007-06-21	ENSG00000059122	ENSG00000059122		"""Zinc fingers"""	25404	protein-coding gene	gene with protein product						11230166, 10997877	Standard	XM_006720959		Approved	DKFZp761A132	uc002csc.3	Q4VC44		ENST00000253928.9:c.1149C>G	16.37:g.2983483C>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_020912	D3DUA1|Q6ZSQ1|Q8WV62|Q9BQG6|Q9BUS5|Q9HCM0	Silent	SNP	ENST00000253928.9	37																																																																																				C|0.704;G|0.296	0.296	strong		0.677	FLYWCH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000436479.1	NM_032296	
FTL	2512	hgsc.bcm.edu	37	19	49469087	49469087	+	Silent	SNP	T	T	C	rs2230267	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49469087T>C	ENST00000331825.6	+	2	370	c.163T>C	c.(163-165)Ttg>Ctg	p.L55L	CTD-2639E6.9_ENST00000599784.1_lincRNA	NM_000146.3	NP_000137.2	P02792	FRIL_HUMAN	ferritin, light polypeptide	55	Catalytic site for iron oxidation.|Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular ferritin complex (GO:0008043)|membrane (GO:0016020)	ferric iron binding (GO:0008199)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)			cervix(1)|kidney(3)|lung(5)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000152)|all cancers(93;0.000435)|GBM - Glioblastoma multiforme(486;0.0171)|Epithelial(262;0.0267)	Iron Dextran(DB00893)	CTTCCGCGAATTGGCCGAGGA	0.582													T|||	2307	0.460663	0.4849	0.5	5008	,	,		19910	0.4246		0.5398	False		,,,				2504	0.3558				p.L55L		Atlas-SNP	.											.	FTL	19	.	0			c.T163C						PASS	.	T		2088,2318	571.8+/-383.2	512,1064,627	56.0	60.0	58.0		163	-2.2	0.8	19	dbSNP_98	58	4669,3931	602.4+/-394.5	1278,2113,909	no	coding-synonymous	FTL	NM_000146.3		1790,3177,1536	CC,CT,TT		45.7093,47.3899,48.0471		55/176	49469087	6757,6249	2203	4300	6503	SO:0001819	synonymous_variant	2512	exon2			CGCGAATTGGCCG	AY207005	CCDS33070.1	19q13.33	2014-05-19			ENSG00000087086	ENSG00000087086			3999	protein-coding gene	gene with protein product	"""ferritin light polypeptide-like 3"", ""L apoferritin"", ""ferritin L subunit"", ""ferritin light chain"", ""ferritin L-chain"", ""neurodegeneration with brain iron accumulation 3"""	134790				3000916, 9526618	Standard	NM_000146		Approved	MGC71996, NBIA3	uc002plo.3	P02792		ENST00000331825.6:c.163T>C	19.37:g.49469087T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	79	77	0.974684	NM_000146	B2R4B9|Q6IBT7|Q7Z2W1|Q86WI9|Q8WU07|Q96AU9|Q96CU0|Q9BTZ8	Silent	SNP	ENST00000331825.6	37	CCDS33070.1																																																																																			T|0.480;C|0.520	0.520	strong		0.582	FTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466233.1	NM_000146	
REG3A	5068	hgsc.bcm.edu	37	2	79385786	79385786	+	Silent	SNP	T	T	C	rs76653007	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:79385786T>C	ENST00000409839.3	-	3	222	c.186A>G	c.(184-186)acA>acG	p.T62T	REG3A_ENST00000393878.1_Silent_p.T62T|AC011754.1_ENST00000415201.1_RNA|REG3A_ENST00000305165.2_Silent_p.T62T	NM_002580.2|NM_138937.2	NP_002571.1|NP_620354.1	Q06141	REG3A_HUMAN	regenerating islet-derived 3 alpha	62	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|cell proliferation (GO:0008283)|heterophilic cell-cell adhesion (GO:0007157)|multicellular organismal development (GO:0007275)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)			breast(2)|large_intestine(4)|lung(41)|prostate(2)|skin(1)	50						CATCTGCATCTGTCCAGGATT	0.552																																					p.T62T		Atlas-SNP	.											.	REG3A	76	.	0			c.A186G						PASS	.						129.0	118.0	122.0					2																	79385786		2203	4300	6503	SO:0001819	synonymous_variant	5068	exon2			TGCATCTGTCCAG	S51768	CCDS1965.1	2p12	2008-02-05	2005-02-11	2005-02-11	ENSG00000172016	ENSG00000172016			8601	protein-coding gene	gene with protein product		167805	"""pancreatitis-associated protein"""	PAP		8188210	Standard	NM_002580		Approved	HIP, REG-III, REG3, PBCGF, PAP1	uc002sof.2	Q06141	OTTHUMG00000130017	ENST00000409839.3:c.186A>G	2.37:g.79385786T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	213	35	0.164319	NM_138938		Silent	SNP	ENST00000409839.3	37	CCDS1965.1																																																																																			T|0.894;C|0.106	0.106	strong		0.552	REG3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252290.2	NM_002580	
BSN	8927	hgsc.bcm.edu	37	3	49690496	49690496	+	Silent	SNP	C	C	T	rs11709525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49690496C>T	ENST00000296452.4	+	5	3621	c.3507C>T	c.(3505-3507)tcC>tcT	p.S1169S		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1169					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		AGACACCCTCCGGCAGCTCCA	0.602													C|||	1039	0.207468	0.2632	0.1657	5008	,	,		19657	0.0565		0.3241	False		,,,				2504	0.1973				p.S1169S		Atlas-SNP	.											BSN,NS,carcinoma,0,1	BSN	272	1	0			c.C3507T						scavenged	.	C		1179,3227	381.6+/-324.1	150,879,1174	33.0	35.0	35.0		3507	-9.8	0.0	3	dbSNP_120	35	2556,6044	384.5+/-341.1	405,1746,2149	no	coding-synonymous	BSN	NM_003458.3		555,2625,3323	TT,TC,CC		29.7209,26.759,28.7175		1169/3927	49690496	3735,9271	2203	4300	6503	SO:0001819	synonymous_variant	8927	exon5			ACCCTCCGGCAGC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3507C>T	3.37:g.49690496C>T		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			C|0.731;G|0.000;T|0.269	0.269	strong		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
OR2AG2	338755	hgsc.bcm.edu	37	11	6790106	6790106	+	Missense_Mutation	SNP	T	T	C	rs7102536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6790106T>C	ENST00000338569.2	-	1	180	c.83A>G	c.(82-84)tAt>tGt	p.Y28C		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	28			Y -> C (in dbSNP:rs7102536).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AAATGTAGCATAGAGCAGTTC	0.507													C|||	4393	0.877196	0.9002	0.8415	5008	,	,		19437	0.9286		0.8141	False		,,,				2504	0.8834				p.Y28C		Atlas-SNP	.											.	OR2AG2	55	.	0			c.A83G						PASS	.	C	CYS/TYR	3969,433	208.2+/-229.3	1786,397,18	105.0	101.0	102.0		83	3.4	0.8	11	dbSNP_116	102	7152,1440	276.3+/-292.2	2990,1172,134	yes	missense	OR2AG2	NM_001004490.1	194	4776,1569,152	CC,CT,TT		16.7598,9.8364,14.4143	benign	28/317	6790106	11121,1873	2201	4296	6497	SO:0001583	missense	338755	exon1			GTAGCATAGAGCA	AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.83A>G	11.37:g.6790106T>C	ENSP00000342697:p.Tyr28Cys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001004490		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	1897	0.8685897435897436	442	0.8983739837398373	303	0.8370165745856354	532	0.9300699300699301	620	0.8179419525065963	C	1.145	-0.648419	0.03506	0.901636	0.832402	ENSG00000188124	ENST00000338569	T	0.03212	4.01	4.28	3.36	0.38483	.	0.115660	0.39834	N	0.001242	T	0.00012	0.0000	N	0.19112	0.55	0.54753	P	1.3000000000040757E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.17745	-1.0359	9	0.27082	T	0.32	.	5.4004	0.16293	0.3556:0.5503:0.0:0.0941	rs7102536;rs17179069;rs52820109;rs58664598;rs7102536	28	A6NM03	O2AG2_HUMAN	C	28	ENSP00000342697:Y28C	ENSP00000342697:Y28C	Y	-	2	0	OR2AG2	6746682	0.066000	0.20996	0.833000	0.33012	0.327000	0.28475	0.488000	0.22371	0.749000	0.32854	-0.119000	0.15052	TAT	T|0.137;C|0.863	0.863	strong		0.507	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
PCDHGA6	56109	hgsc.bcm.edu	37	5	140755387	140755387	+	Silent	SNP	C	C	T	rs62378422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140755387C>T	ENST00000517434.1	+	1	1737	c.1737C>T	c.(1735-1737)ccC>ccT	p.P579P	PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	579	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTGGCGCCCCGCTCCGCAG	0.662													.|||	499	0.0996406	0.202	0.0576	5008	,	,		15180	0.0397		0.0815	False		,,,				2504	0.0716				p.P579P		Atlas-SNP	.											.	PCDHGA6	219	.	0			c.C1737T						PASS	.	C	,,,,,,,,,	778,3624		67,644,1490	79.0	96.0	90.0		,,,,,1737,,,,1737	-3.3	0.2	5	dbSNP_129	90	773,7819		29,715,3552	no	intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,coding-synonymous	PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032086.1	,,,,,,,,,	96,1359,5042	TT,TC,CC		8.9967,17.6738,11.9363	,,,,,,,,,	,,,,,579/933,,,,579/819	140755387	1551,11443	2201	4296	6497	SO:0001819	synonymous_variant	56109	exon1			GGCGCCCCGCTCC	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"""Cadherins / Protocadherins : Clustered"""	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.1737C>T	5.37:g.140755387C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Silent	SNP	ENST00000517434.1	37	CCDS54926.1																																																																																			C|0.918;T|0.082	0.082	strong		0.662	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919	
NRSN2	80023	hgsc.bcm.edu	37	20	330408	330408	+	Missense_Mutation	SNP	C	C	G	rs11556643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:330408C>G	ENST00000382291.3	+	3	361	c.121C>G	c.(121-123)Ctc>Gtc	p.L41V	NRSN2_ENST00000608736.1_Missense_Mutation_p.L41V|RP5-1103G7.4_ENST00000442637.1_RNA|NRSN2_ENST00000492242.1_Intron|NRSN2_ENST00000382285.2_Missense_Mutation_p.L41V	NM_024958.2	NP_079234.1	Q9GZP1	NRSN2_HUMAN	neurensin 2	41			L -> V (in dbSNP:rs11556643).			integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				endometrium(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8		all_cancers(10;0.0834)				AGGCACTGCTCTCAGCGACGA	0.642													C|||	635	0.126797	0.3222	0.0663	5008	,	,		15562	0.0119		0.0457	False		,,,				2504	0.1074				p.L41V		Atlas-SNP	.											.	NRSN2	20	.	0			c.C121G						PASS	.	C	VAL/LEU	1219,3187	416.5+/-337.6	182,855,1166	59.0	57.0	58.0		121	4.2	0.7	20	dbSNP_120	58	483,8117	139.8+/-196.4	15,453,3832	yes	missense	NRSN2	NM_024958.2	32	197,1308,4998	GG,GC,CC		5.6163,27.6668,13.0863	probably-damaging	41/205	330408	1702,11304	2203	4300	6503	SO:0001583	missense	80023	exon3			ACTGCTCTCAGCG	AL136915	CCDS12996.1	20p13	2008-02-04	2006-07-04	2006-07-04	ENSG00000125841	ENSG00000125841			16229	protein-coding gene	gene with protein product		610666	"""chromosome 20 open reading frame 98"""	C20orf98		16527258	Standard	NM_024958		Approved	dJ1103G7.6	uc002wdi.4	Q9GZP1	OTTHUMG00000031628	ENST00000382291.3:c.121C>G	20.37:g.330408C>G	ENSP00000371728:p.Leu41Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_024958	A8K3B2|Q6FII5|Q9NUD3	Missense_Mutation	SNP	ENST00000382291.3	37	CCDS12996.1	208	0.09523809523809523	143	0.29065040650406504	20	0.055248618784530384	7	0.012237762237762238	38	0.05013192612137203	C	10.27	1.305091	0.23736	0.276668	0.056163	ENSG00000125841	ENST00000382291;ENST00000382285	T;T	0.17854	2.25;2.25	4.25	4.25	0.50352	.	0.422192	0.22997	N	0.053131	T	0.00012	0.0000	L	0.54323	1.7	0.36941	P	0.10761500000000002	D	0.67145	0.996	D	0.79108	0.992	T	0.31223	-0.9951	9	0.39692	T	0.17	-26.8864	12.0091	0.53276	0.0:1.0:0.0:0.0	rs11556643;rs60937200	41	Q9GZP1	NRSN2_HUMAN	V	41	ENSP00000371728:L41V;ENSP00000371722:L41V	ENSP00000371722:L41V	L	+	1	0	NRSN2	278408	0.922000	0.31269	0.665000	0.29768	0.422000	0.31414	1.965000	0.40471	2.177000	0.69029	0.643000	0.83706	CTC	C|0.879;G|0.121	0.121	strong		0.642	NRSN2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077446.1	NM_024958	
CATSPER4	378807	hgsc.bcm.edu	37	1	26527884	26527884	+	Silent	SNP	G	G	A	rs41310785	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:26527884G>A	ENST00000456354.2	+	9	1306	c.1239G>A	c.(1237-1239)gaG>gaA	p.E413E		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	413					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		TCAACCAGGAGCAGGAGTCAG	0.602													G|||	114	0.0227636	0.0023	0.036	5008	,	,		18556	0.0		0.0805	False		,,,				2504	0.0051				p.E413E		Atlas-SNP	.											.	CATSPER4	59	.	0			c.G1239A						PASS	.	G		64,4342	60.5+/-97.4	0,64,2139	87.0	79.0	82.0		1239	2.0	1.0	1	dbSNP_127	82	757,7843	180.6+/-229.5	31,695,3574	no	coding-synonymous	CATSPER4	NM_198137.1		31,759,5713	AA,AG,GG		8.8023,1.4526,6.3125		413/473	26527884	821,12185	2203	4300	6503	SO:0001819	synonymous_variant	378807	exon9			CCAGGAGCAGGAG	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.1239G>A	1.37:g.26527884G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	246	123	0.5	NM_198137	A1A4W6|Q5VY71	Silent	SNP	ENST00000456354.2	37	CCDS30645.1																																																																																			G|0.947;A|0.053	0.053	strong		0.602	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
POU6F2	11281	hgsc.bcm.edu	37	7	39379325	39379325	+	Missense_Mutation	SNP	C	C	T	rs2074936	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:39379325C>T	ENST00000403058.1	+	6	750	c.596C>T	c.(595-597)cCg>cTg	p.P199L	POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000559001.1_Missense_Mutation_p.P191L|POU6F2_ENST00000518318.2_Missense_Mutation_p.P199L	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	199	Gln-rich.|Pro-rich.		P -> L (in dbSNP:rs2074936).		central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P199L(1)		NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						cagcCTCCCCCGTCAACCAAC	0.672													C|||	1354	0.270367	0.1921	0.1844	5008	,	,		12095	0.5833		0.159	False		,,,				2504	0.229				p.P199L		Atlas-SNP	.											POU6F2,NS,NS,0,1	POU6F2	117	1	1	Substitution - Missense(1)	NS(1)	c.C596T						PASS	.	C	LEU/PRO,LEU/PRO	799,3603		62,675,1464	16.0	20.0	19.0		596,596	2.7	0.2	7	dbSNP_96	19	1184,7406		98,988,3209	yes	missense,missense	POU6F2	NM_007252.3,NM_001166018.1	98,98	160,1663,4673	TT,TC,CC		13.7835,18.1508,15.2632	benign,benign	199/692,199/656	39379325	1983,11009	2201	4295	6496	SO:0001583	missense	11281	exon6			CTCCCCCGTCAAC	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"""Homeoboxes / POU class"""	21694	protein-coding gene	gene with protein product	"""Retina-derived POU-domain factor-1"""	609062	"""POU domain, class 6, transcription factor 2"""			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.596C>T	7.37:g.39379325C>T	ENSP00000384004:p.Pro199Leu	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	12	5	0.416667	NM_007252	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Missense_Mutation	SNP	ENST00000403058.1	37	CCDS34620.2	634	0.2902930402930403	98	0.1991869918699187	75	0.20718232044198895	342	0.5979020979020979	119	0.15699208443271767	C	1.926	-0.447208	0.04572	0.181508	0.137835	ENSG00000106536	ENST00000403058;ENST00000518318	T;D	0.85411	1.06;-1.98	4.66	2.69	0.31865	.	2.961890	0.02261	U	0.067581	T	0.00012	0.0000	N	0.08118	0	0.40517	P	0.01920900000000003	P;B	0.43885	0.82;0.118	B;B	0.32928	0.155;0.016	T	0.38950	-0.9637	9	0.39692	T	0.17	.	12.6303	0.56653	0.4736:0.5264:0.0:0.0	rs2074936;rs10338353;rs52791432;rs2074936	199;199	P78424-2;P78424	.;PO6F2_HUMAN	L	199	ENSP00000384004:P199L;ENSP00000430514:P199L	ENSP00000384004:P199L	P	+	2	0	POU6F2	39345850	0.204000	0.23447	0.199000	0.23439	0.287000	0.27160	1.173000	0.31920	0.899000	0.36444	0.557000	0.71058	CCG	C|0.764;T|0.236	0.236	strong		0.672	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252	
GLIS1	148979	hgsc.bcm.edu	37	1	53995515	53995515	+	Silent	SNP	G	G	A	rs12021912	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:53995515G>A	ENST00000312233.2	-	4	1472	c.906C>T	c.(904-906)gcC>gcT	p.A302A		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						AGTTGCTGAAGGCCTTCTGGC	0.657													G|||	907	0.18111	0.1036	0.1888	5008	,	,		16095	0.4683		0.0169	False		,,,				2504	0.1534				p.A302A		Atlas-SNP	.											.	GLIS1	52	.	0			c.C906T						PASS	.	G		444,3962	212.8+/-232.6	17,410,1776	88.0	89.0	88.0		906	2.6	1.0	1	dbSNP_120	88	196,8404	86.9+/-149.2	4,188,4108	no	coding-synonymous	GLIS1	NM_147193.2		21,598,5884	AA,AG,GG		2.2791,10.0772,4.9208		302/621	53995515	640,12366	2203	4300	6503	SO:0001819	synonymous_variant	148979	exon4			GCTGAAGGCCTTC	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"""Zinc fingers, C2H2-type"""	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.906C>T	1.37:g.53995515G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_147193		Silent	SNP	ENST00000312233.2	37	CCDS582.1																																																																																			G|0.915;A|0.085	0.085	strong		0.657	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
TAB1	10454	hgsc.bcm.edu	37	22	39813800	39813800	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:39813800G>A	ENST00000216160.6	+	5	558	c.496G>A	c.(496-498)Gcc>Acc	p.A166T	TAB1_ENST00000331454.3_Missense_Mutation_p.A166T	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	166	PP2C-like.				activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						TTCGGGAGGGGCCATGGCCGT	0.577																																					p.A166T		Atlas-SNP	.											.	TAB1	36	.	0			c.G496A						PASS	.						86.0	73.0	77.0					22																	39813800		2203	4300	6503	SO:0001583	missense	10454	exon5			GGAGGGGCCATGG	U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"""TAK1-binding protein 1"", ""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	602615	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.496G>A	22.37:g.39813800G>A	ENSP00000216160:p.Ala166Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	131	68	0.519084	NM_153497	Q2PP09|Q8IZW2	Missense_Mutation	SNP	ENST00000216160.6	37	CCDS13993.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.541345	0.65085	.	.	ENSG00000100324	ENST00000216160;ENST00000331454	T;T	0.05382	3.45;3.45	5.34	5.34	0.76211	Protein phosphatase 2C-like (4);	0.225313	0.44097	D	0.000492	T	0.11324	0.0276	N	0.16098	0.37	0.80722	D	1	B;B;D	0.71674	0.017;0.29;0.998	B;B;D	0.81914	0.015;0.173;0.995	T	0.31971	-0.9924	10	0.07030	T	0.85	.	19.0356	0.92976	0.0:0.0:1.0:0.0	.	166;166;310	Q15750-2;Q15750;Q59FT7	.;TAB1_HUMAN;.	T	166	ENSP00000216160:A166T;ENSP00000333049:A166T	ENSP00000216160:A166T	A	+	1	0	TAB1	38143746	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	8.488000	0.90458	2.496000	0.84212	0.655000	0.94253	GCC	.	.	none		0.577	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497	
ASB18	401036	hgsc.bcm.edu	37	2	237149941	237149941	+	Missense_Mutation	SNP	C	C	T	rs6756597	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:237149941C>T	ENST00000409749.3	-	2	309	c.310G>A	c.(310-312)Gcc>Acc	p.A104T	AC079135.1_ENST00000415226.1_RNA|ASB18_ENST00000330842.6_Missense_Mutation_p.A75T	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	104			A -> T (in dbSNP:rs6756597).		intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					large_intestine(1)|lung(3)|ovary(1)|prostate(1)	6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		CCAAACGTGGCTGGAGATTTC	0.473													C|||	2216	0.442492	0.2995	0.4813	5008	,	,		17421	0.5655		0.508	False		,,,				2504	0.4141				p.A104T		Atlas-SNP	.											.	ASB18	34	.	0			c.G310A						PASS	.	C	THR/ALA	1127,2687		158,811,938	122.0	123.0	123.0		310	4.8	0.9	2	dbSNP_116	123	3962,4280		948,2066,1107	yes	missense	ASB18	NM_212556.2	58	1106,2877,2045	TT,TC,CC		48.0709,29.549,42.2113	benign	104/467	237149941	5089,6967	1907	4121	6028	SO:0001583	missense	401036	exon2			ACGTGGCTGGAGA	AK123854	CCDS46548.1	2q37.2	2013-01-10	2011-01-25		ENSG00000182177	ENSG00000182177		"""Ankyrin repeat domain containing"""	19770	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 18"""			12076535	Standard	NM_212556		Approved		uc010znh.2	Q6ZVZ8	OTTHUMG00000153086	ENST00000409749.3:c.310G>A	2.37:g.237149941C>T	ENSP00000386532:p.Ala104Thr	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	183	76	0.415301	NM_212556	B6ZDL7	Missense_Mutation	SNP	ENST00000409749.3	37	CCDS46548.1	1026	0.4697802197802198	150	0.3048780487804878	172	0.47513812154696133	329	0.5751748251748252	375	0.4947229551451187	C	16.45	3.125352	0.56721	0.29549	0.480709	ENSG00000182177	ENST00000330842;ENST00000409749	T;T	0.38077	1.16;1.17	4.82	4.82	0.62117	Ankyrin repeat-containing domain (1);	0.602490	0.14610	N	0.309108	T	0.00012	0.0000	L	0.31664	0.95	0.34321	P	0.313427	P;P	0.41710	0.76;0.644	B;B	0.41440	0.357;0.192	T	0.41448	-0.9508	9	0.18710	T	0.47	.	17.8766	0.88827	0.0:1.0:0.0:0.0	rs6756597;rs52814791;rs59869358;rs6756597	104;75	Q6ZVZ8;Q6ZVZ8-2	ASB18_HUMAN;.	T	75;104	ENSP00000329970:A75T;ENSP00000386532:A104T	ENSP00000329970:A75T	A	-	1	0	ASB18	236814680	0.979000	0.34478	0.928000	0.36995	0.956000	0.61745	2.676000	0.46883	2.377000	0.81083	0.655000	0.94253	GCC	C|0.535;T|0.465	0.465	strong		0.473	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556	
MCM3AP	8888	hgsc.bcm.edu	37	21	47692531	47692531	+	Silent	SNP	T	T	C	rs17182739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47692531T>C	ENST00000397708.1	-	9	2663	c.2409A>G	c.(2407-2409)gaA>gaG	p.E803E	MCM3AP_ENST00000291688.1_Silent_p.E803E			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	803	SAC3 homology.				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)					GGAACTCCGCTTCGCTGGCAC	0.478													T|||	97	0.019369	0.0015	0.0346	5008	,	,		21993	0.001		0.0646	False		,,,				2504	0.0051				p.E803E		Atlas-SNP	.											MCM3AP,colon,carcinoma,-2,1	MCM3AP	146	1	0			c.A2409G						PASS	.	T		62,4344	57.4+/-93.9	1,60,2142	170.0	148.0	155.0		2409	-7.0	0.0	21	dbSNP_123	155	560,8040	153.3+/-207.7	13,534,3753	no	coding-synonymous	MCM3AP	NM_003906.3		14,594,5895	CC,CT,TT		6.5116,1.4072,4.7824		803/1981	47692531	622,12384	2203	4300	6503	SO:0001819	synonymous_variant	8888	exon8			CTCCGCTTCGCTG	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.2409A>G	21.37:g.47692531T>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	200	95	0.475	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			T|0.959;C|0.041	0.041	strong		0.478	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
CDHR3	222256	hgsc.bcm.edu	37	7	105662690	105662690	+	Silent	SNP	T	T	C	rs10258293	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:105662690T>C	ENST00000317716.9	+	14	1952	c.1872T>C	c.(1870-1872)aaT>aaC	p.N624N	CDHR3_ENST00000542731.1_Silent_p.N624N|CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000478080.1_Silent_p.N536N|CDHR3_ENST00000343407.5_Intron	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	624	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						CTGGTTCCAATGTCACACGCC	0.428													t|||	879	0.175519	0.2186	0.1311	5008	,	,		23774	0.0813		0.2018	False		,,,				2504	0.2188				p.N624N		Atlas-SNP	.											.	CDHR3	153	.	0			c.T1872C						PASS	.	T		846,3206		81,684,1261	185.0	172.0	176.0		1872	-6.0	0.0	7	dbSNP_119	176	1404,6972		132,1140,2916	no	coding-synonymous	CDHR3	NM_152750.4		213,1824,4177	CC,CT,TT		16.7622,20.8786,18.1043		624/886	105662690	2250,10178	2026	4188	6214	SO:0001819	synonymous_variant	222256	exon14			TTCCAATGTCACA	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1872T>C	7.37:g.105662690T>C		Somatic	403	0	0		WXS	Illumina HiSeq	Phase_I	410	199	0.485366	NM_152750	Q8TCI7	Silent	SNP	ENST00000317716.9	37	CCDS47684.1	347	0.15888278388278387	98	0.1991869918699187	58	0.16022099447513813	40	0.06993006993006994	151	0.19920844327176782	C	5.913	0.352602	0.11182	0.208786	0.167622	ENSG00000128536	ENST00000468477	.	.	.	5.23	-5.99	0.02213	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.99999885036	.	.	.	.	.	.	T	0.33394	-0.9870	3	.	.	.	-18.1293	18.9616	0.92679	0.0:0.252:0.0:0.748	rs10258293;rs56524808;rs10258293	.	.	.	T	93	.	.	M	+	2	0	CDHR3	105449926	0.000000	0.05858	0.002000	0.10522	0.787000	0.44495	-1.882000	0.01624	-1.794000	0.01256	-0.699000	0.03677	ATG	T|0.839;C|0.161	0.161	strong		0.428	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
ZNF234	10780	hgsc.bcm.edu	37	19	44660967	44660967	+	Silent	SNP	A	A	G	rs12609635	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:44660967A>G	ENST00000426739.2	+	6	1056	c.798A>G	c.(796-798)ggA>ggG	p.G266G	ZNF234_ENST00000592437.1_Silent_p.G266G	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	266					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)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)	23		Prostate(69;0.0435)				AGGAATGTGGAAGGGCCTTCA	0.418													G|||	2851	0.569289	0.9418	0.4726	5008	,	,		23488	0.4931		0.3668	False		,,,				2504	0.4213				p.G266G		Atlas-SNP	.											.	ZNF234	132	.	0			c.A798G						PASS	.	G	,	3702,704	272.5+/-270.8	1568,566,69	136.0	144.0	142.0		798,798	-4.3	0.0	19	dbSNP_120	142	3162,5438	643.0+/-399.9	577,2008,1715	no	coding-synonymous,coding-synonymous	ZNF234	NM_001144824.1,NM_006630.2	,	2145,2574,1784	GG,GA,AA		36.7674,15.9782,47.2244	,	266/701,266/701	44660967	6864,6142	2203	4300	6503	SO:0001819	synonymous_variant	10780	exon6			ATGTGGAAGGGCC	X78927	CCDS46101.1	19q13	2013-01-08				ENSG00000263002		"""Zinc fingers, C2H2-type"", ""-"""	13027	protein-coding gene	gene with protein product		604750		ZNF269		7865130	Standard	NM_006630		Approved	HZF4	uc002oyl.4	Q14588		ENST00000426739.2:c.798A>G	19.37:g.44660967A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	79	49	0.620253	NM_006630	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Silent	SNP	ENST00000426739.2	37	CCDS46101.1																																																																																			A|0.448;G|0.552	0.552	strong		0.418	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2		
PABPC1	26986	hgsc.bcm.edu	37	8	101727716	101727716	+	Missense_Mutation	SNP	C	C	T	rs201157005		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:101727716C>T	ENST00000318607.5	-	4	1745	c.617G>A	c.(616-618)cGc>cAc	p.R206H	PABPC1_ENST00000522387.1_Missense_Mutation_p.R174H|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000519004.1_Missense_Mutation_p.R161H	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	206	CSDE1-binding.|RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|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 translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			ATCCTTAAGGCGCTCATCATC	0.353																																					p.R206H		Atlas-SNP	.											PABPC1,NS,carcinoma,-1,1	PABPC1	76	1	0			c.G617A						scavenged	.																																			SO:0001583	missense	26986	exon4			TTAAGGCGCTCAT	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.617G>A	8.37:g.101727716C>T	ENSP00000313007:p.Arg206His	Somatic	80	2	0.025		WXS	Illumina HiSeq	Phase_I	80	5	0.0625	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	130|130	0.05952380952380952|0.05952380952380952	45|45	0.09146341463414634|0.09146341463414634	8|8	0.022099447513812154|0.022099447513812154	29|29	0.050699300699300696|0.050699300699300696	48|48	0.0633245382585752|0.0633245382585752	C|C	15.89|15.89	2.967520|2.967520	0.53507|0.53507	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519100|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|D;D;T	.|0.84370	.|-1.84;-1.84;2.38	5.03|5.03	5.03|5.03	0.67393|0.67393	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.56097	.|D	.|0.000024	T|T	0.14184|0.14184	0.0343|0.0343	N|N	0.25647|0.25647	0.755|0.755	0.44736|0.44736	D|D	0.997731|0.997731	.|B;B;B	.|0.24920	.|0.005;0.053;0.114	.|B;B;B	.|0.20384	.|0.008;0.029;0.026	T|T	0.56890|0.56890	-0.7904|-0.7904	5|10	.|0.49607	.|T	.|0.09	.|.	18.734|18.734	0.91748|0.91748	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|174;206;206	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	T|H	78|206;206;161;174	.|ENSP00000313007:R206H;ENSP00000429594:R161H;ENSP00000429395:R174H	.|ENSP00000313007:R206H	A|R	-|-	1|2	0|0	PABPC1|PABPC1	101796892|101796892	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.004000|6.004000	0.70709|0.70709	2.482000|2.482000	0.83794|0.83794	0.585000|0.585000	0.79938|0.79938	GCC|CGC	C|0.940;T|0.060	0.060	strong		0.353	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
PCSK7	9159	hgsc.bcm.edu	37	11	117097952	117097952	+	Silent	SNP	C	C	T	rs2306473	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:117097952C>T	ENST00000320934.3	-	5	1320	c.690G>A	c.(688-690)acG>acA	p.T230T		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	230	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CTGCACATCGCGTGCCATGGT	0.587			T	IGH@	MLCLS								C|||	1049	0.209465	0.3971	0.232	5008	,	,		18916	0.0675		0.1332	False		,,,				2504	0.1646				p.T230T		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	PCSK7,NS,carcinoma,0,1	PCSK7	59	1	0			c.G690A						PASS	.	C		1516,2886	480.4+/-358.8	241,1034,926	119.0	104.0	109.0		690	-7.5	0.0	11	dbSNP_100	109	1311,7281	258.8+/-282.3	94,1123,3079	no	coding-synonymous	PCSK7	NM_004716.2		335,2157,4005	TT,TC,CC		15.2584,34.4389,21.7562		230/786	117097952	2827,10167	2201	4296	6497	SO:0001819	synonymous_variant	9159	exon5			ACATCGCGTGCCA	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.690G>A	11.37:g.117097952C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	112	61	0.544643	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			C|0.788;T|0.212	0.212	strong		0.587	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
IGSF21	84966	hgsc.bcm.edu	37	1	18692089	18692089	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18692089C>T	ENST00000251296.1	+	6	1296	c.913C>T	c.(913-915)Ctc>Ttc	p.L305F		NM_032880.4	NP_116269.3	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	305						extracellular region (GO:0005576)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	40		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		ACGTGCCCTGCTCACCTGGAC	0.647																																					p.L305F		Atlas-SNP	.											.	IGSF21	87	.	0			c.C913T						PASS	.						117.0	95.0	103.0					1																	18692089		2203	4300	6503	SO:0001583	missense	84966	exon6			GCCCTGCTCACCT	AK075316	CCDS184.1	1p36.13	2013-01-29			ENSG00000117154	ENSG00000117154		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28246	protein-coding gene	gene with protein product						12477932	Standard	NM_032880		Approved	MGC15730, RP11-121A23.1	uc001bau.2	Q96ID5	OTTHUMG00000002432	ENST00000251296.1:c.913C>T	1.37:g.18692089C>T	ENSP00000251296:p.Leu305Phe	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	194	97	0.5	NM_032880	Q8NBR8	Missense_Mutation	SNP	ENST00000251296.1	37	CCDS184.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.6|25.6	4.654766|4.654766	0.88056|0.88056	.|.	.|.	ENSG00000117154|ENSG00000117154	ENST00000412684|ENST00000251296	.|T	.|0.31510	.|1.49	4.28|4.28	4.28|4.28	0.50868|0.50868	.|Immunoglobulin-like fold (1);	.|0.120807	.|0.56097	.|D	.|0.000037	T|T	0.35451|0.35451	0.0932|0.0932	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D	.|0.65815	.|0.995	.|P	.|0.56278	.|0.795	T|T	0.03231|0.03231	-1.1058|-1.1058	5|10	.|0.22109	.|T	.|0.4	-13.5806|-13.5806	15.7859|15.7859	0.78304|0.78304	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|305	.|Q96ID5	.|IGS21_HUMAN	V|F	257|305	.|ENSP00000251296:L305F	.|ENSP00000251296:L305F	A|L	+|+	2|1	0|0	IGSF21|IGSF21	18564676|18564676	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	4.004000|4.004000	0.57068|0.57068	2.383000|2.383000	0.81215|0.81215	0.561000|0.561000	0.74099|0.74099	GCT|CTC	.	.	none		0.647	IGSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006924.1	NM_032880	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121653250	121653250	+	Missense_Mutation	SNP	G	G	A	rs61732005	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:121653250G>A	ENST00000393386.2	+	12	4561	c.4150G>A	c.(4150-4152)Gat>Aat	p.D1384N	PTPRZ1_ENST00000483028.1_3'UTR|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1384					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TCCCCACAGAGATGGTTCTGT	0.438													G|||	393	0.0784744	0.0567	0.0447	5008	,	,		22228	0.2093		0.0557	False		,,,				2504	0.0204				p.D1384N		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G4150A						PASS	.	G	,,ASN/ASP	342,4064	179.4+/-207.9	9,324,1870	169.0	160.0	163.0		,,4150	3.3	0.0	7	dbSNP_129	163	646,7954	165.5+/-217.6	23,600,3677	yes	intron,intron,missense	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,23	32,924,5547	AA,AG,GG		7.5116,7.7621,7.5965	,,benign	,,1384/2316	121653250	988,12018	2203	4300	6503	SO:0001583	missense	5803	exon12			CACAGAGATGGTT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.4150G>A	7.37:g.121653250G>A	ENSP00000377047:p.Asp1384Asn	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	226	103	0.455752	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	196	0.08974358974358974	21	0.042682926829268296	18	0.049723756906077346	117	0.20454545454545456	40	0.052770448548812667	G	12.01	1.808443	0.31961	0.077621	0.075116	ENSG00000106278	ENST00000393386	T	0.45276	0.9	5.1	3.29	0.37713	.	0.832539	0.10667	N	0.648025	T	0.00039	0.0001	L	0.31294	0.92	0.54753	P	1.0999999999983245E-5	B	0.06786	0.001	B	0.04013	0.001	T	0.08391	-1.0724	9	0.46703	T	0.11	.	7.9809	0.30183	0.1449:0.1332:0.7218:0.0	rs61732005	1384	P23471	PTPRZ_HUMAN	N	1384	ENSP00000377047:D1384N	ENSP00000377047:D1384N	D	+	1	0	PTPRZ1	121440486	0.861000	0.29849	0.007000	0.13788	0.897000	0.52465	3.354000	0.52254	0.732000	0.32470	0.555000	0.69702	GAT	G|0.926;A|0.074	0.074	strong		0.438	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
PRKCB	5579	hgsc.bcm.edu	37	16	24104188	24104188	+	Silent	SNP	C	C	T	rs3729896	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:24104188C>T	ENST00000321728.7	+	6	781	c.606C>T	c.(604-606)ccC>ccT	p.P202P	PRKCB_ENST00000303531.7_Silent_p.P202P|PRKCB_ENST00000482000.1_3'UTR	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	202	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	AACTGATTCCCGATCCCAAAA	0.418													C|||	304	0.0607029	0.0265	0.0231	5008	,	,		22128	0.1369		0.0398	False		,,,				2504	0.0767				p.P202P		Atlas-SNP	.											.	PRKCB	383	.	0			c.C606T						PASS	.	C	,	117,4277	90.2+/-128.9	1,115,2081	175.0	150.0	159.0		606,606	1.5	1.0	16	dbSNP_107	159	337,8263	116.6+/-176.3	6,325,3969	no	coding-synonymous,coding-synonymous	PRKCB	NM_002738.6,NM_212535.2	,	7,440,6050	TT,TC,CC		3.9186,2.6627,3.4939	,	202/674,202/672	24104188	454,12540	2197	4300	6497	SO:0001819	synonymous_variant	5579	exon6			GATTCCCGATCCC	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"""protein kinase C, beta 1"""	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.606C>T	16.37:g.24104188C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Silent	SNP	ENST00000321728.7	37	CCDS10618.1																																																																																			C|0.960;T|0.040	0.040	strong		0.418	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
DIS3	22894	hgsc.bcm.edu	37	13	73349359	73349359	+	Missense_Mutation	SNP	G	G	C	rs7332388	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:73349359G>C	ENST00000377767.4	-	6	1077	c.977C>G	c.(976-978)aCa>aGa	p.T326R	DIS3_ENST00000377780.4_Missense_Mutation_p.T296R|DIS3_ENST00000545453.1_Missense_Mutation_p.T164R	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	326			T -> R (in dbSNP:rs7332388). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15489334}.		CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		CATTCGTTCTGTCTCTTCTTC	0.383										Multiple Myeloma(4;0.011)			C|||	2167	0.432708	0.7005	0.2839	5008	,	,		16735	0.2946		0.4215	False		,,,				2504	0.3303				p.T326R		Atlas-SNP	.											DIS3,colon,carcinoma,+1,1	DIS3	103	1	0			c.C977G						PASS	.	C	ARG/THR,ARG/THR	2984,1422	463.6+/-353.6	1015,954,234	104.0	108.0	107.0		887,977	-3.7	0.7	13	dbSNP_116	107	3570,5030	628.9+/-398.2	765,2040,1495	yes	missense,missense	DIS3	NM_001128226.1,NM_014953.3	71,71	1780,2994,1729	CC,CG,GG		41.5116,32.2742,49.6079	benign,benign	296/929,326/959	73349359	6554,6452	2203	4300	6503	SO:0001583	missense	22894	exon6			CGTTCTGTCTCTT	AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"""exosome component 11"""	607533	"""KIAA1008"", ""DIS3 mitotic control homolog (S. cerevisiae)"""	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.977C>G	13.37:g.73349359G>C	ENSP00000366997:p.Thr326Arg	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	309	146	0.472492	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	37	CCDS9447.1	940	0.43040293040293043	342	0.6951219512195121	111	0.30662983425414364	182	0.3181818181818182	305	0.4023746701846966	C	7.510	0.654453	0.14580	0.677258	0.415116	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.46451	0.87;0.87;0.87	6.06	-3.74	0.04385	.	1.139410	0.06233	N	0.689042	T	0.00012	0.0000	N	0.12182	0.205	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.40001	-0.9586	9	0.16420	T	0.52	.	8.482	0.33049	0.0:0.1279:0.316:0.556	rs7332388;rs17178684;rs17857453;rs52823965;rs56756337;rs7332388	296;326	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	R	326;296;164	ENSP00000366997:T326R;ENSP00000367011:T296R;ENSP00000440058:T164R	ENSP00000366997:T326R	T	-	2	0	DIS3	72247360	0.994000	0.37717	0.733000	0.30861	0.693000	0.40251	0.304000	0.19228	-1.012000	0.03387	-0.786000	0.03341	ACA	G|0.526;C|0.474	0.474	strong		0.383	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953	
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049941	69049941	+	Missense_Mutation	SNP	T	T	C	rs10177248	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:69049941T>C	ENST00000295381.3	+	10	2086	c.1667T>C	c.(1666-1668)aTg>aCg	p.M556T	ARHGAP25_ENST00000409202.3_Missense_Mutation_p.M557T|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.M250T|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.M550T|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.M549T|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.M517T	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	556			M -> T (in dbSNP:rs10177248). {ECO:0000269|PubMed:14702039}.		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						TTGCAGAGGATGGTCCAAGAG	0.453													t|||	1603	0.320088	0.3525	0.3213	5008	,	,		20565	0.4097		0.335	False		,,,				2504	0.1677				p.M557T		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.T1670C						PASS	.	T	THR/MET,THR/MET,THR/MET,THR/MET	1578,2826	454.7+/-350.8	286,1006,910	69.0	77.0	75.0		1670,1649,1550,1646	-1.1	0.7	2	dbSNP_119	75	2743,5857	409.6+/-349.9	454,1835,2011	yes	missense,missense,missense,missense	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	81,81,81,81	740,2841,2921	CC,CT,TT		31.8953,35.8311,33.2282	benign,benign,benign,benign	557/647,550/640,517/607,549/639	69049941	4321,8683	2202	4300	6502	SO:0001583	missense	9938	exon10			AGAGGATGGTCCA	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1667T>C	2.37:g.69049941T>C	ENSP00000295381:p.Met556Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	80	28	0.35	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		809|809	0.37042124542124544|0.37042124542124544	194|194	0.3943089430894309|0.3943089430894309	99|99	0.27348066298342544|0.27348066298342544	279|279	0.48776223776223776|0.48776223776223776	237|237	0.31266490765171506|0.31266490765171506	t|t	0.793|0.793	-0.758089|-0.758089	0.03019|0.03019	0.358311|0.358311	0.318953|0.318953	ENSG00000163219|ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000543533;ENST00000479844|ENST00000497259	T;T;T;T;T;T|.	0.44083|.	2.89;2.89;2.63;0.93;0.93;0.93|.	5.42|5.42	-1.08|-1.08	0.09936|0.09936	.|.	1.099060|.	0.06758|.	N|.	0.781298|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	P|P	0.99999229651|0.99999229651	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0;0.0|.	T|T	0.47699|0.47699	-0.9097|-0.9097	9|4	0.21014|.	T|.	0.42|.	.|.	9.614|9.614	0.39681|0.39681	0.0:0.3108:0.0:0.6892|0.0:0.3108:0.0:0.6892	rs10177248|rs10177248	517;557;550;549;556|.	E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331|.	.;.;.;.;RHG25_HUMAN|.	T|R	556;557;517;549;550;550;541;250|416	ENSP00000295381:M556T;ENSP00000386911:M557T;ENSP00000420583:M517T;ENSP00000386863:M549T;ENSP00000386241:M550T;ENSP00000417467:M250T|.	ENSP00000295381:M556T|.	M|W	+|+	2|1	0|0	ARHGAP25|ARHGAP25	68903445|68903445	0.003000|0.003000	0.15002|0.15002	0.678000|0.678000	0.29963|0.29963	0.441000|0.441000	0.31987|0.31987	-0.142000|-0.142000	0.10311|0.10311	-0.347000|-0.347000	0.08299|0.08299	-1.438000|-1.438000	0.01074|0.01074	ATG|TGG	T|0.655;C|0.345	0.345	strong		0.453	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
TLK1	9874	hgsc.bcm.edu	37	2	171910313	171910313	+	Silent	SNP	C	C	T	rs11553951	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:171910313C>T	ENST00000431350.2	-	8	1094	c.690G>A	c.(688-690)caG>caA	p.Q230Q	TLK1_ENST00000521943.1_Silent_p.Q182Q|TLK1_ENST00000442919.2_Silent_p.Q182Q|TLK1_ENST00000434911.2_Silent_p.Q134Q|TLK1_ENST00000360843.3_Silent_p.Q251Q|TLK1_ENST00000486857.1_5'UTR			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	230				Q -> L (in Ref. 1; BAA20562). {ECO:0000305}.	cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TTTCCAGGTCCTGGATTTTAT	0.313													C|||	563	0.11242	0.0189	0.1484	5008	,	,		18239	0.0437		0.2783	False		,,,				2504	0.1135				p.Q230Q		Atlas-SNP	.											.	TLK1	134	.	0			c.G690A						PASS	.	C	,,	241,4163	141.9+/-177.2	1,239,1962	162.0	174.0	170.0		546,402,690	-0.4	1.0	2	dbSNP_120	170	2326,6274	388.4+/-342.6	311,1704,2285	no	coding-synonymous,coding-synonymous,coding-synonymous	TLK1	NM_001136554.1,NM_001136555.1,NM_012290.4	,,	312,1943,4247	TT,TC,CC		27.0465,5.4723,19.7401	,,	182/719,134/671,230/767	171910313	2567,10437	2202	4300	6502	SO:0001819	synonymous_variant	9874	exon8			CAGGTCCTGGATT	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.690G>A	2.37:g.171910313C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_012290	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Silent	SNP	ENST00000431350.2	37	CCDS2241.1																																																																																			C|0.814;T|0.186	0.186	strong		0.313	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290	
SLC9C2	284525	hgsc.bcm.edu	37	1	173516903	173516903	+	Silent	SNP	A	A	G	rs10494490	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:173516903A>G	ENST00000367714.3	-	13	1904	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Silent_p.N392N	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	494					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TCTTCATATCATTATGTGAAA	0.338													G|||	2430	0.485224	0.671	0.3732	5008	,	,		18236	0.6448		0.2147	False		,,,				2504	0.4274				p.N494N		Atlas-SNP	.											SLC9A11,NS,carcinoma,-2,1	.	.	1	0			c.T1482C						PASS	.	G		2607,1799	529.7+/-372.7	790,1027,386	148.0	131.0	137.0		1482	-3.2	0.0	1	dbSNP_119	137	1797,6803	733.2+/-406.9	188,1421,2691	no	coding-synonymous	SLC9A11	NM_178527.3		978,2448,3077	GG,GA,AA		20.8953,40.8307,33.8613		494/1125	173516903	4404,8602	2203	4300	6503	SO:0001819	synonymous_variant	284525	exon13			CATATCATTATGT	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1482T>C	1.37:g.173516903A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	127	51	0.401575	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	37	CCDS1308.1																																																																																			A|0.637;G|0.363	0.363	strong		0.338	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
CDRT15	146822	hgsc.bcm.edu	37	17	14140080	14140080	+	Missense_Mutation	SNP	C	C	T	rs17679866	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:14140080C>T	ENST00000420162.2	-	1	86	c.71G>A	c.(70-72)cGa>cAa	p.R24Q	CDRT15_ENST00000431716.2_5'UTR	NM_001007530.1	NP_001007531.1	Q96T59	CDRTF_HUMAN	CMT1A duplicated region transcript 15	24			R -> Q (in dbSNP:rs17679866).							endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		TCGGCATCGTCGGAAAAGGCT	0.582													C|||	348	0.0694888	0.0061	0.0692	5008	,	,		20897	0.0754		0.1243	False		,,,				2504	0.093				p.R24Q		Atlas-SNP	.											.	CDRT15	20	.	0			c.G71A						PASS	.	C	GLN/ARG	106,4300	80.9+/-119.3	5,96,2102	51.0	48.0	49.0		71	-0.6	0.0	17	dbSNP_123	49	1045,7551	219.5+/-257.5	53,939,3306	no	missense	CDRT15	NM_001007530.1	43	58,1035,5408	TT,TC,CC		12.1568,2.4058,8.8525	probably-damaging	24/189	14140080	1151,11851	2203	4298	6501	SO:0001583	missense	146822	exon1			CATCGTCGGAAAA	AF355097	CCDS32569.1	17p12	2012-11-19			ENSG00000223510	ENSG00000223510			14395	protein-coding gene	gene with protein product						11381029	Standard	NM_001007530		Approved		uc010vvu.2	Q96T59	OTTHUMG00000179686	ENST00000420162.2:c.71G>A	17.37:g.14140080C>T	ENSP00000402355:p.Arg24Gln	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	225	100	0.444444	NM_001007530	B2RUU5	Missense_Mutation	SNP	ENST00000420162.2	37	CCDS32569.1	142	0.06501831501831502	3	0.006097560975609756	29	0.08011049723756906	29	0.050699300699300696	81	0.10686015831134564	C	12.63	1.996689	0.35226	0.024058	0.121568	ENSG00000223510	ENST00000420162	T	0.59502	0.26	0.675	-0.604	0.11626	.	.	.	.	.	T	0.00524	0.0017	L	0.29908	0.895	0.09310	N	1	P	0.50943	0.94	B	0.35240	0.198	T	0.02059	-1.1221	8	0.87932	D	0	.	.	.	.	rs17679866;rs52796367;rs17679866	24	Q96T59	CDRTF_HUMAN	Q	24	ENSP00000402355:R24Q	ENSP00000402355:R24Q	R	-	2	0	CDRT15	14080805	0.951000	0.32395	0.000000	0.03702	0.003000	0.03518	0.124000	0.15728	-0.187000	0.10516	-0.763000	0.03452	CGA	C|0.921;T|0.079	0.079	strong		0.582	CDRT15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252853.1	NM_001007530	
FNDC9	408263	hgsc.bcm.edu	37	5	156770209	156770209	+	Silent	SNP	G	G	A	rs10214194	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:156770209G>A	ENST00000312349.4	-	2	523	c.336C>T	c.(334-336)tcC>tcT	p.S112S	CYFIP2_ENST00000377576.3_Intron|CYFIP2_ENST00000442283.2_Intron|CYFIP2_ENST00000521420.1_Intron|CYFIP2_ENST00000347377.6_Intron|CYFIP2_ENST00000541131.1_Intron|CYFIP2_ENST00000435847.2_Intron|CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000318218.6_Intron	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9	112						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						GCACCCAAAGGGAGATCTGGG	0.587											OREG0016977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1367	0.272963	0.3911	0.1556	5008	,	,		20194	0.2986		0.171	False		,,,				2504	0.2751				p.S112S		Atlas-SNP	.											.	FNDC9	22	.	0			c.C336T						PASS	.	G	,,,	1515,2891	482.3+/-359.4	242,1031,930	74.0	76.0	75.0		336,,,	0.4	1.0	5	dbSNP_119	75	1391,7209	269.8+/-288.6	109,1173,3018	no	coding-synonymous,intron,intron,intron	CYFIP2,FNDC9	NM_001001343.3,NM_001037332.2,NM_001037333.1,NM_014376.2	,,,	351,2204,3948	AA,AG,GG		16.1744,34.3849,22.3435	,,,	112/225,,,	156770209	2906,10100	2203	4300	6503	SO:0001819	synonymous_variant	408263	exon2			CCAAAGGGAGATC	BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"""Fibronectin type III domain containing"""	33547	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 40"""	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248	ENST00000312349.4:c.336C>T	5.37:g.156770209G>A		Somatic	105	0	0	1781	WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_001001343	A8K0Y6	Silent	SNP	ENST00000312349.4	37	CCDS4337.1																																																																																			G|0.764;A|0.236	0.236	strong		0.587	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343	
MEF2D	4209	hgsc.bcm.edu	37	1	156450740	156450740	+	Silent	SNP	G	G	A	rs1925950	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156450740G>A	ENST00000348159.4	-	4	762	c.282C>T	c.(280-282)aaC>aaT	p.N94N	MEF2D_ENST00000340875.5_Intron|MEF2D_ENST00000464356.2_Intron|MEF2D_ENST00000353795.3_Intron|MEF2D_ENST00000368240.2_Silent_p.N94N|MEF2D_ENST00000360595.3_Silent_p.N94N	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	94					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGTCGCAGCCGTTGAAGCCCT	0.672											OREG0013874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2866	0.572284	0.2368	0.5951	5008	,	,		14671	0.756		0.673	False		,,,				2504	0.7168				p.N94N		Atlas-SNP	.											.	MEF2D	43	.	0			c.C282T						PASS	.	G		1385,3021	437.0+/-344.8	237,911,1055	79.0	88.0	85.0		282	-1.4	1.0	1	dbSNP_92	85	5655,2941	642.9+/-399.9	1854,1947,497	no	coding-synonymous	MEF2D	NM_005920.2		2091,2858,1552	AA,AG,GG		34.2136,31.4344,45.8545		94/522	156450740	7040,5962	2203	4298	6501	SO:0001819	synonymous_variant	4209	exon4			GCAGCCGTTGAAG	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"""Myocyte enhancer factors"""	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.282C>T	1.37:g.156450740G>A		Somatic	115	0	0	1778	WXS	Illumina HiSeq	Phase_I	145	145	1	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Silent	SNP	ENST00000348159.4	37	CCDS1143.1																																																																																			G|0.452;A|0.548	0.548	strong		0.672	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920	
PASK	23178	hgsc.bcm.edu	37	2	242080119	242080119	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242080119A>C	ENST00000405260.1	-	3	944	c.246T>G	c.(244-246)atT>atG	p.I82M	PASK_ENST00000358649.4_Missense_Mutation_p.I82M|PASK_ENST00000234040.4_Missense_Mutation_p.I82M|PASK_ENST00000403638.3_Missense_Mutation_p.I82M|PASK_ENST00000544142.1_Intron|PASK_ENST00000539818.1_Intron	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	82					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		TACTTGTACAAATATTCTGGG	0.557																																					p.I82M		Atlas-SNP	.											.	PASK	230	.	0			c.T246G						PASS	.						70.0	70.0	70.0					2																	242080119		2203	4300	6503	SO:0001583	missense	23178	exon3			TGTACAAATATTC	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.246T>G	2.37:g.242080119A>C	ENSP00000384016:p.Ile82Met	Somatic	426	0	0		WXS	Illumina HiSeq	Phase_I	483	211	0.436853	NM_001252122	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.015499	0.35511	.	.	ENSG00000115687	ENST00000234040;ENST00000405260;ENST00000358649;ENST00000403638;ENST00000452907	T;T;T;T	0.74842	-0.88;-0.88;-0.84;0.1	4.54	-2.86	0.05717	.	0.000000	0.52532	D	0.000076	T	0.78572	0.4304	M	0.61703	1.905	0.42674	D	0.993524	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.87578	0.981;0.998;0.982;0.981	T	0.75470	-0.3306	10	0.87932	D	0	.	6.5076	0.22204	0.4255:0.1261:0.4485:0.0	.	82;82;82;82	B7Z7R6;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;PASK_HUMAN	M	82	ENSP00000234040:I82M;ENSP00000384016:I82M;ENSP00000351475:I82M;ENSP00000384438:I82M	ENSP00000234040:I82M	I	-	3	3	PASK	241728792	0.204000	0.23447	0.036000	0.18154	0.265000	0.26407	-0.645000	0.05409	-0.426000	0.07360	-0.464000	0.05259	ATT	.	.	none		0.557	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
RFPL4A	342931	hgsc.bcm.edu	37	19	56273293	56273293	+	Missense_Mutation	SNP	G	G	A	rs2019946	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56273293G>A	ENST00000434937.2	+	2	298	c.127G>A	c.(127-129)Gat>Aat	p.D43N		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	43							zinc ion binding (GO:0008270)	p.D43N(1)		haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						GAAGGAGCCCGATGGGGAAGG	0.502													G|||	1154	0.230431	0.1089	0.281	5008	,	,		23158	0.2758		0.2575	False		,,,				2504	0.2843				p.D43N		Atlas-SNP	.											ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	1	Substitution - Missense(1)	stomach(1)	c.G127A						scavenged	.						3.0	2.0	2.0					19																	56273293		554	1272	1826	SO:0001583	missense	342931	exon2			GAGCCCGATGGGG		CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638		"""RING-type (C3HC4) zinc fingers"""	16449	protein-coding gene	gene with protein product		612601	"""ret finger protein-like 4"""	RFPL4		11850190	Standard	NM_001145014		Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.127G>A	19.37:g.56273293G>A	ENSP00000392936:p.Asp43Asn	Somatic	561	2	0.00356506		WXS	Illumina HiSeq	Phase_I	648	112	0.17284	NM_001145014		Missense_Mutation	SNP	ENST00000434937.2	37	CCDS46201.1	.	.	.	.	.	.	.	.	.	.	G	1.780	-0.482237	0.04383	.	.	ENSG00000223638	ENST00000434937	T	0.16196	2.36	3.31	-6.62	0.01813	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);RDM domain, Ret finger protein-like (1);	.	.	.	.	T	0.05777	0.0151	N	0.03608	-0.345	0.80722	P	0.0	B	0.12630	0.006	B	0.14578	0.011	T	0.35425	-0.9789	8	0.34782	T	0.22	-5.3823	6.2307	0.20734	0.2073:0.1271:0.5744:0.0912	rs2019946	43	A6NLU0	RFPLA_HUMAN	N	43	ENSP00000392936:D43N	ENSP00000392936:D43N	D	+	1	0	RFPL4A	60965105	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-4.030000	0.00310	-3.052000	0.00259	-0.538000	0.04264	GAT	G|0.500;A|0.500	0.500	strong		0.502	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384184.1	XM_292796	
TRIOBP	11078	hgsc.bcm.edu	37	22	38164106	38164106	+	Silent	SNP	C	C	T	rs4821708	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38164106C>T	ENST00000406386.3	+	19	6753	c.6498C>T	c.(6496-6498)taC>taT	p.Y2166Y	TRIOBP_ENST00000403663.2_Silent_p.Y453Y	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	2166					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					AGAAGGCCTACCAGGAAGAGC	0.612													C|||	1326	0.264776	0.0408	0.2997	5008	,	,		18755	0.2927		0.336	False		,,,				2504	0.4407				p.Y2166Y		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	0			c.C6498T						PASS	.	C	,	303,3729		11,281,1724	33.0	37.0	35.0		6498,1359	1.0	1.0	22	dbSNP_111	35	2561,5783		367,1827,1978	no	coding-synonymous,coding-synonymous	TRIOBP	NM_001039141.2,NM_007032.5	,	378,2108,3702	TT,TC,CC		30.6927,7.5149,23.1416	,	2166/2366,453/653	38164106	2864,9512	2016	4172	6188	SO:0001819	synonymous_variant	11078	exon19			GGCCTACCAGGAA	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.6498C>T	22.37:g.38164106C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.739;T|0.261	0.261	strong		0.612	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
LRCH4	4034	hgsc.bcm.edu	37	7	100175010	100175010	+	Missense_Mutation	SNP	C	C	T	rs140761835	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100175010C>T	ENST00000310300.6	-	11	1233	c.1181G>A	c.(1180-1182)cGg>cAg	p.R394Q	LRCH4_ENST00000497245.1_5'UTR	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	394					nervous system development (GO:0007399)	PML body (GO:0016605)				NS(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	23	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CGGCTCCTCCCGCCTGAGGGA	0.741													C|||	25	0.00499201	0.0008	0.0115	5008	,	,		13720	0.0		0.0119	False		,,,				2504	0.0041				p.R394Q		Atlas-SNP	.											LRCH4,caecum,carcinoma,+1,1	LRCH4	53	1	0			c.G1181A						PASS	.	C	GLN/ARG	15,4287		0,15,2136	15.0	19.0	18.0		1181	3.2	1.0	7	dbSNP_134	18	139,8325		1,137,4094	yes	missense	LRCH4	NM_002319.3	43	1,152,6230	TT,TC,CC		1.6422,0.3487,1.2063	benign	394/684	100175010	154,12612	2151	4232	6383	SO:0001583	missense	4034	exon11			TCCTCCCGCCTGA	AF053356	CCDS34706.1	7q22	2008-05-20	2004-05-27	2004-05-28	ENSG00000077454	ENSG00000077454			6691	protein-coding gene	gene with protein product				LRN, LRRN1		9799793	Standard	XM_005250346		Approved		uc003uvj.3	O75427	OTTHUMG00000159544	ENST00000310300.6:c.1181G>A	7.37:g.100175010C>T	ENSP00000309689:p.Arg394Gln	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	28	20	0.714286	NM_002319	A4D2D5|Q8WV85|Q96ID0	Missense_Mutation	SNP	ENST00000310300.6	37	CCDS34706.1	16	0.007326007326007326	0	0.0	6	0.016574585635359115	0	0.0	10	0.013192612137203167	C	13.57	2.276222	0.40294	0.003487	0.016422	ENSG00000077454	ENST00000310300	T	0.34275	1.37	5.21	3.2	0.36748	.	0.501717	0.17581	N	0.169125	T	0.07863	0.0197	N	0.17312	0.475	0.80722	D	1	P	0.48998	0.918	B	0.34180	0.177	T	0.01492	-1.1341	10	0.29301	T	0.29	-22.7983	7.2591	0.26193	0.172:0.565:0.263:0.0	.	394	O75427	LRCH4_HUMAN	Q	394	ENSP00000309689:R394Q	ENSP00000309689:R394Q	R	-	2	0	LRCH4	100012946	1.000000	0.71417	1.000000	0.80357	0.435000	0.31806	0.771000	0.26633	2.460000	0.83146	0.536000	0.68110	CGG	C|0.991;T|0.009	0.009	strong		0.741	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319	
PSG2	5670	hgsc.bcm.edu	37	19	43585111	43585111	+	Missense_Mutation	SNP	C	C	G	rs149579909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:43585111C>G	ENST00000406487.1	-	2	450	c.352G>C	c.(352-354)Gga>Cga	p.G118R	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	118	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.G118R(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				GTGTAGGATCCTGCGTCCTCC	0.458																																					p.G118R		Atlas-SNP	.											PSG2,NS,carcinoma,0,2	PSG2	84	2	2	Substitution - Missense(2)	pancreas(2)	c.G352C						PASS	.	C	ARG/GLY	130,4270		6,118,2076	109.0	109.0	109.0		352	-1.0	0.0	19	dbSNP_134	109	928,7630		54,820,3405	no	missense	PSG2	NM_031246.3	125	60,938,5481	GG,GC,CC		10.8437,2.9545,8.1648		118/336	43585111	1058,11900	2200	4279	6479	SO:0001583	missense	5670	exon2			AGGATCCTGCGTC		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.352G>C	19.37:g.43585111C>G	ENSP00000385706:p.Gly118Arg	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	164	76	0.463415	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	162	0.07417582417582418	10	0.02032520325203252	59	0.16298342541436464	2	0.0034965034965034965	91	0.12005277044854881	N	9.270	1.045500	0.19748	0.029545	0.108437	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.11821	2.74	0.569	-1.01	0.10169	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00144	0.0004	M	0.88906	2.99	0.80722	P	0.0	D;D	0.76494	0.999;0.997	D;D	0.87578	0.998;0.994	T	0.02081	-1.1217	7	0.59425	D	0.04	.	.	.	.	.	118;118	B5MCM8;P11465	.;PSG2_HUMAN	R	118	ENSP00000385706:G118R	ENSP00000332984:G118R	G	-	1	0	PSG2	48276951	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.134000	0.10436	-0.398000	0.07679	0.184000	0.17185	GGA	C|0.920;G|0.080	0.080	strong		0.458	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
TMEM132B	114795	hgsc.bcm.edu	37	12	125900095	125900095	+	Silent	SNP	T	T	A	rs3809261	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:125900095T>A	ENST00000299308.3	+	3	971	c.963T>A	c.(961-963)ggT>ggA	p.G321G		NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	321						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CGGCAGCAGGTGTGAAGATAA	0.463													T|||	504	0.100639	0.0666	0.0677	5008	,	,		18057	0.1419		0.0994	False		,,,				2504	0.1288				p.G321G		Atlas-SNP	.											.	TMEM132B	207	.	0			c.T963A						PASS	.	T		236,4070		6,224,1923	79.0	92.0	88.0		963	-7.4	0.6	12	dbSNP_107	88	732,7782		34,664,3559	no	coding-synonymous	TMEM132B	NM_052907.2		40,888,5482	AA,AT,TT		8.5976,5.4807,7.5507		321/1079	125900095	968,11852	2153	4257	6410	SO:0001819	synonymous_variant	114795	exon3			AGCAGGTGTGAAG	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.963T>A	12.37:g.125900095T>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	136	63	0.463235	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																			T|0.901;A|0.099	0.099	strong		0.463	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
OR5H1	26341	hgsc.bcm.edu	37	3	97851968	97851968	+	Missense_Mutation	SNP	C	C	T	rs139235176	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:97851968C>T	ENST00000354565.2	+	1	427	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						ACTGTGCATCCGGCTATTAAT	0.388																																					p.R143W		Atlas-SNP	.											OR5H1,colon,carcinoma,0,1	OR5H1	71	1	0			c.C427T						scavenged	.						63.0	72.0	69.0					3																	97851968		2182	4277	6459	SO:0001583	missense	26341	exon1			TGCATCCGGCTAT	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"""GPCR / Class A : Olfactory receptors"""	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.427C>T	3.37:g.97851968C>T	ENSP00000346575:p.Arg143Trp	Somatic	483	2	0.00414079		WXS	Illumina HiSeq	Phase_I	603	46	0.0762852	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	37	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	C	0.086	-1.174883	0.01646	.	.	ENSG00000231192	ENST00000354565	T	0.00130	8.69	3.57	-0.653	0.11447	GPCR, rhodopsin-like superfamily (1);	1.510900	0.04359	N	0.357065	T	0.00144	0.0004	L	0.39633	1.23	0.09310	N	1	B	0.18166	0.026	B	0.15870	0.014	T	0.26815	-1.0092	10	0.32370	T	0.25	.	2.721	0.05201	0.3436:0.343:0.0:0.3134	.	143	A6NKK0	OR5H1_HUMAN	W	143	ENSP00000346575:R143W	ENSP00000346575:R143W	R	+	1	2	OR5H1	99334658	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.591000	0.00421	-0.433000	0.07286	-1.098000	0.02139	CGG	C|0.989;T|0.011	0.011	strong		0.388	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338	
GAN	8139	hgsc.bcm.edu	37	16	81398635	81398635	+	Silent	SNP	C	C	T	rs2608555	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81398635C>T	ENST00000568107.2	+	8	1455	c.1293C>T	c.(1291-1293)taC>taT	p.Y431Y		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	431					cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				GAGGCTCCTACGGAAAGCTTT	0.498													c|||	757	0.151158	0.1778	0.1225	5008	,	,		17016	0.0407		0.2644	False		,,,				2504	0.1329				p.Y431Y	GBM(106;1239 1507 7582 9741 33976)	Atlas-SNP	.											.	GAN	59	.	0			c.C1293T						PASS	.	T		844,3560	333.3+/-302.9	74,696,1432	72.0	68.0	69.0		1293	-0.5	0.4	16	dbSNP_100	69	2144,6456	367.9+/-334.9	267,1610,2423	no	coding-synonymous	GAN	NM_022041.3		341,2306,3855	TT,TC,CC		24.9302,19.1644,22.9775		431/598	81398635	2988,10016	2202	4300	6502	SO:0001819	synonymous_variant	8139	exon8			CTCCTACGGAAAG	AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"""Kelch-like"", ""BTB/POZ domain containing"""	4137	protein-coding gene	gene with protein product	"""kelch-like family member 16"""	605379	"""giant axonal neuropathy (gigaxonin)"""			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.1293C>T	16.37:g.81398635C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_022041		Silent	SNP	ENST00000568107.2	37	CCDS10935.1																																																																																			C|0.800;T|0.200	0.200	strong		0.498	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3		
MUC21	394263	hgsc.bcm.edu	37	6	30955929	30955929	+	Silent	SNP	C	C	A	rs2517416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30955929C>A	ENST00000376296.3	+	3	1900	c.1659C>A	c.(1657-1659)tcC>tcA	p.S553S	MUC21_ENST00000486149.2_Silent_p.S99S	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	553	Cytoplasmic tail.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GACCAGTATCCTCGATAGCCA	0.612													C|||	771	0.153954	0.1536	0.2622	5008	,	,		15981	0.1181		0.1451	False		,,,				2504	0.1237				p.S553S		Atlas-SNP	.											.	MUC21	98	.	0			c.C1659A						PASS	.	C		457,2561		37,383,1089	43.0	46.0	45.0		1659	2.7	0.0	6	dbSNP_100	45	795,4621		59,677,1972	no	coding-synonymous	MUC21	NM_001010909.2		96,1060,3061	AA,AC,CC		14.6787,15.1425,14.8447		553/567	30955929	1252,7182	1509	2708	4217	SO:0001819	synonymous_variant	394263	exon3			AGTATCCTCGATA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1659C>A	6.37:g.30955929C>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	82	48	0.585366	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			C|0.857;A|0.143	0.143	strong		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
STIM2	57620	hgsc.bcm.edu	37	4	27024524	27024524	+	Missense_Mutation	SNP	G	G	A	rs147362228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:27024524G>A	ENST00000467087.1	+	12	2675	c.2147G>A	c.(2146-2148)aGa>aAa	p.R716K	STIM2_ENST00000465503.1_Missense_Mutation_p.R724K|STIM2_ENST00000382009.3_Missense_Mutation_p.R811K|STIM2_ENST00000467011.1_3'UTR|STIM2_ENST00000237364.5_Missense_Mutation_p.R803K|STIM2_ENST00000412829.2_3'UTR			Q9P246	STIM2_HUMAN	stromal interaction molecule 2	716					activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				AGTGTTGCCAGAATAAGCAGC	0.458													G|||	3	0.000599042	0.0008	0.0	5008	,	,		20105	0.0		0.002	False		,,,				2504	0.0				p.R724K		Atlas-SNP	.											.	STIM2	77	.	0			c.G2171A						PASS	.	G	LYS/ARG,LYS/ARG,	0,4406		0,0,2203	99.0	100.0	99.0		2171,2147,	5.0	1.0	4	dbSNP_134	99	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,utr-3	STIM2	NM_001169118.1,NM_020860.3,NM_001169117.1	26,26,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	possibly-damaging,possibly-damaging,	724/755,716/747,	27024524	3,13003	2203	4300	6503	SO:0001583	missense	57620	exon13			TTGCCAGAATAAG	AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"""Sterile alpha motif (SAM) domain containing"""	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467087.1:c.2147G>A	4.37:g.27024524G>A	ENSP00000419073:p.Arg716Lys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_001169118	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Missense_Mutation	SNP	ENST00000467087.1	37	CCDS3440.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	14.37	2.515082	0.44763	0.0	3.49E-4	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000465503	T;T;T;T	0.76968	-1.03;-1.06;-1.06;-1.04	5.87	5.02	0.67125	.	0.254762	0.44902	D	0.000414	T	0.67813	0.2933	N	0.24115	0.695	0.80722	D	1	P;P	0.48640	0.858;0.913	B;B	0.42593	0.22;0.392	T	0.71856	-0.4466	10	0.54805	T	0.06	.	14.2358	0.65925	0.0:0.0:0.7287:0.2713	.	811;803	E9PGD0;F5GXJ4	.;.	K	716;811;803;724	ENSP00000419073:R716K;ENSP00000371439:R811K;ENSP00000237364:R803K;ENSP00000417569:R724K	ENSP00000237364:R803K	R	+	2	0	STIM2	26633622	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.921000	0.48852	1.583000	0.49898	0.655000	0.94253	AGA	G|0.999;A|0.001	0.001	strong		0.458	STIM2-001	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215063.2	NM_020860	
OLFML1	283298	hgsc.bcm.edu	37	11	7507182	7507182	+	Missense_Mutation	SNP	A	A	G	rs118163706	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7507182A>G	ENST00000329293.3	+	1	470	c.76A>G	c.(76-78)Acc>Gcc	p.T26A	CTD-2516F10.2_ENST00000530201.1_RNA|OLFML1_ENST00000528758.1_Missense_Mutation_p.T26A|OLFML1_ENST00000530135.1_Missense_Mutation_p.T26A	NM_198474.3	NP_940876.2	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1	26						extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(3)|prostate(2)	24				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GCCGCAGTGTACCCAGGACCC	0.547													G|||	80	0.0159744	0.0053	0.0115	5008	,	,		18910	0.0		0.0517	False		,,,				2504	0.0133				p.T26A		Atlas-SNP	.											.	OLFML1	54	.	0			c.A76G						PASS	.	G	ALA/THR	71,4331	819.6+/-416.4	1,69,2131	129.0	116.0	120.0		76	5.6	0.8	11	dbSNP_132	120	593,7999	792.1+/-407.5	16,561,3719	yes	missense	OLFML1	NM_198474.3	58	17,630,5850	GG,GA,AA		6.9018,1.6129,5.1101	benign	26/403	7507182	664,12330	2201	4296	6497	SO:0001583	missense	283298	exon1			CAGTGTACCCAGG	AY358591	CCDS7779.1	11p15	2008-02-05			ENSG00000183801	ENSG00000183801			24473	protein-coding gene	gene with protein product							Standard	NM_198474		Approved	UNQ564	uc001mfi.3	Q6UWY5	OTTHUMG00000165527	ENST00000329293.3:c.76A>G	11.37:g.7507182A>G	ENSP00000332511:p.Thr26Ala	Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	228	113	0.495614	NM_198474	B4DP03|Q569G4	Missense_Mutation	SNP	ENST00000329293.3	37	CCDS7779.1	49	0.022435897435897436	3	0.006097560975609756	6	0.016574585635359115	0	0.0	40	0.052770448548812667	G	5.656	0.305689	0.10733	0.016129	0.069018	ENSG00000183801	ENST00000530135;ENST00000329293;ENST00000534244;ENST00000528758	D;D	0.86627	-2.15;-2.15	5.59	5.59	0.84812	.	0.272836	0.35096	N	0.003445	T	0.08179	0.0204	N	0.00146	-1.995	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39121	-0.9629	10	0.02654	T	1	.	10.7027	0.45937	0.0878:0.0:0.9122:0.0	.	26;26	Q6UWY5;Q5HYE3	OLFL1_HUMAN;.	A	26	ENSP00000433455:T26A;ENSP00000332511:T26A	ENSP00000332511:T26A	T	+	1	0	OLFML1	7463758	0.836000	0.29430	0.814000	0.32528	0.621000	0.37620	1.491000	0.35583	1.377000	0.46286	-0.186000	0.12905	ACC	A|0.959;G|0.041	0.041	strong		0.547	OLFML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384656.1	NM_198474	
ZNF645	158506	hgsc.bcm.edu	37	X	22291732	22291732	+	Silent	SNP	C	C	T	rs6629461	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:22291732C>T	ENST00000323684.1	+	1	668	c.624C>T	c.(622-624)atC>atT	p.I208I		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	208					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						ATAAGGATATCCAGGCTCCTC	0.438													T|||	1014	0.268609	0.202	0.2608	3775	,	,		15996	0.3403		0.0885	False		,,,				2504	0.137				p.I208I		Atlas-SNP	.											.	ZNF645	67	.	0			c.C624T						PASS	.	T		937,2898		103,585,146,944,425	141.0	97.0	112.0		624	-2.1	0.0	X	dbSNP_116	112	795,5933		44,493,214,1891,1658	no	coding-synonymous	ZNF645	NM_152577.3		147,1078,360,2835,2083	TT,TC,T,CC,C		11.8163,24.4329,16.3969		208/426	22291732	1732,8831	2203	4300	6503	SO:0001819	synonymous_variant	158506	exon1			GGATATCCAGGCT	AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.624C>T	X.37:g.22291732C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	86	83	0.965116	NM_152577	A0AV29|A0AV31|E3SBK4|Q6DJY9	Silent	SNP	ENST00000323684.1	37	CCDS14205.1																																																																																			C|0.774;T|0.226	0.226	strong		0.438	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577	
METTL21C	196541	hgsc.bcm.edu	37	13	103339363	103339363	+	Missense_Mutation	SNP	C	C	G	rs148307139	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:103339363C>G	ENST00000267273.6	-	3	332	c.327G>C	c.(325-327)ttG>ttC	p.L109F		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	109					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)			breast(1)|large_intestine(3)|lung(2)|skin(1)	7						CTTGGAAATTCAATTCCTCGG	0.388																																					p.L109F		Atlas-SNP	.											METTL21C,NS,carcinoma,0,1	METTL21C	23	1	0			c.G327C						PASS	.	C	PHE/LEU	0,4406		0,0,2203	83.0	77.0	79.0		327	2.1	1.0	13	dbSNP_134	79	10,8590	7.7+/-29.5	0,10,4290	yes	missense	METTL21C	NM_001010977.1	22	0,10,6493	GG,GC,CC		0.1163,0.0,0.0769	benign	109/265	103339363	10,12996	2203	4300	6503	SO:0001583	missense	196541	exon3			GAAATTCAATTCC		CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"""chromosome 13 open reading frame 39"""	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.327G>C	13.37:g.103339363C>G	ENSP00000267273:p.Leu109Phe	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_001010977		Missense_Mutation	SNP	ENST00000267273.6	37	CCDS32003.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.554827	0.27739	0.0	0.001163	ENSG00000139780	ENST00000267273	T	0.06528	3.29	5.96	2.13	0.27403	.	0.144833	0.48286	D	0.000182	T	0.04543	0.0124	N	0.20766	0.605	0.31573	N	0.656042	B	0.22541	0.071	B	0.22152	0.038	T	0.23833	-1.0177	10	0.20046	T	0.44	-0.0013	12.4417	0.55629	0.0:0.2593:0.6587:0.082	.	109	Q5VZV1	MT21C_HUMAN	F	109	ENSP00000267273:L109F	ENSP00000267273:L109F	L	-	3	2	METTL21C	102137364	0.993000	0.37304	0.974000	0.42286	0.493000	0.33554	0.487000	0.22356	0.381000	0.24851	0.650000	0.86243	TTG	C|0.999;G|0.001	0.001	strong		0.388	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520254	72520254	+	Missense_Mutation	SNP	C	C	T	rs61736607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:72520254C>T	ENST00000373207.1	+	22	3317	c.3317C>T	c.(3316-3318)cCt>cTt	p.P1106L	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.P1109L	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1106	Pro-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						ggcccagaccctggcccaacc	0.637													C|||	140	0.0279553	0.0038	0.0461	5008	,	,		15277	0.001		0.0805	False		,,,				2504	0.0215				p.P1109L		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.C3326T						PASS	.	C	LEU/PRO,LEU/PRO	62,4344	57.4+/-93.9	1,60,2142	54.0	52.0	53.0		3317,3326	3.5	0.0	10	dbSNP_129	53	733,7867	177.2+/-226.9	35,663,3602	yes	missense,missense	ADAMTS14	NM_080722.3,NM_139155.2	98,98	36,723,5744	TT,TC,CC		8.5233,1.4072,6.1126	benign,benign	1106/1224,1109/1227	72520254	795,12211	2203	4300	6503	SO:0001583	missense	140766	exon22			CAGACCCTGGCCC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.3317C>T	10.37:g.72520254C>T	ENSP00000362303:p.Pro1106Leu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	78	0.03571428571428571	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	55	0.07255936675461741	C	9.658	1.143274	0.21205	0.014072	0.085233	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.61859	0.07;0.1	4.44	3.53	0.40419	.	0.685543	0.12145	N	0.495514	T	0.01189	0.0039	N	0.02916	-0.46	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.08055	0.003;0.003	T	0.01591	-1.1317	10	0.15066	T	0.55	.	12.2683	0.54691	0.0:0.9166:0.0:0.0834	rs61736607	1106;1109	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	L	1109;1106	ENSP00000362304:P1109L;ENSP00000362303:P1106L	ENSP00000362303:P1106L	P	+	2	0	ADAMTS14	72190260	0.002000	0.14202	0.017000	0.16124	0.263000	0.26337	1.076000	0.30729	1.220000	0.43490	0.655000	0.94253	CCT	C|0.944;T|0.056	0.056	strong		0.637	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
PLEC	5339	hgsc.bcm.edu	37	8	144993324	144993324	+	Silent	SNP	C	C	T	rs6984820	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144993324C>T	ENST00000322810.4	-	32	11245	c.11076G>A	c.(11074-11076)acG>acA	p.T3692T	PLEC_ENST00000398774.2_Silent_p.T3523T|PLEC_ENST00000345136.3_Silent_p.T3555T|PLEC_ENST00000354589.3_Silent_p.T3555T|PLEC_ENST00000354958.2_Silent_p.T3533T|PLEC_ENST00000436759.2_Silent_p.T3582T|PLEC_ENST00000527096.1_Silent_p.T3578T|PLEC_ENST00000356346.3_Silent_p.T3541T|PLEC_ENST00000357649.2_Silent_p.T3559T	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3692	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TGTACACCTGCGTGGTCTCCA	0.642													C|||	1172	0.234026	0.0348	0.2983	5008	,	,		17797	0.1349		0.4235	False		,,,				2504	0.365				p.T3692T		Atlas-SNP	.											.	PLEC	1144	.	0			c.G11076A						PASS	.	C	,,,,,,,	378,3836		25,328,1754	105.0	122.0	117.0		10746,10623,10599,11076,10569,10665,10677,10665	-4.8	0.6	8	dbSNP_116	117	3444,4994		721,2002,1496	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	746,2330,3250	TT,TC,CC		40.8154,8.9701,30.2087	,,,,,,,	3582/4575,3541/4534,3533/4526,3692/4685,3523/4516,3555/4548,3559/4552,3555/4548	144993324	3822,8830	2107	4219	6326	SO:0001819	synonymous_variant	5339	exon32			CACCTGCGTGGTC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.11076G>A	8.37:g.144993324C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	115	46	0.4	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			C|0.730;T|0.270	0.270	strong		0.642	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
CACNA1B	774	hgsc.bcm.edu	37	9	140777299	140777299	+	Missense_Mutation	SNP	G	G	T	rs71238527	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140777299G>T	ENST00000371372.1	+	3	639	c.494G>T	c.(493-495)gGc>gTc	p.G165V	CACNA1B_ENST00000277549.5_5'UTR|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371355.4_Missense_Mutation_p.G165V|CACNA1B_ENST00000371363.1_Missense_Mutation_p.G165V|CACNA1B_ENST00000277551.2_Missense_Mutation_p.G165V|CACNA1B_ENST00000371357.1_Missense_Mutation_p.G165V	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	165					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CTGCGGAACGGCTGGAACGTC	0.587																																					p.G165V		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G494T						PASS	.	G	VAL/GLY	95,4135		0,95,2020	195.0	208.0	204.0		494	4.6	1.0	9	dbSNP_130	204	992,7488		0,992,3248	yes	missense	CACNA1B	NM_000718.3	109	0,1087,5268	TT,TG,GG		11.6981,2.2459,8.5523	probably-damaging	165/2340	140777299	1087,11623	2115	4240	6355	SO:0001583	missense	774	exon3			GGAACGGCTGGAA	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.494G>T	9.37:g.140777299G>T	ENSP00000360423:p.Gly165Val	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	194	45	0.231959	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.738315	0.30774	0.022459	0.116981	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.98381	-4.9;-4.9;-4.9;-4.9;-4.9	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.66005	0.2746	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60490	-0.7253	10	0.62326	D	0.03	.	17.3563	0.87336	0.0:0.0:1.0:0.0	.	165	B1AQK6	.	V	165	ENSP00000360423:G165V;ENSP00000277551:G165V;ENSP00000360414:G165V;ENSP00000360408:G165V;ENSP00000360406:G165V	ENSP00000277551:G165V	G	+	2	0	CACNA1B	139897120	1.000000	0.71417	0.999000	0.59377	0.154000	0.21943	9.633000	0.98432	2.070000	0.61991	0.467000	0.42956	GGC	G|0.947;T|0.053	0.053	strong		0.587	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
TNXB	7148	hgsc.bcm.edu	37	6	32017242	32017242	+	Missense_Mutation	SNP	C	C	T	rs41258944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32017242C>T	ENST00000375244.3	-	28	9763	c.9562G>A	c.(9562-9564)Gtc>Atc	p.V3188I	TNXB_ENST00000375247.2_Missense_Mutation_p.V3186I			P22105	TENX_HUMAN	tenascin XB	3233	Fibronectin type-III 23. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCCTGGGGGACGGTCCAGGAG	0.677													C|||	364	0.0726837	0.1263	0.0317	5008	,	,		14429	0.0089		0.0686	False		,,,				2504	0.0992				p.V3186I		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,0,2	TNXB	553	2	0			c.G9556A						PASS	.	C	ILE/VAL	283,2221		18,247,987	61.0	67.0	65.0		9556	3.5	0.9	6	dbSNP_127	65	313,4721		14,285,2218	no	missense	TNXB	NM_019105.6	29	32,532,3205	TT,TC,CC		6.2177,11.3019,7.9066	probably-damaging	3186/4243	32017242	596,6942	1252	2517	3769	SO:0001583	missense	7148	exon28			GGGGGACGGTCCA	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.9562G>A	6.37:g.32017242C>T	ENSP00000364393:p.Val3188Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	154	72	0.467532	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		154	0.07051282051282051	83	0.16869918699186992	9	0.024861878453038673	6	0.01048951048951049	56	0.07387862796833773	C	16.71	3.199498	0.58126	0.113019	0.062177	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.56776	0.44;0.44	4.39	3.51	0.40186	.	0.164586	0.28871	N	0.013875	T	0.53334	0.1790	M	0.64170	1.965	0.43814	P	0.003627000000000047	D	0.61697	0.99	D	0.64595	0.927	T	0.54050	-0.8351	9	0.36615	T	0.2	.	9.9009	0.41346	0.0:0.8985:0.0:0.1015	rs41258944;rs62402695	3186	P22105-3	.	I	3188;3186	ENSP00000364393:V3188I;ENSP00000364396:V3186I	ENSP00000364393:V3188I	V	-	1	0	TNXB	32125220	0.002000	0.14202	0.927000	0.36925	0.813000	0.45954	0.228000	0.17814	2.006000	0.58801	0.306000	0.20318	GTC	C|0.855;T|0.145	0.145	strong		0.677	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
CYB5A	1528	hgsc.bcm.edu	37	18	71928150	71928150	+	Splice_Site	SNP	C	C	T	rs7238987	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:71928150C>T	ENST00000340533.4	-	3	428	c.288G>A	c.(286-288)ccG>ccA	p.P96P	CYB5A_ENST00000494131.2_Splice_Site_p.P96P|CYB5A_ENST00000299438.9_Splice_Site_p.P22P|CYB5A_ENST00000579064.1_5'UTR|CYB5A_ENST00000397914.4_Intron	NM_148923.3	NP_683725.1	P00167	CYB5_HUMAN	cytochrome b5 type A (microsomal)	96					hydrogen ion transmembrane transport (GO:1902600)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	aldo-keto reductase (NADP) activity (GO:0004033)|cytochrome-c oxidase activity (GO:0004129)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(1)|lung(1)|skin(1)	4		Esophageal squamous(42;0.0749)|Prostate(75;0.157)|Melanoma(33;0.211)				TCACACTTACCGGAGGCTTGT	0.383													C|||	707	0.141174	0.1596	0.2248	5008	,	,		18057	0.0813		0.1332	False		,,,				2504	0.1268				p.P96P	NSCLC(176;1530 2076 2606 27426 50572)|Ovarian(151;328 1870 2837 37860 52175)	Atlas-SNP	.											.	CYB5A	9	.	0			c.G288A						PASS	.	C	,,	653,3753	278.1+/-274.1	47,559,1597	139.0	128.0	132.0		,288,288	3.6	0.9	18	dbSNP_116	132	1294,7306	256.5+/-280.9	92,1110,3098	yes	intron,coding-synonymous-near-splice,coding-synonymous-near-splice	CYB5A	NM_001190807.2,NM_001914.3,NM_148923.3	,,	139,1669,4695	TT,TC,CC		15.0465,14.8207,14.97	,,	,96/99,96/135	71928150	1947,11059	2203	4300	6503	SO:0001630	splice_region_variant	1528	exon3			ACTTACCGGAGGC	M22865	CCDS12004.1, CCDS12005.1, CCDS54188.1	18q23	2006-01-30	2006-01-30	2006-01-30	ENSG00000166347	ENSG00000166347		"""Cytochrome b genes"""	2570	protein-coding gene	gene with protein product		613218	"""cytochrome b-5"", ""cytochrome b5 (microsomal)"""	CYB5		1840560	Standard	NM_148923		Approved		uc002lli.3	P00167	OTTHUMG00000132843	ENST00000340533.4:c.288+1G>A	18.37:g.71928150C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	83	47	0.566265	NM_148923	A8MV91|F8WEU4|Q6IB14	Silent	SNP	ENST00000340533.4	37	CCDS12004.1																																																																																			C|0.860;T|0.140	0.140	strong		0.383	CYB5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256316.1	NM_001914, NM_148923	Silent
LRP4	4038	hgsc.bcm.edu	37	11	46898771	46898771	+	Missense_Mutation	SNP	T	T	C	rs6485702	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:46898771T>C	ENST00000378623.1	-	23	3498	c.3256A>G	c.(3256-3258)Att>Gtt	p.I1086V	LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1086			I -> V (in dbSNP:rs6485702). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9693030, ECO:0000269|Ref.1}.		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)	p.I1086V(1)		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)		TCTACTCCAATGGCAATGGTG	0.512													T|||	2233	0.445887	0.1256	0.572	5008	,	,		20720	0.2927		0.6769	False		,,,				2504	0.7096				p.I1086V		Atlas-SNP	.											LRP4,NS,carcinoma,0,1	LRP4	160	1	1	Substitution - Missense(1)	stomach(1)	c.A3256G						PASS	.	T	VAL/ILE	977,3425	367.1+/-318.1	126,725,1350	258.0	189.0	212.0		3256	3.9	1.0	11	dbSNP_116	212	5733,2865	674.0+/-403.1	1898,1937,464	yes	missense	LRP4	NM_002334.3	29	2024,2662,1814	CC,CT,TT		33.3217,22.1945,48.3846	benign	1086/1906	46898771	6710,6290	2201	4299	6500	SO:0001583	missense	4038	exon23			CTCCAATGGCAAT	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.3256A>G	11.37:g.46898771T>C	ENSP00000367888:p.Ile1086Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	936	0.42857142857142855	62	0.12601626016260162	193	0.5331491712707183	177	0.3094405594405594	504	0.6649076517150396	T	4.937	0.174078	0.09391	0.221945	0.666783	ENSG00000134569	ENST00000378623	D	0.90955	-2.76	6.17	3.91	0.45181	Six-bladed beta-propeller, TolB-like (1);	0.226336	0.46145	N	0.000309	T	0.00012	0.0000	N	0.08118	0	0.23107	P	0.99828233	B	0.02656	0.0	B	0.06405	0.002	T	0.47649	-0.9101	9	0.19147	T	0.46	.	8.3038	0.32029	0.0:0.2068:0.0:0.7932	rs6485702;rs17790144;rs52801120;rs60959018;rs6485702	1086	O75096	LRP4_HUMAN	V	1086	ENSP00000367888:I1086V	ENSP00000367888:I1086V	I	-	1	0	LRP4	46855347	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.139000	0.42149	1.165000	0.42670	0.533000	0.62120	ATT	T|0.523;C|0.477	0.477	strong		0.512	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
RYR1	6261	hgsc.bcm.edu	37	19	38949904	38949904	+	Silent	SNP	C	C	T	rs3745847	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:38949904C>T	ENST00000359596.3	+	19	2286	c.2286C>T	c.(2284-2286)ccC>ccT	p.P762P	RYR1_ENST00000360985.3_Silent_p.P762P|RYR1_ENST00000355481.4_Silent_p.P762P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	762	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACGGCTGCCCCGTGCAGGGTG	0.622													C|||	2775	0.554113	0.497	0.6686	5008	,	,		18731	0.5933		0.6759	False		,,,				2504	0.3845				p.P762P		Atlas-SNP	.											.	RYR1	708	.	0			c.C2286T						PASS	.	C	,	2367,2039	611.7+/-391.8	623,1121,459	111.0	91.0	98.0		2286,2286	-8.7	0.5	19	dbSNP_107	98	5658,2942	668.3+/-402.5	1857,1944,499	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	2480,3065,958	TT,TC,CC		34.2093,46.2778,38.2977	,	762/5039,762/5034	38949904	8025,4981	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon19			CTGCCCCGTGCAG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.2286C>T	19.37:g.38949904C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	217	217	1	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			C|0.386;T|0.614	0.614	strong		0.622	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
OR5AC2	81050	hgsc.bcm.edu	37	3	97806944	97806944	+	Nonstop_Mutation	SNP	T	T	C	rs80220955	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:97806944T>C	ENST00000358642.2	+	1	928	c.928T>C	c.(928-930)Taa>Caa	p.*310Q		NM_054106.1	NP_473447.1	Q9NZP5	O5AC2_HUMAN	olfactory receptor, family 5, subfamily AC, member 2	0					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	28						TATAAGGAAGTAAACAGTTCC	0.343													T|||	555	0.110823	0.0976	0.1254	5008	,	,		21484	0.0069		0.2366	False		,,,				2504	0.0961				p.X310Q		Atlas-SNP	.											.	OR5AC2	64	.	0			c.T928C						PASS	.	T	GLN/stop	608,3796		46,516,1640	41.0	43.0	42.0		928	1.5	0.0	3	dbSNP_131	42	2059,6539		249,1561,2489	yes	stop-lost	OR5AC2	NM_054106.1		295,2077,4129	CC,CT,TT		23.9474,13.8056,20.5122		310/310	97806944	2667,10335	2202	4299	6501	SO:0001578	stop_lost	81050	exon1			AGGAAGTAAACAG	AF179759	CCDS33796.1	3q11.2	2013-09-23			ENSG00000196578	ENSG00000196578		"""GPCR / Class A : Olfactory receptors"""	15431	protein-coding gene	gene with protein product							Standard	NM_054106		Approved	HSA1	uc011bgs.2	Q9NZP5	OTTHUMG00000160083	ENST00000358642.2:c.928T>C	3.37:g.97806944T>C	ENSP00000351466:p.*310Glnext*?	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	13	0.276596	NM_054106		Missense_Mutation	SNP	ENST00000358642.2	37	CCDS33796.1	273	0.125	40	0.08130081300813008	51	0.1408839779005525	5	0.008741258741258742	177	0.23350923482849603	T	7.475	0.647572	0.14516	0.138056	0.239474	ENSG00000196578	ENST00000358642	.	.	.	4.08	1.53	0.23141	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7376	0.18075	0.1674:0.0:0.1744:0.6581	.	.	.	.	Q	310	.	.	X	+	1	0	OR5AC2	99289634	0.001000	0.12720	0.005000	0.12908	0.013000	0.08279	0.719000	0.25881	0.138000	0.18790	-0.782000	0.03352	TAA	T|0.824;C|0.176	0.176	strong		0.343	OR5AC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359116.1		
ZNF25	219749	hgsc.bcm.edu	37	10	38241067	38241067	+	Missense_Mutation	SNP	A	A	C	rs1208606	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:38241067A>C	ENST00000302609.7	-	6	1571	c.1359T>G	c.(1357-1359)aaT>aaG	p.N453K	AL117337.1_ENST00000582458.1_RNA|ZNF25_ENST00000374633.1_5'UTR	NM_145011.2	NP_659448.1	P17030	ZNF25_HUMAN	zinc finger protein 25	453			N -> K (in dbSNP:rs1208606). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				ACTTCTCAGCATTCCTCTTCT	0.418													C|||	158	0.0315495	0.0015	0.0648	5008	,	,		19419	0.0		0.1024	False		,,,				2504	0.0082				p.N453K		Atlas-SNP	.											.	ZNF25	66	.	0			c.T1359G						PASS	.	C	LYS/ASN	80,4326	819.0+/-416.3	1,78,2124	161.0	141.0	148.0		1359	-0.7	0.0	10	dbSNP_87	148	757,7843	784.7+/-407.6	32,693,3575	yes	missense	ZNF25	NM_145011.2	94	33,771,5699	CC,CA,AA		8.8023,1.8157,6.4355	benign	453/457	38241067	837,12169	2203	4300	6503	SO:0001583	missense	219749	exon6			CTCAGCATTCCTC	AK056452	CCDS7195.1	10p11.2	2013-01-08	2006-05-10		ENSG00000175395	ENSG00000175395		"""Zinc fingers, C2H2-type"", ""-"""	13043	protein-coding gene	gene with protein product		194528	"""zinc finger protein 25 (KOX 19)"""			1639412, 8464732	Standard	NM_145011		Approved	KOX19, FLJ31890, Zfp9	uc001ize.1	P17030	OTTHUMG00000019344	ENST00000302609.7:c.1359T>G	10.37:g.38241067A>C	ENSP00000302222:p.Asn453Lys	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	212	89	0.419811	NM_145011	A9Z1X5|Q8IYE3|Q8NDD6|Q96MU2	Missense_Mutation	SNP	ENST00000302609.7	37	CCDS7195.1	107	0.04899267399267399	1	0.0020325203252032522	32	0.08839779005524862	0	0.0	74	0.09762532981530343	C	1.557	-0.537804	0.04082	0.018157	0.088023	ENSG00000175395	ENST00000302609;ENST00000374633	T	0.04502	3.61	4.46	-0.696	0.11287	Zinc finger, C2H2 (1);	1.517950	0.04479	N	0.377442	T	0.00109	0.0003	N	0.17248	0.465	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46034	-0.9220	9	0.66056	D	0.02	14.094	1.1582	0.01800	0.1446:0.2805:0.1489:0.426	rs1208606;rs17608680;rs17857088;rs52833070;rs61682660;rs1208606	453	P17030	ZNF25_HUMAN	K	453;417	ENSP00000302222:N453K	ENSP00000302222:N453K	N	-	3	2	ZNF25	38281073	.	.	0.000000	0.03702	0.036000	0.12997	.	.	-0.512000	0.06505	-1.078000	0.02229	AAT	A|0.939;C|0.061	0.061	strong		0.418	ZNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051214.1	NM_145011, NM_006966	
TARBP1	6894	hgsc.bcm.edu	37	1	234582651	234582651	+	Missense_Mutation	SNP	T	T	C	rs4920246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:234582651T>C	ENST00000040877.1	-	12	2031	c.2032A>G	c.(2032-2034)Agt>Ggt	p.S678G		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	678			S -> G (in dbSNP:rs4920246).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			GCATTGGTACTAAACTTCATA	0.448													C|||	1518	0.303115	0.3101	0.3804	5008	,	,		13837	0.3036		0.2932	False		,,,				2504	0.2485				p.S678G		Atlas-SNP	.											.	TARBP1	111	.	0			c.A2032G						PASS	.	C	GLY/SER	1452,2954	681.9+/-404.1	242,968,993	182.0	160.0	168.0		2032	4.3	0.0	1	dbSNP_111	168	2344,6256	703.8+/-405.4	305,1734,2261	yes	missense	TARBP1	NM_005646.3	56	547,2702,3254	CC,CT,TT		27.2558,32.9551,29.1865	benign	678/1622	234582651	3796,9210	2203	4300	6503	SO:0001583	missense	6894	exon12			TGGTACTAAACTT		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"""tRNA methyltransferase 3 homolog (S. cerevisiae)"""	605052	"""Tar (HIV-1) RNA binding protein 1"""			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.2032A>G	1.37:g.234582651T>C	ENSP00000040877:p.Ser678Gly	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	245	245	1	NM_005646	Q9H581	Missense_Mutation	SNP	ENST00000040877.1	37	CCDS1601.1	678	0.31043956043956045	157	0.31910569105691056	131	0.36187845303867405	174	0.3041958041958042	216	0.2849604221635884	C	0.008	-1.913982	0.00503	0.329551	0.272558	ENSG00000059588	ENST00000040877	T	0.05025	3.51	5.2	4.29	0.51040	.	0.101514	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45702	-0.9243	9	0.02654	T	1	-9.3057	9.3067	0.37878	0.0:0.8321:0.0:0.1679	rs4920246;rs56505431;rs4920246	678	Q13395	TARB1_HUMAN	G	678	ENSP00000040877:S678G	ENSP00000040877:S678G	S	-	1	0	TARBP1	232649274	0.643000	0.27269	0.022000	0.16811	0.150000	0.21749	1.530000	0.36007	0.804000	0.34136	-0.726000	0.03593	AGT	T|0.703;C|0.297	0.297	strong		0.448	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
C5orf60	285679	hgsc.bcm.edu	37	5	179072006	179072006	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:179072006A>G	ENST00000448248.2	-	1	41	c.16T>C	c.(16-18)Ttg>Ctg	p.L6L	C5orf60_ENST00000506142.1_5'UTR	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	6						integral component of membrane (GO:0016021)		p.L6L(1)		NS(1)|breast(1)|kidney(5)	7						TCCTCAGGCAACTGAGCCCTG	0.577																																					p.L6L		Atlas-SNP	.											C5orf60,NS,carcinoma,0,1	C5orf60	24	1	1	Substitution - coding silent(1)	kidney(1)	c.T16C						scavenged	.						35.0	33.0	34.0					5																	179072006		692	1591	2283	SO:0001819	synonymous_variant	285679	exon1			CAGGCAACTGAGC	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.16T>C	5.37:g.179072006A>G		Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	230	81	0.352174	NM_001142306	A1L488|B7ZM52|B7ZM53	Silent	SNP	ENST00000448248.2	37	CCDS47353.1																																																																																			.	.	weak		0.577	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
OR51I1	390063	hgsc.bcm.edu	37	11	5462085	5462085	+	Silent	SNP	G	G	A	rs11037444	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5462085G>A	ENST00000380211.1	-	1	659	c.660C>T	c.(658-660)taC>taT	p.Y220Y	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	220					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGATCAATGCGTAGGAAAGCA	0.463													G|||	1130	0.225639	0.1203	0.2262	5008	,	,		24335	0.373		0.2256	False		,,,				2504	0.2157				p.Y220Y		Atlas-SNP	.											.	OR51I1	66	.	0			c.C660T						PASS	.	G		573,3829	254.6+/-260.1	35,503,1663	73.0	67.0	69.0		660	0.5	0.8	11	dbSNP_120	69	1798,6796	322.6+/-315.6	198,1402,2697	no	coding-synonymous	OR51I1	NM_001005288.2		233,1905,4360	AA,AG,GG		20.9216,13.0168,18.2441		220/315	5462085	2371,10625	2201	4297	6498	SO:0001819	synonymous_variant	390063	exon1			CAATGCGTAGGAA	BK004429	CCDS31382.1	11p15.4	2012-08-09			ENSG00000167359	ENSG00000167359		"""GPCR / Class A : Olfactory receptors"""	15200	protein-coding gene	gene with protein product							Standard	NM_001005288		Approved		uc010qze.2	Q9H343	OTTHUMG00000066908	ENST00000380211.1:c.660C>T	11.37:g.5462085G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	174	86	0.494253	NM_001005288	B9EKW2|Q6IF33	Silent	SNP	ENST00000380211.1	37	CCDS31382.1																																																																																			G|0.801;A|0.199	0.199	strong		0.463	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288	
CD248	57124	hgsc.bcm.edu	37	11	66083263	66083263	+	Silent	SNP	C	C	T	rs78560344	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:66083263C>T	ENST00000311330.3	-	1	1252	c.1236G>A	c.(1234-1236)ccG>ccA	p.P412P	RP11-867G23.13_ENST00000534065.1_RNA	NM_020404.2	NP_065137.1	Q9HCU0	CD248_HUMAN	CD248 molecule, endosialin	412	Pro-rich.				anatomical structure regression (GO:0060033)|cell migration (GO:0016477)|lymph node development (GO:0048535)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	26						CTGGGAAGCTCGGTCTATAGG	0.647													C|||	27	0.00539137	0.0166	0.0029	5008	,	,		17487	0.0		0.003	False		,,,				2504	0.0				p.P412P		Atlas-SNP	.											CD248,NS,carcinoma,-1,1	CD248	69	1	0			c.G1236A						PASS	.	C		62,4338	57.4+/-93.9	0,62,2138	88.0	91.0	90.0		1236	-3.5	0.2	11	dbSNP_131	90	9,8581	7.1+/-27.0	0,9,4286	no	coding-synonymous	CD248	NM_020404.2		0,71,6424	TT,TC,CC		0.1048,1.4091,0.5466		412/758	66083263	71,12919	2200	4295	6495	SO:0001819	synonymous_variant	57124	exon1			GAAGCTCGGTCTA	AF279142	CCDS8134.1	11q13	2006-04-12	2006-03-28	2005-02-11	ENSG00000174807	ENSG00000174807		"""CD molecules"""	18219	protein-coding gene	gene with protein product	"""endosialin"", ""tumor endothelial marker 1"""	606064	"""CD164 sialomucin-like 1"", ""CD248 antigen, endosialin"""	CD164L1		10947988, 11084048	Standard	NM_020404		Approved	TEM1	uc001ohm.1	Q9HCU0	OTTHUMG00000167073	ENST00000311330.3:c.1236G>A	11.37:g.66083263C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_020404	Q2M2V5|Q3SX55|Q96KB6	Silent	SNP	ENST00000311330.3	37	CCDS8134.1																																																																																			C|0.994;T|0.006	0.006	strong		0.647	CD248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392922.2	NM_020404	
C7orf57	136288	hgsc.bcm.edu	37	7	48081095	48081095	+	Missense_Mutation	SNP	G	G	T	rs10951942	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:48081095G>T	ENST00000348904.3	+	3	432	c.220G>T	c.(220-222)Gcg>Tcg	p.A74S	C7orf57_ENST00000435376.1_5'UTR|C7orf57_ENST00000430738.1_Missense_Mutation_p.A119S|C7orf57_ENST00000420324.1_Missense_Mutation_p.A119S|C7orf57_ENST00000539619.1_Missense_Mutation_p.A74S	NM_001100159.2	NP_001093629.1	Q8NEG2	CG057_HUMAN	chromosome 7 open reading frame 57	74			A -> S (in dbSNP:rs10951942).							breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						TGTGAAGCTCGCGAAACAAGG	0.557													G|||	1790	0.357428	0.2383	0.3559	5008	,	,		16754	0.3294		0.4513	False		,,,				2504	0.4519				p.A74S		Atlas-SNP	.											C7orf57_ENST00000348904,colon,carcinoma,-1,2	C7orf57	59	2	0			c.G220T						PASS	.	G	SER/ALA	878,2922		94,690,1116	30.0	34.0	33.0		220	5.7	0.5	7	dbSNP_120	33	3534,4720		734,2066,1327	yes	missense	C7orf57	NM_001100159.1	99	828,2756,2443	TT,TG,GG		42.8156,23.1053,36.602	probably-damaging	74/296	48081095	4412,7642	1900	4127	6027	SO:0001583	missense	136288	exon3			AAGCTCGCGAAAC	BC031107	CCDS47583.1, CCDS59054.1, CCDS75594.1	7p12.3	2011-11-25			ENSG00000164746	ENSG00000164746			22247	protein-coding gene	gene with protein product							Standard	NM_001100159		Approved		uc003toh.5	Q8NEG2	OTTHUMG00000155808	ENST00000348904.3:c.220G>T	7.37:g.48081095G>T	ENSP00000335500:p.Ala74Ser	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_001100159	C9JBJ8	Missense_Mutation	SNP	ENST00000348904.3	37	CCDS47583.1	796	0.36446886446886445	123	0.25	128	0.35359116022099446	213	0.3723776223776224	332	0.43799472295514513	G	18.43	3.621309	0.66787	0.231053	0.428156	ENSG00000164746	ENST00000420324;ENST00000430738;ENST00000348904;ENST00000539619	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.76002	2.32	0.20074	P	0.9999323842	D	0.61080	0.989	D	0.69142	0.962	T	0.35968	-0.9767	9	0.87932	D	0	-24.527	17.2972	0.87173	0.0:0.0:1.0:0.0	rs10951942;rs12702410;rs17547034;rs52805538;rs56638263;rs10951942	74	Q8NEG2	CG057_HUMAN	S	119;119;74;74	ENSP00000394648:A119S;ENSP00000410944:A119S;ENSP00000335500:A74S;ENSP00000442474:A74S	ENSP00000335500:A74S	A	+	1	0	C7orf57	48047620	1.000000	0.71417	0.501000	0.27601	0.148000	0.21650	6.127000	0.71642	2.670000	0.90874	0.563000	0.77884	GCG	G|0.632;T|0.368	0.368	strong		0.557	C7orf57-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341745.1	NM_001100159	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552921	43552921	+	Silent	SNP	C	C	T	rs12452273	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:43552921C>T	ENST00000430334.3	-	4	601	c.468G>A	c.(466-468)cgG>cgA	p.R156R	PLEKHM1_ENST00000421073.2_Silent_p.R67R	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	156	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CCTCAGCATCCCGGAGCAGGG	0.602													C|||	412	0.0822684	0.0378	0.1556	5008	,	,		19188	0.001		0.1958	False		,,,				2504	0.0573				p.R156R		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.G468A						PASS	.	C		276,4128	141.9+/-177.2	10,256,1936	43.0	42.0	42.0		468	-4.5	0.2	17	dbSNP_120	42	1606,6992	272.0+/-289.9	155,1296,2848	no	coding-synonymous	PLEKHM1	NM_014798.2		165,1552,4784	TT,TC,CC		18.6788,6.267,14.4747		156/1057	43552921	1882,11120	2202	4299	6501	SO:0001819	synonymous_variant	9842	exon4			AGCATCCCGGAGC	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.468G>A	17.37:g.43552921C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	243	116	0.477366	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			C|0.865;T|0.135	0.135	strong		0.602	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
ZDHHC20	253832	hgsc.bcm.edu	37	13	21955582	21955582	+	Missense_Mutation	SNP	C	C	T	rs185661667	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:21955582C>T	ENST00000400590.3	-	11	1249	c.1051G>A	c.(1051-1053)Gtc>Atc	p.V351I	ZDHHC20_ENST00000415724.1_Missense_Mutation_p.V351I|ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.V288I|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.V350I|ZDHHC20_ENST00000320220.9_3'UTR			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	351					protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		CCTGATTTGACGATGCCTTCT	0.368													c|||	3	0.000599042	0.0008	0.0	5008	,	,		14111	0.001		0.001	False		,,,				2504	0.0				p.V350I		Atlas-SNP	.											.	ZDHHC20	36	.	0			c.G1048A						PASS	.	T	ILE/VAL	8,3764		0,8,1878	79.0	75.0	76.0		1048	-2.7	0.0	13		76	13,8195		0,13,4091	yes	missense	ZDHHC20	NM_153251.3	29	0,21,5969	TT,TC,CC		0.1584,0.2121,0.1753	benign	350/355	21955582	21,11959	1886	4104	5990	SO:0001583	missense	253832	exon11			ATTTGACGATGCC	AK090979	CCDS45017.1, CCDS73551.1	13q12.11	2008-10-21			ENSG00000180776	ENSG00000180776		"""Zinc fingers, DHHC-type"""	20749	protein-coding gene	gene with protein product							Standard	NM_153251		Approved	FLJ25952	uc001uoa.2	Q5W0Z9	OTTHUMG00000017410	ENST00000400590.3:c.1051G>A	13.37:g.21955582C>T	ENSP00000383433:p.Val351Ile	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	57	37	0.649123	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	c	0.034	-1.315557	0.01331	0.002121	0.001584	ENSG00000180776	ENST00000400590;ENST00000382466;ENST00000542645;ENST00000415724	T;T;T;T	0.52057	0.96;0.94;0.68;0.96	5.24	-2.7	0.06004	.	2.147630	0.01524	N	0.018465	T	0.41858	0.1177	L	0.47716	1.5	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.23511	-1.0186	10	0.22706	T	0.39	-10.2651	11.1755	0.48596	0.0:0.493:0.0:0.507	.	288;350	B4DRN8;Q5W0Z9-3	.;.	I	351;350;288;351	ENSP00000383433:V351I;ENSP00000371905:V350I;ENSP00000443236:V288I;ENSP00000401232:V351I	ENSP00000371905:V350I	V	-	1	0	ZDHHC20	20853582	0.000000	0.05858	0.000000	0.03702	0.486000	0.33341	0.041000	0.13927	-0.958000	0.03622	-0.735000	0.03563	GTC	C|0.998;T|0.002	0.002	strong		0.368	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251	
KIAA1522	57648	hgsc.bcm.edu	37	1	33235626	33235626	+	Silent	SNP	G	G	A	rs3737995	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:33235626G>A	ENST00000373480.1	+	6	772	c.669G>A	c.(667-669)gcG>gcA	p.A223A	KIAA1522_ENST00000401073.2_Silent_p.A282A|KIAA1522_ENST00000373481.3_Silent_p.A234A|KIAA1522_ENST00000294521.3_Intron	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	223										breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				AGGCGGAGGCGGAGGCTGGCG	0.706													G|||	1542	0.307907	0.0333	0.438	5008	,	,		14338	0.4484		0.3648	False		,,,				2504	0.3834				p.A282A		Atlas-SNP	.											.	KIAA1522	68	.	0			c.G846A						PASS	.	G	,,	408,3616		29,350,1633	15.0	21.0	19.0		669,,846	-8.9	0.0	1	dbSNP_107	19	2943,5379		531,1881,1749	no	coding-synonymous,intron,coding-synonymous	KIAA1522	NM_001198972.1,NM_001198973.1,NM_020888.2	,,	560,2231,3382	AA,AG,GG		35.3641,10.1392,27.1424	,,	223/1036,,282/1095	33235626	3351,8995	2012	4161	6173	SO:0001819	synonymous_variant	57648	exon6			GGAGGCGGAGGCT	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.669G>A	1.37:g.33235626G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	82	56	0.682927	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Silent	SNP	ENST00000373480.1	37	CCDS55588.1																																																																																			A|0.328;C|0.000;G|0.672	0.328	strong		0.706	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1		
NDNF	79625	hgsc.bcm.edu	37	4	121958187	121958187	+	Silent	SNP	A	A	G	rs3822230	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:121958187A>G	ENST00000379692.4	-	4	1465	c.939T>C	c.(937-939)gaT>gaC	p.D313D	NDNF_ENST00000506900.1_5'Flank	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	313	Fibronectin type-III 1.				cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)	p.D313D(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						CCACAAATACATCAAAGTAGT	0.448													A|||	2130	0.425319	0.0756	0.4726	5008	,	,		22211	0.6458		0.6113	False		,,,				2504	0.4458				p.D313D		Atlas-SNP	.											NDNF,NS,carcinoma,0,2	NDNF	72	2	1	Substitution - coding silent(1)	prostate(1)	c.T939C						PASS	.	A		731,3675	301.3+/-286.8	61,609,1533	156.0	135.0	142.0		939	-3.2	0.9	4	dbSNP_107	142	5341,3259	649.4+/-400.6	1672,1997,631	no	coding-synonymous	NDNF	NM_024574.3		1733,2606,2164	GG,GA,AA		37.8953,16.591,46.6861		313/569	121958187	6072,6934	2203	4300	6503	SO:0001819	synonymous_variant	79625	exon4			AAATACATCAAAG	BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 31"""	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.939T>C	4.37:g.121958187A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	247	116	0.469636	NM_024574	A8K0Q0|Q6UWE5|Q9H5P7	Silent	SNP	ENST00000379692.4	37	CCDS3717.2																																																																																			A|0.538;G|0.462	0.462	strong		0.448	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574	
POT1	25913	hgsc.bcm.edu	37	7	124493081	124493081	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:124493081C>T	ENST00000357628.3	-	10	1412	c.814G>A	c.(814-816)Ggt>Agt	p.G272S	POT1_ENST00000393329.1_Missense_Mutation_p.G141S	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	272	DNA binding.				DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47						ATTCCCCGACCGTAACTGGTA	0.353																																					p.G272S	Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)	Atlas-SNP	.											POT1_ENST00000357628,NS,carcinoma,+1,4	POT1	186	4	0			c.G814A						scavenged	.						115.0	109.0	111.0					7																	124493081		2203	4300	6503	SO:0001583	missense	25913	exon10			CCCGACCGTAACT	AK022580	CCDS5793.1	7q31.33	2013-01-21	2013-01-21		ENSG00000128513	ENSG00000128513			17284	protein-coding gene	gene with protein product		606478	"""protection of telomeres 1 homolog (S. pombe)"""			11349150, 12391173	Standard	NR_003102		Approved	hPot1, DKFZp586D211	uc003vlm.3	Q9NUX5	OTTHUMG00000157194	ENST00000357628.3:c.814G>A	7.37:g.124493081C>T	ENSP00000350249:p.Gly272Ser	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	126	2	0.015873	NM_015450	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Missense_Mutation	SNP	ENST00000357628.3	37	CCDS5793.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.983213	0.93044	.	.	ENSG00000128513	ENST00000357628;ENST00000393329;ENST00000451720;ENST00000440969;ENST00000393326;ENST00000265391	T;T	0.58797	0.4;0.31	6.07	6.07	0.98685	Nucleic acid-binding, OB-fold-like (1);	0.047635	0.85682	D	0.000000	T	0.77103	0.4081	M	0.78801	2.425	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.74070	-0.3783	10	0.36615	T	0.2	3.5018	18.1532	0.89682	0.0:1.0:0.0:0.0	.	272	Q9NUX5	POTE1_HUMAN	S	272;141;272;272;272;271	ENSP00000350249:G272S;ENSP00000377002:G141S	ENSP00000265391:G271S	G	-	1	0	POT1	124280317	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.800000	0.62524	2.885000	0.99019	0.655000	0.94253	GGT	.	.	none		0.353	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1		
NBAS	51594	hgsc.bcm.edu	37	2	15542352	15542352	+	Missense_Mutation	SNP	C	C	T	rs16862653	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:15542352C>T	ENST00000281513.5	-	26	3036	c.3011G>A	c.(3010-3012)cGa>cAa	p.R1004Q	NBAS_ENST00000441750.1_Missense_Mutation_p.R884Q	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1004			R -> Q (in dbSNP:rs16862653).		negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TTGATCATTTCGTTCACAGGT	0.373													C|||	339	0.0676917	0.0908	0.0447	5008	,	,		16794	0.1131		0.0616	False		,,,				2504	0.0123				p.R1004Q		Atlas-SNP	.											.	NBAS	246	.	0			c.G3011A						PASS	.	C	GLN/ARG	354,4052	183.3+/-210.9	18,318,1867	156.0	149.0	151.0		3011	4.8	0.2	2	dbSNP_123	151	458,8142	136.7+/-193.7	15,428,3857	yes	missense	NBAS	NM_015909.2	43	33,746,5724	TT,TC,CC		5.3256,8.0345,6.2433	probably-damaging	1004/2372	15542352	812,12194	2203	4300	6503	SO:0001583	missense	51594	exon26			TCATTTCGTTCAC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.3011G>A	2.37:g.15542352C>T	ENSP00000281513:p.Arg1004Gln	Somatic	388	1	0.00257732		WXS	Illumina HiSeq	Phase_I	450	192	0.426667	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	183|183	0.08379120879120878|0.08379120879120878	49|49	0.09959349593495935|0.09959349593495935	23|23	0.06353591160220995|0.06353591160220995	60|60	0.1048951048951049|0.1048951048951049	51|51	0.06728232189973615|0.06728232189973615	C|C	22.8|22.8	4.332903|4.332903	0.81801|0.81801	0.080345|0.080345	0.053256|0.053256	ENSG00000151779|ENSG00000151779	ENST00000442506|ENST00000441750;ENST00000281513;ENST00000441755	.|T;T;T	.|0.15603	.|2.41;2.41;2.41	5.65|5.65	4.77|4.77	0.60923|0.60923	.|Secretory pathway Sec39 (1);	.|0.050312	.|0.85682	.|D	.|0.000000	T|T	0.00998|0.00998	0.0033|0.0033	L|L	0.53249|0.53249	1.67|1.67	0.09310|0.09310	P|P	0.99999633665|0.99999633665	.|D;D	.|0.89917	.|1.0;0.997	.|D;D	.|0.67725	.|0.953;0.945	T|T	0.03717|0.03717	-1.1010|-1.1010	4|9	.|0.87932	.|D	.|0	.|.	13.3248|13.3248	0.60452|0.60452	0.0:0.9231:0.0:0.0769|0.0:0.9231:0.0:0.0769	rs16862653;rs56526315;rs16862653|rs16862653;rs56526315;rs16862653	.|884;1004	.|A2RRP1-2;A2RRP1	.|.;NBAS_HUMAN	K|Q	52|884;1004;51	.|ENSP00000413201:R884Q;ENSP00000281513:R1004Q;ENSP00000396501:R51Q	.|ENSP00000281513:R1004Q	E|R	-|-	1|2	0|0	NBAS|NBAS	15459803|15459803	1.000000|1.000000	0.71417|0.71417	0.188000|0.188000	0.23233|0.23233	0.770000|0.770000	0.43624|0.43624	5.449000|5.449000	0.66619|0.66619	1.374000|1.374000	0.46228|0.46228	0.655000|0.655000	0.94253|0.94253	GAA|CGA	C|0.924;T|0.076	0.076	strong		0.373	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
OR5D18	219438	hgsc.bcm.edu	37	11	55587212	55587212	+	Missense_Mutation	SNP	A	A	G	rs7948629	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55587212A>G	ENST00000333976.4	+	1	127	c.107A>G	c.(106-108)tAc>tGc	p.Y36C		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	36			Y -> C (in dbSNP:rs7948629).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				CTGGCCATCTACAATGTCACT	0.458													N|||	123	0.0245607	0.003	0.0259	5008	,	,		17251	0.001		0.0616	False		,,,				2504	0.0389				p.Y36C		Atlas-SNP	.											.	OR5D18	121	.	0			c.A107G						PASS	.	A	CYS/TYR	42,4358		0,42,2158	161.0	150.0	154.0		107	3.6	0.2	11	dbSNP_116	154	535,8057		23,489,3784	yes	missense	OR5D18	NM_001001952.1	194	23,531,5942	GG,GA,AA		6.2267,0.9545,4.4412	probably-damaging	36/314	55587212	577,12415	2200	4296	6496	SO:0001583	missense	219438	exon1			CCATCTACAATGT	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.107A>G	11.37:g.55587212A>G	ENSP00000335025:p.Tyr36Cys	Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	274	135	0.492701	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	37	CCDS31510.1	50	0.022893772893772892	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	43	0.05672823218997362	.	14.11	2.437675	0.43224	0.009545	0.062267	ENSG00000186119	ENST00000333976	T	0.04706	3.57	4.79	3.64	0.41730	.	0.000000	0.35677	N	0.003044	T	0.02888	0.0086	M	0.92649	3.33	0.09310	N	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.02263	-1.1186	10	0.87932	D	0	-30.0673	10.1492	0.42782	0.8503:0.0:0.0:0.1497	rs7948629;rs56831774;rs7948629	36	Q8NGL1	OR5DI_HUMAN	C	36	ENSP00000335025:Y36C	ENSP00000335025:Y36C	Y	+	2	0	OR5D18	55343788	0.971000	0.33674	0.157000	0.22605	0.859000	0.49053	2.534000	0.45676	0.801000	0.34066	0.514000	0.50259	TAC	A|0.964;G|0.036	0.036	strong		0.458	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952	
PTK2	5747	hgsc.bcm.edu	37	8	141900790	141900790	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:141900790G>A	ENST00000522684.1	-	3	276	c.47C>T	c.(46-48)tCg>tTg	p.S16L	PTK2_ENST00000519881.1_Missense_Mutation_p.S16L|PTK2_ENST00000519419.1_Missense_Mutation_p.S60L|PTK2_ENST00000535192.1_Missense_Mutation_p.S16L|PTK2_ENST00000340930.3_Missense_Mutation_p.S16L|PTK2_ENST00000517887.1_Missense_Mutation_p.S60L|PTK2_ENST00000521059.1_Missense_Mutation_p.S16L|PTK2_ENST00000520892.1_Missense_Mutation_p.S16L|PTK2_ENST00000395218.2_Missense_Mutation_p.S16L	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	16					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			CTTAGTACTCGAATTTGGTGT	0.393																																					p.S38L		Atlas-SNP	.											PTK2_ENST00000395218,NS,carcinoma,0,5	PTK2	311	5	0			c.C113T						scavenged	.						122.0	100.0	107.0					8																	141900790		2203	4300	6503	SO:0001583	missense	5747	exon3			GTACTCGAATTTG	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.47C>T	8.37:g.141900790G>A	ENSP00000429911:p.Ser16Leu	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	272	4	0.0147059	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	37	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.236349	0.58886	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000517887;ENST00000521059;ENST00000395218;ENST00000340930;ENST00000519419;ENST00000524357;ENST00000520475;ENST00000519881;ENST00000520892;ENST00000523803;ENST00000521907;ENST00000517453;ENST00000520045;ENST00000521395;ENST00000521332;ENST00000524040	T;T;T;T;T;T;T	0.77877	-1.09;-1.09;-1.13;-1.09;-1.08;-1.08;-1.13	5.68	5.68	0.88126	.	0.302295	0.37261	N	0.002173	T	0.66416	0.2787	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.25486	0.081;0.127;0.127;0.103	B;B;B;B	0.15870	0.004;0.014;0.014;0.006	T	0.64394	-0.6418	10	0.72032	D	0.01	.	19.7969	0.96490	0.0:0.0:1.0:0.0	.	16;16;38;16	B4E2N6;Q05397;Q658W2;Q8IYN9	.;FAK1_HUMAN;.;.	L	16;16;60;16;16;16;60;16;16;16;16;16;16;16;16;16;16;16	ENSP00000429911:S16L;ENSP00000438009:S16L;ENSP00000429082:S60L;ENSP00000429474:S16L;ENSP00000378644:S16L;ENSP00000341189:S16L;ENSP00000429129:S60L	ENSP00000341189:S16L	S	-	2	0	PTK2	141969972	1.000000	0.71417	0.862000	0.33874	0.909000	0.53808	5.326000	0.65875	2.679000	0.91253	0.650000	0.86243	TCG	.	.	none		0.393	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187692983	187692983	+	Missense_Mutation	SNP	T	T	C	rs17856918	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:187692983T>C	ENST00000295131.2	-	9	1669	c.1630A>G	c.(1630-1632)Atg>Gtg	p.M544V		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	544				M -> V (in Ref. 4; AAH31094). {ECO:0000305}.	apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			CCTTTGGTCATCCGGCTTAGA	0.398													T|||	873	0.174321	0.4213	0.1066	5008	,	,		14139	0.0218		0.1103	False		,,,				2504	0.1115				p.M544V		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.A1630G						PASS	.	T	VAL/MET	1752,2654	511.2+/-367.7	346,1060,797	97.0	92.0	94.0		1630	5.5	0.0	2	dbSNP_123	94	977,7623	209.8+/-250.9	44,889,3367	yes	missense	ZSWIM2	NM_182521.2	21	390,1949,4164	CC,CT,TT		11.3605,39.764,20.9826	benign	544/634	187692983	2729,10277	2203	4300	6503	SO:0001583	missense	151112	exon9			TGGTCATCCGGCT	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1630A>G	2.37:g.187692983T>C	ENSP00000295131:p.Met544Val	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	225	100	0.444444	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	326	0.14926739926739926	193	0.39227642276422764	41	0.1132596685082873	10	0.017482517482517484	82	0.10817941952506596	T	1.692	-0.503653	0.04261	0.39764	0.113605	ENSG00000163012	ENST00000295131	T	0.21361	2.01	5.46	5.46	0.80206	.	0.613366	0.15829	N	0.242594	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.12630	0.006	B	0.08055	0.003	T	0.45352	-0.9267	9	0.26408	T	0.33	0.2554	11.9266	0.52823	0.0:0.0:0.0:1.0	rs17856918;rs17856918	544	Q8NEG5	ZSWM2_HUMAN	V	544	ENSP00000295131:M544V	ENSP00000295131:M544V	M	-	1	0	ZSWIM2	187401228	0.950000	0.32346	0.013000	0.15412	0.031000	0.12232	2.484000	0.45242	2.088000	0.63022	0.402000	0.26972	ATG	T|0.813;C|0.187	0.187	strong		0.398	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
OR8S1	341568	hgsc.bcm.edu	37	12	48919660	48919660	+	Silent	SNP	G	G	A	rs35367885|rs71439450	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48919660G>A	ENST00000310194.1	+	1	246	c.246G>A	c.(244-246)ctG>ctA	p.L82L	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	82			L -> P (in dbSNP:rs4075258).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						CCAAGATGCTGGAGAACCTCC	0.488													G|||	1136	0.226837	0.0371	0.2622	5008	,	,		21342	0.1488		0.4384	False		,,,				2504	0.3211				p.L82L		Atlas-SNP	.											.	OR8S1	47	.	0			c.G246A						PASS	.	G		452,3954	215.8+/-234.7	25,402,1776	134.0	128.0	130.0		246	0.7	0.2	12	dbSNP_126	130	3977,4623	552.1+/-386.1	909,2159,1232	no	coding-synonymous	OR8S1	NM_001005203.2		934,2561,3008	AA,AG,GG		46.2442,10.2587,34.0535		82/360	48919660	4429,8577	2203	4300	6503	SO:0001819	synonymous_variant	341568	exon1			GATGCTGGAGAAC		CCDS31789.1	12q13.2	2012-08-09				ENSG00000197376		"""GPCR / Class A : Olfactory receptors"""	19628	protein-coding gene	gene with protein product							Standard	NM_001005203		Approved		uc010slu.2	Q8NH09		ENST00000310194.1:c.246G>A	12.37:g.48919660G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	184	90	0.48913	NM_001005203		Silent	SNP	ENST00000310194.1	37	CCDS31789.1																																																																																			G|0.692;A|0.308	0.308	strong		0.488	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1		
C15orf57	90416	hgsc.bcm.edu	37	15	40855210	40855210	+	Missense_Mutation	SNP	T	T	A	rs10152546	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:40855210T>A	ENST00000358005.3	-	2	278	c.5A>T	c.(4-6)aAa>aTa	p.K2I	C15orf57_ENST00000561011.1_Missense_Mutation_p.K2I|C15orf57_ENST00000416810.2_Missense_Mutation_p.K2I|C15orf57_ENST00000559911.1_Missense_Mutation_p.K2I|C15orf57_ENST00000558871.1_Missense_Mutation_p.K2I|C15orf57_ENST00000558750.1_Missense_Mutation_p.K11I|C15orf57_ENST00000560109.1_5'UTR|C15orf57_ENST00000560305.1_Missense_Mutation_p.K2I|C15orf57_ENST00000558113.1_Missense_Mutation_p.K2I	NM_001080791.1|NM_052849.2	NP_001074260.1|NP_443081.1	Q9BV29	CO057_HUMAN	chromosome 15 open reading frame 57	2			K -> I (in dbSNP:rs10152546). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.					p.K2I(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	9						CTCAAACATTTTCATTTGGAA	0.448													T|||	1294	0.258387	0.2027	0.2925	5008	,	,		21813	0.0923		0.4742	False		,,,				2504	0.2587				p.K11I		Atlas-SNP	.											C15orf57,NS,carcinoma,0,1	C15orf57	20	1	1	Substitution - Missense(1)	stomach(1)	c.A32T						PASS	.	T	ILE/LYS,ILE/LYS,ILE/LYS	1108,3298	396.3+/-330.0	151,806,1246	115.0	122.0	119.0		32,5,5	4.1	1.0	15	dbSNP_119	119	3846,4754	540.9+/-383.9	839,2168,1293	yes	missense,missense,missense	C15orf57	NM_001080791.1,NM_001080792.1,NM_052849.2	102,102,102	990,2974,2539	AA,AT,TT		44.7209,25.1475,38.0901	probably-damaging,probably-damaging,probably-damaging	11/195,2/186,2/186	40855210	4954,8052	2203	4300	6503	SO:0001583	missense	90416	exon2			AACATTTTCATTT	BC012189	CCDS10060.1, CCDS42022.1, CCDS73706.1	15q15.1	2008-05-30	2008-05-30	2008-05-30	ENSG00000128891	ENSG00000128891			28295	protein-coding gene	gene with protein product			"""coiled-coil domain containing 32"""	CCDC32		12477932	Standard	NM_001080791		Approved	MGC20481	uc001zma.1	Q9BV29	OTTHUMG00000129993	ENST00000358005.3:c.5A>T	15.37:g.40855210T>A	ENSP00000350695:p.Lys2Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	36	34	0.944444	NM_001080791	A8KAL4|Q86TC4|Q8N788|Q8NAR7	Missense_Mutation	SNP	ENST00000358005.3	37	CCDS10060.1	597	0.2733516483516483	98	0.1991869918699187	122	0.3370165745856354	38	0.06643356643356643	339	0.4472295514511873	T	8.192	0.796261	0.16327	0.251475	0.447209	ENSG00000128891	ENST00000358005;ENST00000416810	T	0.50277	0.75	5.22	4.08	0.47627	.	0.215176	0.39834	N	0.001251	T	0.00012	0.0000	L	0.48642	1.525	0.26379	P	0.9767653	B;B	0.28783	0.091;0.222	B;B	0.26202	0.039;0.067	T	0.45644	-0.9247	9	0.45353	T	0.12	-15.767	2.9313	0.05800	0.1436:0.0822:0.1497:0.6245	rs10152546;rs16970825;rs52833420;rs10152546	2;11	Q9BV29;Q9BV29-2	CO057_HUMAN;.	I	2;11	ENSP00000350695:K2I	ENSP00000350695:K2I	K	-	2	0	C15orf57	38642502	1.000000	0.71417	1.000000	0.80357	0.027000	0.11550	1.454000	0.35178	0.805000	0.34159	-0.478000	0.04885	AAA	T|0.660;A|0.340	0.340	strong		0.448	C15orf57-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252259.2	NM_052849	
TIMELESS	8914	hgsc.bcm.edu	37	12	56815922	56815922	+	Missense_Mutation	SNP	C	C	T	rs774047	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56815922C>T	ENST00000553532.1	-	20	2642	c.2492G>A	c.(2491-2493)cGg>cAg	p.R831Q	TIMELESS_ENST00000229201.4_Missense_Mutation_p.R830Q|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						GTACAGCTCCCGAAGATGAGC	0.532													C|||	2498	0.498802	0.2262	0.6772	5008	,	,		21940	0.7371		0.4503	False		,,,				2504	0.545				p.R831Q		Atlas-SNP	.											TIMELESS,NS,carcinoma,+1,1	TIMELESS	107	1	0			c.G2492A						PASS	.	C	GLN/ARG	1078,3328	388.6+/-327.0	123,832,1248	104.0	97.0	99.0		2492	-1.1	1.0	12	dbSNP_86	99	3895,4705	546.2+/-384.9	867,2161,1272	yes	missense	TIMELESS	NM_003920.3	43	990,2993,2520	TT,TC,CC		45.2907,24.4666,38.2362	benign	831/1209	56815922	4973,8033	2203	4300	6503	SO:0001583	missense	8914	exon20			AGCTCCCGAAGAT	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.2492G>A	12.37:g.56815922C>T	ENSP00000450607:p.Arg831Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	104	41	0.394231	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	1059	0.4848901098901099	103	0.20934959349593496	217	0.5994475138121547	401	0.701048951048951	338	0.44591029023746703	C	12.08	1.829831	0.32329	0.244666	0.452907	ENSG00000111602	ENST00000229201;ENST00000553532	T;T	0.12255	2.7;2.7	4.55	-1.07	0.09968	Timeless C-terminal (1);	0.467638	0.22929	N	0.053924	T	0.00012	0.0000	N	0.03967	-0.31	0.09310	P	0.999999999999715	B	0.12013	0.005	B	0.09377	0.004	T	0.20773	-1.0265	9	0.10902	T	0.67	-2.5193	9.4952	0.38984	0.0:0.5777:0.0:0.4223	rs774047;rs1063962;rs3204992;rs3816941;rs17441717;rs52816475;rs58232886;rs774047	831	Q9UNS1	TIM_HUMAN	Q	830;831	ENSP00000229201:R830Q;ENSP00000450607:R831Q	ENSP00000229201:R831Q	R	-	2	0	TIMELESS	55102189	0.759000	0.28416	0.997000	0.53966	0.731000	0.41821	-0.241000	0.08940	-0.079000	0.12707	0.555000	0.69702	CGG	C|0.576;T|0.424	0.424	strong		0.532	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
SLC28A1	9154	hgsc.bcm.edu	37	15	85476441	85476441	+	Silent	SNP	G	G	A	rs2305367	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:85476441G>A	ENST00000286749.3	+	12	1239	c.1149G>A	c.(1147-1149)aaG>aaA	p.K383K	SLC28A1_ENST00000394573.1_Silent_p.K383K|SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000537216.1_Silent_p.K383K|SLC28A1_ENST00000537624.1_Silent_p.K383K			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	383					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	CCCTCTCCAAGCTGGTCTACC	0.572													G|||	2846	0.568291	0.3812	0.5504	5008	,	,		19205	0.8958		0.3847	False		,,,				2504	0.6851				p.K383K		Atlas-SNP	.											.	SLC28A1	118	.	0			c.G1149A						PASS	.	G		1783,2623	527.6+/-372.2	361,1061,781	148.0	126.0	134.0		1149	3.3	1.0	15	dbSNP_100	134	3188,5410	483.2+/-371.1	589,2010,1700	no	coding-synonymous	SLC28A1	NM_004213.3		950,3071,2481	AA,AG,GG		37.0784,40.4675,38.2267		383/650	85476441	4971,8033	2203	4299	6502	SO:0001819	synonymous_variant	9154	exon13			CTCCAAGCTGGTC	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.1149G>A	15.37:g.85476441G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	37	CCDS10334.1																																																																																			G|0.569;A|0.431	0.431	strong		0.572	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
LAMB4	22798	hgsc.bcm.edu	37	7	107746265	107746265	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:107746265T>C	ENST00000388781.3	-	8	950	c.867A>G	c.(865-867)ggA>ggG	p.G289G	LAMB4_ENST00000205386.4_Silent_p.G289G|LAMB4_ENST00000388780.3_Silent_p.G289G|LAMB4_ENST00000414450.2_Silent_p.G289G|LAMB4_ENST00000418464.1_Silent_p.G289G	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	289	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						AACTCACCATTCCAGGAGGGC	0.478																																					p.G289G		Atlas-SNP	.											.	LAMB4	253	.	0			c.A867G						PASS	.						80.0	72.0	75.0					7																	107746265		2203	4300	6503	SO:0001819	synonymous_variant	22798	exon8			CACCATTCCAGGA	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.867A>G	7.37:g.107746265T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	119	48	0.403361	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			.	.	none		0.478	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
FJX1	24147	hgsc.bcm.edu	37	11	35641312	35641312	+	Silent	SNP	G	G	A	rs3740799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:35641312G>A	ENST00000317811.4	+	1	1578	c.1128G>A	c.(1126-1128)ctG>ctA	p.L376L	FJX1_ENST00000532914.1_3'UTR	NM_014344.3	NP_055159.2	Q86VR8	FJX1_HUMAN	four jointed box 1 (Drosophila)	376					retina layer formation (GO:0010842)	extracellular space (GO:0005615)				lung(1)|urinary_tract(1)	2	all_cancers(35;0.177)|all_lung(20;0.0238)|Lung NSC(22;0.0494)|all_epithelial(35;0.0739)	all_hematologic(20;0.107)				GGCGCGTCCTGGAGCTGCACC	0.711													G|||	459	0.0916534	0.0076	0.1153	5008	,	,		12160	0.0794		0.1839	False		,,,				2504	0.1063				p.L376L	Melanoma(161;10 2587 27165 47356)	Atlas-SNP	.											FJX1_ENST00000317811,NS,carcinoma,0,4	FJX1	32	4	0			c.G1128A						scavenged	.	G		122,3572		7,108,1732	5.0	7.0	6.0		1128	5.2	1.0	11	dbSNP_107	6	1424,6522		123,1178,2672	no	coding-synonymous	FJX1	NM_014344.3		130,1286,4404	AA,AG,GG		17.921,3.3027,13.2818		376/438	35641312	1546,10094	1847	3973	5820	SO:0001819	synonymous_variant	24147	exon1			CGTCCTGGAGCTG	AJ245599	CCDS44570.1	11p13	2012-05-18				ENSG00000179431			17166	protein-coding gene	gene with protein product	"""putative secreted ligand homologous to fjx1"""	612206				7647465, 10072791	Standard	NM_014344		Approved	FLJ22416, FLJ25593	uc001mwh.3	Q86VR8		ENST00000317811.4:c.1128G>A	11.37:g.35641312G>A		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	11	3	0.272727	NM_014344	B2RCA9|Q9UGK6	Silent	SNP	ENST00000317811.4	37	CCDS44570.1																																																																																			G|0.896;A|0.104	0.104	strong		0.711	FJX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389078.1	NM_014344	
MOV10L1	54456	hgsc.bcm.edu	37	22	50582630	50582630	+	Silent	SNP	G	G	A	rs11704548	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50582630G>A	ENST00000262794.5	+	18	2546	c.2463G>A	c.(2461-2463)ccG>ccA	p.P821P	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Silent_p.P821P|MOV10L1_ENST00000540615.1_Silent_p.P801P|MOV10L1_ENST00000395852.1_5'Flank|MOV10L1_ENST00000545383.1_Silent_p.P821P	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	821					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGCTACAGCCGGCCACCATGG	0.612													A|||	136	0.0271565	0.0038	0.0447	5008	,	,		19960	0.0		0.0726	False		,,,				2504	0.0276				p.P821P		Atlas-SNP	.											.	MOV10L1	238	.	0			c.G2463A						PASS	.	A	,,	55,4351	821.3+/-416.4	2,51,2150	103.0	90.0	94.0		2463,2403,2463	-11.0	0.0	22	dbSNP_120	94	624,7976	790.9+/-407.6	17,590,3693	no	coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	19,641,5843	AA,AG,GG		7.2558,1.2483,5.2207	,,	821/1166,801/1166,821/1212	50582630	679,12327	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon18			ACAGCCGGCCACC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2463G>A	22.37:g.50582630G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			G|0.952;A|0.048	0.048	strong		0.612	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
ABCG8	64241	hgsc.bcm.edu	37	2	44099433	44099433	+	Missense_Mutation	SNP	C	C	A	rs4148217	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:44099433C>A	ENST00000272286.2	+	8	1289	c.1199C>A	c.(1198-1200)aCg>aAg	p.T400K		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	400			T -> K (in dbSNP:rs4148217). {ECO:0000269|PubMed:11452359, ECO:0000269|PubMed:11668628, ECO:0000269|PubMed:12111378}.		ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	CAGCAGTTTACGACGCTGATC	0.502													C|||	1080	0.215655	0.2912	0.3228	5008	,	,		18266	0.1141		0.2008	False		,,,				2504	0.1575				p.T400K		Atlas-SNP	.											ABCG8,colon,carcinoma,0,1	ABCG8	98	1	0			c.C1199A	GRCh37	CM042913	ABCG8	M	rs4148217	PASS	.	C	LYS/THR	1202,3204	413.7+/-336.6	178,846,1179	46.0	44.0	45.0		1199	3.9	0.0	2	dbSNP_110	45	1647,6953	300.6+/-305.0	162,1323,2815	yes	missense	ABCG8	NM_022437.2	78	340,2169,3994	AA,AC,CC		19.1512,27.281,21.9053	benign	400/674	44099433	2849,10157	2203	4300	6503	SO:0001583	missense	64241	exon8			AGTTTACGACGCT	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"""ATP binding cassette transporters / subfamily G"""	13887	protein-coding gene	gene with protein product	"""gallbladder disease 4"", ""sterolin 2"""	605460	"""ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"""			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.1199C>A	2.37:g.44099433C>A	ENSP00000272286:p.Thr400Lys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_022437	Q53QN8	Missense_Mutation	SNP	ENST00000272286.2	37	CCDS1815.1	476	0.21794871794871795	154	0.3130081300813008	117	0.32320441988950277	60	0.1048951048951049	145	0.19129287598944592	C	9.876	1.200333	0.22121	0.27281	0.191512	ENSG00000143921	ENST00000272286	T	0.69806	-0.43	4.81	3.93	0.45458	ABC-2 type transporter (1);	0.400469	0.29451	N	0.012101	T	0.00012	0.0000	N	0.17474	0.49	0.58432	P	1.999999999946489E-6	B;B	0.21688	0.009;0.059	B;B	0.23419	0.016;0.046	T	0.19647	-1.0299	9	0.27785	T	0.31	.	9.9542	0.41657	0.0:0.9036:0.0:0.0964	rs4148217;rs59591548;rs4148217	399;400	Q9H221-2;Q9H221	.;ABCG8_HUMAN	K	400	ENSP00000272286:T400K	ENSP00000272286:T400K	T	+	2	0	ABCG8	43952937	0.001000	0.12720	0.011000	0.14972	0.089000	0.18198	1.368000	0.34216	1.015000	0.39444	0.591000	0.81541	ACG	A|0.212;C|0.788	0.212	strong		0.502	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
UBE2E3	10477	hgsc.bcm.edu	37	2	181846844	181846844	+	Silent	SNP	A	A	T	rs146744789	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:181846844A>T	ENST00000410062.4	+	2	468	c.75A>T	c.(73-75)cgA>cgT	p.R25R	UBE2E3_ENST00000602475.1_Silent_p.R25R|UBE2E3_ENST00000392415.2_Silent_p.R25R|AC104076.3_ENST00000428080.1_RNA|UBE2E3_ENST00000602710.1_Silent_p.R25R|UBE2E3_ENST00000602959.1_Silent_p.R25R|UBE2E3_ENST00000602632.1_Silent_p.R25R	NM_006357.2	NP_006348.1	Q969T4	UB2E3_HUMAN	ubiquitin-conjugating enzyme E2E 3	25					protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(3)|lung(4)|ovary(1)|skin(1)	11						CGGACCAGCGAGACCCAGCCG	0.507													A|||	47	0.00938498	0.0008	0.0086	5008	,	,		15694	0.0		0.0169	False		,,,				2504	0.0235				p.R25R		Atlas-SNP	.											.	UBE2E3	26	.	0			c.A75T						PASS	.	A	,	11,4393	14.3+/-33.2	0,11,2191	37.0	45.0	42.0		75,75	0.9	1.0	2	dbSNP_134	42	146,8416	70.3+/-132.9	0,146,4135	no	coding-synonymous,coding-synonymous	UBE2E3	NM_006357.2,NM_182678.1	,	0,157,6326	TT,TA,AA		1.7052,0.2498,1.2109	,	25/208,25/208	181846844	157,12809	2202	4281	6483	SO:0001819	synonymous_variant	10477	exon2			CCAGCGAGACCCA	AB017644	CCDS2282.1	2q31.3	2011-05-19	2011-05-19		ENSG00000170035	ENSG00000170035		"""Ubiquitin-conjugating enzymes E2"""	12479	protein-coding gene	gene with protein product		604151	"""ubiquitin-conjugating enzyme E2E 3 (homologous to yeast UBC4/5)"", ""ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast)"""			10343118	Standard	NM_006357		Approved	UbcH9	uc002unq.1	Q969T4	OTTHUMG00000132585	ENST00000410062.4:c.75A>T	2.37:g.181846844A>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	203	189	0.931035	NM_006357	B2RAD6|D3DPG3|Q5U0R7|Q7Z4W4	Silent	SNP	ENST00000410062.4	37	CCDS2282.1																																																																																			A|0.985;T|0.015	0.015	weak		0.507	UBE2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255795.6	NM_006357	
TRIOBP	11078	hgsc.bcm.edu	37	22	38120095	38120095	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38120095G>A	ENST00000406386.3	+	7	1787	c.1532G>A	c.(1531-1533)aGa>aAa	p.R511K		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	511					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.R511K(2)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GACAATCCCAGAGCCTCCAGA	0.592																																					p.R511K		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,2	TRIOBP	262	2	2	Substitution - Missense(2)	kidney(1)|skin(1)	c.G1532A						scavenged	.						16.0	27.0	24.0					22																	38120095		1746	3975	5721	SO:0001583	missense	11078	exon7			ATCCCAGAGCCTC	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1532G>A	22.37:g.38120095G>A	ENSP00000384312:p.Arg511Lys	Somatic	272	2	0.00735294		WXS	Illumina HiSeq	Phase_I	309	6	0.0194175	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	-	12.91	2.079188	0.36662	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.20200	2.09	0.725	0.725	0.18242	.	.	.	.	.	T	0.14442	0.0349	L	0.44542	1.39	0.80722	D	1	.	.	.	.	.	.	T	0.10894	-1.0610	7	0.05620	T	0.96	.	4.9132	0.13833	0.0:0.0:1.0:0.0	.	511	Q9H2D6	TARA_HUMAN	K	511	ENSP00000384312:R511K	ENSP00000384312:R511K	R	+	2	0	TRIOBP	36450041	0.001000	0.12720	0.176000	0.23000	0.248000	0.25809	0.139000	0.16036	0.721000	0.32231	0.289000	0.19496	AGA	.	.	none		0.592	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
DNAH14	127602	hgsc.bcm.edu	37	1	225534219	225534219	+	Missense_Mutation	SNP	T	T	C	rs7527925	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:225534219T>C	ENST00000445597.2	+	49	8471	c.8471T>C	c.(8470-8472)gTa>gCa	p.V2824A	DNAH14_ENST00000439375.2_Missense_Mutation_p.V3627A|DNAH14_ENST00000430092.1_Missense_Mutation_p.V3627A			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2824					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CTTTGCACTGTAATCATGCAA	0.323													C|||	2650	0.529153	0.6407	0.4697	5008	,	,		17450	0.5089		0.4046	False		,,,				2504	0.5695				p.V3627A		Atlas-SNP	.											.	DNAH14	300	.	0			c.T10880C						PASS	.	C	ALA/VAL	842,542		268,306,118	70.0	60.0	63.0		10880	3.5	0.2	1	dbSNP_116	63	1404,1770		323,758,506	yes	missense	DNAH14	NM_001373.1	64	591,1064,624	CC,CT,TT		44.2344,39.1618,49.276	benign	3627/4516	225534219	2246,2312	692	1587	2279	SO:0001583	missense	127602	exon69			GCACTGTAATCAT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.8471T>C	1.37:g.225534219T>C	ENSP00000409472:p.Val2824Ala	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	278	135	0.485611	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	C	2.312	-0.357714	0.05138	0.608382	0.442344	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.50001	0.76;0.76;0.76	5.48	3.53	0.40419	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.45086	-0.9285	7	0.15066	T	0.55	.	3.7279	0.08481	0.1327:0.5895:0.1289:0.1488	rs7527925;rs52797267;rs56543759;rs61045802;rs7527925	3627	Q0VDD8-4	.	A	2824;3627;3627	ENSP00000409472:V2824A;ENSP00000414402:V3627A;ENSP00000392061:V3627A	ENSP00000414402:V3627A	V	+	2	0	DNAH14	223600842	0.000000	0.05858	0.155000	0.22561	0.949000	0.60115	0.067000	0.14510	0.662000	0.31006	-0.294000	0.09567	GTA	T|0.500;C|0.500	0.500	strong		0.323	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
RBM19	9904	hgsc.bcm.edu	37	12	114374887	114374887	+	Missense_Mutation	SNP	T	T	C	rs2290787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:114374887T>C	ENST00000545145.2	-	16	2071	c.1993A>G	c.(1993-1995)Aca>Gca	p.T665A	RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.T665A|RBM19_ENST00000392561.3_Missense_Mutation_p.T665A	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	665			T -> A (in dbSNP:rs2290787). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T665A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TGTGGGGCTGTGCTGGAGAAG	0.527													C|||	579	0.115615	0.0514	0.0418	5008	,	,		17578	0.1885		0.1103	False		,,,				2504	0.1851				p.T665A		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - Missense(1)	stomach(1)	c.A1993G						PASS	.	C	ALA/THR,ALA/THR,ALA/THR	194,4212		13,168,2022	130.0	129.0	129.0		1993,1993,1993	-7.4	0.1	12	dbSNP_100	129	875,7725		37,801,3462	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	58,58,58	50,969,5484	CC,CT,TT		10.1744,4.4031,8.2193	benign,benign,benign	665/961,665/961,665/961	114374887	1069,11937	2203	4300	6503	SO:0001583	missense	9904	exon16			GGGCTGTGCTGGA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1993A>G	12.37:g.114374887T>C	ENSP00000442053:p.Thr665Ala	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	160	76	0.475	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	C	7.721	0.697212	0.15106	0.044031	0.101744	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05081	3.5;3.5;3.5	4.5	-7.42	0.01388	Nucleotide-binding, alpha-beta plait (1);	0.638273	0.16199	N	0.225012	T	0.00073	0.0002	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28522	-1.0041	10	0.07990	T	0.79	0.174	2.1166	0.03715	0.1533:0.1255:0.303:0.4182	rs2290787;rs17856103;rs17856172	665	Q9Y4C8	RBM19_HUMAN	A	665	ENSP00000442053:T665A;ENSP00000376344:T665A;ENSP00000261741:T665A	ENSP00000261741:T665A	T	-	1	0	RBM19	112859270	0.076000	0.21285	0.052000	0.19188	0.226000	0.24999	-0.181000	0.09740	-2.257000	0.00695	-1.557000	0.00889	ACA	A|0.076;C|0.019;T|0.905	0.019	strong		0.527	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
SYT7	9066	hgsc.bcm.edu	37	11	61291922	61291922	+	Silent	SNP	A	A	G	rs10897167	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61291922A>G	ENST00000263846.4	-	6	1032	c.705T>C	c.(703-705)atT>atC	p.I235I	SYT7_ENST00000540677.1_Silent_p.I310I|SYT7_ENST00000539008.1_Silent_p.I518I|SYT7_ENST00000540831.1_5'UTR|SYT7_ENST00000542670.1_Silent_p.I443I|SYT7_ENST00000542836.1_Silent_p.I279I|SYT7_ENST00000535826.1_Silent_p.I354I	NM_004200.3	NP_004191.2	O43581	SYT7_HUMAN	synaptotagmin VII	235	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|plasma membrane repair (GO:0001778)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			kidney(2)|large_intestine(3)|lung(4)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						ACACCTCCCCAATGGGGTCGT	0.557													G|||	758	0.151358	0.4455	0.0504	5008	,	,		20942	0.002		0.0348	False		,,,				2504	0.0992				p.I310I		Atlas-SNP	.											.	SYT7	39	.	0			c.T930C						PASS	.	G		1686,2718	653.9+/-399.7	348,990,864	87.0	80.0	83.0		705	-7.1	0.6	11	dbSNP_120	83	378,8220	802.4+/-407.3	8,362,3929	no	coding-synonymous	SYT7	NM_004200.2		356,1352,4793	GG,GA,AA		4.3964,38.2834,15.8745		235/404	61291922	2064,10938	2202	4299	6501	SO:0001819	synonymous_variant	9066	exon7			CTCCCCAATGGGG	AF038535	CCDS31577.1, CCDS58139.1, CCDS73298.1	11q12-q13.1	2013-01-21			ENSG00000011347	ENSG00000011347		"""Synaptotagmins"""	11514	protein-coding gene	gene with protein product		604146	"""prostate cancer associated protein 7"""	PCANAP7		9615227	Standard	NM_001252065		Approved	IPCA-7, SYT-VII, MGC150517	uc009ynr.3	O43581	OTTHUMG00000168199	ENST00000263846.4:c.705T>C	11.37:g.61291922A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_001252065	F5GZU9|Q08AH6	Silent	SNP	ENST00000263846.4	37	CCDS31577.1																																																																																			A|0.836;G|0.164	0.164	strong		0.557	SYT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398733.1	NM_004200	
MERTK	10461	hgsc.bcm.edu	37	2	112755001	112755001	+	Missense_Mutation	SNP	A	A	G	rs2230515	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:112755001A>G	ENST00000295408.4	+	10	1809	c.1552A>G	c.(1552-1554)Att>Gtt	p.I518V	MERTK_ENST00000409780.1_Missense_Mutation_p.I342V|MERTK_ENST00000421804.2_Missense_Mutation_p.I518V			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	518			I -> V (in dbSNP:rs2230515). {ECO:0000269|PubMed:11062461, ECO:0000269|PubMed:17344846}.		apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						GATTGGGTTGATTTTATACAT	0.453													G|||	2812	0.561502	0.6657	0.6037	5008	,	,		18954	0.2758		0.6252	False		,,,				2504	0.6196				p.I518V		Atlas-SNP	.											.	MERTK	112	.	0			c.A1552G						PASS	.	G	VAL/ILE	2857,1549	488.3+/-361.2	928,1001,274	140.0	125.0	130.0		1552	-2.0	0.0	2	dbSNP_98	130	5388,3212	484.9+/-371.5	1704,1980,616	yes	missense	MERTK	NM_006343.2	29	2632,2981,890	GG,GA,AA		37.3488,35.1566,36.6062	benign	518/1000	112755001	8245,4761	2203	4300	6503	SO:0001583	missense	10461	exon10			GGGTTGATTTTAT	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1552A>G	2.37:g.112755001A>G	ENSP00000295408:p.Ile518Val	Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_006343	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	1131	0.5178571428571429	318	0.6463414634146342	218	0.6022099447513812	124	0.21678321678321677	471	0.6213720316622692	G	0.093	-1.164191	0.01673	0.648434	0.626512	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000393237;ENST00000409780	T;T;T	0.74106	-0.81;-0.81;-0.81	5.85	-2.03	0.07365	.	0.568040	0.13239	N	0.403004	T	0.00012	0.0000	N	0.04636	-0.2	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.39663	-0.9603	9	0.06494	T	0.89	-5.0568	12.1572	0.54083	0.6774:0.0:0.3226:0.0	rs2230515;rs3811635;rs17809697;rs52805200;rs57338807;rs3811635	518	Q12866	MERTK_HUMAN	V	518;518;160;342	ENSP00000295408:I518V;ENSP00000389152:I518V;ENSP00000387277:I342V	ENSP00000295408:I518V	I	+	1	0	MERTK	112471472	0.002000	0.14202	0.000000	0.03702	0.316000	0.28119	-0.141000	0.10327	-0.584000	0.05913	-0.761000	0.03458	ATT	A|0.415;G|0.584	0.584	strong		0.453	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
IL4R	3566	hgsc.bcm.edu	37	16	27373964	27373964	+	Missense_Mutation	SNP	T	T	C	rs1805012	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:27373964T>C	ENST00000395762.2	+	11	1550	c.1291T>C	c.(1291-1293)Tgc>Cgc	p.C431R	IL4R_ENST00000380922.3_Missense_Mutation_p.C416R|IL4R_ENST00000543915.2_Missense_Mutation_p.C431R|IL4R_ENST00000170630.2_Missense_Mutation_p.C431R	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	431			C -> R (in dbSNP:rs1805012). {ECO:0000269|PubMed:11285129, ECO:0000269|PubMed:9070874, ECO:0000269|Ref.5}.		defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						GGGGGAGTCATGCCTTCTTCC	0.622													T|||	441	0.0880591	0.0885	0.111	5008	,	,		19533	0.0833		0.1024	False		,,,				2504	0.0613				p.C431R		Atlas-SNP	.											IL4R,lymph_node,lymphoid_neoplasm,0,1	IL4R	70	1	0			c.T1291C	GRCh37	CM993666	IL4R	M	rs1805012	PASS	.	T	ARG/CYS	391,4003	195.3+/-220.0	22,347,1828	75.0	75.0	75.0		1291	0.8	0.0	16	dbSNP_89	75	925,7675	204.9+/-247.5	57,811,3432	yes	missense	IL4R	NM_000418.2	180	79,1158,5260	CC,CT,TT		10.7558,8.8985,10.1278	probably-damaging	431/826	27373964	1316,11678	2197	4300	6497	SO:0001583	missense	3566	exon11			GAGTCATGCCTTC	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1291T>C	16.37:g.27373964T>C	ENSP00000379111:p.Cys431Arg	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	222	0.10164835164835165	54	0.10975609756097561	42	0.11602209944751381	42	0.07342657342657342	84	0.11081794195250659	T	14.34	2.506626	0.44558	0.088985	0.107558	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	4.68	0.809	0.18725	.	12.972700	0.00166	N	0.000000	T	0.00271	0.0008	M	0.62723	1.935	0.53005	P	3.6000000000036E-5	P;D;D	0.56035	0.944;0.974;0.974	P;P;P	0.45913	0.497;0.497;0.497	T	0.28038	-1.0056	9	0.39692	T	0.17	-8.1819	10.0945	0.42466	0.0:0.0:0.5003:0.4997	rs1805012;rs4134682;rs17548789;rs57980476;rs1805012	416;431;431	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	R	431;431;416;431	ENSP00000379111:C431R;ENSP00000441667:C431R;ENSP00000370309:C416R;ENSP00000170630:C431R	ENSP00000170630:C431R	C	+	1	0	IL4R	27281465	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.548000	0.06048	-0.069000	0.12931	0.533000	0.62120	TGC	T|0.902;C|0.098	0.098	strong		0.622	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
KRT72	140807	hgsc.bcm.edu	37	12	52994955	52994955	+	Silent	SNP	G	G	A	rs61747192	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:52994955G>A	ENST00000537672.2	-	1	292	c.282C>T	c.(280-282)ccC>ccT	p.P94P	KRT72_ENST00000354310.4_Silent_p.P94P|KRT72_ENST00000293745.2_Silent_p.P94P|KRT72_ENST00000398066.3_5'UTR|RP11-641A6.2_ENST00000551089.1_RNA	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	94	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		GGATGCCCCCGGGTGGGCACA	0.746													G|||	876	0.17492	0.0862	0.0879	5008	,	,		14031	0.4444		0.1223	False		,,,				2504	0.1329				p.P94P		Atlas-SNP	.											.	KRT72	70	.	0			c.C282T						PASS	.	G	,,	506,3900	229.8+/-244.2	34,438,1731	35.0	36.0	36.0		282,282,282	-8.3	0.1	12	dbSNP_131	36	1080,7520	223.3+/-260.1	68,944,3288	no	coding-synonymous,coding-synonymous,coding-synonymous	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	,,	102,1382,5019	AA,AG,GG		12.5581,11.4843,12.1944	,,	94/512,94/470,94/512	52994955	1586,11420	2203	4300	6503	SO:0001819	synonymous_variant	140807	exon1			GCCCCCGGGTGGG	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.282C>T	12.37:g.52994955G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Silent	SNP	ENST00000537672.2	37	CCDS8833.1	424	0.19413919413919414	42	0.08536585365853659	33	0.09116022099447514	254	0.44405594405594406	95	0.12532981530343007	G	13.71	2.316979	0.40996	0.114843	0.125581	ENSG00000170486	ENST00000549979	.	.	.	4.49	-8.29	0.01009	.	0.000000	0.52532	D	0.000075	T	0.00012	0.0000	.	.	.	0.22446	P	0.999095179	.	.	.	.	.	.	T	0.28038	-1.0056	4	.	.	.	.	3.2959	0.06966	0.2814:0.4304:0.1238:0.1645	.	.	.	.	L	80	.	.	P	-	2	0	KRT72	51281222	0.000000	0.05858	0.051000	0.19133	0.895000	0.52256	-7.169000	0.00042	-1.814000	0.01224	-0.311000	0.09066	CCG	G|0.856;A|0.144	0.144	strong		0.746	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
ZNF80	7634	hgsc.bcm.edu	37	3	113955187	113955187	+	Nonsense_Mutation	SNP	A	A	C	rs3732781	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:113955187A>C	ENST00000482457.2	-	1	1238	c.735T>G	c.(733-735)taT>taG	p.Y245*	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	245					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				CAAGGCACTCATAAGGTTTCT	0.448													A|||	929	0.185503	0.025	0.2435	5008	,	,		19496	0.1567		0.2803	False		,,,				2504	0.2935				p.Y245X	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.T735G						PASS	.	A	stop/TYR	280,4126	155.2+/-188.4	9,262,1932	98.0	98.0	98.0		735	-2.2	0.0	3	dbSNP_107	98	2404,6196	399.7+/-346.5	321,1762,2217	yes	stop-gained	ZNF80	NM_007136.3		330,2024,4149	CC,CA,AA		27.9535,6.355,20.6366		245/274	113955187	2684,10322	2203	4300	6503	SO:0001587	stop_gained	7634	exon1			GCACTCATAAGGT	X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"""Zinc fingers, C2H2-type"""	13155	protein-coding gene	gene with protein product		194553	"""zinc finger protein 80 (pT17)"""			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.735T>G	3.37:g.113955187A>C	ENSP00000417192:p.Tyr245*	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_007136	Q6NSW4|Q6NT14	Nonsense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	408	0.18681318681318682	20	0.04065040650406504	74	0.20441988950276244	96	0.16783216783216784	218	0.287598944591029	A	26.6	4.753196	0.89753	0.06355	0.279535	ENSG00000174255	ENST00000482457	.	.	.	3.14	-2.2	0.06994	.	.	.	.	.	.	.	.	.	.	.	0.24628	P	0.99363169	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.594	0.39563	0.6231:0.0:0.3769:0.0	rs3732781;rs17606507;rs52838282;rs60910931;rs3732781	.	.	.	X	245	.	ENSP00000309812:Y245X	Y	-	3	2	ZNF80	115437877	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.759000	0.04761	-0.899000	0.03901	-2.109000	0.00356	TAT	C|0.195;N|0.000	0.195	strong		0.448	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
CRISPLD2	83716	hgsc.bcm.edu	37	16	84879464	84879464	+	Missense_Mutation	SNP	A	A	G	rs12051468	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:84879464A>G	ENST00000262424.5	+	3	537	c.313A>G	c.(313-315)Agt>Ggt	p.S105G	CRISPLD2_ENST00000564567.1_Missense_Mutation_p.S105G|CRISPLD2_ENST00000567845.1_Missense_Mutation_p.S105G|CRISPLD2_ENST00000569090.1_Missense_Mutation_p.S105G|CRISPLD2_ENST00000566431.1_3'UTR	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	105	SCP.		S -> G (in dbSNP:rs12051468). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)			endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						CGGGCCCACCAGTCTGCTGGT	0.647													A|||	1870	0.373403	0.4123	0.3501	5008	,	,		15685	0.1925		0.4443	False		,,,				2504	0.4509				p.S105G		Atlas-SNP	.											.	CRISPLD2	36	.	0			c.A313G						PASS	.	A	GLY/SER	1760,2638	522.2+/-370.7	348,1064,787	63.0	53.0	57.0		313	-5.8	0.0	16	dbSNP_120	57	3675,4925	525.5+/-380.8	796,2083,1421	yes	missense	CRISPLD2	NM_031476.3	56	1144,3147,2208	GG,GA,AA		42.7326,40.0182,41.8141	benign	105/498	84879464	5435,7563	2199	4300	6499	SO:0001583	missense	83716	exon3			CCCACCAGTCTGC	AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"""LCCL domain containing cysteine-rich secretory protein 2"""	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.313A>G	16.37:g.84879464A>G	ENSP00000262424:p.Ser105Gly	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_031476	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Missense_Mutation	SNP	ENST00000262424.5	37	CCDS10949.1	747	0.34203296703296704	197	0.40040650406504064	131	0.36187845303867405	92	0.16083916083916083	327	0.4313984168865435	a	0.506	-0.868859	0.02570	0.400182	0.427326	ENSG00000103196	ENST00000262424	T	0.10099	2.91	5.21	-5.79	0.02354	CAP domain (3);	0.847289	0.10943	N	0.616969	T	0.00012	0.0000	N	0.16130	0.375	0.80722	P	0.0	B;B;B;B	0.10296	0.0;0.003;0.0;0.001	B;B;B;B	0.14578	0.005;0.011;0.005;0.006	T	0.47005	-0.9150	9	0.14656	T	0.56	.	3.9831	0.09503	0.2369:0.225:0.4277:0.1104	rs12051468;rs17855777;rs52807121;rs60792077;rs12051468	105;105;105;105	Q9H0B8;Q9H0B8-5;Q9H0B8-2;Q9H0B8-3	CRLD2_HUMAN;.;.;.	G	105	ENSP00000262424:S105G	ENSP00000262424:S105G	S	+	1	0	CRISPLD2	83436965	0.001000	0.12720	0.014000	0.15608	0.177000	0.22998	0.257000	0.18369	-1.629000	0.01546	-1.418000	0.01112	AGT	A|0.613;G|0.387	0.387	strong		0.647	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476	
NCKAP5	344148	hgsc.bcm.edu	37	2	133540605	133540605	+	Missense_Mutation	SNP	G	G	T	rs13016342	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:133540605G>T	ENST00000409261.1	-	14	4152	c.3779C>A	c.(3778-3780)cCa>cAa	p.P1260Q	NCKAP5_ENST00000317721.6_Missense_Mutation_p.P1260Q|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1260			P -> Q (in dbSNP:rs13016342).							NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TTTTAGGTGTGGTTTGCTGGA	0.527													G|||	606	0.121006	0.1702	0.1225	5008	,	,		17556	0.0655		0.1441	False		,,,				2504	0.0869				p.P1260Q		Atlas-SNP	.											.	NCKAP5	322	.	0			c.C3779A						PASS	.	G	GLN/PRO,	695,3293		59,577,1358	120.0	118.0	119.0		3779,	4.6	1.0	2	dbSNP_121	119	1380,6962		118,1144,2909	yes	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	76,	177,1721,4267	TT,TG,GG		16.5428,17.4273,16.8289	possibly-damaging,	1260/1910,	133540605	2075,10255	1994	4171	6165	SO:0001583	missense	344148	exon14			AGGTGTGGTTTGC	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.3779C>A	2.37:g.133540605G>T	ENSP00000387128:p.Pro1260Gln	Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	331	154	0.465257	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	266	0.12179487179487179	79	0.16056910569105692	53	0.1464088397790055	33	0.057692307692307696	101	0.13324538258575197	G	17.72	3.458367	0.63401	0.174273	0.165428	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.15718	2.4;2.4	5.5	4.61	0.57282	.	0.206066	0.24098	U	0.041577	T	0.00073	0.0002	L	0.32530	0.975	0.09310	P	1.0	D	0.67145	0.996	D	0.65010	0.931	T	0.11991	-1.0565	9	0.35671	T	0.21	.	14.0477	0.64714	0.0:0.0:0.8493:0.1507	rs13016342;rs58366400;rs13016342	1260	O14513	NCKP5_HUMAN	Q	1260	ENSP00000387128:P1260Q;ENSP00000380603:P1260Q	ENSP00000380603:P1260Q	P	-	2	0	NCKAP5	133257075	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.500000	0.73687	1.500000	0.48636	0.655000	0.94253	CCA	G|0.868;T|0.132	0.132	strong		0.527	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
MET	4233	hgsc.bcm.edu	37	7	116436022	116436022	+	Silent	SNP	G	G	A	rs2023748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116436022G>A	ENST00000318493.6	+	21	4258	c.4071G>A	c.(4069-4071)gcG>gcA	p.A1357A	MET_ENST00000397752.3_Silent_p.A1339A|MET_ENST00000539704.1_Silent_p.A209A			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A1357A(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GGATATCAGCGATCTTCTCTA	0.443			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	1772	0.353834	0.034	0.4697	5008	,	,		21305	0.4673		0.4433	False		,,,				2504	0.4949				p.A1357A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.G4071A						PASS	.	G	,	405,3531		16,373,1579	140.0	130.0	133.0		4017,4071	-11.4	0.0	7	dbSNP_94	133	3536,4748		773,1990,1379	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	789,2363,2958	AA,AG,GG		42.6847,10.2896,32.2504	,	1339/1391,1357/1409	116436022	3941,8279	1968	4142	6110	SO:0001819	synonymous_variant	4233	exon21	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ATCAGCGATCTTC	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.4071G>A	7.37:g.116436022G>A		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	262	132	0.503817	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.618;A|0.382	0.382	strong		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
RPH3A	22895	hgsc.bcm.edu	37	12	113319600	113319600	+	Silent	SNP	C	C	T	rs2240194	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:113319600C>T	ENST00000389385.4	+	15	1772	c.1275C>T	c.(1273-1275)aaC>aaT	p.N425N	RPH3A_ENST00000420983.2_Silent_p.N425N|RPH3A_ENST00000551052.1_Silent_p.N421N|RPH3A_ENST00000543106.2_Silent_p.N425N|RPH3A_ENST00000415485.3_Silent_p.N425N|RPH3A_ENST00000548866.1_Silent_p.N376N|RPH3A_ENST00000549913.2_3'UTR|RPH3A_ENST00000447659.2_Silent_p.N376N	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	425	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		TGGATTCAAACGGCTTGGCTG	0.612													C|||	2846	0.568291	0.7148	0.6066	5008	,	,		19674	0.6181		0.4264	False		,,,				2504	0.4376				p.N425N		Atlas-SNP	.											.	RPH3A	98	.	0			c.C1275T						PASS	.	C	,	2914,1492	677.4+/-403.4	969,976,258	110.0	102.0	105.0		1275,1263	-9.4	0.5	12	dbSNP_98	105	3534,5066	513.9+/-378.3	785,1964,1551	no	coding-synonymous,coding-synonymous	RPH3A	NM_001143854.1,NM_014954.3	,	1754,2940,1809	TT,TC,CC		41.093,33.8629,49.5771	,	425/695,421/691	113319600	6448,6558	2203	4300	6503	SO:0001819	synonymous_variant	22895	exon15			TTCAAACGGCTTG	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"""Synaptotagmins"""	17056	protein-coding gene	gene with protein product		612159	"""rabphilin 3A homolog (mouse)"""			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.1275C>T	12.37:g.113319600C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_001143854	B7Z3C3|Q96AE0	Silent	SNP	ENST00000389385.4	37	CCDS44979.1																																																																																			C|0.479;T|0.521	0.521	strong		0.612	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954	
SFXN1	94081	hgsc.bcm.edu	37	5	174936038	174936038	+	Silent	SNP	A	A	G	rs35420613	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:174936038A>G	ENST00000321442.5	+	3	422	c.168A>G	c.(166-168)caA>caG	p.Q56Q	SFXN1_ENST00000502393.1_Silent_p.Q56Q	NM_022754.5	NP_073591.2	Q9H9B4	SFXN1_HUMAN	sideroflexin 1	56					erythrocyte differentiation (GO:0030218)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|skin(3)	15	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TTCTTAGGCAAGGAATTGTTC	0.373													A|||	257	0.0513179	0.0045	0.0994	5008	,	,		20639	0.0228		0.0706	False		,,,				2504	0.09				p.Q56Q		Atlas-SNP	.											.	SFXN1	23	.	0			c.A168G						PASS	.	A		55,4351	48.9+/-83.8	0,55,2148	118.0	117.0	118.0		168	5.2	1.0	5	dbSNP_126	118	634,7966	154.6+/-208.8	34,566,3700	no	coding-synonymous	SFXN1	NM_022754.5		34,621,5848	GG,GA,AA		7.3721,1.2483,5.2976		56/323	174936038	689,12317	2203	4300	6503	SO:0001819	synonymous_variant	94081	exon3			TAGGCAAGGAATT	AF327346	CCDS4394.1	5q35.3	2008-02-05			ENSG00000164466	ENSG00000164466		"""Sideroflexins"""	16085	protein-coding gene	gene with protein product		615569					Standard	NM_022754		Approved	FLJ12876	uc003mda.2	Q9H9B4	OTTHUMG00000130555	ENST00000321442.5:c.168A>G	5.37:g.174936038A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	184	182	0.98913	NM_022754	B3KPW3|D3DQN2|Q9HA53	Silent	SNP	ENST00000321442.5	37	CCDS4394.1																																																																																			A|0.947;G|0.053	0.053	strong		0.373	SFXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252980.2	NM_022754	
SLC14A2	8170	hgsc.bcm.edu	37	18	43204744	43204744	+	Missense_Mutation	SNP	C	C	G	rs149251757	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:43204744C>G	ENST00000255226.6	+	2	931	c.115C>G	c.(115-117)Cca>Gca	p.P39A	SLC14A2_ENST00000586448.1_Missense_Mutation_p.P39A	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	39					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GGATACTCACCCAGCTCTGCC	0.567													C|||	3	0.000599042	0.0	0.0	5008	,	,		20005	0.0		0.001	False		,,,				2504	0.002				p.P39A		Atlas-SNP	.											.	SLC14A2	121	.	0			c.C115G						PASS	.	C	ALA/PRO,ALA/PRO	4,4402	8.1+/-20.4	0,4,2199	81.0	78.0	79.0		115,115	4.2	1.0	18	dbSNP_134	79	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	27,27	0,18,6485	GG,GC,CC		0.1628,0.0908,0.1384	benign,benign	39/921,39/921	43204744	18,12988	2203	4300	6503	SO:0001583	missense	8170	exon3			ACTCACCCAGCTC	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.115C>G	18.37:g.43204744C>G	ENSP00000255226:p.Pro39Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	10.95	1.496199	0.26861	9.08E-4	0.001628	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.54279	1.26;0.58	5.08	4.2	0.49525	.	0.077891	0.49305	D	0.000142	T	0.47820	0.1466	M	0.63428	1.95	0.35661	D	0.812527	P;P	0.40970	0.455;0.734	B;B	0.40165	0.142;0.321	T	0.56469	-0.7974	10	0.25751	T	0.34	-7.9968	9.6267	0.39754	0.0:0.9023:0.0:0.0977	.	39;39	Q15849;E7EPU1	UT2_HUMAN;.	A	39	ENSP00000255226:P39A;ENSP00000320689:P39A	ENSP00000255226:P39A	P	+	1	0	SLC14A2	41458742	0.100000	0.21855	0.995000	0.50966	0.555000	0.35460	0.953000	0.29162	1.269000	0.44280	0.462000	0.41574	CCA	C|0.999;G|0.001	0.001	strong		0.567	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
TUBGCP6	85378	hgsc.bcm.edu	37	22	50658424	50658424	+	Missense_Mutation	SNP	T	T	C	rs11703226	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50658424T>C	ENST00000248846.5	-	17	4233	c.4129A>G	c.(4129-4131)Act>Gct	p.T1377A	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_Silent_p.T1396T			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1377			T -> A (in dbSNP:rs11703226). {ECO:0000269|PubMed:11694571}.		G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		AGGTCCTCAGTGTCCCCGCTC	0.642													T|||	2139	0.427117	0.4629	0.4481	5008	,	,		17636	0.3948		0.4414	False		,,,				2504	0.3824				p.T1377A		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.A4129G						PASS	.	T	ALA/THR	2146,2260	575.5+/-384.0	526,1094,583	88.0	74.0	79.0		4129	-1.4	0.0	22	dbSNP_120	79	3807,4793	533.1+/-382.3	839,2129,1332	yes	missense	TUBGCP6	NM_020461.3	58	1365,3223,1915	CC,CT,TT		44.2674,48.7063,45.7712	benign	1377/1820	50658424	5953,7053	2203	4300	6503	SO:0001583	missense	85378	exon17			CCTCAGTGTCCCC	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.4129A>G	22.37:g.50658424T>C	ENSP00000248846:p.Thr1377Ala	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	119	58	0.487395	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	929	0.42536630036630035	227	0.4613821138211382	153	0.42265193370165743	217	0.3793706293706294	332	0.43799472295514513	T	9.274	1.046404	0.19748	0.487063	0.442674	ENSG00000128159	ENST00000248846;ENST00000425018	T;T	0.20463	3.14;2.07	5.31	-1.43	0.08884	.	3.336720	0.00639	N	0.000517	T	0.00012	0.0000	N	0.11201	0.11	0.58432	P	1.0000000000287557E-6	B;B;B	0.12013	0.005;0.003;0.002	B;B;B	0.16722	0.016;0.01;0.006	T	0.46162	-0.9211	9	0.08381	T	0.77	.	0.8927	0.01257	0.145:0.1885:0.2313:0.4353	rs11703226;rs59456356;rs11703226	1369;1377;1377	B2RWN4;Q96RT7;Q96RT7-3	.;GCP6_HUMAN;.	A	1377;63	ENSP00000248846:T1377A;ENSP00000405979:T63A	ENSP00000248846:T1377A	T	-	1	0	TUBGCP6	49000551	0.118000	0.22208	0.001000	0.08648	0.022000	0.10575	0.876000	0.28092	0.022000	0.15160	-0.441000	0.05720	ACT	T|0.561;C|0.439	0.439	strong		0.642	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
MAGEB16	139604	hgsc.bcm.edu	37	X	35821055	35821055	+	Missense_Mutation	SNP	A	A	G	rs4829390|rs370444095	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:35821055A>G	ENST00000399989.1	+	2	1021	c.742A>G	c.(742-744)Atg>Gtg	p.M248V	MAGEB16_ENST00000399992.1_Missense_Mutation_p.M280V|MAGEB16_ENST00000399985.1_Missense_Mutation_p.M248V|MAGEB16_ENST00000399987.1_Missense_Mutation_p.M248V|MAGEB16_ENST00000399988.1_Missense_Mutation_p.M248V	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	248	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		M -> K (in dbSNP:rs4829391).|M -> V (in dbSNP:rs4829390).							breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						AGAGCCCAGAATGCTCATCAC	0.502													G|||	2342	0.620397	0.4478	0.4121	3775	,	,		15852	0.5694		0.4195	False		,,,				2504	0.4785				p.M248V		Atlas-SNP	.											.	MAGEB16	64	.	0			c.A742G						PASS	.	G	VAL/MET	423,3332		76,144,127,1372,444	45.0	44.0	44.0		742	-6.1	0.0	X	dbSNP_111	44	767,5940		105,231,326,2086,1537	yes	missense	MAGEB16	NM_001099921.1	21	181,375,453,3458,1981	GG,GA,G,AA,A		11.4358,11.265,11.3745	benign	248/325	35821055	1190,9272	2163	4285	6448	SO:0001583	missense	139604	exon2			CCCAGAATGCTCA		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.742A>G	X.37:g.35821055A>G	ENSP00000382871:p.Met248Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	124	10	0.0806452	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	906	0.546112115732369	144	0.391304347826087	94	0.3700787401574803	192	0.49740932642487046	201	0.3338870431893688	G	4.024	0.001860	0.07819	0.11265	0.114358	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04502	3.61;3.61;3.61;3.61;3.61	3.06	-6.12	0.02124	.	0.726440	0.13630	N	0.373788	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.11235	0.004	B	0.10450	0.005	T	0.48969	-0.8987	9	0.87932	D	0	.	7.4099	0.27011	0.4068:0.38:0.2132:0.0	rs4829390	248	A2A368	MAGBG_HUMAN	V	248;280;248;248;248	ENSP00000382870:M248V;ENSP00000382874:M280V;ENSP00000382869:M248V;ENSP00000382871:M248V;ENSP00000382867:M248V	ENSP00000382867:M248V	M	+	1	0	MAGEB16	35730976	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.986000	0.01484	-4.139000	0.00070	-0.346000	0.07831	ATG	A|0.455;G|0.545	0.545	strong		0.502	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
ADCY3	109	hgsc.bcm.edu	37	2	25141538	25141538	+	Missense_Mutation	SNP	A	A	G	rs11676272	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:25141538A>G	ENST00000260600.5	-	1	1170	c.319T>C	c.(319-321)Tcc>Ccc	p.S107P		NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	107			S -> P (in dbSNP:rs11676272). {ECO:0000269|PubMed:9920776}.		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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					ACGGCGAGGGAAGCCAGCTTG	0.612													G|||	2839	0.566893	0.913	0.3876	5008	,	,		19699	0.4286		0.4642	False		,,,				2504	0.4744				p.S107P		Atlas-SNP	.											.	ADCY3	114	.	0			c.T319C						PASS	.	G	PRO/SER	3701,705	291.8+/-281.7	1553,595,55	100.0	107.0	104.0		319	2.9	0.0	2	dbSNP_120	104	4059,4541	593.7+/-393.2	964,2131,1205	yes	missense	ADCY3	NM_004036.3	74	2517,2726,1260	GG,GA,AA		47.1977,16.0009,40.3352	benign	107/1145	25141538	7760,5246	2203	4300	6503	SO:0001583	missense	109	exon1			CGAGGGAAGCCAG	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.319T>C	2.37:g.25141538A>G	ENSP00000260600:p.Ser107Pro	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	196	97	0.494898	NM_004036	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	37	CCDS1715.1	1184	0.5421245421245421	443	0.9004065040650406	155	0.4281767955801105	242	0.4230769230769231	344	0.45382585751978893	G	0.005	-2.164073	0.00318	0.839991	0.471977	ENSG00000138031	ENST00000260600;ENST00000415879;ENST00000435135;ENST00000438445	T;T;T	0.80653	-1.4;-0.96;0.93	4.8	2.94	0.34122	.	0.487586	0.22034	N	0.065548	T	0.00012	0.0000	N	0.03115	-0.41	0.48571	P	3.229999999999622E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.31420	-0.9944	9	0.29301	T	0.29	.	4.9246	0.13887	0.2557:0.1545:0.5898:0.0	rs11676272;rs11676272	107	O60266	ADCY3_HUMAN	P	107;82;107;107	ENSP00000260600:S107P;ENSP00000389799:S107P;ENSP00000406153:S107P	ENSP00000260600:S107P	S	-	1	0	ADCY3	24995042	0.799000	0.28903	0.047000	0.18901	0.382000	0.30200	1.285000	0.33261	0.099000	0.17552	-0.213000	0.12676	TCC	A|0.421;G|0.579	0.579	strong		0.612	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
FREM1	158326	hgsc.bcm.edu	37	9	14842557	14842557	+	Missense_Mutation	SNP	T	T	C	rs1353223	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:14842557T>C	ENST00000380880.3	-	9	2278	c.1495A>G	c.(1495-1497)Ata>Gta	p.I499V	FREM1_ENST00000422223.2_Missense_Mutation_p.I499V|FREM1_ENST00000380881.4_Missense_Mutation_p.I500V			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	499			I -> V (in dbSNP:rs1353223).		cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		CCATCAAATATCCGGAAGACC	0.498													T|||	327	0.0652955	0.149	0.049	5008	,	,		20672	0.0		0.0765	False		,,,				2504	0.0194				p.I499V		Atlas-SNP	.											.	FREM1	261	.	0			c.A1495G						PASS	.	T	VAL/ILE	561,3519		41,479,1520	131.0	134.0	133.0		1495	5.6	1.0	9	dbSNP_88	133	599,7797		17,565,3616	yes	missense	FREM1	NM_144966.5	29	58,1044,5136	CC,CT,TT		7.1343,13.75,9.2979	probably-damaging	499/2180	14842557	1160,11316	2040	4198	6238	SO:0001583	missense	158326	exon10			CAAATATCCGGAA	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.1495A>G	9.37:g.14842557T>C	ENSP00000370262:p.Ile499Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	162	0.07417582417582418	88	0.17886178861788618	16	0.04419889502762431	0	0.0	58	0.07651715039577836	T	26.1	4.703239	0.88924	0.1375	0.071343	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.28454	1.61;1.61;1.61	5.63	5.63	0.86233	.	0.052976	0.85682	D	0.000000	T	0.00073	0.0002	L	0.35414	1.06	0.09310	P	0.99999626827	D	0.65815	0.995	P	0.58172	0.834	T	0.05037	-1.0910	9	0.14656	T	0.56	-17.6089	16.1485	0.81594	0.0:0.0:0.0:1.0	rs1353223;rs1353223	499	Q5H8C1	FREM1_HUMAN	V	500;499;499	ENSP00000370263:I500V;ENSP00000412940:I499V;ENSP00000370262:I499V	ENSP00000370257:I502V	I	-	1	0	FREM1	14832557	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.914000	0.69964	2.281000	0.76405	0.533000	0.62120	ATA	T|0.917;C|0.083	0.083	strong		0.498	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
OR10Q1	219960	hgsc.bcm.edu	37	11	57995777	57995777	+	Missense_Mutation	SNP	G	G	A	rs11229301	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:57995777G>A	ENST00000316770.2	-	1	613	c.571C>T	c.(571-573)Cgc>Tgc	p.R191C		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	191			R -> C (in dbSNP:rs11229301).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				CAGGCCAGGCGCAGGACGGGA	0.612													G|||	776	0.154952	0.1513	0.1873	5008	,	,		21565	0.123		0.163	False		,,,				2504	0.1616				p.R191C		Atlas-SNP	.											OR10Q1,NS,carcinoma,+1,2	OR10Q1	79	2	0			c.C571T						PASS	.	G	CYS/ARG	624,3778	271.9+/-270.5	53,518,1630	73.0	63.0	67.0		571	1.4	1.0	11	dbSNP_120	67	1199,7391	241.9+/-272.1	91,1017,3187	yes	missense	OR10Q1	NM_001004471.2	180	144,1535,4817	AA,AG,GG		13.9581,14.1754,14.0317	benign	191/320	57995777	1823,11169	2201	4295	6496	SO:0001583	missense	219960	exon1			CCAGGCGCAGGAC	AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475		"""GPCR / Class A : Olfactory receptors"""	15134	protein-coding gene	gene with protein product							Standard	NM_001004471		Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.571C>T	11.37:g.57995777G>A	ENSP00000314324:p.Arg191Cys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_001004471	Q6IFG4	Missense_Mutation	SNP	ENST00000316770.2	37	CCDS31547.1	325	0.1488095238095238	56	0.11382113821138211	71	0.19613259668508287	78	0.13636363636363635	120	0.158311345646438	G	5.949	0.359011	0.11239	0.141754	0.139581	ENSG00000180475	ENST00000316770	T	0.00158	8.65	4.47	1.43	0.22495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41097	D	0.000943	T	0.00012	0.0000	M	0.80847	2.515	0.80722	P	0.0	B	0.29301	0.241	B	0.28784	0.094	T	0.36335	-0.9752	9	0.72032	D	0.01	.	6.7485	0.23474	0.0889:0.0:0.3361:0.575	rs11229301;rs56678494;rs11229301	191	Q8NGQ4	O10Q1_HUMAN	C	191	ENSP00000314324:R191C	ENSP00000314324:R191C	R	-	1	0	OR10Q1	57752353	0.000000	0.05858	0.986000	0.45419	0.101000	0.19017	-1.080000	0.03407	0.113000	0.18004	0.585000	0.79938	CGC	G|0.865;A|0.135	0.135	strong		0.612	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471	
PCK1	5105	hgsc.bcm.edu	37	20	56138648	56138648	+	Missense_Mutation	SNP	G	G	A	rs11552145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:56138648G>A	ENST00000319441.4	+	6	990	c.826G>A	c.(826-828)Gag>Aag	p.E276K	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Missense_Mutation_p.E144K	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	276			E -> K (in dbSNP:rs11552145). {ECO:0000269|Ref.3}.		carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CCCTGAGGGTGAGAAGAAGTA	0.557													G|||	431	0.0860623	0.0272	0.1052	5008	,	,		17730	0.0079		0.172	False		,,,				2504	0.1442				p.E276K		Atlas-SNP	.											.	PCK1	95	.	0			c.G826A						PASS	.	G	LYS/GLU	229,4177	134.1+/-170.4	3,223,1977	62.0	63.0	63.0		826	-2.2	0.3	20	dbSNP_120	63	1673,6927	307.3+/-308.3	172,1329,2799	yes	missense	PCK1	NM_002591.3	56	175,1552,4776	AA,AG,GG		19.4535,5.1975,14.624	benign	276/623	56138648	1902,11104	2203	4300	6503	SO:0001583	missense	5105	exon6			GAGGGTGAGAAGA		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.826G>A	20.37:g.56138648G>A	ENSP00000319814:p.Glu276Lys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	37	CCDS13460.1	189	0.08653846153846154	7	0.014227642276422764	53	0.1464088397790055	4	0.006993006993006993	125	0.16490765171503957	G	1.662	-0.511127	0.04231	0.051975	0.194535	ENSG00000124253	ENST00000319441;ENST00000535860	T;T	0.10005	2.92;2.92	5.27	-2.16	0.07080	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.289017	0.37530	N	0.002042	T	0.00012	0.0000	N	0.05078	-0.115	0.42755	P	0.006217999999999946	B	0.02656	0.0	B	0.08055	0.003	T	0.44128	-0.9348	9	0.02654	T	1	-18.3718	7.5477	0.27777	0.4186:0.2498:0.3316:0.0	rs11552145;rs28359545;rs52823511;rs11552145	276	P35558	PCKGC_HUMAN	K	276;144	ENSP00000319814:E276K;ENSP00000444342:E144K	ENSP00000319814:E276K	E	+	1	0	PCK1	55572054	0.008000	0.16893	0.257000	0.24404	0.272000	0.26649	0.080000	0.14802	-0.018000	0.14079	-0.254000	0.11334	GAG	G|0.881;A|0.119	0.119	strong		0.557	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
MUC17	140453	hgsc.bcm.edu	37	7	100679715	100679715	+	Missense_Mutation	SNP	C	C	T	rs143909059	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100679715C>T	ENST00000306151.4	+	3	5082	c.5018C>T	c.(5017-5019)aCa>aTa	p.T1673I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1673	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCATCTCCTACACCTGCTGAA	0.498													C|||	3	0.000599042	0.0	0.0	5008	,	,		26255	0.0		0.003	False		,,,				2504	0.0				p.T1673I		Atlas-SNP	.											.	MUC17	804	.	0			c.C5018T						PASS	.	C	ILE/THR	0,4406		0,0,2203	210.0	221.0	217.0		5018	0.9	0.0	7	dbSNP_134	217	7,8593	4.3+/-15.6	0,7,4293	no	missense	MUC17	NM_001040105.1	89	0,7,6496	TT,TC,CC		0.0814,0.0,0.0538	possibly-damaging	1673/4494	100679715	7,12999	2203	4300	6503	SO:0001583	missense	140453	exon3			CTCCTACACCTGC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5018C>T	7.37:g.100679715C>T	ENSP00000302716:p.Thr1673Ile	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	54	34	0.62963	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	2.860	-0.236376	0.05944	0.0	8.14E-4	ENSG00000169876	ENST00000306151	T	0.03242	4.0	0.932	0.932	0.19466	.	.	.	.	.	T	0.01730	0.0055	N	0.17082	0.46	0.09310	N	1	P	0.42757	0.789	B	0.28849	0.095	T	0.48614	-0.9020	9	0.23891	T	0.37	.	5.3368	0.15961	0.0:1.0:0.0:0.0	.	1673	Q685J3	MUC17_HUMAN	I	1673	ENSP00000302716:T1673I	ENSP00000302716:T1673I	T	+	2	0	MUC17	100466435	0.004000	0.15560	0.001000	0.08648	0.004000	0.04260	1.442000	0.35046	0.857000	0.35407	0.134000	0.15878	ACA	C|1.000;T|0.000	0.000	weak		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418275	105418275	+	Silent	SNP	T	T	C	rs2819441	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105418275T>C	ENST00000333244.5	-	7	3632	c.3513A>G	c.(3511-3513)ccA>ccG	p.P1171P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1171						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCCCGAACGATGGCATCTTGA	0.617													.|||	117	0.0233626	0.0408	0.0058	5008	,	,		18029	0.0516		0.004	False		,,,				2504	0.0031				p.P1171P		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A3513G						PASS	.	T		1112,2754		226,660,1047	188.0	191.0	190.0		3513	-8.8	0.0	14	dbSNP_100	190	1855,6381		286,1283,2549	no	coding-synonymous	AHNAK2	NM_138420.2		512,1943,3596	CC,CT,TT		22.5231,28.7636,24.5166		1171/5796	105418275	2967,9135	1933	4118	6051	SO:0001819	synonymous_variant	113146	exon7			GAACGATGGCATC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3513A>G	14.37:g.105418275T>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.267;T|0.733	0.267	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
LRP2	4036	hgsc.bcm.edu	37	2	170053505	170053505	+	Missense_Mutation	SNP	C	C	T	rs2228171	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:170053505C>T	ENST00000263816.3	-	46	8899	c.8614G>A	c.(8614-8616)Gca>Aca	p.A2872T		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2872	LDL-receptor class A 20. {ECO:0000255|PROSITE-ProRule:PRU00124}.		A -> T (in dbSNP:rs2228171).		cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CGCCCAGATGCGCATTGGAAC	0.458													T|||	1342	0.267971	0.1974	0.196	5008	,	,		21800	0.5268		0.2594	False		,,,				2504	0.1564				p.A2872T		Atlas-SNP	.											.	LRP2	751	.	0			c.G8614A						PASS	.	T	THR/ALA	855,3551	745.0+/-411.6	84,687,1432	89.0	79.0	82.0		8614	-10.7	0.0	2	dbSNP_98	82	2261,6339	708.1+/-405.6	304,1653,2343	yes	missense	LRP2	NM_004525.2	58	388,2340,3775	TT,TC,CC		26.2907,19.4054,23.9582	benign	2872/4656	170053505	3116,9890	2203	4300	6503	SO:0001583	missense	4036	exon46			CAGATGCGCATTG		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.8614G>A	2.37:g.170053505C>T	ENSP00000263816:p.Ala2872Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	35	0.57377	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	704	0.32234432234432236	107	0.21747967479674796	73	0.20165745856353592	313	0.5472027972027972	211	0.2783641160949868	T	8.682	0.905469	0.17760	0.194054	0.262907	ENSG00000081479	ENST00000263816	D	0.95656	-3.77	6.17	-10.7	0.00240	.	0.652839	0.17358	N	0.177138	T	0.00012	0.0000	N	0.04820	-0.15	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44390	-0.9331	9	0.11794	T	0.64	.	3.9395	0.09321	0.3942:0.3601:0.0806:0.1651	rs2228171;rs2302697;rs4668123;rs17848174;rs52816657;rs57579868;rs4668123	2872	P98164	LRP2_HUMAN	T	2872	ENSP00000263816:A2872T	ENSP00000263816:A2872T	A	-	1	0	LRP2	169761751	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-2.346000	0.01096	-3.062000	0.00256	-2.179000	0.00317	GCA	T|0.232;G|0.108;C|0.608;A|0.053	0.232	strong		0.458	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
PLEKHA3	65977	hgsc.bcm.edu	37	2	179358665	179358665	+	Silent	SNP	A	A	G	rs2303536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179358665A>G	ENST00000234453.5	+	4	801	c.399A>G	c.(397-399)acA>acG	p.T133T	PLEKHA3_ENST00000461474.1_3'UTR	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	133						Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			AAGTTCATACAATACAGGAAT	0.403													G|||	1527	0.304912	0.2095	0.1945	5008	,	,		20258	0.63		0.1551	False		,,,				2504	0.3313				p.T133T		Atlas-SNP	.											PLEKHA3,NS,carcinoma,+1,1	PLEKHA3	25	1	0			c.A399G						PASS	.	G		883,3523	741.1+/-411.2	90,703,1410	126.0	118.0	120.0		399	-11.7	0.4	2	dbSNP_100	120	1271,7329	760.0+/-407.6	99,1073,3128	no	coding-synonymous	PLEKHA3	NM_019091.3		189,1776,4538	GG,GA,AA		14.7791,20.0409,16.5616		133/301	179358665	2154,10852	2203	4300	6503	SO:0001819	synonymous_variant	65977	exon4			TCATACAATACAG	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"""Pleckstrin homology (PH) domain containing"""	14338	protein-coding gene	gene with protein product	"""four-phosphate-adaptor protein 1"""	607774	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"""			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.399A>G	2.37:g.179358665A>G		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	268	124	0.462687	NM_019091	Q4ZG69|Q86TQ1|Q9NXT3	Silent	SNP	ENST00000234453.5	37	CCDS33336.1																																																																																			A|1.000;|0.000	.	weak		0.403	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091	
FPR1	2357	hgsc.bcm.edu	37	19	52250216	52250216	+	Missense_Mutation	SNP	A	A	G	rs5030878	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52250216A>G	ENST00000595042.1	-	3	173	c.32T>C	c.(31-33)aTc>aCc	p.I11T	FPR1_ENST00000304748.4_Missense_Mutation_p.I11T	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	11			I -> T (in dbSNP:rs5030878). {ECO:0000269|Ref.7}.		activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	CCCTCCAGAGATGTTCGTGGG	0.502													A|||	4177	0.834065	0.7852	0.7896	5008	,	,		20800	0.9613		0.7684	False		,,,				2504	0.8681				p.I11T		Atlas-SNP	.											.	FPR1	64	.	0			c.T32C	GRCh37	CM074875	FPR1	M	rs5030878	PASS	.	A	THR/ILE,THR/ILE	3488,918		1370,748,85	58.0	56.0	57.0		32,32	-6.9	0.0	19	dbSNP_113	57	6559,2041		2506,1547,247	yes	missense,missense	FPR1	NM_001193306.1,NM_002029.3	89,89	3876,2295,332	GG,GA,AA		23.7326,20.8352,22.751	benign,benign	11/351,11/351	52250216	10047,2959	2203	4300	6503	SO:0001583	missense	2357	exon3			CCAGAGATGTTCG	M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"""GPCR / Class A : Formyl peptide receptors"""	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.32T>C	19.37:g.52250216A>G	ENSP00000471493:p.Ile11Thr	Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	37	CCDS12839.1	1805	0.8264652014652014	377	0.766260162601626	290	0.8011049723756906	549	0.9597902097902098	589	0.7770448548812665	.	5.381	0.255528	0.10185	0.791648	0.762674	ENSG00000171051	ENST00000304748	T	0.37752	1.18	3.62	-6.88	0.01665	.	2.217780	0.02646	N	0.105855	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.13594	0.008	B	0.15484	0.013	T	0.28364	-1.0046	9	0.14252	T	0.57	.	0.3369	0.00327	0.245:0.2994:0.1958:0.2598	rs5030878;rs5030878	11	P21462	FPR1_HUMAN	T	11	ENSP00000302707:I11T	ENSP00000302707:I11T	I	-	2	0	FPR1	56942028	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.070000	0.01380	-1.802000	0.01244	0.533000	0.62120	ATC	A|0.201;G|0.799	0.799	strong		0.502	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029	
ADAR	103	hgsc.bcm.edu	37	1	154573526	154573526	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:154573526T>C	ENST00000368474.4	-	2	1791	c.1592A>G	c.(1591-1593)cAt>cGt	p.H531R	ADAR_ENST00000368471.3_Missense_Mutation_p.H236R|ADAR_ENST00000292205.5_Missense_Mutation_p.H574R|ADAR_ENST00000471068.1_5'Flank	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	531	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		CCGAGGTTCATGGGGTGGTCC	0.527																																					p.H531R		Atlas-SNP	.											ADAR,NS,malignant_melanoma,-1,1	ADAR	113	1	0			c.A1592G						PASS	.						108.0	115.0	113.0					1																	154573526		2203	4300	6503	SO:0001583	missense	103	exon2			GGTTCATGGGGTG	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.1592A>G	1.37:g.154573526T>C	ENSP00000357459:p.His531Arg	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	242	102	0.421488	NM_015840	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.978122	0.74360	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	4.77	3.62	0.41486	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.154749	0.56097	D	0.000026	D	0.88332	0.6408	M	0.91354	3.2	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.91635	0.999;0.999;0.994	D	0.89488	0.3755	10	0.66056	D	0.02	-17.755	10.7753	0.46346	0.1421:0.0:0.0:0.8579	.	531;531;531	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	R	574;531;236;526	ENSP00000292205:H574R;ENSP00000357459:H531R;ENSP00000357456:H236R;ENSP00000431794:H526R	ENSP00000292205:H574R	H	-	2	0	ADAR	152840150	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.312000	0.78968	0.815000	0.34398	0.459000	0.35465	CAT	.	.	none		0.527	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
MT-ND5	4540	hgsc.bcm.edu	37	M	13602	13602	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:13602T>C	ENST00000361567.2	+	1	1266	c.1266T>C	c.(1264-1266)taT>taC	p.Y422Y	MT-TE_ENST00000387459.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	422					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ACAAGCGCCTATAGCACTCGA	0.448																																					p.Y422Y		Atlas-SNP	.											.	.	.	.	0			c.T1266C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CGCCTATAGCACT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1266T>C	M.37:g.13602T>C		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.448	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
SPANXD	64648	hgsc.bcm.edu	37	X	140785741	140785741	+	Missense_Mutation	SNP	A	A	C	rs144554749		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:140785741A>C	ENST00000370515.3	-	2	508	c.175T>G	c.(175-177)Ttt>Gtt	p.F59V		NM_032417.2|NM_145665.1	NP_115793.1|NP_663698.1	Q9BXN6	SPNXD_HUMAN	SPANX family, member D	59						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	Acute lymphoblastic leukemia(192;7.65e-05)					GTTCTTTTAAAGTTCCTCCTG	0.488																																					p.F59V		Atlas-SNP	.											.	.	.	.	0			c.T175G						PASS	.						233.0	182.0	199.0					X																	140785741		2202	4287	6489	SO:0001583	missense	171489	exon2			TTTTAAAGTTCCT	AJ457791	CCDS14675.1	Xq27.2	2014-06-19			ENSG00000196406	ENSG00000196406			14332	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 4"""	300670, 300671	"""SPANX family, member E"""	SPANXE			Standard	NM_032417		Approved	CT11.4		Q9BXN6	OTTHUMG00000022563	ENST00000370515.3:c.175T>G	X.37:g.140785741A>C	ENSP00000359546:p.Phe59Val	Somatic	409	1	0.00244499		WXS	Illumina HiSeq	Phase_I	525	339	0.645714	NM_145665	Q5JWI1	Missense_Mutation	SNP	ENST00000370515.3	37	CCDS14675.1	.	.	.	.	.	.	.	.	.	.	N	0	-2.675089	0.00104	.	.	ENSG00000196406	ENST00000370515	T	0.05319	3.46	.	.	.	.	.	.	.	.	T	0.02380	0.0073	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45011	-0.9290	6	0.15952	T	0.53	.	.	.	.	rs1059178;rs2933670;rs3176111;rs17845057;rs17857836;rs17859693	59	Q9BXN6	SPNXD_HUMAN	V	59	ENSP00000359546:F59V	ENSP00000359546:F59V	F	-	1	0	SPANXD	140613407	0.004000	0.15560	0.004000	0.12327	0.004000	0.04260	-2.376000	0.01070	-2.341000	0.00625	-2.441000	0.00211	TTT	.	.	weak		0.488	SPANXD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058598.1		
CHIA	27159	hgsc.bcm.edu	37	1	111862078	111862078	+	Silent	SNP	C	C	T	rs12094378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:111862078C>T	ENST00000369740.1	+	11	1268	c.1165C>T	c.(1165-1167)Ctg>Ttg	p.L389L	CHIA_ENST00000430615.1_Silent_p.L281L|CHIA_ENST00000343320.6_Silent_p.L389L|CHIA_ENST00000483391.1_Silent_p.L228L|CHIA_ENST00000451398.2_Silent_p.L228L|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000353665.6_Silent_p.L228L	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	389					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		GGCCCTCGGCCTGCAGAGTGC	0.542													C|||	511	0.102037	0.1884	0.0821	5008	,	,		19909	0.0		0.1093	False		,,,				2504	0.0971				p.L389L		Atlas-SNP	.											.	CHIA	115	.	0			c.C1165T						PASS	.	C	,	753,3653	302.7+/-287.5	61,631,1511	64.0	60.0	61.0		841,1165	3.5	0.0	1	dbSNP_120	61	1013,7587	212.0+/-252.4	51,911,3338	no	coding-synonymous,coding-synonymous	CHIA	NM_021797.2,NM_201653.2	,	112,1542,4849	TT,TC,CC		11.7791,17.0903,13.5783	,	281/369,389/477	111862078	1766,11240	2203	4300	6503	SO:0001819	synonymous_variant	27159	exon11			CTCGGCCTGCAGA	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.1165C>T	1.37:g.111862078C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	158	70	0.443038	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	37	CCDS41368.1																																																																																			C|0.872;T|0.128	0.128	strong		0.542	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
ZCCHC3	85364	hgsc.bcm.edu	37	20	279185	279185	+	Silent	SNP	C	C	T	rs45569040	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:279185C>T	ENST00000382352.3	+	1	1449	c.958C>T	c.(958-960)Ctg>Ttg	p.L320L		NM_033089.6	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	320							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			GGCCTTCTTCCTGGGGGCCGA	0.632													C|||	20	0.00399361	0.0	0.0029	5008	,	,		16576	0.0		0.0149	False		,,,				2504	0.0031				p.L320L		Atlas-SNP	.											.	ZCCHC3	20	.	0			c.C958T						PASS	.	C		13,3825		0,13,1906	40.0	47.0	45.0		958	2.2	1.0	20	dbSNP_127	45	144,8088		4,136,3976	no	coding-synonymous	ZCCHC3	NM_033089.6		4,149,5882	TT,TC,CC		1.7493,0.3387,1.3007		320/405	279185	157,11913	1919	4116	6035	SO:0001819	synonymous_variant	85364	exon1			TTCTTCCTGGGGG	AL034548	CCDS42844.1	20p13-p12.2	2014-04-10	2004-07-14	2004-07-14	ENSG00000177764	ENSG00000247315		"""Zinc fingers, CCHC domain containing"""	16230	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 99"""	C20orf99			Standard	NM_033089		Approved	dJ1103G7.7	uc002wdf.3	Q9NUD5	OTTHUMG00000188280	ENST00000382352.3:c.958C>T	20.37:g.279185C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	163	163	1	NM_033089	Q3B7J3|Q6NT79	Silent	SNP	ENST00000382352.3	37	CCDS42844.1																																																																																			C|0.995;T|0.005	0.005	strong		0.632	ZCCHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077447.1		
AKR1C2	1646	hgsc.bcm.edu	37	10	5042789	5042789	+	Silent	SNP	A	A	G	rs145355870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:5042789A>G	ENST00000380753.4	-	3	509	c.322T>C	c.(322-324)Ttg>Ctg	p.L108L	AKR1C2_ENST00000455190.1_Silent_p.L108L|AKR1C2_ENST00000407674.1_Silent_p.L108L|AKR1C2_ENST00000421196.3_Silent_p.L108L	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	108					cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	ACATAGTCCAATTGAAGATTT	0.398													A|||	15	0.00299521	0.0015	0.0115	5008	,	,		18331	0.003		0.002	False		,,,				2504	0.0				p.L108L		Atlas-SNP	.											.	AKR1C2	68	.	0			c.T322C						PASS	.	A	,,	7,4399	12.9+/-30.5	0,7,2196	128.0	118.0	122.0		322,322,322	-3.0	0.0	10	dbSNP_134	122	30,8570	21.0+/-64.5	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	AKR1C2	NM_001135241.1,NM_001354.4,NM_205845.1	,,	0,37,6466	GG,GA,AA		0.3488,0.1589,0.2845	,,	108/140,108/324,108/324	5042789	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	1646	exon5			AGTCCAATTGAAG	L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1.3.1.20, 1.1.1.213	"""Aldo-keto reductases"""	385	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III"""	600450	"""aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)"", ""testicular 17,20-desmolase deficiency"""	DDH2, TDD		9716498, 21802064	Standard	NM_001354		Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.322T>C	10.37:g.5042789A>G		Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	256	130	0.507812	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Silent	SNP	ENST00000380753.4	37	CCDS7062.1																																																																																			A|0.997;G|0.003	0.003	strong		0.398	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354	
KRT76	51350	hgsc.bcm.edu	37	12	53165949	53165949	+	Missense_Mutation	SNP	C	C	T	rs12296548	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53165949C>T	ENST00000332411.2	-	5	1119	c.1066G>A	c.(1066-1068)Gag>Aag	p.E356K		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	356	Coil 2.|Rod.			E -> K (in Ref. 3; BAG61375). {ECO:0000305}.	cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GCGCGGACCTCGGCAATGATG	0.597													C|||	690	0.13778	0.0817	0.0965	5008	,	,		20630	0.0972		0.1014	False		,,,				2504	0.3221				p.E356K		Atlas-SNP	.											.	KRT76	72	.	0			c.G1066A						PASS	.	C	LYS/GLU	476,3930	223.3+/-239.8	33,410,1760	88.0	75.0	79.0		1066	4.4	0.9	12	dbSNP_120	79	1043,7557	221.2+/-258.7	71,901,3328	yes	missense	KRT76	NM_015848.4	56	104,1311,5088	TT,TC,CC		12.1279,10.8034,11.6792	probably-damaging	356/639	53165949	1519,11487	2203	4300	6503	SO:0001583	missense	51350	exon5			GGACCTCGGCAAT	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.1066G>A	12.37:g.53165949C>T	ENSP00000330101:p.Glu356Lys	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	230	125	0.543478	NM_015848	B4DRR3|Q7Z795	Missense_Mutation	SNP	ENST00000332411.2	37	CCDS8838.1	218	0.09981684981684982	45	0.09146341463414634	42	0.11602209944751381	62	0.10839160839160839	69	0.09102902374670185	C	21.6	4.179986	0.78564	0.108034	0.121279	ENSG00000185069	ENST00000332411	D	0.92199	-2.99	4.42	4.42	0.53409	Filament (1);	0.000000	0.44902	D	0.000406	T	0.42245	0.1194	M	0.89904	3.07	0.09310	P	0.99999385671	D	0.89917	1.0	D	0.81914	0.995	T	0.66555	-0.5894	9	0.72032	D	0.01	.	17.8977	0.88893	0.0:1.0:0.0:0.0	rs12296548	356	Q01546	K22O_HUMAN	K	356	ENSP00000330101:E356K	ENSP00000330101:E356K	E	-	1	0	KRT76	51452216	1.000000	0.71417	0.920000	0.36463	0.272000	0.26649	6.020000	0.70826	2.398000	0.81561	0.462000	0.41574	GAG	C|0.889;T|0.111	0.111	strong		0.597	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
ABCC3	8714	hgsc.bcm.edu	37	17	48753423	48753423	+	Silent	SNP	C	C	T	rs4148416	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:48753423C>T	ENST00000285238.8	+	22	3119	c.3039C>T	c.(3037-3039)ggC>ggT	p.G1013G	ABCC3_ENST00000510891.1_3'UTR	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1013	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	TGAGGCTGGGCGTCTATGCTG	0.562													C|||	686	0.136981	0.2254	0.0951	5008	,	,		21999	0.1567		0.0497	False		,,,				2504	0.1166				p.G1013G		Atlas-SNP	.											.	ABCC3	138	.	0			c.C3039T						PASS	.	C		850,3556	336.0+/-304.2	79,692,1432	84.0	74.0	77.0		3039	-11.8	0.0	17	dbSNP_110	77	463,8137	137.0+/-194.0	9,445,3846	no	coding-synonymous	ABCC3	NM_003786.3		88,1137,5278	TT,TC,CC		5.3837,19.2919,10.0953		1013/1528	48753423	1313,11693	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon22			GCTGGGCGTCTAT	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.3039C>T	17.37:g.48753423C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1	223	0.1021062271062271	80	0.16260162601626016	35	0.09668508287292818	75	0.13111888111888112	33	0.04353562005277045	C	0.502	-0.870347	0.02570	0.192919	0.053837	ENSG00000108846	ENST00000513745	.	.	.	5.88	-11.8	0.00035	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.99999999076842	.	.	.	.	.	.	T	0.02617	-1.1133	3	.	.	.	-18.5963	4.1202	0.10101	0.431:0.1244:0.0553:0.3894	rs4148416;rs4148416	.	.	.	C	162	.	.	R	+	1	0	ABCC3	46108422	0.000000	0.05858	0.028000	0.17463	0.177000	0.22998	-3.861000	0.00348	-3.862000	0.00098	-0.812000	0.03155	CGT	C|0.893;T|0.107	0.107	strong		0.562	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
ITPKB	3707	hgsc.bcm.edu	37	1	226923938	226923938	+	Missense_Mutation	SNP	A	A	C	rs6667260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:226923938A>C	ENST00000272117.3	-	1	1221	c.1222T>G	c.(1222-1224)Tcc>Gcc	p.S408A	ITPKB_ENST00000429204.1_Missense_Mutation_p.S408A|ITPKB_ENST00000366784.1_Missense_Mutation_p.S408A			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	408			S -> A (in dbSNP:rs6667260). {ECO:0000269|PubMed:11846419, ECO:0000269|PubMed:15489334}.		cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				CAGCTCAGGGAATCAGAGGAC	0.677													C|||	3057	0.610423	0.6067	0.6599	5008	,	,		16260	0.6786		0.5258	False		,,,				2504	0.5971				p.S408A	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	0			c.T1222G						scavenged	.	C	ALA/SER	2536,1860		729,1078,391	33.0	40.0	38.0		1222	1.0	0.0	1	dbSNP_116	38	4146,4452		1040,2066,1193	yes	missense	ITPKB	NM_002221.3	99	1769,3144,1584	CC,CA,AA		48.2205,42.3112,48.5763	benign	408/947	226923938	6682,6312	2198	4299	6497	SO:0001583	missense	3707	exon2			TCAGGGAATCAGA	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1222T>G	1.37:g.226923938A>C	ENSP00000272117:p.Ser408Ala	Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	1305	0.5975274725274725	282	0.573170731707317	229	0.6325966850828729	387	0.6765734265734266	407	0.5369393139841688	C	0.132	-1.111789	0.01813	0.576888	0.482205	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.20598	2.07;2.07;2.06	4.1	1.01	0.19927	.	0.990786	0.08197	N	0.982952	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42649	-0.9439	9	0.02654	T	1	-1.6525	3.0407	0.06138	0.324:0.3961:0.0:0.28	rs6667260;rs17856474;rs58231934;rs6667260	408	P27987	IP3KB_HUMAN	A	408	ENSP00000272117:S408A;ENSP00000411152:S408A;ENSP00000355748:S408A	ENSP00000272117:S408A	S	-	1	0	ITPKB	224990561	0.000000	0.05858	0.001000	0.08648	0.072000	0.16883	0.079000	0.14782	-0.121000	0.11787	-0.323000	0.08544	TCC	A|0.444;C|0.556	0.556	strong		0.677	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
SMCR8	140775	hgsc.bcm.edu	37	17	18226177	18226177	+	Silent	SNP	G	G	T	rs4925171	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:18226177G>T	ENST00000406438.3	+	2	3087	c.2607G>T	c.(2605-2607)ctG>ctT	p.L869L	RP1-178F10.3_ENST00000577764.1_lincRNA	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	869						nucleus (GO:0005634)		p.L869L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						ACCTGCACCTGCCTACCCACG	0.587													G|||	1152	0.230032	0.3396	0.2695	5008	,	,		18525	0.0605		0.3082	False		,,,				2504	0.1483				p.L869L		Atlas-SNP	.											SMCR8,NS,carcinoma,0,1	SMCR8	62	1	1	Substitution - coding silent(1)	stomach(1)	c.G2607T						PASS	.	G		1386,2802		206,974,914	61.0	64.0	63.0		2607	5.2	1.0	17	dbSNP_111	63	2552,5914		369,1814,2050	no	coding-synonymous	SMCR8	NM_144775.2		575,2788,2964	TT,TG,GG		30.1441,33.0946,31.1206		869/938	18226177	3938,8716	2094	4233	6327	SO:0001819	synonymous_variant	140775	exon2			GCACCTGCCTACC	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.2607G>T	17.37:g.18226177G>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	195	89	0.45641	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Silent	SNP	ENST00000406438.3	37	CCDS11195.2																																																																																			G|0.744;T|0.256	0.256	strong		0.587	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
MAP1S	55201	hgsc.bcm.edu	37	19	17835917	17835917	+	Silent	SNP	C	C	T	rs141175074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17835917C>T	ENST00000324096.4	+	4	514	c.363C>T	c.(361-363)tgC>tgT	p.C121C	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000544059.2_Silent_p.C95C|MAP1S_ENST00000597681.1_Intron	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	121	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CTGGGCCCTGCCTGGAGGAGA	0.612													C|||	2	0.000399361	0.0	0.0014	5008	,	,		19191	0.0		0.0	False		,,,				2504	0.001				p.C121C		Atlas-SNP	.											.	MAP1S	74	.	0			c.C363T						PASS	.	C		0,4406		0,0,2203	95.0	94.0	94.0		363	3.2	1.0	19	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MAP1S	NM_018174.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		121/1060	17835917	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55201	exon4			GCCCTGCCTGGAG	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.363C>T	19.37:g.17835917C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Silent	SNP	ENST00000324096.4	37	CCDS32954.1																																																																																			C|1.000;T|0.000	0.000	strong		0.612	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
TNC	3371	hgsc.bcm.edu	37	9	117835899	117835899	+	Missense_Mutation	SNP	C	C	T	rs1138545	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:117835899C>T	ENST00000350763.4	-	10	3608	c.3197G>A	c.(3196-3198)cGt>cAt	p.R1066H	TNC_ENST00000537320.1_Missense_Mutation_p.R1066H|TNC_ENST00000340094.3_Missense_Mutation_p.R1066H|TNC_ENST00000535648.1_Missense_Mutation_p.R1066H|TNC_ENST00000341037.4_Missense_Mutation_p.R1066H|TNC_ENST00000345230.3_Missense_Mutation_p.R1066H|TNC_ENST00000346706.3_Missense_Mutation_p.R1066H|TNC_ENST00000423613.2_Missense_Mutation_p.R1066H|TNC_ENST00000542877.1_Missense_Mutation_p.R1066H	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1066	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.			R -> H (in Ref. 1; no nucleotide entry, 3; AAA88083 and 7; AAA52703). {ECO:0000305}.	bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TGCCTTCACACGTGCGGGCTT	0.542													C|||	592	0.118211	0.1513	0.0893	5008	,	,		20027	0.0952		0.1501	False		,,,				2504	0.0849				p.R1066H		Atlas-SNP	.											.	TNC	282	.	0			c.G3197A						PASS	.	C	HIS/ARG	566,3840	252.1+/-258.6	35,496,1672	116.0	104.0	108.0		3197	3.0	0.0	9	dbSNP_127	108	1243,7357	248.3+/-276.0	104,1035,3161	yes	missense	TNC	NM_002160.3	29	139,1531,4833	TT,TC,CC		14.4535,12.8461,13.909	benign	1066/2202	117835899	1809,11197	2203	4300	6503	SO:0001583	missense	3371	exon10			TTCACACGTGCGG		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.3197G>A	9.37:g.117835899C>T	ENSP00000265131:p.Arg1066His	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	257	0.11767399267399267	65	0.13211382113821138	37	0.10220994475138122	32	0.055944055944055944	123	0.16226912928759896	C	5.666	0.307551	0.10733	0.128461	0.144535	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.53423	0.64;0.66;0.87;0.85;0.68;0.76;0.66;0.85;0.62	5.9	3.05	0.35203	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.342173	0.31963	N	0.006798	T	0.00178	0.0005	L	0.52573	1.65	0.58432	P	1.0000000000287557E-6	B;B	0.18013	0.025;0.001	B;B	0.13407	0.009;0.004	T	0.08953	-1.0697	9	0.25106	T	0.35	.	7.86	0.29504	0.0:0.644:0.1461:0.2099	rs45602433;rs61738260	1066;1066	E9PC84;P24821	.;TENA_HUMAN	H	1066	ENSP00000344400:R1066H;ENSP00000438152:R1066H;ENSP00000344555:R1066H;ENSP00000345861:R1066H;ENSP00000265131:R1066H;ENSP00000339553:R1066H;ENSP00000411406:R1066H;ENSP00000443478:R1066H;ENSP00000442242:R1066H	ENSP00000344400:R1066H	R	-	2	0	TNC	116875720	0.211000	0.23529	0.005000	0.12908	0.034000	0.12701	1.000000	0.29770	0.387000	0.25024	0.655000	0.94253	CGT	C|0.864;T|0.136	0.136	strong		0.542	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
APOL2	23780	hgsc.bcm.edu	37	22	36623920	36623920	+	Missense_Mutation	SNP	G	G	A	rs7285167	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:36623920G>A	ENST00000249066.6	-	6	1020	c.544C>T	c.(544-546)Cgc>Tgc	p.R182C	APOL2_ENST00000451256.2_Missense_Mutation_p.R294C|APOL2_ENST00000358502.5_Missense_Mutation_p.R182C	NM_145637.1	NP_663612.1	Q9BQE5	APOL2_HUMAN	apolipoprotein L, 2	182			R -> C (in dbSNP:rs7285167).		acute-phase response (GO:0006953)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|maternal process involved in female pregnancy (GO:0060135)|multicellular organismal development (GO:0007275)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|membrane (GO:0016020)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(2)	9						TCCAAGTTGCGGGCTTGGGCT	0.522													N|||	757	0.151158	0.3381	0.0576	5008	,	,		20870	0.0367		0.0865	False		,,,				2504	0.1493				p.R182C		Atlas-SNP	.											.	APOL2	20	.	0			c.C544T						PASS	.	G	CYS/ARG,CYS/ARG	1172,2976		145,882,1047	74.0	76.0	76.0		544,544	-0.0	0.0	22	dbSNP_116	76	650,7788		28,594,3597	yes	missense,missense	APOL2	NM_030882.2,NM_145637.1	180,180	173,1476,4644	AA,AG,GG		7.7032,28.2546,14.4764	probably-damaging,probably-damaging	182/338,182/338	36623920	1822,10764	2074	4219	6293	SO:0001583	missense	23780	exon5			AGTTGCGGGCTTG	AF324224	CCDS43014.1	22q12.3	2013-09-20			ENSG00000128335	ENSG00000128335		"""Apolipoproteins"""	619	protein-coding gene	gene with protein product	"""apolipoprotein L-II"""	607252				10591208, 11374903	Standard	NM_145637		Approved	APOL-II	uc003apa.3	Q9BQE5	OTTHUMG00000150634	ENST00000249066.6:c.544C>T	22.37:g.36623920G>A	ENSP00000249066:p.Arg182Cys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_030882	B0QYK7|O95915|Q59GW9|Q5TH96|Q969T6|Q9BT28|Q9UGT1|Q9UH10	Missense_Mutation	SNP	ENST00000249066.6	37	CCDS43014.1	242	0.1108058608058608	137	0.2784552845528455	23	0.06353591160220995	15	0.026223776223776224	67	0.08839050131926121	G	9.300	1.052840	0.19907	0.282546	0.077032	ENSG00000128335	ENST00000358502;ENST00000249066;ENST00000451256	T;T;T	0.03635	3.86;3.86;3.86	3.66	-0.00713	0.14010	.	0.766380	0.12807	N	0.437490	T	0.00012	0.0000	L	0.58101	1.795	0.80722	P	0.0	B;B	0.15141	0.012;0.012	B;B	0.10450	0.005;0.005	T	0.41034	-0.9531	9	0.59425	D	0.04	.	4.7381	0.12999	0.0:0.1125:0.3888:0.4987	rs7285167;rs52814068;rs56937731;rs7285167	294;182	B4E1T5;Q9BQE5	.;APOL2_HUMAN	C	182;182;294	ENSP00000351292:R182C;ENSP00000249066:R182C;ENSP00000403153:R294C	ENSP00000249066:R182C	R	-	1	0	APOL2	34953866	0.000000	0.05858	0.007000	0.13788	0.001000	0.01503	-0.067000	0.11579	-0.179000	0.10654	-0.718000	0.03613	CGC	G|0.885;A|0.115	0.115	strong		0.522	APOL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319279.1	NM_145637	
FMN1	342184	hgsc.bcm.edu	37	15	33359370	33359370	+	Intron	SNP	C	C	T	rs11072170	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:33359370C>T	ENST00000559047.1	-	3	2043				FMN1_ENST00000559150.1_Intron|FMN1_ENST00000558197.1_Missense_Mutation_p.G239E|FMN1_ENST00000334528.9_Missense_Mutation_p.G239E|FMN1_ENST00000561249.1_Intron			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.G239E(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GTCTTGGGACCCTTCTTCTCC	0.512													C|||	1305	0.260583	0.1929	0.4337	5008	,	,		18120	0.1478		0.3569	False		,,,				2504	0.2464				p.G239E		Atlas-SNP	.											FMN1_ENST00000334528,NS,carcinoma,0,1	FMN1	174	1	1	Substitution - Missense(1)	stomach(1)	c.G716A						PASS	.	C	GLU/GLY	781,3349		69,643,1353	85.0	90.0	88.0		716	0.4	0.0	15	dbSNP_120	88	2934,5482		520,1894,1794	yes	missense	FMN1	NM_001103184.2	98	589,2537,3147	TT,TC,CC		34.8622,18.9104,29.611	benign	239/1197	33359370	3715,8831	2065	4208	6273	SO:0001627	intron_variant	342184	exon1			TGGGACCCTTCTT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-2095G>A	15.37:g.33359370C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	110	54	0.490909	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		617	0.2825091575091575	85	0.17276422764227642	154	0.425414364640884	96	0.16783216783216784	282	0.3720316622691293	C	0	-2.721836	0.00092	0.189104	0.348622	ENSG00000248905	ENST00000334528	T	0.34667	1.35	4.57	0.42	0.16444	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B;B	0.14012	0.009;0.001	B;B	0.10450	0.005;0.001	T	0.48019	-0.9071	7	0.27082	T	0.32	.	6.6807	0.23119	0.0:0.5879:0.1238:0.2883	rs11072170;rs52836692;rs61639257;rs11072170	239;239	Q68DA7-3;Q68DA7-5	.;.	E	239	ENSP00000333950:G239E	ENSP00000333950:G239E	G	-	2	0	FMN1	31146662	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-0.333000	0.07894	0.141000	0.18875	-0.136000	0.14681	GGG	C|0.730;T|0.270	0.270	strong		0.512	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
SLC12A7	10723	hgsc.bcm.edu	37	5	1065514	1065514	+	Missense_Mutation	SNP	A	A	G	rs56350427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1065514A>G	ENST00000264930.5	-	18	2364	c.2321T>C	c.(2320-2322)aTg>aCg	p.M774T	MIR4635_ENST00000583759.1_RNA	NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	774					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CAGGTGGGACATGCCATCCCG	0.627													A|||	26	0.00519169	0.0	0.0014	5008	,	,		18614	0.0		0.0209	False		,,,				2504	0.0041				p.M774T		Atlas-SNP	.											.	SLC12A7	97	.	0			c.T2321C						PASS	.	A	THR/MET	14,4392	21.2+/-45.6	0,14,2189	67.0	69.0	68.0		2321	0.5	0.8	5	dbSNP_129	68	195,8405	85.6+/-148.0	4,187,4109	yes	missense	SLC12A7	NM_006598.2	81	4,201,6298	GG,GA,AA		2.2674,0.3177,1.607	benign	774/1084	1065514	209,12797	2203	4300	6503	SO:0001583	missense	10723	exon18			TGGGACATGCCAT	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2321T>C	5.37:g.1065514A>G	ENSP00000264930:p.Met774Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	37	CCDS34129.1	21	0.009615384615384616	0	0.0	2	0.0055248618784530384	0	0.0	19	0.025065963060686015	a	8.557	0.876903	0.17395	0.003177	0.022674	ENSG00000113504	ENST00000264930	D	0.93426	-3.22	4.49	0.507	0.16967	.	0.552015	0.20357	N	0.093925	T	0.64349	0.2590	N	0.10645	0.015	0.24364	N	0.994864	B	0.02656	0.0	B	0.04013	0.001	T	0.64588	-0.6372	10	0.33141	T	0.24	.	7.1786	0.25760	0.5848:0.0:0.4152:0.0	rs56350427	774	Q9Y666	S12A7_HUMAN	T	774	ENSP00000264930:M774T	ENSP00000264930:M774T	M	-	2	0	SLC12A7	1118514	0.090000	0.21635	0.789000	0.31954	0.693000	0.40251	1.824000	0.39072	-0.143000	0.11334	0.383000	0.25322	ATG	A|0.987;G|0.013	0.013	strong		0.627	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189387	11189387	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11189387G>A	ENST00000382435.4	+	1	991	c.772G>A	c.(772-774)Gca>Aca	p.A258T		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	258						integral component of membrane (GO:0016021)		p.A258T(1)									TTGTGTGGGGGCAGAGGGGAT	0.632																																					p.A258T		Atlas-SNP	.											AMAC1L2,trunk,malignant_melanoma,0,1	.	.	1	1	Substitution - Missense(1)	skin(1)	c.G772A						scavenged	.						113.0	111.0	111.0					8																	11189387		2203	4300	6503	SO:0001583	missense	83650	exon1			GTGGGGGCAGAGG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.772G>A	8.37:g.11189387G>A	ENSP00000371872:p.Ala258Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	167	7	0.0419162	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	G	9.059	0.994027	0.19043	.	.	ENSG00000177710	ENST00000382435	T	0.52983	0.64	.	.	.	.	0.157695	0.28865	N	0.013888	T	0.37156	0.0993	M	0.61703	1.905	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.22034	-1.0228	9	0.23302	T	0.38	-0.0577	5.8679	0.18786	8.0E-4:0.0:0.9992:0.0	.	258	Q96KT7	S35G5_HUMAN	T	258	ENSP00000371872:A258T	ENSP00000371872:A258T	A	+	1	0	SLC35G5	11226797	0.004000	0.15560	0.149000	0.22428	0.151000	0.21798	1.286000	0.33273	0.088000	0.17205	0.089000	0.15464	GCA	A|1.000;|0.000	1.000	weak		0.632	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
IL1RAP	3556	hgsc.bcm.edu	37	3	190363594	190363594	+	Silent	SNP	G	G	A	rs34879831	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:190363594G>A	ENST00000412504.2	+	10	1560	c.1308G>A	c.(1306-1308)aaG>aaA	p.K436K	IL1RAP_ENST00000447382.1_Silent_p.K436K|IL1RAP_ENST00000443369.2_Silent_p.K436K|IL1RAP_ENST00000439062.1_Silent_p.K436K|IL1RAP_ENST00000317757.3_Silent_p.K436K|IL1RAP_ENST00000072516.3_Silent_p.K436K			Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein	436	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-2 biosynthetic process (GO:0042094)|protein complex assembly (GO:0006461)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		TTGGATACAAGCTGTGCATCT	0.408													G|||	817	0.163139	0.3109	0.111	5008	,	,		19560	0.0179		0.1541	False		,,,				2504	0.1595				p.K436K		Atlas-SNP	.											.	IL1RAP	96	.	0			c.G1308A						PASS	.	G	,,,	1217,3189	423.0+/-339.9	158,901,1144	99.0	94.0	96.0		1308,1308,1308,1308	4.8	1.0	3	dbSNP_126	96	1390,7210	269.7+/-288.6	115,1160,3025	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL1RAP	NM_001167928.1,NM_001167929.1,NM_001167931.1,NM_002182.3	,,,	273,2061,4169	AA,AG,GG		16.1628,27.6214,20.0446	,,,	436/571,436/571,436/688,436/571	190363594	2607,10399	2203	4300	6503	SO:0001819	synonymous_variant	3556	exon10			ATACAAGCTGTGC	AB006537	CCDS3298.1, CCDS46982.1, CCDS54696.1	3q28	2013-01-11			ENSG00000196083	ENSG00000196083		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5995	protein-coding gene	gene with protein product		602626				9479509, 9065432	Standard	NM_002182		Approved	IL-1RAcP, IL1R3, C3orf13	uc003fsq.3	Q9NPH3	OTTHUMG00000156211	ENST00000412504.2:c.1308G>A	3.37:g.190363594G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_001167929	B1NLD0|D3DNW0|O14915|Q86WJ7	Silent	SNP	ENST00000412504.2	37	CCDS3298.1																																																																																			G|0.811;A|0.189	0.189	strong		0.408	IL1RAP-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343497.1		
AIFM3	150209	hgsc.bcm.edu	37	22	21328568	21328568	+	Missense_Mutation	SNP	G	G	A	rs56179977	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:21328568G>A	ENST00000399167.2	+	6	733	c.493G>A	c.(493-495)Gtc>Atc	p.V165I	AIFM3_ENST00000440238.2_Missense_Mutation_p.V165I|AIFM3_ENST00000335375.5_Missense_Mutation_p.V153I|AIFM3_ENST00000399163.2_Missense_Mutation_p.V165I|AIFM3_ENST00000333607.6_Missense_Mutation_p.V165I|AIFM3_ENST00000405089.1_Missense_Mutation_p.V171I	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	165	Rieske. {ECO:0000255|PROSITE- ProRule:PRU00628}.			V -> A (in Ref. 3; BAC04434). {ECO:0000305}.	cell redox homeostasis (GO:0045454)|execution phase of apoptosis (GO:0097194)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	21	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			GAAGGTGTACGTCCGGGCCAG	0.632													G|||	53	0.0105831	0.0015	0.0216	5008	,	,		15475	0.0		0.0328	False		,,,				2504	0.0031				p.V171I		Atlas-SNP	.											.	AIFM3	49	.	0			c.G511A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	27,4379	33.5+/-64.1	0,27,2176	51.0	49.0	50.0		493,511,493	-1.5	0.1	22	dbSNP_129	50	214,8386	87.4+/-149.7	1,212,4087	yes	missense,missense,missense	AIFM3	NM_001018060.2,NM_001146288.1,NM_144704.2	29,29,29	1,239,6263	AA,AG,GG		2.4884,0.6128,1.853	,,	165/599,171/605,165/606	21328568	241,12765	2203	4300	6503	SO:0001583	missense	150209	exon6			GTGTACGTCCGGG	AK094844	CCDS13786.1, CCDS33605.1, CCDS54503.1	22q11.21	2007-05-03			ENSG00000183773	ENSG00000183773			26398	protein-coding gene	gene with protein product						15764604	Standard	NM_144704		Approved	AIFL, FLJ30473		Q96NN9	OTTHUMG00000150804	ENST00000399167.2:c.493G>A	22.37:g.21328568G>A	ENSP00000382120:p.Val165Ile	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	139	80	0.57554	NM_001146288	B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Missense_Mutation	SNP	ENST00000399167.2	37	CCDS13786.1	36	0.016483516483516484	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	28	0.036939313984168866	G	8.866	0.948115	0.18356	0.006128	0.024884	ENSG00000183773	ENST00000399167;ENST00000399163;ENST00000434714;ENST00000405089;ENST00000335375;ENST00000440238;ENST00000333607	T;T;T;T;T;T	0.55234	0.57;0.53;0.58;0.67;0.57;0.53	4.44	-1.5	0.08691	Rieske [2Fe-2S] iron-sulphur domain (3);	0.124775	0.51477	N	0.000096	T	0.07999	0.0200	L	0.33245	0.995	0.20638	N	0.99987	B;B;B;B	0.32800	0.385;0.03;0.03;0.018	B;B;B;B	0.22753	0.041;0.028;0.028;0.013	T	0.11324	-1.0592	10	0.18276	T	0.48	-2.8262	8.5786	0.33614	0.5459:0.0:0.4541:0.0	rs56179977	153;171;165;165	B7Z9S7;Q96NN9-2;Q96NN9-3;Q96NN9	.;.;.;AIFM3_HUMAN	I	165;165;165;171;153;165;165	ENSP00000382120:V165I;ENSP00000382116:V165I;ENSP00000385800:V171I;ENSP00000335369:V153I;ENSP00000390798:V165I;ENSP00000327671:V165I	ENSP00000327671:V165I	V	+	1	0	AIFM3	19658568	0.793000	0.28825	0.108000	0.21378	0.994000	0.84299	1.671000	0.37513	-0.243000	0.09653	0.655000	0.94253	GTC	G|0.983;A|0.017	0.017	strong		0.632	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704	
ATG7	10533	hgsc.bcm.edu	37	3	11400019	11400019	+	Missense_Mutation	SNP	T	T	C	rs36117895	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:11400019T>C	ENST00000354449.3	+	13	1437	c.1412T>C	c.(1411-1413)gTc>gCc	p.V471A	ATG7_ENST00000354956.5_Missense_Mutation_p.V471A|ATG7_ENST00000446450.2_Missense_Mutation_p.V432A	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7	471			V -> A (in dbSNP:rs36117895).		adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						CATGATGTCGTCTTCCTATTG	0.517													T|||	150	0.0299521	0.0484	0.0202	5008	,	,		18526	0.0		0.0348	False		,,,				2504	0.0378				p.V471A		Atlas-SNP	.											.	ATG7	56	.	0			c.T1412C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	228,4178	135.7+/-171.8	6,216,1981	95.0	90.0	92.0		1412,1295,1412	5.8	0.9	3	dbSNP_126	92	323,8277	114.0+/-174.0	6,311,3983	yes	missense,missense,missense	ATG7	NM_001136031.2,NM_001144912.1,NM_006395.2	64,64,64	12,527,5964	CC,CT,TT		3.7558,5.1748,4.2365	possibly-damaging,possibly-damaging,possibly-damaging	471/677,432/624,471/704	11400019	551,12455	2203	4300	6503	SO:0001583	missense	10533	exon13			ATGTCGTCTTCCT	AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"""Ubiquitin-like modifier activating enzymes"""	16935	protein-coding gene	gene with protein product	"""ubiquitin-activating enzyme E1-like protein"""	608760	"""APG7 autophagy 7-like (S. cerevisiae)"", ""ATG7 autophagy related 7 homolog (S. cerevisiae)"""	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740	ENST00000354449.3:c.1412T>C	3.37:g.11400019T>C	ENSP00000346437:p.Val471Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_001136031	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Missense_Mutation	SNP	ENST00000354449.3	37	CCDS2605.1	52	0.023809523809523808	18	0.036585365853658534	9	0.024861878453038673	0	0.0	25	0.032981530343007916	T	25.4	4.638717	0.87760	0.051748	0.037558	ENSG00000197548	ENST00000446450;ENST00000354956;ENST00000354449	T;T;T	0.55413	0.52;0.52;0.52	5.79	5.79	0.91817	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.411116	0.27846	N	0.017610	T	0.26521	0.0648	M	0.83118	2.625	0.24457	N	0.994457	P;B;P	0.42941	0.794;0.386;0.794	P;B;P	0.47528	0.549;0.184;0.549	T	0.53143	-0.8480	10	0.72032	D	0.01	-11.1728	16.1224	0.81369	0.0:0.0:0.0:1.0	rs36117895	432;471;471	E9PB95;O95352-2;O95352	.;.;ATG7_HUMAN	A	432;471;471	ENSP00000412580:V432A;ENSP00000347042:V471A;ENSP00000346437:V471A	ENSP00000346437:V471A	V	+	2	0	ATG7	11375019	0.988000	0.35896	0.876000	0.34364	0.589000	0.36550	7.527000	0.81931	2.208000	0.71279	0.533000	0.62120	GTC	T|0.965;C|0.035	0.035	strong		0.517	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395	
COL11A2	1302	hgsc.bcm.edu	37	6	33153528	33153528	+	Missense_Mutation	SNP	C	C	T	rs9277934	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:33153528C>T	ENST00000341947.2	-	6	1053	c.826G>A	c.(826-828)Gag>Aag	p.E276K	COL11A2_ENST00000374713.1_Intron|COL11A2_ENST00000374712.1_Missense_Mutation_p.E276K|COL11A2_ENST00000374714.1_Intron|COL11A2_ENST00000395197.1_Missense_Mutation_p.E276K|COL11A2_ENST00000357486.1_Missense_Mutation_p.E276K|COL11A2_ENST00000361917.1_Intron|COL11A2_ENST00000374708.4_Intron	NM_080680.2	NP_542411.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	276	Nonhelical region.		E -> K (in dbSNP:rs9277934).		cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TAGGGGGGCTCGTAGTCATAG	0.552													C|||	1612	0.321885	0.3858	0.2738	5008	,	,		13574	0.2421		0.2773	False		,,,				2504	0.3978				p.E276K	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											COL11A2,NS,lymphoid_neoplasm,+1,1	COL11A2	124	1	0			c.G826A						PASS	.	C	,LYS/GLU,	1108,1910		198,712,599	80.0	102.0	94.0		,826,	3.8	1.0	6	dbSNP_118	94	1703,3715		260,1183,1266	yes	intron,missense,intron	COL11A2	NM_080679.2,NM_080680.2,NM_080681.2	,56,	458,1895,1865	TT,TC,CC		31.4323,36.7131,33.3215	,possibly-damaging,	,276/1737,	33153528	2811,5625	1509	2709	4218	SO:0001583	missense	1302	exon6			GGGGCTCGTAGTC	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000341947.2:c.826G>A	6.37:g.33153528C>T	ENSP00000339915:p.Glu276Lys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000341947.2	37		630	0.28846153846153844	192	0.3902439024390244	80	0.22099447513812154	151	0.263986013986014	207	0.27308707124010556	C	10.48	1.361885	0.24684	0.367131	0.314323	ENSG00000204248	ENST00000341947;ENST00000357486;ENST00000395197;ENST00000374712;ENST00000457788	D;D;D;D;D	0.90069	-2.32;-2.46;-2.42;-2.57;-2.61	3.8	3.8	0.43715	.	0.604873	0.13823	U	0.360284	T	0.75554	0.3865	N	0.22421	0.69	0.09310	P	1.0	D	0.56521	0.976	P	0.50825	0.651	T	0.69239	-0.5197	9	0.07644	T	0.81	.	11.3457	0.49559	0.0:1.0:0.0:0.0	rs9277934;rs17689612;rs52813564;rs60573261;rs9277934	276	P13942	COBA2_HUMAN	K	276	ENSP00000339915:E276K;ENSP00000350079:E276K;ENSP00000378623:E276K;ENSP00000363844:E276K;ENSP00000405520:E276K	ENSP00000339915:E276K	E	-	1	0	COL11A2	33261506	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	3.916000	0.56416	2.121000	0.65114	0.297000	0.19635	GAG	C|0.684;N|0.000	.	strong		0.552	COL11A2-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
CH25H	9023	hgsc.bcm.edu	37	10	90966393	90966393	+	Silent	SNP	G	G	A	rs17382301	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:90966393G>A	ENST00000371852.2	-	1	678	c.657C>T	c.(655-657)aaC>aaT	p.N219N		NM_003956.3	NP_003947.1	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	219					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol 25-hydroxylase activity (GO:0001567)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)	p.N219N(1)		kidney(1)|large_intestine(2)|lung(3)|stomach(1)	7		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		ACCAAGGGAAGTTGTAGCCGG	0.587													G|||	415	0.0828674	0.0053	0.0706	5008	,	,		19855	0.0337		0.1233	False		,,,				2504	0.2055				p.N219N		Atlas-SNP	.											CH25H,NS,carcinoma,0,1	CH25H	19	1	1	Substitution - coding silent(1)	stomach(1)	c.C657T						PASS	.	G		134,4272	98.5+/-137.1	3,128,2072	119.0	100.0	106.0		657	3.1	1.0	10	dbSNP_123	106	1227,7373	247.2+/-275.4	92,1043,3165	no	coding-synonymous	CH25H	NM_003956.3		95,1171,5237	AA,AG,GG		14.2674,3.0413,10.4644		219/273	90966393	1361,11645	2203	4300	6503	SO:0001819	synonymous_variant	9023	exon1			AGGGAAGTTGTAG	AF059212	CCDS7400.1	10q23	2013-03-04			ENSG00000138135	ENSG00000138135	1.14.99.38	"""Fatty acid hydroxylase domain containing"""	1907	protein-coding gene	gene with protein product		604551				9852097	Standard	NM_003956		Approved		uc001kfz.3	O95992	OTTHUMG00000018705	ENST00000371852.2:c.657C>T	10.37:g.90966393G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	85	8	0.0941176	NM_003956	B2RBY3	Silent	SNP	ENST00000371852.2	37	CCDS7400.1																																																																																			G|0.910;A|0.090	0.090	strong		0.587	CH25H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049291.1	NM_003956	
GLOD4	51031	hgsc.bcm.edu	37	17	685640	685640	+	5'Flank	SNP	G	G	T	rs2273454|rs11546732	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:685640G>T	ENST00000301328.5	-	0	0				GLOD4_ENST00000536578.1_5'Flank|RNMTL1_ENST00000304478.4_Missense_Mutation_p.A8S|GLOD4_ENST00000301329.6_5'Flank			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GGTGAGACCCGCGAGGTTTGT	0.701													G|||	1323	0.264177	0.0809	0.3314	5008	,	,		15716	0.505		0.1988	False		,,,				2504	0.2832				p.A8S		Atlas-SNP	.											RNMTL1,NS,carcinoma,-1,1	RNMTL1	25	1	0			c.G22T						PASS	.	G	SER/ALA	487,3919	217.1+/-235.6	28,431,1744	27.0	31.0	29.0		22	-8.4	0.0	17	dbSNP_100	29	1717,6881	299.0+/-304.2	171,1375,2753	yes	missense	RNMTL1	NM_018146.2	99	199,1806,4497	TT,TG,GG		19.9698,11.0531,16.9486	benign	8/421	685640	2204,10800	2203	4299	6502	SO:0001631	upstream_gene_variant	55178	exon1			AGACCCGCGAGGT	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 25"""	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38			17.37:g.685640G>T	Exception_encountered	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_018146	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	37		565	0.2586996336996337	46	0.09349593495934959	107	0.2955801104972376	254	0.44405594405594406	158	0.20844327176781002	G	12.65	2.002514	0.35320	0.110531	0.199698	ENSG00000171861	ENST00000304478	T	0.17854	2.25	4.97	-8.41	0.00961	.	1.317790	0.04892	N	0.449707	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43327	-0.9398	9	0.07325	T	0.83	.	1.9843	0.03433	0.4602:0.0985:0.1421:0.2992	rs2273454;rs17845293;rs17858127;rs17859517;rs52816295;rs58876583	8	Q9HC36	RMTL1_HUMAN	S	8	ENSP00000306080:A8S	ENSP00000306080:A8S	A	+	1	0	RNMTL1	632390	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.782000	0.04643	-1.851000	0.01168	-0.217000	0.12591	GCG	G|0.803;T|0.197	0.197	strong		0.701	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080	
ETFB	2109	hgsc.bcm.edu	37	19	51857738	51857738	+	Intron	SNP	G	G	A	rs79338777	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51857738G>A	ENST00000309244.4	-	2	149				ETFB_ENST00000354232.4_Missense_Mutation_p.P52L|CTD-2616J11.9_ENST00000600974.1_RNA|CTD-2616J11.11_ENST00000600067.1_Intron	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		tgtaggcagGGGCAGGTCACC	0.582													g|||	387	0.0772764	0.0439	0.0403	5008	,	,		16395	0.1181		0.0696	False		,,,				2504	0.1145				p.P52L		Atlas-SNP	.											.	ETFB	46	.	0			c.C155T						PASS	.	G	LEU/PRO,	196,4210	122.5+/-159.9	3,190,2010	79.0	72.0	74.0		155,	-5.5	0.0	19	dbSNP_131	74	591,8009	156.7+/-210.5	22,547,3731	yes	missense,intron	ETFB	NM_001014763.1,NM_001985.2	98,	25,737,5741	AA,AG,GG		6.8721,4.4485,6.0511	probably-damaging,	52/347,	51857738	787,12219	2203	4300	6503	SO:0001627	intron_variant	2109	exon1			GGCAGGGGCAGGT	X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379			3482	protein-coding gene	gene with protein product		130410					Standard	NM_001014763		Approved		uc002pwg.3	P38117		ENST00000309244.4:c.58-176C>T	19.37:g.51857738G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	156	0.07142857142857142	23	0.046747967479674794	13	0.03591160220994475	69	0.12062937062937062	51	0.06728232189973615	g	12.18	1.860517	0.32884	0.044485	0.068721	ENSG00000105379	ENST00000354232	D	0.85955	-2.05	2.77	-5.53	0.02552	.	.	.	.	.	T	0.01905	0.0060	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.15954	-1.0419	6	.	.	.	.	1.673	0.02816	0.2749:0.125:0.4452:0.1549	.	52	P38117-2	.	L	52	ENSP00000346173:P52L	.	P	-	2	0	ETFB	56549550	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.733000	0.00803	-1.622000	0.01560	-0.290000	0.09829	CCC	G|0.937;A|0.063	0.063	strong		0.582	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
RBM19	9904	hgsc.bcm.edu	37	12	114377877	114377877	+	Missense_Mutation	SNP	T	T	C	rs2290789	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:114377877T>C	ENST00000545145.2	-	15	1904	c.1826A>G	c.(1825-1827)cAt>cGt	p.H609R	RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.H609R|RBM19_ENST00000392561.3_Missense_Mutation_p.H609R	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	609	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.		H -> R (in dbSNP:rs2290789). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GCTGCCAAAATGGCCGAAGGT	0.642													C|||	996	0.198882	0.3464	0.0764	5008	,	,		17496	0.1885		0.1133	False		,,,				2504	0.1851				p.H609R		Atlas-SNP	.											.	RBM19	117	.	0			c.A1826G						PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS	1442,2964	676.6+/-403.3	255,932,1016	63.0	69.0	67.0		1826,1826,1826	0.2	0.0	12	dbSNP_100	67	886,7714	776.2+/-407.7	38,810,3452	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	29,29,29	293,1742,4468	CC,CT,TT		10.3023,32.7281,17.8994	benign,benign,benign	609/961,609/961,609/961	114377877	2328,10678	2203	4300	6503	SO:0001583	missense	9904	exon15			CCAAAATGGCCGA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1826A>G	12.37:g.114377877T>C	ENSP00000442053:p.His609Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	362	0.16575091575091574	147	0.29878048780487804	27	0.07458563535911603	102	0.17832167832167833	86	0.11345646437994723	C	0	-2.782507	0.00079	0.327281	0.103023	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05319	3.46;3.46;3.46	4.29	0.25	0.15535	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.381500	0.26387	N	0.024675	T	0.00012	0.0000	N	0.00280	-1.71	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40961	-0.9535	9	0.05833	T	0.94	-0.08	6.9575	0.24580	0.0:0.4211:0.1156:0.4633	rs2290789;rs17856105;rs17856174;rs2290789	609	Q9Y4C8	RBM19_HUMAN	R	609	ENSP00000442053:H609R;ENSP00000376344:H609R;ENSP00000261741:H609R	ENSP00000261741:H609R	H	-	2	0	RBM19	112862260	0.437000	0.25593	0.025000	0.17156	0.040000	0.13550	0.866000	0.27954	-0.236000	0.09753	-1.007000	0.02485	CAT	T|0.830;C|0.170	0.170	strong		0.642	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
